@article {pmid40168325, year = {2025}, author = {Yun, H and Seo, JH and Kim, YK and Yang, J}, title = {Examining the bacterial diversity including extracellular vesicles in air and soil: implications for human health.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0320916}, doi = {10.1371/journal.pone.0320916}, pmid = {40168325}, issn = {1932-6203}, mesh = {*Extracellular Vesicles/metabolism ; *Soil Microbiology ; Humans ; *Bacteria/genetics/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; Air Microbiology ; Microbiota ; Biodiversity ; Metagenomics/methods ; }, abstract = {As the significance of human health continues to rise, the microbiome has shifted its focus from microbial composition to the functional roles it plays. In parallel, interest in ultrafine particles associated with clinically important impact has been increasing. Bacterial extracellular vesicles (BEVs), involved in systemic microbiome activity, are nano-sized spherical vesicles (20 - 100 nm in diameter) containing DNA, RNA, proteins, and lipids. They are known to be absorbed into the body potentially through air and soil, circulate in the blood, and directly impact diseases by affecting organs. Therefore, the aim of this study is to examine the biodiversity of bacteria and BEVs and predicted functional pathways. We sampled air and soil samples in Seoul, Korea and analyzed metagenomics based on 16S rRNA sequencing. At the phylum levels, Firmicutes in BEVs from soil and air were significantly higher than in bacteria, and Acidobacteria in both bacteria and BEVs from soil were significantly higher than from air (p < 0.05). The most dominant genera were Pseudomonas in bacteria from air and soil; and Escherichia-Shigella in BEVs from air and soil. In addition, Two-component system (ko02020) and ATP-binding cassette transporters (ko02010) were dominant functional pathways in both air and soil. The most functional pathways and orthologous groups were significantly different between air and soil (p < 0.05). In conclusion, human health can be affected differently depending on type of environment. Future study is necessary to have a better understanding of human health effects from environmental microbiota.}, } @article {pmid40167332, year = {2025}, author = {Curto, M and Veríssimo, A and Riccioni, G and Santos, CD and Ribeiro, F and Jentoft, S and Alves, MJ and Gante, HF}, title = {Improving Whole Biodiversity Monitoring and Discovery With Environmental DNA Metagenomics.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14105}, doi = {10.1111/1755-0998.14105}, pmid = {40167332}, issn = {1755-0998}, support = {CEEC/0482/2020//Fundação para a Ciência e a Tecnologia/ ; DL 57/2016/CP1440/CP1646/CT0001//Fundação para a Ciência e a Tecnologia/ ; LA/P/0069/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/BIA-CBI/31644/2017//Fundação para a Ciência e a Tecnologia/ ; UID/04292/2020//Fundação para a Ciência e a Tecnologia/ ; UID/BIA/00329/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/50027/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0048/2020//Fundação para a Ciência e a Tecnologia/ ; 857251//Horizon 2020 Framework Programme/ ; STG/21/044//KU Leuven/ ; }, abstract = {Environmental DNA (eDNA) metagenomics sequences all DNA molecules present in environmental samples and has the potential of identifying virtually any organism from which they are derived. However, due to unacceptable levels of false positives and negatives, this approach is underexplored as a tool for biodiversity monitoring across the tree of life, particularly for non-microscopic eukaryotes. We present SeqIDist, a framework that combines multilocus BLAST matches against several reference databases followed by an analysis of sequence identity distribution patterns to disentangle false positives while revealing new biodiversity and increasing the accuracy of metagenomic approaches. We tested SeqIDist on an eDNA metagenomic dataset from a riverine site and compared the results to those obtained with an eDNA metabarcoding approach for benchmarking purposes. We start by characterising the biological community (~2000 taxa) across the tree of life at low taxonomic levels and show that eDNA metagenomics has a higher sensitivity than eDNA metabarcoding in discovering new diversity. We show that limited representation of whole genome sequences in reference databases can lead to false positives. For non-microscopic eukaryotes, eDNA metagenomic data often consist of a few sparse, anonymous sequences scattered across the genome, making metagenome assembly methods unfeasible. Finally, we infer eDNA source and residency time using read length distributions as a measure of decay status. The higher accuracy of SeqIDist opens the discussion of the potential of eDNA metagenomics for archived samples and its implementation in long-term biodiversity monitoring at a planetary scale.}, } @article {pmid40165946, year = {2025}, author = {Guo, Z and Wang, X and Li, Y and Zhang, Y and Guo, P and Zhang, J and Zhang, Z and Ma, X}, title = {Evaluation of the therapeutic effect of pomegranate peel ginger ultrafine powder on chronic enteritis in mice by regulating intestinal microbiota.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1563225}, pmid = {40165946}, issn = {1664-3224}, mesh = {Animals ; Mice ; *Pomegranate/chemistry ; *Zingiber officinale ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Enteritis/drug therapy/microbiology/veterinary ; *Aquaporins/metabolism/genetics ; Cytokines/metabolism ; Chronic Disease ; Disease Models, Animal ; Powders ; Plant Extracts/pharmacology/administration & dosage ; Aquaporin 3 ; Aquaporin 4 ; }, abstract = {To explore the efficacy and mechanism of Pomegranate peel Ginger ultrafine powder (PG) in treating chronic enteritis in mice. Sixty SPF-grade mice were randomly divided into a blank group, a model group, loperamide hydrochloride group (5 mg/kg), a high-dose PG group (100 mg/kg), a medium-dose group (50 mg/kg), and a low-dose group (25 mg/kg), with 10 mice in each group and an equal number of males and females. A chronic enteritis mouse model was established using a multifactorial method of low temperature + ice water + castor oil. The blank group was given an equal amount of physiological saline intragastrically, while the other groups were intervened with corresponding drugs for 7 consecutive days. After 7 days, samples were collected, and Enzyme-linked immunosorbent assay (ELISA) was used to detect the levels of interleuckin 1β (IL-1β), IL-6, and Tumor necrosis factorα(TNF-α) in mouse serum. HE staining was used to examine the pathological changes in the small intestine. oxidative reagent kits were used to detect the content of total superoxide dismutase(T-SOD) and Malondialdehyde (MDA) in the small intestine. Western blot was used to detect the expression of Aquaporin 8(AQP8) proteins in the small intestine. Real time quantitative reverse transcription polymerase chain reaction (RT-qPCR) was used to detect the expression of AQP3, AQP4, AQP8, and Sodium/hydrogen exchanger 8 (NHE8) genes in the small intestine. metagenomics was used to detect the gut microbiota in mouse feces. Compared with the model group, all doses of PG groups reduced the levels of IL-1β, IL-6, and TNF-α in mouse serum (P<0.05), improved pathological changes in the small intestine, increased the content of T-SOD in the small intestine tissue, reduced the content of MDA, increased the expression of AQP4 and AQP8 mRNA, and decreased the expression of AQP3 and NHE8 mRNA (P<0.05), increased the expression of AQP8 protein. PG could improve the pathological changes of chronic enteritis in mice, enhance antioxidant capacity, and alleviate diarrhea caused by chronic enteritis by downregulating the expression of intestinal epithelial transport proteins and acute-phase proteins, and altering gut microbiota.}, } @article {pmid40165255, year = {2025}, author = {Xie, B and Dong, C and Zhao, X and Qu, L and Lv, Y and Liu, H and Xu, J and Yu, Z and Shen, H and Shang, Y and Zhao, X and Zhang, J}, title = {Structural and functional alteration of the gut microbiomes in ICU staff: a cross-sectional analysis.}, journal = {Critical care (London, England)}, volume = {29}, number = {1}, pages = {141}, pmid = {40165255}, issn = {1466-609X}, support = {82402568//National Natural Science Foundation of China/ ; 82472223//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/physiology ; *Intensive Care Units/organization & administration/statistics & numerical data ; Male ; Female ; Prospective Studies ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/analysis/genetics ; Cohort Studies ; Feces/microbiology ; Health Personnel/statistics & numerical data ; }, abstract = {BACKGROUND: 16S rRNA sequencing has revealed structural alterations in the gut microbiomes of medical workers, particularly those working in intensive care unit (ICU). This study aims to further compare the taxonomic and functional characteristics of gut microbiomes between ICU staff and non-medical individuals using metagenomic sequencing.

METHODS: A prospective cross-sectional cohort study was conducted, fecal samples from 39 individuals in each group-ICU staff and non-medical subjects were analyzed using metagenomic sequencing. PERMANOVA (using the adonis function) was employed to analyze the genus-level profiles and assess the impact of individual parameters on the gut microbiome. Multiple databases were utilized to annotate and compare the functional differences in gut microbiomes between the two groups.

RESULTS: We observed that ICU staff exhibited a significant decrease in gut microbiome diversity, characterized by a marked decline in Actinobacteria and a substantial increase in Bacteroides and Bacteroidaceae. CAZy annotation revealed a notable increase in carbohydrate-active enzymes within the ICU staff cohort. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis further indicated an elevated risk of endocrine and metabolic disorders, along with enhanced glycan biosynthesis and metabolism. Additionally, KEGG pathway enrichment analysis highlighted significant enrichment in cancer-related pathways. Analysis using the Virulence Factor Database (VFDB) showed a higher abundance of virulence factors associated with immune modulation, invasion, and antimicrobial activity/competitive advantage among ICU staff. Notably, no discernible difference in the presence of antibiotic resistance genes within the gut microbiomes was observed between the two groups. Importantly, all aforementioned differences demonstrated clear gender disparities.

CONCLUSIONS: Our findings indicated that ICU staff exhibited a reduction in gut microbiome diversity which was associated with an increase in virulence factors and carbohydrate-active enzymes, as well as with a heightened susceptibility to endocrine and metabolic diseases and cancers.}, } @article {pmid40164980, year = {2025}, author = {Otani, S and Louise Jespersen, M and Brinch, C and Duus Møller, F and Pilgaard, B and Egholm Bruun Jensen, E and Leekitcharoenphon, P and Aaby Svendsen, C and Aarestrup, AH and Sonda, T and Sylvina, TJ and Leach, J and Piel, A and Stewart, F and Sapountzis, P and Kazyoba, PE and Kumburu, H and Aarestrup, FM}, title = {Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2484385}, doi = {10.1080/19490976.2025.2484385}, pmid = {40164980}, issn = {1949-0984}, mesh = {Animals ; *Diet ; *Hominidae/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome ; *Life Style ; Humans ; Adaptation, Physiological ; Pan troglodytes/microbiology ; Metagenome ; Phylogeny ; Africa ; }, abstract = {In the diverse landscape of African hominids, the obligate relationship between the host and its microbiome narrates signals of adaptation and co-evolution. Sequencing 546 African hominid metagenomes, including those from indigenous Hadza and wild chimpanzees, identified similar bacterial richness and diversity surpassing those of westernized populations. While hominids share core bacterial communities, they also harbor distinct, population-specific bacterial taxa tailored to specific diets, ecology and lifestyles, differentiating non-indigenous and indigenous humans and chimpanzees. Even amongst shared bacterial communities, several core bacteria have co-diversified to fulfil unique dietary degradation functions within their host populations. These co-evolutionary trends extend to non-bacterial elements, such as mitochondrial DNA, antimicrobial resistance, and parasites. Our findings indicate that microbiome-host co-adaptations have led to both taxonomic and within taxa functional displacements to meet host physiological demands. The microbiome, in turn, transcends its taxonomic interchangeable role, reflecting the lifestyle, ecology and dietary history of its host.}, } @article {pmid40164860, year = {2025}, author = {Adawiah, A and Meryandini, A and Ridwan, R and Fidriyanto, R and Sarwono, KA and Wiryawan, KG}, title = {The rumen microbiome and metabolome profile of Ongole crossbreed cattle fed probiotics and protected amino acids.}, journal = {Tropical animal health and production}, volume = {57}, number = {3}, pages = {148}, pmid = {40164860}, issn = {1573-7438}, mesh = {Animals ; *Rumen/microbiology/metabolism ; Cattle ; *Amino Acids/metabolism ; *Animal Feed/analysis ; Male ; *Metabolome ; *Diet/veterinary ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/administration & dosage/pharmacology ; Cross-Over Studies ; Dietary Supplements/analysis ; Bacteria/classification/metabolism/genetics ; }, abstract = {This study aimed to investigate the microbial population dynamics and metabolite profiles of Ongole crossbreed cattle (OCC) fed a combination of feed additives using metagenomic and metabolomic analyses. A crossover design was employed, involving four 3-year-old fistulated OCC bulls, each receiving four distinct dietary treatments per experimental period, followed by a washout phase with a basal diet. The treatments consisted of a basal diet (G1) as control, and the addition of feed additives as follows: G2: probiotics (Lactiplantibacillus plantarum); G3: premix; G4: G2 + G3 + amino acids lysine and methionine; and G5: G2 + G3 + amino acids protected with tannin. Rumen fluid was collected for the analysis of microbiome dynamics and metabolite profiles. The bacterial communities in diets G1, G2, G3, and G5 exhibited similar compositions, dominated by Bacteroidota, particularly the genus Prevotella. The G5 diet successfully suppressed the population of archaea, notably Methanosarcinales and Methanobacteriales, which are associated with methane production. A total of 28 significant metabolites (VIP > 1) was identified in rumen fluid, including lipid prenols, phenolic compounds, indoles and derivatives, saturated and unsaturated hydrocarbons, fatty acyls, benzene derivatives, and organooxygen compounds. The volatile compounds profile of rumen fluid showed a marked increase in prenol lipid compounds, especially in the G5 diet. Additionally, Methanosarcinales and Methanobacteriales were negatively correlated with prenol lipid levels. The inclusion of probiotics and protected amino acids alters the microbiome community structure and metabolites, positively affecting ruminant productivity.}, } @article {pmid40164638, year = {2025}, author = {Mills, S and Ijaz, UZ and Lens, PNL}, title = {Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {54}, pmid = {40164638}, issn = {2055-5008}, support = {15/RP/2763//Science Foundation Ireland (SFI)/ ; 16/RI/3401//Science Foundation Ireland (SFI)/ ; 15/RP/2763//Science Foundation Ireland (SFI)/ ; 16/RI/3401//Science Foundation Ireland (SFI)/ ; EP/P029329/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/V030515/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Bioreactors/microbiology ; *Metagenomics/methods ; Bacteria/genetics/classification/isolation & purification ; Microbiota ; High-Throughput Nucleotide Sequencing ; Microbial Consortia/genetics ; Methane/metabolism ; Metagenome ; Phylogeny ; }, abstract = {Different microbial communities are impacted disproportionately by environmental disturbances. The degree to which a community can remain unchanged under a disturbance is referred to as resistance[1]. However, the contributing ecological factors, which infer a community's resistance are unknown. In this study, the impact of historical environmental stability on ecological phenomena and microbial community resistance to shocks was investigated. Three separate methanogenic bioreactor consortia, which were subjected to varying degrees of historical environmental stability, and displayed different levels of resistance to an organic loading rate (OLR) shock were sampled. Their community composition was assessed using high throughput sequencing of 16S rRNA genes and assembly based metagenomics. The effect environmental instability on ecological phenomena such as microbial community assembly, microbial niche breadth and the rare biosphere were assessed in the context of each reactor's demonstrated resistance to an OLR shock. Additionally, metagenome assembled genomes were analysed for functional effects of prolonged stability/instability. The system which was subjected to more environmental instability experienced more temporal variation in community beta diversity and a proliferation of specialists, with more abundant two component regulatory systems. This community was more susceptible to deterministic community assembly and demonstrated a lower degree of resistance, indicating that microbial communities experiencing longer term environmental instability (e.g. variations in pH or temperature) are less able to resist a large disturbance.}, } @article {pmid40158160, year = {2025}, author = {Zhu, M and Wang, Q and Yang, Y and Liu, X and Zhang, J and Li, G and Liu, W and Xiang, X and Chen, J}, title = {Multiomics approach reveals the comprehensive interactions between nutrition and children's gut microbiota, and microbial and host metabolomes.}, journal = {Nutrition journal}, volume = {24}, number = {1}, pages = {50}, pmid = {40158160}, issn = {1475-2891}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Child ; Male ; Cross-Sectional Studies ; *Metabolome/physiology ; Female ; Child, Preschool ; *Feces/microbiology ; China ; *Diet/methods ; Metabolomics/methods ; Nutritional Status ; Multiomics ; }, abstract = {The gut microbiome can modulate nutrient metabolism to produce many metabolites interacting with the host. However, the intricate interactions among dietary intake, the gut microbiome and metabolites, and host metabolites need to be further explored although some studies have been devoted to it. Here, in a cross-sectional studies, 88 children aged 2-12 years were enrolled from northwestern China. The dietary intake data were collected via a designed food frequency questionnaire to calculate plant-based diet indices (PDIs). Stool and plasma samples were collected for metagenomic and broad-targeted metabolomic analysis. Spearman's rank correlation was used to describe the associations between nutrients/PDIs and the gut microbiota and metabolites. PDI was significantly positively associated with Bilophila wadsworthia, Bacteroides thetaiotaomicron, and Alistipes indistinctus, etc., but was obviously negatively correlated with Roseburia intestinalis, Faecalibacterium prausnitzii, etc. However, these species showed no significant associations with either healthy PDI (hPDI) or unhealthy PDI (uPDI). Interestingly, hPDI was significantly positively related to species, including Ruminococcus bicirculans, and was significantly negatively associated with uPDI, and vice versa. The above correlation trends were also observed between PDIs and predicted gut microbial functional pathways, microbial metabolites and the host metabolome. Notably, the significantly related pathways were focused mainly on substances and energy metabolism. PDI was significantly positively associated with the fecal contents of P-aminobenzoate, chenodeoxycholic acid, 4,6-dihydroxyquinoline, quinoline-4,8-diol, etc., but was significantly negatively associated with those of TMAO, FFA, creatine phosphate, etc. In plasma, PDI was significantly positively associated with sarcosine, ornithine, L-histidine, etc., but was distinctly negatively correlated with FFAs, carnitine C2:0, etc. Strikingly, the healthy plant-based diet index (hPDI) is correlated with increased levels of metabolites related to tryptophan metabolism, whereas the unhealthy PDI (uPDI) is linked to increased levels of metabolites associated with tyrosine and sphingolipid metabolism, which are pathways commonly associated with Western diets. Our studies provide reliable data support and a comprehensive understanding of the effects of dietary intake on the gut microbiome and microbial and host metabolites and lay a foundation for further studies of the diet-gut microbiota-microbial metabolites and host metabolism.}, } @article {pmid39998261, year = {2025}, author = {Woh, PY and Chen, Y and Kumpitsch, C and Mohammadzadeh, R and Schmidt, L and Moissl-Eichinger, C}, title = {Reevaluation of the gastrointestinal methanogenic archaeome in multiple sclerosis and its association with treatment.}, journal = {Microbiology spectrum}, volume = {13}, number = {4}, pages = {e0218324}, doi = {10.1128/spectrum.02183-24}, pmid = {39998261}, issn = {2165-0497}, support = {F83, P32697, COE7//Austrian Science Fund (FWF)/ ; }, mesh = {Humans ; Middle Aged ; Female ; *Multiple Sclerosis/microbiology/drug therapy ; Adult ; *Gastrointestinal Microbiome/genetics ; Male ; Aged ; Methanobrevibacter/genetics/isolation & purification/metabolism ; Archaea/classification/genetics ; Metagenomics ; Methane/metabolism ; Metagenome ; }, abstract = {The role of the gut archaeal microbiome (archaeome) in health and disease remains poorly understood. Methanogenic archaea have been linked to multiple sclerosis (MS), but prior studies were limited by small cohorts and inconsistent methodologies. To address this, we re-evaluated the association between methanogenic archaea and MS using metagenomic data from the International Multiple Sclerosis Microbiome Study. We analyzed gut microbiome profiles from 115 MS patients and 115 healthy household controls across Buenos Aires (27.8%), Edinburgh (33.9%), New York (10.4%), and San Francisco (27.8%). Metagenomic sequences were taxonomically classified using kraken2/bracken and a curated profiling database to detect archaea, specifically Methanobrevibacter species. Most MS patients were female (80/115), aged 25-72 years (median: 44.5), and 70% were undergoing treatment, including dimethyl fumarate (n = 21), fingolimod (n = 20), glatiramer acetate (n = 14), interferon (n = 18), natalizumab (n = 6), or ocrelizumab/rituximab (n = 1). We found no significant differences in overall archaeome profiles between MS patients and controls. However, treated MS patients exhibited higher abundances of Methanobrevibacter smithii and M. sp900766745 compared to untreated patients. Notably, M. sp900766745 abundance correlated with lower disease severity scores in treated patients. Our results suggest that gut methanogens are not directly associated with MS onset or progression but may reflect microbiome health during treatment. These findings highlight potential roles for M. smithii and M. sp900766745 in modulating treatment outcomes, warranting further investigation into their relevance to gut microbiome function and MS management.IMPORTANCEMultiple sclerosis (MS) is a chronic neuroinflammatory disease affecting the central nervous system, with approximately 2.8 million people diagnosed worldwide, mainly young adults aged 20-30 years. While recent studies have focused on bacterial changes in the MS microbiome, the role of gut archaea has been less explored. Previous research suggested a potential link between methanogenic archaea and MS disease status, but these findings remained inconclusive. Our study addresses this gap by investigating the gut archaeal composition in MS patients and examining how it changes in response to treatment. By focusing on methanogens, we aim to uncover novel insights into their role in MS, potentially revealing new biomarkers or therapeutic targets. This research is crucial for enhancing our understanding of the gut microbiome's impact on MS and improving patient management.}, } @article {pmid39998243, year = {2025}, author = {Brochu, HN and Zhang, Q and Song, K and Wang, L and Deare, EA and Williams, JD and Icenhour, CR and Iyer, LK}, title = {Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples.}, journal = {Microbiology spectrum}, volume = {13}, number = {4}, pages = {e0258224}, doi = {10.1128/spectrum.02582-24}, pmid = {39998243}, issn = {2165-0497}, mesh = {Humans ; *Vaginosis, Bacterial/microbiology/diagnosis ; Female ; *Vagina/microbiology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; DNA, Bacterial/genetics ; Adult ; Polymerase Chain Reaction/methods ; Actinobacteria ; }, abstract = {Bacterial vaginosis (BV) is a type of vaginal inflammation caused by bacterial overgrowth, upsetting the healthy microbiome of the vagina. Existing clinical testing for BV is primarily based upon physical and microscopic examination of vaginal secretions. Modern PCR-based clinical tests target panels of BV-associated microbes, such as the Labcorp NuSwab test that targets Atopobium (Fannyhessea) vaginae, Megasphaera-1, and Bacterial Vaginosis Associated Bacterium (BVAB)-2. Remnant clinician-collected NuSwab vaginal swabs underwent DNA extraction and 16S V3-V4 rRNA gene sequencing to profile microbes in addition to those included in the Labcorp NuSwab test. Community state types (CSTs) were determined using the most abundant taxon detected in each sample. PCR results for NuSwab panel microbial targets were compared against the corresponding microbiome profiles. Metabolic pathway abundances were characterized via metagenomic prediction from amplicon sequence variants (ASVs). 16S V3-V4 rRNA gene sequencing of 75 remnant vaginal swabs yielded 492 unique 16S V3-V4 ASVs, identifying 83 unique genera. NuSwab microbe quantification was strongly concordant with quantification by sequencing (P < 0.01). Samples in CST-I (18 of 18, 100%), CST-II (three of three, 100%), CST-III (15 of 17, 88%), and CST-V (one of one, 100%) were largely categorized as BV-negative via the NuSwab panel, while most CST-IV samples (28 of 36, 78%) were BV-positive or BV-indeterminate. BV-associated microbial and predicted metabolic signatures were shared across multiple CSTs. These findings highlight robust sequencing-based quantification of Labcorp NuSwab BV microbes, accurate discrimination of vaginal microbiome CSTs dominated by distinct Lactobacilli, and expanded the identification of BV-associated bacterial and metabolic biomarkers.IMPORTANCEBacterial vaginosis (BV) poses a significant health burden for women during reproductive years and onward. Current BV diagnostics rely on either panels of select microbes or on physical and microscopic evaluations by technicians. Here, we sequenced the microbiome profiles of samples previously diagnosed by the Labcorp NuSwab test to better understand disruptions to the vaginal microbiome during BV. We show that microbial sequencing can faithfully reproduce targeted PCR diagnostic results and can improve our knowledge of healthy and BV-associated microbial and metabolic biomarkers. This work highlights a robust, agnostic BV classification scheme with potential for future development of sequencing-based BV diagnostic tools.}, } @article {pmid40158141, year = {2025}, author = {Jiang, Y and Aton, M and Zhu, Q and Lu, YY}, title = {Modeling microbiome-trait associations with taxonomy-adaptive neural networks.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {87}, pmid = {40158141}, issn = {2049-2618}, support = {RGPIN-03270-2023//Canadian NSERC Discovery Grant/ ; RGPIN-03270-2023//Canadian NSERC Discovery Grant/ ; }, mesh = {Humans ; *Neural Networks, Computer ; *Microbiota ; Metagenomics/methods ; Bacteria/classification/genetics ; Computer Simulation ; }, abstract = {The human microbiome, a complex ecosystem of microorganisms inhabiting the body, plays a critical role in human health. Investigating its association with host traits is essential for understanding its impact on various diseases. Although shotgun metagenomic sequencing technologies have produced vast amounts of microbiome data, analyzing such data is highly challenging due to its sparsity, noisiness, and high feature dimensionality. Here, we develop MIOSTONE, an accurate and interpretable neural network model for microbiome-disease association that simulates a real taxonomy by encoding the relationships among microbial features. The taxonomy-encoding architecture provides a natural bridge from variations in microbial taxa abundance to variations in traits, encompassing increasingly coarse scales from species to domains. MIOSTONE has the ability to determine whether taxa within the corresponding taxonomic group provide a better explanation in a data-driven manner. MIOSTONE serves as an effective predictive model, as it not only accurately predicts microbiome-trait associations across extensive simulated and real datasets but also offers interpretability for scientific discovery. Both attributes are crucial for facilitating in silico investigations into the biological mechanisms underlying such associations among microbial taxa. Video Abstract.}, } @article {pmid40157532, year = {2025}, author = {Pienaar, RD and Herrero, S and Cerqueira de Araujo, A and Krupa, F and Abd-Alla, AMM and Herniou, EA}, title = {High-throughput screening reveals high diversity and widespread distribution of viruses in black soldier flies (Hermetia illucens).}, journal = {Journal of invertebrate pathology}, volume = {}, number = {}, pages = {108322}, doi = {10.1016/j.jip.2025.108322}, pmid = {40157532}, issn = {1096-0805}, abstract = {Virus discovery in mass-reared insects is a growing topic of interest due to outbreak risks and for insect welfare concerns. In the case of black soldier flies (Hermetia illucens, BSF), pioneering bioinformatic studies have uncovered exogenous viruses from the orders Ghabrivirales and Bunyavirales, as well as endogenous viral elements from five virus families. This prompted further virome investigation of BSF metagenomes and metatranscriptomes, including from BSF individuals displaying signs and symptoms of disease. A high-throughput pipeline allowed the simultaneous investigation of 203 next generation sequencing datasets. This revealed the presence of seven viruses belonging to the families Dicistroviridae, Iflaviridae, Rhabdoviridae, Solinviviridae, Inseviridae, Lebotiviridae, and an unclassified Bunyavirales. Here we describe five viruses, which were detected in BSF from multiple origins, outlining the diversity of naturally occurring viruses associated with BSF colonies. As this viral community may also include BSF pathogens, we developed molecular detection tools which could be used for viral surveillance, both in mass-reared and wild populations of BSF.}, } @article {pmid40156577, year = {2025}, author = {Kop, LFM and Koch, H and Martins, PD and Suarez, C and Karačić, S and Persson, F and Wilén, BM and Hagelia, P and Jetten, MSM and Lücker, S}, title = {High diversity of nitrifying bacteria and archaea in biofilms from a subsea tunnel.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf032}, pmid = {40156577}, issn = {1574-6941}, abstract = {Microbial biofilm formation can contribute to the accelerated deterioration of steel-reinforced concrete structures and significantly impact their service life, making it critical to understand the diversity of the biofilm community and prevailing processes in these habitats. Here, we analyzed 16S rRNA gene amplicon and metagenomics sequencing data to study the abundance and diversity of nitrifiers within biofilms on the concrete surface of the Oslofjord subsea road tunnel in Norway. We showed that the abundance of nitrifiers varied greatly in time and space, with a mean abundance of 24.7±15% but a wide range between 1.2-61.4%. We hypothesize that niche differentiation allows the coexistence of several nitrifier groups and that their high diversity increases the resilience to fluctuating environmental conditions. Strong correlations were observed between the nitrifying families Nitrosomonadaceae and Nitrospinaceae, and the iron-oxidizing family Mariprofundaceae. Metagenome-assembled genome (MAG) analyses suggested that early Mariprofundaceae colonizers may provide a protected environment for nitrifiers in exchange for nitrogen compounds and vitamin B12, but further studies are needed to elucidate the spatial organization of the biofilms and the cooperative and competitive interactions in this environment. Together, this research provides novel insights into the diverse communities of nitrifiers living within biofilms on concrete surfaces and establishes a foundation for future experimental studies of concrete biofilms.}, } @article {pmid40150979, year = {2025}, author = {Yildirim, EA and Laptev, GY and Ilina, LA and Ponomareva, ES and Brazhnik, EA and Smetannikova, TS and Novikova, NI and Turina, DG and Filippova, VA and Dubrovin, AV and Dubrovina, AS and Kalitkina, KA and Klyuchnikova, IA and Zaikin, VA and Griffin, DK and Romanov, MN}, title = {Metagenomic Composition and Predicted Metabolic Pathway Analyses of the Endometrial and Rectal Microbiota in Dairy Cows Following the Introduction of a Complex Feed Additive.}, journal = {Frontiers in bioscience (Elite edition)}, volume = {17}, number = {1}, pages = {25725}, doi = {10.31083/FBE25725}, pmid = {40150979}, issn = {1945-0508}, support = {24-16-00131//Russian Science Foundation/ ; }, mesh = {Animals ; Cattle/microbiology ; Female ; *Animal Feed ; *Rectum/microbiology ; *Endometrium/microbiology/metabolism ; *Microbiota ; Metabolic Networks and Pathways ; Metagenomics ; Dairying ; }, abstract = {BACKGROUND: The microbiome composition in dairy cows (Bos taurus) directly impacts on health and reproductive performance. This study aimed to determine the metagenomic composition and predicted microbial community functions in the endometrium and rectal chyme of cows fed a complex feed additive (CFA). The latter included the Bacillus mucilaginosus 159 strain, a short-chain fatty acid, plus essential oils.

METHODS: Clinically healthy cows were divided into two groups (n = 15 in each): (I) a control group fed the standard diet, and (II) an experimental group. CFA was introduced into the diet of Group II during the entire transit period at a dose of 50 g per animal per day; moreover, all animals received Pen-Strep 400 antibiotics to prevent endometritis and other pathologies. The microbial community composition from the endometrium and rectal chyme biotopes was assessed using targeted next-generation sequencing.

RESULTS: Significant changes were observed in the composition and predicted metabolic pathways due to the CFA administration, with the endometrial microbiota being more responsive to CFA than the intestinal chyme microbiome. Remarkably, the Actinobacteriota representatives disappeared in the endometrium of Group II animals compared to controls, whose content ranged from 0.34 to 3.3%. The use of CFA also resulted in a less pronounced effect in four predicted metabolic pathways for microbial degradation of catechol in the endometrium compared to controls (p < 0.05).

CONCLUSIONS: Our findings support the concept of a relationship between the gut microbiome and the reproductive system microflora of cows, as we observed changes in the composition and predicted metabolic pathways of the endometrial microbiota after orally administering CFA. This emphasizes the need for an integrated approach combining the correction of microecological disorders in the intestines and the reproductive system simultaneously.}, } @article {pmid40090450, year = {2025}, author = {Wu, H and Chen, S and Deng, Y and Shen, J and Xu, Y and Wen, T and Yuan, J and Shen, Q and Xue, C}, title = {Dynamics of antibiotic resistance genes and the bacterial community after stress from a single Dazomet fumigation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {372}, number = {}, pages = {126048}, doi = {10.1016/j.envpol.2025.126048}, pmid = {40090450}, issn = {1873-6424}, mesh = {*Fumigation ; *Soil Microbiology ; *Bacteria/genetics/drug effects ; Thiadiazines/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; RNA, Ribosomal, 16S/genetics ; Soil Pollutants/toxicity ; Microbiota/drug effects/genetics ; Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; }, abstract = {Although chemical fumigants are widely applied in agriculture to control soil-borne diseases, their influence on soil antibiotic resistance genes (ARGs) remains poorly understood. This study employed metagenomic sequencing to investigate the dynamic response and recovery processes of soil bacterial communities and ARGs after the end of fumigation with Dazomet. The results revealed that the effects of Dazomet were both phased and recoverable. Initially, no significant shifts in bacterial community diversity were observed; however, by day 10 of recovery (Dazomet10), diversity had decreased by 3.1 %. By contrast, ARG levels surged by 17.3 % and 10.9 % on days 10 and 20 (Dazomet20), respectively, before reverting to the baseline by day 50 (Dazomet50). These patterns were corroborated by qPCR data, which showed a 90.8 % reduction in 16S rRNA gene abundance, alongside a 4.17- to 4.38-fold increase in the relative abundance of ARGs at Dazomet10 and Dazomet20. Approximately 63 % of the variation in ARGs was attributed to bacterial community composition and mobile genetic elements (MGEs). Combined with community analysis and host-tracking analysis, it was found that Streptomyces and Nocardioides were identified as key ARGs hosts. Overall, the microbial communities and resistome required at least 50 days after the end of fumigation to recover to their pre-fumigation state. This study sheds light on the dynamic interactions between bacterial communities and ARGs during recovery from Dazomet fumigation and underscores the critical need for the rational use of fumigants in agricultural practices.}, } @article {pmid40086705, year = {2025}, author = {Ma, G and Chai, Y and Tye, KD and Xie, H and Meng, L and Tang, X and Luo, H and Xiao, X}, title = {Predictive analysis of the impact of probiotic administration during pregnancy on the functional pathways of the gut microbiome in healthy infants based on 16S rRNA gene sequencing.}, journal = {Gene}, volume = {952}, number = {}, pages = {149414}, doi = {10.1016/j.gene.2025.149414}, pmid = {40086705}, issn = {1879-0038}, mesh = {Humans ; *Probiotics/administration & dosage ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; Infant, Newborn ; Infant ; *Feces/microbiology ; Adult ; Bacteria/classification/genetics ; }, abstract = {Maternal probiotic supplementation altered the microbial composition in infants' gut, yet its effect on the functional pathways of the microbiota remains unclear. This study aimed to explore the potential impact of maternal probiotic intake on the predicted functional pathways of the gut microbiome in healthy infants. A total of 24 pregnant women were randomly allocated to either the control group or the probiotic group. The women in the probiotic group began receiving probiotics at the 32nd week of pregnancy and continued until delivery. Meconium and fecal samples were collected from infants at birth, as well as on the 3rd day, 14th day, and 6th month after birth. The functional characteristics of the microbial community were inferred using 16S rRNA gene analysis, processed with PICRUSt software, and cross-referenced with the KEGG database. The probiotic group had lower levels of Actinobacteria and Bacteroidetes, while Bifidobacterium growth was notably increased in the infant gut microbiota. At day 0 postpartum, the control group exhibited higher levels of Prevotellaceae compared to the probiotic group (P < 0.05). However, no significant differences were found by day 3. At day 14, the control group exhibited higher levels of Bacteroidaceae and Bacteroides, while Bacteroides_thetaiotaomicron was more abundant in the probiotic group (P < 0.05). By 6 months, the control group showed a higher abundance of Firmicutes (P < 0.05). On day 0 postpartum, maternal probiotic consumption increased the Environmental information processing pathway at KEGG Level 1, and increased Energy metabolism, Metabolism of cofactors and vitamins, and Cell growth and death pathways at KEGG Level 2. It also increased Histidine metabolism, One carbon pool by folate, and Folate biosynthesis at KEGG Level 3. No changes were observed in the infant gut microbiota's functional metabolic pathways at 3 days postpartum. At 14 days postpartum, probiotics reduced Lipid metabolism pathways at KEGG Level 2 and the Citrate cycle at KEGG Level 3. At 6 months postpartum, probiotics decreased Carbohydrate metabolism pathways at KEGG Level 2. Our findings suggest that probiotic supplementation during pregnancy affects the functional metabolism of the gut microbiota in healthy infants. This, in turn, may influence the development of the infant's immune system, metabolism, and overall health by modifying the gut microbial environment.}, } @article {pmid40074067, year = {2025}, author = {Pragasam, AK and Maurya, S and Jain, K and Pal, S and Raja, C and Yadav, R and Kumar, S and Purohit, A and Pradhan, D and Kajal, K and Talukdar, D and Singh, AN and Verma, J and Jana, P and Rawat, S and Kshetrapal, P and Krishna, A and Kumar, S and Bansal, VK and Das, B and Srikanth, CV and Garg, PK}, title = {Invasive Salmonella Typhimurium colonizes gallbladder and contributes to gallbladder carcinogenesis through activation of host epigenetic modulator KDM6B.}, journal = {Cancer letters}, volume = {618}, number = {}, pages = {217621}, doi = {10.1016/j.canlet.2025.217621}, pmid = {40074067}, issn = {1872-7980}, mesh = {Animals ; *Salmonella typhimurium/pathogenicity/genetics ; *Gallbladder Neoplasms/microbiology/pathology/genetics ; Humans ; Mice ; *Salmonella Infections/microbiology/pathology/genetics ; *Epigenesis, Genetic ; Gallbladder/microbiology/pathology ; Histone Demethylases/genetics/metabolism ; Gastrointestinal Microbiome ; Female ; Carcinogenesis/genetics ; Male ; Cell Line, Tumor ; }, abstract = {Gallbladder stones alone do not explain the risk of gallbladder cancer (GBC) as the sole etiological factor. Chronic microbial infection, particularly Salmonella, has been implicated in GB carcinogenesis, but its causative role and the underlying mechanisms are largely unknown. We studied gut and gallbladder tissue microbiome through targeted metagenomics to identify pathogenic bacteria in GBC. Virulence and pathogenicity of identified Salmonella Typhimurium from GBC tissue were studied after culture by whole genome sequencing, phylogenetic analysis, mutational profiling, and pangenome analysis. Mechanistic studies for GBC carcinogenesis were carried out in a mouse model of gallstones and chronic Salmonella infection, a cellular model using GBC (NOZ) cell lines, and a xenograft tumor model. We found an increased abundance of Salmonella in the gut microbiome of patients with GBC and culturable S. Typhimurium from the gallbladder cancer tissue. Comparative genomics of S. Typhimurium isolated from the GBC tissue showed a high invasive index. S. Typhimurium isolates harbored horizontally acquired virulence functions in their accessory genome. Chronic S. Typhimurium infection caused chronic inflammation, pre-malignant changes, and tumor-promoting mechanisms in the mouse model with gallbladder stones with activation of the epigenetic modulator KDM6B both in the mouse model and human GBC. Inhibition of KDM6B reduced engrafted tumor size in SCID mice. Of the differentially regulated genes in human GBC tissue, ADAMTSL5, CX3CR1, and SPSB4 were also significantly dysregulated in NOZ cells infected with Salmonella. Chronic Salmonella infection contributes to gallbladder carcinogenesis through a host epigenetic mechanism involving KDM6B.}, } @article {pmid40064231, year = {2025}, author = {Jia, Y and Huang, D and Lan, X and Sun, X and Lin, W and Sun, W and Wang, Y}, title = {Community structure and metabolic potentials of keystone taxa and their associated bacteriophages within rice root endophytic microbiome in response to metal(loid)s contamination.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {372}, number = {}, pages = {126028}, doi = {10.1016/j.envpol.2025.126028}, pmid = {40064231}, issn = {1873-6424}, mesh = {*Oryza/microbiology ; *Plant Roots/microbiology ; *Endophytes/physiology ; *Metals, Heavy ; *Microbiota ; *Soil Pollutants/metabolism ; *Bacteriophages/physiology ; Bacteria/genetics/classification/metabolism/isolation & purification ; Soil Microbiology ; }, abstract = {Heavy metal (HM) contamination of agricultural products is of global environmental concern as it directly threatened the food safety. Plant-associated microbiome, particularly endophytic microbiome, hold the potential for mitigating HM stress as well as promoting plant growth. The metabolic potentials of the endophytes, especially those under the HM stresses, have not been well addressed. Rice, a major staple food worldwide, is more vulnerable to HM contamination compared to other crops and therefore requires special attentions. Therefore, this study selected rice as the target plants. Geochemical analysis and amplicon sequencing were combined to characterize the rice root endophytic bacterial communities and identify keystone taxa in two HM-contaminated rice fields. Metagenomic analysis was employed to investigate the metabolic potentials of these keystone taxa. Burkholderiales and Rhizobiales were identified as predominant keystone taxa. The metagenome-assembled genome (MAG)s associated with these keystone populations suggested that they possessed diverse genetic potentials related to metal resistance and transformation (e.g., As resistance and cycling, V reduction, Cr efflux and reduction), and plant growth promotion (nitrogen fixation, phosphate solubilization, oxidative stress resistance, indole-3-acetic acid, and siderophore production). Moreover, bacteriophages encoding auxiliary metabolism genes (AMGs) associated with the HM resistance as well as nitrogen and phosphate acquisition were identified, suggesting that these phages may contribute to these crucial biogeochemical processes within rice roots. The current findings revealed the beneficial roles of rice endophytic keystone taxa and their associated bacteriophages within HM-contaminated rice root endophytic microbiome, which may provide valuable insights on future applications of employing root microbiome for safety management of agriculture productions.}, } @article {pmid40054424, year = {2025}, author = {Ding, C and Sun, J}, title = {The potential contribution of microbial communities to carbon fixation and nitrogen cycle in the Eastern Indian Ocean.}, journal = {Marine environmental research}, volume = {207}, number = {}, pages = {107056}, doi = {10.1016/j.marenvres.2025.107056}, pmid = {40054424}, issn = {1879-0291}, mesh = {Indian Ocean ; *Carbon Cycle ; *Nitrogen Cycle ; *Microbiota ; *Seawater/microbiology/chemistry ; *Nitrogen Fixation ; RNA, Ribosomal, 16S/genetics ; Nitrogen/metabolism/analysis ; Bacteria/metabolism/genetics/classification ; }, abstract = {This study investigated the diversity and metabolic potential of microbial communities in the Eastern Indian Ocean (EIO) through 16S rDNA gene sequencing and metagenomics analyses. Water samples were collected from the surface waters (5 m depth) and 150 m depth layer in the EIO between March 20th and June 6th, 2019. This study reveals microbial-driven biogeochemical dynamics in the oligotrophic Eastern Indian Ocean, where vertically stratified communities (Cyanobacteria/Proteobacteria-dominated surface vs. diversified Proteobacteria at 150 m) and latitudinal diversity gradients reflect nutrient limitations. Metagenomics identified four carbon fixation strategies: the Calvin cycle dominated epipelagic CO2 assimilation, while the 3-hydroxypropionate bicycle showed elevated surface activity, alongside reductive citrate and Wood-Ljungdahl pathways involving novel Actinobacteria. Nitrogen cycling exhibited spatial heterogeneity: nifH-dominated nitrogen fixation in the surface waters, prevalent narGHI nitrate reduction, and divergent nirS/nirK/nosZ distributions tied to nutrient gradients. Proteobacteria and Actinobacteria were key nitrogen fixers, with novel Actinobacteriota diazotrophs expanding known diversity. Elevated nosZ abundance in the Bay of Bengal underscored regional nitrous oxide consumption hotspots. These findings underscore microbial mediation of carbon-nitrogen fluxes in oligotrophic systems, providing genomic insights into ecosystem responses to climate-driven ocean changes.}, } @article {pmid38847202, year = {2025}, author = {Sharma, P and Singh, S and Singh, AV and Das, K and Bhaskar, Y and Goel, I and Singh, H and Das, R}, title = {Alteration of gastric microbiota in Helicobacter pylori - infected individuals suffering from gastroesophageal reflux disease, duodenal ulcer, and gastritis.}, journal = {Indian journal of pathology & microbiology}, volume = {68}, number = {1}, pages = {61-68}, pmid = {38847202}, issn = {0974-5130}, mesh = {Humans ; *Helicobacter Infections/microbiology ; *Duodenal Ulcer/microbiology ; *Gastritis/microbiology ; *Gastroesophageal Reflux/microbiology ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; Adult ; Middle Aged ; *Helicobacter pylori/genetics/pathogenicity/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification ; Young Adult ; Aged ; }, abstract = {BACKGROUND/AIM: Helicobacter pylori (H. pylori) colonization affects the gastric microbiome, causing gastrointestinal (GI) diseases. Modern sequencing technology provides insights into GI microbe interaction with H. pylori and their metabolic pathways in causing GI diseases. We aim to compare the gastric microbiota alteration due to H. pylori infection in patients suffering from GI diseases.

MATERIALS AND METHODS: Genomic DNA were isolated from gastric antrum tissue from 37 H . pylori -infected patients diagnosed with GERD, duodenal ulcers, and gastritis. We conducted the genomic library preparation and sequencing of the amplified product using 16S rRNA NGS analysis. Using microbiome analyst tool diversity analysis, random forest analysis and ANOVA were conducted to find out the comparison of microbial abundance. We have also conducted functional pathway prediction analysis using PICRUSt.

RESULTS: Metagenomic analysis shows high bacterial diversity in H. pylori -positive gastritis patients. Streptococcus infantis and Neisseria subflava were significantly higher in duodenal ulcer (DU) and gastritis groups. Acinetobacter lwoffii and Helicobacter pullorum were significantly high in the gastritis group only. The functional metabolic pathway analyses revealed that gastroesophageal reflux disease (GERD) samples were significantly enriched with the energy metabolism and xenobiotic biodegradation and metabolism pathways, whereas fructose-1,6-bisphosphatase III was found less in gastritis and DU groups.

CONCLUSION: There is a difference in microbiota composition in different disease outcomes. We found positive association between microbial diversity and H. pylori in gastritis group only, whereas negative association was found in DU and GERD groups. The functional metabolic pathway analysis revealed significant differences in various disease outcomes.}, } @article {pmid40149936, year = {2025}, author = {Zhan, J and Cheng, J and Chang, W and Su, Y and Yue, X and Wu, C}, title = {Absolute Quantitative Metagenomic Analysis Provides More Accurate Insights for the Anti-Colitis Effect of Berberine via Modulation of Gut Microbiota.}, journal = {Biomolecules}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/biom15030400}, pmid = {40149936}, issn = {2218-273X}, mesh = {*Berberine/pharmacology ; *Gastrointestinal Microbiome/drug effects/genetics ; Animals ; *Metagenomics/methods ; Colitis, Ulcerative/microbiology/drug therapy ; Mice ; Bacteria/drug effects/genetics/classification ; Male ; Butyric Acid/pharmacology ; Disease Models, Animal ; }, abstract = {Current gut microbiota studies often rely on relative quantitative sequencing. However, under certain circumstances, while the relative quantitative abundance of these bacteria may remain stable, the absolute quantities of specific bacteria can vary considerably. Since the function of bacteria is directly linked to their total numbers, absolute quantification is crucial. This study aims to identify the optimal method for microbiome analysis by comparing relative and absolute quantitative sequencing. Using ulcerative colitis, which is closely associated with gut microbiota, as a disease model and berberine (which affects microbiota) versus sodium butyrate (which does not) as drugs, relative and absolute quantitative methods were used to evaluate the varying effects of the different drugs on the regulation of gut microbiota in UC-affected animals. The regulatory effects of BBR on gut microbiota were further synthesized as identified in earlier studies using an individual-based meta-analysis, and we compared these findings with our absolute sequencing results. The results from absolute sequencing were more consistent with the actual microbial community, suggesting that relative abundance measurements might not accurately reflect the true abundance of microbial species. Moreover, meta-analysis results were only partially consistent with absolute quantitative sequencing and sometimes directly opposed, suggesting that relative quantitative sequencing analyses are prone to misinterpretation and incorrect correlation of results. This study underscores the importance of absolute quantitative analysis in accurately representing the true microbial counts in a sample and evaluating the modulatory effects of drugs on the microbiome, which plays a vital role in the study of the microbiome.}, } @article {pmid40050500, year = {2025}, author = {Dave, M and Tattar, R}, title = {Antimicrobial resistance genes in the oral microbiome.}, journal = {Evidence-based dentistry}, volume = {26}, number = {1}, pages = {42-43}, pmid = {40050500}, issn = {1476-5446}, mesh = {*Mouth/microbiology ; Humans ; *Microbiota/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Polymerase Chain Reaction ; Biofilms/drug effects ; }, abstract = {A COMMENTARY ON: Sukumar S, Rahmanyar Z, El Jurf H Q et al. Mapping the oral resistome: a systematic review. J Med Microbiol 2024; https://doi.org/10.1099/jmm.0.001866 .

DESIGN: This systematic review, without meta-analysis, aimed to map the oral resistome by analysing clinical studies that detected bacterial antimicrobial resistance genes (ARGs) in the oral cavity using molecular techniques.

DATA SOURCES: The researchers used Medline, Embase, Web of Science, CINAHL and Scopus databases from January 2015 to August 2023.

STUDY SELECTION: This systematic review included cross-sectional or longitudinal clinical studies that detected ARGs using molecular techniques; specifically polymerase chain reaction (PCR) or next-generation sequencing (NGS) metagenomics for samples from the oral cavity (saliva, gingival biofilm, pulp, or oral mucosa). Studies were excluded if they were in vitro or animal studies, literature reviews and not focused on ARG detection.

DATA EXTRACTION AND SYNTHESIS: Five reviewers independently screened titles and abstracts based on inclusion criteria. Full-text reports were then independently assessed for eligibility by three reviewers. Extracted data encompassed publication details, sample size, country, molecular methods used, number of ARGs detected, participants' health status, antibiotic exposure, and sample location within the oral cavity.

RESULTS: Out of 580 initially identified studies, 15 met the inclusion criteria. These studies, published between 2015 and 2023 from 12 different countries, employed either PCR (n = 10) or NGS metagenomics (n = 5) to detect ARGs from a pool of 1486 participants (1 study did not report on the number of participants). PCR-based studies identified an average of 7 ARGs (range 1-20), while NGS studies identified an average of 34 ARGs (range 7-70). In total, 159 unique ARGs conferring resistance to 22 antibiotic classes were identified across six regions of the oral cavity. The supragingival biofilm and saliva exhibited the highest richness of ARGs, defined by the number of unique ARGs detected. Genes conferring resistance to 19 antibiotic classes were present in the supragingival biofilm. Notably, 49 ARGs, including tetracycline and macrolide resistance genes, were found across all sampled locations, indicating a widespread distribution within the oral cavity. Thirteen studies reported on bacterial species associated with ARGs. NGS studies identified a mean of 65 ARG-carrying bacterial species, compared to a mean of 4 species in PCR studies. Specifically, 25 ARG-carrying species were identified in PCR studies, while NGS studies identified 177 species. Four studies reported ARGs associated with streptococcal species implicated in distant-site infections such as infective endocarditis. ESKAPE pathogens (group of highly virulent multidrug-resistant bacteria) were detected with ARGs in various oral sites using both PCR and NGS methods. Comparisons between healthy and diseased states revealed that a healthy oral microbiome harbours a more diverse resistome at the antibiotic class level. The supragingival resistome demonstrated the richest composition in both health and disease, with tetracycline ARGs predominating in the supragingival and saliva resistomes in cases of dental caries.

CONCLUSIONS: The analysis of the oral resistome from these 15 studies identified three ARGs present in all sites of the oral cavity, suggesting the presence of a core resistome. NGS studies provided greater insights compared to PCR studies; however, the overall research base is limited. Further comprehensive studies are necessary to fully map the oral resistome.}, } @article {pmid40149437, year = {2025}, author = {Alharbi, SM and Al-Sulami, N and Al-Amrah, H and Anwar, Y and Gadah, OA and Bahamdain, LA and Al-Matary, M and Alamri, AM and Bahieldin, A}, title = {Metagenomic Characterization of the Maerua crassifolia Soil Rhizosphere: Uncovering Microbial Networks for Nutrient Acquisition and Plant Resilience in Arid Ecosystems.}, journal = {Genes}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/genes16030285}, pmid = {40149437}, issn = {2073-4425}, mesh = {*Rhizosphere ; *Soil Microbiology ; Mycorrhizae/genetics/classification ; Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics/methods ; Metagenome ; Ecosystem ; Microbiota/genetics ; Plant Roots/microbiology ; Fungi/genetics/classification ; }, abstract = {Background/Objectives:Maerua crassifolia, a threatened medicinal species endemic to drylands, exhibits a pronounced drought sensitivity. Despite the critical role of microorganisms, particularly bacteria and fungi, the microbial consortia in M. crassifolia's rhizosphere remain underexplored. Methods: Metagenomic whole genome shotgun sequencing (WGS) was employed to elucidate the taxonomic composition of bacterial and fungal communities inhabiting the soil rhizosphere of M. crassifolia. Results: The data revealed a marked predominance of bacterial genomes relative to fungal communities, as evidenced by non-redundant gene analysis. Notably, arbuscular mycorrhizal fungi (AMF), specifically Rhizophagus clarus, Rhizophagus irregularis and Funneliformis geosporum, are key rhizosphere colonizers. This study confirmed the presence of phosphate-solubilizing bacteria (PSB), such as Sphingomonas spp., Cyanobacteria and Pseudomonadota, underscoring the critical role of these microorganisms in the phosphorus cycle. Additionally, the study uncovered the presence of previously uncharacterized species within the phylum Actinobacteria, as well as unidentified taxa from the Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla, which may represent novel microbial taxa with potential plant growth-promoting properties. Conclusions: Findings suggest a complex, symbiotic network where AMF facilitate phosphorus uptake through plant-root interactions. In a tripartite symbiosis, PSB enhance inorganic phosphorus solubilization, increasing bioavailability, which AMF assimilate and deliver to plant roots, optimizing nutrition. This bacterial-fungal interplay is essential for plant resilience in arid environments. Future investigations should prioritize the isolation and characterization of underexplored microbial taxa residing in the rhizosphere of M. crassifolia, with particular emphasis on members of the Actinobacteria, Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla to uncover their roles in nutrient acquisition and sustainability.}, } @article {pmid40146796, year = {2025}, author = {Li, J and Zhu, Y and Chang, Q and Gong, Y and Wan, J and Xu, S}, title = {Comparative Analysis of Microbiological Profiles and Antibiotic Resistance Genes in Subjects with Colorectal Cancer and Healthy Individuals.}, journal = {Polish journal of microbiology}, volume = {74}, number = {1}, pages = {71-81}, pmid = {40146796}, issn = {2544-4646}, mesh = {Humans ; *Colorectal Neoplasms/microbiology ; Male ; Middle Aged ; Female ; *Bacteria/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome ; Feces/microbiology ; Aged ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Adult ; }, abstract = {Alteration of the gut microbiota (GM) is associated with various diseases, including colorectal cancer (CRC). With the development of next-generation sequencing techniques, metagenomic sequencing, along with metabolic function and antibiotic-resistant gene analyses, has been used to investigate differences in GM between CRC patients and healthy controls. Fecal samples were obtained from seven CRC patients and six healthy subjects, and the sequencing data were analyzed for similarity, a-diversity, principal component analysis (PCA), and linear discriminant analyses (LDA). Regarding Actinobacteria, 3 orders, 5 families, 9 genera, and 19 species were identified with no differences between the CRC and control groups, while the levels of Bifidobacterium bifidum and Bifidobacterium dentium were higher, and the level of Bifidobacterium breve was lower in the CRC group compared to the healthy controls (p = 0.053). Otherwise, 2 genera (Leuco-nostoc and Salmonella) and 7 species of bacteria (Parabacteroides merdae, Alistipes shahii, Alistipes finegoldii, Clostridium nexile, Salmonella enterica, unclassified Salmonella, Enterobacter cloacae) were found to be significantly differently distributed between CRC patients and healthy controls. PCA-LDA successfully classified these 2 groups with satisfactory accuracy (84.52% for metabolic function and 77.38% for resistant genes). These findings underscore the potential of GM as a diagnostic tool for CRC, offering a promising avenue for non-invasive screening and risk assessment. The identification of specific microbial signatures, particularly those linked to metabolic functions and resistance traits, could open new doors for understanding the role of the microbiome in CRC progression and treatment resistance.}, } @article {pmid40144403, year = {2025}, author = {Li, Z and Zou, D and Liu, R and Pan, J and Huang, J and Ma, J and Huang, L and He, J and Fu, L and Zheng, X and Wang, M and Fang, J and Dong, H and Li, M and Huang, L and Dai, X}, title = {A hunting ground for predatory bacteria at the Zhenbei seamount in the South China Sea.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf042}, pmid = {40144403}, issn = {2730-6151}, abstract = {Seamounts are critical marine biodiversity hot spots, while the metabolic activity of their microbial community remains largely unknown. In this study, we investigated the diversity and activity of free-living and particle-attached microorganisms in the surface, middle, and bottom layers of seawater at the Zhenbei seamount in the South China Sea using omics approaches, including 16S ribosomal RNA (rRNA)/16S rDNA ratio analysis. Over 20 phyla were detected, with Proteobacteria, Actinobacteriota, Cyanobacteria, Bacteroidota, Thaumarchaeota, and Planctomycetota being predominant. Surprisingly, Bdellovibrionota and Myxococcota, the two well-known predatory bacteria, exhibited exceptionally higher rRNA/rDNA ratios than the other phyla, with rRNA abundances being 10- or even 200-fold higher than their rDNA abundances. These metabolically active predatory bacteria are mainly uncultured species. A total of 23 Myxococcota metagenome-assembled genomes (MAGs) and 12 Bdellovibrionota MAGs were assembled. The most highly overexpressed genes frequently detected in these MAGs were those that encode flagellum and pilus proteins as well as T4-like virus tail tube protein, indicating that these predator bacteria were likely active in hunting. Our results suggest that seamounts may serve as hunting grounds for predatory bacteria, which may be involved in controlling the flows of elements and energy in the seamount microbial communities and, thus, in shaping the seamount ecosystems.}, } @article {pmid40122128, year = {2025}, author = {Zhang, D and Wang, Q and Li, D and Chen, S and Chen, J and Zhu, X and Bai, F}, title = {Gut microbiome composition and metabolic activity in metabolic-associated fatty liver disease.}, journal = {Virulence}, volume = {16}, number = {1}, pages = {2482158}, doi = {10.1080/21505594.2025.2482158}, pmid = {40122128}, issn = {2150-5608}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; Female ; Adult ; China ; Bacteria/classification/genetics/metabolism/isolation & purification ; Eubacterium/metabolism/genetics ; Fatty Liver/microbiology/metabolism ; Metagenomics ; Metabolomics ; Case-Control Studies ; Metabolome ; Metagenome ; }, abstract = {Metabolic Associated Fatty Liver Disease (MAFLD) impacts approximately 25% of the global population. Between April 2023 and July 2023, 60 patients with MAFLD, along with 60 age, ethnicity, and sex-matched healthy controls (HCs), were enrolled from the Inner Mongolia Autonomous Region, China. Analysis of gut microbiota composition and plasma metabolic profiles was conducted using metagenome sequencing and LC-MS. LEfSe analysis identified five pivotal species: Eubacterium rectale, Dialister invisus, Pseudoruminococcus massiliensis, GGB3278 SGB4328, and Ruminococcaceae bacteria. In subgroup analysis, Eubacterium rectale tended to increase by more than 2 times and more than double in the non-obese MAFLD group, and MAFLD with moderate hepatic steatosis (HS), respectively. Plasma samples identified 172 metabolites mainly composed of fatty acid metabolites such as propionic acid and butyric acid analogues. Ruminococcaceae bacteria have a strong positive correlation with β-alanine, uric acid, and L-valine. Pseudoruminococcus massiliensis has a strong positive correlation with β-alanine. Combinations of phenomics and metabolomics yielded the highest accuracy (AUC = 0.97) in the MAFLD diagnosis. Combinations of phenomics and metagenomics yielded the highest accuracy (AUC = 0.94) in the prediction of the MAFLD HS progress. Increases in Eubacterium rectale and decreases in Dialister invisus seem to be indicative of MAFLD patients. Eubacterium rectale may predict HS degree of MAFLD and play an important role in the development of non-obese MAFLD. Eubacterium rectale can generate more propionic acid and butyric acid analogues to absorb energy and increase lipid synthesis and ultimately cause MAFLD.}, } @article {pmid40142589, year = {2025}, author = {Chen, X and Gao, L and Kou, Y and Wang, X and Li, X and He, H and Wang, M}, title = {Composition, Distribution and Mobility Potential of the Antibiotic Resistome in Sediments from the East China Sea Revealed by Metagenomic Analysis.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030697}, pmid = {40142589}, issn = {2076-2607}, support = {41806131//National Natural Science Foundation of China/ ; 42120104006//National Natural Science Foundation of China/ ; ZR2024QD036//Natural Science Foundation of Shandong Province/ ; }, abstract = {Marine sediments are recognized as crucial reservoirs of antibiotic resistance genes (ARGs). However, the antibiotic resistome in sediments of the East China Sea, an area heavily impacted by human activities, has not been thoroughly studied. Here, we conducted a systematic investigation into the antibiotic resistome in these sediments using metagenomic analysis. Overall, we detected eighty ARG subtypes and nineteen ARG types. Beta-lactams were the dominant ARG type, and Gammaproteobacteria was the main ARG host in this study. Mobile genetic elements (MGEs) were not major drivers of ARG profiles. Although the ARG host communities significantly differed between the spring and autumn (p < 0.05), the antibiotic resistome remained stable across the two seasons. The assembly of ARGs and their hosts was governed by stochastic processes, and a high ratio of stochastic processes implied its crucial role in the assembly and stabilization of the antibiotic resistome. Co-occurrence network analysis revealed an important role of Deltaproteobacteria in the stabilization of ARG profiles across seasons. Environmental parameters (e.g., temperature and density) played certain roles in the stabilization of the antibiotic resistome between spring and autumn. Moreover, nine human pathogen bacteria (HPB) were detected in this study. We also found that the health risks caused by ARGs were relatively higher in the spring. Our results will provide a strong foundation for the development of targeted management strategies to mitigate the further dissemination and spread of ARGs in marine sediments.}, } @article {pmid40141768, year = {2025}, author = {Ghobashy, MOI and Al-Otaibi, AS and Alharbi, BM and Alshehri, D and Ghabban, H and Albalawi, DA and Alenzi, AM and Alatawy, M and Alatawi, FA and Algammal, AM and Mir, R and Mahrous, YM}, title = {Metagenomic Characterization of Microbiome Taxa Associated with Coral Reef Communities in North Area of Tabuk Region, Saudia Arabia.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/life15030423}, pmid = {40141768}, issn = {2075-1729}, support = {Research no.0144-1444-S//Deanship of Research and Graduate Studies at University of Tabuk/ ; }, abstract = {The coral microbiome is highly related to the overall health and the survival and proliferation of coral reefs. The Red Sea's unique physiochemical characteristics, such a significant north-south temperature and salinity gradient, make it a very intriguing research system. However, the Red Sea is rather isolated, with a very diversified ecosystem rich in coral communities, and the makeup of the coral-associated microbiome remains little understood. Therefore, comprehending the makeup and dispersion of the endogenous microbiome associated with coral is crucial for understanding how the coral microbiome coexists and interacts, as well as its contribution to temperature tolerance and resistance against possible pathogens. Here, we investigate metagenomic sequencing targeting 16S rRNA using DNAs from the sediment samples to identify the coral microbiome and to understand the dynamics of microbial taxa and genes in the surface mucous layer (SML) microbiome of the coral communities in three distinct areas close to and far from coral communities in the Red Sea. These findings highlight the genomic array of the microbiome in three areas around and beneath the coral communities and revealed distinct bacterial communities in each group, where Pseudoalteromonas agarivorans (30%), Vibrio owensii (11%), and Pseudoalteromonas sp. Xi13 (10%) were the most predominant species in samples closer to coral (a coral-associated microbiome), with the domination of Pseudoalteromonas_agarivorans and Vibrio_owensii in Alshreah samples distant from coral, while Pseudoalteromonas_sp._Xi13 was more abundant in closer samples. Moreover, Proteobacteria such as Pseudoalteromonas, Pseudomonas and Cyanobacteria were the most prevalent phyla of the coral microbiome. Further, Saweehal showed the highest diversity far from corals (52.8%) and in Alshreah (7.35%) compared to Marwan (1.75%). The microbial community was less diversified in the samples from Alshreah Far (5.99%) and Marwan Far (1.75%), which had comparatively lower values for all indices. Also, Vibrio species were the most prevalent microorganisms in the coral mucus, and the prevalence of these bacteria is significantly higher than those found in the surrounding saltwater. These findings reveal that there is a notable difference in microbial diversity across the various settings and locales, revealing that geographic variables and coral closeness affect the diversity of microbial communities. There were significant differences in microbial community composition regarding the proximity to coral. In addition, there were strong positive correlations between genera Pseudoalteromonas and Vibrio in close-to-coral environments, suggesting that these bacteria may play a synergistic role in Immunizing coral, raising its tolerance towards environmental stress and overall coral health.}, } @article {pmid40140988, year = {2025}, author = {Yan, Q and Huang, L and Li, S and Zhang, Y and Guo, R and Zhang, P and Lei, Z and Lv, Q and Chen, F and Li, Z and Meng, J and Li, J and Wang, G and Chen, C and Ullah, H and Cheng, L and Fan, S and You, W and Zhang, Y and Ma, J and Sha, S and Sun, W}, title = {The Chinese gut virus catalogue reveals gut virome diversity and disease-related viral signatures.}, journal = {Genome medicine}, volume = {17}, number = {1}, pages = {30}, pmid = {40140988}, issn = {1756-994X}, mesh = {Humans ; *Virome/genetics ; *Viruses/genetics/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; China ; Female ; Feces/virology ; Male ; Metagenomics/methods ; Genome, Viral ; Asian People/genetics ; East Asian People ; }, abstract = {BACKGROUND: The gut viral community has been increasingly recognized for its role in human physiology and health; however, our understanding of its genetic makeup, functional potential, and disease associations remains incomplete.

METHODS: In this study, we collected 11,286 bulk or viral metagenomes from fecal samples across large-scale Chinese populations to establish a Chinese Gut Virus Catalogue (cnGVC) using a de novo virus identification approach. We then examined the diversity and compositional patterns of the gut virome in relation to common diseases by analyzing 6311 bulk metagenomes representing 28 disease or unhealthy states.

RESULTS: The cnGVC contains 93,462 nonredundant viral genomes, with over 70% of these being novel viruses not included in existing gut viral databases. This resource enabled us to characterize the functional diversity and specificity of the gut virome. Using cnGVC, we profiled the gut virome in large-scale populations, assessed sex- and age-related variations, and identified 4238 universal viral signatures of diseases. A random forest classifier based on these signatures achieved high accuracy in distinguishing diseased individuals from controls (AUC = 0.698) and high-risk patients from controls (AUC = 0.761), and its predictive ability was also validated in external cohorts.

CONCLUSIONS: Our resources and findings significantly expand the current understanding of the human gut virome and provide a comprehensive view of the associations between gut viruses and common diseases. This will pave the way for novel strategies in the treatment and prevention of these diseases.}, } @article {pmid40140473, year = {2025}, author = {Brown, AA and Widdowson, M and Brandt, S and Mohammadzadeh, P and Rosenberg, JB and Jepsen, JRM and Ebdrup, BH and Hernández-Lorca, M and Bønnelykke, K and Chawes, B and Stokholm, J and Thorsen, J and Ibrahimi, P and Li, X and Sørensen, SJ and Rasmussen, MA}, title = {Associations of the gut microbiome and inflammatory markers with mental health symptoms: a cross-sectional study on Danish adolescents.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {10378}, pmid = {40140473}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Adolescent ; Cross-Sectional Studies ; Female ; Denmark/epidemiology ; *Inflammation/metabolism ; *Attention Deficit Disorder with Hyperactivity/metabolism/microbiology ; *Biomarkers ; *Depression/metabolism ; Anxiety/microbiology ; Mental Health ; Stress, Psychological/metabolism ; Feces/microbiology ; }, abstract = {Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental disorder that often persists into adulthood and is accompanied by comorbid mental health problems. This cross-sectional cohort study analyzed 411 18-year-olds from the Danish COPSAC2000 birth cohort to investigate the relationship between the gut microbiome, fasting and postprandial systemic inflammation, ADHD symptoms, and symptoms of anxiety, stress, and depression. ADHD was assessed using the Adult ADHD Self-Report Scale (ASRS), while depression, stress, and anxiety were evaluated with the Depression, Anxiety, and Stress Scale 21 (DASS-21). Fecal metagenomic data and inflammation levels, measured as glycosylated protein A (GlycA), were analyzed following a standardized meal challenge. In males, higher ADHD symptom scores correlated significantly with increased abundance of a tryptophan biosynthesis pathway (MetaCyc Metabolic Pathways Database) and elevated fasting and postprandial GlycA levels (p < 0.05). While the severity of depression, anxiety, and stress symptoms showed weak associations with GlycA and the gut microbiome, our findings indicate a significant link between ADHD symptoms and postprandial inflammation, warranting further investigation into underlying mechanisms.}, } @article {pmid40139249, year = {2025}, author = {Taylor, JT and Lee, V and Dearlove, T and Jolly, M and Wierenga, JR and Dubrulle, J and Hodgkinson-Bean, J and Hunter, S and Gartrell, B and Morgan, K and McInnes, K and French, N and Holmes, EC and Geoghegan, JL}, title = {A Metagenomic Investigation into Apteryx rowi Dermatosis Identifies Multiple Novel Viruses and a Highly Abundant Nematode.}, journal = {Journal of wildlife diseases}, volume = {}, number = {}, pages = {}, doi = {10.7589/JWD-D-24-00115}, pmid = {40139249}, issn = {1943-3700}, abstract = {Sporadic cases of dermatosis have been reported in wild Ōkārito Rowi (Apteryx rowi), a species of brown kiwi, for over a decade. The disease exhibits distinctive features, including lesions, lichenification, and feather loss. Swab samples and full-thickness skin biopsies were collected during a survey of affected kiwi in 2023 for a metatranscriptome-based, total infectome investigation to identify any possible microbial agents associated with the disease. Our approach identified novel viruses as well as a species of nematode in high relative abundance. We found a highly abundant hepacivirus within the Flaviviridae, but only in some mild cases of dermatitis across all sample types, and in both active and chronic infections. In addition, we found a significant shift in the taxonomic composition of the nonviral microbiome within severe chronic dermatitis cases, particularly an increased abundance of transcripts from a Eucoleus sp. parasitic. Although determining the primary cause of disease in critically endangered wildlife such as Rowi remains challenging, our detection of novel and highly abundant microorganisms opens new lines of inquiry to investigate their potential association with dermatosis in this nationally iconic species.}, } @article {pmid40138008, year = {2025}, author = {Davasaz Tabrizi, E and Sevil, M and Arican, E}, title = {Bioinformatic strategies in metagenomics of chronic prostatitis.}, journal = {World journal of urology}, volume = {43}, number = {1}, pages = {188}, pmid = {40138008}, issn = {1433-8726}, mesh = {Male ; *Prostatitis/microbiology ; Humans ; Adult ; *Metagenomics ; *Computational Biology ; Chronic Disease ; Young Adult ; Middle Aged ; Microbiota/genetics ; }, abstract = {PURPOSE: Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) is a prevalent urological condition in young men, significantly affecting quality of life due to persistent discomfort and neuropsychological symptoms. Despite its high prevalence, the etiology of CP/CPPS remains poorly understood. This study investigated urinary microbiota differences between CP/CPPS patients and healthy controls to identify microbial contributors, antibiotic resistance genes (ARGs), and virulence factors of dominant bacteria, as well as to explore potential therapeutic targets.

METHODS: Urine samples were collected from 58 CP/CPPS patients and 25 controls. Symptom severity was assessed by a specialist urologist using the NIH Chronic Prostatitis Symptom Index and UPOINT classification. Bacterial-specific 16 S rRNA sequencing was performed using nanopore technology, with bioinformatics analyses conducted via ONT guppy 5.0.11, NCBI and SLV 16 S bacterial taxonomic databases, UPGMA hierarchical clustering, and the Bacterial and Viral Bioinformatics Resource Center (BV-BRC). Pairwise comparisons were analyzed using the Mann-Whitney U test.

RESULTS: Distinct microbial diversity patterns were observed between patients and controls. Bacillus species were significantly enriched in CP/CPPS patients, while Enterococcus species predominated in controls. Younger patients exhibited unique microbiome profiles compared to older groups. Bioinformatics analyses identified ARGs and virulence factors associated with Bacillus species, implicating them in localized inflammation. Antibiotics like pleuromutilin or vancomycin were identified as potential therapeutic options, though experimental validation was beyond the study's scope.

CONCLUSION: These findings highlight microbial imbalances and provide a foundation for microbiome-targeted therapeutic strategies for CP/CPPS management in the future. Additionally, the identification of bacterial virulence factors and ARG provides insights into the potential mechanisms driving persistent symptoms. Future research with larger cohorts and experimental validation of the suggested therapeutic options may contribute to more effective treatment for CP/CPPS.}, } @article {pmid40137713, year = {2025}, author = {Shaw, CA and Soltero-Rivera, M and Profeta, R and Weimer, BC}, title = {Case Report: Shift from Aggressive Periodontitis to Feline Chronic Gingivostomatitis Is Linked to Increased Microbial Diversity.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/pathogens14030228}, pmid = {40137713}, issn = {2076-0817}, support = {UL1 TR001860/NH/NIH HHS/United States ; }, mesh = {Animals ; Cats ; *Microbiota/genetics ; *Cat Diseases/microbiology/diagnosis ; *Aggressive Periodontitis/microbiology ; Stomatitis/microbiology/veterinary ; Bacteria/genetics/classification/isolation & purification ; Disease Progression ; Mouth/microbiology ; Metagenomics ; Male ; }, abstract = {Aggressive Periodontitis (AP) and Feline Chronic Gingivostomatitis (FCGS) are two oral inflammatory diseases in cats with unknown etiology. Both conditions present with severe inflammation of the oral cavity and in FCGS it is found with additional deterioration of the non-keratinized mucosa. The oral microbiome is increasingly implicated in disease progression, but little is known about shifts in the microbial community during the AP and FCGS progression. To that end, we used deep metagenomic sequencing with total RNA on three longitudinal samples of the oral microbiome in a cat first diagnosed with AP that progressed to FCGS. This deep sequencing approach revealed that increased diversity at both the genus and species levels marked the shift from AP to FCGS, including increases in Porphyromonas and Treponema species, and decreased Streptobacillus species. The metatranscriptomes were then probed for expression of antimicrobial resistance genes and virulence factors. Disease-related genes that include cheY, and ompP5 were expressed in early AP and FCGS, while others like galU were only expressed in one or the other disease state. Both genus and species-level shifts were observed along the longitudinal microbiome samples with a noted increase in species diversity in the FCGS-associated microbiome. Corroborating that functional shifts accompany taxonomic changes, the AMR and virulence factor expression similarly changed between the sampling points. Together, these taxonomic and functional shifts indicate that AP and FCGS are potentially linked and may be marked by changes in the oral microbiome, which supports the development of microbial-based clinical diagnostics and therapeutics.}, } @article {pmid40136549, year = {2025}, author = {Pizzi, S and Conti, A and Di Canito, A and Casagrande Pierantoni, D and Foschino, R and Setati, ME and Vigentini, I}, title = {Endophytic Diversity in Vitis vinifera with Different Vineyard Managements and Vitis sylvestris Populations from Northern Italy: A Comparative Study of Culture-Dependent and Amplicon Sequencing Methods.}, journal = {Biology}, volume = {14}, number = {3}, pages = {}, pmid = {40136549}, issn = {2079-7737}, support = {150549//Italy/South Africa Joint Research Programme (ISARP) 2023-2025/ ; }, abstract = {This study aimed to investigate the endophytic microbial populations associated with wild and domesticated grapevines using both culture-based and culture-independent methods. Through culture-based methods, 148 endophytes were identified. The dominant fungal species included Aureobasidium pullulans, Alternaria alternata, and Cladosporium allicinum, while predominant bacterial species were Ralstonia pikettii, Nocardia niigatensis, and Sphingomonas echinoides. Culture-independent methods employed metagenomic techniques to explore microbial biodiversity, focusing on targeted amplification of bacterial 16S rRNA as well as fungal ITS and 26S rRNA gene regions. The main bacterial species identified included Halomonas sp., Sphingomonas sp. and Massilia sp., whereas the fungal population was dominated by Cladosporium sp., Malassezia sp. and Mucor sp. The findings revealed that vineyard management practices did not lead to statistically significant variations in microbial communities. The consistent presence of these genera across all samples suggests that they are stable components of the grapevine endophytic microbiota, remaining relatively unaffected by external environmental factors.}, } @article {pmid40135504, year = {2025}, author = {Pelto, J and Auranen, K and Kujala, JV and Lahti, L}, title = {Elementary methods provide more replicable results in microbial differential abundance analysis.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, pmid = {40135504}, issn = {1477-4054}, support = {952914//European Union's Horizon 2020 research and innovation programme/ ; }, mesh = {*Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Humans ; Reproducibility of Results ; Computational Biology/methods ; Bacteria/genetics/classification ; }, abstract = {Differential abundance analysis (DAA) is a key component of microbiome studies. Although dozens of methods exist, there is currently no consensus on the preferred methods. While the correctness of results in DAA is an ambiguous concept and cannot be fully evaluated without setting the ground truth and employing simulated data, we argue that a well-performing method should be effective in producing highly reproducible results. We compared the performance of 14 DAA methods by employing datasets from 53 taxonomic profiling studies based on 16S rRNA gene or shotgun metagenomic sequencing. For each method, we examined how the results replicated between random partitions of each dataset and between datasets from separate studies. While certain methods showed good consistency, some widely used methods were observed to produce a substantial number of conflicting findings. Overall, when considering consistency together with sensitivity, the best performance was attained by analyzing relative abundances with a nonparametric method (Wilcoxon test or ordinal regression model) or linear regression/t-test. Moreover, a comparable performance was obtained by analyzing presence/absence of taxa with logistic regression.}, } @article {pmid40133298, year = {2025}, author = {Bhanu, P and Buchke, S and Hemandhar-Kumar, N and Varsha, P and Kiran, SKR and Vikneswaran, G and Alva, A and Basavaraj, GS and Kumar, J}, title = {Comparative metagenomic analysis of the oral microbiome in COVID-19 patients and healthy individuals.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {10303}, pmid = {40133298}, issn = {2045-2322}, support = {20210001//Bangalore Bioinnovation Centre/ ; }, mesh = {Humans ; *COVID-19/microbiology/virology ; *Mouth/microbiology/virology ; *Microbiota/genetics ; *Metagenomics/methods ; *SARS-CoV-2/genetics/isolation & purification ; Male ; Female ; Adult ; Middle Aged ; Metagenome ; Aged ; }, abstract = {COVID-19, caused by SARS-CoV-2, affects multiple body systems, including the oral cavity, where it may disrupt the oral microbiome in ways that contribute to disease pathology. Understanding the long-term interaction between SARS-CoV-2 and the oral microbiome is crucial, as it may reveal microbial markers valuable for diagnosing or monitoring persistent health issues in COVID-19 survivors. Metagenomic sequencing revealed significant microbial shifts in the oral microbiome of COVID-19 patients, showing reduced microbial diversity and increased prevalence of opportunistic pathogens compared to healthy individuals. Alpha diversity measures indicated lower microbial diversity and evenness, while beta diversity analyses demonstrated distinct microbial community compositions. Core microbiome analysis identified unique taxa in COVID-19 patients that may contribute to disease pathology, while differential abundance analysis highlighted specific taxa shifts, including an increase in potential pathogens. Our findings advance the understanding of microbial changes in the oral microbiome associated with COVID-19 and suggest potential targets for microbiome-based interventions. While these results indicate associations with possible health impacts, further research is needed to determine causative links and long-term implications for COVID-19 survivors. This foundational research highlights the potential for microbiome science to inform diagnostic tools, such as microbial markers for disease progression, and therapeutic approaches, including targeted probiotics, which could ultimately support better patient outcomes and public health strategies.}, } @article {pmid40101714, year = {2025}, author = {Lynn, HM and Gordon, JI}, title = {Sequential co-assembly reduces computational resources and errors in metagenome-assembled genomes.}, journal = {Cell reports methods}, volume = {5}, number = {3}, pages = {101005}, doi = {10.1016/j.crmeth.2025.101005}, pmid = {40101714}, issn = {2667-2375}, mesh = {Animals ; Humans ; *Metagenome/genetics ; Mice ; *Gastrointestinal Microbiome/genetics ; Bangladesh ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Metagenomics/methods ; }, abstract = {Generating metagenome-assembled genomes from DNA shotgun sequencing datasets can demand considerable computational resources. Here, we describe a sequential co-assembly method that reduces the assembly of duplicate reads through successive application of single-node computing tools for read assembly and mapping. Using a simulated mouse microbiome DNA shotgun sequencing dataset, we demonstrated that this approach shortens assembly time, uses less memory than traditional co-assembly, and produces significantly fewer assembly errors. Applying sequential co-assembly to shotgun sequencing reads from (1) a longitudinal study of gut microbiomes from undernourished Bangladeshi children and (2) a 2.3-terabyte dataset generated from gnotobiotic mice colonized with pooled microbiomes from these children that was too large to be handled by a traditional co-assembly approach also demonstrated significant reductions in assembly time and memory requirements. These results suggest that this approach should be useful in resource-constrained settings, including in low- and middle-income countries.}, } @article {pmid40077957, year = {2025}, author = {Ma, Z and Wen, X and Zhang, Y and Ai, Z and Zhao, X and Dong, N and Dou, X and Shan, A}, title = {Thymol Alleviates Colitis by Modulating Intestinal Barrier Damage, Gut Microbiota, and Amino Acid Metabolic Pathways.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {12}, pages = {7211-7227}, doi = {10.1021/acs.jafc.4c10406}, pmid = {40077957}, issn = {1520-5118}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Colitis/chemically induced/metabolism/drug therapy/microbiology ; *Amino Acids/metabolism ; Humans ; *Mice, Inbred C57BL ; *Intestinal Mucosa/metabolism/drug effects ; *Thymol/pharmacology/administration & dosage/metabolism ; Male ; Bacteria/classification/genetics/metabolism/isolation & purification/drug effects ; Metabolic Networks and Pathways/drug effects ; Dextran Sulfate/adverse effects ; Colon/metabolism/microbiology/drug effects ; Cytokines/metabolism/genetics ; }, abstract = {Thymol (THY) is a phenolic monoterpene compound that has garnered attention due to its various biological properties, including antioxidant, anti-inflammatory, and immune-regulatory effects. The purpose of this study was to determine the therapeutic and protective effects of THY in colitic mice, with a particular focus on the mechanisms involving gut microbiota. The results showed that early intervention with THY (40 and 80 mg/kg) not only alleviated the clinical symptoms and colonic damage in mice with dextran sodium sulfate (DSS)-induced colitis but also suppressed the colonic production of inflammatory cytokines (IL-1β, IL-6, and IL-18) and enhanced the expression of mucins (MUC1 and MUC2) and trefoil factor family 3 (TFF3), thereby improving the integrity of the intestinal epithelial barrier. In addition, THY altered the composition of the gut microbiota in colitis mice by increasing the abundance of Bacteroides and reducing the abundance of Proteobacteria. Fecal microbial transplantation (FMT) results demonstrated that FM from THY donor mice significantly improved symptoms of inflammatory bowel disease (IBD), confirming the crucial role of the gut microbiota. Metagenomic and untargeted metabolomic studies found that the characteristic microbiota of THY is Prevotellaceae, and THY significantly upregulated the amino acid metabolic pathways related to arginine and proline metabolism, arginine biosynthesis, and glycerophospholipid metabolism. In summary, THY holds significant potential as a functional additive to enhance host intestinal activity.}, } @article {pmid40015021, year = {2025}, author = {Velásquez-Reyes, D and García-Alamilla, P and Kirchmayr, MR and Lugo-Cervantes, E and Gschaedler, A}, title = {Contribution of post-harvest processing in cocoa bean: Chemometric and metagenomic analysis in fermentation step.}, journal = {Food chemistry}, volume = {477}, number = {}, pages = {143458}, doi = {10.1016/j.foodchem.2025.143458}, pmid = {40015021}, issn = {1873-7072}, mesh = {*Cacao/microbiology/chemistry/metabolism ; *Fermentation ; *Volatile Organic Compounds/metabolism/chemistry/analysis ; *Metagenomics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Microbiota ; Mexico ; Gas Chromatography-Mass Spectrometry ; Food Handling ; Odorants/analysis ; Taste ; }, abstract = {Cocoa fermentation is a heterogeneous process, exhibiting a high degree of diversity of flavor, aroma, and microbial communities. A study was conducted to examine cocoa fermentations in five municipalities of a region in Mexico, with the objective of associating post-harvest practices, geographic area, and chemical and microbiological profiles. Through the application of high-performance DNA sequencing, the microbial diversity was identified, and the non-volatile and volatile compounds were identified and quantified by UHPLC-RID/PDA and HS-SPME/GC-MS, respectively. Using PCA, PLS regression and Pearson correlation, post-harvest practices, geographical factors, microbial communities, and volatile and non-volatile compounds were made. The absence of control in cocoa fermentation was associated to Aspergillus, Escherichia, and Bacillus, and reduced the production of essential acids for aroma. This study provides data on the diversity of post-harvest practices and their impact on cocoa quality.}, } @article {pmid40011766, year = {2025}, author = {Proctor, DM and Sansom, SE and Deming, C and Conlan, S and Blaustein, RA and Atkins, TK and , and Dangana, T and Fukuda, C and Thotapalli, L and Kong, HH and Lin, MY and Hayden, MK and Segre, JA}, title = {Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes.}, journal = {Nature}, volume = {639}, number = {8056}, pages = {1016-1023}, pmid = {40011766}, issn = {1476-4687}, mesh = {Humans ; *Nursing Homes ; *Skin/microbiology ; *Candida auris/genetics ; Klebsiella pneumoniae/isolation & purification/genetics/drug effects ; Metagenomics ; Female ; Male ; Enterococcus faecium/genetics/isolation & purification/drug effects ; Staphylococcus aureus/genetics/drug effects/isolation & purification ; Pseudomonas aeruginosa/genetics/isolation & purification/drug effects ; Acinetobacter baumannii/genetics/drug effects/isolation & purification ; Microbiota ; Bacterial Proteins/genetics/metabolism ; Candidiasis/microbiology/epidemiology ; beta-Lactamases ; }, abstract = {Antimicrobial resistance is a public health threat associated with increased morbidity, mortality and financial burden in nursing homes and other healthcare settings[1]. Residents of nursing homes are at increased risk of pathogen colonization and infection owing to antimicrobial-resistant bacteria and fungi. Nursing homes act as reservoirs, amplifiers and disseminators of antimicrobial resistance in healthcare networks and across geographical regions[2]. Here we investigate the genomic epidemiology of the emerging, multidrug-resistant human fungal pathogen Candida auris in a ventilator-capable nursing home. Coupling strain-resolved metagenomics with isolate sequencing, we report skin colonization and clonal spread of C. auris on the skin of nursing home residents and throughout a metropolitan region. We also report that most Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Entobacter species (ESKAPE) pathogens and other high-priority pathogens (including Escherichia coli, Providencia stuartii, Proteus mirabilis and Morganella morganii) are shared in a nursing home. Integrating microbiome and clinical microbiology data, we detect carbapenemase genes at multiple skin sites on residents identified as carriers of these genes. We analyse publicly available shotgun metagenomic samples (stool and skin) collected from residents with varying medical conditions living in seven other nursing homes and provide additional evidence of previously unappreciated bacterial strain sharing. Taken together, our data suggest that skin is a reservoir for colonization by C. auris and ESKAPE pathogens and their associated antimicrobial-resistance genes.}, } @article {pmid39983731, year = {2025}, author = {Saha, S and Kalathera, J and Sumi, TS and Mane, V and Zimmermann, S and Waschina, S and Pande, S}, title = {Mass lysis of predatory bacteria drives the enrichment of antibiotic resistance in soil microbial communities.}, journal = {Current biology : CB}, volume = {35}, number = {6}, pages = {1258-1268.e6}, doi = {10.1016/j.cub.2025.01.068}, pmid = {39983731}, issn = {1879-0445}, mesh = {*Soil Microbiology ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial ; Microbial Interactions ; Drug Resistance, Microbial ; }, abstract = {Numerous studies have investigated the effects of antibiotics on the evolution and maintenance of antimicrobial resistance (AMR). However, the impact of microbial interactions in antibiotic-free environments on resistance within complex communities remains unclear. We investigated whether the predatory bacterium M. xanthus, which can produce antimicrobials and employ various contact-dependent and -independent prey-killing mechanisms, influences the abundance of antibiotic-resistant bacteria in its local environment simply through its presence, regardless of active predation. We observed an association between the presence of M. xanthus in soil and the frequency of antibiotic-resistant bacteria. Additionally, culture-based and metagenomic analysis showed that coculturing M. xanthus with soil-derived communities in liquid cultures enriched AMR among non-myxobacterial isolates. This is because the lysis of M. xanthus, triggered during the starvation phase of the coculture experiments, releases diffusible growth-inhibitory compounds that enrich pre-existing resistant bacteria. Furthermore, our results show that death during multicellular fruiting body formation-a starvation-induced stress response in M. xanthus that results in over 90% cell death-also releases growth-inhibitory molecules that enrich resistant bacteria. Hence, the higher abundance of resistant bacteria in soil communities, where M. xanthus can be detected, was because of the diffusible growth-inhibitory substances that were released due to the death of M. xanthus cells during fruiting body formation. Together, our findings demonstrate how the death of M. xanthus, an important aspect of its life cycle, can impact antibiotic resistomes in natural soil communities without the anthropogenic influx of antibiotics.}, } @article {pmid39966520, year = {2025}, author = {Diener, C and Holscher, HD and Filek, K and Corbin, KD and Moissl-Eichinger, C and Gibbons, SM}, title = {Metagenomic estimation of dietary intake from human stool.}, journal = {Nature metabolism}, volume = {7}, number = {3}, pages = {617-630}, pmid = {39966520}, issn = {2522-5812}, support = {R01 DK133468/DK/NIDDK NIH HHS/United States ; R01DK133468//U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)/ ; Cluster of Excellence COE7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; }, mesh = {Humans ; *Feces/microbiology ; *Metagenomics/methods ; *Diet ; Adult ; Gastrointestinal Microbiome/genetics ; Infant ; Metagenome ; Male ; Female ; Metabolic Syndrome/microbiology ; Eating ; }, abstract = {Dietary intake is tightly coupled to gut microbiota composition, human metabolism and the incidence of virtually all major chronic diseases. Dietary and nutrient intake are usually assessed using self-reporting methods, including dietary questionnaires and food records, which suffer from reporting biases and require strong compliance from study participants. Here, we present Metagenomic Estimation of Dietary Intake (MEDI): a method for quantifying food-derived DNA in human faecal metagenomes. We show that DNA-containing food components can be reliably detected in stool-derived metagenomic data, even when present at low abundances (more than ten reads). We show how MEDI dietary intake profiles can be converted into detailed metabolic representations of nutrient intake. MEDI identifies the onset of solid food consumption in infants, shows significant agreement with food frequency questionnaire responses in an adult population and shows agreement with food and nutrient intake in two controlled-feeding studies. Finally, we identify specific dietary features associated with metabolic syndrome in a large clinical cohort without dietary records, providing a proof-of-concept for detailed tracking of individual-specific, health-relevant dietary patterns without the need for questionnaires.}, } @article {pmid40132013, year = {2025}, author = {Halo, BA and Aljabri, YAS and Yaish, MW}, title = {Drought-induced microbial dynamics in cowpea rhizosphere: Exploring bacterial diversity and bioinoculant prospects.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0320197}, doi = {10.1371/journal.pone.0320197}, pmid = {40132013}, issn = {1932-6203}, mesh = {*Rhizosphere ; *Vigna/microbiology/genetics ; *Droughts ; *Soil Microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Biodiversity ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; Microbiota ; Plant Roots/microbiology ; }, abstract = {Rhizospheric bacterial communities in plants contribute to drought resilience by promoting plant-soil interactions, yet their biodiversity and ecological impacts are not fully characterized. In cowpeas, these interactions may be crucial in enhancing tolerance to drought conditions. In this study, cowpea plants were subjected to drought treatment, the soil attached to the roots was collected, environmental DNA (e-DNA) was extracted, and the bacterial communities were identified as amplicon sequence variants (ASVs) by metagenomics analysis of the 16S rRNA gene. Microbial communities under drought and control conditions were analyzed using taxonomy and diversity metrics. The sequencing results revealed 5,571 ASVs, and taxonomic analysis identified 1,752 bacterial species. Alpha and beta diversity analyses showed less conserved microbial community structures and compositions among the samples isolated from the rhizosphere under drought conditions compared to untreated samples, implying the enhancement effect of drought on species' biodiversity and richness. The differential accumulation analysis of the bacterial community identified 75 species that accumulated significantly (P ≤ 0.05) in response to drought, including 13 species exclusively present, seven absent, and 46 forming a high-abundance cluster within the hierarchical heatmap. These species were also grouped into specific clades in the phylogenetic tree, suggesting common genetic ancestry and potentially shared traits associated with drought tolerance. The differentially accumulated bacterial list included previously characterized species from drought and saline habitats. These findings suggest that drought stress significantly alters the composition and abundance of epiphytic bacterial communities, potentially impacting the rhizosphere's ecological balance and interactions with cowpeas. The results highlight microbial adaptations that enhance plant resilience through improved stress mitigation, providing meaningful understandings for advancing sustainable agriculture and developing microbial-based strategies to boost crop productivity in drought-prone regions.}, } @article {pmid40129931, year = {2025}, author = {Lee, G and Rosa, BA and Fernandez-Baca, MV and Martin, J and Ore, RA and Ortiz, P and Cabada, MM and Mitreva, M}, title = {Distinct gut microbiome features characterize Fasciola hepatica infection and predict triclabendazole treatment outcomes in Peruvian patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1555171}, pmid = {40129931}, issn = {2235-2988}, mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Humans ; Peru ; Animals ; *Fasciola hepatica/drug effects/genetics ; *Fascioliasis/drug therapy/microbiology ; *Triclabendazole/therapeutic use ; Treatment Outcome ; *Anthelmintics/pharmacology/therapeutic use ; Female ; Male ; Adult ; Middle Aged ; Bacteria/classification/genetics/drug effects/isolation & purification ; Metagenomics ; Young Adult ; Feces/microbiology/parasitology ; }, abstract = {BACKGROUND: Fasciola hepatica, a globally distributed helminth, causes fasciolosis, a disease with significant health and economic impacts. Variability in triclabendazole (TCBZ) efficacy and emerging resistance are remaining challenges. Evidence suggests that the gut microbiome influences host-helminth interactions and is associated with anthelmintic effects, but its association with human F. hepatica infection and TCBZ efficacy is not well understood.

METHODS: In this study, we investigated the relationship between Fasciola hepatica infection and the gut microbiome through metagenomic shotgun sequencing of 30 infected and 60 age- and sex-matched uninfected individuals from Peru. Additionally, we performed a longitudinal analysis to evaluate microbiome dynamics in relation to TCBZ treatment response.

RESULTS AND DISCUSSION: Infection was associated with specific microbial taxonomic and functional features, including higher abundance of Negativibacillus sp900547015, Blautia A sp000285855, and Prevotella sp002299635 species, and enrichment of microbial pathways linked to survival under stress and depletion of pathways for microbial growth. Unexpectedly, we identified that responders to TCBZ treatment (who cleared infection) harbored many microbiome features significantly different relative to non-responders, both before and after treatment. Specifically, the microbiomes of responders had a higher abundance Firmicutes A and Bacteroides species as well as phospholipid synthesis and glucuronidation pathways, while non-responders had higher abundance of Actinobacteria species including several from the Parolsenella and Bifidobacterium genera, and Bifidobacterium shunt and amino acid biosynthesis pathways.

CONCLUSIONS: Our findings underscore the impact of helminth infection on gut microbiome and suggest a potential role of gut microbiota in modulating TCBZ efficacy, offering novel insights into F. hepatica-microbiome interactions and paving the way for microbiome-informed treatment approaches.}, } @article {pmid40129261, year = {2025}, author = {Boden, JS and Som, SM and Brazelton, WJ and Anderson, RE and Stüeken, EE}, title = {Evaluating Serpentinization as a Source of Phosphite to Microbial Communities in Hydrothermal Vents.}, journal = {Geobiology}, volume = {23}, number = {2}, pages = {e70016}, doi = {10.1111/gbi.70016}, pmid = {40129261}, issn = {1472-4669}, support = {NE/V010824/1//Natural Environment Research Council/ ; 80NSSC19K1427//NASA Planetary Science Division ISFM Program/ ; OCE-1536405//National Science Foundation/ ; 80NSSC18K0829//NASA Astrobiology Program/ ; 80NSSC19K1427//NASA Astrobiology Program/ ; }, mesh = {*Hydrothermal Vents/microbiology ; *Phosphites/chemistry/metabolism ; Microbiota ; Bacteria/genetics/metabolism/classification ; Phosphorus/metabolism/analysis ; }, abstract = {Previous studies have documented the presence of phosphite, a reduced and highly soluble form of phosphorus, in serpentinites, which has led to the hypothesis that serpentinizing hydrothermal vents could have been an important source of bioavailable phosphorus for early microbial communities in the Archean. Here, we test this hypothesis by evaluating the genomic hallmarks of phosphorus usage in microbial communities living in modern hydrothermal vents with and without influence from serpentinization. These genomic analyses are combined with results from a geochemical model that calculates phosphorus speciation during serpentinization as a function of temperature, water:rock ratio, and lithology at thermodynamic equilibrium. We find little to no genomic evidence of phosphite use in serpentinizing environments at the Voltri Massif or the Von Damm hydrothermal field at the Mid Cayman Rise, but relatively more in the Lost City hydrothermal field, Coast Range Ophiolite Microbial Observatory, The Cedars, and chimney samples from Old City hydrothermal field and Prony Bay hydrothermal field, as well as in the non-serpentinizing hydrothermal vents at Axial Seamount. Geochemical modeling shows that phosphite production is favored at ca 275°C-325°C and low water:rock ratios, which may explain previous observations of phosphite in serpentinite rocks; however, most of the initial phosphate is trapped in apatite during serpentinization, suppressing the absolute phosphite yield. As a result, phosphite from serpentinizing vents could have supported microbial growth around olivine minerals in chimney walls and suspended aggregates, but it is unlikely to have fueled substantial primary productivity in diffusely venting fluids during life's origin and evolution in the Archean unless substrates equivalent to dunites (composed of > 90 wt% olivine) were more common.}, } @article {pmid40128855, year = {2025}, author = {DeVeaux, AL and Hall-Moore, C and Shaikh, N and Wallace, M and Burnham, CD and Schnadower, D and Kuppermann, N and Mahajan, P and Ramilo, O and Tarr, PI and Dantas, G and Schwartz, DJ}, title = {Metagenomic signatures of extraintestinal bacterial infection in the febrile term infant gut microbiome.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {82}, pmid = {40128855}, issn = {2049-2618}, support = {R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; T32GM139774/GM/NIGMS NIH HHS/United States ; P30DK052574/DK/NIDDK NIH HHS/United States ; P30DK052574/DK/NIDDK NIH HHS/United States ; P30DK052574/DK/NIDDK NIH HHS/United States ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; U03MC00007/HRSA/HRSA HHS/United States ; U03MC00007/HRSA/HRSA HHS/United States ; U03MC00007/HRSA/HRSA HHS/United States ; U03MC00007/HRSA/HRSA HHS/United States ; 2021081/DDCF/Doris Duke Charitable Foundation/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Female ; Male ; *Metagenomics/methods ; Infant, Newborn ; *Fever/microbiology ; *Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; Urinary Tract Infections/microbiology ; Case-Control Studies ; Bacterial Infections/microbiology ; Metagenome ; }, abstract = {BACKGROUND: Extraintestinal bacterial infections (EBIs), e.g., urinary tract infection, bacteremia, and meningitis, occur in approximately 10% of febrile infants younger than 60 days. Although many EBI-causing species commonly reside in the infant gut, proof that the digestive system is a pre-infection habitat remains unestablished.

RESULTS: We studied a cohort of febrile term infants < 60 days old who presented to one of thirteen US emergency departments in the Pediatric Emergency Care Applied Research Network from 2016 to 2019. Forty EBI cases and 74 febrile controls matched for age, sex, and race without documented EBIs were selected for analysis. Shotgun sequencing was performed of the gut microbiome and of strains cultured from the gut and extraintestinal site(s) of EBI cases, including blood, urine, and/or cerebrospinal fluid. Using a combination of EBI isolate genomics and fecal metagenomics, we detected an intestinal strain presumptively isogenic to the EBI pathogen (> 99.999% average nucleotide identity) in 63% of infants with EBIs. Although there was no difference in gut microbiome diversity between cases and controls, we observed significantly increased Escherichia coli relative abundance in the gut microbiome of infants with EBIs caused by E. coli. Infants with E. coli infections who were colonized by the putatively isogenic pathogen strain had significantly higher E. coli phylogroup B2 abundance in their gut, and their microbiome was more likely to contain virulence factor loci associated with adherence, exotoxin production, and nutritional/metabolic function.

CONCLUSIONS: The intestine plausibly serves as a reservoir for EBI pathogens in a subset of febrile term infants, prompting consideration of new opportunities for surveillance and EBI prevention among colonized, pre-symptomatic infants. Video Abstract.}, } @article {pmid40128848, year = {2025}, author = {Byrne, SR and DeMott, MS and Yuan, Y and Ghanegolmohammadi, F and Kaiser, S and Fox, JG and Alm, EJ and Dedon, PC}, title = {Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {81}, pmid = {40128848}, issn = {2049-2618}, support = {T32-ES007020//NIEHS Training Grant in Environmental Toxicology/ ; R01-OD028099-01//NIH Transformative Award/ ; R01-OD028099-01//NIH Transformative Award/ ; P30-ES002109//NIEHS Core Center Grant/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Feces/microbiology ; *Bacteria/genetics/classification/metabolism ; Mice ; Animals ; Epigenesis, Genetic ; Epigenome ; Female ; Male ; Phosphates/metabolism ; }, abstract = {BACKGROUND: Epigenetic regulation of gene expression and host defense is well established in microbial communities, with dozens of DNA modifications comprising the epigenomes of prokaryotes and bacteriophage. Phosphorothioation (PT) of DNA, in which a chemically reactive sulfur atom replaces a non-bridging oxygen in the sugar-phosphate backbone, is catalyzed by dnd and ssp gene families widespread in bacteria and archaea. However, little is known about the role of PTs or other microbial epigenetic modifications in the human microbiome. Here we optimized and applied fecal DNA extraction, mass spectrometric, and metagenomics technologies to characterize the landscape and temporal dynamics of gut microbes possessing PT modifications.

RESULTS: Exploiting the nuclease-resistance of PTs, mass spectrometric analysis of limit digests of PT-containing DNA reveals PT dinucleotides as part of genomic consensus sequences, with 16 possible dinucleotide combinations. Analysis of mouse fecal DNA revealed a highly uniform spectrum of 11 PT dinucleotides in all littermates, with PTs estimated to occur in 5-10% of gut microbes. Though at similar levels, PT dinucleotides in fecal DNA from 11 healthy humans possessed signature combinations and levels of individual PTs. Comparison with a widely distributed microbial epigenetic mark, m[6]dA, suggested temporal dynamics consistent with expectations for gut microbial communities based on Taylor's Power Law. Application of PT-seq for site-specific metagenomic analysis of PT-containing bacteria in one fecal donor revealed the larger consensus sequences for the PT dinucleotides in Bacteroidota, Bacillota (formerly Firmicutes), Actinomycetota (formerly Actinobacteria), and Pseudomonadota (formerly Proteobacteria), which differed from unbiased metagenomics and suggested that the abundance of PT-containing bacteria did not simply mirror the spectrum of gut bacteria. PT-seq further revealed low abundance PT sites not detected as dinucleotides by mass spectrometry, attesting to the complementarity of the technologies. Video Abstract CONCLUSIONS: The results of our studies provide a benchmark for understanding the behavior of an abundant and chemically reactive epigenetic mark in the human gut microbiome, with implications for inflammatory conditions of the gut.}, } @article {pmid40128575, year = {2025}, author = {Yun, H and Seo, JH and Kim, YG and Yang, J}, title = {Impact of scented candle use on indoor air quality and airborne microbiome.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {10181}, pmid = {40128575}, issn = {2045-2322}, support = {RS-2023-00244833//National Research Foundation of Korea/ ; }, mesh = {*Air Pollution, Indoor/analysis ; *Microbiota ; *Particulate Matter/analysis ; *Air Microbiology ; Humans ; Bacteria/classification/isolation & purification ; Environmental Monitoring/methods ; Extracellular Vesicles ; }, abstract = {Indoor air quality has become a growing concern worldwide due to its significant impact on human health, particularly in residential environments where people spend most of their time. Many studies have examined particulate matter (PM) in indoor air and indoor bioaerosols. However, there is a significant lack of research on airborne micro-sized bacteria (m-AB) and nano-sized bacterial extracellular vesicles (n-ABE), particularly those produced by common household activities, such as burning scented candles. This study investigates changes in PM concentrations and indoor microbiome composition resulting from candle use. Air samples were collected from three locations in residential homes: at the candle-lit spot (CL), 3 m away (3m_CL), and 6 m away (6m_CL). PM10 concentrations peaked at 1.52 times the baseline at the source after 5 min of burning, while PM2.5 and PM1 remained elevated at 3m_CL and 6m_CL over time. Before burning, dominant m-AB genera included Phyllobacterium and Pseudomonas, while post-burning, Phyllobacterium myrsinacearum in n-ABE significantly increased, marking its first detection in indoor air. This suggests that existing airborne bacteria may undergo growth or apoptosis due to combustion byproducts. These findings highlight the importance of improving ventilation in indoor spaces to minimize health risks from prolonged exposure to airborne particles and bacterial vesicles.}, } @article {pmid40128181, year = {2025}, author = {Yan, W and Shi, X and Zhao, Y and Liu, X and Jia, X and Gao, L and Yuan, J and Liao, A and Yasui, H and Wang, X and Wang, X and Zhang, R and Wang, H}, title = {Microbiota-reprogrammed phosphatidylcholine inactivates cytotoxic CD8 T cells through UFMylation via exosomal SerpinB9 in multiple myeloma.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2863}, pmid = {40128181}, issn = {2041-1723}, support = {2022-YGJC-61;2022-MS-219//Natural Science Foundation of Liaoning Province (Liaoning Provincial Natural Science Foundation)/ ; }, mesh = {Female ; Animals ; Mice ; Humans ; Cell Line ; *T-Lymphocytes, Cytotoxic/immunology ; *Gastrointestinal Microbiome ; *Phosphatidylcholines/immunology/metabolism ; *Multiple Myeloma/genetics/immunology/metabolism/pathology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; *Exosomes/immunology/metabolism ; *Serpins/genetics/immunology/metabolism ; *Membrane Proteins/genetics/immunology/metabolism ; }, abstract = {Gut microbiome influences tumorigenesis and tumor progression through regulating the tumor microenvironment (TME) and modifying blood metabolites. However, the mechanisms by which gut microbiome and blood metabolites regulate the TME in multiple myeloma (MM) remain unclear. By employing16S rRNA gene sequencing coupled with metagenomics and ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry, we find that Lachnospiraceae are high and phosphatidylcholine (PC) are low in MM patients. We further show that Lachnospiraceae inhibits PC production from MM cells and enhances cytotoxic CD8 T cell function. Mechanistically, PC promotes Sb9 mRNA maturation in MM cells by LIN28A/B via lysophosphatidic acid, thus enhances exosamal Sb9 production. Exosamal Sb9 then reduces GZMB expression by suppressing tumor protein p53 (TP53) UFMylation via the competitive binding of TP53 with the ubiquitin-fold modifier conjugating enzyme 1 in CD8 T cells. We thus show that Lachnospiraceae and PC may be potential therapeutic targets for MM treatment.}, } @article {pmid40124740, year = {2025}, author = {Brucato, N and Lisant, V and Kinipi, C and Kik, A and Besnard, G and Leavesley, M and Ricaut, FX}, title = {Influence of betel nut chewing on oral microbiome in Papua New Guinea.}, journal = {Evolution, medicine, and public health}, volume = {13}, number = {1}, pages = {36-44}, pmid = {40124740}, issn = {2050-6201}, abstract = {BACKGROUND AND OBJECTIVES: For thousands of years, betel nut has been used as a psychoactive agent in Asian and Oceanian populations. Betel nut chewing was associated with the alteration of human oral microbiome and with diseases such as oral cancer and periodontitis, but only in populations of Asian cultural background. We studied the influence of betel nut chewing on the oral microbiome in Papua New Guinea, where half of the population uses betel nut and the prevalence of these diseases is one of the highest in the world.

METHODOLOGY: We characterized the oral microbiomes of 100 Papua New Guineans. We defined two cohorts of betel chewers (n = 50) and non-chewers (n = 50) based on a genetic approach to identify the presence of betel nut in saliva. We statistically compared the alpha and beta microbial diversities between the two cohorts. We performed linear discriminant analyses to identify bacterial species more prevalent in each cohort.

RESULTS: We found that oral microbial diversity is significantly different between betel chewers and non-chewers. The dysbiosis observed in betel chewers, led to an increase of pathogenic bacterial species including Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia, known to be in the aetiology of periodontal diseases.

CONCLUSIONS AND IMPLICATIONS: Our study strongly supports the alteration of human oral microbiome by betel nut use, potentially leading to periodontal diseases. It also shows the need to consider local specificities (e.g. different habits, betel nut types, and oral microbial diversities) to better characterize the impact of betel nut chewing on health.}, } @article {pmid40122890, year = {2025}, author = {Nori, SRC and Walsh, CJ and McAuliffe, FM and Moore, RL and Van Sinderen, D and Feehily, C and Cotter, PD}, title = {Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {49}, pmid = {40122890}, issn = {2055-5008}, support = {H2020-MSCA-COFUND-2019-945385//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; 18/CRT/6214//Science Foundation Ireland (SFI)/ ; }, mesh = {Female ; *Vagina/microbiology ; Humans ; *Lactobacillus/genetics/classification/isolation & purification ; *Metagenomics/methods ; *Lactobacillus crispatus/genetics/isolation & purification ; Pregnancy ; Microbiota ; Ireland ; Host Microbial Interactions ; Metagenome ; Genome, Bacterial ; Gardnerella vaginalis/genetics/isolation & purification/classification ; }, abstract = {The vaginal microbiome, a relatively simple, low diversity ecosystem crucial for female health, is often dominated by Lactobacillus spp. Detailed strain-level data, facilitated by shotgun sequencing, can provide a greater understanding of the mechanisms of colonization and host-microbe interactions. We analysed 354 vaginal metagenomes from pregnant women in Ireland to investigate metagenomic community state types and strain-level variation, focusing on cell surface interfaces. Our analysis revealed multiple subspecies, with Lactobacillus crispatus and Lactobacillus iners being the most dominant. We found genes, including putative mucin-binding genes, distinct to L. crispatus subspecies. Using 337 metagenome-assembled genomes, we observed a higher number of strain-specific genes in L. crispatus related to cell wall biogenesis, carbohydrate and amino acid metabolism, many under positive selection. A cell surface glycan gene cluster was predominantly found in L. crispatus but absent in L. iners and Gardnerella vaginalis. These findings highlight strain-specific factors associated with colonisation and host-microbe interactions.}, } @article {pmid39950811, year = {2025}, author = {Kwon, J and Tanner, W and Kong, Y and Wade, M and Bitler, C and Chiavegato, MB and Pettigrew, MM}, title = {Prospective comparison of the digestive tract resistome and microbiota in cattle raised in grass-fed versus grain-fed production systems.}, journal = {mSphere}, volume = {10}, number = {3}, pages = {e0073824}, doi = {10.1128/msphere.00738-24}, pmid = {39950811}, issn = {2379-5042}, support = {20-006612//Greenacres Foundation/ ; }, mesh = {Animals ; Cattle ; *Animal Feed/analysis ; *Edible Grain/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Bacteria/classification/drug effects/genetics/isolation & purification ; *Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; Gastrointestinal Tract/microbiology ; Diet/veterinary ; Poaceae/microbiology ; Prospective Studies ; Animal Husbandry/methods ; Drug Resistance, Bacterial/genetics ; Male ; Female ; }, abstract = {Most antimicrobials sold in the United States are used in food animals. Farm management practices contribute to antibacterial resistance (AR). Controversially, grass-fed diets have been recommended over grain-fed diets to reduce AR in beef cattle. Ionophore feed additives (non-therapeutic antibiotics that enhance feed efficiency) may contribute to AR development. We used shotgun metagenomic sequencing of fecal swabs to prospectively compare the cattle gastrointestinal resistome and microbiota in two different production systems over five periods from pre-weaning to pre-harvest. Cattle were grass-fed and pasture-raised (system A, n = 33) or grain-fed with ionophore additives in feedlots (system B, n = 34). System A cattle averaged 639 lb and 22.8 months of age, and system B cattle averaged 1,173 lb and 12.4 months of age preharvest. In total, 367 antibiotic resistance genes (ARGs) and 329 bacterial species were identified. The resistome of system A cattle had higher alpha diversity than system B cattle over their lifespan (P = 0.008). Beta-diversity estimates indicated overlap in the pre-weaning resistome and microbiota in both systems, which diverged post-weaning, with increases in several medically important ARGs when system B cattle transitioned to a grain diet. Analysis of compositions of microbiomes with bias correction indicated that levels of tetracycline, macrolide, aminoglycoside, beta-lactam, and bacitracin ARGs were significantly higher in system B cattle pre-harvest. Resistome changes were highly correlated with bacterial community changes (Procrustes, M[2] = 0.958; P = 0.001). Potentially modifiable farm management strategies, including diet and ionophores, may influence abundance and diversity of ARGs in fecal samples from cattle.IMPORTANCEAntibiotic resistance is a One Health threat. More antibiotics are used in agriculture than in human medicine. We compared the relative abundance of antibiotic resistance genes (ARGs) and bacterial species in cattle raised in two different cattle production systems (grass- and grain-fed). Fecal swab samples were collected at five time points spanning pre-weaning and prior to harvest. The antibiotic resistance gene and bacterial communities were relatively similar in the pre-weaning period when cattle in both systems were milking and on pasture. Resistance genes and bacterial communities diverged post-weaning when system B cattle were given a grain diet with feed additives for growth promotion containing non-medically important antibiotics (i.e., ionophores). The levels of medically important ARGs (e.g., macrolides) increased in system B grain-fed cattle post-weaning and were higher than in system A just prior to slaughter. These data provide additional evidence that farm management strategies impact the level of antibiotic resistance.}, } @article {pmid39945541, year = {2025}, author = {Lapid, R and Motro, Y and Craddock, H and Salah, I and King, R and Winner, K and Kahila Bar-Gal, G and Moran-Gilad, J}, title = {Abundance of clinically relevant antimicrobial resistance genes in the golden jackal (Canis aureus) gut.}, journal = {mSphere}, volume = {10}, number = {3}, pages = {e0081924}, doi = {10.1128/msphere.00819-24}, pmid = {39945541}, issn = {2379-5042}, mesh = {Animals ; *Feces/microbiology ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Gastrointestinal Microbiome/genetics ; beta-Lactamases/genetics ; Metagenomics ; Genes, Bacterial/genetics ; Israel ; Bacteria/genetics/drug effects/classification/isolation & purification ; }, abstract = {UNLABELLED: The spread of antimicrobial resistance (AMR) is a critical One Health issue. Wildlife could act as reservoirs or vehicles of AMR bacteria (ARBs) and AMR genes (ARGs) but are relatively understudied. We sought to investigate clinically relevant ARGs in golden jackals (Canis aureus) thriving near human settlements in Israel. Fecal samples were collected from 111 jackals across four regions over a 10-month period. Various animal and spatio-temporal metadata were collected. Samples were analyzed by quantitative PCR (qPCR) for beta-lactamases (blaTEM, blaCTX-M15, and blaSHV), qnrS and int1. A subset of samples was subject to shotgun metagenomic sequencing followed by resistome and microbiome analyses. qPCR detected a high prevalence of ARGs, including beta-lactamases (blaTEM-1, 96.4%; blaCTX-M-15, 51.4%, blaSHV, 15.3%), fluoroquinolone resistance (qnrS, 87.4%), and class 1 integrons (Int1, 94.6%). The blaTEM-1 gene was found to be more prevalent in adult jackals compared to younger ones. Metagenomic analysis of a subset of samples revealed a diverse gut microbiome harboring a rich resistome with tetracycline resistance genes being the most prevalent. Metagenome-assembled genome analysis further identified several ARGs associated with clinically relevant bacteria. These findings highlight the potential role of golden jackals as reservoirs for AMR and emphasize the need for ongoing surveillance to better understand AMR transmission dynamics at the wildlife-human interface.

IMPORTANCE: The research highlights the potential role of the golden jackals as reservoirs for antimicrobial resistance (AMR). The high prevalence of clinically relevant AMR genes in these jackals emphasizes the need for ongoing surveillance and monitoring to better understand AMR transmission dynamics at the wildlife-human interface.}, } @article {pmid40121033, year = {2025}, author = {Wong, MK and Boukhaled, GM and Armstrong, E and Liu, R and Heirali, AA and Yee, NR and Tsang, J and Spiliopoulou, P and Schneeberger, PHH and Wang, BX and Cochrane, K and Sherriff, K and Allen-Vercoe, E and Siu, LL and Spreafico, A and Coburn, B}, title = {Microbial Ecosystem Therapeutics 4 (MET4) elicits treatment-specific IgG responses associated with changes in gut microbiota in immune checkpoint inhibitor recipients with advanced solid tumors.}, journal = {Journal for immunotherapy of cancer}, volume = {13}, number = {3}, pages = {}, doi = {10.1136/jitc-2024-010681}, pmid = {40121033}, issn = {2051-1426}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Neoplasms/immunology/drug therapy/therapy ; *Immunoglobulin G/blood/immunology ; Male ; Female ; Middle Aged ; Aged ; }, abstract = {BACKGROUND: Gut microbiome modulation has shown promise in its potential to treat cancer in combination with immunotherapy. Mechanistically, the pathways and routes by which gut microbiota may influence systemic and antitumor immunity remain uncertain. Here, we used blood and stool samples from Microbial Ecosystem Therapeutic 4 (MET4)-IO, an early-phase trial testing the safety and engraftment of the MET4 bacterial consortium in immune checkpoint inhibitor recipients, to assess how MET4 may affect systemic immunity.

METHODS: Circulating antibody responses induced by MET4 were assessed using an antimicrobial antibody flow cytometry assay on pretreatment and post-treatment plasma. Antibody responses were associated with taxonomic changes in stool identified by metagenomic sequencing. Mass cytometry was performed on peripheral blood mononuclear cells to identify shifts in circulating immune subsets associated with antibody responses.

RESULTS: Increases in circulating anti-MET4 immunoglobulin G (IgG) responses were measured by flow cytometry post-consortium treatment in MET4 recipients, but not untreated control participants, with five individuals displaying notably higher antibody responses. Stronger IgG responses were associated with greater increases in multiple taxa, including MET4 microbe Collinsella aerofaciens, which was previously linked with immune checkpoint response. However, these taxa were not enriched in the IgG-bound fraction post-MET4 treatment. Greater increases in circulating B cells and FoxP3[+] CD4[+] T cells post-MET4 treatment were observed in the blood of high IgG responders, while CD14[+] and CD16[+] monocyte populations were decreased in these individuals.

CONCLUSION: These results demonstrate the induction of treatment-specific circulating humoral immunity by a bacterial consortium and suggest potential mechanisms by which gut microbes may contribute to antitumor immunity.}, } @article {pmid40117176, year = {2025}, author = {Zielińska, K and Udekwu, KI and Rudnicki, W and Frolova, A and Łabaj, PP}, title = {Healthy microbiome-moving towards functional interpretation.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, pmid = {40117176}, issn = {2047-217X}, support = {2020/38/E/NZ2/00598//NCN/ ; PLG/2023/016234//Jagiellonian University in Krakow/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; *Metagenomics/methods ; Metagenome ; Phylogeny ; Dysbiosis/microbiology ; Principal Component Analysis ; COVID-19/virology ; }, abstract = {BACKGROUND: Microbiome-based disease prediction has significant potential as an early, noninvasive marker of multiple health conditions linked to dysbiosis of the human gut microbiota, thanks in part to decreasing sequencing and analysis costs. Microbiome health indices and other computational tools currently proposed in the field often are based on a microbiome's species richness and are completely reliant on taxonomic classification. A resurgent interest in a metabolism-centric, ecological approach has led to an increased understanding of microbiome metabolic and phenotypic complexity, revealing substantial restrictions of taxonomy-reliant approaches.

FINDINGS: In this study, we introduce a new metagenomic health index developed as an answer to recent developments in microbiome definitions, in an effort to distinguish between healthy and unhealthy microbiomes, here in focus, inflammatory bowel disease (IBD). The novelty of our approach is a shift from a traditional Linnean phylogenetic classification toward a more holistic consideration of the metabolic functional potential underlining ecological interactions between species. Based on well-explored data cohorts, we compare our method and its performance with the most comprehensive indices to date, the taxonomy-based Gut Microbiome Health Index (GMHI), and the high-dimensional principal component analysis (hiPCA) methods, as well as to the standard taxon- and function-based Shannon entropy scoring. After demonstrating better performance on the initially targeted IBD cohorts, in comparison with other methods, we retrain our index on an additional 27 datasets obtained from different clinical conditions and validate our index's ability to distinguish between healthy and disease states using a variety of complementary benchmarking approaches. Finally, we demonstrate its superiority over the GMHI and the hiPCA on a longitudinal COVID-19 cohort and highlight the distinct robustness of our method to sequencing depth.

CONCLUSIONS: Overall, we emphasize the potential of this metagenomic approach and advocate a shift toward functional approaches to better understand and assess microbiome health as well as provide directions for future index enhancements. Our method, q2-predict-dysbiosis (Q2PD), is freely available (https://github.com/Kizielins/q2-predict-dysbiosis).}, } @article {pmid40037293, year = {2025}, author = {Delherbe, NA and Gomez, O and Plominsky, AM and Oliver, A and Manzanera, M and Kalyuzhnaya, MG}, title = {Atmospheric methane consumption in arid ecosystems acts as a reverse chimney and is accelerated by plant-methanotroph biomes.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf026}, pmid = {40037293}, issn = {1751-7370}, support = {DE-SC0024289//U.S. Department of Energy/ ; }, mesh = {*Methane/metabolism ; *Soil Microbiology ; California ; *Microbiota ; Metagenomics ; Ecosystem ; Desert Climate ; Metagenome ; Bacteria/genetics/classification/isolation & purification/metabolism ; Plants/microbiology ; Phylogeny ; Atmosphere ; }, abstract = {Drylands cover one-third of the Earth's surface and are one of the largest terrestrial sinks for methane. Understanding the structure-function interplay between members of arid biomes can provide critical insights into mechanisms of resilience toward anthropogenic and climate-change-driven environmental stressors-water scarcity, heatwaves, and increased atmospheric greenhouse gases. This study integrates in situ measurements with culture-independent and enrichment-based investigations of methane-consuming microbiomes inhabiting soil in the Anza-Borrego Desert, a model arid ecosystem in Southern California, United States. The atmospheric methane consumption ranged between 2.26 and 12.73 μmol m2 h-1, peaking during the daytime at vegetated sites. Metagenomic studies revealed similar soil-microbiome compositions at vegetated and unvegetated sites, with Methylocaldum being the major methanotrophic clade. Eighty-four metagenome-assembled genomes were recovered, six represented by methanotrophic bacteria (three Methylocaldum, two Methylobacter, and uncultivated Methylococcaceae). The prevalence of copper-containing methane monooxygenases in metagenomic datasets suggests a diverse potential for methane oxidation in canonical methanotrophs and uncultivated Gammaproteobacteria. Five pure cultures of methanotrophic bacteria were obtained, including four Methylocaldum. Genomic analysis of Methylocaldum isolates and metagenome-assembled genomes revealed the presence of multiple stand-alone methane monooxygenase subunit C paralogs, which may have functions beyond methane oxidation. Furthermore, these methanotrophs have genetic signatures typically linked to symbiotic interactions with plants, including tryptophan synthesis and indole-3-acetic acid production. Based on in situ fluxes and soil microbiome compositions, we propose the existence of arid-soil reverse chimneys, an empowered methane sink represented by yet-to-be-defined cooperation between desert vegetation and methane-consuming microbiomes.}, } @article {pmid39961017, year = {2025}, author = {Colman, DR and Templeton, AS and Spear, JR and Boyd, ES}, title = {Microbial ecology of serpentinite-hosted ecosystems.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf029}, pmid = {39961017}, issn = {1751-7370}, support = {80NSSC21K0489//NASA Exobiology and Evolutionary Biology program/ ; }, mesh = {*Ecosystem ; *Microbiota ; Hydrothermal Vents/microbiology ; Bacteria/genetics/classification/metabolism ; Metagenomics ; Seawater/microbiology ; Geologic Sediments/microbiology ; }, abstract = {Serpentinization, the collective set of geochemical reactions initiated by the hydration of ultramafic rock, has occurred throughout Earth history and is inferred to occur on several planets and moons in our solar system. These reactions generate highly reducing conditions that can drive organic synthesis reactions potentially conducive to the emergence of life, while concomitantly generating fluids that challenge life owing to hyperalkalinity and limited inorganic carbon (and oxidant) availability. Consequently, the serpentinite-hosted biosphere offers insights into the earliest life, the habitable limits for life, and the potential for life on other planets. However, the support of abundant microbial communities by serpentinites was only recognized ~20 years ago with the discovery of deep-sea hydrothermal vents emanating serpentinized fluids. Here, we review the microbial ecology of both marine and continental serpentinization-influenced ecosystems in conjunction with a comparison of publicly available metagenomic sequence data from these communities to provide a global perspective of serpentinite microbial ecology. Synthesis of observations across global systems reveal consistent themes in the diversity, ecology, and functioning of communities. Nevertheless, individual systems exhibit nuances due to local geology, hydrology, and input of oxidized, near-surface/seawater fluids. Further, several new (and old) questions remain including the provenance of carbon to support biomass synthesis, the physical and chemical limits of life in serpentinites, the mode and tempo of in situ evolution, and the extent that modern serpentinites serve as analogs for those on early Earth. These topics are explored from a microbial perspective to outline key knowledge-gaps for future research.}, } @article {pmid40115125, year = {2025}, author = {Pavloudi, C and Santi, I and Azua, I and Baña, Z and Bastianini, M and Belser, C and Bilbao, J and Bitz-Thorsen, J and Broudin, C and Camusat, M and Cancio, I and Caray-Counil, L and Casotti, R and Castel, J and Comtet, T and Cox, CJ and Daguin, C and Díaz de Cerio, O and Exter, K and Fauvelot, C and Frada, MJ and Galand, PE and Garczarek, L and González Fernández, J and Guillou, L and Hablützel, PI and Heynderickx, H and Houbin, C and Kervella, AE and Krystallas, A and Lagaisse, R and Laroquette, A and Lescure, L and Lopes, E and Loulakaki, M and Louro, B and Magalhaes, C and Maidanou, M and Margiotta, F and Montresor, M and Not, F and Paredes, E and Percopo, I and Péru, E and Poulain, J and Præbel, K and Rigaut-Jalabert, F and Romac, S and Stavroulaki, M and Souza Troncoso, J and Thiébaut, E and Thomas, W and Tkacz, A and Trano, AC and Wincker, P and Pade, N}, title = {First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e143585}, pmid = {40115125}, issn = {1314-2828}, abstract = {The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory amongst designated European coastal marine sites, sharing the same protocols for sampling and data curation. Environmental samples are collected from the water column and, at some sites, soft sediments and hard substrates (Autonomous Reef Monitoring Structures - ARMS), together with a set of mandatory and discretionary metadata (including Essential Ocean Variables - EOVs). Samples are collected following standardised protocols at regular and specified intervals and sequenced in large six-monthly batches at a centralised sequencing facility. The use of standard operating procedures (SOPs) during data collection, library preparation and sequencing aims to provide uniformity amongst the data collected from the sites. Coupled with strict adherence to open and FAIR (Findable, Accessible, Interoperable, Reusable) data principles, this ensures maximum comparability amongst samples and enhances reusability and interoperability of the data with other data sources. The observatory network was launched in June 2021, when the first sampling campaign took place.}, } @article {pmid40086306, year = {2025}, author = {Russo, A and D'Alessandro, A and Di Paola, M and Cerasuolo, B and Renzi, S and Meriggi, N and Conti, L and Costa, J and Pogni, R and Martellini, T and Cincinelli, A and Ugolini, A and Cavalieri, D}, title = {On the role of bacterial gut microbiota from supralittoral amphipod Talitrus saltator (Montagu, 1808) in bioplastic degradation.}, journal = {The Science of the total environment}, volume = {972}, number = {}, pages = {179109}, doi = {10.1016/j.scitotenv.2025.179109}, pmid = {40086306}, issn = {1879-1026}, mesh = {Animals ; *Amphipoda/physiology ; *Gastrointestinal Microbiome/drug effects ; *Water Pollutants, Chemical ; Plastics ; Bacteria ; Biodegradation, Environmental ; }, abstract = {Despite the promise of a reduced environmental impact, bioplastics are subjected to dispersion and accumulation similarly to traditional plastics, especially in marine and coastal environments. The environmental impact of bioplastics is attracting increasing attention due to the growing market demand. The ability of the supralittoral amphipod Talitrus saltator to ingest and survive on pristine starch-based bioplastic has already been assessed. However, the involvement of the gut microbiota of this key coastal species in making bioplastics a dietary supplement, remains unknown. In this study, we investigated the modification of T. saltator gut microbiota following bioplastic ingestion and the effect of this change on the modification of their chemical composition. Groups of adult amphipods were fed with: 1 - two different kinds of starch-based bioplastic; 2 - a 50 %/50 % chitosan-starch mixture; and 3 - paper and dry-fish-food. Freshly collected, unfed individuals were used as control group. Faecal pellets from the amphipods were collected and characterized using ATR-FTIR spectroscopy. DNA was extracted from gut samples for metagenomic analysis. Spectroscopic investigation suggested a partial digestion of polysaccharide components in the experimental polymeric materials. The analysis of the gut microbiota revealed that bioplastic feeding induced modification of sandhopper's gut microbial communities, shifting the abundance of specific microbial genera already present in the gut, towards bacterial genera associated with plastic/bioplastic degradation, especially in groups fed with starch-based bioplastics. Overall, our results highlight the involvement of T. saltator's gut microbiota in bioplastic modification, providing new insights into the potential role of microbial consortia associated to sandhoppers in bioplastic management.}, } @article {pmid39983413, year = {2025}, author = {Li, Q and Li, H and Tian, L and Wang, Y and Ouyang, Z and Li, L and Mao, Y}, title = {Genomic insights and metabolic pathways of an enriched bacterial community capable of degrading polyethylene.}, journal = {Environment international}, volume = {197}, number = {}, pages = {109334}, doi = {10.1016/j.envint.2025.109334}, pmid = {39983413}, issn = {1873-6750}, mesh = {*Biodegradation, Environmental ; *Bacteria/metabolism/genetics ; *Polyethylene/metabolism ; *Metabolic Networks and Pathways ; Sewage/microbiology ; Metagenome ; Microbiota ; Genomics ; }, abstract = {In the face of mounting global plastic pollution, especially concerning microplastics, biodegradation must be a sustainable solution. The key factor driving this technology is to explore efficient plastic-biodegraders from different habitats, among which activated sludge (AS) may be an important option since it holds diverse microorganisms occupying various ecological niches. Here we intend to enrich the plastic-degrading microorganisms from AS by using polyethylene (PE) plastic as the carbon and energy source. After a 28-day incubation, the weight loss of PE films reached 3% and the hydrophobicity decreased, indicating physical biodegradation. Moreover, Fourier-transform infrared spectroscopy (FTIR) results showed the formation of several new oxygen-containing functional groups on PE. Microbial analysis extracted 26 metagenome-assembled genomes (MAGs) from the enriched microbial communities. Among them MAG10, MAG21 and MAG26 displayed the increased abundance upon PE addition and harbored abundant genes related to carbohydrate transport and metabolism, suggesting their potential to degrade PE. Additionally, functional analysis revealed 14 plastic degradation-related genes, including oxidase, laccase, and lipase, indicating the significant potential in plastic degradation. Furthermore, a pathway for synergistic biodegradation of PE was proposed based on the potential PE degradation genes retrieved from MAGs. This work offers a promising and sustainable solution to plastic pollution by enriching the potential biodegraders from AS.}, } @article {pmid39985228, year = {2025}, author = {Song, MJ and Freund, F and Tribble, CM and Toffelmier, E and Miller, C and Bradley Shaffer, H and Li, FW and Rothfels, CJ}, title = {The nitrogen-fixing fern Azolla has a complex microbiome characterized by varying degrees of cophylogenetic signal.}, journal = {American journal of botany}, volume = {112}, number = {3}, pages = {e70010}, doi = {10.1002/ajb2.70010}, pmid = {39985228}, issn = {1537-2197}, support = {//California Conservation Genomics Project, with funding provided to the University of California by the State of California, State Budget Act of 2019 [UC Award ID RSI-19-690224]./ ; }, mesh = {*Ferns/microbiology/genetics/physiology ; *Microbiota ; *Symbiosis ; *Nitrogen Fixation ; California ; }, abstract = {PREMISE: Azolla is a genus of floating ferns that has closely evolved with a vertically transmitted obligate cyanobacterium endosymbiont-Anabaena azollae-that fixes nitrogen. There are also other lesser-known Azolla symbionts whose role and mode of transmission are unknown.

METHODS: We sequenced 112 Azolla specimens collected across the state of California and characterized their metagenomes to identify the common bacterial endosymbionts and assess their patterns of interaction.

RESULTS: Four genera were found across all samples, establishing that multiple Azolla endosymbionts were consistently present. We found varying degrees of cophylogenetic signal across these taxa as well as varying degrees of isolation by distance and of pseudogenation, which demonstrates that multiple processes underlie how this endosymbiotic community is constituted. We also characterized the entire Azolla leaf pocket microbiome.

CONCLUSIONS: These results show that the Azolla symbiotic community is complex and features members at potentially different stages of symbiosis evolution, further supporting the utility of the Azolla microcosm as a system for studying the evolution of symbioses.}, } @article {pmid40115072, year = {2025}, author = {Li, J and Hu, X and Tao, X and Li, Y and Jiang, W and Zhao, M and Ma, Z and Chen, B and Sheng, S and Tong, J and Zhang, H and Shen, B and Gao, X}, title = {Deconstruct the link between gut microbiota and neurological diseases: application of Mendelian randomization analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1433131}, pmid = {40115072}, issn = {2235-2988}, mesh = {Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; *Nervous System Diseases/genetics/microbiology ; Brain-Gut Axis ; Genome-Wide Association Study ; }, abstract = {BACKGROUND: Recent research on the gut-brain axis has deepened our understanding of the correlation between gut bacteria and the neurological system. The inflammatory response triggered by gut microbiota may be associated with neurodegenerative diseases. Additionally, the impact of gut microbiota on emotional state, known as the "Gut-mood" relationship, could play a role in depression and anxiety disorders.

RESULTS: This review summarizes recent data on the role of gut-brain axis in the pathophysiology of neuropsychiatric and neurological disorders including epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke. Also, we conducted a Mendelian randomization study on seven neurological disorders (Epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke). MR-Egger and MR-PRESSO tests confirmed the robustness of analysis against horizontal pleiotropy.

CONCLUSIONS: By comparing the protective and risk factors for neurological disorders found in our research and other researches, we can furtherly determine valuable indicators for disease evolution tracking and potential treatment targets. Future research should explore extensive microbiome genome-wide association study datasets using metagenomics sequencing techniques to deepen our understanding of connections and causality between neurological disorders.}, } @article {pmid40114290, year = {2025}, author = {Demina, T and Marttila, H and Pessi, IS and Männistö, MK and Dutilh, BE and Roux, S and Hultman, J}, title = {Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {79}, pmid = {40114290}, issn = {2049-2618}, mesh = {*Soil Microbiology ; *Genome, Viral ; *Virome ; *Tundra ; *Phylogeny ; *Metagenome ; Arctic Regions ; Finland ; Bacteriophages/genetics/classification/isolation & purification ; Acidobacteria/genetics/classification/isolation & purification ; Soil ; DNA, Viral/genetics ; }, abstract = {BACKGROUND: Arctic soils are climate-critical areas, where microorganisms play crucial roles in nutrient cycling processes. Acidobacteriota are phylogenetically and physiologically diverse bacteria that are abundant and active in Arctic tundra soils. Still, surprisingly little is known about acidobacterial viruses in general and those residing in the Arctic in particular. Here, we applied both culture-dependent and -independent methods to study the virome of Acidobacteriota in Arctic soils.

RESULTS: Five virus isolates, Tunturi 1-5, were obtained from Arctic tundra soils, Kilpisjärvi, Finland (69°N), using Tunturiibacter spp. strains originating from the same area as hosts. The new virus isolates have tailed particles with podo- (Tunturi 1, 2, 3), sipho- (Tunturi 4), or myovirus-like (Tunturi 5) morphologies. The dsDNA genomes of the viral isolates are 63-98 kbp long, except Tunturi 5, which is a jumbo phage with a 309-kbp genome. Tunturi 1 and Tunturi 2 share 88% overall nucleotide identity, while the other three are not related to one another. For over half of the open reading frames in Tunturi genomes, no functions could be predicted. To further assess the Acidobacteriota-associated viral diversity in Kilpisjärvi soils, bulk metagenomes from the same soils were explored and a total of 1881 viral operational taxonomic units (vOTUs) were bioinformatically predicted. Almost all vOTUs (98%) were assigned to the class Caudoviricetes. For 125 vOTUs, including five (near-)complete ones, Acidobacteriota hosts were predicted. Acidobacteriota-linked vOTUs were abundant across sites, especially in fens. Terriglobia-associated proviruses were observed in Kilpisjärvi soils, being related to proviruses from distant soils and other biomes. Approximately genus- or higher-level similarities were found between the Tunturi viruses, Kilpisjärvi vOTUs, and other soil vOTUs, suggesting some shared groups of Acidobacteriota viruses across soils.

CONCLUSIONS: This study provides acidobacterial virus isolates as laboratory models for future research and adds insights into the diversity of viral communities associated with Acidobacteriota in tundra soils. Predicted virus-host links and viral gene functions suggest various interactions between viruses and their host microorganisms. Largely unknown sequences in the isolates and metagenome-assembled viral genomes highlight a need for more extensive sampling of Arctic soils to better understand viral functions and contributions to ecosystem-wide cycling processes in the Arctic. Video Abstract.}, } @article {pmid40114168, year = {2025}, author = {Wu, Y and Qu, Z and Wu, Z and Zhuang, J and Wang, Y and Wang, Z and Chu, J and Qi, Q and Han, S}, title = {Multiple primary malignancies and gut microbiome.}, journal = {BMC cancer}, volume = {25}, number = {1}, pages = {516}, pmid = {40114168}, issn = {1471-2407}, support = {2022E50008, 2024ZY01056//Zhejiang Provincial Clinical Research Center for CANCER/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; *Metagenomics/methods ; *Neoplasms, Multiple Primary/microbiology/virology ; Colorectal Neoplasms/microbiology/virology ; Adult ; Aged ; Bacteria/classification/genetics/isolation & purification ; Enterovirus/isolation & purification/genetics ; Case-Control Studies ; Feces/microbiology/virology ; }, abstract = {BACKGROUND: Multiple primary malignancies (MPM) are two or more independent primary malignancies. Recently, the relationship between microbiome and various tumors has been gradually focused on.

OBJECTIVE: To describe the relationship between MPM patients (MPMs) and gut microbiome.

METHODS: A total of 27 MPMs, 30 colorectal cancer patients (CRCs), and 30 healthy individuals were included to obtain metagenomic sequencing data. The knowledge graphs of gut bacteria and enteroviruses were plotted based on metagenomics. Wilcoxon rank-sum test was used to screen the characteristic gut microbiome.

RESULTS: The knowledge graph of gut microbiome in MPM patients was plotted. A total of 26 different gut bacteria, including Dialister, Fecalibacterium and Mediterraneibacter, were found between MPMs and healthy individuals. Twenty gut bacteria, including Parvimonas, Dialister and Mediterraneibacter, were more abundant in MPM complicated by CRC compared with CRCs. Twenty-one different enterovirus, including Triavirus, Punavirus and Lilyvirus, were screened between MPMs and healthy individuals. Triavirus, Punavirus and Lilyvirus were less abundant in MPM than healthy individuals. The abundance of Triavirus, Punavirus and Lilyvirus in CRC patients were also lower than MPM complicated by CRC patients.

CONCLUSION: The knowledge graph of gut microbiome in MPM patients was plotted. It may provide basic data support for future research of MPM.}, } @article {pmid40111684, year = {2025}, author = {de Barros Santos, HS and Pagnussatti, MEL and Arthur, RA}, title = {Symbiosis Between the Oral Microbiome and the Human Host: Microbial Homeostasis and Stability of the Host.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {31-51}, pmid = {40111684}, issn = {0065-2598}, mesh = {Humans ; *Symbiosis ; *Mouth/microbiology ; *Microbiota/physiology ; *Homeostasis ; *Host Microbial Interactions ; Bacteria/metabolism/genetics/classification ; Metagenomics/methods ; Oral Health ; }, abstract = {The oral cavity presents a highly diverse microbial composition. All the three domains of life, Bacteria, Eukarya, and Archaea, as well as viruses constitute the oral microbiome. Bacteria are among the most abundant microorganisms in the oral cavity, followed by viruses, fungi, and Archaea. These microorganisms tend to live in harmony with each other and with the host by preventing the colonization of oral sites by exogenous microorganisms. Interactions between the host and its microbiota are crucial for keeping ecological stability in the oral cavity and a condition compatible with oral health. This chapter focuses on describing the oral microbiota in healthy individuals based on both targeted and nontargeted genome sequencing methods and the functional activity played by those microorganisms based on metagenomic, metatranscriptomic, metaproteomic, and metabolomic analyses. Additionally, this chapter explores mutualistic and antagonistic microbe-microbe relationships. These interactions are mediated by complex mechanisms like cross-feeding networks, production of bacteriocins and secondary metabolites, synthesis of pH-buffering compounds, and the use of universal signaling molecules. At last, the role played by host-microbe interactions on colonization resistance and immune tolerance will help provide a better understanding about the harmonious and peaceful coexistence among host and microbial cells under oral health-related conditions.}, } @article {pmid40108202, year = {2025}, author = {Redgwell, TA and Thorsen, J and Petit, MA and Deng, L and Vestergaard, G and Russel, J and Chawes, B and Bønnelykke, K and Bisgaard, H and Nielsen, DS and Sørensen, S and Stokholm, J and Shah, SA}, title = {Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {46}, pmid = {40108202}, issn = {2055-5008}, mesh = {*Gastrointestinal Microbiome ; *Prophages/genetics/physiology ; Humans ; Infant ; *Metagenome ; Virome ; Female ; Feces/microbiology/virology ; Bacteria/genetics/classification/virology ; Bacteroides/genetics/virology ; }, abstract = {Gut microbiome (GM) composition and function is pivotal for human health and disease, of which the virome's importance is increasingly recognised. However, prophages and their induction patterns in the infant gut remain understudied. Here, we identified 10645 putative prophages in 662 metagenomes from 1-year-old children in the COPSAC2010 mother-child cohort and investigated their potential functions. No core provirome was found as the most prevalent vOTU was identified in only ~70% of the samples. The most dominant cluster of vOTUs in the cohort was related to Bacteroides phage Hanky p00', and it carried both diversity generating retroelements and genes involved in capsular polysaccharide synthesis. Paired analysis of viromes and metagenomes from the same samples revealed that most prophages within the infant gut were induced and that induction was unaffected by a range of environmental perturbers. In summary, prophages are major components of the infant gut that may have far reaching influences on the microbiome and its host.}, } @article {pmid40037607, year = {2025}, author = {Antaliya, K and Godhaniya, M and Galawala, J and Vansia, A and Mangrola, A and Ghelani, A and Patel, R}, title = {Microbial community transition in Surti buffalo-based fermented formulations sustainably enhances soil fertility and plant growth.}, journal = {Letters in applied microbiology}, volume = {78}, number = {3}, pages = {}, doi = {10.1093/lambio/ovaf030}, pmid = {40037607}, issn = {1472-765X}, support = {GSBTM/JD(R&D)661/2022-2023/00172813//Gujarat State Biotechnology Mission/ ; }, mesh = {*Soil Microbiology ; Animals ; *Fermentation ; *Soil/chemistry ; *Buffaloes/growth & development ; Microbiota ; Fertilizers/analysis ; Bacteria/classification/genetics/metabolism/growth & development/isolation & purification ; Plant Development ; Vigna/growth & development/microbiology ; }, abstract = {This study investigates the role of microbial dynamics during the fermentation of buffalo dung and urine-fermented plant growth-promoting formulation, a natural biofertilizer, and its impact on plant growth and soil health. This formulation was prepared using Surti buffalo dung, urine, jaggery, gram flour, and soil and fermented for up to 14 days. Metagenomic analysis revealed microbial succession from a diverse initial community to a Bacillus-dominated population, especially the Lactic Acid Bacteria, after 8 days of fermentation. The changes were accompanied by increases in the plant growth-promoting genes related to nutrient acquisition, phytohormone production, and stress resistance. The pot experiment revealed a significant increase in mung bean growth, with the maximum effect obtained from the eighth-day fermented formulation. The experiment showed considerable improvement in the physicochemical properties of soil, including increased organic carbon and nutrient availability. These findings underscore the ecological importance of microbial input preparation in enhancing soil fertility and plant growth sustainably. Future research should delve deeper into the specific mechanisms these microbes facilitate nutrient cycling and resilience in various agroclimatic conditions.}, } @article {pmid39999339, year = {2025}, author = {Hohmann, M and Iliasov, D and Larralde, M and Johannes, W and Janßen, KP and Zeller, G and Mascher, T and Gulder, TAM}, title = {Heterologous Expression of a Cryptic BGC from Bilophila sp. Provides Access to a Novel Family of Antibacterial Thiazoles.}, journal = {ACS synthetic biology}, volume = {14}, number = {3}, pages = {967-978}, doi = {10.1021/acssynbio.5c00042}, pmid = {39999339}, issn = {2161-5063}, mesh = {*Thiazoles/metabolism ; *Anti-Bacterial Agents/pharmacology ; Humans ; Gastrointestinal Microbiome/drug effects ; Multigene Family ; Siderophores/metabolism ; }, abstract = {Human health is greatly influenced by the gut microbiota and microbiota imbalance can lead to the development of diseases. It is widely acknowledged that the interaction of bacteria within competitive ecosystems is influenced by their specialized metabolites, which act, e.g., as antibacterials or siderophores. However, our understanding of the occurrence and impact of such natural products in the human gut microbiome remains very limited. As arylthiazole siderophores are an emerging family of growth-promoting molecules in pathogenic bacteria, we analyzed a metagenomic data set from the human microbiome and thereby identified the bil-BGC, which originates from an uncultured Bilophila strain. Through gene synthesis and BGC assembly, heterologous expression and mutasynthetic experiments, we discovered the arylthiazole natural products bilothiazoles A-F. While established activities of related molecules indicate their involvement in metal-binding and -uptake, which could promote the growth of pathogenic strains, we also found antibiotic activity for some bilothiazoles. This is supported by biosensor-experiments, where bilothiazoles C and E show PrecA-suppressing activity, while bilothiazole F induces PblaZ, a biosensor characteristic for β-lactam antibiotics. These findings serve as a starting point for investigating the role of bilothiazoles in the pathogenicity of Bilophila species in the gut.}, } @article {pmid39864798, year = {2025}, author = {Nehra, C and Harshini, V and Shukla, N and Chavda, P and Bhure, M and Savaliya, K and Patil, S and Shah, T and Pandit, R and Patil, NV and Patel, AK and Kachhawaha, S and Kumawat, RN and Joshi, M and Joshi, CG}, title = {Ruminal microbial responses to Moringa oleifera feed in lactating goats (Capra hircus): A metagenomic exploration.}, journal = {New biotechnology}, volume = {86}, number = {}, pages = {87-96}, doi = {10.1016/j.nbt.2025.01.006}, pmid = {39864798}, issn = {1876-4347}, mesh = {Animals ; *Goats/microbiology ; *Moringa oleifera ; *Lactation/drug effects ; *Animal Feed ; *Metagenomics ; *Rumen/microbiology/metabolism ; Female ; Bacteria/genetics/metabolism/classification ; Milk/metabolism/microbiology ; Gastrointestinal Microbiome/drug effects ; }, abstract = {The purpose of the current study was to explore the effects of Moringa oleifera feed on the taxonomy and function of the rumen microbial community, and further to evaluate its impact on milk yield and body weight in lactating goats. Nineteen goats were divided into moringa leaf diet (ML; n = 10) and masoor straw (MS; n = 9) groups. For each group fortnight milk yield and body weight was recorded. Rumen solid and liquid fraction samples were processed for metagenomic shotgun sequencing and further analysed. The pairwise comparison between the two groups showed a significant increase (p-value- <0.01) in milk yield of the ML goats after the 4th fortnight interval onwards. The metagenomic analysis revealed Bacteroidetes and Firmicutes are the most abundant phyla, with increased Bacteroidetes in response to the moringa diet. The ML group exhibited a reduction in microbial diversity, with an increase in Prevetolla and Bacteroidales populations which are positively associated with carbohydrate, protein, and VFA metabolism, and an increased proportions of Treponema sp., Ruminococcus sp., Ruminobacter amylophilus, and Aeromonas, indicating improved cellulose and nitrogen metabolism. KEGG analysis revealed significant changes in microbial gene pool and metabolic pathways, particularly in carbohydrate metabolism, propanoate metabolism, and fatty acid synthesis genes. These microbial and functional shifts are correlated with improvements in milk yield, growth rates, and potentially reduced methane emissions.This study highlighted the potential benefits of feeding moringa in the animal production system. However, furthermore experimental evidence including genetic and environmental effects is needed for a comprehensive understanding of moringa feed's impact on goat health and productivity.}, } @article {pmid38735389, year = {2025}, author = {Tan, X and Wu, J and Zhang, H and Li, Y and Huang, Y and Zheng, P and Xie, P}, title = {Biogeography of intestinal mucus-associated microbiome: Depletion of genus Pseudomonas is associated with depressive-like behaviors in female cynomolgus macaques.}, journal = {Journal of advanced research}, volume = {70}, number = {}, pages = {393-404}, doi = {10.1016/j.jare.2024.05.013}, pmid = {38735389}, issn = {2090-1224}, mesh = {Animals ; Female ; *Gastrointestinal Microbiome ; *Depression/microbiology ; *Macaca fascicularis/microbiology ; *Pseudomonas ; Dysbiosis/microbiology ; Intestinal Mucosa/microbiology/metabolism ; Behavior, Animal ; Mucus/metabolism/microbiology ; }, abstract = {INTRODUCTION: Depression is a debilitating and poorly understood mental disorder. There is an urgency to explore new potential biological mechanisms of depression and the gut microbiota is a promising research area.

OBJECTIVES: Our study was aim to understand regional heterogeneity and potential molecular mechanisms underlying depression induced by dysbiosis of mucus-associated microbiota.

METHODS: Here, we only selected female macaques because they are more likely to form a natural social hierarchy in a harem-like environment. Because high-ranking macaques rarely displayed depressive-like behaviors, we selected seven monkeys from high-ranking individuals as control group (HC) and the same number of low-ranking ones as depressive-like group (DL), which displayed significant depressive-like behaviors. Then, we collected mucus from the duodenum, jejunum, ileum, cecum and colon of DL and HC monkeys for shotgun metagenomic sequencing, to profile the biogeography of mucus-associated microbiota along duodenum to colon.

RESULTS: Compared with HC, DL macaques displayed noticeable depressive-like behaviors such as longer duration of huddle and sit alone behaviors (negative emotion behaviors), and fewer duration of locomotion, amicable and ingestion activities (positive emotion behaviors). Moreover, the alpha diversity index (Chao) could predict aforementioned depressive-like behaviors along duodenum to colon. Further, we identified that genus Pseudomonas was consistently decreased in DL group throughout the entire intestinal tract except for the jejunum. Specifically, there were 10, 18 and 28 decreased Pseudomonas spp. identified in ileum, cecum and colon, respectively. Moreover, a bacterial module mainly composed of Pseudomonas spp. was positively associated with three positive emotion behaviors. Functionally, Pseudomonaswas mainly involved in microbiota derived lipid metabolisms such as PPAR signaling pathway, cholesterol metabolism, and fat digestion and absorption.

CONCLUSION: Different regions of intestinal mucus-associated microbiota revealed that depletion of genus Pseudomonas is associated with depressive-like behaviors in female macaques, which might induce depressive phenotypes through regulating lipid metabolism.}, } @article {pmid40102546, year = {2025}, author = {Lechleiter, N and Wedemeyer, J and Schütz, A and Sehl-Ewert, J and Schaufler, K and Homeier-Bachmann, T}, title = {Metagenomic analysis of the faecal microbiota and AMR in roe deer in Western Pomerania.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9288}, pmid = {40102546}, issn = {2045-2322}, mesh = {Animals ; *Deer/microbiology ; *Feces/microbiology ; *Metagenomics/methods ; Escherichia coli/genetics/isolation & purification ; Microbiota/genetics ; Drug Resistance, Bacterial/genetics ; Germany ; Metagenome ; Gastrointestinal Microbiome/genetics ; Bacteria/genetics/classification ; Anti-Bacterial Agents/pharmacology ; }, abstract = {As an integral part of the global wellbeing, the health of wild animals should be regarded just as important as that of humans and livestock. The investigation of wildlife health, however, is limited by the availability of samples. In an attempt to implement a method with little invasiveness and broad areas of application, shotgun metagenomics were utilised to investigate the faecal microbiome and its antimicrobial resistance genes (AMRG) in roe deer. These genes can facilitate antimicrobial resistances (AMR) in bacteria and are therefore of increasing importance in global health. Accordingly, the abundance in potential vectors like wildlife needs to be assessed. The samples were additionally investigated for ESBL-E. coli, an antibiotic resistant pathogen of global concern, via cultivation. Twenty-seven hunt-harvested animals in Western Pomerania were sampled. This study is the first to our knowledge to describe the faecal microbiome of the European roe deer (Capreolus capreolus), providing insights into the bacterial and archaeal composition. Among the animals, the microbiome was mostly similar and showed a comparable composition to what has been reported in related species, with a ratio of 1.76 between Bacillota and Bacteroidota. The normalised abundance of AMR genes was found to be 0.035 on average, which is similar to other investigations on wild ruminants. Selective cultivation found no ESBL-E. coli in the animals. The prevalence of AMRG in roe deer of Western Pomerania was found to be in line with previous results. The use of shotgun metagenomics allowed for the simultaneous investigation of composition and AMR genes in the faecal microbiome of roe deer, which suggests it as a promising method for the health monitoring of wildlife. This study is the first to describe the prokaryotic assemblage in the faeces of roe deer and its differences to the microbiomes published on other cervids were discussed.}, } @article {pmid40102379, year = {2025}, author = {Deng, L and Taelman, S and Olm, MR and Toe, LC and Balini, E and Ouédraogo, LO and Bastos-Moreira, Y and Argaw, A and Tesfamariam, K and Sonnenburg, ED and Hanley-Cook, GT and Ouédraogo, M and Ganaba, R and Van Criekinge, W and Huybregts, L and Stock, M and Kolsteren, P and Sonnenburg, JL and Lachat, C and Dailey-Chwalibóg, T}, title = {Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2683}, pmid = {40102379}, issn = {2041-1723}, support = {OPP1175213//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Female ; *Dietary Supplements ; Infant ; Pregnancy ; Adult ; Burkina Faso ; *Carbohydrate Metabolism ; Infant, Newborn ; Feces/microbiology ; Dietary Proteins/metabolism ; Male ; Lactation ; }, abstract = {Balanced energy-protein (BEP) supplementation during pregnancy and lactation can improve birth outcomes and infant growth, with the gut microbiome as a potential mediator. The MISAME-III randomized controlled trial (ClinicalTrial.gov: NCT03533712) assessed the effect of BEP supplementation, provided during pregnancy and the first six months of lactation, on small-for-gestational age prevalence and length-for-age Z-scores at six months in rural Burkina Faso. Nested within MISAME-III, this sub-study examines the impact of BEP supplementation on maternal and infant gut microbiomes and their mediating role in birth outcomes and infant growth. A total of 152 mother-infant dyads (n = 71 intervention, n = 81 control) were included for metagenomic sequencing, with stool samples collected at the second and third trimesters, and at 1-2 and 5-6 months postpartum. BEP supplementation significantly altered maternal gut microbiome diversity, composition, and function, particularly those with immune-modulatory properties. Pathways linked to lipopolysaccharide biosynthesis were depleted and the species Bacteroides fragilis was enriched in BEP-supplemented mothers. Maternal BEP supplementation also accelerated infant microbiome changes and enhanced carbohydrate metabolism. Causal mediation analyses identified specific taxa mediating the effect of BEP on birth outcomes and infant growth. These findings suggest that maternal supplementation modulates gut microbiome composition and influences early-life development in resource-limited settings.}, } @article {pmid40056581, year = {2025}, author = {Wu, Y and Xu, L and He, F and Song, X and Ding, J and Ma, J}, title = {Effects of micro-magnetite on anaerobic co-digestion of waste activated sludge and slaughterhouse waste: Microbial community and metabolism analyses.}, journal = {Journal of environmental management}, volume = {379}, number = {}, pages = {124896}, doi = {10.1016/j.jenvman.2025.124896}, pmid = {40056581}, issn = {1095-8630}, mesh = {*Sewage/microbiology ; Anaerobiosis ; *Abattoirs ; *Ferrosoferric Oxide/metabolism ; *Methane/metabolism ; Bacteria/metabolism ; Bioreactors ; Microbiota ; }, abstract = {Micro-magnetite has been widely applied to improve anaerobic digestion (AD) performance, while comprehensive investigation of microbial community succession, metabolic pathway and magnetite fate remains unclear. In the current study, the effects of micro-magnetite (Fe3O4) on anaerobic co-digestion (AcD) of waste activated sludge and slaughterhouse waste were investigated. Experimental results indicated that the cumulative methane production was significantly increased from 484.6 mL/g VS to 524.4 mL/g VS with 0.8 g/L Fe3O4 addition. Recycled magnetite remained the initial physicochemical properties, including morphology, particle size and crystal structure, as evidenced by various characterization methods. Microbial community analysis indicated that magnetite addition enriched syntrophic bacteria (Armatimonadota, Syntrophomonas and Petrimonas) and methanogens (Methanosarcina). Metagenomic sequencing analysis demonstrated that hydrolysis and acidogenesis metabolic pathways were reinforced by magnetite addition. Meanwhile, the magnetite stimulated the direct interspecies electron transfer via enriching syntrophic microbes (Syntrophomonas and Methanosarcina) and conductive pili functional genes (pilA, mshA and mshC), finally achieving higher cumulative methane yield. This study provided in-depth investigation of the methane production facilitated by micro-magnetite addition and the magnetite fate during the AcD process.}, } @article {pmid39946816, year = {2025}, author = {Laredo-Tiscareño, SV and Garza-Hernandez, JA and Tangudu, CS and Dankaona, W and Rodríguez-Alarcón, CA and Gonzalez-Peña, R and Adame-Gallegos, JR and Beristain-Ruiz, DM and Barajas-López, IN and Hargett, AM and Munderloh, UG and Blitvich, BJ}, title = {Detection of multiple novel viruses in argasid and ixodid ticks in Mexico.}, journal = {Ticks and tick-borne diseases}, volume = {16}, number = {2}, pages = {102455}, doi = {10.1016/j.ttbdis.2025.102455}, pmid = {39946816}, issn = {1877-9603}, mesh = {Animals ; Mexico ; *Argasidae/virology ; Ixodidae/virology ; Virome ; Viruses/classification/isolation & purification/genetics ; Metagenomics ; }, abstract = {We examined ticks from Mexico using viral metagenomics to increase our understanding of the composition and diversity of the tick virome. The analysis was performed using 3,127 ticks of four Ixodidae spp. and one Argasidae spp. collected in 2019 to 2021 from domestic animals in four states of Mexico (Chiapas, Chihuahua, Guerrero, and Michoacán). All ticks were homogenized and tested for viruses using two approaches. In the first approach, an aliquot of each homogenate underwent two blind passages in Ixodes scapularis (ISE6) cells. Supernatants from all second passage cultures were subjected to polyethylene glycol (PEG) precipitation to enrich for virions then RNAs were extracted from the precipitates and analyzed by unbiased high-throughput sequencing (UHTS). In the second approach, an aliquot of every homogenate was subjected to PEG precipitation then RNAs were extracted and analyzed by UHTS, allowing for the detection of viruses unable to replicate in ISE6 cells. We identified seven novel species of viruses from multiple taxonomic groups (Bunyavirales, Flaviviridae, Nodaviridae, Nyamivirdae, Rhabdoviridae, Solemoviridae, and Totiviridae), some of which are highly divergent from all classified viruses and cannot be assigned to any established genus. Twelve recognized species of viruses were also identified. In summary, multiple novel and recognized viruses were detected in ticks from Mexico, highlighting the remarkable diversity of the tick virome.}, } @article {pmid39377977, year = {2025}, author = {Tufail, MA and Schmitz, RA}, title = {Exploring the Probiotic Potential of Bacteroides spp. Within One Health Paradigm.}, journal = {Probiotics and antimicrobial proteins}, volume = {17}, number = {2}, pages = {681-704}, pmid = {39377977}, issn = {1867-1314}, support = {031B0846D//Bundesministerium für Bildung und Forschung/ ; }, mesh = {*Probiotics ; Humans ; *Bacteroides/genetics ; *Gastrointestinal Microbiome ; One Health ; Animals ; }, abstract = {Probiotics are pivotal in maintaining or restoring the balance of human intestinal microbiota, a crucial factor in mitigating diseases and preserving the host's health. Exploration into Bacteroides spp. reveals substantial promise in their development as next-generation probiotics due to their profound interaction with host immune cells and capability to regulate the microbiome's metabolism by significantly impacting metabolite production. These beneficial bacteria exhibit potential in ameliorating various health issues such as intestinal disorders, cardiovascular diseases, behavioral disorders, and even cancer. Though it's important to note that a high percentage of them are as well opportunistic pathogens, posing risks under certain conditions. Studies highlight their role in modifying immune responses and improving health conditions by regulating lymphocytes, controlling metabolism, and preventing inflammation and cancer. The safety and efficacy of Bacteroides strains are currently under scrutiny by the European Commission for authorization in food processing, marking a significant step towards their commercialization. The recent advancements in bacterial isolation and sequencing methodologies, coupled with the integration of Metagenome-Assembled Genomes (MAGs) binning from metagenomics data, continue to unveil the potential of Bacteroides spp., aiding in the broader understanding and application of these novel probiotics in health and disease management.}, } @article {pmid38214674, year = {2025}, author = {Zhang, H and Zhang, H and Du, H and Yu, X and Xu, Y}, title = {The insights into the phage communities of fermented foods in the age of viral metagenomics.}, journal = {Critical reviews in food science and nutrition}, volume = {65}, number = {9}, pages = {1656-1668}, doi = {10.1080/10408398.2023.2299323}, pmid = {38214674}, issn = {1549-7852}, mesh = {*Bacteriophages/genetics/physiology ; *Metagenomics/methods ; *Fermented Foods/microbiology ; *Fermentation ; *Food Microbiology ; Microbiota ; Bacteria/virology/genetics/classification ; }, abstract = {Phages play a critical role in the assembly and regulation of fermented food microbiome through lysis and lysogenic lifestyle, which in turn affects the yield and quality of fermented foods. Therefore, it is important to investigate and characterize the diversity and function of phages under complex microbial communities and nutrient substrate conditions to provide novel insights into the regulation of traditional spontaneous fermentation. Viral metagenomics has gradually garnered increasing attention in fermented food research to elucidate phage functions and characterize the interactions between phages and the microbial community. Advances in this technology have uncovered a wide range of phages associated with the production of traditional fermented foods and beverages. This paper reviews the common methods of viral metagenomics applied in fermented food research, and summarizes the ecological functions of phages in traditional fermented foods. In the future, combining viral metagenomics with culturable methods and metagenomics will broaden the scope of research on fermented food systems, revealing the complex role of phages and intricate phage-bacterium interactions.}, } @article {pmid40100697, year = {2025}, author = {Sun, J and Hirai, M and Takaki, Y and Evans, PN and Nunoura, T and Rinke, C}, title = {Metagenomic insights into taxonomic and functional patterns in shallow coastal and deep subseafloor sediments in the Western Pacific.}, journal = {Microbial genomics}, volume = {11}, number = {3}, pages = {}, doi = {10.1099/mgen.0.001351}, pmid = {40100697}, issn = {2057-5858}, mesh = {*Geologic Sediments/microbiology ; *Archaea/genetics/classification ; *Metagenomics/methods ; *Bacteria/genetics/classification ; *Metagenome ; Phylogeny ; Pacific Ocean ; Microbiota/genetics ; }, abstract = {Marine sediments are vast, underexplored habitats and represent one of the largest carbon deposits on our planet. Microbial communities drive nutrient cycling in these sediments, but the full extent of their taxonomic and metabolic diversity remains to be explored. Here, we analysed shallow coastal and deep subseafloor sediment cores from 0.01 to nearly 600 metres below the seafloor, in the Western Pacific Region. Applying metagenomics, we identified several taxonomic clusters across all samples, which mainly aligned with depth and sediment type. Inferring functional patterns provided insights into possible ecological roles of the main microbial taxa. These included Chloroflexota, the most abundant phylum across all samples, whereby the classes Dehalococcoida and Anaerolineae dominated deep-subsurface and most shallow coastal sediments, respectively. Thermoproteota and Asgardarchaeota were the most abundant phyla among Archaea, contributing to high relative abundances of Archaea reaching over 50% in some samples. We recovered high-quality metagenome-assembled genomes for all main prokaryotic lineages and proposed names for three phyla, i.e. Tangaroaeota phyl. nov. (former RBG-13-66-14), Ryujiniota phyl. nov. (former UBA6262) and Spongiamicota phyl. nov. (former UBA8248). Metabolic capabilities across all samples ranged from aerobic respiration and photosynthesis in the shallowest sediment layers to heterotrophic carbon utilization, sulphate reduction and methanogenesis in deeper anoxic sediments. We also identified taxa with the potential to be involved in nitrogen and sulphur cycling and heterotrophic carbon utilization. In summary, this study contributes to our understanding of the taxonomic and functional diversity in benthic prokaryotic communities across marine sediments in the Western Pacific Region.}, } @article {pmid40098558, year = {2025}, author = {Di Rienzi, SC and Danhof, HA and Forshee, MD and Roberts, A and Britton, RA}, title = {Limosilactobacillus reuteri promotes the expression and secretion of enteroendocrine- and enterocyte-derived hormones.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {39}, number = {6}, pages = {e70408}, pmid = {40098558}, issn = {1530-6860}, support = {T15 LM007093/LM/NLM NIH HHS/United States ; F32 AI136404/AI/NIAID NIH HHS/United States ; //Weston Family Foundation (WFF)/ ; //BioGaia/ ; }, mesh = {*Limosilactobacillus reuteri/metabolism ; *Enteroendocrine Cells/metabolism ; *Enterocytes/metabolism/microbiology ; Humans ; Organoids/metabolism ; Gastrointestinal Hormones/metabolism/genetics ; Gastrointestinal Microbiome ; Animals ; }, abstract = {Intestinal microbes can beneficially impact host physiology, prompting investigations into the therapeutic usage of such microbes in a range of diseases. For example, human intestinal microbe Limosilactobacillus reuteri strains ATCC PTA 6475 and DSM 17938 are being considered for use for intestinal ailments, including colic, infection, and inflammation, as well as for non-intestinal ailments, including osteoporosis, wound healing, and autism spectrum disorder. While many of their beneficial properties are attributed to suppressing inflammatory responses, we postulated that L. reuteri may also regulate intestinal hormones to affect physiology within and outside of the gut. To determine if L. reuteri secreted factors impact the secretion of enteric hormones, we treated an engineered jejunal organoid line, NGN3-HIO, which can be induced to be enriched in enteroendocrine cells, with L. reuteri 6475 or 17938 conditioned medium and performed transcriptomics. Our data suggest that these L. reuteri strains affect the transcription of many gut hormones, including vasopressin and luteinizing hormone subunit beta, which have not been previously recognized as produced in the gut epithelium. Moreover, we find that these hormones appear to be produced in enterocytes, in contrast to canonical gut hormones produced in enteroendocrine cells. Finally, we show that L. reuteri conditioned media promote the secretion of enteric hormones, including serotonin, GIP, PYY, vasopressin, and luteinizing hormone subunit beta, and identify by metabolomics metabolites potentially mediating these effects on hormones. These results support L. reuteri affecting host physiology through intestinal hormone secretion, thereby expanding our understanding of the mechanistic actions of this microbe.}, } @article {pmid40019271, year = {2025}, author = {Milani, C and Longhi, G and Alessandri, G and Fontana, F and Viglioli, M and Tarracchini, C and Mancabelli, L and Lugli, GA and Petraro, S and Argentini, C and Anzalone, R and Viappiani, A and Carli, E and Vacondio, F and van Sinderen, D and Turroni, F and Mor, M and Ventura, M}, title = {Functional modulation of the human gut microbiome by bacteria vehicled by cheese.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {3}, pages = {e0018025}, doi = {10.1128/aem.00180-25}, pmid = {40019271}, issn = {1098-5336}, support = {GR-2018-12365988//Ministero della Salute (Italy Ministry of Health)/ ; SFI/12/RC/2273a//Science Foundation Ireland (SFI)/ ; SFI/12/RC/2273b//Science Foundation Ireland (SFI)/ ; }, mesh = {*Cheese/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Feces/microbiology ; }, abstract = {Since cheese is one of the most commonly and globally consumed fermented foods, scientific investigations in recent decades have focused on determining the impact of this dairy product on human health and well-being. However, the modulatory effect exerted by the autochthonous cheese microbial community on the taxonomic composition and associated functional potential of the gut microbiota of human is still far from being fully dissected or understood. Here, through the use of an in vitro human gut-simulating cultivation model in combination with multi-omics approaches, we have shown that minor rather than dominant bacterial players of the cheese microbiota are responsible for gut microbiota modulation of cheese consumers. These include taxa from the genera Enterococcus, Bacillus, Clostridium, and Hafnia. Indeed, they contribute to expand the functional potential of the intestinal microbial ecosystem by introducing genes responsible for the production of metabolites with relevant biological activity, including genes involved in the synthesis of vitamins, short-chain fatty acids, and amino acids. Furthermore, tracing of cheese microbiota-associated bacterial strains in fecal samples from cheese consumers provided evidence of horizontal transmission events, enabling the detection of particular bacterial strains transferred from cheese to humans. Moreover, transcriptomic and metabolomic analyses of a horizontally transmitted (cheese-to-consumer) bacterial strain, i.e., Hafnia paralvei T10, cultivated in a human gut environment-simulating medium, confirmed the concept that cheese-derived bacteria may expand the functional arsenal of the consumer's gut microbiota. This highlights the functional and biologically relevant contributions of food microbes acquired through cheese consumption on the human health.IMPORTANCEDiet is universally recognized as the primary factor influencing and modulating the human intestinal microbiota both taxonomically and functionally. In this context, cheese, being a fermented food with its own microbiota, serves not only as a source of nourishment for humans, but also as a source of nutrients for the consumer's gut microbiota. Additionally, it may act as a vehicle for autochthonous food-associated microorganisms which undergo transfer from cheese to the consumer, potentially influencing host gut health. The current study highlights not only that cheese microbiota-associated bacteria can be traced in the human gut microbiota, but also that they may expand the functional repertoire of the human gut microbiota, with potentially significant implications for human health.}, } @article {pmid39912643, year = {2025}, author = {Hotchkiss, MZ and Poulain, AJ and Forrest, JRK}, title = {Bumble bee gut microbial community structure differs between species and commercial suppliers, but metabolic potential remains largely consistent.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {3}, pages = {e0203624}, doi = {10.1128/aem.02036-24}, pmid = {39912643}, issn = {1098-5336}, support = {//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; }, mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Species Specificity ; }, abstract = {Bumble bees are key pollinators for natural and agricultural plant communities. Their health and performance are supported by a core gut microbiota composed of a few bacterial taxa. However, the taxonomic composition and community structure of bumble bee gut microbiotas can vary with bee species, environment, and origin (i.e., whether colonies come from the wild or a commercial rearing facility), and it is unclear whether metabolic capabilities therefore vary as well. Here we used metagenomic sequencing to examine gut microbiota community composition, structure, and metabolic potential across bumble bees from two different commercial Bombus impatiens suppliers, wild B. impatiens, and three other wild bumble bee species sampled from sites within the native range of all four species. We found that the community structure of gut microbiotas varied between bumble bee species, between populations from different origins within species, and between commercial suppliers. Notably, we found that Apibacter is consistently present in some wild bumble bee species-suggesting it may be a previously unrecognized core phylotype of bumble bees-and that commercial B. impatiens colonies can lack core phylotypes consistently found in wild populations. However, despite variation in community structure, the high-level metabolic potential of gut microbiotas was largely consistent across all hosts, including for metabolic capabilities related to host performance, though metabolic activity remains to be investigated.IMPORTANCEOur study is the first to compare genome-level taxonomic structure and metabolic potential of whole bumble bee gut microbiotas between commercial suppliers and between commercial and wild populations. In addition, we profiled the full gut microbiotas of three wild bumble bee species for the first time. Overall, our results provide new insight into bumble bee gut microbiota community structure and function and will help researchers evaluate how well studies conducted in one bumble bee population will translate to other populations and species. Research on taxonomic and metabolic variation in bumble bee gut microbiotas across species and origins is of increasing relevance as we continue to discover new ways that social bee gut microbiotas influence host health, and as some bumble bee species decline in range and abundance.}, } @article {pmid39804518, year = {2025}, author = {Claytor, JD and Lin, DL and Magnaye, KM and Guerrero, YS and Langelier, CR and Lynch, SV and El-Nachef, N}, title = {Effect of Fecal Microbiota Transplant on Antibiotic Resistance Genes Among Patients with Chronic Pouchitis.}, journal = {Digestive diseases and sciences}, volume = {70}, number = {3}, pages = {982-990}, pmid = {39804518}, issn = {1573-2568}, mesh = {Humans ; *Pouchitis/microbiology/therapy ; *Fecal Microbiota Transplantation ; Male ; Female ; Adult ; Middle Aged ; Chronic Disease ; Anti-Bacterial Agents/therapeutic use ; Gastrointestinal Microbiome ; Colitis, Ulcerative/microbiology/surgery/therapy ; Feces/microbiology ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {BACKGROUND: Pouchitis is common among patients with ulcerative colitis (UC) who have had colectomy with ileal pouch-anal anastomosis. Antibiotics are first-line therapy for pouch inflammation, increasing the potential for gut colonization with multi-drug resistant organisms (MDRO). Fecal microbial transplant (FMT) is being studied in the treatment of pouchitis and in the eradication of MDRO. Prior work using aerobic antibiotic culture disks suggests that some patients with chronic pouchitis may regain fluoroquinolone sensitivity after FMT. However, gut MDRO include anaerobic, fastidious organisms that are difficult to culture using traditional methods.

AIM: We aimed to assess whether FMT reduced the abundance of antibiotic resistance genes (ARG) or affected resistome diversity, evenness, or richness in patients with chronic pouchitis.

METHODS: We collected clinical characteristics regarding infections and antibiotic exposures for 18 patients who had previously been enrolled in an observational study investigating FMT as a treatment for pouchitis. Twenty-six pre- and post-FMT stool samples were analyzed using FLASH (Finding Low Abundance Sequences by Hybridization), a CRISPR/Cas9-based shotgun metagenomic sequence enrichment technique that detects acquired and chromosomal bacterial ARGs. Wilcoxon rank sum tests were used to assess differences in clinical characteristics, ARG counts, resistome diversity and ARG richness, pre- and post-FMT.

RESULTS: All 13 of the patients with sufficient stool samples for analysis had recently received antibiotics for pouchitis prior to a single endoscopic FMT. Fecal microbiomes of all patients had evidence of multi-drug resistance genes and ESBL resistance genes at baseline; 62% encoded fluoroquinolone resistance genes. A numerical decrease in overall ARG counts was noted post-FMT, but no statistically significant differences were noted (P = 0.19). Richness and diversity were not significantly altered. Three patients developed infections during the 5-year follow-up period, none of which were associated with MDRO.

CONCLUSION: Antibiotic resistance genes are prevalent among antibiotic-exposed patients with chronic pouchitis. FMT led to a numerical decrease, but no statistically significant change in ARG, nor were there significant changes in the diversity, richness, or evenness of ARGs. Further investigations to improve FMT engraftment and to optimize FMT delivery in patients with inflammatory pouch disorders are warranted.}, } @article {pmid39410870, year = {2025}, author = {Matsubara, K and Li, J and Enomoto, Y and Takahashi, T and Ma, M and Ninomiya, R and Kazami, D and Miura, K and Hirayama, K}, title = {Beneficial Role of Heat-Treated Lactobacillus sakei HS-1 on Growth Performance, Nutritional Status and Gut Microbiota in Weaned Piglets.}, journal = {Journal of animal physiology and animal nutrition}, volume = {109}, number = {2}, pages = {362-375}, doi = {10.1111/jpn.14056}, pmid = {39410870}, issn = {1439-0396}, support = {//The authors received no specific funding for this work./ ; }, mesh = {Animals ; Swine ; *Gastrointestinal Microbiome/drug effects ; *Animal Feed/analysis ; *Animal Nutritional Physiological Phenomena ; *Diet/veterinary ; *Probiotics/pharmacology/administration & dosage ; *Hot Temperature ; *Latilactobacillus sakei ; Nutritional Status ; Weaning ; }, abstract = {In the swine industry, there is a strong need to replace an antibiotic growth promoter (AGP) used as feed additives in weaned piglets to enhance nutrient utilization in their diets and improve growth performance. Lactobacillus sakei HS-1 strain is a microbial preparation isolated from pickles. The study aim is to investigate the effectiveness of heat-treated L. sakei HS-1 strain (HT-LS) as a growth promoter in weaned piglets compared to colistin (CS), a widely used AGP. Eighteen crossbred weaned piglets (Landrace × Yorkshire × Duroc) of 21 days (average body weight [BW]: 7.06 ± 0.59 kg) were divided into three groups: fed the control diet (CT group), fed a diet supplemented with 30 ppm colistin sulphate (CS group), fed a diet supplemented with HT-LS at a concentration of 2.0 × 10[5] cells/g (LS group) until 49 days. The results indicated that LS group exhibited significantly higher average daily gain (p < 0.05) and higher BW (p < 0.1) compared with CT group, even higher than CS group. CS group showed higher growth performance compared to CT group but the differences were not statistically significant. In addition, LS group had higher (p < 0.05) or tended to higher (p < 0.1) concentrations of several plasma amino acids than the other two groups at 35 and 49 days. Faecal acetate concentration was higher (p < 0.1) in LS group than in CT group at 35 days. Blood immunoglobulin G concentration in LS group was significantly lower (p < 0.05) than in CT group at 35 and 49 days, and blood immunoglobulin A tended to be lower (p < 0.1) at 35 days than in CT group. LS group showed an increased abundance of g_Prevotella 7, g_Streptococcus and g_Lactobacillus (linear discriminant analysis [LDA] score ≥ 2.0). Predictive metagenomic analysis revealed an enrichment of the mixed acid fermentation pathway (LDA score ≥ 2.0). Furthermore, several gut microbes exhibited correlations with plasma amino acids (p < 0.01) and short-chain fatty acids in faeces (p < 0.01). These findings demonstrate that HT-LS improves the growth performance of weaned piglets by enhancing the efficient utilization of nutrients through gut microbiota modification.}, } @article {pmid38902926, year = {2025}, author = {Niosi, A and Võ, NH and Sundaramurthy, P and Welch, C and Penn, A and Yuldasheva, Y and Alfareh, A and Rausch, K and Amin-Rahbar, T and Cavanaugh, J and Yadav, P and Peterson, S and Brown, R and Hu, A and Ardon-Castro, A and Nguyen, D and Crawford, R and Lee, W and Morris, EJ and Jensen, MH and Mulligan, K}, title = {Kismet/CHD7/CHD8 affects gut microbiota, mechanics, and the gut-brain axis in Drosophila melanogaster.}, journal = {Biophysical journal}, volume = {124}, number = {6}, pages = {933-941}, doi = {10.1016/j.bpj.2024.06.016}, pmid = {38902926}, issn = {1542-0086}, mesh = {Animals ; *Drosophila melanogaster/microbiology/physiology ; *Gastrointestinal Microbiome ; *Drosophila Proteins/metabolism/genetics ; Brain-Gut Axis/physiology ; Biomechanical Phenomena ; Mutation ; DNA-Binding Proteins/genetics/metabolism ; DNA Helicases/metabolism/genetics ; Mechanical Phenomena ; }, abstract = {The gut microbiome affects brain and neuronal development and may contribute to the pathophysiology of neurodevelopmental disorders. However, it is unclear how risk genes associated with such disorders affect gut physiology in a manner that could impact microbial colonization and how the mechanical properties of the gut tissue might play a role in gut-brain bidirectional communication. To address this, we used Drosophila melanogaster with a null mutation in the gene kismet, an ortholog of chromodomain helicase DNA-binding protein (CHD) family members CHD7 and CHD8. In humans, these are risk genes for neurodevelopmental disorders with co-occurring gastrointestinal symptoms. We found that kismet mutant flies have a significant increase in gastrointestinal transit time, indicating the functional homology of kismet with CHD7/CHD8 in vertebrates. Rheological characterization of dissected gut tissue revealed significant changes in the mechanics of kismet mutant gut elasticity, strain stiffening behavior, and tensile strength. Using 16S rRNA metagenomic sequencing, we also found that kismet mutants have reduced diversity and abundance of gut microbiota at every taxonomic level. To investigate the connection between the gut microbiome and behavior, we depleted gut microbiota in kismet mutant and control flies and quantified the flies' courtship behavior. Depletion of gut microbiota rescued courtship defects of kismet mutant flies, indicating a connection between gut microbiota and behavior. In striking contrast, depletion of the gut microbiome in the control strain reduced courtship activity, demonstrating that antibiotic treatment can have differential impacts on behavior and may depend on the status of microbial dysbiosis in the gut prior to depletion. We propose that Kismet influences multiple gastrointestinal phenotypes that contribute to the gut-microbiome-brain axis to influence behavior. We also suggest that gut tissue mechanics should be considered as an element in the gut-brain communication loop, both influenced by and potentially influencing the gut microbiome and neurodevelopment.}, } @article {pmid40098172, year = {2025}, author = {Raziq, MF and Khan, N and Manzoor, H and Tariq, HMA and Rafiq, M and Rasool, S and Kayani, MUR and Huang, L}, title = {Prioritizing gut microbial SNPs linked to immunotherapy outcomes in NSCLC patients by integrative bioinformatics analysis.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {343}, pmid = {40098172}, issn = {1479-5876}, mesh = {Humans ; *Polymorphism, Single Nucleotide/genetics ; *Carcinoma, Non-Small-Cell Lung/genetics/microbiology/drug therapy ; *Computational Biology/methods ; *Gastrointestinal Microbiome/genetics ; *Lung Neoplasms/genetics/drug therapy/microbiology ; *Immunotherapy ; Treatment Outcome ; Male ; Female ; Metagenome/genetics ; }, abstract = {BACKGROUND: The human gut microbiome has emerged as a potential modulator of treatment efficacy for different cancers, including non-small cell lung cancer (NSCLC) patients undergoing immune checkpoint inhibitor (ICI) therapy. In this study, we investigated the association of gut microbial variations with response against ICIs by analyzing the gut metagenomes of NSCLC patients.

METHODS: Strain identification from the publicly available metagenomes of 87 NSCLC patients, treated with nivolumab and collected at three different timepoints (T0, T1, and T2), was performed using StrainPhlAn3. Variant calling and annotations were performed using Snippy and associations between microbial genes and genomic variations with treatment responses were evaluated using MaAsLin2. Supervised machine learning models were developed to prioritize single nucleotide polymorphisms (SNPs) predictive of treatment response. Structural bioinformatics approaches were employed using MUpro, I-Mutant 2.0, CASTp and PyMOL to access the functional impact of prioritized SNPs on protein stability and active site interactions.

RESULTS: Our findings revealed the presence of strains for several microbial species (e.g., Lachnospira eligens) exclusively in Responders (R) or Non-responders (NR) (e.g., Parabacteroides distasonis). Variant calling and annotations for the identified strains from R and NR patients highlighted variations in genes (e.g., ftsA, lpdA, and nadB) that were significantly associated with the NR status of patients. Among the developed models, Logistic Regression performed best (accuracy > 90% and AUC ROC > 95%) in prioritizing SNPs in genes that could distinguish R and NR at T0. These SNPs included Ala168Val (lpdA) in Phocaeicola dorei and Tyr233His (lpdA), Leu330Ser (lpdA), and His233Arg (obgE) in Parabacteroides distasonis. Lastly, structural analyses of these prioritized variants in objE and lpdA revealed their involvement in the substrate binding site and an overall reduction in protein stability. This suggests that these variations might likely disrupt substrate interactions and compromise protein stability, thereby impairing normal protein functionality.

CONCLUSION: The integration of metagenomics, machine learning, and structural bioinformatics provides a robust framework for understanding the association between gut microbial variations and treatment response, paving the way for personalized therapies for NSCLC in the future. These findings emphasize the potential clinical implications of microbiome-based biomarkers in guiding patient-specific treatment strategies and improving immunotherapy outcomes.}, } @article {pmid40097931, year = {2025}, author = {Boutin, S and Käding, N and Belheouane, M and Merker, M and Rupp, J and Nurjadi, D}, title = {Towards unraveling antimicrobial resistance dynamics: a longitudinal exploration of rectal swab metagenomes.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {150}, pmid = {40097931}, issn = {1471-2180}, mesh = {Humans ; *Rectum/microbiology ; *Metagenome ; *Metagenomics/methods ; Bacteria/genetics/drug effects/isolation & purification/classification ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Whole Genome Sequencing ; Longitudinal Studies ; Male ; Microbial Sensitivity Tests ; Female ; Middle Aged ; Microbiota/genetics/drug effects ; Aged ; Genome, Bacterial/genetics ; Adult ; }, abstract = {The increasing prevalence of antimicrobial resistance (AMR) poses significant challenges in clinical settings. In particular, early screening and detection of colonization by multidrug-resistant organisms (MDROs) in patients at admission is crucial. In this context, the clinical use of metagenomics (mNGS) holds promise for fast and untargeted diagnostic methods. Here, we aimed to evaluate the long-term stability of the rectal microbiome and the diagnostic accuracy of mNGS in comparison to culture and whole-genome sequencing (WGS) of MDROs. We analyzed rectal swabs from 26 patients with two consecutive admissions over a four-year period. The detected antimicrobial resistance genes and assembled metagenomes were compared to those obtained via classical culture-based antimicrobial susceptibility testing and WGS of isolated MDROs. Our results showed that the rectal microbiome is variable during the two timepoints, highlighting the variability in the niche. Nevertheless, we also observed strong co-occurrence of taxa, suggesting that the rectal swab microbiome is also a regulated environment with cooperative biotic interactions. In total, we isolated and sequenced 6 MDROs from 6 patients at individual timepoints. Almost all AMR genes from the genomes of the isolates (median: 100%, range: 84.6-100%) could be detected by mNGS of the rectal swabs at the time of isolation of the MDRO but not at the time of culture negativity. In addition, we detected AMR genes and potentially pathogenic species in patients with negative cultures. In conclusion, our study showed that, in principle, mNGS of rectal swabs can detect clinically relevant AMR profiles. However, the cooccurrence of AMR genes and potentially-pathogenic species does not always correlate with culture-based diagnostic results but rather indicates a potential risk of horizontal AMR gene transfer. However, it is unclear whether the observed discrepancies are due to transient or locally confined colonization of MDROs, limits of detection, or variability of the sampling method and specimens.}, } @article {pmid40097230, year = {2025}, author = {Nair, SS and Kutty Narayanan, A and Nair, K and Mallick, S and Zackariah, NM and Biswas, L and Praseedom, R and G Nair, BK and Surendran, S}, title = {Microbiota-directed intervention in living donor liver transplant recipients: protocol for a randomised double-blind placebo-controlled trial.}, journal = {BMJ open}, volume = {15}, number = {3}, pages = {e092984}, doi = {10.1136/bmjopen-2024-092984}, pmid = {40097230}, issn = {2044-6055}, mesh = {Humans ; *Liver Transplantation ; *Living Donors ; Double-Blind Method ; *Synbiotics/administration & dosage ; *Gastrointestinal Microbiome ; Randomized Controlled Trials as Topic ; Acute-On-Chronic Liver Failure/therapy ; Probiotics/therapeutic use ; Adult ; Postoperative Complications/microbiology ; Male ; Female ; }, abstract = {INTRODUCTION: Acute-on-chronic liver failure (ACLF) patients have the highest propensity for post-liver transplantation (LT) infections and mortality. Liver-associated diseases have been one of the primary targets for synbiotic therapy to augment immunity and mitigate infections. However, despite multiple studies showing benefits of synbiotics in liver diseases, data on their use following LT are sparse.

METHODS AND ANALYSIS: This randomised placebo-controlled study aims to assess the impact of synbiotics in ACLF patients undergoing living donor liver transplantation (LDLT). Following randomisation by computer-generated block number sequence, 3 days prior to LDLT, the intervention arm will receive standard medical treatment and synbiotics (VSL#3 a probiotic, and Yogut, prebiotic and probiotic combination) for 6 weeks, while the control arm will receive standard medical treatment with a placebo. The patients will be followed up for 6 months to study the clinical and biochemical outcomes. The primary objective is to compare the difference in the occurrence of infectious complications between the patients who receive synbiotics versus placebo during the 6-month period following LDLT. The secondary objectives include assessing the qualitative and quantitative change in microbiota with synbiotics and LDLT, adverse reactions due to synbiotics, and post-LT morbidity and mortality. The minimum sample size comes to 71 in each group. The first 50 patients in the study protocol will undergo gut microbiome analysis using 16s metagenomic and nanopore sequencing to analyse the microbial composition before starting synbiotics/placebo and at 6 weeks after LDLT.

ETHICS AND DISSEMINATION: The study is approved by the Research Ethics Committee of Amrita Institute of Medical Sciences, Kochi, India (IEC-AIMS-2022-GISUR-203) and registered in the Clinical Trial Registry of India (CTRI) CTRI/2022/10/046327. The results of the trial will be disseminated by presentation at national/international conferences and publication in peer-reviewed journals.

TRIAL REGISTRATION NUMBER: CTRI/2022/10/046327 - Clinical Trial Registry of India.}, } @article {pmid40094563, year = {2025}, author = {Cheng, W and Yi, L and Xu, T and Xie, Y and Zhu, J and Guan, X and Li, Q and Huang, Y and Zhao, Y and Zhao, S}, title = {The stems and leaves of Panax notoginseng reduce the abundance of antibiotic resistance genes by regulating intestinal microbiota in Duzang pigs.}, journal = {Animal biotechnology}, volume = {36}, number = {1}, pages = {2471785}, doi = {10.1080/10495398.2025.2471785}, pmid = {40094563}, issn = {1532-2378}, mesh = {Animals ; *Panax notoginseng/microbiology ; Swine ; *Gastrointestinal Microbiome/drug effects ; *Plant Leaves ; *Plant Stems ; Drug Resistance, Microbial/genetics ; Animal Feed/analysis ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics/classification ; Genes, Bacterial/genetics ; Cecum/microbiology ; Drug Resistance, Bacterial/genetics ; }, abstract = {In order to study the distribution characteristics of intestinal microbiota and antibiotic resistance genes (ARGs) in Duzang pigs after adding stems and leaves of Panax notoginseng to the feed, the characteristics of intestinal microbiota were explored by metagenomic sequencing, and 14 ARGs and 2 integrase genes were detected by qPCR. The results showed that the addition of stems and leaves of P. notoginseng increased the relative abundance of Firmicutes, Lactobacillus and Pediococcus in the cecum of Duzang pigs. A total of 10 ARGs and 2 integrase genes were detected in the cecal contents of pigs. The addition of stems and leaves of P. notoginseng reduced the relative abundance of total ARGs, ermB, tetO and tetW in the cecum of Duzang pigs. The results of network analysis showed that multiple genera were potential hosts of ARGs. The addition of stems and leaves of P. notoginseng may reduce the relative abundance of ARGs by reducing the relative abundance of genera such as Corynebacterium and Flavonifractor, thereby reducing the risk of ARGs spread. This study provides a theoretical basis for the rational use of stems and leaves of P. notoginseng to control ARGs.}, } @article {pmid40013797, year = {2025}, author = {Bai, Y and Hu, Y and Chen, X and Hu, L and Wu, K and Liang, S and Zheng, J and Gänzle, MG and Chen, C}, title = {Comparative metagenome-associated analysis of gut microbiota and antibiotic resistance genes in acute gastrointestinal injury patients with the risk of in-hospital mortality.}, journal = {mSystems}, volume = {10}, number = {3}, pages = {e0144424}, doi = {10.1128/msystems.01444-24}, pmid = {40013797}, issn = {2379-5077}, support = {200221115835503//the Office of Talent Work Leading Group in Maoming/ ; 2022A1515220065//GDSTC | Basic and Applied Basic Research Foundation of Guangdong Province/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; Male ; Female ; Middle Aged ; *Metagenome/genetics ; Aged ; *Hospital Mortality ; *Drug Resistance, Microbial/genetics ; Prospective Studies ; Feces/microbiology ; Metagenomics ; Intensive Care Units ; Gastrointestinal Diseases/microbiology/mortality/drug therapy ; Drug Resistance, Bacterial/genetics ; }, abstract = {UNLABELLED: Acute gastrointestinal injury (AGI) is known for its poor long-term prognosis and the associated increase in mortality among intensive care unit (ICU) patients. As the role of the gut microbiome and resistome in AGI remains unclear, the present study aimed to explore the possible associations between dysbacteriosis and in-hospital mortality in ICU patients with gastrointestinal dysfunction. Fecal samples were collected from a prospective cohort of 210 ICU patients with AGI, and shotgun metagenomic sequencing was used to determine the taxonomic composition of gut microbiota and the differences of antibiotic resistance genes (ARGs) between the Death and Survival groups. Compared to the Survival group, patients in the Death group shifted from strict anaerobes to facultative anaerobes in the fecal microbial community, with more Klebsiella but less Prevotella. The co-occurrence patterns revealed that more ARG subtypes were enriched in microbial taxa in the Death group, especially for Clostridium and Methanobrevibacter. Furthermore, the ARG type had large area under the curve (AUCs) in receiver operating characteristic for predicting the disease severity, and a combined gut microbiota-ARG subtype classifiers showed better performance than either of them. Thus, comparative metagenome-associated analysis can help to obtain valuable information about gut microbiota and gene coding for antibiotic resistance in AGI patients.

IMPORTANCE: A metagenomic-related strategy was conducted to obtain a highly valuable resource to improve understanding of intestinal microbiota dysbiosis and antibiotic resistance genes (ARGs) profiles. The results indicate that intestinal microbiota, including Klebsiella and Prevotella, changed dramatically in intensive care unit (ICU) patients with acute gastrointestinal injury (AGI). Due to longer ICU stays and receiving more antibiotic treatment, the types and correlations of ARGs in the Death group were significantly higher than those in the Survival group. The findings of this study are expected to expand our knowledge of gut microbiota and resistome profiles reflecting gastrointestinal status, accelerate the identification of disease biomarkers, and provide new insights into the prevention and treatment of AGI-related diseases.}, } @article {pmid40013792, year = {2025}, author = {Qin, Y and Wang, Q and Lin, Q and Liu, F and Pan, X and Wei, C and Chen, J and Huang, T and Fang, M and Yang, W and Pan, L}, title = {Multi-omics analysis reveals associations between gut microbiota and host transcriptome in colon cancer patients.}, journal = {mSystems}, volume = {10}, number = {3}, pages = {e0080524}, doi = {10.1128/msystems.00805-24}, pmid = {40013792}, issn = {2379-5077}, support = {AD22035214//Guangxi Clinical Research Center for Anesthesiology/ ; 2022GXNSFAA035510//National Science Foundation of Guangxi/ ; 8236080196//National Science Foundation of China/ ; 81760530//National Science Foundation of China/ ; 2021M693803//Postdoctoral Science Foundation of China/ ; }, mesh = {Humans ; *Colonic Neoplasms/genetics/microbiology/pathology/immunology ; *Gastrointestinal Microbiome/genetics ; *Transcriptome ; *RNA, Ribosomal, 16S/genetics ; Male ; Female ; Middle Aged ; Metagenomics ; Aged ; Bacteria/genetics/classification ; Multiomics ; }, abstract = {UNLABELLED: Colon cancer (CC) is one of the most common cancers globally, which is associated with the gut microbiota intimately. In current research, exploring the complex interaction between microbiomes and CC is a hotspot. However, the information on microbiomes in most previous studies is based on fecal, which does not fully display the microbial environment of CC. Herein, we collected mucosal and tissue samples from both the tumor and normal regions of 19 CC patients and clarified the composition of mucosal microbiota by 16S rRNA and metagenomic sequencing. Additionally, RNA-Seq was also conducted to identify the different expression genes between tumor and normal tissue samples. We revealed significantly different microbial community structures and expression profiles to CC. Depending on correlation analysis, we demonstrated that 1,472 genes were significantly correlated with CC tumor microbiota. Our study reveals a significant enrichment of Campylobacter jejuni in the mucosa of CC, which correlates with bile secretion. Additionally, we observe a negative correlation between C. jejuni and immune cells CD4+ Tem and mast cells. Finally, we discovered that metabolic bacterial endosymbiont of Bathymodiolus sp., Bacillus wiedmannii, and Mycobacterium tuberculosis had a significant survival value for CC, which was ignored by previous research. Overall, our study expands the understanding of the complex interplay between microbiota and CC and provides new targets for the treatment of CC.

IMPORTANCE: This study contributes to our understanding of the interaction between microbiota and colon cancer (CC). By examining mucosal and tissue samples rather than solely relying on fecal samples, we have uncovered previously unknown aspects of CC-associated microbiota. Our findings reveal distinct microbial community structures and gene expression profiles correlated with CC progression. Notably, the enrichment of Campylobacter jejuni in CC mucosa, linked to bile secretion, underscores potential mechanisms in CC pathogenesis. Additionally, observed correlations between microbial taxa and immune cell populations offer new avenues for immunotherapy research in CC. Importantly, this study introduces CC-associated microbiota with survival implications for CC, expanding therapeutic targets beyond conventional strategies. By elucidating these correlations, our study not only contributes to uncovering the potential role of gut microbiota in colon cancer but also establishes a foundation for mechanistic studies of gut microbiota in colon cancer, emphasizing the broader impact of microbiota research on cancer biology.}, } @article {pmid40013791, year = {2025}, author = {Walter, JM and Greses, S and Hagen, LH and Schiml, VC and Pope, PB and González-Fernández, C and Arntzen, M}, title = {Anaerobic digestion of microalgae: microbial response and recovery after organic loading disturbances.}, journal = {mSystems}, volume = {10}, number = {3}, pages = {e0167424}, doi = {10.1128/msystems.01674-24}, pmid = {40013791}, issn = {2379-5077}, support = {101007006//EC | Horizon 2020 Framework Programme (H2020)/ ; 295910//Norges Forskningsråd (Forskningsrådet)/ ; }, mesh = {*Microalgae/metabolism ; Anaerobiosis/physiology ; *Bioreactors/microbiology ; Fermentation/physiology ; Biofuels/microbiology ; Methane/metabolism ; Microbiota/physiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {UNLABELLED: Industrial anaerobic digestion (AD) represents a relevant energy source beyond today's fossil fuels, wherein organic matter is recycled to methane gas via an intricate and complex microbial food web. Despite its potential, anaerobic reactors often undergo process instability over time, which is frequently caused by substrate composition perturbations, making the system unreliable for stable energy production. To ensure the reliability of AD technologies, it is crucial to identify microbial and system responses to better understand the effect of such perturbations and ultimately detect signatures indicative of process failure. Here, we investigate the effect of the microalgal organic loading rate (OLR) on the fermentation product profile, microbiome dynamics, and disruption/recovery of major microbial metabolisms. Reactors subjected to low- and high-OLR disturbances were operated and monitored for fermentation products and biogas production over time, while microbial responses were investigated via 16S rRNA gene amplicon data, shotgun metagenomics, and metagenome-centric metaproteomics. Both low- and high-ORL fed systems encountered a sudden decline in methane production during OLR disturbances, followed by a recovery of the methanogenic activity within the microbiome. In the high-OLR disturbances, system failure triggered an upregulation of hydrolytic enzymes, an accumulation of fermentation products, and a shift in the methanogenic population from hydrogenotrophic to acetoclastic methanogens, with the latter being essential for recovery of the system after collapse.

IMPORTANCE: Anaerobic digestion (AD) with microalgae holds great potential for sustainable energy production, but process instability caused by substrate disturbances remains a significant barrier. This study highlights the importance of understanding the microbial dynamics and system responses during organic loading rate perturbations. By identifying key shifts in microbial populations and enzyme activity, particularly the transition from hydrogenotrophic to acetoclastic methanogens during recovery, this research provides critical insights for improving AD system stability and can contribute to optimizing microalgae-based AD processes for more reliable and efficient methane production.}, } @article {pmid39992132, year = {2025}, author = {Rodríguez-Ramos, J and Sadler, N and Zegeye, EK and Farris, Y and Purvine, S and Couvillion, S and Nelson, WC and Hofmockel, KS}, title = {Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation.}, journal = {mSystems}, volume = {10}, number = {3}, pages = {e0161624}, doi = {10.1128/msystems.01616-24}, pmid = {39992132}, issn = {2379-5077}, support = {FWP 70880//Department of Energy, Office of Science, Genomic Sciences Program/ ; 60461//DOE | SC | PNNL | Environmental Molecular Sciences Laboratory (EMSL)/ ; 508623//Joint Genome Institute (JGI)/ ; }, mesh = {*Soil Microbiology ; Porosity ; *Chitin/metabolism ; *Phenotype ; Soil/chemistry ; Microbial Consortia/physiology/genetics ; Streptomyces/genetics/metabolism ; Water/metabolism ; Metagenome ; }, abstract = {Soil moisture and porosity regulate microbial metabolism by influencing factors, such as system chemistry, substrate availability, and soil connectivity. However, accurately representing the soil environment and establishing a tractable microbial community that limits confounding variables is difficult. Here, we use a reduced-complexity microbial consortium grown in a glass bead porous media amended with chitin to test the effects of moisture and a structural matrix on microbial phenotypes. Leveraging metagenomes, metatranscriptomes, metaproteomes, and metabolomes, we saw that our porous media system significantly altered microbial phenotypes compared with the liquid incubations, denoting the importance of incorporating pores and surfaces for understanding microbial phenotypes in soils. These phenotypic shifts were mainly driven by differences in expression of Streptomyces and Ensifer, which included a significant decrease in overall chitin degradation between porous media and liquid. Our findings suggest that the success of Ensifer in porous media is likely related to its ability to repurpose carbon via the glyoxylate shunt amidst a lack of chitin degradation byproducts while potentially using polyhydroxyalkanoate granules as a C source. We also identified traits expressed by Ensifer and others, including motility, stress resistance, and carbon conservation, that likely influence the metabolic profiles observed across treatments. Together, these results demonstrate that porous media incubations promote structure-induced microbial phenotypes and are likely a better proxy for soil conditions than liquid culture systems. Furthermore, they emphasize that microbial phenotypes encompass not only the multi-enzyme pathways involved in metabolism but also include the complex interactions with the environment and other community members.IMPORTANCESoil moisture and porosity are critical in shaping microbial metabolism. However, accurately representing the soil environment in tractable laboratory experiments remains a challenging frontier. Through our reduced complexity microbial consortium experiment in porous media, we reveal that predicting microbial metabolism from gene-based pathways alone often falls short of capturing the intricate phenotypes driven by cellular interactions. Our findings highlight that porosity and moisture significantly affect chitin decomposition, with environmental matrix (i.e., glass beads) shifting community metabolism towards stress tolerance, reduced resource acquisition, and increased carbon conservation, ultimately invoking unique microbial strategies not evident in liquid cultures. Moreover, we find evidence that changes in moisture relate to community shifts regarding motility, transporters, and biofilm formation, which likely influence chitin degradation. Ultimately, our incubations showcase how reduced complexity communities can be informative of microbial metabolism and present a useful alternative to liquid cultures for studying soil microbial phenotypes.}, } @article {pmid39936903, year = {2025}, author = {Elena, AX and Orel, N and Fang, P and Herndl, GJ and Berendonk, TU and Tinta, T and Klümper, U}, title = {Jellyfish blooms-an overlooked hotspot and potential vector for the transmission of antimicrobial resistance in marine environments.}, journal = {mSystems}, volume = {10}, number = {3}, pages = {e0101224}, doi = {10.1128/msystems.01012-24}, pmid = {39936903}, issn = {2379-5077}, support = {01DO2200, 01KI2404A//Bundesministerium für Bildung und Forschung (BMBF)/ ; 16GW0355//Bundesministerium für Bildung und Forschung (BMBF)/ ; 202004910327//China Scholarship Council (CSC)/ ; 793778//H2020 Marie Skłodowska-Curie Actions/ ; I04978//Austrian Science Fund (FWF)/ ; ARRS J7-2599, P1-0237//Javna Agencija za Raziskovalno Dejavnost RS (ARRS)/ ; Project ID: 57747282//DAAD/ ; Project ID: B|-DE/25-27-001//Public Agency for Scientific Research and Innovation of the Republic of Slovenia (ARIS)/ ; }, mesh = {Animals ; *Scyphozoa/microbiology/genetics ; RNA, Ribosomal, 16S/genetics ; Microbiota/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; Metagenome ; Bacteria/drug effects/genetics ; Zooplankton/drug effects/genetics ; Interspersed Repetitive Sequences/genetics ; }, abstract = {Gelatinous zooplankton (GZ) represents an important component of marine food webs, capable of generating massive blooms with severe environmental impact. When these blooms collapse, considerable amounts of organic matter (GZ-OM) either sink to the seafloor or can be introduced into the ocean's interior, promoting bacterial growth and providing a colonizable surface for microbial interactions. We hypothesized that GZ-OM is an overlooked marine hotspot for transmitting antimicrobial resistance genes (ARGs). To test this, we first re-analyzed metagenomes from two previous studies that experimentally evolved marine microbial communities in the presence and absence of OM from Aurelia aurita and Mnemiopsis leidyi recovered from bloom events and thereafter performed additional time-resolved GZ-OM degradation experiments to improve sample size and statistical power of our analysis. We analyzed these communities for composition, ARG, and mobile genetic element (MGE) content. Communities exposed to GZ-OM displayed up to fourfold increased relative ARG and up to 10-fold increased MGE abundance per 16S rRNA gene copy compared to the controls. This pattern was consistent across ARG and MGE classes and independent of the GZ species, indicating that nutrient influx and colonizable surfaces drive these changes. Potential ARG carriers included genera containing potential pathogens raising concerns of ARG transfer to pathogenic strains. Vibrio was pinpointed as a key player associated with elevated ARGs and MGEs. Whole-genome sequencing of a Vibrio isolate revealed the genetic capability for ARG mobilization and transfer. This study establishes the first link between two emerging issues of marine coastal zones, jellyfish blooms and ARG spread, both likely increasing with future ocean change. Hence, jellyfish blooms are a quintessential "One Health" issue where decreasing environmental health directly impacts human health.IMPORTANCEJellyfish blooms are, in the context of human health, often seen as mainly problematic for oceanic bathing. Here we demonstrate that they may also play a critical role as marine environmental hotspots for the transmission of antimicrobial resistance (AMR). This study employed (re-)analyses of microcosm experiments to investigate how particulate organic matter introduced to the ocean from collapsed jellyfish blooms, specifically Aurelia aurita and Mnemiopsis leidyi, can significantly increase the presence of antimicrobial resistance genes and mobile genetic elements in marine microbial communities by up to one order of magnitude. By providing abundant nutrients and surfaces for bacterial colonization, organic matter from these blooms enhances ARG proliferation, including transfer to and mobility in potentially pathogenic bacteria like Vibrio. Understanding this connection highlights the importance of monitoring jellyfish blooms as part of marine health assessments and developing strategies to mitigate the spread of AMR in coastal ecosystems.}, } @article {pmid39927795, year = {2025}, author = {Huang, D and Chen, Y and Li, C and Yang, S and Lin, L and Zhang, X and Su, X and Liu, L and Zhao, H and Luo, T and Cai, S and Ren, Q and Dong, H}, title = {Variations in salivary microbiome and metabolites are associated with immunotherapy efficacy in patients with advanced NSCLC.}, journal = {mSystems}, volume = {10}, number = {3}, pages = {e0111524}, doi = {10.1128/msystems.01115-24}, pmid = {39927795}, issn = {2379-5077}, support = {No. 82302919//MOST | National Natural Science Foundation of China (NSFC)/ ; No. 82270024//MOST | National Natural Science Foundation of China (NSFC)/ ; No. 82170032//MOST | National Natural Science Foundation of China (NSFC)/ ; No. 2023A1515110216//GDSTC |Guangdong Basic and Applied Basic Research Foundation ()/ ; No. 2023A1515012879//GDSTC |Guangdong Basic and Applied Basic Research Foundation ()/ ; 2023M731556//China Postdoctoral Science Foundation (China Postdoctoral Foundation Project)/ ; 2023M731546//China Postdoctoral Science Foundation (China Postdoctoral Foundation Project)/ ; 2024T170385//China Postdoctoral Science Foundation (China Postdoctoral Foundation Project)/ ; 2021CR012//Clinical Research Program of Nanfang Hospital, Southern Medical University/ ; }, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/immunology/microbiology/drug therapy/therapy/metabolism ; *Saliva/microbiology/immunology/chemistry/metabolism ; *Lung Neoplasms/immunology/microbiology/drug therapy/metabolism/pathology ; *Microbiota/drug effects ; *Immunotherapy/methods ; Male ; Female ; Middle Aged ; Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Aged ; Treatment Outcome ; Actinomyces/immunology/metabolism ; B7-H1 Antigen/metabolism ; }, abstract = {Lung cancer is a leading cause of cancer mortality, with non-small cell lung cancer (NSCLC) comprising the majority of cases. Despite the advent of immune checkpoint inhibitors (ICIs), a significant number of patients fail to achieve a durable response, highlighting the need to understand the factors influencing treatment efficacy. Saliva samples and tumor samples were collected from 20 NSCLC patients. The salivary microbiota was profiled using metagenomic next-generation sequencing, and metabolites were analyzed via liquid chromatography-mass spectrometry to identify correlations among bacteria, metabolites, and immunotherapy responses. Immunohistochemistry (IHC) analysis of tissue samples verified the result. Besides, in vitro experiments and tumor tissue microarray, including 70 NSCLC patients, were utilized to further explore the potential mechanism linking the oral microbiome and immunotherapy efficacy. The study revealed several differential species and distinct metabolite compositions between responders and non-responders to ICI therapy in NSCLC and explored correlations and mechanisms between microbiota metabolites and immunotherapy resistance. Notably, it was found that several Neisseria and Actinomyces species were significantly enriched in responders and identified lipids and lipid-like molecules associated with PD-L1 expression levels and treatment outcomes. Importantly, several differential lipid molecules were associated with differential species. Further, in vitro experiments and IHC experiments indicated that abnormal fat metabolism linked to dysbiosis is correlated with immunotherapy resistance through regulation of CD8[+] T cell activity/infiltration and PD-L1 expression. Specific saliva microbiome and its associated lipids metabolites are significantly associated with the efficacy of ICI-based therapy in lung cancer. Our findings suggest that oral microbiome modulation and targeting lipid metabolism could improve immunotherapy responses, offering new avenues for personalized treatment strategies.IMPORTANCEIn non-small cell lung cancer, our study links specific salivary microbiome profiles and related lipid metabolites to the efficacy of immune checkpoint inhibitor (ICI) therapies. Responders showed enrichment of certain Neisseria and Actinomyces species and distinct lipid compositions. These lipids correlate with PD-L1 expression and CD8[+] T cell activity, affecting treatment outcomes. Our results imply that modulating the oral microbiome and targeting lipid metabolism may enhance ICI effectiveness, suggesting novel personalized therapeutic approaches.}, } @article {pmid39914332, year = {2025}, author = {Rossi, M and Vergara, A and Troisi, R and Alberico, M and Carraturo, F and Salamone, M and Giordano, S and Capozzi, F and Spagnuolo, V and de Magistris, FA and Donadio, C and Scognamiglio, V and Vedi, V and Guida, M}, title = {Microplastics, microfibers and associated microbiota biofilm analysis in seawater, a case study from the Vesuvian Coast, southern Italy.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137468}, doi = {10.1016/j.jhazmat.2025.137468}, pmid = {39914332}, issn = {1873-3336}, mesh = {Italy ; *Microplastics/toxicity ; *Seawater/microbiology ; *Biofilms ; *Microbiota ; *Water Pollutants, Chemical/analysis ; *Environmental Monitoring ; Bacteria/genetics/classification ; }, abstract = {The growing concerns regarding pollution from microplastics (MPs) and microfibers (MFs) have driven the scientific community to develop new solutions for monitoring ecosystems. However, many of the proposed technologies still include protocols for treating environmental samples that may alter plastic materials, leading to inaccurate results both in observation and in counting. For this reason, we are refining a protocol, based on optical microscopy without the use of pretreatments, applicable to different environmental matrices, which allows not only counting but also a complete morphological characterization of MPs and MFs. Previously, the protocol has successfully been tested on marine sediments from the Vesuvian area of the Gulf of Naples (Italy) with good results. In the present study, we tested the protocol on MPs and MFs in seawater samples collected from the same geographical area to provide a comprehensive overview of their distribution in the marine environments. The protocol enabled not only the morphological characterization of MPs and MFs but also the collection of information on the colonies of microorganisms present on the microparticles. Next Generation Sequencing (NGS) metagenomic technologies enabled us to characterize the microbiota composition of the sampled MPs, the so-called Plastisphere. The analytical approach allowed the characterization of several potentially pathogenic bacteria, which represent a potential threat to the environment and human health. In fact, they may exploit their ability to form biofilms on plastics to proliferate in marine ecosystems.}, } @article {pmid39909254, year = {2025}, author = {Yan, Q and Wang, W and Fan, Z and Wei, Y and Yu, R and Pan, T and Wang, N and Lu, W and Li, B and Fang, Z}, title = {Chickpea-resistant starch exhibits bioactive function for alleviating atopic dermatitis via regulating butyrate production.}, journal = {International journal of biological macromolecules}, volume = {303}, number = {}, pages = {140661}, doi = {10.1016/j.ijbiomac.2025.140661}, pmid = {39909254}, issn = {1879-0003}, mesh = {Animals ; *Cicer/chemistry ; *Dermatitis, Atopic/drug therapy/pathology/metabolism ; Mice ; *Butyrates/metabolism/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Resistant Starch/pharmacology/metabolism ; Starch/chemistry/pharmacology ; Fatty Acids, Volatile/metabolism ; Disease Models, Animal ; Female ; Calcitriol/analogs & derivatives ; }, abstract = {Resistant starch (RS) is one of the bioactive polysaccharides to produce Short-chain fatty acids (SCFAs) in the colon and contributes to allergic diseases including atopic dermatitis (AD). However, the bioactive mechanism of RS relieving AD needs to be elucidated. In this study, RS was prepared using chickpeas. Its microstructure and crystal structure were thoroughly characterized. Chickpea RS significantly improved the clinical symptoms and restored Th1/Th2 immune balance in mice with AD induced by calcipotriol. These benefits were eliminated by antibiotic cocktail treatment, suggesting that gut microbiota mediated the alleviation effects of chickpea RS on AD. Based on metagenomic sequencing and untargeted metabolomic analysis, chickpea RS treatment significantly increased the proportions of Butyricimonas virosa, Bifidobacterium pseudolongum, and Faecalibaculum rodentium, and a total of 206 differential metabolites were altered, especially the increase in propionate and butyrate production. Furthermore, we found that acylated butyrate, but not propionate, improved the pathological characteristics by activating GPR109A, which inhibit the phosphorylation levels of IκB-α, p50, p65, JNK, and p-JNK. Collectively, chickpea RS exhibited the bioactive function for regulating the communication of the gut-skin axis via regulating butyrate production to activate GPR109A.}, } @article {pmid39902937, year = {2025}, author = {Tian, C and Zhang, T and Zhuang, D and Luo, Y and Li, T and Zhao, F and Sang, J and Tang, Z and Jiang, P and Zhang, T and Liu, P and Zhu, L and Zhang, Z}, title = {Industrialization drives the gut microbiome and resistome of the Chinese populations.}, journal = {mSystems}, volume = {10}, number = {3}, pages = {e0137224}, doi = {10.1128/msystems.01372-24}, pmid = {39902937}, issn = {2379-5077}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; China ; *Industrial Development ; Adult ; Metagenomics ; Male ; Female ; Middle Aged ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects/classification/isolation & purification ; Virulence Factors/genetics ; Young Adult ; Metagenome ; Drug Resistance, Bacterial/genetics ; }, abstract = {UNLABELLED: Industrialization has driven lifestyle changes in eastern and western Chinese populations, yet we have a poor understanding of the dynamic changes in their gut microbiome and resistome under industrialization, which is essential for the scientific management of public health. Here, this study employed metagenomics to analyze the gut microbiota of 1,382 healthy individuals from China, including 415 individuals from the eastern region of advanced industrialization and 967 individuals from the western region of developing industrialization. Compared with western populations, eastern populations show a significant increase in interindividual dissimilarity of microbial species composition and metabolic pathways but a significant decrease in intraindividual species and functional diversity. Furthermore, our results found significantly less abundance and richness of antibiotic resistance genes (ARGs) in the gut microbiota of eastern populations, alongside a lower prevalence of unique core ARG subtypes. For the 12 core ARG types shared between eastern and western populations, the mean relative abundance of two types was notably higher in the eastern populations, while eight core ARG types had significantly higher mean relative abundance in the western populations. Based on the reconstruction of metagenomic assembled genomes, we found that Escherichia coli genomes from western populations carried more virulence factor genes (VFGs) and mobile genetic elements (MGEs) compared to those from eastern populations. This large-scale study for the first time revealed industrialization potentially led to unexpected alterations of the gut microbiome and resistome between eastern and western populations that provide a vital implication for Chinese public health and may aid in the development of region-specific strategies for managing pathogenic infections.

IMPORTANCE: As China experiences rapid but uneven industrialization, understanding its effect on people's gut bacteria is critical for public health. This study reveals how industrialization may reshape the health risks related to gut bacteria and antibiotic resistance. This work provides crucial information to help create customized public health policies for different regions.}, } @article {pmid39893982, year = {2025}, author = {Zhong, YQ and He, XL and Li, YH and Zhu, H and Li, JW and Xu, H and Liu, C and Lin, LC and Wang, JF}, title = {Enhancing antibiotic removal in constructed wetlands: A MgFe-LDHs-based strategy for optimizing microbial communities and metabolic functions.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137412}, doi = {10.1016/j.jhazmat.2025.137412}, pmid = {39893982}, issn = {1873-3336}, mesh = {*Wetlands ; *Anti-Bacterial Agents/metabolism ; *Water Pollutants, Chemical/metabolism ; *Biodegradation, Environmental ; Wastewater/microbiology ; Iron/metabolism ; Bacteria/metabolism ; Oxytetracycline/metabolism ; Phosphorus/metabolism ; Magnesium/metabolism/chemistry ; Microbiota ; Hydroxides/chemistry/metabolism ; Nitrogen/metabolism ; Waste Disposal, Fluid/methods ; Ofloxacin/metabolism ; Tetracycline/metabolism ; }, abstract = {To efficiently remove antibiotics from domestic and livestock wastewater in southern China, vertical flow constructed wetlands (CWs) were designed with and without magnesium-iron layered double hydroxides (MgFe-LDHs). Their removal efficiencies for three typical antibiotics (tetracycline, oxytetracycline, and ofloxacin) were evaluated. Results showed that MgFe-LDHs significantly improved nitrogen and phosphorus removal (18.7 %-25.6 %) and enhanced the degradation of tetracycline, oxytetracycline, and ofloxacin (13.1 %-17.8 %). High-resolution LC-MS analysis indicated significant biodegradation through various pathways, such as oxidation, hydrolysis, and dealkylation. Analysis of the Shannon diversity index demonstrated that the introduction of novel MgFe-LDHs enhanced microbial diversity and evenness at the phylum, class, and genus levels. The introduction of MgFe-LDHs increased microbial diversity and enriched antibiotic-degrading genera like Xanthobacter, Ochrobactrum, and Stenotrophomonas. Moreover, MgFe-LDHs may have enhanced the metabolic pathways of glycolysis and the tricarboxylic acid cycle, thereby improving the microbial degradation of organic matter. In summary, MgFe-LDHs exhibited a multifaceted role in enhancing antibiotic removal in CWs by inducing the enrichment of antibiotic-degrading bacteria and regulating the metabolic functions of the microbial community, while also ensuring higher nitrogen and phosphorus removal efficiency.}, } @article {pmid39874761, year = {2025}, author = {Wang, R and Chen, J and Chen, H}, title = {Metagenomic insights into efficiency and mechanism of antibiotic resistome reduction by electronic mediators-enhanced microbial electrochemical system.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137350}, doi = {10.1016/j.jhazmat.2025.137350}, pmid = {39874761}, issn = {1873-3336}, mesh = {*Bioelectric Energy Sources ; Nanotubes, Carbon/chemistry ; Bacteria/genetics/drug effects/metabolism ; Graphite/chemistry ; Drug Resistance, Microbial/genetics ; Iron/chemistry ; Charcoal/chemistry ; Anti-Bacterial Agents/pharmacology/chemistry ; Electrochemical Techniques ; Electrons ; Microbiota/drug effects ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Metagenome ; }, abstract = {Electronic mediators are an effective means of enhancing the efficiency of microbial electrochemical electron transfer; however, there are still gaps in understanding the strengthening mechanisms and the efficiency of removing antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). This study systematically elucidates the effects of various electron mediators on bioelectrochemical processes, electron transfer efficiency, and the underlying mechanisms that inhibit ARG propagation within sediment microbial fuel cell systems (SMFCs). The results indicate that the addition of electron mediators significantly increased the output voltage (33.3 %-61.1 %) and maximum power density (14 %-106 %) of SMFCs, while also reducing ARB abundance and transmission risk. The enhancement effect follows the order of biochar, nanoscale zero-valent iron, graphene, and carbon nanotubes, with biochar emerging as the most economical and efficient choice for generating electricity and removing human pathogenic bacteria carrying ARGs. Procrustes analysis revealed that electron mediators facilitated the removal of ARGs by altering the structure of the microbiome, particularly the electricity-generating microorganisms (EGMs). Voltage and mobile genetic elements were the primary drivers of ARGs in the SMFCs. The network analysis results show that multiple carbohydrate-active enzymes, cluster of orthologous groups, and EGMs were negatively correlated with ARGs, indicating that the electron mediator-enhanced SMFCs mainly inhibit the spread of ARGs by promoting cell division, carbohydrate metabolism, and electricity generation. This study provides novel insights into how electron mediators affect ARG removal in microbial electrochemistry, which can inform economically viable strategies for sustainable environmental remediation.}, } @article {pmid39854991, year = {2025}, author = {Pei, Y and Lei, A and Wang, M and Sun, M and Yang, S and Liu, X and Liu, L and Chen, H}, title = {Novel tetracycline-degrading enzymes from the gut microbiota of black soldier fly: Discovery, performance, degradation pathways, mechanisms, and application potential.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137286}, doi = {10.1016/j.jhazmat.2025.137286}, pmid = {39854991}, issn = {1873-3336}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Tetracycline/metabolism/chemistry ; *Biodegradation, Environmental ; Anti-Bacterial Agents/metabolism ; Diptera/metabolism ; Larva/metabolism ; Water Pollutants, Chemical/metabolism/chemistry ; Wastewater ; }, abstract = {The antibiotic tetracycline (TC) is an emerging pollutant frequently detected in various environments. Although enzymatic remediation is a promising strategy for mitigating TC contamination, the availability of effective TC-degrading enzymes remains limited, and their mechanisms and applications are not fully understood. This study developed a comprehensive TC-degrading enzyme library from the gut microbiome of the highly TC-resistant saprophagous insect, black soldier fly larvae (BSFL), using an integrated metagenomic and comparative metatranscriptomic approach, identifying 105 potential novel TC-degradation genes. Bioinformatics analysis of 10 selected genes underscored the novelty of the identified enzymes. Among these, Trg2 demonstrated strong binding affinity and significant degradation capacity for TC. Key functional amino acid residues, including Thr231, Ala64, Ala82, Gly68, Gly79, and Ser81, were identified as essential for the interaction between TC and Trg2. Six TC degradation pathways were proposed, involving the transformation of TC into 19 metabolites through de-grouping, ring opening, oxidation, reduction, and addition reactions, effectively reducing TC toxicity. Furthermore, Trg2 exhibited resilience under harsh conditions, maintaining the capacity to remove about 45 % of the total TC in mariculture wastewater across eight successive batches. This study advances the understanding of TC degradation mechanisms and highlights the potential application of novel enzymes for bioremediation purposes.}, } @article {pmid40094201, year = {2025}, author = {Masaadeh, AH and Eletrebi, M and Parajuli, B and De Jager, N and Bosch, DE}, title = {Human colitis-associated colorectal carcinoma progression is accompanied by dysbiosis with enriched pathobionts.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2479774}, doi = {10.1080/19490976.2025.2479774}, pmid = {40094201}, issn = {1949-0984}, mesh = {Humans ; *Dysbiosis/microbiology ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; *Disease Progression ; *Colorectal Neoplasms/microbiology/pathology ; *Bacteria/classification/isolation & purification/genetics ; Inflammatory Bowel Diseases/microbiology/pathology/complications ; Colitis-Associated Neoplasms/microbiology/pathology ; Adult ; RNA, Ribosomal, 16S/genetics ; Colitis/microbiology/pathology ; Metagenomics ; Intestinal Mucosa/microbiology/pathology ; }, abstract = {Dysbiosis and pathobionts contribute to inflammation and the risk of colitis-associated carcinoma (CAC) in animal models, but their roles in humans with this uncommon disease are unknown. We identified microbiome differences in human CAC compared with longstanding inflammatory bowel disease (IBD) and sporadic colorectal carcinoma (CRC). Twenty-four CAC resections were matched with CRC and IBD controls. Methods included histopathology, 16S rDNA metagenomics, and pathobiont-specific qPCR. Beta diversity differed by diagnosis (PERMANOVA p = 0.007). The distinguishing taxa included Akkermansia enriched in CRC, and Bacteroides spp. enriched in IBD. The non-neoplastic mucosae presented distinct beta diversity (p = 0.005), but the CAC/CRC tumor microbiomes were similar (p = 0.7). Within metastases and margins, Enterobacteriaceae were enriched in CAC, and Bacteroidales in CRC. Pathobiont-specific qPCR confirmed a greater frequency of pks+ E. coli and enterotoxigenic Bacteroides fragilis in CAC than IBD. High alpha diversity was associated with active inflammation, advanced cancer stage, and shorter overall survival (log-rank p = 0.008). Mucosal microbiomes distinguish CAC from longstanding IBD, implicating pathobionts as markers for disease progression. Integrating our findings with prior animal model research, pathobionts promote carcinogenesis in IBD patients through genotoxicity and host cell signaling.}, } @article {pmid40091534, year = {2025}, author = {Lu, YM and Lu, JQ and Zhao, Q and Chen, J and Xiong, JB}, title = {Pathogenic mechanisms of Enterocytozoon hepatopenaei through the parasite-gut microbiome-shrimp (Litopenaeus vannamei) physiology axis.}, journal = {Zoological research}, volume = {46}, number = {2}, pages = {401-413}, doi = {10.24272/j.issn.2095-8137.2024.411}, pmid = {40091534}, issn = {2095-8137}, mesh = {Animals ; *Penaeidae/microbiology ; *Gastrointestinal Microbiome/physiology ; *Enterocytozoon/physiology/genetics ; Host-Parasite Interactions ; }, abstract = {The progressive impact of Enterocytozoon hepatopenaei (EHP) infection on gut microbial function in Litopenaeus vannamei remains poorly understood beyond static comparisons between healthy and infected individuals. To close this knowledge gap, metagenomic sequencing was used to characterize the gut microbiomes of normal, long, medium, and short-sized adult shrimp categorized by increasing severity of infection. EHP infection suppressed digestive activity while inducing immune responses compared with healthy shrimp. Increasing infection severity was associated with a gradual decline in gut α-diversity and an expansion of potential pathogens and virulence factors (VFs). In addition, dysbiosis in gut microbiota composition and function, as well as reduced network stability among differential species, intensified with infection severity. Accordingly, we identified 24 EHP-discriminatory species that contributed an overall 83.3% accuracy in diagnosing infection severity without false negatives. Functional pathway analysis revealed significant suppression of metabolic, degradative, and biosynthetic processes in EHP-infected shrimp compared with healthy controls. Among them, map00630 glyoxylate and dicarboxylate metabolism and map00280 valine, leucine and isoleucine degradation were consistently depleted in infected individuals, thereby impairing their digestive function and anti-inflammatory responses. Additionally, EHP infection diversified VFs directly affecting shrimp gut microbiome. These findings support a conceptual model linking EHP pathogenesis to the parasite-gut microbiome-shrimp physiology axis.}, } @article {pmid40091083, year = {2025}, author = {Honda, H and Suzuki, T and Kitajima, M and Kondo, NI and Miyata, K and Utsumi, S and Yamada, M}, title = {The new era shaped by environmental genome monitoring - symposium of the japanese environmental mutagen and genome society (JEMS), 2024.}, journal = {Genes and environment : the official journal of the Japanese Environmental Mutagen Society}, volume = {47}, number = {1}, pages = {6}, pmid = {40091083}, issn = {1880-7046}, abstract = {The symposium "The New Era Shaped by Environmental Genome Monitoring," held in December 2024 by the Japanese Environmental Mutagen and Genome Society (JEMS), aimed to explore the interdisciplinary collaborations that are essential for the development of new scopes in environmental genome monitoring. This event highlighted the necessity of integrating mutagenicity research with ecological assessments to enhance public health and biodiversity conservation. Presentations focused on the evolving landscape of environmental genomics, including metagenomic analyses for antibiotic resistance, viral genomic surveillance in wastewater, and innovations in noninvasive biodiversity and stress monitoring through environmental DNA and RNA. This report summarizes the key discussions and presentations from the symposium, underscoring the critical role of environmental genome monitoring in shaping future safety research.}, } @article {pmid40090954, year = {2025}, author = {Lund, D and Parras-Moltó, M and Inda-Díaz, JS and Ebmeyer, S and Larsson, DGJ and Johnning, A and Kristiansson, E}, title = {Genetic compatibility and ecological connectivity drive the dissemination of antibiotic resistance genes.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2595}, pmid = {40090954}, issn = {2041-1723}, support = {2018-02835//Vetenskapsrådet (Swedish Research Council)/ ; 2018-05771//Vetenskapsrådet (Swedish Research Council)/ ; 2019-03482//Vetenskapsrådet (Swedish Research Council)/ ; 2022-00945//Vetenskapsrådet (Swedish Research Council)/ ; }, mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Humans ; *Phylogeny ; Wastewater/microbiology ; Genome, Bacterial ; Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Microbiota/genetics/drug effects ; Genes, Bacterial ; Metagenome ; Drug Resistance, Bacterial/genetics ; }, abstract = {The dissemination of mobile antibiotic resistance genes (ARGs) via horizontal gene transfer is a significant threat to public health globally. The flow of ARGs into and between pathogens, however, remains poorly understood, limiting our ability to develop strategies for managing the antibiotic resistance crisis. Therefore, we aim to identify genetic and ecological factors that are fundamental for successful horizontal ARG transfer. We used a phylogenetic method to identify instances of horizontal ARG transfer in ~1 million bacterial genomes. This data was then integrated with >20,000 metagenomes representing animal, human, soil, water, and wastewater microbiomes to develop random forest models that can reliably predict horizontal ARG transfer between bacteria. Our results suggest that genetic incompatibility, measured as nucleotide composition dissimilarity, negatively influences the likelihood of transfer of ARGs between evolutionarily divergent bacteria. Conversely, environmental co-occurrence increases the likelihood, especially in humans and wastewater, in which several environment-specific dissemination patterns are observed. This study provides data-driven ways to predict the spread of ARGs and provides insights into the mechanisms governing this evolutionary process.}, } @article {pmid40087549, year = {2025}, author = {Wang, X and Shang, Y and Xing, Y and Chen, Y and Wu, X and Zhang, H}, title = {Captive environments reshape the compositions of carbohydrate active enzymes and virulence factors in wolf gut microbiome.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {142}, pmid = {40087549}, issn = {1471-2180}, support = {2022KJ177//the Youth Innovation Team in Colleges and Universities of Shandong Province/ ; 32001228//the National Natural Science Foundation of China/ ; 32270444//the National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Virulence Factors/genetics ; *Wolves/microbiology ; *Bacteria/classification/genetics/isolation & purification/enzymology ; Dogs ; *Foxes/microbiology ; Animals, Zoo/microbiology ; Animals, Wild/microbiology ; Carbohydrate Metabolism ; Metagenomics ; }, abstract = {Species in the family Canidae occupy different spatial ecological niches, and some (e.g., wolf) can be kept in zoos. The gut microbiome may differ among various wild and captive canids. Therefore, we compared the gut microbiomes of wild canids (wolf, red fox, and corsac fox) in the Hulun Lake area, captive wolves, and domestic dogs in different regions using metagenomic data. A random forest analysis revealed significant enrichment for bacterial species producing short-chain fatty acids and the thermogenesis pathway (ko04714) in the gut microbiome of wild wolf, potentially providing sufficient energy for adaptation to a wide range of spatial ecological niches. The significantly enriched bacterial species and functional pathways in the gut microbiome of corsac foxes were related to physiological stability and adaptation to arid environments. Alpha diversity of carbohydrate-active enzymes in the gut microbiome was higher in the red fox than in the corsac fox and wild wolf, which may be related to the abundance of plant seeds (containing carbohydrates) in their diets (red foxes inhabit seed-rich willow bosk habitats). However, the influence of host genetic factors cannot be excluded, and further experimental studies are needed to verify the study results. In addition, captive environments drove similarity in carbohydrate-active enzymes (CAZymes) and virulence factors (VFs) in the gut microbiomes of captive wolf and domestic dog, and increased the diversity of CAZymes and VFs in the gut microbiome of captive wolf. Increased VFs diversity may increase the pathogenic potential of the gut microbiome in captive wolves. Therefore, it is necessary to continue monitoring the health status of captive wolves and develop appropriate management strategies.}, } @article {pmid40086988, year = {2025}, author = {Peng, Q and Quan, L and Zheng, H and Li, J and Xie, G}, title = {Analyzing the contribution of top-down and bottom-up methods to the construction of synthetic microbial communities in Jiuyao.}, journal = {Food microbiology}, volume = {129}, number = {}, pages = {104759}, doi = {10.1016/j.fm.2025.104759}, pmid = {40086988}, issn = {1095-9998}, mesh = {*Fermentation ; *Microbiota ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Food Microbiology ; Fermented Foods/microbiology ; Metagenomics ; Fungi/genetics/classification/metabolism/isolation & purification ; Saccharomyces cerevisiae/genetics/metabolism ; Taste ; }, abstract = {The construction of synthetic microbial communities is a crucial strategy for improving the stability of microbial populations and the quality of fermented foods. Jiuyao, an essential saccharification and fermentation starter in Huangjiu production, was the focus of this study. Using metagenomics combined with culture-dependent methods, we identified 11 microbial species involved in Huangjiu fermentation. Through metagenomic analysis and simulated fermentation, Rhizopus delemar, Rhizopus microspores, Rhizopus stolonife, Rhizopus azygosporus, Saccharomycopsis fibuligera, Saccharomyces cerevisiae, Wickerhamomyces anomalus and Pediococcus pentosaceus were determined to be the core microbial species driving the Jiuyao fermentation process. A synthetic microbial community was constructed based on these species, successfully reproducing the flavor and sensory qualities of Huangjiu while enhancing fermentation efficiency. This study provides valuable insights into the functional roles of Jiuyao-associated microbes and offers a framework for improving microbial community stability and fermentation quality in Huangjiu production.}, } @article {pmid40018976, year = {2025}, author = {Yu, T and Gao, J and Yuan, J and Yin, Z and Chen, X and Wu, Y and Dai, R and Yan, D and Chen, H and Wu, Y}, title = {Dietary methionine restriction restores wheat gluten-induced celiac-associated small intestine damage in association with affecting butyric acid production by intestinal flora.}, journal = {Food & function}, volume = {16}, number = {6}, pages = {2461-2473}, doi = {10.1039/d4fo05757k}, pmid = {40018976}, issn = {2042-650X}, mesh = {Animals ; *Methionine/metabolism ; *Intestine, Small/metabolism/microbiology ; Mice ; *Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; *Butyric Acid/metabolism ; *Glutens/adverse effects ; *Celiac Disease/diet therapy/metabolism ; *Triticum ; Male ; Disease Models, Animal ; Humans ; }, abstract = {Methionine restriction has received some attention in recent years as a novel mode of dietary intervention. Our previous study found that methionine restriction could inhibit the celiac toxic effects of wheat gluten in an in vitro model. However, the role of methionine restriction in gluten-induced celiac intestinal damage remains unclear. The aim of this study was to explore whether dietary methionine restriction could suppress the celiac toxic effects of gluten in an in vivo model, thereby mitigating intestine damage. This study systematically investigated the effects of dietary methionine restriction on celiac characteristic indicators such as symptoms, small intestine damage, and intestinal TG2 and IL-15 expression in a gluten-induced C57BL/6 mouse model. The availability of dietary methionine restriction in different ages (adolescent and adult) was also evaluated. Moreover, mouse cecum contents were assayed and co-analyzed for the metagenome of intestinal flora and target short-chain fatty acid metabolomics, with the goal of further exploring and elucidating critical pathways by which dietary methionine restriction plays a role. We discovered that dietary methionine restriction could effectively ameliorate the gluten-induced celiac-associated small intestine damage by modulating intestinal flora to inhibit butyric acid production. Specifically, dietary methionine restriction could inhibit butyric acid production with the help of s_CAG-485 sp002493045 and s_CAG-475 sp910577815, which in turn affected the mitochondrial function within the intestinal epithelial cells to assist in the repair of intestine damage. This study might provide new insights into modulating dietary patterns to mitigate intestinal damage in celiac disease and the production of novel gluten-free products.}, } @article {pmid39662821, year = {2025}, author = {Groenewegen, B and van Lingen, E and Kovynev, A and van den Berg, AJ and Berssenbrugge, EKL and Sanders, IMJG and van Prehn, J and van Nood, E and Goorhuis, A and Kuijper, EJ and Smits, WK and Wiese, M and Keller, JJ and Ducarmon, QR and Terveer, EM and , }, title = {The presence of Clostridioides difficile in faeces before and after faecal microbiota transplantation and its relation with recurrent C. difficile infection and the gut microbiota in a Dutch cohort.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {31}, number = {4}, pages = {568-574}, doi = {10.1016/j.cmi.2024.12.003}, pmid = {39662821}, issn = {1469-0691}, mesh = {Humans ; *Fecal Microbiota Transplantation ; *Feces/microbiology ; *Clostridioides difficile ; *Clostridium Infections/therapy/microbiology ; Male ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Aged ; *Recurrence ; Netherlands/epidemiology ; Adult ; Aged, 80 and over ; Risk Factors ; Treatment Outcome ; Cohort Studies ; Anti-Bacterial Agents/therapeutic use ; Vancomycin/therapeutic use/pharmacology ; }, abstract = {OBJECTIVES: The objectives of this study are to investigate the presence of Clostridioides difficile in faeces of patients with recurrent C. difficile infection (rCDI) before and after faecal microbiota transplantation (FMT) and to identify risk factors for faecal C. difficile and C. difficile infection (CDI) recurrence.

METHODS: n = 83 faecal sample triads (pre-FMT [∼1 day], post-FMT [∼3 weeks], and a corresponding FMT donor sample), and n = 22 long-term (∼1-3 years) follow-up faecal samples were collected from FMT-treated patients. The presence of C. difficile in faeces was assessed by enrichment broth culture and PCR (tcdB gene) and associated with patient characteristics, FMT outcome, duration of pre-FMT vancomycin, FMT donor, post-FMT antibiotic use, and faecal microbiota composition (shotgun metagenomics).

RESULTS: The FMT cure rate for rCDI was 92.8% (77/83), with six early CDI recurrences (<2 months post-FMT). Toxigenic C. difficile was cultured in 27.7% (23/83) of all patients post-FMT, 23.4% (18/77) of patients cured 2 months post-FMT, and 13.6% (3/22) at long-term follow-up. Early CDI recurrence (n = 6) was associated with positive C. difficile culture post-FMT (21.7% [5/23] vs. 1.7% [1/60], p 0.01), post-FMT antibiotics (30.0% [3/10] vs. 4.6% [3/65], p 0.03), and a short course of pre-FMT vancomycin (median 6.0 days, IQR [5-12] vs. 18 days, IQR [10.8-29], p < 0.05). Additionally, positive C. difficile culture directly pre-FMT was associated with a short course of pre-FMT vancomycin (median 9 days IQR [5-18] vs. 17 days, IQR [10-29.2], p 0.04). Gut microbiota analyses did not reveal signatures associated with C. difficile culture result, despite statistically non-significant trends in relative abundances of the Enterobacteriaceae family, and Dorea, Roseburia, and Clostridiales species.

DISCUSSION: Although eradication of C. difficile is not required for clinical cure of rCDI by FMT, it is associated with reduced prevalence of early CDI recurrence, as are the full completion of pre-FMT vancomycin (at least 10 days) and avoiding post-FMT antibiotics.}, } @article {pmid39080821, year = {2025}, author = {Wang, S and Chen, L and Ma, Z and Zhao, L and Lu, Y and Fu, Y and Liu, H}, title = {Gut microbiota mediates the anti-inflammatory effects of supplemental infrared irradiation in mice.}, journal = {Photochemistry and photobiology}, volume = {101}, number = {2}, pages = {458-470}, doi = {10.1111/php.14008}, pmid = {39080821}, issn = {1751-1097}, support = {JCTD-2020-04//Chinese Academy of Sciences (CAS) Interdisciplinary Innovation Team/ ; 32261133528//National Natural Science Foundation of China/ ; 82271921//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/radiation effects ; Mice ; *Infrared Rays ; Male ; Cytokines/metabolism ; Inflammation/metabolism ; Feces/microbiology ; Mice, Inbred C57BL ; Anti-Inflammatory Agents/pharmacology ; }, abstract = {In recent years, studies have shown that low-dose supplemental infrared (IR) irradiation exhibits systemic anti-inflammatory effects. The gut microbiota is increasingly recognized as a potential mediator of these effects due to its role in regulating host metabolism and inflammatory responses. To investigate the role of gut microbiota diversity and metabolite changes in the mechanism of light-emitting diodes (LED) infrared's anti-inflammatory action, we conducted IR irradiation on mice. Serum inflammatory cytokines were measured using ELISA, and fecal samples were subjected to metagenomic, untargeted, and targeted metabolomic analyses. Our results demonstrated a significant increase in the anti-inflammatory cytokine IL-10 in the IR group, accompanied by a declining trend in pro-inflammatory cytokines. Gut microbiome analysis revealed distinct alterations in composition and functional genes between the groups, including the enrichment of beneficial bacteria like various species of Parabacteroides and Akkermansia muciniphila in the IR group. Notably, the IR group exhibited enrichment in carbohydrate metabolism pathways and a reduction in DNA damage and repair pathways. Furthermore, targeted metabolomic analysis highlighted a notable increase in short-chain fatty acids (SCFAs), including butyric acid and isobutyric acid, which positively correlated with the abundance of several beneficial bacteria. These findings suggest a potential interplay between gut microbiota-derived SCFAs and the anti-inflammatory response. In conclusion, our study provides comprehensive insights into the changes in gut microbiota species and functions associated with IR irradiation. Moreover, we emphasize the significance of altered SCFAs levels in the IR group, which may contribute to the observed anti-inflammatory effects. Our findings contribute valuable evidence supporting the role of low-dose infrared light irradiation as an anti-inflammatory therapy.}, } @article {pmid39017204, year = {2024}, author = {Fernández-Trapote, E and Oliveira, M and Cobo-Díaz, JF and Alvarez-Ordóñez, A}, title = {The resistome of the food chain: A One Health perspective.}, journal = {Microbial biotechnology}, volume = {17}, number = {7}, pages = {e14530}, pmid = {39017204}, issn = {1751-7915}, support = {PID2020-118813GB-I00//Ministerio de Ciencia e Innovación/ ; }, mesh = {*Drug Resistance, Microbial ; Livestock ; Animals ; *Food Chain ; Microbiota ; Dairy Products ; Vegetables ; Meat Products ; Fish Products ; *Food Microbiology ; Global Health ; }, abstract = {Antimicrobial resistance (AMR) represents a significant global health problem which challenges Sustainable Development Goal 3 of the United Nations, with growing concerns about the possibility of AMR transmission through the food chain. The indiscriminate use of antimicrobials for the treatment of food production animals and for agricultural crop improvement, in addition to the direct discharge of livestock farm residues to sewage and the use of animal manure in agriculture, are among the factors that can facilitate the selection and transmission of AMR throughout the food chain. The study of food microbiomes has been boosted by the advent of next-generation sequencing techniques, which have enabled gaining in-depth understanding of the diversity of antimicrobial resistance genes present in food and associated environments (the so-called resistome). The aim of this review is to provide an accurate and comprehensive overview of the knowledge currently available on the resistome of the most frequently consumed foods worldwide, from a One Health perspective. To this end, the different metagenomic studies which have been conducted to characterize the resistome of foods are compiled and critically discussed.}, } @article {pmid40086981, year = {2025}, author = {Kothe, CI and Renault, P}, title = {Metagenomic driven isolation of poorly culturable species in food.}, journal = {Food microbiology}, volume = {129}, number = {}, pages = {104722}, doi = {10.1016/j.fm.2025.104722}, pmid = {40086981}, issn = {1095-9998}, mesh = {*Metagenomics ; *Cheese/microbiology ; *Food Microbiology ; *Bacteria/isolation & purification/classification/genetics ; Microbiota ; Metagenome ; Phylogeny ; }, abstract = {Although isolating microorganisms from food microbiota may appear less challenging than from the gut or environmental sources, recovering all representative species from food remains a difficult task. Here, we showed by metagenomic analysis that several abundant species had escaped isolation in a previous study of ten cheeses, including several previously uncharacterized species. This highlights the ongoing challenge of achieving a comprehensive recovery of microbes from food. To address this gap, we designed a novel strategy integrating metagenomics-based probes targeting the species of interest, coupled with an incremental culturing approach using pooled samples. As proof of concept, we applied this strategy to two cheeses containing species that were not isolated in our previous study, with the objective of isolating all species present at levels above 2% and, in particular, potential novel food species. Through this approach, we successfully performed the targeted isolation of two Psychrobacter and two Vibrio species from the first cheese, and four Halomonas and two Pseudoalteromonas species from the second one. Notably, P. undina and V. litoralis represented, as far as we know, the first cheese isolates characterized for these species. However, we were unable to isolate a novel species of Pseudoalteromonas, with no characterized representative to date, and Marinomonas foliarum, previously isolated from marine environment. Using metagenome-assembled genomes (MAGs) and metagenomic analysis, we discussed the possible reasons for their non-recovery. Finally, this strategy offers a promising approach for isolating a set of strains representative of the microbial diversity present in food ecosystems. These isolates can serve as a basis for investigating their roles in the communities, their impact on product development, safety implications and their potential in the development of starter cultures.}, } @article {pmid40037072, year = {2025}, author = {Meng, JX and Li, MH and Wang, XY and Li, S and Zhang, Y and Ni, HB and Ma, H and Liu, R and Yan, JC and Li, XM and Sun, YZ and Yang, X and Zhang, XX}, title = {Temporal variability in the diversity, function and resistome landscapes in the gut microbiome of broilers.}, journal = {Ecotoxicology and environmental safety}, volume = {292}, number = {}, pages = {117976}, doi = {10.1016/j.ecoenv.2025.117976}, pmid = {40037072}, issn = {1090-2414}, mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome/drug effects ; Bacteria/drug effects/genetics/classification ; Metagenomics ; }, abstract = {Understanding the dynamic and stability of gut microbiota over the course of production cycle of broiler chicken can help identify microbial features that associate with better health and productivity. In the present study, we profile the changes in the composition and stability of gut microbiota of commercially raised broilers at nine distinct time points using shotgun metagenomics and culturomics approaches. We demonstrate, within the first week post-hatching, a rapid decline in relative abundance of 122 pioneer microbial species including Bacteroides fragilis, Lachnospira eligens and Ruminococcus gnavus, accompanied by a substantial decrease in both microbial richness and diversity. This was followed by a gradual increase and stabilization in the microbial diversity and population structure that persisted until the broilers reached the marketing age. Throughout the production cycle, key bacterial families such as Lachnospiraceae, Bacteroidaceae, and Ruminococcaceae were identified. However, significant shifts at the lower taxonomic levels occurred at different production stages, influencing the functional capacities and resistance profiles of the microbiota. During the rapid growth phase, enzymes crucial to vitamin and amino acid metabolism dominated, whereas enzymes associated with carbohydrate and energy metabolism were notably more abundant during the fattening stage. Many predicted antibiotic resistance genes were detected in association with typical commensal bacterial species in the gut microbiota, indicating a sustained resistance of the gut microbiota to antibiotic classes such as aminoglycosides and tetracyclines, which persist even in the absence of antibiotic selection pressure. Our research carries important implications for the management and health surveillance of broiler production.}, } @article {pmid40023333, year = {2025}, author = {Liu, H and Zhou, Z and Long, C and Qing, T and Feng, B and Zhang, P and Chen, YP}, title = {Light/dark synergy enhances cyanophycin accumulation in algal-bacterial consortia: Boosted strategy for nitrogen recovery from wastewater.}, journal = {Bioresource technology}, volume = {425}, number = {}, pages = {132309}, doi = {10.1016/j.biortech.2025.132309}, pmid = {40023333}, issn = {1873-2976}, mesh = {*Wastewater ; *Nitrogen ; Bacterial Proteins/metabolism ; Microbial Consortia/physiology ; Light ; Bacteria/metabolism ; Water Purification/methods ; }, abstract = {Recovering the nitrogen-rich biopolymer cyanophycin [(β-Asp-Arg)n] from algal-bacterial consortia enhances the reclamation of value-added chemicals from wastewater. However, the modulation of light/dark conditions on cyanophycin accumulation remain unknown. In this study, the trends and mechanisms of cyanophycin synthesis in algal-bacterial consortia under light/dark conditions were investigated. The results showed that cyanophycin production during the dark periods ranged from 137-150 mg/g MLSS (mixed liquid suspended solids), which was 32 %-38 % higher than those during the light period (p < 0.001). Metatranscriptomics results demonstrated that 50 metagenome-assembled genomes contribute to cyanophycin production, with the Planktothrix genus being the dominant contributor. Metabolomics findings suggested that algal-bacterial consortia produce higher level of arginine for cyanophycin synthesis under light conditions. This study demonstrates the feasibility of increasing cyanophycin production by merging light/dark cycles, and offers a novel strategy for high yield of valuable biopolymers from wastewater substrate.}, } @article {pmid39983259, year = {2025}, author = {Lyte, JM and Jia, X and Caputi, V and Zhang, D and Daniels, KM and Phillips, GJ and Lyte, M}, title = {Heat stress in chickens induces temporal changes in the cecal microbiome concomitant with host enteric serotonin responses.}, journal = {Poultry science}, volume = {104}, number = {3}, pages = {104886}, pmid = {39983259}, issn = {1525-3171}, mesh = {Animals ; *Chickens/physiology ; *Serotonin/metabolism ; *Gastrointestinal Microbiome ; *Cecum/microbiology ; *Heat-Shock Response/physiology ; Male ; Hot Temperature/adverse effects ; }, abstract = {Heat stress is a potent modulator of the avian neuroendocrine system with concomitant impact on the gut microbiome. As an interkingdom signaling molecule, serotonin is largely derived from the gut and found in large concentrations in the avian gut lumen. Despite the role of serotonin in animal stress physiology and related host-microbe interactions, whether heat stress alters avian enteric concentrations of serotonin is unknown. As such, the present study sought to determine whether acute or chronic exposure to moderate heat stress alters both enteric serotonin concentrations and the microbiome in the chicken gut. Chickens were, or were not, subjected to an acute (1 day), repeated acute (2 days) or chronic (6 days) moderate ambient cyclic heat stress (12h per day, 31°C). Enteric concentrations of serotonin were significantly decreased in the acute heat stress group (P < 0.05), and rebounded to become elevated in the chronic heat stress group (P < 0.05). Shotgun metagenomic sequencing revealed heat stress caused both functional and taxonomic changes in the cecal microbiome. Abundances of bacterial taxa that are known to interact with the host via the serotonergic system, including Lactobacillus spp., and Bifidobacterium spp., were significantly (P < 0.05) altered by heat stress. As these findings demonstrate that heat stress can alter serotonin concentrations in the chicken intestinal tract, with distinct outcomes depending on duration of the stressor, serotonergic signaling may serve as potential leverageable point of intervention in host-microbe interactions including foodborne pathogen colonization in the chicken gut. In addition, this study provides novel insight into the impact of acute and chronic heat stress on the avian microbiome, and its relationship to stress-driven changes in the enteric serotonergic system.}, } @article {pmid39847933, year = {2025}, author = {Malla, MA and Nomalihle, M and Featherston, J and Kumar, A and Amoah, ID and Ismail, A and Bux, F and Kumari, S}, title = {Comprehensive profiling and risk assessment of antibiotic resistomes in surface water and plastisphere by integrated shotgun metagenomics.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137180}, doi = {10.1016/j.jhazmat.2025.137180}, pmid = {39847933}, issn = {1873-3336}, mesh = {*Metagenomics ; *Water Pollutants, Chemical/toxicity/analysis ; *Microbiota/drug effects ; Risk Assessment ; *Bacteria/genetics/drug effects/classification ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Water Microbiology ; Microplastics/toxicity ; Genes, Bacterial/drug effects ; Drug Resistance, Bacterial/genetics ; Environmental Monitoring/methods ; }, abstract = {The ever-increasing microplastics (MPs) and antibiotic-resistance genes (ARGs) in aquatic ecosystems has become a serious global challenging issue. However, the impact of different pollution sources on microbiome and antibiotic resistome in surface water (SW) and plastisphere (PS) remains largely elusive. Here, shotgun metagenomics was used to analyze microbiome structure and antibiotic resistome in SW and PS under the influence of different pollution sources. Pseudomonas were the most abundant genus, followed by Flavobacterium, Acinetobacter, Acidovorax, and Limnohabitans. However, their relative abundance varied significantly both across the sampling sites and habitats i.e. SW and PS (p < 0.05). Additionally, various ARGs were detected in SW and PS, with PS (372) having significantly more potential ARGs than SW (293). The results further showed significant variations in the relative abundance of potential pathogenic bacteria across the sampling sites and habitats (p < 0.05). Further moreover, significant differences were observed in antibiotic resistome risk scores, ARGs and MGEs across different habitats. Over all, this study suggests that pollution source and water quality parameters had a significant impact on microbiome composition and antibiotic resistome in SW and PS.}, } @article {pmid39827796, year = {2025}, author = {He, LX and He, LY and Tang, YJ and Qiao, LK and Xu, MC and Zhou, ZY and Bai, H and Zhang, M and Ying, GG}, title = {Deciphering spread of quinolone resistance in mariculture ponds: Cross-species and cross-environment transmission of resistome.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137198}, doi = {10.1016/j.jhazmat.2025.137198}, pmid = {39827796}, issn = {1873-3336}, mesh = {*Quinolones/pharmacology ; Animals ; *Ponds/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Bacteria/drug effects/genetics ; Aquaculture ; Gills/microbiology ; Genes, Bacterial ; Fishes/microbiology ; Seawater/microbiology ; Geologic Sediments/microbiology ; Microbiota/drug effects ; Water Pollutants, Chemical/toxicity ; }, abstract = {Mariculture is known to harbor antibiotic resistance genes (ARGs), which can be released into marine ecosystems via oceanic farming ponds, posing a public health concern. In this study, metagenomic sequencing was used to decipher the profiles of quinolone-resistant microbiomes and the mechanisms of quinolone resistance in sediment, seawater, and fish gill samples from five mariculture ponds. Residues of both veterinary-specific (enrofloxacin and sarafloxacin) and prohibited quinolones (ofloxacin, ciprofloxacin, pefloxacin, norfloxacin, and lomefloxacin) were detected. We identified a total of 285 subtypes of ARGs across all samples. Pathogens played a crucial role in the prevalence and distribution of these ARGs. Out of the annotated 629 bacterial species, 42 were identified as pathogenic, predominantly belonging to the Proteobacteria phylum. Notably, the Acinetobacter genus was prevalent in the gills and exhibited correlations with various ARGs. The presence of the plasmid-mediated quinolone resistance (PMQR) genes in various bacterial species and the identification of sulfonamide resistance genes across different samples indicated the potential for cross-species and cross-environment transmission of ARGs. Metagenomic binning revealed that Exiguobacterium harbored five ARGs (vanA, vanB, fexA, msr(G), mefF), while Shewanella carried six ARGs (blaOXA-436, adeF, qacl, ANT (2'')-Ia, dfrA1, rsmA). Mutations in gyrA and parC contributed to quinolone resistance in these multidrug-resistant Exiguobacterium and Shewanella. Our findings suggest a potential for ARG transmission across various bacterial species and environments in mariculture. This study emphasized the risk of resistance spread within the mariculture ecosystem.}, } @article {pmid39813926, year = {2025}, author = {Qu, C and Tang, J and Liu, J and Wang, W and Song, F and Cheng, S and Tang, X and Tang, CJ}, title = {Quorum sensing-enhanced electron transfer in anammox consortia: A mechanism for improved resistance to variable-valence heavy metals.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137130}, doi = {10.1016/j.jhazmat.2025.137130}, pmid = {39813926}, issn = {1873-3336}, mesh = {*Quorum Sensing ; Electron Transport ; *Metals, Heavy/metabolism/toxicity ; *Acyl-Butyrolactones/metabolism ; Chromium/metabolism/toxicity ; Bacteria/metabolism/drug effects ; Microbial Consortia ; }, abstract = {Quorum sensing (QS) is recognized for enhancing bacterial resistance against heavy metals by regulating the production of extracellular substances that hinder metal penetration into the intracellular environment. However, it remains unclear whether QS contributes to resistance by regulating electron transfer, thereby transforming metals from more toxic to less toxic forms. This study investigated the regulatory mechanism of acyl-homoserine lactone (AHL)-mediated QS on electron transfer under As(III) and Cr(VI) stress. Metagenomic binning results revealed that Candidatus Brocadia sinica serves as a major contributor to AHL production for regulating heavy metal resistance, while other symbiotic bacteria offer complementary resistance pathways. In these bacteria, the AHL synthesis gene htdS plays a pivotal role in QS regulation of electron transfer and heavy metal resistance. Experimental findings demonstrated that AHL increased the electron transport system activity by 19.8 %, and upregulated electron transfer gene expression by 1.1- to 6.9-fold. The enhanced electron transfer facilitated a 28.7 % increase in the transformation of As(III) to less toxic As(V) and monomethylarsonic acid, ultimately achieving efficient nitrogen removal under As(III) stress. This study expands our understanding of how QS strengthens bacterial resistance to heavy metals, offering novel strategies for enhancing nitrogen removal of anammox in heavy metal-contaminated environments.}, } @article {pmid39798310, year = {2025}, author = {Zhou, HZ and Wang, BQ and Ma, YH and Sun, YY and Zhou, HL and Song, Z and Zhao, Y and Chen, W and Min, J and Li, JW and He, T}, title = {The combination of metagenomics and metabolomics reveals the effect of nitrogen fertilizer application driving the remobilization of immobilization remediation cadmium and rhizosphere microbial succession in rice.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137117}, doi = {10.1016/j.jhazmat.2025.137117}, pmid = {39798310}, issn = {1873-3336}, mesh = {*Oryza/metabolism/microbiology/growth & development ; *Fertilizers ; *Cadmium/metabolism ; *Rhizosphere ; *Nitrogen/metabolism ; *Soil Microbiology ; *Soil Pollutants/metabolism ; Metagenomics ; Metabolomics ; Microbiota/drug effects ; Plant Roots/metabolism/microbiology ; Bacteria/metabolism/genetics ; }, abstract = {The remobilization of cadmium (Cd) in contaminated farmland soil due to nitrogen fertilizer addition has raised significant concerns regarding the effectiveness of immobilization remediation. This study investigated the effects of ammonia nitrogen (NH4[+]-N) and nitrogen (NO3[-]-N) application (100 kg/ha) on the remobilization of immobilization of remediation Cd (bound to clay palygorskite) during various growth stages of rice through field experiments. Our findings revealed that increased organic acid secretion (e.g., benzoic acid and malic acid) from rice roots, induced by NH4[+]-N, significantly enhanced the NH4NO3-extractable Cd content. Consequently, the concentration of Cd in brown rice varied from 39.84 to 43.25 μg/kg to 78.31-90.44 μg/kg. While NO3[-]-N exhibited a relatively weaker capacity for Cd remobilization (Cd content in brown rices: 50.17-65.23 μg/kg). Meanwhile, the organic acid secretion in roots inhibited the expression of most functional genes (e.g., nifK and napA), leading to shifts in microbial communities and functional metabolism (e.g., Cd[2+] exporting). According to the results of metagenome-assembled genome (MAG) composition, specific MAGs with fewer functional annotations were enriched under NH4[+]-N treatment, may further increased risk of Cd exposure in rice by stimulating amt expression. Interaction analysis of metabolic products and microbial communities indicated acids linked to branched-chain amino acid (BCAA) metabolism and urea cycle might serve as a potentially key process influencing microbial dynamics.}, } @article {pmid39692041, year = {2025}, author = {Yang, Z and Zhang, Z and Jiang, S and Li, A and Song, H and Zhang, J}, title = {Diet shapes and maintains the personalized native gut microbiomes in mice.}, journal = {Journal of the science of food and agriculture}, volume = {105}, number = {5}, pages = {2987-3000}, doi = {10.1002/jsfa.14073}, pmid = {39692041}, issn = {1097-0010}, support = {//National Natural Science Foundation of China (No. 32222066 and No. 32160545)/ ; }, mesh = {*Gastrointestinal Microbiome ; Animals ; Mice ; *Mice, Inbred C57BL ; *Diet/veterinary ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Male ; Feces/microbiology ; Humans ; Akkermansia/metabolism ; }, abstract = {BACKGROUND: The gut microbiome plays a critical role in human health and disease. Different dietary backgrounds play an important role in the uniqueness and diversity of the gut microbiota in different individuals, which promotes heterogeneity in disease phenotypes and treatment responses. Here, we explored how diet affects the composition and function of the native gut microbiome of model mice, based on the shotgun metagenomic and metabolomic, by analyzing the gut microbiome of C57B/6J mice in different dietary backgrounds.

RESULTS: The gut microbiomes of mice receiving different diets consistently exhibit distinct compositions across bacterial species, strains, fungi and phages. This implies that native microbial communities cannot 'homogenize' rapidly becaise of priority effects and unchanging diets. Notably, hotspot bacteria such as Limosilactobacillus reuteri, Parabacteroides distasonis and Akkermansia muciniphila were significantly different among the groups. These species harbor diverse adaptive mutations, reflecting genomic evolutionary diversity. The functional profiles of the gut microbiota also exhibit selective differences, involving the capacity for carbohydrate, branched-chain amino acid and fatty acid synthesis, as well as virulence factors, carbohydrate-active enzymes and antibiotic resistance. Furthermore, the differences in the gut microbiota also propagate to the host's serum, where structural and specific metabolite differences were observed. Metabolites that directly impact host health, such as d-glucosamine 6-phosphate and testolic acid, also show significant differences between the different dietary groups.

CONCLUSION: Our findings underscore the profound influence of different dietary the composition and functionality of the gut microbiome, offering valuable insights into optimizing health outcomes through personalized nutritional interventions. © 2024 Society of Chemical Industry.}, } @article {pmid39581260, year = {2025}, author = {Lee, YH and Park, HJ and Jeong, SJ and Auh, QS and Jung, J and Lee, GJ and Shin, S and Hong, JY}, title = {Oral microbiome profiles of gingivitis and periodontitis by next-generation sequencing among a group of hospital patients in Korea: A cross-sectional study.}, journal = {Journal of oral biosciences}, volume = {67}, number = {1}, pages = {100591}, doi = {10.1016/j.job.2024.100591}, pmid = {39581260}, issn = {1880-3865}, mesh = {Humans ; Cross-Sectional Studies ; Female ; Male ; *Gingivitis/microbiology ; *Microbiota/genetics ; Adult ; Middle Aged ; *Periodontitis/microbiology ; Republic of Korea ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; Saliva/microbiology ; Case-Control Studies ; Mouth/microbiology ; }, abstract = {OBJECTIVES: The oral microbiome plays an important role in the development and progression of periodontal disease. The purpose of this study was to compare microbial profiles of oral cavities in good health, with gingivitis, and in a state of periodontitis, and to identify novel pathogens involved in periodontal diseases.

METHODS: One hundred and two participants, including 33 healthy controls, 41 patients with gingivitis, and 28 patients with periodontitis, were included in this cross-sectional study. Salivary oral microbiomes were investigated using 16S rRNA metagenomic sequencing, and the microbial profiles of each group were compared using age- and sex-adjusted general linear models.

RESULTS: The abundance of amplicon sequence variants and Chao1 diversity were significantly elevated in the gingivitis and periodontitis groups relative to healthy controls (p = 0.046). Based on linear discriminant analysis (LDA) scores (>2), Tenericutes, Mollicutes, Mycoplasmatales, Mycoplasmataceae, Mycoplasma, Bacteroidaceae, and Phocaeicola were significantly enriched in the gingivitis group, and Synergistetes, Synergistia, Synergistales, Synergistaceae, Fretibacterium, Sinanaerobacter, and Filifactor were enriched in the periodontitis group. The relative abundances of Fretibacterium fastidiosum, Sinanaerobacter chloroacetimidivorans, and Filifactor alocis (q = 0.008, all bacteria) were highest in the periodontitis group and lowest in the control group. The relative abundance of Treponema denticola was significantly elevated in the periodontitis group compared to the other two groups (q = 0.024).

CONCLUSIONS: Oral microbiomes differed between groups. T. denticola, F. fastidiosum, S. chloroacetimidivorans and F. alocis were significantly more abundant in the periodontitis group than in the control group. Additionally, the abundance of T. denticola and F. fastidiosum in the periodontitis group was significantly different from that in the gingivitis group.}, } @article {pmid39515321, year = {2025}, author = {Lin, Y and Xie, M and Lau, HC and Zeng, R and Zhang, R and Wang, L and Li, Q and Wang, Y and Chen, D and Jiang, L and Damsky, W and Yu, J}, title = {Effects of gut microbiota on immune checkpoint inhibitors in multi-cancer and as microbial biomarkers for predicting therapeutic response.}, journal = {Med (New York, N.Y.)}, volume = {6}, number = {3}, pages = {100530}, doi = {10.1016/j.medj.2024.10.007}, pmid = {39515321}, issn = {2666-6340}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Immune Checkpoint Inhibitors/pharmacology/therapeutic use ; Animals ; Humans ; Mice ; *Carcinoma, Non-Small-Cell Lung/drug therapy/immunology ; *Lung Neoplasms/drug therapy/immunology ; Carcinoma, Renal Cell/drug therapy/immunology/microbiology ; Melanoma/drug therapy/immunology/microbiology ; Feces/microbiology ; Kidney Neoplasms/drug therapy/immunology/microbiology/pathology ; Biomarkers ; Carcinoma, Hepatocellular/drug therapy/microbiology/immunology ; Liver Neoplasms/drug therapy/immunology/microbiology ; Neoplasms/drug therapy/microbiology/immunology ; Faecalibacterium prausnitzii/drug effects ; Female ; }, abstract = {BACKGROUND: Gut bacteria are related to immune checkpoint inhibitors (ICIs). However, there is inconsistency in ICI-associated species, while the role of non-bacterial microbes in immunotherapy remains elusive. Here, we evaluated the association of trans-kingdom microbes with ICIs by multi-cohort multi-cancer analyses.

METHODS: We retrieved fecal metagenomes from 1,359 ICI recipients with four different cancers (metastatic melanoma [MM], non-small cell lung carcinoma [NSCLC], renal cell cancer [RCC], and hepatocellular carcinoma) from 12 published datasets. Microbiota composition was analyzed using the Wilcoxon rank test. The performance of microbial biomarkers in predicting ICI response was assessed by random forest. Key responder-associated microbes were functionally examined in vitro and in mice.

FINDINGS: Trans-kingdom gut microbiota (bacteria, eukaryotes, viruses, and archaea) was significantly different between ICI responders and non-responders in multi-cancer. Bacteria (Faecalibacterium prausnitzii, Coprococcus comes) and eukaryotes (Nemania serpens, Hyphopichia pseudoburtonii) were consistently enriched in responders of ≥2 cancer types or from ≥3 cohorts, contrasting with the depleted bacterium Hungatella hathewayi. Responder-associated species in each cancer were revealed, such as F. prausnitzii in MM and 6 species in NSCLC. These signature species influenced ICI efficacy by modulating CD8[+] T cell activity in vitro and in mice. Moreover, bacterial and eukaryotic biomarkers showed great performance in predicting ICI response in patients from discovery and two validation cohorts (MM: area under the receiver operating characteristic curve [AUROC] = 72.27%-80.19%; NSCLC: AUROC = 72.70%-87.98%; RCC: AUROC = 83.33%-89.58%).

CONCLUSIONS: This study identified trans-kingdom microbial signatures associated with ICI in multi-cancer and specific cancer types. Trans-kingdom microbial biomarkers are potential predictors of ICI response in patients with cancer.

FUNDING: Funding information is shown in the acknowledgments.}, } @article {pmid39447963, year = {2025}, author = {Lee, S and Arefaine, B and Begum, N and Stamouli, M and Witherden, E and Mohamad, M and Harzandi, A and Zamalloa, A and Cai, H and Williams, R and Curtis, MA and Edwards, LA and Chokshi, S and Mardinoglu, A and Proctor, G and Moyes, DL and McPhail, MJ and Shawcross, DL and Uhlen, M and Shoaie, S and Patel, VC}, title = {Oral-gut microbiome interactions in advanced cirrhosis: characterisation of pathogenic enterotypes and salivatypes, virulence factors and antimicrobial resistance.}, journal = {Journal of hepatology}, volume = {82}, number = {4}, pages = {622-633}, doi = {10.1016/j.jhep.2024.09.046}, pmid = {39447963}, issn = {1600-0641}, mesh = {Humans ; *Liver Cirrhosis/microbiology/complications ; *Gastrointestinal Microbiome/physiology/drug effects ; *Virulence Factors/genetics ; Male ; Middle Aged ; Female ; Saliva/microbiology ; Aged ; Feces/microbiology ; Adult ; Severity of Illness Index ; Mouth/microbiology ; Case-Control Studies ; Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND & AIMS: Cirrhosis complications are often triggered by bacterial infections with multidrug-resistant organisms. Alterations in the gut and oral microbiome in decompensated cirrhosis (DC) influence clinical outcomes. We interrogated: (i) gut and oral microbiome community structures, (ii) virulence factors (VFs) and antimicrobial resistance genes (ARGs) and (iii) oral-gut microbial overlap in patients with differing cirrhosis severity.

METHODS: Fifteen healthy controls (HCs), as well as 26 patients with stable cirrhosis (SC), 46 with DC, 14 with acute-on-chronic liver failure (ACLF) and 14 with severe infection without cirrhosis participated. Metagenomic sequencing was undertaken on paired saliva and faecal samples. 'Salivatypes' and 'enterotypes' based on genera clustering were assessed against cirrhosis severity and clinical parameters. VFs and ARGs were evaluated in oral and gut niches, and distinct resistotypes identified.

RESULTS: Salivatypes and enterotypes revealed a greater proportion of pathobionts with concomitant reduction in autochthonous genera with increasing cirrhosis severity and hyperammonaemia. Increasing overlap between oral and gut microbiome communities was observed in DC and ACLF vs. SC and HCs, independent of antimicrobial, beta-blocker and gastric acid-suppressing therapies. Two distinct gut microbiome clusters harboured genes encoding for the PTS (phosphoenolpyruvate:sugar phosphotransferase system) and other VFs in DC and ACLF. Substantial ARGs (oral: 1,218 and gut: 672) were detected (575 common to both sites). The cirrhosis resistome was distinct, with three oral and four gut resistotypes identified, respectively.

CONCLUSIONS: The degree of oral-gut microbial community overlap, frequency of VFs and ARGs all increase significantly with cirrhosis severity, with progressive dominance of pathobionts and loss of commensals. Despite similar antimicrobial exposure, patients with DC and ACLF have reduced microbial richness compared to patients with severe infection without cirrhosis, supporting the additive pathobiological effect of cirrhosis.

IMPACT AND IMPLICATIONS: This research underscores the crucial role of microbiome alterations in the progression of cirrhosis in an era of escalating multidrug resistant infections, highlighting the association and potential impact of increased oral-gut microbial overlap, virulence factors, and antimicrobial resistance genes on clinical outcomes. These findings are particularly significant for patients with decompensated cirrhosis and acute-on-chronic liver failure, as they reveal the intricate relationship between microbiome alterations and cirrhosis complications. This is relevant in the context of multidrug-resistant organisms and reduced oral-gut microbial diversity that exacerbate cirrhosis severity, drive hepatic decompensation and complicate treatment. For practical applications, these insights could guide the development of targeted microbiome-based therapeutics and personalised antimicrobial regimens for patients with cirrhosis to mitigate infectious complications and improve clinical outcomes.}, } @article {pmid40083550, year = {2025}, author = {Ng, HY and Liao, Y and Cheung, CL and Zhang, R and Chan, KH and Seto, WK and Leung, WK and Hung, IFN and Lam, TTY and Cheung, KS}, title = {Gut microbiota is associated with persistence of longer-term BNT162b2 vaccine immunogenicity.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1534787}, pmid = {40083550}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Male ; Female ; Middle Aged ; Adult ; *BNT162 Vaccine/immunology ; *SARS-CoV-2/immunology ; *COVID-19/immunology ; Antibodies, Neutralizing/blood/immunology ; Immunogenicity, Vaccine ; Prospective Studies ; Antibodies, Viral/blood/immunology ; Hong Kong ; Feces/microbiology ; }, abstract = {INTRODUCTION: BNT162b2 immunogenicity wanes with time and we investigated association between gut microbiota and longer-term immunogenicity.

METHODS: This cohort study prospectively recruited adult BNT162b2 two-dose recipients from three vaccination centers in Hong Kong. Blood samples were collected at baseline and day 180 after first dose, and tested for neutralizing antibodies (NAb) against receptor-binding domain (RBD) of wild type SARS-CoV-2 virus using chemiluminescence immunoassay. Shotgun DNA metagenomic sequencing was performed to characterize baseline stool microbiome. Baseline metabolites were measured by gas and liquid chromatography-tandem mass spectrometry (GC-MS/MS and LC-MS/MS). Primary outcome was persistent high NAb response (defined as top 25% of NAb level) at day 180. Putative bacterial species and metabolic pathways were identified using linear discriminant analysis [LDA] effect size analysis. Multivariable logistic regression adjusting for clinical factors was used to derive adjusted odds ratio (aOR) of outcome with bacterial species and metabolites.

RESULTS: Of 242 subjects (median age: 50.2 years [IQR:42.5-55.6]; male:85 [35.1%]), 61 (25.2%) were high-responders while 33 (13.6%) were extreme-high responders (defined as NAb≥200AU/mL). None had COVID-19 at end of study. Ruminococcus bicirculans (log10LDA score=3.65), Parasutterella excrementihominis (score=2.82) and Streptococcus salivarius (score=2.31) were enriched in high-responders, while Bacteroides thetaiotaomicron was enriched in low-responders (score=-3.70). On multivariable analysis, bacterial species (R. bicirculans-aOR: 1.87, 95% CI: 1.02-3.51; P. excrementihominis-aOR: 2.2, 95% CI: 1.18-4.18; S. salivarius-aOR: 2.09, 95% CI: 1.13-3.94) but not clinical factors associated with high response. R. bicirculans positively correlated with most metabolic pathways enriched in high-responders, including superpathway of L-cysteine biosynthesis (score=2.25) and L-isoleucine biosynthesis I pathway (score=2.16) known to benefit immune system. Baseline serum butyrate (aOR:10.00, 95% CI:1.81-107.2) and isoleucine (aOR:1.17, 95% CI:1.04-1.35) significantly associated with extreme-high vaccine response.

CONCLUSION: Certain gut bacterial species, metabolic pathways and metabolites associate with longer-term COVID-19 vaccine immunogenicity.}, } @article {pmid40082612, year = {2025}, author = {Đokić, J and Dinić, M and Soković Bajić, S and Bisenić, A and Mitrović, H and Jakovljević, S and Radojević, D and Brdarić, E and Lukić, J and Živković, M and Tolinački, M and Terzić-Vidojević, A and Golić, N}, title = {High-throughput workflow for cultivation and characterization of gut microbiota strains with anti-inflammatory properties and metabolite signature associated with gut-brain communication.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8741}, pmid = {40082612}, issn = {2045-2322}, support = {Grant IDEAS No. 7744507, NextGenBiotics//Science Fund of the Republic of Serbia/ ; Grant No. 451-03-66/2024-03/200042//Ministry of Science, Technological Development and Innovations of the Republic of Serbia/ ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; *Brain-Gut Axis ; Anti-Inflammatory Agents/metabolism/pharmacology ; Workflow ; Bacteria/metabolism/classification/genetics ; Brain/metabolism ; Probiotics ; Metagenome ; }, abstract = {The gut microbiota is deeply interconnected with the brain, a phenomenon often referred to as the gut-brain axis. Dysfunction in the microbiota-gut-brain axis can cause various neurological and psychiatric disorders associated with chronic inflammation and gut microbiota dysbiosis. Therefore, cultivation of anaerobic human gut microbiota strains, and characterization of their safety status and immunomodulatory potential could contribute to deciphering the molecular mechanisms underlying the microbiota-gut-brain communication and revealed their biotherapeutic potential. However, poor cultivability of gut microbiota members, makes research into their physiological role challenging. Hence, we report a high-throughput workflow based on targeted cultivation linked to metagenome sequencing, combined with the bioinformatic search for gut members with anti-inflammatory properties which produce the most important microbial metabolites that affect brain function. With this approach, we isolated 147 bacterial strains, and 41 were characterized for their immunomodulatory status with 12 strains showing immunosuppressive features with ability of producing brain important metabolites. Through this workflow we established the best growing conditions essential for cultivation, archiving, phenotyping, and characterization of anaerobic gut bacteria important for microbiota-gut-brain-axis research, and characterized the safety and probiotic potential of 7 extremely oxygen-sensitive strains.}, } @article {pmid40082024, year = {2025}, author = {Yin, F and Ge, T and Zalucki, MP and Xiao, Y and Peng, Z and Li, Z}, title = {Gut symbionts affect Plutella xylostella (L.) susceptibility to chlorantraniliprole.}, journal = {Pesticide biochemistry and physiology}, volume = {209}, number = {}, pages = {106327}, doi = {10.1016/j.pestbp.2025.106327}, pmid = {40082024}, issn = {1095-9939}, mesh = {Animals ; *ortho-Aminobenzoates/pharmacology ; *Moths/drug effects/microbiology ; *Insecticides/pharmacology ; *Insecticide Resistance/genetics ; *Gastrointestinal Microbiome/drug effects ; *Symbiosis ; Bacteria/drug effects/genetics/metabolism ; Larva/drug effects/microbiology ; }, abstract = {Plutella xylostella, a globally economically important pest of cruciferous crops, has varying degrees of resistance to almost all insecticides. Insect gut microbiotas have a variety of physiological functions, and recent studies have shown that they have some potential connection with insecticide resistance. Here, we use metagenomics to analyze the differences in gut microbiota among 5 different populations of P. xylostella resistant to chlorantraniliprole. Differential gene expression was enriched in various metabolic pathways including carbohydrate metabolism, amino acid metabolism, energy metabolism, metabolism of cofactors and vitamins, nucleotide metabolism and so on. Proteobacteria was the dominate phyla, and the relative abundance of common dominant genera in the treated group (CL, Bt, and BtCL) was higher than that in susceptible controls. We successfully isolated 15 species of bacteria, in which the Enterobacter hormaechei was associated with enhanced insecticide resistance. The population we isolated can metabolize chlorantraniliprole in vitro, with a metabolic rate of 34.8 % within 4 days. Our work advances understanding of the evolution of insecticide resistance and lays a foundation for the further exploration of symbiotic microbial associations of lepidopteran insects and their ecological consequences.}, } @article {pmid40082000, year = {2025}, author = {Massaro, CA and Meade, S and Lemarié, FL and Kaur, G and Bressler, B and Rosenfeld, G and Leung, Y and Williams, AJ and Lunken, G}, title = {Gut microbiome predictors of advanced therapy response in Crohn's disease: protocol for the OPTIMIST prospective, longitudinal, observational pilot study in Canada.}, journal = {BMJ open}, volume = {15}, number = {3}, pages = {e094280}, doi = {10.1136/bmjopen-2024-094280}, pmid = {40082000}, issn = {2044-6055}, mesh = {Humans ; *Crohn Disease/microbiology/therapy ; *Gastrointestinal Microbiome ; Pilot Projects ; Prospective Studies ; Longitudinal Studies ; Observational Studies as Topic ; Feces/microbiology ; British Columbia/epidemiology ; Canada ; }, abstract = {INTRODUCTION: Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis, is characterised by chronic and relapsing inflammation of the gastrointestinal tract, leading to significant morbidity and reduced quality of life. The global rise in IBD incidence is driven by a complex interplay of genetic, environmental, dietary and microbiome-related factors. Despite advancements in treatment, such as biologics, response rates remain variable, highlighting the need for personalised approaches. Recent research suggests that specific microbiome signatures may serve as biomarkers for predicting therapeutic efficacy, offering a potential tool for optimising treatment strategies in CD. The aim of the Optimising IBD Patient Treatment with Integrated Microbiome Investigation for Specialised Therapeutics (OPTIMIST) study is to evaluate microbiome profiles across various sample types in a Canadian CD cohort starting or already on advanced therapy, with the goal of developing predictive models for personalised therapeutics.

METHODS AND ANALYSIS: This study is a two-phase, longitudinal, prospective observational pilot study conducted in British Columbia, Canada, involving both CD patients and non-IBD controls. Phase 1 focuses on baseline microbiome differences across participant cohorts through cross-sectional analysis. Phase 2 follows participants over 12 months to assess microbiome changes and their association with treatment response. Stool samples, intestinal biopsies from the left colon, right colon and ileum, as well as mucosal wash samples from the proximal part of the distal colon, will undergo metagenomics, metaproteomics and metabolomics analyses to explore compositional and functional differences. Data will be analysed using alpha and beta diversity metrics, differential abundance analyses and multivariate analyses to identify microbiome-based predictors of therapeutic response.

ETHICS AND DISSEMINATION: Ethical approval was received by the Research Ethics Board (REB) of University of British Columbia-Providence Healthcare (UBC-PHC) with a REB number H23-02927. All amendments to the protocol are reported and adapted based on the requirements of the REB. The results of this study will be submitted to peer-reviewed journals and will be communicated in editorials/articles by the IBD Centre of BC and BC Children's Hospital Research Institute.

TRIAL REGISTRATION NUMBER: NCT06453720.

PROTOCOL VERSION: 2024-06-21, version 3.0.}, } @article {pmid40077671, year = {2025}, author = {Gao, Y and Borjihan, Q and Zhang, W and Li, L and Wang, D and Bai, L and Zhu, S and Chen, Y}, title = {Complex Probiotics Ameliorate Fecal Microbiota Transplantation-Induced IBS in Mice via Gut Microbiota and Metabolite Modulation.}, journal = {Nutrients}, volume = {17}, number = {5}, pages = {}, pmid = {40077671}, issn = {2072-6643}, support = {2022-Science and Technology Xing Meng-Quality improvement-02//the Science and Technology Xing Meng action focus project of Inner Mongolia Autonomous Region/ ; 2022-Science and Technology Xing Meng-Quality improvement-02//the Science and Technology Xing Meng action focus project of Inner Mongolia Autonomous Region/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Irritable Bowel Syndrome/therapy/microbiology ; *Fecal Microbiota Transplantation ; *Probiotics/pharmacology ; Mice ; *Feces/microbiology ; *Disease Models, Animal ; Mice, Inbred C57BL ; Male ; Dysbiosis/therapy ; Serotonin/metabolism ; Serotonin Plasma Membrane Transport Proteins/metabolism ; Acetic Acid ; Constipation/therapy/microbiology/metabolism ; Butyric Acid/metabolism ; Tryptophan/metabolism ; }, abstract = {Background/Objectives: Irritable bowel syndrome (IBS) is a highly prevalent functional gastrointestinal disorder. Emerging evidence implicates gut microbiota dysbiosis in IBS pathogenesis, and probiotic interventions targeting microbial modulation hold therapeutic promise. Methods: this study used fecal microbiota transplantation to establish a mouse model of IBS before evaluating the effects of the complex probiotic by using metagenomics and targeted metabolomics to explore the potential mechanism. Results: After 14 days, the probiotic relieved constipation, reduced inflammation and intestinal permeability, lowered 5-HT levels and increased serotonin transporter (SERT) expression in tissues. Metagenomic analysis showed a reduced inflammation-related species abundance. It also decreased fecal butyric acid, acetic acid and tryptophan levels in IBS mice. Conclusions: The probiotic complex effectively alleviated IBS symptoms in mice by modulating gut microbiota and fecal metabolites, providing insights for future IBS research and treatment.}, } @article {pmid40076957, year = {2025}, author = {Kumagai, K and Ishikawa, S and Iino, M and Edamatsu, K and Okuyama, N and Yusa, K and Shimizu, Y and Aoki, R and Masuda, C and Ohashi, Y and Horie, A and Hoshi, K and Hamada, Y}, title = {Characterization of Salivary Microbiota in Japanese Patients with Oral Cancer.}, journal = {International journal of molecular sciences}, volume = {26}, number = {5}, pages = {}, pmid = {40076957}, issn = {1422-0067}, support = {JP 22K10113//JSPS KAKENHI Grant-in-Aid for Scientific Research (C)/ ; }, mesh = {Humans ; *Saliva/microbiology ; Male ; Female ; *Microbiota/genetics ; Middle Aged ; *RNA, Ribosomal, 16S/genetics ; *Mouth Neoplasms/microbiology ; Aged ; Bacteria/classification/genetics/isolation & purification ; Japan ; Case-Control Studies ; Adult ; Metagenomics/methods ; East Asian People ; }, abstract = {This study aimed to characterize salivary microbiota in patients with oral cancer using 16S rRNA amplicon sequencing. DNA was extracted from saliva samples of 23 patients with oral cancer and 95 age-matched controls. A metagenomic analysis was performed using 16S rRNA amplicon sequencing. Patients with oral cancer exhibited lower α-diversity, as indicated by the Chao-1 index, compared to the control group, and significant differences in β-diversity were observed between the two groups. At the genus level, 25 bacterial species such as Lautropia, Megasphaera, Lactobacillus, Kingella, Gemella, Staphylococcus, and Propionibacterium were identified in patients with oral cancer, with more than half being Gram-positive facultative anaerobes or anaerobes. The reduced bacterial diversity in saliva of patients with oral cancer suggests dysbiosis during oral carcinogenesis may contribute to changes in bacterial distribution within the oral cavity.}, } @article {pmid40036345, year = {2024}, author = {Hemeda, AA and Zahran, SA and Ali-Tammam, M and Ewida, MA and Kashef, MT and Yassin, AS and Mitra, A and Youssef, NH and Elshahed, MS}, title = {Metagenomic mining unveils a novel GH130 enzyme with exclusive xylanase activity over a wide temperature and pH ranges.}, journal = {Journal of industrial microbiology & biotechnology}, volume = {52}, number = {}, pages = {}, pmid = {40036345}, issn = {1476-5535}, support = {//United States Agency for International Development/ ; P20GM152333//US National Institutes of Health/ ; P20GM134973/GF/NIH HHS/United States ; }, mesh = {Animals ; Hydrogen-Ion Concentration ; *Temperature ; *Metagenomics ; *Enzyme Stability ; Male ; Horses ; *Metagenome ; Molecular Dynamics Simulation ; Feces/microbiology ; Gastrointestinal Microbiome ; Endo-1,4-beta Xylanases/genetics/metabolism/chemistry ; Molecular Docking Simulation ; Cloning, Molecular ; }, abstract = {UNLABELLED: The equine gut harbors a diverse microbial community and represents a rich source of carbohydrate-active enzymes (CAZymes). To identify and characterize potentially novel CAZymes from a horse's hindgut metagenome, shotgun metagenomic sequencing was performed on DNA extracted from a stool sample of a male horse, followed by CAZyme annotation. Here, we report on the characterization of a novel enzyme (AH2) that was identified, synthesized, cloned, and characterized from the obtained CAZyme dataset. AH2 was identified as a GH130 family member and displayed exclusive xylanase activity, a trait hitherto unreported in prior characterization of GH130 CAZymes. AH2 displayed an optimal activity at a pH of 5.6 and a temperature of 50°C. AH2 maintained significant activity across a pH range of 4-10 (62-72%) and temperatures of 30-70°C (77-86%). The enzyme had remarkable stability, with minimal reductions in activity across a temperature range of 4-70°C and pH levels of 3, 7, and 9. Docking studies identified AH2's amino acids (Glu90 and Glu149) to be involved in substrate binding. Molecular dynamics simulation confirmed the structural stability of AH2 at pH 5.6 and 50°C, further supporting its resilience under these conditions. Our results expand on the known activities associated with the GH130 CAZyme family and demonstrate that the horse gut metagenome represents an unexplored source of novel CAZymes.

ONE-SENTENCE SUMMARY: A novel activity for members of the CAZyme family GH130.}, } @article {pmid40023235, year = {2025}, author = {Fang, J and Yin, B and Wang, X and Pan, K and Wang, WX}, title = {Clamworm bioturbation reduces mercury methylation through alteration of methylator composition in sediment.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {371}, number = {}, pages = {125947}, doi = {10.1016/j.envpol.2025.125947}, pmid = {40023235}, issn = {1873-6424}, mesh = {Animals ; *Geologic Sediments/chemistry ; *Mercury/metabolism ; *Methylmercury Compounds/metabolism ; Methylation ; *Water Pollutants, Chemical/metabolism ; Polychaeta/metabolism ; Microbiota ; Ecosystem ; Environmental Monitoring ; }, abstract = {Coastal sediment has been recognized as a hotspot of mercury (Hg) methylation and acts as an important reservoir for Hg-methylating microbes. The bioturbation behaviors of benthic organisms can significantly influence sediment properties and potentially affect the mobility and availability of contaminants within the sediment. However, the effects of bioturbation on Hg speciation and disposition in sediment have not been well addressed. This study investigated the influence of clamworm activities on the Hg-methylation process and the composition of methylators in sediment. The results showed that the presence of clamworms greatly suppressed the growth of Hg-methylators and led to a significant decrease in the production rate of methylmercury (MeHg) (from 0.61 to 0.36 ng g[-1] dw d[-1]). Metagenomic results indicate that bioturbation significantly decreased the abundance and diversity of putative Hg methylators and altered the dominant contributors to Hg methylation process. Furthermore, clamworm activities influenced the metabolic traits of Hg methylators and shifted the community toward greater oxygen tolerance. Overall, bioturbation by clamworms suppressed the Hg methylation process and increased the abundance of eco-friendly microbiome, which ultimately contributed to making the sedimentary ecosystem more diverse and resilient. These findings highlight the vital role of bioturbation in mitigating MeHg contamination in sediment and provide a deeper understanding of Hg-methylating microbes and the Hg cycling processes in coastal environments.}, } @article {pmid40020898, year = {2025}, author = {Chen, F and Chen, J and Chen, Y and He, Y and Li, H and Li, J and Tian, YS}, title = {Mechanistic insight into degradation of dibutyl phthalate by microorganism in sediment-water environment: Metabolic pathway, community succession, keystone phylotypes and functional genes.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {371}, number = {}, pages = {125932}, doi = {10.1016/j.envpol.2025.125932}, pmid = {40020898}, issn = {1873-6424}, mesh = {*Dibutyl Phthalate/metabolism ; *Water Pollutants, Chemical/metabolism ; *Geologic Sediments/microbiology ; *Biodegradation, Environmental ; *Metabolic Networks and Pathways ; Bacteria/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Microbiota ; }, abstract = {Despite extensive studies on dibutyl phthalate (DBP) degradation in isolated bacterial cultures, the primary degraders, community dynamics, and metabolic pathways involved in its biotransformation within complex sediment microbial communities remain poorly understood. In this study, we aimed to investigate the biotransformation mechanism of DBP by microorganisms in a sediment-water system by employing gas chromatography-mass spectrometry, 16S rRNA gene sequencing, metagenomic analysis, and bacterial isolation techniques. We observed that DBP biotransformation has three distinct phases: lag, degradative, and stationary. During the degradative phase, DBP gets progressively degraded by microorganisms, resulting in a microbial community with reduced stability and ambiguous boundaries. DBP, primarily metabolised by key phylotypes into monobutyl phthalate (MBP), phthalic acid (PA), and protocatechuic acid, subsequently enters the tricarboxylic acid (TCA) cycle. Through metagenomic analysis, ten functional genes from five genera were identified as crucial for DBP metabolism. Firstly, Arthrobacter degrades DBP into MBP and PA using pheA. Subsequently, Acinetobacter, Massilia, and Arthrobacter convert PA into TCA cycle intermediates using phtBAaAbAcAd and pcaCH. Concurrently, Hydrogenophaga and Acidovorax degrade PA to TCA cycle intermediates through pht1234 and ligAB. Genes related to amino acid synthesis, ABC transporters, and two-component regulatory systems also contribute significantly. Thus, the listed key bacteria, along with their diverse functional genes, collectively exhibit a high capacity for DBP degradation. This study provides insights into the bacterial responses to DBP degradation and offers a theoretical basis for the prevention and control of this pollutant.}, } @article {pmid39983954, year = {2025}, author = {Guo, J and Guan, A and Chen, M and Chen, Y and Qi, W and Cao, X and Peng, J and Liu, H and Qu, J and Jia, Z and Hu, H}, title = {Spatial distribution of potential nitrogen reduction rates and associated microbial communities revealed by metagenomic analysis in Yangtze River sediments.}, journal = {Environmental research}, volume = {272}, number = {}, pages = {121170}, doi = {10.1016/j.envres.2025.121170}, pmid = {39983954}, issn = {1096-0953}, mesh = {*Geologic Sediments/microbiology/chemistry ; *Rivers/microbiology/chemistry ; *Nitrogen/metabolism/analysis ; China ; Microbiota ; Metagenomics ; Denitrification ; Bacteria/genetics/metabolism/classification ; Oxidation-Reduction ; }, abstract = {Understanding the intricacies of nitrogen reduction processes and the composition of associated microbial communities is crucial for illuminating the reactions of ecosystems and their functions to persistent nitrogen inputs. To enhance research on the nitrogen reduction process, we determined the potential rates, quantified the relevant genes, and analyzed the macro factors in the sediments of the Yangtze River. The results showed that dissimilatory reduction of nitrate to ammonium (DNRA) dominated the N-reduction processes in the Yangtze River sediment, with average rates of 0.89 ± 0.71 nmol N g[-1] h[-1]. Meanwhile, denitrification and anammox rates were 0.73 ± 0.74 and 0.07 ± 0.07 nmol N g[-1] h[-1], respectively. The Three Gorges Dam (TGD) caused higher potential rates (nmol N g[-1] h[-1]) of denitrification (1.38), anammox (0.12), DNRA (1.48), and N2O depletion (1.49 nmol g[-1] h[-1]) in the Three Gorges Reservoir (TGR) compared to other river reaches. The average copy numbers (copies·g[-1]) of nrfA (2.96 × 10[6]), narG (8.17 × 10[5]), nirS (6.10 × 10[6]), nosZ (2.77 × 10[6]), and hzsB (3.68 × 10[5]) in TGR sediments were higher than those in the other reaches. The TGD's interception of fine sediments and nutrients enhanced microbial gene abundance, thereby favoring N-reduction processes and resulting in N2O depletion in reservoir sediments. Moreover, the TGD caused a decreased contribution gap between DNRA and denitrification in the TGR (2%) compared with the upper (35%) and lower (18%) reaches, while causing predominant anammox (50%) in the middle reach. Metagenomic results suggested that sediment particle size, along with organic carbon and inorganic nitrogen concentrations, influenced N reduction rates by affecting narG, norB and C, nrfA and H, and hzsB and C. This study reveals the spatial pattern of the N-reduction rate in the Yangtze River sediments and quantitatively defines the intensity of dam effects on sediment N-reduction rate.}, } @article {pmid39978531, year = {2025}, author = {Perrotta, BG and Kidd, KA and Marcarelli, AM and Paterson, G and Walters, DM}, title = {Effects of chronic metal exposure and metamorphosis on the microbiomes of larval and adult insects and riparian spiders through the aquatic-riparian food web.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {371}, number = {}, pages = {125867}, doi = {10.1016/j.envpol.2025.125867}, pmid = {39978531}, issn = {1873-6424}, mesh = {Animals ; *Microbiota/drug effects ; *Insecta ; *Metamorphosis, Biological/drug effects ; *Food Chain ; *Larva/growth & development/microbiology ; *Water Pollutants, Chemical/toxicity ; *Spiders/microbiology/drug effects/physiology ; Michigan ; Metals/toxicity ; Copper/toxicity ; Mining ; Lakes/microbiology ; Ecosystem ; }, abstract = {The macroinvertebrate microbiome controls various aspects of the host's physiology, from regulation of environmental contaminants to reproductive output. Aquatic insects provide critical nutritional subsidies linking aquatic and riparian food webs while simultaneously serving as a contaminant pathway for riparian insectivores in polluted ecosystems. Previous studies have characterized the transport and transfer of contaminants from aquatic to riparian ecosystems through insect metamorphosis, but both contaminant exposure and metamorphosis are energetically intensive processes that may cause host microbiomes to undergo radical transformation in structure and function, potentially affecting the host's physiology. We collected arthropods from three sites within Torch Lake, a historical copper mine in the Keweenaw Peninsula, Michigan, USA, and three sites within a nearby reference lake. Our objectives were to: 1) characterize the variation in microbiome communities and predicted metagenomic functions with legacy copper mining activity across space, among host types and family-level host taxonomy, 2) characterize how insect metamorphosis alters the microbiome community, including the degree of endosymbiotic infection, and predicted metagenomic function. We field-collected organisms, extracted their DNA, and sequenced the 16S region of the rRNA gene to characterize microbiome communities, then predicted metagenomic function. Site, lake, and host taxonomy affected the host microbiome community composition. Copper exposure increased the abundance of xenobiotic and lipid metabolism pathways in the Araneidae spider microbiome. Insect metamorphosis reduced the alpha diversity, altered the community composition, and predicted metagenomic function. We observed a bioconcentration of endosymbiotic bacteria in adult insects, especially holometabolous insects. Through metamorphosis, we observed a transition in function from xenobiotic degradation pathways to carbohydrate metabolism. Overall, contaminant exposure alters the microbiome composition in aquatic insects and riparian spiders and alters the function of the microbiome across the aquatic-riparian interface. Furthermore, metamorphosis is a critical element in shaping the aquatic insect microbiome across its life history.}, } @article {pmid39954816, year = {2025}, author = {Ladyhina, V and Rajala, E and Sternberg-Lewerin, S and Nasirzadeh, L and Bongcam-Rudloff, E and Dicksved, J}, title = {Methodological aspects of investigating the resistome in pig farm environments.}, journal = {Journal of microbiological methods}, volume = {230-231}, number = {}, pages = {107103}, doi = {10.1016/j.mimet.2025.107103}, pmid = {39954816}, issn = {1872-8359}, mesh = {Animals ; *Farms ; Swine ; *Metagenomics/methods ; *Bacteria/genetics/drug effects/isolation & purification/classification ; *Drug Resistance, Bacterial/genetics ; *Computational Biology/methods ; Anti-Bacterial Agents/pharmacology ; Metagenome ; Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {A typical One Health issue, antimicrobial resistance (AMR) development and its spread among people, animals, and the environment attracts significant research attention. The animal sector is one of the major contributors to the development and dissemination of AMR and accounts for more than 50 % of global antibiotics usage. The use of antibiotics exerts a selective pressure for resistant bacteria in the exposed microbiome, but many questions about the epidemiology of AMR in farm environments remain unanswered. This is connected to several methodological challenges and limitations, such as inconsistent sampling methods, complexity of farm environment samples and the lack of standardized protocols for sample collection, processing and bioinformatical analysis. In this project, we combined metagenomics and bioinformatics to optimise the methodology for reproducible research on the resistome in complex samples from the indoor farm environment. The work included optimizing sample collection, transportation, and storage, as well as DNA extraction, sequencing, and bioinformatic analysis, such as metagenome assembly and antibiotic resistance gene (ARG) detection. Our studies suggest that the current most optimal and cost-effective pipeline for ARG search should be based on Illumina sequencing of sock sample material at high depth (at least 25 M 250 bp PE for AMR gene families and 43 M for gene variants). We present a computational analysis utilizing MEGAHIT assembly to balance the identification of bacteria carrying ARGs with the potential loss of diversity and abundance of resistance genes. Our findings indicate that searching against multiple ARG databases is essential for detecting the highest diversity of ARGs.}, } @article {pmid39938727, year = {2025}, author = {Braga, CM and da Silva, SP and Neto, JPN and Medeiros, DBA and Cruz, ACR and Nascimento, BLSD and Pinheiro, LRS and Martins, LC}, title = {Viral metagenomics of hematophagous insects collected in the Carajas mining complex, Pará State, Brazil.}, journal = {Acta tropica}, volume = {263}, number = {}, pages = {107551}, doi = {10.1016/j.actatropica.2025.107551}, pmid = {39938727}, issn = {1873-6254}, mesh = {Animals ; Brazil ; *Metagenomics ; *Psychodidae/virology/classification ; *Phylogeny ; *Culicidae/virology/classification ; Ceratopogonidae/virology/classification ; Insect Vectors/virology/classification ; Virome/genetics ; High-Throughput Nucleotide Sequencing ; Viruses/classification/isolation & purification/genetics ; Insect Viruses/genetics/classification/isolation & purification ; }, abstract = {Hematophagous insects are vectors of viruses that cause diseases in humans and animals worldwide. Mosquitoes (Culicidae), biting midges (Ceratopogonidae), and sandflies (Psychodidae) were collected in three municipalities (Marabá, Canaã dos Carajás, and Curionópolis) in the state of Pará, Brazil, in 2019. Morphological keys were used for the taxonomic identification of insect species. High-throughput sequencing and metagenomic analysis were employed to characterize the viromes of the hematophagous insects. We characterized the virome of 839 insects grouped into 14 pools. A total of 729 million paired reads were generated, with 12 million viral sequences (3 % of the reads). The families Reoviridae, Myoviridae, Retroviridae, and Poxviridae were found in all samples of this study. Phylogenies of RNA-dependent RNA polymerase (RdRp) from viruses of the families Chuviridae, Dicistroviridae, Flaviviridae, Iflaviridae, Mesoniviridae, Phenuiviridae, and Rhabdoviridae were performed. In this study, the first isolation of the Guaico Culex Virus (GCXV) in the northern region of Brazil was obtained from a pool of Culex (Melanoconion) spp. mosquitoes collected in Curionópolis. The data obtained in this study demonstrate that the Carajás region has an ecosystem rich in viruses. Additional studies are needed to understand the dynamics of viruses in vectors, vertebrates, and the human population in the region.}, } @article {pmid39893935, year = {2025}, author = {Luo, Y and Gao, J and Su, X and Li, H and Li, Y and Qi, W and Han, X and Han, J and Zhao, Y and Zhang, A and Zheng, Y and Qian, F and He, H}, title = {Unraveling the immunological landscape and gut microbiome in sepsis: a comprehensive approach to diagnosis and prognosis.}, journal = {EBioMedicine}, volume = {113}, number = {}, pages = {105586}, pmid = {39893935}, issn = {2352-3964}, mesh = {Humans ; *Sepsis/diagnosis/immunology/microbiology ; Prognosis ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome/immunology ; Aged ; *Biomarkers ; *Immunophenotyping ; Killer Cells, Natural/immunology/metabolism ; ROC Curve ; Case-Control Studies ; Adult ; }, abstract = {BACKGROUND: Comprehensive and in-depth research on the immunophenotype of septic patients remains limited, and effective biomarkers for the diagnosis and treatment of sepsis are urgently needed in clinical practice.

METHODS: Blood samples from 31 septic patients in the Intensive Care Unit (ICU), 25 non-septic ICU patients, and 18 healthy controls were analyzed using flow cytometry for deep immunophenotyping. Metagenomic sequencing was performed in 41 fecal samples, including 13 septic patients, 10 non-septic ICU patients, and 18 healthy controls. Immunophenotype shifts were evaluated using differential expression sliding window analysis, and random forest models were developed for sepsis diagnosis or prognosis prediction.

FINDINGS: Septic patients exhibited decreased proportions of natural killer (NK) cells and plasmacytoid dendritic cells (pDCs) in CD45[+] leukocytes compared with non-septic ICU patients and healthy controls. These changes statistically mediated the association of Bacteroides salyersiae with sepsis, suggesting a potential underlying mechanism. A combined diagnostic model incorporating B.salyersia, NK cells in CD45[+] leukocytes, and C-reactive protein (CRP) demonstrated high accuracy in distinguishing sepsis from non-sepsis (area under the receiver operating characteristic curve, AUC = 0.950, 95% CI: 0.811-1.000). Immunophenotyping and disease severity analysis identified an Acute Physiology and Chronic Health Evaluation (APACHE) II score threshold of 21, effectively distinguishing mild (n = 19) from severe (n = 12) sepsis. A prognostic model based on the proportion of total lymphocytes, Helper T (Th) 17 cells, CD4[+] effector memory T (TEM) cells, and Th1 cells in CD45[+] leukocytes achieved robust outcome prediction (AUC = 0.906, 95% CI: 0.732-1.000), with further accuracy improvement when combined with clinical scores (AUC = 0.938, 95% CI: 0.796-1.000).

INTERPRETATION: NK cell subsets within innate immunity exhibit significant diagnostic value for sepsis, particularly when combined with B. salyersiae and CRP. In addition, T cell phenotypes within adaptive immunity are correlated with sepsis severity and may serve as reliable prognostic markers.

FUNDING: This project was supported by the National Key R&D Program of China (2023YFC2307600, 2021YFA1301000), Shanghai Municipal Science and Technology Major Project (2023SHZDZX02, 2017SHZDZX01), Shanghai Municipal Technology Standards Project (23DZ2202600).}, } @article {pmid39628107, year = {2025}, author = {Zou, Y and Zou, X and Lin, C and Han, C and Zou, Q}, title = {Inference of functional differentiation of intestinal microbes between two wild zokor species based on metagenomics.}, journal = {Pest management science}, volume = {81}, number = {4}, pages = {1860-1872}, doi = {10.1002/ps.8587}, pmid = {39628107}, issn = {1526-4998}, support = {//National Promoted Program of scientific and technological achievements in Forestry and Grassland/ ; //the National Key Program of Research and Development/ ; }, mesh = {*Gastrointestinal Microbiome ; *Metagenomics ; Animals ; Bacteria/genetics/metabolism/classification ; Cellulose/metabolism ; Species Specificity ; }, abstract = {BACKGROUND: Currently, there are fewer studies on the intestinal microbes of wild zokors, and it is unclear how zokors adapt to special underground environments by regulating their intestinal microbes. Here, we explored the function of intestinal microbes of Eospalax cansus and Eospalax rothschildi based on metagenomics.

RESULTS: Both zokor species have similar intestinal microbial composition, but E. cansus has a higher proportion of bacteria involved in carbohydrate degradation. Functional analysis based on KEGG and CAZy databases indicated that the intestinal microbes of E. cansus harboured stronger carbohydrate degradation ability, mainly in starch and sucrose metabolism, and further in cellulose degradation. Furthermore, the cellulase activity was significantly higher in E. cansus than that in E. rothschildi. Eospalax cansus has a stronger microbial fermentation ability due to an increase in fibre-degrading bacteria like unclassified_f_Lachnospiraceae, Ruminococcus, and Clostridium. In addition, the dominant bacteria isolated from zokor were Bacillus, some of which could degrade both cellulose and hemicellulose.

CONCLUSION: Metagenomic analysis and bacterial isolation experiments indicate that E. cansus has a stronger microbial cellulose-degrading capacity, possibly as an adaptation to its limited food resources underground. © 2024 Society of Chemical Industry.}, } @article {pmid40076673, year = {2025}, author = {Velazquez-Meza, ME and Galarde-López, M and Cornejo-Juárez, P and Bobadilla-Del-Valle, M and Godoy-Lozano, E and Aguilar-Vera, E and Carrillo-Quiroz, BA and Ponce de León-Garduño, A and Velazquez Acosta, C and Alpuche-Aranda, CM}, title = {Bacterial Communities and Resistance and Virulence Genes in Hospital and Community Wastewater: Metagenomic Analysis.}, journal = {International journal of molecular sciences}, volume = {26}, number = {5}, pages = {}, doi = {10.3390/ijms26052051}, pmid = {40076673}, issn = {1422-0067}, support = {682339//CONAHCYT, México/ ; }, mesh = {*Wastewater/microbiology ; *Metagenomics/methods ; *Virulence Factors/genetics ; *Drug Resistance, Bacterial/genetics ; Hospitals ; Bacteria/genetics/pathogenicity ; Metagenome ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Virulence/genetics ; Genes, Bacterial ; Humans ; Microbiota/genetics ; }, abstract = {Metagenomic studies have made it possible to deepen the analysis of the abundance of bacterial populations that carry resistance and virulence determinants in the wastewater environment. In this study, a longitudinal collection of samples of community and hospital wastewater from August 2021 to September 2022 was obtained. Shotgun metagenomic sequencing and bioinformatic analysis were performed to characterize the bacterial abundance, antimicrobial resistance genes (ARGs), plasmids, and virulence factor genes (VFGs) contained in the wastewater. The microbial composition of the community and hospital wastewater showed that the most abundant bacterial phyla detected in all samples were: Proteobacteria, Bacteroides, Firmicutes, Campylobacterota, and Actinobacteria. Seasonal differences in the relative abundances of species, ARGs, plasmids, and VFGs were observed. In this study, a total of 270 ARGs were detected, and it was found that the absolute abundance of ARGs only showed a 39% reduction in the treated wastewater. Furthermore, the ARGs detected in this study were found to encode resistance to antibiotics of the last choice. Our results showed that plasmids carrying resistance genes were more abundant in raw wastewater, and 60% more abundant in hospital wastewater compared to community wastewater. Several of the VFGs detected in this study encode for adhesion, motility, and biofilm formation, which likely allows bacteria to remain and persist in the wastewater environment and survive WWTP treatment systems, thus managing to escape into the environment via treated wastewater.}, } @article {pmid40076252, year = {2025}, author = {Gao, Y and Xu, Y and Dong, Z and Guo, Y and Luo, J and Wang, F and Yan, L and Zou, X}, title = {Endophytic Fungal Diversity and Its Interaction Mechanism with Medicinal Plants.}, journal = {Molecules (Basel, Switzerland)}, volume = {30}, number = {5}, pages = {}, doi = {10.3390/molecules30051028}, pmid = {40076252}, issn = {1420-3049}, support = {BS0050//Heilongjiang Province Postdoctoral Research Fund/ ; LH2022H001//Heilongjiang Natural Science Foundation Joint Guidance Project/ ; ZYW2023-073//Heilongjiang Province Traditional Chinese Medicine Research Project/ ; GZ20210110//Key Research and Development Guidance Project of Heilongjiang Province/ ; }, mesh = {*Plants, Medicinal/microbiology/chemistry ; *Endophytes/metabolism ; *Fungi/metabolism ; Biodiversity ; Metabolomics/methods ; Metagenomics/methods ; Proteomics/methods ; }, abstract = {This paper reviewed the diversity of endophytic fungi and their interactions with medicinal plants, along with the research methodologies utilized to investigate these interactions. It mainly includes the diversity of endophytic fungi, as well as distribution diversity, species diversity, and the diversity of their metabolites and functions, including antibacterial, anti-inflammatory, anti-tumor, insecticidal, antioxidant capabilities, and so on. The research methodologies employed to investigate the interactions between endophytic fungi and medicinal plants are categorized into metagenomics, transcriptomics, metatranscriptomics, proteomics, and metabolomics. Furthermore, this study anticipates the potential applications of secondary metabolites derived from endophytic fungi in both medicine and agriculture.}, } @article {pmid40075266, year = {2025}, author = {Cao, H and Xu, J and Wang, H and Yi, W and Yang, D and Yang, J and Sun, J and Wang, Y and Zhang, F and Yan, J and Li, D}, title = {Fecal microbiota transplantation mitigates postdieting weight regain in mice by modulating the gut-liver axis.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {135}, pmid = {40075266}, issn = {1471-2180}, support = {2023YFF1104305//National Key Research and Development Program of China/ ; 2022YFF1100601//National Key Research and Development Program of China/ ; K2023004//Key Research project of Health Commission of Jiangsu Province/ ; M2021055//Key Research project of Health Commission of Jiangsu Province/ ; Y2021001//Wuxi Science and Technology Bureau, "Taihu Light" Science and Technology Research program/ ; K20221026//Wuxi Science and Technology Bureau, "Taihu Light" Science and Technology Research program/ ; CXTD2021003//Key discipline construction program of Wuxi Commission of Health/ ; KX-23-B050//Soft Science Project of Wuxi Science and Technology Association/ ; KX-23-C196//Soft Science Project of Wuxi Science and Technology Association/ ; YJZ202305//Medical research projects in research-oriented hospitals of Affiliated Hospital of Jiangnan University/ ; HB2023062//"Shuangbai Talents" research program of Wuxi Commission of Health/ ; HB2023063//"Shuangbai Talents" research program of Wuxi Commission of Health/ ; HB2023061//"Shuangbai Talents" research program of Wuxi Commission of Health/ ; LCYJ202347//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; LCYJ202310//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; LCYJ202322//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; LCYJ202303//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; BK20210468//Natural Science Foundation of Jiangsu Province/ ; BK20210060//Natural Science Foundation of Jiangsu Province/ ; 82370809//National Natural Science Foundation of China/ ; 32101033//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Mice ; *Weight Gain ; *Liver/metabolism ; Male ; Bacteria/classification/isolation & purification/genetics/metabolism ; Mice, Inbred C57BL ; Feces/microbiology ; Dysbiosis/therapy/microbiology ; Fatty Acids, Volatile/metabolism ; Lipid Metabolism ; }, abstract = {BACKGROUND: Dysbiosis of the microbiome is strongly associated with weight rebound after dieting. However, the interactions between the host and microbiome and their relevance to the pathogenesis of post-diet weight rebound remain unclear.

PURPOSE: This study aimed to evaluate the effects of fecal microbiota transplantation (FMT) on post-diet weight regain and to investigate the underlying mechanisms by which FMT inhibits weight regain.

METHODS: FMT was administered once daily to mice for 5 weeks. Gas chromatography tandem mass spectrometry was employed to analyze short-chain fatty acid levels in serum, ultrahigh-performance liquid chromatography tandem mass spectrometry was utilized for analyzing hepatic lipid metabolites, and shotgun metagenomic sequencing was applied to examine the intestinal microbiome.

RESULTS: FMT reduced weight regain and prevented lipid accumulation in both liver and adipose tissue while also improving glucose intolerance in mice. Furthermore, FMT increased the abundance of Enterorhabdus caecimuris and decreased the abundances of Burkholderiales, Sutterellaceae, Turicimonas muris, Bacteroides stercorirosoris, and Acetivibrio ethanolgignens within the gut microbiota. Additionally, elevated propionic acid levels and significant alterations in hepatic lipid metabolites were observed following FMT administration.

CONCLUSIONS: Our findings demonstrate that FMT effectively mitigates post-diet weight regain and associated complications. These effects are mediated through interactions between the gut microbiota and the liver via the gut-propionic acid-liver axis.

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid40075219, year = {2025}, author = {Sun, Y and Huang, S and Li, M and Yang, Y and Ma, J and Xie, R and Wang, J and Zhao, Q and Qin, S and He, L and Jiang, J and Zhao, Q and Jin, G and Liu, X and Huang, H and Yang, Y and Wei, J and Liu, W and Wang, B and Yang, R and Su, X and Cao, H}, title = {Maternal high-fat diet disrupts intestinal mucus barrier of offspring by regulating gut immune receptor LRRC19.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {420}, pmid = {40075219}, issn = {2399-3642}, support = {82270574//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82070545//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82400632//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81970488//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Female ; Mice ; *Intestinal Mucosa/metabolism/immunology/microbiology ; Mice, Inbred C57BL ; Pregnancy ; Mice, Knockout ; Male ; Interleukin-22 ; Receptors, Immunologic/metabolism/genetics ; }, abstract = {Maternal high fat diet (MHFD) increased colitis susceptibility in adulthood. However, the mechanism remains unclear. We sought to explore whether novel gut immune receptor leucine-rich repeat C19 (LRRC19) contributed to the impaired mucus barrier of offspring exposed to MHFD via gut immune response and microbiota. The results showed that MHFD significantly impaired the intestinal mucus barrier of offspring, and up-regulated the expression of LRRC19. Lrrc19 deletion alleviated the mucus barrier disruption. Mechanistically, metagenome sequencing revealed that the MHFD-induced gut microbiota alteration was partly restored in Lrrc19[-/-] offspring. Muc2-associated bacteria were decreased in the MHFD group, such as Akkermansia_muciniphila_CAG_154, which increased in the Lrrc19-deficient offspring. Moreover, Lrrc19[-/-] offspring had a higher rate of indole-3-acetic acid (IAA)-producing bacterium, such as Lactobacillus reuteri. A targeted metabolomics analysis revealed that IAA emerged as the top candidate that might mediate the protective effects. IAA was found to improve the mucus barrier function by increasing the ratio of interleukin-22 (IL-22)[+] ILC3 cells in an aryl hydrocarbon receptor (AhR)-dependent manner. These results suggest that MHFD disrupts the intestinal mucus barrier of offspring through regulating gut immune receptor LRRC19 and inducing an imbalance of gut microbiota and microbiota-derived metabolites.}, } @article {pmid40072675, year = {2025}, author = {Verma, N and Chavan, N and Aulakh, KS and Sharma, A and Shouche, Y and Ramana, VV}, title = {Temporal Dynamics of Microbial Community Composition and Antimicrobial Resistance in a Mass Gathering Setting Using Culturomics and Metagenomic Approaches.}, journal = {Journal of epidemiology and global health}, volume = {15}, number = {1}, pages = {41}, pmid = {40072675}, issn = {2210-6014}, support = {OLP-805//CSIR - Institute of Microbial Technology/ ; GAP-233//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {Humans ; India/epidemiology ; *Metagenomics/methods ; Microbiota/drug effects ; Bacteria/drug effects/genetics/isolation & purification/classification ; Water Microbiology ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {INTRODUCTION: Antimicrobial resistance (AMR) is one of the major global concerns in the current scenario. Mass-gathering events in fast-developing and densely populated areas may contribute to antibiotic resistance. Despite meticulous planning and infrastructure development, the effect of mass gatherings on microbial ecosystems and antibiotic resistance must be investigated. This study used culture and metagenome-based methods to investigate and compare the bacterial diversity, AMR profile & mechanism of resistance for bacteria in water samples collected from the mass gathering event (2019 Prayagraj Kumbh Mela in Uttar Pradesh, India) with the control samples, collected during no mass gathering.

METHODS: This study analyzed the water samples collected from a mass gathering event held in February 2019. Water samples collected in this study were grouped into "Test" (mass gathering event) and "Control" (no mass gathering event) groups. This study involved methods including culturomics, antibiotyping, phenotypic & genotypic identification methods, and metagenomics.

RESULTS: There is a significant variation observed in the evenness and richness of bacterial diversity and MDR profile, expressed in terms of the relative abundance of the bacterial species between test and control samples. Out of the total multi-drug resistant (MDR) strains identified in the Prayagraj sample, the majority were derived from the test sample. A pathway-based analysis of MDR strains revealed the highest levels of acquired resistance were related to the inhibition of cell wall synthesis primarily in Pseudomonas spp., followed by resistance to protein synthesis and nucleic acid synthesis pathways. Additionally, the overall resistance profile of the test sample demonstrated a significantly elevated resistome for beta-lactams, particularly in the Pseudomonas spp. Additionally, several ESBL (Extended-spectrum beta-lactamase)-associated gene variants were identified. The test sample showed a two-fold increase in the prevalence and diversity of common beta-lactam gene variants in addition to the presence of unique variants. Using the metagenomics approach, we investigated the mechanism of antibiotic resistance, and it revealed a dominant trend in antibiotic efflux and inactivation pathways within both the test and control samples. Overall, the bacterial diversity, abundance (including AMR strains of human origin), and ARGs were relatively higher in the Test sample compared to the control sample which was collected 3 months after the mass gathering event.

CONCLUSION: Our study found significant variations in microbial communities, MDR strains, and ARGs due to environmental and human influences. Pseudomonas spp. was the most abundant MDR strain, primarily resistant to cell wall synthesis inhibitors. The test sample showed an increased resistome for beta-lactams, while the control sample had reduced bacterial species, ARGs, and MDR strains linked to human microflora. This shift could be due to the re-establishment of native bacterial communities in the Ganges River which may be attributed to its bacteriophage activity, biomolecules, and inherent antimicrobial properties. The study highlights the need for surveillance, monitoring AMR emergence to develop new strategies to combat it.}, } @article {pmid40072088, year = {2025}, author = {Świdnicka-Siergiejko, A and Daniluk, J and Miniewska, K and Daniluk, U and Guzińska-Ustymowicz, K and Pryczynicz, A and Dąbrowska, M and Rusak, M and Ciborowski, M and Dąbrowski, A}, title = {Inflammatory Stimuli and Fecal Microbiota Transplantation Accelerate Pancreatic Carcinogenesis in Transgenic Mice, Accompanied by Changes in the Microbiota Composition.}, journal = {Cells}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/cells14050361}, pmid = {40072088}, issn = {2073-4409}, support = {No NCN 2017/27/B/NZ5/02904//National Science Center/ ; }, mesh = {Animals ; *Fecal Microbiota Transplantation ; *Mice, Transgenic ; *Pancreatic Neoplasms/microbiology/genetics/pathology ; Mice ; *Inflammation/pathology/microbiology ; *Gastrointestinal Microbiome/genetics ; *Carcinoma, Pancreatic Ductal/microbiology/genetics/pathology ; Carcinogenesis/genetics/pathology ; Feces/microbiology ; Proto-Oncogene Proteins p21(ras)/genetics ; Pancreas/pathology ; }, abstract = {An association between gut microbiota and the development of pancreatic ductal adenocarcinoma (PDAC) has been previously described. To better understand the bacterial microbiota changes accompanying PDAC promotion and progression stimulated by inflammation and fecal microbiota transplantation (FMT), we investigated stool and pancreatic microbiota by 16s RNA-based metagenomic analysis in mice with inducible acinar transgenic expressions of KrasG12D, and age- and sex-matched control mice that were exposed to inflammatory stimuli and fecal microbiota obtained from mice with PDAC. Time- and inflammatory-dependent stool and pancreatic bacterial composition alterations and stool alpha microbiota diversity reduction were observed only in mice with a Kras mutation that developed advanced pancreatic changes. Stool Actinobacteriota abundance and pancreatic Actinobacteriota and Bifidobacterium abundances increased. In contrast, stool abundance of Firmicutes, Verrucomicrobiota, Spirochaetota, Desulfobacterota, Butyricicoccus, Roseburia, Lachnospiraceae A2, Lachnospiraceae unclassified, and Oscillospiraceae unclassified decreased, and pancreatic detection of Alloprevotella and Oscillospiraceae uncultured was not observed. Furthermore, FMT accelerated tumorigenesis, gradually decreased the stool alpha diversity, and changed the pancreatic and stool microbial composition in mice with a Kras mutation. Specifically, the abundance of Actinobacteriota, Bifidobacterium and Faecalibaculum increased, while the abundance of genera such as Lachnospiraceace A2 and ASF356, Desulfovibrionaceace uncultured, and Roseburia has decreased. In conclusion, pancreatic carcinogenesis in the presence of an oncogenic Kras mutation stimulated by chronic inflammation and FMT dynamically changes the stool and pancreas microbiota. In particular, a decrease in stool microbiota diversity and abundance of bacteria known to be involved in short-fatty acids production were observed. PDAC mouse model can be used for further research on microbiota-PDAC interactions and towards more personalized and effective cancer therapies.}, } @article {pmid40072031, year = {2025}, author = {Huang, YJ}, title = {The Microbiome in Asthma Heterogeneity: The Role of Multi-Omic Investigations.}, journal = {Immunological reviews}, volume = {330}, number = {1}, pages = {e70015}, doi = {10.1111/imr.70015}, pmid = {40072031}, issn = {1600-065X}, support = {U01TR004066/TR/NCATS NIH HHS/United States ; 75N92024D00012-0-759202400001-1/HL/NHLBI NIH HHS/United States ; }, mesh = {*Asthma/microbiology/immunology/etiology ; Humans ; *Microbiota/immunology ; Animals ; Biomarkers ; Genomics/methods ; Proteomics ; Metabolomics/methods ; Disease Susceptibility ; Metagenomics/methods ; Multiomics ; }, abstract = {Asthma is one of the most prevalent and extensively studied chronic respiratory conditions, yet the heterogeneity of asthma remains biologically puzzling. Established factors like exogenous exposures and treatment adherence contribute to variability in asthma risk and clinical outcomes. It is also clear that the endogenous factors of genetics and immune system response patterns play key roles in asthma. Despite significant existing knowledge in the above, divergent clinical trajectories and outcomes are still observed, even among individuals with similar risk profiles, biomarkers, and optimal medical management. This suggests uncaptured biological interactions that contribute to asthma's heterogeneity, for which the role of host microbiota has lately attracted much research attention. This review will highlight recent evidence in this area, focusing on bedside-to-bench investigations that have leveraged omic technologies to uncover microbiome links to asthma outcomes and immunobiology. Studies centered on the respiratory system and the use of multi-omics are noted in particular. These represent a new generation of reverse-translational investigations revealing potential functional crosstalk in host microbiomes that may drive phenotypic heterogeneity in chronic diseases like asthma. Multi-omic data offer a wide lens into ecosystem interactions within a host. This informs new hypotheses and experimental work to elucidate mechanistic pathways for unresolved asthma endotypes. Further incorporation of multi-omics into patient-centered investigations can yield new insights that hopefully lead to even more precise, microbiome-informed strategies to reduce asthma burden.}, } @article {pmid40069605, year = {2025}, author = {Zhang, H and Wang, Y and Luo, Z and Zhang, B and Lan, X and Xu, L and Li, X and Huang, Z and Bai, J and Hu, D}, title = {Gut microbiome reveals the trophic variation and significant adaption of three sympatric forest-dwelling ungulates on the eastern Qinghai-Xizang Plateau.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {128}, pmid = {40069605}, issn = {1471-2180}, support = {YC-20018//Zhangzhou Pientzehuang Pharmaceutical Co., Ltd./ ; 2023I0046//Supported by Science and Technology Planning Project of Fujian Province, China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; China ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Phylogeny ; Forests ; Metagenomics ; Sympatry ; Adaptation, Physiological ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Ruminants/microbiology ; }, abstract = {BACKGROUND: The gut microbiome of herbivorous mammals regulates numerous physiological processes, including digestion and energy metabolism. The complex stomach architecture of ruminants, in conjunction with the metabolic capabilities of their microbiota, confers a considerable adaptive advantage to these animals. Nevertheless, a significant gap persists in comparative studies on the variations in the gut microbiome among sympatric ruminants and their potential adaptive implications. Accordingly, in this study, 16S rRNA gene sequencing and metagenomic approaches were used to analyse the composition and functional attributes of the gut microbiome of sympatric Moschus chrysogaster, Capricornis sumatraensis, and Cervus albirostris inhabiting the eastern periphery of the Qinghai-Xizang Plateau.

RESULTS: The gut microbiome of C. albirostris exhibited a higher diversity than that of M. chrysogaster and C. sumatraensis, whereas those of M. chrysogaster and C. sumatraensis were similar. Although species-specific variations existed among the three mammalian microbiomes, the microbiomes of C. albirostris and C. sumatraensis were more similar, whereas that of M. chrysogaster was markedly distinct. Metagenomic analysis revealed a pattern of functional convergence in the gut microbiome of the three species, with the gut microbiome of C. albirostris exhibiting a pronounced emphasis on carbohydrate metabolism, significantly surpassing that of M. chrysogaster and C. sumatraensis. Compared to the other two species, the gut microbiome of C. sumatraensis presented significantly elevated levels of amino acids and energy metabolism, whereas that of M. chrysogaster presented an increased capacity for 3-hydroxyacyl- [acyl carrier protein]-dehydratase production.

CONCLUSION: These findings suggest that the gut microbiome of sympatric M. chrysogaster, C. sumatraensis, and C. albirostris tend to converge. Metabolic variations within their gut microbiome may result in differential food resource utilisation, potentially indicating significant nutritional and ecological trait characteristics for stable coexistence.}, } @article {pmid40069560, year = {2025}, author = {Breselge, S and Skibinska, I and Yin, X and Brennan, L and Kilcawley, K and Cotter, PD}, title = {The core microbiomes and associated metabolic potential of water kefir as revealed by pan multi-omics.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {415}, pmid = {40069560}, issn = {2399-3642}, support = {818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; SFI/12/RC/2273_P2//Science Foundation Ireland (SFI)/ ; USIRL-2019-1//Science Foundation Ireland (SFI)/ ; SFI/16/RC/3835//Department of Agriculture, Food and the Marine (DAFM)/ ; TC/2018/0025//Enterprise Ireland/ ; }, mesh = {*Fermentation ; *Kefir/microbiology ; *Microbiota/genetics ; Metagenomics/methods ; Bacteria/metabolism/genetics/classification ; Metabolomics/methods ; Food Microbiology ; Water/metabolism ; Multiomics ; }, abstract = {Water kefir (WK) is an artisanal fermented beverage made from sugary water, optional fruits and WK grains. WK grains can be reused to start new fermentations. Here we investigate the microbial composition and function of 69 WK grains and their ferments by shotgun metagenomics. A subset of samples was subjected to metabolomic, including volatilomic, analysis. The impact of different fermentation practices on microbial composition and fermentation characteristics was analysed and it was noted that, for example, the common practice of drying water kefir grains significantly reduces microbial diversity and negatively impacts subsequent grain growth. Metagenomic analysis allowed the detection of 96 species within WK, the definition of core genera and the detection of different community states after 48 h of fermentation. A total of 485 bacterial metagenome assembled genomes were obtained and 18 putatively novel species were predicted. Metabolite and volatile analysis show associations between key species with flavour compounds. We show the complex microbial composition of WK and links between fermentation practices, microbes and the fermented product. The results can be used as a foundation for the selection of species for large scale WK production with desired flavour profiles and to guide the regulatory framework for commercial WK production.}, } @article {pmid40068396, year = {2025}, author = {Guo, M and Wu, Y and Huang, H and Li, S and Zhao, L and Cao, J and Wang, C}, title = {Revealing the critical role of rare bacterial communities in shaping antibiotic resistance genes in saline soils through metagenomic analysis.}, journal = {Journal of hazardous materials}, volume = {491}, number = {}, pages = {137848}, doi = {10.1016/j.jhazmat.2025.137848}, pmid = {40068396}, issn = {1873-3336}, abstract = {Salinity is considered one of the basic abiotic factors influencing the diversity and distribution of antibiotic resistance genes (ARGs) in soils, yet little is known about the distribution and driving factors of ARGs in naturally saline soils. In this study, metagenomic analysis was conducted to explore the intricate dynamics among soil salinity, microbial community structure and ARGs propagation, with a particular focus on the key contribution of rare potential-hosts of ARGs in light and heavy saline soils. The findings revealed that salinity was significantly negatively correlated with the abundance of ARGs, light saline soils hosted a greater abundance of ARGs than high saline soils, with particularly significant enrichment in genes conferring resistance to multidrug, vancomycin, bacitracin and tetracenomycin C. Proteobacteria and Actinobacteria were identified as primary hosts for ARGs. Notably, rare potential hosts of ARGs play a crucial role in shaping the abundance of ARGs despite their low relative abundance (0.85 %), significantly influencing the relative abundance of ARGs in light and heavy saline soils. The average degree of rare potential-hosts of ARGs was found to be higher in light saline soils (average degree = 45.729 and 25.923 in light and heavy saline soils, respectively), and there was stronger interaction connected between microorganisms (edges = 35,760 and 20,259 in light and heavy saline soils, respectively). Also, microbial community niche width and niche overlap of rare potential-hosts of ARGs in light saline soils were significantly greater than that in heavy saline soils. This work emphasizes the importance of bacterial communities of rare potential-hosts of ARGs on antibiotic resistome, and provides advanced insights into the fate and dissemination of ARGs in saline soils.}, } @article {pmid40065594, year = {2025}, author = {Sun, Y and Yu, YT and Castillo, XO and Anderson, R and Wang, M and Sun, Q and Tallmadge, R and Sams, K and Reboul, G and Zehr, J and Brown, J and Wang, X and Marra, N and Stanhope, B and Grenier, J and Pusterla, N and Divers, T and Mittel, L and Goodman, LB}, title = {Investigation of the Blood Microbiome in Horses With Fever of Unknown Origin.}, journal = {Veterinary medicine and science}, volume = {11}, number = {2}, pages = {e70272}, doi = {10.1002/vms3.70272}, pmid = {40065594}, issn = {2053-1095}, support = {//Harry M. Zweig Memorial Fund for Equine Research/ ; 1U18FD006993//US Food and Drug Administration's Veterinary Laboratory Investigation and Response Network/ ; 1U18FD006716//US Food and Drug Administration's Veterinary Laboratory Investigation and Response Network/ ; W81XWH-22-1-0891//Department of Defense/ ; }, mesh = {Horses ; Animals ; *Horse Diseases/microbiology/virology/blood/epidemiology ; Case-Control Studies ; *Fever of Unknown Origin/veterinary/microbiology/etiology ; Microbiota ; Male ; Female ; }, abstract = {BACKGROUND: Fever of unknown origin (FUO) without a respiratory component is a frequent clinical presentation in horses. Multiple pathogens, both tick-borne and enteric, can be involved as etiologic agents. An additional potential mechanism is intestinal barrier dysfunction.

OBJECTIVES: This case-control study aimed to detect and associate microbial taxa in blood with disease state.

STUDY DESIGN: Areas known for a high prevalence of tick-borne diseases in humans were chosen to survey horses with FUO, which was defined as fever of 101.5°F or higher with no signs of respiratory illness or other recognisable diseases. Blood samples and clinical parameters were obtained from 52 FUO cases and also from matched controls from the same farms. An additional 23 febrile horses without matched controls were included.

METHODS: Broadly targeted polymerase chain reaction (PCR) amplification directed at conserved sequence regions of bacterial 16S rRNA, parasite 18S rRNA, coronavirus RdRp and parvovirus NS1 was performed, followed by deep sequencing. To control for contamination and identify taxa unique to the cases, metagenomic sequences from the controls were subtracted from those of the cases, and additional targeted molecular testing was performed. Sera were also tested for antibodies to equine coronavirus.

RESULTS: Over 60% of cases had intestinal microbial DNA circulating in the blood. Nineteen percent of cases were attributed to infection with Anaplasma phagocytophilum, of which two were subtyped as human-associated strains. A novel Erythroparvovirus was detected in two cases and two controls. Serum titres for equine coronavirus were elevated in some cases but not statistically different overall between the cases and controls.

MAIN LIMITATIONS: Not all pathogens are expected to circulate in blood, which was the sole focus of this study.

CONCLUSIONS: The presence of commensal gut microbes in blood of equine FUO cases is consistent with a compromised intestinal barrier, which is highlighted as a direction for future study.}, } @article {pmid40064739, year = {2025}, author = {Thakur, SS and González, SS and Suravajhala, P and Jain, SK and Yadav, S and Narayan, KS and Esack, E and Kuzyakov, Y and Ratnasari, A}, title = {Metagenomic insights of microbial functions under conventional and conservation agriculture.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {3}, pages = {100}, pmid = {40064739}, issn = {1573-0972}, support = {Grant ID: 3203/SKMCCC/EPCO/2021//Environmental Planning & Coordination Organisation (EPCO), Ministry of Environment, Government of Madhya Pradesh, India/ ; }, mesh = {*Soil Microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Metagenomics ; *Agriculture ; *Archaea/genetics/classification ; *Soil/chemistry ; Metagenome ; Phylogeny ; Biodiversity ; Carbon/metabolism ; Nitrogen/metabolism ; }, abstract = {Agricultural practices such as conventional (CN) and conservation agriculture (CA) influence the composition and structure of soil microorganisms. We used short reads and genome-resolved metagenomic-based dual sequencing approaches to create a profile of bacterial and archaeal communities in hyperthermic Typic Haplustepts soil after seven years of CA and CN. The most differences in the physico-chemical and biological properties of soil were higher pH, organics carbon, available nitrogen and microbial biomass contents, activities of dehydrogenase, β-glucosidase, and arylsulfatase, found in CA soil. The dominant bacterial taxa under both management types were Pseudomonadota (46-48%), Acidobacteriota (12-13%), Planctomycetota (8-10%), Bacteroidota (7-8%), and Actinomycetota (6-7%). Nitrososphaerota (1.1-1.5%) was the predominant archaeal phyla in CA and CN soils. The alpha diversity was 1.5 times higher in CA compared to CN soils. Fourteen high-quality (HQ) metagenomic-assembled genomes (MAGs) were recovered from both groups. Four HQ metagenome-assembled genomes (MAGs) from the Pseudomonadota phylum were exclusively recovered from the CA soil. The dominance of this phylum in the CA soil might be correlated with its nutrient richness, as certain classes of Pseudomonadota, such as Alpha, Beta-, Gamma-, and Deltaproteobacteria, are known to be copiotrophic. Copiotrophic organisms thrive in nutrient-rich environments, which could explain their prevalence in the CA soil. CAZyme gene analysis showed that Glycoside Hydrolases (GH) and GlycosylTransferases (GT) classes are dominant in the CA group, possibly due to higher substrate availability from the application of crop residues, which provide a rich source of complex carbohydrates. Several biogeochemical gene families related to C1 compounds, hydrogen, oxygen, and sulfur metabolism were enriched in CA soils, suggesting these practices may contribute to a soil environment with increased organic matter content, microbial diversity, and nutrient availability. Overall, CA practices seemed to improve soil health by supporting soil microbial communities abundance.}, } @article {pmid39945545, year = {2025}, author = {Verster, AJ and Salerno, P and Valls, R and Barrack, K and Price, CE and McClure, EA and Madan, JC and O'Toole, GA and Sanville, JL and Ross, BD}, title = {Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis.}, journal = {mBio}, volume = {16}, number = {3}, pages = {e0342024}, doi = {10.1128/mbio.03420-24}, pmid = {39945545}, issn = {2150-7511}, support = {ROSS20R3, OTOOLE19GO, MADAN18GO, MADAN18AO, 00389A122MADAN, STANTO19R0//Cystic Fibrosis Foundation (CFF)/ ; P30-DK117469, T32-AI007363, T32-HL134598, UH3OD023275, R35GM142685//HHS | National Institutes of Health (NIH)/ ; }, mesh = {Humans ; *Cystic Fibrosis/microbiology ; *Gastrointestinal Microbiome ; Infant ; *Feces/microbiology ; Infant, Newborn ; Bacteria/classification/genetics/isolation & purification ; Longitudinal Studies ; Metagenomics ; Male ; Female ; Child, Preschool ; Anti-Bacterial Agents/pharmacology/therapeutic use ; }, abstract = {The healthy human infant gut microbiome undergoes stereotypical changes in taxonomic composition between birth and maturation to an adult-like stable state. During this time, extensive communication between microbiota and the host immune system contributes to health status later in life. Although there are many reported associations between microbiota compositional alterations and disease in adults, less is known about how microbiome development is altered in pediatric diseases. One pediatric disease linked to altered gut microbiota composition is cystic fibrosis (CF), a multi-organ genetic disease involving impaired chloride secretion across epithelia and heightened inflammation both in the gut and at other body sites. Here, we use shotgun metagenomics to profile the strain-level composition and developmental dynamics of the infant fecal microbiota from several CF and non-CF longitudinal cohorts spanning from birth to greater than 36 months of life. We identify a set of keystone species that define microbiota development in early life in non-CF infants but are missing or decreased in relative abundance in infants with CF, resulting in a delayed pattern of microbiota maturation, persistent entrenchment in a transitional developmental phase, and subsequent failure to attain an adult-like stable microbiota. Delayed maturation is strongly associated with cumulative antibiotic treatments, and we also detect the increased relative abundance of oral-derived bacteria and higher levels of fungi in infants with CF, features that are associated with decreased gut bacterial density. These findings suggest the potential for future directed therapies targeted at overcoming developmental delays in microbiota maturation for infants with CF.IMPORTANCEThe human gastrointestinal tract harbors a diversity of microbes that colonize upon birth and collectively contribute to host health throughout life. Infants with the disease cystic fibrosis (CF) harbor altered gut microbiota compared to non-CF counterparts, with lower levels of beneficial bacteria. How this altered population is established in infants with CF and how it develops over the first years of life is not well understood. By leveraging multiple large non-CF infant fecal metagenomic data sets and samples from a CF cohort collected prior to highly effective modulator therapy, we define microbiome maturation in infants up to 3 years of age. Our findings identify conserved age-diagnostic species in the non-CF infant microbiome that are diminished in abundance in CF counterparts that instead exhibit an enrichment of oral-derived bacteria and fungi associated with antibiotic exposure. Together, our study builds toward microbiota-targeted therapy to restore healthy microbiota dynamics in infants with CF.}, } @article {pmid39581825, year = {2025}, author = {Isali, I and Almassi, N and Nizam, A and Campbell, R and Weight, C and Gupta, S and Pooja, G and Fulmes, A and Mishra, K and Abbosh, P and Bukavina, L}, title = {State of the Art: The Microbiome in Bladder Cancer.}, journal = {Urologic oncology}, volume = {43}, number = {4}, pages = {199-208}, doi = {10.1016/j.urolonc.2024.11.008}, pmid = {39581825}, issn = {1873-2496}, mesh = {Humans ; *Urinary Bladder Neoplasms/microbiology ; *Microbiota ; Gastrointestinal Microbiome ; }, abstract = {This review assesses the current understanding of the relationship between the human microbiome and BCa. Recognizing how the microbiome affects the tumor microenvironment provides valuable insights into cancer biology, potentially uncovering interactions that could be leveraged to develop innovative therapeutic approaches. By clarifying these intricate microbial-tumor dynamics, novel targets for microbiome-based interventions can be identified, ultimately improving treatment effectiveness and patient outcomes. Current literature lacks comprehensive insights into the effects of BCa treatment on the microbiome and the prevalence of immunotherapy-related toxicities. Further research into the microbiome's role in BCa development could bridge the gap between fundamental research and therapeutic applications. Implementing microbiome surveillance, metagenomic sequencing, and metabolomics in clinical trials could deepen our understanding of BCa and its treatment. This review explores the existing understanding of the urine, tissue, and gut microbiomes and their connections to BCa. Enhanced knowledge of these relationships can pave the way for future research to identify reliable disease predictors, prognostic markers, and novel therapeutic targets.}, } @article {pmid39216617, year = {2025}, author = {Borrego, A and Koury Cabrera, WH and Souza, AT and Eto, SF and de Oliveira, SL and Rodrigues, J and Jensen, JR}, title = {Microbiota transfer early after birth modulates genetic susceptibility to chronic arthritis in mice.}, journal = {Microbes and infection}, volume = {27}, number = {2}, pages = {105411}, doi = {10.1016/j.micinf.2024.105411}, pmid = {39216617}, issn = {1769-714X}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Genetic Predisposition to Disease ; Disease Models, Animal ; Female ; Terpenes/metabolism ; Arthritis/microbiology/genetics ; Mice, Inbred C57BL ; Bacteria/genetics/classification ; Arthritis, Experimental/microbiology/immunology/genetics ; Male ; Metagenomics ; Chronic Disease ; }, abstract = {Genetics is central to the susceptibility or resistance to autoimmunity, and mounting evidence indicates that the intestinal microbiota also plays an essential role. In murine arthritis models, short-chain fat acid supplementation reduces disease severity by modulating tryptophan-metabolizing bacteria. Common microbiota transfer methods modulate arthritis severity, however, they are not practical for chronic models such as pristane-induced arthritis (PIA). PIA-resistant (HIII) and PIA-susceptible (LIII) mice harbor diverse intestinal microbiomes, which might be implicated in their divergent susceptibility. To investigate this hypothesis, we used cross-fostering to stably transfer the microbiota. In this study, we show that extreme susceptibility to arthritis can be modulated by early microbiota transfer, with long-lasting effects. HIII and LIII pups were cross-fostered and injected with pristane after weaning. PIA severity in cross-fostered LIII mice was significantly reduced in the chronic phase. Metagenomic analyses showed that HIII and LIII microbiomes were partly shifted by cross-fostering. Microbial groups whose abundance was associated with either HIII or LIII mice presented similar composition in cross-fostered mice of the opposite strains, suggesting a role in PIA susceptibility. Identification of bacterial groups that modulate chronic arthritis will contribute novel insights on the pathogenesis of human rheumatoid arthritis and targets for replication and functional studies.}, } @article {pmid39095306, year = {2025}, author = {Zugman, M and Wong, M and Jaime-Casas, S and Pal, SK}, title = {The gut microbiome and dietary metabolites in the treatment of renal cell carcinoma.}, journal = {Urologic oncology}, volume = {43}, number = {4}, pages = {244-253}, doi = {10.1016/j.urolonc.2024.07.003}, pmid = {39095306}, issn = {1873-2496}, mesh = {Humans ; *Carcinoma, Renal Cell/therapy/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Kidney Neoplasms/therapy/microbiology/metabolism ; Probiotics/therapeutic use ; Diet ; Fecal Microbiota Transplantation/methods ; Dietary Supplements ; }, abstract = {The gut microbiome is interlinked with renal cell carcinoma (RCC) and its response to systemic treatment. Mounting data suggests that certain elements of the gut microbiome may correlate with improved outcomes. New generation sequencing techniques and advanced bioinformatic data curation are accelerating the investigation of specific markers and metabolites that could predict treatment response. A variety of new therapeutic strategies, such as fecal microbiota transplantation, probiotic supplements, and dietary interventions, are currently being developed to modify the gut microbiome and improve anticancer therapies in patients with RCC. This review discusses the preliminary evidence indicating the role of the microbiome in cancer treatment, the techniques and tools necessary for its proper study and some of the current forms with which the microbiome can be modulated to improve patient outcomes.}, } @article {pmid40063888, year = {2025}, author = {Saraphol, B and Hinthong, W and Chienwichai, P and Pumipuntu, N and Reamtong, O and Srisook, T and Premsuriya, J}, title = {Analysis of the fecal microbiome and metabolome in dairy cows with different body condition scores.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0319461}, pmid = {40063888}, issn = {1932-6203}, mesh = {Animals ; Cattle ; *Feces/microbiology ; *Metabolome ; Female ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; }, abstract = {Holstein Friesian is the most popular breed of dairy cows worldwide due to its exceptional milk production capabilities. In dairy cow management, the body condition score (BCS) is a useful tool, serving as a reliable indicator of a cow's nutritional status and overall health. It is determined via a subjective visual and tactile assessment of fat cover and muscle mass. A low BCS is associated with decreased milk production and fertility. While genetic and nutritional factors have previously been associated with BCS, their effects are often moderate. In this study, we compared the fecal microbiome and the untargeted fecal metabolome of normal (BCS ≥ 3, n = 16) and thin (BCS < 3, n = 16) Holstein Friesian dairy cows. The 16S rRNA gene-based metagenomic analysis revealed that thin cows had significantly higher levels of Clostridiaceae, Erysipelotrichales, Erysipelotrichaceae, and Turicibacter, while normal cows had higher levels of Clostridiales_vadinBB60_group, UCG-010, Bacteroidaceae, Ruminococcaceae, Paludibacteraceae, Alistipes, and Bacteroides. The fecal metabolomic analysis showed that key signaling pathways, including the mechanistic target of rapamycin (mTOR), phosphatidylinositol 3-kinase (PI3K)-Akt, and AMP-activated protein kinase (AMPK) pathways, were enriched in thin cows. In addition, a significant correlation was observed between differential microbial taxa and metabolites. Notably, Clostridiaceae and Erysipelotrichaceae species are linked to inflammation, infectious diseases, and conditions such as ruminal acidosis. Additionally, the mTOR, PI3K-Akt, and AMPK pathways are known to be activated by both nutrient deficiencies and inflammation. We propose that, in addition to genetic and nutritional factors, gut microbiome dysbiosis may contribute to subclinical health conditions, such as chronic inflammation and acidosis, which indirectly affect the cow's BCS. These findings are guiding our ongoing research on the underlying health conditions in thin cows to better understand the role that the gut microbiome plays in the regulation of the body condition.}, } @article {pmid40063675, year = {2025}, author = {Chavarria, X and Park, HS and Oh, S and Kang, D and Choi, JH and Kim, M and Cho, YH and Yi, MH and Kim, JY}, title = {Using gut microbiome metagenomic hypervariable features for diabetes screening and typing through supervised machine learning.}, journal = {Microbial genomics}, volume = {11}, number = {3}, pages = {}, doi = {10.1099/mgen.0.001365}, pmid = {40063675}, issn = {2057-5858}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Supervised Machine Learning ; *Diabetes Mellitus, Type 1/microbiology ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Adult ; Bacteria/genetics/classification/isolation & purification ; Metagenome ; Support Vector Machine ; Aged ; Algorithms ; }, abstract = {Diabetes mellitus is a complex metabolic disorder and one of the fastest-growing global public health concerns. The gut microbiota is implicated in the pathophysiology of various diseases, including diabetes. This study utilized 16S rRNA metagenomic data from a volunteer citizen science initiative to investigate microbial markers associated with diabetes status (positive or negative) and type (type 1 or type 2 diabetes mellitus) using supervised machine learning (ML) models. The diversity of the microbiome varied according to diabetes status and type. Differential microbial signatures between diabetes types and negative group revealed an increased presence of Brucellaceae, Ruminococcaceae, Clostridiaceae, Micrococcaceae, Barnesiellaceae and Fusobacteriaceae in subjects with diabetes type 1, and Veillonellaceae, Streptococcaceae and the order Gammaproteobacteria in subjects with diabetes type 2. The decision tree, elastic net, random forest (RF) and support vector machine with radial kernel ML algorithms were trained to screen and type diabetes based on microbial profiles of 76 subjects with type 1 diabetes, 366 subjects with type 2 diabetes and 250 subjects without diabetes. Using the 1000 most variable features, tree-based models were the highest-performing algorithms. The RF screening models achieved the best performance, with an average area under the receiver operating characteristic curve (AUC) of 0.76, although all models lacked sensitivity. Reducing the dataset to 500 features produced an AUC of 0.77 with sensitivity increasing by 74% from 0.46 to 0.80. Model performance improved for the classification of negative-status and type 2 diabetes. Diabetes type models performed best with 500 features, but the metric performed poorly across all model iterations. ML has the potential to facilitate early diagnosis of diabetes based on microbial profiles of the gut microbiome.}, } @article {pmid39993154, year = {2025}, author = {Yang, K and Zhang, L and Ruiz-Valencia, A and Song, X and Vogel, TM and Zhang, X}, title = {Heterogeneity in the Composition and Catabolism of Indigenous Microbiomes in Subsurface Soils Cocontaminated with BTEX and Chlorinated Aliphatic Hydrocarbons.}, journal = {Environmental science & technology}, volume = {59}, number = {9}, pages = {4540-4550}, doi = {10.1021/acs.est.4c10071}, pmid = {39993154}, issn = {1520-5851}, mesh = {*Microbiota ; *Soil Pollutants/metabolism ; *Biodegradation, Environmental ; *Soil/chemistry ; Soil Microbiology ; Hydrocarbons, Chlorinated/metabolism ; RNA, Ribosomal, 16S ; Benzene/metabolism ; Xylenes/metabolism ; Toluene/metabolism ; Benzene Derivatives ; }, abstract = {The effectiveness of in situ bioremediation can be affected by an insufficient understanding of high site/soil heterogeneity, especially in cocontaminated soils and sediments. In this study, samples from multiple locations within a relatively small area (20 × 20 m[2]) contaminated with benzene, toluene, ethylbenzene, and xylene (BTEX) and chlorinated aliphatic hydrocarbons (CAHs) were compared to examine their physicochemical and microbial properties. Unsupervised clustering analysis of 16S rRNA gene amplicon and metagenome shotgun sequencing data indicates that the indigenous community differentiated into three distinct patterns. In Cluster 1, Pseudomonas, with multiple monooxygenases and glutathione S-transferase (GST), was enriched in samples contaminated with high concentrations of BTEX and CAHs. Cluster 2 contained a high fraction of cometabolic degraders. Cluster 3 was dominated by Ralstonia and organohalide-respiring bacteria (OHRBs) mediating the reductive dechlorination of CAHs. Significant differences in composition and function among microbiomes were attributed to the differential distribution of organic pollutants, even in such a small area. Incorporating genomic features with physicochemical data can significantly enhance the understanding of the heterogeneities in soil and their impacts on microbial communities, thereby providing valuable information for the optimization of bioremediation strategies.}, } @article {pmid39805250, year = {2025}, author = {Bortoluzzi, C and Ghanbari, M and Gonzáles, JC and Bohórquez, JO and Paredes, R and Mauri, Y and Lozano-Poveda, CA}, title = {Precision biotic as an effective replacement of hydrolyzed yeast and butyrate in antibiotic free diets of broiler chickens raised under field conditions.}, journal = {Poultry science}, volume = {104}, number = {2}, pages = {104664}, pmid = {39805250}, issn = {1525-3171}, mesh = {Animals ; *Chickens/growth & development/physiology ; *Animal Feed/analysis ; *Gastrointestinal Microbiome/drug effects ; *Diet/veterinary ; Dietary Supplements/analysis ; Cecum/microbiology ; Male ; Animal Nutritional Physiological Phenomena/drug effects ; Butyrates/metabolism/administration & dosage ; Random Allocation ; }, abstract = {A total of 1,436,000 Ross 380 AP broiler chicks were included in the experiment, which was conducted in two cycles with 20 houses per cycle and 35,900 birds per house. The objective was to evaluate, under field conditions, the impact of a precision biotic (PB) on the growth performance and cecal microbiome of broiler chickens, in comparison to enzymatically hydrolyzed yeast (EHY) and butyrate (BT) in an antibiotic-free diet. Each cycle consisted of six (6) houses under PB supplementation, and 14 houses under the regular dietary program used by the integration. Body weight (BW), feed intake (FI), and feed conversion ratio (FCR) were assessed at processing age, ranging from 39 to 45 d. Birds had ad libitum access to water and feed. On day 29, cecal content from 7 birds per house (42 birds per treatment) were collected for microbiome analysis by applying shotgun metagenomics approach. The performance data were analyzed by ANCOVA, house was considered as the experimental unit for growth performance (n = 20; P < 0.05), and the bird for microbiome analysis (n = 84; P < 0.05). Both treatment groups performed below the strain target in terms of BW, but better in terms of FCR. There were no significant differences (P > 0.05) between both groups on the growth performance, indicating that PB effectively replaced EHY and BT without compromising growth. However, significant functional changes were observed in the microbiome of birds fed PB, with enrichment in the pathways related to carbon and nitrogen metabolism. These changes were associated with an increased carbon metabolism index (P = 0.05), which can lead to higher endogenous short-chain fatty acids (SCFAs) production. Overall, by potentially increasing SCFA production by the intestinal microbiome, PB supported the growth performance of chickens similar to that achieved with EHY and BT.}, } @article {pmid39752831, year = {2025}, author = {Li, Z and Liu, B and Cao, B and Cun, S and Liu, R and Liu, X}, title = {The potential role of viruses in antibiotic resistance gene dissemination in activated sludge viromes.}, journal = {Journal of hazardous materials}, volume = {486}, number = {}, pages = {137046}, doi = {10.1016/j.jhazmat.2024.137046}, pmid = {39752831}, issn = {1873-3336}, mesh = {*Sewage/virology/microbiology ; *Bacteriophages/genetics/isolation & purification ; *Drug Resistance, Microbial/genetics ; Virome/genetics ; China ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Wastewater/virology/microbiology ; }, abstract = {The dissemination of antibiotic resistance genes (ARGs) in activated sludge (AS) systems poses significant environmental and public health challenges. The role of viruses, primarily bacteriophages, in storing and spreading ARGs in AS systems remains largely unexplored. This study characterized the viral community, virus-associated ARGs (vir_ARGs), and mobile genetic elements (MGEs) of aerobic AS viromes from eight wastewater treatment plants (WWTPs) in eastern China. 78,604 viral operational taxonomic units (vOTUs) were identified, including 1685 temperate vOTUs (T-vOTUs). Five ARG types were detected in 37 vOTUs, indicating a low proportion of ARG-carrying viruses. The co-occurrence rate between vir_ARGs and MGEs was 37.83 %, and six ARG-carrying vOTUs contained multiple MGEs, indicating a transfer potential of vir_ARGs. Additionally, ARG and MGE profiles of AS metagenomes were analyzed to evaluate the transfer potential of phage activity on ARGs. The results showed that phage-associated MGEs showed a significant coupling with both the abundance and composition of ARGs, suggesting a potential role of phages in ARG propagation. These findings offer preliminary insights into understanding the viral resistome and its transfer potential in AS systems. Future research necessitates rigorous pure culture and molecular biology experiments to elucidate the precise mechanisms through which viruses contribute to the dissemination and persistence of ARGs.}, } @article {pmid39731892, year = {2025}, author = {Zhao, J and Huang, Y and Hu, S and Chen, Z and Chen, B and Qi, W and Wang, L and Liu, H}, title = {Impact of adaptation time on lincomycin removal in riverbank filtration: A long-term sand column study.}, journal = {Journal of hazardous materials}, volume = {486}, number = {}, pages = {136950}, doi = {10.1016/j.jhazmat.2024.136950}, pmid = {39731892}, issn = {1873-3336}, mesh = {*Lincomycin ; *Water Pollutants, Chemical/analysis ; *Filtration ; *Water Purification/methods ; Anti-Bacterial Agents ; Sand/chemistry ; Bacteria/metabolism/genetics ; Biodegradation, Environmental ; Rivers/chemistry/microbiology ; Archaea/metabolism/genetics ; Microbiota ; }, abstract = {Riverbank filtration (RBF) is an effective pretreatment technology for drinking water, removing organic micropollutants (OMPs) mainly through biodegradation. Despite documented improvements in OMP removal with extended adaptation time, the mechanisms remain poorly understood. This study assessed the removal of 128 OMPs over 82 d in a simulated RBF system, identified those with improved removal, and analyzed their properties. Additionally, microbial community shifts after 400 d of lincomycin exposure were studied to understand the underlying mechanisms. We found that the removal efficiencies of 24 OMPs, including lincomycin and fluconazole, improved by 3-77 % over 82 d while being positively correlated with the presence of tertiary amides and secondary sulfonamides. Lincomycin removal efficiency rose from 20 % to 95 % over 68 days and stayed high. We identified eight potential degradation products of lincomycin, occurring primarily via hydroxylation, N-demethylation, and amide hydrolysis. Additionally, lincomycin notably increased the abundances of specific antibiotic-resistant bacteria (e.g., Thiobacillus, 8.3-fold) and ammonia-oxidizing archaea (e.g., Nitrososphaera, 46.8-fold). The β-lactam resistance gene in Thiobacillus and the amoA gene in Nitrososphaera may enhance lincomycin's removal by promoting its hydrolysis and hydroxylation. Overall, this study provides insights into OMP biodegradation mechanisms and the impact of ng/L levels of lincomycin on microbial communities.}, } @article {pmid39693773, year = {2025}, author = {Shen, D and Li, C and Guo, Z}, title = {Dynamics of antibiotic resistance in poultry farms via multivector analysis.}, journal = {Poultry science}, volume = {104}, number = {2}, pages = {104673}, pmid = {39693773}, issn = {1525-3171}, mesh = {Animals ; *Animal Husbandry/methods ; *Chickens ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Microbiota/drug effects ; Drug Resistance, Bacterial/genetics ; Particulate Matter/analysis ; Soil Microbiology ; Genes, Bacterial ; Poultry ; }, abstract = {This study examines the distribution of microbial communities and antibiotic resistance genes (ARGs) across various vectors in poultry farm environments. The results show that airborne particulate matter (PM) and soil harbor the highest counts of microbial genes, exceeding those found in poultry visceral samples, which display lower microbial diversity and ARG levels. This highlights environmental vectors, particularly soil and PM, as major reservoirs for ARGs. Proteobacteria, predominantly present in feces and feed, are identified as key carriers of ARGs, with resistance mechanisms primarily involving efflux and target modification. Notably, Chlamydia spp. in visceral samples, despite lower overall abundance, show a high proportion of ARGs, raising concerns about ARG persistence in poultry microbiota. Furthermore, a significant correlation between different ARGs was detected, indicating the possibility of cooperative transmission processes. The findings underline the role of PM in ARG transmission due to its mobility and capacity to retain ARGs across distances. Additionally, therapeutic antibiotics in feed may contribute to ARG proliferation in animal microbiomes, suggesting a need for improved management practices to mitigate ARG spread in poultry farming environments.}, } @article {pmid40060112, year = {2024}, author = {Wei, B and Xu, Q and Kong, J and Su, X and Chen, K and Wang, H}, title = {Metagenomics-based study of rhizospheric microorganisms of Poa alpigena L. in Qinghai Lake, Ganzi River Plateau.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1518637}, pmid = {40060112}, issn = {1664-462X}, abstract = {INTRODUCTION: Poa alpigena Lindm., a dominant forage grass on the Tibetan Plateau, plays a critical role in livestock production and grassland restoration. This study investigates the rhizospheric and non-rhizospheric soil microorganisms of Poa alpigena L. in the Ganzi River area of the Qinghai Lake basin using metagenomic sequencing to understand their diversity and potential ecological functions.

METHODS: Soil samples were collected from rhizospheric and non-rhizospheric areas of Poa alpigena L. using the S-type five-point sampling method. DNA was extracted, and metagenomic sequencing was performed using the BGISEQ-500 platform. Alpha and Beta diversity analyses were conducted, and LEfSe analysis was used to identify differentially abundant microbial taxa and metabolic pathways.

RESULTS: A total of 5,681 microbial species across 1,606 genera, 521 families, 61 phyla, and 246 orders were identified. Non-rhizospheric soils exhibited higher species richness than rhizospheric soils. Proteobacteria was the most abundant phylum in both soil types. Rhizospheric soils showed significant enrichment in pathways related to antibiotic biosynthesis, carbon metabolism, and methane metabolism, while non-rhizospheric soils were enriched in quorum sensing and drug-metabolizing pathways.

DISCUSSION: The findings highlight the selective influence of Poa alpigena L. on soil microbial communities and their potential role in mitigating methane emissions. The study provides a foundation for understanding the ecological functions of soil microorganisms in alpine meadows and supports sustainable grassland management practices.}, } @article {pmid40059174, year = {2025}, author = {Jin, X and Cheng, AG and Chanin, RB and Yu, FB and Dimas, A and Jasper, M and Weakley, A and Yan, J and Bhatt, AS and Pollard, KS}, title = {Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {71}, pmid = {40059174}, issn = {2049-2618}, support = {1563159//National Science Foundation/ ; HL160862/HL/NHLBI NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Bacteria/genetics/classification/isolation & purification ; *Bacterial Adhesion/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Animals ; Metagenome ; Mice ; Promoter Regions, Genetic ; Intestines/microbiology ; }, abstract = {BACKGROUND: Bacteria use invertible genetic elements known as invertons to generate heterogeneity among a population and adapt to new and changing environments. In human gut bacteria, invertons are often found near genes associated with cell surface modifications, suggesting key roles in modulating dynamic processes such as surface adhesion and intestinal colonization. However, comprehensive testing of this hypothesis across complex bacterial communities like the human gut microbiome remains challenging. Metagenomic sequencing holds promise for detecting inversions without isolation and culturing, but ambiguity in read alignment limits the accuracy of the resulting inverton predictions.

RESULTS: Here, we developed a customized bioinformatic workflow-PhaseFinderDC-to identify and track invertons in metagenomic data. Applying this method to a defined yet complex gut community (hCom2) across different growth environments over time using both in vitro and in vivo metagenomic samples, we detected invertons in most hCom2 strains. These include invertons whose orientation probabilities change over time and are statistically associated with environmental conditions. We used motif enrichment to identify putative inverton promoters and predict genes regulated by inverton flipping during intestinal colonization and surface adhesion. Analysis of inverton-proximal genes also revealed candidate invertases that may regulate flipping of specific invertons.

CONCLUSIONS: Collectively, these findings suggest that surface adhesion and intestinal colonization in complex gut communities directly modulate inverton dynamics, offering new insights into the genetic mechanisms underlying these processes. Video Abstract.}, } @article {pmid40058902, year = {2025}, author = {Revelo-Romo, DM and Hurtado Gutiérrez, NH and Hidalgo Troya, A and Amaya-Gómez, CV and Flórez-Martínez, DH and Overmann, J and Villegas Torres, MF and González Barrios, AF}, title = {Omics approaches to explore the coffee fermentation microecosystem and its effects on cup quality.}, journal = {Food research international (Ottawa, Ont.)}, volume = {206}, number = {}, pages = {116035}, doi = {10.1016/j.foodres.2025.116035}, pmid = {40058902}, issn = {1873-7145}, mesh = {*Fermentation ; *Coffee/microbiology ; *Coffea/microbiology/chemistry/metabolism ; Microbiota ; Metagenomics/methods ; Seeds/microbiology/metabolism ; Food Handling/methods ; }, abstract = {The cultivation and postharvest processing of coffee constitute the basis of the subsistence and traditional culture for rural family-owned farms, as well as for the economic success of commercial enterprises in many coffee-producing countries worldwide. The quality of the final beverage is determined by a multitude of variables. A key post-harvest factor is the spontaneous fermentation of the coffee beans, conducted directly on the farm, to remove the mucilage that firmly adheres to the beans. The effect of this fermentation step on the aromatic profile of the coffee is not yet sufficiently understood. All of the above have drawn the attention of researchers on the application of various omics approaches to elucidate fermentation processes in more detail. These approaches have been used to study the fermentation of Arabica (Coffea arabica) beans, as this species is economically most important worldwide. It is known that Arabica mild coffee is obtained through the wet method, which involves fermenting depulped coffee beans using various strategies and then washing the fermented coffee with clean water. In contrast, the fermentation of Canephora coffee beans has been much less studied using omics technologies. This review highlights the trends and future research in coffee fermentation based on a scientometric analysis, supplemented by a traditional systematic literature review. It highlights the composition of the coffee fermentation microbiome, as elucidated by metagenomics applications, in light of several factors that can influence its structure. Additionally, it considers the metabolites associated with microbial metabolism that can influence the chemical composition of coffee beans and, consequently, the cup quality. In this way, this review evidences the promising path in understanding microbial functions in coffee fermentation and in particular in the development of microbial inocula and in the refinement of fermentation processes to improve coffee quality.}, } @article {pmid40058900, year = {2025}, author = {Wang, X and Li, Q and Li, W and Cai, G and Wu, D and Xie, G and Lu, J}, title = {Metagenomics unveils the roles of microbes in the metabolic network of purine formation during Huangjiu fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {206}, number = {}, pages = {116031}, doi = {10.1016/j.foodres.2025.116031}, pmid = {40058900}, issn = {1873-7145}, mesh = {*Fermentation ; *Purines/metabolism ; *Metagenomics ; Metabolic Networks and Pathways ; Bacteria/metabolism/genetics/classification ; Microbiota/physiology ; Fermented Foods/microbiology ; }, abstract = {Purine is a major factor contributing to the development of hyperuricemia and gout, and it is found in large quantities in Huangjiu as free bases. Purine production in Huangjiu is strongly associated with microbial metabolism. However, to the best of our knowledge the microorganisms responsible for and the mechanisms of purine formation during Huangjiu fermentation are yet to be evaluated. Herein, changes in purine levels during Huangjiu fermentation were analyzed. Further, the microbes responsible for purine production were identified and their gene abundance was studied. Results revealed that adenine, guanine, hypoxanthine, and xanthine are produced during Huangjiu fermentation. The total purines content on day 0 (27.99 mg/L) was found to be considerably lower than that produced on day 24 (122.15 mg/L) during Huangjiu fermentation. Metagenomics showed that the composition of the microbial community fluctuates sharply during five fermentation periods of Huangjiu, with the microbial community richness and diversity being the most prominent on day 3. At the genus level, Klebsiella, Lactobacillus, Staphylococcus, Saccharopolyspora, and Saccharomyces were abundant during Huangjiu fermentation and were involved in purine metabolism. Relationships between the dominant microorganisms and key enzyme genes of the purine pathways were also established based on the Kyoto Encyclopedia of Genes and Genomes database. Correlation analysis showed that Lactobacillus and Saccharomyces were the main genera involved in purine formation. Saccharomyces cerevisiae, Lactobacillus paralimentarius, and Lactiplantibacillus plantarum were involved in purine formation during Huangjiu fermentation. Overall, this study improves our understanding of the purine formation mechanism during Huangjiu fermentation and provides valuable insights into the regulation of purine formation by microorganisms.}, } @article {pmid40057571, year = {2025}, author = {Adams, SE and Cawley, AK and Arnold, D and Hoptroff, MJ and Slomka, V and Matheson, JR and Marriott, RE and Gemmell, MR and Marsh, PD}, title = {A randomised, double-blind clinical study into the effect of zinc citrate trihydrate toothpaste on oral plaque microbiome ecology and function.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8136}, pmid = {40057571}, issn = {2045-2322}, mesh = {Humans ; *Toothpastes/pharmacology/therapeutic use ; *Dental Plaque/microbiology ; Male ; Female ; Adult ; *Microbiota/drug effects ; Double-Blind Method ; Middle Aged ; Zinc Compounds/pharmacology/therapeutic use/administration & dosage ; Young Adult ; Bacteria/classification/drug effects/genetics/isolation & purification ; }, abstract = {The oral microbiome is a diverse community of microbes residing on all oral surfaces. A balanced oral microbiome is associated with good oral health, and disruption can result in imbalance associated with diseases including gingivitis and dental caries. It is important, therefore, to understand how daily use of oral hygiene products impacts the microbiome. Composition and activity of dental plaque microbiome from 115 participants was analysed after brushing with one of two toothpastes, one containing zinc citrate trihydrate and the other a control toothpaste, in a parallel design. Each participant brushed twice daily for 6-weeks, with samples collected at baseline, 2 and 6-weeks. Metataxonomic analysis demonstrated changes in bacterial communities with use of the zinc toothpaste compared to the control product at community and species level. Increases at the species level were observed for taxa from the genus Veillonella with decrease in a taxon from the genus Fusobacterium for the zinc toothpaste. Analysis of microbiome function based on predicted metagenomic and metatranscriptomic analysis show that use of the zinc toothpaste is associated with an in-vivo reduction in glycolysis, consistent with the mode of action of zinc and, increases in processes linked to gum-health (lysine biosynthesis), and to whole-body health (nitrate reduction). Our findings provide the first understanding of the beneficial modulation of microbiome composition and function by zinc-containing toothpaste in-vivo for oral care benefits.}, } @article {pmid40056814, year = {2025}, author = {Yasemi, M and Jalali, A and Asadzadeh, M and Komijani, M}, title = {Organophosphate pesticides and their potential in the change of microbial population and frequency of antibiotic resistance genes in aquatic environments.}, journal = {Chemosphere}, volume = {376}, number = {}, pages = {144296}, doi = {10.1016/j.chemosphere.2025.144296}, pmid = {40056814}, issn = {1879-1298}, abstract = {Heavy metals (HMs) and pesticides disrupt aquatic biodiversity and microbial communities, contributing to antibiotic resistance via cross-resistance and co-selection mechanisms. This study investigates the relationship between organophosphorus pesticides (OPs), HMs, microbial diversity, and antibiotic resistance genes (ARGs) in eight lakes and wetlands. Microbial communities were analyzed via metagenomics methods, and data were processed using CLC Genomics Workbench 22. ARGs, including tetA, tetB, qnrA, qnrS, CIT, Fox, KPC, CTX-M1, DHA, GES, OXA, IMP, VEB, NDM1, SHV, TEM, CTX-M, PER, and MOX, were identified through polymerase chain reaction (PCR). Element concentrations and pesticide were quantified using inductively coupled plasma mass spectrometry and gas chromatography-mass spectrometry, respectively. The results indicate that environmental elements and pesticides significantly influence microbial diversity. Proteobacteria (Gamma, Beta, Alpha) dominate over other bacteria in all locations. β-Lactamase resistance genes have a significant positive correlations with the concentrations of boron, iron, lithium, magnesium, sodium, and phosphorus (P-value<0.05). Positive correlations between phosphorus, iron, and beta-lactamase genes suggest that higher concentrations of these elements may increase resistance likelihood by promoting resistant bacterial growth or facilitating gene transfer. Additionally, tetA and tetB exhibited a significant positive correlation with parathion concentration. The results showed that OPs and HMs increase antibiotic resistance by causing gene mutations, altering gene expression, and promoting horizontal gene transfer, resulting in multidrug-resistant strains. This highlights the need for monitoring these pollutants as they affect microbial diversity and accelerate antibiotic resistance. Targeted measures, such as bioremediation and pollution control, are essential to mitigate risks to the environment and public health.}, } @article {pmid39965412, year = {2025}, author = {Secomandi, E and De Gregorio, MA and Garcia-Perez, P and Vaccari, F and Puglisi, E and Lucini, L}, title = {Waterlogging alone and combined with other abiotic stresses provides unique metabolic signatures at the plant-rhizosphere interface: A multi-omics perspective on root metabolome, root exudation and rhizomicrobiome.}, journal = {Plant physiology and biochemistry : PPB}, volume = {221}, number = {}, pages = {109646}, doi = {10.1016/j.plaphy.2025.109646}, pmid = {39965412}, issn = {1873-2690}, mesh = {*Rhizosphere ; *Plant Roots/microbiology/metabolism ; *Arabidopsis/microbiology/metabolism/genetics ; *Stress, Physiological ; *Metabolome ; Metabolomics ; Microbiota ; Multiomics ; }, abstract = {Despite the growing evidence on unique and unpredictable impact of stress combination over plants, waterlogging-combined stresses effects are still underexplored. Under those conditions, besides the impairment of plant aerial parts, the root system is particularly vulnerable, leading to consequences on plant survival. Here, we report on the short-term exposure of soil-grown Arabidopsis thaliana L. to waterlogging alone and combined with cold, heat, and salinity to inspect their antagonistic, additive or synergistic effects in the rhizosphere. To this aim, root metabolic changes, exudation profiles, and microbial diversity were investigated using a combination of metabolomics and metagenomics, and their interaction was analysed through multi-omics data integration. In roots, waterlogging strongly affected metabolism compared to other single stresses, causing a down-accumulation of targeted classes of compounds including, phenylpropanoids, sterols, terpenoids, and alkaloids. Additive and synergistic effects were reported in roots under waterlogging combined with heat and cold stresses, respectively. Regarding root exudates, flavonoids, terpenoids, and alkaloids were the main classes of compounds affected. Waterlogging caused a down-accumulation of all classes except for coumarins, and mixed trends were observed in waterlogging-combined stresses, with waterlogging-salinity stresses resulting in an ameliorating effect. Even though microbial communities' alpha- and beta-diversity remained stable, suggesting their resilience under short-term exposure, specific taxa modulation was recorded under each condition. Overall, these results contribute to understanding the hierarchical impact of waterlogging on root metabolism and exudation, influencing rhizosphere interactions. This multi-omics approach advances our understanding of plant stress responses and microbial dynamics, paving the way for future studies on adaptive mechanisms.}, } @article {pmid39920962, year = {2025}, author = {Wang, X and Gao, L and Wang, S and Zhang, X and Feng, R and Jia, S}, title = {Metagenomic insights into the assembly, function, and key taxa of bacterial community in full-scale pesticide wastewater treatment processes.}, journal = {Environmental research}, volume = {271}, number = {}, pages = {121037}, doi = {10.1016/j.envres.2025.121037}, pmid = {39920962}, issn = {1096-0953}, mesh = {*Pesticides/analysis ; *Wastewater/microbiology ; *Bacteria/genetics/classification ; *Waste Disposal, Fluid/methods ; Water Pollutants, Chemical/analysis ; Metagenomics ; Microbiota ; }, abstract = {Pesticide wastewater emerges as a typical refractory wastewater, characterized by complex composition and high toxicity, posing significant treatment challenges. Bacterial communities are responsible for biological treatment of refractory wastewater in full-scale pesticide wastewater treatment plants (PWWTPs), providing important implications for optimizing system performance and improving management strategies. However, the knowledge of their composition, diversity, function, assembly patterns, and biological interactions remains limited. Therefore, this study applied high-throughput sequencing, machine learning models, and statistical analysis to investigate key features of bacterial communities in eight PWWTPs. We found that Proteobacteria and Bacteroidota were the most abundant phyla, with Pseudomonas, Hyphomicrobium, Comamonas, and Thauera being dominant genera. Bacterial community distribution and diversity varied significantly among influents, sludges, and effluents, with sludges and effluents exhibiting higher diversity, richness, and evenness compared to influents. Deterministic processes primarily shaped the bacterial communities, accounting for 77.12%, 61.44%, and 64.05% of variation in influents, sludges, and effluents, respectively. Homogeneous selection explained 47.71%, 31.37%, and 31.37% of variation across these communities. Key modules (Module 1 in influents, Modules 3 and 4 in sludges, and Module 1 in effluents) were significantly associated with various metabolic and degradative functions (p < 0.05). Core taxa identified by Random Forest analysis were strongly linked to key metabolic and degradation functions, such as the metabolism of cofactors and vitamins, carbohydrates, and amino acids as well as the degradation of benzoate, aminobenzoate, nitrotoluene, chloroalkane, and chloroalkene. This study deepens our understanding of bacterial community dynamics and key features in pesticide wastewater treatment systems, offering scientific guidance for process optimization, efficiency improvement, and system stability assessment.}, } @article {pmid39884534, year = {2025}, author = {Zhou, M and Luo, C and Zhang, J and Li, R and Chen, J and Ren, P and Tang, Y and Suo, Z and Chen, K}, title = {Potential risk of microplastics in plateau karst lakes: Insights from metagenomic analysis.}, journal = {Environmental research}, volume = {270}, number = {}, pages = {120984}, doi = {10.1016/j.envres.2025.120984}, pmid = {39884534}, issn = {1096-0953}, mesh = {*Lakes/microbiology/chemistry ; *Microplastics/analysis/toxicity ; *Water Pollutants, Chemical/analysis ; *Metagenomics ; Environmental Monitoring ; Geologic Sediments/microbiology/chemistry ; Microbiota/drug effects ; Tibet ; Drug Resistance, Microbial/genetics ; Biofilms ; }, abstract = {Microplastic (MP) pollution has become one of global concern. While MP pollution in lakes has been well studied, research on MP sources, distribution, and ecological risks in the Tibetan Plateau is limited. We systematically investigated the MP abundance and distribution in alpine travertine lakes in Jiuzhai nature reserve located in east edge of Qinghai-Tibetan Plateau and assessed the distributions of microbiomes, antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) in water, sediments, and MPs, using macrogenomics. MP abundance was 20.27-58.80 n/L in water and 583.33-996.67 n/kg in sediments. MPs were dominantly fibrous and transparent. The particle size distribution was 0.1-0.5 mm for MPs in water, and 0.5-1 mm in sediments. MPs were mainly composed of polyethylene and polyethylene terephthalate. The microbial community of MP biofilms differed from that in the surrounding environmental medium, and Proteobacteria were more abundant in biofilm than in water and sediment. MP biofilms exhibited more cooperative behavior with microorganisms in water than with those in sediments. MPs were selectively enriched for ARGs and VFGs, and MP biofilms had a higher diversity of ARGs, the most abundant isoform being msbA, which is a multidrug resistance gene. VFGs were more abundant in MP biofilms than in water and sediment. The study results are useful for understanding MP sources and ecological risks in plateau karst lakes and provide a valuable dataset and theoretical basis for studies on MP pollution in other alpine calcareous lakes.}, } @article {pmid39880110, year = {2025}, author = {Chen, N and Wang, L and Zhao, Z and Zhu, M and Li, Y}, title = {Impacts of aquaculture on nitrogen cycling and microbial community dynamics in coastal tidal flats.}, journal = {Environmental research}, volume = {270}, number = {}, pages = {120973}, doi = {10.1016/j.envres.2025.120973}, pmid = {39880110}, issn = {1096-0953}, mesh = {*Aquaculture ; *Nitrogen Cycle ; *Microbiota ; Nitrogen/metabolism/analysis ; Seasons ; Seawater/microbiology/chemistry ; Bacteria/genetics/metabolism/classification ; China ; }, abstract = {The expansion of aquaculture areas has encroached upon vast areas of coastal wetlands and introduced excessive nitrogen inputs, disrupting microbial communities and contributing to various environmental issues. However, investigations on how aquaculture affects microbial communities and nitrogen metabolism mechanisms in coastal tidal flats remain scarce. Hence, we explored the composition, diversity, and assembly processes of nitrogen-cycling (N-cycling) microbial communities in tidal flats in Jiangsu using metagenomic assembly methods. Our study further delved into the seasonal variations of these microbial characteristics to better explore the effects of seasonal changes in aquaculture areas on microbial community. Nitrogen metabolism-related processes and functional genes were identified through the KEGG and NCyc databases. The results revealed significant seasonal variation in the relative abundance and composition of microbial communities. Higher diversity was observed in winter, while the co-occurrence network of microbial communities was more complex in summer. Pseudomonadota emerged as the most abundant phylum in the N-cycling community. Furthermore, pH and NO3-N were identified as the primary factors influencing bacterial community composition, whereas NO2-N was more strongly associated with the N-cycling community. Regarding the nitrogen metabolism processes, nitrogen mineralization and nitrification were predominant in the tidal flat regions. NO2-N and NO3-N exhibited significant effects on several N-cycling functional genes (e.g., nirB, hao, and narG). Finally, neutral and null modeling analyses indicated that bacterial communities were predominantly shaped by stochastic processes, whereas N-cycling communities were largely driven by deterministic processes. These findings highlighted the significant role that aquaculture pollution plays in shaping the N-cycling communities in tidal flats. This underscored the importance of understanding microbial community dynamics and nitrogen metabolism in tidal flats to improve environmental management in coastal aquaculture areas.}, } @article {pmid39861970, year = {2025}, author = {Saati-Santamaría, Z and Navarro-Gómez, P and Martínez-Mancebo, JA and Juárez-Mugarza, M and Flores, A and Canosa, I}, title = {Genetic and species rearrangements in microbial consortia impact biodegradation potential.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf014}, pmid = {39861970}, issn = {1751-7370}, support = {//University of Seville from the Ministry of Universities/ ; CLU-2018-04//Regional Government of Castilla y León/ ; //European NextGenerationEU program/ ; //University of Salamanca/ ; 101090267//EU Horizon Europe program/ ; ProyExcel_00358//Programa de Excelencia de la Junta de Andalucía/ ; //V Plan Propio de investigación of the University Pablo de Olavide/ ; }, mesh = {*Biodegradation, Environmental ; *Microbial Consortia/genetics ; *Plasmids/genetics ; *Ibuprofen/metabolism ; Wastewater/microbiology ; Gene Rearrangement ; Bacteria/genetics/metabolism/classification ; Gene Transfer, Horizontal ; Metagenome ; DNA Transposable Elements ; }, abstract = {Genomic reorganisation between species and horizontal gene transfer have been considered the most important mechanism of biological adaptation under selective pressure. Still, the impact of mobile genes in microbial ecology is far from being completely understood. Here we present the collection and characterisation of microbial consortia enriched from environments contaminated with emerging pollutants, such as non-steroidal anti-inflammatory drugs. We have obtained and further enriched two ibuprofen-degrading microbial consortia from two unrelated wastewater treatment plants. We have also studied their ability to degrade the drug and the dynamics of the re-organisations of the genetic information responsible for its biodegradation among the species within the consortium. Our results show that genomic reorganisation within microorganisms and species rearrangements occur rapidly and efficiently during the selection process, which may be facilitated by plasmids and/or transposable elements located within the sequences. We show the evolution of at least two different plasmid backbones on samples from different locations, showing rearrangements of genomic information, including genes encoding activities for IBU degradation. As a result, we found variations in the expression pattern of the consortia after evolution under selective pressure, as an adaptation process to the new conditions. This work provides evidence for changes in the metagenomes of microbial communities that allow adaptation under a selective constraint -ibuprofen as a sole carbon source- and represents a step forward in knowledge that can inspire future biotechnological developments for drug bioremediation.}, } @article {pmid39842302, year = {2025}, author = {Li, H and Zhang, X and Zhaxi, Y and Pan, C and Zhang, Z and Pan, J and Shahzad, K and Sun, F and Zhen, Y and Jinmei, J and Zhao, W and Song, T}, title = {Integrative multi-omics analysis reveals liver-gut axis adaptation in high-altitude goats.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {54}, number = {}, pages = {101422}, doi = {10.1016/j.cbd.2025.101422}, pmid = {39842302}, issn = {1878-0407}, mesh = {Animals ; *Goats/physiology/metabolism ; *Altitude ; *Liver/metabolism ; *Gastrointestinal Microbiome ; *Adaptation, Physiological ; Transcriptome ; Metabolomics ; Metabolome ; Acclimatization ; Multiomics ; }, abstract = {The liver-gut axis is an important regulatory axis for the host's metabolic functions. The study of liver gene expression, changes in metabolic products and the regulation of gut microbial communities in plateau animals under harsh environments can reveal the mechanisms by which Tibetan goats adapt to the plateau environment. This study employs transcriptome, metabolome and metagenomic analyses to reveal the differences in genes, metabolism, and gut microbiota between Jianzhou big-eared goats (JBG) and Xizang cashmere goats (TCG), which is of significant importance for improving survival models of high-altitude ruminants. The results showed that there were 553 DEGs in the liver of JBG and TCG. Hepatic metabolomic analysis revealed significant differences in metabolic activity between the JBG and TCG groups, with notable increases in glycerophospholipid and retinol metabolic pathways. The gut microbiota, including Andreesenia, Dielma, Oscillibacter, Agrobacterium, Hyella and Thermosinus, interact with liver metabolites and can regulate the high-altitude adaptability of goats. This study reveals that TCG enhance immune regulation and energy utilization efficiency by regulating liver gene expression, modulating metabolic pathways, and improving gut microbiota, thereby helping TCG maintain healthy survival capabilities in hypoxic and high-radiation environments.}, } @article {pmid39805403, year = {2025}, author = {Wolf, PG and Welsh, C and Binion, B and Dai, H and Oliveira, ML and Hamm, A and Goldberg, S and Buobu, PS and Schering, T and Vergis, S and Kessee, N and Gomez, SL and Yazici, C and Maienschein-Cline, M and Byrd, DA and Gaskins, HR and Ridlon, JM and Mutlu, E and Greening, C and Tussing-Humphreys, L}, title = {Secondary Bile Acid Derivatives Are Contributors to the Fecal Bile Acid Pool and Associated With Bile Acid-Modulating Nutrients.}, journal = {The Journal of nutrition}, volume = {155}, number = {3}, pages = {826-838}, doi = {10.1016/j.tjnut.2024.12.035}, pmid = {39805403}, issn = {1541-6100}, mesh = {Humans ; Middle Aged ; *Feces/chemistry/microbiology ; Male ; Female ; Aged ; *Bile Acids and Salts/metabolism ; *Diet ; *Dietary Fiber/pharmacology ; Deoxycholic Acid ; Lithocholic Acid/metabolism ; Nutrients ; Gastrointestinal Microbiome ; Coffee/chemistry ; }, abstract = {BACKGROUND: Accumulation of hydrophobic bile acids (BAs) is linked with cancer development. However, derivatives of deoxycholic acid (DCA) and lithocholic acid (LCA) produced via bacterial metabolism may mitigate the proinflammatory and cytotoxic effects of hydrophobic BAs. The impact of diet on secondary BA derivative production has not been determined.

OBJECTIVES: This study aimed to study the associations between BA-modulating nutrients and the composition of secondary BAs and their derivatives.

METHODS: Stool and blood were collected from 138 participants aged 45-75 y that self-identified as Black or non-Hispanic White. BAs were extracted from stool and serum and quantified using LC/ESI-MS/MS. Energy, macronutrients, micronutrients, and specific dietary nutrients were estimated from two 24-h diet recalls. The abundance of genes for microbial BA metabolism was assessed from stool metagenomes. Kendall τ correlation and regression-based modeling were performed to determine associations between BA categories, microbial genes, and select energy-adjusted dietary variables (alcohol, calcium, coffee, fiber, fat, and protein).

RESULTS: Participants had a mean age of 60 y and a mean BMI of 31 kg/m[2]. BA derivatives were present in all participant stools, with lagodeoxycholic acid being the most abundant derivative quantified. Analysis of stool microbial metagenomes revealed the presence of genes for secondary BA derivative production in all participants. Protein is positively associated with the accumulation of secondary BAs. monounsaturated fatty acids (MUFA)s were negatively associated with high abundant derivatives of DCA in regression models. Total fiber and coffee intake were positively correlated with increased conversion of BAs to derivatives. Race and smoking status were significant predictors of associations between dietary variables and BA derivatives.

CONCLUSION: Protein, MUFAs, total fiber and coffee are significantly associated with concentrations of secondary BAs and their derivatives. Future work should account for social and structural influences on dietary intake and its relationship with BA-elicited cancer risk.}, } @article {pmid39732438, year = {2025}, author = {Alhasani, AT and Modasia, AA and Anodiyil, M and Corsetti, M and Aliyu, AI and Crooks, C and Marciani, L and Reid, J and Yakubov, GE and Taylor, M and Avery, A and Harris, H and Warren, FJ and Spiller, RC}, title = {Mode of Action of Psyllium in Reducing Gas Production from Inulin and its Interaction with Colonic Microbiota: A 24-hour, Randomized, Placebo-Controlled Trial in Healthy Human Volunteers.}, journal = {The Journal of nutrition}, volume = {155}, number = {3}, pages = {839-848}, doi = {10.1016/j.tjnut.2024.12.017}, pmid = {39732438}, issn = {1541-6100}, mesh = {Humans ; *Inulin/administration & dosage/pharmacology ; *Psyllium/administration & dosage ; Adult ; Male ; Female ; *Gastrointestinal Microbiome/drug effects ; *Colon/metabolism/microbiology ; *Cross-Over Studies ; *Fermentation ; Young Adult ; Feces/microbiology/chemistry ; Hydrogen/metabolism ; Single-Blind Method ; Healthy Volunteers ; Middle Aged ; Breath Tests ; }, abstract = {BACKGROUND: Recent studies show that the increase in breath hydrogen (BH2) and symptoms after ingestion of inulin are reduced by coadministering psyllium (PI).

OBJECTIVES: To determine if slowing delivery of inulin to the colon by administering it in divided doses would mimic the effect of PI. Primary endpoint was the BH2 area under the curve AUC0-24 h. Secondary endpoints included BH2 AUC0-6 h, 6-12 h, and 12-24 h. Exploratory endpoints included the correlation of BH2 AUC0-24 h with dietary fermentable oligo-, di-, monosaccharides, and polyols (FODMAPs) intake and in vitro fermentation results.

METHODS: A total of 17 healthy adults were randomly assigned to a single-blind, 3-arm, crossover trial. All consumed 20 g inulin (I) powder dissolved in 500 mL water and mixed with either 20 g maltodextrin (control) or 20 g PI consumed as a single dose or 20 g inulin given in divided doses (DDI), 62.5 mL every 45 min over 6 h. Twenty-four-hour BH2, dietary FODMAP intake, stool microbiota, and gas production in vitro were measured. Responders were defined as those whose AUC0-24 h BH2 was reduced by PI, whereas nonresponders showed no reduction.

RESULTS: Compared with control, PI did not reduce mean BH2 AUC0-24 h, whereas DDI increased it, P < 0.0002. DDI and PI both significantly reduced BH2 AUC0-6 h compared with the control, P < 0.0001. However, subsequently, DDI significantly increased BH2 from 6 to 12 h (P < 0.0001) and overnight (12-24 h) (P < 0.0001), whereas PI did so only overnight (P = 0.0002). Nonresponders showed greater release of arabinose during in vitro fermentation and higher abundance of 2 species, Clostridium spp. AM22_11AC and Phocaeicola dorei, which also correlated with BH2 production on PI. Dietary FODMAP intake tended to correlate inversely with BH2 AUC0-24 h (r = -0.42, P = 0.09) and correlated with microbiome community composition.

CONCLUSIONS: DDI, like PI, reduces early BH2 production. PI acts by delaying transit to the colon but not reducing colonic fermentation over 24 h. Dietary FODMAP intake correlates with BH2 response to inulin and the microbiome. This trial was registered at www.

CLINICALTRIALS: gov as NCT05619341.}, } @article {pmid39731826, year = {2025}, author = {Zhou, G and Wang, YS and Wang, HJ and Sun, TL and Peng, RQ and Li, SJ and Peng, H and Wen, X and Zhu, XX and Zhu, YQ and Cui, ZB and Shi, QS and Xie, XB}, title = {Exploring the gut microbiota and metabolome of Lateolabrax japonicus: A multi-omics approach.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {54}, number = {}, pages = {101408}, doi = {10.1016/j.cbd.2024.101408}, pmid = {39731826}, issn = {1878-0407}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Metabolome ; Metabolomics ; Fishes/microbiology/metabolism ; Metagenomics ; Aquaculture ; Multiomics ; }, abstract = {The intestinal microbiota plays a crucial role in the health and development of fish, engaging in intricate interactions with the host organism. As a significant species in aquaculture, Lateolabrax japonicus serves as an exemplary model for investigating these interactions and their subsequent effects on growth and health. This study utilized a multi-omics approach, incorporating metagenomic sequencing and non-targeted metabolomics, to delineate the gut microbiota and metabolome of L. japonicus throughout various developmental phases. Collected from a meticulously controlled aquaculture setting, the intestinal microbiota of L. japonicus underwent high-throughput sequencing to scrutinize microbial DNA and enumerate metabolites. The metagenomic analysis uncovered a heterogeneous gut microbiota in L. japonicus, predominantly composed of Proteobacteria and Firmicutes, with marked heterogeneity in microbial composition across developmental stages. A particularly noteworthy discovery was the prevalence of the genus Acinetobacter, which may significantly influence health and disease resistance. The metabolomic profiling discerned 4479 metabolites, each exhibiting pronounced stage-specific metabolic signatures, particularly within lipid, amino acid, and energy metabolism pathways. The correlation analysis between microbiota and metabolites highlighted the substantial impact of specific genera, such as Acinetobacter and Gaeumannomyces, on the metabolic milieu. This study provides a comprehensive overview of the dynamic shifts in the gut microbiota and metabolome of L. japonicus, highlighting stage-specific transitions that could be pivotal for refining aquaculture practices. The findings underscore the complex interdependence between microbiota composition and metabolic function, providing valuable insights into the modulation of fish health and growth.}, } @article {pmid40056186, year = {2025}, author = {Chen, XX and Ju, Q and Qiu, D and Zhou, Y and Wang, Y and Zhang, XX and Li, JG and Wang, M and Chang, N and Xu, XR and Zhang, YB and Zhao, T and Wang, K and Zhang, Y and Zhang, J}, title = {Microbial dysbiosis with tryptophan metabolites alteration in lower respiratory tract is associated with clinical responses to anti-PD-1 immunotherapy in advanced non-small cell lung cancer.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {74}, number = {4}, pages = {140}, pmid = {40056186}, issn = {1432-0851}, support = {82103446//National Natural Science Foundation of China/ ; 82273226//National Natural Science Foundation of China/ ; 82473215//National Natural Science Foundation of China/ ; 2020QNRC001//China Association for Science and Technology/ ; 2021LC2115//Fourth Military Medical University/ ; }, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/immunology/drug therapy/metabolism/therapy ; *Tryptophan/metabolism ; *Lung Neoplasms/immunology/drug therapy/therapy/metabolism ; *Dysbiosis/immunology ; Female ; Male ; Middle Aged ; Aged ; *Immunotherapy/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; Microbiota/drug effects/immunology ; Programmed Cell Death 1 Receptor/antagonists & inhibitors/metabolism ; Respiratory System/immunology/metabolism/microbiology ; Adult ; }, abstract = {Lower respiratory tract microbiome constitutes a unique immune microenvironment for advanced non-small cell lung cancer as one of dominant localized microbial components. However, there exists little knowledge on the associations between this regional microbiome and clinical responses to anti-PD-1 immunotherapy from clinical perspectives. Here, we equivalently collected bronchoalveolar lavage fluids from 56 advanced NSCLC participants treated with none (untreated, n = 28) or anti-PD-1 immunotherapy (treated, n = 28), which was further divided into responder (n = 17) and non-responder (n = 11) subgroups according to clinical responses, aiming to compare their microbial discrepancy by performing metagenomic sequencing and targeted metabolic alterations by tryptophan sequencing. Correspondingly, microbial diversities transformed significantly after receiving immunotherapeutic agents, where Gammaproteobacteria and Campylobacter enriched, but Escherichia, Streptococcus, Chlamydia, and Staphylococcus reduced at the genus level, differences of which failed to be achieved among subgroups with various clinical responses (responder or non-responder; LDA > 2, P < 0.05[*]). And the relative abundance of Staphylococcus and Streptomyces was escalated in response subgroup to anti-PD-1 immunotherapy by microbial compositional analysis (as relative abundance ≥ 3%, P < 0.05[*]), no significance of which was achieved among treated and untreated groups. In addition, relative abundances of bacterial tryptophan metabolites and its derivatives were also higher in the responder subgroup, distinctively being associated with divergent genera (VIP > 1, P < 0.05[*]). Our study revealed predictive performance of lower respiratory tract microbiome to antitumoral immunotherapy and further suggested that anti-PD-1 immunotherapy may alter lower respiratory tract microbiome composition and interact with its tryptophan metabolites to regulate therapeutic efficacy in advanced NSCLC, performing as potential biomarkers to prognosis and interventional strategies.}, } @article {pmid40055835, year = {2025}, author = {Yin, CF and Pan, P and Li, T and Song, X and Xu, Y and Zhou, NY}, title = {The universal accumulation of p-aminophenol during the microbial degradation of analgesic and antipyretic acetaminophen in WWTPs: a novel metagenomic perspective.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {68}, pmid = {40055835}, issn = {2049-2618}, support = {32400079//the National Natural Science Foundation of China/ ; 2024YFA0919000//the National Key R&D Program of China/ ; 2024YFA0919000//the National Key R&D Program of China/ ; }, mesh = {*Acetaminophen/metabolism ; *Metagenomics ; *Biodegradation, Environmental ; *Aminophenols/metabolism ; *Antipyretics ; Wastewater/microbiology ; Water Pollutants, Chemical/metabolism ; China ; Bacteria/genetics/classification/metabolism/isolation & purification ; Humans ; Microbiota ; Analgesics ; Metagenome ; }, abstract = {BACKGROUND: Acetaminophen, a widely used analgesic and antipyretic drug, has become a significant aquatic micro-pollutant due to its extensive global production and increased consumption, particularly during the COVID-19 pandemic. Its high-water solubility leads to its pervasive presence in wastewater treatment plants (WWTPs), posing substantial risks to the environment and human health. Biological treatment is one of the promising approaches to remove such pollutants. Although previous studies have isolated acetaminophen-degrading pure cultures and proposed catabolic pathways, the interactions between microbiotas and acetaminophen, the distribution feature of acetaminophen degradation genes, and the gene-driven fate of acetaminophen in the real-world environment remain largely unexplored.

RESULTS: Among the water samples from 20 WWTPs across China, acetaminophen was detected from 19 samples at concentrations ranging from 0.06 to 29.20 nM. However, p-aminophenol, a more toxic metabolite, was detected in all samples at significantly higher concentrations (23.93 to 108.68 nM), indicating the presence of a catabolic bottleneck in WWTPs. Metagenomic analysis from both the above 20 samples and global datasets revealed a consistently higher abundance of initial acetaminophen amidases compared to downstream enzymes, potentially having explained the reason for the bottleneck. Meanwhile, a close correlation between initial amidases and Actinomycetota revealed by genome-based taxonomy suggests a species-dependent degradation pattern. Additionally, a distinct amidase ApaA was characterized by newly isolated Rhodococcus sp. NyZ502 (Actinomycetota), represents a predominant category of amidase in WWTPs. Significant phylogenetic and structural diversity observed among putative amidases suggest versatile acetaminophen hydrolysis potential in WWTPs.

CONCLUSIONS: This study enhances our understanding of acetaminophen's environmental fate and highlights the possible occurrence of ecological risks driven by imbalanced genes in the process of acetaminophen degradation in global WWTPs. Video Abstract.}, } @article {pmid40055808, year = {2025}, author = {Avershina, E and Qureshi, AI and Winther-Larsen, HC and Rounge, TB}, title = {Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {66}, pmid = {40055808}, issn = {2049-2618}, support = {2022067//Helse Sør-Øst RHF/ ; }, mesh = {*Software ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Humans ; *Mycobiome ; *Fungi/genetics/classification/isolation & purification ; *Metagenomics/methods ; Computational Biology/methods ; Ascomycota/genetics/classification/isolation & purification ; Basidiomycota/genetics/isolation & purification/classification ; Databases, Genetic ; }, abstract = {BACKGROUND: The mycobiome, representing the fungal component of microbial communities, is increasingly acknowledged as an integral part of the gut microbiome. However, research in this area remains relatively limited. The characterization of mycobiome taxa from metagenomic data is heavily reliant on the quality of the software and databases. In this study, we evaluated the feasibility of mycobiome profiling using existing bioinformatics tools on simulated fungal metagenomic data.

RESULTS: We identified seven tools claiming to perform taxonomic assignment of fungal shotgun metagenomic sequences. One of these was outdated and required substantial modifications of the code to be functional and was thus excluded. To evaluate the accuracy of identification and relative abundance of the remaining tools (Kraken2, MetaPhlAn4, EukDetect, FunOMIC, MiCoP, and HumanMycobiomeScan), we constructed 18 mock communities of varying species richness and abundance levels. The mock communities comprised up to 165 fungal species belonging to the phyla Ascomycota and Basidiomycota, commonly found in gut microbiomes. Of the tools, FunOMIC and HumanMycobiomeScan needed source code modifications to run. Notably, only one species, Candida orthopsilosis, was consistently identified by all tools across all communities where it was included. Increasing community richness improved precision of Kraken2 and the relative abundance accuracy of all tools on species, genus, and family levels. MetaPhlAn4 accurately identified all genera present in the communities and FunOMIC identified most species. The top three tools for overall accuracy in both identification and relative abundance estimation were EukDetect, MiCoP, and FunOMIC, respectively. Adding 90% and 99% bacterial background did not significantly impact these tools' performance. Among the whole genome reference tools (Kraken2, HMS, and MiCoP), MiCoP exhibited the highest accuracy when the same reference database was used.

CONCLUSION: Our survey of mycobiome-specific software revealed a very limited selection of such tools and their poor robustness due to error-prone software, along with a significant lack of comprehensive databases enabling characterization of the mycobiome. None of the implemented tools fully agreed on the mock community profiles. FunOMIC recognized most of the species, but EukDetect and MiCoP provided predictions that were closest to the correct compositions. The bacterial background did not impact these tools' performance. Video Abstract.}, } @article {pmid40054447, year = {2025}, author = {Xiao, X and Zhao, W and Song, Z and Qi, Q and Wang, B and Zhu, J and Lin, J and Wang, J and Hu, A and Huang, S and Wang, Y and Chen, J and Fang, C and Ji, Q and Zhang, N and Meng, L and Wei, X and Chen, C and Cai, S and Chen, S and Ding, K and Li, D and Liu, S and Song, T and Tian, L and Zhang, H and Zhang, Y and Xu, S and Chen, J and Chen, H and Cen, Q and Jiang, F and Hu, G and Tang, C and Guo, W and Wang, X and Zhan, L and Fan, J and Wang, J and Zhou, C and Li, L and Lv, Z and Hu, Y and Lin, X and Mai, G and Luo, L and Yang, T and Wang, W and Kristiansen, K and Chen, L and Yang, H and Ni, M and Gu, Y and Mu, F and Yang, Y and Zhou, J and Wang, J and Zhang, WJ and Han, M and Xu, X and Liu, S}, title = {Microbial ecosystems and ecological driving forces in the deepest ocean sediments.}, journal = {Cell}, volume = {188}, number = {5}, pages = {1363-1377.e9}, doi = {10.1016/j.cell.2024.12.036}, pmid = {40054447}, issn = {1097-4172}, mesh = {*Geologic Sediments/microbiology/chemistry ; *Oceans and Seas ; *RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Phylogeny ; Bacteria/genetics/classification/metabolism ; Microbiota/genetics ; Metagenome ; Metagenomics ; }, abstract = {Systematic exploration of the hadal zone, Earth's deepest oceanic realm, has historically faced technical limitations. Here, we collected 1,648 sediment samples at 6-11 km in the Mariana Trench, Yap Trench, and Philippine Basin for the Mariana Trench Environment and Ecology Research (MEER) project. Metagenomic and 16S rRNA gene amplicon sequencing generated the 92-Tbp MEER dataset, comprising 7,564 species (89.4% unreported), indicating high taxonomic novelty. Unlike in reported environments, neutral drift played a minimal role, while homogeneous selection (HoS, 50.5%) and dispersal limitation (DL, 43.8%) emerged as dominant ecological drivers. HoS favored streamlined genomes with key functions for hadal adaptation, e.g., aromatic compound utilization (oligotrophic adaptation) and antioxidation (high-pressure adaptation). Conversely, DL promoted versatile metabolism with larger genomes. These findings indicated that environmental factors drive the high taxonomic novelty in the hadal zone, advancing our understanding of the ecological mechanisms governing microbial ecosystems in such an extreme oceanic environment.}, } @article {pmid40054445, year = {2025}, author = {Turjeman, S and Rozera, T and Elinav, E and Ianiro, G and Koren, O}, title = {From big data and experimental models to clinical trials: Iterative strategies in microbiome research.}, journal = {Cell}, volume = {188}, number = {5}, pages = {1178-1197}, doi = {10.1016/j.cell.2025.01.038}, pmid = {40054445}, issn = {1097-4172}, mesh = {*Microbiota ; Humans ; *Big Data ; Animals ; Clinical Trials as Topic ; Metagenomics/methods ; Metabolomics/methods ; }, abstract = {Microbiome research has expanded significantly in the last two decades, yet translating findings into clinical applications remains challenging. This perspective discusses the persistent issue of correlational studies in microbiome research and proposes an iterative method leveraging in silico, in vitro, ex vivo, and in vivo studies toward successful preclinical and clinical trials. The evolution of research methodologies, including the shift from small cohort studies to large-scale, multi-cohort, and even "meta-cohort" analyses, has been facilitated by advancements in sequencing technologies, providing researchers with tools to examine multiple health phenotypes within a single study. The integration of multi-omics approaches-such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics-provides a comprehensive understanding of host-microbe interactions and serves as a robust hypothesis generator for downstream in vitro and in vivo research. These hypotheses must then be rigorously tested, first with proof-of-concept experiments to clarify the causative effects of the microbiota, and then with the goal of deep mechanistic understanding. Only following these two phases can preclinical studies be conducted with the goal of translation into the clinic. We highlight the importance of combining traditional microbiological techniques with big-data approaches, underscoring the necessity of iterative experiments in diverse model systems to enhance the translational potential of microbiome research.}, } @article {pmid40056745, year = {2025}, author = {Zhu, S and Mao, H and Yang, X and Zhao, W and Sheng, L and Sun, S and Du, X}, title = {Resilience mechanisms of rhizosphere microorganisms in lead-zinc tailings: Metagenomic insights into heavy metal resistance.}, journal = {Ecotoxicology and environmental safety}, volume = {292}, number = {}, pages = {117956}, doi = {10.1016/j.ecoenv.2025.117956}, pmid = {40056745}, issn = {1090-2414}, abstract = {This study investigates the impact of heavy metal contamination in lead-zinc tailings on plant and soil microbial communities, focusing on the resilience mechanisms of rhizosphere microorganisms in these extreme environments. Utilizing metagenomic techniques, we identified a significant association between Coriaria nepalensis Wall. rhizosphere microbial communities and metal(loid) resistance genes. Our results reveal a notable diversity and abundance of bacteria within the rhizosphere of tailings, primarily consisting of Proteobacteria, Actinobacteria, and Chloroflexi. The presence of metal-resistant bacterial taxa, including Afipia, Bradyrhizobium, Sphingomonas, and Miltoncostaea, indicates specific evolutionary adaptations to metal-rich, nutrient-deficient environments. Elevated expression of resistance genes such as znuD, zntA, pbrB, and pbrT underscores the microorganisms' ability to endure these harsh conditions. These resistance genes are crucial for maintaining biodiversity, ecosystem stability, and adaptability. Our findings enhance the understanding of interactions between heavy metal contamination, microbial community structure, and resistance gene dynamics in lead-zinc tailings. Additionally, this research provides a theoretical and practical foundation for employing plant-microbial synergies in the in-situ remediation of contaminated sites.}, } @article {pmid40053579, year = {2025}, author = {Wöhlbrand, L and Dörries, M and Siani, R and Medrano-Soto, A and Schnaars, V and Schumacher, J and Hilbers, C and Thies, D and Kube, M and Reinhardt, R and Schloter, M and Saier, MH and Winklhofer, M and Rabus, R}, title = {Key role of Desulfobacteraceae in C/S cycles of marine sediments is based on congeneric catabolic-regulatory networks.}, journal = {Science advances}, volume = {11}, number = {10}, pages = {eads5631}, pmid = {40053579}, issn = {2375-2548}, support = {R01 GM077402/GM/NIGMS NIH HHS/United States ; }, mesh = {*Geologic Sediments/microbiology ; *Deltaproteobacteria/metabolism/genetics ; *Carbon Cycle ; Sulfur/metabolism ; Gene Regulatory Networks ; Phylogeny ; Metagenome ; Carbon/metabolism ; Proteome/metabolism ; Oxidation-Reduction ; Metabolic Networks and Pathways ; }, abstract = {Marine sediments are highly bioactive habitats, where sulfate-reducing bacteria contribute substantially to seabed carbon cycling by oxidizing ~77 Tmol Corg year[-1]. This remarkable activity is largely attributable to the deltaproteobacterial family Desulfobacteraceae of complete oxidizers (to CO2), which our biogeography focused meta-analysis verified as cosmopolitan. However, the catabolic/regulatory networks underlying this ecophysiological feat at the thermodynamic limit are essentially unknown. Integrating cultivation-based (80 conditions) proteogenomics of six representative Desulfobacteraceae spp., we identify molecular commonalities explaining the family's environmental relevance and success. Desulfobacteraceae genomes are specifically enriched in substrate uptake, degradation capacities, and regulatory functions including fine-tuned sulfate uptake. Conserved gene arrangements and shared regulatory patterns translate into strikingly similar (sub-)proteome profiles. From 319 proteins, we constructed a meta-network for catabolizing 35 substrates. Therefrom, we defined a Desulfobacteraceae characteristic gene subset, which we found prevalent in metagenomes of organic-rich, marine sediments. These genes are promising targets to advance our mechanistic understanding of Desulfobacteraceae-driven biogeochemical processes in marine sediments and beyond.}, } @article {pmid40052474, year = {2025}, author = {Bamigbade, GB and Abdin, M and Subhash, A and Arachchi, MP and Ullah, N and Gan, RY and Ali, A and Kamal-Eldin, A and Ayyash, M}, title = {Plant polysaccharide-capped nanoparticles: A sustainable approach to modulate gut microbiota and advance functional food applications.}, journal = {Comprehensive reviews in food science and food safety}, volume = {24}, number = {2}, pages = {e70156}, pmid = {40052474}, issn = {1541-4337}, support = {//United Arab Emirates University/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects ; *Nanoparticles/chemistry ; *Polysaccharides/chemistry ; *Functional Food ; Humans ; Plants/chemistry ; }, abstract = {Plant-derived polysaccharides have emerged as sustainable biopolymers for fabricating nanoparticles (polysaccharide-based nanomaterials [PS-NPs]), presenting unique opportunities to enhance food functionality and human health. PS-NPs exhibit exceptional biocompatibility, biodegradability, and structural versatility, enabling their integration into functional foods to positively influence gut microbiota. This review explores the mechanisms of PS-NPs interaction with gut microbiota, highlighting their ability to promote beneficial microbial populations, such as Lactobacilli and Bifidobacteria, and stimulate the production of short-chain fatty acids. Key synthesis and stabilization methods of PS-NPs are discussed, focusing on their role in improving bioavailability, stability, and gastrointestinal delivery of bioactive compounds in food systems. The potential of PS-NPs to address challenges in food science, including enhancing nutrient absorption, mitigating intestinal dysbiosis, and supporting sustainable food production through innovative nanotechnology, is critically evaluated. Barriers such as enzymatic degradation and physicochemical stability are analyzed, alongside strategies to optimize their functionality within complex food matrices. The integration of PS-NPs in food systems offers a novel approach to modulate gut microbiota, improve intestinal health, and drive the development of next-generation functional foods. Future research should focus on bridging knowledge gaps in metagenomic and metabolomic profiling of PS-NPs, optimizing their design for diverse applications, and advancing their role in sustainable and health-promoting food innovations.}, } @article {pmid39987648, year = {2025}, author = {Zampieri, A and Carraro, L and Mohammadpour, H and Rovere, GD and Milan, M and Fasolato, L and Cardazzo, B}, title = {Presence and characterization of the human pathogenic Vibrio species in the microbiota of Manila clams using cultural and molecular methods.}, journal = {International journal of food microbiology}, volume = {433}, number = {}, pages = {111113}, doi = {10.1016/j.ijfoodmicro.2025.111113}, pmid = {39987648}, issn = {1879-3460}, mesh = {*Bivalvia/microbiology ; Animals ; *Vibrio/genetics/classification/isolation & purification/pathogenicity ; *Microbiota ; *Shellfish/microbiology ; Humans ; Metagenomics ; }, abstract = {The North Adriatic lagoons and the Po River Delta are important areas for farming Manila clams (Ruditapes philippinarum). These areas have been heavily impacted by climate change, reducing livestock numbers and increasing pathogen spread. Shellfish, particularly clams, are primary vectors for Vibrio pathogens affecting humans. In this study, the occurrence of human pathogenic Vibrio species on Manila clams was investigated using an integrated approach that combined culture-dependent and culture-independent techniques. Samples were collected over three years from farming areas in the northeastern Adriatic lagoons and the Po River Delta, regions seriously impacted by climate change and pollution. In this study, species of the human pathogen Vibrio were analyzed in the clam microbiota and characterized using recA-pyrH metabarcoding and shotgun metagenomics. Human pathogenic Vibrio species were widespread in the clam microbiota, especially in summer, demonstrating that the environmental conditions on the northern Adriatic coasts allowed the growth of these bacteria. V. parahaemolyticus and V. vulnificus were also quantified using qPCR in <50 % of summer samples Shotgun metagenomics revealed the similarity of V. parahaemolyticus strains to other worldwide genomes, enabling improved pathogen identification and tracking. In the future, climate change could cause these conditions to become even more favorable to these bacteria, potentially increasing pathogen spread. Consequently, enhanced monitoring and control of both the environment and seafood products should be planned to ensure food safety.}, } @article {pmid39962619, year = {2025}, author = {Foucault, P and Halary, S and Duval, C and Goto, M and Marie, B and Hamlaoui, S and Jardillier, L and Lamy, D and Lance, E and Raimbault, E and Allouti, F and Troussellier, M and Bernard, C and Leloup, J and Duperron, S}, title = {A summer in the greater Paris: trophic status of peri-urban lakes shapes prokaryotic community structure and functional potential.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {24}, pmid = {39962619}, issn = {2524-6372}, support = {COM2LIFE (ANR-20-CE32-0006)//Agence Nationale de la Recherche/ ; COM2LIFE (ANR-20-CE32-0006)//Agence Nationale de la Recherche/ ; }, abstract = {With more than 12 million inhabitants, the Greater Paris offers a "natural laboratory" to explore the effects of eutrophication on freshwater lake's microbiomes within a relative restricted area (~ 70 km radius). Here, a 4-months survey was carried out during summertime to monitor planktonic microbial communities of nine lakes located around Paris (Île-de-France, France) of comparable morphologies, yet distinct trophic statuses from mesotrophic to hypereutrophic. By thus minimizing the confounding factors, we investigated how trophic status could influence prokaryotic community structures (16S rRNA gene sequencing) and functions (shotgun metagenomics). These freshwater lakes harbored highly distinct and diverse prokaryotic communities, and their trophic status appears as the main driver explaining both differences in community structure and functional potential. Although their gene pool was quite stable and shared among lakes, taxonomical and functional changes were correlated. According to trophic status, differences in phosphorus metabolism-related genes were highlighted among the relevant functions involved in the biogeochemical cycles. Overall, hypereutrophic lakes microbiomes displayed the highest contrast and heterogeneity over time, suggesting a specific microbial regime shift compared to eutrophic and mesotrophic lakes.}, } @article {pmid40052450, year = {2025}, author = {Qian, Z and Chen, S and Liao, X and Xie, J and Xu, Y and Zhong, H and Ou, L and Zuo, X and Xu, X and Peng, J and Wu, J and Cai, S}, title = {Decreased intestinal abundance of Akkermansia muciniphila is associated with metabolic disorders among people living with HIV.}, journal = {Annals of medicine}, volume = {57}, number = {1}, pages = {2474730}, doi = {10.1080/07853890.2025.2474730}, pmid = {40052450}, issn = {1365-2060}, mesh = {Humans ; Male ; *HIV Infections/complications/microbiology ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; *Akkermansia ; *Non-alcoholic Fatty Liver Disease/microbiology/metabolism ; Prospective Studies ; Feces/microbiology ; Metagenomics/methods ; Hyperlipidemias/microbiology ; Metabolic Diseases/microbiology/epidemiology ; Verrucomicrobia/isolation & purification ; Overweight/microbiology/complications ; }, abstract = {BACKGROUND: Previous studies have shown changes in gut microbiota after human immunodeficiency virus (HIV) infection, but there is limited research linking the gut microbiota of people living with HIV (PLWHIV) to metabolic diseases.

METHODS: A total of 103 PLWHIV were followed for 48 weeks of anti-retroviral therapy (ART), with demographic and clinical data collected. Gut microbiome analysis was conducted using metagenomic sequencing of fecal samples from 12 individuals. Nonalcoholic fatty liver disease (NAFLD) was diagnosed based on controlled attenuation parameter (CAP) values of 238 dB/m from liver fibro-scans. Participants were divided based on the presence of metabolic disorders, including NAFLD, overweight, and hyperlipidemia. Akkermansia abundance in stool samples was measured using RT-qPCR, and Pearson correlation and logistic regression were applied for analysis.

RESULTS: Metagenomic sequencing revealed a significant decline in gut Akkermansia abundance in PLWHIV with NAFLD. STAMP analysis of public datasets confirmed this decline after HIV infection, while KEGG pathway analysis identified enrichment of metabolism-related genes. A prospective cohort study with 103 PLWHIV followed for 48 weeks validated these findings. Akkermansia abundance was significantly lower in participants with NAFLD, overweight, and hyperlipidemia at baseline, and it emerged as an independent predictor of NAFLD and overweight. Negative correlations were observed between Akkermansia abundance and both CAP values and body mass index (BMI) at baseline and at week 48. At the 48-week follow-up, Akkermansia remained a predictive marker for NAFLD.

CONCLUSIONS: Akkermansia abundance was reduced in PLWHIV with metabolic disorders and served as a predictive biomarker for NAFLD progression over 48 weeks of ART.}, } @article {pmid40052334, year = {2025}, author = {Lu, Y and Dong, Y and Zhang, M and Mao, L}, title = {Genome and Metagenome Skimming: Future Sequencing Methods for Environmental DNA (eDNA) Studies.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14095}, doi = {10.1111/1755-0998.14095}, pmid = {40052334}, issn = {1755-0998}, support = {2023YFF0805800//the National Key Research and Development Program of China/ ; BE2022792//Jiangsu Social Development Program/ ; }, abstract = {Genome skimming (GS), also referred to as low-coverage shotgun sequencing, is an efficient and cost-effective sequencing method that targets high-copy regions in genomes. It is most commonly used for species identification, phylogenetic analysis and expansion of reference libraries. GS can be applied to single species or composite DNA samples representing multiple species; the latter is termed metagenome skimming (MGS). GS/MGS shows promise as an effective approach for environmental DNA (eDNA) studies, but it is currently limited to ancient sedimentary samples. There is the potential to expand this methodology to other eDNA sources, including water, soil and airborne samples. In this paper, we introduce GS/MGS and briefly review its current applications. We also discuss the potential benefits and challenges of using GS/MGS to assay eDNA. eDNA GS/MGS is a promising technology that could broaden eDNA studies if some methodological challenges can be addressed.}, } @article {pmid40050382, year = {2025}, author = {Liu, C and Wang, H and Wang, Z and Liang, L and Li, Y and Liu, D and Lu, Q}, title = {Distinct assembly processes of intestinal and non-intestinal microbes of bark beetles from clues of metagenomic insights.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {7910}, pmid = {40050382}, issn = {2045-2322}, support = {32230071//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Coleoptera/microbiology/genetics ; Metagenome ; Bacteria/genetics/classification/metabolism ; Microbiota ; Symbiosis ; Weevils/microbiology/genetics ; Phylogeny ; }, abstract = {Ips (Curculionidae: Scolytinae) bark beetles (BBs) are ecologically and economically devastating coniferous pests in the Northern Hemisphere. Although the microbial diversity associated with these beetles has been well studied, mechanisms of community assembly and the functional roles of key microbes remain poorly understood. This study investigates the microbial community structures and functions in both intestinal and non-intestinal environments of five Ips BBs using a metagenomic approach. The findings reveal similar microbial community compositions, though the α-diversity of dominant taxa differs between intestinal and non-intestinal environments due to the variability in bark beetle species, host trees, and habitats. Intestinal microbial communities are predominantly shaped homogenizing dispersal (HD) and undominated processes (UP), whereas non-intestinal microbial communities are primarily driven by heterogeneous selection (HS). Functional analysis shows that genes and enzymes associated with steroid biosynthesis and oxidative phosphorylation are primarily found in non-intestinal fungal symbionts Ogataea, Wickerhamomyce, Ophiostoma, and Ceratocystis of Ips species. Genes and enzymes involved in degrading terpenoids, phenolic compounds, and polysaccharides are predominately found in the intestinal Acinetobacter, Erwinia, and Serratia. This study provides valuable and in-depth insights into the symbiotic relationships between Ips BBs and their microbial partners, enhancing our understanding of insect-microbe coevolution and suggesting new strategies for pest management.}, } @article {pmid40049907, year = {2025}, author = {Jia, Z and Li, C and Zhang, S and Tang, Y and Ma, S and Liu, X and Zhang, J}, title = {Microbial inoculants modify the functions of soil microbes to optimize plant growth at abandoned mine sites.}, journal = {Journal of environmental sciences (China)}, volume = {154}, number = {}, pages = {678-690}, doi = {10.1016/j.jes.2024.10.002}, pmid = {40049907}, issn = {1001-0742}, mesh = {*Soil Microbiology ; *Mining ; *Plant Development ; *Soil/chemistry ; Phosphorus/metabolism ; Carbon/metabolism ; Biodegradation, Environmental ; Nitrogen/metabolism ; Microbiota ; Bacillus thuringiensis ; }, abstract = {Mining activities have caused significant land degradation globally, emphasizing the need for effective restoration. Microbial inoculants offer a promising solution for sustainable remediation by enhancing soil nutrients, enzyme activities, and microbial communities to support plant growth. However, the mechanisms by which inoculants influence soil microbes and their relationship with plant growth require further investigation. Metagenomic sequencing was employed for this study, based on a one-year greenhouse experiment, to elucidate the effects of Bacillus thuringiensis NL-11 on the microbial functions of abandoned mine soils. Our findings revealed that the application of microbial inoculants significantly enhanced the soil total carbon (TC), total sulfur (TS), organic carbon (SOC), available phosphorus (AP), ammonium (NH4[+]), urease, arylsulfatase, phosphatase, β-1,4-glucosidase (BG), β-1,4-N-acetylglucosaminidase (NAG). Moreover, this led to substantial improvements in plant height, as well as aboveground and belowground biomass. Microbial inoculants impacted functional gene structures without altering diversity. The normalized abundance of genes related to the degradation of carbon and nitrogen, methane metabolism, and nitrogen fixation were observed to increase, as well as the functional genes related to phosphorus cycling. Significant correlations were found between nutrient cycling gene abundance and plant biomass. Partial Least Squares Path Model analysis showed that microbial inoculants not only directly influenced plant biomass but also indirectly affected the plant biomass through C cycle modifications. This study highlights the role of microbial inoculants in promoting plant growth and soil restoration by improving soil properties and enhancing normalized abundance of nutrient cycling gene, making them essential for the recovery of abandoned mine sites.}, } @article {pmid39726137, year = {2025}, author = {Schwesig, K and Zizka, V and Scherber, C and Hölzel, N}, title = {Comparing eDNA and Transect Methods for Aquatic Biodiversity Assessment in Lakes and Ponds.}, journal = {Molecular ecology resources}, volume = {25}, number = {3}, pages = {e14060}, doi = {10.1111/1755-0998.14060}, pmid = {39726137}, issn = {1755-0998}, support = {01UT2101C//Bundesministerium für Bildung und Forschung/ ; 01UT2101B//Bundesministerium für Bildung und Forschung/ ; }, mesh = {*Biodiversity ; Animals ; *Amphibians/genetics/classification ; *Ponds ; Germany ; *DNA Barcoding, Taxonomic/methods ; *Lakes ; Odonata/genetics/classification ; Metagenomics/methods ; DNA, Environmental/genetics ; Aquatic Organisms/genetics/classification ; }, abstract = {Biodiversity monitoring increasingly relies on molecular methods such as eDNA metabarcoding. However, sound applications have so far been only established for a limited number of taxonomic groups. More information on the strengths and weaknesses of eDNA methods, especially for poorly covered groups, is essential for practical applications to achieve the highest possible reliability. We compared amphibian and Odonata data from eDNA metabarcoding and traditional transect walks on N = 56 plots in 38 water bodies distributed over six extraction sites for building materials in Northwest Germany. The traditional amphibian assessment included visual encounters, dip netting and acoustic detection, while Odonata were assessed through exuviae. In total, both methods detected 8 out of 11 amphibian species, while the remaining three species were detected by eDNA only. We did not find differences in amphibian species numbers per plot, but mean detection probabilities were higher with metabarcoding. In contrast, both methods detected 10 out of 29 Odonata species, while the remaining 19 species were detected by exuviae only. Species numbers per plot were higher for exuviae and only 30% of species were detected with metabarcoding. The species identified by eDNA were those with high abundance, and their detection probabilities were similar to transect walks. The results for amphibians show equal suitability and high complementarity of the compared methods. Metabarcoding detected species more efficiently and therefore offers a suitable protocol for biodiversity monitoring. For Odonata, eDNA metabarcoding showed considerable gaps, implying the need for protocol evaluation and improvement in assessment of ecological communities based on eDNA.}, } @article {pmid40049896, year = {2025}, author = {Yu, Q and Hu, X and Qian, Y and Wang, Y and Shi, C and Qi, R and Heděnec, P and Nan, Z and Li, H}, title = {Virus communities rather than bacterial communities contribute more on nutrient pool in polluted aquatic environment.}, journal = {Journal of environmental sciences (China)}, volume = {154}, number = {}, pages = {550-562}, doi = {10.1016/j.jes.2024.08.026}, pmid = {40049896}, issn = {1001-0742}, mesh = {*Bacteria/metabolism/classification/genetics ; *Viruses ; Phosphorus/analysis ; RNA, Ribosomal, 16S/genetics ; Nitrogen/analysis ; Carbon/metabolism ; Water Microbiology ; Water Pollutants, Chemical/analysis ; Nutrients/analysis ; }, abstract = {The degradation of animal carcasses can lead to rapid waste release (e.g., pathogenic bacteria, viruses, prions, or parasites) and also result in nutrient accumulation in the surrounding environment. However, how viral profile responds and influences nutrient pool (carbon (C), nitrogen (N), phosphorus (P) and sulfur (S)) in polluted water caused by animal carcass decomposition had not been explored. Here, we combined metagenomic analysis, 16S rRNA gene sequencing and water physicochemical assessment to explore the response of viral communities under different temperatures (23 °C, 26 °C, 29 °C, 32 °C, and 35 °C) in water polluted by cadaver, as well as compare the contribution of viral/bacterial communities on water nutrient pool. We found that a total of 15,240 viral species were classified and mainly consisted of Siphoviridae. Both temperature and carrion reduced the viral diversity and abundance. Only a small portion of the viruses (∼8.8 %) had significant negative correlations with temperature, while most were not sensitive. Our results revealed that the viruses had lager contribution on nutrient pool than bacteria. Besides, viral-related functional genes involved in C, N, P and S cycling. These functional genes declined during carcass decomposition and covered part of the central nutrient cycle metabolism (including carbon sugar transformation, denitrification, P mineralization and extracelluar sulfate transfer, etc.). Our result implies that human regulation of virus communities may be more important than bacterial communities in regulating and managing polluted water quality and nutrition.}, } @article {pmid40047330, year = {2025}, author = {Gong, S and Li, M and Gao, J and Huang, S and Song, W and Sun, L}, title = {Cucumaria frondosa intestines and ovum hydrolysates intervention ameliorates the symptoms of dextran sulfate sodium-induced colitis by modulating gut microbiota and its metabolites.}, journal = {Journal of food science}, volume = {90}, number = {3}, pages = {e70106}, doi = {10.1111/1750-3841.70106}, pmid = {40047330}, issn = {1750-3841}, support = {42106111//National Natural Science Foundation of China/ ; ZR2021QD030//Natural Science Foundation of Shandong Province/ ; NYJG202303//Fund of Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, China/ ; 2023KJ241//Program for Scientific Research Innovation Team of Young Scholar in Colleges and Universities of Shandong Province/ ; R20076//Doctoral Startup Project of Guangdong Ocean University funded by W.S/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Colitis/chemically induced ; *Dextran Sulfate ; Mice ; Male ; Disease Models, Animal ; Mice, Inbred C57BL ; Colon/metabolism/microbiology/drug effects ; Cytokines/metabolism ; Intestines/microbiology/drug effects ; }, abstract = {Colitis, a troublesome inflammatory disease that significantly impacts daily life, has garnered considerable attention in recent times. Protolysates play a crucial role in the treatment of colitis, and the intestines and ovum of Cucumaria frondosa represent a readily available source of these hydrolysates. However, the effects of C. frondosa intestines and ovum hydrolysates (CFHs) on colitis have not been thoroughly investigated. We initially examined the molecular weight distribution of CFHs and found that the fraction of molecules with a weight less than 1000 Da accounted for 86.98%, indicating that the hydrolysis primarily produced oligopeptides. Subsequently, we employed a dextran sulfate sodium-induced experimental colitis model to assess the therapeutic potential of CFHs. The findings indicated that preventive administration of CFHs dramatically attenuated the pathological manifestations associated with colitis in mice, including weight loss, colon shortening, and tissue damage. Furthermore, CFHs suppressed the secretion of pro-inflammatory cytokines IL-6, TNF-α, and IL-1β, as well as MPO in colon tissue. Metagenomic sequencing demonstrated that CFHs could restore balance to the dysregulated gut microbiota by reinforcing Bacteroidota and suppressing Verrucomicrobia populations, impacting various microbial functions. Metabolomic analyses further revealed that CFHs exhibited a more efficacious modulatory effect on DSS-induced metabolic abnormalities, including amino acid biosynthesis, linoleic acid metabolism, and dopaminergic synapses. In conclusion, CFHs showed promise in alleviating colitis, laying the groundwork for the development and application of CFHs as functional food for colitis relief.}, } @article {pmid40045185, year = {2025}, author = {Freund, L and Hung, C and Topacio, TM and Diamond, C and Fresquez, A and Lyons, TW and Aronson, EL}, title = {Diversity of sulfur cycling halophiles within the Salton Sea, California's largest lake.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {120}, pmid = {40045185}, issn = {1471-2180}, support = {NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; }, mesh = {California ; *Sulfur/metabolism ; *Microbiota ; *Lakes/microbiology ; *Seawater/microbiology/chemistry ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Seasons ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Biodiversity ; }, abstract = {BACKGROUND: Microorganisms are the biotic foundation for nutrient cycling across ecosystems, and their assembly is often based on the nutrient availability of their environment. Though previous research has explored the seasonal lake turnover and geochemical cycling within the Salton Sea, California's largest lake, the microbial community of this declining ecosystem has been largely overlooked. We collected seawater from a single location within the Salton Sea at 0 m, 3 m, 4 m, 5 m, 7 m, 9 m, 10 m, and 10.5 m depths in August 2021, December 2021, and April 2022.

RESULTS: We observed that the water column microbiome significantly varied by season (R[2] = 0.59, P = 0.003). Temperature (R[2] = 0.27, P = 0.004), dissolved organic matter (R[2] = 0.13, P = 0.004), and dissolved oxygen (R[2] = 0.089, P = 0.004) were significant drivers of seasonal changes in microbial composition. In addition, several halophilic mixotrophs and other extremotolerant bacteria were consistently identified in samples across depths and time points, though their relative abundances fluctuated by season. We found that while sulfur cycling genes were present in all metagenomes, their relative coverages fluctuated by pathway and season throughout the water column. Sulfur oxidation and incomplete sulfur oxidation pathways were conserved in the microbiome across seasons.

CONCLUSIONS: Our work demonstrates that the microbiome within the Salton Seawater has the capacity to metabolize sulfur species and utilize multiple trophic strategies, such as alternating between chemorganotrophy and chemolithoautrophy, to survive this harsh, fluctuating environment. Together, these results suggest that the Salton Sea microbiome is integral in the geochemical cycling of this ever-changing ecosystem and thus contributes to the seasonal dynamics of the Salton Sea. Further work is required to understand how these environmental bacteria are implicated relationship between the Salton Sea's sulfur cycle, dust proliferation, and respiratory distress experienced by the local population.}, } @article {pmid40044917, year = {2025}, author = {Štůsková, K and Vavřiník, A and Hakalová, E and Čechová, J and Gramaje, D and Eichmeier, A}, title = {Arbuscular mycorrhizal fungi strongly influence the endorhizosphere of grapevine rootstock with soil type as a key factor.}, journal = {Mycorrhiza}, volume = {35}, number = {2}, pages = {17}, pmid = {40044917}, issn = {1432-1890}, support = {CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; IGA-ZF/2022-ST2-004//Internal Grant Agency, Mendel university in Brno/ ; IGA-ZF/2022-ST2-004//Internal Grant Agency, Mendel university in Brno/ ; }, mesh = {*Mycorrhizae/physiology ; *Vitis/microbiology ; *Soil Microbiology ; *Soil/chemistry ; Czech Republic ; Plant Roots/microbiology ; Mycobiome ; Basidiomycota/genetics/physiology ; Rhizosphere ; Phosphorus/metabolism/analysis ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) play a crucial role in enhancing the health and productivity of host plants, including grapevine. By forming symbiotic relationships with plant roots, AMF significantly improve water uptake and nutrient absorption, particularly phosphorus (P) and nitrogen (N). This study evaluated the microbiome composition and AMF colonization in the grapevine endorhizosphere across five wine-growing sub-regions in the Czech Republic. In all five sub-regions, in terms of composition of the fungal microbiome, the phyla Ascomycetes and Basidiomycetes were most numerous. Additionally, the study confirmed that LSU primers are more sensitive than ITS primers for AMF sequencing. While the representation of the phylum Glomeromycetes ranged from 0.07% to 5.65% in the ITS library, it was significantly higher, ranging from 83.74% to 98.71%, in the LSU library. The most significant difference compared to other sub-regions was observed in the Slovácko sub-region, where the soil had a low pH, a different texture (sandy loam), reduced micronutrient concentration, and low organic matter. The application of chemical plant protection products to grapevines also could have played a significant role, with 49 applications recorded in the Slovácko sub-region during the three years preceding sample collection. In other sub-regions, chemical treatments were conducted only 19-26 times. These factors resulted in only trace amounts of AMF being detected in Slovácko. Furthermore, it was demonstrated that AMF positively influenced the phosphorus concentration in the soil and reduced the presence of certain fungal pathogens.}, } @article {pmid40044690, year = {2025}, author = {Zheng, K and Sun, J and Liang, Y and Kong, L and Paez-Espino, D and Mcminn, A and Wang, M}, title = {VITAP: a high precision tool for DNA and RNA viral classification based on meta-omic data.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2226}, pmid = {40044690}, issn = {2041-1723}, support = {41976117//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42176111//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*RNA, Viral/genetics ; *RNA Viruses/genetics/classification/isolation & purification ; *DNA Viruses/genetics/classification ; *DNA, Viral/genetics ; Software ; Phylogeny ; Genome, Viral/genetics ; Metagenomics/methods ; Virome/genetics ; Computational Biology/methods ; }, abstract = {The rapid growth in the number of newly identified DNA and RNA viral sequences underscores the need for an accurate and comprehensive classification system for all viral realms at different taxonomic levels. Here, we establish the Viral Taxonomic Assignment Pipeline (VITAP), which addresses classification challenges by integrating alignment-based techniques with graphs, offering high precision in classifying both DNA and RNA viral sequences and providing confidence level for each taxonomic unit. This tool automatically updates its database in sync with the latest references from the International Committee on Taxonomy of Viruses (ICTV), efficiently classifying viral sequences as short as 1,000 base pairs to genus level. VITAP possesses good generalization capabilities, maintaining accuracy comparable to other pipelines while achieving higher annotation rates across most DNA and RNA viral phyla. Its application in deep-sea viromes has led to significant taxonomic updates, providing comprehensive diversity information of viruses from deep-sea. VITAP is available at https://github.com/DrKaiyangZheng/VITAP .}, } @article {pmid40044673, year = {2025}, author = {Wood, JR and Zhou, C and Cole, TL and Coleman, M and Anderson, DP and Lyver, PO and Tan, S and Xiang, X and Long, X and Luo, S and Lou, M and Southon, JR and Li, Q and Zhang, G}, title = {Sedimentary DNA insights into Holocene Adélie penguin (Pygoscelis adeliae) populations and ecology in the Ross Sea, Antarctica.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1798}, pmid = {40044673}, issn = {2041-1723}, mesh = {Animals ; Antarctic Regions ; *Spheniscidae/genetics ; *DNA, Mitochondrial/genetics ; *Geologic Sediments ; Phylogeny ; Seals, Earless ; Metagenome ; Ecosystem ; Diet ; }, abstract = {We report 156 sediment metagenomes from Adélie penguin (Pygoscelis adeliae) colonies dating back 6000 years along the Ross Sea coast, Antarctica, and identify marine and terrestrial eukaryotes, including locally occurring bird and seal species. The data reveal spatiotemporal patterns of Adélie penguin diet, including spatial patterns in consumption of cnidarians, a historically overlooked component of Adélie penguin diets. Relative proportions of Adélie penguin mitochondrial lineages detected at each colony are comparable to those previously reported from bones. Elevated levels of Adélie penguin mitochondrial nucleotide diversity in upper stratigraphic samples of several active colonies are consistent with recent population growth. Moreover, the highest levels of Adélie penguin mitochondrial nucleotide diversity recovered from surface sediment layers are from the two largest colonies, indicating that sedaDNA could provide estimates for the former size of abandoned colonies. SedaDNA also reveals prior occupation of the Cape Hallett Adélie penguin colony site by southern elephant seal (Mirounga leonina), demonstrating how terrestrial sedaDNA can detect faunal turnover events in Antarctica driven by past climate or sea ice conditions. Low rates of cytosine deamination indicate exceptional sedaDNA preservation within the region, suggesting there is high potential for recovering much older sedaDNA records from local Pleistocene terrestrial sediments.}, } @article {pmid40043057, year = {2025}, author = {Mercado-Juárez, RA and Valdespino-Castillo, PM and Merino Ibarra, M and Batista, S and Mac Cormack, W and Ruberto, L and Carpenter, EJ and Capone, DG and Falcón, LI}, title = {What defines a photosynthetic microbial mat in western Antarctica?.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0315919}, pmid = {40043057}, issn = {1932-6203}, mesh = {Antarctic Regions ; *Bacteria/genetics/classification/isolation & purification ; Photosynthesis ; Archaea/genetics/classification/isolation & purification ; Biodiversity ; Phylogeny ; Microbiota ; }, abstract = {Antarctic microbial mats, with their significant biodiversity and key role in biogeochemical cycling, were the focus of our study. We employed a metagenomic approach to analyze 14 microbial mats from meltwater streams of western Antarctica, covering the Maritime, Peninsula, and Dry Valleys regions. Our findings revealed that the taxonomic compositional level of the microbial mat communities is characterized by similar bacterial groups, with diatoms being the main distinguishing factor between the rapidly warming Maritime Antarctica and the other mats. Bacteria were found to be the predominant component of all microbial mats (>90%), followed by Eukarya (>3%), Archaea (<1%), and Viruses (<0.1%). The average abundance of the main phyla composing Antarctic microbial mats included Bacteroidota (35%), Pseudomonadota (29%), Cyanobacteriota (19%), Verrucomicrobiota (3%), Bacillariophyta (2%), Planctomycetota (2%), Acidobacteriota (2%), Actinomycetota (2%), Bacillota (1%), and Chloroflexota (1%). We also identified some microeukaryotes that could play essential roles in the functioning of Antarctic microbial mats. Notably, all mats were found in sites with varied environmental characteristics, showed N-limitation, and shared functional patterns.}, } @article {pmid40042126, year = {2025}, author = {Hayden, HS and Nelson, MT and Ross, SE and Verster, AJ and Bouzek, DC and Eng, A and Waalkes, A and Penewit, K and Kopp, BT and Siracusa, C and Rock, MJ and Salipante, SJ and Hoffman, LR and Sanders, DB}, title = {Effects of Therapeutic Antibiotic Exposure on the Oropharyngeal and Fecal Microbiota in Infants With Cystic Fibrosis.}, journal = {Pediatric pulmonology}, volume = {60}, number = {3}, pages = {e71024}, pmid = {40042126}, issn = {1099-0496}, support = {//This work was supported by the Cystic Fibrosis Foundation (CFF; SANDER16Y5, SANDER18A0-I) and the National Institutes of Health (NIH; NIH NHLBI K24HL141669)./ ; }, mesh = {Humans ; *Cystic Fibrosis/microbiology/drug therapy ; *Feces/microbiology ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Infant ; *Oropharynx/microbiology ; Male ; Female ; *Microbiota/drug effects ; beta-Lactams/pharmacology/therapeutic use ; Bacterial Load/drug effects ; Longitudinal Studies ; }, abstract = {BACKGROUND: Systemic antibiotics can impact all microbes inhabiting patients, regardless of the intended target organism(s). We studied the simultaneous effects on respiratory and fecal microbiomes of β-lactam antibiotics administered for respiratory symptoms in infants with cystic fibrosis (IWCF).

OBJECTIVE: To compare the magnitude and duration of intended (respiratory) and unintended (fecal) antimicrobial action by analyzing oropharyngeal (OP) and fecal microbiota in IWCF.

DESIGN: Shotgun metagenomic sequencing and qPCR were performed on OP and fecal samples collected longitudinally from 14 IWCF (ages 1-17 months) during ("On Antibiotics") and after ("Off Antibiotics") β-lactam therapy, and from 5 IWCF (3-16 months) never treated with antibiotics.

RESULTS: Total bacterial loads (TBL) for On Antibiotics samples were lower than for both Never (OP and fecal) and Off Antibiotics samples (fecal only). α-diversities (within-sample) for OP On Antibiotics samples were lower than for Never and Off Antibiotics samples but did not differ between fecal sample groups. β-diversity (between-sample) differed between all OP sample groups and between fecal On and Never Antibiotics and Off and Never antibiotics samples; however, fecal On and Off Antibiotics sample β-diversities did not differ. Patterns of change in antibiotic resistance gene abundances reflected shifts in microbial community composition.

CONCLUSIONS: β-lactam antibiotic exposure was followed by marked alterations in both OP and fecal microbiota. While microbiota appeared to rebound after treatment in both sample types, our results suggest that fecal microbiota recovered less than OP. The clinical consequences of these findings should be studied in IWCF and other populations frequently treated with antibiotics.}, } @article {pmid39893934, year = {2025}, author = {Zeng, S and Mo, S and Wu, X and Meng, C and Peng, P and Kashif, M and Li, J and He, S and Jiang, C}, title = {Microbial-mediated carbon metabolism in the subtropical marine mangroves affected by shrimp pond discharge.}, journal = {Marine environmental research}, volume = {205}, number = {}, pages = {106980}, doi = {10.1016/j.marenvres.2025.106980}, pmid = {39893934}, issn = {1879-0291}, mesh = {*Carbon/metabolism ; *Wetlands ; Animals ; Microbiota ; Aquaculture ; Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/metabolism/genetics/classification ; Ponds/microbiology ; }, abstract = {Mangrove ecosystems exhibit high efficiency in carbon (C) sequestering within the global ecosystem. However, the rapid expansion of the shrimp farming industry poses a significant threat to these delicate ecosystems. The microbial mechanisms driving C metabolism in shrimp-affected sediments remain poorly understood. This study investigates the spatiotemporal dynamics of C metabolism-related microbial communities in shrimp pond and natural mangrove sediments in a subtropical region. Shrimp pond discharge altered soil properties, microbial diversity, and microbial stability, driven by factors such as salinity, sulfide, and total organic C (TOC). Metagenomic analyses reveals shifts in C degradation and oxidation, with a reduction in genes for cellulose and hemicellulose degradation. Microbial markers like Prolixibacteraceae and Nitrosopumilaceae reflect these changes. Co-occurrence network analysis indicates higher connectivity within shrimp pond groups, suggesting nutrient-driven changes in symbiotic relationships. PLS-PM analysis further confirms the interplay between microbial composition, nutrient levels, and C metabolism, with higher 16S rRNA operon copy numbers linked to increased C fixation. These findings demonstrate how shrimp pond discharge alters microbial networks and C metabolism, with implications for ecosystem resilience.}, } @article {pmid39719725, year = {2025}, author = {Deng, K and Shen, L and Xue, Z and Li, BY and Tang, J and Zhao, H and Xu, F and Miao, Z and Cai, X and Hu, W and Fu, Y and Jiang, Z and Liang, X and Xiao, C and Shuai, M and Gou, W and Yue, L and Xie, Y and Sun, TY and Guo, T and Chen, YM and Zheng, JS}, title = {Association of the EAT-Lancet diet, serial measures of serum proteome and gut microbiome, and cardiometabolic health: a prospective study of Chinese middle-aged and elderly adults.}, journal = {The American journal of clinical nutrition}, volume = {121}, number = {3}, pages = {567-579}, doi = {10.1016/j.ajcnut.2024.10.011}, pmid = {39719725}, issn = {1938-3207}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Prospective Studies ; Aged ; *Proteome ; *Diet ; *Blood Proteins/metabolism/analysis ; China ; Cardiovascular Diseases/blood ; Cardiometabolic Risk Factors ; East Asian People ; }, abstract = {BACKGROUND: The EAT-Lancet diet was reported to be mutually beneficial for the human cardiometabolic system and planetary health. However, mechanistic evidence linking the EAT-Lancet diet and human cardiometabolic health is lacking.

OBJECTIVES: We aimed to investigate the role of blood proteins in the association between the EAT-Lancet diet and cardiometabolic health and explore the underlying gut microbiota-blood protein interplay.

METHODS: Our study was based on a prospective cohort including 3742 Chinese participants enrolled from 2008-2013 with serum proteome data repeatedly measured ≤3 times (Nproteome = 7514) and 1195 with gut metagenomic data measured ≤2 times over 9 y (Nmicrobiota = 1695). Least absolute shrinkage and selection operator and multivariable linear regression were used to explore the associations of the EAT-Lancet diet (assessed by semi-quantitative food frequency questionnaire) with serum proteins and gut microbes. Linear mixed-effect model and logistic regression were used to examine the associations of selected proteins with 11 cardiometabolic risk factors and 4 cardiometabolic diseases, respectively. Mediation analysis was used to identify potential mediation effects. Multiple comparisons were adjusted using the Benjamini-Hochberg method.

RESULTS: The mean (standard deviation) age of enrolled participants was 58.4 (6.1) y (31.6% men). The EAT-Lancet diet was prospectively associated with 4 core proteins, including α-2-macroglobulin (A2M) (pooled β: 0.12; 95% confidence interval [CI]: 0.05, 0.2), retinol-binding protein 4 (pooled β: -0.14; 95% CI: -0.24, -0.04), TBC1 domain family member 31 (pooled β: -0.11; 95% CI: -0.22, 0), and adenylate kinase 4 (pooled β: -0.19; 95% CI: -0.3, -0.08). The identified proteins were prospectively associated with cardiometabolic diseases (pooled odds ratio ranged from 0.8-1.18) and risk factors (pooled β ranged from -0.1 to 0.12), mediating the association between the EAT-Lancet diet and blood triglycerides. We then identified 5 gut microbial biomarkers of the EAT-Lancet diet, and discovered a potential gut microbiota-blood protein interplay (EAT-Lancet diet→Rothia mucilaginosa→A2M) underlying the EAT-Lancet diet-cardiometabolic health association.

CONCLUSIONS: Our study presents key molecular evidence to support the role of EAT-Lancet diet adherence in promoting cardiometabolic health.}, } @article {pmid39708826, year = {2025}, author = {Hu, Y and Zhang, ZY and Wang, F and Zhuang, K and Xu, X and Liu, DS and Fan, HZ and Yang, L and Jiang, K and Zhang, DK and Xu, L and Tang, JH and Liu, XM and He, C and Shu, X and Xie, Y and Lau, JYW and Zhu, Y and Du, YQ and Graham, DY and Lu, NH}, title = {Effects of amoxicillin dosage on cure rate, gut microbiota, and antibiotic resistome in vonoprazan and amoxicillin dual therapy for Helicobacter pylori: a multicentre, open-label, non-inferiority randomised controlled trial.}, journal = {The Lancet. Microbe}, volume = {6}, number = {3}, pages = {100975}, doi = {10.1016/j.lanmic.2024.100975}, pmid = {39708826}, issn = {2666-5247}, mesh = {Humans ; *Helicobacter Infections/drug therapy/microbiology ; *Helicobacter pylori/drug effects/genetics ; Middle Aged ; Female ; Male ; *Amoxicillin/administration & dosage/pharmacology/therapeutic use ; *Sulfonamides/administration & dosage/pharmacology/therapeutic use/adverse effects ; Adult ; *Gastrointestinal Microbiome/drug effects ; *Drug Therapy, Combination ; *Pyrroles/administration & dosage/pharmacology/therapeutic use ; *Anti-Bacterial Agents/administration & dosage/pharmacology/therapeutic use/adverse effects ; Aged ; Treatment Outcome ; Young Adult ; Adolescent ; Drug Resistance, Bacterial/genetics ; China ; Proton Pump Inhibitors/administration & dosage/pharmacology/therapeutic use/adverse effects ; }, abstract = {BACKGROUND: Vonoprazan and amoxicillin (VA) dual therapy as a mainstream Helicobacter pylori regimen has gained momentum worldwide, but the optimum dosages remain unclear. We aimed to compare the efficacy and safety of VA dual therapy with 2 g amoxicillin or 3 g amoxicillin, and to assess the short-term effects of therapy on the gut microbiota and antibiotic resistome.

METHODS: We conducted an open-label, non-inferiority randomised controlled trial at 12 centres in China. Individuals infected with H pylori, aged 18-70 years, and without previous eradication therapy were recruited. Participants were randomly assigned at a 1:1 ratio (block size of six) to receive vonoprazan (20 mg twice a day) with either low-dose amoxicillin (1 g twice a day; LVA therapy) or high-dose amoxicillin (1 g three times a day; HVA therapy) for 14 days. Gastric biopsies were collected before treatment for detection of antibiotic resistance. Stool samples were collected at baseline, week 2, and week 8-10 for shotgun metagenomic sequencing. The primary outcome was the eradication rate of H pylori, assessed by [13]C urea breath test, in both intention-to-treat and per-protocol analyses. Secondary outcomes were adverse events, adherence, antibiotic resistance, and alterations to the gut microbiota and antibiotic resistome. The margin used to establish non-inferiority was -0·10. The trial was registered with ClinicalTrials.gov, NCT05649709.

FINDINGS: Between Feb 13, 2023, and Jan 25, 2024, 504 patients (204 [40%] male and 300 [60%] female; mean age 43 years [SD 13]) were randomly assigned to LVA therapy or HVA therapy (n=252 in each group). No infections were resistant to amoxicillin. The H pylori eradication rate was 85·3% (215 of 252; 95% CI 80·4 to 89·2) in the LVA group and 86·5% (218 of 252; 81·7 to 90·2) in the HVA group in the intention-to-treat analysis (p=0·70) and 88·8% (213 of 240; 84·1 to 92·2) and 92·4% (218 of 236; 88·3 to 95·1), respectively, in the per-protocol analysis (p=0·18). The efficacy of LVA was non-inferior to HVA in the intention-to-treat analysis (risk difference -1·2%, 95% CI -7·3 to 4·9, p=0·0022) and the per-protocol analysis (-3·6%, -9·0 to 1·7, p=0·0085). 31 (12%) patients in the LVA group and 43 (17%) patients in the HVA group reported adverse events. Adherence to therapy was 97% in the LVA group and 96% in the HVA group. The diversity of gut microbiota decreased after treatment but was restored to baseline at week 8-10 in both groups. The abundance of beta-lactam-related resistance genes was increased at week 2 after treatment, and was restored to pretreatment level at week 8-10 for the LVA group but not the HVA group.

INTERPRETATION: LVA dual therapy was effective and non-inferior to HVA dual therapy as first-line treatment of H pylori infection and showed a non-lasting effect on the abundance of beta-lactam-related resistance genes. High amoxicillin dosage (eg, 3 g per day) is not required to achieve high cure rates with vonoprazan dual therapy.

FUNDING: National Natural Science Foundation of China, Project for Academic and Technical Leaders of Major Disciplines in Jiangxi Province, and Key Research and Development Program of Jiangxi Province.}, } @article {pmid39653411, year = {2025}, author = {Shi, Z and Li, M and Zhang, C and Li, H and Zhang, Y and Zhang, L and Li, X and Li, L and Wang, X and Fu, X and Sun, Z and Zhang, X and Tian, L and Zhang, M and Chen, WH and Li, Z}, title = {Butyrate-producing Faecalibacterium prausnitzii suppresses natural killer/T-cell lymphoma by dampening the JAK-STAT pathway.}, journal = {Gut}, volume = {74}, number = {4}, pages = {557-570}, doi = {10.1136/gutjnl-2024-333530}, pmid = {39653411}, issn = {1468-3288}, mesh = {Animals ; Humans ; Mice ; *Gastrointestinal Microbiome/physiology ; *Faecalibacterium prausnitzii/metabolism ; *Butyrates/metabolism ; Janus Kinases/metabolism ; Cross-Sectional Studies ; Female ; Male ; STAT Transcription Factors/metabolism ; Signal Transduction ; Lymphoma, Extranodal NK-T-Cell/metabolism/microbiology/pathology ; Probiotics/therapeutic use ; Dysbiosis/microbiology ; Middle Aged ; }, abstract = {BACKGROUND: Natural killer/T-cell lymphoma (NKTCL) is a highly aggressive malignancy with a dismal prognosis, and gaps remain in understanding the determinants influencing disease outcomes.

OBJECTIVE: To characterise the gut microbiota feature and identify potential probiotics that could ameliorate the development of NKTCL.

DESIGN: This cross-sectional study employed shotgun metagenomic sequencing to profile the gut microbiota in two Chinese NKTCL cohorts, with validation conducted in an independent Korean cohort. Univariable and multivariable Cox proportional hazards analyses were applied to assess associations between identified marker species and patient outcomes. Tumour-suppressing effects were investigated using comprehensive in vivo and in vitro models. In addition, metabolomics, RNA sequencing, chromatin immunoprecipitation sequencing, Western blot analysis, immunohistochemistry and lentiviral-mediated gene knockdown system were used to elucidate the underlying mechanisms.

RESULTS: We first unveiled significant gut microbiota dysbiosis in NKTCL patients, prominently marked by a notable reduction in Faecalibacterium prausnitzii which correlated strongly with shorter survival among patients. Subsequently, we substantiated the antitumour properties of F. prausnitzii in NKTCL mouse models. Furthermore, F. prausnitzii culture supernatant demonstrated significant efficacy in inhibiting NKTCL cell growth. Metabolomics analysis revealed butyrate as a critical metabolite underlying these tumour-suppressing effects, validated in three human NKTCL cell lines and multiple tumour-bearing mouse models. Mechanistically, butyrate suppressed the activation of Janus kinase-signal transducer and activator of transcription pathway through enhancing histone acetylation, promoting the expression of suppressor of cytokine signalling 1.

CONCLUSION: These findings uncover a distinctive gut microbiota profile in NKTCL and provide a novel perspective on leveraging the therapeutic potential of F. prausnitzii to ameliorate this malignancy.}, } @article {pmid39643156, year = {2025}, author = {Wang, Y and Zeng, T and Tang, D and Cui, H and Wan, Y and Tang, H}, title = {Integrated Multi-Omics Analyses Reveal Lipid Metabolic Signature in Osteoarthritis.}, journal = {Journal of molecular biology}, volume = {437}, number = {6}, pages = {168888}, doi = {10.1016/j.jmb.2024.168888}, pmid = {39643156}, issn = {1089-8638}, mesh = {Humans ; *Osteoarthritis/genetics/microbiology/metabolism/pathology ; *Lipid Metabolism/genetics ; *Metabolomics/methods ; Chondrocytes/metabolism/pathology ; Gastrointestinal Microbiome ; Male ; Metagenomics ; Gene Regulatory Networks ; Female ; Middle Aged ; Single-Cell Analysis ; Multiomics ; }, abstract = {Osteoarthritis (OA) is the most common degenerative joint disease and the second leading cause of disability worldwide. Single-omics analyses are far from elucidating the complex mechanisms of lipid metabolic dysfunction in OA. This study identified a shared lipid metabolic signature of OA by integrating metabolomics, single-cell and bulk RNA-seq, as well as metagenomics. Compared to the normal counterparts, cartilagesin OA patients exhibited significant depletion of homeostatic chondrocytes (HomCs) (P = 0.03) and showed lipid metabolic disorders in linoleic acid metabolism and glycerophospholipid metabolism which was consistent with our findings obtained from plasma metabolomics. Through high-dimensional weighted gene co-expression network analysis (hdWGCNA), weidentified PLA2G2A as a hub gene associated with lipid metabolic disorders in HomCs. And an OA-associated subtype of HomCs, namely HomC1 (marked by PLA2G2A, MT-CO1, MT-CO2, and MT-CO3) was identified, which also exhibited abnormal activation of lipid metabolic pathways. This suggests the involvement of HomC1 in OA progression through the shared lipid metabolism aberrancies, which were further validated via bulk RNA-Seq analysis. Metagenomic profiling identified specific gut microbial species significantly associated with the key lipid metabolism disorders, including Bacteroides uniformis (P < 0.001, R = -0.52), Klebsiella pneumonia (P = 0.003, R = 0.42), Intestinibacter_bartlettii (P = 0.009, R = 0.38), and Streptococcus anginosus (P = 0.009, R = 0.38). By integrating the multi-omics features, a random forest diagnostic model with outstanding performance was developed (AUC = 0.97). In summary, this study deciphered the crucial role of a integrated lipid metabolic signature in OA pathogenesis, and established a regulatory axis of gut microbiota-metabolites-cell-gene, providing new insights into the gut-joint axis and precision therapy for OA.}, } @article {pmid38508446, year = {2025}, author = {Tao, S and Fan, J and Li, J and Wu, Z and Yao, Y and Wang, Z and Wu, Y and Liu, X and Xiao, Y and Wei, H}, title = {Extracellular vesicles derived from Lactobacillus johnsonii promote gut barrier homeostasis by enhancing M2 macrophage polarization.}, journal = {Journal of advanced research}, volume = {69}, number = {}, pages = {545-563}, doi = {10.1016/j.jare.2024.03.011}, pmid = {38508446}, issn = {2090-1224}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Extracellular Vesicles/metabolism ; Mice ; *Macrophages/metabolism/immunology/microbiology ; Swine ; *Diarrhea/microbiology/therapy ; *Probiotics ; *Lactobacillus johnsonii/metabolism ; Intestinal Mucosa/microbiology/metabolism ; Homeostasis ; Fecal Microbiota Transplantation/methods ; Macrophage Activation ; Humans ; Mice, Inbred C57BL ; Feces/microbiology ; }, abstract = {INTRODUCTION: Diarrheic disease is a common intestinal health problem worldwide, causing great suffering to humans and animals. Precise manipulation strategies based on probiotics to combat diarrheic diseases have not been fully developed.

OBJECTIVES: The aim of this study was to investigate the molecular mechanisms by which probiotics manipulate macrophage against diarrheic disease.

METHODS: Metagenome reveals gut microbiome profiles of healthy and diarrheic piglets. Fecal microbial transplantation (FMT) was employed to explore the causal relationship between gut microbes and diarrhea. The protective role of probiotics and their derived extracellular vesicles (EVs) was investigated in ETEC K88-infected mice. Macrophage depletion was performed to assess the role of macrophages in EVs against diarrhea. Execution of in vitro cell co-culture and transcriptome analyses elucidated the molecular mechanisms by which EVs modulate the macrophage and intestinal epithelial barrier.

RESULTS: Escherichia coli was enriched in weaned diarrheic piglets, while Lactobacillus johnsonii (L. john) showed a negative correlation with Escherichia coli. The transmission of diarrheic illness symptoms was achieved by transferring fecal microbiota, but not metabolites, from diarrheic pigs to germ-free (GF) mice. L. john's intervention prevented the transmission of disease phenotypes from diarrheic piglets to GF mice. L. john also reduces the gut inflammation induced by ETEC K88. The EVs secreted by L. john demonstrated enhanced efficacy in mitigating the adverse impacts induced by ETEC K88 through the modulation of macrophage phenotype. In vitro experiments have revealed that EVs activate M2 macrophages in a manner that shuts down ERK, thereby inhibiting NLRP3 activation in intestinal epithelial cells.

CONCLUSION: Our results reveal that intestinal microbiota drives the onset of diarrheic disease and that probiotic-derived EVs ameliorate diarrheic disease symptoms by modulating macrophage phenotypes. These findings can enhance the advancement of innovative therapeutic approaches for diarrheic conditions based on probiotic-derived EVs.}, } @article {pmid40040342, year = {2025}, author = {Ren, M and Hu, A and Zhao, Z and Yao, X and Kimirei, IA and Zhang, L and Wang, J}, title = {Trait-environmental relationships reveal microbial strategies of environmental adaptation.}, journal = {Ecology}, volume = {106}, number = {3}, pages = {e70047}, doi = {10.1002/ecy.70047}, pmid = {40040342}, issn = {1939-9170}, support = {BK20240111//Basic Research Program of Jiangsu/ ; 067GJHZ2023034MI//the International Collaboration Program of Chinese Academy of Sciences/ ; 151542KYSB20210007//the International Collaboration Program of Chinese Academy of Sciences/ ; SAJC202403//the International Collaboration Program of Chinese Academy of Sciences/ ; 42002304//National Natural Science Foundation of China/ ; 42107445//National Natural Science Foundation of China/ ; 42225708//National Natural Science Foundation of China/ ; 42372353//National Natural Science Foundation of China/ ; 92251304//National Natural Science Foundation of China/ ; 92351303//National Natural Science Foundation of China/ ; }, mesh = {*Lakes/microbiology ; *Adaptation, Physiological ; *Bacteria/classification/genetics ; Bacterial Physiological Phenomena ; Microbiota ; Hydrogen-Ion Concentration ; }, abstract = {Microbial trait variation along environmental gradients is crucial to understanding their ecological adaptation mechanisms. With the increasing availability of microbial genomes, making full use of the genome-based traits to decipher their adaptation strategies becomes promising and urgent. Here, we examined microbial communities in water and sediments of 20 East African lakes with pH values ranging from 7.2 to 10.1 through taxonomic profiling and genome-centric metagenomics. We identified functional traits important for microbial adaptation to the stresses of alkalinity and salinity based on the significant trait-environment relationships (TERs), including those involved in cytoplasmic pH homeostasis, compatible solute accumulation, cell envelope modification, and energy requisition. By integrating these significant traits, we further developed an environmental adaptation index to quantify the species-level adaptive capacity for environmental stresses, such as high pH environments. The adaptation index of pH showed consistently significant positive relationships with species pH optima across regional and global genomic datasets from freshwater, marine, and soda lake ecosystems. The generality of the index for quantifying environmental adaptation was demonstrated by showing significant relationships with the species niche optima for the gradients of soil temperature and seawater salinity. These results highlight the importance of TERs in facilitating the inference of microbial genomic-based adaptation mechanisms and expand our understanding of ecological adaptive strategies along environmental gradients.}, } @article {pmid40038838, year = {2025}, author = {Thiruppathy, D and Moyne, O and Marotz, C and Williams, M and Navarro, P and Zaramela, L and Zengler, K}, title = {Absolute quantification of the living skin microbiome overcomes relic-DNA bias and reveals specific patterns across volunteers.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {65}, pmid = {40038838}, issn = {2049-2618}, support = {S10 OD026929/NH/NIH HHS/United States ; S10 OD026929/NH/NIH HHS/United States ; }, mesh = {Humans ; *Skin/microbiology ; *Microbiota/genetics ; *DNA, Bacterial/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Bacterial Load ; Healthy Volunteers ; Adult ; Female ; Male ; }, abstract = {BACKGROUND: As the first line of defense against external pathogens, the skin and its resident microbiota are responsible for protection and eubiosis. Innovations in DNA sequencing have significantly increased our knowledge of the skin microbiome. However, current characterizations do not discriminate between DNA from live cells and remnant DNA from dead organisms (relic DNA), resulting in a combined readout of all microorganisms that were and are currently present on the skin rather than the actual living population of the microbiome. Additionally, most methods lack the capability for absolute quantification of the microbial load on the skin, complicating the extrapolation of clinically relevant information.

RESULTS: Here, we integrated relic-DNA depletion with shotgun metagenomics and bacterial load determination to quantify live bacterial cell abundances across different skin sites. Though we discovered up to 90% of microbial DNA from the skin to be relic DNA, we saw no significant effect of this on the relative abundances of taxa determined by shotgun sequencing. Relic-DNA depletion prior to sequencing strengthened underlying patterns between microbiomes across volunteers and reduced intraindividual similarity. We determined the absolute abundance and the fraction of population alive for several common skin taxa across body sites and found taxa-specific differential abundance of live bacteria across regions to be different from estimates generated by total DNA (live + dead) sequencing.

CONCLUSIONS: Our results reveal the significant bias relic DNA has on the quantification of low biomass samples like the skin. The reduced intraindividual similarity across samples following relic-DNA depletion highlights the bias introduced by traditional (total DNA) sequencing in diversity comparisons across samples. The divergent levels of cell viability measured across different skin sites, along with the inconsistencies in taxa differential abundance determined by total vs live cell DNA sequencing, suggest an important hypothesis for certain sites being susceptible to pathogen infection. Overall, our study demonstrates a characterization of the skin microbiome that overcomes relic-DNA bias to provide a baseline for live microbiota that will further improve mechanistic studies of infection, disease progression, and the design of therapies for the skin. Video Abstract.}, } @article {pmid40038315, year = {2025}, author = {Chen, Y and Chen, S and Tao, J and Li, M and Wang, W and Chen, M and Fang, X and Kong, L and Wang, Y and Pereira, O and Zhang, C}, title = {Multi-omic stock of surface ocean microbiome built by monthly, weekly and daily sampling in Dapeng Bay, China.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {378}, pmid = {40038315}, issn = {2052-4463}, support = {32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; RCBS20221008093229035//Shenzhen Science and Technology Innovation Commission/ ; 92351301//École Nationale d'Ingénieurs de Saint-Etienne (National Engineering School of Saint-Étienne)/ ; }, mesh = {China ; *Microbiota ; *Archaea/genetics ; *Bacteria/genetics/classification ; *Bays ; Seawater/microbiology ; Metagenome ; Multiomics ; }, abstract = {The coastal ocean is the dynamic interface where terrestrial, atmospheric, and marine systems converge, acting as a hotspot for microbial activity, which underpins the intricate web of carbon and nitrogen cycling. Dapeng Bay, a typical semi-enclosed bay along the southern coastline of China, is strongly influenced by monsoon climates and human activities. Despite its ecological importance, long-term observations and investigations into the microbial community structure in this region are notably lacking. To address this gap, we conducted a two-year continuous sampling from May 2021 to June 2023 to explore shifts in nearshore surface microbial communities and assess the long-term effects of environmental stressors. This study presents comprehensive amplicon, metagenomic, and metatranscriptomic information. We identified 3,600 amplicon sequence variants and recovered 1,216 high-quality metagenome-assembled MAGs, representing 17 bacterial and 3 archaeal phyla. Additionally, 587 MAGs were correlated with transcriptional activity, comprising 539 bacterial and 48 archaeal populations. This dataset is anticipated to provide a multi-dimensional perspective, enhancing our understanding of the complexity, dynamics, and adaptability of microbial communities in coastal environments.}, } @article {pmid40038282, year = {2025}, author = {Li, Z and Riley, WJ and Marschmann, GL and Karaoz, U and Shirley, IA and Wu, Q and Bouskill, NJ and Chang, KY and Crill, PM and Grant, RF and King, E and Saleska, SR and Sullivan, MB and Tang, J and Varner, RK and Woodcroft, BJ and Wrighton, KC and , and Brodie, EL}, title = {A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2186}, pmid = {40038282}, issn = {2041-1723}, support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; SCW1746//DOE | Office of Science (SC)/ ; DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; (#FP00005182//DOE | Office of Science (SC)/ ; 2022070//National Science Foundation (NSF)/ ; }, mesh = {*Ecosystem ; *Methane/metabolism ; *Genomics/methods ; *Microbiota/genetics ; Arctic Regions ; Metagenomics/methods ; Wetlands ; Greenhouse Gases/metabolism ; Climate Change ; Bacteria/genetics/metabolism/classification ; }, abstract = {Microbes drive the biogeochemical cycles of earth systems, yet the long-standing goal of linking emerging genomic information, microbial traits, mechanistic ecosystem models, and projections under climate change has remained elusive despite a wealth of emerging genomic information. Here we developed a general genome-to-ecosystem (G2E) framework for integrating genome-inferred microbial kinetic traits into mechanistic models of terrestrial ecosystems and applied it at a well-studied Arctic wetland by benchmarking predictions against observed greenhouse gas emissions. We found variation in genome-inferred microbial kinetic traits resulted in large differences in simulated annual methane emissions, quantitatively demonstrating that the genomically observable variations in microbial capacity are consequential for ecosystem functioning. Applying microbial community-aggregated traits via genome relative-abundance-weighting gave better methane emissions predictions (i.e., up to 54% decrease in bias) compared to ignoring the observed abundances, highlighting the value of combined trait inferences and abundances. This work provides an example of integrating microbial functional trait-based genomics, mechanistic and pragmatic trait parameterizations of diverse microbial metabolisms, and mechanistic ecosystem modeling. The generalizable G2E framework will enable the use of abundant microbial metagenomics data to improve predictions of microbial interactions in many complex systems, including oceanic microbiomes.}, } @article {pmid39719110, year = {2025}, author = {Koné, A and Kané, F and Neal, A and Konate, I and Coulibaly, B and Dabitao, DK and Diarra, B and Sanogo, I and Sarro, YDS and Coulibaly, TA and Diallo, D and Samake, S and Dicko, I and Diallo, M and Diarra, A and Coulibaly, MD and Keita, D and Coulibaly, N and Koloma, I and Perou, M and Diarra, HB and Cisse, BE and Togo, ACG and Coulibaly, G and Traoré, FG and Sanogo, M and Diakité, M and Aboulhab, J and Akpa, E and Fouth-Tchos, K and Shaw-Saliba, K and Collins, J and Lu, XJ and Nischay, M and Wickiser, JK and Briese, T and Lipkin, WI and Chen, RY and Doumbia, S and Dao, S}, title = {Adding Virome Capture Metagenomic Sequencing to Conventional Laboratory Testing Increases Unknown Fever Etiology Determination in Bamako, Mali.}, journal = {The American journal of tropical medicine and hygiene}, volume = {112}, number = {3}, pages = {626-635}, doi = {10.4269/ajtmh.24-0449}, pmid = {39719110}, issn = {1476-1645}, mesh = {Humans ; Mali/epidemiology ; Male ; Female ; Child ; Adolescent ; Child, Preschool ; Adult ; *Metagenomics/methods ; Young Adult ; Middle Aged ; *Fever of Unknown Origin/diagnosis/virology ; Infant ; Virome ; Measles virus/genetics/isolation & purification/classification ; Metagenome ; Measles/diagnosis/virology ; COVID-19/diagnosis/virology ; SARS-CoV-2/genetics/isolation & purification ; Aged ; }, abstract = {Unexplained fever poses significant diagnostic challenges in resource-limited settings like Bamako, Mali, where overlapping endemic diseases include malaria, HIV/AIDS, yellow fever, typhoid, and others. This study aimed to elucidate the infectious etiologies of acute febrile illnesses in this context. Acute febrile patients of any age were enrolled after informed consent or assent. Baseline clinical and demographic data were collected, and samples were analyzed by using rapid diagnostic tests, reverse transcriptase polymerase chain reaction, ELISA, and virus-targeted metagenomic sequencing (virome capture sequencing platform for vertebrate viruses [VirCapSeq-VERT]). Among 108 enrolled subjects, most were male (51.9%) and under 15 years old (56.5%). Measles virus was identified in 39.8% of cases, primarily among children. Other findings included Plasmodium spp. (12%), Salmonella spp. (13%), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; 8.7%). The virome capture sequencing platform for vertebrate viruses was used for 101 subjects, corroborating many routine test results and identifying additional cases of measles virus (1), SARS-CoV-2 (5), and numerous other agents. Notably, nearly all subjects showed evidence of herpesviruses (90%) and anelloviruses (98%). Hemorrhagic fever viruses were not observed. With the inclusion of VirCapSeq-VERT, identifiable pathogens were found in 79.6% of cases, leaving 20.4% without a clear etiology. The identification of more than one concurrent pathogen was common (41.5%). Integrating metagenomic sequencing with routine laboratory diagnostic testing enhances the detection of pathogens in acute febrile illnesses, highlighting its potential value in identifying infectious etiologies in resource-limited settings.}, } @article {pmid38892504, year = {2024}, author = {Duysburgh, C and Govaert, M and Guillemet, D and Marzorati, M}, title = {Co-Supplementation of Baobab Fiber and Arabic Gum Synergistically Modulates the In Vitro Human Gut Microbiome Revealing Complementary and Promising Prebiotic Properties.}, journal = {Nutrients}, volume = {16}, number = {11}, pages = {}, pmid = {38892504}, issn = {2072-6643}, mesh = {*Gastrointestinal Microbiome ; *Prebiotics ; *Gum Arabic/therapeutic use ; *Adansonia ; *Plant Preparations/therapeutic use ; Metabolome ; Metagenome ; Colon/microbiology ; }, abstract = {Arabic gum, a high molecular weight heteropolysaccharide, is a promising prebiotic candidate as its fermentation occurs more distally in the colon, which is the region where most chronic colonic diseases originate. Baobab fiber could be complementary due to its relatively simple structure, facilitating breakdown in the proximal colon. Therefore, the current study aimed to gain insight into how the human gut microbiota was affected in response to long-term baobab fiber and Arabic gum supplementation when tested individually or as a combination of both, allowing the identification of potential complementary and/or synergetic effects. The validated Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]), an in vitro gut model simulating the entire human gastrointestinal tract, was used. The microbial metabolic activity was examined, and quantitative 16S-targeted Illumina sequencing was used to monitor the gut microbial composition. Moreover, the effect on the gut microbial metabolome was quantitatively analyzed. Repeated administration of baobab fiber, Arabic gum, and their combination had a significant effect on the metabolic activity, diversity index, and community composition of the microbiome present in the simulated proximal and distal colon with specific impacts on Bifidobacteriaceae and Faecalibacterium prausnitzii. Despite the lower dosage strategy (2.5 g/day), co-supplementation of both compounds resulted in some specific synergistic prebiotic effects, including a biological activity throughout the entire colon, SCFA synthesis including a synergy on propionate, specifically increasing abundance of Akkermansiaceae and Christensenellaceae in the distal colon region, and enhancing levels of spermidine and other metabolites of interest (such as serotonin and ProBetaine).}, } @article {pmid40038255, year = {2025}, author = {Cui, B and Luo, H and He, B and Liu, X and Lv, D and Zhang, X and Su, K and Zheng, S and Lu, J and Wang, C and Yang, Y and Zhao, Z and Liu, X and Wang, X and Zhao, Y and Nie, X and Jiang, Y and Zhang, Z and Liu, C and Chen, X and Cai, A and Lv, Z and Liu, Z and An, F and Zhang, Y and Yan, Q and Kelley, KW and Xu, G and Xu, L and Liu, Q and Peng, F}, title = {Gut dysbiosis conveys psychological stress to activate LRP5/β-catenin pathway promoting cancer stemness.}, journal = {Signal transduction and targeted therapy}, volume = {10}, number = {1}, pages = {79}, pmid = {40038255}, issn = {2059-3635}, support = {82373096//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82473131//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Low Density Lipoprotein Receptor-Related Protein-5/genetics/metabolism ; Animals ; Mice ; *Gastrointestinal Microbiome ; Humans ; *Dysbiosis/genetics/microbiology/metabolism ; Female ; *beta Catenin/genetics/metabolism ; *Stress, Psychological/genetics/microbiology/metabolism ; Neoplastic Stem Cells/metabolism/pathology ; Wnt Signaling Pathway/genetics ; Breast Neoplasms/genetics/metabolism/pathology/microbiology ; }, abstract = {Psychological stress causes gut microbial dysbiosis and cancer progression, yet how gut microbiota determines psychological stress-induced tumor development remains unclear. Here we showed that psychological stress promotes breast tumor growth and cancer stemness, an outcome that depends on gut microbiota in germ-free and antibiotic-treated mice. Metagenomic and metabolomic analyses revealed that psychological stress markedly alters the composition and abundance of gut microbiota, especially Akkermansia muciniphila (A. muciniphila), and decreases short-chain fatty acid butyrate. Supplement of active A. muciniphila, butyrate or a butyrate-producing high fiber diet dramatically reversed the oncogenic property and anxiety-like behavior of psychological stress in a murine spontaneous tumor model or an orthotopic tumor model. Mechanistically, RNA sequencing analysis screened out that butyrate decreases LRP5 expression to block the activation of Wnt/β-catenin signaling pathway, dampening breast cancer stemness. Moreover, butyrate as a HDAC inhibitor elevated histone H3K9 acetylation level to transcriptionally activate ZFP36, which further accelerates LRP5 mRNA decay by binding adenine uridine-rich (AU-rich) elements of LRP5 transcript. Clinically, fecal A. muciniphila and serum butyrate were inversely correlated with tumoral LRP5/β-catenin expression, poor prognosis and negative mood in breast cancer patients. Altogether, our findings uncover a microbiota-dependent mechanism of psychological stress-triggered cancer stemness, and provide both clinical biomarkers and potential therapeutic avenues for cancer patients undergoing psychological stress.}, } @article {pmid40037564, year = {2025}, author = {Miller, SJ and Zhang, F and Taylor, S and Woodman, R and Shoubridge, AP and Papanicolas, LE and Rogers, GB}, title = {Oropharyngeal Staphylococcus aureus is linked to higher mortality in long-term aged care residents.}, journal = {Age and ageing}, volume = {54}, number = {3}, pages = {}, doi = {10.1093/ageing/afaf042}, pmid = {40037564}, issn = {1468-2834}, support = {//Australian Medical Research Future Fund/ ; GNT1152268//Australian Department of Health/ ; //Australian Department of Health/ ; GNT119378//National Health and Medical Research Council/ ; //Matthew Flinders Professorial Fellowship/ ; GNT2008625//NHMRC Emerging Leadership/ ; }, mesh = {Humans ; Male ; Female ; *Staphylococcal Infections/mortality/microbiology/diagnosis ; Aged, 80 and over ; Aged ; *Staphylococcus aureus/isolation & purification ; *Oropharynx/microbiology ; *Homes for the Aged/statistics & numerical data ; Risk Factors ; South Australia/epidemiology ; Nursing Homes/statistics & numerical data ; Age Factors ; Long-Term Care/statistics & numerical data ; Carrier State/microbiology/diagnosis ; Time Factors ; Metagenomics ; Microbiota ; Comorbidity ; Cause of Death ; Risk Assessment ; Methicillin-Resistant Staphylococcus aureus/isolation & purification ; }, abstract = {BACKGROUND: Biological ageing, healthcare interactions, and pharmaceutical and environmental exposures in later life alter the characteristics of the oropharyngeal (OP) microbiome. These changes, including an increased susceptibility to colonisation by pathobiont species, have been linked with diverse health outcomes.

OBJECTIVES: To investigate the relationship between OP microbiome characteristics and all-cause mortality in long-term aged care residents.

METHODS: OP swabs were collected from 190 residents of five aged care facilities in South Australia. Microbiota composition was assessed by shotgun metagenomics and related to health outcomes during a 12-month follow-up period. OP carriage of Staphylococcus aureus and methicillin resistance was confirmed by qPCR.

RESULTS: OP carriage of S. aureus was identified in 13 (6.8%) residents. Detection of S. aureus was significantly associated with an increased risk of mortality (adjusted HR [95% CI]: 9.7 [3.8-24.9], P < .0001), compared with non-carriers, independent of methicillin resistance. Staphylococcus aureus carriage demonstrated a stronger association with mortality risk than the total number of comorbidities at the univariate level (S. aureus HR [95% CI]: 7.2 [3.4-15.5], P < .0001 vs. comorbidity count HR [95% CI]: 1.1 [1.0-1.3], P = .03), and remained significant after multivariable adjustment. Staphylococcus aureus detection was significantly associated with total number of comorbidities (adjusted OR [95% CI]: 1.4 [1.0-2.0], P = .04).

CONCLUSION: OP S. aureus carriage predicts all-cause mortality in long-term aged care. We speculate that S. aureus carriage represents a marker of general health, including prior healthcare exposures. OP S. aureus carriage could contribute to estimations of general health in older individuals and thereby inform care strategies.}, } @article {pmid40036691, year = {2025}, author = {Gao, Y and Luo, H and Lyu, H and Yang, H and Yousuf, S and Huang, S and Liu, YX}, title = {Benchmarking short-read metagenomics tools for removing host contamination.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, doi = {10.1093/gigascience/giaf004}, pmid = {40036691}, issn = {2047-217X}, support = {2024M753580//China Postdoctoral Science Foundation/ ; U23A20148//National Natural Science Foundation of China/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; }, mesh = {*Metagenomics/methods ; *Benchmarking ; Microbiota/genetics ; Humans ; DNA Contamination ; Metagenome ; Software ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Reproducibility of Results ; }, abstract = {BACKGROUND: The rapid evolution of metagenomic sequencing technology offers remarkable opportunities to explore the intricate roles of microbiome in host health and disease, as well as to uncover the unknown structure and functions of microbial communities. However, the swift accumulation of metagenomic data poses substantial challenges for data analysis. Contamination from host DNA can substantially compromise result accuracy and increase additional computational resources by including nontarget sequences.

RESULTS: In this study, we assessed the impact of computational host DNA decontamination on downstream analyses, highlighting its importance in producing accurate results efficiently. We also evaluated the performance of conventional tools like KneadData, Bowtie2, BWA, KMCP, Kraken2, and KrakenUniq, each offering unique advantages for different applications. Furthermore, we highlighted the importance of an accurate host reference genome, noting that its absence negatively affected the decontamination performance across all tools.

CONCLUSIONS: Our findings underscore the need for careful selection of decontamination tools and reference genomes to enhance the accuracy of metagenomic analyses. These insights provide valuable guidance for improving the reliability and reproducibility of microbiome research.}, } @article {pmid40032396, year = {2025}, author = {Zimmermann, P and Kurth, S and Giannoukos, S and Stocker, M and Bokulich, NA}, title = {NapBiome trial: Targeting gut microbiota to improve sleep rhythm and developmental and behavioural outcomes in early childhood in a birth cohort in Switzerland - a study protocol.}, journal = {BMJ open}, volume = {15}, number = {3}, pages = {e092938}, doi = {10.1136/bmjopen-2024-092938}, pmid = {40032396}, issn = {2044-6055}, mesh = {Humans ; *Gastrointestinal Microbiome ; Switzerland ; Infant ; Infant, Newborn ; *Sleep/physiology ; Double-Blind Method ; Child Development ; Infant, Premature ; Child, Preschool ; Brain-Gut Axis ; Female ; Randomized Controlled Trials as Topic ; Male ; Probiotics/therapeutic use ; Multicenter Studies as Topic ; }, abstract = {INTRODUCTION: The gut-brain axis plays a crucial role in the regulation and development of psychological and physical processes. The first year of life is a critical period for the development of the gut microbiome, which parallels important milestones in establishing sleep rhythm and brain development. Growing evidence suggests that the gut microbiome influences sleep, cognition and early neurodevelopment. For term-born and preterm-born infants, difficulties in sleep regulation may have consequences on health. Identifying effective interventions on the gut-brain axis in early life is likely to have long-term implications for the health and development of at-risk infants.

METHODS AND ANALYSES: In this multicentre, four-group, double-blinded, placebo (PLC)-controlled randomised trial with a factorial design, 120 preterm-born and 260 term-born infants will be included. The study will investigate whether the administration of daily synbiotics or PLC for a duration of 3 months improves sleep patterns and neurodevelopmental outcomes up to 2 years of age. The trial will also: (1) determine the association between gut microbiota, sleep patterns and health outcomes in children up to 2 years of age; and (2) leverage the interactions between gut microbiota, brain and sleep to develop new intervention strategies for at-risk infants.

ETHICS AND DISSEMINATION: The NapBiome trial has received ethical approval by the Committee of Northwestern and Central Switzerland and Canton Vaud, Switzerland (#2024-01681). Outcomes will be disseminated through publication and will be presented at scientific conferences. Metagenomic data will be shared through the European Nucleotide Archive.

TRIAL REGISTRATION NUMBER: The US National Institutes of Health NCT06396689.}, } @article {pmid40030030, year = {2025}, author = {Ghimire, S and Lehman, PC and Aguilar Meza, LS and Shahi, SK and Hoang, J and Olalde, H and Paullus, M and Cherwin, C and Wang, K and Gill, C and Cho, T and Mangalam, AK}, title = {Specific microbial ratio in the gut microbiome is associated with multiple sclerosis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {10}, pages = {e2413953122}, doi = {10.1073/pnas.2413953122}, pmid = {40030030}, issn = {1091-6490}, support = {R01AI137075//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1I01CX002212//U.S. Department of Veterans Affairs (VA)/ ; P30 ES005605/ES/NIEHS NIH HHS/United States ; T32AI007260//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {*Gastrointestinal Microbiome ; *Multiple Sclerosis/microbiology ; Animals ; Humans ; Mice ; Female ; *Dysbiosis/microbiology ; *Feces/microbiology ; Male ; Akkermansia ; Adult ; Encephalomyelitis, Autoimmune, Experimental/microbiology ; Middle Aged ; Bifidobacterium ; Prevotella/isolation & purification ; Mice, Inbred C57BL ; Case-Control Studies ; }, abstract = {Gut microbiota dysbiosis is associated with multiple sclerosis (MS), but the causal relationship between specific gut bacteria and MS pathogenesis remains poorly understood. Therefore, we profiled the stool microbiome of people with MS (PwMS) and healthy controls (HC) using shotgun metagenomic sequencing. PwMS showed a distinct microbiome compared to HC, with Prevotella copri (PC) and Blautia species as drivers of microbial communities in HC and PwMS, respectively. Administration of MS-driving Blautia species (Blautia wexlerae; BW) to mice resulted in increased levels of gut inflammatory markers and altered microbiota with increased capacity to induce proinflammatory cytokines. Utilizing experimental autoimmune encephalomyelitis (EAE), an animal model of MS, we identified a lower gut Bifidobacterium to Akkermansia ratio as a hallmark of the disease. BW-administered mice also showed a lower Bifidobacterium to Akkermansia ratio pre-EAE induction which correlated with increased disease severity post-EAE induction. The importance of the Bifidobacterium to Akkermansia ratio at the species level, lower Bifidobacterium adolescentis to Akkermansia muciniphila (BA:AM), was validated in our MS cohort and a large International Multiple Sclerosis Microbiome Study. Thus, our findings highlight the BA:AM ratio as a potential gut microbial marker in PwMS, opening avenues for microbiome-based diagnosis, prognosis, and therapy in MS.}, } @article {pmid40028749, year = {2025}, author = {Salahi, A and Abd El-Ghany, WA}, title = {A Spotlight on Archaea in Humans, Livestock and Poultry: A Review.}, journal = {Veterinary medicine and science}, volume = {11}, number = {2}, pages = {e70263}, pmid = {40028749}, issn = {2053-1095}, mesh = {Animals ; *Archaea/physiology ; Humans ; *Poultry ; Livestock ; Gastrointestinal Microbiome ; }, abstract = {The microbiota includes prokaryotes (archaea and bacteria) and eukaryotes. Archaea are single-celled prokaryotes and essential part of gut microbiome. Researches on archaea in ruminants and humans are more than mono-gastric. The low abundance of archaea in the gut depends on the method used (metagenomics or meta-transcriptomic) and age of people or poultry. The lack of complete recognition of archaea is due to their small number and method of identifying them (16S rRNA gene primers). The uses of archaea include analytical kit, reduce oil pollution, archaeosomes or drugs production, vaccines agents, lipid carriers in the pharmaceutical industry and molybdenum extraction in the nuclear industry. The nutritional functions of methanogenic archaea including feed utilization (ruminants) and efficiency, hydrogen reducing (human), fat deposition and enhancement of energy harvesting in mice, CAZymes genes, cecal fermentation, syntrophic potential, carotenoid source and improved transit time and appetite and SCFAs production. Archaea acting as antibiotics (produce archaeocins, sulfolobicins and halocin KPS1) and as probiotics (archaeobiotics) can reduce TMAU (trimethylaminuria) disease, cardiovascular diseases (CVDs), and atherosclerosis, brain abscess, cancer, colorectal cancer, inflammatory bowel disease (IBD), constipation, obesity, food allergies, asthma and anti-inflammation which can be prevented by using archaea, and other functions include energy homeostasis, heat shock protein (HSP) production and reducing aging.}, } @article {pmid39999861, year = {2025}, author = {Mejia, G and Jara-Servin, A and Hernández-Álvarez, C and Romero-Chora, L and Peimbert, M and Cruz-Ortega, R and Alcaraz, LD}, title = {Rhizosphere microbiome influence on tomato growth under low-nutrient settings.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {3}, pages = {}, doi = {10.1093/femsec/fiaf019}, pmid = {39999861}, issn = {1574-6941}, support = {DGAPA-PAPIIT-UNAM IN206824//Universidad Nacional Autónoma de México/ ; }, mesh = {*Solanum lycopersicum/microbiology/growth & development ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/growth & development/isolation & purification ; *Plant Roots/microbiology/growth & development ; Nutrients/metabolism ; Metagenomics ; Hydroponics ; Biomass ; }, abstract = {Studies have suggested that reduced nutrient availability enhances microbial diversity around plant roots, positively impacting plant productivity. However, the specific contributions of rhizosphere microbiomes in nutrient-poor environments still need to be better understood. This study investigates tomato (Solanum lycopersicum L.) root microbiome under low-nutrient conditions. Plants were grown in hydroponics with soil-derived microbial community inoculations. We hypothesized that nutrient limitation would increase the selection of beneficial bacterial communities, compensating for nutrient deficiencies. We identified 12 294 operational taxonomic units across treatments and controls using 16S rRNA gene sequencing. Increased plant biomass was observed in treatments compared to controls, suggesting a role for the microbiome in mitigating nutrient limitations. The relative abundance of genera such as Luteolibacter and Sphingopyxis relative abundance correlated with plant phenotypic traits (P ≤ .05), and their presence was further validated using shotgun metagenomics. We annotated 722 677 protein families and calculated a core set of 48 116 protein families shared across all treatments and assigned them into bacteria (93.7%) and eukaryota (6.2%). Within the core bacterial metagenome, we identified protein families associated with pathways involved in positive plant interactions like the nitrogen fixation. Limited nutrient availability enhanced plant productivity under controlled conditions, offering a path to reduce fertilizer use in agriculture.}, } @article {pmid39983489, year = {2025}, author = {Karlsson, M and Jönsson, HL and Hultberg, M}, title = {Inclusion of biochar in mushroom substrate influences microbial community composition of the substrate and elemental composition of the fruiting bodies.}, journal = {The Science of the total environment}, volume = {968}, number = {}, pages = {178914}, doi = {10.1016/j.scitotenv.2025.178914}, pmid = {39983489}, issn = {1879-1026}, mesh = {*Charcoal/chemistry ; *Fruiting Bodies, Fungal/chemistry ; *Microbiota ; Soil Microbiology ; Pleurotus ; Agaricales/chemistry ; Soil/chemistry ; Bacteria/classification ; }, abstract = {Due to its structure, biochar makes the soil porous and oxygen-rich, enhancing the water-holding capacity and increasing the cation exchange capacity for a longer duration. These aspects could also be favourable for mushroom production. However, biochar has been considerably less investigated within this context. This study investigated the impact of biochar on mushroom production, quality, and the microbial communities of the substrates. Two different biochar's produced from local feedstocks, plant- or sludge based, were evaluated in the production of oyster mushrooms (Pleurotus ostreatus) at two different concentrations (5 % and 10 %). The results showed that inclusion of biochar in the substrate negatively impacted fruiting body production. The elemental composition of the fruiting body was also affected by inclusion of biochar and partly reflected the elemental composition of the biochar. The metagenomics revealed that inclusion of biochar in the substrate altered the microbial community structure. The bacterial diversity based on Shannon indices was higher in the substrate wherein no biochar was added. Bacterial community richness (Chao 1) was higher in samples with biochar compared to the control with no added biochar. Fungal community richness based on Chao 1 indices displayed an increase in samples with an inclusion of biochar. Overall, this study provides novel insights into the impact of biochar in mushroom production regarding its concentration and the effect of the origin material of the biochar.}, } @article {pmid39946886, year = {2025}, author = {Shi, J and Zhang, Q and Sun, Y and Peng, Y and Wang, J and Wang, X}, title = {Microplastic induces microbial nitrogen limitation further alters microbial nitrogentransformation: Insights from metagenomic analysis.}, journal = {The Science of the total environment}, volume = {967}, number = {}, pages = {178825}, doi = {10.1016/j.scitotenv.2025.178825}, pmid = {39946886}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Nitrogen ; *Soil Pollutants ; *Microplastics ; *Metagenomics ; Microbiota/drug effects ; Nitrogen Cycle ; Bacteria/metabolism ; RNA, Ribosomal, 16S ; Soil/chemistry ; Biodegradation, Environmental ; }, abstract = {Microplastic has a significant impact on soil microbial communities, which play crucial roles in soil nitrogen (N) cycles. However, there is a limited understanding of their influences on genes associated with the entire N cycling pathways. Through a 120-day soil incubation using conventional (PE and PET) and biodegradable microplastics (PLA and PBAT), coupled with 16S rRNA and metagenomic sequencing, we investigated the responses of N-cycling genes to microplastics in two contrasting soils (i.e. black soil and loess soil). We found that biodegradable microplastics strongly altered microbial N functional profiles, and enhanced the abundance of numerous key genes involved in N fixation, organic N mineralization, N reduction, and denitrification. Furthermore, biodegradable microplastics significantly decreased net N mineralization (Nm) compared to control and conventional microplastic treatments, suggesting microbial N immobilization outweighed N mineralization. Analysis of the function-taxon bipartite network showed that the Nm was well predicted for the abundances and diversity of bacteria within specific modules, with Nm decreasing, the abundances of specific taxa in a given network modules increasing. These results indicated that biodegradable microplastics act as a carbon source to select specific taxa involved in enhancing N bioavailability (e.g., N fixation and organic N mineralization) to meet microbial N demand, which in turn filtered the bacterial community (decreased diversity but increased abundances) and gradually formed specific function-taxon modules. Comparing the two soils, microbes in the less fertile alkaline loess soil were more sensitive to biodegradable microplastics than those in the nutrient-rich acid black soil. Our study indicated that increasing usage of biodegradable plastics in the future may lead to accelerated soil microbial N limitation and transformation.}, } @article {pmid39946873, year = {2025}, author = {Feng, Y and Li, L and Ma, Q and Liu, S and Wang, P and Li, X and Ma, J}, title = {Effect of microcystin-LR on intestinal microbiota, metabolism, and health of zebrafish (Danio rerio).}, journal = {The Science of the total environment}, volume = {967}, number = {}, pages = {178838}, doi = {10.1016/j.scitotenv.2025.178838}, pmid = {39946873}, issn = {1879-1026}, mesh = {Animals ; *Zebrafish ; *Microcystins/toxicity/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Marine Toxins ; Male ; Water Pollutants, Chemical/toxicity ; Dysbiosis/chemically induced ; }, abstract = {Microcystin-LR (MC-LR) is typically produced along with the occurrence of cyanobacterial blooms, potentially exerting deleterious effects on intestinal microbiota and health in aquatic animals. To date, the underlying mechanism by which MC-LR affects intestinal health remains elusive. In this study, adult male zebrafish were exposed to MC-LR to assess its impact on the microbiome and metabolome. Histopathological and biochemical results indicated that MC-LR damaged intestinal villi and epithelial cells, induced intestinal barrier injury and inflammatory response. Metabolomics results revealed that MC-LR induced amino acid, carbohydrate, lipid, energy metabolisms dysbiosis, and specifically promoted glycine, serine and threonine metabolism. Metagenomics results demonstrated that MC-LR altered the composition of intestinal microbiota, and microbial function prediction suggested that MC-LR promoted the functions associated with amino acid, lipid, carbohydrate and energy metabolisms. Multiomics and Metorigin analyses jointly confirmed that glycine, serine and threonine metabolism was predominantly regulated by dominant Proteobacteria, Firmicutes, Fusobacteriota and Bacteroidota under MC-LR stress. This study offers a comprehensive perspective on the toxicity of microbiota and microbiota-derived metabolism in fish intestines induced by MC-LR and deepens our comprehension of the disruptive influence of MC-LR on intestinal homeostasis in organisms.}, } @article {pmid39932403, year = {2025}, author = {Momo Cabrera, P and Bokulich, NA and Zimmermann, P}, title = {Evaluating stool microbiome integrity after domestic freezer storage using whole-metagenome sequencing, genome assembly, and antimicrobial resistance gene analysis.}, journal = {Microbiology spectrum}, volume = {13}, number = {3}, pages = {e0227824}, doi = {10.1128/spectrum.02278-24}, pmid = {39932403}, issn = {2165-0497}, support = {PZPGP3_193140/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Feces/microbiology ; Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Child, Preschool ; *Specimen Handling/methods ; *Bacteria/genetics/classification/isolation & purification ; Infant ; Metagenomics/methods ; Freezing ; Drug Resistance, Bacterial/genetics ; Female ; Male ; }, abstract = {UNLABELLED: The gut microbiome is crucial for host health. Early childhood is a critical period for the development of a healthy gut microbiome, but it is particularly sensitive to external influences. Recent research has focused on using advanced techniques like shotgun metagenome sequencing to identify key microbial signatures and disruptions linked to disease. For accurate microbiome analysis, samples need to be collected and stored under specific conditions to preserve microbial integrity and composition, with -80°C storage considered the gold standard for stabilization. This study investigates the effect of domestic freezer storage on the microbial composition of stool samples obtained from 20 children under 4 years of age with the use of shotgun metagenome sequencing. Fresh stool samples were aliquoted into sterile tubes, with one aliquot stored at 4°C and analyzed within 24 hours, while others were frozen in domestic freezers (below -18°C) and analyzed after 1 week, 2 months, and 6 months. Assessments of contig assembly quality, microbial diversity, and antimicrobial resistance genes revealed no significant degradation or variation in microbial composition.

IMPORTANCE: Most prior studies on sample storage have relied on amplicon sequencing, which is less applicable to metagenome sequencing-given considerations of contig quality and functional gene detection-and less reliable in representing microbial composition. Moreover, the effects of domestic freezer storage for at-home stool collection on microbiome profiles, contig quality, and antimicrobial resistance gene profiles have not been previously investigated. Our findings suggest that stool samples stored in domestic freezers for up to 6 months maintain the integrity of metagenomic data. These findings indicate that domestic freezer storage does not compromise the integrity or reproducibility of metagenomic data, offering a reliable and accessible alternative for temporary sample storage. This approach enhances the feasibility of large-scale at-home stool collection and citizen science projects, even those focused on the more easily perturbed early life microbiome. This advancement enables more inclusive research into the gut microbiome, enhancing our understanding of its role in human health.}, } @article {pmid39929976, year = {2025}, author = {Sardar, P and Beresford-Jones, BS and Xia, W and Shabana, O and Suyama, S and Ramos, RJF and Soderholm, AT and Tourlomousis, P and Kuo, P and Evans, AC and Imianowski, CJ and Conti, AG and Wesolowski, AJ and Baker, NM and McCord, EAL and Okkenhaug, K and Whiteside, SK and Roychoudhuri, R and Bryant, CE and Cross, JR and Pedicord, VA}, title = {Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses.}, journal = {Nature microbiology}, volume = {10}, number = {3}, pages = {795-807}, pmid = {39929976}, issn = {2058-5276}, support = {206245/Z/17/Z//Wellcome Trust (Wellcome)/ ; 302351/Z/23/Z//Wellcome Trust (Wellcome)/ ; A2194//Rosetrees Trust/ ; EP/X024709/1//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {*Gastrointestinal Microbiome ; Animals ; Mice ; *Lipopolysaccharides/immunology ; *Immunotherapy/methods ; Humans ; *Melanoma/therapy/immunology/drug therapy ; Immune Checkpoint Inhibitors/pharmacology ; Mice, Inbred C57BL ; Bacteria/classification/genetics ; Feces/microbiology ; Female ; Toll-Like Receptor 4/metabolism ; Programmed Cell Death 1 Receptor/antagonists & inhibitors/metabolism/immunology ; Metagenome ; }, abstract = {The gut microbiome modulates immunotherapy treatment responses, and this may explain why immune checkpoint inhibitors, such as anti-PD-1, are only effective in some patients. Previous studies correlated lipopolysaccharide (LPS)-producing gut microbes with poorer prognosis; however, LPS from diverse bacterial species can range from immunostimulatory to inhibitory. Here, by functionally analysing faecal metagenomes from 112 patients with melanoma, we found that a subset of LPS-producing bacteria encoding immunostimulatory hexa-acylated LPS was enriched in microbiomes of clinical responders. In an implanted tumour mouse model of anti-PD-1 treatment, microbiota-derived hexa-acylated LPS was required for effective anti-tumour immune responses, and LPS-binding antibiotics and a small-molecule TLR4 antagonist abolished anti-PD-1 efficacy. Conversely, oral administration of hexa-acylated LPS to mice significantly augmented anti-PD-1-mediated anti-tumour immunity. Penta-acylated LPS did not improve anti-PD-1 efficacy in vivo and inhibited hexa-acylated LPS-induced immune activation in vitro. Microbiome hexa-acylated LPS therefore represents an accessible predictor and potential enhancer of immunotherapy responses.}, } @article {pmid39868792, year = {2025}, author = {Zhou, Z and Yang, M and Fang, H and Niu, Y and Lu, J and Ma, Y and Zhang, B and Zhu, H and Chen, P}, title = {Interspecies interactions mediated by arginine metabolism enhance the stress tolerance of Fusobacterium nucleatum against Bifidobacterium animalis.}, journal = {Microbiology spectrum}, volume = {13}, number = {3}, pages = {e0223524}, doi = {10.1128/spectrum.02235-24}, pmid = {39868792}, issn = {2165-0497}, support = {24ZDFA001//Gansu Provincial Science and Technology Major Project/ ; 2024-8-27,2024-8-30,2024-4-2//The Lanzhou Municipal Science and Technology Program/ ; 20240260001,20240260017//the College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; }, mesh = {Humans ; *Probiotics ; *Fusobacterium nucleatum/metabolism/genetics ; *Colorectal Neoplasms/microbiology/metabolism ; *Bifidobacterium animalis/metabolism/genetics ; *Arginine/metabolism ; Whole Genome Sequencing ; Phylogeny ; Male ; Dysbiosis/microbiology ; Gastrointestinal Microbiome ; Female ; Stress, Physiological ; Middle Aged ; }, abstract = {Colorectal cancer (CRC) is a common cancer accompanied by microbiome dysbiosis. Exploration of probiotics against oncogenic microorganisms is promising for CRC treatment. Here, differential microorganisms between CRC and healthy control were analyzed. Antibacterial experiments, whole-genome sequencing, and metabolic network reconstruction were combined to reveal the anti-Fusobacterium nucleatum mechanism, which was verified by co-culture assay and mendelian randomization analysis. Sequencing results showed that F. nucleatum was enriched in CRC, yet Bifidobacterium animalis decreased gradually from healthy to CRC. Additionally, F. nucleatum could be inhibited by B. animalis. Whole-genome sequencing of B. animalis showed high phylogenetic similarity with known probiotic strains and highlighted its functions for amino acid and carbohydrate metabolism. Metabolic network reconstruction demonstrated that cross-feeding and specific metabolites (acidic molecules, arginine) had a great influence on the coexistence relationship. Finally, the arginine supplement enhanced the competitive ability of F. nucleatum against B. animalis, and the mendelian randomization and metagenomic sequencing analysis confirmed the positive relationship among F. nucleatum, arginine metabolism, and CRC. Thus, whole-genome sequencing and metabolic network reconstruction are valuable for probiotic mining and patient dietary guidance.IMPORTANCEUsing probiotics to inhibit oncogenic microorganisms (Fusobacterium nucleatum) is promising for colorectal cancer (CRC) treatment. In this study, whole-genome sequencing and metabolic network reconstruction were combined to reveal the anti-F. nucleatum mechanism of Bifidobacterium animalis, which was verified by co-culture assay and mendelian randomization analysis. The result indicated that the arginine supplement enhanced the competitive ability of F. nucleatum, which may be harmful to F. nucleatum-infected CRC patients. B. animalis is a potential probiotic to relieve this dilemma. Thus, using in silico simulation methods based on flux balance analysis, such as genome-scale metabolic reconstruction, provides valuable insights for probiotic mining and dietary guidance for cancer patients.}, } @article {pmid39848515, year = {2025}, author = {Zhang, M and Bai, L and Yao, Z and Li, W and Yang, W}, title = {Seasonal lake ice cover drives the restructuring of bacteria-archaea and bacteria-fungi interdomain ecological networks across diverse habitats.}, journal = {Environmental research}, volume = {269}, number = {}, pages = {120907}, doi = {10.1016/j.envres.2025.120907}, pmid = {39848515}, issn = {1096-0953}, mesh = {*Lakes/microbiology ; *Ice Cover/microbiology ; *Bacteria ; *Seasons ; *Fungi ; *Archaea ; *Ecosystem ; Microbiota ; China ; Geologic Sediments/microbiology ; }, abstract = {The coexistence of different microbial communities is fundamental to the sustainability of many ecosystems, yet our understanding of the relationships among microbial communities in plateau cold-region lakes affected by seasonal ice cover remains limited. This research involved investigating three lakes in the Inner Mongolia segment of the Yellow River basin during frozen and unfrozen periods in two habitats: water bodies and sediments. The research examined the composition and function of bacteria, archaea, and fungi across different times and habitats within the basin, their response to environmental variables in water and sediment, and inter-domain interactions between bacteria-archaea and bacteria-fungi were compared using interdomain ecological network (IDEN). The findings indicate significant variations in the structures of bacterial, archaeal, and fungal communities across different periods and habitats, with the pH of the water body being a crucial environmental variable affecting microbial community composition. In the frozen period, the functionality of microbial communities, especially in terms of energy metabolism, was significantly impacted, with water bodies experiencing more pronounced effects than sediments. Archaea and fungi significantly contribute to the stability of bacterial communities across various habitats, especially in ice-covered conditions, where stronger associations between bacterial communities, archaea, and fungi promote the microbial communities' adaptability to cold stress. Furthermore, our results indicate that the primary environmental variable influencing the structure of IDENs is the nutrient salt content in both water bodies and sediments. This study broadens our understanding of the responses and feedback mechanisms of inter-domain microbial interactions in lakes influenced by seasonal ice cover.}, } @article {pmid39710261, year = {2025}, author = {Guerreiro, JF and Pires, AJ and Nunes, M and Esteves, A and Chambel, L and Pascoal, P and Pereira, M and Fangueiro, D and Tavares, L and Dias, R and Bexiga, R and Oliveira, M}, title = {Biochar supplementation affects the microbiome of recycled manure solids for cow bedding: A metagenomic analysis.}, journal = {Journal of dairy science}, volume = {108}, number = {3}, pages = {2620-2631}, doi = {10.3168/jds.2024-25616}, pmid = {39710261}, issn = {1525-3198}, mesh = {Animals ; Cattle ; *Manure/microbiology ; *Microbiota ; *Charcoal ; Female ; }, abstract = {The widespread use of recycled manure solids (RMS) as cow bedding material is not without risks, because cattle manure may act as a vehicle for pathogenic and antimicrobial-resistant bacteria dissemination. Thus, our aim was to evaluate RMS supplemented with a pine biochar produced in Portugal as a new cow bedding material, because the use of biochar has been shown to have the potential to mitigate the effect of relevant bacterial species when added to animal manure microbiota. Our experimental setup consisted on fresh RMS samples that were collected on a commercial dairy farm and placed in naturally-ventilated containers for a total of 4 groups: (1) nonsupplemented RMS, (2) RMS supplemented with 2.5% (wt/wt) of biochar, (3) RMS supplemented with 5% (wt/wt) of biochar, and (4) RMS supplemented with 10% (wt/wt) of biochar. Sampling was performed at 4 different incubation times (0, 5, 15, and 30 d) and in 2 distinct seasons: April through May (humid season) and June through July (dry season). The resulting 32 samples were subjected to DNA extraction and their microbiome profile determined through complete 16S rDNA gene sequencing using Nanopore next-generation sequencing. We observed that biochar supplementation clearly altered the microbiome of RMS, which was reflected in changes in populations' diversity and the relative abundance of relevant pathogenic bacteria. In particular, we found that long-term storage (30 d) was more beneficial than short-term storage, an effect that was more evident for samples supplemented with 2.5% or 5% biochar. In both seasons, those concentrations of biochar led to a decrease in the levels of several mastitis-causing agents (Enterobacteriaceae, streptococci, enterococci, and staphylococci). In addition, we also observed a reduction in the levels of Salmonella spp. and gram-positive bacilli in the biochar-supplemented samples. Unexpectedly, however, those same conditions yielded an increase in the abundance of Brucella spp., a group that includes important infectious agents, highlighting the need for a deeper evaluation of the effect of biochar supplementation of RMS to ensure the future safe and sustainable use of this environmentally-friendly resource in animal production.}, } @article {pmid39604579, year = {2025}, author = {Hao, Z and Lu, Y and Hao, Y and Luo, Y and Wu, K and Zhu, C and Shi, P and Zhu, F and Lin, Y and Zeng, X}, title = {Fungal mycobiome dysbiosis in choledocholithiasis concurrent with cholangitis.}, journal = {Journal of gastroenterology}, volume = {60}, number = {3}, pages = {340-355}, pmid = {39604579}, issn = {1435-5922}, support = {PWZxq2022-06//Key Disciplines Group Construction Project of Shanghai Pudong New Area Health Commission/ ; 82270636//National Natural Science Foundation of China/ ; 82070616//National Natural Science Foundation of China/ ; 82100608//National Natural Science Foundation of China/ ; PW2022D08//Joint Tackling Project of Pudong Health Committee of Shanghai/ ; PW2021A-38//Health and Family Planning Research Project of Pudong Health Committee of Shanghai/ ; PWYgf2021-02//Medical Discipline Construction Project of Pudong Health Committee of Shanghai/ ; 2022XD028//Talent Plan of the Shanghai Municipal Health Commission for Academic Leader/ ; }, mesh = {Humans ; *Dysbiosis/microbiology/complications ; Male ; Retrospective Studies ; Female ; Middle Aged ; Case-Control Studies ; *Gastrointestinal Microbiome ; *Cholangitis/microbiology ; *Choledocholithiasis/microbiology/complications ; *Mycobiome ; Aged ; Adult ; Fungi/isolation & purification/genetics ; Basidiomycota/isolation & purification ; }, abstract = {BACKGROUND: The gut mycobiome might have an important influence on the pathogenesis of choledocholithiasis concurrent with cholangitis (CC). The aim of this study was to characterize the fungal mycobiome profiles, explore the correlation and equilibrium of gut interkingdom network among bacteria-fungi-metabolites triangle in CCs.

METHODS: In a retrospective case-control study, we recruited patients with CC (n = 25) and healthy controls (HCs) (n = 25) respectively to analyze the gut fungal dysbiosis. Metagenomic sequencing was employed to characterize the gut mycobiome profiles, and liquid chromatography/mass spectrometry (LC/MS) analysis was used to quantify the metabolites composition.

RESULTS: The Shannon index displayed a reduction in fungal α-diversity in CCs compared to HCs (p = 0.041), and the overall fungal composition differed significantly between two groups. The dominant 7 fungi species with the remarkable altered abundance were identified (LDA score > 3.0, p < 0.05), including CC-enriched Aspergillus_niger and CC-depleted fungi Saccharomyces_boulardii. In addition, the correlations between CC-related fungi and clinical variables in CCs were analyzed. Moreover, the increased abundance ratio of Basidiomycota-to-Ascomycota and a dense linkage of bacteria-fungi interkingdom network in CCs were demonstrated. Finally, we identified 30 markedly altered metabolites in CCs (VIP > 1.0 and p < 0.05), including low level of acetate and butyrate, and the deeper understanding on the complexity of bacteria-fungi-metabolites triangle involving bile inflammation was verified.

CONCLUSION: Our investigation demonstrated a distinct gut fungal dysbiosis in CCs and proposed that, beyond bacteria, the more attention should be paid to significantly potential influence of fungi and bacteria-fungi-metabolites triangle interkingdom interactions on pathogenesis of CC.}, } @article {pmid39541261, year = {2025}, author = {Golob, J and Rao, K and Berinstein, JA and Singh, P and Chey, WD and Owyang, C and Kamada, N and Higgins, PDR and Young, V and Bishu, S and Lee, AA}, title = {Why Symptoms Linger in Quiescent Crohn's Disease: Investigating the Impact of Sulfidogenic Microbes and Sulfur Metabolic Pathways.}, journal = {Inflammatory bowel diseases}, volume = {31}, number = {3}, pages = {763-776}, doi = {10.1093/ibd/izae238}, pmid = {39541261}, issn = {1536-4844}, support = {K23 DK124567/DK/NIDDK NIH HHS/United States ; R03 DK139095/DK/NIDDK NIH HHS/United States ; /CCF/CCF/United States ; DK124567/NH/NIH HHS/United States ; /CCF/CCF/United States ; DK124567/NH/NIH HHS/United States ; }, mesh = {Humans ; *Crohn Disease/microbiology/metabolism ; Male ; Female ; *Feces/microbiology/chemistry ; Adult ; *Sulfur/metabolism ; *Gastrointestinal Microbiome ; Middle Aged ; *Metabolic Networks and Pathways ; Irritable Bowel Syndrome/metabolism/microbiology ; Case-Control Studies ; Quality of Life ; Metabolome ; }, abstract = {INTRODUCTION: Even in the absence of inflammation, persistent symptoms in patients with Crohn's disease (CD) are prevalent and worsen quality of life. We previously demonstrated enrichment in sulfidogenic microbes in quiescent Crohn's disease patients with (qCD + S) vs without persistent GI symptoms (qCD-S). Thus, we hypothesized that sulfur metabolic pathways would be enriched in stool while differentially abundant microbes would be associated with important sulfur metabolic pathways in qCD + S.

METHODS: We performed a multicenter observational study nested within SPARC IBD. Quiescent inflammation was defined by fecal calprotectin level < 150 mcg/g. Persistent symptoms were defined by CD-PRO2. Active CD (aCD) and non-IBD diarrhea-predominant irritable bowel syndrome (IBS-D) were included as controls.

RESULTS: Thirty-nine patients with qCD + S, 274 qCD-S, 21 aCD, and 40 IBS-D underwent paired shotgun metagenomic sequencing and untargeted metabolomic profiling. The fecal metabolome in qCD + S was significantly different relative to qCD-S and IBS-D but not aCD. Patients with qCD + S were enriched in sulfur-containing amino acid pathways, including cysteine and methionine, as well as serine, glycine, and threonine. Glutathione and nicotinate/nicotinamide pathways were also enriched in qCD + S relative to qCD-S, suggestive of mitochondrial dysfunction, a downstream target of H2S signaling. Multi-omic integration demonstrated that enriched microbes in qCD + S were associated with important sulfur metabolic pathways. Bacterial sulfur metabolic genes, including CTH, isfD, sarD, and asrC, were dysregulated in qCD + S. Finally, sulfur metabolites with and without sulfidogenic microbes showed good accuracy in predicting the presence of qCD + S.

DISCUSSION: Microbial-derived sulfur pathways and downstream mitochondrial function are perturbed in qCD + S, which implicate H2S signaling in the pathogenesis of this condition. Future studies will determine whether targeting H2S pathways results in improved quality of life in qCD + S.}, } @article {pmid40025414, year = {2025}, author = {Izhar, MZ and Nawaz, M and Yaqub, T and Avais, M}, title = {Effect of probiotic Lactobacillus plantarum CM49 on microbial profile and lactobacilli counts in milk of mastitic cattle.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {109}, pmid = {40025414}, issn = {1471-2180}, support = {PHEC/ARA/PIRCA/20211/9//Punjab Higher Education Commission, Pakistan/ ; }, mesh = {Animals ; *Probiotics/administration & dosage/pharmacology ; Cattle ; *Milk/microbiology ; Female ; *Lactobacillus plantarum/isolation & purification/genetics ; *Mastitis, Bovine/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacterial Load ; DNA, Bacterial/genetics ; Microbiota/drug effects ; Lactobacillus/isolation & purification/genetics/classification ; Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification/drug effects ; Streptococcus/genetics/isolation & purification/drug effects ; }, abstract = {BACKGROUND: Bovine mastitis is a common udder disease in cattle, mainly caused by bacteria and other infectious agents. Traditionally antibiotics are used for their treatment, but the development of antibiotic resistance has increased the importance of using non antibiotic alternative such as probiotic. In current study a previously in vitro characterized isolate Lactobacillus plantarum CM49 infused into two groups of cattle suffering from clinical mastitis (n = 5) and sub-clinical mastitis (n = 5).

RESULTS: The bacterial composition and diversity analysis of milk samples before and after probiotic administration was analyzed using 16S rRNA gene base metagenomic analysis and lactobacillus counts were also evaluated using Real time PCR. The results show that there was an increase in abundance of Proteobacteria and decrease in Firmicutes at phylum level in both groups while major mastitogens genera Staphylococcus and Streptococcus abundance was reduced after treatment in sub-clinical mastitis group (SCMG) and clinical mastitis group (CMG) respectively. Lactobacilli counts evaluated through Real time PCR showed an increase in number, furthermore diversity indices showed an increase in diversity after treatment with probiotic.

CONCLUSION: It is concluded from the results that Lactobacillus plantarum CM49 may serve as promising candidate for improving dysbiosis resulting from mastitis and improving microbial diversity.}, } @article {pmid40025399, year = {2025}, author = {Liu, A and Wu, J and Li, J and Li, Q and Zhao, N and Hu, K and Liu, S and Blaiotta, G and Zhou, J}, title = {Uncovering the microbial community dynamics and metabolic pathways of primary organic acids in Sichuan Baoning vinegar through metagenomics.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {3}, pages = {91}, pmid = {40025399}, issn = {1573-0972}, support = {No. 2024NSFSC2079//Science and Technology Department of Sichuan Province/ ; }, mesh = {*Acetic Acid/metabolism ; *Metagenomics ; *Fermentation ; China ; *Metabolic Networks and Pathways ; *Lactic Acid/metabolism ; *Microbiota ; Acetobacter/metabolism/genetics ; Bacteria/genetics/metabolism/classification ; Lactobacillus/metabolism/genetics ; Food Microbiology ; Phylogeny ; }, abstract = {Sichuan Baoning vinegar, a renowned traditional vinegar in China, exhibits a higher lactic acid content compared to acetic acid. The microbiota plays a crucial role in shaping the unique flavor of vinegar, but the species-level succession of key microorganisms and metabolic pathways of major organic acids in this vinegar are still unclear. This study utilized metagenomic sequencing to elucidate microbial succession during fermentation and the functional roles of the microbial community, as well as explore the metabolic network of lactic acid and acetic acid. Our findings revealed that bacteria dominated the fermentation process, with Acetilactobacillus jinshanensis, Lactobacillus amylovorus, and Limosilactobacillus sp. emerging as the top three species. Notably, Acetilactobacillus jinshanensis, Limosilactobacillus sp., Lactobacillus amylovorus, and Limosilactobacillus pontis were key players in lactic acid production, while acetic acid synthesis might be primarily driven by Lactobacillus amylovorus, Limosilactobacillus sp., Lactobacillus acetotolerans, and Acetobacter pasteurianus. This study enhances our understanding of the key microorganisms and organic acids metabolism in vinegar, shedding light on the fermentation mechanism of cereal vinegar.}, } @article {pmid40025082, year = {2025}, author = {Regmi, R and Anderson, J and Burgess, L and Mangelson, H and Liachko, I and Vadakattu, G}, title = {Shotgun and Hi-C Sequencing Datasets for Binning Wheat Rhizosphere Microbiome.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {367}, pmid = {40025082}, issn = {2052-4463}, mesh = {*Triticum/microbiology ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; Metagenome ; Metagenomics ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing ; Archaea/genetics ; South Australia ; }, abstract = {Binning is a crucial process in metagenomics studies, where sequenced reads are combined to form longer contigs and assigned to individual genomes. Conventional methods, such as shotgun binning, rely on similarity measurements and abundance profiles across multiple samples. However, cost constraints for sequencing and limited sample collection capacity hinder their effectiveness. High-throughput chromosome conformation capture (Hi-C), a DNA proximity ligation technique, has been adapted to accurately bin metagenome-assembled genomes (MAGs) from a single sample, addressing challenges like chimeric MAGs. In this study, we generated over 190 Gb of metagenomic data from wheat rhizospheres grown in two highly calcareous soils of South Australian region and compared conventional and Hi-C binning methods. Two shotgun metagenomes and Hi-C libraries were generated, assembling 1089 shotgun MAGs across 39 bacterial and one archaeal taxon, including 94 Hi-C based bins. Binning performed using only short read sequences was prone to high contamination, while the addition of Hi-C binning improved MAG quality and identified mobile element-host-infection interaction. This dataset provides important tools for studying microbial communities in wheat rhizosphere soils.}, } @article {pmid40023383, year = {2025}, author = {Zhang, Y and Zhang, H and Zhang, B}, title = {Biological and terrestrial influences on dissolved organic matter in Antarctic surface waters: insights from mass spectrometry and metagenomic analysis.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121252}, doi = {10.1016/j.envres.2025.121252}, pmid = {40023383}, issn = {1096-0953}, abstract = {Global warming increases the surface waters and biodiversity in polar regions. However, the intrinsic biological sources of dissolved organic matter (DOM) in Antarctic surface waters remain poorly understood. This work evaluated the sources and driving mechanisms of DOM in Antarctic lakes systematically, based on fluorescence excitation-emission matrices, ultrahigh-resolution mass spectra, biological detection, and metagenomic analyses. The most abundant DOM in the water was peptides (37.02%), which differed from those in soil (lignins: 26.33%) and penguin guano (lipids: 50.71%). The relative abundance of CHON and CHOP compounds in water was significantly correlated with the distance from the penguin colony (p < 0.05). Both the fluorescence and mass spectrum fingerprints of water and soil/faeces showed low similarities using end-member source tracking methods. This could be attributed to the facilitation of guano-derived nutrients and organic carbon to phytoplankton proliferation, whereas the concentrations of NH4[+]-N, NO3[-]-N, total phosphorus, and total organic carbon were significantly higher in the penguin-intensive area than in the other areas. Algae had significant positive effects on carbohydrates and amino sugars and positive effects on lignins, compared to zooplankton and bacteria. Zooplankton had significantly more positive effects on peptides than phytoplankton. Secondary bacterial metabolic activity can be positively linked with CHO compounds. Carbohydrates and amino sugars co-occurred with carbohydrate-active enzyme genes and nitrogen cycling genes in one module of the co-occurrence network, whereas the other module was characterised by the co-occurrence patterns of condensed aromatic structures with carbohydrate-active enzyme genes and nitrogen cycling genes. These results emphasise the roles of secondary metabolites from algae and bacteria in species-specific sources of DOM, shedding light on the driving mechanisms of the biogeochemical cycling of DOM in the Antarctic water environment.}, } @article {pmid40022370, year = {2025}, author = {Li, X and You, Y and Xue, B and Chen, J and Du, M and Ibrahim, A and Suo, H and Zhang, F and Zheng, J}, title = {Decoding microbiota and metabolite transformation in inoculated fermented suansun using metagenomics, GC-MS, non-targeted metabolomics, and metatranscriptomics:Impacts of different Lactobacillus plantarum strains.}, journal = {Food research international (Ottawa, Ont.)}, volume = {203}, number = {}, pages = {115847}, doi = {10.1016/j.foodres.2025.115847}, pmid = {40022370}, issn = {1873-7145}, mesh = {*Lactobacillus plantarum/metabolism/genetics ; *Metabolomics/methods ; *Fermentation ; *Gas Chromatography-Mass Spectrometry ; *Metagenomics/methods ; *Microbiota/physiology/genetics ; Flavoring Agents/metabolism ; Transcriptome ; Gene Expression Profiling ; Fermented Foods/microbiology ; Food Microbiology ; }, abstract = {Using metagenomics, GC-MS, non-targeted metabolomics, and metatranscriptomics, we investigated the microbial communities and metabolites in two different Lactobacillus plantarum fermentations. Metagenomics revealed Weissella cibaria dominantly contributed to the DACN766-fermented suansun (LPS1) and Lactiplantibacillus pentosus to the DACN760-fermented suansun (LPS2). GC-MS identified 38 and 40 flavor compounds in LPS1 and LPS2, respectively, with p-cresol, 4-hydroxybenzaldehyde, acetic acid, hexanal, and propionic acid crucial for aroma development. LPS2 exhibited higher levels of p-cresol and acetic acid, contributing to its stronger sour and pungent flavors, which was achieved by regulating many metabolisms like glycolysis and tyrosine metabolism. In contrast, Weissella cibaria plays a role in mitigating off-flavors, resulting in a milder flavor profile in LPS1. Non-targeted metabolomics indicated 70.78% of differential metabolites were upregulated in LPS1. Conversely, the elevated expression of tryptophan and tyrosine underscores the more pronounced sour and odor-producing characteristics observed in LPS2. Metatranscriptomics highlighted the regulation of genes like XFA, XFT, and XFM, which inhibit the formation of the precursors of p-cresol and indole in LPS2. This integrated multi-omics analysis provides deep insights into the fermentation dynamics, facilitating the targeted selection of Lactobacillus plantarum strains with flavor-regulating capabilities.}, } @article {pmid39978123, year = {2025}, author = {Jin, G and Wang, X and Cui, R and Yuan, S and Wang, M and Chen, Z}, title = {Comprehensive assessment of antibiotic impacts and risk thresholds on aquatic microbiomes and resistomes.}, journal = {Water research}, volume = {276}, number = {}, pages = {123262}, doi = {10.1016/j.watres.2025.123262}, pmid = {39978123}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; Bacteria/drug effects/genetics ; Trimethoprim/pharmacology ; Risk Assessment ; Water Pollutants, Chemical ; Lincomycin/pharmacology ; Water Microbiology ; Drug Resistance, Bacterial/genetics ; }, abstract = {Understanding the impacts of environmentally relevant low-level antibiotics on aquatic microbiomes and resistomes is crucial for risk assessment of anthropogenic antibiotic contamination. Here, we investigated the effects of seven subinhibitory concentrations of trimethoprim and lincomycin (10 ng/L to 10 mg/L), individually and in combination, on surface water microcosms over 1 and 7 days, using unspiked samples as controls. Metagenomic sequencing revealed a decrease in bacterial community α-diversity and an increase in resistome α-diversity with rising antibiotic concentrations upon 7 days of exposure. Notably, the β-diversity of both bacterial communities and resistomes exhibited a biphasic response, decreasing and then increasing with breakpoint concentrations of 2.73 µg/L and 0.68 µg/L, respectively. We also observed concentration-dependent increases in certain metagenome-assembled antibiotic-resistant bacteria (MAARB) and antibiotic resistance genes (ARGs), with minimum selective concentrations (MSCs) of 2.28 µg/L for trimethoprim targeting OXA-21 and 32.4 µg/L for lincomycin targeting erm(F). Among various metrics for identifying risk thresholds that induce significant changes in microbial taxa, resistomes, individual ARGs, and MAARB, the breakpoint concentration derived from resistome β-diversity was the most conservative. We propose integrating this metric into environmental risk assessment frameworks for antibiotics. Our study provides a systematic evaluation of antibiotic impacts on aquatic microbiomes and resistomes, offering key insights for refining risk assessments of antibiotic contamination in aquatic environments.}, } @article {pmid39954460, year = {2025}, author = {Luo, S and Yuan, J and Song, Y and Ren, J and Qi, J and Zhu, M and Feng, Y and Li, M and Wang, B and Li, X and Song, C}, title = {Elevated salinity decreases microbial communities complexity and carbon, nitrogen and phosphorus metabolism in the Songnen Plain wetlands of China.}, journal = {Water research}, volume = {276}, number = {}, pages = {123285}, doi = {10.1016/j.watres.2025.123285}, pmid = {39954460}, issn = {1879-2448}, mesh = {*Wetlands ; *Phosphorus/metabolism ; *Nitrogen/metabolism ; *Carbon/metabolism ; *Salinity ; China ; *Soil Microbiology ; Microbiota ; Soil/chemistry ; }, abstract = {Salinity can induce changes in the structure and function of soil microbial communities, which plays an important role in soil carbon (C), nitrogen (N) and phosphorus (P) cycling. However, there are few studies on the relationship between microbial communities and functional properties of wetland soil under elevated salinity. In this study, soil samples from Zhalong, Momoge, Niuxintaobao, and Xianghai wetlands in the Songnen Plain of China were cultured with different salinity and analyzed by metagenomic sequencing to assess the overall impact of salinity on microorganisms. The results showed that increasing soil salinity decreased soil microbial diversity and significantly changed its composition. Elevated salinity led to the replacement of core species (Sphingomonas) by halophilic species (Halomonadaceae, Halomohas campaniensis), reducing the stability of microbial ecological networks. C fixation, denitrification and purine metabolism were the key ways for the maintenance of C, N and P functions in Songnen plain wetlands, and these processes were significantly reduced with increasing salinity. Key genes involved in C, N and P metabolism include EC1.1.1.42, EC4.1.1.31, EC6.4.1.1, nosZ, nirK, purB, purC, adk, purM, and purQ. They were all effectively suppressed due to increased salinity. In summary, elevated salinity reduced the complexity of microorganisms and inhibited the related functions of C, N and P cycling, and affected the stability of wetland ecosystems. Wetland protection should be strengthened to prevent the aggravation of salinization. This study provides a new scientific framework for the restoration and management of salinized wetland ecosystems in the face of upcoming global changes.}, } @article {pmid39953749, year = {2025}, author = {Aizpurua, O and Botnen, AB and Eisenhofer, R and Odriozola, I and Santos-Bay, L and Bjørnsen, MB and Gilbert, MTP and Alberdi, A}, title = {Functional Insights Into the Effect of Feralisation on the Gut Microbiota of Cats Worldwide.}, journal = {Molecular ecology}, volume = {34}, number = {6}, pages = {e17695}, doi = {10.1111/mec.17695}, pmid = {39953749}, issn = {1365-294X}, support = {CF20-0460//Carlsbergfondet/ ; 17417//Villum Fonden/ ; DNRF143//Danmarks Grundforskningsfond/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Cats ; Metagenomics ; Animals, Wild/microbiology ; Male ; Female ; Metagenome ; }, abstract = {Successfully adapting to a feral lifestyle with different access to food, shelter and other resources requires rapid physiological and behavioural changes, which could potentially be facilitated by gut microbiota plasticity. To investigate whether alterations in gut microbiota support this transition to a feral lifestyle, we analysed the gut microbiomes of domestic and feral cats from six geographically diverse locations using genome-resolved metagenomics. By reconstructing 229 non-redundant metagenome-assembled genomes from 92 cats, we identified a typical carnivore microbiome structure, with notable diversity and taxonomic differences across regions. While overall diversity metrics did not differ significantly between domestic and feral cats, hierarchical modelling of species communities, accounting for geographic and sex covariates, revealed significantly larger microbial functional capacities among feral cats. The increased capacity for amino acid and lipid degradation corresponds to feral cats' dietary reliance on crude protein and fat. A second modelling analysis, using behavioural phenotype as the main predictor, unveiled a positive association between microbial production of short-chain fatty acids, neurotransmitters and vitamins and cat aggressiveness, suggesting that gut microbes might contribute to heightened aggression and elusiveness observed in feral cats. Functional microbiome shifts may therefore play a significant role in the development of physiological and behavioural traits advantageous for a feral lifestyle, a hypothesis that warrants validation through microbiota manipulation experiments.}, } @article {pmid39931947, year = {2025}, author = {Liu, Y and Zhao, T and Wang, Z and Zhang, Y and Shen, J and Lu, B}, title = {The microbiome- and metabolome-modulating activity of dietary cholesterol: insights from the small and large intestines.}, journal = {Food & function}, volume = {16}, number = {5}, pages = {1872-1887}, doi = {10.1039/d4fo03049d}, pmid = {39931947}, issn = {2042-650X}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Metabolome ; Humans ; *Cholesterol, Dietary/metabolism ; Mice ; Male ; Intestine, Small/metabolism/microbiology ; Bile Acids and Salts/metabolism ; Mice, Inbred C57BL ; Bacteria/classification/metabolism/genetics ; }, abstract = {Cholesterol is an important lipid molecule that affects the gut microbiome upon ingestion. We systematically investigated the effects of cholesterol on the microbiota of the large and small intestines using ex vivo and in vivo models, combining flow cytometry, metabolomics, and metagenomics. The results showed that cholesterol directly causes a loss of bacterial membrane polarity and integrity, as well as a reduction in microbial metabolic activity. Cholesterol directly affected the global metabolism of the large and small intestinal microbiota, including amino acid, carbohydrate, and nucleotide metabolism. Ex vivo and in vivo studies shared similar results, showing that cholesterol increased the abundance of the primary bile acid-metabolizing bacteria Clostridium and Dorea in the large intestinal microbiota, confirming the enrichment effect of cholesterol on these bacteria. In the in vivo model, increased conjugated bile acids in the small intestine and decreased abundance of BSH-containing Bifidobacterium were observed due to cholesterol. Only in vivo models have demonstrated that cholesterol increases phosphatidylcholine levels in both the small and large intestines, which may be related to the effects of cholesterol on host metabolism. The pro-inflammatory capacity of the intestinal microbiota was enhanced by cholesterol, as evidenced by the increased levels of IL-1β and TNF-α in THP-1 cells upon stimulation with cholesterol-treated microbiota. This study comprehensively elucidates the effects of cholesterol on the composition and metabolic functions of the microbiota in both the large and small intestines. It offers a novel perspective on the ways in which cholesterol affects host metabolism via the gut microbiome.}, } @article {pmid39929376, year = {2025}, author = {Wu, B and Tang, Y and Zhao, L and Gao, Y and Shen, X and Xiao, S and Yao, S and Qi, H and Shen, F}, title = {Integrated network pharmacological analysis and multi-omics techniques to reveal the mechanism of polydatin in the treatment of silicosis via gut-lung axis.}, journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences}, volume = {207}, number = {}, pages = {107030}, doi = {10.1016/j.ejps.2025.107030}, pmid = {39929376}, issn = {1879-0720}, mesh = {Animals ; *Glucosides/pharmacology/therapeutic use ; *Stilbenes/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Male ; *Lung/drug effects/metabolism ; *Network Pharmacology ; *Molecular Docking Simulation ; *Silicosis/drug therapy/metabolism ; Rats ; Metabolomics/methods ; Rats, Sprague-Dawley ; Multiomics ; }, abstract = {Silicosis is a pulmonary disease characterized by inflammation and progressive fibrosis. Previous studies have shown that polydatin (PD) has potential biological activity in key signaling pathways regulating inflammation and apoptosis. To investigate the effect of PD on rats with silicosis, this study used network pharmacology and molecular docking methods to determine the target of PD treatment for silicosis. The therapeutic effect of PD on silicosis was confirmed by measuring the lung injury score, hydroxyproline content, and mRNA expression levels of key targets. In addition, metagenomic sequencing and gas chromatography-mass spectrometry were used to determine the gut microbiota composition and targeted metabolomics analysis, respectively. The results showed that PD could inhibit the expression of inflammation-related indexes and apoptosis-related indexes at protein and mRNA levels. PD also regulates the diversity of the intestinal flora and the content of short-chain fatty acids. In conclusion, the current data suggest that PD has a protective effect against silica-induced lung injury and plays a protective role in regulating intestinal flora diversity and short-chain fatty acid levels through the gut-lung axis.}, } @article {pmid39917835, year = {2025}, author = {Hoffbeck, C and Middleton, DMRL and Wallbank, JA and Boey, JS and Taylor, MW}, title = {Culture-Independent Species-Level Taxonomic and Functional Characterisation of Bacteroides, the Core Bacterial Genus Within Reptile Guts.}, journal = {Molecular ecology}, volume = {34}, number = {6}, pages = {e17685}, doi = {10.1111/mec.17685}, pmid = {39917835}, issn = {1365-294X}, support = {//University of Auckland Doctoral Scholarship/ ; }, mesh = {Animals ; *Reptiles/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; *Bacteroides/genetics/classification ; *Metagenome/genetics ; Phylogeny ; }, abstract = {The genus Bacteroides is a widespread and abundant bacterial taxon associated with gut microbiotas. Species within Bacteroides fill many niches, including as mutualists, commensals and pathogens for their hosts. Within many reptiles, Bacteroides is a dominant, 'core' gut bacterium that sometimes exhibits increased abundance in times of food scarcity, such as during hibernation. Here, we take a two-pronged approach to better characterise Bacteroides populations in reptile guts. Firstly, we leverage published 16S rRNA gene sequence datasets to determine the species-level distributions of Bacteroides members in reptile hosts. Secondly, we mine publicly available metagenomes to extract data for Bacteroides from reptiles, birds, amphibians and mammals, to compare the functional potential of Bacteroides in different host taxa. The 16S rRNA gene analyses revealed that B. acidifaciens is the most common Bacteroides species in reptile guts, and that different orders of reptiles differ in which Bacteroides species they harbour. The taxonomy of Bacteroides species recovered from metagenomic assembly did not differ between reptile orders or substantially across birds, amphibians and mammals. Metagenome-assembled genomes for Bacteroides species were marginally more related when their hosts were more closely related, with reptile hosts in particular harbouring markedly more unique Bacteroides MAGs compared to other hosts. Our findings indicate that hosts harbour similar profiles of Bacteroides species across broad comparisons, but with some differences between reptile groups, and that Bacteroides appears to perform largely similar roles in vertebrate host guts regardless of host relatedness.}, } @article {pmid39855018, year = {2025}, author = {Yu, Y and Huang, W and Tang, S and Xiang, Y and Yuan, L and Zhu, X and Yin, H and Dang, Z and Niu, J}, title = {Metagenomic and enzymatic mechanisms underpinning efficient water treatment of 2-ethylhexyl diphenyl phosphate (EHDPP) by the microbial consortium 8-ZY.}, journal = {Water research}, volume = {275}, number = {}, pages = {123178}, doi = {10.1016/j.watres.2025.123178}, pmid = {39855018}, issn = {1879-2448}, mesh = {*Microbial Consortia ; *Water Purification ; Biodegradation, Environmental ; Metagenomics ; Water Pollutants, Chemical/metabolism ; }, abstract = {The ubiquitous presence, potential toxicity, and persistence of 2-ethylhexyl diphenyl phosphate (EHDPP) in the environment have raised significant concerns. In this study, we successfully isolate a novel microbial consortium, named 8-ZY, and we demonstrate its remarkable ability to degrade EHDPP using an extremely low concentration of the inoculate. A total of 11 degradation metabolites were identified, including hydrolysis, hydroxylated, methylated, glucuronide-conjugated, and previously unreported byproducts, enabling us to propose new transformation pathways. Further, we unveiled the active members of the microbial consortium 8-ZY during the degradation of EHDPP. We observed the presence of diverse active populations, which included Bradyrhizobium, Rhodopseudomonas, Sphingomonas, Hyphomicrobium, Chitinophaga, Aminobacter, and Ralstonia. A metagenomic analysis revealed the presence of genes that encode phosphatase, phosphodiesterase, cytochrome P450, and hydroxylase enzymes, thus indicating their crucial role in EHDPP degradation. Furthermore, we successfully isolated Burkholderia cepacia ZY1, Sphingopyxis terrae ZY2, and Amycolatopsis ZY3 from the 8-ZY consortium, confirming their significance in EHDPP degradation and metabolite formation. These findings underscored the diversity of strains and functional genes responsible for the transformation of EHDPP within the consortium 8-ZY, highlighting the essential role of synergistic interactions during EHDPP biodegradation processes. Molecular docking and dynamics simulation suggested that alkaline phosphatase, cytochrome P450, and hydroxylase stably bonded to EHDPP within their respective active pockets, targeting distinct sites on the EHDPP molecule. These findings provide a comprehensive understanding of the transformation mechanisms of OPEs and contribute valuable insights into their fate in the environment.}, } @article {pmid39204265, year = {2024}, author = {Ariyadasa, S and van Hamelsveld, S and Taylor, W and Lin, S and Sitthirit, P and Pang, L and Billington, C and Weaver, L}, title = {Diversity of Free-Living Amoebae in New Zealand Groundwater and Their Ability to Feed on Legionella pneumophila.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {8}, pages = {}, pmid = {39204265}, issn = {2076-0817}, support = {ESR2023SA1//Ministry of Business, Innovation, and Employment New Zealand/ ; }, mesh = {New Zealand ; *Legionella pneumophila/isolation & purification/genetics ; *Groundwater/microbiology/parasitology ; *Amoeba/microbiology ; Humans ; Biodiversity ; Water Microbiology ; Acanthamoeba/microbiology/isolation & purification/genetics ; Ecosystem ; }, abstract = {Free-living amoebae (FLA) are common in both natural and engineered freshwater ecosystems. They play important roles in biofilm control and contaminant removal through the predation of bacteria and other taxa. Bacterial predation by FLA is also thought to contribute to pathogen dispersal and infectious disease transmission in freshwater environments via the egestion of viable bacteria. Despite their importance in shaping freshwater microbial communities, the diversity and function of FLA in many freshwater ecosystems are poorly understood. In this study, we isolated and characterized FLA from two groundwater sites in Canterbury, New Zealand using microbiological, microscopic, and molecular techniques. Different methods for groundwater FLA isolation and enrichment were trialed and optimized. The ability of these isolated FLA to predate on human pathogen Legionella pneumophila was assessed. FLA were identified by 18S metagenomic amplicon sequencing. Our study showed that Acanthamoeba spp. (including A. polyphaga) and Vermamoeba veriformis were the main FLA species present in both groundwater sites examined. While most of the isolated FLA co-existed with L. pneumophila, the FLA populations in the L. pneumophila co-culture experiments predominantly consisted of A. polyphaga, Acanthamoeba spp., Naegleria spp., V. vermiformis, Paravahlkampfia spp., and Echinamoeba spp. These observations suggest that FLA may have the potential to act as reservoirs for L. pneumophila in Canterbury, New Zealand groundwater systems and could be introduced into the local drinking water infrastructure, where they may promote the survival, multiplication, and dissemination of Legionella. This research addresses an important gap in our understanding of FLA-mediated pathogen dispersal in freshwater ecosystems.}, } @article {pmid38787271, year = {2024}, author = {Lundtorp-Olsen, C and Markvart, M and Twetman, S and Belstrøm, D}, title = {Effect of Probiotic Supplements on the Oral Microbiota-A Narrative Review.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {5}, pages = {}, pmid = {38787271}, issn = {2076-0817}, mesh = {*Probiotics/administration & dosage/pharmacology/therapeutic use ; Humans ; *Microbiota/drug effects ; *Mouth/microbiology ; *Dietary Supplements ; Randomized Controlled Trials as Topic ; Dental Caries/microbiology/prevention & control ; Gingivitis/microbiology/prevention & control ; Periodontitis/microbiology ; }, abstract = {Data from systematic reviews and meta-analyses show that probiotics positively impact clinical parameters of oral diseases such as gingivitis, dental caries, and periodontitis. However, the working mechanism of probiotics is not fully understood, but is hypothesized to be mediated by direct and indirect interactions with the oral microbiota and the human host. In the present narrative review, we focused on the microbiological effect of probiotic supplements based on data retrieved from randomized clinical trials (RCTs). In addition, we assessed to what extent contemporary molecular methods have been employed in clinical trials in the field of oral probiotics. Multiple RCTs have been performed studying the potential effect of probiotics on gingivitis, dental caries, and periodontitis, as evaluated by microbial endpoints. In general, results are conflicting, with some studies reporting a positive effect, whereas others are not able to record any effect. Major differences in terms of study designs and sample size, as well as delivery route, frequency, and duration of probiotic consumption, hamper comparison across studies. In addition, most RCTs have been performed with a limited sample size using relatively simple methods for microbial identification, such as culturing, qPCR, and DNA-DNA checkerboard, while high-throughput methods such as 16S sequencing have only been employed in a few studies. Currently, state-of-the-art molecular methods such as metagenomics, metatranscriptomics, and metaproteomics have not yet been used in RCTs in the field of probiotics. The present narrative review revealed that the effect of probiotic supplements on the oral microbiota remains largely uncovered. One important reason is that most RCTs are performed without studying the microbiological effect. To facilitate future systematic reviews and meta-analyses, an internationally agreed core outcome set for the reporting of microbial endpoints in clinical trials would be desirable. Such a standardized collection of outcomes would most likely improve the quality of probiotic research in the oral context.}, } @article {pmid38392888, year = {2024}, author = {Ford, CE and Dunn, CD and Leis, EM and Thiel, WA and Goldberg, TL}, title = {Five Species of Wild Freshwater Sport Fish in Wisconsin, USA, Reveal Highly Diverse Viromes.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, pmid = {38392888}, issn = {2076-0817}, support = {R/SFA-24//University of Wisconsin Sea Grant Institute/ ; }, mesh = {Animals ; Wisconsin ; *Fishes/virology ; *Virome/genetics ; *Fresh Water/virology ; Phylogeny ; Fish Diseases/virology/epidemiology ; Viruses/genetics/isolation & purification/classification ; }, abstract = {Studies of marine fish have revealed distant relatives of viruses important to global fish and animal health, but few such studies exist for freshwater fish. To investigate whether freshwater fish also host such viruses, we characterized the viromes of five wild species of freshwater fish in Wisconsin, USA: bluegill (Lepomis macrochirus), brown trout (Salmo trutta), lake sturgeon (Acipenser fulvescens), northern pike (Esox lucius), and walleye (Sander vitreus). We analyzed 103 blood serum samples collected during a state-wide survey from 2016 to 2020 and used a metagenomic approach for virus detection to identify known and previously uncharacterized virus sequences. We then characterized viruses phylogenetically and quantified prevalence, richness, and relative abundance for each virus. Within these viromes, we identified 19 viruses from 11 viral families: Amnoonviridae, Circoviridae, Coronaviridae, Hepadnaviridae, Peribunyaviridae, Picobirnaviridae, Picornaviridae, Matonaviridae, Narnaviridae, Nudnaviridae, and Spinareoviridae, 17 of which were previously undescribed. Among these viruses was the first fish-associated coronavirus from the Gammacoronavirus genus, which was present in 11/15 (73%) of S. vitreus. These results demonstrate that, similar to marine fish, freshwater fish also harbor diverse relatives of viruses important to the health of fish and other animals, although it currently remains unknown what effect, if any, the viruses we identified may have on fish health.}, } @article {pmid38392845, year = {2024}, author = {Lamichhane, B and Brockway, C and Evasco, K and Nicholson, J and Neville, PJ and Levy, A and Smith, D and Imrie, A}, title = {Metatranscriptomic Sequencing of Medically Important Mosquitoes Reveals Extensive Diversity of RNA Viruses and Other Microbial Communities in Western Australia.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, pmid = {38392845}, issn = {2076-0817}, mesh = {Animals ; Western Australia ; *RNA Viruses/genetics/isolation & purification ; Microbiota/genetics ; Virome/genetics ; Mosquito Vectors/microbiology/virology ; Culicidae/virology/microbiology ; Aedes/microbiology/virology ; Biodiversity ; Culex/virology/microbiology ; Transcriptome ; Metagenomics/methods ; Phylogeny ; }, abstract = {Mosquitoes harbor a wide diversity of microorganisms, including viruses that are human pathogens, or that are insect specific. We used metatranscriptomics, an unbiased high-throughput molecular approach, to describe the composition of viral and other microbial communities in six medically important mosquito species from across Western Australia: Aedes vigilax, Culex annulirostris, Cx. australicus, Cx. globocoxitus, Cx. pipiens biotype molestus, and Cx. quinquefasciatus. We identified 42 viral species, including 13 novel viruses, from 19 families. Culex mosquitoes exhibited a significantly higher diversity of viruses than Aedes mosquitoes, and no virus was shared between the two genera. Comparison of mosquito populations revealed a heterogenous distribution of viruses between geographical regions and between closely related species, suggesting that geography and host species may play a role in shaping virome composition. We also detected bacterial and parasitic microorganisms, among which Wolbachia bacteria were detected in three members of the Cx. pipiens complex, Cx. australicus, Cx. pipiens biotype molestus, and Cx. quinquefasciatus. In summary, our unbiased metatranscriptomics approach provides important insights into viral and other microbial diversity in Western Australian mosquitoes that vector medically important viruses.}, } @article {pmid40022356, year = {2025}, author = {Li, Y and Wu, Y and Chen, S and Zhao, Y and Li, C and Xiang, H and Wang, D and Wang, Y}, title = {Decoding the aroma landscape of fermented golden pompano: The interplay of ester compounds and symbiotic microbiota as revealed by metagenomics and two-dimensional flavoromics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {203}, number = {}, pages = {115832}, doi = {10.1016/j.foodres.2025.115832}, pmid = {40022356}, issn = {1873-7145}, mesh = {*Metagenomics/methods ; *Fermentation ; *Volatile Organic Compounds/analysis/metabolism ; *Esters/metabolism/analysis ; *Microbiota ; Odorants/analysis ; Taste ; Seafood/microbiology ; Flavoring Agents/metabolism ; Animals ; Fermented Foods/microbiology ; Symbiosis ; }, abstract = {Fermented pompano (Trachinotus ovatus) is a traditionally popular fermented seafood throughout Asia. Its distinctive flavor profile is primarily attributed to the microbial metabolic conversion of nutrients, which produces specific volatile compounds. Two-dimensional flavoromics of mature pompano revealed that various volatile flavor compounds accumulate throughout fermentation, with fruity (predominantly esters) and oleogustus (primarily ketones) being key flavor markers. S-curve analysis further demonstrated synergistic and additive interactions between these compounds, which enhance flavor release. Metagenomics and Kyoto Encyclopedia of Genes and Genome analysis revealed that amino acid metabolism was the pivotal pathway for ethyl ester synthesis, with Staphylococcus equorum being positively correlated with esters such as ethyl isobutyrate and ethyl enanthate. This study elucidated the interrelationship between flavor compounds and the microbial community in fermented pompano, which is expected to provide insights into flavor modulation and guide the selection of strains that produce key esters in fermented seafood products.}, } @article {pmid39922085, year = {2025}, author = {Florio, M and Crudele, L and Sallustio, F and Moschetta, A and Cariello, M and Gadaleta, RM}, title = {Disentangling the nutrition-microbiota liaison in inflammatory bowel disease.}, journal = {Molecular aspects of medicine}, volume = {102}, number = {}, pages = {101349}, doi = {10.1016/j.mam.2025.101349}, pmid = {39922085}, issn = {1872-9452}, mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/diet therapy ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Nutritional Status ; Animals ; Diet ; }, abstract = {Inflammatory Bowel Disease (IBD) is a set of chronic intestinal inflammatory disorders affecting the gastrointestinal (GI) tract. Beside compromised intestinal barrier function and immune hyperactivation, a common IBD feature is dysbiosis, characterized by a reduction of some strains of Firmicutes, Bacteroidetes, Actinobacteria and an increase in Proteobacteria and pathobionts. Emerging evidence points to diet and nutrition-dependent gut microbiota (GM) modulation, as etiopathogenetic factors and adjuvant therapies in IBD. Currently, no nutritional regimen shows universal efficacy, and advice are controversial, especially those involving restrictive diets potentially resulting in malnutrition. This review provides an overview of the role of macronutrients, dietary protocols and GM modulation in IBD patients. A Western-like diet contributes to an aberrant mucosal immune response to commensal bacteria and impairment of the intestinal barrier integrity, thereby triggering intestinal inflammation. Conversely, a Mediterranean nutritional pattern appears to be one of the most beneficial dietetic regimens able to restore the host intestinal physiology, by promoting eubiosis and preserving the intestinal barrier and immune function, which in turn create a virtuous cycle improving patient adherence to the pattern. Further clinical studies are warranted, to corroborate current IBD nutritional guidelines, and develop more accurate models to move forward precision nutrition and ameliorate patients' quality of life.}, } @article {pmid39622769, year = {2025}, author = {Ivan, FX and Tiew, PY and Jaggi, TK and Thng, KX and Pang, PH and Ong, TH and Abisheganaden, JA and Koh, MS and Chotirmall, SH}, title = {Sputum metagenomics reveals a multidrug resistant Pseudomonas-dominant severe asthma phenotype in an Asian population.}, journal = {Respirology (Carlton, Vic.)}, volume = {30}, number = {3}, pages = {217-229}, doi = {10.1111/resp.14863}, pmid = {39622769}, issn = {1440-1843}, support = {AcRF Tier 1 Grant (RT1/22)//Singapore Ministry of Education/ ; MOH-000710//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001275-00//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001356//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001636//Singapore Ministry of Health's National Medical Research Council/ ; }, mesh = {Humans ; *Sputum/microbiology ; *Asthma/microbiology ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; Singapore/epidemiology ; *Phenotype ; Prospective Studies ; *Asian People/genetics ; Adult ; Pseudomonas Infections/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Microbiota/genetics ; Severity of Illness Index ; Pseudomonas aeruginosa/isolation & purification/genetics ; Pseudomonas/genetics/isolation & purification ; Aged ; Bronchiectasis/microbiology ; }, abstract = {BACKGROUND AND OBJECTIVE: While the lung microbiome in severe asthma has been studied, work has employed targeted amplicon-based sequencing approaches without functional assessment with none focused on multi-ethnic Asian populations. Here we investigate the clinical relevance of microbial phenotypes of severe asthma in Asians using metagenomics.

METHODS: Prospective assessment of clinical, radiological, and immunological measures were performed in a multi-ethnic Asian severe asthma cohort (N = 70) recruited across two centres in Singapore. Sputum was subjected to shotgun metagenomic sequencing and patients followed up for a 2-year period. Metagenomic assessment of sputum microbiomes, resistomes and virulomes were related to clinical outcomes.

RESULTS: The lung microbiome in a multi-ethnic Asian cohort with severe asthma demonstrates an increased abundance of Pseudomonas species. Unsupervised clustering of sputum metagenomes identified two patient clusters: C1 (n = 52) characterized by upper airway commensals and C2 (n = 18) dominated by established respiratory pathogens including M. catarrhalis, S. aureus and most significantly P. aeruginosa. C2 patients demonstrated a significantly increased exacerbation frequency on 2-year follow up and an antimicrobial resistome characterized by multidrug resistance. Virulomes appear indistinguishable between severe asthmatics with or without co-existing bronchiectasis, and C2 patients exhibit increased gene expression related to biofilm formation, effector delivery systems and microbial motility. Independent comparison of the C2 cluster to a non-asthmatic bronchiectasis cohort demonstrates analogous airway microbial virulence patterns.

CONCLUSION: Sputum metagenomics demonstrates a multidrug-resistant Pseudomonas-dominant severe asthma phenotype in Asians, characterized by poor clinical outcome including increased exacerbations which is independent of co-existing bronchiectasis.}, } @article {pmid40022320, year = {2025}, author = {Cámara-Martos, F and Bolívar, A and Rabasco-Vílchez, L and Lafont-Déniz, F and Luque-Ojeda, JL and Pérez-Rodríguez, F}, title = {Exploring the bioaccessibility, in vitro colonic fermentation, and the impact on the intestinal microbiota of allyl-and benzyl-isothiocyanate from white and Ethiopian mustard.}, journal = {Food research international (Ottawa, Ont.)}, volume = {203}, number = {}, pages = {115781}, doi = {10.1016/j.foodres.2025.115781}, pmid = {40022320}, issn = {1873-7145}, mesh = {*Gastrointestinal Microbiome ; *Mustard Plant/microbiology/chemistry ; *Colon/microbiology/metabolism ; *Fermentation ; *Isothiocyanates/metabolism ; Humans ; Biological Availability ; Digestion ; Glucosinolates/metabolism/analysis ; Gas Chromatography-Mass Spectrometry ; }, abstract = {The aim of this research was to study the formation and bioaccessibility of allyl- and benzyl-isothiocyanate (ITC) resulting from the gastrointestinal digestion (small and large intestine) of green parts from Ethiopian and white mustard. In addition, a GC-MS methodology was validated to determine these compounds in bioaccessible and non-bioaccessible fraction. Plant clumps were divided into two batches: fresh and freeze-dried samples. ITC bioaccessibility was low in the small intestine, with values ranged between 11 and 53 % and mean values of 26 %. These results are in agreement with the fact that ITCs are poorly water-soluble compounds. Bioaccessibility values for lyophilised samples were lower than those obtained in fresh samples. This could be due to the degradation of the precursor glucosinolates (sinigrin and glucotropaeolin respectively). The simulation of the colonic fermentation reduced allyl - and benzyl - ITC levels from the non-bioaccessible fraction of Ethiopian and white mustard (values between 0.009 and 0.087 mg/g). In both cases, ITCs concentration dropped dramatically, i.e. with a ten-fold reduction. Nevertheless, this result does not necessarily indicate that ITCs have not been produced in the large intestine. Bacterial microbiota plays a key role in generating ITCs; however, ITCs are not always the final products of this process. The metagenomic analysis of colonic samples revealed that ITCs and cruciferous matrix significantly influenced the composition of gut microbiota, inhibiting potentially pathogenic bacteria such as Enterobacter and Klebsiella, while promoting beneficial bacteria such as Bifidobacterium, Faecalibacterium, Blautia, and Ruminococcus. Interestingly, ITCs-rich environments selected bacterial species (i.e. Enterobacter ludwigii) and promoted metabolic pathways involved in glucosinolate/ITCs metabolism.}, } @article {pmid40022097, year = {2025}, author = {Ferneyhough, B and Roddis, M and Millington, S and Quirk, J and Clements, C and West, S and Schilizzi, R and Fischer, MD and Parkinson, NJ}, title = {A highly accurate nanopore-based sequencing workflow for culture and PCR-free microbial metagenomic profiling of urogenital samples.}, journal = {BMC urology}, volume = {25}, number = {1}, pages = {41}, pmid = {40022097}, issn = {1471-2490}, mesh = {Humans ; Female ; Male ; *Metagenomics/methods ; *Microbiota/genetics ; Nanopore Sequencing/methods ; Vagina/microbiology ; Workflow ; Urogenital System/microbiology ; }, abstract = {BACKGROUND: The application of molecular sequencing methods for microbiome profiling of biological samples are largely restricted to research use. However, they require significant resources such as time and cost and can suffer from amplification biases that may hamper interpretation of complex systems. These issues are also a barrier to adoption as standard clinical tools in, for example, diagnosis of urogenital infections. We report a new method that utilises third generation long-read nanopore sequencing to produce fast, accurate and fully quantitated metagenomic microbiome profiles. Here, as proof of principle, we apply this methodology to reassess the healthy urogenital microbiomes of asymptomatic female and male samples.

RESULTS: We show that our method is capable of accurately and reproducibly detecting both levels and composition of a synthetic mixture of ten species comprising known amounts of hard to lyse gram-positive bacteria, gram-negative bacteria and yeast. When applied to urogenital samples, we confirm previous observations that the female asymptomatic vaginal and urinary microbiomes are predominated by Gardnerella spp. or one of several Lactobacillus species (L. crispatus, L. gasseri, L. iners or L. jensenii) that conform to previously defined community state types. We show the tight relationship between vaginal and urinary populations of the same individual at both species and strain level, provide evidence for the previously observed dynamic nature of these microbiomes over a menstrual cycle and compare biomass and complexity of male and female urobiomes.

CONCLUSIONS: We set out to develop an unbiased, amplification and culture-free, fully quantitative metagenomic microbiome profiling tool. Our initial observations suggest our method represents a viable alternative to existing molecular research tools employed in the analysis of complex microbiomes.}, } @article {pmid40022204, year = {2025}, author = {Debray, R and Dickson, CC and Webb, SE and Archie, EA and Tung, J}, title = {Shared environments complicate the use of strain-resolved metagenomics to infer microbiome transmission.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {59}, pmid = {40022204}, issn = {2049-2618}, support = {R01AG071684/NH/NIH HHS/United States ; R01AG071684/NH/NIH HHS/United States ; R61AG078470//National Science Foundation/ ; R61AG078470//National Science Foundation/ ; }, mesh = {Animals ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation ; Humans ; Papio/microbiology ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; }, abstract = {BACKGROUND: In humans and other social animals, social partners have more similar microbiomes than expected by chance, suggesting that social contact transfers microorganisms. Yet, social microbiome transmission can be difficult to identify based on compositional data alone. To overcome this challenge, recent studies have used information about microbial strain sharing (i.e., the shared presence of highly similar microbial sequences) to infer transmission. However, the degree to which strain sharing is influenced by shared traits and environments among social partners, rather than transmission per se, is not well understood.

RESULTS: Here, we first use a fecal microbiota transplant dataset to show that strain sharing can recapitulate true transmission networks under ideal settings when donor-recipient pairs are unambiguous and recipients are sampled shortly after transmission. In contrast, in gut metagenomes from a wild baboon population, we find that demographic and environmental factors can override signals of strain sharing among social partners.

CONCLUSIONS: We conclude that strain-level analyses provide useful information about microbiome similarity, but other facets of study design, especially longitudinal sampling and careful consideration of host characteristics, are essential for inferring the underlying mechanisms of strain sharing and resolving true social transmission network. Video Abstract.}, } @article {pmid40021694, year = {2025}, author = {Gambardella, N and Costa, J and Martins, BM and Folhas, D and Ribeiro, AP and Hintelmann, H and Canário, J and Magalhães, C}, title = {The role of prokaryotic mercury methylators and demethylators in Canadian Arctic thermokarst lakes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {7173}, pmid = {40021694}, issn = {2045-2322}, support = {PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {Arctic Regions ; Canada ; *Lakes/microbiology ; *Mercury/metabolism ; Methylation ; Methylmercury Compounds/metabolism/analysis ; Microbiota ; Geologic Sediments/microbiology ; Bacteria/genetics/metabolism/classification ; Permafrost/microbiology ; Seasons ; Metagenomics/methods ; Water Pollutants, Chemical/metabolism ; Environmental Monitoring/methods ; }, abstract = {Permafrost soils are critical reservoirs for mercury (Hg), with the thawing process leading to the release of this element into the environment, posing significant environmental risks. Of particular concern is the methylated form of mercury, monomethylmercury (MMHg), known for its adverse effects on Human health. Microbial communities play a pivotal role in the formation of MMHg by facilitating Hg methylation and in the demethylation of MMHg, slowing the crossing of toxic threshold concentration in the environment. However, the specific microbes involved still need to be understood. This study aimed to identify the microbial drivers behind changes in Hg speciation (MMHg and Hg) in permafrost thaw lakes and assess the significance of the biotic component in Hg biogeochemistry. Sediment samples from two thermokarst lakes in the Canadian sub-Arctic were collected during the winter and summer of 2022. Gene-centric metagenomics using whole-genome sequencing (WGS) was employed to identify key genes involved in mercury methylation (hgcA and hgcB) and demethylation (merA and merB), supported by qPCR analyses. A seasonal decline in microbial diversity, involved in the Hg methylation, and hgcA gene coverage was observed from winter to summer, mirroring patterns in mercury methylation rates. Notably, hgcA sequences were significantly more abundant than merAB sequences, with contrasting seasonal trends. These results indicate a seasonal shift in the microbial community, transitioning from a dominance of mercury methylation in winter to a predominance of mercury demethylation in summer. Environmental drivers of these dynamics were integrated into a conceptual model. This study provide new insights on the microbial processes influencing the Hg cycle in Arctic permafrost undergoing degradation.}, } @article {pmid40020468, year = {2025}, author = {Huang, Y and Li, XT and Jiang, Z and Liang, ZL and Liu, W and Liu, ZH and Li, LZ and Yang, ZN and Zhang, GQ and Yin, HQ and Liang, JL and Zhou, N and Liu, SJ and Jiang, CY}, title = {Mineral types dominate microbiomes and biogeochemical cycling in acid mine drainage.}, journal = {Water research}, volume = {278}, number = {}, pages = {123367}, doi = {10.1016/j.watres.2025.123367}, pmid = {40020468}, issn = {1879-2448}, abstract = {Acid mine drainage (AMD) environments are typically used as models to study the crucial roles of acidophilic microbes in aquatic environments. Nevertheless, knowledge regarding microbial-driven biogeochemical cycling across mining regions remains limited. In this study, a metagenomics-based approach was employed to explore the diversity, composition, and ecological functions of microbiomes in global AMD environments with different mineral types. A total of 226 metagenomes, covering 12 mineral types of AMD, were analyzed. As a result, 2114 microbial metagenome-assembled genomes (MAGs) were obtained, representing members from 33 bacterial phyla and 8 archaeal phyla. The core taxa and functional groups in AMDs were identified. Additionally, twelve bacterial and two archaeal lineages were discovered for the first time in AMD environments. The specific metabolic potentials of these genomes were also determined. Our results revealed a high level of specialization in the diversity structures and ecological functions of AMD microbial communities based on mineral-type conditions. Mineral type significantly contributed to the dissimilarity in the AMD microbiomes, especially in water environments, underscoring the pivotal role of mineral types in shaping the microbial community in the AMD environment. Collectively, these findings provide novel perspectives on the ecology and metabolism of microbiomes in extreme AMD environments globally.}, } @article {pmid40020117, year = {2025}, author = {Zheng, X and Fan, J and Yin, J and Chu, Y}, title = {The role of gut microbiota and plasma metabolites in ulcerative colitis: Insights from Mendelian randomization analysis.}, journal = {Medicine}, volume = {104}, number = {9}, pages = {e41710}, pmid = {40020117}, issn = {1536-5964}, mesh = {Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome ; *Colitis, Ulcerative/blood/microbiology ; *Genome-Wide Association Study ; }, abstract = {Emerging research suggests that alterations in gut microbiota composition may play a significant role in the pathogenesis of ulcerative colitis (UC). Plasma metabolites, which are influenced by gut microbiota, have also been implicated, but their role in UC remains unclear. This study aims to determine whether specific plasma metabolites mediate the causal relationship between gut microbiota and UC using Mendelian randomization (MR) analysis. This study employed publicly available summary-level data from genome-wide association studies and metagenomic datasets. Gut microbiota data were derived from the FINRISK cohort (5959 participants), plasma metabolite data from the Canadian Longitudinal Study on Aging (8299 individuals), and UC data from multiple consortia (17,030 cases and 883,787 controls). Forward and reverse MR analyses, supplemented by linkage disequilibrium score regression (LDSC), were conducted to assess causal relationships. Mediation effects of plasma metabolites between gut microbiota and UC were analyzed using the product of coefficients method. Various sensitivity analyses, including MR-Egger and MR-PRESSO, were applied to detect pleiotropy and ensure robust results. The study identified 20 bacterial taxa and 93 plasma metabolites linked to UC. Forward MR analysis showed that Clostridium S felsineum increased UC risk via reduced carnitine levels, with a mediation proportion of 39.77%. Eubacterium callanderi was associated with decreased UC risk through the tryptophan to pyruvate ratio (16.02% mediation). Additionally, species CAG-590 sp000431135 increased UC risk through elevated mannitol/sorbitol levels, mediating 28.38% of the effect. Sensitivity analyses confirmed the robustness of these findings, with minimal heterogeneity and pleiotropy detected. This study highlights the significant role of gut microbiota and their associated plasma metabolites in the pathogenesis of UC. Specific microbial species influence UC through metabolites, suggesting potential therapeutic targets. Modulating carnitine, tryptophan metabolism, or sugar alcohols could offer promising avenues for UC management.}, } @article {pmid40016914, year = {2025}, author = {Lu, X and Xu, Y and Liu, Y and Li, F and Feng, Q and Gao, C and Liu, D and Zhou, L and Yang, H and Zhang, J and Cui, F and Chen, Q}, title = {Neutrophil Depletion Reduced the Relative Abundance of Unsaturated Long-Chain Fatty Acid Synthesis Microbiota and Intestinal Lipid Absorption.}, journal = {Cell biochemistry and function}, volume = {43}, number = {3}, pages = {e70060}, doi = {10.1002/cbf.70060}, pmid = {40016914}, issn = {1099-0844}, support = {//This work was supported by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Suzhou Fundamental Research Project (SJC2023001), and Key Laboratory of Radiation Damage and Treatment of Jiangsu Provincial Universities and Colleges. It was funded by the National Natural Science Foundation of China (Grant No. 81773355)./ ; }, mesh = {Animals ; Mice ; *Neutrophils/metabolism ; *Intestinal Absorption ; Male ; Gastrointestinal Microbiome ; Lipid Metabolism ; Mice, Inbred C57BL ; Fatty Acids, Unsaturated/metabolism ; Rats ; }, abstract = {As immune cells, neutrophils serve as the first line of defense against infections; however, the mechanism by which neutrophils regulate lipid metabolism is unknown. The neutrophil depletion group was treated with 100 μg InVivoMAb anti-mouse Ly6G 6 times, whereas the control group mice were intraperitoneally injected with the same quantity of InVivoMAb rat IgG2a. Body fat content, triglycerides (TGs), total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) in the jejunum and ileum, as well as 9 long-chain fatty acids (LCFAs) in the intestinal contents were significantly decreased. Furthermore, genes involved in the absorption of lipids in each segment of the intestine also showed decreased expression. Neutrophil-depletion and control models were administered 25 μCi of [3]H-cholesterol by gavage. The distribution of [3]H cholesterol in the intestinal segment, heart, liver, serum, and feces was not altered by anti-Ly6G antibodies. Metagenomics was applied to investigate uncultured microorganisms in the intestinal contents to identify bacteria containing lipid metabolism genes. At the species level, 12 bacteria were involved in unsaturated LCFA synthesis, among which 2 increased and 10 decreased. The overall relative abundance of these bacteria decreased from 3.102% to 0.734%. Many genes involved in lipid metabolism were also reduced as a result, such as fatty acid synthase and peroxisome proliferator-activated receptor γ. In conclusion, neutrophil depletion does not affect intestinal lipid absorption in the diet but leads to a decrease in the overall relative abundance of gut bacteria involved in unsaturated LCFA synthesis. Consequently, intestinal lipid synthesis and absorption are reduced.}, } @article {pmid39923562, year = {2025}, author = {Solazzo, G and Rovelli, S and Iodice, S and Chung, M and Frimpong, M and Bollati, V and Ferrari, L and Ghedin, E}, title = {The microbiome of Total Suspended Particles and its influence on the respiratory microbiome of healthy office workers.}, journal = {Ecotoxicology and environmental safety}, volume = {291}, number = {}, pages = {117874}, doi = {10.1016/j.ecoenv.2025.117874}, pmid = {39923562}, issn = {1090-2414}, mesh = {Humans ; *Microbiota/drug effects ; *Particulate Matter/analysis ; *Air Pollution, Indoor/analysis ; *Air Microbiology ; Air Pollutants/analysis ; Environmental Monitoring ; Occupational Exposure/analysis ; Bacteria/classification/genetics/isolation & purification ; Respiratory System/microbiology ; Italy ; Adult ; }, abstract = {Air particulate matter (PM) is widely recognized for its potential to negatively affect human health, including changes in the upper respiratory microbiome. However, research on PM-associated microbiota remains limited and mostly focused on PM (e.g., PM2.5 and PM10). This study aims to characterize for the first time the microbiome of Total Suspended Particles (TSP) and investigate the correlations of indoor TSP with the human upper respiratory microbiome. Biological and environmental samples were collected over three collection periods lasting three weeks each, between May and July 2022 at the University of Milan and the University of Insubria Como. TSP were sampled using a filter-based technique, while respiratory samples from both anterior nares (AN) and the nasopharynx (NP) were collected using swabs. Microbiome analysis of both human (N = 145) and TSP (N = 51) samples was conducted on metagenomic sequencing data. A comparison of indoor and outdoor TSP microbiomes revealed differences in microbial diversity and taxonomic composition. The indoor samples had higher relative abundance of environmental bacteria often associated with opportunistic infections like Paracoccus sp., as well as respiratory bacteria such as Staphylococcus aureus and Klebsiella pneumoniae. Additionally, both indoor and outdoor TSP samples contained broad spectrum antibiotic resistance genes. Indoor TSP exposure was negatively associated with commensal bacteria and positively associated with Staphylococcus aureus relative abundance. Finally, a correlation between the relative abundance of respiratory bacteria identified in the indoor TSP and the upper respiratory microbiome was found, suggesting a potential interaction between TSP and the upper airways.}, } @article {pmid39908950, year = {2025}, author = {Alonso-Vásquez, T and Fagorzi, C and Mengoni, A and Oliva, M and Cavalieri, D and Pretti, C and Cangioli, L and Bacci, G and Ugolini, A}, title = {Metagenomic surveys show a widespread diffusion of antibiotic resistance genes in a transect from urbanized to marine protected area.}, journal = {Marine pollution bulletin}, volume = {213}, number = {}, pages = {117640}, doi = {10.1016/j.marpolbul.2025.117640}, pmid = {39908950}, issn = {1879-3363}, mesh = {*Geologic Sediments/microbiology ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects ; RNA, Ribosomal, 16S ; Environmental Monitoring ; Italy ; Metagenomics ; Metagenome ; Microbiota/drug effects ; Urbanization ; }, abstract = {Ports are hot spots of pollution; they receive pollution from land-based sources, marine traffic and port infrastructures. Marine ecosystems of nearby areas can be strongly affected by pollution from port-related activities. Here, we investigated the microbiomes present in sea floor sediments along a transect from the harbour of Livorno (Central Italy) to a nearby marine protected area. Results of 16S rRNA amplicon sequencing and metagenome assembled genomes (MAGs) analyses indicated the presence of different trends of specific bacterial groups (e.g. phyla NB1-j, Acidobacteriota and Desulfobulbales) along the transect, correlating with the measured pollution levels. Human pathogenic bacteria and antibiotic resistance genes (ARGs) were also found. These results demonstrate a pervasive impact of human port activities and highlight the importance of microbiological surveillance of marine sediments, which may constitute a reservoir of ARGs and pathogenic bacteria.}, } @article {pmid39904008, year = {2025}, author = {Bohra, V and Lai, KK and Lam, KL and Tam, NF and Jing-Liang, S and Lee, FW}, title = {Metagenomic surveillance reveals different structure and function of microbial community associated with mangrove pneumatophores and their surrounding matrices.}, journal = {Marine pollution bulletin}, volume = {213}, number = {}, pages = {117614}, doi = {10.1016/j.marpolbul.2025.117614}, pmid = {39904008}, issn = {1879-3363}, mesh = {*Metagenomics ; *Wetlands ; *Avicennia/microbiology ; *Microbiota ; *Bacteria/genetics ; *Geologic Sediments/microbiology ; }, abstract = {Present research employed metagenomics to explore the structural and functional diversity of microorganisms in two matrices of pneumatophore: adhered sediments (PS) and epiphytes (PE) of Avicennia marina. These were compared with microorganisms in surrounding environments: tidal water (TW), mudflat sediment (MF) and mangrove sediment (MS). Results revealed that bacteria made up over 95 % of the microbial community across all five matrices, with the dominance of phylum Proteobacteria, because of their metabolic flexibility and ability to survive in harsh mangrove environment. The bacterial community in PS and PE were similar to TW but differed from those in MF and MS, implying their provenance from TW. The high relative abundance of genes involved in nitrate and sulfur reduction pathways in PS and PE indicates pneumatophore bacteria helps in enhancing nitrogen and sulfur availability. This study is the first to explore the functional significance of pneumatophore-adhered prokaryotic communities using metagenomics.}, } @article {pmid39778631, year = {2025}, author = {Harriman, D and Ng, A and Bronowski, M and Kazakov, H and Nguan, C and Dang, T and Sherwood, K and Miller, A and Lange, D}, title = {Characterizing the urobiome and associated metabolic profiles during acute rejection in renal transplant patients: A pilot study.}, journal = {Transplant immunology}, volume = {89}, number = {}, pages = {102170}, doi = {10.1016/j.trim.2024.102170}, pmid = {39778631}, issn = {1878-5492}, mesh = {Humans ; *Kidney Transplantation ; *Graft Rejection/diagnosis ; Pilot Projects ; Male ; Female ; Middle Aged ; Adult ; Metabolome ; Acute Disease ; Microbiota ; Aged ; }, abstract = {Characteristic alterations in the urinary microbiome, or urobiome, are associated with renal transplant pathology. To date, there has been no direct study of the urobiome during acute allograft rejection. The goal of this study was to determine if unique urobiome alterations are present during acute rejection in renal transplant recipients. We performed shotgun metagenomic sequencing of 32 mid-stream urine samples obtained from 15 transplant recipients pre-transplant, 1- and 3-months post-transplant, and at time of rejection discovered with for-cause biopsy. Within individuals, there was a 40-60 % difference in urobiome composition from pre-to-post-transplant in both rejectors and non-rejectors. The taxa Ureaplasma was enriched in rejectors compared to non-rejectors. However, a greater number of microbial genes were enriched in non-rejectors compared to rejectors, except for genes associated with tetracycline resistance, the lysophosphatidic acid synthesis pathway, and tryptophanyl-tRNA synthetase. Together, our findings suggest that the urobiome is significantly altered post-transplant with certain taxa and/or microbial genes potentially associated with acute allograft rejection/inflammation.}, } @article {pmid38987012, year = {2025}, author = {Caceres Lessa, AY and Edwinson, A and Sato, H and Yang, L and Berumen, A and Breen-Lyles, M and Byale, A and Ryks, M and Keehn, A and Camilleri, M and Farrugia, G and Chen, J and Decuir, M and Smith, K and Dasari, S and Grover, M}, title = {Transcriptomic and Metabolomic Correlates of Increased Colonic Permeability in Postinfection Irritable Bowel Syndrome.}, journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association}, volume = {23}, number = {4}, pages = {632-643.e13}, pmid = {38987012}, issn = {1542-7714}, support = {K23 DK103911/DK/NIDDK NIH HHS/United States ; R01 DK127998/DK/NIDDK NIH HHS/United States ; R03 DK120745/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Irritable Bowel Syndrome/metabolism/genetics/microbiology ; Female ; Male ; Middle Aged ; Adult ; *Permeability ; *Feces/chemistry/microbiology ; *Colon/metabolism/microbiology ; Gastrointestinal Microbiome/physiology ; Transcriptome ; Metabolomics/methods ; Metabolome ; }, abstract = {BACKGROUND & AIMS: Postinfection irritable bowel syndrome (PI-IBS) is well-known epidemiologically; however, its physiological and molecular characteristics are not well studied. We aimed to determine the physiological phenotypes, colonic transcriptome, fecal microbiome, and metabolome in PI-IBS.

METHODS: Fifty-one Rome III Campylobacter PI-IBS patients and 39 healthy volunteers (HV) were enrolled. Participants completed questionnaires, in vivo intestinal permeability, gastrointestinal transit, and rectal sensation. Fecal samples were collected for shotgun metagenomics, untargeted metabolomics, and sigmoid colonic biopsies for bulk RNAseq. Differential gene expression, differences in microbiota composition, and metabolite abundance were determined. Gene and metabolite clusters were identified via weighted gene correlation network analysis and correlations with clinical and physiological parameters determined.

RESULTS: PI-IBS (59% female; 46 ± 2 years) and HV (64% female; 42 ± 2 years) demographics were comparable. Mean IBS-symptom severity score was 227; 94% were nonconstipation. Two- to 24-hour lactulose excretion was increased in PI-IBS, suggesting increased colonic permeability (4.4 ± 0.5 mg vs 2.6 ± 0.3 mg; P = .01). Colonic transit and sensory thresholds were similar between the 2 groups. Overall, expression of 2036 mucosal genes and 223 fecal metabolites were different, with changes more prominent in females. Fecal N-acetylputrescine was increased in PI-IBS and associated with colonic permeability, worse diarrhea, and negatively correlated with abundance of Collinsella aerofaciens. Histamine and N-acetylhistamine positively associated with 2- to 24-hour lactulose excretion. Eight weighted gene coexpression modules significantly correlated with phenotypes (sex, stool frequency, colonic permeability, transit).

CONCLUSIONS: Campylobacter PI-IBS patients demonstrate higher colonic permeability, which associated with changes in polyamine and histamine metabolites. Female patients demonstrated greater molecular changes.}, } @article {pmid40016544, year = {2025}, author = {Zaminhan-Hassemer, M and Zagolin, GB and Aráujo, BC and Perazza, CA and Barbosa, DA and Menegidio, FB and Coutinho, LL and Tizioto, P and Hilsdorf, AWS}, title = {Effect of green propolis crude extract on the modulation of intestinal microbiota and on the productive performance of juvenile Nile tilapia.}, journal = {Veterinary research communications}, volume = {49}, number = {2}, pages = {120}, pmid = {40016544}, issn = {1573-7446}, mesh = {Animals ; *Propolis/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Cichlids/microbiology ; *Animal Feed/analysis ; *Diet/veterinary ; Dietary Supplements/analysis ; }, abstract = {The study aimed to investigate the impact of dietary supplementation with green propolis crude extract on juvenile tilapia's growth and intestinal microbiota. The experiment was conducted in raceway tanks with a volume of 19m[3], comprising two treatments with three replicates each. Fish were assigned to either a control diet or a diet supplemented with 0.67% green propolis crude extract. Each experimental unit consisted of 30 fish, initially averaging 22.38 g ± 0.32 in weight, and which were fed ad libitum for 60 days. Results demonstrated that dietary supplementation with green propolis crude extract significantly improved the growth of juvenile tilapia compared to the control group. Firmicutes, Proteobacteria, Verrucomicrobia, Bacteroidetes, and Cyanobacteria were identified as the predominant bacterial phyla in the intestinal microbiota of both groups. The genera Candidatus xiphinematobacter (Verrucomicrobia) and Somerae (Firmicutes) were consistently abundant across treatments, with Somerae and Dispar as the most prevalent species. Significant differences in alpha diversity were observed between treatments at the genus and species levels according to the Chao 1 index. However, no significant differences were detected in Shannon index diversity between the control and green propolis crude extract groups. Beta diversity analysis revealed distinct clustering between treatments. Linear discriminant analysis Effect Size (LEfSe) highlighted significant differences in bacterial abundance between the control and green propolis crude extract groups. In conclusion, dietary supplementation with green propolis crude extract improved growth. It also modulated the intestinal microbiota of juvenile Thai tilapia.}, } @article {pmid40016229, year = {2025}, author = {Chang, J and Costa, OYA and Sun, Y and Wang, J and Tian, L and Shi, S and Wang, E and Ji, L and Wang, C and Pang, Y and Yao, Z and Ye, L and Zhang, J and Chen, H and Cai, Y and Chen, D and Song, Z and Rong, J and Raaijmakers, JM and Tian, C and Kuramae, EE}, title = {Domesticated rice alters the rhizosphere microbiome, reducing nitrogen fixation and increasing nitrous oxide emissions.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2038}, pmid = {40016229}, issn = {2041-1723}, mesh = {*Oryza/microbiology/metabolism ; *Nitrous Oxide/metabolism ; *Rhizosphere ; *Microbiota/genetics ; *Soil Microbiology ; *Nitrogen Fixation ; *Plant Roots/microbiology/metabolism ; Domestication ; Metagenomics ; Soil/chemistry ; Nitrogenase/metabolism/genetics ; Nitrogen/metabolism ; Bacteria/genetics/metabolism/classification/isolation & purification ; Agriculture/methods ; }, abstract = {Crop domestication has revolutionized food production but increased agriculture's reliance on fertilizers and pesticides. We investigate differences in the rhizosphere microbiome functions of wild and domesticated rice, focusing on nitrogen (N) cycling genes. Shotgun metagenomics and real-time PCR reveal a higher abundance of N-fixing genes in the wild rice rhizosphere microbiomes. Validation through transplanting rhizosphere microbiome suspensions shows the highest nitrogenase activity in soils with wild rice suspensions, regardless of planted rice type. Domesticated rice, however, exhibits an increased number of genes associated with nitrous oxide (N2O) production. Measurements of N2O emissions in soils with wild and domesticated rice are significantly higher in soil with domesticated rice compared to wild rice. Comparative root metabolomics between wild and domesticated rice further show that wild rice root exudates positively correlate with the frequency and abundance of microbial N-fixing genes, as indicated by metagenomic and qPCR, respectively. To confirm, we add wild and domesticated rice root metabolites to black soil, and qPCR shows that wild rice exudates maximize microbial N-fixing gene abundances and nitrogenase activity. Collectively, these findings suggest that rice domestication negatively impacts N-fixing bacteria and enriches bacteria that produce the greenhouse gas N2O, highlighting the environmental trade-offs associated with crop domestication.}, } @article {pmid39923519, year = {2025}, author = {Peng, Q and Cheng, S and Lin, J and Zheng, H and Xie, G}, title = {Metabolic and microbial functionality during the fermentation of traditional Amaranth stems: Insights from metagenomics, flavoromics, and metabolomics.}, journal = {Food chemistry}, volume = {474}, number = {}, pages = {143216}, doi = {10.1016/j.foodchem.2025.143216}, pmid = {39923519}, issn = {1873-7072}, mesh = {*Fermentation ; *Metabolomics ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Microbiota ; *Volatile Organic Compounds/metabolism/chemistry/analysis ; *Metagenomics ; *Flavoring Agents/metabolism/chemistry ; *Amaranthus/metabolism/chemistry ; Plant Stems/chemistry/microbiology/metabolism ; Taste ; }, abstract = {Fermented Amaranth stems is a traditional Chinese fermented vegetable known for its distinctive aroma, produced through natural microbial fermentation. However, the metabolic processes, flavor compounds, and microbial communities involved in its fermentation are not well understood. This study provides a comprehensive analysis using an integrated approach combining flavoromics, untargeted metabolomics, and metagenomics to examine the dynamic changes in metabolites and microbiota during fermentation. A total of 108 volatile organic compounds were identified, with sugar metabolism peaking on the third day of fermentation. The microbial community analysis revealed that key genera such as Pseudomonas, Acinetobacter, Pectobacterium, and Enterobacter play a significant role in flavor formation. The findings offer critical insights into the fermentation mechanisms and the production of flavor compounds, providing a foundation for optimizing fermentation processes and improving the flavor quality of fermented Amaranth stems. This research holds practical significance for enhancing food safety by controlling microbial communities during fermentation.}, } @article {pmid40015896, year = {2025}, author = {Zheng, R and Peng, J and Li, Q and Liu, Y and Huang, D and Sheng, Y and Liu, C and Qi, L and Keyhani, NO and Tang, Q}, title = {Alterations in microbial community structures and metabolic function in soil treated with biological and chemical insecticides.}, journal = {Pesticide biochemistry and physiology}, volume = {208}, number = {}, pages = {106304}, doi = {10.1016/j.pestbp.2025.106304}, pmid = {40015896}, issn = {1095-9939}, mesh = {*Insecticides/pharmacology ; *Soil Microbiology ; *Metarhizium/genetics ; *Ivermectin/analogs & derivatives/pharmacology ; *Neonicotinoids/pharmacology ; Nitro Compounds/pharmacology ; Soil/chemistry ; Microbiota/drug effects ; }, abstract = {Entomopathogenic fungi show significant promise as effective and ecological friendly alternatives to chemical insecticides for insect pest control. However, little is known concerning their effects on soil ecosystems, especially in comparison to application of chemical insecticides. Here, we examined the effects of one biological and two chemical insecticides, Metarhizium anisopliae, imidacloprid (IMI) and emamectin benzoate (EMB) on microbial community structure, metabolic functioning, and soil biochemistry. Treatment with EMB and IMI, reduced Actinobacteriota populations, while increasing that of Acidobacteriota. However, these populations were not significantly altered under M. anisopliae treatment. Chemical pesticides also altered fungal communities including potential pathogens. Activities of soil beneficial nitrogen-cycling-related enzymes were reduced after application of IMI and EMB, but were increased after treatment with M. anisopliae. Metagenomics analysis showed that IMI treatment reduced levels of carbon and nitrogen-related metabolic pathways. However, M. anisopliae treatment increased representation of key enzymes involved in the carbon, nitrogen, and sulfur cycling important for maintenance of soil fertility. Insecticides treatments altered the abundance of a number antibiotic resistance genes (ARGs) but not virulence factors (VFs), whereas application of M. anisopliae resulted had only minimal effects. These findings highlight the consequences of use of biological vs. chemical pesticides on soil microbiology can affect plant and ecosystem health indicating that the fungal biological control agent, M. anisopliae likely has far less detrimental and potentially beneficial effects on soil ecology as compared to chemical pesticides.}, } @article {pmid40008244, year = {2025}, author = {Xu, LL and McIlroy, SE and Ni, Y and Guibert, I and Chen, J and Rocha, U and Baker, DM and Panagiotou, G}, title = {Chemical pollution drives taxonomic and functional shifts in marine sediment microbiome, influencing benthic metazoans.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycae141}, pmid = {40008244}, issn = {2730-6151}, abstract = {Microbial communities in marine sediments contribute significantly to the overall health and resiliency of marine ecosystems. However, increased human disturbance undermines biodiversity and, hence, natural functionality provided by marine sediments. Here, through a deep shotgun metagenomics sequencing of the sediment microbiome and COI metabarcoding of benthic metazoans, we demonstrate that >50% of the microorganisms' and metazoan's taxonomic variation can be explained by specific chemical pollution indices. Interestingly, there was a significant correlation between the similarity in microbiome communities' taxonomical and functional attributes and the similarity of benthic metazoans community composition. Furthermore, mediation analysis was conducted to evaluate the microbiome-mediated indirect effect, suggesting that microbial species and functions accounted for 36% and 26%, respectively, of the total effect of pollution on the benthic metazoans. Our study introduces a multi-level perspective for future studies in urbanized coastal areas to explore marine ecosystems, revealing the impact of pollution stress on microbiome communities and their critical biogeochemical functions, which in turn may influence macrofaunal composition.}, } @article {pmid40007605, year = {2025}, author = {Buffet-Bataillon, S and Durão, G and Le Huërou-Luron, I and Rué, O and Le Cunff, Y and Cattoir, V and Bouguen, G}, title = {Gut microbiota dysfunction in Crohn's disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1540352}, pmid = {40007605}, issn = {2235-2988}, mesh = {*Crohn Disease/microbiology ; Humans ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics ; *Feces/microbiology ; Adult ; Female ; Male ; Virulence Factors/genetics ; Bacteria/classification/genetics/isolation & purification ; Oxidative Stress ; Dysbiosis/microbiology ; Middle Aged ; Young Adult ; }, abstract = {INTRODUCTION: Crohn's disease (CD) results from alterations in the gut microbiota and the immune system. However, the exact metabolic dysfunctions of the gut microbiota during CD are still unclear. Here, we investigated metagenomic functions using PICRUSt2 during the course of CD to better understand microbiota-related disease mechanisms and provide new insights for novel therapeutic strategies.

METHODS: We performed 16S rRNA-based microbial profiling of 567 faecal samples collected from a cohort of 383 CD patients, including 291 remissions (CR), 177 mild-moderate (CM) and 99 severe (CS) disease states. Gene and pathway composition was assessed using PICRUSt2 analyses of 16S data.

RESULTS: As expected, changes in alpha and beta diversity, in interaction networks and increases in Proteobacteria abundance were associated with disease severity. However, microbial function was more consistently disrupted than composition from CR, to CM and then to CS. Major shifts in oxidative stress pathways and reduced carbohydrate and amino acid metabolism in favour of nutrient transport were identified in CS compared to CR. Virulence factors involved in host invasion, host evasion and inflammation were also increased in CS.

CONCLUSIONS: This functional metagenomic information provides new insights into community-wide microbial processes and pathways associated with CD pathogenesis. This study paves the way for new advanced strategies to rebalance gut microbiota and/or eliminate oxidative stress, and biofilm to downregulate gut inflammation.}, } @article {pmid39933221, year = {2025}, author = {Cao, Y and Fan, X and Zang, T and Li, Y and Tu, Y and Wei, Y and Bai, J and Liu, Y}, title = {Gut microbiota causes depressive phenotype by modulating glycerophospholipid and sphingolipid metabolism via the gut-brain axis.}, journal = {Psychiatry research}, volume = {346}, number = {}, pages = {116392}, doi = {10.1016/j.psychres.2025.116392}, pmid = {39933221}, issn = {1872-7123}, mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Sphingolipids/metabolism ; Mice ; *Glycerophospholipids/metabolism ; Female ; Humans ; *Depression/metabolism/microbiology ; Pregnancy ; *Brain-Gut Axis/physiology ; *Brain/metabolism ; Fecal Microbiota Transplantation ; Lipid Metabolism/physiology ; Phenotype ; Mice, Inbred C57BL ; }, abstract = {Emerging evidence suggests that changes in the gut microbiota (GM) are related to prenatal depression onset, but the underlying molecular mechanisms remain obscure. This study was conducted to explore how disordered GM is involved in the onset of prenatal depression through the microbiome-gut-brain (MGB) axis. We transplanted fecal microbiota from women with and without prenatal depression into germ-free mice. Fecal metagenomic sequencing and LC-MS untargeted metabolomics analysis were performed to identify the GM composition, function, and metabolites in mice. Lipid metabolomics analysis was then used to characterize the lipid metabolism of brain tissue in mice. We found that mice transplanted with fecal microbiota from women with prenatal depression exhibited depressive-like behaviors as well as characteristic disorders of the phylum Firmicutes. Weighted Gene Correlation Network Analysis identified three microbial and one metabolic module in the gut, alongside two lipid metabolic modules in the brain, as significantly related to all depressive-like behaviors. These modules were enriched for glycerophospholipid and sphingolipid metabolism. In addition, the GM of mice with depressive-like behaviors were enriched and deficient in relevant functions and enzymes in the glycerophospholipid (mainly phosphatidylethanolamine) and sphingolipid (mainly hexosyl-ceramide) metabolic pathways, respectively. Consistently, glycerophospholipid and sphingolipid metabolites in the brains of depressive-like mice were up- and down-regulated. Increased phosphatidylethanolamine and decreased hexosyl-ceramide were significantly related to differential genera in the gut. Collectively, our findings provide a novel microbial and metabolic framework for understanding the role of the MGB axis in prenatal depression, indicating that the GM may be involved in the onset of depressive phenotypes by modulating central glycerophospholipid and sphingolipid metabolic homeostasis.}, } @article {pmid39908139, year = {2025}, author = {Zhang, Z and Guo, Q and Yang, Z and Sun, Y and Jiang, S and He, Y and Li, J and Zhang, J}, title = {Bifidobacterium adolescentis-derived nicotinic acid improves host skeletal muscle mitochondrial function to ameliorate sarcopenia.}, journal = {Cell reports}, volume = {44}, number = {2}, pages = {115265}, doi = {10.1016/j.celrep.2025.115265}, pmid = {39908139}, issn = {2211-1247}, mesh = {Animals ; *Sarcopenia/metabolism/pathology ; *Niacin/pharmacology/metabolism ; Mice ; *Muscle, Skeletal/metabolism/drug effects ; Humans ; Forkhead Box Protein O3/metabolism ; Male ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism ; Mice, Inbred C57BL ; Muscle Proteins/metabolism ; Sirtuin 1/metabolism ; SKP Cullin F-Box Protein Ligases/metabolism ; Mitochondria, Muscle/metabolism/drug effects ; Ubiquitin-Protein Ligases/metabolism ; NAD/metabolism ; Gastrointestinal Microbiome/drug effects ; Mitochondria/metabolism/drug effects ; Female ; Cell Proliferation/drug effects ; Tripartite Motif Proteins ; }, abstract = {Sarcopenia significantly diminishes quality of life and increases mortality risk in older adults. While the connection between the gut microbiome and muscle health is recognized, the underlying mechanisms are poorly understood. In this study, shotgun metagenomics revealed that Bifidobacterium adolescentis is notably depleted in individuals with sarcopenia, correlating with reduced muscle mass and function. This finding was validated in aged mice. Metabolomics analysis identified nicotinic acid as a key metabolite produced by B. adolescentis, linked to improvements in muscle mass and functionality in individuals with sarcopenia. Mechanistically, nicotinic acid restores nicotinamide adenine dinucleotide (NAD+) levels in muscle, inhibits the FoxO3/Atrogin-1/Murf-1 axis, and promotes satellite cell proliferation, reducing muscle atrophy. Additionally, NAD+ activation enhances the silent-information-regulator 1 (SIRT1)/peroxisome-proliferator-activated-receptor-γ-coactivator 1-alpha (PGC-1α) axis, stimulating mitochondrial biogenesis and promoting oxidative metabolism in slow-twitch fibers, ultimately improving muscle function. Our findings suggest that B. adolescentis-derived nicotinic acid could be a promising therapeutic strategy for individuals with sarcopenia.}, } @article {pmid39894225, year = {2025}, author = {Kim, SY and Woo, SY and Kim, HL and Chang, Y and Ryu, S and Kim, HN}, title = {A shotgun metagenomic study identified short-chain fatty acid-producing species and their functions in the gut microbiome of adults with depressive symptoms: Large-scale shotgun sequencing data of the gut microbiota using a cross-sectional design.}, journal = {Journal of affective disorders}, volume = {376}, number = {}, pages = {26-35}, doi = {10.1016/j.jad.2025.01.149}, pmid = {39894225}, issn = {1573-2517}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Cross-Sectional Studies ; *Fatty Acids, Volatile/metabolism ; Adult ; Middle Aged ; *Metagenomics/methods ; *Depression/microbiology/metabolism ; *Feces/microbiology/chemistry ; Faecalibacterium prausnitzii/metabolism/genetics ; Metagenome ; }, abstract = {BACKGROUND: The gut-brain axis is emerging as a novel mechanism to explain depressive disorders.

METHODS: We performed shotgun metagenomic sequencing of stool samples obtained from 133 individuals with depression and 532 without depression. This study examined the taxonomy, functional pathways, and predicted metabolites profiles associated with depressive symptoms, using generalized linear models. To explore links between the taxonomic and functional pathway results, we compared the relative abundance of specific species contributing to pathways significantly associated with depressive symptoms.

RESULTS: Taxonomic composition suggested a disruption in short-chain fatty acid (SCFA)-producing capacity of the gut microbiome in the depressed group. Pathways related to SCFA biosynthesis were also depleted in this group. Faecalibacterium prausnitzii, a well-known SCFA-producing bacterium, was significantly decreased in the depressed group and was identified as a major contributor to the depleted pathways. When inferring the metabolites related to depression from metagenomic data, higher levels of docosapentaenoic acid, stearoyl ethanolamide, putrescine, and bilirubin were more likely to be found in the depressed group.

CONCLUSION: The present findings highlight the altered gut microbiota and associated SCFA-related pathways in individuals with depression. The depletion of F. prausnitzii and its contribution to SCFA production suggest that it is a potential therapeutic target for depression.}, } @article {pmid38961050, year = {2025}, author = {Bandeira, L and Faria, C and Cavalcante, F and Mesquita, A and Martins, C and Martins, S}, title = {Metabarcoding expands knowledge on diversity and ecology of rare actinobacteria in the Brazilian Cerrado.}, journal = {Folia microbiologica}, volume = {70}, number = {1}, pages = {159-175}, pmid = {38961050}, issn = {1874-9356}, support = {421350/2017-2//Instituto Chico Mendes de Conservação da Biodiversidade/ ; 18/2017//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {*Actinobacteria/chemistry/classification/genetics/isolation & purification ; DNA Barcoding, Taxonomic ; RNA, Ribosomal, 16S/analysis ; Parks, Recreational ; Brazil ; *Soil Microbiology ; Biodiversity ; Soil/chemistry ; Metagenome ; }, abstract = {Rare and unknown actinobacteria from unexplored environments have the potential to produce new bioactive molecules. This study aimed to use 16 s rRNA metabarcoding to determine the composition of the actinobacterial community, particularly focusing on rare and undescribed species, in a nature reserve within the Brazilian Cerrado called Sete Cidades National Park. Since this is an inaccessible area without due legal authorization, it is understudied, and, therefore, its diversity and biotechnological potential are not yet fully understood, and it may harbor species with groundbreaking genetic potential. In total, 543 operational taxonomic units (OTUs) across 14 phyla were detected, with Actinobacteria (41.2%), Proteobacteria (26.5%), and Acidobacteria (14.3%) being the most abundant. Within Actinobacteria, 107 OTUs were found, primarily from the families Mycobacteriaceae, Pseudonocardiaceae, and Streptomycetaceae. Mycobacterium and Streptomyces were the predominant genera across all samples. Seventeen rare OTUs with relative abundance < 0.1% were identified, with 82.3% found in only one sample yet 25.5% detected in all units. Notable rare and transient genera included Salinibacterium, Nocardia, Actinomycetospora_01, Saccharopolyspora, Sporichthya, and Nonomuraea. The high diversity and distribution of Actinobacteria OTUs indicate the area's potential for discovering new rare species. Intensified prospection on underexplored environments and characterization of their actinobacterial diversity could lead to the discovery of new species capable of generating innovative natural products.}, } @article {pmid40006931, year = {2025}, author = {Sarker, S and Talukder, S and Athukorala, A and Whiteley, PL}, title = {The Spleen Virome of Australia's Endemic Platypus Is Dominated by Highly Diverse Papillomaviruses.}, journal = {Viruses}, volume = {17}, number = {2}, pages = {}, doi = {10.3390/v17020176}, pmid = {40006931}, issn = {1999-4915}, mesh = {Animals ; *Phylogeny ; *Platypus/virology ; *Virome ; *Genome, Viral ; Australia ; *Papillomaviridae/genetics/classification/isolation & purification ; *Spleen/virology ; High-Throughput Nucleotide Sequencing ; DNA, Viral/genetics ; Genetic Variation ; }, abstract = {The platypus (Ornithorhynchus anatinus), a unique monotreme, represents a pivotal point in mammalian evolution with its distinctive traits, such as electroreception and venom production. Despite its evolutionary significance, the viral diversity within platypuses remains poorly understood. This study employed next-generation sequencing to investigate the virome of the dead platypuses, uncovering a range of novel and divergent viruses. Among the identified viruses were four complete genomes of papillomaviruses (OaPV1-4) exhibiting substantial divergence from known strains, suggesting a novel genus within the subfamily Secondpapillomavirinae. Additionally, five novel parvoviruses were detected, including two with complete genomes, highlighting the complex viral ecosystem of the platypus. Phylogenetic analysis placed these viruses in unique evolutionary branches, further demonstrating the platypus's evolutionary significance. A circular DNA virus, a tombus-like virus, and a nodamuvirus were also identified, expanding the understanding of viral diversity in monotremes. These findings offer crucial insights into viral evolution in one of the most unique mammalian lineages, emphasising the need for further exploration to assess ecological and pathological impacts on platypus populations.}, } @article {pmid40005640, year = {2025}, author = {Cao, X and Cui, Q and Li, D and Liu, Y and Liu, K and Li, Z}, title = {Characteristics of Soil Microbial Community Structure in Different Land Use Types of the Huanghe Alluvial Plain.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020273}, pmid = {40005640}, issn = {2076-2607}, support = {2022YSKY-57//Integrated analysis of soil hydrologic function of returning farmland to forest (grass) in Basic Scientific Research Youth Exploration Project of Central public welfare research Institute of Chinese Research Academy of Environmental Sciences, China/ ; }, abstract = {The Huanghe alluvial plain plays a crucial role in biodiversity conservation. However, its ecosystem has become sensitive and fragile due to long-term human disturbances. Enhancing the resilience of this ecosystem and promoting the sustainable use of land resources are key to addressing its ecological challenges. Soil microbial communities are vital to ecosystem functioning, and land use is a major human factor influencing their structure and diversity. Existing research on the Huanghe alluvial plain primarily focuses on soil physicochemical properties and moisture content, with relatively limited attention given to soil microorganisms. Therefore, this study, using the Wudi Tanyang Forest Farm in the Huanghe alluvial plain as a case study, employs high-throughput metagenomic sequencing to analyze the composition and diversity of soil bacteria, eukaryota, archaea, and virus communities in five different land use types (Tamarix chinensis forest, Fraxinus chinensis forest, farmland, wetland, and grassland). The results indicate that: (1) At the phylum level, the top three bacteria communities were Pseudomonadota, Acidobacteriota, and Actinomycetota; the top three in the eukaryota communities were Ascomycota, Mucoromycota, and Basidiomycotina; the top three in the archaea communities were Nitrososphaerota, Euryarchaeota, and Candidatus Thermoplasmatota; and the virus communities were dominated by Uroviricota; (2) The microbial community structure of the Tamarix chinensis forest and the Fraxinus chinensis forest was similar, and was significantly different from the other three land use types; (3) The land use type had a significant effect on the diversity of the soil microbial communities, with a higher diversity in the wetland and grassland soils; (4) The dominant species of the soil microbial communities under different land use types showed significant differences. This study provides theoretical support for land use optimization and sustainable soil management in the Huanghe alluvial plain region.}, } @article {pmid40005401, year = {2025}, author = {Straume, Z and Krūmiņa, N and Elbere, I and Rozenberga, M and Erts, R and Rudzīte, D and Proskurina, A and Krumina, A}, title = {Impact of Vitamins, Antibiotics, Probiotics, and History of COVID-19 on the Gut Microbiome in Ulcerative Colitis Patients: A Cross-Sectional Study.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {61}, number = {2}, pages = {}, doi = {10.3390/medicina61020284}, pmid = {40005401}, issn = {1648-9144}, support = {1.1.1.1/21/A/029//the European Regional Development Fund (ERDF)/ ; }, mesh = {Humans ; Cross-Sectional Studies ; Female ; *Colitis, Ulcerative/drug therapy/microbiology ; Male ; *Gastrointestinal Microbiome/drug effects ; *COVID-19 ; *Vitamins/therapeutic use ; Adult ; Middle Aged ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Probiotics/therapeutic use ; *SARS-CoV-2 ; Aged ; }, abstract = {Background and Objectives: The human gut microbiome is essential for the health of the host and is affected by antibiotics and coronavirus disease 2019 (COVID-19). The gut microbiome is recognized as a contributing factor in the development of ulcerative colitis. Specific vitamins and probiotics have been demonstrated to positively influence the microbiome by enhancing the prevalence of expected beneficial microorganisms. Materials and Methods: Forty-nine ulcerative colitis (UC) outpatients from Riga East Clinical University Hospital were enrolled in this cross-sectional study from June 2021 to December 2021. All patients were divided into groups based on history of COVID-19 (COVID-19 positive vs. COVID-19 negative) in the last six months. Information about antibiotic, probiotic, and vitamin intake were outlined, and faecal samples were collected. The MetaPhlAn v.2.6.0 tool was used for the taxonomic classification of the gut microbiome metagenome data. Statistical analysis was performed using R 4.2.1. Results: Of the 49 patients enrolled, 31 (63%) were male and 18 (37%) were female. Coronavirus disease 2019 was found in 14 (28.6%) patients in the last 6 months. Verrucomicrobia was statistically significantly lower in the COVID-19 positive group (M = 0.05; SD = 0.11) compared to the COVID-19 negative group (M = 0.5; SD = 1.22), p = 0.03. Antibiotic non-users had more Firmicutes in their microbiome than antibiotic users (p = 0.008). The most used vitamin supplement was vitamin D (N = 18), fifteen (42.9%) of the patients were COVID-19 negative and 3 (21.4%) were COVID-19 positive over the last six months (p > 0.05). Vitamin C users had more Firmicutes in their gut microbiome compared to non-users (Md = 72.8 [IQR: 66.6; 78.7] vs. Md = 60.1 [IQR: 42.4; 67.7]), p = 0.01. Conclusions: Antibiotic non-users had more Firmicutes than antibiotic users in their gut microbiome. Only vitamin C had statistically significant results; in users, more Firmicutes were observed. A mild course of COVID-19 may not influence ulcerative colitis patients' gut microbiome.}, } @article {pmid40005052, year = {2025}, author = {Zang, P and Chen, P and Chen, J and Sun, J and Lan, H and Dong, H and Liu, W and Xu, N and Wang, W and Hou, L and Sun, B and Zhang, L and Huang, J and Wang, P and Ren, F and Liu, S}, title = {Alteration of Gastrointestinal Function and the Ameliorative Effects of Hericium erinaceus Polysaccharides in Tail Suspension Rats.}, journal = {Nutrients}, volume = {17}, number = {4}, pages = {}, doi = {10.3390/nu17040724}, pmid = {40005052}, issn = {2072-6643}, support = {242300421105//Henan Natural Science Foundation of Excellent Young Scholars/ ; }, mesh = {Animals ; *Rats, Sprague-Dawley ; *Gastrointestinal Microbiome/drug effects ; *Hericium ; Rats ; Male ; *Polysaccharides/pharmacology ; Hindlimb Suspension ; Dysbiosis ; Dietary Supplements ; Gastrointestinal Tract/drug effects ; Gastrointestinal Diseases/drug therapy/prevention & control ; Weightlessness Simulation ; }, abstract = {Background/Objectives: Long-term spaceflight in a microgravity environment frequently results in gastrointestinal dysfunction, presenting substantial challenges to astronauts' health. Hericium erinaceus, a plant recognized for its dual use as food and medicine, contains a key functional component called Hericium erinaceus polysaccharide (HEP), which is purported to promote gastrointestinal health. This study aims to investigate the protective effects of HEP against gastrointestinal disturbances induced by simulated weightlessness and to elucidate its regulatory mechanisms. Methods: Sprague Dawley rats subjected to a tail suspension model were administered either a standard diet or a diet supplemented with 0.125% HEP over a period of 4 weeks (the intake of HEP is approximately 157.5 mg/kg bw/d, n = 8), metagenomics and targeted metabolomics to investigate the effects of HEP on gastrointestinal hormone secretion disorders, gut microbiota dysbiosis, and intestinal barrier damage induced by simulated weightlessness. Results: Dietary supplementation with HEP was observed to significantly alleviate weightlessness-induced gastrointestinal hormone disruptions, enhancing motility and intestinal barrier function while reducing inflammation. In addition, HEP improved gut microbiota by boosting beneficial bacteria as Oscillibacter sp.1-3, Firmicutes bacterium ASF500, and Lactobacillus reuteri, while reducing harmful bacteria like Escherichia coli and Mucispirillum schaedleri at the species level. Furthermore, HEP altered the serum metabolic profile of the rats, reducing inflammation by upregulating the tryptophan metabolism pathway and enhancing the production of short-chain fatty acids. Conclusions: HEP effectively protects against gastrointestinal dysfunction induced by simulated weightlessness by regulating hormone secretion and maintaining intestinal homeostasis.}, } @article {pmid40004244, year = {2025}, author = {Blankestijn, JM and Baalbaki, N and Beijers, RJHCG and Cornelissen, MEB and Wiersinga, WJ and Abdel-Aziz, MI and Maitland-van der Zee, AH and , }, title = {Exploring Heterogeneity of Fecal Microbiome in Long COVID Patients at 3 to 6 Months After Infection.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, doi = {10.3390/ijms26041781}, pmid = {40004244}, issn = {1422-0067}, support = {LSHM20104; LSHM20068//Health Holland/ ; }, mesh = {Humans ; *COVID-19/microbiology/virology ; *Feces/microbiology/virology ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Aged ; *SARS-CoV-2/isolation & purification ; Adult ; Metagenome ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {An estimated 10% of COVID-19 survivors have been reported to suffer from complaints after at least three months. The intestinal microbiome has been shown to impact long COVID through the gut-lung axis and impact the severity. We aimed to investigate the relationship between the gut microbiome and clinical characteristics, exploring microbiome heterogeneity through clustering. Seventy-nine patients with long COVID evaluated at 3 to 6 months after infection were sampled for fecal metagenome analysis. Patients were divided into two distinct hierarchical clusters, based solely on the microbiome composition. Compared to cluster 1 (n = 67), patients in cluster 2 (n = 12) showed a significantly reduced lung function (FEV1, FVC, and DLCO) and during acute COVID-19 showed a longer duration of hospital admissions (48 compared to 7 days) and higher rates of ICU admissions (92% compared to 22%). Additionally, the microbiome composition showed a reduced alpha diversity and lower proportion of butyrate-producing bacteria in cluster 2 together with higher abundances of Ruminococcus gnavus, Escherichia coli, Veillonella spp. and Streptococcus spp. and reduced abundances of Faecalibacterium prausnitzii and Eubacteria spp. Further research could explore the effect of pre- and pro-biotic supplementation and its impact on lung function and societal participation in long COVID.}, } @article {pmid40004174, year = {2025}, author = {Cui, Y and Guan, H and Okyere, SK and Hua, Z and Deng, Y and Deng, H and Ren, Z and Deng, J}, title = {Microbial Guardians or Foes? Metagenomics Reveal Association of Gut Microbiota in Intestinal Toxicity Caused by DON in Mice.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, doi = {10.3390/ijms26041712}, pmid = {40004174}, issn = {1422-0067}, support = {. 32273072//This research was supported by National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Trichothecenes/toxicity ; *Metagenomics/methods ; Cytokines/metabolism ; Intestinal Mucosa/metabolism/microbiology/pathology ; Zonula Occludens-1 Protein/metabolism/genetics ; Male ; Colon/microbiology/metabolism/pathology/drug effects ; Jejunum/microbiology/pathology/metabolism/drug effects ; Occludin/metabolism/genetics ; Intestines/microbiology/pathology/drug effects ; }, abstract = {The role of gut microbiota has become a research hotspot in recent years; however, whether the gut microbiota are involved in the alleviation or exacerbation of Deoxynivalenol (DON) toxicity has not been fully studied. Therefore, the objective of this study was to investigate whether the gut microbiota are involved in reducing or aggravating the intestinal damage induced by DON in mice. Mice that received or did not receive antibiotic-induced intestinal flora clearance were orally given DON (5 mg kg/bw/day) for 14 days. At the end of the experiment, serum, intestinal tissue samples and colon contents were collected for further analysis. DON caused development of severe histopathological damage, such as necrosis and inflammation of the jejunum and colon in mice without gut microbiota clearance. The levels of tight junction proteins ZO-1 and occludin were reduced in the jejunum and colon of mice without gut microbiota clearance. In addition, the mRNA and protein levels of pro-inflammatory cytokines (IL-1β, IL-6, and TNF-α) were increased in mice without gut microbiota clearance. The presence of microbiota exacerbate the intestinal damage induced by DON via changes in gut microbiota abundance and production of gut damaging metabolites.}, } @article {pmid40003915, year = {2025}, author = {Chao, X and Fan, Z and Wu, J and Ye, C and Wang, X and Li, R and Chen, S and Zhang, X and Fang, C and Luo, Q}, title = {Application of mRNA-Seq and Metagenomic Sequencing to Study Salmonella pullorum Infections in Chickens.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, doi = {10.3390/ijms26041448}, pmid = {40003915}, issn = {1422-0067}, support = {2022B0202100002//Key-Area Research and Development Program of Guangdong Province/ ; 2024B03J1353//Science and Technology Program of Guangzhou City/ ; 2023ZD04064//STI2030-Major Projects/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Poultry Diseases/microbiology/genetics ; *Metagenomics/methods ; *Salmonella Infections, Animal/microbiology/genetics ; Cecum/microbiology ; RNA, Messenger/genetics/metabolism ; Gastrointestinal Microbiome/genetics ; Alternative Splicing ; Salmonella/genetics/pathogenicity ; RNA-Seq/methods ; Gene Expression Profiling ; Metagenome ; Gene Expression Regulation ; }, abstract = {The disease caused by Salmonella pullorum has been demonstrated to exert a deleterious effect on the performance of poultry, giving rise to elevated mortality and considerable economic losses within the breeding industry. However, there is a paucity of research investigating the relationship between cecal gene expression and different isomer and Salmonella pullorum infection, and research on the relationship between intestinal microbiota and Salmonella pullorum infection is also limited. In this study, mRNA-Seq and metagenomic sequencing were performed on the cecal tissues and fresh feces of individuals who tested positive (n = 4) and negative (n = 4) for Salmonella pullorum, with the aim of exploring the chickens infected with Salmonella pullorum from two perspectives: the gene transcription level and the microbial level. The mRNA sequencing results revealed 1560 differentially expressed genes (DEGs), of which 380 genes were found to be up-regulated and 1180 genes were down-regulated. A number of genes were reported to be associated with immunity, including AQP8, SLC26A3, CBS, IFI6, DDX60, IL8L1 and IL8L2. Furthermore, a total of 1047 differentially expressed alternative splicings (DEASs) were identified through alternative splicing analysis, including CBS, SLC6A9, ILDR2, OCRL, etc. The joint analysis of DEGs and DEASs revealed 70 genes that exhibited both differentially expressed alternative splicings and differential expression, including CTNND1, TPM1, SPPL2A, etc. The results of metagenomic sequencing demonstrated that the abundances of Bacteroides, Firmicutes, and Verrucobacteria underwent a significant alteration subsequent to the infection of Salmonella pullorum. In summary, the present study conducted a preliminary exploration of the genetic basis of chickens infected with Salmonella pullorum. TPM1 and SPPL2A were found to be differentially expressed by mRNA-Seq, and differences in alternative splicing events. Furthermore, metagenomic sequencing revealed significant changes in the microbial communities of Bacteroidetes, Firmicutes, and Verrucobacteria during infection with Salmonella pullorum.}, } @article {pmid40003912, year = {2025}, author = {Chatzokou, D and Tsarna, E and Davouti, E and Siristatidis, CS and Christopoulou, S and Spanakis, N and Tsakris, A and Christopoulos, P}, title = {Semen Microbiome, Male Infertility, and Reproductive Health.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, doi = {10.3390/ijms26041446}, pmid = {40003912}, issn = {1422-0067}, mesh = {Male ; Humans ; *Microbiota ; *Semen/microbiology ; *Infertility, Male/microbiology ; *Reproductive Health ; Female ; Reproductive Techniques, Assisted ; Spermatozoa/microbiology ; Fertility ; Pregnancy ; }, abstract = {The semen microbiome, once believed to be sterile, is now recognized as a dynamic ecosystem containing a diverse range of microorganisms with potential implications for male fertility and reproductive health. We aimed to examine the relationship between the semen microbiome, male infertility, and reproductive outcomes, highlighting the transformative role of next generation sequencing techniques and bioinformatics in exploring this intricate interaction, and we present a critical review of the published literature on this issue. Current evidence suggests a complex association between the composition of the semen microbiome and male fertility, with certain bacterial genera, such as Lactobacillus and Prevotella that exert opposing effects on sperm quality and DNA integrity. In addition, the influence of the semen microbiome extends beyond natural fertility, affecting assisted reproductive technologies and pregnancy outcomes. Despite considerable progress, challenges remain in standardizing methodologies and interpreting findings. In conclusion, we identify the lack of a definitive management proposal for couples presenting with this phenomenon, and we underline the need for an algorithm and indicate the questions raised that point toward our goal for a strategy. Continued research is essential to clarify the role of the semen microbiome in male reproductive health and to advance the development of personalized fertility management approaches.}, } @article {pmid40000989, year = {2025}, author = {Zhao, M and Zhang, Y and Liu, S and Wang, F and Zhang, P}, title = {Eradication of Helicobacter pylori reshapes gut microbiota and facilitates the evolution of antimicrobial resistance through gene transfer and genomic mutations in the gut.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {90}, pmid = {40000989}, issn = {1471-2180}, support = {32201393//National Natural Science Foundation of China/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Humans ; *Helicobacter pylori/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Helicobacter Infections/microbiology/drug therapy ; *Gene Transfer, Horizontal ; *Feces/microbiology ; Mutation ; Metagenomics ; Klebsiella/genetics/drug effects ; Female ; Male ; Genome, Bacterial/genetics ; Adult ; Escherichia/genetics/drug effects ; Middle Aged ; Genes, Bacterial/genetics ; }, abstract = {Treating Helicobacter pylori (H. pylori) infection requires large quantities of antibiotics, thus dramatically promoting the enrichment and dissemination of antimicrobial resistance (AMR) in feces. However, the influence of H. pylori eradication on the AMR mobility and the gut microbiota evolution has yet to be thoroughly investigated. Here, a study involving 12 H. pylori-positive participants was conducted, and the pre- and post- eradication fecal samples were sequenced. Metagenomic analysis revealed that the eradication treatment drastically altered the gut microbiome, with the Escherichia and Klebsiella genera emerging as the predominant bacteria. Interestingly, the eradication treatment significantly increased the relative abundance and diversity of resistome and mobilome in gut microbiota. Eradication of H. pylori also enriched AMR genes (ARGs) conferring resistance to antibiotics not administered because of the co-location with other ARGs or mobile genetic elements (MGEs). Additionally, the Escherichia and Klebsiella genera were identified as the primary bacterial hosts of these highly transferable ARGs. Furthermore, the genomic variations associated with ARGs in Escherichia coli (E. coli) caused by the eradication treatment were profiled, including the parC, parE, and gyrA genes. These findings revealed that H. pylori eradication promoted the enrichment of ARGs and MGEs in the Escherichia and Klebsiella genera, and further facilitated bacterial evolution through the horizontal transfer of ARGs and genomic variations.}, } @article {pmid39998665, year = {2025}, author = {Szóstak, N and Budnik, M and Tomela, K and Handschuh, L and Samelak-Czajka, A and Pietrzak, B and Schmidt, M and Kaczmarek, M and Galus, Ł and Mackiewicz, J and Mackiewicz, A and Kozlowski, P and Philips, A}, title = {Exploring correlations between gut mycobiome and lymphocytes in melanoma patients undergoing anti-PD-1 therapy.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {74}, number = {4}, pages = {110}, pmid = {39998665}, issn = {1432-0851}, support = {2017/25/B/NZ5/01949//Narodowe Centrum Nauki/ ; POIR.04.01.02-00-0025/17-00//Narodowe Centrum Badań i Rozwoju/ ; }, mesh = {Humans ; *Melanoma/drug therapy/immunology ; *Gastrointestinal Microbiome/immunology/drug effects ; Male ; Female ; Middle Aged ; *Lymphocytes/immunology ; *Immune Checkpoint Inhibitors/therapeutic use ; *Mycobiome ; Aged ; Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Adult ; Skin Neoplasms/immunology/drug therapy/microbiology ; Fungi/immunology ; }, abstract = {Research has shown that the microbiome can influence how the immune system responds to melanoma cells, affecting the course of the disease and the outcome of the therapy. Here, we used the metagenomic approach and flow cytometry analyses of blood cells to discover correlations between gut fungi of metastatic melanoma patients enrolled in anti-PD-1 therapy and lymphocytes in their blood.We analyzed the patterns of associations before the first administration of anti-PD-1 therapy (BT, n = 61) and in the third month of the therapy (T3, n = 37), allowing us to track changes during treatment. To understand the possible impact of gut fungi on the efficacy of anti-PD-1 therapy, we analyzed the associations in clinical beneficiaries (CB, n = 37) and non-beneficiaries (NB, n = 24), as well as responders (R, n = 28) and non-responders (NR, n = 33).Patients with LDH < 338 units/L, overall survival (OS) > 12, CB, as well as R, had lower levels of Shannon diversity (p = 0.02, p = 0.05, p = 0.05, and p = 0.03, respectively). We found that the correlation pattern between intestinal fungi and lymphocytes was specific to the type of response, positive or negative. When comparing CB and NB groups, correlations with opposite directions were detected for C. albicans, suggesting a response-specific immune reaction. For CB, M. restricta exhibited a set of correlations with different types of lymphocytes, with prevalent positive correlations, suggesting a robust immune response in the CB group. This result extends our former research, where M. restricta and C. albicans were associated with an increased risk of melanoma progression and a poorer response to anti-PD-1 treatment.}, } @article {pmid39997957, year = {2025}, author = {Muhie, S and Gautam, A and Mylroie, J and Sowe, B and Campbell, R and Perkins, EJ and Hammamieh, R and Garcia-Reyero, N}, title = {Effects of Environmental Chemical Pollutants on Microbiome Diversity: Insights from Shotgun Metagenomics.}, journal = {Toxics}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/toxics13020142}, pmid = {39997957}, issn = {2305-6304}, abstract = {Chemical exposure in the environment can adversely affect the biodiversity of living organisms, particularly when persistent chemicals accumulate over time and disrupt the balance of microbial populations. In this study, we examined how chemical contaminants influence microorganisms in sediment and overlaying water samples collected from the Kinnickinnic, Milwaukee, and Menomonee Rivers near Milwaukee, Wisconsin, USA. We characterized these samples using shotgun metagenomic sequencing to assess microbiome diversity and employed chemical analyses to quantify more than 200 compounds spanning 16 broad classes, including pesticides, industrial products, personal care products, and pharmaceuticals. Integrative and differential comparative analyses of the combined datasets revealed that microbial density, approximated by adjusted total sequence reads, declined with increasing total chemical concentrations. Protozoan, metazoan, and fungal populations were negatively correlated with higher chemical concentrations, whereas certain bacterial (particularly Proteobacteria) and archaeal populations showed positive correlations. As expected, sediment samples exhibited higher concentrations and a wider dynamic range of chemicals compared to water samples. Varying levels of chemical contamination appeared to shape the distribution of microbial taxa, with some bacterial, metazoan, and protozoan populations present only at certain sites or in specific sample types (sediment versus water). These findings suggest that microbial diversity may be linked to both the type and concentration of chemicals present. Additionally, this study demonstrates the potential roles of multiple microbial kingdoms in degrading environmental pollutants, emphasizing the metabolic versatility of bacteria and archaea in processing complex contaminants such as polyaromatic hydrocarbons and bisphenols. Through functional and resistance gene profiling, we observed that multi-kingdom microbial consortia-including bacteria, fungi, and protozoa-can contribute to bioremediation strategies and help restore ecological balance in contaminated ecosystems. This approach may also serve as a valuable proxy for assessing the types and levels of chemical pollutants, as well as their effects on biodiversity.}, } @article {pmid39950859, year = {2025}, author = {Ma, Y and Zhang, M and Wang, Z and Cao, L and Li, Y and Wan, Z and Kane, Y and Wang, G and Li, X and Zhang, C}, title = {Short-term antiretroviral therapy may not correct the dysregulations of plasma virome and cytokines induced by HIV-1 infection.}, journal = {Virulence}, volume = {16}, number = {1}, pages = {2467168}, doi = {10.1080/21505594.2025.2467168}, pmid = {39950859}, issn = {2150-5608}, mesh = {Humans ; *HIV Infections/drug therapy/virology/blood/immunology ; *Cytokines/blood ; *HIV-1/genetics/drug effects ; Male ; *Virome ; Adult ; Female ; Middle Aged ; Anti-Retroviral Agents/therapeutic use ; Metagenomics ; Anelloviridae/genetics ; Cohort Studies ; }, abstract = {An expansion of plasma anelloviruses and dysregulation of inflammation was associated with HIV-1 infection. However, how antiretroviral therapy (ART) affects the dynamics of plasma virome and cytokine profile remains largely unknown. To characterize the dynamics of plasma virome and cytokines in HIV-1-infected individuals before and during the first year of ART, a cohort of 26 HIV-1-infected individuals and 19 healthy controls was recruited. Blood samples were collected and subjected to metagenomic analysis and the measurement of 27 cytokines. Metagenomic analysis revealed an increased abundance and prevalence of human pegivirus type 1 (HPgV-1) and a slightly decreased diversity and abundance of anellovirus in plasma of HIV-1-infected individuals after ART. No obvious impact was observed on other plasma commensal viruses. Increased abundance and prevalence of HPgV-1 were further confirmed by RT-qPCR assay in a larger cohort of 114 HIV-1-infected individuals. Notably, most dysregulated cytokines were not fully restored by ART, with extremely abnormal levels of IL-10, GM-CSF, VEGF, and eotaxin, and a significantly increased level of plasma I-FABP. Anelloviruses showed significantly negative correlations with other commensal viruses except HPgV-1 but had positive correlations with several anti-inflammatory and Th1 cytokines. These results suggest that short-term ART may not significantly correct the virome and cytokine dysregulations induced by HIV-1 infection. The results highlight a need for further investigation into the long-term effects of ART on virome and cytokine profiles in HIV-1-infected individuals.}, } @article {pmid39938296, year = {2025}, author = {Tan, L and Liang, J and Qin, Z and Ning, T and Wei, X and Yang, B and Wang, Q and Xu, Y and Shen, F}, title = {Unveiling the sustained effects of plant root exudates on soil microbiome and resistome and the related functional traits.}, journal = {Journal of environmental management}, volume = {376}, number = {}, pages = {124485}, doi = {10.1016/j.jenvman.2025.124485}, pmid = {39938296}, issn = {1095-8630}, mesh = {*Soil Microbiology ; *Plant Roots/microbiology/drug effects ; *Microbiota/drug effects ; *Rhizosphere ; *Plant Exudates ; Soil/chemistry ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects/metabolism ; }, abstract = {Investigating the transmission mechanisms and influencing factors of antibiotic resistance genes (ARGs) in the soil-plant continuum is vital for mitigating ARG contamination and safeguarding plant and human health. Rhizosphere soil serves as a crucial interface for ARG propagation and transmission; however, it is unclear whether and how plant involved in regulating ARGs in their rhizosphere environment. Root exudates acting as vital links in the plant-soil-microbe interaction. Here, we examined the fluctuating patterns of the resistome and mobile genetic elements (MGEs) following exposure to four types of common root exudates: amino acids (AAs), sugars, long-chain organic acids (LCOAs), and short-chain organic acids (SCOAs). AAs exerted a rapid and pronounced effect, leading to a significant elevation in total ARG and MGE abundance by 3.18-fold and 21.06-fold, respectively, compared to the control group by day 7. Conversely, the impact of sugars manifested gradually over time. The influence of AAs and sugars persisted beyond 240 days post-treatment cessation. Importantly, the proliferation of ARGs was closely linked to the enrichment of plant growth-promoting bacteria (PGPBs) such as Pseudomonas, Cupriavidus, Azospirillum, Variovorax, and Ensifer. Functional analysis revealed that the potential features of ARGs and MGEs were associated with cell wall/membrane/envelope biogenesis, cell motility, and inorganic ion transport. This study offers novel insights into the factors influencing the dynamics of ARGs in the plant rhizosphere and may contribute to ecologically sustainable agricultural practices.}, } @article {pmid39846163, year = {2025}, author = {Jena, PK and Arditi, M and Noval Rivas, M}, title = {Gut Microbiota Alterations in Patients With Kawasaki Disease.}, journal = {Arteriosclerosis, thrombosis, and vascular biology}, volume = {45}, number = {3}, pages = {345-358}, doi = {10.1161/ATVBAHA.124.321201}, pmid = {39846163}, issn = {1524-4636}, support = {R01 HL139766/HL/NHLBI NIH HHS/United States ; R01 HL159297/HL/NHLBI NIH HHS/United States ; R01 HL149972/HL/NHLBI NIH HHS/United States ; R01 AI157274/AI/NIAID NIH HHS/United States ; R01 HL170580/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/microbiology/immunology ; *Gastrointestinal Microbiome ; *Dysbiosis ; Animals ; Bacteria ; Risk Factors ; Feces/microbiology ; Host-Pathogen Interactions ; }, abstract = {The intestinal microbiota influences many host biological processes, including metabolism, intestinal barrier functions, and immune responses in the gut and distant organs. Alterations in its composition have been associated with the development of inflammatory disorders and cardiovascular diseases, including Kawasaki disease (KD). KD is an acute pediatric vasculitis of unknown etiology and the leading cause of acquired heart disease in children in the United States. The presence of gastrointestinal symptoms in the acute phase of KD has been associated with an increased risk of treatment resistance and the development of coronary artery aneurysms. Studies report alterations in fecal bacterial communities of patients with KD, characterized by the blooming of pathogenic bacteria and decreased relative abundance of short-chain fatty acid-producing bacteria. However, causality and functionality cannot be established from these observational patient cohorts of KD. This highlights the need for more advanced and rigorous studies to establish causality and functionality in both experimental models of KD vasculitis and patient cohorts. Here, we review the evidence linking an altered gut microbiota composition to the development of KD, assess the potential mechanisms involved in this process, and discuss the potential therapeutic value of these observations.}, } @article {pmid39997213, year = {2025}, author = {Calado, R and Leal, MC and Silva, RXG and Borba, M and Ferro, A and Almeida, M and Madeira, D and Vieira, H}, title = {Living Coral Displays, Research Laboratories, and Biobanks as Important Reservoirs of Chemodiversity with Potential for Biodiscovery.}, journal = {Marine drugs}, volume = {23}, number = {2}, pages = {}, doi = {10.3390/md23020089}, pmid = {39997213}, issn = {1660-3397}, support = {UIDB/50017/2020 + UIDP/50017/2020 + LA/P/0094/2020//Fundação para a Ciência e Tecnologia/ ; (Project Nº. C644915664-00000026)//"BLUE BIOECONOMY PACT", co-funded by the Next Gen-eration EU European Fund, under the incentive line "Agendas for Business Innovation" within Component 5-Capitalization and Business Innovation of the Portuguese Recovery and Resili-ence Plan (RRP), specifi/ ; }, mesh = {*Anthozoa/metabolism ; Animals ; *Coral Reefs ; *Biological Specimen Banks ; Bioprospecting ; Laboratories ; Humans ; Biological Products ; }, abstract = {Over the last decades, bioprospecting of tropical corals has revealed numerous bioactive compounds with potential for biotechnological applications. However, this search involves sampling in natural reefs, and this is currently hampered by multiple ethical and technological constraints. Living coral displays, research laboratories, and biobanks currently offer an opportunity to continue to unravel coral chemodiversity, acting as "Noah's Arks" that may continue to support the bioprospecting of molecules of interest. This issue is even more relevant if one considers that tropical coral reefs currently face unprecedent threats and irreversible losses that may impair the biodiscovery of molecules with potential for new products, processes, and services. Living coral displays provide controlled environments for studying corals and producing both known and new metabolites under varied conditions, and they are not prone to common bottlenecks associated with bioprospecting in natural coral reefs, such as loss of the source and replicability. Research laboratories may focus on a particular coral species or bioactive compound using corals that were cultured ex situ, although they may differ from wild conspecifics in metabolite production both in quantitative and qualitative terms. Biobanks collect and preserve coral specimens, tissues, cells, and/or information (e.g., genes, associated microorganisms), which offers a plethora of data to support the study of bioactive compounds' mode of action without having to cope with issues related to access, standardization, and regulatory compliance. Bioprospecting in these settings faces several challenges and opportunities. On one hand, it is difficult to ensure the complexity of highly biodiverse ecosystems that shape the production and chemodiversity of corals. On the other hand, it is possible to maximize biomass production and fine tune the synthesis of metabolites of interest under highly controlled environments. Collaborative efforts are needed to overcome barriers and foster opportunities to fully harness the chemodiversity of tropical corals before in-depth knowledge of this pool of metabolites is irreversibly lost due to tropical coral reefs' degradation.}, } @article {pmid39991687, year = {2025}, author = {Pan, Y and Jiao, FY}, title = {Helicobacter pylori infection and gastric microbiota: Insights into gastric and duodenal ulcer development.}, journal = {World journal of gastroenterology}, volume = {31}, number = {7}, pages = {100044}, pmid = {39991687}, issn = {2219-2840}, mesh = {Humans ; *Helicobacter Infections/microbiology ; *Helicobacter pylori/isolation & purification/genetics/pathogenicity ; *Duodenal Ulcer/microbiology ; *Gastrointestinal Microbiome ; *Stomach Ulcer/microbiology ; *Gastric Mucosa/microbiology/pathology ; Metagenomics/methods ; Stomach/microbiology/pathology ; Dysbiosis/microbiology ; }, abstract = {Helicobacter pylori (H. pylori) infection plays a critical role in gastric diseases, impacting the microbiota structure in gastric and duodenal ulcers. In their study, Jin et al utilized metagenomic sequencing to analyze mucosal samples from patients with ulcers and healthy controls, revealing significant changes in microbial diversity and composition. This article reviews their findings, emphasizing H. pylori's role in gastric ulcers and the need for further research on its impact on duodenal ulcers. We evaluate the study's strengths and limitations, suggesting future research directions to enhance our understanding of H. pylori's contribution to ulcerative diseases.}, } @article {pmid39991683, year = {2025}, author = {Darnindro, N and Abdullah, M and Sukartini, N and Rumende, CM and Pitarini, A and Nursyirwan, SA and Fauzi, A and Makmun, D and Nelwan, EJ and Shatri, H and Rinaldi, I and Tanadi, C}, title = {Differences in diversity and composition of mucosa-associated colonic microbiota in colorectal cancer and non-colorectal cancer in Indonesia.}, journal = {World journal of gastroenterology}, volume = {31}, number = {7}, pages = {100051}, pmid = {39991683}, issn = {2219-2840}, mesh = {Humans ; Indonesia/epidemiology ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Case-Control Studies ; *Colonoscopy ; *Colon/microbiology ; *Intestinal Mucosa/microbiology ; *RNA, Ribosomal, 16S/genetics ; Aged ; Adult ; Metagenomics/methods ; Bacteria/isolation & purification/genetics/classification ; }, abstract = {BACKGROUND: Colorectal cancer is the third most common malignancy and the fourth leading cause of cancer-related deaths worldwide. Several studies have shown an association between gut microbiota and colorectal cancer. Gut microbiota is unique and can be influenced by geographic factors and habits. This study aimed to determine the diversity and composition of colonic mucosal microbiota in patients with and without colorectal cancer.

AIM: To determine the diversity and composition of colonic mucosal microbiota in patients with and without colorectal cancer in Indonesia.

METHODS: This case-control study included 59 subjects (35 colorectal cancer patients and 24 non-colorectal cancer patients indicated for colonoscopy at Dr. Cipto Mangunkusumo Gastrointestinal Endoscopy Center and Fatmawati Hospital. Microbiota examination was performed using 16S rRNA sequencing. Bioinformatics analysis was performed using the wf-metagenomics pipeline from EPI2Me-Labs (Oxford Nanopore Technologies platform).

RESULTS: Patients with colorectal cancer had a higher median index value on the Shannon index (3.28 vs 2.82, P > 0.05) and a lower value on the Simpson index (0.050 vs 0.060, P > 0.05). Significant differences in beta diversity were observed at the genus (P = 0.002) and species levels (P = 0.001). Firmicutes, Proteobacteria, Bacteroidetes, and Fusobacteria were the dominant phyla. The genera Bacteroides, Campylobacter, Peptostreptococcus, and Parvimonas were found more frequently in colorectal cancer, while Faecalibacterium, Haemophilus, and Phocaeicola were more frequently found in non-colorectal cancer. The relative abundance of Fusobacterium nucleatum, Bacteroides fragilis, Enterococcus faecalis, Campylobacter hominis, and Enterococcus faecalis species was significantly elevated in patients with colorectal cancer. Meanwhile, Faecalibacterium prausnitzii, Faecalibacterium duncaniae, and Prevotella copri were more commonly found in non-colorectal cancer.

CONCLUSION: Patients with colorectal cancer exhibit distinct differences in the composition and diversity of their colonic mucosal microbiota compared to those with non-colorectal cancer. This study was reviewed and approved by the Ethics Committee of Faculty of Medicine, Universitas Indonesia (No. KET-1517/UN2.F1/ETIK/PPM.00.02/2023).}, } @article {pmid39919360, year = {2025}, author = {Lemons, JMS and Narrowe, AB and Firrman, J and Mahalak, KK and Liu, L and Higgins, S and Moustafa, AM and Baudot, A and Deyaert, S and Van den Abbeele, P}, title = {The food additive butylated hydroxyanisole minimally affects the human gut microbiome ex vivo.}, journal = {Food chemistry}, volume = {473}, number = {}, pages = {143037}, doi = {10.1016/j.foodchem.2025.143037}, pmid = {39919360}, issn = {1873-7072}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Butylated Hydroxyanisole/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation & purification/metabolism ; Adult ; *Food Additives/pharmacology ; Infant ; Middle Aged ; Aged ; Young Adult ; Child, Preschool ; Child ; Female ; Adolescent ; Male ; }, abstract = {Butylated hydroxyanisole (BHA) continues to raise consumer concerns. All previous evaluations of this additive have failed to consider its effect on the gut microbiome, even though it enters the colon. An ex vivo model was used to assess the effect of BHA on microbial communities from 24 donors, aged infants to older adults. A dose of 0.35 g/L BHA elicited no statistically significant changes in the functional outputs or community structure for any age group. Although not large enough to affect community diversity, there were some significant decreases at the phylum level. Among the genes most significantly affected by treatment with BHA across age groups are those involved in lipopolysaccharide synthesis and bacterial electron transport encoded by Bacteroidota, Proteobacteria, and Verrucomicrobiota. Given what is known about the intracellular activity of BHA, these genes may hint at a mechanism behind BHA's evident, but minimally detrimental effect on the gut microbiota.}, } @article {pmid39909332, year = {2025}, author = {Cheng, Z and He, Y and Wang, N and Wu, L and Xu, J and Shi, J}, title = {Uncovering soil amendment-induced genomic and functional divergence in soybean rhizosphere microbiomes during cadmium-contaminated soil remediation: Novel insights from field multi-omics.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {368}, number = {}, pages = {125787}, doi = {10.1016/j.envpol.2025.125787}, pmid = {39909332}, issn = {1873-6424}, mesh = {*Cadmium/metabolism ; *Glycine max/genetics/microbiology/metabolism ; *Rhizosphere ; *Soil Pollutants/metabolism ; *Soil Microbiology ; *Microbiota ; Soil/chemistry ; Biodegradation, Environmental ; Bacteria/genetics/metabolism ; Metagenomics ; Metagenome ; Multiomics ; }, abstract = {Soil amendments exhibit great potential in reducing cadmium (Cd) bioavailability and its accumulation in crop grains, but their practical implications on microbial characteristics (genomic traits and ecological functions) remain unclear. The objective of this study was to combine metagenomics and metatranscriptomics to track the dynamics of bacterial and viral communities in the soybean rhizosphere during the remediation of Cd-contaminated soil using a commercial Mg-Ca-Si conditioner (CMC), applied at low and high (975 kg ha[-1] and 1950 kg ha[-1]) rates under field conditions. Application of CMC increased the average size and decreased the guanine-cytosine (GC) content of microbial genomes, which were strongly shaped by soil pH and available Cd (ACd). Gene and transcript abundances analysis indicated that CMC promoted the enrichment of Alphaproteobacterial metagenome-assembled genomes (MAGs) carrying czcC gene encoding Cd efflux and dsbB gene encoding disulfide bond oxidoreductase. These genes are closely related to Cd resistance and exhibited notable (p < 0.05) increased expression in CMC-treated soils. Additionally, low and high CMC addition significantly increased viral alpha diversity by 5.7% and 9.6%, and viral activity by 3.3% and 7.8%, respectively, in comparison to the control. Temperate viruses were predicted as the major group (64%) and actively linked to the dominant host, and CMC amendment increased host metabolism and adaptability by enhancing (p < 0.05) the abundance and transcriptional activity of virus-encoded auxiliary metabolic genes (AMGs) involved in heavy metal resistance (ABC transport), sulfur cycling (cysH), and host metabolism (galE and queD) through "piggyback-the-winner" strategy. Structural equation modeling further revealed that CMC application influences Cd accumulation in soybean grains through its direct and indirect effects on soil properties and rhizosphere microbiomes, and highlighted the potential role of rhizosphere viruses in agricultural soil remediation.}, } @article {pmid39887086, year = {2025}, author = {Breton, J and Tu, V and Tanes, C and Wilson, N and Quinn, R and Kachelries, K and Friedman, ES and Bittinger, K and Baldassano, RN and Compher, C and Albenberg, L}, title = {A pro-inflammatory diet is associated with growth and virulence of Escherichia coli in pediatric Crohn's disease.}, journal = {Journal of Crohn's & colitis}, volume = {19}, number = {2}, pages = {}, doi = {10.1093/ecco-jcc/jjaf018}, pmid = {39887086}, issn = {1876-4479}, support = {4100068710//Commonwealth Universal Research Enhancement/ ; 693867//Crohn's and Colitis Foundation Career Development Award/ ; }, mesh = {Humans ; *Crohn Disease/microbiology ; Male ; Child ; Female ; Cross-Sectional Studies ; Adolescent ; *Feces/microbiology ; *Escherichia coli/isolation & purification ; *Gastrointestinal Microbiome/physiology ; Diet/adverse effects/methods ; Case-Control Studies ; Virulence ; Metabolome ; Inflammation/microbiology ; }, abstract = {BACKGROUND AND AIMS: Epidemiological studies have suggested an association between the inflammatory potential of dietary patterns and Crohn's disease (CD). However, the relationships of these inflammatory dietary determinants with the microbiome remain largely unknown. In this cross-sectional study, we evaluate the association between the inflammatory potential of habitual diet, as assessed by the modified Children-Dietary Inflammatory Index (mC-DII), and the fecal microbiome and metabolome of children with CD in comparison to healthy children.

METHODS: A cross-sectional study including 51 children with CD between 6 and 18 years of age and 50 healthy controls was conducted. Dietary inflammatory potential was measured using the mC-DII, and diet quality was assessed by the Healthy Eating Index (HEI)-2015 and alternate Mediterranean Eating Index (aMed). The microbiome was analyzed using shotgun metagenomic sequencing and untargeted metabolomic analysis.

RESULTS: A poor-quality, pro-inflammatory diet, with similar mC-DII, HEI-2015, and aMed scores, was found across healthy children and children with CD. In children with active disease, a pro-inflammatory diet was associated with decreased diversity, increased virulence potential, and expansion of the Proteobacteria phylum dominated by Escherichia coli (E. coli) spp. A positive correlation between E. coli relative abundance and mC-DII was associated with a low intake of a cluster composed of fibers, vitamins, and minerals with anti-inflammatory potential. A negative association between metabolites of fatty acid metabolism and HEI was found.

CONCLUSIONS: In total, our results suggest that a pro-inflammatory diet may potentiate hallmarks of the inflammation-associated dysbiosis in CD and highlight the need for microbiome-targeted dietary interventions optimizing the anti-inflammatory potential of habitual diet in the management of pediatric CD.}, } @article {pmid39550746, year = {2025}, author = {Karaca, C and Takcı, HAM}, title = {Role of gut microbiome in developing necrotizing enterocolitis.}, journal = {Folia microbiologica}, volume = {70}, number = {1}, pages = {197-204}, pmid = {39550746}, issn = {1874-9356}, support = {21-13192//Kilis 7 Aralık University of Research Project Committee/ ; }, mesh = {*Enterocolitis, Necrotizing/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Dysbiosis/microbiology ; Male ; Metagenomics ; Female ; High-Throughput Nucleotide Sequencing ; Infant, Premature ; DNA, Bacterial/genetics ; }, abstract = {Necrotizing enterocolitis (NEC) is one of the most devastating intestinal diseases observed in preterm in the first days of life. Researchers have recently focused on potential predictive biomarkers for early and concomitant diagnoses. Thus, we inquired about the linkage of intestinal dysbiosis, one of the most important factors in NEC development to the gut microbiota. In this study, the systematic differences in the bacterial composition between neonates affected by NEC and healthy newborns were highlighted by metagenomic analysis. The next-generation sequencing of the V3-V4 variable region of the 16S rRNA gene and gene-specific qPCR analyzed the untargeted gut microbiota. Total bacteria, total and fecal coliform loads in stool samples with NEC were higher than control. OTU-level relative abundances of NEC infant was characterized by Firmicutes and Bacteroidetes at phylum levels. At the genus level, NEC stool was identified by the lack of Klebsiella and the presence of Roseburia, Blautia, and Parasutterella. Finally, Clostridium fessum was the predominant species of Clostridium genus in disease and healthy specimens at the species level, whereas Clostridium jeddahitimonense was at NEC diagnosis. Despite a strong relationship between pathophysiology and characterization of gut microbiota at a clinical diagnosis of NEC, our results emphasize the broad difficulty in identifying potential biomarkers.}, } @article {pmid39986751, year = {2025}, author = {Wang, C and Zhao, J and Zhao, W and Xue, L and Chen, Y and Tian, J and Wang, H and Ji, X and Tian, X and Zhang, J and Gu, Y}, title = {A comparative study of the composition of microorganisms and metabolites in different β-casein genetic types of dairy cows based on metagenomics and non-targeted metabolomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {204}, number = {}, pages = {115859}, doi = {10.1016/j.foodres.2025.115859}, pmid = {39986751}, issn = {1873-7145}, mesh = {Animals ; Cattle ; *Caseins/metabolism ; *Metabolomics ; *Metagenomics ; Female ; Rumen/microbiology/metabolism ; Gastrointestinal Microbiome ; Milk/microbiology ; Bacteria/metabolism/classification/genetics ; Genotype ; }, abstract = {β-Casein is the main component of cow's milk protein, with A1 and A2 β-casein being the most common. Of these, A1 β-casein hydrolysate produces BCM-7, which can cause lactose intolerance, while A2 β-casein milk is more gentle on the gut. However, there is limited research on the composition of rumen microbiota, metabolites, and host metabolites in different genotype cows using metagenomics and metabolomics. In this study, we used multi-omics analysis techniques to perform enrichment analysis of differential metabolites, identifying three key metabolic pathways in all three groups: Arachidonic acid metabolism and Tryptophan metabolism. The metabolites in these pathways exhibited unique metabolic characteristics within each group. We then used random forests and ROC to predict key metabolites in these pathways, identifying that the signature metabolites in the A2A2 group were predominantly anti-inflammatory substances, including 12-HETE, PGD2-4d, and Arachidonic Acid. The signature metabolites in the A1A2 group and A2A2 group were Indoleacetaldehyde. The AUC of these signature metabolites was greater than 0.85. Macrogenic linear discriminant analysis (LDA > 2.5) found that the microorganisms with greater contribution were concentrated in the A2A2 group. Compared with the other two groups, g_Bacteroides and g_Parabacteroides were mainly enriched in the A1A2 group. In group A2A2, g_Xanthomonas and g_Acetobacter are mainly enriched. Then, the key microorganisms in A1A2 group were identified by correlation analysis as g_Bacteroides and g_Parabacteroides. The key microorganisms in group A2A2 were g_Acetobacter, g_Xanthomonas and g_Mannheimia, which were consistent with the results of LEfSe analysis. These microorganisms mainly affect the degradation of fiber in the diet, host metabolism and the occurrence of inflammation. In conclusion, our results provide theoretical basis and data support for the study of dairy cows with different genotypes of β-casein, and help to determine the potential biological functions of different genotypes of casein in dairy products and their effects on human health.}, } @article {pmid39986042, year = {2025}, author = {Bacha, LF and Oliveira, MAP and Landuci, F and Vicente, AC and Paz, PH and Lima, M and Hilário, M and Campos, LS and Thompson, M and Chueke, C and Tschoeke, D and Ottoni, A and Teixera, LM and Cosenza, C and de Souza, W and de Rezende, C and Thompson, C and Thompson, F}, title = {Antibiotic-resistance genes and metals increase in polluted tropical rivers of the Baia da Ilha Grande, Rio de Janeiro, Brazil.}, journal = {The Science of the total environment}, volume = {968}, number = {}, pages = {178778}, doi = {10.1016/j.scitotenv.2025.178778}, pmid = {39986042}, issn = {1879-1026}, abstract = {Baia da Ilha Grande (BIG), Rio de Janeiro, Brazil, is one of the largest bays in the world. BIG is important because it serves as a route for the mining and oil industries and plays a vital role in mariculture activities. However, BIG has suffered significant impacts in recent years due to increased pollution and climate change, culminating in a local mariculture collapse. We examined the pollution levels of the bay. Biogeochemical, microbiological, and metagenomics analyses were conducted in ten rivers during the 2022 dry and rainy seasons. Combined data analyses showed that the bay's ten most significant rivers are polluted and classified into three decreasing levels of pollution groups (P1-P3). The P1 group (Centro, Japuíba, Jacuecanga) had the worst-case scenario for all pollution types, and the highest number of the nearby populations, nautical workshops and hospitals. Whereas the P2 (Jacarei, Perequeaçu and Taquari) and P3 (Frade, Bracuí, Mambucaba, São Roque) had relatively reduced pollution, as shown mainly by fecal bacteria. Metals, such as Al (>0.3 mg/L), Fe (>1.4 mg/L), Pb (>0.15 mg/L), and resistance genes (∼2 % metagenomic profile) were also more abundant in P1. High levels of metals and antibiotic resistance genes were a strong indication of pollution. The results from this study shed light on the health status of BIG rivers for further conservation programs and public policies to prevent rivers and marine biodiversity losses, and they serves as a warning on the urgent need to treat effluents in the region.}, } @article {pmid39923290, year = {2025}, author = {Wang, S and Wu, M}, title = {Decoding the link between microbial secondary metabolites and colorectal cancer.}, journal = {Computational biology and chemistry}, volume = {115}, number = {}, pages = {108372}, doi = {10.1016/j.compbiolchem.2025.108372}, pmid = {39923290}, issn = {1476-928X}, mesh = {*Colorectal Neoplasms/metabolism/microbiology ; Humans ; *Gastrointestinal Microbiome ; Feces/microbiology ; }, abstract = {Colorectal cancer (CRC) is a prevalent form of cancer in humans, with the gut microbiota playing a significant role in its pathogenesis. Although previous research has primarily focused on the role of primary metabolites produced by gut microbes in CRC development, the role of secondary metabolites remains largely unexplored. Secondary metabolites are known to mediate crucial interactions between the microbiota and the host, potentially influencing CRC progression. However, their specific relationship to CRC pathogenesis is poorly understood. To address this gap, we performed a meta-analysis using fecal metagenomic data from a cohort of CRC patients and healthy controls, aiming to identify CRC-associated microbial secondary metabolite biosynthetic gene clusters (BGCs). Our findings not only provide valuable insights into the pathogenicity and carcinogenicity of CRC but also shed light on the potential mechanisms underlying its development.}, } @article {pmid39954350, year = {2025}, author = {Dong, Y and Liu, H and Habimana, O}, title = {High risk of Vibrio pathogen and antibiotic resistance transfer in live seafood wet markets of Shantou, China.}, journal = {International journal of food microbiology}, volume = {432}, number = {}, pages = {111098}, doi = {10.1016/j.ijfoodmicro.2025.111098}, pmid = {39954350}, issn = {1879-3460}, mesh = {*Vibrio/genetics/drug effects/isolation & purification ; *Seafood/microbiology ; China ; Animals ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Food Microbiology ; Humans ; Food Contamination/analysis ; Microbiota ; Biofilms/growth & development ; Food Safety ; }, abstract = {The global demand for seafood necessitates robust food safety practices, particularly within traditional wet markets. This study investigated the microbiomes of live Japanese mantis shrimp (JMS) and their associated environments (water and biofilm) in local wet markets to assess the risk of pathogen and antibiotic resistance gene (ARG) transfer. Metagenomic analysis showed a significant link between microbiome composition and the type of sample (shrimp, biofilm, and water). While several known human pathogens were associated with shrimp samples, water and biofilm samples exhibited higher abundances of ARGs, suggesting a high risk of pathogen and ARG transfer from the market environment. Notably, this study focused on the diversity and characterization of poorly understood Vibrio species associated with JMS. The prevalence of β-lactam resistance genes in Vibrio isolates, combined with a comparative genomic analysis of several species, highlights this concern. Our study emphasizes the need to improve hygiene practices in wet markets to reduce foodborne illness risks and address antibiotic resistance. This work represents, to our knowledge, the first comparative genomic analysis of Vibrio species in the context of JMS and wet market seafood safety.}, } @article {pmid39947314, year = {2025}, author = {Zhang, X and Chen, Y and Xia, Y and Lin, S and Zhou, X and Pang, X and Yu, J and Sun, L}, title = {Oral microbiota in colorectal cancer: Unraveling mechanisms and application potential.}, journal = {Life sciences}, volume = {365}, number = {}, pages = {123462}, doi = {10.1016/j.lfs.2025.123462}, pmid = {39947314}, issn = {1879-0631}, mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Microbiota/physiology ; *Mouth/microbiology ; Fusobacterium nucleatum/pathogenicity ; Porphyromonas gingivalis/pathogenicity ; Animals ; }, abstract = {Colorectal cancer (CRC), with a rising prevalence, is the third most commonly diagnosed cancer and the third leading cause of cancer-related death. Studies have shown that a complex interplay between the development of CRC and alterations in the oral microbiome. Recent advancements in genomics and metagenomics have highlighted the significant roles of certain oral microbes, particularly Porphyromonas gingivalis (P. gingivalis) and Fusobacterium nucleatum (F. nucleatum), in the progression of CRC. However, the detailed mechanisms by which the oral microbiota influence CRC development remain unclear. This review aims to elucidate the role of oral microbiota in CRC progression, evaluate their potential as biomarkers, and explore therapeutic strategies targeting these microbes. This review offers insights into the mechanisms underlying the interaction between oral microbiota and CRC, underscoring the potential of oral microbes as diagnostic and prognostic biomarkers, as well as therapeutic targets. Future research should focus on clarifying the exact pathways and developing innovative therapeutic strategies to enhance the diagnosis and treatment.}, } @article {pmid39824262, year = {2025}, author = {Özdemir, A and Sarzhanov, F and Doğruman-Al, F and Gündoğdu, A and Nalbantoğlu, U and Yozgat, A and Yıldız, BD and Büyüktuncer, Z}, title = {Exploring the complex interplay of Blastocystis, morbid obesity, and bariatric surgery on gut microbial dynamics.}, journal = {Microbial pathogenesis}, volume = {200}, number = {}, pages = {107306}, doi = {10.1016/j.micpath.2025.107306}, pmid = {39824262}, issn = {1096-1208}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Bariatric Surgery ; *Obesity, Morbid/surgery/microbiology ; *Blastocystis/isolation & purification/genetics/classification ; Male ; *RNA, Ribosomal, 16S/genetics ; Adult ; Female ; Middle Aged ; Blastocystis Infections/microbiology/parasitology ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology/parasitology ; DNA, Bacterial/genetics ; Gastrectomy ; }, abstract = {This study examines Blastocystis dynamics in 15 individuals undergoing sleeve gastrectomy. Molecular detection involved DNA extraction, RT-PCR, and sequencing, while 16S rRNA sequencing via Illumina MiSeq analyzed the intestinal microbiome. Statistical analysis through SPSS considered a significance level of p < 0.05. Postoperative colonization of Blastocystis was observed in previously negative individuals, revealing subtypes and shifts in microbial taxa. Blastocystis-positive participants post-bariatric surgery showed a significant increase in Lachnospira, alongside higher abundances of Bacteroides, Oscillospira, Barnesiellaceae, and Rikenellaceae, with reduced Lactobacillus levels compared to Blastocystis-negative individuals. Collective analysis highlighted higher Clostridiales and RF32 in Blastocystis-positive post-surgery individuals, coupled with decreased Enterobacteriaceae. The study challenges previous notions, suggesting a complex interplay between Blastocystis, morbid obesity, and bariatric surgery. Despite limitations, including small sample sizes and absent gut microbiome diversity comparisons, this pioneering research calls for further investigation into the intricate mechanisms and implications for metabolic health. This study is registered at clinicaltrials.gov (NCT05085769).}, } @article {pmid39985639, year = {2025}, author = {Zhang, N and Tran, S and Moskatel, LS}, title = {The Gut Microbiome and Migraine: Updates in Understanding.}, journal = {Current neurology and neuroscience reports}, volume = {25}, number = {1}, pages = {20}, pmid = {39985639}, issn = {1534-6293}, mesh = {Humans ; *Migraine Disorders/microbiology ; *Gastrointestinal Microbiome/physiology ; Animals ; *Brain-Gut Axis/physiology ; Dysbiosis/microbiology ; Probiotics/therapeutic use ; }, abstract = {PURPOSE OF REVIEW: We provide an overview of the field of microbiome research, the current understanding of the microbiome-gut-brain axis, and the most recent updates on the interplay between migraine and the gut microbiome.

RECENT FINDINGS: Pre-clinical studies suggest that gut microbiota is required for normal pain sensation. There is also evidence in rodent models that there is potential application of food, herbal medicines, probiotics, and short chain fatty acids (SCFAs) as novel therapies for migraine. Evidence from human cohorts suggests that there is altered gut microbiota in people with migraine, and that the microbiome dysbiosis is from both compositional and functional aspects. Recent metagenome-wide association studies (MWAS) that employ Mendelian Randomization support the causal association between gut microbiota and migraine. The connection between migraine and the gut microbiome remains underexplored, but recent preclinical and clinical studies support the association between gut microbiota and the development of migraine.}, } @article {pmid39984934, year = {2025}, author = {Chen, X and Wei, J and Zhang, L and Wang, H and Zhang, Y and Li, Z and Wang, X and Liu, L and Zhang, Y and Zhang, T}, title = {Association between plasma short-chain fatty acids and inflammation in human immunodeficiency virus-associated neurocognitive disorder: a pilot study.}, journal = {Lipids in health and disease}, volume = {24}, number = {1}, pages = {66}, pmid = {39984934}, issn = {1476-511X}, support = {7222091//Natural Science Foundation of Beijing Municipality/ ; 81873761//National Natural Science Foundation of China/ ; 82241072, 82072271//National Natural Science Foundation of China/ ; 7222095//Beijing Natural Science Foundation/ ; }, mesh = {Humans ; *Fatty Acids, Volatile/blood ; Male ; Female ; Pilot Projects ; Middle Aged ; *Gastrointestinal Microbiome ; *Inflammation/blood ; Adult ; Cytokines/blood ; HIV Infections/blood/complications/virology ; Biomarkers/blood ; Neurocognitive Disorders/blood/virology ; Cognitive Dysfunction/blood ; Case-Control Studies ; ROC Curve ; }, abstract = {BACKGROUND AND AIMS: Short-chain fatty acids (SCFAs), key metabolites produced by gut microbiota, have neuroprotective effects in neurodegenerative diseases by modulating immune responses. However, their role in human immunodeficiency virus (HIV)-associated neurocognitive disorder (HAND) remains largely unexplored.

METHODS: We recruited HAND patients, HIV Control, and healthy controls (HC). Plasma SCFAs and SCFA-producing gut microbiota were quantified via gas chromatography-mass spectrometry and fecal metagenomic analysis. Inflammatory cytokine levels were measured using liquid chromatography. Receiver operating characteristic (ROC) curves were generated to evaluate the predictive accuracy of SCFAs for HAND.

RESULTS: Plasma SCFAs were significantly reduced in HAND patients, correlating with a decrease in SCFA-producing gut bacteria, such as Prevotella and its related species. Reduced SCFAs were positively correlated with pro-inflammatory cytokines and cognitive impairment, while being negatively correlated with anti-inflammatory cytokines. ROC curve analysis demonstrated that several SCFAs exhibited strong predictive accuracy for HAND status.

CONCLUSIONS: SCFAs may influence cognitive function by modulating inflammatory responses, and identifies plasma SCFAs as potential biomarkers and therapeutic targets for HAND. Further investigation is needed to delineate the mechanisms that SCFAs influence HAND pathology.}, } @article {pmid39980208, year = {2025}, author = {Holman, LE and Zampirolo, G and Gyllencreutz, R and Scourse, J and Frøslev, T and Carøe, C and Gopalakrishnan, S and Pedersen, MW and Bohmann, K}, title = {Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14086}, doi = {10.1111/1755-0998.14086}, pmid = {39980208}, issn = {1755-0998}, support = {856488//H2020 European Research Council/ ; }, abstract = {The condition of ancient marine ecosystems provides context for contemporary biodiversity changes in human-impacted oceans. Sequencing sedimentary ancient DNA (sedaDNA) is an emerging method for generating high-resolution biodiversity time-series data, offering insights into past ecosystems. However, few studies directly compare the two predominant sedaDNA sequencing approaches: metabarcoding and shotgun-metagenomics, and it remains unclear if these methodological differences affect diversity metrics. We compared these methods using sedaDNA from an archived marine sediment record sampled in the Skagerrak, North Sea, spanning almost 8000 years. We performed metabarcoding of a eukaryotic 18S rRNA region (V9) and sequenced 153-229 million metagenomic reads per sample. Our results show limited overlap between metabarcoding and metagenomics, with only three metazoan genera detected by both methods. For overlapping taxa, metabarcoding detections became inconsistent for samples older than 2000 years, while metagenomics detected taxa throughout the time series. We observed divergent patterns of alpha diversity, with metagenomics indicating decreased richness towards the present and metabarcoding showing an increase. However, beta diversity patterns were similar between methods, with discrepancies only in metazoan data comparisons. Our findings demonstrate that the choice of sequencing method significantly impacts detected biodiversity in an ancient marine sediment record. While we stress that studies with limited variation in DNA degradation among samples may not be strongly affected, researchers should exonerate methodological explanations for observed biodiversity changes in marine sediment cores, particularly when considering alpha diversity, before making ecological interpretations.}, } @article {pmid39979617, year = {2025}, author = {Ohlsson, C and Lawenius, L and Jiang, Y and Horkeby, K and Wu, J and Nilsson, KH and Koskela, A and Tuukkanen, J and Movérare-Skrtic, S and Henning, P and Sjögren, K}, title = {The beneficial effects of a probiotic mix on bone and lean mass are dependent on the diet in female mice.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {6182}, pmid = {39979617}, issn = {2045-2322}, mesh = {Animals ; Female ; *Probiotics/pharmacology/administration & dosage ; Mice ; *Bone Density/drug effects ; Diet, High-Fat/adverse effects ; Bone and Bones/drug effects ; Mice, Inbred C57BL ; Ovariectomy ; Gastrointestinal Microbiome/drug effects ; Diet ; }, abstract = {Bone mass and lean mass decrease with age and these changes are associated with increased fracture risk and sarcopenia. Previous studies demonstrated that a probiotic mixture of Lacticaseibacillus paracasei DSM13434, Lactiplantibacillus plantarum DSM 15312 and DSM 15313 (L. Mix) prevents bone loss in ovariectomized (ovx) female mice. The purpose of the present study is to test if the beneficial effect of L. Mix is modified by the diet. Female mice were fed either a high-fat (HFD, 60% kcal from fat) or a low-fat (LFD, 10% kcal from fat) diet and subjected to either sham or ovx surgery and treated with L. Mix for 12 weeks. L. Mix treatment increased total body bone mineral density (p ≤ 0.01), by increasing cortical bone area, and total body lean mass (p = 0.035) in mice on LFD but not in mice on HFD. Metagenome sequencing of cecal content showed that L. Mix treatment increased the relative abundance of Lacticaseibacillus paracasei and, Lactiplantibacillus plantarum, demonstrating successful treatment. In addition, the probiotic treatment affected the overall gut microbiota composition and functionality. These findings demonstrate that the L. Mix in combination with a healthy diet is beneficial for musculoskeletal health in female mice.}, } @article {pmid39938449, year = {2025}, author = {Ye, L and Yao, Z and Xuan, Q and Liu, Q and Bo, T}, title = {The impact of sleeve gastrectomy on MASH development by regulating the composition of gut microbiota and metabolic homeostasis.}, journal = {Biochemical and biophysical research communications}, volume = {752}, number = {}, pages = {151466}, doi = {10.1016/j.bbrc.2025.151466}, pmid = {39938449}, issn = {1090-2104}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Gastrectomy ; *Homeostasis ; *Mice, Inbred C57BL ; Mice ; Male ; Fatty Liver/metabolism/pathology ; Disease Models, Animal ; }, abstract = {The prevalence of metabolic dysfunction-associated steatohepatitis (MASH) is increasing annually, which is a global public health issue. Although clinical trials are lacking, observational studies indicate that bariatric surgery can alleviate the progression of MASH. Here, we performed sleeve gastrectomy (SG) and Sham surgery on 8-week-old mice, and then fed a AMLN diet for 24 weeks to construct a diet-inducted MASH mice model after 4-week post-surgery recovery. Applying a multi-omics approach combining metagenomics, metabolomics, and transcriptomics, we found that SG prevents the development of hepatic steatosis, inflammation, and fibrosis in MASH mice not only by significantly altering the structure of gut microbiota including s_Akkermansia muciniphila, s_Alistiples dispar, g_Helicobacter and s_uc_Oscillospiraceae, but also by modulating the levels of serum metabolites including l-arginine and taurocholic acid (TCA). These results suggest that SG and the alteration of gut microbiota and its related serum metabolites can be served as the effective therapeutic strategies for MASH.}, } @article {pmid39490771, year = {2025}, author = {Li, T and Coker, OO and Sun, Y and Li, S and Liu, C and Lin, Y and Wong, SH and Miao, Y and Sung, JJY and Yu, J}, title = {Multi-Cohort Analysis Reveals Altered Archaea in Colorectal Cancer Fecal Samples Across Populations.}, journal = {Gastroenterology}, volume = {168}, number = {3}, pages = {525-538.e2}, doi = {10.1053/j.gastro.2024.10.023}, pmid = {39490771}, issn = {1528-0012}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics/diagnosis ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; *Adenoma/microbiology/genetics ; Female ; Middle Aged ; Case-Control Studies ; Metagenomics ; Aged ; Archaea/genetics/isolation & purification ; Metagenome ; Biomarkers, Tumor/genetics/analysis ; Cohort Studies ; }, abstract = {BACKGROUND & AIMS: Archaea are important components of the host microbiome, but their roles in colorectal cancer (CRC) remain largely unclear. We aimed to elucidate the contribution of gut archaea to CRC across multiple populations.

METHODS: This study incorporated fecal metagenomic data from 10 independent cohorts across 7 countries and an additional in-house cohort, totaling 2101 metagenomes (748 CRC, 471 adenoma, and 882 healthy controls [HCs]). Taxonomic profiling was performed using Kraken2 against the Genome Taxonomy Database. Alterations of archaeal communities and their interactions with bacteria, as well as methanogenic functions were analyzed. A Random Forest model was used to identify multicohort diagnostic microbial biomarkers in CRC.

RESULTS: The overall archaeal alpha diversity shifted from HCs, patients with adenoma, to patients with CRC with the Methanobacteriota phylum enriched while the order Methanomassiliicoccales depleted. At the species level, Methanobrevibacter_A smithii and Methanobrevibacter_A sp002496065 were enriched, whereas 8 species, including Methanosphaera stadtmanae and Methanomassiliicoccus_A intestinalis, were depleted in patients with CRC across multiple cohorts. Among them, M stadtmanae, Methanobrevibacter_A sp900314695, and Methanocorpusculum sp001940805 exhibited a progressive decrease in the HC-adenoma-CRC sequence. CRC-depleted methanogenic archaea exhibited enhanced co-occurring interactions with butyrate-producing bacteria. Consistently, methanogenesis-related genes and pathways were enriched in patients with CRC. A model incorporating archaeal and bacterial biomarkers outperformed single-kingdom models in discriminating patients with CRC from healthy individuals with the area under the curve ranging from 0.744 to 0.931 in leave-one-cohort-out analysis.

CONCLUSIONS: This multicohort analysis uncovered significant alterations in gut archaea and their interactions with bacteria in healthy individuals, patients with adenoma, and patients with CRC. Archaeal biomarkers, combined with bacterial features, have potential as noninvasive diagnostic biomarkers for CRC.}, } @article {pmid39128495, year = {2025}, author = {De Pessemier, B and López, CD and Taelman, S and Verdonck, M and Chen, Y and Stockman, A and Lambert, J and Van de Wiele, T and Callewaert, C}, title = {Comparative Whole Metagenome Analysis in Lesional and Nonlesional Scalp Areas of Patients with Psoriasis Capitis and Healthy Individuals.}, journal = {The Journal of investigative dermatology}, volume = {145}, number = {3}, pages = {605-617.e14}, doi = {10.1016/j.jid.2024.07.020}, pmid = {39128495}, issn = {1523-1747}, mesh = {Humans ; *Psoriasis/microbiology/genetics ; Male ; Female ; *Metagenome ; Adult ; *Scalp/microbiology ; Middle Aged ; Microbiota/genetics ; Scalp Dermatoses/microbiology/genetics ; Metagenomics/methods ; }, abstract = {Psoriasis is an immune-mediated inflammatory disorder, where the majority of the patients suffer from psoriasis capitis or scalp psoriasis. Current therapeutics remain ineffective to treat scalp lesions. In this study, we present a whole-metagenome characterization of the scalp microbiome in psoriasis capitis. We investigated how changes in the homeostatic cutaneous microbiome correlate with the condition and identified metagenomic biomarkers (taxonomic, functional, virulence factors, antimicrobial resistance genes) that could partly explain its emergence. Within this study, 83 top and back scalp samples from healthy individuals and 64 lesional and nonlesional scalp samples from subjects with untreated psoriasis capitis were analyzed. Using qPCR targeting the 16S and 18S ribosomal RNA genes, we found a significant decrease in microbial load within scalp regions affected by psoriasis compared with that in their nonlesional counterparts. Metagenomic analysis revealed that psoriatic lesions displayed significant lower Cutibacterium species (including C. modestum, C. namnetense, C. granulosum, C. porci), along with an elevation in Staphylococcus aureus. A heightened relative presence of efflux pump protein-encoding genes was detected, suggesting potential antimicrobial resistance mechanisms. These mechanisms are known to specifically target human antimicrobial peptides (including cathelicidin LL-37), which are frequently encountered within psoriasis lesions. These shifts in microbial community dynamics may contribute to psoriasis disease pathogenesis.}, } @article {pmid39979340, year = {2025}, author = {Di Costanzo, F and Di Marsico, M and Orefice, I and Kristoffersen, JB and Kasapidis, P and Chaumier, T and Ambrosino, L and Miralto, M and Aiese Cigliano, R and Verret, F and Tirichine, L and Trindade, M and Van Zyl, L and Di Dato, V and Romano, G}, title = {High-quality genome assembly and annotation of Thalassiosira rotula (synonym of Thalassiosira gravida).}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {310}, pmid = {39979340}, issn = {2052-4463}, mesh = {*Diatoms/genetics ; Genome ; Molecular Sequence Annotation ; DNA Methylation ; Transcriptome ; DNA Transposable Elements ; Metagenome ; }, abstract = {Diatoms are unicellular eukaryotic microorganisms thriving in most aquatic environments thanks to the expression of biosynthetic pathways for secondary metabolites involved in defence and adaptation to environmental changes. The sequencing of the transcriptome of the cosmopolitan diatom Thalassiosira rotula Meunier 1910 (synonym of Thalassiosira gravida Cleve 1896) and of the metagenome of its associated microbiome revealed the presence of biosynthetic pathways synthesising molecules and compounds useful for the algae survival and with potential biotechnological applications. Here we present the genome of a Neapolitan T. rotula strain, which is 672 Mbp in size due to a high proportion of repetitive elements (63.59%) and segmental duplications (14%), while the number of predicted genes resulted to be comparable to that of smaller diatom genomes. DNA methylation was predominantly located in transposable elements.}, } @article {pmid39903699, year = {2025}, author = {Roothans, N and van Loosdrecht, MCM and Laureni, M}, title = {Metabolic labour division trade-offs in denitrifying microbiomes.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf020}, pmid = {39903699}, issn = {1751-7370}, support = {JG191217009/732.750/CU//Stichting Toegepast Onderzoek Waterbeheer/ ; 20.0787440//Hoogheemraadschap Hollands Noorderkwartier/ ; Z62737/U131154//Waterschap de Dommel/ ; }, mesh = {*Denitrification ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Nitrates/metabolism ; Nitrites/metabolism ; Metagenome ; Ecosystem ; }, abstract = {Division of metabolic labour is a defining trait of natural and engineered microbiomes. Denitrification-the stepwise reduction of nitrate and nitrite to nitrogenous gases-is inherently modular, catalysed either by a single microorganism (termed complete denitrifier) or by consortia of partial denitrifiers. Despite the pivotal role of denitrification in biogeochemical cycles and environmental biotechnologies, the ecological factors selecting for complete versus partial denitrifiers remain poorly understood. In this perspective, we critically review over 1500 published metagenome-assembled genomes of denitrifiers from diverse and globally relevant ecosystems. Our findings highlight the widespread occurrence of labour division and the dominance of partial denitrifiers in complex ecosystems, contrasting with the prevalence of complete denitrifiers only in simple laboratory cultures. We challenge current labour division theories centred around catabolic pathways, and discuss their limits in explaining the observed niche partitioning. Instead, we propose that labour division benefits partial denitrifiers by minimising resource allocation to denitrification, enabling broader metabolic adaptability to oligotrophic and dynamic environments. Conversely, stable, nutrient-rich laboratory cultures seem to favour complete denitrifiers, which maximise energy generation through denitrification. To resolve the ecological significance of metabolic trade-offs in denitrifying microbiomes, we advocate for mechanistic studies that integrate mixed-culture enrichments mimicking natural environments, multi-meta-omics, and targeted physiological characterisations. These undertakings will greatly advance our understanding of global nitrogen turnover and nitrogenous greenhouse gases emissions.}, } @article {pmid39893570, year = {2025}, author = {Zampieri, G and Santinello, D and Palù, M and Orellana, E and Costantini, P and Favaro, L and Campanaro, S and Treu, L}, title = {Core cooperative metabolism in low-complexity CO2-fixing anaerobic microbiota.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf017}, pmid = {39893570}, issn = {1751-7370}, mesh = {*Carbon Dioxide/metabolism ; *Methane/metabolism ; Anaerobiosis ; *Microbiota ; Formates/metabolism ; Acetates/metabolism ; Hydrogen/metabolism ; Methanobacteriaceae/metabolism/genetics ; Metagenome ; Oxidation-Reduction ; }, abstract = {Biological conversion of carbon dioxide into methane has a crucial role in global carbon cycling and is operated by a specialised set of anaerobic archaea. Although it is known that this conversion is strictly linked with cooperative bacterial activity, such as through syntrophic acetate oxidation, there is also a limited understanding on how this cooperation is regulated and metabolically realised. In this work, we investigate the activity in a microbial community evolved to efficiently convert carbon dioxide into methane and predominantly populated by Methanothermobacter wolfeii. Through multi-omics, biochemical analysis and constraint-based modelling, we identify a potential formate cross-feeding from an uncharacterised Limnochordia species to M. wolfeii, driven by the recently discovered reductive glycine pathway and upregulated when hydrogen and carbon dioxide are limited. The quantitative consistency of this metabolic exchange with experimental data is shown by metagenome-scale metabolic models integrating condition-specific metatranscriptomics, which also indicate a broader three-way interaction involving M. wolfeii, the Limnochordia species, and Sphaerobacter thermophilus. Under limited hydrogen and carbon dioxide, aspartate released by M. wolfeii is fermented by Sphaerobacter thermophilus into acetate, which in turn is convertible into formate by Limnochordia, possibly forming a cooperative loop sustaining hydrogenotrophic methanogenesis. These findings expand our knowledge on the modes of carbon dioxide reduction into methane within natural microbial communities and provide an example of cooperative plasticity surrounding this process.}, } @article {pmid39837331, year = {2025}, author = {Valdés-Mas, R and Leshem, A and Zheng, D and Cohen, Y and Kern, L and Zmora, N and He, Y and Katina, C and Eliyahu-Miller, S and Yosef-Hevroni, T and Richman, L and Raykhel, B and Allswang, S and Better, R and Shmueli, M and Saftien, A and Cullin, N and Slamovitz, F and Ciocan, D and Ouyang, KS and Mor, U and Dori-Bachash, M and Molina, S and Levin, Y and Atarashi, K and Jona, G and Puschhof, J and Harmelin, A and Stettner, N and Chen, M and Suez, J and Honda, K and Lieb, W and Bang, C and Kori, M and Maharshak, N and Merbl, Y and Shibolet, O and Halpern, Z and Shouval, DS and Shamir, R and Franke, A and Abdeen, SK and Shapiro, H and Savidor, A and Elinav, E}, title = {Metagenome-informed metaproteomics of the human gut microbiome, host, and dietary exposome uncovers signatures of health and inflammatory bowel disease.}, journal = {Cell}, volume = {188}, number = {4}, pages = {1062-1083.e36}, doi = {10.1016/j.cell.2024.12.016}, pmid = {39837331}, issn = {1097-4172}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; Animals ; *Proteomics/methods ; *Feces/microbiology/chemistry ; Mice ; *Metagenome ; *Diet ; Dysbiosis/microbiology ; Exposome ; Female ; Male ; Mice, Inbred C57BL ; Biomarkers/metabolism ; }, abstract = {Host-microbiome-dietary interactions play crucial roles in regulating human health, yet their direct functional assessment remains challenging. We adopted metagenome-informed metaproteomics (MIM), in mice and humans, to non-invasively explore species-level microbiome-host interactions during commensal and pathogen colonization, nutritional modification, and antibiotic-induced perturbation. Simultaneously, fecal MIM accurately characterized the nutritional exposure landscape in multiple clinical and dietary contexts. Implementation of MIM in murine auto-inflammation and in human inflammatory bowel disease (IBD) characterized a "compositional dysbiosis" and a concomitant species-specific "functional dysbiosis" driven by suppressed commensal responses to inflammatory host signals. Microbiome transfers unraveled early-onset kinetics of these host-commensal cross-responsive patterns, while predictive analyses identified candidate fecal host-microbiome IBD biomarker protein pairs outperforming S100A8/S100A9 (calprotectin). Importantly, a simultaneous fecal nutritional MIM assessment enabled the determination of IBD-related consumption patterns, dietary treatment compliance, and small intestinal digestive aberrations. Collectively, a parallelized dietary-bacterial-host MIM assessment functionally uncovers trans-kingdom interactomes shaping gastrointestinal ecology while offering personalized diagnostic and therapeutic insights into microbiome-associated disease.}, } @article {pmid39970096, year = {2024}, author = {Begmatov, SA and Beletsky, AV and Rakitin, AL and Lukina, AP and Sokolyanskaya, LO and Rakitin, AV and Glukhova, LB and Mardanov, AV and Karnachuk, OV and Ravin, NV}, title = {[Antibiotic Resistance Genes in Cattle Gut Microbiota: Influence of Housing Conditions].}, journal = {Molekuliarnaia biologiia}, volume = {58}, number = {6}, pages = {996-1006}, pmid = {39970096}, issn = {0026-8984}, mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome/drug effects/genetics ; *Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; Housing, Animal ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics/drug effects ; beta-Lactams/pharmacology ; beta-Lactamases/genetics ; }, abstract = {Resistance to antimicrobial drugs is an urgent problem not only in public health, but also in animal husbandry. The widespread use of antimicrobials in feed additives is one of the main reasons for the rapid spread of antibiotic resistance in the microbiota of the gastrointestinal tract of farm animals. To characterize antibiotic resistance genes (resistome), we performed metagenomic analysis of the feces of 24 cattle from different regions of Russia, including cows of different breeds and yaks. Animals differed in the type of housing: year-round on pastures or in barns of conventional farms, with consumption of feed additives. Although genes of resistance to aminoglycosides, β-lactams, glycopeptides, MLS antibiotics (macrolides, lincosamides, and streptogramins), phenicols, and tetracyclines were detected in samples from both groups of animals, the content of the resistome in the fecal microbiome of stall-bred cattle was about ten times higher than in animals kept on pastures. The resistome of stall cattle was dominated by β-lactamases and tetracycline resistance genes, the content of which in the microbiome was 24 and 60 times higher, respectively, than in animals kept on pastures. Apparently, the spread of resistance to β-lactams and tetracyclines in stall cattle reflects the active use of these antibiotics in livestock production. Metagenomic analysis of livestock feces can be used to quantify antibiotic resistance genes for the purpose of monitoring antimicrobial drugs used in animal husbandry.}, } @article {pmid39969428, year = {2025}, author = {Bloom, PP and Bassis, CM and Crossette, E and Silber, JL and Norman, JM and Young, VB and Lok, ASF}, title = {Safety and efficacy of a defined bacterial consortium, VE303, to treat HE.}, journal = {Hepatology communications}, volume = {9}, number = {3}, pages = {}, doi = {10.1097/HC9.0000000000000650}, pmid = {39969428}, issn = {2471-254X}, mesh = {Humans ; Male ; Middle Aged ; Female ; *Gastrointestinal Microbiome/drug effects ; *Hepatic Encephalopathy/drug therapy ; Aged ; Treatment Outcome ; Vancomycin/therapeutic use/adverse effects ; Anti-Bacterial Agents/therapeutic use/adverse effects/administration & dosage ; Feces/microbiology/chemistry ; Lactulose/therapeutic use ; Rifaximin/therapeutic use ; Adult ; }, abstract = {BACKGROUND: Novel therapies are needed to treat HE, and microbiome modulation is a promising target. VE303 is a defined consortium of 8 purified, clonal bacterial strains, known to produce metabolites that may be beneficial in HE. We evaluated the safety and efficacy of VE303 to treat HE.

METHODS: We performed a single-center, randomized, placebo-controlled trial of VE303 in adult patients with a history of overt HE (NCT04899115). Eligible patients were taking lactulose and rifaximin, had no recent systemic antibiotics, and had MELD ≤20. All patients received 5 days of oral vancomycin followed by randomization to 14 days of VE303 or placebo (2:1). The primary endpoints were incidence of serious adverse events and change in psychometric HE score (PHES) from baseline to 4 weeks after treatment. Stool samples underwent metagenomic sequencing and metabolite quantification.

RESULTS: Eighteen patients completed the trial, 56% men, with a mean age of 59 years and a mean MELD of 11. Patients who received VE303 had a mean change in PHES of +1.5 versus -1.0 in those who received a placebo (p=0.20). Two of the 12 patients who received VE303 had at least 1 serious adverse event (all overt HE hospitalizations), compared with 0/6 patients who received a placebo. In the patients who received VE303, 2 of 8 strains engrafted in >50% of patients. Both VE303 strain engraftment and increased stool butyrate production had a trend toward improved PHES.

CONCLUSIONS: VE303 was well tolerated in patients with cirrhosis and a history of overt HE, leading to the engraftment of certain VE303 strains and a higher percentage of patients with improved PHES.}, } @article {pmid39947184, year = {2025}, author = {Heinken, A and Hulshof, TO and Nap, B and Martinelli, F and Basile, A and O'Brolchain, A and O'Sullivan, NF and Gallagher, C and Magee, E and McDonagh, F and Lalor, I and Bergin, M and Evans, P and Daly, R and Farrell, R and Delaney, RM and Hill, S and McAuliffe, SR and Kilgannon, T and Fleming, RMT and Thinnes, CC and Thiele, I}, title = {A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites.}, journal = {Cell systems}, volume = {16}, number = {2}, pages = {101196}, doi = {10.1016/j.cels.2025.101196}, pmid = {39947184}, issn = {2405-4720}, mesh = {Humans ; *Microbiota/genetics ; Metagenomics/methods ; Metabolic Networks and Pathways/genetics ; Machine Learning ; Metagenome/genetics ; Genome, Microbial ; }, abstract = {Genome-scale modeling of microbiome metabolism enables the simulation of diet-host-microbiome-disease interactions. However, current genome-scale reconstruction resources are limited in scope by computational challenges. We developed an optimized and highly parallelized reconstruction and analysis pipeline to build a resource of 247,092 microbial genome-scale metabolic reconstructions, deemed APOLLO. APOLLO spans 19 phyla, contains >60% of uncharacterized strains, and accounts for strains from 34 countries, all age groups, and multiple body sites. Using machine learning, we predicted with high accuracy the taxonomic assignment of strains based on the computed metabolic features. We then built 14,451 metagenomic sample-specific microbiome community models to systematically interrogate their community-level metabolic capabilities. We show that sample-specific metabolic pathways accurately stratify microbiomes by body site, age, and disease state. APOLLO is freely available, enables the systematic interrogation of the metabolic capabilities of largely still uncultured and unclassified species, and provides unprecedented opportunities for systems-level modeling of personalized host-microbiome co-metabolism.}, } @article {pmid39690119, year = {2025}, author = {Di Gloria, L and Baldi, S and Curini, L and Bertorello, S and Nannini, G and Cei, F and Niccolai, E and Ramazzotti, M and Amedei, A}, title = {Experimental tests challenge the evidence of a healthy human blood microbiome.}, journal = {The FEBS journal}, volume = {292}, number = {4}, pages = {796-808}, doi = {10.1111/febs.17362}, pmid = {39690119}, issn = {1742-4658}, support = {//Ministry of University and Research (MUR)/ ; //FONZIE project (CUP B55F21007810001)/ ; //National Recovery and Resilience Plan (NRRP)/ ; }, mesh = {Humans ; *Microbiota/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *DNA, Bacterial/genetics/blood ; Bacteria/genetics/isolation & purification/classification ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Blood/microbiology ; Sequence Analysis, DNA/methods ; Healthy Volunteers ; Female ; Male ; Adult ; }, abstract = {The advent of next-generation sequencing (NGS) technologies has made it possible to investigate microbial communities in various environments, including different sites within the human body. Therefore, the previously established belief of the sterile nature of several body sites, including human blood, has now been challenged. However, metagenomics investigation of areas with an anticipated low microbial biomass may be susceptible to misinterpretation. Here, we critically evaluate the results of 16S targeted amplicon sequencing performed on total DNA collected from healthy donors' blood samples while incorporating specific negative controls aimed at addressing potential bias to supplement and strengthen the research in this area. We prepared negative controls by increasing the initial DNA quantity through sequences that can be recognized and subsequently discarded. We found that only three organisms were sporadically present among the samples, and this was mostly attributable to bacteria ubiquitously present in laboratory reagents. Despite not fully confirming or denying the existence of healthy blood microbiota, our results suggest that living bacteria, or at least their residual DNA sequences, are not a common feature of human blood in healthy people. Finally, our study poses relevant questions on the design of controls in this research area that must be considered in order to avoid misinterpreted results that appear to contaminate current high-throughput research.}, } @article {pmid39578945, year = {2025}, author = {Li, D and Zhi, J and Ye, J and Yue, W and Yang, Y}, title = {Influence of different diet categories on gut bacterial diversity in Frankliniella occidentalis.}, journal = {Environmental entomology}, volume = {54}, number = {1}, pages = {119-129}, doi = {10.1093/ee/nvae117}, pmid = {39578945}, issn = {1938-2936}, support = {[2016] 5802//Guizhou International Science and Technology Cooperation Base/ ; }, mesh = {Diet ; Gastrointestinal Microbiome ; Metagenome ; Phaseolus ; Rosa ; Sequence Analysis, DNA ; *Thysanoptera/microbiology ; *Bacteria/classification/genetics/isolation & purification ; }, abstract = {The microbial composition of insect guts is typically influenced by the type of food consumed, and conversely, these microbes influence the food habits of insects. Western flower thrips (WFT; Frankliniella occidentalis) is an invasive pest with a wide range of hosts, including vegetables and horticultural crops. To elucidate variations in gut bacteria among WFT feeding on rose (Rosa rugosa) flowers (FF), kidney bean (Phaseolus vulgaris) pods (PF), and kidney bean leaves (LF), we collected adult guts and extracted DNA for 16S ribosomal RNA gene sequencing of microbial communities. The results revealed that the FF population had the highest number of annotations. Alpha diversity analysis revealed that the Chao and Ace indexes were the greatest in the PF population, indicating a higher abundance of gut bacteria. Moreover, the Simpson index was the highest in the FF population, indicating that gut bacterial diversity was the highest in the FF population. Comparison of species composition demonstrated that Proteobacteria dominated all 3 populations at the phylum level, with Actinobacteria being the subdominant phylum. At the genus level, Stenotrophomonas was the dominant bacteria in the PF and LF populations, whereas Rosenbergiella was dominant in the FF population. KEGG pathway annotation predicted that the gut bacteria of adult WFT were mainly involved in carbohydrate and amino acid metabolism. Our results revealed that the diversity and composition of WFT gut microbiota are influenced by diet, offering evidence for future studies on the ecological adaptability of WFT and the mechanisms underlying the interaction between gut microbiota and host.}, } @article {pmid39967175, year = {2025}, author = {Aragão, MOP and Lima, FR and Passamani, FRF and Santos, MAA and Rezende, JP and Batista, LR}, title = {Fungal and bacterial diversity present on the rind and core of Natural Bloomy Rind Artisanal Minas Cheese from the Canastra region, Brazil.}, journal = {Food research international (Ottawa, Ont.)}, volume = {202}, number = {}, pages = {115724}, doi = {10.1016/j.foodres.2025.115724}, pmid = {39967175}, issn = {1873-7145}, mesh = {*Cheese/microbiology ; Brazil ; *Food Microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Fungi/genetics/classification/isolation & purification ; Animals ; Microbiota/genetics ; Geotrichum/genetics ; Milk/microbiology ; Biodiversity ; Cattle ; Lactococcus/genetics/isolation & purification/classification ; }, abstract = {Globally recognized for its unique sensory attributes, Natural Bloomy Rind Artisanal Minas Cheese (NBRAMC) from the Canastra microregion is made from raw cow's milk using a natural starter culture derived from the local environment. During ripening process, microorganisms, predominantly Geotrichum candidum, develop on the surface, with the microbial community playing a crucial role in shaping the cheese's distinctive characteristics. This study aimed to characterize the microbial community, including filamentous fungi, yeasts, and bacteria, present in the rind and core of NBRAMC. Amplicon sequencing of the ITS and 16S rRNA gene regions was performed on rind and core samples from cheeses produced at six distinct producers. Results indicated that G. candidum and Diutina catenulata were the most prevalent fungal species, and Candida intermedia being more abundant exclusively in the interior of the cheeses. The bacterial community displayed greater diversity in the rind, with genera such as Lactococcus, Brevibacterium, and Corynebacterium variabile, while Lactococcus and Streptococcus dominated the core. An inverse relationship between D. catenulata and G. candidum abundance was noted. Significant variations in microbial community profiles were found among producers, despite their geographical proximity. While low levels of undesirable fungi were detected, some samples showed a notable presence of undesirable bacteria, indicating potential hygiene issues during cheese handling. These findings provide valuable insights into the microbial dynamics of NBRAMC, supporting the implementation of strategies that can enhance the quality and safety of the product.}, } @article {pmid39967137, year = {2025}, author = {Espí-Malillos, A and López-Almela, I and Ruiz-García, P and López-Mendoza, MC and Carrón, N and González-Torres, P and Quereda, JJ}, title = {Raw milk at refrigeration temperature displays an independent microbiota dynamic regardless Listeria monocytogenes contamination.}, journal = {Food research international (Ottawa, Ont.)}, volume = {202}, number = {}, pages = {115637}, doi = {10.1016/j.foodres.2024.115637}, pmid = {39967137}, issn = {1873-7145}, mesh = {*Listeria monocytogenes/growth & development/genetics/isolation & purification ; *Milk/microbiology ; Animals ; *Refrigeration ; *Microbiota ; *Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Food Contamination/analysis ; Cold Temperature ; }, abstract = {Dairy products made of raw milk are associated with hypervirulent L. monocytogenes clonal complexes (CCs) CC1, CC4, and CC6, and cause half of the reported listeriosis outbreaks in Europe. However, it is currently unknown whether the overrepresentation of L. monocytogenes hypervirulent clones in dairy products made of raw milk is conditioned by an alteration in the native raw milk microbiota growth and/or composition. In this study, the lag phase, maximal growth rate, and the final maximal concentration of mesophilic aerobic bacteria from native raw milk bacteria were measured at refrigerated temperature (4 °C) in the presence and absence of L. monocytogenes contamination. The raw milk microbiota composition and dynamics were evaluated in the presence and absence of L. monocytogenes hypervirulent (CC1, CC4, CC6), and hypovirulent (CC9 and CC121) clones at 4 °C by using 16S rRNA high-throughput sequencing. Our results showed that the growth and composition of the microbial communities naturally present in raw milk are independent of the contamination with hyper- or hypovirulent L. monocytogenes CCs at refrigeration temperature. Pseudomonas was the most abundant genus in raw milk on days 11 and 21, while Carnobacterium was the second most abundant genus regardless of the contaminant L. monocytogenes CCs. Altogether these results suggest that the overrepresentation of hypervirulent L. monocytogenes CC1, CC4, and CC6 in dairy products is not the consequence of a differential alteration in the native composition of the raw milk microbiota.}, } @article {pmid39966419, year = {2025}, author = {Heidrich, V and Fackelmann, G and Malesevic, M and Armanini, F and Dey, H and Mengoni, C and Stanisavljevic, N and Vukotic, G and Segata, N}, title = {Newly identified species from the dog dental plaque microbiome highlight little overlap with humans.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {30}, pmid = {39966419}, issn = {2055-5008}, mesh = {Animals ; Dogs ; *Dental Plaque/microbiology ; *Microbiota ; Humans ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Metagenomics/methods ; Phylogeny ; Pets/microbiology ; }, abstract = {Understudied pet-associated microbiomes represent a rich source for the discovery of microbial taxa important for pet and human health. From a cohort of 23 dogs, we sampled and metagenomically sequenced 64 dental plaque microbiomes, generating 1945 metagenome-assembled genomes spanning 347 microbial species, including 277 undercharacterized species without cultivated representatives. Integration with human microbiome data revealed the dog plaque microbiome is more diverse than - and shows little overlap (5.9% species in common) with - the human plaque microbiome, even though some shared periodontal pathobionts arise as a potential concern.}, } @article {pmid39964655, year = {2025}, author = {Pitt, A and Lienbacher, S and Schmidt, J and Neumann-Schaal, M and Wolf, J and Wenng, H and Oren, A and Huber, Z and Hahn, MW}, title = {Biodiversity of strains belonging to the freshwater genus Aquirufa in a riparian forest restoration area in Salzburg, Austria, with a focus on the description of Aquirufa salirivi sp. nov. and Aquirufa novilacunae sp. nov.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {39964655}, issn = {1618-1905}, abstract = {During a citizen science project, four freshwater habitats in a riparian forest restoration area in Salzburg, Austria, were sampled. The primary aim was to obtain bacterial strains of the genus Aquirufa, a group of typical and widespread freshwater bacteria. Numerous pure cultures of Aquirufa strains could be obtained, three of them originating from the river Salzach, a newly created pond and the lake Ausee represented new species. Strain 1-SAACH-A3[T] was characterized by a genome size of 3.2 Mbp and a G + C value of 38.4 mol% and encoded genes predicted for nitrate uptake and nitrous oxide utilization. Strains BAHN-186B[T] and 2-AUSEE-184A6 were characterized by a genome size of 2.4 Mbp and a G + C value of 42.4 and 42.2 mol%, respectively, and encoded genes predicted for the light-harvesting rhodopsin system. Calculated whole-genome average nucleotide identity values with Aquirufa type strains resulted in a maximum value of 93.65% for comparison of strain 1-SAACH[T] with the type strain of Aquirufa ecclesiirivi, which is slightly under the proposed threshold of species demarcation. The calculated gANI value comparing strains BAHN-186B[T] and 2-AUSEE-184A6 revealed 95.76%, thus a value slightly above the threshold. Further analyses revealed that the three new strains represent two new species, proposed here as Aquirufa salirivi sp. nov. with type strain 1-SAACH-A3[T] (= DSM 117800[ T] = JCM 37097[ T]) and Aquirufa novilacunae sp. nov. with type strain BAHN-186B[T] (= DSM 118143[ T] = JCM 37099[ T]). Analyses of 123 publicly available metagenomes and a metagenome of the lake Ausee resulted in no detection of A. salirivi sp. nov. In contrast, A. novilacunae sp. nov. could be detected in 15 water samples of rivers, mainly from Asia, but also from North America and Australia. The analyses suggested that the species occurs in most of these samples in low relative abundance, detections derived from metagenomes of water samples from the river Yangtze in the subtropical zone could be interpreted as occurrence in higher abundances.}, } @article {pmid39962698, year = {2025}, author = {Ye, Y and Guo, XW and Yang, MQ and Min, W and Guo, HJ}, title = {[Microbial Community Structure and Functional Genes of Phosphorus Cycling in Cotton Field Soil Under Long-term Saline Drip Irrigation].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {2}, pages = {1225-1235}, doi = {10.13227/j.hjkx.202402036}, pmid = {39962698}, issn = {0250-3301}, mesh = {*Phosphorus/metabolism ; *Gossypium/growth & development/genetics ; *Agricultural Irrigation/methods ; *Soil Microbiology ; *Soil/chemistry ; Microbiota ; Salinity ; Saline Waters ; Bacteria/genetics/classification/metabolism/growth & development ; }, abstract = {Freshwater resources are scarce in arid regions, and the rational use of brackish water resources can alleviate local freshwater shortages, but long-term brackish drip irrigation increases the risk of soil salinization, which in turn affects soil nutrient transformation and microbial diversity. Soil phosphorus availability is critical for crop growth, yet it is unclear how long-term brackish drip irrigation will affect soil phosphorus transformation. Therefore, to investigate the effects of long-term brackish drip irrigation on soil phosphorus-transforming microorganisms and their functional genes in cotton fields, the experiment was set up with two irrigation water salinities, freshwater （0.35 dS·m[-1], FW） and brackish water （8.04 dS·m[-1], SW）. The results showed that long-term brackish drip irrigation significantly decreased cotton dry matter weight, phosphorus uptake, yield, soil pH, and Ca2-P and Ca10-P contents but significantly increased cotton phosphorus content and soil water content； electrical conductivity； quick phosphorus； and Ca8-P, Al-P, Fe-P, and O-P contents. The dominant species in each treatment at the phylum level were Ascomycetes, Actinobacteria, Acidobacteria, Bacillus, and Greenscapes； and at the phylum level, the dominant species were α-Ascomycetes, Actinobacteria, β-Ascomycetes, Oleococcus thermophilus, and γ-Ascomycetes. including Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, and Chloroflexi. Select dominant species at the class level included Alphaproteobacteria, Actinomycetia, Betaproteobacteria, Thermoleophilia, and Gammaproteobacteria. Long-term saline drip irrigation significantly reduced the relative abundance of Actinobacteria, Acidobacteria, and Nitrospirae but significantly increased the relative abundance of Proteobacteria, Gemmatimonadetes, and Bacteroidetes and significantly reduced the expression levels of the organic phosphorus mineralization gene phnA, transport gene pit, and polyphosphate synthesis gene ppaC. Moreover, it significantly increased the expression levels of the polyphosphate degradation gene HDDC3； organic phosphorus mineralization genes phnG, phoA, phnH, phnL, phnM, phnN, phnP, and phnW； transport genes phnK, phnE, phnC, and phnD； and the regulatory gene phoB. Correlation analysis showed that soil phosphorus-cycling microorganisms and functional genes were closely related to soil physicochemical properties and soil inorganic phosphorus content. Therefore, long-term saline drip irrigation changes the composition of soil phosphorus-cycling microorganisms by affecting soil physical and chemical properties and inorganic phosphorus content, which in turn drives the expression of phosphorus-cycling-related functional genes to regulate and adapt to salt stress.}, } @article {pmid39929003, year = {2025}, author = {Bakir-Gungor, B and Temiz, M and Canakcimaksutoglu, B and Yousef, M}, title = {Prediction of colorectal cancer based on taxonomic levels of microorganisms and discovery of taxonomic biomarkers using the Grouping-Scoring-Modeling (G-S-M) approach.}, journal = {Computers in biology and medicine}, volume = {187}, number = {}, pages = {109813}, doi = {10.1016/j.compbiomed.2025.109813}, pmid = {39929003}, issn = {1879-0534}, mesh = {*Colorectal Neoplasms/microbiology ; Humans ; *Gastrointestinal Microbiome/genetics ; *Biomarkers, Tumor/genetics ; Metagenomics/methods ; Algorithms ; Bacteria/genetics/classification ; }, abstract = {Colorectal cancer (CRC) is one of the most prevalent forms of cancer globally. The human gut microbiome plays an important role in the development of CRC and serves as a biomarker for early detection and treatment. This research effort focuses on the identification of potential taxonomic biomarkers of CRC using a grouping-based feature selection method. Additionally, this study investigates the effect of incorporating biological domain knowledge into the feature selection process while identifying CRC-associated microorganisms. Conventional feature selection techniques often fail to leverage existing biological knowledge during metagenomic data analysis. To address this gap, we propose taxonomy-based Grouping Scoring Modeling (G-S-M) method that integrates biological domain knowledge into feature grouping and selection. In this study, using metagenomic data related to CRC, classification is performed at three taxonomic levels (genus, family and order). The MetaPhlAn tool is employed to determine the relative abundance values of species in each sample. Comparative performance analyses involve six feature selection methods and four classification algorithms. When experimented on two CRC associated metagenomics datasets, the highest performance metric, yielding an AUC of 0.90, is observed at the genus taxonomic level. At this level, 7 out of top 10 groups (Parvimonas, Peptostreptococcus, Fusobacterium, Gemella, Streptococcus, Porphyromonas and Solobacterium) were commonly identified for both datasets. Moreover, the identified microorganisms at genus, family, and order levels are thoroughly discussed via refering to CRC-related metagenomic literature. This study not only contributes to our understanding of CRC development, but also highlights the applicability of taxonomy-based G-S-M method in tackling various diseases.}, } @article {pmid39880958, year = {2025}, author = {Maghini, DG and Oduaran, OH and Olubayo, LAI and Cook, JA and Smyth, N and Mathema, T and Belger, CW and Agongo, G and Boua, PR and Choma, SSR and Gómez-Olivé, FX and Kisiangani, I and Mashaba, GR and Micklesfield, L and Mohamed, SF and Nonterah, EA and Norris, S and Sorgho, H and Tollman, S and Wafawanaka, F and Tluway, F and Ramsay, M and Wirbel, J and , and Bhatt, AS and Hazelhurst, S}, title = {Expanding the human gut microbiome atlas of Africa.}, journal = {Nature}, volume = {638}, number = {8051}, pages = {718-728}, pmid = {39880958}, issn = {1476-4687}, support = {R01 AI148623/AI/NIAID NIH HHS/United States ; D43 TW010540/TW/FIC NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; U54 HG006938/HG/NHGRI NIH HHS/United States ; S10 OD023452/OD/NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Female ; *Metagenome ; Cross-Sectional Studies ; HIV Infections/microbiology/epidemiology ; Adult ; Treponema/isolation & purification/genetics/classification ; Africa ; Urban Population/statistics & numerical data ; Life Style ; Metagenomics ; South Africa/epidemiology ; Rural Population/statistics & numerical data ; Atlases as Topic ; Ghana ; }, abstract = {Population studies provide insights into the interplay between the gut microbiome and geographical, lifestyle, genetic and environmental factors. However, low- and middle-income countries, in which approximately 84% of the world's population lives[1], are not equitably represented in large-scale gut microbiome research[2-4]. Here we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,801 women from Burkina Faso, Ghana, Kenya and South Africa. By engaging with communities that range from rural and horticultural to post-industrial and urban informal settlements, we capture a far greater breadth of the world's population diversity. Using shotgun metagenomic sequencing, we identify taxa with geographic and lifestyle associations, including Treponema and Cryptobacteroides species loss and Bifidobacterium species gain in urban populations. We uncover 1,005 bacterial metagenome-assembled genomes, and we identify antibiotic susceptibility as a factor that might drive Treponema succinifaciens absence in urban populations. Finally, we find an HIV infection signature defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals so far, and paired with extensive clinical biomarkers and demographic data, provides extensive opportunity for microbiome-related discovery.}, } @article {pmid39875062, year = {2025}, author = {Zhan, M and Li, Z and Chen, J and Zhao, Y and Bai, Z and Lu, B and Chen, H and Liu, Y}, title = {Indoxyl sulfate (IS) mediates pro-inflammatory responses in severe pneumonia in patients with rheumatoid arthritis associated interstitial lung disease.}, journal = {Clinical immunology (Orlando, Fla.)}, volume = {272}, number = {}, pages = {110430}, doi = {10.1016/j.clim.2025.110430}, pmid = {39875062}, issn = {1521-7035}, mesh = {Humans ; *Arthritis, Rheumatoid/immunology/complications ; *Lung Diseases, Interstitial/immunology ; *COVID-19/immunology/complications ; Male ; Female ; Middle Aged ; Aged ; *Bronchoalveolar Lavage Fluid/immunology ; *Indican ; *SARS-CoV-2 ; *Microbiota ; Neutrophils/immunology ; Lung/immunology ; Pneumonia/immunology/complications/microbiology ; }, abstract = {OBJECT: Patients with rheumatoid arthritis-associated interstitial lung disease (RA-ILD) have a high risk of serious infection, in particular severe pneumonia. This study aimed to investigate the transcriptional landscape, lower respiratory tract (LRT) microbiome and metabolomic profiles in the lung of RA-ILD patients with pneumonia.

METHOD: A total of 10 RA-ILD with pneumonia were enrolled in this study. In addition, 11 patients with COVID-19-associated pneumonia and 6 patients with non-autoimmune and non-COVID-19-related ILD with pneumonia were included as controls. Bronchoalveolar lavage fluid (BALF) was collected and prepared for metagenomic next-generation sequencing (mNGS), non-targeted metabolomics and bulk RNA-seq.

RESULT: Neutrophil-related genes were shared in the BALF cells of RA-ILD patients with pneumonia and patients with COVID-19-associated pneumonia. Carnobacterium, Wujia, Intestinimonas, Apibacter, Anaerotignum and Parvimonas were enriched in the LRT microbiome of RA-ILD, while Wujia, Apibacter, Pseudocitrobacter, and Thermobacillus were enriched in the LRT microbiome of COVID-19. Metabolomics analysis of BALF revealed significant elevation of indoxyl sulfate (IS) in the BALF of RA-ILD patients in comparison to COVID-19. Mechanistically, IS exerts an pro-inflammatory effect on macrophages and bronchial epithelial cells for pro-inflammatory cytokine production and potentiated neutrophils for neutrophil extracellular traps (NETs) formation.

CONCLUSIONS: Our results demonstrated a significant differences in the LRT microbiome and BALF metabolites between RA-ILD and COVID-19 patients with pneumonia, although they displayed similar local immune responses against lung infection. Alterations of LRT microbiome and related metabolites may be implicated in the pathogenesis of pneumonia in RA-ILD.}, } @article {pmid39840975, year = {2025}, author = {Ge, B and McDonald, RC and Yang, Q and Domesle, KJ and Sarria, S and Li, X and Hsu, C-H and Jarvis, KG and Tadesse, DA}, title = {Exploring animal food microbiomes and resistomes via 16S rRNA gene amplicon sequencing and shotgun metagenomics.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {2}, pages = {e0223024}, doi = {10.1128/aem.02230-24}, pmid = {39840975}, issn = {1098-5336}, mesh = {*RNA, Ribosomal, 16S/genetics ; Animals ; *Microbiota ; *Metagenomics ; *Animal Feed/analysis/microbiology ; Dogs ; *Bacteria/genetics/isolation & purification/classification/drug effects ; Cattle ; Food Microbiology ; Drug Resistance, Bacterial/genetics ; Poultry/microbiology ; DNA, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Sequence Analysis, DNA ; }, abstract = {As a diverse and complex food matrix, the animal food microbiota and repertoire of antimicrobial resistance (AMR) genes remain to be better understood. In this study, 16S rRNA gene amplicon sequencing and shotgun metagenomics were applied to three types of animal food samples (cattle feed, dry dog food, and poultry feed). ZymoBIOMICS mock microbial community was used for workflow optimization including DNA extraction kits and bead-beating conditions. The four DNA extraction kits (AllPrep PowerViral DNA/RNA Kit, DNeasy Blood & Tissue Kit, DNeasy PowerSoil Kit, and ZymoBIOMICS DNA Miniprep Kit) were compared in animal food as well as the use of peptide nucleic acid blockers for 16S rRNA gene amplicon sequencing. Distinct microbial community profiles were generated, which varied by animal food type and DNA extraction kit. Employing peptide nucleic acid blockers prior to 16S rRNA gene amplicon sequencing was comparable with post-sequencing in silico filtering at removing chloroplast and mitochondrial sequences. There was a good agreement between 16S rRNA gene amplicon sequencing and shotgun metagenomics on community profiles in animal feed data sets; however, they differed in taxonomic resolution, with the latter superior at resolving at the species level. Although the overall prevalence of AMR genes was low, resistome analysis of animal feed data sets by shotgun metagenomics revealed 10 AMR gene/protein families, including beta-lactamases, erythromycin/lincomycin/pristinamycin/tylosin, fosfomycin, phenicol, and quinolone. Future expansion of microbiome and resistome profiling in animal food will help better understand the bacterial and AMR gene diversity in these commodities and help guide pathogen control and AMR prevention efforts.IMPORTANCEWith the growing interest and application of metagenomics in understanding the structure/composition and function of diverse microbial communities along the One Health continuum, this study represents one of the first attempts to employ these advanced sequencing technologies to characterize the microbiota and AMR genes in animal food. We unraveled the effects of DNA extraction kits on sample analysis by 16S rRNA gene amplicon sequencing and showed similar efficacies of two strategies at removing chloroplast and mitochondrial reads. The in-depth analysis using shotgun metagenomics shed light on the community compositions and the presence of an array of AMR genes in animal food. This exploration of microbiomes and resistomes in representative animal food samples by both sequencing approaches laid important groundwork for future metagenomic investigations to gain a better understanding of the baseline/core microbiomes and associated AMR functions in these diverse commodities and help guide pathogen control and AMR prevention efforts.}, } @article {pmid39840973, year = {2025}, author = {Wu, DG and Harris, CR and Kalis, KM and Bowen, M and Biddle, JF and Farag, IF}, title = {Comparative metagenomics of tropical reef fishes show conserved core gut functions across hosts and diets with diet-related functional gene enrichments.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {2}, pages = {e0222924}, doi = {10.1128/aem.02229-24}, pmid = {39840973}, issn = {1098-5336}, support = {//Midlin Foundation/ ; //W. M. Keck Foundation (WMKF)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Metagenomics ; *Diet/veterinary ; *Fishes/microbiology ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Animal Feed/analysis ; Coral Reefs ; Feces/microbiology ; }, abstract = {UNLABELLED: Fish gut microbial communities are important for the breakdown and energy harvesting of the host diet. Microbes within the fish gut are selected by environmental and evolutionary factors. To understand how fish gut microbial communities are shaped by diet, three tropical fish species (hawkfish, Paracirrhites arcatus; yellow tang, Zebrasoma flavescens; and triggerfish, Rhinecanthus aculeatus) were fed piscivorous (fish meal pellets), herbivorous (seaweed), and invertivorous (shrimp) diets, respectively. From fecal samples, a total of 43 metagenome assembled genomes (MAGs) were recovered from all fish diet treatments. Each host-diet treatment harbored distinct microbial communities based on taxonomy, with Proteobacteria, Bacteroidota, and Firmicutes being the most represented. Based on their metagenomes, MAGs from all three host-diet treatments demonstrated a baseline ability to degrade proteinaceous, fatty acid, and simple carbohydrate inputs and carry out central carbon metabolism, lactate and formate fermentation, acetogenesis, nitrate respiration, and B vitamin synthesis. The herbivorous yellow tang harbored more functionally diverse MAGs with some complex polysaccharide degradation specialists, while the piscivorous hawkfish's MAGs were more specialized for the degradation of proteins. The invertivorous triggerfish's gut MAGs lacked many carbohydrate-degrading capabilities, resulting in them being more specialized and functionally uniform. Across all treatments, several MAGs were able to participate in only individual steps of the degradation of complex polysaccharides, suggestive of microbial community networks that degrade complex inputs.

IMPORTANCE: The benefits of healthy microbiomes for vertebrate hosts include the breakdown of food into more readily usable forms and production of essential vitamins from their host's diet. Compositions of microbial communities in the guts of fish in response to diet have been studied, but there is a lack of a comprehensive understanding of the genome-based metabolic capabilities of specific microbes and how they support their hosts. Therefore, we assembled genomes of several gut microbes collected from the feces of three fish species that were being fed different diets to illustrate how individual microbes can carry out specific steps in the degradation and energy utilization of various food inputs and support their host. We found evidence that fish gut microbial communities share several core functions despite differences in microbial taxonomy. Herbivorous fish harbored a functionally diverse microbial community with plant matter degraders, while the piscivorous and invertivorous fish had microbiomes more specialized in protein degradation.}, } @article {pmid39798664, year = {2025}, author = {Wu, Y and Liu, X and Yin, M and Pei, Y and Cui, Y and Li, J and Zhu, Y and Guo, W and Li, D}, title = {Combining metagenomic sequencing and molecular docking to understand signaling molecule degradation characteristics of quorum quenching consortia.}, journal = {Environmental research}, volume = {268}, number = {}, pages = {120815}, doi = {10.1016/j.envres.2025.120815}, pmid = {39798664}, issn = {1096-0953}, mesh = {*Quorum Sensing ; *Molecular Docking Simulation ; *4-Butyrolactone/analogs & derivatives/metabolism/chemistry ; Metagenomics ; Bacteria/metabolism/genetics ; Microbial Consortia ; }, abstract = {Quorum quenching consortia (QQC) enriched by special substrates for bioaugmentation is a promising QQ technology to reduce biofouling, sludge yield, and sludge bulking. However, the effect of substrate type on the performance of QQC is still a research gap. This study selected three different substrates, regular AHLs (N-octanoyl-l-homoserine lactone, C8), 3-oxo-AHLs (3-oxo-octanoyl)-l-homoserine lactone, 3-oxo-C8), and AHLs analogs (γ-caprolactone, GCL) to enrich three QQC (C8-QQC, 3OC8-QQC, GCL-QQC). Combining metagenomic sequencing, protein prediction, and molecular docking to fill the above gaps from the perspective of bacteria and enzymes. The performance of the three QQC decreased with the increasing complexity of the molecular structure of the substrates. This decline was attributed to more complex substrate enriched with more bacteria, lacking QQ genes in the QQC. All QQC degraded N-acetyl-l-homoserine lactones (AHLs) via acylase and lactonase. C8-QQC and 3OC8-QQC showed stronger degradation capabilities for N-(3-oxo-hexanoyl)-L-homoserine lactone (3OC6) compared to N-hexanoyl-L-homoserine lactone (C6), whereas GCL-QQC exhibited stronger degradation for C6. Molecular docking results showed that in 3OC8-QQC and C8-QQC, most enzymes exhibited stronger degradation capabilities for long-chain and 3OAHLs. However, in GCL-QQC, more QQ enzymes showed stronger degradation for C6 than for 3OC6, explaining the observed differences in AHL degradation. β-Oxidation metabolic pathways in bins revealed differences in their abilities to metabolize octanoic acid from C8 and 3-oxo-octanoic acid from 3OC8, which influenced their abundance in the respective QQC. The study findings offer insights into the relationship between substrates and QQC performance at the gene and protein levels.}, } @article {pmid39779925, year = {2025}, author = {He, X and Hu, M and Xu, Y and Xia, F and Tan, Y and Wang, Y and Xiang, H and Wu, H and Ji, T and Xu, Q and Wang, L and Huang, Z and Sun, M and Wan, Y and Cui, P and Liang, S and Pan, Y and Xiao, S and He, Y and Song, R and Yan, J and Quan, X and Wei, Y and Hong, C and Liao, W and Li, F and El-Omar, E and Chen, J and Qi, X and Gao, J and Zhou, H}, title = {The gut-brain axis underlying hepatic encephalopathy in liver cirrhosis.}, journal = {Nature medicine}, volume = {31}, number = {2}, pages = {627-638}, pmid = {39779925}, issn = {1546-170X}, support = {82372305//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Hepatic Encephalopathy/pathology/microbiology/metabolism ; *Liver Cirrhosis/metabolism/pathology/complications/microbiology ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Brain-Gut Axis ; Male ; Dysbiosis/microbiology ; Brain/metabolism/pathology ; Fecal Microbiota Transplantation ; Liver/metabolism/pathology ; Mice, Inbred C57BL ; Monoamine Oxidase/metabolism/genetics ; Ruminococcus ; }, abstract = {Up to 50-70% of patients with liver cirrhosis develop hepatic encephalopathy (HE), which is closely related to gut microbiota dysbiosis, with an unclear mechanism. Here, by constructing gut-brain modules to assess bacterial neurotoxins from metagenomic datasets, we found that phenylalanine decarboxylase (PDC) genes, mainly from Ruminococcus gnavus, increased approximately tenfold in patients with cirrhosis and higher in patients with HE. Cirrhotic, not healthy, mice colonized with R. gnavus showed brain phenylethylamine (PEA) accumulation, along with memory impairment, symmetrical tremors and cortex-specific neuron loss, typically found in patients with HE. This accumulation of PEA was primarily driven by decreased monoamine oxidase-B activity in both the liver and serum due to cirrhosis. Targeting PDC or PEA reversed the neurological symptoms induced by R. gnavus. Furthermore, fecal microbiota transplantation from patients with HE to germ-free cirrhotic mice replicated these symptoms and further corroborated the efficacy of targeting PDC or PEA. Clinically, high baseline PEA levels were linked to a sevenfold increased risk of HE after intrahepatic portosystemic shunt procedures. Our findings expand the understanding of the gut-liver-brain axis and identify a promising therapeutic and predictive target for HE.}, } @article {pmid39755199, year = {2025}, author = {Liu, L and Zhu, G and Hu, J and Chen, H and Zhai, Y}, title = {An unignorable human health risk posed by antibiotic resistome and microbiome in urban rivers: Insights from Beijing, China.}, journal = {Environmental research}, volume = {268}, number = {}, pages = {120752}, doi = {10.1016/j.envres.2025.120752}, pmid = {39755199}, issn = {1096-0953}, mesh = {*Rivers/microbiology ; Humans ; Beijing ; *Microbiota/drug effects ; Drug Resistance, Microbial/genetics ; Risk Assessment ; Environmental Monitoring ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; China ; }, abstract = {Urban rivers are the main water bodies humans frequently come into contact with, so the risks posed are closely monitored. Antibiotic resistance genes (ARGs) residues in reclaimed water pose serious risks to human health. There are urgent needs to improve the understanding of distribution of and risks posed by ARGs in urban rivers. In this study, shotgun metagenomic approach was used to characterize ARGs, mobile genetic elements (MGEs), and virulence factors (VFs) in water and sediment from Xinfeng River in Beijing and to identify microbes, potential antibiotic resistant bacteria, and human pathogens (HPs). MGE, microbial community, VF, and ARG co-occurrences were used to assess the environmental risks posed by ARGs. The results indicated that quinolone was the most abundant ARG type and that tufA and fusA were the two dominant ARG subtypes. Wetland effluent increased ARG abundance in the river, and the effect was detected even 50 m downstream. ARG abundances and distribution in the river had difference in different seasons. The dominant bacteria in the river were Proteobacteria, Bacteroidetes, and Actinobacteria, and 59 HPs were detected. In total, 69 MGEs and 19 VFs were found. Co-occurrence networks indicated that potential antibiotic resistant bacteria, MGEs, VFs, and ARGs in the river significantly correlated, indicating the potential risks posed by ARGs. The results improve our understanding of ARG distribution and environmental risks in urban river water. More attention should be paid to controlling environmental risks posed by ARGs in urban river and reclaimed water.}, } @article {pmid39662756, year = {2025}, author = {Hodgkiss, R and Acharjee, A}, title = {Unravelling metabolite-microbiome interactions in inflammatory bowel disease through AI and interaction-based modelling.}, journal = {Biochimica et biophysica acta. Molecular basis of disease}, volume = {1871}, number = {3}, pages = {167618}, doi = {10.1016/j.bbadis.2024.167618}, pmid = {39662756}, issn = {1879-260X}, mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/metabolism/pathology ; *Gastrointestinal Microbiome ; Feces/microbiology ; Metabolome ; Dysbiosis/microbiology/metabolism ; }, abstract = {Inflammatory Bowel Diseases (IBDs) are chronic inflammatory disorders of the gastrointestinal tract and colon affecting approximately 7 million individuals worldwide. The knowledge of specific pathology and aetiological mechanisms leading to IBD is limited, however a reduced immune system, antibiotic use and reserved diet may initiate symptoms. Dysbiosis of the gut microbiome, and consequently a varied composition of the metabolome, has been extensively linked to these risk factors and IBD. Metagenomic sequencing and liquid-chromatography mass spectrometry (LC-MS) of N = 220 fecal samples by Fransoza et al., provided abundance data on microbial genera and metabolites for use in this study. Identification of differentially abundant microbes and metabolites was performed using a Wilcoxon test, followed by feature selection of random forest (RF), gradient-boosting (XGBoost) and least absolute shrinkage operator (LASSO) models. The performance of these features was then validated using RF models on the Human Microbiome Project 2 (HMP2) dataset and a microbial community (MICOM) model was utilised to predict and interpret the interactions between key microbes and metabolites. The Flavronifractor genus and microbes of the families Lachnospiraceae and Oscillospiraceae were found differential by all models. Metabolic pathways commonly influenced by such microbes in IBD were CoA biosynthesis, bile acid metabolism and amino acid production and degradation. This study highlights distinct interactive microbiome and metabolome profiles within IBD and the highly potential pathways causing disease pathology. It therefore paves way for future investigation into new therapeutic targets and non-invasive diagnostic tools for IBD.}, } @article {pmid39958933, year = {2025}, author = {Kuźmycz, O and Kowalczyk, A and Bolanowska, A and Drozdzowska, A and Lach, J and Wierzbińska, W and Kluz, T and Stączek, P}, title = {A comprehensive analysis of the uterine microbiome in endometrial cancer patients - identification of Anaerococcus as a potential biomarker and carcinogenic cofactor.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1511625}, pmid = {39958933}, issn = {2235-2988}, mesh = {Humans ; Female ; *Endometrial Neoplasms/microbiology/genetics ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Uterus/microbiology ; Middle Aged ; Phylogeny ; Biomarkers ; Adult ; Aged ; Reactive Oxygen Species/metabolism ; Carcinogenesis ; Fibroblasts/microbiology ; Biomarkers, Tumor/genetics ; Computational Biology/methods ; Oxidative Stress ; }, abstract = {INTRODUCTION: Endometrial cancer (EC) is a significant gynecological malignancy with increasing incidence worldwide. Emerging evidence highlights the role of the uterine microbiome in the pathogenesis of EC. This study aims to characterize the uterine microbiome in EC patients and identify potential microbial biomarkers, with a focus on Anaerococcus as a differentiating taxon.

METHODS: The endocervical canal swabs from patients with EC (n=16) and non-cancerous patients (EM, n=13) were collected. The V3-V4 region of the 16S rRNA gene was sequenced using the Illumina platform. Bioinformatic analyses were performed with QIIME2, and statistical comparisons were conducted to assess differences in microbial composition and diversity. In vitro experiments were conducted to assess the functional impact of Anaerococcus on human uterine fibroblasts, including its ability to adhere to the human cells and induce oxidative stress.

RESULTS: The α-diversity metrics, including Shannon entropy and observed amplicon sequence variants (ASVs), revealed significantly higher microbial diversity in EC samples compared to EM. Anaerococcus was identified as a key taxon differentiating EC from EM groups, showing a higher relative abundance in EC samples. Functional predictions and in vitro assays indicated that Anaerococcus may contribute to carcinogenesis by inducing reactive oxygen species (ROS) production, and has the high ability to adhere to the human endometrial fibroblasts.

DISCUSSION: The study provides evidence of distinct microbial signatures in EC, with Anaerococcus emerging as a potential biomarker. The in vitro findings suggest its role in endometrial carcinogenesis, underscoring its potential as a target for future diagnostic and therapeutic applications.}, } @article {pmid39956110, year = {2025}, author = {Echeveste Medrano, MJ and Smith, GJ and Sánchez-Andrea, I and Jetten, MSM and Welte, CU}, title = {Contrasting Methane, Sulfide and Nitrogen-Loading Regimes in Bioreactors Shape Microbial Communities Originating From Methane-Rich Coastal Sediment of the Stockholm Archipelago.}, journal = {Environmental microbiology}, volume = {27}, number = {2}, pages = {e70056}, pmid = {39956110}, issn = {1462-2920}, support = {854088//European Commission/ ; 024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; VI.Vidi.223.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Bioreactors/microbiology ; *Sulfides/metabolism ; Sweden ; *Nitrogen/metabolism ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Archaea/metabolism/genetics/classification ; Seawater/microbiology ; Bacteria/classification/genetics/metabolism ; Oxidation-Reduction ; Denitrification ; Nitrates/metabolism ; Phylogeny ; Ecosystem ; }, abstract = {Coastal ecosystems are increasingly exposed to high nutrient loads and salinity intrusions due to rising seawater levels. Microbial communities, key drivers of elemental cycles in these ecosystems, consequently, experience fluctuations. This study investigates how the methane-rich coastal sediment microbiome from the Stockholm Archipelago copes with high and low nitrogen and sulfide loading by simulating coastal conditions in two methane-saturated anoxic brackish bioreactors. Over a year, the bioreactors were subjected to the same ratio of nitrate, ammonium and sulfide (2:1:1) under eutrophic or oligotrophic conditions and monitored using 16S rRNA gene amplicon and metagenomic sequencing. Sulfide was depleted in both conditions. Sulfide-dependent denitrification was the predominant process in eutrophic conditions, whereas dissimilatory nitrate reduction to ammonium dominated under oligotrophic conditions. Methane oxidation was driven by Methylobacter and Methylomonas in eutrophic conditions, whereas a more diverse methane-oxidising microbial community developed under oligotrophic conditions, which likely competed for nitrate with anaerobic methanotrophic archaea and the gammaproteobacterial MBAE14. Novel putative copper-dependent membrane-bound monooxygenases (Cu-MMOs) were identified in MBAE14 and co-enriched Rugosibacter genomes, suggesting the need for further physiological and genetic characterisation. This study highlights the importance of understanding coastal anoxic microbiomes under fluctuating conditions, revealing complex interactions and novel pathways crucial for ecosystem functioning.}, } @article {pmid39873521, year = {2025}, author = {Pu, G and Hou, L and Zhao, Q and Liu, G and Wang, Z and Zhou, W and Niu, P and Wu, C and Li, P and Huang, R}, title = {Interactions between gut microbes and host promote degradation of various fiber components in Meishan pigs.}, journal = {mSystems}, volume = {10}, number = {2}, pages = {e0150024}, doi = {10.1128/msystems.01500-24}, pmid = {39873521}, issn = {2379-5077}, support = {32172710//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Dietary Fiber/metabolism ; *Gastrointestinal Microbiome/physiology ; Swine ; Pectins/metabolism ; Fatty Acids, Volatile/metabolism ; Cellulose/metabolism ; Animal Feed/analysis ; Host Microbial Interactions/physiology ; Bacteria/metabolism/genetics/classification ; }, abstract = {UNLABELLED: Although metagenomic investigations into microbial fiber-degrading capabilities are currently prevalent, there is a notable gap in research concerning the regulatory mechanisms underpinning host-microbiota interactions that confer tolerance to high-fiber diets in pigs. In this study, 28 Meishan (MS) and 28 Large White (LW) pigs were subjected to feeding experiments involving various fiber levels. Subsequently, multi-omics was employed to investigate the influence of host-microbiota interactions on the fiber degradation of pigs. MS exhibited superior fiber digestibility compared with LW, particularly evident when fed a high-fiber diet. In MS, positive interactions among Treponema bryantii, Treponema sp., Rikenellaceae bacterium, and Bacteroidales bacterium WCE2004 facilitated the degradation of both cellulose and pectin. The reduced polymerization of polysaccharides and oligosaccharides observed in MS provides compelling evidence for their superior microbial fiber-degrading capability. The concentrations of propionate and butyrate retained in cecal lumen of MS was unchanged, whereas it was significantly increased in LW, indicating a strong absorption of short-chain fatty acids (SCFAs) in MS intestines. Correlation analysis using RNA-seq data revealed distinct patterns in LW and MS. In LW, microbial profiles along with GPR183 and GPR174 exhibited negative correlations with butyrate and propionate, respectively. Conversely, in MS, GPR174 and SLC2A4 were positively correlated with butyrate. Our findings underscore the dynamic collaboration among microbial species in degrading cellulose and pectin, coupled with the synergistic effects of SCFA transport-related genes, as crucial underpinnings for the heightened fiber digestibility observed in MS. These discoveries offer fresh perspectives into the intricate mechanisms governing host-microbiota interactions that influence fiber digestion in pigs.

IMPORTANCE: Studies on porcine intestinal microbiota have been widely conducted, and some microbial taxa with fiber degradation functions have been identified. However, the mechanisms of division among gut microbes in the degradation of complex fiber components are still unclear. In addition, the regulation of fiber digestion by host through absorption of short-chain fatty acids (SCFAs) needs to be further investigated. Our study used apparent total tract digestibility of dietary fiber to assess the utilization efficiency of dietary fiber between Meishan and Large White pigs. Subsequently, through metagenome sequencing and determination of fiber-degrading products, we found that in Meishan pigs, positive interactions among Treponema bryantii, Treponema sp., Rikenellaceae bacterium, and Bacteroidales bacterium WCE2004 facilitated the degradation of both cellulose and pectin. RNA-seq analysis elucidated breed-specific genes associated with SCFA absorption in cecum. By integrating multi-omics data, we constructed a framework outlining host-microbiota interactions that control dietary fiber utilization in pigs. Our data provide novel insights into host-microbiota interactions regulating fiber degradation and lay some theoretical foundations for improving the utilization efficiency of high-fiber cereal feed in pigs through targeted modulation of gut microbial function.}, } @article {pmid39807869, year = {2025}, author = {Sáenz, JS and Rios-Galicia, B and Seifert, J}, title = {Antiviral defense systems in the rumen microbiome.}, journal = {mSystems}, volume = {10}, number = {2}, pages = {e0152124}, doi = {10.1128/msystems.01521-24}, pmid = {39807869}, issn = {2379-5077}, support = {327953272 (SE2059/3-1)//Deutsche Forschungsgemeinschaft (DFG)/ ; 202989534 (SE2059/2-2)//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {*Rumen/microbiology/virology/immunology ; Animals ; *Bacteriophages/genetics ; *Archaea/genetics/virology ; *Bacteria/genetics/immunology/virology ; Genome, Bacterial/genetics ; Microbiota/genetics ; Genome, Archaeal/genetics ; }, abstract = {The continuous interaction between phages and their respective hosts has resulted in the evolution of multiple bacterial immune mechanisms. However, the diversity and prevalence of antiviral defense systems in complex communities are still unknown. We therefore investigated the diversity and abundance of viral defense systems in 3,038 high-quality bacterial and archaeal genomes from the rumen. In total, 14,241 defense systems and 31,948 antiviral-related genes were identified. Those genes represented 114 unique system types grouped into 49 families. We observed a high prevalence of defense systems in the genomes. However, the number of defense systems, defense system families, and system density varied widely from genome to genome. Additionally, the number of defense system per genome correlated positively with the number of defense system families and the genome size. Restriction modification, Abi, and cas system families were the most common, but many rare systems were present in only 1% of the genomes. Antiviral defense systems are prevalent and diverse in the rumen, but only a few are dominant, indicating that most systems are rarely present. However, the collection of systems throughout the rumen may represent a pool of mechanisms that can be shared by different members of the community and modulate the phage-host interaction.IMPORTANCEPhages may act antagonistically at the cell level but have a mutualistic interaction at the microbiome level. This interaction shapes the structure of microbial communities and is mainly driven by the defense mechanism. However, the diversity of such mechanism is larger than previously thought. Because of that, we described the abundance and diversity of the antiviral defense system of a collection of genomes, metagenome-assembled genomes (MAGs) and isolates, from the rumen. While defense mechanisms seem to be prevalent among bacteria and archaea, only a few were common. This suggests that most of these defense mechanisms are not present in many rumen microbes but could be shared among different members of the microbial community. This is consistent with the "pan-immune system" model, which appears to be common across different environments.}, } @article {pmid39745394, year = {2025}, author = {Geers, AU and Michoud, G and Busi, SB and Peter, H and Kohler, TJ and Ezzat, L and , and Battin, TJ}, title = {Deciphering the biosynthetic landscape of biofilms in glacier-fed streams.}, journal = {mSystems}, volume = {10}, number = {2}, pages = {e0113724}, doi = {10.1128/msystems.01137-24}, pmid = {39745394}, issn = {2379-5077}, support = {//NOMIS Stiftung (NOMIS Foundation)/ ; }, mesh = {*Biofilms/growth & development ; *Ice Cover/microbiology ; *Rivers/microbiology/chemistry ; Microbiota ; Multigene Family ; Bacteria/genetics/metabolism ; Metagenome ; }, abstract = {UNLABELLED: Glacier-fed streams are permanently cold, ultra-oligotrophic, and physically unstable environments, yet microbial life thrives in benthic biofilm communities. Within biofilms, microorganisms rely on secondary metabolites for communication and competition. However, the diversity and genetic potential of secondary metabolites in glacier-fed stream biofilms remain poorly understood. In this study, we present the first large-scale exploration of biosynthetic gene clusters (BGCs) from benthic glacier-fed stream biofilms sampled by the Vanishing Glaciers project from the world's major mountain ranges. We found a remarkable diversity of BGCs, with more than 8,000 of them identified within 2,868 prokaryotic metagenome-assembled genomes, some of them potentially conferring ecological advantages, such as UV protection and quorum sensing. The BGCs were distinct from those sourced from other aquatic microbiomes, with over 40% of them being novel. The glacier-fed stream BGCs exhibited the highest similarity to BGCs from glacier microbiomes. BGC composition displayed geographic patterns and correlated with prokaryotic alpha diversity. We also found that BGC diversity was positively associated with benthic chlorophyll a and prokaryotic diversity, indicative of more biotic interactions in more extensive biofilms. Our study provides new insights into a hitherto poorly explored microbial ecosystem, which is now changing at a rapid pace as glaciers are shrinking due to climate change.

IMPORTANCE: Glacier-fed streams are characterized by low temperatures, high turbidity, and high flow. They host a unique microbiome within biofilms, which form the foundation of the food web and contribute significantly to biogeochemical cycles. Our investigation into secondary metabolites, which likely play an important role in these complex ecosystems, found a unique genetic potential distinct from other aquatic environments. We found the potential to synthesize several secondary metabolites, which may confer ecological advantages, such as UV protection and quorum sensing. This biosynthetic diversity was positively associated with the abundance and complexity of the microbial community, as well as concentrations of chlorophyll a. In the face of climate change, our study offers new insights into a vanishing ecosystem.}, } @article {pmid39582241, year = {2025}, author = {Zhang, M and Zhang, L and Suo, B and Wei, Y and Xu, Y and Jiang, M and Dong, J and Li, X and Song, Z and Liu, D}, title = {Distribution Characteristics and Impacting Factors of Drug CYP Enzymes and Transporters in the Gastrointestinal Tract of Chinese Healthy Subjects.}, journal = {Clinical pharmacology and therapeutics}, volume = {117}, number = {3}, pages = {676-689}, doi = {10.1002/cpt.3497}, pmid = {39582241}, issn = {1532-6535}, mesh = {Humans ; Male ; Female ; Adult ; *Healthy Volunteers ; *Asian People/genetics ; Young Adult ; *Cytochrome P-450 Enzyme System/metabolism/genetics ; *Gastrointestinal Tract/metabolism ; Feces/chemistry/microbiology ; Membrane Transport Proteins/metabolism/genetics ; Gastrointestinal Microbiome ; Xenobiotics/metabolism/pharmacokinetics ; Tandem Mass Spectrometry ; China ; Middle Aged ; Chromatography, Liquid ; Genotype ; }, abstract = {The abundance of drug metabolic enzymes (DMEs) and transporters (DTs) in the human gastrointestinal tract significantly affects xenobiotic exposure in the circulating system, the basis of these compounds acting on humans. However, accurately predicting individual exposure in healthy subjects remains challenging due to limited data on protein levels throughout the gastrointestinal tract within the same individuals and inadequate assessment of factors influencing these levels. Therefore, we conducted a clinical study to obtain biopsy samples from 8 different gastrointestinal segments in 24 healthy Chinese volunteers. Concurrently, blood and fecal samples were collected for genotypic analysis and fecal microbiota metagenomic sequencing. Using an optimized LC-MS/MS method, we quantified the absolute protein abundance of CYP2C9, CYP2C19, CYP2D6, CYP3A4, P-gp, and BCRP from the stomach to the colon. Our results revealed significant regional differences in protein expression: CYP3A4 was the most abundant in the small intestine, whereas CYP2C9 was predominantly found in the colon. CYP2D6 was primarily located in the ileum, while other DMEs/DTs showed higher concentrations in the jejunum. Meanwhile, the enzyme abundance in the small intestine and colon and the relative ratio of transporters in different regions to the jejunum were accurately calculated, providing valuable data for refining the physiological parameters in the virtual gastrointestinal tract of Chinese healthy population in PBBMs. Additionally, BMI, IBW, sex, age, genotype, and fecal microbiota were identified as critical factors influencing the protein levels of these DMEs/DTs throughout the gastrointestinal tract, with notable regional differences. Consequently, this study provides a unique foundation for understanding xenobiotic absorption in humans.}, } @article {pmid39955324, year = {2025}, author = {O' Donovan, CM and Nori, SRC and Shanahan, F and Celentano, G and Murphy, TB and Cotter, PD and Sullivan, OO}, title = {Temporal stability and lack of variance in microbiome composition and functionality in fit recreational athletes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {5619}, pmid = {39955324}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Adult ; *Athletes ; Female ; *Feces/microbiology ; Metagenomics/methods ; Prevotella/genetics/isolation & purification ; Young Adult ; Running ; Faecalibacterium prausnitzii/genetics ; }, abstract = {Human gut microbiome composition and function is influenced by environmental and lifestyle factors, including exercise and fitness. We studied the composition and functionality of the faecal microbiome of recreational (non-elite) runners (n = 62) with serial shotgun metagenomics, at 4 time points over a 7-week period. Gut microbiome composition and function was stable over time. Grouping of samples on the basis of their fitness level (fair, good, excellent, and superior) or habitual training (low (4-6 h/week), medium (7-9 h/week), high (10-12 h/week), and extreme (13 + hours/week)) revealed no significant microbiome-related differences. Overall, the species Faecalibacterium prausnitzii, Blautia wexlerae, and Prevotella copri were the most abundant members of the gut microbiome. Analysis of co-abundance groups (CAGs) revealed no significant relationship between CAGs and fitness levels or training subgroups. Functional pathways were similar across all samples and timepoints with no clustering based on associated metadata. The most abundant genes identified within samples corresponded to pathways for nucleoside and nucleotide biosynthesis, amino acid biosynthesis, and cell wall biosynthesis. Collectively, these results describe the microbiome of active recreational runners and note temporal stability amongst participants.}, } @article {pmid39675462, year = {2025}, author = {Wang, H and Liu, Q and Abouelfetouh, MM and Li, H and Zhu, H and Zhu, C and Kiani, FA and Ding, Y}, title = {The role of the hypothalamus-gut microbiota in the pathogenesis of periparturient fatty liver disease in dairy cows.}, journal = {Veterinary journal (London, England : 1997)}, volume = {309}, number = {}, pages = {106290}, doi = {10.1016/j.tvjl.2024.106290}, pmid = {39675462}, issn = {1532-2971}, mesh = {Animals ; Cattle ; Female ; *Gastrointestinal Microbiome ; *Cattle Diseases/microbiology ; *Fatty Liver/veterinary/microbiology ; *Hypothalamus/metabolism ; Peripartum Period ; Pregnancy ; Brain-Gut Axis/physiology ; Liver/metabolism/microbiology ; }, abstract = {During the periparturient period, dairy cows experience negative energy balance due to reduced feed intake, leading to adipose tissue breakdown, liver damage, and fat accumulation. This study examined the gut-liver-brain axis to explore the link between fatty liver disease, changes in hypothalamic appetite-related neurons, and microbiome shifts in dairy cows. Thirty cows were monitored, with daily DMI recordings and blood sampling. Postpartum brain, liver, and ileal contents were collected from 10 selected cows, divided into two groups: H-DMI (slight DMI decrease) and L-DMI (severe DMI decrease). The L-DMI group of cows exhibited higher plasma NEFA, BHBA, ALT, and AST levels, along with severe hepatic steatosis and lipid accumulation. Transcriptome sequencing of the hypothalamic arcuate nucleus (ARC) revealed decreased expression of Hypocretin Neuropeptide Precursor (HCRT), orexin-A (OX-A), Orexin Receptor Type 1 (OX1R), and Cannabinoid Receptor 1 (CB1) in the L-DMI group, while Pro-opiomelanocortin (POMC) and Melanocortin 4 Receptor (MC4R) expression increased. Metagenomic analysis of ileal contents showed reduced abundance of Ruminococcus spp. in the L-DMI group, which may be associated with fatty liver disease (FL). Integrated omics analysis showed that increased MC4R expression was correlated with the elevated abundance of bacteria such as Akkermansia glycaniphila, and reduced abundance of species such as Methanobrevubacter thaueri and Ruminococcus spp. Decreased HCRT expression was also linked to Akkermansia glycaniphila. In conclusion, these changes may affect DMI through the OX-A/POMC pathway, with neurological and gut microbiome alterations potentially leading to appetite suppression, negative energy balance, and the development of fatty liver disease.}, } @article {pmid39673746, year = {2025}, author = {Quraishi, MN and Cheesbrough, J and Rimmer, P and Mullish, BH and Sharma, N and Efstathiou, E and Acharjee, A and Gkoutus, G and Patel, A and Marchesi, JR and Camuzeaux, S and Chappell, K and Valdivia-Garcia, MA and Ferguson, J and Brookes, MJ and Walmsley, M and Rossiter, AE and van Schaik, W and McInnes, RS and Cooney, R and Trauner, M and Beggs, AD and Iqbal, TH and Trivedi, PJ}, title = {Open Label Vancomycin in Primary Sclerosing Cholangitis-Inflammatory Bowel Disease: Improved Colonic Disease Activity and Associations With Changes in Host-Microbiome-Metabolomic Signatures.}, journal = {Journal of Crohn's & colitis}, volume = {19}, number = {2}, pages = {}, doi = {10.1093/ecco-jcc/jjae189}, pmid = {39673746}, issn = {1876-4479}, support = {/MRC_/Medical Research Council/United Kingdom ; MC_PC_12025//National Institute for Health Research/ ; //UK Consortium for MetAbolic Phenotyping/ ; //National Institute for Health Research/ ; //Imperial Biomedical Research Centre/ ; }, mesh = {Humans ; *Vancomycin/therapeutic use/pharmacology ; Female ; Male ; *Gastrointestinal Microbiome/drug effects ; *Cholangitis, Sclerosing/drug therapy/metabolism ; Adult ; Middle Aged ; *Feces/microbiology/chemistry ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Inflammatory Bowel Diseases/drug therapy/microbiology/metabolism ; Remission Induction/methods ; Leukocyte L1 Antigen Complex/analysis/metabolism ; Metabolomics/methods ; }, abstract = {BACKGROUND: We conducted a single-arm interventional study, to explore mucosal changes associated with clinical remission under oral vancomycin (OV) treatment, in primary sclerosing cholangitis-associated inflammatory bowel disease (PSC-IBD); NCT05376228.

METHODS: Fifteen patients with PSC and active colitis (median fecal calprotectin 459 µg/g; median total Mayo score 5) were treated with OV (125 mg QID) for 4 weeks and followed-up for a further 4 weeks of treatment withdrawal (8 weeks, end-of-study). Colonic biopsies were obtained at baseline and Week 4. Clinical assessments, and serum and stool samples (metagenomics, metatranscriptomics, and metabolomics) were collected at Weeks 0, 2, 4, and 8. The primary efficacy outcome measure was the induction of clinical remission.

RESULTS: Oral vancomycin resulted in clinical remission in 12/15 patients and significant reductions in fecal calprotectin. Oral vancomycin was associated with reduced abundances of Lachnospiraceae, genera Blautia and Bacteroides; and enrichment of Enterobacteriaceae, and genera Veillonella, Akkermansia, and Escherichia. Oral vancomycin treatment was associated with the downregulation of multiple metatranscriptomic pathways (including short-chain fatty acid [SCFA] metabolism and bile acid [BA] biotransformation), along with host genes and multiple pathways involved in inflammatory responses and antimicrobial defence; and an upregulation of genes associated with extracellular matrix repair. Oral vancomycin use resulted in the loss of specific fecal SCFAs and secondary BAs, including lithocholic acid derivatives. Colitis activity relapsed following OV withdrawal, with host mucosal and microbial changes trending toward baseline.

CONCLUSIONS: Four weeks of OV induces remission in PSC-IBD activity, associated with a reduction in gut bacterial diversity and compositional changes relating to BA and SCFA homeostasis.}, } @article {pmid37749431, year = {2025}, author = {Arumugam, U and Sudarsanan, GB and Karuppannan, AK and Palaniappan, S}, title = {Metagenomic Studies Reveal the Evidence of Akkermansia muciniphila and Other Probiotic Bacteria in the Gut of Healthy and Enterocytozoon hepatopenaei (EHP)-Infected Farmed Penaeus vannamei.}, journal = {Probiotics and antimicrobial proteins}, volume = {17}, number = {1}, pages = {432-439}, pmid = {37749431}, issn = {1867-1314}, mesh = {Animals ; *Penaeidae/microbiology ; *Enterocytozoon/genetics/isolation & purification/physiology ; *Gastrointestinal Microbiome ; *Probiotics ; *Akkermansia ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Aquaculture ; }, abstract = {Penaeus vannamei (whiteleg shrimp) is the most widely cultured shrimp globally. Enterocytozoon hepatopenaei (EHP), a microsporidian parasite, infects P. vannamei and causes severe growth retardation, subsequent production, and economic losses in the shrimp culture. The influence of EHP infection in the shrimp gut microbiota is poorly studied, and this would be an interesting area to investigate since the gut microbiome of shrimp influences a number of key host processes such as digestion and immunity. In this study, a metagenomic approach was followed to compare the overall species richness of the gut microbiota of EHP-infected and healthy P. vannamei. Bacterial genomic DNA from the healthy and EHP-infected gut sample were profiled for the bacterial 16S rRNA gene, targeting the V3-V4 conserved region. Operational taxonomic units (OTUs), an approximation of definitive taxonomic identity, were identified based on the sequence similarity within the sample reads and clustered together using a cut-off of 97% identity using UCLUST. The OTUs were then used for the computation of alpha diversity and beta diversity for each sample. EHP-infected gut sample showed lower bacterial abundance throughout the family, class, order, genus, and species levels when compared to healthy gut sample. This study shows that the shrimp gut microbiota is sensitive and exhibits a high level of plasticity during a microsporidian infection like EHP. Furthermore, Akkermansia muciniphila, a novel probiotic bacterium, has been reported in the shrimp gut for the first time.}, } @article {pmid39952771, year = {2025}, author = {Cantuti Gendre, J and Le Marrec, C and Chaillou, S and Omhover-Fougy, L and Landaud, S and Dugat-Bony, E}, title = {Exploring viral diversity in fermented vegetables through viral metagenomics.}, journal = {Food microbiology}, volume = {128}, number = {}, pages = {104733}, doi = {10.1016/j.fm.2025.104733}, pmid = {39952771}, issn = {1095-9998}, mesh = {*Metagenomics ; *Vegetables/virology/microbiology ; *Fermentation ; *Bacteriophages/genetics/isolation & purification/classification ; Microbiota ; Brassica/microbiology/virology ; Fermented Foods/microbiology/virology ; Bacteria/genetics/classification/isolation & purification/virology ; Biodiversity ; Daucus carota/microbiology/virology ; Food Microbiology ; Viruses/isolation & purification/classification/genetics ; Enterobacteriaceae/isolation & purification/genetics/virology/classification ; Metagenome ; Lactobacillaceae/isolation & purification/genetics/classification ; }, abstract = {Fermented vegetables are traditionally produced using the endogenous microorganisms present in raw ingredients. While the diversity of bacteria and fungi in fermented vegetables has been relatively well studied, phage communities remain largely unexplored. In this study, we collected twelve samples of fermented cabbage, carrot, and turnip after fermentation and analyzed the microbial and viral communities using shotgun and viral metagenomic approaches. Assessment of the viral diversity also benefited from epifluorescence microscopy to estimate viral load. The viral metagenomics approach targeted dsDNA, ssDNA, and RNA viruses. The microbiome of fermented vegetables was dominated by lactic acid bacteria and varied according to the type of vegetable used as raw material. The analysis of metagenome-assembled-genomes allowed the detection of 22 prophages of which 8 were present as free particles and therefore detected in the metaviromes. The viral community, estimated to range from 5.28 to 7.57 log virus-like particles per gram of fermented vegetables depending on the sample, was mainly composed of dsDNA viruses, although ssDNA and non-bacterial RNA viruses, possibly originating from the phyllosphere, were also detected. The dsDNA viral community, primarily comprising bacteriophages, varied depending on the type of vegetable used for fermentation. The bacterial hosts predicted for these phages mainly belonged to Lactobacillaceae and Enterobacteriaceae families. These results highlighted the complex microbial and viral composition of fermented vegetables, which varied depending on the three types of vegetables used as raw material. Further research is needed to deepen our understanding of the impact of these viruses on the microbial ecology of fermented vegetables and on the quality of the final products.}, } @article {pmid39793486, year = {2025}, author = {Eckermann, H and Lustermans, H and Parnanen, K and Lahti, L and de Weerth, C}, title = {Maternal pre- and postnatal stress and maternal and infant gut microbiota features.}, journal = {Psychoneuroendocrinology}, volume = {172}, number = {}, pages = {107273}, doi = {10.1016/j.psyneuen.2024.107273}, pmid = {39793486}, issn = {1873-3360}, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/physiology ; *Stress, Psychological/microbiology/metabolism ; Pregnancy ; Infant ; Adult ; *Postpartum Period ; *Feces/microbiology ; Mothers/psychology ; Hydrocortisone/analysis/metabolism ; Bifidobacterium ; Male ; Infant, Newborn ; Prenatal Exposure Delayed Effects/microbiology/metabolism ; Hair/chemistry/microbiology ; Anxiety/microbiology ; }, abstract = {BACKGROUND: Maternal stress can have short and long term adverse (mental) health effects for the mother and her child. Previous evidence suggests that the gut microbiota may be a potential mediator and moderator for the effects of stress via various pathways. This study explored the maternal microbiota trajectory during pregnancy as well as the association between pre- and postnatal maternal stress and features of the maternal and infant gut microbiota during and after pregnancy. In line with previous research, we hypothesized that maternal stress would be positively related to maternal and infant microbiota volatility and that infants of highly stressed mothers would show a relative increase in Proteobacteria and a relative decrease in Bifidobacterium.

METHODS: We collected maternal stool samples at 18 and 32 weeks of pregnancy and 8 months postpartum. Infant stools samples were obtained at 2, 6 and 12 weeks and 8 months postpartum. All samples were analyzed using shotgun metagenome sequencing. We also collected several measures of maternal stress (self-reported depression, anxiety, and stress, and hair cortisol and cortisone), most at the same time points as the microbiota samples.

RESULTS: Our data indicated that the maternal microbiota does not undergo drastic changes from the second to the third trimester of pregnancy but that the postpartum microbiota differs significantly from the prenatal microbiota. Furthermore, we identified associations between several stress measures and maternal and infant gut microbiota features at different time points including positive and negative associations with alpha diversity, beta diversity and individual microbial phyla and species relative abundances. Also, the maternal stress composite score, the perceived stress score and the log-ratio of hair cortisol and cortisone were all positively associated with infant microbiota volatility.

CONCLUSION: Our study provides evidence that maternal prenatal and postnatal stress is related to both the maternal and the infant microbiota. Collectively, this and previous studies indicate that maternal stress does not uniformly associate with most gut microbial features. Instead, the associations are highly time point specific. Regarding infant microbiota volatility, we have consistently found a positive association between stress and infant microbiota volatility. This warrants future research investigating this link in more depth.}, } @article {pmid39675160, year = {2025}, author = {Yuan, X and Zhang, Y and Pang, L and Zhang, X and Kang, Y and Hei, G and Li, X and Song, X}, title = {Insulin resistance links dysbiosis of gut microbiota with cognitive impairment in first-episode drug-naïve schizophrenia.}, journal = {Psychoneuroendocrinology}, volume = {172}, number = {}, pages = {107255}, doi = {10.1016/j.psyneuen.2024.107255}, pmid = {39675160}, issn = {1873-3360}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Insulin Resistance/physiology ; Male ; *Schizophrenia/microbiology ; *Dysbiosis/microbiology ; Female ; *Cognitive Dysfunction/microbiology/physiopathology ; Adult ; Case-Control Studies ; Young Adult ; Blood Glucose/analysis/metabolism ; Feces/microbiology ; Insulin/metabolism/blood ; }, abstract = {This study aimed to explore the relationship among gut microbiota imbalance, the homeostasis model of assessment of insulin resistance (HOMA-IR) and cognitive impairments in patients with schizophrenia (SCZ). We conducted a case-control study involving 189 first-episode, drug-naïve SCZ patients and 115 healthy controls (HCs). Main methods adopted included metagenomics analysis, glucose metabolism assessment, and cognitive function evaluation using the MATRICS Consensus Cognitive Battery (MCCB). Fecal microbiota composition was analyzed via high-throughput sequencing of 16S ribosomal RNA. Patients with SCZ showed a higher likelihood of developing IR (23 %), compared to HCs (12 %). The IR group exhibited significantly higher levels of fasting blood glucose (FBG), fasting insulin (FINS), HOMA-IR, and homeostasis model assessment-β (HOMA-β), while showing lower insulin sensitivity index (ISI) levels (all p < 0.05). Patients with IR demonstrated lower scores in working memories (WM), verbal learning (HVLT) and reasoning and problem solving (RPS), compared to those without IR. Additionally, microbiota analysis revealed that IR patients had higher abundance of Negativicutes, Streptococcaceae, Enterobacteriaceae, Lachnoclostridium, Dialister, Klebsiella, and Enterobacter, and lower abundance of Flavonifractor and Rikenellaceae. Notably, Negativicutes, Streptococcaceae, Lachnoclostridium, Flavonifractor, and Rikenellaceae were shared between SCZ and IR conditions. Mediation analysis indicated that the relative abundance of Streptococcaceae have an indirect effect on WM through HOMA-IR (β=-0.148, SE=0.067, 95 %CI=-0.280 to -0.020). The study suggests that IR may play a mediating role in the relationship between gut microbiota dysbiosis and cognitive impairments in patients with SCZ, which could point to potential new avenues for therapeutic interventions.}, } @article {pmid39952762, year = {2025}, author = {Li, Z and Liao, Y and Huang, C and Liu, J and Kong, X and Li, L and Li, Z and Gui, Y}, title = {Analyzing fungal community succession and its correlation to flavor compounds in the Cupei fermentation process of Sichuan shai vinegar.}, journal = {Food microbiology}, volume = {128}, number = {}, pages = {104718}, doi = {10.1016/j.fm.2024.104718}, pmid = {39952762}, issn = {1095-9998}, mesh = {*Fermentation ; *Acetic Acid/metabolism/analysis ; *Volatile Organic Compounds/metabolism/analysis/chemistry ; *Flavoring Agents/metabolism/chemistry ; *Fungi/classification/metabolism/genetics/isolation & purification ; China ; Gas Chromatography-Mass Spectrometry ; Amino Acids/metabolism/analysis ; Solid Phase Microextraction ; Food Microbiology ; Mycobiome ; Chromatography, High Pressure Liquid ; Condiments/microbiology/analysis ; }, abstract = {Sichuan Shai vinegar, a distinctive condiment from Southwest China, is produced through open-air solid-state fermentation, employing a unique Chinese herbal medicine mixture (Yaoqu) as the fermentation starter. Despite its culinary significance, the dynamics and roles of fungal communities within the Cupei fermentation phase remain understudied. This study employed high-performance liquid chromatography (HPLC) to quantify 11 organic acids and 17 amino acids, revealing a significant increase in organic acid content from 2.56 g/100 g-17.47 g/100 g dry weight and a gradual elevation in free amino acid content from 0.53 g/100 g-5.59 g/100 g throughout the fermentation process. Headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME/GC-MS) identified 85 volatile flavor compounds, predominantly consisting of 2 alcohols, 10 acids, 29 esters, 4 ketones, 6 aldehydes, and 14 other types. High-throughput sequencing facilitated the identification of key microorganisms, with Lichtheimia, Brettanomyces, Pichia, Saccharomyces, Kazachstania, and Syncephalastrum emerging as the most abundant fungal genera. Correlation analysis revealed significant positive correlations between 20 fungi and 11 organic acids, 24 fungi and 16 amino acids, and 50 fungi and 76 volatile flavor compounds. Notably, Lichtheimia, Pichia, and Brettanomyces were identified as the most influential in flavor metabolism. These findings elucidate the microbial metabolic mechanisms during Sichuan Shai vinegar fermentation, laying a foundation for further research and potential applications in vinegar production.}, } @article {pmid39952751, year = {2025}, author = {Sequino, G and Cobo-Diaz, JF and Valentino, V and Tassou, C and Volpe, S and Torrieri, E and Nychas, GJ and Álvarez Ordóñez, A and Ercolini, D and De Filippis, F}, title = {Environmental microbiome mapping in poultry processing chain and assessment of microbial dynamics in response to different storage conditions.}, journal = {Food microbiology}, volume = {128}, number = {}, pages = {104734}, doi = {10.1016/j.fm.2025.104734}, pmid = {39952751}, issn = {1095-9998}, mesh = {Animals ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification ; *Chickens/microbiology ; *Food Storage ; Poultry Products/microbiology ; Food Packaging/methods ; Food Microbiology ; Poultry/microbiology ; Drug Resistance, Bacterial ; Temperature ; Meat/microbiology ; Brochothrix/genetics/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Environmental Microbiology ; Metagenomics ; }, abstract = {Poultry production chain comprises a complex network involving various stages from rearing to the final distribution of poultry products. This study explores the intricate dynamics within this chain, using shotgun metagenomics, particularly focusing on taxonomic and functional composition of the microbiome, antibiotic resistance and virulence potential. Moreover, the study of the impact of different packaging and storage conditions provides insights into how diverse packaging strategies and storage temperature can impact the shelf-life of chicken meat. Microbiome mapping in poultry processing facility revealed the dominance of Brochothrix thermosphacta, Pseudomonas fragi and Psychrobacter immobilis on poultry-based products and industrial surfaces. Indeed, surfaces of equipment and tools have a significant impact on the microbial composition of the final food products. Furthermore, the study of the microbiome dynamics in chicken meat stored in different packaging (air, modified atmosphere, under vacuum) and temperatures (0, 4 and 10 °C) revealed temperature-dependent microbiota shifts in chicken meat, highlighting specific spoilage organisms (SSOs) in the different packaging methods. Additionally, our results showed that poultry-based products and industrial surfaces belonging to carcasses processing area hosted elevated levels of Antibiotic Resistance Genes, mainly associated with resistance to aminoglycosides, β-lactams, MLSPs (which includes macrolides, lincosamides, streptogramins and pleuromutilins) amphenicols and tetracyclines classes and several Virulence-associated genes related to adherence, biofilm, effector delivery system, motility, nutritional/metabolic factors and regulation. Finally, our findings underscored a notably mobile resistome, showing multiple AR class correlated with mobile elements. This poses a considerable risk, emphasizing the urgent need for proactive measures in addressing potential antibiotic resistance genes dissemination in the poultry chain.}, } @article {pmid39951448, year = {2025}, author = {Li, Q and Wu, X and Niu, X and Yu, Z and Fang, S and Chu, X and Zhu, J and Song, Q and Hou, C and Wei, X}, title = {Integrated metagenomic and metabolomic analyses of the effects of total flavonoids of Rhizoma Drynariae on reducing ovariectomized-induced osteoporosis by regulating gut microbiota and related metabolites.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0317832}, pmid = {39951448}, issn = {1932-6203}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Female ; *Ovariectomy ; *Osteoporosis/drug therapy/metabolism ; *Metabolomics ; Rats ; *Flavonoids/pharmacology ; *Bone Density/drug effects ; *Polypodiaceae ; Metagenomics ; Rats, Sprague-Dawley ; Drugs, Chinese Herbal/pharmacology ; Rhizome ; }, abstract = {TFRD has been widely used in China to treat osteoporosis (OP). However, the specific molecular mechanism of TFRD against OP has not been fully clarified. Our previous studies have also proved that TFRD could attenuate OP and the clinical equivalent dose of 67.5mg/kg/d is the effective dose for TFRD treating OP. Therefore, this study used 67.5mg/kg as the dosage of TFRD in combination with multi omics to investigate the mechanism of action of TFRD in the treatment of OP. The aim of this study was to further elucidate molecular mechanism of TFRD for treating OP based on metagenomic and metabolomic analyses. In this study, hematoxylin-eosin (H&E) staining, micro computed tomography (micro-CT) and bone mineral density (BMD) analysis were used to observe pharmacological effects of TFRD against ovariectomized (OVX)-induced OP. Subsequently, multiomics analysis including metagenomics, untargeted and short chain fatty acids (SCFAs) metabolomics were carried out to identify whether the anti-osteoporosis mechanism of TFRD correlated with gut microbiota and related metabolites. Our results indicate that TFRD could improve the microstructure and density of trabecular bone in OVX rats. 17 differential species, which mainly from Akkermansia, Bacteroides, and Phascolarctobacterium genus, 14 related differential metabolites and acetic acid in SCFAs were significantly altered by OVX and reversed by TFRD. Furthermore, according to results of untargeted metabolomics analysis, it was found that several metabolic pathways such as phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis and so on might play an important role in TFRD against OP. In order to further study the relationship between gut microbiota and related metabolites, spearman correlation analysis was used, and showed that gut microbiota such as Akkermansia muciniphila might be closely related to several metabolites and metabolic pathways. These findings suggest that TFRD treatment could reduce the effects of OVX-induced OP by altering community composition and abundance of gut microbiota, regulating metabolites and SCFAs. It was speculated that the gut microbiota especially Akkermansia muciniphila and related metabolites might play an important role in TFRD against OP, and deserve further study by follow-up experiment. This conclusion provides new theoretical support for mechanism research of TFRD against OP.}, } @article {pmid39951402, year = {2025}, author = {Reiss, RA and Guerra, PA and Makhnin, O and Kellom, M}, title = {Whole metagenome sequencing and 16S rRNA gene amplicon analyses reveal the complex microbiome responsible for the success of enhanced in-situ reductive dechlorination (ERD) of a tetrachloroethene-contaminated Superfund site.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0306503}, pmid = {39951402}, issn = {1932-6203}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Biodegradation, Environmental ; *Groundwater/microbiology ; *Metagenome ; *Tetrachloroethylene/metabolism ; Water Pollutants, Chemical/metabolism ; Halogenation ; Metagenomics/methods ; Bacteria/genetics/metabolism/classification ; New Mexico ; }, abstract = {The North Railroad Avenue Plume (NRAP) Superfund site in New Mexico, USA exemplifies successful chlorinated solvent bioremediation. NRAP was the result of leakage from a dry-cleaning that operated for 37 years. The presence of tetrachloroethene biodegradation byproducts, organohalide respiring genera (OHRG), and reductive dehalogenase (rdh) genes detected in groundwater samples indicated that enhanced reductive dechlorination (ERD) was the remedy of choice. This was achieved through biostimulation by mixing emulsified vegetable oil into the contaminated aquifer. This report combines metagenomic techniques with site monitoring metadata to reveal new details of ERD. DNA extracts from groundwater samples collected prior to and at four, 23 and 39 months after remedy implementation were subjected to whole metagenome sequencing (WMS) and 16S rRNA gene amplicon (16S) analyses. The response of the indigenous NRAP microbiome to ERD protocols is consistent with results obtained from microcosms, dechlorinating consortia, and observations at other contaminated sites. WMS detects three times as many phyla and six times as many genera as 16S. Both techniques reveal abundance changes in Dehalococcoides and Dehalobacter that reflect organohalide form and availability. Methane was not detected before biostimulation but appeared afterwards, corresponding to an increase in methanogenic Archaea. Assembly of WMS reads produced scaffolds containing rdh genes from Dehalococcoides, Dehalobacter, Dehalogenimonas, Desulfocarbo, and Desulfobacula. Anaerobic and aerobic cometabolic organohalide degrading microbes that increase in abundance include methanogenic Archaea, methanotrophs, Dechloromonas, and Xanthobacter, some of which contain hydrolytic dehalogenase genes. Aerobic cometabolism may be supported by oxygen gradients existing in aquifer microenvironments or by microbes that produce O2 via microbial dismutation. The NRAP model for successful ERD is consistent with the established pathway and identifies new taxa and processes that support this syntrophic process. This project explores the potential of metagenomic tools (MGT) as the next advancement in bioremediation.}, } @article {pmid39903999, year = {2025}, author = {Mondal, A and Parvez, SS and Majumder, A and Sharma, K and Das, B and Bakshi, U and Alam, M and Banik, A}, title = {Co-inoculation of Trichoderma and tea root-associated bacteria enhance flavonoid production and abundance of mycorrhizal colonization in tea (Camellia sinensis).}, journal = {Microbiological research}, volume = {293}, number = {}, pages = {128084}, doi = {10.1016/j.micres.2025.128084}, pmid = {39903999}, issn = {1618-0623}, mesh = {*Camellia sinensis/microbiology ; *Plant Roots/microbiology ; *Flavonoids ; *Rhizosphere ; *Soil Microbiology ; *Mycorrhizae/physiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Trichoderma/isolation & purification/genetics/classification ; India ; Symbiosis ; Microbiota ; Plant Leaves/microbiology ; Tea/microbiology ; Metagenome ; }, abstract = {Tea is one of the most popular nonalcoholic beverages, that contains several medicinally important flavonoids. Due to seasonal variation and various environmental stresses, the overall consistency of tea flavonoids affects the tea quality. To combat stress, plants stimulate symbiotic relationships with root-associated beneficial microbiomes that sustain nutrient allocation. Therefore, a study has been designed to understand the role of the tea root microbiome in sustaining tea leaf flavonoid production. To enumerate the microbiome, tea root and rhizoplane soil were collected from 3 years of healthy plants from Jalpaiguri district, West Bengal, India. A culture-independent approach was adopted to identify root and rhizosphere microbial diversity (BioSample: SAMN31404869; SRA: SRS15503027 [rhizosphere soil metagenome] BioSample: SAMN31404868;SRA:SRS15503030 [root metagenome]. In addition to diverse microbes, four mycorrhiza fungi, i.e., Glomus intraradices, Glomus irregulare, Paraglomus occultum and Scutellospora heterogama were predominant in collected root samples. A culture-dependent approach was also adopted to isolate several plant growth-promoting bacteria [Bacillus sp. D56, Bacillus sp. D42, Bacillus sp. DR15, Rhizobium sp. DR23 (NCBI Accession: OR821747-OR821750)] and one fungal [Trichoderma sp. AM6 (NCBI Accession:OM915414)] strain. A pot experiment was designed to assess the impact of that isolated microbiome on tea seedlings. After six months of microbiome inoculation, tea plants' physicochemical and transcriptional parameters were evaluated. The results confer that the microbiome-treated treatments [(T1-without any microbial inoculation; NCBI Accession: SAMN33591153), Trichoderma sp. AM6 (T2; NCBI Accession: SAMN33591155) and Trichoderma sp. AM6 +VAM containing tea root+synthetic microbial consortia (T5; NCBI Accession: SAMN33591154)] could enhance the total flavonoid content in tea seedlings by upregulating certain transcripts associated with the flavonoid biosynthesis pathway of tea.}, } @article {pmid39892320, year = {2025}, author = {Huang, L and Dai, W and Sun, X and Pu, Y and Feng, J and Jin, L and Sun, K}, title = {Diet-driven diversity of antibiotic resistance genes in wild bats: implications for public health.}, journal = {Microbiological research}, volume = {293}, number = {}, pages = {128086}, doi = {10.1016/j.micres.2025.128086}, pmid = {39892320}, issn = {1618-0623}, mesh = {Animals ; *Chiroptera/microbiology ; *Diet/veterinary ; *Gastrointestinal Microbiome/drug effects/genetics ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; Public Health ; Drug Resistance, Bacterial/genetics ; Metagenomics ; Genes, Bacterial ; Interspersed Repetitive Sequences ; Animals, Wild/microbiology ; Gene Transfer, Horizontal ; Humans ; Drug Resistance, Microbial/genetics ; }, abstract = {Wild bats may serve as reservoirs for antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria, potentially contributing to antibiotic resistance and pathogen transmission. However, current assessments of bats' antibiotic resistance potential are limited to culture-dependent bacterial snapshots. In this study, we present metagenomic evidence supporting a strong association between diet, gut microbiota, and the resistome, highlighting bats as significant vectors for ARG propagation. We characterized gut microbiota, ARGs, and mobile genetic elements (MGEs) in bats with five distinct diets: frugivory, insectivory, piscivory, carnivory, and sanguivory. Our analysis revealed high levels of ARGs in bat guts, with limited potential for horizontal transfer, encompassing 1106 ARGs conferring resistance to 26 antibiotics. Multidrug-resistant and polymyxin-resistant genes were particularly prevalent among identified ARG types. The abundance and diversity of ARGs/MGEs varied significantly among bats with different dietary habits, possibly due to diet-related differences in microbial composition. Additionally, genetic linkage between high-risk ARGs and multiple MGEs was observed on the genomes of various zoonotic pathogens, indicating a potential threat to human health from wild bats. Overall, our study provides a comprehensive analysis of the resistome in wild bats and underscores the role of dietary habits in wildlife-associated public health risks.}, } @article {pmid39884152, year = {2025}, author = {Maphosa, S and Steyn, M and Lebre, PH and Gokul, JK and Convey, P and Marais, E and Maggs-Kölling, G and Cowan, DA}, title = {Rhizosphere bacterial communities of Namib Desert plant species: Evidence of specialised plant-microbe associations.}, journal = {Microbiological research}, volume = {293}, number = {}, pages = {128076}, doi = {10.1016/j.micres.2025.128076}, pmid = {39884152}, issn = {1618-0623}, mesh = {*Rhizosphere ; *Desert Climate ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Plant Roots/microbiology ; *Microbiota ; Plants/microbiology ; Namibia ; DNA, Bacterial/genetics ; Biodiversity ; Ecosystem ; }, abstract = {Rhizosphere microbial communities are intimately associated with plant root surfaces. The rhizosphere microbiome is recruited from the surrounding soil and is known to impact positively on the plant host via enhanced resistance to pathogens, increased nutrient availability, growth stimulation and increased resistance to desiccation. Desert ecosystems harbour a diversity of perennial and annual plant species, generally exhibiting considerable physiological adaptation to the low-water environment. In this study, we explored the rhizosphere bacterial microbiomes associated with selected desert plant species. The rhizosphere bacterial communities of 11 plant species from the central Namib Desert were assessed using 16S rRNA gene-dependent phylogenetic analyses. The rhizosphere microbial community of each host plant species was compared with control soils collected from their immediate vicinity, and with those of all other host plants. Rhizosphere and control soil bacterial communities differed significantly and were influenced by both location and plant species. Rhizosphere-associated genera included 67 known plant growth-promoting taxa, including Rhizobium, Bacillus, Microvirga, Kocuria and Paenibacillus. Other than Kocuria, these genera constituted the 'core' rhizosphere bacterial microbiome, defined as being present in > 90 % of the rhizosphere communities. Nine of the 11 desert plant species harboured varying numbers and proportions of species-specific microbial taxa. Predictive analyses of functional pathways linked to rhizosphere microbial taxa showed that these were significantly enriched in the biosynthesis or degradation of a variety of substances such as sugars, secondary metabolites, phenolic compounds and antimicrobials. Overall, our data suggest that plant species in the Namib Desert recruit unique taxa to their rhizosphere bacterial microbiomes that may contribute to their resilience in this extreme environment.}, } @article {pmid39864304, year = {2025}, author = {Labarga, D and Mairata, A and Puelles, M and Wallner, A and Aziz, A and Alícia, P}, title = {Rootstocks and drought stress impact the composition and functionality of grapevine rhizosphere bacterial microbiota.}, journal = {Microbiological research}, volume = {293}, number = {}, pages = {128073}, doi = {10.1016/j.micres.2025.128073}, pmid = {39864304}, issn = {1618-0623}, mesh = {*Rhizosphere ; *Droughts ; *Microbiota/physiology ; *Soil Microbiology ; *Plant Roots/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Vitis/microbiology ; *Stress, Physiological ; Metagenomics ; }, abstract = {The microbiota, a component of the plant holobiont, plays an active role in the response to biotic and abiotic stresses. Nowadays, with recurrent drought and global warming, a growing challenge in viticulture is being addressed by different practices, including the use of adapted rootstocks. However, the relationships between these practices, abiotic stress and the composition and functions of the rhizosphere microbiota remain to be deciphered. This study aimed to unravel the impact of five rootstocks, water management and the combination of both on the rhizosphere bacterial microbiota in grapevines using shotgun metagenomics approach. The results showed that drought impacted the diversity, composition and functionality of the rhizosphere bacterial community. The genera Mycolicibacterium, Mycobacterium and Rhodococcus, and the bacterial functions, including DNA damage repair, fatty acid synthesis, sugar and amino acid transport, oxidative stress reduction, toxin synthesis and detoxification of exogenous compounds were significantly enriched under drought conditions. Rootstocks also significantly affected the rhizosphere bacterial richness but its influence on diversity and functionality compared to water management was weaker. Some taxa and function could be linked to water managements applied. The interaction between rootstocks and water management further influenced the rhizosphere composition, especially under drought conditions, where distinct clustering was observed for specific rootstocks. The results highlight the importance of conducting multifactorial studies to better understand their impact on shaping functional rhizosphere bacterial communities. This study paves the way for future research on beneficial bacterial inoculation and genetic engineering of rootstock to cope with drought stress.}, } @article {pmid39827519, year = {2025}, author = {Lin, W and Zhao, K and Wu, Q and Xu, F and Cui, L and Lin, H and Ye, C and Yu, X}, title = {Biofilms on pipelines shape the microbiome and antibiotic resistome in drinking water.}, journal = {Water research}, volume = {274}, number = {}, pages = {123136}, doi = {10.1016/j.watres.2025.123136}, pmid = {39827519}, issn = {1879-2448}, mesh = {*Biofilms ; *Drinking Water/microbiology ; *Microbiota ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Biofilms in the drinking water distribution system (DWDS) provide shelter for pathogens and antibiotic resistance genes (ARGs). However, how biofilms alter the microbiome and antibiotic resistome in tap water, as well as the precise quantitative evaluation of their health risks, remains unclear. Herein, biofilm reactors supplied with municipal drinking water were operated for 120 days. Metagenomic sequencing identified significant differences in microbial compositions among the biofilms, influent, and effluents. A total of 69-305 ARGs were detected in this DWDS, and ARG abundances increased in the biofilms (0.246-1.576 cpc) and effluents (0.309-0.503 cpc) compared to the influent (0.131 cpc). Metagenomic assembly pinpointed potential pathogenic ARG hosts such as Acinetobacter, Pseudomonas, and Escherichia. The co-occurrence of ARGs and mobile genetic elements indicated potential mobility, which was further supported by transformation assays demonstrating gene transfers at a frequency of 10[-6]. Furthermore, source tracking revealed that biofilms contributed high proportions (19 %-34 %) to the ARG profiles of effluents. The ARG risk scores increased from the influent (20.39) to the effluents (39.85-55.50), with highest level (55.50) in the cast iron effluent. Overall, this study provides novel insights into the impacts of biofilm growth on the microbiome and antibiotic resistome in tap water, along with their potential health risks in the DWDS.}, } @article {pmid39798533, year = {2025}, author = {Mao, X and Yin, X and Yang, Y and Gao, F and Li, S and Shi, X and Deng, Y and Li, L and Leung, KMY and Zhang, T}, title = {Longitudinal metagenomic analysis on antibiotic resistome, mobilome, and microbiome of river ecosystems in a sub-tropical metropolitan city.}, journal = {Water research}, volume = {274}, number = {}, pages = {123102}, doi = {10.1016/j.watres.2025.123102}, pmid = {39798533}, issn = {1879-2448}, mesh = {*Rivers/microbiology ; *Microbiota/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; Ecosystem ; Hong Kong ; Cities ; Drug Resistance, Bacterial/genetics ; }, abstract = {Rivers play an important role as reservoirs and sinks for antibiotic resistance genes (ARGs). However, it remains underexplored for the resistome and associated mobilome in river ecosystems, and hosts of riverine ARGs particularly the pathogenic ones are rarely studied. This study for the first time conducted a longitudinal metagenomic analysis to unveil the resistome, mobilome, and microbiome in river water, by collecting samples from 16 rivers in Hong Kong over a three-year period and using both short-read and long-read sequencing. Results revealed that aminoglycoside, bacitracin, β-lactam, macrolide lincosamide-streptogramin, and sulfonamide were the predominant ARG types in the river water samples. Riverine ARGs exhibited high spatial variations in abundance and diversity. Environmental factors such as fecal coliform count, Escherichia coli count, 5-day biochemical oxygen demand (BOD5), dissolved oxygen (DO), and total organic carbon (TOC) had a significant correlation to the absolute concentrations of ARGs. Nanopore sequencing was used to reveal the physical genetic linkage of mobile genetic elements (MGEs) with ARGs in river water samples. The results showed that qacEdelta, transposase, integrase, and Tn916 had a high prevalence in ARG-carrying long reads. Host tracking using ARG-carrying reads identified 23 pathogenic bacteria species that harbored ARGs. Some ARGs were shared by different bacterial groups. This study presented a nuanced insight of resistome in river water by a longitudinal metagenomic analysis and deepened our understanding of common and divergent riverine antimicrobial resistant risk across the regional patterns.}, } @article {pmid39730187, year = {2025}, author = {Yan, M and Andersen, TO and Pope, PB and Yu, Z}, title = {Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.}, journal = {Genome research}, volume = {35}, number = {2}, pages = {368-378}, doi = {10.1101/gr.279825.124}, pmid = {39730187}, issn = {1549-5469}, mesh = {Animals ; *Ruminants/microbiology ; *Deep Learning ; *Fungi/genetics/classification ; Rumen/microbiology/parasitology ; Databases, Protein ; Metagenome ; Metagenomics/methods ; Eukaryota/genetics/classification ; Gastrointestinal Microbiome ; Computational Biology/methods ; }, abstract = {Metagenomics, particularly genome-resolved metagenomics, have significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations within various microbiomes, including those in the mammalian gastrointestinal (GI) tract, remain relatively underexplored in metagenomic studies owing to the lack of comprehensive reference genome databases and robust bioinformatic tools. The GI tract of ruminants, particularly the rumen, contains a high eukaryotic biomass but a relatively low diversity of ciliates and fungi, which significantly impacts feed digestion, methane emissions, and rumen microbial ecology. In the present study, we developed GutEuk, a bioinformatics tool that improves upon the currently available Tiara and EukRep in accurately identifying eukaryotic sequences from metagenomes. GutEuk is optimized for high precision across different sequence lengths. It can also distinguish fungal and protozoal sequences, further elucidating their unique ecological, physiological, and nutritional impacts. GutEuk was shown to facilitate comprehensive analyses of protozoa and fungi within more than 1000 rumen metagenomes, revealing a greater genomic diversity among protozoa than previously documented. We further curated several ruminant eukaryotic protein databases, significantly enhancing our ability to distinguish the functional roles of ruminant fungi and protozoa from those of prokaryotes. Overall, the newly developed package GutEuk and its associated databases create new opportunities for the in-depth study of GI tract eukaryotes.}, } @article {pmid39708450, year = {2025}, author = {Gao, B and Chen, L and Wu, L and Zhang, S and Zhao, S and Mo, Z and Chen, Z and Tu, P}, title = {Association between microplastics and the functionalities of human gut microbiome.}, journal = {Ecotoxicology and environmental safety}, volume = {290}, number = {}, pages = {117497}, doi = {10.1016/j.ecoenv.2024.117497}, pmid = {39708450}, issn = {1090-2414}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Microplastics/toxicity ; Humans ; Animals ; Mice ; *Feces/microbiology/chemistry ; Adult ; Female ; Male ; Gas Chromatography-Mass Spectrometry ; Polyvinyl Chloride ; }, abstract = {As an integral part of humans, the gut microbiome plays a significant role in the physiological and pathological processes of the host, and dysbiosis of the gut microbiome is linked to various diseases. The impact of microplastics on the diversity and composition of human gut microbiome has been reported previously. However, effects of microplastics on the functionality of the gut microbiome in humans have not been well studied. In the present study, concentrations of microplastics in human blood were detected through pyrolysis-gas chromatography/mass spectrometry in 39 adults. Five types of microplastics were found in human blood, including polyvinyl chloride, polyethylene, polypropylene, polystyrene, and polyamide 66. Shotgun metagenomic sequencing was further employed to analyze the metagenomes of the human stool samples and fecal samples from mice exposed to microplastics. Associations were found between microplastics and microbial species, as well as microbial genes encoding invasion-related virulence factors, quorum sensing, autoinducer and transporter system, and microplastic biodegradation enzymes. The findings are of significance to improve the understanding of functional changes in the gut microbiome associated with microplastic exposure, as well as raising awareness regarding the health risks of microplastics in the human population.}, } @article {pmid39395412, year = {2025}, author = {Talwar, C and Davuluri, GVN and Kamal, AHM and Coarfa, C and Han, SJ and Veeraragavan, S and Parsawar, K and Putluri, N and Hoffman, K and Jimenez, P and Biest, S and Kommagani, R}, title = {Identification of distinct stool metabolites in women with endometriosis for non-invasive diagnosis and potential for microbiota-based therapies.}, journal = {Med (New York, N.Y.)}, volume = {6}, number = {2}, pages = {100517}, doi = {10.1016/j.medj.2024.09.006}, pmid = {39395412}, issn = {2666-6340}, mesh = {*Endometriosis/metabolism/microbiology/diagnosis ; Female ; Humans ; *Feces/microbiology/chemistry ; Animals ; Mice ; *Gastrointestinal Microbiome ; Adult ; Metabolome ; Indoles/therapeutic use/metabolism ; Disease Models, Animal ; Metabolomics/methods ; Inflammatory Bowel Diseases/metabolism/microbiology/diagnosis ; }, abstract = {BACKGROUND: Endometriosis, a poorly studied gynecological condition, is characterized by the presence of ectopic endometrial lesions resulting in pelvic pain, inflammation, and infertility. These associated symptoms contribute to a significant burden, often exacerbated by delayed diagnosis. Current diagnostic methods involve invasive procedures, and existing treatments provide no cure.

METHODS: Microbiome-metabolome signatures in stool samples from individuals with and without endometriosis were determined using unbiased metabolomics and 16S bacteria sequencing. Functional studies for selected microbiota-derived metabolites were conducted in vitro using patient-derived cells and in vivo by employing murine and human xenograft pre-clinical disease models.

FINDINGS: We discovered a unique bacteria-derived metabolite signature intricately linked to endometriosis. The altered fecal metabolite profile exhibits a strong correlation with that observed in inflammatory bowel disease (IBD), revealing intriguing connections between these two conditions. Notably, we validated 4-hydroxyindole, a gut-bacteria-derived metabolite that is lower in stool samples of endometriosis. Extensive in vivo studies found that 4-hydroxyindole suppressed the initiation and progression of endometriosis-associated inflammation and hyperalgesia in heterologous mouse and in pre-clinical models of the disease.

CONCLUSIONS: Our findings are the first to provide a distinct stool metabolite signature in women with endometriosis, which could serve as stool-based non-invasive diagnostics. Further, the gut-microbiota-derived 4-hydroxyindole poses as a therapeutic candidate for ameliorating endometriosis.

FUNDING: This work was funded by the NIH/NICHD grants (R01HD102680, R01HD104813) and a Research Scholar Grant from the American Cancer Society to R.K.}, } @article {pmid39951352, year = {2025}, author = {Li, Q and Tan, D and Xiong, S and Yu, K and Su, Y and Zhu, W}, title = {Time-restricted feeding promotes glucagon-like peptide-1 secretion and regulates appetite via tryptophan metabolism of gut Lactobacillus in pigs.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2467185}, doi = {10.1080/19490976.2025.2467185}, pmid = {39951352}, issn = {1949-0984}, mesh = {Animals ; *Glucagon-Like Peptide 1/metabolism/blood ; *Gastrointestinal Microbiome ; Swine ; *Tryptophan/metabolism ; *Lactobacillus/metabolism ; *Appetite/physiology ; Enteroendocrine Cells/metabolism ; Feeding Behavior ; Hypothalamus/metabolism ; }, abstract = {Previous clinical trials have shown that time-restricted feeding can be involved in regulating the metabolic health of humans and animals. However, the underlying mechanism has not been fully explored. In this study, the pig model was employed to simulate four prevalent human eating habits, with the aim of investigating the impact of gut microbiota and microbial metabolites on gut hormone secretion and appetite regulation. Compared to the ad libitum feeding (ALF) pattern, three time-restricted feeding patterns reduced total food intake and eating time. Meanwhile, three time-restricted feeding patterns induced elevated levels of serum and hypothalamic glucagon-like peptide-1 (GLP-1), while suppressing reward-related circuits in the hypothalamus. It is noteworthy that the early time-restricted feeding (eTRF) pattern increased the number of intestinal enteroendocrine cells (EECs) compared to ALF. Metagenomic and metabonomic analyses revealed that three time-restricted feeding patterns induced colonization of Lactobacillus and significantly increased the levels of its metabolite, indole-3-lactic acid (ILA). Dietary supplementation with ILA exhibited an increasing trend in fasting serum GLP-1 level of piglets. In vitro studies with pig intestinal organoids showed the Lactobacillus metabolite ILA enhanced GLP-1 secretion through the promotion of intestinal stem cell differentiation into EECs, rather than activating the ability of EECs to secrete GLP-1. Overall, time-restricted feeding promoted GLP-1 secretion and affected long-term appetite regulation by promoting the colonization of Lactobacillus and modulating microbial tryptophan metabolism.}, } @article {pmid39950834, year = {2025}, author = {Ng, HY and Zhang, L and Tan, JT and Hui, RWH and Yuen, MF and Seto, WK and Leung, WK and Cheung, KS}, title = {Gut Microbiota Predicts Treatment Response to Empagliflozin Among MASLD Patients Without Diabetes Mellitus.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {45}, number = {3}, pages = {e70023}, doi = {10.1111/liv.70023}, pmid = {39950834}, issn = {1478-3231}, support = {//General Research Fund, Research Grant Council, The Government of the Hong Kong Special Administrative Region/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Glucosides/therapeutic use ; Middle Aged ; Prospective Studies ; *Benzhydryl Compounds/therapeutic use ; Non-alcoholic Fatty Liver Disease/drug therapy/microbiology ; Treatment Outcome ; Magnetic Resonance Imaging ; Feces/microbiology ; Sodium-Glucose Transporter 2 Inhibitors/therapeutic use ; Logistic Models ; }, abstract = {BACKGROUND AND AIM: We aimed to investigate whether gut microbiota could predict the treatment response to pharmacological agents among metabolic dysfunction-associated steatotic liver disease (MASLD) patients without diabetes mellitus (DM), as data are lacking.

METHODS: We prospectively followed up non-diabetic MASLD patients who used empagliflozin. Clinical, anthropometric, laboratory assessments and magnetic resonance imaging-proton density fat fraction (MRI-PDFF) were performed from baseline to week 52 (EOT). Baseline stool samples were collected, and shotgun DNA metagenomic sequencing was performed to profile microbiome. The primary outcome was treatment response to empagliflozin at EOT, defined as MRI-PDFF decline ≥ 30% at EOT from baseline. Linear discriminant analysis [LDA] effect size was used to identify putative bacterial species. Multivariable logistic regression was used to derive adjusted odds ratio (aOR) of outcome with bacterial species by adjusting for clinical factors.

RESULTS: Twenty-two (48.9%) of 45 patients (median age: 56.9 years [IQR: 51.0-63.2]; male: 23 [51.1%]) achieved treatment response at EOT. There was difference in alpha diversity (Shannon index: p < 0.001; Simpson index: p = 0.001) and beta diversity (p = 0.048) in baseline microbiome between treatment response and non-response groups. Faecalibacterium prausnitzii (log10LDAscore = 4.27), Lachnospira pectinoschiza (log10LDAscore = 3.99), Anaerostipes hadrus (log10LDAscore = 3.98), Roseburia faecis (log10LDAscore = 3.97), Roseburia inulinivorans (log10LDAscore = 3.58) and Agathobaculum butyriciproducens (log10LDAscore = 2.77) were enriched in the treatment response group. L. pectinoschiza (aOR: 34.1; p = 0.015), A. hadrus (aOR:35.0; p = 0.032) and A. butyriciproducens (aOR:22.3; p = 0.023) independently predicted treatment response but not clinical factors. These three species collectively predicted treatment response with AUROC of 0.89 (95% CI: 0.80-0.99).

CONCLUSIONS: Certain gut bacterial species, particularly the combination of A. hadrus, L. pectinoschiza and A. butyriciproducens, may predict treatment response to empagliflozin in MAFLD patients without DM.}, } @article {pmid39948426, year = {2025}, author = {Zang, T and Zhang, Z and Liu, W and Yin, L and Zhao, S and Liu, B and Ma, L and Li, Z and Tang, X}, title = {Structural and functional changes in the oral microbiome of patients with craniofacial microsomia.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {5400}, pmid = {39948426}, issn = {2045-2322}, support = {2021-I2M-1-068//Chinese Academy of Medical Science Innovation Fund for Medical Sciences/ ; }, mesh = {Humans ; Male ; *Microbiota ; Female ; *Mouth/microbiology ; *Saliva/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; Child ; Goldenhar Syndrome/microbiology ; Dysbiosis/microbiology ; Adolescent ; Adult ; Bacteria/classification/genetics/isolation & purification/metabolism ; Young Adult ; Metagenomics/methods ; Child, Preschool ; Case-Control Studies ; }, abstract = {Craniofacial microsomia (CFM) is the second most common congenital craniofacial deformity, presenting diverse clinical manifestations and treatments that may influence oral bacteria dysbiosis (OBD). However, research linking CFM to OBD is limited. Saliva samples were collected from 20 patients with CFM and 24 controls. We compared oral microflora and gene function using 16 S ribosomal RNA sequencing and metagenomics. We also evaluated the correlation between CFM clinical phenotypes and microbiota community structure. Patients with CFM demonstrated greater richness and evenness in their oral microflora. The dominant genera included several pathogenic species, such as Actinomyces, Fusobacterium, and Prevotella. Notably, the severity of CFM correlated positively with the abundance of Neisseria and Porphyromonas. Upregulated pathways were primarily linked to biotin and amino acid metabolism, such as Tryptophan metabolism and Lysine degradation, and further underscored the need for focused oral health interventions in this population. This study is the first to indicate that CFM patients exhibit unique oral bacterial dysbiosis, marked by a higher presence of opportunistic pathogens and increased pathways related to oral and systemic health. These findings highlight the importance of monitoring oral health in patients with CFM.}, } @article {pmid39948184, year = {2025}, author = {Chen, A and Yu, Q and Zheng, L and Yi, J and Tang, Z and Ge, H and Ning, Y and Yin, N and Xie, Y and Chen, S and Shi, W and She, X and Xiang, J and Tang, J}, title = {Dose-dependent M2 macrophage polarization induced by Talaromyces marneffei promotes lung cancer cell growth via arginine-ornithine-cycle activation.}, journal = {Medical microbiology and immunology}, volume = {214}, number = {1}, pages = {11}, pmid = {39948184}, issn = {1432-1831}, support = {81972198, 81773147//National Natural Science Foundation of China/ ; 2019SK2253//Key Research and Development Program of Hunan Province of China/ ; ZLXD2017004//Central South University/ ; ZLXD2017004//Central South University/ ; kq2208299//National Natural Science Foundation of Changsha/ ; }, mesh = {*Talaromyces ; Humans ; Animals ; *Macrophages/microbiology/immunology ; *Lung Neoplasms/microbiology ; Mice ; *Arginine/metabolism ; *Ornithine/metabolism/analogs & derivatives/pharmacology ; Carcinoma, Non-Small-Cell Lung/microbiology/pathology ; Cell Proliferation ; Macrophage Activation ; Female ; Male ; Metagenomics ; Disease Models, Animal ; Cell Line, Tumor ; Mycobiome ; Lung/microbiology/pathology ; }, abstract = {It is now widely accepted that lungs are colonized by diverse microbes. Dysbiosis of the lung microbiota has been found to affect the progression of lung cancer. Fungi are a major component of the lung microbiota. However, the causal links between the mycobiome or specific species and lung cancer remain unclear. To address this, we conducted a study examining the composition of lung mycobiota in Non-Small-Cell Lung Cancer (NSCLC) patients using shotgun metagenomics. The differential taxa between NSCLC patients and non-cancer controls were defined by the Wilcoxon rank-sum test. Nested PCR was used to measure the abundance of specific fungal species. Metabolomics analysis was performed to investigate the metabolic reprogramming of macrophages triggered by intracellular infection of specific fungal species. In vitro and in vivo assays were conducted to examine the effect of the specific fungus on cancer cell growth. Our findings showed that Ascomycota, Microsporidia and Mucoromycota were the dominant fungal taxa in the lungs. Talaromyces marneffei (T.marneffei) was the most significantly differential fungus between lung cancer patients and non-cancer controls, with its abundance positively correlated with lung cancer. The lung cancer animal model demonstrated that T.marneffei promotes lung cancer growth. Our study also demonstrated that T.marneffei promotes lung cancer cell growth by inducing dose-dependent M2 macrophage polarization through arginine-ornithine-cycle activation. Furthermore, inhibition of arginase can reduce M2 polarization of macrophages and the survival of T. marneffei inside macrophages. In summary, our study reveals that the increased abundance of T. marneffei in the lungs affects lung cancer cell growth by triggering arginine-induced M2 polarization of macrophages. These findings provide potential drug targets for the development of therapies aimed at targeting the survival of fungi inside macrophages in the fight against cancer.}, } @article {pmid39947133, year = {2025}, author = {Elmassry, MM and Sugihara, K and Chankhamjon, P and Kim, Y and Camacho, FR and Wang, S and Sugimoto, Y and Chatterjee, S and Chen, LA and Kamada, N and Donia, MS}, title = {A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules.}, journal = {Cell host & microbe}, volume = {33}, number = {2}, pages = {218-234.e12}, doi = {10.1016/j.chom.2025.01.002}, pmid = {39947133}, issn = {1934-6069}, mesh = {*Gastrointestinal Microbiome ; Humans ; Mice ; Animals ; *Inflammatory Bowel Diseases/microbiology ; Feces/microbiology ; Crohn Disease/microbiology ; Disease Models, Animal ; Multigene Family ; Colitis/microbiology ; Metagenomics ; Clostridium/genetics ; Mice, Inbred C57BL ; Female ; }, abstract = {Gut microbiome changes have been associated with several human diseases, but the molecular and functional details underlying these associations remain largely unknown. Here, we performed a meta-analysis of small molecule biosynthetic gene clusters (BGCs) in metagenomic samples of the gut microbiome from inflammatory bowel disease (IBD) patients and matched healthy subjects and identified two Clostridia-derived BGCs that are significantly associated with Crohn's disease (CD), a main IBD type. Using synthetic biology, we discovered and solved the structures of six fatty acid amides as the products of the CD-enriched BGCs, which we subsequently detected in fecal samples from IBD patients. Finally, we show that the discovered molecules disrupt gut permeability and exacerbate disease in chemically or genetically susceptible mouse models of colitis. These findings suggest that microbiome-derived small molecules may play a role in the etiology of IBD and represent a generalizable approach for discovering molecular mediators of disease-relevant microbiome-host interactions.}, } @article {pmid39946339, year = {2025}, author = {Long, C and Wang, P and Wu, J and Liu, J and Tan, Z and Li, W}, title = {Structure and diversity of intestinal methanogens in black carp (Mylopharyngodon piceus), grass carp (Ctenopharyngodon idella) and water samples.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0316456}, doi = {10.1371/journal.pone.0316456}, pmid = {39946339}, issn = {1932-6203}, mesh = {*Carps/microbiology ; Animals ; *Gastrointestinal Microbiome/genetics ; Methane/metabolism ; Intestines/microbiology ; Bacteria/genetics/classification/isolation & purification ; Water Microbiology ; Methanosarcina/genetics/metabolism ; }, abstract = {The present research investigation aims to examine the community features of methanogens in the intestinal tract of black and grass carp, as well as their association with methanogens in water samples. Samples of black carp, grass carp and water in a pond were gathered in Spring 2021. Using the Illumina HiSeq 2500 high-throughput sequencing platform, the metagenomic mcrA gene sequences of black carp, grass carp and cultured water specimens were determined and analyzed. The outcomes indicate that the richness and diversity of methanogens in the intestinal tract of black and carp grass carp were highly correlated with the cultured water. Five bacterial genera were found in the three sets of samples, Methanosarcina, Methanocorpusculum, Methanospirillum, Methanobacterium and Methanofollis, in which Methanosarcina and Methanocorpusculum were the dominant genera. In addition, Methanosarcina had the greatest amount in grass carp and Methanocorpusculum had the greatest quantity in black carp. In conclusion, Methanosarcina and Methanocorpusculum were the main methanogens in the digestive tract of black and grass carp and culture water, and hydrolytic fermentative bacteria were its main metabolic substrate, hydrotrophic was its main metabolic pathway. The results will provide a reference for the relationship between intestinal methanogens and aquaculture and the greenhouse effect.}, } @article {pmid39944722, year = {2025}, author = {Saravanan, C and Gopinath, NK and Ganesan, R and Thirumurugan, D}, title = {Challenges and limitations in using bacterial metabolites as immunomodulators.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1535394}, pmid = {39944722}, issn = {2235-2988}, mesh = {Humans ; *Bacteria/metabolism ; *Immunologic Factors/metabolism ; *Gastrointestinal Microbiome ; Animals ; Metabolomics ; Immunomodulating Agents/metabolism ; Metagenomics ; }, abstract = {Harnessing the immunomodulatory potential of bacterial metabolites opens up exciting possibilities for treating various immune-related disorders. However, turning this potential into a reality presents significant challenges. This review investigates these challenges, focusing on discovery, production, characterization, stability, formulation, safety, and individual variability limitations. The limited bioavailability of many metabolites, as well as potential improvements along with the potential for off-target effects and the importance of precise targeting, are emphasized. Furthermore, the complex interactions between gut bacterial metabolites and the microbiome are investigated, highlighting the importance of personalized approaches. We conclude by discussing promising advances in metagenomics, metabolomics, synthetic biology, and targeted delivery systems, which hold out hope for overcoming these limitations and paving the way for the clinical translation of bacterial metabolites as effective immunomodulators.}, } @article {pmid39940425, year = {2025}, author = {Chen, E and Ajami, NJ and White, DL and Liu, Y and Gurwara, S and Hoffman, K and Graham, DY and El-Serag, HB and Petrosino, JF and Jiao, L}, title = {Dairy Consumption and the Colonic Mucosa-Associated Gut Microbiota in Humans-A Preliminary Investigation.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030567}, pmid = {39940425}, issn = {2072-6643}, support = {RP#140767//Cancer Prevention and Research Institute of Texas/ ; DK56338/DK/NIDDK NIH HHS/United States ; 001//Gillson Longenbaugh Foundation/ ; 001//Gillson Longenbaugh Foundation/ ; CX001430//U.S. Department of Veterans Affairs/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Cross-Sectional Studies ; *Dairy Products/microbiology ; Middle Aged ; *Colon/microbiology ; *Intestinal Mucosa/microbiology ; Adult ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Diet ; Aged ; Yogurt/microbiology ; }, abstract = {BACKGROUND: Dairy consumption has been associated with various health outcomes that may be mediated by changes in gut microbiota.

METHODS: This cross-sectional study investigated the association between the colonic mucosa-associated gut microbiota and the self-reported intake of total dairy, milk, cheese, and yogurt. A total of 97 colonic mucosal biopsies collected from 34 polyp-free individuals were analyzed. Dairy consumption in the past year was assessed using a food frequency questionnaire. The 16S rRNA gene V4 region was amplified and sequenced. Operational taxonomic unit (OTU) classification was performed using the UPARSE and SILVA databases. OTU diversity and relative abundance were compared between lower vs. higher dairy consumption groups. Multivariable negative binomial regression models for panel data were used to estimate the incidence rate ratio and 95% confidence interval for bacterial counts and dairy consumption. False discovery rate-adjusted p values (q value) < 0.05 indicated statistical significance.

RESULTS: Higher total dairy and milk consumption and lower cheese consumption were associated with higher alpha microbial diversity (adjusted p values < 0.05). Higher total dairy and milk consumption was also associated with higher relative abundance of Faecalibacterium. Higher milk consumption was associated with higher relative abundance of Akkermansia. Higher total dairy and cheese consumption was associated with lower relative abundance of Bacteroides.

CONCLUSIONS: Dairy consumption may influence host health by modulating the structure and composition of the colonic adherent gut microbiota.}, } @article {pmid39940254, year = {2025}, author = {Barata, P and Oliveira, A and Soares, R and Fernandes, A}, title = {Gut Microbiota Is Not Significantly Altered by Radioiodine Therapy.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030395}, pmid = {39940254}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/radiation effects ; Female ; Middle Aged ; Male ; *Feces/microbiology ; *Iodine Radioisotopes ; *Hyperthyroidism/radiotherapy/microbiology ; Adult ; Prospective Studies ; Thyroid Neoplasms/radiotherapy/microbiology ; Aged ; Bacteria/classification/radiation effects/genetics/isolation & purification ; Metagenomics/methods ; }, abstract = {Purpose: Radiotherapy treatments are known to alter the gut microbiota. However, little is known regarding the effect of nuclear medicine treatments on gut microbiota, and it is established that nuclear medicine is inherently different from radiotherapy. To address this knowledge gap, we conducted a prospective study to identify changes in the gut microbiota of patients treated with [[131]I]NaI by comparing fecal samples before and after RAIT. Methods: Fecal samples of 64 patients (37 with thyroid cancer and 27 with hyperthyroidism) with indication for RAIT were collected 2 to 3 days before treatment and 8 to 10 days post-treatment. After DNA extraction, the gut microbiota's richness, diversity, and composition were analyzed by shotgun metagenomics. In addition, LEfSe was performed to compare compositional changes in specific bacteria. Results: Gut microbiome richness and diversity remained unchanged after RAIT, with few changes in its composition identified, especially in patients with hyperthyroidism. Conclusions: This study provides a conceptual and analytical basis for increasing our understanding of the effects of radiopharmaceuticals on gut microbiota. Our preliminary results indicate that RAIT, contrary to radiotherapy, does not cause major disruptions to the human gut microbiota.}, } @article {pmid39940045, year = {2025}, author = {Schropp, N and Bauer, A and Stanislas, V and Huang, KD and Lesker, TR and Bielecka, AA and Strowig, T and Michels, KB}, title = {The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {52}, pmid = {39940045}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Cross-Over Studies ; Male ; Female ; Adult ; *Bacteria/classification/genetics/isolation & purification ; *Fatty Acids, Volatile/metabolism ; *Fermented Foods/microbiology ; Middle Aged ; Feces/microbiology ; Metagenomics/methods ; Young Adult ; Metabolome ; Healthy Volunteers ; }, abstract = {BACKGROUND: Sauerkraut is a fermented food that has been suspected to have a beneficial impact on the gut microbiome, but scientific evidence is sparse. In this crossover intervention trial with 87 participants (DRKS00027007), we investigated the impact of daily consumption of fresh or pasteurized sauerkraut for 4 weeks on gut microbial composition and the metabolome in a healthy study population.

RESULTS: Using shotgun metagenomic sequencing, we observed changes in single bacterial species following fresh and pasteurized sauerkraut consumption. More pronounced changes were observed in the pasteurized sauerkraut intervention arm. Only pasteurized sauerkraut consumption increased serum short-chain fatty acids (SCFAs).

CONCLUSIONS: The gut microbiome of healthy individuals is rather resilient to short-term dietary interventions even though single species might be affected by sauerkraut consumption. Video Abstract.}, } @article {pmid39939365, year = {2025}, author = {Soares, KO and Da Rocha, TF and Hale, VL and Vasconcelos, PC and do Nascimento, LJ and da Silva, NMV and Rodrigues, AE and de Oliveira, CJB}, title = {Comparing the impact of landscape on the gut microbiome of Apis mellifera in Atlantic Forest and Caatinga Biomes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {5293}, pmid = {39939365}, issn = {2045-2322}, support = {001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 88881.311776/2018-01//CAPES-PrInt Project "Omic sciences applied to the prevention of antimicrobial resistance at the human-animal-environment interface-a one health approach/ ; 88881.311776/2018-01//CAPES-PrInt Project "Omic sciences applied to the prevention of antimicrobial resistance at the human-animal-environment interface-a one health approach/ ; 3136678/2020-0//Conselho Nacional de Pesquisa e Desenvolvimento/ ; 3136678/2020-0//Conselho Nacional de Pesquisa e Desenvolvimento/ ; }, mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome ; *Forests ; Brazil ; *RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Ecosystem ; }, abstract = {The composition of the gut microbiota in animals can be influenced by a variety of intrinsic and extrinsic factors in the host, such as diet, physiological state, and genetics. This study aimed to compare the structural composition of the gut microbiota of Apis mellifera bees from two distinct Brazilian biomes, the Atlantic Forest and the Caatinga, using high throughput 16 S rRNA sequencing. We identified a core microbiota composed of seven genera present in all samples: Lactobacillus, Commensalibacter, Rhizobiaceae, Snodgrassella, Gilliamella, Orbaceae and Bifidobacterium. These taxa accounted for 63% of all bacterial genera in the dataset. Interestingly, we observed a significantly differential abundance of the genus Apibacter between bees from the two biomes, with a marked increase in bees from Atlantic Forest. However, the overall variance in the gut structural composition attributable to landscape type, while significant, was relatively low. Notably, none of the members of the core microbiota were differently abundant between the biomes. Understanding the magnitude of landscape-associated effects on the microbiota of bees in different biomes is crucial for the accurate assessment of the impact of anthropogenic factors. These findings provide important insights into the resilience and adaptability of the honey bee gut microbiome across contrasting environments, contributing to the development of conservation and sustainable management strategies for these essential pollinators.}, } @article {pmid39938754, year = {2025}, author = {Fernandes, M and Palmieri, O and Castellana, S and Spanetta, M and Latiano, T and Lupo, C and Masi, C and Cardile, C and Calvello, C and Izzi, F and Placidi, F and Mazza, T and Mercuri, NB and Latiano, A and Liguori, C}, title = {Gut microbiome composition changes in obstructive sleep apnoea syndrome also in relation to excessive daytime sleepiness.}, journal = {Brain research bulletin}, volume = {}, number = {}, pages = {111251}, doi = {10.1016/j.brainresbull.2025.111251}, pmid = {39938754}, issn = {1873-2747}, abstract = {INTRODUCTION: Obstructive sleep apnoea syndrome (OSAS) is considered a risk factor for several comorbidities. Alteration in gut microbiome was documented in OSAS animal models and in paediatric patients. This study analysed gut microbiome composition in adult patients with OSAS and compared to controls. Further, the effect of excessive daytime sleepiness (EDS) on gut microbiome was evaluated.

METHODS: Adult patients with OSAS underwent polysomnographic recording and completed the Epworth Sleepiness Scale (ESS) to assess EDS. Faecal samples were collected and compared between patients and healthy controls. Composition, community diversity, differences in taxa abundance profiles and sample dysbiosis were evaluated through 16S metagenomics and multiple bioinformatics algorithms. OSAS patients were distributed in two groups according to EDS (ESS score≥10) to assess differences in clinical, polysomnographic and faecal data.

RESULTS: Twenty-three OSAS patients were compared to 44 controls. Patients presented significant differences of gut microbiome biodiversity, specifically in qualitative alpha diversity metrics (Faith's PD Kruskal-Wallis test, p-value=0.003; Number_of_Observed_Features, p value =0.001). OSAS patients tend to cluster together, at least for Jaccard and Unweighted UniFrac distance-based PERMANOVA tests (q-values=0.02 and =0.003, respectively). Several taxa were detected as different in abundance between OSAS patients and controls, although, globally, OSAS patients cannot be considered as "dysbiotic". Differences in bacteria composition were evident between OSAS patients with and those without EDS.

CONCLUSIONS: OSAS is associated with gut microbiome alteration in adult patients. EDS in OSAS seems to characterize a different gut microbiome composition, although it can be only hypothesized a gut-mediated effect on EDS in OSAS.}, } @article {pmid39909037, year = {2025}, author = {Lim, B and Xu, J and Wierzbicki, IH and Gonzalez, CG and Chen, Z and Gonzalez, DJ and Gao, X and Goodman, AL}, title = {A human gut bacterium antagonizes neighboring bacteria by altering their protein-folding ability.}, journal = {Cell host & microbe}, volume = {33}, number = {2}, pages = {200-217.e24}, doi = {10.1016/j.chom.2025.01.008}, pmid = {39909037}, issn = {1934-6069}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Protein Folding ; *Bacterial Proteins/metabolism/genetics ; *Bacteroides/genetics/metabolism ; Molecular Chaperones/metabolism/genetics ; Animals ; Mice ; Microbial Interactions ; }, abstract = {Antagonistic interactions play a key role in determining microbial community dynamics. Here, we report that one of the most widespread contact-dependent effectors in human gut microbiomes, Bte1, directly targets the PpiD-YfgM periplasmic chaperone complex in related microbes. Structural, biochemical, and genetic characterization of this interaction reveals that Bte1 reverses the activity of the chaperone complex, promoting substrate aggregation and toxicity. Using Bacteroides, we show that Bte1 is active in the mammalian gut, conferring a fitness advantage to expressing strains. Recipient cells targeted by Bte1 exhibit sensitivity to membrane-compromising conditions, and human gut microbes can use this effector to exploit pathogen-induced inflammation in the gut. Further, Bte1 allelic variation in gut metagenomes provides evidence for an arms race between Bte1-encoding and immunity-encoding strains in humans. Together, these studies demonstrate that human gut microbes alter the protein-folding capacity of neighboring cells and suggest strategies for manipulating community dynamics.}, } @article {pmid39805166, year = {2025}, author = {Memon, FU and Zhu, Y and Cui, Y and Feng, X and Ahmad, S and Zeng, P and Nabi, F and Hao, D and Huang, Z and Tettamanti, G and Tian, L}, title = {Gut microbial communities and transcriptional profiles of black soldier fly (Hermitia illucens) larvae fed on fermented sericulture waste.}, journal = {Waste management (New York, N.Y.)}, volume = {194}, number = {}, pages = {158-168}, doi = {10.1016/j.wasman.2025.01.011}, pmid = {39805166}, issn = {1879-2456}, mesh = {Animals ; *Larva/microbiology ; *Fermentation ; *Gastrointestinal Microbiome ; Diptera ; Waste Management/methods ; Transcriptome ; Animal Feed/analysis ; }, abstract = {Sericulture waste poses significant challenges to industrial and environmental safety. Black soldier fly larvae (BSFL) offer a promising solution for organic waste management by converting it into insect protein. This study aimed to develop a microbial fermented method for utilizing sericulture waste to feed BSFL and explore the underlying mechanisms. Our results showed that all fermented sericulture waste groups had positive effects on body weight, survival rate, substrate consumption rate, and substrate conversion rate. Metagenomic analysis revealed a notable increase in the abundances of commensal genera, including Sedimentibacter, Clostridium, Enterococcus, Bacteroides, and Bacillus, in the gut of BSFL fed on sericulture waste fermented with the most effective combination of microbial strains (B. subtilis, B. licheniformis, and E. faecalis). In contrast, BSFL reared on unfermented sericulture waste exhibited higher abundances of potentially pathogenic and harmful genera, including Providencia, Klebsiella, Escherichia, Brucella, and Enterobacter. Clusters of orthologous genes (COG) analysis indicated that altered microbial communities in the fermented group mainly participated in metabolic pathways, defense mechanism, and signal transduction mechanism. Transcriptome analysis further revealed that the upregulated genes were functionally associated with key metabolic pathways and immune mechanisms in the fermented group. These findings underscore the pivotal role of selected microbial fermentation in utilizing sericulture waste as BSFL feed, providing a sustainable solution for organic waste management.}, } @article {pmid39732159, year = {2025}, author = {Yadav, V and Kilambi, R and Sharma, R and Mohapatra, N and Sasturkar, SV and Dawar, A and Rastogi, A and Saini, M and Sharma, D and Trehanpati, N and Kale, PR and Pamecha, V and Ramakrishna, G}, title = {Radiocarbon dating of gallstones for timeline of formation, dormancy analysis, and correlation with chemical/microbial composition: a pilot study on gallstone geobiology.}, journal = {Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract}, volume = {29}, number = {3}, pages = {101937}, doi = {10.1016/j.gassur.2024.101937}, pmid = {39732159}, issn = {1873-4626}, mesh = {*Gallstones/microbiology/pathology ; Pilot Projects ; Humans ; Spectroscopy, Fourier Transform Infrared/methods ; *Carbon Radioisotopes ; *Radiometric Dating ; RNA, Ribosomal, 16S/genetics ; Microscopy, Electron, Scanning ; Time Factors ; Cholesterol/metabolism/analysis ; Gallbladder/microbiology/pathology/chemistry/metabolism ; Microbiota ; Metaplasia/pathology ; }, abstract = {BACKGROUND: India has a high incidence of gallstones, which can cause chronic inflammation and increase the risk of gallbladder cancer. Understanding the age and composition of gallstones can provide insights into their formation and growth. This study used radiocarbon dating ([14]C dating), Fourier transform infrared (FTIR) spectroscopy, and metagenome analysis to explore the natural history, deposition rate, and microbial/chemical composition of gallstones.

METHODS: In this pilot study, 3 cholesterol gallstones were chosen with different tissue histopathologies (normal, metaplasia, and dysplasia), and respective layers were analyzed for [14]C bomb-pulse dating and FTIR for age and chemical composition, respectively. The core of each gallstone was subjected to scanning electron microscopy and further to 16S rRNA sequencing for microbial analysis.

RESULTS: The [14]C data indicated that the largest stone with dysplastic epithelium formed over 6 years, whereas stones with metaplasia and normal pathology took 13 and 12 years to develop, respectively. Furthermore, the largest stone was dormant for 6 years before the individual experienced acute pain, whereas the other 2 stones laid dormant for 7 and 18 years. FTIR analysis revealed that all 3 gallstones were primarily composed of cholesterol. In addition, calcium oxalate, calcium carbonate, and calcium bilirubinate were present in stones with underlying dysplasia. The 16S rRNA analysis revealed an increased abundance of Corynebacterium sp. in stones associated with metaplasia and dysplasia. Moreover, pathogenic Klebsiella and Escherichia coli species were abundant in calcium oxalate-rich gallstones with underlying dysplasia.

CONCLUSION: Overall, the pilot study established the feasibility of [14]C bomb pulse for evaluating the timeline of gallstone formation. In addition, [14]C dating combined with FTIR/metagenome analysis helped in understanding the natural history of gallstone-associated disease.}, } @article {pmid38594229, year = {2025}, author = {Yang, C and Hu, J and Su, Q and Zhang, Z and Du, Y and Wang, J and Sun, H and Han, B and Tang, J and Guo, L and Li, H and Cai, W and Zheng, H and Zhou, X and Zhang, X}, title = {A review on recent taxonomic updates of gut bacteria associated with social bees, with a curated genomic reference database.}, journal = {Insect science}, volume = {32}, number = {1}, pages = {2-23}, doi = {10.1111/1744-7917.13365}, pmid = {38594229}, issn = {1744-7917}, support = {//2115 Talent Development Program of China Agricultural University grants/ ; 32000346//National Natural Science Foundation of China/ ; 32370550//National Natural Science Foundation of China/ ; SYND-2021-30//Sanya Institute of China Agricultural University/ ; }, mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification ; Genome, Bacterial ; Databases, Genetic ; Phylogeny ; }, abstract = {Honeybees and bumblebees play a crucial role as essential pollinators. The special gut microbiome of social bees is a key factor in determining the overall fitness and health of the host. Although bees harbor relatively simple microbial communities at the genus level, recent studies have unveiled significant genetic divergence and variations in gene content within each bacterial genus. However, a comprehensive and refined genomics-based taxonomic database specific to social bee gut microbiomes remains lacking. Here, we first provided an overview of the current knowledge on the distribution and function of social bee gut bacteria, as well as the factors that influence the gut population dynamics. We then consolidated all available genomes of the gut bacteria of social bees and refined the species-level taxonomy, by constructing a maximum-likelihood core genome phylogeny and calculating genome-wide pairwise average nucleotide identity. On the basis of the refined species taxonomy, we constructed a curated genomic reference database, named the bee gut microbe genome sequence database (BGM-GDb). To evaluate the species-profiling performance of the curated BGM-GDb, we retrieved a series of bee gut metagenomic data and inferred the species-level composition using metagenomic intra-species diversity analysis system (MIDAS), and then compared the results with those obtained from a prebuilt MIDAS database. We found that compared with the default database, the BGM-GDb excelled in aligned read counts and bacterial richness. Overall, this high-resolution and precise genomic reference database will facilitate research in understanding the gut community structure of social bees.}, } @article {pmid39933522, year = {2025}, author = {Xu, CCY and Fugère, V and Barbosa da Costa, N and Beisner, BE and Bell, G and Cristescu, ME and Fussmann, GF and Gonzalez, A and Shapiro, BJ and Barrett, RDH}, title = {Pre-exposure to stress reduces loss of community and genetic diversity following severe environmental disturbance.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2025.01.037}, pmid = {39933522}, issn = {1879-0445}, abstract = {Environmental stress caused by anthropogenic impacts is increasing worldwide. Understanding the ecological and evolutionary consequences for biodiversity will be crucial for our ability to respond effectively. Historical exposure to environmental stress is expected to select for resistant species, shifting community composition toward more stress-tolerant taxa. Concurrent with this species sorting process, genotypes within resistant taxa that have the highest relative fitness under severe stress are expected to increase in frequency, leading to evolutionary adaptation. However, empirical demonstrations of these dual ecological and evolutionary processes in natural communities are rare. Here, we provide evidence for simultaneous species sorting and evolutionary adaptation across multiple species within a natural freshwater bacterial community. Using a two-phase stressor experimental design (acidification pre-exposure followed by severe acidification) in aquatic mesocosms, we show that pre-exposed communities were more resistant than naive communities to taxonomic loss when faced with severe acid stress. However, after sustained severe acidification, taxonomic richness of both pre-exposed and naive communities eventually converged. All communities experiencing severe acidification became dominated by an acidophilic bacterium, Acidiphilium rubrum, but this species retained greater genetic diversity and followed distinct evolutionary trajectories in pre-exposed relative to naive communities. These patterns were shared across other acidophilic species, providing repeated evidence for the impact of pre-exposure on evolutionary outcomes despite the convergence of community profiles. Our results underscore the need to consider both ecological and evolutionary processes to accurately predict the responses of natural communities to environmental change.}, } @article {pmid39932999, year = {2025}, author = {Tepekule, B and Barcik, W and Staiger, WI and Bergadà-Pijuan, J and Scheier, T and Brülisauer, L and Hall, AR and Günthard, HF and Hilty, M and Kouyos, RD and Brugger, SD}, title = {Computational and in vitro evaluation of probiotic treatments for nasal Staphylococcus aureus decolonization.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {7}, pages = {e2412742122}, doi = {10.1073/pnas.2412742122}, pmid = {39932999}, issn = {1091-6490}, support = {1449 M//Promedica Stiftung/ ; GRS-09420//Gebert Rüf Stiftung (Gebert Rüf Foundation)/ ; GRS-09420//Gebert Rüf Stiftung (Gebert Rüf Foundation)/ ; BSSGI0_155851//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; K-84804 - 01 - 01//UZH | Foundation for Research in Science and the Humanities (Stiftung für wissenschaftliche Forschung)/ ; }, mesh = {*Probiotics/administration & dosage/pharmacology ; *Staphylococcus aureus/drug effects ; Humans ; *Staphylococcal Infections/microbiology/drug therapy ; *RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology ; Microbiota/drug effects ; Nose/microbiology ; Computer Simulation ; Adult ; }, abstract = {Despite the rising challenge of antibiotic resistance, current approaches to eradicate nasal pathobionts Staphylococcus aureus and Streptococcus pneumoniae rely on antibacterials. An alternative is the artificial inoculation of commensal bacteria, i.e., probiotic treatment, supported by the increasing evidence for commensal-mediated inhibition of pathogens. To systematically investigate the potential of this approach, we developed a quantitative framework simulating the nasal microbiome dynamics by combining mathematical modeling with longitudinal microbiota data. By inferring community parameters using 16S ribosomal RNA (rRNA) amplicon sequencing data and simulating the nasal microbial dynamics of patients colonized with S. aureus, we compared the decolonization performance of probiotic and antibiotic treatments under different assumptions on patients' community composition and susceptibility profile. To further compare the robustness of these treatments, we simulated an S. aureus challenge and quantified the recolonization probability. Through in vitro experiments using nasal swabs of adults colonized with S. aureus, we confirmed that after antibiotic treatment, recolonization of S. aureus was inhibited in samples treated with a probiotic mixture compared to the nontreated control. Our results suggest that probiotic treatment outperforms antibiotics in terms of decolonization performance, recolonization robustness, and leads to less collateral reduction in the microbiome diversity. Thus, probiotic treatment may provide a promising alternative to combat antibiotic resistance, with the additional advantage of personalized treatment options via using the patient's own metagenomic data. The combination of an in silico framework with in vitro experiments using clinical samples reported in this work is an important step forward to further investigate this alternative in clinical trials.}, } @article {pmid39864165, year = {2025}, author = {Wang, XP and Han, NN and Yang, JH and Fan, NS and Jin, RC}, title = {Metagenomic insight into the diffusion signal factor mediated social traits of anammox consortia after starvation.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124270}, doi = {10.1016/j.jenvman.2025.124270}, pmid = {39864165}, issn = {1095-8630}, mesh = {*Oxidation-Reduction ; Quorum Sensing ; Ammonium Compounds/metabolism ; Anaerobiosis ; Metagenomics ; Nitrogen/metabolism ; Microbial Consortia ; Wastewater/microbiology ; Geobacter/metabolism ; Bacteria/metabolism ; }, abstract = {Biomass starvation is common in biological wastewater treatment. As a social trait of microbial community, how quorum sensing (QS) regulated bacterial trade-off through interactions after starvation remains unclear. This study deciphered the mechanism of anaerobic ammonium oxidation (anammox) consortia in response to starvation, including reducing extracellular electron transfer (EET), adenosine 5'-triphosphate (ATP) content and amino acid metabolism. Metagenomic analysis has shown that the addition of the diffusion signal factor (DSF) resulted in a high abundance of antioxidant genes, which contributed to achieving redox balance in anammox bacteria. There was an enrichment of Geobacter and Methanosarcina, which were QS-responsive direct interspecific electron transfer participants. Furthermore, DSF stimulated the nitrogen and carbon metabolism of Ca. Kuenenia_stuttgartiensis, promoting syntrophy of metabolic intermediates within microbial community. This study highlighted the effect of DSF on the microbial interaction patterns and deciphered the QS-based social traits of anammox consortia after starvation, facilitating the stable operation of the anammox process.}, } @article {pmid39671837, year = {2025}, author = {Li, S and Zhen, Y and Chen, Y and Mi, T}, title = {Geochemical and microbial controls on methane distribution in coastal sediments: A case study from the Bohai and South Yellow Seas, China.}, journal = {Marine pollution bulletin}, volume = {211}, number = {}, pages = {117448}, doi = {10.1016/j.marpolbul.2024.117448}, pmid = {39671837}, issn = {1879-3363}, mesh = {*Geologic Sediments/chemistry/microbiology ; *Methane/analysis ; China ; *Oceans and Seas ; Environmental Monitoring ; Microbiota ; Seasons ; }, abstract = {CH4 is among the most potent greenhouse gases. In this study, we investigated one of the important CH4 production hotspots, the continental margins. We examined the spatiotemporal distributions of CH4 in sediment cores from the Bohai and South Yellow Seas, China. Using real-time PCR and metagenomic sequencing, we analyzed the microbial communities related to CH4 production. Our results indicated that concentrations of CH4 generally increased with depth gradually, minimal seasonal variation observed between spring and summer. Notably, spatial heterogeneity, rather than temporal variation, was the predominant factor affecting CH4 distribution and methanogen community differences in sediments. Furthermore, the structure of microbial communities, in conjunction with environmental factors, significantly impacts potential CH4 production. These findings provide valuable insights into the mechanisms underlying methane production and its environmental controls in marine sediments.}, } @article {pmid39623774, year = {2025}, author = {Hu, Y and Wang, ML and Yang, RL and Shao, ZK and Du, YH and Kang, Y and Zhu, YX and Xue, XF}, title = {Symbiotic bacteria play crucial roles in a herbivorous mite host suitability.}, journal = {Pest management science}, volume = {81}, number = {3}, pages = {1657-1668}, doi = {10.1002/ps.8571}, pmid = {39623774}, issn = {1526-4998}, support = {//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Symbiosis ; *Herbivory ; *Solanum lycopersicum/microbiology ; *Mites/physiology/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Solanum melongena/microbiology ; Capsicum/microbiology ; Bacterial Physiological Phenomena ; Microbiota ; }, abstract = {BACKGROUND: The tomato russet mite (TRM), Aculops lycopersici, is a strictly herbivorous and economically significant pest that infests Solanaceae plants, but its host suitability varies, showing high performance on tomatoes. Although symbiotic bacteria have been suggested to play crucial roles in the host adaptation of herbivores, their effects on TRM remain unclear.

RESULTS: In this study, using next generation high-throughput sequencing of the bacterial 16S rRNA data, we identified the bacterial diversity and community composition of TRM feeding on tomato, eggplant, and chili. Our results show no significant difference in the bacterial community composition of TRM across three host plants. However, the relative density of Escherichia coli (TRM_Escherichia) showed 9.36-fold higher on tomato than on eggplant and chili. These results align with the observed TRM performance among three host plants. When TRM_Escherichia was reduced using antibiotics, the treated TRM decreased the population density on tomato. However, when we transferred TRM from eggplant to tomato, the population density of TRM increased, coinciding with an increase of the TRM_Escherichia density. These results indicate that TRM_Escherichia may affect the host suitability of TRM. Our fluorescence in situ hybridization (FISH) results further showed that TRM_Escherichia is primarily distributed in the salivary glands. Metagenomic data results suggest that TRM_Escherichia functions in food digestion and energy metabolism.

CONCLUSION: We provided the first comprehensive analysis of TRM bacterial communities. Our findings demonstrate that the symbiotic bacterium TRM_Escherichia may play crucial roles in the suitability of TRM feeding on different Solanaceae hosts. © 2024 Society of Chemical Industry.}, } @article {pmid39932299, year = {2025}, author = {Cui, H and Wang, S and Fan, S and Long, H and Lin, J and Ding, W and Zhang, W}, title = {Branched-chain amino acid metabolism supports Roseobacteraceae positive interactions in marine biofilms.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0241124}, doi = {10.1128/aem.02411-24}, pmid = {39932299}, issn = {1098-5336}, abstract = {UNLABELLED: Interspecies interactions are key factors affecting the stability of microbial communities. However, microbial interactions in marine biofilms, which constitute up to 80% of the microbial biomass in certain marine environments, are not well understood. We addressed this knowledge gap by coculturing four marine biofilm-derived Roseobacteraceae strains (Leisingera aquaemixtae M597, Roseibium aggregatum S1616, Alloyangia pacifica T6124, and Sulfitobacter indolifex W002) in 14 single carbon sources. Overall, 140 coculture experiments revealed 39.3% positive interactions compared to 8.3% negative interactions. When the carbon source was consumed by only one strain, the interaction between the strains was more likely to be positive. The interaction between S1616 and M597, when cultured in D-gluconic acid, was further studied as an example. S1616-M597 coculture displayed a higher D-gluconic acid consumption rate than S1616 monoculture, whereas M597 could not use D-gluconic acid as the sole carbon source. The supernatant of S1616 monoculture supported the growth of M597, and branched-chain amino acids in the supernatant were consumed. Transcriptomic analysis suggested that M597 induced the expression of genes for branched-chain amino acid biosynthesis in S1616. Additionally, metagenomic analysis revealed the wide distribution and a strongly correlated co-occurrence of the four strains in global oceanic biofilms. Together, our findings show that interspecies positive interactions are prevalent among marine-biofilm Roseobacteraceae, and the interactions are likely to be mediated by branched-chain amino acids metabolism.

IMPORTANCE: Interspecies interactions are crucial for microbial community structure and function. Despite well-studied social behaviors in model microorganisms, species interactions in natural marine biofilms especially Roseobacteraceae with complex metabolic pathways are not well understood. Our findings suggest that positive microbial interactions, which can be mediated by branched-chain amino acid biosynthesis, are common among marine-biofilm Roseobacteraceae. This study provides new insights into microbial interactions and the ecology of marine biofilms.}, } @article {pmid39930446, year = {2025}, author = {Dong, L and Ji, Z and Hu, J and Jiang, Q and Wei, W}, title = {Oral microbiota shifts following tooth loss affect gut health.}, journal = {BMC oral health}, volume = {25}, number = {1}, pages = {213}, pmid = {39930446}, issn = {1472-6831}, support = {YSP202314//Young Scientist Program of Beijing Stomatological Hospital, Capital Medical University/ ; }, mesh = {Animals ; *Tooth Loss/microbiology ; Mice ; *Gastrointestinal Microbiome ; *Mice, Inbred C57BL ; RNA, Ribosomal, 16S ; Saliva/microbiology ; Feces/microbiology ; Microbiota ; Mouth/microbiology ; Male ; }, abstract = {BACKGROUND: Tooth loss not only impairs oral function but also affects gut health by altering the host microbiota. Understanding the oral-gut axis can provide insights into systemic health implications following tooth loss.

METHODS: Using an animal model, we extracted the molars of C57 mice. Saliva and fecal samples were collected for 16S rRNA and metagenomic sequencing to analyze changes in the oral and gut microbiota. Pearson correlation analysis assessed the relationship between altered microbial communities.

RESULTS: The study found a significant reduction in oral microbiota diversity following tooth loss, with increased Proteobacteria and decreased Muribacter. Gut microbiota showed increased Firmicutes and decreased Bacteroidota. Correlations between oral and gut microbiota changes were observed, indicating a potential link between tooth loss and alterations in intestinal microbial balance.

CONCLUSION: In the mouse model, tooth loss disrupted the balance of the oral-gut microbiota, with potential implications for intestinal health. Although these findings are from a murine model, considering the existence of the oral-gut axis balance in the human body, it is reasonable to postulate that following tooth loss in humans, the health of the intestinal microecology may also warrant attention.}, } @article {pmid39927333, year = {2024}, author = {Safika, S and Indrawati, A and Hidayat, R and Puarada, ARR}, title = {Characterizing the gut microbiome of birds-of-paradise in the northwest lowland of Papua Island.}, journal = {Open veterinary journal}, volume = {14}, number = {12}, pages = {3345-3354}, pmid = {39927333}, issn = {2218-6050}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteria/isolation & purification/classification/genetics ; Indonesia ; Feces/microbiology ; Passeriformes/microbiology ; }, abstract = {BACKGROUND: Birds-of-paradise, renowned for their stunning plumage and intricate mating rituals, have been extensively studied for their external characteristics. However, the microbial communities inhabiting their digestive tracts remain largely unexplored. The gut microbiome plays a vital role in host health and physiology, influencing digestion, nutrient absorption, and immune function. Understanding the microbiome of birds-of-paradise, particularly in their unique tropical rainforest habitats, may offer valuable insights into their adaptation and overall health.

AIM: This study aims to characterize the gut microbiome of birds-of-paradise and to explore the relationship between microbiome and host.

METHODS: Fecal samples were collected from Jayapura Regency, Indonesia, with non-invasive sampling methods. DNA was extracted using the DNeasy PowerSoil Pro Kit. Shotgun metagenomic sequencing was performed on the MGI DNBSEQ-G400 platform to obtain DNA sequences. DNA sequences were analyzed using DIAMOND followed by MEGAN6 to provide insights into the relative abundance of bacterial taxa within the microbiome.

RESULTS: Using Operational Taxonomy Unit analysis we identified 1,398,117 sequences from 5,048,280 initial sequences. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria were the dominant phyla, with other phyla present in smaller amounts. Burkholderiales, Hyphomicrobiales, Sphingobacteriales, and Enterobacterales were dominant orders, each with specific functional roles. Family and Genus-Level Abundance: Flavobacteriaceae, Comamonadaceae, and Sphingobacteriaceae were dominant families, while Flavobacterium, Delftia, and Pedobacter were dominant genera. Delftia sp., Pedobacter sp., Klebsiella pneumoniae, Achromobacter sp., Bacillus pumilus, Rhizobium sp., and Brevundimonas sp. were among the most abundant species.

CONCLUSION: The microbiome in the gut of birds-of-paradise is characterized by a diverse community of bacteria, fungi, and other microorganisms. The abundance of specific orders, families, and genera varies between samples, suggesting that differences in diet, habitat, or host genetics may influence microbiome composition. The findings reveal a diverse and complex microbial community that likely plays a crucial role in host health and physiology.}, } @article {pmid39925879, year = {2025}, author = {Gao, Y and Qin, G and Liang, S and Yin, J and Wang, B and Jiang, H and Liu, M and Luo, F and Li, X}, title = {Metagenomic Sequencing Combined with Metabolomics to Explore Gut Microbiota and Metabolic Changes in Mice with Acute Myocardial Infarction and the Potential Mechanism of Allicin.}, journal = {Drug design, development and therapy}, volume = {19}, number = {}, pages = {771-791}, pmid = {39925879}, issn = {1177-8881}, mesh = {Animals ; *Disulfides ; *Gastrointestinal Microbiome/drug effects ; *Sulfinic Acids/pharmacology/administration & dosage ; Mice ; *Myocardial Infarction/drug therapy/metabolism ; Male ; *Metabolomics ; Metagenomics ; Mice, Inbred C57BL ; Administration, Oral ; Disease Models, Animal ; }, abstract = {BACKGROUND: Acute myocardial infarction (AMI) is a significant contributor to global morbidity and mortality. Allicin exhibits promising therapeutic potential in AMI as a primary bioactive component derived from garlic; however, its underlying mechanisms remain incompletely elucidated.

METHODS: Our study induced AMI in mice by ligating the left coronary artery, and administered allicin orally for 28 days. The cardioprotective effects of allicin treatment were comprehensively assessed using echocardiography, histopathological examinations, intestinal barrier function, and serum inflammatory factors. The potential mechanisms of allicin were elucidated through analysis of metagenomics and serum metabolomics. Network pharmacology (NP) was used to further investigate and validate the possible molecular mechanisms of allicin.

RESULTS: Our findings revealed allicin's capacity to ameliorate cardiac impairments, improve intestinal barrier integrity, and reduce serum IL-18 and IL-1β levels after AMI. Further analysis demonstrated that the administration of allicin has the potential to ameliorate intestinal flora disorder following AMI by modulating the abundance of beneficial bacteria, such as g_Lactobacillus, g_Prevotella, g_Alistipes, and g_Limosilactobacillus, while reducing the abundance of harmful bacteria g_Parasutterella. Additionally, it exhibits the ability to enhance myocardial energy metabolism flexibility through modulating metabolites and key enzymes associated with the fatty acid metabolic pathway. Mechanistically, NP and in vivo experiments indicated that allicin might suppress pyroptosis and reduce inflammatory response via blocked activation of the NF-κB-mediated NLRP3/Caspase-1/GSDMD pathway. Moreover, Spearman correlation analysis suggested a significant association between the allicin-induced alterations in microbiota and metabolites with cardiac function and inflammatory cytokines.

CONCLUSION: Our study demonstrated that allicin alleviated myocardial injury and reduced inflammatory response by inhibiting the NF-κB-mediated NLRP3/Caspase-1/GSDMD pathway while remodeling microbiota disturbance, improving serum metabolic disorder, and enhancing the intestinal barrier. These research findings offer a novel perspective on the potential therapeutic value of allicin as an adjunctive dietary supplement to conventional treatments for AMI.}, } @article {pmid39743194, year = {2025}, author = {Ye, G and Chen, G and Avellán-Llaguno, RD and Cao, Y and Huang, Q}, title = {Distinctive gut antibiotic resistome, potential health risks and underlying pathways upon cerebral ischemia-reperfusion injury.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {367}, number = {}, pages = {125614}, doi = {10.1016/j.envpol.2024.125614}, pmid = {39743194}, issn = {1873-6424}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Anti-Bacterial Agents/pharmacology ; *Reperfusion Injury ; Drug Resistance, Microbial/genetics ; Brain Ischemia ; Metagenomics ; Humans ; }, abstract = {Antibiotic resistance genes (ARGs) as emerging pollutants pose health risks to humans and the environment. Gut microbiota is an important reservoir for ARGs and hotspot for ARG acquisition and dissemination. Non-antibiotic factors (such as disease pathophysiology) affect ARG emergence and dissemination. Cerebral ischemia-reperfusion injury (I/R) commonly occurs in stroke patients. However, effects of I/R on ARG emergence and dissemination are unknown. Therefore, metagenomics was used to unveil selective collection of gut antibiotic resistome and its health risks, key ARG hosts and underlying pathways upon I/R. Changes in gut antibiotic resistome upon I/R were characterized by tetracycline ARG accumulation and decreases in aminoglycoside and glycopeptide ARGs. Besides, changes in gut antibiotic resistome were corrected with those in gut microbiota from phylum to species, serum lipid accumulation and glucose depletion upon I/R. Additionally, health risks of gut microbial multidrug ARGs (such as abem, adek and TolC), macA, aph(3')-I and carO, co-localized with mobile gene elements, were increased upon I/R. Moreover, phyla Firmicutes (especially order Eubacteriales, class Clostridia) and Bacteroidota were key ARG hosts in gut microbiota of I/R gerbils. Furthermore, suppression of vancomycin resistance, and lantibiotic biosynthesis and immunity, disturbances in peptidoglycan biosynthesis and hydrolysis, activation of antimicrobial peptide resistance, lipopolysaccharide biosynthesis, teichoic acid biosynthesis, arabinogalactan biosynthesis, aromatic compound degradation, oxidative phosphorylation, the tricarboxylic acid cycle and its anaplerotic pathways were observed in upon I/R. This study provides novel insights and intervention targets related to selective collection of gut antibiotic resistome and its potential health risks upon I/R.}, } @article {pmid39561782, year = {2024}, author = {Lee, D and Ahn, K and Yun, K and Oh, Y and Park, YS and Kim, YS and Gim, JA and Mun, S and Mun, JW and Han, K and Ahn, YJ}, title = {Aerobic bacterial group as an early-stage biomarker from faecal samples of patients with colorectal cancer without distant metastasis.}, journal = {Beneficial microbes}, volume = {16}, number = {2}, pages = {201-219}, doi = {10.1163/18762891-bja00051}, pmid = {39561782}, issn = {1876-2891}, mesh = {Humans ; *Colorectal Neoplasms/pathology/microbiology/diagnosis ; *Feces/microbiology ; *RNA, Ribosomal, 16S/genetics ; Male ; *Gastrointestinal Microbiome/genetics ; Female ; Middle Aged ; *Biomarkers, Tumor/genetics ; Aged ; Early Detection of Cancer/methods ; Adult ; Metagenomics ; }, abstract = {The current approaches for detecting most colorectal polyps and early neoplasms lack sufficient sensitivity and specificity, potentially hindering treatment and ultimately reducing survival rates. Here, we performed a metagenomic analysis to identify microbiome markers in stool samples from patients with early-stage colorectal cancer (CRC). We compared the composition of gut microbiota between patients with CRC and healthy individuals, specifically focusing on patients with early-stage CRC, defined as those without core mutations (KRAS, BRAF) for CRC diagnosis, stable microsatellite instability, and distant metastasis. The aim of our study is to identify potential biomarkers from gut microbiota at different cancer stages in colorectal cancer (CRC) patients through 16S rRNA amplicon sequencing, thereby proposing a novel non-invasive method for the early diagnosis of CRC. Specific microbes were detected from groups divided based on the TNM criteria, with one group classified by tumour size only (named the T group) and another group with lymph node metastasis (named the TN group). Aerobic bacteria, such as Delftia, Stenotrophomonas, Sphingobacterium, Rhodococcus, Devosia, Ensifer, and Psychrobacter were predominantly detected in patients with CRC without lymph node metastasis. The diagnostic prediction was evaluated using the CatBoost algorithm; these microbes presented high diagnostic accuracy with a receiver operating characteristics-area under curve of 0.8, which was validated using qPCR. In conclusion, this study identified specific aerobic microbial groups as non-invasive biomarkers for early diagnosis in patients with CRC without genetic or environmental factors.}, } @article {pmid39924893, year = {2025}, author = {Chen, Y and Fang, H and Chen, H and Liu, X and Zhao, J and Stanton, C and Ross, RP and Chen, W and Yang, B}, title = {Bifidobacterium inhibits the progression of colorectal tumorigenesis in mice through fatty acid isomerization and gut microbiota modulation.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2464945}, doi = {10.1080/19490976.2025.2464945}, pmid = {39924893}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Colorectal Neoplasms/microbiology/metabolism/prevention & control/pathology ; Humans ; *Bifidobacterium/metabolism/physiology ; *Linoleic Acids, Conjugated/metabolism ; Male ; Probiotics/administration & dosage/pharmacology ; Female ; Carcinogenesis ; PPAR gamma/metabolism/genetics ; Fatty Acids/metabolism ; Mice, Inbred C57BL ; NF-kappa B/metabolism ; Middle Aged ; Apoptosis ; Disease Progression ; Butyric Acid/metabolism ; Disease Models, Animal ; }, abstract = {Colorectal cancer (CRC) represents the third most common cancer worldwide. Consequently, there is an urgent need to identify novel preventive and therapeutic strategies for CRC. This study aimed to screen for beneficial bacteria that have a preventive effect on CRC and to elucidate the potential mechanisms. Initially, we compared gut bacteria and bacterial metabolites of healthy volunteers and CRC patients, which demonstrated that intestinal conjugated linoleic acid (CLA), butyric acid, and Bifidobacterium in CRC patients were significantly lower than those in healthy volunteers, and these indicators were significantly negatively correlated with CRC. Next, spontaneous CRC mouse model were conducted to explore the effect of supplemental CLA-producing Bifidobacterium on CRC. Supplementation of mice with CLA-producing Bifidobacterium breve CCFM683 and B. pseudocatenulatum MY40C significantly prevented CRC. Moreover, molecular approaches demonstrated that CLA and the CLA-producing gene, bbi, were the key metabolites and genes for CCFM683 to prevent CRC. Inhibitor intervention results showed that PPAR-γ was the key receptor for preventing CRC. CCFM683 inhibited the NF-κB signaling pathway, up-regulated MUC2, Claudin-1, and ZO-1, and promoted tumor cell apoptosis via the CLA-PPAR-γ axis. Additionally, fecal microbiota transplantation (FMT) and metagenomic analysis showed that CCFM683 up-regulated Odoribacter splanchnicus through CLA production, which then prevented CRC by producing butyric acid, up-regulating TJ proteins, regulating cytokines, and regulating gut microbiota. These results will contribute to the clinical trials of Bifidobacterium and the theoretical research and development of CRC dietary products.}, } @article {pmid39922935, year = {2025}, author = {Das, BK and Gadnayak, A and Chakraborty, HJ and Pradhan, SP and Raut, SS and Das, SK}, title = {Exploring microbial players for metagenomic profiling of carbon cycling bacteria in sundarban mangrove soils.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {4784}, pmid = {39922935}, issn = {2045-2322}, mesh = {*Wetlands ; *Soil Microbiology ; *Metagenomics/methods ; *Bacteria/genetics/metabolism/classification ; *Carbon Cycle ; Carbon/metabolism ; Microbiota/genetics ; Ecosystem ; Metagenome ; Phylogeny ; }, abstract = {The Sundarbans, the world's largest tidal mangrove forest, acts as a crucial ecosystem for production, conservation, and the cycling of carbon and nitrogen. The study explored the hypothesis that microbial communities in mangrove ecosystems exhibit unique taxonomic and functional traits that play a vital part in carbon cycling and ecosystem resilience. Using metagenomic analysis to evaluate microbial communities in mangrove and non-mangrove environment, evaluating their composition, functional functions, and ecological relevance. The analysis revealed distinct microbial profiles, in mangrove and non-mangrove environments, with bacteria, proteobacteria, and viruses being the most prevalent groups, with varying abundances in each environment. Functional and taxonomical analysis identified genes involved in carbon regulation, including Triacylglycerol lipase, NarG, DsrB, DNA-binding transcriptional dual regulator CRP, Vanillate O-demethylase oxygenase, succinate-CoA ligase, Tetrahydrofolate ligase, Carboxylase, Ribulose-1,5-bisphosphate carboxylase/oxygenase, Glycine hydroxymethyltransferase, MAG: urease, Endosymbiont of Oligobrachia haakonmosbiensis, Ribulose bisphosphate carboxylase, Aconitate hydratase AcnA, and nitrous oxide reductase, suggesting the metabolic versatility of these microbial communities for carbon cycling. The findings emphasize the key role of microbial activity in preserving mangrove ecosystem health and resilience, highlighting the intricate interplay between microbial diversity, functional capabilities, and environmental factors.}, } @article {pmid39921224, year = {2025}, author = {Vieira, S and Adão, H and Vicente, CSL}, title = {Assessing spatial and temporal patterns of benthic bacterial communities in response to different sediment conditions.}, journal = {Marine environmental research}, volume = {204}, number = {}, pages = {106963}, doi = {10.1016/j.marenvres.2025.106963}, pmid = {39921224}, issn = {1879-0291}, mesh = {*Geologic Sediments/microbiology ; *Bacteria/classification/genetics ; Portugal ; *Estuaries ; *Ecosystem ; Environmental Monitoring ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Microbiota ; }, abstract = {Benthic bacterial communities are sensitive to habitat condition and present a fast response to environmental stressors, which makes them powerful ecological indicators of estuarine environments. The aim of this work is to study the spatial-temporal patterns of benthic bacterial communities in response to contrasting environmental conditions and assess their potential as ecological indicators of estuarine sediments. We characterized the diversity of bacterial communities in three contrasting sites on Sado Estuary (SW Coast, Portugal) and 4 sampling occasions, using 16S metagenomic approach. Based on previous studies, we hypothesized that diversity patterns of bacterial communities will be distinct between sites and across sampling occasions. Bacterial communities were more influenced by each site conditions than by temporal variations in the sediments. The main drivers of bacterial distribution were sediments' composition, organic contents, and hydrodynamic activity. This work provided an important baseline dataset from Sado estuary to explore bacterial networks concerning benthic ecosystem functioning.}, } @article {pmid39694116, year = {2025}, author = {Zhong, S and Yang, YN and Huo, JX and Sun, YQ and Zhao, H and Dong, XT and Feng, JY and Zhao, J and Wu, CM and Li, YG}, title = {Cyanidin-3-rutinoside from Mori Fructus ameliorates dyslipidemia via modulating gut microbiota and lipid metabolism pathway.}, journal = {The Journal of nutritional biochemistry}, volume = {137}, number = {}, pages = {109834}, doi = {10.1016/j.jnutbio.2024.109834}, pmid = {39694116}, issn = {1873-4847}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Lipid Metabolism/drug effects ; *Anthocyanins/pharmacology ; Male ; *Dyslipidemias/drug therapy/metabolism ; *Mice, Inbred C57BL ; Morus/chemistry ; Mice ; Diet, High-Fat/adverse effects ; Fruit/chemistry ; Liver/metabolism/drug effects ; }, abstract = {Dyslipidemia is responsible for pathologies of cardiovascular diseases and gut microbiota plays an essential role in lipid metabolism. Dietary supplementation is an important supplement to medicine in management of dyslipidemia. Mori Fructus is a popular Asia medical food with various pharmacological benefits including anti-hyperlipidemia. Cyanidin-3-rutinoside (C3R) is the main anthocyanin component in Mori Fructus, but the lipid-lowering effect and underlying mechanism of Mori Fructus-derived C3R remains unknown. In this study, we assessed the beneficial effect of Mori Fructus-derived C3R in HFD-induced hyperlipidemic mice and investigated its potential mechanism through 16S rRNA-based metagenomics and transcriptomics analysis. Our results showed that C3R from Mori Fructus significantly decreased serum lipid levels and attenuated hepatic damage induced by HFD. Analysis of the gut microbiota revealed that C3R altered the specific gut micorbiota but not changed its diversity. Among changed genera, Family_XIII_UCG-001 was significantly enriched by C3R, and it was positively associated with HDL-c, but negatively related with TC, TG, LDL-c, insulin and body weight. Transcriptomic analysis showed that C3R activates the lipid metabolism related pathways including MAPK signaling pathway, Rap1 signaling pathway, Ras signaling pathway and PI3K-Akt signaling pathway. Additionally, correlation analysis unraveled that C3R-enriched Family_XIII_UCG-001 was negatively associated with C3R-inhibited genes of Camk2a, Eef1a2, Gad1, Kif5a and Sv2b, which further positively related with TC, TG, LDL-c, insulin and body weight, but negatively associated with HDL-c. In sum, C3R may inhibit expression of immune-related genes by enriching the Family_XIII_UCG-001 genus, further ameliorating lipid metabolism disorders in HFD-challenged mice. This study provides an optional strategy for the daily management of dyslipidemia.}, } @article {pmid39692191, year = {2025}, author = {Zou, X and Yan, M and Wang, Y and Ni, Y and Zhao, J and Lu, B and Liu, B and Cao, B}, title = {Accurate Diagnosis of Lower Respiratory Infections Using Host Response and Respiratory Microbiome from a Single Metatranscriptome Test of Bronchoalveolar Lavage Fluid.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {12}, number = {6}, pages = {e2405087}, doi = {10.1002/advs.202405087}, pmid = {39692191}, issn = {2198-3844}, support = {2022YFA1304300//National Key R&D Program of China grant/ ; ZRJY2023-GG24//China-Japan Friendship Hospital elite program grant/ ; }, mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; Female ; Male ; *Respiratory Tract Infections/microbiology/diagnosis ; *Microbiota/genetics ; Middle Aged ; Retrospective Studies ; Aged ; Adult ; Transcriptome/genetics ; Gene Expression Profiling/methods ; }, abstract = {Lower respiratory tract infections (LRTIs) diagnosis is challenging because noninfectious diseases mimic its clinical features. The altered host response and respiratory microbiome following LRTIs have the potential to differentiate LRTIs from noninfectious respiratory diseases (non-LRTIs). Patients suspected of having LRTIs are retrospectively enrolled and a clinical metatranscriptome test is performed on bronchoalveolar lavage fluid (BALF). Transcriptomic and metagenomic analysis profiled the host response and respiratory microbiome in patients with confirmed LRTI (n = 126) or non-LRTIs (n = 75). Patients with evidenced LRTIs exhibited enhanced pathways on chemokine and cytokine response, neutrophile recruitment and activation, along with specific gene modules linked to LRTIs status and key blood markers. Moreover, LRTIs patients exhibited reduced diversity and evenness in the lower respiratory microbiome, likely driven by an increased abundance of bacterial pathogens. Host marker genes are selected, and classifiers are developed to distinguish patients with LRTIs, non-LRTIs, and indeterminate status, achieving an area under the receiver operating characteristic curve of 0.80 to 0.86 and validated in a subsequently enrolled cohort. Incorporating respiratory microbiome features further enhanced the classifier's performance. In summary, a single metatranscriptome test of BALF proved detailed profiles of host response and respiratory microbiome, enabling accurate LRTIs diagnosis.}, } @article {pmid39150994, year = {2025}, author = {Malham, M and Vestergaard, MV and Bataillon, T and Villesen, P and Dempfle, A and Bang, C and Engsbro, AL and Jakobsen, C and Franke, A and Wewer, V and Thingholm, LB and Petersen, AM}, title = {The Composition of the Fecal and Mucosa-adherent Microbiota Varies Based on Age and Disease Activity in Ulcerative Colitis.}, journal = {Inflammatory bowel diseases}, volume = {31}, number = {2}, pages = {501-513}, doi = {10.1093/ibd/izae179}, pmid = {39150994}, issn = {1536-4844}, support = {//Aage and Johann Louis-Hansens Foundation/ ; //Aase and Ejnar Danielsens Foundation/ ; //German Research Foundation/ ; }, mesh = {Humans ; *Colitis, Ulcerative/microbiology ; *Feces/microbiology ; Prospective Studies ; Female ; Male ; Adult ; Longitudinal Studies ; *Gastrointestinal Microbiome ; Child ; Adolescent ; *Intestinal Mucosa/microbiology/pathology ; *RNA, Ribosomal, 16S/analysis/genetics ; Young Adult ; Middle Aged ; Age Factors ; }, abstract = {BACKGROUND: Pediatric-onset ulcerative colitis (pUC) represents a more aggressive disease phenotype compared with adult-onset UC. We hypothesized that this difference can, in part, be explained by the composition of the microbiota.

METHODS: In a prospective, longitudinal study, we included pediatric (N = 30) and adult (N = 30) patients with newly or previously (>1 year) diagnosed UC. We analyzed the microbiota composition in the mucosa-adherent microbiota at baseline, using 16S rRNA gene sequencing, and the fecal microbiota at baseline and at 3-month intervals, using shotgun metagenomics.

RESULTS: For fecal samples, the bacterial composition differed between pUC and aUC in newly diagnosed patients (β-diversity, Bray Curtis: R2 = 0.08, P = .02). In colon biopsies, microbial diversity was higher in aUC compared with pUC (α-diversity, Shannon: estimated difference 0.54, P = .006). In the mucosa-adherent microbiota, Alistipes finegoldii was negatively associated with disease activity in pUC while being positively associated in aUC (estimate: -0.255 and 0.098, P = .003 and P = .02 in pUC and aUC, respectively). Finally, we showed reduced stability of the fecal microbiota in pediatric patients, evidenced by a different composition of the fecal microbiota in newly and previously diagnosed pUC, a pattern not found in adults.

CONCLUSIONS: Our results indicate that pediatric UC patients have a more unstable fecal microbiota and a lower α diversity than adult patients and that the microbiota composition differs between aUC and pUC patients. These findings offer some explanation for the observed differences between pUC and aUC and indicate that individualized approaches are needed if microbiota modifications are to be used in the future treatment of UC.}, } @article {pmid39920864, year = {2025}, author = {Kennedy, EA and Weagley, JS and Kim, AH and Antia, A and DeVeaux, AL and Baldridge, MT}, title = {Bacterial community assembly of specific pathogen-free neonatal mice.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {46}, pmid = {39920864}, issn = {2049-2618}, support = {DGE-1745038//National Science Foundation/ ; F31AI167499/NH/NIH HHS/United States ; T32AI007172/NH/NIH HHS/United States ; T32AI007163/NH/NIH HHS/United States ; R01AI139314/NH/NIH HHS/United States ; 1065897//Crohn's and Colitis Foundation/ ; }, mesh = {Animals ; Mice ; *Feces/microbiology ; *Animals, Newborn/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Female ; Specific Pathogen-Free Organisms ; *Mice, Inbred C57BL ; *Mice, Inbred BALB C ; Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Microbiota ; }, abstract = {BACKGROUND: Neonatal mice are frequently used to model diseases that affect human infants. Microbial community composition has been shown to impact disease progression in these models. Despite this, the maturation of the early-life murine microbiome has not been well-characterized. We address this gap by characterizing the assembly of the bacterial microbiota of C57BL/6 and BALB/c litters from birth to adulthood across multiple independent litters.

RESULTS: The fecal microbiome of young pups is dominated by only a few pioneering bacterial taxa. These taxa are present at low levels in the microbiota of multiple maternal body sites, precluding a clear identification of maternal source. The pup microbiota begins diversifying after 14 days, coinciding with the beginning of coprophagy and the consumption of solid foods. Pup stool bacterial community composition and diversity are not significantly different from dams from day 21 onwards. Short-read shotgun sequencing-based metagenomic profiling of young pups enabled the assembly of metagenome-assembled genomes for strain-level analysis of these pioneer Ligilactobacillus, Streptococcus, and Proteus species.

CONCLUSIONS: Assembly of the murine microbiome occurs over the first weeks of postnatal life and is largely complete by day 21. This detailed view of bacterial community development across multiple commonly employed mouse strains informs experimental design, allowing researchers to better target interventions before, during, or after the maturation of the bacterial microbiota. The source of pioneer bacterial strains appears heterogeneous, as the most abundant taxa identified in young pup stool were found at low levels across multiple maternal body sites, suggesting diverse routes for seeding of the murine microbiome. Video Abstract.}, } @article {pmid39742816, year = {2025}, author = {Li, L and Nielsen, J and Chen, Y}, title = {Personalized gut microbial community modeling by leveraging genome-scale metabolic models and metagenomics.}, journal = {Current opinion in biotechnology}, volume = {91}, number = {}, pages = {103248}, doi = {10.1016/j.copbio.2024.103248}, pmid = {39742816}, issn = {1879-0429}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Precision Medicine/methods ; *Metagenomics/methods ; Models, Biological ; }, abstract = {The impact of the gut microbiome on human health is increasingly recognized as dysbiosis has been found to be associated with a spectrum of diseases. Here, we review the databases of genome-scale metabolic models (GEMs), which have paved the way for investigations into the metabolic capabilities of gut microbes and their interspecies dynamics. We further discuss the strategies for developing community-level GEMs, which are crucial for understanding the complex interactions within microbial communities and between the microbiome and its host. Such GEMs can guide the design of synthetic microbial communities for disease treatment. Finally, we explore advances in personalized gut microbiome modeling. These advancements broaden our mechanistic understanding and hold promise for applications in precision medicine and therapeutic interventions.}, } @article {pmid39643107, year = {2025}, author = {Khedpande, N and Barve, K}, title = {Role of gut dysbiosis in drug-resistant epilepsy: Pathogenesis and available therapeutic strategies.}, journal = {Brain research}, volume = {1850}, number = {}, pages = {149385}, doi = {10.1016/j.brainres.2024.149385}, pmid = {39643107}, issn = {1872-6240}, mesh = {Humans ; *Dysbiosis ; *Gastrointestinal Microbiome/physiology/drug effects ; *Drug Resistant Epilepsy/drug therapy ; *Brain-Gut Axis/physiology/drug effects ; Anticonvulsants/therapeutic use ; Animals ; Blood-Brain Barrier/metabolism ; }, abstract = {Over 70 million people worldwide suffer from epilepsy, a persistent brain disorder. Although there are more than 20 antiseizure drugs available for the symptomatic treatment of epilepsy, about one-third of patients with epilepsy experience seizures that show resistance to pharmacotherapy. Since patients with drug-resistant epilepsy are more prone to physical injuries, psychosocial dysfunction, early death, and deteriorated life quality, the development of safer and more effective treatments is a crucial clinical need. The gut-brain axis and microbiome research advances have provided new insights into the pathophysiology of epilepsy, the resistance to anti-seizure medicine, and potential treatment targets. Inflammation, disturbance of the blood-brain barrier, and altered neurotransmitters are key pathways linked to gut dysbiosis. The characterization of microbial species and functional pathways has advanced thanks to metagenomic sequencing and high-throughput analysis. In this review, we elaborate on the gut-mediated molecular pathways involved in drug-resistant epilepsy, the gut- modulatory therapeutic options, and their combination with antiseizure medications for drug-resistant epilepsy.}, } @article {pmid39916938, year = {2024}, author = {Liu, Y and Yang, B and Qi, Q and Liu, S and Du, Y and Ye, L and Zhou, Q}, title = {Metagenomic next-generation sequencing for lung cancer low respiratory tract infections diagnosis and characterizing microbiome features.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1518199}, pmid = {39916938}, issn = {2235-2988}, mesh = {Humans ; *Lung Neoplasms/microbiology/diagnosis ; *Respiratory Tract Infections/microbiology/diagnosis/virology ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Microbiota/genetics ; Male ; *Bacteria/genetics/classification/isolation & purification ; Female ; Middle Aged ; Aged ; Sputum/microbiology ; Fungi/isolation & purification/classification/genetics ; Coinfection/microbiology/diagnosis/virology ; Adult ; Metagenome ; Aged, 80 and over ; }, abstract = {BACKGROUND: The capability of mNGS in diagnosing suspected LRTIs and characterizing the respiratory microbiome in lung cancer patients requires further evaluation.

METHODS: This study evaluated mNGS diagnostic performance and utilized background microbial sequences to characterize LRT microbiome in these patients. GSVA was used to analyze the potential functions of identified genera.

RESULTS: Bacteria were the most common pathogens (n=74) in LRTIs of lung cancer patients, and polymicrobial infections predominated compared to monomicrobial infections (p<0.001). In diagnosing LRTIs in lung cancer patients, the pathogen detection rate of mNGS (83.3%, 70/84) was significantly higher than that of sputum culture (34.5%, 29/84) (p<0.001). This result was consistent with that of non-lung cancer patients (p<0.001). Furthermore, in the specific detection of bacteria (95.7% vs. 22.6%) and fungi (96.0% vs. 22.2%), the detection rate of mNGS was also significantly higher than that of CMTs mainly based on culture (p<0.001, p<0.001). However, in the detection of CMV/EBV viruses, there was no significant difference between the detection rate of mNGS and that of viral DNA quantification (p = 1.000 and 0.152). mNGS analysis revealed Prevotella, Streptococcus, Veillonella, Rothia, and Capnocytophaga as the most prevalent genera in the LRT of lung cancer patients. GSVA revealed significant correlations between these genera and tumor metabolic pathways as well as various signaling pathways including PI3K, Hippo, and p53.

CONCLUSION: mNGS showed a higher pathogen detection rate than culture-based CMTs in lung cancer patients with LRTIs, and also characterizing LRT microbiome composition and revealing potential microbial functions linked to lung carcinogenesis.}, } @article {pmid39915809, year = {2025}, author = {Zhang, Y and Li, HZ and Breed, M and Tang, Z and Cui, L and Zhu, YG and Sun, X}, title = {Soil warming increases the active antibiotic resistome in the gut of invasive giant African snails.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {42}, pmid = {39915809}, issn = {2049-2618}, support = {2022T150635//fellowship of China Postdoctoral Science Foundation/ ; 42407166//National Natural Science Foundation of China/ ; 42307165//National Natural Science Foundation of China/ ; 32361143523//National Natural Science Foundation of China/ ; 2021-DST-004//Ningbo S&T project/ ; 2021-DST-004//Ningbo S&T project/ ; 2021-DST-004//Ningbo S&T project/ ; 2023YFF1304601//National Key Research and Development Program of China/ ; 322GJHZ2022028FN//International Partnership Program of Chinese Academy of Sciences/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics/drug effects ; *Snails/microbiology/genetics ; *Global Warming ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/classification/drug effects ; Soil/chemistry ; Soil Microbiology ; beta-Lactamases/genetics ; Metagenomics ; Metagenome ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: Global warming is redrawing the map for invasive species, spotlighting the globally harmful giant African snail as a major ecological disruptor and public health threat. Known for harboring extensive antibiotic resistance genes (ARGs) and human pathogens, it remains uncertain whether global warming exacerbates these associated health risks.

METHODS: We use phenotype-based single-cell Raman with D2O labeling (Raman-D2O) and genotype-based metagenomic sequencing to investigate whether soil warming increases active antibiotic-resistant bacteria (ARBs) in the gut microbiome of giant African snails.

RESULTS: We show a significant increase in beta-lactam phenotypic resistance of active ARBs with rising soil temperatures, mirrored by a surge in beta-lactamase genes such as SHV, TEM, OCH, OKP, and LEN subtypes. Through a correlation analysis between the abundance of phenotypically active ARBs and genotypically ARG-carrying gut microbes, we identify species that contribute to the increased activity of antibiotic resistome under soil warming. Among 299 high-quality ARG-carrying metagenome-assembled genomes (MAGs), we further revealed that the soil warming enhances the abundance of "supercarriers" including human pathogens with multiple ARGs and virulence factors. Furthermore, we identified elevated biosynthetic gene clusters (BGCs) within these ARG-carrying MAGs, with a third encoding at least one BGC. This suggests a link between active ARBs and secondary metabolism, enhancing the environmental adaptability and competitive advantage of these organisms in warmer environments.

CONCLUSIONS: The study underscores the complex interactions between soil warming and antibiotic resistance in the gut microbiome of the giant African snail, highlighting a potential escalation in environmental health risks due to global warming. These findings emphasize the urgent need for integrated environmental and health strategies to manage the rising threat of antibiotic resistance in the context of global climate change. Video Abstract.}, } @article {pmid39804671, year = {2025}, author = {Broderick, CM and Benucci, GMN and Bachega, LR and Miller, GD and Evans, SE and Hawkes, CV}, title = {Long-term climate establishes functional legacies by altering microbial traits.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39804671}, issn = {1751-7370}, mesh = {*Soil Microbiology ; *Carbon Cycle ; *Metagenomics ; Soil/chemistry ; Droughts ; Climate ; Bacteria/genetics/classification/metabolism/isolation & purification ; Microbiota ; Climate Change ; Seasons ; Carbon/metabolism ; }, abstract = {Long-term climate history can influence rates of soil carbon cycling but the microbial traits underlying these legacy effects are not well understood. Legacies may result if historical climate differences alter the traits of soil microbial communities, particularly those associated with carbon cycling and stress tolerance. However, it is also possible that contemporary conditions can overcome the influence of historical climate, particularly under extreme conditions. Using shotgun metagenomics, we assessed the composition of soil microbial functional genes across a mean annual precipitation gradient that previously showed evidence of strong climate legacies in soil carbon flux and extracellular enzyme activity. Sampling coincided with recovery from a regional, multi-year severe drought, allowing us to document how the strength of climate legacies varied with contemporary conditions. We found increased investment in genes associated with resource cycling with historically higher precipitation across the gradient, particularly in traits related to resource transport and complex carbon degradation. This legacy effect was strongest in seasons with the lowest soil moisture, suggesting that contemporary conditions-particularly, resource stress under water limitation-influences the strength of legacy effects. In contrast, investment in stress tolerance did not vary with historical precipitation, likely due to frequent periodic drought throughout the gradient. Differences in the relative abundance of functional genes explained over half of variation in microbial functional capacity-potential enzyme activity-more so than historical precipitation or current moisture conditions. Together, these results suggest that long-term climate can alter the functional potential of soil microbial communities, leading to legacies in carbon cycling.}, } @article {pmid38291926, year = {2024}, author = {Danckert, NP and Freidin, MB and Granville Smith, I and Wells, PM and Naeini, MK and Visconti, A and Compte, R and MacGregor, A and Williams, FMK}, title = {Treatment response in rheumatoid arthritis is predicted by the microbiome: a large observational study in UK DMARD-naive patients.}, journal = {Rheumatology (Oxford, England)}, volume = {63}, number = {12}, pages = {3486-3495}, pmid = {38291926}, issn = {1462-0332}, support = {21229/VAC_/Versus Arthritis/United Kingdom ; 21227/VAC_/Versus Arthritis/United Kingdom ; }, mesh = {Humans ; *Arthritis, Rheumatoid/drug therapy/microbiology ; *Antirheumatic Agents/therapeutic use ; Female ; Male ; Middle Aged ; Longitudinal Studies ; *Gastrointestinal Microbiome/drug effects ; *Saliva/microbiology ; Treatment Outcome ; United Kingdom ; Feces/microbiology ; Adult ; Aged ; Prevotella/isolation & purification ; Microbiota/drug effects ; }, abstract = {OBJECTIVES: Disease-modifying antirheumatic drugs (DMARDs) are a first-line treatment in rheumatoid arthritis (RA). Treatment response to DMARDs is patient-specific, dose efficacy is difficult to predict and long-term results are variable. The gut microbiota are known to play a pivotal role in prodromal and early-disease RA, manifested by Prevotella spp. enrichment. The clinical response to therapy may be mediated by microbiota, and large-scale studies assessing the microbiome are few. This study assessed whether microbiome signals were associated with, and predictive of, patient response to DMARD treatment. Accurate early identification of those who will respond poorly to DMARD therapy would allow selection of alternative treatment (e.g. biologic therapy) and potentially improve patient outcome.

METHODS: A multicentre, longitudinal, observational study of stool- and saliva microbiome was performed in DMARD-naive, newly diagnosed RA patients during introduction of DMARD treatment. Clinical data and samples were collected at baseline (n = 144) in DMARD-naive patients and at six weeks (n = 117) and 12 weeks (n = 95) into DMARD therapy. Samples collected (n = 365 stool, n = 365 saliva) underwent shotgun sequencing. Disease activity measures were collected at each timepoint and minimal clinically important improvement determined.

RESULTS: In total, 26 stool microbes were found to decrease in those manifesting a minimal clinically important improvement. Prevotella spp. and Streptococcus spp. were the predominant taxa to decline following six weeks and 12 weeks of DMARDs, respectively. Furthermore, baseline microbiota of DMARD-naive patients were indicative of future response.

CONCLUSION: DMARDs appear to restore a perturbed microbiome to a eubiotic state. Moreover, microbiome status can be used to predict likelihood of patient response to DMARD.}, } @article {pmid39915243, year = {2025}, author = {Zhao, S and Lin, H and Li, W and Xu, X and Wu, Q and Wang, Z and Shi, J and Chen, Y and Ye, L and Xi, L and Chen, L and Yuan, M and Su, J and Gao, A and Jin, J and Ying, X and Wang, X and Ye, Y and Sun, Y and Zhang, Y and Deng, X and Shen, B and Gu, W and Ning, G and Wang, W and Hong, J and Wang, J and Liu, R}, title = {Post sleeve gastrectomy-enriched gut commensal Clostridia promotes secondary bile acid increase and weight loss.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2462261}, doi = {10.1080/19490976.2025.2462261}, pmid = {39915243}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Bile Acids and Salts/metabolism ; *Weight Loss ; Mice ; *Gastrectomy ; Humans ; Male ; *Clostridium/metabolism/genetics ; *Mice, Inbred C57BL ; *Obesity/microbiology/metabolism/surgery ; Receptors, G-Protein-Coupled/metabolism/genetics ; Fecal Microbiota Transplantation ; Female ; Adult ; Feces/microbiology ; Symbiosis ; Bariatric Surgery ; Adipose Tissue/metabolism ; }, abstract = {The gut microbiome is altered after bariatric surgery and is associated with weight loss. However, the commensal bacteria involved and the underlying mechanism remain to be determined. We performed shotgun metagenomic sequencing in obese subjects before and longitudinally after sleeve gastrectomy (SG), and found a significant enrichment in microbial species in Clostridia and bile acid metabolizing genes after SG treatment. Bile acid profiling further revealed decreased primary bile acids (PBAs) and increased conjugated secondary bile acids (C-SBAs) after SG. Specifically, glycodeoxycholic acid (GDCA) and taurodeoxycholic acid (TDCA) were increased at different follow-ups after SG, and were associated with the increased abundance of Clostridia and body weight reduction. Fecal microbiome transplantation with post-SG feces increased SBA levels, and alleviated body weight gain in the recipient mice. Furthermore, both Clostridia-enriched spore-forming bacteria and GDCA supplementation increased the expression of genes responsible for lipolysis and fatty acid oxidation in adipose tissue and reduced adiposity via Takeda G-protein-coupled receptor 5 (TGR5) signaling. Our findings reveal post-SG gut microbiome and C-SBAs as contributory to SG-induced weight loss, in part via TGR5 signaling, and suggest SBA-producing gut microbes as a potential therapeutic target for obesity intervention.}, } @article {pmid39910065, year = {2025}, author = {Fumagalli, A and Castells-Nobau, A and Trivedi, D and Garre-Olmo, J and Puig, J and Ramos, R and Ramió-Torrentà, L and Pérez-Brocal, V and Moya, A and Swann, J and Martin-Garcia, E and Maldonado, R and Fernández-Real, JM and Mayneris-Perxachs, J}, title = {Archaea methanogens are associated with cognitive performance through the shaping of gut microbiota, butyrate and histidine metabolism.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2455506}, doi = {10.1080/19490976.2025.2455506}, pmid = {39910065}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/physiology ; *Butyrates/metabolism ; Humans ; *Cognition ; *Histidine/metabolism ; Male ; Female ; Middle Aged ; Aged ; Bacteria/classification/metabolism/genetics/isolation & purification ; Methanobrevibacter/metabolism/genetics ; Metagenomics ; Archaea/metabolism/classification/genetics ; Cohort Studies ; Animals ; Adult ; }, abstract = {The relationship between bacteria, cognitive function and obesity is well established, yet the role of archaeal species remains underexplored. We used shotgun metagenomics and neuropsychological tests to identify microbial species associated with cognition in a discovery cohort (IRONMET, n = 125). Interestingly, methanogen archaeas exhibited the strongest positive associations with cognition, particularly Methanobrevibacter smithii (M. smithii). Stratifying individuals by median-centered log ratios (CLR) of M. smithii (low and high M. smithii groups: LMs and HMs) revealed that HMs exhibited better cognition and distinct gut bacterial profiles (PERMANOVA p = 0.001), characterized by increased levels of Verrucomicrobia, Synergistetes and Lentisphaerae species and reduced levels of Bacteroidetes and Proteobacteria. Several of these species were linked to the cognitive test scores. These findings were replicated in a large-scale validation cohort (Aging Imageomics, n = 942). Functional analyses revealed an enrichment of energy, butyrate, and bile acid metabolism in HMs in both cohorts. Global plasma metabolomics by CIL LC-MS in IRONMET identified an enrichment of methylhistidine, phenylacetate, alpha-linolenic and linoleic acid, and secondary bile acid metabolism associated with increased levels of 3-methylhistidine, phenylacetylgluamine, adrenic acid, and isolithocholic acid in the HMs group. Phenylacetate and linoleic acid metabolism also emerged in the Aging Imageomics cohort performing untargeted HPLC-ESI-MS/MS metabolic profiling, while a targeted bile acid profiling identified again isolithocholic acid as one of the most significant bile acid increased in the HMs. 3-Methylhistidine levels were also associated with intense physical activity in a second validation cohort (IRONMET-CGM, n = 116). Finally, FMT from HMs donors improved cognitive flexibility, reduced weight, and altered SCFAs, histidine-, linoleic acid- and phenylalanine-related metabolites in the dorsal striatum of recipient mice. M. smithii seems to interact with the bacterial ecosystem affecting butyrate, histidine, phenylalanine, and linoleic acid metabolism with a positive impact on cognition, constituting a promising therapeutic target to enhance cognitive performance, especially in subjects with obesity.}, } @article {pmid39567690, year = {2025}, author = {Borton, MA and McGivern, BB and Willi, KR and Woodcroft, BJ and Mosier, AC and Singleton, DM and Bambakidis, T and Pelly, A and Daly, RA and Liu, F and Freiburger, A and Edirisinghe, JN and Faria, JP and Danczak, R and Leleiwi, I and Goldman, AE and Wilkins, MJ and Hall, EK and Pennacchio, C and Roux, S and Eloe-Fadrosh, EA and Good, SP and Sullivan, MB and Wood-Charlson, EM and Miller, CS and Ross, MRV and Henry, CS and Crump, BC and Stegen, JC and Wrighton, KC}, title = {A functional microbiome catalogue crowdsourced from North American rivers.}, journal = {Nature}, volume = {637}, number = {8044}, pages = {103-112}, pmid = {39567690}, issn = {1476-4687}, support = {P30 CA046934/CA/NCI NIH HHS/United States ; }, mesh = {*Crowdsourcing ; *Microbiota/genetics ; *Rivers/microbiology ; United States ; Water Microbiology ; Transcriptome ; Carbon Cycle ; Metagenome ; Databases, Factual ; }, abstract = {Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla, including novel members from 10 families and 128 genera, and defines the core river microbiome at the genome level. GROWdb analyses coupled to extensive geospatial information reveals local and regional drivers of microbial community structuring, while also presenting foundational hypotheses about ecosystem function. Building on the previously conceived River Continuum Concept[1], we layer on microbial functional trait expression, which suggests that the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures[2,3], so that it can be widely accessed across disciplines for watershed predictive modelling and microbiome-based management practices.}, } @article {pmid39547283, year = {2025}, author = {Zelasko, S and Swaney, MH and Sandstrom, S and Lee, KE and Dixon, J and Riley, C and Watson, L and Godfrey, JJ and Ledrowski, N and Rey, F and Safdar, N and Seroogy, CM and Gern, JE and Kalan, L and Currie, C}, title = {Early-life upper airway microbiota are associated with decreased lower respiratory tract infections.}, journal = {The Journal of allergy and clinical immunology}, volume = {155}, number = {2}, pages = {436-450}, doi = {10.1016/j.jaci.2024.11.008}, pmid = {39547283}, issn = {1097-6825}, mesh = {Humans ; *Microbiota ; *Respiratory Tract Infections/microbiology ; Male ; Infant ; Female ; Child, Preschool ; Mouth/microbiology ; Nose/microbiology ; }, abstract = {BACKGROUND: Microbial interactions mediating colonization resistance play key roles within the human microbiome, shaping susceptibility to infection from birth. The role of the nasal and oral microbiome in the context of early life respiratory infections and subsequent allergic disease risk remains understudied.

OBJECTIVES: Our aim was to gain insight into microbiome-mediated defenses and respiratory pathogen colonization dynamics within the upper respiratory tract during infancy.

METHODS: We performed shotgun metagenomic sequencing of nasal (n = 229) and oral (n = 210) microbiomes from our Wisconsin Infant Study Cohort at age 24 months and examined the influence of participant demographics and exposure history on microbiome composition. Detection of viral and bacterial respiratory pathogens by RT-PCR and culture-based studies with antibiotic susceptibility testing, respectively, to assess pathogen carriage was performed. Functional bioassays were used to evaluate pathogen inhibition by respiratory tract commensals.

RESULTS: Participants with early-life lower respiratory tract infection were more likely to be formula fed, attend day care, and experience wheezing. Composition of the nasal, but not oral, microbiome associated with prior lower respiratory tract infection, namely lower alpha diversity, depletion of Prevotella, and enrichment of Moraxella catarrhalis including drug-resistant strains. Prevotella originating from healthy microbiomes had higher biosynthetic gene cluster abundance and exhibited contact-independent inhibition of M catarrhalis.

CONCLUSIONS: These results suggest interbacterial competition affects nasal pathogen colonization. This work advances understanding of protective host-microbe interactions occurring in airway microbiomes that alter infection susceptibility in early life.}, } @article {pmid39433639, year = {2025}, author = {Davidson, IM and Nikbakht, E and Haupt, LM and Ashton, KJ and Dunn, PJ}, title = {Methodological approaches in 16S sequencing of female reproductive tract in fertility patients: a review.}, journal = {Journal of assisted reproduction and genetics}, volume = {42}, number = {1}, pages = {15-37}, pmid = {39433639}, issn = {1573-7330}, mesh = {Female ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Genitalia, Female/microbiology ; Reproductive Techniques, Assisted ; Metagenomics/methods ; Computational Biology/methods ; Fertility/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: The female genital tract microbiome has become a particular area of interest in improving assisted reproductive technology (ART) outcomes with the emergence of next-generation sequencing (NGS) technology. However, NGS assessment of microbiomes currently lacks uniformity and poses significant challenges for accurate and precise bacterial population representation.

OBJECTIVE: As multiple NGS platforms and assays have been developed in recent years for microbiome investigation-including the advent of long-read sequencing technologies-this work aimed to identify current trends and practices undertaken in female genital tract microbiome investigations.

RESULTS: Areas like sample collection and transport, DNA extraction, 16S amplification vs. metagenomics, NGS library preparation, and bioinformatic analysis demonstrated a detrimental lack of uniformity. The lack of uniformity present is a significant limitation characterised by gap discrepancies in generation and interpretation of results. Minimal consistency was observed in primer design, DNA extraction techniques, sample transport, and bioinformatic analyses.

CONCLUSION: With third-generation sequencing technology highlighted as a promising tool in microbiota-based research via full-length 16S rRNA sequencing, there is a desperate need for future studies to investigate and optimise methodological approaches of the genital tract microbiome to ensure better uniformity of methods and results interpretation to improve clinical impact.}, } @article {pmid39908385, year = {2025}, author = {Griffiths, ME and Broos, A and Morales, J and Tu, IT and Bergner, L and Behdenna, A and Valderrama Bazan, W and Tello, C and Carrera, JE and Recuenco, S and Streicker, DG and Viana, M}, title = {Dynamics of influenza transmission in vampire bats revealed by longitudinal monitoring and a large-scale anthropogenic perturbation.}, journal = {Science advances}, volume = {11}, number = {6}, pages = {eads1267}, pmid = {39908385}, issn = {2375-2548}, mesh = {*Chiroptera/virology ; Animals ; Orthomyxoviridae Infections/transmission/virology/veterinary ; Humans ; Bayes Theorem ; Peru/epidemiology ; Zoonoses/transmission/virology ; Longitudinal Studies ; }, abstract = {Interrupting pathogen transmission between species is a priority strategy to mitigate zoonotic threats. However, avoiding counterproductive interventions requires knowing animal reservoirs of infection and the dynamics of transmission within them, neither of which are easily ascertained from the cross-sectional surveys that now dominate investigations into newly discovered viruses. We used biobanked sera and metagenomic data to reconstruct the transmission of recently discovered bat-associated influenza virus (BIV; H18N11) over 12 years in three zones of Peru. Mechanistic models fit under a Bayesian framework, which enabled joint inference from serological and molecular data, showed that common vampire bats maintain BIV independently of the now assumed fruit bat reservoir through immune waning and seasonal transmission pulses. A large-scale vampire bat cull targeting rabies incidentally halved BIV transmission, confirming vampire bats as maintenance hosts. Our results show how combining field studies, perturbation responses, and multi-data-type models can elucidate pathogen dynamics in nature and reveal pathogen-dependent effects of interventions.}, } @article {pmid39643526, year = {2025}, author = {Yen, TY and Hsu, C and Lee, NC and Wu, CS and Wang, H and Lee, KY and Lin, CR and Lu, CY and Tsai, ML and Liu, TY and Lin, C and Chen, CY and Chang, LY and Lai, F and Huang, LM}, title = {Signatures of lower respiratory tract microbiome in children with severe community-acquired pneumonia using shotgun metagenomic sequencing.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {58}, number = {1}, pages = {86-93}, doi = {10.1016/j.jmii.2024.11.011}, pmid = {39643526}, issn = {1995-9133}, mesh = {Humans ; *Community-Acquired Infections/microbiology ; Male ; Prospective Studies ; Child, Preschool ; Female ; *Metagenomics/methods ; Child ; *Microbiota/genetics ; Infant ; *Pneumonia/microbiology ; *High-Throughput Nucleotide Sequencing ; *Metagenome/genetics ; Bacteria/classification/genetics/isolation & purification ; Severity of Illness Index ; Intensive Care Units ; Respiratory System/microbiology ; Adolescent ; }, abstract = {BACKGROUND: Severe community-acquired pneumonia was associated with high morbidity and mortality in children. However, species-level microbiome of lower airway was sparse, and we used shotgun metagenomic next-generation sequencing to explore microbial signatures.

METHODS: We conducted a prospective cohort study to recruit children under 18 who required admission to an intensive care unit for community-acquired pneumonia between December 2019 and February 2022. Lower respiratory specimens were collected on admission for shotgun metagenomic sequencing. The children were divided into two groups. Critical cases were patients with respiratory failure requiring endotracheal ventilator support, and severe cases did not require intubation. Signatures of lower respiratory tract microbiome were compared between groups using an exact k-mer matching metagenomic analysis pipeline (Kraken 2) and a metagenome-assembled genomes pipeline (MetaWRAP).

RESULTS: Totally 66 children were enrolled, and 27 children were critical cases, and the rest were severe cases. There were significant differences in microbial community structure between different severity groups, and microbial abundance was negatively correlated with disease severity. The results showed that Haemophilus influenzae was more prominent in children who were critical, accompanied with increased expression of intracellular transport, secretion, and vesicle transport genes. Rothia mucilaginosa, Dolosigranulum pigrum, and Prevotella melaninogenica tended to be present in less severe community-acquired pneumonia group.

CONCLUSION: This study demonstrated that significantly different microbial community was associated with severity of community-acquired pneumonia requiring intensive care admission. Species-level shotgun metagenomic sequencing facilitates the exploration of potentially pathogenic or protective microbes and shed the light of probiotic development in lower respiratory tract.}, } @article {pmid39907344, year = {2025}, author = {Cuong, NC and Hung, NV and Linh, TK and Loi, NTT and Tung, QN and Tuyen, DT and Anh, DTN}, title = {Structure of fungal community and culturable fungi on the discolored surfaces of pine storage boxes in the tropical region in Dong Nai, Vietnam.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {84}, number = {}, pages = {e289015}, doi = {10.1590/1519-6984.289015}, pmid = {39907344}, issn = {1678-4375}, mesh = {Vietnam ; *Fungi/classification/isolation & purification/genetics ; *Wood/microbiology ; *Pinus/microbiology ; Tropical Climate ; Mycobiome ; }, abstract = {Wood and wood-based materials are commonly used for storage, but their surfaces are prone to biodegradation by microorganisms, especially fungi. This study focuses on the microbial communities on pine wood storage boxes treated with an anti-termite and mold solution in a tropical region in Dong Nai, Vietnam. We isolated 13 fungal strains from these surfaces and classified them into six genera: Rhizopus, Aspergillus, Fusarium, Curvularia, Penicillium, and Trichoderma. Enzyme activity tests revealed that strains Curvularia eragrostidis TD4.2 and Aspergillus sydowii TD5 were the most effective producers of cellulase, amylase, and laccase. Shotgun metagenomics analysis of the biological sample of the discolored surface of pine storage boxes indicated that Ascomycota was the dominant phylum, with Dothideomycetes and Sordariomycetes as the prevalent class. Aureobasidium (0.33%) and Chaetomium (1.1%) were the most abundant genera in the Dothideomycetes and Sordariomycetes, respectively. This research illustrates the complexity of microbial communities on wood surfaces, providing insights into the fungal dynamics affecting wooden storage materials in tropical climates.}, } @article {pmid39907343, year = {2025}, author = {Alifia, L and Zulaika, E and Soeprijanto, S and Hamzah, A and Luqman, A}, title = {Microbial diversity and biotechnological potential of mangrove leaf litter in Kebun Raya Mangrove, Surabaya, Indonesia.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {84}, number = {}, pages = {e288968}, doi = {10.1590/1519-6984.288968}, pmid = {39907343}, issn = {1678-4375}, mesh = {Indonesia ; *Plant Leaves/microbiology ; *Rhizophoraceae/microbiology ; *Avicennia/microbiology ; Biodiversity ; Bacteria/classification/genetics/isolation & purification ; Wetlands ; }, abstract = {Mangrove ecosystems play a crucial role in maintaining ecological balance with leaf litter serving as an important substrate for diverse microbial communities. This study investigates the microbial communities inhabiting leaf litter from four different mangrove species: Rhizophora apiculata, Rhizophora stylosa, Sonneratia caseolaris, and Avicennia marina collected from Kebun Raya Mangrove, Surabaya, Indonesia. Using metagenomic sequencing, we revealed that Proteobacteria were predominant, followed by Chlorobi and Actinobacteria in the samples. Interestingly, we detected notable populations of anaerobic bacteria, including genus of Chlorobaculum and Allochromatium. Metagenomic analyses exhibited high levels of adaptation to stressors, evidenced by the prevalence of genes conferring resistance to antibiotics (e.g., beta-lactams, tetracyclines), heavy metals (e.g., chromium, arsenic), and hydrocarbons. Furthermore, the metagenomic analysis revealed the presence of genes involved in the biosynthesis of polyunsaturated fatty acids (PUFAs), antimicrobial compounds, and plant growth-promoting activities. These findings highlight the potential of mangrove leaf litter as a reservoir of beneficial microbes with diverse biotechnological applications, including bioremediation, nutraceuticals, pharmaceuticals, and agriculture.}, } @article {pmid39906212, year = {2024}, author = {Xi, Z and Chen, J and Wang, L and Lu, A}, title = {Characteristics of lower respiratory microbiota in children's refractory Mycoplasma pneumoniae pneumonia pre- and post-COVID-19 era.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1438777}, pmid = {39906212}, issn = {2235-2988}, mesh = {Humans ; *Microbiota ; *COVID-19/immunology/microbiology ; Male ; Female ; Child ; Child, Preschool ; *Pneumonia, Mycoplasma/microbiology ; Mycoplasma pneumoniae/genetics/isolation & purification ; SARS-CoV-2 ; Infant ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Bacterial ; RNA, Ribosomal, 23S/genetics ; Respiratory System/microbiology/virology ; }, abstract = {INTRODUCTION: Little was known about the characteristics of low respiratory tract (LRT) microbiota of refractory M. pneumoniae pneumonia (RMPP) in children before and after the COVID-19 pandemic.

METHODS: Forty-two children diagnosed with RMPP in 2019 (Y2019 group) and 33 children diagnosed with RMPP in 2023 (Y2023 group), entered into the study. The characteristics of the clinical findings were examined, and the LRT microbiota was analyzed by metagenomic next generation sequencing.

RESULTS: The ratio of consolidate, atelectasis, lung necrosis, and erythema multiforme in Y2023 group was significantly higher than that in Y2019 (P<0.05). Mycoplasmoides pneumoniae was the top species of the LRT microbiota in both groups. The rate of macrolide resistance MP in Y2023 was significantly higher than that in Y2019 (P<0.05), and the mutant site was all 23S rRNA A2063G. There were no significant differences in α-diversity and β-diversity of LRT microbiota between Y2019 and Y2023 group. Trichoderma citrinoviride, Canine mastadenovirus A, Ralstonia pickettii, Lactococcus lactis, Pseudomonas aeruginosa were the biomarkers of LRT microbiota in children with RMPP of Y2023. The abundance of Mycoplasmoides pneumoniae positively correlated with the levels of D-dimer and LDH, negatively correlated with the counts of CD3[+] T cells, CD8[+] T cells, CD19[+] B cells and CD16[+]CD56[+] NK cells.

DISCUSSION: Our study showed that high abundance of MP was correlated with the severity of RMPP and decrease of immune cells. Trichoderma citrinoviride, Canine mastadenovirus A, Ralstonia pickettii, Lactococcus lactis, Pseudomonas aeruginosa were the biomarkers in microbiota of LRT in children with RMPP post COVID-19 era.}, } @article {pmid39905573, year = {2025}, author = {Armstrong, E and Liu, R and Pollock, J and Huibner, S and Udayakumar, S and Irungu, E and Ngurukiri, P and Muthoga, P and Adhiambo, W and Yegorov, S and Kimani, J and Beattie, T and Coburn, B and Kaul, R}, title = {Quantitative profiling of the vaginal microbiota improves resolution of the microbiota-immune axis.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {39}, pmid = {39905573}, issn = {2049-2618}, support = {Canada Graduate Scholarship/CAPMC/CIHR/Canada ; Vanier Canada Graduate Scholarship/CAPMC/CIHR/Canada ; PJT-180629/CAPMC/CIHR/Canada ; MR/R023182/1//Medical Research Council and the UK Foreign, Commonwealth and Development Office/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology/immunology ; *Vaginosis, Bacterial/microbiology/immunology ; Kenya ; *Microbiota ; Adult ; *Sex Workers ; *Bacterial Load ; Bacteria/classification/genetics/isolation & purification ; Young Adult ; Interleukin-1alpha/metabolism ; Cytokines/metabolism ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Lactobacillus/isolation & purification ; }, abstract = {BACKGROUND: The composition of the vaginal microbiota is closely linked to adverse sexual and reproductive health outcomes, due in part to effects on genital immunology. Compositional approaches such as metagenomic sequencing provide a snapshot of all bacteria in a sample and have become the standard for characterizing the vaginal microbiota, but only provide microbial relative abundances. We hypothesized that the addition of absolute abundance data would provide a more complete picture of host-microbe interactions in the female genital tract.

RESULTS: We analyzed cervicovaginal secretions from 196 female sex workers in Kenya and found that bacterial load was elevated among women with diverse, bacterial vaginosis (BV)-type microbiota and lower among women with Lactobacillus predominance. Bacterial load was also positively associated with proinflammatory cytokines, such as IL-1α, and negatively associated with chemokines, such as IP-10. The associations between bacterial load and immune factors differed across bacterial community states, but L. crispatus predominance was the only microbial community where higher bacterial load was not associated with higher proinflammatory cytokines. Total vaginal bacterial load was also a stronger predictor of the genital immune environment than BV by Nugent score, the current clinical standard, in the Kenya-based cohort and in a Uganda-based confirmatory cohort.

CONCLUSIONS: Our results suggest that total vaginal bacterial load is at least as strong a predictor of the genital immune milieu as current BV clinical diagnostic tools, supporting exploration of the vaginal bacterial load as a predictor of adverse reproductive and sexual health outcomes. Video Abstract.}, } @article {pmid39905490, year = {2025}, author = {Molina-Pardines, C and Haro-Moreno, JM and Rodriguez-Valera, F and López-Pérez, M}, title = {Extensive paralogism in the environmental pangenome: a key factor in the ecological success of natural SAR11 populations.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {41}, pmid = {39905490}, issn = {2049-2618}, support = {PRE2021-098122//Ministerio de Economía y Competitividad/ ; PID2020-118052GB-I00//Ministerio de Economía y Competitividad/ ; 2021/PER/00020//Ministerio de Universidades/ ; }, mesh = {*Metagenomics/methods ; Mediterranean Sea ; *Genetic Variation ; Microbiota/genetics ; Genome, Bacterial ; Metagenome ; Phylogeny ; Seawater/microbiology ; }, abstract = {BACKGROUND: The oceanic microbiome is dominated by members of the SAR11 clade. Despite their abundance, challenges in recovering the full genetic diversity of natural populations have hindered our understanding of the eco-evolutionary mechanisms driving intra-species variation. In this study, we employed a combination of single-amplified genomes and long-read metagenomics to recover the genomic diversity of natural populations within the SAR11 genomospecies Ia.3/VII, the dominant group in the Mediterranean Sea.

RESULTS: The reconstruction of the first complete genome within this genomospecies revealed that the core genome represents a significant proportion of the genome (~ 81%), with highly divergent areas that allow for greater strain-dependent metabolic flexibility. The flexible genome was concentrated in small regions, typically containing a single gene, and was located in equivalent regions within the genomospecies. Each variable region was associated with a specific set of genes that, despite exhibiting some divergence, maintained equivalent biological functionality within the population. The environmental pangenome is large and enriched in genes involved in nutrient transport, as well as cell wall synthesis and modification, showing an extremely high degree of functional redundancy in the flexible genome (i.e. paralogisms).

CONCLUSIONS: This genomic architecture promotes polyclonality, preserving genetic variation within the population. This, in turn, mitigates intraspecific competition and enables the population to thrive under variable environmental conditions and selective pressures. Furthermore, this study demonstrates the power of long-read metagenomics in capturing the full genetic diversity of environmental SAR11 populations, overcoming the limitations of second-generation sequencing technologies in genome assembly. Video Abstract.}, } @article {pmid39905038, year = {2025}, author = {Qu, Q and Dou, Q and Xiang, Z and Yu, B and Chen, L and Fan, Z and Zhao, X and Yang, S and Zeng, P}, title = {Population-level gut microbiome and its associations with environmental factors and metabolic disorders in Southwest China.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {24}, pmid = {39905038}, issn = {2055-5008}, mesh = {*Gastrointestinal Microbiome ; Humans ; China ; *Metabolic Diseases/microbiology/etiology ; *Feces/microbiology ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; Diet ; Adult ; Bacteria/classification/genetics/isolation & purification ; Life Style ; Socioeconomic Factors ; }, abstract = {Gut microbiota affects host health and disease. Large-scale cohorts have explored the interactions between the microbiota, host, and environment to reveal the disease-associated microbiota variation. A population-level gut metagenomic cohort is still rare in China. Here, we performed metagenomic sequencing on fecal samples from the CMEC Microbiome Project in Southwest China. In this study, we identified host socioeconomics, diet, lifestyle, and medical measurements that were significantly associated with microbiome function and composition. We revealed extensive novel associations between the host microbiome and common metabolic disorders. Our results provide new insight into associations of gut microbiota with metabolic disorders so as to support the translation of gut microbiome findings into potential clinical practice.}, } @article {pmid39904998, year = {2025}, author = {Boulton, W and Salamov, A and Grigoriev, IV and Calhoun, S and LaButti, K and Riley, R and Barry, K and Fong, AA and Hoppe, CJM and Metfies, K and Oetjen, K and Eggers, SL and Müller, O and Gardner, J and Granskog, MA and Torstensson, A and Oggier, M and Larsen, A and Bratbak, G and Toseland, A and Leggett, RM and Moulton, V and Mock, T}, title = {Metagenome-assembled-genomes recovered from the Arctic drift expedition MOSAiC.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {204}, pmid = {39904998}, issn = {2052-4463}, mesh = {Arctic Regions ; *Metagenome ; Oceans and Seas ; Expeditions ; Ecosystem ; Ice Cover/microbiology ; }, abstract = {The Multidisciplinary Observatory for Study of the Arctic Climate (MOSAiC) expedition consisted of a year-long drifting survey of the Central Arctic Ocean. The ecosystems component of MOSAiC included the sampling of molecular data, with metagenomes collected from a diverse range of environments. The generation of metagenome-assembled-genomes (MAGs) from metagenomes are a starting point for genome-resolved analyses. This dataset presents a catalogue of MAGs recovered from a set of 73 samples from MOSAiC, including 2407 prokaryotic and 56 eukaryotic MAGs, as well as annotations of a near complete eukaryotic MAG using the Joint Genome Institute (JGI) annotation pipeline. The metagenomic samples are from the surface ocean, chlorophyll maximum, mesopelagic and bathypelagic, within leads and under-ice ocean, as well as melt ponds, ice ridges, and first- and second-year sea ice. This set of MAGs can be used to benchmark microbial biodiversity in the Central Arctic Ocean, compare individual strains across space and time, and to study changes in Arctic microbial communities from the winter to summer, at a genomic level.}, } @article {pmid39903340, year = {2025}, author = {Yan, Z and Zheng, Z and Cao, L and Zhu, Z and Zhou, C and Sun, Q and Tang, B and Zhao, G}, title = {Altered gut microbiome and serum metabolome profiles associated with essential tremor.}, journal = {Metabolic brain disease}, volume = {40}, number = {2}, pages = {118}, pmid = {39903340}, issn = {1573-7365}, support = {U20A20355//National Natural Science Foundation of China/ ; WKJ-ZJ-ZZ08//Major Health Science and Technology Program of Zhejiang Province/ ; LZ23H090004//Key Projects of Zhejiang Provincial Natural Science Fund/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Metabolome ; *Essential Tremor/blood/microbiology ; Male ; Female ; Middle Aged ; Aged ; Dysbiosis/blood ; Lipid Metabolism/physiology ; }, abstract = {The genetic predisposition and environmental factors both trigger the complex neurological dyskinesia of essential tremor (ET). Gut dysbiosis may facilitate the occurrence and development of neurological diseases. Therefore, it is worth exploring the inner connections between gut microbiota and ET. First, the gut microbiota of 19 ET patients and 21 healthy controls (HCs) were analysed with metagenomics approach. Second, the potential linkages between gut microbiome and serum metabolome profiles were explored by integrative analysis. The gut microbiota disorders were present in ET patients. The LEfSe method showed a significant decrease in Bacteroides. The functional analysis revealed that there were differences in gut microbial apoptosis, retinol metabolism, and steroid hormone biosynthesis pathways. The levels of various lipids and lipid-like molecules alter in serum of ET patients, which correlated with altered gut microbial abundance, indicating the alterations in lipid metabolism involved in apoptosis pathway in ET. All of these data point to the gut dysbiosis in ET, and some changed gut microbial species were linked to abnormalities in blood lipid metabolism, which open up new avenues for investigation into the pathophysiology of ET.}, } @article {pmid39844349, year = {2025}, author = {Fonseca de Souza, L and Oliveira, HG and Pellegrinetti, TA and Mendes, LW and Bonatelli, ML and Dumaresq, ASR and Sinatti, VVC and Pinheiro, JB and Azevedo, JL and Quecine, MC}, title = {Co-inoculation with Bacillus thuringiensis RZ2MS9 and rhizobia improves the soybean development and modulates soil functional diversity.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {2}, pages = {}, doi = {10.1093/femsec/fiaf013}, pmid = {39844349}, issn = {1574-6941}, support = {2021/12378-4//FAPESP/ ; 166644/2020-0//National Council for Scientific and Technological Development/ ; 69242/2018-8//H.G.O./ ; 22.1.08498.01.0//T.A.P./ ; }, mesh = {*Glycine max/microbiology/growth & development ; *Soil Microbiology ; *Bacillus thuringiensis/genetics/growth & development ; *Soil/chemistry ; Rhizobium/genetics ; Quorum Sensing ; Microbiota ; Phosphorus/metabolism ; Biodiversity ; }, abstract = {Despite the beneficial effects of plant growth-promoting rhizobacteria on agriculture, understanding the consequences of introducing foreign microbes into soil taxonomic and functional diversity is necessary. This study evaluated the effects co-inoculation of soybean with Bacillus thuringiensis (Bt) RZ2MS9 and commercial rhizobia on the natural microbial community structure and functional potential. Our results indicated that soybean development was positively influenced by co-inoculation, plants exhibited greater height and a higher number of pods, and no reductions in productivity estimates. Soil prokaryotic diversity and community structure remained unchanged by Bt RZMS9 inoculation or co-inoculation with rhizobia 147 days after sowing. However, functional diversity was influenced by sole Bt inoculation, potentially due to community quorum sensing disruption by N-acyl homoserine lactone hydrolases. The genes enriched by co-inoculation were mostly related to soil phosphorus cycling, with gcd showing the most pronounced increase. The nifA genes increased when rhizobia alone were inoculated, suggesting that this pathway could be affected by Bt RZ2MS9 inoculation. This study demonstrates the synergistic activity of rhizobia and Bt RZ2MS9 on soybean development, without significantly interfering with natural microbial community, presenting a promising approach for sustainable crop management.}, } @article {pmid39832809, year = {2025}, author = {Miebach, J and Green, D and Strittmatter, M and Mallinger, C and Le Garrec, L and Zhang, QY and Foucault, P and Kunz, C and Gachon, CMM}, title = {Importance, structure, cultivability, and resilience of the bacterial microbiota during infection of laboratory-grown Haematococcus spp. by the blastocladialean pathogen Paraphysoderma sedebokerense: evidence for a domesticated microbiota and its potential for biocontrol.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {2}, pages = {}, doi = {10.1093/femsec/fiaf011}, pmid = {39832809}, issn = {1574-6941}, support = {BB/P027806/1//UK Research and Innovation/ ; H2020-BG1-2016//Horizon Europe/ ; //MNHN/ ; }, mesh = {*Microbiota ; *Chlorophyta/microbiology/growth & development ; *Bacteria/genetics/classification/growth & development/isolation & purification ; Ascomycota/genetics/growth & development/physiology ; Metagenomics ; Biological Control Agents ; }, abstract = {Industrial production of the unicellular green alga Haematococcus lacustris is compromised by outbreaks of the fungal pathogen Paraphysoderma sedebokerense (Blastocladiomycota). Here, using axenic algal and fungal cultures and antibiotic treatments, we show that the bacterial microbiota of H. lacustris is necessary for the infection by P. sedebokerense and that its modulation affects the outcome of the interaction. We combined metagenomics and laboratory cultivation to investigate the diversity of the bacterial microbiota associated to three Haematococcus species and monitor its change upon P. sedebokerense infection. We unveil three types of distinct, reduced bacterial communities, which likely correspond to keystone taxa in the natural Haematococcus spp. microbiota. Remarkably, the taxonomic composition and functionality of these communities remained stable during infection. The major bacterial taxa identified in this study have been cultivated by us or others, paving the way to developing synthetic communities to experimentally explore interactions within this tripartite system. We discuss our results in the light of emerging evidence concerning the structuring and domestication of plant and animal microbiota, thus providing novel experimental tools and a new conceptual framework necessary to enable the engineering of Haematococcus spp. microbiota toward the biocontrol of P. sedebokerense.}, } @article {pmid39826761, year = {2025}, author = {Zhou, Z and Liu, S and Saleem, M and Liu, F and Hu, R and Su, H and Dong, D and Luo, Z and Wu, Y and Zhang, Y and He, Z and Wang, C}, title = {Unraveling phase-dependent variations of viral community, virus-host linkage, and functional potential during manure composting process.}, journal = {Bioresource technology}, volume = {419}, number = {}, pages = {132081}, doi = {10.1016/j.biortech.2025.132081}, pmid = {39826761}, issn = {1873-2976}, mesh = {*Composting/methods ; *Manure/virology ; Bacteria/genetics ; Metagenome ; Virome ; }, abstract = {The temporal dynamics of bacterial and fungal communities significantly impact the manure composting process, yet viral communities are often underexplored. Bulk metagenomes, viromes, metatranscriptomes, and metabolomes were integrated to investigate dynamics of double-stranded DNA (dsDNA) virus and virus-host interactions throughout a 63-day composting process. A total of 473 viral operational taxonomic units (vOTUs), predominantly Caudoviricetes, showed distinct phase-dependent differentiation. In phase I (initial-mesophilic), viruses targeted Gammaproteobacteria and Firmicutes, utilizing restriction-modification (RM) systems. In phase II (thermophilic-maturing), viruses infected Alphaproteobacteria, Chloroflexi, and Planctomycetes, employing CRISPR-Cas systems. Lysogenic and lytic viruses exerting differential effects on bacterial pathogens across phases. Additionally, six types of auxiliary metabolic genes (AMGs) related to galactose and cysteine metabolisms were identified. The homologous lineages of AMGs with bacterial genes, along with the significant temporal correlation observed between virus-host-metabolite interactions, underscore the critical yet often overlooked role of viral communities in modulating microbial metabolisms and pathogenesis within composting ecosystems.}, } @article {pmid39807864, year = {2025}, author = {Nakatsu, G and Ko, D and Michaud, M and Franzosa, EA and Morgan, XC and Huttenhower, C and Garrett, WS}, title = {Virulence factor discovery identifies associations between the Fic gene family and Fap2[+] fusobacteria in colorectal cancer microbiomes.}, journal = {mBio}, volume = {16}, number = {2}, pages = {e0373224}, doi = {10.1128/mbio.03732-24}, pmid = {39807864}, issn = {2150-7511}, support = {//Cancer Research UK (CRUK)/ ; R01CA154426//HHS | NIH | National Cancer Institute (NCI)/ ; }, mesh = {Humans ; *Virulence Factors/genetics ; *Colorectal Neoplasms/microbiology/genetics/pathology ; Bacterial Proteins/genetics/metabolism ; Gastrointestinal Microbiome/genetics ; Fusobacterium/genetics/pathogenicity/metabolism ; Multigene Family ; Genome, Bacterial ; Lectins/genetics/metabolism ; Fusobacteria/genetics/metabolism/pathogenicity ; }, abstract = {Fusobacterium is a bacterium associated with colorectal cancer (CRC) tumorigenesis, progression, and metastasis. Fap2 is a fusobacteria-specific outer membrane galactose-binding lectin that mediates Fusobacterium adherence to and invasion of CRC tumors. Advances in omics analyses provide an opportunity to profile and identify microbial genomic features that correlate with the cancer-associated bacterial virulence factor Fap2. Here, we analyze genomes of Fusobacterium colon tumor isolates and find that a family of post-translational modification enzymes containing Fic domains is associated with Fap2 positivity in these strains. We demonstrate that Fic family genes expand with the presence of Fap2 in the fusobacterial pangenome. Through comparative genomic analysis, we find that Fap2[+] Fusobacteriota are highly enriched with Fic gene families compared to other cancer-associated and human gut microbiome bacterial taxa. Using a global data set of CRC shotgun metagenomes, we show that fusobacterial Fic and Fap2 genes frequently co-occur in the fecal microbiomes of individuals with late-stage CRC. We further characterize specific Fic gene families harbored by Fap2[+] Fusobacterium animalis genomes and detect recombination events and elements of horizontal gene transfer via synteny analysis of Fic gene loci. Exposure of a F. animalis strain to a colon adenocarcinoma cell line increases gene expression of fusobacterial Fic and virulence-associated adhesins. Finally, we demonstrate that Fic proteins are synthesized by F. animalis as Fic peptides are detectable in F. animalis monoculture supernatants. Taken together, our study uncovers Fic genes as potential virulence factors in Fap2[+] fusobacterial genomes.IMPORTANCEAccumulating data support that bacterial members of the intra-tumoral microbiota critically influence colorectal cancer progression. Yet, relatively little is known about non-adhesin fusobacterial virulence factors that may influence carcinogenesis. Our genomic analysis and expression assays in fusobacteria identify Fic domain-containing genes, well-studied virulence factors in pathogenic bacteria, as potential fusobacterial virulence features. The Fic family proteins that we find are encoded by fusobacteria and expressed by Fusobacterium animalis merit future investigation to assess their roles in colorectal cancer development and progression.}, } @article {pmid39798223, year = {2025}, author = {Larsson, SC and Ericson, U and Dekkers, KF and Arage, G and Rašo, LM and Sayols-Baixeras, S and Hammar, U and Baldanzi, G and Nguyen, D and Nielsen, HB and Holm, JB and Risérus, U and Michaëlsson, K and Sundström, J and Smith, JG and Engström, G and Ärnlöv, J and Orho-Melander, M and Fall, T and Ahmad, S}, title = {Meat intake in relation to composition and function of gut microbiota.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {45}, number = {}, pages = {124-133}, doi = {10.1016/j.clnu.2024.12.034}, pmid = {39798223}, issn = {1532-1983}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Male ; Female ; Middle Aged ; Adult ; Diet/methods/statistics & numerical data ; Meat/microbiology ; Aged ; Red Meat/microbiology ; Metagenomics/methods ; Biomarkers/blood ; }, abstract = {OBJECTIVE: Meat intake is suggested to affect gut microbiome composition and the risk of chronic diseases. We aimed to identify meat-associated gut microbiome features and their association with host factors.

DESIGN: Gut microbiota species were profiled by deep shotgun metagenomics sequencing in 9669 individuals. Intake of white meat, unprocessed red meat, and processed red meat was assessed using a food frequency questionnaire. The associations of meat intake with alpha-diversity and relative abundance of gut microbiota species were tested using linear regression models with adjustment for dietary fiber intake, body mass index, and other potential confounders. Meat-associated species were further assessed for association with enrichment of microbial gene function, meat-associated plasma metabolites, and clinical biomarkers.

RESULTS: Higher intake of processed red meat was associated with reduced alpha microbial diversity. White meat, unprocessed, and processed red meat intakes were associated with 36, 14, and 322 microbiota species, respectively. Species associated with processed red meat were enriched for bacterial pathways like amino acid degradation, while those negatively linked were enriched for pathways like homoacetogenesis. Furthermore, species positively associated with processed red meat were to a large extent associated with reduced trimethylamine N-oxide and glutamine levels but increased creatine and carnitine metabolites, fasting insulin and glucose, C-reactive protein, apolipoprotein A1, and triglyceride levels and higher blood pressure.

CONCLUSION: This largest to date population-based study on meat and gut microbiota suggests that meat intake, particularly processed red meat, may modify the gut microbiota composition, functional capacity, and health-related biomarkers.}, } @article {pmid39719199, year = {2025}, author = {Qi, Y and Fu, R and Yan, C and Liu, X and Liu, N}, title = {Enrichment of a heterotrophic nitrifying and aerobic denitrifying bacterial consortium: Microbial community succession and nitrogen removal characteristics and mechanisms.}, journal = {Bioresource technology}, volume = {419}, number = {}, pages = {132013}, doi = {10.1016/j.biortech.2024.132013}, pmid = {39719199}, issn = {1873-2976}, mesh = {*Denitrification ; *Nitrification ; *Nitrogen/metabolism ; Aerobiosis ; *Heterotrophic Processes ; *Microbial Consortia/physiology ; Bacteria/metabolism ; }, abstract = {This study cultivated a bacterial consortium (S60) from landfill leachate that exhibited effective heterotrophic nitrification and aerobic denitrification (HN-AD) properties. Under aerobic conditions, the removal of NH4[+]-N reached 100 % when the S60 consortium utilised NH4[+]-N either as the sole nitrogen source or in combination with NO2[-]-N and NO3[-]-N. Optimal HN-AD performance was achieved with sodium acetate as a carbon source and a pH of 7.0-8.0, dissolved oxygen concentration of 4.0-5.0 mg/L, and a C/N ratio of 10. Furthermore, the presence of functional genes (amoA, hao, napA, nirK, nirS, nosZ), hydroxylamine oxidase, nitrate reductase, and nitrite reductase was confirmed in the S60 consortium. Drawing from these findings, two HN-AD pathways were delineated: NH4[+]-N → NH2OH → NO2[-]-N → NO3[-]-N → NO2[-]-N → NO → N2O → N2 and NH4[+]-N → NH2OH → N2O → N2. Metagenomic binning analysis of the S60 consortium uncovered complete pathways for dissimilatory nitrate reduction and denitrification within Halomonas, Zobellella, Stutzerimonas, Marinobacter, and Pannonibacter. These findings offer new insights into the application of HN-AD bacteria and their collaborative nitrogen removal in environments with varying nitrogen sources.}, } @article {pmid39702789, year = {2025}, author = {Kaur, S and Patel, BCK and Collen, A and Malhotra, R}, title = {The microbiome and the eye: a new era in ophthalmology.}, journal = {Eye (London, England)}, volume = {39}, number = {3}, pages = {436-448}, pmid = {39702789}, issn = {1476-5454}, mesh = {Humans ; *Microbiota/physiology ; *Eye Diseases/microbiology/therapy ; *Ophthalmology ; *Gastrointestinal Microbiome/physiology ; Eye/microbiology ; Fecal Microbiota Transplantation ; }, abstract = {The human microbiome has progressively been recognised for its role in various disease processes. In ophthalmology, complex interactions between the gut and distinct ocular microbiota within each structure and microenvironment of the eye has advanced our knowledge on the multi-directional relationships of these ecosystems. Increasingly, studies have shown that modulation of the microbiome can be achieved through faecal microbiota transplantation and synbiotics producing favourable outcomes for ophthalmic diseases. As ophthalmologists, we are obliged to educate our patients on measures to cultivate a healthy gut microbiome through a range of holistic measures. Further integrative studies combining microbial metagenomics, metatranscriptomics and metabolomics are necessary to fully characterise the human microbiome and enable targeted therapeutic interventions.}, } @article {pmid39487079, year = {2025}, author = {Williams, AD and Leung, VW and Tang, JW and Hidekazu, N and Suzuki, N and Clarke, AC and Pearce, DA and Lam, TT}, title = {Ancient environmental microbiomes and the cryosphere.}, journal = {Trends in microbiology}, volume = {33}, number = {2}, pages = {233-249}, doi = {10.1016/j.tim.2024.09.010}, pmid = {39487079}, issn = {1878-4380}, mesh = {*Microbiota ; *Metagenomics ; *Environmental Microbiology ; Permafrost/microbiology ; Ice ; Bacteria/genetics/classification/isolation & purification ; Computational Biology/methods ; }, abstract = {In this review, we delineate the unique set of characteristics associated with cryosphere environments (namely, ice and permafrost) which present both challenges and opportunities for studying ancient environmental microbiomes (AEMs). In a field currently reliant on several assumptions, we discuss the theoretical and empirical feasibility of recovering microbial nucleic acids (NAs) from ice and permafrost with varying degrees of antiquity. We also summarize contamination control best practices and highlight considerations for the latest approaches, including shotgun metagenomics, and downstream bioinformatic authentication approaches. We review the adoption of existing software and provide an overview of more recently published programs, with reference to their suitability for AEM studies. Finally, we summarize outstanding challenges and likely future directions for AEM research.}, } @article {pmid39901058, year = {2025}, author = {Richardson, M and Zhao, S and Lin, L and Sheth, RU and Qu, Y and Lee, J and Moody, T and Ricaurte, D and Huang, Y and Velez-Cortes, F and Urtecho, G and Wang, HH}, title = {SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.}, journal = {Nature microbiology}, volume = {10}, number = {2}, pages = {527-540}, pmid = {39901058}, issn = {2058-5276}, support = {MCB-2025515//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; 2R01AI132403, 1R01DK118044, 1R01EB031935, 1R21AI146817//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; N00014-18-1-2237//United States Department of Defense | United States Navy | ONR | Office of Naval Research Global (ONR Global)/ ; 1016691//Burroughs Wellcome Fund (BWF)/ ; HR0011-23-2-0001//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; W911NF-22-2-0210//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Feces/microbiology ; Inulin/metabolism ; RNA, Ribosomal, 16S/genetics ; Metagenome ; }, abstract = {The local arrangement of microbes can profoundly impact community assembly, function and stability. However, our understanding of the spatial organization of the human gut microbiome at the micron scale is limited. Here we describe a high-throughput and streamlined method called Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) to capture spatial co-localization in a complex microbial consortium. The method obtains microbial composition of micron-scale subcommunities through split-and-pool barcoding. SAMPL-seq analysis of the healthy human gut microbiome identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These co-localized microbes organize into spatially distinct groups or 'spatial hubs' dominated by Bacteroidaceae, Ruminococcaceae and Lachnospiraceae families. Using inulin as a dietary perturbation, we observed reversible spatial rearrangement of the gut microbiome where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock insights into microbiomes at the micron scale.}, } @article {pmid39807898, year = {2025}, author = {Forry, SP and Servetas, SL and Dootz, JN and Hunter, ME and Kralj, JG and Filliben, JJ and Jackson, SA}, title = {A sensitivity analysis of methodological variables associated with microbiome measurements.}, journal = {Microbiology spectrum}, volume = {13}, number = {2}, pages = {e0069624}, doi = {10.1128/spectrum.00696-24}, pmid = {39807898}, issn = {2165-0497}, mesh = {*Metagenomics/methods ; *Feces/microbiology ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Sequence Analysis, DNA/methods ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; DNA, Bacterial/genetics ; }, abstract = {The experimental methods employed during metagenomic sequencing analyses of microbiome samples significantly impact the resulting data and typically vary substantially between laboratories. In this study, a full factorial experimental design was used to compare the effects of a select set of methodological choices (sample, operator, lot, extraction kit, variable region, and reference database) on the analysis of biologically diverse stool samples. For each parameter investigated, a main effect was calculated that allowed direct comparison both between methodological choices (bias effects) and between samples (real biological differences). Overall, methodological bias was found to be similar in magnitude to real biological differences while also exhibiting significant variations between individual taxa, even between closely related genera. The quantified method biases were then used to computationally improve the comparability of data sets collected under substantially different protocols. This investigation demonstrates a framework for quantitatively assessing methodological choices that could be routinely performed by individual laboratories to better understand their metagenomic sequencing workflows and to improve the scope of the datasets they produce.IMPORTANCEMethod-specific bias is a well-recognized challenge in metagenomic sequencing characterization of microbiome samples, but rigorous bias quantification is challenging. This report details a full factorial exploration of 48 experimental protocols by systematically varying microbiome sample, iterations of material production, laboratory personnel, DNA extraction kit, marker gene selection, and reference databases. Quantification of the biases associated with each parameter revealed similar magnitudes of variation arising from real biological differences and from varied analysis procedures. Furthermore, these measurement biases varied substantially with taxa, even between closely related genera. However, computational correction of method bias using a reference material was demonstrated that significantly harmonized metagenomic sequencing results collected using different analysis protocols.}, } @article {pmid39805953, year = {2025}, author = {Daruka, L and Czikkely, MS and Szili, P and Farkas, Z and Balogh, D and Grézal, G and Maharramov, E and Vu, TH and Sipos, L and Juhász, S and Dunai, A and Daraba, A and Számel, M and Sári, T and Stirling, T and Vásárhelyi, BM and Ari, E and Christodoulou, C and Manczinger, M and Enyedi, MZ and Jaksa, G and Kovács, K and van Houte, S and Pursey, E and Pintér, L and Haracska, L and Kintses, B and Papp, B and Pál, C}, title = {ESKAPE pathogens rapidly develop resistance against antibiotics in development in vitro.}, journal = {Nature microbiology}, volume = {10}, number = {2}, pages = {313-331}, pmid = {39805953}, issn = {2058-5276}, mesh = {*Anti-Bacterial Agents/pharmacology ; Humans ; *Microbial Sensitivity Tests ; Pseudomonas aeruginosa/drug effects/genetics/growth & development ; Drug Resistance, Bacterial/genetics ; Mutation ; Escherichia coli/drug effects/genetics/growth & development ; Metagenomics ; Gastrointestinal Microbiome/drug effects ; Acinetobacter baumannii/drug effects/genetics/growth & development ; Klebsiella pneumoniae/drug effects/genetics/growth & development ; Drug Resistance, Multiple, Bacterial/genetics ; Gram-Negative Bacteria/drug effects/genetics ; }, abstract = {Despite ongoing antibiotic development, evolution of resistance may render candidate antibiotics ineffective. Here we studied in vitro emergence of resistance to 13 antibiotics introduced after 2017 or currently in development, compared with in-use antibiotics. Laboratory evolution showed that clinically relevant resistance arises within 60 days of antibiotic exposure in Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa, priority Gram-negative ESKAPE pathogens. Resistance mutations are already present in natural populations of pathogens, indicating that resistance in nature can emerge through selection of pre-existing bacterial variants. Functional metagenomics showed that mobile resistance genes to antibiotic candidates are prevalent in clinical bacterial isolates, soil and human gut microbiomes. Overall, antibiotic candidates show similar susceptibility to resistance development as antibiotics currently in use, and the corresponding resistance mechanisms overlap. However, certain combinations of antibiotics and bacterial strains were less prone to developing resistance, revealing potential narrow-spectrum antibacterial therapies that could remain effective. Finally, we develop criteria to guide efforts in developing effective antibiotic candidates.}, } @article {pmid39794474, year = {2025}, author = {Yin, Q and da Silva, AC and Zorrilla, F and Almeida, AS and Patil, KR and Almeida, A}, title = {Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations.}, journal = {Nature microbiology}, volume = {10}, number = {2}, pages = {541-553}, pmid = {39794474}, issn = {2058-5276}, support = {MR/W016184/1//RCUK | Medical Research Council (MRC)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Enterobacteriaceae/genetics/classification/isolation & purification ; Metagenome ; Enterobacteriaceae Infections/microbiology ; Feces/microbiology ; Machine Learning ; }, abstract = {Gut bacteria from the Enterobacteriaceae family are a major cause of opportunistic infections worldwide. Given their prevalence among healthy human gut microbiomes, interspecies interactions may play a role in modulating infection resistance. Here we uncover global ecological patterns linked to Enterobacteriaceae colonization and abundance by leveraging a large-scale dataset of 12,238 public human gut metagenomes spanning 45 countries. Machine learning analyses identified a robust gut microbiome signature associated with Enterobacteriaceae colonization status, consistent across health states and geographic locations. We classified 172 gut microbial species as co-colonizers and 135 as co-excluders, revealing a genus-wide signal of colonization resistance within Faecalibacterium and strain-specific co-colonization patterns of the underexplored Faecalimonas phoceensis. Co-exclusion is linked to functions involved in short-chain fatty acid production, iron metabolism and quorum sensing, while co-colonization is linked to greater functional diversity and metabolic resemblance to Enterobacteriaceae. Our work underscores the critical role of the intestinal environment in the colonization success of gut-associated opportunistic pathogens with implications for developing non-antibiotic therapeutic strategies.}, } @article {pmid39745426, year = {2025}, author = {Gulyaeva, A and Liu, L and Garmaeva, S and Kruk, M and Weersma, RK and Harmsen, HJM and Zhernakova, A}, title = {Identification and characterization of Faecalibacterium prophages rich in diversity-generating retroelements.}, journal = {Microbiology spectrum}, volume = {13}, number = {2}, pages = {e0106624}, doi = {10.1128/spectrum.01066-24}, pmid = {39745426}, issn = {2165-0497}, mesh = {*Prophages/genetics/isolation & purification ; *Retroelements ; Humans ; *Metagenomics ; Genome, Viral/genetics ; Gastrointestinal Microbiome ; Computational Biology/methods ; Host Specificity ; Bacteriophages/genetics/classification/isolation & purification/physiology ; Genome, Bacterial/genetics ; Phylogeny ; Genetic Variation ; }, abstract = {Metagenomics has revealed the incredible diversity of phages within the human gut. However, very few of these phages have been subjected to in-depth experimental characterization. One promising method of obtaining novel phages for experimental characterization is through induction of the prophages integrated into the genomes of cultured gut bacteria. Here, we developed a bioinformatic approach to prophage identification that builds on prophage genomic properties, existing prophage-detecting software, and publicly available virome sequencing data. We applied our approach to 22 strains of bacteria belonging to the genus Faecalibacterium, resulting in identification of 15 candidate prophages, and validated the approach by demonstrating the activity of five prophages from four of the strains. The genomes of three active phages were identical or similar to those of known phages, while the other two active phages were not represented in the Viral RefSeq database. Four of the active phages possessed a diversity-generating retroelement (DGR), and one retroelement had two variable regions. DGRs of two phages were active at the time of the induction experiments, as evidenced by nucleotide variation in sequencing reads. We also predicted that the host range of two active phages may include multiple bacterial species. Finally, we noted that four phages were less prevalent in the metagenomes of inflammatory bowel disease patients compared to a general population cohort, a difference mainly explained by differences in the abundance of the host bacteria. Our study highlights the utility of prophage identification and induction for unraveling phage molecular mechanisms and ecological interactions.IMPORTANCEWhile hundreds of thousands of phage genomes have been discovered in metagenomics studies, only a few of these phages have been characterized experimentally. Here, we explore phage characterization through bioinformatic identification of prophages in genomes of cultured bacteria, followed by prophage induction. Using this approach, we detect the activity of five prophages in four strains of commensal gut bacteria Faecalibacterium. We further note that four of the prophages possess diversity-generating retroelements implicated in rapid mutation of phage genome loci associated with phage-host and phage-environment interactions and analyze the intricate patterns of retroelement activity. Our study highlights the potential of prophage characterization for elucidating complex molecular mechanisms employed by the phages.}, } @article {pmid39716679, year = {2025}, author = {Bai, X and Wu, J and Zhang, B and Zhao, H and Tian, F and Wang, B}, title = {Metagenomics reveals functional profiles of soil nitrogen and phosphorus cycling under different amendments in saline-alkali soil.}, journal = {Environmental research}, volume = {267}, number = {}, pages = {120686}, doi = {10.1016/j.envres.2024.120686}, pmid = {39716679}, issn = {1096-0953}, mesh = {*Phosphorus/analysis ; *Soil Microbiology ; *Soil/chemistry ; *Nitrogen/metabolism ; *Metagenomics ; China ; Manure/microbiology ; Nitrogen Cycle ; Fertilizers/analysis ; Salinity ; Alkalies/chemistry ; Microbiota ; }, abstract = {High salinity, low fertility and poor structure in saline-alkali soils led to nutrient cycling slow and microbial activity loss. The application of amendments has proven effective in enhancing soil nutrients, which significantly affects soil nitrogen and phosphorus cycling process. However, the specific impact of different amendments on the microbial functional potential related to nutrient cycling in saline-alkali soils remains unclear. Hence, metagenomics sequencing was used to investigate soil microbial communities and nitrogen and phosphorus cycling genes in response to different amendments, and to examine the influence of soil physicochemical properties on functional genes in the Hetao irrigation district of China. The results showed that amendments application enriched the Proteobacteria abundance, while inhibiting oligotrophic groups such as Chloroflexi. Compared to the control (CK), the combined application of desulfurization gypsum and cattle manure (DC) notably increased nasA (assimilatory nitrate reduction) and nirB (dissimilatory nitrate reduction), as well as phoD and phoA genes (organic P mineralization). Furthermore, soil AK and AP were primary factors affecting microbial communities and N and P cycling genes. Overall, this study offers valuable insights into soil nitrogen and phosphorus cycling genes and their interactions in response to different amendments, where the application of amendments affects nitrogen and phosphorus cycling by altering soil nutrient availability.}, } @article {pmid39701354, year = {2025}, author = {Liu, J and Zhou, M and Zhou, L and Dang, R and Xiao, L and Tan, Y and Li, M and Yu, J and Zhang, P and Hernández, M and Lichtfouse, E}, title = {Methane production related to microbiota in dairy cattle feces.}, journal = {Environmental research}, volume = {267}, number = {}, pages = {120642}, doi = {10.1016/j.envres.2024.120642}, pmid = {39701354}, issn = {1096-0953}, mesh = {Animals ; *Methane/metabolism/biosynthesis ; Cattle ; *Feces/microbiology ; *Archaea/metabolism/genetics ; Bacteria/metabolism/genetics/classification ; Microbiota ; Dairying ; }, abstract = {Methane (CH4) emission from livestock feces, led by ruminants, shows a profound impact on global warming. Despite this, we have almost no information on the syntrophy of the intact microbiome metabolisms, from carbohydrates to the one-carbon units, covering multiple stages of ruminant development. In this study, syntrophic effects of polysaccharide degradation and acetate-producing bacteria, and methanogenic archaea were revealed through metagenome-assembled genomes from water saturated dairy cattle feces. Although CH4 is thought to be produced by archaea, more edges, nodes, and balanced interaction types revealed by network analysis provided a closed bacteria-archaea network. The CH4 production potential and pathways were further evaluated through dynamic, thermodynamic and [13]C stable isotope analysis. The powerful CH4 production potential benefited from the metabolic flux: classical polysaccharides, soluble sugar (glucose, galactose, lactose), acetate, and CH4 produced via typical acetoclastic methanogenesis. In comparison, a cooperative model dominated by hydrogenotrophic methanogenic archaea presented a weak ability to generate CH4. Our findings comprehensively link carbon and CH4 metabolism paradigm to specific microbial lineages which are shaped related to developmental stages of the dairy cattle, directing influencing global warming from livestock and waste treatment.}, } @article {pmid39670752, year = {2025}, author = {Peterson, D and Weidenmaier, C and Timberlake, S and Gura Sadovsky, R}, title = {Depletion of key gut bacteria predicts disrupted bile acid metabolism in inflammatory bowel disease.}, journal = {Microbiology spectrum}, volume = {13}, number = {2}, pages = {e0199924}, doi = {10.1128/spectrum.01999-24}, pmid = {39670752}, issn = {2165-0497}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bile Acids and Salts/metabolism ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Feces/microbiology ; *Clostridium/genetics/metabolism/isolation & purification ; Animals ; Mice ; Bacteria/classification/genetics/metabolism/isolation & purification ; Operon ; Metagenomics ; Metagenome ; }, abstract = {The gut microbiome plays a key role in bile acid (BA) metabolism, where a diversity of metabolic products contribute to human health and disease. In particular, Inflammatory Bowel Disease (IBD) is characterized by a low concentration of secondary bile acids (SBAs), whose transformation from primary bile acids (PBAs) is an essential function performed solely by gut bacteria. BA-transformation activity mediated by the bile acid inducible (bai) operon has been functionally characterized in the genus Clostridium, and homologous bai gene sequences have been found in metagenome-assembled genomes (MAGs) belonging to other taxa in the human gut, but it is unclear which species of bai-carrying bacteria perform physiologically significant amounts of bile acid transformation in healthy and sick individuals. Here, we analyzed hundreds of stool samples with paired metagenomic and metabolomic data from IBD patients and controls and found that the abundance of the bai operon in metagenomic samples was highly predictive of that sample's high- or low-SBA metabolic state. We further found that bai genes from the Clostridium species best characterized as BA transformers were more prevalent in IBD patients than in non-IBD controls, while bai genes from uncharacterized taxa known only from MAGs were much more physiologically relevant in non-IBD samples. These un-isolated clades of BA-transforming bacteria merit further research; as beyond their prevalence in the human population, we found some cases in which they engrafted in IBD patients who had undergone fecal microbiota transplantation and experienced a clinical response.IMPORTANCEIn this paper, we identify specific bacteria that perform an important metabolic function in the human gut and demonstrate that in the guts of a large subset of patients with IBD, these bacteria are missing and the function is defective. This is a rare example where the correlation between the absence of specific bacteria and the dysfunction of metabolism is directly observed, not in mice nor in the lab, but in physiologic microbial communities in the human gut. Our results point to a path for studying how a small but important set of bacteria is affected by conditions in the IBD gut and perhaps to the development of interventions to mitigate the loss of these bacteria in IBD.}, } @article {pmid39665565, year = {2025}, author = {Gao, X and Liang, H and Hu, T and Zou, Y and Xiao, L}, title = {Cultivated genome references for protein database construction and high-resolution taxonomic annotation in metaproteomics.}, journal = {Microbiology spectrum}, volume = {13}, number = {2}, pages = {e0175524}, doi = {10.1128/spectrum.01755-24}, pmid = {39665565}, issn = {2165-0497}, support = {No. 32100009//MOST | National Natural Science Foundation of China (NSFC)/ ; No.XMHT20220104017//Shenzhen Municipal Science and Technology Innovation Council | Shenzhen Key Laboratory Fund ()/ ; }, mesh = {*Proteomics/methods ; *Metagenomics/methods ; *Databases, Protein ; *Gastrointestinal Microbiome/genetics ; Bacterial Proteins/genetics/metabolism ; Peptides/genetics/metabolism ; Molecular Sequence Annotation ; Genome, Bacterial/genetics ; Metagenome ; Bacteria/genetics/classification ; }, abstract = {Metaproteomics offers a profound understanding of the functional dynamics of the gut microbiome, which is crucial for personalized healthcare strategies. The selection of an appropriate database is a critical step for the identification of peptides and proteins, as well as for the provision of accurate taxonomic and functional annotations. The matched metagenomic-derived database is considered to be the best, but its limitations include the identification of low-abundance organisms and taxonomic resolution. Herein, we constructed a protein database (DBCGR2) based on Cultivated Genome Reference 2 (CGR2) and developed a complete peptide-centric analysis workflow for database searching and for the annotation of taxonomy and function. This workflow was subsequently appraised in comparison with metagenomics-derived databases for the analysis of metaproteomic data. Our findings suggested that the performance of DBCGR2 in identification was comparable with metagenomics-derived databases with improvement in identification rates of peptides from low-abundance species. The database searching results could be fully annotated using the pepTaxa taxonomic annotation approach developed in this study, and the taxonomic resolution was enhanced to strain level. Additionally, the results demonstrated that the sensitivity of functional annotation could be enhanced by employing DBCGR2. Overall, the DBCGR2 combined with pepTaxa can be considered an alternative for metaproteomic data analysis with superior analysis performances.IMPORTANCEMass spectrometry-based metaproteomics offers a profound understanding of the gut microbial taxonomy and functionality. The databases utilized in the analysis of metaproteomic data are crucial, as they determine the identification of proteins that can be recognized and linked to overall human health, in addition to the quality of taxonomic and functional annotation. Among the most effective approaches for constructing protein databases is the utilization of metagenomic sequencing to create matched databases. However, the database, derived from isolated genomes, has yet to undergo rigorous testing for their efficacy and accuracy in protein identification and taxonomic and functional annotation. Here, we constructed a protein database DBCGR2 derived from Cultivated Genome Reference 2 (CGR2) and a complete workflow for data analysis. We compared the performances of DBCGR2 and metagenomics-derived databases. Our results indicated that DBCGR2 can be regarded as an alternative to metagenomics-derived databases, which contribute to metaproteomic data analysis.}, } @article {pmid39900940, year = {2025}, author = {Prabhaharan, D and Go, YW and Kim, H and Kang, S and Sang, BI}, title = {Representative Metagenomes of Mesophilic Biogas Reactor Across South Korea.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {198}, pmid = {39900940}, issn = {2052-4463}, support = {MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; }, mesh = {Republic of Korea ; *Biofuels ; *Metagenome ; *Bioreactors ; Microbiota ; Anaerobiosis ; }, abstract = {Biogas production through the anaerobic digestion (AD) of organic waste plays a crucial role in promoting sustainability and closing the carbon cycle. Over the past decade, this has driven global research on biogas-producing microbiomes, leading to significant advances in our understanding of microbial diversity and metabolic pathways within AD plants. However, substantial knowledge gaps persist, particularly in understanding the specific microbial communities involved in biogas production in countries such as South Korea. The present dataset addresses one of these gaps by providing comprehensive information on the metagenomes of five full-scale mesophilic biogas reactors in South Korea. From 110 GB of raw DNA sequences, 401 metagenome-assembled genomes (MAGs) were created, which include 42,301 annotated genes. Of these, 187 MAGs (46.7%) were classified as high-quality based on Minimum Information about Metagenome-Assembled Genome (MIMAG) standards. The data presented here contribute to a broader understanding of biogas-specific microbial communities and offers a significant resource for future studies and advancements in sustainable biogas production.}, } @article {pmid39900569, year = {2025}, author = {Priest, T and Oldenburg, E and Popa, O and Dede, B and Metfies, K and von Appen, WJ and Torres-Valdés, S and Bienhold, C and Fuchs, BM and Amann, R and Boetius, A and Wietz, M}, title = {Seasonal recurrence and modular assembly of an Arctic pelagic marine microbiome.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1326}, pmid = {39900569}, issn = {2041-1723}, mesh = {Arctic Regions ; *Seasons ; *Microbiota/genetics ; *Seawater/microbiology ; *Oceans and Seas ; Metagenomics/methods ; Bacteria/genetics/classification/metabolism ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; DNA Barcoding, Taxonomic ; Metagenome ; Phylogeny ; }, abstract = {Deciphering how microbial communities are shaped by environmental variability is fundamental for understanding the structure and function of ocean ecosystems. While seasonal environmental gradients have been shown to structure the taxonomic dynamics of microbiomes over time, little is known about their impact on functional dynamics and the coupling between taxonomy and function. Here, we demonstrate annually recurrent, seasonal structuring of taxonomic and functional dynamics in a pelagic Arctic Ocean microbiome by combining autonomous samplers and in situ sensors with long-read metagenomics and SSU ribosomal metabarcoding. Specifically, we identified five temporal microbiome modules whose succession within each annual cycle represents a transition across different ecological states. For instance, Cand. Nitrosopumilus, Syndiniales, and the machinery to oxidise ammonia and reduce nitrite are signatures of early polar night, while late summer is characterised by Amylibacter and sulfur compound metabolism. Leveraging metatranscriptomes from Tara Oceans, we also demonstrate the consistency in functional dynamics across the wider Arctic Ocean during similar temporal periods. Furthermore, the structuring of genetic diversity within functions over time indicates that environmental selection pressure acts heterogeneously on microbiomes across seasons. By integrating taxonomic, functional and environmental information, our study provides fundamental insights into how microbiomes are structured under pronounced seasonal changes in understudied, yet rapidly changing polar marine ecosystems.}, } @article {pmid39900484, year = {2025}, author = {Van Etten, J and Stephens, TG and Bhattacharya, D}, title = {Genetic Transfer in Action: Uncovering DNA Flow in an Extremophilic Microbial Community.}, journal = {Environmental microbiology}, volume = {27}, number = {2}, pages = {e70048}, doi = {10.1111/1462-2920.70048}, pmid = {39900484}, issn = {1462-2920}, support = {//U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231/ ; 10.46936/10.25585/60000481//Joint Genome Institute/ ; NJ01180//National Institute of Food and Agriculture/ ; 80NSSC19K1542/NASA/NASA/United States ; NASA (80NSSC19K0462)/NASA/NASA/United States ; }, mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/classification ; Extremophiles/genetics ; Microbiota/genetics ; DNA, Bacterial/genetics ; Genome, Bacterial ; }, abstract = {Horizontal genetic transfer (HGT) is a significant driver of genomic novelty in all domains of life. HGT has been investigated in many studies however, the focus has been on conspicuous protein-coding DNA transfers that often prove to be adaptive in recipient organisms and are therefore fixed longer-term in lineages. These results comprise a subclass of HGTs and do not represent exhaustive (coding and non-coding) DNA transfer and its impact on ecology. Uncovering exhaustive HGT can provide key insights into the connectivity of genomes in communities and how these transfers may occur. In this study, we use the term frequency-inverse document frequency (TF-IDF) technique, that has been used successfully to mine DNA transfers within real and simulated high-quality prokaryote genomes, to search for exhaustive HGTs within an extremophilic microbial community. We establish a pipeline for validating transfers identified using this approach. We find that most DNA transfers are within-domain and involve non-coding DNA. A relatively high proportion of the predicted protein-coding HGTs appear to encode transposase activity, restriction-modification system components, and biofilm formation functions. Our study demonstrates the utility of the TF-IDF approach for HGT detection and provides insights into the mechanisms of recent DNA transfer.}, } @article {pmid39897560, year = {2025}, author = {Zhang, P and Guo, R and Ma, S and Jiang, H and Yan, Q and Li, S and Wang, K and Deng, J and Zhang, Y and Zhang, Y and Wang, G and Chen, L and Li, L and Guo, X and Zhao, G and Yang, L and Wang, Y and Kang, J and Sha, S and Fan, S and Cheng, L and Meng, J and Yu, H and Chen, F and He, D and Wang, J and Liu, S and Shi, H}, title = {A metagenome-wide study of the gut virome in chronic kidney disease.}, journal = {Theranostics}, volume = {15}, number = {5}, pages = {1642-1661}, pmid = {39897560}, issn = {1838-7640}, mesh = {Humans ; *Renal Insufficiency, Chronic/virology ; *Virome/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; *Feces/virology/microbiology ; Middle Aged ; Male ; Female ; Aged ; Dysbiosis/virology/microbiology ; Adult ; Viruses/genetics/classification/isolation & purification ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {Rationale: Chronic kidney disease (CKD) is a progressively debilitating condition leading to kidney dysfunction and severe complications. While dysbiosis of the gut bacteriome has been linked to CKD, the alteration in the gut viral community and its role in CKD remain poorly understood. Methods: Here, we characterize the gut virome in CKD using metagenome-wide analyses of faecal samples from 425 patients and 290 healthy individuals. Results: CKD is associated with a remarkable shift in the gut viral profile that occurs regardless of host properties, disease stage, and underlying diseases. We identify 4,649 differentially abundant viral operational taxonomic units (vOTUs) and reveal that some CKD-enriched viruses are closely related to gut bacterial taxa such as Bacteroides, [Ruminococcus], Erysipelatoclostridium, and Enterocloster spp. In contrast, CKD-depleted viruses include more crAss-like viruses and often target Faecalibacterium, Ruminococcus, and Prevotella species. Functional annotation of the vOTUs reveals numerous viral functional signatures associated with CKD, notably a marked reduction in nicotinamide adenine dinucleotide (NAD[+]) synthesis capacity within the CKD-associated virome. Furthermore, most CKD viral signatures are reproducible in the gut viromes of diabetic kidney disease and several other common diseases, highlighting the considerable universality of disease-associated viromes. Conclusions: This research provides comprehensive resources and novel insights into the CKD-associated gut virome, offering valuable guidance for future mechanistic and therapeutic investigations.}, } @article {pmid39895074, year = {2025}, author = {Lee, KA and Ul-Haq, A and Seo, H and Jo, S and Kim, S and Song, HY and Kim, HS}, title = {Characteristics of skin microbiome associated with disease severity in systemic sclerosis.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {63}, number = {1}, pages = {e.2409018}, doi = {10.71150/jm.2409018}, pmid = {39895074}, issn = {1976-3794}, support = {//Korea Health Industry Development Institute/ ; HI21C1888//Ministry of Health and Welfare/ ; //National Research Foundation of Korea/ ; RS-2023-00219563//Ministry of Science and ICT/ ; //Soonchunhyang University Research Fund/ ; }, mesh = {Humans ; *Scleroderma, Systemic/microbiology ; *Skin/microbiology/pathology ; *Microbiota ; Female ; Middle Aged ; Male ; *RNA, Ribosomal, 16S/genetics ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Severity of Illness Index ; Aged ; Biomarkers ; Metagenomics ; }, abstract = {Systemic sclerosis (SSc) is a chronic autoimmune disorder characterised by skin fibrosis and internal organ involvement. Disruptions in the microbial communities on the skin may contribute to the onset of autoimmune diseases that affect the skin. However, current research on the skin microbiome in SSc is lacking. This study aimed to investigate skin microbiome associated with disease severity in SSc. Skin swabs were collected from the upper limbs of 46 healthy controls (HCs) and 36 patients with SSc. Metagenomic analysis based on the 16S rRNA gene was conducted and stratified by cutaneous subtype and modified Rodnan skin score (mRSS) severity. Significant differences in skin bacterial communities were observed between the HCs and patients with SSc, with further significant variations based on subtype and mRSS severity. The identified biomarkers were Bacteroides and Faecalibacterium for patients with diffuse cutaneous SSc with high mRSS (≥ 10) and Mycobacterium and Parabacteroides for those with low mRSS (< 10). Gardnerella, Abies, Lactobacillus, and Roseburia were the biomarkers in patients with limited cutaneous SSc (lcSS) and high mRSS, whereas Coprococcus predominated in patients with lcSS and low mRSS. Cutaneous subtype analysis identified Pediococcus as a biomarker in the HCs, whereas mRSS analysis revealed the presence of Pseudomonas in conjunction with Pediococcus. In conclusion, patients with SSc exhibit distinct skin microbiota compared with healthy controls. Bacterial composition varies by systemic sclerosis cutaneous subtype and skin thickness.}, } @article {pmid39868213, year = {2025}, author = {Schechter, MS and Trigodet, F and Veseli, IA and Miller, SE and Klein, ML and Sever, M and Maignien, L and Delmont, TO and Light, SH and Eren, AM}, title = {Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39868213}, issn = {2692-8205}, support = {T32 GM007197/GM/NIGMS NIH HHS/United States ; }, abstract = {The increasing availability of microbial genomes is essential to gain insights into microbial ecology and evolution that can propel biotechnological and biomedical advances. Recent advances in genome recovery have significantly expanded the catalogue of microbial genomes from diverse habitats. However, the ability to explain how well a set of genomes account for the diversity in a given environment remains challenging for individual studies or biome-specific databases. Here we present EcoPhylo, a computational workflow to characterize the phylogeography of any gene family through integrated analyses of genomes and metagenomes, and our application of this approach to ribosomal proteins to quantify phylogeny-aware genome recovery rates across three biomes. Our findings show that genome recovery rates vary widely across taxa and biomes, and that single amplified genomes, metagenome-assembled genomes, and isolate genomes have non-uniform yet quantifiable representation of environmental microbes. EcoPhylo reveals highly resolved, reference-free, multi-domain phylogenies in conjunction with distribution patterns of individual clades across environments, providing a means to assess genome recovery in individual studies and benchmark biome-level genome collections.}, } @article {pmid39856391, year = {2025}, author = {Tisza, MJ and Lloyd, RE and Hoffman, K and Smith, DP and Rewers, M and Javornik Cregeen, SJ and Petrosino, JF}, title = {Longitudinal phage-bacteria dynamics in the early life gut microbiome.}, journal = {Nature microbiology}, volume = {10}, number = {2}, pages = {420-430}, pmid = {39856391}, issn = {2058-5276}, support = {U01 DK063821/DK/NIDDK NIH HHS/United States ; U01 DK63865//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; U01 DK63829//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; UC4 DK063821/DK/NIDDK NIH HHS/United States ; U01 DK63821//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Bacteriophages/genetics/physiology/classification ; Infant ; *Bacteria/virology/genetics/classification/isolation & purification ; Child, Preschool ; Longitudinal Studies ; Metagenome ; Diabetes Mellitus, Type 1/microbiology/virology ; Feces/microbiology ; Female ; Male ; Metagenomics ; Infant, Newborn ; }, abstract = {Microbial colonization of the human gut occurs soon after birth, proceeds through well-studied phases and is affected by lifestyle and other factors. Less is known about phage community dynamics during infant gut colonization due to small study sizes, an inability to leverage large databases and a lack of appropriate bioinformatics tools. Here we reanalysed whole microbial community shotgun sequencing data of 12,262 longitudinal samples from 887 children from four countries across four years of life as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We developed an extensive metagenome-assembled genome catalogue using the Marker-MAGu pipeline, which comprised 49,111 phage taxa from existing human microbiome datasets. This was used to identify phage marker genes and their integration into the MetaPhlAn 4 bacterial marker gene database enabled simultaneous assessment of phage and bacterial dynamics. We found that individual children are colonized by hundreds of different phages, which are more transitory than bacteria, accumulating a more diverse phage community over time. Type 1 diabetes correlated with a decreased rate of change in bacterial and viral communities in children aged one and two. The addition of phage data improved the ability of machine learning models to discriminate samples by country. Finally, although phage populations were specific to individuals, we observed trends of phage ecological succession that correlated well with putative host bacteria. This resource improves our understanding of phage-bacteria interactions in the developing early life microbiome.}, } @article {pmid39833544, year = {2025}, author = {Yan, X and Liu, Y and Hu, T and Huang, Z and Li, C and Guo, L and Liu, Y and Li, N and Zhang, H and Sun, Y and Yi, L and Wu, J and Feng, J and Zhang, F and Jiang, T and Tu, C and He, B}, title = {A compendium of 8,176 bat RNA viral metagenomes reveals ecological drivers and circulation dynamics.}, journal = {Nature microbiology}, volume = {10}, number = {2}, pages = {554-568}, pmid = {39833544}, issn = {2058-5276}, support = {32192423//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32022083//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32192424//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32371562//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Chiroptera/virology ; Animals ; China ; *Metagenome ; *Virome/genetics ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; RNA, Viral/genetics ; Humans ; Genetic Variation ; Genome, Viral/genetics ; Metagenomics/methods ; }, abstract = {Bats are natural hosts for many emerging viruses for which spillover to humans is a major risk, but the diversity and ecology of bat viruses is poorly understood. Here we generated 8,176 RNA viral metagenomes by metatranscriptomic sequencing of organ and swab samples from 4,143 bats representing 40 species across 52 locations in China. The resulting database, the BtCN-Virome, expands bat RNA virus diversity by over 3.4-fold. Some viruses in the BtCN-Virome are traced to mammals, birds, arthropods, mollusks and plants. Diet, infection dynamics and environmental parameters such as humidity and forest coverage shape virus distribution. Compared with those in the wild, bats dwelling in human settlements harboured more diverse viruses that also circulated in humans and domestic animals, including Nipah and Lloviu viruses not previously reported in China. The BtCN-Virome provides important insights into the genetic diversity, ecological drivers and circulation dynamics of bat viruses, highlighting the need for surveillance of bats near human settlements.}, } @article {pmid39777507, year = {2025}, author = {Shelton, AN and Yu, FB and Grossman, AR and Bhaya, D}, title = {Abundant and active community members respond to diel cycles in hot spring phototrophic mats.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf001}, pmid = {39777507}, issn = {1751-7370}, support = {2125965//NSF/ ; 1921429//BBSRC-NSF/BIO/ ; //Office of Science of the U.S. Department of Energy/ ; }, mesh = {*Hot Springs/microbiology ; Metagenome ; Photosynthesis ; Phototrophic Processes ; Bacteria/genetics/classification/isolation & purification/metabolism ; Metagenomics ; Microbiota ; Transcriptome ; }, abstract = {Photosynthetic microbial mats in hot springs can provide insights into the diel behaviors of communities in extreme environments. In this habitat, photosynthesis dominates during the day, leading to super-oxic conditions, with a rapid transition to fermentation and anoxia at night. Multiple samples were collected from two springs over several years to generate metagenomic and metatranscriptomic datasets. Metagenome-assembled genomes comprised 71 taxa (in 19 different phyla), of which 12 core taxa were present at high abundance in both springs. The eight most active taxa identified by metatranscriptomics were an oxygenic cyanobacterium (Synechococcus sp.), five anoxygenic phototrophs from three different phyla, and two understudied heterotrophs from phylum Armatimonadota. In all eight taxa, a significant fraction of genes exhibited a diel expression pattern, although peak timing varied considerably. The two abundant heterotrophs exhibit starkly different peak timing of expression, which we propose is shaped by their metabolic and genomic potential to use carbon sources that become differentially available during the diel cycle. Network analysis revealed pathway expression patterns that had not previously been linked to diel cycles, including ribosome biogenesis and chaperones. This provides a framework for analyzing metabolically coupled communities and the dominant role of the diel cycle.}, } @article {pmid39761633, year = {2025}, author = {Lake, BB and McAdams, ZL and Ericsson, AC and Reinero, C and Gull, T and Lyons, BM}, title = {Feline urethral obstruction alters the urinary microbiota and comparison to oral, preputial, and rectal microbiotas.}, journal = {American journal of veterinary research}, volume = {86}, number = {2}, pages = {}, doi = {10.2460/ajvr.24.07.0213}, pmid = {39761633}, issn = {1943-5681}, mesh = {Animals ; Cats ; *Cat Diseases/microbiology/urine ; *Microbiota ; Male ; *Urethral Obstruction/veterinary/microbiology ; *Rectum/microbiology ; *RNA, Ribosomal, 16S/genetics ; Female ; Prospective Studies ; Mouth/microbiology ; Case-Control Studies ; }, abstract = {OBJECTIVE: To document differences in the microbiota of healthy cats versus cats with urethral obstruction (UO); compare the urinary microbiota with the oral, preputial, and rectal microbiota; and demonstrate that 16S rRNA gene sequencing will reveal rich and diverse urinary microbiota.

METHODS: 15 client-owned cats with UO and 15 age-matched healthy cats were included from July 2020 through April 2021. Exclusion criteria were evidence of urinary tract infection, urolithiasis, antimicrobial administration, urinary catheterization in the past 30 days, or a comorbidity. This study was a prospective, observational study. Both groups had a baseline CBC, chemistry panel, urinalysis, urine culture, and focal bladder ultrasound. Swabs of the cystocentesis site, buccal mucosa, rectum, prepuce, and urinary samples were collected, and 16S rRNA gene sequencing was used to compare the groups and sites.

RESULTS: Differences in the microbiota richness and diversity were found in the urine of cats with UO (n = 15) compared to healthy cats (15), along with differences in the preputial and oral samples, supporting the presence of a urinary dysbiosis in cats with UO.

CONCLUSIONS: Our preliminary data demonstrates a dramatic change in the urinary microbiota of cats with UO along with changes in microbiota in other sites compared to healthy cats.

CLINICAL RELEVANCE: A urinary dysbiosis in cats with UO has been minimally supported in prior studies using 16S rRNA gene sequencing. Although these are preliminary results, documenting this dysbiosis in cats with UO provides a potential avenue for novel therapeutics.}, } @article {pmid39693209, year = {2025}, author = {Yamamoto, A and Kawashima, A and Uemura, T and Nakano, K and Matsushita, M and Ishizuya, Y and Jingushi, K and Hase, H and Katayama, K and Yamaguchi, R and Sassi, N and Motoyama, Y and Nojima, S and Mita, M and Kimura, T and Motooka, D and Horibe, Y and Okuda, Y and Oka, T and Yamamichi, G and Tomiyama, E and Koh, Y and Yamamoto, Y and Kato, T and Hatano, K and Uemura, M and Imoto, S and Wada, H and Morii, E and Tsujikawa, K and Nonomura, N}, title = {A novel mouse model of upper tract urothelial carcinoma highlights the impact of dietary intervention on gut microbiota and carcinogenesis prevention despite carcinogen exposure.}, journal = {International journal of cancer}, volume = {156}, number = {7}, pages = {1439-1456}, doi = {10.1002/ijc.35295}, pmid = {39693209}, issn = {1097-0215}, support = {19K09709//Japan Society for the Promotion of Science/ ; 21K20968//Japan Society for the Promotion of Science/ ; 22H03213//Japan Society for the Promotion of Science/ ; 22K09523//Japan Society for the Promotion of Science/ ; 22K18398//Japan Society for the Promotion of Science/ ; JP22ym0126809i0002//Japan Agency for Medical Research and Development/ ; JP23ama121054//Japan Agency for Medical Research and Development/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; Female ; *Disease Models, Animal ; Humans ; *Carcinogens/toxicity ; Male ; *Butylhydroxybutylnitrosamine ; Carcinogenesis ; Mice, Inbred BALB C ; Urinary Bladder Neoplasms/prevention & control/chemically induced/etiology/pathology ; Urologic Neoplasms/prevention & control/diet therapy/etiology/chemically induced/pathology ; Urothelium/pathology/metabolism/microbiology ; }, abstract = {Animal models of N-butyl-N-(4-hydroxy butyl) nitrosamine (BBN)-induced urothelial carcinoma (UC), particularly bladder cancer (BC), have long been established. However, the rare incidence of BBN-induced upper urinary tract UC (UTUC), which originates from the same urothelium as BC, remains elusive. The scarcity of animal models of UTUC has made it challenging to study the biology of UTUC. To address this problem, we tried to establish a novel mouse model of UTUC by treating multiple mice strains and sexes with BBN. The molecular consistency between the UTUC mouse model and human UTUC was confirmed using multi-omics analyses, including whole-exome, whole-transcriptome, and spatial transcriptome sequencing. 16S ribosomal RNA metagenome sequencing, metabolome analysis, and dietary interventions were employed to assess changes in the gut microbiome, metabolome, and carcinogenesis of UTUC. Of all treated mice, only female BALB/c mice developed UTUC over BC. Multi-omics analyses confirmed that the UTUC model reflected the molecular characteristics and heterogeneity of human UTUC with poor prognosis. Furthermore, the model exhibited increased Tnf-related inflammatory gene expression in the upper urinary tract and a low relative abundance of Parabacteroides distasonis in the gut. Dietary intervention, mainly without alanine, led to P. distasonis upregulation and successfully prevented UTUC, as well as suppressed Tnf-related inflammatory gene expression in the upper urinary tract despite the exposure to BBN. This is the first report to demonstrate a higher incidence of UTUC than BC in a non-engineered mouse model using BBN. Overall, this model could serve as a useful tool for comprehensively investigating UTUC in future studies.}, } @article {pmid39893166, year = {2025}, author = {Bourquin, M and Peter, H and Michoud, G and Busi, SB and Kohler, TJ and Robison, AL and Styllas, M and Ezzat, L and Geers, AU and Huss, M and Fodelianakis, S and , and Battin, TJ}, title = {Predicting climate-change impacts on the global glacier-fed stream microbiome.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1264}, pmid = {39893166}, issn = {2041-1723}, mesh = {*Microbiota/genetics ; *Ice Cover/microbiology ; *Climate Change ; *Phylogeny ; *Bacteria/genetics/classification ; *Rivers/microbiology ; Metagenome ; Biodiversity ; Ecosystem ; }, abstract = {The shrinkage of glaciers and the vanishing of glacier-fed streams (GFSs) are emblematic of climate change. However, forecasts of how GFS microbiome structure and function will change under projected climate change scenarios are lacking. Combining 2,333 prokaryotic metagenome-assembled genomes with climatic, glaciological, and environmental data collected by the Vanishing Glaciers project from 164 GFSs draining Earth's major mountain ranges, we here predict the future of the GFS microbiome until the end of the century under various climate change scenarios. Our model framework is rooted in a space-for-time substitution design and leverages statistical learning approaches. We predict that declining environmental selection promotes primary production in GFSs, stimulating both bacterial biomass and biodiversity. Concomitantly, predictions suggest that the phylogenetic structure of the GFS microbiome will change and entire bacterial clades are at risk. Furthermore, genomic projections reveal that microbiome functions will shift, with intensified solar energy acquisition pathways, heterotrophy and algal-bacterial interactions. Altogether, we project a 'greener' future of the world's GFSs accompanied by a loss of clades that have adapted to environmental harshness, with consequences for ecosystem functioning.}, } @article {pmid39893159, year = {2025}, author = {Sampson, TR and Wallen, ZD and Won, WJ and Standaert, DG and Payami, H and Harms, AS}, title = {Alpha synuclein overexpression can drive microbiome dysbiosis in mice.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {4014}, pmid = {39893159}, issn = {2045-2322}, support = {ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-000375//Aligning Science Across Parkinson's/ ; }, mesh = {Animals ; *alpha-Synuclein/metabolism/genetics ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Mice ; *Mice, Transgenic ; *Parkinson Disease/microbiology/metabolism/genetics ; Disease Models, Animal ; Humans ; Aging ; Male ; }, abstract = {Growing evidence indicates that persons with Parkinson disease (PD), have a unique composition of indigenous gut microbes. Given the long prodromal or pre-diagnosed period, longitudinal studies of the human and rodent gut microbiome before symptomatic onset and for the duration of the disease are currently lacking. PD is partially characterized by the accumulation of the protein α-synuclein (α-syn) into insoluble aggregates, in both the central and enteric nervous systems. As such, several experimental rodent and non-human primate models of α-syn overexpression recapitulate some of the hallmark pathophysiologies of PD. These animal models provide an opportunity to assess how the gut microbiome changes with age under disease-relevant conditions. Here, we used a transgenic mouse strain, which overexpress wild-type human α-syn to test how the gut microbiome composition responds in this model of PD pathology during aging. Using shotgun metagenomics, we find significant, age and genotype-dependent bacterial taxa whose abundance becomes altered with age. We reveal that α-syn overexpression can drive alterations to the gut microbiome composition and suggest that it limits diversity through age. Taxa that were most affected by genotype-age interaction were Lactobacillus and Bifidobacteria. In a mouse model, we showed direct link between alpha synuclein geneotype (hallmark of PD), a dysbiotic and low-diversity gut microbiome, and dysbiotic levels of Bifidobacteria and Lactobacillus (most robust features of PD microbiome). Given emerging data on the potential contributions of the gut microbiome to PD pathologies, our data provide an experimental foundation to understand how the PD-associated microbiome may arise as a trigger or co-pathology to disease.}, } @article {pmid39793775, year = {2025}, author = {Li, X and Ning, L and Zhao, H and Gu, C and Han, Y and Xu, W and Si, Y and Xu, Y and Wang, R and Ren, Q}, title = {Jiawei Ermiao Granules (JWEMGs) clear persistent HR-HPV infection though improving vaginal microecology.}, journal = {Journal of ethnopharmacology}, volume = {341}, number = {}, pages = {119342}, doi = {10.1016/j.jep.2025.119342}, pmid = {39793775}, issn = {1872-7573}, mesh = {Female ; Humans ; *Vagina/microbiology/drug effects/pathology ; *Papillomavirus Infections/drug therapy ; *Drugs, Chinese Herbal/pharmacology ; Adult ; Middle Aged ; Microbiota/drug effects ; Antiviral Agents/pharmacology ; Cytokines/metabolism ; Young Adult ; }, abstract = {Jiawei Ermiao Granules (JWEMGs), a traditional Chinese herbal formulation, has been widely used in China for the treatment of human papillomavirus (HPV) infections. However, the underlying mechanisms through which it exerts its antiviral effects remain poorly understood.

AIM OF THE STUDY: This study aimed to investigate the potential mechanisms by which JWEMGs modulate vaginal microecology and clear HPV infections, utilizing clinical trials, metagenomic sequencing, and in vitro models.

MATERIALS AND METHODS: Clinical indicators related to vaginal microecology, such as vaginal pH, cleanliness, Nugent score, Donders score, catalase, neuraminidase, and leukocyte esterase, were evaluated in 65 patients with high-risk HPV (HR-HPV) infection. The study examined the impact of two courses of oral JWEMGs on these clinical parameters. Additionally, metagenomic sequencing was performed on vaginal lavage samples from 33 patients to assess the alteration of the vaginal microbiome following JWEMGs treatment. Immunohistochemistry was used to detect ALPK1 expression in cervical exfoliated cells, and ELISA was employed to measure cytokine levels in vaginal lavage fluid. JWEMGs intervention was applied to HaCaT-HPV E6/E7 cells to evaluate its effects on restoring α-kinase 1 (ALPK1) expression and promoting the secretion of cytokines and chemokines.

RESULTS: Treatment with JWEMGs significantly improved several clinical indicators, including cleanliness, pH, Nugent score, Donders score, catalase, neuraminidase, and leukocyte esterase, in HR-HPV-infected patients. Furthermore, JWEMGs therapy led to an increased abundance of Lactobacillus species, especially Lactobacillus crispatus, and a marked reduction in Gardnerella species. JWEMGs treatment also significantly promoted ALPK1 expression in cervical exfoliated cells and augmented the secretion of key cytokines, including IL-6, IL-8, and TNF-α. In parallel, in vitro results showed that JWEMGs substantially enhanced IL-6, IL-8, TNF-α, CCL2, CCL5, and CCL7 secretion in HaCaT-HPV E6/E7 cells, which correlated with the activation of the ALPK1/NF-κB signaling pathway.

CONCLUSION: In conclusion, JWEMGs treatment effectively remodels the vaginal microbiota and bolsters mucosal immunity in the lower genital tract, thereby improving the vaginal microecology in HR-HPV-infected individuals. In vitro findings further demonstrated that JWEMGs promote cytokine and chemokine expression, activating the ALPK1/NF-κB pathway.}, } @article {pmid39778648, year = {2025}, author = {Bellanco, A and Requena, T and Martínez-Cuesta, MC}, title = {Polysorbate 80 and carboxymethylcellulose: A different impact on epithelial integrity when interacting with the microbiome.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {196}, number = {}, pages = {115236}, doi = {10.1016/j.fct.2025.115236}, pmid = {39778648}, issn = {1873-6351}, mesh = {*Polysorbates/pharmacology ; *Carboxymethylcellulose Sodium/chemistry ; *Gastrointestinal Microbiome/drug effects ; Humans ; Emulsifying Agents ; Bacteria/drug effects/classification/genetics/metabolism ; }, abstract = {The consumption of dietary emulsifiers, including polysorbate 80 (P80) and sodium carboxymethylcellulose (CMC), has raised safety concerns due to its interaction with the intestinal microbiome. This study demonstrated that increasing concentrations of P80 and CMC added to a dynamic four-stage gut microbiota model (BFBL gut simulator) altered the microbiome composition and impacted epithelial integrity in a dose-dependent manner. 16S rDNA amplicon-based metagenomics analysis revealed that these emulsifiers increased microbial groups with proinflammatory capacities while decreasing microbial taxa known to enhance barrier function. Increasing doses of P80 significantly decreased Bacteroides dorei and Akkermansia, taxa associated with anti-inflammatory potential, while increasing doses of CMC were linked to a higher abundance of Ruminococcus torques and Hungatella, which negatively impact barrier function. Both emulsifiers displayed a different impact on epithelial integrity when interacting with the microbiome. On one hand, supernatants from the BFBL simulator fed with P80 disrupted epithelial integrity to a lesser extent than the additive alone. On the other hand, both the microbiota and the supernatants from the BFBL simulator fed with CMC diminished the epithelial integrity, though the additive itself did not. These findings highlight the need to incorporate the gut microbiome in the risk assessment of these additives.}, } @article {pmid39701375, year = {2025}, author = {Corbett, GA and Corcoran, S and Feehily, C and Soldati, B and Rafferty, A and MacIntyre, DA and Cotter, PD and McAuliffe, FM}, title = {Preterm-birth-prevention with Lactobacillus crispatus oral probiotics: Protocol for a double blinded randomised placebo-controlled trial (the PrePOP study).}, journal = {Contemporary clinical trials}, volume = {149}, number = {}, pages = {107776}, doi = {10.1016/j.cct.2024.107776}, pmid = {39701375}, issn = {1559-2030}, mesh = {Humans ; Female ; *Probiotics/administration & dosage/therapeutic use ; Double-Blind Method ; *Vagina/microbiology ; Pregnancy ; *Premature Birth/prevention & control/microbiology ; *Lactobacillus crispatus ; *Lactobacillus ; *Gastrointestinal Microbiome ; *Lacticaseibacillus rhamnosus ; Adult ; Administration, Oral ; Infant, Newborn ; }, abstract = {INTRODUCTION: Effective spontaneous preterm birth (sPTB) prevention is an urgent unmet clinical need. Vaginal depletion of Lactobacillus crispatus is linked to sPTB. This trial will investigate impact of an oral Lactobacillus spp. probiotic product containing an L. crispatus strain with other Lactobacilli spp., on the maternal vaginal and gut microbiome in pregnancies high-risk for sPTB.

METHODS: A double-blind, placebo-controlled, randomised trial will be performed at the National Maternity Hospital Dublin, Ireland. Inclusion criteria are women with history of sPTB or mid-trimester loss, cervical surgery (cone biopsy or two previous large-loop-excision-of-transformation-zone) or uterine anomaly. The intervention is oral supplementation for twelve weeks with probiotic or identical placebo. The probiotic will contains: ◦ 4 billion CFU Lactobacillus crispatus Lbv 88(2x10[9]CFU/Capsule) ◦ 4 billion CFU Lactobacillus rhamnosus Lbv 96(2x10[9]CFU/Capsule) ◦ 0.8 billion CFU Lactobacillus jensenii Lbv 116(0.4x10[9]CFU/Capsule) ◦ 1.2 billion CFU Lactobacillus gasseri Lbv 150(0.6x10[9]CFU/Capsule). Investigators and participants will be blinded to assignment.

RESULTS: The primary outcome is detectable L. crispatus in the vaginal microbiome after twelve weeks of treatment, measured using high-throughput DNA sequencing. A total of 126 women are required to detect a 25 % increase in detectable L. crispatus. Secondary outcomes include impact of intervention on the gut microbiome and metabolome, rate of sPTB and mid-trimester loss, neonatal outcomes and maternal morbidity.

CONCLUSIONS: This randomised trial will investigate ability of an oral probiotic containing L. crispatus to increase its abundance in the vaginal microbiome, both directly by horizontal transfer and indirectly via microbiome and metabolome of the gut.}, } @article {pmid39891205, year = {2025}, author = {Huang, D and Liao, J and Balcazar, JL and Ye, M and Wu, R and Wang, D and Alvarez, PJJ and Yu, P}, title = {Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {34}, pmid = {39891205}, issn = {2049-2618}, support = {42177113//National Natural Science Foundation of China/ ; 42277418//National Natural Science Foundation of China/ ; Y2022084//the Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; 2022YFC3704700//National Key Research and Development Program of China/ ; }, mesh = {*Chromium/pharmacology ; *Soil Microbiology ; *Stress, Physiological ; *Bacteria/genetics/classification/drug effects ; *Microbiota/drug effects ; Soil Pollutants ; Metagenomics/methods ; Viruses/genetics/drug effects/classification ; Soil/chemistry ; }, abstract = {BACKGROUND: The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of prokaryotic antiviral defense systems, their responses to abiotic stress and ecological consequences remain poorly understood in soil ecosystems. We established microcosm systems with varying concentrations of hexavalent chromium (Cr(VI)) to investigate the adaptive modifications of prokaryotic antiviral defense systems under abiotic stress.

RESULTS: Utilizing hybrid metagenomic assembly with long-read and short-read sequencing, we discovered that antiviral defense systems were more diverse and prevalent in heavily polluted soils, which was corroborated by meta-analyses of public datasets from various heavy metal-contaminated sites. As the Cr(VI) concentration increased, prokaryotes with defense systems favoring prokaryote-virus mutualism gradually supplanted those with defense systems incurring high adaptive costs. Additionally, as Cr(VI) concentrations increased, enriched antiviral defense systems exhibited synchronization with microbial heavy metal resistance genes. Furthermore, the proportion of antiviral defense systems carried by mobile genetic elements (MGEs), including plasmids and viruses, increased by approximately 43% and 39%, respectively, with rising Cr concentrations. This trend is conducive to strengthening the dissemination and sharing of defense resources within microbial communities.

CONCLUSIONS: Overall, our study reveals the adaptive modification of prokaryotic antiviral defense systems in soil ecosystems under abiotic stress, as well as their positive contributions to establishing prokaryote-virus mutualism and the evolution of microbial heavy metal resistance. These findings advance our understanding of microbial adaptation in stressful environments and may inspire novel approaches for microbiome manipulation and bioremediation. Video Abstract.}, } @article {pmid39890997, year = {2025}, author = {Marter, P and Freese, HM and Ringel, V and Brinkmann, H and Pradella, S and Rohde, M and Jarek, M and Spröer, C and Wagner-Döbler, I and Overmann, J and Bunk, B and Petersen, J}, title = {Superior Resolution Profiling of the Coleofasciculus Microbiome by Amplicon Sequencing of the Complete 16S rRNA Gene and ITS Region.}, journal = {Environmental microbiology reports}, volume = {17}, number = {1}, pages = {e70066}, doi = {10.1111/1758-2229.70066}, pmid = {39890997}, issn = {1758-2229}, support = {34509606-TRR 51//Deutsche Forschungsgemeinschaft/ ; //Collaborative Research Center Roseobacter (TRR51)/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Cyanobacteria/genetics/classification/isolation & purification ; Sequence Analysis, DNA ; Phylogeny ; DNA, Ribosomal Spacer/genetics ; DNA, Bacterial/genetics ; Bacteria/genetics/classification/isolation & purification ; Metagenomics ; }, abstract = {The filamentous cyanobacterium Coleofasciculus chthonoplastes is the key primary producer of marine microbial mats. We elucidated the microbiomes of 32 non-axenic Coleofasciculus isolates using PacBio-based amplicon sequencing of the complete 16S rRNA gene and the internally transcribed spacer (16S-ITS). The length of authentic amplicon sequence variants (ASVs) ranged from 1827 to 3044 nucleotides (median: 2267 nt). The results, which were complemented by metagenome analyses and cultivation approaches, revealed the presence of more than 70 associated heterotrophs in the culture of Coleofasciculus sp. WW12. The great bacterial diversity in the cyanosphere is dominated by Pseudomonadota (59%) and Bacteroidota (23%). Allelic ribosomal operon variants were detected in 18 Coleofasciculus strains and our analyses proposed the presence of at least four different species. A comparative analysis of cyanobacterial microbiomes documented complementary advantages of amplicon sequencing versus metagenomics with an individual strength of the 16S-ITS approach in terms of (i) ribosomal target sequence quality, (ii) contaminant detection and (iii) identification of rare bacteria. The characterisation of the Coleofasciculus microbiome showed that long-read amplicon sequencing of the 16S-ITS region is the method of choice for rapid profiling of non-axenic cyanobacteria. Its superior resolution allows a reliable differentiation of even very closely related strains.}, } @article {pmid39890137, year = {2025}, author = {Kennedy, EC and Ross, FC and O'Shea, CA and Lavelle, A and Ross, P and Dempsey, E and Stanton, C and Hawkes, CP}, title = {Observational study protocol: the faecal microbiome in the acute stage of new-onset paediatric type 1 diabetes in an Irish cohort.}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e089206}, doi = {10.1136/bmjopen-2024-089206}, pmid = {39890137}, issn = {2044-6055}, mesh = {Humans ; *Diabetes Mellitus, Type 1/microbiology ; *Feces/microbiology ; Child ; *Gastrointestinal Microbiome ; Male ; Female ; Prospective Studies ; Ireland ; Child, Preschool ; Adolescent ; Metabolome ; }, abstract = {INTRODUCTION: Type 1 diabetes (T1D) is an autoimmune-mediated disorder caused by the destruction of pancreatic beta cells. Although there is an underlying genetic predisposition to developing T1D, the trigger is multifactorial and likely includes environmental factors. The intestinal microbiome has been identified as one such factor. Previous studies have illustrated differences in the microbiota of people with T1D compared with healthy controls. This study aims to describe the evolution of the microbiome and metabolome during the first year of clinical T1D, or stage 3 T1D diagnosis, and investigate whether there are differences in the microbiome and metabolome of children who present with and without diabetic ketoacidosis. The study will also explore possible associations between the microbiome, metabolome, glycaemic control and beta cell reserve.

METHODS AND ANALYSIS: This prospective cohort study will include children with newly diagnosed T1D and sibling controls (n=100, males and females) and their faecal microbiome will be characterised using shotgun metagenomic sequencing at multiple time points during the first year of diagnosis. We will develop a microbial culture biobank based on culturomic studies of stool samples from the healthy controls that will support future investigation. Metabolomic analysis will aim to identify additional biomarkers which may be involved in disease presentation and progression. Through this initial exploratory study, we aim to identify specific microbial biomarkers which may be used as future interventional targets throughout the various stages of T1D progression.

ETHICS AND DISSEMINATION: This study has been approved by the Clinical Research Ethics Committee of the Cork Teaching Hospitals. Study results will be available to patients with T1D and their families, carers, support networks and microbiome societies and other researchers.

TRIAL REGISTRATION NUMBER: The clinicaltrials.gov registration number for this trial is NCT06157736.}, } @article {pmid39793444, year = {2025}, author = {Verheijden, RJ and van Eijs, MJM and Paganelli, FL and Viveen, MC and Rogers, MRC and Top, J and May, AM and van de Wijgert, JHHM and Suijkerbuijk, KPM and , }, title = {Gut microbiome and immune checkpoint inhibitor toxicity.}, journal = {European journal of cancer (Oxford, England : 1990)}, volume = {216}, number = {}, pages = {115221}, doi = {10.1016/j.ejca.2025.115221}, pmid = {39793444}, issn = {1879-0852}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Immune Checkpoint Inhibitors/adverse effects ; Male ; Female ; Middle Aged ; Aged ; Prospective Studies ; *Neoplasms/drug therapy/microbiology ; Dysbiosis/chemically induced/microbiology ; Adult ; Feces/microbiology ; }, abstract = {BACKGROUND: Multiple studies have suggested that gut microbiome may influence immune checkpoint inhibitor (ICI) efficacy, but its association with immune-related adverse events (irAEs) is less well studied. In this prospective cohort study, we assessed whether gut microbiome composition at start, or changes during ICI, are associated with severe irAEs.

METHODS: Stool samples of cancer patients treated with anti-PD-1 ± anti-CTLA-4 were analyzed using 16S rRNA gene sequencing and metagenomic shotgun sequencing. Differences in alpha and beta diversity between patients with and without severe irAE were assessed, as well as differential relative abundance (RA) of taxa, MetaCyc pathways, and seven prespecified literature-based bacterial groups including pathobionts and Ruminococcaceae.

FINDINGS: We analyzed 497 samples of 195 patients before and soon after starting ICI, at severe irAE onset and after starting immunosuppression. Mean RA of the pathobionts group was significantly higher in patients who developed a severe irAE (8.2 %) compared to those who did not (4.8 %; odds ratio 1.40; 95 %CI 1.07-1.87) at baseline, and also early during ICI treatment and at severe irAE onset. A significantly stronger decrease in RA of Ruminococcaceae after starting ICI was observed in patients who developed a severe irAE compared to those who did not. RAs of Ruminococcaceae, the genus Ruminococcus, and the species R. bromii and R. callidus were significantly lower at severe irAE onset compared to other time points.

INTERPRETATION: Gut microbiome dysbiosis signaled by higher RA of pathobionts and decrease in RA of Ruminococcaceae may predispose to severe irAEs.}, } @article {pmid39628067, year = {2025}, author = {Fujimoto, S and Hatano, K and Banno, E and Motooka, D and De Velasco, MA and Kura, Y and Toyoda, S and Hashimoto, M and Adomi, S and Minami, T and Yoshimura, K and Oka, T and Hata, J and Matsushita, M and Takao, T and Takada, S and Tsujimura, A and Kojima, Y and Obara, W and Nakamura, S and Uemura, H and Nonomura, N and Fujita, K}, title = {Comparative analysis of gut microbiota in hormone-sensitive and castration-resistant prostate cancer in Japanese men.}, journal = {Cancer science}, volume = {116}, number = {2}, pages = {462-469}, doi = {10.1111/cas.16408}, pmid = {39628067}, issn = {1349-7006}, support = {//Yakult Bio-Science Foundation/ ; //The Japanese Foundation for Prostate Research (JFPR)/ ; //The Japanese Urological Association/ ; }, mesh = {Male ; *Gastrointestinal Microbiome/genetics ; Animals ; Humans ; *Prostatic Neoplasms, Castration-Resistant/microbiology/genetics/pathology ; Mice ; Aged ; Japan ; *RNA, Ribosomal, 16S/genetics ; Mice, Transgenic ; Middle Aged ; Mice, Knockout ; Disease Progression ; Lactobacillus/genetics/isolation & purification ; Aged, 80 and over ; Disease Models, Animal ; East Asian People ; }, abstract = {Gut microbiota plays a crucial role in the development and progression of prostate cancer, with previous studies indicating that certain bacterial taxa are more abundant in castration-resistant prostate cancer (CRPC) compared to hormone-sensitive prostate cancer (HSPC). Notably, the composition of gut microbiota can vary significantly by geographic region, and Japanese individuals have a distinct microbial profile. However, research exploring these differences within Japanese populations remains limited. This study investigated the gut microbiota differences between Japanese men with HSPC and CRPC and further validated these findings using a transgenic mouse model. Rectal swab samples were collected from 140 Japanese men diagnosed with HSPC (n = 84) or CRPC (n = 56) between September 2020 and July 2022. Gut microbiota composition was analyzed using 16S rRNA gene sequencing. Additionally, Pten-KO mice, which model the progression from HSPC to CRPC, underwent similar microbiota analysis. Results revealed significant differences in gut microbiota composition between HSPC and CRPC patients. Specifically, the CRPC group showed a higher abundance of Firmicutes, including Gemella and Lactobacillus, compared to the HSPC group. These differences were mirrored in the mouse model, where CRPC mice also showed an increase in these bacteria. This study identifies distinct microbial differences between HSPC and CRPC in Japanese men, suggesting that Gemella and Lactobacillus may be associated with the progression to castration resistance in prostate cancer. These findings suggest that gut microbiota differences may be associated with prostate cancer progression. Further research is needed to explore the potential of targeting the microbiota as a therapeutic strategy.}, } @article {pmid39745433, year = {2025}, author = {Grüterich, L and Woodhouse, JN and Mueller, P and Tiemann, A and Ruscheweyh, H-J and Sunagawa, S and Grossart, H-P and Streit, WR}, title = {Assessing environmental gradients in relation to dark CO2 fixation in estuarine wetland microbiomes.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0217724}, doi = {10.1128/aem.02177-24}, pmid = {39745433}, issn = {1098-5336}, support = {407270017//Deutsche Forschungsgemeinschaft (DFG)/ ; 502681570//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {*Wetlands ; *Carbon Dioxide/metabolism ; *Microbiota ; *Estuaries ; *Carbon Cycle ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Soil Microbiology ; }, abstract = {UNLABELLED: The rising atmospheric concentration of CO2 is a major concern to society due to its global warming potential. In soils, CO2-fixing microorganisms are preventing some of the CO2 from entering the atmosphere. Yet, the controls of dark CO2 fixation are rarely studied in situ. Here, we examined the gene and transcript abundance of key genes involved in microbial CO2 fixation along major environmental gradients within estuarine wetlands. A combined multi-omics approach incorporating metabarcoding, deep metagenomic, and metatranscriptomic analyses confirmed that wetland microbiota harbor four out of seven known CO2 fixation pathways, namely, the Calvin cycle, reverse tricarboxylic acid cycle, Wood-Ljungdahl pathway, and reverse glycine pathway. These pathways are transcribed at high frequencies along several environmental gradients, albeit at different levels depending on the environmental niche. Notably, the transcription of the key genes for the reverse tricarboxylic acid cycle was associated with high nitrate concentration, while the transcription of key genes for the Wood-Ljungdahl pathway was favored by reducing, O2-poor conditions. The transcript abundance of the Calvin cycle was favored by niches high in organic matter. Taxonomic assignment of transcripts implied that dark CO2 fixation was mainly linked to a few bacterial phyla, namely, Desulfobacterota, Methylomirabilota, Nitrospirota, Chloroflexota, and Pseudomonadota.

IMPORTANCE: The increasing concentration of atmospheric CO2 has been identified as the primary driver of climate change and poses a major threat to human society. This work explores the mostly overlooked potential of light-independent CO2 fixation by soil microbes (a.k.a. dark CO2 fixation) in climate change mitigation efforts. Applying a combination of molecular microbial tools, our research provides new insights into the ecological niches where CO2-fixing pathways are most active. By identifying how environmental factors, like oxygen, salinity and organic matter availability, influence these pathways in an estuarine wetland environment, potential strategies for enhancing natural carbon sinks can be developed. The importance of our research is in advancing the understanding of microbial CO2 fixation and its potential role in the global climate system.}, } @article {pmid39714193, year = {2025}, author = {Midot, F and Goh, KM and Liew, KJ and Lau, SYL and Espenberg, M and Mander, Ü and Melling, L}, title = {Temporal dynamics of soil microbial C and N cycles with GHG fluxes in the transition from tropical peatland forest to oil palm plantation.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0198624}, doi = {10.1128/aem.01986-24}, pmid = {39714193}, issn = {1098-5336}, support = {P015 790102009//The Twelfth Malaysian Plan through Ministry of Education, Innovation, and Talent Development of Sarawak/ ; FRGS/1/2023/STG02/UTM/02/1,Q.J130000.3854.22H63//Ministry of Higher Education of Malaysia through the Fundamental Research Grant Scheme and UTM Fundamental Research Grant/ ; No 101079192 (MLTOM23003R)//European Union Horizon program/ ; No 101096403 (MLTOM23415R)//EC | European Research Council (ERC)/ ; PRG-2302//Estonian Research Council/ ; }, mesh = {*Soil Microbiology ; *Greenhouse Gases/analysis ; *Forests ; Malaysia ; *Microbiota ; Methane/metabolism/analysis ; Nitrogen Cycle ; Carbon Cycle ; Soil/chemistry ; Nitrous Oxide/analysis/metabolism ; Nitrogen/analysis/metabolism ; Carbon/analysis/metabolism ; Wetlands ; Bacteria/classification/genetics/metabolism/isolation & purification ; Arecaceae ; Agriculture ; }, abstract = {Tropical peatlands significantly influence local and global carbon and nitrogen cycles, yet they face growing pressure from anthropogenic activities. Land use changes, such as peatland forests conversion to oil palm plantations, affect the soil microbiome and greenhouse gas (GHG) emissions. However, the temporal dynamics of microbial community changes and their role as GHG indicators are not well understood. This study examines the dynamics of peat chemistry, soil microbial communities, and GHG emissions from 2016 to 2020 in a logged-over secondary peat swamp forest in Sarawak, Malaysia, which transitioned to an oil palm plantation. This study focuses on changes in genetic composition governing plant litter degradation, methane (CH4), and nitrous oxide (N2O) fluxes. Soil CO2 emission increased (doubling from approximately 200 mg C m[-2] h[-1]), while CH4 emissions decreased (from 200 µg C m[-2] h[-1] to slightly negative) following land use changes. The N2O emissions in the oil palm plantation reached approximately 1,510 µg N m[-2] h[-1], significantly higher than previous land uses. The CH4 fluxes were driven by groundwater table, humification levels, and C:N ratio, with Methanomicrobia populations dominating methanogenesis and Methylocystis as the main CH4 oxidizer. The N2O fluxes correlated with groundwater table, total nitrogen, and C:N ratio with dominant nirK-type denitrifiers (13-fold nir to nosZ) and a minor role by nitrification (a threefold increase in amoA) in the plantation. Proteobacteria and Acidobacteria encoding incomplete denitrification genes potentially impact N2O emissions. These findings highlighted complex interactions between microbial communities and environmental factors influencing GHG fluxes in altered tropical peatland ecosystems.IMPORTANCETropical peatlands are carbon-rich environments that release significant amounts of greenhouse gases when drained or disturbed. This study assesses the impact of land use change on a secondary tropical peat swamp forest site converted into an oil palm plantation. The transformation lowered groundwater levels and changed soil properties. Consequently, the oil palm plantation site released higher carbon dioxide and nitrous oxide compared to previous land uses. As microbial communities play crucial roles in carbon and nitrogen cycles, this study identified environmental factors associated with microbial diversity, including genes and specific microbial groups related to nitrous oxide and methane emissions. Understanding the factors driving microbial composition shifts and greenhouse gas emissions in tropical peatlands provides baseline information to potentially mitigate environmental consequences of land use change, leading to a broader impact on climate change mitigation efforts and proper land management practices.}, } @article {pmid39679708, year = {2025}, author = {Liu, Z and Jiang, C and Yin, Z and Ibrahim, IA and Zhang, T and Wen, J and Zhou, L and Jiang, G and Li, L and Yang, Z and Huang, Y and Yang, Z and Gu, Y and Meng, D and Yin, H}, title = {Ecological features of microbial community linked to stochastic and deterministic assembly processes in acid mine drainage.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0102824}, doi = {10.1128/aem.01028-24}, pmid = {39679708}, issn = {1098-5336}, support = {2023YFE0114500//MOST | National Key Research and Development Program of China (NKPs)/ ; 92351303//MOST | National Natural Science Foundation of China (NSFC)/ ; BX20230437//Postdoctoral Fellowship Program of CPSF/ ; }, mesh = {*Microbiota ; *Mining ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Phylogeny ; Stochastic Processes ; Metagenomics ; Acids/metabolism ; Metagenome ; }, abstract = {UNLABELLED: Ecological processes greatly shape microbial community assembly, but the driving factors remain unclear. Here, we compiled a metagenomic data set of microbial communities from global acid mine drainage (AMD) and explored the ecological features of microbial community linked to stochastic and deterministic processes from the perspective of species niche position, interaction patterns, gene functions, and viral infection. Our results showed that dispersal limitation (DL) (48.5%~93.5%) dominated the assembly of phylogenetic bin in AMD microbial community, followed by homogeneous selection (HoS) (3.1%~39.2%), heterogeneous selection (HeS) (1.4%~22.2%), and drift (DR) (0.2%~2.7%). The dominant process of dispersal limitation was significantly influenced by niche position in temperature (r = -0.518, P = 0.007) and dissolved oxygen (r = 0.471, P = 0.015). Network stability had a significantly negative correlation with the relative importance of dispersal limitation, while it had a positive correlation with selection processes, implying changes in network properties could be mediated by ecological processes. Furthermore, we found that ecological processes were mostly related to the gene functions of energy production and conversion (C), and amino acid transport and metabolism (E). Meanwhile, our results showed that the number of proviruses and viral genes involved in arsenic (As) resistance is negatively associated with the relative importance of ecological drift in phylogenetic bin assembly, implying viral infection might weaken ecological drift. Taken together, these results highlight that ecological processes are associated with ecological features at multiple levels, providing a novel insight into microbial community assembly in extremely acidic environments.

IMPORTANCE: Unraveling the forces driving community assemblage is a core issue in microbial ecology, but how ecological constraints impose stochasticity and determinism remains unknown. This study presents a comprehensive investigation to uncover the association of ecological processes with species niche position, interaction patterns, microbial metabolisms, and viral infections, which provides novel insights into community assembly in extreme environments.}, } @article {pmid39665561, year = {2025}, author = {Unzueta-Martínez, A and Girguis, PR}, title = {Taxonomic diversity and functional potential of microbial communities in oyster calcifying fluid.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0109424}, doi = {10.1128/aem.01094-24}, pmid = {39665561}, issn = {1098-5336}, support = {2109473//National Science Foundation (NSF)/ ; 9208//Gordon and Betty Moore Foundation (GBMF)/ ; }, mesh = {Animals ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Archaea/classification/genetics/metabolism ; Metagenomics ; Calcification, Physiologic ; Ostreidae/microbiology ; Biomineralization ; Viruses/classification/genetics ; Biodiversity ; }, abstract = {UNLABELLED: Creating and maintaining an appropriate chemical environment is essential for biomineralization, the process by which organisms precipitate minerals to form their shells or skeletons, yet the mechanisms involved in maintaining calcifying fluid chemistry are not fully defined. In particular, the role of microorganisms in facilitating or hindering animal biomineralization is poorly understood. Here, we investigated the taxonomic diversity and functional potential of microbial communities inhabiting oyster calcifying fluid. We used shotgun metagenomics to survey calcifying fluid microbial communities from three different oyster harvesting sites. There was a striking consistency in taxonomic composition across the three collection sites. We also observed archaea and viruses that had not been previously identified in oyster calcifying fluid. Furthermore, we identified microbial energy-conserving metabolisms that could influence the host's calcification, including genes involved in sulfate reduction and denitrification that are thought to play pivotal roles in inorganic carbon chemistry and calcification in microbial biofilms. These findings provide new insights into the taxonomy and functional capacity of oyster calcifying fluid microbiomes, highlighting their potential contributions to shell biomineralization, and contribute to a deeper understanding of the interplay between microbial ecology and biogeochemistry that could potentially bolster oyster calcification.

IMPORTANCE: Previous research has underscored the influence of microbial metabolisms in carbonate deposition throughout the geological record. Despite the ecological importance of microbes to animals and inorganic carbon transformations, there have been limited studies characterizing the potential role of microbiomes in calcification by animals such as bivalves. Here, we use metagenomics to investigate the taxonomic diversity and functional potential of microbial communities in calcifying fluids from oysters collected at three different locations. We show a diverse microbial community that includes bacteria, archaea, and viruses, and we discuss their functional potential to influence calcifying fluid chemistry via reactions like sulfate reduction and denitrification. We also report the presence of carbonic anhydrase and urease, both of which are critical in microbial biofilm calcification. Our findings have broader implications in understanding what regulates calcifying fluid chemistry and consequentially the resilience of calcifying organisms to 21st century acidifying oceans.}, } @article {pmid39651865, year = {2025}, author = {Howland, KE and Mouradian, JJ and Uzarski, DR and Henson, MW and Uzarski, DG and Learman, DR}, title = {Nutrient amendments enrich microbial hydrocarbon degradation metagenomic potential in freshwater coastal wetland microcosm experiments.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0197224}, doi = {10.1128/aem.01972-24}, pmid = {39651865}, issn = {1098-5336}, mesh = {*Wetlands ; *Biodegradation, Environmental ; *Fresh Water/microbiology ; *Hydrocarbons/metabolism ; Bacteria/genetics/metabolism/classification ; Metagenomics ; Petroleum/metabolism ; Geologic Sediments/microbiology ; Nutrients/metabolism ; Microbiota ; Metagenome ; Benzene Derivatives/metabolism ; Volatile Organic Compounds/metabolism ; Toluene/metabolism ; Benzene/metabolism ; Water Pollutants, Chemical/metabolism ; }, abstract = {UNLABELLED: Biostimulating native microbes with fertilizers has proven to be a highly effective strategy to speed up biodegradation rates in microbial communities. This study investigates the genetic potential of microbes to degrade light synthetic crude oil in a freshwater coastal wetland. Experimental sediment microcosms were exposed to a variety of conditions (biological control, a light synthetic crude oil amendment, and light synthetic crude oil with nutrient amendment) and incubated for 30 days before volatile organic compounds (BTEX) were quantified and DNA was sequenced for metagenomic analysis. The resulting DNA sequences were binned into metagenome-assembled genomes (MAGs). Analyses of MAGs uncovered a 13-fold significant increase in the abundance of rate-limiting hydrocarbon degrading monooxygenases and dioxygenases, identified only in MAGs from the light synthetic crude oil with nutrient amendments. Further, complete degradation pathways for BTEX compounds were found only in MAGs resulting from the light synthetic crude with nutrient amendment. Moreover, volatile organic compounds (BTEX, cyclohexane, and naphthalene) analyses of microcosm sediments in the presence of nutrients documented that benzene was degraded below detection limits, toluene (98%) and ethylbenzene (67%) were predominantly reduced within 30 days. Results indicate that the genetic potential to degrade BTEX compounds in this freshwater wetland can be linked to the functional potential for bioremediation. BTEX compounds are typically more recalcitrant and tougher to degrade than alkanes. This study demonstrated that stimulating a microbial community with nutrients to enhance its ability to biodegrade hydrocarbons, even in a relatively nutrient-rich habitat like a freshwater wetland, is an effective remediation tactic.

IMPORTANCE: The impact of oil spills in a freshwater aquatic environment can pose dire social, economic, and ecological effects on the region. An oil spill in the Laurentian Great Lakes region has the potential to affect the drinking water of more than 30 million people. The light synthetic crude oil used in this experimental microcosm study is transported through an underground pipeline crossing the waterway between two Laurentian Great Lakes. This study collected metagenomic data (experiments in triplicate) and assessed the quantity of BTEX compounds, which connected microbial degradation function to gene potential. The resulting data documented the bioremediation capabilities of native microbes in a freshwater coastal wetland. This study also provided evidence for this region that bioremediation can be a viable remediation strategy instead of invasive physical methods.}, } @article {pmid39641605, year = {2025}, author = {Bao, Z and Chen, B and Yu, K and Wei, Y and Liang, X and Yao, H and Liao, X and Xie, W and Yin, K}, title = {Microbiome dynamics and functional profiles in deep-sea wood-fall micro-ecosystem: insights into drive pattern of community assembly, biogeochemical processes, and lignocellulose degradation.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0216524}, doi = {10.1128/aem.02165-24}, pmid = {39641605}, issn = {1098-5336}, support = {42090041, 42030502//MOST | National Natural Science Foundation of China (NSFC)/ ; 42306165//MOST | National Natural Science Foundation of China (NSFC)/ ; No. 2023JJB150027//| Natural Science Foundation of Guangxi Zhuang Autonomous Region (Guangxi Natural Science Foundation)/ ; No. 311022005//Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2021SP204, SML2023SP215, SML2023SP218, SML2023SP205//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; }, mesh = {*Lignin/metabolism ; *Wood/microbiology/metabolism ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Fungi/genetics/classification/metabolism ; *Seawater/microbiology ; China ; Ecosystem ; Geologic Sediments/microbiology ; }, abstract = {Wood-fall micro-ecosystems contribute to biogeochemical processes in the oligotrophic deep ocean. However, the community assembly processes and biogeochemical functions of microbiomes in wood fall remain unclear. This study investigated the diversity, community structure, assembly processes, and functional profiles of bacteria and fungi in a deep-sea wood fall from the South China Sea using physicochemical indices, amplicon sequencing, and metagenomics. The results showed that distinct wood-fall contact surfaces exhibit habitat heterogeneity. The bacterial community of all contact surfaces and the fungal community of seawater contact surface (SWCS) were affected by homogeneous selection. In SWCS and transition region (TR), bacterial communities were influenced by dispersal limitation, whereas fungal communities were affected by homogenizing dispersal. The Venn diagram visualization revealed that the shared fungal community between SWCS and TR was dominated by Aspergillaceae. Additionally, the bacterial community demonstrated a higher genetic potential for sulfur, nitrogen, and methane metabolism than fungi. The sediment contact surface enriched modules were associated with dissimilatory sulfate reduction and methanogenesis, whereas the modules related to nitrate reduction exhibited enrichment characteristics in TR. Moreover, fungi showed a stronger potential for lignocellulase production compared to bacteria, with Microascaceae and Nectriaceae identified as potential contributors to lignocellulose degradation. These results indicate that environmental filtering and organism exchange levels regulated the microbial community assembly of wood fall. The biogeochemical cycling of sulfur, nitrogen, and methane was mainly driven by the bacterial community. Nevertheless, the terrestrial fungi Microascaceae and Nectriaceae might degrade lignocellulose via the combined action of multiple lignocellulases.IMPORTANCEThe presence and activity of microbial communities may play a crucial role in the biogeochemical cycle of deep-sea wood-fall micro-ecosystems. Previous studies on wood falls have focused on the microbiome diversity, community composition, and environmental impact, while few have investigated wood-fall micro-ecosystems by distinguishing among distinct contact surfaces. Our study investigated the microbiome dynamics and functional profiles of bacteria and fungi among distinct wood-fall contact surfaces. We found that the microbiome community assembly was regulated by environmental filtering and organism exchange levels. Bacteria drive the biogeochemical cycling of sulfur, nitrogen, and methane in wood fall through diverse metabolic pathways, whereas fungi are crucial for lignocellulose degradation. Ultimately, this study provides new insights into the driving pattern of community assembly, biogeochemical processes, and lignocellulose degradation in the microbiomes of deep-sea wood-fall micro-ecosystems, enhancing our comprehension of the ecological impacts of organic falls on deep-sea oligotrophic environments.}, } @article {pmid37480259, year = {2024}, author = {Ahmad, V and Jamal, A and Khan, MI and Alzahrani, FA and Albiheyri, R and Jamal, QMS}, title = {Cefoperazone targets D-alanyl-D-alanine carboxypeptidase (DAC) to control Morganella morganii-mediated infection: a subtractive genomic and molecular dynamics approach.}, journal = {Journal of biomolecular structure & dynamics}, volume = {42}, number = {13}, pages = {6799-6812}, doi = {10.1080/07391102.2023.2238088}, pmid = {37480259}, issn = {1538-0254}, mesh = {*Morganella morganii/drug effects/enzymology ; *Enterobacteriaceae Infections/drug therapy ; *Cefoperazone/pharmacology ; Humans ; *Serine-Type D-Ala-D-Ala Carboxypeptidase/chemistry/metabolism ; *Metagenome ; Gastrointestinal Microbiome ; Escherichia coli Proteins/chemistry/metabolism ; Penicillin-Binding Proteins/chemistry/metabolism ; Escherichia coli/enzymology ; *Molecular Dynamics Simulation ; Molecular Conformation ; }, abstract = {Morganella morganii is a Gram-negative bacterial pathogen that causes bacteremia, urinary tract infections, intra-abdominal infections, chorioamnionitis, neonatal sepsis, and newborn meningitis. To control this bacterial pathogen a total of 3565 putative proteins targets in Morganella morganii were screened using comparative subtractive analysis of biochemical pathways annotated by the KEGG that did not share any similarities with human proteins. One of the targets, D-alanyl-D-alanine carboxypeptidase DacB [Morganella] was observed to be implicated in the majority of cell wall synthesis pathways, leading to its selection as a novel pharmacological target. The drug that interacted optimally with the identified target was observed to be Cefoperazone (DB01329) with the estimated free energy of binding -8.9 Kcal/mol. During molecular dynamics simulations; it was observed that DB01328-2exb and DB01329-2exb complexes showed similar values as the control FMX-2exb complex near 0.2 nm with better stability. Furthermore, MMPBSA total free energy calculation showed better binding energy than the control complex for DB01329-2exb interaction i.e. -31.50 (±0.93) kcal/mol. Our presented research suggested that D-alanyl-D-alanine carboxypeptidase DacB could be a therapeutic target and cefoperazone could be a promising ligand to inhibit the D-alanyl-D-alanine carboxypeptidase DacB protein of Morganella morganii. To identify prospective therapeutic and vaccine targets in Morganella morganii, this is the first computational and subtractive genomics investigation of various metabolic pathways exploring other therapeutic targets of Morganella morganii. In vitro/in vivo experimental validation of the identified target D-alanyl-D-alanine carboxypeptidase and the design of its inhibitors is suggested to figure out the best dose, the drug's effectiveness, and its toxicity.Communicated by Ramaswamy H. Sarma.}, } @article {pmid39885140, year = {2025}, author = {Shao, B and Xie, YG and Zhang, L and Ruan, Y and Liang, B and Zhang, R and Xu, X and Wang, W and Lin, Z and Pei, X and Wang, X and Zhao, L and Zhou, X and Wu, X and Xing, D and Wang, A and Lee, DJ and Ren, N and Canfield, DE and Hedlund, BP and Hua, ZS and Chen, C}, title = {Versatile nitrate-respiring heterotrophs are previously concealed contributors to sulfur cycle.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1202}, pmid = {39885140}, issn = {2041-1723}, support = {52076063//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52100035//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52400025//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52300155//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52321005//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32170014//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023DX04//State Key Laboratory of Urban Water Resource and Environment (SKLUWRE)/ ; 2024M754204//China Postdoctoral Science Foundation/ ; 2023M740917//China Postdoctoral Science Foundation/ ; }, mesh = {*Sulfur/metabolism ; *Nitrates/metabolism ; *Heterotrophic Processes ; *Denitrification ; *Oxidation-Reduction ; Bacteria/metabolism/genetics ; Geologic Sediments/microbiology ; Nitrous Oxide/metabolism ; Microbiota ; Sulfides/metabolism ; Metagenomics ; Greenhouse Gases/metabolism ; }, abstract = {Heterotrophic denitrifiers play crucial roles in global carbon and nitrogen cycling. However, their inability to oxidize sulfide renders them vulnerable to this toxic molecule, which inhibits the key enzymatic reaction responsible for reducing nitrous oxide (N2O), thereby raising greenhouse gas emissions. Here, we applied microcosm incubations, community-isotope-corrected DNA stable-isotope probing, and metagenomics to characterize a cohort of heterotrophic denitrifiers in estuarine sediments that thrive by coupling sulfur oxidation with denitrification through chemolithoheterotrophic metabolism. Remarkably, ecophysiology experiments from enrichments demonstrate that such heterotrophs expedite denitrification with sulfur acting as alternative electron sources and substantially curtail N2O emissions in both organic-rich and organic-limited environments. Their flexible, non-sulfur-dependent physiology may confer competitive advantages over conventional heterotrophic denitrifiers in detoxifying sulfide, adapting to organic matter fluctuations, and mitigating greenhouse gas emissions. Our study provides insights into the ecological role of heterotrophic denitrifiers in microbial communities with implications for sulfur cycling and climate change.}, } @article {pmid39885121, year = {2025}, author = {Nooij, S and Plomp, N and Sanders, IMJG and Schout, L and van der Meulen, AE and Terveer, EM and Norman, JM and Karcher, N and Larralde, MF and Vossen, RHAM and Kloet, SL and Faber, KN and Harmsen, HJM and Zeller, GF and Kuijper, EJ and Smits, WK and Ducarmon, QR}, title = {Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1182}, pmid = {39885121}, issn = {2041-1723}, mesh = {Humans ; *Crohn Disease/microbiology/genetics ; *Metagenomics/methods ; *Genome, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; Health Status ; Genome-Wide Association Study ; Clostridiales/genetics/isolation & purification ; Life Style ; Phylogeny ; Infant, Newborn ; Genomics ; Female ; Male ; Adult ; Virulence Factors/genetics ; }, abstract = {Ruminococcus gnavus is a gut bacterium found in > 90% of healthy individuals, but its increased abundance is also associated with chronic inflammatory diseases, particularly Crohn's disease. Nevertheless, its global distribution and intraspecies genomic variation remain understudied. By surveying 12,791 gut metagenomes, we recapitulated known associations with metabolic diseases and inflammatory bowel disease. We uncovered a higher prevalence and abundance of R. gnavus in Westernized populations and observed bacterial relative abundances up to 83% in newborns. Next, we built a resource of R. gnavus isolates (N = 45) from healthy individuals and Crohn's disease patients and generated complete R. gnavus genomes using PacBio circular consensus sequencing. Analysis of these genomes and publicly available high-quality draft genomes (N = 333 genomes) revealed multiple clades which separated Crohn's-derived isolates from healthy-derived isolates. Presumed R. gnavus virulence factors could not explain this separation. Bacterial genome-wide association study revealed that Crohn's-derived isolates were enriched in genes related to mobile elements and mucin foraging. Together, we present a large R. gnavus resource that will be available to the scientific community and provide novel biological insights into the global distribution and genomic variation of R. gnavus.}, } @article {pmid39881417, year = {2025}, author = {Ye, GC and Peng, H and Xiang, JC and Miao, LT and Liu, CZ and Wang, SG and Xia, QD}, title = {Comprehensive analysis of the interaction microbiome and prostate cancer: an initial exploration from multi-cohort metagenome and GWAS studies.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {130}, pmid = {39881417}, issn = {1479-5876}, mesh = {Humans ; Male ; *Prostatic Neoplasms/microbiology/genetics/pathology ; *Metagenome/genetics ; *Genome-Wide Association Study ; *Gastrointestinal Microbiome/genetics ; Cohort Studies ; Neoplasm Metastasis ; Mendelian Randomization Analysis ; }, abstract = {INTRODUCTION: Prostate cancer is one of the most common cancers in the United States with a high mortality rate. In recent years, the traditional opinion about prostate microbiome was challenged. Although there still are some arguments, an escalating number of researchers are shifting their focus toward the microbiome within the prostate tumor environment.

METHODS: We mined the data of the microbiome extracted from the metagenome, and it offers a broader taxonomic coverage and accurate functional profiling. We used Kraken2, a mapping tool, to mine the gut microbiota of prostate cancer patients. A two-sample Mendelian Randomization was conducted to reflect the association between gut microbiome and cancer.

RESULTS: In the study, we found the consistency of the special intratumor microbiome of both non-metastatic tumors and metastatic tumors. And we dig the gut microbiome in patients with different treatments. We found that some microbiotas may be associated with prostate cancer progression and a special microbiome in metastatic prostate cancer may exist. The anti-androgen therapy can significantly change both the intratumor and gut microbiome.

CONCLUSION: With the progression and metastasis of prostate cancer, some intratumor microbiome changes. And anti-androgen influences both the intratumor and gut microbiome. Our discovery may help researchers further understand the progression, metastasis, and resistance of prostate cancer from the perspective of microbiome level.}, } @article {pmid39881387, year = {2025}, author = {Pangga, GM and Star-Shirko, B and Psifidi, A and Xia, D and Corcionivoschi, N and Kelly, C and Hughes, C and Lavery, U and Richmond, A and Ijaz, UZ and Gundogdu, O}, title = {Impact of commercial gut health interventions on caecal metagenome and broiler performance.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {30}, pmid = {39881387}, issn = {2049-2618}, support = {BB/T008709/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; EP/V030515/1//Engineering and Physical Sciences Research Council/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome ; *Cecum/microbiology ; *Metagenome ; *Probiotics/administration & dosage ; Prebiotics ; Bacteria/classification/genetics/isolation & purification ; Animal Feed/microbiology ; Vaccination/veterinary ; Dietary Supplements ; }, abstract = {BACKGROUND: Maintaining gut health is a persistent and unresolved challenge in the poultry industry. Given the critical role of gut health in chicken performance and welfare, there is a pressing need to identify effective gut health intervention (GHI) strategies to ensure optimal outcomes in poultry farming. In this study, across three broiler production cycles, we compared the metagenomes and performance of broilers provided with ionophores (as the control group) against birds subjected to five different GHI combinations involving vaccination, probiotics, prebiotics, essential oils, and reduction of ionophore use.

RESULTS: Using a binning strategy, 84 (≥ 75% completeness, ≤ 5% contamination) metagenome-assembled genomes (MAGs) from 118 caecal samples were recovered and annotated for their metabolic potential. The majority of these (n = 52, 61%) had a differential response across all cohorts and are associated with the performance parameter - European poultry efficiency factor (EPEF). The control group exhibited the highest EPEF, followed closely by the cohort where probiotics are used in conjunction with vaccination. The use of probiotics B, a commercial Bacillus strain-based formulation, was determined to contribute to the superior performance of birds. GHI supplementation generally affected the abundance of microbial enzymes relating to carbohydrate and protein digestion and metabolic pathways relating to energy, nucleotide synthesis, short-chain fatty acid synthesis, and drug-transport systems. These shifts are hypothesised to differentiate performance among groups and cycles, highlighting the beneficial role of several bacteria, including Rikenella microfusus and UBA7160 species.

CONCLUSIONS: All GHIs are shown to be effective methods for gut microbial modulation, with varying influences on MAG diversity, composition, and microbial functions. These metagenomic insights greatly enhance our understanding of microbiota-related metabolic pathways, enabling us to devise strategies against enteric pathogens related to poultry products and presenting new opportunities to improve overall poultry performance and health. Video Abstract.}, } @article {pmid39765196, year = {2025}, author = {Caballero-Gómez, J and Ávalos, G and Matas-Méndez, P and Figueiredo, AM and Castro-Scholten, S and Jiménez-Martín, D and Köster, PC and Santín, M and Bailo, B and Cano-Terriza, D and Sarmento, P and Neves, N and Carrapato, C and González-Barrio, D and Mateo, M and García-Bocanegra, I and Dashti, A and Sánchez, S and Carmena, D}, title = {Dietary profiles of wild carnivores and Blastocystis occurrence: The case of the endangered Iberian lynx (Lynx pardinus) and systematic review.}, journal = {Research in veterinary science}, volume = {184}, number = {}, pages = {105518}, doi = {10.1016/j.rvsc.2024.105518}, pmid = {39765196}, issn = {1532-2661}, mesh = {Animals ; *Lynx/parasitology ; *Blastocystis/genetics/isolation & purification ; Portugal ; Spain ; *Feces/parasitology ; *Endangered Species ; *Animals, Wild/parasitology ; Diet/veterinary ; Blastocystis Infections/veterinary/epidemiology ; }, abstract = {Recent molecular and metagenomic studies have revealed that the obligate anaerobic protist Blastocystis is found more prevalently and with higher subtype diversities in herbivore species than in carnivore species. However, information on wild carnivore species is scarce. Here, we investigated the presence of Blastocystis by molecular methods in fecal DNA samples of free-ranging and captive Iberian lynxes from Spain (n = 243) and Portugal (n = 30). In addition, a systematic review was conducted to obtain information on the Blastocystis prevalence rates and subtype diversities reported in free-living and captive wild carnivores worldwide during the period 2000-2024. Blastocystis was not detected by PCR in any of the samples investigated. Analyses of the data gathered from our systematic review revealed that Blastocystis is uncommon either in free-living (2.1 %, 29/1377) or captive (8.5 %, 100/1175) wild carnivore species. Many of these findings seem to result from accidental acquisition via prey animals, scavenging, contaminated water/feed (free-ranging wild carnivores), or cross-species transmission among animals sharing enclosures (captive wild carnivores). Comparative metagenomic studies analyzing gut microbiota profiles of carnivores are needed to fully understand how microbial communities affect Blastocystis colonization.}, } @article {pmid38490247, year = {2025}, author = {Ahmed, S and Mahapatra, S and Mishra, R and Murmu, KC and Padhan, P and Prasad, P and Misra, R}, title = {16s RNA-based metagenomics reveal previously unreported gut microbiota associated with reactive arthritis and undifferentiated peripheral spondyloarthritis.}, journal = {Rheumatology (Oxford, England)}, volume = {64}, number = {2}, pages = {870-879}, doi = {10.1093/rheumatology/keae165}, pmid = {38490247}, issn = {1462-0332}, support = {//APLAR/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Arthritis, Reactive/microbiology ; Female ; Male ; Adult ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Prohibitins ; *Spondylarthritis/microbiology ; Middle Aged ; Case-Control Studies ; Feces/microbiology ; Young Adult ; }, abstract = {OBJECTIVES: Reactive arthritis (ReA) provides a unique opportunity to comprehend how a mucosal infection leads to inflammatory arthritis at a distant site without the apparent invasion of the pathogen. Unfortunately, conventional stool cultures after ReA provide limited information, and there is a dearth of metagenomic studies in ReA. The objective of this study was to identify gut microbiota associated with the development of ReA.

METHODS: Patients with ReA or undifferentiated peripheral spondyloarthritis (UpSpA) were included if they presented within 4 weeks of the onset of the current episode of arthritis. Metagenomic DNA was extracted from the stools of these patients and of 36 age- and sex-similar controls. Sequencing and analysis were done using a standard 16S ribosomal pipeline.

RESULTS: Of 55 patients, there was no difference between the gut microbiota of postdiarrheal ReA (n = 20) and of upSpA (n = 35). Comparing the gut microbiota of patients vs healthy controls, the patients had significantly higher alpha and beta diversity measures. After stringency filters, Proteobacteria had high abundance while Firmicutes had lesser as compared with the controls. Six families were overexpressed in patients, while another five were overexpressed in controls. Sixteen genera and 18 species were significantly different between patients and controls. At the species level there was strong association of Staphylococcus aureus, Clostridium septicum Klebsiella pneumoniae, Escherichia coli, Empedobacter brevis, Roseburia hominis, Bacillus velezensis and Crassaminicella with ReA.

CONCLUSION: The microbiota of classical gut-associated ReA and upSpA is similar. Patients have higher diversities in their gut microbiota compared with healthy controls. Both known and previously unreported species associated with ReA/upSpA were identified.}, } @article {pmid39881163, year = {2025}, author = {Dash, M and Thiyageshwari, S and Selvi, D and Johnson, HKV and Ariyan, M and Rajan, K and Anandham, R}, title = {Unveiling microbial diversity in slightly and moderately magnesium deficient acidic soils.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {3696}, pmid = {39881163}, issn = {2045-2322}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Magnesium/metabolism/analysis ; *RNA, Ribosomal, 16S/genetics ; India ; Bacteria/genetics/classification/metabolism ; Metagenomics/methods ; Biodiversity ; Magnesium Deficiency/genetics ; Phosphorus/deficiency/metabolism ; Microbiota/genetics ; }, abstract = {Magnesium (Mg) an essential plant nutrient is widespread deficient in the acidic soils of Nilgiris of Tamil nadu, India. The vegetable yield and quality is especially affected due to deficiency of nutrients like Mg. This study investigates soil characteristics and bacterial diversity in the Nilgiris district of Tamil Nadu, India, with respect to Mg deficiency. The soil samples were collected from different vegetable growing regions of the Nilgiris to assess soil physiocochemical parameters, soil enzymes and soil Mg status. 16S rRNA gene-based metagenomic analysis used to investigate the functional potential and structural diversity of the bacterial communities in high Mg and low Mg deficiency soil. Results indicated mildly acidic soils with a sandy loam texture and high organic carbon content. While nitrogen (N), phosphorus (P), and potassium (K) levels were adequate, Mg deficiency was consistent. Soil enzymes such as dehydrogenase, acid phosphatase, urease and aryl sulfatase, varied across the soil samples. Additionally, 16S rRNA gene-based metagenomics analysis revealed the bacterial diversity and functional pathways in soils with high and low Mg deficiency. Low Mg levels were associated with increased bacterial richness, dominated by Proteobacteria, Gemmatimonadetes, Actinobacteria, Bacteroidetes, and Acidobacteria. Functional pathways related to carbon metabolism, amino acid biosynthesis, and various metabolic processes were more abundant in low Mg deficient soils. This research highlights the significant influence of Mg levels on bacterial diversity and functional potentials in acidic soils, providing insights into soil management strategies in Mg-deficient regions.}, } @article {pmid39876003, year = {2025}, author = {Li, Q and Huo, J and Ni, G and Zhang, F and Zhang, S and Zhang, X and Wang, R and Jiao, J and Yu, Z and Pu, X and Yue, Y and Ungerfeld, EM and Zhang, X and Wu, J and Tan, Z and Greening, C and Wang, M}, title = {Reductive acetogenesis is a dominant process in the ruminant hindgut.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {28}, pmid = {39876003}, issn = {2049-2618}, mesh = {Animals ; *Rumen/microbiology ; *Goats/microbiology ; *Cecum/microbiology ; *Hydrogen/metabolism ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Gastrointestinal Microbiome ; *Fermentation ; *Acetates/metabolism ; *Fatty Acids, Volatile/metabolism ; Archaea/classification/metabolism/genetics ; Ruminants/microbiology ; Methane/metabolism ; }, abstract = {BACKGROUND: The microbes residing in ruminant gastrointestinal tracts play a crucial role in converting plant biomass to volatile fatty acids, which serve as the primary energy source for ruminants. This gastrointestinal tract comprises a foregut (rumen) and hindgut (cecum and colon), which differ in structures and functions, particularly with respect to feed digestion and fermentation. While the rumen microbiome has been extensively studied, the cecal microbiome remains much less investigated and understood, especially concerning the assembling microbial communities and overriding pathways of hydrogen metabolism.

RESULTS: To address this gap, we comparatively investigated the composition, capabilities, and activities of the rumen and the cecum microbiome using goats as an experimental ruminant model. In situ measurements showed significantly higher levels of dissolved hydrogen and acetate in the cecum than in the rumen. Increased dissolved hydrogen indicated distinct processes and reduced coupling between fermentative H2 production and utilization, whereas higher levels of acetate could be caused by slower VFA absorption through cecal papillae than through the rumen papillae. Microbial profiling indicated that the cecum harbors a greater abundance of mucin-degrading microbes and fermentative hydrogen producers, whereas the rumen contains a higher abundance of fibrolytic fermentative bacteria, hydrogenotrophic respiratory bacteria, and methanogenic archaea. Most strikingly, reductive acetogenic bacteria were 12-fold more abundant in the cecum. Genome-resolved metagenomic analysis unveiled that the cecum acetogens are both phylogenetically and functionally distinct from those found in the rumen. Further supporting these findings, two in vitro experiments demonstrated a marked difference in hydrogen metabolism pathways between the cecum and the rumen, with increased acetate production and reduced methanogenesis in the cecum. Moreover, comparative analysis across multiple ruminant species confirmed a strong enrichment of reductive acetogens in the hindguts, suggesting a conserved functional role.

CONCLUSIONS: These findings highlight an enrichment of acetogenesis in a key region of the gastrointestinal tract and reshape our understanding of ruminant hydrogen metabolism and how the H2 can be managed in accord to livestock methane mitigation efforts. Video Abstract.}, } @article {pmid39742975, year = {2025}, author = {Dougherty, PE and Pedersen, MS and Forero-Junco, LM and Carstens, AB and Raaijmakers, JM and Riber, L and Hansen, LH}, title = {Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks.}, journal = {Virus research}, volume = {352}, number = {}, pages = {199524}, doi = {10.1016/j.virusres.2024.199524}, pmid = {39742975}, issn = {1872-7492}, mesh = {*Triticum/microbiology/virology ; *Bacteriophages/genetics/classification/isolation & purification/physiology ; *Phylogeny ; *Genome, Viral ; DNA, Viral/genetics ; DNA Breaks, Single-Stranded ; Erwinia/virology/genetics ; Pseudomonas/virology/genetics ; Metagenome ; Microbiota ; Pseudomonas Phages/genetics/classification/isolation & purification ; Bacteria/virology/genetics/classification ; }, abstract = {The phyllosphere microbiome can positively or negatively impact plant health and growth, but we currently lack the tools to control microbiome composition. Contributing to a growing collection of bacteriophages (phages) targeting bacteria living in the wheat phyllosphere, we here isolate and sequence eight novel phages targeting common phyllosphere Erwinia and Pseudomonas strains, including two jumbo phages. We characterize genomic, phylogenetic, and morphological traits from these phages and argue for establishing four novel viral genera. We also search the genomes for anti-defense systems and investigate DNA modifications using Nanopore sequencing. In Pseudomonas phage Rembedalsseter we find evidence of 13 motif-associated single-stranded DNA breaks. A bioinformatics search revealed that 60 related Pseudomonas phages are enriched in the same motif, suggesting these single-stranded nicks may be widely distributed in this family of phages. Finally, we also search the Sequence Read Archive for similar phages in public metagenomes. We find close hits to the Erwinia jumbo-phage Kaldavass in a wide variety of plant, food, and wastewater metagenomes including a near-perfect hit from a Spanish spinach sample, illustrating how interconnected geographically distant phages can be.}, } @article {pmid39875829, year = {2025}, author = {Zhang, Z and Zong, X and Liu, Z and Dong, X and Bai, H and Fan, L and Li, T}, title = {Comprehensive analysis of vaginal microbiota in Chinese women with genital tuberculosis: implications for diagnosis and treatment.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {52}, pmid = {39875829}, issn = {1471-2180}, support = {2024-4-2119//Capital's Funds for Health Improvement and Research/ ; FCYY201916//Special Training Program for Young and Middle-aged Subject Backbone of Beijing Obstetrics and Gynecology Hospital, Capital Medical University/ ; YQRC201906//"Excellent young Talents" project of Beijing Obstetrics and Gynecology Hospital, Capital Medical University/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology ; Adult ; *Tuberculosis, Female Genital/microbiology/diagnosis ; *Microbiota ; China ; Middle Aged ; Young Adult ; Antitubercular Agents/therapeutic use ; Lactobacillus/isolation & purification/genetics ; Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; East Asian People ; }, abstract = {BACKGROUND: Tuberculosis remains an infectious disease of global concern, with potential impacts on respiratory and intestinal microbiota owing to prolonged broad-spectrum antibiotic therapy. Despite its potential to cause infertility, the vaginal microbiota of women with genital tuberculosis remains poorly understood. We comprehensively analyzed the vaginal microbiota in Chinese women with genital tuberculosis.

RESULTS: We recruited women with pelvic (n = 28), endometrial (n = 16), and pulmonary (n = 12) tuberculosis as the research group, and healthy women (n = 11) as the control group. Vaginal discharges were collected for metagenomic analysis of its microbiota. The alpha diversity of the vaginal microbiota in women with genital tuberculosis was slightly higher than that in healthy women, though the difference was not statistically significant (P = 0.23). Similarly, no significant differences in alpha diversity were observed between women with genital and pulmonary tuberculosis (P = 0.82) or between those with pelvic and endometrial tuberculosis (P = 0.82). Notably, the lowest alpha diversity was recorded six months to one year after initiating anti-tuberculosis treatment, with this decline being statistically significant (P = 0.023). The dominance of Lactobacillus iners in the vaginal microbiota was more common in women with genital tuberculosis than that of Lactobacillus crispatus. Furthermore, the abundance of short-chain fatty acid -producing anaerobes, such as Actinomycetes, Streptococcus, and Finegoldia, were significantly increased. Short-chain fatty acid precursor pathways, including the ko03010 ribosome pathway, ko00970 aminoacyl-tRNA synthesis, ko00230 purine metabolism, ko00240 pyrimidine metabolism, and ko00010 glycolysis gluconeogenesis pathway, were significantly upregulated in women with endometrial tuberculosis.

CONCLUSIONS: Extrapulmonary tuberculosis, particularly genital tuberculosis and its associated vaginal dysbiosis impacts female fecundity. Vaginal dysbiosis is more pronounced when M. tuberculosis invades the endometrium. Given the effect of antibiotics on vaginal flora, probiotic combined interventions could be used as a future research direction.

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid39875095, year = {2025}, author = {Moeller, AH}, title = {Partner fidelity, not geography, drives co-diversification of gut microbiota with hominids.}, journal = {Biology letters}, volume = {21}, number = {1}, pages = {20240454}, doi = {10.1098/rsbl.2024.0454}, pmid = {39875095}, issn = {1744-957X}, support = {/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Phylogeny ; Hominidae/microbiology ; Bacteria/classification/genetics/isolation & purification ; Genome, Bacterial ; Geography ; }, abstract = {Bacterial strains that inhabit the gastrointestinal tracts of hominids have diversified in parallel (co-diversified) with their host species. The extent to which co-diversification has been mediated by partner fidelity between strains and hosts or by geographical distance between hosts is not clear due to a lack of strain-level data from clades of hosts with unconfounded phylogenetic relationships and geographical distributions. Here, I tested these competing hypotheses through meta-analyses of 7121 gut bacterial genomes assembled from wild-living ape species and subspecies sampled throughout their ranges in equatorial Africa. Across the gut bacterial phylogeny, strain diversification was more strongly associated with host phylogeny than with geography. In total, approximately 14% of the branch length of the gut bacterial phylogeny showed significant evidence of co-diversification independent of geography, whereas only approximately 4% showed significant evidence of diversification associated with geography independent of host phylogeny. Geographically co-occurring heterospecific hosts (Pan and Gorilla) universally maintained distinct co-diversified bacterial strains. Strains whose diversification was associated with geography independent of host phylogeny included clades of Proteobacteria known to adopt free-living lifestyles (e.g. Escherichia). These results show that co-diversification of gut bacterial strains with hominids has been driven primarily by fidelity of strains to host lineages rather than geography.}, } @article {pmid39874239, year = {2025}, author = {Zhou, H and Balint, D and Shi, Q and Vartanian, T and Kriegel, MA and Brito, I}, title = {Lupus and inflammatory bowel disease share a common set of microbiome features distinct from other autoimmune disorders.}, journal = {Annals of the rheumatic diseases}, volume = {84}, number = {1}, pages = {93-105}, doi = {10.1136/ard-2024-225829}, pmid = {39874239}, issn = {1468-2060}, mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/immunology ; *Lupus Erythematosus, Systemic/microbiology/immunology ; *Gastrointestinal Microbiome/genetics ; *Autoimmune Diseases/microbiology/immunology ; Biomarkers ; Female ; Metagenomics/methods ; Metagenome ; Male ; Receptors, Glucocorticoid/genetics ; }, abstract = {OBJECTIVES: This study aims to elucidate the microbial signatures associated with autoimmune diseases, particularly systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD), compared with colorectal cancer (CRC), to identify unique biomarkers and shared microbial mechanisms that could inform specific treatment protocols.

METHODS: We analysed metagenomic datasets from patient cohorts with six autoimmune conditions-SLE, IBD, multiple sclerosis, myasthenia gravis, Graves' disease and ankylosing spondylitis-contrasting these with CRC metagenomes to delineate disease-specific microbial profiles. The study focused on identifying predictive biomarkers from species profiles and functional genes, integrating protein-protein interaction analyses to explore effector-like proteins and their targets in key signalling pathways.

RESULTS: Distinct microbial signatures were identified across autoimmune disorders, with notable overlaps between SLE and IBD, suggesting shared microbial underpinnings. Significant predictive biomarkers highlighted the diverse microbial influences across these conditions. Protein-protein interaction analyses revealed interactions targeting glucocorticoid signalling, antigen presentation and interleukin-12 signalling pathways, offering insights into possible common disease mechanisms. Experimental validation confirmed interactions between the host protein glucocorticoid receptor (NR3C1) and specific gut bacteria-derived proteins, which may have therapeutic implications for inflammatory disorders like SLE and IBD.

CONCLUSIONS: Our findings underscore the gut microbiome's critical role in autoimmune diseases, offering insights into shared and distinct microbial signatures. The study highlights the potential importance of microbial biomarkers in understanding disease mechanisms and guiding treatment strategies, paving the way for novel therapeutic approaches based on microbial profiles.

TRIAL REGISTRATION NUMBER: NCT02394964.}, } @article {pmid39871406, year = {2025}, author = {Noell, SE and Abbaszadeh, J and Richards, H and Labat Saint Vincent, M and Lee, CK and Herbold, CW and Stott, MB and Cary, SC and McDonald, IR}, title = {Antarctic Geothermal Soils Exhibit an Absence of Regional Habitat Generalist Microorganisms.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70032}, doi = {10.1111/1462-2920.70032}, pmid = {39871406}, issn = {1462-2920}, support = {18-UOW-028//Marsden Fund/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Archaea/classification/genetics ; *Bacteria/classification/isolation & purification/genetics ; *Ecosystem ; Microbiota ; Phylogeny ; Hot Springs/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Active geothermal systems are relatively rare in Antarctica and represent metaphorical islands ideal to study microbial dispersal. In this study, we tested the macro-ecological concept that high dispersal rates result in communities being dominated by either habitat generalists or specialists by investigating the microbial communities on four geographically separated geothermal sites on three Antarctic volcanoes (Mts. Erebus, Melbourne, and Rittman). We found that the microbial communities at higher temperature (max 65°C) sites (Tramway Ridge on Erebus and Rittmann) were unique from each other and were dominated by a variety of novel Archaea from class Nitrososphaeria, while lower temperature (max 50°C) sites (Western Crater on Erebus and Melbourne) had characteristically mesophilic communities (Planctomycetes, Acidobacteriota, etc.) that were highly similar. We found that 97% of the detected microbial taxa were regional habitat specialists, with no generalists, with community assembly driven by high dispersal rates and drift (25% and 30% of community assembly, respectively), not environmental selection. Our results indicate that for microbial communities experiencing high dispersal rates between isolated communities, habitat specialists may tend to out-compete habitat generalists.}, } @article {pmid39765072, year = {2025}, author = {Khan, M and Nizamani, MM and Asif, M and Kamran, A and He, G and Li, X and Yang, S and Xie, X}, title = {Comprehensive approaches to heavy metal bioremediation: Integrating microbial insights and genetic innovations.}, journal = {Journal of environmental management}, volume = {374}, number = {}, pages = {123969}, doi = {10.1016/j.jenvman.2024.123969}, pmid = {39765072}, issn = {1095-8630}, mesh = {*Biodegradation, Environmental ; *Metals, Heavy/metabolism ; Microbiota ; Ecosystem ; Humans ; }, abstract = {The increasing contamination of ecosystems with heavy metals (HMs) due to industrial activities raises significant jeopardies to environmental health and human well-being. Addressing this issue, recent advances in the field of bioremediation have highlighted the potential of plant-associated microbiomes and genetically engineered organisms (GEOs) to mitigate HMs pollution. This review explores recent advancements in bioremediation strategies for HMs detoxification, with particular attention to omics technologies such as metagenomics, metabolomics, and metaproteomics in deepening the understanding of microbial interactions and their potential for neutralizing HMs. Additionally, Emerging strategies and technologies in GEOs and microorganism-aided nanotechnology have proven to be effective bioremediation tools, particularly for alleviating HM contamination. Despite the promising strategies developed in laboratory settings, several challenges impede their practical application, including ecological risks, regulatory limitations, and public concerns regarding the practice of genetically modified organisms. A comprehensive approach that involves interdisciplinary research is essential to enhance the efficacy and safety of bioremediation technologies. This approach should be coupled with robust regulatory frameworks and active public engagement to ensure environmental integrity and societal acceptance. This review underscores the importance of developing sustainable bioremediation strategies that align with ecological conservation goals and public health priorities.}, } @article {pmid39723822, year = {2025}, author = {Beauchemin, ET and Hunter, C and Maurice, CF}, title = {Dextran sodium sulfate-induced colitis alters the proportion and composition of replicating gut bacteria.}, journal = {mSphere}, volume = {10}, number = {1}, pages = {e0082524}, doi = {10.1128/msphere.00825-24}, pmid = {39723822}, issn = {2379-5042}, support = {Frederick Banting and Charles Best Canada Graduate Scholarship-Master's//Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; Ferrings Pharmaceuticals Fellowship//Faculty of Medicine, McGill University (McGill Faculty of Medicine)/ ; Doctoral Research grant//FRQ | Fonds de recherche du Québec - Nature et technologies (FRQNT)/ ; 950-230748 X-242502//Canada Research Chairs (Chaires de recherche du Canada)/ ; PJT-149098//Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; Innovators award//Kenneth Rainin Foundation (KRF)/ ; Owens Catchpaugh IBD Graduate Research Award//McGill University Health Centre (MUHC)/ ; }, mesh = {Animals ; *Dextran Sulfate ; *Gastrointestinal Microbiome ; *Colitis/microbiology/chemically induced ; Mice ; *Disease Models, Animal ; *Bacteria/classification/isolation & purification/genetics/metabolism ; *Mice, Inbred C57BL ; Metagenomics ; Female ; Male ; Single-Cell Analysis ; }, abstract = {The bacteria living in the human gut are essential for host health. Though the composition and metabolism of these bacteria are well described in both healthy hosts and those with intestinal disease, less is known about the metabolic activity of the gut bacteria prior to, and during, disease development-especially regarding gut bacterial replication. Here, we use a recently developed single-cell technique alongside existing metagenomics-based tools to identify, track, and quantify replicating gut bacteria both ex vivo and in situ in the dextran sodium sulfate (DSS) mouse model of colitis. We show that the proportion of replicating gut bacteria decreases when mice have the highest levels of inflammation and returns to baseline levels as mice begin recovering. In addition, we report significant alterations in the composition of the replicating gut bacterial community ex vivo during colitis development. On the taxa level, we observe significant changes in the abundance of taxa such as the mucus-degrading Akkermansia and the poorly described Erysipelatoclostridium genus. We further demonstrate that many taxa exhibit variable replication rates in situ during colitis, including Akkermansia muciniphila. Lastly, we show that colitis development is positively correlated with increases in the presence and abundance of bacteria in situ which are predicted to be fast replicators. This could suggest that taxa with the potential to replicate quickly may have an advantage during intestinal inflammation. These data support the need for additional research using activity-based approaches to further characterize the gut bacterial response to intestinal inflammation and its consequences for both the host and the gut microbial community.IMPORTANCEIt is well known that the bacteria living inside the gut are important for human health. Indeed, the type of bacteria that are present and their metabolism are different in healthy people versus those with intestinal disease. However, less is known about how these gut bacteria are replicating, especially as someone begins to develop intestinal disease. This is particularly important as it is thought that metabolically active gut bacteria may be more relevant to health. Here, we begin to address this gap using several complementary approaches to characterize the replicating gut bacteria in a mouse model of intestinal inflammation. We reveal which gut bacteria are replicating, and how quickly, as mice develop and recover from inflammation. This work can serve as a model for future research to identify how actively growing gut bacteria may be impacting health, or why these particular bacteria tend to thrive during intestinal inflammation.}, } @article {pmid39699190, year = {2025}, author = {Prattico, C and Gonzalez, E and Dridi, L and Jazestani, S and Low, KE and Abbott, DW and Maurice, CF and Castagner, B}, title = {Identification of novel fructo-oligosaccharide bacterial consumers by pulse metatranscriptomics in a human stool sample.}, journal = {mSphere}, volume = {10}, number = {1}, pages = {e0066824}, doi = {10.1128/msphere.00668-24}, pmid = {39699190}, issn = {2379-5042}, support = {DO-16//UofA | Canadian Glycomics Network (GlycoNet)/ ; PJT-437944//Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; }, mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome ; *Oligosaccharides/metabolism ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Prebiotics ; Gene Expression Profiling ; Metagenomics/methods ; Fermentation ; RNA, Ribosomal, 16S/genetics ; Transcriptome ; Dietary Fiber/metabolism ; }, abstract = {UNLABELLED: Dietary fibers influence the composition of the human gut microbiota and directly contribute to its downstream effects on host health. As more research supports the use of glycans as prebiotics for therapeutic applications, the need to identify the gut bacteria that metabolize glycans of interest increases. Fructo-oligosaccharide (FOS) is a common diet-derived glycan that is fermented by the gut microbiota and has been used as a prebiotic. Despite being well studied, we do not yet have a complete picture of all FOS-consuming gut bacterial taxa. To identify new bacterial consumers, we used a short exposure of microbial communities in a stool sample to FOS or galactomannan as the sole carbon source to induce glycan metabolism genes. We then performed metatranscriptomics, paired with whole metagenomic sequencing, and 16S amplicon sequencing. The short incubation was sufficient to cause induction of genes involved in carbohydrate metabolism, like carbohydrate-active enzymes (CAZymes), including glycoside hydrolase family 32 genes, which hydrolyze fructan polysaccharides like FOS and inulin. Interestingly, FOS metabolism transcripts were notably overexpressed in Blautia species not previously reported to be fructan consumers. We therefore validated the ability of different Blautia species to ferment fructans by monitoring their growth and fermentation in defined media. This pulse metatranscriptomics approach is a useful method to find novel consumers of prebiotics and increase our understanding of prebiotic metabolism by CAZymes in the gut microbiota.

IMPORTANCE: Complex carbohydrates are key contributors to the composition of the human gut microbiota and play an essential role in the microbiota's effects on host health. Understanding which bacteria consume complex carbohydrates, or glycans, provides a mechanistic link between dietary prebiotics and their beneficial health effects, an essential step for their therapeutic application. Here, we used a pulse metatranscriptomics pipeline to identify bacterial consumers based on glycan metabolism induction in a human stool sample. We identified novel consumers of fructo-oligosaccharide among Blautia species, expanding our understanding of this well-known glycan. Our approach can be applied to identify consumers of understudied glycans and expand our prebiotic repertoire. It can also be used to study prebiotic glycans directly in stool samples in distinct patient populations to help delineate the prebiotic mechanism.}, } @article {pmid39653637, year = {2025}, author = {Lepcha, A and Kumar, R and Dindhoria, K and Bhargava, B and Pati, AM and Kumar, R}, title = {Metagenomic insights into the functional potential of non-sanitary landfill microbiomes in the Indian Himalayan region, highlighting key plastic degrading genes.}, journal = {Journal of hazardous materials}, volume = {484}, number = {}, pages = {136642}, doi = {10.1016/j.jhazmat.2024.136642}, pmid = {39653637}, issn = {1873-3336}, mesh = {India ; *Waste Disposal Facilities ; *Microbiota/genetics ; *Plastics ; *Metagenomics ; Biodegradation, Environmental ; Bacteria/genetics/metabolism/classification ; Metals, Heavy ; Soil Microbiology ; Soil Pollutants/metabolism ; Refuse Disposal ; }, abstract = {Solid waste management in the Indian Himalayan Region (IHR) is a growing challenge, intensified by increasing population and tourism, which strain non-sanitary landfills. This study investigates microbial diversity and functional capabilities within these landfills using a high-throughput shotgun metagenomic approach. Physicochemical analysis revealed that the Manali and Mandi landfill sites were under heavy metal contamination and thermal stress. Taxonomic annotation identified a dominance of bacterial phyla, including Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes, with genera like Pseudomonas and Bacillus prevalent. Squeezemeta analysis generated 9,216,983 open reading frames (ORFs) across the sampling sites, highlighting diverse metabolic potentials for heavy metal resistance and degrading organic, xenobiotics and plastic wastes. Hierarchical clustering and principal component analysis (PCA) identified distinct gene clusters in Manali and Mandi landfill sites, reflecting differences in pollution profiles. Functional redundancy of landfill microbiome was observed with notable xenobiotic and plastic degradation pathways. This is the first comprehensive metagenomic assessment of non-sanitary landfills in the IHR, providing valuable insights into the microbial roles in degrading persistent pollutants, plastic waste, and other contaminants in these stressed environments.}, } @article {pmid39642737, year = {2025}, author = {Medriano, CA and Kim, S and Kim, LH and Bae, S}, title = {Chronic Exposure of Adult Zebrafish to Polyethylene and Polyester-based Microplastics: Metabolomic and Gut Microbiome Alterations Reflecting Dysbiosis and Resilience.}, journal = {Journal of hazardous materials}, volume = {484}, number = {}, pages = {136691}, doi = {10.1016/j.jhazmat.2024.136691}, pmid = {39642737}, issn = {1873-3336}, mesh = {Animals ; *Zebrafish ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/chemically induced ; *Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; *Metabolomics ; *Polyesters ; *Polyethylene/toxicity ; }, abstract = {The study explored the ecotoxicological effects of chronic exposure to microplastic (MP) on adult zebrafish, focusing on environmentally relevant concentrations of polyethylene (PE) beads and polyester (PES). High-throughput untargeted metabolomics via UPLC-QToF-MS and 16S metagenomics for gut microbiota analysis were used to assess ecotoxicity in zebrafish exposed to varying concentrations of PE and PES. The VIP (Variable Importance in Projection) scores indicated PE exposure primarily impacted phospholipids, ceramides, and nucleotide-related compounds, while PES exposure led to alterations in lipid-related compounds, chitin, and amino acid derivatives. From MSEA (Metabolite Set Enrichment Analysis) and Mummichog analyses, PE and PES significantly disrupted key metabolomic pathways associated with inflammation, immune responses, and apoptosis, including leukotriene and arachidonic acid metabolism and the formation of putative anti-inflammatory metabolites from EPA. PE caused physical disruption and inflammation of the epithelial barrier, whereas PES affected gut microbiota interactions, impairing digestion and metabolism. Although alpha diversity within the gut microbiome remained stable, beta diversity analysis revealed significant shifts in microbial composition and structure, suggesting a disruption of functional balance and an increased susceptibility to pathogens. Chronic PE and PES exposures induced shifts in the gut microbial community and interaction network with potential increases in pathogenic bacteria and alteration in commensal bacteria, demonstrating the microbiome's resilience and adaptability to stressors of MPs exposure. High-throughput metabolomics and 16S metagenomics revealed potential chronic diseases associated with inflammation, immune system disorders, metabolic dysfunction, and gut dysbiosis, highlighting the complex relationship between gut microbiome resilience and metabolic disruption under MP-induced stress, with significant ecological implications.}, } @article {pmid39571716, year = {2025}, author = {González-Parra, JA and Barrera-Conde, M and Kossatz, E and Veza, E and de la Torre, R and Busquets-Garcia, A and Robledo, P and Pizarro, N}, title = {Microbiota and social behavior alterations in a mouse model of down syndrome: Modulation by a synbiotic treatment.}, journal = {Progress in neuro-psychopharmacology & biological psychiatry}, volume = {136}, number = {}, pages = {111200}, doi = {10.1016/j.pnpbp.2024.111200}, pmid = {39571716}, issn = {1878-4216}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; *Down Syndrome/genetics ; Mice ; *Synbiotics ; *Disease Models, Animal ; *Social Behavior ; Mice, Inbred C57BL ; Behavior, Animal/physiology ; Sex Characteristics ; }, abstract = {Sex differences in the composition and functionality of gut microbiota are an emerging field of interest in neurodevelopmental disorders, as they may help in understanding the phenotypic disparities between males and females. This study aimed to characterize sex-related specific alterations in gut microbiota composition in a mouse model of Down syndrome (Ts65Dn mice, TS mice) through the sequencing of the PCR-amplified 16S ribosomal DNA fraction. Moreover, it intended to examine whether the modulation of gut microbiota by the administration of a synbiotic (SYN) treatment would be beneficial for the behavioral alterations observed in male and female TS mice. Our results show that male, but not female, TS mice exhibit alterations in beta diversity compared to their wild-type (WT) littermates. Sex-dependent differences are also observed in the relative abundance of the classes Bacilli and Clostridia. Administering the SYN effectively counteracts hypersociability in females, and normalizes the overall abundance of Bacilli, specifically by increasing Lactobacillaceae. On the contrary, it rescues emotional recognition deficits in male TS mice and increases the relative abundance of the families Lactobacillaceae, Streptococcaceae and Atopobiaceae. In addition, a metagenome KEGG analysis of differentially enriched pathways shows relevant changes in the cofactor biosynthesis and the amino acid synthesis categories. Finally, following SYN treatment, both male and female TS mice exhibit a robust increase in propionic acid levels compared to WT littermates. These findings suggest sex-specific mechanisms that could link gut microbiota composition with behavior in TS mice, and underscore the potential of targeted gut microbiota interventions to modulate social abnormalities in neurodevelopmental disorders.}, } @article {pmid38760649, year = {2025}, author = {Kumar, A and Sharma, S and Dindhoria, K and Thakur, A and Kumar, R}, title = {Insight into physico-chemical properties and microbial community structure of biogas slurry from household biogas plants of sub-Himalaya for its implications in improved biogas production.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {28}, number = {1}, pages = {187-200}, pmid = {38760649}, issn = {1618-1905}, mesh = {*Biofuels ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *RNA, Ribosomal, 16S/genetics ; *Bioreactors/microbiology ; *Microbiota ; Phylogeny ; Anaerobiosis ; Manure/microbiology/analysis ; Carbon/analysis/metabolism ; Nitrogen/analysis ; Metagenomics ; Biodiversity ; }, abstract = {Numerous metagenomics studies, conducted in both full-scale anaerobic digesters and household biogas plants, have shed light on the composition and activity of microbial flora essential for optimizing the performance of biogas reactors, underscoring the significance of microbial community composition in biogas plant efficiency. Although the efficiency of household biogas plants in the sub-Himalayan region has been reported, there is no literature evidence on the microbial community structure of such household biogas plants in the sub-Himalayan region. The current study evaluated the physico-chemical properties and bacterial community structure from the slurry samples of household biogas plants prevalent in the sub-Himalayan region. The slurry samples were observed to be rich in nutrients; however, their carbon and nitrogen contents were higher than the recommended standard values of liquid-fermented organic manure. The species richness and diversity indices (Chao1, Shannon, and Simpson) of household biogas plants were quite similar to the advanced biogas reactors operating at mesophilic conditions. 16S rRNA gene amplicon sequencing reveals microbial diversity, showing a higher abundance of Firmicutes (70.9%) and Euryarchaeota (9.52%) in advanced biogas reactors compared to household biogas plants. Microbial analysis shows a lack of beneficial microbes for anaerobic digestion, which might be the reason for inefficient biogas production in household biogas plants of the sub-Himalayan region. The lack of efficient bacterial biomass may also be attributed to the digester design, feedstock, and ambient temperatures. This study emphasized the establishment of efficient microbial consortia for enhanced degradation rates that may increase the methane yield in biogas plants.}, } @article {pmid38758414, year = {2025}, author = {Xiao, Z and Zhang, Y and Zhang, W and Zhang, A and Wang, G and Chen, C and Ullah, H and Ayaz, T and Li, S and Zhaxi, D and Yan, Q and Kang, J and Xu, X}, title = {Characterizations of gut bacteriome, mycobiome, and virome of healthy individuals living in sea-level and high-altitude areas.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {28}, number = {1}, pages = {173-186}, pmid = {38758414}, issn = {1618-1905}, support = {82370563//National Natural Science Foundation of China/ ; 31700697//National Natural Science Foundation of China/ ; QYXTZX-NQ2022-03//Characteristic Technology of Polysaccharides Research Programme of Naqu, Tibet/ ; }, mesh = {Humans ; *Altitude ; *Gastrointestinal Microbiome ; *Virome ; *Mycobiome ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/isolation & purification/genetics ; Adult ; Male ; Viruses/classification/isolation & purification/genetics ; Healthy Volunteers ; Female ; Feces/microbiology/virology ; Middle Aged ; Metagenome ; }, abstract = {BACKGROUND: The contribution of gut microbiota to human high-altitude adaptation remains inadequately understood.

METHODS: Here a comparative analysis of gut microbiota was conducted between healthy individuals living at sea level and high altitude using deep whole-metagenome shotgun sequencing, to investigate the adaptive mechanisms of gut microbiota in plateau inhabitants.

RESULTS: The results showed the gut bacteriomes in high-altitude individuals exhibited greater within-sample diversity and significant alterations in both bacterial compositional and functional profiles when compared to those of sea-level individuals, indicating the potential selection of unique bacteria associated with high-altitude environments. The strain-level investigation revealed enrichment of Collinsella aerofaciens and Akkermansia muciniphila in high-altitude populations. The characteristics of gut virome and gut mycobiome were also investigated. Compared to sea-level subjects, high-altitude subjects exhibited a greater diversity in their gut virome, with an increased number of viral operational taxonomic units (vOTUs) and unique annotated genes. Finally, correlation analyses revealed 819 significant correlations between 42 bacterial species and 375 vOTUs, while no significant correlations were observed between bacteria and fungi or between fungi and viruses.

CONCLUSION: The findings have significantly contributed to an enhanced comprehension of the mechanisms underlying the high-altitude geographic adaptation of the human gut microbiota.}, } @article {pmid39867343, year = {2024}, author = {Guimarães, LO and Ribeiro, GO and da Couto, R and Ramos, EDSF and Morais, VDS and Telles-de-Deus, J and Helfstein, VC and Dos Santos, JM and Deng, X and Delwart, E and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Kirchgatter, K and Leal, É}, title = {Exploring mosquito virome dynamics within São Paulo Zoo: insights into mosquito-virus-environment interactions.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1496126}, pmid = {39867343}, issn = {2235-2988}, mesh = {Animals ; Brazil ; *Virome ; *Mosquito Vectors/virology ; *Metagenomics ; Animals, Zoo/virology ; Arboviruses/genetics/classification/isolation & purification ; Culicidae/virology ; Aedes/virology ; Anopheles/virology ; Culex/virology ; Ecosystem ; }, abstract = {BACKGROUND: Mosquito-borne diseases have a significant public health threat worldwide, with arboviruses accounting for a high proportion of infectious diseases and mortality annually. Brazil, in particular, has been suffering outbreaks of diseases transmitted by mosquito viruses, notably those of the Aedes genus, such as dengue, Zika, and chikungunya. Against this background, the São Paulo Zoo is an intriguing ecological niche to explore the virome of mosquitoes, potentially shedding light on the dynamics of arbovirus transmission within a confined setting.

METHODS: In this study, we conducted a comprehensive metagenomic analysis of mosquitoes collected from diverse habitats within the zoo, focusing on the Aedes, Anopheles, and Culex genera. From 1,039 contigs of viral origin, we identified 229 viral species infecting mosquitoes, with the orders Picornavirales, Nodamuvirales and Sobelivirales being the most prevalent and abundant. The difference in virome composition was primarily driven by mosquito host species rather than specific collection sites or trap height.

RESULTS: Despite environmental disparities, the virome remained remarkably uniform across different areas of the zoo, emphasizing the strong association between mosquito species and their viral communities. Furthermore, we identified a core virome shared among mosquito species, highlighting potential cross-species transmission events and underscoring the need for targeted surveillance and control measures.

CONCLUSION: These results contribute to our understanding of the interplay between mosquitoes, the environment, and viruses, providing valuable insights for disease intervention strategies in mosquito-borne diseases.}, } @article {pmid39866568, year = {2025}, author = {Pucci, N and Ujčič-Voortman, J and Verhoeff, AP and Mende, DR}, title = {Priority effects, nutrition and milk glycan-metabolic potential drive Bifidobacterium longum subspecies dynamics in the infant gut microbiome.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18602}, pmid = {39866568}, issn = {2167-8359}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Milk, Human/microbiology/chemistry/metabolism ; Infant ; *Bifidobacterium/metabolism/genetics ; *Bifidobacterium longum/metabolism ; Female ; *Polysaccharides/metabolism ; Infant, Newborn ; Feces/microbiology ; Metagenome ; Breast Feeding ; Male ; }, abstract = {BACKGROUND: The initial colonization of the infant gut is a complex process that defines the foundation for a healthy microbiome development. Bifidobacterium longum is one of the first colonizers of newborns' gut, playing a crucial role in the healthy development of both the host and its microbiome. However, B. longum exhibits significant genomic diversity, with subspecies (e.g., Bifidobacterium longum subsp. infantis and subsp. longum) displaying distinct ecological and metabolic strategies including differential capabilities to break down human milk glycans (HMGs). To promote healthy infant microbiome development, a good understanding of the factors governing infant microbiome dynamics is required.

METHODOLOGY: We analyzed newly sequenced gut microbiome samples of mother-infant pairs from the Amsterdam Infant Microbiome Study (AIMS) and four publicly available datasets to identify important environmental and bifidobacterial features associated with the colonization success and succession outcomes of B. longum subspecies. Metagenome-assembled genomes (MAGs) were generated and assessed to identify characteristics of B. longum subspecies in relation to early-life gut colonization. We further implemented machine learning tools to identify significant features associated with B. longum subspecies abundance.

RESULTS: B. longum subsp. longum was the most abundant and prevalent gut Bifidobacterium at one month, being replaced by B. longum subsp. infantis at six months of age. By utilizing metagenome-assembled genomes (MAGs), we reveal significant differences between and within B. longum subspecies in their potential to break down HMGs. We further combined strain-tracking, meta-pangenomics and machine learning to understand these abundance dynamics and found an interplay of priority effects, milk-feeding type and HMG-utilization potential to govern them across the first six months of life. We find higher abundances of B. longum subsp. longum in the maternal gut microbiome, vertical transmission, breast milk and a broader range of HMG-utilizing genes to promote its abundance at one month of age. Eventually, we find B. longum subsp. longum to be replaced by B. longum subsp. infantis at six months of age due to a combination of nutritional intake, HMG-utilization potential and a diminishment of priority effects.

DISCUSSION: Our results establish a strain-level ecological framework explaining early-life abundance dynamics of B. longum subspecies. We highlight the role of priority effects, nutrition and significant variability in HMG-utilization potential in determining the predictable colonization and succession trajectories of B. longum subspecies, with potential implications for promoting infant health and well-being.}, } @article {pmid39814067, year = {2024}, author = {Ji, J and Jung, S}, title = {PredCMB: predicting changes in microbial metabolites based on the gene-metabolite network analysis of shotgun metagenome data.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {1}, pages = {}, doi = {10.1093/bioinformatics/btaf020}, pmid = {39814067}, issn = {1367-4811}, support = {//National Research Foundation of Korea/ ; 2022R1A2C1007345//Korea government/ ; }, mesh = {*Metagenome ; *Metagenomics/methods ; Humans ; Metabolomics/methods ; Metabolic Networks and Pathways ; Microbiota/genetics ; Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Metabolome ; Stomach Neoplasms/metabolism/microbiology/genetics ; }, abstract = {MOTIVATION: Microbiota-derived metabolites significantly impact host biology, prompting extensive research on metabolic shifts linked to the microbiota. Recent studies have explored both direct metabolite analyses and computational tools for inferring metabolic functions from microbial shotgun metagenome data. However, no existing tool specifically focuses on predicting changes in individual metabolite levels, as opposed to metabolic pathway activities, based on shotgun metagenome data. Understanding these changes is crucial for directly estimating the metabolic potential associated with microbial genomic content.

RESULTS: We introduce Predicting Changes in Microbial metaBolites (PredCMB), a novel method designed to predict alterations in individual metabolites between conditions using shotgun metagenome data and enzymatic gene-metabolite networks. PredCMB evaluates differential enzymatic gene abundance between conditions and estimates its influence on metabolite changes. To validate this approach, we applied it to two publicly available datasets comprising paired shotgun metagenomics and metabolomics data from inflammatory bowel disease cohorts and the cohort of gastrectomy for gastric cancer. Benchmark evaluations revealed that PredCMB outperformed a previous method by demonstrating higher correlations between predicted metabolite changes and experimentally measured changes. Notably, it identified metabolite classes exhibiting major alterations between conditions. By enabling the prediction of metabolite changes directly from shotgun metagenome data, PredCMB provides deeper insights into microbial metabolic dynamics than existing methods focused on pathway activity evaluation. Its potential applications include refining target metabolite selection in microbial metabolomic studies and assessing the contributions of microbial metabolites to disease pathogenesis.

Freely available to non-commercial users at https://www.sysbiolab.org/predcmb.}, } @article {pmid39556491, year = {2025}, author = {Shete, O and Ghosh, TS}, title = {Normal Gut Microbiomes in Diverse Populations: Clinical Implications.}, journal = {Annual review of medicine}, volume = {76}, number = {1}, pages = {95-114}, doi = {10.1146/annurev-med-051223-031809}, pmid = {39556491}, issn = {1545-326X}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; }, abstract = {The human microbiome is a sensor and modulator of physiology and homeostasis. Remarkable tractability underpins the promise of therapeutic manipulation of the microbiome. However, the definition of a normal or healthy microbiome has been elusive. This is in part due to the underrepresentation of minority groups and major global regions in microbiome studies to date. We review studies of the microbiome in different populations and highlight a commonality among health-associated microbiome signatures along with major drivers of variation. We also provide an overview of microbiome-associated therapeutic interventions for some widespread, widely studied diseases. We discuss sources of bias and the challenges associated with defining population-specific microbiome reference bases. We propose a roadmap for defining normal microbiome references that can be used for population-customized microbiome therapeutics and diagnostics.}, } @article {pmid39865153, year = {2025}, author = {Wu, Z and Jiang, M and Jia, M and Sang, J and Wang, Q and Xu, Y and Qi, L and Yang, W and Feng, L}, title = {The difference of oropharyngeal microbiome during acute respiratory viral infections in infants and children.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {127}, pmid = {39865153}, issn = {2399-3642}, support = {2022-I2M-CoV19-006//Chinese Academy of Medical Sciences (CAMS)/ ; }, mesh = {Humans ; *Respiratory Tract Infections/microbiology/virology ; Infant ; *Oropharynx/microbiology/virology ; *Microbiota ; Child, Preschool ; Male ; Female ; Child ; Acute Disease ; Virus Diseases/virology/microbiology/epidemiology ; }, abstract = {Acute respiratory infections (ARI) with multiple types of viruses are common in infants and children. This study was conducted to assess the difference of oropharyngeal microbiome during acute respiratory viral infection using whole-genome shotgun metagenomic sequencing. The overall taxonomic alpha diversity did not differ by the types of infected virus. The beta diversity differed by disease severity, disease-related symptoms, and types of infected virus. Nine species had significantly higher abundance in outpatients than in inpatients, with five of them in the genus Achromobacter. Three microbial community types were identified. The prevalence of community type (CT) 1 was higher among patients with influenza virus, enterovirus, and human adenvirus; CT2 was higher among patients with human metapneumovirus; and CT3 was higher among patients with respiratory syncytial virus and human adenvirus infections. Our results suggest that the oropharyngeal microbiome is associated with ARI disease severity, disease-related symptoms, and the types of infected virus.}, } @article {pmid38385313, year = {2025}, author = {Iqbal, S and Begum, F and Ullah, I and Jalal, N and Shaw, P}, title = {Peeling off the layers from microbial dark matter (MDM): recent advances, future challenges, and opportunities.}, journal = {Critical reviews in microbiology}, volume = {51}, number = {1}, pages = {1-21}, doi = {10.1080/1040841X.2024.2319669}, pmid = {38385313}, issn = {1549-7828}, mesh = {*Metagenomics ; *Bacteria/genetics/classification/metabolism ; Genomics ; Microbiota ; Metagenome ; }, abstract = {Microbes represent the most common organisms on Earth; however, less than 2% of microbial species in the environment can undergo cultivation for study under laboratory conditions, and the rest of the enigmatic, microbial world remains mysterious, constituting a kind of "microbial dark matter" (MDM). In the last two decades, remarkable progress has been made in culture-dependent and culture-independent techniques. More recently, studies of MDM have relied on culture-independent techniques to recover genetic material through either unicellular genomics or shotgun metagenomics to construct single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs), respectively, which provide information about evolution and metabolism. Despite the remarkable progress made in the past decades, the functional diversity of MDM still remains uncharacterized. This review comprehensively summarizes the recently developed culture-dependent and culture-independent techniques for characterizing MDM, discussing major challenges, opportunities, and potential applications. These activities contribute to expanding our knowledge of the microbial world and have implications for various fields including Biotechnology, Bioprospecting, Functional genomics, Medicine, Evolutionary and Planetary biology. Overall, this review aims to peel off the layers from MDM, shed light on recent advancements, identify future challenges, and illuminate the exciting opportunities that lie ahead in unraveling the secrets of this intriguing microbial realm.}, } @article {pmid39861468, year = {2025}, author = {Fricker, AD and Sejane, K and Desai, M and Snyder, MW and Duran, L and Mackelprang, R and Bode, L and Ross, MG and Flores, GE}, title = {A Pilot Study Exploring the Relationship Between Milk Composition and Microbial Capacity in Breastfed Infants.}, journal = {Nutrients}, volume = {17}, number = {2}, pages = {}, doi = {10.3390/nu17020338}, pmid = {39861468}, issn = {2072-6643}, support = {SC1GM136546/GM/NIGMS NIH HHS/United States ; R21HD104028/HD/NICHD NIH HHS/United States ; R01HD099813/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; *Milk, Human/chemistry/microbiology ; Pilot Projects ; Female ; *Gastrointestinal Microbiome ; Infant ; *Breast Feeding ; *Oligosaccharides/analysis ; Adult ; *Feces/microbiology/chemistry ; Cross-Sectional Studies ; Male ; Body Mass Index ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Overweight/microbiology ; Infant, Newborn ; Obesity/microbiology ; }, abstract = {BACKGROUND: Maternal obesity may contribute to childhood obesity in a myriad of ways, including through alterations of the infant gut microbiome. For example, maternal obesity may contribute both directly by introducing a dysbiotic microbiome to the infant and indirectly through the altered composition of human milk that fuels the infant gut microbiome. In particular, indigestible human milk oligosaccharides (HMOs) are known to shape the composition of the infant gut microbiome. The goal of this study was to characterize the HMO profiles of normal-weight and overweight mothers and to quantitatively link HMO concentrations to the taxonomic composition and functional potential of the infant gut microbiome.

METHODS: Normal-weight (BMI = 18.5-24.9; n = 9) and overweight/obese (OW/OB; BMI > 25; n = 11) breastfeeding mothers and their infants were enrolled in this single-center, cross-sectional pilot study. Human milk from the mothers and rectal stool swabs from the infants were collected 7-9 weeks postpartum. The HMO composition, microbiome composition, and microbial functions were assessed using HPLC, 16S rRNA gene sequencing, and metagenomic sequencing, respectively.

RESULTS: Neither the HMO profiles nor the infant microbiome composition varied according to maternal BMI status. Taxonomically, the gut microbiota of infants were dominated by typical gut lineages including Bifidobacterium. Significant correlations between individual HMOs and bacterial genera were identified, including for Prevotella, a genus of the Bacteroidota phylum that was positively correlated with the concentrations of lacto-N-neotetraose (LNnT) and lacto-N-hexaose (LNH). Using metagenomic assembled genomes, we were also able to identify the broad HMO-degradative capacity across the Bifidobacterium and Prevotella genera.

CONCLUSIONS: These results suggest that the maternal BMI status does not impact the HMO profiles of human milk. However, select HMOs were correlated with specific bacterial taxa, suggesting that the milk composition influences both the taxonomic composition and the functional capacity of the infant gut microbiome.}, } @article {pmid39860966, year = {2024}, author = {Laryushina, Y and Samoilova-Bedych, N and Turgunova, L and Marchenko, A and Turgunov, Y and Kozhakhmetov, S and Suieubayev, M and Mukhanbetzhanov, N and Kabdulina, N}, title = {Interrelationships of the Intestinal Microbiome, Trimethylamine N-Oxide and Lipopolysaccharide-Binding Protein with Crohn's Disease Activity.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/pathogens14010005}, pmid = {39860966}, issn = {2076-0817}, support = {AP14871959//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, mesh = {Humans ; *Methylamines/metabolism ; *Gastrointestinal Microbiome/physiology ; *Crohn Disease/microbiology/metabolism ; Female ; Male ; Adult ; *Acute-Phase Proteins/metabolism/analysis ; *Feces/microbiology/chemistry ; Middle Aged ; *Membrane Glycoproteins/metabolism ; Carrier Proteins/metabolism ; Young Adult ; Lipopolysaccharides/metabolism ; }, abstract = {UNLABELLED: Crohn's disease (CD) is a multifactorial inflammatory bowel disease whose pathogenetic mechanisms are a field of ongoing study. Changes in the intestinal microbiome in CD may influence metabolite production and reflect the disease's severity. We investigate the relationship between trimethylamine N-oxide (TMAO) and lipopolysaccharide-binding protein (LPS) levels and changes in the gut microbiome in patients with CD of various degrees of activity.

METHODS: In total, 29 CD patients and 15 healthy individuals were investigated for their levels of TMAO by HPLC-MS, and LPS protein by ELISA and metagenomic 16 s-sequencing of feces was performed.

RESULTS: We found significant differences in TMAO levels in patients in the remission/mild and moderate/severe groups compared to the control group (p = 0.02 and p = 0.014), changes in alpha diversity with the Shannon index (p = 0. 0151 and p = 0.0018) and in beta diversity (ANOSIM p = 0.009 and PERMANOVA p = 0.005) in both groups compared to controls. Strongly positive correlations in TMAO levels and mixed correlations of LPS with alpha diversity metrics were found, as well as significant correlations with microbiota species.

CONCLUSIONS: Changes in the level of metabolites may reflect specific disturbances in the composition of the intestinal microbiome at different degrees of severity of CD.}, } @article {pmid39859429, year = {2025}, author = {Vicente-Valor, J and Tesolato, S and Paz-Cabezas, M and Gómez-Garre, D and Ortega-Hernández, A and de la Serna, S and Domínguez-Serrano, I and Dziakova, J and Rivera, D and Jarabo, JR and Gómez-Martínez, AM and Hernando, F and Torres, A and Iniesta, P}, title = {Fecal Microbiota Strongly Correlates with Tissue Microbiota Composition in Colorectal Cancer but Not in Non-Small Cell Lung Cancer.}, journal = {International journal of molecular sciences}, volume = {26}, number = {2}, pages = {}, doi = {10.3390/ijms26020717}, pmid = {39859429}, issn = {1422-0067}, support = {PI19/00073//Carlos III Health Institute (Ministerio de Economía y Competitividad), Spain and co-funded by the European Union through the European Regional Development Fund (ERDF) 'A way to make Europe'/ ; }, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/microbiology ; *Feces/microbiology ; *Colorectal Neoplasms/microbiology ; *Lung Neoplasms/microbiology ; Female ; Male ; Middle Aged ; Aged ; RNA, Ribosomal, 16S/genetics ; Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Adult ; }, abstract = {Microbiota could be of interest in the diagnosis of colorectal and non-small cell lung cancer (CRC and NSCLC). However, how the microbial components of tissues and feces reflect each other remains unknown. In this work, our main objective is to discover the degree of correlation between the composition of the tissue microbiota and that of the feces of patients affected by CRC and NSCLC. Specifically, we investigated tumor and non-tumor tissues from 38 recruited patients with CRC and 19 with NSCLC. DNA from samples was submitted for 16S rDNA metagenomic sequencing, followed by data analysis through the QIIME2 pipeline and further statistical processing with STATA IC16. Tumor and non-tumor tissue selected genera were highly correlated in both CRC and NSCLC (100% and 81.25%). Following this, we established tissue-feces correlations, using selected genera from a LEfSe analysis previously published. In CRC, we found a strong correlation between the taxa detected in feces and those from colorectal tissues. However, our data do not demonstrate this correlation in NSCLC. In conclusion, our findings strongly reinforce the utility of fecal microbiota as a non-invasive biomarker for CRC diagnosis, while highlighting critical distinctions for NSCLC. Furthermore, our data demonstrate that the microbiota components of tumor and non-tumor tissues are similar, with only minor differences being detected.}, } @article {pmid39856742, year = {2025}, author = {Benitez, AJ and Tanes, C and Friedman, ES and Zackular, JP and Ford, E and Gerber, JS and DeRusso, PA and Kelly, A and Li, H and Elovitz, MA and Wu, GD and Zemel, B and Bittinger, K}, title = {Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {21}, pmid = {39856742}, issn = {2049-2618}, support = {KL2TR001879/TR/NCATS NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R35GM138369/GM/NIGMS NIH HHS/United States ; UL1TR001878//NIH National Center for Research Resources Clinical and Translational Science Program/ ; unrestricted donation//American Beverage Foundation for a Healthy America/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/adverse effects/pharmacology ; Infant ; *Feces/microbiology/chemistry ; Female ; *Bile Acids and Salts/metabolism ; Male ; Prospective Studies ; *Breast Feeding ; Longitudinal Studies ; Infant, Newborn ; Metagenomics ; Bacteria/classification/genetics/drug effects/isolation & purification ; Child, Preschool ; Black or African American ; Amoxicillin ; Bifidobacterium/drug effects/isolation & purification/genetics ; White ; }, abstract = {BACKGROUND: The evolving infant gut microbiome influences host immune development and later health outcomes. Early antibiotic exposure could impact microbiome development and contribute to poor outcomes. Here, we use a prospective longitudinal birth cohort of n = 323 healthy term African American children to determine the association between antibiotic exposure and the gut microbiome through shotgun metagenomics sequencing as well as bile acid profiles through liquid chromatography-mass spectrometry.

RESULTS: Stool samples were collected at ages 4, 12, and 24 months for antibiotic-exposed (n = 170) and unexposed (n = 153) participants. A short-term substudy (n = 39) collected stool samples at first exposure, and over 3 weeks following antibiotics initiation. Antibiotic exposure (predominantly amoxicillin) was associated with minimal microbiome differences, whereas all tested taxa were modified by breastfeeding. In the short-term substudy, we observed microbiome differences only in the first 2 weeks following antibiotics initiation, mainly a decrease in Bifidobacterium bifidum. The differences did not persist a month after antibiotic exposure. Four species were associated with infant age. Antibiotic exposure was not associated with an increase in antibiotic resistance gene abundance or with differences in microbiome-derived fecal bile acid composition.

CONCLUSIONS: Short-term and long-term gut microbiome perturbations by antibiotic exposure were detectable but substantially smaller than those associated with breastfeeding and infant age.}, } @article {pmid39856709, year = {2025}, author = {Li, D and Chen, W and Luo, W and Zhang, H and Liu, Y and Shu, D and Wei, G}, title = {Seed microbiomes promote Astragalus mongholicus seed germination through pathogen suppression and cellulose degradation.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {23}, pmid = {39856709}, issn = {2049-2618}, support = {42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; }, mesh = {*Seeds/microbiology ; *Germination ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Cellulose/metabolism ; Astragalus Plant/microbiology ; Soil Microbiology ; Metagenome ; }, abstract = {BACKGROUND: Seed-associated microorganisms play crucial roles in maintaining plant health by providing nutrients and resistance to biotic and abiotic stresses. However, their functions in seed germination and disease resistance remain poorly understood. In this study, we investigated the microbial community assembly features and functional profiles of the spermosphere and endosphere microbiomes related to germinated and ungerminated seeds of Astragalus mongholicus by using amplicon and shotgun metagenome sequencing techniques. Additionally, we aimed to elucidate the relationship between beneficial microorganisms and seed germination through both in vitro and in vivo pot experiments.

RESULTS: Our findings revealed that germination significantly enhances the diversity of microbial communities associated with seeds. This increase in diversity is driven through environmental ecological niche differentiation, leading to the enrichment of potentially beneficial probiotic bacteria such as Pseudomonas and Pantoea. Conversely, Fusarium was consistently enriched in ungerminated seeds. The co-occurrence network patterns revealed that the microbial communities within germinated and ungerminated seeds presented distinct structures. Notably, germinated seeds exhibit more complex and interconnected networks, particularly for bacterial communities and their interactions with fungi. Metagenome analysis showed that germinated seed spermosphere soil had more functions related to pathogen inhibition and cellulose degradation. Through a combination of culture-dependent and germination experiments, we identified Fusarium solani as the pathogen. Consistent with the metagenome analysis, germination experiments further demonstrated that bacteria associated with pathogen inhibition and cellulose degradation could promote seed germination and vigor. Specifically, Paenibacillus sp. significantly enhanced A. mongholicus seed germination and plant growth.

CONCLUSIONS: Our study revealed the dynamics of seed-associated microorganisms during seed germination and confirmed their ecological role in promoting A. mongholicus seed germination by suppressing pathogens and degrading cellulose. This study offers a mechanistic understanding of how seed microorganisms facilitate successful seed germination, highlighting the potential for leveraging these microbial communities to increase plant health. Video Abstract.}, } @article {pmid39856104, year = {2025}, author = {Özcan, E and Yu, KB and Dinh, L and Lum, GR and Lau, K and Hsu, J and Arino, M and Paramo, J and Lopez-Romero, A and Hsiao, EY}, title = {Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {987}, pmid = {39856104}, issn = {2041-1723}, support = {R01NS115537//U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS)/ ; }, mesh = {*Diet, Ketogenic ; Animals ; *Gastrointestinal Microbiome ; *Dietary Fiber/administration & dosage ; *Seizures/diet therapy/metabolism ; Mice ; Male ; Humans ; Mice, Inbred C57BL ; Disease Models, Animal ; Infant Formula ; Female ; }, abstract = {The gut microbiome modulates the anti-seizure effects of the ketogenic diet, but how specific dietary formulations differentially modify the gut microbiome in ways that impact seizure outcome is poorly understood. We find that medical ketogenic infant formulas vary in macronutrient ratio, fat source, and fiber content and differentially promote resistance to 6-Hz seizures in mice. Dietary fiber, rather than fat ratio or source, drives substantial metagenomic shifts in a model human infant microbial community. Addition of fiber to a fiber-deficient ketogenic formula restores seizure resistance, and supplementing protective formulas with excess fiber potentiates seizure resistance. By screening 13 fiber sources and types, we identify metagenomic responses in the model community that correspond with increased seizure resistance. Supplementing with seizure-protective fibers enriches microbial genes related to queuosine biosynthesis and preQ0 biosynthesis and decreases genes related to sucrose degradation and TCA cycle, which are also seen in seizure-protected mice that are fed fiber-containing ketogenic formulas. This study reveals that different formulations of ketogenic diets, and dietary fiber content in particular, differentially impact seizure outcome in mice, likely by modifying the gut microbiome. Understanding interactions between diet, microbiome, and host susceptibility to seizures could inform novel microbiome-guided approaches to treat refractory epilepsy.}, } @article {pmid39856097, year = {2025}, author = {Pidgeon, R and Mitchell, S and Shamash, M and Suleiman, L and Dridi, L and Maurice, CF and Castagner, B}, title = {Diet-derived urolithin A is produced by a dehydroxylase encoded by human gut Enterocloster species.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {999}, pmid = {39856097}, issn = {2041-1723}, support = {PJT-437944//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; }, mesh = {Humans ; *Coumarins/metabolism ; *Gastrointestinal Microbiome ; *Operon/genetics ; Feces/microbiology ; Diet ; Bacterial Proteins/metabolism/genetics ; Proteomics ; }, abstract = {Urolithin A (uroA) is a polyphenol derived from the multi-step metabolism of dietary ellagitannins by the human gut microbiota. Once absorbed, uroA can trigger mitophagy and aryl hydrocarbon receptor signaling pathways, altering host immune function, mitochondrial health, and intestinal barrier integrity. Most individuals harbor a microbiota capable of uroA production; however, the mechanisms underlying the dehydroxylation of its catechol-containing precursor (uroC) are unknown. Here, we use a combination of untargeted bacterial transcriptomics, proteomics, and comparative genomics to uncover an inducible uroC dehydroxylase (ucd) operon in Enterocloster species. We show that the ucd operon encodes a predicted molybdopterin-dependent enzyme complex that dehydroxylates urolithins at a specific position (9-OH). By interrogating publicly available metagenomics datasets, we observed that uroC-metabolizing Enterocloster species and ucd operon genes are prevalent in human feces. In ex vivo experiments with human fecal samples, only samples actively transcribing ucd could produce uroA, possibly explaining differences in urolithin metabolism between individuals. Collectively, this work identifies Enterocloster species and the ucd operon as important contributors to uroA production and establishes a multi-omics framework to further our mechanistic understanding of polyphenol metabolism by the human gut microbiota.}, } @article {pmid39856057, year = {2025}, author = {Hu, H and Huang, Y and Yang, F and Ma, L and Zhang, J and Deng, X and Ma, N and Wang, K and Tao, Y and Lin, Q and Li, Y and Bai, X and Pan, H}, title = {Metagenome-assembled microbial genomes (n = 3,448) of the oral microbiomes of Tibetan and Duroc pigs.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {141}, pmid = {39856057}, issn = {2052-4463}, mesh = {Animals ; *Metagenome ; Swine/microbiology ; *Mouth/microbiology ; *Microbiota ; Genome, Microbial ; Metagenomics ; Tibet ; }, abstract = {Compared with leaner breeds, local Chinese pig breeds have distinct intestinal microbial, as determined by metagenomic techniques, and the interactions between oral microorganisms and their hosts are also gradually being clarified. However, the high host genome content means that few metagenome-based oral microbiomes have been reported. Here, we combined dilution-based metagenomic sequencing and binning approaches to extract the microbial genomes from the oral microbiomes of Tibetan and Duroc pigs. The host contamination rates were reduced to 13.64%, a quarter of the normal metagenomic level (65.25% on average). Medium-high-quality metagenome-assembled genomes (MAGs; n = 3,448) spanning nine phyla were retrieved and 70.79% were novel species. Of the nonredundant MAGs, only 13.37% were shared, revealing the strong disparities between Tibetan and Duroc pigs. The oral microbial diversity of the Duroc pig was greater than that of the Tibetan pig. We present the first large-scale dilute-based metagenomic data on the pig oral microbiome, which should facilitate further investigation of the functions of oral microorganisms in pigs.}, } @article {pmid39536492, year = {2025}, author = {Chu, J and Ye, Y and Wu, YH}, title = {A glimpse of microbial potential in metal metabolism in the Clarion-Clipperton Fracture Zone in the eastern Pacific Ocean based on metagenomic analysis.}, journal = {Marine genomics}, volume = {79}, number = {}, pages = {101159}, doi = {10.1016/j.margen.2024.101159}, pmid = {39536492}, issn = {1876-7478}, mesh = {Pacific Ocean ; *Metagenome ; *Bacteria/genetics/metabolism/classification ; *Archaea/genetics/metabolism ; *Metagenomics ; Metals/metabolism ; Geologic Sediments/microbiology ; Microbiota ; }, abstract = {The polymetallic nodules distributed in the abyssal ocean floor are full of economic value, rich in manganese, iron, copper and rare-earth elements. Little is currently known about the diversity and the metabolic potential of microorganisms inhabiting the Clarion-Clipperton Fracture Zone (CCFZ) in eastern Pacific Ocean. In this study, the surface sediments (0-8 cm), which were divided into eight parts at 1 cm intervals were collected from the CCFZ. The microbial diversity and the metabolic potential of metal were examined by metagenomic sequencing and binning. The metal redox genes and metal transporter genes also showed a certain trend at different depths, the highest in the surface layer, about the same at 0-6 cm, and greater changes after >6 cm. 58 high- and medium metagenome-assembled genomes (MAGs) were recovered and assigned to 14 bacterial phyla and 1 archaeal phylum after dereplication. Alphaproteobacteria mainly carried out the oxidation of Fe/Mn and the reduction of Hg, Gammaproteobacteria mainly for the oxidation of Mn/Cu and the reduction of Cr/Hg and Methylomirabilota mainly for the oxidation of Mn and the reduction of As/Cr/Hg. Among the five Thermoproteota MAGs identified, only one had genes annotated for Mn oxidation, suggesting a limited but potentially significant role in this process at the bottom layer. By identifying the microbial diversity and the metabolic potential of metal in different depth, our study strengthens the understanding of metal metabolism in CCFZ and provides the foundation for further analyses of metal metabolism in such ecosystems.}, } @article {pmid39853798, year = {2025}, author = {Lutz, KC and Neugent, ML and Bedi, T and De Nisco, NJ and Li, Q}, title = {A Generalized Bayesian Stochastic Block Model for Microbiome Community Detection.}, journal = {Statistics in medicine}, volume = {44}, number = {3-4}, pages = {e10291}, doi = {10.1002/sim.10291}, pmid = {39853798}, issn = {1097-0258}, support = {2113674//National Science Foundation/ ; 2210912//National Science Foundation/ ; AT-2030-20200401//Welch Foundation/ ; 1F32DK128975-01A1/NH/NIH HHS/United States ; 1R01DK131267-01/NH/NIH HHS/United States ; 1R01GM141519/NH/NIH HHS/United States ; }, mesh = {*Bayes Theorem ; Humans ; *Microbiota/genetics ; *Markov Chains ; Computer Simulation ; Female ; Monte Carlo Method ; Stochastic Processes ; Models, Statistical ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; }, abstract = {Advances in next-generation sequencing technology have enabled the high-throughput profiling of metagenomes and accelerated microbiome studies. Recently, there has been a rise in quantitative studies that aim to decipher the microbiome co-occurrence network and its underlying community structure based on metagenomic sequence data. Uncovering the complex microbiome community structure is essential to understanding the role of the microbiome in disease progression and susceptibility. Taxonomic abundance data generated from metagenomic sequencing technologies are high-dimensional and compositional, suffering from uneven sampling depth, over-dispersion, and zero-inflation. These characteristics often challenge the reliability of the current methods for microbiome community detection. To study the microbiome co-occurrence network and perform community detection, we propose a generalized Bayesian stochastic block model that is tailored for microbiome data analysis where the data are transformed using the recently developed modified centered-log ratio transformation. Our model also allows us to leverage taxonomic tree information using a Markov random field prior. The model parameters are jointly inferred by using Markov chain Monte Carlo sampling techniques. Our simulation study showed that the proposed approach performs better than competing methods even when taxonomic tree information is non-informative. We applied our approach to a real urinary microbiome dataset from postmenopausal women. To the best of our knowledge, this is the first time the urinary microbiome co-occurrence network structure in postmenopausal women has been studied. In summary, this statistical methodology provides a new tool for facilitating advanced microbiome studies.}, } @article {pmid39853685, year = {2025}, author = {Sun, Y and Gan, Z and Liu, S and Zhang, S and Zhong, W and Liu, J and Huang, X and He, W and Zhong, H and Cao, Q}, title = {Metagenomic and Transcriptomic Analysis Reveals Crosstalk Between Intratumor Mycobiome and Hosts in Early-Stage Nonsmoking Lung Adenocarcinoma Patients.}, journal = {Thoracic cancer}, volume = {16}, number = {2}, pages = {e15527}, doi = {10.1111/1759-7714.15527}, pmid = {39853685}, issn = {1759-7714}, support = {220904094208//Fifth Affiliated Hospital of Sun Yat-sen University Qingdong Cao's talent-attracting fund/ ; 3320104100430//Exploration and Practice of a Tri-Party Personalized Oncology Strategy Based on Precision Medicine in Patient-Doctor-Research Collaboration/ ; }, mesh = {Humans ; *Lung Neoplasms/microbiology/genetics/pathology ; *Adenocarcinoma of Lung/microbiology/genetics/pathology ; *Mycobiome ; Female ; *Metagenomics/methods ; Male ; Middle Aged ; Gene Expression Profiling ; Aged ; Transcriptome ; Prognosis ; Tumor Microenvironment ; Case-Control Studies ; }, abstract = {BACKGROUND: The mycobiome in the tumor microenvironment of non-smokers with early-stage lung adenocarcinoma (ES-LUAD) has been minimally investigated.

METHODS: In this study, we conducted ultra-deep metagenomic and transcriptomic sequencing on 128 samples collected from 46 nonsmoking ES-LUAD patients and 41 healthy controls (HC), aiming to characterize the tumor-resident mycobiome and its interactions with the host.

RESULTS: The results revealed that ES-LUAD patients exhibited fungal dysbiosis characterized by reduced species diversity and significant imbalances in specific fungal abundances. Concurrently, microbial functional analysis revealed significant alterations associated with genes such as ribosomal proteins and histones. We observed correlations between Yarrowia lipolytica, Saccharomyces paradoxus, and tumor-infiltrating immune cells (TIICs), and identified a strong association (|rho| > 0.7) between S. paradoxus and 14 transcription factors. A signature of three prognostic genes (GRIA1, CDO1, FHL1) closely associated with S. paradoxus was identified and they suggest that the interaction between the mycobiome and the host may contribute to prolonged overall survival (OS). Finally, a predictive model based on six fungi demonstrated decent classification performance in distinguishing ES-LUAD cases from HCs (AUC = 0.724).

CONCLUSIONS: Our study demonstrates that the interactions between the mycobiome and transcriptome within tumors may help elucidate the pathogenic mechanisms of ES-LUAD. Fungi, as a potential predictive tool, can be used as an additional resource for accurately detecting and discriminating individuals with ES-LUAD.}, } @article {pmid39850835, year = {2025}, author = {Zhang, Q and Zhen, M and Wang, X and Zhao, F and Dong, Y and Wang, X and Gao, S and Wang, J and Shi, W and Zhang, Y}, title = {Antibiotic exposure enriches streptococci carrying resistance genes in periodontitis plaque biofilms.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18835}, pmid = {39850835}, issn = {2167-8359}, mesh = {Humans ; *Biofilms/drug effects/growth & development ; *Periodontitis/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Streptococcus/drug effects/genetics ; Female ; Male ; Adult ; *Dental Plaque/microbiology ; *Amoxicillin/pharmacology/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Drug Resistance, Bacterial/genetics ; Microbiota/drug effects/genetics ; Tetracycline/pharmacology/therapeutic use ; Metronidazole/pharmacology/therapeutic use ; Clindamycin/pharmacology/therapeutic use ; }, abstract = {BACKGROUND: Periodontitis is not always satisfactorily treated with conventional scaling and root planing, and adjunctive use of antibiotics is required in clinical practice. Therefore, it is important for clinicians to understand the diversity and the antibiotic resistance of subgingival microbiota when exposed to different antibiotics.

MATERIALS AND METHODS: In this study, subgingival plaques were collected from 10 periodontitis patients and 11 periodontally healthy volunteers, and their microbiota response to selective pressure of four antibiotics (amoxicillin, metronidazole, clindamycin, and tetracycline) were evaluated through 16S rRNA gene amplicon and metagenomic sequencing analysis. Additionally, sensitive and resistant strains were isolated and cultured in vitro for resistance evaluation.

RESULTS: Cultivation of subgingival microbiota revealed the oral microbiota from periodontitis patients were more resistant to antibiotics than that of healthy. Significant differences were also observed for the microbial community between with and without antibiotics (especially amoxicillin and tetracycline) treated in periodontitis group.

CONCLUSION: Overall, after the two antibiotics (amoxicillin and tetracycline) exposed, the oral subgingival microbiota in periodontitis patients exhibited different diversity and composition. Streptococcus may account for oral biofilm-specific antibiotic resistance in periodontitis. This provides information for personalized treatment of periodontitis.}, } @article {pmid39849759, year = {2025}, author = {Peng, Q and Huang, J and Li, S and Chen, Z and Zhu, Q and Yuan, H and Li, J and Massou, BB and Xie, G}, title = {Dynamics of microbial communities and metabolites during the fermentation of Ningxia goji berry wine: An integrated metagenomics and metabolomics approach.}, journal = {Food research international (Ottawa, Ont.)}, volume = {201}, number = {}, pages = {115609}, doi = {10.1016/j.foodres.2024.115609}, pmid = {39849759}, issn = {1873-7145}, mesh = {*Fermentation ; *Wine/analysis/microbiology ; *Metabolomics ; *Metagenomics ; *Microbiota ; Volatile Organic Compounds/analysis/metabolism ; Bacteria/metabolism/genetics/classification ; Fruit ; Taste ; Food Microbiology ; }, abstract = {Ningxia Goji Berry Wine (NGBW), a traditional Chinese fermented beverage, exhibits complex flavor quality changes during fermentation, the mechanisms of which remain insufficiently elucidated. This study aimed to elucidate the dynamic shifts in physicochemical properties, metabolites, and microbial communities throughout the controlled fermentation process of NGBW. Metabolomic analysis identified 8 key differential volatile metabolites (VOCs) and 406 differential non-volatile metabolites. The enrichment analysis of KEGG metabolic pathways revealed that, during the fermentation of NGBW, ten critical metabolic pathways-Purine metabolism, Glycine, Serine, and Threonine metabolism, Galactose metabolism, and the Citric Acid (TCA) Cycle-play essential roles. Amplicon sequencing indicated that 25 bacterial genera dominated the microbial ecosystem (relative abundance ≥ 0.1 %). Spearman correlation analysis revealed significant associations between 5 core microorganism and flavor compounds, and 25 core microbes with non-volatile metabolites, suggesting their pivotal roles in flavor formation. This study provides a theoretical basis for optimizing the fermentation process and enhancing the flavor quality of NGBW.}, } @article {pmid39849445, year = {2025}, author = {Xie, H and Chen, Z and Wu, G and Wei, P and Gong, T and Chen, S and Xu, Z}, title = {Application of metagenomic next-generation sequencing (mNGS) to describe the microbial characteristics of diabetic foot ulcers at a tertiary medical center in South China.}, journal = {BMC endocrine disorders}, volume = {25}, number = {1}, pages = {18}, pmid = {39849445}, issn = {1472-6823}, support = {[2021]76//the High-level Hospital and Clinical Specialty Discipline Construction Programme for Fujian Medical Development, China/ ; 2023J01692//Fujian Provincial Natural Science Foundation of China/ ; 2022J01243//Fujian Provincial Natural Science Foundation of China/ ; 2020Y9094//the Joint Funds for the innovation of science and Technology，Fujian province, China/ ; 2023Y9213//the Joint Funds for the innovation of science and Technology，Fujian province, China/ ; 2021Y9068//the Joint Funds for the innovation of science and Technology，Fujian province, China/ ; 82002034//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Diabetic Foot/microbiology/diagnosis ; China/epidemiology ; *High-Throughput Nucleotide Sequencing/methods ; *Tertiary Care Centers ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; Aged ; Microbiota/genetics ; Adult ; }, abstract = {BACKGROUND: Diabetic foot ulcers (DFUs) are characterized by dynamic wound microbiome, the timely and accurate identification of pathogens in the clinic is required to initiate precise and individualized treatment. Metagenomic next-generation sequencing (mNGS) has been a useful supplement to routine culture method for the etiological diagnosis of DFUs. In this study, we utilized a routine culture method and mNGS to analyze the same DFU wound samples and the results were compared.

METHODS: Forty samples from patients with DFUs at a tertiary medical center in South China were collected, the microorganisms were identified with mNGS and routine culture method simultaneously.

RESULTS: The results showed that the positive detection rate of microorganisms in DFUs with mNGS was much higher (95% vs. 60%). Thirteen strains of microorganisms were detected with routine culture method, and seventy-seven strains were detected with mNGS. Staphylococcus aureus was the most common microorganism detected with culture method, while Enterococcus faecalis was the most common microorganism detected with mNGS. The false negative rate of the culture method was 35%, that was, 14 samples with negative results with culture method were found to be positive with mNGS.

CONCLUSION: The mNGS method had a higher positive detection rate and identified a broader spectrum of microorganisms in DFUs, thus, mNGS provided a more comprehensive understanding of the microbiome of DFUs to facilitate the development of timely and optimal treatment.

TRIAL REGISTRATION: The study was conducted in accordance with the Declaration of Helsinki and approved by the Ethical Review Committee of the Fujian Medical University Union Hospital (approval number 2021KY054).}, } @article {pmid39693966, year = {2025}, author = {Li, T and Wang, P and Zhi, Z and Guo, T and Zhou, J and Zhang, H and Cao, C and Cai, Y and Li, Y and Zhang, J}, title = {Free-caged rearing modes regulate chicken intestinal metabolism by influencing gut microbial homeostasis.}, journal = {Poultry science}, volume = {104}, number = {1}, pages = {104381}, pmid = {39693966}, issn = {1525-3171}, mesh = {Animals ; *Chickens ; *Gastrointestinal Microbiome/physiology ; *Homeostasis ; *Animal Husbandry/methods ; Cecum/microbiology/metabolism ; Housing, Animal ; Bacteria/classification/metabolism/genetics ; Male ; }, abstract = {Free-caged rearing modes, which prioritize animal welfare, are believed to enhance the quality of animal products. The impact of rearing modes on meat quality may play a key role in the superior quality of local chicken breeds. This study analyzed the cecal contents of free-range and caged black-bone chickens at different ages using metagenomic and metabolomic sequencing. We identified 32 metabolites and 367 microbial species significantly affected by the rearing mode. Linear discriminant analysis Effect Size (LefSe) highlighted five key microorganisms, Gemmiger formicilis, Bacteria unclassified, Bacteroides sp. ET225, Massilistercora timonensis, and Bacteroidales unclassified, that showed distinct abundance patterns across all age points. Among them, Bacteroides sp. ET225 and Massilistercora timonensis were positively associated with certain phospholipids and plant-derived metabolites, while negatively correlated with others like demissidine and acylcarnitine. Functional analysis revealed that rearing modes impact gut metabolites involved in gut metabolism as well as broader processes such as signal transduction, protein digestion, and autophagy. This study offers new insights into how rearing modes influence gut microbiota and metabolites, shedding light on the study of rearing mode-mediated muscle development and fat deposition.}, } @article {pmid39849165, year = {2025}, author = {Sandhu, S and Kumar, S and Singh, P and Singh, BP and Jurel, SK and Lal, N and Mohit, and Sharma, V and Rai, N and Chand, P}, title = {Metagenomic profiling of plaque microbiota in Indian subjects: identified hidden ecological tapestry.}, journal = {Current genetics}, volume = {71}, number = {1}, pages = {3}, pmid = {39849165}, issn = {1432-0983}, mesh = {Humans ; *Dental Plaque/microbiology ; *Metagenomics/methods ; Male ; *Microbiota/genetics ; Female ; India/epidemiology ; Adult ; *Metagenome ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; Young Adult ; Adolescent ; Bacteria/genetics/classification/isolation & purification ; Streptococcus/genetics/isolation & purification/classification ; }, abstract = {Dental plaque biofilms are the primary etiologic factor for various chronic oral infectious diseases. In recent years, dental plaque shows enormous potential to know about an individual microbiota. Various microbiome studies of oral cavity from different geographical locations reveals abundance of microbial species. Although, the representation of Indian population in this respect is limited, which make us curious to undergo this study. This study investigates the dental plaque microbiota of North Indian individuals based on their age, gender, and dietary patterns; specifically, food preference and availability of water source using 16 S rRNA metagenomics analysis. The findings from this study revealed that Streptococcus levels are high across genders, age groups, and water source, highlighting its role as a predominant dental caries associated species like Streptococcus mutans, Streptococcus pyogenes, Streptococcus sobrinus and Streptococcus oralis in the studied population groups. Additionally, the abundance of Actinomyces is observed higher in young individuals and females whereas Fusobacterium and Leptotrichia were high in elderly individuals. Moreover, non-vegetarians have higher abundance of Streptococcus and Fusobacterium, whereas vegetarians show higher abundance of Prevotella and Leptotrichia. The study also highlights the influence of water type on bacterial composition of dental plaque in the studied population i.e., individuals consuming underground water has high abundance of Streptococcus, whereas individuals consuming RO water exhibit elevated Prevotella and Leptotrichia. Insights emerged from the analysis illuminates the complex dynamics of microbiota in dental plaque among North Indians. This study also highlight that this variation of microbiome is influenced by age, gender, and dietary habits (vegetarian or non-vegetarian lifestyle). These results will fill a significant knowledge gap regarding the Indian dental plaque microbiome but also offer a foundation to conduct metagenome studies and potential therapeutic implications for future personalized oral health interventions.}, } @article {pmid39844180, year = {2025}, author = {Chen, J and Pan, Q and Lu, L and Huang, X and Wang, S and Liu, X and Lun, J and Xu, X and Su, H and Guo, F and Yang, L and You, L and Xiao, H and Luo, W and Liu, HF and Pan, Q}, title = {Atg5 deficiency in basophils improves metabolism in lupus mice by regulating gut microbiota dysbiosis.}, journal = {Cell communication and signaling : CCS}, volume = {23}, number = {1}, pages = {40}, pmid = {39844180}, issn = {1478-811X}, support = {No. 82070757, 82270770//National Natural Science Foundation of China/ ; No. 82070757, 82270770//National Natural Science Foundation of China/ ; 2022B1212030003//Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Noncommunicable Diseases/ ; 2022B1212030003//Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Noncommunicable Diseases/ ; 2022B1212030003//Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Noncommunicable Diseases/ ; 2021A05067//Science and Technology Planning Project of Zhanjiang City/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Lupus Erythematosus, Systemic/metabolism ; *Basophils/metabolism ; *Dysbiosis ; Mice ; *Autophagy-Related Protein 5/genetics/metabolism ; Mice, Inbred MRL lpr ; Mice, Knockout ; Female ; Autophagy ; Mice, Inbred C57BL ; }, abstract = {Autophagic activation in immune cells, gut microbiota dysbiosis, and metabolic abnormalities have been reported separately as characteristics of systemic lupus erythematosus (SLE). Elucidating the crosstalk among the immune system, commensal microbiota, and metabolites is crucial to understanding the pathogenesis of autoimmune diseases. Emerging evidence shows that basophil activation plays a critical role in the pathogenesis of SLE; however, the underlying mechanisms remain largely unknown. Here, we investigated the effects of autophagic inhibition on the pathogenesis of basophils in SLE using Autophagy-related gene 5 (Atg5) knockout (Atg5[-/-]) as an autophagic inhibitor. Specifically, we knocked out basophilic Atg5 in vivo to investigate its impact on lupus metabolism. Furthermore, Atg5[-/-] basophils were transferred to basophil-depleted MRL/MpJ-Fas[lpr] (MRL/lpr) mice to study their effect on disease metabolism. Metagenomic and targeted metabolomic sequencing results indicated considerable reduction in the levels of plasma autoantibodies and inflammatory cytokines in the Atg5[-/-] basophil transfer group compared with that in the control group. Transplanting Atg5[-/-] basophils improved the gut microbiota balance in MRL/lpr mice, increasing the abundance of beneficial bacteria, such as Ligilactobacillus murinus and Faecalitalea rodentium, and reducing that of potentially pathogenic bacteria such as Phocaeicola salanitronis. The transplantation of Atg5-deficient basophils improved lupus symptoms by modulating lipid and amino acid metabolism. This improvement was linked to changes in the gut microbiota, particularly an increase in Ligilactobacillus murinus and Faecalitalea rodentium populations. These microbial shifts are believed to promote the production of beneficial metabolites, such as γ-linolenic acid and oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine, while reducing the levels of harmful metabolites such as arginine. These alterations in the metabolic profile contribute to the alleviation of lupus symptoms. Collectively, these findings reveal a novel role of basophil autophagy in SLE, highlighting its potential as a therapeutic target.}, } @article {pmid39843539, year = {2025}, author = {Laczkó, L and Nagy, NA and Nagy, Á and Maroda, Á and Sály, P}, title = {An updated reference genome of Barbatula barbatula (Linnaeus, 1758).}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {137}, pmid = {39843539}, issn = {2052-4463}, support = {OTKA PD142602//Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal (NKFI Office)/ ; }, mesh = {Animals ; *Genome ; *Microsatellite Repeats ; Cypriniformes/genetics ; }, abstract = {The stone loach Barbatula barbatula is a benthic fish species widely distributed throughout Europe, primarily inhabiting stony upper sections of stream networks. This study presents an updated genome assembly of B. barbatula, contributing to the species' available genomic resources for downstream applications such as conservation genetics. The draft assembly was 550 Mbp in size, with an N50 of 11.21 Mbp. We used the species' available chromosome scaffolds to finish the genome. The final assembly had a BUSCO score of 96.7%. We identified 23270 protein-coding genes, and the proteome exhibited high completeness with BUSCO (93.1%) and OMArk (90.81%). Despite using multiple approaches to reduce duplicate contigs, we observed a relatively high duplicate ratio of 6.1% (BUSCO) and 8.52% (OMArk) in the annotations. We aimed to find microsatellite loci present in both the species' publicly available genome and the new assembly to aid marker development for downstream analyses. This dataset serves as a reference for genomic analysis and is useful for developing markers to study the species' biodiversity and support conservation efforts.}, } @article {pmid39843522, year = {2025}, author = {Bray, AS and Broberg, CA and Hudson, AW and Wu, W and Nagpal, RK and Islam, M and Valencia-Bacca, JD and Shahid, F and Hernandez, GE and Nutter, NA and Walker, KA and Bennett, EF and Young, TM and Barnes, AJ and Ornelles, DA and Miller, VL and Zafar, MA}, title = {Klebsiella pneumoniae employs a type VI secretion system to overcome microbiota-mediated colonization resistance.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {940}, pmid = {39843522}, issn = {2041-1723}, support = {AI178595//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI166642//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI173244//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {*Klebsiella pneumoniae/genetics/metabolism ; *Type VI Secretion Systems/genetics/metabolism ; Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Klebsiella Infections/microbiology ; Gene Expression Regulation, Bacterial ; Gastrointestinal Tract/microbiology ; Bacterial Proteins/metabolism/genetics ; DNA Transposable Elements/genetics ; Female ; Mice, Inbred C57BL ; }, abstract = {Microbial species must compete for space and nutrients to persist in the gastrointestinal (GI) tract, and our understanding of the complex pathobiont-microbiota interactions is far from complete. Klebsiella pneumoniae, a problematic, often drug-resistant nosocomial pathogen, can colonize the GI tract asymptomatically, serving as an infection reservoir. To provide insight on how K. pneumoniae interacts with the resident gut microbiome, we conduct a transposon mutagenesis screen using a murine model of GI colonization with an intact microbiota. Among the genes identified were those encoding a type VI secretion system (T6SS), which mediates contact-dependent killing of gram-negative bacteria. From several approaches, we demonstrate that the T6SS is critical for K. pneumoniae gut colonization. Metagenomics and in vitro killing assays reveal that K. pneumoniae reduces Betaproteobacteria species in a T6SS-dependent manner, thus identifying specific species targeted by K. pneumoniae. We further show that T6SS gene expression is controlled by several transcriptional regulators and that expression only occurs in vitro under conditions that mimic the gut environment. By enabling K. pneumoniae to thrive in the gut, the T6SS indirectly contributes to the pathogenic potential of this organism. These observations advance our molecular understanding of how K. pneumoniae successfully colonizes the GI tract.}, } @article {pmid39843444, year = {2025}, author = {Bechtold, EK and Ellenbogen, JB and Villa, JA and de Melo Ferreira, DK and Oliverio, AM and Kostka, JE and Rich, VI and Varner, RK and Bansal, S and Ward, EJ and Bohrer, G and Borton, MA and Wrighton, KC and Wilkins, MJ}, title = {Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {944}, pmid = {39843444}, issn = {2041-1723}, support = {EAR-2029686//National Science Foundation (NSF)/ ; PRFB-2109592//National Science Foundation (NSF)/ ; DEB-1754756//National Science Foundation (NSF)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; DE-SC000054//U.S. Department of Energy (DOE)/ ; DE-SC0007144//U.S. Department of Energy (DOE)/ ; DE-SC0012088//U.S. Department of Energy (DOE)/ ; DESC0023297//U.S. Department of Energy (DOE)/ ; DE-SC0023456//U.S. Department of Energy (DOE)/ ; DE-SC0023456//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC000054//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC000054//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; DE-SC0022191//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0021350//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0021350//U.S. Department of Energy (DOE)/ ; DESC000054//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; }, mesh = {*Methane/metabolism ; *Wetlands ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Fresh Water/microbiology ; Metagenome ; Bacteria/metabolism/genetics/classification ; Climate Change ; }, abstract = {Current estimates of wetland contributions to the global methane budget carry high uncertainty, particularly in accurately predicting emissions from high methane-emitting wetlands. Microorganisms drive methane cycling, but little is known about their conservation across wetlands. To address this, we integrate 16S rRNA amplicon datasets, metagenomes, metatranscriptomes, and annual methane flux data across 9 wetlands, creating the Multi-Omics for Understanding Climate Change (MUCC) v2.0.0 database. This resource is used to link microbiome composition to function and methane emissions, focusing on methane-cycling microbes and the networks driving carbon decomposition. We identify eight methane-cycling genera shared across wetlands and show wetland-specific metabolic interactions in marshes, revealing low connections between methanogens and methanotrophs in high-emitting wetlands. Methanoregula emerged as a hub methanogen across networks and is a strong predictor of methane flux. In these wetlands it also displays the functional potential for methylotrophic methanogenesis, highlighting the importance of this pathway in these ecosystems. Collectively, our findings illuminate trends between microbial decomposition networks and methane flux while providing an extensive publicly available database to advance future wetland research.}, } @article {pmid39809266, year = {2025}, author = {Wang, D and Jiang, Y and Jiang, J and Pan, Y and Yang, Y and Fang, X and Liang, L and Li, H and Dong, Z and Fan, S and Ma, D and Zhang, XS and Li, H and He, Y and Li, N}, title = {Gut microbial GABA imbalance emerges as a metabolic signature in mild autism spectrum disorder linked to overrepresented Escherichia.}, journal = {Cell reports. Medicine}, volume = {6}, number = {1}, pages = {101919}, doi = {10.1016/j.xcrm.2024.101919}, pmid = {39809266}, issn = {2666-3791}, mesh = {*Gastrointestinal Microbiome/genetics ; *Autism Spectrum Disorder/metabolism/microbiology/genetics ; *gamma-Aminobutyric Acid/metabolism ; Humans ; Animals ; Female ; Male ; Mice ; Child ; Child, Preschool ; Metabolomics/methods ; RNA, Ribosomal, 16S/genetics ; Escherichia/metabolism/genetics ; Feces/microbiology ; Glutamic Acid/metabolism ; Mice, Inbred C57BL ; Escherichia coli/genetics/metabolism ; Metabolome ; }, abstract = {Gut microbiota (GM) alterations have been implicated in autism spectrum disorder (ASD), yet the specific functional architecture remains elusive. Here, employing multi-omics approaches, we investigate stool samples from two distinct cohorts comprising 203 children with mild ASD or typical development. In our screening cohort, regression-based analysis for metabolomic profiling identifies an elevated γ-aminobutyric acid (GABA) to glutamate (Glu) ratio as a metabolic signature of ASD, independent of age and gender. In the validating cohort, we affirm the GABA/Glu ratio as an ASD diagnostic indicator after adjusting for geography, age, gender, and specific food-consuming frequency. Integrated analysis of metabolomics, 16S rRNA sequencing, and metagenomics reveals a correlation between overrepresented Escherichia and disrupted GABA metabolism. Furthermore, we observe social behavioral impairments in weaning mice transplanted with E. coli, suggesting a potential link to ASD symptomatology. Collectively, these findings provide insights into potential diagnostic and therapeutic strategies aimed at evaluating and restoring gut microbial neurotransmitter homeostasis.}, } @article {pmid39739308, year = {2024}, author = {Chaabane, F and Pillonel, T and Bertelli, C}, title = {MeSS and assembly_finder: a toolkit for in silico metagenomic sample generation.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {1}, pages = {}, doi = {10.1093/bioinformatics/btae760}, pmid = {39739308}, issn = {1367-4811}, mesh = {*Metagenomics/methods ; *Software ; Microbiota/genetics ; Computational Biology/methods ; Humans ; Computer Simulation ; Metagenome ; Sequence Analysis, DNA/methods ; }, abstract = {SUMMARY: The intrinsic complexity of the microbiota combined with technical variability render shotgun metagenomics challenging to analyze for routine clinical or research applications. In silico data generation offers a controlled environment allowing for example to benchmark bioinformatics tools, to optimize study design, statistical power, or to validate targeted applications. Here, we propose assembly_finder and the Metagenomic Sequence Simulator (MeSS), two easy-to-use Bioconda packages, as part of a benchmarking toolkit to download genomes and simulate shotgun metagenomics samples, respectively. Outperforming existing tools in speed while requiring less memory, MeSS reproducibly generates accurate complex communities based on a list of taxonomic ranks and their abundance.

All code is released under MIT License and is available on https://github.com/metagenlab/MeSS and https://github.com/metagenlab/assembly_finder.}, } @article {pmid39523638, year = {2024}, author = {Munjita, SM and Mubemba, B and Tembo, J and Bates, M and Munsaka, S}, title = {Rhipicephalus simus ticks: new hosts for phleboviruses.}, journal = {Parasitology}, volume = {151}, number = {9}, pages = {962-970}, doi = {10.1017/S0031182024001033}, pmid = {39523638}, issn = {1469-8161}, support = {RIA2016E-1609//European and Developing Countries Clinical Trials Partnership/ ; }, mesh = {*Rhipicephalus/microbiology/virology ; *Phlebovirus/classification/genetics ; Metagenome/genetics ; Genome, Viral/genetics ; Zambia ; Phylogeny ; Biodiversity ; Animals ; Disease Vectors ; }, abstract = {Ticks are widespread arthropods that transmit microorganisms of veterinary and medical significance to vertebrates, including humans. Rhipicephalus simus, an ixodid tick frequently infesting and feeding on humans, may play a crucial role in transmitting infectious agents across species. Despite the known association of many Rhipicephalus ticks with phleboviruses, information on R. simus is lacking. During a study in a riverine area in Lusaka Zambia, ten R. simus ticks were incidentally collected from the grass and bushes and subjected to metagenomic next generation sequencing (mNGS) in 2 pools of 5. Analysis detected a diverse microbial profile, including bacteria 82% (32/39), fungi 15.4% (6/39), and viruses 2.6% (1/39). Notably, viral sequence LSK-ZM-102022 exhibited similarity to tick phleboviruses, sharing 74.92% nucleotide identity in the RdRp gene and 72% in the NP gene with tick-borne phlebovirus (TBPV) from Greece and Romania, respectively. Its RNA-dependent RNA polymerase (RdRp) encoding region carried conserved RdRp and endonuclease domains characteristic of phenuiviridae viruses. Phylogenetic analysis positioned LSK-ZM-102022 in a distinct but lone lineage within tick phleboviruses basal to known species like brown dog tick phlebovirus and phlebovirus Antigone. Pair-wise genetic distance analysis revealed similar findings. This study emphasizes the urgency of further research on the ecology, transmission dynamics, and pathogenic potential of LSK-ZM-102022 and related TBPVs, crucial for local and global preparedness against emerging tick-borne diseases.}, } @article {pmid38709227, year = {2025}, author = {Unzueta-Medina, JA and González-Chávez, SA and Salas-Leiva, JS and Silva-Sánchez, SE and Pacheco-Tena, C}, title = {Differential Composition and Structure of the Microbiota from Active and Inactive Stages of HLA-B27-associated Uveitis by Paired Fecal Metagenomes.}, journal = {Ocular immunology and inflammation}, volume = {33}, number = {1}, pages = {56-64}, doi = {10.1080/09273948.2024.2346818}, pmid = {38709227}, issn = {1744-5078}, mesh = {Humans ; *HLA-B27 Antigen/genetics/immunology ; Male ; *Feces/microbiology ; Prospective Studies ; Adult ; Female ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; *Uveitis, Anterior/microbiology/immunology ; Metagenome ; Bacteria/genetics/isolation & purification ; DNA, Bacterial/genetics ; Microbiota ; Acute Disease ; }, abstract = {PURPOSE: To compare the diversities and abundances of bacterial taxa in the microbiome of patients with HLA B27-positive acute anterior uveitis (AAU) in the active and inactive phases.

METHODS: An observational descriptive prospective and comparative study was conducted in ten HLA-B27-positive AAU patients (44.6 ± 13.4 years). The microbiome of the stool samples obtained in the active and inactive stages was analyzed by sequencing the V3 region of the 16S rRNA gene.

RESULTS: The differences in the bacteria profile between active and inactive stages in each individual were confirmed (p < 0.0001). Ten OTUs were found exclusively in the active phase of 90% of the individuals, suggesting a proinflammatory association. Blautia OUT_4 and Faecalibacterium OUT_2 abundances showed a direct relationship between abundance and severity of ocular inflammation. Two OTUs were exclusive of the inactive stage, suggesting an anti-inflammatory role.

CONCLUSION: The metagenomic profile of the fecal microbiota differs in the acute phase of the AAU compared to when the inflammation subsides, despite being the same individual and a short time-lapse. AAU is a fertile field for studying the connection between subtle rapid changes in microbiota and their systemic consequences.}, } @article {pmid39841201, year = {2025}, author = {Geng, P and Zhao, N and Zhou, Y and Harris, RS and Ge, Y}, title = {Faecalibacterium prausnitzii regulates carbohydrate metabolic functions of the gut microbiome in C57BL/6 mice.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2455503}, doi = {10.1080/19490976.2025.2455503}, pmid = {39841201}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Mice, Inbred C57BL ; Mice ; *Carbohydrate Metabolism ; *Faecalibacterium prausnitzii/metabolism/genetics ; *Phylogeny ; *Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Probiotics/administration & dosage ; Male ; Metagenome ; }, abstract = {The probiotic impact of microbes on host metabolism and health depends on both host genetics and bacterial genomic variation. Faecalibacterium prausnitzii is the predominant human gut commensal emerging as a next-generation probiotic. Although this bacterium exhibits substantial intraspecies diversity, it is unclear whether genetically distinct F. prausnitzii strains might lead to functional differences in the gut microbiome. Here, we isolated and characterized a novel F. prausnitzii strain (UT1) that belongs to the most prevalent but underappreciated phylogenetic clade in the global human population. Genome analysis showed that this butyrate-producing isolate carries multiple putative mobile genetic elements, a clade-specific defense system, and a range of carbohydrate catabolic enzymes. Multiomic approaches were used to profile the impact of UT1 on the gut microbiome and associated metabolic activity of C57BL/6 mice at homeostasis. Both 16S rRNA and metagenomic sequencing demonstrated that oral administration of UT1 resulted in profound microbial compositional changes including a significant enrichment of Lactobacillus, Bifidobacterium, and Turicibacter. Functional profiling of the fecal metagenomes revealed a markedly higher abundance of carbohydrate-active enzymes (CAZymes) in UT1-gavaged mice. Accordingly, UT1-conditioned microbiota possessed the elevated capability of utilizing starch in vitro and exhibited a lower availability of microbiota-accessible carbohydrates in the gut. Further analysis uncovered a functional network wherein UT1 reduced the abundance of mucin-degrading CAZymes and microbes, which correlated with a concomitant reduction of fecal mucin glycans. Collectively, our results reveal a crucial role of UT1 in facilitating the carbohydrate metabolism of the gut microbiome and expand our understanding of the genetic and phenotypic diversity of F. prausnitzii.}, } @article {pmid39838431, year = {2025}, author = {Sun, Q and Li, BR and Li, DH and Wang, XY and Wang, QY and Jiang, ZM and Ning, SB and Sun, T}, title = {WKB ameliorates DSS-induced colitis through inhibiting enteric glial cells activation and altering the intestinal microbiota.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {93}, pmid = {39838431}, issn = {1479-5876}, support = {No. 22YXQN034//Air Force Medical Center Youth Talent Program Project/ ; No. 2020-4-5123//Capital's Funds for Health Improvement and Research/ ; }, mesh = {Animals ; *Dextran Sulfate ; *Gastrointestinal Microbiome ; *Colitis/pathology/microbiology/chemically induced/complications ; *Mice, Inbred C57BL ; Male ; *Neuroglia/metabolism/pathology ; Cytokines/metabolism ; Colon/pathology/microbiology ; Permeability ; Body Weight ; Inflammation/pathology ; Intestinal Mucosa/pathology/microbiology/metabolism ; Mice ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic condition influenced by diet, which affects gut microbiota and immune functions. The rising prevalence of IBD, linked to Western diets in developing countries, highlights the need for dietary interventions. This study aimed to assess the impact of white kidney beans (WKB) on gut inflammation and microbiota changes, focusing on their effects on enteric glial cells (EGCs) and immune activity in colitis.

METHODS: Male C57BL/6 mice were divided into four groups: normal diet (ND), ND with 2.5% dextran sulfate sodium (DSS) for colitis induction, ND with 20% WKB, and WKB with 2.5% DSS. The dietary intervention lasted 17 weeks, with DSS given in the final week. Colonic inflammation was assessed by body weight, disease activity index, and histopathology. Epithelial barrier integrity was evaluated using immunofluorescence, transmission electron microscopy, and permeability assays. EGCs activity was analyzed via immunofluorescence and quantitative real-time PCR. Immune responses were measured using flow cytometry and cytokine profiling, while gut microbiota changes were examined through metagenomic sequencing.

RESULTS: WKB supplementation significantly alleviated DSS-induced colitis in mice, evidenced by reduced weight loss, disease activity, and improved colonic histology. This effect was linked to enhanced mucosal barrier integrity, seen through increased tight junction protein and Muc2 expression, accompanied by favorable ultrastructural changes. WKB modulated EGCs activity via TNF-like cytokine 1 A inhibition, resulting in reduced glial fibrillary acidic protein expression. Immunologically, it downregulated Th1 and Th17 pro-inflammatory cells, increased Treg cells, and altered cytokine profiles (reduced TNF-α, IFN-γ, IL-17; increased IL-10). Metagenomic analysis showed that WKB restored gut microbiota balance, particularly enhancing beneficial bacteria like Akkermansia. KEGG pathway analysis further indicated that WKB supplementation improved key metabolic pathways, notably those related to phenylalanine, tyrosine, and tryptophan biosynthesis, thereby countering DSS-induced metabolic disruptions.

CONCLUSIONS: WKB shows promise for treating IBD by enhancing mucosal barriers, inhibiting EGCs activity, balancing Th1/Th17/Treg cells, and restoring gut microbiota and metabolic homeostasis, thereby alleviating colitis symptoms.}, } @article {pmid39838419, year = {2025}, author = {Liu, X and Ding, H and Zhang, X and Ta, N and Zhao, J and Zhang, Q and Liu, H and Sun, M and Zhang, X}, title = {Dynamic changes in the gastrointestinal microbial communities of Gangba sheep and analysis of their functions in plant biomass degradation at high altitude.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {17}, pmid = {39838419}, issn = {2049-2618}, mesh = {Animals ; Sheep/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Altitude ; *Biomass ; Metagenome ; Animal Feed/microbiology ; Archaea/genetics/classification ; Gastrointestinal Tract/microbiology ; Plants/microbiology ; }, abstract = {BACKGROUND: While Gangba sheep being well known for their unique flavour and nutritional value, harsh environmental factors negatively affect their growth and development, leading to poor productivity. The gastrointestinal tract microbiota plays an important role in host nutrient absorption and metabolism. The identification of dynamic changes in the gastrointestinal microbial communities and their functions is an important step towards improving animal production performance and health.

RESULTS: A comprehensive multi-omics survey of the microbial communities of the Gangba sheep gastrointestinal tract was performed under three distinct feeding strategies: natural grazing, semi-grazing with supplementation, and barn feeding. The dynamic changes, cross-kingdom partnerships and functional potential profiles were analysed and the results revealed that the feeding strategies had a greater impact on the microbial communities than the site of the gastrointestinal tract. The different microbial associations among the groups were revealed by co-occurrence networks based on the amplicon sequence variants (ASVs). Moreover, a Gangba sheep gastrointestinal microbial genomic catalogue was constructed for the first time, including 1146 metagenome-assembled genomes (MAGs) with completeness > 50% and contamination < 10%, among which, 504 bacterial and 15 archaeal MAGs were of high quality with completeness > 80% and contamination < 10%. About 40% of the high-quality MAGs displaying enzyme activity were related to the microbial species that contribute to plant biomass degradation. Most of these enzymes were expressed in rumen metatranscriptome datasets, especially in Prevotella spp. and Ruminococcus spp., suggesting that gastrointestinal microbial communities in ruminants play major roles in the digestion of plant biomass to provide nutrition and energy for the host.

CONCLUSIONS: These findings suggest that feeding strategies are the primary cause of changes in the gastrointestinal microbiome. Diversification of livestock feed might be an effective strategy to maintain the diversity and ecological multifunctionality of microbial communities in the gastrointestinal tract. Additionally, the catalogue of microbial genomes and the encoded biomass-degrading enzymes identified here provide insights into the potential microbial functions of the gastrointestinal tract of Gangba sheep at high altitudes. This paves the way for microbial interventions to improve the growth performance, productivity and product quality of ruminant livestock. Video Abstract.}, } @article {pmid39838369, year = {2025}, author = {Fan, J and Zeng, F and Zhong, H and Cai, J and Shen, W and Cheng, C and He, C and Liu, Y and Zhou, Y and Chen, S and Zhu, Y and Liu, T and Zheng, JS and Wang, L and Chen, YM and Ma, W and Zhou, D}, title = {Potential roles of cigarette smoking on gut microbiota profile among Chinese men.}, journal = {BMC medicine}, volume = {23}, number = {1}, pages = {25}, pmid = {39838369}, issn = {1741-7015}, mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Cigarette Smoking/adverse effects ; Middle Aged ; Adult ; China ; RNA, Ribosomal, 16S/genetics ; Asian People ; Actinomyces ; Aged ; East Asian People ; }, abstract = {BACKGROUND: Cigarette smoking is posited as a potential factor in disrupting the balance of the human gut microbiota. However, existing studies with limited sample size have yielded inconclusive results.

METHODS: Here, we assessed the association between cigarette smoking and gut microbial profile among Chinese males from four independent studies (N total = 3308). Both 16S rRNA and shotgun metagenomic sequencing methods were employed, covering 206 genera and 237 species. Microbial diversity and abundance were compared among non-smokers, current smokers, and former smokers.

RESULTS: Actinomyces[g], Atopobium[g], Haemophilus[g], Turicibacter[g], and Lachnospira[g] were found to be associated with smoking status (current smokers vs. non-smokers). Metagenomic data provided a higher resolution at the species level, particularly for the Actinomyces[g] branch. Additionally, serum γ-glutamylcysteine (γ-Glu-Cys) was found to have a potential role in connecting smoking and Actinomyces[g]. Furthermore, we revealed putative mediation roles of the gut microbiome in the associations between smoking and common diseases including cholecystitis and type 2 diabetes.

CONCLUSIONS: We characterized the gut microbiota profile in male smokers and further revealed their potential involvement in mediating the impact of smoking on health outcomes. These findings advance our understanding of the intricate association between cigarette smoking and the gut microbiome.}, } @article {pmid39838275, year = {2025}, author = {Nabisubi, P and Kanyerezi, S and Kebirungi, G and Sserwadda, I and Nsubuga, M and Kisitu, G and Nahirya, PN and Mulindwa, B and Akabwai, GP and Nantongo, S and Kekitiinwa, A and Kigozi, E and Luutu, NM and Katabazi, FA and Kalema, L and Katabalwa, A and Jjingo, D and Mboowa, G}, title = {Beyond the fever: shotgun metagenomic sequencing of stool unveils pathogenic players in HIV-infected children with non-malarial febrile illness.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {96}, pmid = {39838275}, issn = {1471-2334}, support = {TMA2020CDF-3159//European and Developing Countries Clinical Trials Partnership/ ; TMA2020CDF-3159//European and Developing Countries Clinical Trials Partnership/ ; TMA2020CDF-3159//European and Developing Countries Clinical Trials Partnership/ ; TMA2020CDF-3159//European and Developing Countries Clinical Trials Partnership/ ; TMA2020CDF-3159//European and Developing Countries Clinical Trials Partnership/ ; }, mesh = {Humans ; *Feces/microbiology/virology ; *Metagenomics ; Female ; *HIV Infections/complications/microbiology/virology ; Male ; Child, Preschool ; Child ; Fever/microbiology ; Uganda/epidemiology ; Infant ; Candida albicans/genetics/isolation & purification/classification/pathogenicity ; Giardia/genetics/isolation & purification/classification ; Bacteroides/genetics/isolation & purification/classification ; Gastrointestinal Microbiome/genetics ; }, abstract = {BACKGROUND: Non-malarial febrile illnesses (NMFI) pose significant challenges in HIV-infected children, often leading to severe complications and increased morbidity. While traditional diagnostic approaches focus on specific pathogens, shotgun metagenomic sequencing offers a comprehensive tool to explore the microbial landscape underlying NMFI in this vulnerable population ensuring effective management.

METHODS: In this study, we employed shotgun metagenomics to analyse stool samples from HIV-infected children at the Baylor Children's Clinic Uganda presenting with non-malarial febrile illness. Samples were collected and subjected to DNA extraction at the Molecular and Genomics Laboratory, Makerere University followed by shotgun metagenomics sequencing at the Chan Zuckerberg Biohub San Francisco. Bioinformatics analysis was conducted to identify and characterise the microbial composition and potential pathogenic taxa associated with NMFI using the CZID pipeline.

RESULTS: Our findings reveal a diverse array of microbial taxa in the stool samples of HIV-infected children with NMFI. Importantly, shotgun metagenomics revealed potentially pathogenic players including Trichomonas vaginalis, Candida albicans, Giardia, and Bacteroides in stool from this patient population. This sheds light on the complexities of microbial interactions that potentially underpin non-malarial febrile illness in this group. Taxonomic profiling identified recognised pathogens and comorbidities and revealed possible new correlations with NMFI, shedding light on the pathophysiology of fever in HIV-infected children.

CONCLUSION: Shotgun metagenomics is a valuable method for understanding the gut microbial landscape of NMFI in HIV-infected children, providing a comprehensive approach to pathogen identification and characterisation. By revealing potential pathogenic actors beyond the fever, this work demonstrates how metagenomic sequencing may improve our knowledge of infectious illnesses in vulnerable groups and inspire targeted therapies for better clinical care and outcomes.}, } @article {pmid39838107, year = {2025}, author = {Teso-Pérez, C and López-Gazcón, A and Peralta-Sánchez, JM and Martínez-Bueno, M and Valdivia, E and Fárez-Vidal, ME and Martín-Platero, AM}, title = {Bacteriocin-Producing Enterococci Modulate Cheese Microbial Diversity.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {175}, pmid = {39838107}, issn = {1432-184X}, support = {PEJ2018-003019-A//Plan Estatal de Garantía Juvenil (Fondo Social Europeo, Gobierno de España/ ; Group BIO 309//PAIDI Program/ ; A-BIO-083-UGR18//Programa Operativo FEDER Andalucía 2014-2020/ ; }, mesh = {*Cheese/microbiology ; *Bacteriocins/metabolism/biosynthesis ; *Enterococcus/metabolism/genetics ; *Microbiota ; Biodiversity ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Milk/microbiology ; Animals ; }, abstract = {Cheese production involves various lactic acid bacteria (LAB) that break down lactose, milk proteins, and fats, producing key nutrients and influencing the cheese's flavor. They form communities that play a crucial role in determining the cheese's organoleptic properties. The composition of cheeses' microbial communities is shaped by physicochemical factors (e.g., temperature, pH, and salinity) and biological factors (i.e. microbial interactions). While starter cultures are introduced to control these communities, non-starter LAB represent a significant portion of the final microbial assemblage, but their interactions remain unclear. LAB often produce bacteriocins, antimicrobial peptides that antagonize other bacteria, but their role within LAB communities is not fully understood. This study aimed to assess the impact of bacteriocin production on LAB diversity in cheese, using Enterococcus as a model organism, a common bacteriocin producer. We analyzed enterocin production of enterococcal isolates by antimicrobial assays and microbial diversity differences in raw milk cheeses by two approaches: 16S RNA gene amplicon metagenomic sequencing for the whole microbial community and multi-locus sequence analysis (MLSA) for the enterococcal diversity. Our results revealed that LAB communities were dominated by lactococci, lactobacilli, and streptococci, with enterococci present in lower numbers. However, cheeses containing bacteriocin-producing enterococci exhibited higher microbial diversity. Interestingly, the highest diversity occurred at low levels of bacteriocin producers, but this effect was not observed within enterococcal populations. These findings suggest that bacteriocin production plays a key role in shaping LAB communities during cheese ripening, although further research is needed to understand its broader implications in other microbial ecosystems.}, } @article {pmid39772525, year = {2025}, author = {Yum, SJ and Yu, SY and Kim, SM and Jeong, HG}, title = {Antibiotic Resistance Genes and Microbiota in Brassica oleracea var. acephala Cultivated in South Korea: Potential for Resistance Transmission.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {3}, pages = {2156-2166}, doi = {10.1021/acs.jafc.4c11161}, pmid = {39772525}, issn = {1520-5118}, mesh = {*Brassica/microbiology ; Republic of Korea ; *Microbiota/drug effects ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Antimicrobial resistance (AMR) poses a critical global public health challenge. This study investigates the microbiome of Brassica oleracea var. acephala (kale) to evaluate the role of food production systems, particularly plant-derived foods, in AMR dissemination. Using 16S rRNA gene sequencing and metagenomic shotgun sequencing, we analyzed microbial diversity and antimicrobial resistance genes (ARGs) in kale samples. Results showed significant regional differences in microbiota composition and ARG distribution, with traditional fertilizer use linked to higher ARG prevalence in coliform bacteria compared to farms using other fertilization methods. Additionally, we confirmed ARG transfer potential by Klebsiella pneumoniae within coliform populations. Storage conditions notably affected microbial dynamics, with higher temperatures promoting K. pneumoniae growth in washed samples. These findings revealed the importance of AMR research in plant-derived foods and highlight the need for improved agricultural practices to mitigate the risks associated with high ARG abundance in coliform bacteria.}, } @article {pmid39722326, year = {2025}, author = {Liu, X and Chen, Y and Liu, Y and Hu, Y and Wang, K and Huang, L and Ke, X and Peng, L and Guo, Z}, title = {Protective effects and mechanisms of extracts of Gleditsia sinensis Lam. Thorn on DSS-induced colitis in mice.}, journal = {Journal of ethnopharmacology}, volume = {340}, number = {}, pages = {119244}, doi = {10.1016/j.jep.2024.119244}, pmid = {39722326}, issn = {1872-7573}, mesh = {Animals ; *Dextran Sulfate ; *Plant Extracts/pharmacology ; Mice ; Male ; *Gastrointestinal Microbiome/drug effects ; *Cytokines/metabolism ; *Mice, Inbred C57BL ; Colitis/chemically induced/drug therapy/pathology ; Disease Models, Animal ; Colon/drug effects/pathology/metabolism ; Anti-Inflammatory Agents/pharmacology ; Colitis, Ulcerative/chemically induced/drug therapy/pathology ; }, abstract = {Inflammatory Bowel Disease (IBD), encompassing Ulcerative Colitis (UC) and Crohn's Disease (CD), stems from a multifaceted interaction of hereditary, immunological, ecological, and microbial elements. Current treatments have limitations, necessitating new therapeutic approaches.

AIM OF THE STUDY: This study investigates the safeguarding impacts and fundamental processes of extracts of Gleditsia sinensis Lam. thorn (EGST) in a dextran sulfate sodium (DSS)-induced colitis model in mice.

MATERIALS AND METHODS: A total of 180g of dried EGST were prepared, and untargeted metabolomic profiling using high-resolution liquid chromatography electrospray ionization orbitrap mass spectrometry (HR-LC-ESI-Orbitrap-MS) identified 930 compounds. UC model mice were administered 3% DSS for 7 d, followed by EGST treatment. The analysis encompassed physiological and pathological evaluations, serum cytokine ELISA, gut microbiota (GM) metagenomic sequencing, GC-MS metabolomics, mRNA sequencing, and Western Blot.

RESULTS: EGST markedly mitigated colitis symptoms, evidenced by reduced weight loss, lower DAI scores, and less colon shortening. It also decreased levels of pro-inflammatory cytokines (TNF-α, IL-6, IL-1β) while boosting IL-10. Histological examination revealed diminished tissue damage, restoration of crypts, and reduced inflammation, with barrier integrity maintained via upregulation of occludin and ZO-1. Metagenomic sequencing demonstrated that EGST modulated the GM, enhancing the levels of Firmicutes and Bacteroidetes while reducing the levels of Proteobacteria and Verrucomicrobia. Metabolomic analysis indicated that EGST influenced critical pathways, including those involving D-amino acids, glutathione, cysteine, and methionine metabolism. Furthermore, mRNA sequencing identified 2625 differentially expressed genes (DEGs), comprising 1729 with increased and 896 with decreased expression, and highlighted EGST's impact on the PPARγ/AMPK/NF-κB pathway.

CONCLUSION: Overall, EGST mitigates DSS-induced colitis through modulation of GM, metabolic profiles, and gene expression, suggesting its promise as a naturally derived treatment for colitis.}, } @article {pmid39675450, year = {2025}, author = {Ye, X and Niu, X and Li, L and Lv, M and Zhang, D and Chen, D and Line, Y and Yang, Z}, title = {Insights into the impact of 6PPD-Q and 6PPD on nitrogen metabolism and microbial community in the anammox system.}, journal = {Environmental research}, volume = {266}, number = {}, pages = {120485}, doi = {10.1016/j.envres.2024.120485}, pmid = {39675450}, issn = {1096-0953}, mesh = {*Nitrogen/metabolism ; Water Pollutants, Chemical/metabolism ; Microbiota/drug effects ; Bacteria/metabolism/genetics ; Waste Disposal, Fluid/methods ; Wastewater/microbiology ; Bioreactors/microbiology ; Oxidation-Reduction ; Anaerobiosis ; }, abstract = {N-(1,3-Dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD) is an antioxidant commonly used in tire manufacturing, and its release into the environment has significantly increased due to rapid urbanization. When subjected to ozonation, 6PPD converts into the harmful pollutant 6PPD quinone (6PPDQ). These substances enter wastewater treatment plants (WWTPs) via stormwater runoff and pipelines, posing significant risks to the functional microorganisms. Anammox, a strictly controlled and sensitive microbial nitrogen removal process, is especially susceptible to the effects of the pollutants. This study investigates the comprehensive impact of 6PPD-Q and 6PPD on anammox communities based on characterization analysis and metagenomics. At environmental concentrations, 6PPD-Q at 200 ng/L-1000 ng/L led to the disintegration of anammox granules. Extended exposure to both 6PPD-Q and 6PPD significantly reduces the population of anammox bacteria (AnAOB). By utilizing organic matter from dead cells and incoming carbonate as a carbon source, the system evolved into a nitrogen metabolism network primarily focused on denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This transformation was accompanied by a reshuffling of the microbial community and associated genes, resulting in an accumulation of NH4[+]-N. These findings underscore the toxicity of 6PPD-Q and 6PPD to anammox and stress the importance of incorporating 6PPD into regulatory and preventive strategies.}, } @article {pmid39672497, year = {2025}, author = {Zhou, L and Zhang, L and Dang, R and Han, G and Liu, J and Zhou, M and Xiao, L}, title = {Microbiota-induced asymmetry in coastal methane emission potential under experimental precipitation gradients.}, journal = {Environmental research}, volume = {266}, number = {}, pages = {120601}, doi = {10.1016/j.envres.2024.120601}, pmid = {39672497}, issn = {1096-0953}, mesh = {*Methane/metabolism ; *Microbiota ; China ; *Rain ; Wetlands ; Soil Microbiology ; Air Pollutants/analysis/toxicity ; }, abstract = {Climate models predict that the frequency and intensity of extreme precipitation events will increase globally. Despite carbon budget in coastal wetlands is known to be sensitive to precipitation variability, in where CH4 productions and potential mechanisms remain poorly understood. We investigated CH4 emission potential and its drivers after 7-year of field experiments with five precipitation gradients (-60%, -40%, ambient condition, +40%, +60%) in Yellow River Delta, China. The response of CH4 emission potential to precipitation gradients exhibited significant asymmetry, with the highest emission potential occurring under +40% precipitation. [13]C-isotope tracing experiment discovered the primary contribution of acetoclastic methanogenic pathway. +40% precipitation significantly improved the accumulation of aboveground biomass, soil organic carbon and total nitrogen. Microbial community abundance, but not composition, referring to metagenome-assembled genomes also actively responded to precipitation changes. For example, +40% precipitation increased the relative abundance of Methanosarcinia and Methanobacteria. Furthermore, CH4 emission potential was also promoted by higher microbial enzyme activity. Collectively, CH4 emission potential in response to 7-year experimental precipitations was regulated by microbiota-driven, showing obvious asymmetry.}, } @article {pmid39363100, year = {2025}, author = {Chu, VT and Glascock, A and Donnell, D and Grabow, C and Brown, CE and Ward, R and Love, C and Kalantar, KL and Cohen, SE and Cannon, C and Woodworth, MH and Kelley, CF and Celum, C and Luetkemeyer, AF and Langelier, CR}, title = {Impact of doxycycline post-exposure prophylaxis for sexually transmitted infections on the gut microbiome and antimicrobial resistome.}, journal = {Nature medicine}, volume = {31}, number = {1}, pages = {207-217}, pmid = {39363100}, issn = {1546-170X}, support = {K23 AI144036/AI/NIAID NIH HHS/United States ; R01 AI143439/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Doxycycline/pharmacology ; Male ; Female ; Adult ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; Post-Exposure Prophylaxis ; Sexually Transmitted Diseases/microbiology/prevention & control ; Drug Resistance, Bacterial/genetics ; Homosexuality, Male ; Transgender Persons ; Middle Aged ; }, abstract = {Doxycycline post-exposure prophylaxis (doxy-PEP) reduces bacterial sexually transmitted infections among men who have sex with men and transgender women. Although poised for widespread clinical implementation, the impact of doxy-PEP on antimicrobial resistance remains a primary concern as its effects on the gut microbiome and resistome, or the antimicrobial resistance genes (ARGs) present in the gut microbiome, are unknown. To investigate these effects, we studied participants from the DoxyPEP trial, a randomized clinical trial comparing doxy-PEP use, a one-time doxycycline 200-mg dose taken after condomless sex (DP arm, n = 100), to standard of care (SOC arm, n = 50) among men who have sex with men and transgender women. From self-collected rectal swabs at enrollment (day-0) and after 6 months (month-6), we performed metagenomic DNA sequencing (DNA-seq) or metatranscriptomic RNA sequencing (RNA-seq). DNA-seq data were analyzable from 127 samples derived from 89 participants, and RNA-seq data were analyzable from 86 samples derived from 70 participants. We compared the bacterial microbiome and resistome between the two study arms and over time. The median number of doxycycline doses taken since enrollment by participants with DNA-seq data was zero (interquartile range (IQR): 0-7 doses) for the SOC arm and 42 (IQR: 27-64 doses) for the DP arm. Tetracycline ARGs were detected in all day-0 DNA-seq samples and in 85% of day-0 RNA-seq samples. The proportional mass of tetracycline ARGs in the resistome increased between day-0 and month-6 in DP participants from 46% to 51% in the metagenome (P = 2.3 × 10[-2]) and from 4% to 15% in the metatranscriptome (P = 4.5 × 10[-6]), but no statistically significant increases in other ARG classes were observed. Exposure to a higher number of doxycycline doses correlated with proportional enrichment of tetracycline ARGs in the metagenome (Spearman's ρ = 0.23, P = 9.0 × 10[-3]) and metatranscriptome (Spearman's ρ = 0.55, P = 3.7 × 10[-8]). Bacterial microbiome alpha diversity, beta diversity and total bacterial mass did not differ between day-0 and month-6 samples from DP participants when assessed by either DNA-seq or RNA-seq. In an abundance-based correlation analysis, we observed an increase over time in the strength of the correlation between tetracycline ARGs and specific bacterial taxa, including some common human pathogens. In sum, doxy-PEP use over a 6-month period was associated with an increase in the proportion of tetracycline ARGs comprising the gut resistome and an increase in the expression of tetracycline ARGs. At 6 months of doxy-PEP use, no residual differences were observed in alpha and beta diversity or taxonomic composition of the gut microbiome. As doxy-PEP is implemented as a public health strategy, further studies and population-level surveillance of doxycycline-resistant pathogens are needed to understand the implications of these findings. ClinicalTrials.gov registration number: NCT03980223 .}, } @article {pmid39078977, year = {2025}, author = {Ismail, HM and Perera, D and Mandal, R and DiMeglio, LA and Evans-Molina, C and Hannon, T and Petrosino, J and Javornik Cregeen, S and Schmidt, NW}, title = {Gut Microbial Changes Associated With Obesity in Youth With Type 1 Diabetes.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {110}, number = {2}, pages = {364-373}, pmid = {39078977}, issn = {1945-7197}, support = {K23 DK129799/DK/NIDDK NIH HHS/United States ; /NH/NIH HHS/United States ; //(NIH)/ ; /TR/NCATS NIH HHS/United States ; KL2TR002530//Clinical and Translational Sciences Award/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetes Mellitus, Type 1/microbiology/metabolism/complications ; Female ; Male ; Adolescent ; Pilot Projects ; *Feces/microbiology ; Fatty Acids, Volatile/metabolism/analysis ; Body Mass Index ; Obesity/microbiology/metabolism ; Pediatric Obesity/microbiology/metabolism ; Child ; Young Adult ; }, abstract = {CONTEXT: Obesity is prevalent in type 1 diabetes (T1D) and is problematic with higher risk for diabetes complications. It is unknown to what extent gut microbiome changes are associated with obesity and T1D.

OBJECTIVE: This work aimed to describe the gut microbiome and microbial metabolite changes associated with obesity in T1D. We hypothesized statistically significant gut microbial and metabolite differences in lean T1D youth (body mass index [BMI]: 5%-<85%) vs those with obesity (BMI: ≥95%).

METHODS: We analyzed stool samples for gut microbial (using metagenomic shotgun sequencing) and short-chain fatty acid (SCFA) differences in lean (n = 27) and obese (n = 21) T1D youth in a pilot study. The mean ± SD age was 15.3 ± 2.2 years, glycated hemoglobin A1c 7.8 ± 1.3%, diabetes duration 5.1 ± 4.4 years, 42.0% female, and 94.0% were White.

RESULTS: Bacterial community composition showed between sample diversity differences (β-diversity) by BMI group (P = .013). There was a higher ratio of Prevotella to Bacteroides in the obese group (P = .0058). There was a differential distribution of significantly abundant taxa in either the lean or obese groups, including increased relative abundance of Prevotella copri, among other taxa in the obese group. Functional profiling showed an upregulation of branched-chain amino acid (BCAA) biosynthesis in the obese group and upregulation of BCAA degradation, tyrosine metabolism, and secondary bile acid biosynthesis in the lean group. Stool SCFAs were higher in the obese vs the lean group (P < .05 for all).

CONCLUSION: Our findings identify a gut microbiome and microbial metabolite signature associated with obesity in T1D. These findings could help identify gut microbiome-targeted therapies to manage obesity in T1D.}, } @article {pmid39835966, year = {2025}, author = {Levine, BH and Hoffman, JM}, title = {Microbiome transplants may not improve health and longevity in Drosophila melanogaster.}, journal = {Biology open}, volume = {14}, number = {1}, pages = {}, doi = {10.1242/bio.061745}, pmid = {39835966}, issn = {2046-6390}, support = {R00AG059920/NH/NIH HHS/United States ; //Augusta University; University of South Carolina/ ; }, mesh = {Animals ; *Drosophila melanogaster/microbiology/physiology ; *Longevity ; *Gastrointestinal Microbiome ; Female ; Male ; Microbiota ; }, abstract = {The gut microbiome, which is composed of bacteria, viruses, and fungi, and is involved in multiple essential physiological processes, changes measurably as a person ages, and can be associated with negative health outcomes. Microbiome transplants have been proposed as a method to improve gut function and reduce or reverse multiple disorders, including age-related diseases. Here, we take advantage of the laboratory model organism, Drosophila melanogaster, to test the effects of transplanting the microbiome of a young fly into middle-aged flies, across multiple genetic backgrounds and both sexes, to test whether age-related lifespan could be increased, and late-life physical health declines mitigated. Our results suggest that, overall, microbiome transplants do not improve longevity and may even be detrimental in flies, and the health effects of microbiome transplants were minor, but sex- and genotype-dependent. This discovery supports previous evidence that axenic flies, those with no gut microbiome, live healthier and longer lives than their non-axenic counterparts. The results of this study suggest that, at least for fruit flies, microbiome transplants may not be a viable intervention to improve health and longevity, though more research is still warranted.}, } @article {pmid39833973, year = {2025}, author = {Rampanelli, E and Romp, N and Troise, AD and Ananthasabesan, J and Wu, H and Gül, IS and De Pascale, S and Scaloni, A and Bäckhed, F and Fogliano, V and Nieuwdorp, M and Bui, TPN}, title = {Gut bacterium Intestinimonas butyriciproducens improves host metabolic health: evidence from cohort and animal intervention studies.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {15}, pmid = {39833973}, issn = {2049-2618}, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Mice ; Feces/microbiology ; Male ; Lysine/metabolism ; Female ; Fermentation ; Butyrates/metabolism ; Cohort Studies ; Clostridiales/metabolism/classification ; Fructose/metabolism ; Mice, Inbred C57BL ; Middle Aged ; Obesity/microbiology/metabolism ; Probiotics/administration & dosage/metabolism ; Disease Models, Animal ; }, abstract = {BACKGROUND: The human gut microbiome strongly influences host metabolism by fermenting dietary components into metabolites that signal to the host. Our previous work has shown that Intestinimonas butyriciproducens is a prevalent commensal bacterium with the unique ability to convert dietary fructoselysine to butyrate, a well-known signaling molecule with proven health benefits. Dietary fructoselysine is an abundant Amadori product formed in foods during thermal treatment and is part of foods rich in dietary advanced glycation end products which have been associated with cardiometabolic disease. It is therefore of interest to investigate the causal role of this bacterium and fructoselysine metabolism in metabolic disorders.

RESULTS: We assessed associations of I. butyriciproducens with metabolic risk biomarkers at both strain and functional levels using a human cohort characterized by fecal metagenomic analysis. We observed that the level of the bacterial strain as well as fructoselysine fermentation genes were negatively associated with BMI, triglycerides, HbA1c, and fasting insulin levels. We also investigated the fructoselysine degradation capacity within the Intestinimonas genus using a culture-dependent approach and found that I. butyriciproducens is a key player in the butyrogenic fructoselysine metabolism in the gut. To investigate the function of I. butyriciproducens in host metabolism, we used the diet-induced obesity mouse model to mimic the human metabolic syndrome. Oral supplementation with I. butyriciproducens counteracted body weight gain, hyperglycemia, and adiposity. In addition, within the inguinal white adipose tissue, bacterial administration reduced inflammation and promoted pathways involved in browning and insulin signaling. The observed effects may be partly attributable to the formation of the short-chain fatty acids butyrate from dietary fructoselysine, as butyrate plasma and cecal levels were significantly increased by the bacterial strain, thereby contributing to the systemic effects of the bacterial treatment.

CONCLUSIONS: I. butyriciproducens ameliorates host metabolism in the context of obesity and may therefore be a good candidate for new microbiota-therapeutic approaches to prevent or treat metabolic diseases. Video Abstract.}, } @article {pmid39833341, year = {2025}, author = {Zhang, C and Yu, Y and Yue, L and Chen, Y and Chen, Y and Liu, Y and Guo, C and Su, Q and Xiang, Z}, title = {Gut microbiota profiles of sympatric snub-nosed monkeys and macaques in Qinghai-Tibetan Plateau show influence of phylogeny over diet.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {95}, pmid = {39833341}, issn = {2399-3642}, support = {32171487//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31870509//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32400413//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Phylogeny ; *Diet ; Tibet ; RNA, Ribosomal, 16S/genetics ; Colobinae/microbiology ; Macaca mulatta ; Macaca/microbiology ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {The unique environment of the Qinghai-Tibetan Plateau provides a great opportunity to study how primate intestinal microorganisms adapt to ecosystems. The 16S rRNA gene amplicon and metagenome analysis were conducted to investigate the correlation between gut microbiota in primates and other sympatric animal species living between 3600 and 4500 m asl. Results showed that within the same geographical environment, Macaca mulatta and Rhinopithecus bieti exhibited a gut microbiome composition similar to that of Tibetan people, influenced by genetic evolution of host, while significantly differing from other distantly related animals. The gut microbiota of plateau species has developed similar strategies to facilitate their hosts' adaptation to specific environments, including broadening its dietary niche and enhancing energy absorption. These findings will enhance our comprehension of the significance of primate gut microbiota in adapting to specific habitats.}, } @article {pmid39756329, year = {2025}, author = {Dai, J and Li, M and He, J and Duan, L and Zhu, X and Liu, L and Meng, M and Shao, X and Zhu, G}, title = {Gut microbiota changes are associated with abnormal metabolism activity in children and adolescents with obsessive-compulsive disorder.}, journal = {Journal of psychiatric research}, volume = {181}, number = {}, pages = {728-737}, doi = {10.1016/j.jpsychires.2024.12.041}, pmid = {39756329}, issn = {1879-1379}, mesh = {Humans ; *Obsessive-Compulsive Disorder/metabolism/microbiology ; Adolescent ; *Gastrointestinal Microbiome/physiology ; Male ; Child ; Female ; *Feces/microbiology ; *RNA, Ribosomal, 16S ; Metabolomics ; Metagenomics ; }, abstract = {Obsessive-compulsive disorder (OCD) is a chronic and disabling psychiatric disorder characterized by recurrent intrusive thoughts or repetitive behaviors. We sought to better understand the structure of gut microbiota in first visit registration, treatment-naive children and adolescents with OCD, and the relationship between gut microbiota and fecal metabolites. Thus we studied the gut microbial population using 16 S rRNA sequencing in 49 children (8-17 years of age) with OCD, 42 healthy controls (HCs). We found a significant decrease in α-diversity in the OCD group, and the OCD and HC groups had distinctive intestinal flora. To further investigate the potential interaction effects between OCD and functional pathways of the intestinal flora, the 19 OCD patients and 18 aged-matched HCs were selected to undergo metagenomics analysis. We showed that several functional pathways of gut microbiota in patients with OCD were disrupted, such as glucolipid metabolism, amino acid metabolism, steroid biosynthesis, and the second messenger system. Changes in the clinical characteristics of OCD patients were associated with specific bacteria. Metabolomics analysis was also performed on stool samples from 91 subjects. Intestinal microflora metabolite expression in OCD patients was disturbed, and the related metabolic pathway functions were abnormal. Abnormal metabolites of gut microbiota in OCD patients are mainly involved in folate biosynthesis, the prion disease pathway, and the amino acid metabolic network. This study detailed the intestinal microbiota of children and adolescents with OCD. Our study suggests possible modalities for early OCD intervention by targeting the specific bacteria associated with neurotransmitter metabolism.}, } @article {pmid39714212, year = {2025}, author = {Fang, Y and Meng, L and Xia, J and Gotoh, Y and Hayashi, T and Nagasaki, K and Endo, H and Okazaki, Y and Ogata, H}, title = {Genome-resolved year-round dynamics reveal a broad range of giant virus microdiversity.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0116824}, doi = {10.1128/msystems.01168-24}, pmid = {39714212}, issn = {2379-5077}, support = {21H05057//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; Nos. 2018-31//Kyoto University | Institute for Chemical Research, Kyoto University (ICR)/ ; Nos. 2017-25//Kyoto University | Institute for Chemical Research, Kyoto University (ICR)/ ; 22H00384//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22H00385//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 16H06279//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 16H06429//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; 16K21723//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; 16H06437//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; Nos. 2021-33//Kyoto University | Institute for Chemical Research, Kyoto University (ICR)/ ; Nos. 2019-33//Kyoto University | Institute for Chemical Research, Kyoto University (ICR)/ ; }, mesh = {*Genome, Viral ; *Seawater/virology ; *Giant Viruses/genetics ; Metagenome ; Metagenomics ; Phylogeny ; Genetic Variation/genetics ; Seasons ; Biodiversity ; }, abstract = {Giant viruses are crucial for marine ecosystem dynamics because they regulate microeukaryotic community structure, accelerate carbon and nutrient cycles, and drive the evolution of their hosts through co-evolutionary processes. Previously reported long-term observations revealed that these viruses display seasonal fluctuations in abundance. However, the underlying genetic mechanisms driving such dynamics of these viruses remain largely unknown. In this study, we investigated the dynamics of giant viruses using time-series metagenomes from eutrophic coastal seawater samples collected over 20 months. A newly developed computational pipeline generated 1,065 high-quality genomes covering six major giant virus lineages. These genomic data revealed year-round recovery of the viral community structure at the study site and distinct dynamics of viral populations that were classified as persistent (n = 9), seasonal (n = 389), sporadic (n = 318), or others. By profiling the intra-species nucleotide-resolved microdiversity through read mapping, we also identified year-round recovery dynamics at subpopulation level for viruses classified as persistent or seasonal. Our results further indicated that giant viruses with broader niche breadth tended to exhibit higher levels of microdiversity. We argue that greater microdiversity of viruses likely enhances adaptability and thus survival under the virus-host arms race during prolonged interactions with their hosts.IMPORTANCERecent genome-resolved metagenomic surveys have uncovered the vast genomic diversity of giant viruses, which play significant roles in aquatic ecosystems by acting as bloom terminators and influencing biogeochemical cycles. However, the relationship between the ecological dynamics of giant viruses and underlying genetic structures of viral populations remains unresolved. In this study, we performed deep metagenomic sequencing of seawater samples collected across a time-series from a coastal area in Japan. The results revealed a significant positive correlation between microdiversity and temporal persistence of giant virus populations, suggesting that population structure is a crucial factor for adaptation and survival in the interactions with their hosts.}, } @article {pmid39714168, year = {2025}, author = {Bhosle, A and Jackson, MI and Walsh, AM and Franzosa, EA and Badri, DV and Huttenhower, C}, title = {Response of the gut microbiome and metabolome to dietary fiber in healthy dogs.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0045224}, doi = {10.1128/msystems.00452-24}, pmid = {39714168}, issn = {2379-5077}, support = {A-2019-687-HL//Hill's Pet Nutrition (Hill's)/ ; }, mesh = {Animals ; *Dietary Fiber/metabolism ; Dogs/microbiology ; *Gastrointestinal Microbiome/physiology ; *Metabolome/physiology ; *Feces/microbiology ; Male ; Female ; }, abstract = {UNLABELLED: Dietary fiber confers multiple health benefits originating from the expansion of beneficial gut microbial activity. However, very few studies have established the metabolic consequences of interactions among specific fibers, microbiome composition, and function in either human or representative animal models. In a study design reflective of realistic population dietary variation, fecal metagenomic and metabolomic profiles were analyzed from healthy dogs fed 12 test foods containing different fiber sources and quantities (5-13% as-fed basis). Taxa and functions were identified whose abundances were associated either with overall fiber intake or with specific fiber compositions. Fourteen microbial species were significantly enriched in response to ≥1 specific fiber source; enrichment of fiber-derived metabolites was more pronounced in response to these fiber sources. Positively associated fecal metabolites, including short-chain fatty acids, acylglycerols, fiber bound sugars, and polyphenols, co-occurred with microbes enriched in specific food groups. Critically, the specific metabolite pools responsive to differential fiber intake were dependent on differences both in individual microbial community membership and in overall ecological configuration. This helps to explain, for the first time, differences in microbiome-diet associations observed in companion animal epidemiology. Thus, our study corroborates findings in human cohorts and reinforces the role of personalized microbiomes even in seemingly phenotypically homogeneous subjects.

IMPORTANCE: Consumption of dietary fiber changes the composition of the gut microbiome and, to a larger extent, the associated metabolites. Production of health-relevant metabolites such as short-chain fatty acids from fiber depends both on the consumption of a specific fiber and on the enrichment of beneficial metabolite-producing species in response to it. Even in a seemingly homogeneous population, the benefit received from fiber consumption is personalized and emphasizes specific fiber-microbe-host interactions. These observations are relevant for both population-wide and personalized nutrition applications.}, } @article {pmid39714161, year = {2025}, author = {Neumann, CJ and Mohammadzadeh, R and Woh, PY and Kobal, T and Pausan, M-R and Shinde, T and Haid, V and Mertelj, P and Weiss, E-C and Kolovetsiou-Kreiner, V and Mahnert, A and Kumpitsch, C and Jantscher-Krenn, E and Moissl-Eichinger, C}, title = {First-year dynamics of the anaerobic microbiome and archaeome in infants' oral and gastrointestinal systems.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0107124}, doi = {10.1128/msystems.01071-24}, pmid = {39714161}, issn = {2379-5077}, support = {10.55776/KLI784 and 10.55776/DOC31//Austrian Science Fund (FWF)/ ; }, mesh = {Humans ; Infant ; *Mouth/microbiology ; *Gastrointestinal Microbiome/physiology ; *Breast Feeding ; Female ; Male ; Archaea/classification ; Gastrointestinal Tract/microbiology ; Anaerobiosis/physiology ; Microbiota/physiology ; Longitudinal Studies ; }, abstract = {UNLABELLED: Recent research provides new insights into the early establishment of the infant gut microbiome, emphasizing the influence of breastfeeding on the development of gastrointestinal microbiomes. In our study, we longitudinally examined the taxonomic and functional dynamics of the oral and gastrointestinal tract (GIT) microbiomes of healthy infants (n = 30) in their first year, focusing on the often-over-looked aspects, the development of archaeal and anaerobic microbiomes. Breastfed (BF) infants exhibit a more defined transitional phase in their oral microbiome compared to non-breastfed (NBF) infants, marked by a decrease in Streptococcus and the emergence of anaerobic genera such as Granulicatella. This phase, characterized by increased alpha-diversity and significant changes in beta-diversity, occurs earlier in NBF infants (months 1-3) than in BF infants (months 4-6), suggesting that breastfeeding supports later, more defined microbiome maturation. We demonstrated the presence of archaea in the infant oral cavity and GIT microbiome from early infancy, with Methanobrevibacter being the predominant genus. Still, transient patterns show that no stable archaeome is formed. The GIT microbiome exhibited gradual development, with BF infants showing increased diversity and complexity between the third and eighth months, marked by anaerobic microbial networks. NBF infants showed complex microbial co-occurrence patterns from the start. These strong differences between BF and NBF infants' GIT microbiomes are less pronounced on functional levels than on taxonomic levels. Overall, the infant microbiome differentiates and stabilizes over the first year, with breastfeeding playing a crucial role in shaping anaerobic microbial networks and overall microbiome maturation.

IMPORTANCE: The first year of life is a crucial period for establishing a healthy human microbiome. Our study analyses the role of archaea and obligate anaerobes in the development of the human oral and gut microbiome, with a specific focus on the impact of breastfeeding in this process. Our findings demonstrated that the oral and gut microbiomes of breastfed infants undergo distinct phases of increased dynamics within the first year of life. In contrast, the microbiomes of non-breastfed infants are more mature from the first month, leading to a steadier development without distinct transitional phases in the first year. Additionally, we found that archaeal signatures are present in infants under 1 year of age, but they do not form a stable archaeome. In contrast to this, we could track specific bacterial strains transitioning from oral to gut or persisting in the gut over time.}, } @article {pmid39699181, year = {2025}, author = {Olson, N and Lamar, F and Mucache, H and Fafetine, J and Saíde, J and Milisse, A and Brito, DRA and Jesser, KJ and Levy, K and Freeman, MC and Nadimpalli, ML}, title = {Farm-to-fork changes in poultry microbiomes and resistomes in Maputo City, Mozambique.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0103724}, doi = {10.1128/msystems.01037-24}, pmid = {39699181}, issn = {2379-5077}, support = {//Rollins School of Public Health Dean's Pilot and Innovation Award/ ; OPP 1189339//Bill and Melinda Gates Foundation (GF)/ ; 5T32ES007032-37, 5T32ES012870-15//HHS | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; T32AI138952//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 5T32ES012870//HHS | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; }, mesh = {Animals ; Mozambique/epidemiology ; *Chickens/microbiology ; *Feces/microbiology ; Microbiota/genetics ; Farms ; Drug Resistance, Bacterial/genetics ; Humans ; Poultry/microbiology ; Gastrointestinal Microbiome/genetics ; Bacteria/genetics/drug effects/isolation & purification/classification ; Metagenomics ; }, abstract = {UNLABELLED: Increasing demand for poultry has spurred poultry production in low- and middle-income countries like Mozambique. Poultry may be an important source of foodborne, antimicrobial-resistant bacteria to consumers in settings with limited water, sanitation, and hygiene infrastructure. The Chicken Exposures and Enteric Pathogens in Children Exposed through Environmental Pathways (ChEEP ChEEP) study was conducted in Maputo City, Mozambique from 2019 to 2021 to quantify enteric pathogen exposures along the supply chain for commercial and local (i.e., scavenger) chicken breeds. Here, we performed metagenomic sequencing of total DNA from banked ChEEP ChEEP samples to characterize fecal and carcass microbiomes and resistome diversity between chicken breeds and along the supply chain. Fecal samples (n = 26) were collected from commercial and local chickens at production sites and markets and carcass (n = 49) and rinse bucket samples (n = 26) from markets. We conducted taxonomic profiling and identified antimicrobial resistance genes (ARGs) from metagenomic sequence data, focusing especially on potential human pathogens and "high-risk" ARGs. We estimated alpha diversity for each sample and compared by site and breed. We estimated Bray-Curtis dissimilarity between samples and examined clustering. We found that commercial and local chickens harbored distinct fecal potential pathogens and resistomes at production and market sites. Many potentially pathogenic bacteria and ARGs present in chicken fecal samples are also present on carcasses sold to consumers. Finally, commercial chicken carcasses contain high-risk ARGs that are not necessarily introduced from chicken feces. These results indicate markets are an important site of exposure to potentially pathogenic bacteria and high-risk ARGs.

IMPORTANCE: While chicken eggs and meat are a critical protein source in low-income settings, antibiotics are routinely fed to chickens with consequences for selection of antimicrobial resistance. Evaluating how poultry gut bacterial communities, including potential human pathogens and high-risk antimicrobial resistance genes, differ from farm to market could help identify where to target interventions to minimize transmission risks to human populations. In this study in Maputo City, Mozambique, we found compositional differences between commercial and local chicken breeds at production and market sites. We also found that while all potentially pathogenic bacteria and many high-risk antimicrobial resistance genes persisted from production and market through processing, some resistance genes were detected on carcass samples only after processing, suggesting human or environmental contamination is occurring within markets. Overall, our findings indicate that open-air markets may represent a critical juncture for human exposures to pathogens and antimicrobial resistance genes from poultry and poultry products.}, } @article {pmid39611812, year = {2025}, author = {Shi, M and Zhao, B and Cai, W and Yuan, H and Liang, X and Li, Z and Liu, X and Jin, Y and Liu, X and Wei, C}, title = {Multi-omics mechanical analysis of gut microbiota, carboxylic acids, and cardiac gene expression interaction triggering diabetic cardiomyopathy.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0145024}, doi = {10.1128/msystems.01450-24}, pmid = {39611812}, issn = {2379-5077}, support = {82170268,82200482//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Diabetic Cardiomyopathies/genetics/microbiology/metabolism ; Mice ; Male ; Carboxylic Acids/metabolism ; Metabolomics ; Diabetes Mellitus, Type 2/microbiology/genetics/metabolism ; Metagenomics ; Receptors, Leptin/genetics/metabolism ; Myocardium/metabolism ; Mice, Inbred C57BL ; Diabetes Mellitus, Experimental/microbiology/genetics/metabolism ; Multiomics ; }, abstract = {UNLABELLED: It is well known that gut microbial imbalance is a potential factor for the occurrence and development of diabetes mellitus (DM) and its complications. Moreover, the heart and gut microbiota can regulate each other through the gut-metabolite-heart axis. In this study, metagenomics, metabolomics, and transcriptomics were chosen to sequence the changes in gut microbiota, serum metabolite levels, and differentially expressed genes (DEGs) in leptin receptor-deficient db/db mice and analyze the correlation between serum metabolites and gut microbiota or DEGs. According to the results, there were significant differences in the 1,029 cardiac genes and 353 serum metabolites in diabetic mice of the db/db group, including DEGs enriched in the PPAR signaling pathway and increased short-chain carboxylic acids (CAs), when compared with the normal db/m group. According to metagenomics, the gut microbiota of mice in the db/db group were disrupted, and particularly Lachnospiraceae bacteria and Oscillospiraceae bacteria significantly decreased. Also, according to the Pearson correlation analysis, a significant positive correlation was found between CAs and PPAR signaling pathway-related DEGs, and a negative correlation was found between CAs and the abundance of the above-mentioned species. To sum up, type 2 diabetes mellitus (T2DM) can upregulate the expression of partial cardiac genes through the levels of serum short-chain CAs affected by gut microbiota, thus playing a role in the occurrence and development of diabetic cardiomyopathy (DCM).

IMPORTANCE: Our research results clearly link the changes in heart genes of T2DM and normal mice with changes in serum metabolites and gut microbiota, indicating that some genes in biological processes are closely related to the reduction of protective microbiota in the gut microbiota. This study provides a theoretical basis for investigating the mechanism of DCM and may provide preliminary evidence for the future use of gut microbiota therapy for DCM.}, } @article {pmid39828685, year = {2025}, author = {Chen, Y and Yi, ZT and Yu, HL and Wu, XY and Wang, JP and Nie, C and Li, H and Li, SH and Yan, QL and He, TW and Chen, MC and Yang, XY and Wen, JY and Lv, LJ}, title = {Does preeclampsia impact the gut microbiota of preterm offspring during early infancy?.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {84}, pmid = {39828685}, issn = {1479-5876}, support = {2019A1515110389//Basic and Applied Basic Research Foundation of Guangdong Province/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; *Pre-Eclampsia/microbiology ; Pregnancy ; Infant, Newborn ; *Infant, Premature ; Adult ; Feces/microbiology ; Biodiversity ; }, abstract = {Preeclampsia (PE) is a pregnancy complication characterized by high blood pressure and organ damage. This study investigates the differences in the gut microbiota between preterm neonates born to mothers with PE and those born to mothers without PE (PR), aiming to understand how maternal health conditions like PE influence neonatal gut microbiota. The early gut microbiota plays a crucial role in neonatal health, and disturbances in its development can have long-term consequences. Fecal samples were collected from preterm neonates of PE and PR mothers at 2 and 6 weeks postpartum and analyzed using shotgun metagenomic sequencing. We found that PE significantly affected the gut microbial composition of preterm neonates, particularly at 2 weeks postpartum. The gut microbial diversity in the PE_2 group was notably lower compared to the PR_2 group, with no significant difference observed between the PR_6 and PE_6 groups. At the phylum level, Firmicutes and Proteobacteria were predominant, with significant differences observed, particularly a lower abundance of Actinobacteria in the PE_2 group. At the genus level, Escherichia, Enterococcus, and Klebsiella were more prevalent in the PE_2 group, whereas Bifidobacterium and Cutibacterium dominated the PR_2 group. The gut virome analysis showed no significant differences among the groups. Functional analysis revealed distinct metabolic pathway activities across the groups, suggesting that early disturbances due to PE impact the establishment of healthy gut microbiota. These findings underscore the substantial influence of maternal health on the early development of the neonatal gut microbiota and highlight the potential long-term health consequences. Additionally, the differences in metabolic pathways further emphasize the impact of preeclampsia on gut microbiota functionality.}, } @article {pmid39828574, year = {2025}, author = {Ma, XY and A, XR and Ma, JD and Zhou, JW and Cheng, P and Tang, Y}, title = {[Differential analysis of intestinal flora in patients with hepatic blastomycosis based on second-generation sequencing].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {59}, number = {1}, pages = {101-109}, doi = {10.3760/cma.j.cn112150-20240620-00487}, pmid = {39828574}, issn = {0253-9624}, support = {2022‑ZJ‑T01//Qinghai Province 2022 Innovation Platform Construction Special Project/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Case-Control Studies ; *Feces/microbiology ; High-Throughput Nucleotide Sequencing ; Echinococcosis, Hepatic/microbiology ; Metagenomics/methods ; }, abstract = {Exploring the variability of the intestinal flora of patients with hepatic blastocysticercosis and searching for members of the intestinal microflora that may play a role in the disease process by means of macro-genome sequencing technology. A case-control study was used to include fecal samples from patients with hepatic vesicular schistosomiasis admitted to Qinghai Provincial People's Hospital between October 2023 and January 2024 and individuals attending health checkups. The experimental group (AE group) consisted of 10 patients with liver vesicular schistosomiasis and the control group (NC group) consisted of 9 individuals attending health checkups. Macrogenomic sequencing was performed on these two groups of samples using the Illumina Novaseq 6000 sequencing platform, using fastp (v0.20.1) to remove junctions, and bbmap (v38.93-0) to remove the hosted sequences, followed by sequence splicing using MEGAHIT (v1.2.9), and then using prodigal (v2.6.3) to The spliced scaffold was subjected to ORF prediction and translated into amino acid sequences, followed by the construction of a non-redundant gene set using MMSeqs2 (v13.45111), and finally compared with the non-redundant gene set using salmon (v1.8.0). Species were annotated by the non-redundant database, species abundance was calculated in each sample, and the two sets were tested using Wilcoxon rank sum test. Finally, the differences in intestinal flora between the two groups were statistically analyzed using linear discriminant analysis, and the correlation between the differential intestinal flora and clinical indicators was analyzed using redundancy analysis (RDA). The results showed that the effective data volume of each sample was distributed from 10.41 to 12.46 G. The number of ORFs in the de-redundantly constructed gene catalogue (non-redundant gene set) was 4 951 408, and the annotation rate of the non-redundant genes was 97.97% when compared with the NR database. The ages of the study subjects in the two groups were (44.78±4.58) years in the NC group and (42.90±10.44) years in the AE group, and the difference was not statistically significant (t=0.530, P=0.476). The two groups were matched for body mass index (BMI) (t=2.368, P=0.142), gender (χ[2]=0.200, P=0.655), and dietary habits. There was no statistically significant difference in alpha diversity in the AE group (ACE index, t=0.942; chao1 index, t=0.947; shannon index, t=0.813, the simpson's index, t=0.613, P>0.05), while beta diversity analysis showed significant differences in the overall structure of the two communities (Stress=0.054 5). A total of 120 species were annotated at the phylum level, of which two differed. While 1 736 species were annotated at the genus level, 69 were different, and 309 were different at the species level. The AE group ranked the top 6 in terms of abundance of Anaplasma, Escherichiaceae, Clostridium, Alternaria, Ruminalia, and Treponema spp. at the genus level; whereas, Segatella, Prevotella, E. faecalis, Rossella, and beneficial rod-shaped bacteria were more abundant in the NC group. There were differences in the abundance and diversity of intestinal flora between the two groups, and the structure of community composition was significantly different. Statistical results by linear discriminant analysis (LDA) showed that LDA scores >2 in the NC group included beneficial bacillus spp. and E. faecalis spp. in young infants, etc. LDA scores >2 in the AE group at the mid-species level included Clostridium polterococcus, unknown microorganisms in the genus Clostridium intestinalis, Hathaway's Henkett's bacillus, and Clostridium oryzae in the genus Clostridium refractory to culture and small Clostridium spp. in the AE group. Clostridium intestinalis. The RDA results showed a negative correlation between beneficial rod genera and liver function indices, and a positive correlation between Clostridium intestinalis genera and liver function indices. In conclusion, patients with hepatic blastomycosis have altered intestinal flora abundance and diversity, with significant structural changes in community composition and differences in several genera, including Mycobacterium anisopliae and Clostridium intestinalis, and imbalances in the intestinal flora may affect hepatic function by influencing intestinal metabolites and may have an impact on the development of hepatic blastomycosis, a finding that warrants further in-depth study.}, } @article {pmid39827261, year = {2025}, author = {Guccione, C and Patel, L and Tomofuji, Y and McDonald, D and Gonzalez, A and Sepich-Poore, GD and Sonehara, K and Zakeri, M and Chen, Y and Dilmore, AH and Damle, N and Baranzini, SE and Hightower, G and Nakatsuji, T and Gallo, RL and Langmead, B and Okada, Y and Curtius, K and Knight, R}, title = {Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {825}, pmid = {39827261}, issn = {2041-1723}, support = {P30 CA023100/CA/NCI NIH HHS/United States ; NIH/NIGMS T32GM007198//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; NIH Pioneer DP1AT010885//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; NCI U24CA248454//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; CDC award 75D301-22-C-14717//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; AGA Research Scholar Award AGA2022-13-05//AGA Research Foundation/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Genome, Human ; Female ; Male ; Feces/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Microbiota/genetics ; Metagenome/genetics ; Computational Biology/methods ; Skin/microbiology ; }, abstract = {As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. We find that insufficient host filtration using prior human genome references can introduce false sex biases and inadvertently permit flow-through of host-specific DNA during bioinformatic analyses, which could be exploited for individual identification. To address these issues, we introduce and benchmark three host filtration methods of varying throughput, with concomitant applications across low biomass samples such as skin and high microbial biomass datasets including fecal samples. We find that these methods are important for obtaining accurate results in low biomass samples (e.g., tissue, skin). Overall, we demonstrate that rigorous host filtration is a key component of privacy-minded analyses of patient microbiomes and provide computationally efficient pipelines for accomplishing this task on large-scale datasets.}, } @article {pmid39827180, year = {2025}, author = {Van Goethem, MW and Bezuidt, OKI and Pierneef, R and Vikram, S and Hopkins, DW and Aspray, T and Hall, G and Woodborne, S and Hogg, ID and Northen, TR and Kong, W and Daffonchio, D and Cowan, DA and Van de Peer, Y and Delgado-Baquerizo, M and Makhalanyane, TP}, title = {Novel adaptive immune systems in pristine Antarctic soils.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2368}, pmid = {39827180}, issn = {2045-2322}, support = {118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Phylogeny ; *CRISPR-Cas Systems ; Microbiota/genetics ; Metagenomics/methods ; Adaptive Immunity/genetics ; Genome, Bacterial ; Bacteria/genetics ; Prophages/genetics ; Metagenome ; }, abstract = {Antarctic environments are dominated by microorganisms, which are vulnerable to viral infection. Although several studies have investigated the phylogenetic repertoire of bacteria and viruses in these poly-extreme environments with freezing temperatures, high ultra violet irradiation levels, low moisture availability and hyper-oligotrophy, the evolutionary mechanisms governing microbial immunity remain poorly understood. Using genome-resolved metagenomics, we test the hypothesis that Antarctic poly-extreme high-latitude microbiomes harbour diverse adaptive immune systems. Our analysis reveals the prevalence of prophages in bacterial genomes (Bacteroidota and Verrucomicrobiota), suggesting the significance of lysogenic infection strategies in Antarctic soils. Furthermore, we demonstrate the presence of diverse CRISPR-Cas arrays, including Class 1 arrays (Types I-B, I-C, and I-E), alongside systems exhibiting novel gene architecture among their effector cas genes. Notably, a Class 2 system featuring type V variants lacks CRISPR arrays, encodes Cas1 and Cas2 adaptation module genes. Phylogenetic analysis of Cas12 effector proteins hints at divergent evolutionary histories compared to classified type V effectors and indicates that TnpB is likely the ancestor of Cas12 nucleases. Our findings suggest substantial novelty in Antarctic cas sequences, likely driven by strong selective pressures. These results underscore the role of viral infection as a key evolutionary driver shaping polar microbiomes.}, } @article {pmid39763865, year = {2024}, author = {Gonzalez, FL and Ranaivoson, HC and Andrianiaina, A and Andry, S and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Dussart, P and Héraud, JM and Brook, CE}, title = {Genomic characterization of novel bat kobuviruses in Madagascar: implications for viral evolution and zoonotic risk.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39763865}, issn = {2692-8205}, support = {DP2 AI171120/AI/NIAID NIH HHS/United States ; R01 AI129822/AI/NIAID NIH HHS/United States ; R25 GM066522/GM/NIGMS NIH HHS/United States ; }, abstract = {Kobuviruses (family Picornaviridae, genus Kobuvirus) are enteric viruses that infect a wide range of both human and animal hosts. Much of the evolutionary history of kobuviruses remains elusive, largely due to limited screening in wildlife. Bats have been implicated as major sources of virulent zoonoses, including coronaviruses, henipaviruses, and filoviruses, though much of the bat virome still remains uncharacterized. While most bat virus research has historically focused on immediately recognizable zoonotic clades (e.g. SARS-related coronaviruses), a handful of prior reports catalog kobuvirus infection in bats and posit the role of bats as potential progenitors of downstream kobuvirus evolution. As part of a multi-year study, we carried out metagenomic Next Generation Sequencing (mNGS) on fecal samples obtained from endemic, wild-caught Madagascar fruit bats to characterize potentially zoonotic viruses circulating within these populations. The wild bats of Madagascar represent diverse Asian and African phylogeographic histories, presenting a unique opportunity for viruses from disparate origins to mix, posing significant public health threats. Here, we report detection of kobuvirus RNA in Malagasy fruit bat (Eidolon dupreanum) feces and undertake phylogenetic characterization of one full genome kobuvirus sequence, which nests within the Aichivirus A clade - a kobuvirus clade known to infect a wide range of hosts including humans, rodents, canids, felids, birds, and bats. Given the propensity of kobuviruses for recombination and cross-species infection, further characterization of this clade is critical to accurate evaluation of future zoonotic threats.}, } @article {pmid39742897, year = {2025}, author = {Jumaylawee, HRH and Komijani, M and Shahrjerdi, S and Sargolzaei, J}, title = {The interplay of gut microbiota and heavy metals in multiple sclerosis patients.}, journal = {Microbial pathogenesis}, volume = {199}, number = {}, pages = {107269}, doi = {10.1016/j.micpath.2024.107269}, pmid = {39742897}, issn = {1096-1208}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Metals, Heavy/blood ; *Multiple Sclerosis/microbiology ; *Feces/microbiology/chemistry ; *RNA, Ribosomal, 16S/genetics ; Male ; Adult ; Female ; Arsenic/analysis ; Interleukin-10/blood/metabolism ; Middle Aged ; Bacteria/classification/isolation & purification/genetics ; Metagenomics ; Mass Spectrometry ; Young Adult ; Nickel ; }, abstract = {Multiple Sclerosis (MS) is a chronic inflammatory disease characterized by central nervous system (CNS). In this study, the concentration of heavy metals was measured in stool samples of MS patients by Inductively Coupled Plasma-Mass Spectroscopy (ICP-MS) method and compared with healthy people. Also, another goal of this study is to investigate the alteration of the gut microbiome of MS patients by metagenomics technique based on the 16S rRNA gene sequencing. The IL-10 ELISA assay showed no significant differences between the serum level of the IL-10 in the patients and the control group (p = 0.510). Heavy metal measurement by ICP-MS showed significantly higher levels of arsenic (As, Mean = 32.77 μg/kg), nickel (Ni, Mean = 7.154 μg/kg), manganese (Mn, Mean = 3723 μg/kg), and zinc (Zn, Mean = 5508 μg/kg) in the stool samples of the MS group compared to the control group, while concentrations of iron (Fe, Mean = 9585 μg/kg), lead (Pb, Mean = 18.54 μg/kg), titanium (Ti, Mean = 69.69 μg/kg), and tin (Sn, Mean = 13.92 μg/kg) were significantly lower. The result of gut microbiome analysis showed an increase in the abundance of the Verrumicrobiaceae, Lachnospiraceae and Ruminococcaceae families was considerably increased in MS patients compared to the control group (p < 0.05). This study reports that high levels of heavy metals such as Ars, Ni, Mn, and Zn, deficiency of Fe, Pb, Ti, and Sn, and alteration of the gut microbiome are involved in the pathogenesis of MS. The novelty of this study lies in its multi-faceted approach to understanding MS by integrating the measurement of heavy metals in stool samples with the analysis of gut microbiome alterations, thereby providing comprehensive insights into heavy metals, the gut microbiome, and potential therapeutic avenues. This study suggests several potential applications and practical implications based on its findings regarding heavy metals, gut microbiome alterations, and IL-10 levels in MS. First, the identification of elevated levels of specific heavy metals and deficiencies in others may lead to targeted screening and monitoring, informing preventive strategies for MS patients. Additionally, the observed gut microbiome changes could facilitate the development of microbiome-based therapies, such as probiotics or dietary interventions, aimed at restoring microbial balance. Finally, exploring the interplay between heavy metals, gut microbiome, and immune response may guide the creation of novel therapeutic interventions, ultimately enhancing treatment efficacy and providing new avenues for managing MS, thereby alleviating the burden of this chronic condition.}, } @article {pmid39716651, year = {2025}, author = {Xu, K and Liu, P and Qin, X and Wang, X and Shi, L and Wang, P and Wu, X and Xiao, H and Zhao, H and Zhong, Y and Zhang, C}, title = {Bacteriophage diversity and novelty revealed by metaviromic analysis of the gut virome in the medicinal Blaps rynchopetera.}, journal = {Microbial pathogenesis}, volume = {199}, number = {}, pages = {107249}, doi = {10.1016/j.micpath.2024.107249}, pmid = {39716651}, issn = {1096-1208}, mesh = {*Bacteriophages/genetics/isolation & purification/classification ; Animals ; *Genome, Viral ; *Virome ; *Gastrointestinal Microbiome ; *Coleoptera/virology ; *High-Throughput Nucleotide Sequencing ; Phylogeny ; DNA Viruses/genetics ; DNA, Viral/genetics ; Metagenomics ; }, abstract = {The medicinal beetle Blaps rynchopetera is recognized for its antibacterial, anti-inflammatory, and immune-regulating properties. This study utilized metaviromics technology to systematically characterize the viral community within the gut of B. rynchopetera through high-throughput sequencing of gut contents, with a specific focus on the composition of its bacteriophage community. The sequencing generated 15,394 contigs exceeding 200 bp, which were assembled into 577 viral operational taxonomic units. Among these, dsDNA viruses constituted 52.33%, ssDNA viruses 11.09%, and Nucleo-Cytoplasmic Large DNA Viruses 11.78%, with 24.80% remaining unknown. Bacteriophages were the predominant viral community members, comprising 65.86% of the total, mainly distributed among five families: Peduoviridae, Schitoviridae, Drexlerviridae, Autographiviridae, and Casjensviridae, with 40.21% of the bacteriophages belonging to unclassified genera. Deep genomic assembly yielded 34 complete bacteriophage sequences, including nine sequences lacking significant similarity to existing viral genomes in BLAST analysis. The remaining sequences were classified as follows: four in Stephanstirmvirinae, three in Schitoviridae, three in Peduoviridae, one in Autographiviridae, one in Guernseyvirinae, one in Herelleviridae, one in Gordonclarkvirinae, one in Chaseviridae, and one in Salmondvirus, while nine bacteriophages remained unclassified. The results indicate that the gut bacteriophage community of B. rynchopetera is diverse and species-rich, exhibiting distinct characteristics compared to bacteriophage communities from honey bees and mosquitoes. These findings lay a foundation for further investigation into virus-microbiota interactions and virus-host relationships within the gut of B. rynchopetera.}, } @article {pmid39675442, year = {2025}, author = {Tian, C and Yang, Q and Lv, H and Yue, F}, title = {Integrative analysis of gut microbiota and fecal metabolites in cynomolgus monkeys with spontaneous type 2 diabetes mellitus.}, journal = {Microbial pathogenesis}, volume = {199}, number = {}, pages = {107228}, doi = {10.1016/j.micpath.2024.107228}, pmid = {39675442}, issn = {1096-1208}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Feces/microbiology/chemistry ; *Macaca fascicularis ; *Diabetes Mellitus, Type 2/microbiology/metabolism ; *Fatty Acids, Volatile/metabolism/analysis ; *Metabolomics ; *Dysbiosis/microbiology ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Biomarkers ; Disease Models, Animal ; Metagenomics ; Male ; Metabolome ; }, abstract = {BACKGROUND: Accumulating evidence suggests that gut microbiota (GM) is clearly associated with the pathogenesis of type 2 diabetes mellitus (T2DM). However, the underlying mechanism of GM dysbiosis participates the onset of T2DM is not fully understood. The spontaneous T2DM cynomolgus monkeys are a powerful model for understanding the pathological mechanism of T2DM.

METHODS: Fecal samples were collected from 7 spontaneous T2DM cynomolgus monkeys and 7 healthy controls matched with similar age for multi-omics analysis, including shotgun metagenomic sequencing, untargeted metabolomics profiling, and targeted metabolomics focusing on short chain fatty acids (SCFAs). Lastly, the correlation network between differential gut microbial species and fecal metabolites was performed to explore the potential biomarkers of T2DM.

RESULTS: We found that 17 low-abundance species showed significant differences between the two groups. Analysis of gut microbial functions revealed that 16 KEGG pathways and 51 KEGG modules were significantly different in the two groups. Meanwhile, 276 fecal DEMs were identified, and these DEMs were enriched in the KEGG pathways, including Nucleotide metabolism, ABC transporters, Purine metabolism and so on. Lastly, Spearman correlation network analysis showed that the species of Anaerostipes_hadrus and Lachnoanaerobaculum_umeaense, and the metabolites including Glycerophospho-N-palmitoyl ethanolamine and 2-Hydroxycinnamic acid might serve as potential biomarkers of T2DM.

CONCLUSIONS: Our study provides novel insights into specific alterations in the GM composition, gene functions, and fecal metabolic profiles in spontaneous T2DM cynomolgus monkeys.}, } @article {pmid39468772, year = {2025}, author = {Chero-Sandoval, L and Higuera-Gómez, A and Martínez-Urbistondo, M and Castejón, R and Mellor-Pita, S and Moreno-Torres, V and de Luis, D and Cuevas-Sierra, A and Martínez, JA}, title = {Comparative assessment of phenotypic markers in patients with chronic inflammation: Differences on Bifidobacterium concerning liver status.}, journal = {European journal of clinical investigation}, volume = {55}, number = {2}, pages = {e14339}, doi = {10.1111/eci.14339}, pmid = {39468772}, issn = {1365-2362}, support = {CD22/00011//Instituto de Salud Carlos III/ ; Y2020/6600//Consejería de Educación, Juventud y Deporte, Comunidad de Madrid/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; Male ; Adult ; Middle Aged ; *Bifidobacterium ; *Biomarkers/metabolism ; *Inflammation ; *Lupus Erythematosus, Systemic/microbiology/immunology ; Phenotype ; Feces/microbiology ; Liver ; Fatty Liver/microbiology ; }, abstract = {BACKGROUND: The relationship between systemic lupus erythematosus (SLE) and low-grade metabolic inflammation (MI) with the microbiota is crucial for understanding the pathogenesis of these diseases and developing effective therapeutic interventions. In this context, it has been observed that the gut microbiota plays a key role in the immune regulation and inflammation contributing to the exacerbation through inflammatory mediators. This research aimed to describe similarities/differences in anthropometric, biochemical, inflammatory, and hepatic markers as well as to examine the putative role of gut microbiota concerning two inflammatory conditions: SLE and MI.

METHODS: Data were obtained from a cohort comprising adults with SLE and MI. Faecal samples were determined by 16S technique. Statistical analyses compared anthropometric and clinical variables, and LEfSe and MetagenomeSeq were used for metagenomic data. An interaction analysis was fitted to investigate associations of microbiota with fatty liver index (FLI) depending on the inflammatory condition.

RESULTS: Participants with low-grade MI showed worse values in anthropometry and biochemicals compared with patients with SLE. The liver profile of patients with MI was unhealthier, while no relevant differences were found in most of the inflammatory markers between groups. LEfSe analysis revealed an overrepresentation of Bifidobacteriaceae family in SLE group. An interactive association between gut Bifidobacterium abundance and type of disease was identified for FLI values, suggesting an effect modification of the gut microbiota concerning liver markers depending on the inflammatory condition.

CONCLUSION: This study found phenotypical and microbial similarities and disparities between these two inflammatory conditions, evidenced in clinical and hepatic markers, and showed the interactive interplay between gut Bifidobacterium and liver health (measured by FLI) that occur in a different manner depending on the type of inflammatory disease. These results underscore the importance of personalized approaches and individual microbiota in the screening of different inflammatory situations, considering unique hepatic and microbiota profiles.}, } @article {pmid39363651, year = {2025}, author = {Vazquez Bucheli, JE and Lee, Y and Kim, B and Azevedo, NF and Azevedo, AS and Todorov, SD and Ji, Y and Kang, H and Holzapfel, WH}, title = {Use of FISH-FLOW as a Method for the Identification and Quantification of Bacterial Populations.}, journal = {Molecular nutrition & food research}, volume = {69}, number = {2}, pages = {e2400494}, doi = {10.1002/mnfr.202400494}, pmid = {39363651}, issn = {1613-4133}, support = {NRF-2018M3A9F3021964//NRF Korea/ ; RS-2023-00222687//NRF Korea/ ; 739489//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; 2023/05394-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; LA/P/0045/2020UIDP/00511/2020,POCI-01-0145-FEDER-030431//FCT Portugal/ ; }, mesh = {*In Situ Hybridization, Fluorescence/methods ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Flow Cytometry/methods ; *Bacteria/isolation & purification/genetics/classification ; Proteobacteria/isolation & purification/genetics ; Gastrointestinal Tract/microbiology ; Bacteroidetes/isolation & purification/genetics ; Actinobacteria/isolation & purification/genetics ; Firmicutes/isolation & purification/genetics ; Female ; Male ; }, abstract = {The gastrointestinal tract (GIT) harbors the largest group of microbiotas among the microbial communities of the human host. The resident organisms typical of a healthy gut are well adapted to the gastrointestinal environment while alteration of these populations can trigger disorders that may affect the health and well-being of the host. Various investigations have applied different tools to study bacterial communities in the gut and their correlation with gastrointestinal disorders such as inflammatory bowel disease (IBD), obesity, and diabetes. This study proposes fluorescent in situ hybridization, combined with flow cytometry (FISH-FLOW), as an alternative approach for phylum level identification of Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria and quantification of target bacteria from the GIT based on analysis of fecal samples, where results are validated by quantitative polymerase chain reaction (qPCR) and 16S ribosomal ribonucleic acid (16s rRNA) sequencing. The results obtained via FISH-FLOW experimental approach show high specificity for the developed probes for hybridization with the target bacteria. The study, therefore, suggests the FISH-FLOW as a reliable method for studying bacterial communities in the gut with results correlating well with those of metagenomic investigations of the same fecal samples.}, } @article {pmid38458256, year = {2025}, author = {Mishra, S and Tejesvi, MV and Hekkala, J and Turunen, J and Kandikanti, N and Kaisanlahti, A and Suokas, M and Leppä, S and Vihinen, P and Kuitunen, H and Sunela, K and Koivunen, J and Jukkola, A and Kalashnikov, I and Auvinen, P and Kääriäinen, OS and Peñate Medina, T and Peñate Medina, O and Saarnio, J and Meriläinen, S and Rautio, T and Aro, R and Häivälä, R and Suojanen, J and Laine, M and Erawijattari, PP and Lahti, L and Karihtala, P and Ruuska, TS and Reunanen, J}, title = {Gut microbiome-derived bacterial extracellular vesicles in patients with solid tumours.}, journal = {Journal of advanced research}, volume = {68}, number = {}, pages = {375-386}, doi = {10.1016/j.jare.2024.03.003}, pmid = {38458256}, issn = {2090-1224}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Extracellular Vesicles/metabolism ; *Neoplasms/microbiology/metabolism ; *Feces/microbiology ; *Bacteria/metabolism/classification/genetics ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Proteomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Adult ; Proteome/metabolism/analysis ; Aged ; }, abstract = {INTRODUCTION: Gut microbiome-derived nanoparticles, known as bacterial extracellular vesicles (bEVs), have garnered interest as promising tools for studying the link between the gut microbiome and human health. The diverse composition of bEVs, including their proteins, mRNAs, metabolites, and lipids, makes them useful for investigating diseases such as cancer. However, conventional approaches for studying gut microbiome composition alone may not be accurate in deciphering host-gut microbiome communication. In clinical microbiome research, there is a gap in the knowledge on the role of bEVs in solid tumor patients.

OBJECTIVES: Analyzing the functionality of bEVs using (meta)genomics and proteomics could highlight the unique aspects of host-gut microbiome interactions in solid tumor patients. Therefore, we performed a comparative analysis of the proteome and microbiota composition of gut microbiome-derived bEVs isolated from patients with solid tumors and healthy controls.

METHODS: After isolating bEVs from the feces of solid tumor patients and healthy controls, we performed spectrometry analysis of their proteomes and next-generation sequencing (NGS) of the 16S gene. We also investigated the gut microbiomes of feces from patients and controls using 16S sequencing and used machine learning to classify the samples into patients and controls based on their bEVs and fecal microbiomes.

RESULTS: Solid tumor patients showed decreased microbiota richness and diversity in both the bEVs and feces. However, the bEV proteomes were more diverse in patients than in the controls and were enriched with proteins associated with the metabolism of amino acids and carbohydrates, nucleotide binding, and oxidoreductase activity. Metadata classification of samples was more accurate using fecal bEVs (100%) compared with fecal samples (93%).

CONCLUSION: Our findings suggest that bEVs are unique functional entities. There is a need to explore bEVs together with conventional gut microbiome analysis in functional cancer research to decipher the potential of bEVs as cancer diagnostic or therapeutic biomarkers.}, } @article {pmid39826029, year = {2025}, author = {Reuben, RC and Torres, C}, title = {Integrating the milk microbiome signatures in mastitis: milk-omics and functional implications.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {2}, pages = {41}, pmid = {39826029}, issn = {1573-0972}, mesh = {*Milk/microbiology ; Animals ; *Microbiota ; Female ; *Metagenomics/methods ; *Mastitis/microbiology ; Mastitis, Bovine/microbiology ; Proteomics ; Humans ; Cattle ; Bacteria/classification/genetics/isolation & purification ; Dysbiosis/microbiology ; }, abstract = {Mammalian milk contains a variety of complex bioactive and nutritional components and microorganisms. These microorganisms have diverse compositions and functional roles that impact host health and disease pathophysiology, especially mastitis. The advent and use of high throughput omics technologies, including metagenomics, metatranscriptomics, metaproteomics, metametabolomics, as well as culturomics in milk microbiome studies suggest strong relationships between host phenotype and milk microbiome signatures in mastitis. While single omics studies have undoubtedly contributed to our current understanding of milk microbiome and mastitis, they often provide limited information, targeting only a single biological viewpoint which is insufficient to provide system-wide information necessary for elucidating the biological footprints and molecular mechanisms driving mastitis and milk microbiome dysbiosis. Therefore, integrating a multi-omics approach in milk microbiome research could generate new knowledge, improve the current understanding of the functional and structural signatures of the milk ecosystem, and provide insights for sustainable mastitis control and microbiome management.}, } @article {pmid39825576, year = {2025}, author = {Fouché, J and Lebre, PH and Melville, HA and Cowan, DA}, title = {The Functional and Structural Succession of Mesic-Grassland Soil Microbiomes Beneath Decomposing Large Herbivore Carcasses.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70022}, doi = {10.1111/1462-2920.70022}, pmid = {39825576}, issn = {1462-2920}, mesh = {*Soil Microbiology ; Animals ; *Microbiota ; *Herbivory ; *Grassland ; *Bacteria/classification/genetics/metabolism ; *RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Carbon/metabolism ; }, abstract = {Plant detritus is abundant in grasslands but decomposes slowly and is relatively nutrient-poor, whereas animal carcasses are labile and nutrient-rich. Recent studies have demonstrated that labile nutrients from carcasses can significantly alter the long-term soil microbial function at an ecosystem scale. However, there is a paucity of knowledge on the functional and structural response and temporal scale of soil microbiomes beneath large herbivore carcasses. This study compared microbiome functions and structures of soil beneath Connochaetes taurinus (hereafter 'wildebeest') carcasses at various postmortem intervals of decomposition to matched control samples over 18 months. Microbial functions were compared by their community-level physiological profiles determined by sole-carbon substrate utilisation and structures by metagenomic sequences using 16S rRNA gene markers. Overall metabolism and metabolic diversity remained increased and functionally dissimilar to control soils throughout the experimental period, with successive sole-carbon substrate utilisation observed. Conversely, diversity was initially reduced and structurally dissimilar from the control soil but recovered within the experimental period. The study contributes to the knowledge of carcass decomposition by investigating the long-term soil microbiome dynamics resulting from large herbivore carcasses decomposing in a mesic grassland. Microbial functional succession and ecologically relevant bacterial biomarkers of soil beneath the decomposing carcasses were identified for various postmortem intervals.}, } @article {pmid39824780, year = {2025}, author = {Wu, X and Peng, J and Malik, AA and Peng, Z and Luo, Y and Fan, F and Lu, Y and Wei, G and Delgado-Baquerizo, M and Liesack, W and Jiao, S}, title = {A Global Relationship Between Genome Size and Encoded Carbon Metabolic Strategies of Soil Bacteria.}, journal = {Ecology letters}, volume = {28}, number = {1}, pages = {e70064}, doi = {10.1111/ele.70064}, pmid = {39824780}, issn = {1461-0248}, support = {42122050//National Science Foundation for Excellent Young Scholars of China/ ; 42277307 & 41977038//National Natural Science Foundation of China/ ; 2021YFD1900500//National Key Research and Development Program of China/ ; }, mesh = {*Soil Microbiology ; *Carbon/metabolism ; *Bacteria/metabolism/genetics ; *Genome, Bacterial ; *Genome Size ; Gene Transfer, Horizontal ; Microbiota ; Biomass ; }, abstract = {Microbial traits are critical for carbon sequestration and degradation in terrestrial ecosystems. Yet, our understanding of the relationship between carbon metabolic strategies and genomic traits like genome size remains limited. To address this knowledge gap, we conducted a global-scale meta-analysis of 2650 genomes, integrated whole-genome sequencing data, and performed a continental-scale metagenomic field study. We found that genome size was tightly associated with an increase in the ratio between genes encoding for polysaccharide decomposition and biomass synthesis that we defined as the carbon acquisition-to-biomass yield ratio (A/Y). We also show that horizontal gene transfer played a major evolutionary role in the expanded bacterial capacities in carbon acquisition. Our continental-scale field study further revealed a significantly negative relationship between the A/Y ratio and soil organic carbon stocks. Our work demonstrates a global relationship between genome size and the encoded carbon metabolic strategies of soil bacteria across terrestrial microbiomes.}, } @article {pmid39793467, year = {2025}, author = {Cardacino, A and Turco, S and Balestra, GM}, title = {Seasonal dynamics of kiwifruit microbiome: A case study in a KVDS-affected orchard.}, journal = {Microbiological research}, volume = {292}, number = {}, pages = {128044}, doi = {10.1016/j.micres.2024.128044}, pmid = {39793467}, issn = {1618-0623}, mesh = {*Soil Microbiology ; *Plant Diseases/microbiology ; *Microbiota ; *Seasons ; *Actinidia/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; *Plant Roots/microbiology ; Italy ; Metagenomics ; Temperature ; }, abstract = {Over the past decade, Italian kiwifruit orchards and overall production have faced a significant threat from Kiwifruit Vine Decline Syndrome (KVDS). Despite the insights gained from metagenomics studies into the microbial communities associated with the disease, unanswered questions still remain. In this study, the evolution of bacterial, fungal, and oomycetes communities in soil and root endosphere at three different time points during the vegetative season was investigated for the first time in a KVDS-affected orchard in the Lazio Region. The fungal and oomycetes genera previously associated with the syndrome, including Fusarium, Ilyonectria, Thelonectria, Phytophthora, Pythium and Globisporangium, were identified in both groups. In contrast, the characterization of bacterial communities revealed the first instance of the presence of the genus Ralstonia in soil and root samples. The microbiome composition shifts between KVDS-affected and asymptomatic plants were significant as evidenced by the results, particularly after a temperature increase. This temperature change coincided with the onset of severe disease symptoms and may indicate a key role in the progression of KVDS.}, } @article {pmid39761739, year = {2025}, author = {Yavorov-Dayliev, D and Milagro, FI and Ayo, J and Oneca, M and Goyache, I and López-Yoldi, M and FitzGerald, JA and Crispie, F and Cotter, PD and Aranaz, P}, title = {Pediococcus acidilactici CECT 9879 (pA1c®) and heat inactivated pA1c® (pA1c® HI) ameliorate gestational diabetes mellitus in mice.}, journal = {Life sciences}, volume = {362}, number = {}, pages = {123359}, doi = {10.1016/j.lfs.2024.123359}, pmid = {39761739}, issn = {1879-0631}, mesh = {Animals ; Female ; Pregnancy ; Mice ; *Diabetes, Gestational/metabolism/microbiology ; *Mice, Inbred C57BL ; *Probiotics/therapeutic use/administration & dosage ; *Gastrointestinal Microbiome ; *Pediococcus acidilactici/metabolism ; Insulin Resistance ; Blood Glucose/metabolism ; Hot Temperature ; }, abstract = {AIMS: Gestational diabetes mellitus (GDM) is the most common complication of pregnancy and is known to be associated with an increased risk of postpartum metabolic disease. Based on the important role that the intestinal microbiota plays in blood glucose regulation and insulin sensitivity, supplementation of probiotic and postbiotic strains could improve glucose metabolism and tolerance in GDM.

MAIN METHODS: 56 4-week-old female C57BL/6J-mice were divided into 4 groups (n = 14 animals/group): control (CNT), high-fat/high-sucrose (HFS), pA1c® alive (pA1c®) and heat-inactivated pA1c® (pA1c®HI). Serum biochemical parameters were analyzed, gene expression analyses were conducted, and fecal microbiota composition was evaluated by shot-gun sequencing.

KEY FINDINGS: pA1c®- and pA1c® HI-supplemented groups presented reduced fasting blood glucose levels and reduced insulin resistance during gestation and exhibited lower visceral adiposity and increased muscle tissue, together with an improvement in intrahepatic TGs content and ALT levels. Liver gene expression analyses demonstrated that pA1c® and pA1c® HI activities were mediated by modulation of the insulin receptor, but also by an overexpression of beta-oxidation genes, and downregulation of fatty acid biosynthesis genes. Shot-gun metagenomics demonstrated that Pediococcus acidilactici was detected in the feces of all the pA1c® and pA1c® HI-group after the supplementation period (75 % of the microbial profile was Pediococcus acidilactici) in only nine weeks of supplementation, and modulated gut microbiota composition.

SIGNIFICANCE: These results may be considered as future perspectives for the development of preventive, even therapeutic options for GDM based on hyperglycemia reduction, blood glucose regulation, hepatic steatosis attenuation and insulin resistance alleviation.}, } @article {pmid39427267, year = {2025}, author = {Singh, AB and Paul, T and Shukla, SP and Kumar, S and Kumar, S and Kumar, G and Kumar, K}, title = {Gut microbiome as biomarker for triclosan toxicity in Labeo rohita: bioconcentration, immunotoxicity and metagenomic profiling.}, journal = {Ecotoxicology (London, England)}, volume = {34}, number = {1}, pages = {102-111}, pmid = {39427267}, issn = {1573-3017}, support = {DST/TMD-EWO-WTI/2K19/EWFH/2019/214//Department of Science and Technology, Ministry of Science and Technology, India/ ; }, mesh = {Animals ; *Triclosan/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Water Pollutants, Chemical/toxicity ; *Cyprinidae ; *Biomarkers ; Metagenomics ; }, abstract = {Triclosan (TCS) is a lipophilic, broad spectrum antimicrobial agent commonly used in personal care products with a projected continuous escalation in aquatic environments in the post COVID 19 era. There is rich documentation in the literature on the alteration of physiological responses in fish due to TCS exposure; however, studies on gut associated bacteria of fish are still scarce. This is the first attempt to determine changes in bacterial community structure due to exposure of TCS on Labeo rohita, a commercially essential freshwater species, using 16S V3-V4 region ribosomal RNA (rRNA) next-generation sequencing (NGS). Chronic exposure of TCS at environmentally realistic concentrations viz. 1/5th (T1: 0.129 mg/L) and 1/10th (T2: 0.065 mg/L) of LC50 for 28 days resulted in the dose dependent bioconcentration of TCS in the fish gut. Prolonged exposure to TCS leads to disruption of gut bacteria evidenced by down regulation of the host immune system. Additionally, high-throughput sequencing analysis showed alternation in the abundance and diversity of microbial communities in the gut, signifying Proteobacteria and Verrucomicrobia as dominant phyla. Significant changes were also observed in the relative abundance of Chloroflexi and Gammatimonadetes phyla in TCS exposed groups. The study revealed that gut microbiome can be used as a biomarker in assessing the degree of TCS toxicity in commercially important fish species.}, } @article {pmid39181210, year = {2025}, author = {Zhang, YH and Xie, R and Dai, CS and Gao, HW and Zhou, G and Qi, TT and Wang, WY and Wang, H and Cui, YM}, title = {Thyroid hormone receptor-beta agonist HSK31679 alleviates MASLD by modulating gut microbial sphingolipids.}, journal = {Journal of hepatology}, volume = {82}, number = {2}, pages = {189-202}, doi = {10.1016/j.jhep.2024.08.008}, pmid = {39181210}, issn = {1600-0641}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Sphingolipids/metabolism ; *Thyroid Hormone Receptors beta/agonists/metabolism ; Male ; Humans ; Spiro Compounds/pharmacology/administration & dosage/therapeutic use ; Double-Blind Method ; Disease Models, Animal ; Liver/metabolism/drug effects ; Mice, Inbred C57BL ; Pyridazines ; Uracil/analogs & derivatives ; }, abstract = {BACKGROUND & AIMS: As the first approved medication for metabolic dysfunction-associated steatohepatitis (MASH), the thyroid hormone receptor-β (THR-β) agonist MGL-3196 (resmetirom) has garnered much attention as a liver-directed, bioactive oral drug. However, studies on MGL-3196 have also identified remarkable heterogeneity of individual clinical efficacy and its interference with gut microbiota in host hepatoenteral circulation remains to be elucidated.

METHODS: We compared MASH attenuation by MGL-3196 and its derivative drug HSK31679 between germ-free (GF) and specific-pathogen free (SPF) mice to evaluate the role of gut microbiota. Then cross-omics analyses of microbial metagenome, metabolome and single-cell RNA-sequencing were applied to a randomized, double-blind, placebo-controlled multiple ascending dose cohort receiving HSK31679 treatment (n = 32) or placebo (n = 8), to comprehensively investigate the altered gut microbiota metabolism and circulating immune signatures.

RESULTS: HSK31679 outperformed MGL-3196 in ameliorating MASH diet-induced steatohepatitis of SPF mice but not GF mice. In the multiple ascending dose cohort of HSK31679, the relative abundance of B. thetaiotaomicron was significantly enriched, impairing glucosylceramide synthase (GCS)-catalyzed monoglucosylation of microbial Cer(d18:1/16:0) and Cer(d18:1/24:1). In contrast to the non-inferior effect of MGL-3196 and HSK31679 on MASH resolution in GF[BTΔGCS] mice, HSK31679 led to superior benefit on steatohepatitis in GF[BTWT] mice, due to its steric hindrance of R123 and Y401 of gut microbial GCS. For participants with high fecal GCS activity, the administration of 160 mg HSK31679 induced a shift in peripheral compartments towards an immunosuppressive niche, characterized by decreased CD8α[+] dendritic cells and MINCLE[+] macrophages.

CONCLUSIONS: This study provided novel insights into the gut microbiota that are key to the efficacy of HSK31679 treatment, revealing microbial GCS as a potential predictive biomarker in MASH, as well as a new target for further microbiota-based treatment strategies for MASH.

IMPACT AND IMPLICATIONS: Remarkable heterogeneity in individual clinical efficacy of thyroid hormone receptor-β agonists and their interferences with the microbiome in host hepatoenteral circulation are poorly understood. In our current germ-free mouse models and a randomized, double-blind, multiple-dose cohort study, we identified microbial glucosylceramide synthase as a key mechanistic node in the resolution of metabolic dysfunction-associated steatohepatitis. Microbial glucosylceramide synthase activity could be a predictive biomarker of response to HSK31679 treatment or a new target for microbiota-based therapeutics in metabolic dysfunction-associated steatohepatitis.}, } @article {pmid39823339, year = {2025}, author = {van der Loos, LM and Steinhagen, S and Stock, W and Weinberger, F and D'hondt, S and Willems, A and De Clerck, O}, title = {Low functional change despite high taxonomic turnover characterizes the Ulva microbiome across a 2000-km salinity gradient.}, journal = {Science advances}, volume = {11}, number = {3}, pages = {eadr6070}, doi = {10.1126/sciadv.adr6070}, pmid = {39823339}, issn = {2375-2548}, mesh = {*Ulva/genetics ; *Salinity ; *Microbiota ; Bacteria/genetics/classification/metabolism ; Metagenome ; Metagenomics/methods ; }, abstract = {The green seaweed Ulva relies on associated bacteria for morphogenesis and is an important model to study algal-bacterial interactions. Ulva-associated bacteria exhibit high turnover across environmental gradients, leading to the hypothesis that bacteria contribute to the acclimation potential of the host. However, the functional variation of these bacteria in relation to environmental changes remains unclear. We analyzed 91 Ulva samples across a 2000-kilometer Atlantic-Baltic Sea salinity gradient using metagenomic sequencing. Metabolic reconstruction of 639 metagenome-assembled genomes revealed widespread potential for carbon, nitrogen, sulfur, and vitamin metabolism. Although the R[2] value for salinity explained 70% of taxonomic variation, it accounted only for 17% of functional variation. The limited variation was attributed to typical high-salinity bacteria exhibiting enrichment in genes for thiamine, pyridoxal, and betaine biosynthesis, which likely contribute to stress mitigation and osmotic homeostasis in response to salinity variations. Our results emphasize the importance of functional profiling to understand the seaweed holobiont and its collective response to environmental change.}, } @article {pmid39823335, year = {2025}, author = {Santoro, EP and Cárdenas, A and Villela, HDM and Vilela, CLS and Ghizelini, AM and Duarte, GAS and Perna, G and Saraiva, JP and Thomas, T and Voolstra, CR and Peixoto, RS}, title = {Inherent differential microbial assemblages and functions associated with corals exhibiting different thermal phenotypes.}, journal = {Science advances}, volume = {11}, number = {3}, pages = {eadq2583}, doi = {10.1126/sciadv.adq2583}, pmid = {39823335}, issn = {2375-2548}, mesh = {*Anthozoa/microbiology/metabolism/physiology ; Animals ; *Microbiota ; *Phenotype ; Symbiosis ; Metagenomics/methods ; Bacteria/metabolism/genetics ; }, abstract = {Certain coral individuals exhibit enhanced resistance to thermal bleaching, yet the specific microbial assemblages and their roles in these phenotypes remain unclear. We compared the microbial communities of thermal bleaching-resistant (TBR) and thermal bleaching-sensitive (TBS) corals using metabarcoding and metagenomics. Our multidomain approach revealed stable distinct microbial compositions between thermal phenotypes. Notably, TBR corals were inherently enriched with microbial eukaryotes, particularly Symbiodiniaceae, linked to photosynthesis, and the biosynthesis of antibiotic and antitumor compounds and glycosylphosphatidylinositol-anchor proteins, crucial for cell wall regulation and metabolite exchange. In contrast, TBS corals were dominated by bacterial metabolic genes related to nitrogen, amino acid, and lipid metabolism. The inherent microbiome differences between TBR and TBS corals, already observed before thermal stress, point to distinct holobiont phenotypes associated to thermal bleaching resistance, offering insights into mechanisms underlying coral response to climate-induced stress.}, } @article {pmid39821458, year = {2025}, author = {Mathew, DE and Soni, A and Dhimmar, A and Gajjar, A and Parab, AS and Phakatkar, SS and Sahastrabudhe, H and Manohar, CS and Shinde, PB and Mantri, VA}, title = {Characterization, Bio-Prospection, and Comparative Metagenomics of Bacterial Communities Revealing the Predictive Functionalities in Wild and Cultured Samples of Industrially Important Red Seaweed Gracilaria dura.}, journal = {Current microbiology}, volume = {82}, number = {2}, pages = {85}, pmid = {39821458}, issn = {1432-0991}, support = {HCP 024//Council for Scientific and Industrial Research, India/ ; }, mesh = {*Gracilaria/microbiology ; *Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; *Phylogeny ; Microbiota ; Seaweed/microbiology ; Metagenome ; Proteobacteria/genetics/isolation & purification/classification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The present study explores the microbial community associated with the industrially important red seaweed Gracilaria dura to determine the diversity and biotechnological potential through culture and metagenomics approaches. In the first part of the investigation, we isolated and characterized 75 bacterial morphotypes, with varied colony characteristics and metabolic diversity from the wild seaweed. Phylogenetic analysis identified isolates in Proteobacteria, Firmicutes, and Actinobacteria, with Bacillus sp. being prevalent. B. licheniformis and Streptomyces sp. were notable in producing important enzymes like L-asparaginase, and polysaccharide lyases. Antimicrobial activity was significant in 21% of isolates, effective against seaweed pathogens such as Vibrio and Xanthomonas. Rhodococcus pyridinivorans showed strong pyridine degradation, suggesting bioremediation potential. Several isolates exhibited phosphate solubilization and nitrate indicating the roles of bacteria as algal growth promoters and biocontrol agents. Subsequent metagenome analysis of wild and cultured samples provides insights into bacterial communities associated with G. dura, revealing their distribution and functional roles. Proteobacteria (~ 95%) dominated the communities, further bacterial groups involved in algal growth, carpospore liberation, stress resistance, biogeochemical cycles, and biomedical applications were identified. A notable difference in bacteriomes was observed between the samples, with 25% remaining stable. The samples are cultured in the lab to generate seedlings for farming and serve as germplasm storage during the monsoon season. Microbiome surveys are crucial for understanding the association of pathogens and the overall health of the seedlings, supporting successful seaweed farming. Our findings provide valuable insights into G. dura-associated microbial communities and their role in algal growth, which has aquacultural implications.}, } @article {pmid39820425, year = {2025}, author = {Huang, H and Cheng, Z and Wang, Y and Qiao, G and Wang, X and Yue, Y and Gao, Q and Peng, S}, title = {Multi-omics dataset of individual variations in growth performance of large yellow croaker.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {90}, pmid = {39820425}, issn = {2052-4463}, mesh = {Animals ; *Perciformes/genetics/growth & development ; *Gastrointestinal Microbiome ; Metabolomics ; Transcriptome ; Metagenomics ; China ; Multiomics ; }, abstract = {Large yellow croaker (Larimichthys crocea) is a highly economically important marine fish species in China. However, substantial individual variations in growth performance have emerged as a limiting factor for the sustainable development of the large yellow croaker industry. Gut microbiota plays a crucial role in fish growth and development by regulating metabolic processes. To explore these dynamics, we employed metagenomics, transcriptomics, and untargeted metabolomics to comprehensively analyze the structure of the intestinal microbiome and its relationship with intestinal metabolism and host gene expression. We constructed association models for "gut microbiota-differentially expressed genes", "differentially expressed genes-metabolites," and "gut microbiota-metabolites." Sequencing data and LC-MS/MS raw data have been deposited in NCBI and MetaboLights databases for public access. Our findings offer critical insights into the molecular mechanisms underlying growth variations in L. crocea and provide valuable data for the selective breeding of improved strains.}, } @article {pmid39819730, year = {2025}, author = {Liu, X and Tang, Y and Chen, H and Liu, JX and Sun, HZ}, title = {Rumen DNA virome and its relationship with feed efficiency in dairy cows.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {14}, pmid = {39819730}, issn = {2049-2618}, support = {32322077//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Rumen/virology/microbiology ; Cattle ; *Virome ; *High-Throughput Nucleotide Sequencing ; *Animal Feed/virology ; Female ; DNA, Viral/genetics ; Metagenome ; Viruses/classification/genetics/isolation & purification ; }, abstract = {BACKGROUND: The rumen harbors a diverse virome that interacts with other microorganisms, playing pivotal roles in modulating metabolic processes within the rumen environment. However, the characterization of rumen viruses remains incomplete, and their association with production traits, such as feed efficiency (FE), has not been documented. In this study, rumen fluid from 30 Chinese Holstein dairy cows was analyzed using next-generation sequencing (NGS) and High-Fidelity (HiFi) sequencing to elucidate the rumen DNA virome profile and uncover potential viral mechanisms influencing FE.

RESULTS: Integrated NGS and HiFi sequencing enhanced the length, completeness, and resolution of viral operational taxonomic units (vOTUs) compared to NGS. A total of 6,922 vOTUs were identified, including 4,716 lytic and 1,961 temperate vOTUs. At the family level, lytic viruses were predominantly from Siphoviridae (30.35%) and Schitoviridae (23.93%), while temperate viruses were primarily Siphoviridae (67.21%). The study annotated 2,382 auxiliary metabolic genes (AMGs), comprising 1,752 lytic virus-associated AMGs across 51 functional categories and 589 temperate virus-associated AMGs across 29 categories. Additionally, 2,232 vOTU-host metagenome-assembled genome (hMAG) linkages were predicted, with Firmicutes_A (33.60%) and Bacteroidota (33.24%) being the most prevalent host phyla. Significant differences in viral populations were observed between high and low FE groups across multiple taxonomic levels (P < 0.05). Two pathways were proposed to explain how rumen viruses might modulate FE: (1) Lytic viruses could lyse beneficial host bacteria linked to favorable cattle phenotypes, such as vOTU1836 targeting Ruminococcaceae, resulting in diminished organic acid production and consequently lower FE; (2) AMG-mediated host metabolism modulation, exemplified by GT2 carried by vOTU0897, which may enhance Lachnospiraceae fermentation capacity, increasing organic acid production and thereby improving FE.

CONCLUSIONS: This study constructed a comprehensive rumen DNA virome profile for Holstein dairy cows, elucidating the structural and functional complexity of rumen viruses, the roles of AMGs, and vOTU-hMAG linkages. The integration of these data offers novel insights into the mechanisms by which rumen viruses may regulate nutrient utilization, potentially influencing FE in dairy cows. Video Abstract.}, } @article {pmid39819379, year = {2025}, author = {Terzin, M and Robbins, SJ and Bell, SC and Lê Cao, KA and Gruber, RK and Frade, PR and Webster, NS and Yeoh, YK and Bourne, DG and Laffy, PW}, title = {Gene content of seawater microbes is a strong predictor of water chemistry across the Great Barrier Reef.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {11}, pmid = {39819379}, issn = {2049-2618}, mesh = {*Seawater/microbiology ; *Coral Reefs ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics/methods ; *Microbiota/genetics ; Archaea/genetics/classification ; Salinity ; Seasons ; Synechococcus/genetics/classification ; }, abstract = {BACKGROUND: Seawater microbes (bacteria and archaea) play essential roles in coral reefs by facilitating nutrient cycling, energy transfer, and overall reef ecosystem functioning. However, environmental disturbances such as degraded water quality and marine heatwaves, can impact these vital functions as seawater microbial communities experience notable shifts in composition and function when exposed to stressors. This sensitivity highlights the potential of seawater microbes to be used as indicators of reef health. Microbial indicator analysis has centered around measuring the taxonomic composition of seawater microbial communities, but this can obscure heterogeneity of gene content between taxonomically similar microbes, and thus, microbial functional genes have been hypothesized to have more scope for predictive potential, though empirical validation for this hypothesis is still pending. Using a metagenomics study framework, we establish a functional baseline of seawater microbiomes across offshore Great Barrier Reef (GBR) sites to compare the diagnostic value between taxonomic and functional information in inferring continuous physico-chemical metrics in the surrounding reef.

RESULTS: Integrating gene-centric metagenomics analyses with 17 physico-chemical variables (temperature, salinity, and particulate and dissolved nutrients) across 48 reefs revealed that associations between microbial functions and environmental parameters were twice as stable compared to taxonomy-environment associations. Distinct seasonal variations in surface water chemistry were observed, with nutrient concentrations up to threefold higher during austral summer, explained by enhanced production of particulate organic matter (POM) by photoautotrophic picocyanobacteria, primarily Synechococcus. In contrast, nutrient levels were lower in winter, and POM production was also attributed to Prochlorococcus. Additionally, heterotrophic microbes (e.g., Rhodospirillaceae, Burkholderiaceae, Flavobacteriaceae, and Rhodobacteraceae) were enriched in reefs with elevated dissolved organic carbon (DOC) and phytoplankton-derived POM, encoding functional genes related to membrane transport, sugar utilization, and energy metabolism. These microbes likely contribute to the coral reef microbial loop by capturing and recycling nutrients derived from Synechococcus and Prochlorococcus, ultimately transferring nutrients from picocyanobacterial primary producers to higher trophic levels.

CONCLUSION: This study reveals that functional information in reef-associated seawater microbes more robustly associates with physico-chemical variables than taxonomic data, highlighting the importance of incorporating microbial function in reef monitoring initiatives. Our integrative approach to mine for stable seawater microbial biomarkers can be expanded to include additional continuous metrics of reef health (e.g., benthic cover of corals and macroalgae, fish counts/biomass) and may be applicable to other large-scale reef metagenomics datasets beyond the GBR. Video Abstract.}, } @article {pmid39680298, year = {2025}, author = {Han, L and Lin, C and Lan, Y and Hua, Y and Wu, J and Fan, Z and Li, Y}, title = {Metagenomic Analysis of Gut Microbiome of Persistent Pulmonary Hypertension of the Newborn.}, journal = {Cardiovascular toxicology}, volume = {25}, number = {1}, pages = {135-147}, pmid = {39680298}, issn = {1559-0259}, support = {2021YFQ0061//Technology Project of Sichuan Province of China/ ; 82270249//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Infant, Newborn ; *Gastrointestinal Microbiome ; *Metagenomics ; *Feces/microbiology ; Case-Control Studies ; Male ; *Bacteria/genetics/isolation & purification/classification/metabolism/growth & development ; Female ; Persistent Fetal Circulation Syndrome/microbiology/genetics ; Dysbiosis ; Host-Pathogen Interactions ; Intestines/microbiology ; }, abstract = {Persistent pulmonary hypertension of the newborn (PPHN) is one of the most common diseases in the neonatal intensive care unit which severely affects neonatal survival. Gut microbes play an increasingly important role in human health, but there are rarely reported how gut microbiota contribute to PPHN. In our study, the metagenomic sequencing of feces from 12 PPHN's neonates and 8 controls were performed to expose the relation between neonatal gut microbes and PPHN disease. Firstly, we found that the abundance of Actinobacteria, Proteobacteria, Bacteroidetes were significantly increased in PPHN compared with controls, but the Firmicutes components was reduced. And some pathogenic strains (like Vibrio metschnikovii) were significantly enriched in the PPHN compared with controls. Secondly, functional annotation of genes found that PPHN up-regulated transmembrane transport, but down-regulated ribosome and ATP binding. Lastly, microbial metabolic pathway enrichment analysis indicated that some metabolic pathway in PPHN were conflicting and contradictory, showed that an abnormally increased metabolism, disturbed protein synthesis and genomic instability in the PPHN neonate. Our results contribute to understanding the changes in the species and function of gut microbiota in PPHN, thus providing a theoretical basis for the explanation and treatment of PPHN.}, } @article {pmid39520618, year = {2025}, author = {Men, Z and Chen, Z and Gu, X and Wang, Y and Zhang, X and Fang, F and Shen, M and Huang, S and Wu, S and Zhou, L and Bai, Z}, title = {Clinical relevance of lung microbiota composition in critically ill children with acute lower respiratory tract infections: insights from a retrospective analysis of metagenomic sequencing.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {44}, number = {1}, pages = {83-98}, pmid = {39520618}, issn = {1435-4373}, support = {H2023106//Medical Research Project of Jiangsu Provincial Commission of Health/ ; SKY2022178//Science and Technology Development Project of Suzhou/ ; SKJY2021108//Science and Technology Development Project of Suzhou/ ; BK20211077//Natural Science Foundation of Jiangsu Province/ ; BE2023714//Science and Technology Support Program of Jiangsu Province/ ; GSWS2019015//Gusu Health Talent Program/ ; ML13100423//Suzhou Medical College Clinician Scientist Program/ ; }, mesh = {Humans ; Retrospective Studies ; Male ; Female ; Child, Preschool ; *Metagenomics/methods ; Child ; *Lung/microbiology ; Infant ; *Microbiota/genetics ; *Respiratory Tract Infections/microbiology ; *Critical Illness ; *Bronchoalveolar Lavage Fluid/microbiology ; High-Throughput Nucleotide Sequencing ; Bacteria/classification/genetics/isolation & purification ; Prognosis ; Metagenome ; Severity of Illness Index ; Clinical Relevance ; }, abstract = {PURPOSE: Acute lower respiratory tract infections (ALRIs) is a leading cause of child mortality worldwide. Metagenomic next-generation sequencing (mNGS) identifies ALRIs pathogens and explores the lung microbiota's role in disease severity and clinical outcomes. This study examines the association between lung microbiota and ALRIs outcomes in children, exploring its potential as a prognostic biomarker.

METHODS: We retrospectively analyzed mNGS data from the bronchoalveolar lavage fluid (BALF) of 83 pediatric ALRIs patients from 2019 to 2023. Microbial diversity and relative abundances of specific taxa were compared between survivor and non-survivor groups, as well as between varying severity levels. LEfSe was employed to identify key biomarkers related to survival and disease severity.

RESULTS: Among the 83 patients, 68 survived and 15 died. Patients were also divided into a low severity group (n = 38) and a moderate-to-very-high severity group (n = 45) according to mPIRO score at admission. Significant differences in beta diversity were observed between the survival groups and across different severity levels. Prevotella, Haemophilus and Veillonella exhibited higher abundances in both the survivor and low severity groups, suggesting their potential as predictors of better outcomes. Conversely, Enterococcus and Acinetobacter baumannii were more prevalent in the non-survivor and moderate-to-very-high severity groups. Additionally, Streptococcus pneumoniae and Streptococcus mitis showed increased abundances in survivors. LEfSe further revealed that these microorganisms may predict outcomes and severity in ALRIs.

CONCLUSION: Our findings underscore the complex relationship between lung microbiota and ALRIs, with specific microbial profiles associated with disease severity and clinical outcomes. This underscores the need for further research to explore and validate its prognostic predictive capacity.

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid39096471, year = {2025}, author = {Maharana, B and Mahalle, S and Bhende, R and Dafale, NA}, title = {Repercussions of Prolonged Pesticide Use on Natural Soil Microbiome Dynamics Using Metagenomics Approach.}, journal = {Applied biochemistry and biotechnology}, volume = {197}, number = {1}, pages = {73-93}, pmid = {39096471}, issn = {1559-0291}, mesh = {*Soil Microbiology ; *Microbiota/drug effects ; *Pesticides ; *Metagenomics ; Soil/chemistry ; Bacteria/genetics/drug effects/isolation & purification/classification ; }, abstract = {The residual pesticides in soil can affect the natural microbiome composition and genetic profile that drive nutrient cycling and soil fertility. In the present study, metagenomic approach was leveraged to determine modulations in nutrient cycling and microbial composition along with connected nexus of pesticide, antibiotic, and heavy metal resistance in selected crop and fallow soils having history of consistent pesticide applications. GC-MS analysis estimated residuals of chlorpyrifos, hexachlorbenzene, and dieldrin showing persistent nature of pesticides that pose selective pressure for microbial adaptation. Taxonomic profiling showed increased abundance of pesticide degrading Streptomyces, Xanthomonas, Cupriavidus, and Pseudomonas across the selected soils. Genes encoding for pesticide degrading cytochrome p450, organophosphorus hydrolase, aldehyde dehydrogenase, and oxidase were predominant and positively correlated with Bacillus, Sphingobium, and Burkholderia. Nitrogen-fixing genes (nifH, narB, and nir) were relatively less abundant in crop soils, correlating to the decrease in nitrogen-fixing bacteria (Anabaena, Pantoea, and Azotobacter). Microbial enzymes involved in carbon (pfkA, gap, pgi, and tpiA) and phosphorus cycle (gmbh and phnJ) were significantly higher in crop soils indicating extensive utilization of pesticide residuals as a nutrient source by the indigenous soil microbiota. Additionally, presence of antibiotic and heavy metal resistance genes suggested potential cross-resistance under pressure from pesticide residues. The results implied selective increase in pesticide degrading microbes with decrease in beneficial bacteria that resulted in reduced soil health and fertility. The assessment of agricultural soil microbial profile will provide a framework to develop sustainable agriculture practices to conserve soil health and fertility.}, } @article {pmid39724786, year = {2025}, author = {Ma, X and Zhang, J and Jiang, Q and Li, YX and Yang, G}, title = {Human microbiome-derived peptide affects the development of experimental autoimmune encephalomyelitis via molecular mimicry.}, journal = {EBioMedicine}, volume = {111}, number = {}, pages = {105516}, pmid = {39724786}, issn = {2352-3964}, mesh = {*Encephalomyelitis, Autoimmune, Experimental/immunology/etiology/microbiology/metabolism ; Animals ; Humans ; *Molecular Mimicry ; Mice ; *Myelin-Oligodendrocyte Glycoprotein/immunology ; *Gastrointestinal Microbiome ; Multiple Sclerosis/etiology/immunology/microbiology/metabolism ; Peptides/immunology/chemistry ; Disease Models, Animal ; Protein Binding ; CD4-Positive T-Lymphocytes/immunology/metabolism ; Receptors, Antigen, T-Cell/metabolism ; Microbiota ; Peptide Fragments/immunology/metabolism ; Histocompatibility Antigens Class II/metabolism/immunology ; Female ; Computational Biology/methods ; }, abstract = {BACKGROUND: Gut commensal microbiota has been identified as a potential environmental risk factor for multiple sclerosis (MS), and numerous studies have linked the commensal microorganism with the onset of MS. However, little is known about the mechanisms underlying the gut microbiome and host-immune system interaction.

METHODS: We employed bioinformatics methodologies to identify human microbial-derived peptides by analyzing their similarity to the MHC II-TCR binding patterns of self-antigens. Subsequently, we conducted a range of in vitro and in vivo assays to assess the encephalitogenic potential of these microbial-derived peptides.

FINDINGS: We analyzed 304,246 human microbiome genomes and 103 metagenomes collected from the MS cohort and identified 731 nonredundant analogs of myelin oligodendrocyte glycoprotein peptide 35-55 (MOG35-55). Of note, half of these analogs could bind to MHC II and interact with TCR through structural modeling of the interaction using fine-tuned AlphaFold. Among the 8 selected peptides, the peptide (P3) shows the ability to activate MOG35-55-specific CD4[+] T cells in vitro. Furthermore, P3 shows encephalitogenic capacity and has the potential to induce EAE in some animals. Notably, mice immunized with a combination of P3 and MOG35-55 develop severe EAE. Additionally, dendritic cells could process and present P3 to MOG35-55-specific CD4[+] T cells and activate these cells.

INTERPRETATION: Our data suggests the potential involvement of a MOG35-55-mimic peptide derived from the gut microbiota as a molecular trigger of EAE pathogenesis. Our findings offer direct evidence of how microbes can initiate the development of EAE, suggesting a potential explanation for the correlation between certain gut microorganisms and MS prevalence.

FUNDING: National Natural Science Foundation of China (82371350 to GY).}, } @article {pmid39647263, year = {2025}, author = {Fu, Y and Gou, W and Zhong, H and Tian, Y and Zhao, H and Liang, X and Shuai, M and Zhuo, LB and Jiang, Z and Tang, J and Ordovas, JM and Chen, YM and Zheng, JS}, title = {Diet-gut microbiome interaction and its impact on host blood glucose homeostasis: a series of nutritional n-of-1 trials.}, journal = {EBioMedicine}, volume = {111}, number = {}, pages = {105483}, pmid = {39647263}, issn = {2352-3964}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Blood Glucose/metabolism ; *Homeostasis ; Female ; Male ; Adult ; Metagenomics/methods ; Diet ; Middle Aged ; Metagenome ; Dietary Carbohydrates/metabolism ; }, abstract = {BACKGROUND: The interplay between diet and gut microbiome substantially influences host metabolism, but uncertainties remain regarding their relationships tailored for each subject given the huge inter-individual variability. Here we aim to investigate diet-gut microbiome interaction at single-subject resolution and explore its effects on blood glucose homeostasis.

METHODS: We conducted a series of nutritional n-of-1 trials (NCT04125602), in which 30 participants were assigned high-carbohydrate (HC) and low-carbohydrate (LC) diets in a randomized sequence across 3 pair of cross-over periods lasting 72 days. We used shotgun metagenomic sequencing and continuous glucose monitoring systems to profile the gut microbiome and blood glucose, respectively. An independent cohort of 1219 participants with available metagenomics data are included as a validation cohort.

FINDINGS: We demonstrated that the gut microbiome exhibited both intra-individually dynamic and inter-individually personalized signatures during the interventions. At the single-subject resolution, we observed person-specific response patterns of gut microbiota to interventional diets. Furthermore, we discovered a personal gut microbial signature represented by a carb-sensitivity score, which was closely correlated with glycemic phenotypes during the HC intervention, but not LC intervention. We validate the role of this score in the validation cohort and find that it reflects host glycemic sensitivity to the personal gut microbiota profile when sensing the dietary carbohydrate inputs.

INTERPRETATION: Our finding suggests that the HC diet modulates gut microbiota in a person-specific manner and facilitates the connection between gut microbiota and glycemic sensitivity. This study represents a new paradigm for investigating the diet-microbiome interaction in the context of precision nutrition.

FUNDING: This work was supported by the National Key R&D Program of China, National Natural Science Foundation of China and Zhejiang Provincial Natural Science Foundation of China.}, } @article {pmid39644773, year = {2025}, author = {Hu, Y and Hu, X and Jiang, L and Luo, J and Huang, J and Sun, Y and Qiao, Y and Wu, H and Zhou, S and Li, H and Li, J and Zhou, L and Zheng, S}, title = {Microbiome and metabolomics reveal the effect of gut microbiota on liver regeneration of fatty liver disease.}, journal = {EBioMedicine}, volume = {111}, number = {}, pages = {105482}, pmid = {39644773}, issn = {2352-3964}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Liver Regeneration ; Mice ; *Metabolomics/methods ; *Fatty Liver/metabolism/etiology/microbiology ; Male ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Metabolome ; Hepatectomy ; Mice, Inbred C57BL ; Metagenomics/methods ; Liver/metabolism ; RNA, Ribosomal, 16S/genetics ; Akkermansia ; }, abstract = {BACKGROUND: Metabolic dysfunction-associated fatty liver disease (MAFLD) is associated with impaired regenerative capacity and poor postoperative prognosis following hepatectomy. Previous research has highlighted the importance of the gut-liver axis in the physiological and pathological processes of the liver. However, the contribution of gut bacteria to the regeneration of livers with MAFLD and its metabolic regulatory mechanisms remain elusive.

METHODS: Partial hepatectomy (PHx) was performed on C57Bl/6J mice fed with high-fat diet (HFD) for 12 weeks. Pathological examination, immunohistochemistry, and qRT-PCR analysis were performed to assess the severity of steatosis and proliferative potential. The gut microbiome was examined by 16S rRNA gene sequencing and shotgun metagenomics, whereas liver metabolomics was analysed via untargeted and targeted metabolomics using liquid chromatography-tandem mass spectrometry (LC-MS).

FINDINGS: HFD-induced hepatic steatosis in mice led to impaired liver regeneration following PHx. The gut microbiota and liver metabolites were altered along with the liver regeneration process. Longitudinal time-series analysis revealed dynamic alterations in these data, whereas correlation analysis screened out bacterial candidates that potentially influence liver regeneration in MAFLD by modulating metabolic pathways. Among these bacteria, the dominant bacterium Akkermansia was selected for subsequent investigation. MAFLD mice gavaged with Akkermansia muciniphila (A. muciniphila) exhibited reduced liver lipid accumulation and accelerated liver regeneration, possibly through the regulation of the tricarboxylic acid (TCA) cycle.

INTERPRETATION: These data demonstrated the interplay between the gut microbiome, liver metabolomics, and liver regeneration in mice with MAFLD. A. muciniphila has the potential to serve as a clinical intervention agent to accelerate postoperative recovery in MAFLD.

FUNDING: This work was supported by the Research Project of Jinan Microecological Biomedicine Shandong Laboratory [JNL-2022008B]; the Zhejiang Provincial Natural Science Foundation of China [LZ21H180001]; the Fundamental Research Funds for the Central Universities [No. 2022ZFJH003].}, } @article {pmid39813598, year = {2025}, author = {Ren, M and Xia, Y and Pan, H and Zhou, X and Yu, M and Ji, F}, title = {Duodenal-jejunal bypass ameliorates MASLD in rats by regulating gut microbiota and bile acid metabolism through FXR pathways.}, journal = {Hepatology communications}, volume = {9}, number = {2}, pages = {}, doi = {10.1097/HC9.0000000000000615}, pmid = {39813598}, issn = {2471-254X}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Receptors, Cytoplasmic and Nuclear/metabolism ; Rats ; *Bile Acids and Salts/metabolism ; *Duodenum/surgery/metabolism/microbiology ; Male ; *Fecal Microbiota Transplantation ; Jejunum/surgery/metabolism ; Rats, Sprague-Dawley ; Disease Models, Animal ; Fatty Liver/metabolism ; Anti-Bacterial Agents/pharmacology ; Diet, High-Fat ; Gastric Bypass ; Insulin Resistance ; }, abstract = {BACKGROUND: Although bariatric and metabolic surgical methods, including duodenal-jejunal bypass (DJB), were shown to improve metabolic dysfunction-associated steatotic liver disease (MASLD) in clinical trials and experimental rodent models, their underlying mechanisms remain unclear. The present study therefore evaluated the therapeutic effects and mechanisms of action of DJB in rats with MASLD.

METHODS: Rats with MASLD were randomly assigned to undergo DJB or sham surgery. Rats were orally administered a broad-spectrum antibiotic cocktail (Abx) or underwent fecal microbiota transplantation to assess the role of gut microbiota in DJB-induced improvement of MASLD. Gut microbiota were profiled by 16S rRNA gene sequencing and metagenomic sequencing, and bile acids (BAs) were analyzed by BA-targeted metabolomics.

RESULTS: DJB alleviated hepatic steatosis and insulin resistance in rats with diet-induced MASLD. Abx depletion of bacteria abrogated the ameliorating effects of DJB on MASLD. Fecal microbiota transplantation from rats that underwent DJB improved MASLD in high-fat diet-fed recipients by reshaping the gut microbiota, especially by significantly reducing the abundance of Clostridium. This, in turn, suppressed secondary BA biosynthesis and activated the hepatic BA receptor, farnesoid X receptor. Inhibition of farnesoid X receptor attenuated the ameliorative effects of post-DJB microbiota on MASLD.

CONCLUSIONS: DJB ameliorates MASLD by regulating gut microbiota and BA metabolism through hepatic farnesoid X receptor pathways.}, } @article {pmid39812347, year = {2025}, author = {Gustafson, KL and Rodriguez, TR and McAdams, ZL and Coghill, LM and Ericsson, AC and Franklin, CL}, title = {Failure of colonization following gut microbiota transfer exacerbates DSS-induced colitis.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2447815}, doi = {10.1080/19490976.2024.2447815}, pmid = {39812347}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Colitis/microbiology/chemically induced/pathology ; *Dextran Sulfate ; Mice ; *Disease Models, Animal ; *Mice, Inbred C57BL ; *Fecal Microbiota Transplantation ; Bacteria/classification/isolation & purification/genetics/metabolism ; Female ; Specific Pathogen-Free Organisms ; Feces/microbiology ; Inflammatory Bowel Diseases/microbiology ; Male ; }, abstract = {To study the impact of differing specific pathogen-free gut microbiomes (GMs) on a murine model of inflammatory bowel disease, selected GMs were transferred using embryo transfer (ET), cross-fostering (CF), and co-housing (CH). Prior work showed that the GM transfer method and the microbial composition of donor and recipient GMs can influence microbial colonization and disease phenotypes in dextran sodium sulfate-induced colitis. When a low richness GM was transferred to a recipient with a high richness GM via CH, the donor GM failed to successfully colonize, and a more severe disease phenotype resulted when compared to ET or CF, where colonization was successful. By comparing CH and gastric gavage for fecal material transfer, we isolated the microbial component of this effect and determined that differences in disease severity and survival were associated with microbial factors rather than the transfer method itself. Mice receiving a low richness GM via CH and gastric gavage exhibited greater disease severity and higher expression of pro-inflammatory immune mediators compared to those receiving a high richness GM. This study provides valuable insights into the role of GM composition and colonization in disease modulation.}, } @article {pmid39709798, year = {2025}, author = {Wang, RX and Zhou, HB and Gao, JX and Bai, WF and Wang, J and Bai, YC and Jiang, SY and Chang, H and Shi, SL}, title = {Metagenomics and metabolomics to investigate the effect of Amygdalus mongolica oil on intestinal microbiota and serum metabolites in rats.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {136}, number = {}, pages = {156335}, doi = {10.1016/j.phymed.2024.156335}, pmid = {39709798}, issn = {1618-095X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Male ; *Metabolomics ; *Rats, Sprague-Dawley ; Rats ; Metagenomics ; Plant Oils/pharmacology ; Fibrosis ; Kidney/drug effects ; Renal Insufficiency, Chronic/blood/drug therapy/microbiology ; }, abstract = {BACKGROUND: Renal fibrosis (RF) is an inevitable consequence of multiple manifestations of progressive chronic kidney diseases (CKDs). Mechanism of Amygdalus mongolica (Maxim.) in the treatment of RF needs further investigation.

PURPOSE: The study further investigated the potential mechanism of A. mongolica in the treatment of RF.

METHODS: A rat model of RF was induced by unilateral ureteral obstruction (UUO), followed by treatment with varying dosages of A. mongolica oil for 4 weeks. Body weight was measured weekly. We detected serum levels of interleukin (IL)-6, IL-1β, type Ⅲ procollagen (Col-Ⅲ), type IV collagen (Col-Ⅳ), laminin (LN), hyaluronidase (HA), and tissue levels of albumin (ALB), blood urea nitrogen (BUN), creatinine (Cre), superoxide dismutase (SOD), malondialdehyde (MDA), and hydroxyproline (HYP). Shotgun metagenomics analyzed the composition of the intestinal microbiota. High-performance liquid chromatography coupled with a quadrupole-exactive mass spectrometer (HPLC-Q-Exactive-MS) monitored changes in metabolite levels in serum and gut. Multiple reaction monitoring-mass spectrometry (MRM-MS) determined the levels of amino acids in serum.

RESULTS: A. mongolica oil significantly alleviated indicators related to RF (p < 0.05). A. mongolica oil reduced the ratio of Firmicutes to Bacteroidetes and restored the balance of intestinal microbiota in rats with RF. A. mongolica oil modulated levels of metabolites in gut content and serum. It regulated 11 metabolic pathways including arachidonic acid metabolism. Targeted metabolomics of amino acids showed that 17 amino acids were significantly changed by A. mongolica oil, including L-glycine, L-serine and L-glutamine.

CONCLUSION: A. mongolica oil regulates intestinal microbiota and metabolites, restoring amino acid metabolism to treat RF.}, } @article {pmid39591767, year = {2025}, author = {Geng, Q and Wang, Z and Shi, T and Wen, C and Xu, J and Jiao, Y and Diao, W and Gu, J and Wang, Z and Zhao, L and Deng, T and Xiao, C}, title = {Cannabidiol regulates L-carnitine and butyric acid metabolism by modulating the gut microbiota to ameliorate collagen-induced arthritis.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {136}, number = {}, pages = {156270}, doi = {10.1016/j.phymed.2024.156270}, pmid = {39591767}, issn = {1618-095X}, mesh = {Animals ; *Cannabidiol/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Arthritis, Experimental/drug therapy/metabolism ; *Carnitine/pharmacology ; *Butyric Acid/pharmacology ; Rats ; *Dysbiosis/drug therapy ; Male ; *Arthritis, Rheumatoid/drug therapy ; }, abstract = {BACKGROUND: Rheumatoid arthritis (RA) is one of the most common autoimmune diseases, affecting multiple systems in the body. Cannabidiol (CBD) is one of the most medically valuable active ingredients in cannabis. At present, CBD has been shown to alleviate the progression of RA; however, owing to its multiple targets, the mechanism of CBD is not clear.

METHODS: On the basis of the gut microbiota, we explored the mechanism by which CBD inhibits RA progression. Metagenomic and nontargeted metabolomic analyses were used to determine the changes in the intestinal ecology and plasma metabolites of collagen-induced arthritis (CIA) rats after CBD treatment.

RESULTS: CBD reversed gut dysbiosis in CIA rats, notably altering the abundances of Allobaculum_unclassified, Allobaculum_fili, and Prevotella_unclassified. In addition, metabolomic analysis confirmed that CBD increased the contents of butyric acid and L-carnitine. Allobaculum could produce butyric acid and Prevotella could accelerate the metabolism of L-carnitine. In addition, in vitro experiments demonstrated that L-carnitine participated in the regulation of neutrophils, macrophages and RA-fibroblast-like synoviocytes (RA-FLSs), which was consistent with the synovial changes in CIA rats caused by CBD.

CONCLUSION: In summary, CBD increased the plasma contents of butyric acid and L-carnitine by altering the abundances of gut microbiota, thereby inhibiting inflammation in neutrophils, macrophages and RA-FLSs. Our study is the first to explain the mechanism by which CBD alleviates progression in CIA rats from the perspective of gut microbes and metabolites, providing new views into CBD mechanisms, which warrants clinical attention.}, } @article {pmid39810263, year = {2025}, author = {Nychas, E and Marfil-Sánchez, A and Chen, X and Mirhakkak, M and Li, H and Jia, W and Xu, A and Nielsen, HB and Nieuwdorp, M and Loomba, R and Ni, Y and Panagiotou, G}, title = {Discovery of robust and highly specific microbiome signatures of non-alcoholic fatty liver disease.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {10}, pmid = {39810263}, issn = {2049-2618}, mesh = {*Non-alcoholic Fatty Liver Disease/microbiology ; Humans ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Middle Aged ; Bacteria/classification/genetics/isolation & purification ; Machine Learning ; Metagenomics/methods ; Adult ; Obesity/microbiology ; Metagenome ; }, abstract = {BACKGROUND: The pathogenesis of non-alcoholic fatty liver disease (NAFLD) with a global prevalence of 30% is multifactorial and the involvement of gut bacteria has been recently proposed. However, finding robust bacterial signatures of NAFLD has been a great challenge, mainly due to its co-occurrence with other metabolic diseases.

RESULTS: Here, we collected public metagenomic data and integrated the taxonomy profiles with in silico generated community metabolic outputs, and detailed clinical data, of 1206 Chinese subjects w/wo metabolic diseases, including NAFLD (obese and lean), obesity, T2D, hypertension, and atherosclerosis. We identified highly specific microbiome signatures through building accurate machine learning models (accuracy = 0.845-0.917) for NAFLD with high portability (generalizable) and low prediction rate (specific) when applied to other metabolic diseases, as well as through a community approach involving differential co-abundance ecological networks. Moreover, using these signatures coupled with further mediation analysis and metabolic dependency modeling, we propose synergistic defined microbial consortia associated with NAFLD phenotype in overweight and lean individuals, respectively.

CONCLUSION: Our study reveals robust and highly specific NAFLD signatures and offers a more realistic microbiome-therapeutics approach over individual species for this complex disease. Video Abstract.}, } @article {pmid39809768, year = {2025}, author = {Fahur Bottino, G and Bonham, KS and Patel, F and McCann, S and Zieff, M and Naspolini, N and Ho, D and Portlock, T and Joos, R and Midani, FS and Schüroff, P and Das, A and Shennon, I and Wilson, BC and O'Sullivan, JM and Britton, RA and Murray, DM and Kiely, ME and Taddei, CR and Beltrão-Braga, PCB and Campos, AC and Polanczyk, GV and Huttenhower, C and Donald, KA and Klepac-Ceraj, V}, title = {Early life microbial succession in the gut follows common patterns in humans across the globe.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {660}, pmid = {39809768}, issn = {2041-1723}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; *Feces/microbiology ; Female ; Metagenome ; Male ; Bifidobacterium/genetics/isolation & purification ; Infant, Newborn ; Faecalibacterium prausnitzii/genetics ; Child Development ; }, abstract = {Characterizing the dynamics of microbial community succession in the infant gut microbiome is crucial for understanding child health and development, but no normative model currently exists. Here, we estimate child age using gut microbial taxonomic relative abundances from metagenomes, with high temporal resolution (±3 months) for the first 1.5 years of life. Using 3154 samples from 1827 infants across 12 countries, we trained a random forest model, achieving a root mean square error of 2.56 months. We identified key taxonomic predictors of age, including declines in Bifidobacterium spp. and increases in Faecalibacterium prausnitzii and Lachnospiraceae. Microbial succession patterns are conserved across infants from diverse human populations, suggesting universal developmental trajectories. Functional analysis confirmed trends in key microbial genes involved in feeding transitions and dietary exposures. This model provides a normative benchmark of "microbiome age" for assessing early gut maturation that may be used alongside other measures of child development.}, } @article {pmid39809763, year = {2025}, author = {Armetta, J and Li, SS and Vaaben, TH and Vazquez-Uribe, R and Sommer, MOA}, title = {Metagenome-guided culturomics for the targeted enrichment of gut microbes.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {663}, pmid = {39809763}, issn = {2041-1723}, support = {NNF20CC0035580//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17CO0028232//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20CC0035580//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17CO0028232//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20CC0035580//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17CO0028232//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20CC0035580//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17CO0028232//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; grant agreement No. 813781//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; grant agreement No. 813781//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; no. ALTF 137-2018//European Molecular Biology Organization (EMBO)/ ; no. GNT1166180//Department of Health | National Health and Medical Research Council (NHMRC)/ ; }, mesh = {*Gastrointestinal Microbiome/genetics/drug effects ; Humans ; *Metagenome ; *Phylogeny ; Culture Media/chemistry ; Bacteria/genetics/metabolism/classification ; Feces/microbiology ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Caffeine ; }, abstract = {The gut microbiome significantly impacts human health, yet cultivation challenges hinder its exploration. Here, we combine deep whole-metagenome sequencing with culturomics to selectively enrich for taxa and functional capabilities of interest. Using a modified commercial base medium, 50 growth modifications were evaluated, spanning antibiotics, physico-chemical conditions, and bioactive compounds. Whole-metagenome sequencing identified medium additives, like caffeine, that enhance taxa often associated with healthier subjects (e.g., Lachnospiraceae, Oscillospiraceae, Ruminococcaceae). We also explore the impact of modifications on the composition of cultured communities and establish a link between medium preference and microbial phylogeny. Leveraging these insights, we demonstrate that combinations of media modifications can further enhance the targeted enrichment of taxa and metabolic functions, such as Collinsella aerofaciens, or strains harboring biochemical pathways involved in dopamine metabolism. This streamlined, scalable approach unlocks the potential for selective enrichment, advancing microbiome research by understanding the impact of different cultivation parameters on gut microbes.}, } @article {pmid39806507, year = {2025}, author = {Zhang, D and Cao, Y and Dai, B and Zhang, T and Jin, X and Lan, Q and Qian, C and He, Y and Jiang, Y}, title = {The virome composition of respiratory tract changes in school-aged children with Mycoplasma pneumoniae infection.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {10}, pmid = {39806507}, issn = {1743-422X}, support = {No. Q202342//Scientific Research Program of Wuxi Health Commission/ ; No. 32201990//National Natural Science Foundation of China/ ; No. BK20210461//Natural Science Foundation of Jiangsu Province of China/ ; No. SBQN22013//Hospital-level project of Northern Jiangsu People's Hospital/ ; }, mesh = {Humans ; Child ; *Virome ; Male ; Female ; *Mycoplasma pneumoniae/genetics/isolation & purification/classification ; *Pneumonia, Mycoplasma/epidemiology/microbiology/virology ; Viruses/classification/isolation & purification/genetics ; Metagenomics ; Bronchoalveolar Lavage Fluid/virology/microbiology ; Respiratory System/virology/microbiology ; COVID-19/virology/epidemiology ; Respiratory Tract Infections/virology/microbiology/epidemiology ; Adolescent ; }, abstract = {BACKGROUND: Mycoplasma pneumoniae (MP) is a common pathogen for respiratory infections in children. Previous studies have reported respiratory tract microbial disturbances associated with MP infection (MPI); however, since the COVID-19 pandemic, respiratory virome data in school-aged children with MPI remains insufficient. This study aims to explore the changes in the respiratory virome caused by MPI after the COVID-19 pandemic to enrich local epidemiological data.

METHODS: Clinical samples from 70 children with MPI (70 throat swab samples and 70 bronchoalveolar lavage fluid (BALF) samples) and 78 healthy controls (78 throat swab samples) were analyzed using viral metagenomics. Virus reads were calculated and normalized using MEGAN.6, followed by statistical analysis.

RESULTS: Principal Coordinate Analysis (PCoA) showed that viral community diversity is a significant difference between disease cohorts and healthy controls. After MPI, the number of virus species in the upper respiratory tract (URT) increased obviously, and the abundance of families Poxviridae, Retroviridae, and Iridoviridae, which infect vertebrates, rose evidently, particularly the species BeAn 58,085 virus (BAV). Meanwhile, phage alterations in the disease cohorts were predominantly characterized by increased Myoviridae and Ackermannviridae families and decreased Siphoviridae and Salasmaviridae families (p < 0.01). In addition, some new viruses, such as rhinovirus, respirovirus, dependoparvovirus, and a novel gemykibvirus, were also detected in the BALF of the disease cohort.

CONCLUSIONS: This cross-sectional research highlighted the respiratory virome characteristics of school-aged children with MPI after the COVID-19 outbreak and provided important epidemiological information. Further investigation into the impact of various microorganisms on diseases will aid in developing clinical treatment strategies.}, } @article {pmid39806455, year = {2025}, author = {Liu, Z and Yao, X and Chen, C and Zhao, Y and Dong, C and Sun, L and Zhao, J and Zhang, B and Yu, Z and Cheng, D and Zhu, L and Hu, B}, title = {Growth of microbes in competitive lifestyles promotes increased ARGs in soil microbiota: insights based on genetic traits.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {8}, pmid = {39806455}, issn = {2049-2618}, support = {22206166//National Natural Science Foundation of China/ ; 22193061//National Natural Science Foundation of China/ ; 22193061//National Natural Science Foundation of China/ ; 2020YFC1806903//National Key Research and Development Program of China/ ; 2023M733056//China Postdoctoral Science Foundation awards the fellowship/ ; ES202118//Open Project of State Key Laboratory of Urban Water Resource and Environment, Harbin Institute and Technology/ ; 2022HT0025//Zhejiang Province Ecological Environment Research and Results Promotion Project/ ; }, mesh = {*Soil Microbiology ; *Bacteria/genetics/classification/isolation & purification/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/genetics ; Metagenomics ; Genes, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Oxytetracycline/pharmacology ; Soil/chemistry ; Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: The widespread selective pressure of antibiotics in the environment has led to the propagation of antibiotic resistance genes (ARGs). However, the mechanisms by which microbes balance population growth with the enrichment of ARGs remain poorly understood. To address this, we employed microcosm cultivation at different antibiotic (i.e., Oxytetracycline, OTC) stresses across the concentrations from the environmental to the clinical. Paired with shot-gun metagenomics analysis and quantification of bacterial growth, trait-based assessment of soil microbiota was applied to reveal the association between key ARG subtypes, representative bacterial taxa, and functional-gene features that drive the growth of ARGs.

RESULTS: Our results illuminate that resistome variation is closely associated with bacterial growth. A non-monotonic change in ARG abundance and richness was observed over a concentration gradient from none to 10 mg/l. Soil microbiota exposed to intermediate OTC concentrations (i.e., 0.1 and 0.5 mg/l) showed greater increases in the total abundance of ARGs. Community compositionally, the growth of representative taxa, i.e., Pseudomonadaceae was considered to boost the increase of ARGs. It has chromosomally carried kinds of multidrug resistance genes such as mexAB-oprM and mexCD-oprJ could mediate the intrinsic resistance to OTC. Streptomycetaceae has shown a better adaptive ability than other microbes at the clinical OTC concentrations. However, it contributed less to the ARGs growth as it represents a stress-tolerant lifestyle that grows slowly and carries fewer ARGs. In terms of community genetic features, the community aggregated traits analysis further indicates the enhancement in traits of resource acquisition and growth yield is driving the increase of ARGs abundance. Moreover, optimizations in energy production and conversion, alongside a streamlining of bypass metabolic pathways, further boost the growth of ARGs in sub-inhibitory antibiotic conditions.

CONCLUSION: The results of this study suggest that microbes with competitive lifestyles are selected under the stress of environmental sub-inhibitory concentrations of antibiotics and nutrient scarcity. They possess greater substrate utilization capacity and carry more ARGs, due to this they were faster growing and leading to a greater increase in the abundance of ARGs. This study has expanded the application of trait-based assessments in understanding the ecology of ARGs propagation. And the finding illustrated changes in soil resistome are accompanied by the lifestyle switching of the microbiome, which theoretically supports the ARGs control approach based on the principle of species competitive exclusion. Video Abstract.}, } @article {pmid39806416, year = {2025}, author = {Chen, L and Ye, Z and Li, J and Wang, L and Chen, Y and Yu, M and Han, J and Huang, J and Li, D and Lv, Y and Xiong, K and Tian, D and Liao, J and Seidler, U and Xiao, F}, title = {Gut bacteria Prevotellaceae related lithocholic acid metabolism promotes colonic inflammation.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {55}, pmid = {39806416}, issn = {1479-5876}, support = {81873556//National Natural Science Foundation of China/ ; 82170546//National Natural Science Foundation of China/ ; CCCF-QF-2022B67-3//China Crohn's & Colitis Foundation/ ; 2023B02//Tongji Hospital Fund/ ; }, mesh = {Animals ; *Lithocholic Acid/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Colitis/microbiology/pathology/chemically induced/metabolism ; Humans ; *Dextran Sulfate ; *Mice, Inbred C57BL ; Male ; Inflammation/pathology ; Feces/microbiology ; Female ; Colon/pathology/microbiology/metabolism ; Bile Acids and Salts/metabolism ; Inflammatory Bowel Diseases/microbiology/pathology/metabolism ; Mice ; Signal Transduction ; Middle Aged ; }, abstract = {BACKGROUND: The conversion of primary bile acids to secondary bile acids by the gut microbiota has been implicated in colonic inflammation. This study investigated the role of gut microbiota related bile acid metabolism in colonic inflammation in both patients with inflammatory bowel disease (IBD) and a murine model of dextran sulfate sodium (DSS)-induced colitis.

METHODS: Bile acids in fecal samples from patients with IBD and DSS-induced colitis mice, with and without antibiotic treatment, were analyzed using ultraperformance liquid chromatography-mass spectrometry (UPLC-MS). The composition of the microbiota in fecal samples from IBD patients and DSS-colitis mice was characterized via Illumina MiSeq sequencing of the bacterial 16S rRNA gene V3-V4 region. Metagenomic profiling further identified metabolism-related gene signatures in stool samples from DSS-colitis mice. Histological analysis, quantitative PCR (qPCR) and Western Blotting were conducted on colonic samples from DSS-induced colitis mice to assess colonic inflammation, mucosal barrier integrity, and associated signaling pathways. The multivariate analysis of bile acids was conducted using Soft Independent Modelling of Class Analogy (SIMCA, Umetrics, Sweden). The relation between the relative abundance of specific phyla/genera and bile acid concentration was assess through Spearman's correlation analyses. Finally, lithocholic acid (LCA), the key bile acid, was administered via gavage to evaluate its effect on colonic inflammation and mucosal barrier integrity.

RESULTS: In patients with IBD, the composition of colonic bile acids and gut microbiota was altered. Moreover, changes in the gut microbiota further modulate the composition of bile acids in the intestine. As the gut microbiota continues to shift, the bile acid profile undergoes additional alterations. The aforementioned alterations were also observed in mice with DSS-induced colitis. The study revealed a correlation between dysbiosis of the gut microbiota and modifications in the profile of colonic bile acids, notably LCA observed in both patients with IBD and mice with DSS-induced colitis. Through multivariate analysis, LCA was identified as the key bile acid that significantly affects colonic inflammation and the integrity of mucosal barrier. Subsequent experiments confirmed that LCA supplementation effectively mitigated the inhibitory effects of gut microbiota on colitis progression in mice, primarily through the activation of the sphingosine-1-phosphate receptor 2 (S1PR2)/NF-κB p65 signaling pathway. Analysis of the microbiome and metagenomic data revealed changes in the gut microbiota, notably an increased abundance of an unclassified genus within the family Prevotellaceae in DSS-induced colitis mice. Furthermore, a positive correlation was observed between the relative abundance of Prevotellaceae and bile acid biosynthesis pathways, as well as colonic LCA level.

CONCLUSIONS: These findings suggest that LCA and its positively correlated gut bacteria, Prevotellaceae, are closely associated with intestinal inflammation. Targeting colonic inflammation may involve inhibiting LCA and members of the Prevotellaceae family as potential therapeutic strategies.}, } @article {pmid39740461, year = {2025}, author = {Rana, S and Pandey, H and Shridhar, V and Tiwary, P and Kukreti, S and Arunachalam, K and Singh, V}, title = {Structural and functional analysis of rhizospheric bacterial diversity in the Pranmati basin, Himalayan critical zone observatory.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123872}, doi = {10.1016/j.jenvman.2024.123872}, pmid = {39740461}, issn = {1095-8630}, mesh = {*Soil Microbiology ; *Rhizosphere ; Bacteria ; Soil/chemistry ; Microbiota ; Ecosystem ; Biodiversity ; Forests ; }, abstract = {The study explores the structural and functional dynamics of rhizospheric bacterial diversity in the Pranmati basin, focusing on their ecological significance, diversity, and functional roles across dominant vegetation types; Rhododendron arboreum, Myrica esculenta, and Quercus leucotrichophora. The research provides critical insights into soil health and ecosystem functioning by analysing rhizospheric soil properties among the selected vegetations. The research findings reveal that Myrica esculenta exhibits the highest root colonization (95.8%) and moisture content (92.6%), while Quercus leucotrichophora shows the lowest (76.2% and 83.2%), respectively. The microbial community is predominantly composed of Proteobacteria, with 62-65% abundance across different vegetation types. Key genera such as Bacillus, Acinetobacter, and Paenibacillus are notably enriched, highlighting their significant role in phosphate solubilization and nutrient cycling. Venn diagram analysis identified 136 common bacterial species among vegetation types reflecting ecological significance in forest ecosystem. The functional metabolism, diversity indices, and core microbiome analysis underscore the distinct microbial profiles associated with different vegetation types, which are crucial for overall forest soil health. The importance of this research lies in its contribution to environmental management by providing a comprehensive understanding of how microbial communities interact with various vegetation types and influence soil health in the Pranmati basin. These insights are essential for developing targeted strategies to enhance soil fertility and manage forest ecosystems in terms of conservation and restoration efforts in sensitive ecological regions. This study is pioneer as it establishes a functional analysis of rhizospheric bacterial diversity in the Pranmati basin, offering a baseline data for future research on bacterial community structure and their functional role in Himalayan Critical Zone Observatory to the best of our knowledge.}, } @article {pmid39733577, year = {2025}, author = {Heisi, HD and Nkuna, R and Matambo, T}, title = {Rhizosphere microbial community structure and PICRUSt2 predicted metagenomes function in heavy metal contaminated sites: A case study of the Blesbokspruit wetland.}, journal = {The Science of the total environment}, volume = {959}, number = {}, pages = {178147}, doi = {10.1016/j.scitotenv.2024.178147}, pmid = {39733577}, issn = {1879-1026}, mesh = {*Wetlands ; *Metals, Heavy/analysis ; *Biodegradation, Environmental ; *Microbiota ; *Rhizosphere ; South Africa ; *Soil Microbiology ; Soil Pollutants/analysis ; Metagenome ; Bacteria/classification/genetics ; Eichhornia/microbiology ; Fungi ; Poaceae/microbiology ; Typhaceae ; }, abstract = {This study investigated the microbial diversity inhabiting the roots (rhizosphere) of macrophytes thriving along the Blesbokspruit wetland, South Africa's least conserved Ramsar site. The wetland suffers from decades of pollution from mining wastewater, agriculture, and sewage. The current study focused on three macrophytes: Phragmites australis (common reed), Typha capensis (bulrush), and Eichhornia crassipes (water hyacinth). The results revealed a greater abundance and diversity of microbes (Bacteria and Fungi) associated with the free-floating E. crassipes compared to P. australis and T. capensis. Furthermore, the correlation between microbial abundance and metals, showed a strong correlation between fungal communities and metals such as nickel (Ni) and arsenic (As), while bacterial communities correlated more with lead (Pb) and chromium (Cr). The functional analysis predicted by PICRUSt2 identified genes related to xenobiotic degradation, suggesting the potential of these microbes to break down pollutants. Moreover, specific bacterial groups - Proteobacteria, Verrucomicrobia, Cyanobacteria, and Bacteroidetes - were linked to this degradation pathway. These findings suggest a promising avenue for microbe-assisted phytoremediation, a technique that utilizes plants and their associated microbes to decontaminate polluted environments.}, } @article {pmid39729842, year = {2025}, author = {Wang, M and Zhao, J and Gu, Y and Wu, Y and Liu, Y and Tang, Z and Xu, Y and Mao, X and Zhang, J and Tian, W}, title = {Deciphering the mechanism of rhizosphere microecosystem in modulating rice cadmium accumulation via integrating metabolomics and metagenomics.}, journal = {The Science of the total environment}, volume = {959}, number = {}, pages = {178181}, doi = {10.1016/j.scitotenv.2024.178181}, pmid = {39729842}, issn = {1879-1026}, mesh = {*Cadmium/metabolism/analysis ; *Oryza/microbiology/metabolism ; *Rhizosphere ; *Soil Pollutants/metabolism/analysis ; Metabolomics ; Metagenomics ; Soil Microbiology ; Microbiota ; }, abstract = {Cadmium (Cd) accumulation in rice poses significant risks to human health. The Cd accumulation levels vary widely among cultivars and are strongly associated with the rhizosphere microecosystem. However, the underlying mechanisms remain poorly understood. Here, we conducted a field experiment in Cd-contaminated areas with 24 popular regional cultivars. These cultivars were categorized into high Cd accumulation (HA) and low Cd accumulation (LA) groups based on their grain Cd content. Rhizosphere soil physicochemical properties were monitored, and key metabolites, microbiomes, and their interaction contributing to Cd accumulation were analyzed using omics-sequencing technologies and bioinformatics analysis. Metabolomic analysis identified distinct rhizosphere metabolite profiles between the HA and LA groups, with key metabolites showing strong correlations with Cd accumulation. Key metabolites in the LA group were linked to reduced Cd uptake and enhanced antioxidant defense mechanisms, while those in the HA group were associated with increased Cd mobility and uptake. Metagenomic analysis of the rhizosphere soil showed that the LA group harbored a more diverse and interconnected microbial community, with tax such as Syntrophaceae, Anaerolineae, Thermoflexales, and Syntrophales, along with metabolite such as disopyramide, playing central roles in Cd immobilization and detoxification. Additionally, the enhanced carbon, nitrogen, and phosphorus cycling in the LA group suggests a more robust nutrient assimilation process that supports plant growth and reduces Cd uptake. This study highlights the critical role of the rhizosphere microecosystem in regulating Cd accumulation and underscores the potential of selecting rice cultivars with favorable rhizosphere traits as a strategy for reducing Cd uptake.}, } @article {pmid39721532, year = {2025}, author = {Chauhan, A and Jain, A and Kolton, M and Pathak, A}, title = {Impacts of long-term irrigation of municipally-treated wastewater to the soil microbial and nutrient properties.}, journal = {The Science of the total environment}, volume = {959}, number = {}, pages = {178143}, doi = {10.1016/j.scitotenv.2024.178143}, pmid = {39721532}, issn = {1879-1026}, mesh = {*Wastewater ; *Soil Microbiology ; *Agricultural Irrigation/methods ; *Soil/chemistry ; *Waste Disposal, Fluid/methods ; Microbiota ; Nitrogen/analysis ; }, abstract = {Reusing treated wastewater (TWW) for crop irrigation has shown to provide environmental and economic benefits as well as drawbacks. This study was conducted using soils collected from a wastewater reuse facility in Tallahassee, FL, mainly to elucidate the long-term impact(s) of TWW irrigation on soil microbiome and nutrient status. Approximately 890 ha of land have been spray-irrigated with TWW since the 1980's to grow fodder crops. Soil cores were collected from six irrigated and six control sites at depths of 0-15, 15-30, and 30-60 cm during summer and winter, followed by nutrient analysis and assessment of bacterial, fungal, and denitrifier communities using SSU rRNA, ITS, nirK, nirS, and nosZ phylogenetic markers. TWW irrigation significantly increased soil pH, soluble salts, nitrate, phosphate, calcium, magnesium, and organic matter, alongside shifts in the prokaryotic and fungal community structures, particularly in summer. Beta-diversity analyses indicated that wastewater quality and season collectively explained 23 % of prokaryotic community similarity and 9.8 % of fungal community dissimilarity. Indicator species analysis, supported by random forest machine learning, identified 37 prokaryotic and 11 fungal bioindicators whose occurrences varied significantly with wastewater quality and season. Key nitrogen-cycling microbes included ammonia-oxidizing families of Nitrosomonadaceae, Nitrosopumilaceae, Nitrososphaeraceae, Nitrosotaleaceae, and comammox-performing Nitrospiraceae. The fungal community was predominated by Ascomycota (78.6 % ± 4.2 %). FUNGuild analysis showed dominant trophic levels of symbiotrophs, saprotrophs, and pathotrophs, averaging 42 % ± 7.1 %. Overall, this study points to the long-term impacts of TWW irrigation on the studied soil properties and microbial communities.}, } @article {pmid39700995, year = {2025}, author = {Xu, X and Hao, Y and Cai, Z and Cao, Y and Jia, W and Zhao, J and White, JC and Ma, C}, title = {Nanoscale‑boron nitride positively alters rhizosphere microbial communities and subsequent cucumber (Cucumis sativa) growth: A metagenomic analysis.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {178115}, doi = {10.1016/j.scitotenv.2024.178115}, pmid = {39700995}, issn = {1879-1026}, mesh = {*Rhizosphere ; *Soil Microbiology ; *Cucumis sativus/microbiology ; *Microbiota/drug effects ; Metagenomics ; Boron Compounds ; Plant Growth Regulators ; Soil/chemistry ; }, abstract = {Boron (B) deficiency affects over 132 crop species globally, making effective B supplement crucial for enhancing agricultural yield and health. This study explores an innovative application of nanoscale boron nitride (nano-BN) as a sustainable solution for addressing B deficiency in crops. Cucumber seedlings were treated with different contents of nano-BN under greenhouse conditions and both B and N ionic treatments were set as comparisons. Results show that soil application of 10 mg/kg nano-BN achieved a remarkable 15.8 % increase in fresh weight compared to the control. Notably, nano-BN exhibited superior efficiency in providing essential micronutrients without inducing toxicity as compared to traditional ionic B sources. Phytohormone correlation analysis reveals that nano-BN application significantly enhances levels of indole-3-acetic acid (IAA) and cytokinins while reducing abscisic acid (ABA), fostering optimal plant growth conditions. Furthermore, increases in dissolved organic matter (DOM) and dissolved organic carbon (DOC) levels in the rhizosphere improve nutrient availability and promote beneficial microbial activity in the soil as affected by nano-BN. Metagenomics techniques were used to investigate the impact of nano-BN on soil carbon and nitrogen cycling, alongside its effects on the soil microbiome. The upregulation of genes associated with fermentation pathways as affected by nano-BN suggests the enhanced carbon cycling. Additionally, nano-BN upregulated a number of functional genes involved in nitrogen-based processes, leading to a significant increase in microorganisms harboring nitrogen-fixing genes, including Phenylobacterium, Novosphingobium, and Reyranella. Overall, these findings provide valuable insight into the application of nano-BN in agriculture to sustainably increase crop productivity and enhance the efficiency of carbon and nitrogen cycling.}, } @article {pmid39700989, year = {2025}, author = {Liu, F and Zeng, J and Ding, J and Wang, C and He, Z and Liu, Z and Shu, L}, title = {Microbially-driven phosphorus cycling and its coupling mechanisms with nitrogen cycling in mangrove sediments.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {178118}, doi = {10.1016/j.scitotenv.2024.178118}, pmid = {39700989}, issn = {1879-1026}, mesh = {*Phosphorus/metabolism ; *Geologic Sediments/microbiology ; *Nitrogen/metabolism ; *Nitrogen Cycle ; Microbiota ; Wetlands ; Bacteria/metabolism ; }, abstract = {The phosphorus (P) cycle plays a crucial role in the biogeochemical cycling of mangrove sediments. However, the diversity of microbially-driven P-cycling and its coupling with nitrogen (N)-cycling remain poorly understood. In this study, we used metagenomic approaches to investigate microbial P-cycling and its potential interactions with N-cycling in mangrove sediments. Our results revealed that pH, total carbon, and total nitrogen were key environmental factors influencing the diversity of P-cycling microbial communities. Phosphorus metabolic pathways differed among mangrove sediment depths. In surface sediments (0-5 cm), microbial communities primarily acquired readily available inorganic phosphorus, whereas, in deeper sediments (>60 cm), they hydrolyzed more persistent triphosphates, reabsorbed nucleotides, and sourced free phosphate, reflecting a shift in phosphorus transport modes. We also identified glutamate metabolism as a potential pathway linking P-cycling with N-cycling, with these functions co-occurring in both contigs and genomes. Additionally, the diversity of microbial communities associated with the P-cycling increased with sediment depth, suggesting that microbially-driven P-cycling diversifies as depth increases. This study provides new insights into P-cycling and its potential coupling with N-cycling through glutamate metabolism, its coupling with N-cycling through glutamate metabolism.}, } @article {pmid39674156, year = {2025}, author = {Erkorkmaz, BA and Zeevi, D and Rudich, Y}, title = {Dust storm-driven dispersal of potential pathogens and antibiotic resistance genes in the Eastern Mediterranean.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {178021}, doi = {10.1016/j.scitotenv.2024.178021}, pmid = {39674156}, issn = {1879-1026}, mesh = {*Dust/analysis ; *Drug Resistance, Microbial/genetics ; *Air Microbiology ; Environmental Monitoring ; Iran ; Saudi Arabia ; Iraq ; Microbiota/drug effects ; Air Pollutants/analysis ; }, abstract = {The atmosphere hosts a microbiome that connects distant ecosystems yet remains relatively unexplored. In this study, we tested the hypothesis that dust storms enhance the spread of pathogenic microorganisms and whether these microorganisms carry antibiotic resistance and virulence-related genes in the Eastern Mediterranean. We collected air samples during a seasonal transition period, capturing data from 13 dusty days originating from Middle Eastern sources, including the Saharan Desert, Iraq, Iran, and Saudi Arabia, and 32 clear days, with temperatures ranging from 16.5 to 27.1 °C. Using metagenomic analysis, we identified several facultative pathogens like Klebsiella pneumoniae, Stenotrophomonas maltophilia, and Aspergillus fumigatus, which are linked to human respiratory diseases, and others like Zymoseptoria tritici, Fusarium poae, and Puccinia striiformis, which are harmful to wheat. The abundance of these pathogens increased during dust storms and with rising temperatures. Although we did not find strong evidence that these species harbored antibiotic resistance or virulence-related genes, which could be linked to their pathogenic potential, dust storms transported up to 125 times more total antibiotic resistance genes, as measured by RPKM abundance, compared to clear conditions. These levels during dust storms far exceeded those found in other ecosystems. While further research is needed to determine whether dust storms and temperature variations pose an immediate threat to public health and the environment, our findings underscore the importance of continuous monitoring of atmospheric microbiomes. This surveillance is crucial for assessing potential risks to human health and ecosystem stability, particularly in the face of accelerating global climate change.}, } @article {pmid39671945, year = {2025}, author = {Justine, EE and Lee, HJ and Jung, KH and Lee, YS and Kim, YJ}, title = {Methane emission mitigation of Paenibacillus yonginensis DCY84[T] incorporated with silicate on paddy rice (Oryzae sativa L.) plantation revealed in soil microbiome profiling.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177996}, doi = {10.1016/j.scitotenv.2024.177996}, pmid = {39671945}, issn = {1879-1026}, mesh = {*Oryza/microbiology ; *Soil Microbiology ; *Silicates ; *Methane/metabolism ; *Paenibacillus/physiology/metabolism ; *Microbiota ; Biodegradation, Environmental ; Agriculture/methods ; }, abstract = {Anthropogenic methane emissions from paddy cultivation contribute to greenhouse gas levels owing to the anaerobic conditions in flooded rice fields, which promotes the activity of methanogenic bacteria. This study explored bioremediation strategies to mitigate methane release through the application of plant growth-promoting rhizobacteria combined with silicate in rice cultivation. Rice seeds were coated with Paenibacillus yonginensis DCY84[T], with and without the addition of silicate, prior to sowing. Results revealed notable reduction in methane flux during the peak growth stage of rice in seeds treated with DCY84[T] (27.215 ± 1.975 mg m[-2] h[-1]), with a further reduction observed when silicate was also applied (23.592 ± 3.112 mg m[-2] h[-1]), compared to untreated seeds (37.305 ± 2.990 mg m[-2] h[-1]). Additionally, treatment with DCY84[T] (28.24 ± 0.55 g) resulted in an increase in rice yield (p < 0.05), as evidenced by a greater 1000-grain weight compared to both the control group (26.91 ± 0.09 g) and the application of silicate (27.37 ± 0.57 g). The beta diversity of the soil microbial community highlighted distinct differences between the treated and control groups, indicating DCY84[T] inoculation with or without silicate altered the soil microbial structure. Particularly, the treated groups showed dominance of the phylum Proteobacteria, especially the classes Alphaproteobacteria and Deltaproteobacteria. Furthermore, the addition of silicate to DCY84[T]-coated rice seeds resulted in a higher abundance of bacterial families, such as Anaerolinaceae, Clostridiceae, and Nitrospirae which compete with methanogens for organic substrates, thereby reducing their methane production. Notably, the DCY84[T]-silicate treatment group showed higher levels of methane metabolism biomarkers such as formate dehydrogenase within the soil microbiome, which correlated with the observed reduction in methane emissions. These findings suggest that coating rice seeds with DCY84[T] and silicate prior to sowing effectively mediates methane production and release during rice cultivation by promoting beneficial soil bacterial communities.}, } @article {pmid39667337, year = {2025}, author = {Chen, YT and Reid, T and Weisener, C}, title = {Microbial community and functional shifts across agricultural and urban landscapes within a Lake Erie watershed.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123683}, doi = {10.1016/j.jenvman.2024.123683}, pmid = {39667337}, issn = {1095-8630}, mesh = {*Lakes/microbiology ; *Agriculture ; *Nitrogen/metabolism/analysis ; *Microbiota ; Ontario ; Ecosystem ; }, abstract = {The role of sediment microbial communities in regulating the loss and retention of nutrients in aquatic ecosystems has been increasingly recognised. However, in the Great Lakes, where nutrient mitigation focuses on harmful algal blooms, there are limited studies examining the fundamental role of water/sediment microbes in nutrient biogeochemical cycling. Little is understood in this regard considering the increase in anthropogenic pressure on in-stream biological processes impacting nutrient flux to lakes. In this study, metagenomic and metatranscriptomic approaches were used to investigate the microbial community and gene regulation. The study focused on nitrogen (N) metabolism in a nutrient-polluted watershed of Lake Erie in southwestern Ontario, Canada. Nutrients and microbial analyses of water and sediments were collected in 2020 and 2021 from Sturgeon Creek headwaters to the nearshore of Lake Erie. Results showed no significant shifts in community structure with nutrient concentrations or land use. Metabolically, active genes involved in denitrification (consisting of 32-53% of N metabolic transcripts) showed the highest expression within agricultural and wetland dominant locations. Based on active gene expression patterns, the urbanised location coinciding with peak nitrate (NO3[-]) concentrations showed the greatest potential for nitrous oxide (N2O) emission and nitrogen loss along this transect. In contrast to denitrification, direct nitrification (5-21% of N metabolic transcripts) increased two-fold approaching downstream and nearshore lake locations. Across this river-lake corridor, expression of key functional genes associated with N transformation showed strong correlation with the change in concentrations of aqueous NO3[-] and nitrite (NO2[-]) and the ratio of NO2[-]/NO3[-]. Our findings demonstrated a clear link between sediment microbial metabolism and overlying water chemistry in this lotic system. We suggest that future studies assessing nutrient mitigation consider sediment biogeochemical processes and N-metabolising bacteria, and their fundamental role and cooperative relationship with nutrient and hydrological dynamics of overlying waters.}, } @article {pmid39662407, year = {2025}, author = {Wang, Y and Yi, H and Li, G and Li, A and Wang, H and Ding, D}, title = {Influence of enriched nitrate reducing bacteria communities on bacterial community structure and groundwater condition during in situ bioremediation of nitrate in acidic uranium-contaminated groundwater.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177896}, doi = {10.1016/j.scitotenv.2024.177896}, pmid = {39662407}, issn = {1879-1026}, mesh = {*Groundwater/microbiology/chemistry ; *Nitrates/metabolism ; *Biodegradation, Environmental ; *Uranium/metabolism ; *Bacteria/metabolism ; China ; *Water Pollutants, Radioactive/metabolism ; Microbiota ; Water Pollutants, Chemical/metabolism/analysis ; }, abstract = {In-situ leaching (ISL) is the predominant technology used in uranium mining currently, although it leads to significant environmental challenges. Nitrates, a key component in leaching agents, not only pose a threat to human health but also impede the bioreduction of U(VI) in uranium-contaminated water. In this study, the nitrate reducing bacterial (NRB) communities adapted to acidic uranium-contaminated groundwater from a site in Northwest China were gained by an enrichment micro-model. The effects of the NRB communities on the groundwater parameters and microbial diversity were evaluated using the groundwater-core column leaching system during the in-situ bioremediation of nitrate. The enrichment experiments revealed that NRB communities adapted to acidic uranium-contaminated groundwater were successfully enriched, of which Tumebacillus was the main functional bacterium. The column leaching experiment results showed that adding NRB communities successfully reduced nitrate levels from 100.91 mg/L to 0.7 mg/L in just 8 days, improved groundwater acidity and redox conditions. Additionally, the metagenomic analysis showed that introducing NRB communities increased biomass and indigenous NRB, but decreased microbial diversity. The KEGG enrichment analysis suggested that butanoate metabolism and valine, leucine and isoleucine degradation were promoted by adding enriched NRB communities. This research lays the groundwork for nitrate removal from contaminated groundwater in areas affected by ISL in uranium mines, setting the stage for future in situ bioremediation of U(VI).}, } @article {pmid39647796, year = {2025}, author = {Zhu, Y and Zhao, S and Qi, S and Zhang, H and Zhang, X and Li, S and Wang, X and Gu, J and Zhang, T and Xi, H and Liu, X}, title = {Effects of energetic compounds on soil microbial communities and functional genes at a typical ammunition demolition site.}, journal = {Chemosphere}, volume = {370}, number = {}, pages = {143913}, doi = {10.1016/j.chemosphere.2024.143913}, pmid = {39647796}, issn = {1879-1298}, mesh = {*Soil Microbiology ; *Trinitrotoluene/toxicity ; *Soil Pollutants/toxicity ; *Triazines ; *Microbiota/drug effects ; *Azocines ; Explosive Agents/toxicity ; Soil/chemistry ; Proteobacteria/genetics/drug effects ; Metagenomics ; }, abstract = {High concentrations of energetic compounds such as 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) in military-contaminated sites pose a serious threat to human health and ecosystems. Better understanding about their effects on microbial diversity and functional genes in soil of ammunition demolition sites is required. In this study, the information of soil microbial community composition was obtained by metagenomic sequencing, and the impacts of energetic compounds on microbial community structure at the level of functional genes and enzymes based on Nr (Non-Redundant Protein Sequence Database), KEGG (Kyoto Encyclopedia of Genes and Genomes), CAZy (Carbohydrate-Active enZymes Database) and other databases were discussed. The results showed that soil microbial diversity and functional gene abundance decreased significantly with the increase of the concentrations of energetic compounds. Conversely, the relative abundance of Proteobacteria increased significantly, reaching over 80% in the heavily TNT-contaminated area near explosive-wastewater pool. Furthermore, functional gene analysis indicated that Proteobacteria had an advantage in degrading energetic compounds, and thus had the potential to improve the soil quality at ammunition demolition sites. This study provides a scientific basis for the future remediation and management of contaminated soils at ammunition demolition sites, as well as for the selection of efficient degraders of energetic compounds.}, } @article {pmid39642837, year = {2025}, author = {Li, Y and Liu, K and Qiu, H and Chen, F and Zhang, J and Zheng, Z}, title = {Dynamics of antibiotic resistance genes and bacterial community structure within substrate biofilms.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123512}, doi = {10.1016/j.jenvman.2024.123512}, pmid = {39642837}, issn = {1095-8630}, mesh = {*Biofilms/drug effects ; Drug Resistance, Microbial/genetics ; Wastewater/microbiology ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Microbiota ; }, abstract = {Biofilms that develop on the surface of substrates are critical for treating wastewater. The accumulation of antibiotic resistance genes (ARGs) within these biofilms is particularly noteworthy. Despite their importance, studies that focus on biofilms attached to substrate surfaces remain scarce. This investigation explored the prevalence and succession of ARGs and microbial dynamics in biofilms on different substrates (ceramic, biomass filter, and steel slag) versus water biofilms over a year. Results showed distinct differences in ARG profiles between water and substrate biofilms. Multidrug ARGs constituted 39.14-46.73% of all ARGs in the substrate biofilms, with macrolide ARGs making up 11.98-14.52%. Seasonal variations influenced the diversity of the ARGs, notably increasing during the spring. The neutral community model suggested that the ARG assembly was dominantly driven by stochastic process. Proteobacteria, Actinobacteria and Campylobacter emerged as the predominant phyla within these biofilms. The microbial community distribution was predominantly influenced by ammonium nitrogen (NH4[+]-N) (R[2] = 0.4113), temperature and total nitrogen (TN). Notably, temperature exerted a critical impact on the microbial community distribution (P = 0.001), identifying it as the principal factor for spatial arrangement. Furthermore, the structural variations of ARGs were primarily driven by total organic carbon (TOC) (R[2] = 0.3988), temperature, oxidation-reduction potential (ORP) and NH4[+]-N. Our findings provided new insights into the optimization of substrate selection and ecological management to manage ARG enrichment, offering a promising strategy for aquatic ecological restoration and pollution control.}, } @article {pmid39639495, year = {2024}, author = {Alanzi, AR}, title = {Exploring Microbial Dark Matter for the Discovery of Novel Natural Products: Characteristics, Abundance Challenges and Methods.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2407064}, doi = {10.4014/jmb.2407.07064}, pmid = {39639495}, issn = {1738-8872}, mesh = {*Biological Products/metabolism ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Phylogeny ; Microbiota ; }, abstract = {The objective of this review is to investigate microbial dark matter (MDM) with a focus on its potential for discovering novel natural products (NPs). This first part will examine the characteristics and abundance of these previously unexplored microbial communities, as well as the challenges faced in identifying and harnessing their unique biochemical properties and novel methods in this field. MDMs are thought to hold great potential for the discovery of novel NPs, which could have significant applications in medicine, agriculture, and industry. In recent years, there has been a growing interest in exploring MDM to unlock its potential. In fact, developments in genome-sequencing technologies and sophisticated phylogenetic procedures and metagenomic techniques have contributed to drastically make important changes in our sights on the diversity of microbial life, including the very outline of the tree of life. This has led to the development of novel technologies and methodologies for studying these elusive microorganisms, such as single-cell genomics, metagenomics, and culturomics. These approaches enable researchers to isolate and analyze individual microbial cells, as well as entire communities, providing insights into their genetic and metabolic potential. By delving into the MDM, scientists hope to uncover new compounds and biotechnological advancements that could have far-reaching impacts on various fields.}, } @article {pmid39626398, year = {2025}, author = {Song, A and Si, Z and Xu, D and Wei, B and Wang, E and Chong, F and Fan, F}, title = {Lanthanum and cerium added to soil influence microbial carbon and nitrogen cycling genes.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123509}, doi = {10.1016/j.jenvman.2024.123509}, pmid = {39626398}, issn = {1095-8630}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism ; *Cerium ; *Nitrogen/metabolism ; *Lanthanum ; *Nitrogen Cycle ; Microbiota ; }, abstract = {The soil microbiome plays an important role in carbon (C) and nitrogen (N) processing and storage and is influenced by rare earth elements (REEs), which can have both direct and indirect effects on plant metabolic processes. Using conventional physicochemical methods and metagenomic-based analyses, we investigated REEs effects on soil respiration, soil mineral N, soil microbial community structure and functional genes related to C and N metabolism. High doses of cerium (0.16 and 0.32 mmol kg[-1] soil) increased CO2 net production rate by 59 and 42%, and N2O net production rate by 255 and 609%, respectively, compared to no REEs. Similarly, high doses of lanthanum (0.16 and 0.32 mmol kg[-1] soil) increased CO2 net production rate by 47 and 39%, and N2O net production rate by 105 and 187%, respectively. Increased soil respiration from altered relative abundances of key soil microorganisms associated with soil N cycling and organic matter degradation and functional genes encoding enzymes involved in C and N metabolism, accelerated N mineralization. Elevated REEs levels substantially increased the relative abundances of functional genes related to cellulose, chitin, glucans, hemicellulose, lignin, and peptidoglycan degradation. REEs also influenced multiple functional genes associated with the N cycle. The abundance of genes responsible for organic N degradation and synthesis, such as asnB, gdh_K15371, glsA, and gs, increased with elevated cerium and lanthanum concentrations. Similarly, the abundances of denitrification genes, including narl, narJ, narZ, and nosZ, also rose with increasing amounts of cerium and lanthanum. However, the decrease in narB and nirB gene abundance with increasing REE concentrations was attributed to the reduction of nitrate to amino groups. Our findings highlight the influence of REEs on key soil microorganisms associated with soil N cycling and organic matter degradation and key functional genes in soil C and N metabolism, with implications for agriculture, environmental protection, and human health.}, } @article {pmid39615467, year = {2025}, author = {Khandeparker, L and Kale, D and Hede, N and Anil, AC}, title = {Application of functional metagenomics in the evaluation of microbial community dynamics in the Arabian Sea: Implications of environmental settings.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123449}, doi = {10.1016/j.jenvman.2024.123449}, pmid = {39615467}, issn = {1095-8630}, mesh = {*Metagenomics ; Cyanobacteria/genetics/metabolism ; Microbiota ; Seawater/microbiology ; Chlorophyll A/metabolism ; Climate Change ; }, abstract = {Ocean microbial communities form the base of marine food webs, facilitating energy transfer and nutrient cycling, thereby supporting higher trophic levels. We investigated their composition and functional profiles across depths (surface waters 0, 29, and 63 m and bottom waters 100, 150, and 200 m) in the central-eastern Arabian Sea (CEAS) using next-generation sequencing. It was hypothesized that the composition and functional diversity of these communities would be influenced by depth and environmental parameters. Our research showed that microbial communities vary with depth and are shaped by environmental factors like irradiance, temperature, dissolved oxygen, suspended particulate matter, chlorophyll a, and ammonia concentrations. Cyanobacteria (Prochlorococcus sp) and Mamiellaceae, belonging to picoeukaryotes, exhibited distinct depth-specific distributions up to subsurface chlorophyll maxima (SCM) at 63 m. On the other hand, a community shift in the microbial communities comprising Firmicutes, Bacteroidetes, and Actinobacteria phyla was observed at the deeper water depths. The profiling of functional genes pointed out the expression of carbon fixation by photosynthetic organisms at the surface (0, 29, and 63 m), which shifted to prokaryotic carbon fixation in deeper waters (0, 150, and 200 m). Microcosm experiments (mixing of surface water with water from the SCM) carried out simulating disturbances such as climate change forced mixing (cyclones), revealed shifts in microbial structure and function. It was observed that within 48 h, the carbon fixation activity changed from photosynthetic organisms to prokaryotes and indicated an increase in stress-related biosynthetic pathways such as expression of quorum sensing, biosynthesis of antibiotics, lipopolysaccharides, and secondary metabolites. These findings have implications for predictive modelling of food web dynamics and fisheries management in the context of climate change.}, } @article {pmid39806046, year = {2025}, author = {Sun, L and Liu, X and Zhou, L and Wang, H and Lian, C and Zhong, Z and Wang, M and Chen, H and Li, C}, title = {Shallow-water mussels (Mytilus galloprovincialis) adapt to deep-sea environment through transcriptomic and metagenomic insights.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {46}, pmid = {39806046}, issn = {2399-3642}, support = {42276153, 42106134, 42106100, 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Mytilus/microbiology/genetics/immunology ; *Transcriptome ; *Microbiota ; Metagenomics ; Symbiosis/genetics ; Adaptation, Physiological/genetics ; Seawater/microbiology ; Metagenome ; }, abstract = {Recent studies have unveiled the deep sea as a rich biosphere, populated by species descended from shallow-water ancestors post-mass extinctions. Research on genomic evolution and microbial symbiosis has shed light on how these species thrive in extreme deep-sea conditions. However, early adaptation stages, particularly the roles of conserved genes and symbiotic microbes, remain inadequately understood. This study examined transcriptomic and microbiome changes in shallow-water mussels Mytilus galloprovincialis exposed to deep-sea conditions at the Site-F cold seep in the South China Sea. Results reveal complex gene expression adjustments in stress response, immune defense, homeostasis, and energy metabolism pathways during adaptation. After 10 days of deep-sea exposure, shallow-water mussels and their microbial communities closely resembled those of native deep-sea mussels, demonstrating host and microbiome convergence in response to adaptive shifts. Notably, methanotrophic bacteria, key symbionts in native deep-sea mussels, emerged as a dominant group in the exposed mussels. Host genes involved in immune recognition and endocytosis correlated significantly with the abundance of these bacteria. Overall, our analyses provide insights into adaptive transcriptional regulation and microbiome dynamics of mussels in deep-sea environments, highlighting the roles of conserved genes and microbial community shifts in adapting to extreme environments.}, } @article {pmid39804694, year = {2025}, author = {Puller, V and Plaza Oñate, F and Prifti, E and de Lahondès, R}, title = {Impact of simulation and reference catalogues on the evaluation of taxonomic profiling pipelines.}, journal = {Microbial genomics}, volume = {11}, number = {1}, pages = {}, doi = {10.1099/mgen.0.001330}, pmid = {39804694}, issn = {2057-5858}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Computer Simulation ; Benchmarking ; Bacteria/classification/genetics ; Metagenomics/methods ; Microbiota/genetics ; }, abstract = {Microbiome profiling tools rely on reference catalogues, which significantly affect their performance. Comparing them is, however, challenging, mainly due to differences in their native catalogues. In this study, we present a novel standardized benchmarking framework that makes such comparisons more accurate. We decided not to customize databases but to translate results to a common reference to use the tools with their native environment. Specifically, we conducted two realistic simulations of gut microbiome samples, each based on a specific taxonomic profiler, and used two different taxonomic references to project their results, namely the Genome Taxonomy Database and the Unified Human Gastrointestinal Genome. To demonstrate the importance of using such a framework, we evaluated four established profilers as well as the impact of the simulations and that of the common taxonomic references on the perceived performance of these profilers. Finally, we provide guidelines to enhance future profiler comparisons for human microbiome ecosystems: (i) use or create realistic simulations tailored to your biological context (BC), (ii) identify a common feature space suited to your BC and independent of the catalogues used by the profilers and (iii) apply a comprehensive set of metrics covering accuracy (sensitivity/precision), overall representativity (richness/Shannon) and quantification (UniFrac and/or Aitchison distance).}, } @article {pmid39804408, year = {2025}, author = {Macdonald, JFH and Han, Y and Astafyeva, Y and Bergmann, L and Gurschke, M and Dirksen, P and Blümke, P and Schneider, YKH and Alawi, M and Lippemeier, S and Andersen, JH and Krohn, I}, title = {Exploring Tetraselmis chui microbiomes-functional metagenomics for novel catalases and superoxide dismutases.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {6}, pmid = {39804408}, issn = {1432-0614}, support = {AquaHealth FKZ 031B0945C//Bundesministerium für Bildung und Forschung/ ; SuReMetS FKZ 031B0944A//Bundesministerium für Bildung und Forschung/ ; }, mesh = {*Superoxide Dismutase/genetics/metabolism ; *Metagenomics ; *Antioxidants/metabolism ; *Catalase/metabolism/genetics ; *Microbiota ; Microalgae/genetics/enzymology ; Chlorophyta/genetics/enzymology ; Bacteria/genetics/enzymology/classification/isolation & purification ; }, abstract = {The focus on microalgae for applications in several fields, e.g. resources for biofuel, the food industry, cosmetics, nutraceuticals, biotechnology, and healthcare, has gained increasing attention over the last decades. In this study, we investigate the microbiome of the cultured microalga Tetraselmis chui (T. chui) to highlight their potential for health benefits. In this context, biomolecules like antioxidants play a crucial role in the well-being of living organisms as they metabolise harmful reactive oxygen species (ROS) to reduce oxidative stress. Impaired processing of ROS leads to damaged cells and increases the risk of cancer, inflammatory diseases, and diabetes, among others. Here, we identify, characterise, and test bacterial antioxidants derived from the T. chui microbiome metagenome dataset. We identified 258 genes coding for proteins with potential antioxidant activity. Of those, four novel enzymes are expressed and identified as two superoxide dismutases (SOD), TcJM_SOD2 and TcIK_SOD3, and two catalases (CAT), TcJM_CAT2 and TcIK_CAT3. Extensive analyses characterised all implemented enzymes as active even in concentrations down to 25 ng*ml[-1] for the SODs and 15 ng*ml[-1] for the CATs. Furthermore, sequence-based analyses assign TcJM_SOD2 and TcIK_SOD3 to iron superoxide dismutases (Fe SODs) and TcJM_CAT2 and TcIK_CAT3 to heme-containing catalases. These candidates are phylogenetically classified within the phylum Pseudomonadota. Regarding the biotechnological potential, a toxicity assay did not indicate any harmful effects. The introduced enzymes may benefit medical applications and expand the potential of microalgae microbiomes. KEY POINTS: • Omics-based discoveries of antioxidant enzymes from Tetraselmis chui microbiome • Two superoxide dismutases and two catalases are identified and tested for activity • Enzyme sensitivity highlights biotechnological potential of microalgae microbiomes.}, } @article {pmid39801456, year = {2025}, author = {Torozan, DA and Laczny, CC and Roomp, K and Wilmes, P and Fleckenstein, J and Schneider, JG}, title = {Metagenomic Profiling of Oral Microbiome Dynamics During Chemoradiotherapy in Head and Neck Squamous Cell Carcinoma Patients.}, journal = {Cancer medicine}, volume = {14}, number = {1}, pages = {e70589}, doi = {10.1002/cam4.70589}, pmid = {39801456}, issn = {2045-7634}, support = {863664//H2020 European Research Council/ ; }, mesh = {Humans ; Male ; *Chemoradiotherapy/adverse effects ; Female ; Middle Aged ; *Squamous Cell Carcinoma of Head and Neck/microbiology/therapy ; *Microbiota/radiation effects ; Aged ; *Metagenomics/methods ; *Head and Neck Neoplasms/microbiology/therapy ; *Saliva/microbiology ; Prospective Studies ; Mouth/microbiology ; Adult ; Case-Control Studies ; Metagenome ; }, abstract = {BACKGROUND: We explored the interaction between the oral microbiome and the development of radiation-induced mucositis in patients with head and neck squamous cell cancer (HNSCC) undergoing chemoradiotherapy (CRT). We prospectively studied the oral microbiome and compared it to healthy controls. Additionally, we compared patients with low-grade (LGM) vs. high-grade mucositis (HGM).

METHODS: Ten HNSCC patients scheduled for CRT were included. Saliva samples were characterized prior to, during, and nine months after CRT using metagenomic sequencing. We similarly characterized samples from seven healthy controls. We assessed alpha and beta diversity and examined abundances at different taxonomic levels between (sub)groups.

RESULTS: Patients exhibited significantly reduced alpha diversity compared to controls at all times (p ⟨ 0.05). Differential abundance of taxa between patients and controls was observed at baseline. In patients, the relative abundance of Staphylococcus aureus and Escherichia coli increased significantly during CRT. Capnocytophaga spp. was associated with the definitive CRT patients' subgroup. At baseline, two fungal families (Melampsoraceae and Herpotrichiellaceaea) were more abundant in patients who later developed HGM. No differentially abundant taxa were found between LGM vs. HGM during irradiation.

CONCLUSION: Our findings support the hypothesis that CRT, as well as HNSCC itself, influences the composition of the oral microbiome. Microbial markers found in patients who later developed HGM should be evaluated using independent cohorts to qualify their specific biomarker potential.}, } @article {pmid39760260, year = {2025}, author = {You, H and Yang, B and Liu, H and Wu, W and Yu, F and Lin, N and Yang, W and Hu, B and Liu, Y and Zou, H and Hao, S and Xiao, Y and Xu, T and Jiang, Y}, title = {Unravelling distinct patterns of metagenomic surveillance and respiratory microbiota between two P1 genotypes of Mycoplasma pneumoniae.}, journal = {Emerging microbes & infections}, volume = {14}, number = {1}, pages = {2449087}, doi = {10.1080/22221751.2024.2449087}, pmid = {39760260}, issn = {2222-1751}, mesh = {Humans ; *Mycoplasma pneumoniae/genetics/isolation & purification ; *Pneumonia, Mycoplasma/epidemiology/microbiology ; Retrospective Studies ; Child ; Female ; Male ; Child, Preschool ; *Microbiota ; Adolescent ; *Metagenomics ; *Genotype ; Middle Aged ; Adult ; COVID-19/epidemiology/microbiology ; Young Adult ; Infant ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {To unravel distinct patterns of metagenomic surveillance and respiratory microbiota between Mycoplasma pneumoniae (M. pneumoniae) P1-1 and P1-2 and to explore the impact of the COVID-19 pandemic on epidemiological features, we conducted a multicentre retrospective study which spanned 90,886 pneumonia patients, among which 3164 cases M. pneumoniae were identified. Our findings revealed a concurrent outbreak of M. pneumoniae, with the positivity rate rising sharply to 9.62% from July 2023, compared to the 0.16% to 4.06% positivity rate observed during the 2020-2022 COVID-19 pandemic. P1-1 had a higher odds ratio of co-detecting opportunistic pathogens. However, no significant differences were observed in the co-detection odds ratio between children and other age groups in P1-2. This study is the first to demonstrate differences in relative abundance, diversity of respiratory microbiota and co-detection rate of opportunistic pathogen between M. pneumoniae P1-1 and P1-2. Through bronchoalveolar lavage (BAL) metagenomic and host transcriptomic analyses, we identified variations in co-detection rates of M. pneumoniae P1-1 genotype with opportunistic pathogens like S. pneumoniae, alterations in respiratory microbiota composition, lung inflammation, and disruption of ciliary function. Consistent with the results of host transcriptome, we found that P1-1 infections were associated with significantly higher rates of requiring respiratory support and mechanical ventilation compared to P1-2 infections (Fisher's exact test, p-value = 0.035/0.004). Our study provides preliminary evidence of clinical severity between M. pneumoniae strains, underscoring the need for ongoing research and development of targeted therapeutic strategies.}, } @article {pmid39126385, year = {2025}, author = {Jangi, S and Zhao, N and Hsia, K and Park, YS and Michaud, DS and Yoon, H}, title = {Specific Bacterial Co-abundance Groups Are Associated With Inflammatory Status in Patients With Ulcerative Colitis.}, journal = {Journal of Crohn's & colitis}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ecco-jcc/jjae125}, pmid = {39126385}, issn = {1876-4479}, support = {/TR/NCATS NIH HHS/United States ; /NH/NIH HHS/United States ; //National Research Foundation/ ; }, mesh = {Humans ; *Colitis, Ulcerative/microbiology ; *Gastrointestinal Microbiome ; Male ; Adult ; Female ; Prospective Studies ; Middle Aged ; Clostridiales/isolation & purification ; Candida/isolation & purification ; Republic of Korea ; Feces/microbiology ; }, abstract = {BACKGROUND AND AIMS: While there is increasing interest in microbiome-directed therapies for patients with ulcerative colitis (UC), the identification of microbial targets remains elusive, underlining the need for novel approaches.

METHODS: Utilizing metagenomic data from the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease (SPARC IBD), available via the IBD Plexus Program of the Crohn's & Colitis Foundation, we used a tree-based dichotomous approach to assemble distinct clusters of species-level bacterial co-abundance groups (CAGs). We evaluated the abundance of bacterial CAGs and fungal taxa during remission (n = 166) and activity (n = 46). We examined if the bacterial CAGs identified in our cohorts were conserved in 2 healthy cohorts and a Korean UC cohort.

RESULTS: CAG3 and CAG8, dominated by bacteria from the family Lachnospiraceae, were associated with remission. Low abundance of CAG8 and elevated abundance of Candida genus were predictive of active UC. Constituents from CAG8 were influential hub species of the remission-associated microbial UC network, including Ruminococcus gnavus, Erysipelatoclostridium ramosum, Blautia, and Dorea species. These hub species interactions were preserved in 2 healthy cohorts and were partially recapitulated in a Korean UC cohort. CAG8 abundance correlated with the secondary bile acid production pathway. Bacterial CAGs did not correlate with Candida; however, Bifidobacterium adolescentis and Alistipes putredinis were negatively associated with Candida.

CONCLUSIONS: Lachnospiraceae-dominated bacterial CAGs were associated with remission in UC, with key bacterial interactions within the CAG also observed in 2 healthy cohorts and a Korean UC cohort. Bacterial CAG-based analyses may aid in designing candidate consortia for microbiome-based therapeutics.}, } @article {pmid39800795, year = {2025}, author = {Pagac, MP and Davient, B and Plado, LA and Lam, HYI and Lee, SM and Ravikrishnan, A and Chua, WLE and Muralidharan, S and Sridharan, A and Irudayaswamy, AS and Srinivas, R and Wearne, S and Mohamed Naim, AN and Ho, EXP and Ng, HQA and Kwah, JS and Png, E and Bendt, AK and Wenk, MR and Torta, F and Nagarajan, N and Common, J and Chong, YS and Tham, EH and Shek, LP and Loo, EXL and Chambers, J and Yew, YW and Loh, M and Dawson, TL}, title = {Life stage impact on the human skin ecosystem: lipids and the microbial community.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {13}, pmid = {39800795}, issn = {2055-5008}, mesh = {Humans ; *Skin/microbiology ; Female ; Adult ; *Microbiota ; *Oxylipins/metabolism ; *Lipid Metabolism ; *Lipidomics/methods ; Child ; Malassezia ; Keratinocytes/microbiology/metabolism ; Middle Aged ; Male ; Metagenomics/methods ; Sebum/metabolism ; Interleukin-6/metabolism ; Interleukin-1beta/metabolism ; Aged ; Coculture Techniques ; Adolescent ; Bacteria/classification/metabolism/genetics/isolation & purification ; Young Adult ; Host Microbial Interactions ; Ecosystem ; }, abstract = {Sebaceous free fatty acids are metabolized by multiple skin microbes into bioactive lipid mediators termed oxylipins. This study investigated correlations between skin oxylipins and microbes on the superficial skin of pre-pubescent children (N = 36) and adults (N = 100), including pre- (N = 25) and post-menopausal females (N = 25). Lipidomics and metagenomics revealed that Malassezia restricta positively correlated with the oxylipin 9,10-DiHOME on adult skin and negatively correlated with its precursor, 9,10-EpOME, on pre-pubescent skin. Co-culturing Malassezia with keratinocytes demonstrated a link between 9,10-DiHOME and pro-inflammatory cytokines IL-1β and IL-6 production. We also observed strong correlations between other skin oxylipins and microbial taxa, highlighting life stage differences in sebum production and microbial community composition. Our findings imply a complex host-microbe communication system mediated by lipid metabolism occurring on human skin, warranting further research into its role in skin health and disease and paving the way towards novel therapeutic targets and treatments.}, } @article {pmid39700725, year = {2025}, author = {Petersen, JF and Valk, LC and Verhoeven, MD and Nierychlo, MA and Singleton, CM and Dueholm, MKD and Nielsen, PH}, title = {Diversity and physiology of abundant Rhodoferax species in global wastewater treatment systems.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {1}, pages = {126574}, doi = {10.1016/j.syapm.2024.126574}, pmid = {39700725}, issn = {1618-0984}, mesh = {*Wastewater/microbiology/chemistry ; *Phylogeny ; *RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Metagenome ; Water Purification ; Sequence Analysis, DNA ; Denmark ; Biodiversity ; Oxidation-Reduction ; Genome, Bacterial/genetics ; }, abstract = {Wastewater treatment plants rely on complex microbial communities for bioconversion and removal of pollutants, but many process-critical species are still poorly investigated. One of these genera is Rhodoferax, an abundant core genus in wastewater treatment plants across the world. The genus has been associated with many metabolic traits such as iron reduction and oxidation and denitrification. We used 16S rRNA gene amplicon data to uncover the diversity and abundance of Rhodoferax species in Danish and global treatment plants. Publicly available metagenome-assembled genomes were analyzed based on phylogenomics to delineate species and assign taxonomies based on the SeqCode. The phylogenetic analysis of "Rhodoferax" revealed that species previously assigned to Rhodoferax in wastewater treatment plants should be considered as at least eight different genera, with five representing previously undescribed genera. Genome annotation showed potential for several key-bioconversions in wastewater treatment, such as nitrate reduction, carbohydrate degradation, and accumulations of various storage compounds. Iron oxidation and reduction capabilities were not predicted for abundant species. Species-resolved FISH-Raman was performed to gain an overview of the morphology and ecophysiology of selected taxa to clarify their potential role in global wastewater treatment systems. Our study provides a first insight into the functional and ecological characteristics of several novel genera abundant in global wastewater treatment plants, previously assigned to the Rhodoferax genus.}, } @article {pmid39528052, year = {2025}, author = {Jiang, Q and Zhu, X and Sun, L and Xie, C and Wang, X and Ma, L and Yan, X}, title = {Akkermansia muciniphila Promotes SIgA Production and Alters the Reactivity Toward Commensal Bacteria in Early-Weaned Piglets.}, journal = {The Journal of nutrition}, volume = {155}, number = {1}, pages = {52-65}, doi = {10.1016/j.tjnut.2024.11.002}, pmid = {39528052}, issn = {1541-6100}, mesh = {Animals ; Swine ; *Immunoglobulin A, Secretory/metabolism ; *Weaning ; *Akkermansia ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Verrucomicrobia ; Bacteria/classification ; Intestines/microbiology/immunology ; }, abstract = {BACKGROUND: Secretory IgA (SIgA) is the first line of defense in protecting the intestinal epithelium against pathogenic bacteria, regulating gut microbiota composition, and maintaining intestinal homeostasis. Early weaning strategies may disrupt SIgA levels in piglet intestines, causing a decline in immune response and early weaning stress. However, the specific microbial mechanisms modulating SIgA in early-weaned piglets are not well understood.

OBJECTIVES: We hypothesized that Akkermansia muciniphila increases intestinal SIgA production in the early-weaned piglets.

METHODS: Fecal SIgA levels, SIgA-coated bacteria abundance, and fecal metagenomes were compared between 6 Huanjiang miniature (HM) and 6 Duroc×Landrace×Yorkshire (DLY) early-weaned piglets to identify bacterial species involved in SIgA modulation. Four bacterial species were investigated using 5 groups (Control, A. muciniphila, L. amylovorus, L. crispatus, and L. acidophilus) of male specific pathogen-free C57BL/6J mice, weaned 3 wk postbirth (n = 8/group). Subsequently, 10-d-old Landrace×Yorkshire (LY) piglets were randomly assigned to 3 groups (Control, 10[9]A. muciniphila, and 10[8]A. muciniphila) (n = 10/group) to evaluate the effect of orally administered A. muciniphila on intestinal SIgA production and microbial composition.

RESULTS: HM early-weaned piglets showed significantly higher SIgA levels [7.59 μg/mg, 95% confidence interval (CI): 3.2, 12, P = 0.002] and SIgA-coated bacteria abundance (8.64%, 95% CI: 3.2, 14, P = 0.014) than DLY piglets. In the mouse model, the administration of A. muciniphila significantly increased SIgA levels (3.50 μg/mg, 95% CI: 0.59, 6.4, P = 0.018), SIgA-coated bacteria abundance (9.06%, 95% CI: 4, 14, P = 0.018), and IgA[+] plasma cell counts (6.1%, 95% CI: 4.3, 8, P = 0.005). In the pig experiments, the oral administration of A. muciniphila to LY piglets significantly enhanced intestinal SIgA concentrations (4.22 μg/mg, 95% CI: 0.37, 8.5, P = 0.034) and altered the SIgA-coated bacterial landscape.

CONCLUSIONS: Early intervention with A. muciniphila in nursing piglets can increases intestinal SIgA production and alter the reactivity toward commensal bacteria upon early weaning.}, } @article {pmid39305900, year = {2025}, author = {Liu, Q and Huang, B and Zhou, Y and Wei, Y and Li, Y and Li, B and Li, Y and Zhang, J and Qian, Q and Chen, R and Lyu, Z and Wang, R and Cao, Q and Xu, Q and Wang, Q and Miao, Q and You, Z and Lian, M and Gershwin, ME and Jin, Q and Xiao, X and Ma, X and Tang, R}, title = {Gut microbiome pattern impacts treatment response in primary biliary cholangitis.}, journal = {Med (New York, N.Y.)}, volume = {6}, number = {1}, pages = {100504}, doi = {10.1016/j.medj.2024.08.003}, pmid = {39305900}, issn = {2666-6340}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Liver Cirrhosis, Biliary/drug therapy/microbiology ; *Ursodeoxycholic Acid/therapeutic use ; Female ; Male ; Middle Aged ; Prospective Studies ; Dysbiosis/microbiology ; Feces/microbiology ; Aged ; Cholagogues and Choleretics/therapeutic use ; Clostridium/isolation & purification/drug effects/genetics ; Adult ; Metagenomics/methods ; Metagenome/drug effects ; Metabolomics ; }, abstract = {BACKGROUND: Primary biliary cholangitis (PBC) is a progressive autoimmune liver disease. An inadequate response to ursodeoxycholic acid (UDCA) poses a high risk of progression toward end-stage liver disease. Gut dysbiosis has been implicated in PBC. Here, we aimed to investigate microbial signatures that permit risk stratification and provide mechanistic insights into novel therapies for PBC.

METHODS: We prospectively recruited UDCA treatment-naive patients with PBC and performed metagenomic sequencing and metabolomic profiling using stool and serum samples obtained before (n = 132) and after (n = 59) treatment. PBC microbiome subtypes were identified using unsupervised machine learning methods and validated in two independent cohorts.

FINDINGS: PBC baseline metagenomes clustered into two community subtypes characterized by varying abundances of Clostridia taxa. Compared with Clostridia[low] microbiomes, Clostridia[high] microbiomes were more similar to healthy controls. Notably, patients in the Clostridia[low] subtype exhibited a 2-fold higher UDCA non-response rate compared to those in the Clostridia[high] subtype (41% vs. 20%, p = 0.015). Integrative analysis of metagenomic and metabolomic data revealed divergent functional modules and metabolic activities between the two metacommunities. In particular, anaerobic fermentation and the production of bioactive metabolites, including tryptophan derivatives and secondary bile acids, crucial for immune regulation and gut barrier maintenance, were markedly diminished in the Clostridia[low] subtype. Moreover, UDCA administration reconfigured the fecal microbial and metabolic profiles only in the Clostridia[high] group. Importantly, the microbiome subtypes and their associations with UDCA response were reproducible in two independent treatment-naive PBC cohorts.

CONCLUSIONS: Characterizing baseline microbiota patterns may enable the prediction of treatment outcomes in PBC and facilitate personalized treatment strategies.

FUNDING: This research was mainly supported by the National Natural Science Foundation of China.}, } @article {pmid39797569, year = {2025}, author = {Rogers, AB and Kale, V and Baldi, G and Alberdi, A and Gilbert, MTP and Gupta, D and Limborg, MT and Li, S and Payne, T and Petersen, B and Rasmussen, JA and Richardson, L and Finn, RD}, title = {HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production.}, journal = {Database : the journal of biological databases and curation}, volume = {2025}, number = {}, pages = {}, doi = {10.1093/database/baae112}, pmid = {39797569}, issn = {1758-0463}, mesh = {Animals ; *Chickens/microbiology ; Host Microbial Interactions/genetics ; Salmon/microbiology ; Microbiota ; Databases, Genetic ; Gastrointestinal Microbiome ; }, abstract = {The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues. The HoloFood Data Portal is a web resource that simplifies access to the project datasets. For example, users can conveniently access multiomic datasets derived from the same individual or retrieve host phenotypic data with a linked gut microbiome sample. Project-specific metagenome-assembled genome and viral catalogues are also provided, linking to broader datasets in MGnify. The portal stores only data necessary to provide these relationships, with possible linking to the underlying repositories. The portal showcases a model approach for how future multiomics datasets can be made available. Database URL: https://www.holofooddata.org.}, } @article {pmid39797470, year = {2025}, author = {Záhonová, K and Kaur, H and Furgason, CC and Smirnova, AV and Dunfield, PF and Dacks, JB}, title = {Comparative Analysis of Protist Communities in Oilsands Tailings Using Amplicon Sequencing and Metagenomics.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70029}, doi = {10.1111/1462-2920.70029}, pmid = {39797470}, issn = {1462-2920}, support = {e-INFRA CZ (90254)//the Ministry of Education, Youth and Sports of the Czech Republic/ ; CRDPJ 542973-19//Natural Sciences and Engineering Research Council of Canada/ ; RES0021028//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Alberta ; *Metagenomics/methods ; *Oil and Gas Fields ; *Eukaryota/genetics/classification ; RNA, Ribosomal, 18S/genetics ; Biodiversity ; Phylogeny ; }, abstract = {The Canadian province of Alberta contains substantial oilsands reservoirs, consisting of bitumen, clay and sand. Extracting oil involves separating bitumen from inorganic particles using hot water and chemical diluents, resulting in liquid tailings waste with ecotoxicologically significant compounds. Ongoing efforts aim to reclaim tailings-affected areas, with protist colonisation serving as one assessment method of reclamation progress. Oilsands-associated protist communities have mainly been evaluated using amplicon sequencing of the 18S rRNA V4 region; however, this barcode may overlook important protist groups. This study examined how community assessment methods between the V4 and V9 regions differ in representing protist diversity across four oilsands-associated environments. The V9 barcode identified more operational taxonomical units (OTUs) for Discoba, Metamonada and Amoebozoa compared with the V4. A comparative shotgun metagenomics approach revealed few eukaryotic contigs but did recover a complete Paramicrosporidia mitochondrial genome, only the second publicly available from microsporidians. Both V4 and V9 markers were informative for assessing community diversity in oilsands-associated environments and are most effective when combined for a comprehensive taxonomic estimate, particularly in anoxic environments.}, } @article {pmid39796619, year = {2025}, author = {Johnson, AJ and Alvear, A and Knights, D and Chow, LS and Bantle, AE}, title = {A Randomized Pilot Study of Time-Restricted Eating Shows Minimal Microbiome Changes.}, journal = {Nutrients}, volume = {17}, number = {1}, pages = {}, doi = {10.3390/nu17010185}, pmid = {39796619}, issn = {2072-6643}, support = {KL2TR002492//National Institutes of Health, National Center of Advancing Translational Sciences/ ; UL1TR002494//National Institutes of Health, National Center for Advancing Translational Sciences/ ; K23DK115906/DK/NIDDK NIH HHS/United States ; 17SFR-2YR50LC//Healthy Foods, Healthy Lives Institute at the University of Minnesota/ ; }, mesh = {Humans ; Pilot Projects ; *Gastrointestinal Microbiome ; Male ; *Feces/microbiology ; Female ; Adult ; Obesity/microbiology ; Middle Aged ; Body Composition ; Fasting ; Time Factors ; }, abstract = {OBJECTIVE: TRE is an emerging approach in obesity treatment, yet there is limited data on how it influences gut microbiome composition in humans. Our objective was to characterize the gut microbiome of human participants before and after a TRE intervention. This is a secondary analysis of a previously published clinical trial examining the effects of time-restricted eating (TRE).

METHODS: In a previously published, 12-week randomized controlled trial, Chow et al. evaluated the effects of an 8-h TRE intervention on body composition in human participants. Chow et al. demonstrated significant reductions in weight, lean mass, and visceral fat in the TRE group compared to those following time-unrestricted eating (non-TRE). Stool samples were collected by a subset of those participants using home kits at both baseline and post-intervention for shotgun metagenomic sequencing for this secondary analysis. Microbiome community composition was compared before and after intervention as alpha and beta diversity.

RESULTS: Sixteen participants provided stool samples (eight in the TRE group and eight in the non-TRE group). Stool samples were collected from all participants at at least one time point, but both pre- and post-treatment samples were available from only five participants who completed both baseline and post-treatment collections. In alignment with the findings of Chow et al., the participants in the TRE group of the secondary analysis who collected microbiome sample(s) successfully reduced their eating window from an average of 15.3 ± 0.8 h at baseline to 9.3 ± 1.7 h during the intervention (mean ± SD, p < 0.001) and the non-TRE group's eating window remained unchanged. While the TRE group lost weight and visceral fat mass, no effect of the TRE intervention was observed on alpha diversity (Shannon index, Simpson index, and number of taxa, linear mixed models), beta diversity (Bray-Curtis, PERMANOVA), even after controlling for weight and visceral fat changes.

CONCLUSIONS: Our analysis did not detect any significant differences in gut microbiome composition or diversity indices between participants undergoing a TRE intervention and those in the control group. The study's findings are limited by a small sample size, short duration, and the collection of stool samples at only two time points. Future studies with larger sample sizes, longer durations, and more frequent sampling, and collection of detailed dietary data are needed to better understand the relationship between TRE and gut microbiome dynamics.}, } @article {pmid39796584, year = {2024}, author = {Firrman, J and Deyaert, S and Mahalak, KK and Liu, L and Baudot, A and Joossens, M and Poppe, J and Cameron, SJS and Van den Abbeele, P}, title = {The Bifidogenic Effect of 2'Fucosyllactose Is Driven by Age-Specific Bifidobacterium Species, Demonstrating Age as an Important Factor for Gut Microbiome Targeted Precision Medicine.}, journal = {Nutrients}, volume = {17}, number = {1}, pages = {}, doi = {10.3390/nu17010151}, pmid = {39796584}, issn = {2072-6643}, support = {8072-41000-102-00D//United States Department of Agriculture/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Trisaccharides/pharmacology ; *Bifidobacterium/drug effects ; Infant ; *Feces/microbiology ; Aged ; Adult ; Child, Preschool ; *Precision Medicine ; Middle Aged ; Child ; Female ; Male ; Age Factors ; Young Adult ; Adolescent ; Milk, Human/chemistry ; Oligosaccharides/pharmacology ; Lactose ; }, abstract = {BACKGROUND: The human gut microbiota develops in concordance with its host over a lifetime, resulting in age-related shifts in community structure and metabolic function. Little is known about whether these changes impact the community's response to microbiome-targeted therapeutics. Providing critical information on this subject, faecal microbiomes of subjects from six age groups, spanning from infancy to 70-year-old adults (n = six per age group) were harvested. The responses of these divergent communities to treatment with the human milk oligosaccharide 2'-fucosyllactose (2'FL), fructo-oligosaccharides (FOS), and lactose was investigated using the Ex vivo SIFR[®] technology that employs bioreactor fermentation and is validated to be predictive of clinical findings. Additionally, it was evaluated whether combining faecal microbiomes of a given age group into a single pooled microbiome produced similar results as the individual microbiomes.

RESULTS: First, marked age-dependent changes in community structure were identified. Bifidobacterium levels strongly declined as age increased, and Bifidobacterium species composition was age-dependent: B. longum, B. catenulatum/pseudocatenulatum, and B. adolescentis were most prevalent for breastfed infants, toddlers/children, and adults, respectively. Metabolomic analyses (LA-REIMS) demonstrated that these age-dependent differences particularly impacted treatment effects of 2'FL (more than FOS/lactose). Further analysis revealed that while 2'FL enhanced production of short-chain fatty acids (SCFAs) and exerted potent bifidogenic effects, regardless of age, the specific Bifidobacterium species enhanced by 2'FL, as well as subsequent cross-feeding interactions, were highly age-dependent. Furthermore, single-pooled microbiomes produced results that were indicative of the average treatment response for each age group. Nevertheless, pooled microbiomes had an artificially high diversity, thus overestimating treatment responses (especially for infants), did not recapitulate interindividual variation, and disallowed for the correlative analysis required to unravel mechanistic actions.

CONCLUSIONS: Age is an important factor in shaping the gut microbiome, with the dominant taxa and their metabolites changing over a lifetime. This divergence affects the response of the microbiota to therapeutics, demonstrated in this study using 2'FL. These results evidence the importance of screening across multiple age groups separately to provide granularity of how therapeutics impact the microbiome and, consequently, human health.}, } @article {pmid39796532, year = {2024}, author = {Paterson, S and Majchrzak, M and Gómez-Garre, D and Ortega-Hernández, A and Sánchez-González, S and de la Fuente, MÁ and Gómez-Cortés, P and Hernández-Ledesma, B}, title = {Role of Simulated Nannochloropsis gaditana Digests in Shaping Gut Microbiota and Short-Chain Fatty Acid Levels.}, journal = {Nutrients}, volume = {17}, number = {1}, pages = {}, doi = {10.3390/nu17010099}, pmid = {39796532}, issn = {2072-6643}, support = {PID2021-122989OB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; PIPF-2022/BIO-24996//Comunidad Autónoma de Madrid/ ; }, mesh = {*Gastrointestinal Microbiome/physiology/drug effects ; Humans ; *Fatty Acids, Volatile/metabolism ; *Microalgae ; *Fermentation ; Stramenopiles/metabolism ; RNA, Ribosomal, 16S ; Bacteria/metabolism/classification/genetics ; Colon/microbiology/metabolism ; }, abstract = {The connection between gut microbiota and factors like diet is crucial for maintaining intestinal balance, which in turn impacts the host's overall health. Nannochloropsis gaditana microalgae is a sustainable source of bioactive compounds, mainly known for its used in aquaculture and extraction of bioactive lipids, with potential health benefits whose effects on human gut microbiota are still unknown. Therefore, the goal of this work was to assess the impact of N. gaditana on human gut microbiota composition and derived metabolites by combining the INFOGEST protocol and in vitro colonic fermentation process to evaluate potential effects on human gut microbiota conformation through 16S rRNA gene sequencing and its metabolic functionality. The results have demonstrated the ability of the digests from N. gaditana to significantly modify gut microbiota composition, promoting an increase in beneficial bacterial genera such as Akkermansia, Butyricicoccus, Eisenbergiella, Lachnoclostridium, and Marvinbryantia, in contrast to inulin, after 48 h of colonic fermentation. Additionally, the digests increased the levels of both major and minor short-chain fatty acids (SCFAs), particularly butyric and valeric acids, considered as intestinal biomarkers, and increased ammonium production. This research has demonstrated, for the first time, the potential of N. gaditana microalgae as a sustainable agent for influencing the composition and functionality of human gut microbiota.}, } @article {pmid39796518, year = {2024}, author = {Vega-Rojas, A and Haro, C and Molina-Abril, H and Guil-Luna, S and Santos-Marcos, JA and Gutierrez-Mariscal, FM and Garcia-Fernandez, H and Caballero-Villarraso, J and Rodriguez-Ariza, A and Lopez-Miranda, J and Perez-Martinez, P and Hervas, A and Camargo, A}, title = {Gut Microbiota Interacts with Dietary Habits in Screenings for Early Detection of Colorectal Cancer.}, journal = {Nutrients}, volume = {17}, number = {1}, pages = {}, doi = {10.3390/nu17010084}, pmid = {39796518}, issn = {2072-6643}, support = {PI-0055-2021//Consejería de Salud y Consumo/ ; PI-0156-2016//Consejería de Salud y Consumo/ ; AGL2015-67896-P//Ministerio de Ciencia, Innovación y Universidades/ ; n.a.//European Union/ ; CP14/00114//Instituto de Salud Carlos III/ ; PI19/00299//Instituto de Salud Carlos III/ ; DTS19/00007//Instituto de Salud Carlos III/ ; PI22/00925//Instituto de Salud Carlos III/ ; C1-0001-2022//Andalusian Health Service/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/diagnosis ; *Gastrointestinal Microbiome ; *Early Detection of Cancer/methods ; Male ; Female ; Middle Aged ; *Feeding Behavior ; *Colonoscopy ; Aged ; Adenocarcinoma/microbiology ; Occult Blood ; Diet ; Colonic Polyps/microbiology/diagnosis ; Feces/microbiology ; }, abstract = {BACKGROUND/OBJECTIVES: Gut microbiota interacts with nutrients, which may be relevant to assigning a microbial signature to colorectal cancer (CRC). We aim to evaluate the potential of gut microbiota combined with dietary habits in the early detection of pathological findings related to CRC in the course of a screening program.

METHODOLOGY: The colonoscopy performed on 152 subjects positive for fecal occult blood test showed that 6 subjects had adenocarcinoma, 123 had polyps, and 23 subjects had no pathological findings. Gut microbiota was analyzed by 16S metagenomic. Caret package was used to build the classification models in R.

RESULTS: Random forest (RF) classifier models were used to test the potential of gut microbiota alone or combined with dietary habits as a biomarker to discern between individuals with CRC-related lesions (polyps or adenocarcinoma) versus individuals without pathological findings. RF classifier models yielded an area under the curve of 0.790 using gut microbiota data, 0.710 using dietary habits data, and 0.804 in the combined model including gut microbiota and dietary habits data. The abundance of Suterella, Oscillospirales, Proteobacteria, and Burkholderiales was highly discriminant between groups, together with the consumption of fruit and vegetables and the consumption of carbonated and/or sweetened beverages.

CONCLUSIONS: Our results suggest that the interaction between gut microbiota and dietary habits is relevant when a microbial signature is used as a marker in CRC. Moreover, gut microbiota signature and information about the dietary habits of the individuals seem to be important for improving screening programs for the early detection of CRC.}, } @article {pmid39796082, year = {2024}, author = {Kim, DG and Lee, CM and Lee, YS and Yoon, SH and Kim, SY}, title = {Isolation of a Novel Low-Temperature-Active and Organic-Solvent-Stable Mannanase from the Intestinal Metagenome of Hermetia illucens.}, journal = {International journal of molecular sciences}, volume = {26}, number = {1}, pages = {}, doi = {10.3390/ijms26010216}, pmid = {39796082}, issn = {1422-0067}, support = {Project No. PJ008604//Rural Development Administration/ ; }, mesh = {*Mannans/metabolism ; Animals ; Phylogeny ; Metagenome ; Diptera/microbiology ; Mannosidases/metabolism/genetics/chemistry ; Gastrointestinal Microbiome ; Substrate Specificity ; Amino Acid Sequence ; Galactans/metabolism ; Enzyme Stability ; Cold Temperature ; Plant Gums/chemistry/metabolism ; Hydrogen-Ion Concentration ; Intestines/microbiology ; Solvents/chemistry ; Recombinant Proteins/metabolism/genetics/chemistry ; Galactose/analogs & derivatives ; }, abstract = {The black soldier fly, Hermetia illucens, is a voracious scavenger of various organic materials; therefore, it could be exploited as a biological system for processing daily food waste. In order to survey novel hydrolytic enzymes, we constructed a fosmid metagenome library using unculturable intestinal microorganisms from H. illucens. Through functional screening of the library on carboxymethyl cellulose plates, we identified a fosmid clone, the product of which displayed hydrolytic activity. Sequence analysis of the fosmid revealed a novel mannan-degrading gene, ManEM6, composed of 1185 base pairs encoding 394 amino acids, with a deduced 20-amino-acid N-terminal signal peptide sequence. The conceptual translation of ManEM6 exhibited the highest identity (78%) to endo-1,4-β-mannosidase from Dysgonomonas mossii. Phylogenetic and domain analyses indicated that ManEM6 encodes a novel mannanase with a glycoside hydrolase family 26 domain. The recombinant protein rManEM6 showed its highest activity at 40 °C and pH 7.0, and it remained stable in the range of pH 5-10.0. rManEM6 hydrolyzed substrates with β-1,4-glycosidic mannoses, showing maximum enzymatic activity toward locust bean gum galactomannan, while it did not hydrolyze p-nitrophenyl-β-pyranosides, demonstrating endo-form mannosidase activity. rManEM6 was highly stable under stringent conditions, including those of polar organic solvents, as well as reducing and denaturing reagents. Therefore, ManEM6 may be an attractive candidate for the degradation of mannan under high-organic-solvent and protein-denaturing processes in the food and feed industries.}, } @article {pmid39794871, year = {2025}, author = {Samodova, D and Stankevic, E and Søndergaard, MS and Hu, N and Ahluwalia, TS and Witte, DR and Belstrøm, D and Lubberding, AF and Jagtap, PD and Hansen, T and Deshmukh, AS}, title = {Salivary proteomics and metaproteomics identifies distinct molecular and taxonomic signatures of type-2 diabetes.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {5}, pmid = {39794871}, issn = {2049-2618}, support = {74550801//European Foundation for the Study of Diabetes/ ; NNF18CC0034900; NNF23SA0084103//Novo Nordisk Fonden/ ; NNF18CC0034900; NNF23SA0084103//Novo Nordisk Fonden/ ; }, mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/metabolism ; *Saliva/microbiology ; *Proteomics/methods ; Male ; Middle Aged ; Female ; *Microbiota ; Biomarkers/metabolism ; Bacterial Proteins/genetics ; Adult ; Bacteria/classification/metabolism/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Computational Biology/methods ; Salivary Proteins and Peptides/metabolism ; Case-Control Studies ; Aged ; }, abstract = {BACKGROUND: Saliva is a protein-rich body fluid for noninvasive discovery of biomolecules, containing both human and microbial components, associated with various chronic diseases. Type-2 diabetes (T2D) imposes a significant health and socio-economic burden. Prior research on T2D salivary microbiome utilized methods such as metagenomics, metatranscriptomics, 16S rRNA sequencing, and low-throughput proteomics.

RESULTS: We conducted ultrafast, in-depth MS-based proteomic and metaproteomic profiling of saliva from 15 newly diagnosed T2D individuals and 15 age-/BMI-matched healthy controls (HC). Using state-of-the-art proteomics, over 4500 human and bacterial proteins were identified in a single 21-min run. Bioinformatic analysis revealed host signatures of altered immune-, lipid-, and glucose-metabolism regulatory systems, increased oxidative stress, and possible precancerous changes in T2D saliva. Abundance of peptides for bacterial genera such as Neisseria and Corynebacterium were altered showing biomarker potential, offering insights into disease pathophysiology and microbial applications for T2D management.

CONCLUSIONS: This study presents a comprehensive mapping of salivary proteins and microbial communities, serving as a foundational resource for enhancing understanding of T2D pathophysiology. The identified biomarkers hold promise for advancing diagnostics and therapeutic approaches in T2D and its associated long-term complication Video Abstract.}, } @article {pmid39794618, year = {2025}, author = {Nguyen, HP and Le, BT and Nguyen, HN and Nguyen, TT and Duong, TH and Hoang, TC and Duy, NPT and Nguyen, MV and Duong, LN and Le, LQ and Pham, TT}, title = {Demonstration of adapted packed-bed bioreactor for accurate and rapid estimation of biochemical oxygen demand: insights into the influence of microbial community structure and functions.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {2}, pages = {31}, pmid = {39794618}, issn = {1573-0972}, support = {NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; }, mesh = {*Bioreactors/microbiology ; *Wastewater/microbiology/chemistry ; *Biological Oxygen Demand Analysis ; *Microbial Consortia ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics/methods ; Biodegradation, Environmental ; Cocos/microbiology ; Glucose/metabolism ; Azo Compounds/metabolism ; Metagenome ; }, abstract = {This study demonstrated a novel approach to accurately estimate 5-day biochemical oxygen demand (BOD5) in textile wastewater using a microbial consortium from food processing wastewater fixed on coconut fibers. Although glucose-glutamic acid (GGA) has been widely known as the most preferred substrates for microbial respiration, its calibration surprisingly resulted in an overestimation of BOD5 in textile wastewater due to its lower utilization rate compared to that of textile wastewater. After being adapted with a new nutrient environment composed of GGA and textile wastewater, the adapted packed-bed bioreactors (PBBRs) was capable of accurate estimation of BOD5 in textile wastewater using GGA standard solution. Metagenomic analysis revealed the dominance of the genera Enterobacter, Acinetobacter, Chryseobacterium, and Comamonas in the adapted microbial community, which are recognized for their significant potential in azo dye degradation. The imputed metagenome showed an enhanced showed an enhanced abundance of "Amino Acid Degradation" and "Carbohydrate Degradation" functions, confirming the improved ability of adapted community to utilization of GGA in the standard solution. These findings suggest that adaptation of exogenous microbial consortium to a nutrient environment composed of GGA and target wastewater may shift the community to that dominated by strains having both utilization ability of GGA and target compounds which, in turn, enhance the accuracy of the adapted PBBRs for estimation of BOD5 in target wastewater.}, } @article {pmid39762435, year = {2025}, author = {Fackelmann, G and Manghi, P and Carlino, N and Heidrich, V and Piccinno, G and Ricci, L and Piperni, E and Arrè, A and Bakker, E and Creedon, AC and Francis, L and Capdevila Pujol, J and Davies, R and Wolf, J and Bermingham, KM and Berry, SE and Spector, TD and Asnicar, F and Segata, N}, title = {Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals.}, journal = {Nature microbiology}, volume = {10}, number = {1}, pages = {41-52}, pmid = {39762435}, issn = {2058-5276}, support = {microTOUCH-101045015)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; *Diet ; *Diet, Vegetarian ; *Diet, Vegan ; *Bacteria/classification/genetics/isolation & purification ; Female ; Vegans ; Male ; Adult ; Metagenomics ; Feces/microbiology ; Middle Aged ; Diet, Western/adverse effects ; }, abstract = {As plant-based diets gain traction, interest in their impacts on the gut microbiome is growing. However, little is known about diet-pattern-specific metagenomic profiles across populations. Here we considered 21,561 individuals spanning 5 independent, multinational, human cohorts to map how differences in diet pattern (omnivore, vegetarian and vegan) are reflected in gut microbiomes. Microbial profiles distinguished these common diet patterns well (mean AUC = 0.85). Red meat was a strong driver of omnivore microbiomes, with corresponding signature microbes (for example, Ruminococcus torques, Bilophila wadsworthia and Alistipes putredinis) negatively correlated with host cardiometabolic health. Conversely, vegan signature microbes were correlated with favourable cardiometabolic markers and were enriched in omnivores consuming more plant-based foods. Diet-specific gut microbes partially overlapped with food microbiomes, especially with dairy microbes, for example, Streptococcus thermophilus, and typical soil microbes in vegans. The signatures of common western diet patterns can support future nutritional interventions and epidemiology.}, } @article {pmid39753668, year = {2025}, author = {Rohwer, RR and Kirkpatrick, M and Garcia, SL and Kellom, M and McMahon, KD and Baker, BJ}, title = {Two decades of bacterial ecology and evolution in a freshwater lake.}, journal = {Nature microbiology}, volume = {10}, number = {1}, pages = {246-257}, pmid = {39753668}, issn = {2058-5276}, support = {DEB-0822700//National Science Foundation (NSF)/ ; DEB-1440297//National Science Foundation (NSF)/ ; MCB-9977903//National Science Foundation (NSF)/ ; DEB-1344254//National Science Foundation (NSF)/ ; WIS01789//U.S. Department of Agriculture (United States Department of Agriculture)/ ; WIS01516//U.S. Department of Agriculture (United States Department of Agriculture)/ ; R01-GM116853//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; DBI-2011002//National Science Foundation (NSF)/ ; DEB-1831730//National Science Foundation (NSF)/ ; R01 GM116853/GM/NIGMS NIH HHS/United States ; DEB-0702395//National Science Foundation (NSF)/ ; DEB-2025982//National Science Foundation (NSF)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DEB-9632853//National Science Foundation (NSF)/ ; DEB-0217533//National Science Foundation (NSF)/ ; }, mesh = {*Lakes/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota/genetics ; Metagenome ; Seasons ; Phylogeny ; Genome, Bacterial ; Evolution, Molecular ; Biological Evolution ; }, abstract = {Ecology and evolution are considered distinct processes that interact on contemporary time scales in microbiomes. Here, to observe these processes in a natural system, we collected a two-decade, 471-metagenome time series from Lake Mendota (Wisconsin, USA). We assembled 2,855 species-representative genomes and found that genomic change was common and frequent. By tracking strain composition via single nucleotide variants, we identified cyclical seasonal patterns in 80% and decadal shifts in 20% of species. In the dominant freshwater family Nanopelagicaceae, environmental extremes coincided with shifts in strain composition and positive selection of amino acid and nucleic acid metabolism genes. These genes identify organic nitrogen compounds as potential drivers of freshwater responses to global change. Seasonal and long-term strain dynamics could be regarded as ecological processes or, equivalently, as evolutionary change. Rather than as distinct interacting processes, we propose a conceptualization of ecology and evolution as a continuum to better describe change in microbial communities.}, } @article {pmid39747695, year = {2025}, author = {Wang, X and Fang, Y and Liang, W and Cai, Y and Wong, CC and Wang, J and Wang, N and Lau, HC and Jiao, Y and Zhou, X and Ye, L and Mo, M and Yang, T and Fan, M and Song, L and Zhou, H and Zhao, Q and Chu, ES and Liang, M and Liu, W and Liu, X and Zhang, S and Shang, H and Wei, H and Li, X and Xu, L and Liao, B and Sung, JJY and Kuang, M and Yu, J}, title = {Gut-liver translocation of pathogen Klebsiella pneumoniae promotes hepatocellular carcinoma in mice.}, journal = {Nature microbiology}, volume = {10}, number = {1}, pages = {169-184}, pmid = {39747695}, issn = {2058-5276}, support = {82173191//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; }, mesh = {Animals ; *Carcinoma, Hepatocellular/microbiology/pathology ; *Klebsiella pneumoniae/pathogenicity/genetics ; Mice ; *Liver Neoplasms/microbiology/pathology/metabolism ; Humans ; *Toll-Like Receptor 4/metabolism/genetics ; *Gastrointestinal Microbiome ; *Klebsiella Infections/microbiology ; *Bacterial Translocation ; *Liver/microbiology/pathology ; Fecal Microbiota Transplantation ; Disease Models, Animal ; Mice, Inbred C57BL ; Male ; Carcinogenesis ; Cell Proliferation ; Bacterial Proteins/metabolism/genetics ; }, abstract = {Hepatocellular carcinoma (HCC) is accompanied by an altered gut microbiota but whether the latter contributes to carcinogenesis is unclear. Here we show that faecal microbiota transplantation (FMT) using stool samples from patients with HCC spontaneously initiate liver inflammation, fibrosis and dysplasia in wild-type mice, and accelerate disease progression in a mouse model of HCC. We find that HCC-FMT results in gut barrier injury and translocation of live bacteria to the liver. Metagenomic analyses and bacterial culture of liver tissues reveal enrichment of the gut pathogen Klebsiella pneumoniae in patients with HCC and mice transplanted with the HCC microbiota. Moreover, K. pneumoniae monocolonization recapitulates the effect of HCC-FMT in promoting liver inflammation and hepatocarcinogenesis. Mechanistically, K. pneumoniae surface protein PBP1B interacts with and activates TLR4 on HCC cells, leading to increased cell proliferation and activation of oncogenic signalling. Targeting gut colonization using K. oxytoca or TLR4 inhibition represses K. pneumoniae-induced HCC progression. These findings indicate a role for an altered gut microbiota in hepatocarcinogenesis.}, } @article {pmid39747694, year = {2025}, author = {Hsu, TY and Nzabarushimana, E and Wong, D and Luo, C and Beiko, RG and Langille, M and Huttenhower, C and Nguyen, LH and Franzosa, EA}, title = {Profiling lateral gene transfer events in the human microbiome using WAAFLE.}, journal = {Nature microbiology}, volume = {10}, number = {1}, pages = {94-111}, pmid = {39747694}, issn = {2058-5276}, support = {K23DK125838//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R24DK110499//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; Research Scholars Award//American Gastroenterological Association (AGA)/ ; Career Development Award//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; T32CA009001//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; U54DE023798//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; }, mesh = {Humans ; *Gene Transfer, Horizontal ; *Microbiota/genetics ; *Metagenome ; *Phylogeny ; *Algorithms ; Bacteria/genetics/classification/isolation & purification ; Metagenomics/methods ; Genome, Bacterial ; Computational Biology/methods ; }, abstract = {Lateral gene transfer (LGT), also known as horizontal gene transfer, facilitates genomic diversification in microbial populations. While previous work has surveyed LGT in human-associated microbial isolate genomes, the landscape of LGT arising in personal microbiomes is not well understood, as there are no widely adopted methods to characterize LGT from complex communities. Here we developed, benchmarked and validated a computational algorithm (WAAFLE or Workflow to Annotate Assemblies and Find LGT Events) to profile LGT from assembled metagenomes. WAAFLE prioritizes specificity while maintaining high sensitivity for intergenus LGT. Applying WAAFLE to >2,000 human metagenomes from diverse body sites, we identified >100,000 high-confidence previously uncharacterized LGT (~2 per microbial genome-equivalent). These were enriched for mobile elements, as well as restriction-modification functions associated with the destruction of foreign DNA. LGT frequency was influenced by biogeography, phylogenetic similarity of involved pairs (for example, Fusobacterium periodonticum and F. nucleatum) and donor abundance. These forces manifest as networks in which hub taxa donate unequally with phylogenetic neighbours. Our findings suggest that human microbiome LGT may be more ubiquitous than previously described.}, } @article {pmid39747693, year = {2025}, author = {Michoud, G and Peter, H and Busi, SB and Bourquin, M and Kohler, TJ and Geers, A and Ezzat, L and , and Battin, TJ}, title = {Mapping the metagenomic diversity of the multi-kingdom glacier-fed stream microbiome.}, journal = {Nature microbiology}, volume = {10}, number = {1}, pages = {217-230}, pmid = {39747693}, issn = {2058-5276}, support = {Vanishing Glaciers Project//NOMIS Stiftung (NOMIS Foundation)/ ; }, mesh = {*Microbiota/genetics ; *Rivers/microbiology ; *Metagenome ; *Bacteria/genetics/classification/isolation & purification ; *Ice Cover/microbiology ; Biofilms/growth & development ; Metagenomics ; Fungi/genetics/classification ; Geologic Sediments/microbiology ; Ecosystem ; Viruses/genetics/classification ; Biodiversity ; Phylogeny ; }, abstract = {Glacier-fed streams (GFS) feature among Earth's most extreme aquatic ecosystems marked by pronounced oligotrophy and environmental fluctuations. Microorganisms mainly organize in biofilms within them, but how they cope with such conditions is unknown. Here, leveraging 156 metagenomes from the Vanishing Glaciers project obtained from sediment samples in GFS from 9 mountains ranges, we report thousands of metagenome-assembled genomes (MAGs) encompassing prokaryotes, algae, fungi and viruses, that shed light on biotic interactions within glacier-fed stream biofilms. A total of 2,855 bacterial MAGs were characterized by diverse strategies to exploit inorganic and organic energy sources, in part via functional redundancy and mixotrophy. We show that biofilms probably become more complex and switch from chemoautotrophy to heterotrophy as algal biomass increases in GFS owing to glacier shrinkage. Our MAG compendium sheds light on the success of microbial life in GFS and provides a resource for future research on a microbiome potentially impacted by climate change.}, } @article {pmid39747692, year = {2025}, author = {Olm, MR and Spencer, SP and Takeuchi, T and Silva, EL and Sonnenburg, JL}, title = {Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut.}, journal = {Nature microbiology}, volume = {10}, number = {1}, pages = {112-125}, pmid = {39747692}, issn = {2058-5276}, support = {T32DK007056//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; K08DK134856//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; K08 DK134856/DK/NIDDK NIH HHS/United States ; DP1AT009892//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; T32 DK007056/DK/NIDDK NIH HHS/United States ; F32DK128865//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; }, mesh = {Humans ; *Immunoglobulin A/immunology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/immunology/metabolism ; Host Microbial Interactions/immunology ; Healthy Volunteers ; Intestinal Mucosa/microbiology/immunology/metabolism ; }, abstract = {IgA, the primary human antibody secreted from the gut mucosa, shapes the intestinal microbiota. Methodological limitations have hindered defining which microbial strains are targeted by IgA and the implications of binding. Here we develop a technique, metagenomic immunoglobulin sequencing (MIg-seq), that provides strain-level resolution of microbes coated by IgA and use it to determine IgA coating levels for 3,520 gut microbiome strains in healthy human faeces. We find that both health and disease-associated bacteria are targeted by IgA. Microbial genes are highly predictive of IgA binding levels; in particular, mucus degradation genes are correlated with high binding, and replication rates are significantly reduced for microbes bound by IgA. We demonstrate that IgA binding is more correlated with host immune status than traditional relative abundance measures of microbial community composition. This study introduces a powerful technique for assessing strain-level IgA binding in human stool, paving the way for deeper understanding of IgA-based host-microbe interactions.}, } @article {pmid39718972, year = {2025}, author = {Pittaluga, AM and Miccoli, FE and Guerrero, LD and Relling, AE}, title = {Effect of multispecies fungal extract supplementation on growth performance, nutrient digestibility, ruminal fermentation, and the rumen microbiome composition of beef cattle fed forage-based diets.}, journal = {Journal of animal science}, volume = {103}, number = {}, pages = {}, doi = {10.1093/jas/skae387}, pmid = {39718972}, issn = {1525-3163}, support = {//Biopremix Technologies LLC/ ; OHO01461//USDA National Institute of Food and Agriculture/ ; }, mesh = {Animals ; Cattle/physiology/growth & development ; *Rumen/microbiology/metabolism ; *Animal Feed/analysis ; *Digestion/drug effects ; *Diet/veterinary ; *Fermentation ; *Dietary Supplements/analysis ; Male ; *Gastrointestinal Microbiome/drug effects ; *Animal Nutritional Physiological Phenomena ; Female ; Cross-Over Studies ; Fungi ; Random Allocation ; Nutrients/metabolism ; }, abstract = {Our objective was to evaluate the effect of a multispecies fungal extract (MFE) on growth performance, apparent total tract digestibility (ATTD), fermentation characteristics, and rumen microbiome composition of beef cattle fed forage-based diets. For experiment 1, ruminally cannulated Angus × SimAngus cows (n = 4; body weight [BW] = 569 ± 21 kg) were used in a randomized crossover design with two 21-d study periods and a 23-d washout period to evaluate the effect of dietary inclusion of an MFE on in situ digestion, ruminal fermentation, and the composition of the rumen microbiome. Treatments consisted of a forage-based diet with or without the inclusion of a MFE. Rumen samples were collected on days 5, 10, and 20. Experiment 2 evaluated different inclusion rates of the MFE in a randomized complete block design using Angus × SimAngus-crossbred steers (n = 80; BW = 370 ± 44 kg). Steers were blocked by BW and randomly assigned to one of four treatments (2 pens/treatment): diet with no MFE, 0.02%, 0.04%, and 0.08% of the MFE (dry matter [DM] basis). Steers were fed a forage-based diet for 122 d. Subsets of 10 steers/treatment were randomly selected for the determination of ATTD on d 20, 40, and 60. All data were analyzed using the MIXED procedure of SAS. In exp 1, adding the MFE to the diet tended to increase the ruminal disappearance rate of the DM on day 10 (P = 0.06). No interactions or treatment effects were observed for the short-chain fatty acid profile of the rumen fluid (P ≥ 0.13). Metagenomic analysis of the rumen microbiome showed an MFE × d interaction for the Fibrobacter genus (P = 0.01), which on day 20 was less abundant in the rumen of cows fed the MFE. In exp 2, steers supplemented with 0.04% of MFE had a lower average daily gain and were lighter at the end of the experiment (cubic, P ≤ 0.04) compared to steers supplemented with 0.02% MFE. Steers fed the diet with 0.02% of MFE had the greatest gain-to-feed ratio among the MFE-supplemented groups (cubic, P < 0.01). Dietary inclusion of the MFE increased neutral detergent fiber digestibility (linear, P = 0.05). Steers supplemented with 0.04% of MFE had the greatest acid detergent fiber digestibility among treatments (quadratic, P = 0.03). Collectively, results showed that ruminal disappearance rate and digestibility of forage-based diets increased due to MFE supplementation, but did not translate into growth performance improvements or beneficially alter rumen fermentation.}, } @article {pmid39635985, year = {2025}, author = {Mulders, MCF and Van Koetsveld, PM and Feelders, RA and Hofland, LJ and de Herder, WW and Kraaij, R and Hofland, J}, title = {Gut microbial and functional alterations lead to metagenomic signatures for midgut neuroendocrine tumor patients and for carcinoid syndrome.}, journal = {Endocrine-related cancer}, volume = {32}, number = {2}, pages = {}, doi = {10.1530/ERC-24-0145}, pmid = {39635985}, issn = {1479-6821}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Neuroendocrine Tumors/microbiology/genetics/pathology ; Female ; Male ; Middle Aged ; Aged ; Malignant Carcinoid Syndrome/microbiology/genetics ; Adult ; Intestinal Neoplasms/microbiology/genetics/pathology ; Metagenomics/methods ; Feces/microbiology ; Metagenome ; }, abstract = {Midgut neuroendocrine tumors (NET) derive from enterochromaffin cells, which have a close interrelationship with intestinal microbiota. Recently, we have utilized 16S rRNA sequencing to uncover that midgut NET patients have a depleted gut microbiome and a specific fecal microbial signature. This study aims to validate these findings and to further characterize the role of microbes and microbial metabolic pathways in midgut NET patients with and without carcinoid syndrome (CS). Fecal samples from 60 midgut NET patients and 20 household-matched controls were subjected to whole metagenome sequencing. The gut microbial community composition of midgut NET patients differed from that of controls, with 2 genera, 17 species and 9 microbial pathways showing differential abundance (P < 0.001). No differences in the microbial composition were observed between midgut NET patients with and without CS (P > 0.05). However, we did observe changes in inter-genus correlations of Bacteroides, Odoribacter, Parasutterella, Klebsiella, Ruminococcus and Proteobacteria when comparing these two patient groups. A signature of 16 microbial species (area under the receiver operating characteristics (AUROC) curve 0.892) or 18 microbial pathways (AUROC 0.909) accurately predicted the presence of a midgut NET. Furthermore, a microbial signature consisting of 14 functional microbial pathways distinguished CS patients from non-CS patients (AUROC 0.807). Thus, this study confirms that the gut microbiome of midgut NET patients is altered at the metagenomic level, which is not related to the presence of CS. A fecal microbial signature could constitute a novel biomarker for the diagnosis of midgut NET or CS.}, } @article {pmid39541968, year = {2025}, author = {Nishijima, S and Stankevic, E and Aasmets, O and Schmidt, TSB and Nagata, N and Keller, MI and Ferretti, P and Juel, HB and Fullam, A and Robbani, SM and Schudoma, C and Hansen, JK and Holm, LA and Israelsen, M and Schierwagen, R and Torp, N and Telzerow, A and Hercog, R and Kandels, S and Hazenbrink, DHM and Arumugam, M and Bendtsen, F and Brøns, C and Fonvig, CE and Holm, JC and Nielsen, T and Pedersen, JS and Thiele, MS and Trebicka, J and Org, E and Krag, A and Hansen, T and Kuhn, M and Bork, P and , }, title = {Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations.}, journal = {Cell}, volume = {188}, number = {1}, pages = {222-236.e15}, doi = {10.1016/j.cell.2024.10.022}, pmid = {39541968}, issn = {1097-4172}, mesh = {*Gastrointestinal Microbiome ; *Feces/microbiology ; Humans ; Machine Learning ; Female ; Bacteria/classification/genetics/isolation & purification ; Male ; Metagenomics/methods ; Adult ; }, abstract = {The microbiota in individual habitats differ in both relative composition and absolute abundance. While sequencing approaches determine the relative abundances of taxa and genes, they do not provide information on their absolute abundances. Here, we developed a machine-learning approach to predict fecal microbial loads (microbial cells per gram) solely from relative abundance data. Applying our prediction model to a large-scale metagenomic dataset (n = 34,539), we demonstrated that microbial load is the major determinant of gut microbiome variation and is associated with numerous host factors, including age, diet, and medication. We further found that for several diseases, changes in microbial load, rather than the disease condition itself, more strongly explained alterations in patients' gut microbiome. Adjusting for this effect substantially reduced the statistical significance of the majority of disease-associated species. Our analysis reveals that the fecal microbial load is a major confounder in microbiome studies, highlighting its importance for understanding microbiome variation in health and disease.}, } @article {pmid39042247, year = {2024}, author = {Çalık Koç, G and Rezaei, F and Kahraman Ilıkkan, Ö and Bağdat, EŞ}, title = {Effect of seed priming with polyethylene glycol, distilled water, and sorbitol on physical, chemical quality parameters, and nodule microbiota of lentil.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {55}, number = {4}, pages = {3997-4008}, pmid = {39042247}, issn = {1678-4405}, support = {21/07//Baskent Üniversitesi/ ; }, mesh = {*Lens Plant/microbiology/chemistry ; *Seeds/microbiology/chemistry ; *Polyethylene Glycols/pharmacology/chemistry ; *Microbiota/drug effects ; *Water/chemistry ; *Sorbitol/pharmacology/metabolism ; Bacteria/classification/genetics/drug effects/isolation & purification ; Root Nodules, Plant/microbiology ; Germination/drug effects ; }, abstract = {The aim of this study was to investigate the effects of different seed priming solutions on physical and chemical quality parameters of lentils as well as nodule bacterial diversity before sowing. Therefore, lentil seeds were treated with polyethylene glycol (PEG 6000) (15%), sorbitol (6%), and distilled water, and none pretreated lentils (Lens culinaris) were used as control. The seeds were kept in these solutions for 24 h, then dried on toweling paper for 24 h, and used for the experiment. For nodule microbiota analysis, the plant root was divided into two equal parts, upper and lower, according to the root length and all nodules were collected from each region. According to the results, it was observed that emergence and flowering started late in the control compared to other seed priming treatments. Sorbitol application was found to provide advantages in terms of germination and seedling development. PEG and distilled water (DW) treatments showed an increase in total phenolic component activity; however, no significant change was observed in DPPH radical scavenging activity. Amplicon-based metagenomic analysis revealed that sorbitol and distilled water were the seed priming solutions altering the species diversity, especially Rhizobium sp. as the genus. In the comparison of samples taken from different parts of the root nodules, more Rhizobium sp. as a genus and Rhizobium leguminosarum as the species were found in the nodules collected from the top of the root. According to the overall results of lentil pod, lentil plant, and microbiota, sorbitol and DW can be considered to be a good priming solutions.}, } @article {pmid39789436, year = {2025}, author = {Cao, T and Guo, Y and Lin, L and Wang, D and Liu, Z and Zou, X and Ke, Y and Lv, Z}, title = {Effect of folpet on hypoglycaemia, intestinal microbiota, and drug resistance genes in mice.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {11}, pmid = {39789436}, issn = {1471-2180}, support = {JCYJ20210324124014040//Shenzhen Science and Technology Program/ ; JCYJ20210324124201004//Shenzhen Science and Technology Program/ ; SZSM202011008//Sanming Project of Medicine in Shenzhen/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; Mice ; *Hypoglycemia/genetics/chemically induced ; Blood Glucose/metabolism/drug effects ; Sulfonamides/pharmacology ; Bacteria/drug effects/genetics/classification/isolation & purification ; Male ; Metagenomics ; }, abstract = {BACKGROUND: Folpet is a nonspecific sulfonamide fungicide widely used to protect crops from mildew. However, the in vivo effects of folpet on glucose metabolism homeostasis, gut microbiota, and abundance of drug resistance genes remain unknown. The purpose of this study was to assess the effects of the pesticide, folpet, on glucose metabolism homeostasis, and folpet-induced changes in the intestinal microbiota and resistance genes in mice.

METHODS: Mice were orally administered folpet at 0, 1, 10, and 100 mg/kg body weight/day for 5 weeks. Blood sugar levels in mice were measured after 5 weeks of folpet administration. Metagenomic sequencing and drug resistance gene analyses were performed to explore changes in the abundance of gut microbiota members and drug resistance genes in mice after folpet administration. Correlation analysis was performed using metabolomics to explore the relationship between intestinal microbiota, drug resistance genes, and glucose metabolism.

RESULTS: Mice in the folpet group had significantly lower blood glucose levels than those in the control group. The abundance of Atopobium, Libanicoccus, Collinsella, and Parabacteroides in the intestinal microbiota of folpet-treated mice was significantly higher than that in the control group. However, the abundance of Mailhella, Bilophila, Roseburia, and Bacteroides were reduced in folpet-treated mice. Compared with the control group, the abundance of APH6-Ic and AAC6-Ie-APH2-Ia resistance genes in mice treated with folpet significantly increased. The abundance of tetQ, ermE, and BahA resistance genes was significantly reduced after folpet treatment.

CONCLUSIONS: Folpet is associated with changes in the abundance of gut microbiota in mice and may also affect the abundance of drug-resistance genes and the regulation of blood glucose levels.}, } @article {pmid39788986, year = {2025}, author = {Patova, A and Ribeiro, PA and Murillo, FJ and Riesgo, A and Taboada, S and Pomponi, SA and Rapp, HT and Kenchington, E and Xavier, JR}, title = {Population genomics and connectivity of Vazella pourtalesii sponge grounds of the northwest Atlantic with conservation implications of deep sea vulnerable marine ecosystems.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1540}, pmid = {39788986}, issn = {2045-2322}, mesh = {*Metagenomics ; *Porifera/genetics/metabolism ; Atlantic Ocean ; *Ecosystem ; *Aquatic Organisms/genetics/metabolism ; *Conservation of Natural Resources ; Hunting/statistics & numerical data ; Animal Distribution ; Animals ; Polymorphism, Single Nucleotide/genetics ; Nova Scotia ; }, abstract = {Sponges are key ecosystem engineers that shape, structure and enhance the biodiversity of marine benthic communities globally. Sponge aggregations and reefs are recognized as vulnerable marine ecosystems (or VMEs) due to their susceptibility to damage from bottom-contact fishing gears. Ensuring their long-term sustainability, preservation, and ecosystem functions requires the implementation of sound scientific conservation tools. Here, the genetic diversity, structure, and connectivity of the deep-sea glass sponge, Vazella pourtalesii (Schmidt, 1870), was investigated using 1,102 neutral SNPs obtained in RADseq. This species is distributed across the northwest Atlantic from Florida, USA to Nova Scotia, Canada and we sequenced samples covering this full distribution and provided evidence of strong genetic structure with two distinct clusters: Florida together with the Carolina Shelves and the Scotian Shelf. We estimated moderate levels of diversity with low migration across large distances (> 1000 kms) and high connectivity at smaller scales (< 300 kms). Further, fishing pressure on genetic diversity was evaluated, within two Sponge Conservation Areas (SCAs) on the Scotian Shelf. Those areas have different disturbance histories, and cumulative fishing pressure. Slightly lower levels of genetic diversity were found inside the SCAs, and yet they encompassed a high proportion of the diversity observed within the Scotian Shelf. We provide baseline data for future monitoring of the SCAs, discussing our findings in the light of existing area-based management tools.}, } @article {pmid39788961, year = {2025}, author = {Banerjee, G and Papri, SR and Huang, H and Satapathy, SK and Banerjee, P}, title = {Deep sequencing-derived Metagenome Assembled Genomes from the gut microbiome of liver transplant patients.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {39}, pmid = {39788961}, issn = {2052-4463}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Liver Transplantation ; *Metagenome ; High-Throughput Nucleotide Sequencing ; Akkermansia ; Fatty Liver/microbiology ; }, abstract = {Recurrence of metabolic dysfunction-associated steatotic liver disease (MASLD) after liver transplantation (LT) is a continuing concern. The role of gut microbiome dysbiosis in MASLD initiation and progression has been well established. However, there is a lack of comprehensive gut microbiome shotgun sequence data for patients experiencing MASLD recurrence after LT. In this data descriptor, we describe a dataset of deep metagenomic sequences of a well-defined LT recipient population. Community-based analysis revealed a high abundance of Akkermansia muciniphila, consistently observed in most patient samples with a low (0-2) MASLD Activity Score (NAS). We constructed 357 metagenome-assembled genomes (MAGs), including 220 high-quality MAGs (>90% completion). The abundance of different species of Bacteroides MAGs dominated in patient samples with NAS > 5 ("definite MASH"). In contrast, the MAGs of A. muciniphila, Akkermansia sp., and Blutia sp. dominated in samples from patients without MASH (NAS = 0-2). In addition, the phylogenetic analysis of A. muciniphila and Akkermansia sp. MAGs identified two new phylogroups of Akkermansia that are distinct from the previously reported three phylogroups.}, } @article {pmid39788783, year = {2025}, author = {Franz, K and Markó, L and Mähler, A and Chakaroun, R and Heinitz, S and Schlögl, H and Sacher, J and Steckhan, N and Dechend, R and Adams, N and Andersen, M and Glintborg, D and Viehweger, M and Bahr, LS and Forslund-Startceva, SK}, title = {Sex hormone-dependent host-microbiome interactions and cardiovascular risk (XCVD): design of a longitudinal multi-omics cohort study.}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e087982}, doi = {10.1136/bmjopen-2024-087982}, pmid = {39788783}, issn = {2044-6055}, mesh = {Humans ; *Cardiovascular Diseases/microbiology/epidemiology ; Longitudinal Studies ; Male ; Female ; *Gonadal Steroid Hormones/metabolism/blood ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; Transgender Persons ; Research Design ; Heart Disease Risk Factors ; Adult ; Sex Reassignment Procedures ; Multiomics ; }, abstract = {INTRODUCTION: Cardiovascular diseases (CVDs) present differently in women and men, influenced by host-microbiome interactions. The roles of sex hormones in CVD outcomes and gut microbiome in modifying these effects are poorly understood. The XCVD study examines gut microbiome mediation of sex hormone effects on CVD risk markers by observing transgender participants undergoing gender-affirming hormone therapy (GAHT), with findings expected to extrapolate to cisgender populations.

METHODS AND ANALYSES: This observational, longitudinal cohort study includes baseline, 1- and 2-year follow-ups with transgender participants beginning GAHT. It involves comprehensive phenotyping and microbiome genotyping, integrating computational analyses of high-dimensional data. Microbial diversity will be assessed using gut, skin, and oral samples via 16S rRNA and shotgun metagenomic sequencing of gut samples. Blood measurements will include sex hormones, CVD risk markers, cardiometabolic parameters, cytokines, and immune cell counts. Hair samples will be analysed for cortisol. Participants will complete online questionnaires on physical activity, mental health, stress, quality of life, fatigue, sleep, pain, and gender dysphoria, tracking medication use and diet to control for confounders. Statistical analyses will integrate phenomic, lifestyle, and multi-omic data to model health effects, testing gut microbiome mediation of CVD risk as the endocrine environment shifts between that typical for cisgender men to women and vice versa.

ETHICS AND DISSEMINATION: The study adheres to Good Clinical Practice and the Declaration of Helsinki. The protocol was approved by the Charité Ethical Committee (EA1/339/21). Signed informed consent will be obtained. Results will be published in peer-reviewed journals and conferences and shared as accessible summaries for participants, community groups, and the public, with participants able to view their data securely after public and patient involvement review for accessibility.

TRIAL REGISTRATION NUMBER: The XCVD study was registered on ClinicalTrials.gov (NCT05334888) as 'Sex-differential host-microbiome CVD risk - a longitudinal cohort approach (XCVD)" on 4 April 2022. Data set link can be found at https://classic.

CLINICALTRIALS: gov/ct2/show/NCT05334888.}, } @article {pmid39786931, year = {2025}, author = {Ni, B and Xiao, L and Lin, D and Zhang, TL and Zhang, Q and Liu, Y and Chen, Q and Zhu, D and Qian, H and Rillig, MC and Zhu, YG}, title = {Increasing pesticide diversity impairs soil microbial functions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {2}, pages = {e2419917122}, doi = {10.1073/pnas.2419917122}, pmid = {39786931}, issn = {1091-6490}, support = {41991332//MOST | National Natural Science Foundation of China (NSFC)/ ; 42307027//MOST | National Natural Science Foundation of China (NSFC)/ ; 42222701//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; 2021-DST-004//Ningbo S&T project/ ; 2023321//Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; }, mesh = {*Soil Microbiology ; *Pesticides ; *Bacteria/genetics/metabolism/classification/drug effects ; *Soil/chemistry ; *Fertilizers ; *Nitrogen/metabolism ; Phosphorus/metabolism ; Carbon/metabolism ; Sulfur/metabolism ; Agriculture/methods ; Metagenomics/methods ; Microbiota/drug effects ; }, abstract = {Pesticide application is essential for stabilizing agricultural production. However, the effects of increasing pesticide diversity on soil microbial functions remain unclear, particularly under varying nitrogen (N) fertilizer management practices. In this study, we investigated the stochasticity of soil microbes and multitrophic networks through amplicon sequencing, assessed soil community functions related to carbon (C), N, phosphorus (P), and sulfur (S) cycling, and characterized the dominant bacterial life history strategies via metagenomics along a gradient of increasing pesticide diversity under two N addition levels. Our findings show that higher pesticide diversity enriches the abundance of bacterial specialists and opportunists capable of degrading or resisting pesticides, reducing the proportion of bacterial generalists in the absence of N addition. These shifts can complicate multitrophic microbial networks. Under increased pesticide diversity, selective pressure may drive bacteria to streamline their average genome size to conserve energy while enhancing C, N, P, and S metabolic capacities, thus accelerating soil nutrient loss. In comparison, N addition was found to reduce bacterial niche differentiation at higher pesticide diversity, mitigating the impacts of network complexity and functional traits associated with pesticide diversity, ultimately alleviating soil nutrient loss. Our results reveal the contrasting impacts of pesticide diversity on microbial functions under different N input scenarios and emphasize that strategic N fertilizer management can mitigate the ecological effects of pesticide use in agricultural systems.}, } @article {pmid39781512, year = {2025}, author = {Sato, N and Katayama, K and Miyaoka, D and Uematsu, M and Saito, A and Fujimoto, K and Uematsu, S and Imoto, S}, title = {stana: an R package for metagenotyping analysis and interactive application based on clinical data.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {1}, pages = {lqae191}, pmid = {39781512}, issn = {2631-9268}, mesh = {Humans ; *Software ; *Gastrointestinal Microbiome/genetics ; Crohn Disease/genetics/microbiology ; Metagenomics/methods ; Parkinson Disease/genetics ; Kidney Failure, Chronic/genetics ; Metagenome/genetics ; }, abstract = {Metagenotyping of metagenomic data has recently attracted increasing attention as it resolves intraspecies diversity by identifying single nucleotide variants. Furthermore, gene copy number analysis within species provides a deeper understanding of metabolic functions in microbial communities. However, a platform for examining metagenotyping results based on relevant grouping data is lacking. Here, we have developed the R package, stana, for the processing and analysis of metagenotyping results. The package consists of modules for preprocessing, statistical analysis, functional analysis and visualization. An interactive analysis environment for exploring the metagenotyping results was also developed and publicly released with over 1000 publicly available metagenome samples related to human diseases. Three examples exploring the relationship between the metagenotypes of the gut microbiome and human diseases are presented-end-stage renal disease, Crohn's disease and Parkinson's disease. The results suggest that stana facilitated the confirmation of the original study's findings and the generation of a new hypothesis. The GitHub repository for the package is available at https://github.com/noriakis/stana.}, } @article {pmid39779932, year = {2025}, author = {Wei, Y and Zhu, Y and Yang, L and Chen, C and Yue, M and Mao, Z and Wang, Y and Li, Q and Li, Y and Lv, J and Xue, W}, title = {Effects of oil pollution on the growth and rhizosphere microbial community of Calamagrostis epigejos.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1278}, pmid = {39779932}, issn = {2045-2322}, support = {22NYYF029//Xi'an Agricultural Technology R&D Projects/ ; S2024-JC-YB-2574//Natural Science Foundation of Science and Technology Department of Shaanxi Province/ ; 2020ZDLSF06-01//Natural Science Foundation of Science and Technology Department of Shaanxi Province/ ; 2021K-25//Strategic Reserve Talent Training Program of Shaanxi Academy of Sciences/ ; 2023JH-NJGG-0167//Xi'an Science Technology Bureau Fund/ ; KRDL K6-2207039//the Project of the First Investigation of Wild Plants Resources in Xi'an/ ; }, mesh = {*Soil Microbiology ; *Rhizosphere ; *Fungi/genetics ; *Bacteria/genetics/classification ; *Archaea/genetics/growth & development/metabolism ; Petroleum Pollution/adverse effects ; Petroleum ; Microbiota/drug effects ; Soil Pollutants ; }, abstract = {Bacteria, fungi, archaea, and viruses are reflective organisms that indicate soil health. Investigating the impact of crude oil pollution on the community structure and interactions among bacteria, fungi, archaea, and viruses in Calamagrostis epigejos soil can provide theoretical support for remediating crude oil pollution in Calamagrostis epigejos ecosystems. In this study, Calamagrostis epigejos was selected as the research subject and subjected to different levels of crude oil addition (0 kg/hm[2], 10 kg/hm[2], 40 kg/hm[2]). Metagenomic sequencing technology was employed to analyze the community structure and diversity of soil bacteria, fungi, archaea, and viruses. Additionally, molecular ecological network analysis was integrated to explore species interactions and ecosystem stability within these microbial communities. The functional profiles of soil microorganisms were elucidated based on data from the KEGG database. Results demonstrated a significant increase in petroleum hydrocarbon content, polyphenol oxidase activity, hydrogen peroxide enzyme activity, and acid phosphatase activity upon crude oil addition, while β-glucosidase content, fiber disaccharide hydrolase content, and tiller number decreased (P < 0.05). Proteobacteria and Actinobacteria were identified as dominant bacterial phyla; Ascomycota, Basidiomycota, and Mucoromycota were found to be dominant fungal phyla; Thaumarchaeota emerged as a dominant archaeal phylum; and Uroviricota represented a dominant viral phylum. The diversity of soil bacterial, fungal, archaeal, and viral communities increased with higher amounts of added crude oil. Ecological network analysis revealed a robust collaborative relationship among bacterial, fungal, archaeal, and viral community species in the control treatment (CK), while strong competitive relationships were observed among these species in the treatments with 10% (F10) and 40% (F40) crude oil concentrations. Structural equation modeling analysis indicated significant positive correlations between fungal community, viral community, enzyme activity, and plant growth; conversely, bacterial and archaeal communities showed significant negative correlations with plant growth (P < 0.05). Correlation analysis identified acid phosphatase as the primary environmental factor influencing soil microbial function. Acid phosphatase levels along with tiller number, aboveground biomass, and petroleum hydrocarbons significantly influenced the fungal community (P < 0.05), while underground biomass had a significant impact on the archaeal community (P < 0.05). Acid phosphatase levels along with cellulose-hydrolyzing enzymes, tiller number, and petroleum hydrocarbons exhibited significant effects on the viral community (P < 0.05). This study investigated variations in bacterial, fungal, archaeal, and viral communities under different crude oil concentrations as well as their driving factors, providing a theoretical foundation for evaluating Calamagrostis epigejos' potential to remediate crude oil pollution.}, } @article {pmid39779716, year = {2025}, author = {Gałęcka, I and Rychlik, A and Całka, J}, title = {Influence of selected dosages of plastic microparticles on the porcine fecal microbiome.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1269}, pmid = {39779716}, issn = {2045-2322}, support = {2020/37/N/NZ7/01383//Narodowe Centrum Nauki/ ; The Regional Initiative of Excellence Program//Minister of Science Poland/ ; }, mesh = {Animals ; Swine ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Microplastics/toxicity ; Female ; Plastics ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Studies conducted so far have shown that nano- and microplastic may disturb the intestinal microenvironment by interacting with the intestinal epithelium and the gut microbiota. Depending on the research model used, the effect on the microbiome is different-an increase or decrease in selected taxa resulting in the development of dysbiosis. Dysbiosis may be associated with intestinal inflammation, development of mental disorders or diabetes. The aim of the study was to analyze the intestinal microbiome in 15 gilts divided into 3 research groups (n = 5; control group, receiving micropartices at a dose 0.1 g/day (LD) and 1 g/day (HD)). Feaces were collected before and after 28 days of exposure to PET microplastics. The analysis of the intestinal microbiome was performed using next-generation sequencing. Alpha and beta diversity indices were compared, showing, that repetition affected only the abundance indices in the control and LD groups, but not in the HD group. The relationships between the number of reads at the phylum, genus and species level and the microplastic dose were calculated using statistical methods (r-Pearson correlation, generalized regression model, analysis of variance). The statistical analysis revealed, that populations of Family XIII AD3011 group, Coprococcus, V9D2013 group, UCG-010 and Sphaerochaeta increased with increasing MP-PET dose. The above-mentioned taxa are mainly responsible for the production of short-chain fatty acids (SCFA). It may be assumed, that SCFA are one of the mechanisms involved in the response to oral exposure to MP-PET.}, } @article {pmid39779118, year = {2025}, author = {Wang, C and Bin, Z and Wang, L and Zhu, G and Tang, S and Chen, Y and Xiao, D and Guo, X}, title = {Metagenomic and metabolomic profiling analyses to unravel the formation mechanism of n-propanol during the first and second round of Jiangxiangxing Baijiu fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {200}, number = {}, pages = {115459}, doi = {10.1016/j.foodres.2024.115459}, pmid = {39779118}, issn = {1873-7145}, mesh = {*Fermentation ; *Metabolomics/methods ; *1-Propanol/metabolism ; *Metagenomics/methods ; Lactobacillus/metabolism/genetics ; Alcoholic Beverages/microbiology ; Pichia/metabolism/genetics ; Saccharomyces cerevisiae/metabolism/genetics ; Food Microbiology ; Microbiota ; }, abstract = {N-propanol is one of the higher alcohols, a moderate amount of n-propanol is beneficial for the harmony of the liquor body, whereas excessive or repeated intake will lead to discomfort and pose significant harm to human health. In actual production process of Jiangxiangxing Baijiu, the n-propanol content of the base baijiu in first round (FR) is far higher than that of second round (SR). Nevertheless, the formation mechanism and the key n-propanol producing microbials remain unclear and this limits the quality control of baijiu fermentation. Here, we combined metagenomics and metabolomics to verify the biosynthesis pathway of n-propanol and to identify characteristic microorganisms in FR and SR. The results showed that the preliminary period of pit fermentation was critical for the accumulation of n-propanol. FR was enriched in Lactobacillus plantarum, Lactobacillus ponits, Lactobacillus brevis and Lactobacillus panis, while it was harbored greater abundances of Pichia kudriazevii, Saccharomyces cerevisiae and Lactobacillus acetotolerans in SR. Function analysis combined with KEGG providing comprehensive evidence for the main synthetic pathways of n-propanol in Jiangxiangxing baijiu, and L. panis was key microbial. In addition, the experiments of inoculating L. panis and L. acetotolerans in situ indicated L. panis was mainly responsible for n-propanol production while L. acetotolerans not conducive to the production of n-propanol. Besides, the bioturbation effect on microbiota and flavor compounds were also analyzed. These results are useful for elucidating the mechanism of flavor formation in baijiu fermentation and promoting the further application of bioturbation technology in the traditional fermentation industry.}, } @article {pmid39778056, year = {2025}, author = {Silva, JK and Hervé, V and Mies, US and Platt, K and Brune, A}, title = {A Novel Lineage of Endosymbiotic Actinomycetales: Genome Reduction and Acquisition of New Functions in Bifidobacteriaceae Associated With Termite Gut Flagellates.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70010}, pmid = {39778056}, issn = {1462-2920}, support = {//Max-Planck-Gesellschaft/ ; }, mesh = {*Symbiosis ; Animals ; *Isoptera/microbiology ; *Genome, Bacterial ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Actinomycetales/genetics/metabolism ; Gene Transfer, Horizontal ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/parasitology ; Metagenome ; }, abstract = {Cellulolytic flagellates are essential for the symbiotic digestion of lignocellulose in the gut of lower termites. Most species are associated with host-specific consortia of bacterial symbionts from various phyla. 16S rRNA-based diversity studies and taxon-specific fluorescence in situ hybridization revealed a termite-specific clade of Actinomycetales that colonise the cytoplasm of Trichonympha spp. and other gut flagellates, representing the only known case of intracellular Actinomycetota in protists. Comparative analysis of eleven metagenome-assembled genomes from lower termites allowed us to describe them as new genera of Bifidobacteriaceae. Like the previously investigated Candidatus Ancillula trichonymphae, they ferment sugars via the bifidobacterium shunt but, unlike their free-living relatives, experienced significant genome erosion. Additionally, they acquired new functions by horizontal gene transfer from other gut bacteria, including the capacity to produce hydrogen. Members of the genus Ancillula (average genome size 1.56 ± 0.2 Mbp) retained most pathways for the synthesis of amino acids, including a threonine/serine exporter, providing concrete evidence for the basis of the mutualistic relationship with their host. By contrast, Opitulatrix species (1.23 ± 0.1 Mbp) lost most of their biosynthetic capacities, indicating that an originally mutualistic symbiosis is on the decline.}, } @article {pmid39777846, year = {2025}, author = {Liu, R and He, X and Ren, G and Li, DW and Zhao, M and Lehtovirta-Morley, L and Todd, JD and Zhang, XH and Liu, J}, title = {Niche Partitioning and Intraspecific Variation of Thaumarchaeota in Deep Ocean Sediments.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70018}, doi = {10.1111/1462-2920.70018}, pmid = {39777846}, issn = {1462-2920}, support = {41976101//National Natural Science Foundation of China/ ; 92051115//National Natural Science Foundation of China/ ; 92251303//National Natural Science Foundation of China/ ; 202141009//Fundamental Research Funds for the Central Universities/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 2022QNLM030004-3//Laoshan Laboratory/ ; LSKJ202203206//Laoshan Laboratory/ ; ZR2022YQ38//Natural Science Foundation of Shandong Province/ ; ZR2024JQ006//Natural Science Foundation of Shandong Province/ ; }, mesh = {*Geologic Sediments/microbiology ; *Archaea/genetics/classification ; *Phylogeny ; Oceans and Seas ; Metagenome ; Ecosystem ; Seawater/microbiology ; Metagenomics ; Ammonia/metabolism ; Genome, Archaeal ; }, abstract = {Deep-sea sediments contain a large number of Thaumarchaeota that are phylogenetically distinct from their pelagic counterparts. However, their ecology and evolutionary adaptations are not well understood. Metagenomic analyses were conducted on samples from various depths of a 750-cm sediment core collected from the Mariana Trench Challenger Deep. The abundance of Thaumarchaeota and archaeal amoA generally decreased with depth, except for an unexpected peak midway through the core. The thaumarchaeotal metagenome-assembled genomes were classified into diverse phylogenetic clusters associated with amoA-NP-γ, amoA-NP-θ, and amoA-NP-δ of ammonia-oxidising Thaumarchaeota and non-ammonia-oxidising lineages. The most abundant group was within amoA-NP-γ, which is usually found in coastal and shallow habitats, indicating potential niche expansion from marine shallow to hadal environments. This benthic group showed within-species genomic variations compared to the previously identified Hadal water group, suggesting microdiversification of hadal Thaumarchaeota along with niche separation between benthic and pelagic environments. Evolutionary adaptations associated with the benthic-to-pelagic transition included reduced genome size, loss of motility/cell adhesion, altered energy metabolism, and different mechanisms for substrate acquisition and regulation (e.g., ammonium). These findings offer new insights into the evolution of hadal Thaumarchaeota and demonstrate, for the first time, intraspecies-level genomic variation in Thaumarchaeota related to the benthic-versus-pelagic niche partitioning in the deep ocean.}, } @article {pmid39777550, year = {2025}, author = {Byers, AK and Wakelin, SA and Condron, L and Black, A}, title = {Land Use Change Disrupts the Network Complexity and Stability of Soil Microbial Carbon Cycling Genes Across an Agricultural Mosaic Landscape.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {167}, pmid = {39777550}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Carbon Cycle ; New Zealand ; *Agriculture ; *Soil/chemistry ; *Microbiota ; *Bacteria/genetics/classification/metabolism ; Carbon/metabolism ; Gene Regulatory Networks ; Forests ; Ecosystem ; }, abstract = {To understand the effects of agricultural land use change and management on soil carbon (C) cycling, it is crucial to examine how these changes can influence microbial soil C cycling. Network analysis can offer insights into the structure, complexity, and stability of the soil microbiome in response to environmental disturbances, including land use change. Using SparCC-based co-occurrence networks, we studied how land use change impacts the connectivity, complexity, and stability of microbial C-cycling gene networks across an agricultural mosaic landscape in Canterbury, New Zealand. The most densely connected networks were found in land uses that were under the most intensive agricultural management, or under naturally regenerating vegetation. The microbial C-cycling gene networks from both land uses presented high network connectivity, low modularity, and a low proportion of negative gene interactions. In contrast, microbial C-cycling genes from native forests, which had the most stable and undisturbed plant cover, had the lowest network connectivity, highest modularity, and a greater proportion of negative gene interactions. Although the differences in total soil C content between land uses were small, the large effects of land use on the network structure of microbial C-cycling genes may have important implications for long-term microbial soil C cycling. Furthermore, this research highlights the value of using microbial network analysis to study the metabolic gene interactions shaping the functional structure of soil microbial communities in a manner not typically captured by more traditional forms of microbial diversity analysis.}, } @article {pmid39774426, year = {2024}, author = {Segura, D and Sharma, D and Espin-Garcia, O}, title = {Comparing subsampling strategies for metagenomic analysis in microbial studies using amplicon sequence variants versus operational taxonomic units.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0315720}, pmid = {39774426}, issn = {1932-6203}, mesh = {Humans ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; Gastrointestinal Microbiome/genetics ; Microbiota/genetics ; Infant ; Sequence Analysis, DNA/methods ; Bacteria/genetics/classification ; Metagenome/genetics ; }, abstract = {The microbiome is increasingly regarded as a key component of human health, and analysis of microbiome data can aid in the development of precision medicine. Due to the high cost of shotgun metagenomic sequencing (SM-seq), microbiome analyses can be done cost-effectively in two phases: Phase 1-sequencing of 16S ribosomal RNA, and Phase 2-SM-seq of an informative subsample. Existing research suggests strategies to select the subsample based on biological diversity and dissimilarity metrics calculated using operational taxonomic units (OTUs). However, the microbiome field has progressed towards amplicon sequencing variants (ASVs), as they provide more precise microbe identification and sample diversity information. The aim of this work is to compare the subsampling strategies for two-phase metagenomic studies when using ASVs instead of OTUs, and to propose data driven strategies for subsample selection through dimension reduction techniques. We used 199 samples of infant-gut microbiome data from the DIABIMMUNE project to generate ASVs and OTUs, then generated subsamples based on five existing biologically driven subsampling methods and two data driven methods. Linear discriminant analysis Effect Size (LEfSe) was used to assess differential representation of taxa between the subsamples and the overall sample. The use of ASVs showed a 50-93% agreement in the subsample selection with the use of OTUs for the subsampling methods evaluated, and showed a similar bacterial representation across all methods. Although sampling using ASVs and OTUs typically lead to similar results for each subsample, ASVs had more clades that differed in expression levels between allergic and non-allergic individuals across all sample sizes compared to OTUs, and led to more biomarkers discovered at Phase 2-SM-seq level.}, } @article {pmid39770890, year = {2024}, author = {Wells, RK and Torres, A and Mau, MK and Maunakea, AK}, title = {Racial-Ethnic Disparities of Obesity Require Community Context-Specific Biomedical Research for Native Hawaiians and Other Pacific Islanders.}, journal = {Nutrients}, volume = {16}, number = {24}, pages = {}, pmid = {39770890}, issn = {2072-6643}, support = {P20GM139753//NIH-NIGMS/ ; R01MD016593//NIH-NIMHD/ ; R56MD014630//NIH-NIMHD/ ; UG03HL169657//NIH-NHLBI/ ; }, mesh = {Humans ; *Native Hawaiian or Other Pacific Islander ; *Obesity/ethnology ; Hawaii/epidemiology ; *Biomedical Research ; Health Status Disparities ; Gastrointestinal Microbiome ; Pacific Island People ; }, abstract = {Compared to the general population of Hawai'i, Native Hawaiians and Other Pacific Islanders (NHPI) shoulder a disproportionately high risk for obesity-related cardiometabolic disorders, such as type 2 diabetes and cardiovascular disease. The gut microbiome is an area of rapid research interest for its role in regulating adjacent metabolic pathways, offering novel opportunities to better understand the etiology of these health disparities. Obesity and the gut microbiome are influenced by regional, racial-ethnic, and community-specific factors, limiting the generalizability of current literature for understudied populations. Additionally, anthropometric and directly measured obesity indices are variably predictive of adiposity and metabolic health risk in this diverse population. Thus, further NHPI-inclusive research is required to adequately characterize community-specific factors in the context of obesity-related disease etiology. Culturally responsible research ethics and scientific communication are crucial to conducting such research, especially among indigenous and understudied populations. In this review, we explore these limitations in current literature, emphasizing the urgent need for NHPI-inclusive research to assess community-specific factors accurately. Such accuracy in Indigenous health research may ensure that findings relevant to individual or public health recommendations and/or policies are meaningful to the communities such research aims to serve.}, } @article {pmid39770772, year = {2024}, author = {Long, Y and Zhang, X and Peng, X and Yang, H and Ni, H and Zou, L and Long, Z}, title = {Metagenomic Analysis Revealing the Impact of Water Contents on the Composition of Soil Microbial Communities and the Distribution of Major Ecological Functional Genes in Poyang Lake Wetland Soil.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770772}, issn = {2076-2607}, support = {31960015//The National Natural Science Foundation of China/ ; 20192BAB204001//Natural Science Foundation of Jiangxi Province, China/ ; }, abstract = {Poyang Lake is the largest freshwater lake in China, which boasts unique hydrological conditions and rich biodiversity. In this study, metagenomics technology was used to sequence the microbial genome of soil samples S1 (sedimentary), S2 (semi-submerged), and S3 (arid) with different water content from the Poyang Lake wetland; the results indicate that the three samples have different physicochemical characteristics and their microbial community structure and functional gene distribution are also different, resulting in separate ecological functions. The abundance of typical ANME archaea Candidatus Menthanoperedens and the high abundance of mcrA in S1 mutually demonstrate prominent roles in the methane anaerobic oxidation pathway during the methane cycle. In S2, the advantageous bacterial genus Nitrospira with ammonia oxidation function is validated by a large number of nitrification functional genes (amoA, hao, nxrA), manifesting in that it plays a monumental role in nitrification in the nitrogen cycle. In S3, the dominant bacterial genus Nocardioides confirms a multitude of antibiotic resistance genes, indicating their crucial role in resistance and their emphatic research value for microbial resistance issues. The results above have preliminarily proved the role of soil microbial communities as indicators predicting wetland ecological functions, which will help to better develop plans for restoring ecological balance and addressing climate change.}, } @article {pmid39770743, year = {2024}, author = {Peng, X and Li, S and Dou, W and Li, M and Gontcharov, AA and Peng, Z and Qi, B and Wang, Q and Li, Y}, title = {Metagenomic Insight into the Associated Microbiome in Plasmodia of Myxomycetes.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770743}, issn = {2076-2607}, support = {31770011//National Natural Science Foundation of China/ ; }, abstract = {During the trophic period of myxomycetes, the plasmodia of myxomycetes can perform crawling feeding and phagocytosis of bacteria, fungi, and organic matter. Culture-based studies have suggested that plasmodia are associated with one or several species of bacteria; however, by amplicon sequencing, it was shown that up to 31-52 bacteria species could be detected in one myxomycete, suggesting that the bacterial diversity associated with myxomycetes was likely to be underestimated. To fill this gap and characterize myxomycetes' microbiota and functional traits, the diversity and functional characteristics of microbiota associated with the plasmodia of six myxomycetes species were investigated by metagenomic sequencing. The results indicate that the plasmodia harbored diverse microbial communities, including eukaryotes, viruses, archaea, and the dominant bacteria. The associated microbiomes represented more than 22.27% of the plasmodia genome, suggesting that these microbes may not merely be parasitic or present as food but rather may play functional roles within the plasmodium. The six myxomycetes contained similar bacteria, but the bacteria community compositions in each myxomycete were species-specific. Functional analysis revealed a highly conserved microbial functional profile across the six plasmodia, suggesting they may serve a specific function for the myxomycetes. While the host-specific selection may shape the microbial community compositions within plasmodia, functional redundancy ensures functional stability across different myxomycetes.}, } @article {pmid39769095, year = {2024}, author = {Mohan, B and Majeed, A and Thingujam, D and Burton, SS and Cowart, KE and Pajerowska-Mukhtar, KM and Mukhtar, MS}, title = {Amplicon Sequencing Analysis of Submerged Plant Microbiome Diversity and Screening for ACC Deaminase Production by Microbes.}, journal = {International journal of molecular sciences}, volume = {25}, number = {24}, pages = {}, doi = {10.3390/ijms252413330}, pmid = {39769095}, issn = {1422-0067}, support = {IOS-2038872//National Science Foundation/ ; 2418230//National Science Foundation/ ; }, mesh = {*Carbon-Carbon Lyases/genetics/metabolism ; *Microbiota/genetics ; *Plants/microbiology ; Bacteria/genetics/classification/enzymology ; Metagenomics/methods ; Phylogeny ; Biodiversity ; }, abstract = {Submerged plants can thrive entirely underwater, playing a crucial role in maintaining water quality, supporting aquatic organisms, and enhancing sediment stability. However, they face multiple challenges, including reduced light availability, fluctuating water conditions, and limited nutrient access. Despite these stresses, submerged plants demonstrate remarkable resilience through physiological and biochemical adaptations. Additionally, their interactions with microbial communities are increasingly recognized as pivotal in mitigating these environmental stresses. Understanding the diversity of these microbial communities is crucial for comprehending the complex interactions between submerged plants and their environments. This research aims to identify and screen microbes from submerged plant samples capable of producing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and to explore microbial diversity through metagenomic analysis. Microbes were isolated and screened for ACC deaminase production, and metagenomic techniques, including co-occurrence network analysis, were used to examine microbial diversity and interactions within the communities. ACC deaminase-producing microbes can significantly enhance plant metabolism under stress conditions. The identification of the culturable bacteria revealed that most of these microbes belong to the genera Pseudomonas, Bacillus, and Acinetobacter. A total of 177 microbial strains were cultured, with molecular identification revealing 79 reductant, 86 non-reductant, and 12 uncultured strains. Among 162 samples screened for ACC deaminase activity, 50 tested positive. To further understand microbial dynamics, samples were collected from both natural sources and artificial pond reservoirs to assess the impact of the location on flood-associated microbiomes in submerged plants. Metagenomic analysis was conducted on both the epiphytic and endophytic samples. By exploring the overall composition and dynamics of microbial communities associated with submerged plants, this research seeks to deepen our understanding of plant-microbe interactions in aquatic environments. The microbial screening helped to identify the diverse microbes associated with ACC deaminase activity in submerged plants and amplicon sequencing analysis paved the way towards identifying the impact of the location in shaping the microbiome and the diversity associated with endophytic and epiphytic microbes. Co-occurrence network analysis further highlighted the intricate interactions within these microbial communities. Notably, ACC deaminase activity was observed in plant-associated microbes across different locations, with distinct variations between epiphytic and endophytic populations as identified through co-occurrence network analysis.}, } @article {pmid39768398, year = {2024}, author = {Al-Awthan, YS and Mir, R and Alatawi, FA and Alatawi, AS and Almutairi, FM and Khafaga, T and Shohdi, WM and Fakhry, AM and Alharbi, BM}, title = {Metagenome Analysis Identified Novel Microbial Diversity of Sandy Soils Surrounded by Natural Lakes and Artificial Water Points in King Salman Bin Abdulaziz Royal Natural Reserve, Saudi Arabia.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {12}, pages = {}, pmid = {39768398}, issn = {2075-1729}, abstract = {BACKGROUND: Soil microbes play a vital role in the ecosystem as they are able to carry out a number of vital tasks. Additionally, metagenomic studies offer valuable insights into the composition and functional potential of soil microbial communities. Furthermore, analyzing the obtained data can improve agricultural restoration practices and aid in developing more effective environmental management strategies.

METHODOLOGY: In November 2023, sandy soil samples were collected from ten sites of different geographical areas surrounding natural lakes and artificial water points in the Tubaiq conservation area of King Salman Bin Abdulaziz Royal Natural Reserve (KSRNR), Saudi Arabia. In addition, genomic DNA was extracted from the collected soil samples, and 16S rRNA sequencing was conducted using high-throughput Illumina technology. Several computational analysis tools were used for gene prediction and taxonomic classification of the microbial groups.

RESULTS: In this study, sandy soil samples from the surroundings of natural and artificial water resources of two distinct natures were used. Based on 16S rRNA sequencing, a total of 24,563 OTUs were detected. The metagenomic information was then categorized into 446 orders, 1036 families, 4102 genera, 213 classes, and 181 phyla. Moreover, the phylum Pseudomonadota was the most dominant microbial community across all samples, representing an average relative abundance of 34%. In addition, Actinomycetes was the most abundant class (26%). The analysis of clustered proteins assigned to COG categories provides a detailed understanding of the functional capabilities and adaptation of microbial communities in soil samples. Amino acid metabolism and transport were the most abundant categories in the soil environment.

CONCLUSIONS: Metagenome analysis of sandy soils surrounding natural lakes and artificial water points in the Tubaiq conservation area of KSRNR (Saudi Arabia) has unveils rich microbial activity, highlighting the complex interactions and ecological roles of microbial communities in these environments.}, } @article {pmid39768341, year = {2024}, author = {Maffia, A and Scotti, R and Wood, T and Muscolo, A and Lepore, A and Acocella, E and Celano, G}, title = {Transforming Agricultural and Sulfur Waste into Fertilizer: Assessing the Short-Term Effects on Microbial Biodiversity via a Metagenomic Approach.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {12}, pages = {}, pmid = {39768341}, issn = {2075-1729}, support = {FARB2023//University of Salerno and the doctoral research funds of the Mediterranean University of Reggio Calabria./ ; }, abstract = {Fungi and soil bacteria are vital for organic matter decomposition and biogeochemical cycles, but excessive synthetic fertilizer use contributes to soil degradation and loss of biodiversity. Despite this, about 97% of soil microorganisms are unculturable, making them difficult to study. Metagenomics offers a solution, enabling the direct extraction of DNA from soil to uncover microbial diversity and functions. This study utilized metagenomics to analyze the rhizosphere of two-year-old Tonda di Giffoni hazelnut saplings treated with synthetic NPK, composted olive pomace, and an innovative fertilizer derived from sulfur-based agro-industrial waste stabilized with bentonite clay. Using 16S rDNA for bacteria and ITS2 for fungi, Illumina sequencing provided insights into microbial responses to different fertilizer treatments. The results highlighted a significant increase in the abundance of beneficial microorganisms such as Thiobacillus, Pseudoxanthomonas, and Thermomyces, especially when organic materials were included. Additionally, microbial biodiversity improved with organic inputs, as shown by increased species richness (Chao1) and diversity (Bray-Curtis) greater than 20% compared with NPK and unfertilized soils (CTR). These findings emphasize the importance of organic fertilization in enhancing soil microbial health, offering a sustainable approach to improving soil quality and hazelnut productivity.}, } @article {pmid39766799, year = {2024}, author = {Xu, X and Gao, X and Gui, C and Wang, H and Liu, X and Wu, G}, title = {Metagenomic Insights into the Enhancement of Bioavailable Nitrogen in Continuous Cropping Soil Through the Application of Traditional Chinese Medicine Residue Following Fumigation.}, journal = {Genes}, volume = {15}, number = {12}, pages = {}, pmid = {39766799}, issn = {2073-4425}, support = {32060639//National Natural Science Foundation of China/ ; 32060640//National Natural Science Foundation of China/ ; 32260704//National Natural Science Foundation of China/ ; 202105AC160037//Reserve Talents Project for Yunnan Young and Middle-aged Academic and Technical Leaders c/ ; 202205AC160077//Reserve Talents Project for Yunnan Young and Middle-aged Academic and Technical Leadersc/ ; NA//Hunan Engineering Research Center for Green Prevention and Control of Soil-borne Diseases/ ; NA//Hunan Engineering Research Center for Research and Development of plant resources in Nanling area, Hunan Province/ ; }, mesh = {*Soil Microbiology ; *Fumigation/methods ; *Nitrogen/metabolism ; *Rhizosphere ; *Soil/chemistry ; *Fertilizers/analysis ; Metagenomics/methods ; Medicine, Chinese Traditional/methods ; Bacteria/genetics/drug effects/growth & development ; Microbiota/drug effects ; Metagenome ; Capsicum/growth & development/microbiology/drug effects/genetics ; }, abstract = {Background/Objectives: Chemical fumigation can effectively inhibit the occurrence of soil-borne diseases; however, this approach can negatively affect the structure of the soil microbial community. The combination of soil fumigant and organic fertilizer application thus represents a widely adopted strategy in agricultural practice. Traditional Chinese medicine residue (TCMR) is a high-quality organic fertilizer; however, the impact of post-fumigation TCMR application on keystone taxa and their functional traits remains uncertain. Methods: This study examined the effects of five fertilization treatments on the diversity, key species, and related functional genes of microbial communities in rhizosphere soil of continuous cropping pepper. Results: Chemical fumigation followed by TCMR application markedly enhanced soil nutrient content in the rhizosphere and significantly influenced microbial community composition as well as functional gene patterns associated with microbial nitrogen cycling. It was also strongly correlated with soil bioavailable nitrogen content. The abundance of keystone bacterial species (Pseudomonadota, Actinomycetota, and Bacillota) substantially increased following TCMR application, alongside a notable rise in Ascomycota abundance within the fungal community. This shift contributed to an increase in beneficial bacterial abundance while reducing that of harmful bacteria. Additionally, TCMR addition affected the abundance of denitrification and DNRA genes involved in nitrogen cycling; specifically, nirB and nirK were strongly associated with soil organic nitrogen content. Conclusions: The combined application of chemical fumigants and TCMR modified the composition of keystone microbial community species by influencing rhizosphere soil TN and other nutrients, and these alterations were linked to multiple nitrogen-cycling functional genes.}, } @article {pmid39763701, year = {2025}, author = {Hereira-Pacheco, S and Arias-Del Razo, I and Miranda-Carrazco, A and Dendooven, L and Estrada-Torres, A and Navarro-Noya, YE}, title = {Metagenomic analysis of fungal assemblages at a regional scale in high-altitude temperate forest soils: alternative methods to determine diversity, composition and environmental drivers.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18323}, pmid = {39763701}, issn = {2167-8359}, mesh = {*Soil Microbiology ; *Forests ; *Metagenomics/methods ; *Fungi/genetics/classification/isolation & purification ; *Altitude ; Mexico ; Mycobiome/genetics ; Biodiversity ; }, abstract = {BACKGROUND: Understanding the diversity and distribution of fungal communities at a regional scale is important since fungi play a crucial role in ecosystem functioning. Our study used environmental metagenomics to determine fungal communities in mountainous forest soils in the central highlands of Mexico.

METHODS: We used four different bioinformatic workflows to profile fungal assemblages, i.e., Geneious+UNITE, single- and paired-end microbial community profiling (MiCoP), and Kraken2.

RESULTS: The workflows yielded different results; one detected a higher abundance of ectomycorrhizal (EcM) and saprophytic fungi, while the other identified more saprophytic and pathogenic fungi. Environmental, vegetation, and geographical factors determined the spatial distribution of soil fungi at a regional scale. Potential hydrogen (pH), calcium (Ca), magnesium (Mg), and silt content were detected as common drivers of fungal communities across different datasets enriched towards a functional guild. Vegetation traits were found to be more influential in shaping symbiotrophic fungi composition than saprotrophic and pathogenic fungi. This highlights the importance of considering vegetation traits when studying fungal community diversity and distribution. Clustering patterns of sampling points near the volcanoes indicated shared environmental and vegetation characteristics. A weak but significant distance decay in taxonomic similarity revealed that dispersal limitation contributed to fungal community composition, although it was not the primary factor in this study. Overall, this study provides important insights into the challenges and opportunities of studying fungal communities at a regional scale using metagenomic data.}, } @article {pmid39762979, year = {2025}, author = {Oh, S and Kim, J and Shin, CM and Lee, HJ and Lee, HS and Park, KU}, title = {Metagenomic characterization of oral microbiome signatures to predict upper gastrointestinal and pancreaticobiliary cancers: a case-control study.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {20}, pmid = {39762979}, issn = {1479-5876}, support = {16-2021-0007//Seoul National University Bundang Hospital/ ; }, mesh = {Humans ; Case-Control Studies ; *Metagenomics/methods ; *Pancreatic Neoplasms/microbiology/diagnosis ; Female ; Male ; Middle Aged ; *Microbiota/genetics ; Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Aged ; Metagenome ; Saliva/microbiology ; Biliary Tract Neoplasms/microbiology/diagnosis ; Gastrointestinal Neoplasms/microbiology/diagnosis ; }, abstract = {BACKGROUND: This study investigated the oral microbiome signatures associated with upper gastrointestinal (GI) and pancreaticobiliary cancers.

METHODS: Saliva samples from cancer patients and age- and sex-matched healthy controls were analyzed using 16S rRNA-targeted sequencing, followed by comprehensive bioinformatics analysis.

RESULTS: Significant dissimilarities in microbial composition were observed between cancer patients and controls across esophageal cancer (EC), gastric cancer (GC), biliary tract cancer (BC), and pancreatic cancer (PC) groups (R[2] = 0.067, = 0.075, = 0.068, and = 0.044; p = 0.001, = 0.001, = 0.002, and = 0.004, respectively). Additionally, the oral microbiome composition significantly differed by the four cancer sites (p = 0.001 for EC vs. GC, EC vs. BC, EC vs. PC, GC vs. BC, and GC vs. PC; p = 0.013 for BC vs. PC). We built oral metagenomic classifiers to predict cancer and selected specific microbial taxa with diagnostic properties. For EC, the classifier differentiated cancer patients and controls with good accuracy (area under the curve [AUC] = 0.791) and included three genera: Akkermansia, Escherichia-Shigella, and Subdoligranulum. For GC, the classifier exhibited high discriminative power (AUC = 0.961); it included five genera (Escherichia-Shigella, Gemella, Holdemanella, Actinomyces, and Stomatobaculum) and three species (Eubacterium sp. oral clone EI074, Ruminococcus sp. Marseille-P328, and Leptotrichia wadei F0279). However, microbial taxa with diagnostic features for BC and PC were not identified.

CONCLUSIONS: These findings suggested that the oral microbiome composition may serve as an indicator of tumorigenesis in upper GI and pancreaticobiliary cancers. The development of oral metagenomic classifiers for EC and GC demonstrates the potential value of microbial biomarkers in cancer screening.}, } @article {pmid39762302, year = {2025}, author = {Kim, MJ and Song, MH and Ji, YS and Park, JW and Shin, YK and Kim, SC and Kim, G and Cho, B and Park, H and Ku, JL and Jeong, SY}, title = {Cell free supernatants of Bifidobacterium adolescentis and Bifidobacterium longum suppress the tumor growth in colorectal cancer organoid model.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {935}, pmid = {39762302}, issn = {2045-2322}, support = {2021M3H9A1030151//National Research Foundation, South Korea/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology/metabolism ; *Bifidobacterium longum/metabolism ; *Organoids/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Bifidobacterium adolescentis/metabolism ; Female ; Male ; Probiotics ; Middle Aged ; Aged ; Cell Proliferation ; Cell Line, Tumor ; }, abstract = {The probiotic gut microbiome and its metabolites are pivotal in regulating host metabolism, inflammation, and immunity. Host genetics, colonization at birth, the host lifestyle, and exposure to diseases and drugs determine microbial composition. Dysbiosis and disruption of homeostasis in the beneficial microbiome have been reported to be involved in the tumorigenesis and progression of colorectal cancer (CRC). However, the influence of bacteria-secreted metabolites on CRC growth is yet to be fully elucidated. In this study, we compared the microbial composition of CRC patients to healthy controls to identify distinct patterns of microbiota-derived metabolites in CRC patients. Metagenomic analysis demonstrated that beneficial bacteria strains; Blautia producta, Bifidobacterium adolescentis, and Bifidobacterium longum decreased, while Parabacteroides distasonis and Bacteroides ovatus were more prevalent in the CRC patient group. Treatment of cancer organoid lines with microbial culture supernatants from Blautia producta, Bifidobacterium adolescentis, and Bifidobacterium longum showed remarkable inhibition of cancer growth. This study demonstrates that the bacterial metabolites depleted in CRC patients may inhibit cancer growth and highlights the effects of microbiome-derived metabolites on CRC growth.}, } @article {pmid39762227, year = {2025}, author = {Ding, J and Liu, F and Zeng, J and Gu, H and Huang, J and Wu, B and Shu, L and Yan, Q and He, Z and Wang, C}, title = {Depth heterogeneity of lignin-degrading microbiome and organic carbon processing in mangrove sediments.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {5}, pmid = {39762227}, issn = {2055-5008}, mesh = {*Geologic Sediments/microbiology ; *Lignin/metabolism ; *Microbiota ; *Carbon/metabolism ; *Wetlands ; *Metagenomics/methods ; Bacteria/genetics/classification/metabolism/isolation & purification ; Biomass ; Metagenome ; Sequence Analysis, DNA ; }, abstract = {Mangrove ecosystems are globally recognized for their blue carbon (C) sequestration capacity. Lignocellulosic detritus constitutes the primary C input to mangrove sediments, but the microbial processes involved in its bioprocessing remain unclear. Using lignocellulosic analysis and metagenomic sequencing across five 100-cm sediment cores, we found a high proportion of lignin (95.0-97.7%) within sediments' lignocellulosic detritus, with a small fraction of lignin-degrading genes (1.24-1.98%) of lignin-degrading genes within the carbohydrate-active enzyme coding genes. Depth stratification was observed in genes and microbial communities involved in lignin depolymerization and mineralization of lignin monomer derivatives. Further microbe-centered analyses of biomass production rates and adaptive metabolism revealed diminished microbial C use efficiency potential and augmented "enzyme latch" with increasing sediment depths. These findings enhance our understanding of sedimentary organic C cycling and storage in coastal blue C ecosystems.}, } @article {pmid39762111, year = {2025}, author = {Al-Shakhshir, S and Quraishi, MN and Mullish, B and Patel, A and Vince, A and Rowe, A and Homer, V and Jackson, N and Gyimah, D and Shabir, S and Manzoor, S and Cooney, R and Alrubaiy, L and Quince, C and van Schaik, W and Hares, M and Beggs, AD and Efstathiou, E and Rimmer, P and Weston, C and Iqbal, T and Trivedi, PJ}, title = {FAecal micRobiota transplantation in primary sclerosinG chOlangitis (FARGO): study protocol for a randomised, multicentre, phase IIa, placebo-controlled trial.}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e095392}, doi = {10.1136/bmjopen-2024-095392}, pmid = {39762111}, issn = {2044-6055}, mesh = {Adult ; Female ; Humans ; Male ; *Cholangitis, Sclerosing/therapy ; Clinical Trials, Phase II as Topic ; *Fecal Microbiota Transplantation/methods ; Gastrointestinal Microbiome ; Inflammatory Bowel Diseases/therapy/microbiology ; Multicenter Studies as Topic ; Randomized Controlled Trials as Topic ; Treatment Outcome ; }, abstract = {INTRODUCTION: Primary sclerosing cholangitis (PSC) is the classical hepatobiliary manifestation of inflammatory bowel disease (IBD). The strong association between gut and liver inflammation has driven several pathogenic hypotheses to which the intestinal microbiome is proposed to contribute. Pilot studies of faecal microbiota transplantation (FMT) in PSC and IBD are demonstrated to be safe and associated with increased gut bacterial diversity. However, the longevity of such changes and the impact on markers of disease activity and disease progression have not been studied. The aim of this clinical trial is to determine the effects of repeated FMT as a treatment for PSC-IBD.

METHODS AND ANALYSIS: FAecal micRobiota transplantation in primary sclerosinG chOlangitis (FARGO) is a phase IIa randomised placebo-controlled trial to assess the efficacy and safety of repeated colonic administration of FMT in patients with non-cirrhotic PSC-IBD. Fifty-eight patients will be recruited from six sites across England and randomised in a 1:1 ratio between active FMT or FMT placebo arms. FMT will be manufactured by the University of Birmingham Microbiome Treatment Centre, using stool collected from rigorously screened healthy donors. A total of 8 weekly treatments will be delivered; the first through colonoscopic administration (week 1) and the remaining seven via once-weekly enema (up to week 8). Participants will then be followed on a 12-weekly basis until week 48 from the first treatment visit. The primary efficacy outcome will be to determine the effect of FMT on serum alkaline phosphatase values over time (end of study at 48 weeks). Key secondary outcomes will be to evaluate the impact of FMT on other liver biochemical parameters, PSC risk scores, circulating and imaging markers of liver fibrosis, health-related quality of life measures, IBD activity and the incidence of PSC-related clinical events. Key translational objectives will be to identify mucosal metagenomic, metatranscriptomic, metabolomic and immunological pathways associated with the administration of FMT.

ETHICS AND DISSEMINATION: The protocol was approved by the South Central-Hampshire B Research Ethics Committee (REC 23/SC/0147). Participants will be required to provide written informed consent. The results of this trial will be disseminated through national and international presentations and peer-reviewed publications.

TRIAL REGISTRATION NUMBER: The trial was registered at ClinicalTrials.gov on 23 February 2024 (NCT06286709). Weblink: Study Details | FAecal Microbiota Transplantation in primaRy sclerosinG chOlangitis | ClinicalTrials.gov.}, } @article {pmid39762107, year = {2025}, author = {Weldegebreal, F and Ayana, DA and Wilfong, T and Dheresa, M and Yadeta, TA and Negesa, AS and Demmu, YM and Tesfa, T and Alemu, TN and Eticha, TG and Geremew, A and Roba, KT and Abdissa, A and Assefa, N and Negash, AA and Cools, P and Tura, AK}, title = {Relationship between vaginal and gut microbiome and pregnancy outcomes in eastern Ethiopia: a protocol for a longitudinal maternal-infant cohort study (the EthiOMICS study).}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e092461}, doi = {10.1136/bmjopen-2024-092461}, pmid = {39762107}, issn = {2044-6055}, mesh = {Humans ; Female ; Ethiopia ; Pregnancy ; *Gastrointestinal Microbiome/genetics ; *Vagina/microbiology ; Infant, Newborn ; Longitudinal Studies ; *Pregnancy Outcome ; Infant ; Feces/microbiology ; Research Design ; Milk, Human/microbiology ; Adult ; }, abstract = {INTRODUCTION: Although evidence exists on the impact of microbiota on pregnancy outcomes in many high-resource settings, there is a lack of research in many low-resource settings like Ethiopia. This study aims to fill this gap by studying the gut and vaginal microbiota changes throughout pregnancy and assess how these changes relate to pregnancy outcomes among a cohort of pregnant women in eastern Ethiopia.

METHODS AND ANALYSIS: Vaginal and stool samples will be collected using DNA/RNA Shield Collection kits three times starting at 12-22 weeks, 28-36 weeks and at birth (within 7 days). Postnatally, newborns' skin swabs (at birth) and rectal swabs will be obtained until 2 years of age. Moreover, breast milk samples at birth and 6 months and environmental samples (water, indoor air and soil) will be collected at enrolment, birth, 6, 12 and 24 months post partum. DNA will be extracted using Roche kits. Metagenomic sequencing will be performed to identify metataxonomic profiling and assess variations in microbial profiles, and α and β diversity of the microbiota. Information on socioeconomic, behavioural, household and biological factors will be collected at enrolment. The collected data will be coded, entered into EpiData 3.1 and analysed using Stata 17.

ETHICS AND DISSEMINATION: The Institutional Health Research Ethics Review Committee (Ref No. IHRERC/033/2022) of Haramaya University, Ethiopia has approved this study ethically. Written informed consent regarding the study and sample storage for biobanking will be obtained from all participants. Results will be published in international peer-reviewed journals, and summaries will be provided to the study funders. Clinical study data will be submitted to Data Compass (https://datacompass.lshtm.ac.uk/), and molecular profiles of the microbiome and whole-genome sequences will be submitted to the European Nucleotide Archive (https://www. ebi.ac.uk/ena). Requests for data should be directed to daberaf@gmail.com. The decision to share data will be made by the study steering committee under the College of Health and Medical Sciences, Haramaya University, Ethiopia.}, } @article {pmid39761113, year = {2025}, author = {Kardailsky, A and Durán-Vinet, B and Nester, G and Ayad, ME and Raes, EJ and Jeunen, GJ and Miller, AK and McVey, P and Corrigan, S and Fraser, M and Goncalves, P and Burnell, S and Bennett, A and Rauschert, S and Bayer, PE}, title = {Monitoring the Land and Sea: Enhancing Efficiency Through CRISPR-Cas Driven Depletion and Enrichment of Environmental DNA.}, journal = {The CRISPR journal}, volume = {}, number = {}, pages = {}, doi = {10.1089/crispr.2024.0050}, pmid = {39761113}, issn = {2573-1602}, abstract = {Characterizing biodiversity using environmental DNA (eDNA) represents a paradigm shift in our capacity for biomonitoring complex environments, both aquatic and terrestrial. However, eDNA biomonitoring is limited by biases toward certain species and the low taxonomic resolution of current metabarcoding approaches. Shotgun metagenomics of eDNA enables the collection of whole ecosystem data by sequencing all molecules present, allowing characterization and identification. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated proteins (Cas)-based methods have the potential to improve the efficiency of eDNA metagenomic sequencing of low-abundant target organisms and simplify data analysis by enrichment of target species or nontarget DNA depletion before sequencing. Implementation of CRISPR-Cas in eDNA has been limited due to a lack of interest and support in the past. This perspective synthesizes current approaches of CRISPR-Cas to study underrepresented taxa and advocate for further application and optimization of depletion and enrichment methods of eDNA using CRISPR-Cas, holding promise for eDNA biomonitoring.}, } @article {pmid39758340, year = {2024}, author = {Shang, X and Fu, Y and Wang, Y and Yan, S}, title = {Ramulus Mori (Sangzhi) alkaloids ameliorate high-fat diet induced obesity in rats by modulating gut microbiota and bile acid metabolism.}, journal = {Frontiers in endocrinology}, volume = {15}, number = {}, pages = {1506430}, pmid = {39758340}, issn = {1664-2392}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Diet, High-Fat/adverse effects ; *Obesity/metabolism/drug therapy ; Rats ; Male ; *Bile Acids and Salts/metabolism ; *Rats, Sprague-Dawley ; *Alkaloids/pharmacology ; Lipid Metabolism/drug effects ; Liver/metabolism/drug effects ; Receptors, G-Protein-Coupled/metabolism ; }, abstract = {OBJECTIVE: The objective of this study is to investigate the ability of Ramulus Mori (Sangzhi) alkaloid tablets (SZ-A) to ameliorate obesity and lipid metabolism disorders in rats subjected to a high-fat diet (HFD) through metagenomics, untargeted lipidomics, targeted metabolism of bile acid (BA), and BA pathways, providing a novel perspective on the management of metabolic disorders.

METHODS: In this research, HFD-fed rats were concurrently administered SZ-A orally. We measured changes in body weight (BW), blood lipid profiles, and liver function to assess therapeutic effects. Liver lipid status was visualized through H&E and Oil Red O. Gut microbiota composition was elucidated using metagenomics. The LC-MS-targeted metabolomics approach was utilized to define the fecal BA profiles. Furthermore, the lipid metabolomics of adipose tissue samples was investigated using an LC-MS analysis platform. The expression levels of the BA receptor were determined by western blotting. Additionally, serum insulin (INS), glucagon-like peptide-1 (GLP-1), and inflammatory cytokines were quantified using an ELISA kit. The integrity of the colonic epithelial barrier was assessed using immunofluorescence.

RESULTS: SZ-A notably decreased BW and blood lipid levels in obese rats while also alleviating liver injury. Additionally, SZ-A reduced the serum levels of leptin (LEP), INS, and GLP-1, indicating its potential to modulate key metabolic hormones. Most notably, SZ-A substantially improved gut microbiota composition. Specifically, it reshaped the gut microbiota structure in HFD-fed rats by increasing the relative abundance of beneficial bacteria, such as Bacteroides, while decreasing the populations of potentially harmful bacteria, such as Dorea and Blautia. At the BA level, SZ-A decreased the levels of harmful BAs, including hyodeoxycholic acid (HDCA), deoxycholic acid (DCA), 12-keto lithocholic acid (12-KLCA), lithocholic acid (LCA), and muricholic acid (MDCA). Between the model group and SZ-A, 258 differentially abundant metabolites were detected, with 72 upregulated and 186 downregulated. Furthermore, these BAs are implicated in the activation of the FXR-FGF15 and TGR5-GLP-1 pathways in the intestine. This activation helps to alleviate HFD-fed intestinal inflammation and restore intestinal barrier damage by modulating inflammatory cytokines and bolstering the intestinal barrier's capabilities.

CONCLUSIONS: Our findings indicate that SZ-A effectively modulates BW, serum lipid profiles, and liver function in HFD-fed rats. Moreover, SZ-A exerts a positive influence on inflammatory cytokines, thereby mitigating inflammation and promoting the restoration of the intestinal barrier. Significantly, our research indicates that adjusting the gut microbiome and BA levels could serve as an effective approach for both preventing and treating obesity and related metabolic dyslipidemia.}, } @article {pmid39754646, year = {2025}, author = {Shaffer, M and North, D and Bibby, K}, title = {Evaluating Nanotrap Microbiome Particles as A Wastewater Viral Concentration Method.}, journal = {Food and environmental virology}, volume = {17}, number = {1}, pages = {10}, pmid = {39754646}, issn = {1867-0342}, support = {1748019//National Science Foundation/ ; }, mesh = {*Wastewater/virology/microbiology ; *Microbiota ; *Viruses/isolation & purification/classification/genetics ; Metagenomics/methods ; Bacteria/isolation & purification/classification/genetics/virology ; Tobamovirus/isolation & purification/genetics/classification ; }, abstract = {Wastewater-based surveillance has emerged as a powerful approach to monitoring infectious diseases within a community. Typically, wastewater samples are concentrated before viral analyses to improve sensitivity. Current concentration methods vary in time requirements, costs, and efficiency. Here, we evaluated the concentration efficiency and bias of a novel viral concentration approach, Nanotrap Microbiome Particles (NMP), in wastewater. NMP concentration efficiency was target-specific, with significantly lower concentrations of the bacterial indicator HF183 and viral indicator Carjivirus (formerly crAssphage) relative to direct extraction (1.2 × 10[5] vs. 3.4 × 10[5] GC/mL and 2.0 × 10[5] vs. 1.2 × 10[5] GC/mL, respectively), but significantly higher concentrations of the viral fecal indicator Pepper Mild Mottle Virus (PMMoV) relative to direct extraction (1.4 × 10[5] vs. 8.4 × 10[3] GC/mL). Targeted metagenomic sequencing showed that NMP resulted in significantly more unique species reads per sample than direct extractions (p < 0.001) by detecting species that went undetected by direct extractions. Key viral families identified with high abundances were Adenoviridae, Caliciviridae, Herpesviridae, Papillomaviridae, and Polyomaviridae. NMP showed differential ability for concentrating clinically relevant viral families, suggesting that the technology should be evaluated and optimized for specific viral targets before implementation.}, } @article {pmid39754220, year = {2025}, author = {Karwowska, Z and Aasmets, O and , and Kosciolek, T and Org, E}, title = {Effects of data transformation and model selection on feature importance in microbiome classification data.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {2}, pmid = {39754220}, issn = {2049-2618}, mesh = {Humans ; *Machine Learning ; *Gastrointestinal Microbiome/genetics ; *Algorithms ; *Metagenomics/methods ; Microbiota/genetics ; Bacteria/classification/genetics ; Biomarkers ; Metagenome ; }, abstract = {BACKGROUND: Accurate classification of host phenotypes from microbiome data is crucial for advancing microbiome-based therapies, with machine learning offering effective solutions. However, the complexity of the gut microbiome, data sparsity, compositionality, and population-specificity present significant challenges. Microbiome data transformations can alleviate some of the aforementioned challenges, but their usage in machine learning tasks has largely been unexplored.

RESULTS: Our analysis of over 8500 samples from 24 shotgun metagenomic datasets showed that it is possible to classify healthy and diseased individuals using microbiome data with minimal dependence on the choice of algorithm or transformation. Presence-absence transformations performed comparably to abundance-based transformations, and only a small subset of predictors is necessary for accurate classification. However, while different transformations resulted in comparable classification performance, the most important features varied significantly, which highlights the need to reevaluate machine learning-based biomarker detection.

CONCLUSIONS: Microbiome data transformations can significantly influence feature selection but have a limited effect on classification accuracy. Our findings suggest that while classification is robust across different transformations, the variation in feature selection necessitates caution when using machine learning for biomarker identification. This research provides valuable insights for applying machine learning to microbiome data and identifies important directions for future work.}, } @article {pmid39753925, year = {2025}, author = {Bora, SS and Ronghang, R and Das, P and Naorem, RS and Hazarika, DJ and Gogoi, R and Banu, S and Barooah, M}, title = {Endophytic Microbial Community Structure and Dynamics Influence Agarwood Formation in Aquilaria malaccensis Lam.}, journal = {Current microbiology}, volume = {82}, number = {2}, pages = {66}, pmid = {39753925}, issn = {1432-0991}, mesh = {*Thymelaeaceae/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Endophytes/genetics/classification/isolation & purification ; *Fungi/genetics/classification/isolation & purification ; Microbiota ; Metagenomics ; Wood/microbiology ; Metagenome ; }, abstract = {Aquilaria malaccensis Lam., an Agarwood-producing tree native to Southeast Asia, secretes oleoresin, a resin with diverse applications, in response to injuries. To explore the role of endosphere microbial communities during Agarwood development, we utilized a metagenomics approach across three stages: non-symptomatic (NC), symptomatic early (IN), and symptomatic mature (IN1). The NC metagenome was dominated by Bacillus (19.15%), Klebsiella (13.25%), and Pantoea (12.46%) among bacteria and Saccharomyces (15.92%) among fungi. Notably, bacterial chemotaxis pathway genes were more prevalent in NC (2.14%) compared to IN (0.92%) and IN1 (1.16%), suggesting microbial chemotactic behavior. In the IN stage, Klebsiella (27.05%) and Saccharomyces (34.81%) were the dominant genera. The IN1 metagenome featured Pantoea (8.92%) and Neurospora (8.24%) as leading bacterial and fungal genera, respectively. Functional genes associated with defense mechanisms, lipid transport, and secondary metabolite biosynthesis were increasingly represented in IN1, indicating an enhanced microbial response as infection progresses. Ecological indices, including a high Shannon-Wiener index (H' = 4.467) and Simpson's dominance (1 - D = 0.9697), alongside Pielou's evenness index (J = 0.7034), highlighted a dynamic and diverse microbial community at the mature infection stage, reflecting the complex interactions within the Aquilaria endosphere during Agarwood formation.}, } @article {pmid39753565, year = {2025}, author = {Chen, YC and Su, YY and Chu, TY and Wu, MF and Huang, CC and Lin, CC}, title = {PreLect: Prevalence leveraged consistent feature selection decodes microbial signatures across cohorts.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {3}, pmid = {39753565}, issn = {2055-5008}, support = {NSTC 112-2221-E-A49 -106 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 112-2221-E-A49 -106 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; MOHW112-TDU-B-222-124013//Ministry of Health and Welfare (Ministry of Health and Welfare, Taiwan)/ ; MOHW111-TDU-B-221-114007//Ministry of Health and Welfare (Ministry of Health and Welfare, Taiwan)/ ; MOHW112-TDU-B-222-124013//Ministry of Health and Welfare (Ministry of Health and Welfare, Taiwan)/ ; MOHW111-TDU-B-221-114007//Ministry of Health and Welfare (Ministry of Health and Welfare, Taiwan)/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology ; Microbiota ; Bacteria/genetics/classification/isolation & purification ; Machine Learning ; Gastrointestinal Microbiome ; Cohort Studies ; Glycerophospholipids ; Computational Biology/methods ; Lipopolysaccharides ; Metagenomics/methods ; }, abstract = {The intricate nature of microbiota sequencing data-high dimensionality and sparsity-presents a challenge in identifying informative and reproducible microbial features for both research and clinical applications. Addressing this, we introduce PreLect, an innovative feature selection framework that harnesses microbes' prevalence to facilitate consistent selection in sparse microbiota data. Upon rigorous benchmarking against established feature selection methodologies across 42 microbiome datasets, PreLect demonstrated superior classification capabilities compared to statistical methods and outperformed machine learning-based methods by selecting features with greater prevalence and abundance. A significant strength of PreLect lies in its ability to reliably identify reproducible microbial features across varied cohorts. Applied to colorectal cancer, PreLect identifies key microbes and highlights crucial pathways, such as lipopolysaccharide and glycerophospholipid biosynthesis, in cancer progression. This case study exemplifies PreLect's utility in discerning clinically relevant microbial signatures. In summary, PreLect's accuracy and robustness make it a significant advancement in the analysis of complex microbiota data.}, } @article {pmid39749666, year = {2024}, author = {Defazio, G and Tangaro, MA and Pesole, G and Fosso, B}, title = {kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39749666}, issn = {1477-4054}, support = {CN_00000013//National Centre on High-Performance Computing, Big Data and Quantum Computing/ ; PNC0000002//Complementary National Plan PNC-I.1/ ; CUP H93C22000560003//Life Science Hub Puglia/ ; }, mesh = {*Metagenome ; *Software ; *Metagenomics/methods ; *Algorithms ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Microbiota/genetics ; }, abstract = {The advent of high-throughput sequencing (HTS) technologies unlocked the complexity of the microbial world through the development of metagenomics, which now provides an unprecedented and comprehensive overview of its taxonomic and functional contribution in a huge variety of macro- and micro-ecosystems. In particular, shotgun metagenomics allows the reconstruction of microbial genomes, through the assembly of reads into MAGs (metagenome-assembled genomes). In fact, MAGs represent an information-rich proxy for inferring the taxonomic composition and the functional contribution of microbiomes, even if the relevant analytical approaches are not trivial and still improvable. In this regard, tools like CAMITAX and GTDBtk have implemented complex approaches, relying on marker gene identification and sequence alignments, requiring a large processing time. With the aim of deploying an effective tool for fast and reliable MAG taxonomic classification, we present here kMetaShot, a taxonomy classifier based on k-mer/minimizer counting. We benchmarked kMetaShot against CAMITAX and GTDBtk by using both in silico and real mock communities and demonstrated how, while implementing a fast and concise algorithm, it outperforms the other tools in terms of classification accuracy. Additionally, kMetaShot is an easy-to-install and easy-to-use bioinformatic tool that is also suitable for researchers with few command-line skills. It is available and documented at https://github.com/gdefazio/kMetaShot.}, } @article {pmid39748884, year = {2024}, author = {Zhou, H and Pei, Y and Xie, Q and Nie, W and Liu, X and Xia, H and Jiang, J}, title = {Diagnosis and insight into the unique lung microbiota of pediatric pulmonary tuberculosis patients by bronchoalveolar lavage using metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1492881}, pmid = {39748884}, issn = {2235-2988}, mesh = {Humans ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing ; Male ; Child ; *Microbiota/genetics ; *Lung/microbiology ; Child, Preschool ; *Metagenomics/methods ; Sensitivity and Specificity ; Adolescent ; Mycobacterium tuberculosis/genetics/isolation & purification ; Infant ; Bronchoalveolar Lavage ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Although previous studies have reported the dysregulation of respiratory tract microbiota in infectious diseases, insufficient data exist regarding respiratory microbiota imbalances in the lower respiratory tracts of children with pulmonary tuberculosis (PTB). In this study, we assessed the value of mNGS in the pathogen diagnosis and microbiome analysis of PTB patients using bronchoalveolar lavage fluid (BALF) samples.

METHODS: A total of 64 participants, comprising 43 pediatric PTB and 21 pediatric pneumonia patients were recruited in the present study. BALF samples were collected from the above participants. Parallel comparisons between mNGS and conventional microbial test (CMT) pathogen detection were performed. Moreover, the diversity and structure of all 64 patients' lung BALF microbiomes were explored using the mNGS data.

RESULTS: Comparing to the final clinical diagnosis, mNGS in BALF samples produced a sensitivity of 46.51%, which was lower than that of TB-PCR (55.00%) and Xpert (55.00%). The diagnostic efficacy of PTB can be highly enhanced by mNGS combined with TB-PCR (AUC=0.8140, P<0.0001). There were no significant differences in the diversity either between patients with TB and pneumonia. Positive mNGS pathogen results in pediatric PTB patients significantly affect the β-diversity of the pulmonary microbiota. In addition, significant taxonomic differences were found in BALF specimens from patients with PTB and pneumonia, both of which have unique bacterial compositions.

CONCLUSIONS: mNGS is valuable in the etiological diagnosis of PTB, and can reveal pulmonary microecological characteristics. For pediatric PTB patients, the mNGS should be implemented early and complementary to CMTs.}, } @article {pmid39748068, year = {2025}, author = {Li, S and Ma, X and Mei, H and Chang, X and He, P and Sun, L and Xiao, H and Wang, S and Li, R}, title = {Association between gut microbiota and short-chain fatty acids in children with obesity.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {483}, pmid = {39748068}, issn = {2045-2322}, support = {2019ZYYD051//the Special Projects for the Central Government to Guide the Development of Local Science and Technology/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Child ; Male ; *Fatty Acids, Volatile/metabolism/blood ; Female ; Adolescent ; *Pediatric Obesity/microbiology/metabolism/blood ; Case-Control Studies ; Feces/microbiology ; Metabolome ; Metagenomics/methods ; Body Mass Index ; }, abstract = {The gut microbiome and its metabolites may be important role in regulating the pathogenesis of obesity. This study aimed to characterize the gut microbiome and short-chain fatty acid (SCFA) metabolome in obese children. This case-control study recruited children aged 7‒14 years and divided them into a normal group (NG) and an obese group (OG) based on their body mass index. Whole-genome shotgun metagenomic analysis was performed on fecal samples from the OG and NG groups to characterize the signatures and functional potential of the gut microbiota. Serum metabolite profiles were analyzed using high-performance liquid chromatography/mass spectrometry (LC/MS). The Statistical Package for the Social Sciences (SPSS, version 26) and R software were used for data analysis. A total of 99 children were recruited, with 49 in the OG and 50 in the NG. At the phylum level, Proteobacteria were significantly more abundant in children in the OG than those in the NG. At the genus level, Oscillibacter and Alistipes were significantly lower in children in the OG than those in the NG. Caproate levels significantly increased, whereas butyrate and isobutyrate levels decreased in children in the OG than those in the NG. Kyoto encyclopedia of genes and genomes (KEGG) functional analysis revealed 28 enriched KEGG pathways, of which/with the phosphotransferase system (PTS) and enhanced biofilm formation by Escherichia coli were particularly significant in the OG. Spearman's correlation analysis indicated that the genus Oscillibacter and species Clostridium_sp._CAG:302 connect serum metabolites and the gut microbiota in childhood obesity. Childhood obesity is correlated with the symbiotic status of the gut microbiota. The microbiota influences human metabolism via specific pathways, particularly butyrate, caproate, and the genus Oscillibacter, all closely associated with obesity.}, } @article {pmid39747535, year = {2025}, author = {Wongsamart, R and Somboonna, N and Cheibchalard, T and Klankeo, P and Ruampatana, J and Nuntapaitoon, M}, title = {Probiotic Bacillus licheniformis DSMZ 28710 improves sow milk microbiota and enhances piglet health outcomes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {17}, pmid = {39747535}, issn = {2045-2322}, support = {764002-DT//Ratchadapisek Sompoch Endowment Fund 2021/ ; 764002-DT//Ratchadapisek Sompoch Endowment Fund 2021/ ; //the Second Century Fund (C2F)/ ; //the Second Century Fund (C2F)/ ; //the Second Century Fund (C2F)/ ; //the Second Century Fund (C2F)/ ; CU_FRB65_hea(68)_131_23_61//Thailand Research Fund, Thailand Science Research and Innovation Fund Chulalongkorn University/ ; FOOD_FF_68_013_3100_003//Thailand Research Fund, Thailand Science Research and Innovation Fund Chulalongkorn University/ ; }, mesh = {Animals ; *Probiotics/administration & dosage ; Swine ; *Milk/microbiology ; *Microbiota ; *Bacillus licheniformis ; RNA, Ribosomal, 16S/genetics ; Female ; Colostrum/microbiology ; Dietary Supplements ; Animal Feed ; }, abstract = {Maintaining a diverse and balanced sow milk microbiome is essential to piglet development. Thus, this study aimed to examine the effects of probiotic Bacillus licheniformis supplementation on the microbiome composition of sow colostrum and milk, and to review associated health findings in piglets. B. licheniformis DSMZ 28710 was supplemented at 10 g/day as feed additive before predicted farrowing until weaning by top dressing. Colostrum and milk samples were collected for metagenomic DNA extraction, 16s rRNA sequencing, and bioinformatics analyses for bacterial microbiota diversity. Results indicated that the supplementation increased the abundances of beneficial bacteria, such as Lactobacillus, Pediococcus, Bacteroides, and Bifidobacterium, while decreasing the abundances of pathogenic bacteria, such as Staphylococcus aureus, Enterobacteriaceae, and Campylobacter in the colostrum. The supplementation increased diversity while maintaining richness and evenness. Moreover, the rise in predicted microbial community metabolic function in membrane transport pathways provides crucial evidence showing that the supplementation is potentially beneficial to piglets, as these pathways are important for providing nutrients and immunity to offspring. This research highlights the importance of microbiome composition in sow milk and the potential of B. licheniformis supplementation as a means to improve piglet health and development.}, } @article {pmid39747287, year = {2025}, author = {Delgadillo, DR and Borelli, JL and Mayer, EA and Labus, JS and Cross, MP and Pressman, SD}, title = {Biological, environmental, and psychological stress and the human gut microbiome in healthy adults.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {362}, pmid = {39747287}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Adult ; *Stress, Psychological/microbiology ; Male ; *RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Phylogeny ; Middle Aged ; Metagenome ; }, abstract = {Emerging research suggests that the gut microbiome plays a crucial role in stress. We assess stress-microbiome associations in two samples of healthy adults across three stress domains (perceived stress, stressful life events, and biological stress /Respiratory Sinus Arrhythmia; RSA). Study 1 (n = 62; mean-age = 37.3 years; 68% female) and Study 2 (n = 74; mean-age = 41.6 years; female only) measured RSA during laboratory stressors and used 16S rRNA pyrosequencing to classify gut microbial composition from fecal samples. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States was used to predict functional pathways of metagenomes. Results showed differences in beta diversity between high and low stressful life events groups across both studies. Study 1 revealed differences in beta diversity between high and low RSA groups. In Study 1, the low perceived stress group was higher in alpha diversity than the high perceived stress group. Levels of Clostridium were negatively associated with RSA in Study 1 and levels Escherichia/Shigella were positively associated with perceived stress in Study 2. Associations between microbial functional pathways (L-lysine production and formaldehyde absorption) and RSA are discussed. Findings suggest that certain features of the gut microbiome are differentially associated with each stress domain.}, } @article {pmid39746973, year = {2025}, author = {Inskeep, WP and Jay, ZJ and McKay, LJ and Dlakić, M}, title = {Respiratory processes of early-evolved hyperthermophiles in sulfidic and low-oxygen geothermal microbial communities.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {277}, pmid = {39746973}, issn = {2041-1723}, support = {1950770//National Science Foundation (NSF)/ ; }, mesh = {Hot Springs/microbiology ; *Pyrobaculum/classification/enzymology/genetics ; *Microbiota ; *Hot Temperature ; *Bacteria/classification/enzymology/genetics ; Anaerobiosis ; Electron Transport ; *Sulfur/metabolism ; *Arsenic/metabolism ; *Cytochrome b Group/metabolism ; *Oxidoreductases/metabolism ; Geothermal Energy ; Phylogeny ; Energy Metabolism ; }, abstract = {Thermophilic microbial communities growing in low-oxygen environments often contain early-evolved archaea and bacteria, which hold clues regarding mechanisms of cellular respiration relevant to early life. Here, we conducted replicate metagenomic, metatranscriptomic, microscopic, and geochemical analyses on two hyperthermophilic (82-84 °C) filamentous microbial communities (Conch and Octopus Springs, Yellowstone National Park, WY) to understand the role of oxygen, sulfur, and arsenic in energy conservation and community composition. We report that hyperthermophiles within the Aquificota (Thermocrinis), Pyropristinus (Caldipriscus), and Thermoproteota (Pyrobaculum) are abundant in both communities; however, higher oxygen results in a greater diversity of aerobic heterotrophs. Metatranscriptomics revealed major shifts in respiratory pathways of keystone chemolithotrophs due to differences in oxygen versus sulfide. Specifically, early-evolved hyperthermophiles express high levels of high-affinity cytochrome bd and CydAA' oxidases in suboxic sulfidic environments and low-affinity heme Cu oxidases under microaerobic conditions. These energy-conservation mechanisms using cytochrome oxidases in high-temperature, low-oxygen habitats likely played a crucial role in the early evolution of microbial life.}, } @article {pmid39744910, year = {2024}, author = {de Moura Barbosa Leite, D and de Paula, TS and Hajdu, E}, title = {The complete mitochondrial genome of the deep-sea methanotrophic sponges Hymedesmia methanophila and Iophon methanophila: leveraging 'waste' in metagenomic data.}, journal = {Journal of genetics}, volume = {103}, number = {}, pages = {}, pmid = {39744910}, issn = {0973-7731}, mesh = {*Genome, Mitochondrial ; Animals ; *Porifera/microbiology/genetics ; *Phylogeny ; *Metagenomics/methods ; Methane/metabolism ; Metagenome ; High-Throughput Nucleotide Sequencing ; DNA, Mitochondrial/genetics ; RNA, Transfer/genetics ; }, abstract = {A significant proportion of next-generation sequencing (NGS) data ends up not being used since they comprise information out-of-scope of the primary studies. This 'waste' of potential can be harnessed to explore organellar genomes, such as the mitochondrial DNA, and be used for evolutionary, conservation and biodiversity research. We present the complete mitochondrial genomes of the deep-sea methanotrophic sponges Hymedesmia methanophila and Iophon methanophila (Demospongiae, Poecilosclerida) retrieved from previously published whole metagenome sequencing data. The predicted mitogenome of H. methanophila (18,657 bp) and I. methanophila (18,718 bp) present the characteristic arrangement observed among Poecilosclerida sponges. These mtDNAs encode the usual set of 14 proteins, two ribosomal RNA, and 24 or 23 transfer RNA genes, respectively, with intergenic regions amounting ~5% of their total length. The overall similarity of these mitogenomes to those of phylogenetic relatives, both in organization and divergence, suggests that neither their extremophilic habitat in asphalt seeps within the deep sea nor their symbiotic association with methaneoxidizing bacteria imposed a major influence on the evolution of their mitochondrial genome. This research shows how metagenomic data can be leveraged to extract additional genetic knowledge from primary metagenome sources, and by exploiting previously unexplored sequencing data, valuable information can be unlocked to shed light on the evolutionary dynamics of diverse organisms inhabiting extreme environments.}, } @article {pmid39744158, year = {2024}, author = {Jiménez-Arroyo, C and Molinero, N and Sabater, C and Margolles, A and Terrón-Camero, LC and Andrés-León, E and Ramos, M and Del Val, M and Moreno-Arribas, MV}, title = {Gut microbiome and clinical and lifestyle host factors associated with recurrent positive RT-PCR for SARS-CoV-2.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1494193}, pmid = {39744158}, issn = {2235-2988}, mesh = {Humans ; *COVID-19/microbiology/virology/diagnosis ; *Gastrointestinal Microbiome/genetics ; *SARS-CoV-2/genetics/isolation & purification ; Male ; Female ; Middle Aged ; *Feces/microbiology/virology ; Adult ; Metagenomics/methods ; Life Style ; Aged ; }, abstract = {BACKGROUND: SARS-CoV-2 and COVID-19 are still active in the population. Some patients remained PCR-positive for more than 4 weeks, called "persistently PCR-positive". Recent evidence suggests a link between the gut microbiota and susceptibility to COVID-19, although no studies have explored persistent PCR conditions. We aimed to evaluate the relationship between persistent positive SARS-CoV-2 RT-PCR, the gut microbiome, and individual host determinants.

METHODS: A shotgun metagenomic analysis was conducted on fecal samples from 28 individuals affected by COVID-19. Patients were divided into two groups: those who had cleared the virus within 30 days (designated as the control group) (n = 15), and those who remained PCR-positive beyond 30 days (called the PCR+ group) (n = 13). We also investigated the correlation between prolonged viral clearance and several additional factors, including clinical parameters, immune responses, microbial metabolites, and dietary habits.

RESULTS: The composition and functionality of the microbiome varied based on the duration of positivity as determined by PCR. Compared to the control group, the persistent PCR+ group exhibited elevated pathogen levels and augmented diversity in functional gene families (p-value < 0.05). A multi-omics analysis integrating metagenomics, metabolites, and metadata also revealed the specific contribution of certain blood markers in this group, including basophils, IgM, IgG (both general and specific for SARS-CoV-2), and markers of liver damage. Unhealthy diet was identified as a significant factor influencing the duration of PCR positivity.

CONCLUSIONS: These findings indicate that the gut microbiome may play a role in delayed viral clearance and persistent positive RT-PCR results. Our study also contributes to the understanding of the role of host factors as mediators linking the gut microbiota and disease outcomes. Further large-scale studies must confirm these data; however, they suggest the relevance of monitoring microbiome changes in the early post-viral years to control SARS-CoV-2 and providing individual healthcare support.}, } @article {pmid39743584, year = {2025}, author = {Ezzat, L and Peter, H and Bourquin, M and Busi, SB and Michoud, G and Fodelianakis, S and Kohler, TJ and Lamy, T and Geers, A and Pramateftaki, P and Baier, F and Marasco, R and Daffonchio, D and Deluigi, N and Wilmes, P and Styllas, M and Schön, M and Tolosano, M and De Staercke, V and Battin, TJ}, title = {Diversity and biogeography of the bacterial microbiome in glacier-fed streams.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {39743584}, issn = {1476-4687}, abstract = {The rapid melting of mountain glaciers and the vanishing of their streams is emblematic of climate change[1,2]. Glacier-fed streams (GFSs) are cold, oligotrophic and unstable ecosystems in which life is dominated by microbial biofilms[2,3]. However, current knowledge on the GFS microbiome is scarce[4,5], precluding an understanding of its response to glacier shrinkage. Here, by leveraging metabarcoding and metagenomics, we provide a comprehensive survey of bacteria in the benthic microbiome across 152 GFSs draining the Earth's major mountain ranges. We find that the GFS bacterial microbiome is taxonomically and functionally distinct from other cryospheric microbiomes. GFS bacteria are diverse, with more than half being specific to a given mountain range, some unique to single GFSs and a few cosmopolitan and abundant. We show how geographic isolation and environmental selection shape their biogeography, which is characterized by distinct compositional patterns between mountain ranges and hemispheres. Phylogenetic analyses furthermore uncovered microdiverse clades resulting from environmental selection, probably promoting functional resilience and contributing to GFS bacterial biodiversity and biogeography. Climate-induced glacier shrinkage puts this unique microbiome at risk. Our study provides a global reference for future climate-change microbiology studies on the vanishing GFS ecosystem.}, } @article {pmid39741524, year = {2024}, author = {Khatiebi, S and Kiprotich, K and Onyando, Z and Mwaura, J and Wekesa, C and Chi, CN and Mulambalah, C and Okoth, P}, title = {High-Throughput Shotgun Metagenomics of Microbial Footprints Uncovers a Cocktail of Noxious Antibiotic Resistance Genes in the Winam Gulf of Lake Victoria, Kenya.}, journal = {Journal of tropical medicine}, volume = {2024}, number = {}, pages = {7857069}, pmid = {39741524}, issn = {1687-9686}, abstract = {Background: A diverse range of pollutants, including heavy metals, agrochemicals, pharmaceutical residues, illicit drugs, personal care products, and other anthropogenic contaminants, pose a significant threat to aquatic ecosystems. The Winam Gulf of Lake Victoria, heavily impacted by surrounding human activities, faces potential contamination from these pollutants. However, studies exploring the presence of antibiotic resistance genes (ARGs) in the lake remain limited. In the current study, a shotgun metagenomics approach was employed to identify ARGs and related pathways. Genomic DNA was extracted from water and sediment samples and sequenced using the high-throughput Illumina NovaSeq platform. Additionally, phenotypic antibiotic resistance was assessed using the disk diffusion method with commonly used antibiotics. Results: The analysis of metagenomes sequences from the Gulf ecosystem and Comprehensive Antibiotic Resistance Database (CARD) revealed worrying levels of ARGs in the lake. The study reported nine ARGs from the 37 high-risk resistant gene families previously documented by the World Health Organization (WHO). Proteobacteria had the highest relative abundance of antibiotic resistance (53%), Bacteriodes (4%), Verrucomicrobia (2%), Planctomycetes Chloroflexi, Firmicutes (2%), and other unclassified bacteria (39%). Genes that target protection, replacement, change, and antibiotic-resistant efflux were listed in order of dominance. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed antibiotic resistance to beta-lactamase and vancomycin. Phenotypic resistance to vancomycin, tetracycline, sulfamethoxazole, erythromycin, trimethoprim, tetracycline, and penicillin was reported through the zone of inhibition. Conclusions: This study highlights that the Winam Gulf of Lake Victoria in Kenya harbors a diverse array of antibiotic-resistant genes, including those conferring multidrug resistance. These findings suggest that the Gulf could be serving as a reservoir for more antibiotic-resistant genes, posing potential risks to both human health and aquatic biodiversity. The insights gained from this research can guide policy development for managing antibiotic resistance in Kenya.}, } @article {pmid39741321, year = {2024}, author = {Shao, L and Cai, G and Fu, J and Zhang, W and Ye, Y and Ling, Z and Ye, S}, title = {Gut microbial 'TNFα-sphingolipids-steroid hormones' axis in children with autism spectrum disorder: an insight from meta-omics analysis.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {1165}, pmid = {39741321}, issn = {1479-5876}, support = {LY22C010001//Natural Science Foundation of Zhejiang Province/ ; 2022KY1451//Zhejiang Provincial Medical and Health Science and Technology Plan/ ; 2022KY971//Zhejiang Provincial Medical and Health Science and Technology Plan/ ; 31870839//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Autism Spectrum Disorder/microbiology/blood/metabolism ; *Gastrointestinal Microbiome ; *Tumor Necrosis Factor-alpha/metabolism/blood ; *Sphingolipids/blood/metabolism ; Child ; *Steroids/blood/metabolism ; Metabolomics ; Male ; Female ; Hormones/blood/metabolism ; Metagenomics ; Child, Preschool ; Dysbiosis/microbiology ; Feces/microbiology ; }, abstract = {BACKGROUND: Autism spectrum disorder (ASD) is a persistent neurodevelopmental disorder affecting brains of children. Mounting evidences support the associations between gut microbial dysbiosis and ASD, whereas detailed mechanisms are still obscure.

METHODS: Here we probed the potential roles of gut microbiome in ASD using fecal metagenomics and metabolomics.

RESULTS: Children with ASD were found to be associated with augmented serum cytokines milieu, especially TNFα. Metagenomic analysis generated 29 differential species and 18 dysregulated functional pathways such as Bifidobacterium bifidum, Segatella copri, and upregulated 'Sphingolipid metabolism' in children with ASD. Metabolomics revealed steroid hormone dysgenesis in children with ASD with lower abundances of metabolites such as estriol, estradiol and deoxycorticosterone. A three-way association analysis showed positive correlations between TNFα and microbial function potentials such as 'Bacterial toxins' and 'Lysosome', indicating the contribution of microbial dysbiosis to neuroinflammation. TNFα also correlated positively with 'Sphingolipid metabolism', which further showed negative correlations with metabolites estriol and deoxycorticosterone. Such results, in consistent with current findings, revealed the contribution of increased TNFα to upregulated sphingolipid metabolism, which further impaired steroid hormone biosynthesis.

CONCLUSION: Our study proposed the gut microbial 'TNFα-sphingolipids-steroid hormones' axis in children with ASD, which may provide new perspectives for developing gut microbiome-based treatments in the future.}, } @article {pmid39738315, year = {2024}, author = {Ecklu-Mensah, G and Miller, R and Maseng, MG and Hawes, V and Hinz, D and Kim, C and Gilbert, JA}, title = {Modulating the human gut microbiome and health markers through kombucha consumption: a controlled clinical study.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31647}, pmid = {39738315}, issn = {2045-2322}, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Biomarkers ; Diet, Western/adverse effects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Probiotics/administration & dosage ; Kombucha Tea ; Cholesterol, HDL/blood ; Insulin Resistance ; Inflammation ; }, abstract = {Fermented foods are becoming more popular due to their purported links to metabolic health and the gut microbiome. However, direct clinical evidence for the health claims is lacking. Here, we describe an eight-week clinical trial that explored the effects of a four-week kombucha supplement in healthy individuals consuming a Western diet, randomized into the kombucha (n = 16) or control (n = 8) group. We collected longitudinal stool and blood samples to profile the human microbiome and inflammation markers. We did not observe significant changes in either biochemical parameters or levels of circulating markers of inflammation across the entire cohort. However, paired analysis between baseline and end of intervention time points within kombucha or control groups revealed increases in fasting insulin and in HOMA-IR in the kombucha group whereas reductions in HDL cholesterol were associated with the control group. Shotgun metagenomic analysis revealed the relative abundance of Weizmannia, a kombucha-enriched probiotic and several SCFA producing taxa to be overrepresented in consumers at the end of the intervention. Collectively, in our healthy cohort consuming a Western diet, a short-term kombucha intervention induced modest impacts on human gut microbiome composition and biochemical parameters, which may be attributed to relatively small number of participants and the extensive inter-participant variability.}, } @article {pmid39738309, year = {2024}, author = {Tawfiq, R and Niu, K and Hoehndorf, R and Kulmanov, M}, title = {DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31813}, pmid = {39738309}, issn = {2045-2322}, support = {URF/1/4675-01-01, URF/1/4355-01- 01, URF/1/4697-01-01, URF/1/5041-01- 01, REI/1/5334-01-01, FCC/1/1976-46-01, and FCC/1/1976- 34-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; URF/1/4675-01-01, URF/1/4355-01- 01, URF/1/4697-01-01, URF/1/5041-01- 01, REI/1/5334-01-01, FCC/1/1976-46-01, and FCC/1/1976- 34-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; URF/1/4675-01-01, URF/1/4355-01- 01, URF/1/4697-01-01, URF/1/5041-01- 01, REI/1/5334-01-01, FCC/1/1976-46-01, and FCC/1/1976- 34-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; URF/1/4675-01-01, URF/1/4355-01- 01, URF/1/4697-01-01, URF/1/5041-01- 01, REI/1/5334-01-01, FCC/1/1976-46-01, and FCC/1/1976- 34-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; }, mesh = {*Deep Learning ; *Microbiota ; Gene Ontology ; Computational Biology/methods ; Proteins/metabolism ; Bacteria/metabolism/genetics ; Bacterial Proteins/metabolism/genetics ; Software ; }, abstract = {Analyzing microbial samples remains computationally challenging due to their diversity and complexity. The lack of robust de novo protein function prediction methods exacerbates the difficulty in deriving functional insights from these samples. Traditional prediction methods, dependent on homology and sequence similarity, often fail to predict functions for novel proteins and proteins without known homologs. Moreover, most of these methods have been trained on largely eukaryotic data, and have not been evaluated on or applied to microbial datasets. This research introduces DeepGOMeta, a deep learning model designed for protein function prediction as Gene Ontology (GO) terms, trained on a dataset relevant to microbes. The model is applied to diverse microbial datasets to demonstrate its use for gaining biological insights. Data and code are available at https://github.com/bio-ontology-research-group/deepgometa.}, } @article {pmid39738126, year = {2024}, author = {Zhang, S and Song, W and Marinos, G and Waschina, S and Zimmermann, J and Kaleta, C and Thomas, T}, title = {Genome-scale metabolic modelling reveals interactions and key roles of symbiont clades in a sponge holobiont.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10858}, pmid = {39738126}, issn = {2041-1723}, mesh = {*Symbiosis ; *Porifera/microbiology/metabolism ; Animals ; *Microbiota/genetics ; *Metabolic Networks and Pathways/genetics ; Bacteria/metabolism/genetics/classification ; Phylogeny ; Genome ; Genome, Bacterial ; Models, Biological ; Metagenomics/methods ; }, abstract = {Sponges harbour complex microbiomes and as ancient metazoans and important ecosystem players are emerging as powerful models to understand the evolution and ecology of symbiotic interactions. Metagenomic studies have previously described the functional features of sponge symbionts, however, little is known about the metabolic interactions and processes that occur under different environmental conditions. To address this issue, we construct here constraint-based, genome-scale metabolic networks for the microbiome of the sponge Stylissa sp. Our models define the importance of sponge-derived nutrients for microbiome stability and discover how different organic inputs can result in net heterotrophy or autotrophy of the symbiont community. The analysis further reveals the key role that a newly discovered bacterial taxon has in cross-feeding activities and how it dynamically adjusts with nutrient inputs. Our study reveals insights into the functioning of a sponge microbiome and provides a framework to further explore and define metabolic interactions in holobionts.}, } @article {pmid39732868, year = {2024}, author = {Liu, Y and Wang, F and Zhou, Z and Liu, B and Wu, Z and Pan, X}, title = {Profiling and comprehensive analysis of microbiome and ARGs of nurses and nursing workers in China: a cross-sectional study.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31301}, pmid = {39732868}, issn = {2045-2322}, support = {2018YFC2000500//National Key Research and Development Program of China/ ; }, mesh = {Humans ; Cross-Sectional Studies ; China/epidemiology ; *Nurses ; *Microbiota/genetics ; Female ; Adult ; Male ; Feces/microbiology ; Cross Infection/microbiology/epidemiology ; Gastrointestinal Microbiome ; Hand/microbiology ; Bacteria/genetics/isolation & purification/drug effects/classification ; Metagenomics/methods ; Hand Hygiene ; }, abstract = {Hospital-acquired infection (HAI) and antimicrobial resistance (AMR) represent major challenges in healthcare system. Despite numerous studies have assessed environmental and patient samples, very few studies have explored the microbiome and resistome profiles of medical staff including nursing workers. This cross-sectional study was performed in a tertiary hospital in China and involved 25 nurses (NSs), 25 nursing workers (NWs), and 55 non-medical control (NC). Stool samples from all participants and hand samples (i.e., the microbiome sample from hand skin, which were collected by swabbing both hands with a sponge-swab soaked with neutralized buffer and centrifuging the liquid buffer) from NSs and NWs were collected for metagenomic analysis. Metagenomic analysis revealed that medical staff exhibited lower abundances of beneficial species such as Blautia, and Bifidobacterium in the gut microbiome. However, an important potential pathogen, Staphylococcus haemolyticus, was enriched in the hands of NWs, suggesting a considerable prevalence of pathogenesis and multi-drug resistance. Accordantly, ARG analysis revealed worse hand hygiene among NWs than among NSs, characterized by a higher diversity of ARGs and a higher abundance of ARGs conferring multi-drug resistance including mdtF, acrB, AcrF and evgS. This study provides a comprehensive overview of the microbial and ARG profiles in the gut and hands of NSs and NWs. The higher abundance of potential pathogens and diverse multi-drug resistant ARGs in NWs hands indicates insufficient hand hygiene and a higher risk of HAI in this subgroup. This study is the first to highlight the critical need to improve hand hygiene among NWs, thus mitigating the risks of AMR and HAI.}, } @article {pmid39732792, year = {2024}, author = {Pan, J and Zhang, X and Shi, D and Tian, X and Xu, L and Lu, X and Dong, M and Yao, P and Pan, Z and Ling, Z and Wu, N and Yao, H}, title = {Short-chain fatty acids play a key role in antibody response to SARS-CoV-2 infection in people living with HIV.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31211}, pmid = {39732792}, issn = {2045-2322}, support = {SYS202202//Shandong Provincial Laboratory Project/ ; 2022ZFJH003//Fundamental Research Funds for the Central Universities/ ; 2022R52029//Zhejiang Plan for the Special Support for Top-notch Talents/ ; }, mesh = {Humans ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome/immunology ; *HIV Infections/immunology/virology/microbiology ; *COVID-19/immunology/blood/virology ; *SARS-CoV-2/immunology ; Male ; Female ; Middle Aged ; *Antibodies, Viral/blood/immunology ; Adult ; Antibody Formation/immunology ; }, abstract = {High SARS-CoV-2-specific antibody levels can protect against SARS-CoV-2 reinfection. The gut microbiome can affect a host's immune response. However, its role in the antibody response to SARS-CoV-2 in people living with HIV (PLWH) remains poorly understood. Here, we categorised PLWH and healthy individuals into high- and low-antibody-response groups. Shotgun metagenomic sequencing and targeted metabolomic assays were used to investigate the differences in the gut microbiome and metabolic functions between the high- and low-antibody-response groups. PLWH demonstrated a higher abundance of short-chain fatty acid (SCFA)-producing species, accompanied by high serum levels of several SCFAs, in the high-antibody-response group than in the low-antibody-response group. In contrast, healthy individuals demonstrated higher enrichment of pilus-bearing bacterial species, with flagella-expressing genes, in the high-antibody-response group than in the low-antibody-response group. Therefore, gut-microbiota-derived SCFAs play a key role in antibody responses in PLWH but not in healthy individuals. Our results afford a novel understanding of how the gut microbiome and its metabolites are associated with host immunity. Moreover, they may facilitate the exploration of modalities to prevent SARS-CoV-2 reinfection through various gut-microbiota-targeted interventions tailored to different populations.}, } @article {pmid39732609, year = {2025}, author = {Tegegne, HA and Savidge, TC}, title = {Leveraging human microbiomes for disease prediction and treatment.}, journal = {Trends in pharmacological sciences}, volume = {46}, number = {1}, pages = {32-44}, doi = {10.1016/j.tips.2024.11.007}, pmid = {39732609}, issn = {1873-3735}, mesh = {Humans ; *Microbiota ; Precision Medicine/methods ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Computational Biology ; Animals ; }, abstract = {The human microbiome consists of diverse microorganisms that inhabit various body sites. As these microbes are increasingly recognized as key determinants of health, there is significant interest in leveraging individual microbiome profiles for early disease detection, prevention, and drug efficacy prediction. However, the complexity of microbiome data, coupled with conflicting study outcomes, has hindered its integration into clinical practice. This challenge is partially due to demographic and technological biases that impede the development of reliable disease classifiers. Here, we examine recent advances in 16S rRNA and shotgun-metagenomics sequencing, along with bioinformatics tools designed to enhance microbiome data integration for precision diagnostics and personalized treatments. We also highlight progress in microbiome-based therapies and address the challenges of establishing causality to ensure robust diagnostics and effective treatments for complex diseases.}, } @article {pmid39731160, year = {2024}, author = {Virtanen, S and Saqib, S and Kanerva, T and Ventin-Holmberg, R and Nieminen, P and Holster, T and Kalliala, I and Salonen, A}, title = {Metagenome-validated combined amplicon sequencing and text mining-based annotations for simultaneous profiling of bacteria and fungi: vaginal microbiota and mycobiota in healthy women.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {273}, pmid = {39731160}, issn = {2049-2618}, mesh = {Humans ; *Vagina/microbiology ; Female ; *RNA, Ribosomal, 16S/genetics ; *Fungi/genetics/classification/isolation & purification ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota/genetics ; *Metagenome ; *Data Mining ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Mycobiome ; Healthy Volunteers ; DNA, Bacterial/genetics ; }, abstract = {BACKGROUND: Amplicon sequencing of kingdom-specific tags such as 16S rRNA gene for bacteria and internal transcribed spacer (ITS) region for fungi are widely used for investigating microbial communities. So far most human studies have focused on bacteria while studies on host-associated fungi in health and disease have only recently started to accumulate. To enable cost-effective parallel analysis of bacterial and fungal communities in human and environmental samples, we developed a method where 16S rRNA gene and ITS1 amplicons were pooled together for a single Illumina MiSeq or HiSeq run and analysed after primer-based segregation. Taxonomic assignments were performed with Blast in combination with an iterative text-extraction-based filtration approach, which uses extensive literature records from public databases to select the most probable hits that were further validated by shotgun metagenomic sequencing.

RESULTS: Using 50 vaginal samples, we show that the combined run provides comparable results on bacterial composition and diversity to conventional 16S rRNA gene amplicon sequencing. The text-extraction-based taxonomic assignment-guided tool provided ecosystem-specific bacterial annotations that were confirmed by shotgun metagenomic sequencing (VIRGO, MetaPhlAn, Kraken2). Fungi were identified in 39/50 samples with ITS sequencing while in the metagenome data fungi largely remained undetected due to their low abundance and database issues. Co-abundance analysis of bacteria and fungi did not show strong between-kingdom correlations within the vaginal ecosystem of healthy women.

CONCLUSION: Combined amplicon sequencing for bacteria and fungi provides a simple and cost-effective method for simultaneous analysis of microbiota and mycobiota within the same samples. Conventional metagenomic sequencing does not provide sufficient fungal genome coverage for their reliable detection in vaginal samples. Text extraction-based annotation tool facilitates ecosystem-specific characterization and interpretation of microbial communities by coupling sequence homology to microbe metadata readily available through public databases. Video Abstract.}, } @article {pmid39731152, year = {2024}, author = {Liang, L and Kong, C and Li, J and Liu, G and Wei, J and Wang, G and Wang, Q and Yang, Y and Shi, D and Li, X and Ma, Y}, title = {Distinct microbes, metabolites, and the host genome define the multi-omics profiles in right-sided and left-sided colon cancer.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {274}, pmid = {39731152}, issn = {2049-2618}, support = {No. 22PJD013//Shanghai Pujiang Program/ ; Nos. 81920108026 and 82372594//National Natural Science Foundation of China/ ; No.23410710500//Shanghai Science and Technology Development Foundation/ ; }, mesh = {Humans ; *Colonic Neoplasms/microbiology/genetics/metabolism ; *Gastrointestinal Microbiome/genetics ; Male ; *RNA, Ribosomal, 16S/genetics ; Female ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Middle Aged ; Metabolomics ; Metabolome ; Feces/microbiology ; Aged ; Exome Sequencing ; Metagenomics/methods ; Multiomics ; }, abstract = {BACKGROUND: Studies have reported clinical heterogeneity between right-sided colon cancer (RCC) and left-sided colon cancer (LCC). However, none of these studies used multi-omics analysis combining genetic regulation, microbiota, and metabolites to explain the site-specific difference.

METHODS: Here, 494 participants from a 16S rRNA gene sequencing cohort (50 RCC, 114 LCC, and 100 healthy controls) and a multi-omics cohort (63 RCC, 79 LCC, and 88 healthy controls) were analyzed. 16S rRNA gene, metagenomic sequencing, and metabolomics analyses of fecal samples were evaluated to identify tumor location-related bacteria and metabolites. Whole-exome sequencing (WES) and transcriptome sequencing (RNA-seq) were conducted to obtain the mutation burden and genomic expression pattern.

RESULTS: We found unique profiles of the intestinal microbiome, metabolome, and host genome between RCC and LCC. The bacteria Flavonifractor plautii (Fp) and Fusobacterium nucleatum, the metabolites L-phenylalanine, and the host genes PHLDA1 and WBP1 were the key omics features of RCC; whereas the bacteria Bacteroides sp. A1C1 (B.A1C1) and Parvimonas micra, the metabolites L-citrulline and D-ornithine, and the host genes TCF25 and HLA-DRB5 were considered the dominant omics features in LCC. Multi-omics correlation analysis indicated that RCC-enriched Fp was related to the accumulation of the metabolite L-phenylalanine and the suppressed WBP1 signal in RCC patients. In addition, LCC-enriched B.A1C1 was associated with the accumulation of the metabolites D-ornithine and L-citrulline as well as activation of the genes TCF25, HLA-DRB5, and AC079354.1.

CONCLUSION: Our findings identify previously unknown links between intestinal microbiota alterations, metabolites, and host genomics in RCC vs. LCC, suggesting that it may be possible to treat colorectal cancer (CRC) by targeting the gut microbiota-host interaction. Video Abstract.}, } @article {pmid39724227, year = {2024}, author = {Shahid, U and Hooi, SL and Lim, SY and Mohd Aris, A and Khor, BC and Ayub, Q and Tan, HS}, title = {Metagenomic surveillance of microbial community and antibiotic resistant genes associated with Malaysian wastewater during the COVID-19 pandemic.}, journal = {Current genetics}, volume = {71}, number = {1}, pages = {1}, pmid = {39724227}, issn = {1432-0983}, mesh = {*Wastewater/microbiology ; *COVID-19/epidemiology ; Malaysia/epidemiology ; *Metagenomics/methods ; *SARS-CoV-2/genetics ; Humans ; Drug Resistance, Microbial/genetics ; Pandemics ; Microbiota/genetics ; Metagenome ; Bacteria/genetics/classification/drug effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; }, abstract = {Wastewater is a reservoir of pathogens and hotspots for disseminating antibiotic resistance genes across species. The metagenomic surveillance of wastewater provides insight into the native microbial community, antibiotic-resistance genes (ARGs) and mobile genetic elements. t. The COVID-19 pandemic has caused wider dissemination of ARGs and resistant bacteria in wastewater. Although immensely significant, no research has been performed on the Malaysian wastewater microbial community and ARGs or their correlation with COVID-19 infections. This study utilised a 16S metagenomics approach to characterise the microbial community in Malaysian wastewater during high and low-case phases of the pandemic. Bacteria belonging to Bacteriodales, Bacillales, Actinomycetales and opportunistic pathogens-Arcobacters, Flavobacteria, and Campylobacterales, Neisseriales, were enriched during higher COVID-19 pandemic (active cases). Additionally, copy number profiling of ARGs in water samples showed the prevalence of elements conferring resistance to antibiotics like sulphonamides, cephalosporins, and colistin. The high prevalence of intI1 and other ion-based transporters in samples highlights an extensive risk of horizontal gene transfer to previously susceptible species. Our study emphasises the importance of wastewater surveillance in understanding microbial community dynamics and ARG dissemination, particularly during public health crises like the COVID-19 pandemic.}, } @article {pmid39724159, year = {2024}, author = {Ulbrich, J and Jobe, NE and Jones, DS and Kieft, TL}, title = {Cave Pools in Carlsbad Caverns National Park Contain Diverse Bacteriophage Communities and Novel Viral Sequences.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {163}, pmid = {39724159}, issn = {1432-184X}, support = {NCKRI-NMT Internal Seed Grant Program//National Cave and Karst Research Institute/ ; }, mesh = {*Caves ; *Parks, Recreational ; *Bacteriophages/genetics/isolation & purification/classification ; *Bacteria/genetics/classification/isolation & purification/virology ; *RNA, Ribosomal, 16S/genetics ; California ; Metagenome ; Phylogeny ; Virome ; Biodiversity ; }, abstract = {Viruses are the most abundant biological entities on Earth, and they play a critical role in the environment and biosphere where they regulate microbial populations and contribute to nutrient cycling. Environmental viruses have been the most studied in the ocean, but viral investigations have now spread to other environments. Here, viral communities were characterized in four cave pools in Carlsbad Caverns National Park to test the hypotheses that (i) viral abundance is ten-fold higher than prokaryotic cell abundance in cavern pools, (ii) cavern pools contain novel viral sequences, and (iii) viral communities in pools from developed portions of the cave are distinct from those of pools in undeveloped parts of the same cave. The relationship between viral and microbial abundance was determined through direct epifluorescence microscopy counts. Viral metagenomes were constructed to examine viral diversity among pools, identify novel viruses, and characterize auxiliary metabolic genes (AMGs). Bacterial communities were characterized by 16S rRNA gene amplicon sequencing. Epifluorescence microscopy showed that the ratio of viral-like particles (VLPs) to microorganisms was approximately 22:1 across all sites. Viral communities from pools with higher tourist traffic were more similar to each other than to those from less visited pools, although surprisingly, viruses did not follow the same pattern as bacterial communities, which reflected pool geochemistry. Bacterial hosts predicted from viral sequences using iPHoP showed overlap with both rare and abundant genera and families in the 16S rRNA gene dataset. Gene-sharing network analysis revealed high viral diversity compared to a reference viral database as well as to other aquatic environments. AMG presence showed variation in metabolic potential among the four pools. Overall, Carlsbad Cavern harbors novel viruses with substantial diversity among pools within the same system, indicating that caves are likely an important repository for unexplored viromes.}, } @article {pmid39722590, year = {2025}, author = {Wu, WK and Lo, YL and Chiu, JY and Hsu, CL and Lo, IH and Panyod, S and Liao, YC and Chiu, THT and Yang, YT and Kuo, HC and Zou, HB and Chen, YH and Chuang, HL and Yen, JJY and Wang, JT and Chiu, HM and Hsu, CC and Kuo, CH and Sheen, LY and Kao, HL and Wu, MS}, title = {Gut microbes with the gbu genes determine TMAO production from L-carnitine intake and serve as a biomarker for precision nutrition.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2446374}, doi = {10.1080/19490976.2024.2446374}, pmid = {39722590}, issn = {1949-0984}, mesh = {*Methylamines/metabolism ; *Gastrointestinal Microbiome ; *Carnitine/metabolism ; Humans ; *Biomarkers/analysis ; Male ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Feces/microbiology ; Female ; Animals ; Adult ; Mice ; Multigene Family ; Middle Aged ; Metagenomics ; Precision Medicine ; }, abstract = {Gut microbial metabolism of L-carnitine, which leads to the production of detrimental trimethylamine N-oxide (TMAO), offers a plausible link between red meat consumption and cardiovascular risks. Several microbial genes, including cntA/B, the cai operon, and the recently identified gbu gene cluster, have been implicated in the conversion of dietary L-carnitine into TMA(O). However, the key microbial genes and associated gut microbes involved in this pathway have not been fully explored. Utilizing the oral carnitine challenge test (OCCT), which specifically measures TMAO production from L-carnitine intake and identifies TMAO producer phenotypes, we compared the abundance of microbial genes between low- and high-TMAO producers across three independent cohorts. Our findings consistently revealed that the gbu gene cluster, rather than cntA/B or the cai operon, was significantly enriched in high-TMAO producers. We further analyzed 292 paired multi-omic datasets from OCCT and shotgun metagenomic sequencing, which demonstrated a significant positive correlation between the abundance of fecal gbu genes and L-carnitine-induced TMAO production, with gbuB showing the strongest correlation. Interestingly, these fecal gbu genes were found to increase with L-carnitine supplementation and decrease with a plant-based diet. Notably, we verified a previously uncultured gbu-containing bacterium, JAGTTR01 sp018223385, as the major contributor to TMA formation in the human gut. We isolated these gbu-containing gut microbes and confirmed their role in TMA/TMAO production using anaerobic incubation and a gnotobiotic mouse model. Using an in-house collection of gbu-containing isolates, we developed a qPCR-based method to quantify fecal gbuB and validated its correlation with L-carnitine-mediated TMAO production as measured by OCCT. Overall, these findings suggest that gbu-containing gut microbes are crucial for TMAO increases following L-carnitine intake and may serve as biomarkers or targets for personalized nutrition.}, } @article {pmid39722539, year = {2025}, author = {Zepeda-Rivera, MA and Eisele, Y and Baryiames, A and Wu, H and Mengoni, C and Piccinno, G and McMahon, EF and LaCourse, KD and Jones, DS and Hauner, H and Minot, SS and Segata, N and Dewhirst, FE and Johnston, CD and Bullman, S}, title = {Fusobacterium sphaericum sp. nov., isolated from a human colon tumor adheres to colonic epithelial cells and induces IL-8 secretion.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2442522}, doi = {10.1080/19490976.2024.2442522}, pmid = {39722539}, issn = {1949-0984}, mesh = {Humans ; *Interleukin-8/metabolism/genetics ; *Colonic Neoplasms/microbiology/pathology ; *Fusobacterium/isolation & purification/genetics ; *Epithelial Cells/microbiology ; *Phylogeny ; Bacterial Adhesion ; Colon/microbiology/pathology ; Feces/microbiology ; Adenocarcinoma/microbiology/pathology ; Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; }, abstract = {Cancerous tissue is a largely unexplored microbial niche that provides a unique environment for the colonization and growth of specific bacterial communities, and with it, the opportunity to identify novel bacterial species. Here, we report distinct features of a novel Fusobacterium species, F. sphaericum sp. nov. (Fs), isolated from primary colon adenocarcinoma tissue. We acquire the complete closed genome and associated methylome of this organism and phylogenetically confirm its classification into the Fusobacterium genus, with F. perfoetens as its closest neighbor. Fs is phenotypically and genetically distinct, with morphological analysis revealing its coccoid shape, that while similar to F. perfoetens is rare for most Fusobacterium members. Fs displays a metabolic profile and antibiotic resistance repertoire consistent with other Fusobacterium species. In vitro, Fs has adherent and immunomodulatory capabilities, as it intimately associates with human colon cancer epithelial cells and promotes IL-8 secretion. An analysis of the prevalence and abundance of Fs in > 20,000 human metagenomic samples shows that it is a rarely detected member within human stool with variable relative abundance, found in both healthy controls and patients with colorectal cancer (CRC). Our study sheds light on a novel bacterial species isolated directly from the human CRC tumor niche and given its in vitro interaction with cancer epithelial cells suggests that its role in human health and disease warrants further investigation.}, } @article {pmid39720963, year = {2024}, author = {Guha, SK and Niyogi, S}, title = {Microbial Dynamics in COVID-19: Unraveling the Impact of Human Microbiome on Disease Susceptibility and Therapeutic Strategies.}, journal = {Current microbiology}, volume = {82}, number = {1}, pages = {59}, pmid = {39720963}, issn = {1432-0991}, mesh = {Humans ; *COVID-19/microbiology/virology ; *SARS-CoV-2 ; *Microbiota ; *Dysbiosis/microbiology ; Disease Susceptibility ; Probiotics/therapeutic use ; Gastrointestinal Microbiome ; }, abstract = {This review explores the bidirectional relationship between the human microbiome and SARS-CoV-2 infection, elucidating its implications for COVID-19 susceptibility, severity, and therapeutic strategies. Metagenomic analyses reveal notable alterations in microbiome composition associated with SARS-CoV-2 infection, impacting disease severity and clinical outcomes. Dysbiosis within the respiratory, gastrointestinal, oral, and skin microbiomes exacerbates COVID-19 pathology through immune dysregulation and inflammatory pathways. Understanding these microbial shifts is pivotal for devising targeted therapeutic interventions. Notably, co-infection of oral pathogens with SARS-CoV-2 worsens lung pathology, while gut microbiome dysbiosis influences viral susceptibility and severity. Potential therapeutic approaches targeting the microbiome include probiotics, antimicrobial agents, and immunomodulatory strategies. This review underscores the importance of elucidating host-microbiota interactions to advance precision medicine and public health initiatives in combating COVID-19 and other infectious diseases.}, } @article {pmid39719706, year = {2025}, author = {Zhang, AN and Gaston, JM and Cárdenas, P and Zhao, S and Gu, X and Alm, EJ}, title = {CRISPR-Cas spacer acquisition is a rare event in human gut microbiome.}, journal = {Cell genomics}, volume = {5}, number = {1}, pages = {100725}, doi = {10.1016/j.xgen.2024.100725}, pmid = {39719706}, issn = {2666-979X}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *CRISPR-Cas Systems/genetics ; Gene Transfer, Horizontal/genetics ; Bacteriophages/genetics ; Bifidobacterium longum/genetics ; Metagenome/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Genome, Bacterial/genetics ; }, abstract = {Host-parasite relationships drive the evolution of both parties. In microbe-phage dynamics, CRISPR functions as an adaptive defense mechanism, updating immunity via spacer acquisition. Here, we investigated these interactions within the human gut microbiome, uncovering low frequencies of spacer acquisition at an average rate of one spacer every ∼2.9 point mutations using isolates' whole genomes and ∼2.7 years using metagenome time series. We identified a highly prevalent CRISPR array in Bifidobacterium longum spreading via horizontal gene transfer (HGT), with six spacers found in various genomic regions in 15 persons from the United States and Europe. These spacers, targeting two prominent Bifidobacterium phages, comprised 76% of spacer occurrence of all spacers targeting these phages in all B. longum populations. This result suggests that HGT of an entire CRISPR-Cas system introduced three times more spacers than local CRISPR-Cas acquisition in B. longum. Overall, our findings identified key ecological and evolutionary factors in prokaryote adaptive immunity.}, } @article {pmid39719433, year = {2024}, author = {Jia, M and Fan, Y and Ma, Q and Yang, D and Wang, Y and He, X and Zhao, B and Zhan, X and Qi, Z and Ren, Y and Dong, Z and Zhu, F and Wang, W and Gao, Y and Ma, X}, title = {Gut microbiota dysbiosis promotes cognitive impairment via bile acid metabolism in major depressive disorder.}, journal = {Translational psychiatry}, volume = {14}, number = {1}, pages = {503}, pmid = {39719433}, issn = {2158-3188}, support = {82230044//National Science Foundation of China | Key Programme/ ; 82171505//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Depressive Disorder, Major/metabolism/microbiology ; *Bile Acids and Salts/metabolism ; Male ; Female ; *Dysbiosis/metabolism/complications ; *Cognitive Dysfunction/metabolism/etiology/microbiology ; Adult ; Middle Aged ; Feces/microbiology ; Metabolomics ; Case-Control Studies ; Brain-Gut Axis ; }, abstract = {Evidence suggests that complex interactions among the gut microbiome, metabolic abnormalities, and brain have important etiological and therapeutic implications in major depressive disorder (MDD). However, the influence of microbiome-gut-brain cross-talk on cognitive impairment in MDD remains poorly characterized. We performed serum metabolomic profiling on 104 patients with MDD and 77 healthy controls (HCs), and also performed fecal metagenomic sequencing on a subset of these individuals, including 79 MDD patients and 60 HCs. The findings were validated in a separate cohort that included 40 patients with MDD and 40 HCs using serum-targeted metabolomics. Abnormal bile acid metabolism was observed in patients with MDD, which is related to cognitive dysfunction. The following gut microbiota corresponded to changes in bile acid metabolism and enzyme activities involved in the bile acid metabolic pathway, including Lachnospiraceae (Blautia_massiliensis, Anaerostipes_hadrus, Dorea_formicigenerans, and Fusicatenibacter_saccharivorans), Ruminococcaceae (Ruminococcus_bromii, Flavonifractor_plautii, and Ruthenibacterium_lactatiformans), and Escherichia_coli. Furthermore, a combinatorial marker classifier that robustly differentiated patients with MDD from HCs was identified. In conclusion, this study provides insights into the gut-brain interactions in the cognitive phenotype of MDD, indicating a potential therapeutic strategy for MDD-associated cognitive impairment by targeting the gut microbiota and bile acid metabolism.}, } @article {pmid39716092, year = {2024}, author = {Chapman, JA and Wroot, E and Brown, T and Beck, LC and Embleton, ND and Berrington, JE and Stewart, CJ}, title = {Characterising the metabolic functionality of the preterm neonatal gut microbiome prior to the onset of necrotising enterocolitis: a pilot study.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {533}, pmid = {39716092}, issn = {1471-2180}, mesh = {Humans ; *Enterocolitis, Necrotizing/microbiology/metabolism ; *Gastrointestinal Microbiome ; Pilot Projects ; Infant, Newborn ; *Infant, Premature ; Female ; Male ; Bacteria/classification/metabolism/isolation & purification/genetics ; Feces/microbiology ; Case-Control Studies ; Metagenome ; }, abstract = {BACKGROUND: Necrotising enterocolitis (NEC) is a devastating bowel disease that primarily occurs in infants born prematurely and is associated with abnormal gut microbiome development. While gut microbiome compositions associated with NEC have been well studied, there is a lack of experimental work investigating microbiota functions and their associations with disease onset. The aim of this pilot study was to characterise the metabolic functionality of the preterm gut microbiome prior to the onset of NEC compared with healthy controls.

RESULTS: Eight NEC infants were selected of median gestation 26.5 weeks and median day of life (DOL) of NEC onset 20, with one sample used per infant, collected within one to eight days (median four) before NEC onset. Each NEC case was matched to a control infant based on gestation and sample DOL, the main driver of microbiome composition in this population, giving a total cohort of 16 infants for this study. Dietary exposures were well matched. The microbiota of NEC and control infants showed similar wide-ranging metabolic functionalities. All 94 carbon sources were utilised to varying extents but NEC and control samples clustered separately by supervised ordination based on carbon source utilisation profiles. For a subset of eight samples (four NEC, four control) for which pre-existing metagenome data was available, microbiome composition was found to correlate significantly with metabolic activity measured on Biolog plates (p = 0.035). Comparisons across all 16 samples showed the NEC microbiota to have greater utilisation of carbon sources that are the products of proteolytic fermentation, specifically amino acids. In pairwise comparisons, L-methionine was highly utilised in NEC samples, but poorly utilised in controls (p = 0.043). Carbon sources identified as discriminatory for NEC also showed a greater enrichment for established markers of inflammatory disease, such as inflammatory bowel disease, irritable bowel syndrome and diverticular disease.

CONCLUSIONS: Before NEC onset, the preterm gut microbiota showed greater metabolic utilisation of amino acids, potentially indicating a shift from predominantly saccharolytic to proteolytic fermentation. Products of amino acid breakdown could therefore act as biomarkers for NEC development. A larger study is warranted, ideally with infants from multiple sites.}, } @article {pmid39716039, year = {2025}, author = {Du, Q and Liu, X and Zhang, R and Hu, G and Liu, Q and Wang, R and Ma, W and Hu, Y and Fan, Z and Li, J}, title = {Placental and Fetal Microbiota in Rhesus Macaque: A Case Study Using Metagenomic Sequencing.}, journal = {American journal of primatology}, volume = {87}, number = {1}, pages = {e23718}, doi = {10.1002/ajp.23718}, pmid = {39716039}, issn = {1098-2345}, support = {//This work was supported by the National Natural Science Foundation of China (32171607)/ ; }, mesh = {Animals ; *Macaca mulatta/microbiology ; Female ; Pregnancy ; *Fetus/microbiology ; *Placenta/microbiology ; *Microbiota ; *Metagenomics ; Umbilical Cord/microbiology ; Gastrointestinal Microbiome ; }, abstract = {Recent evidence challenging the notion of a sterile intrauterine environment has sparked research into the origins and effects of fetal microbiota on immunity development during gestation. Rhesus macaques (RMs) serve as valuable nonhuman primate models due to their similarities to humans in development, placental structure, and immune response. In this study, metagenomic analysis was applied to the placenta, umbilical cord, spleen, gastrointestinal tissues of an unborn RM fetus, and the maternal intestine, revealing the diversity and functionality of microbes in these tissues. Additionally, gut metagenomic data of adult Rhesus macaques from our previous study, along with data from a human fetus obtained from public databases, were included for comparison. We observed substantial microbial sharing between the mother and fetus, with the microbial composition of the placenta and umbilical cord more closely resembling that of the fetal organs than the maternal intestine. Notably, compared with other adult RMs, there was a clear convergence between maternal and fetal microbiota, alongside distinct differences between the microbiota of adults and the fetus, which underscores the unique microbial profiles in fetal environments. Furthermore, the fetal microbiota displayed a less developed carbohydrate metabolism capacity than adult RMs. It also shared antibiotic resistance genes with both maternal and adult RM microbiomes, indicating potential vertical transmission. Comparative analysis of the metagenomes between the RM fetus and a human fetus revealed significant differences in microbial composition and genes, yet also showed similarities in certain abundant microbiota. Collectively, our results contribute to a more comprehensive understanding of the intrauterine microbial environment in macaques.}, } @article {pmid39715919, year = {2024}, author = {Jiang, ZB and Zhang, H and Tian, JJ and Guo, HH and Zhou, LR and Ma, XL}, title = {The Microbial Diversity of Biological Moss Crust: Application in Saline-Alkali Soil Management.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {162}, pmid = {39715919}, issn = {1432-184X}, support = {82160672//the National Natural Science Foundation of China/ ; 2022AAC05041 and 2023AAC05048//Outstanding Youth Program of Ningxia Natural Science Foundation/ ; 2021BEB04019//the Key R&D Projects in Ningxia/ ; 2021AAC03210 and 2019AAC03113//the Ningxia Natural Science Foundation/ ; }, mesh = {*Soil/chemistry ; *Soil Microbiology ; *Bryophyta/microbiology ; China ; Biodiversity ; Alkalies/analysis ; Salinity ; Bacteria/classification/genetics/isolation & purification/metabolism ; Chlorophyll/analysis ; }, abstract = {Soil salinization poses a substantial threat to global food security, particularly under the influence of climate change, and is recognized as one of the most urgent challenges in land degradation. This study aims to elucidate the challenges associated with managing arid and semi-arid saline-alkali lands in China's Ningxia province and propose feasible solutions. To assess moss crust colonization, we measured changes in organic matter and chlorophyll levels. Additionally, we investigated the impact of an interlayer composed of Goji berry root bark using liquid chromatography-mass spectrometry analysis, biological enzyme activity analysis, and metagenomic sequencing. A total of 45 endophytes were isolated from the moss crust. The most significant colonization of moss crusts was observed when the Goji berry root bark was used as the interlayer, resulting in a significant increase in chlorophyll content. Several responses were identified as pivotal factors facilitating moss crust growth when the Goji berry root bark was used as the interlayer. In saline-alkali soil, the Goji berry root bark interlayer increased the activities of sucrase, urease, and alkaline phosphatase. Metagenomic data analysis revealed variations in the relative abundance of microorganisms at the phylum level, although these differences were not statistically significant. Evaluation of the impact of physical isolation and moss crust transplantation on the ecological restoration of saline-alkali soil using liquid chromatography-tandem mass spectrometry and metagenomic sequencing indicated that the Goji berry root bark as a physical isolation method promotes moss crust colonization in saline-alkali soil and increases soil organic matter and nutrient elements, offering valuable insights for the ecological management of saline-alkali land and serving as a reference for future research in this field.}, } @article {pmid39714548, year = {2024}, author = {Wang, W and Zhang, Z and Sun, M and Li, C and Yan, M and Wang, C}, title = {Mechanism of decolorization and degradation of direct brown D3G by a halo-thermophilic consortium.}, journal = {Extremophiles : life under extreme conditions}, volume = {29}, number = {1}, pages = {11}, pmid = {39714548}, issn = {1433-4909}, support = {22B610001//the Key Scientific Research Project in Colleges and Universities of Henan Province of China/ ; HDXJJG2023-058//the teaching reform project of Henan University/ ; }, mesh = {*Azo Compounds/metabolism/chemistry ; Microbial Consortia ; Biodegradation, Environmental ; Halomonas/metabolism ; Coloring Agents/metabolism/chemistry ; Laccase/metabolism ; Bacillus/metabolism ; }, abstract = {Azo dye wastewater has garnered significant attention from researchers because of its association with high-temperature, high-salt, and high-alkali conditions. In this study, consortium ZZ efficiently decolorized brown D3G under halophilic and thermophilic conditions. he results indicated that consortium ZZ, which was mainly dominated by Marinobacter, Bacillus, and Halomonas, was achieved decolorization rates ranging from 1 to 10% at temperatures between 40 °C and 50 °C, while maintaining a pH range of 7 to 10 for direct brown D3G degradation. Through the comprehensive utilization of UV-vis spectral analysis, Fourier transform infrared (FTIR), gas chromatography mass spectrometric (GC-MS) techniques, as well as metagenomic analysis, the decolorization and degradation pathway of direct brown by consortium ZZ was proposed. The azo dye reductase, lignin peroxidase, and laccase were also highly expressed in the decolorization process. Additionally, phytotoxicity tests using seeds of Cucumis sativus and Oryza sativa revealed that the intermediates generated showed no significant toxicity compared with distilled water. This investigation elucidated the pivotal contribution of consortium ZZ to azo dye degradation and provided novel theoretical insights along with practical guidance for azo dye treatment at halo-thermophilic conditions.}, } @article {pmid39713824, year = {2024}, author = {Karesh, WB}, title = {Shifting from wildlife disease threats to wildlife health.}, journal = {Revue scientifique et technique (International Office of Epizootics)}, volume = {Special Edition}, number = {}, pages = {141-144}, doi = {10.20506/rst.SE.3568}, pmid = {39713824}, issn = {0253-1933}, mesh = {Animals ; *Animals, Wild ; Humans ; Zoonoses/prevention & control ; Conservation of Natural Resources ; Animal Diseases/prevention & control/epidemiology ; }, abstract = {The evolution of wildlife disease management and surveillance, as documented in the World Organisation for Animal Health's Scientific and Technical Review, reflects a deepening understanding of the links between wildlife health, ecosystem integrity and human well-being. Early work, beginning with the World Assembly of Delegates in 1954, primarily focused on diseases like rabies. This focus expanded over time to include broader concerns such as the impacts of climate change, habitat loss and increased human-wildlife interactions on wildlife health. By the late 20th century, the emphasis had shifted towards improved practices for wildlife disease control and the development of advanced diagnostic methods and vaccines. Articles in the Review highlight the growing complexity of wildlife diseases and the need for holistic management strategies. The adoption in recent years of cutting-edge technologies like CRISPR-Cas systems and metagenomics points to a future of more proactive and integrated approaches to wildlife disease management. There is still a need to address not just the consequences of wildlife diseases but also their anthropogenic drivers. The latest perspectives advocate for nature-based solutions, expanded partnerships and systems-level thinking to effectively tackle 21st-century challenges in wildlife and biodiversity conservation.}, } @article {pmid39711113, year = {2025}, author = {Olivares, C and Ruppé, E and Ferreira, S and Corbel, T and Andremont, A and de Gunzburg, J and Guedj, J and Burdet, C}, title = {A modelling framework to characterize the impact of antibiotics on the gut microbiota diversity.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2442523}, doi = {10.1080/19490976.2024.2442523}, pmid = {39711113}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; *Feces/microbiology ; *Bacteria/classification/genetics/drug effects/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; Adult ; Ceftazidime/pharmacology/administration & dosage ; Male ; Moxifloxacin/pharmacology/administration & dosage ; Drug Combinations ; Ceftriaxone/pharmacology/administration & dosage ; Female ; Azabicyclo Compounds/pharmacology/administration & dosage ; Biodiversity ; Young Adult ; Healthy Volunteers ; Piperacillin, Tazobactam Drug Combination ; }, abstract = {Metagenomic sequencing deepened our knowledge about the role of the intestinal microbiota in human health, and several studies with various methodologies explored its dynamics during antibiotic treatments. We compared the impact of four widely used antibiotics on the gut bacterial diversity. We used plasma and fecal samples collected during and after treatment from healthy volunteers assigned to a 5-day treatment either by ceftriaxone (1 g every 24 h through IV route), ceftazidime/avibactam (2 g/500 mg every 8 h through IV route), piperacillin/tazobactam (1 g/500 mg every 8 h through IV route) or moxifloxacin (400 mg every 24 h through oral route). Antibiotic concentrations were measured in plasma and feces, and bacterial diversity was assessed by the Shannon index from 16S rRNA gene profiling. The relationship between the evolutions of antibiotic fecal exposure and bacterial diversity was modeled using non-linear mixed effects models. We compared the impact of antibiotics on gut microbiota diversity by simulation, using various reconstructed pharmacodynamic indices. Piperacillin/tazobactam was characterized by the highest impact in terms of intensity of perturbation (maximal [IQR] loss of diversity of 27.3% [1.9; 40.0]), while moxifloxacin had the longest duration of perturbation, with a time to return to 95% of baseline value after the last administration of 13.2 d [8.3; 19.1]. Overall, moxifloxacin exhibited the highest global impact, followed by piperacillin/tazobactam, ceftazidime/avibactam and ceftriaxone. Their AUC between day 0 and day 42 of the change of diversity indices from day 0 were, respectively, -13.2 Shannon unit.day [-20.4; -7.9], -10.9 Shannon unit.day [-20.4; -0.6] and -10.1 Shannon unit.day [-18.3; -4.6]. We conclude that antibiotics alter the intestinal diversity to varying degrees, both within and between antibiotics families. Such studies are needed to help antibiotic stewardship in using the antibiotics with the lowest impact on the intestinal microbiota.}, } @article {pmid39710013, year = {2025}, author = {He, B and Xu, S and Schooling, CM and Leung, GM and Ho, JWK and Au Yeung, SL}, title = {Gut microbiome and obesity in late adolescence: A case-control study in "Children of 1997" birth cohort.}, journal = {Annals of epidemiology}, volume = {101}, number = {}, pages = {58-66}, doi = {10.1016/j.annepidem.2024.12.009}, pmid = {39710013}, issn = {1873-2585}, mesh = {Humans ; *Gastrointestinal Microbiome ; Case-Control Studies ; Female ; Male ; Adolescent ; *Pediatric Obesity/microbiology/epidemiology ; *Feces/microbiology ; Diabetes Mellitus, Type 2/microbiology/epidemiology ; Birth Cohort ; Bacteroides/isolation & purification ; }, abstract = {PURPOSE: Although the gut microbiome is important in human health, its relation to adolescent obesity remains unclear. Here we assessed the associations of the gut microbiome with adolescent obesity in a case-control study.

METHODS: In the "Children of 1997" birth cohort, participants with and without obesity at ∼17.4 years were 1:1 matched on sex, physical activity, parental education and occupation (n = 312). Fecal gut microbiome composition and pathways were assessed via shotgun metagenomic sequencing. The association of microbiota species with obesity was evaluated using conditional logistic regression. We explored the association of the obesity-relevant species with adolescent metabolomics using multivariable linear regression, and causal relationships with type 2 diabetes using Mendelian randomization analysis.

RESULTS: Gut microbiota in the adolescents with obesity exhibited lower richness (p = 0.031) and evenness (p = 0.014) compared to controls. Beta diversity revealed differences in the microbiome composition in two groups (p = 0.034). Lower relative abundance of Clostridium spiroforme, Clostridium phoceensis and Bacteroides uniformis were associated with higher obesity risk (q<0.15). Lower Bacteroides uniformis was associated with higher branched-chain amino acid, potentially contributing to higher type 2 diabetes risk.

CONCLUSION: Adolescents with obesity had a distinct gut microbiota profile compared to the controls, possibly linked to metabolic pertubation and related diseases.}, } @article {pmid39709651, year = {2025}, author = {Cheng, E and Hung, SC and Lin, TY}, title = {Association of trimethylamine N-oxide and metabolites with kidney function decline in patients with chronic kidney disease.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {44}, number = {}, pages = {239-247}, doi = {10.1016/j.clnu.2024.12.001}, pmid = {39709651}, issn = {1532-1983}, mesh = {Humans ; *Methylamines/blood ; Female ; *Renal Insufficiency, Chronic/blood/physiopathology ; Male ; Aged ; *Gastrointestinal Microbiome/physiology ; *Glomerular Filtration Rate ; Prospective Studies ; *Carnitine/blood ; Middle Aged ; *Choline/blood ; Kidney/physiopathology ; Disease Progression ; Betaine/blood/analogs & derivatives ; }, abstract = {BACKGROUND: Trimethylamine N-oxide (TMAO) is a gut microbial metabolite derived from dietary l-carnitine and choline. High plasma TMAO levels are associated with cardiovascular disease and overall mortality, but little is known about the associations of TMAO and related metabolites with the risk of kidney function decline among patients with chronic kidney disease (CKD).

METHODS: We prospectively followed 152 nondialysis patients with CKD stages 3-5 and measured plasma TMAO and related metabolites (trimethylamine [TMA], choline, carnitine, and γ-butyrobetaine) via liquid chromatography‒mass spectrometry. An estimated glomerular filtration rate (eGFR) slope >3 ml/min/per 1.73 m[2] per year was defined as a rapid decline. We performed logistic regression to determine the probability of rapid or slow eGFR decline, with each metabolite as the main predictor. The gut microbiota was profiled via whole metagenomic sequencing.

RESULTS: The participants had a median age of 66 years, 41.4 % were women, 39.5 % had diabetes, and the median eGFR was 23 mL/min/1.73 m[2]. A rapid decrease in the eGFR occurred in 65 patients (42.8 %) over a median follow-up of 3.3 years. After adjustment for baseline eGFR, proteinuria, and clinical factors, plasma TMAO levels were independently associated with increased odds of rapid eGFR decline (odds ratio, 2.42; 95 % CI, 1.36-4.32), whereas plasma TMA, choline, carnitine, and γ-butyrobetaine levels were not. Patients who exhibited rapid eGFR decline had a distinct gut microbial composition characterized by increased α-diversity and an abundance of TMA-producing bacteria, including those of the genera Desulfovibrio and Collinsella tanakaei, as well as increased expression of the TMA-producing enzymes bbuA and cutC.

CONCLUSION: Our findings suggest the relevance of plasma TMAO in the progression of kidney disease among patients with CKD.}, } @article {pmid39709594, year = {2025}, author = {Smith, MZ and York, M and Townsend, KS and Martin, LM and Gull, T and Coghill, LM and Ericsson, AC and Johnson, PJ}, title = {Effects of orally administered clioquinol on the fecal microbiome of horses.}, journal = {Journal of veterinary internal medicine}, volume = {39}, number = {1}, pages = {e17276}, pmid = {39709594}, issn = {1939-1676}, mesh = {Animals ; Horses ; *Feces/microbiology ; *Clioquinol/pharmacology/administration & dosage ; Female ; Male ; Administration, Oral ; Prospective Studies ; Gastrointestinal Microbiome/drug effects ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; }, abstract = {BACKGROUND: Whereas restoration of fecal consistency after treatment with clioquinol for chronic diarrhea and free fecal water syndrome has been attributed to its antiprotozoal properties, actions of clioquinol on the colonic bacterial microbiota have not been investigated.

OBJECTIVES: Characterize the dynamics of fecal microbial diversity before, during, and after PO administration of clioquinol to healthy horses.

STUDY DESIGN: Experimental prospective cohort study using a single horse group.

METHODS: Eight healthy adult horses received PO clioquinol (10 g, daily) for 7 days. Feces were obtained daily for 7 days before, during, and after conclusion of treatment, and again 3 months later. Libraries of 16S rRNA V4 region amplicons generated from fecal DNA were sequenced using the Illumina sequencing platform. Bioinformatic analysis was undertaken with QIIME2 and statistical analyses included analysis of variance (ANOVA) and permutational multivariate ANOVA (PERMANOVA).

RESULTS: The richness and composition of the fecal microbiome was altered after administration of clioquinol, reaching a maximum effect by the fifth day of administration. Changes included a 90% decrease in richness, and compensatory expansion of facultative anaerobes including Streptococcaceae, Enterococcaceae, and Enterobacteriaceae. Multiple horses had Salmonella cultured from feces.

MAIN LIMITATIONS: Limitations including lack of control group and modest sample size are obviated by robust longitudinal study design and strong effect size associated with drug exposure.

CONCLUSIONS: Clioquinol has broad-spectrum antibacterial effects on the fecal microbiome of horses, but spares certain bacterial families including several pathogens and pathobionts. Clioquinol should be used with caution in horses, in an environment free of contamination with fecal pathogens.}, } @article {pmid39709449, year = {2024}, author = {Dos Santos, SJ and Copeland, C and Macklaim, JM and Reid, G and Gloor, GB}, title = {Vaginal metatranscriptome meta-analysis reveals functional BV subgroups and novel colonisation strategies.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {271}, pmid = {39709449}, issn = {2049-2618}, support = {20170705//Weston Family Foundation/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology ; *Vaginosis, Bacterial/microbiology ; *Microbiota/genetics ; *Transcriptome ; *Bacteria/genetics/classification/isolation & purification ; Biofilms/growth & development ; Metagenomics/methods ; }, abstract = {BACKGROUND: The application of '-omics' technologies to study bacterial vaginosis (BV) has uncovered vast differences in composition and scale between the vaginal microbiomes of healthy and BV patients. Compared to amplicon sequencing and shotgun metagenomic approaches focusing on a single or few species, investigating the transcriptome of the vaginal microbiome at a system-wide level can provide insight into the functions which are actively expressed and differential between states of health and disease.

RESULTS: We conducted a meta-analysis of vaginal metatranscriptomes from three studies, split into exploratory (n = 42) and validation (n = 297) datasets, accounting for the compositional nature of sequencing data and differences in scale between healthy and BV microbiomes. Conducting differential expression analyses on the exploratory dataset, we identified a multitude of strategies employed by microbes associated with states of health and BV to evade host cationic antimicrobial peptides (CAMPs); putative mechanisms used by BV-associated species to resist and counteract the low vaginal pH; and potential approaches to disrupt vaginal epithelial integrity so as to establish sites for adherence and biofilm formation. Moreover, we identified several distinct functional subgroups within the BV population, distinguished by genes involved in motility, chemotaxis, biofilm formation and co-factor biosynthesis. After defining molecular states of health and BV in the validation dataset using KEGG orthology terms rather than community state types, differential expression analysis confirmed earlier observations regarding CAMP resistance and compromising epithelial barrier integrity in healthy and BV microbiomes and also supported the existence of motile vs. non-motile subgroups in the BV population. These findings were independent of the enzyme classification system used (KEGG or EggNOG).

CONCLUSIONS: Our findings highlight a need to focus on functional rather than taxonomic differences when considering the role of microbiomes in disease and identify pathways for further research as potential BV treatment targets. Video Abstract.}, } @article {pmid39708838, year = {2024}, author = {Luo, Q and Zhang, S and Butt, H and Chen, Y and Jiang, H and An, L}, title = {PhyImpute and UniFracImpute: two imputation approaches incorporating phylogeny information for microbial count data.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39708838}, issn = {1477-4054}, support = {R01ES027013//National Institute of Health/ ; ARZT-1361620-H22-149//United States Department of Agriculture/ ; }, mesh = {*Phylogeny ; Algorithms ; Humans ; Computational Biology/methods ; Microbiota/genetics ; }, abstract = {Sequencing-based microbial count data analysis is a challenging task due to the presence of numerous non-biological zeros, which can impede downstream analysis. To tackle this issue, we introduce two novel approaches, PhyImpute and UniFracImpute, which leverage similar microbial samples to identify and impute non-biological zeros in microbial count data. Our proposed methods utilize the probability of non-biological zeros and phylogenetic trees to estimate sample-to-sample similarity, thus addressing this challenge. To evaluate the performance of our proposed methods, we conduct experiments using both simulated and real microbial data. The results demonstrate that PhyImpute and UniFracImpute outperform existing methods in recovering the zeros and empowering downstream analyses such as differential abundance analysis, and disease status classification.}, } @article {pmid39707929, year = {2024}, author = {Shahzaib, M and Muaz, M and Zubair, MH and Kayani, MUR}, title = {MiCK: a database of gut microbial genes linked with chemoresistance in cancer patients.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {39707929}, issn = {1758-0463}, mesh = {Humans ; *Neoplasms/genetics/drug therapy ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Neoplasm/genetics ; *Databases, Genetic ; }, abstract = {Cancer remains a global health challenge, with significant morbidity and mortality rates. In 2020, cancer caused nearly 10 million deaths, making it the second leading cause of death worldwide. The emergence of chemoresistance has become a major hurdle in successfully treating cancer patients. Recently, human gut microbes have been recognized for their role in modulating drug efficacy through their metabolites, ultimately leading to chemoresistance. The currently available databases are limited to knowledge regarding the interactions between gut microbiome and drugs. However, a database containing the human gut microbial gene sequences, and their effect on the efficacy of chemotherapy for cancer patients has not yet been developed. To address this challenge, we present the Microbial Chemoresistance Knowledgebase (MiCK), a comprehensive database that catalogs microbial gene sequences associated with chemoresistance. MiCK contains 1.6 million sequences of 29 gene types linked to chemoresistance and drug metabolism, curated manually from recent literature and sequence databases. The database can support downstream analysis as it provides a user-friendly web interface for sequence search and download functionalities. MiCK aims to facilitate the understanding and mitigation of chemoresistance in cancers by serving as a valuable resource for researchers. Database URL: https://microbialchemreskb.com/.}, } @article {pmid39707568, year = {2024}, author = {Yang, X and Yuan, R and Yang, S and Dai, Z and Di, N and Yang, H and He, Z and Wei, M}, title = {A salt-tolerant growth-promoting phyllosphere microbial combination from mangrove plants and its mechanism for promoting salt tolerance in rice.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {270}, pmid = {39707568}, issn = {2049-2618}, mesh = {*Oryza/microbiology/growth & development ; *Salt Tolerance ; *Plant Leaves/microbiology ; Microbiota ; Rhizosphere ; Pantoea/genetics ; Soil Microbiology ; Bacillus/genetics/isolation & purification/physiology ; Bacteria/genetics/classification/isolation & purification ; Wetlands ; Rhizophoraceae/microbiology ; Quorum Sensing ; }, abstract = {BACKGROUND: Mangrove plants growing in the high salt environment of coastal intertidal zones colonize a variety of microorganisms in the phyllosphere, which have potential salt-tolerant and growth-promoting effects. However, the characteristics of microbial communities in the phyllosphere of mangrove species with and without salt glands and the differences between them remain unknown, and the exploration and the agricultural utilization of functional microbial resources from the leaves of mangrove plants are insufficient.

RESULTS: In this study, we examined six typical mangrove species to unravel the differences in the diversity and structure of phyllosphere microbial communities between mangrove species with or without salt glands. Our results showed that a combination of salt-tolerant growth-promoting strains of Pantoea stewartii A and Bacillus marisflavi Y25 (A + Y25) was constructed from the phyllosphere of mangrove plants, which demonstrated an ability to modulate osmotic substances in rice and regulate the expression of salt-resistance-associated genes. Further metagenomic analysis revealed that exogenous inoculation with A + Y25 increased the rice rhizosphere's specific microbial taxon Chloroflexi, thereby elevating microbial community quorum sensing and ultimately enhancing ionic balance and overall microbial community function to aid salt resistance in rice.

CONCLUSIONS: This study advances our understanding of the mutualistic and symbiotic relationships between mangrove species and their phyllosphere microbial communities. It offers a paradigm for exploring agricultural beneficial microbial resources from mangrove leaves and providing the potential for applying the salt-tolerant bacterial consortium to enhance crop adaptability in saline-alkaline land. Video Abstract.}, } @article {pmid39707567, year = {2024}, author = {Feng, X and Xing, P and Tao, Y and Wang, X and Wu, QL and Liu, Y and Luo, H}, title = {Functional traits and adaptation of lake microbiomes on the Tibetan Plateau.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {264}, pmid = {39707567}, issn = {2049-2618}, support = {2023A1515012162//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2022M712195//the China Postdoctoral Science Foundation/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; U2102216//the National Natural Science Foundation of China/ ; 92251304//the National Natural Science Foundation of China/ ; 92251304//the National Natural Science Foundation of China/ ; AoE/M-403/16//the Hong Kong Research Grants Council Area of Excellence Scheme/ ; }, mesh = {*Lakes/microbiology ; Tibet ; *Microbiota/genetics ; *Phylogeny ; *Bacteria/classification/genetics ; Metagenome ; Salinity ; Climate Change ; Ecosystem ; Adaptation, Physiological ; }, abstract = {BACKGROUND: Tibetan Plateau is credited as the "Third Pole" after the Arctic and the Antarctic, and lakes there represent a pristine habitat ideal for studying microbial processes under climate change.

RESULTS: Here, we collected 169 samples from 54 lakes including those from the central Tibetan region that was underrepresented previously, grouped them to freshwater, brackish, and saline lakes, and generated a genome atlas of the Tibetan Plateau Lake Microbiome. This genomic atlas comprises 8271 metagenome-assembled genomes featured by having significant phylogenetic and functional novelty. The microbiomes of freshwater lakes are enriched with genes involved in recalcitrant carbon degradation, carbon fixation, and energy transformation, whereas those of saline lakes possess more genes that encode osmolyte transport and synthesis and enable anaerobic metabolism. These distinct metabolic features match well with the geochemical properties including dissolved organic carbon, dissolved oxygen, and salinity that distinguish between these lakes. Population genomic analysis suggests that microbial populations in saline lakes are under stronger functional constraints than those in freshwater lakes. Although microbiomes in the Tibet lakes, particularly the saline lakes, may be subject to changing selective regimes due to ongoing warming, they may also benefit from the drainage reorganization and metapopulation reconnection.

CONCLUSIONS: Altogether, the Tibetan Plateau Lake Microbiome atlas serves as a valuable microbial genetic resource for biodiversity conservation and climate research. Video Abstract.}, } @article {pmid39707560, year = {2024}, author = {Wang, H and Sun, C and Li, Y and Chen, J and Zhao, XM and Chen, WH}, title = {Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {260}, pmid = {39707560}, issn = {2049-2618}, support = {T2225015//National Natural Science Foundation of China/ ; 32070660//National Natural Science Foundation of China/ ; 2020YFA0712403//National Key Research and Development Program of China/ ; 2019YFA0905600//National Key Research and Development Program of China/ ; 82161138017//NNSF-VR Sino-Swedish Joint Research Programme/ ; }, mesh = {*Genome, Viral/genetics ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; *Feces/virology ; Metagenomics/methods ; Virome/genetics ; Viruses/genetics/classification ; Benchmarking ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Metagenome-assembled viral genomes have significantly advanced the discovery and characterization of the human gut virome. However, we lack a comparative assessment of assembly tools on the efficacy of viral genome identification, particularly across next-generation sequencing (NGS) and third-generation sequencing (TGS) data.

RESULTS: We evaluated the efficiency of NGS, TGS, and hybrid assemblers for viral genome discovery using 95 viral-like particle (VLP)-enriched fecal samples sequenced on both Illumina and PacBio platforms. MEGAHIT, metaFlye, and hybridSPAdes emerged as the optimal choices for NGS, TGS, and hybrid datasets, respectively. Notably, these assemblers recovered distinct viral genomes, demonstrating a remarkable degree of complementarity. By combining individual assembler results, we expanded the total number of nonredundant high-quality viral genomes by 4.83 ~ 21.7-fold compared to individual assemblers. Among them, viral genomes from NGS and TGS data have the least overlap, indicating the impact of data type on viral genome recovery. We also evaluated four binning methods, finding that CONCOCT incorporated more unrelated contigs into the same bins, while MetaBAT2, AVAMB, and vRhyme balanced inclusiveness and taxonomic consistency within bins.

CONCLUSIONS: Our findings highlight the challenges in metagenome-driven viral discovery, underscoring tool limitations. We advocate for combined use of multiple assemblers and sequencing technologies when feasible and highlight the urgent need for specialized tools tailored to gut virome assembly. This study contributes essential insights for advancing viral genome research in the context of gut metagenomics. Video Abstract.}, } @article {pmid39707557, year = {2024}, author = {Santamarina-García, G and Yap, M and Crispie, F and Amores, G and Lordan, C and Virto, M and Cotter, PD}, title = {Shotgun metagenomic sequencing reveals the influence of artisanal dairy environments on the microbiomes, quality, and safety of Idiazabal, a raw ewe milk PDO cheese.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {262}, pmid = {39707557}, issn = {2049-2618}, support = {IT1568-22//Eusko Jaurlaritza/ ; IT1568-22//Eusko Jaurlaritza/ ; IT1568-22//Eusko Jaurlaritza/ ; PIF19/31//Euskal Herriko Unibertsitatea/ ; }, mesh = {*Cheese/microbiology ; Animals ; *Milk/microbiology ; *Microbiota ; *Metagenomics ; Sheep/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Female ; Dairying ; Food Microbiology ; Metagenome ; }, abstract = {BACKGROUND: Numerous studies have highlighted the impact of bacterial communities on the quality and safety of raw ewe milk-derived cheeses. Despite reported differences in the microbiota among cheese types and even producers, to the best of our knowledge, no study has comprehensively assessed all potential microbial sources and their contributions to any raw ewe milk-derived cheese, which could suppose great potential for benefits from research in this area. Here, using the Protected Designation of Origin Idiazabal cheese as an example, the impact of the environment and practices of artisanal dairies (including herd feed, teat skin, dairy surfaces, and ingredients) on the microbiomes of the associated raw milk, whey, and derived cheeses was examined through shotgun metagenomic sequencing.

RESULTS: The results revealed diverse microbial ecosystems across sample types, comprising more than 1300 bacterial genera and 3400 species. SourceTracker analysis revealed commercial feed and teat skin as major contributors to the raw milk microbiota (45.6% and 33.5%, respectively), being a source of, for example, Lactococcus and Pantoea, along with rennet contributing to the composition of whey and cheese (17.4% and 41.0%, respectively), including taxa such as Streptococcus, Pseudomonas_E or Lactobacillus_H. Functional analysis linked microbial niches to cheese quality- and safety-related metabolic pathways, with brine and food contact surfaces being most relevant, related to genera like Brevibacterium, Methylobacterium, or Halomonas. With respect to the virulome (virulence-associated gene profile), in addition to whey and cheese, commercial feed and grass were the main reservoirs (related to, e.g., Brevibacillus_B or CAG-196). Similarly, grass, teat skin, or rennet were the main contributors of antimicrobial resistance genes (e.g., Bact-11 or Bacteriodes_B). In terms of cheese aroma and texture, apart from the microbiome of the cheese itself, brine, grass, and food contact surfaces were key reservoirs for hydrolase-encoding genes, originating from, for example, Lactococcus, Lactobacillus, Listeria or Chromohalobacter. Furthermore, over 300 metagenomic assembled genomes (MAGs) were generated, including 60 high-quality MAGs, yielding 28 novel putative species from several genera, e.g., Citricoccus, Corynebacterium, or Dietzia.

CONCLUSION: This study emphasizes the role of the artisanal dairy environments in determining cheese microbiota and, consequently, quality and safety. Video Abstract.}, } @article {pmid39707494, year = {2024}, author = {Li, C and Liu, K and Gu, C and Li, M and Zhou, P and Chen, L and Sun, S and Li, X and Wang, L and Ni, W and Li, M and Hu, S}, title = {Gastrointestinal jumbo phages possess independent synthesis and utilization systems of NAD.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {268}, pmid = {39707494}, issn = {2049-2618}, mesh = {*Bacteriophages/genetics/classification/isolation & purification ; Animals ; *Genome, Viral/genetics ; *NAD/metabolism ; *Phylogeny ; Humans ; Gastrointestinal Microbiome ; Swine ; Sheep ; Metagenomics ; Horses ; Cattle ; Bacteria/virology/genetics ; Deer/virology ; DNA Replication ; }, abstract = {BACKGROUND: Jumbo phages, phages with genomes > 200 kbp, contain some unique genes for successful reproduction in their bacterial hosts. Due to complex and massive genomes analogous to those of small-celled bacteria, how jumbo phages complete their life cycle remains largely undefined.

RESULTS: In this study, we assembled 668 high-quality jumbo phage genomes from over 15 terabytes (TB) of intestinal metagenomic data from 955 samples of 5 animal species (cow, sheep, pig, horse, and deer). Within them, we obtained a complete genome of 716 kbp in length, which is the largest phage genome so far reported in the gut environments. Interestingly, 174 out of the 668 jumbo phages were found to encode all genes required for the synthesis of NAD[+] by the salvage pathway or Preiss-Handler pathway, referred to as NAD-jumbo phage. Besides synthesis genes of NAD[+], these NAD-jumbo phages also encode at least 15 types of NAD[+]-consuming enzyme genes involved in DNA replication, DNA repair, and counterdefense, suggesting that these phages not only have the capacity to synthesize NAD[+] but also redirect NAD[+] metabolism towards phage propagation need in hosts. Phylogenetic analysis and environmental survey indicated NAD-jumbo phages are widely present in the Earth's ecosystems, including the human gut, lakes, salt ponds, mine tailings, and seawater.

CONCLUSION: In summary, this study expands our understanding of the diversity and survival strategies of phages, and an in-depth study of the NAD-jumbo phages is crucial for understanding their role in ecological regulation. Video Abstract.}, } @article {pmid39707478, year = {2024}, author = {He, Z and Hou, Y and Li, Y and Bei, Q and Li, X and Zhu, YG and Liesack, W and Rillig, MC and Peng, J}, title = {Increased methane production associated with community shifts towards Methanocella in paddy soils with the presence of nanoplastics.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {259}, pmid = {39707478}, issn = {2049-2618}, mesh = {*Methane/metabolism ; *Soil Microbiology ; *Soil/chemistry ; *Oryza/microbiology ; Microbiota ; Polyethylene ; Soil Pollutants ; Metagenomics ; Archaea/metabolism/genetics/classification ; Carbon/metabolism ; Plastics ; }, abstract = {BACKGROUND: Planetary plastic pollution poses a major threat to ecosystems and human health in the Anthropocene, yet its impact on biogeochemical cycling remains poorly understood. Waterlogged rice paddies are globally important sources of CH4. Given the widespread use of plastic mulching in soils, it is urgent to unravel whether low-density polyethylene (LDPE) will affect the methanogenic community in flooded paddy soils. Here, we employed a combination of process measurements, short-chain and long-chain fatty acid (SCFAs and LCFAs) profiling, Fourier-transform ion cyclotron resonance mass spectrometry, quantitative PCR, metagenomics, and mRNA profiling to investigate the impact of LDPE nanoplastics (NPs) on dissolved organic carbon (DOC) and CH4 production in both black and red paddy soils under anoxic incubation over a 160-day period.

RESULTS: Despite significant differences in microbiome composition between the two soil types, both exhibited similar results to NPs exposure. NPs induced a change in DOC content and CH4 production up to 1.8-fold and 10.1-fold, respectively. The proportion of labile dissolved organic matter decreased, while its recalcitrance increased. Genes associated with the degradation of complex carbohydrates and aromatic carbon were significantly enriched. The elevated CH4 production was significantly correlated to increases in both the PCR-quantified mcrA gene copy numbers and the metagenomic methanogen-to-bacteria abundance ratio. Notably, the latter was linked to an enrichment of the hydrogenotrophic methanogenesis pathway. Among 391 metagenome-assembled genomes (MAGs), the abundance of several Syntrophomonas and Methanocella MAGs increased concomitantly, suggesting that the NPs treatments stimulated the syntrophic oxidation of fatty acids. mRNA profiling further identified Methanosarcinaceae and Methanocellaceae to be the key players in the NPs-induced CH4 production.

CONCLUSIONS: The specific enrichment of Syntrophomonas and Methanocella indicates that LDPE NPs stimulate the syntrophic oxidation of LCFAs and SCFAs, with Methanocella acting as the hydrogenotrophic methanogen partner. Our findings enhance the understanding of how LDPE NPs affect the methanogenic community in waterlogged paddy soils. Given the importance of this ecosystem, our results are crucial for elucidating the mechanisms that govern carbon fluxes, which are highly relevant to global climate change.}, } @article {pmid39706917, year = {2024}, author = {Chang, WS and Harvey, E and Mahar, JE and Firth, C and Shi, M and Simon-Loriere, E and Geoghegan, JL and Wille, M}, title = {Improving the reporting of metagenomic virome-scale data.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1687}, pmid = {39706917}, issn = {2399-3642}, mesh = {Animals ; Humans ; Genome, Viral ; Metagenome ; *Metagenomics/methods ; *Virome/genetics ; *Viruses/genetics/classification ; }, abstract = {Over the last decade metagenomic sequencing has facilitated an increasing number of virome-scale studies, leading to an exponential expansion in understanding of virus diversity. This is partially driven by the decreasing costs of metagenomic sequencing, improvements in computational tools for revealing novel viruses, and an increased understanding of the key role that viruses play in human and animal health. A central concern associated with this remarkable increase in the number of virome-scale studies is the lack of broadly accepted "gold standards" for reporting the data and results generated. This is of particular importance for animal virome studies as there are a multitude of nuanced approaches for both data presentation and analysis, all of which impact the resulting outcomes. As such, the results of published studies can be difficult to contextualise and may be of reduced utility due to reporting deficiencies. Herein, we aim to address these reporting issues by outlining recommendations for the presentation of virome data, encouraging a transparent communication of findings that can be interpreted in evolutionary and ecological contexts.}, } @article {pmid39705954, year = {2024}, author = {Basile, A and Riggio, FP and Tescari, M and Chebbi, A and Sodo, A and Bartoli, F and Imperi, F and Caneva, G and Visca, P}, title = {Metagenome-resolved functional traits of Rubrobacter species implicated in rosy discoloration of ancient frescoes in two Georgian Cathedrals.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {178135}, doi = {10.1016/j.scitotenv.2024.178135}, pmid = {39705954}, issn = {1879-1026}, abstract = {Pink biofilm formation on stone monuments and mural paintings poses serious harm to cultural heritage preservation. Pink biofilms are globally widespread and recalcitrant to eradication, often causing recurrences after restoration. Yet, the ecological drivers of pink biofilm formation and the metabolic functions sustaining the growth of pigment-producing biodeteriogens remain unclear. In this study, a combined approach integrating physicochemical investigations, scanning electron microscopy, 16S rRNA sequence-based analysis of the prokaryotic community, metagenomic deep sequencing, and metabolic profiling, was applied to determine the etiology of rosy discoloration of ancient frescoes in the Gelati and the Martvili Cathedrals (Georgia). Martvili samples showed greater diversity than Gelati samples, though Actinomycetota predominated in both samples. Rubrobacter-related sequences were detected in all sampling sites, showing an overwhelming abundance in Gelati samples. Reconstruction of metagenome-assembled genomes (MAGs) and phylogenetic analyses highlighted significant intra-genus diversity for Rubrobacter-related sequences, most of which could not be assigned to any formally described Rubrobacter species. Metabolic profiling of the Gelati metagenomes suggests that carbon-fixing autotrophic bacteria and proteinaceous substances in the plaster could contribute to sustaining the chemoorganotrophic members of the community. Complete pathways for β-carotene and bacterioruberin synthesis were identified in Rubrobacter MAGs, consistent with the Raman spectroscopy-based detection of these pigments in fresco samples. Gene clusters for the synthesis of secondary metabolites endowed with antibiotic activity were predicted from the annotation of Rubrobacter MAGs, along with genes conferring resistance to several antimicrobials and biocides. In conclusion, genome-resolved metagenomics provided robust evidence of a causal relationship between contamination by Rubrobacter-related carotenoid-producing bacteria and the rosy discoloration of Georgian frescoes, with relevant implications for rational biodeteriogen-targeted restoration strategies.}, } @article {pmid39705480, year = {2024}, author = {Lu, S and Sun, L and Cao, L and Zhao, M and Guo, Y and Li, M and Duan, S and Zhai, Y and Zhang, X and Wang, Y and Gai, W and Cui, X}, title = {Analysis of lung microbiota in pediatric pneumonia patients using BALF metagenomic next-generation sequencing: A retrospective observational study.}, journal = {Medicine}, volume = {103}, number = {51}, pages = {e40860}, pmid = {39705480}, issn = {1536-5964}, support = {202139//Clinical Medical peronnel training programs/ ; }, mesh = {Child ; Child, Preschool ; Female ; Humans ; Infant ; Male ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Lung/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; *Pneumonia/genetics/microbiology ; Pneumonia, Mycoplasma/microbiology/diagnosis ; Retrospective Studies ; Severity of Illness Index ; }, abstract = {The contribution of the lung microbiota to pneumonia in children of varying severity remains poorly understood. This study utilized metagenomic next-generation sequencing (mNGS) technology to elucidate the characteristics of lung microbiota and their association with disease severity. This retrospective study analyzed bronchoalveolar lavage fluid (BALF) mNGS data of 92 children diagnosed with pneumonia between January 2021 and July 2022. A comparative analysis of the lung microbiota was conducted between the severe pneumonia (SP) (n = 44) and non-severe pneumonia (NSP) (n = 48) groups. Compared to conventional microbiological tests (CMT), mNGS had a higher positivity rate in etiology detection (68% vs 100%). In the NSP group, the predominant type of infection was Mycoplasma pneumoniae single infection, whereas in the SP group, the main type involved a combination of M pneumoniae and bacterial infection. The top 3 identified microbial taxa in both the groups were M pneumoniae, Rothia mucilaginosa, and Schaalia odontolyticus. Although there were no significant differences in the α and β diversity of the lung microbiota between the SP and NSP groups, the abundance of M pneumoniae was higher in the SP group (P = .053). Spearman analysis indicated a highly significant positive correlation between the abundance of Prevotella melaninogenica and M pneumoniae (P < .001). Our analysis identified an association between M pneumoniae infections and disease severity. This study provides a foundation for a better understanding of the pathogenesis of pediatric pneumonia and the relationship between microorganisms.}, } @article {pmid39705298, year = {2024}, author = {Oliveira, V and Cleary, DFR and Polónia, ARM and Huang, YM and Rocha, U and Voogd, NJ and Gomes, NCM}, title = {Unravelling a Latent Pathobiome Across Coral Reef Biotopes.}, journal = {Environmental microbiology}, volume = {26}, number = {12}, pages = {e70008}, doi = {10.1111/1462-2920.70008}, pmid = {39705298}, issn = {1462-2920}, support = {VH-NG-1248 Micro "BigData"//Helmholtz Young Investigator Grant/ ; MNPH 104403//Marine National Parks Headquarter, Taiwan/ ; MOST 105-2621-B-346-002//Ministry of Science and Technology, Taiwan/ ; DOI: 10.54499/DL57/2016/CP1482/CT0109//Foundation for Science and Technology/ ; PTDC/BIA29/MIC/6473/2014 - POCI-01-0145-FEDER-01//Foundation for Science and Technology/ ; SFRH/BPD/117563/2016//Foundation for Science and Technology/ ; UIDP/50017/2020 + UIDB/50017/2020 + LA/P/0094/2020//Foundation for Science and Technology/ ; }, mesh = {*Coral Reefs ; Animals ; *Anthozoa/microbiology ; *Bacteria/genetics/classification ; *Microbiota ; Virulence Factors/genetics ; }, abstract = {Previous studies on disease in coral reef organisms have neglected the natural distribution of potential pathogens and the genetic factors that underlie disease incidence. This study explores the intricate associations between hosts, microbial communities, putative pathogens, antibiotic resistance genes (ARGs) and virulence factors (VFs) across diverse coral reef biotopes. We observed a substantial compositional overlap of putative bacterial pathogens, VFs and ARGs across biotopes, consistent with the 'everything is everywhere, but the environment selects' hypothesis. However, flatworms and soft corals deviated from this pattern, harbouring the least diverse microbial communities and the lowest diversity of putative pathogens and ARGs. Notably, our study revealed a significant congruence between the distribution of putative pathogens, ARGs and microbial assemblages across different biotopes, suggesting an association between pathogen and ARG occurrence. This study sheds light on the existence of this latent pathobiome, the disturbance of which may contribute to disease onset in coral reef organisms.}, } @article {pmid39702650, year = {2024}, author = {Vriend, EMC and Galenkamp, H and Herrema, H and Nieuwdorp, M and van den Born, BH and Verhaar, BJH}, title = {Machine learning analysis of sex and menopausal differences in the gut microbiome in the HELIUS study.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {152}, pmid = {39702650}, issn = {2055-5008}, support = {189235//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 09150182010020/ZONMW_/ZonMw/Netherlands ; 101141346/ERC_/European Research Council/International ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Female ; *Machine Learning ; Male ; Middle Aged ; *Menopause ; Aged ; Sex Factors ; Metagenomics/methods ; Adult ; Cohort Studies ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; }, abstract = {Sex differences in the gut microbiome have been examined previously, but results are inconsistent, often due to small sample sizes. We investigated sex and menopausal differences in the gut microbiome in a large multi-ethnic population cohort study, including 5166 participants. Using machine learning models, we revealed modest associations between sex and menopausal status, and gut microbiota composition (AUC 0.61-0.63). After adjustments for age, cardiovascular risk factors, and diet, a part of the associations of the highest-ranked gut microbes with sex were attenuated, but most associations remained significant. In contrast, most associations with menopausal status were driven by age and lost significance after adjustment. Using pathway analyses on metagenomic data, we identified sex differences in vitamin B6 synthesis and stachyose degradation pathways. Since some of sex differences in gut microbiome composition and function could not be explained by covariates, we recommend sex stratification in future microbiome studies.}, } @article {pmid39702405, year = {2024}, author = {Soufi, HH and Porch, R and Korchagina, MV and Abrams, JA and Schnider, JS and Carr, BD and Williams, MA and Louca, S}, title = {Taxonomic variability and functional stability across Oregon coastal subsurface microbiomes.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1663}, pmid = {39702405}, issn = {2399-3642}, mesh = {Oregon ; *Microbiota/genetics ; *Geologic Sediments/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Phylogeny ; Metagenomics/methods ; Biodiversity ; }, abstract = {The factors shaping microbial communities in marine subsurface sediments remain poorly understood. Here, we analyzed the microbiome of subsurface sediments within a depth range of 1.6-1.9 m, at 10 locations along the Oregon coast. We used metagenomics to reconstruct the functional structure and 16S rRNA gene amplicon sequencing to estimate the taxonomic composition of microbial communities, accompanied by physicochemical measurements. Functional community structure, in terms of the proportions of various gene groups, was remarkably stable across samples, despite the latter covering a region spanning over 300 km. In contrast, taxonomic composition was highly variable, especially at the level of amplicon sequence variants (ASVs) and operational taxonomic units (OTUs). Mantel correlation tests between compositional dissimilarities and geographic distances revealed only a moderate influence of distance on composition. Regression models predicting taxonomic dissimilarities and considering up to 20 physicochemical variables as predictors, almost always failed to select a significant predictor, suggesting that variation in local conditions does not explain the high taxonomic variability. Permutation null models of community assembly revealed that taxa tend to strongly segregate, i.e., exclude each other. We conclude that biological interactions are important drivers of taxonomic variation in subsurface sediments, and that this variation can decouple from functional structure.}, } @article {pmid39702006, year = {2024}, author = {Demirkan, A and van Dongen, J and Finnicum, CT and Westra, HJ and Jankipersadsing, S and Willemsen, G and Ijzerman, RG and Boomsma, DI and Ehli, EA and Bonder, MJ and Fu, J and Franke, L and Wijmenga, C and de Geus, EJC and Kurilshikov, A and Zhernakova, A}, title = {Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1224}, pmid = {39702006}, issn = {1471-2164}, mesh = {*DNA Methylation ; *Gastrointestinal Microbiome/genetics ; Humans ; *Epigenome ; *Genome-Wide Association Study ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; CpG Islands/genetics ; Middle Aged ; Adult ; Netherlands ; }, abstract = {Microbiome influences multiple human systems, but its effects on gene methylation is unknown. We investigated the relations between gene methylation in blood and the abundance of common gut bacteria profiled by 16s rRNA gene sequencing in two population-based Dutch cohorts: LifeLines-Deep (LLD, n = 616, discovery) and the Netherlands Twin Register (NTR, n = 296, replication). In LLD, we also explored microbial pathways using data generated by shotgun metagenomic sequencing (n = 683). Methylation in both cohorts was profiled in blood samples using the Illumina 450K array. Discovery and replication analysis identified two independent CpGs associated with the genus Eggerthella: cg16586104 (Pmeta-analysis = 3.21 × 10[-11]) and cg12234533 (Pmeta-analysis = 4.29 × 10[-10]). We also show that microbiome can mediate the effect of environmental factors on host gene methylation. In this first association study linking epigenome to microbiome, we found and replicated the associations of two CpGs to the abundance of genus Eggerthella and identified microbiome as a mediator of the exposome. These associations are observational and suggest further investigation in larger and longitudinal set-ups.}, } @article {pmid39701966, year = {2024}, author = {Oskolkov, N and Sandionigi, A and Götherström, A and Canini, F and Turchetti, B and Zucconi, L and Mimmo, T and Buzzini, P and Borruso, L}, title = {Unraveling the ancient fungal DNA from the Iceman gut.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1225}, pmid = {39701966}, issn = {1471-2164}, mesh = {*DNA, Ancient/analysis ; Humans ; *DNA, Fungal/genetics ; Metagenomics/methods ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Mummies/microbiology ; Computational Biology/methods ; Fungi/genetics/classification ; }, abstract = {BACKGROUND: Fungal DNA is rarely reported in metagenomic studies of ancient samples. Although fungi are essential for their interactions with all kingdoms of life, limited information is available about ancient fungi. Here, we explore the possibility of the presence of ancient fungal species in the gut of Ötzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria).

METHODS: A robust bioinformatic pipeline has been developed to detect and authenticate fungal ancient DNA (aDNA) from muscle, stomach, small intestine, and large intestine samples.

RESULTS: We revealed the presence of ancient DNA associated with Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, which were abundant in the stomach and small intestine and absent in the large intestine and muscle samples.

CONCLUSION: We suggest that Ötzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they persisted in his gut after his death due to their adaptability to harsh and cold environments. This suggests the potential co-occurrence of ancient humans with opportunistic fungal species and proposes and validates a conservative bioinformatic approach for detecting and authenticating fungal aDNA in historical metagenomic samples.}, } @article {pmid39701829, year = {2025}, author = {McAlister, JS and Blum, MJ and Bromberg, Y and Fefferman, NH and He, Q and Lofgren, E and Miller, DL and Schreiner, C and Candan, KS and Szabo-Rogers, H and Reed, JM}, title = {An interdisciplinary perspective of the built-environment microbiome.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {1}, pages = {}, pmid = {39701829}, issn = {1574-6941}, support = {CCF 2200140//U.S. National Science Foundation/ ; }, mesh = {*Microbiota ; *Built Environment ; Humans ; Interdisciplinary Research ; }, abstract = {The built environment provides an excellent setting for interdisciplinary research on the dynamics of microbial communities. The system is simplified compared to many natural settings, and to some extent the entire environment can be manipulated, from architectural design to materials use, air flow, human traffic, and capacity to disrupt microbial communities through cleaning. Here, we provide an overview of the ecology of the microbiome in the built environment. We address niche space and refugia, population, and community (metagenomic) dynamics, spatial ecology within a building, including the major microbial transmission mechanisms, as well as evolution. We also address landscape ecology, connecting microbiomes between physically separated buildings. At each stage, we pay particular attention to the actual and potential interface between disciplines, such as ecology, epidemiology, materials science, and human social behavior. We end by identifying some opportunities for future interdisciplinary research on the microbiome of the built environment.}, } @article {pmid39701698, year = {2024}, author = {Bao, YY and Li, MX and Gao, XX and Wei, WJ and Huang, WJ and Lin, LZ and Wang, H and Zheng, NN and Li, HK}, title = {[Astragalus polysaccharides improve adipose tissue aging in naturally aged mice via indole-3-lactic acid].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {49}, number = {22}, pages = {5998-6007}, doi = {10.19540/j.cnki.cjcmm.20240508.401}, pmid = {39701698}, issn = {1001-5302}, mesh = {Animals ; Mice ; *Aging/drug effects ; *Adipose Tissue/drug effects/metabolism ; *Polysaccharides/pharmacology ; *Indoles/pharmacology ; Male ; *Astragalus Plant/chemistry ; 3T3-L1 Cells ; Humans ; Adipocytes/drug effects/metabolism/cytology ; Mice, Inbred C57BL ; Cellular Senescence/drug effects ; Drugs, Chinese Herbal/pharmacology/administration & dosage ; Gastrointestinal Microbiome/drug effects ; }, abstract = {Plant polysaccharides are effective components that widely present in traditional Chinese medicine(TCM), exhibiting rich biological activities. However, as most plant polysaccharides cannot be directly absorbed and utilized by the human digestive system, it is now believed that their mode of action mainly involves interaction with intestinal microbiota, leading to the production of functional small molecules. The efficacy of Astragalus polysaccharide(APS) is extensive, including weight loss, improvement of fatty liver, reduction of blood lipids, and enhancement of insulin sensitivity, which may also be related to the regulation of intestinal microbiota. Adipose tissue senescence is an important characteristic of the physiological aging process in the body, often occurring prior to the aging of other important organs. Its main features include the accumulation of senescent cells and exacerbation of inflammation within the tissue. Therefore, to explore the potential protective effects of APS on aging, the improvement of adipose tissue aging phenotype in naturally aging mice was observed using APS, and combined with metagenomic metabolomics, corresponding microbial metabolic functional molecules were identified. Furthermore, functional tests in cell aging models were conducted. The results showed that APS significantly improved the adipocyte aging characteristics of naturally aging mice: specifically reducing aging-induced adipocyte hypertrophy; decreasing the protein expression of aging markers cyclin-dependent kinase inhibitor p21(P21) and multiple tumor suppressor 1(P16); lowering the tissue inflammation reaction. Metagenomic metabolomic analysis of serum from mice in each group revealed that APS significantly increased the content of indole-3-lactic acid(ILA) in naturally aging mice. Further in vitro studies showed that ILA could improve the aging of 3T3-L1 mouse embryonic fibroblasts induced by bleomycin, reduce the protein expression of the aging marker P21, alleviate inflammation, and enhance the ability of preadipocytes to mature. Therefore, APS had the efficacy of protecting naturally aging mice, and its action may be related to the increase in the intestinal microbiota metabolite ILA. This study suggested that TCM may serve as an important entry point for explaining the mechanism of action of TCM by regulating intestinal microbiota and their functional metabolites.}, } @article {pmid39696556, year = {2024}, author = {Amano, Y and Sachdeva, R and Gittins, D and Anantharaman, K and Lei, S and Valentin-Alvarado, LE and Diamond, S and Beppu, H and Iwatsuki, T and Mochizuki, A and Miyakawa, K and Ishii, E and Murakami, H and Jaffe, AL and Castelle, C and Lavy, A and Suzuki, Y and Banfield, JF}, title = {Diverse microbiome functions, limited temporal variation and substantial genomic conservation within sedimentary and granite rock deep underground research laboratories.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {105}, pmid = {39696556}, issn = {2524-6372}, support = {JPJ007597//The Ministry of Economy, Trade and Industry of Japan/ ; 19K05342//the Japan Society for the Promotion of Science/ ; OCE2049478//National Science Foundation/ ; DE-AC02-05CH11231//the Watershed Function Scientific Focus Area funded by the U.S. Department of Energy/ ; 2230766//NSF "Four Networks for Geologic Hydrogen Storage"/ ; }, abstract = {BACKGROUND: Underground research laboratories (URLs) provide a window on the deep biosphere and enable investigation of potential microbial impacts on nuclear waste, CO2 and H2 stored in the subsurface. We carried out the first multi-year study of groundwater microbiomes sampled from defined intervals between 140 and 400 m below the surface of the Horonobe and Mizunami URLs, Japan.

RESULTS: We reconstructed draft genomes for > 90% of all organisms detected over a four year period. The Horonobe and Mizunami microbiomes are dissimilar, likely because the Mizunami URL is hosted in granitic rock and the Horonobe URL in sedimentary rock. Despite this, hydrogen metabolism, rubisco-based CO2 fixation, reduction of nitrogen compounds and sulfate reduction are well represented functions in microbiomes from both URLs, although methane metabolism is more prevalent at the organic- and CO2-rich Horonobe URL. High fluid flow zones and proximity to subsurface tunnels select for candidate phyla radiation bacteria in the Mizunami URL. We detected near-identical genotypes for approximately one third of all genomically defined organisms at multiple depths within the Horonobe URL. This cannot be explained by inactivity, as in situ growth was detected for some bacteria, albeit at slow rates. Given the current low hydraulic conductivity and groundwater compositional heterogeneity, ongoing inter-site strain dispersal seems unlikely. Alternatively, the Horonobe URL microbiome homogeneity may be explained by higher groundwater mobility during the last glacial period. Genotypically-defined species closely related to those detected in the URLs were identified in three other subsurface environments in the USA. Thus, dispersal rates between widely separated underground sites may be fast enough relative to mutation rates to have precluded substantial divergence in species composition. Species overlaps between subsurface locations on different continents constrain expectations regarding the scale of global subsurface biodiversity.

CONCLUSIONS: Our analyses reveal microbiome stability in the sedimentary rocks and surprising microbial community compositional and genotypic overlap over sites separated by hundreds of meters of rock, potentially explained by dispersal via slow groundwater flow or during a prior hydrological regime. Overall, microbiome and geochemical stability over the study period has important implications for underground storage applications.}, } @article {pmid39695983, year = {2024}, author = {Su, L and Guo, J and Shi, W and Tong, W and Li, X and Yang, B and Xiang, Z and Qin, C}, title = {Metagenomic analysis reveals the community composition of the microbiome in different segments of the digestive tract in donkeys and cows: implications for microbiome research.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {530}, pmid = {39695983}, issn = {1471-2180}, support = {2021YFF0702900//National Key Research and Development Program of China/ ; 2023-PT180-01//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; 2021-I2M-1-039, 2021-I2M-1-034//CAMS initiative for Innovative Medicine of China/ ; }, mesh = {Animals ; *Equidae/microbiology ; Cattle/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Tract/microbiology ; Sequence Analysis, DNA/methods ; Metagenome ; Bacteroidetes/genetics/isolation & purification/classification ; }, abstract = {INTRODUCTION: The intestinal microbiota plays a crucial role in health and disease. This study aimed to assess the composition and functional diversity of the intestinal microbiota in donkeys and cows by examining samples collected from different segments of the digestive tract using two distinct techniques: direct swab sampling and faecal sampling.

RESULTS: In this study, we investigated and compared the effects of multiple factors on the composition and function of the intestinal microbial community. Approximately 300 GB of metagenomic sequencing data from 91 samples obtained from various segments of the digestive tract were used, including swabs and faecal samples from monogastric animals (donkeys) and polygastric animals (cows). We assembled 4,004,115 contigs for cows and 2,938,653 contigs for donkeys, with a total of 9,060,744 genes. Our analysis revealed that, compared with faecal samples, swab samples presented a greater abundance of Bacteroidetes, whereas faecal samples presented a greater abundance of Firmicutes. Additionally, we observed significant variations in microbial composition among different digestive tract segments in both animals. Our study identified key bacterial species and pathways via different methods and provided evidence that multiple factors can influence the microbial composition. These findings provide new insights for the accurate characterization of the composition and function of the gut microbiota in microbiome research.

CONCLUSIONS: The results obtained by both sampling methods in the present study revealed that the composition and function of the intestinal microbiota in donkeys and cows exhibit species-specific and region-specific differences. These findings highlight the importance of using standardized sampling protocols to ensure accurate and consistent characterization of the intestinal microbiota in various animal species. The implications and underlying mechanisms of these associations provide multiple perspectives for future microbiome research.}, } @article {pmid39695885, year = {2024}, author = {Galic, I and Bez, C and Bertani, I and Venturi, V and Stankovic, N}, title = {Herbicide-treated soil as a reservoir of beneficial bacteria: microbiome analysis and PGP bioinoculants in maize.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {107}, pmid = {39695885}, issn = {2524-6372}, support = {451-03-47/2023-01/ 200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; 451-03-47/2023-01/ 200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; Research and Training Grant 1818//FEMS/ ; }, abstract = {BACKGROUND: Herbicides are integral to agricultural weed management but can adversely affect non-target organisms, soil health, and microbiome. We investigated the effects of herbicides on the total soil bacterial community composition using 16S rRNA gene amplicon community profiling. Further, we aimed to identify herbicide-tolerant bacteria with plant growth-promoting (PGP) capabilities as a mitigative strategy for these negative effects, thereby promoting sustainable agricultural practices.

RESULTS: A bacterial community analysis explored the effects of long-term S-metolachlor application on soil bacterial diversity, revealing that the herbicide's impact on microbial communities is less significant than the effects of temporal factors (summer vs. winter) or agricultural practices (continuous maize cultivation vs. maize-winter wheat rotation). Although S-metolachlor did not markedly alter the overall bacteriome structure in our environmental context, the application of enrichment techniques enabled the selection of genera such as Pseudomonas, Serratia, and Brucella, which were rare in metagenome analysis of soil samples. Strain isolation revealed a rich source of herbicide-tolerant PGP bacteria within the culturable microbiome fraction, termed the high herbicide concentration tolerant (HHCT) bacterial culture collection. Within the HHCT collection, we isolated 120 strains that demonstrated significant in vitro PGP and biocontrol potential, and soil quality improvement abilities. The most promising HHCT isolates were combined into three consortia, each exhibiting a comprehensive range of plant-beneficial traits. We evaluated the efficacy and persistence of these multi-strain consortia during 4-week in pot experiments on maize using both agronomic parameters and 16S rRNA gene community analysis assessing early-stage plant development, root colonization, and rhizosphere persistence. Notably, 7 out of 10 inoculated consortia partners successfully established themselves and persisted in the maize root microbiome without significantly altering host root biodiversity. Our results further evidenced that all three consortia positively impacted both seed germination and early-stage plant development, increasing shoot biomass by up to 47%.

CONCLUSIONS: Herbicide-treated soil bacterial community analysis revealed that integrative agricultural practices can suppress the effects of continuous S-metolachlor application on soil microbial diversity and stabilize microbiome fluctuations. The HHCT bacterial collection holds promise as a source of beneficial bacteria that promote plant fitness while maintaining herbicide tolerance.}, } @article {pmid39695297, year = {2024}, author = {Conteville, LC and Silva, JVD and Andrade, BGN and Coutinho, LL and Palhares, JCP and Regitano, LCA}, title = {Recovery of metagenome-assembled genomes from the rumen and fecal microbiomes of Bos indicus beef cattle.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1385}, pmid = {39695297}, issn = {2052-4463}, mesh = {Animals ; Cattle/microbiology ; *Feces/microbiology ; *Metagenome ; *Rumen/microbiology ; *Phylogeny ; Gastrointestinal Microbiome ; Brazil ; Male ; Archaea/genetics/classification ; Bacteria/genetics/classification ; Microbiota ; }, abstract = {Nelore is a Bos indicus beef breed that is well-adapted to tropical environments and constitutes most of the world's largest commercial cattle herd: the Brazilian bovine herd. Despite its significance, microbial genome recovery from ruminant microbiomes has largely excluded representatives from Brazilian Nelore cattle. To address this gap, this study presents a comprehensive dataset of microbial genomes recovered from the rumen and feces of 52 Brazilian Nelore bulls. A total of 1,526 non-redundant metagenome-assembled genomes (MAGs) were recovered from their gastrointestinal tract, with 497 ruminal and 486 fecal classified as high-quality. Phylogenetic analysis revealed that the bacterial MAGs fall into 12 phyla, with Firmicutes and Bacteroidota being the most predominant, while all archaeal MAGs belong to the genus Methanobrevibacter. The exploration of these microbial genomes will provide valuable insights into the metabolic potential and functional roles of individual microorganisms within host-microbiome interactions, contributing to a better understanding of the microbiome's roles in bovine performance.}, } @article {pmid39695203, year = {2024}, author = {Jeon, J and Park, Y and Lee, DH and Kim, JH and Jin, YK and Hong, JK and Lee, YM}, title = {Microbial profiling of the East Siberian Sea sediments using 16S rRNA gene and metagenome sequencing.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1350}, pmid = {39695203}, issn = {2052-4463}, mesh = {*Geologic Sediments/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Metagenome ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; Arctic Regions ; Microbiota ; Oceans and Seas ; Siberia ; }, abstract = {The Arctic Ocean is experiencing significant global warming, leading to reduced sea-ice cover, submarine permafrost thawing, and increased river discharge. The East Siberian Sea (ESS) undergoes more significant terrestrial inflow from coastal erosion and river runoff than other Arctic seas. Despite extensive research on environmental changes, microbial communities and their functions in the ESS, which are closely related to environmental conditions, remain largely unexplored. Here, we investigated microbial communities in ESS surface sediments spanning latitudes from 73°N to 77°N using 16S rRNA amplicon sequencing, and reconstructed 211 metagenome-assembled genomes (MAGs) using shotgun metagenome sequencing. Taxonomic analysis identified 209 bacterial MAGs, with the predominant phyla Pseudomonadota (n = 82), Actinobacteriota (n = 38), Desulfobacterota (n = 23), along with 2 archaeal MAGs of Thermoproteota. Notably, 86% of the MAGs (n = 183) could not be classified into known species, indicating the potential presence of novel and unidentified microorganisms in the ESS. This dataset provides invaluable information on the microbial diversity and ecological functions in the rapidly changing ESS.}, } @article {pmid39693444, year = {2024}, author = {Ruff, SE and de Angelis, IH and Mullis, M and Payet, JP and Magnabosco, C and Lloyd, KG and Sheik, CS and Steen, AD and Shipunova, A and Morozov, A and Reese, BK and Bradley, JA and Lemonnier, C and Schrenk, MO and Joye, SB and Huber, JA and Probst, AJ and Morrison, HG and Sogin, ML and Ladau, J and Colwell, F}, title = {A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide.}, journal = {Science advances}, volume = {10}, number = {51}, pages = {eadq0645}, pmid = {39693444}, issn = {2375-2548}, mesh = {*Microbiota/genetics ; *Biodiversity ; *Archaea/genetics/classification ; *Phylogeny ; *Bacteria/genetics/classification ; Metagenome ; Seawater/microbiology ; Ecosystem ; }, abstract = {Subsurface environments are among Earth's largest habitats for microbial life. Yet, until recently, we lacked adequate data to accurately differentiate between globally distributed marine and terrestrial surface and subsurface microbiomes. Here, we analyzed 478 archaeal and 964 bacterial metabarcoding datasets and 147 metagenomes from diverse and widely distributed environments. Microbial diversity is similar in marine and terrestrial microbiomes at local to global scales. However, community composition greatly differs between sea and land, corroborating a phylogenetic divide that mirrors patterns in plant and animal diversity. In contrast, community composition overlaps between surface to subsurface environments supporting a diversity continuum rather than a discrete subsurface biosphere. Differences in microbial life thus seem greater between land and sea than between surface and subsurface. Diversity of terrestrial microbiomes decreases with depth, while marine subsurface diversity and phylogenetic distance to cultured isolates rivals or exceeds that of surface environments. We identify distinct microbial community compositions but similar microbial diversity for Earth's subsurface and surface environments.}, } @article {pmid39688845, year = {2024}, author = {Oteo-García, G and Mutti, G and Caldon, M and Oosthuitzen, O and ManfrediniK, M and Capelli, C}, title = {Reconstructing micro-evolutionary dynamics shaping local variation in southern African populations using genomics, metagenomics and personal metadata.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {102}, number = {}, pages = {123-143}, doi = {10.4436/JASS.10204}, pmid = {39688845}, issn = {2037-0644}, mesh = {Humans ; Namibia ; *Metagenomics ; *Saliva/microbiology/virology ; *Microbiota/genetics ; Male ; Female ; Adult ; Lesotho ; Genomics ; Genetic Variation ; Young Adult ; Middle Aged ; Adolescent ; Black People/genetics ; }, abstract = {Geography is a well-known factor shaping genetic variation in human populations. However, the potential role played by cultural variables remains much understudied. This study investigates the impact of socio-cultural variables on genomic similarity and the saliva microbiome, using data from populations in Lesotho and Namibia. Geographic distance within Lesotho increases genetic differentiation, while shared clan affiliation surprisingly increases it. In Namibia, ethnicity is the predominant factor influencing genetic affinity. Saliva metagenomic data shows a negative correlation between age and alpha diversity, with notable differences in host-interacting taxa and viral load. These findings highlight the role of geography in shaping genetic affinity even at small scales and the complex influences of cultural factors. The saliva microbiome appears primarily affected by unrecorded individual behaviors rather than geographic or cultural variables. At population-level these oral microbiomes reveal insights into some dietary habits, oral health, and also the communal viral load, which appears to have greater incidence in Lesotho possibly related to the long-term effects of the HIV epidemic in the country.}, } @article {pmid39684893, year = {2024}, author = {Parkar, N and Young, W and Olson, T and Hurst, C and Janssen, P and Spencer, NJ and McNabb, WC and Dalziel, JE}, title = {Peripherally Restricted Activation of Opioid Receptors Influences Anxiety-Related Behaviour and Alters Brain Gene Expression in a Sex-Specific Manner.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684893}, issn = {1422-0067}, support = {C10X1706//Ministry of Business, Innovation and Employment/ ; }, mesh = {Animals ; Male ; Female ; *Anxiety/metabolism ; Rats ; *Loperamide/pharmacology ; *Brain/metabolism/drug effects ; *Rats, Sprague-Dawley ; *Receptors, Opioid/metabolism/genetics ; Behavior, Animal/drug effects ; Gastrointestinal Microbiome/drug effects ; Hippocampus/metabolism/drug effects ; Enteric Nervous System/metabolism ; Gene Expression Regulation/drug effects ; Sex Factors ; Sex Characteristics ; }, abstract = {Although effects of stress-induced anxiety on the gastrointestinal tract and enteric nervous system (ENS) are well studied, how ENS dysfunction impacts behaviour is not well understood. We investigated whether ENS modulation alters anxiety-related behaviour in rats. We used loperamide, a potent μ-opioid receptor agonist that does not cross the blood-brain barrier, to manipulate ENS function and assess changes in behaviour, gut and brain gene expression, and microbiota profile. Sprague Dawley (male/female) rats were acutely dosed with loperamide (subcutaneous) or control solution, and their behavioural phenotype was examined using open field and elevated plus maze tests. Gene expression in the proximal colon, prefrontal cortex, hippocampus, and amygdala was assessed by RNA-seq and caecal microbiota composition determined by shotgun metagenome sequencing. In female rats, loperamide treatment decreased distance moved and frequency of supported rearing, indicating decreased exploratory behaviour and increased anxiety, which was associated with altered hippocampal gene expression. Loperamide altered proximal colon gene expression and microbiome composition in both male and female rats. Our results demonstrate the importance of the ENS for communication between gut and brain for normo-anxious states in female rats and implicate corticotropin-releasing hormone and gamma-aminobutyric acid gene signalling pathways in the hippocampus. This study also sheds light on sexually dimorphic communication between the gut and the brain. Microbiome and colonic gene expression changes likely reflect localised effects of loperamide related to gut dysmotility. These results suggest possible ENS pharmacological targets to alter gut to brain signalling for modulating mood.}, } @article {pmid39684853, year = {2024}, author = {Tynior, W and Kłósek, M and Salatino, S and Cuber, P and Hudy, D and Nałęcz, D and Chan, YT and Gustave, C and Strzelczyk, JK}, title = {Metagenomic Analysis of the Buccal Microbiome by Nanopore Sequencing Reveals Structural Differences in the Microbiome of a Patient with Molar Incisor Hypomineralization (MIH) Compared to a Healthy Child-Case Study.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684853}, issn = {1422-0067}, support = {PCN-1-111/N/2/O//Medical University of Silesia/ ; }, mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; *Nanopore Sequencing/methods ; *Dental Enamel Hypoplasia/microbiology/genetics ; Child ; Mouth Mucosa/microbiology/pathology ; Male ; Female ; Bacteria/genetics/classification/isolation & purification ; Case-Control Studies ; Metagenome ; Incisor/microbiology ; Molar Hypomineralization ; }, abstract = {Molar incisor hypomineralization (MIH) is a qualitative developmental defect that affects the enamel tissue of permanent molars and can also occur in permanent incisors. Enamel affected by MIH has reduced hardness, increased porosity, and a higher organic content than unaffected enamel. These characteristics predispose the enamel to accumulation of bacteria and a higher prevalence of caries lesions. Through a groundbreaking metagenomic analysis of the buccal mucosal sample from a patient with MIH, we explored the intricacies of its microbiome compared to a healthy control using state-of-the-art nanopore long-read sequencing. Out of the 210 bacterial taxa identified in the MIH microbiome, we found Streptococcus and Haemophilus to be the most abundant genera. The bacteria with the highest read counts in the patient with MIH included Streptococcus mitis, Haemophilus parainfluenzae, Streptococcus pneumoniae, Rothia dentocariosa, and Gemella haemolysans. Our results revealed a striking contrast between healthy and MIH affected children, with a higher dominance and number of pathogenic species (S. pneumoniae, H. influenzae, and N. meningitidis) and reduced diversity in the MIH-affected patient. This distinct microbial profile not only sheds light on MIH-affected patients, but paves the way for future research, inspiring deeper understanding and larger scale studies.}, } @article {pmid39684458, year = {2024}, author = {Salini, A and Zuliani, L and Gonnelli, PM and Orlando, M and Odoardo, A and Ragno, D and Aulitto, M and Zaccone, C and Fusco, S}, title = {Plastic-Degrading Microbial Consortia from a Wastewater Treatment Plant.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684458}, issn = {1422-0067}, support = {CUP B53D23015130001//MUR - Italian Ministry of University and Research in the framework of the Next Generation EU action/ ; }, mesh = {*Microbial Consortia ; *Wastewater/microbiology ; *Biodegradation, Environmental ; Sewage/microbiology ; Plastics/metabolism ; Bacteria/metabolism/classification/genetics/isolation & purification ; Microbiota ; }, abstract = {Plastic waste pollution has become a global crisis, with millions of tons of plastic expected to accumulate in landfills and in natural environments, posing a serious threat to wildlife and human health. As current recycling methods remain inefficient, there is an urgent need for innovative enzymatic solutions to break down plastics and enable a circular economy approach. In this study, we explore the plastic-degrading potential of microorganisms enriched from activated sludge (AS) sourced from a municipal wastewater treatment plant (WWTP)-a known microplastic-contaminated industrial niche. Five microbial consortia (i.e., microbiomes) were enriched under selective pressure using low-carbon conditions and high concentrations of polyester polymers, including post-consumer PET, post-consumer PLA, and virgin PLA. Enrichment was performed for 100 days at 37 °C and 50 °C, followed by microbiomes isolation and metagenomic analysis to identify plastic-active bacteria and their enzymes. The results revealed that PLA polymers, but not post-consumer PET, were effectively degraded by the microbiomes, as confirmed by nuclear magnetic resonance (NMR) and gel permeation chromatography (GPC), showing significant molecular weight reduction compared to the abiotic controls. Microbial community analysis highlighted a distinct enrichment profile driven by the polymer composition and the temperature. At 50 °C, the Bacillales order became the predominant population, whereas at 37 °C, a more diverse community within the Proteobacteria and Actinobacteria phyla were selected. Nonetheless, the enriched microbial communities at both temperatures included phyla with members known for polyester degradation. Moreover, at 50 °C, enrichment of putative PET/PLA hydrolases was also observed. These findings suggest that AS microorganisms are a reservoir of polyester-active enzymes, particularly PLA-depolymerases, and hold promise for advancing biotechnological strategies to mitigate plastic pollution through re- and up-cycling.}, } @article {pmid39684246, year = {2024}, author = {Domínguez-Pino, M and Mellado, S and Cuesta, CM and Grillo-Risco, R and García-García, F and Pascual, M}, title = {Metagenomics Reveals Sex-Based Differences in Murine Fecal Microbiota Profiles Induced by Chronic Alcohol Consumption.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684246}, issn = {1422-0067}, support = {2023-I024//the Spanish Ministry of Health-PNSD/ ; CIAICO/2021/203//GVA/ ; RD21/0009/0005//the Primary Addiction Care Research Network/ ; pro-ject IMPaCT-Data, exp. IMP/00019//FGG and RGR were supported by and partially funded by the Institute of Health Carlos III/ ; PID2023-146865OB-I00 and PID2021-124430OA-I00//MCIN/AEI/10.13039/501100011033/ FEDER/ ; }, mesh = {Animals ; Female ; Male ; *Feces/microbiology ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Toll-Like Receptor 4/genetics/metabolism ; *Metagenomics/methods ; *Mice, Knockout ; *RNA, Ribosomal, 16S/genetics ; *Ethanol/adverse effects ; Alcohol Drinking/adverse effects ; Mice, Inbred C57BL ; Sex Factors ; Dysbiosis/microbiology/chemically induced ; Sex Characteristics ; }, abstract = {Chronic ethanol exposure induces an inflammatory response within the intestinal tract, compromising mucosal and epithelial integrity and leading to dysbiosis of the gut microbiome. However, the specific roles of the gut microbiota in mediating ethanol-induced effects, as well as their interactions with the immune system, remain poorly characterized. This study aimed to evaluate sex-based differences in fecal microbiota profiles induced by chronic alcohol consumption and to assess whether TLR4 is involved in these effects. We analyzed the 16S rRNA gene sequencing of fecal samples from male and female wild-type (WT) and TLR4-knockout (TLR4-KO) mice with and without chronic ethanol exposure over a three-month period. Our findings provide evidence, for the first time, that male mice are more susceptible to the effects of ethanol on the fecal microbiota, since ethanol exposure induced greater alterations in the Gram-negative and -positive bacteria with immunogenic capacity in the WT male mice than in the female mice. We also demonstrate that the absence of immune receptor TLR4 leads to different microbiota in both sexes, showing anti-inflammatory and protective properties for intestinal barrier function and resulting in a phenotype more resistant to ethanol's effects. These findings may open new avenues for understanding the relationship between gut microbiota profiles and inflammation in the digestive system induced by chronic alcohol consumption.}, } @article {pmid39683635, year = {2024}, author = {Ouédraogo, LO and Deng, L and Ouattara, CA and Compaoré, A and Ouédraogo, M and Argaw, A and Lachat, C and Houpt, ER and Saidi, Q and Haerynck, F and Sonnenburg, J and Azad, MB and Tavernier, SJ and Bastos-Moreira, Y and Toe, LC and Dailey-Chwalibóg, T}, title = {Describing Biological Vulnerability in Small, Vulnerable Newborns in Urban Burkina Faso (DenBalo): Gut Microbiota, Immune System, and Breastmilk Assembly.}, journal = {Nutrients}, volume = {16}, number = {23}, pages = {}, pmid = {39683635}, issn = {2072-6643}, support = {INV-035474 & INV-036154/GATES/Bill & Melinda Gates Foundation/United States ; }, mesh = {Humans ; Burkina Faso ; Female ; Infant, Newborn ; *Gastrointestinal Microbiome ; *Milk, Human/immunology ; Prospective Studies ; *Vagina/microbiology/immunology ; *Immune System ; Pregnancy ; Breast Feeding ; Infant, Small for Gestational Age ; Adult ; }, abstract = {Background: Small vulnerable newborns (SVNs), including those born preterm, small for gestational age, or with low birth weight, are at higher risk of neonatal mortality and long-term health complications. Early exposure to maternal vaginal microbiota and breastfeeding plays a critical role in the development of the neonatal microbiota and immune system, especially in low-resource settings like Burkina Faso, where neonatal mortality rates remain high. Objectives: The DenBalo study aims to investigate the role of maternal and neonatal factors, such as vaginal and gut microbiota, immune development, and early nutrition, in shaping health outcomes in SVNs and healthy infants. Methods: This prospective cohort observational study will recruit 141 mother-infant pairs (70 SVNs and 71 healthy controls) from four health centers in Bobo-Dioulasso, Burkina Faso. The mother-infant pairs will be followed for six months with anthropometric measurements and biospecimen collections, including blood, breast milk, saliva, stool, vaginal swabs, and placental biopsies. Multi-omics approaches, encompassing metagenomics, metabolomics, proteomics, and immune profiling, will be used to assess vaginal and gut microbiota composition and functionality, immune cell maturation, and cytokine levels at critical developmental stages. Conclusions: This study will generate comprehensive data on how microbiota, metabolomic, and proteomic profiles, along with immune system development, differ between SVNs and healthy infants. These findings will guide targeted interventions to improve neonatal health outcomes and reduce mortality, particularly in vulnerable populations.}, } @article {pmid39682735, year = {2024}, author = {Hemmati, MA and Monemi, M and Asli, S and Mohammadi, S and Foroozanmehr, B and Haghmorad, D and Oksenych, V and Eslami, M}, title = {Using New Technologies to Analyze Gut Microbiota and Predict Cancer Risk.}, journal = {Cells}, volume = {13}, number = {23}, pages = {}, pmid = {39682735}, issn = {2073-4409}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Neoplasms/microbiology ; Machine Learning ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; }, abstract = {The gut microbiota significantly impacts human health, influencing metabolism, immunological responses, and disease prevention. Dysbiosis, or microbial imbalance, is linked to various diseases, including cancer. It is crucial to preserve a healthy microbiome since pathogenic bacteria, such as Escherichia coli and Fusobacterium nucleatum, can cause inflammation and cancer. These pathways can lead to the formation of tumors. Recent advancements in high-throughput sequencing, metagenomics, and machine learning have revolutionized our understanding of the role of gut microbiota in cancer risk prediction. Early detection is made easier by machine learning algorithms that improve the categorization of cancer kinds based on microbiological data. Additionally, the investigation of the microbiome has been transformed by next-generation sequencing (NGS), which has made it possible to fully profile both cultivable and non-cultivable bacteria and to understand their roles in connection with cancer. Among the uses of NGS are the detection of microbial fingerprints connected to treatment results and the investigation of metabolic pathways implicated in the development of cancer. The combination of NGS with machine learning opens up new possibilities for creating customized medicine by enabling the development of diagnostic tools and treatments that are specific to each patient's microbiome profile, even in the face of obstacles like data complexity. Multi-omics studies reveal microbial interactions, biomarkers for cancer detection, and gut microbiota's impact on cancer progression, underscoring the need for further research on microbiome-based cancer prevention and therapy.}, } @article {pmid39681310, year = {2024}, author = {Tobar, Z and Lee, KY and Gaa, ME and Moore, BP and Li, X and Pitesky, ME}, title = {Evaluation of 16s Long Read Metabarcoding for Characterizing the Microbiome and Salmonella Contamination of Retail Poultry Meat.}, journal = {Journal of food protection}, volume = {88}, number = {2}, pages = {100434}, doi = {10.1016/j.jfp.2024.100434}, pmid = {39681310}, issn = {1944-9097}, abstract = {The traditional gold standard for detection of Salmonella in meat products is bacterial culture with enrichment. While this method is highly sensitive, it is slow and provides an incomplete assessment of isolate taxonomy in positive samples. This study presents a novel PCR-based detection assay which amplifies the 16s-ITS-23s region which is an approximately 2,500 base pair region of the larger ribosomal rrn operon. Intra-assay variation was assessed by splitting each biological sample into 3 technical replicates. Limits of detection (LOD) were assessed by utilizing a serial dilution of a pure culture of Salmonella enterica subsp. enterica serovar Heidelberg spiked into either sterile 1 × PBS or 1 × PBS rinsate of a Salmonella culture-negative chicken meat sample. Results indicate the 16s metabarcoding assay evaluated here could not be reliably used for the detection of Salmonella in adulterated retail meat samples as the LOD observed, 4.70 log colony forming units (CFU)/ml, is above the expected concentration of Salmonella in retail poultry meat samples which previous studies have shown range from under 1 to 2 log CFU/ml. However, due to greater taxonomic resolution afforded by using 16s long reads, the assay allowed alpha diversity assessment of the microbiome of raw poultry meat with the ability to assign taxonomy to the species and strain level for some amplicon sequence variants (ASV). This indicates this process may have value characterizing biodiversity and pathogen contamination of poultry samples in earlier steps of the poultry meat production process where bacterial contamination concentrations are likely to be higher.}, } @article {pmid39679737, year = {2024}, author = {Zhao, H and Wang, T}, title = {Debiased high-dimensional regression calibration for errors-in-variables log-contrast models.}, journal = {Biometrics}, volume = {80}, number = {4}, pages = {}, doi = {10.1093/biomtc/ujae153}, pmid = {39679737}, issn = {1541-0420}, mesh = {Humans ; Calibration ; *Models, Statistical ; Gastrointestinal Microbiome ; Computer Simulation ; Regression Analysis ; Bias ; Linear Models ; Biometry/methods ; Data Interpretation, Statistical ; Metagenomics/methods/statistics & numerical data ; }, abstract = {Motivated by the challenges in analyzing gut microbiome and metagenomic data, this work aims to tackle the issue of measurement errors in high-dimensional regression models that involve compositional covariates. This paper marks a pioneering effort in conducting statistical inference on high-dimensional compositional data affected by mismeasured or contaminated data. We introduce a calibration approach tailored for the linear log-contrast model. Under relatively lenient conditions regarding the sparsity level of the parameter, we have established the asymptotic normality of the estimator for inference. Numerical experiments and an application in microbiome study have demonstrated the efficacy of our high-dimensional calibration strategy in minimizing bias and achieving the expected coverage rates for confidence intervals. Moreover, the potential application of our proposed methodology extends well beyond compositional data, suggesting its adaptability for a wide range of research contexts.}, } @article {pmid39679619, year = {2024}, author = {Steinbach, E and Belda, E and Alili, R and Adriouch, S and Dauriat, CJG and Donatelli, G and Dumont, JL and Pacini, F and Tuszynski, T and Pelloux, V and Jacques, F and Creusot, L and Coles, E and Taillandier, P and Vazquez Gomez, M and Masi, D and Mateo, V and André, S and Kordahi, M and Rouault, C and Zucker, JD and Sokol, H and Genser, L and Chassaing, B and Le Roy, T and Clément, K}, title = {Comparative analysis of the duodenojejunal microbiome with the oral and fecal microbiomes reveals its stronger association with obesity and nutrition.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2405547}, pmid = {39679619}, issn = {1949-0984}, mesh = {Humans ; *Obesity/microbiology ; *Feces/microbiology ; Female ; Male ; Middle Aged ; *Gastrointestinal Microbiome ; Adult ; *Duodenum/microbiology ; *Bacteria/classification/isolation & purification/genetics/metabolism ; Jejunum/microbiology ; Mouth/microbiology ; Nutritional Status ; }, abstract = {The intestinal microbiota is increasingly recognized as a crucial player in the development and maintenance of various chronic conditions, including obesity and associated metabolic diseases. While most research focuses on the fecal microbiota due to its easier accessibility, the small intestine, as a major site for nutrient sensing and absorption, warrants further investigation to determine its microbiota composition and functions. Here, we conducted a clinical research project in 30 age- and sex-matched participants with (n = 15) and without (n = 15) obesity. Duodenojejunal fluid was obtained by aspiration during endoscopy. Phenotyping included clinical variables related to metabolic status, lifestyle, and psychosocial factors using validated questionnaires. We performed metagenomic analyses of the oral, duodenojejunal, and fecal microbiome, alongside metabolomic data from duodenojejunal fluid and feces, integrating these data with clinical and lifestyle information. Our results highlight significant associations between duodenojejunal microbiota composition and usual dietary intake, as well as clinical phenotypes, with larger effect sizes than the associations between these variables and fecal microbiota. Notably, we found that the duodenojejunal microbiota of patients with obesity exhibited higher diversity and showed distinct differences in the abundance of several duodenojejunal microbiota species compared with individuals without obesity. Our findings support the relevance of studying the role of the small intestinal microbiota in the pathogenesis of nutrition-related diseases.}, } @article {pmid39679617, year = {2024}, author = {McAdams, ZL and Gustafson, KL and Russell, AL and Self, R and Petry, AL and Lever, TE and Ericsson, AC}, title = {Supplier-origin gut microbiomes affect host body weight and select autism-related behaviors.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2385524}, pmid = {39679617}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; Animals ; Mice ; Male ; *Autism Spectrum Disorder/microbiology ; *Body Weight ; Female ; *Behavior, Animal ; Disease Models, Animal ; Humans ; Brain-Gut Axis/physiology ; Bacteria/classification/isolation & purification/genetics ; Autistic Disorder/microbiology/psychology ; }, abstract = {Autism spectrum disorders (ASD) are complex human neurodiversities increasing in prevalence within the human population. In search of therapeutics to improve quality-of-life for ASD patients, the gut microbiome (GM) has become a promising target as a growing body of work supports roles for the complex community of microorganisms in influencing host behavior via the gut-brain-axis. However, whether naturally-occurring microbial diversity within the host GM affects these behaviors is often overlooked. Here, we applied a model of population-level differences in the GM to a classic ASD model - the BTBR T[+] Itpr3[tf]/J mouse - to assess how complex GMs affect host behavior. Leveraging the naturally occurring differences between supplier-origin GMs, our data demonstrate that differing, complex GMs selectively effect host ASD-related behavior - especially neonatal ultrasonic communication - and reveal a male-specific effect on behavior not typically observed in this strain. We then identified that the body weight of BTBR mice is influenced by the postnatal GM which was potentially mediated by microbiome-dependent effects on energy harvest in the gut. These data provide insight into how variability within the GM affects host behavior and growth, thereby emphasizing the need to incorporate microbial diversity within the host GM as an experimental factor in biomedical research.}, } @article {pmid39679616, year = {2024}, author = {Seki, D and Kirkegaard, R and Osvatic, J and Hausmann, B and Séneca, J and Pjevac, P and Berger, A and J Hall, L and Wisgrill, L and Berry, D}, title = {Gut microbiota genome features associated with brain injury in extremely premature infants.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2410479}, pmid = {39679616}, issn = {1949-0984}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Infant, Extremely Premature ; *Brain Injuries/microbiology/genetics ; *Feces/microbiology ; Female ; Male ; Bacteria/genetics/classification/isolation & purification/metabolism ; Genome, Bacterial ; Cohort Studies ; }, abstract = {Severe brain damage is common among premature infants, and the gut microbiota has been implicated in its pathology. Although the order of colonizing bacteria is well described, the mechanisms underlying aberrant assembly of the gut microbiota remain elusive. Here, we employed long-read nanopore sequencing to assess abundances of microbial species and their functional genomic potential in stool samples from a cohort of 30 extremely premature infants. We identify several key microbial traits significantly associated with severe brain damage, such as the genomic potential for nitrate respiration and iron scavenging. Members of the Enterobacteriaceae were prevalent across the cohort and displayed a versatile metabolic potential, including pathogenic and nonpathogenic traits. Predominance of Enterobacter hormaechei and Klebsiella pneumoniae were associated with an overall loss of genomic functional redundancy as well as poor neurophysiological outcome. These findings reveal microbial traits that may be involved in exacerbating brain injury in extremely premature infants and provide suitable targets for therapeutic interventions.}, } @article {pmid39678952, year = {2024}, author = {Sinha, T and Talukdar, NC}, title = {Phylum Level Diversity of Plant Interior Bacteria in Seeds, Supernatant and Pellet Phases of Seed Suspension of Mustard Plant.}, journal = {Indian journal of microbiology}, volume = {64}, number = {4}, pages = {1587-1597}, pmid = {39678952}, issn = {0046-8991}, abstract = {Our previous study explored the bacterial endophytic diversity in a certain quantity of mustard seeds using culture dependent method by development of new isolation strategies. No bacterial colony was initially observed in supernatant obtained after centrifugation of mustard seed suspension. This was later overcome by usage of surfactant whereas pellet part showed presence of bacterial colonies on media. In our present study, presence of bacteria was examined in supernatant and whether the diversity was similar to that of pellet and seeds by culture independent approach. In addition, growth of bacterial colonies on media is explained using GC-MS. In this study, Proteobacteria was the dominant bacterial phyla followed by Firmicutes in pellet, supernatant and seed. This indicated that bacteria were present in supernatant but may not be viable when plated on media. This is either due to antimicrobial compounds or oil-imposed difficulty during their isolation which might have hindered their survival. GC-MS study revealed the presence of compounds with antimicrobial property as suggested by previous literature. Our research conducts fundamental investigations to address the primary objective of understanding the bacterial diversity in mustard seed, pellet, and supernatant. Further research using workflows of metagenomics and metabolomics approaches can enrich our understanding ofthe diversity of microorganisms in seeds.}, } @article {pmid39676101, year = {2024}, author = {Wang, C and Zhang, C and He, S and Wang, Q and Gao, H}, title = {The microbiome alterations of supragingival plaque among adolescents using clear aligners: a metagenomic sequencing analysis.}, journal = {Progress in orthodontics}, volume = {25}, number = {1}, pages = {48}, pmid = {39676101}, issn = {2196-1042}, support = {PY2023038//Science research cultivation program of stomatological hospital, Southern medical university/ ; PY2023043//Science research cultivation program of stomatological hospital, Southern medical university/ ; B2023274//Guangdong Medical Research Fund/ ; B2022013//Guangdong Medical Research Fund/ ; }, mesh = {Humans ; Adolescent ; *Dental Plaque/microbiology ; Male ; *Microbiota ; Female ; *Biofilms ; Child ; *Capnocytophaga ; Neisseria ; Metagenomics/methods ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: White spot lesions (WSLs) may develop in adolescents undergoing clear aligner (CA) therapy with poor oral hygiene. The specific effects of CAs on the microbial composition and functional characteristics of supragingival plaques remain unclear. The present study investigated the shift in the supragingival microbial community induced by CAs in adolescents through metagenomic technology.

METHODS: Fifteen adolescents (12-15 years old) with Invisalign appliances were recruited. Supragingival plaque specimens were obtained twice, before treatment (T1) and three months after treatment (T2). All the bacterial plaque specimens were analyzed for microbial communities and functions using metagenomic analyses.

RESULTS: A total of 2,840,242,722 reads disclosed 180 phyla, 3,975 genera, and 16,497 microbiome species. During the first three months, the microbial community was relatively stable. The genus level revealed a higher relative abundance of Capnocytophaga, Neisseria, and Arachnia in the T2 period. Furthermore, the functional analysis suggested that the relative abundances of folate biosynthesis, biotin metabolism and biofilm formation-vibrio cholerae were increased in the T2 period compared to the T1 period. Finally, virulence factor analysis demonstrated that the relative abundance of genes associated with type IV pili (VF0082) and polar flagella (VF0473) was higher in the T2 period than in the T1 period.

CONCLUSION: In adolescents undergoing CA therapy with poor plaque control, caries progresses quickly within three months and noticeable WSLs develop on the tooth surface. Although the microbial community remained relatively steady and CA therapy did not cause significant changes in the overall functional gene composition in the first three months, virulence factors, including type IV pili and flagella, were more abundant and actively contributed to microorganism adhesion and biofilm formation.}, } @article {pmid39674265, year = {2024}, author = {Ravishankar, S and Perez, V and Davidson, R and Roca-Rada, X and Lan, D and Souilmi, Y and Llamas, B}, title = {Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39674265}, issn = {1477-4054}, support = {CE170100015//Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage/ ; GA204260//NHMRC SYNERGY/ ; //Australian Government Research Training Program Scholarship/ ; //Portuguese National Funds/ ; }, mesh = {*DNA, Ancient/analysis ; *Metagenomics/methods ; *Sequence Analysis, DNA/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Workflow ; DNA Contamination ; }, abstract = {Contamination with exogenous DNA presents a significant challenge in ancient DNA (aDNA) studies of single organisms. Failure to address contamination from microbes, reagents, and present-day sources can impact the interpretation of results. Although field and laboratory protocols exist to limit contamination, there is still a need to accurately distinguish between endogenous and exogenous data computationally. Here, we propose a workflow to reduce exogenous contamination based on a metagenomic classifier. Unlike previous methods that relied exclusively on DNA sequencing reads mapping specificity to a single reference genome to remove contaminating reads, our approach uses Kraken2-based filtering before mapping to the reference genome. Using both simulated and empirical shotgun aDNA data, we show that this workflow presents a simple and efficient method that can be used in a wide range of computational environments-including personal machines. We propose strategies to build specific databases used to profile sequencing data that take into consideration available computational resources and prior knowledge about the target taxa and likely contaminants. Our workflow significantly reduces the overall computational resources required during the mapping process and reduces the total runtime by up to ~94%. The most significant impacts are observed in low endogenous samples. Importantly, contaminants that would map to the reference are filtered out using our strategy, reducing false positive alignments. We also show that our method results in a negligible loss of endogenous data with no measurable impact on downstream population genetics analyses.}, } @article {pmid39673707, year = {2024}, author = {Huang, KD and Müller, M and Sivapornnukul, P and Bielecka, AA and Amend, L and Tawk, C and Lesker, TR and Hahn, A and Strowig, T}, title = {Dietary selective effects manifest in the human gut microbiota from species composition to strain genetic makeup.}, journal = {Cell reports}, volume = {43}, number = {12}, pages = {115067}, doi = {10.1016/j.celrep.2024.115067}, pmid = {39673707}, issn = {2211-1247}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diet ; Adult ; Male ; Bacteria/genetics/classification ; Female ; Genetic Variation ; Middle Aged ; }, abstract = {Diet significantly influences the human gut microbiota, a key player in health. We analyzed shotgun metagenomic sequencing data from healthy individuals with long-term dietary patterns-vegan, flexitarian, or omnivore-and included detailed dietary surveys and blood biomarkers. Dietary patterns notably affected the bacterial community composition by altering the relative abundances of certain species but had a minimal impact on microbial functional repertoires. However, diet influenced microbial functionality at the strain level, with diet type linked to strain genetic variations. We also found molecular signatures of selective pressure in species enriched by specific diets. Notably, species enriched in omnivores exhibited stronger positive selection, such as multiple iron-regulating genes in the meat-favoring bacterium Odoribacter splanchnicus, an effect that was also validated in independent cohorts. Our findings offer insights into how diet shapes species and genetic diversity in the human gut microbiota.}, } @article {pmid39671861, year = {2025}, author = {Buzzanca, D and Giordano, M and Chiarini, E and Ferrocino, I and Cocolin, L and Zeppa, G and Alessandria, V}, title = {Delving into Roccaverano PDO cheese: A comprehensive examination of microbial diversity and flavour profiles compared to non-PDO cheeses.}, journal = {International journal of food microbiology}, volume = {429}, number = {}, pages = {111014}, doi = {10.1016/j.ijfoodmicro.2024.111014}, pmid = {39671861}, issn = {1879-3460}, mesh = {*Cheese/microbiology ; *Volatile Organic Compounds/analysis ; *Taste ; Italy ; *Microbiota ; Humans ; Food Microbiology ; Flavoring Agents/analysis ; Bacteria/classification/isolation & purification/genetics ; Fungi/isolation & purification/classification/genetics ; Odorants/analysis ; Gas Chromatography-Mass Spectrometry ; }, abstract = {Roccaverano Protected Designation of Origin (PDO) is a fresh soft cheese produced in Roccaverano area (Italy). This study aimed to evaluate Roccaverano PDO microbiota, together with aromatic profile and sensory analysis to be compared with 15 non-PDO cheeses of the same type. Microbiota was evaluated through shotgun metagenomics sequencing, while GC-MS analysis was conducted to study volatile organic compounds (VOCs) presence and concentration. Sensory analyses were conducted through ONAF (Italian National Organization of Cheese Tasters) evaluation parameters followed by flash profile sensory analysis of selected cheeses. The results demonstrated Lactococcus lactis predominance in both non-PDO and PDO cheeses, while Streptococcus thermophilus was more abundant in non-PDO group. A higher abundance of Kluyveromyces lactis was observed in Roccaverano PDO, which exhibited greater fungal diversity compared to non-PDO cheeses. Metagenome-Assembled Genomes of 26 L. lactis and 19 Leuconostoc mesenteroides showed absence of significant differences in terms of average nucleotide identity and pangenomes partitions. The ONAF sensory evaluation demonstrated a higher average score of Roccaverano PDO group. Flash profile analysis demonstrated that lactic aroma/odour, acid, astringent, vegetal odour, exotic fruit and fermented aroma, hazelnut flavour and sweet were associated with high ONAF scores. The concentration of butanoic acid, 2-methyl-, ethyl ester and butanoic acid, 3-methyl- (sweat, acid, rancid related) were higher in PDO cheeses, while reads related to butanoate metabolism were less abundant compared to non-PDO samples. Several fungal species (included K. lactis) were associated with astringents, acid and chalky flavours. Roccaverano PDO demonstrates unique characteristics even maintaining a certain degree of variability between samples.}, } @article {pmid39669269, year = {2024}, author = {Lee, KH and Kim, YO and Dho, SH and Yong, JJH and Oh, HS and Lee, JH and Yang, SJ and Cha, I and Chun, J and Lee, EH and Jeong, SJ and Woo, W and Choi, JP and Han, SH and Choi, GB and Huh, JR and Kim, LK and Song, YG}, title = {Altered gut microbiome in convalescent patients with coronavirus disease 2019.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1455295}, pmid = {39669269}, issn = {2235-2988}, mesh = {Humans ; *COVID-19/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; *Feces/microbiology/virology ; Middle Aged ; Prospective Studies ; *SARS-CoV-2/isolation & purification ; Longitudinal Studies ; *RNA, Ribosomal, 16S/genetics ; Adult ; Severity of Illness Index ; Convalescence ; Bacteria/classification/isolation & purification/genetics ; Aged ; }, abstract = {INTRODUCTION: Coronavirus disease 2019 (COVID-19) alters the gut microbiome. This study aimed to assess the association between the disease severity of COVID-19 and changes in stool microbes through a seven-month follow-up of stool collection.

METHODS: We conducted a multicentre, prospective longitudinal study of 58 COVID-19 patients and 116 uninfected controls. Differences in the gut microbiota were analysed using 16S ribosomal RNA sequencing. The first stool samples were collected at an early convalescent phase of COVID-19, and the second sample was collected at least seven months after COVID-19 infection.

RESULTS AND DISCUSSION: At the order level, Eubacteriales and Bifidobacteriales decreased, while Bacteroidales and Burkholderiales increased in the COVID-19 group compared to the controls. Alpha diversity also decreased in COVID-19 patients compared to controls, with imperfect recovery of the gut microbiome after seven months. The compositional change in the gut microbiome between the early and late convalescent phases was largest in the moderate and severe groups. The severity of COVID-19 was the most influential clinical variable for microbiome composition (Sum of Sqs = 0.686, P = 0.006), and its effect persisted even after partialling out other effects such as antibiotic use and age. Thus, our study indicates a possible interaction between respiratory viral infection and the composition of the gut microbiota community, warranting future mechanistic and prospective longitudinal studies. Additionally, we were able to detect microbiome changes in patients who were re-infected with SARS-CoV-2. Notably, the dominant bacteria in the re-infected group were Lachnospiraceae and Faecalimonas umbilicata, compared to the one-time infected group.}, } @article {pmid39660920, year = {2025}, author = {Zavarzina, DG and Maslov, AA and Merkel, AY and Kharitonova, NA and Klyukina, AA and Baranovskaya, EI and Baydariko, EA and Potapov, EG and Zayulina, KS and Bychkov, AY and Chernyh, NA and Bonch-Osmolovskaya, EA and Gavrilov, SN}, title = {Analogs of Precambrian microbial communities formed de novo in Caucasian mineral water aquifers.}, journal = {mBio}, volume = {16}, number = {1}, pages = {e0283124}, pmid = {39660920}, issn = {2150-7511}, mesh = {*Groundwater/microbiology/chemistry ; *Mineral Waters/microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Microbiota ; Archaea/genetics/classification/metabolism ; Phylogeny ; Metagenomics ; }, abstract = {The microbiome of deep continental aquifers is considered the most slowly evolving part of the biosphere. The Yessentukskoye Mineral Water Basin (YMWB), located in the pre-Caucasus region, contains three closely spaced but distinct aquifers, the Upper Cretaceous, the Lower Cretaceous, and the Upper Jurassic, which represent unique objects for subsurface biosphere research due to gas-hydrogeochemical and thermal anomalies of the area. We analyzed the geological and hydrogeochemical parameters of the three aquifers and a recharge area of the YMWB and investigated their microbial communities using metagenomic and cultivation-based approaches within a long-term survey. Correlation analysis of the obtained data revealed stable and highly stratified microbial communities inhabiting four distinct ecosystems. Their structure and the metabolic traits of their prokaryotic populations were similar to those presumed to have dominated the Earth's biosphere during several critical periods of its evolutionary history, that is, the Early Archean, the period of banded iron formations accumulation, and the Great Oxidation Event. Among the YMWB strata, the Upper Jurassic aquifer, supersaturated with CO2, influenced by magmatic activity, and highly enriched with thermophilic autotrophic hydrogenotrophic acetogens, turned out to be the first described modern ecosystem based on the primary production by a process predicted to support the Last Universal Common Ancestor (LUCA). The characterization of the YMWB microbial communities reveals a contemporary model environment of the early stages of Earth's development and thus contributes to the understanding of the evolutionary traits in microbial populations that may have played a critical role in the formation of the modern biosphere.IMPORTANCEContinental subsurface environments are estimated to harbor up to one-fifth of the planet's total biomass, representing the most stable and slowly evolving part of the biosphere. Among the deep subsurface inhabitants, the microbial communities of drinking mineral waters remain the least studied. Our interdisciplinary study of the Yessentukskoye Mineral Water Basin shows how hydrochemical and hydrodynamic factors shape different subsurface ecosystems, whose microbial populations influence the composition of mineral waters. A comprehensive analysis reveals the similarity of these ecosystems to those predicted for the early Earth. The deepest of the studied aquifers is the first described modern ecosystem with the most probable primary producer performing hydrogenotrophic acetogenesis. Thus, our results contribute to the understanding of the genesis of modern drinking water resources and expand the knowledge of the evolutionary traits that may have played a critical role in the formation of the Earth's biosphere.}, } @article {pmid39660898, year = {2025}, author = {Su, G and Huang, P and Liu, D and Xing, G and Guo, R and Li, S and Fan, S and Cheng, L and Yan, Q and Yang, W}, title = {Gut mycobiome alterations and network interactions with the bacteriome in patients with atherosclerotic cardiovascular disease.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0218224}, pmid = {39660898}, issn = {2165-0497}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Mycobiome ; Male ; Female ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; *Fungi/classification/genetics/isolation & purification ; Aged ; *Atherosclerosis/microbiology ; Cardiovascular Diseases/microbiology ; Metagenomics ; Feces/microbiology ; }, abstract = {The connection between the gut mycobiome and atherosclerotic cardiovascular disease (ACVD) is largely uncharted. In our study, we compared the gut fungal communities of 214 ACVD patients with those of 171 healthy controls using shotgun metagenomic sequencing and examined their interactions with gut bacterial communities and network key taxa. The gut mycobiome composition in ACVD patients is significantly different, showing a rise in opportunistic pathogens like Candida albicans, Exophiala spinifera, and Malassezia restricta, with Exophiala and Malassezia showing the most significant changes (Wilcoxon rank-sum test, P < 0.001, fold change >10). Network analysis revealed a less interconnected and more uneven gut microbial network in ACVD patients. Network key taxa identified in the ACVD gut microbiome network include Malassezia globosa c182, Nakaseomyces glabratus c88, Malassezia arunalokei c192, and Penicillium sumatraense c22. Predictive models that integrated both bacterial and fungal taxa enhanced prediction accuracy, underscoring the critical role of gut fungi in ACVD. Our findings offer a thorough understanding of the link between the gut mycobiome and ACVD progression, which is vital for directing future therapeutic research.IMPORTANCEACVD is a leading cause of death and morbidity worldwide. While the role of the gut microbiome in ACVD development is recognized, the contribution of the gut mycobiome remains largely unexplored. Our study reveals significant alterations in the gut mycobiome of ACVD patients and identifies key fungal taxa associated with the disease. These findings underscore the importance of the gut mycobiome in the pathogenesis of ACVD and offer new avenues for developing preventive and therapeutic strategies targeting the gut fungal community. Our results provide valuable insights into the complex interplay between gut fungi and bacteria in ACVD, paving the way for novel therapeutic approaches.}, } @article {pmid39660058, year = {2024}, author = {Boer, MD and Melkonian, C and Zafeiropoulos, H and Haas, AF and Garza, DR and Dutilh, BE}, title = {Improving genome-scale metabolic models of incomplete genomes with deep learning.}, journal = {iScience}, volume = {27}, number = {12}, pages = {111349}, pmid = {39660058}, issn = {2589-0042}, abstract = {Deciphering microbial metabolism is essential for understanding ecosystem functions. Genome-scale metabolic models (GSMMs) predict metabolic traits from genomic data, but constructing GSMMs for uncultured bacteria is challenging due to incomplete metagenome-assembled genomes, resulting in many gaps. We introduce the deep neural network guided imputation of reactomes (DNNGIOR), which uses AI to improve gap-filling by learning from the presence and absence of metabolic reactions across diverse bacterial genomes. Key factors for prediction accuracy are: (1) reaction frequency across all bacteria and (2) phylogenetic distance of the query to the training genomes. DNNGIOR predictions achieve an average F1 score of 0.85 for reactions present in over 30% of training genomes. DNNGIOR guided gap-filling was 14 times more accurate for draft reconstructions and 2-9 times for curated models than unweighted gap-filling.}, } @article {pmid39658189, year = {2024}, author = {Dufault-Thompson, K and Levy, S and Hall, B and Jiang, X}, title = {Bilirubin reductase shows host-specific associations in animal large intestines.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39658189}, issn = {1751-7370}, mesh = {Animals ; *Phylogeny ; *Gastrointestinal Microbiome ; *Intestine, Large/microbiology ; *Oxidoreductases Acting on CH-CH Group Donors/genetics/metabolism ; Bilirubin/metabolism ; Heme/metabolism ; Bacteria/genetics/classification/isolation & purification/enzymology ; Metagenomics ; }, abstract = {Animal gastrointestinal tracts contain diverse metabolites, including various host-derived compounds that gut-associated microbes interact with. Here, we explore the diversity and evolution of bilirubin reductase, a bacterial enzyme that metabolizes the host-derived tetrapyrrole bilirubin, performing a key role in the animal heme degradation pathway. Through an analysis of the bilirubin reductase phylogeny and predicted structures, we found that the enzyme family can be divided into three distinct clades with different structural features. Using these clade definitions, we analyzed metagenomic sequencing data from multiple animal species, finding that bilirubin reductase is significantly enriched in the large intestines of animals and that the clades exhibit differences in distribution among animals. Combined with phylogenetic signal analysis, we find that the bilirubin reductase clades exhibit significant associations with specific animals and animal physiological traits like gastrointestinal anatomy and diet. These patterns demonstrate that bilirubin reductase is specifically adapted to the anoxic lower gut environment of animals and that its evolutionary history is complex, involving adaptation to a diverse collection of animals harboring bilirubin-reducing microbes. The findings suggest that bilirubin reductase evolution has been shaped by the host environment, providing a new perspective on heme metabolism in animals and highlighting the importance of the microbiome in animal physiology and evolution.}, } @article {pmid39657789, year = {2025}, author = {Zdouc, MM and Blin, K and Louwen, NLL and Navarro, J and Loureiro, C and Bader, CD and Bailey, CB and Barra, L and Booth, TJ and Bozhüyük, KAJ and Cediel-Becerra, JDD and Charlop-Powers, Z and Chevrette, MG and Chooi, YH and D'Agostino, PM and de Rond, T and Del Pup, E and Duncan, KR and Gu, W and Hanif, N and Helfrich, EJN and Jenner, M and Katsuyama, Y and Korenskaia, A and Krug, D and Libis, V and Lund, GA and Mantri, S and Morgan, KD and Owen, C and Phan, CS and Philmus, B and Reitz, ZL and Robinson, SL and Singh, KS and Teufel, R and Tong, Y and Tugizimana, F and Ulanova, D and Winter, JM and Aguilar, C and Akiyama, DY and Al-Salihi, SAA and Alanjary, M and Alberti, F and Aleti, G and Alharthi, SA and Rojo, MYA and Arishi, AA and Augustijn, HE and Avalon, NE and Avelar-Rivas, JA and Axt, KK and Barbieri, HB and Barbosa, JCJ and Barboza Segato, LG and Barrett, SE and Baunach, M and Beemelmanns, C and Beqaj, D and Berger, T and Bernaldo-Agüero, J and Bettenbühl, SM and Bielinski, VA and Biermann, F and Borges, RM and Borriss, R and Breitenbach, M and Bretscher, KM and Brigham, MW and Buedenbender, L and Bulcock, BW and Cano-Prieto, C and Capela, J and Carrion, VJ and Carter, RS and Castelo-Branco, R and Castro-Falcón, G and Chagas, FO and Charria-Girón, E and Chaudhri, AA and Chaudhry, V and Choi, H and Choi, Y and Choupannejad, R and Chromy, J and Donahey, MSC and Collemare, J and Connolly, JA and Creamer, KE and Crüsemann, M and Cruz, AA and Cumsille, A and Dallery, JF and Damas-Ramos, LC and Damiani, T and de Kruijff, M and Martín, BD and Sala, GD and Dillen, J and Doering, DT and Dommaraju, SR and Durusu, S and Egbert, S and Ellerhorst, M and Faussurier, B and Fetter, A and Feuermann, M and Fewer, DP and Foldi, J and Frediansyah, A and Garza, EA and Gavriilidou, A and Gentile, A and Gerke, J and Gerstmans, H and Gomez-Escribano, JP and González-Salazar, LA and Grayson, NE and Greco, C and Gomez, JEG and Guerra, S and Flores, SG and Gurevich, A and Gutiérrez-García, K and Hart, L and Haslinger, K and He, B and Hebra, T and Hemmann, JL and Hindra, H and Höing, L and Holland, DC and Holme, JE and Horch, T and Hrab, P and Hu, J and Huynh, TH and Hwang, JY and Iacovelli, R and Iftime, D and Iorio, M and Jayachandran, S and Jeong, E and Jing, J and Jung, JJ and Kakumu, Y and Kalkreuter, E and Kang, KB and Kang, S and Kim, W and Kim, GJ and Kim, H and Kim, HU and Klapper, M and Koetsier, RA and Kollten, C and Kovács, ÁT and Kriukova, Y and Kubach, N and Kunjapur, AM and Kushnareva, AK and Kust, A and Lamber, J and Larralde, M and Larsen, NJ and Launay, AP and Le, NT and Lebeer, S and Lee, BT and Lee, K and Lev, KL and Li, SM and Li, YX and Licona-Cassani, C and Lien, A and Liu, J and Lopez, JAV and Machushynets, NV and Macias, MI and Mahmud, T and Maleckis, M and Martinez-Martinez, AM and Mast, Y and Maximo, MF and McBride, CM and McLellan, RM and Bhatt, KM and Melkonian, C and Merrild, A and Metsä-Ketelä, M and Mitchell, DA and Müller, AV and Nguyen, GS and Nguyen, HT and Niedermeyer, THJ and O'Hare, JH and Ossowicki, A and Ostash, BO and Otani, H and Padva, L and Paliyal, S and Pan, X and Panghal, M and Parade, DS and Park, J and Parra, J and Rubio, MP and Pham, HT and Pidot, SJ and Piel, J and Pourmohsenin, B and Rakhmanov, M and Ramesh, S and Rasmussen, MH and Rego, A and Reher, R and Rice, AJ and Rigolet, A and Romero-Otero, A and Rosas-Becerra, LR and Rosiles, PY and Rutz, A and Ryu, B and Sahadeo, LA and Saldanha, M and Salvi, L and Sánchez-Carvajal, E and Santos-Medellin, C and Sbaraini, N and Schoellhorn, SM and Schumm, C and Sehnal, L and Selem, N and Shah, AD and Shishido, TK and Sieber, S and Silviani, V and Singh, G and Singh, H and Sokolova, N and Sonnenschein, EC and Sosio, M and Sowa, ST and Steffen, K and Stegmann, E and Streiff, AB and Strüder, A and Surup, F and Svenningsen, T and Sweeney, D and Szenei, J and Tagirdzhanov, A and Tan, B and Tarnowski, MJ and Terlouw, BR and Rey, T and Thome, NU and Torres Ortega, LR and Tørring, T and Trindade, M and Truman, AW and Tvilum, M and Udwary, DW and Ulbricht, C and Vader, L and van Wezel, GP and Walmsley, M and Warnasinghe, R and Weddeling, HG and Weir, ANM and Williams, K and Williams, SE and Witte, TE and Rocca, SMW and Yamada, K and Yang, D and Yang, D and Yu, J and Zhou, Z and Ziemert, N and Zimmer, L and Zimmermann, A and Zimmermann, C and van der Hooft, JJJ and Linington, RG and Weber, T and Medema, MH}, title = {MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D678-D690}, pmid = {39657789}, issn = {1362-4962}, support = {//Conahcyt Mexico International PhD Studentship/ ; 32170080//National Natural Science Foundation of China/ ; 547394769//German Research Foundation/ ; 101066127//European Union/ ; NNF19SA0059360//Novo Nordisk Foundation INTERACT/ ; //Swedish Pharmaceutical Society PostDoc/ ; F32AT011475/AT/NCCIH NIH HHS/United States ; //Werner Siemens Foundation/ ; 027/E5/PG.02.00.PL/2024//Ministry of Education/ ; ANR-17-EUR-0007//EUR Saclay Plant Sciences-SPS/ ; PROYEXCEL_00012//Spanish "Junta de Andalucía"/ ; 1347411//CONAHCYT/ ; IM230100154//Australian Research Council Industry Fellowship/ ; 1229222N//Research Foundation-Flanders (FWO)/ ; R01 GM146224/GM/NIGMS NIH HHS/United States ; //Swiss Federal Government/ ; OSF.23.1.044//NWO Open Science Project 'BiG-CODEC'/ ; //NWO Merian/ ; 024.004.014//MiCRop Consortium/ ; CZIF2022-007203//Chan Zuckerberg Initiative Foundation/ ; BB/T007222/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DP230102668//Australian Research Council Discovery Project/ ; 57/0009//Ministry of Education and Science of Ukraine/ ; //Delta Stewardship Council Delta Science Program/ ; T32 GM136629/GM/NIGMS NIH HHS/United States ; //Basic Science Research Program/ ; R01-GM146224/GM/NIGMS NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; AUFF-E-2022-9-42//AUFF/ ; 10062709//UK Innovation Funding Agency (UKRI)/ ; CBET-2032243//U.S. National Science Foundation/ ; //University of Illinois/ ; //HZI POF IV Cooperativity and Creativity Project Call/ ; //Horizon Europe Marie Skłodowska-Curie Actions Postdoctoral Fellowship/ ; NE/T010959/1//Signals in the Soil/ ; ANR-24-CE20-7299-01//Agence Nationale de la Recherche/ ; DNRF137//Danish National Research Foundation/ ; OCENW.GROOT.2019.063//NWO-XL/ ; BB/V005723/2//BBSRC/ ; 101087181//EU/ ; 101000392//Horizon 2020/ ; 101072485//European Union's Horizon/ ; 10.55776/P 34036//Austrian Science Fund/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; 23/01956-2//São Paulo Research Foundation/ ; //Department of Biotechnology/ ; 222676//USDA Evans-Allen Research/ ; //Saarland University/ ; 102022750//SINTEF/ ; //Hans Fischer Society/ ; 21K06336//KAKENHI/ ; CF22-1239//Carlsberg Foundation/ ; ANR-22-CE44-0011-01 UMISYN//Agence Nationale de la Recherche/ ; 495740318//German Research Foundation/ ; 802736//European Union Horizon 2020/ ; //Strathclyde University Global Research Scholarship/ ; NNF22OC0079021//Novo Nordisk Foundation Postdoctoral Fellowship/ ; 101055020-COMMUNITY//ERC Advanced/ ; 101099528//European Innovation Council/ ; GNT2021638//National Health and Medical Research Council/ ; 757173//Consejo Nacional de Ciencia y Tecnología/ ; NA22NOS4200050//NERRS/ ; 865738/ERC_/European Research Council/International ; DGE 2241144//NSF GRFP/ ; //National Research Fund of Ukraine/ ; RYC2020-029240-I//Ministerio de Ciencia, Innovación y Universidades/ ; MR/V022334/1//UKRI Future Leaders Fellowship/ ; 102029187//SEP AGREE/ ; NNF22OC0078997//Novo Nodisk Foundation/ ; F31 ES036421/ES/NIEHS NIH HHS/United States ; KICH1.LWV04.21.013//NWO/ ; DM60066//Italian Ministry of Research/ ; 101117891-MeDiSyn//ERC Starting/ ; //European Union's Horizon 2020 Research/ ; NRF 2018R1A5A2023127//Korea Government (MSIT)/ ; PS00349981//Fulbright/ ; NRF-2020R1A6A1A03044512//Korean Government (MSIT)/ ; 735867//Consejo Nacional de Ciencia y Tecnología/ ; 3141-00013A//Innovation Fund Denmark/ ; CFB 2.0//Novo Nordisk Foundation/ ; 21/07038-0//São Paulo Research Foundation/ ; 2021YFA0909500//National Key Research and Development Program of China/ ; 101072485//European Union's Horizon Europe/ ; OCENW.XL21.XL21.088//NWO-XL/ ; //University Grants Commission/ ; //Natural Science and Research Council of Canada/ ; TTU 09.826//German Center for Infection Research/ ; //European Regional Development Fund/ ; 101072485//Horizon Europe Marie Skłodowska-Curie/ ; DNRF137//Danish National Research Foundation CeMiSt/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; BB/X01097X/1//BBSRC Institute Strategic Program/ ; 802736//European Union's Horizon 2020/ ; //Alexander von Humboldt-Stiftung/ ; //UK Government Department for Environment, Food & Rural Affairs (DEFRA) Global Centre on Biodiversity for the Climate/ ; //Shanghai Pilot Program for Basic Research - Shanghai Jiao Tong University/ ; 102024676-14//POS BIOINFO 2024/ ; MR/W011247/1//UKRI Future Leaders Fellowship/ ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; 101106349//Marie Sklodowska-Curie/ ; T32-GM136629//Chemical-Biology Interface Training/ ; //University of Sydney/ ; 101000794//SECRETed EU Project Horizon 2020/ ; 2022R1C1C2004118//National Research Foundation of Korea/ ; //Indonesia Endowment Fund for Education Agency (LPDP)/ ; 101130799//European Union's Horizon/ ; 852600//Innovation Program ERC St/ ; //National Agri-Food Biotechnology Institute/ ; //German Academic Scholarship Foundation/ ; 205320_219638/SNSF_/Swiss National Science Foundation/Switzerland ; EXC-2124/1-09.029_0//Cluster of Excellence: Controlling Microbes to Fight Infection/ ; F32 AT011475/AT/NCCIH NIH HHS/United States ; 398967434-TRR 261//Deutsche Forschungsgemeinschaft/ ; 212747/SNSF_/Swiss National Science Foundation/Switzerland ; K445/2022//Leibniz Association/ ; NRF-RS-2024-00352229//Ministry of Science and ICT/ ; //Natural Sciences and Engineering Research Council of Canada Discovery/ ; VI.Veni.202.130//NWO Talent/ ; 106/IV/KS/11/2023//National Research and Innovation Agency/ ; T32GM136583/NH/NIH HHS/United States ; DE-AC02-05CH11231//U.S. Department of Energy/ ; }, mesh = {*Multigene Family ; *Databases, Genetic ; Biosynthetic Pathways/genetics ; Molecular Sequence Annotation ; Biological Products/metabolism/chemistry ; Data Curation ; }, abstract = {Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.}, } @article {pmid39654977, year = {2024}, author = {Wu, J and Wang, D and He, WJ and Li, JY and Mo, X and Li, YJ}, title = {Allergen-specific sublingual immunotherapy altered gut microbiota in patients with allergic rhinitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1454333}, pmid = {39654977}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Sublingual Immunotherapy/methods ; *Rhinitis, Allergic/therapy/microbiology/immunology ; Male ; Female ; Adult ; *Feces/microbiology ; Allergens/immunology ; Young Adult ; Animals ; Middle Aged ; Antigens, Dermatophagoides/immunology ; Dermatophagoides farinae/immunology ; Treatment Outcome ; Adolescent ; Metagenomics/methods ; }, abstract = {INTRODUCTION: Allergen-specific immunotherapy (AIT) induces long-term immune tolerance to allergens and is effective for treating allergic rhinitis (AR). However, the impact of sublingual immunotherapy (SLIT) on gut microbiota from AR patients and its correlation with treatment efficacy remains unclear.

METHODS: In the present study, we enrolled 24 AR patients sensitized to Dermatophagoides farinae (Der-f) and 6 healthy donors (HD). All AR patients received SLIT treatment using standardized Der-f drops. Stool samples were collected from AR patients before treatment, and 1- and 3-months post-treatment, as well as from HD, for metagenomic sequencing analysis.

RESULTS: AR patients had significantly lower richness and diversity in gut microbiota compared to HD, with notable alterations in composition and function. Besides, three months post-SLIT treatment, significant changes in gut microbiota composition at the genus and species levels were observed in AR patients. Streptococcus parasanguinis_B and Streptococcus parasanguinis, which were significantly lower in AR patients compared to HD, increased notably after three months of treatment. LEfSe analysis identified these species as markers distinguishing HD from AR patients and AR patients pre- from post-SLIT treatment. Furthermore, changes in the relative abundance of S. parasanguinis_B were negatively correlated with changes in VAS scores but positively correlated with changes in RCAT scores, suggesting a positive correlation with effective SLIT treatment.

DISCUSSION: SLIT treatment significantly alters the gut microbiota of AR patients, with S. parasanguinis_B potentially linked to its effectiveness. This study offers insights into SLIT mechanisms and suggests that specific strains may serve as biomarkers for predicting SLIT efficacy and as modulators for improving SLIT efficacy.}, } @article {pmid39654975, year = {2024}, author = {Jarmukhanov, Z and Mukhanbetzhanov, N and Vinogradova, E and Kozhakhmetov, S and Kushugulova, A}, title = {Gut metagenomic features of frailty.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1486579}, pmid = {39654975}, issn = {2235-2988}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Frailty/microbiology/metabolism ; Male ; Female ; Aged ; Middle Aged ; *Feces/microbiology ; *Metagenomics/methods ; Kazakhstan ; Adult ; Metagenome ; Bacteria/classification/genetics/isolation & purification/metabolism ; Aged, 80 and over ; Metabolic Networks and Pathways/genetics ; }, abstract = {This study investigates the relationship between frailty severity and gut microbiome characteristics in adults in Kazakhstan. We analyzed 158 participants across four frailty severity (mild to very severe) using metagenomic sequencing of stool samples. Frailty was significantly correlated with age, weight, and functional measures like walking speed and grip strength. Microbial diversity decreased significantly with increasing frailty. Beta diversity analysis revealed distinct clustering patterns based at phylum level. Taxonomically, we observed a significant inverse correlation between Firmicutes abundance and frailty. Classes like Clostridia and Erysipelotrichia decreased with frailty, while Bacteroidia and Actinobacteria increased. At the family level, Oscillospiraceae showed a positive correlation with frailty. Functionally, we identified significant correlations between frailty measures and specific metabolic pathways. The frailty index negatively correlated with pathways involved in cobalamin, arginine and molybdenum cofactor biosynthesis and positively correlated with folate biosynthesis. Physical performance measures strongly correlated with pathways related to nucleotide biosynthesis, and one-carbon metabolism. We propose these identified features may constitute a "frailty-associated metabolic signature" in the gut microbiome. This signature suggests multiple interconnected mechanisms through which the microbiome may influence frailty development, including modulation of inflammation, alterations in energy metabolism, and potential impacts on muscle function through microbial metabolites.}, } @article {pmid39653697, year = {2024}, author = {Palladino, G and Nanetti, E and Scicchitano, D and Cinti, N and Foresto, L and Cozzi, A and Gonzalez Vara Rodriguez, A and Interino, N and Fiori, J and Turroni, S and Candela, M and Rampelli, S}, title = {Zonation of the Vitis vinifera microbiome in Vino Nobile di Montepulciano PDO production area.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1626}, pmid = {39653697}, issn = {2399-3642}, support = {818290//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {*Vitis/microbiology ; *Microbiota/genetics ; Italy ; *Wine/microbiology ; Soil Microbiology ; Bacteria/genetics/classification/metabolism/isolation & purification ; Fungi/genetics/classification/metabolism ; Rhizosphere ; }, abstract = {The microbial dimension of the terroir is crucial for wine quality, as microbiomes contribute to plant biofertilization, stress tolerance and pathogen suppression. While microbial terroir can act as a biological signature at large scale, data for local contexts is lacking, hindering the characterization of regional microbial diversity in vineyards. Here, we define the microbial terroir of vineyards across the 12 sub-areas (Additional Geographic Units -AGUs) of the "Consorzio del Vino Nobile di Montepulciano DOCG" PDO area (Italy), a world-renowned wine-producing region. Rhizospheres of Vitis vinifera cultivar Sangiovese and soil samples were collected throughout the 2022 viticultural season and analyzed through an integrated metabarcoding/shotgun metagenomic approach, targeting bacteria and fungi. Wine metabolomics was also perfomed, projecting compositional and functional variations of the microbial terroir at the AGUs level into a corresponding variation in the product metabolic profile. Our findings reveal a unique taxonomic configuration of the Vino Nobile di Montepulciano terroir compared to other vineyards, with microbiomes being "AGU-specific" in taxonomic abundances and plant growth-promoting functions, confirming the potential relevance of characterizing and preserving the microbial terroir to safeguard high-quality traditional wines.}, } @article {pmid39653684, year = {2024}, author = {Chen, Y and Yang, C and Deng, Z and Xiang, T and Tan, J and Xu, J and Sun, D and Luo, F}, title = {Alterations of gut virome with close interaction in the progression of estrogen deficiency-induced osteoporosis.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2437250}, pmid = {39653684}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; Animals ; Female ; *Virome ; Mice ; *Osteoporosis/virology ; Humans ; *Estrogens/metabolism ; Ovariectomy ; Bacteria/classification/genetics/isolation & purification/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; Disease Progression ; }, abstract = {Previous research has established a link between gut microbiota and osteoporosis (OP) advancement. However, there remains a limited understanding of the crucial contribution of the gut virome in the onset and progression of OP. We employed metagenomic shotgun sequencing and gut virome sequencing to process the ovariectomy (OVX)-induced OP murine model, which revealed significant disparities in bacteriome and virome compositions between subjects with OP and healthy controls. One hundred and seventy-four altered viral strains were identified to participate in the multifaceted regulation of bone loss, involving immune modulation, microbial metabolic activity, and intricate host-virus dynamics. Our findings suggested that the gut virome may influence bone metabolism, potentially altering the balance of bone-modulating compounds like short-chain fatty acids. This comprehensive analysis of the gut virome in OP highlighted the diagnostic potential of combined gut viral and bacterial biomarkers for OP.}, } @article {pmid39648978, year = {2025}, author = {Ribero, MN and Schiaffino, MR and Filloy, J}, title = {Grassland Afforestation Drives Biotic Homogenisation of Soil Microbial Communities at a Regional Scale.}, journal = {Molecular ecology}, volume = {34}, number = {2}, pages = {e17617}, doi = {10.1111/mec.17617}, pmid = {39648978}, issn = {1365-294X}, support = {2018//Secretaría de Ciencia y Técnica, Universidad de Buenos Aires/ ; //Neotropical Grassland Conservancy/ ; PICT 2017//Agencia Nacional de Promoción Científica y Tecnológica/ ; //Consejo Nacional de Investigaciones Científicas y Técnicas/ ; }, mesh = {*Soil Microbiology ; *Grassland ; *Biodiversity ; Argentina ; *Microbiota/genetics ; *Fungi/genetics/classification ; Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; }, abstract = {Grassland afforestation poses a threat to biodiversity beyond land-use conversion. Diversity patterns are shaped by temporal dynamics, particularly, time since afforestation can decline beta diversity and lead to biotic homogenisation. Our study examines the effect of grassland afforestation on soil prokaryotic and fungal beta diversity. We evaluate the contributions of colonisation and extinction processes to beta diversity, as well as the replacement of endemic species by ubiquitous ones. Along a 200 km climatic gradient in Argentina's Pampas region, we analysed grasslands and mature eucalypt plantations at different times since afforestation. Soil samples were collected at each site and analysed using 16S (V3-V4) and ITS2 amplicon sequencing to identify prokaryotic and fungal communities, respectively. The analyses revealed biotic homogenisation at the transition from grassland to newly planted stands, evidenced by a decrease in intratreatment beta diversity. Increasing time since afforestation did not exacerbate this decline. However, our findings indicate that there are different responses between prokaryotes and fungi. The homogenisation of prokaryotes in young stands is due to the low heterogeneity in colonising communities. On the other hand, the decline in fungal beta diversity is likely caused by other mechanisms beyond extinction or replacement. The study highlights the impacts of the afforestation process on the beta diversity of soil microbial communities of grasslands, affecting taxonomic groups in different ways. Although microbial diversity may be partially restored in time in eucalypt plantations, it is important to investigate its underlying mechanisms and the ecological implications for microbial diversity and its spatial distribution.}, } @article {pmid39647426, year = {2024}, author = {Ge, H and Li, C and Huang, C and Zhao, L and Cong, B and Liu, S}, title = {Bacterial community composition and metabolic characteristics of three representative marine areas in northern China.}, journal = {Marine environmental research}, volume = {204}, number = {}, pages = {106892}, doi = {10.1016/j.marenvres.2024.106892}, pmid = {39647426}, issn = {1879-0291}, abstract = {Bacteria are essential components of ecosystems, participating in nutrient cycling and biogeochemical processes, and playing a crucial role in maintaining the stability of marine ecosystems. However, the biogeographic distribution patterns of bacterial diversity and metabolic functions in the estuarine and coastal areas of northern China remain unclear. Here, we used metagenomic sequencing to investigate the bacterial community composition and metabolic functions in sediments from the adjacent waters of the Yellow River Estuary, the Yellow Sea Cold Water Mass, and the adjacent waters of the Yangtze River Estuary. Among the 9164 species that were found, the most dominant microbial communities are Pseudomonadota, Actinomycetota, Bacteroidota, and Bacillota, but there are significant differences in the species composition in these three typical habitats. Amino acid metabolism and carbohydrate metabolic pathways were highly enriched. Glycoside hydrolases (GHs) predominate in carbon metabolism across all samples. In nitrogen metabolic pathway, genes related to organic degradation and synthesis are more abundant in the Yellow River Estuary than the other two habitats. In sulfur metabolic pathway, genes involved in assimilatory sulfate reduction are significantly enriched. Assimilatory sulfate reduction might be crucial for sulfur metabolism in coastal regions, with a full assimilatory nitrate reduction pathway found in Desulfobacterota. This research offers insights into the compositional diversity, metabolic functions, and biogeographic distribution patterns of bacterial communities in sediments from typical marine areas of northern China.}, } @article {pmid39647412, year = {2024}, author = {He, T and Xie, J and Jin, L and Zhao, J and Zhang, X and Liu, H and Li, XD}, title = {Seasonal dynamics of the phage-bacterium linkage and associated antibiotic resistome in airborne PM2.5 of urban areas.}, journal = {Environment international}, volume = {194}, number = {}, pages = {109155}, doi = {10.1016/j.envint.2024.109155}, pmid = {39647412}, issn = {1873-6750}, mesh = {*Bacteriophages/genetics ; *Particulate Matter ; China ; *Bacteria/genetics/drug effects ; *Seasons ; Humans ; Air Microbiology ; Cities ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Air Pollutants/analysis ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Microbiota ; }, abstract = {Inhalable microorganisms in airborne fine particulate matter (PM2.5), including bacteria and phages, are major carriers of antibiotic resistance genes (ARGs) with strong ecological linkages and potential health implications for urban populations. A full-spectrum study on ARG carriers and phage-bacterium linkages will shed light on the environmental processes of antibiotic resistance from airborne dissemination to the human lung microbiome. Our metagenomic study reveals the seasonal dynamics of phage communities in PM2.5, their impacts on clinically important ARGs, and potential implications for the human respiratory microbiome in selected cities of China. Gene-sharing network comparisons show that air harbours a distinct phage community connected to human- and water-associated viromes, with 57 % of the predicted hosts being potential bacterial pathogens. The ARGs of common antibiotics, e.g., peptide and tetracycline, dominate both the antibiotic resistome associated with bacteria and phages in PM2.5. Over 60 % of the predicted hosts of vARG-carrying phages are potential bacterial pathogens, and about 67 % of these hosts have not been discovered as direct carriers of the same ARGs. The profiles of ARG-carrying phages are distinct among urban sites, but show a significant enrichment in abundance, diversity, temperate lifestyle, and matches of CRISPR (short for 'clustered regularly interspaced short palindromic repeats') to identified bacterial genomes in winter and spring. Moreover, phages putatively carry 52 % of the total mobile genetic element (MGE)-ARG pairs with a unique 'flu season' pattern in urban areas. This study highlights the role that phages play in the airborne dissemination of ARGs and their delivery of ARGs to specific opportunistic pathogens in human lungs, independent of other pathways of horizontal gene transfer. Natural and anthropogenic stressors, particularly wind speed, UV index, and level of ozone, potentially explained over 80 % of the seasonal dynamics of phage-bacterial pathogen linkages on antibiotic resistance. Therefore, understanding the phage-host linkages in airborne PM2.5, the full-spectrum of antibiotic resistomes, and the potential human pathogens involved, will be of benefit to protect human health in urban areas.}, } @article {pmid39643877, year = {2024}, author = {Cui, Z and Wang, S and Niu, J and Ma, J and Yang, H}, title = {Bifidobacterium species serve as key gut microbiome regulators after intervention in gestational diabetes mellitus.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {520}, pmid = {39643877}, issn = {1471-2180}, support = {22cz020401-4811009//National High Level Hospital Clinical Research/ ; 81830044//National Natural Science Foundation of China/ ; 2021YFC2700700//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Diabetes, Gestational/microbiology/metabolism/blood ; Pregnancy ; *Gastrointestinal Microbiome/genetics ; Female ; *Bifidobacterium/genetics ; Adult ; *Feces/microbiology ; Fatty Acids, Volatile/metabolism ; Dysbiosis/microbiology ; Genome-Wide Association Study ; Metagenome ; }, abstract = {Gut microbiome dysbiosis is associated with gestational diabetes mellitus (GDM), and its modulation represents a promising approach for enhancing glycemic control. In this study, we aimed to discover specific alterations in the gut microbiome through lifestyle management. We performed metagenome sequencing on fecal samples and measured short-chain fatty acid (SCFA) in plasma samples from 27 well-controlled GDM pregnancies before and after glycemic control. At the same time, 38 normal glucose tolerance (NGT) samples served as controls. Additionally, we employed two-sample Mendelian Randomization (MR) to validate our findings against Genome-Wide Association Study (GWAS) database. Our dynamic analysis revealed Bifidobacterium genus increased in GDM patients after intervention. The MR analysis confirmed that the family of Bifidobacteriaceae (OR 0.929, 95% CI, 0.886-0.975; P = 0.003) was the only negatively associated family with GDM. Further analysis indicated the increased abundance of Bifidobacterium species were negatively correlated with glycemic traits (Spearman rho mean - 0.32 ± 0.34) but positively correlated with plasma SCFA levels (Spearman rho mean 0.24 ± 0.19). Functional analysis revealed that the quorum-sensing pathway had the strongest effect on the ability of Bifidobacterium to promote glucose homeostasis (Spearman rho = -0.34), suggesting its role in regulating intestinal microbiota. Finally, the multivariable MR analysis demonstrated that two pathways, COLANSYN PWY and PWY 7323, responsible for cell surface compound synthesis in gram-negative bacteria, mediated 14.83% (P = 0.017) and 16.64% (P = 0.049) of the protective effects of Bifidobacteriaceae against GDM, respectively. In summary, Bifidobacterium is an effective gut microbiota regulator for GDM-related glucose homeostasis.}, } @article {pmid39643362, year = {2024}, author = {Shen, C and Yu, Y and Zhang, X and Zhang, H and Chu, M and Yuan, B and Guo, Y and Li, Y and Zhou, J and Mao, J and Xu, X}, title = {The dynamic of physicochemical properties, volatile compounds and microbial community during the fermentation of Chinese rice wine with diverse cereals.}, journal = {Food research international (Ottawa, Ont.)}, volume = {198}, number = {}, pages = {115319}, doi = {10.1016/j.foodres.2024.115319}, pmid = {39643362}, issn = {1873-7145}, mesh = {Amino Acids/analysis/metabolism ; Bacteria/classification/metabolism ; Edible Grain/chemistry/microbiology ; Esters/analysis/metabolism ; *Fermentation ; Gas Chromatography-Mass Spectrometry ; Microbiota ; *Odorants/analysis ; *Oryza/chemistry ; Taste ; *Volatile Organic Compounds/analysis ; *Wine/analysis/microbiology ; }, abstract = {This study investigates the impact of liquid state fermentation on the key flavor compounds and microbial community structure in Chinese rice wine brewed from five different raw materials: buckwheat, sorghum, japonica rice, glutinous rice, and black rice. Using HS-SPME-GC-MS and HPLC, the volatile compounds were analyzed across various grain liquefaction methods, detecting 82 volatiles, including esters, alcohols, aldehydes, and acids. The concentration of flavor compounds such as esters, amino acids, phenolic acids, and organic acids varied significantly depending on the raw material used. Based on odor activity values, 31 key compounds were identified, including 15 ethyl esters, like ethyl laurate, responsible for the unique and complex aroma of the rice wines. Bitter amino acids, making up over 50 % of the total amino acids, were predominant. Among the varieties, the buckwheat-fermented wine exhibited the highest ester content (27.39 mg/L), nearly double that of other samples, along with elevated amino acids (1.47 mg/mL) and phenolic acids (904.29 mg/L). Black rice ranked second in amino acid content (0.93 mg/mL), while glutinous rice had the highest organic acid content (239.76 mg/mL). Metagenomic sequencing on the fifth day of fermentation revealed significant differences in microbial community structure among the raw materials. Saccharomyces, Aspergillus, Thermomyces, Epicoccus, and Albertella were dominant fungi, while Weissella, Thermoactinomyces, Bacillus, and Saccharopolyspora were dominant bacteria. Sensory analysis showed that buckwheat-fermented rice wine was distinguished by its honey, floral, creamy, and umami attributes, while balancing alcohol, acidity, bitterness, and Qu aroma. The results demonstrate the significant influence of raw material selection and liquefaction method on both flavor profile and microbial diversity in Chinese rice wine.}, } @article {pmid39643360, year = {2024}, author = {Li, N and Xu, W and Meng, L and Zhao, Y and Zhao, X and Zheng, N and Zhang, Y and Wang, J}, title = {Metagenomics reveals differences in spore-forming bacterial diversity in raw milk in different regions and seasons in China.}, journal = {Food research international (Ottawa, Ont.)}, volume = {198}, number = {}, pages = {115317}, doi = {10.1016/j.foodres.2024.115317}, pmid = {39643360}, issn = {1873-7145}, mesh = {*Seasons ; Animals ; *Milk/microbiology ; China ; *Spores, Bacterial/genetics ; *Metagenomics ; Food Microbiology ; Bacteria/genetics/classification/isolation & purification ; Biodiversity ; }, abstract = {The spore-forming bacteria in the dairy industry are notable for their spores resilience and capacity to survive heating processes, allowing them to germinate and enter the vegetative stage, potentially leading to spoilage of the milk. Additionally, these spores can form biofilms, becoming a persistent source of contamination in processing environments. In this study, we collected a total of 165 raw milk from six different parts in China in spring, summer, autumn, and winter, respectively. Metagenomics sequencing method was used to explore and compare the differences in spore-forming bacterial composition and diversity in raw milk samples. Among these samples, four genera and 207 species of spore-forming bacteria were identified, with the genus Bacillus and the species Paenibacillus darwinianus dominant. Seasonal variations had a greater impact on the composition and abundance of spore-forming bacteria in raw milk than regional differences. Notable, raw milk samples collected during the spring and summer exhibited a higher number of unique spore-forming bacterial species compared to those collected in other seasons. Moreover, different regions and seasons have their own dominant bacteria. Metabolism of cofactors and vitamins, energy metabolism, carbohydrate metabolism, and amino acid metabolism were the main metabolic pathways. Hence, specific strategies need to be adopted to prevent and control spore-forming bacteria in raw milk in different regions and seasons.}, } @article {pmid39643345, year = {2024}, author = {Jian, C and Sun, M and Ma, T and Wang, W and Lv, B and Wang, J and Su, X and Li, S and Guo, Y}, title = {Revealing the formation mechanisms of key flavor components during the fermentation of bamboo shoots by combining flavoromics and metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {198}, number = {}, pages = {115361}, doi = {10.1016/j.foodres.2024.115361}, pmid = {39643345}, issn = {1873-7145}, mesh = {*Fermentation ; *Metagenomics ; *Taste ; *Volatile Organic Compounds/analysis/metabolism ; *Odorants/analysis ; *Metabolomics ; Flavoring Agents/metabolism ; Plant Shoots ; Fermented Foods/microbiology ; Bacteria/genetics/classification/metabolism ; Food Microbiology ; Amino Acids/analysis/metabolism ; Microbiota ; }, abstract = {Microbial metabolism plays a critical role in the flavor development of Guangxi fermented bamboo shoots (GFBS). To clarify the role of microorganisms in flavor formation and predict the metabolic pathways of key characteristic flavor compounds, this study employed metabolomics, Odor Activity Value (OAV), and Taste Activity Value (TAV) calculations, integrated with Partial Least Squares Discriminant Analysis (PLS-DA), to investigate changes in GFBS flavors-represented by volatile flavor compounds, organic acids, and free amino acids-across a 30-day fermentation period. Metagenomic datasets were used to identify taxonomic and functional changes in the microbial community. As a result, 26 characteristic flavor compounds (OAV or TAV > 1) were identified in mature GFBS, and 23 differential flavor compounds were identified at different fermentation stages using PLS-DA (VIP > 1.2). The top 10 microbial genera associated with these characteristic flavor compounds were identified, including Acinetobacter, Enterobacter, Raoultella, Enterococcus, Klebsiella, Lactococcus, Leuconostoc, Weissella, Lactiplantibacillus and Limosilactobacillus. Based on these findings, a predictive metabolic network of key flavor compounds in GFBS was constructed, providing a comprehensive understanding of the diverse metabolic roles of microorganisms during fermentation. This work lays a theoretical foundation for the standardized production and quality control of GFBS flavor.}, } @article {pmid39643336, year = {2024}, author = {Li, T and Cao, W and Li, D and Wei, C and Yan, Y and Zeng, X}, title = {Metagenomic insights into quorum sensing-associated microbial profiling and its correlations with flavor compounds of Maotai-flavor liquor: A case study of stacking fermented grains.}, journal = {Food research international (Ottawa, Ont.)}, volume = {198}, number = {}, pages = {115324}, doi = {10.1016/j.foodres.2024.115324}, pmid = {39643336}, issn = {1873-7145}, mesh = {*Quorum Sensing ; *Fermentation ; *Flavoring Agents/metabolism ; *Metagenomics/methods ; Taste ; Food Microbiology ; Bacteria/genetics/metabolism/classification ; Fungi/genetics/metabolism ; Edible Grain/microbiology ; Alcoholic Beverages/microbiology ; Microbiota ; }, abstract = {Stacking fermentation is typical process of Maotai-flavor Baijiu and microbial composition determine content of flavors. To date, the knowledge on the driving force of microbial composition was as yet unknown. Since quorum sensing molecule (QSM) plays an important role in modifying microbial interactions. Therefore, the objectives of the present study were: (1) to describe the microbial profile associated with QSM in stacking grains using metagenomics; (2) to elucidate how QSM shapes microbial interactions and accordingly regulates flavor synthesis. Results indicated that bacterial QSM including AI-2, DSF, and AHL as well as fungal QSM aromatic alcohols and farnesol were prevalent in the stacking fermented grains. Thereinto, AI-2 might be an important driving force of microbial composition due to its highest abundance. AI-2 in Limosilactobacillus fermentum, Pediococcus pentosaceus, and Weissella cibaria perhaps modified microbial interactions together with fungal QSM in Schizosaccharomyces pombe and Pichia membranifaciens. The role of AI-2 was much higher than that of fungal QSM. Furthermore, QSM indirectly influenced the synthesis of important flavors such as ethyl lactate, phenylethanol, and ethyl phenylacetate through the dynamic of microbial composition. Together, this current study for the first time explored the effects of QSM on microbial composition and flavor synthesis in the Baijiu field.}, } @article {pmid39642431, year = {2024}, author = {Bertini, F and Catania, V and Scirè Calabrisotto, L and Dara, M and Bisanti, L and La Corte, C and Staropoli, M and Piazzese, D and Parisi, MG and Parrinello, D and Cammarata, M}, title = {A multi-comprehensive approach to assess the responses of the Mediterranean mussel Mytilus galloprovincialis (Lamarck, 1919) to a simulation of a diesel-oil mixture spill.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {279}, number = {}, pages = {107188}, doi = {10.1016/j.aquatox.2024.107188}, pmid = {39642431}, issn = {1879-1514}, abstract = {Oil spills are a major cause of pollution impacting marine ecosystems. In this work, the effects of short-term exposure to three different concentrations of a hydrocarbon mixture (HC), that simulated the action of such an event, were investigated on Mytilus galloprovincialis specimens. Physiological effects were measured using a battery of biomarkers consisting of cellular activity (phagocytosis), immune-related enzymes, chaperonins (HSP70 and HSC70), and histomorphological alterations. Different concentrations of HC led to a significant decrease in phagocytosis, especially following high concentrations. Immune-related enzymes evaluated in hemolymph and digestive gland extract showed up-regulation, suggesting the activation of antioxidant, detoxicant, and inflammatory responses. Morphological alterations of digestive gland tubules were observed after exposure to the HC. HSP70 and HSC70 activity was up regulated following the treatments, indicating their involvement in maintaining organism homeostasis. In addition, the diversity and composition of hemolymph and digestive gland microbiota exposed to HC were analyzed by automated ribosomal intergenic spacer analysis (ARISA) and a Next Generation Sequencing (NGS) approach to evaluate the connection with hydrocarbon contamination. Metagenomic analysis revealed significant differences in the hemolymph and digestive gland microbiota composition between mussels exposed and unexposed to HC. Exposure to increasing HC concentrations had a positive effect on microbial diversity with clear adaptative responses, and an increase in the relative abundance of several known degrading bacterial genera, including Alcanivorax, Roseovarius, Pseudomonas, Vibrio, Oleibacter. These results show the utility of a multi-comprehensive approach to evaluating functional adaptation in terms of immunological dysfunctions and microbiota alteration in the sentinel organism M. galloprovincialis.}, } @article {pmid39641169, year = {2025}, author = {Yang, J and Lei, OK and Bhute, S and Kris-Etherton, PM and Lichtenstein, AH and Matthan, NR and Petersen, KS and Sabaté, J and Reboussin, DM and Lovato, L and Vitolins, MZ and Rajaram, S and Jacobs, JP and Huang, J and Taw, M and Yang, S and Li, Z}, title = {Impact of daily avocado consumption on gut microbiota in adults with abdominal obesity: an ancillary study of HAT, a randomized controlled trial.}, journal = {Food & function}, volume = {16}, number = {1}, pages = {168-180}, doi = {10.1039/d4fo03806a}, pmid = {39641169}, issn = {2042-650X}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Persea ; Female ; Male ; Adult ; Middle Aged ; *Obesity, Abdominal/diet therapy/metabolism/microbiology ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification/metabolism ; Diet ; }, abstract = {Objectives: This study aimed to investigate short-term and long-term impact of avocado consumption without caloric restriction on the gut microbiota of free-living adults with abdominal obesity. Methods: The Habitual Diet and Avocado Trial (HAT) was a 26-week, multi-center, randomized, controlled trial involving 1008 individuals with abdominal obesity. Participants were randomly assigned to the Avocado Supplemented Diet Group (AVO), receiving one avocado per day, or the Habitual Diet group (HAB), maintaining their usual dietary habits. Fecal samples were collected at baseline, week 4 and week 26 from a subset of participants recruited at a University of California Los Angeles site (n = 230). Fecal microbiota was assessed with shotgun metagenomics sequencing. Alpha diversity was assessed using the Chao1 and Shannon indices; beta diversity was assessed using Bray-Curtis dissimilarity with significance determined by repeated measures permutational multivariat analysis of variance. Potential association of intervention at week 4 and 26 with alpha diversity, species and metabolic pathways was examined using linear mixed effect models. Results: Compared to the HAB group, the AVO group had higher alpha diversity by 4 weeks, which persisted through the 26-week study period. Exploratory analysis based on healthy eating index-2015 (HEI-2015) indicated that participants with a low HEI score at baseline (≤52.7), had an increase in alpha diversity in the AVO group vs. HAB group. The AVO group had a significant change in beta diversity at week 26 compared to the HAB group. At the species level, the AVO group had significantly increased Faecalibacterium prausnitzii and Bacterium AF16_15 at week 26 compared to the HAB group. Functional analysis showed no significant difference in metabolic pathways between the HAB and AVO groups. Conclusions: Our findings document a potentially favorable effect of avocados on gut microbiota diversity. The prebiotic potential of avocados is more pronounced in individuals with a low diet quality score. This trial is registered at clinicaltrials.gov as NCT03528031 (https://clinicaltrials.gov/study/NCT03528031).}, } @article {pmid39640900, year = {2024}, author = {Pahirah, N and Narkwichean, A and Taweechotipatr, M and Wannaiampikul, S and Duang-Udom, C and Laosooksathit, W}, title = {Comparison of Gut Microbiomes Between Neonates Born by Cesarean Section and Vaginal Delivery: Prospective Observational Study.}, journal = {BioMed research international}, volume = {2024}, number = {}, pages = {8302361}, pmid = {39640900}, issn = {2314-6141}, mesh = {Humans ; *Cesarean Section ; *Gastrointestinal Microbiome ; Infant, Newborn ; Female ; Prospective Studies ; *Delivery, Obstetric ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; Male ; Feces/microbiology ; Thailand ; Bifidobacterium ; }, abstract = {Background: Balanced diversity and abundance of gut microbiome play important roles in human health, including neonatal health. Though not established, there is evidence that the delivery route could alter the diversity of neonatal gut microbiomes. Objective: The objective of the study was to investigate the differences in the gut microbiomes of neonates delivered via cesarean section compared to those born by vaginal delivery and to identify the predominant microbial taxa present in each group. Study Design: A prospective observational study of 281 healthy neonates born between February 2021 and April 2023 at Her Royal Highness Maha Chakri Sirindhorn Medical Center, Srinakharinwirot University, Thailand, was performed. The study population was divided into two groups: 139 neonates born via vaginal delivery and 141 neonates born via cesarean section. The microbiota composition of each neonate's fecal sample was identified by using 16S ribosomal ribonucleic acid metagenomic sequencing. Results: Neonates delivered vaginally exhibited a gut microbiome with higher abundance and diversity than those delivered by cesarean delivery. Bifidobacterium was the dominant genus in both groups. Bifidobacterium breve was the dominant species and was significantly higher in cesarean-delivered neonates compared to those delivered vaginally (24.0% and 9.2%, respectively) (p < 0.001). However, the taxonomy of only 89 (64.0%) and 44 (31.43%) fecal samples could be identified from the vaginal and cesarean delivery groups, respectively. Conclusion: Route of delivery is associated with neonatal gut microbiome abundance and diversity. Neonates delivered via vaginal delivery exhibited higher diversity but lower abundance of the dominant species in the gut microbiome. Trial Registration: Thai Clinical Trials Registry identifier: TCTR20221024003.}, } @article {pmid39639355, year = {2024}, author = {Benga, L and Rehm, A and Gougoula, C and Westhoff, P and Wachtmeister, T and Benten, WPM and Engelhardt, E and Weber, APM and Köhrer, K and Sager, M and Janssen, S}, title = {The host genotype actively shapes its microbiome across generations in laboratory mice.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {256}, pmid = {39639355}, issn = {2049-2618}, mesh = {Animals ; Mice ; Female ; *Genotype ; *Mice, Inbred BALB C ; *Mice, Inbred C57BL ; *Microbiota ; Male ; Maternal Inheritance ; Embryo, Mammalian/microbiology ; Host Microbial Interactions ; Pregnancy ; }, abstract = {BACKGROUND: The microbiome greatly affects health and wellbeing. Evolutionarily, it is doubtful that a host would rely on chance alone to pass on microbial colonization to its offspring. However, the literature currently offers only limited evidence regarding two alternative hypotheses: active microbial shaping by host genetic factors or transmission of a microbial maternal legacy.

RESULTS: To further dissect the influence of host genetics and maternal inheritance, we collected two-cell stage embryos from two representative wild types, C57BL6/J and BALB/c, and transferred a mixture of both genotype embryos into hybrid recipient mice to be inoculated by an identical microbiome at birth.

CONCLUSIONS: Observing the offspring for six generations unequivocally emphasizes the impact of host genetic factors over maternal legacy in constant environments, akin to murine laboratory experiments. Interestingly, maternal legacy solely controlled the microbiome in the first offspring generation. However, current evidence supporting maternal legacy has not extended beyond this initial generation, resolving the aforementioned debate. Video Abstract.}, } @article {pmid39639104, year = {2025}, author = {Knuth, MM and Campos, CV and Smith, K and Hutchins, EK and Lewis, S and York, M and Coghill, LM and Franklin, C and MacFarlane, AJ and Ericsson, AC and Magnuson, T and Ideraabdullah, F}, title = {Timing of standard chow exposure determines the variability of mouse phenotypic outcomes and gut microbiota profile.}, journal = {Lab animal}, volume = {54}, number = {1}, pages = {24-36}, pmid = {39639104}, issn = {1548-4475}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Mice, Inbred C57BL ; Male ; Mice ; Female ; *Diet/veterinary ; Phenotype ; Time Factors ; Animal Feed/analysis ; }, abstract = {Standard chow diets influence reproducibility in animal model experiments because chows have different nutrient compositions, which can independently influence phenotypes. However, there is little evidence of the role of timing in the extent of variability caused by chow exposure. Here we measured the impact of different diets (5V5M, 5V0G, 2920X and 5058) and timing of exposure (adult exposure (AE), lifetime exposure (LE) and developmental exposure (DE)) on growth and development, metabolic health indicators and gut bacterial microbiota profiles across genetically identical C57BL/6J mice. Diet drove differences in macro- and micronutrient intake for all exposure models. AE had no effect on phenotypic outcomes. However, LE mice exhibited significant sex-dependent diet effects on growth, body weight and body composition. LE effects were mostly absent in the DE model, where mice were exposed to chow differences only from conception to weaning. Both AE and LE models exhibited similar diet-driven beta diversity profiles for the gut bacterial microbiota, with 5058 diet driving the most distinct profile. However, compared with AE, LE effects on beta diversity were sex dependent, and LE mice exhibited nine times more differentially abundant bacterial genera, the majority of which were inversely affected by 2920X and 5058 diets. Our findings demonstrate that LE to different chow diets has the greatest impact on the reproducibility of several experimental measures commonly used in preclinical mouse model studies. Importantly, weaning mice from different diets onto the same diet for maturation may be an effective way to reduce unwanted phenotypic variability among experimental models.}, } @article {pmid39637857, year = {2024}, author = {Vaher, K and Cabez, MB and Parga, PL and Binkowska, J and van Beveren, GJ and Odendaal, ML and Sullivan, G and Stoye, DQ and Corrigan, A and Quigley, AJ and Thrippleton, MJ and Bastin, ME and Bogaert, D and Boardman, JP}, title = {The neonatal gut microbiota: A role in the encephalopathy of prematurity.}, journal = {Cell reports. Medicine}, volume = {5}, number = {12}, pages = {101845}, doi = {10.1016/j.xcrm.2024.101845}, pmid = {39637857}, issn = {2666-3791}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Infant, Newborn ; Female ; Male ; *Infant, Premature ; Feces/microbiology ; Brain/pathology/microbiology ; Brain Diseases/microbiology/pathology ; Gestational Age ; Magnetic Resonance Imaging/methods ; Premature Birth/microbiology ; }, abstract = {Preterm birth correlates with brain dysmaturation and neurocognitive impairment. The gut microbiome associates with behavioral outcomes in typical development, but its relationship with neurodevelopment in preterm infants is unknown. We characterize fecal microbiome in a cohort of 147 neonates enriched for very preterm birth using 16S-based and shotgun metagenomic sequencing. Delivery mode strongly correlates with the preterm microbiome shortly after birth. Low birth gestational age, infant sex assigned at birth, and antibiotics associate with microbiome composition at neonatal intensive care unit discharge. We integrate these data with term-equivalent structural and diffusion brain MRI. Bacterial community composition associates with MRI features of encephalopathy of prematurity. Particularly, abundances of Escherichia coli and Klebsiella spp. correlate with microstructural parameters in deep and cortical gray matter. Metagenome functional capacity analyses suggest that these bacteria may interact with brain microstructure via tryptophan and propionate metabolism. This study indicates that the gut microbiome associates with brain development following preterm birth.}, } @article {pmid39637856, year = {2025}, author = {Caty, SN and Alvarez-Buylla, A and Vasek, C and Tapia, EE and Martin, NA and McLaughlin, T and Golde, CL and Weber, PK and Mayali, X and Coloma, LA and Morris, MM and O'Connell, LA}, title = {Alkaloids are associated with increased microbial diversity and metabolic function in poison frogs.}, journal = {Current biology : CB}, volume = {35}, number = {1}, pages = {187-197.e8}, doi = {10.1016/j.cub.2024.10.069}, pmid = {39637856}, issn = {1879-0445}, mesh = {Animals ; *Alkaloids/metabolism ; *Microbiota ; *Anura/microbiology/metabolism ; Skin/microbiology/metabolism ; Bacteria/metabolism/classification/genetics/isolation & purification ; Poison Frogs ; }, abstract = {Shifts in host-associated microbiomes can impact both host and microbes.[1][,][2][,][3][,][4][,][5][,][6] It is of interest to understand how perturbations, like the introduction of exogenous chemicals,[7][,][8][,][9][,][10][,][11][,][12][,][13] impact microbiomes. In poison frogs (family Dendrobatidae), the skin microbiome is exposed to alkaloids that the frogs sequester for defense.[14][,][15][,][16][,][17][,][18][,][19] These alkaloids are antimicrobial[20][,][21][,][22]; however, their effect on the frogs' skin microbiome is unknown. To test this, we characterized microbial communities from field-collected dendrobatid frogs. Then, we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of two frog species with contrasting alkaloid loads in nature. In both datasets, we found that alkaloid-exposed microbiomes were more phylogenetically diverse, with an increase in diversity among rare taxa. To better understand the isolate-specific response to alkaloids, we cultured microbial isolates from poison frog skin and found that many isolates exhibited enhanced growth or were not impacted by the addition of DHQ. To further explore the microbial response to alkaloids, we sequenced the metagenomes from high- and low-alkaloid frogs and observed a greater diversity of genes associated with nitrogen and carbon metabolism in high-alkaloid frogs. From these data, we hypothesized that some strains may metabolize the alkaloids. We used stable isotope tracing coupled to nanoSIMS (nanoscale secondary ion mass spectrometry), which supported the idea that some of these isolates are able to metabolize DHQ. Together, these data suggest that poison frog alkaloids open new niches for skin-associated microbes with specific adaptations, such as alkaloid metabolism, that enable survival in this environment.}, } @article {pmid39636804, year = {2024}, author = {Calderon, MS and Bustamante, DE and Perez, J and Fernandez-Güimac, SLJ and Mendoza, JE and Barboza, JI and Ayala, RY and Carrion, JV}, title = {Diversity and functional role of bacterial microbiota in spontaneous coffee fermentation in northern Peru using shotgun metagenomics.}, journal = {Journal of food science}, volume = {89}, number = {12}, pages = {9692-9710}, doi = {10.1111/1750-3841.17583}, pmid = {39636804}, issn = {1750-3841}, support = {//Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica/ ; N° 030-2018-FONDECYT-BM-IADT-MU//Peruvian CONCYTEC under the projects Metacafé/ ; N° PE501081184-2022-PROCIENCIA//Metacafé 2.0/ ; //Vicerrectorado de Investigación (VRIN) de la UNTRM/ ; }, mesh = {*Fermentation ; Peru ; *Coffee/microbiology ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; Taste ; Coffea/microbiology ; Food Microbiology/methods ; }, abstract = {Peru is the ninth-largest coffee producer and the largest organic coffee exporter worldwide. Specific modifications in the microbial consortia during fermentation control the flavor of coffee. It is still unclear how fermentation duration affects microbial communities. This study aimed to provide insights into the diversity and functional behavior of the bacterial microbiome during coffee fermentation in northern Peru using shotgun metagenomics. Accordingly, metagenomic DNA was extracted and sequenced from samples of the liquid fraction during the short fermentation process (SFP) in Amazonas (6 and 12 h) and long fermentation process (LFP) in Cajamarca (6, 12, 18, 24, and 36 h). Our findings indicate that common (e.g., Acetobacter, Lactobacillus, Leuconostoc, and Weissella) and unique (e.g., Acidiphilium and Methylobacterium) acid-tolerant bacteria from the SFP and LFP play crucial roles and have a positive impact on the sensory qualities of coffee. Specifically, the LFP from San Ignacio might be associated with the high sensory quality of coffee based on the release of catalytic, hydrolase, oxidoreductase, transferase, and transporter enzymes in the InterPro and KEGG profiles. Additionally, these bacterial microorganisms metabolize several compounds (e.g., isoleucine, betaine, galactose, tryptophan, arginine, and cobalamin) into volatile compounds, mainly in the LFP, enhancing the flavor and aroma of coffees. This characteristic suggests that the LFP has a stronger effect on coffee quality than does the SFP on the basis of bacterial diversity and functional prediction. These findings provide new perspectives on the potential biotechnological uses of autochthonous microorganisms to produce superior-quality coffee beans from northern Peru.}, } @article {pmid39635041, year = {2024}, author = {Dora, D and Revisnyei, P and Mihucz, A and Kiraly, P and Szklenarik, G and Dulka, E and Galffy, G and Lohinai, Z}, title = {Metabolic pathways from the gut metatranscriptome are associated with COPD and respiratory function in lung cancer patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1381170}, pmid = {39635041}, issn = {2235-2988}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/metabolism/physiopathology ; *Gastrointestinal Microbiome/genetics ; *Metabolic Networks and Pathways/genetics ; *Lung Neoplasms/microbiology/genetics ; Male ; *Feces/microbiology ; Female ; Aged ; Middle Aged ; Carcinoma, Non-Small-Cell Lung/genetics/microbiology ; Transcriptome ; Metagenomics/methods ; Bacteria/genetics/classification/isolation & purification/metabolism ; Streptococcus/genetics/isolation & purification/metabolism ; }, abstract = {INTRODUCTION: Changes in the human gut microbiome have been linked to various chronic diseases, including chronic obstructive pulmonary disease (COPD). While substantial knowledge is available on the genomic features of fecal communities, little is known about the microbiome's transcriptional activity. Here, we analyzed the metatranscriptomic (MTR) abundance of MetaCyc pathways, SuperPathways, and protein domain families (PFAM) represented by the gut microbiome in a cohort of non-small cell lung cancer (NSCLC) patients with- or without COPD comorbidity.

METHODS: Fecal samples of 40 NSCLC patients with- or without COPD comorbidity were collected at the time of diagnosis. Data was preprocessed using the Metaphlan3/Humann3 pipeline and BioCyc[©] to identify metabolic SuperPathways. LEfSe analysis was conducted on Pathway- and PFAM abundance data to determine COPD- and non-COPD-related clusters.

RESULTS: Key genera Streptococcus, Escherichia, Gemella, and Lactobacillus were significantly more active transcriptionally compared to their metagenomic presence. LEfSe analysis identified 11 MetaCyc pathways that were significantly overrepresented in patients with- and without COPD comorbidity. According to Spearman's rank correlation, Smoking PY showed a significant negative correlation with Glycolysis IV, Purine Ribonucleoside Degradation and Glycogen Biosynthesis I, and a significant positive correlation with Superpathway of Ac-CoA Biosynthesis and Glyoxylate cycle, whereas forced expiratory volume in the first second (FEV1) showed a significant negative correlation with Glycolysis IV and a significant positive correlation with Glycogen Biosynthesis I. Furthermore, COPD patients showed a significantly increased MTR abundance in ~60% of SuperPathways, indicating a universally increased MTR activity in this condition. FEV1 showed a significant correlation with SuperPathways Carbohydrate degradation, Glycan biosynthesis, and Glycolysis. Taxonomic analysis suggested a more prominent MTR activity from multiple Streptococcus species, Enterococcus (E.) faecalis, E. faecium and Escherichia (E.) coli than expected from their metagenomic abundance. Multiple protein domain families (PFAMs) were identified as more associated with COPD, E. faecium, E.coli, and Streptococcus salivarius, contributing the most to these PFAMs.

CONCLUSION: Metatranscriptome analysis identified COPD-related subsets of lung cancer with potential therapeutic relevance.}, } @article {pmid39632378, year = {2024}, author = {Li, Y and Hu, W and Lin, B and Ma, T and Zhang, Z and Hu, W and Zhou, R and Kwok, LY and Sun, Z and Zhu, C and Zhang, H}, title = {Omic characterizing and targeting gut dysbiosis in children with autism spectrum disorder: symptom alleviation through combined probiotic and medium-carbohydrate diet intervention - a pilot study.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2434675}, pmid = {39632378}, issn = {1949-0984}, mesh = {Humans ; *Autism Spectrum Disorder/diet therapy/microbiology ; Pilot Projects ; *Probiotics/administration & dosage ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/diet therapy/therapy ; Male ; Child ; Female ; *Feces/microbiology/chemistry ; Child, Preschool ; Bacteria/classification/isolation & purification/genetics/metabolism ; Dietary Carbohydrates/metabolism/administration & dosage ; Bifidobacterium animalis ; }, abstract = {Autism spectrum disorder (ASD) currently lacks effective diagnostic and therapeutic approaches. Disruptions in the gut ecosystem have been observed in individuals with ASD, suggesting that targeting gut microbiota through probiotic and dietary supplementation may serve as a potential treatment strategy. This two-phase study aimed to characterize the fecal metagenome of children with ASD and investigate the beneficial effects of a combined probiotic and medium-carbohydrate intervention in ASD. Fecal metagenomes of children with ASD were compared to those of typically developing children, revealing intestinal dysbiosis in ASD, characterized by reduced levels of Prevotella sp. Dialister invisus, and Bacteroides sp. along with increased predicted abundances of inosine, glutamate, xanthine, and methylxanthine. The gut bacteriome and phageome exhibited high cooperativity. In a 3-month pilot study, Bifidobacterium animalis subsp. lactis Probio-M8 (Probio-M8) was administered alongside a medium-carbohydrate diet to Chinese children with ASD. The primary endpoint was the Childhood Autism Rating Scale (CARS), while the secondary endpoint was the Gastrointestinal Symptom Rating Scale (GSRS). A total of 72 autistic children were initially recruited for the intervention study, but only 53 completed the intervention. Probio-M8, in combination with dietary intervention, significantly improved CARS and GSRS scores, increased fecal levels of Bifidobacterium animalis, Akkermansia muciniphila, Fusicatenibacter saccharivorans, and Sutterella sp. while also reducing Blautia obeum (Benjamini-Hochberg corrected p ≤ 0.05 for all cases). The intervention also modulated fecal metabolites associated with the metabolism of amino acids (lysine), neurotransmitters (glutamate, γ-aminobutyric acid), polyunsaturated fatty acids (arachidonate, myristic acid), and vitamin B3. In conclusion, Probio-M8 combined with medium-carbohydrate diet effectively improved ASD symptoms, with associated changes in the gut microbiome and metabolome, supporting its potential as an adjunctive therapy for ASD.}, } @article {pmid39631543, year = {2024}, author = {Qu, M and Zheng, Y and Cheng, Z and Shi, Y and Wang, W and Wu, X and Chen, J}, title = {Mechanism of chlorobenzene removal in biotrickling filter enhanced by non-thermal plasma: Insights from biodiversity and functional gene perspectives.}, journal = {Bioresource technology}, volume = {418}, number = {}, pages = {131931}, doi = {10.1016/j.biortech.2024.131931}, pmid = {39631543}, issn = {1873-2976}, abstract = {Biotrickling filter (BTF) technology is inefficient in the treatment of Cl-containing volatile organic compounds (VOCs) such as chlorobenzene (CB). This study adopted non-thermal plasma (NTP) as a pretreatment and conducted in-depth analyses, especially in microorganisms, to investigate strengthening mechanism of a NTP to a BTF in the process. The introduction of NTP enhance efficiency of CB removal from 65 % to 90 %, and CO2 generation from 60 % to 85 %. It is found that the protein content of the extracellular polymeric substances increases from 212 × 10[-3] mg·g[-1] filler to 299 × 10[-3] mg·g[-1] filler, thus CB capturing and utilization enhanced. Metagenomic analysis showed that bacteria with CB-degrading properties were enriched in BTF, and CB was involved in cellular metabolism as a carbon source. The presence of active substances from NTP is found to stimulate the ability of BTF treatment. The findings of this study will provide theoretical support for the application of NTP-BTF technology.}, } @article {pmid39630952, year = {2024}, author = {Gao, F and Shen, Y and Wu, H and Laue, HE and Lau, FK and Gillet, V and Lai, Y and Shrubsole, MJ and Prada, D and Zhang, W and Liu, Z and Bellenger, JP and Takser, L and Baccarelli, AA}, title = {Associations of Stool Metal Exposures with Childhood Gut Microbiome Multiomics Profiles in a Prospective Birth Cohort Study.}, journal = {Environmental science & technology}, volume = {58}, number = {50}, pages = {22053-22063}, doi = {10.1021/acs.est.4c09642}, pmid = {39630952}, issn = {1520-5851}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Child ; *Metals ; Prospective Studies ; Female ; Male ; Birth Cohort ; Environmental Exposure ; Multiomics ; }, abstract = {Metal exposures are closely related to childhood developmental health. However, their effects on the childhood gut microbiome, which also impacts health, are largely unexplored using microbiome multiomics including the metagenome and metatranscriptome. This study examined the associations of fecal profiles of metal/element exposures with gut microbiome species and active functional pathways in 8- to 12-year-old children (N = 116) participating in the GESTation and Environment (GESTE) cohort study. We analyzed 19 stool metal and element concentrations (B, Na, Mg, Al, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Mo, Cd, Ba, and Pb). Covariate-adjusted linear regression models identified several significant microbiome associations with continuous stool metal/element concentrations. For instance, Zn was positively associated with Turicibacter sanguinis (coef = 1.354, q-value = 0.039) and negatively associated with Eubacterium eligens (coef = -0.794, q-value = 0.044). Higher concentrations of Cd were associated with lower Eubacterium eligens (coef = -0.774, q-value = 0.045). Additionally, a total of 490 significant functional pathways such as biosynthesis and degradation/utilization/assimilation were identified, corresponding to different functions, including amino acid synthesis and carbohydrate degradation. Our results suggest links among metal exposures, pediatric gut microbiome multiomics, and potential health implications. Future work will further explore their relation to childhood health.}, } @article {pmid39629792, year = {2024}, author = {González-García, S and Hamdan-Partida, A and Pérez-Ramos, J and Aguirre-Garrido, JF and Bustos-Hamdan, A and Bustos-Martínez, J}, title = {Comparison of the bacterial microbiome in the pharynx and nasal cavity of persistent, intermittent carriers and non-carriers of Staphylococcus aureus.}, journal = {Journal of medical microbiology}, volume = {73}, number = {12}, pages = {}, pmid = {39629792}, issn = {1473-5644}, mesh = {Humans ; *Pharynx/microbiology ; *Staphylococcus aureus/isolation & purification/genetics ; *Carrier State/microbiology ; *Nasal Cavity/microbiology ; *Microbiota ; *Staphylococcal Infections/microbiology ; Male ; Female ; Adult ; Young Adult ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; }, abstract = {Introduction. Staphylococcus aureus is a bacterium that colonizes various human sites. The pharynx has been considered as a site of little clinical relevance and little studied. Recently, it has been reported that S. aureus can colonize more the pharynx than the nose. In addition, S. aureus can persist in these sites for prolonged periods of time.Hypothesis. The composition of the pharyngeal and nasal microbiome will differ between persistent, intermittent carriers and non-carriers of S. aureus.Aim. Determine whether the pharyngeal and nasal microbiome is different between carriers and non-carriers of S. aureus.Methodology. S. aureus carriers were monitored by means of pharyngeal and nasal exudates of apparently healthy adult university students for 3 months. Samples from individuals of the same carrier type were pooled, and DNA was extracted and the 16S rRNA was sequenced. The sequences were analysed in MOTHUR v.1.48.0 software, by analysing the percentages of relative abundance in the STAMP 2.1.3 program, in addition to the predictive analysis of metabolic pathways in PICRUSt2.Results. A greater colonization of S. aureus was found in the pharynx than in the nose. The microbiomes of S. aureus carriers and non-carriers do not show significant differences. The main microbiome difference found was between pharyngeal and nasal microbiomes. No significant differences were found in the abundance of the genus Staphylococcus in pharyngeal and nasal S. aureus carriers and non-carriers. The nasal microbiome was found to have more variation compared to the pharyngeal microbiome, which appears to be more stable between individuals and pools. Predictive analysis of metabolic pathways showed a greater presence of Staphylococcus-associated pathways in the nose than in the pharynx.Conclusion. S. aureus can colonize and persist in the pharynx in equal or greater proportion than in the nose. No statistically significant differences were found in the microbiome of the pharyngeal and nasal carriers and non-carriers of S. aureus, but the pharyngeal and nasal microbiomes are different independent of the type of S. aureus carrier or non-carrier. Therefore, the microbiome apparently does not influence the persistence of S. aureus.}, } @article {pmid39629129, year = {2024}, author = {Zhao, Q and Lu, Y and Duan, J and Du, D and Pu, Q and Li, F}, title = {Gut microbiota depletion and FXR inhibition exacerbates zonal hepatotoxicity of sunitinib.}, journal = {Theranostics}, volume = {14}, number = {18}, pages = {7219-7240}, pmid = {39629129}, issn = {1838-7640}, mesh = {Animals ; *Sunitinib/toxicity ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Chemical and Drug Induced Liver Injury/pathology/etiology ; *Liver/drug effects/pathology ; *Mice, Knockout ; *Receptors, Cytoplasmic and Nuclear/metabolism ; Male ; Hepatocytes/drug effects ; Mice, Inbred C57BL ; Endothelial Cells/drug effects ; Apoptosis/drug effects ; Bacteroidetes/drug effects ; Autophagy/drug effects ; }, abstract = {Rationale: Sunitinib is a small-molecule tyrosine kinase inhibitor associated with the side-effect of liver injury. The impaired cell type in liver and the hepatotoxicity mechanisms is still unclear. Methods: Spatial metabolomics, transmission electron microscopy, immunofluorescence co-staining, and isolation of bile duct cells and liver sinusoidal endothelial cells (LSECs) were used to evaluate the zonated hepatotoxicity of sunitinib. Farnesoid X receptor (FXR) conditional knockout mice, metagenomics analysis, bacteria clearance, bacterial culture, Parabacteroides distasonis and 3-oxolithocholic acid supplementation were used to evaluate the hepatotoxicity mechanisms of sunitinib. Results: Phenotype analysis found that hepatic autophagy, apoptosis, and mitochondrial injury were observed in vivo or in vitro after sunitinib treatment. By using spatial metabolomics and isolation of bile duct cells and LSECs, the zonated drug toxicity was observed around the portal vein. Hepatocytes, bile duct cells, and LSECs were damaged after sunitinib treatment. FXR inhibition and gut microbiota depletion aggravated sunitinib-induced liver injury. For diurnal variation, sunitinib-induced liver injury was enhanced at night compared with that at day, and FXR and gut microbiota participated in circadian rhythmic hepatotoxicity induced by sunitinib. Conclusions: Our data suggested activation of FXR and Parabacteroides distasonis supplementation may be used to improve sunitinib-induced hepatotoxicity.}, } @article {pmid39628196, year = {2024}, author = {Li, ZX and Li, JH and Zhang, Q and Lu, JJ and Gao, CH and Jin, DS and Xu, MG}, title = {[Response and Assembly Process of Soil Microbial Communities Under Different Reclamation Measures].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {45}, number = {12}, pages = {7326-7336}, doi = {10.13227/j.hjkx.202312247}, pmid = {39628196}, issn = {0250-3301}, mesh = {*Soil Microbiology ; *Fungi/classification ; *Bacteria/classification/genetics/growth & development/isolation & purification ; Mining ; Nitrogen ; Soil/chemistry ; Phosphorus ; Environmental Restoration and Remediation/methods ; Microbiota ; Ecosystem ; }, abstract = {Reclamation is essential for restoring the ecological function of soil in mining areas. However, the microbiological mechanism of soil ecological function reconstruction under different reclamation measures still needs to be clarified. Clarifying the characteristics of soil bacterial and fungal communities, assembly mechanisms, and their relationship with physicochemical properties under different reclamation measures is crucial for reshaping the ecological stability of soil in mining areas. Metagenomic sequencing technology was combined with the null model and neutral model to analyze the differences in soil microbial diversity, community composition, network structure, and community assembly process between the reclaimed natural recovery area （LH） and the reclamation fertilization area （MM）. The results suggested that： ① Compared with that in the LH treatment, the MM treatment significantly increased the soil nutrient content, and the total nitrogen （TN）, total phosphorus （TP）, available phosphorus （AP）, and available potassium （AK） contents increased by 34.70%, 72.72%, 468.98%, and 45.74%, respectively （P<0.05）. ② The dominant bacterial and fungal communities did not change under the LH and MM treatments； however, the abundance of bacterial communities changed significantly. Compared with that in the LH treatment, the relative abundance of Acidobacteria increased significantly by 5.4% in the MM treatment, while the relative abundance of Candidatus Rokubacteria decreased significantly by 235.72% （P<0.05）. Under different reclamation measures, the indicator microorganisms of bacterial and fungal communities changed. ③ Compared with that in the LH treatment, the MM treatment increased the complexity of bacterial networks, decreased the complexity of fungal networks, and increased the number of soil bacterial nodes and links. The reclamation measures transformed the key bacterial groups from Proteobacteria to Candidatus Rokubacteria and Planctomycetes. The key group of fungi was Ascomycota. 4.） The deterministic process dominated the assembly of bacterial and fungal communities. Homogeneous selection contributed the most to the bacterial community assembly in the LH treatment, and heterogeneous selection contributed the most to the MM treatment. The fungal communities were all dominated by heterogeneous selection. These results provide new insights into the soil microbial community structure and ecological function restoration in coal mining subsidence reclamation areas.}, } @article {pmid39626557, year = {2025}, author = {Peng, Q and Cheng, S and Huang, X and Pu, Y and Xie, G}, title = {Comprehensive multi-omics analysis of fermented Chinese artichoke: Insights from Flavoromics, metagenomics, and untargeted metabolomics.}, journal = {Food chemistry}, volume = {467}, number = {}, pages = {142278}, doi = {10.1016/j.foodchem.2024.142278}, pmid = {39626557}, issn = {1873-7072}, mesh = {*Fermentation ; *Metabolomics ; *Metagenomics ; *Flavoring Agents/metabolism/chemistry ; *Volatile Organic Compounds/metabolism/chemistry/analysis ; *Taste ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Cynara scolymus/chemistry/metabolism ; Microbiota ; Fermented Foods/analysis/microbiology ; Multiomics ; East Asian People ; }, abstract = {Fermented Chinese Artichoke, a traditional Chinese fermented vegetable, has a distinctive flavor profile shaped by its fermentation process. This study applied flavoromics, metagenomics, and untargeted metabolomics to comprehensively analyze flavor compounds, microbial communities, and metabolic transformations during fermentation. We identified 43 volatile organic compounds (VOCs), with Terpineol, 1-Hexanol, and Linalool as the predominant components. Metagenomic analysis highlighted Lactiplantibacillus plantarum, Priestia megaterium, and Pediococcus pentosaceus as the dominant species, while Lactiplantibacillus, Pediococcus, and Bacillus were key in flavor development. Untargeted metabolomics further revealed increases in organic acids, amino acids, and umami compounds, contributing to flavor enhancement. These findings offer valuable insights into flavor formation mechanisms in Fermented Chinese Artichoke and provide guidance for improving its industrial fermentation quality.}, } @article {pmid39626551, year = {2025}, author = {Xu, C and Han, A and Tian, Y and Sun, S}, title = {Based on computer simulation and experimental verification: mining and characterizing novel antimicrobial peptides from soil microbiome.}, journal = {Food chemistry}, volume = {467}, number = {}, pages = {142275}, doi = {10.1016/j.foodchem.2024.142275}, pmid = {39626551}, issn = {1873-7072}, mesh = {*Soil Microbiology ; *Antimicrobial Peptides/chemistry/pharmacology ; Microbiota ; Anti-Bacterial Agents/pharmacology/chemistry ; Computer Simulation ; Microbial Sensitivity Tests ; Klebsiella pneumoniae/drug effects ; Staphylococcus aureus/drug effects/growth & development ; Molecular Docking Simulation ; Escherichia coli/drug effects/genetics ; Bacteria/drug effects/genetics ; Molecular Dynamics Simulation ; }, abstract = {Antimicrobial peptides (AMPs) show great promise for enhancing food safety and extending shelf life, but traditional screening methods are complex and costly. To address these issues, we developed a deep learning-based prediction pipeline to identify potential AMPs from soil metagenomic data, achieving high accuracy (92.71 %) and precision (91.29 %). Based on model scoring, surface charge, and Hemopred and ToxinPred screenings, we identified nine candidate peptides. Peptide P4 (GTAWRWHYRARS) showed the best binding affinity to MrkH in molecular docking studies and was validated through molecular dynamics simulations. The chemically synthesized P4 demonstrated significant antimicrobial activity against Klebsiella pneumoniae, Escherichia coli, and Staphylococcus aureus, indicating its potential as an effective alternative to traditional food antimicrobial agents. This study highlights the effectiveness of our integrated prediction pipeline for discovering new AMPs.}, } @article {pmid39626421, year = {2024}, author = {Wang, J and Wu, D and Wu, Q and Chen, J and Zhao, Y and Wang, H and Liu, F and Yuan, Q}, title = {Vertical profiles of community and activity of methanotrophs in large lake and reservoir of Southwest China.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177782}, doi = {10.1016/j.scitotenv.2024.177782}, pmid = {39626421}, issn = {1879-1026}, mesh = {China ; *Lakes/microbiology/chemistry ; *Methane/metabolism/analysis ; *Geologic Sediments/microbiology/chemistry ; Methylococcaceae/genetics/metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S ; Environmental Monitoring ; Microbiota ; }, abstract = {Microbial methane oxidation plays a significant role in regulating methane emissions from lakes and reservoirs. However, the differences in methane oxidation activity and methanotrophic community between lakes and reservoirs remain inadequately characterized. In this study, sediment and water samples were collected from the large shallow lake (Dianchi) and deep reservoirs (Dongfeng and Hongjiadu) located in karst area, Southwest China. The results indicated that the rates of aerobic oxidation of methane (AeOM) in lake sediment ranged from 7.1 to 27.7 μg g[-1] d[-1], which was higher than that in reservoirs sediment (1.92 to 11.56 μg g[-1] d[-1]). Similarly, the average AeOM in the water column of lake (104.7 μg L[-1] d[-1]) was much higher than that of reservoirs (46 μg L[-1] d[-1]). The content of sediment organic carbon and dissolved inorganic carbon were important factors that influenced the rates of AeOM in sediment and water column, respectively. 16S rRNA genes sequencing revealed a higher relative abundance of methanotrophs in lake sediments compared to reservoir sediments. The dominant methanotrophic taxa in lake was Methylococcaceae (type Ib), while Methylomonadaceae (type Ia) was predominant in reservoirs. Meanwhile, anaerobic methane-oxidizing microorganisms Candidatus Methylomirabilis and Candidatus Methanoperedens were also abundant in sediments of reservoirs. However, metatranscriptomic analysis revealed that the type I methanotrophs, especially Methylobacter, was most active in the sediment of both lake and reservoir. Water depth and conductivity could be the key controlling factors of the structures of methanotrophic communities in sediment and water column, respectively. Metagenome-assembled genomes suggested that type I methanotrophs exhibited greater motility, as evidenced by a higher number of flagellar assembly genes, while type II methanotrophs demonstrated advantages in metabolic processes such as carbon, phosphorus, and methane metabolism.}, } @article {pmid39625614, year = {2024}, author = {Saeng-Kla, K and Mhuantong, W and Termsaithong, T and Pinyakong, O and Sonthiphand, P}, title = {Biodegradation of Di-2-Ethylhexyl Phthalate by Mangrove Sediment Microbiome Impacted by Chronic Plastic Waste.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {27}, number = {1}, pages = {19}, pmid = {39625614}, issn = {1436-2236}, support = {FF-072/2567//Mahidol University (Fundamental Fund: fiscal year 2024 by National Science Research and Innovation Fund (NSRF)/ ; }, mesh = {*Diethylhexyl Phthalate/metabolism ; *Geologic Sediments/microbiology ; *Biodegradation, Environmental ; *Microbiota ; Water Pollutants, Chemical/metabolism ; Plastics/metabolism ; Gordonia Bacterium/metabolism/genetics ; Plasticizers/metabolism ; Wetlands ; Bacteria/metabolism/classification/genetics/isolation & purification ; }, abstract = {Plastic pollution through the leaching of di(2-ethylhexyl) phthalate (DEHP), a widely used plasticizer, has led to the emergence of mangrove pollution. This study aimed to assess the DEHP removal efficiency of indigenous mangrove sediment microbiomes and identify key DEHP degraders using microcosm construction and metagenomic analysis. During the 35-day incubation period, the indigenous mangrove sediment microbiome, affected by chronic plastic pollution, demonstrated a 99% degradation efficiency of 200 mg/kg DEHP. Spearman's correlation analysis suggested that Myxococcales, Methyloligellaceae, Mycobacterium, and Micromonospora were potentially responsible for DEHP degradation. Based on PICRUSt2, the DEHP-degrading pathway in the sediment was predicted to be an anaerobic process involving catechol metabolism through catC, pcaD, pcaI, pcaF, and fadA. Efficient bacterial isolates from the mangrove sediment, identified as Gordonia sp. and Gordonia polyisoprenivorans, were able to degrade DEHP (65-97%) within 7 days and showed the ability to degrade other phthalate esters (PAEs).}, } @article {pmid39623529, year = {2024}, author = {Ma, J and Sun, S and Cheng, X and Meng, C and Zhao, H and Fu, W and Gao, Y and Ma, L and Yang, Z and Yao, H and Su, J}, title = {Unraveling the role of gut microbiome in predicting adverse events in neoadjuvant therapy for rectal cancer.}, journal = {Human vaccines & immunotherapeutics}, volume = {20}, number = {1}, pages = {2430087}, pmid = {39623529}, issn = {2164-554X}, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Chemoradiotherapy/adverse effects/methods ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Immunotherapy/methods/adverse effects ; Metabolome ; Metabolomics ; Metagenomics/methods ; *Neoadjuvant Therapy/adverse effects/methods ; *Rectal Neoplasms/therapy/microbiology ; }, abstract = {Some patients may develop adverse events during neoadjuvant chemoradiotherapy combined with immunotherapy, influencing response rates. The roles of intestinal microbiome and its metabolites in therapeutic adverse events remain unclear. We collected baseline fecal samples from 21 patients with adverse events (AE group) and 11 patients without adverse events (Non-AE group). Their microbiota and metabolome were characterized using metagenomic shotgun sequencing and untargeted metabolomics. At the species level, the gut microbiota in the Non-AE group exhibits significantly higher abundance of Clostridium sp. Alistipes sp. and lower abundance of Lachnoclostridium sp. Weissella cibaria, Weissella confusa, compared to the AE group (p < .05). A total of 58 discriminative metabolites were identified between groups. Beta-alanine metabolism was scattered. Boc-beta-cyano-L-alanine and CoQ9 were significantly increased in patients without adverse events, while linoleic acid increased in patients with adverse events. The increased Alistipes sp. in the Non-AE group was positively correlated with Boc-beta-cyano-L-alanine and negatively correlated with linoleic acid (p < .05). We constructed a combined microbiome-metabolite model to distinguish Non-AE and AE patients with an AUC of 0.963 via the random forest algorithm. Our findings provided a novel insight into the interplay of multispecies microbial cluster and metabolites of rectal patients with adverse events in neoadjuvant chemoradiotherapy combined with immunotherapy. These microbiota and metabolites deserve further investigations to reveal their roles in adverse events, providing clues for better treatment scenarios.Trial registration number: ClinicalTrials.gov identifier: NCT05368051.}, } @article {pmid39621710, year = {2024}, author = {Mangoma, N and Zhou, N and Ncube, T}, title = {Metagenome-assembled genomes provide insight into the microbial taxonomy and ecology of the Buhera soda pans, Zimbabwe.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0299620}, pmid = {39621710}, issn = {1932-6203}, mesh = {Zimbabwe ; *Metagenome ; *Phylogeny ; Metagenomics/methods ; Bacteria/genetics/classification ; Genome, Bacterial ; Ecosystem ; Microbiota/genetics ; Extreme Environments ; }, abstract = {The use of metagenomics has substantially improved our understanding of the taxonomy, phylogeny and ecology of extreme environment microbiomes. Advances in bioinformatics now permit the reconstruction of almost intact microbial genomes, called metagenome-assembled genomes (MAGs), from metagenomic sequence data, allowing for more precise cell-level taxonomic, phylogenetic and functional profiling of uncultured extremophiles. Here, we report on the recovery and characterisation of metagenome-assembled genomes from the Buhera soda pans located in eastern Zimbabwe. This ecosystem has not been studied despite its unique geochemistry and potential as a habitat for unique microorganisms. Metagenomic DNA from the soda pan was sequenced using the DNA Nanoball Sequencing (DNBSEQR) technique. Sequence analysis, done on the Knowledgebase (KBase) platform, involved quality assessment, read assembly, contig binning, and MAG extraction. The MAGs were subjected to taxonomic placement, phylogenetic profiling and functional annotation in order to establish their possible ecological roles in the soda pan ecosystem. A total of 16 bacterial MAGs of medium to high quality were recovered, all distributed among five phyla dominated by Pseudomonadota and Bacillota. Of the ten MAGs that were taxonomically classified up to genus level, five of them belonged to the halophilic/ haloalkaliphilic genera Alkalibacterium, Vibrio, Thioalkalivibrio, Cecembia and Nitrincola, underscoring the importance of haloalkaliphiles in the Buhera soda pans. Functional profiling revealed the possession of diverse carbohydrate-metabolising pathways by the MAGs, with glycolysis and the pentose phosphate pathways appearing to be key pathways in this ecosystem. Several MAGs possessed pathways that implicated them in some key aspects of the nitrogen and sulphur cycle. Some MAGs harboured both sulphate reduction and respiratory pathways, suggesting a possible mechanism of ATP biosynthesis through sulphate respiration. This study demonstrates the feasibility of the recovery and taxonomic and functional annotation of high quality microbial genomes from extreme environments, making it possible to establish the ecological roles and biotechnological potential of uncultured microorganisms.}, } @article {pmid39621607, year = {2024}, author = {Deel, HL and Manter, DK and Moore, JM}, title = {Rethreading the needle: A novel molecular index of soil health (MISH) using microbial functional genes to predict soil health management.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0314072}, pmid = {39621607}, issn = {1932-6203}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *RNA, Ribosomal, 16S/genetics ; Metagenome ; Bacteria/genetics/classification/isolation & purification ; Microbiota/genetics ; Machine Learning ; Ecosystem ; Genes, Microbial ; }, abstract = {Soil health relies on the actions and interactions of an abundant and diverse biological community. Current soil health assessments rely heavily on a suite of soil biological, chemical, and physical indicators, often excluding molecular information. Soil health is critical for sustainable agricultural production, and a comprehensive understanding of how microbial communities provide ecosystem services can help guide management practices. To explore the role of microbial function in soil health, 536 soil samples were collected from 26 U.S. states, representing 52 different crops and grazing lands, and analyzed for various soil health indicators. The bacterial functional profile was characterized using 16S ribosomal RNA gene sequencing paired with PICRUSt2 to predict metagenome functions. Functional data were used as predictors in eXtreme Gradient Boosting (XGBoost), a powerful machine learning algorithm, and enzymes important to soil health indicators were compiled into a Molecular Index of Soil Health (MISH). The overall MISH score significantly correlated with non-molecular measures of soil health and management practice adoption. Additionally, several new enzymes were identified as potential targets to better understand microbial mediation of soil health. This low-cost, DNA-based approach to measuring soil health is robust and generalizable across climates.}, } @article {pmid39621089, year = {2024}, author = {Singh, K and Gupta, JK and Chanchal, DK and Shinde, MG and Kumar, S and Jain, D and Almarhoon, ZM and Alshahrani, AM and Calina, D and Sharifi-Rad, J and Tripathi, A}, title = {Natural products as drug leads: exploring their potential in drug discovery and development.}, journal = {Naunyn-Schmiedeberg's archives of pharmacology}, volume = {}, number = {}, pages = {}, pmid = {39621089}, issn = {1432-1912}, abstract = {Natural products have been pivotal in drug discovery, offering a wealth of bioactive compounds that significantly contribute to therapeutic developments. Despite the rise of synthetic chemistry, natural products continue to play a crucial role due to their unique chemical structures and diverse biological activities. This study reviews and evaluates the potential of natural products in drug discovery and development, emphasizing the integration of traditional knowledge with modern drug discovery methodologies and addressing the associated challenges. A comprehensive literature search was conducted across PubMed/MedLine, Scopus, Web of Science, Google Scholar, and Cochrane Library, covering publications from 2000 to 2023. Inclusion criteria focused on studies related to natural products, bioactive compounds, medicinal plants, phytochemistry, and AI applications in drug discovery. Data were categorized into source, extraction methods, bioactivity assays, and technological advances. The current review underscores the historical and ongoing importance of natural products in drug discovery. Technological advancements in chromatographic and spectroscopic techniques have improved the isolation and structural elucidation of bioactive compounds. AI and machine learning have streamlined the identification and optimization of natural product leads. Challenges such as biodiversity sustainability and development complexities are discussed, alongside innovative approaches like biosynthetic engineering and metagenomics. Natural products remain a vital source of novel therapeutic agents, providing unique chemical diversity and specific biological activities. Integrating traditional knowledge with modern scientific methods is essential for maximizing the potential of natural products in drug discovery. Despite existing challenges, ongoing research and technological advancements are expected to enhance the efficiency and success of natural product-based drug development.}, } @article {pmid39620486, year = {2024}, author = {Luo, Y and Sheikh, TMM and Li, X and Yuan, Y and Yao, F and Wang, M and Guo, X and Wu, J and Shafiq, M and Xie, Q and Jiao, X}, title = {Exploring the dynamics of gut microbiota, antibiotic resistance, and chemotherapy impact in acute leukemia patients: A comprehensive metagenomic analysis.}, journal = {Virulence}, volume = {15}, number = {1}, pages = {2428843}, pmid = {39620486}, issn = {2150-5608}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Metagenomics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Male ; Female ; Adult ; Middle Aged ; Feces/microbiology ; Bacteria/genetics/drug effects/classification/isolation & purification ; Leukemia/drug therapy/microbiology/complications ; Drug Resistance, Microbial/genetics ; Aged ; Young Adult ; Antineoplastic Agents/adverse effects ; }, abstract = {Leukemia poses significant challenges to its treatment, and understanding its complex pathogenesis is crucial. This study used metagenomic sequencing to investigate the interplay between chemotherapy, gut microbiota, and antibiotic resistance in patients with acute leukemia (AL). Pre- and post-chemotherapy stool samples from patients revealed alterations in microbial richness, taxa, and antibiotic resistance genes (ARGs). The analysis revealed a decreased alpha diversity, increased dispersion in post-chemotherapy samples, and changes in the abundance of specific bacteria. Key bacteria such as Enterococcus, Klebsiella, and Escherichia coli have been identified as prevalent ARG carriers. Correlation analysis between gut microbiota and blood indicators revealed potential links between microbial species and inflammatory biomarkers, including C-reactive protein (CRP) and adenosine deaminase (ADA). This study investigated the impact of antibiotic dosage on microbiota and ARGs, revealing networks connecting co-occurring ARGs with microbial species (179 nodes, 206 edges), and networks associated with ARGs and antibiotic dosages (50 nodes, 50 edges). Antibiotics such as cephamycin and sulfonamide led to multidrug-resistant Klebsiella colonization. Our analyses revealed distinct microbial profiles with Salmonella enterica elevated post-chemotherapy in NF patients and Akkermansia muciniphila elevated pre-chemotherapy. These microbial signatures could inform strategies to modulate the gut microbiome, potentially mitigating the risk of neutropenic fever in patients undergoing chemotherapy. Finally, a comprehensive analysis of KEGG modules shed light on disrupted metabolic pathways after chemotherapy, providing insights into potential targets for managing side effects. Overall, this study revealed intricate relationships between gut microbiota, chemotherapy, and antibiotic resistance, providing new insights into improving therapy and enhancing patient outcomes.}, } @article {pmid39620359, year = {2024}, author = {López-Agudelo, VA and Falk-Paulsen, M and Bharti, R and Rehman, A and Sommer, F and Wacker, EM and Ellinghaus, D and Luzius, A and Sievers, LK and Liebeke, M and Kaser, A and Rosenstiel, P}, title = {Defective Atg16l1 in intestinal epithelial cells links to altered fecal microbiota and metabolic shifts during pregnancy in mice.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2429267}, pmid = {39620359}, issn = {1949-0984}, mesh = {Animals ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; Mice ; *Feces/microbiology ; *Autophagy-Related Proteins/genetics/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Intestinal Mucosa/microbiology/metabolism ; Epithelial Cells/microbiology/metabolism ; Crohn Disease/microbiology/metabolism ; Mice, Inbred C57BL ; Metagenomics ; Chemokine CXCL1/genetics/metabolism ; }, abstract = {Throughout gestation, the female body undergoes a series of transformations, including profound alterations in intestinal microbial communities. Changes gradually increase toward the end of pregnancy and comprise reduced α-diversity of microbial communities and an increased propensity for energy harvest. Despite the importance of the intestinal microbiota for the pathophysiology of inflammatory bowel diseases, very little is known about the relationship between these microbiota shifts and pregnancy-associated complications of the disease. Here, we explored the longitudinal dynamics of gut microbiota composition and functional potential during pregnancy and after lactation in Atg16l1[∆IEC] mice carrying an intestinal epithelial deletion of the Crohn's disease risk gene Atg16l1. Using 16S rRNA amplicon and shotgun metagenomic sequencing, we demonstrated divergent temporal shifts in microbial composition between Atg16l1 wildtype and Atg16l1[∆IEC] pregnant mice in trimester 3, which was validated in an independent experiment. Observed differences included microbial genera implicated in IBD such as Lachnospiraceae, Roseburia, Ruminococcus, and Turicibacter. Changes partially recovered after lactation. Additionally, metagenomic and metabolomic analyses suggest an increased capacity for chitin degradation, resulting in higher levels of free N-acetyl-glucosamine products in feces, alongside reduced glucose and myo-inositol levels in serum around the time of delivery. On the host side, we found that the immunological response of Atg16l1[∆IEC] mice is characterized by higher colonic mRNA levels of TNFα and CXCL1 in trimester 3 and a lower weight of offspring at birth. Understanding pregnancy-dependent microbiome changes in the context of IBD may constitute the first step in the identification of fecal microbial biomarkers and microbiota-directed therapies that could help improve precision care for managing pregnancies in IBD patients.}, } @article {pmid39619205, year = {2024}, author = {Hewson, I and Brandt, M and Budd, K and Breitbart, M and DeRito, C and Gittens, S and Henson, MW and Hylkema, A and Sevier, M and Souza, M and Vilanova-Cuevas, B and Von Hoene, S}, title = {Viral metagenomic investigation of two Caribbean echinoderms, Diadema antillarum (Echinoidea) and Holothuria floridana (Holothuria).}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18321}, pmid = {39619205}, issn = {2167-8359}, mesh = {Animals ; *Metagenomics ; Caribbean Region ; *Genome, Viral/genetics ; Echinodermata/virology ; Metagenome ; Holothuria/virology/genetics ; Coral Reefs ; Viruses/genetics/isolation & purification/classification ; Virome/genetics ; }, abstract = {BACKGROUND: Echinoderms play crucial roles in coral reef ecosystems, where they are significant detritivores and herbivores. The phylum is widely known for its boom and bust cycles, driven by food availability, predation pressure and mass mortalities. Hence, surveillance of potential pathogens and associates of grossly normal specimens is important to understanding their roles in ecology and mass mortality.

METHODS: We performed viral surveillance in two common coral reef echinoderms, Diadema antillarum and Holothuria floridana, using metagenomics. Urchin specimens were obtained during the 2022 Diadema antillarum scuticociliatosis mass mortality event from the Caribbean and grossly normal H. floridana specimens from a reef in Florida. Viral metagenomes were assembled and aligned against viral genomes and protein encoding regions. Metagenomic reads and previously sequenced transcriptomes were further investigated for putative viral elements by Kraken2.

RESULTS: D. antillarum was devoid of viruses typically seen in echinoderms, but H. floridana yielded viral taxa similar to those found in other sea cucumbers, including Pisoniviricetes (Picornaviruses), Ellioviricetes (Bunyaviruses), and Magsaviricetes (Nodaviruses). The lack of viruses detected in D. antillarum may be due to the large amount of host DNA in viral metagenomes, or because viruses are less abundant in D. antillarum tissues when compared to H. floridana tissues. Our results also suggest that RNA amplification approach may influence viral representation in viral metagenomes. While our survey was successful in describing viruses associated with both echinoderms, our results indicate that viruses are less pronounced in D. antillarum than in other echinoderms. These results are important in context of wider investigation on the association between viruses and D. antillarum mass mortalities, since the conventional method used in this study was unsuccessful.}, } @article {pmid39616358, year = {2024}, author = {Dell'Olio, A and Scott, WT and Taroncher-Ferrer, S and San Onofre, N and Soriano, JM and Rubert, J}, title = {Tailored impact of dietary fibers on gut microbiota: a multi-omics comparison on the lean and obese microbial communities.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {250}, pmid = {39616358}, issn = {2049-2618}, support = {79441//'European Union's Horizon 2020 Research and Innovation programme' for the Marie Skłodowska-Curie/ ; RYC2018-024850-I//Spanish Ministry of Science and Innovation for the Ramón y Cajal fellowship/ ; }, mesh = {*Dietary Fiber/metabolism ; *Obesity/microbiology ; *Gastrointestinal Microbiome ; *Malus/microbiology ; Humans ; Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics ; Pectins/metabolism ; Metabolomics ; Cellulose/metabolism ; Bioreactors/microbiology ; Multiomics ; }, abstract = {BACKGROUND: Previous studies have shown that microbial communities differ in obese and lean individuals, and dietary fiber can help reduce obesity-related conditions through diet-gut microbiota interactions. However, the mechanisms by which dietary fibers shape the gut microbiota still need to be elucidated. In this in vitro study, we examined how apple fibers affect lean and obese microbial communities on a global scale. We employed a high-throughput micro-matrix bioreactor system and a multi-omics approach to identify the key microorganisms and metabolites involved in this process.

RESULTS: Initially, metagenomics and metabolomics data indicated that obese and lean microbial communities had distinct starting microbial communities. We found that obese microbial community had different characteristics, including higher levels of Ruminococcus bromii and lower levels of Faecalibacterium prausnitzii, along with an increased Firmicutes:Bacteroides ratio. Afterward, we exposed obese and lean microbial communities to an apple as a representative complex food matrix, apple pectin as a soluble fiber, and cellulose as an insoluble fiber. Dietary fibers, particularly apple pectin, reduced Acidaminococcus intestini and boosted Megasphaera and Akkermansia in the obese microbial community. Additionally, these fibers altered the production of metabolites, increasing beneficial indole microbial metabolites. Our results underscored the ability of apple and apple pectin to shape the obese gut microbiota.

CONCLUSION: We found that the obese microbial community had higher branched-chain amino acid catabolism and hexanoic acid production, potentially impacting energy balance. Apple dietary fibers, especially pectin, influenced the obese microbial community, altering both species and metabolites. Notably, the apple pectin feeding condition affected species like Klebsiella pneumoniae and Bifidobacterium longum. By using genome-scale metabolic modeling, we discovered a mutualistic cross-feeding relationship between Megasphaera sp. MJR8396C and Bifidobacterium adolescentis. This in vitro study suggests that incorporating apple fibers into the diets of obese individuals can help modify the composition of gut bacteria and improve metabolic health. This personalized approach could help mitigate the effects of obesity. Video Abstract.}, } @article {pmid39616151, year = {2024}, author = {Wang, J and Zhong, H and Chen, Q and Ni, J}, title = {Adaption mechanism and ecological role of CPR bacteria in brackish-saline groundwater.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {141}, pmid = {39616151}, issn = {2055-5008}, support = {52070002, 51721006, 51925901//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52209078//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023T160020//China Postdoctoral Science Foundation/ ; }, mesh = {*Groundwater/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Phylogeny ; Salinity ; Biodiversity ; Metagenome ; Adaptation, Physiological ; Nitrogen/metabolism ; Carbon/metabolism ; Sulfur/metabolism ; Metagenomics/methods ; Bacterial Physiological Phenomena ; }, abstract = {Candidate phyla radiation (CPR) constitutes a substantial fraction of bacterial diversity, yet their survival strategies and biogeochemical roles in brackish-saline groundwater remain unknown. By reconstructing 399 CPR metagenome-assembled genomes (MAGs) and 2007 non-CPR MAGs, we found that CPR, affiliated with 44 previously proposed phyla and 8 putative novel phyla, played crucial roles in maintaining the microbial stability and complexity in groundwater. Metabolic reconstructions revealed that CPR participated in diverse processes, including carbon, nitrogen, and sulfur cycles. Adaption of CPR to high-salinity conditions could be attributed to abundant genes associated with heat shock proteins, osmoprotectants, and sulfur reduction, as well as their cooperation with Co-CPR (non-CPR bacteria co-occurred with CPR) for metabolic support and resource exchange. Our study enhanced the understanding of CPR biodiversity in high-salinity groundwater, highlighting the collaborative roles of self-adaptive CPR bacteria and their reciprocal partners in coping with salinity stress, maintaining ecological stability, and mediating biogeochemical cycling.}, } @article {pmid39615045, year = {2024}, author = {Valentino, V and De Filippis, F and Marotta, R and Pasolli, E and Ercolini, D}, title = {Genomic features and prevalence of Ruminococcus species in humans are associated with age, lifestyle, and disease.}, journal = {Cell reports}, volume = {43}, number = {12}, pages = {115018}, doi = {10.1016/j.celrep.2024.115018}, pmid = {39615045}, issn = {2211-1247}, mesh = {Humans ; *Ruminococcus/genetics ; *Life Style ; Genome, Bacterial ; Adult ; Gastrointestinal Microbiome/genetics ; Metagenome ; Phylogeny ; Genomics/methods ; Male ; Middle Aged ; Female ; Aged ; }, abstract = {The genus Ruminococcus is dominant in the human gut, but higher levels of some species, such as R. gnavus, R. torques, and R. bromii, have been linked to health or disease. In this study, we analyzed >9,000 Ruminococcus metagenome-assembled genomes (MAGs) reconstructed from >5,000 subjects and revealed significant links between the prevalence of some species/subspecies and geographic origin, age, lifestyle, and disease, with subspecies prevalent in specific subpopulations showing divergent metabolic potential. Furthermore, Ruminococcus species from Lachnospiraceae encoded for carbohydrate-active enzymes (CAZy) potentially involved in the metabolism of human N- and O-glycans, whereas those from Oscillospiraceae appear to be more adapted toward fiber metabolism. These new findings contribute to elucidating the potential functional role of Ruminococcus in specific lifestyles and diseases and to decipher the diversity and the adaptation of members of this genus to the human gut.}, } @article {pmid39614549, year = {2024}, author = {Wicaksono, WA and Akinyemi, OE and Wassermann, B and Bickel, S and Suwanto, A and Berg, G}, title = {Traditionally produced tempeh harbors more diverse bacteria with more putative health-promoting properties than industrially produced tempeh.}, journal = {Food research international (Ottawa, Ont.)}, volume = {196}, number = {}, pages = {115030}, doi = {10.1016/j.foodres.2024.115030}, pmid = {39614549}, issn = {1873-7145}, mesh = {*Bacteria/genetics/classification/metabolism ; *Food Microbiology ; Humans ; Soy Foods/microbiology ; Fermentation ; Rhizopus/genetics/metabolism ; Hygiene ; Indonesia ; Microbiota ; Fermented Foods/microbiology ; }, abstract = {In recent years, there has been a significant shift towards industrialization in food production, resulting in the implementation of higher hygiene standards globally. Our study focused on examining the impact of hygiene standards on tempeh, a popular Rhizopus-based fermented soybean product native to Indonesia, and now famous around the world. We observed that tempeh produced with standardized hygiene measures exhibited a microbiome with comparable bacterial abundances but a markedly different community structure and function than traditionally produced tempeh. In detail, we found a decreased bacterial abundance of lactobacilli and enterobacteria, bacterial diversity, different indicator taxa, and significantly changed community structure in industrial tempeh. A similar picture was found for functional analysis: the quantity of bacterial genes was similar but qualitative changes were found for genes associated with human health. The resistome of tempeh varied based on its microbiome composition. The higher number of antimicrobial resistance genes in tempeh produced without standardized hygiene measures mainly belong to multidrug efflux pumps known to occur in plant-based food. Our findings were confirmed by functional insights into genomes and metagenome-assembled genomes from the dominant bacteria, e.g. Leuconostoc, Limosilactobacillus, Lactobacillus, Enterococcus, Paenibacillus, Azotobacter and Enterobacter. They harboured an impressive spectrum of genes important for human health, e.g. for production of vitamin B1, B7, B12, and K, iron and zinc transport systems and short chain fatty acid production. In conclusion, industrially produced tempeh harbours a less diverse microbiome than the traditional one. Although this ensures production at large scales as well as biosafety, in the long-term it can lead to potential effects for human gut health.}, } @article {pmid39614478, year = {2024}, author = {Yu, H and Li, Z and Zheng, D and Chen, C and Ge, C and Tian, H}, title = {Exploring microbial dynamics and metabolic pathways shaping flavor profiles in Huangjiu through metagenomic analysis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {196}, number = {}, pages = {115036}, doi = {10.1016/j.foodres.2024.115036}, pmid = {39614478}, issn = {1873-7145}, mesh = {*Taste ; *Metagenomics/methods ; *Fermentation ; *Wine/microbiology/analysis ; *Metabolic Networks and Pathways ; Microbiota/genetics ; Oryza/microbiology ; Flavoring Agents/metabolism ; Humans ; Food Microbiology ; Odorants/analysis ; Male ; }, abstract = {In the production of Huangjiu (Chinese rice wine), fermentation microbiota plays a crucial role in flavor formation. This study investigates the microbial dynamics and metabolic pathways that shape the flavor profiles of Huangjiu using different starters. Sensory evaluation and metabolite analysis of six starters revealed significant differences in ester, fruity, and sweet aromas. Saccharomyces, Aspergillus, and Rhizopus were identified as the dominant genera significantly impacting fermentation. Metagenomic species and functional gene annotations of Huangjiu starters elucidated the metabolic pathways for key flavor compounds synthesis pathways. Enzyme genes involved in these pathways were classified and annotated to microbial genera using the NR database, identifying 231 classes of relevant catalytic enzymes and 154 microbial genera. A metabolic relationship between flavor compound formation and different microbial genera was established using catalytic enzymes as a bridge. This study highlights the impact of starter composition on the final product and provides new insights for optimizing starters to enhance Huangjiu flavor quality.}, } @article {pmid39614477, year = {2024}, author = {Yang, L and Fan, W and Xu, Y}, title = {Effects of storage period and season on the microecological characteristics of Jiangxiangxing high-temperature Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {196}, number = {}, pages = {115034}, doi = {10.1016/j.foodres.2024.115034}, pmid = {39614477}, issn = {1873-7145}, mesh = {*Seasons ; *Hot Temperature ; *Food Storage/methods ; *Microbiota ; Fermentation ; Bacteria/metabolism/classification ; Food Microbiology ; Metabolomics ; Proteomics ; China ; Metagenomics ; Camellia sinensis/microbiology/metabolism ; Fungi/metabolism/classification ; }, abstract = {Metagenomics, non-targeted metabolomics, and metaproteomics were employed to analyze the microecological succession of high-temperature Daqu during storage, elucidate the adaptation mechanism of the microbial community of Daqu to storage environments, and clarify the microecological characteristics of Daqu during different seasons. During storage, the relative abundances of Bacillus, Oceanobacillus, Staphylococcus, and Aspergillus in Daqu had significantly increased, while those of Kroppenstedtia, Saccharopolyspora, Thermoascus, and Thermomyces had significantly decreased. During the first 3 months of storage, compound metabolism of Daqu was primarily dominated by generation of small molecular substances and then shifted to metabolism of amino sugars. During the storage process, homogeneous selection (15.57 %) and homogeneous diffusion (14.86 %) of the microbial communities of Daqu were much larger than during the fermentation process, while the variable selection assembly (29.43 %) was smaller than during the fermentation process. Among the 2509 proteins identified in the four-season Daqu, bacterial protein expression was 1.46-fold greater than that of fungi. Seasonal factors influenced the function of Daqu by alterations to Bacillus subtilis, Oceanobacillus iheyensis, and Aspergillus nidulans and other microbial functions. Carbon and benzoic acid metabolism of Daqu was relatively increased during the spring, while metabolism of alkaloids and tyrosine was upregulated during the summer, amino acid synthesis and starch metabolism were enriched during the autumn, and peptidoglycan synthesis was relatively greater during the winter. Adjusting the moisture content of Daqu during the storage period was shown to reduce microecological differentiation caused by seasonal temperature variations.}, } @article {pmid39614169, year = {2024}, author = {Tang, H and Du, S and Niu, Z and Zhang, D and Tang, Z and Chen, H and Chen, Z and Zhang, M and Xu, Y and Sun, Y and Fu, X and Norback, D and Shao, J and Zhao, Z}, title = {Nasal, dermal, oral and indoor dust microbe and their interrelationship in children with allergic rhinitis.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {505}, pmid = {39614169}, issn = {1471-2180}, mesh = {Humans ; *Dust/analysis ; Male ; Child ; Female ; *Rhinitis, Allergic/microbiology ; Case-Control Studies ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/isolation & purification/genetics ; *Skin/microbiology ; *Mouth/microbiology ; *Microbiota ; Nasal Cavity/microbiology ; Air Pollution, Indoor/analysis ; Child, Preschool ; Metagenomics/methods ; Nose/microbiology ; }, abstract = {BACKGROUND: Allergic rhinitis (AR) subjects might have their microenvironment changed due to pathogenesis and living environment. Whether the nasal microbe in AR children differs from healthy subjects and how it interplays with dermal, oral and indoor dust microbe needs to be elucidated.

METHODS: In this case-control study, we analyzed and compared the bacterial characterization and associations in nasal, dermal, oral swab samples and dust samples in 62 children with physician-diagnosed AR(cases) and 51 age- and gender-matched healthy ones with no history of allergic diseases(controls). Full-length 16S rRNA sequencing(swabs) and shotgun metagenomics(dust) were applied. Bacterial diversity, composition, abundance difference characteristics and fast expectation-maximization for microbial source tracking(FEAST) analysis were performed and compared between cases and controls.

RESULTS: The α-diversity of dust microorganisms in AR was lower than that in control group (P = 0.034), and the β-diversity indices of microorganisms in nasal cavity (P = 0.020), skin (P = 0.001) and dust (P = 0.004) were significantly different from those in control group. At species levels, a total of 10, 15, 12, and 15 bacterial species were differentially enriched in either cases or controls in nasal, dermal, oral, and dust samples, respectively(Linear Discriminant Analysis(LDA) score > 2, P < 0.05). Staphylococcus epidermidis was the single species simultaneously more abundant in nasal, dermal and dust samples in AR children. By FEAST analysis, 8.85% and 10.11% of S. epidermidis in AR dermal and dust samples came from nasal cavity. These proportions were significantly higher than those in controls (2.70% and 3.86%) (P < 0.05). The same significantly higher transfer proportions(P < 0.05) were observed for Staphylococcus aureus enriched in the nasal cavity in AR children. Classification models by random forest regression at species levels showed, bacterial species enriched in indoor dust, nasal and dermal samples had substantial power in distinguishing AR children from healthy ones, with the highest power in the dust samples (AUC = 0.88) followed by nasal(AUC = 0.81) and dermal ones(AUC = 0.80).

CONCLUSIONS: Our study presented the microbial enrichment characteristics in AR children both in the living environment(dust) and body sites exposed to environment through inhalation(nasal cavity), contact(skin) and ingestion(oral cavity) pathways, respectively. Nasal S.epidermidis and S.aureus had dominant influences on dust and other body sites in AR children.}, } @article {pmid39614167, year = {2024}, author = {Mangoma, N and Zhou, N and Ncube, T}, title = {Metagenomic insights into the microbial community of the Buhera soda pans, Zimbabwe.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {510}, pmid = {39614167}, issn = {1471-2180}, mesh = {Zimbabwe ; *Metagenomics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Microbiota/genetics ; Salinity ; Phylogeny ; Hydrogen-Ion Concentration ; Archaea/genetics/classification/metabolism/isolation & purification ; Water Microbiology ; }, abstract = {BACKGROUND: Soda pans are unique, natural aquatic environments characterised by elevated salinity and alkalinity, creating a distinctive and often extreme geochemistry. The microbiomes of soda pans are unique, with extremophiles such as halophiles, alkaliphiles and haloalkaliphiles being important. Despite being dominated by mostly unculturable inhabitants, soda pans hold immense biotechnological potential. The application of modern "omics-based" techniques helps us better understand the ecology and true extend of the biotechnological potential of soda pan microbiomes. In this study, we used a shotgun metagenomic approach to determine the microbial diversity and functional profile of previously unexplored soda pans located in Buhera, Eastern Zimbabwe. A combination of titrimetry and inductively coupled plasma optical emission spectroscopy (ICP‒OES) was used to perform physico-chemical analysis of the soda pan water.

RESULTS: Physicochemical analysis revealed that the Buhera soda pans are highly alkaline, with a pH range of 8.74 to 11.03, moderately saline (2.94 - 7.55 g/L), and have high carbonate (3625 mg/L) and bicarbonate ion (1325 mg/L) alkalinity. High levels of sulphate, phosphate, chloride and fluoride ions were detected. Metagenomic analysis revealed that domain Bacteria dominated the soda pan microbial community, with Pseudomonadota and Bacillota being the dominant phyla. Vibrio was shown to be the predominant genus, followed by Clostridium, Candidatus Brevefilum, Acetoanaerobium, Thioalkalivibrio and Marinilactibacillus. Archaea were also detected, albeit at a low prevalence of 1%. Functional profiling revealed that the Buhera soda pan microbiome is functionally diverse, has hydrolytic-enzyme production potential and is capable of supporting a variety of geochemical cycles.

CONCLUSIONS: The results of this pioneering study showed that despite their extreme alkalinity and moderate salinity, the Buhera soda pans harbour a taxonomically and functionally diverse microbiome dominated by bacteria. Future work will aim towards establishing the full extent of the soda pan's biotechnological potential, with a particular emphasis on potential enzyme production.}, } @article {pmid39612821, year = {2025}, author = {Rosenqvist, T and Hilding, J and Suarez, C and Paul, CJ}, title = {Microbial communities in slow sand filters for drinking water treatment adapt to organic matter altered by ozonation.}, journal = {Water research}, volume = {270}, number = {}, pages = {122843}, doi = {10.1016/j.watres.2024.122843}, pmid = {39612821}, issn = {1879-2448}, mesh = {*Ozone ; *Drinking Water/microbiology ; *Water Purification/methods ; *Filtration ; Sand ; Bacteria/genetics ; Microbiota ; }, abstract = {Changing natural organic matter quality from anthropogenic activity and stricter requirements for micropollutant removal challenges existing systems for drinking water production. Ozonation of water followed by biofiltration, such as passage through a slow sand filter (SSF), is a partial solution. Biofiltration relies on biofilms (microbial communities within extracellular matrices). However, the effects of ozonation on SSF microbial communities are unknown. In this study, genome-resolved and read-based metagenomics were used to compare the microbial communities of two full-scale SSFs employing conventional pre-treatment to a 20 m[2] SSF operated in parallel with ozonation as additional pre-treatment. The SSF microbial community receiving ozonated water was less diverse than those receiving non-ozonated water. Families Hyphomicrobiaceae, Acetobacteraceae, Sphingomonadaceae and Burkholderiaceae were more abundant when ozone was used, as were genes for metabolism of single-carbon organic compounds. Conversely, genes for metabolism of aromatic compounds and fatty acids were less abundant. Metagenome assembled genomes associated with the non-ozonated SSFs were enriched with several glycoside hydrolases, while those associated with the ozonated SSF were enriched with genes for 1-2 carbon compound metabolism. No indications of increased microbial risk (pathogens or antibiotic resistance genes) were detected as a consequence of ozonation. This study shows how microbial communities of SSFs adapt to changes in organic matter quality, highlighting the key role of biofilters for production of safe and sustainable drinking water in a changing climate.}, } @article {pmid39611142, year = {2024}, author = {Zhang, L and Zhang, H and Su, S and Jia, Y and Liang, C and Fang, Y and Hong, D and Li, T and Ma, F}, title = {Risk factor assessment and microbiome analysis in peritoneal dialysis-related peritonitis reveal etiological characteristics.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1443468}, pmid = {39611142}, issn = {1664-3224}, mesh = {Humans ; *Peritonitis/microbiology/etiology/diagnosis ; *Peritoneal Dialysis/adverse effects ; Male ; Female ; Middle Aged ; Risk Factors ; *Gastrointestinal Microbiome ; Aged ; Risk Assessment ; Adult ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Peritoneal dialysis-related peritonitis (PDRP) is one of the most common complications of peritoneal dialysis (PD). Understanding the risk factors and etiological characteristics is indispensable for infection prevention and improving the outcome and life quality.

METHODS: A total of 70 PD patients were separated into the PDRP group (n=25) and the control group (n=45). Variables, including gender, age, body mass index, primary diseases, and history of basic diseases, in the two groups were analyzed to assess the risk factors of PDRP. Metagenomic next-generation sequencing (mNGS) and microbial culture were compared in detecting pathogenic microorganisms. Gut microbiota analysis was performed in 35 PDRP patients based on mNGS data.

RESULTS: Dialysis time and times of dialysate change were the risk factors of PDRP, and times of dialysate change was the independent risk factor of PDRP (p = 0.046). mNGS produced higher sensitivity (65.79%) than microbial culture (36.84%) in identifying pathogenic microorganisms. Staphylococcus aureus and Klebsiella pneumoniae (four cases) were the most frequent pathogens causing PDRP, followed by Staphylococcus capitis (three cases). β diversity of the gut microbiota was significantly different between patients with fewer times of dialysate change (≤4) and more (>5), as well as between patients with gram-positive (G+) bacterial and gram-negative (G-) bacterial infection.

CONCLUSION: The dialysis time and times of dialysate changes not only are risk factors for peritonitis in PD patients but also stimulate significant changes in the gut microbiome structure in PDRP patients. These findings may provide a novel viewpoint for the management of patients with PDRP.}, } @article {pmid39611041, year = {2024}, author = {Liu, L and Lian, ZH and Lv, AP and Salam, N and Zhang, JC and Li, MM and Sun, WM and Tan, S and Luo, ZH and Gao, L and Yuan, Y and Ming, YZ and OuYang, YT and Li, YX and Liu, ZT and Hu, CJ and Chen, Y and Hua, ZS and Shu, WS and Hedlund, BP and Li, WJ and Jiao, JY}, title = {Insights into chemoautotrophic traits of a prevalent bacterial phylum CSP1-3, herein Sysuimicrobiota.}, journal = {National science review}, volume = {11}, number = {11}, pages = {nwae378}, pmid = {39611041}, issn = {2053-714X}, abstract = {Candidate bacterial phylum CSP1-3 has not been cultivated and is poorly understood. Here, we analyzed 112 CSP1-3 metagenome-assembled genomes and showed they are likely facultative anaerobes, with 3 of 5 families encoding autotrophy through the reductive glycine pathway (RGP), Wood-Ljungdahl pathway (WLP) or Calvin-Benson-Bassham (CBB), with hydrogen or sulfide as electron donors. Chemoautotrophic enrichments from hot spring sediments and fluorescence in situ hybridization revealed enrichment of six CSP1-3 genera, and both transcribed genes and DNA-stable isotope probing were consistent with proposed chemoautotrophic metabolisms. Ancestral state reconstructions showed that the ancestors of phylum CSP1-3 may have been acetogens that were autotrophic via the RGP, whereas the WLP and CBB were acquired by horizontal gene transfer. Our results reveal that CSP1-3 is a widely distributed phylum with the potential to contribute to the cycling of carbon, sulfur and nitrogen. The name Sysuimicrobiota phy. nov. is proposed.}, } @article {pmid39609882, year = {2024}, author = {Cloarec, LA and Bacchetta, T and Bruto, M and Leboulanger, C and Grossi, V and Brochier-Armanet, C and Flandrois, JP and Zurmely, A and Bernard, C and Troussellier, M and Agogué, H and Ader, M and Oger-Desfeux, C and Oger, PM and Vigneron, A and Hugoni, M}, title = {Lineage-dependent partitioning of activities in chemoclines defines Woesearchaeota ecotypes in an extreme aquatic ecosystem.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {249}, pmid = {39609882}, issn = {2049-2618}, mesh = {*Archaea/classification/genetics/metabolism ; *Lakes/microbiology ; *Phylogeny ; *Ecotype ; Ecosystem ; Metagenomics ; Microbiota ; Genome, Archaeal ; Water Microbiology ; Biodiversity ; }, abstract = {BACKGROUND: DPANN archaea, including Woesearchaeota, encompass a large fraction of the archaeal diversity, yet their genomic diversity, lifestyle, and role in natural microbiomes remain elusive. With an archaeal assemblage naturally enriched in Woesearchaeota and steep vertical geochemical gradients, Lake Dziani Dzaha (Mayotte) provides an ideal model to decipher their in-situ activity and ecology.

RESULTS: Using genome-resolved metagenomics and phylogenomics, we identified highly diversified Woesearchaeota populations and defined novel halophilic clades. Depth distribution of these populations in the water column showed an unusual double peak of abundance, located at two distinct chemoclines that are hotspots of microbial diversity in the water column. Genome-centric metatranscriptomics confirmed this vertical distribution and revealed a fermentative activity, with acetate and lactate as end products, and active cell-to-cell processes, supporting strong interactions with other community members at chemoclines. Our results also revealed distinct Woesearchaeota ecotypes, with different transcriptional patterns, contrasted lifestyles, and ecological strategies, depending on environmental/host conditions.

CONCLUSIONS: This work provides novel insights into Woesearchaeota in situ activity and metabolism, revealing invariant, bimodal, and adaptative lifestyles among halophilic Woesearchaeota. This challenges our precepts of an invariable host-dependent metabolism for all the members of this taxa and revises our understanding of their contributions to ecosystem functioning and microbiome assemblage. Video Abstract.}, } @article {pmid39609616, year = {2024}, author = {Kim, M and Parrish, RC and Tisza, MJ and Shah, VS and Tran, T and Ross, M and Cormier, J and Baig, A and Huang, CY and Brenner, L and Neuringer, I and Whiteson, K and Harris, JK and Willis, AD and Lai, PS}, title = {Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1590}, pmid = {39609616}, issn = {2399-3642}, support = {R01 AI144119/AI/NIAID NIH HHS/United States ; R21 AI175965/AI/NIAID NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; T32 HL116275/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Sputum/microbiology ; *Cystic Fibrosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Freezing ; Adult ; Cryopreservation ; Female ; High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics/isolation & purification/classification ; Sequence Analysis, DNA/methods ; Male ; Respiratory System/microbiology ; }, abstract = {Most respiratory microbiome studies use amplicon sequencing due to high host DNA. Metagenomics sequencing offers finer taxonomic resolution, phage assessment, and functional characterization. We evaluated five host DNA depletion methods on frozen nasal swabs from healthy adults, sputum from people with cystic fibrosis (pwCF), and bronchoalveolar lavage (BAL) from critically ill patients. Median sequencing depth was 76.4 million reads per sample. Untreated nasal, sputum, and BAL had 94.1%, 99.2%, and 99.7% host reads, respectively. Host depletion effects varied by sample type, generally increasing microbial reads, species and functional richness; this was mediated by higher effective sequencing depth. Rarefaction curves showed species richness saturation at 0.5-2 million microbial reads. Most methods did not change Morisita-Horn dissimilarity for BAL and nasal samples although the proportion of gram-negative bacteria decreased for sputum from pwCF. Freezing did not affect the viability of Staphylococcus aureus but reduced the viability of Pseudomonas aeruginosa and Enterobacter spp.; this was mitigated by adding a cryoprotectant. QIAamp-based host depletion minimally impacted gram-negative viability even in non-cryoprotected frozen isolates. While some host depletion methods may shift microbial composition, metagenomics sequencing without host depletion severely underestimates microbial diversity of respiratory samples due to shallow effective sequencing depth and is not recommended.}, } @article {pmid39608999, year = {2024}, author = {Climacosa, FMM and Anlacan, VMM and Gordovez, FJA and Reyes, JCB and Tabios, IKB and Manalo, RVM and Cruz, JMC and Asis, JLB and Razal, RB and Abaca, MJM and Dacasin, AB and Espiritu, APN and Gapaz, NCLL and Lee Yu, MHL}, title = {Monitoring drug Efficacy through Multi-Omics Research initiative in Alzheimer's Disease (MEMORI-AD): A protocol for a multisite exploratory prospective cohort study on the drug response-related clinical, genetic, microbial and metabolomic signatures in Filipino patients with Alzheimer's disease.}, journal = {BMJ open}, volume = {14}, number = {11}, pages = {e078660}, pmid = {39608999}, issn = {2044-6055}, mesh = {Humans ; *Alzheimer Disease/drug therapy/genetics ; Philippines ; Prospective Studies ; Aged ; Cholinesterase Inhibitors/therapeutic use ; Rivastigmine/therapeutic use ; Donepezil/therapeutic use ; Cross-Sectional Studies ; Memantine/therapeutic use ; Male ; Female ; Metabolomics ; Gastrointestinal Microbiome/drug effects ; Multiomics ; }, abstract = {INTRODUCTION: Dementia is one of the leading causes of disability among older people aged 60 years and above, with majority eventually being diagnosed with Alzheimer's disease (AD). Pharmacological agents approved for dementia include acetylcholinesterase enzyme (AChE) inhibitors like rivastigmine, donepezil and galantamine and the N-methyl-D-aspartate (NMDA) receptor antagonist memantine, prescribed as monotherapy or in combination with each other, depending on the severity of disease. There is currently no available study demonstrating the clinical response to these drugs for AD in the Filipino population. Hence, this protocol aims to characterise the clinical, genetic, microbial and metabolic factors associated with drug responses to donepezil, rivastigmine and/or memantine for AD in a cohort of Filipinos with late-onset AD.

METHODS AND ANALYSIS: This protocol involves a multisite descriptive study that will use two study designs: (1) a descriptive, cross-sectional study to characterise the clinical profile of Filipino dementia patients with AD and (2) an exploratory prospective cohort study to investigate drug response-related genetic, gut microbiome and metabolome signatures of a subset of the recruited AD patients. At least 153 patients with mild or moderate AD aged 65 years old and above will be recruited regardless of their treatment status. A subset of these patients (n=60) who meet inclusion and exclusion criteria will be included further in the exploratory cohort study. These patients will be grouped according to their baseline medications and will be observed for treatment response in 6 months. The cognitive, functional and behavioural domains of patients and levels of functioning will be measured using different assessment tools. Drug responses of Filipino patients will then be investigated employing multi-omics technology to characterise genetic variations via whole exome sequencing, gut microbiome profile via shotgun metagenomic sequencing and metabolome profile via liquid chromatography with mass spectrometry.

ETHICS AND DISSEMINATION: The study has received ethical clearance from the Department of Health Single Joint Research Ethics Board (SJREB-2022-15). Results of psychometric scales will be made available to enrolled patients. The study results will be presented at national/international conferences and published in international peer-reviewed scientific journals, and summaries of the results will be provided to the study funders and institutional review boards of the three tertiary referral hospitals.

TRIAL REGISTRATION NUMBER: Philippine Health Research Registry ID PHRR230220-0054116; ClinicalTrials.gov ID NCT05801380.}, } @article {pmid39608199, year = {2025}, author = {Bhat, AH and Malik, IM and Tak, H and Ganai, BA and Bharti, P}, title = {Host, parasite, and microbiome interaction: Trichuris ovis and its effect on sheep gut microbiota.}, journal = {Veterinary parasitology}, volume = {333}, number = {}, pages = {110356}, doi = {10.1016/j.vetpar.2024.110356}, pmid = {39608199}, issn = {1873-2550}, mesh = {Animals ; Sheep ; *Sheep Diseases/parasitology/microbiology ; *Gastrointestinal Microbiome ; *Trichuris ; *Host-Parasite Interactions ; *Trichuriasis/veterinary/parasitology/microbiology ; RNA, Ribosomal, 16S/genetics ; Cecum/microbiology/parasitology ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Sheep that are infected with gastrointestinal helminths experience a significant impact on their health and productivity. Among the helminths, nematodes like Haemonchus contortus, Oesophagostomum spp., Bunostomum trigonocephalum, Nematodirus battus, Trichostrongylus spp. and Teladorsagia circumcincta are particularly pathogenic. Understanding the interactions among parasites, hosts, and their microbiomes is crucial in developing new approaches in the management of parasites. This study examines the bacterial profile of Trichuris ovis, a highly prevalent nematode among Kashmir Merino sheep, and the influence of nematode infection on the caecal microbiome of its host. Sheep were selected based on T. ovis infection status, and samples were collected from infected and non-infected caecum. The 16S rRNA metagenomic analysis revealed distinct microbial communities in T. ovis, infected caecum, and non-infected caecum. Proteobacteria dominated the T. ovis microbiome, while infected caecum was rich in Bacteroidota and Spirochaetota, and non-infected caecum had a higher proportion of Firmicutes and Verrucomicrobiota. At the genus level, T. ovis was predominantly associated with Escherichia/Shigella, while infected caecum had higher proportions of Bacteroides, Prevotella, and Treponema. Non-infected caecum was characterized by WCHB1-41, Prevotella, and Succiniclasticum like genera. Alpha and beta diversity indicated significant differences in microbiome among the groups, with higher diversity observed in infected caecum. The study found T. ovis infection significantly alters the caecal microbiome of sheep, introducing potentially pathogenic bacteria and reducing beneficial ones. These findings underscore the complex relationship between host, parasite, and microbiome, highlighting the need for comprehensive strategies to manage helminth infections and their broader ecological impacts.}, } @article {pmid39607975, year = {2024}, author = {Abbasi, AM and Nasir, S and Bajwa, AA and Akbar, H and Ali, MM and Rashid, MI}, title = {A comparative study of the microbiomes of the ticks Rhipicephalus microplus and Hyalomma anatolicum.}, journal = {Parasite (Paris, France)}, volume = {31}, number = {}, pages = {74}, pmid = {39607975}, issn = {1776-1042}, support = {HEC-GCF-273//Higher Education Commission, Pakistan/ ; }, mesh = {Animals ; *Rhipicephalus/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Ixodidae/microbiology ; *Microbiota ; Pakistan ; Phylogeny ; Symbiosis ; Female ; Gastrointestinal Microbiome ; Coxiella/genetics/isolation & purification/classification ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Hyalomma anatolicum and Rhipicephalus microplus are tick species that are important vectors of numerous pathogens affecting both humans and livestock. Endosymbionts, such as Coxiella-like endosymbionts (CLE), Francisella-like endosymbionts (FLE), and Candidatus Midichloria, play a crucial role in the physiology and vector competence of these ticks. In this study, we investigated the microbial composition of H. anatolicum and R. microplus from four geographically distinct regions of Pakistan to assess whether environmental differences influence their microbiomes. We analyzed the ticks' gut microbiome targeting the V3-V4 hypervariable region of 16S rRNA for Illumina 16S metagenome NGS sequencing and processed overall 144 ticks. Analysis of gut bacterial composition resulted in observation of 1200 R. microplus and 968 H. anatolicum unique amplicon sequencing variants (ASVs). Relative abundance, Alpha diversity (Shannon, Faith's phylogenetic distance) and beta diversity metrics (Bray-Curtis, Jaccard and UniFrac) were analyzed and revealed that H. anatolicum ticks have significantly unique and diverse microbial communities with Acinetobacter indicus and Francisella-like endosymbionts dominating as opposed to Candidatus Midichloria. Rhipicephalus microplus exhibited results consistent with the previous studies with no major changes in microbiome including Coxiella-like endosymbionts as the major contributor. These findings suggest that geographical and environmental factors play a significant role in shaping the tick microbiome, with potential consequences for disease transmission and tick survivability. Further research is needed to elucidate the functional roles of these microbial shifts and their impact on public health and livestock in affected regions.}, } @article {pmid39604824, year = {2024}, author = {Li, X and Zhang, Z and Bai, H and Liu, Z}, title = {Analysis of vaginal microbiota during postpartum and postmenopausal periods based on metagenomics.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {501}, pmid = {39604824}, issn = {1471-2180}, mesh = {Humans ; Female ; *Vagina/microbiology ; *Postmenopause ; *Postpartum Period ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Postmenopausal and the postpartum periods are essential physiological phases that result in low estrogen levels in women; however, they are important to female reproductive health. Traditional as well as new detection methods (such as 16 S RNA sequencing) have limitations in detecting the composition of vaginal microbiota. Therefore, in this study, we used metagenomic detection technology to study the composition of vaginal microbiota in postmenopausal and postpartum women. Six women were randomly selected from each group (healthy women of childbearing age, postmenopausal group, and postpartum) for vaginal microecology, composition, α-diversity, linear discriminant analysis effect size (LEfSe), and Comprehensive Antibiotic Resistance Database (CARD) analyses.

RESULTS: We discovered that Lactobacillus dominance disappeared in postpartum and postmenopausal group women and that diversity increased. However, the proportions of Atopobium vaginae, Escherichia coli, and Streptococcus agalactiae significantly increased. Diversity was the highest in the postpartum period, with a significant increase in the proportions of A. vaginae, Gardnerella vaginalis, Prevotella, and occasionally, Chlamydia trachomatis. Linear discriminant analysis effect size analysis revealed that Lactobacillus crispatus and L. iners enrichment in the postpartum and menopausal periods was much lower than that in the childbearing age group. CARD analysis revealed that ABC-F ATP-binding cassette ribosomal protection protein subfamily gene abundance was significantly lower in the menopausal than in the childbearing age group, whereas the gimA family macrolide glycosyltransferase gene abundance was significantly higher.

CONCLUSIONS: The dominance of vaginal Lactobacillus in postpartum and menopausal women disappeared, while their diversity increased. In addition, the reproductive tract of postpartum women was susceptible to invasion by pathogenic microorganisms, which deserves clinical attention. When menopausal women receive treatment for vaginal infections, the likelihood that certain bacterial communities develop antibiotic resistance through ribosomal protection mechanisms is lower than that of women in the childbearing age, while the possibility of developing resistance to macrolides through glycosylation may increase. This, however, requires further research.}, } @article {pmid39604809, year = {2025}, author = {Li, Q and Wu, D and Song, Y and Zhang, L and Wang, T and Chen, X and Zhang, M}, title = {In vivo mechanism of the interaction between trimethylamine lyase expression and glycolytic pathways.}, journal = {Food & function}, volume = {16}, number = {1}, pages = {87-101}, doi = {10.1039/d4fo03809f}, pmid = {39604809}, issn = {2042-650X}, mesh = {Animals ; *Glycolysis ; Mice ; *Gastrointestinal Microbiome ; Male ; Glycine/metabolism/pharmacology ; Mice, Inbred C57BL ; Lyases/metabolism/genetics ; Methylamines/metabolism ; Diet ; Bacteria/genetics/classification/metabolism ; RNA, Ribosomal, 16S/genetics ; Choline/metabolism ; }, abstract = {Recent studies confirmed that host-gut microbiota interactions modulate disease-linked metabolite TMA production via TMA lyase. However, microbial enzyme production mechanisms remain unclear. In the present study, we investigated the impact of dietary and intervention factors on gut microbiota, microbial gene expression, and the interplay between TMA lyase and glycolytic pathways in mice. Using 16S rRNA gene sequencing, metagenomics, and metabolomics, the gut microbiota composition and microbial functional gene expression profiles related to TMA lyase and glycolytic enzymes were determined. The results revealed that distinct diets and intervention factors altered gut microbiota, gene expression, and metabolites linked to glycine metabolism and glycolysis. Notably, an arabinoxylan-rich diet suppressed genes linked to choline, glycine, glycolysis, and TMA lyase, favoring glycine utilization via pyruvate pathways. Glycolytic inhibitors amplified these effects, mainly inhibiting pyruvate kinase. Our findings underscored the crosstalk between TMA lyase and glycolytic pathways, regulating glycine levels, and suggested avenues for targeted interventions and personalized diets to curb choline TMA lyase production.}, } @article {pmid39604726, year = {2025}, author = {Chen-Liaw, A and Aggarwala, V and Mogno, I and Haifer, C and Li, Z and Eggers, J and Helmus, D and Hart, A and Wehkamp, J and Lamousé-Smith, ESN and Kerby, RL and Rey, FE and Colombel, JF and Kamm, MA and Olle, B and Norman, JM and Menon, R and Watson, AR and Crossett, E and Terveer, EM and Keller, JJ and Borody, TJ and Grinspan, A and Paramsothy, S and Kaakoush, NO and Dubinsky, MC and Faith, JJ}, title = {Gut microbiota strain richness is species specific and affects engraftment.}, journal = {Nature}, volume = {637}, number = {8045}, pages = {422-429}, pmid = {39604726}, issn = {1476-4687}, support = {R01 DK112978/DK/NIDDK NIH HHS/United States ; R01 DK124133/DK/NIDDK NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation ; Humans ; Animals ; *Species Specificity ; *Feces/microbiology ; Mice ; Metagenome ; Male ; Female ; Lakes/microbiology ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Soil Microbiology ; }, abstract = {Despite the fundamental role of bacterial strain variation in gut microbiota function[1-6], the number of unique strains of a species that can stably colonize the human intestine is still unknown for almost all species. Here we determine the strain richness (SR) of common gut species using thousands of sequenced bacterial isolates with paired metagenomes. We show that SR varies across species, is transferable by faecal microbiota transplantation, and is uniquely low in the gut compared with soil and lake environments. Active therapeutic administration of supraphysiologic numbers of strains per species increases recipient SR, which then converges back to the population average after dosing is ceased. Stratifying engraftment outcomes by high or low SR shows that SR predicts microbial addition or replacement in faecal transplants. Together, these results indicate that properties of the gut ecosystem govern the number of strains of each species colonizing the gut and thereby influence strain addition and replacement in faecal microbiota transplantation and defined live biotherapeutic products.}, } @article {pmid39604394, year = {2024}, author = {Akiyama, S and Nishijima, S and Kojima, Y and Kimura, M and Ohsugi, M and Ueki, K and Mizokami, M and Hattori, M and Tsuchiya, K and Uemura, N and Kawai, T and Bork, P and Nagata, N}, title = {Multi-biome analysis identifies distinct gut microbial signatures and their crosstalk in ulcerative colitis and Crohn's disease.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10291}, pmid = {39604394}, issn = {2041-1723}, mesh = {Humans ; *Colitis, Ulcerative/microbiology/genetics/virology ; *Crohn Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; Male ; *Metagenomics/methods ; Female ; *Bacteriophages/genetics ; Adult ; Escherichia coli/genetics/metabolism ; Middle Aged ; Japan ; Fungi/genetics ; Bacteria/genetics/metabolism/classification ; Metagenome/genetics ; Saccharomyces cerevisiae/genetics ; Bifidobacterium/genetics ; Virome/genetics ; Enterococcus faecium/genetics/pathogenicity ; Fatty Acids, Volatile/metabolism ; Young Adult ; China ; Case-Control Studies ; }, abstract = {The integrative multi-kingdom interaction of the gut microbiome in ulcerative colitis (UC) and Crohn's disease (CD) remains underinvestigated. Here, we perform shotgun metagenomic sequencing of feces from patients with UC and CD, and healthy controls in the Japanese 4D cohort, profiling bacterial taxa, gene functions, and antibacterial genes, bacteriophages, and fungi. External metagenomic datasets from the US, Spain, the Netherlands, and China were analyzed to validate our multi-biome findings. We found that Enterococcus faecium and Bifidobacterium spp. were enriched in both diseases. Enriched Escherichia coli was characteristic of CD and was linked to numerous antibiotic resistance genes involved in efflux pumps and adherent-invasive Escherichia coli virulence factors. Virome changes correlated with shifts in the bacteriome, including increased abundances of phages encoding pathogenic genes. Saccharomyces paradoxus and Saccharomyces cerevisiae were enriched in UC and CD, respectively. Saccharomyces cerevisiae and Escherichia coli had negative associations with short-chain fatty acid (SCFA)-producing bacteria in CD. Multi-biome signatures and their interactions in UC and CD showed high similarities between Japan and other countries. Since bacteria, phages, and fungi formed multiple hubs of intra- or trans-kingdom networks with SCFA producers and pathobionts in UC and CD, an approach targeting the interaction network may hold therapeutic promise.}, } @article {pmid39603713, year = {2024}, author = {Helfrich, PG and Feldman, J and Andrade-Barahona, E and Robertson, I and Foster, J and Hofacker, R and Dahlquist Selking, G and Sheik, CS and Cox, A}, title = {Aqueous copper geochemistry shapes the sediment microbial resistome in a recovering stream.}, journal = {Environmental microbiology reports}, volume = {16}, number = {6}, pages = {e70045}, pmid = {39603713}, issn = {1758-2229}, support = {800015-10297//Montana Department of Justice, Natural Resource Damage Program (NRDP) through the Butte Natural Resource Damage Restoration Council (BNRC)/ ; //Montana Tech Faculty Seed and Faculty Development Initiatives/ ; //Montana Tech Earth Science and Engineering Fellowship/ ; //Montana Water Center, Faculty Seed Grant/ ; }, mesh = {*Copper/metabolism ; *Geologic Sediments/microbiology/chemistry ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/drug effects/classification/metabolism/isolation & purification ; Metagenome ; Water Pollutants, Chemical/metabolism ; Metagenomics ; Arsenic/metabolism ; Microbiota/genetics/drug effects ; }, abstract = {Aqueous metals are pervasive contaminants associated with historical mining. We produced and examined 16 metagenomes from a contaminated creek to investigate how anthropogenic metal contamination shapes the functional profiles of microbial communities. We then incorporated the metagenomic profiles and concurrently collected geochemical context into a multivariate model to examine correlations between stream geochemistry and microbial functional potential. Integrating the metagenomes with full geochemical profiles emphasised that even low metalloid concentrations shaped microbial functionality, seasonal shifts in copper bioavailability and arsenic exposure correlated with genetic variation, and copper resistomes were spatiotemporally distinct. This study provides new insights into microbial metabolic potential and microbe-metal(loid) interactions.}, } @article {pmid39603473, year = {2025}, author = {Li, Y and Tao, C and Li, S and Chen, W and Fu, D and Jafvert, CT and Zhu, T}, title = {Feasibility study of machine learning to explore relationships between antimicrobial resistance and microbial community structure in global wastewater treatment plant sludges.}, journal = {Bioresource technology}, volume = {417}, number = {}, pages = {131878}, doi = {10.1016/j.biortech.2024.131878}, pmid = {39603473}, issn = {1873-2976}, mesh = {*Machine Learning ; *Sewage/microbiology ; *Wastewater/microbiology ; Water Purification/methods ; Feasibility Studies ; Bacteria/drug effects/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/drug effects ; China ; Drug Resistance, Bacterial/genetics ; }, abstract = {Wastewater sludges (WSs) are major reservoirs and emission sources of antibiotic resistance genes (ARGs) in cities. Identifying antimicrobial resistance (AMR) host bacteria in WSs is crucial for understanding AMR formation and mitigating biological and ecological risks. Here 24 sludge data from wastewater treatment plants in Jiangsu Province, China, and 1559 sludge data from genetic databases were analyzed to explore the relationship between 7 AMRs and bacterial distribution. The results of the Procrustes and Spearman correlation analysis were unsatisfactory, with p-value exceeding the threshold of 0.05 and no strong correlation (r > 0.8). In contrast, explainable machine learning (EML) using SHapley Additive exPlanation (SHAP) revealed Pseudomonadota as a major contributor (39.3 %-74.2 %) to sludge AMR. Overall, the application of ML is promising in analyzing AMR-bacteria relationships. Given the different applicable occasions and advantages of various analysis methods, using ML as one of the correlation analysis tools is strongly recommended.}, } @article {pmid39602306, year = {2024}, author = {Pasolli, E and Mauriello, IE and Avagliano, M and Cavaliere, S and De Filippis, F and Ercolini, D}, title = {Bifidobacteriaceae diversity in the human microbiome from a large-scale genome-wide analysis.}, journal = {Cell reports}, volume = {43}, number = {12}, pages = {115027}, doi = {10.1016/j.celrep.2024.115027}, pmid = {39602306}, issn = {2211-1247}, mesh = {Humans ; *Phylogeny ; *Microbiota/genetics ; Metagenome ; Genome, Bacterial ; Genome-Wide Association Study ; Probiotics ; }, abstract = {We performed a large-scale genome-wide analysis aiming to investigate the prevalence and strain-level diversity of Bifidobacteriaceae species in the human microbiome. We considered 9,528 publicly available human metagenomes and integrated them with 1,192 isolate genomes from different sources. The prevalence and abundance of Bifidobacteriaceae species in humans was linked to multiple host characteristics: they were reduced in older people and enriched in populations characterized by Westernized lifestyles with geography-specific patterns. Phylogenetic analysis highlighted 110 Bifidobacteriaceae species-level genome bins (SGBs), with 32 found in humans and 8 in food and probiotic sources. Functional annotation revealed a great diversity in carbohydrate-active enzyme families across these SGBs. We found potential subspecies for most of the SGBs prevalent in humans and identified patterns driven by age and geography. We provided evidence that strains used in probiotics were rarely identified in humans, with the only exception represented by Bifidobacterium animalis. We finally evaluated that the abundance of Bifidobacteriaceae species exhibited moderate and variable capabilities to predict health status in case-control studies.}, } @article {pmid39601988, year = {2024}, author = {Rekadwad, BN and Shouche, YS and Jangid, K}, title = {Oil spill pollution and diversity analyses of resistant bacteria isolated from soil across the Arabian Sea and Bay of Bengal coastlines.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {12}, pages = {1265}, pmid = {39601988}, issn = {1573-2959}, mesh = {*Bacteria/classification/isolation & purification/genetics ; *Petroleum Pollution ; *Environmental Monitoring ; India ; *Soil Microbiology ; Biodiversity ; Bays/microbiology ; Drug Resistance, Bacterial ; }, abstract = {Pelagic transport causes oil pollution via international tanker routes in the open ocean across southern Asia and the Indian Territory. Nutrient-rich runoff from residential, commercial, and industrial wastes, oil tanker mishaps, and sailing flags have all resulted in pollution. The natural flow of ocean water from east to west dragged pollutants into Indian Territory. We have investigated that the severe deposition of oil spills and biohazardous wastes is causing faunal mortality. Microbiome analyses helped us understand the sample's microbial load. 16S amplicon metagenome analysis, followed by enumeration and confirmation using molecular methods, indicates the presence of diverse microbial profiles. The presence of non-native hydrocarbon- and AMR-resistant bacterial taxa, such as Brevundimonas, Staphylococcus spp., Mycolicibacterium, Spingomonas spp., Bacillus spp., Chitinophaga spp., Priestia spp., Domibacillus spp., Rossellomorea spp., and Acinetobacter spp., confirms the impacts of oil and urban pollution. This indicates that the coastal soil of Goa and Andhra Pradesh has hydrocarbon- and antibiotic-resistant bacteria, which confirms that the present pollution status and that high-traffic recreational activities put biodiversity and humans at risk of getting illnesses linked to antibiotic resistance.}, } @article {pmid39601556, year = {2024}, author = {Yang, J and Wang, H and Lin, X and Liu, J and Feng, Y and Bai, Y and Liang, H and Hu, T and Wu, Z and Lai, J and Liu, J and Zou, Y and Wei, S and Yan, P}, title = {Gut microbiota dysbiosis induced by alcohol exposure in pubertal and adult mice.}, journal = {mSystems}, volume = {9}, number = {12}, pages = {e0136624}, pmid = {39601556}, issn = {2379-5077}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/chemically induced/microbiology ; Mice ; *Ethanol ; Male ; Mice, Inbred C57BL ; Metagenome/drug effects ; Liver/metabolism/drug effects/pathology ; Sexual Maturation/drug effects ; }, abstract = {UNLABELLED: Alcohol intake causes many diseases including neuropsychiatric symptoms, nutritional deficiency, progressive pancreatitis, liver cirrhosis, and ischemic heart disease. The gut microbiota changes significantly after alcohol exposure. Alcohol consumption tends to increase in underage and young people, but the feature of the gut microbiota in puberty remains largely unexplored. In this study, we conducted alcohol-exposed pubertal and adult mice model to investigate the intestinal damage and gut microbiota change. Interestingly, the responses of pubertal mice and adult mice after alcohol exposure were different. We found that alcohol dehydrogenase decreased and aldehyde dehydrogenase increased in the liver of pubertal mice, thus reducing the accumulation of toxic acetaldehyde. Furthermore, alcohol exposure caused less intestinal injury in pubertal mice. Through the analysis of metagenome assembly genome, we obtained many unrecognized bacterial genomes. Limosillactobacillus reuteri (cluster_56) and Lactobacillus intestinalis (cluster_57) were assembled from the samples of pubertal mice, which were involved in the production of indole acetic acid and the transformation of bile acids in response to alcohol exposure. This study provided a new insight to investigate the gut microbiota change and explained the difference of the gut microbiota after alcohol exposure between pubertal mice and adult mice.

IMPORTANCE: This study elucidates the significant impact of alcohol exposure on the gut microbiota and metabolic pathways in mice, highlighting the differential responses between adolescent and adult stages. Alcohol exposure was found to damage the intestinal barrier, alter the microbial composition by decreasing beneficial bacteria like Lactobacillus, and increase harmful bacteria such as Alistipes. The study also discovered unique microbial changes and resilience in pubertal mice. Species-level metagenomic analysis revealed specific microbial taxa and metabolic functions affected by alcohol. Metagenome-assembled genomes (MAGs) found many species that could not be annotated by conventional methods including many members of Lachnospiraceae, greatly expanding our understanding of the gut microbiota composition. These findings underscore the need for further research on alcohol's effects on various organs and the implications of microbial metabolites on disease progression.}, } @article {pmid39601555, year = {2024}, author = {Gao, Y and Zhang, H and Zhu, D and Guo, L}, title = {Different artificial feeding strategies shape the diverse gut microbial communities and functions with the potential risk of pathogen transmission to captive Asian small-clawed otters (Aonyx cinereus).}, journal = {mSystems}, volume = {9}, number = {12}, pages = {e0095424}, pmid = {39601555}, issn = {2379-5077}, support = {561119219//Scientific research start-up foundation from Lanzhou University/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Otters/microbiology ; *Feces/microbiology ; *Animal Feed/analysis/microbiology ; Animals, Zoo/microbiology ; Diet/veterinary ; Bacteria/genetics/isolation & purification/classification ; Fatty Acids, Volatile/metabolism ; }, abstract = {UNLABELLED: Captive otters raised in zoos are fed different artificial diets, which may shape gut microbiota. The objective is to evaluate the impacts of two different artificial diets on microbial communities and function capabilities and short-chain fatty acid (SCFA) profiles in healthy otters' feces. A total of 16 Asian small-clawed otters in two groups (n = 8) were selected. Group A otters were fed raw loaches supplemented with commercial cat food (LSCF) diet, and group B otters were fed raw crucian diet. The communities and functional capabilities of microbiota in feces were assessed with metagenomic sequencing. Captive otters fed two kinds of diets possessed different gut microbial communities and functional capabilities. Various pathogenic bacteria, like Escherichia coli and Clostridium perfringens, were enriched in the samples from the two groups, respectively. Most of the differential pathways of nutrient metabolism were significantly enriched in group A, and the distributions of carbohydrate enzymes in the two groups significantly differed from each other. Multiple resistance genes markedly accumulated in fecal samples of the group A otters with LSCF diet. Higher concentrations of SCFAs were also observed in group A otters. Two feeding strategies were both likely to facilitate the colonization and expansion of various pathogenic bacteria and the accumulation of resistance genes in the intestines of captive otters, suggesting that risk of pathogen transmission existed in the current feeding process. Commercial cat food could supplement various nutrients and provide a substrate for the production of SCFAs, which might be beneficial for the otters' intestinal fermentation and metabolism.

IMPORTANCE: Captive otters fed with different diets possessed distinct gut microbial communities and functions, with the enrichment of several pathogens and multiple resistance genes in their gut microbiota. The current artificial feeding strategies had the possibility to accelerate the colonization and proliferation of various pathogenic bacteria in the intestines of otters and the spread of resistance genes, increasing the risk of diseases. In addition, supplementation with commercial cat food had benefits for otters' intestinal fermentation and the metabolism of gut microbiota.}, } @article {pmid39601293, year = {2024}, author = {Liu, L and Cao, S and Lin, W and Gao, Z and Yang, L and Zhu, L and Yang, B and Zhang, G and Zhu, R and Wu, D}, title = {miMatch: a microbial metabolic background matching tool for mitigating host confounding in metagenomics research.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2434029}, pmid = {39601293}, issn = {1949-0984}, mesh = {*Metagenomics/methods ; Humans ; Gastrointestinal Microbiome ; Software ; Case-Control Studies ; Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenome ; Propensity Score ; }, abstract = {Metagenomic research faces a persistent challenge due to the low concordance across studies. While matching host confounders can mitigate the impact of individual differences, the influence of factors such as genetics, environment, and lifestyle habits on microbial profiles makes it exceptionally challenging to create fully matched cohorts. The microbial metabolic background, which modulates microbial composition, reflects a cumulative impact of host confounders, serving as an ideal baseline for microbial sample matching. In this study, we introduced miMatch, an innovative metagenomic sample-matching tool that uses microbial metabolic background as a comprehensive reference for host-related variables and employs propensity score matching to build case-control pairs, even in the absence of host confounders. In the simulated datasets, miMatch effectively eliminated individual metabolic background differences, thereby enhancing the accuracy of identifying differential microbial patterns and reducing false positives. Moreover, in real metagenomic data, miMatch improved result consistency and model generalizability across cohorts of the same disease. A user-friendly web server (https://www.biosino.org/iMAC/mimatch) has been established to promote the integration of multiple metagenomic cohorts, strengthening causal relationships in metagenomic research.}, } @article {pmid39599783, year = {2024}, author = {Vila-Nistal, M and Logares, R and Gasol, JM and Martinez-Garcia, M}, title = {Time Series Data Provide Insights into the Evolution and Abundance of One of the Most Abundant Viruses in the Marine Virosphere: The Uncultured Pelagiphages vSAG 37-F6.}, journal = {Viruses}, volume = {16}, number = {11}, pages = {}, pmid = {39599783}, issn = {1999-4915}, support = {PID2021-125175OB-I00//Agencia Estatal de Investigación/ ; CTM2015-70340-R//Agencia Estatal de Investigación/ ; RTI2018-101025-B-I00//Agencia Estatal de Investigación/ ; }, mesh = {*Seawater/virology ; *Metagenomics/methods ; Genome, Viral ; Phylogeny ; Evolution, Molecular ; Aquatic Organisms/virology ; Virome/genetics ; }, abstract = {Viruses play a pivotal role in ecosystems by influencing biochemical cycles and impacting the structure and evolution of their host cells. The widespread pelagiphages infect Pelagibacter spp., the most abundant marine microbe on Earth, and thus play a significant role in carbon transformation through the viral shunt. Among these viruses, the uncultured lytic pelagiphage vSAG 37-F6, uncovered by single-virus genomics, is likely the most numerous virus in the ocean. While previous research has delved into the diversity and spatial distribution of vSAG 37-F6, there is still a gap in understanding its temporal dynamics, hindering our insight into its ecological impact. We explored the temporal dynamics of vSAG 37-F6, assessing periodic fluctuations in abundance and evolutionary patterns using long- and short-term data series. In the long-term series (7 years), metagenomics showed negative selection acting on all viral genes, with a highly conserved overall diversity over time composed of a pool of yearly emergent, highly similar novel strains that exhibited a seasonal abundance pattern with two peaks during winter and fall and a decrease in months with higher UV radiation. Most non-synonymous polymorphisms occurred in structural viral proteins located in regions with low conformational restrictions, suggesting that many of the viral genes of this population are highly purified over its evolution. At the fine-scale resolution (24 h time series), combining digital PCR and metagenomics, we identified two peaks of cellular infection for the targeted vSAG 37-F6 viral strain (up to approximately 10[3] copies/ng of prokaryotic DNA), one before sunrise and the second shortly after midday. Considering the high number of co-occurring strains of this microdiverse virus, the abundance values at the species or genus level could be orders of magnitudes higher. These findings represent a significant advancement in understanding the dynamics of the potentially most abundant oceanic virus, providing valuable insights into ecologically relevant marine viruses.}, } @article {pmid39599719, year = {2024}, author = {Senaprom, S and Namjud, N and Ondee, T and Bumrungpert, A and Pongpirul, K}, title = {Sugar Composition of Thai Desserts and Their Impact on the Gut Microbiome in Healthy Volunteers: A Randomized Controlled Trial.}, journal = {Nutrients}, volume = {16}, number = {22}, pages = {}, pmid = {39599719}, issn = {2072-6643}, support = {FOODF67300006//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; //The 90th Anniversary of Chulalongkorn University, Ratchadaphisek Somphot Fund/ ; //The Second Century Fund (C2F) for PhD Scholarship, Chulalongkorn University/ ; }, mesh = {Adolescent ; Adult ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; Bacteria/classification/genetics ; *Dietary Sugars ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Healthy Volunteers ; RNA, Ribosomal, 16S/genetics ; Thailand ; }, abstract = {BACKGROUND: The relationship between consuming Thai desserts-predominantly composed of carbohydrates-and gut microbiome profiles remains unclear. This study aimed to evaluate the effects of consuming various Thai desserts with different GI values on the gut microbiomes of healthy volunteers.

METHODS: This open-label, parallel randomized clinical trial involved 30 healthy individuals aged 18 to 45 years. Participants were randomly assigned to one of three groups: Phetchaburi's Custard Cake (192 g, low-GI group, n = 10), Saraburi's Curry Puff (98 g, medium-GI group, n = 10), and Lampang's Crispy Rice Cracker (68 g, high-GI group, n = 10), each consumed alongside their standard breakfast. Fecal samples were collected at baseline and 24 h post-intervention for metagenomic analysis of gut microbiome profiles using 16S rRNA gene sequencing.

RESULTS: After 24 h, distinct trends in the relative abundance of various gut microbiota were observed among the dessert groups. In the high-GI dessert group, the abundance of Collinsella and Bifidobacterium decreased compared to the low- and medium-GI groups, while Roseburia and Ruminococcus showed slight increases. Correlation analysis revealed a significant negative relationship between sugar intake and Lactobacillus abundance in the medium- and high-GI groups, but not in the low-GI group. Additionally, a moderately negative association was observed between Akkermansia abundance and sugar intake in the high-GI group. These bacteria are implicated in energy metabolism and insulin regulation. LEfSe analysis identified Porphyromonadaceae and Porphyromonas as core microbiota in the low-GI group, whereas Klebsiella was enriched in the high-GI group, with no predominant bacteria identified in the medium-GI group.

CONCLUSIONS: The findings suggest that Thai desserts with varying GI levels can influence specific gut bacteria, though these effects may be temporary.}, } @article {pmid39598209, year = {2024}, author = {Al-Awthan, YS and Mir, R and Alharbi, BM and Alatawi, AS and Almutairi, FM and Khafaga, T and Shohdi, WM and Fakhry, AM and Alatawi, MM}, title = {Metagenomic Analysis of Sediment Bacterial Diversity and Composition in Natural Lakes and Artificial Waterpoints of Tabuk Region in King Salman Bin Abdulaziz Royal Natural Reserve, Saudi Arabia.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {11}, pages = {}, pmid = {39598209}, issn = {2075-1729}, abstract = {The Tabuk region is located in the northern part of Saudi Arabia, and it has an area of 117,000 km[2] between longitudes 26° N and 29° N and latitudes 34° E and 38° E. King Salman Bin Abdulaziz Royal Natural Reserve (KSRNR) is the largest natural reserve in Saudi Arabia and covers about 130,700 km[2]. It represents a new tourist attraction area in the Tabuk region. Human activities around the lake may lead to changes in water quality, with subsequent changes in microenvironment components, including microbial diversity. The current study was designed to assess possible changes in bacterial communities of the water sediment at some natural lakes and artificial waterpoints of KSRNR. Water samples were collected from ten different locations within KSRNR: W1, W2, W3 (at the border of the royal reserve); W4, W5, W6, W7 (at the middle); and W8, W9, and W10 (artificial waterpoints). The total DNA of the samples was extracted and subjected to 16S rRNA sequencing and metagenomic analysis; also, the environmental parameters (temperature and humidity) were recorded for all locations. Metagenomic sequencing yielded a total of 24,696 operational taxonomic units (OTUs), which were subsequently annotated to 193 phyla, 215 classes, 445 orders, 947 families, and 3960 genera. At the phylum level, Pseudomonadota dominated the microbial communities across all samples. At the class level, Gammaproteobacteria, Clostridia, Alphaproteobacteria, Bacilli, and Betaproteobacteria were the most prevalent. The dominant families included Enterobacteriaceae, Pseudomonadaceae, Clostridiaceae, Comamonadaceae, and Moraxellaceae. At the genus level, Pseudomonas, Clostridium, Acinetobacter, Paenibacillus, and Acidovorax exhibited the highest relative abundances. The most abundant species were Hungatella xylanolytica, Pseudescherichia vulneris, Pseudorhizobium tarimense, Paenibacillus sp. Yn15, and Enterobacter sp. Sa187. The observed species richness revealed substantial heterogeneity across samples using species richness estimators, Chao1 and ACE, indicating particularly high diversity in samples W3, W5, and W6. Current study results help in recognizing the structure of bacterial communities at the Tubaiq area in relation to their surroundings for planning for environmental protection and future restoration of affected ecosystems. The findings highlight the dominance of various bacterial phyla, classes, families, and genera, with remarkable species richness in some areas. These results underscore the influence of human activities on microbial diversity, as well as the significance of monitoring and conserving the reserve's natural ecosystems.}, } @article {pmid39597714, year = {2024}, author = {Yang, T and He, Y and Yang, M and Gao, Z and Zhou, J and Wang, Y}, title = {Community Structure and Biodiversity of Active Microbes in the Deep South China Sea.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597714}, issn = {2076-2607}, support = {42376149//National Natural Science Foundation of China/ ; }, abstract = {The deep ocean harbors a group of highly diversified microbes, while our understanding of the active microbes that are real contributors to the nutrient cycle remains limited. In this study, we report eukaryotic and prokaryotic communities in ~590 m and 1130 m depths using 16S and 18S rRNA Illumina reads (miTags) extracted from 15 metagenomes (MG) and 14 metatranscriptomes (MT). The metagenomic 16S miTags revealed the dominance of Gammaproteobacteria, Alphaproteobacteria, and Nitrososphaeria, while the metatranscriptomic 16S miTags were highly occupied by Gammaproteobacteria, Acidimicrobiia, and SAR324. The consistency of the active taxa between the two depths suggests the homogeneity of the functional microbial groups across the two depths. The eukaryotic microbial communities revealed by the 18S miTags of the metagenomic data are dominated by Polycystinea; however, they were almost all absent in the 18S metatranscriptomic miTags. The active eukaryotes were represented by the Arthropoda class (at 590 m depth), Dinophyceae, and Ciliophora classes. Consistent eukaryotic communities were also exhibited by the 18S miTags of the metatranscriptomic data of the two depths. In terms of biodiversity, the ACE and Shannon indices of the 590 m depth calculated using the 18S metatranscriptomic miTags were much higher than those of the 1130 m depth, while a reverse trend was shown for the indices based on the metagenomic data. Our study reports the active microbiomes functioning in the nutrient utilization and carbon cycle in the deep-sea zone, casting light on the quantification of the ecological processes occurring in the deep ocean.}, } @article {pmid39597627, year = {2024}, author = {Vilo, C and Fábrega, F and Campos, VL and Gómez-Silva, B}, title = {Microbial Biodiversity in Sediment from the Amuyo Ponds: Three Andean Hydrothermal Lagoons in Northern Chile.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597627}, issn = {2076-2607}, support = {FB 0001//ANID, Chile/ ; }, abstract = {The Amuyo Ponds (APs) are a group of three brackish hydrothermal lagoons located at 3700 m above sea level in a pre-Andean setting in the Atacama Desert. Each pond shows a conspicuous green (GP), red (RP), or yellow (YP) coloration, and discharges water rich in arsenic and boron into the Caritaya River (Camarones Basin, northern Chile). Microorganisms are subjected to harsh environmental conditions in these ponds, and the microbial composition and diversity in the Amuyo Ponds' sediments are unknown. The microbial life colonizing AP sediments was explored by metagenomics analyses, showing a diverse microbial life dominated by members of the bacterial domain, with nearly 800 bacterial genome sequences, and sequences associated with Archaea, Eukarya, and viruses. The genus Pseudomonas was more abundant in GP and YP sediments, while the genera Pseudomonas, Aeromonas, and Shewanella were enriched in RP sediments. Archaeal composition was similar in all sediments, and enriched with methanogens sequences from the Archaeoglobi and Halobacteria classes. Abundant fungi sequences were detected in all sediments from the phyla Blastocladiomycota and Ascomycota. We also report putative functional capabilities related to virulence and defense genes, the biosynthesis of secondary metabolites, and tolerance to arsenic. Thirteen bacterial and fourteen viral metagenome-assembled genomes were reconstructed and informed here. This work expands our knowledge on the richness of the microorganisms in the APs and open further studies on the ecology and genomics of this striking Andean geosite.}, } @article {pmid39596262, year = {2024}, author = {Mang, Q and Gao, J and Li, Q and Sun, Y and Xu, G and Xu, P}, title = {Probiotics Enhance Coilia nasus Growth Performance and Nutritional Value by Regulating Glucolipid Metabolism via the Gut-Liver Axis.}, journal = {International journal of molecular sciences}, volume = {25}, number = {22}, pages = {}, pmid = {39596262}, issn = {1422-0067}, support = {32302976//National Natural Science Foundation of China/ ; BK20230179//Natural Science Foundation of Jiangsu Province/ ; 2022YFD2400904//National Key Research and development Program of China/ ; JSGS[2021]134//Jiangsu Province seed industry revitalization "revealing-list" project/ ; }, mesh = {*Probiotics/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Liver/metabolism ; Nutritive Value ; Lipid Metabolism ; Fishes/metabolism/growth & development ; Animal Feed ; Glycolipids/metabolism ; }, abstract = {Large-scale intensive feeding triggered reduced growth performance and nutritional value. Exogenous probiotics can promote the growth performance and nutritional value of fish through improving the intestinal microbiota. However, detailed research on the correlation between the intestinal microbiota, growth performance, and nutritional value remains to be elucidated. Therefore, we performed metagenomic and metabolomic analysis to investigate the effects of probiotic addition to basal diet (1.0 × 10[8] CFU/g) (PF) and water (1.0 × 10[8] CFU/g) (PW) on the growth performance, muscle nutritional value, intestinal microbiota and their metabolites, and glucolipid metabolism in Coilia nasus. The results showed that FBW, BL, and SGR were enhanced in PF and PW groups. The concentrations of EAAs, TAAs, SFAs, MUFAs, and PUFAs were increased in PF and PW groups. Metagenomic and metabolic analyses revealed that bacterial community structure and metabolism were changed in the PF and PW groups. Moreover, adding probiotics to diet and water increased SCFAs and bile acids in the intestine. The gene expression associated with lipolysis and oxidation (hsl, pparα, cpt1, and acadm) and glycolysis (gck and pfk) was upregulated, while the gene expression associated with lipid synthesis (srebp1, acc, dgat, and elovl6) and gluconeogenesis (g6pca1, g6pca2, and pck) was downregulated in the liver. Correlation analysis displayed that hepatic glucolipid metabolism was regulated through the microbiota-gut-liver axis. Mantel test analysis showed that growth performance and muscle nutritional value were improved by the gut-liver axis. Our findings offered novel insights into the mechanisms that underlie the enhancement of growth performance and nutritional value in C. nasus and other fish by adding probiotics.}, } @article {pmid39593380, year = {2024}, author = {Cardinali, F and Rampanti, G and Paderni, G and Milanović, V and Ferrocino, I and Reale, A and Boscaino, F and Raicevic, N and Ilincic, M and Osimani, A and Aquilanti, L and Martinovic, A and Garofalo, C}, title = {A comprehensive study on the autochthonous microbiota, volatilome, physico-chemical, and morpho-textural features of Montenegrin Njeguški cheese.}, journal = {Food research international (Ottawa, Ont.)}, volume = {197}, number = {Pt 1}, pages = {115169}, doi = {10.1016/j.foodres.2024.115169}, pmid = {39593380}, issn = {1873-7145}, mesh = {*Cheese/microbiology/analysis ; *Food Microbiology ; *Microbiota ; *Volatile Organic Compounds/analysis ; *Biogenic Amines/analysis ; Montenegro ; Bacteria/classification ; Odorants/analysis ; }, abstract = {The present study aims to deepen the knowledge of the microbiota, gross composition, physico-chemical and morpho-textural features, biogenic amines content and volatilome of Njeguški cheese, one of the most popular indigenous cheeses produced in Montenegro. Cheese samples were collected in duplicate from three different batches produced by three Montenegrin artisan producers. For the first time, the microbiota of Njeguški cheese was investigated using both culture-dependent techniques and metagenomic analysis. Coagulase positive staphylococci viable counts were below the detection limit of the analysis (<1 log cfu g[-1]). Salmonella spp., Listeria monocytogenes and staphylococcal enterotoxins were absent. However, relatively high viable counts of Enterobacteriaceae, Escherichia coli, Pseudomonadaceae and eumycetes were detected. Metataxonomic analysis revealed a core microbiome composed of Lactococcus lactis, Streptococcus thermophilus, Debaryomyces hansenii, and Kluyveromyces marxianus. Furthermore, the detection of opportunistic pathogenic yeasts such as Magnusiomyces capitatus and Wickerhamiella pararugosa, along with the variable content of biogenic amines, suggests the need for increased attention to hygienic conditions during Njeguški cheese production. Significant variability was observed in humidity (ranging from 38.37 to 45.58 %), salt content (ranging from 0.70 to 1.78 %), proteins content (ranging from 21.42 to 25.08 %), ash content (ranging from 2.97 to 4.05 %), hardness, springiness, and color among samples from different producers. Gas chromatography-mass spectrometry analysis showed a well-defined and complex volatilome profile of the Njeguški cheese, with alcohols (ethanol, isoamyl alcohol, phenetyl alcol), esters and acetates (ethyl acetate, ethyl butanoate, isoamyl acetate), ketones (acetoin, 2-butanone), and acids (acetic, butanoic, hexanoic acids) being the main chemical groups involved in aroma formation. This research will provide new insights into the still poorly explored identity of Njeguški cheese, thus serving as a first baseline for future studies aimed at protecting its tradition.}, } @article {pmid39593354, year = {2024}, author = {Peng, Q and Zheng, H and Zhou, H and Chen, J and Xu, Y and Wang, Z and Xie, G}, title = {Elucidating core microbiota in yellow wine (Huangjiu) through flavor-oriented synthesis and construction of microbial communities.}, journal = {Food research international (Ottawa, Ont.)}, volume = {197}, number = {Pt 1}, pages = {115139}, doi = {10.1016/j.foodres.2024.115139}, pmid = {39593354}, issn = {1873-7145}, mesh = {*Volatile Organic Compounds/analysis ; *Fermentation ; *Microbiota ; *Wine/analysis/microbiology ; *Taste ; Humans ; Gas Chromatography-Mass Spectrometry ; Solid Phase Microextraction ; Pentanols/metabolism/analysis ; Odorants/analysis ; Flavoring Agents/analysis ; China ; Male ; Saccharomyces cerevisiae/metabolism ; Food Microbiology ; Female ; Phenylethyl Alcohol/metabolism/analysis ; Adult ; Butanols ; }, abstract = {Huangjiu, a traditional Chinese alcoholic beverage with a history spanning thousands of years, holds significant cultural and economic value in China. Despite its importance, the complexity of Huangjiu fermentation and the intricate interactions within its microbial community remain underexplored. This study addresses this gap by identifying the core volatile organic compounds (VOCs) and key microorganisms that define the flavor profile of Huangjiu. We employed HS-SPME-GC-MS along with aroma reconstitution and omission experiments to identify core VOCs, including Isobutanol, Isoamyl alcohol, β-Phenylethanol, and others. Metagenomic sequencing combined with QPCR was used to analyze microbial communities, revealing the temporal and spatial dynamics during fermentation. A synthetic microbial community model was constructed using the core microbes identified: Saccharomyces cerevisiae, Lactobacillus brevis, Saccharopolyspora rectivirgula, Bacillus subtilis, Leuconostoc citreum, Lactobacillus plantarum, Lactobacillus curvatus, Lactobacillus casei, and Aspergillus oryzae. This model successfully replicated Huangjiu's core VOCs and sensory characteristics, increased alcohol content, and reduced acidity. Our study contributes valuable insights into the microbial influences on Huangjiu quality, paving the way for its enhanced production and providing a foundation for future research in fermented beverages.}, } @article {pmid39593339, year = {2024}, author = {Scarano, L and Peruzy, MF and Fallico, V and Blaiotta, G and Aponte, M and Anastasio, A and Murru, N}, title = {Provolone del Monaco PDO cheese: Lactic microflora, biogenic amines and volatilome characterization.}, journal = {Food research international (Ottawa, Ont.)}, volume = {197}, number = {Pt 1}, pages = {115257}, doi = {10.1016/j.foodres.2024.115257}, pmid = {39593339}, issn = {1873-7145}, mesh = {*Cheese/analysis/microbiology ; *Biogenic Amines/analysis ; *Lactobacillales/classification/genetics/isolation & purification ; *Volatile Organic Compounds/analysis ; Metagenome/genetics ; RNA, Ribosomal, 16S ; Microbiota/genetics ; Bacterial Load ; *Food Microbiology ; }, abstract = {One commercial production run of Provolone del Monaco - a long-ripened pasta filata cheese - was followed up to the end of ripening for a total of 20 samples. 371 LAB isolates were subject to genetic characterization followed by 16S rRNA gene sequencing. The dominant species were Lacticaseibacillus casei/paracasei (19.4 %), Streptococcus macedonicus (19.1 %) and Enterococcus faecalis (13.2 %). Strains were screened for features of technological interest or safety relevance. Tyramine-producing cultures were quite common, above all within enterococci. By MALDI TOF Mass Spectrometry, one Lactococcus lactis and one Enterococcus faecium strain proved to be bacteriocin producers. Four further cheese wheels from the same production run at 623 days of ripening were evaluated for volatile organic compounds, biogenic amines, and bacterial community by metagenomic sequencing. Three individual wheel samples shared a rather similar microbiome with Lactobacillus delbrueckii and Streptococcus thermophilus as the most represented species, while the fourth wheel appeared wholly different being dominated by Lentilactobacillus buchneri and St. infantarius. Additionally, this sample had the greatest content of biogenic amines and a different VOCs composition. Given the variance seen among cheese wheels processed and ripened under the same conditions, the search for adjunct cultures in the production of this cheese seems to be of utmost importance.}, } @article {pmid39593310, year = {2024}, author = {Li, X and Du, C and Zhao, Y and Li, J and Hu, Y and Dong, W and Peng, N and Zhao, S}, title = {Differences in microbial communities among different types of zaopei and their effects on quality and flavor of baijiu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {197}, number = {Pt 1}, pages = {115224}, doi = {10.1016/j.foodres.2024.115224}, pmid = {39593310}, issn = {1873-7145}, mesh = {*Fermentation ; *Microbiota ; *Food Microbiology ; *Taste ; Ethanol/metabolism ; Fermented Foods/microbiology ; Lactobacillales/genetics/metabolism/classification ; Lactic Acid/metabolism/analysis ; Fungi/classification/genetics ; Acetic Acid/metabolism/analysis ; Oryza/microbiology ; Bacteria/classification/genetics/metabolism ; Flavoring Agents/analysis ; }, abstract = {Three types of zaopei (fermented grain) of xiaoqu light-flavor baijiu (XQZP), daqu light-flavor baijiu (DQZP), and strong-flavor baijiu (SFZP) at the end of fermentation and their dominant lactic acid bacteria were systematically compared and analyzed in this study. The results showed that these three types of zaopei differed significantly in acidity, reducing sugar content, and ethanol content, and that the main factors influencing their microbial community were acidity and lactic acid. The diversity and contents of flavor substances were significantly higher in SFZP than in DQZP and XQZP. Additionally, there was a strong correlation between dominant lactic acid bacteria and flavor substances in all three zaopei, but the correlation between fungi and flavor substances was higher than that between bacteria and flavor substances. Differential gene analysis revealed that the microbial activities followed the order of SFZP > DQZP > XQZP. The KEGG enrichment analysis indicated that the differential genes from different zaopei were enriched in different metabolic pathways. Furthermore, various microorganisms in 3 types of zaopei contained different functional genes, of which fungi mainly contained genes responsible for the synthesis of ethanol and acetic acid, while lactic acid bacteria mainly contained genes responsible for the synthesis of lactic acid. In XQZP, L. helveticus was dominant lactic acid bacteria prominent in acetic acid tolerance and lactic acid production; in DQZP, L. acetotolerans was remarkable in its tolerance to lactic acid, acetic acid, ethanol and lactic acid production; and in SFZP, A. jinshanensis was superior in acetic acid tolerance and production. Taken together, this study reveals the mechanism underlying flavor differences among three types of baijiu and provides valuable references for the development and utilization of baijiu microbial resources.}, } @article {pmid39592704, year = {2024}, author = {Hai, C and Hao, Z and Bu, L and Lei, J and Liu, X and Zhao, Y and Bai, C and Su, G and Yang, L and Li, G}, title = {Increased rumen Prevotella enhances BCAA synthesis, leading to synergistically increased skeletal muscle in myostatin-knockout cattle.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1575}, pmid = {39592704}, issn = {2399-3642}, support = {32360837, 32341052//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Cattle ; *Myostatin/genetics/metabolism ; *Amino Acids, Branched-Chain/metabolism/biosynthesis ; *Prevotella/genetics/metabolism ; *Muscle, Skeletal/metabolism ; *Rumen/microbiology/metabolism ; Gene Knockout Techniques ; Gastrointestinal Microbiome/genetics ; }, abstract = {Myostatin (MSTN) is a negative regulator of muscle growth, and its relationship with the gut microbiota is not well understood. In this study, we observed increase muscle area and branched-chain amino acids (BCAAs), an energy source of muscle, in myostatin knockout (MSTN-KO) cattle. To explore the link between increased BCAAs and rumen microbiota, we performed metagenomic sequencing, metabolome analysis of rumen fluid, and muscle transcriptomics. MSTN-KO cattle showed a significant increase in the phylum Bacteroidota (formerly Bacteroidetes), particularly the genus Prevotella (P = 3.12e-04). Within this genus, Prevotella_sp._CAG:732, Prevotella_sp._MSX73, and Prevotella_sp._MA2016 showed significant upregulation of genes related to BCAA synthesis. Functional enrichment analysis indicated enrichment of BCAA synthesis-related pathways in both rumen metagenomes and metabolomes. Additionally, muscle transcriptomics indicated enrichment in muscle fiber and amino acid metabolism, with upregulation of solute carrier family genes, enhancing BCAA transport. These findings suggest that elevated rumen Prevotella in MSTN-KO cattle, combined with MSTN deletion, synergistically improves muscle growth through enhanced BCAA synthesis and transport.}, } @article {pmid39591974, year = {2024}, author = {Peng, Y and Zhu, J and Wang, S and Liu, Y and Liu, X and DeLeon, O and Zhu, W and Xu, Z and Zhang, X and Zhao, S and Liang, S and Li, H and Ho, B and Ching, JY and Cheung, CP and Leung, TF and Tam, WH and Leung, TY and Chang, EB and Chan, FKL and Zhang, L and Ng, SC and Tun, HM}, title = {A metagenome-assembled genome inventory for children reveals early-life gut bacteriome and virome dynamics.}, journal = {Cell host & microbe}, volume = {32}, number = {12}, pages = {2212-2230.e8}, doi = {10.1016/j.chom.2024.10.017}, pmid = {39591974}, issn = {1934-6069}, mesh = {*Gastrointestinal Microbiome/genetics ; Infant ; Humans ; *Virome/genetics ; *Metagenome/genetics ; Child, Preschool ; Infant, Newborn ; Child ; Bacteriophages/genetics/isolation & purification ; Bacteria/genetics/virology/classification ; Genome, Viral/genetics ; Feces/microbiology/virology ; Metagenomics/methods ; Female ; Bifidobacterium/genetics/isolation & purification/classification ; Phylogeny ; Male ; Genome, Bacterial ; }, abstract = {Existing microbiota databases are biased toward adult samples, hampering accurate profiling of the infant gut microbiome. Here, we generated a metagenome-assembled genome inventory for children (MAGIC) from a large collection of bulk and viral-like particle-enriched metagenomes from 0 to 7 years of age, encompassing 3,299 prokaryotic and 139,624 viral species-level genomes, 8.5% and 63.9% of which are unique to MAGIC. MAGIC improves early-life microbiome profiling, with the greatest improvement in read mapping observed in Africans. We then identified 54 candidate keystone species, including several Bifidobacterium spp. and four phages, forming guilds that fluctuated in abundance with time. Their abundances were reduced in preterm infants and were associated with childhood allergies. By analyzing the B. longum pangenome, we found evidence of phage-mediated evolution and quorum sensing-related ecological adaptation. Together, the MAGIC database recovers genomes that enable characterization of the dynamics of early-life microbiomes, identification of candidate keystone species, and strain-level study of target species.}, } @article {pmid39591453, year = {2024}, author = {Wang, L and Liu, Y and Ni, H and Zuo, W and Shi, H and Liao, W and Liu, H and Chen, J and Bai, Y and Yue, H and Huang, A and Friedman, J and Si, T and Liu, Y and Chen, M and Dai, L}, title = {Systematic characterization of plant-associated bacteria that can degrade indole-3-acetic acid.}, journal = {PLoS biology}, volume = {22}, number = {11}, pages = {e3002921}, pmid = {39591453}, issn = {1545-7885}, mesh = {*Indoleacetic Acids/metabolism ; *Oryza/microbiology/metabolism ; *Arabidopsis/microbiology/metabolism ; *Plant Roots/microbiology/metabolism ; *Bacteria/metabolism/genetics ; Plant Growth Regulators/metabolism ; Rhizosphere ; Soil Microbiology ; Phylogeny ; Operon/genetics ; Microbiota/physiology ; Seedlings/microbiology/metabolism ; }, abstract = {Plant-associated microbiota affect pant growth and development by regulating plant hormones homeostasis. Indole-3-acetic acid (IAA), a well-known plant hormone, can be produced by various plant-associated bacteria. However, the prevalence of bacteria with the capacity to degrade IAA in the rhizosphere has not been systematically studied. In this study, we analyzed the IAA degradation capabilities of bacterial isolates from the roots of Arabidopsis and rice. Using genomics analysis and in vitro assays, we found that 21 out of 183 taxonomically diverse bacterial isolates possess the ability to degrade IAA. Through comparative genomics and transcriptomic assays, we identified iac-like or iad-like operon in the genomes of these IAA degraders. Additionally, the putative regulator of the operon was found to be highly conserved among these strains through protein structure similarity analysis. Some of the IAA degraders could utilize IAA as their carbon and energy source. In planta, most of the IAA degrading strains mitigated Arabidopsis and rice seedling root growth inhibition (RGI) triggered by exogenous IAA. Moreover, RGI caused by complex synthetic bacterial community can be alleviated by introducing IAA degraders. Importantly, we observed increased colonization preference of IAA degraders from soil to root according to the frequency of the biomarker genes in metagenome-assembled genomes (MAGs) collected from different habitats, suggesting that there is a close association between IAA degraders and IAA producers. In summary, our findings further the understanding of the functional diversity and potential biological roles of plant-associated bacteria in host plant root morphogenesis.}, } @article {pmid39589660, year = {2024}, author = {Xue, X and Zhao, Z and Zhao, LB and Gao, YH and Xu, WH and Cai, WM and Chen, SH and Li, TJ and Nie, TY and Rui, D and Ma, Y and Qian, XS and Lin, JL and Liu, L}, title = {Gut microbiota changes in healthy individuals, obstructive sleep apnea patients, and patients treated using continuous positive airway pressure: a whole-genome metagenomic analysis.}, journal = {Sleep & breathing = Schlaf & Atmung}, volume = {29}, number = {1}, pages = {11}, pmid = {39589660}, issn = {1522-1709}, support = {22BJZ52//Military Health Care Project/ ; 23BJZ27//Military Health Care Project/ ; SYDW_KY[2021]04//Military experimental animal special research project/ ; }, mesh = {Humans ; *Continuous Positive Airway Pressure ; *Sleep Apnea, Obstructive/therapy/microbiology ; *Gastrointestinal Microbiome/physiology/genetics ; Male ; Middle Aged ; Female ; Adult ; *Metagenomics ; Polysomnography ; }, abstract = {PURPOSE: This study investigated variations in gut microbiota among severe obstructive sleep apnea (OSA) patients and changes in gut microbiota after continuous positive airway pressure (CPAP) treatment.

METHOD: From November 2020 to August 2021, laboratory-based polysomnography (PSG) was used to measure sleep parameters in healthy controls, severe OSA patients, and severe OSA patients treated with CPAP for three months. A fully automated biochemical analyzer was used to evaluate routine blood tests and biochemical indicators. Whole-genome metagenomic analysis was used to determine the microbial composition of gut samples from all participants. The relationships between gut microbiota and hypertension were examined using correlation analysis.

RESULT: The relative abundances of Bacteroides, Firmicutes, and Parabacteroides were significantly lower at the species level. Enterobacterales and Turicibacter were significantly higher in participants with severe OSA than healthy controls. Negative correlations were identified between Bacteroides coprocola and systolic blood pressure (SBP) (r =  - 0.710, P = 0.003) and diastolic blood pressure (DBP) (r =  - 0.615, P = 0.015). Conversely, a positive correlation was found between Escherichia coli and SBP (r = 0.568, P = 0.027).

CONCLUSION: The metabolic pathways and gut microbiota differed significantly between the control group and individuals with severe OSA. Additionally, CPAP therapy substantially changed the metabolic pathways and gut microbial composition among patients diagnosed with severe OSA. Correlation analysis further revealed a strong association between Escherichia coli, Bacteroides coprocola, and blood pressure levels.}, } @article {pmid39589588, year = {2024}, author = {Wanna, W and Aucharean, C and Jaeram, N}, title = {Analysis of Gut Microbiota Associated with WSSV Resistance in Litopenaeus vannamei.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {27}, number = {1}, pages = {10}, pmid = {39589588}, issn = {1436-2236}, support = {SCI6601054S//The National Science, Research and Innovation Fund (NSRF) and Prince of Songkla University/ ; SCI6601054S//The National Science, Research and Innovation Fund (NSRF) and Prince of Songkla University/ ; PSU_PHD2565-004//The Graduate School, Prince of Songkla University/ ; }, mesh = {Animals ; *Penaeidae/microbiology/virology ; *White spot syndrome virus 1/genetics ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; Disease Resistance/genetics ; Metagenome ; }, abstract = {Microorganisms in the digestive tract regulate the metabolism of host cells as well as stimulate the immune system of the host. If the microbiota is in good balance, it will promote the good health of the host. In this study, using 16S rRNA sequencing, we analyzed the microbiota of three groups of shrimp: a group of normal shrimp (control group), shrimp that were killed by infection with the white spot syndrome virus (WSSV) (susceptible group), and shrimp that survived WSSV infection (resistant group). The results showed that although the alpha diversity of the microbiota was barely affected by the WSSV, the bacterial communities in the three groups had different prevalences. The resistant group harbored significantly more bacteria than both the other groups. Remarkably, the resistant group had the greatest prevalence of the phylum Bacterioidetes, the families Rhodobacteraceae and Flavobacteriaceae, and the genus Nautella, suggesting their potential as biomarkers for shrimp resistance to WSSV infection. In addition, analysis of functional diversity in bacterial communities showed that the abundance of bacterial metagenomes in two groups infected with WSSV was mostly linked to metabolism and cellular processes. The susceptible WSSV group exhibited a significant reduction in amino acid metabolism. This result suggested that metabolism was the principal factor affecting the alteration in the microbiota after WSSV infection. This overview of the gut microbiota of shrimp infected with the WSSV offers crucial insights for aquaculture management and simplifies the use of control strategies in the future.}, } @article {pmid39589125, year = {2024}, author = {Zhang, Z and Tong, M and Ding, W and Liu, S and Jong, M-C and Radwan, AA and Cai, Z and Zhou, J}, title = {Changes in the diversity and functionality of viruses that can bleach healthy coral.}, journal = {mSphere}, volume = {9}, number = {12}, pages = {e0081624}, pmid = {39589125}, issn = {2379-5042}, mesh = {*Anthozoa/virology/microbiology ; Animals ; *Microbiota/genetics ; *Viruses/genetics/classification ; *Metagenomics ; Bacteria/genetics/classification/virology/isolation & purification ; Symbiosis ; Bacteriophages/genetics/physiology/classification/isolation & purification ; }, abstract = {UNLABELLED: Coral microbiomes play a crucial role in maintaining the health and functionality of holobionts. Disruption in the equilibrium of holobionts, including bacteria, fungi, and archaea, can result in the bleaching of coral. However, little is known about the viruses that can infect holobionts in coral, especially bacteriophages. Here, we employed a combination of amplicon and metagenomic analyses on Acropora muricata and Galaxea astreata to investigate the diversity and functionality of viruses in healthy and bleached corals. Analysis showed that the alpha diversity of holobionts (bacteria, eukaryotes, zooxanthellae, and lysogenic and lytic viruses) was higher in bleached corals than that in healthy corals. Meanwhile, bleached corals exhibited a relatively higher abundance of specific viral classes, including Revtraviricetes, Arfiviricetes, Faserviricetes, Caudoviricetes, Herviviricetes, and Tectiliviricetes; moreover, we found that the expression levels of functional genes involved in carbon and sulfur metabolism were enriched. An increase in Vibrio abundance has been reported as a notable factor in coral bleaching; our analysis also revealed an increased abundance of Vibrio in bleached coral. Finally, bleached corals contained a higher abundance of Vibrio phages and encoded more virulence factor genes to increase the competitiveness of Vibrio after coral bleaching. In conclusion, we attempted to understand the causes of coral bleaching from the perspective of phage-bacteria-coral tripartite interaction.

IMPORTANCE: Viruses, especially bacteriophages, outnumber other microorganisms by approximately 10-fold and represent the most abundant members of coral holobionts. Corals represent a model system for the study of symbiosis, the influence of viruses on organisms inhabiting healthy coral reef, the role of rapid horizontal gene transfer, and the expression of auxiliary metabolic genes. However, the least studied component of coral holobiont are viruses. Therefore, there is a critical need to investigate the viral community of viruses, and their functionality, in healthy and bleached coral. Here, we compared the composition and functionality of viruses in healthy and bleached corals and found that viruses may participate in the induction of coral bleaching by enhancing the expression of virulence genes and other auxiliary metabolic functions.}, } @article {pmid39588334, year = {2024}, author = {Zhang, J and Wu, L and Zhang, Z and Li, D and Han, R and Ye, L and Zhang, Y and Hong, J and Gu, W}, title = {Gut microbiota and metabolic profiles in adults with unclassified diabetes: a cross-sectional study.}, journal = {Frontiers in endocrinology}, volume = {15}, number = {}, pages = {1440984}, pmid = {39588334}, issn = {1664-2392}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Adult ; Case-Control Studies ; Cross-Sectional Studies ; *Diabetes Mellitus, Type 2/microbiology/metabolism/blood ; *Metabolome ; Diabetes Mellitus, Type 1/microbiology/metabolism/blood ; Biomarkers/blood ; Young Adult ; }, abstract = {AIMS: Our study, employing a multi-omics approach, aimed to delineate the distinct gut microbiota and metabolic characteristics in individuals under 30 with unclassified diabetes, thus shedding light on the underlying pathophysiological mechanisms.

METHODS: This age- and sex-matched case-control study involved 18 patients with unclassified diabetes, 18 patients with classic type 1 diabetes, 13 patients with type 2 diabetes, and 18 healthy individuals. Metagenomics facilitated the profiling of the gut microbiota, while untargeted liquid chromatography-mass spectrometry was used to quantify the serum lipids and metabolites.

RESULTS: Our findings revealed a unique gut microbiota composition in unclassified diabetes patients, marked by a depletion of Butyrivibrio proteoclasticus and Clostridium and an increase in Ruminococcus torques and Lachnospiraceae bacterium 8_1_57FAA. Comparative analysis identified the combined marker panel of five bacterial species, seven serum biomarkers, and three clinical parameters could differentiate patients with UDM from HCs with an AUC of 0.94 (95% CI 0.85-1). Notably, the gut microbiota structure of patients with unclassified diabetes resembled that of type 2 diabetes patients, especially regarding disrupted lipid and branched-chain amino acid metabolism.

CONCLUSIONS: Despite sharing certain metabolic features with type 2 diabetes, unclassified diabetes presents unique features. The distinct microbiota and metabolites in unclassified diabetes patients suggest a significant role in modulating glucose, lipid, and amino acid metabolism, potentially influencing disease progression. Further longitudinal studies are essential to explore therapeutic strategies targeting the gut microbiota and metabolites to modify the disease trajectory.}, } @article {pmid39587811, year = {2024}, author = {Xu, N and Chen, B and Wang, Y and Lei, C and Zhang, Z and Ye, Y and Jin, M and Zhang, Q and Lu, T and Dong, H and Shou, J and Penuelas, J and Zhu, YG and Qian, H}, title = {Integrating Anthropogenic-Pesticide Interactions Into a Soil Health-Microbial Index for Sustainable Agriculture at Global Scale.}, journal = {Global change biology}, volume = {30}, number = {11}, pages = {e17596}, doi = {10.1111/gcb.17596}, pmid = {39587811}, issn = {1365-2486}, support = {22376187//National Natural Science Foundation of China/ ; 21777144//National Natural Science Foundation of China/ ; 21976161//National Natural Science Foundation of China/ ; LZ23B070001//Zhejiang Provincial Natural Science Foundation of China/ ; 2021YFA0909500//National Key Research and Development Program of China/ ; MMLKF23-03//Open Funding Project of the State Key Laboratory of Microbial Metabolism/ ; TED2021-132627 B-I00//MCIN, AEI/10.13039/501100011033 European Union Next Generation EU/PRTR/ ; PID2022-140808NB-I00//Spanish Government grants/ ; }, mesh = {*Soil Microbiology ; *Agriculture/methods ; *Pesticides/analysis ; Microbiota ; Sustainable Development ; Soil/chemistry ; Metagenome ; Soil Pollutants/analysis ; Machine Learning ; }, abstract = {Soil microbiota in intensive agriculture are threatened by pesticides, economic activities, and land-use changes. However, the interactions among these anthropogenic factors remain underexplored. By analyzing 2356 soil metagenomes from around the world, we developed a comprehensive soil health-microbial index that integrates microbial diversity, nutrient cycling potential, metabolic potential, primary productivity, and health risks to assess how the soil microbiota respond to anthropogenic factors. Our results indicated that the health-microbial index was the lowest with severe pesticide contamination. Pesticides, in combination with other anthropogenic and climatic factors, exacerbate the decline in this index. Machine learning predictions suggest that the health-microbial index in approximately 26% of global farmland could decline between 2015 and 2040, even under sustainable development scenarios. Even with strategies to reduce pesticide usage, we cannot completely halt the decline in the health-microbial index. Our findings highlight that sustaining soil microbial health on a global scale requires addressing not only pesticide management but also broader anthropogenic impacts.}, } @article {pmid39587335, year = {2024}, author = {Liu, Y and Du, S and Sun, L and Li, Y and Liu, M and Sun, P and Bai, B and Ge, G and Jia, Y and Wang, Z}, title = {Volatile metabolomics and metagenomics reveal the effects of lactic acid bacteria on alfalfa silage quality, microbial communities, and volatile organic compounds.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1565}, pmid = {39587335}, issn = {2399-3642}, mesh = {*Volatile Organic Compounds/metabolism/analysis ; *Silage/microbiology/analysis ; *Metabolomics/methods ; *Microbiota ; *Metagenomics/methods ; *Medicago sativa/microbiology/metabolism ; Lactobacillales/metabolism/genetics ; Lactobacillus plantarum/metabolism/genetics ; }, abstract = {Lactic acid bacteria metabolism affects the composition of volatile organic compounds (VOCs) in alfalfa silage, which results in differences of odor and quality. The aim of this study was to reveal the effects of commercial Lactobacillus plantarum (CL), screened Lactobacillus plantarum (LP), and screened Pediococcus pentosaceus (PP) on quality, microbial community, and VOCs of alfalfa silage based on volatile metabolomics and metagenomics. The results showed that the LP and PP groups had higher sensory and quality grades, and the dominant bacteria were Lactiplantibacillus plantarum and Pediococcus pentosaceus. The main VOCs in alfalfa silage were terpenoids (25.29%), esters (17.08%), and heterocyclic compounds (14.43%), and esters such as methyl benzoate, ethyl benzoate, and ethyl salicylate were significantly increased in the LP and PP groups (P < 0.05). Correlation analysis showed that terpenoids, esters, and alcohols with aromatic odors were positively correlated with Lactiplantibacillus plantarum and Pediococcus pentosaceus. Microbial functions in carbohydrate and amino acid metabolism, biosynthesis of secondary metabolites, and degradation of aromatic compounds were significantly enriched. In conclusion, the addition of lactic acid bacteria can increase the aromatic substances in silage and further improve silage odor and quality.}, } @article {pmid39587088, year = {2024}, author = {Honorato, L and Paião, HGO and da Costa, AC and Tozetto-Mendoza, TR and Mendes-Correa, MC and Witkin, SS}, title = {Viruses in the female lower reproductive tract: a systematic descriptive review of metagenomic investigations.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {137}, pmid = {39587088}, issn = {2055-5008}, mesh = {Female ; Humans ; *Metagenomics/methods ; *Viruses/genetics/classification ; *Virome ; Microbiota ; Genitalia, Female/virology/microbiology ; Metagenome ; }, abstract = {The lower female reproductive tract (FRT) hosts a complex microbial environment, including eukaryotic and prokaryotic viruses (the virome), whose roles in health and disease are not fully understood. This review consolidates findings on FRT virome composition, revealing the presence of various viral families and noting significant gaps in knowledge. Understanding interactions between the virome, microbiome, and immune system will provide novel insights for preventing and managing lower genital tract disorders.}, } @article {pmid39586993, year = {2024}, author = {Zhao, Y and Bhatnagar, S}, title = {Epigenetic Modulations by Microbiome in Breast Cancer.}, journal = {Advances in experimental medicine and biology}, volume = {1465}, number = {}, pages = {55-69}, doi = {10.1007/978-3-031-66686-5_4}, pmid = {39586993}, issn = {0065-2598}, mesh = {Humans ; *Breast Neoplasms/genetics/microbiology ; *Epigenesis, Genetic ; Female ; *Tumor Microenvironment/genetics ; *Gene Expression Regulation, Neoplastic ; Microbiota/genetics ; Animals ; DNA Methylation ; Gastrointestinal Microbiome/genetics ; }, abstract = {Recent studies have identified a critical role of the diverse and dynamic microbiome in modulating various aspects of host physiology and intrinsic processes. However, the altered microbiome has also become a hallmark of cancer, which could influence the tumor microenvironment. Aberrations in epigenetic regulation of tumor suppressors, apoptotic genes, and oncogenes can accentuate breast cancer onset and progression. Interestingly, recent studies have established that the microbiota modulates the epigenetic mechanisms at global and gene-specific levels. While the mechanistic basis is unclear, the cross-talk between the microbiome and epigenetics influences breast cancer trajectory. Here, we review different epigenetic mechanisms of mammalian gene expression and summarize the host-associated microbiota distributed across the human body and their influence on cancer and other disease-related genes. Understanding this complex relationship between epigenetics and the microbiome holds promise for new insights into effective therapeutic strategies for breast cancer patients.}, } @article {pmid39585984, year = {2024}, author = {Padhi, C and Field, CM and Forneris, CC and Olszewski, D and Fraley, AE and Sandu, I and Scott, TA and Farnung, J and Ruscheweyh, HJ and Narayan Panda, A and Oxenius, A and Greber, UF and Bode, JW and Sunagawa, S and Raina, V and Suar, M and Piel, J}, title = {Metagenomic study of lake microbial mats reveals protease-inhibiting antiviral peptides from a core microbiome member.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {49}, pages = {e2409026121}, pmid = {39585984}, issn = {1091-6490}, support = {1-001369-000//Promedica Stiftung/ ; 205320_185077//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 205320_219638//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 310030_212802//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; n/a//Peter und Traudl Engelhorn Stiftung (Peter and Traudl Engelhorn Foundation)/ ; 897571//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, mesh = {*Lakes/microbiology ; *Antiviral Agents/pharmacology/chemistry ; *Microbiota ; *Metagenomics/methods ; Protease Inhibitors/pharmacology/metabolism ; Peptides/metabolism/chemistry ; Multigene Family ; Metagenome ; India ; Bacteria/drug effects/genetics/metabolism ; }, abstract = {In contrast to the large body of work on bioactive natural products from individually cultivated bacteria, the chemistry of environmental microbial communities remains largely elusive. Here, we present a comprehensive bioinformatic and functional study on a complex and interaction-rich ecosystem, algal-bacterial (microbial) mats of Lake Chilika in India, Asia's largest brackish water body. We report the bacterial compositional dynamics over the mat life cycle, >1,300 reconstructed environmental genomes harboring >2,200 biosynthetic gene clusters (BGCs), the successful cultivation of a widespread core microbiome member belonging to the genus Rheinheimera, heterologous reconstitution of two silent Rheinheimera biosynthetic pathways, and new compounds with potent protease inhibitory and antiviral activities. The identified substances, posttranslationally modified peptides from the graspetide and spliceotide families, were targeted among the large BGC diversity by applying a strategy focusing on recurring multi-BGC loci identified in diverse samples, suggesting their presence in successful colonizers. In addition to providing broad insights into the biosynthetic potential of a poorly studied community from sampling to bioactive substances, the study highlights the potential of ribosomally synthesized and posttranslationally modified peptides as a large, underexplored resource for antiviral drug discovery.}, } @article {pmid39584840, year = {2024}, author = {Bernardin, JR and Young, EB and Gray, SM and Bittleston, LS}, title = {Bacterial community function increases leaf growth in a pitcher plant experimental system.}, journal = {mSystems}, volume = {9}, number = {12}, pages = {e0129824}, pmid = {39584840}, issn = {2379-5077}, mesh = {*Plant Leaves/microbiology/growth & development ; *Sarraceniaceae/microbiology ; *Microbiota/physiology ; *Bacteria/genetics ; Metagenomics ; }, abstract = {UNLABELLED: Across diverse ecosystems, bacteria and their hosts engage in complex relationships having negative, neutral, or positive interactions. However, the specific effects of leaf-associated bacterial community functions on plant growth are poorly understood. Although microbes can promote plant growth through various biochemical mechanisms, investigating the community's functional contributions to plant growth remains to be explored. To address this gap, we characterized the relationships between bacterial community function and host plant growth in the purple pitcher plant (Sarracenia purpurea). The main aim of our research was to investigate how different bacterial community functions affect the growth and nutrient content in the plant. Previous research has suggested that microbial communities aid in prey decomposition and subsequent nutrient acquisition in carnivorous plants, including S. purpurea. However, the specific functional roles of bacterial communities in plant growth and nutrient uptake are not well known. In this study, sterile, freshly opened pitchers were inoculated with three functionally distinct, pre-assembled bacterial communities. Bacterial community composition and function were measured over 8 weeks using physiological assays, metagenomics, and metatranscriptomics. Distinct community functions affected plant traits; a bacterial community enriched in decomposition was associated with larger leaves with almost double the biomass of control pitchers. Physiological differences in bacterial communities were supported by metatranscriptomics; for example, the bacterial community with the highest chitinase activity had greater expression of transcripts associated with chitinase enzymes. The relationship between bacterial community function and plant growth observed here indicates potential mechanisms, such as chitinase activity, for host-associated bacterial functions to support pitcher plant growth.

IMPORTANCE: This study addresses a gap in understanding the relationships between bacterial community function and plant growth. We inoculated sterile, freshly opened pitcher plant leaves with three functionally distinct bacterial communities to uncover potential mechanisms through which bacterial functions support plant health and growth. Our findings demonstrate that distinct community functions significantly influence plant traits, with some bacterial communities supporting more plant growth than in control pitchers. These results highlight the ecological roles of microbial communities in plants and thus ecosystems and suggest that nutrient cycling is an important pathway through which microbes support host plant health. This research provides valuable insights into plant-microbe interactions and the effects of diverse microbial community functions.}, } @article {pmid39582065, year = {2024}, author = {Velsko, IM and Fagernäs, Z and Tromp, M and Bedford, S and Buckley, HR and Clark, G and Dudgeon, J and Flexner, J and Galipaud, JC and Kinaston, R and Lewis, CM and Matisoo-Smith, E and Nägele, K and Ozga, AT and Posth, C and Rohrlach, AB and Shing, R and Simanjuntak, T and Spriggs, M and Tamarii, A and Valentin, F and Willie, E and Warinner, C}, title = {Exploring the potential of dental calculus to shed light on past human migrations in Oceania.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10191}, pmid = {39582065}, issn = {2041-1723}, support = {EXC 2051, 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SRC 8038-06//National Geographic Society/ ; }, mesh = {Humans ; *Human Migration/history ; *Dental Calculus/microbiology/history ; Oceania ; *Microbiota/genetics ; Archaeology ; Phylogeny ; Pacific Islands ; Asia, Southeastern ; Metagenomics/methods ; DNA, Ancient/analysis ; History, Ancient ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {The Pacific islands and Island Southeast Asia have experienced multiple waves of human migrations, providing a case study for exploring the potential of ancient microbiomes to study human migration. We perform a metagenomic study of archaeological dental calculus from 102 individuals, originating from 10 Pacific islands and 1 island in Island Southeast Asia spanning ~3000 years. Oral microbiome DNA preservation in calculus is far higher than that of human DNA in archaeological bone, and comparable to that of calculus from temperate regions. Oral microbial community composition is minimally driven by time period and geography in Pacific and Island Southeast Asia calculus, but is found to be distinctive compared to calculus from Europe, Africa, and Asia. Phylogenies of individual bacterial species in Pacific and Island Southeast Asia calculus reflect geography. Archaeological dental calculus shows good preservation in tropical regions and the potential to yield information about past human migrations, complementing studies of the human genome.}, } @article {pmid39581874, year = {2024}, author = {Li, Y and Pan, G and Wang, S and Li, Z and Yang, R and Jiang, Y and Chen, Y and Li, SC and Shen, B}, title = {Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39581874}, issn = {1477-4054}, mesh = {Humans ; *Microbiota/genetics ; Genome, Human ; Metagenome ; Respiratory System/microbiology ; Bacteria/genetics/classification ; }, abstract = {The human respiratory microbiome plays a crucial role in respiratory health, but there is no comprehensive respiratory genome catalogue (RGC) for studying the microbiome. In this study, we collected whole-metagenome shotgun sequencing data from 4067 samples and sequenced long reads of 124 samples, yielding 9.08 and 0.42 Tbp of short- and long-read data, respectively. By submitting these data with a novel assembly algorithm, we obtained a comprehensive human RGC. This high-quality RGC contains 190,443 contigs over 1 kbps and an N50 length exceeding 13 kbps; it comprises 159 high-quality and 393 medium-quality genomes, including 117 previously uncharacterized respiratory bacteria. Moreover, the RGC contains 209 respiratory-specific species not captured by the unified human gastrointestinal genome. Using the RGC, we revisited a study on a pediatric pneumonia dataset and identified 17 pneumonia-specific respiratory pathogens, reversing an inaccurate etiological conclusion due to the previous incomplete reference. Furthermore, we applied the RGC to the data of 62 participants with a clinical diagnosis of infection. Compared to the Nucleotide database, the RGC yielded greater specificity (0 versus 0.444, respectively) and sensitivity (0.852 versus 0.881, respectively), suggesting that the RGC provides superior sensitivity and specificity for the clinical diagnosis of respiratory diseases.}, } @article {pmid39580871, year = {2025}, author = {Kumar, S and Bhatia, Z and Seshadri, S}, title = {Formulated chitosan microspheres remodelled the altered gut microbiota and liver miRNA in diet-induced Type-2 diabetic rats.}, journal = {Carbohydrate research}, volume = {547}, number = {}, pages = {109301}, doi = {10.1016/j.carres.2024.109301}, pmid = {39580871}, issn = {1873-426X}, mesh = {*Chitosan/pharmacology/chemistry ; Animals ; *Gastrointestinal Microbiome/drug effects ; *MicroRNAs/metabolism ; *Microspheres ; Rats ; Male ; *Diabetes Mellitus, Type 2/drug therapy/metabolism ; *Diabetes Mellitus, Experimental/drug therapy/chemically induced/metabolism ; *Liver/drug effects/pathology/metabolism ; Hypoglycemic Agents/pharmacology/chemistry ; Metformin/pharmacology ; Diet, High-Fat/adverse effects ; }, abstract = {Chitosan was formulated into a microsphere and comprehensively characterized and evaluated for its anti-inflammatory potential and anti-diabetic properties against the high sugar fat diet-induced diabetic animals. The diabetic model was induced through feeding with a high-sugar fat diet. Metformin, a standard antidiabetic drug, and CMS (chitosan microspheres) were administered orally for 90 days as reversal strategies. Upon completion of the study, the following parameters, such as serum biochemistry, cytokine analysis, tissue histology, liver miRNA sequencing, and Shotgun metagenomics studies from stool samples, were performed. SEM images of the microsphere indicated a smooth morphology, while FTIR and DSC respectively, confirmed the presence of functional groups of chitosan and the thermal stability of the formulation. Following HSFD induction, all the parameters analyzed were altered compared to the control group. In both reversal groups, serum biochemical parameters were restored, which was at par with the control. A significant increase in the anti-inflammatory cytokine IL-10, and a remarkable reduction in TNF-α and MCP-1 inflammatory cytokines were observed in both reversal groups. Tissue histology indicated improvements in low-grade inflammation, induced in the diabetic group. miR-203 was upregulated in the CMS-treated group, while miR-103 was downregulated. The study further delved into the impact on gut microbiota and KEGG. Major phyla i.e., Bacteroidetes, Cyanobacteria, Firmicutes, Proteobacteria, and Verrucomicrobia showed restoration, while upregulation of DNA polymerase zeta in T2D showed reversal after the treatment. The formulation showed reversal at par with metformin and also confirms its anti-diabetic and anti-inflammatory activities of CMS, with microfloral and miR regulatory functions.}, } @article {pmid39580566, year = {2024}, author = {Gomes, WDS and Partelli, FL and Veloso, TGR and da Silva, MCS and Moreli, AP and Moreira, TR and Pereira, LL}, title = {Effects of Coffea canephora genotypes on the microbial community of soil and fruit.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {29035}, pmid = {39580566}, issn = {2045-2322}, support = {23186000886201801//Sul Serrana of Espírito Santo Free Admission Credit Cooperative- SICOOB/ ; 23186000886201801//Sul Serrana of Espírito Santo Free Admission Credit Cooperative- SICOOB/ ; 23186000886201801//Sul Serrana of Espírito Santo Free Admission Credit Cooperative- SICOOB/ ; }, mesh = {*Coffea/microbiology/genetics ; *Soil Microbiology ; *Fruit/microbiology ; *Genotype ; *Microbiota/genetics ; *Rhizosphere ; Bacteria/genetics/classification/isolation & purification ; Fungi/genetics/classification/isolation & purification ; Brazil ; Soil ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In recent years, the role of microbial communities in agricultural systems has received increasing attention, particularly concerning their impact on plant health and productivity. However, the influence of host plant genetic factors on the microbial composition of coffee plants remains largely unexplored. This study provides the first comprehensive investigation into how genotype affects the microbial communities present in the rhizosphere and fruits of Coffea canephora. Conducted on a commercial coffee farm in Brazil, we analyzed six genotypes of C. canephora var. Conilon. Soil and fruit samples were collected from which microbial DNA was extracted and sequenced, targeting the V3-V4 region of the 16 S rDNA and the ITS1 region for fungi. A total of 12,239,769 reads were generated from the 16 S rDNA and ITS1 regions. The PCoA revealed distinct patterns of beta diversity, with genotype 153 exhibiting significant isolation in soil bacterial communities. The dominant bacterial orders included Rhizobiales and Rhodobacterales, while the fungal community comprised diverse taxa from Saccharomycetales and Hypocreales. LEfSe analysis identified key metagenomic biomarkers, highlighting genotype Baiano 4 for its richness in fruit-associated taxa, whereas genotype 153 exhibited lower diversity in both soil and fruit samples. This work enhances our understanding of the microbiomes associated with different coffee genotypes, providing evidence of how host genetic variation influences microbial community composition. Our findings indicate that specific microbial taxa are enriched in the fruits and soil of various genotypes. Future research should focus on identifying these microorganisms and elucidating their specific functions within the rhizosphere and coffee fruits.}, } @article {pmid39580523, year = {2024}, author = {Li, J and Zhai, X and Chen, C and Zhang, R and Huang, X and Liu, Y}, title = {The intrahepatic bacterial metataxonomic signature of patients with hepatocellular carcinoma.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {29077}, pmid = {39580523}, issn = {2045-2322}, support = {32300081//the National Natural Science Foundation of China/ ; 23QA1406600//Shanghai Science and Technology Committee/ ; }, mesh = {Humans ; *Carcinoma, Hepatocellular/microbiology/pathology/metabolism ; *Liver Neoplasms/microbiology/pathology/metabolism ; Male ; Female ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Aged ; Liver/microbiology/pathology/metabolism ; Microbiota ; Liver Cirrhosis/microbiology/pathology ; Adult ; }, abstract = {Dysbiosis of the gut-liver axis increases the risk of bacterial and metabolite influx into the liver, which may contribute to the development of hepatocellular carcinoma (HCC). In this study, we compared the microbiomes in HCC tumors and adjacent tissues. We examined the HCC tumors and adjacent tissues from 19 patients diagnosed with HCC. We find that the liver tissues from HCC patients with capsule invasion presented higher alpha diversity at the genus level than those without. The bacterial compositions in liver tissues of HCC patients at stage II differed from those at stage I and Advanced, respectively. Metagenomic profiling revealed that order Actinomycetales was enriched in the HCC patients at advanced stages. Order Lactobacillales, family Veillonellaceae, genera Rhodobacter and Megasphaera are enriched in tumors of HCC patients, whereas genus Pseudochrobactrum is enriched in the adjacent tissues from HCC patients. An increased abundance of class Actinobacteria and order Actinomycetales is observed in the HCC patients with cirrhosis. In contrast, phylum Firmicutes, classes Clostridia and Betaproteobacteria, and order Clostridiales are enriched in those without cirrhosis. The presence of various types of bacterial 16S rRNAs in HCC tumors and adjacent tissues indicates the presence of various bacterial communities therein. Our study provides information about differentially abundant intrahepatic bacteria in patients with HCC. The differences found may support possible diagnostic and personalized therapeutic implications for HCC.}, } @article {pmid39579348, year = {2024}, author = {Ramos-Barbero, MD and Aldeguer-Riquelme, B and Viver, T and Villamor, J and Carrillo-Bautista, M and López-Pascual, C and Konstantinidis, KT and Martínez-García, M and Santos, F and Rossello-Mora, R and Antón, J}, title = {Experimental evolution at ecological scales allows linking of viral genotypes to specific host strains.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39579348}, issn = {1751-7370}, support = {PID2021-126114NB-C41//Spanish Ministry of Science and Innovation projects METACIRCLE/ ; CIPROM/2021/006//European Regional Development Fund/ ; }, mesh = {*Genotype ; Metagenomics ; Genome, Viral ; Ponds/virology/microbiology ; Metagenome ; }, abstract = {Viruses shape microbial community structure and activity through the control of population diversity and cell abundances. Identifying and monitoring the dynamics of specific virus-host pairs in nature is hampered by the limitations of culture-independent approaches such as metagenomics, which do not always provide strain-level resolution, and culture-based analyses, which eliminate the ecological background and in-situ interactions. Here, we have explored the interaction of a specific "autochthonous" host strain and its viruses within a natural community. Bacterium Salinibacter ruber strain M8 was spiked into its environment of isolation, a crystallizer pond from a coastal saltern, and the viral and cellular communities were monitored for one month using culture, metagenomics, and microscopy. Metagenome sequencing indicated that the M8 abundance decreased sharply after being added to the pond, likely due to forces other than viral predation. However, the presence of M8 selected for two species of a new viral genus, Phoenicisalinivirus, for which 120 strains were isolated. During this experiment, an assemblage of closely related viral genomic variants was replaced by a single population with the ability to infect M8, a scenario which was compatible with the selection of a genomic variant from the rare biosphere. Further analysis implicated a viral genomic region putatively coding for a tail fiber protein to be responsible for M8 specificity. Our results indicate that low abundance viral genotypes provide a viral seed bank that allows for a highly specialized virus-host response within a complex ecological background.}, } @article {pmid39578870, year = {2024}, author = {Wang, Y and Chen, X and Huws, SA and Xu, G and Li, J and Ren, J and Xu, J and Guan, LL and Yao, J and Wu, S}, title = {Ileal microbial microbiome and its secondary bile acids modulate susceptibility to nonalcoholic steatohepatitis in dairy goats.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {247}, pmid = {39578870}, issn = {2049-2618}, mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/microbiology ; *Goats ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome ; *Ileum/microbiology ; *Liver/metabolism ; Mice ; Bacteria/classification/isolation & purification/genetics ; Disease Susceptibility ; Goat Diseases/microbiology ; Disease Models, Animal ; Female ; }, abstract = {BACKGROUND: Liver damage from nonalcoholic steatohepatitis (NASH) presents a significant challenge to the health and productivity of ruminants. However, the regulatory mechanisms behind variations in NASH susceptibility remain unclear. The gut‒liver axis, particularly the enterohepatic circulation of bile acids (BAs), plays a crucial role in regulating the liver diseases. Since the ileum is the primary site for BAs reabsorption and return to the liver, we analysed the ileal metagenome and metabolome, liver and serum metabolome, and liver single-nuclei transcriptome of NASH-resistant and susceptible goats together with a mice validation model to explore how ileal microbial BAs metabolism affects liver metabolism and immunity, uncovering the key mechanisms behind varied NASH pathogenesis in dairy goats.

RESULTS: In NASH goats, increased total cholesterol (TC), triglyceride (TG), and primary BAs and decreased secondary BAs in the liver and serum promoted hepatic fat accumulation. Increased ileal Escherichia coli, Erysipelotrichaceae bacterium and Streptococcus pneumoniae as well as proinflammatory compounds damaged ileal histological morphology, and increased ileal permeability contributes to liver inflammation. In NASH-tolerance (NASH-T) goats, increased ursodeoxycholic acid (UDCA), isodeoxycholic acid (isoDCA) and isolithocholic acid (isoLCA) in the liver, serum and ileal contents were attributed to ileal secondary BAs-producing bacteria (Clostridium, Bifidobacterium and Lactobacillus) and key microbial genes encoding enzymes. Meanwhile, decreased T-helper 17 (TH17) cells and increased regulatory T (Treg) cells proportion were identified in both liver and ileum of NASH-T goats. To further validate whether these key BAs affected the progression of NASH by regulating the proliferation of TH17 and Treg cells, the oral administration of bacterial UDCA, isoDCA and isoLCA to a high-fat diet-induced NASH mouse model confirmed the amelioration of NASH through the TH17 cell differentiation/IL-17 signalling/PPAR signalling pathway by these bacterial secondary BAs.

CONCLUSION: This study revealed the roles of ileal microbiome and its secondary BAs in resilience and susceptibility to NASH by affecting the hepatic Treg and TH17 cells proportion in dairy goats. Bacterial UDCA, isoDCA and isoLCA were demonstrated to alleviate NASH and could be novel postbiotics to modulate and improve the liver health in ruminants. Video Abstract.}, } @article {pmid39578464, year = {2024}, author = {Nunn, BL and Timmins-Schiffman, E and Mudge, MC and Plubell, DL and Chebli, G and Kubanek, J and Riffle, M and Noble, WS and Harvey, E and Nunn, TA and Huntemann, M and Clum, A and Foster, B and Foster, B and Roux, S and Palaniappan, K and Mukherjee, S and Reddy, TBK and Daum, C and Copeland, A and Chen, IA and Ivanova, NN and Kyrpides, NC and Glavina Del Rio, T and Eloe-Fadrosh, EA}, title = {Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle: High-Resolution Sampling Every 4 Hours Over 22 Days.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1270}, pmid = {39578464}, issn = {2052-4463}, support = {R21ES034337-01//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; F31 ES032733/ES/NIEHS NIH HHS/United States ; 2041497//NSF | BIO | Division of Integrative Organismal Systems (IOS)/ ; IOS 2041497//NSF | BIO | Division of Integrative Organismal Systems (IOS)/ ; R21 ES034337/ES/NIEHS NIH HHS/United States ; }, mesh = {*Phytoplankton/genetics/growth & development ; *Metagenome ; *Bacteria/genetics/growth & development/classification ; *Archaea/genetics ; Eutrophication ; Microbiota ; Viruses/genetics/growth & development ; }, abstract = {In May and June of 2021, marine microbial samples were collected for DNA sequencing in East Sound, WA, USA every 4 hours for 22 days. This high temporal resolution sampling effort captured the last 3 days of a Rhizosolenia sp. bloom, the initiation and complete bloom cycle of Chaetoceros socialis (8 days), and the following bacterial bloom (2 days). Metagenomes were completed on the time series, and the dataset includes 128 size-fractionated microbial samples (0.22-1.2 µm), providing gene abundances for the dominant members of bacteria, archaea, and viruses. This dataset also has time-matched nutrient analyses, flow cytometry data, and physical parameters of the environment at a single point of sampling within a coastal ecosystem that experiences regular bloom events, facilitating a range of modeling efforts that can be leveraged to understand microbial community structure and their influences on the growth, maintenance, and senescence of phytoplankton blooms.}, } @article {pmid39577778, year = {2025}, author = {Chen, Y and Huang, M and Fu, Y and Gao, T and Gan, Z and Meng, F}, title = {Construction of polylactic acid plastisphere microbiota for enhancing nitrate reduction in denitrification biofilters.}, journal = {Bioresource technology}, volume = {417}, number = {}, pages = {131853}, doi = {10.1016/j.biortech.2024.131853}, pmid = {39577778}, issn = {1873-2976}, mesh = {*Denitrification ; *Polyesters/metabolism/chemistry ; *Nitrates/metabolism ; *Biofilms ; *Microbiota ; Bioreactors/microbiology ; Filtration/methods ; Water Purification/methods ; Biodegradation, Environmental ; }, abstract = {Developing methods for reusing biodegradable plastics, like polylactic acid (PLA) straws, is highly needed. Here, PLAs were applied to substitute traditional commercial ceramic media (CCM) in denitrification biofilters. During long-term operation, replacing CCM with PLA significantly enhanced nitrate removal efficiency from 32.68-54.39 % to 41.64-66.26 %. Ammonia nitrogen effluent maintained below 0.5 mg/L in all reactors. PLA plastisphere shaped unique microbial communities, i.e., denitrifying bacteria Bacillus, Pseudomonas and Acidovorax preferred to inhabit or degrade PLA. Compared to CCM biofilms, PLA diminished the importance of stochastic process in biofilm assembly of PLA plastisphere. Metagenomic sequencing suggested that PLA biofilms possessed greater metabolic capabilities of denitrification and glycolysis compared to CCM. Additionally, Bacillus strain P01 isolated from PLA plastisphere demonstrated strong PLA depolymerization. Overall, this study revealed that PLA serves as carbon source and biofilm carrier, offering a promising approach to integrating plastic reuse with wastewater treatment.}, } @article {pmid39577582, year = {2024}, author = {Mukherjee, S and Bhattacharya, R and Sarkar, O and Islam, S and Biswas, SR and Chattopadhyay, A}, title = {Gut microbiota perturbation and subsequent oxidative stress in gut and kidney tissues of zebrafish after individual and combined exposure to inorganic arsenic and fluoride.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177519}, doi = {10.1016/j.scitotenv.2024.177519}, pmid = {39577582}, issn = {1879-1026}, mesh = {Animals ; *Zebrafish ; *Gastrointestinal Microbiome/drug effects ; *Oxidative Stress/drug effects ; *Arsenic/toxicity ; *Kidney/drug effects ; *Fluorides/toxicity ; *Water Pollutants, Chemical/toxicity ; }, abstract = {Chronic exposure to inorganic arsenic (iAs) and fluoride (F) affect gut health and potentially damage organs. The present study investigates the interplay between gut bacteria and oxidative stress (measured by MDA level, GSH level, catalase activity, Nrf2 translocation and expression) in zebrafish exposed to F (NaF 15 ppm) and As (As2O3 50 ppb) alone or in combination. Combined exposure to As and F reduced gut bacterial alteration and imposed less oxidative stress compared to F- exposure alone. V3-V4 metagenomic sequencing revealed Pseudomonas, Aeromonas and Plesiomonas genera dominated in As or F treated groups while As+F treated group was enriched in beneficial Lactococcus and Streptococcus genera. Functional KEGG analysis demonstrated treatment-specific changes in bacterial metabolism, host organismal systems, human diseases, as well as cellular processes of microbial community were significantly affected. When Aeromonas sp. isolated from F-treated fish gut, tagged with GFP-vector and fed (~3.2 × 10[6] CFU/mL) to untreated fish, induced oxidative stress in gut and kidney. Gut bacteria were found to both increase and mitigate iAs or F-toxicity, whereas As+F treatment promoted a protective response. Correlation analysis between gut microbial community at genus level and oxidative stress parameters of gut and kidney, showed Aeromonas and Plesiomonas genera are strongly correlated with oxidative stress (r = 0.5-0.9, p˂0.05). This study identifies microbiome biomarkers of iAs and F toxicity on gut-kidney axis.}, } @article {pmid39577368, year = {2025}, author = {Yang, L and Yao, B and Zhang, S and Yang, Y and Wang, G and Pan, H and Zeng, X and Qiao, S}, title = {Division mechanism of labor in Diqing Tibetan Pigs gut microbiota for dietary fiber efficiently utilization.}, journal = {Microbiological research}, volume = {290}, number = {}, pages = {127977}, doi = {10.1016/j.micres.2024.127977}, pmid = {39577368}, issn = {1618-0623}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Dietary Fiber/metabolism ; Swine ; *Animal Feed ; *Feces/microbiology ; Tibet ; Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics ; Xylose/metabolism ; Glycoside Hydrolases/metabolism ; Lactobacillus/metabolism/genetics ; }, abstract = {The Diqing Tibetan (TP) pig is an roughage tolerance breed that inhabits an area with the highest altitude distribution in the world and can be maintained on a diet containing 90 % forage material in confined production systems. Our results showed that TP pigs had a strong capability for high-efficiency utilization of arabinose and xylose. Metagenomic analysis revealed that the secretion of carbohydrate esterases was mainly undertaken by fecal strains of Microbacterium, Alistipes, Acinetobacter, and Faecalibacterium, while Microbacterium, Prevotella, Turicibacter, Lactobacillus, Clostridium, and Streptococcus were responsible for most of the secretion of glycoside hydrolases. Then, a brand new species, which was named Microbacterium sp. Qiao 01 was captured and appeared to have the highest fiber utilization ability in vitro, degrading 36.54 % of the neutral detergent fiber in corn stover. Our results provide strong evidence that efficient utilization of dietary fiber by TP pigs is due to the emergence of highly specialized microbial strategies in the gut. Microorganisms showed preferences and a clear division of labor in the degradation process of dietary fiber. This study has great practical significance for improving the utilization efficiency of livestock feed and alleviating the tension of food insecurity.}, } @article {pmid39577267, year = {2025}, author = {Ngo, C and Morrell, JM and Tummaruk, P}, title = {Boar semen microbiome: Insights and potential implications.}, journal = {Animal reproduction science}, volume = {272}, number = {}, pages = {107647}, doi = {10.1016/j.anireprosci.2024.107647}, pmid = {39577267}, issn = {1873-2232}, mesh = {Animals ; *Semen/microbiology ; Swine/microbiology/physiology ; Male ; *Microbiota ; Semen Analysis/veterinary ; Bacteria/classification/isolation & purification/genetics ; }, abstract = {The pioneers of next-generation sequencing technology and bioinformatic analyses initiated a new era in microbiology research by offering profound insights into bacterial microbiome communities. In the pig farming sector, while considerable attention has been devoted to the gut microbiome and the microbiome of the female reproductive tract, research on the microbiome of boar semen remains limited. Nonetheless, published studies have provided valuable insights, serving as important references and sparking ideas for further investigations into the seminal microbiome. Factors such as breed, seasons, feed additives, hygiene management, and antibiotic use are believed to exert a notable influence on the diversity and richness of bacterial genera in the boar seminal microbiome, potentially affecting semen quality. Moreover, current shifts towards sustainability in the swine industry, coupled with global guidelines concerning the prudent use of antibiotics in stored boar semen for artificial insemination, underscore the need for insights into factors influencing seminal bacteria. The objective of this review is to elucidate the current understanding of boar bacterial contents using conventional culture methods, as well as the boar seminal microbiome through metagenomics and bioinformatics. It also aims to review specific microbiome communities, such as those in the reproductive tract and gut, and their connections to semen quality. In addition, strategic enhancements for processing boar semen doses through alternative methods to improve seminal quality are proposed.}, } @article {pmid39577061, year = {2024}, author = {Mahanty, S and Pillay, K and Hardouin, EA and Andreou, D and Cvitanović, M and Darbha, GK and Mandal, S and Chaudhuri, P and Majumder, S}, title = {Whispers in the mangroves: Unveiling the silent impact of potential toxic metals (PTMs) on Indian Sundarbans fungi.}, journal = {Marine pollution bulletin}, volume = {209}, number = {Pt B}, pages = {117233}, doi = {10.1016/j.marpolbul.2024.117233}, pmid = {39577061}, issn = {1879-3363}, mesh = {*Wetlands ; *Environmental Monitoring ; *Metals, Heavy/analysis/toxicity ; India ; *Water Pollutants, Chemical/analysis/toxicity ; *Fungi ; Geologic Sediments/chemistry ; Biodiversity ; }, abstract = {This study investigates sediment samples from the Indian Sundarbans' mangrove habitat, where most samples were alkaline and hypersaline, except for one acidic sample. Elemental analysis revealed poor sediment quality, with elevated Enrichment Factors (2.20-9.7), Geo-accumulation indices (-2.19-1.19), Contamination Factors (0.61-3.18), and Pollution Load Indices (1.04-1.32). Toxic metal ions, including Pb, Cu, Ni, Cd, Zn, and Cr, were identified as key contributors to compromised sediment quality. These metals inhibit crucial sediment enzymes, such as CMC-cellulase, β-glucosidase, aryl sulfatase, urease, and phosphatases, essential for nutrient cycling and organic matter decomposition. A negative correlation was found between heavy metals and biodiversity, as indicated by the Shannon index, and a similar trend was observed with fungal load. The study highlights the adverse effects of persistent trace metals on the fungal community, potentially disrupting the mangrove ecosystem and suggests using manglicolous fungi as biological indicators of environmental health.}, } @article {pmid39576476, year = {2024}, author = {Zabolotneva, AA and Laskina, TA and Kharchev, DN and Shestopalov, AV}, title = {Effects of a Short-Term High-Fat Diet on Microbiota Biodiversity of the Small and Large Intestines of C57BL/6SPF Mice.}, journal = {Bulletin of experimental biology and medicine}, volume = {178}, number = {1}, pages = {17-23}, pmid = {39576476}, issn = {1573-8221}, mesh = {Animals ; *Diet, High-Fat/adverse effects ; Mice ; *Mice, Inbred C57BL ; *Gastrointestinal Microbiome/genetics ; Male ; *Intestine, Small/microbiology/metabolism ; *Intestine, Large/microbiology ; Lipid Metabolism ; Biodiversity ; Blood Glucose/metabolism ; }, abstract = {Long-term high-fat diet (HFD) promotes the formation of excess body weight and disorders of lipid metabolism and causes persistent dysbiotic changes in the intestinal microbial community. Changes in eating behavior, endocrine and immune functions of the host are associated with changes in the structure and functional activity of microbial communities. Short-term HFD may also influence the composition and function of the intestinal microbiota, but data on this issue are limited, and most papers are focused on the study of the large intestinal microbiota. The present study examined the effect of short-term HFD (4 weeks) on the structure of microbial communities in the small and large intestines of 24 mice. High-throughput metagenomic sequencing was performed on 48 samples of small and large intestine contents. It was revealed that short-term HFD in mice contributed to impaired glucose tolerance and increased the diversity of microbiota in the colon, but not of the small intestine, and also led to changes in the representation of certain microbial taxa (in particular Tenericutes and Verrucomicrobia). Furthermore, short-term HFD increased blood glucose levels compared to control mice (fed a normal diet), but did not affect lipid metabolism. The results will help to assess the contribution of environmental factors to the structure of microbial communities of the small and large intestines and may also be useful for correcting dysbiotic conditions, including when prescribing therapeutic diets (for example, a ketogenic diet).}, } @article {pmid39574252, year = {2024}, author = {Crombez, L and Descamps, A and Hirmz, H and Lambert, M and Calewaert, J and Siluk, D and Markuszewski, M and Biesemans, M and Petrella, G and Cicero, D and Cesaroni, S and Stokowy, T and Gerber, GK and Tataru, C and Naumovski, P and Elewaut, D and Van De Looverbosch, C and Calders, P and Van Den Noortgate, N and De Spiegeleer, B and Wynendaele, E and De Spiegeleer, A}, title = {The Saliva and Muscle Study (SaMu): Rationale and Protocol for Associations between Salivary Microbiome and Accelerated Muscle Ageing.}, journal = {The Journal of frailty & aging}, volume = {13}, number = {4}, pages = {331-340}, doi = {10.14283/jfa.2024.75}, pmid = {39574252}, issn = {2260-1341}, mesh = {Humans ; *Saliva/microbiology ; *Sarcopenia/microbiology ; Aged ; Cross-Sectional Studies ; Male ; Female ; Muscle Strength/physiology ; Aging/physiology ; Microbiota/physiology ; Muscle, Skeletal/microbiology ; Aged, 80 and over ; }, abstract = {BACKGROUND: The gut microbiome is recognized as a pivotal factor in the pathophysiology of sarcopenia-a condition marked by the accelerated loss of muscle strength, mass and function with ageing. Despite this well-known gut-muscle axis, the potential links between other microbial ecosystems and sarcopenia remain largely unexplored. The oral microbiome has been linked to various age-related health conditions such as rheumatoid arthritis and colorectal cancer. However, its potential association with sarcopenia is unknown. The Saliva and Muscle (SaMu) study seeks to address this knowledge gap.

METHODS: The SaMu study comprises three sequential phases. In phase 1, a cross-sectional analysis will be conducted on a cohort of 200 individuals aged 70 years or older to examine the relationship between salivary microbiome and sarcopenia status. Participants will be recruited in the three main places of living: general community, assisted living facilities and nursing homes. The salivary microbiome composition will be evaluated utilizing shotgun metagenomics sequencing, while sarcopenia status will be determined through muscle mass (determined by whole-body bioelectrical impedance analysis and calf circumference), muscle strength (grip strength and the 5-times-sit-to-stand test) and physical performance (usual walking speed). In addition to investigating the microbiome composition, the study aims to elucidate microbiome functions by exploring potential omic associations with sarcopenia. To achieve this, salivary proteomics, metabolomics and quorum sensing peptidomics will be performed. Covariates that will be measured include clinical variables (sociodemographic factors, health status, health-related behaviours, oral health and quality of life) as well as blood variables (immune profiling, hormones, kidney and liver function, electrolytes and haematocrit). In phase 2, an in-depth mechanistic analysis will be performed on an envisaged subcohort of 50 participants. This analysis will explore pathways in muscle tissue using histology, genomics and transcriptomics, focusing on (maximal) 25 healthy older adults and (maximal) 25 with severe sarcopenia. Phase 3 involves a two-year clinical follow-up of the initial participants from the cross-sectional analysis, along with a resampling of blood and saliva. Additionally, secondary outcomes like falls, hospitalization and mortality will be examined.

DISCUSSION: Using a salivary multi-omics approach, SaMu primarily aims to clarify the associations between the oral microbiome and sarcopenia. SaMu is expected to contribute to the discovery of predictive biomarkers of sarcopenia as well as to the identification of potential novel targets to prevent/tackle sarcopenia. This study-protocol is submitted for registration at the ISRCTN registry.}, } @article {pmid39574009, year = {2024}, author = {Kim, S and Thapa, I and Ali, H}, title = {A novel computational approach for the mining of signature pathways using species co-occurrence networks in gut microbiomes.}, journal = {BMC microbiology}, volume = {24}, number = {Suppl 1}, pages = {490}, pmid = {39574009}, issn = {1471-2180}, mesh = {*Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; Humans ; *Computational Biology/methods ; *Metagenome ; Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Data Mining ; }, abstract = {BACKGROUND: Advances in metagenome sequencing data continue to enable new methods for analyzing biological systems. When handling microbial profile data, metagenome sequencing has proven to be far more comprehensive than traditional methods such as 16s rRNA data, which rely on partial sequences. Microbial community profiling can be used to obtain key biological insights that pave the way for more accurate understanding of complex systems that are critical for advancing biomedical research and healthcare. However, such attempts have mostly used partial or incomplete data to accurately capture those associations.

METHODS: This study introduces a novel computational approach for the identification of co-occurring microbial communities using the abundance and functional roles of species-level microbiome data. The proposed approach is then used to identify signature pathways associated with inflammatory bowel disease (IBD). Furthermore, we developed a computational pipeline to identify microbial species co-occurrences from metagenome data at various granularity levels.

RESULTS: When comparing the IBD group to a control group, we show that certain co-occurring communities of species are enriched for potential pathways. We also show that the identified co-occurring microbial species operate as a community to facilitate pathway enrichment.

CONCLUSIONS: The obtained findings suggest that the proposed network model, along with the computational pipeline, provide a valuable analytical tool to analyze complex biological systems and extract pathway signatures that can be used to diagnose certain health conditions.}, } @article {pmid39572861, year = {2024}, author = {Ding, Y and Ma, RA and Zhang, R and Zhang, H and Zhang, J and Li, S and Zhang, SY}, title = {Increased antibiotic resistance gene abundance linked to intensive bacterial competition in the phyllosphere across an elevational gradient.}, journal = {Environmental microbiology reports}, volume = {16}, number = {6}, pages = {e70042}, pmid = {39572861}, issn = {1758-2229}, support = {52270198//National Natural Science Foundation of China/ ; }, mesh = {*Bacteria/genetics/classification/isolation & purification ; *Phylogeny ; *Microbiota/genetics ; Biodiversity ; Metagenomics ; Genes, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; Altitude ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antibiotic resistance genes (ARGs) are ancient and widespread in natural habitats, providing survival advantages for microbiomes under challenging conditions. In mountain ecosystems, phyllosphere bacterial communities face multiple stress conditions, and the elevational gradients of mountains represent crucial environmental gradients for studying biodiversity distribution patterns. However, the distribution patterns of ARGs in the phyllosphere along elevational gradients, and their correlation with bacterial community structures, remain poorly understood. Here, we applied metagenomic analyses to investigate the abundance and diversity of ARGs in 88 phyllosphere samples collected from Mount Tianmu, a national natural reserve. Our results showed that the abundance of ARGs in the phyllosphere increased along elevational gradients and was dominated by multidrug resistance and efflux pumps. The composition of bacterial communities, rather than plant traits or abiotic factors, significantly affected ARG abundance. Moreover, increased ARG abundance was correlated with greater phylogenetic overdispersion and a greater proportion of negative associations in the bacterial co-occurrence networks, suggesting that bacterial competition primarily shapes phyllosphere resistomes. These findings constitute a major advance in the biodiversity of phyllosphere resistomes along elevations, emphasizing the significant impact of bacterial community structure and assembly on ARG distribution, and are essential for understanding the emergence of ARGs.}, } @article {pmid39572788, year = {2024}, author = {Pereira, FC and Ge, X and Kristensen, JM and Kirkegaard, RH and Maritsch, K and Szamosvári, D and Imminger, S and Seki, D and Shazzad, JB and Zhu, Y and Decorte, M and Hausmann, B and Berry, D and Wasmund, K and Schintlmeister, A and Böttcher, T and Cheng, JX and Wagner, M}, title = {The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration.}, journal = {Nature microbiology}, volume = {9}, number = {12}, pages = {3165-3183}, pmid = {39572788}, issn = {2058-5276}, support = {R01AI141439//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01EB032391//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01 AI141439/AI/NIAID NIH HHS/United States ; R01 EB032391/EB/NIBIB NIH HHS/United States ; Z383-B//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; ZK-57//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; S10 OD024993/OD/NIH HHS/United States ; 10.55776; COE 7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 10.55776 COE 7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; R35GM136223//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35 GM136223/GM/NIGMS NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Iron/metabolism ; *Parkinson Disease/microbiology/metabolism/drug therapy ; *Feces/microbiology ; *Catechols/pharmacology/metabolism ; *Nitriles/pharmacology ; Homeostasis/drug effects ; Bacteria/genetics/drug effects/metabolism/classification/isolation & purification ; Metagenomics ; Antiparkinson Agents/pharmacology ; }, abstract = {Many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, the mechanisms underlying these effects are not well known. Here we combined quantitative microbiome profiling, long-read metagenomics, stable isotope probing and single-cell chemical imaging to investigate the impact of two widely prescribed drugs on the gut microbiome. Physiologically relevant concentrations of entacapone, a treatment for Parkinson's disease, or loxapine succinate, used to treat schizophrenia, were incubated ex vivo with human faecal samples. Both drugs significantly impact microbial activity, more so than microbial abundance. Mechanistically, entacapone can complex and deplete available iron resulting in gut microbiome composition and function changes. Microbial growth can be rescued by replenishing levels of microbiota-accessible iron. Further, entacapone-induced iron starvation selected for iron-scavenging gut microbiome members encoding antimicrobial resistance and virulence genes. These findings reveal the impact of two under-investigated drugs on whole microbiomes and identify metal sequestration as a mechanism of drug-induced microbiome disturbance.}, } @article {pmid39572621, year = {2024}, author = {Rabenhorst, SHB and Ferrasi, AC and Barboza, MMO and Melo, VMM}, title = {Microbial composition of gastric lesions: differences based on Helicobacter pylori virulence profile.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {28890}, pmid = {39572621}, issn = {2045-2322}, support = {07939716/2020//Fundação Cearense de Apoio ao Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Humans ; *Helicobacter pylori/pathogenicity/genetics ; *Helicobacter Infections/microbiology/pathology ; *Stomach Neoplasms/microbiology/pathology ; *Gastritis/microbiology/pathology ; Virulence ; *Gastric Mucosa/microbiology/pathology ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Aged ; Metaplasia/microbiology ; Adult ; Gastrointestinal Microbiome ; }, abstract = {Helicobacter pylori infection is a major risk factor for gastric adenocarcinomas. In the case of the intestinal subtype, chronic gastritis and intestinal metaplasia are well-known sequential steps in carcinogenesis. H. pylori has high genetic diversity that can modulate virulence and pathogenicity in the human host as a cag Pathogenicity Island (cagPAI). However, bacterial gene combinations do not always explain the clinical presentation of the disease, indicating that other factors associated with H. pylori may play a role in the development of gastric disease. In this context, we characterized the microbial composition of patients with chronic gastritis (inactive and active), intestinal metaplasia, and gastric cancer as well as their potential association with H. pylori. To this end, 16 S rRNA metagenomic analysis was performed on gastric mucosa samples from patients with different types of lesions and normal gastric tissues. Our main finding was that H. pylori virulence status can contribute to significant differences in the constitution of the gastric microbiota between the sequential steps of the carcinogenesis cascade. Differential microbiota was observed in inactive and active gastritis dependent of the H. pylori presence and status (p = 0.000575). Pseudomonades, the most abundant order in the gastritis, was associated the presence of non-virulent H. pylori in the active gastritis. Notably, there are indicator genera according to H. pylori status that are poorly associated with diseases and provide additional evidence that the microbiota, in addition to H. pylori, is relevant to gastric carcinogenesis.}, } @article {pmid39572587, year = {2024}, author = {Yang, S and Zheng, J and Mao, H and Vinitchaikul, P and Wu, D and Chai, J}, title = {Multiomics of yaks reveals significant contribution of microbiome into host metabolism.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {133}, pmid = {39572587}, issn = {2055-5008}, mesh = {Animals ; Cattle ; *Rumen/microbiology ; *Metagenomics/methods ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Gastrointestinal Microbiome ; Metabolomics/methods ; Methane/metabolism ; Animal Feed ; Metabolome ; Microbiota ; Multiomics ; }, abstract = {An intensive feeding system might improve the production cycle of yaks. However, how intensive feeding system contributes to yak growth is unclear. Here, multi-omics, including rumen metagenomics, rumen and plasma metabolomics, were performed to classify the regulatory mechanisms of intensive feeding system on yaks. Increased growth performance were observed. Rumen metagenomics revealed that Clostridium, Methanobrevibacter, Piromyces and Anaeromyces increased in the intensively fed yaks, contributing to amino acid and carbohydrate metabolism. The grazing yaks had more cellulolytic microbes. These microbiomes were correlated with the pathways of "Alanine aspartate and glutamate metabolism" and "Pyruvate metabolism". Intensive feeding increased methane degradation functions, while grazing yaks had higher methyl metabolites associated with methane production. These rumen microbiomes and their metabolites resulted in changes in plasma metabolome, finally influencing yaks' growth. Thus, an intensive feeding system altered the rumen microbiome and metabolism as well as host metabolism, resulting in improvements of yak growth.}, } @article {pmid39571816, year = {2024}, author = {Arros, P and Palma, D and Gálvez-Silva, M and Gaete, A and Gonzalez, H and Carrasco, G and Coche, J and Perez, I and Castro-Nallar, E and Galbán, C and Varas, MA and Campos, M and Acuña, J and Jorquera, M and Chávez, FP and Cambiazo, V and Marcoleta, AE}, title = {Life on the edge: Microbial diversity, resistome, and virulome in soils from the union glacier cold desert.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177594}, doi = {10.1016/j.scitotenv.2024.177594}, pmid = {39571816}, issn = {1879-1026}, mesh = {*Soil Microbiology ; Antarctic Regions ; *Ice Cover/microbiology ; *Desert Climate ; *Bacteria/genetics ; *Microbiota ; Soil/chemistry ; Biodiversity ; }, abstract = {The high-latitude regions of Antarctica remain among the most remote, extreme, and least explored areas on Earth. Still, microbial life has been reported in these environments, with limited information on their genetic properties and functional capabilities. Although diverse autochthonous multidrug-resistant bacteria were found in Antarctic Peninsula soils, posing whether these soils could act as a source of resistance determinants that could emerge among pathogens, we still lack information regarding the resistome of areas closer to the South Pole. Moreover, no previous studies have evaluated the pathogenic potential of microbes inhabiting Antarctic soils. In this work, we combined metagenomic and culture-dependent approaches to investigate the microbial diversity, resistome, virulome, and mobile genetic elements (MGEs) in soils from Union Glacier, a cold desert in West Antarctica. Despite the extreme conditions, several bacterial phyla were found, predominating Actinomycetota and Pseudomonadota, with limited archaeal and fungal taxa. Contrastive with Ecology Glacier soils from King George Island, the Union Glacier soil bacterial community is significantly less diverse, mainly attributed to scarce moisture. We recovered >80 species-level representative genomes (SRGs) of predominant bacteria and an ammonia-oxidating nitrogen- and carbon-fixing archaeon from a novel species of Nitrosocosmicus. Several resistance and virulence genes were found in Union Glacier soils, similar to those in other Antarctic cold desert areas but significantly distinct from those observed in maritime Antarctica and other non-cryosphere biomes. Furthermore, we characterized bacterial isolates resistant to up to 24 clinical antibiotics, mainly Pseudomonas, Arthrobacter, Plantibacter, and Flavobacterium. Moreover, some isolates produced putative virulence factors, including siderophores, pyocyanins, and exoenzymes with hemolytic, lecithinase, protease, and DNAse activity. This evidence uncovers a largely unexplored resistome and virulome hosted by deep Antarctica's soil microbial communities and the presence of bacteria with pathogenic potential, highlighting the relevance of One Health approaches for environmental surveillance in this continent.}, } @article {pmid39571342, year = {2024}, author = {Calvani, R and Giampaoli, O and Marini, F and Del Chierico, F and De Rosa, M and Conta, G and Sciubba, F and Tosato, M and Picca, A and Ciciarello, F and Galluzzo, V and Gervasoni, J and Di Mario, C and Santoro, L and Tolusso, B and Spagnoli, M and Tomassini, A and Aureli, W and Toto, F and Pane, S and Putignani, L and Miccheli, A and Marzetti, E and Landi, F and , }, title = {Beetroot juice intake positively influenced gut microbiota and inflammation but failed to improve functional outcomes in adults with long COVID: A pilot randomized controlled trial.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {43}, number = {12}, pages = {344-358}, doi = {10.1016/j.clnu.2024.11.023}, pmid = {39571342}, issn = {1532-1983}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Beta vulgaris/chemistry ; *Fruit and Vegetable Juices ; Pilot Projects ; Adult ; Double-Blind Method ; Middle Aged ; *COVID-19 ; *Inflammation ; Dietary Supplements ; Nitrates ; SARS-CoV-2 ; Young Adult ; }, abstract = {BACKGROUND & AIMS: Long-term effects of coronavirus disease 2019 (long COVID) develop in a substantial number of people following an acute COVID-19 episode. Red beetroot juice may have positive effects on multiple pathways involved in long COVID. The aim of this pilot study was to explore the impact of beetroot juice supplementation on physical function, gut microbiota, and systemic inflammation in adults with long COVID.

METHODS: A single-center, double-blind, placebo-controlled randomized trial was conducted to test the effects of 14 days of beetroot juice supplementation, rich in nitrates and betalains, on functional and biological outcomes in adults aged between 20 and 60 years with long COVID. Participants were randomized 1:1 to receive either daily oral supplementation with 200 mL beetroot juice (∼600 mg nitrate) or placebo (∼60 mg nitrate) for 14 days. The primary endpoint was the change from baseline to day 14 in a fatigue resistance test. Secondary outcomes included the distance walked on the 6-min walk test, handgrip strength, and flow-mediated dilation. Secondary endpoints also included changes from baseline in circulating inflammatory mediators and metagenomic and fecal water metabolomic profiles. Partial least squares discriminant analysis (PLS-DA) models were built to evaluate the differences in biological variables associated with the interventions.

RESULTS: Thirty-one participants were randomized in the study. Twenty-five of them (median (interquartile range) age 40 (10), 14 [56 %] women), received either beetroot juice (15) or placebo (10) and completed the study. At 14 days, fatigue resistance significantly improved from baseline (mean difference [standard error]: +21.8 [3.7] s; p < 0.001) with no significant differences between intervention groups. A significant increase from baseline in the distance walked on the 6-min walk test was observed (mean difference [standard error]: +30.0 [9.4] m; p = 0.03), which was not different between groups. Flow-mediated dilation did not differ between participants who received beetroot juice and those on placebo. PLS-DA models allowed correct classification of participants with 92.2 ± 4.4 % accuracy. Those who ingested red beetroot juice had a greater abundance of bacteria with well-known beneficial effects, including Akkermansia, Oscillospira, Prevotella, Roseburia, Ruminococcaceae, and Turicibacter, compared with placebo. Participants allocated to beetroot juice supplementation were also characterized by significantly higher levels of fecal nicotinate, trimethylamine, and markers of beetroot juice intake (e.g., 5,6-dihydroxyindole). Finally, higher levels of interferon gamma and macrophage inflammatory protein-1β were found in participants who consumed beetroot juice.

CONCLUSION: Beetroot juice supplementation for two weeks did not to induce significant improvements in functional outcomes in adults with long COVID compared with placebo. Beneficial effects were observed in both gut microbiota composition (i.e., increase in probiotic species) and inflammatory mediators.

TRIAL REGISTRATION: Trial was registered under ClinicalTrials.gov. Identifier no. NCT06535165.}, } @article {pmid39571000, year = {2024}, author = {Zapién-Campos, R and Bansept, F and Traulsen, A}, title = {Stochastic models allow improved inference of microbiome interactions from time series data.}, journal = {PLoS biology}, volume = {22}, number = {11}, pages = {e3002913}, pmid = {39571000}, issn = {1545-7885}, mesh = {*Stochastic Processes ; *Microbiota ; Models, Biological ; Metagenome ; Humans ; Microbial Interactions/physiology ; Algorithms ; }, abstract = {How can we figure out how the different microbes interact within microbiomes? To combine theoretical models and experimental data, we often fit a deterministic model for the mean dynamics of a system to averaged data. However, in the averaging procedure a lot of information from the data is lost-and a deterministic model may be a poor representation of a stochastic reality. Here, we develop an inference method for microbiomes based on the idea that both the experiment and the model are stochastic. Starting from a stochastic model, we derive dynamical equations not only for the average, but also for higher statistical moments of the microbial abundances. We use these equations to infer distributions of the interaction parameters that best describe the biological experimental data-improving identifiability and precision. The inferred distributions allow us to make predictions but also to distinguish between fairly certain parameters and those for which the available experimental data does not give sufficient information. Compared to related approaches, we derive expressions that also work for the relative abundance of microbes, enabling us to use conventional metagenome data, and account for cases where not a single host, but only replicate hosts, can be tracked over time.}, } @article {pmid39570026, year = {2024}, author = {Waterworth, SC and Solomons, GM and Kalinski, J-CJ and Madonsela, LS and Parker-Nance, S and Dorrington, RA}, title = {The unique and enigmatic spirochete symbiont of latrunculid sponges.}, journal = {mSphere}, volume = {9}, number = {12}, pages = {e0084524}, pmid = {39570026}, issn = {2379-5042}, support = {87583//National Research Foundation (NRF)/ ; 110612//National Research Foundation (NRF)/ ; 96185//South African Medical Research Council (SAMRC)/ ; 101038//National Research Foundation (NRF)/ ; }, mesh = {*Symbiosis ; Animals ; *Porifera/microbiology ; *Phylogeny ; Metagenome ; Spirochaetales/genetics/classification/physiology ; }, abstract = {Bacterial symbionts are critical members of many marine sponge holobionts. Some sponge-associated bacterial lineages, such as Poribacteria, sponge-associated unclassified lineage (SAUL), and Tethybacterales, appear to have broad-host ranges and associate with a diversity of sponge species, while others are more species-specific, having adapted to the niche environment of their host. Host-associated spirochete symbionts that are numerically dominant have been documented in several invertebrates including termites, starfish, and corals. However, dominant spirochete populations are rare in marine sponges, having thus far been observed only in Clathrina clathrus and various species within the Latrunculiidae family, where they are co-dominant alongside Tethybacterales symbionts. This study aimed to characterize these spirochetes and their potential role in the host sponge. Analysis of metagenome-assembled genomes from eight latrunculid sponges revealed that these unusual spirochetes are relatively recent symbionts and are phylogenetically distinct from other sponge-associated spirochetes. Functional comparative analysis suggests that the host sponge may have selected for these spirochetes due to their ability to produce terpenoids and/or possible structural contributions.IMPORTANCESouth African latrunculid sponges are host to co-dominant Tethybacterales and Spirochete symbionts. While the Tethybacterales are broad-host range symbionts, the spirochetes have not been reported as abundant in any other marine sponge except Clathrina clathrus. However, spirochetes are regularly the most dominant populations in marine corals and terrestrial invertebrates where they are predicted to serve as beneficial symbionts. Here, we interrogated eight metagenome-assembled genomes of the latrunculid-associated spirochetes and found that these symbionts are phylogenetically distinct from all invertebrate-associated spirochetes. The symbiosis between the spirochetes and their sponge host appears to have been established relatively recently.}, } @article {pmid39570022, year = {2024}, author = {Wang, W and Wang, H and Zou, X and Liu, Y and Zheng, K and Chen, X and Wang, X and Sun, S and Yang, Y and Wang, M and Shao, H and Liang, Y}, title = {A novel virus potentially evolved from the N4-like viruses represents a unique viral family: Poorviridae.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {12}, pages = {e0155924}, pmid = {39570022}, issn = {1098-5336}, mesh = {*Genome, Viral ; *Phylogeny ; China ; *Pseudoalteromonas/virology/genetics/isolation & purification ; Seawater/virology ; DNA Viruses/genetics/classification/isolation & purification ; Evolution, Molecular ; Capsid Proteins/genetics ; }, abstract = {UNLABELLED: Pseudoalteromonas are widely distributed in marine extreme habitats and exhibit diverse extracellular protease activity, which is essential for marine biogeochemical cycles. However, our understanding of viruses that infect Pseudoalteromonas remains limited. This study isolated a virus infecting Pseudoalteromonas nigrifaciens from Xiaogang in Qingdao, China. vB_PunP_Y3 comprises a linear, double-strand DNA genome with a length of 48,854 bp, encoding 52 putative open reading frames. Transmission electron microscopy demonstrates the short-tailed morphology of vB_PunP_Y3. Phylogenetic and genome-content-based analysis indicate that vB_PunP_Y3 represents a novel virus family named as Poorviridae, along with three high-quality uncultivated viral genomes. Biogeographical analyses show that Poorviridae is distributed across five viral ecological zones, and is predominantly detected in the Antarctic, Arctic, and bathypelagic zones. Comparative genomics analyses identified three of the seven hallmark proteins of N4-like viruses (DNA polymerase, major capsid protein, and virion-encapsulated RNA polymerase) from vB_PunP_Y3, combing with the protein tertiary structures of the major capsid protein, suggesting that vB_PunP_Y3 might evolve from the N4-like viruses.

IMPORTANCE: vB_PunP_Y3 is a unique strain containing three of the seven hallmark proteins of N4-like viruses, but is grouped into a novel family-level viral cluster with three uncultured viruses from metagenomics, named Poorviridae. This study enhanced the understanding about the genetic diversity, evolution, and distribution of Pseudoalteromonas viruses and provided insights into the novel evolution mechanism of marine viruses.}, } @article {pmid39568064, year = {2024}, author = {Sauma-Sánchez, T and Alcorta, J and Tamayo-Leiva, J and Díez, B and Bezuidenhout, H and Cowan, DA and Ramond, JB}, title = {Functional redundancy buffers the effect of poly-extreme environmental conditions on southern African dryland soil microbial communities.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {12}, pages = {}, pmid = {39568064}, issn = {1574-6941}, support = {FBIS160422162807//National Research Foundation/ ; 1210912//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; }, mesh = {*Soil Microbiology ; *Bacteria/genetics/classification ; *Archaea/genetics/classification ; *Microbiota ; *Salinity ; *Fungi/genetics/classification ; Climate Change ; Desert Climate ; Soil/chemistry ; Extreme Environments ; Africa, Southern ; Biodiversity ; }, abstract = {Drylands' poly-extreme conditions limit edaphic microbial diversity and functionality. Furthermore, climate change exacerbates soil desiccation and salinity in most drylands. To better understand the potential effects of these changes on dryland microbial communities, we evaluated their taxonomic and functional diversities in two Southern African dryland soils with contrasting aridity and salinity. Fungal community structure was significantly influenced by aridity and salinity, while Bacteria and Archaea only by salinity. Deterministic homogeneous selection was significantly more important for bacterial and archaeal communities' assembly in hyperarid and saline soils when compared to those from arid soils. This suggests that niche partitioning drives bacterial and archaeal communities' assembly under the most extreme conditions. Conversely, stochastic dispersal limitations drove the assembly of fungal communities. Hyperarid and saline soil communities exhibited similar potential functional capacities, demonstrating a disconnect between microbial structure and function. Structure variations could be functionally compensated by different taxa with similar functions, as implied by the high levels of functional redundancy. Consequently, while environmental selective pressures shape the dryland microbial community assembly and structures, they do not influence their potential functionality. This suggests that they are functionally stable and that they could be functional even under harsher conditions, such as those expected with climate change.}, } @article {pmid39567665, year = {2024}, author = {Zhang, T and Hasegawa, Y and Waldor, MK}, title = {Enteric bacterial infection stimulates remodelling of bile metabolites to promote intestinal homeostasis.}, journal = {Nature microbiology}, volume = {9}, number = {12}, pages = {3376-3390}, pmid = {39567665}, issn = {2058-5276}, support = {P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 AI042347/AI/NIAID NIH HHS/United States ; MKW//Howard Hughes Medical Institute (HHMI)/ ; }, mesh = {Animals ; Mice ; *Homeostasis ; *Citrobacter rodentium ; *Enterobacteriaceae Infections/microbiology/metabolism ; *Metabolome ; *Gastrointestinal Microbiome ; *Bile/metabolism ; Liver/metabolism/microbiology ; Listeria monocytogenes/genetics ; Mice, Inbred C57BL ; Intestines/microbiology ; Metabolomics ; Listeriosis/microbiology/metabolism ; Bile Acids and Salts/metabolism ; Specific Pathogen-Free Organisms ; }, abstract = {The liver makes bile, an aqueous solution critical for fat absorption, which is secreted into the duodenum. Despite extensive studies on bile salts, other components of bile are less well characterized. Here we used global metabolomic analysis on bile from specific-pathogen-free, germ-free, Citrobacter rodentium-infected or Listeria monocytogenes-infected mice and identified a metabolome of 812 metabolites that were altered by both microbiota and enteric infection. Hepatic transcriptomics identified enteric-infection-triggered pathways that probably underlie bile remodelling. Enteric infection increased levels of four dicarboxylates in bile, including itaconate. Analysis of Acod1[-/-] mice indicated that increased itaconate also increased tuft cell abundance, altered microbiota composition and function as detected by metagenomic analysis, and modulated host defence, leading to reduced Vibrio cholerae colonization. Our data suggest that enteric-infection-associated signals are relayed between the intestine and liver and induce transcriptional programmes that shape the bile metabolome, modifying the immunomodulatory and host defence functions of bile.}, } @article {pmid39567534, year = {2024}, author = {Wang, Z and Li, Z and Zhang, Y and Liao, J and Guan, K and Zhai, J and Meng, P and Tang, X and Dong, T and Song, Y}, title = {Root hair developmental regulators orchestrate drought triggered microbiome changes and the interaction with beneficial Rhizobiaceae.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10068}, pmid = {39567534}, issn = {2041-1723}, mesh = {*Plant Roots/microbiology/metabolism ; *Droughts ; *Microbiota/physiology ; *Stress, Physiological ; Rhizobium/physiology/genetics ; Arabidopsis/microbiology/genetics/metabolism ; Metagenome ; Transcriptome ; Symbiosis ; }, abstract = {Drought is one of the most serious abiotic stresses, and emerging evidence suggest plant microbiome affects plant drought tolerance. However, there is a lack of genetic evidence regarding whether and how plants orchestrate the dynamic assembly of the microbiome upon drought. By utilizing mutants with enhanced or decreased root hair densities, we find that root hair regulators also affect drought induced root microbiome changes. Rhizobiaceae is a key biomarker taxa affected by root hair related mutants. We isolated and sequenced 1479 root associated microbes, and confirmed that several Rhizobium strains presented stress-alleviating activities. Metagenome, root transcriptome and root metabolome studies further reveal the multi-omic changes upon drought stress. We knocked out an ornithine cyclodeaminase (ocd) gene in Rhizobium sp. 4F10, which significantly dampens its stress alleviating ability. Our genetic and integrated multi-omics studies confirm the involvement of host genetic effects in reshaping a stress-alleviating root microbiome during drought, and provide mechanistic insights into Rhizobiaceae mediated abiotic stress protection.}, } @article {pmid39566459, year = {2025}, author = {Xian, Y and Cao, L and Lu, Y and Li, Q and Su, C and He, Y and Zhou, G and Chen, S and Gao, S}, title = {Metagenomics and metaproteomics reveal the effects of sludge types and inoculation modes on N,N-dimethylformamide degradation pathways and the microbial community involved.}, journal = {Journal of hazardous materials}, volume = {481}, number = {}, pages = {136548}, doi = {10.1016/j.jhazmat.2024.136548}, pmid = {39566459}, issn = {1873-3336}, mesh = {*Sewage/microbiology ; *Dimethylformamide/metabolism ; *Metagenomics ; *Biodegradation, Environmental ; *Proteomics ; Microbiota ; Anaerobiosis ; Bacteria/metabolism/genetics/classification ; Aerobiosis ; Methylamines/metabolism ; }, abstract = {This study demonstrated the effects of the sludge type and inoculation method on the N,N-dimethylformamide degradation pathway and associated microbial communities. The sludge type is critical for DMF metabolism, with acclimatized aerobic sludge having a significant advantage in terms of DMF metabolism performance, whereas acclimatized anaerobic sludge has a reduced DMF metabolism capacity. Metagenomic revealed increased abundances of Methanosarcina, Pelomona and Xanthobacter in the adapted anaerobic sludge, suggesting that anaerobic sludge can utilize the methyl products produced by DMF metabolism for growth. Adapted aerobic sludge had high Mycobacterium abundance, significantly boosting DMF hydrolysis. In addition, a large number of dmfA2 genes were found in aerobic sludge, more so in acclimatized sludge, indicating stronger DMF metabolism. Conversely, acclimatized anaerobic sludge showed lower abundance of dmd-tmd and mauA/B, qhpA genes, implying long-term DMF toxicity reduced anaerobic microbial activity. Metaproteomic analysis showed that Methanosarcina and Methanomethylovorans enzymes in anaerobic sludge metabolized dimethylamine and methylamine to methane, aiding DMF degradation. In the aerobic sludge, aminohydrolase proteins, which hydrolyze DMF, were significantly upregulated. These findings provide insights into DMF wastewater treatment.}, } @article {pmid39566458, year = {2025}, author = {Zhang, L and Jiang, L and Yan, W and Tao, H and Yao, C and An, L and Sun, Y and Hu, T and Sun, W and Qian, X and Gu, J}, title = {Exogenous additives reshape the microbiome and promote the reduction of resistome in co-composting of pig manure and mushroom residue.}, journal = {Journal of hazardous materials}, volume = {481}, number = {}, pages = {136544}, doi = {10.1016/j.jhazmat.2024.136544}, pmid = {39566458}, issn = {1873-3336}, mesh = {Animals ; *Composting ; *Manure/microbiology ; *Microbiota/drug effects ; Swine ; *Agaricales/genetics/drug effects ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; Soil Microbiology ; Genes, Bacterial ; }, abstract = {Comprehensive understanding of the microbiome and resistome evolution in compost is crucial for guaranteeing the safety of organic fertilizers. Current studies using different composting systems and sequencing technologies have yielded varying conclusions on the efficacy of exogenous additives (EAs) in reducing antibiotic resistance genes (ARGs) in compost. This study employed metagenomics to investigate the impact of various EAs on microbial communities, ARGs, their coexistence with mobile genetic elements (MGEs), and ARG hosts in co-composting. Our results demonstrated that EAs significantly reshaped the microbial communities and facilitated a notable reduction in total ARG abundance and diversity, primarily by decreasing core ARGs. Cooperative rather than antagonistic relationships among bacteria. The RA changes in total ARGs are mainly caused by a decrease in the prevalence of core ARGs. Furthermore, EAs showed significant efficacy in reducing clinical ARGs, including cfxA, tetX1, cfxA6, vanA, and aac (6')-Ib', with diatomite (5 %) and zeolite (5 %) being the most effective. The effect of EAs on ARGs and microbial community assembly were stochastic processes. Composting stage and EAs jointly reduced the association between ARGs and MGEs in the composting system. The reduction of ARGs attributed to a decreased abundance of potential pathogenic ARG-associated hosts and diminished associations with MGEs. In conclusion, EAs present a straightforward and effective approach for promoting ARGs reduction in compost, offering crucial insights for assessing the environmental risks associated with the release of agricultural ARGs.}, } @article {pmid39565113, year = {2024}, author = {Nowak, VV and Hou, P and Owen, JG}, title = {Microbial communities associated with marine sponges from diverse geographic locations harbor biosynthetic novelty.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {12}, pages = {e0072624}, pmid = {39565113}, issn = {1098-5336}, support = {Doctoral Scholarship//Victoria University of Wellington (WGTN)/ ; Contract 16/172//Manatu Hauora | Health Research Council of New Zealand (HRC)/ ; RDF-VUW1601//Royal Society Te Apārangi (Royal Society of New Zealand)/ ; RTVU1908 and UOAX2010//Ministry for Business Innovation and Employment (MBIE)/ ; }, mesh = {*Porifera/microbiology ; Animals ; New Zealand ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Metagenome ; *Microbiota ; Mediterranean Sea ; Multigene Family ; Metagenomics ; Phylogeny ; }, abstract = {Marine sponges are a prolific source of biologically active small molecules, many of which originate from sponge-associated bacteria. Identifying the producing bacteria is a key step in developing sustainable routes for the production of these metabolites. To facilitate the required computational analyses, we developed MetaSing, a reproducible singularity-based pipeline for assembly, identification of high-quality metagenome-assembled genomes (MAGs), and analysis of biosynthetic gene clusters (BGCs) from metagenomic short-read data. We applied this pipeline to metagenomic sequencing data from 16 marine sponges collected from New Zealand, Tonga, and the Mediterranean Sea. This analysis yielded 643 MAGs representing 510 species. Of the 2,670 BGCs identified across all samples, 70.8% were linked to a MAG. Comparison of BGCs to those identified from previously sequenced bacteria revealed high biosynthetic novelty in variety of underexplored phyla, including Poribacteria, Acidobacteriota, and Dadabacteria. Alongside the observation that each sample contains unique biosynthetic potential, this holds great promise for natural product discovery and for furthering the understanding of different sponge holobionts.IMPORTANCEDiscovery of new chemical compounds such as natural products is a crucial endeavor to combat the increasing resistance to antibiotics and other drugs. This manuscript demonstrates that microbial communities associated with marine sponges investigated in this work encode the potential to produce novel chemistry. Lesser studied bacterial taxa that are often difficult to cultivate are particularly rich in potential.}, } @article {pmid39563700, year = {2024}, author = {Quezada-Romegialli, C and Quiroga-Carmona, M and D'Elía, G and Harrod, C and Storz, JF}, title = {Diet of Andean Leaf-Eared Mice (Phyllotis) Living at Extreme Elevations on Atacama Volcanoes: Insights From Metagenomics, DNA Metabarcoding, and Stable Isotopes.}, journal = {Ecology and evolution}, volume = {14}, number = {11}, pages = {e70591}, pmid = {39563700}, issn = {2045-7758}, support = {R01 HL159061/HL/NHLBI NIH HHS/United States ; }, abstract = {On the flanks of > 6000 m Andean volcanoes that tower over the Atacama Desert, leaf-eared mice (Phyllotis vaccarum) live at extreme elevations that surpass known vegetation limits. The diet of these mice in these barren, hyperarid environments has been the subject of much speculation. According to the arthropod fallout hypothesis, sustenance is provided by windblown insects that accumulate in snowdrifts ("aolian deposits"). Mice may also feed on saxicolous lichen or forms of cryptic vegetation that have yet to be discovered at such high elevations. We tested hypotheses about the diet of mice living at extreme elevations on Atacama volcanoes by combining metagenomic and DNA metabarcoding analyses of gut contents with stable isotope analyses of mouse tissues. Genomic analyses of contents of the gastrointestinal tract of a live-captured mouse from the summit of Volcán Llullaillaco (6739 m) revealed an opportunistic but purely herbivorous diet, including lichens. Although we found no evidence of animal DNA in gut contents of the summit mouse, stable isotope data indicate that mice from elevations at or near vegetation limits (~5100 m) include a larger fraction of animal prey in their diet than mice from lower elevations. Some plant species detected in the gut contents of the summit mouse are known to exist at lower elevations at the base of the volcano and in the surrounding Altiplano, suggesting that they may occur at higher elevations beneath the snowpack or in other cryptic microhabitats.}, } @article {pmid39563409, year = {2024}, author = {Li, M and Chen, K and Chen, Y and Zhang, L and Cui, Y and Xiao, F and Liu, Z and Zhang, W and Jiang, J and Zhou, Q and Yan, J and Sun, Y and Guan, F}, title = {Integrative analysis of gut microbiome and host transcriptome reveal novel molecular signatures in Hashimoto's thyroiditis.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {1045}, pmid = {39563409}, issn = {1479-5876}, support = {82071952//Natural Science Foundation of China/ ; 82171873//Natural Science Foundation of China/ ; 82370806//Natural Science Foundation of China/ ; 82030058//Natural Science Foundation of China/ ; }, mesh = {Humans ; *Hashimoto Disease/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; *Transcriptome/genetics ; Female ; Male ; Adult ; Case-Control Studies ; MicroRNAs/genetics/metabolism ; Middle Aged ; ROC Curve ; RNA, Messenger/genetics/metabolism ; Gene Expression Profiling ; }, abstract = {BACKGROUND: Hashimoto's thyroiditis (HT) is an autoimmune disorder with unclear molecular mechanisms. While current diagnosis is well-established, understanding of the gut-thyroid axis in HT remains limited. This study aimed to uncover novel molecular signatures in HT by integrating gut metagenome and host transcriptome data (miRNA/mRNA), potentially elucidating disease pathogenesis and identifying new therapeutic targets.

METHODS: We recruited 31 early HT patients and 30 healthy controls in a two-stage study (discovery and validation). Blood and fecal samples underwent RNA and metagenomic sequencing, respectively. Integrative analysis included differential expression, weighted correlation network, correlation and random forest analyses. Regression models and ROC curve analysis were used to evaluate the significance of identified molecular signatures in HT.

RESULTS: Integrative analysis revealed subtle changes in gut microbiota diversity and composition in early HT, increased abundance of Bacillota_A and Spirochaetota at the phylum level, and significant differences in 24 genera and 67 species. Ecological network analysis indicated an imbalance in the gut microbiota with reduced inhibitory interactions against pathogenic genera in HT. Functional analysis showed changes in infection- and immune-related pathways. Three characteristic species (Salaquimonas_sp002400845, Clostridium_AI_sp002297865, and Enterocloster_citroniae) were identified as most relevant to HT. Analysis of miRNA and mRNA expression profiles uncovered pathways related to immune response, inflammation, infection, metabolism, proliferation, and thyroid cancer in HT. Based on correlations with HT and interactions between them, six characteristic RNAs (hsa-miR-548aq-3p, hsa-miR-374a-5p, GADD45A, IRS2, SMAD6, WWTR1) were identified. Furthermore, our study uncovered significant gut microbiota-host transcriptome interactions in HT, revealing enrichment in metabolic, immune, and cancer-related pathways, particularly with strong associations among those 9 key molecular signatures. The validation stage confirmed improved HT classification accuracy by combining these signatures (AUC = 0.95, ACC = 0.85), suggesting their potential significance in understanding HT pathogenesis.

CONCLUSION: Our study reveals novel molecular signatures linking gut microbiome and host transcriptome in HT, providing new insights into the disease pathogenesis. These findings not only enhance our understanding of the gut-thyroid axis but also suggest potential new directions for therapeutic interventions in HT.}, } @article {pmid39563023, year = {2025}, author = {Park, HA and Sung, J and Chang, Y and Ryu, S and Yoon, KJ and Kim, HL and Kim, HN}, title = {Metagenomic Analysis Identifies Sex-Related Gut Microbial Functions and Bacterial Taxa Associated With Skeletal Muscle Mass.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {16}, number = {1}, pages = {e13636}, pmid = {39563023}, issn = {2190-6009}, support = {2023R1A2C2006416//National Research Foundation of Korea/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *Muscle, Skeletal/microbiology ; *Metagenomics/methods ; Middle Aged ; Feces/microbiology ; Adult ; Bacteria/classification/genetics ; Metagenome ; }, abstract = {BACKGROUND: This study aimed to explore the association between gut microbiota functional profiles and skeletal muscle mass, focusing on sex-specific differences in a population under 65 years of age.

METHODS: Stool samples from participants were analysed using metagenomic shotgun sequencing. Skeletal muscle mass and skeletal muscle mass index (SMI) were quantified (SMI [%] = total appendage muscle mass [kg]/body weight [kg] × 100) using bioelectrical impedance analysis. Participants were categorized into SMI quartiles, and associations between gut microbiota, functional profiling and SMI were assessed by sex, adjusting for age, BMI and physical activity.

RESULTS: The cohort included 1027 participants (651 men, 376 women). In men, Escherichia coli (log2 fold change 3.08, q = 0.001), Ruminococcus_B gnavus (log2 fold change 2.89, q = 0.014) and Enterocloster sp001517625 (log2 fold change 2.47, q = 0.026) were more abundant in the lowest SMI compared to the highest SMI group. In contrast, Bifidobacterium bifidum (log2 fold change 3.13, q = 0.025) showed higher levels in the second lowest SMI group in women. Microbial pathways associated with amino acid synthesis (MET-SAM-PWY: log2 fold change 0.42; METSYN-PWY: log2 fold change 0.44; SER-GLYSYN-PWY: log2 fold change 0.20; PWY-5347: log2 fold change 0.41; P4-PWY: log2 fold change 0.53), N-acetylneuraminate degradation (log2 fold change 0.43), isoprene biosynthesis (log2 fold change 0.20) and purine nucleotide degradation and salvage (PWY-6353: log2 fold change 0.42; PWY-6608: log2 fold change 0.38; PWY66-409: log2 fold change 0.52; SALVADEHYPOX-PWY: log2 fold change 0.43) were enriched in the lowest SMI in men (q < 0.10). In women, the second lowest SMI group showed enrichment in energy-related pathways, including lactic acid fermentation (ANAEROFRUCAT-PWY: log2 fold change 0.19), pentose phosphate pathway (PENTOSE-P-PWY: log2 fold change 0.30) and carbohydrate degradation (PWY-5484: log2 fold change 0.31; GLYCOLYSIS: log2 fold change 0.29; PWY-6901: log2 fold change 0.27) (q < 0.05).

CONCLUSIONS: This study highlights sex-specific differences in gut microbiota and functional pathways associated with SMI. These findings suggest that gut microbiota may play a role in muscle health and point toward microbiota-targeted strategies for maintaining muscle mass.}, } @article {pmid39562866, year = {2024}, author = {Camacho-Mateu, J and Lampo, A and Ares, S and Cuesta, JA}, title = {Nonequilibrium microbial dynamics unveil a new macroecological pattern beyond Taylor's law.}, journal = {Physical review. E}, volume = {110}, number = {4-1}, pages = {044402}, doi = {10.1103/PhysRevE.110.044402}, pmid = {39562866}, issn = {2470-0053}, mesh = {*Models, Biological ; Microbiota ; }, abstract = {We introduce a comprehensive analytical benchmark, relying on Fokker-Planck formalism, to study microbial dynamics in the presence of both biotic and abiotic forces. In equilibrium, we observe a balance between the two kinds of forces, leading to no correlations between species abundances. This implies that real microbiomes, where correlations have been observed, operate out of equilibrium. Therefore, we analyze nonequilibrium dynamics, presenting an ansatz for an approximate solution that embodies the complex interplay of forces in the system. This solution is consistent with Taylor's law as a coarse-grained approximation of the relation between species abundance and variance, but implies subtler effects, predicting unobserved structure beyond Taylor's law. Motivated by this theoretical prediction, we refine the analysis of existing metagenomic data, unveiling a novel universal macroecological pattern. Finally, we speculate on the physical origin of Taylor's law: building upon an analogy with Brownian motion theory, we propose that Taylor's law emerges as a fluctuation-growth relation resulting from equipartition of environmental resources among microbial species.}, } @article {pmid39562308, year = {2024}, author = {Yang, Y and Xu, P and He, W and Tao, F}, title = {Metagenomic analysis reveals houseflies as indicators for monitoring environmental antibiotic resistance genes.}, journal = {Environmental microbiology reports}, volume = {16}, number = {6}, pages = {e70032}, pmid = {39562308}, issn = {1758-2229}, support = {32170105//National Natural Science Foundation of China/ ; MMLKF20-03//State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University/ ; }, mesh = {*Houseflies/microbiology/genetics ; *Metagenomics ; Animals ; *Anti-Bacterial Agents/pharmacology ; *Environmental Monitoring ; Genes, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/genetics ; Bacteria/genetics/classification/drug effects/isolation & purification ; Drug Resistance, Bacterial/genetics ; }, abstract = {Given the threat to public health posed by antibiotic resistance transmission, environmental monitoring is essential for tracking antibiotic resistance genes (ARGs). Houseflies, being ubiquitous organisms capable of carrying and disseminating ARGs, serve as suitable indicators for environmental monitoring. In this study, we employ metagenomic approaches to investigate housefly body surface samples from five typical sites associated with human activities. The investigation reveals microbiome diversity among the samples, along with variations in the occurrence and mobility potential of ARGs. Metagenomic analysis indicates that the composition of ARGs on housefly body surfaces is influenced by environmental ARGs, which may be enriched on the housefly body surface. The resistance genes related to multidrug, β-lactam, bacitracin, and tetracycline were the predominant ARGs detected, with multidrug-related ARGs consistently exhibiting dominance. Furthermore, the abundance of ARGs in the different housefly body surface samples was found to correlate with the population density and mobility of the sampling site. Natural environments exhibited the lowest ARG abundance, while areas with higher population density and limited population mobility displayed higher ARG abundance. This study emphasizes the effectiveness of houseflies as monitors for environmental ARGs and underscores their potential for assessing and controlling antibiotic resistance risks in urban environments.}, } @article {pmid39560390, year = {2025}, author = {Lin, H and Wu, L and Zhang, L and Ta, QK and Liu, P and Song, J and Yang, X}, title = {Metagenome-based diversity and functional analysis of culturable microbes in sugarcane.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0198224}, pmid = {39560390}, issn = {2165-0497}, mesh = {*Saccharum/microbiology ; *Soil Microbiology ; *Rhizosphere ; *Bacteria/classification/genetics/isolation & purification ; *Metagenome ; *Microbiota/genetics ; *Metagenomics/methods ; Biodiversity ; Burkholderia/genetics/classification/isolation & purification ; Phylogeny ; }, abstract = {UNLABELLED: Sugarcane is a key crop for sugar and energy production, and understanding the diversity of its associated microbes is crucial for optimizing its growth and health. However, there is a lack of thorough investigation and use of microbial resources in sugarcane. This study conducted a comprehensive analysis of culturable microbes and their functional features in different tissues and rhizosphere soil of four diverse sugarcane species using metagenomics techniques. The results revealed significant microbial diversity in sugarcane's tissues and rhizosphere soil, including several important biomarker bacterial taxa identified, which are reported to engage in several processes that support plant growth, such as nitrogen fixation, phosphate solubilization, and the production of plant hormones. The Linear discriminant analysis Effect Size (LEfSe) studies identified unique microbial communities in different parts of the same sugarcane species, particularly Burkholderia, which exhibited significant variations across the sugarcane species. Microbial analysis of carbohydrate-active enzymes (CAZymes) indicated that genes related to sucrose metabolism were mostly present in specific bacterial taxa, including Burkholderia, Pseudomonas, Paraburkholderia, and Chryseobacterium. This study improves understanding of the diversities and functions of endophytes and rhizosphere soil microbes in sugarcane. Moreover, the approaches and findings of this study provide valuable insights for microbiome research and the use of comparable technologies in other agricultural fields.

IMPORTANCE: This work utilized metagenomics techniques for conducting a comprehensive examination of culturable microbes and their functional characteristics in various tissues and rhizosphere soil of four distinct sugarcane species. This study enhances comprehension of the diversity and functions of endophytes and rhizosphere soil microbes in sugarcane. Furthermore, the methodologies and discoveries of this work offer new perspectives for microbiome investigation and the use of similar technologies in other agricultural fields.}, } @article {pmid39558081, year = {2024}, author = {Yang, M and Zhao, Y and Li, L and Qi, Y and Gao, P and Guo, J and Liu, J and Chen, Z and Zhao, J and Yu, L}, title = {Functional dynamics analysis of endophytic microbial communities during Amorphophallus muelleri seed maturation.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {28432}, pmid = {39558081}, issn = {2045-2322}, support = {YJL24014//Talent Introduction Program of Kunming University/ ; 202201AT070113//Yunnan Provincial Science and Technology Dep artment/ ; 202101AO070075//Yunnan Provincial Science and Technology Dep artment/ ; 202401AU070020//Yunnan Provincial Science and Technology Dep artment/ ; 202201AU070043//Yunnan Provincial Science and Technology Dep artment/ ; 202101BA070001-174//Yunnan Provincial Science and Technology Dep artment/ ; 202301AU070136//Yunnan Provincial Science and Technology Dep artment/ ; 2022J0644//Yunnan Education Department Research Project/ ; 2023J0827//Yunnan Education Department Research Project/ ; YNWR-QNBJ-2018-324//Yunnan Province Youth Talent Support Program/ ; }, mesh = {*Seeds/microbiology/growth & development ; *Endophytes/genetics ; *Microbiota/genetics ; *Amorphophallus/microbiology ; Metagenomics/methods ; Bacteria/genetics/classification ; Ascomycota/genetics ; Fungi/genetics/classification ; }, abstract = {Konjac seeds of Amorphophallus muelleri are produced through a unique form of apomixis in triploid parthenogenesis, and typically require a longer maturation period (approximately 8 months). To date, the relevant functions of endophytic microbial taxa during A. muelleri seed development and maturation remain largely unexplored. In this study, we analyzed the functional adaptability and temporal dynamics of endophytic microbial communities during three stages of A. muelleri seed maturation. Through metagenomic sequencing, we determined that the functions of the endophytic microbiome in A. muelleri seeds were driven by the seed maturation status, and the functions of the microbial communities in the seed coats and seeds differed significantly. The species annotation results show that Proteobacteria, Actinobacteria, Ascomycota, and Basidiomycota were the dominant bacterial and fungal communities in A. muelleri seeds at different maturation stages. The KEGG and COG functional gene annotation results revealed that the seed samples during the three maturation stages had higher KO functional diversity than the seed coat samples, and the COG functional diversity of the green and red seed samples was also significantly higher than that of the seed coat samples. At different maturation stages, microbial functional genes involved in energy production and conversion as well as carbon fixation were enriched in the A. muelleri seed coats, while microbial functional genes involved in signal transduction mechanisms, amino acid transport and metabolism, carbohydrate metabolism, and lipid metabolism were more highly expressed in the seeds. Moreover, in the middle to late stages of seed maturation, the microbial functional genes involved in the biosynthesis of resistant compounds such as phenols, flavonoids, and alkaloids were significantly enriched to enhance the resistance and environmental adaptation of A. muelleri seeds. The results verified that the functions of the endophytic microbial communities change dynamically during A. muelleri seed maturation to adapt to the current needs of the host plant, which has significant implications for the exploration and utilization of functional microbial resources in A. muelleri seeds.}, } @article {pmid39557257, year = {2024}, author = {Dong, J and Wang, L and Bai, Y and Huang, X and Chen, C and Liu, Y}, title = {Study on the physicochemical properties and immune regulatory mechanism of polysaccharide fraction from Aronia Melanocarpa fruit.}, journal = {International journal of biological macromolecules}, volume = {283}, number = {Pt 2}, pages = {137696}, doi = {10.1016/j.ijbiomac.2024.137696}, pmid = {39557257}, issn = {1879-0003}, mesh = {*Photinia/chemistry ; *Polysaccharides/pharmacology/chemistry ; Animals ; Mice ; *Fruit/chemistry ; *Gastrointestinal Microbiome/drug effects ; Chemical Phenomena ; Molecular Weight ; }, abstract = {Aronia Melanocarpa (Michx.) Elliott fruit has been extensively used in the food and medicinal fields. This study aimed to analyze the physicochemical properties of a polysaccharide fraction (AMP2) isolated from this fruit for the first time and investigated its immune regulatory mechanism. The physicochemical properties of AMP2 were determined using high-performance gel permeation chromatography, PMP derivatization-high performance liquid chromatography, Ultraviolet spectroscopy, and infrared spectroscopy. The metagenomic technology was applied to investigate the regulatory effects and mechanisms of AMP2 on the gut microbiota of immunosuppressed mice. The results showed that molecular weight of AMP2 was 83,444 Da, which was mainly composed of D-arabinose, D-xylose, D-mannose, D-rhamnose and D-glucose, and both β-type and α-type glycosidic bonds contained in its structure. AMP2 changed the composition of gut microbiota by increasing the number of beneficial and probiotic bacteria, thereby regulated the intestinal mucosal immune system of host. AMP2 improved intestinal immune system response and antimicrobial capacity through positive regulation of the NOD-like receptor signaling pathway and neutrophil extracellular trap formation. The results demonstrate the potential of AMP2 in immune regulation, providing a new perspective for its subsequent development and contributing to the development and application of related health foods.}, } @article {pmid39557245, year = {2024}, author = {Qin, X and Huang, W and Li, Q}, title = {Lignocellulose biodegradation to humic substances in cow manure-straw composting: Characterization of dissolved organic matter and microbial community succession.}, journal = {International journal of biological macromolecules}, volume = {283}, number = {Pt 3}, pages = {137758}, doi = {10.1016/j.ijbiomac.2024.137758}, pmid = {39557245}, issn = {1879-0003}, mesh = {*Humic Substances/analysis ; *Lignin/chemistry/metabolism ; *Manure/microbiology/analysis ; Cattle ; Animals ; *Composting/methods ; *Biodegradation, Environmental ; Microbiota ; }, abstract = {Composting, a sustainable practice, facilitates the biodegradation of organic waste, notably lignocellulosic biomass, into value-added humic substances. Despite its potential, the application of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) to characterize dissolved organic matter (DOM) for assessing the changes in maturity during cow manure-straw composting is underexplored. Furthermore, the link between these changes, microbial community succession, and the biochemical pathways of humus formation is seldom investigated. This study leveraged ESI FT-ICR MS and metagenomic analysis to elucidate the molecular changes in DOM, identified key microbes in humus formation, and traced the humus formation pathway during composting. The results highlighted the crucial role of microorganisms such as Thermobifida, Luteimonas, Ascomycota, and Chloroflexi in accelerating the breakdown and transformation of plant biopolymers. Large molecular nitrogen compounds from cow manure-straw were converted into unsaturated, aromatic oxygen compounds, which resemble humic substances in their chemical properties. The ESI FT-ICR MS data revealed that humus formation occurred through a series of reactions, including protein deamination, lignin delignification, and decarbonylation. This research offered new light on strategies to enhance the stabilization and humification of cow manure-straw composting, contributing to more effective composting processes.}, } @article {pmid39557129, year = {2025}, author = {Drane, K and Huerlimann, R and Jones, R and Whelan, A and Sheehan, M and Ariel, E and Kinobe, R}, title = {Concordance in molecular methods for detection of antimicrobial resistance: A cross sectional study of the influent to a wastewater plant.}, journal = {Journal of microbiological methods}, volume = {228}, number = {}, pages = {107069}, doi = {10.1016/j.mimet.2024.107069}, pmid = {39557129}, issn = {1872-8359}, mesh = {*Wastewater/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Australia ; Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; Microbiota/genetics/drug effects ; Genes, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Methods that are used to characterise microbiomes and antimicrobial resistance genes (ARGs) in wastewater are not standardised. We used shotgun metagenomic sequencing (SM-Seq), RNA sequencing (RNA-seq) and targeted qPCR to compare microbial and ARG diversity in the influent to a municipal wastewater treatment plant in Australia. ARGs were annotated with CARD-RGI and MEGARes databases, and bacterial diversity was characterised by 16S rRNA gene sequencing and SM-Seq, with species annotation in SILVA/GreenGenes databases or Kraken2 and the NCBI nucleotide database respectively. CARD and MEGARes identified evenly distributed ARG profiles but MEGARes detected a richer array of ARGs (richness = 475 vs 320). Qualitatively, ARGs encoding for aminoglycoside, macrolide-lincosamide-streptogramin and multidrug resistance were the most abundant in all examined databases. RNA-seq detected only 32 % of ARGs identified by SM-Seq, but there was concordance in the qualitative identification of aminoglycoside, macrolide-lincosamide, phenicol, sulfonamide and multidrug resistance by SM-Seq and RNA-seq. qPCR confirmed the detection of some ARGs, including OXA, VEB and EREB, that were identified by SM-Seq and RNA-seq in the influent. For bacteria, SM-Seq or 16S rRNA gene sequencing were equally effective in population profiling at phyla or class level. However, SM-Seq identified a significantly higher species richness (richness = 15,000 vs 3750). These results demonstrate that SM-Seq with gene annotation in CARD and MEGARes are equally sufficient for surveillance of antimicrobial resistance in wastewater. For more precise ARG identification and quantification however, MEGARes presented a better resolution. The functionality of detected ARGs was not confirmed, but general agreement on the putative phenotypic resistance profile by antimicrobial class was observed between RNA-Seq and SM-Seq.}, } @article {pmid39551951, year = {2024}, author = {Yao, L and Devotta, H and Li, J and Lunjani, N and Sadlier, C and Lavelle, A and Albrich, WC and Walter, J and O'Toole, PW and O'Mahony, L}, title = {Dysrupted microbial tryptophan metabolism associates with SARS-CoV-2 acute inflammatory responses and long COVID.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2429754}, pmid = {39551951}, issn = {1949-0984}, mesh = {Humans ; *Tryptophan/metabolism/blood ; *COVID-19/immunology/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; *SARS-CoV-2/immunology ; *Cytokines/blood/metabolism ; Middle Aged ; Aged ; *Feces/microbiology/virology ; Post-Acute COVID-19 Syndrome ; Indoles/metabolism ; Indoleacetic Acids/metabolism/blood ; Inflammation ; Adult ; Dysbiosis/microbiology ; }, abstract = {Protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and risk of long COVID has been associated with the depletion or over-abundance of specific taxa within the gut microbiome. However, the microbial mechanisms mediating these effects are not yet known. We hypothesized that altered microbial production of tryptophan and its downstream derivatives might contribute to inappropriate immune responses to viral infection. In patients hospitalized with COVID-19 (n = 172), serum levels of tryptophan and indole-3-propionate (IPA) negatively correlated with serum levels of many proinflammatory mediators (including C-reactive protein and Serum amyloid A), while C-glycosyltryptophan (C-Trp), indole-3-lactic acid (ILA) and indole-3-acetic acid (IAA) levels were positively correlated with levels of acute phase proteins, proinflammatory cytokines, alarmins and chemokines. A similar pattern was observed in long COVID patients (n = 20) where tryptophan and IPA were negatively associated with a large number of serum cytokines, while C-Trp and IAA were positively associated with circulating cytokine levels. Metagenomic analysis of the fecal microbiota showed the relative abundance of genes encoding the microbial enzymes required for tryptophan production (e.g. anthranilate synthase) and microbial tryptophan metabolism was significantly lower in patients hospitalized with COVID-19 (n = 380) compared to healthy controls (n = 270). Microbial tryptophan metabolites reduced innate cell proinflammatory responses to cytosolic DNA sensor Stimulator of interferon genes (STING), toll-like receptor (TLR)-3 and TLR-4 stimulation in vitro, while IL-10 secretion was enhanced. Microbial tryptophan metabolites also modified ex vivo human lymphocyte responses by limiting the production of TH1 and TH17 associated cytokines, while enhancing secretion of IL-22. These data suggest that lower levels of tryptophan production and tryptophan metabolism by gut microbes may increase the risk of severe and chronic outcomes to SARS-CoV-2 infection due to impaired innate and adaptive responses to infection. Screening patients for lower-level microbiome capacity for tryptophan metabolism may help identify at-risk individuals.}, } @article {pmid39551884, year = {2024}, author = {Mamo, Z and Abera, S and Tafesse, M}, title = {Taxonomic and functional profiling of microbial community in municipal solid waste dumpsite.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {12}, pages = {384}, pmid = {39551884}, issn = {1573-0972}, support = {EN-1/17-1/18//Addis Ababa Science and Technology University/ ; }, mesh = {*Solid Waste ; *Bacteria/classification/genetics/metabolism ; *Waste Disposal Facilities ; *Microbiota ; *Metagenomics ; Phylogeny ; Refuse Disposal ; Biodegradation, Environmental ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; }, abstract = {Understanding the microbial ecology of landfills is crucial for improving waste management strategies and utilizing the potential of these microbial communities for biotechnological applications. This study aimed to conduct a comprehensive taxonomic and functional profiling of the microbial community present in the Addis Ababa municipal solid waste dumpsite using a shotgun metagenomics sequencing approach. The taxonomic analysis of the sample revealed the significant presence of bacteria, with the Actinomycetota (56%), Pseudomonadota (23%), Bacillota (3%), and Chloroflexota (3%) phyla being particularly abundant. The most abundant KEGG categories were carbohydrates metabolism, membrane transport, signal transduction, and amino acid metabolism. The biodegradation and metabolism of xenobiotics, as well as terpenoids and polyketides, were also prevalent. Moreover, the Comprehensive Antibiotic Resistance Database (CARD) identified 52 antibiotic resistance gene (ARG) subtypes belonging to 14 different drug classes, with the highest abundances observed for glycopeptide, phosphonic acid, and multidrug resistance genes. Actinomycetota was the dominant phylum harboring ARGs, followed by Pseudomonadota and Chloroflexota. This study offers valuable insights into the taxonomic and functional diversity of the microbial community in the Addis Ababa municipal solid waste dumpsite. It sheds light on the widespread presence of metabolically versatile microbes, antibiotic resistance genes, mobile genetic elements, and pathogenic bacteria. This understanding can contribute to the creation of efficient waste management strategies and the investigation of possible biotechnological uses for these microbial communities.}, } @article {pmid39551356, year = {2025}, author = {Lalli, MK and Salo, TE and Hakola, L and Knip, M and Virtanen, SM and Vatanen, T}, title = {Associations between dietary fibers and gut microbiome composition in the EDIA longitudinal infant cohort.}, journal = {The American journal of clinical nutrition}, volume = {121}, number = {1}, pages = {83-99}, doi = {10.1016/j.ajcnut.2024.11.011}, pmid = {39551356}, issn = {1938-3207}, mesh = {Humans ; *Dietary Fiber/administration & dosage ; *Gastrointestinal Microbiome ; Infant ; Longitudinal Studies ; Female ; Male ; Cross-Sectional Studies ; Infant Nutritional Physiological Phenomena ; Cohort Studies ; Milk, Human/chemistry ; Bacteria/classification/genetics ; Diet ; Feces/microbiology ; }, abstract = {BACKGROUND: The infant gut microbiome undergoes rapid changes in the first year of life, supporting normal development and long-term health. Although diet shapes this process, the role of fibers in complementary foods on gut microbiome maturation is poorly understood.

OBJECTIVES: We explored how the transition from human milk to fibers in complementary foods shapes the taxonomic and functional maturation of the gut microbiome within the first year of life.

METHODS: We assessed the longitudinal and cross-sectional development of infant gut microbiomes (N = 68 infants) and metabolomes (N = 33 infants) using linear mixed models to uncover their associations to dietary fibers and their food sources. Fiber intakes were assessed with 3-d food records (months 3, 6, 9, and 12) relying on CODEX-compliant fiber fraction values, and questionnaires tracked the overall complementary food introduction. Bacterial species were identified and quantified via MetaPhlAn2 from metagenomic data, and metabolomic profiles were obtained using 4 LC-MS methods.

RESULTS: We identified 176 complementary food fiber-bacterial species associations. First plant-based fibers associated with microbiota compositions similar to breastfeeding, and further associated with aromatic amino acid-derived metabolites, including 5-hydroxyindoleacetic acid (total dietary fiber - complementary foods (g) - β = 3.50, CI: 2.48, 4.52, P = 6.53 × 10[-5]). Distinct fibers from different food categories showed unique associations with specific bacterial taxa. Key species, such as Faecalibacterium prausnitznii, associated with oat fibers (g/MJ, β = 2.18, confidence interval: 1.36, 2.84, P = 6.12 × 10[-6]), reflective of maturing microbial communities. Fiber intake during weaning associated with shifts in metabolite profiles, including immunomodulatory metabolites, with fiber effects observed in a source- and timing-dependent manner, implicated in gradual microbiome diversification.

CONCLUSIONS: Introducing complementary dietary fibers during the weaning period supports gut microbiome diversification and stabilization. Even minor dietary variations shows significant associations with microbial taxa and functions from the onset of weaning, highlighting the importance of infant dietary recommendations that support the gut microbiome maturation during early life. This trial was registered at clinicaltrials.gov as registration number NCT01735123.}, } @article {pmid39551294, year = {2024}, author = {Zhang, G and Du, J and Zhang, C and Zhao, Z and Chen, Y and Liu, M and Chen, J and Fan, G and Ma, L and Li, S and Liu, K}, title = {Identification of a PET hydrolytic enzyme from the human gut microbiome unveils potential plastic biodegradation in human digestive tract.}, journal = {International journal of biological macromolecules}, volume = {283}, number = {Pt 3}, pages = {137732}, doi = {10.1016/j.ijbiomac.2024.137732}, pmid = {39551294}, issn = {1879-0003}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Polyethylene Terephthalates/metabolism/chemistry ; *Biodegradation, Environmental ; Hydrolysis ; Gastrointestinal Tract/microbiology/metabolism ; Metagenome ; Hydrolases/metabolism/genetics ; Plastics/chemistry ; Nanoparticles/chemistry ; }, abstract = {Widespread use of polyethylene terephthalate (PET) plastics and their recycling challenges have led to substantial accumulation of PET wastes in global environments, with inevitable consequences for their entry into the food chains. Recent studies have increasingly documented the ingestion of microplastics by humans through food and beverages. However, the fate of these microplastics within the gastrointestinal tract, particularly the role of the human gut microbiota, remains inadequately understood. To address this knowledge gap, we employed a bioinformatics workflow integrated with functional verification to investigate the PET digestion/degradation capabilities of intestinal microorganisms. This approach identified a novel PET hydrolase-HGMP01 from the human gut metagenome, which exhibits the capacity to hydrolyze PET nanoparticles. Moreover, comprehensive exploration for HGMP01 homologues in the human gut metagenome and metatranscriptome unveil their distribution in diverse intestinal microorganisms. This study provides biochemical evidence for an unforeseen role of human gut microbiome in plastic digestion, thus holding substantial implications for human health.}, } @article {pmid39551110, year = {2025}, author = {Adenaike, AS and Akpan, U and Oyedun, IO and Adewole, FA and Agbaje, M and Olusanya, OM and Arowosegbe, MO and Ikeobi, CON}, title = {Gut microbial composition differs among FUNAAB Alpha broiler chicken genotypes raised in a tropical environment.}, journal = {Microbial pathogenesis}, volume = {198}, number = {}, pages = {107126}, doi = {10.1016/j.micpath.2024.107126}, pmid = {39551110}, issn = {1096-1208}, mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; *Genotype ; *Tropical Climate ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; Feathers/microbiology ; Bacteroidetes/genetics/isolation & purification/classification ; Phylogeny ; Firmicutes/genetics/isolation & purification/classification ; Actinobacteria/genetics/classification/isolation & purification ; Biodiversity ; DNA, Bacterial/genetics ; Gastrointestinal Tract/microbiology ; }, abstract = {The gut microbiota of FUNAAB Alpha chickens plays a crucial role in determining their overall health and performance. Understanding the various types and diversity of microbiota in the gut of different genotypes of chickens is crucial for enhancing their well-being, productivity, and disease resistance. This study employed 16S rRNA and metagenomics analysis to examine the gut bacteria of three genotypes of FUNAAB Alpha broiler chickens, namely Naked neck, Frizzle, and Normal feather. There were three phyla observed in the three genotypes: Bacteroidetes, Actinobacteria, and Firmicutes. Through the utilisation of 16S rRNA sequencing, we successfully identified and categorised the various microbiota present within the gastrointestinal tract. Our study revealed notable variations in the composition and quantity of microbiota across the three genotypes, suggesting that each genotype possesses a distinct collection of gut bacteria. A wide range of microbiological diversity was observed within the community. Interestingly, the Normal feather chicken exhibited a greater number of operational taxonomic units (OTUs) compared to the Naked neck and Frizzle feather chicken. This study presents significant findings regarding the ceacal microbiota of FUNAAB Alpha chickens, emphasising the variations observed among different genotypes. It is crucial to study composition-modification techniques to enhance host health and performance, as well as to control zoonotic pathogens that can contaminate poultry products and threaten consumers' health.}, } @article {pmid39550955, year = {2024}, author = {Liu, S and Cao, J and Yu, J and Jian, M and Zou, L}, title = {Microplastics exacerbate the ecological risk of antibiotic resistance genes in wetland ecosystem.}, journal = {Journal of environmental management}, volume = {372}, number = {}, pages = {123359}, doi = {10.1016/j.jenvman.2024.123359}, pmid = {39550955}, issn = {1095-8630}, mesh = {*Wetlands ; *Drug Resistance, Microbial/genetics ; *Microplastics/toxicity ; China ; Ecosystem ; Lakes/microbiology ; }, abstract = {Wetlands are vital components of the global ecosystem, significantly influencing the retention and dissemination of microplastics (MPs) and antibiotic resistance genes (ARGs). However, the effects of different types of MPs on the environmental dynamics of ARGs within these ecosystems remain poorly understood. This study focused on the distribution and composition of ARGs associated with two primary types of MPs-polyethylene and polypropylene-within the Poyang Lake wetland, the largest freshwater lake in China, utilizing metagenomic analysis. The findings demonstrated that the bacterial communities and ARG profiles in the plastisphere were markedly distinct from those in the surrounding water. Specifically, thirteen opportunistic pathogens and forty subtypes of ARGs, primarily related to multidrug, bacitracin, and β-lactam resistance, were identified in the plastisphere. Notably, polyethylene exhibited four times more specific ARG subtypes than polypropylene. Procrustes analysis combined with network analysis indicated a lack of strong correlation between ARG abundance and bacterial populations, suggesting potential horizontal transfer of ARGs within the microbiota of the plastisphere. Additionally, three novel and functional β-lactamase genes were identified within this environment. This investigation highlights the role of MPs as reservoirs for ARGs, facilitating their exchange and posing risks to both ecological integrity and human health, thereby underscoring the need for increased attention in future research efforts.}, } @article {pmid39550949, year = {2024}, author = {Wu, ZL and Shi, WJ and Zhang, L and Xia, ZY and Gou, M and Sun, ZY and Tang, YQ}, title = {Investigating the robustness of microbial communities in municipal sludge anaerobic digestion under organic loading rate disturbance.}, journal = {Journal of environmental management}, volume = {372}, number = {}, pages = {123326}, doi = {10.1016/j.jenvman.2024.123326}, pmid = {39550949}, issn = {1095-8630}, mesh = {*Sewage/microbiology ; Anaerobiosis ; *Bioreactors/microbiology ; Waste Disposal, Fluid/methods ; Bacteria/metabolism/genetics/classification ; Microbiota ; }, abstract = {Anaerobic digestion (AD) frequently encounters disturbances due to variations in organic loading rates (OLRs), which can result in the failure of the sludge treatment process. However, there is a lack of comprehensive studies on the robustness of AD systems against OLR disturbances and the underlying mechanisms. In this study, the responses of reactor performance and active microbial communities in mesophilic AD were investigated and compared under conditions of OLR shock and OLR fluctuation. Statistical analysis confirmed that all reactors recovered from both types of OLR disturbance, indicating both functional and structural robustness of the mesophilic community. Based on metagenomics and metatranscriptomics analyses, it was observed that high diversity within the microbial community led to functional redundancy, which appears to be a key mechanism contributing to the robustness against OLR disturbances. Additionally, for the first time, the potential metabolic diversity of aerobic autotrophy bacteria in AD reactors was identified, including their roles in the utilization of glucose and acetate. Furthermore, the analysis of topological properties within the microbial interaction network was conducted, and the robustness of the community network was verified through the application of random node deletion attacks. The findings from this study provide valuable information for the effective regulation of microbial communities and the design of practical AD systems.}, } @article {pmid39550371, year = {2024}, author = {Yang, JX and Peng, Y and Yu, QY and Yang, JJ and Zhang, YH and Zhang, HY and Adams, CA and Willing, CE and Wang, C and Li, QS and Han, XG and Gao, C}, title = {Gene horizontal transfers and functional diversity negatively correlated with bacterial taxonomic diversity along a nitrogen gradient.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {128}, pmid = {39550371}, issn = {2055-5008}, mesh = {*Soil Microbiology ; Soil/chemistry ; *Nitrogen/metabolism/pharmacology ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/metabolism ; Metagenome ; *Gene Transfer, Horizontal/drug effects ; }, abstract = {Horizontal gene transfer (HGT) mediated diversification is a critical force driving evolutionary and ecological processes. However, how HGT might relate to anthropogenic activity such as nitrogen addition, and its subsequent effect on functional diversity and cooccurrence networks remain unknown. Here we approach this knowledge gap by blending bacterial 16S rRNA gene amplicon and shotgun metagenomes from a platform of cessation of nitrogen additions and continuous nitrogen additions. We found that bacterial HGT events, functional genes, and virus diversities increased whereas bacterial taxonomic diversity decreased by nitrogen additions, resulting in a counterintuitive strong negative association between bacterial taxonomic and functional diversities. Nitrogen additions, especially the ceased one, complexified the cooccurrence network by increasing the contribution of vitamin B12 auxotrophic Acidobacteria, indicating cross-feeding. These findings advance our perceptions of the causes and consequences of the diversification process in community ecology.}, } @article {pmid39549663, year = {2024}, author = {Méndez, A and Maisto, F and Pavlović, J and Rusková, M and Pangallo, D and Sanmartín, P}, title = {Microbiome shifts elicited by ornamental lighting of granite facades identified by MinION sequencing.}, journal = {Journal of photochemistry and photobiology. B, Biology}, volume = {261}, number = {}, pages = {113065}, doi = {10.1016/j.jphotobiol.2024.113065}, pmid = {39549663}, issn = {1873-2682}, mesh = {*Microbiota ; *Silicon Dioxide/chemistry ; *Bacteria/genetics/radiation effects/isolation & purification/classification ; *Fungi/genetics ; Lighting ; Nanopore Sequencing ; Pilot Projects ; Archaea/genetics/radiation effects ; }, abstract = {Night-time outdoor illumination in combination with natural sunlight can influence the visible phototrophic colonizers (mainly algae) growing on stone facades; however, the effects on the microbiome (invisible to the naked eye) are not clear. The presence of stone-dwelling microbes, such as bacteria, diatoms, fungi, viruses and archaea, drives further biological colonization, which may exacerbate the biodeterioration of substrates. Considering the microbiome is therefore important for conservation of the built heritage. The impact of the following types of lighting on the relative abundance and diversity of the microbiome on granite ashlars was evaluated in a year-long outdoor pilot study: no lighting; lighting with a metal halide lamp (a traditional lighting system currently used to illuminate monuments); and lighting with a novel LED lamp (an environmentally sound prototype lamp with a biostatic effect, halting biological colonization by phototrophs, currently under trial). Culturable fractions of microbiome and whole-genome sequencing by metabarcoding with Oxford Nanopore Sequencing (MinION) was conducted for bacteria and fungi in order to complement both community characterization strategies. In addition, the possible biodeteriorative profiles of the isolated strains, relative to calcium carbonate precipitation/solubilisation and iron oxidation/reduction, were investigated by plate assays. Alpha and beta diversity indexes were also determined, along with the abundance of biocide and antibiotic resistance genes. Culture-dependent microbiological analysis failed to properly show changes in community composition, for which metagenomic approaches like MinION are better suited. Thus, MinION analysis identified shifts in the granite microbiome elicited by ornamental lighting. The novel LED lamp with the biostatic effect on phototrophs caused an increase in the diversity of bacteria and fungi. In this case, the microbiome was more similar to that in the unlit samples. In the samples illuminated by the metal halide lamp, dominance of bacteria was favoured and the presence of fungi was negligible.}, } @article {pmid39549023, year = {2024}, author = {Xiang, J and Chai, N and Li, L and Hao, X and Linghu, E}, title = {Alterations of Gut Microbiome in Patients with Colorectal Advanced Adenoma by Metagenomic Analyses.}, journal = {The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology}, volume = {35}, number = {11}, pages = {859-868}, pmid = {39549023}, issn = {2148-5607}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/microbiology/pathology ; Female ; Male ; *Adenoma/microbiology/pathology ; Middle Aged ; *Dysbiosis/microbiology ; *Feces/microbiology ; *Metagenomics/methods ; Case-Control Studies ; Aged ; Tryptophan/metabolism ; }, abstract = {BACKGROUND/AIMS: Colorectal cancer (CRC) is one of the deadliest cancers worldwide, mostly arising from adenomatous polyps. Mounting evidence has demonstrated that changes in the gut microbiome play key roles in CRC progression, while quite few studies focused on the altered microbiota architecture of advanced adenoma (AA), a crucial precancerous stage of CRC. Thus, we aimed to investigate the microbial profiles of AA patients.

MATERIALS AND METHODS: Fecal samples were collected from 26 AA patients and 26 age- and sex-matched normal controls (NC), and analyzed by shotgun metagenomic sequencing.

RESULTS: Gut microbial dysbiosis was observed in AA patients with lower alpha diversity. Advanced adenoma was characterized by an increased Bacillota/Bacteroidota ratio and higher Pseudomonadota levels compared to normal individuals. Linear discriminant analysis effect size (LEfSe) analysis was performed and identified 14 microbiota with significantly different abundance levels between AA and NC groups. Functional analysis revealed that tryptophan metabolism was upregulated in AA. Correspondingly, the expressions of gut microbes implicated in tryptophan metabolism also changed, including Akkermansia muciniphila, Bacteroides ovatus, Clostridium sporogenes, and Limosilactobacillus reuteri. The microbial network suggested that AA exhibited decreased correlation complexity, with Escherichia coli and Enterobacteriaceae unclassified harboring the strongest connectivity. A diagnostic model consisting of 3 microbial species was established based on random forest, yielding an area under the curve (AUC) of 0.799.

CONCLUSION: Our study profiled the alterations of the gut microbiome in AA patients, which may enrich the knowledge of microbial signatures along with colorectal tumorigenesis and provide promising biomarkers for AA diagnosis.}, } @article {pmid39548565, year = {2024}, author = {Grønbæk, IMB and Mollerup, S and Halkjær, SI and Paulsen, SJ and Pinholt, M and Westh, H and Petersen, AM}, title = {Faecal sample storage without ethanol for up to 24 h followed by freezing performs better than storage with ethanol for shotgun metagenomic microbiome analysis in patients with inflammatory and non-inflammatory intestinal diseases and healthy controls.}, journal = {BMC research notes}, volume = {17}, number = {1}, pages = {340}, pmid = {39548565}, issn = {1756-0500}, mesh = {Humans ; *Feces/microbiology ; *Ethanol ; *Gastrointestinal Microbiome/genetics ; *Specimen Handling/methods ; *Freezing ; Male ; Adult ; *Inflammatory Bowel Diseases/microbiology ; Female ; Metagenomics/methods ; Middle Aged ; Metagenome ; Case-Control Studies ; }, abstract = {OBJECTIVE: The influence of different faecal collection methods on metagenomic analyses remains under discussion, and there is no general agreement on which collection method is preferable for gut microbiome research. We compared faecal samples collected in tubes without preservatives with those containing 10 mL of 96% ethanol for gut microbiome research when the timeframe from defecation to freezing at - 80 °C was up to 24 h. We aimed to compare the collection methods on faeces from participants with inflammatory and non-inflammatory gastrointestinal disorders and healthy controls to investigate the most suitable method when considering data yield, human fraction of sequencing reads, and ease of use. We also examined the faecal sample homogeneity.

RESULTS: Faeces collected in tubes without preservatives resulted in more sequencing reads compared to faeces collected in tubes with 96% ethanol and were also easier to handle. The human fraction of total reads in faeces collected in ethanol from participants with inflammatory bowel disease was higher than all other samples. DNA extraction and sequencing from two different locations in the same faecal sample gave similar results and showed sample homogeneity.}, } @article {pmid39546167, year = {2024}, author = {Rajeev, M and Cho, JC}, title = {Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {62}, number = {11}, pages = {985-997}, pmid = {39546167}, issn = {1976-3794}, mesh = {*Aquaculture ; *RNA, Ribosomal, 16S/genetics ; *Rhodobacteraceae/genetics/classification/isolation & purification/metabolism ; Animals ; Republic of Korea ; China ; Metagenomics ; Vietnam ; Phylogeny ; Microbiota ; Metagenome ; Seawater/microbiology ; }, abstract = {Bioflocs are microbial aggregates primarily composed of heterotrophic bacteria that play essential ecological roles in maintaining animal health, gut microbiota, and water quality in biofloc aquaculture systems. Despite the global adoption of biofloc aquaculture for shrimp and fish cultivation, our understanding of biofloc microbiota-particularly the dominant bacterial members and their ecological functions-remains limited. In this study, we employed integrated metataxonomic and metagenomic approaches to demonstrate that the family Rhodobacteraceae of Alphaproteobacteria consistently dominates the biofloc microbiota and plays essential ecological roles. We first analyzed a comprehensive metataxonomic dataset consisting of 200 16S rRNA gene amplicons collected across three Asian countries: South Korea, China, and Vietnam. Taxonomic investigation identified Rhodobacteraceae as the dominant and consistent bacterial members across the datasets. The predominance of this taxon was further validated through metagenomics approaches, including read taxonomy and read recruitment analyses. To explore the ecological roles of Rhodobacteraceae, we applied genome-centric metagenomics, reconstructing 45 metagenome-assembled genomes. Functional annotation of these genomes revealed that dominant Rhodobacteraceae genera, such as Marivita, Ruegeria, Dinoroseobacter, and Aliiroseovarius, are involved in vital ecological processes, including complex carbohydrate degradation, aerobic denitrification, assimilatory nitrate reduction, ammonium assimilation, and sulfur oxidation. Overall, our study reveals that the common practice of carbohydrate addition in biofloc aquaculture systems fosters the growth of specific heterotrophic bacterial communities, particularly Rhodobacteraceae. These bacteria contribute to maintaining water quality by removing toxic nitrogen and sulfur compounds and enhance animal health by colonizing gut microbiota and exerting probiotic effects.}, } @article {pmid39545702, year = {2024}, author = {Zhang, M and Ma, L and Luo, J and Ren, T and Liu, S and Pan, L and Bao, Y and Li, F and Dai, Y and Pi, Z and Yue, H and Zheng, F}, title = {Low-Medium Polarity Ginsenosides from Wild Ginseng Improves Immunity by Activating the AhR/MAPK Pathway through Tryptophan Metabolism Driven by Gut Microbiota.}, journal = {Journal of agricultural and food chemistry}, volume = {72}, number = {47}, pages = {26142-26154}, doi = {10.1021/acs.jafc.4c06019}, pmid = {39545702}, issn = {1520-5118}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Panax/chemistry ; Mice ; *Tryptophan/metabolism ; *Ginsenosides/pharmacology/administration & dosage ; *Plant Extracts/pharmacology/administration & dosage ; *Receptors, Aryl Hydrocarbon/metabolism/genetics ; Male ; Bacteria/classification/genetics/metabolism/isolation & purification/drug effects ; Humans ; Immunity/drug effects ; MAP Kinase Signaling System/drug effects ; Spleen/drug effects/metabolism/immunology ; Intestinal Mucosa/metabolism/immunology/drug effects ; Mice, Inbred BALB C ; }, abstract = {The gut microbiota contribute significantly to the immune system. Low-medium polarity ginsenosides from wild ginseng (LWG) have potential immunomodulatory effects. However, how the LWG regulates gut microbiota to enhance immunity remains unclear. To explore the interaction between gut microbes and metabolites mediating LWG's immunomodulatory effects, this study examined LWG's impact on splenocytes and CTX-induced immunosuppressed mice. Metabolomic and metagenomic analyses were conducted in vivo to explore the mechanism by which LWG regulates gut microbiota to enhance immunity. In vitro data suggest that LWG at 4 μg/mL enhances the splenocyte activity. Furthermore, LWG effectively reduces symptoms in immunocompromised mice, including weight loss and intestinal mucosal damage. LWG alleviated gut microbiota disturbance, restored tryptophan metabolites (IA, IAA, and IPA), and significantly increased JNK, ERK, and p38MAPK protein levels, which were downstream of AhR. Our study demonstrated that LWG improves the immunity by reshaping gut microbiota, restoring intestinal mucosa, and boosting the gut microbiota-related metabolism of tryptophan to activate the AhR/MAPK pathway. This research offers new insights into the mechanism by which LWG regulates immune function.}, } @article {pmid39544492, year = {2024}, author = {Xiao, S and Zhou, W and Caldwell, R and Decker, S and Oh, J and Milstone, AM}, title = {Association of Neonatal and Maternal Nasal Microbiome Among Neonates in the Intensive Care Unit.}, journal = {Open forum infectious diseases}, volume = {11}, number = {11}, pages = {ofae644}, pmid = {39544492}, issn = {2328-8957}, abstract = {The neonatal nasal microbiota may help protect neonates in the neonatal intensive care unit from pathogen colonization and infection. This preliminary study characterized the biodiversity of nasal microbiota comparing neonates in the neonatal intensive care unit and their mothers, highlighting the potential of strain sharing between mother-neonate pairs.}, } @article {pmid39544283, year = {2024}, author = {Li, S and Fan, S and Ma, Y and Xia, C and Yan, Q}, title = {Influence of gender, age, and body mass index on the gut microbiota of individuals from South China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1419884}, pmid = {39544283}, issn = {2235-2988}, mesh = {Humans ; *Body Mass Index ; China ; Female ; Male ; Adult ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; Age Factors ; *Feces/microbiology ; Sex Factors ; Young Adult ; Aged ; Bacteria/classification/genetics/isolation & purification ; Phylogeny ; }, abstract = {BACKGROUND: The symbiotic gut microbiota is pivotal for human health, with its composition linked to various diseases and metabolic disorders. Despite its significance, there remains a gap in systematically evaluating how host phenotypes, such as gender, age, and body mass index (BMI), influence gut microbiota.

We conducted an analysis of the gut microbiota of 185 Chinese adults based on whole-metagenome shotgun sequencing of fecal samples. Our investigation focused on assessing the effects of gender, age, and BMI on gut microbiota across three levels: diversity, gene/phylogenetic composition, and functional composition. Our findings suggest that these phenotypes have a minor impact on shaping the gut microbiome compared to enterotypes, they do not correlate significantly within- or between-sample diversity. We identified a substantial number of phenotype-associated genes and metagenomic linkage groups (MLGs), indicating variations in gut microflora composition. Specifically, we observed a decline in beneficial Firmicutes microbes, such as Eubacterium, Roseburia, Faecalibacterium and Ruminococcus spp., in both older individuals and those with higher BMI, while potentially harmful microbes like Erysipelotrichaceae, Subdoligranulum and Streptococcus spp. increased with age. Additionally, Blautia and Dorea spp. were found to increase with BMI, aligning with prior research. Surprisingly, individuals who were older or overweight exhibited a lack of Bacteroidetes, a dominant phylum in the human gut microbiota that includes opportunistic pathogens, while certain species of the well-known probiotics Bifidobacterium were enriched in these groups, suggesting a complex interplay of these bacteria warranting further investigation. Regarding gender, several gender-associated MLGs from Bacteroides, Parabacteroides, Clostridium and Akkermansia were enriched in females. Functional analysis revealed a multitude of phenotype-associated KEGG orthologs (KOs).

CONCLUSIONS/SIGNIFICANCE: Our study underscores the influence of gender, age, and BMI on gut metagenomes, affecting both phylogenetic and functional composition. However, further investigation is needed to elucidate the precise roles of these bacteria, including both pathogens and probiotics.}, } @article {pmid39544279, year = {2024}, author = {Hong, R and Lin, S and Zhang, S and Yi, Y and Li, L and Yang, H and Du, Z and Cao, X and Wu, W and Ren, R and Yao, X and Xie, B}, title = {Pathogen spectrum and microbiome in lower respiratory tract of patients with different pulmonary diseases based on metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1320831}, pmid = {39544279}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; *Metagenomics/methods ; Middle Aged ; Female ; Male ; Lung Diseases/microbiology ; Aged ; Lung/microbiology ; Bacteria/genetics/classification/isolation & purification ; Adult ; Respiratory System/microbiology ; Metagenome/genetics ; }, abstract = {INTRODUCTION: The homeostasis of the microbiome in lower respiratory tract is crucial in sustaining normal physiological functions of the lung. Different pulmonary diseases display varying degrees of microbiome imbalance; however, the specific variability and clinical significance of their microbiomes remain largely unexplored.

METHODS: In this study, we delineated the pathogen spectrum and commensal microorganisms in the lower respiratory tract of various pulmonary diseases using metagenomic sequencing. We analyzed the disparities and commonalities of the microbial features and examined their correlation with disease characteristics.

RESULTS: We observed distinct pathogen profiles and a diversity in lower airway microbiome in patients diagnosed with cancer, interstitial lung disease, bronchiectasis, common pneumonia, Nontuberculous mycobacteria (NTM) pneumonia, and severe pneumonia.

DISCUSSION: This study illustrates the utility of Metagenomic Next-generation Sequencing (mNGS) in identifying pathogens and analyzing the lower respiratory microbiome, which is important for understanding the microbiological aspect of pulmonary diseases and essential for their early and precise diagnosis.}, } @article {pmid39544117, year = {2024}, author = {Roslund, MI and Galitskaya, P and Saarenpää, M and Sinkkonen, A}, title = {Cultivar-dependent differences in plant bud microbiome and functional gene pathways in woody plants commonly used in urban green space.}, journal = {Letters in applied microbiology}, volume = {77}, number = {12}, pages = {}, doi = {10.1093/lambio/ovae110}, pmid = {39544117}, issn = {1472-765X}, support = {346 136//Strategic Research Council/ ; }, mesh = {*Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Metagenome ; Archaea/genetics/classification ; Plants/microbiology ; Humans ; Phylogeny ; Metagenomics ; }, abstract = {Plant richness and microbiota have been associated with plant health; hardly any studies have investigated how plant taxa differs in microbiota in the context of human health. We investigated the microbial differences in buds of 83 woody plant taxa used in urban green spaces in hemiboreal climate, using 16S rRNA and whole metagenome shotgun sequencing. Bud microbial community was the richest in Cotoneaster Nanshan and C. integerrimus, and Malus domestica cultivars "Sandra" and "Lobo" and poorest in Ribes glandulosum. Metagenomic shotgun sequencing of two M. domestica and four Ribes varieties confirmed differences in taxa in bud microbiota and indicated higher siderophore synthesis in Malus. Microbial richness, including bacteria, archaea, and viruses, and functional richness of gene pathways was higher in Malus compared to Ribes. The 10 most abundant amplicon sequence units, often referred as species, belonged to the phylum Proteobacteria. The differences between plant taxa were evident in classes Alpha- and Gammaproteobacteria, known for potential human health benefits. Since environmental microbiota contributes to human microbiota and immunoregulation, horticultural cultivars hosting rich microbiota may have human health benefits. Further studies are needed to confirm the effectiveness of microbially-oriented plant selection in optimizing human microbiota and planetary health.}, } @article {pmid39543781, year = {2024}, author = {Samuthpongtorn, C and Chan, AA and Ma, W and Wang, F and Nguyen, LH and Wang, DD and Okereke, OI and Huttenhower, C and Chan, AT and Mehta, RS}, title = {F. prausnitzii potentially modulates the association between citrus intake and depression.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {237}, pmid = {39543781}, issn = {2049-2618}, support = {U01 CA176726/CA/NCI NIH HHS/United States ; U01 CA176726 to WW/CA/NCI NIH HHS/United States ; U01 CA176726 to WW/NH/NIH HHS/United States ; R01MH091448/NH/NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Female ; *Depression/microbiology ; Male ; *Citrus ; *Feces/microbiology ; Middle Aged ; *Faecalibacterium prausnitzii/genetics ; Diet ; Adult ; Metagenomics ; Longitudinal Studies ; S-Adenosylmethionine/metabolism ; Monoamine Oxidase/genetics/metabolism ; Prospective Studies ; }, abstract = {BACKGROUND: The gut microbiome modulates the effects of diet on host health, but it remains unclear which specific foods and microbial features interact to influence risk of depression. To understand this interplay, we leveraged decades of dietary and depression data from a longitudinal cohort of women (n = 32,427), along with fecal metagenomics and plasma metabolomics from a substudy (n = 207) nested in this cohort, as well as an independent validation cohort of men (n = 307).

RESULTS: We report that citrus intake and its components are prospectively associated with a lower risk of depression and altered abundance of 15 gut microbial species, including enriched Faecalibacterium prausnitzii. In turn, we found a lower abundance of F. prausnitzii and its metabolic pathway, S-adenosyl-L-methionine (SAM) cycle I in participants with depression. To explore causality, we found that lower SAM production by F. prausnitzii may decrease intestinal monoamine oxidase A gene expression implicated in serotonin and dopamine synthesis.

CONCLUSIONS: These data underscore the role of diet in the prevention of depression and offer a plausible explanation for how the intestinal microbiome modulates the influence of citrus on mental health. Video Abstract.}, } @article {pmid39543780, year = {2024}, author = {Zhao, XD and Gao, ZY and Peng, J and Konstantinidis, KT and Zhang, SY}, title = {Various microbial taxa couple arsenic transformation to nitrogen and carbon cycling in paddy soils.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {238}, pmid = {39543780}, issn = {2049-2618}, mesh = {*Soil Microbiology ; *Arsenic/metabolism ; *Bacteria/metabolism/classification/genetics ; *Oryza/metabolism ; *Nitrogen/metabolism ; *Oxidation-Reduction ; *Archaea/metabolism/genetics/classification ; *Soil/chemistry ; Carbon/metabolism ; Carbon Cycle ; Microbiota ; Arsenites/metabolism ; Arsenates/metabolism ; }, abstract = {BACKGROUND: Arsenic (As) metabolism pathways and their coupling to nitrogen (N) and carbon (C) cycling contribute to elemental biogeochemical cycling. However, how whole-microbial communities respond to As stress and which taxa are the predominant As-transforming bacteria or archaea in situ remains unclear. Hence, by constructing and applying ROCker profiles to precisely detect and quantify As oxidation (aioA, arxA) and reduction (arrA, arsC1, arsC2) genes in short-read metagenomic and metatranscriptomic datasets, we investigated the dominant microbial communities involved in arsenite (As(III)) oxidation and arsenate (As(V)) reduction and revealed their potential pathways for coupling As with N and C in situ in rice paddies.

RESULTS: Five ROCker models were constructed to quantify the abundance and transcriptional activity of short-read sequences encoding As oxidation (aioA and arxA) and reduction (arrA, arsC1, arsC2) genes in paddy soils. Our results revealed that the sub-communities carrying the aioA and arsC2 genes were predominantly responsible for As(III) oxidation and As(V) reduction, respectively. Moreover, a newly identified As(III) oxidation gene, arxA, was detected in genomes assigned to various phyla and showed significantly increased transcriptional activity with increasing soil pH, indicating its important role in As(III) oxidation in alkaline soils. The significant correlation of the transcriptional activities of aioA with the narG and nirK denitrification genes, of arxA with the napA and nirS denitrification genes and of arrA/arsC2 with the pmoA and mcrA genes implied the coupling of As(III) oxidation with denitrification and As(V) reduction with methane oxidation. Various microbial taxa including Burkholderiales, Desulfatiglandales, and Hyphomicrobiales (formerly Rhizobiales) are involved in the coupling of As with N and C metabolism processes. Moreover, these correlated As and N/C genes often co-occur in the same genome and exhibit greater transcriptional activity in paddy soils with As contamination than in those without contamination.

CONCLUSIONS: Our results revealed the comprehensive detection and typing of short-read sequences associated with As oxidation and reduction genes via custom-built ROCker models, and shed light on the various microbial taxa involved in the coupling of As and N and C metabolism in situ in paddy soils. The contribution of the arxA sub-communities to the coupling of As(III) oxidation with nitrate reduction and the arsC sub-communities to the coupling of As(V) reduction with methane oxidation expands our knowledge of the interrelationships among As, N, and C cycling in paddy soils. Video Abstract.}, } @article {pmid39543707, year = {2024}, author = {Wang, T and Ruan, Y and Xu, Q and Shen, Q and Ling, N and Vandenkoornhuyse, P}, title = {Effect of plant-derived microbial soil legacy in a grafting system-a turn for the better.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {234}, pmid = {39543707}, issn = {2049-2618}, mesh = {*Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/metabolism ; Soil/chemistry ; Metagenome ; }, abstract = {BACKGROUND: Plant-soil feedback arises from microbial legacies left by plants in the soil. Grafting is a common technique used to prevent yield declines in monocultures. Yet, our understanding of how grafting alters the composition of soil microbiota and how these changes affect subsequent crop performance remains limited. Our experiment involved monoculturing ungrafted and grafted watermelons to obtain conditioned soils, followed by growing the watermelons on the conditioned soils to investigate plant-soil feedback effects.

RESULTS: Ungrafted plants grew better in soil previously conditioned by a different plant (heterospecific soil) while grafted plants grew better in soil conditioned by the same plant (conspecific soil). We demonstrated experimentally that these differences in growth were linked to changes in microorganisms. Using a supervised machine learning algorithm, we showed that differences in the relative abundance of certain genera, such as Rhizobium, Chryseobacterium, Fusarium, and Aspergillus, significantly influenced the conspecific plant-soil feedback. Metabolomic analyses revealed that ungrafted plants in heterospecific soil enriched arginine biosynthesis, whereas grafted plants in conspecific soil increased sphingolipid metabolism. Elsewhere, the metagenome-assembled genomes (MAGs) of ungrafted plants identified in heterospecific soil include Chryseobacterium and Lysobacter, microorganisms having been prominently identified in earlier research as contributors to plant growth. Metabolic reconstruction revealed the putative ability of Chryseobacterium to convert D-glucono-1,5-lactone to gluconic acid, pointing to distinct disease-suppressive mechanisms and hence distinct microbial functional legacies between grafted and ungrafted plants.

CONCLUSIONS: Our findings show a deep impact of the soil microbial reservoir on plant growth and suggest the necessity to protect and improve this microbial community in agricultural soils. The work also suggests possibilities of optimizing microbiota-mediated benefits through grafting herein, a way that "engineered" soil microbial communities for better plant growth. Video Abstract.}, } @article {pmid39543265, year = {2024}, author = {Stevens, BR and Roesch, LFW}, title = {Interplay of human ABCC11 transporter gene variants with axillary skin microbiome functional genomics.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {28037}, pmid = {39543265}, issn = {2045-2322}, mesh = {Humans ; *Microbiota/genetics ; *Polymorphism, Single Nucleotide ; *Skin/microbiology/metabolism ; Female ; *ATP-Binding Cassette Transporters/genetics/metabolism ; Male ; Haplotypes ; Genomics/methods ; Axilla/microbiology ; Adult ; Pedigree ; }, abstract = {The human armpit microbiome is metabolically entangled with skin cell physiology. This "meta-organism" symbiotic mutualism results in sweat either with or without odor (osmidrosis), depending on host ABCC11 gene haplotypes. Apocrine metabolism produces odorless S-glutathione conjugate that is transferred by ABCC11 transporters into secretory vesicles, deglutamylated to S-Cys-Gly-3M3SH thiol, and exuded to skin surface. An anthropogenic clade of skin bacteria then takes up the thiol and bioconverts it to malodorous 3-methyl-3-sulfanylhexan-1-ol (3M3SH). We hypothesized a familial meta-organism association of human ABCC11 gene non-synonymous SNP rs17822931 interplaying with skin microbiome 3M3SH biosynthesis. Subjects were genotyped for ABCC11 SNPs, and their haplotypes were correlated with axilla microbiome DNA sequencing profiles and predicted metagenome functions. A multigeneration family pedigree revealed a Mendelian autosomal recessive pattern: the C allele of ABCC11 correlated with bacterial Cys-S-conjugate β-lyase (PatB) gene known for Staphylococcus hominis biosynthesis of 3M3SH from human precursor; PatB was rescinded in hosts with homozygous TT alleles encoding ABCC11 loss-of-function mutation. We posit that a C allele encoding functional ABCC11 is key to delivering host conjugate precursors that shape heritable skin niche conditions favorable to harboring Staphylococcus having genomics of odor thiol production. This provides existential insights into human evolution and global regional population ancestries.}, } @article {pmid39543167, year = {2024}, author = {Sumithra, TG and Sharma, SRK and Suresh, G and Suja, G and Prasad, V and Gop, AP and Patil, PK and Gopalakrishnan, A}, title = {Gut microbes of a high-value marine fish, Snubnose Pompano (Trachinotus blochii) are resilient to therapeutic dosing of oxytetracycline.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {27949}, pmid = {39543167}, issn = {2045-2322}, support = {Grant No. CIBA/AINP-FH/2015-16//Indian Council of Agricultural Research/ ; BT/AAQ/3/SP28267/2018//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {*Oxytetracycline/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; Fishes/microbiology ; Aquaculture/methods ; Dysbiosis/microbiology ; Metagenomics/methods ; Bacteria/drug effects/genetics/classification ; }, abstract = {Trachinotus blochii is a high-value tropical mariculture species. The present study evaluated the gut microbial impact of therapeutic exposure (80 mg/day/kg biomass for 10 days) to oxytetracycline, the most common aquaculture antibiotic in T. blochii. The cultivable counts, α-diversity measures of taxonomic and functional metagenomics, microbial dysbiosis (MD) index, and microbial taxon abundances showed the resilience of gut microbiota at 16-26 days of treatment. A significant reduction in bacterial abundance, diversity measures, Firmicutes and Actinobacteria and an increase in γ-Proteobacteria was recorded on the 6th and 11th day of treatment. The increased metagenomic stress signatures, decreased beneficial bacterial abundances, decreased abundance of microbial pathways on energy metabolism, and MD index indicated short-term transient stress during the initial days of therapeutic withdrawal, warranting health management measures. Therapeutic exposure reduced the abundance of fish pathogens, including Vibrio spp., kanamycin and ampicillin-resistant bacteria. Strikingly, oxytetracycline treatment did not increase tetracycline-resistant bacterial counts and the predicted abundance of tetracycline resistance encoding genes in the gut, illustrating that therapeutic application would not pose a risk in the context of antimicrobial resistance in short term. Altogether, the present study provides a foundation for oxytetracycline treatment to develop suitable risk minimization tactics in sustainable aquaculture.}, } @article {pmid39542187, year = {2025}, author = {Gurumayum, N and Devi, MB and Khound, P and Bhattacharya, A and Sarma, H and Khan, MR and Devi, R}, title = {Bioactive fraction of Musa balbisiana seed mitigates D-galactose-induced brain aging via SIRT1/PGC-1α/FoxO3a activation and intestinal barrier dysfunction by modulating gut microbiota and core metabolites.}, journal = {Free radical biology & medicine}, volume = {226}, number = {}, pages = {43-55}, doi = {10.1016/j.freeradbiomed.2024.11.016}, pmid = {39542187}, issn = {1873-4596}, mesh = {Animals ; *Galactose/adverse effects/toxicity ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Seeds/chemistry ; *Sirtuin 1/metabolism/genetics ; *Plant Extracts/pharmacology ; *Aging/drug effects ; *Oxidative Stress/drug effects ; *Brain/metabolism/drug effects/pathology ; *Forkhead Box Protein O3/metabolism/genetics ; *Musa/chemistry ; *Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism/genetics ; Male ; Rats, Sprague-Dawley ; Glycation End Products, Advanced/metabolism ; Antioxidants/pharmacology/metabolism ; }, abstract = {Aging is an inevitable biological process, and emerging research has highlighted the potential of dietary and pharmacological interventions to decelerate the trajectory of age-related diseases and prolong the health span. This study evaluates the protective effects of Musa balbisiana seed on healthy aging using D-galactose-induced accelerated aging rats. The results suggested that the bioactive ethyl acetate fraction of Musa balbisiana seed extract (BF) exhibited protective effects against aging-induced oxidative stress by reducing oxidative DNA damage, advanced glycation end-product formation, and malondialdehyde levels while restoring antioxidant and glyoxalase enzyme activities. BF also ameliorated neurodegeneration by decreasing acetylcholinesterase enzyme activity and amyloid beta plaque formation. Histopathological analysis demonstrated the protective effects of BF against brain aging, liver disruption, renal damage, and intestinal barrier dysfunction. BF further restored intestinal permeability by upregulating the tight junctions (zonula occludens 1 and 2, claudin 1,2,3 and 4, and occludin) and mucin (mucin 2 and mucin 5ac) gene expression while downregulating the expression of inflammatory cytokines (IL-1β, IL-6, and TNF-α). BF significantly induced the phosphorylation of FoxO3a proteins and upregulated the gene expression of SIRT1, PGC-1α, and TFAM in the hippocampus. Next-generation sequencing (NGS) of 16s rRNA amplicons of fecal metagenomics DNA and metabolites profiling showed that BF intervention restructured the gut microbiota and altered core metabolites related to cholesterol metabolism. Overall, our findings demonstrated the multifaceted protective effects of Musa balbisiana seed against D-galactose-induced aging.}, } @article {pmid39541983, year = {2024}, author = {Urtecho, G and Moody, T and Huang, Y and Sheth, RU and Richardson, M and Descamps, HC and Kaufman, A and Lekan, O and Zhang, Z and Velez-Cortes, F and Qu, Y and Cohen, L and Ricaurte, D and Gibson, TE and Gerber, GK and Thaiss, CA and Wang, HH}, title = {Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut.}, journal = {Cell systems}, volume = {15}, number = {11}, pages = {1002-1017.e4}, doi = {10.1016/j.cels.2024.10.007}, pmid = {39541983}, issn = {2405-4720}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Fecal Microbiota Transplantation/methods ; Mice, Inbred C57BL ; Gastrointestinal Tract/microbiology ; Dysbiosis/microbiology ; Mammals/microbiology ; Feces/microbiology ; }, abstract = {While fecal microbiota transplantation (FMT) has been shown to be effective in reversing gut dysbiosis, we lack an understanding of the fundamental processes underlying microbial engraftment in the mammalian gut. Here, we explored a murine gut colonization model leveraging natural inter-individual variations in gut microbiomes to elucidate the spatiotemporal dynamics of FMT. We identified a natural "super-donor" consortium that robustly engrafts into diverse recipients and resists reciprocal colonization. Temporal profiling of the gut microbiome showed an ordered succession of rapid engraftment by early colonizers within 72 h, followed by a slower emergence of late colonizers over 15-30 days. Moreover, engraftment was localized to distinct compartments of the gastrointestinal tract in a species-specific manner. Spatial metagenomic characterization suggested engraftment was mediated by simultaneous transfer of spatially co-localizing species from the super-donor consortia. These results offer a mechanism of super-donor colonization by which nutritional niches are expanded in a spatiotemporally dependent manner. A record of this paper's transparent peer review process is included in the supplemental information.}, } @article {pmid39541817, year = {2024}, author = {Czatzkowska, M and Wolak, I and Harnisz, M and Korzeniewska, E}, title = {Microbial diversity and biosafety judgment of digestates derived from different biogas plants for agricultural applications.}, journal = {Journal of environmental management}, volume = {371}, number = {}, pages = {123329}, doi = {10.1016/j.jenvman.2024.123329}, pmid = {39541817}, issn = {1095-8630}, mesh = {*Biofuels ; *Agriculture ; *Soil Microbiology ; Microbiota ; Biodegradation, Environmental ; Anaerobiosis ; Soil/chemistry ; Bacteria/classification ; }, abstract = {The composition of microbial communities is the key to effective anaerobic digestion (AD). The microbiome driving the AD process has been extensively researched, whereas the influence of specific substrates on the microbiome of digestate remains insufficiently investigated. Digestate has considerable potential for use in soil fertilization and bioremediation, therefore its biological safety should be monitored. Moreover, the knowledge about the composition of microbial communities and their interconnections in digestate should be extended, due to the impact on soil microbiota and its functionality. The aim of this study was a comprehensive assessment of the (1) sanitary quality, (2) core microbiome, and (3) microbial interactions in digestates collected from three full-scale agricultural biogas plants, with particular emphasis on their applicability from the perspective of the resident microbiota. Analyzed samples of digestate were derived from various substrates used for AD, including plant- and animal-based materials, and industrial waste. The study demonstrated that the phyla Bacillota, Bacteroidota, and Cloacimonadota were the most dominant in digestates regardless of the composition of the processed substrates, however, member composition at the genus level differed significantly between samples. In addition, we observed that microbial genera belonging to the less prevalent phyla play an integral role in the forming of microbial community interactions. Dominant microbial taxa with broad metabolic capabilities, potentially improving soil quality and functionality, have been identified. Moreover, we confirmed, that digestate samples were free of analyzed pathogenic bacteria and parasites. The study results indicate that digestate may have an immense fertilizing and bioremediation potential that has not been fully availed of to date.}, } @article {pmid39540836, year = {2024}, author = {Charles, P and Kumar, S and Girish Kumar, CP and Parameswaran, S and Viswanathan, P and Nachiappa Ganesh, R}, title = {Association of gut microbiota with allograft injury in kidney transplant recipients: a comparative profiling through 16S metagenomics and quantitative PCR.}, journal = {Journal of medical microbiology}, volume = {73}, number = {11}, pages = {}, doi = {10.1099/jmm.0.001934}, pmid = {39540836}, issn = {1473-5644}, mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Gastrointestinal Microbiome ; Male ; *RNA, Ribosomal, 16S/genetics ; Female ; Middle Aged ; *Metagenomics/methods ; Adult ; Prospective Studies ; Longitudinal Studies ; *Graft Rejection/microbiology ; Real-Time Polymerase Chain Reaction/methods ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; Allografts/microbiology ; Transplant Recipients ; }, abstract = {Introduction. The existence of a mutual relationship between gut microbiota and immune homeostasis highlights its importance in the context of kidney transplantation.Gap statement. The translational utility of gut microbiota as a biomarker for allograft injury has not been assessed before.Aim. In this study, we aimed to characterize the gut microbial diversity in kidney transplant recipients and investigate the alterations in the gut microbial composition in association with allograft injury such as histopathological graft rejection and calcineurin inhibitor toxicity. In addition, we compared the gut microbial quantitation using 16S metagenomics and quantitative PCR (qPCR) to assess its translational utility.Methodology. In this prospective longitudinal cohort study, we enrolled 38 kidney transplant recipients and collected serial faecal specimens (n=114), once before the induction therapy, and twice after transplant, during the first and third month. We characterized the gut microbial composition through 16S rRNA sequencing and qPCR from the DNA isolates of the samples. The recipients were clinically followed up for a median of 600 days post-transplant. Histopathological evidence of allograft rejection and calcineurin inhibitor toxicity were used for the correlational analysis with gut microbial diversity.Results. Significant differences in the gut microbial diversity were observed between the pre- and post-transplant samples. Pre-transplant gut microbiota revealed a higher relative abundance of phylum Bacteroidetes in the allograft rejection group, and a higher relative abundance of phylum Firmicutes was observed in the histopathological features of calcineurin inhibitor toxicity (hCNI toxicity) group. We found a high concordance between 16S metagenomics and qPCR outputs for assessing the gut microbial diversity. Furthermore, the receiver operating characteristic curve analysis has also proven that the pre-transplant levels of gut microbial dysbiosis, as a potential predictive biomarker for allograft injury.Conclusion. Our pilot study found a strong statistical association of gut microbial dysbiosis with kidney allograft injury, highlighting the potential of gut microbiota as a predictive biomarker and that qPCR serves as a more reliable and economic tool for assessing dysbiosis paving the way for its translational utility.}, } @article {pmid39540551, year = {2024}, author = {Vepštaitė-Monstavičė, I and Lukša, J and Strazdaitė-Žielienė, Ž and Serva, S and Servienė, E}, title = {Distinct microbial communities associated with health-relevant wild berries.}, journal = {Environmental microbiology reports}, volume = {16}, number = {6}, pages = {e70048}, pmid = {39540551}, issn = {1758-2229}, support = {S-PD-22-85//Lithuanian Research Council (LMTLT)/ ; }, mesh = {*Fruit/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; *Microbiota ; Vaccinium vitis-idaea/chemistry/microbiology/genetics ; High-Throughput Nucleotide Sequencing ; Rosa/microbiology ; Phylogeny ; }, abstract = {Lingonberries (Vaccinium vitis-idaea L.), rowanberries (Sorbus aucuparia L.) and rosehips (Rosa canina L.) positively affect human health due to their healing properties, determined by a high content of bioactive compounds. The consumption of unprocessed wild berries is relevant and encouraged, making their in-depth microbiological characterization essential for food safety. This study presents the first high-throughput sequencing analysis of bacterial and fungal communities distributed on the surface of lingonberries, rowanberries and rosehips. Significant plant-defined differences in the taxonomic composition of prokaryotic and eukaryotic microbiota were observed. The bacterial community on rosehips was shown to be prevalent by Enterobacteriaceae, lingonberries by Methylobacteriaceae and rowanberries by Sphingomonadaceae representatives. Among the fungal microbiota, Dothioraceae dominated on rosehips and Exobasidiaceae on lingonberries; meanwhile, rowanberries were inhabited by a similar level of a broad spectrum of fungal families. Cultivable yeast profiling revealed that lingonberries were distinguished by the lowest amount and most distinct yeast populations. Potentially pathogenic to humans or plants, as well as beneficial and relevant biocontrol microorganisms, were identified on tested berries. The combination of metagenomics and a cultivation-based approach highlighted the wild berries-associated microbial communities and contributed to uncovering their potential in plant health, food and human safety.}, } @article {pmid39538984, year = {2024}, author = {Zhang, Y and Song, Z and Schilling, JS}, title = {Evaluation of DNA Extraction Methods for Microbial Community Profiling in Deadwood Decomposition.}, journal = {MicrobiologyOpen}, volume = {13}, number = {6}, pages = {e70007}, pmid = {39538984}, issn = {2045-8827}, support = {//Funding for the study was provided by a Jr. Faculty grant to J.S.S. from the Andrew W. Mellon Foundation (New York, NY)./ ; }, mesh = {*Wood/microbiology ; *Fungi/genetics/classification/isolation & purification ; *Bacteria/genetics/classification/isolation & purification ; *Betula/microbiology ; *DNA, Fungal/genetics ; *Microbiota/genetics ; Pinus/microbiology ; DNA, Bacterial/genetics ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; }, abstract = {As technologies advance alongside metabarcoding and metagenomic resources, particularly for larger fungal genomes, DNA extraction methods must be optimized to meet higher thresholds, especially from complex environmental substrates. This study focused on extracting fungal genomic compounds from woody substrates, a challenge due to the embedment of endophytic and saprotrophic fungi within wood cells, the physical recalcitrance of wood, the adsorption of nucleic acids to wood polymers, and the release of downstream inhibitors. Hypothesizing that cetyltrimethylammonium bromide would be the best option, we compared prominent methods by extracting and sequencing microbial DNA from sound and decayed birch (Betula papyrifera) and pine (Pinus resinosa). DNA quantities varied significantly depending on extraction methods and decay stage. The quality of DNA, in terms of purity and integrity, significantly impacted whether the samples could be amplified and sequenced. However, amplicon sequencing of bacterial and fungal communities revealed no significant extraction bias. This, along with the sequencing effectiveness and cost/time efficiency, indicates that Qiagen is the gold standard for woody substrates. This study increases confidence in published amplicon data sets regardless of the extraction methods, provides a cost-benefit table for making protocol decisions, and offers guidance on fungal DNA extractions from complex organic substrates (sound and decayed wood) that would best suit future metagenomic efforts.}, } @article {pmid39537963, year = {2024}, author = {Sitthideatphaiboon, P and Somlaw, N and Zungsontiporn, N and Ouwongprayoon, P and Sukswai, N and Korphaisarn, K and Poungvarin, N and Aporntewan, C and Hirankarn, N and Vinayanuwattikun, C and Chanida, V}, title = {Dietary pattern and the corresponding gut microbiome in response to immunotherapy in Thai patients with advanced non-small cell lung cancer (NSCLC).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {27791}, pmid = {39537963}, issn = {2045-2322}, support = {N35A660426//National Research Council of Thailand/ ; RA-MF-04/67//Rachadapisek Sompote Matching fund, Chulalongkorn University/ ; }, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; *Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology/pathology ; *Diet ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Immune Checkpoint Inhibitors/therapeutic use ; *Immunotherapy/methods ; *Lung Neoplasms/microbiology/drug therapy/pathology ; Progression-Free Survival ; Prospective Studies ; Southeast Asian People ; Thailand ; }, abstract = {Gut microbiota is considered a key player modulating the response to immune checkpoint inhibitors (ICI) in cancer. The effects of dietary pattern on this interaction is not well-studied. A prospective multicenter cohort of 95 patients with advanced non-small cell lung cancer (NSCLC) undergoing ICI therapy were enrolled. Stool shotgun metagenomic sequencing was performed. Three-day dietary patterns before ICI were assessed. Patients were categorized as hyperprogressive disease (HPD) if they exhibited a time to treatment failure of less than 2 months. All others were categorized as non-hyperprogressive disease (non-HPD). The correlation between dietary patterns, gut microbiome, and response to ICI therapy was analyzed. In the multivariate analysis, a high abundance of Firmicutes unclassified and the Ruminococcaceae family correlated with a significantly diminished progression-free survival (PFS) with an HR of 2.40 [P = 0.006] and 4.30 [P = 0.005], respectively. More specifically, within the subset of NSCLC patients treated solely with ICI therapy, a high abundance of Intestinimonas and the Enterobacteriaceae family were associated with substantially reduced PFS with an HR of 2.61 [P = 0.02] and HR 3.34 [P = 0.005], respectively. In our comprehensive dietary pattern analysis, the HPD group showed increased consumption of cholesterol, sodium, and fats beyond recommended levels compared to the non-HPD group. This group also displayed a tendency towards higher food pattern scores characterized by a high intake of fat and dairy products. Our study revealed a distinct association between the gut microbiome composition and treatment outcomes. The overall composition of diet might be related to ICI therapeutic outcomes.}, } @article {pmid39537661, year = {2024}, author = {Li, Z and Chen, J and Li, Y and Li, L and Zhan, Y and Yang, J and Wu, H and Li, S and Mo, X and Wang, X and Mi, Y and Zhou, X and Li, Y and Wang, J and Li, Y and Sun, R and Cai, W and Ye, F}, title = {Impact of SARS-CoV-2 infection on respiratory and gut microbiome stability: a metagenomic investigation in long-term-hospitalized COVID-19 patients.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {126}, pmid = {39537661}, issn = {2055-5008}, mesh = {Humans ; *COVID-19/microbiology/virology ; *Gastrointestinal Microbiome/genetics ; *SARS-CoV-2/genetics ; Male ; Middle Aged ; Female ; Aged ; *Metagenomics/methods ; Feces/microbiology/virology ; High-Throughput Nucleotide Sequencing ; Adult ; Hospitalization ; Bacteria/classification/genetics/isolation & purification ; Sputum/microbiology/virology ; Respiratory System/microbiology/virology ; Metagenome ; }, abstract = {During the coronavirus disease 2019 (COVID-19) pandemic, the exploration of microecology has been essential for elucidating the intricacies of infection mechanisms and the recovery of afflicted individuals. To decipher the interplay of microorganisms between the intestinal and respiratory tracts, we collected sputum and throat swabs and feces from COVID-19 patients and explored the mutual migration among intestinal and respiratory microorganisms. Using next-generation sequencing (NGS) technology, we investigated intestinal and respiratory microorganism intermigration in two patients with severe COVID-19 during their hospitalization. Notably, we observed an expedited recovery of microecological equilibrium in one patient harboring Mycobacterium avium. Comparative analyses between 32 healthy controls and 110 COVID-19 patients with different disease severities revealed alterations in predominant microorganisms inhabiting the respiratory and intestinal tracts of COVID-19 patients. Among the alterations, intestinal Bacteroides vulgatus (BV) was identified as a noteworthy microorganism that exhibited marked enrichment in patients with severe COVID-19. BV, when highly abundant, may inhibit the transitional growth of Escherichia coli/Enterococcus, indirectly prevent the overgrowth of salivary streptococci, and maintain lung/intestinal microecology stability. In summary, this study elucidates the bidirectional microbial intermigration between the intestinal and respiratory tracts in COVID-19 patients. These findings are expected to provide new ideas for the treatment and management of COVID-19, underscoring the essential role of microecology in infectious diseases. Nevertheless, a systematic study of the roles of BV in recovery from infection is required to gain a deeper understanding of the mechanisms of microbial migration.}, } @article {pmid39537082, year = {2024}, author = {Chettri, D and Verma, AK and Chirania, M and Verma, AK}, title = {Metagenomic approaches in bioremediation of environmental pollutants.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {363}, number = {Pt 2}, pages = {125297}, doi = {10.1016/j.envpol.2024.125297}, pmid = {39537082}, issn = {1873-6424}, mesh = {*Biodegradation, Environmental ; *Metagenomics/methods ; *Environmental Pollutants/metabolism ; Artificial Intelligence ; Microbiota ; }, abstract = {Metagenomics has emerged as a pivotal tool in bioremediation, providing a deeper understanding of the structure and function of the microbial communities involved in pollutant degradation. By circumventing the limitations of traditional culture-based methods, metagenomics enables comprehensive analysis of microbial ecosystems and facilitates the identification of new genes and metabolic pathways that are critical for bioremediation. Advanced sequencing technologies combined with computational and bioinformatics approaches have greatly enhanced our ability to detect sources of pollution and monitor dynamic changes in microbial communities during the bioremediation process. These tools enable the precise identification of key microbial players and their functional roles, and provide a deeper understanding of complex biodegradation networks. The integration of artificial intelligence (AI) with machine learning algorithms has accelerated the process of discovery of novel genes associated with bioremediation and has optimized metabolic pathway prediction. Novel strategies, including sequencing techniques and AI-assisted analysis, have the potential to revolutionize bioremediation by enabling the development of highly efficient, targeted, and sustainable remediation strategies for various contaminated environments. However, the complexity of microbial interactions, data interpretation, and high cost of these advanced technologies remain challenging. Future research should focus on improving computational tools, reducing costs, and integrating multidisciplinary approaches to overcome these limitations.}, } @article {pmid39537028, year = {2025}, author = {Liu, L and Nguyen, SM and Wang, L and Shi, J and Long, J and Cai, Q and Shrubsole, MJ and Shu, XO and Zheng, W and Yu, D}, title = {Associations of alcohol intake with gut microbiome: a prospective study in a predominantly low-income Black/African American population.}, journal = {The American journal of clinical nutrition}, volume = {121}, number = {1}, pages = {134-140}, doi = {10.1016/j.ajcnut.2024.11.007}, pmid = {39537028}, issn = {1938-3207}, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Alcohol Drinking ; *Black or African American ; Feces/microbiology ; *Gastrointestinal Microbiome ; Poverty ; Prospective Studies ; }, abstract = {BACKGROUND: Alcohol intake can alter gut microbiome, which may subsequently affect human health. However, limited population-based, prospective studies have investigated associations of habitual and recent alcohol intake with the gut microbiome, particularly among Black/African American individuals.

OBJECTIVE: We examined the association of alcohol intake with gut microbiome in a predominantly low-income Black/African American population.

METHODS: We investigated the dose- and type-specific associations of habitual and recent alcohol intake with the gut microbiome among 538 Black/African American adults (150 males and 388 females). Habitual and recent alcohol intakes were assessed at cohort baseline (2002-2009) and stool collection (2018-2021), respectively. Gut microbiome was profiled using shotgun metagenomic sequencing. Generalized linear models were employed to evaluate the associations between alcohol intakes and gut microbiome composition, with adjustments for sociodemographic characteristics, other lifestyle factors, and comorbidities. False discovery rate (FDR) <0.1 was considered statistically significant.

RESULTS: The mean age at enrollment was 53.2 ± 7.7 y, with a mean interval of 13.8 y (range: 9.0-18.1 y) between baseline and stool sample collection. Recent alcohol intake was not significantly associated with microbial taxa abundance. However, habitual alcohol intake, both total amount and types of alcoholic beverages, showed significant associations with several microbial taxa abundance, primarily in males, including species within classes Clostridia, Bacilli, and Mahellia within Firmicutes. Specifically, total alcohol, beer, and red wine intakes were all inversely associated with genus MGYG-HGUT-02719 within class Clostridia (β = -2.26 to -0.09 per 1 drink/d increase). Red wine consumption was also inversely associated with the abundance of genera CAG-110, Oscillibacter, and Gemmiger within class Clostridia (β = -3.88 to -2.69), whereas positively associated with genus Absiella (β = 1.81) within class Bacilli. Most of these associations remained significant after additionally adjusting for BMI and baseline comorbidities.

CONCLUSIONS: We identified gut microbial taxa associated with habitual alcohol intake among Black/African American males, although the magnitudes of these associations were generally small. Further research is needed to determine if these bacteria modify alcohol-disease relationships.}, } @article {pmid39536991, year = {2025}, author = {Li, Z and Gao, W and Yuan, H and Pan, X and Yuan, R and Wang, W and Guan, L and Hu, L and Chen, Y and Cheng, Z and He, R and Zhang, L and Yang, B and Zhu, Q and Liang, M and Seki, E and Lin, R and Chu, H and Yang, L}, title = {Suppression of intestinal Ticam1 ameliorated MASH via Akkermansia muciniphila QAA37749.1 mediated betaine transformation.}, journal = {Biochimica et biophysica acta. Molecular basis of disease}, volume = {1871}, number = {1}, pages = {167571}, doi = {10.1016/j.bbadis.2024.167571}, pmid = {39536991}, issn = {1879-260X}, mesh = {Animals ; Mice ; *Akkermansia ; *Gastrointestinal Microbiome ; *Mice, Knockout ; Intestinal Mucosa/metabolism/microbiology/immunology/pathology ; Diet, High-Fat/adverse effects ; Male ; Fatty Liver/metabolism/pathology ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND & AIMS: Gut inflammation caused by diets could damage the intestinal barrier, which increases the liver exposition to pathogenic substances. Toll-IL-1 receptor (TIR) domain-containing adaptor molecule-1 (Ticam1) is a key molecule in the Toll-like receptors (TLRs) pathway, which is important for the immune defense against pathogens such as bacteria or viruses. In this study, mouse intestinal epithelial cell (IEC) Ticam1 was knocked out to suppress the intestinal inflammation response in metabolic dysfunction-associated steatohepatitis (MASH) to investigate its influence on the development of MASH.

METHODS: The IEC-specific Ticam1 knockout (Ticam1[ΔIEC]) mice and the control (Ticam1[fl/fl]) mice were fed with high-fat high-fructose diet (HFD) for 22 weeks to evaluate the gut alteration and the MASH-associated disorders. The intestinal secreted immunoglobulin A (sIgA) and IgA-secreting immune cells were detected. Shotgun metagenomic sequencing was used to find the gut microbiome shift in different groups. Liquid chromatography mass spectrometry was also performed to evaluate the change of serum metabolites caused by the gut microbiome alteration.

RESULTS: The gut inflammation and gut barrier dysfunction were both alleviated in HFD-fed Ticam1[ΔIEC] mice, which had improved MASH disorders compared with Ticam1[fl/fl]. Additionally, HFD-fed Ticam1[ΔIEC] mice had increased sIgA and intestinal IgA-secreting immune cells. It showed a significantly higher content of Akkermansia muciniphila. We proved that Akkermansia muciniphila encoded a protein named QAA37749.1 that could promote the conversion of choline to betaine, through which the development of MASH was inhibited in HFD-Ticam1[ΔIEC] mice.

CONCLUSION: Deletion of IEC Ticam1 alleviated MASH disorder and gut dysfunction in mice. It enhanced the level of intestinal sIgA and the growth of Akkermansia muciniphila, which supported the betaine transformation by QAA37749.1. Suppressing IEC Ticam1 might be a promising strategy for MASH disorder.}, } @article {pmid39536943, year = {2024}, author = {Fadell, F and Saliba, R and El-Solh, AA}, title = {Bacteriology of Aspiration Pneumonia: The Lung Microbiome and the Changing Microbial Etiology.}, journal = {Seminars in respiratory and critical care medicine}, volume = {45}, number = {6}, pages = {626-633}, doi = {10.1055/s-0044-1792111}, pmid = {39536943}, issn = {1098-9048}, mesh = {Humans ; *Pneumonia, Aspiration/microbiology ; *Microbiota ; Lung/microbiology ; Dysbiosis/microbiology ; }, abstract = {Aspiration pneumonia refers to the process of alveolar inflammation induced by the inhalation of oropharyngeal secretions into the lower respiratory tract. Predisposing factors comprise swallowing dysfunction, impaired cough reflex, and degenerative neurological diseases. Accumulating evidence projects a fading contribution of anaerobic bacteria in aspiration pneumonia at the expense of Gram-negative bacilli, with Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa, becoming the predominant organisms recovered from respiratory specimens. Aspiration of oropharyngeal secretions colonized with respiratory pathogens induces a profound disequilibrium of the lung microbiota resulting in a state of dysbiosis. Understanding this complex temporal variability between microbiome-host associations was only made possible with the introduction of metagenomic sequencing. In this narrative review, we summarize existing knowledge and elaborate on the evolving microbiology of aspiration pneumonia including the link between oral microbiome and pulmonary aspiration. We also highlight the progress and challenges in instituting microbiome-targeted strategies for preventing and treating the sequelae of aspiration pneumonia.}, } @article {pmid39533168, year = {2024}, author = {Zhang, Z and Wang, K and Zou, C and Zhao, T and Wu, W and Wang, C and Hua, Y}, title = {Comparison of microbial diversity and carbohydrate-active enzymes in the hindgut of two wood-feeding termites, Globitermes sulphureus (Blattaria: Termitidae) and Coptotermes formosanus (Blattaria: Rhinotermitidae).}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {470}, pmid = {39533168}, issn = {1471-2180}, support = {2024A1515012617//Guangdong Natural Science Foundation-General Program/ ; }, mesh = {Animals ; *Isoptera/microbiology ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/genetics ; *Wood/microbiology ; *Bacteria/classification/genetics/enzymology/isolation & purification ; Phylogeny ; Glycoside Hydrolases/genetics/metabolism ; Lignin/metabolism ; Biodiversity ; }, abstract = {BACKGROUND: Wood-feeding termites have been employed as sources of novel and highly efficient lignocellulolytic enzymes due to their ability to degrade lignocellulose efficiently. As a higher wood-feeding termite, Globitermes sulphureus (Blattaria: Termitidae) plays a crucial role as a decomposer in regions such as Vietnam, Singapore, Myanmar, and Yunnan, China. However, the diversity of its gut microbiome and carbohydrate-active enzymes (CAZymes) remains unexplored. Here, we analyzed the diversity of hindgut microbial communities and CAZymes in a higher wood-feeding termite, G. sulphureus, and a lower wood-feeding termite, Coptotermes formosanus (Blattaria: Rhinotermitidae).

RESULTS: 16S rRNA sequencing revealed that Spirochaetota, Firmicutes, and Fibrobacterota were the dominant microbiota in the hindgut of the two termite species. At the phylum level, the relative abundances of Proteobacteria and Bacteroidota were significantly greater in the hindgut of C. formosanus than in G. sulphureus. At the genus level, the relative abundances of Candidatus_Azobacteroides and Escherichia-Shigella were significantly lower in the hindgut of G. sulphureus than in C. formosanus. Metagenomic analysis revealed that glycoside hydrolases (GHs) with cellulases and hemicellulases functions were not significantly different between G. sulphureus and C. formosanus. Interestingly, the cellulases in G. sulphureus were mainly GH5_2, GH5_4, GH6, GH9, and GH45, while the hemicellulases were mainly GH11, GH8, GH10, GH11, GH26, and GH53. In C. formosanus, the cellulases were mainly GH6 and GH9, and the hemicellulases were mainly GH5_7, GH5_21, GH10, GH12, and GH53. In addition, β-glucosidase, exo-β-1,4-glucanase, and endo-β-1,4-glucanase activities did not differ significantly between the two termite species, while xylanase activity was higher in G. sulphureus than in C. formosanus. The bacteria encoding GHs in G. sulphureus were mainly Firmicutes, Fibrobacterota, and Proteobacteria, whereas Bacteroidota and Spirochaetota were the main bacteria encoding GHs in C. formosanus.

CONCLUSIONS: Our findings characterized the microbial composition and differences in the hindgut microbiota of G. sulphureus and C. formosanus. Compared to C. formosanus, G. sulphureus is enriched in genes encoding for hemicellulase and debranching enzymes. It also highlights the rich diversity of GHs in the hindgut microbiota of G. sulphureus, including the GH5 subfamily, GH6, and GH48, with the GH6 and GH48 not previously reported in other higher termites. These results strengthen the understanding of the diversity of termite gut microbiota and CAZymes.}, } @article {pmid39529146, year = {2024}, author = {Zhang, C and Liu, H and Jiang, X and Zhang, Z and Hou, X and Wang, Y and Wang, D and Li, Z and Cao, Y and Wu, S and Huws, SA and Yao, J}, title = {An integrated microbiome- and metabolome-genome-wide association study reveals the role of heritable ruminal microbial carbohydrate metabolism in lactation performance in Holstein dairy cows.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {232}, pmid = {39529146}, issn = {2049-2618}, mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Lactation ; Female ; *Genome-Wide Association Study ; *Polymorphism, Single Nucleotide ; *Carbohydrate Metabolism/genetics ; *Fatty Acids, Volatile/metabolism ; *Metabolome ; Gastrointestinal Microbiome/genetics ; Milk/microbiology/metabolism ; Microbiota/genetics ; Bacteria/classification/genetics/metabolism ; }, abstract = {BACKGROUND: Despite the growing number of studies investigating the connection between host genetics and the rumen microbiota, there remains a dearth of systematic research exploring the composition, function, and metabolic traits of highly heritable rumen microbiota influenced by host genetics. Furthermore, the impact of these highly heritable subsets on lactation performance in cows remains unknown. To address this gap, we collected and analyzed whole-genome resequencing data, rumen metagenomes, rumen metabolomes and short-chain fatty acids (SCFAs) content, and lactation performance phenotypes from a cohort of 304 dairy cows.

RESULTS: The results indicated that the proportions of highly heritable subsets (h[2] ≥ 0.2) of the rumen microbial composition (55%), function (39% KEGG and 28% CAZy), and metabolites (18%) decreased sequentially. Moreover, the highly heritable microbes can increase energy-corrected milk (ECM) production by reducing the rumen acetate/propionate ratio, according to the structural equation model (SEM) analysis (CFI = 0.898). Furthermore, the highly heritable enzymes involved in the SCFA synthesis metabolic pathway can promote the synthesis of propionate and inhibit the acetate synthesis. Next, the same significant SNP variants were used to integrate information from genome-wide association studies (GWASs), microbiome-GWASs, metabolome-GWASs, and microbiome-wide association studies (mWASs). The identified single nucleotide polymorphisms (SNPs) of rs43470227 and rs43472732 on SLC30A9 (Zn[2+] transport) (P < 0.05/nSNPs) can affect the abundance of rumen microbes such as Prevotella_sp., Prevotella_sp._E15-22, Prevotella_sp._E13-27, which have the oligosaccharide-degradation enzymes genes, including the GH10, GH13, GH43, GH95, and GH115 families. The identified SNPs of chr25:11,177 on 5s_rRNA (small ribosomal RNA) (P < 0.05/nSNPs) were linked to ECM, the abundance alteration of Pseudobutyrivibrio_sp. (a genus that was also showed to be linked to the ECM production via the mWASs analysis), GH24 (lysozyme), and 9,10,13-TriHOME (linoleic acid metabolism). Moreover, ECM, and the abundances of Pseudobutyrivibrio sp., GH24, and 9,10,13-TRIHOME were significantly greater in the GG genotype than in the AG genotype at chr25:11,177 (P < 0.05). By further the SEM analysis, GH24 was positively correlated with Pseudobutyrivibrio sp., which was positively correlated with 9,10,13-triHOME and subsequently positively correlated with ECM (CFI = 0.942).

CONCLUSION: Our comprehensive study revealed the distinct heritability patterns of rumen microbial composition, function, and metabolism. Additionally, we shed light on the influence of host SNP variants on the rumen microbes with carbohydrate metabolism and their subsequent effects on lactation performance. Collectively, these findings offer compelling evidence for the host-microbe interactions, wherein cows actively modulate their rumen microbiota through SNP variants to regulate their own lactation performance. Video Abstract.}, } @article {pmid39524440, year = {2024}, author = {Ozaka, S and Sonoda, A and Kudo, Y and Ito, K and Kamiyama, N and Sachi, N and Chalalai, T and Kagoshima, Y and Soga, Y and Ekronarongchai, S and Ariki, S and Mizukami, K and Ishizawa, S and Nishiyama, M and Murakami, K and Takeda, K and Kobayashi, T}, title = {Daikenchuto, a Japanese herbal medicine, ameliorates experimental colitis in a murine model by inducing secretory leukocyte protease inhibitor and modulating the gut microbiota.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1457562}, pmid = {39524440}, issn = {1664-3224}, mesh = {Animals ; Humans ; Male ; Mice ; Anti-Inflammatory Agents/pharmacology ; *Colitis/chemically induced/drug therapy/microbiology ; Colon/drug effects/immunology/microbiology ; Cytokines/metabolism ; Dextran Sulfate ; Disease Models, Animal ; *Gastrointestinal Microbiome/drug effects ; Intestinal Mucosa/drug effects/immunology/microbiology ; Mice, Inbred C57BL ; Mice, Knockout ; *Panax/chemistry ; *Plant Extracts/pharmacology ; *Secretory Leukocyte Peptidase Inhibitor/metabolism/genetics ; *Zanthoxylum/chemistry ; *Zingiberaceae/chemistry ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a refractory inflammatory disorder of the intestine, which is probably triggered by dysfunction of the intestinal epithelial barrier. Secretory leukocyte protease inhibitor (SLPI) secreted by colon epithelial cells protects against intestinal inflammation by exerting anti-protease and anti-microbial activities. Daikenchuto (DKT) is one of the most commonly prescribed Japanese traditional herbal medicines for various digestive diseases. Although several animal studies have revealed that DKT exerts anti-inflammatory effects, its detailed molecular mechanism is unclear. This study aimed to clarify the anti-inflammatory mechanism of DKT using a murine colitis model, and to evaluate its potential as a therapeutic agent for IBD.

METHODS: Experimental colitis was induced in wild-type (WT) mice and SLPI-deficient (KO) mice by dextran sulfate sodium (DSS) after oral administration of DKT. The resultant clinical symptoms, histological changes, and pro-inflammatory cytokine levels in the colon were assessed. Expression of SLPI in the colon was detected by Western blotting and immunohistochemistry. Composition of the gut microbiota was analyzed by 16S rRNA metagenome sequencing and intestinal metabolites were measured by gas chromatography-mass spectrometry analysis. Intestinal epithelial barrier function was assessed by oral administration of FITC-dextran and immunostaining of tight junction proteins (TJPs).

RESULTS: Oral administration of DKT increased the number of butyrate-producing bacteria, such as Parabacteroides, Allobaculum, and Akkermansia, enhanced the levels of short-chain fatty acids, including butyrate, in the colon, induced SLPI expression, and ameliorated DSS-induced colitis in WT mice. We found that mouse colon carcinoma cell line treatment with either DKT or butyrate significantly enhanced the expression of SLPI. Moreover, supplementation of DKT protected the intestinal epithelial barrier with augmented expression of TJPs in WT mice, but not in KO mice. Finally, the composition of the gut microbiota was changed by DKT in WT mice, but not in KO mice, suggesting that DKT alters the colonic bacterial community in an SLPI-dependent manner.

CONCLUSION: These results indicate that DKT exerts anti-inflammatory effects on the intestinal epithelial barrier by SLPI induction, due, at least in part, to increased butyrate-producing bacteria and enhanced butyrate levels in the colon. These results provide insight into the mechanism of the therapeutic effects of DKT on IBD.}, } @article {pmid39535126, year = {2024}, author = {Gao, P and Rinott, E and Dong, D and Mei, Z and Wang, F and Liu, Y and Kamer, O and Yaskolka Meir, A and Tuohy, KM and Blüher, M and Stumvoll, M and Stampfer, MJ and Shai, I and Wang, DD}, title = {Gut microbial metabolism of bile acids modifies the effect of Mediterranean diet interventions on cardiometabolic risk in a randomized controlled trial.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2426610}, pmid = {39535126}, issn = {1949-0984}, support = {R01 NR019992/NR/NINR NIH HHS/United States ; P30 DK046200/DK/NIDDK NIH HHS/United States ; R01 AG077489/AG/NIA NIH HHS/United States ; RF1 AG083764/AG/NIA NIH HHS/United States ; R00 DK119412/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Diet, Mediterranean ; *Bile Acids and Salts/metabolism ; Male ; Female ; *Feces/microbiology/chemistry ; Middle Aged ; Adult ; Cardiometabolic Risk Factors ; Body Mass Index ; Bacteria/classification/metabolism/isolation & purification/genetics ; Lipids/blood ; Cardiovascular Diseases/prevention & control/metabolism ; Adiposity ; }, abstract = {Bile acids (BAs) undergo extensive microbial metabolism in the gut and exert hormone-like functions on physiological processes underlying metabolic risk. However, the extent to which gut BA profiles predict cardiometabolic risk and explain individual responses to dietary interventions in humans is still unclear. In the DIRECT-PLUS Trial, we conducted a multi-omics analysis of 284 participants randomized into three groups: healthy dietary guidelines and two Mediterranean diet (MedDiet) groups. We longitudinally measured 44 fecal BAs using liquid chromatography-mass spectrometry, the gut microbiome through shotgun metagenomic sequencing, and body adiposity and serum lipids at baseline, 6, and 18 months. Fecal levels of 14 BAs, such as lithocholic acid and ursodeoxycholic acid, were prospectively associated with body mass index (BMI) and serum lipid profiles (false discovery rate [q]<0.05). Baseline fecal BA levels significantly modified the beneficial effects of the MedDiet; for example, BMI reduction induced by MedDiet interventions was more pronounced in individuals with lower 12-dehydrocholic acid levels (q-interaction <0.001). We confirmed that the gut microbiome is a major modifier of the secondary BA pool in humans. Furthermore, the association of fecal BAs with body adiposity and serum lipids varied significantly in individuals with different abundances of gut microbes carrying BA metabolism enzymes, e.g. several Ruminococcus spp. In summary, our study identifies novel predictive biomarkers for cardiometabolic risk and offers new mechanistic insights to guide personalized dietary interventions.}, } @article {pmid39532872, year = {2024}, author = {Wang, YF and Liu, YJ and Fu, YM and Xu, JY and Zhang, TL and Cui, HL and Qiao, M and Rillig, MC and Zhu, YG and Zhu, D}, title = {Microplastic diversity increases the abundance of antibiotic resistance genes in soil.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9788}, pmid = {39532872}, issn = {2041-1723}, mesh = {*Soil Microbiology ; *Microplastics ; *Drug Resistance, Microbial/genetics ; Soil/chemistry ; Soil Pollutants ; Metagenomics ; Genes, Bacterial ; Virulence Factors/genetics ; Bacteria/genetics/drug effects/classification ; Interspersed Repetitive Sequences/genetics ; Genetic Variation ; Metagenome/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The impact of microplastics on antibiotic resistance has attracted widespread attention. However, previous studies primarily focused on the effects of individual microplastics. In reality, diverse microplastic types accumulate in soil, and it remains less well studied whether microplastic diversity (i.e., variations in color, shape or polymer type) can be an important driver of increased antibiotic resistance gene (ARG) abundance. Here, we employed microcosm studies to investigate the effects of microplastic diversity on soil ARG dynamics through metagenomic analysis. Additionally, we evaluated the associated potential health risks by profiling virulence factor genes (VFGs) and mobile genetic elements (MGEs). Our findings reveal that as microplastic diversity increases, there is a corresponding rise in the abundance of soil ARGs, VFGs and MGEs. We further identified microbial adaptive strategies involving genes (changed genetic diversity), community (increased specific microbes), and functions (enriched metabolic pathways) that correlate with increased ARG abundance and may thus contribute to ARG dissemination. Additional global change factors, including fungicide application and plant diversity reduction, also contributed to elevated ARG abundance. Our findings suggest that, in addition to considering contamination levels, it is crucial to monitor microplastic diversity in ecosystems due to their potential role in driving the dissemination of antibiotic resistance through multiple pathways.}, } @article {pmid39531444, year = {2024}, author = {Ghosh, S and Ghosh, AJ and Islam, R and Sarkar, S and Saha, T}, title = {Lactobacillus plantarum KAD protects against high-fat diet-induced hepatic complications in Swiss albino mice: Role of inflammation and gut integrity.}, journal = {PloS one}, volume = {19}, number = {11}, pages = {e0313548}, pmid = {39531444}, issn = {1932-6203}, mesh = {Animals ; *Lactobacillus plantarum ; Mice ; *Diet, High-Fat/adverse effects ; *Probiotics/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Liver/pathology/metabolism/drug effects ; *Inflammation ; Male ; Oxidative Stress/drug effects ; }, abstract = {Hepatic complications are the major health issues associated with dietary intake of calorie saturated food e.g. high-fat diet (HFD). Recent studies have revealed the beneficial effects of probiotics in HFD fed mice with hepatic complications. Some probiotic Lactic acid bacteria (LAB) e.g. Lactobacillus plantarum have drawn our attention in managing hepatic complications. Here, we aim to elucidate the protective effects of L. plantarum KAD strain, isolated from ethnic fermented food 'Kinema' in HFD-fed mice as, a preventive approach. Eighteen Swiss albino mice were equally divided into 3 groups: Normal Diet (ND), negative control (HFD), and HFD-fed with oral L. plantarum KAD supplementation (LP). All the experimental groups were subjected to specific diet according to grouping for eight weeks. After completion of the regime, subjects were anesthetized and sacrificed. Organs, blood, and fecal samples were collected and stored appropriately. Physical indices, including body weight gain, organ co-efficients were calculated along with assessment of glycemic, lipidomic, hepatic, oxidative stress, inflammatory, and histological parameters. Gut microbiota analysis was performed using 16s V3-V4 fecal metagenomic profiling, and sequencing were done using Illumina Miseq system. Oral administration of L. plantarum KAD is found to significantly (p<0.05) restore metabolic health by normalizing glycemic, lipidomic, hepatic parameters, oxidative stress and inflammatory parameters. Moreover, LP group (7.08±0.52 mg/g) showed significantly (p<0.001) decreased hepatic triglyceride level compared to HFD group (20.07±1.32 mg/g). L. plantarum KAD improved the adipocytic, and colonic histomorphology with significantly better scoring pattern. LP group (1.83±0.41) showed a significantly (p<0.001) reduced hepatic score compared to negative control group (5.00±0.63), showing reduced hepatosteatosis, and immune infiltration. The strain modulated gut health by altering its microbial composition positively towards normalization. In conclusion, the results of the experiment suggest that prophylactic L. plantarum KAD administration has beneficial effects on the onset of HFD induced hepatic complications in mice. Further studies are needed, on this strain for its clinical use as dietary supplement.}, } @article {pmid39530358, year = {2024}, author = {Arandia-Gorostidi, N and Jaffe, AL and Parada, AE and Kapili, BJ and Casciotti, KL and Salcedo, RSR and Baumas, CMJ and Dekas, AE}, title = {Urea assimilation and oxidation support activity of phylogenetically diverse microbial communities of the dark ocean.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39530358}, issn = {1751-7370}, support = {507798//Simons Foundation Early Career Investigator Award AED/ ; 2143035//National Science Foundation CAREER Award to AED/ ; 1634297//NSF/ ; ECCS-2026822//National Science Foundation/ ; CEX2019-000928-S//Severo Ochoa Centre of Excellence/ ; 2020-BP-00179//Beatriu de Pinós Program/ ; //Stanford Science Fellows Program/ ; //National Science Foundation Postdoctoral Research Fellowship in Ocean Sciences/ ; }, mesh = {*Urea/metabolism ; *Oxidation-Reduction ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Pacific Ocean ; *Microbiota ; *Seawater/microbiology ; *Nitrification ; *Archaea/metabolism/genetics/classification ; *Metagenomics ; Phylogeny ; Metagenome ; Nitrogen/metabolism ; Ammonia/metabolism ; Urease/metabolism/genetics ; Ammonium Compounds/metabolism ; }, abstract = {Urea is hypothesized to be an important source of nitrogen and chemical energy to microorganisms in the deep sea; however, direct evidence for urea use below the epipelagic ocean is lacking. Here, we explore urea utilization from 50 to 4000 meters depth in the northeastern Pacific Ocean using metagenomics, nitrification rates, and single-cell stable-isotope-uptake measurements with nanoscale secondary ion mass spectrometry. We find that on average 25% of deep-sea cells assimilated urea-derived N (60% of detectably active cells), and that cell-specific nitrogen-incorporation rates from urea were higher than that from ammonium. Both urea concentrations and assimilation rates relative to ammonium generally increased below the euphotic zone. We detected ammonia- and urea-based nitrification at all depths at one of two sites analyzed, demonstrating their potential to support chemoautotrophy in the mesopelagic and bathypelagic regions. Using newly generated metagenomes we find that the ureC gene, encoding the catalytic subunit of urease, is found within 39% of deep-sea cells in this region, including the Nitrososphaeria (syn., Thaumarchaeota; likely for nitrification) as well as members of thirteen other phyla such as Proteobacteria, Verrucomicrobia, Plantomycetota, Nitrospinota, and Chloroflexota (likely for assimilation). Analysis of public metagenomes estimated ureC within 10-46% of deep-sea cells around the world, with higher prevalence below the photic zone, suggesting urea is widely available to the deep-sea microbiome globally. Our results demonstrate that urea is a nitrogen source to abundant and diverse microorganisms in the dark ocean, as well as a significant contributor to deep-sea nitrification and therefore fuel for chemoautotrophy.}, } @article {pmid39530242, year = {2025}, author = {Liu, F and Cai, B and Lian, S and Chang, X and Chen, D and Pu, Z and Bao, L and Wang, J and Lv, J and Zheng, H and Bao, Z and Zhang, L and Wang, S and Li, Y}, title = {MolluscDB 2.0: a comprehensive functional and evolutionary genomics database for over 1400 molluscan species.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D1075-D1086}, pmid = {39530242}, issn = {1362-4962}, support = {2022YFD2400301//National Key R&D Program of China/ ; 32222085//National Natural Science Foundation of China/ ; 842341005//Fundamental Research Funds for the Central Universities/ ; 32130107//National Natural Science Foundation of China/ ; LSKJ202202804//Science & Technology Innovation Project of Laoshan Laboratory/ ; 2021ZLGX03//Key Research and Development Program of Shandong Province/ ; GML20220018//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; //Taishan Scholar Project of Shandong Province/ ; }, mesh = {Animals ; *Mollusca/genetics/classification ; *Genomics/methods ; *Databases, Genetic ; Transcriptome ; Evolution, Molecular ; Genome/genetics ; Proteome/genetics ; Software ; Molecular Sequence Annotation ; }, abstract = {Mollusca represents the second-largest animal phylum but remains less explored genomically. The increase in high-quality genomes and diverse functional genomic data holds great promise for advancing our understanding of molluscan biology and evolution. To address the opportunities and challenges facing the molluscan research community in managing vast multi-omics resources, we developed MolluscDB 2.0 (http://mgbase.qnlm.ac), which integrates extensive functional genomic data and offers user-friendly tools for multilevel integrative and comparative analyses. MolluscDB 2.0 covers 1450 species across all eight molluscan classes and compiles ∼4200 datasets, making it the most comprehensive multi-omics resource for molluscs to date. MolluscDB 2.0 expands the layers of multi-omics data, including genomes, bulk transcriptomes, single-cell transcriptomes, proteomes, epigenomes and metagenomes. MolluscDB 2.0 also more than doubles the number of functional modules and analytical tools, updating 14 original modules and introducing 20 new, specialized modules. Overall, MolluscDB 2.0 provides highly valuable, open-access multi-omics platform for the molluscan research community, expediting scientific discoveries and deepening our understanding of molluscan biology and evolution.}, } @article {pmid39529629, year = {2024}, author = {Smith, GJ and van Alen, TA and van Kessel, MAHJ and Lücker, S}, title = {Simple, reference-independent assessment to empirically guide correction and polishing of hybrid microbial community metagenomic assembly.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18132}, pmid = {39529629}, issn = {2167-8359}, mesh = {*Metagenomics/methods ; *Microbiota/genetics ; Metagenome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Bioreactors/microbiology ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {Hybrid metagenomic assembly of microbial communities, leveraging both long- and short-read sequencing technologies, is becoming an increasingly accessible approach, yet its widespread application faces several challenges. High-quality references may not be available for assembly accuracy comparisons common for benchmarking, and certain aspects of hybrid assembly may benefit from dataset-dependent, empiric guidance rather than the application of a uniform approach. In this study, several simple, reference-free characteristics-particularly coding gene content and read recruitment profiles-were hypothesized to be reliable indicators of assembly quality improvement during iterative error-fixing processes. These characteristics were compared to reference-dependent genome- and gene-centric analyses common for microbial community metagenomic studies. Two laboratory-scale bioreactors were sequenced with short- and long-read platforms, and assembled with commonly used software packages. Following long read assembly, long read correction and short read polishing were iterated up to ten times to resolve errors. These iterative processes were shown to have a substantial effect on gene- and genome-centric community compositions. Simple, reference-free assembly characteristics, specifically changes in gene fragmentation and short read recruitment, were robustly correlated with advanced analyses common in published comparative studies, and therefore are suitable proxies for hybrid metagenome assembly quality to simplify the identification of the optimal number of correction and polishing iterations. As hybrid metagenomic sequencing approaches will likely remain relevant due to the low added cost of short-read sequencing for differential coverage binning or the ability to access lower abundance community members, it is imperative that users are equipped to estimate assembly quality prior to downstream analyses.}, } @article {pmid39529240, year = {2024}, author = {Liu, S and Zhang, Z and Wang, X and Ma, Y and Ruan, H and Wu, X and Li, B and Mou, X and Chen, T and Lu, Z and Zhao, W}, title = {Biosynthetic potential of the gut microbiome in longevous populations.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2426623}, pmid = {39529240}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Feces/microbiology ; Aged ; *Metagenomics ; Multigene Family ; Aged, 80 and over ; Terpenes/metabolism ; Longevity ; Akkermansia/metabolism ; Adult ; Male ; Female ; Middle Aged ; Cohort Studies ; Biological Products/metabolism ; Metagenome ; Young Adult ; }, abstract = {Gut microbiome plays a pivotal role in combating diseases and facilitating healthy aging, and natural products derived from biosynthetic gene clusters (BGCs) of the human microbiome exhibit significant biological activities. However, the natural products of the gut microbiome in long-lived populations remain poorly understood. Here, we integrated six cohorts of long-lived populations, encompassing a total of 1029 fecal metagenomic samples, and employed the metagenomic single sample assembled BGCs (MSSA-BGCs) analysis pipeline to investigate the natural products and their associated species. Our findings reveal that the BGC composition of the extremely long-lived group differed significantly from that of younger elderly and young individuals across five cohorts. Terpene and Type I PKS BGCs were enriched in the extremely long-lived, whereas cyclic-lactone-autoinducer BGCs were more prevalent in the young. Association analysis indicated that terpene BGCs were strongly associated with the abundance of Akkermansia muciniphila, which was also more abundant in the long-lived elderly across at least three cohorts. We assembled 18 A. muciniphila draft genomes using metagenomic data from the extremely long-lived group across six cohorts and discovered that they all harbor two classes of terpene BGCs, which aligns with the 97 complete genomes of A. muciniphila strains retrieved from the NCBI database. The core domains of these two BGC classes are squalene/phytoene synthases involved in the biosynthesis of tri- and tetraterpenes. Furthermore, the abundance of fecal A. muciniphila was significantly associated with eight types of triterpenoids. Targeted terpenoid metabolomic analysis revealed that two triterpenoids, Holstinone C and colubrinic acid, were enriched in the A. muciniphila culture solution compared to the medium, thereby confirming the production of triterpenoids by A. muciniphila. The natural products derived from the gut of long-lived populations provide intriguing indications of their potential beneficial roles in regulating health.}, } @article {pmid39529113, year = {2024}, author = {Guo, M and He, S and Song, W and Mai, J and Yuan, X and Huang, Y and Xi, H and Sun, G and Chen, Y and Du, B and Liu, X}, title = {The Lachnospiraceae-butyric acid axis and its role in glucocorticoid-associated osteonecrosis.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {1015}, pmid = {39529113}, issn = {1479-5876}, support = {82074471//National Natural Science Foundation of China/ ; 81804117//National Natural Science Foundation of China/ ; MS202220//Jiangsu Administration of Traditional Chinese Medicine/ ; JSDW202252//Jiangsu Provincial Medical Key Discipline(Laboratory)Cultivation Unit/ ; }, mesh = {Humans ; *Glucocorticoids/adverse effects ; *Osteonecrosis/chemically induced/pathology ; *Gastrointestinal Microbiome/drug effects ; *Butyric Acid ; Male ; Female ; Middle Aged ; Inflammation ; }, abstract = {Glucocorticoids (GCs) are key inducers of osteonecrosis, yet not all patients treated with GCs develop glucocorticoid-associated osteonecrosis (GAON). The factors mediating this relationship are unclear. Studies have shown that gut microbiota and their metabolites influence bone metabolism, but their role in GAON is unclear. This study aimed to explore the connection between GAON and gut microbiota. Through bidirectional Mendelian randomization analysis, we identified 14 gut microbial taxa, including Lachnospiraceae (IVW, P = 0.011), associated with GAON. RNA-seq analysis revealed that GAON differentially expressed genes (DEGs) were enriched for intestinal inflammatory response mechanisms. We then compared patients who developed GAON (17 cases), those who did not (GAnON, 15 cases), and those untreated with GCs (Blank, 15 cases) for gut microbiota composition, short-chain fatty acids (SCFAs), and serum inflammatory factors. Our findings indicated a decrease in Lachnospiraceae abundance (GAON 17.13%, GAnON 12.51%, Blank 24.52%) in GC-treated patients. Serum inflammatory factors (IL-17 A, IL-33, and TNF-α) associated with GAON (59.603 ± 12.147, 89.337 ± 20.714, 42.584 ± 9.185) showed significant differences between Blank (1.446 ± 0.683, 11.534 ± 4.705, 4.682 ± 1.48) and GAnON (25.353 ± 8.181, 32.527 ± 7.352, 12.49 ± 3.217) groups, with a negative correlation between these factors and Lachnospiraceae levels. Butyric acid levels in SCFAs varied among groups (P<0.01) and correlated with Lachnospiraceae and inflammatory factors. Controlled experiments in GAON rats demonstrated butyric acid's osteoprotective role in GAON development (P<0.01). In conclusion, our study suggests that reduced Lachnospiraceae and butyric acid levels, along with increased inflammation due to GCs use, contribute to GAON. Butyric acid may mediate the effects of Lachnospiraceae and inflammation. Butyrate supplementation could potentially reduce GAON incidence, offering a novel approach for its clinical management.}, } @article {pmid39528484, year = {2024}, author = {Manghi, P and Filosi, M and Zolfo, M and Casten, LG and Garcia-Valiente, A and Mattevi, S and Heidrich, V and Golzato, D and Perini, S and Thomas, AM and Montalbano, S and Cancellieri, S and Waldron, L and Hall, JB and Xu, S and Volfovsky, N and Green Snyder, L and Feliciano, P and Asnicar, F and Valles-Colomer, M and Michaelson, JJ and Segata, N and Domenici, E}, title = {Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9743}, pmid = {39528484}, issn = {2041-1723}, support = {MASTER-818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; ONCOBIOME-825410//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 1U01CA230551//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; }, mesh = {Humans ; *Autism Spectrum Disorder/microbiology ; Male ; Child ; Female ; *Mouth/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; *Saliva/microbiology ; Cross-Sectional Studies ; *Biomarkers ; Siblings ; Metagenome ; Child, Preschool ; Adolescent ; }, abstract = {The link between the oral microbiome and neurodevelopmental disorders remains a compelling hypothesis, still requiring confirmation in large-scale datasets. Leveraging over 7000 whole-genome sequenced salivary samples from 2025 US families with children diagnosed with autism spectrum disorders (ASD), our cross-sectional study shows that the oral microbiome composition can discriminate ASD subjects from neurotypical siblings (NTs, AUC = 0.66), with 108 differentiating species (q < 0.005). The relative abundance of these species is highly correlated with cognitive impairment as measured by Full-Scale Intelligence Quotient (IQ). ASD children with IQ < 70 also exhibit lower microbiome strain sharing with parents (p < 10[-6]) with respect to NTs. A two-pronged functional enrichment analysis suggests the contribution of enzymes from the serotonin, GABA, and dopamine degradation pathways to the distinct microbial community compositions observed between ASD and NT samples. Although measures of restrictive eating diet and proxies of oral hygiene show relatively minor effects on the microbiome composition, the observed associations with ASD and IQ may still represent unaccounted-for underlying differences in lifestyle among groups. While causal relationships could not be established, our study provides substantial support to the investigation of oral microbiome biomarkers in ASD.}, } @article {pmid39528483, year = {2024}, author = {Sánchez, O and Stefanni, S and Bhadury, P}, title = {The deep sea biodiversity and conservation collection.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {27559}, pmid = {39528483}, issn = {2045-2322}, abstract = {The deep sea, defined as ocean depths below 200 m, encompasses vast and largely unexplored habitats, such as abyssal plains, hydrothermal vents, cold seeps, and ocean trenches. This environment supports a remarkable diversity of life forms adapted to extreme conditions, including high pressure, low temperatures, and complete darkness. The Deep Sea Biodiversity and Conservation Collection highlights the importance of these ecosystems and the unique adaptations of the organisms inhabiting these extreme environments, ranging from invertebrates like corals and sponges to diverse microbial communities. The Collection includes studies on coral distribution and ecosystem services, trophic dynamics at cold-water coral reefs, and microbial diversity using metabarcoding and metagenomics. Notable findings include insights into hydrothermal vent communities, the role of chemosynthesis in sustaining deep-sea life, and the adaptation of deep-sea invertebrates to varying depths. These studies underscore the critical need for conservation strategies for these fragile and understudied oceanic ecosystems to ensure their sustainability.}, } @article {pmid39527509, year = {2024}, author = {Illidge, S and Kort, R and Hertzberger, R and , }, title = {'From women for women': A citizen science approach engaging women in the isolation and application of the vaginal health-associated bacterium Lactobacillus crispatus.}, journal = {PloS one}, volume = {19}, number = {11}, pages = {e0308526}, pmid = {39527509}, issn = {1932-6203}, mesh = {Humans ; Female ; *Vagina/microbiology ; *Probiotics ; *Lactobacillus crispatus/isolation & purification/genetics ; Adult ; *Vaginosis, Bacterial/microbiology/diagnosis ; *Microbiota ; Middle Aged ; Young Adult ; }, abstract = {A vaginal microbiome rich in Lactobacillus crispatus is associated with good reproductive and sexual health outcomes. Dysbiosis, indicated by the loss of Lactobacillus crispatus, is a risk factor for urogenital infections, such as the clinical diagnosis of bacterial vaginosis (BV) or urinary tract infections. While many scientists have explored probiotics using a conventional pharmaceutical approach, concerns about accessibility and affordability prompt an investigation into a preventive approach using this naturally occurring bacterium. Our study aimed to explore a potential woman-friendly vaginal probiotic product using the naturally occurring bacterium, Lactobacillus crispatus. Citizen scientists actively participated in a two-day practicum and successfully performed the procedures using self-collected vaginal swabs. The practicum received positive responses from participants who demonstrated notable engagement and enthusiasm. With expert guidance, participants without a laboratory background were able to execute assigned tasks successfully. From the Dutch crispatus Citizen Science Collective of 48 women, 22 succeeded in isolating their own Lactobacillus crispatus strains using a Loop-Mediated Isothermal Amplification (LAMP) protocol for identification. Additionally, 48 metagenomes and 54 whole genomes from 22 individuals were sequenced for comparative analysis. This project effectively engaged a community of women in the isolation of Lactobacillus crispatus strains from their vaginal microbiota, followed by in vitro characterization experiments and a hackathon for the development of a probiotic product. Our citizen science approach opens up collaboration possibilities and new avenues for exploration of vaginal health, facilitating community involvement and the development of targeted interventions to enhance women's well-being.}, } @article {pmid39526896, year = {2024}, author = {Wei, F and Jiang, H and Zhu, C and Zhong, L and Lin, Z and Wu, Y and Song, L}, title = {The co-fermentation of whole-grain black barley and quinoa improves murine cognitive impairment induced by a high-fat diet via altering gut microbial ecology and suppressing neuroinflammation.}, journal = {Food & function}, volume = {15}, number = {23}, pages = {11667-11685}, doi = {10.1039/d4fo02704c}, pmid = {39526896}, issn = {2042-650X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Diet, High-Fat/adverse effects ; *Cognitive Dysfunction ; *Mice, Inbred C57BL ; *Chenopodium quinoa/chemistry ; Male ; *Hordeum/chemistry ; *Fermentation ; Neuroinflammatory Diseases/metabolism ; Lactobacillus ; Hippocampus/metabolism ; Brain-Gut Axis ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {A high-fat diet (HFD) is associated with various adverse health outcomes, including cognitive impairment and an elevated risk of neurodegenerative conditions. This relationship is partially attributed to the influence of an HFD on the gut microbiota. The objective of this research was to evaluate the neuroprotective benefits of co-fermented black barley and quinoa with Lactobacillus (FG) against cognitive impairments triggered by an HFD and to investigate the microbiota-gut-brain axis mechanisms involved. C57BL/6J mice were randomized into four groups: the normal control group (NC, n = 10), the high-fat diet group (HFD, n = 10), the high-fat diet group supplemented with FG (HFG, 10 mL per kg BW, n = 10), and the high-fat diet group supplemented with Lactobacillus (HFL, 10 mL per kg BW, n = 10). Our results showed that the FG intervention enhanced the behavioral and locomotor skills of the mice, elevated the levels of dopamine (DA) and norepinephrine (NPI) in brain tissues, and alleviated synaptic ultrastructural damage in the hippocampus. Furthermore, FG intervention was observed to exert a protective effect on both the blood-brain barrier and the colonic barrier, as evidenced by an increase in the mRNA levels of Zona occludens-1 (ZO-1), Claudin-4, and Occludin in the hippocampus and colon. These beneficial effects may be attributed to FG's regulation of gut microbiota dysbiosis, which involves the restoration of intestinal flora diversity, reduction of the Firmicutes/Bacteroidetes (F/B) ratio, and a decrease in the levels of pro-inflammatory bacteria such as s_Escherichia coli E and g_Escherichia; moreover, there was an increase in the abundances of anti-inflammatory bacteria, such as s_Bacteroides thetaiotaomicron and s_Parabacteroides goldsteinii. Metagenomic analysis revealed that the FG treatment downregulated the lipopolysaccharide (LPS) pathway and upregulated neurotransmitter biosynthetic pathways. These probiotic effects of FG resulted in reduced production and "leakage" of LPS and decreased mRNA expression of Toll-like receptor 4 (Tlr4), cluster of differentiation 14 (CD14), and myeloid differentiation factor 88 (Myd88) in hippocampal and colon tissues. Consequently, a reduction was observed in the levels of inflammatory cytokines in the serum, hippocampus, and colon, along with suppression of the immunoreactivity of microglia and astrocytes. Our results suggest that FG may serve as an intervention strategy for preventing cognitive impairments caused by an HFD.}, } @article {pmid39526401, year = {2025}, author = {Jiang, Y and Wang, Y and Che, L and Yang, S and Zhang, X and Lin, Y and Shi, Y and Zou, N and Wang, S and Zhang, Y and Zhao, Z and Li, SC}, title = {GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D772-D782}, pmid = {39526401}, issn = {1362-4962}, support = {20220814183301001//Shenzhen Science and Technology Program/ ; }, mesh = {*Gene Transfer, Horizontal ; Humans ; *Gastrointestinal Microbiome/genetics ; *Databases, Genetic ; Metagenome/genetics ; Metagenomics/methods ; Bacteria/genetics/classification ; }, abstract = {Metagenomic studies have revealed the critical roles of complex microbial interactions, including horizontal gene transfer (HGT) and functional redundancy (FR), in shaping the gut microbiome's functional capacity and resilience. However, the lack of comprehensive data integration and systematic analysis approaches has limited the in-depth exploration of HGT and FR dynamics across large-scale gut microbiome datasets. To address this gap, we present GutMetaNet (https://gutmetanet.deepomics.org/), a first-of-its-kind database integrating extensive human gut microbiome data with comprehensive HGT and FR analyses. GutMetaNet contains 21 567 human gut metagenome samples with whole-genome shotgun sequencing data related to various health conditions. Through systematic analysis, we have characterized the taxonomic profiles and FR profiles, and identified 14 636 HGT events using a shared reference genome database across the collected samples. These HGT events have been curated into 8049 clusters, which are annotated with categorized mobile genetic elements, including transposons, prophages, integrative mobilizable elements, genomic islands, integrative conjugative elements and group II introns. Additionally, GutMetaNet incorporates automated analyses and visualizations for the HGT events and FR, serving as an efficient platform for in-depth exploration of the interactions among gut microbiome taxa and their implications for human health.}, } @article {pmid39526369, year = {2025}, author = {Dmitrijeva, M and Ruscheweyh, HJ and Feer, L and Li, K and Miravet-Verde, S and Sintsova, A and Mende, DR and Zeller, G and Sunagawa, S}, title = {The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D797-D805}, pmid = {39526369}, issn = {1362-4962}, support = {//ETH Zurich/ ; 51NF40_180575//NCCR/ ; //European Molecular Biology Laboratory/ ; 031A537B//Federal Ministry of Education and Research/ ; LT0050/2023-L//Human Frontier Science Program/ ; 205321_184955/SNSF_/Swiss National Science Foundation/Switzerland ; 101118531/ERC_/European Research Council/International ; /SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Internet ; *Databases, Genetic ; *Metagenome ; *Microbiota/genetics ; Genomics/methods ; Bacteria/genetics/classification ; Metagenomics/methods ; Phylogeny ; Software ; Genome, Bacterial ; }, abstract = {Determining the taxonomic composition (taxonomic profiling) is a fundamental task in studying environmental and host-associated microbial communities. However, genome-resolved microbial diversity on Earth remains undersampled, and accessing the genomic context of taxa detected during taxonomic profiling remains a challenging task. Here, we present the mOTUs online database (mOTUs-db), which is consistent with and interfaces with the mOTUs taxonomic profiling tool. It comprises 2.83 million metagenome-assembled genomes (MAGs) and 919 090 single-cell and isolate genomes from 124 295 species-level taxonomic units. In addition to being one of the largest prokaryotic genome resources to date, all MAGs in the mOTUs-db were reconstructed de novo in 117 902 individual samples by abundance correlation of scaffolds across multiple samples for improved quality metrics. The database complements the Genome Taxonomy Database, with over 50% of its species-level taxonomic groups being unique. It also offers interactive querying, enabling users to explore and download genomes at various taxonomic levels. The mOTUs-db is accessible at https://motus-db.org.}, } @article {pmid39523762, year = {2025}, author = {El Mouzan, M and Al Quorain, A and Assiri, A and Almasoud, A and Alsaleem, B and Aladsani, A and Al Sarkhy, A}, title = {Gut fungal profile in new onset treatment-naïve ulcerative colitis in Saudi children.}, journal = {Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association}, volume = {31}, number = {1}, pages = {28-33}, pmid = {39523762}, issn = {1998-4049}, mesh = {Humans ; *Colitis, Ulcerative/microbiology/epidemiology ; Child ; Male ; Saudi Arabia/epidemiology ; Adolescent ; Female ; *Feces/microbiology ; Child, Preschool ; Gastrointestinal Microbiome ; Infant ; Young Adult ; Candida/isolation & purification/genetics ; Case-Control Studies ; DNA, Fungal/genetics/analysis ; Saccharomyces cerevisiae/genetics/isolation & purification ; Dysbiosis/microbiology/epidemiology ; }, abstract = {BACKGROUND: Although the role of fungi in gut inflammation in IBD has been suggested, data are still limited in ulcerative colitis (UC). Our aim was to describe the gut fungal profile in a pediatric UC in Saudi Arabia.

METHODS: Fecal samples from children with UC and control samples provided by healthy school children were collected. The fungal DNA was analyzed using Shotgun metagenomic procedures. Shannon alpha diversity, beta diversity, differential abundance, random forest classification algorithm, and area under the curve were analyzed.

RESULTS: There were 20 children with UC and 20 healthy school children. The median age and range were 13 (0.5-21) and 13 (7-16) years for children with UC and controls, respectively. Male subjects were 40% and 35% for UC and controls, respectively. At diagnosis, the UC extent was E4 (38%); E3 (25%); E2 (37%) and 35% had a PUCAI ≥65. The reduction of alpha diversity and the significant dissimilarity in children with UC were similar to those of most published studies. However, a significant difference was found at all taxa levels with a remarkable enhancement of Candida genus and Saccharomyces cerevisiae in children with UC. Three species were identified as fungal signatures and an area under the curve of 98.4% (95.1-100% CI), indicating an association with UC that has not been reported thus far.

CONCLUSION: We report significant fungal dysbiosis in children with UC consistent with published literature. However, the report of potential fungal signature and a strong association with UC deserves further studies with a bigger sample size from other populations.}, } @article {pmid39523457, year = {2024}, author = {Chen, Y and Liu, S and Tan, S and Zheng, Y and Chen, Y and Yang, C and Lin, S and Mi, Y and Li, W}, title = {KRAS mutations promote the intratumoral colonization of enterotoxigenic bacteroides fragilis in colorectal cancer through the regulation of the miRNA3655/SURF6/IRF7/IFNβ axis.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2423043}, pmid = {39523457}, issn = {1949-0984}, mesh = {*Colorectal Neoplasms/microbiology/genetics/metabolism/pathology ; Humans ; *Bacteroides fragilis/genetics/metabolism ; *Proto-Oncogene Proteins p21(ras)/genetics/metabolism ; *MicroRNAs/genetics/metabolism ; *Mutation ; Animals ; Mice ; *Interferon-beta/metabolism/genetics ; *Interferon Regulatory Factor-7/metabolism/genetics ; Cell Line, Tumor ; Gastrointestinal Microbiome ; Mice, Nude ; Gene Expression Regulation, Neoplastic ; Female ; }, abstract = {KRAS mutations are associated with poor prognosis in colorectal cancer (CRC). Although the association between the gut microbiota and CRC has been extensively documented, it is unclear whether KRAS mutations can regulate the gut microbiota. Metagenomics has identified changes in the diversity of the gut microbiota in CRC due to KRAS mutations. Specifically, KRAS mutations positively correlate with the abundance of the bacteroides. Understanding how to regulate the classic carcinogenic bacterium within the bacteroides, such as enterotoxigenic bacteroides fragilis (ETBF), to enhance treatment efficacy of tumors is a key focus of research. Mechanistically, we found that the reduction of miR3655 is indispensable for KRAS mutation-promoted proliferation of CRC and the abundance of ETBF. miR3655 targets SURF6 to inhibit its transcription. Further transcriptomic sequencing revealed that SURF6 promotes intratumoral colonization of ETBF in CRC by inhibiting the nuclear translocation and transcription levels of the IRF7, affecting the activation of the IFNβ promoter. Regulating miR3655 and SURF6 can promote IFNβ secretion in CRC, directly killing ETBF. These data indicate that KRAS mutations affect the intratumoral colonization of ETBF in CRC through the miR3655/SURF6/IRF7/IFNβ axis. This provides new potential strategies for treating CRC associated with KRAS mutations or high levels of ETBF.}, } @article {pmid39523344, year = {2024}, author = {You, X and Yan, J and Herzog, J and Nobakhti, S and Campbell, R and Hoke, A and Hammamieh, R and Sartor, RB and Shefelbine, S and Kacena, MA and Chakraborty, N and Charles, JF}, title = {Bone loss with aging is independent of gut microbiome in mice.}, journal = {Bone research}, volume = {12}, number = {1}, pages = {65}, pmid = {39523344}, issn = {2095-4700}, support = {R01-AG046257//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; R01 AG046257/AG/NIA NIH HHS/United States ; P30-AR070253//U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)/ ; 997397//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; P40-OD010995//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P30-DK034987//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Aging/physiology ; Male ; Mice ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Bone Resorption/microbiology ; Germ-Free Life ; }, abstract = {Emerging evidence suggests a significant role of gut microbiome in bone health. Aging is well recognized as a crucial factor influencing the gut microbiome. In this study, we investigated whether age-dependent microbial change contributes to age-related bone loss in CB6F1 mice. The bone phenotype of 24-month-old germ-free (GF) mice was indistinguishable compared to their littermates colonized by fecal transplant at 1-month-old. Moreover, bone loss from 3 to 24-month-old was comparable between GF and specific pathogen-free (SPF) mice. Thus, GF mice were not protected from age-related bone loss. 16S rRNA gene sequencing of fecal samples from 3-month and 24-month-old SPF males indicated an age-dependent microbial shift with an alteration in energy and nutrient metabolism potential. An integrative analysis of 16S predicted metagenome function and LC-MS fecal metabolome revealed an enrichment of protein and amino acid biosynthesis pathways in aged mice. Microbial S-adenosyl methionine metabolism was increased in the aged mice, which has previously been associated with the host aging process. Collectively, aging caused microbial taxonomic and functional alteration in mice. To demonstrate the functional importance of young and old microbiome to bone, we colonized GF mice with fecal microbiome from 3-month or 24-month-old SPF donor mice for 1 and 8 months. The effect of microbial colonization on bone phenotypes was independent of the microbiome donors' age. In conclusion, our study indicates age-related bone loss occurs independent of gut microbiome.}, } @article {pmid39522897, year = {2024}, author = {Zhang, H and Yang, X and Chen, J and Jiang, Q and Yao, S and Chen, L and Xiang, X}, title = {Investigation of the mechanism by which Tegillarca granosa polysaccharide regulates non-alcoholic fatty liver disease in mice by modulating Lactobacillus Johnsonii.}, journal = {International journal of biological macromolecules}, volume = {282}, number = {Pt 6}, pages = {137259}, doi = {10.1016/j.ijbiomac.2024.137259}, pmid = {39522897}, issn = {1879-0003}, mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/metabolism/drug therapy ; *Polysaccharides/pharmacology/chemistry ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Diet, High-Fat/adverse effects ; *Lactobacillus johnsonii/metabolism ; *Lipid Metabolism/drug effects ; Male ; Disease Models, Animal ; Liver/drug effects/metabolism ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred C57BL ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD), a prevalent chronic liver disease, is marked by excessive lipid deposition in the liver without alcohol abuse. Scapharca subcrenatum, a major Chinese farmed bivalve, yields S. subcrenatum polysaccharide (TGP), an active substance with known biological activity. Previous studies revealed TGP's significant regulatory effect on a high-fat diet (HFD)-induced NAFLD in mice. However, the precise mechanisms, particularly involving gut microbiota, remain unclear. In the current study, an antibiotic-treated mouse model was established to determine the mechanistic role of the gut microbiota in the observed anti-obesity effects of TGP. In addition, 16S rRNA genomic and metagenome-derived taxonomic analyses were performed to assess the gut microbial populations. The results showed that TGP selectively enhanced the number of the eosinophilic bacterium Lactobacillus johnsonii, which was reduced in HFD mice. Of note, the oral administration of L. johnsonii formulations to HFD mice alleviated NAFLD, and this was related to regulating lipid metabolism and the accumulation of lipids in the liver. Therefore, the current study uncovered a potential pathway for developing NAFLD treatment strategies based on the interaction between TGP and the gut microbiota.}, } @article {pmid39522830, year = {2025}, author = {Matamoros, BR and Serna, C and Wedel, E and Montero, N and Kirpekar, F and Gonzalez-Zorn, B}, title = {NpmC - a novel A1408 16S rRNA methyltransferase in the gut of humans and animals.}, journal = {International journal of antimicrobial agents}, volume = {65}, number = {1}, pages = {107382}, doi = {10.1016/j.ijantimicag.2024.107382}, pmid = {39522830}, issn = {1872-7913}, mesh = {*Methyltransferases/genetics/metabolism ; *RNA, Ribosomal, 16S/genetics ; *Aminoglycosides/pharmacology/metabolism ; Humans ; Animals ; *Escherichia coli/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Sisomicin/analogs & derivatives/pharmacology ; Gastrointestinal Microbiome ; Escherichia coli Proteins/genetics/metabolism ; Methylation ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; }, abstract = {NpmA and NpmB are 16S rRNA methyltransferases that act on residue A1408 and confer high-level resistance to almost all aminoglycosides; however, these methyltransferases are rarely reported. A novel gene, npmC, was identified after analysisng all world-wide available metagenomic projects in a One Health context. This gene has a high level of similarity (91.5%) with npmA and up to 92.7% similarity at amino acidic level. The protein encoded by this gene presents the conserved motifs required for A1408 methylation. npmC was synthesized and its expression in Escherichia coli resulted in a high level of resistance to 4,5-disubstituted 2-deoxystreptamine (2-DOS) and 4-monosubstituted 2-DOS aminoglycosides, as well as moderate resistance to 4,6-disusbstituted 2-DOS aminoglycosides, including the last resort aminoglycoside, plazomicin. Methylation at residue A1408 was confirmed by mass spectrometry assays. Analysis of the npmC gene background revealed that its genetic context was associated with different insertion sequences that could mobilise the gene. Similarities in the genetic context between npmC and npmA indicate that they share a common ancestor. The immediate genetic context of this methyltransferase indicates a high relationship to the Eubacteriales order. This finding reveals the dark matter of the microbiome as a potential source of novel resistance genes, expands the list of the true pan-aminoglycoside 16S rRNA methyltransferases, which threaten the usefulness and development of next-generation aminoglycosides.}, } @article {pmid39522205, year = {2024}, author = {Wang, Z and Cao, H and Jin, J and Thorley, E and Cava, J and Sun, Y and Zhang, L and Wang, N and Yang, Z}, title = {Diel asynchrony in the expanded characteristics of toxic cyanobacterial blooms revealed by integrated metabolomics and metagenomics.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136403}, doi = {10.1016/j.jhazmat.2024.136403}, pmid = {39522205}, issn = {1873-3336}, mesh = {*Metabolomics ; *Cyanobacteria/genetics/metabolism ; *Metagenomics ; *Lakes/microbiology ; China ; Biomass ; Microbiota ; Phytoplankton/genetics/metabolism ; }, abstract = {We establish a field metabolomics protocol in Lake Taihu (China) and determined two critical parameters: the minimum amount of biomass for metabolomics and the daytime when metabolomes are stable. The minimum biomass is 475-950 µg dry weight (DW) or 204-408 ng DNA for F (phytoplankton) samples, and 940-1760 µg DW or 193-514 ng DNA for W (whole-water) samples. In a diel cycle, temporal taxonomical composition, metabolic state, and response to physiochemical factors progressed asynchronously between the F and W microbiomes. F peak growth (metabolic steady state) occurred 12-17 pm while W around 12 pm in metabolite identity, concentration, and molecular weight. 482 (∼50 %) metabolites highly correlated between the F and W microbiomes. Integrated analysis revealed different systematic changes between F and W sample, in taxon-associated metabolites, reactions, and biological functions: e.g., carbon metabolism and bioenergetics in F and amino acid metabolism and central metabolism in W samples. Metagenomics discovered important interspecific and intraspecific diversity using single-nucleotide polymorphism, and interactions between cyanobacteria and epibiotic bacteria. Diel intraspecific diversity shift inferred Microcystis aeruginosa and Anabaena sp. have different temperature optima experimentally verified. This integrated multi-omics protocol expands water microbiome analyses from conventional structure and function to diversity dynamics and interspecific metabolism and ecophysiology.}, } @article {pmid39522045, year = {2024}, author = {Cabezas, MP and Fonseca, NA and Muñoz-Mérida, A}, title = {MIMt: a curated 16S rRNA reference database with less redundancy and higher accuracy at species-level identification.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {88}, pmid = {39522045}, issn = {2524-6372}, support = {UIDB/04050/2020//FCT/ ; NORTE-01-0246-FEDER-000063//NORTE2020/ ; NORTE-01-0246-FEDER-000063//NORTE2020/ ; }, abstract = {MOTIVATION: Accurate determination and quantification of the taxonomic composition of microbial communities, especially at the species level, is one of the major issues in metagenomics. This is primarily due to the limitations of commonly used 16S rRNA reference databases, which either contain a lot of redundancy or a high percentage of sequences with missing taxonomic information. This may lead to erroneous identifications and, thus, to inaccurate conclusions regarding the ecological role and importance of those microorganisms in the ecosystem.

RESULTS: The current study presents MIMt, a new 16S rRNA database for archaea and bacteria's identification, encompassing 47 001 sequences, all precisely identified at species level. In addition, a MIMt2.0 version was created with only curated sequences from RefSeq Targeted loci with 32 086 sequences. MIMt aims to be updated twice a year to include all newly sequenced species. We evaluated MIMt against Greengenes, RDP, GTDB and SILVA in terms of sequence distribution and taxonomic assignments accuracy. Our results showed that MIMt contains less redundancy, and despite being 20 to 500 times smaller than existing databases, outperforms them in completeness and taxonomic accuracy, enabling more precise assignments at lower taxonomic ranks and thus, significantly improving species-level identification.}, } @article {pmid39521075, year = {2024}, author = {Oliveira, OA and Estrada, CSD and Vidal, LO and Junior, LCC and Abril, G and Rezende, CE and Thompson, CC and Thompson, FL and Tschoeke, DA and Garcia, GD}, title = {Insights into the water microbiome dynamics of a large tropical estuary transition.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177411}, doi = {10.1016/j.scitotenv.2024.177411}, pmid = {39521075}, issn = {1879-1026}, mesh = {*Estuaries ; *Microbiota ; Tropical Climate ; Environmental Monitoring ; Bacteria/classification/genetics ; Seasons ; Water Microbiology ; Brazil ; Biodiversity ; Methane/metabolism ; }, abstract = {Tropical estuarine systems play several ecological roles, such as acting as a nursery for biodiversity and cycling nutrients and greenhouse gases. However, the phylogenetic and metabolic diversity of estuarine microbiomes is not completely known. Furthermore, it is unclear how seasonal patterns may affect microbial diversity in these systems. The aim of the present study was to determine the metagenomic diversity and its major drivers in a large tropical estuarine system dominated by a mangrove forest in the South Atlantic around the Paraiba do Sul River. In total, 12.16 million shotgun sequences were generated (dry season: n = 8; wet season: n = 5), and water-quality parameters were evaluated for all locations. Metagenomic sequences were distributed between two patterns: (1) the dry season, in which the families Rhodobactereaceae and Flavobactereaceae increased, and (2) the wet season, in which Moraxellaceae, Pseudomonadaceae, Pseudoalteromonadaceae were more abundant. The dry season was characterized by higher salinity, nitrogen fixation, nitrification, and photosynthetic potential. In contrast, the wet season had higher carbon dioxide (CO2) and methane (CH4) production and a higher abundance of methanogenic, methylotrophic, and chemoorganotrophic bacteria in samples with low salinity. These findings suggest a possible relationship with the production of greenhouse gases during the wet period.}, } @article {pmid39520912, year = {2024}, author = {Zhao, L and Weng, W and Ni, M and Shen, H and Zhang, S and Chen, Y and Jia, R and Fan, L and Mao, Y and Qin, L and Liu, S and Wang, Y}, title = {Rubidium salt can effectively relieve the symptoms of DSS-induced ulcerative colitis.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {181}, number = {}, pages = {117574}, doi = {10.1016/j.biopha.2024.117574}, pmid = {39520912}, issn = {1950-6007}, mesh = {*Colitis, Ulcerative/drug therapy/microbiology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Dextran Sulfate ; Male ; Mice ; Mice, Inbred C57BL ; Salts ; Colon/drug effects/pathology/metabolism/microbiology ; Disease Models, Animal ; }, abstract = {Inflammatory bowel disease (IBD) is a chronic condition that afflicts individuals repeatedly and cannot be cured at present, which has seriously affected the quality of life of patients. Minerals Containing Rubidium (MCR) from Guangxi Yuechengling, which Professor Zhao Lichun purified, were explored. Against this backdrop, the present study investigates the efficacy of rubidium salt in ulcerative colitis. Rubidium salt reduced levels of inflammatory markers and improved intestinal barrier function through the Elisa kit, immunohistochemistry, and qPCR. Next, we detected the level of short-chain fatty acid and found that the content of propanoic acid, butyric acid, and n-butyric acid increased after treatment with rubidium salt. We used fecal metagenomics to explore the underlying reasons further and found that rubidium salt significantly adjusted the structure of intestinal flora, increased the abundance of beneficial bacteria such as lactobacillus and bifidobacterium, and inhibited the abundance of harmful bacteria such as Enterobacteriaceae and Escherichia coli. We also learned that rubidium salt directly weakened pathogenic bacteria's infection and survival ability by reducing the expression of virulence factors such as fimH, invA, and hilA and virulence genes such as acrA and ompR. Overall, rubidium salt can reduce harmful bacteria and increase beneficial bacteria. The increased beneficial bacteria help enhance the gut barrier and regulate inflammatory factors by raising the levels of short-chain fatty acids. A strengthened gut barrier further stabilizes microbial homeostasis, ultimately alleviating ulcerative colitis.}, } @article {pmid39520707, year = {2024}, author = {Lu, T and Ericsson, AC and Dietz, ZK and Cato, AK and Coghill, LM and Picking, WD and Picking, WL}, title = {Impact of an intranasal L-DBF vaccine on the gut microbiota in young and elderly mice.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2426619}, pmid = {39520707}, issn = {1949-0984}, support = {R01 AI138970/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Administration, Intranasal ; Mice ; *Feces/microbiology ; Female ; Shigella Vaccines/immunology/administration & dosage/genetics ; Lung/microbiology/immunology ; Shigella/immunology/genetics ; RNA, Ribosomal, 16S/genetics ; Age Factors ; Mice, Inbred BALB C ; Vaccination ; }, abstract = {Shigella spp. cause bacillary dysentery (shigellosis) with high morbidity and mortality in low- and middle-income countries. Infection occurs through the fecal-oral route and can be devastating for vulnerable populations, including infants and the elderly. These bacteria invade host cells using a type III secretion system (T3SS). No licensed vaccine yet exists for shigellosis, but we have generated a recombinant fusion protein, L-DBF, combining the T3SS needle tip protein (IpaD), translocator protein (IpaB), and the LTA1 subunit of enterotoxigenic E. coli labile toxin, which offers broad protection in a mouse model of lethal pulmonary infection. The L-DBF vaccine protects high-risk groups, including young and elderly mice. Here, we investigated how the gut microbiota of young and elderly mice responds to intranasal L-DBF vaccination formulated in an oil-in-water emulsion (ME). Samples from lungs, small intestines, and feces were collected on day 14 after 2 or 3 doses of L-DBF in ME. 16S rRNA gene sequencing revealed age-dependent changes in gut microbiota post-vaccination. The vaccine-induced changes were more prominent in the elderly mice and were most significant in the intestinal tract, indicating that vaccination by the intranasal route can have a tremendous impact on the gut environment. These findings provide insight into the communication between the intranasal mucosal surface following subunit vaccination and the microbiota at a distant mucosal site, thereby highlighting the impact of vaccination and the host's microbiome.}, } @article {pmid39520096, year = {2024}, author = {Logel, M and Tope, P and El-Zein, M and Gonzalez, E and Franco, EL}, title = {A Narrative Review of the Putative Etiologic Role and Diagnostic Utility of the Cervicovaginal Microbiome in Human Papillomavirus-Associated Cervical Carcinogenesis.}, journal = {Journal of medical virology}, volume = {96}, number = {11}, pages = {e70027}, pmid = {39520096}, issn = {1096-9071}, support = {//This work was supported by the Canadian Institutes of Health Research (grant FDN-143347 to E.L.F.) and Fonds de Recherche du Québec - Santé./ ; }, mesh = {Humans ; Female ; *Microbiota ; *Uterine Cervical Neoplasms/virology/diagnosis/microbiology ; *Papillomavirus Infections/diagnosis/virology/microbiology ; *Vagina/microbiology/virology ; *Cervix Uteri/microbiology/virology ; *Papillomaviridae/genetics/isolation & purification/classification ; Metagenomics/methods ; Carcinogenesis ; RNA, Ribosomal, 16S/genetics ; Bacteria/isolation & purification/genetics/classification ; Human Papillomavirus Viruses ; }, abstract = {The cervicovaginal microbiome (CVM) may contribute to human papillomavirus (HPV)-associated cervical carcinogenesis. We summarized the literature on the CVM in cervical carcinogenesis by searching Medline, Web of Science, and Embase for articles that sequenced the CVM using metagenomics. Additionally, we identified studies assessing the diagnostic role of the CVM in cervical carcinogenesis by searching PubMed. We performed an environmental scan of Google and Google Scholar to review common CVM characterization techniques. Twenty-eight records presented or summarized associations between the CVM and HPV acquisition, prevalence, persistence, clearance, and cervical lesions or cancer, while three studies identified bacterial taxa detecting high-risk HPV prevalence or cervical lesions. The area under the curve ranged from 0.802 to 0.952. 16S ribosomal RNA gene sequencing and whole metagenome sequencing have sufficient resolution to study the CVM bacteriome. Bacterial communities may have important implications in cervical cancer; however, there is a need for methodological standardization for CVM characterization.}, } @article {pmid39519025, year = {2024}, author = {Zhang, T and Zhao, C and Li, N and He, Q and Gao, G and Sun, Z}, title = {Longitudinal and Multi-Kingdom Gut Microbiome Alterations in a Mouse Model of Alzheimer's Disease.}, journal = {International journal of molecular sciences}, volume = {25}, number = {21}, pages = {}, pmid = {39519025}, issn = {1422-0067}, support = {32325040//National Natural Science Foundation of China/ ; U22A20540//National Natural Science Foundation of China/ ; 2022YFD2100700//National Key R&D Program of China/ ; 2022YFSJ0017//Inner Mongolia Science & Technology Planning Project/ ; 2022110//Research support funds for high-level talents in public institutions at the autonomous region level in Inner Mongolia/ ; }, mesh = {Animals ; *Alzheimer Disease/microbiology/virology ; *Gastrointestinal Microbiome/genetics ; Mice ; *Disease Models, Animal ; Dysbiosis/microbiology ; Feces/microbiology ; Bacteria/classification/genetics ; Archaea/genetics ; Metagenomics/methods ; Fungi/genetics/classification ; Metagenome ; Longitudinal Studies ; }, abstract = {Gut microbial dysbiosis, especially bacteriome, has been implicated in Alzheimer's disease (AD). However, nonbacterial members of the gut microbiome in AD, such as the mycobiome, archaeome, and virome, are unexplored. Here, we perform higher-resolution shotgun metagenomic sequencing on fecal samples collected longitudinally from a mouse model of AD to investigate longitudinal and multi-kingdom gut microbiome profiling. Shotgun metagenomic sequencing of fecal samples from AD mice and healthy mice returns 41,222 bacterial, 414 fungal, 1836 archaeal, and 1916 viral species across all time points. The ecological network pattern of the gut microbiome in AD mice is characterized by more complex bacterial-bacterial interactions and fungal-fungal interactions, as well as simpler archaeal-archaeal interactions and viral-viral interactions. The development of AD is accompanied by multi-kingdom shifts in the gut microbiome composition, as evidenced by the identification of 1177 differential bacterial, 84 differential fungal, 59 differential archaeal, and 10 differential viral species between healthy and AD mice across all time points. In addition, the functional potential of the gut microbiome is partially altered in the development of AD. Collectively, our findings uncover longitudinal and multi-kingdom gut microbiome alterations in AD and provide a motivation for considering microbiome-based therapeutics during the prevention and treatment of AD.}, } @article {pmid39518901, year = {2024}, author = {Nahon, SMR and Trindade, FC and Yoshiura, CA and Martins, GC and Costa, IRCD and Costa, PHO and Herrera, H and Balestrin, D and Godinho, TO and Marchiori, BM and Valadares, RBDS}, title = {Impact of Agroforestry Practices on Soil Microbial Diversity and Nutrient Cycling in Atlantic Rainforest Cocoa Systems.}, journal = {International journal of molecular sciences}, volume = {25}, number = {21}, pages = {}, pmid = {39518901}, issn = {1422-0067}, support = {//VALE Research Institute/ ; }, mesh = {*Soil Microbiology ; *Cacao/microbiology/metabolism/genetics ; *Rainforest ; Soil/chemistry ; Agriculture/methods ; Nitrogen/metabolism ; Nitrogen Cycle ; Biodiversity ; Forestry/methods ; Microbiota ; Metagenomics/methods ; Ecosystem ; }, abstract = {Microorganisms are critical indicators of soil quality due to their essential role in maintaining ecosystem services. However, anthropogenic activities can disrupt the vital metabolic functions of these microorganisms. Considering that soil biology is often underestimated and traditional assessment methods do not capture its complexity, molecular methods can be used to assess soil health more effectively. This study aimed to identify the changes in soil microbial diversity and activity under different cocoa agroforestry systems, specially focusing on taxa and functions associated to carbon and nitrogen cycling. Soils from three different cocoa agroforestry systems, including a newly established agroforestry with green fertilization (GF), rubber (Hevea brasiliensis)-cocoa intercropping (RC), and cocoa plantations under Cabruca (cultivated under the shave of native forest) (CAB) were analyzed and compared using metagenomic and metaproteomic approaches. Samples from surrounding native forest and pasture were used in the comparison, representing natural and anthropomorphic ecosystems. Metagenomic analysis revealed a significant increase in Proteobacteria and Basidiomycota and the genes associated with dissimilatory nitrate reduction in the RC and CAB areas. The green fertilization area showed increased nitrogen cycling activity, demonstrating the success of the practice. In addition, metaproteomic analyses detected enzymes such as dehydrogenases in RC and native forest soils, indicating higher metabolic activity in these soils. These findings underscore the importance of soil management strategies to enhance soil productivity, diversity, and overall soil health. Molecular tools are useful to demonstrate how changes in agricultural practices directly influence the microbial community, affecting soil health.}, } @article {pmid39516921, year = {2024}, author = {Cheng, L and Tao, J and Lu, P and Liang, T and Li, X and Chang, D and Su, H and He, W and Qu, Z and Li, H and Mu, W and Zhang, W and Liu, N and Zhang, J and Cao, P and Jin, J}, title = {Manipulation in root-associated microbiome via carbon nanosol for plant growth improvements.}, journal = {Journal of nanobiotechnology}, volume = {22}, number = {1}, pages = {685}, pmid = {39516921}, issn = {1477-3155}, mesh = {*Microbiota/drug effects ; *Plant Roots/microbiology ; *Carbon/metabolism/chemistry ; *Soil Microbiology ; *Bacteria/metabolism ; *Rhizosphere ; *Plant Development/drug effects ; *Fungi ; Nicotiana/microbiology ; Soil/chemistry ; Nanostructures/chemistry ; Biomass ; }, abstract = {BACKGROUND: Modulating the microbiome with nanomaterials has been proposed to improve plant growth, and reduce reliance on external inputs. Carbon Nanosol (CNS) was attracted for its potential to improve plant productivity. However, the mechanism between CNS and rhizosphere microorganisms remained largely elusive.

RESULTS: Here, we tried to systematically explore the effects of CNS (600 and 1200 mg/L by concentration) on tobacco growth, soil physical properties, and root-associated microbiome. The influence of CNS on soil physicochemical properties and plant growth was significant and dose-dependent, leading to a 28.82% increase in biomass accumulation by 600 mg/L CNS. Comparison between the CNS-treated and control plants revealed significant differences in microbiome composition, including 1148 distinct ASVs (923 bacteria and 225 fungi), microbiome interactions, and metabolic function of root-associated microbiomes. Fungal and bacterial communities had different response patterns for CNS treatment, with phased and dose-dependent effects, with the most significant changes in microbial community structure observed at 1200 mg/L after 10 days of treatment. Microbial networks of CNS-treated plants had more nodes and edges, higher connectivity, and more hub microorganisms than those of control plants. Compared with control, CNS significantly elevated abundances of various bacterial biomarkers (such as Sphingomonas and Burkholderia) and fungi biomarkers (including Penicillium, Myceliophthora, and Talaromyces), which were potential plant-beneficial organisms. Functional prediction based on metagenomic data demonstrated pathways related to nutrient cycling being greatly enriched under CNS treatment. Furthermore, 391 culturable bacteria and 44 culturable fungi were isolated from soil and root samples. Among them, six bacteria and two fungi strains enriched upon CNS treatment were validated to have plant growth promotion effect, and two fungi (Cladosporium spp. and Talaromyces spp.) played their roles by mediating volatile organic compounds (VOCs). To some extent, the driving and shaping of the microbiome by CNS contributed to its impact on plant growth and development.

CONCLUSION: Our results revealed the key role of root-associated microbiota in mediating the interaction between CNS and plants, thus providing valuable insights and strategies for harnessing CNS to enhance plant growth.}, } @article {pmid39516585, year = {2024}, author = {Karlsson, ME and Forsberg, G and Rosberg, AK and Thaning, C and Alsanius, B}, title = {Impact of thermal seed treatment on spermosphere microbiome, metabolome and viability of winter wheat.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {27197}, pmid = {39516585}, issn = {2045-2322}, mesh = {*Triticum/microbiology/metabolism ; *Seeds/microbiology/metabolism ; *Microbiota ; *Metabolome ; Seedlings/microbiology/metabolism/growth & development ; Fusarium ; Hot Temperature ; }, abstract = {Thermal seed treatment can be used as an alternative method to prevent infection by seed-borne diseases, but exposure duration and temperature during thermal treatment are important to maintain high seed viability and emergence whilst decreasing infection rate. A method for predicting suitable treatment parameters to maintain viability and eliminate seed-borne pathogens is therefore needed. Seeds of winter wheat were subjected to thermal treatment at four levels of intensity and pre-treatments with or without imbibition. Treatment impact was measured by metabolome analysis using LC-MS and GC-MS, analysis of spermosphere bacterial and fungal metagenomes using Illumina MiSeq, and detection of presence of Fusarium spp. and Microdochium spp. using ddPCR. The results showed that moderate treatment intensity reduced signs of infection and increased seedling emergence. In imbibed samples, myo-inositol concentration and myo-inositol: glucose ratio were positively correlated with treatment intensity, whereas concentrations of glucose and citric acid were negatively correlated. No correlations were found for non-imbibed samples. Imbibition had a large significant impact on microbial community composition of the wheat spermosphere. Imbibition of wheat seeds prior to thermal treatment altered wheat spermosphere microbiota. The concentration of myo-inositol, potentially in combination with glucose, could be a candidate predictor for suitable thermal treatment intensity of wheat seeds.}, } @article {pmid39515382, year = {2024}, author = {Shan, E and Zhang, X and Yu, Z and Hou, C and Pang, L and Guo, S and Liu, Y and Dong, Z and Zhao, J and Wang, Q and Yuan, X}, title = {Seawater warming rather than acidification profoundly affects coastal geochemical cycling mediated by marine microbiome.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177365}, doi = {10.1016/j.scitotenv.2024.177365}, pmid = {39515382}, issn = {1879-1026}, mesh = {*Seawater/microbiology/chemistry ; *Microbiota ; *Climate Change ; Hydrogen-Ion Concentration ; Global Warming ; Denitrification ; Bacteria ; }, abstract = {The most concerning consequences of climate change include ocean acidification and warming, which can affect microbial communities and thus the biogeochemical cycling they mediate. Therefore, it is urgent to study the impact of ocean acidification and warming on microbial communities. In the current study, metagenomics was utilized to reveal how the structure and function of marine microorganisms respond to ocean warming and acidification. In terms of community structure, Non-metric Multidimensional Scaling analysis visualized the similarity or difference between the control and the warming or acidification treatments, but the inter-group differences were not significant. In terms of gene functionality, warming treatments showed greater effects on microbial communities than acidification. After treatment with warming, the relative abundance of genes associated with denitrification increased, suggesting that ocean nitrogen loss can increase with increased temperature. Conversely, acidification treatments apparently inhibited denitrification. Warming treatment also greatly affected sulfur-related microorganisms, increasing the relative abundance of certain sulfate-reducing prokaryote, and enriched microbial carbon-fixation pathways. These results provide information on the response strategies of coastal microorganisms in the changing marine environments.}, } @article {pmid39515333, year = {2024}, author = {Li, X and Zhang, J and Ma, D and Fan, X and Zheng, X and Liu, YX}, title = {Exploring protein natural diversity in environmental microbiomes with DeepMetagenome.}, journal = {Cell reports methods}, volume = {4}, number = {11}, pages = {100896}, pmid = {39515333}, issn = {2667-2375}, mesh = {*Microbiota/genetics ; Metagenome/genetics ; Deep Learning ; Metallothionein/genetics/metabolism ; Humans ; Software ; }, abstract = {Protein natural diversity offers a vast sequence space for protein engineering, and deep learning enables its detection from metagenomes/proteomes without prior assumptions. DeepMetagenome, a Python-based method, explores protein diversity through modules for training and analyzing sequence datasets. The deep learning model includes Embedding, Conv1D, LSTM, and Dense layers, with sequence feature analysis for data cleaning. Applied to metallothioneins from a database of over 146 million coding features, DeepMetagenome identified over 500 high-confidence metallothionein sequences, outperforming DIAMOND and CNN-based models. It showed stable performance compared to a Transformer-based model over 25 epochs. Among 23 synthesized sequences, 20 exhibited metal resistance. The tool also successfully explored the diversity of three additional protein families and is freely available on GitHub with detailed instructions.}, } @article {pmid39515242, year = {2025}, author = {Wang, Y and Chen, S and Chen, Y and Xu, J and Zhou, J and He, Q and Lin, Z and Xu, KQ and Fan, G}, title = {Structure-activity relationship between crystal plane and pyrite-driven autotrophic denitrification efficacy: Electron transfer and metagenome-based microbial mechanism.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122756}, doi = {10.1016/j.watres.2024.122756}, pmid = {39515242}, issn = {1879-2448}, mesh = {*Denitrification ; Structure-Activity Relationship ; *Sulfides/chemistry/metabolism ; Nitrates/metabolism ; Water Purification ; *Electron Transport/genetics ; *Metagenome/genetics ; Bacteria/enzymology/genetics ; *Iron/chemistry/metabolism ; Electrochemistry ; Oxidation-Reduction ; *Microbiota ; }, abstract = {Pyrite-driven autotrophic denitrification (PAD) has been recognized as a promising treatment technology for nitrate removal. Although the occurrence of PAD has been found in recent years, there is a knowledge gap about effects of crystal plane of pyrite on the performance and mechanism of PAD system. Here, this study investigated the effects of crystal planes ({100}, {111} and {210} ) of single-crystal pyrite on denitrification performance, electron transfer, and microbial mechanism in PAD system. The removal efficiency of nitrate in B-{210} reached 100%, which was 1.67-fold and 2.86-fold higher than that of B-{100} and B-{111}, respectively. X-ray photoelectron spectroscopy and electrochemical results indicated that Fe-S bonds of pyrite with {210} crystal plane were more susceptible to breakage by Fe[3+] oxidation assault, and leaching microbially available Fe[2+] and sulfur intermediates to drive autotrophic denitrification. Metagenomic results suggested that community of functional pyrite-driven denitrifiers varied in response to crystal plane, and abundances of N-S transformation and EET-related microbes and genes in B-{210} notably up-regulated compared to B-{100} and B-{111} . In addition, this work proposed a dual-mode for electron transfer pathway during pyrite oxidation and nitrogen transformation in PAD system. In B-{210}, Fe(II)- and sulfur-driven denitrifiers obtained electron after pyrite oxidation-dissolution, and the enrichment of pyrite-oxidizing bacteria in B-{210} could enhance the electron transfer from pyrite through electron shuttles. This work highlighted that stronger surface reactivity and electron shuttle effect in B-{210} enhanced electron transfer, leading to favorable PAD performance in B-{210} . Overall, this study provides novel insights into the structure-activity relationship between the crystal plane structure of pyrite and denitrification activity in PAD system.}, } @article {pmid39515198, year = {2024}, author = {De Jaeghere, EA and Hamerlinck, H and Tuyaerts, S and Lippens, L and Van Nuffel, AMT and Baiden-Amissah, R and Vuylsteke, P and Henry, S and Trinh, XB and van Dam, PA and Aspeslagh, S and De Caluwé, A and Naert, E and Lambrechts, D and Hendrix, A and De Wever, O and Van de Vijver, KK and Amant, F and Vandecasteele, K and Verhasselt, B and Denys, HG}, title = {Associations of the gut microbiome with outcomes in cervical and endometrial cancer patients treated with pembrolizumab: Insights from the phase II PRIMMO trial.}, journal = {Gynecologic oncology}, volume = {191}, number = {}, pages = {275-286}, doi = {10.1016/j.ygyno.2024.10.020}, pmid = {39515198}, issn = {1095-6859}, mesh = {Humans ; Female ; *Antibodies, Monoclonal, Humanized/adverse effects/therapeutic use/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Middle Aged ; *Uterine Cervical Neoplasms/drug therapy/microbiology/pathology ; *Endometrial Neoplasms/drug therapy/microbiology/pathology ; *Antineoplastic Agents, Immunological/adverse effects/therapeutic use ; Aged ; Adult ; Feces/microbiology ; }, abstract = {BACKGROUND: The phase II PRIMMO trial investigated a pembrolizumab-based regimen in patients with recurrent and/or metastatic cervical (CC) or endometrial (EC) carcinoma who had at least one prior line of systemic therapy. Here, exploratory studies of the gut microbiome (GM) are presented.

METHODS: The microbial composition of 77 longitudinal fecal samples obtained from 35 patients (CC, n = 15; EC, n = 20) was characterized using 16S rRNA gene sequencing. Analyses included assessment of alpha (Shannon index) and beta diversity (weighted UniFrac), unbiased hierarchical clustering, and linear discriminant analysis effect size. Correlative studies with demographics, disease characteristics, safety, efficacy, and immune monitoring data were performed.

RESULTS: Significant enrichment in multiple bacterial taxa was associated with the occurrence or resistance to severe treatment-related adverse events (overall or gastrointestinal toxicity specifically). Consistent differences in GM taxonomic composition before pembrolizumab initiation were observed between patients with favorable efficacy (e.g., enriched with Blautia genus) and those with poor efficacy (e.g., enriched with Enterobacteriaceae family and its higher-level taxa up to the phylum level, as well as Clostridium genus and its Clostridiaceae family). Two naturally occurring GM clusters with distinct bacterial compositions were identified. These clusters showed a more than four-fold differential risk for death (hazard ratio, 4.4 [95 % confidence interval, 1.9 to 10.3], P < 0.001) and were associated with interesting (but non-significant) trends in peripheral immune monitoring data.

CONCLUSION: Although exploratory, this study offers initial insights into the intricate interplay between the GM and clinical outcomes in patients with CC and EC treated with a pembrolizumab-based regimen.

TRIAL REGISTRATION: ClinicalTrials.gov (identifier NCT03192059) and EudraCT Registry (number 2016-001569-97).}, } @article {pmid39513860, year = {2024}, author = {Stupak, A and Kwiatek, M and Gęca, T and Kwaśniewska, A and Mlak, R and Nawrot, R and Goździcka-Józefiak, A and Kwaśniewski, W}, title = {A Virome and Proteomic Analysis of Placental Microbiota in Pregnancies with and without Fetal Growth Restriction.}, journal = {Cells}, volume = {13}, number = {21}, pages = {}, pmid = {39513860}, issn = {2073-4409}, support = {DS 128//Medical University of Lublin/ ; }, mesh = {Humans ; Female ; *Fetal Growth Retardation/virology/metabolism/microbiology ; Pregnancy ; *Proteomics/methods ; *Placenta/virology/metabolism/microbiology ; *Virome ; Adult ; Microbiota ; Proteome/metabolism ; Viral Proteins/metabolism ; Case-Control Studies ; }, abstract = {INTRODUCTION: Metagenomic research has allowed the identification of numerous viruses present in the human body. Viruses may significantly increase the likelihood of developing intrauterine fetal growth restriction (FGR). The goal of this study was to examine and compare the virome of normal and FGR placentas using proteomic techniques.

METHODS: The study group of 18 women with late FGR was compared with 18 control patients with physiological pregnancy and eutrophic fetus. Proteins from the collected afterbirth placentas were isolated and examined using liquid chromatography linked to a mass spectrometer.

RESULTS: In this study, a group of 107 viral proteins were detected compared to 346 in the controls. In total, 41 proteins were common in both groups. In total, 64 proteins occurred only in the study group and indicated the presence of bacterial phages: E. coli, Bacillus, Mediterranenean, Edwardsiella, Propionibacterium, Salmonella, Paenibaciilus and amoebae Mimiviridae, Acanthamoeba polyphaga, Mimivivirus, Pandoravirdae, Miroviridae, Pepper plant virus golden mosaic virus, pol proteins of HIV-1 virus, and proteins of Pandoravirdae, Microviridae, and heat shock proteins of the virus Faustoviridae. Out of 297 proteins found only in the control group, only 2 viral proteins occurred statistically significantly more frequently: 1/hypothetical protein [uncultured Mediterranean phage uvMED] and VP4 [Gokushovirus WZ-2015a].

DISCUSSION: The detection of certain viral proteins exclusively in the control group suggests that they may play a protective role. Likewise, the proteins identified only in the study group could indicate a potentially pathogenic function. A virome study may be used to identify an early infection, evaluate its progress, and possible association with fetal growth restriction. Utilizing this technology, an individualized patient therapy is forthcoming, e.g., vaccines.}, } @article {pmid39513726, year = {2024}, author = {Zou, L and Zhang, Z and Chen, J and Guo, R and Tong, X and Ju, Y and Lu, H and Yang, H and Wang, J and Zong, Y and Xu, X and Jin, X and Xiao, L and Jia, H and Zhang, T and Liu, X}, title = {Unraveling the impact of host genetics and factors on the urinary microbiome in a young population.}, journal = {mBio}, volume = {15}, number = {12}, pages = {e0277324}, pmid = {39513726}, issn = {2150-7511}, mesh = {Humans ; Female ; *Microbiota/genetics ; Male ; Adult ; *Bacteria/genetics/classification/isolation & purification ; Young Adult ; Metagenomics ; China ; Host Microbial Interactions/genetics ; Urinary Tract/microbiology ; Whole Genome Sequencing ; Urine/microbiology ; Cohort Studies ; Adolescent ; }, abstract = {UNLABELLED: The significance of the urinary microbiome in maintaining health and contributing to disease development is increasingly recognized. However, a comprehensive understanding of this microbiome and its influencing factors remains elusive. Utilizing whole metagenomic and whole-genome sequencing, along with detailed metadata, we characterized the urinary microbiome and its influencing factors in a cohort of 1,579 Chinese individuals. Our findings unveil the distinctiveness of the urinary microbiome from other four body sites, delineating five unique urotypes dominated by Gardnerella vaginalis, Sphingobium fluviale, Lactobacillus iners, Variovorax sp. PDC80, and Acinetobacter junii, respectively. We identified 108 host factors significantly influencing the urinary microbiome, collectively explaining 12.92% of the variance in microbial composition. Notably, gender-related factors, including sex hormones, emerged as key determinants in defining urotype groups, microbial composition and pathways, with the urinary microbiome exhibiting strong predictive ability for gender (area under the curve [AUC] = 0.843). Furthermore, we discovered 43 genome-wide significant associations between host genetic loci and specific urinary bacteria, Acinetobacter in particular, linked to eight host loci (P < 5 × 10[-8]). These associations were also modulated by gender and sex hormone levels. In summary, our study provides novel insights into the impact of host genetics and other factors on the urinary microbiome, shedding light on its implications for host health and disease.

IMPORTANCE: The urinary microbiome, essential to human health, reveals its unique qualities in our study of 1,579 Chinese individuals. We identified distinctive microbial profiles, or "urotypes," and uncovered strong gender-related influences, particularly from sex hormones, on these microbial communities. Our research highlights significant genetic associations affecting specific urinary bacteria, indicating a deep interaction between our genetics and our microbiome. These insights not only enhance our understanding of the urinary microbiome's role in health and disease but also open new pathways for personalized medical strategies, making our findings crucial for future diagnostic and therapeutic innovations. This work underscores the intricate relationship between our body's biological processes and the microorganisms within, providing valuable knowledge for both scientific and medical communities.}, } @article {pmid39511594, year = {2024}, author = {Gui, L and Zuo, X and Feng, J and Wang, M and Chen, Z and Sun, Y and Qi, J and Chen, Z and Pathak, JL and Zhang, Y and Cui, C and Zhang, P and Guo, X and Lv, Q and Zhang, X and Zhang, Y and Gu, J and Lin, Z}, title = {Outgrowth of Escherichia is susceptible to aggravation of systemic lupus erythematosus.}, journal = {Arthritis research & therapy}, volume = {26}, number = {1}, pages = {191}, pmid = {39511594}, issn = {1478-6362}, support = {2024A1515010590//Natural Science Foundation of Guangdong Province, China/ ; JCYJ20220530154601004//Shenzhen Science and Technology Innovation Bureau/ ; 2020B1111170008//Guangdong Clinical Research Center of Immune disease/ ; SW201901//Ten & Five Project of the Third Affiliated Hospital of Sun Yat-Sen University/ ; A2675//Distinguished Young Scholar Candidates Program for The Third Affiliated Hospital of Sun Yat-Sen University/ ; }, mesh = {*Lupus Erythematosus, Systemic/microbiology/immunology/metabolism ; *Gastrointestinal Microbiome/physiology/immunology ; Animals ; Humans ; Female ; Mice ; *Mice, Inbred MRL lpr ; Adult ; *Feces/microbiology ; Male ; Dysbiosis/immunology/microbiology ; Middle Aged ; Escherichia coli/genetics/immunology ; Metagenomics/methods ; }, abstract = {BACKGROUND: Systemic lupus erythematosus (SLE) is linked to host gut dysbiosis. Here we performed faecal gut microbiome sequencing to investigate SLE-pathogenic gut microbes and their potential mechanisms.

METHODS: There were 134 healthy controls (HCs) and 114 SLE cases for 16 S ribosomal RNA (rRNA) sequencing and 97 HCs and 124 SLE cases for shotgun metagenomics. Faecal microbial changes and associations with clinical phenotypes were evaluated, and SLE-associated microbial genera were identified in amplicon analysis. Next, metagenomic sequencing was applied for accurate identification of microbial species and discovery of their metabolic pathways and immunogenic peptides both relevant to SLE. Finally, contribution of specific taxa to disease development was confirmed by oral gavage into lupus-prone MRL/lpr mice.

RESULTS: SLE patients had gut microbiota richness reduction and composition alteration, particularly lupus nephritis and active patients. Proteobacteria/Bacteroidetes (P/B) ratio was remarkably up-regulated, and Escherichia was identified as the dominantly expanded genus in SLE, followed by metagenomics accurately located Escherichia coli and Escherichia unclassified species. Significant associations primarily appeared among Escherichia coli, metabolic pathways of purine nucleotide salvage or peptidoglycan maturation and SLE disease activity index (SLEDAI), and between multiple epitopes from Escherichia coli and disease activity or renal involvement phenotype. Finally, gavage with faecal Escherichia revealed that it upregulated lupus-associated serum traits and aggravated glomerular lesions in MRL/lpr mice.

CONCLUSION: We characterize a novel SLE exacerbating Escherichia outgrowth and suggest its contribution to SLE procession may be partially associated with metabolite changes and cross-reactivity of gut microbiota-associated epitopes and host autoantigens. The findings could provide a deeper insight into gut Escherichia in the procession of SLE.}, } @article {pmid39510376, year = {2025}, author = {Huang, Y and You, Y and Wang, W and Chen, YH and Zhang, H and Li, QP and Liu, L and Tong, K and Sun, N and Hao, JR and Gao, C}, title = {Adenosine regulates depressive behavior in mice with chronic social defeat stress through gut microbiota.}, journal = {Neuropharmacology}, volume = {262}, number = {}, pages = {110209}, doi = {10.1016/j.neuropharm.2024.110209}, pmid = {39510376}, issn = {1873-7064}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology/drug effects ; *Adenosine/metabolism ; Male ; Mice ; *Stress, Psychological/metabolism ; *Fecal Microbiota Transplantation ; *Social Defeat ; *Depression/therapy/metabolism ; Dysbiosis ; Humans ; Mice, Inbred C57BL ; Depressive Disorder, Major/metabolism/therapy ; Probiotics/administration & dosage/pharmacology ; Female ; }, abstract = {Major depressive disorder (MDD) is recognized as the most prevalent affective disorder worldwide. Metagenomic studies increasingly support a critical role for dysbiosis of gut microbiota in the development of depression. Previous studies have demonstrated that adenosine alleviates gut dysbiosis, suggesting that elevating adenosine levels could be a novel intervention for MDD; however, the mechanisms underlying this effect remain unclear. This study utilized 16S rRNA gene sequencing, fecal microbiota transplantation (FMT) and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) to test the hypothesis that increased adenosine alleviates depressive behaviors in male mice subjected to chronic social defeat stress (CSDS) through alterations to gut microbiota. The data showed that depression-susceptible (SUS) mice exhibited gut dysbiosis, and FMT from SUS mice increased depression-like behaviors in healthy recipients. In SUS mice, adenosine supplementation ameliorated both depression-like behaviors and abnormalities in gut microbiota, and co-administration of probiotics and adenosine not only mitigated depression-like behaviors but also enhanced gut barrier integrity. By including 83 depressed adolescents and 67 healthy controls, this study found that the level of short-chain fatty acids (SCFAs) in the depression group was reduced, this finding parallels reductions seen in SUS mice and in recipient mice after FMT from SUS donors. Conversely, supplementation with either adenosine or probiotics led increased SCFAs concentrations in the serum of SUS mice. These findings suggest that adenosine may alleviate depression-like behaviors in CSDS mice by modulating the gut microbiota. This effect is likely associated with increased serum SCFAs, metabolites produced by the gut microbiota, following adenosine supplementation. This article is part of the Special Issue on "Personality Disorders".}, } @article {pmid39510362, year = {2024}, author = {Deng, YP and Yao, C and Fu, YT and Zhuo, Y and Zou, JL and Pan, HY and Peng, YY and Liu, GH}, title = {Analyses of the gut microbial composition of domestic pig louse Haematopinus suis.}, journal = {Microbial pathogenesis}, volume = {197}, number = {}, pages = {107106}, doi = {10.1016/j.micpath.2024.107106}, pmid = {39510362}, issn = {1096-1208}, mesh = {Animals ; Swine ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation & purification ; Symbiosis ; Phylogeny ; Swine Diseases/microbiology/parasitology ; Metagenomics ; Computational Biology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Haematopinus suis is an obligatory ectoparasite of the domestic pig, serving as a vector of several swine pathogens and posing great threats to the pig industry. The gut microbiome of lice is thought of an important mediator of their healthy physiology. However, there is a great paucity of lice-associated microbial communities' structure and function. The current study aimed to profile the gut microbiome and to understand the microbial functions of swine lice by metagenomic sequencing and bioinformatics analyses. In total, 102,358 (77.2 %) nonredundant genes were cataloged, by contrast, only a small proportion of genes were assigned to microbial taxa and functional assemblages. Bacteria of known or potential public health significance such as Anaplasma phagocytophilum, Chlamydia trachomatis, Waddlia chondrophila, Bacillus cereus, and Leptotrichia goodfellowii were observed in all samples. The integrated microbial profile further illustrated the evolutionary relevance of endosymbionts and detailed the functional composition, and findings suggested H. suis may acquire adenosylcobalamin by feeding due to an adenosylcobalamin synthesis defect and a lack of complete synthases of endosymbionts. Sucking lice contained fewer functional genes compared with ticks and fleas probably because of the obligate host specificity of parasitic lice. In addition, the genes from the intestines contained encompassed most of the microbial functional genes in sucking lice. A wide range of unknown taxonomic and functional assemblages were discovered, which improves our understanding related to microbial features and physiological activities of sucking lice. In general, this study increases the characterization of the microbiota of lice and offers clues for preventing and controlling lice infestation in swine production in the future.}, } @article {pmid39509330, year = {2024}, author = {Wang, M and Fontaine, S and Jiang, H and Li, G}, title = {ADAPT: Analysis of Microbiome Differential Abundance by Pooling Tobit Models.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {11}, pages = {}, doi = {10.1093/bioinformatics/btae661}, pmid = {39509330}, issn = {1367-4811}, support = {R03DE031296/DE/NIDCR NIH HHS/United States ; }, mesh = {*Microbiota ; Humans ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; *Saliva/microbiology ; Software ; Infant ; Dental Caries/microbiology ; }, abstract = {MOTIVATION: Microbiome differential abundance analysis (DAA) remains a challenging problem despite multiple methods proposed in the literature. The excessive zeros and compositionality of metagenomics data are two main challenges for DAA.

RESULTS: We propose a novel method called "Analysis of Microbiome Differential Abundance by Pooling Tobit Models" (ADAPT) to overcome these two challenges. ADAPT interprets zero counts as left-censored observations to avoid unfounded assumptions and complex models. ADAPT also encompasses a theoretically justified way of selecting non-differentially abundant microbiome taxa as a reference to reveal differentially abundant taxa while avoiding false discoveries. We generate synthetic data using independent simulation frameworks to show that ADAPT has more consistent false discovery rate control and higher statistical power than competitors. We use ADAPT to analyze 16S rRNA sequencing of saliva samples and shotgun metagenomics sequencing of plaque samples collected from infants in the COHRA2 study. The results provide novel insights into the association between the oral microbiome and early childhood dental caries.

The R package ADAPT can be installed from Bioconductor at https://bioconductor.org/packages/release/bioc/html/ADAPT.html or from Github at https://github.com/mkbwang/ADAPT. The source codes for simulation studies and real data analysis are available at https://github.com/mkbwang/ADAPT_example.}, } @article {pmid39509322, year = {2024}, author = {Rödelsperger, C and Röseler, W and Athanasouli, M and Wighard, S and Herrmann, M and Sommer, RJ}, title = {Genome Assembly of the Nematode Rhabditoides Inermis From a Complex Microbial Community.}, journal = {Genome biology and evolution}, volume = {16}, number = {11}, pages = {}, pmid = {39509322}, issn = {1759-6653}, support = {//Max Planck Society/ ; }, mesh = {Animals ; *Phylogeny ; *Genome, Helminth ; Rhabditoidea/genetics/microbiology ; Microbiota ; }, abstract = {Free-living nematodes such as Caenorhabditis elegans and Pristionchus pacificus are powerful model systems for linking specific traits to their underlying genetic basis. To trace the evolutionary history of specific traits or genes, a robust phylogenomic framework is indispensable. In the context of the nematode family Diplogastridae to which P. pacificus belongs, the identity of a sister group has long been debated. In this work, we generated a pseudochromosome level genome assembly of the nematode Rhabditoides inermis, which has previously been proposed as the sister taxon. The genome was assembled from a complex microbial community that is stably associated with R. inermis isolates and that consists of multiple bacteria and a fungus, which we identified as a strain of Vanrija albida. The R. inermis genome spans 173.5Mb that are largely assembled into five pseudochromosomes. This chromosomal configuration likely arose from two recent fusions of different Nigon elements. Phylogenomic analysis did not support a sister group relationship between R. inermis and diplogastrids, but rather supports a sister group relationship between the monophyletic Diplogastridae and a group of genera of Rhabditidae including C. elegans and R. inermis. Thus, our work addresses for the first time the long lasting question about the sister group to diplogastrids at the phylogenomic level and provides with the genomes of R. inermis and the associated fungus V. albida valuable resources for future genomic comparisons.}, } @article {pmid39508593, year = {2024}, author = {Tran, TH and F Escapa, I and Roberts, AQ and Gao, W and Obawemimo, AC and Segre, JA and Kong, HH and Conlan, S and Kelly, MS and Lemon, KP}, title = {Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses.}, journal = {mSystems}, volume = {9}, number = {12}, pages = {e0113224}, pmid = {39508593}, issn = {2379-5077}, support = {//HHS | NIH | National Human Genome Research Institute (NHGRI)/ ; //HHS | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)/ ; R35 GM141806/GM/NIGMS NIH HHS/United States ; K23 AI135090/AI/NIAID NIH HHS/United States ; R01 GM117174/GM/NIGMS NIH HHS/United States ; FPILOT45//Forsyth Institute/ ; R35 GM141806, R01 GM117174//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {*Corynebacterium/genetics/metabolism ; Humans ; *Genome, Bacterial ; *Phylogeny ; Microbiota/genetics ; Genomics ; United States ; Nose/microbiology ; Botswana ; }, abstract = {UNLABELLED: Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum, C. pseudodiphtheriticum, C. accolens, and C. tuberculostearicum. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the United States. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution spanning Africa and North America. All species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent versus accessory genome of each species indicating limited strain-level variability in metabolic capacity. Based on prevalence data, at least two Corynebacterium species likely coexist in the nasal microbiota of 82% of adults. So, it was surprising that core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the U.S. clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in most of the strains in the Botswana clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.

IMPORTANCE: Pangenomic analysis with estimation of functional capabilities facilitates our understanding of the full biologic diversity of bacterial species. We performed systematic genomic, phylogenomic, and pangenomic analyses with qualitative estimation of the metabolic capabilities of four common human nasal Corynebacterium species, along with focused experimental validations, generating a foundational resource. The prevalence of each species in human nasal microbiota is consistent with the common coexistence of at least two species. We identified a notably high level of metabolic conservation within and among species indicating limited options for species to occupy distinct metabolic niches, highlighting the importance of investigating interactions among nasal Corynebacterium species. Comparing strains from two continents, C. pseudodiphtheriticum had restricted geographic strain distribution characterized by an evolutionarily recent loss of assimilatory sulfate reduction in U.S. strains. Our findings contribute to understanding the functions of Corynebacterium within human nasal microbiota and to evaluating their potential for future use as biotherapeutics.}, } @article {pmid39507669, year = {2024}, author = {Buytaers, FE and Berger, N and Van der Heyden, J and Roosens, NHC and De Keersmaecker, SCJ}, title = {The potential of including the microbiome as biomarker in population-based health studies: methods and benefits.}, journal = {Frontiers in public health}, volume = {12}, number = {}, pages = {1467121}, pmid = {39507669}, issn = {2296-2565}, mesh = {Humans ; *Biomarkers/analysis ; *Microbiota ; Population Health ; Health Status ; Public Health ; }, abstract = {The key role of our microbiome in influencing our health status, and its relationship with our environment and lifestyle or health behaviors, have been shown in the last decades. Therefore, the human microbiome has the potential to act as a biomarker or indicator of health or exposure to health risks in the general population, if information on the microbiome can be collected in population-based health surveys or cohorts. It could then be associated with epidemiological participant data such as demographic, clinical or exposure profiles. However, to our knowledge, microbiome sampling has not yet been included as biological evidence of health or exposure to health risks in large population-based studies representative of the general population. In this mini-review, we first highlight some practical considerations for microbiome sampling and analysis that need to be considered in the context of a population study. We then present some examples of topics where the microbiome could be included as biological evidence in population-based health studies for the benefit of public health, and how this could be developed in the future. In doing so, we aim to highlight the benefits of having microbiome data available at the level of the general population, combined with epidemiological data from health surveys, and hence how microbiological data could be used in the future to assess human health. We also stress the challenges that remain to be overcome to allow the use of this microbiome data in order to improve proactive public health policies.}, } @article {pmid39507397, year = {2024}, author = {Wang, H and Wang, H and Crowther, TW and Isobe, K and Reich, PB and Tateno, R and Shi, W}, title = {Metagenomic insights into inhibition of soil microbial carbon metabolism by phosphorus limitation during vegetation succession.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae128}, pmid = {39507397}, issn = {2730-6151}, abstract = {There is growing awareness of the need for regenerative practices in the fight against biodiversity loss and climate change. Yet, we lack a mechanistic understanding of how microbial community composition and functioning are likely to change alongside transition from high-density tillage to large-scale vegetation restoration. Here, we investigated the functional dynamics of microbial communities following a complete vegetation successional chronosequence in a subtropical zone, Southwestern China, using shotgun metagenomics approaches. The contents of total soil phosphorus (P), available P, litter P, and microbial biomass P decreased significantly during vegetation succession, indicating that P is the most critical limiting nutrient. The abundance of genes related to P-uptake and transport, inorganic P-solubilization, organic P-mineralization, and P-starvation response regulation significantly increased with successional time, indicating an increased microbial "mining" for P under P limitation. Multi-analysis demonstrated microbial P limitation strongly inhibits carbon (C) catabolism potential, resulting in a significant decrease in carbohydrate-active enzyme family gene abundances. Nevertheless, over successional time, microorganisms increased investment in genes involved in degradation-resistant compounds (lignin and its aromatic compounds) to acquire P resources in the litter. Our study provides functional gene-level insights into how P limitation during vegetation succession in subtropical regions inhibits soil microbial C metabolic processes, thereby advancing our understanding of belowground C cycling and microbial metabolic feedback during forest restoration.}, } @article {pmid39507337, year = {2024}, author = {Rizzo, C and Dastager, SG and Ay, H}, title = {Editorial: Microbial biodiversity and bioprospecting in polar ecosystems in the genomics era.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1504105}, pmid = {39507337}, issn = {1664-302X}, } @article {pmid39508239, year = {2024}, author = {Dames, NR and Rocke, E and Pitcher, G and Rybicki, E and Pfaff, M and Moloney, CL}, title = {Ecological roles of nano-picoplankton in stratified waters of an embayment in the southern Benguela.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, pmid = {39508239}, issn = {1574-6968}, support = {116142//National Research Foundation/ ; }, mesh = {South Africa ; *Archaea/classification/metabolism/isolation & purification/genetics ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Plankton/classification ; Microbiota ; Seawater/microbiology/chemistry ; Bays/microbiology ; Ecosystem ; Eukaryota/classification/physiology ; }, abstract = {Nano-picoplankton are the dominant primary producers during the postupwelling period in St Helena Bay, South Africa. Their dynamics on short timescales are not well-understood and neither are the community composition, structure, and potential functionality of the surrounding microbiome. Samples were collected over five consecutive days in March 2018 from three depths (1, 25, and 50 m) at a single sampling station in St Helena Bay. There was clear depth-differentiation between the surface and depth in both diversity and function throughout the sampling period for the archaea, bacteria, and eukaryotes. Daily difference in eukaryote diversity, was more pronounced at 1 and 25 m with increased abundances of Syndiniales and Bacillariophyta. Surface waters were dominated by photosynthetic and photoheterotrophic microorganisms, while samples at depth were linked to nitrogen cycling processes, with high abundances of nitrifiers and denitrifiers. Strong depth gradients found in the nutrient transporters for ammonia were good indicators of measured uptake rates. This study showed that nano-picoplankton dynamics were driven by light availability, nutrient concentrations, carbon biomass, and oxygenation. The nano-picoplankton help sustain ecosystem functioning in St Helena Bay through their ecological roles, which emphasizes the need to monitor this size fraction of the plankton.}, } @article {pmid39506101, year = {2024}, author = {Beránková, T and Arora, J and Romero Arias, J and Buček, A and Tokuda, G and Šobotník, J and Hellemans, S and Bourguignon, T}, title = {Termites and subsocial roaches inherited many bacterial-borne carbohydrate-active enzymes (CAZymes) from their common ancestor.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1449}, pmid = {39506101}, issn = {2399-3642}, mesh = {*Isoptera/microbiology/enzymology ; Animals ; *Bacteria/enzymology/genetics ; *Phylogeny ; Gastrointestinal Microbiome ; Cockroaches/microbiology/enzymology ; Metagenome ; Evolution, Molecular ; Bacterial Proteins/metabolism/genetics ; Carbohydrate Metabolism ; }, abstract = {Termites digest wood using Carbohydrate-Active Enzymes (CAZymes) produced by gut bacteria with whom they have cospeciated at geological timescales. Whether CAZymes were encoded in the genomes of their ancestor's gut bacteria and transmitted to modern termites or acquired more recently from bacteria not associated with termites is unclear. We used gut metagenomes from 195 termites and one Cryptocercus, the sister group of termites, to investigate the evolution of termite gut bacterial CAZymes. We found 420 termite-specific clusters in 81 bacterial CAZyme gene trees, including 404 clusters showing strong cophylogenetic patterns with termites. Of the 420 clusters, 131 included at least one bacterial CAZyme sequence associated with Cryptocercus or Mastotermes, the sister group of all other termites. Our results suggest many bacterial CAZymes have been encoded in the genomes of termite gut bacteria since termite origin, indicating termites rely upon many bacterial CAZymes endemic to their guts to digest wood.}, } @article {pmid39505993, year = {2024}, author = {Gulyás, G and Kakuk, B and Dörmő, Á and Járay, T and Prazsák, I and Csabai, Z and Henkrich, MM and Boldogkői, Z and Tombácz, D}, title = {Cross-comparison of gut metagenomic profiling strategies.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1445}, pmid = {39505993}, issn = {2399-3642}, support = {LP2020-8/2020//Magyar Tudományos Akadémia (Hungarian Academy of Sciences)/ ; FK 142676//Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal (NKFI Office)/ ; }, mesh = {*Metagenomics/methods ; Animals ; *Gastrointestinal Microbiome/genetics ; Dogs ; *Feces/microbiology ; Computational Biology/methods ; Software ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Gene Library ; }, abstract = {The rapid advancements in sequencing technologies and bioinformatics have enabled metagenomic research of complex microbial systems, but reliable results depend on consistent laboratory and bioinformatics approaches. Current efforts to identify best practices often focus on optimizing specific steps, making it challenging to understand the influence of each stage on microbial population analysis and compare data across studies. This study evaluated DNA extraction, library construction methodologies, sequencing platforms, and computational approaches using a dog stool sample, two synthetic microbial community mixtures, and various sequencing data sources. Our work, the most comprehensive evaluation of metagenomic methods to date. We developed a software tool, termed minitax, which provides consistent results across the range of platforms and methodologies. Our findings showed that the Zymo Research Quick-DNA HMW MagBead Kit, Illumina DNA Prep library preparation method, and the minitax bioinformatics tool were the most effective for high-quality microbial diversity analysis. However, the effectiveness of pipelines or method combinations is sample-specific, making it difficult to identify a universally optimal approach. Therefore, employing multiple approaches is crucial for obtaining reliable outcomes in microbial systems.}, } @article {pmid39505912, year = {2024}, author = {Mi, J and Jing, X and Ma, C and Shi, F and Cao, Z and Yang, X and Yang, Y and Kakade, A and Wang, W and Long, R}, title = {A metagenomic catalogue of the ruminant gut archaeome.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9609}, pmid = {39505912}, issn = {2041-1723}, mesh = {Animals ; *Ruminants/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Archaea/genetics/classification ; *Genome, Archaeal ; *Metagenome ; Methane/metabolism ; Phylogeny ; Gastrointestinal Tract/microbiology ; }, abstract = {While the ruminant gut archaeome regulates the gut microbiota and hydrogen balance, it is also a major producer of the greenhouse gas methane. However, ruminant gut archaeome diversity within the gastrointestinal tract (GIT) of ruminant animals worldwide remains largely underexplored. Here, we construct a catalogue of 998 unique archaeal genomes recovered from the GITs of ruminants, utilizing 2270 metagenomic samples across 10 different ruminant species. Most of the archaeal genomes (669/998 = 67.03%) belong to Methanobacteriaceae and Methanomethylophilaceae (198/998 = 19.84%). We recover 47/279 previously undescribed archaeal genomes at the strain level with completeness of >80% and contamination of <5%. We also investigate the archaeal gut biogeography across various ruminants and demonstrate that archaeal compositional similarities vary significantly by breed and gut location. The catalogue contains 42,691 protein clusters, and the clustering and methanogenic pathway analysis reveal strain- and host-specific dependencies among ruminant animals. We also find that archaea potentially carry antibiotic and metal resistance genes, mobile genetic elements, virulence factors, quorum sensors, and complex archaeal viromes. Overall, this catalogue is a substantial repository for ruminant archaeal recourses, providing potential for advancing our understanding of archaeal ecology and discovering strategies to regulate methane production in ruminants.}, } @article {pmid39505908, year = {2024}, author = {Xu, B and Song, P and Jiang, F and Cai, Z and Gu, H and Gao, H and Li, B and Liang, C and Qin, W and Zhang, J and Yan, J and Liu, D and Sun, G and Zhang, T}, title = {Large-scale metagenomic assembly provide new insights into the genetic evolution of gut microbiomes in plateau ungulates.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {120}, pmid = {39505908}, issn = {2055-5008}, support = {U20A2012//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023M743743//China Postdoctoral Science Foundation/ ; }, mesh = {*Gastrointestinal Microbiome ; Animals ; *Metagenomics/methods ; *Evolution, Molecular ; China ; *Metagenome ; Bacteria/genetics/classification/isolation & purification ; Phylogeny ; Fatty Acids, Volatile/metabolism ; Genome, Bacterial ; }, abstract = {Trillions of microbes colonize the ungulate gastrointestinal tract, playing a pivotal role in enhancing host nutrient utilization by breaking down cellulose and hemicellulose present in plants. Here, through large-scale metagenomic assembly, we established a catalog of 131,416 metagenome-assembled genomes (MAGs) and 11,175 high-quality species-level genome bins (SGBs) from 17 species of ungulates in China. Our study revealed the convergent evolution of high relative abundances of carbohydrate-active enzymes (CAZymes) in the gut microbiomes of plateau-dwelling ungulates. Notably, two significant factors contribute to this phenotype: structural variations in their gut microbiome genomes, which contain more CAZymes, and the presence of novel gut microbiota species, particularly those in the genus Cryptobacteroides, which are undergoing independent rapid evolution and speciation and have higher gene densities of CAZymes. Furthermore, these enrichment CAZymes in the gut microbiomes are highly enrichment in known metabolic pathways for short-chain fatty acid (SCFA) production. Our findings not only provide a valuable genomic resource for understanding the gut microbiomes of ungulates but also offer fresh insights into the interaction between gut microbiomes and their hosts, as well as the co-adaptation of hosts and their gut microbiomes to their environments.}, } @article {pmid39505900, year = {2024}, author = {Bontemps, Z and Abrouk, D and Venier, S and Vergne, P and Michalet, S and Comte, G and Moënne-Loccoz, Y and Hugoni, M}, title = {Microbial diversity and secondary metabolism potential in relation to dark alterations in Paleolithic Lascaux Cave.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {121}, pmid = {39505900}, issn = {2055-5008}, mesh = {*Caves/microbiology ; *Secondary Metabolism ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Microbiota ; Biodiversity ; Metagenome ; Melanins/metabolism ; }, abstract = {Tourism in Paleolithic caves can cause an imbalance in cave microbiota and lead to cave wall alterations, such as dark zones. However, the mechanisms driving dark zone formation remain unclear. Using shotgun metagenomics in Lascaux Cave's Apse and Passage across two years, we tested metabarcoding-derived functional hypotheses regarding microbial diversity and metabolic potential in dark zones vs unmarked surfaces nearby. Taxonomic and functional metagenomic profiles were consistent across years but divergent between cave locations. Aromatic compound degradation genes were prevalent inside and outside dark zones, as expected from past biocide usage. Dark zones exhibited enhanced pigment biosynthesis potential (melanin and carotenoids) and melanin was evidenced chemically, while unmarked surfaces showed genes for antimicrobials production, suggesting that antibiosis might restrict the development of pigmented microorganisms and dark zone extension. Thus, this work revealed key functional microbial traits associated with dark zone formation, which helps understand cave alteration processes under severe anthropization.}, } @article {pmid39505046, year = {2024}, author = {Liu, Y and Wang, Y and Shi, W and Wu, N and Liu, W and Francis, F and Wang, X}, title = {Enterobacter-infecting phages in nitrogen-deficient paddy soil impact nitrogen-fixation capacity and rice growth by shaping the soil microbiome.}, journal = {The Science of the total environment}, volume = {956}, number = {}, pages = {177382}, doi = {10.1016/j.scitotenv.2024.177382}, pmid = {39505046}, issn = {1879-1026}, mesh = {*Oryza/virology/microbiology ; *Soil Microbiology ; *Enterobacter/virology/physiology ; *Microbiota/physiology ; *Bacteriophages/physiology ; *Soil/chemistry ; *Nitrogen Fixation ; *Nitrogen ; Phylogeny ; }, abstract = {Bacteriophages ("phage") play important roles in nutrient cycling and ecology in environments by regulating soil microbial community structure. Here, metagenomic sequencing showed that a low relative abundance of nitrogen-fixing bacteria but high abundance of Enterobacter-infecting phages in paddy soil where rice plants showed nitrogen deficiency. From soil in the same field, we also isolated and identified a novel virulent phage (named here as Apdecimavirus NJ2) that infects several species of Enterobacter and characterized its impact on nitrogen fixation in the soil and in plants. It has the morphology of the Autographiviridae family, with a dsDNA genome of 39,605 bp, 47 predicted open reading frames and 52.64 % GC content. Based on genomic characteristics, comparative genomics and phylogenetic analysis, Apdecimavirus NJ2 should be a novel species in the genus Apdecimavirus, subfamily Studiervirinae. After natural or sterilized field soil was potted and inoculated with the phage, soil nitrogen-fixation capacity and rice growth were impaired, the abundance of Enterobacter decreased, along with the bacterial community composition and biodiversity changed compared with that of the unadded control paddy soil. Our work provides strong evidence that phages can affect the soil nitrogen cycle by changing the bacterial community. Controlling phages in the soil could be a useful strategy for improving soil nitrogen fixation.}, } @article {pmid39503478, year = {2024}, author = {Sun, H and Liu, X and Wang, T and Liu, S and Zhang, R and Guo, X and Yu, Z and Zhao, Y and Shen, P and Zhang, Y}, title = {Rhizosphere microbiomes are closely linked to seagrass species: a comparative study of three coastal seagrasses.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {12}, pages = {e0175424}, pmid = {39503478}, issn = {1098-5336}, support = {U2106208//NSFC-Shandong Joint Fund/ ; 41976147//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Rhizosphere ; *Microbiota ; *Zosteraceae/microbiology ; China ; Bacteria/classification/genetics/isolation & purification/metabolism ; Soil Microbiology ; Alismatales/microbiology ; Metagenome ; }, abstract = {UNLABELLED: Seagrass meadows are important marine ecosystems in coastal areas, offering ecological and economic services to the mankind. However, these ecosystems are facing declines due to climate changes and human activities. Rhizosphere-associated microbiomes play critical roles in the survival and adaptation of seagrasses. While prior studies have explored the general microbial communities and their roles in seagrass meadows, there is a gap in understanding the specific rhizosphere microbiomes of different seagrass species and their interdependent relationships. Our study analyzed the microbial community composition and their metabolism in the rhizosphere of Ruppia sinensis (RS), Zostera japonica (ZJ), and Zostera marina (ZM) obtained from the coastal area of Shandong, China, using high throughput and metagenome sequencing. We found that Rhodobacteraceae, Desulfocapsaceae, and Sulfurovaceae were enriched in RS, ZJ, and ZM samples, respectively, compared with the other two seagrass species, and the bacterial connections were decreased from RS to ZM and ZJ samples. The abundances of nirKS and norBC, mediating denitrification, were higher in RS samples with 2.38% ± 0.59% and 2.14% ± 0.24%, respectively. RS samples also showed a higher level of genes in assimilatory sulfate reduction but lower levels in dissimilatory sulfate reduction and oxidation, with a greater ability to convert sulfide into L-cysteine and acetate. Metagenome-assembled genomes from metagenome of RS rhizosphere had a higher diversity and were assigned to eight phyla. Our study could provide a typical project to analyze the bacterial community structures and metabolic functions in the rhizosphere microbiomes of different seagrasses.

IMPORTANCE: Seagrasses are indispensable in marine ecosystems, offering numerous critical services, with their health significantly influenced by associated rhizosphere microbiomes. Although studies have investigated the microbial communities and their ecological roles in seagrass meadows, the correlations between rhizosphere microbiome and seagrass species from a particular geographic region are limited. Some studies concentrated on the bacterial composition within the rhizosphere of various seagrasses, but the functional aspects of these microbiomes remain unexplored. Our research delves into this void, revealing that Ruppia sinensis, Zostera japonica, and Zostera marina host diverse bacterial community in the composition, connections, functions, and metabolism, such as nitrogen and sulfur metabolism. Our study revealed that seagrass species play an important role in shaping the rhizosphere microbiomes in an equivalent environment, emphasizing the importance of seagrass species in shaping the rhizosphere microbial communities.}, } @article {pmid39503092, year = {2025}, author = {Wu, Y and You, Y and Wu, L and Du, M and Ibrahim, A and Suo, H and Zhang, F and Zheng, J}, title = {Integrated metagenomics and metatranscriptomics analyses reveal the impacts of different Lactiplantibacillus plantarum strains on microbial communities and metabolic profiles in pickled bamboo shoots.}, journal = {Food chemistry}, volume = {464}, number = {Pt 2}, pages = {141772}, doi = {10.1016/j.foodchem.2024.141772}, pmid = {39503092}, issn = {1873-7072}, mesh = {*Fermentation ; *Metagenomics ; *Lactobacillus plantarum/metabolism/genetics ; *Microbiota ; Plant Shoots/metabolism/chemistry/microbiology ; Metabolome ; Sasa/microbiology/metabolism ; }, abstract = {Effects of two different Lactobacillus plantarum fermentation processes on microbial communities and metabolic functions were evaluated using metagenomics and metatranscriptomics. Dominant species in Lactobacillus plantarum DACN4208 (LPIF8) and DACN4120 (LPIF10) were Lactobacillus pentosus and Lactobacillus plantarum, with Lactiplantibacillus comprised 75.31 % of the microbial community in LPIF10. Metatranscriptomic revealed that LPIF8 had more genes associated with carbohydrate-binding modules and auxiliary activities, totaling 7500 and 4000 genes, respectively. Metabolic reconstruction further showed that LPIF8 had the most genes involved in pyruvate and lactose metabolism, with 633 and 389 genes, respectively. In contrast, LPIF10 fewer genes related to the biosynthesis and metabolism of phenylalanine, tyrosine, and tryptophan. These results indicate that LPIF8 could efficiently improve fermentation efficiency and increase metabolic activity, while LPIF10 exhibited a more moderate and controlled metabolic process. These provide valuable insights into how different starter cultures influence the structure and metabolic functions of microbial communities in pickled bamboo shoots.}, } @article {pmid39500921, year = {2024}, author = {Stewart, RD and Oluwalana-Sanusi, AE and Munzeiwa, WA and Magoswana, L and Chaukura, N}, title = {Profiling the bacterial microbiome diversity and assessing the potential to detect antimicrobial resistance bacteria in wastewater in Kimberley, South Africa.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {26867}, pmid = {39500921}, issn = {2045-2322}, mesh = {*Wastewater/microbiology ; South Africa ; *Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/classification/isolation & purification/drug effects ; RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology ; Phylogeny ; }, abstract = {Wastewater treatment plants (WWTPs) are hotspots for pathogens, and can facilitate horizontal gene transfer, potentially releasing harmful genetic material and antimicrobial resistance genes into the environment. Little information exists on the composition and behavior of microbes in WWTPs, especially in developing countries. This study used environmental DNA (eDNA) techniques to examine the microbiome load of wastewater from WWTPs. The DNA was isolated from wastewater samples collected from the treatment trains of three WWTPs in Kimberley, South Africa, and the microbial diversity and composition was compared through 16 S rRNA gene sequencing. The microbes detected were of the Kingdom Bacteria, and of these, 48.27% were successfully identified to genus level. The majority of reads from the combined bacterial data fall within the class Gammaproteobacteria, which is known to adversely impact ecological and human health. Arcobacteraceae constituted 19% of the bacterial reads, which is expected as this family is widespread in aquatic environments. Interestingly, the most abundant bacterial group was Bacteroides, which contain a variety of antibiotic-resistant members. Overall, various antibiotic-resistant taxa were detected in the wastewater, indicating a concerning level of antibiotic resistance within the bacterial community. Therefore, eDNA analysis can be a valuable tool in monitoring and assessing the bacterial microbiome in wastewater, thus providing important information for the optimization and improvement of wastewater treatment systems and mitigate public health risks.}, } @article {pmid39500545, year = {2024}, author = {Hu, X and Bi, J and Yu, Q and Li, H}, title = {Metagenomics reveals the divergence of gut microbiome composition and function in two common pika species (Ochotona curzoniae and Ochotona daurica) in China.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, doi = {10.1093/femsle/fnae092}, pmid = {39500545}, issn = {1574-6968}, support = {42007026//National Natural Science Foundation of China/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; *Metagenomics ; China ; Animals ; *Lagomorpha/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Archaea/classification/genetics/isolation & purification ; Viruses/genetics/classification/isolation & purification ; }, abstract = {Gut microbiome plays crucial roles in animal adaptation and evolution. However, research on adaptation and evolution of small wild high-altitude mammals from the perspective of gut microbiome is still limited. In this study, we compared differences in intestinal microbiota composition and function in Plateau pikas (Ochotona curzoniae) and Daurian pikas (O. daurica) using metagenomic sequencing. Our results showed that microbial community structure had distinct differences in different pika species. Prevotella, Methanosarcina, Rhizophagus, and Podoviridae were abundant bacteria, archaea, eukaryotes, and viruses in Plateau pikas, respectively. However, Prevotella, Methanosarcina, Ustilago, and Retroviridae were dominated in Daurian pikas. Functional pathways related to carbohydrate metabolism that refer to the utilization of pectin, hemicellulose, and debranching enzymes were abundant in Plateau pikas, while the function for degradation of chitin, lignin, and cellulose was more concentrated in Daurian pikas. Pika gut had abundant multidrug resistance genes, followed by glycopeptide and beta-lactamase resistance genes, as well as high-risk antibiotic resistance genes, such as mepA, tetM, and bacA. Escherichia coli and Klebsiella pneumoniae may be potential hosts of mepA. This research provided new insights for adaptation and evolution of wild animals from perspective of gut microbiome and broadened our understanding of high-risk antibiotic resistance genes and potential pathogens of wild animals.}, } @article {pmid39500537, year = {2024}, author = {Slizovskiy, IB and Bonin, N and Bravo, JE and Ferm, PM and Singer, J and Boucher, C and Noyes, NR}, title = {Factors impacting target-enriched long-read sequencing of resistomes and mobilomes.}, journal = {Genome research}, volume = {34}, number = {11}, pages = {2048-2060}, pmid = {39500537}, issn = {1549-5469}, support = {R01 AI141810/AI/NIAID NIH HHS/United States ; R01 AI173928/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Animals ; *Metagenomics/methods ; Cattle ; Feces/microbiology ; Drug Resistance, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Gastrointestinal Microbiome/genetics ; Interspersed Repetitive Sequences ; Sequence Analysis, DNA/methods ; Metagenome ; Bacteria/genetics/drug effects/classification ; Soil Microbiology ; }, abstract = {We investigated the efficiency of target-enriched long-read sequencing (TELSeq) for detecting antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) within complex matrices. We aimed to overcome limitations associated with traditional antimicrobial resistance (AMR) detection methods, including short-read shotgun metagenomics, which can lack sensitivity, specificity, and the ability to provide detailed genomic context. By combining biotinylated probe-based enrichment with long-read sequencing, we facilitated the amplification and sequencing of ARGs, eliminating the need for bioinformatic reconstruction. Our experimental design included replicates of human fecal microbiota transplant material, bovine feces, pristine prairie soil, and a mock human gut microbial community, allowing us to examine variables including genomic DNA input and probe set composition. Our findings demonstrated that TELSeq markedly improves the detection rates of ARGs and MGEs compared to traditional sequencing methods, underlining its potential for accurate AMR monitoring. A key insight from our research is the importance of incorporating mobilome profiles to better predict the transferability of ARGs within microbial communities, prompting a recommendation for the use of combined ARG-MGE probe sets for future studies. We also reveal limitations for ARG detection from low-input workflows, and describe the next steps for ongoing protocol refinement to minimize technical variability and expand utility in clinical and public health settings. This effort is part of our broader commitment to advancing methodologies that address the global challenge of AMR.}, } @article {pmid39500412, year = {2024}, author = {Regar, RK and Kamthan, M and Gaur, VK and Singh, SP and Mishra, S and Dwivedi, S and Mishra, A and Manickam, N and Nautiyal, CS}, title = {Microbiome divergence across four major Indian riverine water ecosystems impacted by anthropogenic contamination: A comparative metagenomic analysis.}, journal = {Chemosphere}, volume = {368}, number = {}, pages = {143672}, doi = {10.1016/j.chemosphere.2024.143672}, pmid = {39500412}, issn = {1879-1298}, mesh = {*Rivers/microbiology/chemistry ; *Microbiota/drug effects ; India ; *Metagenomics ; *Water Pollutants, Chemical/analysis ; Bacteria/genetics/classification/isolation & purification ; Environmental Monitoring/methods ; Biodiversity ; Ecosystem ; Metals, Heavy/analysis ; Water Microbiology ; Bacteriophages ; }, abstract = {Rivers are critical ecosystems that support biodiversity and local livelihoods. This study aimed to evaluate the effects of metal contamination and anthropogenic activities on microbial and phage community dynamics within major Indian river ecosystems, focusing on the Ganga, Narmada, Cauvery, and Gomti rivers -using metagenomic techniques, Biolog, and ICP-MS analysis. Significant variations in microbial communities were observed both within each river and across the four systems, influenced by ecological factors like geography and hydrology, as well as anthropogenic pressures. Downstream sites consistently exhibited higher microbial diversity, with prevalence of Acidobacteria, Actinobacteria, Verrucomicrobia, Firmicutes, and Nitrospirae dominating, while Proteobacteria and Bacteroides declined. The Ganga River showed a higher abundance of bacteriophages compared to other rivers, which gradually reduced with the increment of anthropogenic impact. Functional gene analysis revealed correlations between carbon utilization and metal resistance in contaminated sites. ICP-MS analysis indicates elevated chromium and lead levels in downstream sites of all rivers compared to upstream sites. Interestingly, pristine upstream sites in the Ganga had higher trace element levels than those in Narmada and Cauvery, likely due to its Himalayan origin. Both the Ganga and Cauvery rivers contained numerous metal resistance genes. The Alaknanda was identified as the primary source of microbial communities, bacteriophages, trace elements, and heavy metals in the Ganga. These findings offer new insights into anthropogenic influences on river microbial dynamics and highlight the need for targeted monitoring and management strategies to preserve river health.}, } @article {pmid39499979, year = {2024}, author = {Zheng, X and Xu, M and Zhang, Z and Yang, L and Liu, X and Zhen, Y and Ye, Z and Wen, J and Liu, P}, title = {Microbial signatures in chronic thromboembolic pulmonary hypertension thrombi: Insights from metagenomic profiling of fresh and organized thrombi.}, journal = {Thrombosis research}, volume = {244}, number = {}, pages = {109204}, doi = {10.1016/j.thromres.2024.109204}, pmid = {39499979}, issn = {1879-2472}, mesh = {Humans ; Female ; Male ; Middle Aged ; *Hypertension, Pulmonary/microbiology ; *Metagenomics/methods ; *Pulmonary Embolism/microbiology ; Thrombosis/microbiology ; Aged ; Chronic Disease ; Adult ; Microbiota ; }, abstract = {OBJECTIVE: Many studies have reported microbial signatures in thrombi at major vascular sites, such as the coronary artery and the middle cerebral artery, which are critical for maintaining proper blood flow and oxygenation. Chronic thromboembolic pulmonary hypertension (CTEPH) is a condition involving non-resolving thrombosis that has not been fully studied. This study explored the microbial taxonomy and functional profiles of both fresh and organized thrombi associated with CTEPH to investigate the role of microbiota in thrombus non-resolving.

METHODS: In this study, 12 CTEPH fresh thrombi and 12 organized thrombi were collected from 14 patients with CTEPH. Metagenomic sequencing was employed to explore the genomic information of all microorganisms in the thrombus samples.

RESULTS: Our data demonstrated a diverse range of microorganisms in CTEPH thrombi, whether fresh or organized. Notably, a considerable proportion (54.7 %) of sequencing data could not be classified into the relative microbial taxa, highlighting the complexity and novelty of the thrombus ecosystem. Although there were no significant differences in microbial community structure between the two groups, the abundance of dominant microbial species varied. Leuconostoc sp. DORA 2, Staphylococcus aureus, and Aliidongia dinghuensis were common dominant species in CTEPH thrombus. Organized thrombus significantly increased the relative abundance of Staphylococcus aureus, which was confirmed to effectively distinguish between organized and fresh thrombi by LeFSe analysis and random forest analysis. Functional annotation using both the KEGG and eggNOG databases revealed that organized thrombi exhibit stronger metabolic functions, particularly in amino acid metabolism.

CONCLUSIONS: Our findings suggest that microbial composition and function may play an important role in thrombus organization. Targeting inflammation to prevent thrombosis presents promising opportunities for further research in this area.}, } @article {pmid39497924, year = {2024}, author = {Li, L and Shao, J and Tong, C and Gao, W and Pan, P and Qi, C and Gao, C and Zhang, Y and Zhu, Y and Chen, C}, title = {Non-tuberculous mycobacteria enhance the tryptophan-kynurenine pathway to induce immunosuppression and facilitate pulmonary colonization.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1455605}, pmid = {39497924}, issn = {2235-2988}, mesh = {Humans ; *Tryptophan/metabolism ; *Kynurenine/metabolism ; *Nontuberculous Mycobacteria ; *Mycobacterium Infections, Nontuberculous/microbiology ; *Lung/microbiology/immunology ; Bronchoalveolar Lavage Fluid/microbiology ; Microbiota ; Metabolic Networks and Pathways ; Pseudomonas aeruginosa/genetics/metabolism ; Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism ; Metabolomics ; Immune Tolerance ; Metagenomics ; }, abstract = {The increasing prevalence of non-tuberculous mycobacterium (NTM) infections alongside tuberculosis (TB) underscores a pressing public health challenge. Yet, the mechanisms governing their infection within the lung remain poorly understood. Here, we integrate metagenomic sequencing, metabolomic sequencing, machine learning classifiers, SparCC, and MetOrigin methods to profile bronchoalveolar lavage fluid (BALF) samples from NTM/TB patients. Our aim is to unravel the intricate interplay between lung microbial communities and NTM/Mycobacterium tuberculosis infections. Our investigation reveals a discernible reduction in the compositional diversity of the lung microbiota and a diminished degree of mutual interaction concomitant with NTM/TB infections. Notably, NTM patients exhibit a distinct microbial community characterized by marked specialization and notable enrichment of Pseudomonas aeruginosa and Staphylococcus aureus, driving pronounced niche specialization for NTM infection. Simultaneously, these microbial shifts significantly disrupt tryptophan metabolism in NTM infection, leading to an elevation of kynurenine. Mycobacterium intracellulare, Mycobacterium paraintracellulare, Mycobacterium abscessus, and Pseudomonas aeruginosa have been implicated in the metabolic pathways associated with the conversion of indole to tryptophan via tryptophan synthase within NTM patients. Additionally, indoleamine-2,3-dioxygenase converts tryptophan into kynurenine, fostering an immunosuppressive milieu during NTM infection. This strategic modulation supports microbial persistence, enabling evasion from immune surveillance and perpetuating a protracted state of NTM infection. The elucidation of these nuanced microbial and metabolic dynamics provides a profound understanding of the intricate processes underlying NTM and TB infections, offering potential avenues for therapeutic intervention and management.}, } @article {pmid39497628, year = {2024}, author = {Steffen, KJ and Sorgen, AA and Fodor, AA and Carroll, IM and Crosby, RD and Mitchell, JE and Bond, DS and Heinberg, LJ}, title = {Early changes in the gut microbiota are associated with weight outcomes over 2 years following metabolic and bariatric surgery.}, journal = {Obesity (Silver Spring, Md.)}, volume = {32}, number = {11}, pages = {1985-1997}, doi = {10.1002/oby.24168}, pmid = {39497628}, issn = {1930-739X}, support = {1R01DK112585/DK/NIDDK NIH HHS/United States ; 3R01DK112585-01S1/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Bariatric Surgery/methods ; Female ; Male ; Middle Aged ; Adult ; *Weight Loss ; Longitudinal Studies ; Body Mass Index ; Treatment Outcome ; Obesity/surgery/microbiology ; Body-Weight Trajectory ; }, abstract = {OBJECTIVE: Metabolic and bariatric surgery (MBS) is associated with substantial, but variable, weight outcomes. The gut microbiome may be a factor in determining weight trajectory, but examination has been limited by a lack of longitudinal studies with robust microbiome sequencing. This study aimed to describe changes in the microbiome and associations with weight outcomes more than 2 years post surgery.

METHODS: Data were collected at two Midwestern U.S.

CENTERS: Adults undergoing primary MBS were assessed before and 1, 6, 12, 18, and 24 months after surgery. BMI and metagenomic sequencing occurred at each assessment. A linear growth mixture model determined class structure for weight trajectory.

RESULTS: A linear growth mixture model of participants (N = 124) revealed a two-class structure; one class had greater sustained weight loss relative to the other. Greater genus-level taxonomic changes in the microbiome composition at each time point were associated with being in the more favorable weight trajectory class, after controlling for surgery type. Higher Proteobacteria relative abundance at 1 month was predictive of percentage weight change at 6, 12, 18, and 24 months (p < 0.05 for all).

CONCLUSIONS: Greater genus-level taxonomic changes in the gut microbiota are associated with improved weight trajectory. Early changes in the gut microbiota may be an important indicator of MBS outcomes and durability.}, } @article {pmid39496275, year = {2024}, author = {Lazar, A and Phillips, RP and Kivlin, S and Bending, GD and Mushinski, RM}, title = {Understanding the ecological versatility of Tetracladium species in temperate forest soils.}, journal = {Environmental microbiology}, volume = {26}, number = {11}, pages = {e70001}, doi = {10.1111/1462-2920.70001}, pmid = {39496275}, issn = {1462-2920}, support = {DESC0016188//U.S. Department of Energy Office of Biological and Environmental Research, Terrestrial Ecosystem Science Program/ ; NE/S007350/1//UK Research and Innovation Natural Environment Research Council/ ; }, mesh = {*Soil Microbiology ; *Forests ; *Soil/chemistry ; Biodiversity ; Mycorrhizae/classification/genetics ; }, abstract = {Although Tetracladium species have traditionally been studied as aquatic saprotrophs, the growing number of metagenomic and metabarcoding reports detecting them in soil environments raises important questions about their ecological adaptability and versatility. We investigated the factors associated with the relative abundance, diversity and ecological dynamics of Tetracladium in temperate forest soils. Through amplicon sequencing of soil samples collected from 54 stands in six forest sites across the eastern United States, we identified 29 distinct Amplicon Sequence Variants (ASVs) representing Tetracladium, with large differences in relative abundance and small changes in ASV community composition among sites. Tetracladium richness was positively related to soil pH, soil temperature, total sulphur and silt content, and negatively related to plant litter quality, such as the lignin-to-nitrogen ratio and the lignocellulose index. Co-occurrence network analysis indicated negative relationships between Tetracladium and other abundant fungal groups, including ectomycorrhizal and arbuscular mycorrhizal fungi. Collectively, our findings highlight the ecological significance of Tetracladium in temperate forest soils and emphasize the importance of site-specific factors and microbial interactions in shaping their distribution patterns and ecological dynamics.}, } @article {pmid39494496, year = {2024}, author = {Su, Q and Li, YC and Zhuang, DH and Liu, XY and Gao, H and Li, D and Chen, Y and Ge, MX and Han, YM and Gao, ZL and Yin, FQ and Zhao, L and Zhang, YX and Yang, LQ and Zhao, Q and Luo, YJ and Zhang, Z and Kong, QP}, title = {Rewiring of Uric Acid Metabolism in the Intestine Promotes High-Altitude Hypoxia Adaptation in Humans.}, journal = {Molecular biology and evolution}, volume = {41}, number = {11}, pages = {}, pmid = {39494496}, issn = {1537-1719}, mesh = {Humans ; *Uric Acid/metabolism ; Male ; Adult ; *Acclimatization ; *Altitude ; *Gastrointestinal Microbiome ; Hypoxia/metabolism ; Altitude Sickness/metabolism ; Intestines/metabolism ; Feces ; Adaptation, Physiological ; Longitudinal Studies ; China ; }, abstract = {Adaptation to high-altitude hypoxia is characterized by systemic and organ-specific metabolic changes. This study investigates whether intestinal metabolic rewiring is a contributing factor to hypoxia adaptation. We conducted a longitudinal analysis over 108 days, with seven time points, examining fecal metabolomic data from a cohort of 46 healthy male adults traveling from Chongqing (a.s.l. 243 m) to Lhasa (a.s.l. 3,658 m) and back. Our findings reveal that short-term hypoxia exposure significantly alters intestinal metabolic pathways, particularly those involving purines, pyrimidines, and amino acids. A notable observation was the significantly reduced level of intestinal uric acid, the end product of purine metabolism, during acclimatization (also called acclimation) and additional two long-term exposed cohorts (Han Chinese and Tibetans) residing in Shigatse, Xizang (a.s.l. 4,700 m), suggesting that low intestinal uric acid levels facilitate adaptation to high-altitude hypoxia. Integrative analyses with gut metagenomic data showed consistent trends in intestinal uric acid levels and the abundance of key uric acid-degrading bacteria, predominantly from the Lachnospiraceae family. The sustained high abundance of these bacteria in the long-term resident cohorts underscores their essential role in maintaining low intestinal uric acid levels. Collectively, these findings suggest that the rewiring of intestinal uric acid metabolism, potentially orchestrated by gut bacteria, is crucial for enhancing human resilience and adaptability in extreme environments.}, } @article {pmid39494289, year = {2024}, author = {Rueangmongkolrat, N and Uthaipaisanwong, P and Kusonmano, K and Pruksangkul, S and Sonthiphand, P}, title = {The role of microbiomes in cooperative detoxification mechanisms of arsenate reduction and arsenic methylation in surface agricultural soil.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18383}, pmid = {39494289}, issn = {2167-8359}, mesh = {*Soil Microbiology ; *Microbiota ; *Arsenates/metabolism ; *Arsenic/metabolism ; *Soil Pollutants/metabolism ; Methylation ; *Agriculture/methods ; Soil/chemistry ; Bacteria/metabolism/genetics/classification/isolation & purification ; Metagenomics ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbial arsenic (As) transformations play a vital role in both driving the global arsenic biogeochemical cycle and determining the mobility and toxicity of arsenic in soils. Due to the complexity of soils, variations in soil characteristics, and the presence and condition of overlying vegetation, soil microbiomes and their functional pathways vary from site to site. Consequently, key arsenic-transforming mechanisms in soil are not well characterized. This study utilized a combination of high-throughput amplicon sequencing and shotgun metagenomics to identify arsenic-transforming pathways in surface agricultural soils. The temporal and successional variations of the soil microbiome and arsenic-transforming bacteria in agricultural soils were examined during tropical monsoonal dry and wet seasons, with a six-month interval. Soil microbiomes of both dry and wet seasons were relatively consistent, particularly the relative abundance of Chloroflexi, Gemmatimonadota, and Bacteroidota. Common bacterial taxa present at high abundance, and potentially capable of arsenic transformations, were Bacillus, Streptomyces, and Microvirga. The resulting shotgun metagenome indicated that among the four key arsenic-functional genes, the arsC gene exhibited the highest relative abundance, followed by the arsM, aioA, and arrA genes, in declining sequence. Gene sequencing data based on 16S rRNA predicted only the arsC and aioA genes. Overall, this study proposed that a cooperative mechanism involving detoxification through arsenate reduction and arsenic methylation was a key arsenic transformation in surface agricultural soils with low arsenic concentration (7.60 to 10.28 mg/kg). This study significantly advances our knowledge of arsenic-transforming mechanisms interconnected with microbial communities in agricultural soil, enhancing pollution control measures, mitigating risks, and promoting sustainable soil management practices.}, } @article {pmid39490992, year = {2024}, author = {Cansdale, A and Chong, JPJ}, title = {MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {226}, pmid = {39490992}, issn = {2049-2618}, mesh = {*Metagenomics/methods ; *Metagenome ; Software ; Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics/classification ; Humans ; }, abstract = {BACKGROUND: Metagenomics, the whole genome sequencing of microbial communities, has provided insight into complex ecosystems. It has facilitated the discovery of novel microorganisms, explained community interactions and found applications in various fields. Advances in high-throughput and third-generation sequencing technologies have further fuelled its popularity. Nevertheless, managing the vast data produced and addressing variable dataset quality remain ongoing challenges. Another challenge arises from the number of assembly and binning strategies used across studies. Comparing datasets and analysis tools is complex as it requires the quantitative assessment of metagenome quality. The inherent limitations of metagenomic sequencing, which often involves sequencing complex communities, mean community members are challenging to interrogate with traditional culturing methods leading to many lacking reference sequences. MIMAG standards aim to provide a method to assess metagenome quality for comparison but have not been widely adopted.

RESULTS: To address the need for simple and quick metagenome quality assignation, here we introduce the pipeline MAGqual (Metagenome-Assembled Genome qualifier) and demonstrate its effectiveness at determining metagenomic dataset quality in the context of the MIMAG standards.

CONCLUSIONS: The MAGqual pipeline offers an accessible way to evaluate metagenome quality and generate metadata on a large scale. MAGqual is built in Snakemake to ensure readability and scalability, and its open-source nature promotes accessibility, community development, and ease of updates. MAGqual is built in Snakemake, R, and Python and is available under the MIT license on GitHub at https://github.com/ac1513/MAGqual . Video Abstract.}, } @article {pmid39490825, year = {2024}, author = {Liang, W and Yan, D and Zhang, M and Wang, J and Ni, D and Yun, S and Wei, X and Zhang, L and Fu, H}, title = {Unraveling methanogenesis processes and pathways for Quaternary shallow biogenic gas in aquifer systems through geochemical, genomic and transcriptomic analyses.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {177189}, doi = {10.1016/j.scitotenv.2024.177189}, pmid = {39490825}, issn = {1879-1026}, mesh = {*Methane/metabolism ; *Groundwater/chemistry/microbiology ; China ; Transcriptome ; Microbiota ; Gene Expression Profiling ; Genomics ; Environmental Monitoring ; }, abstract = {Shallow biogenic gas is crucial in global warming and carbon cycling. Considering the knowledge gap in the understanding of methanogenesis and metabolic mechanisms within shallow groundwater systems, we investigated Quaternary shallow biogenic gas resources from the Hetao Basin in North China, which were previously underexplored. We systematically analyzed the genesis of gas and formation water, microbial communities, methanogenic processes, and pathways using geochemistry, genomics, and transcriptomics. Our findings indicated that active freshwater environments are conducive to microbial activity and the generation of primary microbial gases. A diverse range of microbes with functions, such as hydrolysis (e.g., Caulobacter), acidogenesis, and hydrogen production (e.g., Sediminibacterium), synergistically contributed to the methanogenic process. Methanogens predominantly comprised hydrogenotrophic methanogens (e.g., Methanobacteriales), although H2-dependent methylotrophic methanogens (e.g., Methanofastidiosa) were also prevalent. The metabolic processes of the different methanogenic pathways were revealed based on functional gene analysis and mapping results. Furthermore, the composition of the community structure, functional predictions, metagenomics, and metatranscriptomics underscored the contribution of the hydrogenotrophic pathway, which ranged from 52.22 % to 79.23 %. The aceticlastic pathway exhibited high gene abundance and was primarily associated with methylotrophs and other potential pathways. The H2-dependent methylotrophic methanogenesis pathway was constrained by low metabolic activity. By revealing the methane production mechanism of biogenic gas in shallow aquifer systems, this study provides a new perspective and profound comprehension of its ecological and environmental implications worldwide.}, } @article {pmid39490764, year = {2024}, author = {Witkabel, P and Abendroth, C}, title = {A systematic literature review of microbial anammox consortia in UASB/ EGSB-reactors.}, journal = {Chemosphere}, volume = {367}, number = {}, pages = {143630}, doi = {10.1016/j.chemosphere.2024.143630}, pmid = {39490764}, issn = {1879-1298}, mesh = {*Bioreactors/microbiology ; *Bacteria/metabolism/genetics/classification ; *Oxidation-Reduction ; *Waste Disposal, Fluid/methods ; *Wastewater/microbiology ; *Archaea/metabolism/genetics ; Ammonium Compounds/metabolism ; Microbial Consortia ; Anaerobiosis ; Ammonia/metabolism ; }, abstract = {Anaerobic ammonium oxidation (anammox) poses an emerging research field as it can outstand previous processes of biological wastewater treatment in terms of efficiency and costs. Anammox bacteria have the ability to metabolise NH4[+] and NO2[-] to produce N2 under anaerobic conditions. Despite numerous studies, there is a lack of research on the co-occurrence and interrelationship of the predominant microbes that inhabit anammox-related processes. This systematic literature review follows the PSALSAR approach to assess metagenomic data on anammox bacteria and functional microbes in upstream reactors. Essential information on the physiology, metabolic pathways and inhibitory effects of anammox bacteria are reviewed and functional bacteria such as ammonia-oxidising bacteria (AOB), nitrite-oxidising bacteria (NOB), ammonia-oxidising Archaea (AOA) and denitrifying bacteria are identified. Candidatus Kuenenia and Candidatus Brocadia were the most frequently sequenced genera in the observed literature. Pseudomonadota, Chloroflexota and Bacteroidota were prevalent regardless of crucial operational parameters and configurations that affect the microbial community. Interrelationship analysis revealed a positive association between the versatility of a phylum's metabolism and its presence in the observed wastewater treatment literature. Several groups, such as Calditrichota, Myxococcota and Deinococcota are highly underrepresented, a finding that should be investigated in more detail. No evidence was found to suggest that high anammox ratios are correlated with high nitrogen removal efficiencies, as some studies found high efficiency despite low anammox abundance (<1%).}, } @article {pmid39490442, year = {2024}, author = {Gregoris, K and Pope, WH}, title = {Extraction of high-quality metagenomic DNA from the lichens Flavoparmelia caperata and Peltigera membranacea.}, journal = {Journal of microbiological methods}, volume = {227}, number = {}, pages = {107065}, doi = {10.1016/j.mimet.2024.107065}, pmid = {39490442}, issn = {1872-8359}, mesh = {*Lichens ; *Metagenomics/methods ; DNA, Fungal/genetics/isolation & purification ; Polymerase Chain Reaction/methods ; Microbiota/genetics ; Metagenome ; Ascomycota/genetics/classification/isolation & purification/chemistry ; }, abstract = {Lichens are composite organisms found throughout temperate terrestrial forests, with species-specific associations with industrial air pollution. Metagenomic analysis of lichen samples requires robust nucleic acid extraction methodology, a process that is challenging due to the protective cortex layers, high polysaccharide content, and the vast diversity of the internal microbiome. Our method includes physical lysis through garnet bead beating, chemical lysis using a sodium dodecyl sulfate buffer, phenol:chloroform:isoamyl alcohol extraction, and ethanol precipitation. The method was tested on three different lichen samples from two distinct species and yielded metagenomic DNA suitable for sequencing and PCR amplification. This procedure addresses the issues associated with DNA extraction from lichen using common laboratory equipment and reagents without the utilization of liquid nitrogen. This paper presents a cost-effective and accessible DNA extraction method for obtaining high-quality genetic material from dried and preserved lichen specimens.}, } @article {pmid39490096, year = {2025}, author = {Ji, J and Zhao, Y and Wu, G and Hu, F and Yang, H and Bai, Z and Jin, B and Yang, X}, title = {Responses of endogenous partial denitrification process to acetate and propionate as carbon sources: Nitrite accumulation performance, microbial community dynamic changes, and metagenomic insights.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122680}, doi = {10.1016/j.watres.2024.122680}, pmid = {39490096}, issn = {1879-2448}, mesh = {*Denitrification ; *Nitrites/metabolism ; *Propionates/metabolism ; *Carbon/metabolism ; *Acetates/metabolism ; Bioreactors ; Microbiota ; Nitrates/metabolism ; }, abstract = {Endogenous partial denitrification (EPD) offered a promising pathway for supplying nitrite to anammox, and it also enabled energy-efficient and cost-effective nitrogen removal. However, information about the impact of different carbon sources on the EPD system was limited, and the metabolic mechanisms remained unclear. This study operated the EPD system for 180 days with various acetate and propionate ratios over eight phases. The nitrate-to-nitrite transformation ratio (NTR) decreased from 81.7 % to 0.4 % as the acetate/propionate (Ac/Pr) ratio shifted from 3:0 to 0:3, but the NTR returned to 86.1 % after propionate was replaced with acetate. Typical cycles indicated that PHB (126.8 and 133.9 mg COD/g VSS, respectively) was mainly stored, facilitating a higher NTR (87.8 % and 67.7 %, respectively) on days 58 and 180 in the presence of acetate. In contrast, on day 158 in the presence of propionate, PHV (84.8 mg COD/g VSS) was predominantly stored, resulting in negligible nitrite accumulation (0.2 mg N/L). Metagenomic analysis revealed that the microbial community structure did not significantly change, and the (narGHI+napAB)/nirKS ratio consistently exceeded 7:2, despite variations in the carbon source. Compared with acetate, propionate as carbon source reduced the abundance of genes encoding NADH-producing enzymes (e.g., mdh), likely owing to a shift in PHAs synthesis and degradation pathways. Consequently, limited NADH affected electron distribution and transfer rates, thereby decreasing the nitrate reduction rate and causing nitrite produced by narGHI and napAB to be immediately reduced by nirKS. This study provided new insights and guidance for EPD systems to manage the conditions of carbon deficiency or complex carbon sources.}, } @article {pmid39487149, year = {2024}, author = {Sato, T and Abe, K and Koseki, J and Seto, M and Yokoyama, J and Akashi, T and Terada, M and Kadowaki, K and Yoshida, S and Yamashiki, YA and Shimamura, T}, title = {Survivability and life support in sealed mini-ecosystems with simulated planetary soils.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {26322}, pmid = {39487149}, issn = {2045-2322}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Ecosystem ; Ecological Systems, Closed ; Microbiota ; Life Support Systems ; Space Flight ; Extraterrestrial Environment ; Groundwater/microbiology ; Plants/microbiology/metabolism ; Cyanobacteria/growth & development/metabolism/physiology ; Animals ; }, abstract = {Establishing a sustainable life-support system for space exploration is a formidable challenge due to the vast distances, high costs, and environmental differences from Earth. Building upon the lessons from the Biosphere 2 experiment, we introduce the novel "Ecosphere" and "Biosealed" systems, self-sustaining ecosystems within customizable, enclosed containers. These systems incorporate terrestrial ecosystems and groundwater layers, offering a potential model for transplanting Earth-like biomes to extraterrestrial environments. Over 4 years, we conducted rigorous experiments and analyses to understand the dynamics of these enclosed ecosystems. We successfully mitigated moisture deficiency, a major obstacle to plant growth, by incorporating groundwater layers. Additionally, we quantified microbial communities proliferating in specific soils, including simulated lunar and Ryugu asteroid regolith, enhance plant cultivation in space environments. Metagenomic analysis of these simulated space soils revealed diverse microbial populations and their crucial role in plant growth and ecosystem stability. Notably, we identified symbiotic relationships between plants and Cyanobacteria, enhancing oxygen production, and demonstrated the potential of LED lighting as an alternative light source for plant cultivation in sun-limited space missions. We also confirmed the survival of fruit flies within these systems, relying on plant-produced oxygen and photosynthetic bacteria. Our research provides a comprehensive framework for developing future space life-support systems. The novelty of our work lies in the unique design of our enclosed ecosystems, incorporating groundwater layers and simulated extraterrestrial soils, and the detailed analysis of microbial communities within these systems. These findings offer valuable insights into the challenges and potential solutions for establishing sustainable human habitats in space, including the importance of microbial management and potential health concerns related to microbial exposure.}, } @article {pmid39483461, year = {2024}, author = {Chen, G and Ren, Q and Zhong, Z and Li, Q and Huang, Z and Zhang, C and Yuan, H and Feng, Z and Chen, B and Wang, N and Feng, Y}, title = {Exploring the gut microbiome's role in colorectal cancer: diagnostic and prognostic implications.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1431747}, pmid = {39483461}, issn = {1664-3224}, mesh = {*Colorectal Neoplasms/microbiology/diagnosis/immunology/etiology ; Humans ; *Gastrointestinal Microbiome/immunology ; Prognosis ; Animals ; Biomarkers, Tumor ; Early Detection of Cancer ; Metagenomics/methods ; }, abstract = {The intricate interplay between the gut microbiome and colorectal cancer (CRC) presents novel avenues for early diagnosis and prognosis, crucial for improving patient outcomes. This comprehensive review synthesizes current findings on the gut microbiome's contribution to CRC pathogenesis, highlighting its potential as a biomarker for non-invasive CRC screening strategies. We explore the mechanisms through which the microbiome influences CRC, including its roles in inflammation, metabolism, and immune response modulation. Furthermore, we assess the viability of microbial signatures as predictive tools for CRC prognosis, offering insights into personalized treatment approaches. Our analysis underscores the necessity for advanced metagenomic studies to elucidate the complex microbiome-CRC nexus, aiming to refine diagnostic accuracy and prognostic assessment in clinical settings. This review propels forward the understanding of the microbiome's diagnostic and prognostic capabilities, paving the way for microbiome-based interventions in CRC management.}, } @article {pmid39482450, year = {2024}, author = {Gao, L and Rao, MPN and Liu, YH and Wang, PD and Lian, ZH and Abdugheni, R and Jiang, HC and Jiao, JY and Shurigin, V and Fang, BZ and Li, WJ}, title = {SALINITY-Induced Changes in Diversity, Stability, and Functional Profiles of Microbial Communities in Different Saline Lakes in Arid Areas.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {135}, pmid = {39482450}, issn = {1432-184X}, support = {2021FY100900//National Science and Technology Fundamental Resources Investigation Program of China/ ; 2022D01A154//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022B0202110001//Key-Area Research and Development Programof Guangdong Province/ ; }, mesh = {*Lakes/microbiology/chemistry ; *Salinity ; *Archaea/genetics/classification/isolation & purification ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Biodiversity ; Geologic Sediments/microbiology ; Phylogeny ; Desert Climate ; Ecosystem ; }, abstract = {Saline lakes, characterized by high salinity and limited nutrient availability, provide an ideal environment for studying extreme halophiles and their biogeochemical processes. The present study examined prokaryotic microbial communities and their ecological functions in lentic sediments (with the salinity gradient and time series) using 16S rRNA amplicon sequencing and a metagenomic approach. Our findings revealed a negative correlation between microbial diversity and salinity. The notable predominance of Archaea in high-salinity lakes signified a considerable alteration in the composition of the microbial community. The results indicate that elevated salinity promotes homogeneous selection pressures, causing substantial alterations in microbial diversity and community structure, and simultaneously hindering interactions among microorganisms. This results in a notable decrease in the complexity of microbial ecological networks, ultimately influencing the overall ecological functional responses of microbial communities such as carbon fixation, sulfur, and nitrogen metabolism. Overall, our findings reveal salinity drives a notable predominance of Archaea, selects for species adapted to extreme conditions, and decreases microbial community complexity within saline lake ecosystems.}, } @article {pmid39488668, year = {2024}, author = {Geat, N and Singh, D and Saha, P and Jatoth, R and Babu, PL and Devi, GSR and Lakhran, L and Singh, D}, title = {Deciphering Phyllomicrobiome of Cauliflower Leaf: Revelation by Metagenomic and Microbiological Analysis of Tolerant and Susceptible Genotypes Against Black Rot Disease.}, journal = {Current microbiology}, volume = {81}, number = {12}, pages = {439}, pmid = {39488668}, issn = {1432-0991}, mesh = {*Plant Diseases/microbiology ; *Plant Leaves/microbiology ; *Microbiota/genetics ; *Genotype ; *Brassica/microbiology ; *Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Xanthomonas campestris/genetics ; Phylogeny ; High-Throughput Nucleotide Sequencing ; }, abstract = {Understanding the phyllomicrobiome dynamics in cauliflower plants holds significant promise for enhancing crop resilience against black rot disease, caused by Xanthomonas campestris pv. campestris. In this study, the culturable microbiome and metagenomic profile of tolerant (BR-161) and susceptible (Pusa Sharad) cauliflower genotypes were investigated to elucidate microbial interactions associated with disease tolerance. Isolation of phyllospheric bacteria from asymptomatic and black rot disease symptomatic leaves of tolerant and susceptible cultivars yielded 46 diverse bacterial isolates. Molecular identification via 16S rRNA sequencing revealed differences in the diversity of microbial taxa between genotypes and health conditions. Metagenomic profiling using next-generation sequencing elucidated distinct microbial communities, with higher diversity observed in black rot disease symptomatic leaf of BR-161. Alpha and beta diversity indices highlighted differences in microbial community structure and composition between genotypes and health conditions. Taxonomic analysis revealed a core microbiome consisting of genera such as Xanthomonas, Psychrobacillus, Lactobacillus, and Pseudomonas across all the samples. Validation through microbiological methods confirmed the presence of these key genera. The findings provide novel insights into the phyllomicrobiome of black rot-tolerant and susceptible genotypes of cauliflower. Harnessing beneficial microbial communities identified in this study offers promising avenues for developing sustainable strategies to manage black rot disease and enhance cauliflower crop health and productivity.}, } @article {pmid39487448, year = {2024}, author = {Kosch, TA and Torres-Sánchez, M and Liedtke, HC and Summers, K and Yun, MH and Crawford, AJ and Maddock, ST and Ahammed, MS and Araújo, VLN and Bertola, LV and Bucciarelli, GM and Carné, A and Carneiro, CM and Chan, KO and Chen, Y and Crottini, A and da Silva, JM and Denton, RD and Dittrich, C and Espregueira Themudo, G and Farquharson, KA and Forsdick, NJ and Gilbert, E and Che, J and Katzenback, BA and Kotharambath, R and Levis, NA and Márquez, R and Mazepa, G and Mulder, KP and Müller, H and O'Connell, MJ and Orozco-terWengel, P and Palomar, G and Petzold, A and Pfennig, DW and Pfennig, KS and Reichert, MS and Robert, J and Scherz, MD and Siu-Ting, K and Snead, AA and Stöck, M and Stuckert, AMM and Stynoski, JL and Tarvin, RD and Wollenberg Valero, KC and , }, title = {The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1025}, pmid = {39487448}, issn = {1471-2164}, mesh = {Animals ; *Amphibians/genetics ; *Genomics/methods ; Conservation of Natural Resources/methods ; Genome ; }, abstract = {Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to "leap" to the next level.}, } @article {pmid39486340, year = {2024}, author = {Zhang, H and Cheng, S and Yan, W and Zhang, Q and Jiang, B and Xing, Y and Zhang, B}, title = {Interplay between vanadium distribution and microbial community in soil-plant system.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136303}, doi = {10.1016/j.jhazmat.2024.136303}, pmid = {39486340}, issn = {1873-3336}, mesh = {*Vanadium/metabolism ; *Soil Microbiology ; *Soil Pollutants/metabolism ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Microbiota ; Bacteria/metabolism/genetics/classification ; Biodegradation, Environmental ; Plant Roots/microbiology/metabolism ; }, abstract = {Soil-plant system play an essential role in distribution and transformation of vanadium (V). V shapes the diversity of soil communities, while soil microorganisms mediate V transformation. Plants also absorb V from surrounding soil. However, the study of microbial response to V stress in different soil-plant compartments is limited, and the metabolic functions driving V transformation across these systems remain elusive. The study investigates the distribution of V in soil-plant systems nearby a V smelter. 16S rRNA sequencing and metagenomics are utilized to reveal the microbial adaptation and V transformation in bulk soil, rhizosphere, and endosphere. Bothriochloa ischaemum (L.) Keng. (BK) exhibits higher phytoextraction potential (TF = 0.74 ± 0.26). Environmental variables, including pH, V, OM, and AP, show significant (p < 0.05) influence in soil community composition, with homogeneous selection governing the assembly processes in bulk soil and rhizosphere, while stochastic process dominates endospheric assembly. Metagenomic investigation revealed a coordinated metabolic pathway between functional taxa in soil and plants, which lead to root uptake and translocation. V stress is mitigated through Nocardioide, Microvirga, and Solirubrobacter, putatively harboring V(V) reduction genes n arG and mtrC in soil. In rhizosphere, citrate synthase gltA and alkaline phosphatase phoD exhibit functional potential to facilitate formation of V-complexation to increase V mobility. In endoshere, endophytic Enterobacter further detoxifies V(V), and likely promotes V translocation through siderophore biosynthesis gene, iucA. These findings enhance our understanding on interplay between V and microbial community in soil-plant systems, which is instrumental in developing mitigation plan for V contaminated sites.}, } @article {pmid39485561, year = {2024}, author = {Achudhan, AB and Saleena, LM}, title = {Comparative genomic analysis and characterization of novel high-quality draft genomes from the coal metagenome.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {12}, pages = {370}, pmid = {39485561}, issn = {1573-0972}, mesh = {*Coal/microbiology ; *Metagenome ; *Phylogeny ; *Bacteria/genetics/classification ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Genomics/methods ; Metagenomics/methods ; Microbiota/genetics ; DNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Coal, a sedimentary rock harbours a complex microbial community that plays a significant role in its formation and characteristics. However, coal metagenome sequencing and studies were less, limiting our understanding of this complex ecosystem. This study aimed to reconstruct high-quality metagenome-assembled genomes (MAGs) from the coal sample collected in the Neyveli mine to explore the unrevealed diversity of the coal microbiome. Using Illumina sequencing, we obtained high-quality raw reads in FASTQ format. Subsequently, de novo assembly and binning with metaWRAP software facilitated the reconstruction of coal MAGs. Quality assessment using CheckM identified 10 High-Quality MAGs (HQ MAGs), 7 medium-quality MAGs (MQ MAGs), and 6 low-quality MAGs (LQ MAGs). Further analysis using GTDB-Tk revealed four HQ MAGs as known species like Dermacoccus abyssi, Sphingomonas aquatilis, Acinetobacter baumannii, and Burkholderia cenocepacia. The remaining six HQ MAGs were classified as Comamonas, Arthrobacter, Noviherbaspirillum, Acidovorax, Oxalicibacterium, and Bordetella and designated as novel genomes by the validation of digital DNA-DNA hybridization (dDDH). Phylogenetic analysis and further pangenome analysis across the phylogenetic groups revealed a similar pattern with a high proportion of cloud genes. We further analysed the functional potential of these MAGs and closely related genomes using COG. The comparative functional genomics revealed that novel genomes are highly versatile, potentially reflecting adaptations to the coal environment. BlastKOALA was used to conduct a detailed analysis of the metabolic pathways associated with the MAGs. This study highlights the comparative genomic analysis of novel coal genomes with their closely related genomes to understand the evolutionary relationships and functional properties.}, } @article {pmid39485064, year = {2024}, author = {Feng, L and Guo, Z and Yao, W and Mu, G and Zhu, X}, title = {Metagenomics and Untargeted Metabolomics Analysis Revealed the Probiotic and Postbiotic Derived from Lactiplantibacillus plantarum DPUL F232 Alleviate Whey Protein-Induced Food Allergy by Reshaping Gut Microbiota and Regulating Key Metabolites.}, journal = {Journal of agricultural and food chemistry}, volume = {72}, number = {45}, pages = {25436-25448}, doi = {10.1021/acs.jafc.4c08203}, pmid = {39485064}, issn = {1520-5118}, mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Metabolomics ; *Whey Proteins/metabolism ; *Metagenomics ; *Rats, Sprague-Dawley ; Male ; Humans ; Immunoglobulin E/immunology/blood ; Food Hypersensitivity/immunology ; Lactobacillus plantarum ; Female ; }, abstract = {Postbiotics have emerged as a promising alternative to probiotics. However, it remains unclear whether postbiotics can exert regulatory effects on intestinal flora and metabolism as probiotics. Thus, we investigated the effects of probiotic and postbiotic in rats with whey protein-induced food allergy, which demonstrated that postbiotic intervention effectively alleviated allergy symptoms, reduced serum immunoglobulin E (IgE) and mast cell protease-1 (mMCP-1) levels, and regulated the type helper 1 cell/2 cell (Th1/Th2) balance in both serum and spleen. Metagenomic analysis revealed that postbiotics induced more significant changes in intestinal flora. Untargeted metabolomics analysis showed that both probiotics and postbiotics significantly up-regulated various differential metabolites, which were negatively correlated with immune indices, including malvidin-3-glucoside, 3,4-dihydroxymandelic acid, nicotinamide, triterpenoids, pirbuterol, and 4-hydroxybenzoic acid. This study confirms that postbiotics can alleviate food allergies and regulate intestinal flora and metabolites, which provides a valuable reference for the use of postbiotics in mitigating allergic diseases through gut microbiota and metabolite modulation.}, } @article {pmid39482414, year = {2024}, author = {Virachabadoss, VRA and Appavoo, MS and Paramasivam, KS and Karthikeyan, SV and Govindan, D}, title = {The addition of humic acid into soil contaminated with microplastics enhanced the growth of black gram (Vigna mungo L. Hepper) and modified the rhizosphere microbial community.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {54}, pages = {63343-63359}, pmid = {39482414}, issn = {1614-7499}, mesh = {*Humic Substances ; *Rhizosphere ; *Soil Pollutants ; *Soil Microbiology ; *Vigna/drug effects/growth & development ; *Microplastics ; *Soil/chemistry ; Microbiota/drug effects ; }, abstract = {Microplastics have polluted agricultural soils, posing a substantial risk to crop productivity. Moreover, the presence of microplastic pollution has caused a disturbance in the composition of the microbial community in the soil surrounding plant roots, therefore impacting the growth of beneficial bacteria. A study was conducted to examine if humic acid (HA) can counteract the harmful effects of microplastics (MPs) on the growth of black gram crops and the composition of the rhizosphere soil microbial community, to reduce the negative impacts of microplastics on these microorganisms and crops. The research was carried out using mud pots and the plastic utilized for the experiment consisted of 60% high-density polyethylene (HDPE) and 40% polypropylene (PP). The soil was enriched with lignite-based potassium humate, which had a pH range of 8.0-9.5 and with 65% humic acid. The experiment consisted of six treatments: T1, which served as the control without HA and MP; T2, which involved the use of HA at a concentration of 0.15% w/w; T3, which involved the use of MP at a concentration of 0.2% w/w; T4, which involved the use of MP at a concentration of 0.4% w/w; T5, which involved the combination of HA at a concentration of 0.15% w/w and MP at a concentration of 0.2% w/w; and T6, which involved the combination of HA at a concentration of 0.15% w/w and MP at a concentration of 0.4% w/w. The plant growth characteristics, including germination percentage, nodule number, and chlorophyll content, were measured. In addition, the DNA obtained from the rhizosphere soil was analyzed using metagenomics techniques to investigate the organization of the microbial population. Seedlings in soil polluted with MP exhibited delayed germination compared to seedlings in uncontaminated soil. Following 60 days of growth, the soil samples treated with T5 (0.2% MP and 0.15% HA w/w) had the highest population of bacteria and rhizobium, with counts 5.58 ± 0.02 and 4.90 ± 0.02 CFU g[-1] soil. The plants cultivated in T5 had the most elevated chlorophyll-a concentration (1.340 ± 0.06 mg g[-1]), and chlorophyll-b concentration (0.62 ± 0.02 mg g[-1]) while those cultivated in T3 displayed the lowest concentration of chlorophyll-a (0.59 ± 0.02 mg g[-1]) and chlorophyll-b (0.21 ± 0.04 mg g[-1]). Within the phylum, Proteobacteria had the highest prevalence in all treatments. However, when the soil was polluted with MPs, its relative abundance was reduced by 8.4% compared to the control treatment (T1). Conversely, treatment T5 had a 3.76% rise in relative abundance when compared to treatment T3. The predominant taxa found in soil polluted with MP were Sphingomonas and Bacillus, accounting for 19.3% of the total. Sphingomonas was the predominant genus (21.2%) in soil polluted with MP and supplemented with humic acid. Humic acid can be used as a soil amendment to mitigate the negative effects of MPs and enhance their positive advantages. Research has demonstrated that incorporating humic acid into soil is a viable method for maintaining the long-term integrity of soil's physical, chemical, and biological characteristics.}, } @article {pmid39481794, year = {2024}, author = {Li, X and Li, Y and Wang, Y and Liu, Y and Riaz, L and Wang, Q and Zeng, X and Qin, Z and Irfan, M and Yang, Q}, title = {Methodology comparison of environmental sediment fungal community analysis.}, journal = {Environmental research}, volume = {263}, number = {Pt 3}, pages = {120260}, doi = {10.1016/j.envres.2024.120260}, pmid = {39481794}, issn = {1096-0953}, mesh = {*Geologic Sediments/microbiology ; *Fungi/genetics/isolation & purification/classification ; *RNA, Ribosomal, 18S/genetics ; *High-Throughput Nucleotide Sequencing ; DNA, Fungal/analysis ; DNA, Ribosomal Spacer/genetics ; Mycobiome ; Rivers/microbiology ; }, abstract = {Fungi play important roles in ecosystems. Analyzing fungal communities in environments has long been a challenge due to the large difference in compositions retrieved using different methods or sequencing regions, obscuring the true abundance and species information. Our study aimed to compare and determine more accurate approach for evaluating fungal populations in river sediment. To achieve this, different primer sets in the internal transcribed spacer (ITS) (ITS5/ITS1R, ITS1F/ITS2), 18S rRNA gene (0817F/1196R) for High-throughput sequencing (HTS), metagenomic shotgun sequencing (MS) directly from environmental samples, and HTS using ITS primers for the fungal samples collected from plate cultivation were used to characterize the fungal communities. We calculated diversity index and used FungalTraits to analyze methods preferences for fungal species. The study revealed that when analyzing the fungal species directly from environmental samples, amplification and sequencing of ITS region demonstrated more accuracy than MS and 18S rRNA gene sequencing methods, but displayed significant primer preference. Over 30 % fungal species from HTS after plate cultivation were not present in HTS from the environmental samples. NMDS analysis demonstrated significant disparities in species diversity among different methods, suggesting potential complementarity between them. Over 85% species identified by HTS using ITS primers belonged to filamentous fungi, while the MS mostly identified yeast (62%). Therefore, to get more accurate fungal community information in sediment, multiple methods were recommended by using cultivation, molecular biological methods dependent on PCR techniques like ITS1F/ITS2 primer for HTS and PCR independent method such as metagenomic shotgun sequencing techniques.}, } @article {pmid39478626, year = {2024}, author = {Favero, F and Re, A and Dason, MS and Gravina, T and Gagliardi, M and Mellai, M and Corazzari, M and Corà, D}, title = {Characterization of gut microbiota dynamics in an Alzheimer's disease mouse model through clade-specific marker-based analysis of shotgun metagenomic data.}, journal = {Biology direct}, volume = {19}, number = {1}, pages = {100}, pmid = {39478626}, issn = {1745-6150}, mesh = {Animals ; *Alzheimer Disease/microbiology/genetics ; *Gastrointestinal Microbiome ; Mice ; *Metagenomics/methods ; *Disease Models, Animal ; Mice, Transgenic ; Feces/microbiology ; Metagenome ; }, abstract = {Alzheimer's disease (AD) is a complex neurodegenerative disorder significantly impairing cognitive faculties, memory, and physical abilities. To characterize the modulation of the gut microbiota in an in vivo AD model, we performed shotgun metagenomics sequencing on 3xTgAD mice at key time points (i.e., 2, 6, and 12 months) of AD progression. Fecal samples from both 3xTgAD and wild-type mice were collected, DNA extracted, and sequenced. Quantitative taxon abundance assessment using MetaPhlAn 4 ensured precise microbial community representation. The analysis focused on species-level genome bins (SGBs) including both known and unknown SGBs (kSGBs and uSGBs, respectively) and also comprised higher taxonomic categories such as family-level genome bins (FGBs), class-level genome bins (CGBs), and order-level genome bins (OGBs). Our bioinformatic results pinpointed the presence of extensive gut microbial diversity in AD mice and showed that the largest proportion of AD- and aging-associated microbiome changes in 3xTgAD mice concern SGBs that belong to the Bacteroidota and Firmicutes phyla, along with a large set of uncharacterized SGBs. Our findings emphasize the need for further advanced bioinformatic studies for accurate classification and functional analysis of these elusive microbial species in relation to their potential bridging role in the gut-brain axis and AD pathogenesis.}, } @article {pmid39478562, year = {2024}, author = {Lai, X and Liu, S and Miao, J and Shen, R and Wang, Z and Zhang, Z and Gong, H and Li, M and Pan, Y and Wang, Q}, title = {Eubacterium siraeum suppresses fat deposition via decreasing the tyrosine-mediated PI3K/AKT signaling pathway in high-fat diet-induced obesity.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {223}, pmid = {39478562}, issn = {2049-2618}, mesh = {Animals ; Male ; Mice ; Diet, High-Fat/adverse effects ; *Eubacterium/metabolism ; *Gastrointestinal Microbiome ; *Obesity/microbiology/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Proto-Oncogene Proteins c-akt/metabolism ; *Signal Transduction ; Swine ; }, abstract = {BACKGROUND: Obesity in humans can lead to chronic diseases such as diabetes and cardiovascular disease. Similarly, subcutaneous fat (SCF) in pigs affects feed utilization, and excessive SCF can reduce the feed efficiency of pigs. Therefore, identifying factors that suppress fat deposition is particularly important. Numerous studies have implicated the gut microbiome in pigs' fat deposition, but research into its suppression remains scarce. The Lulai black pig (LL) is a hybrid breed derived from the Laiwu pig (LW) and the Yorkshire pig, with lower levels of SCF compared to the LW. In this study, we focused on these breeds to identify microbiota that regulate fat deposition. The key questions were: Which microbial populations reduce fat in LL pigs compared to LW pigs, and what is the underlying regulatory mechanism?

RESULTS: In this study, we identified four different microbial strains, Eubacterium siraeum, Treponema bryantii, Clostridium sp. CAG:413, and Jeotgalibaca dankookensis, prevalent in both LW and LL pigs. Blood metabolome analysis revealed 49 differential metabolites, including tanshinone IIA and royal jelly acid, known for their anti-adipogenic properties. E. siraeum was strongly correlated with these metabolites, and its genes and metabolites were enriched in pathways linked to fatty acid degradation, glycerophospholipid, and glycerolipid metabolism. In vivo mouse experiments confirmed that E. siraeum metabolites curb weight gain, reduce SCF adipocyte size, increase the number of brown adipocytes, and regulate leptin, IL-6, and insulin secretion. Finally, we found that one important pathway through which E. siraeum inhibits fat deposition is by suppressing the phosphorylation of key proteins in the PI3K/AKT signaling pathway through the reduction of tyrosine.

CONCLUSIONS: We compared LW and LL pigs using fecal metagenomics, metabolomics, and blood metabolomics, identifying E. siraeum as a strain linked to fat deposition. Oral administration experiments in mice demonstrated that E. siraeum effectively inhibits fat accumulation, primarily through the suppression of the PI3K/AKT signaling pathway, a critical regulator of lipid metabolism. These findings provide a valuable theoretical basis for improving pork quality and offer insights relevant to the study of human obesity and related chronic metabolic diseases. Video Abstract.}, } @article {pmid39478083, year = {2024}, author = {Mehlferber, EC and Arnault, G and Joshi, B and Partida-Martinez, LP and Patras, KA and Simonin, M and Koskella, B}, title = {A cross-systems primer for synthetic microbial communities.}, journal = {Nature microbiology}, volume = {9}, number = {11}, pages = {2765-2773}, pmid = {39478083}, issn = {2058-5276}, support = {U19 AI157981/AI/NIAID NIH HHS/United States ; DBI-2209151//National Science Foundation (NSF)/ ; 1838299//NSF | BIO | Division of Integrative Organismal Systems (IOS)/ ; }, mesh = {*Microbiota ; Synthetic Biology/methods ; Microbial Consortia ; Humans ; Microbial Interactions ; }, abstract = {The design and use of synthetic communities, or SynComs, is one of the most promising strategies for disentangling the complex interactions within microbial communities, and between these communities and their hosts. Compared to natural communities, these simplified consortia provide the opportunity to study ecological interactions at tractable scales, as well as facilitating reproducibility and fostering interdisciplinary science. However, the effective implementation of the SynCom approach requires several important considerations regarding the development and application of these model systems. There are also emerging ethical considerations when both designing and deploying SynComs in clinical, agricultural or environmental settings. Here we outline current best practices in developing, implementing and evaluating SynComs across different systems, including a focus on important ethical considerations for SynCom research.}, } @article {pmid39477611, year = {2024}, author = {Hua, Q and Chi, X and Wang, Y and Xu, B}, title = {Biological damage of monocrotaline on the brain and intestinal tissues of Apis mellifera.}, journal = {Pesticide biochemistry and physiology}, volume = {205}, number = {}, pages = {106158}, doi = {10.1016/j.pestbp.2024.106158}, pmid = {39477611}, issn = {1095-9939}, mesh = {Animals ; Bees/drug effects ; *Brain/drug effects/metabolism ; *Monocrotaline/toxicity ; *Intestines/drug effects ; Oxidative Stress/drug effects ; Apoptosis/drug effects ; Gastrointestinal Microbiome/drug effects ; Antioxidants/metabolism ; }, abstract = {Monocrotaline (MCT) is a toxic alkaloid present in plants, posing a threat to animals in terrestrial ecosystems. However, little is known about its potential impacts on pollinating insects. Here, we report the effects of of MCT on the brains and intestines of foraging honeybees (Apis mellifera). MCT exposure resulted in a reduction in head weight and swelling of the abdomen in honeybees. Additionally, MCT exposure caused morphological damage to the brain, characterized by decreased antioxidant capacity and increased apoptosis, along with intestinal tissue damage that was accompanied by increased antioxidant capacity and apoptosis. Moreover, MCT altered the core gut microbial community structure in honeybees and increased the expression of antimicrobial peptide (AMP) genes in the midgut. These findings indicate that exposure to MCT activates the immune response in the honeybee gut, while the brain does not exhibit an immune response but instead experiences oxidative stress. This study provides a resource for future research exploring interactions between MCT and other insects, and can help deepen our understanding of MCT's potential impacts in ecosystems.}, } @article {pmid39477048, year = {2024}, author = {Vinayagam, S and Sekar, K and Rajendran, D and Meenakshisundaram, K and Panigrahi, A and Arumugam, DK and Bhowmick, IP and Sattu, K}, title = {The genetic composition of Anopheles mosquitoes and the diverse population of gut-microbiota within the Anopheles subpictus and Anopheles vagus mosquitoes in Tamil Nadu, India.}, journal = {Acta tropica}, volume = {260}, number = {}, pages = {107439}, doi = {10.1016/j.actatropica.2024.107439}, pmid = {39477048}, issn = {1873-6254}, mesh = {Animals ; *Anopheles/microbiology/genetics ; India ; *Phylogeny ; *Gastrointestinal Microbiome ; Mosquito Vectors/microbiology/genetics ; Bacteria/classification/genetics/isolation & purification ; Sequence Analysis, DNA ; Female ; DNA, Ribosomal Spacer/genetics ; }, abstract = {In recent days, in tropical and subtropical regions, secondary vectors of Anopheles mosquitoes are becoming more important in transmitting diseases to humans as primary vectors. Various molecular techniques have separated closely related Anopheles subpictus and Anopheles vagus mosquitoes based on their diversity with other mosquito species. Despite their widespread distribution, the An. subpictus and An. vagus mosquitoes, which carry Plasmodium in their salivary glands, were not considered primary malaria vectors in India. An. vagus mosquitoes are zoophilic and physically similar to An. subpictus. We intend to identify An. subpictus and An. vagus mosquito's sister species based on their Interspaced Transcribed Region-2 (ITS2). We isolated the midgut gDNA from each mosquito and used ITS2-PCR and Sanger sequencing to characterize the mosquito species. BioEdit software aligned the sequences, and MEGA7 built a phylogenetic tree from them. According to this study, the information gathered from these mosquito samples fits the An. subpictus species A form and the An. vagus Indian form. Furthermore, gut microbiome plays an important role in providing nutrients, immunity, and food processing, whereas mosquitoes' midgut microbiota changes their hosts and spreads illnesses. So, we used the Illumina sequencer to look at the gut microbiome diversity of An. subpictus and An. vagus mosquitoes using 16S rRNA-based metagenomic sequencing. Both mosquito species had an abundant phylum of Pseudomonadota (Proteobacteria), Bacillota, Bacteroidota, and Actinomycetota in their gut microbiomes. Notably, both mosquito species had the genus Serratia in their gut. In the subpictus midgut, the genus of Haematosprillum bacteria was dominant, whereas in the vagus mosquito, the genus of Salmonella was dominant. Notably, current research has observed the Sodalis spp. Bacterial genus for the first time.}, } @article {pmid39476326, year = {2024}, author = {Khan, FZA and Ahmed, S and Powell, AM}, title = {Vaginal Microbiome and the Risk of Preterm Birth in Women Living With HIV: A Scoping Review.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {92}, number = {5}, pages = {e70011}, doi = {10.1111/aji.70011}, pmid = {39476326}, issn = {1600-0897}, support = {K23AI155296//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology ; *HIV Infections/immunology/complications/microbiology ; *Premature Birth/microbiology ; *Microbiota ; Pregnancy ; Pregnancy Complications, Infectious/microbiology/immunology ; }, abstract = {There are sparse data on the role of the vaginal microbiome (VMB) in pregnancy among pregnant women living with HIV (PWLWH) and its association with spontaneous preterm birth (sPTB). We conducted a scoping review to assess associations between vaginal microbiota and sPTB among PWLWH. Three studies were included, representing a total of 180 PWLWH out of 652 total pregnancies. All studies used modern DNA sequencing methods (16S rRNA amplification, metagenomics, or metatranscriptomics). PWLWH had higher VMB richness and diversity compared to HIV-uninfected pregnant women and higher sPTB rates in two of three studies. A higher proportion of sPTB among PWLWH was observed in those with Lactobacillus-deficient, anaerobe-dominant vaginal microbiota. In two of three studies, higher concentrations of vaginal inflammation markers were associated with increased VMB richness and diversity. HIV status was independently associated with sPTB. It is unclear if increased vaginal microbial diversity among PWLWH or increased vaginal inflammation contributes more to PTB, but HIV does appear to alter the VMB in pregnant individuals and may also affect PTB rates in microbiome-independent pathways. Given the limited number of studies, heterogeneity in sample size, sample collection methods, and inconsistent results it is difficult to causally link HIV, VMB, inflammatory cytokines, and sPTB.}, } @article {pmid39475924, year = {2024}, author = {Liu, S and Ren, J and Li, J and Yu, D and Xu, H and He, F and Li, N and Zou, L and Cao, Z and Wen, J}, title = {Characterizing the gut microbiome of diarrheal mink under farmed conditions: A metagenomic analysis.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0312821}, pmid = {39475924}, issn = {1932-6203}, mesh = {Animals ; *Mink/microbiology ; *Gastrointestinal Microbiome/genetics ; *Diarrhea/microbiology/veterinary ; *Metagenomics/methods ; Metagenome ; Bacteria/genetics/classification/isolation & purification ; Bacteroidetes/genetics/isolation & purification ; Farms ; Feces/microbiology ; }, abstract = {This study aimed to comprehensively characterize the gut microbiota in diarrheal mink. We conducted Shotgun metagenomic sequencing on samples from five groups of diarrheal mink and five groups of healthy mink. The microbiota α-diversity and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology did not show significant differences between the groups. However, significant differences were observed in microbiota β-diversity and the function of carbohydrate-active enzymes (CAZymes) between diarrheal and healthy mink. Specifically, The relative abundance of Firmicutes was lower, whereas that of Bacteroidetes was higher in diarrheal mink. Fusobacteria were enriched as invasive bacteria in the gut of diarrheal mink compared with healthy mink. In addition, Escherichia albertii was identified as a new bacterium in diarrheal mink. Regarding functions, nicotinate and nicotinamide metabolism and glycoside hydrolases 2 (GH2) family were the enhanced KEGG orthology and CAZymes in diarrheal mink. Furthermore, the diversity and number of antibiotic-resistant genes were significantly higher in the diarrheal mink group than in the healthy group. These findings enhance our understanding of the gut microbiota of adult mink and may lead to new approaches to the diagnosis and treatment of mink diarrhea.}, } @article {pmid39475341, year = {2024}, author = {Sánchez-Terrón, G and Martínez, R and Freire, MJ and Molina-Infante, J and Estévez, M}, title = {Gastrointestinal fate of proteins from commercial plant-based meat analogs: Silent passage through the stomach, oxidative stress in intestine, and gut dysbiosis in Wistar rats.}, journal = {Journal of food science}, volume = {89}, number = {12}, pages = {10294-10316}, pmid = {39475341}, issn = {1750-3841}, support = {//Ministerio de Ciencia e Innovación/ ; //Junta de Extremadura/ ; //Junta de Andalucía/ ; }, mesh = {Animals ; *Rats, Wistar ; Rats ; *Oxidative Stress ; *Gastrointestinal Microbiome/physiology ; Male ; *Dysbiosis ; Gastrointestinal Tract/metabolism/microbiology ; Dietary Proteins/metabolism ; Stomach/microbiology ; Digestion ; Meat Substitutes ; }, abstract = {Plant-based meat analogs (PBMAs) are common ultra-processed foods (UPFs) included in the vegan/vegetarian diets as presumed healthy alternatives to meat and meat products. However, such health claims need to be supported by scientific evidence. To gain further insight into this topic, two commercial UPFs typically sold as meat analogs, namely, seitan (S) and tofu (T), were included in a cereal-based chow and provided to Wistar rats for 10 weeks. A group of animals had, simultaneously, an isocaloric and isoprotein experimental diet formulated with cooked beef (B). In all cases, experimental chows (∼4 kcal/g feed) had their basal protein concentration increased from 14% to 30% using proteins from S, T, or B. Upon slaughter, in vivo protein digestibility was assessed, and the entire gastrointestinal tract (digests and tissues) was analyzed for markers of oxidative stress and untargeted metabolomics. Metagenomics was also applied to assess the variation of microbiota composition as affected by dietary protein. Diets based on PBMAs showed lower protein digestibility than those containing meat and promoted an intense luminal glycoxidative stress and an inflammatory intestinal response. The fermentation of undigested oxidized proteins from T in the colon of Wistar rats likely led to formation of mutagenic metabolites such as p-cresol. The presence of these compounds in the animal models raises concerns about the potential effects of full replacement of meat by certain PBMAs in the diet. Therefore, future research might target on translational human studies to shed light on these findings.}, } @article {pmid39474927, year = {2024}, author = {Milesi, VP}, title = {Redox Gradient Shapes the Chemical Composition of Peatland Microbial Communities.}, journal = {Geobiology}, volume = {22}, number = {6}, pages = {e70001}, doi = {10.1111/gbi.70001}, pmid = {39474927}, issn = {1472-4669}, support = {//Agence Nationale de la Recherche/ ; }, mesh = {*Oxidation-Reduction ; *Soil Microbiology ; *Soil/chemistry ; *Microbiota ; Bacteria/classification/genetics/metabolism ; Carbon/metabolism/analysis ; }, abstract = {The response of soil carbon to climate change and anthropogenic forcing depends on the relationship between the physicochemical variables of the environment and microbial communities. In anoxic soils that store large amounts of organic carbon, it can be hypothesized that the low amount of catabolic energy available leads microbial organisms to minimize the energy costs of biosynthesis, which may shape the composition of microbial communities. To test this hypothesis, thermodynamic modeling was used to assess the link between redox gradients in the ombrotrophic peatland of the Marcell Experimental Forest (Minnesota, USA) and the chemical and taxonomic composition of microbial communities. The average amino acid composition of community-level proteins, called hereafter model proteins, was calculated from shotgun metagenomic sequencing. The carbon oxidation state of model proteins decreases linearly from -0.14 at 10 cm depth to -0.17 at 150 cm depth. Calculating equilibrium activities of model proteins for a wide range of chemical conditions allows identification of the redox potential of maximum chemical activity. Consistent with redox measurements across peat soils, this model Eh decreases logarithmically from an average value of 300 mV at 10 cm depth, close to the stability domain of goethite relative to Fe[2+], to an average value of -200 mV at 150 cm, within the stability domain of CH4 relative to CO2. The correlation identified between the taxonomic abundance and the carbon oxidation state of model proteins enables predicting the evolution of taxonomic abundance as a function of model Eh. The model taxonomic abundance is consistent with the measured gene and taxonomic abundance, which evolves from aerobic bacteria at the surface including Acidobacteria, Proteobacteria, and Verrumicrobia, to anaerobes at depth dominated by Crenarchaeota. These results indicate that the thermodynamic forcing imposed by redox gradient across peat soils shapes both the chemical and taxonomic composition of microbial communities. By providing a mechanistic understanding of the relationship between microbial community and environmental conditions, this work sheds new light on the mechanisms that govern soil microbial life and opens up prospects for predicting geochemical and microbial evolution in changing environments.}, } @article {pmid39473051, year = {2024}, author = {Wang, Y and Chen, J and Ni, Y and Liu, Y and Gao, X and Tse, MA and Panagiotou, G and Xu, A}, title = {Exercise-changed gut mycobiome as a potential contributor to metabolic benefits in diabetes prevention: an integrative multi-omics study.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2416928}, pmid = {39473051}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; *Exercise ; Middle Aged ; *Mycobiome ; *Fungi/classification/genetics/isolation & purification ; *Feces/microbiology ; Proteomics ; Prediabetic State/microbiology/metabolism ; Metabolomics ; Bacteria/classification/isolation & purification/genetics/metabolism ; Adult ; Diabetes Mellitus, Type 2/microbiology/prevention & control ; Metagenomics ; Multiomics ; }, abstract = {BACKGROUND: The importance of gut microbes in mediating the benefits of lifestyle intervention is increasingly recognized. However, compared to the bacterial microbiome, the role of intestinal fungi in exercise remains elusive. With our established randomized controlled trial of exercise intervention in Chinese males with prediabetes (n = 39, ClinicalTrials.gov:NCT03240978), we investigated the dynamics of human gut mycobiome and further interrogated their associations with exercise-elicited outcomes using multi-omics approaches.

METHODS: Clinical variations and biological samples were collected before and after training. Fecal fungal composition was analyzed using the internal transcribed spacer 2 (ITS2) sequencing and integrated with paired shotgun metagenomics, untargeted metabolomics, and Olink proteomics.

RESULTS: Twelve weeks of exercise training profoundly promoted fungal ecological diversity and intrakingdom connection. We further identified exercise-responsive genera with potential metabolic benefits, including Verticillium, Sarocladium, and Ceratocystis. Using multi-omics approaches, we elucidated comprehensive associations between changes in gut mycobiome and exercise-shaped metabolic phenotypes, bacterial microbiome, and circulating metabolomics and proteomics profiles. Furthermore, a machine-learning algorithm built using baseline microbial signatures and clinical characteristics predicted exercise responsiveness in improvements of insulin sensitivity, with an area under the receiver operating characteristic (AUROC) of 0.91 (95% CI: 0.85-0.97) in the discovery cohort and of 0.79 (95% CI: 0.74-0.86) in the independent validation cohort (n = 30).

CONCLUSIONS: Our findings suggest that intense exercise training significantly remodels the human fungal microbiome composition. Changes in gut fungal composition are associated with the metabolic benefits of exercise, indicating gut mycobiome is a possible molecular transducer of exercise. Moreover, baseline gut fungal signatures predict exercise responsiveness for diabetes prevention, highlighting that targeting the gut mycobiome emerges as a prospective strategy in tailoring personalized training for diabetes prevention.}, } @article {pmid39472959, year = {2024}, author = {Martin-Cuadrado, AB and Rubio-Portillo, E and Rosselló, F and Antón, J}, title = {The coral Oculina patagonica holobiont and its response to confinement, temperature, and Vibrio infections.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {222}, pmid = {39472959}, issn = {2049-2618}, mesh = {*Anthozoa/microbiology ; Animals ; *Coral Reefs ; *Microbiota ; *Vibrio/genetics/classification/physiology/isolation & purification ; Symbiosis ; Temperature ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Rhodobacteraceae/genetics/classification/isolation & purification/physiology ; Fungi/classification/genetics/isolation & purification ; Vibrionaceae/genetics/classification/isolation & purification ; Vibrio Infections/microbiology ; Climate Change ; }, abstract = {BACKGROUND: Extensive research on the diversity and functional roles of the microorganisms associated with reef-building corals has been promoted as a consequence of the rapid global decline of coral reefs attributed to climate change. Several studies have highlighted the importance of coral-associated algae (Symbiodinium) and bacteria and their potential roles in promoting coral host fitness and survival. However, the complex coral holobiont extends beyond these components to encompass other entities such as protists, fungi, and viruses. While each constituent has been individually investigated in corals, a comprehensive understanding of their collective roles is imperative for a holistic comprehension of coral health and resilience.

RESULTS: The metagenomic analysis of the microbiome of the coral Oculina patagonica has revealed that fungi of the genera Aspergillus, Fusarium, and Rhizofagus together with the prokaryotic genera Streptomyces, Pseudomonas, and Bacillus were abundant members of the coral holobiont. This study also assessed changes in microeukaryotic, prokaryotic, and viral communities under three stress conditions: aquaria confinement, heat stress, and Vibrio infections. In general, stress conditions led to an increase in Rhodobacteraceae, Flavobacteraceae, and Vibrionaceae families, accompanied by a decrease in Streptomycetaceae. Concurrently, there was a significant decline in both the abundance and richness of microeukaryotic species and a reduction in genes associated with antimicrobial compound production by the coral itself, as well as by Symbiodinium and fungi.

CONCLUSION: Our findings suggest that the interplay between microeukaryotic and prokaryotic components of the coral holobiont may be disrupted by stress conditions, such as confinement, increase of seawater temperature, or Vibrio infection, leading to a dysbiosis in the global microbial community that may increase coral susceptibility to diseases. Further, microeukaryotic community seems to exert influence on the prokaryotic community dynamics, possibly through predation or the production of secondary metabolites with anti-bacterial activity. Video Abstract.}, } @article {pmid39471749, year = {2024}, author = {Liu, X and Lu, B and Tang, H and Jia, X and Zhou, Q and Zeng, Y and Gao, X and Chen, M and Xu, Y and Wang, M and Tan, B and Li, J}, title = {Gut microbiome metabolites, molecular mimicry, and species-level variation drive long-term efficacy and adverse event outcomes in lung cancer survivors.}, journal = {EBioMedicine}, volume = {109}, number = {}, pages = {105427}, pmid = {39471749}, issn = {2352-3964}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Lung Neoplasms/drug therapy/immunology/pathology ; Male ; Female ; Middle Aged ; Aged ; Cancer Survivors ; Metabolome ; Metagenome ; Metagenomics/methods ; Immune Checkpoint Inhibitors/therapeutic use/adverse effects ; Treatment Outcome ; }, abstract = {BACKGROUND: The influence of the gut microbiota on long-term immune checkpoint inhibitor (ICI) efficacy and immune-related adverse events (irAEs) is poorly understood, as are the underlying mechanisms.

METHODS: We performed gut metagenome and metabolome sequencing of gut microbiotas from patients with lung cancer initially treated with anti-PD-1/PD-L1 therapy and explored the underlying mechanisms mediating long-term (median follow-up 1167 days) ICI responses and immune-related adverse events (irAEs). Results were validated in external, publicly-available datasets (Routy, Lee, and McCulloch cohorts).

FINDINGS: The ICI benefit group was enriched for propionate (P = 0.01) and butyrate/isobutyrate (P = 0.12) compared with the resistance group, which was validated in the McCulloch cohort (propionate P < 0.001, butyrate/isobutyrate P = 0.002). The acetyl-CoA pathway (P = 0.02) in beneficial species mainly mediated butyrate production. Microbiota sequences from irAE patients aligned with antigenic epitopes found in autoimmune diseases. Microbiotas of responsive patients contained more lung cancer-related antigens (P = 0.07), which was validated in the Routy cohort (P = 0.02). Escherichia coli and SGB15342 of Faecalibacterium prausnitzii showed strain-level variations corresponding to clinical phenotypes. Metabolome validation reviewed more abundant acetic acid (P = 0.03), propionic acid (P = 0.09), and butyric acid (P = 0.02) in the benefit group than the resistance group, and patients with higher acetic, propionic, and butyric acid levels had a longer progression-free survival and lower risk of tumor progression after adjusting for histopathological subtype and stage (P < 0.05).

INTERPRETATION: Long-term ICI survivors have coevolved a compact microbial community with high butyrate production, and molecular mimicry of autoimmune and tumor antigens by microbiota contribute to outcomes. These results not only characterize the gut microbiotas of patients who benefit long term from ICIs but pave the way for "smart" fecal microbiota transplantation. Registered in the Chinese Clinical Trial Registry (ChiCTR2000032088).

FUNDING: This work was supported by Beijing Natural Science Foundation (7232110), National High Level Hospital Clinical Research Funding (2022-PUMCH-A-072, 2023-PUMCH-C-054), CAMS Innovation Fund for Medical Sciences (CIFMS) (2022-I2M-C&T-B-010).}, } @article {pmid39470190, year = {2024}, author = {Toyomane, K and Kimura, Y and Fukagawa, T and Yamagishi, T and Watanabe, K and Akutsu, T and Asahi, A and Kubota, S and Sekiguchi, K}, title = {Metagenomic sequencing of CRISPRs as a new marker to aid in personal identification with low-biomass samples.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0103824}, pmid = {39470190}, issn = {2379-5077}, support = {20K18991,24K20264//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {Humans ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; *Metagenomics/methods ; *Skin/microbiology ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Metagenome/genetics ; Genetic Markers/genetics ; }, abstract = {The high specificity of the human skin microbiome is expected to provide a new marker for personal identification. Metagenomic sequencing of clustered regularly interspaced short palindromic repeats (CRISPRs), which we call metaCRISPR typing, was shown to achieve personal identification accurately. However, the intra-individual variability observed in previous studies, which may be due to poor DNA yields from skin samples, has resulted in non-reproducible results. Furthermore, whether metaCRISPR typing can assist in the forensic human DNA analysis of low-biomass samples, from which the information obtained is insufficient, is unknown. In the present study, we sequenced serially diluted control streptococcal CRISPRs cloned into plasmids to determine the minimum copy number required to obtain reproducible results from metaCRISPR typing. We found that at least 10[2] copies of CRISPRs are necessary to obtain reproducible results. We then analyzed the skin swab samples using both metaCRISPR typing and human DNA typing. When the DNA extracted from the skin swabs was diluted, no information was obtained from six out of eight samples by human DNA typing. On the other hand, beta diversity indices of spacer sequences compared with reference samples were below 0.8 for three out of six samples, for which no information was obtained from human DNA analysis, indicating that the spacers observed in these samples were similar to those in the references. These results indicate that metaCRISPR typing may contribute to the identification of individuals from whom the samples were obtained, even in cases where human DNA yields are insufficient to perform human DNA analysis.IMPORTANCEPrevious studies have developed new personal identification methods utilizing personal differences in the skin microbiome. However, intra-individual diversity of skin microbiome may preclude the application of microbiome-based personal identification. Moreover, no study has compared microbiome-based personal identification and practical human DNA analysis. Here, we revealed that the results of metaCRISPR typing, a previously developed microbiome-based personal identification method, are stable if the copy number of the marker gene is sufficient. We then analyzed the skin swab samples using both metaCRISPR typing and human DNA analysis. Our results indicate that metaCRISPR typing may provide additional information for personal identification using low-biomass samples that cannot be used for conventional human DNA analysis.}, } @article {pmid39468837, year = {2024}, author = {Wan, Y and Wong, OWH and Tun, HM and Su, Q and Xu, Z and Tang, W and Ma, SL and Chan, S and Chan, FKL and Ng, SC}, title = {Fecal microbial marker panel for aiding diagnosis of autism spectrum disorders.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2418984}, pmid = {39468837}, issn = {1949-0984}, mesh = {Humans ; *Feces/microbiology ; *Autism Spectrum Disorder/diagnosis/microbiology ; Female ; *Gastrointestinal Microbiome ; Male ; Child ; Child, Preschool ; *Biomarkers/analysis ; *Bacteria/isolation & purification/classification/genetics ; Metagenome ; Machine Learning ; }, abstract = {Accumulating evidence suggests that gut microbiota alterations influence brain function and could serve as diagnostic biomarkers and therapeutic targets. The potential of using fecal microbiota signatures to aid autism spectrum disorder (ASD) detection is still not fully explored. Here, we assessed the potential of different levels of microbial markers (taxonomy and genome) in distinguishing children with ASD from age and gender-matched typically developing peers (n = 598, ASD vs TD = 273 vs 325). A combined microbial taxa and metagenome-assembled genome (MAG) markers showed a better performance than either microbial taxa or microbial MAGs alone for detecting ASD. A machine-learning model comprising 5 bacterial taxa and 44 microbial MAG markers (2 viral MAGs and 42 bacterial MAGs) achieved an area under the receiving operator curve (AUROC) of 0.886 in the discovery cohort and 0.734 in an independent validation cohort. Furthermore, the identified biomarkers and predicted ASD risk score also significantly correlated with the core symptoms measured by the Social Responsiveness Scale-2 (SRS-2). The microbiome panel showed a superior classification performance in younger children (≤6 years old) with an AUROC of 0.845 than older children (>6 years). The model was broadly applicable to subjects across genders, with or without gastrointestinal tract symptoms (constipation and diarrhea) and with or without psychiatric comorbidities (attention deficit and hyperactivity disorder and anxiety). This study highlights the potential clinical validity of fecal microbiome to aid in ASD diagnosis and will facilitate studies to understand the association of disturbance of human gut microbiota and ASD symptom severity.}, } @article {pmid39468445, year = {2024}, author = {Chen, Q and Chen, Z and Tan, Y and Wu, S and Zou, S and Liu, J and Song, S and Du, Q and Wang, M and Liang, K}, title = {Blood microbiota in HIV-infected and HIV-uninfected patients with suspected sepsis detected by metagenomic next-generation sequencing.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1210}, pmid = {39468445}, issn = {1471-2334}, support = {PTXM2020008//Medical Science and Technology Innovation Platform Support Project of Zhongnan Hospital, Wuhan University/ ; cxpy2017043//Science and Technology Innovation Cultivation Fund of Zhongnan Hospital, Wuhan University/ ; TFJC2018004//Medical Science Advancement Program (Basic Medical Sciences) of Wuhan University/ ; 2020-PT320-004//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; }, mesh = {Humans ; *HIV Infections/complications/microbiology ; Male ; Female ; Middle Aged ; *Sepsis/microbiology/blood ; *High-Throughput Nucleotide Sequencing ; Retrospective Studies ; Adult ; *Metagenomics/methods ; *Microbiota ; China ; Bacteria/classification/genetics/isolation & purification ; Aged ; }, abstract = {BACKGROUND: Information on the comparison of blood microbiota between human immunodeficiency virus (HIV)-infected and HIV-uninfected patients with suspected sepsis by metagenomic next-generation sequencing (mNGS) is limited.

METHODS: Retrospectively analysis was conducted in HIV-infected and HIV-uninfected patients with suspected sepsis at Changsha First Hospital (China) from March 2019 to August 2022. Patients who underwent blood mNGS testing were enrolled. The blood microbiota detected by mNGS were analyzed.

RESULTS: A total of 233 patients with suspected sepsis who performed blood mNGS were recruited in this study, including 79 HIV-infected and 154 HIV-uninfected patients. Compared with HIV-uninfected patients, the proportions of mycobacterium (p = 0.001), fungus (p < 0.001) and viruses (p < 0.001) were significantly higher, while the proportion of bacteria (p = 0.001) was significantly lower in HIV-infected patients. The higher positive rates of non-tuberculous mycobacteriosis (NTM, p = 0.022), Pneumocystis jirovecii (P. jirovecii) (p = 0.014), Talaromyces marneffei (T. marneffei) (p < 0.001) and cytomegalovirus (CMV) (p < 0.001) were observed in HIV-infected patients, compared with HIV-uninfected patients. In addition, compared with HIV-uninfected patients, the constituent ratio of T. marneffei (p < 0.001) in the fungus spectrum were significantly higher, while the constituent ratios of Candida (p < 0.001) and Aspergillus (p = 0.001) were significantly lower in HIV-infected patients.

CONCLUSIONS: Significant differences in the blood microbiota profiles exist between HIV-infected and HIV-uninfected patients with suspected sepsis.}, } @article {pmid39468253, year = {2024}, author = {Luna, N and Páez-Triana, L and Ramírez, AL and Muñoz, M and Goméz, M and Medina, JE and Urbano, P and Barragán, K and Ariza, C and Martínez, D and Hernández, C and Patiño, LH and Ramirez, JD}, title = {Microbial community dynamics in blood, faeces and oral secretions of neotropical bats in Casanare, Colombia.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {25808}, pmid = {39468253}, issn = {2045-2322}, support = {Internal funds//Universidad del Rosario/ ; }, mesh = {Animals ; *Chiroptera/microbiology/virology ; *Feces/microbiology/virology ; Colombia/epidemiology ; Microbiota/genetics ; Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing ; Fungi/genetics/isolation & purification/classification ; Metagenomics/methods ; Mouth/microbiology/virology ; RNA, Ribosomal, 16S/genetics ; Viruses/genetics/isolation & purification/classification ; Saliva/microbiology/virology ; }, abstract = {Bats are known reservoirs for a wide range of pathogenic microorganisms, including viruses, bacteria, fungi, helminths, and protozoa, which can be transmitted and infect other zoonotic organisms. Various studies have utilised next-generation sequencing (NGS) to describe the pathogens associated with bats. Although most have characterised microbial communities in specific body fluids, few have analysed the composition and diversity of these microbial communities across different body fluids at the individual level. In this study, we employed two next-generation sequencing techniques: amplicon-based sequencing of the V4 hypervariable region of the 16S- and 18S-rRNA genes and viral metagenomics, to describe the prokaryotic, eukaryotic, and viral communities present in blood, faeces, and oral swab samples collected from two genera of bats (Carollia and Phyllostomus) in the department of Casanare, eastern Colombia. A total of 60 samples corresponding to the three bodily fluids were processed and analysed. The results indicated that the microbial communities across the body fluids were mainly composed of bacteria, fungi, protozoa, and various DNA and RNA viruses, showing a variability of microbial genera and species. The abundances, diversity metrics, and correlations of these microorganisms displayed patterns associated with bat genus and body fluids, suggesting that the ecological characteristics of these microbial communities may be influenced by the ecological and physiological traits of the bats. Additionally, we found similar community compositions of bacteria, some fungal genera, and viruses in the three body fluids, indicating a possible circulation of these microbes within the same bat. This could be due to microbial movement from the gut microbiota to other physiological systems or transmission via blood-feeding vectors. Furthermore, our results revealed the presence of various microbes of public health concern, including Bartonella spp., Mannheimia haemolytica, Rhodotorula spp., Piroplasmida spp., Toxoplasma gondii, Alphacoronavirus spp., and Bat circovirus. The abundance of these pathogenic microbial species across the three bodily fluids suggests potential transmission routes from bats to other organisms, which may contribute to the emergence of zoonotic disease outbreaks. These findings highlight the variability of microorganisms present within the same bat and the different pathogen-host interactions that may regulate the presence and transmission of these zoonotic microbes. Further research is required to elucidate the genomic features, ecological interactions, and biological activities of these microbial communities in bats.}, } @article {pmid39467883, year = {2024}, author = {Saini, N and Aamir, M and Khan, ZA and Singh, VK and Sah, P and Mona, S}, title = {Deciphering Toxic Pollutants Breakdown Potential in Microbial Community of Chumathang Hot Spring, Ladakh, India via Shotgun Metagenome Sequencing.}, journal = {Current microbiology}, volume = {81}, number = {12}, pages = {430}, pmid = {39467883}, issn = {1432-0991}, mesh = {*Hot Springs/microbiology ; India ; *Biodegradation, Environmental ; *Metagenome ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics ; Microbiota/genetics ; Phylogeny ; Persistent Organic Pollutants/metabolism ; Xenobiotics/metabolism ; High-Throughput Nucleotide Sequencing ; }, abstract = {Persistent Organic Pollutants (POPs) have been in focus of research due to their massive contamination of environment and bio-accumulation. Bioremediation and high-throughput research have gained momentum to curb the harmful effects of POPs. The present research has explored the microbial diversity of Chumathang Hot Spring, Ladakh, India, through Illumina metagenomic HiSeq 4000 sequencing platform and their potential to degrade persistent pollutants, especially xenobiotics. Taxonomic characterization based on raw metagenomic data illuminated the abundance of members of Pseudomonadota and Actinomyceota. The re-construction of the microbial genomes from assembled contigs and scaffolds using de novo assembler metaSPAdes and their further annotation through contig alignment with available reference genomes elucidated the landscape of the hot spring's microbes. The predominantly occupied key genera reported were Pannonibacter and Novosphingobium. Comparative genomic analysis established evolutionary relationships and functional diversities among hot spring microbial communities. The function annotation through MG-RAST has revealed their metabolic versatility of degrading a wide array of xenobiotic compounds, including caprolactam, dioxin, chlorobenzene, benzoate, and. Further, the hydroxylating dioxygenase (Saro_3901) was identified as a pivotal component in the aromatic degradation pathways, showcasing extensive metabolic interconnectivity. Interestingly, protein interaction network analysis identified hub genes like Saro_1233 (protocatechuate 4,5-dioxygenase alpha subunit), while Saro_3057 (amidase) was noted for its critical role in network communication and control. The resilience of thermal ecosystems, evidenced by robust enzymatic activity and degradation capability among organisms with < 95% genetic similarity, underscores their potential for industrial and bioremediation exploration, emphasizing the importance of preserving and studying biodiverse habitats.}, } @article {pmid39467681, year = {2024}, author = {Wang, HM and Zhang, MM and Lin, Y and Liu, Y and Xue, GH and Shi, L and Yuan, J and Li, XH}, title = {[Characteristics of intestinal microbiota in the acute phase of Kawasaki disease in infants and children].}, journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics}, volume = {26}, number = {10}, pages = {1101-1107}, pmid = {39467681}, issn = {1008-8830}, mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/microbiology ; *Gastrointestinal Microbiome ; Infant ; Child, Preschool ; Male ; Female ; Acute Disease ; Feces/microbiology ; Infant, Newborn ; }, abstract = {OBJECTIVES: To study the composition, abundance, and functional profiles of the intestinal microbiota in infants and young children with Kawasaki disease (KD) during the acute phase, and to explore the potential role of intestinal microbiota in the pathogenesis of KD.

METHODS: Six children aged 0-3 years with acute KD admitted to the Department of Cardiology, Children's Hospital Affiliated to Capital Institute of Pediatrics from July to October 2021 were prospectively included as the KD group. Six age- and sex-matched healthy children who underwent physical examinations at the hospital during the same period were selected as the healthy control group. Metagenomics sequencing was used to detect and compare the differences in the microflora structure and functional profiles of fecal samples between the two groups.

RESULTS: There were significant differences in the structural composition and diversity of intestinal microbiota between the two groups (P<0.05). Compared with the healthy control group, the abundance of Listeria_monocytogenes (family Listeriaceae and genus Listeria), Bifidobacterium_rousetti, Enterococcus_avium, and Enterococcus_hirae was significantly higher in the intestinal microbiota in the KD group (|LDA|>2.0, P<0.05). The steroid degradation and apoptosis pathways were significantly upregulated in the KD group compared with the healthy control group, while the Bacterial_secretion_system, Sulfur_metabolism, Butanoate_metabolism, Benzoate_degradation, β-alanine metabolism, and α-linolenic acid pathways were significantly downregulated (|LDA|>2, P<0.05).

CONCLUSIONS: There are significant differences in the structure and diversity of intestinal microbiota between children aged 0-3 years with acute KD and healthy children, suggesting that disturbances in intestinal microbiota occur during the acute phase of KD. In particular, Listeria_monocytogenes, Enterococcus_avium, and Enterococcus_hirae may be involved in the pathogenesis of KD through steroid degradation and apoptosis pathways.}, } @article {pmid39465298, year = {2024}, author = {Xiao, X and Singh, A and Giometto, A and Brito, IL}, title = {Segatella clades adopt distinct roles within a single individual's gut.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {114}, pmid = {39465298}, issn = {2055-5008}, support = {DP2 HL141007/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Fatty Acids, Volatile/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Genetic Variation ; Anti-Bacterial Agents/pharmacology ; Host Microbial Interactions ; Metagenomics/methods ; Drug Resistance, Bacterial ; Epithelial Cells/microbiology ; }, abstract = {Segatella is a prevalent genus within individuals' gut microbiomes worldwide, especially in non-Western populations. Although metagenomic assembly and genome isolation have shed light on its genetic diversity, the lack of available isolates from this genus has resulted in a limited understanding of how members' genetic diversity translates into phenotypic diversity. Within the confines of a single gut microbiome, we have isolated 63 strains from diverse lineages of Segatella. We performed comparative analyses that exposed differences in cellular morphologies, preferences in polysaccharide utilization, yield of short-chain fatty acids, and antibiotic resistance across isolates. We further show that exposure to Segatella isolates either evokes strong or muted transcriptional responses in human intestinal epithelial cells. Our study exposes large phenotypic differences within related Segatella isolates, extending this to host-microbe interactions.}, } @article {pmid39465163, year = {2024}, author = {Premsuriya, J and Leerach, N and Laosena, P and Hinthong, W}, title = {The effects of livestock grazing on physicochemical properties and bacterial communities of perlite-rich soil.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18433}, pmid = {39465163}, issn = {2167-8359}, mesh = {*Soil Microbiology ; Animals ; Thailand ; *Soil/chemistry ; *Livestock/microbiology ; *Aluminum Oxide ; *Silicon Dioxide ; Mining ; Bacteria/genetics/classification/isolation & purification ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; }, abstract = {Livestock grazing has been proposed as a cost-effective way to reclaim post-mining lands. It can enhance soil fertility and biodiversity, but its impacts on soil quality and microbial communities vary across soil types. Moreover, waste from grazing raises concerns about pathogens that could pose risks to animal and human health. This study investigated the effects of grazing on post-mining perlite-rich soil in central Thailand. A comparative analysis of soil physicochemical properties and bacterial diversity was conducted between grazed and ungrazed sites. Bacterial diversity was assessed using 16S amplicon sequencing. The perlite-rich soil was found to be sandy, acidic, and to have low nutritional content. Grazing significantly improved the soil texture and nutrient content, suggesting its potential as a cost-effective reclamation strategy. The 16S metagenomic sequencing analysis revealed that microbial communities were impacted by livestock grazing. Specifically, shifts in the dominant bacterial phyla were identified, with increases in Firmicutes and Chloroflexi and a decrease in Actinobacteria. Concerns about increased levels of pathogenic Enterobacteriaceae due to grazing were not substantiated in perlite-rich soil. These bacteria were consistently found at low levels in all soil samples, regardless of livestock grazing. This study also identified a diverse population of Streptomycetaceae, including previously uncharacterized strains/species. This finding could be valuable given that this bacterial family is known for producing antibiotics and other secondary metabolites. However, grazing adversely impacted the abundance and diversity of Streptomycetaceae in this specific soil type. In line with previous research, this study demonstrated that the response of soil microbial communities to grazing varies significantly depending on the soil type, with unique responses appearing to be associated with perlite-rich soil. This emphasizes the importance of soil-specific research in understanding how grazing affects microbial communities. Future research should focus on optimizing grazing practices for perlite-rich soil and characterizing the Streptomycetaceae community for potential antibiotic and secondary metabolite discovery. The obtained findings should ultimately contribute to sustainable post-mining reclamation through livestock grazing and the preservation of valuable microbial resources.}, } @article {pmid39462143, year = {2024}, author = {Boutouchent, N and Vu, TNA and Landraud, L and Kennedy, SP}, title = {Urogenital colonization and pathogenicity of E. Coli in the vaginal microbiota during pregnancy.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {25523}, pmid = {39462143}, issn = {2045-2322}, support = {Bourse Année Recherche (BAR) 2023-24//University Hospital of Rouen Normandy/ ; DOS0053477 SUB & DOS0053473 AR//Programme d'Investissements d'avenir and BPIfrance/ ; DOS0053477 SUB & DOS0053473 AR//Programme d'Investissements d'avenir and BPIfrance/ ; DOS0053477 SUB & DOS0053473 AR//Programme d'Investissements d'avenir and BPIfrance/ ; }, mesh = {Female ; Humans ; *Vagina/microbiology ; Pregnancy ; *Escherichia coli/genetics/pathogenicity ; *Microbiota ; *Escherichia coli Infections/microbiology ; Adult ; Bacteriuria/microbiology ; Pregnancy Complications, Infectious/microbiology ; Lactobacillus/genetics/isolation & purification ; }, abstract = {This study explores the role of the vaginal microbiota (VM) in the pathophysiology of asymptomatic bacteriuria (ASB) in a cohort of 1,553 pregnant women. Worldwide, E. coli remains the most common etiological agent of bacteriuria during pregnancy and also a major causative agent of newborn infections. A healthy VM is typically characterized by low diversity and is dominated by lactic acid-producing species, notably those from the Lactobacillus genus. Our results point to decreases in Lactobacillus spp associated with an increase of gut-microbiota-associated species from the Enterobacterales order. Escherichia coli exhibited the most pronounced increase in abundance within the VM during bacteriuria and was notably associated with ASB. Molecular typing and antimicrobial resistance characterization of 72 metagenome assembled E. coli genomes (MAGs) from these pregnant women revealed a genomic signature of extraintestinal pathogenic E. coli ("ExPEC") strains, which are involved in various extraintestinal infections such as urinary tract infections, newborn infections and bacteremia. Microbial diversity within the vaginal samples from which an E. coli MAG was obtained showed a substantial variation, primarily marked by a decrease in abundance of Lactobacillus species. Overall, our study shows how disruption in key bacterial group within the VM can disrupt its stability, potentially leading to the colonization by opportunistic pathogens.}, } @article {pmid39462132, year = {2024}, author = {Siallagan, ZL and Fadli, M and de Fretes, CE and Opier, RDA and Susanto, RD and Wei, Z and Suhardi, VSH and Nugrahapraja, H and Radjasa, OK and Dwivany, FM}, title = {Metagenomic analysis of deep-sea bacterial communities in the Makassar and Lombok Straits.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {25472}, pmid = {39462132}, issn = {2045-2322}, support = {#80NSSC18K0777//Physical Oceanography Program of the U.S. National Aeronautics and Space Administration (NASA) and through the University of Maryland/ ; }, mesh = {*Bacteria/genetics/classification ; *Metagenomics/methods ; *Seawater/microbiology ; *RNA, Ribosomal, 16S/genetics ; Phylogeny ; Biodiversity ; High-Throughput Nucleotide Sequencing ; Indonesia ; Metagenome ; Microbiota/genetics ; }, abstract = {The extreme conditions of the deep-sea environment, including limited light, low oxygen levels, high pressure, and nutrient scarcity, create a natural habitat for deep-sea bacteria. These remarkable microorganisms have developed unique strategies to survive and adapt to their surroundings. However, research on the diversity of deep-sea bacteria, both culture-dependent and culture-independent, in Indonesian waters remains insufficient. This study focused on exploring the biodiversity of deep-sea bacteria, specifically in the Makassar and Lombok Strait, the main Indonesian throughflow pathway characterized by relatively fertile water, which serves as an important deep-sea region. High-throughput DNA sequencing of full-length 16S rRNA was employed to construct a genomic database. The results of the bioinformatic analysis revealed that two stations, 48 and 50 (Makassar Strait), exhibited a more similar community structure of deep-sea bacteria than did station 33 (Lombok Strait). Among the predominant phyla found at a depth of 1000 m, the top ten were Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Planctomycetes, Acidobacteria, Nitrospinae, Verrucomicrobia, Candidatus Melainabacteria, and Cyanobacteria. Furthermore, the genera Colwellia, Moritella, Candidatus Pelagibacter, Alteromonas, and Psychrobacter consistently appeared at all three stations, albeit with varying relative abundance values. These bacterial genera share common characteristics, such as psychrophilic, halophilic, and piezophilic tendencies, and are commonly found in deep-sea ecosystem. The environmental conditions at a depth of 1000 m were relatively stable, with an average pressure 10 MPa, temperature 4.68 °C, salinity 34.58 PSU, pH 8.06, chlorophyll-a 0.29 µg/L, nitrate 3.19 µmol/L, phosphate 6.32 µmol/L and dissolved oxygen (DO) 2.90 mg/L. The bacterial community structures at the three sampling stations located at the same depth (1000 m) exhibited similarities, as indicated by the closely aligned similarity index values.}, } @article {pmid39461939, year = {2024}, author = {Gardiner, LJ and Marshall, M and Reusch, K and Dearden, C and Birmingham, M and Carrieri, AP and Pyzer-Knapp, EO and Krishna, R and Neal, AL}, title = {DGCNN approach links metagenome-derived taxon and functional information providing insight into global soil organic carbon.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {113}, pmid = {39461939}, issn = {2055-5008}, support = {BBS/E/RH/230003B//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/X010953/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {*Soil Microbiology ; *Carbon/metabolism ; *Soil/chemistry ; *Metagenomics/methods ; *Metagenome ; Machine Learning ; Microbiota ; Carbon Cycle ; Bacteria/genetics/classification/isolation & purification/metabolism ; Neural Networks, Computer ; }, abstract = {Metagenomics can provide insight into the microbial taxa present in a sample and, through gene identification, the functional potential of the community. However, taxonomic and functional information are typically considered separately in downstream analyses. We develop interpretable machine learning (ML) approaches for modelling metagenomic data, combining the biological representation of species with their associated genetically encoded functions within models. We apply our methods to investigate soil organic carbon (SOC) stocks. First, we combine a diverse global set of soil microbiome samples with environmental data, improving the predictive performance of classic ML and providing new insights into the role of soil microbiomes in global carbon cycling. Our network analysis of predictive taxa identified by classical ML models provides context for their ecological significance, extending the focus beyond just the most predictive taxa to 'hidden' features within the model that might be considered less predictive using standard methods for explainability. We next develop unique graph representations for individual microbiomes, linking microbial taxa to their associated functions directly, enabling predictions of SOC via deep graph convolutional neural networks (DGCNNs). Interpretation of the DGCNNs distinguished between the importance of functions of key individual species, providing genome sequence differences, e.g., gene loss/acquisition, that associate with SOC. These approaches identify several members of the Verrucomicrobiaceae family and a range of genetically encoded functions, e.g., related to carbohydrate metabolism, as important for SOC stocks and effective global SOC predictors. These relatively understudied but widespread organisms could play an important role in SOC dynamics globally.}, } @article {pmid39461337, year = {2024}, author = {Häcker, D and Siebert, K and Smith, BJ and Köhler, N and Riva, A and Mahapatra, A and Heimes, H and Nie, J and Metwaly, A and Hölz, H and Manz, Q and De Zen, F and Heetmeyer, J and Socas, K and Le Thi, G and Meng, C and Kleigrewe, K and Pauling, JK and Neuhaus, K and List, M and Pollard, KS and Schwerd, T and Haller, D}, title = {Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease.}, journal = {Cell host & microbe}, volume = {32}, number = {11}, pages = {2019-2034.e8}, doi = {10.1016/j.chom.2024.10.001}, pmid = {39461337}, issn = {1934-6069}, mesh = {*Crohn Disease/microbiology/therapy ; Animals ; Humans ; *Gastrointestinal Microbiome ; *Enteral Nutrition ; Mice ; *Feces/microbiology ; Child ; Female ; Male ; Germ-Free Life ; Adolescent ; Prospective Studies ; Interleukin-10/metabolism/genetics ; Metagenomics ; Fatty Acids/metabolism ; Disease Models, Animal ; Remission Induction ; Mice, Inbred C57BL ; Clostridiales ; Bacteria/classification/genetics ; }, abstract = {Exclusive enteral nutrition (EEN) is a first-line therapy for pediatric Crohn's disease (CD), but protective mechanisms remain unknown. We established a prospective pediatric cohort to characterize the function of fecal microbiota and metabolite changes of treatment-naive CD patients in response to EEN (German Clinical Trials DRKS00013306). Integrated multi-omics analysis identified network clusters from individually variable microbiome profiles, with Lachnospiraceae and medium-chain fatty acids as protective features. Bioorthogonal non-canonical amino acid tagging selectively identified bacterial species in response to medium-chain fatty acids. Metagenomic analysis identified high strain-level dynamics in response to EEN. Functional changes in diet-exposed fecal microbiota were further validated using gut chemostat cultures and microbiota transfer into germ-free Il10-deficient mice. Dietary model conditions induced individual patient-specific strain signatures to prevent or cause inflammatory bowel disease (IBD)-like inflammation in gnotobiotic mice. Hence, we provide evidence that EEN therapy operates through explicit functional changes of temporally and individually variable microbiome profiles.}, } @article {pmid39460431, year = {2024}, author = {Lin, B and Melnikov, V and Guo, S and Cao, Z and Ye, Z and Ye, Z and Ji, C and Chen, J and Wang, J and Zhang, H and Jiang, Y and Shi, C and Chen, Z and Zhang, Q and Ma, Z and Qiao, N and Chen, L and Wang, M and Wang, Y and Zhang, Z and Ye, H and Li, Y and Zhang, Y and Gao, R and Yu, Y}, title = {Concomitant gut dysbiosis and defective gut barrier serve as the bridges between hypercortisolism and chronic systemic inflammation in Cushing's disease.}, journal = {European journal of endocrinology}, volume = {191}, number = {5}, pages = {509-522}, doi = {10.1093/ejendo/lvae139}, pmid = {39460431}, issn = {1479-683X}, support = {82202906, 81972221, 81970716, 82170841, 82200921, 82370656, U21A20389, 82073640//National Natural Science Foundation of China/ ; SHDC12018X04//Shanghai Hospital Development Center/ ; 2023-I2M-C&T-B-125//CAMS Innovation Fund for Medical Sciences/ ; //National Project for Promoting the Diagnosis and Treatment of Major Diseases/ ; //MDT/ ; }, mesh = {Humans ; *Dysbiosis/metabolism ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Adult ; Middle Aged ; Caco-2 Cells ; *Inflammation/metabolism ; Feces/microbiology/chemistry ; Intestinal Mucosa/metabolism/microbiology ; Pituitary ACTH Hypersecretion/metabolism ; Cushing Syndrome/metabolism/microbiology ; Carrier Proteins/metabolism ; }, abstract = {OBJECTIVE: The aim of this study was to investigate the gut microbial signatures and related pathophysiological implications in patients with Cushing's disease (CD).

DESIGN AND METHODS: Twenty-seven patients with CD and 45 healthy controls were enrolled. Based on obtained metagenomics data, we performed correlation, network study, and genome interaction group (GIG) analysis. Fecal metabolomics and serum enzyme linked immunosorbent assay (ELISA) analysis were conducted in dichotomized CD patients. Caco-2 cells were incubated with gradient concentrations of cortisol for subsequent transepithelial electrical resistance (TEER) measurement, FITC-dextran transwell permeability assay, qPCR, and western blot analysis.

RESULTS: Gut microbial composition in patients with CD was notably different from that in healthy controls. Network analysis revealed that Eubacterium siraeum might serve as the core specie in the gut microbial system of CD patients. Subsequent GIG analysis identified the positive correlations between GIG9 and UFC. Further serum ELISA and fecal metabolomics uncovered that CD patients with elevated UFC levels were characterized with increased lipopolysaccharide binding protein (LBP). Moreover, remarkable positive association was found between LBP level and relative abundance of E. siraeum. TEER and FITC-dextran transwell assays demonstrated that hypercortisolism induced increased gut permeability. Further qPCR and western blot analysis suggested that dysregulated AhR/Claudin 2 axis might be involved in the development of hypercortisolism-induced defective gut barrier function.

CONCLUSIONS: Disease activity associated dysbiosis and defective gut barrier might jointly facilitate the development of systemic inflammation in patients with CD.}, } @article {pmid39459947, year = {2024}, author = {Vansia, R and Smadi, M and Phelan, J and Wang, A and Bilodeau, GJ and Pernal, SF and Guarna, MM and Rott, M and Griffiths, JS}, title = {Viral Diversity in Mixed Tree Fruit Production Systems Determined through Bee-Mediated Pollen Collection.}, journal = {Viruses}, volume = {16}, number = {10}, pages = {}, pmid = {39459947}, issn = {1999-4915}, support = {J-002323//Agriculture and Agri-Food Canada/ ; N-000212//Canadian Food Inspection Agency/ ; GRDI-SID-P-1903//Canadian Food Inspection Agency/ ; }, mesh = {*Pollen/virology ; Bees/virology ; Animals ; *Fruit/virology ; *Plant Diseases/virology ; *Plant Viruses/genetics/isolation & purification/classification ; *Pollination ; Virome/genetics ; Prunus/virology ; Metagenomics ; Trees/virology ; Malus/virology ; Ilarvirus/genetics/isolation & purification/classification ; Phylogeny ; Nepovirus/genetics/isolation & purification/classification/physiology ; }, abstract = {Commercially cultivated Prunus species are commonly grown in adjacent or mixed orchards and can be infected with unique or commonly shared viruses. Apple (Malus domestica), another member of the Rosacea and distantly related to Prunus, can share the same growing regions and common pathogens. Pollen can be a major route for virus transmission, and analysis of the pollen virome in tree fruit orchards can provide insights into these virus pathogen complexes from mixed production sites. Commercial honey bee (Apis mellifera) pollination is essential for improved fruit sets and yields in tree fruit production systems. To better understand the pollen-associated virome in tree fruits, metagenomics-based detection of plant viruses was employed on bee and pollen samples collected at four time points during the peak bloom period of apricot, cherry, peach, and apple trees at one orchard site. Twenty-one unique viruses were detected in samples collected during tree fruit blooms, including prune dwarf virus (PDV) and prunus necrotic ringspot virus (PNRSV) (Genus Ilarvirus, family Bromoviridae), Secoviridae family members tomato ringspot virus (genus Nepovirus), tobacco ringspot virus (genus Nepovirus), prunus virus F (genus Fabavirus), and Betaflexiviridae family member cherry virus A (CVA; genus Capillovirus). Viruses were also identified in composite leaf and flower samples to compare the pollen virome with the virome associated with vegetative tissues. At all four time points, a greater diversity of viruses was detected in the bee and pollen samples. Finally, the nucleotide sequence diversity of the coat protein regions of CVA, PDV, and PNRSV was profiled from this site, demonstrating a wide range of sequence diversity in pollen samples from this site. These results demonstrate the benefits of area-wide monitoring through bee pollination activities and provide new insights into the diversity of viruses in tree fruit pollination ecosystems.}, } @article {pmid39458495, year = {2024}, author = {Ohkusa, T and Kato, K and Sekizuka, T and Sugiyama, T and Sato, N and Kuroda, M}, title = {Comparison of the Gut Microbiota of Patients Who Improve with Antibiotic Combination Therapy for Ulcerative Colitis and Those Who Do Not: Investigation by Fecal Metagenomic Analyses.}, journal = {Nutrients}, volume = {16}, number = {20}, pages = {}, pmid = {39458495}, issn = {2072-6643}, mesh = {Humans ; *Colitis, Ulcerative/microbiology/drug therapy ; *Gastrointestinal Microbiome/drug effects ; *Feces/microbiology ; *Anti-Bacterial Agents/administration & dosage/pharmacology ; Male ; Female ; Adult ; Middle Aged ; *Metronidazole/administration & dosage ; *Drug Therapy, Combination ; Metagenomics/methods ; Amoxicillin/administration & dosage/pharmacology ; Tetracycline/pharmacology/administration & dosage ; Dysbiosis/microbiology ; Young Adult ; Treatment Outcome ; }, abstract = {Background/Objectives: The cause of ulcerative colitis (UC) may be related to commensal bacteria in genetically susceptible patients. We previously demonstrated that triple antibiotic combination therapy induces remission in patients with active UC in randomized controlled trials (RCTs). Now, we investigate changes in the gut microbiota of patients who responded to the antibiotic combination therapy. Methods: Thirty-one patients with UC given ATM/AFM (amoxicillin, metronidazole, and tetracycline or fosfomycin) therapy for two weeks were enrolled in this study. The clinical conditions of these UC patients were evaluated by the partial Mayo score. The gut microbiota was compared via the metagenomic shot gun analysis of fecal samples. Results: Of the 31 patients, 16 and 8 experienced complete and partial remission, respectively, over three months in response to ATM/AFM therapy, whereas ATM/AFM showed no efficacy in 7 patients. The dysbiosis before treatment in the active stage could be associated with increased populations of Bacteroides, Parabacteroides, Rickenella, Clostridium, Flavonifractor, Pelagibacter, Bordetella, Massilia, and Piscrickettsia species. Metagenomic analysis revealed dramatic changes in the gut microbiota at an early stage, that is, just two weeks after starting ATM/AFM therapy. After treatment in the responder group, the populations of bifidobacterium and lactobacilli species were significantly increased, while the population of bacteroides decreased. Conclusions: These results suggest that metagenomic analysis demonstrated a marked change in the gut microbiota after antibiotic combination treatment. In the triple antibiotic combination therapy, remission was associated with an increase in bifidobacterium and lactobacilli species.}, } @article {pmid39458465, year = {2024}, author = {Filardo, S and Di Pietro, M and Mastromarino, P and Porpora, MG and Sessa, R}, title = {A Multi-Strain Oral Probiotic Improves the Balance of the Vaginal Microbiota in Women with Asymptomatic Bacterial Vaginosis: Preliminary Evidence.}, journal = {Nutrients}, volume = {16}, number = {20}, pages = {}, pmid = {39458465}, issn = {2072-6643}, mesh = {Humans ; Female ; *Probiotics/administration & dosage ; *Vaginosis, Bacterial/microbiology/drug therapy/therapy ; *Vagina/microbiology ; Adult ; Prospective Studies ; Pilot Projects ; *Microbiota/drug effects ; Administration, Oral ; Young Adult ; Lactobacillus ; }, abstract = {BACKGROUND/OBJECTIVES: the vaginal microbiota is known to confer protection in the genital ecosystem, due to the predominance of different Lactobacillus species, playing a crucial role in women's health; alterations in the composition of the microbial communities in the vagina can be associated with the development of bacterial vaginosis (BV). Current therapy for BV involves oral or intravaginal administration of metronidazole or clindamycin, albeit the high recurrence rates suggest a need for alternative therapeutic tools, such as probiotics. Herein, the diversity and composition of vaginal microbiota in women with asymptomatic BV was investigated before and after the oral administration of a multi-strain probiotic formulation.

METHODS: a prospective observational pilot study with pre-post design was carried out from 1 June 2022, to 31 December 2022, on reproductive-age women with asymptomatic BV, as diagnosed via Nugent score, and matched healthy controls. The probiotic was administered to all study participants as acid-resistant oral capsules (twice daily), and a vaginal swab was collected at baseline and after 2 months of treatment, for the metagenomic analysis of 16s rDNA.

RESULTS: the diversity and richness of the vaginal microbiota in women with BV were significantly reduced after 2 months of supplementation with the oral probiotic, as evidenced by measures of α-diversity. Interestingly, some bacterial genera typically associated with dysbiosis, such as Megasphaera spp., were significantly decreased; whereas, at the same time, Lactobacillus spp. Doubled.

CONCLUSIONS: our preliminary results suggest that the multi-strain oral probiotic is a beneficial treatment specifically targeting the dysbiotic vaginal microenvironment.}, } @article {pmid39457438, year = {2024}, author = {Wei, Q and Song, Z and Chen, Y and Yang, H and Chen, Y and Liu, Z and Yu, Y and Tu, Q and Du, J and Li, H}, title = {Metagenomic Sequencing Elucidated the Microbial Diversity of Rearing Water Environments for Sichuan Taimen (Hucho bleekeri).}, journal = {Genes}, volume = {15}, number = {10}, pages = {}, pmid = {39457438}, issn = {2073-4425}, support = {(YSCX2035-011)//the Project of Original Innovation 2035/ ; (2022ZZCX093)//Sichuan Province financial independent innovation special project/ ; (SCCXTD-2024-15)//Sichuan Fresh Water Fish Innovation Team/ ; (cjb2024wzbh-011)//Ministry of Agriculture and Rural Affairs of the Yangtze River Basin Fisheries Administration Office-Artificial Breeding and Habitat Restoration of Sichuan taimen/ ; }, mesh = {Animals ; China ; *Metagenomics/methods ; Microbiota/genetics ; Water Microbiology ; Bacteria/genetics/classification ; Metagenome ; Biodiversity ; Fishes/microbiology/genetics ; Aquaculture/methods ; }, abstract = {BACKGROUND: Sichuan taimen (Hucho bleekeri) is a fish species endemic to China's upper Yangtze River drainage and has significant value as an aquatic resource. It was listed as a first-class state-protected wild animal by the Chinese government due to its very limited distribution and wild population at present.

METHODS: To elucidate the diversity of microorganisms in rearing water environments for H. bleekeri, metagenomic sequencing was applied to water samples from the Maerkang and Jiguanshan fish farms, where H. bleekeri were reared.

RESULTS: The results revealed that Pseudomonadota was the dominant phylum in the microbial communities of the water samples. Among the shared bacterial groups, Cyanobacteriota, Actinomycetota, Planctomycetota, Nitrospirota, and Verrucomicrobiota were significantly enriched in the water environment of Jiguanshan (p < 0.01), while Bacteroidota was more enriched in that of Maerkang (p < 0.01). Additionally, the Shannon diversity and Simpson index of the microbial community in the water environment of Maerkang were lower than in that of Jiguanshan.

CONCLUSIONS: The present study demonstrated the similarities and differences in the microbial compositions of rearing water environments for H. bleekeri, which are expected to benefit the artificial breeding of H. bleekeri in the future.}, } @article {pmid39457400, year = {2024}, author = {Arciuch-Rutkowska, M and Nowosad, J and Łuczyński, MK and Hussain, SM and Kucharczyk, D}, title = {Next-Generation Sequencing to Determine Changes in the Intestinal Microbiome of Juvenile Sturgeon Hybrid (Acipenser gueldenstaedtii♀ × Acipenser baerii♂) Resulting from Sodium Butyrate, Β-Glucan and Vitamin Supplementation.}, journal = {Genes}, volume = {15}, number = {10}, pages = {}, pmid = {39457400}, issn = {2073-4425}, support = {DWD/4/80/2020//Polish Ministry of Education and Science/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; *beta-Glucans/pharmacology/administration & dosage ; *Butyric Acid/metabolism/pharmacology ; *Fishes/genetics/microbiology ; *High-Throughput Nucleotide Sequencing ; *Dietary Supplements ; *Vitamins/pharmacology/administration & dosage ; Animal Feed/analysis ; Male ; Female ; Hydrocortisone ; Muramidase/genetics ; }, abstract = {BACKGROUND/OBJECTIVES: The effect of sodium butyrate (NaB), β-glucan (βG) and vitamins in the diet on gut microbiome, cortisol level, lysozyme activity and growth parameters of juvenile hybrid sturgeon (Acipenser gueldenstaedtii♀ × Acipenser baerii♂) was determined.

METHODS: Sturgeon hybrids (n = 144) were divided into three groups with enriched feeding (mg/kg of feed): FQV1 (50 NaB; 20 βG; const. vitamins), FQV2 (150 NaB; 20 βG; const. vitamins), FQV3 (50 NaB; 60 βG; const. vitamins) and control (not supplemented), each group in triplicate, 12 fish in each repetition. Rearing was carried out for 30 days in controlled conditions. Gut microbiome was characterized using Next Generation Sequencing (NGS) of DNA samples isolated from intestinal content. Cortisol level was determined using the ELISA test. Lysozyme activity was measured by turbidimetric test.

RESULTS: Based on data obtained from NGS, it was determined that the FQV1 group is characterized by the highest values of diversity indices (Shannon, Simpson and Chao-1) and the largest number of ASVs (Amplicon Sequence Variants). The highest abundance of probiotic bacteria (Lactobacillus, Lactococcus) was determined in the FQV1 group. The highest cortisol concentration was determined in the control (33.26 ng/mL), while the lowest was in FQV3 (27.75 ng/mL). The highest lysozyme activity was observed in FQV1 (154.64 U/mL), and the lowest in FQV2 (104.39 U/mL) and control (121.37 U/mL) (p < 0.05). FQV2 was characterized by significantly more favorable values of breeding indicators (p < 0.05).

CONCLUSIONS: The obtained results prove that an appropriate composition of NaB, βG and vitamins can be used in the commercial breeding of juvenile hybrid sturgeons.}, } @article {pmid39457387, year = {2024}, author = {Naumova, OY and Dobrynin, PV and Khafizova, GV and Grigorenko, EL}, title = {The Association of the Oral Microbiota with Cognitive Functioning in Adolescence.}, journal = {Genes}, volume = {15}, number = {10}, pages = {}, pmid = {39457387}, issn = {2073-4425}, support = {P20HD091005//the Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; }, mesh = {Humans ; Male ; Adolescent ; *Cognition ; *Mouth/microbiology ; Child ; *Microbiota ; Saliva/microbiology ; Metagenomics/methods ; Bacteria/genetics/classification ; }, abstract = {Background: A growing body of research supports the role of the microbial communities residing in the digestive system in the host's cognitive functioning. Most of these studies have been focused on the gut microbiome and its association with clinical phenotypes in middle-aged and older adults. There is an insufficiency of population-based research exploring the association of normative cognitive functioning with the microbiome particularly with the oral microbiota. Methods: In this study, using metagenomics and metabolomics, we characterized the salivary microbiome diversity in a sample of 51 males of Hispanic and African American origin aged 12-18 years and explored the associations between the microbiome and the youths' cognitive performance captured with the Kaufman Assessment Battery for Children II (KABC-II). Results: Several bacterial species of the oral microbiota and related metabolic pathways were associated with cognitive function. In particular, we found negative associations between indicators of general intelligence and the relative abundance of Bacteroidetes and Lachnospiraceae and positive associations with Bifidobacteriaceae and Prevotella histicola sp. Among metabolic pathways, the super pathways related to bacterial cell division and GABA metabolism were linked to cognitive function. Conclusions: The results of our work are consistent with the literature reporting on the association between microbiota and cognitive function and support further population work to elucidate the potential for a healthy oral microbiome to improve cognitive health.}, } @article {pmid39456970, year = {2024}, author = {Yang, C and Wusigale, and You, L and Li, X and Kwok, LY and Chen, Y}, title = {Inflammation, Gut Microbiota, and Metabolomic Shifts in Colorectal Cancer: Insights from Human and Mouse Models.}, journal = {International journal of molecular sciences}, volume = {25}, number = {20}, pages = {}, pmid = {39456970}, issn = {1422-0067}, support = {2022YFHH0060//Inner Mongolia Autonomous Region Key R&D Plan Project/ ; NMGIRT2220//Inner Mongolia Autonomous Region Higher Education Institutions Innovation Team Development Plan/ ; }, mesh = {Animals ; *Colorectal Neoplasms/metabolism/microbiology/pathology ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Inflammation/metabolism/microbiology ; *Disease Models, Animal ; Male ; Female ; Metabolomics/methods ; Metabolome ; Middle Aged ; Dextran Sulfate ; Dysbiosis/microbiology/metabolism ; Aged ; Feces/microbiology ; }, abstract = {Colorectal cancer (CRC) arises from aberrant mutations in colorectal cells, frequently linked to chronic inflammation. This study integrated human gut metagenome analysis with an azoxymethane and dextran sulfate sodium-induced CRC mouse model to investigate the dynamics of inflammation, gut microbiota, and metabolomic profiles throughout tumorigenesis. The analysis of stool metagenome data from 30 healthy individuals and 40 CRC patients disclosed a significant escalation in both gut microbiota diversity and abundance in CRC patients compared to healthy individuals (p < 0.05). Marked structural disparities were identified between the gut microbiota of healthy individuals and those with CRC (p < 0.05), characterized by elevated levels of clostridia and diminished bifidobacteria in CRC patients (p < 0.05). In the mouse model, CRC mice exhibited distinct gut microbiota structures and metabolite signatures at early and advanced tumor stages, with subtle variations noted during the intermediate phase. Additionally, inflammatory marker levels increased progressively during tumor development in CRC mice, in contrast to their stable levels in healthy counterparts. These findings suggest that persistent inflammation might precipitate gut dysbiosis and altered microbial metabolism. Collectively, this study provides insights into the interplay between inflammation, gut microbiota, and metabolite changes during CRC progression, offering potential biomarkers for diagnosis. While further validation with larger cohorts is warranted, the data obtained support the development of CRC prevention and diagnosis strategies.}, } @article {pmid39456772, year = {2024}, author = {Vilà-Quintana, L and Fort, E and Pardo, L and Albiol-Quer, MT and Ortiz, MR and Capdevila, M and Feliu, A and Bahí, A and Llirós, M and García-Velasco, A and Morell Ginestà, M and Laquente, B and Pozas, D and Moreno, V and Garcia-Gil, LJ and Duell, EJ and Pimenoff, VN and Carreras-Torres, R and Aldeguer, X}, title = {Metagenomic Study Reveals Phage-Bacterial Interactome Dynamics in Gut and Oral Microbiota in Pancreatic Diseases.}, journal = {International journal of molecular sciences}, volume = {25}, number = {20}, pages = {}, pmid = {39456772}, issn = {1422-0067}, support = {201912-31//Fundació la Marató de TV3/ ; 9986//European Molecular Biology Organization/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Metagenomics/methods ; *Bacteriophages/genetics ; *Feces/microbiology ; Pancreatic Neoplasms/microbiology/metabolism ; Male ; Mouth/microbiology ; Saliva/microbiology/metabolism ; Female ; Middle Aged ; Carcinoma, Pancreatic Ductal/microbiology/metabolism/virology ; Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenome ; Pancreatitis, Chronic/microbiology/metabolism/virology ; Pancreatic Diseases/microbiology/metabolism/virology ; Aged ; Microbiota/genetics ; Adult ; }, abstract = {Individuals with pancreatic-related health conditions usually show lower diversity and different composition of bacterial and viral species between the gut and oral microbiomes compared to healthy individuals. We performed a thorough microbiome analysis, using deep shotgun sequencing of stool and saliva samples obtained from patients with chronic pancreatitis (CP), pancreatic ductal adenocarcinoma (PDAC), and healthy controls (HCs).We observed similar microbiota composition at the species level in both the gut and oral samples in PDAC patients compared to HCs, among which the most distinctive finding was that the abundance of oral-originated Fusobacterium nucleatum species did not differ between the oral and the gut samples. Moreover, comparing PDAC patients with HCs, Klebsiella oxytoca was significantly more abundant in the stool samples of PDAC patients, while Streptococcus spp. showed higher abundance in both the oral and stool samples of PDAC patients. Finally, the most important finding was the distinctive gut phage-bacterial interactome pattern among PDAC patients. CrAssphages, particularly Blohavirus, showed mutual exclusion with K. oxytoca species, while Burzaovirus showed co-occurrence with Enterobacteriaceae spp., which have been shown to be capable of inducing DNA damage in human pancreatic cells ex vivo. The interactome findings warrant further mechanistic studies, as our findings may provide new insights into developing microbiota-based diagnostic and therapeutic methods for pancreatic diseases.}, } @article {pmid39456745, year = {2024}, author = {Chen, Y and Chen, Z and Li, X and Malik, K and Li, C}, title = {Metagenomic Analysis: Alterations of Soil Microbial Community and Function due to the Disturbance of Collecting Cordyceps sinensis.}, journal = {International journal of molecular sciences}, volume = {25}, number = {20}, pages = {}, pmid = {39456745}, issn = {1422-0067}, support = {2021-SF-A4//Major Science and Technology Project of Qinghai Province/ ; LHZX-2022-01//Chinese Academy of Sciences-People's Government of Qinghai Province on Sanjiangyuan National Park/ ; 〔2021〕794//Gansu Province Grassland Monitoring and Evaluation Technology Support Project of Gansu Province Forestry and Grassland Administration/ ; }, mesh = {*Soil Microbiology ; *Cordyceps/genetics/metabolism/growth & development ; *Metagenomics/methods ; *Microbiota/genetics ; Archaea/genetics/metabolism/classification ; Bacteria/genetics/classification/metabolism ; Metagenome ; Soil/chemistry ; }, abstract = {Soil microorganisms are critical to the occurrence of Cordyceps sinensis (Chinese Cordyceps), a medicinal fungi used in Traditional Chinese Medicine. The over-collection of Chinese Cordyceps has caused vegetation degradation and impacted the sustainable occurrence of Cordyceps. The effects of Chinese Cordyceps collection on soil microorganisms have not been reported. Metagenomic analysis was performed on the soil of collecting and non-collecting areas of production and non-production areas, respectively. C. sinensis collection showed no alteration in alpha-diversity but significantly affected beta-diversity and the community composition of soil microorganisms. In Cordyceps production, Thaumarchaeota and Crenarchaeota were identified as the dominant archaeal phyla. DNA repair, flagellar assembly, propionate metabolism, and sulfur metabolism were affected in archaea, reducing the tolerance of archaea in extreme habitats. Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Nitrospirae were identified as the dominant bacterial phyla. The collection of Chinese Cordyceps enhanced the bacterial biosynthesis of secondary metabolites and suppressed ribosome and carbon metabolism pathways in bacteria. A more complex microbial community relationship network in the Chinese Cordyceps production area was found. The changes in the microbial community structure were closely related to C, N, P and enzyme activities. This study clarified soil microbial community composition and function in the Cordyceps production area and established that collection clearly affects the microbial community function by altering microbial community structure. Therefore, it would be important to balance the relationship between cordyceps production and microbiology.}, } @article {pmid39456741, year = {2024}, author = {He, H and Fang, C and Liu, L and Li, M and Liu, W}, title = {Environmental Driving of Adaptation Mechanism on Rumen Microorganisms of Sheep Based on Metagenomics and Metabolomics Data Analysis.}, journal = {International journal of molecular sciences}, volume = {25}, number = {20}, pages = {}, pmid = {39456741}, issn = {1422-0067}, support = {No. 2021YFD1600702//the National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Rumen/microbiology/metabolism ; Sheep/microbiology ; *Metabolomics/methods ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; Adaptation, Physiological ; Metabolome ; Metagenome ; Altitude ; }, abstract = {Natural or artificial selection causes animals to adapt to their environment. The adaptive changes generated by the rumen population and metabolism form the basis of ruminant evolution. In particular, the adaptive drive for environmental adaptation reflects the high-quality traits of sheep that have migrated from other places or have been distant from their origins for a long time. The Hu sheep is the most representative sheep breed in the humid and low-altitude environments (Tai Lake region) in East Asia and has been widely introduced into the arid and high-altitude environments (Tibetan Plateau and Hotan region), resulting in environmental adaptive changes in the Hu sheep. In this study, a joint analysis of the rumen microbial metagenome and metabolome was conducted on Hu sheep from different regions (area of origin and area of introduction) with the objective of investigating the quality traits of Hu sheep and identifying microorganisms that influence the adaptive drive of ruminants. The results demonstrated that the growth performance of Hu sheep was altered due to changes in rumen tissue and metabolism following their introduction to the arid area at relatively high altitude. Metagenomic and metabolomic analyses (five ramsper area) revealed that 3580 different microorganisms and 732 different metabolites were identified in the rumen fluid of arid sheep. Among these, the representative upregulated metabolites were 4,6-isocanedione, methanesulfonic acid and N2-succinyl-L-arginine, while the dominant microorganism was Prevotella ruminicola. The downregulated metabolites were identified as campesterol, teprenone and dihydroclavaminic acid, while the disadvantaged microorganisms were Dialister_succinatiphilus, Prevotella_sp._AGR2160, Prevotella_multisaccharivorax and Selenomonas_bovis. The results of the Pearson analysis indicated that the rumen microbiota and metabolite content of sheep were significantly altered and highly correlated following their relocation from a humid lowland to an arid upland. In particular, the observed changes in rumen microorganisms led to an acceleration of body metabolism, rendering sheep highly adaptable to environmental stress. Prevotella_ruminicola was identified as playing an important role in this process. These findings provide insights into the environmental adaptation mechanisms of sheep.}, } @article {pmid39456706, year = {2024}, author = {Adnane, M and Chapwanya, A}, title = {Microbial Gatekeepers of Fertility in the Female Reproductive Microbiome of Cattle.}, journal = {International journal of molecular sciences}, volume = {25}, number = {20}, pages = {}, pmid = {39456706}, issn = {1422-0067}, mesh = {Animals ; Cattle ; Female ; *Fertility ; *Microbiota ; Reproduction ; Dysbiosis/microbiology ; Genitalia, Female/microbiology ; }, abstract = {This review paper delves into the intricate relationship between the genital microbiome and fertility outcomes in livestock, with a specific focus on cattle. Drawing upon insights derived from culture-independent metagenomics studies, the paper meticulously examines the composition and dynamics of the genital microbiome. Through advanced techniques such as high-throughput sequencing, the review illuminates the temporal shifts in microbial communities and their profound implications for reproductive health. The analysis underscores the association between dysbiosis-an imbalance in microbial communities-and the development of reproductive diseases, shedding light on the pivotal role of microbial gatekeepers in livestock fertility. Furthermore, the paper emphasizes the need for continued exploration of uncharted dimensions of the female reproductive microbiome to unlock new insights into its impact on fertility. By elucidating the complex interplay between microbial communities and reproductive health, this review underscores the importance of innovative strategies aimed at enhancing fertility and mitigating reproductive diseases in livestock populations.}, } @article {pmid39456701, year = {2024}, author = {Yan, K and Sun, X and Fan, C and Wang, X and Yu, H}, title = {Unveiling the Role of Gut Microbiota and Metabolites in Autoimmune Thyroid Diseases: Emerging Perspectives.}, journal = {International journal of molecular sciences}, volume = {25}, number = {20}, pages = {}, pmid = {39456701}, issn = {1422-0067}, support = {82160154, 81670844//National Natural Science Foundation Project of China/ ; QKH-PTRC-GCC[2023]041//The Hundred-level Innovative Talent Foundation of Guizhou Province/ ; 18-ZY-001//The Program for Excellent Young Talents of Zunyi Medical University/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Animals ; Graves Disease/microbiology/metabolism/immunology ; Autoimmune Diseases/microbiology/metabolism ; Thyroid Hormones/metabolism ; Hashimoto Disease/microbiology/metabolism/immunology ; Thyroid Gland/metabolism/microbiology ; Fatty Acids, Volatile/metabolism ; }, abstract = {Autoimmune thyroid diseases (AITDs) are among the most prevalent organ-specific autoimmune disorders, with thyroid hormones playing a pivotal role in the gastrointestinal system's structure and function. Emerging evidence suggests a link between AITDs and the gut microbiome, which is a diverse community of organisms that are essential for digestion, absorption, intestinal homeostasis, and immune defense. Recent studies using 16S rRNA and metagenomic sequencing of fecal samples from AITD patients have revealed a significant correlation between a gut microbiota imbalance and the severity of AITDs. Progress in animal models of autoimmune diseases has shown that intervention in the gut microbiota can significantly alter the disease severity. The gut microbiota influences T cell subgroup differentiation and modulates the pathological immune response to AITDs through mechanisms involving short-chain fatty acids (SCFAs), lipopolysaccharides (LPSs), and mucosal immunity. Conversely, thyroid hormones also influence gut function and microbiota composition. Thus, there is a bidirectional relationship between the thyroid and the gut ecosystem. This review explores the pathogenic mechanisms of the gut microbiota and its metabolites in AITDs, characterizes the gut microbiota in Graves' disease (GD) and Hashimoto's thyroiditis (HT), and examines the interactions between the gut microbiota, thyroid hormones, T cell differentiation, and trace elements. The review aims to enhance understanding of the gut microbiota-thyroid axis and proposes novel approaches to mitigate AITD severity through gut microbiota modulation.}, } @article {pmid39453910, year = {2024}, author = {Mondal, N and Dutta, S and Chatterjee, S and Sarkar, J and Mondal, M and Roy, C and Chakraborty, R and Ghosh, W}, title = {Aquificae overcomes competition by archaeal thermophiles, and crowding by bacterial mesophiles, to dominate the boiling vent-water of a Trans-Himalayan sulfur-borax spring.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0310595}, pmid = {39453910}, issn = {1932-6203}, mesh = {*Hot Springs/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/metabolism ; *Sulfur/metabolism ; Archaea/genetics/metabolism ; Phylogeny ; Microbiota/genetics ; Boron/metabolism ; Water Microbiology ; }, abstract = {Trans-Himalayan hot spring waters rich in boron, chlorine, sodium and sulfur (but poor in calcium and silicon) are known based on PCR-amplified 16S rRNA gene sequence data to harbor high diversities of infiltrating bacterial mesophiles. Yet, little is known about the community structure and functions, primary productivity, mutual interactions, and thermal adaptations of the microorganisms present in the steaming waters discharged by these geochemically peculiar spring systems. We revealed these aspects of a bacteria-dominated microbiome (microbial cell density ~8.5 × 104 mL-1; live:dead cell ratio 1.7) thriving in the boiling (85°C) fluid vented by a sulfur-borax spring called Lotus Pond, situated at 4436 m above the mean sea-level, in the Puga valley of eastern Ladakh, on the Changthang plateau. Assembly, annotation, and population-binning of >15-GB metagenomic sequence illuminated the numeral predominance of Aquificae. While members of this phylum accounted for 80% of all 16S rRNA-encoding reads within the metagenomic dataset, 14% of such reads were attributed to Proteobacteria. Post assembly, only 25% of all protein-coding genes identified were attributable to Aquificae, whereas 41% was ascribed to Proteobacteria. Annotation of metagenomic reads encoding 16S rRNAs, and/or PCR-amplified 16S rRNA genes, identified 163 bacterial genera, out of which 66 had been detected in past investigations of Lotus Pond's vent-water via 16S amplicon sequencing. Among these 66, Fervidobacterium, Halomonas, Hydrogenobacter, Paracoccus, Sulfurihydrogenibium, Tepidimonas, Thermus and Thiofaba (or their close phylogenomic relatives) were presently detected as metagenome-assembled genomes (MAGs). Remarkably, the Hydrogenobacter related MAG alone accounted for ~56% of the entire metagenome, even though only 15 out of the 66 genera consistently present in Lotus Pond's vent-water have strains growing in the laboratory at >45°C, reflecting the continued existence of the mesophiles in the ecosystem. Furthermore, the metagenome was replete with genes crucial for thermal adaptation in the context of Lotus Pond's geochemistry and topography. In terms of sequence similarity, a majority of those genes were attributable to phylogenetic relatives of mesophilic bacteria, while functionally they rendered functions such as encoding heat shock proteins, molecular chaperones, and chaperonin complexes; proteins controlling/modulating/inhibiting DNA gyrase; universal stress proteins; methionine sulfoxide reductases; fatty acid desaturases; different toxin-antitoxin systems; enzymes protecting against oxidative damage; proteins conferring flagellar structure/function, chemotaxis, cell adhesion/aggregation, biofilm formation, and quorum sensing. The Lotus Pond Aquificae not only dominated the microbiome numerically but also acted potentially as the main primary producers of the ecosystem, with chemolithotrophic sulfur oxidation (Sox) being the fundamental bioenergetic mechanism, and reductive tricarboxylic acid (rTCA) cycle the predominant carbon fixation pathway. The Lotus Pond metagenome contained several genes directly or indirectly related to virulence functions, biosynthesis of secondary metabolites including antibiotics, antibiotic resistance, and multi-drug efflux pumping. A large proportion of these genes being attributable to Aquificae, and Proteobacteria (very few were ascribed to Archaea), it could be worth exploring in the future whether antibiosis helped the Aquificae overcome niche overlap with other thermophiles (especially those belonging to Archaea), besides exacerbating the bioenergetic costs of thermal endurance for the mesophilic intruders of the ecosystem.}, } @article {pmid39450991, year = {2024}, author = {Du, S and Tong, X and Leung, MHY and Betts, RJ and Woo, AC and Bastien, P and Misra, N and Aguilar, L and Clavaud, C and Lee, PKH}, title = {Chronic exposure to polycyclic aromatic hydrocarbons alters skin virome composition and virus-host interactions.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39450991}, issn = {1751-7370}, support = {7020049//L'Oréal Research & Innovation, Pudong, China, and the City University of Hong Kong/ ; //L'Oréal Research & Innovation, Pudong, China/ ; 7020049//City University of Hong Kong/ ; }, mesh = {*Skin/virology/microbiology ; Female ; Humans ; *Virome ; *Polycyclic Aromatic Hydrocarbons/metabolism ; *Microbiota/drug effects ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Viruses/classification/drug effects/genetics/isolation & purification ; China ; Adult ; Metagenome ; Host Microbial Interactions ; Air Pollutants ; }, abstract = {Exposure to polycyclic aromatic hydrocarbons (PAHs) in polluted air influences the composition of the skin microbiome, which in turn is associated with altered skin phenotypes. However, the interactions between PAH exposure and viromes are unclear. This study aims to elucidate how PAH exposure affects the composition and function of skin viruses, their role in shaping the metabolism of bacterial hosts, and the subsequent effects on skin phenotype. We analyzed metagenomes from cheek skin swabs collected from 124 Chinese women in our previous study and found that the viruses associated with the two microbiome cutotypes had distinct diversities, compositions, functions, and lifestyles following PAH exposure. Moreover, exposure to high concentrations of PAHs substantially increased interactions between viruses and certain biodegrading bacteria. Under high-PAH exposure, the viruses were enriched in xenobiotic degradation functions, and there was evidence suggesting that the insertion of bacteriophage-encoded auxiliary metabolic genes into hosts aids biodegradation. Under low-PAH exposure conditions, the interactions followed the "Piggyback-the-Winner" model, with Cutibacterium acnes being "winners," whereas under high-PAH exposure, they followed the "Piggyback-the-Persistent" model, with biodegradation bacteria being "persistent." These findings highlight the impact of air pollutants on skin bacteria and viruses, their interactions, and their modulation of skin health. Understanding these intricate relationships could provide insights for developing targeted strategies to maintain skin health in polluted environments, emphasizing the importance of mitigating pollutant exposure and harnessing the potential of viruses to help counteract the adverse effects.}, } @article {pmid39450961, year = {2024}, author = {Sansonetti, PJ and Doré, J}, title = {[The human microbiome proofed by the Anthropocene: from correlation to causality and intervention].}, journal = {Medecine sciences : M/S}, volume = {40}, number = {10}, pages = {757-765}, doi = {10.1051/medsci/2024121}, pmid = {39450961}, issn = {1958-5381}, mesh = {Humans ; *Microbiota/physiology ; Animals ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; Biodiversity ; Causality ; Climate Change ; }, abstract = {The deleterious effects of human activities on biodiversity in the vegetal and animal world, and on climate changes are now well-established facts. However, little is yet known on the impact of human activities on microbial diversity on the planet and more specifically on the human microbiota Large implementation of metagenomics allows exaustive microbial cataloguing with broad spatio-temporal resolution of human microbiota. A reduction in bacterial richness and diversity in the human microbiota, particularly in the intestinal tract, is now established and particularly obvious in the most industrialized regions of the planet. Massive, uncontrolled use of antibiotics, drastic changes in traditional food habits and some elements of the "global exposome" that remain to identify are usually considered as stressors accounting for this situation of "missing microbes". As a consequence, a dysbiotic situation develops, a "dysbiosis" being characterized by the erosion of the central core of shared bacterial species across individuals and the development of opportunistic "pathobionts" in response to a weaker barrier capacity of these impoverished microbiota. The current challenge is to establish a causality link between the extension of these dysbiotic situations and the steady emergence of epidemic, non-communicable diseases such as asthma, allergy, obesity, diabetes, autoimmune diseases and some cancers. Experimental animal models combined with controlled, prospective clinical interventions are in demand to consolidate causality links, with the understanding that in the deciphering of the mechanisms of alteration of the human-microbiome symbiosis resides a novel exciting chapter of medicine: "microbial medicine".}, } @article {pmid39449105, year = {2024}, author = {Rahlff, J and Westmeijer, G and Weissenbach, J and Antson, A and Holmfeldt, K}, title = {Surface microlayer-mediated virome dissemination in the Central Arctic.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {218}, pmid = {39449105}, issn = {2049-2618}, support = {2023-03310_VR//Vetenskapsrådet/ ; CTS20:128//Carl Tryggers Foundation/ ; 2022-04340//Vetenskapsrådet/ ; 224665/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; RA3432/1-1, project number: 446702140//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Arctic Regions ; *Virome ; Viruses/classification/genetics/isolation & purification ; Greenland ; Genome, Viral/genetics ; Water Microbiology ; Metagenomics/methods ; Ecosystem ; Microbiota ; }, abstract = {BACKGROUND: Aquatic viruses act as key players in shaping microbial communities. In polar environments, they face significant challenges such as limited host availability and harsh conditions. However, due to the restricted accessibility of these ecosystems, our understanding of viral diversity, abundance, adaptations, and host interactions remains limited.

RESULTS: To fill this knowledge gap, we studied viruses from atmosphere-close aquatic ecosystems in the Central Arctic and Northern Greenland. Aquatic samples for virus-host analysis were collected from ~60 cm depth and the submillimeter surface microlayer (SML) during the Synoptic Arctic Survey 2021 on icebreaker Oden in the Arctic summer. Water was sampled from a melt pond and open water before undergoing size-fractioned filtration, followed by genome-resolved metagenomic and cultivation investigations. The prokaryotic diversity in the melt pond was considerably lower compared to that of open water. The melt pond was dominated by a Flavobacterium sp. and Aquiluna sp., the latter having a relatively small genome size of 1.2 Mb and the metabolic potential to generate ATP using the phosphate acetyltransferase-acetate kinase pathway. Viral diversity on the host fraction (0.2-5 µm) of the melt pond was strikingly limited compared to that of open water. From the 1154 viral operational taxonomic units (vOTUs), of which two-thirds were predicted bacteriophages, 17.2% encoded for auxiliary metabolic genes (AMGs) with metabolic functions. Some AMGs like glycerol-3-phosphate cytidylyltransferase and ice-binding like proteins might serve to provide cryoprotection for the host. Prophages were often associated with SML genomes, and two active prophages of new viral genera from the Arctic SML strain Leeuwenhoekiella aequorea Arc30 were induced. We found evidence that vOTU abundance in the SML compared to that of ~60 cm depth was more positively correlated with the distribution of a vOTU across five different Arctic stations.

CONCLUSIONS: The results indicate that viruses employ elaborate strategies to endure in extreme, host-limited environments. Moreover, our observations suggest that the immediate air-sea interface serves as a platform for viral distribution in the Central Arctic. Video Abstract.}, } @article {pmid39448846, year = {2024}, author = {Wu, Z and Liu, S and Ni, J}, title = {Metagenomic characterization of viruses and mobile genetic elements associated with the DPANN archaeal superphylum.}, journal = {Nature microbiology}, volume = {9}, number = {12}, pages = {3362-3375}, pmid = {39448846}, issn = {2058-5276}, support = {U2240205//National Natural Science Foundation of China (National Science Foundation of China)/ ; 51721006//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92047303//National Natural Science Foundation of China (National Science Foundation of China)/ ; 423B2703//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Archaea/genetics/virology ; *Metagenomics ; *Interspersed Repetitive Sequences ; *Archaeal Viruses/genetics/classification ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Phylogeny ; Metagenome ; Genome, Viral/genetics ; Genome, Archaeal ; Virome/genetics ; Symbiosis ; }, abstract = {The archaeal superphylum DPANN (an acronym formed from the initials of the first five phyla discovered: Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota and Nanoarchaeota) is a group of ultrasmall symbionts able to survive in extreme ecosystems. The diversity and dynamics between DPANN archaea and their virome remain largely unknown. Here we use a metagenomic clustered regularly interspaced short palindromic repeats (CRISPR) screening approach to identify 97 globally distributed, non-redundant viruses and unclassified mobile genetic elements predicted to infect hosts across 8 DPANN phyla, including 7 viral groups not previously characterized. Genomic analysis suggests a diversity of viral morphologies including head-tailed, tailless icosahedral and spindle-shaped viruses with the potential to establish lytic, chronic or lysogenic infections. We also find evidence of a virally encoded Cas12f1 protein (probably originating from uncultured DPANN archaea) and a mini-CRISPR array, which could play a role in modulating host metabolism. Many metagenomes have virus-to-host ratios >10, indicating that DPANN viruses play an important role in controlling host populations. Overall, our study illuminates the underexplored diversity, functional repertoires and host interactions of the DPANN virome.}, } @article {pmid39448159, year = {2025}, author = {Diaz, M and Aird, H and Le Viet, T and Gutiérrez, AV and Larke-Mejia, N and Omelchenko, O and Moragues-Solanas, L and Fritscher, J and Som, N and McLauchlin, J and Hildebrand, F and Jørgensen, F and Gilmour, M}, title = {Microbial composition and dynamics in environmental samples from a ready-to-eat food production facility with a long-term colonization of Listeria monocytogenes.}, journal = {Food microbiology}, volume = {125}, number = {}, pages = {104649}, doi = {10.1016/j.fm.2024.104649}, pmid = {39448159}, issn = {1095-9998}, mesh = {*Listeria monocytogenes/genetics/isolation & purification/growth & development/classification ; *Fast Foods/microbiology ; Food Microbiology ; Microbiota ; Bacteria/genetics/classification/isolation & purification/growth & development ; Environmental Microbiology ; Metagenomics ; Pseudomonas fluorescens/genetics/isolation & purification/growth & development/classification ; Food Contamination/analysis ; }, abstract = {Listeria monocytogenes is a foodborne pathogen of significant concern for the food industry due to its remarkable ability to persist through safety control efforts, posing a subsequent health threat to consumers. Understanding the microbial communities coexisting with L. monocytogenes in food processing environments provides insights into its persistence mechanisms. We investigated the microbial communities on non-food contact surfaces in a facility producing ready-to-eat foods, known to harbour a ST121 L. monocytogenes strain over multiple years. A 10-week sampling period was coordinated with the company and public health authorities. Metagenomic analysis revealed a stable microbial composition dominated by Pseudomonas fluorescens. While highly related populations were present in high-care production zones, distinctive taxa characteristic of specific areas were observed (e.g., Sphingomonas aerolata). Although Listeria spp. were not detected in metagenomes, they were detected in cultured samples, suggesting low relative abundance in factory settings. The findings suggest that a stable resident microbiota, with distinct adaptations to different areas within the factory, was selected for by their collective ability to survive control efforts in this environment. Listeria spp. was a member of this microbial community, albeit at low abundance, and may likewise benefit from the mutualism of the overall microbial community.}, } @article {pmid39448157, year = {2025}, author = {Hou, S and Liang, Z and Wu, Q and Cai, Q and Weng, Q and Guo, W and Ni, L and Lv, X}, title = {Metagenomics reveals the differences in flavor quality of rice wines with Hongqu and Maiqu as the fermentation starters.}, journal = {Food microbiology}, volume = {125}, number = {}, pages = {104647}, doi = {10.1016/j.fm.2024.104647}, pmid = {39448157}, issn = {1095-9998}, mesh = {*Wine/analysis/microbiology ; *Fermentation ; *Oryza/microbiology/chemistry ; *Flavoring Agents/metabolism/chemistry/analysis ; *Taste ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Metagenomics ; *Volatile Organic Compounds/analysis/metabolism ; Biogenic Amines/analysis/metabolism ; Microbiota ; Fungi/classification/genetics/metabolism/isolation & purification ; }, abstract = {Chinese rice wine (CRW) is an alcoholic beverage made mainly from rice or grain through saccharification and fermentation with Jiuqu (starter). Jiuqu makes an important contribution to the formation of the flavor characteristics of rice wine. Hongqu and Maiqu are two kinds of Jiuqu commonly used in CRW brewing. This study compared the microbial community, biogenic amines (BAs), and volatile flavor components (VFCs) of two types of rice wine brewed with Hongqu and Maiqu as fermentation agents. The results showed that the amino acid content of rice wine fermented with Maiqu (MQW) was significantly lower than that of rice wine fermented with Hongqu (HQW). On the contrary, the majority of BAs in MQW were significantly higher than those in HQW, except for putrescine. Multivariate statistical analysis indicated that most of the VFCs detected were enriched in HQW, while ethyl 3-phenylpropanoate and citronellol were enriched in MQW. The results of metagenomic analysis showed that Weissiella, Enterobacter, Leuconostoc, Kosakonia, Saccharomyces, Aspergilus and Monascus were identified as the predominant microbial genera in HQW brewing process, while Saccharopolyspora, Lactococcus, Enterobacter, Leuconostoc, Kosakonia, Pediococcus, Pantoea, Saccharomyces, Aspergillus, Lichtheimia and Nakaseomyces were the predominant microbial genera in MQW brewing. In addition, some VFCs and BAs were strongly correlated with dominant microbial genera in HQW and MQW brewing. Bioinformatics analysis showed that the abundance of genes involved in BAs synthesis in MQW brewing was much higher than that in HQW brewing, while the abundances of genes related to metabolic pathway of characteristic VFCs in HQW brewing were obviously higher than those in MQW, which explained the differences in flavor quality between HQW and MQW from the perspective of microbial genes. Collectively, these findings provide scientific evidence for elucidating the contribution of different microbial genera to the formation of flavor quality of CRW, and is helpful for screening beneficial microbes to enhance flavor quality and drinking comfort of CRW.}, } @article {pmid39448156, year = {2025}, author = {Ren, D and Liu, S and Qin, H and Huang, M and Bai, X and Han, X and Zhang, S and Mao, J}, title = {Metagenomics-based insights into the microbial community dynamics and flavor development potentiality of artificial and natural pit mud.}, journal = {Food microbiology}, volume = {125}, number = {}, pages = {104646}, doi = {10.1016/j.fm.2024.104646}, pmid = {39448156}, issn = {1095-9998}, mesh = {*Metagenomics ; *Bacteria/genetics/classification/metabolism/isolation & purification/growth & development ; *Flavoring Agents/metabolism ; *Microbiota ; Fermentation ; Metagenome ; Taste ; Fermented Foods/microbiology ; Brassica/microbiology ; Food Microbiology ; }, abstract = {Strong-flavor Baijiu (SFB) production has relied on pit mud (PM) as a starter culture. The maturation time of natural PM (NPM) is about 30 years, so artificial PM (APM) with a shorter maturation time has attracted widespread attention. This study reveals the microbial and functional dissimilarities of APM and NPM, and helps to elucidate the different metabolic roles of microbes during substrate degradation and flavor formation. Significant differences in the microbial community were observed between APM and NPM, manifesting as variations in the abundance of core microorganisms. Total of 187 high-quality metagenome-assembled genomes (MAGs) were obtained based on the metagenomic binning technology, mainly including Firmicutes (n = 106), Bacteroidota (n = 15) and Chloroflexota (n = 14). Furthermore, the relative concentration of flavor compounds in 4-year APM was similar to those in 30-year NPM, but different from those in 100-year NPMs. Methanosarcina, Methanobacterium, Methanoculleus, Anaerolineae bacterium and Aminobacterium were the key bacteria responsible for the flavor differences. From a functional perspective, amino acid and carbohydrate metabolism were key functions of PM microbial, and showed differences between APM and NPM. Finally, substrate degradation and flavor generation pathways were found to exist in multiple microorganisms. Combine the relative abundance of microorganisms with the absolute abundance of enzymes, Clostridium, Lactobacillus, Petrimonas, Methanoculleus, Prevotella, Methanobacterium, Methanosarcina, Methanothrix, Proteiniphilum, Bellilinea, Anaerolinea, Anaeromassilibacillus, Syntrophomonas and Brevefilum were identified as the key microorganisms in APM and NPM.}, } @article {pmid39446191, year = {2024}, author = {Shi, K and Liu, Q and Ji, Q and He, Q and Zhao, XM}, title = {MicroHDF: predicting host phenotypes with metagenomic data using a deep forest-based framework.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {6}, pages = {}, pmid = {39446191}, issn = {1477-4054}, support = {62162019//National Natural Science Foundation of China/ ; 2018SHZDZX01//Shanghai Municipal Science and Technology Major Project/ ; //Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence/ ; //ZJLab/ ; //Guangxi Key Laboratory Fund of Embedded Technology and Intelligent System/ ; ZY22096025//Special Funds for Guiding Local Scientific and Technological Development by the Central Government/ ; YCSW2024357//Guilin University of Technology, Innovation Project of Guangxi Graduate Education/ ; }, mesh = {Humans ; *Phenotype ; *Deep Learning ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology/genetics ; Autism Spectrum Disorder/genetics/microbiology ; Liver Cirrhosis/genetics/microbiology ; Computational Biology/methods ; Machine Learning ; Metagenome ; ROC Curve ; }, abstract = {The gut microbiota plays a vital role in human health, and significant effort has been made to predict human phenotypes, especially diseases, with the microbiota as a promising indicator or predictor with machine learning (ML) methods. However, the accuracy is impacted by a lot of factors when predicting host phenotypes with the metagenomic data, e.g. small sample size, class imbalance, high-dimensional features, etc. To address these challenges, we propose MicroHDF, an interpretable deep learning framework to predict host phenotypes, where a cascade layers of deep forest units is designed for handling sample class imbalance and high dimensional features. The experimental results show that the performance of MicroHDF is competitive with that of existing state-of-the-art methods on 13 publicly available datasets of six different diseases. In particular, it performs best with the area under the receiver operating characteristic curve of 0.9182 ± 0.0098 and 0.9469 ± 0.0076 for inflammatory bowel disease (IBD) and liver cirrhosis, respectively. Our MicroHDF also shows better performance and robustness in cross-study validation. Furthermore, MicroHDF is applied to two high-risk diseases, IBD and autism spectrum disorder, as case studies to identify potential biomarkers. In conclusion, our method provides an effective and reliable prediction of the host phenotype and discovers informative features with biological insights.}, } @article {pmid39445812, year = {2024}, author = {Soueidan, A and Idiri, K and Becchina, C and Esparbès, P and Legrand, A and Le Bastard, Q and Montassier, E}, title = {Pooled analysis of oral microbiome profiles defines robust signatures associated with periodontitis.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0093024}, pmid = {39445812}, issn = {2379-5077}, support = {RC 21_0250//Centre Hospitalier Universitaire de Nantes (CHU de Nantes)/ ; }, mesh = {Humans ; *Periodontitis/microbiology ; *Microbiota/genetics ; *Dysbiosis/microbiology ; Female ; *RNA, Ribosomal, 16S/genetics ; Adult ; Male ; Mouth/microbiology ; Middle Aged ; Metagenomics/methods ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {UNLABELLED: Oral microbial dysbiosis has been associated with periodontitis in studies using 16S rRNA gene sequencing analysis. However, this technology is not sufficient to consistently separate the bacterial species to species level, and reproducible oral microbiome signatures are scarce. Obtaining these signatures would significantly enhance our understanding of the underlying pathophysiological processes of this condition and foster the development of improved therapeutic strategies, potentially personalized to individual patients. Here, we sequenced newly collected samples from 24 patients with periodontitis, and we collected available oral microbiome data from 24 samples in patients with periodontitis and from 214 samples in healthy individuals (n = 262). Data were harmonized, and we performed a pooled analysis of individual patient data. By metagenomic sequencing of the plaque microbiome, we found microbial signatures for periodontitis and defined a periodontitis-related complex, composed by the most discriminative bacteria. A simple two-factor decision tree, based on Tannerella forsythia and Fretibacterium fastidiosum, was associated with periodontitis with high accuracy (area under the curve: 0.94). Altogether, we defined robust oral microbiome signatures relevant to the pathophysiology of periodontitis that can help define promising targets for microbiome therapeutic modulation when caring for patients with periodontitis.

IMPORTANCE: Oral microbial dysbiosis has been associated with periodontitis in studies using 16S rRNA gene sequencing analysis. However, this technology is not sufficient to consistently separate the bacterial species to species level, and reproducible oral microbiome signatures are scarce. Here, using ultra-deep metagenomic sequencing and machine learning tools, we defined a simple two-factor decision tree, based on Tannerella forsythia and Fretibacterium fastidiosum, that was highly associated with periodontitis. Altogether, we defined robust oral microbiome signatures relevant to the pathophysiology of periodontitis that can help define promising targets for microbiome therapeutic modulation when caring for patients with periodontitis.}, } @article {pmid39444361, year = {2024}, author = {Bravo, JE and Slizovskiy, I and Bonin, N and Oliva, M and Noyes, N and Boucher, C}, title = {The TELCoMB Protocol for High-Sensitivity Detection of ARG-MGE Colocalizations in Complex Microbial Communities.}, journal = {Current protocols}, volume = {4}, number = {10}, pages = {e70031}, pmid = {39444361}, issn = {2691-1299}, support = {R01 AI141810/AI/NIAID NIH HHS/United States ; R01 AI173928/AI/NIAID NIH HHS/United States ; 1R01AI173928-01A1//National Institute of Allergy and Infectious Diseases/ ; 5R01AI141810-04//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {*Microbiota/genetics ; Metagenomics/methods ; Interspersed Repetitive Sequences/genetics ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects/isolation & purification/classification ; Genes, Bacterial/genetics ; }, abstract = {Understanding the genetic basis of antimicrobial resistance is crucial for developing effective mitigation strategies. One necessary step is to identify the antimicrobial resistance genes (ARGs) within a microbial population, referred to as the resistome, as well as the mobile genetic elements (MGEs) harboring ARGs. Although shotgun metagenomics has been successful in detecting ARGs and MGEs within a microbiome, it is limited by low sensitivity. Enrichment using cRNA biotinylated probes has been applied to address this limitation, enhancing the detection of rare ARGs and MGEs, especially when combined with long-read sequencing. Here, we present the TELCoMB protocol, a Snakemake workflow that elucidates resistome and mobilome composition and diversity and uncovers ARG-MGE colocalizations. The protocol supports both short- and long-read sequencing and does not require enrichment, making it versatile for various genomic data types. TELCoMB generates publication-ready figures and CSV files for comprehensive analysis, improving our understanding of antimicrobial resistance mechanisms and spread. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Installing TELCOMB Locally Alternate Protocol: Installing TELCOMB on a SLURM Cluster Basic Protocol 2: Data Preprocessing Basic Protocol 3: Calculation of Resistome Distribution and Composition Basic Protocol 4: Identification of ARG-MGE Colocalizations.}, } @article {pmid39443951, year = {2024}, author = {Guo, W and Zhou, M and Li, F and Neves, ALA and Ma, T and Bi, S and Wang, W and Long, R and Guan, LL}, title = {Seasonal stability of the rumen microbiome contributes to the adaptation patterns to extreme environmental conditions in grazing yak and cattle.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {240}, pmid = {39443951}, issn = {1741-7007}, support = {31672453//National Natural Science Foundation of China/ ; 32402705//National Natural Science Foundation of China/ ; 2018F095R//Ministry of Alberta Agriculture and Forestry/ ; }, mesh = {Animals ; Cattle ; *Rumen/microbiology ; *Seasons ; *Gastrointestinal Microbiome/physiology ; Microbiota ; Adaptation, Physiological ; Bacteria/genetics/classification ; }, abstract = {BACKGROUND: The rumen microbiome plays an essential role in maintaining ruminants' growth and performance even under extreme environmental conditions, however, which factors influence rumen microbiome stability when ruminants are reared in such habitats throughout the year is unclear. Hence, the rumen microbiome of yak (less domesticated) and cattle (domesticated) reared on the Qinghai-Tibetan Plateau through the year were assessed to evaluate temporal changes in their composition, function, and stability.

RESULTS: Rumen fermentation characteristics and pH significantly shifted across seasons in both cattle and yak, but the patterns differed between the two ruminant species. Ruminal enzyme activity varied with season, and production of xylanase and cellulase was greater in yak compared to cattle in both fall and winter. The rumen bacterial community varied with season in both yak and cattle, with higher alpha diversity and similarity (beta diversity) in yak than cattle. The diversity indices of eukaryotic community did not change with season in both ruminant species, but higher similarity was observed in yak. In addition, the similarity of rumen microbiome functional community was higher in yak than cattle across seasons. Moreover, yak rumen microbiome encoded more genes (GH2 and GH3) related to cellulose and hemicellulose degradation compared to cattle, and a new enzyme family (GH160) gene involved in oligosaccharides was uniquely detected in yak rumen. The season affected microbiome attenuation and buffering values (stability), with higher buffering value in yak rumen microbiome than cattle. Positive correlations between antimicrobial resistance gene (dfrF) and CAZyme family (GH113) and microbiome stability were identified in yak, but such relationship was negatively correlated in cattle.

CONCLUSIONS: The findings of the potential of cellulose degradation, the relationship between rumen microbial stability and the abundance of functional genes varied differently across seasons and between yak and cattle provide insight into the mechanisms that may underpin their divergent adaptation patterns to the harsh climate of the Qinghai-Tibetan Plateau. These results lay a solid foundation for developing strategies to maintain and improve rumen microbiome stability and dig out the potential candidates for manufacturing lignocellulolytic enzymes in the yak rumen to enhance ruminants' performance under extreme environmental conditions.}, } @article {pmid39443495, year = {2024}, author = {Wright, JR and Chen See, JR and Ly, TT and Tokarev, V and Pellegrino, J and Peachey, L and Anderson, SLC and Walls, CY and Hosler, M and Shope, AJ and Gulati, S and Toler, KO and Lamendella, R}, title = {Application of a metatranscriptomics technology, CSI-Dx, for the detection of pathogens associated with prosthetic joint infections.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {25100}, pmid = {39443495}, issn = {2045-2322}, mesh = {Humans ; *Prosthesis-Related Infections/diagnosis/microbiology ; *Synovial Fluid/microbiology ; Female ; Male ; Aged ; Middle Aged ; Bacteria/genetics/isolation & purification ; Gene Expression Profiling/methods ; Metagenomics/methods ; Transcriptome ; Sensitivity and Specificity ; Microbiota/genetics ; }, abstract = {Preoperative identification of causal organism(s) is crucial for effective prosthetic joint infection treatment. Herein, we explore the clinical application of a novel metatranscriptomic (MT) workflow, CSI-Dx, to detect pathogens associated with prosthetic joint infection. MT provides insight into transcriptionally active microbes, overcoming limitations of culture-based and available molecular methods. This study included 340 human synovial fluid specimens subjected to CSI-Dx and traditional culture-based methods. Exploratory analyses were conducted to determine sensitivity and specificity of CSI-Dx for detecting clinically-relevant taxa. Our findings provide insights into the active microbial community composition of synovial fluid from arthroplasty patients and demonstrate the potential clinical utility of CSI-Dx for aiding prosthetic joint infection diagnosis. This approach offers potential for improved sensitivity and acceptable specificity compared to synovial fluid culture, enabling detection of culturable and non-culturable microorganisms. Furthermore, CSI-Dx provides valuable information on antimicrobial resistance gene expression. While further optimization is needed, integrating metatranscriptomic technologies like CSI-Dx into routine clinical practice can revolutionize prosthetic joint infection diagnosis by offering a comprehensive and active snapshot of associated pathogens.}, } @article {pmid39443316, year = {2024}, author = {Zheng, HY and Wu, HX and Du, ZQ}, title = {Gut metagenome-derived image augmentation and deep learning improve prediction accuracy of metabolic disease classification.}, journal = {Yi chuan = Hereditas}, volume = {46}, number = {10}, pages = {886-896}, doi = {10.16288/j.yczz.24-086}, pmid = {39443316}, issn = {0253-9772}, mesh = {Humans ; *Deep Learning ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; *Support Vector Machine ; *Metabolic Diseases/genetics/microbiology ; Neural Networks, Computer ; Bayes Theorem ; }, abstract = {In recent years, statistics and machine learning methods have been widely used to analyze the relationship between human gut microbial metagenome and metabolic diseases, which is of great significance for the functional annotation and development of microbial communities. In this study, we proposed a new and scalable framework for image enhancement and deep learning of gut metagenome, which could be used in the classification of human metabolic diseases. Each data sample in three representative human gut metagenome datasets was transformed into image and enhanced, and put into the machine learning models of logistic regression (LR), support vector machine (SVM), Bayesian network (BN) and random forest (RF), and the deep learning models of multilayer perceptron (MLP) and convolutional neural network (CNN). The accuracy performance of the overall evaluation model for disease prediction was verified by accuracy (A), accuracy (P), recall (R), F1 score (F1), area under ROC curve (AUC) and 10 fold cross-validation. The results showed that the overall performance of MLP model was better than that of CNN, LR, SVM, BN, RF and PopPhy-CNN, and the performance of MLP and CNN models was further improved after data enhancement (random rotation and adding salt-and-pepper noise). The accuracy of MLP model in disease prediction was further improved by 4%-11%, F1 by 1%-6% and AUC by 5%-10%. The above results showed that human gut metagenome image enhancement and deep learning could accurately extract microbial characteristics and effectively predict the host disease phenotype. The source code and datasets used in this study can be publicly accessed in https://github.com/HuaXWu/GM_ML_Classification.git.}, } @article {pmid39441997, year = {2024}, author = {Bolaños, LM and Michelsen, M and Temperton, B}, title = {Metagenomic time series reveals a Western English Channel viral community dominated by members with strong seasonal signals.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39441997}, issn = {1751-7370}, support = {NE/R010935/1//UK Natural Environment Research Council/ ; NE/R015953/1//National Capability Long-term Single Centre Science Programme, Climate Linked Atlantic Sector Science/ ; }, mesh = {*Seasons ; *Metagenomics ; *Seawater/virology/microbiology ; *Metagenome ; Viruses/genetics/classification/isolation & purification ; Virome/genetics ; }, abstract = {Marine viruses are key players of ocean biogeochemistry, profoundly influencing microbial community ecology and evolution. Despite their importance, few studies have explored continuous inter-seasonal viral metagenomic time series in marine environments. Viral dynamics are complex, influenced by multiple factors such as host population dynamics and environmental conditions. To disentangle the complexity of viral communities, we developed an unsupervised machine learning framework to classify viral contigs into "chronotypes" based on temporal abundance patterns. Analysing an inter-seasonal monthly time series of surface viral metagenomes from the Western English Channel, we identified chronotypes and compared their functional and evolutionary profiles. Results revealed a consistent annual cycle with steep compositional changes from winter to summer and steadier transitions from summer to winter. Seasonal chronotypes were enriched in potential auxiliary metabolic genes of the ferrochelatases and 2OG-Fe(II) oxygenase orthologous groups compared to non-seasonal types. Chronotypes clustered into four groups based on their correlation profiles with environmental parameters, primarily driven by temperature and nutrients. Viral contigs exhibited a rapid turnover of polymorphisms, akin to Red Queen dynamics. However, within seasonal chronotypes, some sequences exhibited annual polymorphism recurrence, suggesting that a fraction of the seasonal viral populations evolve more slowly. Classification into chronotypes revealed viral genomic signatures linked to temporal patterns, likely reflecting metabolic adaptations to environmental fluctuations and host dynamics. This novel framework enables the identification of long-term trends in viral composition, environmental influences on genomic structure, and potential viral interactions.}, } @article {pmid39441989, year = {2024}, author = {Bustos-Caparros, E and Viver, T and Gago, JF and Rodriguez-R, LM and Hatt, JK and Venter, SN and Fuchs, BM and Amann, R and Bosch, R and Konstantinidis, KT and Rossello-Mora, R}, title = {Ecological success of extreme halophiles subjected to recurrent osmotic disturbances is primarily driven by congeneric species replacement.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39441989}, issn = {1751-7370}, support = {PGC2018-096956-B-C41//Spanish Ministry of Science, Innovation and Universities/ ; //European Regional Development Funds/ ; PRE2019-088016//Spanish Government Ministry for Science and Innovation/ ; FEMS-GO-2020-254//Federation of European Microbiological Societies/ ; //DiSC of University of Innsbruck/ ; }, mesh = {*Osmotic Pressure ; Halobacteriaceae/genetics ; Biodiversity ; Salinity ; }, abstract = {To understand how extreme halophiles respond to recurrent disturbances, we challenged the communities thriving in salt-saturated (~36% salts) ~230 L brine mesocosms to repeated dilutions down to 13% (D13 mesocosm) or 20% (D20 mesocosm) salts each time mesocosms reached salt saturation due to evaporation (for 10 and 17 cycles, respectively) over 813 days. Depending on the magnitude of dilution, the most prevalent species, Haloquadratum walsbyi and Salinibacter ruber, either increased in dominance by replacing less competitive populations (for D20, moderate stress conditions), or severely decreased in abundance and were eventually replaced by other congeneric species better adapted to the higher osmotic stress (for D13, strong stress conditions). Congeneric species replacement was commonly observed within additional abundant genera in response to changes in environmental or biological conditions (e.g. phage predation) within the same system and under a controlled perturbation of a relevant environmental parameter. Therefore, a genus is an ecologically important level of diversity organization, not just a taxonomic rank, that persists in the environment based on congeneric species replacement due to relatively high functional overlap (gene sharing), with important consequences for the success of the lineage, and similar to the success of a species via strain-replacement. Further, our results showed that successful species were typically accompanied by the emergence of their own viral cohorts, whose intra-cohort diversity appeared to strongly covary with, and likely drive, the intra-host diversity. Collectively, our results show that brine communities are ecologically resilient and continuously adapting to changing environments by transitioning to alternative stable states.}, } @article {pmid39440963, year = {2024}, author = {Wang, Y and Sun, Y and Huang, K and Gao, Y and Lin, Y and Yuan, B and Wang, X and Xu, G and Nussio, LG and Yang, F and Ni, K}, title = {Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0068224}, pmid = {39440963}, issn = {2379-5077}, support = {32171686//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Medicago sativa/microbiology/metabolism ; *Silage/microbiology ; *Fermentation ; *Microbiota/genetics ; Animals ; Biomarkers/metabolism ; Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Cattle ; Multiomics ; }, abstract = {UNLABELLED: Alfalfa (Medicago sativa L.) is one of the most extensively cultivated forage crops globally, and its nutritional quality critically influences the productivity of dairy cows. Silage fermentation is recognized as a crucial technique for the preservation of fresh forage, ensuring the retention of its vital nutrients. However, the detailed microbial components and their functions in silage fermentation are not fully understood. This study integrated large-scale microbial culturing with high-throughput sequencing to thoroughly examine the microbial community structure in alfalfa silage and explored the potential pathways of nutritional degradation via metagenomic analysis. The findings revealed an enriched microbial diversity in silage, indicated by the identification of amplicon sequence variants. Significantly, the large-scale culturing approach recovered a considerable number of unique microbes undetectable by high-throughput sequencing. Predominant genera, such as Lactiplantibacillus, Leuconostoc, Lentilactobacillus, Weissella, and Liquorilactobacillus, were identified based on their abundance and prevalence. Additionally, genes associated with Enterobacteriaceae were discovered, which might be involved in pathways leading to the production of ammonia-N and butyric acid. Overall, this study offers a comprehensive insight into the microbial ecology of silage fermentation and provides valuable information for leveraging microbial consortia to enhance fermentation quality.

IMPORTANCE: Silage fermentation is a microbial-driven anaerobic process that efficiently converts various substrates into nutrients readily absorbable and metabolizable by ruminant animals. This study, integrating culturomics and metagenomics, has successfully identified core microorganisms involved in silage fermentation, including those at low abundance. This discovery is crucial for the targeted cultivation of specific microorganisms to optimize fermentation processes. Furthermore, our research has uncovered signature microorganisms that play pivotal roles in nutrient metabolism, significantly advancing our understanding of the intricate relationships between microbial communities and nutrient degradation during silage fermentation.}, } @article {pmid39438987, year = {2024}, author = {Rosenstein, R and Torres Salazar, BO and Sauer, C and Heilbronner, S and Krismer, B and Peschel, A}, title = {The Staphylococcus aureus-antagonizing human nasal commensal Staphylococcus lugdunensis depends on siderophore piracy.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {213}, pmid = {39438987}, issn = {2049-2618}, support = {GRK1708//Deutsche Forschungsgemeinschaft/ ; Cluster of Excellence EXC2124//Deutsche Forschungsgemeinschaft/ ; GRK1708//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; *Staphylococcus lugdunensis/metabolism/isolation & purification ; *Staphylococcus aureus/genetics ; *Nose/microbiology ; *Siderophores/metabolism ; *Staphylococcal Infections/microbiology ; Microbiota ; Adult ; Male ; Female ; Healthy Volunteers ; Symbiosis ; Carrier State/microbiology ; Middle Aged ; }, abstract = {BACKGROUND: Bacterial pathogens such as Staphylococcus aureus colonize body surfaces of part of the human population, which represents a critical risk factor for skin disorders and invasive infections. However, such pathogens do not belong to the human core microbiomes. Beneficial commensal bacteria can often prevent the invasion and persistence of such pathogens by using molecular strategies that are only superficially understood. We recently reported that the commensal bacterium Staphylococcus lugdunensis produces the novel antibiotic lugdunin, which eradicates S. aureus from the nasal microbiomes of hospitalized patients. However, it has remained unclear if S. lugdunensis may affect S. aureus carriage in the general population and which external factors might promote S. lugdunensis carriage to enhance its S. aureus-eliminating capacity.

RESULTS: We could cultivate S. lugdunensis from the noses of 6.3% of healthy human volunteers. In addition, S. lugdunensis DNA could be identified in metagenomes of many culture-negative nasal samples indicating that cultivation success depends on a specific bacterial threshold density. Healthy S. lugdunensis carriers had a 5.2-fold lower propensity to be colonized by S. aureus indicating that lugdunin can eliminate S. aureus also in healthy humans. S. lugdunensis-positive microbiomes were dominated by either Staphylococcus epidermidis, Corynebacterium species, or Dolosigranulum pigrum. These and further bacterial commensals, whose abundance was positively associated with S. lugdunensis, promoted S. lugdunensis growth in co-culture. Such mutualistic interactions depended on the production of iron-scavenging siderophores by supportive commensals and on the capacity of S. lugdunensis to import siderophores. Video Abstract CONCLUSIONS: These findings underscore the importance of microbiome homeostasis for eliminating pathogen colonization. Elucidating mechanisms that drive microbiome interactions will become crucial for microbiome-precision editing approaches.}, } @article {pmid39438902, year = {2024}, author = {Díaz-García, C and Moreno, E and Talavera-Rodríguez, A and Martín-Fernández, L and González-Bodí, S and Martín-Pedraza, L and Pérez-Molina, JA and Dronda, F and Gosalbes, MJ and Luna, L and Vivancos, MJ and Huerta-Cepas, J and Moreno, S and Serrano-Villar, S}, title = {Fecal microbiota transplantation alters the proteomic landscape of inflammation in HIV: identifying bacterial drivers.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {214}, pmid = {39438902}, issn = {2049-2618}, mesh = {Humans ; *Fecal Microbiota Transplantation ; *HIV Infections/therapy ; *Gastrointestinal Microbiome ; *Inflammation ; Male ; Middle Aged ; Female ; *Proteomics/methods ; Adult ; *Feces/microbiology ; Pilot Projects ; Double-Blind Method ; Bacteria/classification/isolation & purification/metabolism ; }, abstract = {BACKGROUND: Despite effective antiretroviral therapy, people with HIV (PWH) experience persistent systemic inflammation and increased morbidity and mortality. Modulating the gut microbiome through fecal microbiota transplantation (FMT) represents a novel therapeutic strategy. We aimed to evaluate proteomic changes in inflammatory pathways following repeated, low-dose FMT versus placebo.

METHODS: This double-masked, placebo-controlled pilot study assessed the proteomic impacts of weekly FMT versus placebo treatment over 8 weeks on systemic inflammation in 29 PWH receiving stable antiretroviral therapy (ART). Three stool donors with high Faecalibacterium and butyrate profiles were selected, and their individual stools were used for FMT capsule preparation. Proteomic changes in 345 inflammatory proteins in plasma were quantified using the proximity extension assay, with samples collected at baseline and at weeks 1, 8, and 24. Concurrently, we characterized shifts in the gut microbiota composition and annotated functions through shotgun metagenomics. We fitted generalized additive models to evaluate the dynamics of protein expression. We selected the most relevant proteins to explore their correlations with microbiome composition and functionality over time using linear mixed models.

RESULTS: FMT significantly reduced the plasma levels of 45 inflammatory proteins, including established mortality predictors such as IL6 and TNF-α. We found notable reductions persisting up to 16 weeks after the final FMT procedure, including in the expression of proteins such as CCL20 and CD22. We identified changes in 46 proteins, including decreases in FT3LG, IL6, IL10RB, IL12B, and IL17A, which correlated with multiple bacterial species. We found that specific bacterial species within the Ruminococcaceae, Succinivibrionaceae, Prevotellaceae families, and the Clostridium genus, in addition to their associated genes and functions, were significantly correlated with changes in inflammatory markers.

CONCLUSIONS: Targeting the gut microbiome through FMT effectively decreased inflammatory proteins in PWH, with sustained effects. These findings suggest the potential of the microbiome as a therapeutic target to mitigate inflammation-related complications in this population, encouraging further research and development of microbiome-based interventions. Video Abstract.}, } @article {pmid39438539, year = {2024}, author = {Guo, J and Li, Z and Liu, X and Jin, Y and Sun, Y and Yuan, Z and Zhang, W and Wang, J and Zhang, M}, title = {Response of the gut microbiota to changes in the nutritional status of red deer during winter.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {24961}, pmid = {39438539}, issn = {2045-2322}, support = {2572023AW20//National Key Fundamental Research Funds for the Central Universities, China/ ; 2572020BE02//National Key Fundamental Research Funds for the Central Universities, China/ ; QLKH [2023] 11//the Guizhou Forestry Administration Scientific Research Project/ ; 2023GZJB005//the Reward and Subsidy Fund Project of Guizhou Education University, Ministry of Science and Technology of the People's Republic of China and National Natural Science Foundation of China/ ; 32071512//the National Natural Science Foundation of China, NSFC/ ; 2023YFF1305000//National Key Research and Development Program of China: Migration and diffusion mechanism of wild animals and population control technology/ ; ZKKF2022179//the Opening Research Projects for the Think Tanks of Heilongjiang Provincial Universities/ ; }, mesh = {Animals ; *Deer/microbiology ; *Gastrointestinal Microbiome ; *Seasons ; *Nutritional Status ; Feces/microbiology ; Nitrogen/metabolism/analysis ; Creatinine ; }, abstract = {Unravelling abrupt alterations in the gut microbiota of wild species associated with nutritional stress is imperative but challenging for wildlife conservation. This study assessed the nutritional status of wild red deer during winter on the basis of changes in faecal nitrogen (FN) and urea nitrogen/creatinine (UN: C) levels and identified gut microbes associated with nutritional status via nutritional control experiments and metagenomic sequencing. The FN of wild red deer in winter 2022 was significantly lower than that in winter 2021 (p < 0.05, winter 2021: 1.37 ± 0.16% and winter 2022: 1.26 ± 0.22%), and the UN: C ratio increased (winter 2021: 2.19 ± 1.65 and winter 2022: 3.05 ± 3.50). Similar trends were found in late winter, which indicated greater nutritional pressure in winter (2022) and late winter. Compared with winter 2021, abundances of Ructibacterium and Butyrivibrio significantly increased, and Acetatifactor and Cuneatibacter significantly decreased during winter 2022 (p < 0.05). Compared with early winter, the cell growth and death pathways increased and lipid metabolism and its subpathway of secondary bile acid synthesis (ko00121) significantly decreased during late winter (p < 0.05), which was similar to the changes in malnourished experimental red deer. Abrupt alterations in the gut microbiota should receive increased attention when monitoring the nutritional health of wild ungulates. This study provides new insights and critical implications for the conservation of wild ungulate populations.}, } @article {pmid39438328, year = {2024}, author = {Varghese, P and Kumar, K and Sarkar, P and Karmakar, S and Shukla, SP and Kumar, S and Bharti, VS and Paul, T and Kantal, D}, title = {Impact of Triclosan on Bacterial Biodiversity and Sediment Enzymes - A Microcosm Study.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {113}, number = {5}, pages = {59}, pmid = {39438328}, issn = {1432-0800}, support = {DST/TMD-EWO-WTI/2K19/EWFH/2019/214//Department of Science and Technology, Govt. of India/ ; }, mesh = {*Triclosan/toxicity ; *Geologic Sediments/microbiology/chemistry ; *Biodiversity ; *Water Pollutants, Chemical/analysis/toxicity ; *Bacteria/drug effects ; }, abstract = {Triclosan (TCS), a widely used antimicrobial biocide, has raised serious concern among the scientific community in recent years owing to its ubiquitous presence around the globe and toxicity to aquatic organisms. The current study investigated the alterations in bacterial diversity, nutrients, and sediment enzyme activity in TCS-exposed sediment. TCS concentrations of 3 mg/L (T1) and 6 mg/L (T2) were applied in a microcosm setup for 28 days to sediment collected from Versova Creek, Mumbai. Among sediment enzymes, dehydrogenase activity exhibited the greatest degree of variability in 3 mg/L exposed sediment. Nitrite, total nitrogen and urease exhibited higher concentrations in 6 mg/L TCS exposed sediment. The concentration of ammonia was observed to be decreasing in treatments exposed to 6 mg/L TCS. Total heterotrophic bacteria exhibited an increase in count in T1 and a decrease in T2. Metagenomics data showed a higher relative abundance of bacteria in T1 compared to T2 on the 28th day of sampling. Proteobacteria was found to be the most abundant phylum in all samples, and their relative abundance was reduced by 0.14% in T1 and 5.48% in T2. The results confirm the alterations in the composition of sediment bacterial communities and their enzymatic activities due to TCS exposure.}, } @article {pmid39436938, year = {2024}, author = {Rocha, U and Kasmanas, JC and Toscan, R and Sanches, DS and Magnusdottir, S and Saraiva, JP}, title = {Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery.}, journal = {PLoS computational biology}, volume = {20}, number = {10}, pages = {e1012530}, pmid = {39436938}, issn = {1553-7358}, mesh = {*Metagenome/genetics ; *Microbiota/genetics ; *Computer Simulation ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Bacteria/genetics/classification ; Genome, Bacterial/genetics ; }, abstract = {We hypothesize that sample species abundance, sequencing depth, and taxonomic relatedness influence the recovery of metagenome-assembled genomes (MAGs). To test this hypothesis, we assessed MAG recovery in three in silico microbial communities composed of 42 species with the same richness but different sample species abundance, sequencing depth, and taxonomic distribution profiles using three different pipelines for MAG recovery. The pipeline developed by Parks and colleagues (8K) generated the highest number of MAGs and the lowest number of true positives per community profile. The pipeline by Karst and colleagues (DT) showed the most accurate results (~ 92%), outperforming the 8K and Multi-Metagenome pipeline (MM) developed by Albertsen and collaborators. Sequencing depth influenced the accurate recovery of genomes when using the 8K and MM, even with contrasting patterns: the MM pipeline recovered more MAGs found in the original communities when employing sequencing depths up to 60 million reads, while the 8K recovered more true positives in communities sequenced above 60 million reads. DT showed the best species recovery from the same genus, even though close-related species have a low recovery rate in all pipelines. Our results highlight that more bins do not translate to the actual community composition and that sequencing depth plays a role in MAG recovery and increased community resolution. Even low MAG recovery error rates can significantly impact biological inferences. Our data indicates that the scientific community should curate their findings from MAG recovery, especially when asserting novel species or metabolic traits.}, } @article {pmid39436609, year = {2025}, author = {Singer, F and Kuhring, M and Renard, BY and Muth, T}, title = {Moving Toward Metaproteogenomics: A Computational Perspective on Analyzing Microbial Samples via Proteogenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2859}, number = {}, pages = {297-318}, pmid = {39436609}, issn = {1940-6029}, mesh = {*Proteogenomics/methods ; *Microbiota/genetics ; Computational Biology/methods ; Proteomics/methods ; Software ; Databases, Protein ; Metagenomics/methods ; Algorithms ; Metagenome ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Mass Spectrometry/methods ; Proteome/genetics ; }, abstract = {Microbial sample analysis has received growing attention within the last decade, driven by important findings in microbiome research and promising applications in the biotechnological field. Modern mass spectrometry-based methodology has been established in this context, providing sufficient sensitivity, resolution, dynamic range, and throughput to analyze the so-called metaproteome of complex microbial mixtures from clinical or environmental samples. While proteomic analyses were previously restricted to common model organisms, next-generation sequencing technologies nowadays allow for the rapid and cost-efficient characterization of whole metagenomes of microbial consortia and specific genomes from non-model organisms to which microbes contribute by significant amounts. This proteogenomic approach, meaning the combined application of genomic and proteomic methods, enables researchers to create a protein database that presents a tailored blueprint of the microbial sample under investigation. This contribution provides an overview of the computational challenges and opportunities in proteogenomics and metaproteomics as of January 2018. For practical application, we first showcase an integrative proteogenomic method that circumvents existing reference databases by creating sample-specific transcripts. The underlying algorithm uses a graph network approach that combines RNA-Seq and peptide information. As a second example, we provide a tutorial for a simulation tool that estimates the computational limits of detecting microbial non-model organisms. This method evaluates the potential influence of error-tolerant searches and proteogenomic approaches on databases of interest. Finally, we discuss recommendations for developing future strategies that may help overcome present limitations by combining the strengths of genome- and proteome-based methods and moving toward an integrated metaproteogenomics approach.}, } @article {pmid39436239, year = {2024}, author = {Cheng, M and Zhou, H and Zhang, H and Zhang, X and Zhang, S and Bai, H and Zha, Y and Luo, D and Chen, D and Chen, S and Ning, K and Liu, W}, title = {Hidden Links Between Skin Microbiome and Skin Imaging Phenome.}, journal = {Genomics, proteomics & bioinformatics}, volume = {22}, number = {4}, pages = {}, doi = {10.1093/gpbjnl/qzae040}, pmid = {39436239}, issn = {2210-3244}, support = {32071465//National Natural Science Foundation of China/ ; 2018YFC0910502//National Key R&D Program of China/ ; }, mesh = {Humans ; *Skin/microbiology/metabolism/diagnostic imaging ; *Microbiota/genetics ; Male ; Female ; *Phenotype ; *Skin Aging ; Adult ; Middle Aged ; Metagenome ; }, abstract = {Despite the skin microbiome has been linked to skin health and diseases, its role in modulating human skin appearance remains understudied. Using a total of 1244 face imaging phenomes and 246 cheek metagenomes, we first established three skin age indices by machine learning, including skin phenotype age (SPA), skin microbiota age (SMA), and skin integration age (SIA) as surrogates of phenotypic aging, microbial aging, and their combination, respectively. Moreover, we found that besides aging and gender as intrinsic factors, skin microbiome might also play a role in shaping skin imaging phenotypes (SIPs). Skin taxonomic and functional α diversity was positively linked to melanin, pore, pigment, and ultraviolet spot levels, but negatively linked to sebum, lightening, and porphyrin levels. Furthermore, certain species were correlated with specific SIPs, such as sebum and lightening levels negatively correlated with Corynebacterium matruchotii, Staphylococcus capitis, and Streptococcus sanguinis. Notably, we demonstrated skin microbial potential in predicting SIPs, among which the lightening level presented the least error of 1.8%. Lastly, we provided a reservoir of potential mechanisms through which skin microbiome adjusted the SIPs, including the modulation of pore, wrinkle, and sebum levels by cobalamin and heme synthesis pathways, predominantly driven by Cutibacterium acnes. This pioneering study unveils the paradigm for the hidden links between skin microbiome and skin imaging phenome, providing novel insights into how skin microbiome shapes skin appearance and its healthy aging.}, } @article {pmid39435818, year = {2024}, author = {He, L and Yan, YT and Yuan, CY and Lin, QS and Yu, DT}, title = {Characteristics of soil viral communities in Cunninghamia lanceolata plantations with different stand ages.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {9}, pages = {2543-2551}, doi = {10.13287/j.1001-9332.202409.007}, pmid = {39435818}, issn = {1001-9332}, mesh = {*Soil Microbiology ; *Cunninghamia/growth & development/virology ; Soil/chemistry ; Viruses/classification/isolation & purification/genetics ; China ; Virome ; Phosphorus/analysis ; }, abstract = {We investigated the dynamics of soil viral community in Cunninghamia lanceolata plantations with different stand ages (8, 21, 27, and 40 years old) in a subtropical region. The viral metagenomics and bioinformatics analysis were used to analyze the compositional and functional differences of soil viral communities across different stand ages, and to explore the environmental driving factors. The results showed that tailed phages dominated soil viral community in subtropical C. lanceolata plantations, with the highest proportion of Siphoviridae (19.6%-39.5%). There was significant difference in soil viral community structure among different stand ages, with the main driving factors being electrical conductance and available phosphorus. The metabolic functional genes encoded by viruses exhibited higher relative abundance. The α-diversity of soil viral function in mature C. lanceolata plantations was higher than other stands. There were significant differences in soil viral functional structure among different stand ages, which were mainly driven by ammonium nitrogen. During the development of C. lanceolata plantations, auxiliary metabolic genes encoded by virus related to nitrogen and phosphorus may regulate the metabolism of host microorganisms, thereby potentially impacting biogeochemical cycling of these elements.}, } @article {pmid39434799, year = {2024}, author = {Ghabban, H and Albalawi, DA and Al-Otaibi, AS and Alshehri, D and Alenzi, AM and Alatawy, M and Alatawi, HA and Alnagar, DK and Bahieldin, A}, title = {Investigating the bacterial community of gray mangroves (Avicennia marina) in coastal areas of Tabuk region.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18282}, pmid = {39434799}, issn = {2167-8359}, mesh = {*Soil Microbiology ; *Avicennia/microbiology ; Saudi Arabia ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Wetlands ; }, abstract = {Mangrove vegetation, a threatened and unique inter-tidal ecosystem, harbours a complex and largely unexplored bacterial community crucial for nutrient cycling and the degradation of toxic pollutants in coastal areas. Despite its importance, the bacterial community composition of the gray mangrove (Avicennia marina) in the Red Sea coastal regions remains under-studied. This study aims to elucidate the structural and functional diversity of the microbiome in the bulk and rhizospheric soils associated with A. marina in the coastal areas of Ras Alshabaan-Umluj (Umluj) and Almunibrah-Al-Wajh (Al-Wajh) within the Tabuk region of Saudi Arabia. Amplicon sequencing targeting the 16S rRNA was performed using the metagenomic DNAs from the bulk and rhizospheric soil samples from Umluj and Al-Wajh. A total of 6,876 OTUs were recovered from all samples, of which 1,857 OTUs were common to all locations while the total number of OTUs unique to Al-wajh was higher (3,011 OTUs) than the total number of OTUs observed (1,324 OTUs) at Umluj site. Based on diversity indices, overall bacterial diversity was comparatively higher in rhizospheric soil samples of both sites. Comparing the diversity indices for the rhizosphere samples from the two sites revealed that the diversity was much higher in the rhizosphere samples from Al-Wajh as compared to those from Umluj. The most dominant genera in rhizosphere sample of Al-Wajh were Geminicoccus and Thermodesulfovibrio while the same habitat of the Umluj site was dominated by Propionibacterium, Corynebacterium and Staphylococcus. Bacterial functional potential prediction analyses showed that bacteria from two locations have almost similar patterns of functional genes including amino acids and carbohydrates metabolisms, sulfate reduction and C-1 compound metabolism and xenobiotics biodegradation. However, the rhizosphere samples of both sites harbour more genes involved in the utilization and assimilation of C-1 compounds. Our results reveal that bacterial communities inhabiting the rhizosphere of A. marina differed significantly from those in the bulk soil, suggesting a possible role of A. marina roots in shaping these bacterial communities. Additionally, not only vegetation but also geographical location appears to influence the overall bacterial composition at the two sites.}, } @article {pmid39434565, year = {2025}, author = {Blattner, LA and Lapellegerie, P and Courtney-Mustaphi, C and Heiri, O}, title = {Sediment Core DNA-Metabarcoding and Chitinous Remain Identification: Integrating Complementary Methods to Characterise Chironomidae Biodiversity in Lake Sediment Archives.}, journal = {Molecular ecology resources}, volume = {25}, number = {1}, pages = {e14035}, pmid = {39434565}, issn = {1755-0998}, mesh = {Animals ; *Chironomidae/genetics/classification ; *Lakes ; *DNA Barcoding, Taxonomic/methods ; *Geologic Sediments/chemistry ; *Biodiversity ; Switzerland ; Larva/genetics/classification ; DNA/genetics/chemistry ; Chitin ; Metagenomics/methods ; }, abstract = {Chironomidae, so-called non-biting midges, are considered key bioindicators of aquatic ecosystem variability. Data derived from morphologically identifying their chitinous remains in sediments document chironomid larvae assemblages, which are studied to reconstruct ecosystem changes over time. Recent developments in sedimentary DNA (sedDNA) research have demonstrated that molecular techniques are suitable for determining past and present occurrences of organisms. Nevertheless, sedDNA records documenting alterations in chironomid assemblages remain largely unexplored. To close this gap, we examined the applicability of sedDNA metabarcoding to identify Chironomidae assemblages in lake sediments by sampling and processing three 21-35 cm long sediment cores from Lake Sempach in Switzerland. With a focus on developing analytical approaches, we compared an invertebrate-universal (FWH) and a newly designed Chironomidae-specific metabarcoding primer set (CH) to assess their performance in detecting Chironomidae DNA. We isolated and identified chitinous larval remains and compared the morphotype assemblages with the data derived from sedDNA metabarcoding. Results showed a good overall agreement of the morphotype assemblage-specific clustering among the chitinous remains and the metabarcoding datasets. Both methods indicated higher chironomid assemblage similarity between the two littoral cores in contrast to the deep lake core. Moreover, we observed a pronounced primer bias effect resulting in more Chironomidae detections with the CH primer combination compared to the FWH combination. Overall, we conclude that sedDNA metabarcoding can supplement traditional remain identifications and potentially provide independent reconstructions of past chironomid assemblage changes. Furthermore, it has the potential of more efficient workflows, better sample standardisation and species-level resolution datasets.}, } @article {pmid39434181, year = {2024}, author = {Chen, CZ and Li, P and Liu, L and Sun, YJ and Ju, WM and Li, ZH}, title = {Seasonal variations of microbial communities and viral diversity in fishery-enhanced marine ranching sediments: insights into metabolic potentials and ecological interactions.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {209}, pmid = {39434181}, issn = {2049-2618}, support = {42277269//National Natural Science Foundation of China/ ; 42277269//National Natural Science Foundation of China/ ; 42277269//National Natural Science Foundation of China/ ; 42277269//National Natural Science Foundation of China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; }, mesh = {*Geologic Sediments/microbiology/virology ; *Seasons ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Viruses/classification/genetics/isolation & purification ; *Fisheries ; *Biodiversity ; Ecosystem ; Metagenome ; Sulfur/metabolism ; Metagenomics ; Carbon/metabolism ; Nitrogen/metabolism ; }, abstract = {BACKGROUND: The ecosystems of marine ranching have enhanced marine biodiversity and ecological balance and have promoted the natural recovery and enhancement of fishery resources. The microbial communities of these ecosystems, including bacteria, fungi, protists, and viruses, are the drivers of biogeochemical cycles. Although seasonal changes in microbial communities are critical for ecosystem functioning, the current understanding of microbial-driven metabolic properties and their viral communities in marine sediments remains limited. Here, we employed amplicon (16S and 18S) and metagenomic approaches aiming to reveal the seasonal patterns of microbial communities, bacterial-eukaryotic interactions, whole metabolic potential, and their coupling mechanisms with carbon (C), nitrogen (N), and sulfur (S) cycling in marine ranching sediments. Additionally, the characterization and diversity of viral communities in different seasons were explored in marine ranching sediments.

RESULTS: The current study demonstrated that seasonal variations dramatically affected the diversity of microbial communities in marine ranching sediments and the bacterial-eukaryotic interkingdom co-occurrence networks. Metabolic reconstruction of the 113 medium to high-quality metagenome-assembled genomes (MAGs) was conducted, and a total of 8 MAGs involved in key metabolic genes and pathways (methane oxidation - denitrification - S oxidation), suggesting a possible coupling effect between the C, N, and S cycles. In total, 338 viral operational taxonomic units (vOTUs) were identified, all possessing specific ecological characteristics in different seasons and primarily belonging to Caudoviricetes, revealing their widespread distribution and variety in marine sediment ecosystems. In addition, predicted virus-host linkages showed that high host specificity was observed, with few viruses associated with specific hosts.

CONCLUSIONS: This finding deepens our knowledge of element cycling and viral diversity in fisheries enrichment ecosystems, providing insights into microbial-virus interactions in marine sediments and their effects on biogeochemical cycling. These findings have potential applications in marine ranching management and ecological conservation. Video Abstract.}, } @article {pmid39434178, year = {2024}, author = {van Gogh, M and Louwers, JM and Celli, A and Gräve, S and Viveen, MC and Bosch, S and de Boer, NKH and Verheijden, RJ and Suijkerbuijk, KPM and Brand, EC and Top, J and Oldenburg, B and de Zoete, MR}, title = {Next-generation IgA-SEQ allows for high-throughput, anaerobic, and metagenomic assessment of IgA-coated bacteria.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {211}, pmid = {39434178}, issn = {2049-2618}, mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome ; *Metagenomics/methods ; *Immunoglobulin A/immunology ; *Bacteria/genetics/classification/immunology ; High-Throughput Nucleotide Sequencing/methods ; Inflammatory Bowel Diseases/microbiology/immunology ; }, abstract = {BACKGROUND: The intestinal microbiota plays a significant role in maintaining systemic and intestinal homeostasis, but can also influence diseases such as inflammatory bowel disease (IBD) and cancer. Certain bacterial species within the intestinal tract can chronically activate the immune system, leading to low-grade intestinal inflammation. As a result, plasma cells produce high levels of secretory antigen-specific immunoglobulin A (IgA), which coats the immunostimulatory bacteria. This IgA immune response against intestinal bacteria may be associated with the maintenance of homeostasis and health, as well as disease. Unraveling this dichotomy and identifying the immunostimulatory bacteria is crucial for understanding the relationship between the intestinal microbiota and the immune system, and their role in health and disease. IgA-SEQ technology has successfully identified immunostimulatory, IgA-coated bacteria from fecal material. However, the original technology is time-consuming and has limited downstream applications. In this study, we aimed to develop a next-generation, high-throughput, magnet-based sorting approach (ng-IgA-SEQ) to overcome the limitations of the original IgA-SEQ protocol.

RESULTS: We show, in various settings of complexity ranging from simple bacterial mixtures to human fecal samples, that our magnetic 96-well plate-based ng-IgA-SEQ protocol is highly efficient at sorting and identifying IgA-coated bacteria in a high-throughput and time efficient manner. Furthermore, we performed a comparative analysis between different IgA-SEQ protocols, highlighting that the original FACS-based IgA-SEQ approach overlooks certain nuances of IgA-coated bacteria, due to the low yield of sorted bacteria. Additionally, magnetic-based ng-IgA-SEQ allows for novel downstream applications. Firstly, as a proof-of-concept, we performed metagenomic shotgun sequencing on 10 human fecal samples to identify IgA-coated bacterial strains and associated pathways and CAZymes. Secondly, we successfully isolated and cultured IgA-coated bacteria by performing the isolation protocol under anaerobic conditions.

CONCLUSIONS: Our magnetic 96-well plate-based high-throughput next-generation IgA-SEQ technology efficiently identifies a great number of IgA-coated bacteria from fecal samples. This paves the way for analyzing large cohorts as well as novel downstream applications, including shotgun metagenomic sequencing, culturomics, and various functional assays. These downstream applications are essential to unravel the role of immunostimulatory bacteria in health and disease. Video Abstract.}, } @article {pmid39432998, year = {2024}, author = {Ma, ZS and Li, L}, title = {Identifications of the potential in-silico biomarkers in lung cancer tissue microbiomes.}, journal = {Computers in biology and medicine}, volume = {183}, number = {}, pages = {109231}, doi = {10.1016/j.compbiomed.2024.109231}, pmid = {39432998}, issn = {1879-0534}, mesh = {Humans ; *Lung Neoplasms/microbiology/metabolism ; *Microbiota ; *Biomarkers, Tumor/genetics/metabolism ; Metagenome ; Computer Simulation ; }, abstract = {It is postulated that the tumor tissue microbiome is one of the enabling characteristics that can either promote or suppress the ability of tumors to acquire certain hallmarks of cancer. This underscores its critical importance in carcinogenesis, cancer progression, and therapy responses. However, characterizing the tumor microbiomes is extremely challenging because of their low biomass and severe difficulties in controlling laboratory-borne contaminants, which is further aggravated by lack of comprehensively effective computational approaches to identify unique or enriched microbial species associated with cancers. Here we take advantage of a recent computational framework by Ma (2024), termed metagenome comparison (MC) framework (MCF), which can detect treatment-specific, unique or enriched OMUs (operational metagenomic unit), or US/ES (unique/enriched species) when adapted for this study. We apply the MCF to reanalyze four lung cancer tissue microbiome datasets, which include samples from Lung Adenocarcinoma (LUAD), Lung Squamous Cell Carcinoma (LUSC), and their adjacent normal tissue (NT) controls. Our analysis is structured around three distinct schemes: Scheme I-separately detecting the US/ES for each of the four lung cancer microbiome datasets; Scheme II-consolidation of the four datasets followed by detection of US/ES in the combined datasets; Scheme III-construction of the union and intersection sets of US/ES derived from the results of the preceding two schemes. The generated lists of US/ES, including enriched microbial phyla, likely hold significant biomedical value for developing diagnostic and prognostic biomarkers for lung cancer risk assessment, improving the efficacy of immunotherapy, and designing novel microbiome-based therapies in lung cancer research.}, } @article {pmid39432783, year = {2024}, author = {Oguro-Igashira, E and Murakami, M and Mori, R and Kuwahara, R and Kihara, T and Kohara, M and Fujiwara, M and Motooka, D and Okuzaki, D and Arase, M and Toyota, H and Peng, S and Ogino, T and Kitabatake, Y and Morii, E and Hirota, S and Ikeuchi, H and Umemoto, E and Kumanogoh, A and Takeda, K}, title = {The pyruvate-GPR31 axis promotes transepithelial dendrite formation in human intestinal dendritic cells.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {44}, pages = {e2318767121}, pmid = {39432783}, issn = {1091-6490}, support = {JP21H050430//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP21K07895//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP21gm1010004//Japan Agency for Medical Research and Development (AMED)/ ; JPMJSP213//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; J178501002//BD Biosciences (Becton Dickenson Biosciences)/ ; }, mesh = {Humans ; *Receptors, G-Protein-Coupled/metabolism ; *Dendritic Cells/metabolism ; *Pyruvic Acid/metabolism ; Intestinal Mucosa/metabolism/cytology ; Dendrites/metabolism ; Gastrointestinal Microbiome ; Signal Transduction ; Induced Pluripotent Stem Cells/metabolism/cytology ; Organoids/metabolism ; Intestines/cytology ; }, abstract = {The intestinal lumen is rich in gut microbial metabolites that serve as signaling molecules for gut immune cells. G-protein-coupled receptors (GPCRs) sense metabolites and can act as key mediators that translate gut luminal signals into host immune responses. However, the impacts of gut microbe-GPCR interactions on human physiology have not been fully elucidated. Here, we show that GPR31, which is activated by the gut bacterial metabolite pyruvate, is specifically expressed on type 1 conventional dendritic cells (cDC1s) in the lamina propria of the human intestine. Using human induced pluripotent stem cell-derived cDC1s and a monolayer human gut organoid coculture system, we show that cDC1s extend their dendrites toward pyruvate on the luminal side, forming transepithelial dendrites (TED). Accordingly, GPR31 activation via pyruvate enhances the fundamental function of cDC1 by allowing efficient uptake of gut luminal antigens, such as dietary compounds and bacterial particles through TED formation. Our results highlight the role of GPCRs in tuning the human gut immune system according to local metabolic cues.}, } @article {pmid39432094, year = {2024}, author = {Shafana Farveen, M and Narayanan, R}, title = {Omic-driven strategies to unveil microbiome potential for biodegradation of plastics: a review.}, journal = {Archives of microbiology}, volume = {206}, number = {11}, pages = {441}, pmid = {39432094}, issn = {1432-072X}, mesh = {*Biodegradation, Environmental ; *Plastics/metabolism ; *Microbiota ; Bacteria/metabolism/genetics/classification ; Proteomics ; Genomics ; Microbial Consortia ; }, abstract = {Plastic waste accumulation has lately been identified as the leading and pervasive environmental concern, harming all living beings, natural habitats, and the global market. Given this issue, developing ecologically friendly solutions, such as biodegradation instead of standard disposal, is critical. To effectively address and develop better strategies, it is critical to understand the inter-relationship between microorganisms and plastic, the role of genes and enzymes involved in this process. However, the complex nature of microbial communities and the diverse mechanisms involved in plastic biodegradation have hindered the development of efficient plastic waste degradation strategies. Omics-driven approaches, encompassing genomics, transcriptomics and proteomics have revolutionized our understanding of microbial ecology and biotechnology. Therefore, this review explores the application of omics technologies in plastic degradation studies and discusses the key findings, challenges, and future prospects of omics-based approaches in identifying novel plastic-degrading microorganisms, enzymes, and metabolic pathways. The integration of omics technologies with advanced molecular technologies such as the recombinant DNA technology and synthetic biology would guide in the optimization of microbial consortia and engineering the microbial systems for enhanced plastic biodegradation under various environmental conditions.}, } @article {pmid39432083, year = {2024}, author = {Xu, X and Liu, X and Liu, L and Chen, J and Guan, J and Luo, D}, title = {Metagenomic and transcriptomic profiling of the hypoglycemic and hypotriglyceridemic actions of Tremella fuciformis-derived polysaccharides in high-fat-diet- and streptozotocin-treated mice.}, journal = {Food & function}, volume = {15}, number = {22}, pages = {11096-11114}, doi = {10.1039/d4fo01870b}, pmid = {39432083}, issn = {2042-650X}, mesh = {Animals ; Mice ; *Diet, High-Fat/adverse effects ; *Hypoglycemic Agents/pharmacology ; Male ; *Basidiomycota/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Diabetes Mellitus, Experimental/drug therapy ; *Polysaccharides/pharmacology ; Gene Expression Profiling ; Streptozocin ; Blood Glucose/metabolism ; Metagenomics ; Transcriptome ; }, abstract = {Mushroom polysaccharides have great anti-diabetes potential. The fruiting body of Tremella fuciformis is rich in polysaccharides. However, few studies have been performed to date on T. fuciformis-derived polysaccharides (TPs) in terms of anti-diabetes potential. Our previous studies showed that novel TPs with medium molecular weights exhibited the highest anti-skin aging activities among the tested samples in D-galactose-treated mice. In the present study, the effects of these novel TPs, named TP, on high-fat-diet- and streptozotocin-treated mice were assessed, and their potential biological mechanisms were explored by metagenomic and transcriptomic analyses. Oral administration of TP markedly reduced blood glucose and TG levels, alleviated emaciation, improved anti-oxidant capacity, and protected the functions of β-cells at a dose of 100 mg kg[-1] in diabetic mice. Meanwhile, the taxonomic compositions and functional properties of fecal microbiota were altered considerably by TP, as evidenced by partial restoration of the imbalanced gut microbiota and the higher abundances of Bacteroides, Phocaeicola, Bifidobacterium, and Alistipes compared to the model mice, corresponding to the upregulation of four enriched KEGG pathways of microbial communities such as the digestive system, cardiovascular disease, parasitic infectious disease, and cell growth and death. Further transcriptomic analysis of liver tissues identified 35 enriched KEGG pathways associated with metabolism and cellular signaling processes in response to TP. These results demonstrated the biological mechanisms underlying the hypoglycemic and hypotriglyceridemic activities of TP. The findings expanded our understanding of the anti-diabetic mechanisms for mushroom polysaccharides and provided new clues for future studies.}, } @article {pmid39431789, year = {2024}, author = {Bickerstaff, JRM and Walsh, T and Court, L and Pandey, G and Ireland, K and Cousins, D and Caron, V and Wallenius, T and Slipinski, A and Rane, R and Escalona, HE}, title = {Chromosome Structural Rearrangements in Invasive Haplodiploid Ambrosia Beetles Revealed by the Genomes of Euwallacea fornicatus (Eichhoff) and Euwallacea similis (Ferrari) (Coleoptera, Curculionidae, Scolytinae).}, journal = {Genome biology and evolution}, volume = {16}, number = {11}, pages = {}, pmid = {39431789}, issn = {1759-6653}, support = {//ResearchPlus CSIRO Early Research Career Fellowship/ ; //Zimmerman Trust/ ; //ANIC-NRCA-CSIRO/ ; }, mesh = {Animals ; *Weevils/microbiology/genetics ; *Genome, Insect ; *Introduced Species ; Haploidy ; Chromosomes, Insect ; Coleoptera/microbiology/genetics ; }, abstract = {Bark and ambrosia beetles are among the most ecologically and economically damaging introduced plant pests worldwide. Life history traits including polyphagy, haplodiploidy, inbreeding polygyny, and symbiosis with fungi contribute to their dispersal and impact. Species vary in their interactions with host trees, with many attacking stressed or recently dead trees, such as the globally distributed Euwallacea similis (Ferrari). Other species, like the Polyphagous Shot Hole Borer Euwallacea fornicatus (Eichhoff), can attack over 680 host plants and is causing considerable economic damage in several countries. Despite their notoriety, publicly accessible genomic resources for Euwallacea Hopkins species are scarce, hampering our understanding of their invasive capabilities as well as modern control measures, surveillance, and management. Using a combination of long and short read sequencing platforms, we assembled and annotated high quality (BUSCO > 98% complete) pseudo-chromosome-level genomes for these species. Comparative macrosynteny analysis identified an increased number of pseudo-chromosome scaffolds in the haplodiploid inbreeding species of Euwallacea compared to diploid outbred species, due to fission events. This suggests that life history traits can impact chromosome structure. Further, the genome of E. fornicatus had a higher relative proportion of repetitive elements, up to 17% more, than E. similis. Metagenomic assembly pipelines identified microbiota associated with both species including Fusarium fungal symbionts and a novel Wolbachia strain. These novel genomes of haplodiploid inbreeding species will contribute to the understanding of how life history traits are related to their evolution and to the management of these invasive pests.}, } @article {pmid39431768, year = {2024}, author = {Tutagata, J and Pocquet, N and Trouche, B and Reveillaud, J}, title = {Dissection of Mosquito Ovaries, Midgut, and Salivary Glands for Microbiome Analyses at the Organ Level.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {212}, pages = {}, doi = {10.3791/67128}, pmid = {39431768}, issn = {1940-087X}, mesh = {Animals ; Female ; *Salivary Glands/microbiology ; *Microbiota/physiology ; *Ovary/microbiology ; Dissection/methods ; Culicidae/microbiology ; }, abstract = {The global burden of mosquito-transmitted diseases, including malaria, dengue, West Nile, Zika, Usutu, and yellow fever, continues to increase, posing a significant public health threat. With the rise of insecticide resistance and the absence of effective vaccines, new strategies are emerging that focus on the mosquito's microbiota. Nevertheless, the majority of symbionts remain resistant to cultivation. Characterizing the diversity and function of bacterial genomes in mosquito specimens, therefore, relies on metagenomics and subsequent assembly and binning strategies. The obtention and analysis of Metagenome-Assembled Genomes (MAGs) from separated organs can notably provide key information about the specific role of mosquito-associated microbes in the ovaries (the reproductive organs), the midgut (key for food digestion and immunity), or the salivary glands (essential for the transmission of vector-borne diseases as pathogens must colonize them to enter the saliva and reach the bloodstream during a blood meal). These newly reconstructed genomes can then pave the way for the development of novel vector biocontrol strategies. To this aim, it is required to isolate mosquito organs while avoiding cross-contamination between them or with microorganisms present in other mosquito organs. Here, we describe an optimized and contamination-free dissection protocol for studying mosquito microbiome at the organ level.}, } @article {pmid39431465, year = {2024}, author = {Hagan, J}, title = {Mapping the spread of antibiotic resistance genes in the coastal microbiome.}, journal = {BioTechniques}, volume = {76}, number = {9}, pages = {411-414}, doi = {10.1080/07366205.2024.2416379}, pmid = {39431465}, issn = {1940-9818}, mesh = {*Microbiota/genetics/drug effects ; *Metagenomics/methods ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; Seawater/microbiology ; Genes, Bacterial/genetics ; Metagenome/genetics ; }, abstract = {StandfirstCoastal environments are becoming increasingly exposed to antibiotics through anthropogenic inputs. But how could emerging metagenomic techniques be used to map the spread of antibiotic resistance genes in the coastal microbiome?[Formula: see text].}, } @article {pmid39431056, year = {2024}, author = {Han, L and Hu, C and Du, Z and Yu, H and Du, Y and Li, L and Li, F and Wang, Y and Gao, X and Sun, X and Zhang, Z and Qin, Y}, title = {Association of glycerolipid metabolism with gut microbiota disturbances in a hamster model of high-fat diet-induced hyperlipidemia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1439744}, pmid = {39431056}, issn = {2235-2988}, mesh = {Animals ; *Hyperlipidemias/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Diet, High-Fat/adverse effects ; Cricetinae ; *Disease Models, Animal ; *Liver/metabolism ; Male ; *Lipid Metabolism ; *Feces/microbiology ; Metabolomics ; Bacteria/classification/isolation & purification/metabolism/genetics ; Metagenomics ; Lipids/blood ; }, abstract = {BACKGROUND: High-fat diet (HFD)-induced hyperlipidemia, which is associated with gut microbiota disturbances, remains a major public health challenge. Glycerolipid metabolism is responsible for lipid synthesis and is thus involved in the development of hyperlipidemia. However, possible association between the HFD-modulated gut microbiome and the glycerolipid metabolism pathway remains unclear.

METHODS: Hamsters were fed a HFD for 4 weeks to establish a hyperlipidemia model. Fecal, plasma and liver samples collected from hamsters fed a HFD or a normal chow diet (NCD) were used for integrative metagenomic and untargeted metabolomic analyses to explore changes in the composition and functions of the gut microbiota, and relevant metabolites. Spearman rank correlation analysis was used to explore correlations between gut microbes and circulating glycerolipid metabolites, gut microbes and lipids, and circulating glycerolipid metabolites and lipids.

RESULTS: The gut microbial composition of HFD hamsters showed significant alterations at the phylum, genus, and species levels that were skewed toward metabolic disorders compared with that of NCD hamsters. Functional characterization by KEGG analysis identified enrichment of the glycerolipid metabolism pathway in the gut microbiome of HFD hamsters. Plasma and liver metabolomics further indicated the upregulation and enrichment of glycerolipid metabolites in HFD hamsters. The Faecalibaculum, Allobaculum, and Eubacterium genera were positively correlated with plasma glycerolipid metabolites and lipid indices.

CONCLUSION: The findings of this study suggest an association between glycerolipid metabolism and the HFD-modulated gut microbiome that is involved in the development of hyperlipidemia.}, } @article {pmid39428758, year = {2024}, author = {Minot, SS and Mayer-Blackwell, K and Fiore-Gartland, A and Johnson, A and Self, S and Bhatti, P and Yao, L and Liu, L and Sun, X and Jinfa, Y and Kublin, J}, title = {Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2414975}, pmid = {39428758}, issn = {1949-0984}, support = {R01 AI127100/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Male ; Female ; Metagenomics ; Microbial Consortia ; Metagenome ; Infant, Newborn ; Cohort Studies ; Cystic Fibrosis/microbiology ; }, abstract = {BACKGROUND: The human gut microbiome develops rapidly during infancy, a key window of development coinciding with the maturation of the adaptive immune system. However, little is known about the microbiome growth dynamics over the first few months of life and whether there are any generalizable patterns across human populations. We performed metagenomic sequencing on stool samples (n = 94) from a cohort of infants (n = 15) at monthly intervals in the first 6 months of life, augmenting our dataset with seven published studies for a total of 4,441 metagenomes from 1,162 infants.

RESULTS: Strain-level de novo analysis was used to identify 592 of the most abundant organisms in the infant gut microbiome. Previously unrecognized consortia were identified which exhibited highly correlated abundances across samples and were composed of diverse species spanning multiple genera. Analysis of a published cohort of infants with cystic fibrosis identified one such novel consortium of diverse Enterobacterales which was positively correlated with weight gain. While all studies showed an increased community stability during the first year of life, microbial dynamics varied widely in the first few months of life, both by study and by individual.

CONCLUSION: By augmenting published metagenomic datasets with data from a newly established cohort, we were able to identify novel groups of organisms that are correlated with measures of robust human development. We hypothesize that the presence of these groups may impact human health in aggregate in ways that individual species may not in isolation.}, } @article {pmid39427542, year = {2024}, author = {Kuai, Y and Yao, Z and Pang, T and Wang, L and Gong, X and Cheng, Y and Liu, X and Fu, Q and Wang, S}, title = {Chronic dietary deoxynivalenol exposure interferes the intestinal microbial community structure and antibiotic resistome in laying hens.}, journal = {Ecotoxicology and environmental safety}, volume = {286}, number = {}, pages = {117213}, doi = {10.1016/j.ecoenv.2024.117213}, pmid = {39427542}, issn = {1090-2414}, mesh = {Animals ; *Trichothecenes/toxicity ; *Chickens/microbiology ; *Gastrointestinal Microbiome/drug effects ; Female ; *Animal Feed/analysis ; Drug Resistance, Microbial/genetics ; Intestines/drug effects/microbiology ; Diet/veterinary ; Dietary Exposure ; }, abstract = {Antibiotic resistance genes (ARGs) are critical emerging pollutants that have attracted considerable attention. Deoxynivalenol (DON) is one of the most prevalent mycotoxins in cereal crops worldwide, arising severe health hazards to both humans and animals. Even if numerous researches argue in favor of a notorious influence of DON on the gut, the effects of dietary DON exposure on the ARG profile in poultry intestine remain obscure. In this study, two separate feeding experiments using Jing Tint 6 laying hens exposed to 4.5 or 9.0 mg/kg DON were performed to explore the impact of dietary DON exposure on the microbial community structure and the profiles of ARGs in the intestine via 16S rDNA sequencing and metagenomics sequencing, respectively. In addition, growth performance and intestinal barrier function were also determined to assess the feasibility of using DON-contaminated feedstuffs inappropriate for pigs' consumption in laying hens. Chronic ingestion of DON at 9.0 mg/kg did not alter zootechnical parameters. However, histomorphological impairments were observed in liver and jejunum. Additionally, metagenomic sequencing revealed that dietary DON exposure at 9.0 mg/kg level dramatically changed the gut microbial structure and shifted the ARG profile. The abundance of tetracycline ARG subtype in the layer cecum was decreased, whereas the abundance of vancomycin ARG subtype was increased upon DON exposure. Co-occurrence network analysis identified that Prevotella was the major ARG host in the intestine of laying hens. In summary, our findings demonstrated that DON-contaminated feedstuffs inappropriate for pigs' consumption should be prudently used in hen production, and shed new light on the interactions between mycotoxins and ARGs in the poultry intestine.}, } @article {pmid39427349, year = {2025}, author = {Zhou, L and Zhang, X and Zhang, X and Wu, P and Wang, A}, title = {Insights into the carbon and nitrogen metabolism pathways in mixed-autotrophy/heterotrophy anammox consortia in response to temperature reduction.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122642}, doi = {10.1016/j.watres.2024.122642}, pmid = {39427349}, issn = {1879-2448}, mesh = {*Nitrogen/metabolism ; *Carbon/metabolism ; *Temperature ; *Autotrophic Processes ; Denitrification ; Heterotrophic Processes ; Microbial Consortia ; Oxidation-Reduction ; }, abstract = {While the multi-coupled anammox system boasts a substantial research foundation, the specific characteristics of its synergistic metabolic response to decreased temperatures, particularly within the range of 13-15 °C, remained elusive. In this study, we delve into the intricate carbon and nitrogen metabolism pathways of mixed-autotrophy/heterotrophy anammox consortia under conditions of temperature reduction. Our macrogenomic analyses reveal a compelling phenomenon: the stimulation of functional genes responsible for complete denitrification, suggesting an enhancement of this process during temperature reduction. This adaptation likely contributes to maintaining system performance amidst environmental challenges. Further metabolic functional recombination analyses highlight a dramatic shift in microbial community composition, with denitrifying MAGs (metagenome-assembled genomes) experiencing a substantial increase in abundance (up to 200 times) compared to autotrophic MAGs. This proliferation underscores the strong stimulatory effect of temperature reduction on denitrifying species. Notably, autotrophic MAGs play a pivotal role in supporting the glycolytic processes of denitrifying MAGs, underscoring the intricate interdependencies within the consortia. Moreover, metabolic variations in amino acid composition among core MAGs emerge as a crucial adaptation mechanism. These differences facilitate the preservation of enzyme activity and enhance the consortia's resilience to low temperatures. Together, these findings offer a comprehensive understanding of the microbial synergistic metabolism within mixed-autotrophy/heterotrophy anammox consortia under temperature reduction, shedding light on their metabolic flexibility and resilience in dynamic environments.}, } @article {pmid39426981, year = {2024}, author = {Lu, C and Liu, D and Wu, Q and Zeng, J and Xiong, Y and Luo, T}, title = {EphA2 blockage ALW-II-41-27 alleviates atherosclerosis by remodeling gut microbiota to regulate bile acid metabolism.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {108}, pmid = {39426981}, issn = {2055-5008}, support = {2023NSFSC1631//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; 2023YFS0116//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; 2022YFS0604//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; Q22066//Education Department of Sichuan Province/ ; }, mesh = {Animals ; *Atherosclerosis/metabolism/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Bile Acids and Salts/metabolism ; Mice ; *Receptor, EphA2/metabolism ; *Diet, High-Fat/adverse effects ; Male ; Humans ; Disease Models, Animal ; Plaque, Atherosclerotic/etiology ; Mice, Inbred C57BL ; Bacteria/classification/isolation & purification/genetics/metabolism ; Dysbiosis ; }, abstract = {Coronary artery disease (CAD), a critical condition resulting from systemic inflammation, metabolic dysfunction, and gut microbiota dysbiosis, poses a global public health challenge. ALW-II-41-27, a specific inhibitor of the EphA2 receptor, has shown anti-inflammatory prosperities. However, the impact of ALW-II-41-27 on atherosclerosis has not been elucidated. This study aimed to examine the roles of pharmacologically inhibiting EphA2 and the underlying mechanism in ameliorating atherosclerosis. ALW-II-41-27 was administered to apoE[-/-] mice fed a high-fat diet via intraperitoneal injection. We first discovered that ALW-II-41-27 led to a significant reduction in atherosclerotic plaques, evidenced by reduced lipid and macrophage accumulation, alongside an increase in collagen and smooth muscle cell content. ALW-II-41-27 also significantly lowered plasma and hepatic cholesterol levels, as well as the colonic inflammation. Furthermore, gut microbiota was analyzed by metagenomics and plasma metabolites by untargeted metabolomics. ALW-II-41-27-treated mice enriched Enterococcus, Akkermansia, Eggerthella and Lactobaccilus, accompanied by enhanced secondary bile acids production. To explore the causal link between ALW-II-41-27-associated gut microbiota and atherosclerosis, fecal microbiota transplantation was employed. Mice that received ALW-II-41-27-treated mouse feces exhibited the attenuated atherosclerotic plaque. In clinical, lower plasma DCA and HDCA levels were determined in CAD patients using quantitative metabolomics and exhibited a negative correlation with higher monocytes EphA2 expression. Our findings underscore the potential of ALW-II-41-27 as a novel therapeutic agent for atherosclerosis, highlighting its capacity to modulate gut microbiota composition and bile acid metabolism, thereby offering a promising avenue for CAD.}, } @article {pmid39426578, year = {2025}, author = {Tao, Y and Zeng, Y and Zeng, R and Gou, X and Zhou, X and Zhang, J and Nhamdriel, T and Fan, G}, title = {The total alkaloids of Berberidis Cortex alleviate type 2 diabetes mellitus by regulating gut microbiota, inflammation and liver gluconeogenesis.}, journal = {Journal of ethnopharmacology}, volume = {337}, number = {Pt 3}, pages = {118957}, doi = {10.1016/j.jep.2024.118957}, pmid = {39426578}, issn = {1872-7573}, mesh = {Animals ; *Diabetes Mellitus, Type 2/drug therapy/metabolism ; *Alkaloids/pharmacology ; Male ; *Gastrointestinal Microbiome/drug effects ; *Liver/drug effects/metabolism ; *Diabetes Mellitus, Experimental/drug therapy ; Rats ; *Rats, Sprague-Dawley ; *Hypoglycemic Agents/pharmacology ; *Gluconeogenesis/drug effects ; Inflammation/drug therapy ; Diet, High-Fat/adverse effects ; Plant Extracts/pharmacology ; Blood Glucose/drug effects ; }, abstract = {Type 2 diabetes mellitus (T2DM) has become a public health problem worldwide. There is growing interest in finding drugs to treat T2DM from herbal medicine. Berberidis Cortex is a traditional Tibetan herb commonly used in the treatment of T2DM, and alkaloids are its main active components. However, the anti-diabetic mechanisms of the total alkaloids of Berberidis Cortex (TBC) remain unclear.

AIM OF THE STUDY: The aim of this study was to evaluate the anti-T2DM efficacy of TBC and reveal the mechanisms behind its effects.

MATERIALS AND METHODS: UPLC-Q-Exactive Orbitrap MS technology was employed to qualitatively identify alkaloid components in TBC. T2DM rat models were induced by high-fat diet combined with streptozotocin, and then treated with different doses of TBC (43.5, 87, 174 mg/kg/d) for 40 days. Biochemical parameters, such as fasting blood glucose (FBG), oral glucose tolerance test (OGTT), glycated serum protein (GSP), homeostatic model assessment of insulin resistance (HOMA-IR), total cholesterol (TC), triglycerides (TG), and low-density lipoprotein cholesterol (LDL-C), alongside H&E and PAS staining were used to evaluate the anti-diabetic activity of TBC. More importantly, metagenomics, transcriptomics, targeted metabolomics, and Western blot analysis were integrated to reveal the underlying mechanisms of TBC for T2DM treatment.

RESULTS: TBC significantly reduced the levels of FBG, OGTT, GSP, HOMA-IR, TC, TG, and LDL-C, and improved the histopathological alterations of pancreatic and liver tissues in T2D rats. It also reduced serum levels of lipopolysaccharide (LPS) and several pro-inflammatory cytokines (IL-6, IL-1β and TNF-α). Gut microbiome analysis by metagenomics proved that TBC could improve gut microbiota dysbiosis, including an increase in some beneficial bacteria (e.g., Bifidobacterium pseudolongum and Lactobacillus acidophilus) and a decrease in some harmful bacteria (e.g., Marvinbryantia and Parabacteroides). Western blot analysis found that TBC significantly up-regulated the expression of three intestinal barrier related tight junction proteins (ZO-1, occludin, and claudin-1), and effectively suppressed several key proteins in the TLR4/MyD88/NF-κB inflammatory cascade, including TLR4, MyD88 and p-NF-κB p65. Moreover, hepatic transcriptomics analysis further revealed the regulatory role of TBC on gluconeogenesis related genes, such as Pgc, and Creb1. Targeted metabolomics and Western blot analysis showed that TBC improved BAs dysregulation in T2DM rats, specifically increasing TCDCA and CA levels, thereby activating several proteins in the FXR/FGF15 signaling axis (i.e., FXR, FGF15 and FGFR4), and then decreased the expression of p-CREB1 and PGC-1α to inhibit liver gluconeogenesis.

CONCLUSIONS: TBC can significantly improve hyperglycemia, insulin resistance, hyperlipidemia, and inflammation in T2DM rats. The mechanism is related to the regulation of multiple links, including improving gut microbiota dysbiosis, protecting the intestinal barrier by up-regulating the expression of three tight junction proteins, reducing inflammation by inhibiting the LPS/TLR4/MyD88/NF-κB pathway, and inhibiting liver gluconeogenesis by regulating BAs/FXR/FGF15 and CREB1/PGC-1α signaling pathways.}, } @article {pmid39426111, year = {2024}, author = {Shang, KM and Elsheikha, HM and Ma, H and Wei, YJ and Zhao, JX and Qin, Y and Li, JM and Zhao, ZY and Zhang, XX}, title = {Metagenomic profiling of cecal microbiota and antibiotic resistome in rodents.}, journal = {Ecotoxicology and environmental safety}, volume = {286}, number = {}, pages = {117186}, doi = {10.1016/j.ecoenv.2024.117186}, pmid = {39426111}, issn = {1090-2414}, mesh = {Animals ; *Cecum/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Rodentia/microbiology ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects/classification ; Drug Resistance, Microbial/genetics ; Metagenomics ; Rats ; Drug Resistance, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Metagenome ; }, abstract = {The rodent gut microbiota is a known reservoir of antimicrobial resistance, yet the distribution of antibiotic resistance genes (ARGs) within rodent cecal microbial communities and the specific bacterial species harboring these ARGs remain largely underexplored. This study employed high-throughput sequencing of 122 samples from five distinct rodent species to comprehensively profile the diversity and distribution of ARGs and to identify the bacterial hosts of these genes. A gene catalog of the rodent cecal microbiome was constructed, comprising 22,757,369 non-redundant genes. Analysis of the microbial composition and diversity revealed that Bacillota and Bacteroidota were the dominant bacterial phyla across different rodent species, with significant variations in species composition among the rodents. In total, 3703 putative antimicrobial resistance protein-coding genes were identified, corresponding to 392 unique ARG types classified into 32 resistance classes. The most enriched ARGs in the rodent cecal microbiome were associated with multidrug resistance, followed by glycopeptide and elfamycin antibiotics. Procrustes analysis demonstrated a correlation between the structure of the microbial community and the resistome. Metagenomic assembly-based host tracking indicated that most ARG-carrying contigs originated from the bacterial family Oscillospiraceae. Additionally, 130 ARGs showed significant correlations with mobile genetic elements. These findings provide new insights into the cecal microbiota and the prevalence of ARGs across five rodent species. Future research on a wider range of wild rodent species carrying ARGs will further elucidate the mechanisms underlying the transmission of antimicrobial resistance.}, } @article {pmid39425237, year = {2024}, author = {Zelasko, S and Swaney, MH and Sandstrom, S and Davenport, TC and Seroogy, CM and Gern, JE and Kalan, LR and Currie, CR}, title = {Upper respiratory microbial communities of healthy populations are shaped by niche and age.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {206}, pmid = {39425237}, issn = {2049-2618}, support = {U19AI142720/NH/NIH HHS/United States ; U19AI104317/NH/NIH HHS/United States ; F30AI169759/NH/NIH HHS/United States ; U19 AI142720/AI/NIAID NIH HHS/United States ; T32AI055397/NH/NIH HHS/United States ; U19 AI104317/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; Adult ; Infant ; Female ; *Bacteria/classification/genetics/isolation & purification ; Male ; Age Factors ; Child, Preschool ; Healthy Volunteers ; Metagenomics/methods ; Respiratory System/microbiology ; Metagenome ; }, abstract = {BACKGROUND: Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and intermicrobial interactions across healthy 24-month-old infant (n = 229) and adult (n = 100) populations.

RESULTS: We find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity.

CONCLUSIONS: In summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functions related to colonization resistance, with important implications for host health across the lifespan. Video Abstract.}, } @article {pmid39425038, year = {2024}, author = {Woldeyohannis, NN and Desta, AF}, title = {Metagenome-based microbial community analysis of urine-derived fertilizer.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {418}, pmid = {39425038}, issn = {1471-2180}, mesh = {Humans ; *Fertilizers/analysis ; *Urine/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Struvite ; *Metagenome ; Microbiota/genetics ; Metagenomics/methods ; DNA, Bacterial/genetics ; Phylogeny ; }, abstract = {Phosphorus is essential for food production and its supply is limited. Urine is an excellent source of phosphorus and one way to produce fertilizer is through conversion of urine to struvite (MgNH3PO4.6H2O). The present study aimed to understand the bacterial portion of the microbial community composition and dynamics of plasmid-mediated antimicrobial resistant genes during the optimized process of struvite production from composite human urine. Samples for DNA extraction was collected from fresh urine, stored urine and struvite during the process of struvite production. Shotgun metagenomic analysis was employed to understand the bacterial community. The most dominant phyla in the fresh and stored urine samples were Pseudomonadata, which comprised of 60% and 43% respectively, followed by Bacillota, comprised of 25% and 39% respectively. The struvite sample was dominated by the phylum Bacilliota (61%), Pseudomonadota (18%) and bacteroidota (12%). Members of the above phyla persisted in dominating each sample accordingly. Member of the family Morganellaceae was dominant in the fresh sample while the stored urine and struvite samples were dominated by the family Clostridiaceae. A decrease of members of the class Gammaproteobacteria was observed from the fresh to the struvite sample though not statistically significant. The genus Pseudomonas remained to be the most dominant member of Gammaproteobacteria in the fresh and stored urine sample with OTU count of 12,116 and 6,155 with a marked decrease by half in the stored sample. On the other hand, members of the genera Clostridium, Enterococcus, Bacteroides in the stored samples and Clostridium, Alkaliphilus and Pseudomonas in the struvite samples were dominant. 96% of the identified genera were shared in all the samples and the antimicrobial resistance genes (ARGs) identified in the fresh urine were shared by the struvite but not by the stored urine (e.g. sul, cat, aph and aac members). The presence of high abundance of ARGs in struvite needs attention in the persistence and transmissibility of the ARGs before application for agriculture.}, } @article {pmid39423892, year = {2024}, author = {Ouyang, W and Huang, Y and Li, C and Huang, W and Yuan, S and Liu, H}, title = {Control of dissolved H2 concentration enhances electron generation, transport and TCE reduction by indigenous microbial community.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {177014}, doi = {10.1016/j.scitotenv.2024.177014}, pmid = {39423892}, issn = {1879-1026}, mesh = {*Trichloroethylene/metabolism ; *Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism/analysis ; Hydrogen/metabolism ; Microbiota ; Electron Transport ; Bacteria/metabolism ; Oxidation-Reduction ; Electrons ; Groundwater/chemistry/microbiology ; }, abstract = {Electrokinetic enhanced bioremediation (EK-Bio) is practical for trichloroethene (TCE) dechlorination because the cathode can produce a wide range of dissolved H2 (DH) concentrations of 1.3-0 mg/L from the electrode to the aquifer. In this study, TCE dechlorination was investigated under different DH concentrations. The mechanisms were discussed by analyzing the microbial community structure and abundance of organohalide-respiring bacteria (OHRB) using 16S rRNA, and the gene abundances of key enzymes in the TCE electron transport chain using metagenomic analysis. The results showed that the moderate DH concentration of 0.19-0.53 mg/L exhibited the most pronounced TCE dechlorination, even better than the higher DH concentrations, due to the optimal redox environment, the enrichments of OHRB, reductive dehalogenase (rdhA) genes and key enzyme genes in the electron generation and transport chain. More electrons were obtained from H2 metabolism by Dehalobacter by promoting the formation of [NiFe] hydrogenase (HupS/L/C) or from glycolysis by versatile OHRB by stimulating the formation of formate and enriching formate dehydrogenase (FDH) under moderate DH conditions. In addition, the enhanced amino acid metabolism improved the vitamin K cycle for electron transport and enriched the reductive dechlorinating enzyme (RDase) genes. This study identifies the optimal DH concentration that facilitates bioremediation efficiency, provides insights into microbial community shifts and key enzymatic pathways in EK-Bio remediation.}, } @article {pmid39423213, year = {2024}, author = {Ma, J and Yang, X and He, J}, title = {Comprehensive gut microbiota composition and microbial interactions among the three age groups.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0305583}, pmid = {39423213}, issn = {1932-6203}, mesh = {Humans ; *Gastrointestinal Microbiome ; Aged ; Aged, 80 and over ; Adult ; Middle Aged ; Male ; Aging ; Young Adult ; Microbial Interactions ; Female ; Bacteria/genetics/classification ; Age Factors ; Archaea/genetics ; }, abstract = {There is a growing interest in studying the microbiota associated with aging by integrating multiple longevity researches while minimizing the influence of confounding factors. Here, we reprocessed metagenomic sequencing data from four different aging research studies and evaluated potential confounding factors in order to minimize the batch effect. Subsequently, we detected the diversity and abundance of the gut microbiome in three different age cohorts. Out of 1053 different bacteria species, only four showed substantial depletion across different age groups: Ligilactobacillus ruminis, Turicibacter sp. H121, Blautia massiliensis, and Anaerostipes hadrus. Archaea accumulated more in young individuals compared to elderly and centenarians. Candida albicans was more prevalent in centenarians, but Nakaseomyces glabratus (also known as Candida glabrata) was more common in elderly adults. Shuimuvirus IME207 showed a significant increase in centenarians compared to both control groups. In addition, we utilized a Fisher's exact test to investigate topological properties of differentially abundant microbiota in the co-occurrence network of each age group. Microbial signatures specific to different age stages were identified based on the condition: the reads showing differential abundance were higher compared to the other age groups. Lastly, we selected Methanosarcina sp. Kolksee for the Y group, Prevotella copri for the E group and Shuimuvirus IME207 for the C group as representatives of age-related characteristics to study how their interactions change during the aging process. Our results provide crucial insights into the gut microbiome's ecological dynamics in relation to the aging process.}, } @article {pmid39422129, year = {2024}, author = {Kanti Nath, B and Gupta, SD and Talukder, S and Tonu, NS and Raidal, SR and Forwood, JK and Sarker, S}, title = {Metagenomic Detection of Multiple Viruses in Monk Parakeet (Myiopsitta monachus) in Australia.}, journal = {Veterinary medicine and science}, volume = {10}, number = {6}, pages = {e70083}, pmid = {39422129}, issn = {2053-1095}, mesh = {Animals ; *Feces/virology/microbiology ; *Parakeets/virology ; Bird Diseases/virology/epidemiology/microbiology ; Australia ; Adenoviridae/isolation & purification/classification/genetics ; Parvoviridae/isolation & purification/genetics/classification ; Phylogeny ; Circovirus/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing/veterinary ; Victoria ; Circoviridae/isolation & purification/genetics/classification ; Virome ; Metagenomics ; }, abstract = {BACKGROUND: Birds are known to harbour many pathogens, including circovirus, herpesviruses, adenoviruses and Chlamydia psittaci. Some of these pose zoonotic risks, while others, such as beak and feather disease virus (BFDV), have a significant impact on the conservation of endangered bird species.

OBJECTIVES: This study was aimed to determine the faecal virome of a group of apparently healthy Monk parakeet using high-throughput sequencing.

METHODS: Fresh faecal samples were collected from four Monk parakeets at a pet shop in Melbourne, Australia. Virus enrichment and nucleic acid extraction were performed on the faecal samples, followed by high-throughput sequencing at the Australian Genome Research Facility (AGRF).

RESULTS: Utilising an established pipeline for high-throughput sequencing data analysis, this study revealed the presence of three viruses of the families Circoviridae, Parvoviridae and Adenoviridae. Subsequent sequence comparison and phylogenetic analyses further confirmed that the detected viruses belong to the genera Chaphamaparvovirus (unassigned species), Circovirus (species Circovirus parrot) and Siadenovirus (species Siadenovirus viridis).

CONCLUSION: Despite non-pathogenicity, the existence of multiple viruses within a bird species underscores the risk of these viruses spreading into the pet trade. Detection and a better understanding of avian viruses are crucial for the establishment of appropriate management and biosecurity measures in the domestic and international bird trade, which ultimately supports the conservation of vulnerable bird species.}, } @article {pmid39420635, year = {2025}, author = {Li, C and Sun, L and Jia, Z and Tang, Y and Liu, X and Zhang, J and Müller, C}, title = {Microbial Inoculants Drive Changes in Soil and Plant Microbiomes and Improve Plant Functions in Abandoned Mine Restoration.}, journal = {Plant, cell & environment}, volume = {48}, number = {2}, pages = {1162-1178}, doi = {10.1111/pce.15215}, pmid = {39420635}, issn = {1365-3040}, support = {//Jinchi Zhang acknowledges the funding support from Jiangsu Science and Technology Plan Project (BE2022420); the Innovation and Promotion of Forestry Science and Technology Program of Jiangsu Province (LYKJ[2021]30); the Scientific Research Project of Baishanzu National Park (2021ZDLY01); and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD). Chong Li is grateful for the partial financial support from the Postgraduate Research and Practice Innovation Program of Jiangsu Province (KYCX21_0915), and the China Scholarship Council (202108320300)./ ; }, mesh = {*Soil Microbiology ; *Microbiota ; *Mining ; *Plant Roots/microbiology/physiology ; Plants/microbiology/metabolism ; Soil/chemistry ; Bacteria/metabolism ; Fungi/physiology ; Environmental Restoration and Remediation/methods ; }, abstract = {The application of microbial inoculants holds promise for the sustainable restoration of abandoned mine sites by affecting soil nutrients and microbial communities. However, the responses of plant microbial communities to microbial inoculants in mine restoration remain largely unknown. To bridge this knowledge gap, we conducted a 4-year field experiment at an abandoned carbonate mine site to assess the impacts of microbial inoculants on the soil-plant microbiome. Our findings revealed that microbial inoculants significantly changed roots, fine root bacterial and fungal communities. Further, no significant correlations were observed between the soil-plant nutrient content (Z-score) and microbial alpha diversity. However, a significantly positive correlation was found between the relative abundance of the keystone ecological cluster (Module #1) and soil-plant nutrient content. The application of microbial inoculants also increased complexity, albeit decreased stability of plant microbiome networks, alongside a reduction in stochastic assembly. Conversely, they decreased the complexity but increased the stability of soil microbiome networks, accompanied by an increase in stochastic assembly. Notably, the number of specifically enriched microbiome functional traits of roots and root nodules under the microbial inoculant treatments surpassed that of the control. In summary, our findings underscored the potential of microbial inoculants to enhance soil-plant functionality at abandoned mine restoration sites.}, } @article {pmid39420033, year = {2024}, author = {Majzoub, ME and Paramsothy, S and Haifer, C and Parthasarathy, R and Borody, TJ and Leong, RW and Kamm, MA and Kaakoush, NO}, title = {The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8979}, pmid = {39420033}, issn = {2041-1723}, support = {988415//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; APP2011047//Department of Health | National Health and Medical Research Council (NHMRC)/ ; Investigator grant//Department of Health | National Health and Medical Research Council (NHMRC)/ ; Scientia fellowship//University of New South Wales (UNSW Australia)/ ; }, mesh = {Humans ; *Colitis, Ulcerative/therapy/microbiology/virology ; *Fecal Microbiota Transplantation ; *Bacteriophages/genetics/isolation & purification/physiology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology/virology ; Double-Blind Method ; Male ; Female ; Metagenomics/methods ; Adult ; Dysbiosis/microbiology/therapy ; Middle Aged ; Virome/genetics ; Remission Induction ; Anti-Bacterial Agents/therapeutic use ; Biomarkers ; }, abstract = {Bacteriophages are influential within the human gut microbiota, yet they remain understudied relative to bacteria. This is a limitation of studies on fecal microbiota transplantation (FMT) where bacteriophages likely influence outcome. Here, using metagenomics, we profile phage populations - the phageome - in individuals recruited into two double-blind randomized trials of FMT in ulcerative colitis. We leverage the trial designs to observe that phage populations behave similarly to bacterial populations, showing temporal stability in health, dysbiosis in active disease, modulation by antibiotic treatment and by FMT. We identify a donor bacteriophage putatively associated with disease remission, which on genomic analysis was found integrated in a bacterium classified to Oscillospiraceae, previously isolated from a centenarian and predicted to produce vitamin B complex except B12. Our study provides an in-depth assessment of phage populations during different states and suggests that bacteriophage tracking has utility in identifying determinants of disease activity and resolution.}, } @article {pmid39419193, year = {2024}, author = {Chen, H and Zeng, M and Batool, SS and Zhao, Y and Yu, Z and Zhou, J and Liu, K and Huang, J}, title = {Metagenomic analysis reveals effects of gut microbiome in response to neoadjuvant chemoradiotherapy in advanced rectal cancer.}, journal = {Genomics}, volume = {116}, number = {6}, pages = {110951}, doi = {10.1016/j.ygeno.2024.110951}, pmid = {39419193}, issn = {1089-8646}, mesh = {Humans ; *Rectal Neoplasms/therapy/microbiology/genetics/metabolism ; *Gastrointestinal Microbiome ; *Neoadjuvant Therapy ; Chemoradiotherapy ; Female ; Male ; Middle Aged ; Metagenomics ; Aged ; Metagenome ; Feces/microbiology ; Bacteria/genetics/classification/metabolism ; }, abstract = {Neoadjuvant chemoradiotherapy can enhance survival rate of patients with advanced rectal cancer, but its effectiveness varies considerably. Previous studies have indicated that gut microbes may serve as biomarkers for predicting treatment efficacy. However, the specific roles of the gut microbiome in patients who have good response to nCRT remains unclear. In this study, shotgun metagenomic sequencing technology was used to analyze the fecal microbiome of patients with varying responses to nCRT. Our findings revealed that beneficial intestinal bacteria and genes from different metabolic pathways (carbohydrate metabolism, amino acid metabolism, and sulfur metabolism) were significantly enriched in patients with good response. Additionally, causal relationship in which microbial-derived GDP-D-rhamnose and butyrate could influence the response to nCRT was clarified. Our results offered new insights into the different response to nCRT, and provided valuable reference points for improving the effectiveness of nCRT in patients with advanced colorectal cancer.}, } @article {pmid39418776, year = {2024}, author = {Xie, Q and Sun, J and Sun, M and Wang, Q and Wang, M}, title = {Perturbed microbial ecology in neuromyelitis optica spectrum disorder: Evidence from the gut microbiome and fecal metabolome.}, journal = {Multiple sclerosis and related disorders}, volume = {92}, number = {}, pages = {105936}, doi = {10.1016/j.msard.2024.105936}, pmid = {39418776}, issn = {2211-0356}, mesh = {*Neuromyelitis Optica/microbiology/immunology ; Humans ; *Gastrointestinal Microbiome/physiology ; *Feces/microbiology ; Animals ; Female ; Adult ; *Fecal Microbiota Transplantation ; Mice ; Male ; Metabolome/physiology ; Middle Aged ; }, abstract = {BACKGROUND: Neuromyelitis optica spectrum disorder (NMOSD) is a central nervous system inflammatory demyelinating immune-mediated ailment, which is influenced by genetic, epigenetic, and environmental elements. The escalating incidence of NMOSD in recent years implies alterations in environmental risk factors. Recent research has established a correlation between gut microbiomes and the development of NMOSD.

METHODS: Metagenomic shotgun sequencing and gas chromatography-mass spectrometry (GC-MS) were employed to assess alterations of the structure and function in the fecal microbiome, as well as levels of short-chain fatty acids (SCFAs) in fecal and blood samples, among individuals with neuromyelitis optica spectrum disorder (NMOSD) during the acute phase (n = 25), the remission phase (n = 11), and a group of healthy controls (HCs) (n = 24). We further explored the correlation between gut microbiota and the pathogenesis of NMOSD through fecal microbiota transplantation (FMT). The gut microbiome from human donors diagnosed with NMOSD or HCs was transplanted into germ-free mice, followed by an analysis of the alterations in the structure and functionality of the transplanted mice's gut microbiome. Additionally, the impact of microbiome transfer on the immunity and spinal cord of germ-free mice was assessed through various techniques, including ELISA, flow cytometry, western blot, histopathology, and transcriptome sequencing.

RESULTS: (1) At the taxonomic levels of genus and species, there were significant differences in the α-diversity of the microbiome between HCs and NMOSD patients in the acute phase, with NMOSD patients having higher species diversity. (2) In the acute phase, the gut microbiota of NMOSD patients was characterized by Ruminococcaceae_unclassified, Campylobacter, Parabacteroides, Lactobacillus, Akkermansia, Streptococcus oralis, Clostridium leptum, Clostridium asparagiforme, Firmicutes bacterium CAG 238, and Lactobacillus fermentum. (3) The relative abundances of Coprobacter, Turicimonas, Gemmiger, Enterobacter, Roseburia sp.CAG 471, Veillonella tobetsuensis, Proteobacteria bacterium CAG 139, Ruminococcus bicirculans, Lactococcus lactis, Flavonifractor plautii, and Streptococcus cristatus were notably lower in patients experiencing remission compared to NMOSD patients in the acute phase, On the other hand, the relative abundances of Flavonifractor (P = 0.049) and Clostridium aldenense (P = 0.049) were significantly higher. Following medication, the gut microbiome distribution in NMOSD patients during remission closely resembled that of healthy controls (HCs). (4) Compared with HCs, acetate levels in the feces of patients with NMOSD in the acute phase were significantly lower. (5) In addition, we transplanted feces from NMOSD patients into germ-free mice and revealed a significant increase in the levels of IL-6, IL-17A, and IL-23 in the blood of mice belonging to the NMOSD fecal transplantation (NFMT) group. Additionally, the IL-10 level exhibited a significant reduction. Moreover, the proportion of Th17 cells displayed a significant increase, while the proportion of Treg cells exhibited a significant decrease in the spleens of NFMT mice.

CONCLUSION: Patients in the acute phase of neuromyelitis optica spectrum disorder (NMOSD) exhibited imbalances in their gut microbiota and a deficiency in short-chain fatty acids (SCFAs). Following drug treatment, the composition of intestinal microbes in NMOSD patients during the remission phase closely resembled that of the healthy control population. The FMT experiment provided evidence of the significant association between intestinal flora and the pathogenesis of NMOSD. Consequently, investigating gut microbiota and identifying novel microbial markers hold promise for the diagnosis and treatment of NMOSD patients.}, } @article {pmid39418241, year = {2024}, author = {Song, C and Liu, F and Mei, Y and Cai, W and Cheng, K and Guo, D and Liu, Y and Shi, H and Duan, DD and Liu, Z}, title = {Integrated metagenomic and metabonomic mechanisms for the therapeutic effects of Duhuo Jisheng decoction on intervertebral disc degeneration.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0310014}, pmid = {39418241}, issn = {1932-6203}, mesh = {Animals ; *Intervertebral Disc Degeneration/drug therapy/metabolism/microbiology ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Metabolomics/methods ; Rats ; *Gastrointestinal Microbiome/drug effects ; Male ; *Rats, Sprague-Dawley ; *Metagenomics/methods ; Metabolome/drug effects ; Feces/microbiology ; Disease Models, Animal ; }, abstract = {Intervertebral disc degeneration (IVDD) is a prevalent orthopedic condition with lower back pain as the predominant clinical presentation that challenges clinical treatment with few therapeutic options. Duhuo Jisheng Decoction (DHJSD) has been proven effective in the therapy of IVDD, but the precise underlying mechanisms remain not fully elucidated. The current study was designed to test our hypothesis that DHJSD may systematically correct the phenotypic disruption of the gut microbiota and changes in the serum metabolome linked to IVDD. Analysis of the active ingredients of DHJSD by ultra high performance liquid chromatography. An integrated metagenomic and metabonomic approach was used to analyze feces and blood samples from normal and IVDD rats. Compared to the control group, fiber ring pinning on the caudal 3 to caudal 5 segments of the rats caused IVDD and significantly altered the compositions of the intestinal microbiota and serum metabolites. Integrated analysis revealed commonly-altered metabolic pathways shared by both intestinal microbiota and serum metabolome of the IVDD rats. DHJSD inhibited the degenerative process and restored the compositions of the perturbed gut microbiota, particularly the relative abundance of commensal microbes of the Prevotellaceae family. DHJSD also corrected the altered metabolic pathways involved in the metabolism of glycine, serine, threonine, valine, the citric acid cycle, and biosynthesis of leucine and isoleucine. DHJSD inhibited the disc degeneration process by an integrated metagenomic and metabonomic mechanism to restore the microbiome profile and normalize the metabonomic pathways.}, } @article {pmid39417540, year = {2024}, author = {Ginatt, AA and Berihu, M and Castel, E and Medina, S and Carmi, G and Faigenboim-Doron, A and Sharon, I and Tal, O and Droby, S and Somera, T and Mazzola, M and Eizenberg, H and Freilich, S}, title = {A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39417540}, issn = {2050-084X}, support = {US-5390-21//United States-Israel Binational Agricultural Research and Development Fund/ ; }, mesh = {*Rhizosphere ; *Malus/microbiology/metabolism ; *Microbiota ; Plant Roots/microbiology/metabolism ; Soil Microbiology ; Bacteria/metabolism/genetics/classification ; Crops, Agricultural/microbiology ; Metabolomics/methods ; Models, Biological ; }, abstract = {The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other types of microbial communities, would open the door to the optimization of specific predefined functions of interest, and therefore to the harnessing of the functionality of various types of microbiomes. However, mechanistic knowledge regarding the gathering and interpretation of these interactions is limited. Here, we present a framework utilizing genomics and constraint-based modeling approaches, aiming to interpret the hierarchical trophic interactions in the soil environment. 243 genome scale metabolic models of bacteria associated with a specific disease-suppressive vs disease-conducive apple rhizospheres were drafted based on genome-resolved metagenomes, comprising an in silico native microbial community. Iteratively simulating microbial community members' growth in a metabolomics-based apple root-like environment produced novel data on potential trophic successions, used to form a network of communal trophic dependencies. Network-based analyses have characterized interactions associated with beneficial vs non-beneficial microbiome functioning, pinpointing specific compounds and microbial species as potential disease supporting and suppressing agents. This framework provides a means for capturing trophic interactions and formulating a range of testable hypotheses regarding the metabolic capabilities of microbial communities within their natural environment. Essentially, it can be applied to different environments and biological landscapes, elucidating the conditions for the targeted manipulation of various microbiomes, and the execution of countless predefined functions.}, } @article {pmid39415203, year = {2024}, author = {Tong, X and Luo, D and Leung, MHY and Lee, JYY and Shen, Z and Jiang, W and Mason, CE and Lee, PKH}, title = {Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {198}, pmid = {39415203}, issn = {2049-2618}, support = {BK20230230//Jiangsu Science and Technology Programme/ ; 11214721//Hong Kong Research Grants Council, General Research Fund/ ; R1016-20F//Hong Kong Research Grants Council, Research Impact Fund/ ; }, mesh = {Humans ; Hong Kong ; *Microbiota ; *Built Environment ; *Metagenome ; *Phylogeny ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Skin/microbiology ; Micrococcus luteus/genetics/metabolism ; Genome, Bacterial ; }, abstract = {BACKGROUND: Built environments (BEs) are typically considered to be oligotrophic and harsh environments for microbial communities under normal, non-damp conditions. However, the metabolic functions of microbial inhabitants in BEs remain poorly understood. This study aimed to shed light on the functional capabilities of microbes in BEs by analyzing 860 representative metagenome-assembled genomes (rMAGs) reconstructed from 738 samples collected from BEs across the city of Hong Kong and from the skin surfaces of human occupants. The study specifically focused on the metabolic functions of rMAGs that are either phylogenetically novel or prevalent in BEs.

RESULTS: The diversity and composition of BE microbiomes were primarily shaped by the sample type, with Micrococcus luteus and Cutibacterium acnes being prevalent. The metabolic functions of rMAGs varied significantly based on taxonomy, even at the strain level. A novel strain affiliated with the Candidatus class Xenobia in the Candidatus phylum Eremiobacterota and two novel strains affiliated with the superphylum Patescibacteria exhibited unique functions compared with their close relatives, potentially aiding their survival in BEs and on human skins. The novel strains in the class Xenobia possessed genes for transporting nitrate and nitrite as nitrogen sources and nitrosative stress mitigation induced by nitric oxide during denitrification. The two novel Patescibacteria strains both possessed a broad array of genes for amino acid and trace element transport, while one of them carried genes for carotenoid and ubiquinone biosynthesis. The globally prevalent M. luteus in BEs displayed a large and open pangenome, with high infraspecific genomic diversity contributed by 11 conspecific strains recovered from BEs in a single geographic region. The versatile metabolic functions encoded in the large accessory genomes of M. luteus may contribute to its global ubiquity and specialization in BEs.

CONCLUSIONS: This study illustrates that the microbial inhabitants of BEs possess metabolic potentials that enable them to tolerate and counter different biotic and abiotic conditions. Additionally, these microbes can efficiently utilize various limited residual resources from occupant activities, potentially enhancing their survival and persistence within BEs. A better understanding of the metabolic functions of BE microbes will ultimately facilitate the development of strategies to create a healthy indoor microbiome. Video Abstract.}, } @article {pmid39414630, year = {2024}, author = {Córdoba-Agudelo, M and Arboleda-Rivera, JC and Borrego-Muñoz, DA and Ramírez-Cuartas, CA and Pérez-Jaramillo, JE}, title = {Key Chemical Soil Parameters for the Assembly of Rhizosphere Bacteria Associated with Avocado Cv Hass Grafted on Landrace Rootstocks.}, journal = {Current microbiology}, volume = {81}, number = {12}, pages = {412}, pmid = {39414630}, issn = {1432-0991}, mesh = {*Persea/microbiology ; *Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Soil/chemistry ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Plant Roots/microbiology ; Colombia ; Phylogeny ; }, abstract = {Avocado cultivation holds significant economic importance in many countries, ranking Colombia as the fifth largest global producer. Particularly, the Hass cultivar plays a pivotal role in Colombia's avocado industry, especially in the Department of Antioquia, the primary export region. This cultivar is grown under diverse soil and climate conditions and exhibits considerable genetic polymorphism due to the hybridization of varieties of agronomic significance, leading to a diverse array of landrace rootstocks. However, the role of soil conditions and rootstock genotype in structuring rhizosphere bacterial communities is still lacking. In addressing this knowledge gap, we investigated the influence of two soil conditions on the structure of rhizosphere bacterial communities associated with two landrace genotypes of Persea americana cv. Hass, utilizing 16S rRNA sequencing. Notably, no significant differences related to genotypes were observed. This study reports that the rhizosphere bacterial microbiome remains consistent across avocado landrace rootstocks, while variations in key parameters such as phosphorus, pH, Mg, and Ca drive distinct rhizosphere effects. Our results reveal that despite the soils having similar management, increases in these crucial parameters can lead to bacterial communities with lower alpha diversity and a more complex co-occurrence network. In addition, we found substantial variations in beta diversity, bacterial composition, and metagenome predictions between the two farms, underscoring the role of soil variables in shaping the bacterial microbiome. These findings provide valuable insights into the factors influencing the bacterial communities that may play a role in the health and productivity of crops with agro-industrial potential, such as Hass avocado.}, } @article {pmid39413681, year = {2025}, author = {Wu, X and Qin, L and Song, M and Zhang, C and Guo, J and Yang, Z and Gao, Z and Qiu, M}, title = {Metagenomics combined with untargeted metabolomics to study the mechanism of miRNA-150-5p on SiO2 -induced acute lung injury.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {252}, number = {}, pages = {116515}, doi = {10.1016/j.jpba.2024.116515}, pmid = {39413681}, issn = {1873-264X}, mesh = {Animals ; *Acute Lung Injury/chemically induced/metabolism ; Mice ; *Metabolomics/methods ; *Metagenomics/methods ; *MicroRNAs ; *Silicon Dioxide ; *Gastrointestinal Microbiome/drug effects ; Male ; Disease Models, Animal ; }, abstract = {Acute lung injury is a significant global health issue, and its treatment is becoming a hot topic of the researchers. To investigate the feasibility of miRNA-150-5p tail vein injection in the treatment of SiO2-induced acute lung injury through the regulation of gut microbiota and serum metabolites based on multiomics technology. Twenty-four mice were randomly divided into the control, SiO2 and miRNA-150-5p intervention groups. The SiO2 and miRNA-150-5p intervention groups received a single intranasal dose of 100 µL 4 % SiO2 suspension. Meanwhile, the miRNA-150-5p intervention group was administered with two tail vein injections of miRNA-150-5p (15 nmol each per mouse) on the day of successful modelling and on the third day post modelling. Metagenomics and metabolomics techniques were used to measure gut microbiota and serum metabolites, respectively. Tail vein injection of miRNA-150-5p improved SiO2-induced acute lung injury and reduced the secretion of inflammatory factors interleukin (IL)-6, tumour necrosis factor-α and IL-1β. These conditions altered the structure of gut microbiota, which resulted in the notable modulation of eight species at the species level. In addition, tail vein injection of miRNA-150-5p considerably reduced the levels of substances, such as phosphatidylethanolamine, phosphatidylcholine and phosphatidylinositol, in the glycerophospholipid metabolism and glycosylphosphatidylinositol-anchor biosynthesis pathways. Tail vein injection of miRNA-150-5p can alleviate acute lung injury. Combined metagenomics and untargeted metabolomics revealed the miRNA-150-5p-mitigated SiO2-induced acute lung injury that occurred through the regulation of gut microbiota and serum metabolites.}, } @article {pmid39413245, year = {2024}, author = {Wang, L and Yin, Z and Yan, W and Hao, J and Tian, F and Shi, J}, title = {Nitrate-dependent antimony oxidase in an uncultured Symbiobacteriaceae member.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39413245}, issn = {1751-7370}, support = {2023YFC3710004//National Key Research and Development Program of China/ ; 22276206//National Natural Science Foundation of China/ ; }, mesh = {*Antimony/metabolism ; *Nitrates/metabolism ; *Oxidation-Reduction ; *Oxidoreductases/metabolism/genetics ; *RNA, Ribosomal, 16S/genetics ; Phylogeny ; Metagenomics ; Rhodopseudomonas/enzymology/genetics/metabolism ; Microbiota ; }, abstract = {Autotrophic antimony (Sb) oxidation coupled to nitrate reduction plays an important role in the transformation and detoxification of Sb. However, the specific oxidase involved in this process has yet to be identified. Herein, we enriched the microbiota capable of nitrate-dependent Sb(III) oxidation and identified a new Sb(III) oxidase in an uncultured member of Symbiobacteriaceae. Incubation experiments demonstrated that nitrate-dependent Sb(III) oxidation occurred in the microcosm supplemented with Sb(III) and nitrate. Both the 16S rRNA gene and metagenomic analyses indicated that a species within Symbiobacteriaceae played a crucial role in this process. Furthermore, carbon-13 isotope labeling with carbon dioxide-fixing Rhodopseudomonas palustris in combination with nanoscale secondary ion mass spectrometry revealed that a newly characterized oxidase from the dimethylsulfoxide reductase family, designated as NaoABC, was responsible for autotrophic Sb(III) oxidation coupled with nitrate reduction. The NaoABC complex functions in conjunction with the nitrate reductase NarGHI, forming a redox loop that transfers electrons from Sb(III) to nitrate, thereby generating the energy necessary for autotrophic growth. This research offers new insights into the understanding of how microbes link Sb and nitrogen biogeochemical cycles in the environment.}, } @article {pmid39409167, year = {2024}, author = {Evseev, P and Gutnik, D and Evpak, A and Kasimova, A and Miroshnikov, K}, title = {Origin, Evolution and Diversity of φ29-like Phages-Review and Bioinformatic Analysis.}, journal = {International journal of molecular sciences}, volume = {25}, number = {19}, pages = {}, pmid = {39409167}, issn = {1422-0067}, mesh = {*Bacteriophages/genetics/classification ; *Computational Biology/methods ; *Genome, Viral ; Evolution, Molecular ; Phylogeny ; Archaea/virology/genetics ; Capsid Proteins/genetics ; }, abstract = {Phage φ29 and related bacteriophages are currently the smallest known tailed viruses infecting various representatives of both Gram-positive and Gram-negative bacteria. They are characterised by genomic content features and distinctive properties that are unique among known tailed phages; their characteristics include protein primer-driven replication and a packaging process characteristic of this group. Searches conducted using public genomic databases revealed in excess of 2000 entries, including bacteriophages, phage plasmids and sequences identified as being archaeal that share the characteristic features of phage φ29. An analysis of predicted proteins, however, indicated that the metagenomic sequences attributed as archaeal appear to be misclassified and belong to bacteriophages. An analysis of the translated polypeptides of major capsid proteins (MCPs) of φ29-related phages indicated the dissimilarity of MCP sequences to those of almost all other known Caudoviricetes groups and a possible distant relationship to MCPs of T7-like (Autographiviridae) phages. Sequence searches conducted using HMM revealed the relatedness between the main structural proteins of φ29-like phages and an unusual lactococcal phage, KSY1 (Chopinvirus KSY1), whose genome contains two genes of RNA polymerase that are similar to the RNA polymerases of phages of the Autographiviridae and Schitoviridae (N4-like) families. An analysis of the tail tube proteins of φ29-like phages indicated their dissimilarity of the lower collar protein to tail proteins of all other viral groups, but revealed its possible distant relatedness with proteins of toxin translocation complexes. The combination of the unique features and distinctive origin of φ29-related phages suggests the categorisation of this vast group in a new order or as a new taxon of a higher rank.}, } @article {pmid39409144, year = {2024}, author = {Donchev, D and Stoikov, I and Diukendjieva, A and Ivanov, IN}, title = {Assessment of Skimmed Milk Flocculation for Bacterial Enrichment from Water Samples, and Benchmarking of DNA Extraction and 16S rRNA Databases for Metagenomics.}, journal = {International journal of molecular sciences}, volume = {25}, number = {19}, pages = {}, pmid = {39409144}, issn = {1422-0067}, support = {BG05M2OP001-1.002-0001-C04//European Regional Development Fund through the Operational Program Science and Education for Smart Growth 2014-2020/ ; not applicable//Biocampus Sofia Association/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Milk/microbiology ; *Metagenomics/methods ; Animals ; *DNA, Bacterial/genetics/isolation & purification ; *Bacteria/genetics/classification/isolation & purification ; Flocculation ; Microbiota/genetics ; Water Microbiology ; }, abstract = {Water samples for bacterial microbiome studies undergo biomass concentration, DNA extraction, and taxonomic identification steps. Through benchmarking, we studied the applicability of skimmed milk flocculation (SMF) for bacterial enrichment, an adapted in-house DNA extraction protocol, and six 16S rRNA databases (16S-DBs). Surface water samples from two rivers were treated with SMF and vacuum filtration (VF) and subjected to amplicon or shotgun metagenomics. A microbial community standard underwent five DNA extraction protocols, taxonomical identification with six different 16S-DBs, and evaluation by the Measurement Integrity Quotient (MIQ) score. In SMF samples, the skimmed milk was metabolized by members of lactic acid bacteria or genera such as Polaromonas, Macrococcus, and Agitococcus, resulting in increased relative abundance (p < 0.5) up to 5.0 log fold change compared to VF, rendering SMF inapplicable for bacterial microbiome studies. The best-performing DNA extraction protocols were FastSpin Soil, the in-house method, and EurX. All 16S-DBs yielded comparable MIQ scores within each DNA extraction kit, ranging from 61-66 (ZymoBIOMICs) up to 80-82 (FastSpin). DNA extraction kits exert more bias toward the composition than 16S-DBs. This benchmarking study provided valuable information to inform future water metagenomic study designs.}, } @article {pmid39408280, year = {2024}, author = {Nguyen, SM and Tran, TDC and Tran, TM and Wang, C and Wu, J and Cai, Q and Ye, F and Shu, XO}, title = {Influence of Peanut Consumption on the Gut Microbiome: A Randomized Clinical Trial.}, journal = {Nutrients}, volume = {16}, number = {19}, pages = {}, pmid = {39408280}, issn = {2072-6643}, support = {N/A//The Peanut Institute/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Arachis ; Male ; Female ; *Feces/microbiology ; Adult ; Bacteria/classification/genetics ; Vietnam ; Diet ; Middle Aged ; }, abstract = {Background: Peanut consumption could impact cardiometabolic health through gut microbiota, a hypothesis that remains to be investigated. A randomized clinical trial in Vietnam evaluated whether peanut consumption alters gut microbiome communities. Methods: One hundred individuals were included and randomly assigned to the peanut intervention and control groups. A total of 51 participants were provided with and asked to consume 50 g of peanuts daily, while 49 controls maintained their usual dietary intake for 16 weeks. Stool samples were collected before and on the last day of the trial. After excluding 22 non-compliant participants and those who received antibiotic treatment, 35 participants from the intervention and 43 from the control were included in the analysis. Gut microbiota composition was measured by shotgun metagenomic sequencing. Associations of changes in gut microbial diversity with peanut intervention were evaluated via linear regression analysis. Linear mixed-effects models were used to analyze associations of composition, sub-community structure, and microbial metabolic pathways with peanut intervention. We also performed beta regression analysis to examine the impact of peanut intervention on the overall and individual stability of microbial taxa and metabolic pathways. All associations with false discovery rate (FDR)-corrected p-values of <0.1 were considered statistically significant. Results: No significant changes were found in α- and β-diversities and overall gut microbial stability after peanut intervention. However, the peanut intervention led to lower enrichment of five phyla, five classes, two orders, twenty-four metabolic pathways, and six species-level sub-communities, with a dominant representation of Bifidobacterium pseudocatenulatum, Escherichia coli D, Holdemanella biformis, Ruminococcus D bicirculans, Roseburia inulinivorans, and MGYG-HGUT-00200 (p < 0.05 and FDR < 0.1). The peanut intervention led to the short-term stability of several species, such as Faecalibacterium prausnitzii F and H, and a metabolic pathway involved in nitrate reduction V (p < 0.05; FDR < 0.1), known for their potential roles in human health, especially cardiovascular health. Conclusions: In summary, a 16-week peanut intervention led to significant changes in gut microbial composition, species-level sub-communities, and the short-term stability of several bacteria, but not overall gut microbial diversity and stability. Further research with a larger sample size and a longer intervention period is needed to confirm these findings and investigate the direct impact of gut-microbiome-mediated health effects of peanut consumption. Trial registration: The International Traditional Medicine Clinical Trial Registry (ITMCTR). Registration number: ITMCTR2024000050. Retrospectively Registered 24 April 2024.}, } @article {pmid39407346, year = {2024}, author = {Barcenilla, C and Cobo-Díaz, JF and Puente, A and Valentino, V and De Filippis, F and Ercolini, D and Carlino, N and Pinto, F and Segata, N and Prieto, M and López, M and Alvarez-Ordóñez, A}, title = {In-depth characterization of food and environmental microbiomes across different meat processing plants.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {199}, pmid = {39407346}, issn = {2049-2618}, support = {BOCYL-D-07072020-6//Junta de Castilla y León and the European Social Fund/ ; PRE2021-098910//Ministerio de Ciencia e Innovación, Spain/ ; }, mesh = {*Microbiota ; *Food Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Meat Products/microbiology ; *Food Handling ; Environmental Microbiology ; Meat/microbiology ; RNA, Ribosomal, 16S/genetics ; Animals ; Phylogeny ; }, abstract = {BACKGROUND: Processing environments can be an important source of pathogenic and spoilage microorganisms that cross contaminate meat and meat products. The aim of this study was to characterize the microbiome of raw materials, processing environments and end products from 19 facilities producing different meat products.

RESULTS: The taxonomic profiles of the microbial communities evolved along processing, from raw materials to end products, suggesting that food contact (FC) surfaces play an important role in modulating the microbiome of final products. Some species persisted with the highest relative abundance in raw materials, food processing environments and/or in the final product, including species from the genera Pseudomonas, Staphylococcus, Brochothrix, Acinetobacter and Psychrobacter. Processing environments showed a very diverse core microbiota, partially shared with the products. Pseudomonas fragi and Pseudomonas sp. Lz4W (in all sample and facility types) and Brochothrix thermosphacta, Psychrobacter sp. and Psychrobacter sp. P11F6 (in raw materials, FC surfaces and end products) were prominent members of the core microbiota for all facilities, while Latilactobacillus sakei was found as a dominant species exclusively in end products from the facilities producing fermented sausages. Processing environments showed a higher amount of antimicrobial resistance genes and virulence factors than raw materials and end products. One thousand four hundred twenty-one medium/high-quality metagenome-assembled genomes (MAGs) were reconstructed. Of these, 274 high-quality MAGs (completeness > 90%) corresponded to 210 putative new species, mostly found in processing environments. For two relevant taxa in meat curing and fermentation processes (S. equorum and L. sakei, respectively), phylogenetic variation was observed associated with the specific processing facility under study, which suggests that specific strains of these taxa may be selected in different meat processing plants, likely contributing to the peculiar sensorial traits of the end products produced in them.

CONCLUSIONS: Overall, our findings provide the most detailed metagenomics-based perspective up to now of the microbes that thrive in meat, meat products and associated environments and open avenues for future research activities to better understand the microbiome functionality and potential contribution to meat quality and safety. Video Abstract.}, } @article {pmid39407345, year = {2024}, author = {Salgado, JFM and Hervé, V and Vera, MAG and Tokuda, G and Brune, A}, title = {Unveiling lignocellulolytic potential: a genomic exploration of bacterial lineages within the termite gut.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {201}, pmid = {39407345}, issn = {2049-2618}, mesh = {Animals ; *Isoptera/microbiology ; *Lignin/metabolism ; *Gastrointestinal Microbiome ; Phylogeny ; Bacteria/genetics/classification/isolation & purification/enzymology ; Metagenome ; Polysaccharides/metabolism ; Genome, Bacterial ; Genomics ; Cellulose/metabolism ; }, abstract = {BACKGROUND: The microbial landscape within termite guts varies across termite families. The gut microbiota of lower termites (LT) is dominated by cellulolytic flagellates that sequester wood particles in their digestive vacuoles, whereas in the flagellate-free higher termites (HT), cellulolytic activity has been attributed to fiber-associated bacteria. However, little is known about the role of individual lineages in fiber digestion, particularly in LT.

RESULTS: We investigated the lignocellulolytic potential of 2223 metagenome-assembled genomes (MAGs) recovered from the gut metagenomes of 51 termite species. In the flagellate-dependent LT, cellulolytic enzymes are restricted to MAGs of Bacteroidota (Dysgonomonadaceae, Tannerellaceae, Bacteroidaceae, Azobacteroidaceae) and Spirochaetota (Breznakiellaceae) and reflect a specialization on cellodextrins, whereas their hemicellulolytic arsenal features activities on xylans and diverse heteropolymers. By contrast, the MAGs derived from flagellate-free HT possess a comprehensive arsenal of exo- and endoglucanases that resembles that of termite gut flagellates, underlining that Fibrobacterota and Spirochaetota occupy the cellulolytic niche that became vacant after the loss of the flagellates. Furthermore, we detected directly or indirectly oxygen-dependent enzymes that oxidize cellulose or modify lignin in MAGs of Pseudomonadota (Burkholderiales, Pseudomonadales) and Actinomycetota (Actinomycetales, Mycobacteriales), representing lineages located at the hindgut wall.

CONCLUSIONS: The results of this study refine our concept of symbiotic digestion of lignocellulose in termite guts, emphasizing the differential roles of specific bacterial lineages in both flagellate-dependent and flagellate-independent breakdown of cellulose and hemicelluloses, as well as a so far unappreciated role of oxygen in the depolymerization of plant fiber and lignin in the microoxic periphery during gut passage in HT. Video Abstract.}, } @article {pmid39406897, year = {2024}, author = {Westmeijer, G and van Dam, F and Kietäväinen, R and González-Rosales, C and Bertilsson, S and Drake, H and Dopson, M}, title = {Candidatus Desulforudis audaxviator dominates a 975 m deep groundwater community in central Sweden.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1332}, pmid = {39406897}, issn = {2399-3642}, support = {2018-04311//Vetenskapsrådet (Swedish Research Council)/ ; }, mesh = {*Groundwater/microbiology ; Sweden ; Microbiota/genetics ; Metagenome ; Phylogeny ; Deltaproteobacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The continental bedrock contains groundwater-bearing fractures that are home to microbial populations that are vital in mediating the Earth's biogeochemical cycles. However, their diversity is poorly understood due to the difficulty of obtaining samples from this environment. Here, a groundwater-bearing fracture at 975 m depth was isolated by employing packers in order to characterize the microbial community via metagenomes combined with prokaryotic and eukaryotic marker genes (16S and 18S ribosomal RNA gene). Genome-resolved analyses revealed a community dominated by sulfate-reducing Bacillota, predominantly represented by Candidatus Desulforudis audaxviator and with Wood-Ljungdahl as the most prevalent pathway for inorganic carbon fixation. Moreover, the eukaryotic community had a considerable diversity and was comprised of mainly flatworms, chlorophytes, crustaceans, ochrophytes, and fungi. These findings support the important role of the Bacillota, with the sulfate reducer Candidatus Desulforudis audaxviator as its main representative, as primary producers in the often energy-limited groundwaters of the continental subsurface.}, } @article {pmid39405686, year = {2024}, author = {Zhang, S and Hou, R and Wang, Y and Huang, Q and Lin, L and Li, H and Liu, S and Jiang, Z and Huang, X and Xu, X}, title = {Xenobiotic metabolism activity of gut microbiota from six marine species: Combined taxonomic, metagenomic, and in vitro transformation analysis.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136152}, doi = {10.1016/j.jhazmat.2024.136152}, pmid = {39405686}, issn = {1873-3336}, mesh = {Animals ; *Xenobiotics/metabolism/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/genetics/metabolism/classification ; Water Pollutants, Chemical/metabolism/toxicity ; RNA, Ribosomal, 16S/genetics ; Fishes/microbiology/metabolism ; Metagenomics ; Bivalvia/microbiology/metabolism ; Biotransformation ; }, abstract = {The xenobiotic metabolism driven by the gut microbiota significantly regulates the bioavailability and toxic effects of environmental pollutants such as plasticizers on aquatic organisms. However, it is still unknown whether the gut microbiota can exhibit variable metabolic ability across host species and which functional bacteria and genes are involved in xenobiotic transformation. This study investigated the enriched gut microbiota community composition and diversity of in vitro enrichment cultures from 6 marine species, namely, yellowfin seabream (Acanthopagrus latus), thorn fish (Terapon jarbua), shortnose ponyfish (Leiognathus brevirostris), mussel (Perna viridis), prawn (Parapenaeopsis hungerfordi) and crab (Charybdis riversandersoni). Pseudomonadota, Bacteroidota and Bacillota were the dominant phyla and Enterobacter, Raoultella, Klebsiella, Dysgonomanas and Lactococcus were the dominant genera in the enriched flora according to 16S rRNA sequencing. Furthermore, the metagenomic results revealed that all enriched gut microbiota presented metabolic genes for carbohydrates, amino acids, lipids, and xenobiotics. In particular, the gut microbiota of yellowfin seabream had the highest abundance of glycoside hydrolase family genes and CYP450 enzyme genes. Klebsiella was identified as a common potential degrader of xenobiotic metabolism. In addition, the Biolog plate test system confirmed that the gut microbiota can metabolize various carbon sources and drive the xenobiotic transformation. According to AWCD analysis of community level physiological profiling (CLPP), yellowfin seabream > mussel > prawn > shortnose ponyfish > crab > thorn fish. The gut microbiota of yellowfin seabream presented a stronger metabolic profile of phthalates and bisphenol analogs which reflected by their AWCD results and concentration variations. Overall, our results demonstrated the diverse metabolic abilities of the gut microbiota from six marine organisms and their potential for altering of the fate of xenobiotics in the ecosystem on the basis of combined taxonomic, metagenomic, and in vitro transformation analysis.}, } @article {pmid39405675, year = {2024}, author = {Xing, BS and Su, YM and Fu, YL and Wu, YF and Yan, CH and Wang, XC and Li, YY and Chen, R}, title = {Comparison of the short- and long-term effects of zinc ions on the anaerobic mesophilic co-digestion of food waste and waste activated sludge: Digester performance, antibiotic resistance gene reduction and the microbial community.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136119}, doi = {10.1016/j.jhazmat.2024.136119}, pmid = {39405675}, issn = {1873-3336}, mesh = {*Zinc ; *Sewage/microbiology ; Anaerobiosis ; *Bioreactors ; *Methane/metabolism ; *Drug Resistance, Microbial/genetics ; *Microbiota/drug effects ; Food ; Waste Disposal, Fluid/methods ; Food Loss and Waste ; }, abstract = {Heavy metals contained in waste activated sludge (WAS), especially zinc ions, have an inhibitory effect on the anaerobic digestion. However, the effects of zinc ions on digester performance, antibiotic resistance genes (ARGs) reduction, and the microbial community involved in the anaerobic mesophilic co-digestion (AcoD) of WAS and food waste (FW) have not been fully characterized. Therefore, batch trials and continuous stirred tank reactors were used under different zinc-ion concentrations. Findings showed that the AcoD system can tolerate a maximum zinc ion of 540 mg/L in a short-term batch and 470 mg/L in a long-term AcoD system, promoting methane production of approximately 1.0-17.0 %. Metagenomic analysis revealed that syntrophic H2 transfer occurred between Syntrophomonas and Methanoculleus and the aceticlastic and hydrogenotrophic methanogenic pathways were both enhanced by 1.18- and 1.16 times, respectively. Moreover, the relative abundance of Methanosarcina increased from 58.4 % to 72.5 % at 470 mg/L to adapt to the high zinc ion concentration during long-term continuous operation. These results revealed that AcoD with a low zinc ion concentration can effectively increase the removal percentage of ARGs. The results provide guidance for biogas recovery and use of mesophilic AcoD with FW and WAS containing high zinc ion concentrations without pretreatment process.}, } @article {pmid39404262, year = {2024}, author = {Zhong, C and Yamanouchi, S and Li, Y and Chen, J and Wei, T and Wang, R and Zhou, K and Cheng, A and Hao, W and Liu, H and Konhauser, KO and Iwasaki, W and Qian, P-Y}, title = {Marine biofilms: cyanobacteria factories for the global oceans.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0031724}, pmid = {39404262}, issn = {2379-5077}, support = {2021HJ01, SMSEGL20SC01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) ()/ ; JPMJCR19S2//MEXT | Japan Science and Technology Agency (JST)/ ; 19H05688, 18H04136//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; HKUST PDFS2223-6S03//Research Grants Council, University Grants Committee ()/ ; }, mesh = {*Biofilms/growth & development ; *Cyanobacteria/genetics/physiology/classification/isolation & purification ; *Seawater/microbiology ; *Oceans and Seas ; Metagenome ; Phylogeny ; Metagenomics ; }, abstract = {UNLABELLED: Marine biofilms were newly revealed as a giant microbial diversity pool for global oceans. However, the cyanobacterial diversity in marine biofilms within the upper seawater column and its ecological and evolutionary implications remains undetermined. Here, we reconstructed a full picture of modern marine cyanobacteria habitats by re-analyzing 9.3 terabyte metagenomic data sets and 2,648 metagenome-assembled genomes (MAGs). The abundances of cyanobacteria lineages exclusively detected in marine biofilms were up to ninefold higher than those in seawater at similar sample size. Analyses revealed that cyanobacteria in marine biofilms are specialists with strong geographical and environmental constraints on their genome and functional adaption, which is in stark contrast to the generalistic features of seawater-derived cyanobacteria. Molecular dating suggests that the important diversifications in biofilm-forming cyanobacteria appear to coincide with the Great Oxidation Event (GOE), "boring billion" middle Proterozoic, and the Neoproterozoic Oxidation Event (NOE). These new insights suggest that marine biofilms are large and important cyanobacterial factories for the global oceans.

IMPORTANCE: Cyanobacteria, highly diverse microbial organisms, play a crucial role in Earth's oxygenation and biogeochemical cycling. However, their connection to these processes remains unclear, partly due to incomplete surveys of oceanic niches. Our study uncovered significant cyanobacterial diversity in marine biofilms, showing distinct niche differentiation compared to seawater counterparts. These patterns reflect three key stages of marine cyanobacterial diversification, coinciding with major geological events in the Earth's history.}, } @article {pmid39402236, year = {2024}, author = {Vera-Ponce de León, A and Hensen, T and Hoetzinger, M and Gupta, S and Weston, B and Johnsen, SM and Rasmussen, JA and Clausen, CG and Pless, L and Veríssimo, ARA and Rudi, K and Snipen, L and Karlsen, CR and Limborg, MT and Bertilsson, S and Thiele, I and Hvidsten, TR and Sandve, SR and Pope, PB and La Rosa, SL}, title = {Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health.}, journal = {Nature microbiology}, volume = {9}, number = {11}, pages = {3059-3074}, pmid = {39402236}, issn = {2058-5276}, support = {300846//Norges Forskningsråd (Research Council of Norway)/ ; 757922//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 12/RC/2273-P2//Science Foundation Ireland (SFI)/ ; }, mesh = {Animals ; *Salmo salar/microbiology ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Metagenomics ; *Aquaculture ; *Genome, Bacterial/genetics ; Seawater/microbiology ; Fresh Water/microbiology ; Phylogeny ; Genomics/methods ; }, abstract = {To ensure sustainable aquaculture, it is essential to understand the path 'from feed to fish', whereby the gut microbiome plays an important role in digestion and metabolism, ultimately influencing host health and growth. Previous work has reported the taxonomic composition of the Atlantic salmon (Salmo salar) gut microbiome; however, functional insights are lacking. Here we present the Salmon Microbial Genome Atlas consisting of 211 high-quality bacterial genomes, recovered by cultivation (n = 131) and gut metagenomics (n = 80) from wild and farmed fish both in freshwater and seawater. Bacterial genomes were taxonomically assigned to 14 different orders, including 35 distinctive genera and 29 previously undescribed species. Using metatranscriptomics, we functionally characterized key bacterial populations, across five phyla, in the salmon gut. This included the ability to degrade diet-derived fibres and release vitamins and other exometabolites with known beneficial effects, which was supported by genome-scale metabolic modelling and in vitro cultivation of selected bacterial species coupled with untargeted metabolomic studies. Together, the Salmon Microbial Genome Atlas provides a genomic and functional resource to enable future studies on salmon nutrition and health.}, } @article {pmid39400741, year = {2024}, author = {Lemieux-Labonté, V and Pathmanathan, JS and Terrat, Y and Tromas, N and Simard, A and Haase, CG and Lausen, CL and Willis, CKR and Lapointe, FJ}, title = {Pseudogymnoascus destructans invasion stage impacts the skin microbial functions of highly vulnerable Myotis lucifugus.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {11}, pages = {}, pmid = {39400741}, issn = {1574-6941}, support = {RGPIN-2015-05219//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; *Chiroptera/microbiology ; *Skin/microbiology ; *Ascomycota/genetics/pathogenicity ; *Microbiota ; Hibernation ; Mycoses/microbiology/veterinary ; }, abstract = {The role of the skin microbiome in resistance and susceptibility of wildlife to fungal pathogens has been examined from a taxonomic perspective but skin microbial function, in the context of fungal infection, has yet to be studied. Our objective was to understand effects of a bat fungal pathogen site infection status and course of invasion on skin microbial function. We sampled seven hibernating colonies of Myotis lucifugus covering three-time points over the course of Pseudogymnoascus destructans (Pd) invasion and white nose syndrome (pre-invasion, epidemic, and established). Our results support three new hypotheses about Pd and skin functional microbiome: (1) there is an important effect of Pd invasion stage, especially at the epidemic stage; (2) disruption by the fungus at the epidemic stage could decrease anti-fungal functions with potential negative effects on the microbiome and bat health; (3) the collection site might have a larger influence on microbiomes at the pre-invasion stage rather than at epidemic and established stages. Future studies with larger sample sizes and using meta-omics approaches will help confirm these hypotheses, and determine the influence of the microbiome on wildlife survival to fungal disease.}, } @article {pmid39399973, year = {2024}, author = {Simpson, A and Wood-Charlson, EM and Smith, M and Koch, BJ and Beilsmith, K and Kimbrel, JA and Kellom, M and Hunter, CI and Walls, RL and Schriml, LM and Wilhelm, RC}, title = {MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {39399973}, issn = {2047-217X}, support = {IND90024429//USDA/ ; //Purdue University/ ; //Lawrence Berkeley National Laboratory/ ; }, mesh = {*Isotope Labeling/methods ; Reproducibility of Results ; Microbiota/genetics ; Metadata ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; }, abstract = {DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields-isotope, isotopolog, isotopolog label, labeling approach, and gradient position-and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.}, } @article {pmid39399231, year = {2024}, author = {Scicchitano, D and Foresto, L and Laczny, CC and Cinti, N and Vitagliano, R and Halder, R and Morri, G and Turroni, S and D'Amico, F and Palladino, G and Fiori, J and Wilmes, P and Rampelli, S and Candela, M}, title = {A 15-day pilot biodiversity intervention with horses in a farm system leads to gut microbiome rewilding in 10 urban Italian children.}, journal = {One health (Amsterdam, Netherlands)}, volume = {19}, number = {}, pages = {100902}, pmid = {39399231}, issn = {2352-7714}, abstract = {To provide some glimpses on the possibility of shaping the human gut microbiome (GM) through probiotic exchange with natural ecosystems, here we explored the impact of 15 days of daily interaction with horses on the GM of 10 urban-living Italian children. Specifically, the children were in close contact with the horses in an "educational farm", where they spent almost 10 h/day interacting with the animals. The children's GM was assessed before and after the horse interaction using metabarcoding sequencing and shotgun metagenomics, along with the horses' skin, oral and fecal microbiomes. Targeted metabolomic analysis for GM-produced beneficial metabolites (i.e., short-chain fatty acids) in the children's feces was also performed. Interaction with horses facilitated the acquisition of health-related traits in the children's GM, such as increased diversity, enhanced butyrate production and an increase in several health-promoting species considered to be next-generation probiotics. Among these, the butyrate producers Facecalibacterium prausnitzii and F. duncaniae and a species belonging to the order Christensenellales. Interaction with horses was also associated with increased proportions of Eggerthella lenta, Gordonibacter pamelae and G. urolithinfaciens, GM components known to play a role in the bioconversion of dietary plant polyphenols into beneficial metabolites. Notably, no increase in potentially harmful traits, including toxin genes, was observed. Overall, our pilot study provides some insights on the existence of possible health-promoting exchanges between children and horses microbiomes. It lays the groundwork for an implemented and more systematic enrollment effort to explore the full complexity of human GM rewilding through exchange with natural ecosystems, aligning with the One Health approach.}, } @article {pmid39396785, year = {2024}, author = {Su, XS and Zhang, YB and Jin, WJ and Zhang, ZJ and Xie, ZK and Wang, RY and Wang, YJ and Qiu, Y}, title = {Lily viruses regulate the viral community of the Lanzhou lily rhizosphere and indirectly affect rhizosphere carbon and nitrogen cycling.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {176808}, doi = {10.1016/j.scitotenv.2024.176808}, pmid = {39396785}, issn = {1879-1026}, mesh = {*Rhizosphere ; *Soil Microbiology ; *Lilium/virology/microbiology ; *Nitrogen/metabolism ; Nitrogen Cycle ; Carbon/metabolism ; Plant Viruses/physiology ; Virome ; China ; Plant Roots/virology/microbiology/metabolism ; Soil/chemistry ; Carbon Cycle ; Metagenomics ; Cucumovirus/physiology ; }, abstract = {The rhizosphere, where plant roots interact intensely with the soil, is a crucial but understudied area in terms of the impact of virus infection. In this study, we investigated the effects of lily symptomless virus (LSV) and cucumber mosaic virus (CMV) on the Lanzhou lily (Lilium davidii var. unicolor) rhizosphere using metagenomics and bioinformatics analysis. We found that virus infection significantly altered soil pH, inorganic carbon, nitrate nitrogen, and total sulfur. Co-infection with LSV and CMV had a greater influence than single infections on the α- and β-diversity of the rhizosphere viral community in which the absolute abundance of certain virus families (Siphoviridae, Podoviridae, and Myoviridae) increased significantly, whereas bacteria, fungi, and archaea remained relatively unaffected. These altered virus populations influenced the rhizosphere microbial carbon and nitrogen cycles by exerting top-down control on bacteria. Co-infection potentially weakened rhizosphere carbon fixation and promoted processes such as methane oxidation, nitrification, and denitrification. In addition, the co-occurrence network of bacteria and viruses in the rhizosphere revealed substantial changes in microbial community composition under co-infection. Our partial-least-squares path model confirmed that the diversity of the rhizosphere viral community indirectly regulated the carbon and nitrogen cycling functions of the microbial community, thus affecting the accumulation of carbon and nitrogen nutrients in the soil. Our results are the first report of the effects of virus infection on the lily rhizosphere, particularly for co-infection; they therefore complement research on the plant virus pathogenic mechanisms, and increase our understanding of the ecological role of rhizosphere soil viruses.}, } @article {pmid39396767, year = {2024}, author = {Zhao, F and Tie, N and Kwok, LY and Ma, T and Wang, J and Man, D and Yuan, X and Li, H and Pang, L and Shi, H and Ren, S and Yu, Z and Shen, X and Li, H and Zhang, H}, title = {Baseline gut microbiome as a predictive biomarker of response to probiotic adjuvant treatment in gout management.}, journal = {Pharmacological research}, volume = {209}, number = {}, pages = {107445}, doi = {10.1016/j.phrs.2024.107445}, pmid = {39396767}, issn = {1096-1186}, mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; *Gout/drug therapy/blood ; *Gastrointestinal Microbiome/drug effects ; Male ; Double-Blind Method ; Middle Aged ; *Uric Acid/blood ; Female ; *Biomarkers/blood ; Aged ; Gout Suppressants/therapeutic use ; Febuxostat/therapeutic use ; Adult ; Treatment Outcome ; Feces/microbiology ; }, abstract = {Gout is characterized by dysregulation of uric acid (UA) metabolism, and the gut microbiota may serve as a regulatory target. This two-month randomized, double-blind, placebo-controlled trial aimed to investigate the additional benefits of coadministering Probio-X alongside febuxostat. A total of 160 patients with gout were randomly assigned to either the probiotic group (n = 120; Probio-X [3 × 10[10] CFU/day] with febuxostat) or the placebo group (n = 40; placebo material with febuxostat). Coadministration of Probio-X significantly decreased serum UA levels and the rate of acute gout attacks (P < 0.05). Based on achieving a target sUA level (360 μmol/L) after the intervention, the probiotic group was further subdivided into probiotic-responsive (ProA; n = 54) and probiotic-unresponsive (ProB; n = 66) subgroups. Post-intervention clinical indicators, metagenomic, and metabolomic changes in the ProB and placebo groups were similar, but differed from those in the ProA group, which exhibited significantly lower levels of acute gout attack, gout impact score, serum indicators (UA, XOD, hypoxanthine, and IL-1β), and fecal gene abundances of UA-producing pathways (KEGG orthologs of K13479 and K01487; gut metabolic modules for formate conversion and lactose and galactose degradation). Additionally, the ProA group showed significantly higher levels (P < 0.05) of gut SCFAs-producing bacteria and UA-related metabolites (xanthine, hypoxanthine, bile acids) after the intervention. Finally, we established a gout metagenomic classifier to predict probiotic responsiveness based on subjects' baseline gut microbiota composition. Our results indicate that probiotic-driven therapeutic responses are highly individual, with the probiotic-responsive cohort benefitting significantly from probiotic coadministration.}, } @article {pmid39387577, year = {2024}, author = {Beck, KL and Haiminen, N and Agarwal, A and Carrieri, AP and Madgwick, M and Kelly, J and Pylro, V and Kawas, B and Wiedmann, M and Ganda, E}, title = {Development and evaluation of statistical and artificial intelligence approaches with microbial shotgun metagenomics data as an untargeted screening tool for use in food production.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0084024}, pmid = {39387577}, issn = {2379-5077}, support = {#PEN04752, #PEN04731//U.S. Department of Agriculture (USDA)/ ; }, mesh = {*Metagenomics/methods ; *Artificial Intelligence ; *Milk/microbiology/chemistry ; Animals ; Food Microbiology/methods ; Microbiota/genetics ; Algorithms ; Principal Component Analysis ; Machine Learning ; }, abstract = {UNLABELLED: The increasing knowledge of microbial ecology in food products relating to quality and safety and the established usefulness of machine learning algorithms for anomaly detection in multiple scenarios suggests that the application of microbiome data in food production systems for anomaly detection could be a valuable approach to be used in food systems. These methods could be used to identify ingredients that deviate from their typical microbial composition, which could indicate food fraud or safety issues. The objective of this study was to assess the feasibility of using shotgun sequencing data as input into anomaly detection algorithms using fluid milk as a model system. Contrastive principal component analysis (PCA), cluster-based methods, and explainable artificial intelligence (AI) were evaluated for the detection of two anomalous sample classes using longitudinal metagenomic profiling of fluid milk compared to baseline (BL) samples collected under comparable circumstances. Traditional methods (alpha and beta diversity, clustering-based contrastive PCA, multidimensional scaling, and dendrograms) failed to differentiate anomalous sample classes; however, explainable AI was able to classify anomalous vs baseline samples and indicate microbial drivers in association with antibiotic use. We validated the potential for explainable AI to classify different milk sources using larger publicly available fluid milk 16S rDNA sequencing data sets and demonstrated that explainable AI is able to differentiate between milk storage methods, processing stages, and seasons. Our results indicate that the application of artificial intelligence continues to hold promise in the realm of microbiome data analysis and could present further opportunities for downstream analytic automation to aid in food safety and quality.

IMPORTANCE: We evaluated the feasibility of using untargeted metagenomic sequencing of raw milk for detecting anomalous food ingredient content with artificial intelligence methods in a study specifically designed to test this hypothesis. We also show through analysis of publicly available fluid milk microbial data that our artificial intelligence approach is able to successfully predict milk in different stages of processing. The approach could potentially be applied in the food industry for safety and quality control.}, } @article {pmid39394961, year = {2024}, author = {Branck, T and Hu, Z and Nickols, WA and Walsh, AM and Bhosle, A and Short, MI and Nearing, JT and Asnicar, F and McIver, LJ and Maharjan, S and Rahnavard, A and Louyakis, AS and Badri, DV and Brockel, C and Thompson, KN and Huttenhower, C}, title = {Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39394961}, issn = {1751-7370}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Dogs/microbiology ; Cats ; *Pets/microbiology ; *Feces/microbiology ; *Phylogeny ; *Metagenome ; Humans ; *Metagenomics ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {The gut microbiome of companion animals is relatively underexplored, despite its relevance to animal health, pet owner health, and basic microbial community biology. Here, we provide the most comprehensive analysis of the canine and feline gut microbiomes to date, incorporating 2639 stool shotgun metagenomes (2272 dog and 367 cat) spanning 14 publicly available datasets (n = 730) and 8 new study populations (n = 1909). These are compared with 238 and 112 baseline human gut metagenomes from the Human Microbiome Project 1-II and a traditionally living Malagasy cohort, respectively, processed in a manner identical to the animal metagenomes. All microbiomes were characterized using reference-based taxonomic and functional profiling, as well as de novo assembly yielding metagenomic assembled genomes clustered into species-level genome bins. Companion animals shared 184 species-level genome bins not found in humans, whereas 198 were found in all three hosts. We applied novel methodology to distinguish strains of these shared organisms either transferred or unique to host species, with phylogenetic patterns suggesting host-specific adaptation of microbial lineages. This corresponded with functional divergence of these lineages by host (e.g. differences in metabolic and antibiotic resistance genes) likely important to companion animal health. This study provides the largest resource to date of companion animal gut metagenomes and greatly contributes to our understanding of the "One Health" concept of a shared microbial environment among humans and companion animals, affecting infectious diseases, immune response, and specific genetic elements.}, } @article {pmid39394504, year = {2024}, author = {Passarini, MRZ and Robayo, MIG and Ottoni, JR and Duarte, AWF and Rosa, LH}, title = {Biotechnological potential in agriculture of soil Antarctic microorganisms revealed by omics approach.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {11}, pages = {345}, pmid = {39394504}, issn = {1573-0972}, support = {Nº 205/2021//Program Institutional Triple Agenda EDITAL PRPPG/ ; }, mesh = {*Soil Microbiology ; Antarctic Regions ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Agriculture ; *Fungi/classification/genetics/isolation & purification/metabolism ; *Biotechnology ; *Metagenomics ; High-Throughput Nucleotide Sequencing ; Soil/chemistry ; Phylogeny ; Nitrogen/metabolism ; Microbiota ; }, abstract = {The biotechnological potential for agricultural applications in the soil in the thawing process on Whalers Bay, Deception Island, Antarctica was evaluated using a metagenomic approach through high-throughput sequencing. Approximately 22.70% of the sequences were affiliated to the phyla of the Bacteria dominion, followed by 0.26% to the Eukarya. Proteobacteria (Bacteria) and Ascomycota (Fungi) were the most abundant phyla. Thirty-two and thirty-six bacterial and fungal genera associated with agricultural biotechnological applications were observed. Streptomyces and Pythium were the most abundant genera related to the Bacteria and Oomycota, respectively. The main agricultural application associated with bacteria was nitrogen affixation; in contrast for fungi, was associated with phytopathogenic capabilities. The present study showed the need to use metagenomic technology to understand the dynamics and possible metabolic pathways associated with the microbial communities present in the soil sample in the process of thawing recovered from the Antarctic continent, which presented potential application in processes of agro-industrial interest.}, } @article {pmid39393653, year = {2024}, author = {Li, Y and Huang, F and Dong, S and Liu, L and Lin, L and Li, Z and Zheng, Y and Hu, Z}, title = {Microbiota succession, species interactions, and metabolic functions during autotrophic biofloc formation in zero-water-exchange shrimp farming without organic carbon supplements.}, journal = {Bioresource technology}, volume = {414}, number = {}, pages = {131584}, doi = {10.1016/j.biortech.2024.131584}, pmid = {39393653}, issn = {1873-2976}, mesh = {Animals ; *Aquaculture/methods ; *Microbiota ; *Carbon ; *Nitrogen ; *Bacteria/metabolism ; *Autotrophic Processes ; Penaeidae ; Microalgae/metabolism ; Ammonia/metabolism ; }, abstract = {Autotrophic bioflocs (ABF) exhibits lower energy consumption, more environment-friendly and cost-effective than heterotrophic bioflocs depending on organic carbon supplements. Whereas ABF has not been widely applied to aquaculture production. Here, ABF successfully performed to control ammonia and nitrite under harmless levels even when carbon-to-nitrogen ratio reduced to 2.0, during 12-week shrimp farming in commercial scale. ABF was mainly dominated by bacteria of Proteobacteria, Bacteroidota, Chloroflexi and eukaryotes of Bacillariophyta, Rotifera, Ciliophora. A notable shift occurred in ABF with the significant decreases of Proteobacteria and Rotifera replaced by Bacteroidota, Chloroflexi, and Bacillariophyta after four weeks. Nitrogen metabolism was synergistically executed by bacteria and microalgae, especially the positive interaction between Nitrospira and Halamphora for ABF nitrification establishment. Metagenomics confirmed the complete functional genes of key bacteria related to the cycling of carbon, nitrogen, and phosphorus by ABF. This study may promote the development application of ABF in low-carbon shrimp aquaculture.}, } @article {pmid39393228, year = {2024}, author = {Dey, G and Maity, JP and Banerjee, P and Sharma, RK and Das, K and Gnanachandrasamy, G and Wang, CW and Lin, PY and Wang, SL and Chen, CY}, title = {Evaluation and mitigation of potentially toxic elements contamination in mangrove ecosystem: Insights into phytoremediation and microbial perspective.}, journal = {Marine pollution bulletin}, volume = {209}, number = {Pt A}, pages = {117035}, doi = {10.1016/j.marpolbul.2024.117035}, pmid = {39393228}, issn = {1879-3363}, mesh = {*Biodegradation, Environmental ; *Wetlands ; *Water Pollutants, Chemical/analysis ; Taiwan ; Avicennia ; Environmental Monitoring ; Geologic Sediments/chemistry/microbiology ; Microbiota ; Ecosystem ; }, abstract = {Mangroves, essential coastal ecosystems, are threatened by human-induced Potentially-toxic-elements (PTEs) pollution. This study analyzed PTEs distribution, phytoremediation potential, and rhizosphere microbial communities in Taiwan's Xinfeng mangrove forest. Significant variations in physicochemical and PTEs concentrations were observed across adjacent water bodies, with moderate contamination in the river, estuary, and overlying water of mangroves sediment. The partition-coefficient showed the mobility of Bi, Pb, Co, and Sr at the water-sediment interface. The geochemical-indices revealed high Bi and Pb contamination and moderate Zn, Sr, Cu, and Cd contamination in sediment. The overall pollution indices indicated the significant contamination, while moderate ecological risk was found for Cd (40 ≤ Er[i] < 80). Mangroves Kandelia obovata and Avicennia marina exhibited promising PTEs phytoremediation potential (Bi, Cd, Mn, Sr, and Co). Metagenomics indicated a diverse microbial community with N-fixation, P-solubilization, IAA synthesis, and PTEs-resistance genes. These findings underscore the need for targeted conservation to protect these critical habitats.}, } @article {pmid39390034, year = {2024}, author = {Delanghe, L and De Boeck, I and Van Malderen, J and Allonsius, CN and Van Rillaer, T and Bron, PA and Claes, I and Hagendorens, M and Lebeer, S and Leysen, J}, title = {Mild atopic dermatitis is characterized by increase in non-staphylococcus pathobionts and loss of specific species.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {23659}, pmid = {39390034}, issn = {2045-2322}, support = {HBC.2020.2873//Agentschap Innoveren en Ondernemen/ ; HBC.2020.2873//Agentschap Innoveren en Ondernemen/ ; 12S4222N//Fonds Wetenschappelijk Onderzoek/ ; 1S08523N//Fonds Wetenschappelijk Onderzoek/ ; 852600/ERC_/European Research Council/International ; }, mesh = {*Dermatitis, Atopic/microbiology ; Humans ; *Microbiota ; *Skin/microbiology/pathology ; Female ; Adult ; Male ; Staphylococcus aureus/genetics/isolation & purification/pathogenicity ; Bacteria/classification/genetics ; Middle Aged ; Metagenomics/methods ; }, abstract = {Atopic dermatitis is the most common inflammatory skin condition with a severe negative impact on patients' quality of life. The etiology of AD is complex and depends on age, genetics, the immune system, environmental factors, and the skin microbiome, with a key role for pathogenic Staphylococcus aureus in the development of severe AD. However, the composition of the skin microbiome in mild AD is understudied. Here, using metagenomic shallow shotgun sequencing, we showed that mild AD lesions did not show a significant difference in the diversity of the skin microbiome compared to samples from non-AD patients and that the relative abundance of S. aureus did not differ in these mild AD lesions. However, when we assessed other taxa, Mycobacterium ostraviense, Pedobacter panaciterrae_A and four Streptomyces species were identified with higher abundances in mild AD lesions and species of 15 genera were decreased in abundance. The highest fold decreases were observed for Paracoccus marcusii, Microbacterium lacticum, Micrococcus luteus, and Moraxella sp002478835. These microbiome compositional insights are a first step towards novel microbiome-based diagnostics and therapeutics for early intervention at the stage of mild AD and provide a path forward for the functional study of species involved in this often-overlooked patient population.}, } @article {pmid39390025, year = {2024}, author = {Larsson, A and Ericson, U and Jönsson, D and Miari, M and Athanasiadis, P and Baldanzi, G and Brunkwall, L and Hellstrand, S and Klinge, B and Melander, O and Nilsson, PM and Fall, T and Maziarz, M and Orho-Melander, M}, title = {New connections of medication use and polypharmacy with the gut microbiota composition and functional potential in a large population.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {23723}, pmid = {39390025}, issn = {2045-2322}, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Polypharmacy ; Male ; Female ; Middle Aged ; Sweden ; Aged ; Adult ; }, abstract = {Medication can affect the gut microbiota composition and function. The aim of this study was to investigate connections between use of common non-antibiotic medicines and the gut microbiota composition and function in a large Swedish cohort (N = 2223). Use of 67 medications and polypharmacy (≥ 5 medications), based on self-reported and prescription registry data, were associated with the relative abundance of 881 gut metagenomic species (> 5% prevalence) and 103 gut metabolic modules (GMMs). Altogether, 97 associations of 26 medications with 40 species and of four medications with five GMMs were observed (false discovery rate < 5%). Several earlier findings were replicated like the positive associations of proton pump inhibitors (PPIs) with numerous oral species, and those of metformin with Escherichia species and with lactate consumption I and arginine degradation II. Several new associations were observed between, among others, use of antidepressants, beta-blockers, nonsteroidal anti-inflammatory drugs and calcium channel blockers, and specific species. Polypharmacy was positively associated with Enterococcus faecalis, Bacteroides uniformis, Rothia mucilaginosa, Escherichia coli and Limosilactobacillus vaginalis, and with 13 GMMs. We confirmed several previous findings and identified numerous new associations between use of medications/polypharmacy and the gut microbiota composition and functional potential. Further studies are needed to confirm the new findings.}, } @article {pmid39390011, year = {2024}, author = {Kim, HS and Oh, SJ and Kim, BK and Kim, JE and Kim, BH and Park, YK and Yang, BG and Lee, JY and Bae, JW and Lee, CK}, title = {Dysbiotic signatures and diagnostic potential of gut microbial markers for inflammatory bowel disease in Korean population.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {23701}, pmid = {39390011}, issn = {2045-2322}, support = {2017R1A5A2014768//National Research Foundation of Korea/ ; 2021R1C1C2008556//National Research Foundation of Korea/ ; HI23C0661//Korea Health Industry Development Institute/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Dysbiosis/diagnosis/microbiology ; Female ; Male ; Republic of Korea/epidemiology ; Adult ; Middle Aged ; *Biomarkers ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Inflammatory Bowel Diseases/microbiology/diagnosis ; Colitis, Ulcerative/microbiology/diagnosis ; Metagenomics/methods ; Crohn Disease/microbiology/diagnosis ; Case-Control Studies ; Cross-Sectional Studies ; Young Adult ; Aged ; }, abstract = {Fecal samples were collected from 640 individuals in Korea, including 523 patients with IBD (223 with Crohn's disease [CD] and 300 with ulcerative colitis [UC]) and 117 healthy controls. The samples were subjected to cross-sectional gut metagenomic analysis using 16 S rRNA sequencing and bioinformatics analysis. Patients with IBD, particularly those with CD, exhibited significantly lower alpha diversities than the healthy subjects. Differential abundance analysis revealed dysbiotic signatures, characterized by an expansion of the genus Escherichia-Shigella in patients with CD. Functional annotations showed that functional pathways related to bacterial pathogenesis and production of hydrogen sulfide (H2S) were strongly upregulated in patients with CD. A dysbiosis score, calculated based on functional characteristics, highly correlated with disease severity. Markers distinguishing between healthy subjects and patients with IBD showed accurate classification based on a small number of microbial taxa, which may be used to diagnose ambiguous cases. These findings confirm the taxonomic and functional dysbiosis of the gut microbiota in patients with IBD, especially those with CD. Taxa indicative of dysbiosis may have significant implications for future clinical research on the management and diagnosis of IBD.}, } @article {pmid39389770, year = {2024}, author = {Xu, Y and Yan, Y and Zhou, T and Lu, Y and Yang, X and Tang, K and Liu, F}, title = {Synergy between Arbuscular Mycorrhizal Fungi and Rhizosphere Bacterial Communities Increases the Utilization of Insoluble Phosphorus and Potassium in the Soil by Maize.}, journal = {Journal of agricultural and food chemistry}, volume = {72}, number = {42}, pages = {23631-23642}, doi = {10.1021/acs.jafc.4c07428}, pmid = {39389770}, issn = {1520-5118}, mesh = {*Mycorrhizae/metabolism ; *Phosphorus/metabolism ; *Zea mays/microbiology/metabolism ; *Rhizosphere ; *Soil Microbiology ; *Potassium/metabolism ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Soil/chemistry ; Plant Roots/microbiology/metabolism ; }, abstract = {Arbuscular mycorrhizal (AM) fungi can enhance plant uptake of phosphorus (P) and potassium (K), but it is not yet clear whether rhizosphere bacteria can enhance the ability of AM fungi to acquire insoluble P and K from the soil. Here, pot experiments confirmed that AM fungus-promoted insoluble P and K uptake by plants requires rhizosphere bacteria. The changes of rhizosphere bacterial communities associated with AM fungi were explored by 16S rRNA amplicon sequencing and metagenomic sequencing. Five core bacteria genera identified were involved in P and K cycles. Synthetic community (SynCom) inoculation revealed that SynCom increased soil available P and K and its coinoculation with AM fungi increased P and K concentration in the plants. This study revealed that AM fungi interact with rhizosphere bacteria and promote insoluble P and K acquisition, which provided a foundation for the application of AM fungal-bacterial biofertilizers and was beneficial for the sustainable development of agriculture.}, } @article {pmid39389057, year = {2024}, author = {Hou, X and He, Y and Fang, P and Mei, SQ and Xu, Z and Wu, WC and Tian, JH and Zhang, S and Zeng, ZY and Gou, QY and Xin, GY and Le, SJ and Xia, YY and Zhou, YL and Hui, FM and Pan, YF and Eden, JS and Yang, ZH and Han, C and Shu, YL and Guo, D and Li, J and Holmes, EC and Li, ZR and Shi, M}, title = {Using artificial intelligence to document the hidden RNA virosphere.}, journal = {Cell}, volume = {187}, number = {24}, pages = {6929-6942.e16}, doi = {10.1016/j.cell.2024.09.027}, pmid = {39389057}, issn = {1097-4172}, mesh = {*RNA Viruses/genetics/isolation & purification ; *RNA-Dependent RNA Polymerase/genetics ; *RNA, Viral/genetics ; Genome, Viral/genetics ; Artificial Intelligence ; Virome/genetics ; Phylogeny ; Metagenomics/methods ; Algorithms ; Deep Learning ; Hot Springs/virology ; Hydrothermal Vents/virology ; }, abstract = {Current metagenomic tools can fail to identify highly divergent RNA viruses. We developed a deep learning algorithm, termed LucaProt, to discover highly divergent RNA-dependent RNA polymerase (RdRP) sequences in 10,487 metatranscriptomes generated from diverse global ecosystems. LucaProt integrates both sequence and predicted structural information, enabling the accurate detection of RdRP sequences. Using this approach, we identified 161,979 potential RNA virus species and 180 RNA virus supergroups, including many previously poorly studied groups, as well as RNA virus genomes of exceptional length (up to 47,250 nucleotides) and genomic complexity. A subset of these novel RNA viruses was confirmed by RT-PCR and RNA/DNA sequencing. Newly discovered RNA viruses were present in diverse environments, including air, hot springs, and hydrothermal vents, with virus diversity and abundance varying substantially among ecosystems. This study advances virus discovery, highlights the scale of the virosphere, and provides computational tools to better document the global RNA virome.}, } @article {pmid39389029, year = {2024}, author = {Qian, J and Yeo, EN and Olm, MR}, title = {Hospitalization throws the preterm gut microbiome off-key.}, journal = {Cell host & microbe}, volume = {32}, number = {10}, pages = {1651-1653}, doi = {10.1016/j.chom.2024.09.009}, pmid = {39389029}, issn = {1934-6069}, mesh = {*Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Feces/microbiology ; *Intensive Care Units, Neonatal ; *Metagenomics ; *Infant, Premature ; Hospitalization ; Infant ; }, abstract = {Environmental exposures substantially influence the infant gut microbiome. In this issue of Cell Host & Microbe, Thänert et al.[1] characterize how medical interventions in the neonatal intensive care unit (NICU) shape gut microbiome dynamics in the first months of life by analyzing over 2,500 fecal samples with metagenomics and metatranscriptomics.}, } @article {pmid39384807, year = {2024}, author = {Minot, SS and Li, N and Srinivasan, H and Ayers, JL and Yu, M and Koester, ST and Stangis, MM and Dominitz, JA and Halberg, RB and Grady, WM and Dey, N}, title = {Colorectal cancer-associated bacteria are broadly distributed in global microbiomes and drivers of precancerous change.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {23646}, pmid = {39384807}, issn = {2045-2322}, support = {K08 DK111941/DK/NIDDK NIH HHS/United States ; R50 CA233042/CA/NCI NIH HHS/United States ; U54 CA274374/CA/NCI NIH HHS/United States ; R50CA233042//U.S. Department of Health and Human Services | NIH | National Cancer Institute (NCI)/ ; }, mesh = {*Colorectal Neoplasms/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Animals ; Humans ; Mice ; *Bacteria/genetics/classification ; *Precancerous Conditions/microbiology ; Metagenomics/methods ; }, abstract = {The gut microbiome is implicated in the pathogenesis of colorectal cancer (CRC), but the full scope of this dialogue is unknown. Here we aimed to define the scale and membership of the body of CRC- and health-associated gut bacteria in global populations. We performed a microbiome-CRC correlation analysis of published ultra-deep shotgun metagenomic sequencing data from global microbiome surveys, utilizing a de novo (reference-agnostic) gene-level clustering approach to identify protein-coding co-abundant gene (CAGs) clusters. We link an unprecedented ~ 23-40% of gut bacteria to CRC or health, split nearly evenly as CRC- or health-associated. These microbes encode 2319 CAGs encompassing 427,261 bacterial genes significantly enriched or depleted in CRC. We identified many microbes that had not previously been linked to CRC, thus expanding the scope of "known unknowns" of CRC-associated microbes. We performed an agnostic CAG-based screen of bacterial isolates and validated predicted effects of previously unimplicated bacteria in preclinical models, in which we observed differential induction of precancerous adenomas and field effects. Single-cell RNA sequencing disclosed microbiome-induced senescence-associated gene expression signatures in discrete colonic populations including fibroblasts. In organoid co-cultures, primary colon fibroblasts from mice with microbiomes promoted significantly greater growth than fibroblasts from microbiome-depleted mice. These results offer proof-of-principle for gene-level metagenomic analysis enabling discovery of microbiome links to health and demonstrate that the microbiome can drive precancer states, thereby potentially revealing novel cancer prevention opportunities.}, } @article {pmid39383807, year = {2025}, author = {Zhang, Q and Ji, XM and Wang, X and Wang, W and Xu, X and Zhang, Q and Xing, D and Ren, N and Lee, DJ and Chen, C}, title = {Differentiation of the Anammox core microbiome: Unraveling the evolutionary impetus of scalable gene flow.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122580}, doi = {10.1016/j.watres.2024.122580}, pmid = {39383807}, issn = {1879-2448}, mesh = {*Microbiota ; *Gene Flow ; Phylogeny ; Ammonium Compounds/metabolism ; Oxidation-Reduction ; Bacteria/metabolism/genetics ; Anaerobiosis ; }, abstract = {Anaerobic ammonium oxidation bacteria (AAOB), distinguished by their unique autotrophic nitrogen metabolism, hold pivotal positions in the global nitrogen cycle and environmental biotechnologies. However, the ecophysiology and evolution of AAOB remain poorly understood, attributed to the absence of monocultures. Hence, a comprehensive elucidation of the AAOB-dominated core microbiome, anammox core, is imperative to further completing the theory of engineered nitrogen removal and ecological roles of anammox. Performing taxonomic and phylogenetic analyses on collected genome repertoires, we show here that Candidatus Brocadia and Candidatus Kuenenia possesses a more compact core than Candidatus Jettenia, which partly explains why the latter has a less common ecological presence. Evidence of gene flow is particularly striking in functions related to biosynthesis and oxygen detoxification, underscoring the evolutionary forces driving lineage and core differentiation. Furthermore, CRISPR spacer traceback of the AAOB metagenome-assembled genomes (MAGs) reveals a series of genetic traces for the concealed phages. By reconceptualizing the functional divergence of AAOB with the historical role of phages, we ultimately propose a coevolutionary framework to understand the evolutionary trajectory of anammox microecology. The discoveries provided in this study offer new insights into understanding the evolution of AAOB and the ecology of anammox.}, } @article {pmid39381854, year = {2025}, author = {Drahun, I and Morrison, K and Poole, EA and van Herk, WG and Cassone, BJ}, title = {Characterisation of the bacteriomes harboured by major wireworm pest species in the Canadian Prairies.}, journal = {Insect molecular biology}, volume = {34}, number = {1}, pages = {203-217}, pmid = {39381854}, issn = {1365-2583}, support = {RGPIN-2016-04335//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2023-04126//Natural Sciences and Engineering Research Council of Canada/ ; //Brandon University Research Committee/ ; }, mesh = {Animals ; *Coleoptera/microbiology/growth & development ; *Larva/microbiology/growth & development ; *RNA, Ribosomal, 16S/genetics ; Manitoba ; Microbiota ; Bacteria/classification/genetics ; Grassland ; Canada ; }, abstract = {Nearly all insects harbour bacterial communities that can have a profound effect on their life history, including regulating and shaping host metabolism, development, immunity and fitness. The bacteriomes of several coleopterans have been described; however, very little has been reported for wireworms. These long-lived larvae of click beetles (Coleoptera: Elateridae) are major agricultural pests of a variety of crops grown in the Canadian Prairies. Consequently, the goal of this study was to characterise the bacteriomes of five of the most significant pest species within the region: Limonius californicus, Hypnoidus abbreviatus, H. bicolor, Aeolus mellillus and Dalopius spp. To do this, we collected larvae from southern Manitoba fields (pre-seeding) and carried out 16S rRNA sequencing on individual specimens. Our results indicate wireworms have diverse and taxon-rich bacterial communities, with over 400 genera identified predominately from the phyla Proteobacteria, Actinobacteriota, Bacteroidota and Firmicutes. However, each species had nine or fewer genera comprising >80% of their bacteriome. Network analyses revealed some community structuring consistent among species, which may culminate in shaping/regulating host biology. Moreover, the microbial signatures were influenced by both ontogeny (early vs. late stage larvae) and reproductive strategy (sexual vs. parthenogenetic), with a myriad of other factors likely contributing to bacterial diversity that are impossible to resolve from our study. Overall, this metagenomics study represents the first to characterise the bacteriomes of wireworms in the Canadian Prairies and the findings could assist in the development of sustainable management strategies for these important agricultural pests.}, } @article {pmid39380016, year = {2024}, author = {Ju, Y and Zhang, Z and Liu, M and Lin, S and Sun, Q and Song, Z and Liang, W and Tong, X and Jie, Z and Lu, H and Cai, K and Chen, P and Jin, X and Zhang, W and Xu, X and Yang, H and Wang, J and Hou, Y and Xiao, L and Jia, H and Zhang, T and Guo, R}, title = {Integrated large-scale metagenome assembly and multi-kingdom network analyses identify sex differences in the human nasal microbiome.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {257}, pmid = {39380016}, issn = {1474-760X}, mesh = {Humans ; Male ; Female ; *Metagenome ; *Microbiota ; Adult ; Nose/microbiology ; Sex Characteristics ; Young Adult ; Bacteria/genetics/classification ; Sex Factors ; Metagenomics/methods ; }, abstract = {BACKGROUND: Respiratory diseases impose an immense health burden worldwide. Epidemiological studies have revealed extensive disparities in the incidence and severity of respiratory tract infections between men and women. It has been hypothesized that there might also be a nasal microbiome axis contributing to the observed sex disparities.

RESULTS: Here, we study the nasal microbiome of healthy young adults in the largest cohort to date with 1593 individuals, using shotgun metagenomic sequencing. We compile the most comprehensive reference catalog for the nasal bacterial community containing 4197 metagenome-assembled genomes and integrate the mycobiome, to provide a valuable resource and a more holistic perspective for the understudied human nasal microbiome. We systematically evaluate sex differences and reveal extensive sex-specific features in both taxonomic and functional levels in the nasal microbiome. Through network analyses, we capture markedly higher ecological stability and antagonistic potentials in the female nasal microbiome compared to the male's. The analysis of the keystone bacteria reveals that the sex-dependent evolutionary characteristics might have contributed to these differences.

CONCLUSIONS: In summary, we construct the most comprehensive catalog of metagenome-assembled-genomes for the nasal bacterial community to provide a valuable resource for the understudied human nasal microbiome. On top of that, comparative analysis in relative abundance and microbial co-occurrence networks identify extensive sex differences in the respiratory tract community, which may help to further our understanding of the observed sex disparities in the respiratory diseases.}, } @article {pmid39379175, year = {2024}, author = {Zheng, D and Wilén, BM and Öberg, O and Wik, T and Modin, O}, title = {"Metagenomics reveal the potential for geosmin and 2-methylisoborneol production across multiple bacterial phyla in recirculating aquaculture systems".}, journal = {Environmental microbiology}, volume = {26}, number = {10}, pages = {e16696}, doi = {10.1111/1462-2920.16696}, pmid = {39379175}, issn = {1462-2920}, support = {2020-02639//Svenska Forskningsrådet Formas/ ; }, mesh = {*Metagenomics ; *Bacteria/genetics/classification/metabolism ; *Aquaculture ; *Naphthols/metabolism ; *Camphanes/metabolism ; Phylogeny ; Archaea/genetics/metabolism/classification ; Microbiota ; Metagenome ; }, abstract = {Geosmin and 2-methylisoborneol (MIB) are known to cause taste-and-odour problems in recirculating aquaculture systems (RAS). Both geosmin and MIB are microbial metabolites belonging to terpenoids. Precursors for terpenoids are biosynthesized via the methylerythritol phosphate (MEP) and the mevalonate (MVA) pathways. We carried out a metagenomic analysis of 50 samples from five RAS to investigate terpenoid biosynthesis and metabolic potential for geosmin and MIB production in RAS microbiomes. A total of 1008 metagenome-assembled genomes (MAGs) representing 26 bacterial and three archaeal phyla were recovered. Although most archaea are thought to use the MVA pathway for terpenoid precursor biosynthesis, an Iainarchaeota archaeal MAG is shown to harbour a complete set of genes encoding the MEP pathway but lacking genes associated with the MVA pathway. In this study, a total of 16 MAGs affiliated with five bacterial phyla (Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexota, and Myxococcota) were identified as possessing potential geosmin or MIB synthases. These putative taste and odour producers were diverse, many were taxonomically unidentified at the genus or species level, and their relative abundance differed between the investigated RAS farms. The metagenomic study of the RAS microbiomes revealed a previously unknown phylogenetic diversity of the potential to produce geosmin and MIB.}, } @article {pmid39378970, year = {2025}, author = {Zharikova, AA and Andrianova, NV and Silachev, DN and Nebogatikov, VO and Pevzner, IB and Makievskaya, CI and Zorova, LD and Maleev, GV and Baydakova, GV and Chistyakov, DV and Goriainov, SV and Sergeeva, MG and Burakova, IY and Gureev, AP and Popkov, VA and Ustyugov, AA and Plotnikov, EY}, title = {Analysis of the brain transcriptome, microbiome and metabolome in ketogenic diet and experimental stroke.}, journal = {Brain, behavior, and immunity}, volume = {123}, number = {}, pages = {571-585}, doi = {10.1016/j.bbi.2024.10.004}, pmid = {39378970}, issn = {1090-2139}, mesh = {Animals ; *Diet, Ketogenic/methods ; Rats ; *Brain/metabolism ; *Gastrointestinal Microbiome/physiology ; Male ; *Metabolome ; *Transcriptome ; *Stroke/metabolism ; *Infarction, Middle Cerebral Artery/metabolism ; Disease Models, Animal ; Rats, Sprague-Dawley ; }, abstract = {The ketogenic diet (KD) has been shown to be effective in treating various brain pathologies. In this study, we conducted detailed transcriptomic and metabolomic profiling of rat brains after KD and ischemic stroke in order to investigate the effects of KD and its underlying mechanisms. We evaluated the effect of a two-month KD on gene expression in intact brain tissue and after middle cerebral artery occlusion (MCAO). We analyzed the effects of KD on gut microbiome composition and blood metabolic profile as well as investigated the correlation between severity of neurological deficits and KD-induced changes. We found transcriptional reprogramming in the brain after stroke and KD treatment. The KD altered the expression of genes involved in the regulation of glucose and fatty acid metabolism, mitochondrial function, the immune response, Wnt-associated signaling, stem cell development, and neurotransmission, both in intact rats and after MCAO. The KD led to a significant change in the composition of gut microbiome and the levels of amino acids, acylcarnitines, polyunsaturated fatty acids, and oxylipins in the blood. However, the KD slightly worsened the neurological functions after MCAO, so that the therapeutic effect of the diet remained unproven.}, } @article {pmid39378879, year = {2024}, author = {Wu, G and Xu, T and Zhao, N and Lam, YY and Ding, X and Wei, D and Fan, J and Shi, Y and Li, X and Li, M and Ji, S and Wang, X and Fu, H and Zhang, F and Shi, Y and Zhang, C and Peng, Y and Zhao, L}, title = {A core microbiome signature as an indicator of health.}, journal = {Cell}, volume = {187}, number = {23}, pages = {6550-6565.e11}, doi = {10.1016/j.cell.2024.09.019}, pmid = {39378879}, issn = {1097-4172}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2/microbiology ; Case-Control Studies ; Dietary Fiber/metabolism ; Metagenome ; Metagenomics/methods ; Health ; Microbiota ; }, abstract = {The gut microbiota is crucial for human health, functioning as a complex adaptive system akin to a vital organ. To identify core health-relevant gut microbes, we followed the systems biology tenet that stable relationships signify core components. By analyzing metagenomic datasets from a high-fiber dietary intervention in type 2 diabetes and 26 case-control studies across 15 diseases, we identified a set of stably correlated genome pairs within co-abundance networks perturbed by dietary interventions and diseases. These genomes formed a "two competing guilds" (TCGs) model, with one guild specialized in fiber fermentation and butyrate production and the other characterized by virulence and antibiotic resistance. Our random forest models successfully distinguished cases from controls across multiple diseases and predicted immunotherapy outcomes through the use of these genomes. Our guild-based approach, which is genome specific, database independent, and interaction focused, identifies a core microbiome signature that serves as a holistic health indicator and a potential common target for health enhancement.}, } @article {pmid39378072, year = {2024}, author = {Koohi-Moghadam, M and Watt, RM and Leung, WK}, title = {Multi-site analysis of biosynthetic gene clusters from the periodontitis oral microbiome.}, journal = {Journal of medical microbiology}, volume = {73}, number = {10}, pages = {}, doi = {10.1099/jmm.0.001898}, pmid = {39378072}, issn = {1473-5644}, mesh = {Humans ; *Periodontitis/microbiology ; *Multigene Family ; *Mouth/microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Pilot Projects ; Metagenomics/methods ; Saliva/microbiology ; Adult ; Male ; Biosynthetic Pathways/genetics ; Female ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Metagenome ; }, abstract = {Background. Bacteria significantly influence human health and disease, with bacterial biosynthetic gene clusters (BGCs) being crucial in the microbiome-host and microbe-microbe interactions.Gap statement. Despite extensive research into BGCs within the human gut microbiome, their roles in the oral microbiome are less understood.Aim. This pilot study utilizes high-throughput shotgun metagenomic sequencing to examine the oral microbiota in different niches, particularly focusing on the association of BGCs with periodontitis.Methodology. We analysed saliva, subgingival plaque and supragingival plaque samples from periodontitis patients (n=23) and controls (n=16). DNA was extracted from these samples using standardized protocols. The high-throughput shotgun metagenomic sequencing was then performed to obtain comprehensive genetic information from the microbial communities present in the samples.Results. Our study identified 10 742 BGCs, with certain clusters being niche-specific. Notably, aryl polyenes and bacteriocins were the most prevalent BGCs identified. We discovered several 'novel' BGCs that are widely represented across various bacterial phyla and identified BGCs that had different distributions between periodontitis and control subjects. Our systematic approach unveiled the previously unexplored biosynthetic pathways that may be key players in periodontitis.Conclusions. Our research expands the current metagenomic knowledge of the oral microbiota in both healthy and periodontally diseased states. These findings highlight the presence of novel biosynthetic pathways in the oral cavity and suggest a complex network of host-microbe and microbe-microbe interactions, potentially influencing periodontal disease. The BGCs identified in this study pave the way for future investigations into the role of small-molecule-mediated interactions within the human oral microbiota and their impact on periodontitis.}, } @article {pmid39377603, year = {2024}, author = {Colberg, O and Hermes, GDA and Licht, TR and Wichmann, A and Baker, A and Laursen, MF and Wellejus, A}, title = {Development of an infant colon simulating in vitro model, I-TIM-2, to study the effects of modulation strategies on the infant gut microbiome composition and function.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0072424}, pmid = {39377603}, issn = {2165-0497}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/drug effects ; Infant ; *Feces/microbiology ; *Colon/microbiology/metabolism ; *Fatty Acids, Volatile/metabolism/analysis ; *Milk, Human/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification/growth & development ; Oligosaccharides/metabolism ; Female ; Breast Feeding ; Models, Biological ; Infant, Newborn ; Male ; }, abstract = {The early life stages are critical for the development of the gut microbiome. Variables such as antibiotics exposure, birth-mode via Cesarean section, and formula feeding are associated with disruptions in microbiome development and are related to adverse health effects later in life. Studying the effects of microbiome-modulating strategies in infants is challenged by appropriate ethical constraints. Therefore, we developed I-TIM-2, an infant in vitro colonic model based on the validated, computer-controlled, dynamic model of the colon, TIM-2. The system, consisting of four separate compartments, was inoculated with feces from four healthy, primarily breastfed infants, displaying distinctive microbiome profiles. For each infant's fecal sample, a 96-h experiment was performed, with two compartments receiving an infant diet adapted medium and two compartments additionally receiving five human milk oligosaccharides (HMOs) in physiological concentrations and proportions. Bacterial composition was determined by shotgun metagenomics and qPCR. Concentrations of short-chain fatty acids (SCFAs) and HMOs were determined by LC-MS. Microbial diversity and high amounts of inoculum-derived species were preserved in the model throughout each experiment. Microbiome composition and SCFA concentrations were consistent with published data from infants. HMOs strongly modulated the microbiome composition by stimulating relative proportions of Bifidobacterium. This affected the metabolic output and resulted in an increased production of acetic and formic acid, characteristic of bifidobacterial HMO metabolism. In conclusion, these data demonstrate the development of a valid model to study the dynamics and modulations of the infant gut microbiome and metabolome.IMPORTANCEThe infant gut microbiome is intricately linked to the health of its host. This is partly mediated through the bacterial production of metabolites that interact with the host cells. Human milk shapes the establishment of the infant gut microbiome as it contains human milk sugars that select for primarily bifidobacteria. The establishment can be disrupted by modern interventions such as formula feeding. This can alter the microbiome composition and metabolite production profile, which can affect the host. In this article, we set up an infant in vitro colonic model to study microbiome interactions and functions. In this model, we investigated the effects of human milk sugars and their promotion of bifidobacteria at the expense of other bacteria. The model is an ideal system to assess the effects of various modulating strategies on the infant gut microbiome and its interactions with its host.}, } @article {pmid39377587, year = {2024}, author = {McMillan, AS and Zhang, G and Dougherty, MK and McGill, SK and Gulati, AS and Baker, ES and Theriot, CM}, title = {Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent Clostridioides difficile infection.}, journal = {mSphere}, volume = {9}, number = {10}, pages = {e0070624}, pmid = {39377587}, issn = {2379-5042}, support = {RM1 GM145416/GM/NIGMS NIH HHS/United States ; R01 GM141277/GM/NIGMS NIH HHS/United States ; R01 GM141277, RM1 GM145416//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM119438, R35GM149222//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; P42 ES027704/ES/NIEHS NIH HHS/United States ; R35 GM119438/GM/NIGMS NIH HHS/United States ; T32 DK007634/DK/NIDDK NIH HHS/United States ; STAR RD 84003201//Environmental Protection Agency (EPA)/ ; R35 GM149222/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Clostridium Infections/therapy/microbiology ; *Clostridioides difficile/genetics/metabolism ; *Metabolomics ; *Gastrointestinal Microbiome ; *Feces/microbiology ; *Metagenomics/methods ; *Metabolome ; Male ; Lipidomics ; Female ; Bile Acids and Salts/metabolism ; Recurrence ; Middle Aged ; Aged ; Adult ; Metagenome ; }, abstract = {Recurrent C. difficile infection (rCDI) is an urgent public health threat, for which the last resort and lifesaving treatment is a fecal microbiota transplant (FMT). However, the exact mechanisms that mediate a successful FMT are not well-understood. Here, we use longitudinal stool samples collected from patients undergoing FMT to evaluate intra-individual changes in the microbiome, metabolome, and lipidome after successful FMTs relative to their baselines pre-FMT. We show changes in the abundance of many lipids, specifically a decrease in acylcarnitines post-FMT, and a shift from conjugated bile acids pre-FMT to deconjugated secondary bile acids post-FMT. These changes correlate with a decrease in Enterobacteriaceae, which encode carnitine metabolism genes, and an increase in Lachnospiraceae, which encode bile acid altering genes such as bile salt hydrolases (BSHs) and the bile acid-inducible (bai) operon, post-FMT. We also show changes in gut microbe-encoded amino acid biosynthesis genes, of which Enterobacteriaceae was the primary contributor to amino acids C. difficile is auxotrophic for. Liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) revealed a shift from microbial conjugation of primary bile acids pre-FMT to secondary bile acids post-FMT. Here, we define the structural and functional changes associated with a successful FMT and generate hypotheses that require further experimental validation. This information is meant to help guide the development of new microbiota-focused therapeutics to treat rCDI.IMPORTANCERecurrent C. difficile infection is an urgent public health threat, for which the last resort and lifesaving treatment is a fecal microbiota transplant. However, the exact mechanisms that mediate a successful FMT are not well-understood. Here, we show changes in the abundance of many lipids, specifically acylcarnitines and bile acids, in response to FMT. These changes correlate with Enterobacteriaceae pre-FMT, which encodes carnitine metabolism genes, and Lachnospiraceae post-FMT, which encodes bile salt hydrolases and baiA genes. There was also a shift from microbial conjugation of primary bile acids pre-FMT to secondary bile acids post-FMT. Here, we define the structural and functional changes associated with a successful FMT, which we hope will help aid in the development of new microbiota-focused therapeutics to treat rCDI.}, } @article {pmid39375774, year = {2024}, author = {Kosmopoulos, JC and Klier, KM and Langwig, MV and Tran, PQ and Anantharaman, K}, title = {Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {195}, pmid = {39375774}, issn = {2049-2618}, mesh = {*Virome/genetics ; *Viruses/genetics/classification/isolation & purification ; *Metagenomics/methods ; Humans ; *Metagenome ; *Genome, Viral/genetics ; Microbiota/genetics ; Soil Microbiology ; Fresh Water/virology/microbiology ; Gastrointestinal Microbiome/genetics ; }, abstract = {BACKGROUND: Viruses, the majority of which are uncultivated, are among the most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses are fundamental members of microbiomes. While the number of studies leveraging viral metagenomics (viromics) for studying uncultivated viruses is growing, standards for viromics research are lacking. Viromics can utilize computational discovery of viruses from total metagenomes of all community members (hereafter metagenomes) or use physical separation of virus-specific fractions (hereafter viromes). However, differences in the recovery and interpretation of viruses from metagenomes and viromes obtained from the same samples remain understudied.

RESULTS: Here, we compare viral communities from paired viromes and metagenomes obtained from 60 diverse samples across human gut, soil, freshwater, and marine ecosystems. Overall, viral communities obtained from viromes had greater species richness and total viral genome abundances than those obtained from metagenomes, although there were some exceptions. Despite this, metagenomes still contained many viral genomes not detected in viromes. We also found notable differences in the predicted lytic state of viruses detected in viromes vs metagenomes at the time of sequencing. Other forms of variation observed include genome presence/absence, genome quality, and encoded protein content between viromes and metagenomes, but the magnitude of these differences varied by environment.

CONCLUSIONS: Overall, our results show that the choice of method can lead to differing interpretations of viral community ecology. We suggest that the choice of whether to target a metagenome or virome to study viral communities should be dependent on the environmental context and ecological questions being asked. However, our overall recommendation to researchers investigating viral ecology and evolution is to pair both approaches to maximize their respective benefits. Video Abstract.}, } @article {pmid39375368, year = {2024}, author = {Jeong, E and Abdellaoui, N and Lim, JY and Seo, JA}, title = {The presence of a significant endophytic fungus in mycobiome of rice seed compartments.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {23367}, pmid = {39375368}, issn = {2045-2322}, support = {320036-5//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/ ; RS-2023-00230782//Rural Development Administration/ ; }, mesh = {*Seeds/anatomy & histology/microbiology ; *Mycobiome/genetics ; *Oryza/anatomy & histology/classification/microbiology ; *Fungi/classification/isolation & purification/pathogenicity ; Basidiomycota/physiology ; Metagenome/genetics ; Crops, Agricultural/anatomy & histology/microbiology ; Analysis of Variance ; Republic of Korea ; }, abstract = {Seed microbial communities have been known to have a crucial role in the life cycle of a plant. In this study, we examined the distribution of the fungal communities in three compartments (husk, brown rice, and milled rice) of the fourteen rice seed samples. Ten fungal genera distributed throughout the three compartments of the rice seeds were identified as the core mycobiome of the rice seeds, regardless of collecting regions or cultivars. Based on the diversity analysis, the distribution of the fungal community in milled rice was found to be more diversified, evenly distributed, and differently clustered from the other two compartments. Among the core mycobiome, Moesziomyces dominated almost 80% of the fungal communities in the outer compartments of rice seeds, whereas the abundances of other endophytic pathogenic fungi declined. Our results provide that antagonistic yeast Moesziomyces may be able to control the endogenous pathogenic fungal communities in rice seeds, hence maintaining the quality of rice seeds. In addition, the distribution of fungal communities differs depending on the rice seed's compartment, indicating that the compartment can affect the distribution of the seed microbial community.}, } @article {pmid39375348, year = {2024}, author = {Kang, X and Zhang, W and Li, Y and Luo, X and Schönhuth, A}, title = {HyLight: Strain aware assembly of low coverage metagenomes.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8665}, pmid = {39375348}, issn = {2041-1723}, mesh = {*Metagenome/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Bacteria/genetics/classification ; Genome, Bacterial ; Software ; }, abstract = {Different strains of identical species can vary substantially in terms of their spectrum of biomedically relevant phenotypes. Reconstructing the genomes of microbial communities at the level of their strains poses significant challenges, because sequencing errors can obscure strain-specific variants. Next-generation sequencing (NGS) reads are too short to resolve complex genomic regions. Third-generation sequencing (TGS) reads, although longer, are prone to higher error rates or substantially more expensive. Limiting TGS coverage to reduce costs compromises the accuracy of the assemblies. This explains why prior approaches agree on losses in strain awareness, accuracy, tendentially excessive costs, or combinations thereof. We introduce HyLight, a metagenome assembly approach that addresses these challenges by implementing the complementary strengths of TGS and NGS data. HyLight employs strain-resolved overlap graphs (OG) to accurately reconstruct individual strains within microbial communities. Our experiments demonstrate that HyLight produces strain-aware and contiguous assemblies at minimal error content, while significantly reducing costs because utilizing low-coverage TGS data. HyLight achieves an average improvement of 19.05% in preserving strain identity and demonstrates near-complete strain awareness across diverse datasets. In summary, HyLight offers considerable advances in metagenome assembly, insofar as it delivers significantly enhanced strain awareness, contiguity, and accuracy without the typical compromises observed in existing approaches.}, } @article {pmid39375020, year = {2024}, author = {Garritano, AN and Zhang, Z and Jia, Y and Allen, MA and Hill, LJ and Kuzhiumparambil, U and Hinkley, C and Raina, JB and Peixoto, RS and Thomas, T}, title = {Simple Porifera holobiont reveals complex interactions between the host, an archaeon, a bacterium, and a phage.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39375020}, issn = {1751-7370}, support = {BAS/1/1095-01-01//ANP R&D levy as "Compromisso de Investimentos com Pesquisa e Desenvolvimento"/ ; }, mesh = {*Symbiosis ; *Archaea/metabolism/genetics ; Animals ; *Bacteriophages/physiology/genetics ; *Porifera/microbiology ; *Bacteria/metabolism/genetics/classification ; Ammonia/metabolism ; Microbiota ; Phylogeny ; Vitamin B 12/metabolism ; }, abstract = {The basal metazoan phylum Porifera (sponges) is increasingly used as a model to investigate ecological and evolutionary features of microbe-animal symbioses. However, sponges often host complex microbiomes, which has hampered our understanding of their interactions with their microbial symbionts. Here, we describe the discovery and characterization of the simplest sponge holobiont reported to date, consisting of the deep-sea glass sponge Aphrocallistes beatrix and two newly-described microbial symbionts: an autotrophic ammonia-oxidizing archaeon and a bacterial heterotroph. Omics analyses and metabolic modeling revealed the dependency of the ammonia-oxidizing archaea on sponge-derived ammonia to drive primary production, which in turn supports the bacterium's growth by providing the dicarboxylate fumarate. Furthermore, virus-mediated archaeal lysis appears crucial to overcome the bacterium's vitamin B12 auxotrophy. These findings reveal that the exchanges of vitamin B12 and dicarboxylate may be evolutionarily conserved features of symbiosis as they can also be found in interactions between free-living marine bacteria, and between microbes and plants or diatoms.}, } @article {pmid39375018, year = {2024}, author = {Yang, Q and Zhong, Y and Feng, SW and Wen, P and Wang, H and Wu, J and Yang, S and Liang, JL and Li, D and Yang, Q and Tam, NFY and Peng, P}, title = {Temporal enrichment of comammox Nitrospira and Ca. Nitrosocosmicus in a coastal plastisphere.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39375018}, issn = {1751-7370}, support = {42 077 285//National Natural Science Foundation of China/ ; 2024A04J6534//Science and Technology Projects of Guangzhou/ ; ZDYF2023SHFZ171//Key Research and Development Program of Hainan Province/ ; 2023B1212060049//Guangdong Foundation for Program of Science and Technology Research/ ; 2023B0303000007//Guangdong Major Project of Basic and Applied Basic Research/ ; SKLOG2024-01//State Key Laboratory of Organic Geochemistry/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; *Ammonia/metabolism ; *Nitrification ; Microbiota ; Bacteria/classification/genetics/metabolism/isolation & purification ; Oxidation-Reduction ; Phylogeny ; Archaea/metabolism/genetics/classification/isolation & purification ; Metagenome ; }, abstract = {Plastic marine debris is known to harbor a unique microbiome (termed the "plastisphere") that can be important in marine biogeochemical cycles. However, the temporal dynamics in the plastisphere and their implications for marine biogeochemistry remain poorly understood. Here, we characterized the temporal dynamics of nitrifying communities in the plastisphere of plastic ropes exposed to a mangrove intertidal zone. The 39-month colonization experiment revealed that the relative abundances of Nitrospira and Candidatus Nitrosocosmicus representatives increased over time according to 16S rRNA gene amplicon sequencing analysis. The relative abundances of amoA genes in metagenomes implied that comammox Nitrospira were the dominant ammonia oxidizers in the plastisphere, and their dominance increased over time. The relative abundances of two metagenome-assembled genomes of comammox Nitrospira also increased with time and positively correlated with extracellular polymeric substances content of the plastisphere but negatively correlated with NH4+ concentration in seawater, indicating the long-term succession of these two parameters significantly influenced the ammonia-oxidizing community in the coastal plastisphere. At the end of the colonization experiment, the plastisphere exhibited high nitrification activity, leading to the release of N2O (2.52 ng N2O N g-1) in a 3-day nitrification experiment. The predicted relative contribution of comammox Nitrospira to N2O production (17.9%) was higher than that of ammonia-oxidizing bacteria (4.8%) but lower than that of ammonia-oxidizing archaea (21.4%). These results provide evidence that from a long-term perspective, some coastal plastispheres will become dominated by comammox Nitrospira and thereby act as hotspots of ammonia oxidation and N2O production.}, } @article {pmid39374753, year = {2024}, author = {Pushkareva, E and Hejduková, E and Elster, J and Becker, B}, title = {Microbial response to seasonal variation in arctic biocrusts with a focus on fungi and cyanobacteria.}, journal = {Environmental research}, volume = {263}, number = {Pt 2}, pages = {120110}, doi = {10.1016/j.envres.2024.120110}, pmid = {39374753}, issn = {1096-0953}, mesh = {Arctic Regions ; *Seasons ; *Cyanobacteria/genetics ; *Fungi/genetics/classification ; *Microbiota ; Ecosystem ; }, abstract = {Biocrusts are crucial components of Arctic ecosystems, playing significant roles in carbon and nitrogen cycling, especially in regions where plant growth is limited. However, the microbial communities within Arctic biocrusts and their strategies for surviving the harsh conditions remain poorly understood. In this study, the microbial profiles of Arctic biocrusts across different seasons (summer, autumn, and winter) were investigated in order to elucidate their survival strategies in extreme conditions. Metagenomic and metatranscriptomic analyses revealed significant differences in microbial community composition among the sites located in different elevations. The bacterial communities were dominated by Actinobacteria and Proteobacteria, while the fungal communities were mainly represented by Ascomycota and Basidiomycota, with lichenized and saprotrophic traits prevailing. Cyanobacteria were primarily composed of heterocystous cyanobacteria. Furthermore, the study identified molecular mechanisms underlying cold adaptation, including the expression of heat shock proteins and cold-inducible RNA helicases in cyanobacteria and fungi. Overall, the microbial communities appear to be permanently well adapted to the extreme environment.}, } @article {pmid39373498, year = {2024}, author = {Ojeda, A and Akinsuyi, O and McKinley, KL and Xhumari, J and Triplett, EW and Neu, J and Roesch, LFW}, title = {Increased antibiotic resistance in preterm neonates under early antibiotic use.}, journal = {mSphere}, volume = {9}, number = {10}, pages = {e0028624}, pmid = {39373498}, issn = {2379-5042}, support = {//Little Giraffe Foundation (LGF)/ ; }, mesh = {Female ; Humans ; Infant, Newborn ; Male ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Bacteria/drug effects/genetics/classification ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Infant, Premature ; *Metagenomics ; Retrospective Studies ; }, abstract = {UNLABELLED: The standard use of antibiotics in newborns to empirically treat early-onset sepsis can adversely affect the neonatal gut microbiome, with potential long-term health impacts. Research into the escalating issue of antimicrobial resistance in preterm infants and antibiotic practices in neonatal intensive care units is limited. A deeper understanding of the effects of early antibiotic intervention on antibiotic resistance in preterm infants is crucial. This retrospective study employed metagenomic sequencing to evaluate antibiotic resistance genes (ARGs) in the meconium and subsequent stool samples of preterm infants enrolled in the Routine Early Antibiotic Use in Symptomatic Preterm Neonates study. Microbial metagenomics was conducted using a subset of fecal samples from 30 preterm infants for taxonomic profiling and ARG identification. All preterm infants exhibited ARGs, with 175 unique ARGs identified, predominantly associated with beta-lactam, tetracycline, and aminoglycoside resistance. Notably, 23% of ARGs was found in preterm infants without direct or intrapartum antibiotic exposure. Post-natal antibiotic exposure increases beta-lactam/tetracycline resistance while altering mechanisms that aid bacteria in withstanding antibiotic pressure. Microbial profiling revealed 774 bacterial species, with antibiotic-naive infants showing higher alpha diversity (P = 0.005) in their microbiota and resistome compared with treated infants, suggesting a more complex ecosystem. High ARG prevalence in preterm infants was observed irrespective of direct antibiotic exposure and intensifies with age. Prolonged membrane ruptures and maternal antibiotic use during gestation and delivery are linked to alterations in the preterm infant resistome and microbiome, which are pivotal in shaping the ARG profiles in the neonatal gut.This study is registered with ClinicalTrials.gov as NCT02784821.

IMPORTANCE: A high burden of antibiotic resistance in preterm infants poses significant challenges to neonatal health. The presence of antibiotic resistance genes, along with alterations in signaling, energy production, and metabolic mechanisms, complicates treatment strategies for preterm infants, heightening the risk of ineffective therapy and exacerbating outcomes for these vulnerable neonates. Despite not receiving direct antibiotic treatment, preterm infants exhibit a concerning prevalence of antibiotic-resistant bacteria. This underscores the complex interplay of broader influences, including maternal antibiotic exposure during and beyond pregnancy and gestational complications like prolonged membrane ruptures. Urgent action, including cautious antibiotic practices and enhanced antenatal care, is imperative to protect neonatal health and counter the escalating threat of antimicrobial resistance in this vulnerable population.}, } @article {pmid39369676, year = {2024}, author = {Zhuang, Y and Liu, S and Xiao, J and Chen, T and Gao, D and Xu, Y and Jiang, W and Wang, J and Hou, G and Li, S and Zhao, X and Huang, Y and Li, S and Zhang, S and Li, M and Wang, W and Li, S and Cao, Z}, title = {Metagenomics reveals the characteristics and potential spread of microbiomes and virulence factor genes in the dairy cattle production system.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136005}, doi = {10.1016/j.jhazmat.2024.136005}, pmid = {39369676}, issn = {1873-3336}, mesh = {Animals ; Cattle ; *Virulence Factors/genetics ; *Metagenomics ; *Feces/microbiology ; *Dairying ; Microbiota ; Female ; Colostrum/microbiology ; Soil Microbiology ; Wastewater/microbiology ; Rumen/microbiology ; }, abstract = {Virulence factor genes (VFGs) pose a potential threat to ecological security and animal health, and have attracted increasing attention in the livestock industry. As one of the primary livestock types, dairy cattle may be an important source of VFG transmission. However, the distribution, transmission, and evolution of VFGs in the gastrointestinal tract and surrounding environment of dairy cattle remain unclear. In the present study, a total of 263 samples were collected from cows, calves, colostrum, farm wastewater, and soil. Metagenomics was conducted to analyze changes in the microbiome and VFGs characteristics in these ecological niches. The VFGs of the cows showed distinct differences between the rumen and feces, and were influenced by the region. The dominant VFG hosts was regulated by their microbial structure. Colostrum administration of cows increased VFG abundance in their newborn calf feces sharply and Enterobacteriaceae became the primary host. While diet was the primary driving force for the temporal variation in calf VFGs. For samples of the surrounding environment, water and soil had higher VFG concentrations and were more structurally stable. Moreover, extensive interactions between the mobile genetic elements and VFGs and gene mobile analysis map based on metagenomic binning both displayed the potential horizontal transfer ability of VFGs in the cows and environment. Our study revealed the prevalence, diffusion, and regulatory factors of VFGs in dairy cattle production systems, providing novel insights into reducing livestock VFGs and limiting their spread.}, } @article {pmid39369255, year = {2024}, author = {Figueroa-Gonzalez, PA and Bornemann, TLV and Hinzke, T and Maaß, S and Trautwein-Schult, A and Starke, J and Moore, CJ and Esser, SP and Plewka, J and Hesse, T and Schmidt, TC and Schreiber, U and Bor, B and Becher, D and Probst, AJ}, title = {Metaproteogenomics resolution of a high-CO2 aquifer community reveals a complex cellular adaptation of groundwater Gracilibacteria to a host-dependent lifestyle.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {194}, pmid = {39369255}, issn = {2049-2618}, support = {CRC 1439/1 426547801//German Research Foundation (DFG)/ ; }, mesh = {*Groundwater/microbiology ; Carbon Dioxide/metabolism ; Metagenomics ; Bacteria/genetics/classification/isolation & purification/metabolism ; Germany ; Genome, Bacterial ; Phylogeny ; Microbiota/genetics ; Proteogenomics ; Adaptation, Physiological ; Proteomics ; }, abstract = {BACKGROUND: Bacteria of the candidate phyla radiation (CPR), constituting about 25% of the bacterial biodiversity, are characterized by small cell size and patchy genomes without complete key metabolic pathways, suggesting a symbiotic lifestyle. Gracilibacteria (BD1-5), which are part of the CPR branch, possess alternate coded genomes and have not yet been cultivated. The lifestyle of Gracilibacteria, their temporal dynamics, and activity in natural ecosystems, particularly in groundwater, has remained largely unexplored. Here, we aimed to investigate Gracilibacteria activity in situ and to discern their lifestyle based on expressed genes, using the metaproteogenome of Gracilibacteria as a function of time in the cold-water geyser Wallender Born in the Volcanic Eifel region in Germany.

RESULTS: We coupled genome-resolved metagenomics and metaproteomics to investigate a cold-water geyser microbial community enriched in Gracilibacteria across a 12-day time-series. Groundwater was collected and sequentially filtered to fraction CPR and other bacteria. Based on 725 Gbps of metagenomic data, 1129 different ribosomal protein S3 marker genes, and 751 high-quality genomes (123 population genomes after dereplication), we identified dominant bacteria belonging to Gallionellales and Gracilibacteria along with keystone microbes, which were low in genomic abundance but substantially contributing to proteomic abundance. Seven high-quality Gracilibacteria genomes showed typical limitations, such as limited amino acid or nucleotide synthesis, in their central metabolism but no co-occurrence with potential hosts. The genomes of these Gracilibacteria were encoded for a high number of proteins involved in cell to cell interaction, supporting the previously surmised host-dependent lifestyle, e.g., type IV and type II secretion system subunits, transporters, and features related to cell motility, which were also detected on protein level.

CONCLUSIONS: We here identified microbial keystone taxa in a high-CO2 aquifer, and revealed microbial dynamics of Gracilibacteria. Although Gracilibacteria in this ecosystem did not appear to target specific organisms in this ecosystem due to lack of co-occurrence despite enrichment on 0.2-µm filter fraction, we provide proteomic evidence for the complex machinery behind the host-dependent lifestyle of groundwater Gracilibacteria. Video Abstract.}, } @article {pmid39368785, year = {2025}, author = {Malan-Müller, S and Martín-Hernández, D and Caso, JR and Matthijnssens, J and Rodríguez-Urrutia, A and Lowry, CA and Leza, JC}, title = {Metagenomic symphony of the intestinal ecosystem: How the composition affects the mind.}, journal = {Brain, behavior, and immunity}, volume = {123}, number = {}, pages = {510-523}, doi = {10.1016/j.bbi.2024.09.033}, pmid = {39368785}, issn = {1090-2139}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Brain-Gut Axis/physiology ; Neurodegenerative Diseases/microbiology ; Metagenomics/methods ; Mental Disorders/microbiology/metabolism ; Animals ; Probiotics ; Mental Health ; Brain/metabolism/physiology ; Bacteria/metabolism ; Metagenome ; }, abstract = {Mental health disorders and neurodegenerative diseases place a heavy burden on patients and societies, and, although great strides have been made to understand the pathophysiology of these conditions, advancement in drug development is lagging. The importance of gastrointestinal health in maintaining overall health and preventing disease is not a new concept. Hundreds of years ago, healers from various cultures and civilizations recognized the crucial role of the gut in sustaining health. More than a century ago, scientists began exploring the restorative effects of probiotics, marking the early recognition of the importance of gut microbes. The omics era brought more enlightenment and enabled researchers to identify the complexity of the microbial ecosystems we harbour, encompassing bacteria, eukaryotes (including fungi), archaea, viruses, and other microorganisms. The extensive genetic capacity of the microbiota is dynamic and influenced by the environment. The microbiota therefore serves as a significant entity within us, with evolutionarily preserved functions in host metabolism, immunity, development, and behavior. The significant role of the bacterial gut microbiome in mental health and neurodegenerative disorders has been realized and described within the framework of the microbiota-gut-brain axis. However, the bacterial members do not function unaccompanied, but rather in concert, and there is a substantial knowledge gap regarding the involvement of non-bacterial microbiome members in these disorders. In this review, we will explore the current literature that implicates a role for the entire metagenomic ensemble, and how their complex interkingdom relationships could influence CNS functioning in mental health disorders and neurodegenerative diseases.}, } @article {pmid39368784, year = {2024}, author = {McCoubrey, LE and Shen, C and Mwasambu, S and Favaron, A and Sangfuang, N and Thomaidou, S and Orlu, M and Globisch, D and Basit, AW}, title = {Characterising and preventing the gut microbiota's inactivation of trifluridine, a colorectal cancer drug.}, journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences}, volume = {203}, number = {}, pages = {106922}, doi = {10.1016/j.ejps.2024.106922}, pmid = {39368784}, issn = {1879-0720}, mesh = {*Trifluridine/pharmacology ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/drug therapy/microbiology/prevention & control ; *Feces/microbiology ; *Uridine/pharmacology/analogs & derivatives/metabolism ; Antineoplastic Agents/pharmacology ; Male ; Female ; Clostridium perfringens/drug effects ; Adult ; Colon/microbiology/metabolism/drug effects ; Middle Aged ; }, abstract = {The gut microbiome can metabolise hundreds of drugs, potentially affecting their bioavailability and pharmacological effect. As most gut bacteria reside in the colon, drugs that reach the colon in significant proportions may be most impacted by microbiome metabolism. In this study the anti-colorectal cancer drug trifluridine was used as a model drug for characterising metabolism by the colonic microbiota, identifying correlations between bacterial species and individuals' rates of microbiome drug inactivation, and developing strategies to prevent drug inactivation following targeted colonic delivery. High performance liquid chromatography and ultra-high performance liquid chromatography coupled with high resolution tandem mass spectrometry demonstrated trifluridine's variable and multi-route metabolism by the faecal microbiota sourced from six healthy humans. Here, four drug metabolites were linked to the microbiome for the first time. Metagenomic sequencing of the human microbiota samples revealed their composition, which facilitated prediction of individual donors' microbial trifluridine inactivation. Notably, the abundance of Clostridium perfringens strongly correlated with the extent of trifluridine inactivation by microbiota samples after 2 hours (R[2] = 0.8966). Finally, several strategies were trialled for the prevention of microbial trifluridine metabolism. It was shown that uridine, a safe and well-tolerated molecule, significantly reduced the microbiota's metabolism of trifluridine by acting as a competitive enzyme inhibitor. Further, uridine was found to provide prebiotic effects. The findings in this study greatly expand knowledge on trifluridine's interactions with the gut microbiome and provide valuable insights for investigating the microbiome metabolism of other drugs. The results demonstrate how protection strategies could enhance the colonic stability of microbiome-sensitive drugs.}, } @article {pmid39368512, year = {2024}, author = {Niu, X and Lin, L and Zhang, T and An, X and Li, Y and Yu, Y and Hong, M and Shi, H and Ding, L}, title = {Research on antibiotic resistance genes in wild and artificially bred green turtles (Chelonia mydas).}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176716}, doi = {10.1016/j.scitotenv.2024.176716}, pmid = {39368512}, issn = {1879-1026}, mesh = {*Turtles/microbiology/genetics ; Animals ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Gastrointestinal Microbiome/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; }, abstract = {Sea turtles, vital to marine ecosystems, face population decline. Artificial breeding is a recovery strategy, yet it risks introducing antibiotic resistance genes (ARGs) to wild populations and ecosystems. This study employed metagenomic techniques to compare the distribution characteristics of ARGs in the guts of wild and artificially bred green turtles (Chelonia mydas). The findings revealed that the total abundance of ARGs in C. mydas that have been artificially bred was significantly higher than that in wild individuals. Additionally, the abundance of mobile genetic elements (MGEs) co-occurring with ARGs in artificially bred C. mydas was significantly higher than in wild C. mydas. In the analysis of bacteria carrying ARGs, wild C. mydas exhibited greater bacterial diversity. Furthermore, in artificially bred C. mydas, we discovered 23 potential human pathogenic bacteria (HPB) that contain antibiotic resistance genes. In contrast, in wild C. mydas, only one type of HPB carrying an antibiotic resistance gene was found. The findings of this study not only enhance our understanding of the distribution and dissemination of ARGs within the gut microbial communities of C. mydas, but also provide vital information for assessing the potential impact of releasing artificially bred C. mydas on the spread of antibiotic resistance.}, } @article {pmid39368509, year = {2024}, author = {Wen, M and Liu, Y and Yang, C and Dou, Y and Zhu, S and Tan, G and Wang, J}, title = {Effects of manure and nitrogen fertilization on soil microbial carbon fixation genes and associated communities in the Loess Plateau of China.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176581}, doi = {10.1016/j.scitotenv.2024.176581}, pmid = {39368509}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Fertilizers ; China ; *Nitrogen/analysis ; *Soil/chemistry ; *Carbon Cycle ; *Manure ; *Carbon/analysis ; Bacteria/genetics ; Agriculture/methods ; Microbiota ; }, abstract = {The effects of long-term fertilization on soil carbon (C) cycling have been a key focus of agricultural sustainable development research. However, the influences of different fertilization treatments on soil microbial C fixation profiles are still unclear. Metagenomics technology and multivariate analysis were employed to inquire changes in soil properties, soil microbial C fixation genes and associated bacterial communities, and the influence of dominant soil properties on C fixation genes. The contents of soil C and nitrogen fractions were signicficantly higher in manure or combined with nitrogen fertilization (NM) than other treatments. The composition of soil microbial C fixation genes and associated bacterial communities varied among different fertilization treatments. Compared with other treatments, the total abundance of microbial C fixation genes and the abundance of Proteobacteria were significantly higher in NM than in other treatments, as well as the abundances of C fixation genes involved in dicarboxylate/4-hydroxybutyrate cycle and reductive citrate cycle. Key functional genes and main bacterial communities presented in the middle of the co-occurrence network. Soil organic carbon, total nitrogen, and microbial biomass nitrogen were the dominant soil properties influencing microbial C fixation genes and associated bacterial communitis. Fertilization increased the abundance of C fixation genes by affecting the changes in bacterial communities abundance mediated by soil properties. Overall, elucidating the responses of soil microbial C fixation genes and associated communities to different fertilization will enhance our understanding of the processes of soil C fixation in farmland.}, } @article {pmid39367927, year = {2024}, author = {Wang, Q and Wang, M and Chen, Y and Miao, Q and Jin, W and Ma, Y and Pan, J and Hu, B}, title = {Deciphering microbiome and fungi-bacteria interactions in chronic wound infections using metagenomic sequencing.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {43}, number = {12}, pages = {2383-2396}, pmid = {39367927}, issn = {1435-4373}, support = {20YF1407700//Science and Technology Innovation Plan Of Shanghai Science and Technology Commission/ ; }, mesh = {Humans ; Male ; Female ; *Wound Infection/microbiology ; Middle Aged ; *Fungi/classification/genetics/isolation & purification ; Aged ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota/genetics ; *High-Throughput Nucleotide Sequencing ; Chronic Disease ; Adult ; Microbial Interactions ; Mycobiome/genetics ; Aged, 80 and over ; }, abstract = {PURPOSE: Chronic wounds caused by infections impose a considerable global healthcare burden. The microbial features of these infections and possible correlations between bacteria and fungi may influence wound healing. However, metagenomic next-generation sequencing (mNGS) analyses of these features remain sparse. Therefore, we performed mNGS on chronic wound infection samples to investigate features and correlations between the bacteriome and mycobiome in 66 patients (28: chronic wounds; 38: non-chronic wounds).

METHODS: Microbial community characteristics in patients with wound infections, microbiome-systemic inflammation associations, and bacteria-fungi correlations were analyzed.

RESULTS: Infections constituted the primary cause of wounds in this study. Nontuberculous mycobacteria (23%) and Mycobacterium tuberculosis (13%) were the most common pathogens associated with chronic wounds, whereas Staphylococcus aureus (15%) was the most prevalent in non-chronic wound infections. Patients with chronic wound infections had a higher abundance of Pseudomonas aeruginosa than those without chronic wounds. Microbes with a high relative abundance in chronic wound infections were less significantly associated with plasma inflammatory factors than those in non-chronic wound infections. Additionally, a positive correlation between Candida glabrata and P. aeruginosa and an association between Malassezia restricta and anaerobic species were detected in patients with chronic wound infections.

CONCLUSION: Our results further support the hypothesis that P. aeruginosa is a microbial biomarker of chronic wound infection regardless of the causative pathogens. Moreover, we propose a positive correlation between C. glabrata and P. aeruginosa in chronic wound infections, which advances the current understanding of fungi-bacteria correlations in patients with chronic wound infections.}, } @article {pmid39367431, year = {2024}, author = {Gaber, M and Wilson, AS and Millen, AE and Hovey, KM and LaMonte, MJ and Wactawski-Wende, J and Ochs-Balcom, HM and Cook, KL}, title = {Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {192}, pmid = {39367431}, issn = {2049-2618}, support = {W81XWH-20-1-0014//Congressionally Directed Medical Research Programs/ ; W81XWH-20-1-0014//Congressionally Directed Medical Research Programs/ ; W81XWH-20-1-0014//Congressionally Directed Medical Research Programs/ ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; HHSN268201600018C, HHSN268201600001C, HHSN268201600002C, HHSN268201600003C, and HHSN268201600004C/HL/NHLBI NIH HHS/United States ; HHSN268201600018C, HHSN268201600001C, HHSN268201600002C, HHSN268201600003C, and HHSN268201600004C/HL/NHLBI NIH HHS/United States ; }, mesh = {Female ; *Gastrointestinal Microbiome/drug effects ; *Endotoxemia/immunology/microbiology ; Humans ; *Postmenopause ; Animals ; Aged ; Mice ; *Lipopolysaccharides ; Intra-Abdominal Fat/metabolism/immunology ; Inflammation ; Aged, 80 and over ; Mice, Inbred C57BL ; Adiposity ; Bacteria/classification/isolation & purification/metabolism/genetics ; Acute-Phase Proteins/metabolism ; Feces/microbiology ; Obesity, Abdominal/microbiology/immunology ; Absorptiometry, Photon ; Carrier Proteins ; Membrane Glycoproteins ; }, abstract = {BACKGROUND: Obesity, and in particular abdominal obesity, is associated with an increased risk of developing a variety of chronic diseases. Obesity, aging, and menopause are each associated with differential shifts in the gut microbiome. Obesity causes chronic low-grade inflammation due to increased lipopolysaccharide (LPS) levels which is termed "metabolic endotoxemia." We examined the association of visceral adiposity tissue (VAT) area, circulating endotoxemia markers, and the gut bacterial microbiome in a cohort of aged postmenopausal women.

METHODS: Fifty postmenopausal women (mean age 78.8 ± 5.3 years) who had existing adipose measurements via dual x-ray absorptiometry (DXA) were selected from the extremes of VAT: n = 25 with low VAT area (45.6 ± 12.5 cm[2]) and n = 25 with high VAT area (177.5 ± 31.3 cm[2]). Dietary intake used to estimate the Healthy Eating Index (HEI) score was assessed with a food frequency questionnaire. Plasma LPS, LPS-binding protein (LBP), anti-LPS antibodies, anti-flagellin antibodies, and anti-lipoteichoic acid (LTA) antibodies were measured by ELISA. Metagenomic sequencing was performed on fecal DNA. Female C57BL/6 mice consuming a high-fat or low-fat diet were treated with 0.4 mg/kg diet-derived fecal isolated LPS modeling metabolic endotoxemia, and metabolic outcomes were measured after 6 weeks.

RESULTS: Women in the high VAT group showed increased Proteobacteria abundance and a lower Firmicutes/Bacteroidetes ratio. Plasma LBP concentration was positively associated with VAT area. Plasma anti-LPS, anti-LTA, and anti-flagellin IgA antibodies were significantly correlated with adiposity measurements. Women with high VAT showed significantly elevated LPS-expressing bacteria compared to low VAT women. Gut bacterial species that showed significant associations with both adiposity and inflammation (anti-LPS IgA and LBP) were Proteobacteria (Escherichia coli, Shigella spp., and Klebsiella spp.) and Veillonella atypica. Healthy eating index (HEI) scores negatively correlated with % body fat and anti-LPS IgA antibodies levels. Preclinical murine model showed that high-fat diet-fed mice administered a low-fat diet fecal-derived LPS displayed reduced body weight, decreased % body fat, and improved glucose tolerance test parameters when compared with saline-injected or high-fat diet fecal-derived LPS-treated groups consuming a high-fat diet.

CONCLUSIONS: Increased VAT in postmenopausal women is associated with elevated gut Proteobacteria abundance and immunogenic metabolic endotoxemia markers. Low-fat diet-derived fecal-isolated LPS improved metabolic parameters in high-fat diet-fed mice giving mechanistic insights into potential pro-health signaling mediated by under-acylated LPS isoforms. Video Abstract.}, } @article {pmid39367251, year = {2024}, author = {Zheng, J and Sun, Q and Zhang, M and Liu, C and Su, Q and Zhang, L and Xu, Z and Lu, W and Ching, J and Tang, W and Cheung, CP and Hamilton, AL and Wilson O'Brien, AL and Wei, SC and Bernstein, CN and Rubin, DT and Chang, EB and Morrison, M and Kamm, MA and Chan, FKL and Zhang, J and Ng, SC}, title = {Noninvasive, microbiome-based diagnosis of inflammatory bowel disease.}, journal = {Nature medicine}, volume = {30}, number = {12}, pages = {3555-3567}, pmid = {39367251}, issn = {1546-170X}, support = {R4030-22//Research Grants Council, University Grants Committee (RGC, UGC)/ ; 14121322//Research Grants Council, University Grants Committee (RGC, UGC)/ ; 2017PG-IBD003//Leona M. and Harry B. Helmsley Charitable Trust (Helmsley Charitable Trust)/ ; 10210816//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; 82100573//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *Feces/microbiology ; *Inflammatory Bowel Diseases/microbiology/diagnosis ; *Crohn Disease/microbiology/diagnosis ; *Gastrointestinal Microbiome/genetics ; *Biomarkers ; *Colitis, Ulcerative/microbiology/diagnosis ; Female ; Male ; Adult ; Leukocyte L1 Antigen Complex/analysis/metabolism ; Bacteria/genetics/isolation & purification ; Metagenomics/methods ; Middle Aged ; Case-Control Studies ; Microbiota/genetics ; }, abstract = {Despite recent progress in our understanding of the association between the gut microbiome and inflammatory bowel disease (IBD), the role of microbiome biomarkers in IBD diagnosis remains underexplored. Here we developed a microbiome-based diagnostic test for IBD. By utilization of metagenomic data from 5,979 fecal samples with and without IBD from different geographies and ethnicities, we identified microbiota alterations in IBD and selected ten and nine bacterial species for construction of diagnostic models for ulcerative colitis and Crohn's disease, respectively. These diagnostic models achieved areas under the curve >0.90 for distinguishing IBD from controls in the discovery cohort, and maintained satisfactory performance in transethnic validation cohorts from eight populations. We further developed a multiplex droplet digital polymerase chain reaction test targeting selected IBD-associated bacterial species, and models based on this test showed numerically higher performance than fecal calprotectin in discriminating ulcerative colitis and Crohn's disease from controls. Here we discovered universal IBD-associated bacteria and show the potential applicability of a multibacteria biomarker panel as a noninvasive tool for IBD diagnosis.}, } @article {pmid39367018, year = {2024}, author = {Baldi, A and Braat, S and Hasan, MI and Bennett, C and Barrios, M and Jones, N and Abdul Azeez, I and Wilcox, S and Roy, PK and Bhuiyan, MSA and Ataide, R and Clucas, D and Larson, LM and Hamadani, J and Zimmermann, M and Bowden, R and Jex, A and Biggs, BA and Pasricha, SR}, title = {Effects of iron supplements and iron-containing micronutrient powders on the gut microbiome in Bangladeshi infants: a randomized controlled trial.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8640}, pmid = {39367018}, issn = {2041-1723}, support = {GNT1158696//Department of Health | National Health and Medical Research Council (NHMRC)/ ; GNT2009047//Department of Health | National Health and Medical Research Council (NHMRC)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Infant ; Bangladesh ; *Dietary Supplements ; *Micronutrients/administration & dosage ; Female ; *Iron/metabolism/administration & dosage ; Male ; *RNA, Ribosomal, 16S/genetics ; *Powders ; Diarrhea/microbiology ; Feces/microbiology ; Anemia, Iron-Deficiency/microbiology ; }, abstract = {Anemia is highly prevalent globally, especially in young children in low-income countries, where it often overlaps with a high burden of diarrheal disease. Distribution of iron interventions (as supplements or iron-containing multiple micronutrient powders, MNPs) is a key anemia reduction strategy. Small studies in Africa indicate iron may reprofile the gut microbiome towards pathogenic species. We seek to evaluate the safety of iron and MNPs based on their effects on diversity, composition, and function of the gut microbiome in children in rural Bangladesh as part of a large placebo-controlled randomized controlled trial of iron or MNPs given for 3 months (ACTRN12617000660381). In 923 infants, we evaluate the microbiome before, immediately following, and nine months after interventions, using 16S rRNA gene sequencing and shotgun metagenomics in a subset. We identify no increase in diarrhea with either treatment. In our primary analysis, neither iron nor MNPs alter gut microbiome diversity or composition. However, when not adjusting for multiple comparisons, compared to placebo, children receiving iron and MNPs exhibit reductions in commensal species (e.g., Bifidobacterium, Lactobacillus) and increases in potential pathogens, including Clostridium. These increases are most evident in children with baseline iron repletion and are further supported by trend-based statistical analyses.}, } @article {pmid39365058, year = {2024}, author = {Corbett, GA and Moore, R and Feehily, C and Killeen, SL and O'Brien, E and Van Sinderen, D and Matthews, E and O'Flaherty, R and Rudd, PM and Saldova, R and Walsh, CJ and Lawton, EM and MacIntyre, DA and Corcoran, S and Cotter, PD and McAuliffe, FM}, title = {Dietary amino acids, macronutrients, vaginal birth, and breastfeeding are associated with the vaginal microbiome in early pregnancy.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0113024}, pmid = {39365058}, issn = {2165-0497}, support = {12/RC/2273//Science Foundation Ireland (SFI)/ ; 16/SP/3827//Science Foundation Ireland (SFI)/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology ; Pregnancy ; Adult ; *Amino Acids/metabolism ; *Microbiota ; *Breast Feeding ; Nutrients ; Bacteria/classification/genetics/isolation & purification/metabolism ; Diet ; Young Adult ; Premature Birth/microbiology ; Delivery, Obstetric ; }, abstract = {UNLABELLED: The vaginal microbiome is a key player in the etiology of spontaneous preterm birth. This study aimed to illustrate maternal environmental factors associated with vaginal microbiota composition and function in pregnancy. Women in healthy pregnancy had vaginal microbial sampling from the posterior vaginal fornix performed at 16 weeks gestation. After shotgun metagenomic sequencing, heatmaps of relative abundance data were generated. Community state type (CST) was assigned, and alpha diversity was calculated. Demography, obstetric history, well-being, exercise, and diet using food frequency questionnaires were collected and compared against microbial parameters. A total of 119 pregnant participants had vaginal metagenomic sequencing performed. Factors with strongest association with beta diversity were dietary lysine (adj-R[2] 0.113, P = 0.002), valine (adj-R[2] 0.096, P = 0.004), leucine (adj-R[2] 0.086, P = 0.003), and phenylalanine (adj-R[2] 0.085, P = 0.005, Fig. 2D). Previous vaginal delivery and breastfeeding were associated with vaginal beta diversity (adj-R[2] 0.048, P = 0.003; adj-R[2] 0.045, P = 0.004), accounting for 8.5% of taxonomy variation on redundancy analysis. Dietary fat, starch, and maltose were positively correlated with alpha diversity (fat +0.002 SD/g, P = 0.025; starch +0.002 SD/g, P = 0.043; maltose +0.440 SD/g, P = 0.013), particularly in secretor-positive women. Functional signature was associated with CST, maternal smoking, and dietary phenylalanine, accounting for 8.9%-11% of the variation in vaginal microbiome functional signature. Dietary amino acids, previous vaginal delivery, and breastfeeding history were associated with vaginal beta diversity. Functional signature of the vaginal microbiome differed with community state type, smoking, dietary phenylalanine, and vitamin K. Increased alpha diversity correlated with dietary fat and starch. These data provide a novel snapshot into the associations between maternal environment, nutrition, and the vaginal microbiome.

IMPORTANCE: This secondary analysis of the MicrobeMom randomized controlled trial reveals that dietary amino acids, macronutrients, previous vaginal birth, and breastfeeding have the strongest associations with vaginal taxonomy in early pregnancy. Function of the vaginal niche is associated mainly by species composition, but smoking, vitamin K, and phenylalanine also play a role. These associations provide an intriguing and novel insight into the association between host factors and diet on the vaginal microbiome in pregnancy and highlight the need for further investigation into the complex interactions between the diet, human gut, and vaginal microbiome.}, } @article {pmid39365049, year = {2024}, author = {Won, S and Cho, S and Kim, H}, title = {rRNA operon improves species-level classification of bacteria and microbial community analysis compared to 16S rRNA.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0093124}, pmid = {39365049}, issn = {2165-0497}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota/genetics ; *rRNA Operon/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {UNLABELLED: Precise identification of species is fundamental in microbial genomics and is crucial for understanding the microbial communities. While the 16S rRNA gene, particularly its V3-V4 regions, has been extensively employed for microbial identification, however has limitations in achieving species-level resolution. Advancements in long-read sequencing technologies have highlighted the rRNA operon as a more accurate marker for microbial classification and analysis than the 16S rRNA gene. This study aims to compare the accuracy of species classification and microbial community analysis using the rRNA operon versus the 16S rRNA gene. We evaluated the species classification accuracy of the rRNA operon,16S rRNA gene, and 16S rRNA V3-V4 regions using a BLAST-based method and a k-mer matching-based method with public data available from NCBI. We further performed simulations to model microbial community analysis. We accessed the performance using each marker in community composition estimation and differential abundance analysis. Our findings demonstrate that the rRNA operon offers an advantage over the 16S rRNA gene and its V3-V4 regions for species-level classification within the genus. When applied to microbial community analysis, the rRNA operon enables a more accurate determination of composition. Using the rRNA operon yielded more reliable results in differential abundance analysis as well.

IMPORTANCE: We quantitatively demonstrated that the rRNA operon outperformed the 16S rRNA and its V3-V4 regions in accuracy for both individual species identification and species-level microbial community analysis. Our findings can provide guidelines for selecting appropriate markers in the field of microbial research.}, } @article {pmid39363816, year = {2024}, author = {Sarker, S and Klukowski, N and Talukder, S and Gupta, SD and Vaughan-Higgins, R}, title = {Evidence of a highly divergent novel parvovirus in Australia's critically endangered western ground parrot/kyloring (Pezoporus flaviventris).}, journal = {Australian veterinary journal}, volume = {102}, number = {11}, pages = {570-575}, doi = {10.1111/avj.13378}, pmid = {39363816}, issn = {1751-0813}, mesh = {Animals ; *Parrots/virology ; *Endangered Species ; *Phylogeny ; *Parvoviridae Infections/veterinary/virology/epidemiology ; Australia/epidemiology ; *Feces/virology ; Parvovirus/genetics/classification/isolation & purification ; Bird Diseases/virology/epidemiology ; Genome, Viral ; }, abstract = {Detecting pathogens in endangered animal populations is vital for understanding and mitigating threats to their survival. The critically endangered western ground parrot (Pezoporus flaviventris, WGP), with a population as low as 150 individuals in Australia, faces an imminent risk of extinction. Despite this urgency, research on viral pathogens in this species remains limited. This study aimed to identify and characterise viruses present in faecal samples from seven individual WGP using a viral metagenomic approach. Analysis of the sequenced datasets revealed the presence of a novel virus belonging to the Parvoviridae family, named psittaciform chaphamaparvovirus 7 (PsChPV-7). The genome of PsChPV-7 contains typical structural and functional gene sequences found in Parvoviridae but is highly divergent, indicating its classification as a distinct species. Phylogenetic analysis placed PsChPV-7 within a unique sub-clade of the Chaphamaparvovirus genus, suggesting its evolutionary significance as an ancient lineage within this group. These findings may contribute to the development of strategic management and biosecurity plans aimed at conserving this endangered WGP.}, } @article {pmid39362120, year = {2024}, author = {Gao, S and Li, S and Cao, S and Zhong, H and He, Z}, title = {Disclosing the key role of Fe/As/Cu in community co-occurrence and microbial recruitment in metallurgical ruins.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135889}, doi = {10.1016/j.jhazmat.2024.135889}, pmid = {39362120}, issn = {1873-3336}, mesh = {*Iron/metabolism ; *Microbiota/drug effects ; Metallurgy ; Arsenic/metabolism ; Mining ; Copper ; Bacteria/metabolism/genetics ; Metals, Heavy/toxicity ; Soil Microbiology ; Soil Pollutants/metabolism/toxicity ; }, abstract = {Mining activities have led to the persistent presence of substantial heavy metals at metallurgical sites. However, the impact of long-term and complex heavy metal pollution in metallurgical ruins on the structure and spatial shift of microbiome remains unclear. In this study, we focused on various types of metallurgical sites to uncover the occurrence of heavy metals in abandoned mines and the response patterns of microbial communities. The results indicate that mining activities have caused severe exceedances of multiple heavy metals, with AsBio, CuBio, and FeBio being the primary factors affecting community structure and function. Co-occurrence network analyses suggest that several genera, including Ellin6515, Cupriavidus, Acidobacteria genus RB41, Vicinamibacteraceae, Blastococcus, and Sphingomonas, may play significant roles in the synergistic metabolism of communities responding to Fe-Cu-As stress. Although random dispersal contributed to community migration, null models emphasized that variable selection predominates in the spatial turnover of community composition. Additionally, metagenomic prediction (PICRUSt2) identified key genes involved in stress and detoxification strategies of heavy metals. The composite heavy metal stress strengthened the relationship between network structure and the potential function of the community, along with critical ecosystem functions. Our findings demonstrated that microbial interactions were crucial for ecosystem management and the ecological consequences of heavy metal pollution remediation.}, } @article {pmid39361891, year = {2024}, author = {Ramos-Barbero, MD and Gómez-Gómez, C and Vique, G and Sala-Comorera, L and Rodríguez-Rubio, L and Muniesa, M}, title = {Recruitment of complete crAss-like phage genomes reveals their presence in chicken viromes, few human-specific phages, and lack of universal detection.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39361891}, issn = {1751-7370}, mesh = {Humans ; *Bacteriophages/genetics/classification/isolation & purification ; Animals ; *Genome, Viral ; *Phylogeny ; *Virome/genetics ; *Chickens/virology ; Feces/virology ; Host Specificity ; }, abstract = {The order Crassvirales, which includes the prototypical crAssphage (p-crAssphage), is predominantly associated with humans, rendering it the most abundant and widely distributed group of DNA phages in the human gut. The reported human specificity and wide global distribution of p-crAssphage makes it a promising human fecal marker. However, the specificity for the human gut as well as the geographical distribution around the globe of other members of the order Crassvirales remains unknown. To determine this, a recruitment analysis using 91 complete, non-redundant genomes of crAss-like phages in human and animal viromes revealed that only 13 crAss-like phages among the 91 phages analyzed were highly specific to humans, and p-crAssphage was not in this group. Investigations to elucidate whether any characteristic of the phages was responsible for their prevalence in humans showed that the 13 human crAss-like phages do not share a core genome. Phylogenomic analysis placed them in three independent families, indicating that within the Crassvirales group, human specificity is likely not a feature of a common ancestor but rather was introduced on separate/independent occasions in their evolutionary history. The 13 human crAss-like phages showed variable geographical distribution across human metagenomes worldwide, with some being more prevalent in certain countries than in others, but none being universally identified. The varied geographical distribution and the absence of a phylogenetic relationship among the human crAss-like phages are attributed to the emergence and dissemination of their bacterial host, the symbiotic human strains of Bacteroides, across various human populations occupying diverse ecological niches worldwide.}, } @article {pmid39358810, year = {2024}, author = {Meng, L and Jin, H and Yulug, B and Altay, O and Li, X and Hanoglu, L and Cankaya, S and Coskun, E and Idil, E and Nogaylar, R and Ozsimsek, A and Shoaie, S and Turkez, H and Nielsen, J and Zhang, C and Borén, J and Uhlén, M and Mardinoglu, A}, title = {Multi-omics analysis reveals the key factors involved in the severity of the Alzheimer's disease.}, journal = {Alzheimer's research & therapy}, volume = {16}, number = {1}, pages = {213}, pmid = {39358810}, issn = {1758-9193}, mesh = {Humans ; *Alzheimer Disease/genetics/microbiology/metabolism/blood ; *Proteomics ; Female ; Male ; Aged ; *Metabolomics/methods ; *Gastrointestinal Microbiome ; Severity of Illness Index ; Artificial Intelligence ; Aged, 80 and over ; Biomarkers/blood ; Metagenomics/methods ; Multiomics ; }, abstract = {Alzheimer's disease (AD) is a debilitating neurodegenerative disorder with a global impact, yet its pathogenesis remains poorly understood. While age, metabolic abnormalities, and accumulation of neurotoxic substances are potential risk factors for AD, their effects are confounded by other factors. To address this challenge, we first utilized multi-omics data from 87 well phenotyped AD patients and generated plasma proteomics and metabolomics data, as well as gut and saliva metagenomics data to investigate the molecular-level alterations accounting the host-microbiome interactions. Second, we analyzed individual omics data and identified the key parameters involved in the severity of the dementia in AD patients. Next, we employed Artificial Intelligence (AI) based models to predict AD severity based on the significantly altered features identified in each omics analysis. Based on our integrative analysis, we found the clinical relevance of plasma proteins, including SKAP1 and NEFL, plasma metabolites including homovanillate and glutamate, and Paraprevotella clara in gut microbiome in predicting the AD severity. Finally, we validated the predictive power of our AI based models by generating additional multi-omics data from the same group of AD patients by following up for 3 months. Hence, we observed that these results may have important implications for the development of potential diagnostic and therapeutic approaches for AD patients.}, } @article {pmid39358791, year = {2024}, author = {Wirajana, IN and Ariantari, NP and Shyu, DJH and Vaghamshi, N and Antaliya, K and Dudhagara, P}, title = {Prokaryotic communities profiling of Indonesian hot springs using long-read Oxford Nanopore sequencing.}, journal = {BMC research notes}, volume = {17}, number = {1}, pages = {286}, pmid = {39358791}, issn = {1756-0500}, support = {B/530-4/UN14.4A/PT.01.03/2023//Udayana University International Senior Fellowship (UNISERF) grant for year 2023 (Grant Number: B/530-4/UN14.4A/PT.01.03/2023), Udayana University, Bali, Indonesia/ ; }, mesh = {*Hot Springs/microbiology ; Indonesia ; *RNA, Ribosomal, 16S/genetics ; *Nanopore Sequencing/methods ; Microbiota/genetics ; Bacteria/genetics/isolation & purification/classification ; Metagenome/genetics ; Metagenomics/methods ; Water Microbiology ; Phylogeny ; DNA, Bacterial/genetics/analysis ; Sequence Analysis, DNA/methods ; }, abstract = {OBJECTIVES: Indonesia's location at the convergence of multiple tectonic plates results in a unique geomorphological feature with abundant hot springs. This study pioneers the metagenomic exploration of Indonesian hot springs, harbouring unique life forms despite high temperatures. The microbial community of hot springs is taxonomically versatile and biotechnologically valuable. 16s rRNA amplicon sequencing of the metagenome is a viable option for the microbiome investigation. This study utilized Oxford Nanopore's long-read 16 S rRNA sequencing for enhanced species identification, improved detection of rare members, and a more detailed community composition profile.

DATA DESCRIPTION: Water samples were taken from three hot springs of the Bali, Indonesia (i) Angseri, 8.362503 S, 115.133452 E; (ii) Banjar, 8.210270 S, 114.967063 E; and (iii) Batur, 8.228806 S, 115.404829 E. BioLit Genomic DNA Extraction Kit (SRL, Mumbai, India) was used to isolate DNA from water samples. The quantity and quality of the DNA were determined using a NanoDrop™ spectrophotometer and a Qubit fluorometer (Thermo Fisher Scientific, USA). The library was created using Oxford Nanopore Technology kits, and the sequencing was done using Oxford Nanopore's GridION platform. All sequencing data was obtained in FASTQ files and filtered using NanoFilt software. This dataset is valuable for searching novel bacteria diversity and their existence.}, } @article {pmid39358771, year = {2024}, author = {Kawano-Sugaya, T and Arikawa, K and Saeki, T and Endoh, T and Kamata, K and Matsuhashi, A and Hosokawa, M}, title = {A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {188}, pmid = {39358771}, issn = {2049-2618}, mesh = {Humans ; *Bacteria/genetics/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; *Mouth/microbiology ; *Genome, Bacterial ; Interspersed Repetitive Sequences/genetics ; Microbiota/genetics ; Drug Resistance, Bacterial/genetics ; Metagenomics/methods ; Phylogeny ; }, abstract = {BACKGROUND: The increase in metagenome-assembled genomes (MAGs) has advanced our understanding of the functional characterization and taxonomic assignment within the human microbiome. However, MAGs, as population consensus genomes, often aggregate heterogeneity among species and strains, thereby obfuscating the precise relationships between microbial hosts and mobile genetic elements (MGEs). In contrast, single amplified genomes (SAGs) derived via single-cell genome sequencing can capture individual genomic content, including MGEs.

RESULTS: We introduce the first substantial SAG dataset (bbsag20) from the human oral and gut microbiome, comprising 17,202 SAGs above medium-quality without co-assembly. This collection unveils a diversity of bacterial lineages across 312 oral and 647 gut species, demonstrating different taxonomic compositions from MAGs. Moreover, the SAGs showed cellular-level evidence of the translocation of oral bacteria to the gut. We also identified broad-host-range MGEs harboring antibiotic resistance genes (ARGs), which were not detected in the MAGs.

CONCLUSIONS: The difference in taxonomic composition between SAGs and MAGs indicates that combining both methods would be effective in expanding the genome catalog. By connecting mobilomes and resistomes in individual samples, SAGs could meticulously chart a dynamic network of ARGs on MGEs, pinpointing potential ARG reservoirs and their spreading patterns in the microbial community. Video Abstract.}, } @article {pmid39357281, year = {2024}, author = {Zhang, J and Gao, T and Chen, G and Liang, Y and Nie, X and Gu, W and Li, L and Tong, H and Huang, W and Lu, T and Bian, Z and Su, L}, title = {Vinegar-processed Schisandra Chinensis enhanced therapeutic effects on colitis-induced depression through tryptophan metabolism.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {135}, number = {}, pages = {156057}, doi = {10.1016/j.phymed.2024.156057}, pmid = {39357281}, issn = {1618-095X}, mesh = {Animals ; *Schisandra/chemistry ; *Depression/drug therapy ; Male ; Mice ; *Tryptophan/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Acetic Acid ; *Colitis, Ulcerative/drug therapy/chemically induced ; *Disease Models, Animal ; Mice, Inbred C57BL ; Blood-Brain Barrier/drug effects ; Dextran Sulfate ; Colon/drug effects/metabolism ; Cytokines/metabolism ; Hippocampus/drug effects/metabolism ; Plant Extracts/pharmacology ; Intestinal Mucosa/drug effects/metabolism ; }, abstract = {BACKGROUND: Ulcerative colitis (UC) is an inflammatory bowel disease characterized by its incurable nature and undefined etiology, which is often accompanied by a high prevalence of comorbid depression. The gut-brain axis has emerged as a promising treatment target in recent years.

PURPOSE: This study aimed to investigate how vinegar-processed Schisandra Chinensis (VSC) enhances therapeutic effects on depressive behavior in chronic UC mice.

METHODS: A chronic UC model was induced in mice using dextran sulfate sodium. The therapeutic effects of both raw and vinegar-processed Schisandra Chinensis on UC and associated depressive symptoms were assessed. Colonic mucosal damage was evaluated using hematoxylin and eosin (H&E) and Alcian blue staining. The integrity of the blood-brain barrier (BBB) and synaptic structures was visualized via transmission electron microscopy (TEM). Enzyme-linked immunosorbent assay (ELISA) was employed to quantify inflammatory cytokine levels in the colon, serum, and brain, while western blotting was performed for protein expression analysis. Additionally, metagenomic analysis was conducted to investigate gut microbiota composition. Nissl staining and immunofluorescence were used to assess hippocampal neuronal damage, and behavioral assessments including the morris water maze, open field test, forced swimming test and tail suspension test, were implemented to evaluate depressive states. Serum metabolites were analyzed using UPLC-MS/MS.

RESULTS: Both raw and vinegar-processed Schisandra Chinensis significantly upregulated aryl hydrocarbon receptor (AhR), inhibited NF-κB p-p65 activation, and reduced levels of pro-inflammatory cytokine. These treatments also enhanced the expression of tight junction proteins, restored colonic mucosal and BBB integrity, alleviated damage to hippocampal neurons, and improved synaptic structure. Behavioral assessments indicated that VSC was particularly effective in ameliorating depressive-like behaviors in chronic UC mice. In the gut, both treatments reshaped the gut microbial composition, restoring the relative abundance of Duncaniella, Candidatus_Amulumruptor, Alistipes, Parabacteroides, Lachnospiraceae_bacterium, uncultured_Bacteroides_sp., Candidatus_Amulumruptor_caecigallinarius, with VSC showing more pronounced effects. Serum metabolomics revealed an increase in tryptophan levels and a decrease in kynurenine and xanthurenic acid levels with VSC, indicating that tryptophan metabolism shifted from the kynurenine pathway to the 5-HT or indole pathway. However, this phenomenon did not occur with Schisandra Chinensis (SC).

CONCLUSION: This study demonstrated that the disruption of tryptophan metabolic balance served as a biological mechanism underlying the occurrence of depressive behaviors induced by UC. The application of SC following vinegar processing enhanced its regulatory effects on gut microbiota and tryptophan metabolism. This findings provided a new insight for the clinical management of gut-brain comorbidities.}, } @article {pmid39353343, year = {2024}, author = {Zheng, X and Li, J and Ouyang, Y and Wu, G and He, X and Wang, D and Zhang, XX}, title = {Ecological linkages between top-down designed benzothiazole-degrading consortia and selection strength: From performance to community structure and functional genes.}, journal = {Water research}, volume = {267}, number = {}, pages = {122491}, doi = {10.1016/j.watres.2024.122491}, pmid = {39353343}, issn = {1879-2448}, mesh = {*Benzothiazoles ; *Biodegradation, Environmental ; Microbial Consortia ; Rhodococcus/genetics/metabolism ; }, abstract = {The inefficient biodegradation and incomplete mineralization of nitrogenous heterocyclic compounds (NHCs) have emerged as a pressing environmental concern. The top-down design offers potential solutions to this issue by targeting improvements in community function, but the ecological linkages between selection strength and the structure and function of desired microbiomes remain elusive. Herein, the integration of metagenomics, culture-based approach, non-targeted metabolite screening and enzymatic verification experiments revealed the effect of enrichment concentration on the top-down designed benzothiazole (BTH, a typical NHC)-degrading consortia. Significant differences were observed for the degradation efficiency and community structure under varying BTH selections. Notably, the enriched consortia at high concentrations of BTH were dominated by genus Rhodococcus, possessing higher degradation rates. Moreover, the isolate Rhodococcus pyridinivorans Rho48 displayed excellent efficiencies in BTH removal (98 %) and mineralization (∼ 60 %) through the hydroxylation and cleavage of thiazole and benzene rings, where cytochrome P450 enzyme was firstly reported to participate in BTH conversion. The functional annotation of 460 recovered genomes from the enriched consortia revealed diverse interspecific cooperation patterns that accounted for the BTH mineralization, particularly Nakamurella and Micropruina under low selection strength, and Rhodococcus and Marmoricola under high selection strength. This study highlights the significance of selection strength in top-down design of synthetic microbiomes for degrading refractory organic pollutants, providing valuable guidance for designing functionally optimized microbiomes used in environmental engineering.}, } @article {pmid39356745, year = {2024}, author = {Hartman, SJ and Hibberd, MC and Mostafa, I and Naila, NN and Islam, MM and Zaman, MU and Huq, S and Mahfuz, M and Islam, MT and Mukherji, K and Moghaddam, VA and Chen, RY and Province, MA and Webber, DM and Henrissat, S and Henrissat, B and Terrapon, N and Rodionov, DA and Osterman, AL and Barratt, MJ and Ahmed, T and Gordon, JI}, title = {A microbiome-directed therapeutic food for children recovering from severe acute malnutrition.}, journal = {Science translational medicine}, volume = {16}, number = {767}, pages = {eadn2366}, pmid = {39356745}, issn = {1946-6242}, support = {R01 DK030292/DK/NIDDK NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Severe Acute Malnutrition/diet therapy/therapy ; Infant ; Microbiota ; Male ; Female ; Bangladesh ; Gastrointestinal Microbiome ; }, abstract = {Globally, severe acute malnutrition (SAM), defined as a weight-for-length z-score more than three SDs below a reference mean (WLZ < -3), affects 14 million children under 5 years of age. Complete anthropometric recovery after standard, short-term interventions is rare, with children often left with moderate acute malnutrition (MAM; WLZ -2 to -3). We conducted a randomized controlled trial (RCT) involving 12- to 18-month-old Bangladeshi children from urban and rural sites, who, after initial hospital-based treatment for SAM, received a 3-month intervention with a microbiome-directed complementary food (MDCF-2) or a calorically more dense, standard ready-to-use supplementary food (RUSF). The rate of WLZ improvement was significantly greater in MDCF-2-treated children (P = 8.73 × 10[-3]), similar to our previous RCT of Bangladeshi children with MAM without antecedent SAM (P = 0.032). A correlated meta-analysis of plasma levels of 4520 proteins in both RCTs revealed 215 positively associated with WLZ (largely representing musculoskeletal and central nervous system development) and 44 negatively associated (primarily related to immune activation). Moreover, the positively associated proteins were significantly enriched by MDCF-2 (q = 1.1 × 10[-6]). Characterizing the abundances of 754 bacterial metagenome-assembled genomes in serially collected fecal samples disclosed the effects of acute rehabilitation for SAM on the microbiome and how, during treatment for MAM, specific strains of Prevotella copri function at the intersection between MDCF-2 glycan metabolism and anthropometric recovery. These results provide a rationale for further testing the generalizability of MDCF efficacy and for identifying biomarkers to define treatment responses.}, } @article {pmid39354675, year = {2024}, author = {Šardzíková, S and Gajewska, M and Gałka, N and Štefánek, M and Baláž, A and Garaiová, M and Holič, R and Świderek, W and Šoltys, K}, title = {Can longer lifespan be associated with gut microbiota involvement in lipid metabolism?.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {11}, pages = {}, pmid = {39354675}, issn = {1574-6941}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Lipid Metabolism ; Mice ; Male ; Female ; *Longevity ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/metabolism/classification ; Mice, Inbred C57BL ; Feces/microbiology ; Cholesterol Esters/metabolism ; }, abstract = {Biological aging is linked to altered body composition and reduced neuroactive steroid hormones like dehydroepiandrosterone sulfate (DHEAS), which can stimulate the GABA signaling pathway via gut microbiota. Our study examined the association of gut microbiota with lifespan in mice through comprehensive analysis of its composition and functional involvement in cholesterol sulfate, a precursor of DHEAS, metabolism. We used 16S rRNA and metagenomic sequencing, followed by metabolic pathway prediction and thin layer chromatography and MALDI-TOF cholesterol sulfate identification. Significant increases in bacteria such as Bacteroides, typical for long-lived and Odoribacter and Colidextribacter, specific for short-lived mice were detected. Furthermore, for males (Rikenella and Alloprevotella) and females (Lactobacillus and Bacteroides), specific bacterial groups emerged as predictors (AUC = 1), highlighting sex-specific patterns. Long-lived mice showed a strong correlation of Bacteroides (0.918) with lipid and steroid hormone metabolism, while a negative correlation of GABAergic synapse with body weight (-0.589). We found that several Bacteroides species harboring the sulfotransferase gene and gene cluster for sulfonate donor synthesis are involved in converting cholesterol to cholesterol sulfate, significantly higher in the feces of long-lived individuals. Overall, we suggest that increased involvement of gut bacteria, mainly Bacteroides spp., in cholesterol sulfate synthesis could ameliorate aging through lipid metabolism.}, } @article {pmid39354152, year = {2024}, author = {Freire-Zapata, V and Holland-Moritz, H and Cronin, DR and Aroney, S and Smith, DA and Wilson, RM and Ernakovich, JG and Woodcroft, BJ and Bagby, SC and , and , and Rich, VI and Sullivan, MB and Stegen, JC and Tfaily, MM}, title = {Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient.}, journal = {Nature microbiology}, volume = {9}, number = {11}, pages = {2892-2908}, pmid = {39354152}, issn = {2058-5276}, support = {DE-SC0021349//DOE | SC | Biological and Environmental Research (BER)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; }, mesh = {*Permafrost/microbiology ; *Greenhouse Gases/metabolism/analysis ; *Microbiota ; *Methane/metabolism ; *Metagenomics ; *Carbon Dioxide/metabolism ; *Bacteria/metabolism/genetics/classification ; Sweden ; Ecosystem ; Soil Microbiology ; }, abstract = {Interactions between microbiomes and metabolites play crucial roles in the environment, yet how these interactions drive greenhouse gas emissions during ecosystem changes remains unclear. Here we analysed microbial and metabolite composition across a permafrost thaw gradient in Stordalen Mire, Sweden, using paired genome-resolved metagenomics and high-resolution Fourier transform ion cyclotron resonance mass spectrometry guided by principles from community assembly theory to test whether microorganisms and metabolites show concordant responses to changing drivers. Our analysis revealed divergence between the inferred microbial versus metabolite assembly processes, suggesting distinct responses to the same selective pressures. This contradicts common assumptions in trait-based microbial models and highlights the limitations of measuring microbial community-level data alone. Furthermore, feature-scale analysis revealed connections between microbial taxa, metabolites and observed CO2 and CH4 porewater variations. Our study showcases insights gained by using feature-level data and microorganism-metabolite interactions to better understand metabolic processes that drive greenhouse gas emissions during ecosystem changes.}, } @article {pmid39354019, year = {2024}, author = {Oaikhena, AO and Coker, ME and Cyril-Okoh, D and Wicaksono, WA and Olimi, E and Berg, G and Okeke, IN}, title = {The phyllosphere of Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii is inhabited by a specific microbiota.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {22806}, pmid = {39354019}, issn = {2045-2322}, mesh = {*Euphorbia ; *Ficus/microbiology ; *Microbiota/genetics ; *Plants, Medicinal/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; *Plant Leaves/microbiology ; *Fungi/genetics/classification/isolation & purification ; Nigeria ; Phylogeny ; }, abstract = {The microbiota of medicinal plants is known to be highly specific and can contribute to medicinal activity. However, the majority of plant species have not yet been studied. Here, we investigated the phyllosphere composition of two common Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii, by a polyphasic approach combining analyses of metagenomic DNA and isolates. Microbial abundance estimated via qPCR using specific marker gene primers showed that all leaf samples were densely colonized, with up to 10[8] per gram of leaf, with higher bacterial and fungal abundance than Archaea. While no statistically significant differences between both plant species were found for abundance, amplicon sequencing of 16S rRNA and ITS genes revealed distinct microbiota compositions. Only seven of the 27 genera isolated were represented on both plants, e.g. dominant Sphingomonas spp., and numerous members of Xanthomonadaceae and Enterobacteriaceae. The most dominant fungal families on both plants were Cladosporiaceae, Mycosphaerellaceae and Trichosphaeriaceae. In addition, 225 plant-specific isolates were identified, with Pseudomonadota and Enterobacteriaceae being dominant. Interestingly, 29 isolates are likely species previously unknown, and 14 of these belong to Burkholderiales. However, a high proportion, 56% and 40% of the isolates from E. lateriflora and F. thonningii, respectively, were characterized as various Escherichia coli. The growth of most of the bacterial isolates was not influenced by extractable secondary metabolites of plants. Our results suggest that a specific and diverse microbial community inhabits the leaves of both E. lateriflora and F. thonningii, including potentially new species and producers of antimicrobials.}, } @article {pmid39354003, year = {2024}, author = {Li, Y and Liu, H and Xiao, Y and Jing, H}, title = {Metagenome sequencing and 982 microbial genomes from Kermadec and Diamantina Trenches sediments.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1067}, pmid = {39354003}, issn = {2052-4463}, mesh = {*Geologic Sediments/microbiology ; *Metagenome ; *Archaea/genetics ; *Phylogeny ; *Bacteria/genetics/classification ; Genome, Microbial ; Microbiota ; Genome, Archaeal ; }, abstract = {Deep-sea trenches representing an intriguing ecosystem for exploring the survival and evolutionary strategies of microbial communities in the highly specialized deep-sea environments. Here, 29 metagenomes were obtained from sediment samples collected from Kermadec and Diamantina trenches. Notably, those samples covered a varying sampling depths (from 5321 m to 9415 m) and distinct layers within the sediment itself (from 0~40 cm in Kermadec trench and 0~24 cm in Diamantina trench). Through metagenomic binning process, we reconstructed 982 metagenome assembled genomes (MAGs) with completeness >60% and contamination <5%. Within them, completeness of 351 MAGs were >90%, while an additional 331 were >80%. Phylogenomic analysis for the MAGs revealed nearly all of them were distantly related to known cultivated isolates. The abundant bacterial MAGs affiliated to phyla of Proteobacteria, Planctomycetota, Nitrospirota, Acidobacteriota, Actinobacteriota, and Chlorofexota, while the abundant archaeal phyla affiliated with Nanoarchaeota and Thermoproteota. These results provide a dataset available for further interrogation of diversity, distribution and ecological function of deep-sea microbes existed in the trenches.}, } @article {pmid39352141, year = {2024}, author = {Coclet, C and Camargo, AP and Roux, S}, title = {MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0088824}, pmid = {39352141}, issn = {2379-5077}, mesh = {*Metagenome/genetics ; *Genome, Viral/genetics ; *Metagenomics/methods ; *Viruses/genetics/classification/isolation & purification ; Software ; Virome/genetics ; Computational Biology/methods ; Molecular Sequence Annotation ; }, abstract = {While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.IMPORTANCEThe significance of our work lies in the development of Modular Viromics Pipeline (MVP), an integrated and user-friendly pipeline tailored exclusively for viromics analyses. MVP stands out due to its modular design, which ensures easy installation, execution, and integration of new tools and databases. By combining state-of-the-art tools such as geNomad and CheckV, MVP provides high-quality viral genome recovery and taxonomy and host assignment, and functional annotation, addressing the limitations of existing pipelines. MVP's ability to handle diverse sample types, including environmental, human microbiome, and plant-associated samples, makes it a versatile tool for the broader microbiome research community. By standardizing the analysis process and providing easily interpretable results, MVP enables researchers to perform comprehensive studies of viral communities, significantly advancing our understanding of viral ecology and its impact on various ecosystems.}, } @article {pmid39351905, year = {2024}, author = {Feng, M and Robinson, S and Qi, W and Edwards, A and Stierli, B and van der Heijden, M and Frey, B and Varliero, G}, title = {Microbial genetic potential differs among cryospheric habitats of the Damma glacier.}, journal = {Microbial genomics}, volume = {10}, number = {10}, pages = {}, pmid = {39351905}, issn = {2057-5858}, mesh = {*Ice Cover/microbiology ; *Ecosystem ; Soil Microbiology ; Nitrogen Fixation/genetics ; Microbiota/genetics ; Metagenomics ; Geologic Sediments/microbiology ; Bacteria/genetics/classification/isolation & purification ; Metagenome ; Nitrogen Cycle/genetics ; }, abstract = {Climate warming has led to glacier retreat worldwide. Studies on the taxonomy and functions of glacier microbiomes help us better predict their response to glacier melting. Here, we used shotgun metagenomic sequencing to study the microbial functional potential in different cryospheric habitats, i.e. surface snow, supraglacial and subglacial sediments, subglacial ice, proglacial stream water and recently deglaciated soils. The functional gene structure varied greatly among habitats, especially for snow, which differed significantly from all other habitats. Differential abundance analysis revealed that genes related to stress responses (e.g. chaperones) were enriched in ice habitat, supporting the fact that glaciers are a harsh environment for microbes. The microbial metabolic capabilities related to carbon and nitrogen cycling vary among cryospheric habitats. Genes related to auxiliary activities were overrepresented in the subglacial sediment, suggesting a higher genetic potential for the degradation of recalcitrant carbon (e.g., lignin). As for nitrogen cycling, genes related to nitrogen fixation were more abundant in barren proglacial soils, possibly due to the presence of Cyanobacteriota in this habitat. Our results deepen our understanding of microbial processes in glacial ecosystems, which are vulnerable to ongoing global warming, and they have implications for downstream ecosystems.}, } @article {pmid39351368, year = {2024}, author = {Tolstoganov, I and Chen, Z and Pevzner, P and Korobeynikov, A}, title = {SpLitteR: diploid genome assembly using TELL-Seq linked-reads and assembly graphs.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18050}, pmid = {39351368}, issn = {2167-8359}, mesh = {*Diploidy ; Animals ; Humans ; Genome, Human/genetics ; Sheep/genetics ; Software ; Sequence Analysis, DNA/methods ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Genome/genetics ; }, abstract = {BACKGROUND: Recent advances in long-read sequencing technologies enabled accurate and contiguous de novo assemblies of large genomes and metagenomes. However, even long and accurate high-fidelity (HiFi) reads do not resolve repeats that are longer than the read lengths. This limitation negatively affects the contiguity of diploid genome assemblies since two haplomes share many long identical regions. To generate the telomere-to-telomere assemblies of diploid genomes, biologists now construct their HiFi-based phased assemblies and use additional experimental technologies to transform them into more contiguous diploid assemblies. The barcoded linked-reads, generated using an inexpensive TELL-Seq technology, provide an attractive way to bridge unresolved repeats in phased assemblies of diploid genomes.

RESULTS: We developed the SpLitteR tool for diploid genome assembly using linked-reads and assembly graphs and benchmarked it against state-of-the-art linked-read scaffolders ARKS and SLR-superscaffolder using human HG002 genome and sheep gut microbiome datasets. The benchmark showed that SpLitteR scaffolding results in 1.5-fold increase in NGA50 compared to the baseline LJA assembly and other scaffolders while introducing no additional misassemblies on the human dataset.

CONCLUSION: We developed the SpLitteR tool for assembly graph phasing and scaffolding using barcoded linked-reads. We benchmarked SpLitteR on assembly graphs produced by various long-read assemblers and have demonstrated that TELL-Seq reads facilitate phasing and scaffolding in these graphs. This benchmarking demonstrates that SpLitteR improves upon the state-of-the-art linked-read scaffolders in the accuracy and contiguity metrics. SpLitteR is implemented in C++ as a part of the freely available SPAdes package and is available at https://github.com/ablab/spades/releases/tag/splitter-preprint.}, } @article {pmid39349606, year = {2024}, author = {Guo, X and Lin, S and Zhang, X and Li, M and Wang, Z and Peng, Y and He, X and Liu, J}, title = {Integrated metabolomic and microbiome analysis identifies Cupriavidus metallidurans as a potential therapeutic target for β-thalassemia.}, journal = {Annals of hematology}, volume = {103}, number = {12}, pages = {5169-5179}, pmid = {39349606}, issn = {1432-0584}, support = {21B0827//The Hunan Provincial Department of Education/ ; 202201065317//The Hunan Provincial Health Commission/ ; kq2004076//The Changsha Science and Technology Bureau/ ; 81920108004//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *beta-Thalassemia/metabolism/microbiology/therapy ; Mice ; *Gastrointestinal Microbiome ; *Metabolomics/methods ; *Cupriavidus/metabolism ; Disease Models, Animal ; Bilirubin/metabolism/blood ; Mice, Inbred C57BL ; Metabolome ; Feces/microbiology ; }, abstract = {β-thalassemia(β-TH) is an inherited hemoglobin disorder marked by ineffective erythropoiesis, anemia, splenomegaly, and systemic iron overload, predominantly affecting developing countries in tropical and subtropical regions. Despite extensive research on its pathogenesis, the interactions between gut microbiota and metabolites in β-TH remain poorly understood. This study compares fecal metabolomics and metagenomics between wildtype (Wt) and heterozygous Th3/+ mice, a model for non-transfusion-dependent β-thalassemia intermedia. Our results show increased intestinal bilirubin metabolism, with significant elevations in metabolites such as biliverdin, bilirubin, and stercobilin. Metagenomic analysis revealed notable differences in bacterial composition between Th3/+ and Wt mice. Specifically, Cupriavidus metallidurans was identified as a key bacterium that mitigates anemia by reducing liver and spleen iron deposition. This is the first study to ameliorate anemia in mice by altering gut microbiota, presenting new strategies for β-TH management.}, } @article {pmid39349486, year = {2024}, author = {Sun, W and Zhang, Y and Guo, R and Sha, S and Chen, C and Ullah, H and Zhang, Y and Ma, J and You, W and Meng, J and Lv, Q and Cheng, L and Fan, S and Li, R and Mu, X and Li, S and Yan, Q}, title = {A population-scale analysis of 36 gut microbiome studies reveals universal species signatures for common diseases.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {96}, pmid = {39349486}, issn = {2055-5008}, support = {5050071720001//Beijing University of Chinese Medicine (BUCM)/ ; 2180072120049//Beijing University of Chinese Medicine (BUCM)/ ; 81503455//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Case-Control Studies ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Metagenomics/methods ; China ; Biodiversity ; }, abstract = {The gut microbiome has been implicated in various human diseases, though findings across studies have shown considerable variability. In this study, we reanalyzed 6314 publicly available fecal metagenomes from 36 case-control studies on different diseases to investigate microbial diversity and disease-shared signatures. Using a unified analysis pipeline, we observed reduced microbial diversity in many diseases, while some exhibited increased diversity. Significant alterations in microbial communities were detected across most diseases. A meta-analysis identified 277 disease-associated gut species, including numerous opportunistic pathogens enriched in patients and a depletion of beneficial microbes. A random forest classifier based on these signatures achieved high accuracy in distinguishing diseased individuals from controls (AUC = 0.776) and high-risk patients from controls (AUC = 0.825), and it also performed well in external cohorts. These results offer insights into the gut microbiome's role in common diseases in the Chinese population and will guide personalized disease management strategies.}, } @article {pmid39347544, year = {2024}, author = {Yergaliyev, T and Künzel, S and Hanauska, A and Rees, A and Wild, KJ and Pétursdóttir, ÁH and Gunnlaugsdóttir, H and Reynolds, CK and Humphries, DJ and Rodehutscord, M and Camarinha-Silva, A}, title = {The effect of Asparagopsis taxiformis, Ascophyllum nodosum, and Fucus vesiculosus on ruminal methanogenesis and metagenomic functional profiles in vitro.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0394223}, pmid = {39347544}, issn = {2165-0497}, support = {19084,19084-20//EC | H2020 | H2020 European Institute of Innovation and Technology (EIT)/ ; }, mesh = {*Methane/metabolism ; Animals ; *Seaweed/microbiology ; *Rumen/microbiology ; *Ascophyllum/metabolism ; *Fucus/microbiology/metabolism ; *Bacteria/classification/genetics/metabolism/drug effects/isolation & purification ; Metagenomics ; Scotland ; Archaea/classification/metabolism/genetics/drug effects/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Portugal ; Ruminants/microbiology ; Microbiota/drug effects ; Animal Feed/analysis ; Gastrointestinal Microbiome/drug effects ; Rhodophyta ; }, abstract = {UNLABELLED: The ruminant-microorganism symbiosis is unique by providing high-quality food from fibrous materials but also contributes to the production of one of the most potent greenhouse gases-methane. Mitigating methanogenesis in ruminants has been a focus of interest in the past decades. One of the promising strategies to combat methane production is the use of feed supplements, such as seaweeds, that might mitigate methanogenesis via microbiome modulation and direct chemical inhibition. We conducted in vitro investigations of the effect of three seaweeds (Ascophyllum nodosum, Asparagopsis taxiformis, and Fucus vesiculosus) harvested at different locations (Iceland, Scotland, and Portugal) on methane production. We applied metataxonomics (16S rRNA gene amplicons) and metagenomics (shotgun) methods to uncover the interplay between the microbiome's taxonomical and functional states, methanogenesis rates, and seaweed supplementations. Methane concentration was reduced by A. nodosum and F. vesiculosus, both harvested in Scotland and A. taxiformis, with the greatest effect of the latter. A. taxiformis acted through the reduction of archaea-to-bacteria ratios but not eukaryotes-to-bacteria. Moreover, A. taxiformis application was accompanied by shifts in both taxonomic and functional profiles of the microbial communities, decreasing not only archaeal ratios but also abundances of methanogenesis-associated functions. Methanobrevibacter "SGMT" (M. smithii, M. gottschalkii, M. millerae or M. thaueri; high methane yield) to "RO" (M. ruminantium and M. olleyae; low methane yield) clades ratios were also decreased, indicating that A. taxiformis application favored Methanobrevibacter species that produce less methane. Most of the functions directly involved in methanogenesis were less abundant, while the abundances of the small subset of functions that participate in methane assimilation were increased.

IMPORTANCE: The application of A. taxiformis significantly reduced methane production in vitro. We showed that this reduction was linked to changes in microbial function profiles, the decline in the overall archaeal community counts, and shifts in ratios of Methanobrevibacter "SGMT" and "RO" clades. A. nodosum and F. vesiculosus, obtained from Scotland, also decreased methane concentration in the total gas, while the same seaweed species from Iceland did not.}, } @article {pmid39347539, year = {2024}, author = {Yuan, Y and Hu, H and Sun, Z and Wang, W and Wang, Z and Zheng, M and Xing, Y and Zhang, W and Wang, M and Lu, X and Li, Y and Liang, C and Lin, Z and Xie, C and Li, J and Mao, T}, title = {Combining Metagenomics, Network Pharmacology and RNA-Seq Strategies to Reveal the Therapeutic Effects and Mechanisms of Qingchang Wenzhong Decoction on Inflammatory Bowel Disease in Mice.}, journal = {Drug design, development and therapy}, volume = {18}, number = {}, pages = {4273-4289}, pmid = {39347539}, issn = {1177-8881}, mesh = {Animals ; Mice ; *Drugs, Chinese Herbal/pharmacology/chemistry ; *Inflammatory Bowel Diseases/drug therapy ; *Metagenomics ; *Gastrointestinal Microbiome/drug effects ; *Network Pharmacology ; *Dextran Sulfate ; *Mice, Inbred C57BL ; Disease Models, Animal ; Male ; RNA-Seq ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic and recurrent inflammatory disease that lacks effective treatments. Qingchang Wenzhong Decoction (QCWZD) is a clinically effective herbal prescription that has been proven to attenuate intestinal inflammation in IBD. However, its molecular mechanism of action has not been clearly elucidated.

PURPOSE: We aimed to probe the mechanism of QCWZD for the treatment of IBD.

METHODS: The dextran sulfate sodium (DSS)-induced mouse model of IBD was used to identify the molecular targets involved in the mechanism of action of QCWZD. Metagenomics sequencing was utilized to analyze the differences in gut microbiota and the functional consequences of these changes. Network pharmacology combined with RNA sequencing (RNA-seq) were employed to predict the molecular targets and mechanism of action of QCWZD, and were validated through in vivo experiments.

RESULTS: Our results demonstrated that QCWZD treatment alleviated intestinal inflammation and accelerated intestinal mucosal healing that involved restoration of microbial homeostasis. This hypothesis was supported by the results of bacterial metagenomics sequencing that showed attenuation of gut dysbiosis by QCWZD treatment, especially the depletion of the pathogenic bacterial genus Bacteroides, while increasing the beneficial microorganism Akkermansia muciniphila that led to altered bacterial gene functions, such as metabolic regulation. Network pharmacology and RNA-seq analyses showed that Th17 cell differentiation plays an important role in QCWZD-based treatment of IBD. This was confirmed by in vivo experiments showing a marked decrease in the percentage of CD3[+]CD4[+]IL-17[+] (Th17) cells. Furthermore, our results also showed that the key factors associated with Th17 cell differentiation (IL-17, NF-κB, TNF-α and IL-6) in the colon were significantly reduced in QCWZD-treated colitis mice.

CONCLUSION: QCWZD exerted beneficial effects in the treatment of IBD by modulating microbial homeostasis while inhibiting Th17 cell differentiation and its associated pathways, providing a novel and promising therapeutic strategy for the treatment of IBD.}, } @article {pmid39346055, year = {2024}, author = {Knobloch, S and Salimi, F and Buaya, A and Ploch, S and Thines, M}, title = {RAPiD: a rapid and accurate plant pathogen identification pipeline for on-site nanopore sequencing.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17893}, pmid = {39346055}, issn = {2167-8359}, mesh = {*Nanopore Sequencing/methods ; Metagenomics/methods ; Plant Diseases/microbiology ; Bacteria/genetics/isolation & purification/classification ; Sequence Analysis, DNA/methods ; Fungi/genetics/isolation & purification/classification ; Plants/microbiology ; Computational Biology/methods ; }, abstract = {Nanopore sequencing technology has enabled the rapid, on-site taxonomic identification of samples from anything and anywhere. However, sequencing errors, inadequate databases, as well as the need for bioinformatic expertise and powerful computing resources, have hampered the widespread use of the technology for pathogen identification in the agricultural sector. Here we present RAPiD, a lightweight and accurate real-time taxonomic profiling pipeline. Compared to other metagenomic profilers, RAPiD had a higher classification precision achieved through the use of a curated, non-redundant database of common agricultural pathogens and extensive quality filtering of alignments. On a fungal, bacterial and mixed mock community RAPiD was the only pipeline to detect all members of the communities. We also present a protocol for in-field sample processing enabling pathogen identification from plant sample to sequence within 3 h using low-cost equipment. With sequencing costs continuing to decrease and more high-quality reference genomes becoming available, nanopore sequencing provides a viable method for rapid and accurate pathogen identification in the field. A web implementation of the RAPiD pipeline for real-time analysis is available at https://agrifuture.senckenberg.de.}, } @article {pmid39345197, year = {2024}, author = {Wei, Y and Zhang, Y and Zhuang, Y and Tang, Y and Nie, H and Haung, Y and Liu, T and Yang, W and Yan, F and Zhu, Y}, title = {Veillonella parvula acts as a pathobiont promoting the biofilm virulence and cariogenicity of Streptococcus mutans in adult severe caries.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0431823}, pmid = {39345197}, issn = {2165-0497}, support = {82201055//MOST | National Natural Science Foundation of China (NSFC)/ ; 0223A205//2015 cultivation program for reserve talents for academic leaders of Nanjing Stomatological Hospital/ ; 2022-R-203 0222C116//3456 cultivation program for junior talents of Nanjing Stomatological Hospital/ ; ZKX23053//Nanjing Medical Science and Technique Development Foundation/ ; }, mesh = {*Biofilms/growth & development ; *Streptococcus mutans/genetics/pathogenicity/physiology ; *Dental Caries/microbiology ; *Dental Plaque/microbiology ; Humans ; Virulence ; Animals ; Adult ; *Veillonella/genetics/physiology/pathogenicity ; Rats ; Male ; Mice ; Female ; Microbiota ; }, abstract = {Adult severe caries (ASC) brings severe oral dysfunction and treatment difficulties to patients, and yet no clear pathogenic mechanism for it has been found. This study is focused on the composition of dental plaque microbiome profiles in order to identify disease-relevant species and to investigate into their interactions with the S. mutans. Samples of dental plaque were collected for metagenomic analysis. The acidification, aciduricity, oxidative stress tolerance, and gtf (glucosyltransferase) gene expression of S. mutans cocultured with V. parvula which was identified as ASC-related dominant bacterium. The biofilm formation and extracellular exopolysaccharide (EPS) synthesis of dual-strain were analyzed with scanning electron microscopy (SEM), crystal violet (CV) staining, live/dead bacterial staining, and confocal laser scanning microscopy (CLSM). Furthermore, rodent model experiments were performed to validate the in vivo cariogenicity of the dual-species biofilm. The most significantly abundant taxon found associated with ASC was V. parvula. In vitro experiments found that V. parvula can effectively promote S. mutans mature biofilm formation with enhanced acid resistance, hydrogen peroxide detoxicity, and biofilm virulence. Rodent model experiments revealed that V. parvula was incapable of causing disease on its own, but it significantly heightened the biofilm virulence of S. mutans when being co-infected and augmented the progression, quantity, and severity of dental caries. Our findings demonstrated that V. parvula may act as a synergistic pathobiont to modulate the metabolic activity, spatial structure, and pathogenicity of biofilms of S. mutans in the context of ASC.IMPORTANCEAdult severe caries (ASC), as a special type of acute caries, is rarely reported and its worthiness of further study is still in dispute. Yet studies on the etiology of severe caries in adults have not found a clear pathogenic mechanism for it. Knowledge of the oral microbiota is important for the treatment of dental caries. We discovered that the interaction between V. parvula and S. mutans augments the severity of dental caries in vivo, suggesting V. parvula may act as a synergistic pathobiont exacerbating biofilm virulence of S. mutans in ASC. Our findings may improve the understanding of ASC pathogenesis and are likely to provide a basis for planning appropriate therapeutic strategies.}, } @article {pmid39343535, year = {2024}, author = {Masuda, N and Kato, S and Ohkuma, M and Endo, K}, title = {Metagenomic Insights into Ecophysiology of Zetaproteobacteria and Gammaproteobacteria in Shallow Zones within Deep-sea Massive Sulfide Deposits.}, journal = {Microbes and environments}, volume = {39}, number = {3}, pages = {}, pmid = {39343535}, issn = {1347-4405}, mesh = {*Sulfides/metabolism ; *Gammaproteobacteria/genetics/classification/isolation & purification ; *Metagenomics ; *Seawater/microbiology ; *Metagenome ; Geologic Sediments/microbiology/chemistry ; Phylogeny ; Ecosystem ; Pacific Ocean ; Oxidation-Reduction ; Microbiota/genetics ; Carbon Cycle ; }, abstract = {Deep-sea massive sulfide deposits serve as energy sources for chemosynthetic ecosystems in dark, cold environments even after hydrothermal activity ceases. However, the vertical distribution of microbial communities within sulfide deposits along their depth from the seafloor as well as their ecological roles remain unclear. We herein conducted a culture-independent metagenomic ana-lysis of a core sample of massive sulfide deposits collected in a hydrothermally inactive field of the Southern Mariana Trough, Western Pacific, by drilling (sample depth: 0.52‍ ‍m below the seafloor). Based on the gene context of the metagenome-assembled genomes (MAGs) obtained, we showed the metabolic potential of as-yet-uncultivated microorganisms, particularly those unique to the shallow zone rich in iron hydroxides. Some members of Gammaproteobacteria have potential for the oxidation of reduced sulfur species (such as sulfide and thiosulfate) to sulfate coupled to nitrate reduction to ammonia and carbon fixation via the Calvin-Benson-Bassham (CBB) cycle, as the primary producers. The Zetaproteobacteria member has potential for iron oxidation coupled with microaerobic respiration. A comparative ana-lysis with previously reported metagenomes from deeper zones (~2‍ ‍m below the seafloor) of massive sulfide deposits revealed a difference in the relative abundance of each putative primary producer between the shallow and deep zones. Our results expand knowledge on the ecological potential of uncultivated microorganisms in deep-sea massive sulfide deposits and provide insights into the vertical distribution patterns of chemosynthetic ecosystems.}, } @article {pmid39342753, year = {2024}, author = {Zou, S and Hu, R and Liang, S and Lu, T and Kang, D and Li, D}, title = {Assessment of health risk of antibiotics resistance genes from human disturbed habitat to wild animals: Metagenomic insights into availability and functional changes of gut microbiome.}, journal = {Ecotoxicology and environmental safety}, volume = {285}, number = {}, pages = {117117}, doi = {10.1016/j.ecoenv.2024.117117}, pmid = {39342753}, issn = {1090-2414}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Ecosystem ; *Drug Resistance, Microbial/genetics ; Humans ; *Animals, Wild/microbiology ; Risk Assessment ; Colobinae/microbiology/genetics ; Metagenomics ; Metagenome ; Environmental Monitoring ; Anti-Bacterial Agents/pharmacology/toxicity ; }, abstract = {Not all antibiotic resistance genes (ARGs) pose an ecological risk to their host animals. A standard should be developed to study which types of ARGs posed an ecological risk to wild animals under human disturbances (HDs). In this study, the golden snub-nosed monkeys (Rhinopithecus roxellana) were used as sentinel species. According to the animals-associated enrichment, mobility, and pathogenicity, the ARGs in habitat of sentinel species were divided into four levels. If the mobile and pathogenic ARGs that could be collinear with the metagenome-assembled genome (MAGs) in the gut of the sentinel species, the ARGs were defined as Rank I ARGs and they were considered to have ecological risk to sentinel species. Functional genes in the MAGs that collinear with the Rank I ARGs were used to predict the health risks of sentinel species. The ecological risk to sentinel species was present in 0.158 % of the ARGs-contigs in the habitat. Cultivation and villages, but not grazing, agriculture and ecotourism, increased the ecological risk of the ARGs to wild animals, The ability of gut microbiome to acquire mobile and pathogenic ARGs increased, as did the collinear functional genes, and the health risks of the wild animals also enhanced by the disturbances of cultivation and villages. Cultivation and villages increased the nutrient content of the soil, and they had a positive effect on the ecological risk of Rank I ARGs by affecting the mobile genetic elements (MGEs), microbiome and the resistant group in the habitat, which was why the cultivation and villages increased the health risks of wild animals. We proposed that cultivation and living should be controlled, while grazing, agriculture and ecotourism could be developed in nature reserves of wild animals, but the nutrients in the wild animals' habitat should be monitored.}, } @article {pmid39342284, year = {2024}, author = {Seitz, VA and McGivern, BB and Borton, MA and Chaparro, JM and Schipanski, ME and Prenni, JE and Wrighton, KC}, title = {Cover crop root exudates impact soil microbiome functional trajectories in agricultural soils.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {183}, pmid = {39342284}, issn = {2049-2618}, support = {P30 CA046934/CA/NCI NIH HHS/United States ; 507580//Facilities Integrating Collaborations for User Science/ ; 2021-67019-34814//U.S. Department of Agriculture/ ; P30CA046934//Cancer Center Support Grant/ ; }, mesh = {*Soil Microbiology ; *Plant Roots/microbiology ; *Crops, Agricultural/microbiology ; *Microbiota ; *Rhizosphere ; *Soil/chemistry ; Bacteria/classification/metabolism/isolation & purification ; Agriculture ; Plant Growth Regulators/metabolism ; Plant Exudates/metabolism ; Sorghum/metabolism/microbiology ; }, abstract = {BACKGROUND: Cover cropping is an agricultural practice that uses secondary crops to support the growth of primary crops through various mechanisms including erosion control, weed suppression, nutrient management, and enhanced biodiversity. Cover crops may elicit some of these ecosystem services through chemical interactions with the soil microbiome via root exudation, or the release of plant metabolites from roots. Phytohormones are one metabolite type exuded by plants that activate the rhizosphere microbiome, yet managing this chemical interaction remains an untapped mechanism for optimizing plant-soil-microbiome interactions. Currently, there is limited understanding on the diversity of cover crop phytohormone root exudation patterns and our aim was to understand how phytochemical signals selectively enrich specific microbial taxa and functionalities in agricultural soils.

RESULTS: Here, we link variability in cover crop root exudate composition to changes in soil microbiome functionality. Exudate chemical profiles from 4 cover crop species (Sorghum bicolor, Vicia villosa, Brassica napus, and Secale cereal) were used as the chemical inputs to decipher microbial responses. These distinct exudate profiles, along with a no exudate control, were amended to agricultural soil microcosms with microbial responses tracked over time using metabolomes and genome-resolved metatranscriptomes. Our findings illustrated microbial metabolic patterns were unique in response to cover crop exudate inputs over time, particularly by sorghum and cereal rye amended microcosms. In these microcosms, we identify novel microbial members (at the genera and family level) who produced IAA and GA4 over time. Additionally, we identified cover crop exudates exclusively enriched for bacterial nitrite oxidizers, while control microcosms were discriminated for nitrogen transport, mineralization, and assimilation, highlighting distinct changes in microbial nitrogen cycling in response to chemical inputs.

CONCLUSIONS: We highlight that root exudate amendments alter microbial community function (i.e., N cycling) and microbial phytohormone metabolisms, particularly in response to root exudates isolated from cereal rye and sorghum plants. Additionally, we constructed a soil microbial genomic catalog of microorganisms responding to commonly used cover crops, a public resource for agriculturally relevant microbes. Many of our exudate-stimulated microorganisms are representatives from poorly characterized or novel taxa, revealing the yet to be discovered metabolic reservoir harbored in agricultural soils. Our findings emphasize the tractability of high-resolution multi-omics approaches to investigate processes relevant for agricultural soils, opening the possibility of targeting specific soil biogeochemical outcomes through biological precision agricultural practices that use cover crops and the microbiome as levers for enhanced crop production. Video Abstract.}, } @article {pmid39342129, year = {2024}, author = {García-Estrada, DA and Selem-Mojica, N and Martínez-Hernández, A and Lara-Reyna, J and Dávila-Ramos, S and Verdel-Aranda, K}, title = {Diversity of bacterial communities in wetlands of Calakmul Biosphere Reserve: a comparative analysis between conserved and semi-urbanized zones in pre-Mayan Train era.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {376}, pmid = {39342129}, issn = {1471-2180}, support = {No. 320237//Consejo Nacional de Humanidades, Ciencias y Tecnologías, México/ ; }, mesh = {*Wetlands ; *Bacteria/classification/genetics/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Biodiversity ; Metagenomics ; Phylogeny ; DNA, Bacterial/genetics ; Soil Microbiology ; }, abstract = {BACKGROUND: The Calakmul Biosphere Reserve (CBR) is known for its rich animal and plant biodiversity, yet its microbial communities remain largely unknown. The reserve does not possess permanent bodies of water; nevertheless, seasonal depressions associated with fractures create wetlands, known locally as aguadas. Given the recent construction of the Maya train that crosses the CRB, it is essential to assess the biodiversity of its microorganisms and recognize their potential as a valuable source of goods. This evaluation is pivotal in mitigating potential mismanagement of the forest ecosystem. To enhance comprehension of microbial communities, we characterized the microbiota in three different wetlands. Ag-UD1 and Ag-UD2 wetlands are located in a zone without human disturbances, while the third, Ag-SU3, is in a semi-urbanized zone. Sampling was carried out over three years (2017, 2018, and 2019), enabling the monitoring of spatiotemporal variations in bacterial community diversity. The characterization of microbiome composition was conducted using 16S rRNA metabarcoding. Concurrently, the genomic potential of select samples was examined through shotgun metagenomics.

RESULTS: Statistical analysis of alpha and beta diversity indices showed significant differences among the bacterial communities found in undisturbed sites Ag-UD1 and Ag-UD2 compared to Ag-SU3. However, no significant differences were observed among sites belonging to the undisturbed area. Furthermore, a comparative analysis at the zone level reveals substantial divergence among the communities, indicating that the geographic location of the samples significantly influences these patterns. The bacterial communities in the CBR wetlands predominantly consist of genera from phyla Actinobacteria, Acidobacteria, and Proteobacteria.

CONCLUSION: This characterization has identified the composition of microbial communities and provided the initial overview of the metabolic capacities of the microbiomes inhabiting the aguadas across diverse conservation zones. The three sites exhibit distinct microbial compositions, suggesting that variables such as chemical composition, natural and anthropogenic disturbances, vegetation, and fauna may play a pivotal role in determining the microbial structure of the aguadas. This study establishes a foundational baseline for evaluating the impact of climatic factors and human interventions on critical environments such as wetlands.}, } @article {pmid39342083, year = {2024}, author = {Wang, X and Yao, S and Yang, X and Li, Y and Yu, Z and Huang, J and Wang, J}, title = {Peritoneal dialysis promotes microbial-driven biosynthesis pathways of sesquiterpenes and triterpenes compounds in end-stage renal disease patients.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {377}, pmid = {39342083}, issn = {1471-2180}, support = {32170071//National Natural Science Foundation of China/ ; 32300051//National Natural Science Foundation of China/ ; 2022JJ40663//Natural Science Foundation of Hunan Province/ ; C2023045//Hunan Province Traditional Chinese Medicine Research Program Project/ ; }, mesh = {Humans ; *Kidney Failure, Chronic/therapy/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Peritoneal Dialysis ; *Sesquiterpenes/metabolism ; Male ; Female ; *Feces/microbiology ; Middle Aged ; *Triterpenes/metabolism ; Bacteria/metabolism/classification/genetics/isolation & purification ; Biosynthetic Pathways ; Adult ; Metagenomics ; Aged ; }, abstract = {The concept of the gut-kidney axis is gaining significant attention due to the close relationship between gut microbiota and kidney disease. Peritoneal dialysis is recognized as a crucial renal replacement therapy for end-stage renal disease (ESRD). The alterations in gut microbiota and related mechanisms after receiving this dialysis method are not fully understood. This study conducted shotgun metagenomic sequencing on fecal samples from 11 end-stage renal disease patients who did not receive dialysis (ESRD_N) and 7 patients who received peritoneal dialysis (ESRD_P). After quality control and correlation analysis of the data, our study is aimed at exploring the impact of peritoneal dialysis on the gut microbiota and health of ESRD patients. Our research findings indicate that the complexity and aggregation characteristics of gut microbiota interactions increase in ESRD_P. In addition, the gut microbiota drives the biosynthesis pathways of sesquiterpenes and triterpenes in ESRD_P patients, which may contribute to blood purification and improve circulation. Therefore, our research will lay the foundation for the prevention and treatment of ESRD.}, } @article {pmid39341403, year = {2024}, author = {Chen, X and Balliew, J and Bauer, CX and Deegan, J and Gitter, A and Hanson, BM and Maresso, AW and Tisza, MJ and Troisi, CL and Rios, J and Mena, KD and Boerwinkle, E and Wu, F}, title = {Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater.}, journal = {The Journal of infection}, volume = {89}, number = {5}, pages = {106284}, doi = {10.1016/j.jinf.2024.106284}, pmid = {39341403}, issn = {1532-2742}, mesh = {*Wastewater/virology ; *SARS-CoV-2/genetics/isolation & purification ; Humans ; *COVID-19/epidemiology/virology ; Texas/epidemiology ; Genome, Viral ; Evolution, Molecular ; Spike Glycoprotein, Coronavirus/genetics ; }, abstract = {OBJECTIVES: Rapid evolution of SARS-CoV-2 has resulted in the emergence of numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, has limitations in capturing the full epidemiological dynamics of circulating variants in the general population. This study aimed to monitor the SARS-CoV-2 variant community dynamics and evolution using receptor-binding domain (RBD) amplicon sequencing of wastewater samples.

METHODS: We sequenced wastewater from El Paso, Texas, over 17 months, compared the sequencing data with clinical genome data, and performed biodiversity analysis to reveal SARS-CoV-2 variant dynamics and evolution.

RESULTS: We identified 91 variants and observed waves of dominant variants transitioning from BA.2 to BA.2.12.1, BA.4&5, BQ.1, and XBB.1.5. Comparison with clinical genome sequencing data revealed earlier detection of variants and identification of unreported outbreaks. Our results also showed strong consistency with clinical data for dominant variants at the local, state, and national levels. Alpha diversity analyses revealed significant seasonal variations, with the highest diversity observed in winter. By segmenting the outbreak into lag, growth, stationary, and decline phases, we found higher variant diversity during the lag phase, likely due to lower inter-variant competition preceding outbreak growth.

CONCLUSIONS: Our findings underscore the importance of low transmission periods in facilitating rapid mutation and variant evolution. Our approach, integrating RBD amplicon sequencing with wastewater surveillance, demonstrates effectiveness in tracking viral evolution and understanding variant emergence, thus enhancing public health preparedness.}, } @article {pmid39341204, year = {2024}, author = {Takewaki, D and Kiguchi, Y and Masuoka, H and Manu, MS and Raveney, BJE and Narushima, S and Kurokawa, R and Ogata, Y and Kimura, Y and Sato, N and Ozawa, Y and Yagishita, S and Araki, T and Miyake, S and Sato, W and Suda, W and Yamamura, T}, title = {Tyzzerella nexilis strains enriched in mobile genetic elements are involved in progressive multiple sclerosis.}, journal = {Cell reports}, volume = {43}, number = {10}, pages = {114785}, doi = {10.1016/j.celrep.2024.114785}, pmid = {39341204}, issn = {2211-1247}, mesh = {Animals ; Humans ; *Encephalomyelitis, Autoimmune, Experimental/genetics/pathology ; Mice ; *Multiple Sclerosis/genetics/pathology/microbiology ; Female ; Interspersed Repetitive Sequences/genetics ; Male ; Gastrointestinal Microbiome/genetics ; Mice, Inbred C57BL ; Clostridiales/genetics ; Middle Aged ; Adult ; }, abstract = {Multiple sclerosis (MS) is an autoimmune-demyelinating disease with an inflammatory pathology formed by self-reactive lymphocytes with activated glial cells. Progressive MS, characterized by resistance to medications, significantly differs from the non-progressive form in gut microbiome profiles. After confirming an increased abundance of "Tyzzerella nexilis" in various cohorts of progressive MS, we identified a distinct cluster of T. nexilis strains enriched in progressive MS based on long-read metagenomics. The distinct T. nexilis cluster is characterized by a large number of mobile genetic elements (MGEs) and a lack of defense systems against MGEs. Microbial genes for sulfate reduction and flagella formation with pathogenic implications are specific to this cluster. Moreover, these flagellar genes are encoded on MGEs. Mono-colonization with MGE-enriched T. nexilis made germ-free mice more susceptible to experimental autoimmune encephalomyelitis. These results indicate that the progression of MS may be promoted by MGE-enriched T. nexilis with potentially pathogenic properties.}, } @article {pmid39341154, year = {2024}, author = {Gough, EK and Edens, TJ and Carr, L and Robertson, RC and Mutasa, K and Ntozini, R and Chasekwa, B and Geum, HM and Baharmand, I and Gill, SK and Mutasa, B and Mbuya, MNN and Majo, FD and Tavengwa, N and Francis, F and Tome, J and Evans, C and Kosek, M and Prendergast, AJ and Manges, AR and , }, title = {Bifidobacterium longum and microbiome maturation modify a nutrient intervention for stunting in Zimbabwean infants.}, journal = {EBioMedicine}, volume = {108}, number = {}, pages = {105362}, pmid = {39341154}, issn = {2352-3964}, mesh = {Humans ; Infant ; *Gastrointestinal Microbiome ; *Growth Disorders/prevention & control/microbiology ; Female ; Male ; Zimbabwe ; Fucosyltransferases/genetics ; Feces/microbiology ; Bifidobacterium ; Dietary Supplements ; Nutrients ; }, abstract = {BACKGROUND: Small-quantity lipid-based nutrient supplements (SQ-LNS), which has been widely tested to reduce child stunting, has largely modest effects to date, but the mechanisms underlying these modest effects are unclear. Child stunting is a longstanding indicator of chronic undernutrition and it remains a prevalent public health problem. The infant gut microbiome may be a key contributor to stunting; and mother and infant fucosyltransferase (FUT) phenotypes are important determinants of infant microbiome composition.

METHODS: We investigated whether mother-infant FUT status (n = 792) and infant gut microbiome composition (n = 354 fecal specimens from 172 infants) modified the impact of an infant and young child feeding (IYCF) intervention, that included SQ-LNS, on stunting at age 18 months in secondary analysis of a randomized trial in rural Zimbabwe.

FINDINGS: We found that the impact of the IYCF intervention on stunting was modified by: (i) mother-infant FUT2+/FUT3- phenotype (difference-in-differences -32.6% [95% CI: -55.3%, -9.9%]); (ii) changes in species composition that reflected microbiome maturation (difference-in-differences -68.1% [95% CI: -99.0%, -28.5%); and (iii) greater relative abundance of B. longum (differences-in-differences 49.1% [95% CI: 26.6%, 73.6%]). The dominant strains of B. longum when the intervention started were most similar to the proficient milk oligosaccharide utilizer subspecies infantis, which decreased with infant age and differed by mother-infant FUT2+/FUT3- phenotypes.

INTERPRETATION: These findings indicate that a persistently "younger" microbiome at initiation of the intervention reduced its benefits on stunting in areas with a high prevalence of growth restriction.

FUNDING: Bill and Melinda Gates Foundation, UK DFID/Aid, Wellcome Trust, Swiss Agency for Development and Cooperation, US National Institutes of Health, UNICEF, and Nutricia Research Foundation.}, } @article {pmid39340684, year = {2024}, author = {Vinothini, K and Nakkeeran, S and Saranya, N and Jothi, P and Richard, JI and Perveen, K and Bukhari, NA and Glick, BR and Sayyed, RZ and Mastinu, A}, title = {Rhizosphere Engineering of Biocontrol Agents Enriches Soil Microbial Diversity and Effectively Controls Root-Knot Nematodes.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {120}, pmid = {39340684}, issn = {1432-184X}, mesh = {Animals ; *Solanum lycopersicum/microbiology/parasitology ; *Soil Microbiology ; *Rhizosphere ; *Bacillus/genetics/physiology ; *Plant Roots/microbiology/parasitology ; *Pest Control, Biological ; Plant Diseases/parasitology/prevention & control/microbiology ; Trichoderma/physiology/genetics ; Tylenchoidea/physiology ; Microbiota ; Antinematodal Agents/pharmacology ; Biological Control Agents/pharmacology ; Bacteria/genetics/classification ; }, abstract = {The root-knot nematode (RKN) causes significant yield loss in tomatoes. Understanding the interaction of biocontrol agents (BCAs)-nematicides-soil microbiomes and RKNs is essential for enhancing the efficacy of biocontrol agents and nematicides to curb RKN damage to crops. The present study aimed to evaluate the in vitro effectiveness of BACa and nematicide against RKN and to apply the amplicon sequencing to assess the interaction of Bacillus velezensis (VB7) and Trichoderma koningiopsis (TK) against RKNs. Metagenomic analysis revealed the relative abundance of three phyla such as Proteobacteria (42.16%), Firmicutes (19.57%), and Actinobacteria (17.69%) in tomato rhizospheres. Those tomato rhizospheres treated with the combined application of B. velezensis VB7 + T. koningiopsis TK and RKN had a greater frequency of diversity and richness than the control. RKN-infested tomato rhizosphere drenched with bacterial and fungal antagonists had the maximum diversity index of bacterial communities. A strong correlation with a maximum number of interconnection edges in the phyla Proteobacteria, Firmicutes, and Actinobacteria was evident in soils treated with both B. velezensis VB7 and T. koningiopsis TK challenged against RKN in infected soil. The present study determined a much greater diversity of bacterial taxa observed in tomato rhizosphere soils treated with B. velezensis VB7 and T. koningiopsis TK than in untreated soil. It is suggested that the increased diversity and abundance of bacterial communities might be responsible for increased nematicidal properties in tomato plants. Hence, the combined applications of B. velezensis VB7 and T. koningiopsis TK can enhance the nematicidal action to curb RKN infecting tomatoes.}, } @article {pmid39340212, year = {2024}, author = {Avellaneda-Franco, L and Xie, L and Nakai, M and Barr, JJ and Marques, FZ}, title = {Dietary fiber intake impacts gut bacterial and viral populations in a hypertensive mouse model.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2407047}, pmid = {39340212}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Dietary Fiber/administration & dosage ; Mice ; Male ; *Hypertension/virology ; *Mice, Inbred C57BL ; *Bacteria/classification/genetics/isolation & purification ; *Bacteriophages/physiology/genetics ; *Disease Models, Animal ; Angiotensin II/metabolism ; Genome, Viral ; }, abstract = {The gut microbiome is an emerging factor in preventing hypertension, yet the influence of gut bacteriophages, viruses infecting bacteria, on this condition remains unclear. Bacteriophage-bacteria interactions, which impact the gut microbiome, are influenced differentially by temperate and virulent bacteriophages. However, the standard technique for studying viral populations, viral-like particles (VLPs)-metagenomes, often overlook prophages, the intracellular stage of temperate bacteriophages, creating a knowledge gap. To address this, we investigated alterations in extracellular and intracellular bacteriophages, alongside bacterial populations, in the angiotensin II-hypertension model. We sequenced VLPs and bulk DNA from cecal-colonic samples collected from male C57BL/6J mice implanted with minipumps containing saline or angiotensin II. We assembled 106 bacterial and 816 viral genomes and found that gut viral and bacterial populations remained stable between hypertensive and normotensive mice. A higher number of temperate viruses were observed across all treatments. Although temperate viruses outnumbered virulent viruses, sequencing of both VLPs and bulk revealed that virions from virulent viruses were more abundant in the murine gut. We then evaluated the impact of low- and high-fiber intake on gut microbiome composition in the angiotensin II model. Fiber intake significantly influenced the gut microbiome composition and hypertension development. Mice receiving high-fiber had lower blood pressure, a higher bacterial-encoded carbohydrate-associated enzyme, and a higher total relative abundance of temperate viruses than those receiving low-fiber. Our findings suggest that phages are not associated with hypertension development in the angiotensin II model. However, they support a complex diet-bacteria/phage interaction that may be involved in blood pressure regulation.}, } @article {pmid39338979, year = {2024}, author = {Opitz-Ríos, C and Burgos-Pacheco, A and Paredes-Cárcamo, F and Campanini-Salinas, J and Medina, DA}, title = {Metagenomics Insight into Veterinary and Zoonotic Pathogens Identified in Urban Wetlands of Los Lagos, Chile.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, pmid = {39338979}, issn = {2076-0817}, support = {11230295//Agencia Nacional de Investigación y Desarrollo/ ; VRID_FAPPE21-07//Universidad San Sebastián/ ; VRID_INTER23/02//Universidad San Sebastián/ ; VRID_DocI22/06//Universidad San Sebastián/ ; }, abstract = {Wetlands are ecosystems that are essential to ecological balance and biodiversity; nevertheless, human activity is a constant threat to them. Excess nutrients are caused by intensive livestock and agricultural operations, pollution, and population growth, which in turn leads to uncontrolled microbiological development. This impairment in water quality can constitute a risk to animal, human, and environmental health. To thoroughly characterize the microbial communities, shotgun metagenomics was used to characterize the taxonomic and functional pattern of microorganisms that inhabit urban wetlands in the Los Lagos Region of Chile. The main objective was to identify microorganisms of veterinary relevance, assess their potential antibiotic resistance, and characterize the main virulence mechanism. As expected, a high diversity of microorganisms was identified, including bacteria described as animal or human pathogens, such as Pasteurella multocida, Pseudomonas aeruginosa, Staphylococcus aureus, and Escherichia coli. Also, a diverse repertory of antimicrobial-resistant genes (ARGs) was detected in metagenomic assembled sequences and inside the sequence of mobile genetic elements, genes that confer mainly resistance to beta-lactams, consistent with the families of antibiotics most used in Chile. In addition, a diverse collection of virulence mechanisms was also identified. Given the significance of the relationship between environmental, animal, and human health-a concept known as One Health-there is a need to establish molecular surveillance programs that monitor the environmental biohazard elements using molecular tools. This work is the first report of the presence of these harmful biological elements in urban wetlands subjected to anthropogenic pressure, located in the south of Chile.}, } @article {pmid39338129, year = {2024}, author = {Mayer, MH and Woldemariam, S and Gisinger, C and Dorner, TE}, title = {Association of Gut Microbiome with Muscle Mass, Muscle Strength, and Muscle Performance in Older Adults: A Systematic Review.}, journal = {International journal of environmental research and public health}, volume = {21}, number = {9}, pages = {}, pmid = {39338129}, issn = {1660-4601}, mesh = {Aged ; Aged, 80 and over ; Humans ; *Gastrointestinal Microbiome/physiology ; *Muscle Strength/physiology ; *Muscle, Skeletal/physiology ; *Sarcopenia/microbiology/physiopathology ; }, abstract = {Sarcopenia, characterized by reduced muscle mass, strength, or performance, is a common condition in older adults. The association between the gut microbiome and sarcopenia remains poorly understood. This systematic review aims to evaluate the relationship between muscle parameters and the intestinal microbiome. A systematic search was conducted in PubMed, EMBASE, Cochrane Library, and Google Scholar for studies published between 2002 and 2022 involving participants aged 50+. Studies were included if they assessed sarcopenia using at least one measure of muscle mass (skeletal muscle mass, bioelectrical impedance analysis, MRI), muscle strength, or muscle performance (SARC-F questionnaire, Timed-Up-and-Go Test, Chair Stand Test, grip strength, gait speed, Short Physical Performance Battery, 400 m Walk Test). The microbiome was measured using at least RNA/DNA sequencing or shotgun metagenomic sequencing. Twelve studies were analyzed. Findings revealed that a higher abundance of bacterial species such as Desulfovibrio piger, and Clostridium symbiosum and reduced diversity of butyrate-producing bacteria was associated with sarcopenia severity, as indicated by decreased grip strength, muscle mass, or physical performance. The gut microbiome plays a significant role in age-related muscle loss. Probiotics, prebiotics, and bacterial products could be potential interventions to improve muscle health in older adults.}, } @article {pmid39334245, year = {2024}, author = {Van Herzele, C and Coppens, S and Vereecke, N and Theuns, S and de Graaf, DC and Nauwynck, H}, title = {New insights into honey bee viral and bacterial seasonal infection patterns using third-generation nanopore sequencing on honey bee haemolymph.}, journal = {Veterinary research}, volume = {55}, number = {1}, pages = {118}, pmid = {39334245}, issn = {1297-9716}, support = {1SB3123N//Fonds Wetenschappelijk Onderzoek/ ; Baekeland mandate HBC.2020.2889//Agentschap Innoveren en Ondernemen/ ; }, mesh = {Animals ; Bees/virology/microbiology ; *Seasons ; *Hemolymph/virology/microbiology ; Nanopore Sequencing/methods/veterinary ; Bacteria/genetics/isolation & purification/classification ; Virome ; }, abstract = {Honey bees are rapidly declining, which poses a significant threat to our environment and agriculture industry. These vital insects face a disease complex believed to be caused by a combination of parasites, viruses, pesticides, and nutritional deficiencies. However, the real aetiology is still enigmatic. Due to the conventional analysis methods, we still lack complete insights into the honey bee virome and the presence of pathogenic bacteria. To fill this knowledge gap, we employed third-generation nanopore metagenomic sequencing on honey bee haemolymph to monitor the presence of pathogens over almost a year. This study provides valuable insights into the changes in bacterial and viral loads within honey bee colonies. We identified different pathogens in the honey bee haemolymph, which are not included in honey bee screenings. These pathogens comprise the Apis mellifera filamentous virus, Apis rhabdoviruses, and various bacteria such as Frischella sp. and Arsenophonus sp. Furthermore, a sharp contrast was observed between young and old bees. Our research proposes that transgenerational immune priming may play a role in shaping infection patterns in honey bees. We observed a significant increase in pathogen loads in the spring, followed by a notable decrease in pathogen presence during the summer and autumn months. However, certain pathogens seem to be able to evade this priming effect, making them particularly intriguing as potential factors contributing to mortality. In the future, we aim to expand our research on honey bee transgenerational immune priming and investigate its potential in natural settings. This knowledge will ultimately enhance honey bee health and decrease colony mortality.}, } @article {pmid39333778, year = {2024}, author = {Msango, K and Gouda, MNR and Ramakrishnan, B and Kumar, A and Subramanian, S}, title = {Variation and functional profile of gut bacteria in the scarab beetle, Anomala dimidiata, under a cellulose-enriched microenvironment.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {22400}, pmid = {39333778}, issn = {2045-2322}, mesh = {Animals ; *Coleoptera/microbiology ; *Cellulose/metabolism ; *Gastrointestinal Microbiome ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Larva/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Symbiosis ; }, abstract = {This study utilized cultivable methods and 16 S amplicon sequencing to compare taxonomic profiles and functional potential of gut bacteria in the scarab beetle, Anomola dimidiata, under cellulose-enriched conditions. Eight culturable cellulolytic gut bacteria were isolated from the midgut and hindgut of the scarab larvae, respectively. 16 S amplicon sequencing evinced that the most represented taxonomic profiles at phylum level in the fermentation chamber and midgut were Bacillota (71.62 and 56.76%), Pseudomonadota (22.66 and 36.89%) and Bacteroidota (2.7 and 2.81%). Bacillota (56.74 and 91.39%) were significantly enriched in the midgut with the addition of cellulose. In contrast, Bacillota and Psedomonadota were significantly enriched in the fermentation chamber. Carbohydrate metabolism was up-regulated in the midgut, while nitrogen and phosphorus metabolism were up-regulated in the fermentation chamber, suggesting these symbionts' possible metabolic roles to the host. An analysis of total cellulases as well as amplicon sequence variants indicated that the gut bacteria belonging to Acinetobacter, Bacillus, Brucella, Brevibacillus, Enterobacter, Lysinibacillus and Paenibacillus are involved in nutrition provisioning. These results have provided additional insights into the gut bacteria associated with cellulose digestion in A. dimidiata and created a platform for bioprospecting novel isolates to produce biomolecules for biotechnological use, besides identifying eco-friendly targets for its management.}, } @article {pmid39333734, year = {2024}, author = {Ishak, S and Rondeau-Leclaire, J and Faticov, M and Roy, S and Laforest-Lapointe, I}, title = {Boreal moss-microbe interactions are revealed through metagenome assembly of novel bacterial species.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {22168}, pmid = {39333734}, issn = {2045-2322}, mesh = {*Bryophyta/microbiology ; *Bacteria/genetics/metabolism/classification ; *Metagenome ; Taiga ; Metagenomics/methods ; Microbiota ; Quebec ; Nitrogen Fixation ; Photosynthesis ; }, abstract = {Moss-microbe interactions contribute to ecosystem processes in boreal forests. Yet, how host-specific characteristics and the environment drive the composition and metabolic potential of moss microbiomes is still poorly understood. In this study, we use shotgun metagenomics to identify the taxonomy and metabolic potential of the bacteria of four moss species of the boreal forests of Northern Québec, Canada. To characterize moss bacterial community composition and diversity, we assembled the genomes of 110 potentially novel bacterial species. Our results highlight that moss genus, species, gametophyte section, and to a lesser extent soil pH and soil temperature, drive moss-associated bacterial community composition and diversity. In the brown gametophyte section, two Stigonema spp. showed partial pathway completeness for photosynthesis and nitrogen fixation, while all brown-associated Hyphomicrobiales had complete assimilatory nitrate reduction pathways and many nearly complete carbon fixation pathways. Several brown-associated species showed partial to complete pathways for coenzyme M and F420 biosynthesis, important for methane metabolism. In addition, green-associated Hyphomicrobiales (Methylobacteria spp.) displayed potential for the anoxygenic photosystem II pathway. Overall, our findings demonstrate how host-specific characteristics and environmental factors shape the composition and metabolic potential of moss bacteria, highlighting their roles in carbon fixation, nitrogen cycling, and methane metabolism in boreal forests.}, } @article {pmid39333577, year = {2024}, author = {Zhao, B and Zi, M and Zhang, X and Wang, Y}, title = {Microbial communities and metagenomes in methane-rich deep coastal sediments.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1043}, pmid = {39333577}, issn = {2052-4463}, support = {U22B2012//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Microbiota ; *Metagenome ; *Archaea/genetics ; *RNA, Ribosomal, 16S/genetics ; Phylogeny ; }, abstract = {Coastal sediments are rich in embedded recalcitrant organic carbons that are biotransformed into methane. In this study, gas composition (carbon dioxide, methane and nitrogen) and chemical indicators (total nitrogen, total carbon, and total sulfate) were examined in five deep sediment cores (up to 130 m in length) obtained from the Hangzhou Bay. The V3-V4 region of the 16S rRNA gene amplicons was amplified and sequenced for the prokaryotic community analysis. The species composition, along with the physicochemical factors of the sediments, revealed a strong correlation with methane content in one of the sediment cores. We then obtained metagenomes of the two sediment samples selected for their high methane content and enrichment of methanogenic Bathyarchaeota with phylogenetic evidence. A total of 27 draft genomes were retrieved through metagenomic binning methodologies and were classified into Bathyarchaeota, Asgard archaea, Planctomycetes, and other microbial groups. The data provided are valuable for understanding the relationship between methane generation and microbial community composition in deep sediment core samples from coastal to marine environments.}, } @article {pmid39333527, year = {2024}, author = {Cheng, M and Xu, Y and Cui, X and Wei, X and Chang, Y and Xu, J and Lei, C and Xue, L and Zheng, Y and Wang, Z and Huang, L and Zheng, M and Luo, H and Leng, Y and Jiang, C}, title = {Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8361}, pmid = {39333527}, issn = {2041-1723}, mesh = {Humans ; *Critical Illness ; *Microbiota/genetics ; *Intensive Care Units ; *Metagenome/genetics ; Metagenomics/methods ; Longitudinal Studies ; Male ; Female ; Plasmids/genetics ; Genome, Bacterial/genetics ; Respiratory System/microbiology ; Aged ; Middle Aged ; Bacteria/genetics/classification/isolation & purification ; Pneumonia/microbiology ; Evolution, Molecular ; }, abstract = {The lower respiratory tract (LRT) microbiome impacts human health, especially among critically ill patients. However, comprehensive characterizations of the LRT microbiome remain challenging due to low microbial mass and host contamination. We develop a chelex100-based low-biomass microbial-enrichment method (CMEM) that enables deep metagenomic profiling of LRT samples to recover near-complete microbial genomes. We apply the method to 453 longitudinal LRT samples from 157 intensive care unit (ICU) patients in three geographically distant hospitals. We recover 120 high-quality metagenome-assembled genomes (MAGs) and associated plasmids without culturing. We detect divergent longitudinal microbiome dynamics and hospital-specific dominant opportunistic pathogens and resistomes in pneumonia patients. Diagnosed pneumonia and the ICU stay duration were associated with the abundance of specific antibiotic-resistance genes (ARGs). Moreover, CMEM can serve as a robust tool for genome-resolved analyses. MAG-based analyses reveal strain-specific resistome and virulome among opportunistic pathogen strains. Evolutionary analyses discover increased mobilome in prevailing opportunistic pathogens, highly conserved plasmids, and new recombination hotspots associated with conjugative elements and prophages. Integrative analysis with epidemiological data reveals frequent putative inter-patient strain transmissions in ICUs. In summary, we present a genome-resolved functional, transmission, and evolutionary landscape of the LRT microbiota in critically ill patients.}, } @article {pmid39333204, year = {2024}, author = {Martin Říhová, J and Gupta, S and Nováková, E and Hypša, V}, title = {Fur microbiome as a putative source of symbiotic bacteria in sucking lice.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {22326}, pmid = {39333204}, issn = {2045-2322}, support = {GA20-07674S//Grantová Agentura České Republiky/ ; }, mesh = {Animals ; *Symbiosis ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Phthiraptera/microbiology ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {Symbiosis between insects and bacteria has been established countless times. While it is well known that the symbionts originated from a variety of different bacterial taxa, it is usually difficult to determine their environmental source and a route of their acquisition by the host. In this study, we address this question using a model of Neisseriaceae symbionts in rodent lice. These bacteria established their symbiosis independently with different louse taxa (Polyplax, Hoplopleura, Neohaematopinus), most likely from the same environmental source. We first applied amplicon analysis to screen for candidate source bacterium in the louse environment. Since lice are permanent ectoparasites, often specific to the particular host, we screened various microbiomes associated with three rodent species (Microtus arvalis, Clethrionomys glareolus, and Apodemus flavicollis). The analyzed samples included fur, skin, spleen, and other ectoparasites sampled from these rodents. The fur microbiome data revealed a Neisseriaceae bacterium, closely related to the known louse symbionts. The draft genomes of the environmental Neisseriaceae, assembled from all three rodent hosts, converged to a remarkably small size of approximately 1.4 Mbp, being even smaller than the genomes of the related symbionts. Our results suggest that the rodent fur microbiome can serve as a source for independent establishment of bacterial symbiosis in associated louse species. We further propose a hypothetical scenario of the genome evolution during the transition of a free-living bacterium to the member of the rodent fur-associated microbiome and subsequently to the facultative and obligate louse symbionts.}, } @article {pmid39333145, year = {2024}, author = {Boie, W and Schemmel, M and Ye, W and Hasler, M and Goll, M and Verreet, JA and Cai, D}, title = {An assessment of the species diversity and disease potential of Pythium communities in Europe.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8369}, pmid = {39333145}, issn = {2041-1723}, support = {031B0910-A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 221NR-058B//Fachagentur Nachwachsende Rohstoffe (Agency for Renewable Resources)/ ; }, mesh = {*Pythium/genetics/isolation & purification ; Europe ; *Plant Diseases/microbiology ; *Zea mays/microbiology ; Soil Microbiology ; Biodiversity ; Metagenomics/methods ; }, abstract = {Pythium sensu lato (s.l.) is a genus of parasitic oomycetes that poses a serious threat to agricultural production worldwide, but their severity is often neglected because little knowledge about them is available. Using an internal transcribed spacer (ITS) amplicon-based-metagenomics approach, we investigate the occurrence, abundance, and diversity of Pythium spp. s.l. in 127 corn fields of 11 European countries from the years 2019 to 2021. We also identify 73 species, with up to 20 species in a single soil sample, and the prevalent species, which show high species diversity, varying disease potential, and are widespread in most countries. Further, we show species-species co-occurrence patterns considering all detected species and link species abundance to soil parameter using the LUCAS topsoil dataset. Infection experiments with recovered isolates show that Pythium s.l. differ in disease potential, and that effective interference with plant hormone networks suppressing JA (jasmonate)-mediated defenses is an essential component of the virulence mechanism of Pythium s.l. species. This study provides a valuable dataset that enables deep insights into the structure and species diversity of Pythium s.l. communities in European corn fields and knowledge for better understanding plant-Pythium interactions, facilitating the development of an effective strategy to cope with this pathogen.}, } @article {pmid39331712, year = {2024}, author = {Fellows, RC and Chun, SK and Larson, N and Fortin, BM and Mahieu, AL and Song, WA and Seldin, MM and Pannunzio, NR and Masri, S}, title = {Disruption of the intestinal clock drives dysbiosis and impaired barrier function in colorectal cancer.}, journal = {Science advances}, volume = {10}, number = {39}, pages = {eado1458}, pmid = {39331712}, issn = {2375-2548}, support = {R01 CA244519/CA/NCI NIH HHS/United States ; R01 CA259370/CA/NCI NIH HHS/United States ; R01 CA276470/CA/NCI NIH HHS/United States ; R37 CA266042/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Colorectal Neoplasms/microbiology/metabolism/pathology ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Mice ; *Circadian Clocks/genetics ; Intestinal Mucosa/metabolism/microbiology ; Disease Models, Animal ; Humans ; Permeability ; }, abstract = {Diet is a robust entrainment cue that regulates diurnal rhythms of the gut microbiome. We and others have shown that disruption of the circadian clock drives the progression of colorectal cancer (CRC). While certain bacterial species have been suggested to play driver roles in CRC, it is unknown whether the intestinal clock impinges on the microbiome to accelerate CRC pathogenesis. To address this, genetic disruption of the circadian clock, in an Apc-driven mouse model of CRC, was used to define the impact on the gut microbiome. When clock disruption is combined with CRC, metagenomic sequencing identified dysregulation of many bacterial genera including Bacteroides, Helicobacter, and Megasphaera. We identify functional changes to microbial pathways including dysregulated nucleic acid, amino acid, and carbohydrate metabolism, as well as disruption of intestinal barrier function. Our findings suggest that clock disruption impinges on microbiota composition and intestinal permeability that may contribute to CRC pathogenesis.}, } @article {pmid39331699, year = {2024}, author = {Yang, Z and Shan, Y and Liu, X and Chen, G and Pan, Y and Gou, Q and Zou, J and Chang, Z and Zeng, Q and Yang, C and Kong, J and Sun, Y and Li, S and Zhang, X and Wu, WC and Li, C and Peng, H and Holmes, EC and Guo, D and Shi, M}, title = {VirID: Beyond Virus Discovery-An Integrated Platform for Comprehensive RNA Virus Characterization.}, journal = {Molecular biology and evolution}, volume = {41}, number = {10}, pages = {}, pmid = {39331699}, issn = {1537-1719}, support = {82341118//National Natural Science Foundation of China/ ; 2022A1515011854//Natural Science Foundation of Guangdong Province of China/ ; JCYJ20210324124414040//Shenzhen Science and Technology Program/ ; //Hong Kong Innovation and Technology Fund (ITF/ ; GZNL2023A01001//Major Project of Guangzhou National Laboratory/ ; 2019ZT08Y464//Guangdong Province "Pearl River Talent Plan" Innovation, Entrepreneurship Team Project/ ; ZDSYS20220606100803007//Fund of Shenzhen Key Laboratory/ ; GNT2017197//NHMRC (Australia) Investigator Award/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; }, mesh = {*RNA Viruses/genetics ; *Software ; *Metagenomics/methods ; *Phylogeny ; Humans ; RNA-Dependent RNA Polymerase/genetics ; Computational Biology/methods ; }, abstract = {RNA viruses exhibit vast phylogenetic diversity and can significantly impact public health and agriculture. However, current bioinformatics tools for viral discovery from metagenomic data frequently generate false positive virus results, overestimate viral diversity, and misclassify virus sequences. Additionally, current tools often fail to determine virus-host associations, which hampers investigation of the potential threat posed by a newly detected virus. To address these issues we developed VirID, a software tool specifically designed for the discovery and characterization of RNA viruses from metagenomic data. The basis of VirID is a comprehensive RNA-dependent RNA polymerase database to enhance a workflow that includes RNA virus discovery, phylogenetic analysis, and phylogeny-based virus characterization. Benchmark tests on a simulated data set demonstrated that VirID had high accuracy in profiling viruses and estimating viral richness. In evaluations with real-world samples, VirID was able to identify RNA viruses of all types, but also provided accurate estimations of viral genetic diversity and virus classification, as well as comprehensive insights into virus associations with humans, animals, and plants. VirID therefore offers a robust tool for virus discovery and serves as a valuable resource in basic virological studies, pathogen surveillance, and early warning systems for infectious disease outbreaks.}, } @article {pmid39329490, year = {2024}, author = {Maday, SDM and Kingsbury, JM and Weaver, L and Pantos, O and Wallbank, JA and Doake, F and Masterton, H and Hopkins, M and Dunlop, R and Gaw, S and Theobald, B and Risani, R and Abbel, R and Smith, D and Handley, KM and Lear, G}, title = {Taxonomic variation, plastic degradation, and antibiotic resistance traits of plastisphere communities in the maturation pond of a wastewater treatment plant.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {10}, pages = {e0071524}, pmid = {39329490}, issn = {1098-5336}, support = {C03X1802//Ministry of Business, Innovation and Employment (MBIE)/ ; }, mesh = {*Plastics ; *Wastewater/microbiology ; *Ponds/microbiology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Biodegradation, Environmental ; *RNA, Ribosomal, 16S/genetics ; Biofilms/drug effects/growth & development ; Microbiota/drug effects ; Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid ; Water Pollutants, Chemical/analysis ; Water Purification ; }, abstract = {Wastewater treatment facilities can filter out some plastics before they reach the open environment, yet microplastics often persist throughout these systems. As they age, microplastics in wastewater may both leach and sorb pollutants and fragment to provide an increased surface area for bacterial attachment and conjugation, possibly impacting antimicrobial resistance (AMR) traits. Despite this, little is known about the effects of persistent plastic pollution on microbial functioning. To address this knowledge gap, we deployed five different artificially weathered plastic types and a glass control into the final maturation pond of a municipal wastewater treatment plant in Ōtautahi-Christchurch, Aotearoa/New Zealand. We sampled the plastic-associated biofilms (plastisphere) at 2, 6, 26, and 52 weeks, along with the ambient pond water, at three different depths (20, 40, and 60 cm from the pond water surface). We investigated the changes in plastisphere microbial diversity and functional potential through metagenomic sequencing. Bacterial 16S ribosomal RNA genes composition did not vary among plastic types and glass controls (P = 0.997) but varied among sampling times [permutational multivariate analysis of variance (PERMANOVA), P = 0.001] and depths (PERMANOVA, P = 0.011). Overall, there was no polymer-substrate specificity evident in the total composition of genes (PERMANOVA, P = 0.67), but sampling time (PERMANOVA, P = 0.002) and depth were significant factors (PERMANOVA, P = 0.001). The plastisphere housed diverse AMR gene families, potentially influenced by biofilm-meditated conjugation. The plastisphere also harbored an increased abundance of genes associated with the biodegradation of nylon, or nylon-associated substances, including nylon oligomer-degrading enzymes and hydrolases.IMPORTANCEPlastic pollution is pervasive and ubiquitous. Occurrences of plastics causing entanglement or ingestion, the leaching of toxic additives and persistent organic pollutants from environmental plastics, and their consequences for marine macrofauna are widely reported. However, little is known about the effects of persistent plastic pollution on microbial functioning. Shotgun metagenomics sequencing provides us with the necessary tools to examine broad-scale community functioning to further investigate how plastics influence microbial communities. This study provides insight into the functional consequence of continued exposure to waste plastic by comparing the prokaryotic functional potential of biofilms on five types of plastic [linear low-density polyethylene (LLDPE), nylon-6, polyethylene terephthalate, polylactic acid, and oxygen-degradable LLDPE], glass, and ambient pond water over 12 months and at different depths (20, 40, and 60 cm) within a tertiary maturation pond of a municipal wastewater treatment plant.}, } @article {pmid39329142, year = {2024}, author = {Khomutovska, N and Jasser, I and Sarapultseva, P and Spirina, V and Zaitsev, A and Masłowiecka, J and Isidorov, VA}, title = {Seasonal dynamics in leaf litter decomposing microbial communities in temperate forests: a whole-genome- sequencing-based study.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17769}, pmid = {39329142}, issn = {2167-8359}, mesh = {*Plant Leaves/microbiology/metabolism ; *Forests ; *Seasons ; *Microbiota/genetics/physiology ; Bacteria/genetics/classification/metabolism ; Fungi/genetics/classification/metabolism/isolation & purification ; Whole Genome Sequencing ; Metagenome/genetics ; Trees/microbiology ; }, abstract = {Leaf litter decomposition, a crucial component of the global carbon cycle, relies on the pivotal role played by microorganisms. However, despite their ecological importance, leaf-litter-decomposing microorganism taxonomic and functional diversity needs additional study. This study explores the taxonomic composition, dynamics, and functional role of microbial communities that decompose leaf litter of forest-forming tree species in two ecologically unique regions of Europe. Twenty-nine microbial metagenomes isolated from the leaf litter of eight forest-forming species of woody plants were investigated by Illumina technology using read- and assembly-based approaches of sequences analysis. The taxonomic structure of the microbial community varies depending on the stage of litter decomposition; however, the community's core is formed by Pseudomonas, Sphingomonas, Stenotrophomonas, and Pedobacter genera of Bacteria and by Aureobasidium, Penicillium, Venturia genera of Fungi. A comparative analysis of the taxonomic structure and composition of the microbial communities revealed that in both regions, seasonal changes in structure take place; however, there is no clear pattern in its dynamics. Functional gene analysis of MAGs revealed numerous metabolic profiles associated with leaf litter degradation. This highlights the diverse metabolic capabilities of microbial communities and their implications for ecosystem processes, including the production of volatile organic compounds (VOCs) during organic matter decomposition. This study provides important advances in understanding of ecosystem processes and the carbon cycle, underscoring the need to unravel the intricacies of microbial communities within these contexts.}, } @article {pmid39327897, year = {2024}, author = {Dai, Z and Wang, H and Xu, J and Lu, X and Ni, P and Yang, S and Shen, Q and Wang, X and Li, W and Wang, X and Zhou, C and Zhang, W and Shan, T}, title = {Unveiling the Virome of Wild Birds: Exploring CRESS-DNA Viral Dark Matter.}, journal = {Genome biology and evolution}, volume = {16}, number = {10}, pages = {}, pmid = {39327897}, issn = {1759-6653}, support = {2023YFD1801301//National Key Research and Development Programs of China/ ; 82341106//National Natural Science Foundation of China/ ; 20229152//The Special Funds for Science Development of the Clinical Teaching Hospitals of Jiangsu Vocational College of Medicine/ ; }, mesh = {Animals ; *Birds/virology ; *Virome/genetics ; *DNA Viruses/genetics/classification ; Phylogeny ; Animals, Wild/virology ; Metagenomics ; DNA, Viral/genetics ; }, abstract = {Amid global health concerns and the constant threat of zoonotic diseases, this study delves into the diversity of circular replicase-encoding single-stranded DNA (CRESS-DNA) viruses within Chinese wild bird populations. Employing viral metagenomics to tackle the challenge of "viral dark matter," the research collected and analyzed 3,404 cloacal swab specimens across 26 bird families. Metagenomic analysis uncovered a rich viral landscape, with 67.48% of reads classified as viral dark matter, spanning multiple taxonomic levels. Notably, certain viral families exhibited host-specific abundance patterns, with Galliformes displaying the highest diversity. Diversity analysis categorized samples into distinct groups, revealing significant differences in viral community structure, particularly noting higher diversity in terrestrial birds compared to songbirds and unique diversity in migratory birds versus perching birds. The identification of ten novel Circoviridae viruses, seven Smacoviridae viruses, and 167 Genomoviridae viruses, along with 100 unclassified CRESS-DNA viruses, underscores the expansion of knowledge on avian-associated circular DNA viruses. Phylogenetic and structural analyses of Rep proteins offered insights into evolutionary relationships and potential functional variations among CRESS-DNA viruses. In conclusion, this study significantly enhances our understanding of the avian virome, shedding light on the intricate relationships between viral communities and host characteristics in Chinese wild bird populations. The diverse array of CRESS-DNA viruses discovered opens avenues for future research into viral evolution, spread factors, and potential ecosystem impacts.}, } @article {pmid39327438, year = {2024}, author = {Schmartz, GP and Rehner, J and Gund, MP and Keller, V and Molano, LG and Rupf, S and Hannig, M and Berger, T and Flockerzi, E and Seitz, B and Fleser, S and Schmitt-Grohé, S and Kalefack, S and Zemlin, M and Kunz, M and Götzinger, F and Gevaerd, C and Vogt, T and Reichrath, J and Diehl, L and Hecksteden, A and Meyer, T and Herr, C and Gurevich, A and Krug, D and Hegemann, J and Bozhueyuek, K and Gulder, TAM and Fu, C and Beemelmanns, C and Schattenberg, JM and Kalinina, OV and Becker, A and Unger, M and Ludwig, N and Seibert, M and Stein, ML and Hanna, NL and Martin, MC and Mahfoud, F and Krawczyk, M and Becker, SL and Müller, R and Bals, R and Keller, A}, title = {Decoding the diagnostic and therapeutic potential of microbiota using pan-body pan-disease microbiomics.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8261}, pmid = {39327438}, issn = {2041-1723}, mesh = {Humans ; *Microbiota/genetics ; *Metagenome/genetics ; *Metagenomics/methods ; Bacteria/genetics/isolation & purification/classification ; Feces/microbiology ; Male ; Female ; Multigene Family ; Saliva/microbiology ; Adult ; }, abstract = {The human microbiome emerges as a promising reservoir for diagnostic markers and therapeutics. Since host-associated microbiomes at various body sites differ and diseases do not occur in isolation, a comprehensive analysis strategy highlighting the full potential of microbiomes should include diverse specimen types and various diseases. To ensure robust data quality and comparability across specimen types and diseases, we employ standardized protocols to generate sequencing data from 1931 prospectively collected specimens, including from saliva, plaque, skin, throat, eye, and stool, with an average sequencing depth of 5.3 gigabases. Collected from 515 patients, these samples yield an average of 3.7 metagenomes per patient. Our results suggest significant microbial variations across diseases and specimen types, including unexpected anatomical sites. We identify 583 unexplored species-level genome bins (SGBs) of which 189 are significantly disease-associated. Of note, the existence of microbial resistance genes in one specimen was indicative of the same resistance genes in other specimens of the same patient. Annotated and previously undescribed SGBs collectively harbor 28,315 potential biosynthetic gene clusters (BGCs), with 1050 significant correlations to diseases. Our combinatorial approach identifies distinct SGBs and BGCs, emphasizing the value of pan-body pan-disease microbiomics as a source for diagnostic and therapeutic strategies.}, } @article {pmid39327429, year = {2024}, author = {Schmartz, GP and Rehner, J and Schuff, MJ and Molano, LG and Becker, SL and Krawczyk, M and Tagirdzhanov, A and Gurevich, A and Francke, R and Müller, R and Keller, V and Keller, A}, title = {Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8263}, pmid = {39327429}, issn = {2041-1723}, support = {469073465//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Animals ; *Animals, Wild/microbiology ; *Animals, Zoo/microbiology ; *Gastrointestinal Microbiome/genetics ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/genetics/drug effects ; Bacteria/genetics/metabolism/classification/drug effects ; Multigene Family ; Humans ; Biodiversity ; Drug Resistance, Bacterial/genetics ; Vancomycin/pharmacology ; Biosynthetic Pathways/genetics ; }, abstract = {Understanding human, animal, and environmental microbiota is essential for advancing global health and combating antimicrobial resistance (AMR). We investigate the oral and gut microbiota of 48 animal species in captivity, comparing them to those of wildlife animals. Specifically, we characterize the microbiota composition, metabolic pathways, AMR genes, and biosynthetic gene clusters (BGCs) encoding the production of specialized metabolites. Our results reveal a high diversity of microbiota, with 585 novel species-level genome bins (SGBs) and 484 complete BGCs identified. Functional gene analysis of microbiomes shows diet-dependent variations. Furthermore, by comparing our findings to wildlife-derived microbiomes, we observe the impact of captivity on the animal microbiome, including examples of converging microbiome compositions. Importantly, our study identifies AMR genes against commonly used veterinary antibiotics, as well as resistance to vancomycin, a critical antibiotic in human medicine. These findings underscore the importance of the 'One Health' approach and the potential for zoonotic transmission of pathogenic bacteria and AMR. Overall, our study contributes to a better understanding of the complexity of the animal microbiome and highlights its BGC diversity relevant to the discovery of novel antimicrobial compounds.}, } @article {pmid39327011, year = {2024}, author = {Ruff, SE and Schwab, L and Vidal, E and Hemingway, JD and Kraft, B and Murali, R}, title = {Widespread occurrence of dissolved oxygen anomalies, aerobic microbes, and oxygen-producing metabolic pathways in apparently anoxic environments.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {11}, pages = {}, pmid = {39327011}, issn = {1574-6941}, support = {RGEC34/2023//Human Frontier Science Program/ ; 824763//Simons Foundation/ ; 946150/ERC_/European Research Council/International ; }, mesh = {*Oxygen/metabolism ; *Metabolic Networks and Pathways ; Groundwater/microbiology ; Phylogeny ; Bacteria/metabolism/genetics/classification ; Ecosystem ; Anaerobiosis ; }, abstract = {Nearly all molecular oxygen (O2) on Earth is produced via oxygenic photosynthesis by plants or photosynthetically active microorganisms. Light-independent O2 production, which occurs both abiotically, e.g. through water radiolysis, or biotically, e.g. through the dismutation of nitric oxide or chlorite, has been thought to be negligible to the Earth system. However, recent work indicates that O2 is produced and consumed in dark and apparently anoxic environments at a much larger scale than assumed. Studies have shown that isotopically light O2 can accumulate in old groundwaters, that strictly aerobic microorganisms are present in many apparently anoxic habitats, and that microbes and metabolisms that can produce O2 without light are widespread and abundant in diverse ecosystems. Analysis of published metagenomic data reveals that the enzyme putatively capable of nitric oxide dismutation forms four major phylogenetic clusters and occurs in at least 16 bacterial phyla, most notably the Bacteroidota. Similarly, a re-analysis of published isotopic signatures of dissolved O2 in groundwater suggests in situ production in up to half of the studied environments. Geochemical and microbiological data support the conclusion that "dark oxygen production" is an important and widespread yet overlooked process in apparently anoxic environments with far-reaching implications for subsurface biogeochemistry and ecology.}, } @article {pmid39326312, year = {2025}, author = {Wang, X and Cui, J and Gu, Z and Guo, L and Liu, R and Guo, Y and Qin, N and Yang, Y}, title = {Aged garlic oligosaccharides modulate host metabolism and gut microbiota to alleviate high-fat and high-cholesterol diet-induced atherosclerosis in ApoE[-/-] mice.}, journal = {Food chemistry}, volume = {463}, number = {Pt 3}, pages = {141409}, doi = {10.1016/j.foodchem.2024.141409}, pmid = {39326312}, issn = {1873-7072}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Atherosclerosis/metabolism/microbiology/drug therapy ; Mice ; *Oligosaccharides/pharmacology/administration & dosage/metabolism ; *Diet, High-Fat/adverse effects ; Male ; *Apolipoproteins E/genetics/metabolism ; *Garlic/chemistry ; Mice, Inbred C57BL ; Bacteria/isolation & purification/classification/genetics/metabolism/drug effects ; Humans ; Mice, Knockout ; Fatty Acids, Volatile/metabolism ; Feces/microbiology/chemistry ; }, abstract = {Atherosclerosis (AS) is a cardiovascular disease caused by excessive accumulation of lipids in arterial walls. In this study, we developed an AS model in ApoE[-/-] mice using a high-fat, high-cholesterol diet and investigated the anti-AS mechanism of aged garlic oligosaccharides (AGOs) by focusing on the gut microbiota. Results revealed that AGOs exhibited significant anti-AS effects, reduced trimethylamine N-oxide levels from 349.9 to 189.2 ng/mL, and reduced aortic lipid deposition from 31.7 % to 9.5 %. AGOs significantly increased the levels of short-chain fatty acids in feces, in which acetic, propionic, and butyric acids were increased from 1.580, 0.364, and 0.469 mg/g to 2.233, 0.774, and 0.881 mg/g, respectively. An analysis of the gut microbiota indicated that AGOs restored alpha and beta diversity, decreased the Firmicutes/Bacteroidetes ratio, and promoted the dominance of the genus Akkermansia. A metagenomic analysis revealed that AGOs alleviated AS through the ABC transporter pathway and the lipopolysaccharide biosynthesis pathway.}, } @article {pmid39324818, year = {2024}, author = {Li, F and Jia, M and Chen, H and Chen, M and Su, R and Usman, S and Ding, Z and Hao, L and Franco, M and Guo, X}, title = {Responses of microbial community composition and CAZymes encoding gene enrichment in ensiled Elymus nutans to altitudinal gradients in alpine region.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {10}, pages = {e0098624}, pmid = {39324818}, issn = {1098-5336}, support = {U20A2002//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Altitude ; *Silage/microbiology/analysis ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification ; *Elymus/microbiology/genetics ; Fermentation ; Tibet ; Acetic Acid/metabolism ; }, abstract = {UNLABELLED: High-throughput metagenomic sequence technology was employed to evaluate changes in microbial community composition and carbohydrate-active enzymes encoding gene enrichment status in Elymus nutans silages to altitudinal gradients in the world's highest alpine region of Qinghai-Tibetan Plateau (QTP). E. nutans were collected from three different altitudes in QTP: 2,600 m (low altitude), 3600 m (moderate altitude), and 4,600 m [high (H) altitude], and ensiled for 7, 14, 30, and 60 d. Results indicated an improvement in silage quality with the increasing altitude, although the acetic acid concentration and dry matter loss were greater in H altitude silages after 30 d of ensiling. Harmful bacteria or potential pathogens predominated in the microbial community on d 7 and 14 of fermentation, while genera belonging to lactic acid bacteria gradually became the main microorganisms with the increasing altitude on d 30 and 60 of ensiling. The abundance of carbohydrate-active enzymes genes responsible for macromolecular carbohydrate degradation in silage increased with increasing altitude, and those genes were mainly carried by Lactiplantibacillus and Pediococcus at 30 and 60 d of ensiling. The abundance of key enzymatic genes associated with glycolysis and organic acid production in carbohydrate metabolism pathway was higher in H altitude silages, and Lactiplantibacillus and Pediococcus were also the main hosts after 30 d of silage fermentation, except for the fact that acetic acid production was also related to genera Leuconostoc, Latilactobacillus, and Levilactobacillus.

IMPORTANCE: The fermentation quality of Elymus nutans silage was getting better with the increase of altitude in the Qinghai-Tibetan Plateau. The abundance of hosts carrying carbohydrate-active enzymes genes and key enzyme genes related to organic acid production increased with increasing altitude during the later stages of fermentation. Lactiplantibacillus and Pediococcus were the core microorganisms responsible for both polysaccharide hydrolysis and silage fermentation in the late stage of ensiling. This study provided insights on the influence of different altitudes on the composition and function of silage microbiome in the Qinghai-Tibetan Plateau, and provided a reference approach for improving the quality and controllability of silage production in high altitude areas of the Qinghai-Tibetan Plateau.}, } @article {pmid39324627, year = {2024}, author = {Bigatton, ED and Verdenelli, RA and Haro, RJ and Ayoub, I and Barbero, FM and Martín, MP and Dubini, LE and Jorrín Novo, JV and Lucini, EI and Castillejo, MÁ}, title = {Metagenomic Analysis to Assess the Impact of Plant Growth-Promoting Rhizobacteria on Peanut (Arachis hypogaea L.) Crop Production and Soil Enzymes and Microbial Diversity.}, journal = {Journal of agricultural and food chemistry}, volume = {72}, number = {40}, pages = {22385-22397}, pmid = {39324627}, issn = {1520-5118}, mesh = {*Arachis/microbiology/growth & development/metabolism/genetics ; *Soil Microbiology ; *Bacillus/genetics/metabolism ; *Bradyrhizobium/genetics/metabolism/growth & development/physiology ; *Pseudomonas/genetics/physiology/growth & development ; *Metagenomics ; *Rhizosphere ; *Soil/chemistry ; Crop Production/methods ; Bacteria/genetics/classification/metabolism/enzymology/isolation & purification ; Biodiversity ; Nitrogen Fixation ; Plant Roots/microbiology/growth & development/metabolism ; }, abstract = {Peanut production could be increased through plant growth-promoting rhizobacteria (PGPR). In this regard, the present field research aimed at elucidating the impact of PGPR on peanut yield, soil enzyme activity, microbial diversity, and structure. Three PGPR strains (Bacillus velezensis, RI3; Bacillus velezensis, SC6; Pseudomonas psychrophila, P10) were evaluated, along with Bradyrhizobium japonicum (BJ), taken as a control. PGPR increased seed yield by 8%, improving the radiation use efficiency (4-14%). PGPR modified soil enzymes (fluorescein diacetate activity by 17% and dehydrogenase activity by 28%) and microbial abundance (12%). However, PGPR did not significantly alter microbial diversity; nonetheless, it modified the relative abundance of key phyla (Actinobacteria > Proteobacteria > Firmicutes) and genera (Bacillus > Arthrobacter > Pseudomonas). PGPRs modified the relative abundance of genes associated with N-fixation and nitrification while increasing genes related to N-assimilation and N-availability. PGPR improved agronomic traits without altering rhizosphere diversity.}, } @article {pmid39322959, year = {2024}, author = {Wirbel, J and Essex, M and Forslund, SK and Zeller, G}, title = {A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {247}, pmid = {39322959}, issn = {1474-760X}, mesh = {Humans ; *Microbiota ; *Benchmarking ; RNA, Ribosomal, 16S/genetics ; Computer Simulation ; }, abstract = {BACKGROUND: In microbiome disease association studies, it is a fundamental task to test which microbes differ in their abundance between groups. Yet, consensus on suitable or optimal statistical methods for differential abundance testing is lacking, and it remains unexplored how these cope with confounding. Previous differential abundance benchmarks relying on simulated datasets did not quantitatively evaluate the similarity to real data, which undermines their recommendations.

RESULTS: Our simulation framework implants calibrated signals into real taxonomic profiles, including signals mimicking confounders. Using several whole meta-genome and 16S rRNA gene amplicon datasets, we validate that our simulated data resembles real data from disease association studies much more than in previous benchmarks. With extensively parametrized simulations, we benchmark the performance of nineteen differential abundance methods and further evaluate the best ones on confounded simulations. Only classic statistical methods (linear models, the Wilcoxon test, t-test), limma, and fastANCOM properly control false discoveries at relatively high sensitivity. When additionally considering confounders, these issues are exacerbated, but we find that adjusted differential abundance testing can effectively mitigate them. In a large cardiometabolic disease dataset, we showcase that failure to account for covariates such as medication causes spurious association in real-world applications.

CONCLUSIONS: Tight error control is critical for microbiome association studies. The unsatisfactory performance of many differential abundance methods and the persistent danger of unchecked confounding suggest these contribute to a lack of reproducibility among such studies. We have open-sourced our simulation and benchmarking software to foster a much-needed consolidation of statistical methodology for microbiome research.}, } @article {pmid39322110, year = {2024}, author = {Liu, K and Li, Y and Ge, Z and Huang, D and Zhang, J}, title = {Microbial communities and mobile genetic elements determine the variations of antibiotic resistance genes for a continuous year in the urban river deciphered by metagenome assembly.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {362}, number = {}, pages = {125018}, doi = {10.1016/j.envpol.2024.125018}, pmid = {39322110}, issn = {1873-6424}, mesh = {*Rivers/microbiology/chemistry ; *Drug Resistance, Microbial/genetics ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics ; Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Environmental Monitoring/methods ; }, abstract = {Antibiotic resistance genes (ARGs) have become emerging environmental contaminants influenced by intricate regulatory factors. However, there is a lack of comprehensive studies on the evolution and distribution of ARGs over a full year in urban rivers, which serve as significant reservoirs of ARGs due to dynamic human activities. In this study, we conducted a 12-month metagenomic assembly to explore the microbial communities, ARGs, mobile genetic elements (MGEs) coexisting with ARGs, ARGs hosts, and the impact of environmental factors. Bacitracin (32%-47%) and multidrug (13%-24%) were detected throughout the year, constituting over 60% of the total abundance, making them the primary ARGs types. The assembly mechanisms of microbial communities and ARGs were primarily driven by stochastic processes. Integrase, IntI1, recombinase, and transposase were identified as the main MGEs coexisting with ARGs. Procrustes analysis revealed a significant structural association, indicating that the composition of host communities likely plays crucial roles in the seasonal composition and distribution of ARGs. Human pathogenic bacteria (HPBs) were identified in the summer, autumn, and winter, with Escherichia coli, Klebsiella pneumoniae, Acinetobacter lwoffii, and Burkholderiales bacterium being the primary HPBs. Mantle tests and PLS-PM equation analysis indicated that microbial communities and MGEs are the most critical factors determining the distribution and composition of ARGs in the river. Environmental factors (including water properties and nutrients) and ARGs hosts influence the evolution and abundance of ARGs by directly regulating microbial communities and MGEs. This study provides critical insights into risk assessment and management of ARGs in urban rivers.}, } @article {pmid39320367, year = {2024}, author = {Kayser, E and He, F and Nixon, S and Howard-Varona, A and Lamelas, A and Martinez-Blanch, J and Chenoll, E and Davenport, GM and de Godoy, MRC}, title = {Effects of supplementation of live and heat-treated Bifidobacterium animalis subspecies lactis CECT 8145 on glycemic and insulinemic response, fecal microbiota, systemic biomarkers of inflammation, and white blood cell gene expression of adult dogs.}, journal = {Journal of animal science}, volume = {102}, number = {}, pages = {}, pmid = {39320367}, issn = {1525-3163}, mesh = {Animals ; Dogs ; *Bifidobacterium animalis ; *Feces/microbiology/chemistry ; *Probiotics/pharmacology/administration & dosage ; Male ; Female ; *Diet/veterinary ; Dietary Supplements/analysis ; Animal Feed/analysis ; Biomarkers/blood ; Inflammation/veterinary ; Gastrointestinal Microbiome ; Blood Glucose ; Leukocytes/metabolism ; Hot Temperature ; Insulin/blood/metabolism ; Gene Expression ; }, abstract = {The popularity of functional ingredients such as probiotics and postbiotics has increased as pet owners seek ways to improve the health quality and longevity of their pets. Limited research has been conducted regarding the use of probiotics and postbiotics and their effects on canine health. The objective of this study was to evaluate the effects of daily supplementation of Bifidobacterium animalis subsp. lactis CECT 8145, in both live probiotic (PRO) and heat-treated postbiotic (POST) forms, on fecal fermentative end-products and microbiome, insulin sensitivity, serum gut hormones, oxidative stress, inflammatory biomarkers, and white blood cell gene expression of adult dogs. Eighteen adult beagles and 18 adult English pointers were used in a double-blinded placebo-controlled parallel group design, with 12 animals per group (6 English pointers and 6 beagles). The study began with a 60 d adaptation period followed by a 90 d period of daily supplementation with either PRO, POST, or placebo (maltodextrin; CON). Longitudinal assessment of body weight, body condition score, and pelvic circumference did not differ among dietary supplements (P > 0.05). Throughout the experimental period, fecal scores did not differ (P > 0.05); however, fecal pH was lower (P = 0.0049) in the dogs fed POST compared with CON. A higher fecal concentration of propionate (P = 0.043) was observed in dogs fed PRO and POST when compared with CON. While PRO and POST supplementation were associated with changes in bacterial composition at the family and genus level, the overall richness and diversity of the microbiome were not significantly affected. Functional analysis of the metagenome also suggests that PRO and POST supplementation induced potentially beneficial changes in the abundance of pathways involved in pathogenicity, amino acid biosynthesis, and DNA repair. No differences in glycemic or insulinemic responses were observed among the groups (P > 0.05). Dogs supplemented with PRO had a higher (P < 0.05) mean white blood cell leptin relative fold gene expression compared with groups POST and CON. Serum metabolites and complete blood cell counts were within normal ranges and all dogs remained healthy throughout the study. Together, these data suggest that the PRO and POST can safely be supplemented for dogs. Moreover, the results of this study support further investigation of the role of PRO and POST in supporting parameters related to gut health and hormonal regulation.}, } @article {pmid39320101, year = {2024}, author = {Xue, H and Wang, Y and Mei, C and Han, L and Lu, M and Li, X and Chen, T and Wang, F and Tang, X}, title = {Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP).}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0083924}, pmid = {39320101}, issn = {2379-5077}, mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; Male ; Case-Control Studies ; *Metabolome ; Humans ; *Lactose Intolerance/microbiology ; Rats ; Female ; Adult ; Fecal Microbiota Transplantation ; Rats, Sprague-Dawley ; Middle Aged ; }, abstract = {UNLABELLED: Lactose intolerance (LI) is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption. Recent evidence suggests that the gut microbiome may influence lactose levels in the gut. However, there is limited understanding regarding the alterations in microbiota and metabolism between individuals with LI and non-LI. This study conducted a paired-sample investigation utilizing data from the American Gut Project (AGP) and performed metagenomic and untargeted metabolomic analyses in a Chinese cohort to explore the interaction between the gut microbiome and serum metabolites. In addition, fecal microbiota transplantation (FMT) experiments were conducted to further examine the impact of the LI-associated gut microbiome on inflammatory outcomes. We identified 14 microbial genera that significantly differed between LI and controls from AGP data. Using a machine learning approach, group separation was predicted based on seven species and nine metabolites in the Chinese cohort. Notably, increased levels of Escherichia coli in the LI group were negatively correlated with several metabolites, including PC (22:6/0:0), indole, and Lyso PC, while reduced levels of Faecalibacterium prausnitzii and Eubacterium rectale were positively correlated with indole and furazolidone. FMT-LI rats displayed visceral hypersensitivity and an altered gut microbiota composition compared to FMT-HC rats. Metagenomic and metabolomic analyses revealed an enrichment of MAPK signaling in LI, which was confirmed by FMT-LI rats showing higher expression of ERK and RAS, along with increased concentrations of proinflammatory cytokines. This study provides valuable insights into the disrupted microbial and metabolic traits associated with LI, emphasizing potential microbiome-based approaches for its prevention and treatment.

IMPORTANCE: Lactose intolerance (LI) is a prevalent condition characterized by gastrointestinal symptoms after lactose consumption due to a deficiency of lactase. There is limited understanding regarding the microbiota and metabolic alterations between individuals with LI and non-LI. This study represents the first exploration to investigate metagenomic and metabolomic signatures among subjects with lactose intolerance as far as our knowledge. We identified 14 microbial genera in the Western cohort and 7 microbial species, along with 9 circulating metabolites in the Chinese cohort, which significantly differed in LI patients. Metagenomic and metabolomic analyses revealed an enrichment of MAPK signaling in LI patients. This finding was confirmed by FMT-LI rats, exhibiting increased expression of ERK and RAS, along with higher concentrations of pro-inflammatory cytokines. Our study provides insights into the disrupted functional and metabolic traits of the gut microbiome in LI, highlighting potential microbiome-based approaches for preventing and treating LI.}, } @article {pmid39319624, year = {2025}, author = {Shi, Q and Fu, Q and Zhang, J and Hao, G and Liang, C and Duan, F and Ma, J and Zhao, H and Song, W}, title = {Paenibacillus polymyxa J2-4 induces cucumber to enrich rhizospheric Pseudomonas and contributes to Meloidogyne incognita management under field conditions.}, journal = {Pest management science}, volume = {81}, number = {1}, pages = {266-276}, doi = {10.1002/ps.8429}, pmid = {39319624}, issn = {1526-4998}, support = {2023YFD1400400//National Key R&D Program of China/ ; 2022CXGC020710-6//Subproject of Shandong Province Key R&D Plan Project/ ; QNYCX23027//Qingdao Agricultural University Graduate Student Innovation Program/ ; QNYCX24076//Qingdao Agricultural University Graduate Student Innovation Program/ ; }, mesh = {*Tylenchoidea/physiology ; Animals ; *Paenibacillus polymyxa/genetics/physiology ; *Pseudomonas/physiology ; *Rhizosphere ; *Cucumis sativus/microbiology/parasitology ; *Plant Diseases/prevention & control/parasitology/microbiology ; Soil Microbiology ; Pest Control, Biological ; Microbiota ; }, abstract = {BACKGROUND: Root knot nematodes (RKNs) pose a great threat to agricultural production worldwide. The bacterial nematocides have received increasing attention due to their safe and efficient control against RKNs. Here, we investigated the biocontrol efficacy of Paenibacillus polymyxa J2-4 against Meloidogyne incognita in the field and analyzed the rhizosphere microbiome of cucumber under nematode infection after application of the J2-4 strain. Furthermore, a biomarker strain of Pseudomonas spp. was isolated from the J2-4-inoculated rhizosphere soil, and its nematocidal activity and growth-promoting effect on host plants were determined. In addition, chemotaxis assay of P. fluroescens ZJ5 toward root exudates was carried out.

RESULTS: The field experiment demonstrated that P. polymyxa J2-4 could effectively suppressed gall formation in cucumber plants, with the galling index reduced by 67.63% in 2022 and 65.50% in 2023, respectively, compared with controls. Meanwhile, plant height and yield were significantly increased in J2-4 treated plants compared with controls. Metagenomic analysis indicated that J2-4 altered the rhizosphere microbial communities. The relative abundance of Pseudomonas spp. was notably enhanced in the J2-4 group, which was consistent with Linear discriminant analysis Effect Size results that Pseudomonas was determined as one of the biomarkers in the J2-4 group. Furthermore, the ZJ5 strain, one of the biomarker Pseudomonas strains, was isolated from the J2-4-inoculated rhizosphere soil and was identified as Pseudomonas fluorescens. In addition, P. fluorescens ZJ5 exhibited high nematicidal activity in vitro and in vivo, with 99.20% of the mortality rate of M. incognita at 24 h and 69.75% of gall index reduction. The biocontrol efficiency of the synthetic community of ZJ5 plus J2-4 was superior to that of any other single bacteria against M. incognita. Additionally, ZJ5 exhibited great chemotaxis ability toward root exudates inoculated with J2-4.

CONCLUSION: Paenibacillus polymyxa J2-4 has good potential in the biological control against M. incognita under field conditions. Enrichment of the beneficial bacteria Pseudomonas fluorescens ZJ5 in the J2-4-inoculated rhizosphere soil contributes to M. incognita management. © 2024 Society of Chemical Industry.}, } @article {pmid39316987, year = {2024}, author = {Yang, H and Liu, Y and Cao, G and Liu, J and Xiao, S and Xiao, P and Tao, Y and Gao, H}, title = {Effects of lycopene on the growth performance, meat quality, cecal metagenome, and hepatic untargeted metabolome in heat stressed broilers.}, journal = {Poultry science}, volume = {103}, number = {12}, pages = {104299}, pmid = {39316987}, issn = {1525-3171}, mesh = {Animals ; *Chickens/physiology/growth & development ; *Animal Feed/analysis ; *Diet/veterinary ; *Meat/analysis ; *Liver/drug effects/metabolism ; *Lycopene/pharmacology/administration & dosage ; *Cecum/microbiology/drug effects/metabolism ; *Dietary Supplements/analysis ; *Metabolome/drug effects ; Male ; Metagenome ; Random Allocation ; Gastrointestinal Microbiome/drug effects ; Heat-Shock Response/drug effects ; }, abstract = {The occurrence of heat stress in poultry houses is inevitable and leads to oxidative stress in the birds. Lycopene, a natural hydrocarbon carotenoid, possesses potent antioxidant properties. This study aimed to investigate the impact of lycopene on growth performance, meat quality, cecal microflora, and liver metabolome in broilers subjected to heat stress. A total of 480 yellow feather broilers were randomly allocated into 4 treatment groups: birds fed standard diet (Con), birds fed standard diet and supplemented with lycopene (Lyc), birds fed standard diet and subjected to heat stress (Hs), and birds fed with lycopene and subjected to heat stress (Hs-Lyc). As compared with the normal temperature groups, Hs decreased the average daily gain (ADG) of birds during d 1 to 28, lowered the pH value either in breast meat or thigh meat, increased the L* value of breast meat, and decreased the a* value of thigh meat. In comparison with non-Lyc feeding birds, Lyc supplement elevated the ADG during d 1 to 56, increased the pH of breast meat, decrease the L* and b* values of thigh meat, simultaneously increase the a* value of thigh meat. The L* of breast meat and pH of thigh meat exhibited significant differences under Hs-Lyc treatment. Lyc-treated birds exhibited higher elasticity, gumminess, and resilience in breast meat than those in non-Lyc feeding birds. The cecal metagenome analysis indicated that Hs-Lyc treatment increased the abundance of Phocaeicola salanitronis and Prevotella sp.CAG:1058, Bacteroides sp.An269, and Bacteroides sp.An19 at the species level compared with other treatments. The hepatic untargeted metabolome analysis showed that administration of Lyc upregulated 20 metabolites and downregulated 60 metabolites compared to the Con birds. Futhermore, the Hs-Lyc treatment upregulated 34 metabolites and downregulated 45 metabolites compared to the Hs birds. The correlation between the metagenome and metabolome showed that Lyc supplementation induced significant alterations in the citrate cycle, metabolism of butanoate, glycolysis/gluconeogenesis, glyoxylate and dicarboxylate, alanine, aspartate, and glutamate compared with standard supplement. In contrast, Hs-Lyc treatment induced alterations in the citrate cycle, metabolism of pyruvate, glyoxylate, and dicarboxylate, glycolysis/gluconeogenesis, arginine, proline, alanine, aspartate, and glutamate compared with the standard supplement of heat-challenged broilers. In summary, dietary Lyc supplementation promoted the growth performance, changed the meat quality, modulated the cecal metagenome and hepatic metabolome in heat-stressed broilers.}, } @article {pmid39315850, year = {2024}, author = {Yao, G and Zhang, X and Zhang, T and Jin, J and Qin, Z and Ren, X and Wang, X and Zhang, S and Yin, X and Tian, Z and Zhang, Y and Zhang, J and Wang, Z and Zhang, Q}, title = {The role of dysbiotic gut mycobiota in modulating risk for abdominal aortic aneurysm.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0177624}, pmid = {39315850}, issn = {2165-0497}, support = {2021YFA1301102//MOST | National Key Research and Development Program of China (NKPs)/ ; 82170495, 82070820, 82370481//MOST | National Natural Science Foundation of China (NSFC)/ ; ZR2023ZD58//SDMOST|Natural Science Foundation of Shandong Province（SDNSF）/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Animals ; *Aortic Aneurysm, Abdominal/microbiology/pathology ; Mice ; Male ; *Feces/microbiology ; Female ; Aged ; Fungi/isolation & purification/classification/genetics/physiology ; Saccharomyces cerevisiae/genetics ; Mycobiome ; Mice, Inbred C57BL ; Candida/isolation & purification/genetics/physiology/pathogenicity ; Metagenomics ; }, abstract = {UNLABELLED: Abdominal aortic aneurysm (AAA) is a large-vessel disease with high mortality, characterized by complex pathogenic mechanisms. Current therapeutic approaches remain insufficient to halt its progression. Fungi are important members of the gut microbiota. However, their characteristic alterations and roles in AAA remain unclear. This study investigated the role of gut fungal communities in the development of AAA through metagenomic sequencing of fecal samples from 31 healthy individuals and 33 AAA patients. We observed significant dysbiosis in the gut mycobiomes of AAA patients compared to healthy individuals, characterized by an increase in pathogenic fungi like Candida species and a decrease in beneficial yeasts such as Saccharomyces cerevisiae. The changes in fungal populations correlated strongly with clinical indicators of AAA, highlighting their potential for diagnosing and predicting AAA progression. Furthermore, our animal experiments demonstrated that Saccharomyces cerevisiae significantly ameliorated pathological alterations in AAA mice, suggesting a protective role for specific yeast strains against AAA development. These findings underscore the significant impact of gut mycobiomes on AAA and suggest that modulating these fungal communities could offer a novel therapeutic approach. Our research advances the understanding of the influence of gut microbiome on vascular diseases and suggests potential non-surgical approaches for managing AAA. By elucidating the diagnostic and therapeutic potential of gut fungi in AAA, this study provided important clues for future clinical strategies and therapeutic developments in the field of vascular medicine.

IMPORTANCE: Our research highlights the crucial role of gut fungi in abdominal aortic aneurysm (AAA) development. By analyzing fecal samples from AAA patients and healthy controls, we discovered significant dysbiosis in gut fungal communities, characterized by an increase in harmful Candida species and a decrease in beneficial yeasts like Saccharomyces cerevisiae. This dysbiosis was correlated with the severity of AAA. Importantly, in animal experiments, supplementing with Saccharomyces cerevisiae significantly slowed AAA progression. These findings suggest that modulating gut fungi may offer a novel, non-surgical approach to the diagnosis and treatment of AAA, potentially reducing the need for invasive procedures.}, } @article {pmid39315792, year = {2024}, author = {Gu Liu, C and Thompson, BE and Chang, JD and Min, L and Maresso, AW}, title = {Construction and characterization of DNA libraries from cultured phages and environmental viromes.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {10}, pages = {e0117124}, pmid = {39315792}, issn = {1098-5336}, support = {VA I01-RX002595//U.S. Department of Veterans Affairs (VA)/ ; //The Mike Hogg Foundation/ ; I01 RX002595/RX/RRD VA/United States ; Roderick D. MacDonald Research Fund//Baylor St. Luke's Medical Center/ ; Levy-Longenbaugh fund//Baylor College of Medicine/ ; Seed Funds to TAILΦR//Baylor College of Medicine (BCM)/ ; }, mesh = {*Gene Library ; *Bacteriophages/genetics/isolation & purification/classification ; *Metagenomics ; Virome/genetics ; Wastewater/virology/microbiology ; Seawater/virology/microbiology ; DNA, Viral/genetics ; High-Throughput Nucleotide Sequencing ; Genome, Viral ; Fresh Water/virology/microbiology ; Escherichia coli/genetics/virology ; }, abstract = {Despite many efforts to understand and leverage the functional potential of environmental viromes, most bacteriophage genes are largely uncharacterized. To explore novel biology from uncultivated microbes like phages, metagenomics has emerged as a powerful tool to directly mine new genes without the need to culture the diverse microbiota and the viruses within. When a pure computational approach cannot infer gene function, it may be necessary to create a DNA library from environmental genomic DNA, followed by the screening of that library for a particular function. However, these screens are often initiated without a metagenomic analysis of the completed DNA library being reported. Here, we describe the construction and characterization of DNA libraries from a single cultured phage (ΦT4), five cultured Escherichia coli phages, and three metagenomic viral sets built from freshwater, seawater, and wastewater samples. Through next-generation sequencing of five independent samplings of the libraries, we found a consistent number of recovered genes per replicate for each library, with many genes classifiable via the KEGG and Pharokka databases. By characterizing the size of the genes and inserts, we found that our libraries contain a median of one to two genes per contig with a median gene length of 303-381 bp for all libraries, reflective of the small genomes of viruses. The environmental libraries were genetically diverse compared to the single phage and multi-phage libraries. Additionally, we found reduced coverage of individual genomes when five phages were used as opposed to one. Taken together, this work provides a comprehensive analysis of the DNA libraries from phage genomes that can be used for metagenomic exploration and functional screens to infer and identify new biology.IMPORTANCEFunctional metagenomics is an approach that aims to characterize the putative biological function of genes in the microbial world. This includes an examination of the sequencing data collected from a pooled source of diverse microbes and inference of gene function by comparison to annotated and studied genes from public databases. At times, DNA libraries are made from these genes, and the library is screened for a specific function. Hits are validated using a combination of biological, computational, and structural analysis. Left unresolved is a detailed characterization of the library, both its diversity and content, for the purposes of imputing function entirely by computational means, a process that may yield findings that aid in designing useful screens to identify novel gene functions. In this study, we constructed libraries from cultured phages and uncultured viromes from the environment and characterized some important parameters, such as gene number, genes per contig, ratio of hypothetical to known proteins, total genomic coverage and recovery, and the effect of pooling genetic information from multiple sources, to provide a better understanding of the nature of these libraries. This work will aid the design and implementation of future screens of pooled DNA libraries to discover and isolate viral genes with novel biology across various biomes.}, } @article {pmid39315779, year = {2024}, author = {Rajeev, M and Jung, I and Kang, I and Cho, J-C}, title = {Genome-centric metagenomics provides insights into the core microbial community and functional profiles of biofloc aquaculture.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0078224}, pmid = {39315779}, issn = {2379-5077}, support = {KIMST-20210646//Korea Institute of Marine Science and Technology promotion (KIMST)/ ; NRF-2022R1A2C3008502,NRF-2018R1A5A1025077//National Research Foundation of Korea (NRF)/ ; }, mesh = {*Aquaculture ; *Metagenomics/methods ; Animals ; *Microbiota/genetics ; Bacteria/genetics/metabolism/classification ; Archaea/genetics/metabolism/classification ; Metagenome ; Phylogeny ; Penaeidae/microbiology/genetics ; }, abstract = {UNLABELLED: Bioflocs are microbial aggregates that play a pivotal role in shaping animal health, gut microbiota, and water quality in biofloc technology (BFT)-based aquaculture systems. Despite the worldwide application of BFT in aquaculture industries, our comprehension of the community composition and functional potential of the floc-associated microbiota (FAB community; ≥3 µm size fractions) remains rudimentary. Here, we utilized genome-centric metagenomic approach to investigate the FAB community in shrimp aquaculture systems, resulting in the reconstruction of 520 metagenome-assembled genomes (MAGs) spanning both bacterial and archaeal domains. Taxonomic analysis identified Pseudomonadota and Bacteroidota as core community members, with approximately 93% of recovered MAGs unclassified at the species level, indicating a large uncharacterized phylogenetic diversity hidden in the FAB community. Functional annotation of these MAGs unveiled their complex carbohydrate-degrading potential and involvement in carbon, nitrogen, and sulfur metabolisms. Specifically, genomic evidence supported ammonium assimilation, autotrophic nitrification, denitrification, dissimilatory nitrate reduction to ammonia, thiosulfate oxidation, and sulfide oxidation pathways, suggesting the FAB community's versatility for both aerobic and anaerobic metabolisms. Conversely, genes associated with heterotrophic nitrification, anaerobic ammonium oxidation, assimilatory nitrate reduction, and sulfate reduction were undetected. Members of Rhodobacteraceae emerged as the most abundant and metabolically versatile taxa in this intriguing community. Our MAGs compendium is expected to expand the available genome collection from such underexplored aquaculture environments. By elucidating the microbial community structure and metabolic capabilities, this study provides valuable insights into the key biogeochemical processes occurring in biofloc aquacultures and the major microbial contributors driving these processes.

IMPORTANCE: Biofloc technology has emerged as a sustainable aquaculture approach, utilizing microbial aggregates (bioflocs) to improve water quality and animal health. However, the specific microbial taxa within this intriguing community responsible for these benefits are largely unknown. Compounding this challenge, many bacterial taxa resist laboratory cultivation, hindering taxonomic and genomic analyses. To address these gaps, we employed metagenomic binning approach to recover over 500 microbial genomes from floc-associated microbiota of biofloc aquaculture systems operating in South Korea and China. Through taxonomic and genomic analyses, we deciphered the functional gene content of diverse microbial taxa, shedding light on their potential roles in key biogeochemical processes like nitrogen and sulfur metabolisms. Notably, our findings underscore the taxa-specific contributions of microbes in aquaculture environments, particularly in complex carbon degradation and the removal of toxic substances like ammonia, nitrate, and sulfide.}, } @article {pmid39313592, year = {2024}, author = {Hemapriya, M and Nataraja, KN and Suryanarayanan, TS and Uma Shaanker, R}, title = {Comparative Metagenomic Analysis of Seed Endobiome of Domesticated and Wild Finger Millet Species (Eleusine spp.): Unveiling Microbial Diversity and Composition.}, journal = {Current microbiology}, volume = {81}, number = {11}, pages = {373}, pmid = {39313592}, issn = {1432-0991}, mesh = {*Seeds/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics ; *Eleusine/microbiology/genetics ; *Domestication ; *Microbiota ; Biodiversity ; Fungi/classification/genetics/isolation & purification ; }, abstract = {Domestication, which involves selective breeding, modern agricultural practices, and specific growing conditions, can influence the microbial and endophytic communities in crop plants. In this study, we examined the microbial diversity and community composition in the seeds of wild and domesticated finger millet species. We employed a metagenomic approach to investigate the seed microbial diversity and community composition of wild (Eleusine africana) and domesticated finger millet species (Eleusine coracana (L.) Gaertn) grown in the same habitat. While our findings indicated no significant change in seed endobiome diversity due to domestication, there were differences in microbial community composition between wild and domesticated species. Seeds of domesticated species had higher relative abundance of certain bacterial genera including Helicobacter, Akkermansia, Streptococcus, Bacteroides, and Pseudomonas, whereas seeds of wild species had higher relative abundance of unclassified Streptophyta. The seed-associated microbiota also varied among domesticated finger millet accessions. Co-occurrence network analysis revealed a strong relationship between bacteria and fungi in domesticated compared to wild species. We discuss the results obtained in the larger context of the importance of seed endobiome and how domestication processes in crop plants may have impacted the seed endobiome diversity, composition, and function compared to their wild counterparts.}, } @article {pmid39313228, year = {2024}, author = {Kirtipal, N and Seo, Y and Son, J and Lee, S}, title = {Systems Biology of Human Microbiome for the Prediction of Personal Glycaemic Response.}, journal = {Diabetes & metabolism journal}, volume = {48}, number = {5}, pages = {821-836}, pmid = {39313228}, issn = {2233-6087}, support = {//Ministry of Science ICT/ ; 2021R1C1C1006336//National Research Foundation of Korea/ ; 2021M3A9G8022959//National Research Foundation of Korea/ ; RS-2024-00419699//National Research Foundation of Korea/ ; //Korea Health Industry Development Institute/ ; HR22C141105//Ministry of Health and Welfare/ ; 2024-ER2108-00//Korea National Institute of Health/ ; 2024-ER0608-00//Korea National Institute of Health/ ; //GIST Research Institute/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Precision Medicine/methods ; *Systems Biology/methods ; Machine Learning ; Dysbiosis ; Blood Glucose/analysis ; Diabetes Mellitus/microbiology ; Diabetes Mellitus, Type 2/microbiology ; Hypoglycemic Agents/therapeutic use ; }, abstract = {The human gut microbiota is increasingly recognized as a pivotal factor in diabetes management, playing a significant role in the body's response to treatment. However, it is important to understand that long-term usage of medicines like metformin and other diabetic treatments can result in problems, gastrointestinal discomfort, and dysbiosis of the gut flora. Advanced sequencing technologies have improved our understanding of the gut microbiome's role in diabetes, uncovering complex interactions between microbial composition and metabolic health. We explore how the gut microbiota affects glucose metabolism and insulin sensitivity by examining a variety of -omics data, including genomics, transcriptomics, epigenomics, proteomics, metabolomics, and metagenomics. Machine learning algorithms and genome-scale modeling are now being applied to find microbiological biomarkers associated with diabetes risk, predicted disease progression, and guide customized therapy. This study holds promise for specialized diabetic therapy. Despite significant advances, some concerns remain unanswered, including understanding the complex relationship between diabetes etiology and gut microbiota, as well as developing user-friendly technological innovations. This mini-review explores the relationship between multiomics, precision medicine, and machine learning to improve our understanding of the gut microbiome's function in diabetes. In the era of precision medicine, the ultimate goal is to improve patient outcomes through personalized treatments.}, } @article {pmid39311770, year = {2024}, author = {Zhou, B and Wang, C and Putzel, G and Hu, J and Liu, M and Wu, F and Chen, Y and Pironti, A and Li, H}, title = {An integrated strain-level analytic pipeline utilizing longitudinal metagenomic data.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0143124}, pmid = {39311770}, issn = {2165-0497}, support = {R01 CA159036/CA/NCI NIH HHS/United States ; R01CA204113//HHS | National Institutes of Health (NIH)/ ; P20 CA252728/CA/NCI NIH HHS/United States ; R01 LM014085/LM/NLM NIH HHS/United States ; P20CA252728,R01LM014085//HHS | National Institutes of Health (NIH)/ ; R01 CA204113/CA/NCI NIH HHS/United States ; R01 CA164964/CA/NCI NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; Humans ; Longitudinal Studies ; Software ; Microbiota/genetics ; Polymorphism, Single Nucleotide ; High-Throughput Nucleotide Sequencing ; Metagenome ; Gastrointestinal Microbiome/genetics ; Bacteria/genetics/classification/isolation & purification ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; }, abstract = {UNLABELLED: With the development of sequencing technology and analytic tools, studying within-species variations enhances the understanding of microbial biological processes. Nevertheless, most existing methods designed for strain-level analysis lack the capability to concurrently assess both strain proportions and genome-wide single nucleotide variants (SNVs) across longitudinal metagenomic samples. In this study, we introduce LongStrain, an integrated pipeline for the analysis of large-scale metagenomic data from individuals with longitudinal or repeated samples. In LongStrain, we first utilize two efficient tools, Kraken2 and Bowtie2, for the taxonomic classification and alignment of sequencing reads, respectively. Subsequently, we propose to jointly model strain proportions and shared haplotypes across samples within individuals. This approach specifically targets tracking a primary strain and a secondary strain for each subject, providing their respective proportions and SNVs as output. With extensive simulation studies of a microbial community and single species, our results demonstrate that LongStrain is superior to two genotyping methods and two deconvolution methods across a majority of scenarios. Furthermore, we illustrate the potential applications of LongStrain in the real data analysis of The Environmental Determinants of Diabetes in the Young study and a gastric intestinal metaplasia microbiome study. In summary, the proposed analytic pipeline demonstrates marked statistical efficiency over the same type of methods and has great potential in understanding the genomic variants and dynamic changes at strain level. LongStrain and its tutorial are freely available online at https://github.com/BoyanZhou/LongStrain.

IMPORTANCE: The advancement in DNA-sequencing technology has enabled the high-resolution identification of microorganisms in microbial communities. Since different microbial strains within species may contain extreme phenotypic variability (e.g., nutrition metabolism, antibiotic resistance, and pathogen virulence), investigating within-species variations holds great scientific promise in understanding the underlying mechanism of microbial biological processes. To fully utilize the shared genomic variants across longitudinal metagenomics samples collected in microbiome studies, we develop an integrated analytic pipeline (LongStrain) for longitudinal metagenomics data. It concurrently leverages the information on proportions of mapped reads for individual strains and genome-wide SNVs to enhance the efficiency and accuracy of strain identification. Our method helps to understand strains' dynamic changes and their association with genome-wide variants. Given the fast-growing longitudinal studies of microbial communities, LongStrain which streamlines analyses of large-scale raw sequencing data should be of great value in microbiome research communities.}, } @article {pmid39308020, year = {2024}, author = {Kong, X and Dong, Z and Hu, W and Mi, J and Xiao, J and Wang, Y and Chen, W and Pei, Z and Hao, Z and Liang, C and Wang, Q and Wang, Z}, title = {The role of gut microbiota involved in prostate microenvironment and symptoms improvement in chronic prostatitis/chronic pelvic pain syndrome patients treated with low-intensity extracorporeal shock wave.}, journal = {The Prostate}, volume = {84}, number = {16}, pages = {1525-1536}, doi = {10.1002/pros.24794}, pmid = {39308020}, issn = {1097-0045}, support = {2020QN-15//"Cuiying Science and Technology Innovation" Program/ ; CYXZ2022-40, CYXZ2022-23//Of the Second Hospital of Lanzhou University, The "Cuiying Scholars" Program of the Second Hospital of Lanzhou University/ ; 2021B-042//The Innovation Fund Project of the Gansu Provincial Education Department/ ; PRO133011//National Natural Science Foundation of China/ ; lzujbky-2021-kb29//The Fundamental Research Funds for the Central Universities of Lanzhou University/ ; //and Natural Science Foundation of G/ ; }, mesh = {Humans ; Male ; *Prostatitis/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; Adult ; *Extracorporeal Shockwave Therapy/methods ; *Pelvic Pain/therapy/microbiology ; *Prostate/microbiology ; Treatment Outcome ; Chronic Pain/therapy/microbiology ; Semen/microbiology ; }, abstract = {BACKGROUND: Low-intensity extracorporeal shockwave therapy (Li-ESWT) is emerging as a promising and safe treatment for Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS). In this study, we aimed to investigate the role of the gut microbiota involved in the prostate microenvironment and symptom improvement during the Li-ESWT for CP/CPPS patients.

METHODS: CP/CPPS patients not taking antibiotics or other treatments were included. NIH-Chronic Prostatitis Symptom Index (NIH-CPSI), International Prostate Symptom Score (IPSS), and International Index of Erectile Function (IIEF-5) were used to evaluate the effectiveness of Li-ESWT at the end of treatment. Visual analogue scale/score was used to evaluate the pain during procedure. Stool and semen samples were collected before and after Li-ESWT. Shotgun metagenomics analyzed gut microbiota, while ELISA and other diagnostic kits detected biochemical changes in seminal plasma.

RESULT: Of the 60 enrolled patients, 52 completed treatment. Li-ESWT response rate was 78.8% (41/52) at end of treatment. Among responders, the subitems of the NIH-CPSI; IPSS; and IIEF-5 scores improved significantly, and the seminal plasma analysis showed decreased TNF-a and MDA levels and increased SOD and Zn[2+] levels posttreatment. Gut microbiome analysis indicated that posttreatment, both α and β diversity increased, and the abundance of certain specific species significantly increased. Fifty-eight pathways significantly enriched posttreatment, notably in branched-chain amino acid synthesis and butyrate synthesis. The abundance of several specific species was found to be significantly higher in non-responders than responders. Among responders, at the species level, some bacteria associated with NIH-CPSI and its subscales, IPSS, IIEF-5, and prostate microenvironment markers (TNF-a, MDA, Zn[2+], and SOD) were identified.

CONCLUSIONS: Our study demonstrates for the first time that Li-ESWT improves the prostate microenvironment and gut microbiota in CP/CPPS patients. Treatment nonresponse may be associated with a high abundance of specific pathogens before treatment. The gut microbiota could have a significant impact on Li-ESWT response and the prostate microenvironment.}, } @article {pmid39307865, year = {2024}, author = {Gundogdu, A and Nalbantoglu, OU and Karis, G and Sarikaya, I and Erdogan, MN and Hora, M and Aslan, H}, title = {Comparing microbial communities in mucilage and seawater samples: Metagenomic insights into mucilage formation in the Marmara Sea.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {48}, pages = {58363-58374}, pmid = {39307865}, issn = {1614-7499}, support = {121G128//The Scientific and Technological Research Council of Turkey (TUBITAK)/ ; }, mesh = {*Seawater/microbiology ; *Microbiota ; Metagenomics ; Bacteria/genetics ; }, abstract = {Marine environments are subject to various naturally occurring phenomena, including marine snow and mucilage. In 2021, the rapid emergence of mucilage in the Marmara Sea raised concerns about its environmental impact. This study investigates the microbial communities in mucilage and seawater samples from the Marmara Sea using metagenomic-scale comparative analyses. The results indicate significant differences in microbial composition and diversity, with mucilage samples showing higher levels of polysaccharide biosynthesis-related enzymes. Over 50% of reads in mucilage samples remained unclassified (dark matter), highlighting unknown microbial taxa. Clean seawater was characterized by a higher presence of Euryarchaeota, Proteobacteria, and Rhodothermaeota, while Chlamydiae and Fusobacteria were dominant in mucilage. The study underscores the necessity for comprehensive metagenomic analyses to understand microbial roles in mucilage formation and persistence. Early detection of microbial shifts could serve as a warning system for mucilage outbreaks, aiding in the development of management strategies.}, } @article {pmid39307589, year = {2025}, author = {Koike, Y and Kuwatsuka, S and Motooka, D and Murota, H}, title = {Dysbiosis of the human skin mycobiome in patients receiving systemic IL-23 inhibitors.}, journal = {Allergology international : official journal of the Japanese Society of Allergology}, volume = {74}, number = {1}, pages = {72-77}, doi = {10.1016/j.alit.2024.06.003}, pmid = {39307589}, issn = {1440-1592}, mesh = {Humans ; *Mycobiome ; *Skin/microbiology ; *Dysbiosis/microbiology ; Female ; Male ; Middle Aged ; Adult ; Interleukin-23/antagonists & inhibitors/immunology ; Psoriasis/drug therapy/microbiology ; Aged ; }, abstract = {BACKGROUND: Systemic inhibition of pro-inflammatory cytokines affects the skin microbiome; however, the impact of systemic anti-inflammatory therapy on the skin fungal microbiome is poorly understood. To examine the effects of cytokine inhibition on the fungal community on human skin and oral mucosa, we analyzed the composition of the skin mycobiome before and after IL-23 inhibition.

METHODS: The study enrolled 15 psoriasis patients. Swab samples were collected from the psoriasis-free skin of antecubital fossa, post-auricular, and the tongue surface before and after 16 weeks of treatment with anti-IL-23 antibodies. Fungal DNA was sequenced by ITS1 metagenomic analysis, and taxonomic classification was performed.

RESULTS: Data from samples collected from the antecubital fossa revealed that the α diversity of the skin mycobiome decreased significantly after treatment with anti-IL-23 antibodies (p = 0.0120). Fungal DNAs were not amplified in 6/15 swab samples after 16 weeks of IL-23 inhibition; by contrast, sufficiently detected in all 15 samples before treatment (p = 0.0554). A comparison of 9/15 paired samples containing well-detected reads revealed that the percentage of genus Malassezia in the mycobiome fell significantly after treatment with IL-23 inhibitors (before, 29.3% ± 9.9%; after; 8.5% ± 3.4%, p = 0.0137). The mycobiome on post-auricular skin and on the tongue surface showed no marked changes after IL-23 inhibition.

CONCLUSIONS: Taken together, the data suggest that inhibition of systemic IL-23 provokes dysbiosis of the mycobiome at the antecubital fossa skin, a finding characterized by reduced fungal diversity and a reduction in the percentage of the genus Malassezia.}, } @article {pmid39306146, year = {2024}, author = {Martínez-Aranzales, JR and Córdoba-Agudelo, M and Pérez-Jaramillo, JE}, title = {Fecal microbiome and functional prediction profiles of horses with and without crib-biting behavior: A comparative study.}, journal = {Journal of equine veterinary science}, volume = {142}, number = {}, pages = {105198}, doi = {10.1016/j.jevs.2024.105198}, pmid = {39306146}, issn = {0737-0806}, mesh = {Animals ; Horses/microbiology ; *Feces/microbiology ; Male ; Female ; Bacteria/genetics/classification/isolation & purification ; Behavior, Animal/physiology ; Gastrointestinal Microbiome/physiology/genetics ; RNA, Bacterial/genetics/analysis ; }, abstract = {Crib-biting is a stereotyped oral behavior with poorly understood etiology and pathophysiology. The relationship between the gut microbiome and brain function has been described in behavioral disorders such as schizophrenia, depression and anxiety in humans. In horses, studies of behavioral problems and the microbiome are very limited. This study aimed to characterize the fecal microbiome and the predicted functional profile of horses with and without aerophagia. Fecal samples were collected from 12 Colombian Creole Horses of both sexes, divided into two groups: group 1, composed of six horses with crib-biting (3 females and 3 males), average body weight of 330 ± 10 kg, age of 7.0 ± 1.2 years and body condition score (BCS) of 5/9 ± 1 and group 2, consisting of six horses without crib-biting (3 females and 3 males), average body weight of 335 ± 5 kg, age 6.5 ± 1 years and BCS of 6/9 ± 1. From each horse in both groups fecal total DNA was obtained and 16S ribosomal RNA gene amplicons were sequenced to characterize the bacterial community structure. Community structure and differential abundance analyses revealed significant differences between the two conditions (p < 0.05). Specifically, the fecal microbiota at the family level in crib-biting horses, showing a decrease in Bacteroidales and an increase in Bacillota and Clostridia, differed from that of healthy horses without crib-biting, consistent with findings from previous studies. Furthermore, metagenome prediction suggests metabolic profile changes in bacterial communities between both conditions in horses. Further studies are required to validate the role of the microbiota-gut-brain axis in the etiology of crib-biting and other abnormal and stereotyped behaviors.}, } @article {pmid39305897, year = {2024}, author = {Zampirolo, G and Holman, LE and Sawafuji, R and Ptáková, M and Kovačiková, L and Šída, P and Pokorný, P and Pedersen, MW and Walls, M}, title = {Tracing early pastoralism in Central Europe using sedimentary ancient DNA.}, journal = {Current biology : CB}, volume = {34}, number = {20}, pages = {4650-4661.e4}, doi = {10.1016/j.cub.2024.08.047}, pmid = {39305897}, issn = {1879-0445}, mesh = {*DNA, Ancient/analysis ; Animals ; *Archaeology ; Forests ; Sheep/genetics ; Microbiota/genetics ; Agriculture/history ; Geologic Sediments/analysis ; Europe ; }, abstract = {Central European forests have been shaped by complex human interactions throughout the Holocene, with significant changes following the introduction of domesticated animals in the Neolithic (∼7.5-6.0 ka before present [BP]). However, understanding early pastoral practices and their impact on forests is limited by methods for detecting animal movement across past landscapes. Here, we examine ancient sedimentary DNA (sedaDNA) preserved at the Velký Mamuťák rock shelter in northern Bohemia (Czech Republic), which has been a forested enclave since the early Holocene. We find that domesticated animals, their associated microbiomes, and plants potentially gathered for fodder have clear representation by the Late Neolithic, around 6.0 ka BP, and persist throughout the Bronze Age into recent times. We identify a change in dominant grazing species from sheep to pigs in the Bronze Age (∼4.1-3.0 ka BP) and interpret the impact this had in the mid-Holocene retrogressions that still define the structure of Central European forests today. This study highlights the ability of ancient metagenomics to bridge archaeological and paleoecological methods and provide an enhanced perspective on the roots of the "Anthropocene."}, } @article {pmid39305601, year = {2024}, author = {Wang, F and Hu, Z and Wang, W and Wang, J and Xiao, Y and Shi, J and Wang, C and Mai, W and Li, G and An, T}, title = {Selective enrichment of high-risk antibiotic resistance genes and priority pathogens in freshwater plastisphere: Unique role of biodegradable microplastics.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135901}, doi = {10.1016/j.jhazmat.2024.135901}, pmid = {39305601}, issn = {1873-3336}, mesh = {*Microplastics/toxicity ; *Drug Resistance, Microbial/genetics ; *Fresh Water/microbiology ; Water Pollutants, Chemical/toxicity ; Biofilms/drug effects ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Virulence Factors/genetics ; Polyhydroxyalkanoates ; Polyesters/metabolism ; Microbiota/drug effects/genetics ; Biodegradation, Environmental ; Biodegradable Plastics ; }, abstract = {Microplastics (MPs) has been concerned as emerging vectors for spreading antibiotic resistance and pathogenicity in aquatic environments, but the role of biodegradable MPs remains largely unknown. Herein, field in-situ incubation method combined with metagenomic sequencing were employed to reveal the dispersal characteristics of microbial community, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factors (VFs) enriched by MPs biofilms. Results showed that planktonic microbes were more prone to enrich on biodegradable MPs (i.e., polyhydroxyalkanoate and polylactic acid) than non-biodegradable MPs (i.e., polystyrene, polypropylene and polyethylene). Distinctive microbial communities were assembled on biodegradable MPs, and the abundances of ARGs, MGEs, and VFs on biofilms of biodegradable MPs were much higher than that of non-biodegradable MPs. Notably, network analysis showed that the biodegradable MPs selectively enriched pathogens carrying ARGs, VFs and MGEs concurrently, suggesting a strong potential risks of co-spreading antibiotic resistance and pathogenicity through horizontal gene transfer. According to WHO priority list of Antibiotic Resistant Pathogens (ARPs) and ARGs health risk assessment framework, the highest abundances of Priority 1 ARPs and Rank I risk ARGs were found on polylactic acid and polyhydroxyalkanoate, respectively. These findings elucidate the unique and critical role of biodegradable MPs for selective enrichment of high-risk ARGs and priority pathogens in freshwater environments.}, } @article {pmid39305563, year = {2024}, author = {Albuquerque, L and Viver, T and Barroso, C and Claudino, R and Galvan, M and Simões, G and Lobo-da-Cunha, A and Egas, C}, title = {Halorubrum miltondacostae sp. nov., a potential polyhydroxyalkanoate producer isolated from an inland solar saltern in Rio Maior, Portugal.}, journal = {Systematic and applied microbiology}, volume = {47}, number = {6}, pages = {126553}, doi = {10.1016/j.syapm.2024.126553}, pmid = {39305563}, issn = {1618-0984}, mesh = {*Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Sequence Analysis, DNA ; *Polyhydroxyalkanoates ; *Halorubrum/genetics/classification/isolation & purification ; Portugal ; *DNA, Archaeal/genetics/chemistry ; Random Amplified Polymorphic DNA Technique ; Base Composition ; Fatty Acids/analysis/chemistry ; Genes, Essential/genetics ; Phospholipids/analysis/chemistry ; }, abstract = {One hundred and sixty-three extreme halophiles were recovered from a single sample collected from an inland solar saltern in Rio Maior. Based on random amplified polymorphic DNA (RAPD) profiles and partial 16S rRNA gene sequencing 125 isolates were identified as members of the Archaea domain within the genus Halorubrum. Two strains, RMP-11[T] and RMP-47, showed 99.1 % sequence similarity with the species Halorubrum californiense based on phylogenetic analysis of the 16S rRNA gene sequence. However, phylogenetic analysis based on five housekeeping genes, atpB, EF-2, glnA, ppsA and rpoB', showed Halorubrum coriense as the closest related species with 96.7 % similarity. The average nucleotide identity (ANI) of strains RMP-11[T], RMP-47 and species Hrr. coriense were within the range of 90.0-90.5 %, supporting that strains RMP-11[T] and RMP-47 represent a novel species of the genus Halorubrum. These strains formed red-pigmented colonies that were able to grow in a temperature range of 25-50 °C. Polyhydroxyalkanoate (PHA) granules were detected in both strains. The polar lipid profile was identical to the neutrophilic species of the genus Halorubrum. The Rio Maior sample from which both strains were isolated was metagenome sequenced. We identified five metagenome-assembled genomes representing novel Halorubrum species but distinct from the species represented by strains RMP-11[T] and RMP-47. Based on phylogenetic, phylogenomic, comparative genomics, physiological and chemotaxonomic parameters, we describe a new species of the genus Halorubrum represented by strains RMP-11[T] (=CECT 30760[T] = DSM 115521[T]) and RMP-47 (=CECT 30761 = DSM 115541) for which we propose the name Halorubrum miltondacostae sp. nov.}, } @article {pmid39304820, year = {2024}, author = {Silva, MH and Batista, LL and Malta, SM and Santos, ACC and Mendes-Silva, AP and Bonetti, AM and Ueira-Vieira, C and Dos Santos, AR}, title = {Unveiling the Brazilian kefir microbiome: discovery of a novel Lactobacillus kefiranofaciens (LkefirU) genome and in silico prospection of bioactive peptides with potential anti-Alzheimer properties.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {884}, pmid = {39304820}, issn = {1471-2164}, mesh = {*Kefir/microbiology ; *Alzheimer Disease ; *Lactobacillus/genetics ; *Genome, Bacterial ; *Microbiota ; Brazil ; *Peptides/chemistry/pharmacology ; Humans ; Molecular Docking Simulation ; Amyloid beta-Peptides/metabolism/genetics ; Amyloid Precursor Protein Secretases/metabolism ; Aspartic Acid Endopeptidases/genetics/metabolism ; Metagenomics/methods ; }, abstract = {BACKGROUND: Kefir is a complex microbial community that plays a critical role in the fermentation and production of bioactive peptides, and has health-improving properties. The composition of kefir can vary by geographic localization and weather, and this paper focuses on a Brazilian sample and continues previous work that has successful anti-Alzheimer properties. In this study, we employed shotgun metagenomics and peptidomics approaches to characterize Brazilian kefir further.

RESULTS: We successfully assembled the novel genome of Lactobacillus kefiranofaciens (LkefirU) and conducted a comprehensive pangenome analysis to compare it with other strains. Furthermore, we performed a peptidome analysis, revealing the presence of bioactive peptides encrypted by L. kefiranofaciens in the Brazilian kefir sample, and utilized in silico prospecting and molecular docking techniques to identify potential anti-Alzheimer peptides, targeting β-amyloid (fibril and plaque), BACE, and acetylcholinesterase. Through this analysis, we identified two peptides that show promise as compounds with anti-Alzheimer properties.

CONCLUSIONS: These findings not only provide insights into the genome of L. kefiranofaciens but also serve as a promising prototype for the development of novel anti-Alzheimer compounds derived from Brazilian kefir.}, } @article {pmid39304351, year = {2025}, author = {Jiménez, DJ and Chaparro, D and Sierra, F and Custer, GF and Feuerriegel, G and Chuvochina, M and Diaz-Garcia, L and Mendes, LW and Ortega Santiago, YP and Rubiano-Labrador, C and Salcedo Galan, F and Streit, WR and Dini-Andreote, F and Reyes, A and Rosado, AS}, title = {Engineering the mangrove soil microbiome for selection of polyethylene terephthalate-transforming bacterial consortia.}, journal = {Trends in biotechnology}, volume = {43}, number = {1}, pages = {162-183}, doi = {10.1016/j.tibtech.2024.08.013}, pmid = {39304351}, issn = {1879-3096}, mesh = {*Polyethylene Terephthalates/metabolism ; *Soil Microbiology ; *Microbiota/genetics ; Microbial Consortia/genetics ; Biodegradation, Environmental ; Wetlands ; Bacteria/genetics/metabolism/classification ; Seawater/microbiology ; Metagenome/genetics ; }, abstract = {Mangroves are impacted by multiple environmental stressors, including sea level rise, erosion, and plastic pollution. Thus, mangrove soil may be an excellent source of as yet unknown plastic-transforming microorganisms. Here, we assess the impact of polyethylene terephthalate (PET) particles and seawater intrusion on the mangrove soil microbiome and report an enrichment culture experiment to artificially select PET-transforming microbial consortia. The analysis of metagenome-assembled genomes of two bacterial consortia revealed that PET catabolism can be performed by multiple taxa, of which particular species harbored putative novel PET-active hydrolases. A key member of these consortia (Mangrovimarina plasticivorans gen. nov., sp. nov.) was found to contain two genes encoding monohydroxyethyl terephthalate hydrolases. This study provides insights into the development of strategies for harnessing soil microbiomes, thereby advancing our understanding of the ecology and enzymology involved in microbial-mediated PET transformations in marine-associated systems.}, } @article {pmid39303138, year = {2024}, author = {Boukheloua, R and Mukherjee, I and Park, H and Šimek, K and Kasalický, V and Ngochera, M and Grossart, HP and Picazo-Mozo, A and Camacho, A and Cabello-Yeves, PJ and Rodriguez-Valera, F and Callieri, C and Andrei, AS and Pernthaler, J and Posch, T and Alfreider, A and Sommaruga, R and Hahn, MW and Sonntag, B and López-García, P and Moreira, D and Jardillier, L and Lepère, C and Biderre-Petit, C and Bednarska, A and Ślusarczyk, M and Tóth, VR and Banciu, HL and Kormas, K and Orlić, S and Šantić, D and Muyzer, G and Herlemann, DPR and Tammert, H and Bertilsson, S and Langenheder, S and Zechmeister, T and Salmaso, N and Storelli, N and Capelli, C and Lepori, F and Lanta, V and Vieira, HH and Kostanjšek, F and Kabeláčová, K and Chiriac, MC and Haber, M and Shabarova, T and Fernandes, C and Rychtecký, P and Znachor, P and Szőke-Nagy, T and Layoun, P and Wong, HL and Kavagutti, VS and Bulzu, PA and Salcher, MM and Piwosz, K and Ghai, R}, title = {Global freshwater distribution of Telonemia protists.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39303138}, issn = {1751-7370}, support = {20-12496X//Grant Agency of the Czech Republic/ ; 017/2022/P//GAJU/ ; 2021/03/Y/NZ8/00076//National Science Centre/ ; }, mesh = {*Fresh Water/microbiology/parasitology ; *Phylogeny ; *RNA, Ribosomal, 18S/genetics ; *In Situ Hybridization, Fluorescence ; Metagenome ; Lakes/microbiology/parasitology ; Biodiversity ; Metagenomics ; }, abstract = {Telonemia are one of the oldest identified marine protists that for most part of their history have been recognized as a distinct incertae sedis lineage. Today, their evolutionary proximity to the SAR supergroup (Stramenopiles, Alveolates, and Rhizaria) is firmly established. However, their ecological distribution and importance as a natural predatory flagellate, especially in freshwater food webs, still remain unclear. To unravel the distribution and diversity of the phylum Telonemia in freshwater habitats, we examined over a thousand freshwater metagenomes from all over the world. In addition, to directly quantify absolute abundances, we analyzed 407 samples from 97 lakes and reservoirs using Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). We recovered Telonemia 18S rRNA gene sequences from hundreds of metagenomic samples from a wide variety of habitats, indicating a global distribution of this phylum. However, even after this extensive sampling, our phylogenetic analysis did not reveal any new major clades, suggesting current molecular surveys are near to capturing the full diversity within this group. We observed excellent concordance between CARD-FISH analyses and estimates of abundances from metagenomes. Both approaches suggest that Telonemia are largely absent from shallow lakes and prefer to inhabit the colder hypolimnion of lakes and reservoirs in the Northern Hemisphere, where they frequently bloom, reaching 10%-20% of the total heterotrophic flagellate population, making them important predatory flagellates in the freshwater food web.}, } @article {pmid39303118, year = {2024}, author = {Doré, J and Sansonetti, PJ}, title = {[The human microbiome: 340 years of history, 140 years of interrogations, technological innovations and emergence of "microbial medicine"].}, journal = {Medecine sciences : M/S}, volume = {40}, number = {8-9}, pages = {654-660}, doi = {10.1051/medsci/2024101}, pmid = {39303118}, issn = {1958-5381}, mesh = {Humans ; Gastrointestinal Microbiome/physiology ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Inventions/history/trends ; *Microbiota/physiology ; Symbiosis ; History, 17th Century ; }, abstract = {For 350 years, we have known that the human body hosts microbes, then called "animalcules". For over a century, following the demonstration of the role of some of these microbes in diseases, questions have arisen about the role of the largely predominant ones colonizing human skin and mucous surfaces, particularly the rich microbial ecosystem of the intestine, the gut microbiota. From the invention of germ-free life - axenism - which experimentally validated the human-microbe symbiosis, resulting from a long coevolution, to the development of anaerobic culture methods, then to the invention of molecular diagnosis, deep sequencing opening up metagenomic and omics approaches in general, a remarkable race has taken place between technological innovations and conceptual advances. This race, beyond the exhaustive description of the microbiota in its intra- and inter-human diversity, and the essential symbiotic functions of the microbiome, has paved the way for a new field of medicine: microbial medicine.}, } @article {pmid39300577, year = {2024}, author = {Lezcano, MÁ and Bornemann, TLV and Sánchez-García, L and Carrizo, D and Adam, PS and Esser, SP and Cabrol, NA and Probst, AJ and Parro, V}, title = {Hyperexpansion of genetic diversity and metabolic capacity of extremophilic bacteria and archaea in ancient Andean lake sediments.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {176}, pmid = {39300577}, issn = {2049-2618}, support = {FJC2018-037246-I//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RYC2018-023943-I//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RYC-2014-19446//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RTI2018-094368-B-I0//Spanish Ministry of Science and Innovation/State Agency of Research/ ; PEJD-2017- POST/TIC-4119//Spanish Ministry of Science and Innovation/State Agency of Research (EU Youth Employment Initiative)/ ; NAI-CAN7, 13NAI7_2-0018//NASA Astrobiology Institute/ ; DFG PR1603/2-1//German Research Foundation/ ; 161L0285E//German Federal Ministry of Education and Research/ ; }, mesh = {*Lakes/microbiology ; *Archaea/genetics/metabolism/classification ; *Geologic Sediments/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Genetic Variation ; Chile ; Phylogeny ; Microbiota ; Extremophiles/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The Andean Altiplano hosts a repertoire of high-altitude lakes with harsh conditions for life. These lakes are undergoing a process of desiccation caused by the current climate, leaving terraces exposed to extreme atmospheric conditions and serving as analogs to Martian paleolake basins. Microbiomes in Altiplano lake terraces have been poorly studied, enclosing uncultured lineages and a great opportunity to understand environmental adaptation and the limits of life on Earth. Here we examine the microbial diversity and function in ancient sediments (10.3-11 kyr BP (before present)) from a terrace profile of Laguna Lejía, a sulfur- and metal/metalloid-rich saline lake in the Chilean Altiplano. We also evaluate the physical and chemical changes of the lake over time by studying the mineralogy and geochemistry of the terrace profile.

RESULTS: The mineralogy and geochemistry of the terrace profile revealed large water level fluctuations in the lake, scarcity of organic carbon, and high concentration of SO4[2-]-S, Na, Cl and Mg. Lipid biomarker analysis indicated the presence of aquatic/terrestrial plant remnants preserved in the ancient sediments, and genome-resolved metagenomics unveiled a diverse prokaryotic community with still active microorganisms based on in silico growth predictions. We reconstructed 591 bacterial and archaeal metagenome-assembled genomes (MAGs), of which 98.8% belonged to previously unreported species. The most abundant and widespread metabolisms among MAGs were the reduction and oxidation of S, N, As, and halogenated compounds, as well as aerobic CO oxidation, possibly as a key metabolic trait in the organic carbon-depleted sediments. The broad redox and CO2 fixation pathways among phylogenetically distant bacteria and archaea extended the knowledge of metabolic capacities to previously unknown taxa. For instance, we identified genomic potential for dissimilatory sulfate reduction in Bacteroidota and α- and γ-Proteobacteria, predicted an enzyme for ammonia oxidation in a novel Actinobacteriota, and predicted enzymes of the Calvin-Benson-Bassham cycle in Planctomycetota, Gemmatimonadota, and Nanoarchaeota.

CONCLUSIONS: The high number of novel bacterial and archaeal MAGs in the Laguna Lejía indicates the wide prokaryotic diversity discovered. In addition, the detection of genes in unexpected taxonomic groups has significant implications for the expansion of microorganisms involved in the biogeochemical cycles of carbon, nitrogen, and sulfur. Video Abstract.}, } @article {pmid39300575, year = {2024}, author = {Li, Q and Ruscheweyh, HJ and Østergaard, LH and Libertella, M and Simonsen, KS and Sunagawa, S and Scoma, A and Schwab, C}, title = {Trait-based study predicts glycerol/diol dehydratases as a key function of the gut microbiota of hindgut-fermenting carnivores.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {178}, pmid = {39300575}, issn = {2049-2618}, support = {9152//EMBO/ ; AUFF-F-2020-7//Aarhus Universitet Forsknings Fonden/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Feces/microbiology ; *Fermentation ; *Glycerol/metabolism ; *Metagenomics/methods ; Hydro-Lyases/genetics/metabolism ; Propylene Glycols/metabolism ; Vitamin B 12/metabolism ; Bacteria/classification/genetics/isolation & purification/enzymology ; Phylogeny ; Animals, Wild/microbiology ; }, abstract = {BACKGROUND: Microbial pdu and cob-cbi-hem gene clusters encode the key enzyme glycerol/diol dehydratase (PduCDE), which mediates the transformation of dietary nutrients glycerol and 1,2-propanediol (1,2-PD) to a variety of metabolites, and enzymes for cobalamin synthesis, a co-factor and shared good of microbial communities. It was the aim of this study to relate pdu as a multipurpose functional trait to environmental conditions and microbial community composition. We collected fecal samples from wild animal species living in captivity with different gut physiology and diet (n = 55, in total 104 samples), determined occurrence and diversity of pdu and cob-cbi-hem using a novel approach combining metagenomics with quantification of metabolic and genetic biomarkers, and conducted in vitro fermentations to test for trait-based activity.

RESULTS: Fecal levels of the glycerol transformation product 1,3-propanediol (1,3-PD) were higher in hindgut than foregut fermenters. Gene-based analyses indicated that pduC harboring taxa are common feature of captive wild animal fecal microbiota that occur more frequently and at higher abundance in hindgut fermenters. Phylogenetic analysis of genomes reconstructed from metagenomic sequences identified captive wild animal fecal microbiota as taxonomically rich with a total of 4150 species and > 1800 novel species but pointed at only 56 species that at least partially harbored pdu and cbi-cob-hem. While taxonomic diversity was highest in fecal samples of foregut-fermenting herbivores, higher pduC abundance and higher diversity of pdu/cbi-cob-hem related to higher potential for glycerol and 1,2-PD utilization of the less diverse microbiota of hindgut-fermenting carnivores in vitro.

CONCLUSION: Our approach combining metabolite and gene biomarker analysis with metagenomics and phenotypic characterization identified Pdu as a common function of fecal microbiota of captive wild animals shared by few taxa and stratified the potential of fecal microbiota for glycerol/1,2-PD utilization and cobalamin synthesis depending on diet and physiology of the host. This trait-based study suggests that the ability to utilize glycerol/1,2-PD is a key function of hindgut-fermenting carnivores, which does not relate to overall community diversity but links to the potential for cobalamin formation. Video Abstract.}, } @article {pmid39300163, year = {2024}, author = {Myeong, NR and Choe, YH and Shin, SC and Kim, J and Sul, WJ and Kim, M}, title = {Genomic profiling of Antarctic geothermal microbiomes using long-read, Hi-C, and single-cell techniques.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1023}, pmid = {39300163}, issn = {2052-4463}, support = {PE24460//Korea Polar Research Institute (KOPRI)/ ; PE24070//Korea Polar Research Institute (KOPRI)/ ; PE24460//Korea Polar Research Institute (KOPRI)/ ; PE24460//Korea Polar Research Institute (KOPRI)/ ; Graduate Research Scholarship in 2017//Chung-Ang University (CAU)/ ; }, mesh = {Antarctic Regions ; *Microbiota ; *Single-Cell Analysis ; Hot Springs/microbiology ; Metagenomics ; Metagenome ; }, abstract = {Geothermal features in Antarctica provide favorable conditions for diverse microorganisms, yet their genomic diversity remains poorly understood. Here, we present an integrated dataset comprising PacBio HiFi and Hi-C metagenomic sequencing, along with single-cell amplified genomes (SAGs) from two high-altitude geothermal sites, Mount Melbourne and Mount Rittmann, in Antarctica. The long-read HiFi sequencing, coupled with Hi-C, enhances the understanding of microbiome diversity and functionality in this unique ecosystem by providing more complete and accurate genomic information. SAGs complement this by recovering rare microbial taxa and offering a strain-resolved perspective. This dataset aims to deepen our understanding of microbial evolution and ecology in Antarctic geothermal environments, and facilitate cross-comparison with other geothermal environments globally.}, } @article {pmid39299446, year = {2024}, author = {Wei, ZY and Feng, M and Zhang, DX and Jiang, CY and Deng, Y and Wang, ZJ and Feng, K and Song, Y and Zhou, N and Wang, YL and Liu, SJ}, title = {Deep insights into the assembly mechanisms, co-occurrence patterns, and functional roles of microbial community in wastewater treatment plants.}, journal = {Environmental research}, volume = {263}, number = {Pt 1}, pages = {120029}, doi = {10.1016/j.envres.2024.120029}, pmid = {39299446}, issn = {1096-0953}, mesh = {*Microbiota ; *Wastewater/microbiology ; Waste Disposal, Fluid/methods ; Seasons ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; Bacteria/genetics/classification ; Phosphorus/analysis ; }, abstract = {The understanding of activated sludge microbial status and roles is imperative for improving and enhancing the performance of wastewater treatment plants (WWTPs). In this study, we conducted a deep analysis of activated sludge microbial communities across five compartments (inflow, effluent, and aerobic, anoxic, anaerobic tanks) over temporal scales, employing high-throughput sequencing of 16S rRNA amplicons and metagenome data. Clearly discernible seasonal patterns, exhibiting cyclic variations, were observed in microbial diversity, assembly, co-occurrence network, and metabolic functions. Notably, summer samples exhibited higher α-diversity and were distinctly separated from winter samples. Our analysis revealed that microbial community assembly is influenced by both stochastic processes (66%) and deterministic processes (34%), with winter samples demonstrating more random assembly compared to summer. Co-occurrence patterns were predominantly mutualistic, with over 96% positive correlations, and summer networks were more organized than those in winter. These variations were significantly correlated with temperature, total phosphorus and sludge volume index. However, no significant differences were found among microbial community across five compartments in terms of β diversity. A core community of keystone taxa was identified, playing key roles in eight nitrogen and eleven phosphorus cycling pathways. Understanding the assembly mechanisms, co-occurrence patterns, and functional roles of microbial communities is essential for the design and optimization of biotechnological treatment processes in WWTPs.}, } @article {pmid39298952, year = {2024}, author = {Liu, J and Shi, J and Hu, Y and Su, Y and Zhang, Y and Wu, X}, title = {Flumethrin exposure perturbs gut microbiota structure and intestinal metabolism in honeybees (Apis mellifera).}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135886}, doi = {10.1016/j.jhazmat.2024.135886}, pmid = {39298952}, issn = {1873-3336}, mesh = {Animals ; Bees/drug effects/metabolism ; *Pyrethrins/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Insecticides/toxicity ; Catalase/metabolism ; Superoxide Dismutase/metabolism ; Glutathione Transferase/metabolism ; Intestines/drug effects/microbiology ; }, abstract = {Flumethrin mitigates Varroa's harm to honeybee colonies; however, its residues in colonies threaten the fitness of honeybee hosts and gut microbiota. Our previous research has shown that flumethrin induces significant physiological effects on honeybee larvae; but the effects of flumethrin on the gut microbiota and metabolism of adult honeybees are still unknown. In this study, 1-day-old honeybees were exposed to 0, 0.01, 0.1, and 1 mg/L flumethrin for 14 days and the impacts of flumethrin on the intestinal system were evaluated. The results showed that exposure to 1 mg/L flumethrin significantly reduced honeybee survival and the activities of antioxidative enzymes (superoxide dismutase and catalase) and detoxification enzymes (glutathione S-transferase) in honeybee heads. Moreover, exposure to 0.01, 0.1, and 1 mg/L flumethrin significantly decreased the diversity of the honeybee gut microbiota. Results from untargeted metabolomics showed that long-term exposure to 0.01, 0.1, and 1 mg/L flumethrin caused changes in the metabolic pathways of honeybee gut microbes. Furthermore, increased metabolism of phenylalanine, tyrosine, and tryptophan derivatives was observed in honeybee gut microbes. These findings underscore the importance of careful consideration in using pesticides in apiculture and provide a basis for safeguarding honeybees from pollutants, considering the effects on gut microbes.}, } @article {pmid39298897, year = {2024}, author = {Wang, N and Li, S and Shi, M and Ni, N and Zhang, X and Guo, X and Lin, H and Luo, Y}, title = {Trajectory of antibiotic resistome response to antibiotics gradients: A comparative study from pharmaceutical and associated wastewater treatment plants to receiving river.}, journal = {Water research}, volume = {266}, number = {}, pages = {122444}, doi = {10.1016/j.watres.2024.122444}, pmid = {39298897}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Wastewater/microbiology ; *Rivers/microbiology/chemistry ; *Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid ; Water Pollutants, Chemical ; Microbiota/drug effects ; }, abstract = {Pharmaceutical wastewater often contains significant levels of antibiotic residues, which continuously induce and promote antibiotic resistance during the sewage treatment process. However, the specific impact of antibiotics on the emergence of antibiotic resistance genes (ARGs), microbiomes, and mobile genetic elements (MGEs), as well as the dose-response relationship remain unclear. Herein, through metagenomic sequencing and analysis, we investigated the fate, transmission, and associated risk of ARGs over a ten-year period of exposure to a gradient of sulfonamide antibiotics at a pharmaceutical wastewater treatment plant (PWWTP), an associated wastewater treatment plant (WWTP), and the receiving river. Through abundance comparison and principal co-ordinates analysis (PCoA), our results revealed distinct ARG, microbiome, and MGE profiles across different antibiotic concentrations. Notably, there was a decreasing trend in the abundance of ARGs and MGEs as the antibiotic concentrations were attenuated (p < 0.05). Further partial least squares path modeling analysis, Procrustes analysis and network analysis indicated that variation in MGEs and microbiomes were the driving forces behind the distribution of ARGs. Based on these findings, we proposed an antibiotic-microbiome-MGE-ARG dissemination paradigm, in which integrons as key drivers were closely associated with prevalent ARGs such as sul1, sul2, and aadA. With a focus on human pathogenic bacteria and the associated health risks of ARGs, we conducted pathogen source analysis and calculated the antibiotic resistome risk index (ARRI). Our findings highlighted potential risks associated with the transition from PWWTP to WWTP, raising concerns regarding risk amplification due to the mixed treatment of antibiotic-laden industrial wastewater and domestic sewage. Overall, the results of our study provide valuable information for optimizing wastewater treatment practices to better manage antibiotic resistance.}, } @article {pmid39298862, year = {2024}, author = {Karadayı, S and Yılmaz, İ and Özbek, T and Karadayı, B}, title = {Transfer and persistence of microbiota markers from the human hand to the knife: A preliminary study.}, journal = {Journal of forensic and legal medicine}, volume = {107}, number = {}, pages = {102757}, doi = {10.1016/j.jflm.2024.102757}, pmid = {39298862}, issn = {1878-7487}, mesh = {Humans ; *Microbiota ; *Hand/microbiology ; *Touch ; RNA, Ribosomal, 16S ; Male ; High-Throughput Nucleotide Sequencing ; Bacteria/isolation & purification/genetics ; Female ; Adult ; }, abstract = {New scientific techniques and methods are always needed to link the perpetrators to the incident or the crime scene. Recent microbiota studies based on NGS (Next-generation sequencing) show that various biological samples from crime scenes have the potential to be used in forensic investigations. Especially when DNA traces belonging to more than one person are insufficient to fully determine the genetic profile, a secret sample, such as a microbiota sample created by the suspect's touch, can be used. In this preliminary study, a fictionalized experimental model was designed to investigate the transfer and persistence of the hand microbiome on the knife handle, which has a high potential to be used in criminal incidents, by metagenomic analysis methods. In addition, it was aimed to determine the transfer of specific bacterial species identified only to the person among the five participants onto the knife handle and their persistence over time. In the first stage of the research, samples were collected from the hands of 5 volunteer participants using the swap method, including their palms. Then, after each participant held a different knife, samples were collected from the knife handles via swabs from different angles of the knives at 4 and 24 h and analyzed by metagenomic methods. The findings of this preliminary study showed that the heatmap graphs generated after UniFrac distance analysis were not successful in establishing any similarity between the hand samples and the post-transfer knife handle samples. Nonetheless, it was observed that the transfer of bacterial species detected in the hand samples to knives differed according to the individuals and some bacterial species were transferred to the knife samples held by the participants. The number of bacterial species detected that are specific to each participant's hand sample was 302 in total, and it was determined that a total of 8.28 % of these bacterial species were transferred to the knife handle samples of the 4th hour and 6.95 % to the knife samples of the 24th hour. In the presented study, considering the transfer of some bacterial species in the hand microbiome, which are effective in the variation between individuals, onto the knife; It has been evaluated that some rare bacterial species can be important potential markers to associate the object with the perpetrator.}, } @article {pmid39298196, year = {2024}, author = {Barber, DG and Davies, CA and Hartley, IP and Tennant, RK}, title = {Evaluation of commercial RNA extraction kits for long-read metatranscriptomics in soil.}, journal = {Microbial genomics}, volume = {10}, number = {9}, pages = {}, pmid = {39298196}, issn = {2057-5858}, mesh = {*Soil Microbiology ; Microbiota/genetics ; Soil/chemistry ; Transcriptome ; Gene Expression Profiling/methods ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, RNA/methods ; RNA/genetics/isolation & purification ; RNA, Bacterial/genetics/isolation & purification ; }, abstract = {Metatranscriptomic analysis of the soil microbiome has the potential to reveal molecular mechanisms that drive soil processes regulated by the microbial community. Therefore, RNA samples must be of sufficient yield and quality to robustly quantify differential gene expression. While short-read sequencing technology is often favoured for metatranscriptomics, long-read sequencing has the potential to provide several benefits over short-read technologies. The ability to resolve complete transcripts on a portable sequencing platform for a relatively low capital expenditure makes Oxford Nanopore Technology an attractive prospect for addressing many of the challenges of soil metatranscriptomics. To fully enable long-read metatranscriptomic analysis of the functional molecular pathways expressed in these diverse habitats, RNA purification methods from soil must be optimised for long-read sequencing. Here we compare RNA samples purified using five commercially available extraction kits designed for use with soil. We found that the Qiagen RNeasy PowerSoil Total RNA Kit performed the best across RNA yield, quality and purity and was robust across different soil types. We found that sufficient sequencing depth can be achieved to characterise the active community for total RNA samples using Oxford Nanopore Technology, and discuss its current limitations for differential gene expression analysis in soil studies.}, } @article {pmid39294312, year = {2024}, author = {Li, D and Wang, Y and Li, X and Zhang, Z and Wang, G and Zhang, Y and Chen, L}, title = {Exploring microbial diversity and function in companion planting systems of white clover and orchard grass.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21609}, pmid = {39294312}, issn = {2045-2322}, support = {32172769//National Natural Science Foundation of China/ ; }, mesh = {*Trifolium/microbiology/genetics/growth & development ; *Soil Microbiology ; *Rhizosphere ; *Microbiota/genetics ; Dactylis/genetics/microbiology ; Metagenomics/methods ; Bacteria/genetics/classification ; Biodiversity ; }, abstract = {Companion planting of white clover (Trifolium repens L.) with orchard grass (Dactylis glomerata L.), a famous hay grass, improves the forage quality of orchard grass. Microbiome profiling techniques can reveal the specific role of white clover companion planting with orchard grass. This study aimed to explore the microbiome distribution and gene functions of rhizosphere and non-rhizosphere soil via companion planting systems of white clover and orchard grass. From metagenomics sequencing analysis, we confirmed the significant role of white clover on soil environment modeling during companion planting with orchard grass. Twenty-eight biomarkers of rhizosphere soil organisms were identified during companion planting, including Proteobacteria, Betaproteobacteria, Flavobacteriia, and Caulobacterales. The number of gene functions of nitrogen and carbon fixation in companion planting was higher than that in single plants, indicating new functional flora for companion planting. We characterized specific rhizosphere effects, typical biomarker flora, and potential regulatory mechanisms for white clover-related companion planting by metagenomics analyses.}, } @article {pmid39294129, year = {2024}, author = {Bozzi, D and Neuenschwander, S and Cruz Dávalos, DI and Sousa da Mota, B and Schroeder, H and Moreno-Mayar, JV and Allentoft, ME and Malaspinas, AS}, title = {Towards predicting the geographical origin of ancient samples with metagenomic data.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21794}, pmid = {39294129}, issn = {2045-2322}, mesh = {Humans ; *DNA, Ancient/analysis ; *Metagenomics/methods ; *Metagenome ; Geography ; Microbiota/genetics ; }, abstract = {Reconstructing the history-such as the place of birth and death-of an individual sample is a fundamental goal in ancient DNA (aDNA) studies. However, knowing the place of death can be particularly challenging when samples come from museum collections with incomplete or erroneous archives. While analyses of human DNA and isotope data can inform us about the ancestry of an individual and provide clues about where the person lived, they cannot specifically trace the place of death. Moreover, while ancient human DNA can be retrieved, a large fraction of the sequenced molecules in ancient DNA studies derive from exogenous DNA. This DNA-which is usually discarded in aDNA analyses-is constituted mostly by microbial DNA from soil-dwelling microorganisms that have colonized the buried remains post-mortem. In this study, we hypothesize that remains of individuals buried in the same or close geographic areas, exposed to similar microbial communities, could harbor more similar metagenomes. We propose to use metagenomic data from ancient samples' shotgun sequencing to locate the place of death of a given individual which can also help to solve cases of sample mislabeling. We used a k-mer-based approach to compute similarity scores between metagenomic samples from different locations and propose a method based on dimensionality reduction and logistic regression to assign a geographical origin to target samples. We apply our method to several public datasets and observe that individual samples from closer geographic locations tend to show higher similarities in their metagenomes compared to those of different origin, allowing good geographical predictions of test samples. Moreover, we observe that the genus Streptomyces commonly infiltrates ancient remains and represents a valuable biomarker to trace the samples' geographic origin. Our results provide a proof of concept and show how metagenomic data can also be used to shed light on the place of origin of ancient samples.}, } @article {pmid39293811, year = {2024}, author = {Liu, Y and Ong, SL and Gedye, K and Truglio, M and Prabakar, S}, title = {Behind the scenes: metagenomic analysis of bacterial communities in sustainable depilation of sheepskin.}, journal = {Journal of applied microbiology}, volume = {135}, number = {11}, pages = {}, doi = {10.1093/jambio/lxae244}, pmid = {39293811}, issn = {1365-2672}, support = {LSRX-1801//the New Zealand Ministry of Business, Innovation and Employment (MBIE)/ ; }, mesh = {*Bacteria/genetics/isolation & purification/classification ; *Metagenomics ; *Microbiota ; Animals ; Acetic Acid/metabolism ; Hair Removal ; }, abstract = {AIM: The leather industry is embracing eco-friendly technologies for both regulatory compliance and sustainable growth. While enzymatic depilation provides a greener alternative to traditional beamhouse methods, its complexity often leads to higher costs. To address this, we examined the performance of sheepskins' native bacterial flora in acetic acid conditions with low-environmental impact.

METHODS AND RESULTS: Utilizing metagenomic techniques, we analyzed the bacterial community dynamics during the depilation process. This investigation revealed a notable increase in microbial diversity and richness in acetic acid treatments compared to water treatments. At the class level, a post-processing decrease in Gammaproteobacteria dominance was observed, while Actinomycetia numbers surged in the acetic acid group. In contrast, the water group showed an increase in Bacteroidia. Order-level analysis indicated reductions in Pseudomonadales and increases in Actinomycetales with acetic acid treatment, whereas Flavobacteriales was more prevalent in water-treated liquors. At the family level, Moraxellaceae decreased and Micrococcaceae increased in the acetic acid group, in contrast to the marked rise of Weeksellaceae in the water group. Temporal analyses further highlighted the evolving bacterial landscapes under different treatments. Moreover, acetic acid treatment fostered a stable microbial community, beneficial for sustainable leather processing. Functional pathways were predicted using PICRUSt2. It showed that significantly enriched degradation pathways in the water group were less abundant in the acetic acid group, potentially preventing substrate matrix damage during depilation.

CONCLUSION: The study underscores the transformative potential of acetic acid for the leather industry, offering a pathway to reduce pollution while maintaining economic viability. By enhancing our understanding of microbial interactions during depilation, this study opens avenues for refining these eco-friendly techniques. Our findings advocate for a shift towards greener depilation methods and contribute to the broader dialogue on sustainable manufacturing practices, emphasizing the importance of leveraging indigenous microbial communities for environmental and economic gains.}, } @article {pmid39293338, year = {2024}, author = {Bakir-Gungor, B and Temiz, M and Inal, Y and Cicekyurt, E and Yousef, M}, title = {CCPred: Global and population-specific colorectal cancer prediction and metagenomic biomarker identification at different molecular levels using machine learning techniques.}, journal = {Computers in biology and medicine}, volume = {182}, number = {}, pages = {109098}, doi = {10.1016/j.compbiomed.2024.109098}, pmid = {39293338}, issn = {1879-0534}, mesh = {*Colorectal Neoplasms/microbiology/genetics/metabolism ; Humans ; *Machine Learning ; *Biomarkers, Tumor/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; Software ; }, abstract = {Colorectal cancer (CRC) ranks as the third most common cancer globally and the second leading cause of cancer-related deaths. Recent research highlights the pivotal role of the gut microbiota in CRC development and progression. Understanding the complex interplay between disease development and metagenomic data is essential for CRC diagnosis and treatment. Current computational models employ machine learning to identify metagenomic biomarkers associated with CRC, yet there is a need to improve their accuracy through a holistic biological knowledge perspective. This study aims to evaluate CRC-associated metagenomic data at species, enzymes, and pathway levels via conducting global and population-specific analyses. These analyses utilize relative abundance values from human gut microbiome sequencing data and robust classification models are built for disease prediction and biomarker identification. For global CRC prediction and biomarker identification, the features that are identified by SelectKBest (SKB), Information Gain (IG), and Extreme Gradient Boosting (XGBoost) methods are combined. Population-based analysis includes within-population, leave-one-dataset-out (LODO) and cross-population approaches. Four classification algorithms are employed for CRC classification. Random Forest achieved an AUC of 0.83 for species data, 0.78 for enzyme data and 0.76 for pathway data globally. On the global scale, potential taxonomic biomarkers include ruthenibacterium lactatiformanas; enzyme biomarkers include RNA 2' 3' cyclic 3' phosphodiesterase; and pathway biomarkers include pyruvate fermentation to acetone pathway. This study underscores the potential of machine learning models trained on metagenomic data for improved disease prediction and biomarker discovery. The proposed model and associated files are available at https://github.com/TemizMus/CCPRED.}, } @article {pmid39289490, year = {2024}, author = {Bai, B and Tuerxun, G and Tuerdi, A and Maimaiti, R and Sun, Y and Abudukerimu, A}, title = {Analysis of vaginal flora diversity and study on the role of Porphyromonas asaccharolytica in promoting IL-1β in regulating cervical cancer.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21731}, pmid = {39289490}, issn = {2045-2322}, support = {2022D01C185//Natural Science Foundation of the Xinjiang Uygur Autonomous Region/ ; }, mesh = {Female ; Humans ; *Uterine Cervical Neoplasms/microbiology/virology/pathology/genetics ; *Vagina/microbiology ; *Porphyromonas/genetics/isolation & purification ; *Interleukin-1beta/genetics/metabolism ; *Microbiota/genetics ; Adult ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Papillomavirus Infections/virology/microbiology/complications ; }, abstract = {Cervical cancer, a prevalent malignancy in the female reproductive tract, exhibits a high incidence. Existing evidence indicates a robust correlation between alterations in vaginal flora composition and the progression of cervical cancer. Nevertheless, there is a lack of clarity concerning the specific microorganisms within the vaginal microbiota that are linked to the onset and development of cervical cancer, as well as the mechanisms through which they exert carcinogenic effects. The 16 S ribosomal (rRNA) and metagenomic sequencing technology were used to analyze vaginal microorganisms, and screening for human papillomavirus (HPV) positive cervical cancer-associated microbial markers using fold change in mean bacterial abundance. Moreover, vaginal microenvironmental factors were detected, and the local vaginal inflammatory state in patients with cervical cancer was subjected to assay via qRT-PCR and ELISA. The hub inflammatory genes were screened by transcriptome sequencing after co-culture of bacteria and normal cervical epithelial cells, and an in vitro model was utilized to assess the impacts of inflammatory factors on cervical cancer. Both cervical cancer patients and HPV-positive patients showed significant changes in the composition of the vaginal flora, characterised by a decrease in the abundance of Lactobacillus and an increase in the abundance of a variety of anaerobic bacteria; The microbial sequencing identified Porphyromonas, Porphyromonas_asaccharolytica, and Porphyromonas_uenonis as microbial markers for HPV-associated cervical cancer. Vaginal inflammatory factors in patients with cervical cancer were overexpressed. After Porphyromonas_asaccharolytica intervention on cervical epithelial H8 cells, interleukin (IL)-1β, a hub differential gene, markedly promoted tumor-associated biological behaviors at the in vitro cytological level in cervical cancer. This study for the first demonstrated that Porphyromonas, Porphyromonas_asaccharolytica, and Porphyromonas_uenonis could serve as novel microbial markers for cervical cancer. Moreover, Porphyromonas_asaccharolytica was identified as having the ability to induce the overexpression of inflammatory genes in cervical epithelial cells to create a favorable microenvironment for the onset and development of cervical cancer. The effects of dysbacteriosis on cervical cancer were microbiologically elucidated.}, } @article {pmid39289365, year = {2024}, author = {Peng, X and Wang, S and Wang, M and Feng, K and He, Q and Yang, X and Hou, W and Li, F and Zhao, Y and Hu, B and Zou, X and Deng, Y}, title = {Metabolic interdependencies in thermophilic communities are revealed using co-occurrence and complementarity networks.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8166}, pmid = {39289365}, issn = {2041-1723}, mesh = {*Metabolic Networks and Pathways/genetics ; *Archaea/genetics/metabolism ; *Bacteria/metabolism/genetics/classification ; *Metagenome/genetics ; *Microbiota ; Hot Springs/microbiology ; Phylogeny ; Microbial Interactions ; Hot Temperature ; }, abstract = {Microbial communities exhibit intricate interactions underpinned by metabolic dependencies. To elucidate these dependencies, we present a workflow utilizing random matrix theory on metagenome-assembled genomes to construct co-occurrence and metabolic complementarity networks. We apply this approach to a temperature gradient hot spring, unraveling the interplay between thermal stress and metabolic cooperation. Our analysis reveals an increase in the frequency of metabolic interactions with rising temperatures. Amino acids, coenzyme A derivatives, and carbohydrates emerge as key exchange metabolites, forming the foundation for syntrophic dependencies, in which commensalistic interactions take a greater proportion than mutualistic ones. These metabolic exchanges are most prevalent between phylogenetically distant species, especially archaea-bacteria collaborations, as a crucial adaptation to harsh environments. Furthermore, we identify a significant positive correlation between basal metabolite exchange and genome size disparity, potentially signifying a means for streamlined genomes to leverage cooperation with metabolically richer partners. This phenomenon is also confirmed by another composting system which has a similar wide range of temperature fluctuations. Our workflow provides a feasible way to decipher the metabolic complementarity mechanisms underlying microbial interactions, and our findings suggested environmental stress regulates the cooperative strategies of thermophiles, while these dependencies have been potentially hardwired into their genomes during co-evolutions.}, } @article {pmid39287376, year = {2024}, author = {Bucher-Johannessen, C and Senthakumaran, T and Avershina, E and Birkeland, E and Hoff, G and Bemanian, V and Tunsjø, H and Rounge, TB}, title = {Species-level verification of Phascolarctobacterium association with colorectal cancer.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0073424}, pmid = {39287376}, issn = {2379-5077}, support = {2020056//Ministry of Health and Care Services | Helse Sør-Øst RHF (sorost)/ ; 2022067//Ministry of Health and Care Services | Helse Sør-Øst RHF (sorost)/ ; 190179//Kreftforeningen (NCS)/ ; 198048//Kreftforeningen (NCS)/ ; 202401/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology ; Male ; Female ; *RNA, Ribosomal, 16S/genetics ; Gastrointestinal Microbiome/genetics ; Norway/epidemiology ; Metagenome ; Middle Aged ; Adenoma/microbiology/genetics ; Aged ; }, abstract = {We have previously demonstrated an association between increased abundance of Phascolarctobacterium and colorectal cancer (CRC) and adenomas in two independent Norwegian cohorts. Here we seek to verify our previous findings using new cohorts and methods. In addition, we characterize lifestyle and sex specificity, the functional potential of the Phascolarctobacterium species, and their interaction with other microbial species. We analyze Phascolarctobacterium with 16S rRNA sequencing, shotgun metagenome sequencing, and species-specific qPCR, using 2350 samples from three Norwegian cohorts-CRCAhus, NORCCAP, and CRCbiome-and a large publicly available data set, curatedMetagenomicData. Using metagenome-assembled genomes from the CRCbiome study, we explore the genomic characteristics and functional potential of the Phascolarctobacterium pangenome. Three species of Phascolarctobacterium associated with adenoma/CRC were consistently detected by qPCR and sequencing. Positive associations with adenomas/CRC were verified for Phascolarctobacterium succinatutens and negative associations were shown for Phascolarctobacterium faecium and adenoma in curatedMetagenomicData. Men show a higher prevalence of P. succinatutens across cohorts. Co-occurrence among Phascolarctobacterium species was low (<6%). Each of the three species shows distinct microbial composition and forms distinct correlation networks with other bacterial taxa, although Dialister invisus was negatively correlated to all investigated Phascolarctobacterium species. Pangenome analyses showed P. succinatutens to be enriched for genes related to porphyrin metabolism and degradation of complex carbohydrates, whereas glycoside hydrolase enzyme 3 was specific to P. faecium.IMPORTANCEUntil now Phascolarctobacterium has been going under the radar as a CRC-associated genus despite having been noted, but overseen, as such for over a decade. We found not just one, but two species of Phascolarctobacterium to be associated with CRC-Phascolarctobacterium succinatutens was more abundant in adenoma/CRC, while Phascolarctobacterium faecium was less abundant in adenoma. Each of them represents distinct communities, constituted by specific microbial partners and metabolic capacities-and they rarely occur together in the same patients. We have verified that P. succinatutens is increased in adenoma and CRC and this species should be recognized among the most important CRC-associated bacteria.}, } @article {pmid39287374, year = {2024}, author = {Vinogradova, E and Mukhanbetzhanov, N and Nurgaziyev, M and Jarmukhanov, Z and Aipova, R and Sailybayeva, A and Bekbossynova, M and Kozhakhmetov, S and Kushugulova, A}, title = {Impact of urbanization on gut microbiome mosaics across geographic and dietary contexts.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0058524}, pmid = {39287374}, issn = {2379-5077}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Urbanization ; Male ; Female ; Kazakhstan/epidemiology ; *Diet ; Adult ; Rural Population/statistics & numerical data ; Middle Aged ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Urban Population/statistics & numerical data ; Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; Young Adult ; }, abstract = {UNLABELLED: This study provides a comprehensive assessment of how urban-rural divides influence gut microbial diversity and composition across the distinct geographical landscapes of Kazakhstan, elucidating the intricate interplay between lifestyle, environment, and gut microbiome. In this prospective cohort study, we enrolled 651 participants from urban centers and rural settlements across Kazakhstan, following ethical approval and informed consent. Comprehensive demographic, dietary, and stool sample data were collected. 16S rRNA gene sequencing and shotgun metagenomics techniques were employed to delineate the intricate patterns of the gut microbiome. A rigorous statistical framework dissected the interplay between urbanization gradients, geography, dietary lifestyles, and microbial dynamics. Our findings demonstrate a stark microbial divide between urban and rural gut ecosystems. The study found significant differences in gut microbiome diversity and composition between urban and rural populations in Kazakhstan. Urban microbiomes exhibited reduced diversity, higher Firmicutes/Bacteroidetes ratios, and increased prevalence of genera Coprococcus and Parasutterella. In contrast, rural populations had greater microbial diversity and abundance of Ligilactobacillus, Sutterella, and Paraprevotella. Urbanization also influenced dietary patterns, with urban areas consuming more salt, cholesterol, and protein, while rural areas had diets richer in carbohydrates and fiber. The study also identified distinct patterns in the prevalence of antibiotic resistance genes and virulence factors between urban and rural gut microbiomes. This study sheds light on how urbanization may be deeply involved in shaping the intricate mosaic of the gut microbiome across Kazakhstan's diverse geographical and dietary landscapes, underscoring the complex interplay between environmental exposures, dietary lifestyles, and the microbial residents inhabiting our intestines.

IMPORTANCE: The study examined gut microbiome composition across diverse geographical locations in Kazakhstan, spanning urban centers and rural settlements. This allows for thoroughly investigating how urbanization gradients and geographic factors shape the gut microbiome. The study's examination of the gut resistome and prevalence of virulence-associated genes provide essential insights into the public health implications of urbanization-driven microbiome alterations. Collecting comprehensive demographic, dietary, and stool sample data enables the researchers to better understand the relationships between urbanization, nutritional patterns, and gut microbiome composition. The findings have important implications for understanding how urbanization-driven microbiome changes may impact human health and well-being, paving the way for tailored interventions to restore a balanced gut microbial ecology.}, } @article {pmid39287279, year = {2024}, author = {Xing, W and Yu, J and Cui, S and Liu, L and Zhi, Y and Zhang, T and Zhou, J}, title = {Analysis of the correlation between gut microbiome imbalance and the development of endometrial cancer based on metagenomics.}, journal = {Medicine}, volume = {103}, number = {37}, pages = {e39596}, pmid = {39287279}, issn = {1536-5964}, mesh = {Humans ; Female ; *Endometrial Neoplasms/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Case-Control Studies ; Middle Aged ; Prospective Studies ; *Metagenomics/methods ; Aged ; Adult ; }, abstract = {Endometrial cancer (EC) is the most prevalent gynecologic malignancy, with a higher risk in obese women, suggesting the potential involvement of gut microbiota in the progression of EC. However, there is no direct evidence of a connection between EC and the human gut microbiota. Using metagenomic sequencing, we investigated the relationship between gut microbiome imbalance and cancer development in patients with EC. In this prospective case-control study, we included 15 patients with EC based on endometrial biopsy in the case group and 15 women admitted to the hospital for female pelvic floor issues during the same time who did not have endometrial lesions from January 2023 to June 2023 in control group. The microbiota structure of EC cases and controls without benign or malignant endometrial lesions during the same time period was analyzed using metagenomic sequencing technology. We employed Alpha diversity analysis to reflect the richness and diversity of microbial communities. Statistical algorithm Bray-Curtis was utilized to calculate pairwise distances between samples, obtaining a beta diversity distance matrix. Subsequently, hierarchical clustering analysis was conducted based on the distance matrix. The results showed that the composition of bacterial colonies in both groups was dominated by Firmicutes, which had a higher proportion in the control group, followed by Bacteroidetes in the control group and Proteobacteria and Bacteroidetes in the case group. The abundance of Klebsiella (P = .02) was significantly higher, and the abundance of Alistipes (P = .04), Anearobutyricum (P = .01), and bacteria in Firmicutes such as Oscillospira and Catenibacterium was markedly lower in the case group than in the control group. These results demonstrated conclusively that a gut microbiome imbalance was associated with the development of EC.}, } @article {pmid39284445, year = {2024}, author = {Huo, C and Zhang, J and Yang, X and Li, X and Su, Y and Chen, Z}, title = {Dry season irrigation promotes nutrient cycling by reorganizing Eucalyptus rhizosphere microbiome.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176307}, doi = {10.1016/j.scitotenv.2024.176307}, pmid = {39284445}, issn = {1879-1026}, mesh = {*Eucalyptus ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; *Agricultural Irrigation/methods ; China ; *Fertilizers ; Phosphorus ; Soil/chemistry ; Nitrogen/metabolism ; Seasons ; Bacteria/metabolism ; }, abstract = {In southern China, seasonal droughts and low soil phosphorus content constrain the productivity of Eucalyptus trees. To understand the rhizosphere microbiome response to the dry season, metagenomic sequencing analysis was used to investigate the 6-year-old Eucalyptus rhizosphere microbiome under four different irrigation and fertilization treatments. The results showed that irrigation and fertilization during the dry season significantly altered the composition of microbiome in the rhizosphere soil of Eucalyptus plantations. The soil physicochemical properties and enzyme activity explained 30.73 % and 29.75 % of the changes in bacterial and fungal community structure in Eucalyptus rhizosphere soil, respectively. Irrigation and fertilization during the dry season significantly altered the physicochemical properties of rhizosphere soil. Compared with the seasonal drought without fertilizer treatment (CK), the dry season irrigation with fertilizer treatment (WF) significantly increased the content of total nitrogen (46.34 %), available nitrogen (37.72 %), available phosphorus (440.9 %), and organic matter (35.34 %). Soil organic matter (OM), pH, and available phosphorus (AP) were key environmental factors influencing the microbial community composition. Moreover, irrigation and fertilization promoted carbon fixation and nitrogen and phosphorus mineralization, increasing soil OM content and the availability of inorganic nitrogen and phosphorus. Meanwhile, compared to the CK, the increase of acid phosphatase (16.81 %), invertase (146.89 %)and urease (59.45 %) in rhizosphere soil under irrigation (W) treatment further proves that dry season irrigation promote the soil carbon, nitrogen and phosphorus cycles. Irrigation and fertilization treatment alleviated the constraints of low phosphorus in southern China's soil, which promoted Eucalyptus productivity. In conclusion, we suggest implementing reasonable irrigation and fertilization strategies in the production practice of Eucalyptus and utilizing microbial resources to improve soil fertility and Eucalyptus productivity.}, } @article {pmid39283121, year = {2024}, author = {Machado, DT and Dias, BdC and Cayô, R and Gales, AC and Marques de Carvalho, F and Vasconcelos, ATR}, title = {Uncovering new Firmicutes species in vertebrate hosts through metagenome-assembled genomes with potential for sporulation.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0211324}, pmid = {39283121}, issn = {2165-0497}, support = {E-26/210.012/2020//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; 88887.677436/2022-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; 402659/2018-0,443805/2018-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; OPP1193112//Bill and Melinda Gates Foundation (GF)/ ; 88887.508687/2020-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; 302023/2024-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 307915/2022-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 312066/2019-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; E-26/201.046/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; }, mesh = {Animals ; *Spores, Bacterial/genetics/growth & development ; *Phylogeny ; *Metagenome ; *Genome, Bacterial/genetics ; *Firmicutes/genetics/classification ; Humans ; Cattle ; Swine ; Gastrointestinal Microbiome/genetics ; Vertebrates/microbiology ; Poultry/microbiology ; }, abstract = {Metagenome-assembled genomes (MAGs) have contributed to identifying non-culturable microorganisms and understanding their ecological functions. MAGs offer an advantage in investigating sporulation-associated genes, especially given the difficulty of isolating many species residing in the gut microbiota of multiple hosts. Bacterial sporulation is a key survival mechanism with implications for pathogenicity and biotechnology. Here, we investigate MAGs from vertebrate hosts, emphasizing taxonomic identification and identifying sporulation-associated genes in potential novel species within the Firmicutes phylum. We identified potential new species in the classes Clostridia (Borkfalkiaceae, Lachnospiraceae, Monoglobaceae, and Oscillospiraceae families) and Bacilli (Bacillaceae and Erysipelotrichaceae families) through phylogenetic and functional pathway analyses, highlighting their sporulation potential. Our study covers 146 MAGs, 124 of them without refined taxonomic assignments at the family level. We found that Clostridia and Bacilli have unique sporulation gene profiles in the refined family MAGs for cattle, swine, poultry, and human hosts. The presence of genes related to Spo0A regulon, engulfment, and spore cortex in MAGs underscores fundamental mechanisms in sporulation processes in currently uncharacterized species with sporulation potential from metagenomic dark matter. Furthermore, genomic analyses predict sporulation potential based on gene presence, genome size, and metabolic pathways involved in spore formation. We emphasize MAGs covering families not yet characterized through the phylogenetic analysis, and with extensive potential for spore-forming bacteria within Clostridia, Bacilli, UBA4882, and UBA994 classes. These findings contribute to exploring spore-forming bacteria, which provides evidence for novel species diversity in multiple hosts, their adaptive strategies, and potential applications in biotechnology and host health.IMPORTANCESpores are essential for bacterial survival in harsh environments, facilitating their persistence and adaptation. Exploring sporulation-associated genes in metagenome-assembled genomes (MAGs) from different hosts contributes to clinical and biotechnological domains. Our study investigated the extent of genes associated with bacterial sporulation in MAGs from poultry, swine, cattle, and humans, revealing these genes in uncultivated bacteria. We identified potential novel Firmicutes species with sporulation capabilities through phylogenetic and functional analyses. Notably, MAGs belonging to Clostridia, Bacilli, and unknown classes, namely UBA4882 and UBA994, remained uncharacterized at the family level, which raises the hypothesis that sporulation would also be present in these genomes. These findings contribute to our understanding of microbial adaptation and have implications for microbial ecology, underlining the importance of sporulation in Firmicutes across different hosts. Further studies into novel species and their sporulation capability can contribute to bacterial maintenance mechanisms in various organisms and their applications in biotechnology studies.}, } @article {pmid39283083, year = {2024}, author = {Brennan, C and Belda-Ferre, P and Zuffa, S and Charron-Lamoureux, V and Mohanty, I and Ackermann, G and Allaband, C and Ambre, M and Boyer, T and Bryant, M and Cantrell, K and Gonzalez, A and McDonald, D and Salido, RA and Song, SJ and Wright, G and Dorrestein, PC and Knight, R}, title = {Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0098524}, pmid = {39283083}, issn = {2379-5077}, support = {U19 AG063744/AG/NIA NIH HHS/United States ; U19AG063744//HHS | National Institutes of Health (NIH)/ ; }, mesh = {*Microbiota/genetics ; Humans ; *RNA, Ribosomal, 16S/genetics ; Specimen Handling/methods ; }, abstract = {UNLABELLED: Large-scale studies are essential to answer questions about complex microbial communities that can be extremely dynamic across hosts, environments, and time points. However, managing acquisition, processing, and analysis of large numbers of samples poses many challenges, with cross-contamination being the biggest obstacle. Contamination complicates analysis and results in sample loss, leading to higher costs and constraints on mixed sample type study designs. While many researchers opt for 96-well plates for their workflows, these plates present a significant issue: the shared seal and weak separation between wells leads to well-to-well contamination. To address this concern, we propose an innovative high-throughput approach, termed as the Matrix method, which employs barcoded Matrix Tubes for sample acquisition. This method is complemented by a paired nucleic acid and metabolite extraction, utilizing 95% (vol/vol) ethanol to stabilize microbial communities and as a solvent for extracting metabolites. Comparative analysis between conventional 96-well plate extractions and the Matrix method, measuring 16S rRNA gene levels via quantitative polymerase chain reaction, demonstrates a notable decrease in well-to-well contamination with the Matrix method. Metagenomics, 16S rRNA gene amplicon sequencing (16S), and untargeted metabolomics analysis via liquid chromatography-tandem mass spectrometry (LC-MS/MS) confirmed that the Matrix method recovers reproducible microbial and metabolite compositions that can distinguish between subjects. This advancement is critical for large-scale study design as it minimizes well-to-well contamination and technical variation, shortens processing times, and integrates with automated infrastructure for enhancing sample randomization and metadata generation.

IMPORTANCE: Understanding dynamic microbial communities typically requires large-scale studies. However, handling large numbers of samples introduces many challenges, with cross-contamination being a major issue. It not only complicates analysis but also leads to sample loss and increased costs and restricts diverse study designs. The prevalent use of 96-well plates for nucleic acid and metabolite extractions exacerbates this problem due to their wells having little separation and being connected by a single plate seal. To address this, we propose a new strategy using barcoded Matrix Tubes, showing a significant reduction in cross-contamination compared to conventional plate-based approaches. Additionally, this method facilitates the extraction of both nucleic acids and metabolites from a single tubed sample, eliminating the need to collect separate aliquots for each extraction. This innovation improves large-scale study design by shortening processing times, simplifying analysis, facilitating metadata curation, and producing more reliable results.}, } @article {pmid39277616, year = {2024}, author = {Jia, Y and Shi, Y and Wang, J and Liu, H and Huang, Y and Wang, H and Liu, Y and Peng, J}, title = {Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21491}, pmid = {39277616}, issn = {2045-2322}, support = {GZC20242045//Postdoctoral Fellowship Program of CPSF/ ; 2023zzts896//Fundamental Research Funds for Central Universities of the Central South University/ ; 82170661//National Natural Science Foundation of China/ ; 2023DK2002//Key Project of Research and Development Plan of Hunan Province/ ; }, mesh = {*Gastrointestinal Microbiome ; *Pancreatitis/microbiology/metabolism ; Animals ; *Metabolomics/methods ; *Metagenomics/methods ; Mice ; Metabolome ; Disease Models, Animal ; Dysbiosis/microbiology/metabolism ; Mice, Inbred C57BL ; Male ; Acute Disease ; }, abstract = {Acute pancreatitis (AP) is an inflammatory disease of the pancreas. Despite of a steadily increasing in morbidity and mortality, there is still no effective therapy. Gut microbial dysbiosis and its derived-metabolites disorder have been shown to play an important role in the development of AP, however, little is known regarding the crosstalk between gut microbiota and metabolites. In this study, we assessed the alterations in gut microbiota and metabolites by constructing three AP mouse models by means of metagenomic and metabolomic sequencing, and further clarified their relationship by correlation analysis. The results revealed that each model exhibited unique flora and metabolite profiles. KEGG analysis showed that the differential flora and metabolite-enriched pathway functions were correlated with lipid metabolism and amino acid metabolism. Moreover, two core differential bacterial species on Burkholderiales bacterium YL45 and Bifidobacterium pseudolongum along with eleven differential metabolites appeared to exert certain effects during the course of AP. In conclusion, further exploration of the crosstalk between microbiota and derived metabolites may provide novel insights and strategies into the diagnosis and treatment of AP.}, } @article {pmid39277613, year = {2024}, author = {da Silva, S and Vuong, P and Amaral, JRV and da Silva, VAS and de Oliveira, SS and Vermelho, AB and Beale, DJ and Bissett, A and Whiteley, AS and Kaur, P and Macrae, A}, title = {The piranha gut microbiome provides a selective lens into river water biodiversity.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21518}, pmid = {39277613}, issn = {2045-2322}, support = {Bolsa de Doutorado//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; Bolsa de Iniciacao Cientifica//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; Bolsa de doutordo//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; PRINT 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, mesh = {*Rivers/microbiology ; *Gastrointestinal Microbiome/genetics ; Animals ; *Biodiversity ; Metagenome ; Metagenomics/methods ; Water Microbiology ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {Advances in omics technologies have enabled the in-depth study of microbial communities and their metabolic profiles from all environments. Here metagenomes were sampled from piranha (Serrasalmus rhombeus) and from river water from the Rio São Benedito (Amazon Basin). Shotgun metagenome sequencing was used to explore diversity and to test whether fish microbiomes are a good proxy for river microbiome studies. The results showed that the fish microbiomes were not significantly different from the river water microbiomes at higher taxonomic ranks. However, at the genus level, fish microbiome alpha diversity decreased, and beta diversity increased. This result repeated for functional gene abundances associated with specific metabolic categories (SEED level 3). A clear delineation between water and fish was seen for beta diversity. The piranha microbiome provides a good and representative subset of its river water microbiome. Variations seen in beta biodiversity were expected and can be explained by temporal variations in the fish microbiome in response to stronger selective forces on its biodiversity. Metagenome assembled genomes construction was better from the fish samples. This study has revealed that the microbiome of a piranha tells us a lot about its river water microbiome and function.}, } @article {pmid39276741, year = {2024}, author = {Kumar, A and Lakhawat, SS and Singh, K and Kumar, V and Verma, KS and Dwivedi, UK and Kothari, SL and Malik, N and Sharma, PK}, title = {Metagenomic analysis of soil from landfill site reveals a diverse microbial community involved in plastic degradation.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135804}, doi = {10.1016/j.jhazmat.2024.135804}, pmid = {39276741}, issn = {1873-3336}, mesh = {*Soil Microbiology ; *Waste Disposal Facilities ; *Biodegradation, Environmental ; *Plastics ; *Bacteria/genetics/classification/metabolism ; *Fungi/genetics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Soil Pollutants/metabolism ; }, abstract = {In this study, we have investigated microbial communities structure and function using high throughput amplicon sequencing and whole metagenomic sequencing of DNA extracted from different depths of a plastic-laden landfill site. With diverse taxonomic groups inhabiting the plastic-rich soil, our study demonstrates the remarkable adaptability of microbes to use this new substrate as a carbon source. FTIR spectroscopic analysis of soil indicated degradation of plastic as perceived from the carbonyl index of 0.16, 0.72, and 0.44 at 0.6, 0.9 and 1.2 m depth, respectively. Similarly, water contact angles of 108.7 degree, 99.7 degree, 62.7 degree, and 77.8 degree of plastic pieces collected at 0.3, 0.6, 0.9, and 1.2 m depths respectively showed increased wettability and hydrophilicity of the plastic. Amplicon analysis of 16S and 18 S rRNA revealed a high abundance of several plastic-degrading bacterial groups, including Pseudomonas, Rhizobiales, Micrococcaceae, Chaetomium, Methylocaldum, Micromonosporaceae, Rhodothermaceae and fungi, including Trichoderma, Aspergillus, Candida at 0.9 m. The co-existence of specific microbial groups at different depths of landfill site indicates importance of bacterial and fungal interactions for plastic. Whole metagenome analysis of soil sample at 0.9 m depth revealed a high abundance of genes encoding enzymes that participate in the biodegradation of PVC, polyethylene, PET, and polyurethane. Curation of the pathways related to the degradation of these materials provided a blueprint for plastic biodegradation in this ecosystem. Altogether, our study has highlighted the importance of microbial cooperation for the biodegradation of pollutants. Our metagenome-based investigation supports the current perception that consortia of fungi-bacteria are preferable to axenic cultures for effective bioremediation of the environment.}, } @article {pmid39267241, year = {2024}, author = {Doni, L and Azzola, A and Oliveri, C and Bosi, E and Auguste, M and Morri, C and Bianchi, CN and Montefalcone, M and Vezzulli, L}, title = {Genome-resolved metagenomics revealed novel microbial taxa with ancient metabolism from macroscopic microbial mat structures inhabiting anoxic deep reefs of a Maldivian Blue Hole.}, journal = {Environmental microbiology reports}, volume = {16}, number = {5}, pages = {e13315}, pmid = {39267241}, issn = {1758-2229}, support = {CN_00000033//Centro Nazionale di Ricerca - Biodiversità (Italy) project (PNRR CN00000033 - Centro Nazionale Biodiversità/ ; CUP D33C22000960007//Italian Ministry of University and Research/ ; }, mesh = {*Metagenomics ; *Phylogeny ; *Metagenome ; Bacteria/classification/genetics/isolation & purification/metabolism ; Geologic Sediments/microbiology ; Genome, Bacterial/genetics ; Anaerobiosis ; Deltaproteobacteria/genetics/classification/isolation & purification/metabolism ; Chloroflexi/genetics/classification/isolation & purification/metabolism ; Proteobacteria/genetics/classification/isolation & purification ; Microbiota ; }, abstract = {Blue holes are vertical water-filled openings in carbonate rock that exhibit complex morphology, ecology, and water chemistry. In this study, macroscopic microbial mat structures found in complete anoxic conditions in the Faanu Mudugau Blue Hole (Maldives) were studied by metagenomic methods. Such communities have likely been evolutionary isolated from the surrounding marine environment for more than 10,000 years since the Blue Hole formation during the last Ice Age. A total of 48 high-quality metagenome-assembled genomes (MAGs) were recovered, predominantly composed of the phyla Chloroflexota, Proteobacteria and Desulfobacterota. None of these MAGs have been classified to species level (<95% ANI), suggesting the discovery of several new microbial taxa. In particular, MAGs belonging to novel bacterial genera within the order Dehalococcoidales accounted for 20% of the macroscopic mat community. Genome-resolved metabolic analysis of this dominant microbial fraction revealed a mixotrophic lifestyle based on energy conservation via fermentation, hydrogen metabolism and anaerobic CO2 fixation through the Wood-Ljungdahl pathway. Interestingly, these bacteria showed a high proportion of ancestral genes in their genomes providing intriguing perspectives on mechanisms driving microbial evolution in this peculiar environment. Overall, our results provide new knowledge for understanding microbial life under extreme conditions in blue hole environments.}, } @article {pmid39275913, year = {2024}, author = {Takada, K and Nakagawa, S and Kryukov, K and Ozawa, M and Watanabe, T}, title = {Metagenomic analysis of the gut microbiota of hooded cranes (Grus monacha) on the Izumi plain in Japan.}, journal = {FEBS open bio}, volume = {14}, number = {12}, pages = {1972-1984}, pmid = {39275913}, issn = {2211-5463}, support = {//Crane Conservation by the City of Izumi/ ; //Tokyo Biochemical Research Foundation/ ; JPMJCR20H6//Core Research for Evolutional Science and Technology/ ; //2020 Tokai University School of Medicine Research Aid/ ; 22gm1610010h0001//Japan Agency for Medical Research and Development/ ; JP223fa627002h//Japan Agency for Medical Research and Development/ ; //Takeda Science Foundation/ ; 16H06429//Japan Society for the Promotion of Science/ ; 16H06434//Japan Society for the Promotion of Science/ ; 16K21723//Japan Society for the Promotion of Science/ ; 19H04843//Japan Society for the Promotion of Science/ ; 19fk0108171//Japan Society for the Promotion of Science/ ; 21J01036//Japan Society for the Promotion of Science/ ; 22K15469//Japan Society for the Promotion of Science/ ; JP19fk0108113//Japan Society for the Promotion of Science/ ; JP22H02521//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; Japan ; *Gastrointestinal Microbiome/genetics ; *Birds/microbiology/virology ; *Metagenomics/methods ; Feces/microbiology ; Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing ; Metagenome/genetics ; }, abstract = {Recent advances in DNA sequencing technology have dramatically improved our understanding of the gut microbiota of various animal species. However, research on the gut microbiota of birds lags behind that of many other vertebrates, and information about the gut microbiota of wild birds such as migratory waterfowl is particularly lacking. Because the ecology of migratory waterfowl (e.g., lifestyle, diet, physiological characteristics) differs from that of other birds, the gut microbiota of migratory waterfowl likely also differs, but much is still unknown. The hooded crane (Grus monacha) is an important representative migratory waterbird species and is listed as endangered on the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species. In this study, we analyzed the bacterial and viral microbiota in the gut of hooded cranes by using deep sequencing data from fecal samples of hooded cranes that winter on the Izumi plain in Japan, and found that Cetobacterium, Clupeiformes, and Pbunavirus were clearly present in the fecal samples of hooded cranes. These findings advance our understanding of the ecology of hooded cranes.}, } @article {pmid39275258, year = {2024}, author = {Wang, M and Chen, Y and Song, AX and Weng, X and Meng, Y and Lin, J and Mao, YH}, title = {The Combination of Exercise and Konjac Glucomannan More Effectively Prevents Antibiotics-Induced Dysbiosis in Mice Compared with Singular Intervention.}, journal = {Nutrients}, volume = {16}, number = {17}, pages = {}, pmid = {39275258}, issn = {2072-6643}, support = {2023A1515010004//Guangdong Basic and Applied Basic Research Foundation/ ; 2023ZDZX2035//Special Funds in Key Areas of Guangdong Provincial Department of Education/ ; S202410585045//The College Students Innovation and Entrepreneurship Training Program/ ; 202410585015//The College Students Innovation and Entrepreneurship Training Program/ ; 82003434//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Mannans/pharmacology ; *Dysbiosis/prevention & control/chemically induced ; *Mice, Inbred C57BL ; *Anti-Bacterial Agents/pharmacology/adverse effects ; *Gastrointestinal Microbiome/drug effects ; *Physical Conditioning, Animal ; Mice ; Male ; Combined Modality Therapy ; }, abstract = {Our previous studies have demonstrated that konjac glucomannan (KGM) can prevent dysbiosis induced by antibiotics. While exercise may also impact the gut microbiome, there are limited studies reporting its protective effect on antibiotic-induced dysbiosis. Therefore, this study investigated the preventive and regulatory effects of a combination of 6-week exercise and KGM intervention on antibiotic-induced dysbiosis in C57BL/6J mice compared with a single intervention. The results showed that combined exercise and KGM intervention could restore the changes in the relative abundance of Bacteroides (3.73% with CTL versus 14.23% with ATBX versus 4.46% with EK) and Prevotellaceae_Prevotella (0.33% with CTL versus 0.00% with ATBX versus 0.30% with EK) induced by antibiotics (p < 0.05), and minimized the Bray-Curtis distance induced by antibiotics (0.55 with CTL versus 0.81 with ATBX versus 0.80 with EXC versus 0.83 with KGM versus 0.75 with EK). Compared with the combined intervention, exercise intervention also produced a certain level of recovery effects; the relative abundance of Rikenellaceae (1.96% with CTL versus 0.09% with ATBX versus 0.49% with EXC) was restored, while KGM supplementation showed the best preventive effect. In addition, the combination of exercise and KGM significantly enriched microbial purine metabolic pathways (p < 0.05). These findings indicate that combining exercise with KGM could be a promising approach to reducing the side effects of antibiotics on the gut microbiome.}, } @article {pmid39273435, year = {2024}, author = {Di Chiano, M and Sallustio, F and Fiocco, D and Rocchetti, MT and Spano, G and Pontrelli, P and Moschetta, A and Gesualdo, L and Gadaleta, RM and Gallone, A}, title = {Psychobiotic Properties of Lactiplantibacillus plantarum in Neurodegenerative Diseases.}, journal = {International journal of molecular sciences}, volume = {25}, number = {17}, pages = {}, pmid = {39273435}, issn = {1422-0067}, support = {1062//PON "RICERCA E INNOVAZIONE" 2014-2020-Innovazione/ ; Call for tender No. 341 of 15 March 2022 of Italian Ministry of University and Research funded by the European Union - Next Generation EU//National Recovery and Resilience Plan (NRRP)/ ; Concession Decree No. 1550 of 11 October 2022 adopted by the Italian Ministry of University and Research, CUP D93C22000890001//Italian Ministry of University and Research, CUP D93C22000890001/ ; Codice progetto n. 2022H9MPZ5//MIUR- PRIN Progetti di Ricerca di Rilevante Interesse Nazionale 2022/ ; Id. 23239//AIRC IG 2019/ ; Call for tender No. 3138 of 16/12/2021 of Italian Ministry of University and Research funded by the European Union//National Recovery and Resilience Plan (NRRP)/ ; Project code: CN00000041, CUP H93C22000430007//NextGenerationEU/ ; PNRR-MR1-2022-12376395//European Union - Next Generation EU - PNRR M6C2/ ; "POFACS" - ARS01_00640 -", D.D. 1211/2020 and 1104/2021//Italian Ministry of University and Research (MIUR)/ ; PRA-HE 2021//University of Foggia/ ; }, mesh = {Humans ; *Neurodegenerative Diseases/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Probiotics/therapeutic use ; Dysbiosis/microbiology ; Brain-Gut Axis ; Animals ; }, abstract = {Neurodegenerative disorders are the main cause of cognitive and physical disabilities, affect millions of people worldwide, and their incidence is on the rise. Emerging evidence pinpoints a disturbance of the communication of the gut-brain axis, and in particular to gut microbial dysbiosis, as one of the contributors to the pathogenesis of these diseases. In fact, dysbiosis has been associated with neuro-inflammatory processes, hyperactivation of the neuronal immune system, impaired cognitive functions, aging, depression, sleeping disorders, and anxiety. With the rapid advance in metagenomics, metabolomics, and big data analysis, together with a multidisciplinary approach, a new horizon has just emerged in the fields of translational neurodegenerative disease. In fact, recent studies focusing on taxonomic profiling and leaky gut in the pathogenesis of neurodegenerative disorders are not only shedding light on an overlooked field but are also creating opportunities for biomarker discovery and development of new therapeutic and adjuvant strategies to treat these disorders. Lactiplantibacillus plantarum (LBP) strains are emerging as promising psychobiotics for the treatment of these diseases. In fact, LBP strains are able to promote eubiosis, increase the enrichment of bacteria producing beneficial metabolites such as short-chain fatty acids, boost the production of neurotransmitters, and support the homeostasis of the gut-brain axis. In this review, we summarize the current knowledge on the role of the gut microbiota in the pathogenesis of neurodegenerative disorders with a particular focus on the benefits of LBP strains in Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, autism, anxiety, and depression.}, } @article {pmid39273112, year = {2024}, author = {Druker, S and Sicsic, R and Ravid, S and Scheinin, S and Raz, T}, title = {Reproductive Tract Microbial Transitions from Late Gestation to Early Postpartum Using 16S rRNA Metagenetic Profiling in First-Pregnancy Heifers.}, journal = {International journal of molecular sciences}, volume = {25}, number = {17}, pages = {}, pmid = {39273112}, issn = {1422-0067}, mesh = {Female ; Animals ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; Cattle ; *Postpartum Period ; *Vagina/microbiology ; *Microbiota/genetics ; *Uterus/microbiology ; Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; Metagenome ; }, abstract = {Studies in recent years indicate that reproductive tract microbial communities are crucial for shaping mammals' health and reproductive outcomes. Following parturition, uterine bacterial contamination often occurs due to the open cervix, which may lead to postpartum uterine inflammatory diseases, especially in primiparous individuals. However, investigations into spatio-temporal microbial transitions in the reproductive tract of primigravid females remain limited. Our objective was to describe and compare the microbial community compositions in the vagina at late gestation and in the vagina and uterus at early postpartum in first-pregnancy heifers. Three swab samples were collected from 33 first-pregnancy Holstein Friesian heifers: one vaginal sample at gestation day 258 ± 4, and vaginal and uterine samples at postpartum day 7 ± 2. Each sample underwent 16S rRNA V4 region metagenetic analysis via Illumina MiSeq, with bioinformatics following Mothur MiSeq SOP. The reproductive tract bacterial communities were assigned to 1255 genus-level OTUs across 30 phyla. Dominant phyla, accounting for approximately 90% of the communities, included Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Fusobacteria. However, the results revealed distinct shifts in microbial composition between the prepartum vagina (Vag-pre), postpartum vagina (Vag-post), and postpartum uterus (Utr-post). The Vag-pre and Utr-post microbial profiles were the most distinct. The Utr-post group had lower relative abundances of Proteobacteria but higher abundances of Bacteroidetes, Fusobacteria, and Tenericutes compared to Vag-pre, while Vag-post displayed intermediate values for these phyla, suggesting a transitional profile. Additionally, the Utr-post group exhibited lower bacterial richness and diversity compared to both Vag-pre and Vag-post. The unsupervised probabilistic Dirichlet Multinomial Mixtures model identified two distinct community types: most Vag-pre samples clustered into one type and Utr-post samples into another, while Vag-post samples were distributed evenly between the two. LEfSe analysis revealed distinct microbial profiles at the genus level. Overall, specific microbial markers were associated with anatomical and temporal transitions, revealing a dynamic microbial landscape during the first pregnancy and parturition. These differences highlight the complexity of these ecosystems and open new avenues for research in reproductive biology and microbial ecology.}, } @article {pmid39271469, year = {2024}, author = {Ciuchcinski, K and Stokke, R and Steen, IH and Dziewit, L}, title = {Landscape of the metaplasmidome of deep-sea hydrothermal vents located at Arctic Mid-Ocean Ridges in the Norwegian-Greenland Sea: ecological insights from comparative analysis of plasmid identification tools.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {10}, pages = {}, pmid = {39271469}, issn = {1574-6941}, support = {UMO-2019/34/H/NZ2/00584//National Science Centre/ ; }, mesh = {*Plasmids/genetics ; *Hydrothermal Vents/microbiology ; Arctic Regions ; *Metagenomics ; Seawater/microbiology ; Bacteria/genetics/classification/isolation & purification ; Microbiota/genetics ; Norway ; Oceans and Seas ; Metagenome ; }, abstract = {Plasmids are one of the key drivers of microbial adaptation and evolution. However, their diversity and role in adaptation, especially in extreme environments, remains largely unexplored. In this study, we aimed to identify, characterize, and compare plasmid sequences originating from samples collected from deep-sea hydrothermal vents located in Arctic Mid-Ocean Ridges. To achieve this, we employed, and benchmarked three recently developed plasmid identification tools-PlasX, GeNomad, and PLASMe-on metagenomic data from this unique ecosystem. To date, this is the first direct comparison of these computational methods in the context of data from extreme environments. Upon recovery of plasmid contigs, we performed a multiapproach analysis, focusing on identifying taxonomic and functional biases within datasets originating from each tool. Next, we implemented a majority voting system to identify high-confidence plasmid contigs, enhancing the reliability of our findings. By analysing the consensus plasmid sequences, we gained insights into their diversity, ecological roles, and adaptive significance. Within the high-confidence sequences, we identified a high abundance of Pseudomonadota and Campylobacterota, as well as multiple toxin-antitoxin systems. Our findings ensure a deeper understanding of how plasmids contribute to shaping microbial communities living under extreme conditions of hydrothermal vents, potentially uncovering novel adaptive mechanisms.}, } @article {pmid39271424, year = {2024}, author = {Bokulich, NA and Robeson, MS}, title = {Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities.}, journal = {Trends in microbiology}, volume = {32}, number = {12}, pages = {1163-1166}, doi = {10.1016/j.tim.2024.08.011}, pmid = {39271424}, issn = {1878-4380}, mesh = {Humans ; *Neoplasms/microbiology ; *Microbiota ; *Computational Biology/methods ; *Metagenomics/methods ; *Machine Learning ; Sequence Analysis, DNA/methods ; }, abstract = {Increasing evidence suggests that the human microbiome plays an important role in cancer risk and treatment. Untargeted 'omics' techniques have accelerated research into microbiome-cancer interactions, supporting the discovery of novel associations and mechanisms. However, these techniques require careful selection and use to avoid biases and other pitfalls. In this essay, we discuss selected challenges involved in the analysis of microbiome data in the context of cancer, including the application of machine learning (ML). We focus on DNA sequencing-based (e.g., metagenomics) methods, but many of the pitfalls and opportunities generalize to other omics technologies as well. We advocate for extended training opportunities, community standards, and best practices for sharing data and code to advance transparency and reproducibility in cancer microbiome research.}, } @article {pmid39270881, year = {2025}, author = {Bai, M and Zhou, Z and Yin, M and Wang, M and Gao, X and Zhao, J}, title = {The use of metagenomic and untargeted metabolomics in the analysis of the effects of the Lycium barbarum glycopeptide on allergic airway inflammation induced by Artemesia annua pollen.}, journal = {Journal of ethnopharmacology}, volume = {337}, number = {Pt 1}, pages = {118816}, doi = {10.1016/j.jep.2024.118816}, pmid = {39270881}, issn = {1872-7573}, mesh = {Animals ; *Pollen ; *Metabolomics ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Artemisia annua/chemistry ; Mice, Inbred BALB C ; Lycium/chemistry ; Anti-Inflammatory Agents/pharmacology ; Metagenomics/methods ; Disease Models, Animal ; Female ; Drugs, Chinese Herbal/pharmacology ; Respiratory Hypersensitivity/drug therapy ; Male ; Plant Extracts/pharmacology ; }, abstract = {The prevalence of allergic airway inflammation (AAI) worldwide is high. Artemisia annua L. pollen is spread worldwide, and allergic diseases caused by its plant polysaccharides, which are closely related to the intestinal microbiota, have anti-inflammatory effects. Further isolation and purification of Lycium barbarum L. yielded its most effective component Lycium barbarum L. glycopeptide (LbGP), which can inhibit inflammation in animal models. However, its therapeutic effect on AAI and its mechanism of regulating the intestinal flora have not been fully investigated.

AIM OF THE STUDY: To explore LbGP in APE-induced immunological mechanisms of AAI and the interaction mechanism of the intestinal flora and metabolites.

METHODS: A mouse model of AAI generated from Artemisia annua pollen was constructed, and immunological indices related to the disease were examined. A combination of macrogenomic and metabolomic analyses was used to investigate the effects of LbGP on the gut microbial and metabolite profiles of mice with airway inflammation.

RESULTS: LbGP effectively alleviated Artemisia. annua pollen extract (APE)-induced AAI, corrected Th1/Th2 immune dysregulation, decreased Th17 cells, increased Treg cells, and altered the composition and function of the intestinal microbiota. LbGP treatment increased the number of OdoribacterandDuncaniella in the intestines of the mice, but the numble of Alistipes and Ruminococcus decreased. Metabolite pathway enrichment analysis were used to determine the effects of taurine and hypotaurine metabolism, bile acid secretion, and pyrimidine metabolism pathways on disease.

CONCLUSION: Our results revealed significant changes in the macrogenome and metabolome following APE and LbGP intervention, revealed potential correlations between gut microbial species and metabolites, and highlighted the beneficial effects of LbGP on AAI through the modulation of the gut microbiome and host metabolism.}, } @article {pmid39269772, year = {2024}, author = {Rahal, Z and Liu, Y and Peng, F and Yang, S and Jamal, MA and Sharma, M and Moreno, H and Damania, AV and Wong, MC and Ross, MC and Sinjab, A and Zhou, T and Chen, M and Tarifa Reischle, I and Feng, J and Chukwuocha, C and Tang, E and Abaya, C and Lim, JK and Leung, CH and Lin, HY and Deboever, N and Lee, JJ and Sepesi, B and Gibbons, DL and Wargo, JA and Fujimoto, J and Wang, L and Petrosino, JF and Ajami, NJ and Jenq, RR and Moghaddam, SJ and Cascone, T and Hoffman, K and Kadara, H}, title = {Inflammation Mediated by Gut Microbiome Alterations Promotes Lung Cancer Development and an Immunosuppressed Tumor Microenvironment.}, journal = {Cancer immunology research}, volume = {12}, number = {12}, pages = {1736-1752}, pmid = {39269772}, issn = {2326-6074}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; R01 CA205608/CA/NCI NIH HHS/United States ; S10 OD024977/OD/NIH HHS/United States ; R01CA248731//National Cancer Institute (NCI)/ ; R01 CA248731/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Tumor Microenvironment/immunology ; *Lung Neoplasms/immunology/microbiology/pathology ; Mice ; Humans ; *Inflammation/immunology ; Adenocarcinoma of Lung/immunology/microbiology/pathology ; Lipocalin-2/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Mice, Knockout ; }, abstract = {Accumulating evidence indicates that the gut microbiome influences cancer progression and therapy. We recently showed that progressive changes in gut microbial diversity and composition are closely coupled with tobacco-associated lung adenocarcinoma in a human-relevant mouse model. Furthermore, we demonstrated that the loss of the antimicrobial protein Lcn2 in these mice exacerbates protumor inflammatory phenotypes while further reducing microbial diversity. Yet, how gut microbiome alterations impinge on lung adenocarcinoma development remains poorly understood. In this study, we investigated the role of gut microbiome changes in lung adenocarcinoma development using fecal microbiota transfer and delineated a pathway by which gut microbiome alterations incurred by loss of Lcn2 fostered the proliferation of proinflammatory bacteria of the genus Alistipes, triggering gut inflammation. This inflammation propagated systemically, exerting immunosuppression within the tumor microenvironment, augmenting tumor growth through an IL6-dependent mechanism and dampening response to immunotherapy. Corroborating our preclinical findings, we found that patients with lung adenocarcinoma with a higher relative abundance of Alistipes species in the gut showed diminished response to neoadjuvant immunotherapy. These insights reveal the role of microbiome-induced inflammation in lung adenocarcinoma and present new potential targets for interception and therapy.}, } @article {pmid39269181, year = {2024}, author = {Quan, Q and Liu, J and Li, C and Ke, Z and Tan, Y}, title = {Insights into prokaryotic communities and their potential functions in biogeochemical cycles in cold seep.}, journal = {mSphere}, volume = {9}, number = {10}, pages = {e0054924}, pmid = {39269181}, issn = {2379-5042}, mesh = {*Bacteria/classification/genetics/metabolism ; *Microbiota ; *Nitrogen/metabolism ; *Geologic Sediments/microbiology ; *Seawater/microbiology/chemistry ; *Sulfur/metabolism ; Phosphorus/metabolism/analysis ; Cold Temperature ; Metagenomics ; }, abstract = {UNLABELLED: Microorganisms are significant drivers of organic matter mineralization and are essential in marine biogeochemical cycles. However, the variations and influencing factors in prokaryotic communities from cold-seep sediments to the water column and the specific role of these microorganisms in biogeochemical cycles in the water column above cold seep remain unclear. Here, we investigated prokaryotic communities and their roles in nitrogen/sulfur cycling processes and conducted in situ dissolved organic matter (DOM) enrichment experiments to explore the effects of diverse sources of DOM on prokaryotic communities. Field investigations showed that the prokaryotic communities in the near-bottom water were more similar to those in the deep layer of the euphotic zone (44.60%) and at a depth of 400 m (50.89%) than those in the sediment (18.00%). DOM enrichment experiments revealed that adding dissolved organic nitrogen (DON) and phosphorus DOP caused a notable increase in the relative abundances of Rhodobacterales and Vibrionales, respectively. A remarkable increase was observed in the relative abundance of Alteromonadales and Pseudomonadales after the addition of dissolved organic sulfur (DOS). The metagenomic results revealed that Proteobacteria served as the keystone taxa in mediating the biogeochemical cycles of nitrogen, phosphorus, and sulfur in the Haima cold seep. This study highlights the responses of prokaryotes to DOM with different components and the microbially driven elemental cycles in cold seeps, providing a foundational reference for further studies on material energy metabolism and the coupled cycling of essential elements mediated by deep-sea microorganisms.

IMPORTANCE: Deep-sea cold seeps are among the most productive ecosystems, sustaining unique fauna and microbial communities through the release of methane and other hydrocarbons. Our study revealed that the influence of seepage fluid on the prokaryotic community in the water column is surprisingly limited, which challenges conventional views regarding the impact of seepage fluids. In addition, we identified that different DOM compositions play a crucial role in shaping the prokaryotic community composition, providing new insights into the factors driving microbial diversity in cold seeps. Furthermore, the study highlighted Proteobacteria as key and multifaceted drivers of biogeochemical cycles in cold seeps, emphasizing their significant contribution to complex interactions and processes. These findings offer a fresh perspective on the dynamics of cold-seep environments and their microbial communities, advancing our understanding of the biogeochemical functions in deep-sea environments.}, } @article {pmid39268238, year = {2024}, author = {Wang, J and Su, C and Qian, M and Wang, X and Chen, C and Liu, Y and Liu, W and Xiang, Z and Xu, B}, title = {Subchronic toxic effects of bisphenol A on the gut-liver-hormone axis in rats via intestinal flora and metabolism.}, journal = {Frontiers in endocrinology}, volume = {15}, number = {}, pages = {1415216}, pmid = {39268238}, issn = {1664-2392}, mesh = {Animals ; *Phenols/toxicity ; Male ; Female ; Rats ; *Gastrointestinal Microbiome/drug effects ; *Benzhydryl Compounds/toxicity ; *Liver/drug effects/metabolism/pathology ; *Endocrine Disruptors/toxicity ; Rats, Sprague-Dawley ; Hormones/blood ; }, abstract = {BACKGROUND: Bisphenol A (BPA), a characteristic endocrine disruptor, is a substance that seriously interferes with the human endocrine system and causes reproductive disorders and developmental abnormalities. However, its toxic effects on the gut-liver-hormone axis are still unclear.

METHOD: Male and female rats were exposed to BPA (300 mg/kg) by oral gavage for 60 consecutive days. H&E staining was used for histopathological evaluation, and the serum biochemical indexes were determined using an automatic analyzer. The 16S rRNA gene sequencing was used to detect the intestinal microbial diversity, and the GC-MS was used to analyze the contents of short-chain fatty acids (SCFAs) in colon contents. UPLC-QTOF MS was used to analyze the related metabolites. The ELISA method was used to assess the levels of serum inflammatory factors.

RESULTS: Histopathological analysis indicated that the liver, heart, and testis were affected by BPA. There was a significant effect on alanine aminotransferase (ALT), triglyceride (TG), total cholesterol (TC), and low-density lipoprotein (LDL) in the male-BPA group (P < 0.05), and globulin (GLB), indirect bilirubin (IBIL), alkaline phosphatase (ALP), ALT, TG, TC, high-density lipoprotein (HDL), and creatinine (Cr) in the female-BPA group (P < 0.05). Metagenomics (16S rRNA gene sequencing) analysis indicated that BPA reduced the diversity and changed the composition of gut microbiota in rats significantly. Compared with the control and blank groups, the contents of caproic acid, isobutyric acid, isovaleric acid, and propanoic acid in the colon contents decreased in the male-BPA group (P < 0.05), and caproic acid, isobutyric acid, isovaleric acid, and valeric acid in the colon contents decreased in the female-BPA group (P < 0.05). Metabolomic analysis of the serum indicated that BPA could regulate bile acid levels, especially ursodeoxycholic acid (UDCA) and its conjugated forms. The contents of amino acids, hormones, and lipids were also significantly affected after exposure to BPA. The increase in interleukin-6 (IL-6), interleukin-23 (IL-23), and transforming growth factor-β (TGF-β) in the serum of the male-BPA group suggests that BPA exposure affects the immune system.

CONCLUSION: BPA exposure will cause toxicity to rats via disrupting the gut-liver-hormone axis.}, } @article {pmid39267171, year = {2024}, author = {Gandasegui, J and Fleitas, PE and Petrone, P and Grau-Pujol, B and Novela, V and Rubio, E and Muchisse, O and Cossa, A and Jamine, JC and Sacoor, C and Brienen, EAT and van Lieshout, L and Muñoz, J and Casals-Pascual, C}, title = {Baseline gut microbiota diversity and composition and albendazole efficacy in hookworm-infected individuals.}, journal = {Parasites & vectors}, volume = {17}, number = {1}, pages = {387}, pmid = {39267171}, issn = {1756-3305}, mesh = {*Albendazole/therapeutic use/pharmacology/administration & dosage ; Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Anthelmintics/therapeutic use/administration & dosage ; *Hookworm Infections/drug therapy ; *Feces/parasitology/microbiology ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Adult ; Treatment Outcome ; Animals ; Young Adult ; Middle Aged ; Ancylostomatoidea/drug effects/genetics ; Adolescent ; Child ; }, abstract = {Soil-transmitted helminth (STH) infections account for a significant global health burden, necessitating mass drug administration with benzimidazole-class anthelmintics, such as albendazole (ALB), for morbidity control. However, ALB efficacy shows substantial variability, presenting challenges for achieving consistent treatment outcomes. We have explored the potential impact of the baseline gut microbiota on ALB efficacy in hookworm-infected individuals through microbiota profiling and machine learning (ML) techniques. Our investigation included 89 stool samples collected from hookworm-infected individuals that were analyzed by microscopy and quantitative PCR (qPCR). Of these, 44 were negative by microscopy for STH infection using the Kato-Katz method and qPCR 21 days after treatment, which entails a cure rate of 49.4%. Microbiota characterization was based on amplicon sequencing of the V3-V4 16S ribosomal RNA gene region. Alpha and beta diversity analyses revealed no significant differences between participants who were cured and those who were not cured, suggesting that baseline microbiota diversity does not influence ALB treatment outcomes. Furthermore, differential abundance analysis at the phylum, family and genus levels yielded no statistically significant associations between bacterial communities and ALB efficacy. Utilizing supervised ML models failed to predict treatment response accurately. Our investigation did not provide conclusive insights into the relationship between gut microbiota and ALB efficacy. However, the results highlight the need for future research to incorporate longitudinal studies that monitor changes in the gut microbiota related to the infection and the cure with ALB, as well as functional metagenomics to better understand the interaction of the microbiome with the drug, and its role, if there is any, in modulating anthelmintic treatment outcomes in STH infections. Interdisciplinary approaches integrating microbiology, pharmacology, genetics and data science will be pivotal in advancing our understanding of STH infections and optimizing treatment strategies globally.}, } @article {pmid39266528, year = {2024}, author = {Liu, S and Chen, Q and Hou, C and Dong, C and Qiu, X and Tang, K}, title = {Recovery of 1559 metagenome-assembled genomes from the East China Sea's low-oxygen region.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {994}, pmid = {39266528}, issn = {2052-4463}, mesh = {China ; *Metagenome ; *Archaea/genetics ; Bacteria/genetics/classification ; Oxygen ; Seawater/microbiology ; Phylogeny ; Metagenomics ; Oceans and Seas ; Microbiota ; }, abstract = {The Changjiang Estuary and adjacent East China Sea are well-known hypoxic aquatic environments. Eutrophication-driven hypoxia frequently occurs in coastal areas, posing a major threat to the ecological environment, including altering community structure and metabolic processes of marine organisms, and enhancing diversion of energy shunt into microbial communities. However, the responses of microbial communities and their metabolic pathways to coastal hypoxia remain poorly understood. Here, we studied the microbial communities collected from spatiotemporal samplings using metagenomic sequencing in the Changjiang Estuary and adjacent East China Sea. This generated 1.31 Tbp of metagenomics data, distributed across 103 samples corresponding to 8 vertical profiles. We further reported 1,559 metagenome-assembled genomes (MAGs), of which 508 were high-quality MAGs (Completeness > 90% and Contamination < 10%). Phylogenomic analysis classified them into 181 archaeal and 1,378 bacterial MAGs. These results provided a valuable metagenomic dataset available for further investigation of the effects of hypoxia on marine microorganisms.}, } @article {pmid39266450, year = {2024}, author = {Gnimpieba, EZ and Hartman, TW and Do, T and Zylla, J and Aryal, S and Haas, SJ and Agany, DDM and Gurung, BDS and Doe, V and Yosufzai, Z and Pan, D and Campbell, R and Huber, VC and Sani, R and Gadhamshetty, V and Lushbough, C}, title = {Biofilm marker discovery with cloud-based dockerized metagenomics analysis of microbial communities.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {Supplement_1}, pages = {}, pmid = {39266450}, issn = {1477-4054}, support = {#1849206//National Science Foundation/ ; //Institutional Development Award/ ; /GM/NIGMS NIH HHS/United States ; P20GM103443/NH/NIH HHS/United States ; }, mesh = {*Biofilms/growth & development ; *Metagenomics/methods ; Microbiota/genetics ; Cloud Computing ; Humans ; Computational Biology/methods ; }, abstract = {In an environment, microbes often work in communities to achieve most of their essential functions, including the production of essential nutrients. Microbial biofilms are communities of microbes that attach to a nonliving or living surface by embedding themselves into a self-secreted matrix of extracellular polymeric substances. These communities work together to enhance their colonization of surfaces, produce essential nutrients, and achieve their essential functions for growth and survival. They often consist of diverse microbes including bacteria, viruses, and fungi. Biofilms play a critical role in influencing plant phenotypes and human microbial infections. Understanding how these biofilms impact plant health, human health, and the environment is important for analyzing genotype-phenotype-driven rule-of-life functions. Such fundamental knowledge can be used to precisely control the growth of biofilms on a given surface. Metagenomics is a powerful tool for analyzing biofilm genomes through function-based gene and protein sequence identification (functional metagenomics) and sequence-based function identification (sequence metagenomics). Metagenomic sequencing enables a comprehensive sampling of all genes in all organisms present within a biofilm sample. However, the complexity of biofilm metagenomic study warrants the increasing need to follow the Findability, Accessibility, Interoperability, and Reusable (FAIR) Guiding Principles for scientific data management. This will ensure that scientific findings can be more easily validated by the research community. This study proposes a dockerized, self-learning bioinformatics workflow to increase the community adoption of metagenomics toolkits in a metagenomics and meta-transcriptomics investigation. Our biofilm metagenomics workflow self-learning module includes integrated learning resources with an interactive dockerized workflow. This module will allow learners to analyze resources that are beneficial for aggregating knowledge about biofilm marker genes, proteins, and metabolic pathways as they define the composition of specific microbial communities. Cloud and dockerized technology can allow novice learners-even those with minimal knowledge in computer science-to use complicated bioinformatics tools. Our cloud-based, dockerized workflow splits biofilm microbiome metagenomics analyses into four easy-to-follow submodules. A variety of tools are built into each submodule. As students navigate these submodules, they learn about each tool used to accomplish the task. The downstream analysis is conducted using processed data obtained from online resources or raw data processed via Nextflow pipelines. This analysis takes place within Vertex AI's Jupyter notebook instance with R and Python kernels. Subsequently, results are stored and visualized in Google Cloud storage buckets, alleviating the computational burden on local resources. The result is a comprehensive tutorial that guides bioinformaticians of any skill level through the entire workflow. It enables them to comprehend and implement the necessary processes involved in this integrated workflow from start to finish. This manuscript describes the development of a resource module that is part of a learning platform named "NIGMS Sandbox for Cloud-based Learning" https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.}, } @article {pmid39265854, year = {2024}, author = {Viglioli, M and Rizzo, SM and Alessandri, G and Fontana, F and Milani, C and Turroni, F and Mancabelli, L and Croci, N and Rivara, S and Vacondio, F and Ventura, M and Mor, M}, title = {Investigating drug-gut microbiota interactions: reductive and hydrolytic metabolism of oral glucocorticoids by in vitro artificial gut microbiota.}, journal = {International journal of pharmaceutics}, volume = {665}, number = {}, pages = {124663}, doi = {10.1016/j.ijpharm.2024.124663}, pmid = {39265854}, issn = {1873-3476}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Glucocorticoids/metabolism/administration & dosage ; Humans ; *Feces/microbiology ; Hydrolysis ; Administration, Oral ; Prodrugs/metabolism ; Fermentation ; }, abstract = {Elucidation of the role of gut microbiota in the metabolism of orally administered drugs may improve therapeutic effectiveness and contribute to the development of personalized medicine. In this study, ten different artificial gut microbiota (AGM), obtained by culturing fecal samples in a continuous fermentation system, were challenged for their metabolizing capacity on a panel of six glucocorticoids selected from either prodrugs or drugs. Data from metabolic stability assays highlighted that, while the hydrolysis-mediated conversion of prodrugs to drugs represented only a minor metabolic pathway, significant differences in the stability of parent compounds and in their conversion rates to multiple reductive metabolites were obtained for the selected drugs. In the latter case, a taxonomic composition-dependent ability to convert parent drugs to metabolites was observed. Indeed, the artificial microbial communities dominated by the genus Bacteroides showed the maximal conversion of parent glucocorticoids to several metabolites. Furthermore, the effect of drugs on AGM was also evaluated through shallow shotgun sequencing and flow cytometry-based total bacterial cell count highlighting that these drugs can affect both the taxonomic composition and growth performances of the human gut microbiota.}, } @article {pmid39265811, year = {2024}, author = {Nataraj, BH and Ranveer, SA and K, J and Nagpal, R and Behare, PV}, title = {Immune and microbiome modulatory effects of Limosilactobacillus fermentum NCDC 400 in an immunocompromised mouse model.}, journal = {Microbial pathogenesis}, volume = {196}, number = {}, pages = {106927}, doi = {10.1016/j.micpath.2024.106927}, pmid = {39265811}, issn = {1096-1208}, mesh = {Animals ; Mice ; *Probiotics/administration & dosage ; *Limosilactobacillus fermentum ; *Immunocompromised Host ; *Disease Models, Animal ; *Cyclophosphamide ; *Gastrointestinal Microbiome/drug effects ; *Spleen/immunology ; Oxidative Stress ; Male ; Cell Differentiation ; }, abstract = {The present study was aimed to assess and validate the safety and functional efficacy of an indigenous probiotic strain Limosilactobacillus fermentum NCDC 400 (hereafter, LFN400) in an immunocompromised murine model. The study included four groups; a normal control (NC) group without immune suppression; an experimental model control (MC) with immune suppression induced via intraperitoneal cyclophosphamide (Cy) administration; and two MC groups orally administered with either low dose (LD) or high dose (HD) of LFN400 at dose 10[8] and 10[10] CFU/mouse/day, respectively, for 15-days. Both control groups received normal saline as placebo control. LFN400 improved specific experimental characteristics including hematological and serum biochemical markers. Compared to MC group, LFN400-fed groups showed markedly (P < 0.05) decreased arrays of detrimental caecal enzymes. We did not observe instances of bacterial translocation of LFN400 from gut to bloodstream or extra-intestinal organs. LFN400 intake significantly (P < 0.05) enhanced spleen cell differentiation, immune and oxidative stress markers, and restored Cy-induced histopathological changes in multiple tissues, including the spleen. There was no genotoxic effect of LFN400 on bone marrow cells. Although not statistically significant, LFN400 feeding moderately increased gut microbiome diversity, supporting the growth of beneficial saccharolytic microorganisms and reducing the presence of pathobionts. The findings demonstrate that the probiotic strain LFN400 possesses in vivo safety and immunomodulatory potency and thus should be considered a potential candidate for future human clinical studies.}, } @article {pmid39265779, year = {2024}, author = {Xiao, X and Wu, Y and Jie, Z and Lin, L and Li, Y and Hu, W and Li, Y and Zhong, S}, title = {Akkermansia Muciniphila supplementation improves hyperlipidemia, cardiac function, and gut microbiota in high fat fed apolipoprotein E-deficient mice.}, journal = {Prostaglandins & other lipid mediators}, volume = {175}, number = {}, pages = {106906}, doi = {10.1016/j.prostaglandins.2024.106906}, pmid = {39265779}, issn = {1098-8823}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Akkermansia ; Mice ; *Hyperlipidemias ; *Diet, High-Fat/adverse effects ; *Apolipoproteins E/deficiency/genetics ; Male ; Atherosclerosis ; Humans ; Mice, Inbred C57BL ; Dietary Supplements ; Mice, Knockout, ApoE ; Verrucomicrobia ; }, abstract = {Hyperlipidemia, obesity and gut dysbiosis are pivotal risk factors for atherosclerotic cardiovascular disease (ACVD). Supplementation of Akkermansia muciniphila (AKK) has also been proven to be effective in the prevention and treatment of obesity and other metabolic disorders. Here we found that AKK was more abundant in healthy control than ACVD patients via metagenomic sequencing on fecal samples. Subsequently, we investigated the role and underlying mechanism of AKK on obesity-associated atherosclerosis. AKK intervention partially reversed the exacerbation of atherosclerotic lesion formation in ApoE[-/-] mice by improving dyslipidemia. Interestingly, replenishment with AKK significantly enhanced cardiac function and reduced the body weight. It also reduced pro-inflammatory cytokine IL-6 and increased anti-inflammatory IL-10 in the circulation. Additionally, AKK colonization dramatically regulated gut microbiota and increased the abundance of Lactobacillaceae. Our findings have provided novel insights into the therapeutic potential of AKK as a beneficial microbe for treating atherosclerotic-associated cardiovascular diseases.}, } @article {pmid39264803, year = {2024}, author = {Tang, D and Hu, W and Fu, B and Zhao, X and You, G and Xie, C and Wang, HY and Guo, X and Zhang, Q and Liu, Z and Ye, L}, title = {Gut microbiota-mediated C-sulfonate metabolism impairs the bioavailability and anti-cholestatic efficacy of andrographolide.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2387402}, pmid = {39264803}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Diterpenes/metabolism/pharmacology ; *Biological Availability ; Mice ; Cholestasis/metabolism/drug therapy/microbiology ; Male ; RNA, Ribosomal, 16S/genetics ; Bile Acids and Salts/metabolism ; Bacteria/metabolism/classification/genetics/drug effects/isolation & purification ; Humans ; Mice, Inbred C57BL ; Liver/metabolism/drug effects ; Receptors, Cytoplasmic and Nuclear/metabolism/genetics ; Disease Models, Animal ; }, abstract = {Cholestatic liver injury results from the accumulation of toxic bile acids in the liver, presenting a therapeutic challenge with no effective treatment available to date. Andrographolide (AP) has exhibited potential as a treatment for cholestatic liver disease. However, its limited oral bioavailability poses a significant obstacle to harnessing its potent therapeutic properties and restricts its clinical utility. This limitation is potentially attributed to the involvement of gut microbiota in AP metabolism. In our study, employing pseudo-germ-free, germ-free and strain colonization animal models, along with 16S rRNA and shotgun metagenomic sequencing analysis, we elucidate the pivotal role played by gut microbiota in the C-sulfonate metabolism of AP, a process profoundly affecting its bioavailability and anti-cholestatic efficacy. Subsequent investigations pinpoint a specific enzyme, adenosine-5'-phosphosulfate (APS) reductase, predominantly produced by Desulfovibrio piger, which catalyzes the reduction of SO4[2-] to HSO3[-]. HSO3[-] subsequently interacts with AP, targeting its C=C unsaturated double bond, resulting in the formation of the C-sulfonate metabolite, 14-deoxy-12(R)-sulfo andrographolide (APM). Inhibition of APS reductase leads to a notable enhancement in AP bioavailability and anti-cholestatic efficacy. Furthermore, employing RNA sequencing analysis and farnesoid X receptor (FXR) knockout mice, our findings suggest that AP may exert its anti-cholestatic effects by activating the FXR pathway to promote bile acid efflux. In summary, our study unveils the significant involvement of gut microbiota in the C-sulfonate metabolism of AP and highlights the potential benefits of inhibiting APS reductase to enhance its therapeutic effects. These discoveries provide valuable insights into enhancing the clinical applicability of AP as a promising treatment for cholestatic liver injury.}, } @article {pmid39264513, year = {2024}, author = {Angebault, C and Botterel, F}, title = {Metagenomics Applied to the Respiratory Mycobiome in Cystic Fibrosis.}, journal = {Mycopathologia}, volume = {189}, number = {5}, pages = {82}, pmid = {39264513}, issn = {1573-0832}, mesh = {*Cystic Fibrosis/microbiology/complications ; Humans ; *Mycobiome ; *Metagenomics/methods ; Fungi/genetics/classification/isolation & purification ; Respiratory System/microbiology ; Bacteria/genetics/classification/isolation & purification ; Lung/microbiology ; Microbiota ; }, abstract = {Cystic fibrosis (CF) is a genetic disorder characterized by chronic microbial colonization and inflammation of the respiratory tract (RT), leading to pulmonary exacerbation (PEx) and lung damage. Although the lung bacterial microbiota has been extensively studied, the mycobiome remains understudied. However, its importance as a contributor to CF pathophysiology has been highlighted. The objective of this review is to provide an overview of the current state of knowledge regarding the mycobiome, as described through NGS-based studies, in patients with CF (pwCF).Several studies have demonstrated that the mycobiome in CF lungs is a dynamic entity, exhibiting a lower diversity and abundance than the bacterial microbiome. Nevertheless, the progression of lung damage is associated with a decrease in fungal and bacterial diversity. The core mycobiome of the RT in pwCFs is mainly composed of yeasts (Candida spp., Malassezia spp.) and molds with lower abundance. Some fungi (Aspergillus, Scedosporium/Pseudallescheria) have been demonstrated to play a role in PEx, while the involvement of others (Candida, Pneumocystis) remains uncertain. The "climax attack" ecological model has been proposed to explain the complexity and interplay of microbial populations in the RT, leading to PEx and lung damage. NGS-based studies also enable the detection of intra- and interkingdom correlations between fungi and bacteria. Further studies are required to ascertain the biological and pathophysiological relevance of these correlations. Finally, with the recent advent of CFTR modulators, our understanding of the pulmonary microbiome and mycobiome in pwCFs is about to change.}, } @article {pmid39264053, year = {2024}, author = {Ho, L and Lai, C and Daim, LDJ and Noh, NM and Yap, Y and Ibrahim, J and Teh, C}, title = {Deciphering root-associated microbial communities in asymptomatic oil palm seedlings exposed to Ganoderma boninense: new insight into disease tolerance of oil palms.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {10}, pages = {}, pmid = {39264053}, issn = {1574-6941}, support = {//SD Guthrie Research Sdn Bhd/ ; }, mesh = {*Ganoderma/genetics ; *Seedlings/microbiology ; *Arecaceae/microbiology ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Microbiota ; *Rhizosphere ; *Plant Roots/microbiology ; Ascomycota/genetics ; Disease Resistance ; Metagenomics ; }, abstract = {Understanding the microbial communities in asymptomatic oil palm seedlings is crucial for developing disease-suppressive microbiota against basal stem rot (BSR) in oil palm. In this study, we compared the microbial communities in bulk soil, rhizosphere, and endosphere of control, asymptomatic, and symptomatic seedlings following inoculation with Ganoderma boninense. Our findings revealed significant shifts in microbial structure and interactions, particularly in asymptomatic seedlings. Both Actinobacteriota and Ascomycota were notably enriched in these samples, with Actinobacteriota identified as keystone taxa. Long-read shotgun metagenomics demonstrated that 67.4% of enriched Actinobacteriota taxa were unique to asymptomatic seedlings. Similarly, Ascomycota members showed significant enrichment, suggesting their potential role in BSR suppression. The consistent identification of these phyla across various analyses underscores their importance in disease resistance. This is the first report detailing the shifts in prokaryotic and fungal communities in asymptomatic and symptomatic seedlings, offering insights into potential disease-suppressive taxa across three compartments: bulk soil, rhizosphere, and endosphere of oil palm seedlings.}, } @article {pmid39260724, year = {2024}, author = {Ke, Y and Sun, W and Xue, Y and Yuan, Z and Zhu, Y and Chen, X and Yan, S and Li, Y and Xie, S}, title = {Pipe material and natural organic matter impact drinking water biofilm microbial community, pathogen profiles and antibiotic resistome deciphered by metagenomics assembly.}, journal = {Environmental research}, volume = {262}, number = {Pt 2}, pages = {119964}, doi = {10.1016/j.envres.2024.119964}, pmid = {39260724}, issn = {1096-0953}, mesh = {*Biofilms/drug effects ; *Drinking Water/microbiology ; *Metagenomics ; Microbiota/drug effects ; Drug Resistance, Microbial/genetics ; Water Supply ; Anti-Bacterial Agents/pharmacology ; Polyethylene ; Water Microbiology ; }, abstract = {Biofilms in drinking water distribution systems (DWDSs) are a determinant to drinking water biosafety. Yet, how and why pipe material and natural organic matter (NOM) affect biofilm microbial community, pathogen composition and antibiotic resistome remain unclear. We characterized the biofilms' activity, microbial community, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and pathogenic ARG hosts in Centers for Disease Control and Prevention (CDC) reactors with different NOM dosages and pipe materials based on metagenomics assembly. Biofilms in cast iron (CI) pipes exhibited higher activity than those in polyethylene (PE) pipes. NOM addition significantly decreased biofilm activity in CI pipes but increased it in PE pipes. Pipe material exerted more profound effects on microbial community structure than NOM. Azospira was significantly enriched in CI pipes and Sphingopyxis was selected in PE pipes, while pathogen (Ralstonia pickettii) increased considerably in NOM-added reactors. Microbial community network in CI pipes showed more edges (CI 13520, PE 7841) and positive correlation proportions (CI 72.35%, PE 61.69%) than those in PE pipes. Stochastic processes drove assembly of both microbial community and antibiotic resistome in DWDS biofilms based on neutral community model. Bacitracin, fosmidomycin and multidrug ARGs were predominant in both PE and CI pipes. Both pipe materials and NOM regulated the biofilm antibiotic resistome. Plasmid was the major MGE co-existing with ARGs, facilitating ARG horizontal transfer. Pathogens (Achromobacter xylosoxidans and Ralstonia pickettii) carried multiple ARGs (qacEdelta1, OXA-22 and aadA) and MGEs (integrase, plasmid and transposase), which deserved more attention. Microbial community contributed more to ARG change than MGEs. Structure equation model (SEM) demonstrated that turbidity and ammonia affected ARGs by directly mediating Shannon diversity and MGEs. These findings might provide a technical guidance for controlling pathogens and ARGs from the point of pipe material and NOM in drinking water.}, } @article {pmid39260494, year = {2024}, author = {Ejaz, MR and Badr, K and Hassan, ZU and Al-Thani, R and Jaoua, S}, title = {Metagenomic approaches and opportunities in arid soil research.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {176173}, doi = {10.1016/j.scitotenv.2024.176173}, pmid = {39260494}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Metagenomics ; *Soil/chemistry ; Desert Climate ; Microbiota ; }, abstract = {Arid soils present unique challenges and opportunities for studying microbial diversity and bioactive potential due to the extreme environmental conditions they bear. This review article investigates soil metagenomics as an emerging tool to explore complex microbial dynamics and unexplored bioactive potential in harsh environments. Utilizing advanced metagenomic techniques, diverse microbial populations that grow under extreme conditions such as high temperatures, salinity, high pH levels, and exposure to metals and radiation can be studied. The use of extremophiles to discover novel natural products and biocatalysts emphasizes the role of functional metagenomics in identifying enzymes and secondary metabolites for industrial and pharmaceutical purposes. Metagenomic sequencing uncovers a complex network of microbial diversity, offering significant potential for discovering new bioactive compounds. Functional metagenomics, connecting taxonomic diversity to genetic capabilities, provides a pathway to identify microbes' mechanisms to synthesize valuable secondary metabolites and other bioactive substances. Contrary to the common perception of desert soil as barren land, the metagenomic analysis reveals a rich diversity of life forms adept at extreme survival. It provides valuable findings into their resilience and potential applications in biotechnology. Moreover, the challenges associated with metagenomics in arid soils, such as low microbial biomass, high DNA degradation rates, and DNA extraction inhibitors and strategies to overcome these issues, outline the latest advancements in extraction methods, high-throughput sequencing, and bioinformatics. The importance of metagenomics for investigating diverse environments opens the way for future research to develop sustainable solutions in agriculture, industry, and medicine. Extensive studies are necessary to utilize the full potential of these powerful microbial communities. This research will significantly improve our understanding of microbial ecology and biotechnology in arid environments.}, } @article {pmid39259188, year = {2024}, author = {Liu, C and Wang, Y and Zhou, Z and Wang, S and Wei, Z and Ravanbakhsh, M and Shen, Q and Xiong, W and Kowalchuk, GA and Jousset, A}, title = {Protist predation promotes antimicrobial resistance spread through antagonistic microbiome interactions.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39259188}, issn = {1751-7370}, support = {42090064//National Natural Science Foundation of China/ ; 2023YFD1901402//National Key Research and Development Program of China/ ; YDZX2023023//Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Microbiota/drug effects ; *Soil Microbiology ; *Bacteria/drug effects/genetics/classification ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Microbial Interactions ; Drug Resistance, Bacterial ; Eukaryota/drug effects ; }, abstract = {Antibiotic resistance has grown into a major public health threat. In this study, we reveal predation by protists as an overlooked driver of antibiotic resistance dissemination in the soil microbiome. While previous studies have primarily focused on the distribution of antibiotic resistance genes, our work sheds light on the pivotal role of soil protists in shaping antibiotic resistance dynamics. Using a combination of metagenomics and controlled experiments in this study, we demonstrate that protists cause an increase in antibiotic resistance. We mechanistically link this increase to a fostering of antimicrobial activity in the microbiome. Protist predation gives a competitive edge to bacteria capable of producing antagonistic secondary metabolites, which secondary metabolites promote in turn antibiotic-resistant bacteria. This study provides insights into the complex interplay between protists and soil microbiomes in regulating antibiotic resistance dynamics. This study highlights the importance of top-down control on the spread of antibiotic resistance and directly connects it to cross-kingdom interactions within the microbiome. Managing protist communities may become an important tool to control outbreaks of antibiotic resistance in the environment.}, } @article {pmid39257028, year = {2024}, author = {Jotta, VFM and García, GJY and Fonseca, PLC and de Mello Ferreira, A and Azevedo, V and Brenig, B and Góes-Neto, A and Badotti, F}, title = {Taxonomic and functional characterization of biofilms from a photovoltaic panel reveals high genetic and metabolic complexity of the communities.}, journal = {Journal of applied microbiology}, volume = {135}, number = {9}, pages = {}, doi = {10.1093/jambio/lxae231}, pmid = {39257028}, issn = {1365-2672}, support = {//Omics Sciences NETWORK/ ; //CEFET-MG/ ; }, mesh = {*Biofilms/growth & development ; Brazil ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics ; Ferric Compounds/metabolism ; Microbiota ; Minerals/metabolism ; Bioelectric Energy Sources/microbiology ; Iron Compounds ; }, abstract = {AIMS: Biofilms are complex microbial cell aggregates that attach to different surfaces in nature, industrial environments, or hospital settings. In photovoltaic panels (PVs), biofilms are related to significant energy conversion losses. In this study, our aim was to characterize the communities of microorganisms and the genes involved in biofilm formation.

METHODS AND RESULTS: In this study, biofilm samples collected from a PV system installed in southeastern Brazil were analyzed through shotgun metagenomics, and the microbial communities and genes involved in biofilm formation were investigated. A total of 2030 different genera were identified in the samples, many of which were classified as extremophiles or producers of exopolysaccharides. Bacteria prevailed in the samples (89%), mainly the genera Mucilaginibacter, Microbacterium, Pedobacter, Massilia, and Hymenobacter. The functional annotation revealed >12 000 genes related to biofilm formation and stress response. Genes involved in the iron transport and synthesis of c-di-GMP and c-AMP second messengers were abundant in the samples. The pathways related to these components play a crucial role in biofilm formation and could be promising targets for preventing biofilm formation in the PV. In addition, Raman spectroscopy analysis indicated the presence of hematite, goethite, and ferrite, consistent with the mineralogical composition of the regional soil and metal-resistant bacteria.

CONCLUSIONS: Taken together, our findings reveal that PV biofilms are a promising source of microorganisms of industrial interest and genes of central importance in regulating biofilm formation and persistence.}, } @article {pmid39256724, year = {2024}, author = {Gamage, BD and Ranasinghe, D and Sahankumari, A and Malavige, GN}, title = {Metagenomic analysis of colonic tissue and stool microbiome in patients with colorectal cancer in a South Asian population.}, journal = {BMC cancer}, volume = {24}, number = {1}, pages = {1124}, pmid = {39256724}, issn = {1471-2407}, support = {ASP/01/RE/MED/2018/52//University of Sri Jayewardenepura/ ; ASP/01/RE/MED/2018/52//University of Sri Jayewardenepura/ ; }, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Bacteria/classification/isolation & purification ; Colon/microbiology ; *Colorectal Neoplasms/microbiology ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; South Asian People ; }, abstract = {BACKGROUND: The gut microbiome is thought to play an important role in the development of colorectal cancer (CRC). However, as the gut microbiome varies widely based on diet, we sought to investigate the gut microbiome changes in patients with CRC in a South Asian population.

METHODS: The gut microbiome was assessed by 16s metagenomic sequencing targeting the V4 hypervariable region of the bacterial 16S rRNA in stool samples (n = 112) and colonic tissue (n = 36) in 112 individuals. The cohort comprised of individuals with CRC (n = 24), premalignant lesions (n = 10), healthy individuals (n = 50) and in those with diabetes (n = 28).

RESULTS: Overall, the relative abundances of genus Fusobacterium (p < 0.001), Acinetobacter (p < 0.001), Escherichia-Shigella (p < 0.05) were significantly higher in gut tissue, while Romboutsia (p < 0.01) and Prevotella (p < 0.05) were significantly higher in stool samples. Bacteroides and Fusobacterium were the most abundant genera found in stool samples in patients with CRC. Patients with pre-malignant lesions had significantly high abundances of Christensenellaceae, Enterobacteriaceae, Mollicutes and Ruminococcaceae (p < 0.001) compared to patients with CRC, and healthy individuals. Romboutsia was significantly more abundant (p < 0.01) in stool samples in healthy individuals compared to those with CRC and diabetes.

CONCLUSION: Despite marked differences in the Sri Lankan diet compared to the typical Western diet, Bacteroides and Fusobacterium species were the most abundant in those with CRC, with Prevotella species, being most abundant in many individuals. We believe these results pave the way for possible dietary interventions for prevention of CRC in the South Asian population.}, } @article {pmid39256682, year = {2024}, author = {Wu, LH and Hu, CX and Liu, TX}, title = {Metagenomic profiling of gut microbiota in Fall Armyworm (Spodoptera frugiperda) larvae fed on different host plants.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {337}, pmid = {39256682}, issn = {1471-2180}, mesh = {Animals ; *Spodoptera/microbiology/genetics ; *Larva/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Zea mays/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Sorghum/microbiology ; Solanum lycopersicum/microbiology ; Capsicum/microbiology ; Metagenome ; }, abstract = {BACKGROUND: The fall armyworm (FAW, Spodoptera frugiperda) is a polyphagous pest known for causing significant crop damage. The gut microbiota plays a pivotal role in influencing the biology, physiology and adaptation of the host. However, understanding of the taxonomic composition and functional characteristics of the gut microbiota in FAW larvae fed on different host plants remains limited.

METHODS: This study utilized metagenomic sequencing to explore the structure, function and antibiotic resistance genes (ARGs) of the gut microbiota in FAW larvae transferred from an artificial diet to four distinct host plants: maize, sorghum, tomato and pepper.

RESULTS: The results demonstrated significant variations in gut microbiota structure among FAW larvae fed on different host plants. Firmicutes emerged as the dominant phylum, with Enterococcaceae as the dominant family and Enterococcus as the prominent genus. Notably, Enterococcus casseliflavus was frequently observed in the gut microbiota of FAW larvae across host plants. Metabolism pathways, particularly those related to carbohydrate and amino acid metabolism, played a crucial role in the adaptation of the FAW gut microbiota to different host plants. KEGG orthologs associated with the regulation of the peptide/nickel transport system permease protein in sorghum-fed larvae and the 6-phospho-β-glucosidase gene linked to glycolysis/gluconeogenesis as well as starch and sucrose metabolism in pepper-fed larvae were identified. Moreover, the study identified the top 20 ARGs in the gut microbiota of FAW larvae fed on different host plants, with the maize-fed group exhibiting the highest abundance of vanRC.

CONCLUSIONS: Our metagenomic sequencing study reveals significant variations in the gut microbiota composition and function of FAW larvae across diverse host plants. These findings underscore the intricate co-evolutionary relationship between hosts and their gut microbiota, suggesting that host transfer profoundly influences the gut microbiota and, consequently, the adaptability and pest management strategies for FAW.}, } @article {pmid39256599, year = {2024}, author = {Chen, Y and Zhang, KX and Liu, H and Zhu, Y and Bu, QY and Song, SX and Li, YC and Zou, H and You, XY and Zhao, GP}, title = {Impact of ginsenoside Rb1 on gut microbiome and associated changes in pharmacokinetics in rats.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21168}, pmid = {39256599}, issn = {2045-2322}, support = {TSBICIP-CXRC-042//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Projects/ ; TSBICIP-CXRC-008//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Projects/ ; E2M9560201//Major Project of Haihe Laboratory of Synthetic Biology/ ; 31200035//National Natural Science Foundation of China/ ; XDC 0110300//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, mesh = {*Ginsenosides/pharmacokinetics/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; Rats ; Male ; *Bacteroides/drug effects ; Rats, Sprague-Dawley ; Glycoside Hydrolases/metabolism ; }, abstract = {Ginsenoside Rb1 exhibits a wide range of biological activities, and gut microbiota is considered the main metabolic site for Rb1. However, the impact of gut microbiota on the pharmacokinetics of Rb1 are still uncertain. In this study, we investigated the gut microbiome changes and the pharmacokinetics after a 30 d Rb1 intervention. Results reveal that the systemic exposure and metabolic clearance rate of Rb1 and Rd were substantially affected after orally supplementing Rb1 (60 mg/kg) to rats. Significant increase in the relative abundance of Bacteroides cellulosilyticus in gut microbiota and specific glycoside hydrolase (GH) families, such as GH2, GH92, and GH20 were observed based on microbiome and metagenomic analysis. Moreover, a robust association was identified between the pharmacokinetic parameters of Rb1 and the relative abundance of specific Bacteroides species, and glycoside hydrolase families. Our study demonstrates that Rb1 administration significantly affects the gut microbiome, revealing a complex relationship between B. cellulosilyticus, key GH families, and Rb1 pharmacokinetics.}, } @article {pmid39256479, year = {2024}, author = {Campese, L and Russo, L and Abagnale, M and Alberti, A and Bachi, G and Balestra, C and Bellardini, D and Buondonno, A and Cardini, U and Carotenuto, Y and Checcucci, G and Chiusano, ML and D'Ambra, I and d'Ippolito, G and Di Capua, I and Donnarumma, V and Fontana, A and Furia, M and Galarza-Verkovitch, D and Gallia, R and Labadie, K and Leone, S and Licandro, P and Longo, A and Maselli, M and Merquiol, L and Murano, C and Oliveira, PH and Passarelli, A and Percopo, I and Perdereau, A and Piredda, R and Raffini, F and Roncalli, V and Ruscheweyh, HJ and Russo, E and Saggiomo, M and Santinelli, C and Sarno, D and Sunagawa, S and Tramontano, F and Trano, AC and Uttieri, M and Wincker, P and Zampicinini, G and Casotti, R and Conversano, F and D'Alelio, D and Iudicone, D and Margiotta, F and Montresor, M}, title = {The NEREA Augmented Observatory: an integrative approach to marine coastal ecology.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {989}, pmid = {39256479}, issn = {2052-4463}, mesh = {*Ecosystem ; Plankton ; Metagenome ; Biodiversity ; Metagenomics ; }, abstract = {The NEREA (Naples Ecological REsearch for Augmented observatories) initiative aims to establish an augmented observatory in the Gulf of Naples (GoN), designed to advance the understanding of marine ecosystems through a holistic approach. Inspired by the Tara Oceans expedition and building on the scientific legacy of the MareChiara Long-Term Ecological Research (LTER-MC) site, NEREA integrates traditional physical, chemical, and biological measurements with state-of-the-art methodologies such as metabarcoding and metagenomics. Here we present the first 10 months of NEREA data, collected from April 2019 to January 2020, encompassing physico-chemical parameters, plankton biodiversity (e.g., microscopy and flow cytometry), prokaryotic and eukaryotic metabarcoding, a prokaryotic gene catalogue, and a collection of 3818 prokaryotic Metagenome-Assembled Genomes (MAGs). NEREA's efforts produce a significant volume of multifaceted data, which enhances our understanding of marine ecosystems and promotes the development of scientific hypotheses and ideas.}, } @article {pmid39256206, year = {2024}, author = {Ashade, AO and Obayori, OS and Salam, LB and Fashola, MO and Nwaokorie, FO}, title = {Effects of anthropogenic activities on the microbial community diversity of Ologe Lagoon sediment in Lagos State, Nigeria.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {10}, pages = {918}, pmid = {39256206}, issn = {1573-2959}, mesh = {Nigeria ; *Geologic Sediments/microbiology/chemistry ; *Environmental Monitoring ; *Microbiota ; *Water Pollutants, Chemical/analysis ; Metals, Heavy/analysis ; Anthropogenic Effects ; Bacteria/classification/genetics ; Hydrocarbons/analysis ; }, abstract = {The impact of pollution on the Ologe Lagoon was assessed by comparing physicochemical properties, hydrocarbon concentrations and microbial community structures of the sediments obtained from distinct sites of the lagoon. The locations were the human activity site (OLHAS), industrial-contaminated sites (OLICS) and relatively undisturbed site (OLPS). The physicochemical properties, heavy metal concentrations and hydrocarbon profiles were determined using standard methods. The microbial community structures of the sediments were determined using shotgun next-generation sequencing (NGS), taxonomic profiling was performed using centrifuge and statistical analysis was done using statistical analysis for metagenomics profile (STAMP) and Microsoft Excel. The result showed acidic pH across all sampling points, while the nitrogen content at OLPS was low (7.44 ± 0.085 mg/L) as compared with OLHAS (44.380 ± 0.962 mg/L) and OLICS (59.485 ± 0.827 mg/L). The levels of the cadmium, lead and nickel in the three sites were above the regulatory limits. The gas chromatography flame ionization detector (GC-FID) profile revealed hydrocarbon contaminations with nC14 tetradecane > alpha xylene > nC9 nonane > acenaphthylene more enriched at OLPS. Structurally, the sediments metagenomes consisted of 43 phyla,75 classes each, 165, 161, 166 orders, 986, 927 and 866 bacterial genera and 1476, 1129, 1327 species from OLHAS, OLICS and OLPS, respectively. The dominant phyla in the sediments were Proteobacteria, Firmicutes, Actinobacteria, and Chloroflexi. The principal component ordination (PCO) showed that OLPS microbial community had a total variance of 87.7% PCO1, setting it apart from OLHAS and OLICS. OLICS and OLHAS were separated by PCO2 accounting for 12.3% variation, and the most polluted site is the OLPS.}, } @article {pmid39255397, year = {2024}, author = {Park, G and Kadyan, S and Hochuli, N and Salazar, G and Laitano, O and Chakrabarty, P and Efron, PA and Zafar, MA and Wilber, A and Nagpal, R}, title = {An Enteric Bacterial Infection Triggers Neuroinflammation and Neurobehavioral Impairment in 3xTg-AD Transgenic Mice.}, journal = {The Journal of infectious diseases}, volume = {230}, number = {Supplement_2}, pages = {S95-S108}, pmid = {39255397}, issn = {1537-6613}, support = {23A02//Florida Department of Health/ ; R01 AG070094/NH/NIH HHS/United States ; R01 AG070094/AG/NIA NIH HHS/United States ; //Foundation/ ; R21 AI166642/AI/NIAID NIH HHS/United States ; 440658//US Department of Agriculture/ ; R01 AI173244/AI/NIAID NIH HHS/United States ; //Infectious Diseases Society of America/ ; //Florida State University/ ; R01AI173244//US Public Health Service/ ; }, mesh = {Animals ; Mice ; *Mice, Transgenic ; *Klebsiella pneumoniae ; *Disease Models, Animal ; *Dysbiosis/microbiology/chemically induced ; *Alzheimer Disease/microbiology ; *Neuroinflammatory Diseases/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Klebsiella Infections/microbiology ; *Blood-Brain Barrier/microbiology ; Brain/pathology/microbiology ; Anti-Bacterial Agents/pharmacology ; Brain-Gut Axis ; Male ; Humans ; }, abstract = {BACKGROUND: Klebsiella pneumoniae is infamous for hospital-acquired infections and sepsis, which have also been linked to Alzheimer disease (AD)-related neuroinflammatory and neurodegenerative impairment. However, its causative and mechanistic role in AD pathology remains unstudied.

METHODS: A preclinical model of K. pneumoniae enteric infection and colonization is developed in an AD model (3xTg-AD mice) to investigate whether and how K. pneumoniae pathogenesis exacerbates neuropathogenesis via the gut-blood-brain axis.

RESULTS: K. pneumoniae, particularly under antibiotic-induced dysbiosis, was able to translocate from the gut to the bloodstream by penetrating the gut epithelial barrier. Subsequently, K. pneumoniae infiltrated the brain by breaching the blood-brain barrier. Significant neuroinflammatory phenotype was observed in mice with K. pneumoniae brain infection. K. pneumoniae-infected mice also exhibited impaired neurobehavioral function and elevated total tau levels in the brain. Metagenomic analyses revealed an inverse correlation of K. pneumoniae with gut biome diversity and commensal bacteria, highlighting how antibiotic-induced dysbiosis triggers an enteroseptic "pathobiome" signature implicated in gut-brain perturbations.

CONCLUSIONS: The findings demonstrate how infectious agents following hospital-acquired infections and consequent antibiotic regimen may induce gut dysbiosis and pathobiome and increase the risk of sepsis, thereby increasing the predisposition to neuroinflammatory and neurobehavioral impairments via breaching the gut-blood-brain barrier.}, } @article {pmid39254351, year = {2024}, author = {Wasmund, K and Singleton, C and Dahl Dueholm, MK and Wagner, M and Nielsen, PH}, title = {The predicted secreted proteome of activated sludge microorganisms indicates distinct nutrient niches.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0030124}, pmid = {39254351}, issn = {2379-5077}, mesh = {*Sewage/microbiology ; *Proteome/metabolism/analysis ; Bacterial Proteins/genetics/metabolism ; Nutrients/metabolism/analysis ; Bacteria/metabolism/genetics/classification ; Metagenome ; Microbiota/genetics ; }, abstract = {In wastewater treatment plants (WWTPs), complex microbial communities process diverse chemical compounds from sewage. Secreted proteins are critical because many are the first to interact with or degrade external (macro)molecules. To better understand microbial functions in WWTPs, we predicted secreted proteomes of WWTP microbiota from more than 1,000 high-quality metagenome-assembled genomes (MAGs) from 23 Danish WWTPs with biological nutrient removal. Focus was placed on examining secreted catabolic exoenzymes that target major classes of macromolecules. We demonstrate that Bacteroidota has a high potential to digest complex polysaccharides, but also proteins and nucleic acids. Poorly understood activated sludge members of Acidobacteriota and Gemmatimonadota also have high capacities for extracellular polysaccharide digestion. Secreted nucleases are encoded by 61% of MAGs indicating an importance for extracellular DNA and/or RNA digestion in WWTPs. Secreted lipases were the least common macromolecule-targeting enzymes predicted, encoded mainly by Gammaproteobacteria and Myxococcota. In contrast, diverse taxa encode extracellular peptidases, indicating that proteins are widely used nutrients. Diverse secreted multi-heme cytochromes suggest capabilities for extracellular electron transfer by various taxa, including some Bacteroidota that encode undescribed cytochromes with >100 heme-binding motifs. Myxococcota have exceptionally large secreted protein complements, probably related to predatory lifestyles and/or complex cell cycles. Many Gammaproteobacteria MAGs (mostly former Betaproteobacteria) encode few or no secreted hydrolases, but many periplasmic substrate-binding proteins and ABC- and TRAP-transporters, suggesting they are mostly sustained by small molecules. Together, this study provides a comprehensive overview of how WWTPs microorganisms interact with the environment, providing new insights into their functioning and niche partitioning.IMPORTANCEWastewater treatment plants (WWTPs) are critical biotechnological systems that clean wastewater, allowing the water to reenter the environment and limit eutrophication and pollution. They are also increasingly important for the recovery of resources. They function primarily by the activity of microorganisms, which act as a "living sponge," taking up and transforming nutrients, organic material, and pollutants. Despite much research, many microorganisms in WWTPs are uncultivated and poorly characterized, limiting our understanding of their functioning. Here, we analyzed a large collection of high-quality metagenome-assembled genomes from WWTPs for encoded secreted enzymes and proteins, with special emphasis on those used to degrade organic material. This analysis showed highly distinct secreted proteome profiles among different major phylogenetic groups of microorganisms, thereby providing new insights into how different groups function and co-exist in activated sludge. This knowledge will contribute to a better understanding of how to efficiently manage and exploit WWTP microbiomes.}, } @article {pmid39254336, year = {2024}, author = {Jung, D and Park, S and Kurban, D and Dufour, S and Ronholm, J}, title = {The occurrence of Aerococcus urinaeequi and non-aureus staphylococci in raw milk negatively correlates with Escherichia coli clinical mastitis.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0036224}, pmid = {39254336}, issn = {2379-5077}, support = {Dairy Research Cluster 3//Dairy Farmers of Canada (DFC)/ ; }, mesh = {Animals ; Female ; *Milk/microbiology ; Cattle ; *Mastitis, Bovine/microbiology ; *Escherichia coli/isolation & purification/genetics ; *Aerococcus/isolation & purification/genetics ; *Escherichia coli Infections/microbiology/veterinary ; *Staphylococcus/isolation & purification/genetics ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Escherichia coli is a common environmental pathogen associated with clinical mastitis (CM) in dairy cattle. There is an interest in optimizing the udder microbiome to increase the resistance of dairy cattle to E. coli CM; however, the details of which members of the healthy udder microbiome may play a role in antagonizing E. coli are unknown. In this study, we characterized the bacterial community composition in raw milk collected from quarters of lactating Holstein dairy cows that developed E. coli CM during lactation, including milk from both healthy and diseased quarters (n = 1,172). The milk microbiome from infected quarters was compared before, during, and after CM. A combination of 16S rRNA gene amplicon and metagenomic sequencing was used generate data sets with a high level of both depth and breadth. The microbial diversity present in raw milk significantly decreased in quarters experiencing E. coli CM, indicating that E. coli displaces other members of the microbiome. However, the diversity recovered very rapidly after infection. Two genera, Staphylococcus and Aerococcus, and the family Oscillospiraceae were significantly more abundant in healthy quarters with low inflammation. Species of these genera, Staphylococcus auricularis, Staphylococcus haemolyticus, and Aerocussus urinaeequi, were identified by metagenomics. Thus, these species are of interest for optimizing the microbiome to discourage E. coli colonization without triggering inflammation.IMPORTANCEIn this study, we show that E. coli outcompetes and displaces several members of the udder microbiome during CM, but that microbial diversity recovers post-infection. In milk from quarters which remained healthy, the community composition was often highly dominated by S. auricularis, S. haemolyticus, A. urinaeequi, and S. marcescens without increases in somatic cell count (SCC). Community dominance by these organisms, without inflammation, could indicate that these species might have potential as prophylactic probiotics which could contribute to colonization resistance and prevent future instances of E. coli CM.}, } @article {pmid39254265, year = {2024}, author = {Anandakumar, H and Rauch, A and Wimmer, MI and Yarritu, A and Koch, G and McParland, V and Bartolomaeus, H and Wilck, N}, title = {Segmental patterning of microbiota and immune cells in the murine intestinal tract.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2398126}, pmid = {39254265}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Mice, Inbred C57BL ; *Bacteria/classification/genetics/isolation & purification/immunology ; Intestines/microbiology/immunology/cytology ; Metagenomics ; Germ-Free Life ; Female ; T-Lymphocyte Subsets/immunology ; Male ; Intestinal Mucosa/microbiology/immunology/cytology ; }, abstract = {The intestine exhibits distinct characteristics along its length, with a substantial immune cell reservoir and diverse microbiota crucial for maintaining health. This study investigates how anatomical location and regional microbiota influence intestinal immune cell abundance. Using conventionally colonized and germ-free mice, segment-specific immune cell composition and microbial communities were assessed. Metagenomic sequencing analyzed microbiome variations, while flow cytometry and immunofluorescence examined immune cell composition. Microbiome composition varied significantly along the intestine, with diversity and abundance increasing from upper to lower segments. Immune cells showed distinct segment-specific patterning influenced by microbial colonization and localization. T cell subsets displayed varied dependence on microbiome presence and anatomical location. This study highlights locoregional differences in intestinal immune cell and microbiome composition, identifying immune subsets susceptible to microbiota presence. The findings provide context for understanding immune cell alterations in disease models.}, } @article {pmid39254049, year = {2024}, author = {Harris, RM and Pace, F and Kuntz, TM and Morgan, XC and Hyland, P and Summers, K and McDermott, E and Blumen, K and Watnick, PI}, title = {Testosterone treatment impacts the intestinal microbiome of transgender individuals.}, journal = {mSphere}, volume = {9}, number = {10}, pages = {e0055724}, pmid = {39254049}, issn = {2379-5042}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Testosterone ; Male ; *Transgender Persons ; Female ; Pilot Projects ; *Feces/microbiology ; Adult ; Metagenomics ; Middle Aged ; Glutamic Acid/metabolism ; Bacteria/classification/genetics/drug effects/metabolism/isolation & purification ; }, abstract = {Medical modulation of sex hormone levels is a cornerstone of treatment for many conditions that impact well-being, including cancer, fertility/infertility, gender dysphoria, and chronic metabolic diseases such as diabetes and obesity. The microbial residents of the intestine, known as the microbiota, interact with sex hormones in the intestine, and there is correlative evidence that this interaction is bidirectional. Based on these published findings, we hypothesized that transgender individuals receiving exogenous testosterone as part of their gender-affirming medical treatment might undergo changes in their intestinal microbiome. To test this, we collected 26 stool samples from nine individuals before and up to 8 months after initiation of treatment with exogenous testosterone and subjected these samples to metagenomic analysis. While no species were significantly associated with the duration of testosterone therapy, pathways that generate glutamate increased in abundance, while those that consume glutamate decreased. Glutamate is a precursor of arginine, and testosterone is known to increase levels of arginine and its metabolites in the plasma. We hypothesize that testosterone increases the uptake of glutamate by enterocytes, thus decreasing access of the microbiota to this amino acid. While this pilot study establishes the impact of testosterone therapy on the intestinal microbiome, a more comprehensive study is necessary to establish the impact of testosterone-driven metagenomic shifts on the stool metatranscriptome, the stool metabolome, and the plasma metabolome.IMPORTANCEThe human intestine is inhabited by a large community of microbes known as the microbiome. Members of the microbiome consume the diet along with their human host. Thus, the metabolomes of the host and microbe are intricately linked. Testosterone alters the plasma metabolome. In particular, plasma levels of arginine and its metabolites and testosterone are positively correlated. To investigate the impact of exogenous testosterone on the microbiome, we analyzed the stool metagenomes of transgender individuals before and after the initiation of testosterone treatment. In this pilot project, we found a modest impact on the microbiome community structure but an increase in the abundance of metabolic pathways that generate glutamate and spare glutamate consumption. We propose that the host uses glutamate to generate arginine, decreasing the amount available for the microbiome.}, } @article {pmid39253815, year = {2024}, author = {Wimmer, MI and Bartolomaeus, H and Anandakumar, H and Chen, CY and Vecera, V and Kedziora, S and Kamboj, S and Schumacher, F and Pals, S and Rauch, A and Meisel, J and Potapenko, O and Yarritu, A and Bartolomaeus, TUP and Samaan, M and Thiele, A and Stürzbecher, L and Geisberger, SY and Kleuser, B and Oefner, PJ and Haase, N and Löber, U and Gronwald, W and Forslund-Startceva, SK and Müller, DN and Wilck, N}, title = {Metformin modulates microbiota and improves blood pressure and cardiac remodeling in a rat model of hypertension.}, journal = {Acta physiologica (Oxford, England)}, volume = {240}, number = {11}, pages = {e14226}, doi = {10.1111/apha.14226}, pmid = {39253815}, issn = {1748-1716}, support = {//Deutsche Forschungsgemeinschaft/ ; //Deutsches Zentrum für Herz-Kreislaufforschung/ ; }, mesh = {Animals ; *Metformin/pharmacology ; *Hypertension/drug therapy/metabolism ; Male ; *Gastrointestinal Microbiome/drug effects ; *Blood Pressure/drug effects ; *Ventricular Remodeling/drug effects ; Rats ; *Rats, Transgenic ; Disease Models, Animal ; Hypoglycemic Agents/pharmacology ; Fatty Acids, Volatile/metabolism ; }, abstract = {AIMS: Metformin has been attributed to cardiovascular protection even in the absence of diabetes. Recent observations suggest that metformin influences the gut microbiome. We aimed to investigate the influence of metformin on the gut microbiota and hypertensive target organ damage in hypertensive rats.

METHODS: Male double transgenic rats overexpressing the human renin and angiotensinogen genes (dTGR), a model of angiotensin II-dependent hypertension, were treated with metformin (300 mg/kg/day) or vehicle from 4 to 7 weeks of age. We assessed gut microbiome composition and function using shotgun metagenomic sequencing and measured blood pressure via radiotelemetry. Cardiac and renal organ damage and inflammation were evaluated by echocardiography, histology, and flow cytometry.

RESULTS: Metformin treatment increased the production of short-chain fatty acids (SCFA) acetate and propionate in feces without altering microbial composition and diversity. It significantly reduced systolic and diastolic blood pressure and improved cardiac function, as measured by end-diastolic volume, E/A, and stroke volume despite increased cardiac hypertrophy. Metformin reduced cardiac inflammation by lowering macrophage infiltration and shifting macrophage subpopulations towards a less inflammatory phenotype. The observed improvements in blood pressure, cardiac function, and inflammation correlated with fecal SCFA levels in dTGR. In vitro, acetate and propionate altered M1-like gene expression in macrophages, reinforcing anti-inflammatory effects. Metformin did not affect hypertensive renal damage or microvascular structure.

CONCLUSION: Metformin modulated the gut microbiome, increased SCFA production, and ameliorated blood pressure and cardiac remodeling in dTGR. Our findings confirm the protective effects of metformin in the absence of diabetes, highlighting SCFA as a potential mediators.}, } @article {pmid39253787, year = {2024}, author = {Cheng, S and Gong, X and Xue, W and Kardol, P and Delgado-Baquerizo, M and Ling, N and Chen, X and Liu, M}, title = {Evolutionarily conserved core microbiota as an extended trait in nitrogen acquisition strategy of herbaceous species.}, journal = {The New phytologist}, volume = {244}, number = {4}, pages = {1570-1584}, doi = {10.1111/nph.20118}, pmid = {39253787}, issn = {1469-8137}, support = {42077047//National Foundation of Sciences in China/ ; lzujbky-2022-ct04//Fundamental Research Funds for the Central University of China/ ; 2021YFD1700202//National Key R&D program/ ; }, mesh = {*Nitrogen/metabolism ; *Rhizosphere ; *Microbiota ; *Phylogeny ; Biological Evolution ; Plants/microbiology/metabolism ; Soil Microbiology ; Species Specificity ; Quantitative Trait, Heritable ; }, abstract = {Microbiota have co-evolved with plants over millions of years and are intimately linked to plants, ranging from symbiosis to pathogenesis. However, our understanding of the existence of a shared core microbiota across phylogenetically diverse plants remains limited. A common garden field experiment was conducted to investigate the rhizosphere microbial communities of phylogenetically contrasting herbaceous families. Through a combination of metagenomic sequencing, analysis of plant economic traits, and soil biochemical properties, we aimed to elucidate the eco-evolutionary role of the core rhizosphere microbiota in light of plant economic strategies. We identified a conserved core microbiota consisting of 278 taxa that was closely associated with the phylogeny of the plants studied. This core microbiota actively participated in multiple nitrogen metabolic processes and showed a strong correlation with the functional potential of rhizosphere nitrogen cycling, thereby serving as an extended trait in the plant nitrogen acquisition. Furthermore, our examination of simulated species loss revealed the crucial role of the core microbiota in maintaining the rhizosphere community's network stability. Our study highlighted that the core microbiota, which exhibited a phylogenetically conserved association with plants, potentially represented an extension of the plant phenotype and played an important role in nitrogen acquisition. These findings held implications for the utilization of microbiota-mediated plant functions.}, } @article {pmid39252078, year = {2024}, author = {Vojvoda Zeljko, T and Kajan, K and Jalžić, B and Hu, A and Cukrov, N and Marguš, M and Cukrov, N and Marković, T and Sabatino, R and Di Cesare, A and Orlić, S}, title = {Genome-centric metagenomes unveiling the hidden resistome in an anchialine cave.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {67}, pmid = {39252078}, issn = {2524-6372}, support = {KK.01.2.1.02.0335//European Union through the European Regional Development Fund/ ; KK.01.1.1.01.0003//European Union through the European Regional Development Fund/ ; KK.01.2.1.02.0335//European Union through the European Regional Development Fund/ ; CN_00000033//European Union - NextGenerationEU/ ; CN_00000033//European Union - NextGenerationEU/ ; }, abstract = {BACKGROUND: Antibiotic resistance is a critical global concern, posing significant challenges to human health and medical treatments. Studying antibiotic resistance genes (ARGs) is essential not only in clinical settings but also in diverse environmental contexts. However, ARGs in unique environments such as anchialine caves, which connect both fresh and marine water, remain largely unexplored despite their intriguing ecological characteristics.

RESULTS: We present the first study that comprehensively explores the occurrence and distribution of ARGs and mobile genetic elements (MGEs) within an anchialine cave. Utilizing metagenomic sequencing we uncovered a wide array of ARGs with the bacitracin resistance gene, bacA and multidrug resistance genes, being the most dominant. The cave's microbial community and associated resistome were significantly influenced by the salinity gradient. The discovery of novel β-lactamase variants revealed the cave's potential as a reservoir for previously undetected resistance genes. ARGs in the cave demonstrated horizontal transfer potential via plasmids, unveiling ecological implications.

CONCLUSIONS: These findings highlight the need for further exploration of the resistome in unique environments like anchialine caves. The interconnected dynamics of ARGs and MGEs within anchialine caves offer valuable insights into potential reservoirs and mechanisms of antibiotic resistance in natural ecosystems. This study not only advances our fundamental understanding but also highlights the need for a comprehensive approach to address antibiotic resistance in diverse ecological settings.}, } @article {pmid39251745, year = {2024}, author = {Serwecińska, L and Font-Nájera, A and Strapagiel, D and Lach, J and Tołoczko, W and Bołdak, M and Urbaniak, M}, title = {Sewage sludge fertilization affects microbial community structure and its resistome in agricultural soils.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21034}, pmid = {39251745}, issn = {2045-2322}, support = {No. 2020/39/B/NZ9/01772//Narodowe Centrum Nauki/ ; No. 2020/39/B/NZ9/01772//Narodowe Centrum Nauki/ ; }, mesh = {*Sewage/microbiology ; *Soil Microbiology ; *Agriculture/methods ; *Fertilizers ; *Soil/chemistry ; *Microbiota/genetics/drug effects ; Bacteria/genetics/drug effects/classification ; Metagenomics/methods ; Drug Resistance, Microbial/genetics ; Poland ; }, abstract = {Global sewage sludge production is rapidly increasing, and its safe disposal is becoming an increasingly serious issue. One of the main methods of municipal sewage sludge management is based on its agricultural use. The wastewater and sewage sludge contain numerous antibiotic resistance genes (ARGs), and its microbiome differs significantly from the soil microbial community. The aim of the study was to assess the changes occurring in the soil microbial community and resistome after the addition of sewage sludge from municipal wastewater treatment plant (WWTP) in central Poland, from which the sludge is used for fertilizing agricultural soils on a regular basis. This study used a high-throughput shotgun metagenomics approach to compare the microbial communities and ARGs present in two soils fertilized with sewage sludge. The two soils represented different land uses and different physicochemical and granulometric properties. Both soils were characterized by a similar taxonomic composition of the bacterial community, despite dissimilarities between soils properties. Five phyla predominated, viz. Planctomycetes, Actinobacteria, Proteobacteria, Chloroflexi and Firmicutes, and they were present in comparable proportions in both soils. Network analysis revealed that the application of sewage sludge resulted in substantial qualitative and quantitative changes in bacterial taxonomic profile, with most abundant phyla being considerably depleted and replaced by Proteobacteria and Spirochaetes. In addition, the ratio of oligotrophic to copiotrophic bacteria substantially decreased in both amended soils. Furthermore, fertilized soils demonstrated greater diversity and richness of ARGs compared to control soils. The increased abundance concerned mainly genes of resistance to antibiotics most commonly used in human and animal medicine. The level of heavy metals in sewage sludge was low and did not exceed the standards permitted in Poland for sludge used in agriculture, and their level in fertilized soils was still inconsiderable.}, } @article {pmid39251728, year = {2024}, author = {Cai, X and Dai, J and Xie, Y and Xu, S and Liu, M}, title = {Multi-omics study unravels gut microbiota and metabolites alteration in patients with Wilson's disease.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21025}, pmid = {39251728}, issn = {2045-2322}, support = {JCYJ20220530165400002//Shenzhen Science and Technology Innovation Program/ ; 2021R01132//Shenzhen Guangming District Economic Development Special Fund/ ; }, mesh = {Humans ; *Hepatolenticular Degeneration/metabolism/microbiology/genetics ; *Gastrointestinal Microbiome ; Female ; Male ; Adult ; RNA, Ribosomal, 16S/genetics ; Metabolomics/methods ; Feces/microbiology ; Metabolome ; Young Adult ; Bacteria/classification/metabolism/genetics/isolation & purification ; Metagenomics/methods ; Adolescent ; Multiomics ; }, abstract = {Hepatolenticular degeneration (HLD), also known as Wilson's disease (WD), is a rare autosomal recessive disorder regarding copper metabolism. Whether gut microbiota imbalance is involved in developing HLD remains unknown. A comprehensive 16S rRNA amplicon sequencing, metagenomic sequencing, and metabonomic analysis were undertaken in patients with WD to analyze the composition and function profiles of gut microbiota in patients with WD. The data demonstrated differences in gut microbiota and metabolic pathways between WD patients and normal individuals, significantly decreasing bacterial richness and diversity. The levels of Selenomonaceae and Megamonas in WD patients are significantly higher than those in healthy individuals. The relative abundances of Roseburia inulinivorans in patients with WD are lower than in healthy individuals. Compared with healthy people, the level of metabolites in patients with WD is abnormal. Leucylproline, 5-Phenylvaleric Acid and N-Desmethylclobazam, which have nutritional and protective effects, are significantly reduced fecal metabolites in patients with WD. D-Gluconic acid, which can chelate metal ions, may be a potential treatment for WD. The positive correlation it demonstrates with Alistipes indistinctus and Prevotella stercora indicates potential bacteria able to treat WD. These metabolites are mainly related to the biosynthesis of antibiotics, alpha-linolenic acid metabolism, one carbon pool by folate, nicotinate and nicotinamide metabolism. In conclusion, the data from this study elucidate novel mechanisms describing how abnormal gut miccrobiota contribute to the pathogenesis of WD and outlines new molecules for the treatment of WD.}, } @article {pmid39250478, year = {2024}, author = {Pusa, T and Rousu, J}, title = {Stable biomarker discovery in multi-omics data via canonical correlation analysis.}, journal = {PloS one}, volume = {19}, number = {9}, pages = {e0309921}, pmid = {39250478}, issn = {1932-6203}, mesh = {Humans ; *Biomarkers/metabolism ; *Inflammatory Bowel Diseases/metabolism ; *Metabolomics/methods ; Metagenomics/methods ; Machine Learning ; Gastrointestinal Microbiome ; Multiomics ; }, abstract = {Multi-omics analysis offers a promising avenue to a better understanding of complex biological phenomena. In particular, untangling the pathophysiology of multifactorial health conditions such as the inflammatory bowel disease (IBD) could benefit from simultaneous consideration of several omics levels. However, taking full advantage of multi-omics data requires the adoption of suitable new tools. Multi-view learning, a machine learning technique that natively joins together heterogeneous data, is a natural source for such methods. Here we present a new approach to variable selection in unsupervised multi-view learning by applying stability selection to canonical correlation analysis (CCA). We apply our method, StabilityCCA, to simulated and real multi-omics data, and demonstrate its ability to find relevant variables and improve the stability of variable selection. In a case study on an IBD microbiome data set, we link together metagenomics and metabolomics, revealing a connection between their joint structure and the disease, and identifying potential biomarkers. Our results showcase the usefulness of multi-view learning in multi-omics analysis and demonstrate StabilityCCA as a powerful tool for biomarker discovery.}, } @article {pmid39250184, year = {2024}, author = {Pallen, MJ}, title = {The dynamic history of prokaryotic phyla: discovery, diversity and division.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {9}, pages = {}, pmid = {39250184}, issn = {1466-5034}, mesh = {Archaea/genetics/classification ; *Bacteria/genetics/classification ; Classification/methods ; History, 20th Century ; History, 21st Century ; *Phylogeny ; Prokaryotic Cells/classification ; History, 19th Century ; }, abstract = {Here, I review the dynamic history of prokaryotic phyla. Following leads set by Darwin, Haeckel and Woese, the concept of phylum has evolved from a group sharing common phenotypes to a set of organisms sharing a common ancestry, with modern taxonomy based on phylogenetic classifications drawn from macromolecular sequences. Phyla came as surprising latecomers to the formalities of prokaryotic nomenclature in 2021. Since then names have been validly published for 46 prokaryotic phyla, replacing some established names with neologisms, prompting criticism and debate within the scientific community. Molecular barcoding enabled phylogenetic analysis of microbial ecosystems without cultivation, leading to the identification of candidate divisions (or phyla) from diverse environments. The introduction of metagenome-assembled genomes marked a significant advance in identifying and classifying uncultured microbial phyla. The lumper-splitter dichotomy has led to disagreements, with experts cautioning against the pressure to create a profusion of new phyla and prominent databases adopting a conservative stance. The Candidatus designation has been widely used to provide provisional status to uncultured prokaryotic taxa, with phyla named under this convention now clearly surpassing those with validly published names. The Genome Taxonomy Database (GTDB) has offered a stable, standardized prokaryotic taxonomy with normalized taxonomic ranks, which has led to both lumping and splitting of pre-existing phyla. The GTDB framework introduced unwieldy alphanumeric placeholder labels, prompting recent publication of over 100 user-friendly Latinate names for unnamed prokaryotic phyla. Most candidate phyla remain 'known unknowns', with limited knowledge of their genomic diversity, ecological roles, or environments. Whether phyla still reflect significant evolutionary and ecological partitions across prokaryotic life remains an area of active debate. However, phyla remain of practical importance for microbiome analyses, particularly in clinical research. Despite potential diminishing returns in discovery of biodiversity, prokaryotic phyla offer extensive research opportunities for microbiologists for the foreseeable future.}, } @article {pmid39248477, year = {2024}, author = {Hu, N-n and Wang, Z-q and Zhang, S-j and Wang, Z-z and Chen, X-x}, title = {Characterization of larval gut microbiota of two endoparasitoid wasps associated with their common host, Plutella xylostella (Linnaeus) (Lepidoptera: Plutellidae).}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0120824}, pmid = {39248477}, issn = {2165-0497}, support = {2023YFD1400800//National Key R&D Program of China/ ; U22A20485//MOST | National Natural Science Foundation of China (NSFC)/ ; 32272607//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Wasps/microbiology/physiology ; *Larva/microbiology/growth & development ; *Moths/parasitology/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Host-Parasite Interactions ; Phylogeny ; }, abstract = {Insect gut microbes play important roles in digestion, metabolism, development, and environmental adaptation. Parasitoid wasps are one of the most important biological control agents in pest control, while the gut microbial species compositions and the associated functions have been poorly investigated. Two endoparasitoid wasps, Cotesia vestalis and Diadromus collaris, parasitize the larval stage and pupal stage of the diamondback moth, Plutella xylostella, respectively. Using whole-genome shotgun metagenomic sequencing, we characterized the gut microbial composition, diversity, and potential functional roles associated with the two parasitoid wasp larvae. The results reveal that Proteobacteria and Firmicutes are the dominant phyla in the gut of C. vestalis and D. collaris larvae, with Rhizobium and Enterococcus being the dominant genera. The putative microbial functions associated with the two parasitoid wasps might play a virtual role in assisting in consuming the host's nutritional composition. The enriched CAZymes family genes are primarily involved in the degradation and synthesis of chitin. Despite the richness of microbial species and communities, the microbes species and the microbial community structure exhibit significant similarity between the two parasitoid wasps and between the parasitoid wasp and the host P. xylostella. Notably, the prevalence of the genus Enterococcus shared among them suggests a possible link of gut microbes between the host and their associated parasitoids. Our study offers insights into the gut microbe-based interactions between the host and parasitoid wasps for the first time, potentially paving the way for the development of an ecologically friendly biocontrol strategy against the pest P. xylostella.IMPORTANCEEndoparasitoid wasps spend the majority of their lifespan within their host and heavily rely on the host's nutrition for survival. There is limited understanding regarding the composition and physiological impacts of gut microbial communities in parasitoid wasps, particularly during the larval stage, which is directly linked to the host. Based on a thorough characterization of the gut microbe and comprehensive comparative analysis, we found the microbial species of the larval parasitoid wasp Cotesia vestalis and the pupal parasitoid wasp Diadromus collaris were similar, sharing 159 genera and 277 species, as were the microbial community structure. Certain of the dominant microbial strains of the two parasitoid wasps were similar to that of their host Plutella xylostella larvae, revealing host insect may affect the microbial community of the parasitoid wasps. The putative microbial functions associated with the parasitoid wasp larvae play an important role in dietary consumption.}, } @article {pmid39248279, year = {2024}, author = {Ohuchi, H and Asano, R and Mori, A and Ishibashi, T and Motooka, D and Nakai, M and Nakaoka, Y}, title = {Gut Dysbiosis in Patients With Fontan Circulation.}, journal = {Journal of the American Heart Association}, volume = {13}, number = {18}, pages = {e034538}, doi = {10.1161/JAHA.124.034538}, pmid = {39248279}, issn = {2047-9980}, mesh = {Humans ; Male ; *Dysbiosis ; *Fontan Procedure/adverse effects ; Female ; *Gastrointestinal Microbiome/physiology ; Adolescent ; Child ; Heart Defects, Congenital/surgery ; Case-Control Studies ; Young Adult ; Feces/microbiology ; Hemodynamics ; Biomarkers/blood/metabolism ; Adult ; }, abstract = {BACKGROUND: The process underlying Fontan pathophysiology is multifactorial and may include gut dysbiosis (GD). We investigated the presence of GD and elucidated its correlation with Fontan pathophysiology.

METHODS AND RESULTS: Gut microbiomes of 155 consecutive patients with Fontan pathophysiology and 44 healthy individuals were analyzed using 16S rRNA sequencing of bacterial DNA extracted from fecal samples. GD was evaluated on the basis of α and ß diversities of the gut microbiome and was compared with natural log-transformed C-reactive protein, hemodynamics, von Willebrand factor antigen (a bacterial translocation marker), Mac-2 binding protein glycosylation isomer (a liver fibrosis indicator), peak oxygen uptake, and heart failure hospitalization. Patients with Fontan exhibited GD in terms of α and ß diversities as compared with controls (P<0.01). Reduced α diversity was associated with a failed hemodynamic phenotype, hypoxia, high natural log-transformed C-reactive protein levels, and elevated von Willebrand factor antigen and Mac-2 binding protein glycosylation isomer levels (P<0.05-0.01). In addition to elevated von Willebrand factor antigen and hypoxia, decreased α diversity was independently correlated with a high natural log-transformed C-reactive protein level (P<0.05), which was associated with liver imaging abnormalities and a heightened risk of heart failure hospitalization (P<0.01 for both).

CONCLUSIONS: Patients with Fontan pathophysiology exhibited GD compared with healthy individuals, and GD was linked to failed hemodynamics and systemic inflammation with a poor prognosis. Therefore, GD may play a pivotal role in a failing Fontan status, including Fontan-associated liver disease, through GD-associated systemic inflammation.}, } @article {pmid39248272, year = {2024}, author = {Chen, X and He, Y and Zhou, L and Li, X and Jiang, M and Wu, M and Li, J and Chen, L and Xu, H and Gui, L and Zhou, Z}, title = {Microbial Heterogeneity Identification of Cerebral Thrombi Via Metagenomic Next-Generation Sequencing-Based Strategy.}, journal = {Journal of the American Heart Association}, volume = {13}, number = {18}, pages = {e033221}, doi = {10.1161/JAHA.123.033221}, pmid = {39248272}, issn = {2047-9980}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; *Intracranial Thrombosis/microbiology/genetics ; Aged ; Ischemic Stroke/microbiology/genetics ; Bacteria/genetics/isolation & purification ; Microbiota/genetics ; }, abstract = {BACKGROUND: Diagnosis of the cause of cerebral thrombi is vital for recurrence prevention but also challenging. The presence of the microbiome has recently been confirmed in thrombus, suggesting a novel approach to distinguish cerebral thrombi of different origins. However, little is known about whether there is heterogeneity in microbiological colonization of cerebral thrombi of different sources.

METHODS AND RESULTS: Forty patients experiencing acute ischemic stroke were included and clinical data were collected. Metagenomic next-generation sequencing was adopted to detect bacterial and genomic signatures of human cerebral thrombi samples. We found similar species diversity between the large-artery atherosclerosis thrombi and cardioembolic thrombi but different species composition and distribution of cerebral thrombus microbiota. Compared with the group with cardioembolism, the group with large-artery atherosclerosis showed a significantly higher relative abundance of Ralstonia insidiosa among the top 10 bacterial species in cerebral thrombi. Twenty operational taxonomy units were correlated with 11 clinical indicators of ischemic stroke. The Gene Ontology enrichment analysis revealed 9 different enriched biological processes (translation and carbohydrate metabolic process, etc). The enriched Kyoto Encyclopedia of Genes and Genomes pathways included ribosome, butanoate metabolism, and sulfur metabolism.

CONCLUSIONS: This study, based on the approach of metagenomic next-generation sequencing, provides a diagnostic microbiological method to discriminate individuals with cardioembolic thrombi from those with large-artery atherosclerosis thrombi with human cerebral thrombi samples. Our findings provide a fresh perspective on microbial heterogeneity of cerebral thrombi and demonstrate biological processes and pathway features of cerebral thrombi.}, } @article {pmid39247916, year = {2024}, author = {Lyu, X and Xu, X and Shen, S and Qin, F}, title = {Genetics causal analysis of oral microbiome on type 2 diabetes in East Asian populations: a bidirectional two-sample Mendelian randomized study.}, journal = {Frontiers in endocrinology}, volume = {15}, number = {}, pages = {1452999}, pmid = {39247916}, issn = {1664-2392}, mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/genetics ; East Asian People/genetics ; Genetic Predisposition to Disease ; *Genome-Wide Association Study ; *Mendelian Randomization Analysis ; *Microbiota/genetics ; Mouth/microbiology ; *Saliva/microbiology ; Tongue/microbiology ; }, abstract = {INTRODUCTION: The dysbiosis of the oral microbiome is associated with the progression of various systemic diseases, including diabetes. However, the precise causal relationships remain elusive. This study aims to investigate the potential causal associations between oral microbiome and type 2 diabetes (T2D) using Mendelian randomization (MR) analyses.

METHODS: We conducted bidirectional two-sample MR analyses to investigate the impact of oral microbiome from saliva and the tongue T2D. This analysis was based on metagenome-genome-wide association studies (mgGWAS) summary statistics of the oral microbiome and a large meta-analysis of GWAS of T2D in East Asian populations. Additionally, we utilized the T2D GWAS summary statistics from the Biobank Japan (BBJ) project for replication. The MR methods employed included Wald ratio, inverse variance weighting (IVW), weighted median, MR-Egger, contamination mixture (ConMix), and robust adjusted profile score (RAPS).

RESULTS: Our MR analyses revealed genetic associations between specific bacterial species in the oral microbiome of saliva and tongue with T2D in East Asian populations. The MR results indicated that nine genera were shared by both saliva and tongue. Among these, the genera Aggregatibacter, Pauljensenia, and Prevotella were identified as risk factors for T2D. Conversely, the genera Granulicatella and Haemophilus D were found to be protective elements against T2D. However, different species within the genera Catonella, Lachnoanaerobaculum, Streptococcus, and Saccharimonadaceae TM7x exhibited multifaceted influences; some species were positively correlated with the risk of developing T2D, while others were negatively correlated.

DISCUSSION: This study utilized genetic variation tools to confirm the causal effect of specific oral microbiomes on T2D in East Asian populations. These findings provide valuable insights for the treatment and early screening of T2D, potentially informing more targeted and effective therapeutic strategies.}, } @article {pmid39246231, year = {2024}, author = {Du, Y and Zuo, W and Sun, F}, title = {Imputing Metagenomic Hi-C Contacts Facilitates the Integrative Contig Binning Through Constrained Random Walk with Restart.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {31}, number = {10}, pages = {1008-1021}, doi = {10.1089/cmb.2024.0663}, pmid = {39246231}, issn = {1557-8666}, mesh = {*Metagenomics/methods ; *Algorithms ; Animals ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; Sheep ; Contig Mapping/methods ; Software ; }, abstract = {Metagenomic Hi-C (metaHi-C) has shown remarkable potential for retrieving high-quality metagenome-assembled genomes from complex microbial communities. Nevertheless, existing metaHi-C-based contig binning methods solely rely on Hi-C interactions between contigs, disregarding crucial biological information such as the presence of single-copy marker genes. To overcome this limitation, we introduce ImputeCC, an integrative contig binning tool optimized for metaHi-C datasets. ImputeCC integrates both Hi-C interactions and the discriminative power of single-copy marker genes to group marker-gene-containing contigs into preliminary bins. It also introduces a novel constrained random walk with restart algorithm to enhance Hi-C connectivity among contigs. Comprehensive assessments using both mock and real metaHi-C datasets from diverse environments demonstrate that ImputeCC consistently outperforms other Hi-C-based contig binning tools. A genus-level analysis of the sheep gut microbiota reconstructed by ImputeCC underlines its capability to recover key species from dominant genera and identify previously unknown genera.}, } @article {pmid39245657, year = {2024}, author = {Lee, S and Meslier, V and Bidkhori, G and Garcia-Guevara, F and Etienne-Mesmin, L and Clasen, F and Park, J and Plaza Oñate, F and Cai, H and Le Chatelier, E and Pons, N and Pereira, M and Seifert, M and Boulund, F and Engstrand, L and Lee, D and Proctor, G and Mardinoglu, A and Blanquet-Diot, S and Moyes, D and Almeida, M and Ehrlich, SD and Uhlen, M and Shoaie, S}, title = {Transient colonizing microbes promote gut dysbiosis and functional impairment.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {80}, pmid = {39245657}, issn = {2055-5008}, support = {EP/S001301/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; BB/S016899/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; N/A//Science for Life Laboratory (SciLifeLab)/ ; }, mesh = {*Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Metagenomics/methods ; Sweden ; *Bacteria/classification/genetics/isolation & purification ; *Feces/microbiology ; Longitudinal Studies ; Metagenome ; Adult ; Bioreactors/microbiology ; Fermentation ; }, abstract = {Species composition of the healthy adult gut microbiota tends to be stable over time. Destabilization of the gut microbiome under the influence of different factors is the main driver of the microbial dysbiosis and subsequent impacts on host physiology. Here, we used metagenomics data from a Swedish longitudinal cohort, to determine the stability of the gut microbiome and uncovered two distinct microbial species groups; persistent colonizing species (PCS) and transient colonizing species (TCS). We validated the continuation of this grouping, generating gut metagenomics data for additional time points from the same Swedish cohort. We evaluated the existence of PCS/TCS across different geographical regions and observed they are globally conserved features. To characterize PCS/TCS phenotypes, we performed bioreactor fermentation with faecal samples and metabolic modeling. Finally, using chronic disease gut metagenome and other multi-omics data, we identified roles of TCS in microbial dysbiosis and link with abnormal changes to host physiology.}, } @article {pmid39245190, year = {2024}, author = {Huang, J and Liu, S and Li, P and Wei, L and Lin, G and Lin, J and Luo, Y and Liu, Y and Mao, Y and Ruan, H and Qin, B and Fan, P and Lu, T and Cai, W and Yi, H and Mou, X and Lu, Z and Zhao, W and Wu, A}, title = {Multi-omics analysis of gut-brain axis reveals novel microbial and neurotransmitter signatures in patients with arteriosclerotic cerebral small vessel disease.}, journal = {Pharmacological research}, volume = {208}, number = {}, pages = {107385}, doi = {10.1016/j.phrs.2024.107385}, pmid = {39245190}, issn = {1096-1186}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Cerebral Small Vessel Diseases/metabolism/microbiology ; Male ; *Brain-Gut Axis ; Female ; Aged ; Middle Aged ; *Neurotransmitter Agents/metabolism ; *Dysbiosis/microbiology ; Metabolomics ; Bacteria/metabolism/genetics ; Metabolome ; Multiomics ; }, abstract = {Arteriosclerotic cerebral small vessel disease (aCSVD) is a major cause of stroke and dementia. Although its underlying pathogenesis remains poorly understood, both inflammaging and gut microbiota dysbiosis have been hypothesized to play significant roles. This study investigated the role of gut microbiota in the pathogenesis of aCSVD through a comparative analysis of the gut microbiome and metabolome between CSVD patients and healthy controls. The results showed that patients with aCSVD exhibited a marked reduction in potentially beneficial bacterial species, such as Faecalibacterium prausnitzli and Roseburia intestinalis, alongside an increase in taxa from Bacteroides and Proteobacteria. Integrated metagenomic and metabolomic analyses revealed that alterations in microbial metabolic pathways, including LPS biosynthesis and phenylalanine-tyrosine metabolism, were associated with the status of aCSVD. Our findings indicated that microbial LPS biosynthesis and phenylalanine-tyrosine metabolism potentially influenced the symptoms and progression of aCSVD via pro-inflammatory effect and modulation of systemic neurotransmitters, respectively. These results imply that gut microbiota characteristics may serve as indicators for early detection of aCSVD and as potential gut-directed therapeutic intervention target.}, } @article {pmid39244633, year = {2024}, author = {Li, F and Liu, J and Maldonado-Gómez, MX and Frese, SA and Gänzle, MG and Walter, J}, title = {Highly accurate and sensitive absolute quantification of bacterial strains in human fecal samples.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {168}, pmid = {39244633}, issn = {2049-2618}, mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Limosilactobacillus reuteri/genetics/classification ; Reproducibility of Results ; DNA, Bacterial/genetics ; Real-Time Polymerase Chain Reaction/methods ; High-Throughput Nucleotide Sequencing/methods ; Limit of Detection ; Sensitivity and Specificity ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {BACKGROUND: Next-generation sequencing (NGS) approaches have revolutionized gut microbiome research and can provide strain-level resolution, but these techniques have limitations in that they are only semi-quantitative, suffer from high detection limits, and generate data that is compositional. The present study aimed to systematically compare quantitative PCR (qPCR) and droplet digital PCR (ddPCR) for the absolute quantification of Limosilactobacillus reuteri strains in human fecal samples and to develop an optimized protocol for the absolute quantification of bacterial strains in fecal samples.

RESULTS: Using strain-specific PCR primers for L. reuteri 17938, ddPCR showed slightly better reproducibility, but qPCR was almost as reproducible and showed comparable sensitivity (limit of detection [LOD] around 10[4] cells/g feces) and linearity (R[2] > 0.98) when kit-based DNA isolation methods were used. qPCR further had a wider dynamic range and is cheaper and faster. Based on these findings, we conclude that qPCR has advantages over ddPCR for the absolute quantification of bacterial strains in fecal samples. We provide an optimized and easy-to-follow step-by-step protocol for the design of strain-specific qPCR assays, starting from primer design from genome sequences to the calibration of the PCR system. Validation of this protocol to design PCR assays for two L. reuteri strains, PB-W1 and DSM 20016[ T], resulted in a highly accurate qPCR with a detection limit in spiked fecal samples of around 10[3] cells/g feces. Applying our strain-specific qPCR assays to fecal samples collected from human subjects who received live L. reuteri PB-W1 or DSM 20016[ T] during a human trial demonstrated a highly accurate quantification and sensitive detection of these two strains, with a much lower LOD and a broader dynamic range compared to NGS approaches (16S rRNA gene sequencing and whole metagenome sequencing).

CONCLUSIONS: Based on our analyses, we consider qPCR with kit-based DNA extraction approaches the best approach to accurately quantify gut bacteria at the strain level in fecal samples. The provided step-by-step protocol will allow scientists to design highly sensitive strain-specific PCR systems for the accurate quantification of bacterial strains of not only L. reuteri but also other bacterial taxa in a broad range of applications and sample types. Video Abstract.}, } @article {pmid39244624, year = {2024}, author = {Yang, X and Feng, K and Wang, S and Yuan, MM and Peng, X and He, Q and Wang, D and Shen, W and Zhao, B and Du, X and Wang, Y and Wang, L and Cao, D and Liu, W and Wang, J and Deng, Y}, title = {Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {166}, pmid = {39244624}, issn = {2049-2618}, support = {No. 2019YFC1905001//National Key Research and Development Program of China/ ; }, mesh = {Anaerobiosis ; *Biodegradation, Environmental ; *Bioreactors/microbiology ; *Metabolomics ; *Microbiota ; Bacteria/metabolism/genetics/classification ; Metagenomics ; Methane/metabolism ; Thermodynamics ; Multiomics ; }, abstract = {BACKGROUND: Microbial anaerobic metabolism is a key driver of biogeochemical cycles, influencing ecosystem function and health of both natural and engineered environments. However, the temporal dynamics of the intricate interactions between microorganisms and the organic metabolites are still poorly understood. Leveraging metagenomic and metabolomic approaches, we unveiled the principles governing microbial metabolism during a 96-day anaerobic bioreactor experiment.

RESULTS: During the turnover and assembly of metabolites, homogeneous selection was predominant, peaking at 84.05% on day 12. Consistent dynamic coordination between microbes and metabolites was observed regarding their composition and assembly processes. Our findings suggested that microbes drove deterministic metabolite turnover, leading to consistent molecular conversions across parallel reactors. Moreover, due to the more favorable thermodynamics of N-containing organic biotransformations, microbes preferentially carried out sequential degradations from N-containing to S-containing compounds. Similarly, the metabolic strategy of C18 lipid-like molecules could switch from synthesis to degradation due to nutrient exhaustion and thermodynamical disadvantage. This indicated that community biotransformation thermodynamics emerged as a key regulator of both catabolic and synthetic metabolisms, shaping metabolic strategy shifts at the community level. Furthermore, the co-occurrence network of microbes-metabolites was structured around microbial metabolic functions centered on methanogenesis, with CH4 as a network hub, connecting with 62.15% of total nodes as 1st and 2nd neighbors. Microbes aggregate molecules with different molecular traits and are modularized depending on their metabolic abilities. They established increasingly positive relationships with high-molecular-weight molecules, facilitating resource acquisition and energy utilization. This metabolic complementarity and substance exchange further underscored the cooperative nature of microbial interactions.

CONCLUSIONS: All results revealed three key rules governing microbial anaerobic degradation. These rules indicate that microbes adapt to environmental conditions according to their community-level metabolic trade-offs and synergistic metabolic functions, further driving the deterministic dynamics of molecular composition. This research offers valuable insights for enhancing the prediction and regulation of microbial activities and carbon flow in anaerobic environments. Video Abstract.}, } @article {pmid39244357, year = {2024}, author = {Abo-Ismail, M and Sadek, MAA and Humagain, K and Banjara, N and Pokharel, S}, title = {Spatiotemporal distribution of environmental microbiota around animal farms adjacent to produce fields in central coast California.}, journal = {Food microbiology}, volume = {124}, number = {}, pages = {104598}, doi = {10.1016/j.fm.2024.104598}, pmid = {39244357}, issn = {1095-9998}, mesh = {Animals ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Seasons ; *Soil Microbiology ; *Farms ; California ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Water Microbiology ; Spatio-Temporal Analysis ; Metagenomics ; }, abstract = {This study aimed to identify different environmental microbiota in animal farms adjacent to produce fields and to understand their potential flow pattern. Soil and water samples were collected from 16 locations during the winter, spring, summer, and fall seasons. In addition, a high-resolution digital elevation model helped to create a stream network to understand the potential flow of the microbiome. Metagenomic analysis of the 16 S rRNA gene revealed that soil and water samples from the four seasons harbor diverse microbiome profiles. The phylogenetic relationship of operational taxonomic units (OTUs) is separated by a maximum of 0.6 Bray-Curtis distance. Similarly, the Principal Component Analysis (P = 0.001) demonstrated the soil and water microbiome clustering across different locations and seasons. The relative abundance of Proteobacteria, Bacteroidetes, and Firmicutes was higher in the water samples than in the soil samples. In contrast, the relative abundance of Actinobacteria and Chloroflexi was higher in the soil compared to the water samples. Soil samples in summer and water samples in spring had the highest abundance of Bacteroidetes and Firmicutes, respectively. A unique microbial community structure was found in water samples, with an increased abundance of Hydrogenophaga and Solirubrobacter. Genera that were significantly abundant at a 1% false discovery rate (FDR) among seasons and soil or water samples, include Nocardioides, Gemmatimonas, JG30-KF-CM45, Massilia, Gaiellales, Sphingomonas, KD4-96, Bacillus, Streptomyces, Gaiella, and Gemmatimonadaceae. The relative abundance of pathogenic genera, including Mycobacterium, Bacteroides, Nocardia, Clostridium, and Corynebacterium, were significantly (at 1% FDR) affected by seasons and environmental type. The elevation-based stream network model suggests the potential flow of microbiomes from the animal farm to the produce fields.}, } @article {pmid39244165, year = {2024}, author = {Choi, MH and Kim, D and Lee, KH and Kim, HJ and Sul, WJ and Jeong, SH}, title = {Dysbiosis of the gut microbiota is associated with in-hospital mortality in patients with antibiotic-associated diarrhoea: A metagenomic analysis.}, journal = {International journal of antimicrobial agents}, volume = {64}, number = {5}, pages = {107330}, doi = {10.1016/j.ijantimicag.2024.107330}, pmid = {39244165}, issn = {1872-7913}, mesh = {Humans ; *Diarrhea/microbiology/mortality ; Male ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; *Anti-Bacterial Agents/adverse effects/therapeutic use ; *Dysbiosis/microbiology ; Aged ; Middle Aged ; *Metagenomics ; *Hospital Mortality ; *Feces/microbiology ; *Clostridium Infections/mortality/microbiology ; Clostridioides difficile/genetics/isolation & purification/drug effects ; Aged, 80 and over ; Adult ; Machine Learning ; }, abstract = {BACKGROUND: The increasing incidence of antibiotic-associated diarrhoea (AAD) is a serious health care problem. Dysbiosis of the gut microbiota is suspected to play a role in the pathogenesis of AAD, but its impact on the clinical outcomes of patients remains unclear.

METHODS: Between May and October 2022, 210 patients with AAD admitted to a university hospital and 100 healthy controls were recruited. DNA extraction from stool specimens and shotgun sequencing were performed. Machine learning was conducted to assess profiling at different taxonomic levels and to select variables for multivariable analyses.

RESULTS: Patients were classified into two groups: Clostridioides difficile infection (CDI, n = 39) and non-CDI AAD (n = 171). The in-hospital mortality rate for the patients was 20.0%, but the presence of C. difficile in the gut microbiota was not associated with mortality. Machine learning showed that taxonomic profiling at the genus level best reflected patient prognosis. The in-hospital mortality of patients was associated with the relative abundance of specific gut microbial genera rather than alpha-diversity: each of the five genera correlated either positively (Enterococcus, Klebsiella, Corynebacterium, Pseudomonas, and Anaerofustis) or negatively (Bifidobacterium, Bacteroides, Streptococcus, Faecalibacterium, and Dorea). Genes for vancomycin resistance were significantly associated with in-hospital mortality in patients with AAD (adjusted hazard ratios, 2.45; 95% CI, 1.20-4.99).

CONCLUSION: This study demonstrates the potential utility of metagenomic studies of the gut microbial community as a biomarker for prognosis prediction in AAD patients.}, } @article {pmid39244052, year = {2024}, author = {Wang, Q and Chen, J and Qi, W and Bai, Y and Mao, J and Qu, J}, title = {Dam construction alters the traits of health-related microbes along the Yangtze River.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {176077}, doi = {10.1016/j.scitotenv.2024.176077}, pmid = {39244052}, issn = {1879-1026}, mesh = {*Rivers/microbiology ; China ; Water Microbiology ; Drug Resistance, Microbial/genetics ; Microbiota ; Environmental Monitoring ; Ecosystem ; Virulence Factors/genetics ; }, abstract = {Dams, constructed globally for energy production and water conservation, fragment rivers, and modify flow regimes, thereby altering the composition of biological communities and ecosystem functions. Despite the extensive use of dams, few studies have explored their potential health impacts, particularly concerning changes in health-related genes, such as antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), and their hosts (i.e., ARB and potential pathogens). Understanding these health-related effects is crucial because they can impact human health through water quality and pathogen prevalence. In this study, we investigated the planktonic microbial community in the Three Gorges Reservoir (TGR) and adjacent upstream and downstream areas of the Yangtze River during both the dry and wet season. Our metagenomic analysis showed that dam construction significantly decreased the abundance of ARGs, but it had an insignificant effect on VFGs. The observed reduction in ARGs abundance could be mainly attributed to the decrease abundance of the major ARGs carrier - Limnohabitansin the TGR and downstream areas due to high grazing pressure and fitness cost. Conversely, the abundance of microbes carrying VFGs (potential pathogens) remained stable from upstream to the dam reservoir, which may explain the negligible impact on VFG abundance. Overall, our results provide a detailed understanding of the ecological health implications of dam construction in large river ecosystems.}, } @article {pmid39243610, year = {2025}, author = {Jiang, L and Shen, S and Zuo, A and Chi, Y and Lu, Y and He, Q}, title = {Characterizing flavor development in low-salt Chinese horse bean-chili paste through integrated metabolomics and metagenomics.}, journal = {Food chemistry}, volume = {463}, number = {Pt 1}, pages = {141076}, doi = {10.1016/j.foodchem.2024.141076}, pmid = {39243610}, issn = {1873-7072}, mesh = {*Bacteria/classification/isolation & purification ; Capsicum/chemistry/microbiology ; Fermentation ; *Fermented Foods/analysis/microbiology ; *Metabolomics ; *Metagenomics ; Microbiota ; Sodium Chloride/analysis ; *Taste ; }, abstract = {This study utilized metabolomics and metagenomics to investigate the microbial composition and functions in low- and high-salt Chinese horse bean-chili pastes (CHCPs). The results showed that 25 key metabolites were identified to distinguish the flavor attributes between the two samples. Leuconostoc was identified as the dominant microbiota in low-salt CHCP, while Pantoea prevailed in the high-salt CHCP. Compared to traditional high-salt fermentation, low-salt and inoculated fermentation promoted the increase in the relative abundances of Companionlactobacillus, Levilactobacillus, Tetragenococcus, Zygosaccharomyces and Wickerhamiella as well as the enrichment of carbohydrate and amino acid metabolic pathways, which contributed to the enhancement of characteristic flavor compounds. Further metabolic pathway reconstruction elucidated 21 potential microbial genera associated with the formation of key metabolites, such as Leuconostoc, Levilactobacillus, Pantoea, and Pectobacterium. This study may provide insights for optimizing the fermentation process and improving the flavor quality of low-salt CHCP and similar fermentation products. KEYWORDS: Low-salt fermentation Hight-salt fermentation Chinese horse-bean chili paste Flavor formation Metabolomics Metagenomics.}, } @article {pmid39243471, year = {2024}, author = {Cai, M and Zhang, H and Zheng, L and Tang, X}, title = {A global microbiome analysis reveals the ecological feature of Tistrella and its production of the bioactive didemnins in the marine ecosystem.}, journal = {Marine pollution bulletin}, volume = {207}, number = {}, pages = {116939}, doi = {10.1016/j.marpolbul.2024.116939}, pmid = {39243471}, issn = {1879-3363}, mesh = {*Microbiota ; *Ecosystem ; Aquatic Organisms ; Metagenomics ; Seawater/microbiology/chemistry ; }, abstract = {Marine microorganisms like Tistrella are essential for producing bioactive compounds, including didemnins with antitumor and antiviral properties. However, our understanding of Tistrella's ecological features and didemnin production in natural environments is limited. In this study, we used genomics and metagenomics to show that Tistrella is widely distributed across natural habitats, especially in marine environments from the surface to 5000 m deep, with distinct non-random distribution patterns revealed by co-occurrence analysis. Importantly, transcriptional profiling of didemnin biosynthetic gene clusters indicates active in situ production of this compound within marine ecosystems. These findings enhance our understanding of Tistrella's ecology and secondary metabolite production in natural environments. Further research is needed to explore the ecological dynamics and functional impacts of Tistrella in these ecosystems.}, } @article {pmid39243463, year = {2024}, author = {Ren, M and Hu, A and Zhang, L and Yao, X and Zhao, Z and Kimirei, IA and Wang, J}, title = {Acidic proteomes are linked to microbial alkaline preference in African lakes.}, journal = {Water research}, volume = {266}, number = {}, pages = {122393}, doi = {10.1016/j.watres.2024.122393}, pmid = {39243463}, issn = {1879-2448}, mesh = {*Lakes/microbiology ; *Proteome ; Hydrogen-Ion Concentration ; Bacteria/metabolism/genetics ; Amino Acids/metabolism ; Microbiota ; }, abstract = {Microbial amino acid composition (AA) reflects adaptive strategies of cellular and molecular regulations such as a high proportion of acidic AAs, including glutamic and aspartic acids in alkaliphiles. It remains understudied how microbial AA content is linked to their pH adaptation especially in natural environments. Here we examined prokaryotic communities and their AA composition of genes with metagenomics for 39 water and sediments of East African lakes along a gradient of pH spanning from 7.2 to 10.1. We found that Shannon diversity declined with the increasing pH and that species abundance were either positively or negatively associated with pH, indicating their distinct habitat preference in lakes. Microbial communities showed higher acidic proteomes in alkaline than neutral lakes. Species acidic proteomes were also positively correlated with their pH preference, which was consistent across major bacterial lineages. These results suggest selective pressure associated with high pH likely shape microbial amino acid composition both at the species and community levels. Comparative genome analyses further revealed that alkaliphilic microbes contained more functional genes with higher acidic AAs when compared to those in neutral conditions. These traits included genes encoding diverse classes of cation transmembrane transporters, antiporters, and compatible solute transporters, which are involved in cytoplasmic pH homeostasis and osmotic stress defense under high pH conditions. Our results provide the field evidence for the strong relationship between prokaryotic AA composition and their habitat preference and highlight amino acid optimization as strategies for environmental adaptation.}, } @article {pmid39243135, year = {2024}, author = {Shi, K and Liu, X and Duan, Y and Ding, J and Jia, Y and Jiang, Z and Feng, C}, title = {Multi-omics analysis reveals associations between host gene expression, gut microbiota, and metabolites in chickens.}, journal = {Journal of animal science}, volume = {102}, number = {}, pages = {}, pmid = {39243135}, issn = {1525-3163}, mesh = {Animals ; *Chickens/microbiology/metabolism ; *Gastrointestinal Microbiome ; Female ; *Metabolome ; Transcriptome ; Liver/metabolism ; Gene Expression Profiling ; Gene Expression ; Multiomics ; }, abstract = {Egg-laying is an important trait in chickens, and it is affected by many factors, such as hormones regulated by the hypothalamic-pituitary axis and precursors synthesized by the liver. Recent studies showed that gut microbiota was associated with egg-laying, however, its underlying mechanism remains unclear. We comprehensively analyzed the host transcriptome, gut microbiota, and metabolome in broiler breeder hens during the pre-laying, peak-laying, and late-laying periods. The transcriptome analysis of the tissues related to the hypothalamic-pituitary-liver (HPL) axis revealed dynamic gene expression during egg-laying periods. Differentially expressed genes (DEGs) (i.e., PENK, NPY, AVP, PRL, RLN3, and FST) from the hypothalamus and pituitary gland were involved in female gonadal development, hormone secretion, response to endogenous stimulus, liver development, and amide metabolism. In liver, DEGs (i.e., FABP3, VTG1, LPL, APOA5, APOV1, and RBP5) were enriched in efferocytosis, sphingolipid metabolism, amide, and peptide biosynthesis. Alpha and beta diversity changed significantly in cecum microbiota during different laying periods. The abundance of Firmicutes was decreased and the abundance of Bacteroidota was increased during the peak-laying period. Functional analysis showed that the biosynthesis of secondary metabolites, amino acids, purine, and steroid hormones was altered during laying. The metabolome analysis from cecal contents showed that amino acid metabolism and steroid hormone biosynthesis changed during laying. Integrated analysis of the cecal microbiota and metabolites showed the genus Megasphaera was involved in amino acid metabolism, which included 3-phenyllatic acid, quinic acid, caffeic acid, and folic acid, and the genus Hungatella participated in steroid hormone biosynthesis through its strong correlation with estradiol. These results explored the dynamic changes in tissues related to the HPL axis and cecal microbiota and provided new insights into the interaction between the host and microbiota during egg-laying in chickens.}, } @article {pmid39242817, year = {2024}, author = {Shao, Y and Garcia-Mauriño, C and Clare, S and Dawson, NJR and Mu, A and Adoum, A and Harcourt, K and Liu, J and Browne, HP and Stares, MD and Rodger, A and Brocklehurst, P and Field, N and Lawley, TD}, title = {Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly.}, journal = {Nature microbiology}, volume = {9}, number = {10}, pages = {2570-2582}, pmid = {39242817}, issn = {2058-5276}, support = {/WT_/Wellcome Trust/United Kingdom ; WT101169MA, 206194 and 108413/A/15/D//Wellcome Trust (Wellcome)/ ; }, mesh = {Humans ; *Feces/microbiology ; Animals ; Infant, Newborn ; *Gastrointestinal Microbiome ; *Bifidobacterium/genetics/isolation & purification ; Mice ; Female ; United Kingdom ; Metagenomics ; Enterococcus faecalis/genetics/isolation & purification ; Milk, Human/microbiology ; Male ; }, abstract = {Human microbiota assembly commences at birth, seeded by both maternal and environmental microorganisms. Ecological theory postulates that primary colonizers dictate microbial community assembly outcomes, yet such microbial priority effects in the human gut remain underexplored. Here using longitudinal faecal metagenomics, we characterized neonatal microbiota assembly for a cohort of 1,288 neonates from the UK. We show that the pioneering neonatal gut microbiota can be stratified into one of three distinct community states, each dominated by a single microbial species and influenced by clinical and host factors, such as maternal age, ethnicity and parity. A community state dominated by Enterococcus faecalis displayed stochastic microbiota assembly with persistent high pathogen loads into infancy. In contrast, community states dominated by Bifidobacterium, specifically B. longum and particularly B. breve, exhibited a stable assembly trajectory and long-term pathogen colonization resistance, probably due to strain-specific functional adaptions to a breast milk-rich neonatal diet. Consistent with our human cohort observation, B. breve demonstrated priority effects and conferred pathogen colonization resistance in a germ-free mouse model. Our findings solidify the crucial role of Bifidobacteria as primary colonizers in shaping the microbiota assembly and functions in early life.}, } @article {pmid39242698, year = {2024}, author = {Lu, X and Gong, G and Zhang, Q and Yang, S and Wu, H and Zhao, M and Wang, X and Shen, Q and Ji, L and Liu, Y and Wang, Y and Liu, J and Suolang, S and Ma, X and Shan, T and Zhang, W}, title = {Metagenomic analysis reveals high diversity of gut viromes in yaks (Bos grunniens) from the Qinghai-Tibet Plateau.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1097}, pmid = {39242698}, issn = {2399-3642}, mesh = {Animals ; Cattle ; *Metagenomics ; *Gastrointestinal Microbiome/genetics ; *Virome/genetics ; Tibet ; Metagenome ; }, abstract = {The Qinghai-Tibet Plateau (QTP), renowned for its exceptional biological diversity, is home to numerous endemic species. However, research on the virology of vulnerable vertebrates like yaks remains limited. In this study, our objective was to use metagenomics to provide a comprehensive understanding of the diversity and evolution of the gut virome in yak populations across different regions of the QTP. Our findings revealed a remarkably diverse array of viruses in the gut of yaks, including those associated with vertebrates and bacteriophages. Notably, some vertebrate-associated viruses, such as astrovirus and picornavirus, showed significant sequence identity across diverse yak populations. Additionally, we observed differences in the functional profiles of genes carried by the yak gut virome across different regions. Moreover, the virus-bacterium symbiotic network that we discovered holds potential significance in maintaining the health of yaks. Overall, this research expands our understanding of the viral communities in the gut of yaks and highlights the importance of further investigating the interactions between viruses and their hosts. These data will be beneficial for revealing the crucial role that viruses play in the yak gut ecology in future studies.}, } @article {pmid39242535, year = {2024}, author = {Attrah, M and Schärer, MR and Esposito, M and Gionchetta, G and Bürgmann, H and Lens, PNL and Fenner, K and van de Vossenberg, J and Robinson, SL}, title = {Disentangling abiotic and biotic effects of treated wastewater on stream biofilm resistomes enables the discovery of a new planctomycete beta-lactamase.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {164}, pmid = {39242535}, issn = {2049-2618}, support = {109070/WT_/Wellcome Trust/United Kingdom ; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, 186531 (ANTIVERSA as part of biodeversa+, European Biodiversity Partnership)//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, 186531 (ANTIVERSA as part of biodeversa+, European Biodiversity Partnership)//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 200021L_201006//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; PZPGP2_209124//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Biofilms/drug effects ; *Wastewater/microbiology ; *beta-Lactamases/genetics ; *Rivers/microbiology ; *Metagenomics ; Microbiota/drug effects ; Bacteria/genetics/classification/drug effects/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Planctomycetales/genetics/drug effects ; Metagenome ; Bacterial Proteins/genetics/metabolism ; }, abstract = {BACKGROUND: Environmental reservoirs of antibiotic resistance pose a threat to human and animal health. Aquatic biofilms impacted by wastewater effluent (WW) are known environmental reservoirs for antibiotic resistance; however, the relative importance of biotic factors and abiotic factors from WW on the abundance of antibiotic resistance genes (ARGs) within aquatic biofilms remains unclear. Additionally, experimental evidence is limited within complex aquatic microbial communities as to whether genes bearing low sequence similarity to validated reference ARGs are functional as ARGs.

RESULTS: To disentangle the effects of abiotic and biotic factors on ARG abundances, natural biofilms were previously grown in flume systems with different proportions of stream water and either ultrafiltered or non-ultrafiltered WW. In this study, we conducted deep shotgun metagenomic sequencing of 75 biofilm, stream, and WW samples from these flume systems and compared the taxonomic and functional microbiome and resistome composition. Statistical analysis revealed an alignment of the resistome and microbiome composition and a significant association with experimental treatment. Several ARG classes exhibited an increase in normalized metagenomic abundances in biofilms grown with increasing percentages of non-ultrafiltered WW. In contrast, sulfonamide and extended-spectrum beta-lactamase ARGs showed greater abundances in biofilms grown in ultrafiltered WW compared to non-ultrafiltered WW. Overall, our results pointed toward the dominance of biotic factors over abiotic factors in determining ARG abundances in WW-impacted stream biofilms and suggested gene family-specific mechanisms for ARGs that exhibited divergent abundance patterns. To investigate one of these specific ARG families experimentally, we biochemically characterized a new beta-lactamase from the Planctomycetota (Phycisphaeraceae). This beta-lactamase displayed activity in the cleavage of cephalosporin analog despite sharing a low sequence identity with known ARGs.

CONCLUSIONS: This discovery of a functional planctomycete beta-lactamase ARG is noteworthy, not only because it was the first beta-lactamase to be biochemically characterized from this phylum, but also because it was not detected by standard homology-based ARG tools. In summary, this study conducted a metagenomic analysis of the relative importance of biotic and abiotic factors in the context of WW discharge and their impact on both known and new ARGs in aquatic biofilms. Video Abstract.}, } @article {pmid39240096, year = {2024}, author = {Ruiz-Perez, D and Gimon, I and Sazal, M and Mathee, K and Narasimhan, G}, title = {Unfolding and de-confounding: biologically meaningful causal inference from longitudinal multi-omic networks using METALICA.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0130323}, pmid = {39240096}, issn = {2379-5077}, support = {R15 AI128714/AI/NIAID NIH HHS/United States ; Dissertation Year Fellowship//University Graduate School, Florida International University (UGS)/ ; 1R15AI128714-01//HHS | NIH | OSC | Common Fund (NIH Common Fund)/ ; }, mesh = {Humans ; *Algorithms ; Microbiota/genetics ; Longitudinal Studies ; Gastrointestinal Microbiome/genetics ; Metabolomics ; Computational Biology/methods ; Multiomics ; }, abstract = {UNLABELLED: A key challenge in the analysis of microbiome data is the integration of multi-omic datasets and the discovery of interactions between microbial taxa, their expressed genes, and the metabolites they consume and/or produce. In an effort to improve the state of the art in inferring biologically meaningful multi-omic interactions, we sought to address some of the most fundamental issues in causal inference from longitudinal multi-omics microbiome data sets. We developed METALICA, a suite of tools and techniques that can infer interactions between microbiome entities. METALICA introduces novel unrolling and de-confounding techniques used to uncover multi-omic entities that are believed to act as confounders for some of the relationships that may be inferred using standard causal inferencing tools. The results lend support to predictions about biological models and processes by which microbial taxa interact with each other in a microbiome. The unrolling process helps identify putative intermediaries (genes and/or metabolites) to explain the interactions between microbes; the de-confounding process identifies putative common causes that may lead to spurious relationships to be inferred. METALICA was applied to the networks inferred by existing causal discovery, and network inference algorithms were applied to a multi-omics data set resulting from a longitudinal study of IBD microbiomes. The most significant unrollings and de-confoundings were manually validated using the existing literature and databases.

IMPORTANCE: We have developed a suite of tools and techniques capable of inferring interactions between microbiome entities. METALICA introduces novel techniques called unrolling and de-confounding that are employed to uncover multi-omic entities considered to be confounders for some of the relationships that may be inferred using standard causal inferencing tools. To evaluate our method, we conducted tests on the inflammatory bowel disease (IBD) dataset from the iHMP longitudinal study, which we pre-processed in accordance with our previous work. From this dataset, we generated various subsets, encompassing different combinations of metagenomics, metabolomics, and metatranscriptomics datasets. Using these multi-omics datasets, we demonstrate how the unrolling process aids in the identification of putative intermediaries (genes and/or metabolites) to explain the interactions between microbes. Additionally, the de-confounding process identifies potential common causes that may give rise to spurious relationships to be inferred. The most significant unrollings and de-confoundings were manually validated using the existing literature and databases.}, } @article {pmid39239875, year = {2024}, author = {Kwan, SY and Gonzales, KA and Jamal, MA and Stevenson, HL and Tan, L and Lorenzi, PL and Futreal, PA and Hawk, ET and McCormick, JB and Fisher-Hoch, SP and Jenq, RR and Beretta, L}, title = {Protection against fibrosis by a bacterial consortium in metabolic dysfunction-associated steatohepatitis and the role of amino acid metabolism.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2399260}, pmid = {39239875}, issn = {1949-0984}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; P50 CA217674/CA/NCI NIH HHS/United States ; UL1 TR000371/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; *Liver Cirrhosis/microbiology/metabolism ; Mice ; *Amino Acids/metabolism ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Male ; *Liver/metabolism/pathology/microbiology ; Female ; Feces/microbiology ; Mice, Inbred C57BL ; Middle Aged ; Fatty Liver/metabolism/microbiology ; Disease Models, Animal ; Metagenome ; Adult ; }, abstract = {The gut microbiota drives progression to liver fibrosis, the main determinant of mortality in metabolic dysfunction-associated steatohepatitis (MASH). In this study, we aimed to identify bacterial species associated with protection against liver fibrosis in a high-risk population, and test their potential to protect against liver fibrosis in vivo. Based on stool shotgun metagenomic sequencing of 340 subjects from a population cohort disproportionally affected by MASH, we identified bacterial species from the Bacteroidales and Clostridiales orders associated with reduced risk of liver fibrosis. A bacterial consortium was subsequently tested in a mouse model of MASH, which demonstrated protective effects against liver fibrosis. Six of the eight inoculated bacteria were detected in mouse stool and liver. Intrahepatic presence of bacteria was further confirmed by bacterial culture of mouse liver tissue. Changes in liver histological parameters, gut functional profiles, and amino acid profiles were additionally assessed. Comparison between fibrosis-associated human metagenome and bacteria-induced metagenome changes in mice identified microbial functions likely to mediate the protective effect against liver fibrosis. Amino acid profiling confirmed an increase in cysteine synthase activity, associated with reduced fibrosis. Other microbiota-induced changes in amino acids associated with reduced fibrosis included increased gut asparaginase activity and decreased hepatic tryptophan-to-kynurenine conversion. This human-to-mouse study identified bacterial species and their effects on amino acid metabolism as innovative strategies to protect against liver fibrosis in MASH.}, } @article {pmid39238368, year = {2024}, author = {Hansen, AK and Argondona, JA and Miao, S and Percy, DM and Degnan, PH}, title = {Rapid Loss of Nutritional Symbionts in an Endemic Hawaiian Herbivore Radiation Is Associated with Plant Galling Habit.}, journal = {Molecular biology and evolution}, volume = {41}, number = {9}, pages = {}, pmid = {39238368}, issn = {1537-1719}, mesh = {Animals ; *Symbiosis ; *Herbivory ; *Hemiptera/microbiology ; RNA, Ribosomal, 16S/genetics ; Hawaii ; Phylogeny ; Biological Evolution ; Microbiota ; }, abstract = {Insect herbivores frequently cospeciate with symbionts that enable them to survive on nutritionally unbalanced diets. While ancient symbiont gain and loss events have been pivotal for insect diversification and feeding niche specialization, evidence of recent events is scarce. We examine the recent loss of nutritional symbionts (in as little as 1 MY) in sap-feeding Pariaconus, an endemic Hawaiian insect genus that has undergone adaptive radiation, evolving various galling and free-living ecologies on a single host-plant species, Metrosideros polymorpha within the last ∼5 MY. Using 16S rRNA sequencing, we investigated the bacterial microbiomes of 19 Pariaconus species and identified distinct symbiont profiles associated with specific host-plant ecologies. Phylogenetic analyses and metagenomic reconstructions revealed significant differences in microbial diversity and functions among psyllids with different host-plant ecologies. Within a few millions of years, Pariaconus species convergently evolved the closed-gall habit twice. This shift to enclosed galls coincided with the loss of the Morganella-like symbiont that provides the essential amino acid arginine to free-living and open-gall sister species. After the Pariaconus lineage left Kauai and colonized younger islands, both open- and closed-gall species lost the Dickeya-like symbiont. This symbiont is crucial for synthesizing essential amino acids (phenylalanine, tyrosine, and lysine) as well as B vitamins in free-living species. The recurrent loss of these symbionts in galling species reinforces evidence that galls are nutrient sinks and, combined with the rapidity of the evolutionary timeline, highlights the dynamic role of insect-symbiont relationships during the diversification of feeding ecologies. We propose new Candidatus names for the novel Morganella-like and Dickeya-like symbionts.}, } @article {pmid39237540, year = {2024}, author = {Ravikrishnan, A and Wijaya, I and Png, E and Chng, KR and Ho, EXP and Ng, AHQ and Mohamed Naim, AN and Gounot, JS and Guan, SP and Hanqing, JL and Guan, L and Li, C and Koh, JY and de Sessions, PF and Koh, WP and Feng, L and Ng, TP and Larbi, A and Maier, AB and Kennedy, BK and Nagarajan, N}, title = {Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7751}, pmid = {39237540}, issn = {2041-1723}, mesh = {Aged, 80 and over ; Female ; Humans ; Male ; *Aging ; Asian People/genetics ; Bacteria/genetics/classification/metabolism/isolation & purification ; Bacteroides/genetics/metabolism ; Cohort Studies ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Metagenomics/methods ; Phenotype ; Singapore ; Octogenarians ; }, abstract = {While rapid demographic changes in Asia are driving the incidence of chronic aging-related diseases, the limited availability of high-quality in vivo data hampers our ability to understand complex multi-factorial contributions, including gut microbial, to healthy aging. Leveraging a well-phenotyped cohort of community-living octogenarians in Singapore, we used deep shotgun-metagenomic sequencing for high-resolution taxonomic and functional characterization of their gut microbiomes (n = 234). Joint species-level analysis with other Asian cohorts identified distinct age-associated shifts characterized by reduction in microbial richness, and specific Alistipes and Bacteroides species enrichment (e.g., Alistipes shahii and Bacteroides xylanisolvens). Functional analysis confirmed these changes correspond to metabolic potential expansion in aging towards alternate pathways synthesizing and utilizing amino-acid precursors, vis-à-vis dominant microbial guilds producing butyrate in gut from pyruvate (e.g., Faecalibacterium prausnitzii, Roseburia inulinivorans). Extending these observations to key clinical markers helped identify >10 robust microbial associations to inflammation, cardiometabolic and liver health, including potential probiotic species (e.g., Parabacteroides goldsteinii) and pathobionts (e.g., Klebsiella pneumoniae), highlighting the microbiome's role as biomarkers and potential targets for promoting healthy aging.}, } @article {pmid39236827, year = {2024}, author = {Xu, W and Xu, Y and Sun, R and Rey Redondo, E and Leung, KK and Wan, SH and Li, J and Yung, CCM}, title = {Revealing the intricate temporal dynamics and adaptive responses of prokaryotic and eukaryotic microbes in the coastal South China Sea.}, journal = {The Science of the total environment}, volume = {952}, number = {}, pages = {176019}, doi = {10.1016/j.scitotenv.2024.176019}, pmid = {39236827}, issn = {1879-1026}, mesh = {China ; *Phytoplankton/physiology/genetics ; *Seawater/microbiology ; Microbiota ; Cyanobacteria/genetics/physiology ; Photosynthesis ; Seasons ; Metagenome ; }, abstract = {This comprehensive two-year investigation in the coastal South China Sea has advanced our understanding of marine microbes at both community and genomic levels. By combining metagenomics and metatranscriptomics, we have revealed the intricate temporal dynamics and remarkable adaptability of microbial communities and phytoplankton metagenome-assembled genomes (MAGs) in response to environmental fluctuations. We observed distinct seasonal shifts in microbial community composition and function: cyanobacteria were predominant during warmer months, whereas photosynthetic protists were more abundant during colder seasons. Notably, metabolic marker KOs of photosynthesis were consistently active throughout the year, underscoring the persistent role of these processes irrespective of seasonal changes. Our analysis reveals that environmental parameters such as temperature, salinity, and nitrate concentrations profoundly influence microbial community composition, while temperature and silicate have emerged as crucial factors shaping their functional traits. Through the recovery and analysis of 37 phytoplankton MAGs, encompassing nine prokaryotic cyanobacteria and 28 eukaryotic protists from diverse phyla, we have gained insights into their genetic diversity and metabolic capabilities. Distinct profiles of photosynthesis-related pathways including carbon fixation, carotenoid biosynthesis, photosynthesis-antenna proteins, and photosynthesis among the MAGs indicated their genetic adaptations to changing environmental conditions. This study not only enhances our understanding of microbial dynamics in coastal marine ecosystems but also sheds light on the ecological roles and adaptive responses of different microbial groups to environmental changes.}, } @article {pmid39236503, year = {2024}, author = {Wang, D and Meng, Y and Huang, LN and Zhang, XX and Luo, X and Meng, F}, title = {A comprehensive catalog encompassing 1376 species-level genomes reveals the core community and functional diversity of anammox microbiota.}, journal = {Water research}, volume = {266}, number = {}, pages = {122356}, doi = {10.1016/j.watres.2024.122356}, pmid = {39236503}, issn = {1879-2448}, mesh = {*Microbiota ; Bacteria/genetics/classification/metabolism ; Metagenome ; Wastewater/microbiology ; }, abstract = {Research on the microbial community and function of the anammox process for environmentally friendly wastewater treatment has achieved certain success, which may mean more universal insights are needed. However, the comprehensive understanding of the anammox process is constrained by the limited taxonomic assignment and functional characterization of anammox microbiota, primarily due to the scarcity of high-quality genomes for most organisms. This study reported a global genome catalog of anammox microbiotas based on numerous metagenomes obtained from both lab- and full-scale systems. A total of 1376 candidate species from 7474 metagenome-assembled genomes were used to construct the genome catalog, providing extensive microbial coverage (averaged of 92.40 %) of anammox microbiota. Moreover, a total of 64 core genera and 44 core species were identified, accounting for approximately 64.25 % and 43.97 %, respectively, of anammox microbiota. The strict core genera encompassed not only functional bacteria (e.g., Brocadia, Desulfobacillus, Zeimonas, and Nitrosomonas) but also two candidate genera (UBA12294 and OLB14) affiliated with the order Anaerolineales. In particular, core denitrifying bacteria with observably taxonomic diversity exhibited diverse functional profiles; for instance, the potential of carbohydrate metabolism in Desulfobacillus and Zeimonas likely improves the mixotrophic lifestyle of anammox microbiota. Besides, a noteworthy association was detected between anammox microbiota and system type. Microbiota in coupling system exhibited complex diversity and interspecies interactions by limiting numerous core denitrifying bacteria. In summary, the constructed catalog substantially expands our understanding of the core community and their functions of anammox microbiota, providing a valuable resource for future studies on anammox systems.}, } @article {pmid39235751, year = {2025}, author = {Lemée, P and Bridier, A}, title = {Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2852}, number = {}, pages = {289-309}, pmid = {39235751}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Food Microbiology/methods ; *Bacteria/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Microbiota/genetics ; }, abstract = {Next-generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize, and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.}, } @article {pmid39235268, year = {2024}, author = {Sudarshan, AS and Dai, Z and Gabrielli, M and Oosthuizen-Vosloo, S and Konstantinidis, KT and Pinto, AJ}, title = {New Drinking Water Genome Catalog Identifies a Globally Distributed Bacterial Genus Adapted to Disinfected Drinking Water Systems.}, journal = {Environmental science & technology}, volume = {58}, number = {37}, pages = {16475-16487}, pmid = {39235268}, issn = {1520-5851}, mesh = {*Drinking Water/microbiology ; Disinfection ; Bacteria/genetics ; Microbiota ; Genome, Bacterial ; Metagenome ; }, abstract = {Genome-resolved insights into the structure and function of the drinking water microbiome can advance the effective management of drinking water quality. To enable this, we constructed and curated thousands of metagenome-assembled and isolate genomes from drinking water distribution systems globally to develop a Drinking Water Genome Catalog (DWGC). The current DWGC disproportionately represents disinfected drinking water systems due to a paucity of metagenomes from nondisinfected systems. Using the DWGC, we identify core genera of the drinking water microbiome including a genus (UBA4765) within the order Rhizobiales that is frequently detected and highly abundant in disinfected drinking water systems. We demonstrate that this genus has been widely detected but incorrectly classified in previous amplicon sequencing-based investigations of the drinking water microbiome. Further, we show that a single genome variant (genomovar) within this genus is detected in 75% of drinking water systems included in this study. We propose a name for this uncultured bacterium as "Raskinella chloraquaticus" and describe the genus as "Raskinella" (endorsed by SeqCode). Metabolic annotation and modeling-based predictions indicate that this bacterium is capable of necrotrophic growth, is able to metabolize halogenated compounds, proliferates in a biofilm-based environment, and shows clear indications of disinfection-mediated selection.}, } @article {pmid39235252, year = {2024}, author = {Sweet, P and Burroughs, M and Jang, S and Contreras, L}, title = {TolRad, a model for predicting radiation tolerance using Pfam annotations, identifies novel radiosensitive bacterial species from reference genomes and MAGs.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0383823}, pmid = {39235252}, issn = {2165-0497}, support = {HDTRA1-17-1-0025//DOD | Defense Threat Reduction Agency (DTRA)/ ; FA9550-20-1-0131//DOD | USAF | AMC | Air Force Office of Scientific Research (AFOSR)/ ; W911NF22S0002//DNI | Intelligence Advanced Research Projects Activity (IARPA)/ ; }, mesh = {*Radiation Tolerance/genetics ; *Bacteria/genetics/radiation effects/classification ; *Genome, Bacterial ; Humans ; Radiation, Ionizing ; Bacterial Proteins/genetics/metabolism ; Microbiota/genetics/radiation effects ; Proteome ; Metagenome ; Molecular Sequence Annotation ; }, abstract = {UNLABELLED: The trait of ionizing radiation (IR) tolerance is variable between bacterium, with species succumbing to acute doses as low as 60 Gy and extremophiles able to survive doses exceeding 10,000 Gy. While survival screens have identified multiple highly radioresistant bacteria, such systemic searches have not been conducted for IR-sensitive bacteria. The taxonomy-level diversity of IR sensitivity is poorly understood, as are genetic elements that influence IR sensitivity. Using the protein domain (Pfam) frequencies from 61 bacterial species with experimentally determined D10 values (the dose at which only 10% of the population survives), we trained TolRad, a random forest binary classifier, to distinguish between radiosensitive (D10 < 200 Gy) and radiation-tolerant (D10 > 200 Gy) bacteria. On untrained species, TolRad had an accuracy of 0.900. We applied TolRad to 152 UniProt-hosted bacterial proteomes associated with the human microbiome, including 37 strains from the ATCC Human Microbiome Collection, and classified 34 species as radiosensitive. Whereas IR-sensitive species (D10 < 200 Gy) in the training data set had been confined to the phylum Proteobacterium, this initial TolRad screen identified radiosensitive bacteria in two additional phyla. We experimentally validated the predicted radiosensitivity of a Bacteroidota species from the human microbiome. To demonstrate that TolRad can be applied to metagenome-assembled genomes (MAGs), we tested the accuracy of TolRad on Egg-NOG assembled proteomes (0.965) and partial proteomes. Finally, three collections of MAGs were screened using TolRad, identifying further phyla with radiosensitive species and suggesting that environmental conditions influence the abundance of radiosensitive bacteria.

IMPORTANCE: Bacterial species have vast genetic diversity, allowing for life in extreme environments and the conduction of complex chemistry. The ability to harness the full potential of bacterial diversity is hampered by the lack of high-throughput experimental or bioinformatic methods for characterizing bacterial traits. Here, we present a computational model that uses de novo-generated genome annotations to classify a bacterium as tolerant of ionizing radiation (IR) or as radiosensitive. This model allows for rapid screening of bacterial communities for low-tolerance species that are of interest for both mechanistic studies into bacterial sensitivity to IR and biomarkers of IR exposure.}, } @article {pmid39233185, year = {2024}, author = {Huang, J and Wang, C and Huang, X and Zhang, Q and Feng, R and Wang, X and Zhang, S and Wang, J}, title = {Long-term effect of phenol, quinoline, and pyridine on nitrite accumulation in the nitrification process: performance, microbial community, metagenomics and molecular docking analysis.}, journal = {Bioresource technology}, volume = {412}, number = {}, pages = {131407}, doi = {10.1016/j.biortech.2024.131407}, pmid = {39233185}, issn = {1873-2976}, mesh = {*Molecular Docking Simulation ; *Nitrification ; *Nitrites/metabolism ; *Quinolines/pharmacology ; *Metagenomics/methods ; *Pyridines/pharmacology/metabolism ; Phenol ; Bacteria/metabolism/drug effects ; Microbiota/drug effects ; Wastewater ; Oxidoreductases/metabolism ; Ammonia/metabolism ; }, abstract = {Phenol, quinoline, and pyridine, commonly found in industrial wastewater, disrupt the nitrification process, leading to nitrite accumulation. This study explores the potential mechanisms through which these biotoxic organic compounds affect nitrite accumulation, using metagenomic and molecular docking analyses. Despite increasing concentrations of these compounds from 40 to 160 mg/L, ammonia nitrogen removal was not hindered, and stable nitrite accumulation rates exceeding 90 % were maintained. Additionally, these compounds inhibited nitrite-oxidizing bacteria (NOB) and enriched ammonia-oxidizing bacteria (AOB) in situ. As the concentration of these compounds rose, protein (PN) and polysaccharide (PS) concentrations also increased, along with a higher PN/PS ratio. Metagenomic analysis further revealed an increase in hao relative abundance, while microbial community analysis showed increased Nitrosomonas abundance, which contributed to nitrite accumulation stability. Molecular docking indicated that these compounds have lower binding energy with hydroxylamine oxidoreductase (HAO) and nitrate reductase (NAR), theoretically supporting the observed sustained nitrite accumulation.}, } @article {pmid39232827, year = {2024}, author = {Sun, C and Hu, G and Yi, L and Ge, W and Yang, Q and Yang, X and He, Y and Liu, Z and Chen, WH}, title = {Integrated analysis of facial microbiome and skin physio-optical properties unveils cutotype-dependent aging effects.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {163}, pmid = {39232827}, issn = {2049-2618}, support = {2019YFA0905600//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Microbiota ; *Skin/microbiology ; *Face/microbiology ; Middle Aged ; *Skin Aging/physiology ; Female ; Adult ; Male ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Aging ; Metagenome ; Young Adult ; High-Throughput Nucleotide Sequencing ; Sebum/metabolism ; }, abstract = {BACKGROUND: Our facial skin hosts millions of microorganisms, primarily bacteria, crucial for skin health by maintaining the physical barrier, modulating immune response, and metabolizing bioactive materials. Aging significantly influences the composition and function of the facial microbiome, impacting skin immunity, hydration, and inflammation, highlighting potential avenues for interventions targeting aging-related facial microbes amidst changes in skin physiological properties.

RESULTS: We conducted a multi-center and deep sequencing survey to investigate the intricate interplay of aging, skin physio-optical conditions, and facial microbiome. Leveraging a newly-generated dataset of 2737 species-level metagenome-assembled genomes (MAGs), our integrative analysis highlighted aging as the primary driver, influencing both facial microbiome composition and key skin characteristics, including moisture, sebum production, gloss, pH, elasticity, and sensitivity. Further mediation analysis revealed that skin characteristics significantly impacted the microbiome, mostly as a mediator of aging. Utilizing this dataset, we uncovered two consistent cutotypes across sampling cities and identified aging-related microbial MAGs. Additionally, a Facial Aging Index (FAI) was formulated based on the microbiome, uncovering the cutotype-dependent effects of unhealthy lifestyles on skin aging. Finally, we distinguished aging related microbial pathways influenced by lifestyles with cutotype-dependent effect.

CONCLUSIONS: Together, our findings emphasize aging's central role in facial microbiome dynamics, and support personalized skin microbiome interventions by targeting lifestyle, skin properties, and aging-related microbial factors. Video Abstract.}, } @article {pmid39232318, year = {2024}, author = {Yadav, P and Kumari, SP and Hooda, S and Gupta, RK and Diwan, P}, title = {Comparative assessment of microbiome and resistome of influent and effluent of sewage treatment plant and common effluent treatment plant located in Delhi, India using shotgun approach.}, journal = {Journal of environmental management}, volume = {369}, number = {}, pages = {122342}, doi = {10.1016/j.jenvman.2024.122342}, pmid = {39232318}, issn = {1095-8630}, mesh = {India ; *Microbiota ; *Sewage/microbiology ; *Wastewater/microbiology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; Waste Disposal, Fluid ; }, abstract = {Antimicrobial resistance (AMR) is a significant threat that demands surveillance to identify and analyze trends of the emerging antibiotic resistance genes (ARGs) and potential microbial carriers. The influent of the wastewater treatment plants (WWTPs) reflects the microbes derived from the population and effluent being the source of dissemination of potential pathogenic microbes and AMR. The present study aimed to monitor microbial communities and antibiotic resistance genes in WWTPs employing a whole metagenome shotgun sequencing approach. The samples were collected from a sewage treatment plant (STP) and a common effluent treatment plant (CETP) in Delhi, India. The results showed the influent of STP to be rich in Bifidobacterium, Bacteroides, Escherichia, Arcobacter, and Pseudomonas residents of gut microbiota and known to cause diseases in humans and animals; whereas the CETP sample was abundant in Aeromonas, Escherichia, and Shewanella known to be involved in the degradation of different compounds. Interestingly, the effluent samples from both STPs and CETP were rich in microbial diversity, comprising organic and xenobiotic compound degrading and disease-causing bacteria, indicating the effluent being the source of dissemination of concerning bacteria to the environment. The functional profile at both sites displayed similarity with an abundance of housekeeping function genes as analyzed by Clusters of Orthologous Genes (COG), KEGG Orthology (KO), and subsystem databases. Resistome profiling by MEGARes showed the dominance of ARGs corresponding to beta-lactams having relative abundance ranging from 16% to 34% in all the metagenome datasets, followed by tetracycline (8%-16%), aminoglycosides (7%-9%), multi-drug (5%-9%), and rifampin (3%-9%). Also, AMR genes oxa, ant3-DPRIME, and rpoB, which are of clinical importance were predominantly and most prevalently present in all the samples. The presence of AMR in effluents from both types of treatment plants indicates that wastewater from both sources contributes to the spread of pathogenic bacteria and resistance genes, increasing the environmental AMR burden and therefore requires tertiary treatment before discharge. This work will facilitate further research towards the identification of suitable biomarkers for monitoring antibiotic resistance.}, } @article {pmid39232160, year = {2024}, author = {Chen, J and Jia, Y and Sun, Y and Liu, K and Zhou, C and Liu, C and Li, D and Liu, G and Zhang, C and Yang, T and Huang, L and Zhuang, Y and Wang, D and Xu, D and Zhong, Q and Guo, Y and Li, A and Seim, I and Jiang, L and Wang, L and Lee, SMY and Liu, Y and Wang, D and Zhang, G and Liu, S and Wei, X and Yue, Z and Zheng, S and Shen, X and Wang, S and Qi, C and Chen, J and Ye, C and Zhao, F and Wang, J and Fan, J and Li, B and Sun, J and Jia, X and Xia, Z and Zhang, H and Liu, J and Zheng, Y and Liu, X and Wang, J and Yang, H and Kristiansen, K and Xu, X and Mock, T and Li, S and Zhang, W and Fan, G}, title = {Global marine microbial diversity and its potential in bioprospecting.}, journal = {Nature}, volume = {633}, number = {8029}, pages = {371-379}, pmid = {39232160}, issn = {1476-4687}, mesh = {Antimicrobial Cationic Peptides/genetics/isolation & purification ; *Aquatic Organisms/classification/genetics/isolation & purification ; Archaea/genetics/classification ; Bacteria/genetics/classification ; *Biodiversity ; Biomedical Technology ; *Bioprospecting/trends ; Biotechnology ; CRISPR-Associated Protein 9/genetics/isolation & purification ; CRISPR-Cas Systems/genetics ; Drug Resistance, Bacterial/genetics ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; *Geographic Mapping ; *Metagenome/genetics ; Oceans and Seas ; Phylogeny ; Seawater/microbiology ; Water Microbiology ; }, abstract = {The past two decades has witnessed a remarkable increase in the number of microbial genomes retrieved from marine systems[1,2]. However, it has remained challenging to translate this marine genomic diversity into biotechnological and biomedical applications[3,4]. Here we recovered 43,191 bacterial and archaeal genomes from publicly available marine metagenomes, encompassing a wide range of diversity with 138 distinct phyla, redefining the upper limit of marine bacterial genome size and revealing complex trade-offs between the occurrence of CRISPR-Cas systems and antibiotic resistance genes. In silico bioprospecting of these marine genomes led to the discovery of a novel CRISPR-Cas9 system, ten antimicrobial peptides, and three enzymes that degrade polyethylene terephthalate. In vitro experiments confirmed their effectiveness and efficacy. This work provides evidence that global-scale sequencing initiatives advance our understanding of how microbial diversity has evolved in the oceans and is maintained, and demonstrates how such initiatives can be sustainably exploited to advance biotechnology and biomedicine.}, } @article {pmid39232089, year = {2024}, author = {Melo, T and Sousa, CA and Delacour-Estrella, S and Bravo-Barriga, D and Seixas, G}, title = {Characterization of the microbiome of Aedes albopictus populations in different habitats from Spain and São Tomé.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {20545}, pmid = {39232089}, issn = {2045-2322}, mesh = {Animals ; *Aedes/microbiology ; Spain ; *Microbiota ; *Wolbachia/genetics/isolation & purification/physiology ; Female ; *RNA, Ribosomal, 16S/genetics ; Mosquito Vectors/microbiology ; Ecosystem ; Male ; }, abstract = {The mosquito microbiome significantly influences vector competence, including in Aedes albopictus, a globally invasive vector. Describing the microbiome and Wolbachia strains of Ae. albopictus from different regions can guide area-specific control strategies. Mosquito samples from Spain and São Tomé were analyzed using 16S rRNA gene sequencing and metagenomic sequencing. Wolbachia infection patterns were observed by sex and population. Female mosquitoes were blood-fed, a factor considered in analyzing their microbiota. Results revealed a dominance of dual Wolbachia infections, strains A and B, in the microbiome of both populations of Ae. albopictus, especially among females. Both populations shared a core microbiome, although 5 and 9 other genera were only present in Spain and São Tomé populations, respectively. Genera like Pelomonas and Nevskia were identified for the first time in Aedes mosquitoes. This study is the first to describe the Ae. albopictus bacteriome in Spain and São Tomé, offering insights for the development of targeted mosquito control strategies. Understanding the specific microbiome composition can help in designing more effective interventions, such as microbiome manipulation and Wolbachia-based approaches, to reduce vector competence and transmission potential of these mosquitoes.}, } @article {pmid39230701, year = {2024}, author = {Hera, MR and Liu, S and Wei, W and Rodriguez, JS and Ma, C and Koslicki, D}, title = {Metagenomic functional profiling: to sketch or not to sketch?.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {Suppl 2}, pages = {ii165-ii173}, pmid = {39230701}, issn = {1367-4811}, support = {R01 GM146462/GM/NIGMS NIH HHS/United States ; R01GM146462/GF/NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; *Software ; *Algorithms ; *Metagenome/genetics ; Humans ; Microbiota/genetics ; Databases, Genetic ; }, abstract = {MOTIVATION: Functional profiling of metagenomic samples is essential to decipher the functional capabilities of microbial communities. Traditional and more widely used functional profilers in the context of metagenomics rely on aligning reads against a known reference database. However, aligning sequencing reads against a large and fast-growing database is computationally expensive. In general, k-mer-based sketching techniques have been successfully used in metagenomics to address this bottleneck, notably in taxonomic profiling. In this work, we describe leveraging FracMinHash (implemented in sourmash, a publicly available software), a k-mer-sketching algorithm, to obtain functional profiles of metagenome samples.

RESULTS: We show how pieces of the sourmash software (and the resulting FracMinHash sketches) can be put together in a pipeline to functionally profile a metagenomic sample. We named our pipeline fmh-funprofiler. We report that the functional profiles obtained using this pipeline demonstrate comparable completeness and better purity compared to the profiles obtained using other alignment-based methods when applied to simulated metagenomic data. We also report that fmh-funprofiler is 39-99× faster in wall-clock time, and consumes up to 40-55× less memory. Coupled with the KEGG database, this method not only replicates fundamental biological insights but also highlights novel signals from the Human Microbiome Project datasets.

This fast and lightweight metagenomic functional profiler is freely available and can be accessed here: https://github.com/KoslickiLab/fmh-funprofiler. All scripts of the analyses we present in this manuscript can be found on GitHub.}, } @article {pmid39230261, year = {2024}, author = {Tu, V and Ren, Y and Tanes, C and Mukhopadhyay, S and Daniel, SG and Li, H and Bittinger, K}, title = {A quantitative approach to measure and predict microbiome response to antibiotics.}, journal = {mSphere}, volume = {9}, number = {9}, pages = {e0048824}, pmid = {39230261}, issn = {2379-5042}, support = {SAP # 4100068710//Pennsylvania Department of Health (PA DOH)/ ; //Children's Hospital of Philadelphia (CHOP)/ ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/drug effects/genetics/classification ; Gastrointestinal Microbiome/drug effects/genetics ; Metagenomics/methods ; Microbial Sensitivity Tests/methods ; Skin/microbiology ; Mouth/microbiology ; Software ; }, abstract = {UNLABELLED: Although antibiotics induce sizable perturbations in the human microbiome, we lack a systematic and quantitative method to measure and predict the microbiome's response to specific antibiotics. Here, we introduce such a method, which takes the form of a microbiome response index (MiRIx) for each antibiotic. Antibiotic-specific MiRIx values quantify the overall susceptibility of the microbiota to an antibiotic, based on databases of bacterial phenotypes and published data on intrinsic antibiotic susceptibility. We applied our approach to five published microbiome studies that carried out antibiotic interventions with vancomycin, metronidazole, ciprofloxacin, amoxicillin, and doxycycline. We show how MiRIx can be used in conjunction with existing microbiome analytical approaches to gain a deeper understanding of the microbiome response to antibiotics. Finally, we generate antibiotic response predictions for the oral, skin, and gut microbiome in healthy humans. Our approach is implemented as open-source software and is readily applied to microbiome data sets generated by 16S rRNA marker gene sequencing or shotgun metagenomics.

IMPORTANCE: Antibiotics are potent influencers of the human microbiome and can be a source for enduring dysbiosis and antibiotic resistance in healthcare. Existing microbiome data analysis methods can quantify perturbations of bacterial communities but cannot evaluate whether the differences are aligned with the expected activity of a specific antibiotic. Here, we present a novel method to quantify and predict antibiotic-specific microbiome changes, implemented in a ready-to-use software package. This has the potential to be a critical tool to broaden our understanding of the relationship between the microbiome and antibiotics.}, } @article {pmid39230075, year = {2024}, author = {Kim, N and Kim, CY and Ma, J and Yang, S and Park, DJ and Ha, SJ and Belenky, P and Lee, I}, title = {MRGM: an enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2393791}, pmid = {39230075}, issn = {1949-0984}, support = {R01 DK125382/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Bacteria/classification/genetics/isolation & purification ; *Genome, Bacterial ; Humans ; Phylogeny ; Diet ; }, abstract = {Mouse gut microbiome research is pivotal for understanding the human gut microbiome, providing insights into disease modeling, host-microbe interactions, and the dietary influence on the gut microbiome. To enhance the translational value of mouse gut microbiome studies, we need detailed and high-quality catalogs of mouse gut microbial genomes. We introduce the Mouse Reference Gut Microbiome (MRGM), a comprehensive catalog with 42,245 non-redundant mouse gut bacterial genomes across 1,524 species. MRGM marks a 40% increase in the known taxonomic diversity of mouse gut microbes, capturing previously underrepresented lineages through refined genome quality assessment techniques. MRGM not only broadens the taxonomic landscape but also enriches the functional landscape of the mouse gut microbiome. Using deep learning, we have elevated the Gene Ontology annotation rate for mouse gut microbial proteins from 3.2% with orthology to 60%, marking an over 18-fold increase. MRGM supports both DNA- and marker-based taxonomic profiling by providing custom databases, surpassing previous catalogs in performance. Finally, taxonomic and functional comparisons between human and mouse gut microbiota reveal diet-driven divergences in their taxonomic composition and functional enrichment. Overall, our study highlights the value of high-quality microbial genome catalogs in advancing our understanding of the co-evolution between gut microbes and their host.}, } @article {pmid39227168, year = {2024}, author = {Salmaso, N and Cerasino, L and Pindo, M and Boscaini, A}, title = {Taxonomic and functional metagenomic assessment of a Dolichospermum bloom in a large and deep lake south of the Alps.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {10}, pages = {}, pmid = {39227168}, issn = {1574-6941}, support = {CN00000033//European Union/ ; }, mesh = {*Lakes/microbiology ; *Metagenomics ; *Metagenome ; *Phylogeny ; Eutrophication ; Cyanobacteria/genetics/classification/growth & development/metabolism ; Aphanizomenon/genetics/growth & development/metabolism ; }, abstract = {Untargeted genetic approaches can be used to explore the high metabolic versatility of cyanobacteria. In this context, a comprehensive metagenomic shotgun analysis was performed on a population of Dolichospermum lemmermannii collected during a surface bloom in Lake Garda in the summer of 2020. Using a phylogenomic approach, the almost complete metagenome-assembled genome obtained from the analysis allowed to clarify the taxonomic position of the species within the genus Dolichospermum and contributed to frame the taxonomy of this genus within the ADA group (Anabaena/Dolichospermum/Aphanizomenon). In addition to common functional traits represented in the central metabolism of photosynthetic cyanobacteria, the genome annotation uncovered some distinctive and adaptive traits that helped define the factors that promote and maintain bloom-forming heterocytous nitrogen-fixing Nostocales in oligotrophic lakes. In addition, genetic clusters were identified that potentially encode several secondary metabolites that were previously unknown in the populations evolving in the southern Alpine Lake district. These included geosmin, anabaenopetins, and other bioactive compounds. The results expanded the knowledge of the distinctive competitive traits that drive algal blooms and provided guidance for more targeted analyses of cyanobacterial metabolites with implications for human health and water resource use.}, } @article {pmid39226954, year = {2024}, author = {Zhang, Z and Yang, H and Linghu, M and Li, J and Chen, C and Wang, B}, title = {Cattle manure composting driven by a microbial agent: A coupled mechanism involving microbial community succession and organic matter conversion.}, journal = {The Science of the total environment}, volume = {952}, number = {}, pages = {175953}, doi = {10.1016/j.scitotenv.2024.175953}, pmid = {39226954}, issn = {1879-1026}, mesh = {*Composting ; *Manure/microbiology ; Animals ; Cattle ; Microbiota ; Soil Microbiology ; Bacillus/physiology ; }, abstract = {Aerobic composting has been used as a mainstream treatment technology for agricultural solid waste resourcing. In the present study, we investigated the effects and potential mechanisms of the addition of a microbial agent (LD) prepared by combining Bacillus subtilis, Bacillus paralicheniformis and Irpex lacteus in improving the efficiency of cattle manure composting. Our results showed that addition of 1.5 % LD significantly accelerated compost humification, i.e., the germination index and lignocellulose degradation rate of the final compost product reached values of 92.20 and 42.29 %, respectively. Metagenomic sequencing results showed that inoculation of cattle manure with LD increased the abundance of functional microorganisms. LD effectively promoted the production of humus precursors, which then underwent reactions through synergistic abiotic and biotic pathways to achieve compost humification. This research provides a theoretical basis for the study of microbial enhancement strategies and humus formation mechanisms in the composting of livestock manure.}, } @article {pmid39226940, year = {2024}, author = {Wang, M and Li, Y and Peng, H and Liu, K and Wang, X and Xiang, W}, title = {A cyclic shift-temperature operation method to train microbial communities of mesophilic anaerobic digestion.}, journal = {Bioresource technology}, volume = {412}, number = {}, pages = {131410}, doi = {10.1016/j.biortech.2024.131410}, pmid = {39226940}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Temperature ; *Biofuels/microbiology ; Bioreactors/microbiology ; Methane/metabolism ; Methanosarcina/metabolism ; Microbiota/physiology ; }, abstract = {Temperature is the critical factor affecting the efficiency and cost of anaerobic digestion (AD). The current work develops a shift-temperature AD (STAD) between 35 °C and 55 °C, intending to optimise microbial community and promote substrate conversion. The experimental results showed that severe inhibition of biogas production occurred when the temperature was firstly increased stepwise from 35 °C to 50 °C, whereas no inhibition was observed at the second warming cycle. When the organic load rate was increased to 6.37 g VS/L/d, the biogas yield of the STAD reached about 400 mL/g VS, nearly double that of the constant-temperature AD (CTAD). STAD promoted the proliferation of Methanosarcina (up to 57.32 %), while severely suppressed hydrogenophilic methanogens. However, when the temperature was shifted to 35 °C, most suppressed species recovered quickly and the excess propionic acid was quickly consumed. Metagenomic analysis showed that STAD also promoted gene enrichment related to pathways metabolism, membrane functions, and methyl-based methanogenesis.}, } @article {pmid39225513, year = {2024}, author = {Han, K and Kuo, B and Khalili, H and Staller, K}, title = {Metagenomics Analysis Reveals Unique Gut Microbiota Signature of Slow-Transit Constipation.}, journal = {Clinical and translational gastroenterology}, volume = {15}, number = {10}, pages = {e1}, pmid = {39225513}, issn = {2155-384X}, support = {K23 DK120945/DK/NIDDK NIH HHS/United States ; KSN2022210 and KSN2211010//Korea Institute of Oriental Medicine/ ; K23 DK120945/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Constipation/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; *Metagenomics/methods ; Male ; Case-Control Studies ; Adult ; Feces/microbiology ; Aged ; Gastrointestinal Transit ; Bile Acids and Salts/metabolism ; Bacteria/genetics/isolation & purification/classification ; }, abstract = {INTRODUCTION: Altered gut microbiota may play a role in slow-transit constipation (STC). We conducted a study of gut microbiota composition and functionality in STC using metagenomic analyses.

METHODS: We assembled a clinical cohort of 24 patients with STC physiology age- and sex-matched to 24 controls. We performed shotgun metagenomic sequencing followed by prediction of metabolite composition from functional profiles.

RESULTS: In a middle-aged (mean 55.3 years), predominantly female cohort, there were no significant differences in α-diversity indices, but permutational multivariate analysis of variance analysis showed significant between-group differences (R 2 = 0.050, P < 0.001) between STC patients and controls. Gordonibacter pamelaeae , Bifidobacterium longum , Firmicutes bacterium co-abundance gene group 94, and Anaerotruncus colihominis were more abundant in STC, whereas Coprococcus comes and Roseburia intestinalis were more abundant in controls. Gut-derived metabolites varying in STC relative to controls were related to bile acid and cholesterol metabolism.

DISCUSSION: We found a unique metagenomic and metabolomic signature of STC.}, } @article {pmid39222347, year = {2024}, author = {Glendinning, L and Wu, Z and Vervelde, L and Watson, M and Balic, A}, title = {Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota.}, journal = {Microbial genomics}, volume = {10}, number = {9}, pages = {}, pmid = {39222347}, issn = {2057-5858}, mesh = {Animals ; *Chickens/microbiology ; *Infectious bronchitis virus/immunology/genetics ; *Cecum/microbiology ; *Gastrointestinal Microbiome ; Vaccination ; Poultry Diseases/microbiology/virology/immunology ; Coronavirus Infections/veterinary/prevention & control/immunology ; Viral Vaccines/immunology/genetics ; Receptors, G-Protein-Coupled/genetics ; Metagenome ; Dendritic Cells/immunology ; Bacteria/classification/genetics ; Metagenomics ; }, abstract = {The chicken immune system and microbiota play vital roles in maintaining gut homeostasis and protecting against pathogens. In mammals, XCR1+ conventional dendritic cells (cDCs) are located in the gut-draining lymph nodes and play a major role in gut homeostasis. These cDCs sample antigens in the gut luminal contents and limit the inflammatory response to gut commensal microbes by generating appropriate regulatory and effector T-cell responses. We hypothesized that these cells play similar roles in sustaining gut homeostasis in chickens, and that chickens lacking XCR1 were likely to contain a dysbiotic caecal microbiota. Here we compare the caecal microbiota of chickens that were either heterozygous or homozygous XCR1 knockouts, that had or had not been vaccinated for infectious bronchitis virus (IBV). We used short-read (Illumina) and long-read (PacBio HiFi) metagenomic sequencing to reconstruct 670 high-quality, strain-level metagenome assembled genomes. We found no significant differences between alpha diversity or the abundance of specific microbial taxa between genotypes. However, IBV vaccination was found to correlate with significant differences in the richness and beta diversity of the microbiota, and to the abundance of 40 bacterial genera. In conclusion, we found that a lack of XCR1 was not correlated with significant changes in the chicken microbiota, but IBV vaccination was.}, } @article {pmid39222062, year = {2024}, author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Kurilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I}, title = {CAIM: coverage-based analysis for identification of microbiome.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {5}, pages = {}, pmid = {39222062}, issn = {1477-4054}, support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; P20GM125503//National Institute of General Medical Sciences of the National Institutes of Health/ ; R01CA143130/NH/NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Software ; Algorithms ; Sequence Analysis, DNA/methods ; }, abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic approach. In this study, we developed a new bioinformatics tool, coverage-based analysis for identification of microbiome (CAIM), for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count-based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consistently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similarity of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and 44 primary liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.}, } @article {pmid39221872, year = {2025}, author = {Wang, Z and Xu, M and Li, Q and Lu, S and Liu, Z}, title = {Subchronic Chloroform Exposure Causes Intestinal Damage and Induces Gut Microbiota Disruption and Metabolic Dysregulation in Mice.}, journal = {Environmental toxicology}, volume = {40}, number = {1}, pages = {5-18}, doi = {10.1002/tox.24417}, pmid = {39221872}, issn = {1522-7278}, support = {LH2021C095//Natural Science Foundation of Heilongjiang Province of China/ ; 1452TD008//Heilongjiang Provincial Department of Education filing project/ ; 1451TD002//Heilongjiang Provincial Department of Education filing project/ ; }, mesh = {Animals ; *Chloroform/toxicity ; *Gastrointestinal Microbiome/drug effects ; Female ; Mice ; Cecum/microbiology/drug effects ; Intestines/drug effects/microbiology/pathology ; Environmental Pollutants/toxicity ; }, abstract = {Chloroform is a prevalent toxic environmental pollutant in urban settings, posing risks to human health through exposure via various mediums such as air and tap water. The gut microbiota plays a pivotal role in maintaining host health. However, there is a paucity of research elucidating the impact of chloroform exposure on the gut microbiota. In this investigation, 18 SPF Kunming female mice were stratified into three groups (n = 6) and subjected to oral gavage with chloroform doses equivalent to 0, 50, and 150 mg/kg of body weight over 30 days. Our findings demonstrate that subchronic chloroform exposure significantly perturbs hematological parameters in mice and induces histopathological alterations in cecal tissues, consequently engendering marked disparities in the functional composition of cecal microbiota and metabolic equilibrium of cecal contents. Ultimately, our investigation revealed a statistically robust correlation, exhibiting a high degree of significance, between the intestinal microbiome composition and the metabolites that were differentially expressed consequent to chloroform exposure.}, } @article {pmid39218875, year = {2024}, author = {Liwinski, T and Auer, MK and Schröder, J and Pieknik, I and Casar, C and Schwinge, D and Henze, L and Stalla, GK and Lang, UE and von Klitzing, A and Briken, P and Hildebrandt, T and Desbuleux, JC and Biedermann, SV and Holterhus, PM and Bang, C and Schramm, C and Fuss, J}, title = {Gender-affirming hormonal therapy induces a gender-concordant fecal metagenome transition in transgender individuals.}, journal = {BMC medicine}, volume = {22}, number = {1}, pages = {346}, pmid = {39218875}, issn = {1741-7015}, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; Metagenome ; Prospective Studies ; *Transgender Persons ; Sex Reassignment Procedures/methods ; Gonadal Steroid Hormones/administration & dosage ; }, abstract = {BACKGROUND: Limited data exists regarding gender-specific microbial alterations during gender-affirming hormonal therapy (GAHT) in transgender individuals. This study aimed to investigate the nuanced impact of sex steroids on gut microbiota taxonomy and function, addressing this gap. We prospectively analyzed gut metagenome changes associated with 12 weeks of GAHT in trans women and trans men, examining both taxonomic and functional shifts.

METHODS: Thirty-six transgender individuals (17 trans women, 19 trans men) provided pre- and post-GAHT stool samples. Shotgun metagenomic sequencing was used to assess the changes in gut microbiota structure and potential function following GAHT.

RESULTS: While alpha and beta diversity remained unchanged during transition, specific species, including Parabacteroides goldsteinii and Escherichia coli, exhibited significant abundance shifts aligned with affirmed gender. Overall functional metagenome analysis showed a statistically significant effect of gender and transition (R[2] = 4.1%, P = 0.0115), emphasizing transitions aligned with affirmed gender, particularly in fatty acid-related metabolism.

CONCLUSIONS: This study provides compelling evidence of distinct taxonomic and functional profiles in the gut microbiota between trans men and women. GAHT induces androgenization in trans men and feminization in trans women, potentially impacting physiological and health-related outcomes.

TRIAL REGISTRATION: Clinicaltrials.gov NCT02185274.}, } @article {pmid39218360, year = {2024}, author = {Park, DG and Kang, W and Shin, IJ and Chalita, M and Oh, HS and Hyun, DW and Kim, H and Chun, J and An, YS and Lee, EJ and Yoon, JH}, title = {Difference in gut microbial dysbiotic patterns between body-first and brain-first Parkinson's disease.}, journal = {Neurobiology of disease}, volume = {201}, number = {}, pages = {106655}, doi = {10.1016/j.nbd.2024.106655}, pmid = {39218360}, issn = {1095-953X}, mesh = {Humans ; *Parkinson Disease/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Cross-Sectional Studies ; Aged ; Middle Aged ; *Dysbiosis/microbiology ; REM Sleep Behavior Disorder/microbiology ; Brain/metabolism/microbiology ; }, abstract = {BACKGROUND: This study aims to identify distinct microbial and functional biomarkers characteristic of body-first or brain-first subtypes of Parkinson's disease (PD). This could illuminate the unique pathogenic mechanisms within these subtypes.

METHODS: In this cross-sectional study, we classified 36 well-characterized PD patients into body-first, brain-first, or undetermined subtypes based on the presence of premotor REM sleep behavior disorder (RBD) and cardiac meta-iodobenzylguanidine (MIBG) uptake. We then conducted an in-depth shotgun metagenomic analysis of the gut microbiome for each subtype and compared the results with those from age- and sex-matched healthy controls.

RESULTS: Significant differences were found in the gut microbiome of body-first PD patients (n = 15) compared to both brain-first PD patients (n = 9) and healthy controls. The gut microbiome in body-first PD showed a distinct profile, characterized by an increased presence of Escherichia coli and Akkermansia muciniphila, and a decreased abundance of short-chain fatty acid-producing commensal bacteria. These shifts were accompanied by a higher abundance of microbial genes associated with curli protein biosynthesis and a lower abundance of genes involved in putrescine and spermidine biosynthesis. Furthermore, the combined use of premotor RBD and MIBG criteria was more strongly correlated with these microbiome differences than the use of each criterion independently.

CONCLUSIONS: Our findings highlight the significant role of dysbiotic and pathogenic gut microbial alterations in body-first PD, supporting the body-first versus brain-first hypothesis. These insights not only reinforce the gut microbiome's potential as a therapeutic target in PD but also suggest the possibility of developing subtype-specific treatment strategies.}, } @article {pmid39217664, year = {2024}, author = {Yu, Y and Wei, R and Yi, S and Teng, Y and Ning, R and Wei, S and Bai, L and Liu, H and Li, L and Xu, H and Han, C}, title = {Research Note: Integrative analysis of transcriptome and gut microbiome reveals foie gras capacity difference between cage and floor rearing systems.}, journal = {Poultry science}, volume = {103}, number = {11}, pages = {104248}, pmid = {39217664}, issn = {1525-3171}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Geese ; *Transcriptome ; *Animal Husbandry/methods ; Housing, Animal ; Liver/metabolism ; Lipid Metabolism ; Male ; Gene Expression Profiling/veterinary ; }, abstract = {To explore the differences in foie gras performance between geese raised in cages and on the ground, we conducted an integrative analysis of liver transcriptome and gut microbial metagenomes. The results showed extremely significant differences in the liver weight (P < 0.01) and liver lipid accumulation of FRS and CRS groups. The levels of triglyceride (TG), high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C) of CRS were significantly higher than those of FRS (P < 0.05). Transcriptome analysis showed that 3,917 upregulated and 1,395 downregulated genes were identified, and lipid metabolism pathway and fatty acid metabolism were significantly enriched. Analysis of cecum microbiota revealed that several inflammation-related bacteria (including Gallibacterium, Escherichia-Shigella, Desulfovibrio, Alistipes, and Fournierella) were enriched in CRS, while beneficial bacteria (including Lactobacillus, Limosilactobacillus, and Ligilactobacillus) were significantly enriched in FRS. In conclusion, CRS was better than FRS in foie gras production, which was more conducive to lipid deposition in the goose liver.}, } @article {pmid39217389, year = {2024}, author = {Zhang, Y and Cheng, TY and Liu, GH and Liu, L and Duan, DY}, title = {Metagenome reveals the midgut microbial community of Haemaphysalis qinghaiensis ticks collected from yaks and Tibetan sheep.}, journal = {Parasites & vectors}, volume = {17}, number = {1}, pages = {370}, pmid = {39217389}, issn = {1756-3305}, support = {No. 31902294//the National Natural Science Foundation of China/ ; }, mesh = {Animals ; Sheep ; Cattle ; Female ; *Metagenome ; *Ixodidae/microbiology ; Gastrointestinal Microbiome ; Bacteria/classification/isolation & purification/genetics ; Tick Infestations/veterinary/parasitology ; Sheep Diseases/microbiology/parasitology ; China ; Metagenomics ; Tibet ; Cattle Diseases/microbiology/parasitology ; }, abstract = {BACKGROUND: Haemaphysalis qinghaiensis is a tick species distributed only in China. Due to its ability to transmit a variety of pathogens, including species of the genera Anaplasma, Rickettsia, Babesia, and Theileria, it seriously endangers livestock husbandry. However, the microbial community of the midgut of H. qinghaiensis females collected from yaks and Tibetan sheep has not yet been characterized using metagenomic sequencing technology.

METHODS: Haemaphysalis qinghaiensis were collected from the skins of yaks and Tibetan sheep in Gansu Province, China. Genomic DNA was extracted from the midguts and midgut contents of fully engorged H. qinghaiensis females collected from the two hosts. Metagenomic sequencing technology was used to analyze the microbial community of the two groups.

RESULTS: Fifty-seven phyla, 483 genera, and 755 species were identified in the two groups of samples. The ticks from the two hosts harbored common and unique microorganisms. At the phylum level, the dominant common phyla were Proteobacteria, Firmicutes, and Mucoromycota. At the genus level, the dominant common genera were Anaplasma, Ehrlichia, and Pseudomonas. At the species level, bacteria including Anaplasma phagocytophilum, Ehrlichia minasensis, and Pseudomonas aeruginosa along with eukaryotes such as Synchytrium endobioticum and Rhizophagus irregularis, and viruses such as the orf virus, Alphadintovirus mayetiola, and Parasteatoda house spider adintovirus were detected in both groups. In addition, the midgut of H. qinghaiensis collected from yaks had unique microbial taxa including two phyla, eight genera, and 23 species. Unique microorganisms in the midgut of H. qinghaiensis collected from Tibetan sheep included two phyla, 14 genera, and 32 species. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that the functional genes of the microbiome of H. qinghaiensis were annotated to six pathways, and the metabolic pathways included 11 metabolic processes, in which the genes involved in carbohydrate metabolism were the most abundant, followed by the genes involved in lipid metabolism.

CONCLUSIONS: These findings indicate that most of the microbial species in the collected H. qinghaiensis ticks were the same in both hosts, but there were also slight differences. The analytical data from this study have enhanced our understanding of the midgut microbial composition of H. qinghaiensis collected from different hosts. The database of H. qinghaiensis microbe constructed from this study will lay the foundation for predicting tick-borne diseases. Furthermore, a comprehensive understanding of tick microbiomes will be useful for understanding vector competency and interactions with ticks and midgut microorganisms.}, } @article {pmid39217229, year = {2024}, author = {Gyaltshen, Y and Ishii, Y and Charvet, S and Goetz, E and Maruyama, S and Kim, E}, title = {Molecular diversity of green-colored microbial mats from hot springs of northern Japan.}, journal = {Extremophiles : life under extreme conditions}, volume = {28}, number = {3}, pages = {43}, pmid = {39217229}, issn = {1433-4909}, support = {KAKENHI 17H05713//Japan Society for the Promotion of Science/ ; 19H04713//Japan Society for the Promotion of Science/ ; CAREER 1453639//Division of Integrative Organismal Systems/ ; }, mesh = {*Hot Springs/microbiology ; Japan ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Microbiota ; Bacteria/genetics/classification/isolation & purification ; Phylogeny ; }, abstract = {We acquired and analyzed metagenome and 16S/18S rRNA gene amplicon data of green-colored microbial mats from two hot springs within the Onikobe geothermal region (Miyagi Prefecture, Japan). The two collection sites-Tamago and Warabi-were in proximity and had the same temperature (40 °C), but the Tamago site was connected to a nearby stream, whereas the Warabi site was isolated. Both the amplicon and metagenome data suggest the bacterial, especially cyanobacterial, dominance of the mats; other abundant groups include Chloroflexota, Pseudomonadota, Bacteroidota/Chlorobiota, and Deinococcota. At finer resolution, however, the taxonomic composition entirely differed between the mats. A total of 5 and 21 abundant bacterial 16S rRNA gene OTUs were identified for Tamago and Warabi, respectively; of these, 12 are putative chlorophyll- or rhodopsin-based phototrophs. The presence of phylogenetically diverse microbial eukaryotes was noted, with ciliates and amoebozoans being the most abundant eukaryote groups for Tamago and Warabi, respectively. Fifteen metagenome-assembled genomes (MAGs) were obtained, represented by 13 bacteria, one ciliate (mitochondrion), and one giant virus. A total of 15 novel taxa, including a new deeply branching Chlorobiota species, is noted from the amplicon and MAG data, highlighting the importance of environmental sequencing in uncovering hidden microorganisms.}, } @article {pmid39216995, year = {2024}, author = {Gekenidis, MT and Vollenweider, V and Joyce, A and Murphy, S and Walser, JC and Ju, F and Bürgmann, H and Hummerjohann, J and Walsh, F and Drissner, D}, title = {Unde venis? Bacterial resistance from environmental reservoirs to lettuce: tracking microbiome and resistome over a growth period.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {10}, pages = {}, pmid = {39216995}, issn = {1574-6941}, support = {407240_167068//National Research Program "Antimicrobial Resistance"/ ; /SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Lactuca/microbiology ; *Manure/microbiology ; Animals ; *Soil Microbiology ; *Microbiota/genetics ; *Bacteria/genetics/growth & development/drug effects/classification/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; Drug Resistance, Bacterial/genetics ; Swine ; Plant Leaves/microbiology ; Wastewater/microbiology ; Water Microbiology ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; Agricultural Irrigation ; Soil/chemistry ; Water Quality ; }, abstract = {Fresh produce is suggested to contribute highly to shaping the gut resistome. We investigated the impact of pig manure and irrigation water quality on microbiome and resistome of field-grown lettuce over an entire growth period. Lettuce was grown under four regimes, combining soil amendment with manure (with/without) with sprinkler irrigation using river water with an upstream wastewater input, disinfected by UV (with/without). Lettuce leaves, soil, and water samples were collected weekly and analysed by bacterial cultivation, 16S rRNA gene amplicon sequencing, and shotgun metagenomics from total community DNA. Cultivation yielded only few clinically relevant antibiotic-resistant bacteria (ARB), but numbers of ARB on lettuce increased over time, while no treatment-dependent changes were observed. Microbiome analysis confirmed a temporal trend. Antibiotic resistance genes (ARGs) unique to lettuce and water included multidrug and β-lactam ARGs, whereas lettuce and soil uniquely shared mainly glycopeptide and tetracycline ARGs. Surface water carried clinically relevant ARB (e.g. ESBL-producing Escherichia coli or Serratia fonticola) without affecting the overall lettuce resistome significantly. Resistance markers including biocide and metal resistance were increased in lettuce grown with manure, especially young lettuce (increased soil contact). Overall, while all investigated environments had their share as sources of the lettuce resistome, manure was the main source especially on young plants. We therefore suggest minimizing soil-vegetable contact to minimize resistance markers on fresh produce.}, } @article {pmid39216430, year = {2024}, author = {Gupta, A and Shivachandran, A and Saleena, LM}, title = {Oral microbiome insights: Tracing acidic culprits in dental caries with functional metagenomics.}, journal = {Archives of oral biology}, volume = {168}, number = {}, pages = {106064}, doi = {10.1016/j.archoralbio.2024.106064}, pmid = {39216430}, issn = {1879-1506}, mesh = {*Dental Caries/microbiology ; Humans ; *Metagenomics/methods ; *Microbiota ; Mouth/microbiology ; Acids/metabolism ; Bacteria/classification/genetics ; DNA, Bacterial ; Sequence Analysis, DNA ; Male ; Female ; }, abstract = {OBJECTIVE: This study aimed to investigate the presence and abundance of acid-producing bacteria in dental caries samples using functional gene prediction techniques.

DESIGN: A total of 24 dental caries samples were collected for analysis. DNA isolation was performed followed by shotgun metagenomic sequencing. Functional gene prediction techniques were used to identify enzymes responsible for acid production from primary metabolites. Enzymes responsible for converting primary metabolites into acids were identified from the KEGG database. Subsequently, 840 contigs were examined, and their genus and species were characterized.

RESULTS: Analysis of the obtained data revealed 31 KEGG IDs corresponding to enzymes involved in the conversion of primary metabolites into acids. All 117 identified genera from the contig analysis were found to be part of the oral microbiome. In addition, A higher prevalence of acid-producing bacteria was noted in dental caries samples compared to earlier reports.

CONCLUSION: The study indicates the significant role of acid-producing bacteria in the initiation and progression of dental caries. The findings highlight the importance of microbial activity in the demineralization process of tooth enamel. Methods for preventing dental decay may be promising if specific measures are implemented to reduce the amount of acid produced by oral bacteria.}, } @article {pmid39216241, year = {2024}, author = {Liao, X and Hou, L and Zhang, L and Grossart, HP and Liu, K and Liu, J and Chen, Y and Liu, Y and Hu, A}, title = {Distinct influences of altitude on microbiome and antibiotic resistome assembly in a glacial river ecosystem of Mount Everest.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135675}, doi = {10.1016/j.jhazmat.2024.135675}, pmid = {39216241}, issn = {1873-3336}, mesh = {*Rivers/microbiology ; *Altitude ; *Microbiota/drug effects ; *Drug Resistance, Microbial/genetics ; Ecosystem ; Bacteria/genetics/drug effects/classification ; Geologic Sediments/microbiology ; Viruses/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Ice Cover/microbiology ; China ; }, abstract = {The profound influences of altitude on aquatic microbiome were well documented. However, differences in the responses of different life domains (bacteria, microeukaryotes, viruses) and antibiotics resistance genes (ARGs) in glacier river ecosystems to altitude remain unknown. Here, we employed shotgun metagenomic and amplicon sequencing to characterize the altitudinal variations of microbiome and ARGs in the Rongbu River, Mount Everest. Our results indicated the relative influences of stochastic processes on microbiome and ARGs assembly in water and sediment were in the following order: microeukaryotes < ARGs < viruses < bacteria. Moreover, distinct assembly patterns of the microbiome and ARGs were found in response to differences in altitude, the latter of which shift from deterministic to stochastic processes with increasing differences in altitude. Partial least squares path modeling revealed that mobile genetic elements (MGEs) and viral β-diversity were the major factors influencing the ARG abundances. Taken together, our work revealed that altitude-caused environmental changes led to significant changes in the composition and assembly processes of the microbiome and ARGs, while ARGs had a unique response pattern to altitude. Our findings provide novel insights into the impacts of altitude on the biogeographic distribution of microbiome and ARGs, and the associated driving forces in glacier river ecosystems.}, } @article {pmid39216231, year = {2024}, author = {Xu, J and Li, P and Li, Z and Liu, S and Guo, H and Lesser, CF and Ke, J and Zhao, W and Mou, X}, title = {Gut bacterial type III secretion systems aggravate colitis in mice and serve as biomarkers of Crohn's disease.}, journal = {EBioMedicine}, volume = {107}, number = {}, pages = {105296}, pmid = {39216231}, issn = {2352-3964}, mesh = {Animals ; Mice ; *Crohn Disease/microbiology/metabolism/pathology ; Humans ; *Biomarkers ; *Disease Models, Animal ; *Gastrointestinal Microbiome ; *Type III Secretion Systems/metabolism/genetics ; Colitis/microbiology/metabolism ; Metagenomics/methods ; Feces/microbiology ; Female ; Male ; }, abstract = {BACKGROUND: Mesenteric adipose tissue (mAT) hyperplasia, known as creeping fat, is a pathologic characteristic of Crohn's disease (CD). In our previously reported cohort, we observed that Achromobacter pulmonis was the most abundant and prevalent bacteria cultivated from creeping fat.

METHODS: A whole genomic sequencing and identification of T3SS orthologs of mAT-derived A. pulmonis were used. A functional type III secretion system (T3SS) mediated the pathogenic potential of A. pulmonis in vitro and in mouse colitis model. Furthermore, a T3SS Finder pipeline was introduced to evaluate gut bacterial T3SS orthologs in the feces of CD patients, ulcerative colitis and colorectal cancer patients.

FINDINGS: Here, we reveal that mAT-derived A. pulmonis possesses a functional T3SS, aggravates colitis in mice via T3SS, and exhibits T3SS-dependent cytotoxicity via a caspase-independent mechanism in macrophages and epithelial cells, which demonstrated the pathogenic potential of the T3SS-harboring A. pulmonis. Metagenomic analyses demonstrate an increased abundance of Achromobacter in the fecal of Crohn's disease patients compared to healthy controls. A comprehensive comparison of total microbial vT3SS abundance in various intestine diseases demonstrated that the specific enrichment of vT3SS genes was shown in fecal samples of CD, neither ulcerative colitis nor colorectal cancer patients, and ten T3SS gene-based biomarkers for CD were discovered and validated in a newly recruited CD cohort. Furthermore, treatment with exclusive enteral nutrition (EEN), an intervention that improves CD patient symptomatology, was found associated with a significant reduction in the prevalence of T3SS genes in fecal samples.

INTERPRETATION: These findings highlight the pathogenic significance of T3SSs in the context of CD and identify specific T3SS genes that could potentially function as biomarkers for diagnosing and monitoring the clinical status of CD patients.

FUNDING: This work is supported by the National Key Research and Development Program of China (2020YFA0907800), the China Postdoctoral Science Foundation (2023M744089), the National Natural Science Foundation of China (32000096), the Shenzhen Science and Technology Programs (KQTD20200820145822023, RCIC20231211085944057, and ZDSYS20220606100803007), National Key Clinical Discipline, Guangdong Provincial Clinical Research Center for Digestive Diseases (2020B1111170004), Qingfeng Scientific Research Fund of the China Crohn's & Colitis Foundation (CCCF) (CCCF-QF-2022B71-1), and the Sixth Affiliated Hospital, Sun Yat-sen University Clinical Research 1010 Program 1010CG(2023)-08. These funding provided well support for this research work, which involved data collection, analysis, interpretation, patient recruitment and so on.}, } @article {pmid39215755, year = {2024}, author = {Cannarozzi, AL and Latiano, A and Massimino, L and Bossa, F and Giuliani, F and Riva, M and Ungaro, F and Guerra, M and Brina, ALD and Biscaglia, G and Tavano, F and Carparelli, S and Fiorino, G and Danese, S and Perri, F and Palmieri, O}, title = {Inflammatory bowel disease genomics, transcriptomics, proteomics and metagenomics meet artificial intelligence.}, journal = {United European gastroenterology journal}, volume = {12}, number = {10}, pages = {1461-1480}, pmid = {39215755}, issn = {2050-6414}, support = {PNRR-MAD-2022-12375729//Italian Next Generation Eu Program/ ; }, mesh = {Humans ; *Artificial Intelligence ; Colitis, Ulcerative/genetics/immunology/microbiology/pathology ; Crohn Disease/genetics/immunology/microbiology/pathology ; Gastrointestinal Microbiome/immunology ; *Inflammatory Bowel Diseases/genetics/immunology/microbiology/pathology ; *Metagenomics/methods ; Precision Medicine/methods ; *Proteomics/methods ; Transcriptome ; Multiomics/methods ; }, abstract = {Various extrinsic and intrinsic factors such as drug exposures, antibiotic treatments, smoking, lifestyle, genetics, immune responses, and the gut microbiome characterize ulcerative colitis and Crohn's disease, collectively called inflammatory bowel disease (IBD). All these factors contribute to the complexity and heterogeneity of the disease etiology and pathogenesis leading to major challenges for the scientific community in improving management, medical treatments, genetic risk, and exposome impact. Understanding the interaction(s) among these factors and their effects on the immune system in IBD patients has prompted advances in multi-omics research, the development of new tools as part of system biology, and more recently, artificial intelligence (AI) approaches. These innovative approaches, supported by the availability of big data and large volumes of digital medical datasets, hold promise in better understanding the natural histories, predictors of disease development, severity, complications and treatment outcomes in complex diseases, providing decision support to doctors, and promising to bring us closer to the realization of the "precision medicine" paradigm. This review aims to provide an overview of current IBD omics based on both individual (genomics, transcriptomics, proteomics, metagenomics) and multi-omics levels, highlighting how AI can facilitate the integration of heterogeneous data to summarize our current understanding of the disease and to identify current gaps in knowledge to inform upcoming research in this field.}, } @article {pmid39209868, year = {2024}, author = {Gonzalez, E and Lee, MD and Tierney, BT and Lipieta, N and Flores, P and Mishra, M and Beckett, L and Finkelstein, A and Mo, A and Walton, P and Karouia, F and Barker, R and Jansen, RJ and Green, SJ and Weging, S and Kelliher, J and Singh, NK and Bezdan, D and Galazska, J and Brereton, NJB}, title = {Spaceflight alters host-gut microbiota interactions.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {71}, pmid = {39209868}, issn = {2055-5008}, mesh = {*Gastrointestinal Microbiome ; Animals ; *Space Flight ; Mice ; *Bacteria/classification/genetics ; Liver/microbiology ; Host Microbial Interactions ; Metagenomics/methods ; Colon/microbiology ; Bile Acids and Salts/metabolism ; Energy Metabolism ; Male ; Humans ; Mice, Inbred C57BL ; }, abstract = {The ISS rodent habitat has provided crucial insights into the impact of spaceflight on mammals, inducing symptoms characteristic of liver disease, insulin resistance, osteopenia, and myopathy. Although these physiological responses can involve the microbiome on Earth, host-microbiota interactions during spaceflight are still being elucidated. We explore murine gut microbiota and host gene expression in the colon and liver after 29 and 56 days of spaceflight using multiomics. Metagenomics revealed significant changes in 44 microbiome species, including relative reductions in bile acid and butyrate metabolising bacteria like Extibacter muris and Dysosmobacter welbionis. Functional prediction indicate over-representation of fatty acid and bile acid metabolism, extracellular matrix interactions, and antibiotic resistance genes. Host gene expression described corresponding changes to bile acid and energy metabolism, and immune suppression. These changes imply that interactions at the host-gut microbiome interface contribute to spaceflight pathology and that these interactions might critically influence human health and long-duration spaceflight feasibility.}, } @article {pmid39209853, year = {2024}, author = {Mi, J and Jing, X and Ma, C and Yang, Y and Li, Y and Zhang, Y and Long, R and Zheng, H}, title = {Massive expansion of the pig gut virome based on global metagenomic mining.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {76}, pmid = {39209853}, issn = {2055-5008}, mesh = {Animals ; Swine ; *Virome/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; *Viruses/genetics/classification/isolation & purification ; *Genome, Viral ; Data Mining ; Metagenome ; Phylogeny ; }, abstract = {The pig gut virome plays a vital role in the gut microbial ecosystem of pigs. However, a comprehensive understanding of their diversity and a reference database for the virome are currently lacking. To address this gap, we established a Pig Virome Database (PVD) that comprised of 5,566,804 viral contig sequences from 4650 publicly available gut metagenomic samples using a pipeline designated "metav". By clustering sequences, we identified 48,299 viral operational taxonomic units (vOTUs) genomes of at least medium quality, of which 92.83% of which were not found in existing major databases. The majority of vOTUs were identified as Caudoviricetes (72.21%). The PVD database contained a total of 2,362,631 protein-coding genes across the above medium-quality vOTUs genomes that can be used to explore the functional potential of the pig gut virome. These findings highlight the extensive diversity of viruses in the pig gut and provide a pivotal reference dataset for forthcoming research concerning the pig gut virome.}, } @article {pmid39209850, year = {2024}, author = {Colman, DR and Keller, LM and Arteaga-Pozo, E and Andrade-Barahona, E and St Clair, B and Shoemaker, A and Cox, A and Boyd, ES}, title = {Covariation of hot spring geochemistry with microbial genomic diversity, function, and evolution.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7506}, pmid = {39209850}, issn = {2041-1723}, support = {80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; }, mesh = {*Hot Springs/microbiology/chemistry ; *Metagenome ; *Phylogeny ; Bacteria/genetics/classification/metabolism ; Hydrogen-Ion Concentration ; Archaea/genetics/classification/metabolism ; Genome, Microbial ; Ecosystem ; Microbiota/genetics ; }, abstract = {The geosphere and the microbial biosphere have co-evolved for ~3.8 Ga, with many lines of evidence suggesting a hydrothermal habitat for life's origin. However, the extent that contemporary thermophiles and their hydrothermal habitats reflect those that likely existed on early Earth remains unknown. To address this knowledge gap, 64 geochemical analytes were measured and 1022 metagenome-assembled-genomes (MAGs) were generated from 34 chemosynthetic high-temperature springs in Yellowstone National Park and analysed alongside 444 MAGs from 35 published metagenomes. We used these data to evaluate co-variation in MAG taxonomy, metabolism, and phylogeny as a function of hot spring geochemistry. We found that cohorts of MAGs and their functions are discretely distributed across pH gradients that reflect different geochemical provinces. Acidic or circumneutral/alkaline springs harbor MAGs that branched later and are enriched in sulfur- and arsenic-based O2-dependent metabolic pathways that are inconsistent with early Earth conditions. In contrast, moderately acidic springs sourced by volcanic gas harbor earlier-branching MAGs that are enriched in anaerobic, gas-dependent metabolisms (e.g. H2, CO2, CH4 metabolism) that have been hypothesized to support early microbial life. Our results provide insight into the influence of redox state in the eco-evolutionary feedbacks between thermophiles and their habitats and suggest moderately acidic springs as early Earth analogs.}, } @article {pmid39215001, year = {2024}, author = {Becsei, Á and Fuschi, A and Otani, S and Kant, R and Weinstein, I and Alba, P and Stéger, J and Visontai, D and Brinch, C and de Graaf, M and Schapendonk, CME and Battisti, A and De Cesare, A and Oliveri, C and Troja, F and Sironen, T and Vapalahti, O and Pasquali, F and Bányai, K and Makó, M and Pollner, P and Merlotti, A and Koopmans, M and Csabai, I and Remondini, D and Aarestrup, FM and Munk, P}, title = {Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7551}, pmid = {39215001}, issn = {2041-1723}, support = {NNF16OC0021856//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF16OC0021856//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 874735//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 874735//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {*Sewage/microbiology ; *Metagenomics/methods ; *Seasons ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Metagenome/genetics ; Europe ; }, abstract = {Sewage metagenomics has risen to prominence in urban population surveillance of pathogens and antimicrobial resistance (AMR). Unknown species with similarity to known genomes cause database bias in reference-based metagenomics. To improve surveillance, we seek to recover sewage genomes and develop a quantification and correlation workflow for these genomes and AMR over time. We use longitudinal sewage sampling in seven treatment plants from five major European cities to explore the utility of catch-all sequencing of these population-level samples. Using metagenomic assembly methods, we recover 2332 metagenome-assembled genomes (MAGs) from prokaryotic species, 1334 of which were previously undescribed. These genomes account for ~69% of sequenced DNA and provide insight into sewage microbial dynamics. Rotterdam (Netherlands) and Copenhagen (Denmark) show strong seasonal microbial community shifts, while Bologna, Rome, (Italy) and Budapest (Hungary) have occasional blooms of Pseudomonas-dominated communities, accounting for up to ~95% of sample DNA. Seasonal shifts and blooms present challenges for effective sewage surveillance. We find that bacteria of known shared origin, like human gut microbiota, form communities, suggesting the potential for source-attributing novel species and their ARGs through network community analysis. This could significantly improve AMR tracking in urban environments.}, } @article {pmid39214983, year = {2024}, author = {Duan, Y and Santos-Júnior, CD and Schmidt, TS and Fullam, A and de Almeida, BLS and Zhu, C and Kuhn, M and Zhao, XM and Bork, P and Coelho, LP}, title = {A catalog of small proteins from the global microbiome.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7563}, pmid = {39214983}, issn = {2041-1723}, support = {61932008//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Microbiota/genetics ; *Open Reading Frames/genetics ; *Bacteria/genetics/classification/metabolism ; *Metagenome/genetics ; *Archaea/genetics/metabolism/classification ; Molecular Sequence Annotation ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Small open reading frames (smORFs) shorter than 100 codons are widespread and perform essential roles in microorganisms, where they encode proteins active in several cell functions, including signal pathways, stress response, and antibacterial activities. However, the ecology, distribution and role of small proteins in the global microbiome remain unknown. Here, we construct a global microbial smORFs catalog (GMSC) derived from 63,410 publicly available metagenomes across 75 distinct habitats and 87,920 high-quality isolate genomes. GMSC contains 965 million non-redundant smORFs with comprehensive annotations. We find that archaea harbor more smORFs proportionally than bacteria. We moreover provide a tool called GMSC-mapper to identify and annotate small proteins from microbial (meta)genomes. Overall, this publicly-available resource demonstrates the immense and underexplored diversity of small proteins.}, } @article {pmid39214976, year = {2024}, author = {Yi, X and Liang, JL and Wen, P and Jia, P and Feng, SW and Liu, SY and Zhuang, YY and Guo, YQ and Lu, JL and Zhong, SJ and Liao, B and Wang, Z and Shu, WS and Li, JT}, title = {Giant viruses as reservoirs of antibiotic resistance genes.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7536}, pmid = {39214976}, issn = {2041-1723}, mesh = {*Phylogeny ; *Giant Viruses/genetics ; *Genome, Viral/genetics ; Drug Resistance, Microbial/genetics ; Bacteriophages/genetics/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Metagenome/genetics ; Gene Transfer, Horizontal ; Trimethoprim/pharmacology ; Drug Resistance, Bacterial/genetics ; }, abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs; also called giant viruses), constituting the phylum Nucleocytoviricota, can infect a wide range of eukaryotes and exchange genetic material with not only their hosts but also prokaryotes and phages. A few NCLDVs were reported to encode genes conferring resistance to beta‑lactam, trimethoprim, or pyrimethamine, suggesting that they are potential vehicles for the transmission of antibiotic resistance genes (ARGs) in the biome. However, the incidence of ARGs across the phylum Nucleocytoviricota, their evolutionary characteristics, their dissemination potential, and their association with virulence factors remain unexplored. Here, we systematically investigated ARGs of 1416 NCLDV genomes including those of almost all currently available cultured isolates and high-quality metagenome-assembled genomes from diverse habitats across the globe. We reveal that 39.5% of them carry ARGs, which is approximately 37 times higher than that for phage genomes. A total of 12 ARG types are encoded by NCLDVs. Phylogenies of the three most abundant NCLDV-encoded ARGs hint that NCLDVs acquire ARGs from not only eukaryotes but also prokaryotes and phages. Two NCLDV-encoded trimethoprim resistance genes are demonstrated to confer trimethoprim resistance in Escherichia coli. The presence of ARGs in NCLDV genomes is significantly correlated with mobile genetic elements and virulence factors.}, } @article {pmid39214237, year = {2025}, author = {Macowan, M and Pattaroni, C and Bonner, K and Chatzis, R and Daunt, C and Gore, M and Custovic, A and Shields, MD and Power, UF and Grigg, J and Roberts, G and Ghazal, P and Schwarze, J and Turner, S and Bush, A and Saglani, S and Lloyd, CM and Marsland, BJ}, title = {Deep multiomic profiling reveals molecular signatures that underpin preschool wheeze and asthma.}, journal = {The Journal of allergy and clinical immunology}, volume = {155}, number = {1}, pages = {94-106}, doi = {10.1016/j.jaci.2024.08.017}, pmid = {39214237}, issn = {1097-6825}, mesh = {Humans ; *Respiratory Sounds/genetics/immunology ; *Asthma/genetics/immunology ; Child, Preschool ; Child ; Female ; Male ; Adolescent ; Infant ; Microbiota ; Gene Expression Profiling ; Transcriptome ; }, abstract = {BACKGROUND: Wheezing in childhood is prevalent, with over one-half of all children experiencing at least 1 episode by age 6. The pathophysiology of wheeze, especially why some children develop asthma while others do not, remains unclear.

OBJECTIVES: This study addresses the knowledge gap by investigating the transition from preschool wheeze to asthma using multiomic profiling.

METHODS: Unsupervised, group-agnostic integrative multiomic factor analysis was performed using host/bacterial (meta)transcriptomic and bacterial shotgun metagenomic datasets from bronchial brush samples paired with metabolomic/lipidomic data from bronchoalveolar lavage samples acquired from children 1-17 years old.

RESULTS: Two multiomic factors were identified: one characterizing preschool-aged recurrent wheeze and another capturing an inferred trajectory from health to wheeze and school-aged asthma. Recurrent wheeze was driven by type 1-immune signatures, coupled with upregulation of immune-related and neutrophil-associated lipids and metabolites. Comparatively, progression toward asthma from ages 1 to 18 was dominated by changes related to airway epithelial cell gene expression, type 2-immune responses, and constituents of the airway microbiome, such as increased Haemophilus influenzae.

CONCLUSIONS: These factors highlighted distinctions between an inflammation-related phenotype in preschool wheeze, and the predominance of airway epithelial-related changes linked with the inferred trajectory toward asthma. These findings provide insights into the differential mechanisms driving the progression from wheeze to asthma and may inform targeted therapeutic strategies.}, } @article {pmid39214080, year = {2024}, author = {Carlino, N and Blanco-Míguez, A and Punčochář, M and Mengoni, C and Pinto, F and Tatti, A and Manghi, P and Armanini, F and Avagliano, M and Barcenilla, C and Breselge, S and Cabrera-Rubio, R and Calvete-Torre, I and Coakley, M and Cobo-Díaz, JF and De Filippis, F and Dey, H and Leech, J and Klaassens, ES and Knobloch, S and O'Neil, D and Quijada, NM and Sabater, C and Skírnisdóttir, S and Valentino, V and Walsh, L and , and Alvarez-Ordóñez, A and Asnicar, F and Fackelmann, G and Heidrich, V and Margolles, A and Marteinsson, VT and Rota Stabelli, O and Wagner, M and Ercolini, D and Cotter, PD and Segata, N and Pasolli, E}, title = {Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome.}, journal = {Cell}, volume = {187}, number = {20}, pages = {5775-5795.e15}, doi = {10.1016/j.cell.2024.07.039}, pmid = {39214080}, issn = {1097-4172}, mesh = {Humans ; *Metagenome/genetics ; *Gastrointestinal Microbiome/genetics ; Microbiota/genetics ; Food Microbiology ; Metagenomics/methods ; Bacteria/genetics/classification ; }, abstract = {Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their role in shaping the human microbiome, and supports future uses of metagenomics for food quality, safety, and authentication.}, } @article {pmid39210613, year = {2024}, author = {Xu, Y and Wu, X and Li, Y and Liu, X and Fang, L and Jiang, Z}, title = {Probiotics and the Role of Dietary Substrates in Maintaining the Gut Health: Use of Live Microbes and Their Products for Anticancer Effects against Colorectal Cancer.}, journal = {Journal of microbiology and biotechnology}, volume = {34}, number = {10}, pages = {1933-1946}, pmid = {39210613}, issn = {1738-8872}, mesh = {*Probiotics/therapeutic use ; *Colorectal Neoplasms/microbiology ; Humans ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; Animals ; Diet ; Bacteria/classification/genetics/metabolism ; Gastrointestinal Tract/microbiology ; Bifidobacterium ; Antineoplastic Agents ; }, abstract = {The gut microbiome is an important and the largest endocrine organ linked to the microbes of the GI tract. The bacterial, viral and fungal communities are key regulators of the health and disease status in a host at hormonal, neurological, immunological, and metabolic levels. The useful microbes can compete with microbes exhibiting pathogenic behavior by maintaining resistance against their colonization, thereby maintaining eubiosis. As diagnostic tools, metagenomic, proteomic and genomic approaches can determine various microbial markers in clinic for early diagnosis of colorectal cancer (CRC). Probiotics are live non-pathogenic microorganisms such as lactic acid bacteria, Bifidobacteria, Firmicutes and Saccharomyces that can help maintain eubiosis when administered in appropriate amounts. In addition, the type of dietary intake contributes substantially to the composition of gut microbiome. The use of probiotics has been found to exert antitumor effects at preclinical levels and promote the antitumor effects of immunotherapeutic drugs at clinical levels. Also, modifying the composition of gut microbiota by Fecal Microbiota Transplantation (FMT), and using live lactic acid producing bacteria such as Lactobacillus, Bifidobacteria and their metabolites (termed postbiotics) can contribute to immunomodulation of the tumor microenvironment. This can lead to tumor-preventive effects at early stages and antitumor effects after diagnosis of CRC. To conclude, probiotics are presumably found to be safe to use in humans and are to be studied further to promote their appliance at clinical levels for management of CRC.}, } @article {pmid39209855, year = {2024}, author = {Whittle, MJ and Castillo-Fernandez, J and Amos, GCA and Watson, P}, title = {Metagenomic characterisation of canine skin reveals a core healthy skin microbiome.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {20104}, pmid = {39209855}, issn = {2045-2322}, mesh = {Dogs ; Animals ; *Skin/microbiology ; *Microbiota ; *Metagenomics/methods ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; }, abstract = {Furthering our knowledge of the skin microbiome is essential to understand health and disease in canines. To date, studies into the canine skin microbiome have focused on 16S rRNA high throughput sequencing however, these lack the granularity of species and strain level taxonomic characterisation and their associated functions. The aim of this study was to provide a comprehensive assessment of the skin microbiome by analysing the skin microbiome of 72 healthy adult colony dogs, across four distinct skin sites and four breeds, using metagenomic sequencing. Our analysis revealed that breed and skin site are drivers of variation, and a core group of taxa and genes are present within the skin microbiome of healthy dogs, comprising 230 taxa and 1219 gene families. We identified 15 species within the core microbiome that are represented by more than one strain. The biosynthesis of secondary metabolites pathway was enriched in the core microbiome suggesting the skin microbiome may play a role in colonisation resistance and protection from invading pathogens. Additionally, we uncovered the novelty of the canine skin microbiome and show that further investigation is required to increase the suitability of current databases for metagenomic sequencing of canine skin samples.}, } @article {pmid39207726, year = {2024}, author = {Lu, C and Wang, X and Ye, P and Lu, Z and Ma, J and Luo, W and Wang, S and Chen, X}, title = {Antimicrobial Peptides From the Gut Microbiome of the Centenarians: Diversification of Biosynthesis and Youthful Development of Resistance Genes.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {79}, number = {11}, pages = {}, doi = {10.1093/gerona/glae218}, pmid = {39207726}, issn = {1758-535X}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Aged, 80 and over ; *Antimicrobial Peptides/genetics ; Male ; Female ; Aged ; Adult ; Drug Resistance, Bacterial/genetics ; Middle Aged ; Probiotics ; }, abstract = {Antimicrobial peptides (AMPs) offer a potential solution to the antibiotic crisis owing to their antimicrobial properties, and the human gut biome may be a source of these peptides. However, the potential AMPs and AMP resistance genes (AMPRGs) of gut microbes in different age groups have not been thoroughly assessed. Here, we investigated the potential development of AMPs and the distribution pattern of AMPRGs in the gut microbiome at different ages by analyzing the intestinal metagenomic data of healthy individuals at different life stages (CG: centenarians group n = 20; OAG: older adults group: n = 15; YG: young group: n = 15). Age-related increases were observed in the potential AMPs within the gut microbiome, with centenarians showing a greater diversity of these peptides. However, the gut microbiome of the CG group had a lower level of AMPRGs compared to that of the OAG group, and it was similar to the level found in the YG group. Additionally, conventional probiotic strains showed a significant positive correlation with certain potential AMPs and were associated with a lower detection of resistance genes. Furthermore, comparing potential AMPs with existing libraries revealed limited similarity, indicating that current machine learning models can identify novel peptides in the gut microbiota. These results indicate that longevity may benefit from the diversity of AMPs and lower resistance genes. Our findings help explain the age advantage of the centenarians and identify the potential for antimicrobial peptide biosynthesis in the human gut microbiome, offering insights into the development of antimicrobial peptide resistance and the screening of probiotic strains.}, } @article {pmid39207108, year = {2024}, author = {Crouch, AL and Monsey, L and Rambeau, M and Ramos, C and Yracheta, JM and Anderson, MZ}, title = {Metagenomic discovery of microbial eukaryotes in stool microbiomes.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0206324}, pmid = {39207108}, issn = {2150-7511}, support = {//Ohio State University (OSU)/ ; 2046863//National Science Foundation (NSF)/ ; //Chan Zuckerberg Initiative (CZI)/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Feces/microbiology ; *Eukaryota/genetics/classification/isolation & purification ; Gastrointestinal Microbiome/genetics ; Metagenome ; Fungi/genetics/classification/isolation & purification ; Sequence Analysis, DNA/methods ; Microbiota/genetics ; }, abstract = {Host-associated microbiota form complex microbial communities that are increasingly associated with host behavior and disease. While these microbes include bacterial, archaeal, viral, and eukaryotic constituents, most studies have focused on bacteria due to their dominance in the human host and available tools for investigation. Accumulating evidence suggests microbial eukaryotes in the microbiome play pivotal roles in host health, but our understandings of these interactions are limited to a few readily identifiable taxa because of technical limitations in unbiased eukaryote exploration. Here, we combined cell sorting, optimized eukaryotic cell lysis, and shotgun sequencing to accelerate metagenomic discovery and analysis of host-associated microbial eukaryotes. Using synthetic communities with a 1% microbial eukaryote representation, the eukaryote-optimized cell lysis and DNA recovery method alone yielded a 38-fold increase in eukaryotic DNA. Automated sorting of eukaryotic cells from stool samples of healthy adults increased the number of microbial eukaryote reads in metagenomic pools by up to 28-fold compared to commercial kits. Read frequencies for identified fungi increased by 10,000× on average compared to the Human Microbiome Project and allowed for the identification of novel taxa, de novo assembly of contigs from previously unknown microbial eukaryotes, and gene prediction from recovered genomic segments. These advances pave the way for the unbiased inclusion of microbial eukaryotes in deciphering determinants of health and disease in the host-associated microbiome.IMPORTANCEMicrobial eukaryotes are common constituents of the human gut where they can contribute to local ecology and host health, but they are often overlooked in microbiome studies. The lack of attention is due to current technical limitations that are heavily biased or poorly recovered DNA from microbial eukaryotes. We developed a method to increase the representation of these eukaryotes in metagenomic sequencing of microbiome samples that allows to improve their detection compared to prior methods and allows for the identification of new species. Application of the technique to gut microbiome samples improved detection of fungi, protists, and helminths. New eukaryotic taxa and their encoded genes could be identified by sequencing a small number of samples. This approach can improve the inclusion of eukaryotes into microbiome research.}, } @article {pmid39206042, year = {2024}, author = {Zhen, J and Zhang, Y and Li, Y and Zhou, Y and Cai, Y and Huang, G and Xu, A}, title = {The gut microbiota intervenes in glucose tolerance and inflammation by regulating the biosynthesis of taurodeoxycholic acid and carnosine.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1423662}, pmid = {39206042}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; *Carnosine/metabolism ; Male ; *Feces/microbiology ; Glucose Intolerance/metabolism ; Inflammation/metabolism ; Hep G2 Cells ; Metagenomics ; Female ; Middle Aged ; Taurochenodeoxycholic Acid/metabolism/pharmacology ; Hyperglycemia/metabolism ; Neutrophils/metabolism ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/metabolism/genetics ; }, abstract = {OBJECTIVE: This study aims to investigate the pathogenesis of hyperglycemia and its associated vasculopathy using multiomics analyses in diabetes and impaired glucose tolerance, and validate the mechanism using the cell experiments.

METHODS: In this study, we conducted a comprehensive analysis of the metagenomic sequencing data of diabetes to explore the key genera related to its occurrence. Subsequently, participants diagnosed with impaired glucose tolerance (IGT), and healthy subjects, were recruited for fecal and blood sample collection. The dysbiosis of the gut microbiota (GM) and its associated metabolites were analyzed using 16S rDNA sequencing and liquid chromatograph mass spectrometry, respectively. The regulation of gene and protein expression was evaluated through mRNA sequencing and data-independent acquisition technology, respectively. The specific mechanism by which GM dysbiosis affects hyperglycemia and its related vasculopathy was investigated using real-time qPCR, Western blotting, and enzyme-linked immunosorbent assay techniques in HepG2 cells and neutrophils.

RESULTS: Based on the published data, the key alterable genera in the GM associated with diabetes were identified as Blautia, Lactobacillus, Bacteroides, Prevotella, Faecalibacterium, Bifidobacterium, Ruminococcus, Clostridium, and Lachnoclostridium. The related metabolic pathways were identified as cholate degradation and L-histidine biosynthesis. Noteworthy, Blautia and Faecalibacterium displayed similar alterations in patients with IGT compared to those observed in patients with diabetes, and the GM metabolites, tauroursodeoxycholic acid (TUDCA) and carnosine (CARN, a downstream metabolite of histidine and alanine) were both found to be decreased, which in turn regulated the expression of proteins in plasma and mRNAs in neutrophils. Subsequent experiments focused on insulin-like growth factor-binding protein 3 and interleukin-6 due to their impact on blood glucose regulation and associated vascular inflammation. Both proteins were found to be suppressed by TUDCA and CARN in HepG2 cells and neutrophils.

CONCLUSION: Dysbiosis of the GM occurred throughout the entire progression from IGT to diabetes, characterized by an increase in Blautia and a decrease in Faecalibacterium, leading to reduced levels of TUDCA and CARN, which alleviated their inhibition on the expression of insulin-like growth factor-binding protein 3 and interleukin-6, contributing to the development of hyperglycemia and associated vasculopathy.}, } @article {pmid39205200, year = {2024}, author = {Santos, JPN and Rodrigues, GVP and Ferreira, LYM and Monteiro, GP and Fonseca, PLC and Lopes, ÍS and Florêncio, BS and da Silva Junior, AB and Ambrósio, PE and Pirovani, CP and Aguiar, ERGR}, title = {The Virome of Cocoa Fermentation-Associated Microorganisms.}, journal = {Viruses}, volume = {16}, number = {8}, pages = {}, pmid = {39205200}, issn = {1999-4915}, support = {Financial code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brazil (CAPES)/ ; Researcher fellowship//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; }, mesh = {*Cacao/virology/microbiology ; *Fermentation ; *Virome ; Viruses/genetics/classification/isolation & purification ; Fungi/virology/genetics/classification ; Phylogeny ; Bacteriophages/genetics/classification/isolation & purification ; Costa Rica ; Bacteria/genetics/classification/virology ; Metagenomics ; Genome, Viral ; }, abstract = {Theobroma cacao plantations are of significant economic importance worldwide, primarily for chocolate production. During the harvest and processing of cocoa beans, they are subjected to fermentation either by microorganisms present in the environment (spontaneous fermentation) or the addition of starter cultures, with different strains directly contributing distinct flavor and color characteristics to the beans. In addition to fungi and bacteria, viruses are ubiquitous and can affect the quality of the fermentation process by infecting fermenting organisms, destabilizing microbial diversity, and consequently affecting fermentation quality. Therefore, in this study, we explored publicly available metatranscriptomic libraries of cocoa bean fermentation in Limon Province, Costa Rica, looking for viruses associated with fermenting microorganisms. Libraries were derived from the same sample at different time points: 7, 20, and 68 h of fermentation, corresponding to yeast- and lactic acid bacteria-driven phases. Using a comprehensive pipeline, we identified 68 viral sequences that could be assigned to 62 new viral species and 6 known viruses distributed among at least nine families, with particular abundance of elements from the Lenarviricota phylum. Interestingly, 44 of these sequences were specifically associated with ssRNA phages (Fiersviridae) and mostly fungi-infecting viral families (Botourmiaviridae, Narnaviridae, and Mitoviridae). Of note, viruses from those families show a complex evolutionary relationship, transitioning from infecting bacteria to infecting fungi. We also identified 10 and 3 viruses classified within the Totiviridae and Nodaviridae families, respectively. The quantification of the virus-derived RNAs shows a general pattern of decline, similar to the dynamic profile of some microorganism genera during the fermentation process. Unexpectedly, we identified narnavirus-related elements that showed similarity to segmented viral species. By exploring the molecular characteristics of these viral sequences and applying Hidden Markov Models, we were capable of associating these additional segments with a specific taxon. In summary, our study elucidates the complex virome associated with the microbial consortia engaged in cocoa bean fermentation that could contribute to organism/strain selection, altering metabolite production and, consequently, affecting the sensory characteristics of cocoa beans.}, } @article {pmid39202331, year = {2024}, author = {Zheng, X and Xu, L and Tang, Q and Shi, K and Wang, Z and Shi, L and Ding, Y and Yin, Z and Zhang, X}, title = {Integrated Metagenomic and Metabolomics Profiling Reveals Key Gut Microbiota and Metabolites Associated with Weaning Stress in Piglets.}, journal = {Genes}, volume = {15}, number = {8}, pages = {}, pmid = {39202331}, issn = {2073-4425}, support = {202103a06020013//Major special science and technology project of Anhui Province/ ; GXXT-2023-059//the Cooperative Innovation Project of Anhui Provincial Universities/ ; 340000211260001000431//the Joint Research Project on Local Pig Breeding in Anhui Province/ ; 2021YFD1301200//National Key research and development Program of China/ ; }, mesh = {Animals ; *Weaning ; *Gastrointestinal Microbiome ; Swine ; *Metabolomics/methods ; *Metagenomics/methods ; Stress, Physiological ; Metabolome ; Animals, Newborn ; Cecum/microbiology/metabolism ; }, abstract = {(1) Background: Weaning is a challenging and stressful event in the pig's life, which disrupts physiological balance and induces oxidative stress. Microbiota play a significant role during the weaning process in piglets. Therefore, this study aimed to investigate key gut microbiota and metabolites associated with weaning stress in piglets. (2) Methods: A total of ten newborn piglet littermates were randomly assigned to two groups: S (suckling normally) and W (weaned at 21 d; all euthanized at 23 d). Specimens of the cecum were dehydrated with ethanol, cleared with xylene, embedded in paraffin, and cut into 4 mm thick serial sections. After deparaffinization, the sections were stained with hematoxylin and eosin (H&E) for morphometric analysis. Cecal metagenomic and liver LC-MS-based metabolomics were employed in this study. Statistical comparisons were performed by a two-tailed Student's t-test, and p < 0.05 indicated statistical significance. (3) Results: The results showed that weaning led to intestinal morphological damage in piglets. The intestinal villi of suckling piglets were intact, closely arranged in an orderly manner, and finger-shaped, with clear contours of columnar epithelial cells. In contrast, the intestines of weaned piglets showed villous atrophy and shedding, as well as mucosal bleeding. Metagenomics and metabolomics analyses showed significant differences in composition and function between suckling and weaned piglets. The W piglets showed a decrease and increase in the relative abundance of Bacteroidetes and Proteobacteria (p < 0.05), respectively. The core cecal flora in W piglets were Campylobacter and Clostridium, while those in S piglets were Prevotella and Lactobacillus. At the phylum level, the relative abundance of Bacteroidetes significantly decreased (p < 0.05) in weaned piglets, while Proteobacteria significantly increased (p < 0.05). Significant inter-group differences were observed in pathways and glycoside hydrolases in databases, such as the KEGG and CAZymes, including fructose and mannose metabolism, salmonella infection, antifolate resistance, GH135, GH16, GH32, and GH84. We identified 757 differential metabolites between the groups through metabolomic analyses-350 upregulated and 407 downregulated (screened in positive ion mode). In negative ion mode, 541 differential metabolites were identified, with 270 upregulated and 271 downregulated. Major differential metabolites included glycerophospholipids, histidine, nitrogen metabolism, glycine, serine, threonine, β-alanine, and primary bile acid biosynthesis. The significant differences in glycine, serine, and threonine metabolites may be potentially related to dysbiosis caused by weaning stress. Taken together, the identification of microbiome and metabolome signatures of suckling and weaned piglets has paved the way for developing health-promoting nutritional strategies, focusing on enhancing bacterial metabolite production in early life stages.}, } @article {pmid39201270, year = {2024}, author = {Su, H and Yang, S and Chen, S and Chen, X and Guo, M and Zhu, L and Xu, W and Liu, H}, title = {What Happens in the Gut during the Formation of Neonatal Jaundice-Underhand Manipulation of Gut Microbiota?.}, journal = {International journal of molecular sciences}, volume = {25}, number = {16}, pages = {}, pmid = {39201270}, issn = {1422-0067}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Jaundice, Neonatal/therapy/microbiology/etiology ; Infant, Newborn ; *Probiotics ; *Bilirubin/metabolism/blood ; Breast Feeding ; Milk, Human/microbiology/metabolism ; }, abstract = {Jaundice is a symptom of high blood bilirubin levels affecting about 80% of neonates. In neonates fed with breast milk, jaundice is particularly prevalent and severe, which is likely multifactorial. With the development of genomics and metagenomics, a deeper understanding of the neonatal gut microbiota has been achieved. We find there are accumulating evidence to indicate the importance of the gut microbiota in the mechanism of jaundice. In this paper, we present new comprehensive insight into the relationship between the microbiota and jaundice. In the new perspective, the gut is a crucial crossroad of bilirubin excretion, and bacteria colonizing the gut could play different roles in the excretion of bilirubin, including Escherichia coli as the main traffic jam causers, some Clostridium and Bacteroides strains as the traffic police, and most probiotic Bifidobacterium and Lactobacillus strains as bystanders with no effect or only a secondary indirect effect on the metabolism of bilirubin. This insight could explain why breast milk jaundice causes a longer duration of blood bilirubin and why most probiotics have limited effects on neonatal jaundice. With the encouragement of breastmilk feeding, our perspective could guide the development of new therapy methods to prevent this side effect of breastfeeding.}, } @article {pmid39201260, year = {2024}, author = {Ryu, HM and Islam, SMS and Riaz, B and Sayeed, HM and Choi, B and Sohn, S}, title = {Immunomodulatory Effects of a Probiotic Mixture: Alleviating Colitis in a Mouse Model through Modulation of Cell Activation Markers and the Gut Microbiota.}, journal = {International journal of molecular sciences}, volume = {25}, number = {16}, pages = {}, pmid = {39201260}, issn = {1422-0067}, mesh = {Animals ; *Probiotics/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Disease Models, Animal ; *Colitis/microbiology/therapy/diet therapy/chemically induced ; *Dextran Sulfate/toxicity ; RNA, Ribosomal, 16S/genetics ; Colitis, Ulcerative/microbiology/therapy/immunology/diet therapy ; Biomarkers ; Mice, Inbred C57BL ; Colon/microbiology/pathology/metabolism ; }, abstract = {Ulcerative colitis (UC) is a persistent inflammatory intestinal disease that consistently affects the colon and rectum. Its exact cause remains unknown. UC causes a considerable challenge in healthcare, prompting research for novel therapeutic strategies. Although probiotics have gained popularity as possible candidates for managing UC, studies are still ongoing to identify the best probiotics or probiotic mixtures for clinical applications. This study aimed to determine the efficacy of a multi-strain probiotic mixture in mitigating intestinal inflammation in a colitis mouse model induced by dextran sulfate sodium. Specifically, a multi-strain probiotic mixture consisting of Tetragenococcus halophilus and Eubacterium rectale was used to study its impact on colitis symptoms. Anti-inflammatory effects were evaluated using ELISA and flow cytometry. The configuration of gut microbial communities was determined using 16S rRNA metagenomic analysis. According to this study, colitis mice treated with the probiotic mixture experienced reduced weight loss and significantly less colonic shortening compared to untreated mice. Additionally, the treated mice exhibited increased levels of forkhead box P3 (Foxp3) and interleukin 10, along with decreased expression of dendritic cell activation markers, such as CD40+, CD80+, and CD83+, in peripheral blood leukocytes and intraepithelial lymphocytes. Furthermore, there was a significant decrease in the frequencies of CD8+N.K1.1+ cells and CD11b+Ly6G+ cells. In terms of the gut microbiota, probiotic-mixture treatment of colitis mice significantly increased the abundance of the phyla Actinobacteria and Verrucomicrobia (p < 0.05). These results provide valuable insights into the therapeutic promise of multi-strain probiotics, shedding light on their potential to alleviate colitis symptoms. This research contributes to the ongoing exploration of effective probiotic interventions for managing inflammatory bowel disease.}, } @article {pmid39201258, year = {2024}, author = {Al-Sarraj, F and Albiheyri, R and Qari, M and Alotaibi, M and Al-Zahrani, M and Anwar, Y and Alghamdi, MA and Nass, NM and Bouback, T and Alotibi, I and Radhwi, O and Sajer, BH and Redhwan, A and Al-Matary, MA and Almanzalawi, EA and Elshafie, HS}, title = {Genetic Patterns of Oral Cavity Microbiome in Patients with Sickle Cell Disease.}, journal = {International journal of molecular sciences}, volume = {25}, number = {16}, pages = {}, pmid = {39201258}, issn = {1422-0067}, support = {grant no. J: 007-130-1443.//Deanship of Scientific Research (DSR) at King Abdulaziz University (KAU), Jeddah/ ; }, mesh = {Humans ; *Anemia, Sickle Cell/microbiology/genetics ; *Mouth/microbiology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Female ; Male ; Adult ; *Saliva/microbiology ; Bacteria/genetics/classification/isolation & purification ; Young Adult ; Case-Control Studies ; Adolescent ; High-Throughput Nucleotide Sequencing ; Middle Aged ; }, abstract = {The Middle Eastern prevalence of sickle cell anemia, a genetic disorder that affects red blood cells, necessitates additional research. On a molecular level, we sought to identify and sort the oral microbiota of healthy individuals and those with sickle cell anemia. Furthermore, it is crucial to comprehend how changes in the genetic makeup of the oral microbiota impact the state of sickle cell anemia. Using next-generation sequencing, the 16S rRNA amplicon was examined using saliva samples from 36 individuals with sickle cell anemia and healthy individuals. These samples were obtained from sickle cell anemia patients (18 samples) and healthy control participants (controls, 18 samples). Various analyses are conducted using bioinformatic techniques to identify distinct species and their relative abundance. Streptococcus, followed by Fusobacterium nucleatum, Prevotella, and Veillonella were the most prevalent genera of bacteria in the saliva of the SCA and non-SCA individuals according to our findings. Rothia mucilaginosa, Prevotella scoposa, and Veillonella dispar species were the dominant species in both sickle cell anemia and non-sickle cell anemia subjects. Streptococcus salivarius, Actinomyces graevenitzii, Actinomyces odontolyticus, and Actinomyces georgiae spp. were the most prevalent bacterial spp. in the studied SCA cases. The sequencing of the 16S rRNA gene yielded relative abundance values that were visualized through a heatmap analysis. Alterations in the oral microflora's constitution can significantly affect the susceptibility of sickle cell anemia patients to develop more severe health complications. Salivary diagnosis is a potential tool for predicting and preventing oral microbiome-related diseases in the future.}, } @article {pmid39198832, year = {2024}, author = {Su, W and Gong, C and Zhong, H and Yang, H and Chen, Y and Wu, X and Jin, J and Xi, H and Zhao, J}, title = {Vaginal and endometrial microbiome dysbiosis associated with adverse embryo transfer outcomes.}, journal = {Reproductive biology and endocrinology : RB&E}, volume = {22}, number = {1}, pages = {111}, pmid = {39198832}, issn = {1477-7827}, support = {437606312//Wenzhou Medical University advantageous and distinctive Discipline Construction Project/ ; }, mesh = {Humans ; Female ; *Embryo Transfer/methods ; *Dysbiosis/microbiology ; Adult ; *Vagina/microbiology ; *Microbiota/genetics/physiology ; *Endometrium/microbiology/metabolism ; *Embryo Implantation/physiology ; Pregnancy ; *Infertility, Female/microbiology/therapy ; Fertilization in Vitro/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Assisted reproductive technology (ART) is the most effective method to treat infertility and the pathogenesis of implantation failure after in vitro fertilization-embryo transfer (IVF-ET) is a challenging filed in infertility. Microbes in the female reproductive tract are considered to be associated with gynecological and obstetric diseases. However, its effects on embryo implantation failure are unsured.

PURPOSE: This study aimed to investigate reproductive tract dysbiosis, identify different bacteria in reproductive tract as potential biomarkers of embryo implantation failure and demonstrate the pathogenesis through metabolites analysis.

METHODS: We compared the data from 16S rRNA gene and metagenome in reproductive tracts through QIIME2 and HUMAnN2 by the times of embryo implantation failure on 239 infertile patients and 17 healthy women.

RESULTS: Our study revealed a strong positive correlation between Lactobacillus abundance and embryo implantation success (IS) after IVF-ET. The microbial community composition and structure in reproductive tract showed substantially difference between the embryo implantation failure (IF) and healthy control. Moreover, we established a diagnostic model through receiver operating characteristic (ROC) with 0.913 area under curve (AUC) in IS and multiple implantation failures (MIF), verified its effectiveness with an AUC = 0.784 demonstrating microbial community alterations could efficiently discriminate MIF patients. Metagenome functional analyses of vaginal samples from another independent infertile patients after IVF-ET revealed the L-lysine synthesis pathway enriched in IF patients, along with ascended vaginal pH and decreased Lactobacillus abundance.

CONCLUSIONS: This study clarifies several independent relationships of bacteria in vagina and endometrial fluid on embryo implantation failure and undoubtedly broadens the understanding about female reproductive health.}, } @article {pmid39198826, year = {2024}, author = {Su, Q and Zhuang, DH and Li, YC and Chen, Y and Wang, XY and Ge, MX and Xue, TY and Zhang, QY and Liu, XY and Yin, FQ and Han, YM and Gao, ZL and Zhao, L and Li, YX and Lv, MJ and Yang, LQ and Xia, TR and Luo, YJ and Zhang, Z and Kong, QP}, title = {Gut microbiota contributes to high-altitude hypoxia acclimatization of human populations.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {232}, pmid = {39198826}, issn = {1474-760X}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Acclimatization ; *Altitude ; Animals ; Adult ; Male ; *Hypoxia/genetics ; Mice ; Female ; Longitudinal Studies ; Altitude Sickness/microbiology/genetics ; Middle Aged ; }, abstract = {BACKGROUND: The relationship between human gut microbiota and high-altitude hypoxia acclimatization remains highly controversial. This stems primarily from uncertainties regarding both the potential temporal changes in the microbiota under such conditions and the existence of any dominant or core bacteria that may assist in host acclimatization.

RESULTS: To address these issues, and to control for variables commonly present in previous studies which significantly impact the results obtained, namely genetic background, ethnicity, lifestyle, and diet, we conducted a 108-day longitudinal study on the same cohort comprising 45 healthy Han adults who traveled from lowland Chongqing, 243 masl, to high-altitude plateau Lhasa, Xizang, 3658 masl, and back. Using shotgun metagenomic profiling, we study temporal changes in gut microbiota composition at different timepoints. The results show a significant reduction in the species and functional diversity of the gut microbiota, along with a marked increase in functional redundancy. These changes are primarily driven by the overgrowth of Blautia A, a genus that is also abundant in six independent Han cohorts with long-term duration in lower hypoxia environment in Shigatse, Xizang, at 4700 masl. Further animal experiments indicate that Blautia A-fed mice exhibit enhanced intestinal health and a better acclimatization phenotype to sustained hypoxic stress.

CONCLUSIONS: Our study underscores the importance of Blautia A species in the gut microbiota's rapid response to high-altitude hypoxia and its potential role in maintaining intestinal health and aiding host adaptation to extreme environments, likely via anti-inflammation and intestinal barrier protection.}, } @article {pmid39198450, year = {2024}, author = {Licht, P and Dominelli, N and Kleemann, J and Pastore, S and Müller, ES and Haist, M and Hartmann, KS and Stege, H and Bros, M and Meissner, M and Grabbe, S and Heermann, R and Mailänder, V}, title = {The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {74}, pmid = {39198450}, issn = {2055-5008}, mesh = {Humans ; *Microbiota ; *Skin/microbiology ; Female ; Middle Aged ; Male ; *Staphylococcus aureus/genetics/pathogenicity/isolation & purification ; *Lymphoma, T-Cell, Cutaneous/microbiology ; Aged ; *Mycosis Fungoides/microbiology ; Dysbiosis/microbiology ; Skin Neoplasms/microbiology/pathology ; Adult ; Aged, 80 and over ; Metagenomics/methods ; Virulence Factors/genetics ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Mycosis fungoides (MF) is the most common entity of Cutaneous T cell lymphomas (CTCL) and is characterized by the presence of clonal malignant T cells in the skin. The role of the skin microbiome for MF development and progression are currently poorly understood. Using shotgun metagenomic profiling, real-time qPCR, and T cell receptor sequencing, we compared lesional and nonlesional skin of 20 MF patients with early and advanced MF. Additionally, we isolated Staphylococcus aureus and other bacteria from MF skin for functional profiling and to study the S. aureus virulence factor spa. We identified a subgroup of MF patients with substantial dysbiosis on MF lesions and concomitant outgrowth of S. aureus on plaque-staged lesions, while the other MF patients had a balanced microbiome on lesional skin. Dysbiosis and S. aureus outgrowth were accompanied by ectopic levels of cutaneous antimicrobial peptides (AMPs), including adaptation of the plaque-derived S. aureus strain. Furthermore, the plaque-derived S. aureus strain showed a reduced susceptibility towards antibiotics and an upregulation of the virulence factor spa, which may activate the NF-κB pathway. Remarkably, patients with dysbiosis on MF lesions had a restricted T cell receptor repertoire and significantly lower event-free survival. Our study highlights the potential for microbiome-modulating treatments targeting S. aureus to prevent MF progression.}, } @article {pmid39198444, year = {2024}, author = {Chang, D and Gupta, VK and Hur, B and Cobo-López, S and Cunningham, KY and Han, NS and Lee, I and Kronzer, VL and Teigen, LM and Karnatovskaia, LV and Longbrake, EE and Davis, JM and Nelson, H and Sung, J}, title = {Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7447}, pmid = {39198444}, issn = {2041-1723}, support = {UL1 TR002377/TR/NCATS NIH HHS/United States ; UL1 TR002494/TR/NCATS NIH HHS/United States ; UL1TR002377//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Feces/microbiology ; *Health Status ; Metagenome ; Bacteria/classification/genetics/isolation & purification ; Female ; }, abstract = {Recent advancements in translational gut microbiome research have revealed its crucial role in shaping predictive healthcare applications. Herein, we introduce the Gut Microbiome Wellness Index 2 (GMWI2), an enhanced version of our original GMWI prototype, designed as a standardized disease-agnostic health status indicator based on gut microbiome taxonomic profiles. Our analysis involves pooling existing 8069 stool shotgun metagenomes from 54 published studies across a global demographic landscape (spanning 26 countries and six continents) to identify gut taxonomic signals linked to disease presence or absence. GMWI2 achieves a cross-validation balanced accuracy of 80% in distinguishing healthy (no disease) from non-healthy (diseased) individuals and surpasses 90% accuracy for samples with higher confidence (i.e., outside the "reject option"). This performance exceeds that of the original GMWI model and traditional species-level α-diversity indices, indicating a more robust gut microbiome signature for differentiating between healthy and non-healthy phenotypes across multiple diseases. When assessed through inter-study validation and external validation cohorts, GMWI2 maintains an average accuracy of nearly 75%. Furthermore, by reevaluating previously published datasets, GMWI2 offers new insights into the effects of diet, antibiotic exposure, and fecal microbiota transplantation on gut health. Available as an open-source command-line tool, GMWI2 represents a timely, pivotal resource for evaluating health using an individual's unique gut microbial composition.}, } @article {pmid39198442, year = {2024}, author = {Campos-Madueno, EI and Aldeia, C and Endimiani, A}, title = {Nanopore R10.4 metagenomic detection of blaCTX-M/blaDHA antimicrobial resistance genes and their genetic environments in stool.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7450}, pmid = {39198442}, issn = {2041-1723}, support = {192514//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {*Feces/microbiology ; *Escherichia coli/genetics/isolation & purification ; Humans ; *beta-Lactamases/genetics/metabolism ; *Metagenomics/methods ; *Nanopores ; Escherichia coli Proteins/genetics ; Plasmids/genetics ; Nanopore Sequencing/methods ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Gastrointestinal Microbiome/genetics ; }, abstract = {The increasing prevalence of gut colonization with CTX-M extended-spectrum β-lactamase- and/or DHA plasmid-mediated AmpC-producing Escherichia coli is a concern. Here, we evaluate Nanopore-shotgun metagenomic sequencing (Nanopore-SMS) latest V14 chemistry to detect blaCTX-M and blaDHA genes from healthy stools. We test 25 paired samples characterized with culture-based methods (native and pre-enriched). Antimicrobial resistant genes (ARGs) are detected from reads and meta-assembled genomes (MAGs) to determine their associated genetic environments (AGEs). Sensitivity and specificity of native Nanopore-SMS are 61.1% and 100%, compared to 81.5% and 75% for pre-enriched Nanopore-SMS, respectively. Native Nanopore-SMS identifies only one sample with an AGE, whereas pre-enriched Nanopore-SMS recognizes 9/18 plasmids and 5/9 E. coli chromosomes. Pre-enriched Nanopore-SMS identifies more ARGs than native Nanopore-SMS (p < 0.001). Notably, blaCTX-Ms and blaDHAs AGEs (plasmid and chromosomes) are identified within 1 hour of sequencing. Furthermore, microbiota analyses show that pre-enriched Nanopore-SMS results in more E. coli classified reads (47% vs. 3.1%), higher differential abundance (5.69 log2 fold) and lower Shannon diversity index (p < 0.0001). Nanopore-SMS has the potential to be used for intestinal colonization screening. However, sample pre-enrichment is necessary to increase sensitivity. Further computational improvements are needed to reduce the turnaround time for clinical applications.}, } @article {pmid39198293, year = {2024}, author = {Joseph, B and Babu, S}, title = {Effect of Organic and Chemical Fertilizer on the Diversity of Rhizosphere and Leaf Microbial Composition in Sunflower Plant.}, journal = {Current microbiology}, volume = {81}, number = {10}, pages = {331}, pmid = {39198293}, issn = {1432-0991}, mesh = {*Fertilizers/analysis ; *Rhizosphere ; *Helianthus/microbiology ; *Bacteria/classification/genetics/isolation & purification/drug effects ; *Plant Leaves/microbiology ; *Soil Microbiology ; *Fungi/classification/genetics/isolation & purification ; *Manure/microbiology ; Microbiota ; Biodiversity ; Metagenomics ; }, abstract = {Applying organic manure to crops positively impacts the soil microbial community which is negatively impacted when chemical fertilizers are used. Organic manures also add new microbes to the soil in addition to influencing the growth of native ones. Metagenomic analysis of different organic manures, soil, and pot culture experiments conducted under various fertilizer conditions constitute the primary methodologies employed in this study. We compared the effect of two organic manure combinations and an inorganic fertilizer combination on microbial community of rhizosphere soil and leaves of sunflower plants. Metagenomic sequencing data analysis revealed that the diversity of bacteria and fungi is higher in organic manure than in chemical fertilizers. Each organic manure combination selectively increased population of some specific microbes and supported new microbes. Application of chemical fertilizer hurts many plant beneficial fungi and bacteria. In summary, our study points out the superiority of organic manure combinations in enhancing microbial diversity and supporting beneficial microbes. These findings enhance the profound influence of fertilizer types on sunflower microbial communities, shedding light on the intricate dynamics within the rhizosphere and leaf microbiome. Bacterial genera such as Bacillus, Serratia, Sphingomonas, Pseudomonas, Methylobacterium, Acinetobacter, Stenotrophomonas, and fungal genera such as Wallemia, Aspergillus, Cladosporium, and Penicillium constitute the key microbes of sunflower plants.}, } @article {pmid39197546, year = {2024}, author = {Kim, H and Lee, E and Park, M and Min, K and Diep, YN and Kim, J and Ahn, H and Lee, E and Kim, S and Kim, Y and Kang, YJ and Jung, JH and Byun, MS and Joo, Y and Jeong, C and Lee, DY and Cho, H and Park, H and Kim, T}, title = {Microbiome-derived indole-3-lactic acid reduces amyloidopathy through aryl-hydrocarbon receptor activation.}, journal = {Brain, behavior, and immunity}, volume = {122}, number = {}, pages = {568-582}, doi = {10.1016/j.bbi.2024.08.051}, pmid = {39197546}, issn = {1090-2139}, mesh = {Animals ; Female ; Humans ; Male ; Mice ; *Alzheimer Disease/metabolism ; *Amyloid beta-Peptides/metabolism ; Amyloidosis/metabolism ; Astrocytes/metabolism ; Brain/metabolism ; Cognitive Dysfunction/metabolism ; *Disease Models, Animal ; *Gastrointestinal Microbiome/drug effects ; *Indoles/pharmacology ; Mice, Transgenic ; Microbiota/drug effects ; Microglia/metabolism ; *Receptors, Aryl Hydrocarbon/metabolism ; Signal Transduction/drug effects ; Tryptophan/metabolism/pharmacology ; }, abstract = {Alzheimer's disease (AD) pathogenesis has been associated with the gut microbiome and its metabolites, though the specific mechanisms have remained unclear. In our study, we used a multi-omics approach to identify specific microbial strains and metabolites that could potentially mitigate amyloidopathy in 5xFAD mice, a widely used model for AD research. Among the microbial strains tested, three showed promising results in reducing soluble amyloid-beta (Aβ) levels. Plasma metabolomics analysis revealed an enrichment of tryptophan (Trp) and indole-3-lactic acid (ILA) in mice with reduced soluble Aβ levels, suggesting a potential preventative role. The administration of a combined treatment of Trp and ILA prevented both Aβ accumulation and cognitive impairment in the 5xFAD mice. Our investigation into the mechanism revealed that ILA's effect on reducing Aβ levels was mediated through the activation of microglia and astrocytes, facilitated by the aryl hydrocarbon receptor (AhR) signaling pathway. These mechanisms were verified through experiments in 5xFAD mice that included an additional group with the administration of ILA alone, as well as in vitro experiments using an AhR inhibitor. Clinical data analysis revealed a greater abundance of Lactobacillus reuteri in the gut of healthy individuals compared to those at early stages of Aβ accumulation or with mild cognitive impairment. Additionally, human post-mortem brain analyses showed an increased expression of genes associated with the AhR signaling pathway in individuals without AD, suggesting a protective effect against AD progression. Our results indicate that ILA from gut microbes could inhibit the progression of amyloidopathy in 5xFAD mice through activation of AhR signaling in the brain.}, } @article {pmid39197484, year = {2024}, author = {Lu, W and Zheng, Y and Wang, Y and Song, J and Weng, Y and Ma, W and Arslan, M and Gamal El-Din, M and Wang, D and Wang, Q and Chen, C}, title = {Survival strategies and assembly mechanisms of microbial communities in petroleum-contaminated soils.}, journal = {Environmental research}, volume = {262}, number = {Pt 1}, pages = {119857}, doi = {10.1016/j.envres.2024.119857}, pmid = {39197484}, issn = {1096-0953}, mesh = {*Soil Microbiology ; *Soil Pollutants/analysis ; *Petroleum ; China ; Bacteria/genetics/classification/metabolism ; Archaea/genetics ; Microbiota ; Fungi/genetics/metabolism ; Soil/chemistry ; }, abstract = {This study analyzed petroleum-contaminated soils from south and north locations in China to explore the structure, diversity, functional genes and assembly processes of microbial communities' . Compared with soils from south locations, soils from northern regions exhibited elevated pH, total nitrogen (TN), and total petroleum hydrocarbon (TPH) levels. Among these, TN and TPH were the most influential on the microbial community. The dominant phyla for bacteria, archaea, and fungi were Proteobacteria, Thaumarchaeota, and Ascomycota, respectively. Among them, Proteobacteria was strongly correlated with various functional genes including alkB and many aromatics degradation and denitrification genes (r > 0.9, p < 0.01), suggesting that Proteobacteria play an important role in petroleum-contaminated soils. Metabolism in northern regions was more active than that in southern regions. The northern regions showed a pronounced tendency for denitrification, while the southern regions were characterized by acetoclastic methanogenesis. The assembly of microbial communities exhibited regional patterns, the deterministic assembly was more prominent in the northern soils, while the stochastic assembly was evident in the southern soils. Overall, these findings provide a new conceptual framework to understand the biosphere in petroleum-contaminated soil, potentially guiding improved management practices in the environmental remediation.}, } @article {pmid39197454, year = {2024}, author = {Thänert, R and Schwartz, DJ and Keen, EC and Hall-Moore, C and Wang, B and Shaikh, N and Ning, J and Rouggly-Nickless, LC and Thänert, A and Ferreiro, A and Fishbein, SRS and Sullivan, JE and Radmacher, P and Escobedo, M and Warner, BB and Tarr, PI and Dantas, G}, title = {Clinical sequelae of gut microbiome development and disruption in hospitalized preterm infants.}, journal = {Cell host & microbe}, volume = {32}, number = {10}, pages = {1822-1837.e5}, pmid = {39197454}, issn = {1934-6069}, support = {K99 AI175674/AI/NIAID NIH HHS/United States ; P30 ES030283/ES/NIEHS NIH HHS/United States ; R01 AI184858/AI/NIAID NIH HHS/United States ; R01 AI155893/AI/NIAID NIH HHS/United States ; UH3 AI083265/AI/NIAID NIH HHS/United States ; 2021081/DDCF/Doris Duke Charitable Foundation/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; K08 AI159384/AI/NIAID NIH HHS/United States ; T32 HD007409/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Infant, Premature ; Infant, Newborn ; *Feces/microbiology ; *Enterocolitis, Necrotizing/microbiology ; Female ; *Metagenomics ; *Anti-Bacterial Agents/pharmacology ; Male ; Clostridioides difficile/genetics ; Intensive Care Units, Neonatal ; Infant ; Hospitalization ; Enterobacteriaceae/genetics ; Enterococcus/genetics ; Staphylococcus epidermidis ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Aberrant preterm infant gut microbiota assembly predisposes to early-life disorders and persistent health problems. Here, we characterize gut microbiome dynamics over the first 3 months of life in 236 preterm infants hospitalized in three neonatal intensive care units using shotgun metagenomics of 2,512 stools and metatranscriptomics of 1,381 stools. Strain tracking, taxonomic and functional profiling, and comprehensive clinical metadata identify Enterobacteriaceae, enterococci, and staphylococci as primarily exploiting available niches to populate the gut microbiome. Clostridioides difficile lineages persist between individuals in single centers, and Staphylococcus epidermidis lineages persist within and, unexpectedly, between centers. Collectively, antibiotic and non-antibiotic medications influence gut microbiome composition to greater extents than maternal or baseline variables. Finally, we identify a persistent low-diversity gut microbiome in neonates who develop necrotizing enterocolitis after day of life 40. Overall, we comprehensively describe gut microbiome dynamics in response to medical interventions in preterm, hospitalized neonates.}, } @article {pmid39197279, year = {2024}, author = {Guo, Y and Cheng, S and Fang, H and Geng, J and Li, Y and Shi, F and Wang, H and Chen, L and Zhou, Y}, title = {Copper and cadmium co-contamination increases the risk of nitrogen loss in red paddy soils.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135626}, doi = {10.1016/j.jhazmat.2024.135626}, pmid = {39197279}, issn = {1873-3336}, mesh = {*Cadmium/toxicity/metabolism ; *Soil Pollutants/metabolism ; *Copper/toxicity ; *Soil Microbiology ; *Nitrogen/metabolism ; China ; Bacteria/metabolism/genetics/classification ; Soil/chemistry ; Oryza/metabolism/growth & development ; Nitrogen Cycle ; Denitrification ; Microbiota/drug effects ; }, abstract = {The microbiome plays a crucial role in soil nitrogen (N) cycling and in regulating its bioavailability. However, the functional and genomic information of microorganisms encoding N cycling in response to copper (Cu) and cadmium (Cd) contamination is largely unknown. Here, metagenomics and genome binning were used to examine microbial N cycling in Cu and Cd co-contaminated red paddy soils collected from a polluted watershed in southern China. The results showed that soil Cu and Cd concentrations induced more drastic changes in microbial N functional and taxonomic traits than soil general properties. Soil Cu and Cd co-contamination stimulated microbial nitrification, denitrification, and dissimilatory nitrate reduction processes mainly by increasing the abundance of Nitrospira (phylum Nitrospirota), while inhibiting N fixation by decreasing the abundance of Desulfobacca. These contrasting changes in microbial N cycling processes suggested a potential risk of N loss in paddy soils. A high-quality genome was identified as belonging to Nitrospirota with the highest abundance in heavily contaminated soils. This novel Nitrospirota strain possessed metabolic capacities for N transformation and metal resistance. These findings elucidate the genetic mechanisms underlying soil N bioavailability under long-term Cu and Cd contamination, which is essential for maintaining agricultural productivity and controlling heavy metal pollution.}, } @article {pmid39197244, year = {2025}, author = {Zhang, C and Gu, C and Wang, M and Chen, J and Chang, H and Chang, Z and Zhou, J and Yue, M and Zhang, W and Zhang, Q and Feng, Z}, title = {Effect of temperature regulation on microbial community, volatile flavours, amino acid profiles, and iridoid glycosides during noni (Morinda citrifolia L.) fruit fermentation.}, journal = {Food chemistry}, volume = {462}, number = {}, pages = {140966}, doi = {10.1016/j.foodchem.2024.140966}, pmid = {39197244}, issn = {1873-7072}, mesh = {*Fermentation ; *Fruit/chemistry/metabolism/microbiology ; *Amino Acids/metabolism/analysis ; *Bacteria/metabolism/classification/genetics/isolation & purification ; *Microbiota ; *Morinda/chemistry/metabolism ; *Iridoid Glycosides/metabolism/analysis/chemistry ; *Temperature ; Volatile Organic Compounds/metabolism/chemistry ; Flavoring Agents/metabolism/chemistry ; }, abstract = {Noni fruit has an unpleasant flavour but is highly bioactive. Therefore, it is necessary to clarify the effect of temperature regulation on quality of fermented noni fruit. In the present study, the formation of flavours, amino acid profiles, and iridoid glycosides during noni fruit fermentation at different temperatures were investigated. We initially found that different temperatures affected core microbial communities. The general evolutionary trends of Acetobacter and Gluconobacter were influenced by different temperatures. Furthermore, high temperature helped maintain low octanoic and hexanoic acids. Subsequently, we found that high temperature improved total amino acids and iridoid glycosides. The correlation network analysis revealed that bacterial communities impacted the quality (volatile flavours, amino acid profiles, and iridoid glycosides) of fermented noni fruit. Overall, altering the temperature induced variations in microbial communities and quality during the noni fruit fermentation process. These results are instrumental in the pursuit of quality control in natural fermentation processes.}, } @article {pmid39197040, year = {2024}, author = {Chen, S and Zhang, Z and Liu, S and Chen, T and Lu, Z and Zhao, W and Mou, X and Liu, S}, title = {Consistent signatures in the human gut microbiome of longevous populations.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2393756}, pmid = {39197040}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Longevity ; Aged, 80 and over ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Female ; Adult ; Male ; Aged ; Young Adult ; Metagenomics ; Middle Aged ; Desulfovibrio/genetics/metabolism ; }, abstract = {Gut microbiota of centenarians has garnered significant attention in recent years, with most studies concentrating on the analysis of microbial composition. However, there is still limited knowledge regarding the consistent signatures of specific species and their biological functions, as well as the potential causal relationship between gut microbiota and longevity. To address this, we performed the fecal metagenomic analysis of eight longevous populations at the species and functional level, and employed the Mendelian randomization (MR) analysis to infer the causal associations between microbial taxa and longevity-related traits. We observed that several species including Eisenbergiella tayi, Methanobrevibacter smithii, Hungatella hathewayi, and Desulfovibrio fairfieldensis were consistently enriched in the gut microbiota of long-lived individuals compared to younger elderly and young adults across multiple cohorts. Analysis of microbial pathways and enzymes indicated that E. tayi plays a role in the protein N-glycosylation, while M. smithii is involved in the 3-dehydroquinate and chorismate biosynthesis. Furthermore, H. hathewayi makes a distinct contribution to the purine nucleobase degradation I pathway, potentially assisting the elderly in maintaining purine homeostasis. D. fairfieldensis contributes to the menaquinone (vitamin K2) biosynthesis, which may help prevent age-related diseases such as osteoporosis-induced fractures. According to MR results, Hungatella was significantly positively correlated with parental longevity, and Desulfovibrio also exhibited positive associations with lifespan and multiple traits related to parental longevity. Additionally, Alistipes and Akkermansia muciniphila were consistently enriched in the gut microbiota of the three largest cohorts of long-lived individuals, and MR analysis also suggests their potential causal relationships with longevity. Our findings reveal longevity-associated gut microbial signatures, which are informative for understanding the role of microbiota in regulating longevity and aging.}, } @article {pmid39196507, year = {2024}, author = {Qian, Y and Sorgen, AA and Steffen, KJ and Heinberg, LJ and Reed, K and Carroll, IM}, title = {Intestinal Energy Harvest Mediates Gut Microbiota-Associated Weight Loss Following Bariatric Surgery.}, journal = {Obesity surgery}, volume = {34}, number = {10}, pages = {3771-3780}, pmid = {39196507}, issn = {1708-0428}, support = {1R01DK112585-01//National Institute of Health/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Weight Loss/physiology ; Female ; Male ; *Bariatric Surgery ; *Obesity, Morbid/surgery/microbiology ; Adult ; Middle Aged ; Energy Metabolism ; Feces/microbiology ; }, abstract = {PURPOSE: Metabolic and bariatric surgery (MBS) is the most effective treatment for class III obesity. The capacity to efficiently extract intestinal energy is potentially a determinant of varying weight loss outcomes post-MBS. Prior research indicated that intestinal energy harvest is correlated with post-MBS weight loss. Studies have also demonstrated that the gut microbiota is associated with weight loss post-MBS. We aim to investigate whether gut microbiota-associated weight loss is mediated by intestinal energy harvest in patients post-MBS.

MATERIALS AND METHODS: We examined the relationship between specific gut microbiota, intestinal energy harvest, diet, and weight loss using fecal metagenomic sequence data, bomb calorimetry (fecal energy content as a proxy for calorie absorption), and a validated dietary questionnaire on 67 individuals before and after MBS. Mediation analysis and a machine learning algorithm were conducted.

RESULTS: Intestinal energy harvest was a mediator in the relationship between the intestinal microbiota (Bacteroides caccae) and weight loss outcomes in patients post-MBS at 18 months (M). The association between the abundance of B. caccae and post-MBS weight loss rate at 18 M was partly mediated by 1 M intestinal energy harvest (β = 0.001 ± 0.001, P = 0.020). This mediation represents 2.83% of the total effect (β = 0.050 ± 0.047; P = 0.028). Intestinal microbiota and energy harvest improved random forest model's accuracy in predicting weight loss results.

CONCLUSION: Energy harvest partly mediates the relationship between the intestinal microbiota and weight loss outcomes among patients post-MBS. This study elucidates a potential mechanism regarding how intestinal energy absorption facilitates the effect of intestinal microbiota on energy metabolism and weight loss outcomes.}, } @article {pmid39195462, year = {2024}, author = {Pan, D and Xiao, P and Li, F and Liu, J and Zhang, T and Zhou, X and Zhang, Y}, title = {High Degree of Polymerization of Chitin Oligosaccharides Produced from Shrimp Shell Waste by Enrichment Microbiota Using Two-Stage Temperature-Controlled Technique of Inducing Enzyme Production and Metagenomic Analysis of Microbiota Succession.}, journal = {Marine drugs}, volume = {22}, number = {8}, pages = {}, pmid = {39195462}, issn = {1660-3397}, support = {32100065//National Natural Science Foundation of China/ ; 32300031//National Natural Science Foundation of China/ ; 2023KJ207//Shandong Province Youth Entrepreneurship Technology Support Program for Higher Education Institutions/ ; ZR2023MB095//Natural Science Foundation of Shandong Province of China/ ; }, mesh = {*Chitin/chemistry ; Animals ; *Oligosaccharides/chemistry ; *Microbiota ; *Chitinases/metabolism ; *Animal Shells/chemistry ; Metagenomics/methods ; Temperature ; Polymerization ; Bacteria ; }, abstract = {The direct enzymatic conversion of untreated waste shrimp and crab shells has been a key problem that plagues the large-scale utilization of chitin biological resources. The microorganisms in soil samples were enriched in two stages with powdered chitin (CP) and shrimp shell powder (SSP) as substrates. The enrichment microbiota XHQ10 with SSP degradation ability was obtained. The activities of chitinase and lytic polysaccharide monooxygenase of XHQ10 were 1.46 and 54.62 U/mL. Metagenomic analysis showed that Chitinolyticbacter meiyuanensis, Chitiniphilus shinanonensis, and Chitinimonas koreensis, with excellent chitin degradation performance, were highly enriched in XHQ10. Chitin oligosaccharides (CHOSs) are produced by XHQ10 through enzyme induction and two-stage temperature control technology, which contains CHOSs with a degree of polymerization (DP) more significant than ten and has excellent antioxidant activity. This work is the first study on the direct enzymatic preparation of CHOSs from SSP using enrichment microbiota, which provides a new path for the large-scale utilization of chitin bioresources.}, } @article {pmid39192744, year = {2024}, author = {Metcalfe-Roach, A and Cirstea, MS and Yu, AC and Ramay, HR and Coker, O and Boroomand, S and Kharazyan, F and Martino, D and Sycuro, LK and Appel-Cresswell, S and Finlay, BB}, title = {Metagenomic Analysis Reveals Large-Scale Disruptions of the Gut Microbiome in Parkinson's Disease.}, journal = {Movement disorders : official journal of the Movement Disorder Society}, volume = {39}, number = {10}, pages = {1740-1751}, doi = {10.1002/mds.29959}, pmid = {39192744}, issn = {1531-8257}, support = {GR008160//Pacific Parkinson's Research Institute/ ; FDN-159935/CAPMC/CIHR/Canada ; PPG-2020-0000000052//Parkinson Canada/ ; FDN-159935/CAPMC/CIHR/Canada ; }, mesh = {Humans ; *Parkinson Disease/microbiology ; *Gastrointestinal Microbiome/genetics/physiology ; Male ; Female ; Aged ; Middle Aged ; *Metagenomics/methods ; *Feces/microbiology ; Disease Progression ; }, abstract = {BACKGROUND: Parkinson's disease (PD) has been consistently linked to alterations within the gut microbiome.

OBJECTIVE: Our goal was to identify microbial features associated with PD incidence and progression.

METHODS: Metagenomic sequencing was used to characterize taxonomic and functional changes to the PD microbiome and to explore their relation to bacterial metabolites and disease progression. Motor and non-motor symptoms were tracked using Movement Disorder Society Unified Parkinson's Disease Rating Scale (MDS-UPDRS) and levodopa equivalent dose across ≤5 yearly study visits. Stool samples were collected at baseline for metagenomic sequencing (176 PD, 100 controls).

RESULTS: PD-derived stool samples had reduced intermicrobial connectivity and seven differentially abundant species compared to controls. A suite of bacterial functions differed between PD and controls, including depletion of carbohydrate degradation pathways and enrichment of ribosomal genes. Faecalibacterium prausnitzii-specific reads contributed significantly to more than half of all differentially abundant functional terms. A subset of disease-associated functional terms correlated with faster progression of MDS-UPDRS part IV and separated those with slow and fast progression with moderate accuracy within a random forest model (area under curve = 0.70). Most PD-associated microbial trends were stronger in those with symmetric motor symptoms.

CONCLUSION: We provide further evidence that the PD microbiome is characterized by reduced intermicrobial communication and a shift to proteolytic metabolism in lieu of short-chain fatty acid production, and suggest that these microbial alterations may be relevant to disease progression. We also describe how our results support the existence of gut-first versus brain-first PD subtypes. © 2024 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.}, } @article {pmid39192682, year = {2024}, author = {Flynn, PJ and Moreau, CS}, title = {Viral diversity and co-evolutionary dynamics across the ant phylogeny.}, journal = {Molecular ecology}, volume = {33}, number = {19}, pages = {e17519}, doi = {10.1111/mec.17519}, pmid = {39192682}, issn = {1365-294X}, support = {2210800//Division of Biological Infrastructure/ ; 1900357//Division of Environmental Biology/ ; //National Science Foundation Graduate Research Fellowship Program/ ; }, mesh = {*Ants/virology/microbiology/genetics ; Animals ; *Phylogeny ; *Biodiversity ; Genome, Viral/genetics ; Metagenome/genetics ; DNA Viruses/genetics/classification ; Bacteria/genetics/virology/classification ; RNA Viruses/genetics/classification ; Ecosystem ; Bacteriophages/genetics/classification ; Virome/genetics ; }, abstract = {Knowledge of viral biodiversity within insects, particularly within ants, is extremely limited with only a few environmental viruses from invasive ant species identified to date. This study documents and explores the viral communities in ants. We comprehensively profile the metagenomes of a phylogenetically broad group of 35 ant species with varied ecological traits and report the discovery of 3710 novel and unique ant-associated viral genomes. These previously unknown viruses discovered within this study constitute over 95% of all currently described ant viruses, significantly increasing our knowledge of the ant virosphere. The identified RNA and DNA viruses fill gaps in insect-associated viral phylogenies and uncover evolutionary histories characterized by both frequent host switching and co-divergence. Many ants also host diverse bacterial communities, and we discovered that approximately one-third of these new ant-associated viruses are bacteriophages. Two ecological categories, bacterial abundance in the host and habitat degradation are both correlated with ant viral diversity and help to structure viral communities within ants. These data demonstrate that the ant virosphere is remarkably diverse phylogenetically and genomically and provide a substantial foundation for studies in virus ecology and evolution within eukaryotes. We highlight the importance of studying insect-associated viruses in natural ecosystems in order to more thoroughly and effectively understand host-microbe evolutionary dynamics.}, } @article {pmid39192352, year = {2024}, author = {Zeng, G and Zeng, L and Wang, Y and Cao, Z and Zeng, X and Xue, Z and Liu, S and Li, Y and He, L}, title = {Correlation between gut microbiota characteristics and non-small cell lung cancer based on macrogenomics sequencing.}, journal = {Hereditas}, volume = {161}, number = {1}, pages = {26}, pmid = {39192352}, issn = {1601-5223}, support = {No. 2023349//Chengdu Municipal Health Commission/ ; }, mesh = {*Carcinoma, Non-Small-Cell Lung/genetics ; Humans ; *Gastrointestinal Microbiome ; *Lung Neoplasms/genetics/microbiology ; Male ; Middle Aged ; Female ; Feces/microbiology ; Aged ; Metagenome ; Metagenomics/methods ; Bacteria/genetics/classification ; }, abstract = {OBJECTIVE: Non-small cell lung cancer (NSCLC) patients undergoing chemotherapy and immunotherapy experience disturbances in the gut microbiota. This study intends to find out the correlation between gut microbiota and clinical indices before and after radiotherapy for NSCLC.

METHODS: Ten patients with primary NSCLC were screened, and plasma and fecal samples were collected before and after radiotherapy, respectively. Inflammatory indices in plasma were detected. Genomic DNA was extracted from fecal specimens and sequenced on on Illumina HiSeq2000 sequencing platform. Thee sequenced data were subjected to Metagenome assembly, gene prediction, species annotation, and gene function analysis to study and analyze gut microbiota and metabolic functions. The correlation between the diversity of gut microbiota and the clinical indicators of NSCLC patients was evaluated, and the changes of gut microbiota before and after radiotherapy were observed.

RESULTS: The diversity of gut microbiota in NSCLC patients did not correlate with smoking, pathology, and inflammatory markers. The abundance of phylum (p)_Bacteroidetes increased; p_Firmicutes and p_Bacteroidetes accounted for the highest proportion in NSCLC patients, and the abundance of both was dominantly exchanged after radiotherapy. There was a decrease in genus (g)_Bifidobacterium after radiotherapy in NSCLC patients. There was no significant correlation between the diversity of gut microbiota after radiotherapy and radiotherapy sensitivity, and the structural composition and abundance of gut microbiota remained stable.

CONCLUSION: The diversity of gut microbiota is altered after radiotherapy in NSCLC patients, showing an increase in harmful bacteria and a decrease in beneficial bacteria.}, } @article {pmid39192220, year = {2024}, author = {Samak, ME and Solyman, SM and Hanora, A and Zakeer, S}, title = {Metagenomic mining of two Egyptian Red Sea sponges associated microbial community.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {315}, pmid = {39192220}, issn = {1471-2180}, support = {59/2020//Academy of Scientific Research and Technology/ ; 6420/2009//SIDA/ ; }, mesh = {*Porifera/microbiology ; Animals ; Indian Ocean ; *Metagenomics ; *Microbiota/genetics ; Egypt ; Bacteria/genetics/classification ; Phylogeny ; Biodiversity ; Multigene Family ; Biological Products/metabolism ; Metagenome ; Proteobacteria/genetics/classification/isolation & purification ; }, abstract = {The Red Sea is a promising habitat for the discovery of new bioactive marine natural products. Sponges associated microorganisms represent a wealthy source of compounds with unique chemical structures and diverse biological activities. Metagenomics is an important omics-based culture-independent technique that is used as an effective tool to get genomic and functional information on sponge symbionts. In this study, we used metagenomic analysis of two Egyptian Red Sea sponges Hyrtios erectus and Phorbas topsenti microbiomes to study the biodiversity and the biosynthetic potential of the Red Sea sponges to produce bioactive compounds. Our data revealed high biodiversity of the two sponges' microbiota with phylum Proteobacteria as the most dominant phylum in the associated microbial community with an average of 31% and 70% respectively. The analysis also revealed high biosynthetic potential of sponge Hyrtios erectus microbiome through detecting diverse types of biosynthetic gene clusters (BGCs) with predicted cytotoxic, antibacterial and inhibitory action. Most of these BGCs were predicted to be novel as they did not show any similarity with any MIBiG database known cluster. This study highlights the importance of the microbiome of the collected Red Sea sponge Hyrtios erectus as a valuable source of new bioactive natural products.}, } @article {pmid39191812, year = {2024}, author = {Feng, Y and Wei, R and Chen, Q and Shang, T and Zhou, N and Wang, Z and Chen, Y and Chen, G and Zhang, G and Dong, K and Zhong, Y and Zhao, H and Hu, F and Zheng, H}, title = {Host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {72}, pmid = {39191812}, issn = {2055-5008}, mesh = {Animals ; *Host Specificity ; *Bacteriophages/genetics/physiology ; *Gastrointestinal Microbiome ; Bees/virology/microbiology ; *Bacteria/virology/genetics/classification ; *Phylogeny ; Metagenomics/methods ; Metagenome ; }, abstract = {Cophylogeny has been identified between gut bacteria and their animal host and is highly relevant to host health, but little research has extended to gut bacteriophages. Here we use bee model to investigate host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system. Through metagenomic sequencing upon different bee species, the gut phageome revealed a more variable composition than the gut bacteriome. Nevertheless, the bacteriome and the phageome showed a significant association of their dissimilarity matrices, indicating a reciprocal interaction between the two kinds of communities. Most of the gut phages were host generalist at the viral cluster level but host specialist at the viral OTU level. While the dominant gut bacteria Gilliamella and Snodgrassella exhibited matched phylogeny with bee hosts, most of their phages showed a diminished level of cophylogeny. The evolutionary rates of the bee, the gut bacteria and the gut phages showed a remarkably increasing trend, including synonymous and non-synonymous substitution and gene content variation. For all of the three codiversified tripartite members, however, their genes under positive selection and genes involving gain/loss during evolution simultaneously enriched the functions into metabolism of nutrients, therefore highlighting the tripartite coevolution that results in an enhanced ecological fitness for the whole holobiont.}, } @article {pmid39191760, year = {2024}, author = {Hartikainen, AK and Jalanka, J and Lahtinen, P and Ponsero, AJ and Mertsalmi, T and Finnegan, L and Crispie, F and Cotter, PD and Arkkila, P and Satokari, R}, title = {Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {73}, pmid = {39191760}, issn = {2055-5008}, support = {316338//Academy of Finland (Suomen Akatemia)/ ; 323156//Academy of Finland (Suomen Akatemia)/ ; }, mesh = {*Irritable Bowel Syndrome/therapy/microbiology ; Humans ; *Fecal Microbiota Transplantation/methods ; *RNA, Ribosomal, 16S/genetics ; Female ; Male ; Adult ; Treatment Outcome ; *Gastrointestinal Microbiome ; Middle Aged ; Feces/microbiology ; Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Imbalanced microbiota may contribute to the pathophysiology of irritable bowel syndrome (IBS), thus fecal microbiota transplantation (FMT) has been suggested as a potential treatment. Previous studies on the relationship between clinical improvement and microbiota after FMT have been inconclusive. In this study, we used 16S rRNA gene amplicon and shotgun metagenomics data from a randomized, placebo controlled FMT trial on 49 IBS patients to analyze changes after FMT in microbiota composition and its functional potential, and to identify connections between microbiota and patients' clinical outcome. As a result, we found that the successful modulation of microbiota composition and functional profiles by FMT from a healthy donor was not associated with the resolution of symptoms in IBS patients. Notably, a donor derived strain of Prevotella copri dominated the microbiota in those patients in the FMT group who had a low relative abundance of P. copri pre-FMT. The results highlight the multifactorial nature of IBS and the role of recipient's microbiota in the colonization of donor's strains.}, } @article {pmid39191378, year = {2024}, author = {da Silva, VG and Smith, NW and Mullaney, JA and Wall, C and Roy, NC and McNabb, WC}, title = {Food-breastmilk combinations alter the colonic microbiome of weaning infants: an in silico study.}, journal = {mSystems}, volume = {9}, number = {9}, pages = {e0057724}, pmid = {39191378}, issn = {2379-5077}, support = {//High-Value Nutrition National Science Challenge/ ; }, mesh = {Humans ; *Milk, Human/chemistry/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Infant ; *Weaning ; *Colon/microbiology/metabolism ; *Computer Simulation ; Fatty Acids, Volatile/metabolism/analysis ; }, abstract = {The introduction of solid foods to infants, also known as weaning, is a critical point for the development of the complex microbial community inhabiting the human colon, impacting host physiology in infancy and later in life. This research investigated in silico the impact of food-breastmilk combinations on growth and metabolite production by colonic microbes of New Zealand weaning infants using the metagenome-scale metabolic model named Microbial Community. Eighty-nine foods were individually combined with breastmilk, and the 12 combinations with the strongest influence on the microbial production of short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs) were identified. Fiber-rich and polyphenol-rich foods, like pumpkin and blackcurrant, resulted in the greatest increase in predicted fluxes of total SCFAs and individual fluxes of propionate and acetate when combined, respectively, with breastmilk. Identified foods were further combined with other foods and breastmilk, resulting in 66 multiple food-breastmilk combinations. These combinations altered in silico the impact of individual foods on the microbial production of SCFAs and BCFAs, suggesting that the interaction between the dietary compounds composing a meal is the key factor influencing colonic microbes. Blackcurrant combined with other foods and breastmilk promoted the greatest increase in the production of acetate and total SCFAs, while pork combined with other foods and breastmilk decreased the production of total BCFAs.IMPORTANCELittle is known about the influence of complementary foods on the colonic microbiome of weaning infants. Traditional in vitro and in vivo microbiome methods are limited by their resource-consuming concerns. Modeling approaches represent a promising complementary tool to provide insights into the behavior of microbial communities. This study evaluated how foods combined with other foods and human milk affect the production of short-chain fatty acids and branched-chain fatty acids by colonic microbes of weaning infants using a rapid and inexpensive in silico approach. Foods and food combinations identified here are candidates for future experimental investigations, helping to fill a crucial knowledge gap in infant nutrition.}, } @article {pmid39189780, year = {2024}, author = {Liu, L and He, X and Wang, J and Li, M and Wei, X and Yang, J and Cheng, G and Du, W and Liu, Z and Xiao, X}, title = {Exploring the associations between gut microbiota composition and SARS-CoV-2 inactivated vaccine response in mice with type 2 diabetes mellitus.}, journal = {mSphere}, volume = {9}, number = {9}, pages = {e0038024}, pmid = {39189780}, issn = {2379-5042}, support = {82002149//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022CFB451//| Natural Science Foundation of Hubei Province ()/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Diabetes Mellitus, Type 2/immunology ; *Mice, Inbred C57BL ; *Vaccines, Inactivated/immunology ; *COVID-19/prevention & control/immunology ; *SARS-CoV-2/immunology ; *Feces/microbiology ; *COVID-19 Vaccines/immunology ; Immunoglobulin G/blood ; RNA, Ribosomal, 16S/genetics ; Lung/microbiology/immunology ; Female ; Male ; Probiotics/administration & dosage ; Antibodies, Viral/blood ; Vaccine Efficacy ; }, abstract = {UNLABELLED: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination is crucial for protecting vulnerable individuals, yet individuals with type 2 diabetes mellitus (T2DM) often exhibit impaired vaccine responses. Emerging evidence suggests that the composition of the host microbiota, crucial in immune regulation and development, influences vaccine efficacy. This study aimed to characterize the relationships between the SARS-CoV-2 inactivated vaccine and the host microbiota (specifically, gut and lung microbiota) of C57BL/6 mice with T2DM. Employing 16S rRNA metagenomic sequencing and ultra-high-performance liquid chromatography-mass spectrometry, we observed lower alpha diversity and distinct beta diversity in fecal microbiota before vaccination and in gut microbiota 28 days post-vaccination between T2DM mice and healthy mice. Compared with healthy mice, T2DM mice showed a higher Firmicutes/Bacteroidetes ratio 28 days post-vaccination. Significant alterations in gut microbiota composition were detected following vaccination, while lung microbiota remained unchanged. T2DM was associated with a diminished initial IgG antibody response against the spike protein, which subsequently normalized after 28 days. Notably, the initial IgG response positively correlated with fecal microbiota alpha diversity pre-vaccination. Furthermore, after 28 days, increased relative abundance of gut probiotics (Bifidobacterium and Lactobacillus) and higher levels of the gut bacterial tryptophan metabolite, indole acrylic acid, were positively associated with IgG levels. These findings suggest a potential link between vaccine efficacy and gut microbiota composition. Nonetheless, further research is warranted to elucidate the precise mechanisms underlying the impact of the gut microbiome on vaccine response. Overall, this study enhances our understanding of the intricate relationships among host microbiota, SARS-CoV-2 vaccination, and T2DM, with potential implications for improving vaccine efficacy.

IMPORTANCE: Over 7 million deaths attributed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by 6 May 2024 underscore the urgent need for effective vaccination strategies. However, individuals with type 2 diabetes mellitus (T2DM) have been identified as particularly vulnerable and display compromised immune responses to vaccines. Concurrently, increasing evidence suggests that the composition and diversity of gut microbiota, crucial regulators of immune function, may influence the efficacy of vaccines. Against this backdrop, our study explores the complex interplay among SARS-CoV-2 inactivated vaccination, T2DM, and host microbiota. We discover that T2DM compromises the initial immune response to the SARS-CoV-2 inactivated vaccine, and this response is positively correlated with specific features of the gut microbiota, such as alpha diversity. We also demonstrate that the vaccination itself induces alterations in the composition and structure of the gut microbiota. These findings illuminate potential links between the gut microbiota and vaccine efficacy in individuals with T2DM, offering valuable insights that could enhance vaccine responses in this high-risk population.}, } @article {pmid39189742, year = {2024}, author = {Wurzbacher, CE and Hammer, J and Haufschild, T and Wiegand, S and Kallscheuer, N and Jogler, C}, title = {"Candidatus Uabimicrobium helgolandensis"-a planctomycetal bacterium with phagocytosis-like prey cell engulfment, surface-dependent motility, and cell division.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0204424}, pmid = {39189742}, issn = {2150-7511}, support = {AWI_BAH_o4//Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (AWI)/ ; EXC 2051 - Project-ID 390713860//German Research foundation/ ; SFB 1076 - Project Number 218627073//German Research foundation/ ; Project-ID 239748522 - CRC 1127 ChemBioSys//German Research foundation/ ; //Studienstiftung des Deutschen Volkes (Studienstiftung)/ ; //Landesgraduiertenstipendium/ ; //Jena School for Microbial Communications/ ; }, mesh = {*Phagocytosis ; *Cell Division ; Phylogeny ; Planctomycetales/genetics/classification/physiology/isolation & purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The unique cell biology presented by members of the phylum Planctomycetota has puzzled researchers ever since their discovery. Initially thought to have eukaryotic-like features, their traits are now recognized as exceptional but distinctly bacterial. However, recently discovered strains again added novel and stunning aspects to the planctomycetal cell biology-shapeshifting by members of the "Saltatorellus" clade to an extent that is unprecedented in any other bacterial phylum, and phagocytosis-like cell engulfment in the bacterium "Candidatus Uabimicrobium amorphum." These recent additions to the phylum Planctomycetota indicate hitherto unexplored members with unique cell biology, which we aimed to make accessible for further investigations. Targeting bacteria with features like "Ca. U. amorphum", we first studied both the morphology and behavior of this microorganism in more detail. While similar to eukaryotic amoeboid organisms at first sight, we found "Ca. U. amorphum" to be rather distinct in many regards. Presenting a detailed description of "Ca. U. amorphum," we furthermore found this organism to divide in a fashion that has never been described in any other organism. Employing the obtained knowledge, we isolated a second "bacterium of prey" from the harbor of Heligoland Island (North Sea, Germany). Our isolate shares key features with "Ca. U. amorphum": phagocytosis-like cell engulfment, surface-dependent motility, and the same novel mode of cell division. Being related to "Ca. U. amorphum" within genus thresholds, we propose the name "Ca. Uabimicrobium helgolandensis" for this strain.IMPORTANCE"Candidatus Uabimicrobium helgolandensis" HlEnr_7 adds to the explored bacterial biodiversity with its phagocytosis-like uptake of prey bacteria. Enrichment of this strain indicates that there might be "impossible" microbes out there, missed by metagenomic analyses. Such organisms have the potential to challenge our understanding of nature. For example, the origin of eukaryotes remains enigmatic, with a contentious debate surrounding both the mitochondrial host entity and the moment of uptake. Currently, favored models involve a proteobacterium as the mitochondrial progenitor and an Asgard archaeon as the fusion partner. Models in which a eukaryotic ancestor engulfed the mitochondrial ancestor via phagocytosis had been largely rejected due to bioenergetic constraints. Thus, the phagocytosis-like abilities of planctomycetal bacteria might influence the debate, demonstrating that prey engulfment is possible in a prokaryotic cellular framework.}, } @article {pmid39189169, year = {2024}, author = {Hejazirad, SP and de Abreu, CM and Carneiro, GHF and Gomes, CR and Spinola Filho, PRC and da Costa, MR and Santos, JBD}, title = {The Impact of Metolachlor Applications and Phytoremediation Processes on Soil Microorganisms: Insights from Functional Metagenomics Analysis.}, journal = {Journal of xenobiotics}, volume = {14}, number = {3}, pages = {970-988}, pmid = {39189169}, issn = {2039-4713}, support = {PQD//National Council for Scientific and Technological Development/ ; 00097-22//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 001//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; }, abstract = {This study assessed the impact of phytoremediation on reducing the residual concentration of metolachlor in soil treated with doses of 530.7 and 1061.4 g/ha and its effect on microbial biodiversity in contaminated areas. For the plant species Avena sativa and Medicago sativa, a significant efficacy of 54.5 and 36.4% was observed in the dissipation of the herbicide, especially at higher doses. Although metolachlor application reduced soil microbial biodiversity, phytoremediating plants, especially M. sativa, promoted greater richness and distribution of microbial species, mitigating the negative effects of the herbicide. Principal component analysis revealed the influence of these plants and metolachlor on the composition of the microbial community. These results highlight the importance of phytoremediation in promoting soil biodiversity and reducing herbicide contamination, providing crucial insights for remediation strategies in contaminated areas.}, } @article {pmid39189041, year = {2024}, author = {Haussmann, AJ and McMahan, ZH and Volkmann, ER}, title = {Understanding the gastrointestinal microbiome in systemic sclerosis: methodological advancements and emerging research.}, journal = {Current opinion in rheumatology}, volume = {36}, number = {6}, pages = {401-409}, pmid = {39189041}, issn = {1531-6963}, support = {K23 HL150237/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Scleroderma, Systemic/microbiology ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; Fecal Microbiota Transplantation/methods ; }, abstract = {PURPOSE OF REVIEW: This review highlights the role of the gastrointestinal (GI) microbiome in systemic sclerosis (SSc). We describe techniques for evaluating the GI microbiome in humans, and emerging research linking GI microbiome alterations (i.e., dysbiosis) and distinct SSc clinical manifestations. We also address the evolving treatment landscape targeting dysbiosis in SSc.

RECENT FINDINGS: Recent literature brings into focus the complex relationship between the GI microbiome and SSc pathogenesis. Advanced techniques (e.g., shotgun metagenomics, meta-transcriptomics) provide deeper insights into microbial taxonomy and active gene expression, exposing dysbiosis as a potential driver of SSc. New studies demonstrate that SSc patients who possess specific SSc clinical features, (e.g., interstitial lung disease), have unique GI microbiome profiles.

SUMMARY: Dysbiosis is associated with specific clinical features in patients with SSc. New tools for studying the GI microbiome have furthered our understanding of the relationship between dysbiosis and SSc complications. Therapeutic avenues such as dietary adjustments, probiotics, antibiotics, mindfulness practices, and fecal transplants offer potential for managing SSc and preventing its progression through GI microbiome modulation. By clarifying what is known about the relationship between the GI dysbiosis, GI dysfunction, and SSc, this review enhances our understanding of SSc pathogenesis and proposes targeted interventions.}, } @article {pmid39187802, year = {2024}, author = {Anitua, E and Murias-Freijo, A and Tierno, R and Tejero, R and Alkhraisat, MH}, title = {Assessing peri-implant bacterial community structure: the effect of microbiome sample collection method.}, journal = {BMC oral health}, volume = {24}, number = {1}, pages = {1001}, pmid = {39187802}, issn = {1472-6831}, mesh = {Humans ; *Microbiota ; *Biofilms ; *Gingival Crevicular Fluid/microbiology ; *Dental Implants/microbiology ; Middle Aged ; Specimen Handling/methods ; Female ; Male ; High-Throughput Nucleotide Sequencing ; Bacteria/classification/isolation & purification ; Aged ; }, abstract = {BACKGROUND: Oral microbiota comprises polymicrobial communities shaped by mutualistic coevolution with the host, contributing to homeostasis and regulating immune function. Nevertheless, dysbiosis of oral bacterial communities is associated with a number of clinical symptoms that ranges from infections to oral cancer. Peri-implant diseases are biofilm-associated inflammatory conditions affecting the soft and hard tissues around dental implants. Characterization and identification of the biofilm community are essential for the understanding of the pathophysiology of such diseases. For that sampling methods should be representative of the biofilm communities Therefore, there is a need to know the effect of different sampling strategies on the biofilm characterization by next generation sequencing.

METHODS: With the aim of selecting an appropriate microbiome sampling procedure for periimplant biofilms, next generation sequencing was used for characterizing the bacterial communities obtained by three different sampling strategies two months after transepithelial abutment placement: adjacent periodontal crevicular fluid (ToCF), crevicular fluid from transepithelial abutment (TACF) and transepithelial abutment (TA).

RESULTS: Significant differences in multiple alpha diversity indices were detected at both the OTU and the genus level between different sampling procedures. Differentially abundant taxa were detected between sample collection strategies, including peri-implant health and disease related taxa. At the community level significant differences were also detected between TACF and TA and also between TA and ToCF. Moreover, differential network properties and association patterns were identified.

CONCLUSIONS: The selection of sample collection strategy can significantly affect the community composition and structure.

TRIAL REGISTRATION: This research is part of a randomized clinical trial that was designed to assess the effect of transepithelial abutment surface on the biofilm formation. The trial was registered at Trial Registration ClinicalTrials.gov under the number NCT03554876.}, } @article {pmid39186442, year = {2024}, author = {Chen, Y and Ma, W and Zhao, J and Stanton, C and Ross, RP and Zhang, H and Chen, W and Yang, B}, title = {Lactobacillus plantarum Ameliorates Colorectal Cancer by Ameliorating the Intestinal Barrier through the CLA-PPAR-γ Axis.}, journal = {Journal of agricultural and food chemistry}, volume = {72}, number = {36}, pages = {19766-19785}, doi = {10.1021/acs.jafc.4c02824}, pmid = {39186442}, issn = {1520-5118}, mesh = {*Lactobacillus plantarum/metabolism ; *PPAR gamma/metabolism/genetics ; Animals ; Mice ; *Colorectal Neoplasms/metabolism ; Humans ; *Probiotics/administration & dosage/pharmacology ; Male ; *Linoleic Acids, Conjugated/pharmacology/metabolism ; *Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; *Intestinal Mucosa/metabolism/microbiology ; Female ; NF-kappa B/metabolism/genetics ; Apoptosis/drug effects ; Claudin-1/metabolism/genetics ; Zonula Occludens-1 Protein/metabolism/genetics ; }, abstract = {Colorectal cancer (CRC) is the third-largest cancer worldwide. Lactobacillus can regulate the intestinal barrier and gut microbiota. However, the mechanisms of Lactobacillus that alleviate CRC remained unknown. This study aimed to explore the regulatory effect of Lactobacillus plantarum on CRC and its potential mechanism. CCFM8661 treatment significantly ameliorated CRC compared with phosphate-buffered solution (PBS) treatment in Apc[Min/+] mice. In addition, conjugated linoleic acid (CLA) was proved to be the key metabolite for CCFM8661 in ameliorating CRC by molecular biology techniques. Peroxisome proliferator-activated receptor γ (PPAR-γ) was proved to be the key receptor in ameliorating CRC by inhibitor intervention experiments. Moreover, supplementation with CCFM8661 ameliorated CRC by producing CLA to inhibit NF-κB pathway and pro-inflammatory cytokines, up-regulate ZO-1, Claudin-1, and MUC2, and promote tumor cell apoptosis in a PPAR-γ-dependent manner. Metagenomic analysis showed that CCFM8661 treatment significantly increased Odoribacter splanchnicus, which could ameliorate CRC by repairing the intestinal barrier. Clinical results showed that intestinal CLA, butyric acid, PPAR-γ, and Lactobacillus were significantly decreased in CRC patients, and these indicators were significantly negatively correlated with CRC. CCFM8661 alleviated CRC by ameliorating the intestinal barrier through the CLA-PPAR-γ axis. These results will promote the development of dietary probiotic supplements for CRC.}, } @article {pmid39185682, year = {2024}, author = {Maqsood, R and Holland, LA and Wu, LI and Begnel, ER and Adhiambo, J and Owiti, P and Chohan, BH and Gantt, S and Kinuthia, J and Wamalwa, D and Ojee, E and Richardson, BA and Slyker, J and Lehman, DA and Lim, ES}, title = {Gut virome and microbiome dynamics before and after SARS-CoV-2 infection in women living with HIV and their infants.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2394248}, pmid = {39185682}, issn = {1949-0984}, support = {R01 HD092311/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; Female ; *COVID-19/microbiology/virology ; *HIV Infections/microbiology/virology ; *Virome ; *Gastrointestinal Microbiome ; *SARS-CoV-2/genetics/isolation & purification ; Adult ; Infant, Newborn ; *Feces/microbiology/virology ; Infant ; Bacteria/classification/isolation & purification/genetics ; Longitudinal Studies ; }, abstract = {Microbiome perturbations can have long-term effects on health. The dynamics of the gut microbiome and virome in women living with HIV (WLHIV) and their newborn infants is poorly understood. Here, we performed metagenomic sequencing analyses on longitudinal stool samples including 23 mothers (13 WLHIV, 10 HIV-negative) and 12 infants that experienced SARS-CoV-2 infection with mild disease, as well as 40 mothers (18 WLHIV, 22 HIV-negative) and 60 infants that remained SARS-CoV-2 seronegative throughout the study follow-up. Regardless of HIV or SARS-CoV-2 status, maternal bacterial and viral profiles were distinct from infants. Using linear mixed effects models, we showed that the microbiome alpha diversity trajectory was not significantly different between SARS-CoV-2 seropositive and seronegative women. However, seropositive women's positive trajectory while uninfected was abruptly reversed after SARS-CoV-2 infection (p = 0.015). Gut virome signatures of women were not associated with SARS-CoV-2. Alterations in infant microbiome and virome diversities were generally not impacted by SARS-CoV-2 but were rather driven by development. We did not find statistically significant interactions between HIV and SARS-CoV-2 on the gut microbiome and virome. Overall, our study provides insights into the complex interplay between maternal and infant bacterial microbiome, virome, and the influence of SARS-CoV-2 and HIV status.}, } @article {pmid39185088, year = {2024}, author = {Hu, L and Xu, Y and Li, J and Zhang, M and Sun, Z and Ban, Y and Tian, X and Liu, D and Hu, L}, title = {Gut microbiome characteristics of women with hypothyroidism during early pregnancy detected by 16S rRNA amplicon sequencing and shotgun metagenomic.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1369192}, pmid = {39185088}, issn = {2235-2988}, mesh = {Humans ; Female ; Pregnancy ; *Hypothyroidism/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Adult ; *Dysbiosis/microbiology ; Bacteria/classification/genetics/isolation & purification ; Pregnancy Complications/microbiology ; Metagenome ; Feces/microbiology ; }, abstract = {OBJECTIVE: This study aimed to explore the correlation between microbiota dysbiosis and hypothyroidism in early pregnancy by 16S rRNA amplicon sequencing combined with metagenomic sequencing.

METHODS: Sixty pregnant women (30 with hypothyroidism and 30 normal controls) were recruited for 16S rRNA amplicon sequencing, and 6 patients from each group were randomly selected for metagenomic sequencing to assess the gut microbiome profile.

RESULTS: The 16S rRNA results showed that beta-diversity in the hypothyroidism group was decreased. The relative abundances of the Prevotella and Paraprevotella genera increased in the hypothyroidism group, and Blautia predominated in the controls. The metagenomics results revealed that Prevotella_stercorea_CAG_629, Prevotella_hominis, Prevotella_sp_AM34_19LB, etc. were enriched in the hypothyroidism group at the species level. Functional analysis revealed that the pyridoxal 5'-phosphate synthase pdxT subunit module was decreased, and the short-chain fatty acid (SCFA) transporter and phospholipase/carboxylesterase modules were strongly enriched in the hypothyroidism group. Hypothyroidism patients had increased C-reactive protein (CRP), interleukin-2 (IL-2), IL-4, IL-10, and tumor necrosis factor (TNF)-α levels. The pyridoxal 5'-phosphate synthase pdxT subunit, the SCFA transporter, and the phospholipase/carboxylesterase module were associated with different Prevotella species.

CONCLUSION: In early pregnancy, women with hypothyroidism exhibit microbiota dysbiosis, and Prevotella may affect the metabolism of glutamate, SCFA, and phospholipases, which could be involved in the development of hypothyroidism during pregnancy.}, } @article {pmid39185086, year = {2024}, author = {Wang, X and Xiao, T and Lu, M and Wu, Z and Chen, L and Zhang, Z and Lu, W}, title = {Lower respiratory tract microbiome and lung cancer risk prediction in patients with diffuse lung parenchymal lesions.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1410681}, pmid = {39185086}, issn = {2235-2988}, mesh = {Humans ; *Lung Neoplasms/microbiology/pathology ; Male ; Female ; *Microbiota ; Middle Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; Retrospective Studies ; Aged ; Lung/microbiology/pathology/diagnostic imaging ; High-Throughput Nucleotide Sequencing ; Adult ; Respiratory System/microbiology ; Metagenomics/methods ; Risk Factors ; }, abstract = {OBJECTIVE: In clinical practice, imaging manifestations of diffuse lung parenchymal lesions are common and indicative of various diseases, making differential diagnosis difficult. Some of these lesions are eventually diagnosed as lung cancer.

METHODS: Because respiratory microorganisms play an important role in lung cancer development, we searched for microbial markers that could predict the risk of lung cancer by retrospectively analyzing the lower respiratory tract (LRT) microbiome of 158 patients who were hospitalized in the First Affiliated Hospital of Guangzhou Medical University (March 2021-March 2023) with diffuse lung parenchymal lesions. The final diagnosis was lung cancer in 21 cases, lung infection in 93 cases, and other conditions (other than malignancy and infections) in 44 cases. The patient's clinical characteristics and the results of metagenomic next-generation sequencing of bronchoalveolar lavage fluid (BALF) were analyzed.

RESULTS: Body mass index (BMI) and LRT microbial diversity (Shannon, Simpson, species richness, and Choa1 index) were significantly lower (P< 0.001, respectively) and Lactobacillus acidophilus relative abundance in the LRT was significantly higher (P< 0.001) in patients with lung cancer. The relative abundance of L. acidophilus in BALF combined with BMI was a good predictor of lung cancer risk (area under the curve = 0.985, accuracy = 98.46%, sensitivity = 95.24%, and specificity = 100.00%; P< 0.001).

CONCLUSION: Our study showed that an imbalance in the component ratio of the microbial community, diminished microbial diversity, and the presence of specific microbial markers in the LRT predicted lung cancer risk in patients with imaging manifestations of diffuse lung parenchymal lesions.}, } @article {pmid39182818, year = {2024}, author = {Fang, C and Liu, KD and Tian, FJ and Li, JY and Li, SJ and Zhang, RM and Sun, J and Fang, LX and Ren, H and Wang, MG and Liao, XP}, title = {Metagenomic analysis unveiled the response of microbial community and antimicrobial resistome in natural water body to duck farm sewage.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {361}, number = {}, pages = {124784}, doi = {10.1016/j.envpol.2024.124784}, pmid = {39182818}, issn = {1873-6424}, mesh = {*Ducks ; Animals ; *Sewage/microbiology ; *Microbiota/drug effects ; Farms ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Environmental Monitoring ; Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Sewages from duck farms are often recognized as a major source of antimicrobial resistance and pathogenic bacteria discharged to natural water bodies, but few studies depicted the dynamic changes in resistome and microbial communities in the rivers under immense exposure of sewage discharge. In this study, we investigated the ecological and environmental risks of duck sewages to the rivers that geographically near to the duck farms with short-distance (<1 km) using 16S rRNA amplicon and metagenomic sequencing. The results showed that a total of 20 ARG types were identified with abundances ranged from 0.61 to 1.33 cpc. Of note, the genes modulate resistances against aminoglycoside, bacitracin and beta-lactam were the most abundant ARGs. Limnohabitans, Fluviibacter and Cyanobium were the top 3 predominant genera in the microbial community. The alpha diversity of overall microbial community decrease while the abundance of pathogen increase during the input of sewage within 200 m. Sul1 and bacA were the dominant ARGs brought from duck farm sewage. The community variations of ARGs and microbiome were primarily driven by pH and temperature. Total phosphorus was significantly correlated to alpha diversity and top 30 ARGs subtype. Stochastic processes was the dominated microbial assembly pattern and did not be altered by sewage. We also highlighted the ecological risk caused by blaGES which possibly could be mitigated by Cyanobacteria, and the natural water body can purify partial ARGs as well as microbiome from duck farms sewage. These findings expanded our knowledge regarding the ecological risks by wastes from the livestock farm, and underscoring the necessity to monitor ARGs in farm-surrounding water bodies.}, } @article {pmid39182764, year = {2024}, author = {Zhao, Y and Tan, J and Fang, L and Jiang, L}, title = {Harnessing meta-omics to unveil and mitigate methane emissions in ruminants: Integrative approaches and future directions.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175732}, doi = {10.1016/j.scitotenv.2024.175732}, pmid = {39182764}, issn = {1879-1026}, mesh = {*Methane/metabolism ; Animals ; *Ruminants ; Metabolomics ; Metagenomics ; Air Pollutants/analysis ; Greenhouse Gases ; Rumen/metabolism ; Gastrointestinal Microbiome ; Genomics ; }, abstract = {Methane emissions from enteric fermentation present a dual challenge globally: they not only contribute significantly to atmospheric greenhouse gases but also represent a considerable energy loss for ruminant animals. Utilizing high-throughput omics technologies to analyze rumen microbiome samples (meta-omics, i.e., metagenomics, metatranscriptomics, metaproteomics, metabolomics) holds vast potential for uncovering the intricate interplay between diet, microbiota, and methane emissions in these animals. The primary obstacle is the effective integration of diverse meta-omic approaches and their broader application across different ruminant species. Genetic variability significantly impacts methane production in ruminants, suggesting that genomic selection could be a viable strategy to reduce emissions. While substantial research has been conducted on the microbiological aspects of methane production, there remains a critical need to delineate the specific genetic interactions between the host and its microbiome. Advancements in meta-omics technologies are poised to shed light on these interactions, enhancing our understanding of the genetic factors that govern methane output. This review explores the potential of meta-omics to accelerate genetic advancements that could lead to reduced methane emissions in ruminants. By employing a systems biology approach, the integration of various omics technologies allows for the identification of key genomic regions and genetic markers linked to methane production. These markers can then be leveraged in selective breeding programs to cultivate traits associated with lower emissions. Moreover, the review addresses current challenges in applying genomic selection for this purpose and discusses how omics technologies can overcome these obstacles. The systematic integration and analysis of diverse biological data provide deeper insights into the genetic underpinnings and overall biology of methane production traits in ruminants. Ultimately, this comprehensive approach not only aids in reducing the environmental impact of agriculture but also contributes to the sustainability and efficiency of livestock management.}, } @article {pmid39182301, year = {2024}, author = {Peruzzo, A and Petrin, S and Boscolo Anzoletti, A and Mancin, M and Di Cesare, A and Sabatino, R and Lavagnolo, MC and Beggio, G and Baggio, G and Danesi, P and Barco, L and Losasso, C}, title = {The integration of omics and cultivation-dependent methods could effectively determine the biological risks associated with the utilization of soil conditioners in agriculture.}, journal = {Journal of hazardous materials}, volume = {478}, number = {}, pages = {135567}, doi = {10.1016/j.jhazmat.2024.135567}, pmid = {39182301}, issn = {1873-3336}, mesh = {*Agriculture ; *Soil Microbiology ; *Sewage/microbiology ; *Bacteria/genetics ; Soil/chemistry ; Composting ; Metagenomics ; Fertilizers ; }, abstract = {In the circular economy, reusing agricultural residues, treated biowaste, and sewage sludges-commonly referred to as soil conditioners-in agriculture is essential for converting waste into valuable resources. However, these materials can also contribute to the spread of antimicrobial-resistant pathogens in treated soils. In this study, we analyzed different soil conditioners categorized into five groups: compost from source-separated biowaste and green waste, agro-industrial digestate, digestate from anaerobic digestion of source-separated biowaste, compost from biowaste digestate, and sludges from wastewater treatment plants. Under Italian law, only the first two categories are approved for agricultural use, despite Regulation 1009/2019/EU allowing the use of digestate from anaerobic digestion of source-separated biowaste in CE-marked fertilizers. We examined the bacterial community and associated resistome of each sample using metagenomic approaches. Additionally, we detected and isolated various pathogens to provide a comprehensive understanding of the potential risks associated with sludge application in agriculture. The compost samples exhibited higher bacterial diversity and a greater abundance of potentially pathogenic bacteria compared to other samples, except for wastewater treatment plant sludges, which had the highest frequency of Salmonella isolation and resistome diversity. Our findings suggest integrating omics and cultivation-dependent methods to accurately assess the biological risks of using sludge in agriculture.}, } @article {pmid39182227, year = {2024}, author = {Chilton, PM and Ghare, SS and Charpentier, BT and Myers, SA and Rao, AV and Petrosino, JF and Hoffman, KL and Greenwell, JC and Tyagi, N and Behera, J and Wang, Y and Sloan, LJ and Zhang, J and Shields, CB and Cooper, GE and Gobejishvili, L and Whittemore, SR and McClain, CJ and Barve, SS}, title = {Age-associated temporal decline in butyrate-producing bacteria plays a key pathogenic role in the onset and progression of neuropathology and memory deficits in 3×Tg-AD mice.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2389319}, pmid = {39182227}, issn = {1949-0984}, support = {P20 GM113226/GM/NIGMS NIH HHS/United States ; R01 AG061065/AG/NIA NIH HHS/United States ; U01 AA022618/AA/NIAAA NIH HHS/United States ; P50 AA024337/AA/NIAAA NIH HHS/United States ; U01 AA026936/AA/NIAAA NIH HHS/United States ; I01 CX002219/CX/CSRD VA/United States ; }, mesh = {Animals ; *Butyrates/metabolism ; *Gastrointestinal Microbiome ; Mice ; *Alzheimer Disease/microbiology/pathology/metabolism ; *Memory Disorders/microbiology/metabolism/pathology ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Disease Models, Animal ; *Dysbiosis/microbiology ; Hippocampus/metabolism/pathology ; Mice, Transgenic ; Male ; Disease Progression ; Brain-Gut Axis/physiology ; Brain/metabolism/pathology ; }, abstract = {Alterations in the gut-microbiome-brain axis are increasingly being recognized to be involved in Alzheimer's disease (AD) pathogenesis. However, the functional consequences of enteric dysbiosis linking gut microbiota and brain pathology in AD progression remain largely undetermined. The present work investigated the causal role of age-associated temporal decline in butyrate-producing bacteria and butyrate in the etiopathogenesis of AD. Longitudinal metagenomics, neuropathological, and memory analyses were performed in the 3×Tg-AD mouse model. Metataxonomic analyses showed a significant temporal decline in the alpha diversity marked by a decrease in butyrate-producing bacterial communities and a concurrent reduction in cecal butyrate production. Inferred metagenomics analysis identified the bacterial acetyl-CoA pathway as the main butyrate synthesis pathway impacted. Concomitantly, there was an age-associated decline in the transcriptionally permissive acetylation of histone 3 at lysines 9 and 14 (H3K9/K14-Ac) in hippocampal neurons. Importantly, these microbiome-gut-brain changes preceded AD-related neuropathology, including oxidative stress, tau hyperphosphorylation, memory deficits, and neuromuscular dysfunction, which manifest by 17-18 months. Initiation of oral administration of tributyrin, a butyrate prodrug, at 6 months of age mitigated the age-related decline in butyrate-producing bacteria, protected the H3K9/K14-Ac status, and attenuated the development of neuropathological and cognitive changes associated with AD pathogenesis. These data causally implicate age-associated decline in butyrate-producing bacteria as a key pathogenic feature of the microbiome-gut-brain axis affecting the onset and progression of AD. Importantly, the regulation of butyrate-producing bacteria and consequent butyrate synthesis could be a significant therapeutic strategy in the prevention and treatment of AD.}, } @article {pmid39182035, year = {2024}, author = {Velázquez-Fernández, JB and Aceves Suriano, CE and Thalasso, F and Montoya-Ciriaco, N and Dendooven, L}, title = {Structural and functional bacterial biodiversity in a copper, zinc and nickel amended bioreactor: shotgun metagenomic study.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {313}, pmid = {39182035}, issn = {1471-2180}, mesh = {*Bioreactors/microbiology ; *Zinc/metabolism ; *Nickel/metabolism ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Metagenomics ; *Copper/metabolism ; *Biodiversity ; Wastewater/microbiology/chemistry ; }, abstract = {BACKGROUND: At lower concentrations copper (Cu), zinc (Zn) and nickel (Ni) are trace metals essential for some bacterial enzymes. At higher concentrations they might alter and inhibit microbial functioning in a bioreactor treating wastewater. We investigated the effect of incremental concentrations of Cu, Zn and Ni on the bacterial community structure and their metabolic functions by shotgun metagenomics. Metal concentrations reported in previous studies to inhibit bacterial metabolism were investigated.

RESULTS: At 31.5 μM Cu, 112.4 μM Ni and 122.3 μM Zn, the most abundant bacteria were Achromobacter and Agrobacterium. When the metal concentration increased 2 or fivefold their abundance decreased and members of Delftia, Stenotrophomonas and Sphingomonas dominated. Although the heterotrophic metabolic functions based on the gene profile was not affected when the metal concentration increased, changes in the sulfur biogeochemical cycle were detected. Despite the large variations in the bacterial community structure when concentrations of Cu, Zn and Ni increased in the bioreactor, functional changes in carbon metabolism were small.

CONCLUSIONS: Community richness and diversity replacement indexes decreased significantly with increased metal concentration. Delftia antagonized Pseudomonas and members of Xanthomonadaceae. The relative abundance of most bacterial genes remained unchanged despite a five-fold increase in the metal concentration, but that of some EPS genes required for exopolysaccharide synthesis, and those related to the reduction of nitrite to nitrous oxide decreased which may alter the bioreactor functioning.}, } @article {pmid39181304, year = {2024}, author = {Yu, Y and Ai, T and Huang, J and Jin, L and Yu, X and Zhu, X and Sun, J and Zhu, L}, title = {Metabolism of isodecyl diphenyl phosphate in rice and microbiome system: Differential metabolic pathways and underlying mechanisms.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {361}, number = {}, pages = {124803}, doi = {10.1016/j.envpol.2024.124803}, pmid = {39181304}, issn = {1873-6424}, mesh = {*Oryza/metabolism/microbiology ; *Microbiota ; *Rhizosphere ; Metabolic Networks and Pathways ; Soil Pollutants/metabolism ; Organophosphorus Compounds/metabolism ; Soil Microbiology ; Organophosphates/metabolism ; }, abstract = {Isodecyl diphenyl phosphate (IDDP) is among the emerging aromatic organophosphate esters (aryl-OPEs) that pose risks to both human beings and other organisms. This study aims to investigate the translocation and biotransformation behavior of IDDP in rice and the rhizosphere microbiome through hydroponic exposure (the duration of hydroponic exposure was 10 days). The rhizosphere microbiome 9-FY was found to efficiently eliminate IDDP, thereby reducing its uptake in rice tissues and mitigating the negative impact of IDDP on rice growth. Furthermore, this study proposed the first-ever transformation pathways of IDDP, identifying hydrolysis, hydroxylation, methylation, methoxylation, carboxylation, and glucuronidation products. Notably, the methylation and glycosylation pathways were exclusively observed in rice, indicating that the transformation of IDDP in rice may be more complex than in microbiome 9-FY. Additionally, the presence of the product COOH-IDDP in rice suggested that there might be an exchange of degradation products between rice and rhizobacteria, implying their potential interaction. This finding highlights the significance of rhizobacteria's role which cannot be overlooked in the accumulation and transformation of organic pollutants in grain crops. The study revealed active members in 9-FY during IDDP degradation, and metagenomic analysis indicated that most of the active populations contained IDDP-degrading genes. Moreover, transcriptome sequencing showed that cytochrome P450, acid phosphatase, glucosyltransferase, and methyltransferases genes in rice were up-regulated, which was further confirmed by RT-qPCR. This provides insight into the intermediate products identified in rice, such as hydrolysis, hydroxylated, glycosylated, and methylated products. These results significantly contribute to our understanding of the translocation and transformation of organophosphate esters (OPEs) in plants and the rhizosphere microbiome, and reveal the fate of OPEs in rice and microbiome system to ensure the paddy yield and rice safety.}, } @article {pmid39181265, year = {2024}, author = {Dong, W and Zhou, J and Zhang, CJ and Yang, Q and Li, M}, title = {Methylotrophic substrates stimulated higher methane production than competitive substrates in mangrove sediments.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175677}, doi = {10.1016/j.scitotenv.2024.175677}, pmid = {39181265}, issn = {1879-1026}, mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Wetlands ; China ; Microbiota ; Bacteria/metabolism/classification ; }, abstract = {Although mangrove forests can uptake atmospheric CO2 and store carbon as organic matter called "blue carbon", it is also an important natural source of greenhouse gas methane. Methanogens are major contributors to methane and play important roles in the global carbon cycle. However, our understanding of the key microbes and metabolic pathways responsible for methanogenesis under specific substrates in mangrove sediments is still very limited. Here, we set an anaerobic incubation to evaluate the responses of methanogens in mangrove sediments from South China to the addition of diverse methanogenic substrates (H2/CO2, acetate, trimethylamine (TMA), and methanethiol (MT)) and further investigated the dynamics of the whole microbial community. Our results showed that diverse substrates stimulated methanogenic activities at different times. The stimulation of methanogenesis was more pronounced at early and late periods by the addition of methylotrophic substrates TMA and MT, respectively. The amplicon sequencing analysis showed that genus Methanococcoides was mainly responsible for TMA-utilized methanogenesis in mangrove sediment, while the multitrophic Methanococcus was most abundant in H2/CO2 and MT treatments. Apart from that, the bacteria enrichments of Syntrophotalea, Clostridium_sensu_stricto_12, Fusibacter in MT treatments might also be associated with the stimulation of methane production. In addition, the metagenomic analysis suggested that Methanosarcinaceae was also one of the key methanogens in MT treatments with different genomic information compared to that in TMA treatments. Finally, the total relative abundances of methanogenesis-related genes were also highest in TMA and MT treatments. These results will help advance our understanding of the contributions of different methanogenesis pathways and methanogens to methane emissions in mangrove sediments.}, } @article {pmid39180723, year = {2024}, author = {Jiang, L and Hao, Y and Han, D and Dong, W and Yang, A and Sun, Z and Ge, Y and Duan, S and Zhang, X and Dai, Z}, title = {Gut microbiota dysbiosis deteriorates immunoregulatory effects of tryptophan via colonic indole and LBP/HTR2B-mediated macrophage function.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39180723}, issn = {1751-7370}, support = {2022YFA1304204//National Key Research and Development Program of China/ ; 32072689//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/microbiology ; Mice ; *Colitis/chemically induced/immunology/microbiology ; *Tryptophan/metabolism ; *Indoles/pharmacology ; *Macrophages/immunology/drug effects ; *Mice, Inbred C57BL ; *Colon/microbiology/immunology ; *Disease Models, Animal ; *Carrier Proteins/genetics/metabolism ; *Dextran Sulfate ; Acute-Phase Proteins/metabolism ; Male ; Fecal Microbiota Transplantation ; Anti-Bacterial Agents/pharmacology ; Signal Transduction ; Membrane Glycoproteins ; }, abstract = {Tryptophan (Trp) has been shown to regulate immune function by modulating gut serotonin (5-HT) metabolism and signaling. However, the mechanisms underlying the microbial modulation of gut 5-HT signaling in gut inflammation with gut microbiota dysbiosis require further investigation. Here, we investigated the effects of Trp supplementation on the composition and metabolism of the gut microbiome and 5-HT signaling-related gut immune function using a dextran sodium sulfate (DSS)-induced colitis mouse model coupled with antibiotic exposure. The results showed that antibiotic treatment before but not during DSS treatment decreased the immunoregulatory effects of Trp and aggravated gut inflammation and body weight loss in mice. Metagenomic analysis revealed that the fecal microbiota transplantation of Trp-enriched gut microbiota to recipient mice subject to antibiotic pre-exposure and DSS treatment alleviated inflammation by increasing the relative abundances of Lactobacillus and Parabacteroides and the microbial production of indole coupled with the activation of the 5-HT receptor 2B (HTR2B) in the colon. Transcriptomic analysis showed that HTR2B agonist administration strengthened the beneficial effects of Trp in DSS-induced colitis mice with antibiotic exposure by reducing gut lipopolysaccharide-binding protein (LBP) production, IκB-α/nuclear factor-κB signaling, and M1 macrophage polarization. Indole treatment reduced LBP production and M1 macrophage polarization both in mice with DSS-induced colitis and in lipopolysaccharide-treated mouse macrophages; however, the HTR2B antagonist reversed the effects of indole. Our findings provide the basis for developing new dietary and therapeutic interventions to improve gut microbiota dysbiosis-associated inflammatory gut disorders and diseases.}, } @article {pmid39180208, year = {2024}, author = {Wang, YC and Jiang, TM and Mo, L and Lu, HZ and Quan, LH and Zhong, P and Guan, Y}, title = {Distribution of Antibiotic-Resistant Genes in Intestines of Infants and Influencing Factors.}, journal = {Critical reviews in eukaryotic gene expression}, volume = {34}, number = {8}, pages = {59-73}, pmid = {39180208}, issn = {1045-4403}, mesh = {Humans ; Female ; *Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Milk, Human/microbiology ; Infant ; Infant, Newborn ; Intestines/microbiology ; Male ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Gastrointestinal Microbiome/genetics/drug effects ; Bacteria/genetics/drug effects ; Drug Resistance, Microbial/genetics ; }, abstract = {The objective of this study is to assess the prevalence of antibiotic-resistant genes (ARGs) in the intestines of infants and the factors affecting their distribution. Breast milk and infant stool samples were collected from nine full-term, healthy mother-infant pairs. The bacterial distribution and various types of ARGs present in the samples were analyzed using metagenomic next-generation sequencing. Over a period spanning from 2 to 240 d after birth, a total of 273 types of ARGs were identified in both infant feces and breast milk, exhibiting a trend of increasing prevalence over time. High concentrations of representative ARG populations were identified in the intestines of infants, especially at 12-15 d after birth. These populations included APH3-Ib, tetW/N/W, mphA, and Haemophilus influenzae PBP3, and multiple ARG Escherichia coli soxS that were resistant to common clinically used aminoglycoside, tetracycline, macrolide, and beta-lactam antibiotics. Gammaproteobacteria and Bacilli, especially Enterococcus, Staphylococcus, Acinetobacter, Streptococcus, and Escherichia were among the identified ARG carriers. Maternal age and body mass index (present and before pregnancy), infant sex, maternal consumption of probiotic yogurt during pregnancy, and lactation might be substantial factors influencing the occurrence of ARG-carrying bacteria and ARG distribution in the infant feces. These results indicate that environmental factors may influence the distribution of ARG-carrying bacteria and ARGs themselves in infants during early life. Providing appropriate recommendations regarding maternal age, body mass index during pregnancy, and use of probiotic products could potentially mitigate the transmission of antibiotic-resistant microbiota and ARGs, thereby diminishing the risk of antibiotic-resistant infections and safeguarding children's health.}, } @article {pmid39180123, year = {2024}, author = {Horigan, S and Kettenburg, G and Kistler, A and Ranaivoson, HC and Andrianiaina, A and Andry, S and Raharinosy, V and Randriambolamanantsoa, TH and Tato, CM and Lacoste, V and Heraud, JM and Dussart, P and Brook, CE}, title = {Detection, characterization, and phylogenetic analysis of novel astroviruses from endemic Malagasy fruit bats.}, journal = {Virology journal}, volume = {21}, number = {1}, pages = {195}, pmid = {39180123}, issn = {1743-422X}, support = {001/WHO_/World Health Organization/International ; GCE/ID OPP1211841//Bill and Melinda Gates Foundation/ ; 1R01A|129822-01/NH/NIH HHS/United States ; PREEMPT Program Cooperative Agreement no D18AC00031//Defense Sciences Office, DARPA/ ; }, mesh = {Animals ; *Chiroptera/virology ; *Phylogeny ; *Astroviridae/genetics/isolation & purification/classification ; *Astroviridae Infections/veterinary/virology/epidemiology ; *Metagenomics ; High-Throughput Nucleotide Sequencing ; Madagascar ; Genome, Viral/genetics ; Sequence Analysis, DNA ; }, abstract = {Bats (order: Chiroptera) are known to host a diverse range of viruses, some of which present a human public health risk. Thorough viral surveillance is therefore essential to predict and potentially mitigate zoonotic spillover. Astroviruses (family: Astroviridae) are an understudied group of viruses with a growing amount of indirect evidence for zoonotic transfer. Astroviruses have been detected in bats with significant prevalence and diversity, suggesting that bats may act as important astrovirus hosts. Most astrovirus surveillance in wild bat hosts has, to date, been restricted to single-gene PCR detection and concomitant Sanger sequencing; additionally, many bat species and many geographic regions have not yet been surveyed for astroviruses at all. Here, we use metagenomic Next Generation Sequencing (mNGS) to detect astroviruses in three species of Madagascar fruit bats, Eidolon dupreanum, Pteropus rufus, and Rousettus madagascariensis. We detect numerous partial sequences from all three species and one near-full length astrovirus sequence from Rousettus madagascariensis, which we use to characterize the evolutionary history of astroviruses both within bats and the broader mammalian clade, Mamastrovirus. Taken together, applications of mNGS implicate bats as important astrovirus hosts and demonstrate novel patterns of bat astrovirus evolutionary history, particularly in the Southwest Indian Ocean region.}, } @article {pmid39180058, year = {2024}, author = {Hua, X and McGoldrick, J and Nakrour, N and Staller, K and Chung, DC and Xavier, RJ and Khalili, H}, title = {Gut microbiome structure and function in asymptomatic diverticulosis.}, journal = {Genome medicine}, volume = {16}, number = {1}, pages = {105}, pmid = {39180058}, issn = {1756-994X}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AG068390/AG/NIA NIH HHS/United States ; DK043351//Center for the study of inflammatory bowel disease/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Aged ; Metagenomics/methods ; Colonoscopy ; Metagenome ; Bacteria/classification/genetics ; }, abstract = {BACKGROUND: Colonic diverticulosis, the most common lesion found in routine colonoscopy, affects more than 50% of individuals aged ≥ 60 years. Emerging evidence suggest that dysbiosis of gut microbiota may play an important role in the pathophysiology of diverticular disease. However, specific changes in microbial species and metabolic functions in asymptomatic diverticulosis remain unknown.

METHODS: In a cohort of US adults undergoing screening colonoscopy, we analyzed the gut microbiota using shotgun metagenomic sequencing. Demographic factors, lifestyle, and medication use were assessed using a baseline questionnaire administered prior to colonoscopy. Taxonomic structures and metabolic pathway abundances were determined using MetaPhlAn3 and HUMAnN3. We used multivariate association with linear models to identify microbial species and metabolic pathways that were significantly different between asymptomatic diverticulosis and controls, while adjusting for confounders selected a priori including age at colonoscopy, sex, body mass index (BMI), and dietary pattern.

RESULTS: Among 684 individuals undergoing a screening colonoscopy, 284 (42%) had diverticulosis. Gut microbiome composition explained 1.9% variation in the disease status of asymptomatic diverticulosis. We observed no significant differences in the overall diversity of gut microbiome between asymptomatic diverticulosis and controls. However, microbial species Bifidobacterium pseudocatenulatum and Prevotella copri were significantly enriched in controls (q value = 0.19 and 0.14, respectively), whereas Roseburia intestinalis, Dorea sp. CAG:317, and Clostridium sp. CAG: 299 were more abundant in those with diverticulosis (q values = 0.17, 0.24, and 0.10, respectively). We observed that the relationship between BMI and diverticulosis appeared to be limited to carriers of Bifidobacterium pseudocatenulatum and Roseburia intestinalis (Pinteraction = 0.09).

CONCLUSIONS: Our study provides the first large-scale evidence supporting taxonomic and functional shifts of the gut microbiome in individuals with asymptomatic diverticulosis. The suggestive interaction between gut microbiota and BMI on prevalent diverticulosis deserves future investigations.}, } @article {pmid39179206, year = {2024}, author = {Barone Lumaga, R and Tagliamonte, S and De Rosa, T and Valentino, V and Ercolini, D and Vitaglione, P}, title = {Consumption of a Sourdough-Leavened Croissant Enriched with a Blend of Fibers Influences Fasting Blood Glucose in a Randomized Controlled Trial in Healthy Subjects.}, journal = {The Journal of nutrition}, volume = {154}, number = {10}, pages = {2976-2987}, doi = {10.1016/j.tjnut.2024.08.015}, pmid = {39179206}, issn = {1541-6100}, mesh = {Humans ; *Dietary Fiber/administration & dosage/pharmacology ; Male ; Female ; *Blood Glucose/analysis ; Adult ; *Bread/analysis ; Gastrointestinal Microbiome ; Middle Aged ; Fasting ; Young Adult ; Healthy Volunteers ; Diet ; }, abstract = {BACKGROUND: An incorrect lifestyle, including diet, is responsible for the worldwide dramatic increase in obesity and type 2 diabetes. Increasing dietary fiber consumption may lead to health benefits, and reformulation of bakery products may be a strategy to globally improve the diet.

OBJECTIVES: This study aimed to assess the impact of a 2-wk breakfast consumption with a sourdough-leavened croissant containing a blend of dietary fiber from 10 sources (4.8 g/100 g, croissant enriched with dietary fibers [FIBCRO]), compared with a control croissant (dietary fibers 1.3 g/100 g, CONCRO) on daily energy intake, appetite, metabolic variables, and the gut microbiome.

METHODS: Thirty-two healthy participants were randomly allocated to 2 groups consuming FIBCRO or CONCRO. Participants self-recorded their diet and appetite through 7-d weighted food diaries and visual analog scales every day over the 2 wk. At baseline and after the intervention, fasting blood and urine samples, and fecal samples were collected beside blood pressure, anthropometry, and body composition. Serum glucose, lipids, C-reactive protein, and insulin according to the official methods and serum dipeptidyl peptidase-4 (DPPIV) activity by photometric method were measured. Polyphenols and urolithins in urines were analyzed by Liquid chromatography-tandem mass spectrometry (LC/MS/MS), whereas gut microbiome in feces by shotgun metagenomics.

RESULTS: FIBCRO consumption improved fasting blood glucose compared with CONCRO (mean changes from baseline -2.0 mg/dL in FIBCRO compared with +3.1 mg/dL in CONCRO, P = 0.022), also reducing serum DPPIV activity by 1.7 IU/L (P = 0.01) and increasing urinary excretion of urolithin A-sulfate by 6.9 ng/mg creatinine (P = 0.04) compared with baseline. No further changes in any of the monitored variables or in the gut microbiome were detected.

CONCLUSIONS: Results suggested that a 2-wk consumption of a sourdough croissant claimed as "source of dietary fiber" improved fasting glycemia compared with a conventional sourdough croissant in healthy subjects. The reduced serum DPPIV activity and increased bioavailability of urolithin likely contributed to determine that effect independently from gut microbiome changes. This trial was registered at clinicaltrials.gov as NCT04999280.}, } @article {pmid39179139, year = {2024}, author = {Gao, N and Zhuang, Y and Zheng, Y and Li, Y and Wang, Y and Zhu, S and Fan, M and Tian, W and Jiang, Y and Wang, Y and Cui, M and Suo, C and Zhang, T and Jin, L and Chen, X and Xu, K}, title = {Investigating the link between gut microbiome and bone mineral density: The role of genetic factors.}, journal = {Bone}, volume = {188}, number = {}, pages = {117239}, doi = {10.1016/j.bone.2024.117239}, pmid = {39179139}, issn = {1873-2763}, mesh = {Humans ; *Bone Density/genetics ; Female ; *Gastrointestinal Microbiome/genetics ; Male ; Middle Aged ; Aged ; *Osteoporosis/genetics/microbiology ; Feces/microbiology ; }, abstract = {Osteoporosis is a complex metabolic bone disease that severely undermines the quality of life and overall health of the elderly. While previous studies have established a close relationship between gut microbiome and host bone metabolism, the role of genetic factors has received less scrutiny. This research aims to identify potential taxa associated with various bone mineral density states, incorporating assessments of genetic factors. Fecal microbiome profiles from 605 individuals (334 females and 271 males) aged 55-65 from the Taizhou Imaging Study with osteopenia (n = 270, 170 women) or osteoporosis (n = 94, 85 women) or normal (n = 241, 79 women) were determined using shotgun metagenomic sequencing. The linear discriminant analysis was employed to identify differentially enriched taxa. Utilizing the Kyoto Encyclopedia of Genes and Genomes for annotation, functional pathway analysis was conducted to identify differentially metabolic pathways. Polygenic risk score for osteoporosis was estimated to represent genetic susceptibility to osteoporosis, followed by stratification and interaction analyses. Gut flora diversity did not show significant differences among various bone mineral groups. After multivariable adjustment, certain species, such as Clostridium leptum, Fusicatenibacter saccharivorans and Roseburia hominis, were enriched in osteoporosis patients. Statistically significant interactions between the polygenic risk score and taxa Roseburia faecis, Megasphaera elsdenii were observed (P for interaction = 0.005, 0.018, respectively). Stratified analyses revealed a significantly negative association between Roseburia faecis and bone mineral density in the low-genetic-risk group (β = -0.045, P < 0.05), while Turicimonas muris was positively associated with bone mineral density in the high-genetic-risk group (β = 4.177, P < 0.05) after multivariable adjustments. Functional predictions of the gut microbiome indicated an increase in pathways related to structural proteins in high-genetic-risk patients, while low-genetic-risk patients exhibited enrichment in enzyme-related pathways. This study emphasizes the association between gut microbes and bone mass, offering new insights into the interaction between genetic background and gut microbiome.}, } @article {pmid39178987, year = {2024}, author = {Shukla, V and Singh, S and Verma, S and Verma, S and Rizvi, AA and Abbas, M}, title = {Targeting the microbiome to improve human health with the approach of personalized medicine: Latest aspects and current updates.}, journal = {Clinical nutrition ESPEN}, volume = {63}, number = {}, pages = {813-820}, doi = {10.1016/j.clnesp.2024.08.005}, pmid = {39178987}, issn = {2405-4577}, mesh = {Humans ; *Precision Medicine ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; *Probiotics/therapeutic use ; *Prebiotics ; *Dysbiosis/therapy ; Microbiota ; Synbiotics ; }, abstract = {The intricate ecosystem of microorganisms residing within and on the human body, collectively known as the microbiome, significantly influences human health. Imbalances in this microbiome, referred to as dysbiosis, have been associated with various diseases, prompting the exploration of novel therapeutic approaches. Personalized medicine, Tailors treatments to individual patient characteristics, offers a promising avenue for addressing microbiome-related health issues. This review highlights recent developments in utilizing personalized medicine to target the microbiome, aiming to enhance health outcomes. Noteworthy strategies include fecal microbiota transplantation (FMT), where healthy donor microbes are transferred to patients, showing promise in treating conditions such as recurrent Clostridium difficile infection. Additionally, probiotics, which are live microorganisms similar to beneficial gut inhabitants, and prebiotics, non-digestible compounds promoting microbial growth, are emerging as tools to restore microbiome balance. The integration of these approaches, known as synbiotics, enhances microbial colonization and therapeutic effects. Advances in metagenomics and sequencing technologies provide the means to understand individual microbiome profiles, enabling tailored interventions. This paper aims to present the latest insights in leveraging personalized medicine to address microbiome-related health concerns, envisioning a future where microbiome-based therapies reshape disease management and promote human health.}, } @article {pmid39178591, year = {2024}, author = {Gao, FZ and Hu, LX and Liu, YS and Qiao, LK and Chen, ZY and Su, JQ and He, LY and Bai, H and Zhu, YG and Ying, GG}, title = {Unveiling the overlooked small-sized microbiome in river ecosystems.}, journal = {Water research}, volume = {265}, number = {}, pages = {122302}, doi = {10.1016/j.watres.2024.122302}, pmid = {39178591}, issn = {1879-2448}, mesh = {*Rivers/microbiology ; *Microbiota ; *Ecosystem ; Metagenomics ; Bacteria/genetics ; }, abstract = {Enriching microorganisms using a 0.22-μm pore size is a general pretreatment procedure in river microbiome research. However, it remains unclear the extent to which this method loses microbiome information. Here, we conducted a comparative metagenomics-based study on microbiomes with sizes over 0.22 μm (large-sized) and between 0.22 μm and 0.1 μm (small-sized) in a subtropical river. Although the absolute concentration of small-sized microbiome was about two orders of magnitude lower than that of large-sized microbiome, sequencing only large-sized microbiome resulted in a significant loss of microbiome diversity. Specifically, the microbial community was different between two sizes, and 347 genera were only detected in small-sized microbiome. Small-sized microbiome had much more diverse viral community than large-sized fraction. The viruses had abundant ecological functions and were hosted by 825 species of 169 families, including pathogen-related families. Small-sized microbiome had distinct antimicrobial resistance risks from large-sized microbiome, showing an enrichment of eight antibiotic resistance gene (ARG) types as well as the detection of 140 unique ARG subtypes and five enriched risk rank I ARGs. Draft genomes of five major resistant pathogens having diverse ecological and pollutant-degrading functions were only assembled in small-sized microbiome. These findings provide novel insights into river ecosystems, and highlight the overlooked small-sized microbiome in the environment.}, } @article {pmid39178288, year = {2024}, author = {Buscaglia, M and Iriarte, JL and Schulz, F and Díez, B}, title = {Adaptation strategies of giant viruses to low-temperature marine ecosystems.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39178288}, issn = {1751-7370}, support = {21190726//ANID/ ; DG_06-20//INACH/ ; RT_04-19//INACH/ ; RT_05-18//INACH/ ; //CONA-SHOA CIMAR 25F/ ; AUB1900003//ANID/ ; ANID-FONDAP 1523A0002//Center for Climate and Resilience Research/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; ANID/FONDAP/151500003//Center for Dynamic Research on High Latitude Marine Ecosystems/ ; }, mesh = {*Cold Temperature ; *Seawater/virology ; *Ecosystem ; Antarctic Regions ; Arctic Regions ; *Genome, Viral ; *Metagenome ; Giant Viruses/genetics/classification/isolation & purification ; Phylogeny ; Adaptation, Physiological ; }, abstract = {Microbes in marine ecosystems have evolved their gene content to thrive successfully in the cold. Although this process has been reasonably well studied in bacteria and selected eukaryotes, less is known about the impact of cold environments on the genomes of viruses that infect eukaryotes. Here, we analyzed cold adaptations in giant viruses (Nucleocytoviricota and Mirusviricota) from austral marine environments and compared them with their Arctic and temperate counterparts. We recovered giant virus metagenome-assembled genomes (98 Nucleocytoviricota and 12 Mirusviricota MAGs) from 61 newly sequenced metagenomes and metaviromes from sub-Antarctic Patagonian fjords and Antarctic seawater samples. When analyzing our data set alongside Antarctic and Arctic giant viruses MAGs already deposited in the Global Ocean Eukaryotic Viral database, we found that Antarctic and Arctic giant viruses predominantly inhabit sub-10°C environments, featuring a high proportion of unique phylotypes in each ecosystem. In contrast, giant viruses in Patagonian fjords were subject to broader temperature ranges and showed a lower degree of endemicity. However, despite differences in their distribution, giant viruses inhabiting low-temperature marine ecosystems evolved genomic cold-adaptation strategies that led to changes in genetic functions and amino acid frequencies that ultimately affect both gene content and protein structure. Such changes seem to be absent in their mesophilic counterparts. The uniqueness of these cold-adapted marine giant viruses may now be threatened by climate change, leading to a potential reduction in their biodiversity.}, } @article {pmid39178040, year = {2024}, author = {Liu, L and Feng, T and Liu, Q and Liao, M and Liu, B and Li, M}, title = {Characterization of the vaginal microbiota in infertile women with repeated implantation failure.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {71}, number = {3}, pages = {263-271}, doi = {10.1556/030.2024.02323}, pmid = {39178040}, issn = {1588-2640}, mesh = {Humans ; Female ; *Vagina/microbiology ; Adult ; *Infertility, Female/microbiology ; *Microbiota ; *Bacteria/classification/isolation & purification/genetics ; Embryo Implantation ; Pregnancy ; Fertilization in Vitro ; }, abstract = {Although the relationship between vaginal microorganisms and fertility has been well established, only few studies have investigated vaginal microorganisms in women undergoing in vitro fertilization (IVF). Our aim was to study the differences in vaginal microbiota between infertile women with repeated implantation failure (RIF) and those who achieved clinical pregnancy in their first frozen embryo transfer cycle. We compared the vaginal microbiota of patients with a history of RIF (n = 37) with that of the control group (n = 43). Following DNA extraction, metagenomic sequencing was employed for the analysis of alpha and beta diversities, distinctions in bacterial species, and the functional annotation of microbial genes. Furthermore, disparities between the two groups were revealed. Alpha diversity analysis revealed that the Shannon index was higher in the RIF group (P < 0.05). There were differences in the beta diversity between groups (P = 0.16). At the bacterial family level, the relative abundance of Actinomycetaceae (P = 0.013) and Ruminococcaceae (P = 0.013) were significantly higher in the RIF group. At the genus level, the abundances of Actinomyces (P = 0.028) and Subdoligranulum (P = 0.013) were significantly higher in the RIF group. At the species level, the abundances of Prevotella timonensis (P = 0.028), Lactobacillus jensenii (P = 0.049), and Subdoligranulum (P = 0.013) were significantly higher in the RIF group. Significant differences in family, genus, species, alpha and beta diversity were observed in the vaginal microbiota between groups. Notably, among these findings, the Subdoligranulum genus emerged as the most prominent correlating factor.}, } @article {pmid39177227, year = {2024}, author = {Deng, Y and Nong, Z and Wei, M and Xu, Y and Luo, Y and Li, X and Zhao, R and Yang, Z and Pan, L}, title = {Characteristics and function of the gut microbiota in patients with IgA nephropathy via metagenomic sequencing technology.}, journal = {Renal failure}, volume = {46}, number = {2}, pages = {2393754}, pmid = {39177227}, issn = {1525-6049}, mesh = {Humans ; *Glomerulonephritis, IGA/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Adult ; *Feces/microbiology ; *Metagenomics/methods ; Case-Control Studies ; Middle Aged ; Moraxella/isolation & purification/genetics ; Escherichia coli/isolation & purification/genetics ; Acinetobacter/isolation & purification/genetics ; Metagenome ; Young Adult ; }, abstract = {OBJECTIVE: The aim of this study was to investigate the characteristics and related functional pathways of the gut microbiota in patients with IgA nephropathy (IgAN) through metagenomic sequencing technology.

METHODS: We enrolled individuals with primary IgAN, including patients with normal and abnormal renal function. Additionally, we recruited healthy volunteers as the healthy control group. Stool samples were collected, and species and functional annotation were performed through fecal metagenome sequencing. We employed linear discriminant analysis effect size (LEfSe) analysis to identify significantly different bacterial microbiota and functional pathways. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was used to annotate microbiota functions, and redundancy analysis (RDA) was performed to analyze the factors affecting the composition and distribution of the gut microbiota.

RESULTS: LEfSe analysis revealed differences in the gut microbiota between IgAN patients and healthy controls. The characteristic microorganisms in the IgAN group were classified as Escherichia coli, with a significantly greater abundance than that in the healthy control group (p < 0.05). The characteristic microorganisms in the IgAN group with abnormal renal function were identified as Enterococcaceae, Moraxella, Moraxella, and Acinetobacter. KEGG functional analysis demonstrated that the functional pathways of the microbiota that differed between IgAN patients and healthy controls were related primarily to bile acid metabolism.

CONCLUSIONS: The status of the gut microbiota is closely associated not only with the onset of IgAN but also with the renal function of IgAN patients. The characteristic gut microbiota may serve as a promising diagnostic biomarker and therapeutic target for IgAN.}, } @article {pmid39175129, year = {2025}, author = {Hotchkiss, MZ and Forrest, JRK and Poulain, AJ}, title = {Changes in bumblebee queen gut microbiotas during and after overwintering diapause.}, journal = {Insect molecular biology}, volume = {34}, number = {1}, pages = {136-150}, pmid = {39175129}, issn = {1365-2583}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; Bees/microbiology/physiology ; *Gastrointestinal Microbiome ; *Diapause, Insect ; Female ; Seasons ; }, abstract = {Bumblebees are key pollinators with gut microbiotas that support host health. After bumblebee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post-diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumblebee queen gut microbiota community structure and metabolic potential shift during and after winter diapause, and whether post-diapause recovery is affected by pesticide exposure. To do so, we placed commercial Bombus impatiens queens into diapause, euthanizing them at 0, 2 and 4 months of diapause. Additionally, we allowed some queens to recover from diapause for 1 week before euthanasia, exposing half to the common herbicide glyphosate. Using whole-community, shotgun metagenomic sequencing, we found that core bee gut phylotypes dominated queen gut microbiotas before, during and after diapause, but that two phylotypes, Schmidhempelia and Snodgrassella, ceased to be detected during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Also, glyphosate exposure did not affect post-diapause microbiota recovery. However, metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways declined alongside microbial abundance, which was substantially reduced during diapause. Our study offers new insights into how bumblebee queen gut microbiotas change taxonomically and functionally during a key life stage and provides guidance for future microbiota studies in diapausing bumblebees.}, } @article {pmid39175056, year = {2024}, author = {Sbardellati, DL and Vannette, RL}, title = {Targeted viromes and total metagenomes capture distinct components of bee gut phage communities.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {155}, pmid = {39175056}, issn = {2049-2618}, support = {2023-67011-40501//U.S. Department of Agriculture/ ; 1929516//National Science Foundation/ ; }, mesh = {Bees/virology/microbiology ; Animals ; *Bacteriophages/genetics/isolation & purification/classification ; *Virome ; *Metagenome ; Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Gastrointestinal Tract/microbiology/virology ; }, abstract = {BACKGROUND: Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens.

RESULTS: We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low occupancy phage, while total metagenomes were biased towards sampling temperate phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments.

CONCLUSIONS: Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage. Video Abstract.}, } @article {pmid39174663, year = {2024}, author = {Jafari, M and Moghimi, H and Tirandaz, H and Ebrahim-Habibi, MB}, title = {Corrosion behavior of predominant Halodesulfovibrio in a marine SRB consortium and its mitigation using ZnO nanoparticles.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {19545}, pmid = {39174663}, issn = {2045-2322}, mesh = {Corrosion ; *Zinc Oxide/chemistry/pharmacology ; *Biofilms/drug effects ; *Bioreactors/microbiology ; Steel/chemistry ; Nanoparticles/chemistry ; Microbial Consortia/drug effects ; }, abstract = {Formation of Sulfate Reducing Bacteria (SRB) biofilm accelerates microbiologically influenced corrosion (MIC). The aim of this study was to investigate both the corrosivity of a marine SRB consortium on carbon steel coupons and its mitigation in the presence of ZnO. Metagenomics analysis revealed that Halodesulfovibrio (78.9%) was predominant and could be related to MIC. The analysis also showed a remarkable shift from a highly corrosive SRB consortium in the control bioreactors to a far less corrosive consortium when ZnO was added to the bioreactors. Further results indicated that the corrosion rate of the SRB consortium was 8.17 mpy on the carbon steel coupons. In the ZnO-treated bioreactors, the count of SRB and MIC in the carbon steel coupons simultaneously reduced. Moreover, Confocal Laser Scanning Microscopy and profilometry analysis determined that ZnO could significantly decrease the amount of biofilm and the corrosion rate. Electrochemical experiments revealed higher corrosion current density (icorr) and lower charge transfer resistance (Rct) in the control bioreactors relative to the ZnO-treated bioreactors. We introduce Halodesulfovibrio as a potentially important corrosive genus in a marine SRB consortium. Additionally, ZnO could be considered a proper candidate to control the corrosion induced by Halodesulfovibrio.}, } @article {pmid39173973, year = {2024}, author = {Oliver, A and Alkan, Z and Stephensen, CB and Newman, JW and Kable, ME and Lemay, DG}, title = {Diet, Microbiome, and Inflammation Predictors of Fecal and Plasma Short-Chain Fatty Acids in Humans.}, journal = {The Journal of nutrition}, volume = {154}, number = {11}, pages = {3298-3311}, pmid = {39173973}, issn = {1541-6100}, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; Biomarkers/blood ; Cohort Studies ; *Diet ; *Fatty Acids, Volatile/metabolism/blood ; *Feces/microbiology/chemistry ; *Gastrointestinal Microbiome ; *Inflammation/blood ; }, abstract = {BACKGROUND: Gut microbes produce short-chain fatty acids (SCFAs), which are associated with broad health benefits. However, it is not fully known how diet and/or the gut microbiome could be modulated to improve SCFA production.

OBJECTIVES: The objective of this study was to identify dietary, inflammatory, and/or microbiome predictors of SCFAs in a cohort of healthy adults.

METHODS: SCFAs were measured in fecal and plasma samples from 359 healthy adults in the United States Department of Agriculture Nutritional Phenotyping Study. Habitual and recent diet was assessed using a Food Frequency Questionnaire and Automated Self-Administered 24-h Dietary Assesment Tool dietary recalls. Markers of systemic and gut inflammation were measured in fecal and plasma samples. The gut microbiome was assessed using shotgun metagenomics. Using statistics and machine learning, we determined how the abundance and composition of SCFAs varied with measures of diet, inflammation, and the gut microbiome.

RESULTS: We show that fecal pH may be a good proxy for fecal SCFA abundance. A higher Healthy Eating Index for a habitual diet was associated with a compositional increase in fecal butyrate relative to acetate and propionate. SCFAs were associated with markers of subclinical gastrointestinal (GI) inflammation. Fecal SCFA abundance was inversely related to plasma lipopolysaccharide-binding protein. When we analyzed hierarchically organized diet and microbiome data with taxonomy-aware algorithms, we observed that diet and microbiome features were far more predictive of fecal SCFA abundances compared to plasma SCFA abundances. The top diet and microbiome predictors of fecal butyrate included potatoes and the thiamine biosynthesis pathway, respectively.

CONCLUSIONS: These results suggest that resistant starch in the form of potatoes and microbially produced thiamine provide a substrate and essential cofactor, respectively, for butyrate synthesis. Thiamine may be a rate-limiting nutrient for butyrate production in adults. Overall, these findings illustrate the complex biology underpinning SCFA production in the gut. This trial was registered at clinicaltrials.gov as NCT02367287.}, } @article {pmid39173234, year = {2024}, author = {Jia, P and Liang, JL and Lu, JL and Zhong, SJ and Xiong, T and Feng, SW and Wang, Y and Wu, ZH and Yi, XZ and Gao, SM and Zheng, J and Wen, P and Li, F and Li, Y and Liao, B and Shu, WS and Li, JT}, title = {Soil keystone viruses are regulators of ecosystem multifunctionality.}, journal = {Environment international}, volume = {191}, number = {}, pages = {108964}, doi = {10.1016/j.envint.2024.108964}, pmid = {39173234}, issn = {1873-6750}, mesh = {*Soil Microbiology ; China ; *Ecosystem ; *Viruses/genetics ; Soil/chemistry ; Microbiota ; Fungi/genetics ; Forests ; Metagenomics ; Biodiversity ; }, abstract = {Ecosystem multifunctionality reflects the capacity of ecosystems to simultaneously maintain multiple functions which are essential bases for human sustainable development. Whereas viruses are a major component of the soil microbiome that drive ecosystem functions across biomes, the relationships between soil viral diversity and ecosystem multifunctionality remain under-studied. To address this critical knowledge gap, we employed a combination of amplicon and metagenomic sequencing to assess prokaryotic, fungal and viral diversity, and to link viruses to putative hosts. We described the features of viruses and their potential hosts in 154 soil samples from 29 farmlands and 25 forests distributed across China. Although 4,460 and 5,207 viral populations (vOTUs) were found in the farmlands and forests respectively, the diversity of specific vOTUs rather than overall soil viral diversity was positively correlated with ecosystem multifunctionality in both ecosystem types. Furthermore, the diversity of these keystone vOTUs, despite being 10-100 times lower than prokaryotic or fungal diversity, was a better predictor of ecosystem multifunctionality and more strongly associated with the relative abundances of prokaryotic genes related to soil nutrient cycling. Gemmatimonadota and Actinobacteria dominated the host community of soil keystone viruses in the farmlands and forests respectively, but were either absent or showed a significantly lower relative abundance in that of soil non-keystone viruses. These findings provide novel insights into the regulators of ecosystem multifunctionality and have important implications for the management of ecosystem functioning.}, } @article {pmid39168346, year = {2024}, author = {Li, J and Li, C and Han, Y and Yang, J and Hu, Y and Xu, H and Zhou, Y and Zuo, J and Tang, Y and Lei, C and Li, C and Wang, H}, title = {Bacterial membrane vesicles from swine farm microbial communities harboring and safeguarding diverse functional genes promoting horizontal gene transfer.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175639}, doi = {10.1016/j.scitotenv.2024.175639}, pmid = {39168346}, issn = {1879-1026}, mesh = {*Gene Transfer, Horizontal ; Animals ; Swine ; Farms ; Microbiota ; Bacteria/genetics ; Feces/microbiology ; Drug Resistance, Microbial/genetics ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; Soil Microbiology ; Genes, Bacterial ; }, abstract = {Antibiotic resistance (AMR) poses a significant global health challenge, with swine farms recognized as major reservoirs of antibiotic resistance genes (ARGs). Recently, bacterial membrane vesicles (BMVs) have emerged as novel carriers mediating horizontal gene transfer. However, little is known about the ARGs carried by BMVs in swine farm environments and their transfer potential. This study investigated the distribution, sources, and microbiological origins of BMVs in three key microbial habitats of swine farms (feces, soil, and fecal wastewater), along with the ARGs and mobile genetic elements (MGEs) they harbor. Characterization of BMVs revealed particle sizes ranging from 20 to 500 nm and concentrations from 10[8] to 10[12] particles/g, containing DNA and proteins. Metagenomic sequencing identified BMVs predominantly composed of members of the Proteobacteria phyla, including Pseudomonadaceae, Moraxellaceae, and Enterobacteriaceae, carrying diverse functional genes encompassing resistance to 14 common antibiotics and 74,340 virulence genes. Notably, multidrug resistance, tetracycline, and chloramphenicol resistance genes were particularly abundant. Furthermore, BMVs harbored various MGEs, primarily plasmids, and demonstrated the ability to protect their DNA cargo from degradation and facilitate horizontal gene transfer, including the transmission of resistance genes. In conclusion, this study reveals widespread presence of BMVs carrying ARGs and potential virulence genes in swine farm feces, soil, and fecal wastewater. These findings not only provide new insights into the role of extracellular DNA in the environment but also highlight concerns regarding the gene transfer potential mediated by BMVs and associated health risks.}, } @article {pmid39167702, year = {2024}, author = {Prins, FM and Hidding, IJ and Klaassen, MAY and Collij, V and Schultheiss, JPD and Uniken Venema, WTC and Bangma, A and Aardema, JB and Jansen, BH and Mares, WGN and Witteman, BJM and Festen, EAM and Dijkstra, G and Visschedijk, MC and Fidder, HH and Vich Vila, A and Oldenburg, B and Gacesa, R and Weersma, RK}, title = {Limited predictive value of the gut microbiome and metabolome for response to biological therapy in inflammatory bowel disease.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2391505}, pmid = {39167702}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Inflammatory Bowel Diseases/drug therapy/microbiology/metabolism ; *Metabolome/drug effects ; *Ustekinumab/therapeutic use ; Prospective Studies ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; *Feces/microbiology ; Female ; Male ; Adult ; Biological Therapy/methods ; Treatment Outcome ; Middle Aged ; Bacteria/genetics/classification/metabolism/drug effects/isolation & purification ; Biomarkers/analysis/metabolism ; }, abstract = {Emerging evidence suggests the gut microbiome's potential in predicting response to biologic treatments in patients with inflammatory bowel disease (IBD). In this prospective study, we aimed to predict treatment response to vedolizumab and ustekinumab, integrating clinical data, gut microbiome profiles based on metagenomic sequencing, and untargeted fecal metabolomics. We aimed to identify predictive biomarkers and attempted to replicate microbiome-based signals from previous studies. We found that the predictive utility of the gut microbiome and fecal metabolites for treatment response was marginal compared to clinical features alone. Testing our identified microbial ratios in an external cohort reinforced the lack of predictive power of the microbiome. Additionally, we could not confirm previously published predictive signals observed in similar sized cohorts. Overall, these findings highlight the importance of external validation and larger sample sizes, to better understand the microbiome's impact on therapy outcomes in the setting of biologicals in IBD before potential clinical implementation.}, } @article {pmid39166878, year = {2024}, author = {Lu, Q and Zhu, R and Zhou, L and Zhang, R and Li, Z and Xu, P and Wang, Z and Wu, G and Ren, J and Jiao, D and Song, Y and Li, J and Wang, W and Liang, R and Ma, X and Sun, Y}, title = {Gut dysbiosis contributes to the development of Budd-Chiari syndrome through immune imbalance.}, journal = {mSystems}, volume = {9}, number = {9}, pages = {e0079424}, pmid = {39166878}, issn = {2379-5077}, support = {81870457//MOST | National Natural Science Foundation of China (NSFC)/ ; 82172944//MOST | National Natural Science Foundation of China (NSFC)/ ; 81900558//MOST | National Natural Science Foundation of China (NSFC)/ ; 232102311048//Key science and technology project s of Henan Province/ ; }, mesh = {*Dysbiosis/microbiology/immunology ; *Gastrointestinal Microbiome/physiology ; *Budd-Chiari Syndrome/immunology/microbiology/pathology ; Humans ; Animals ; Mice ; Male ; Case-Control Studies ; Female ; *Cytokines/metabolism/immunology/genetics ; Adult ; Fecal Microbiota Transplantation ; Middle Aged ; }, abstract = {UNLABELLED: Budd-Chiari syndrome (B-CS) is a rare and lethal condition characterized by hepatic venous outflow tract blockage. Gut microbiota has been linked to numerous hepatic disorders, but its significance in B-CS pathogenesis is uncertain. First, we performed a case-control study (Ncase = 140, Ncontrol = 63) to compare the fecal microbiota of B-CS and healthy individuals by metagenomics sequencing. B-CS patients' gut microbial composition and activity changed significantly, with a different metagenomic makeup, increased potentially pathogenic bacteria, including Prevotella, and disease-linked microbial function. Imbalanced cytokines in patients were demonstrated to be associated with gut dysbiosis, which led us to suspect that B-CS is associated with gut microbiota and immune dysregulation. Next, 16S ribosomal DNA sequencing on fecal microbiota transplantation (FMT) mice models examined the link between gut dysbiosis and B-CS. FMT models showed damaged liver tissues, posterior inferior vena cava, and increased Prevotella in the disturbed gut microbiota of FMT mice. Notably, B-CS-FMT impaired the morphological structure of colonic tissues and increased intestinal permeability. Furthermore, a significant increase of the same cytokines (IL-5, IL-6, IL-9, IL-10, IL-17A, IL-17F, and IL-13) and endotoxin levels in B-CS-FMT mice were observed. Our study suggested that gut microbial dysbiosis may cause B-CS through immunological dysregulation.

IMPORTANCE: This study revealed that gut microbial dysbiosis may cause Budd-Chiari syndrome (B-CS). Gut dysbiosis enhanced intestinal permeability, and toxic metabolites and imbalanced cytokines activated the immune system. Consequently, the escalation of causative factors led to their concentration in the portal vein, thereby compromising both the liver parenchyma and outflow tract. Therefore, we proposed that gut microbial dysbiosis induced immune imbalance by chronic systemic inflammation, which contributed to the B-CS development. Furthermore, Prevotella may mediate inflammation development and immune imbalance, showing potential in B-CS pathogenesis.}, } @article {pmid39166873, year = {2024}, author = {Kwan, S-Y and Sabotta, CM and Cruz, LR and Wong, MC and Ajami, NJ and McCormick, JB and Fisher-Hoch, SP and Beretta, L}, title = {Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes.}, journal = {mSystems}, volume = {9}, number = {9}, pages = {e0043424}, pmid = {39166873}, issn = {2379-5077}, support = {P50 CA217674/CA/NCI NIH HHS/United States ; UL1 TR000371/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics ; Middle Aged ; *Virome/genetics ; *Mexican Americans ; *Fatty Liver/genetics ; Cross-Sectional Studies ; Adult ; Diabetes Mellitus ; Feces/microbiology/virology ; Aged ; }, abstract = {Mexican Americans are disproportionally affected by metabolic dysfunction-associated steatotic liver disease (MASLD), which often co-occurs with diabetes. Despite extensive evidence on the causative role of the gut microbiome in MASLD, studies determining the involvement of the gut phageome are scarce. In this cross-sectional study, we characterized the gut phageome in Mexican Americans of South Texas by stool shotgun metagenomic sequencing of 340 subjects, concurrently screened for liver steatosis by transient elastography. Inter-individual variations in the phageome were associated with gender, country of birth, diabetes, and liver steatosis. The phage signatures for diabetes and liver steatosis were subsequently determined. Enrichment of Inoviridae was associated with both diabetes and liver steatosis. Diabetes was further associated with the enrichment of predominantly temperate Escherichia phages, some of which possessed virulence factors. Liver steatosis was associated with the depletion of Lactococcus phages r1t and BK5-T, and enrichment of the globally prevalent Crassvirales phages, including members of genus cluster IX (Burzaovirus coli, Burzaovirus faecalis) and VI (Kahnovirus oralis). The Lactococcus phages showed strong correlations and co-occurrence with Lactococcus lactis, while the Crassvirales phages, B. coli, B. faecalis, and UAG-readthrough crAss clade correlated and co-occurred with Prevotella copri. In conclusion, we identified the gut phageome signatures for two closely linked metabolic diseases with significant global burden. These phage signatures may have utility in risk modeling and disease prevention in this high-risk population, and identification of potential bacterial targets for phage therapy.IMPORTANCEPhages influence human health and disease by shaping the gut bacterial community. Using stool samples from a high-risk Mexican American population, we provide insights into the gut phageome changes associated with diabetes and liver steatosis, two closely linked metabolic diseases with significant global burden. Common to both diseases was an enrichment of Inoviridae, a group of phages that infect bacterial hosts chronically without lysis, allowing them to significantly influence bacterial growth, virulence, motility, biofilm formation, and horizontal gene transfer. Diabetes was additionally associated with the enrichment of Escherichia coli-infecting phages, some of which contained virulence factors. Liver steatosis was additionally associated with the depletion of Lactococcus lactis-infecting phages, and enrichment of Crassvirales phages, a group of virulent phages with high global prevalence and persistence across generations. These phageome signatures may have utility in risk modeling, as well as identify potential bacterial targets for phage therapy.}, } @article {pmid39164259, year = {2024}, author = {Seong, HJ and Kim, JJ and Kim, T and Ahn, SJ and Rho, M and Lee, KJ and Sul, WJ}, title = {Recovery of 240 metagenome-assembled genomes from coastal mariculture environments in South Korea.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {902}, pmid = {39164259}, issn = {2052-4463}, mesh = {Republic of Korea ; *Metagenome ; *Aquaculture ; Animals ; Bacteria/genetics/classification ; Microbiota ; Ostreidae/microbiology ; Archaea/genetics ; Pectinidae/microbiology/genetics ; Penaeidae/microbiology/genetics ; }, abstract = {The mariculture industry has seen a rapid expansion in recent years due to the increasing global demand for seafood. However, the industry faces challenges from climate change and increased pathogen pressure. Additionally, the chemicals used to enhance mariculture productivity are changing ocean ecosystems. This study analyzed 36 surface-water metagenomes from South Korean mussel, oyster, scallop, and shrimp farms to expand our understanding of aquaculture microbial genetic resources and the potential impacts of these anthropogenic inputs. We recovered 240 non-redundant species-level metagenome-assembled genomes (MAGs), comprising 224 bacteria, 13 archaea, and three eukaryotes. Most MAGs were assigned to Proteobacteria, Bacteroidota, and Actinobacteriota, with 40.7% remaining unclassified at the species level. Among the three eukaryotic MAGs, one was identified as a novel lineage of green algae, highlighting the uncharacterized genetic diversity in mariculture environments. Additionally, 22 prokaryotic MAGs harbored 26 antibiotic and metal resistance genes, with MAGs carrying beta-lactamases being particularly prevalent in most farms. The obtained microbiome data from mariculture environments can be utilized in future studies to foster healthy, sustainable mariculture practices.}, } @article {pmid39163860, year = {2024}, author = {Torres, MDT and Brooks, EF and Cesaro, A and Sberro, H and Gill, MO and Nicolaou, C and Bhatt, AS and de la Fuente-Nunez, C}, title = {Mining human microbiomes reveals an untapped source of peptide antibiotics.}, journal = {Cell}, volume = {187}, number = {19}, pages = {5453-5467.e15}, doi = {10.1016/j.cell.2024.07.027}, pmid = {39163860}, issn = {1097-4172}, mesh = {Humans ; Animals ; Mice ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; *Antimicrobial Peptides/pharmacology/chemistry ; Metagenome ; Female ; Open Reading Frames ; Bacteria/drug effects/genetics/classification ; Prevotella/drug effects ; }, abstract = {Drug-resistant bacteria are outpacing traditional antibiotic discovery efforts. Here, we computationally screened 444,054 previously reported putative small protein families from 1,773 human metagenomes for antimicrobial properties, identifying 323 candidates encoded in small open reading frames (smORFs). To test our computational predictions, 78 peptides were synthesized and screened for antimicrobial activity in vitro, with 70.5% displaying antimicrobial activity. As these compounds were different compared with previously reported antimicrobial peptides, we termed them smORF-encoded peptides (SEPs). SEPs killed bacteria by targeting their membrane, synergizing with each other, and modulating gut commensals, indicating a potential role in reconfiguring microbiome communities in addition to counteracting pathogens. The lead candidates were anti-infective in both murine skin abscess and deep thigh infection models. Notably, prevotellin-2 from Prevotella copri presented activity comparable to the commonly used antibiotic polymyxin B. Our report supports the existence of hundreds of antimicrobials in the human microbiome amenable to clinical translation.}, } @article {pmid39163656, year = {2024}, author = {Sun, F and Yang, H and Zhang, X and Tan, F and Wang, G and Shi, Q}, title = {Significant response of coral-associated bacteria and their carbohydrate-active enzymes diversity to coral bleaching.}, journal = {Marine environmental research}, volume = {201}, number = {}, pages = {106694}, doi = {10.1016/j.marenvres.2024.106694}, pmid = {39163656}, issn = {1879-0291}, mesh = {Animals ; *Anthozoa/microbiology ; *Bacteria/genetics/enzymology ; Symbiosis ; Microbiota ; }, abstract = {Analysis of bacterial carbohydrate-active enzymes (CAZymes) contributes significantly to comprehending the response exhibited by coral symbionts to the external environment. This study explored the impact of bleaching on the bacteria and their CAZymes in coral Favites sp. through metagenomic sequencing. Notably, principal coordinates analysis (PCoA) unveiles substantial difference in bacterial communities between bleached and unbleached corals. Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidota, and Chloroflexi, exhibit noteworthy alterations during coral bleaching. CAZymes profiles in bleached coral disclosed a significant increase in Glycosyltransferases (GTs) abundance, suggesting an intensified biosynthesis of polysaccharides. Conversely, there is a marked reduction in other CAZymes abundance in bleached coral. Proteobacteria, Bacteroidota, Chlorobi, and Planctomycetota exhibit greater contributions to CAZymes in bleached corals, with Rhodobacterales, Cytophagales, Burkholderiales, Caulobacterales, and Hyphomicrobiales being the main contributors. While Acidobacteria, Actinobacteria, and Chloroflexi demonstrate higher contributions to CAZymes in unbleached corals. The changes in bacteria and their CAZymes reflect the ecological adaptability of coral holobionts when facing environmental stress. The alterations in CAZymes composition caused by bleaching events may have profound impacts on coral nutrient absorption and ecosystem stability. Therefore, understanding the dynamic changes in CAZymes is crucial for assessing the health and recovery potential of coral ecosystems.}, } @article {pmid39163484, year = {2024}, author = {Dede, B and Reeves, EP and Walter, M and Bach, W and Amann, R and Meyerdierks, A}, title = {Bacterial chemolithoautotrophy in ultramafic plumes along the Mid-Atlantic Ridge.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39163484}, issn = {1751-7370}, support = {EXC-309-49926684//Deutsche Forschungsgemeinschaft/ ; //Norwegian Research Council/ ; 179560//University of Bergen Centre for Geobiology/ ; //Max Planck Society/ ; }, mesh = {*Hydrothermal Vents/microbiology ; Atlantic Ocean ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Chemoautotrophic Growth ; *Seawater/microbiology ; Microbiota ; Hydrogen/metabolism ; Phylogeny ; Sulfur/metabolism ; Oxidation-Reduction ; In Situ Hybridization, Fluorescence ; Carbon Dioxide/metabolism ; }, abstract = {Hydrothermal vent systems release reduced chemical compounds that act as an important energy source in the deep sea. Chemolithoautotrophic microbes inhabiting hydrothermal plumes oxidize these compounds, in particular, hydrogen and reduced sulfur, to obtain the energy required for CO2 fixation. Here, we analysed the planktonic communities of four hydrothermal systems located along the Mid-Atlantic Ridge: Irinovskoe, Semenov-2, Logatchev-1, and Ashadze-2, by combining long-read 16S rRNA gene analysis, fluorescence in situ hybridization, meta-omics, and thermodynamic calculations. Sulfurimonas and SUP05 dominated the microbial communities in these hydrothermal plumes. Investigation of Sulfurimonas and SUP05 MAGs, and their gene transcription in plumes indicated a niche partitioning driven by hydrogen and sulfur. In addition to sulfur and hydrogen oxidation, a novel SAR202 clade inhabiting the plume, here referred to as genus Carboxydicoccus, harbours the capability for CO oxidation and CO2 fixation via reverse TCA cycle. Both pathways were also highly transcribed in other hydrogen-rich plumes, including the Von Damm vent field. Carboxydicoccus profundi reached up to 4% relative abundance (1.0 x 103 cell ml- 1) in Irinovskoe non-buoyant plume and was also abundant in non-hydrothermally influenced deep-sea metagenomes (up to 5 RPKM). Therefore, CO, which is probably not sourced from the hydrothermal fluids (1.9-5.8 μM), but rather from biological activities within the rising fluid, may serve as a significant energy source in hydrothermal plumes. Taken together, this study sheds light on the chemolithoautotrophic potential of the bacterial community in Mid-Atlantic Ridge plumes.}, } @article {pmid39162524, year = {2024}, author = {Hu, F and Cheng, Y and Fan, B and Li, W and Ye, B and Wu, Z and Tan, Z and He, Z}, title = {Ruminal microbial metagenomes and host transcriptomes shed light on individual variability in the growth rate of lambs before weaning: the regulated mechanism and potential long-term effect on the host.}, journal = {mSystems}, volume = {9}, number = {9}, pages = {e0087324}, pmid = {39162524}, issn = {2379-5077}, support = {XDA26040304, XDA26050102//strategic priority research program/ ; 32072760//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022JJ10054//HSTD | Natural Science Foundation of Hunan Province/ ; 2022JBGS0023//the Inner Mongolia major technology project/ ; 2019RS3021//Innovation province project/ ; }, mesh = {Animals ; *Weaning ; Sheep/growth & development/microbiology ; *Rumen/microbiology/metabolism ; *Transcriptome ; *Metagenome ; Female ; Gastrointestinal Microbiome/physiology ; Amino Acids/metabolism/blood ; Liver/metabolism ; Fermentation ; }, abstract = {UNLABELLED: Weaning weight is a reflection of management during the breastfeeding phase and will influence animal performance in subsequent phases, considered important indicators within production systems. The aims of this study were as follows: (i) to investigate variability in the growth rate among individual lambs from ewes rearing single or twin lambs fed with two different diets and (ii) to explore the molecular mechanisms regulating the growth rate and the potential long-term effects on the host. No significant change in lamb average daily gain (ADG) was observed in litter size and diet treatment, and there were large variations among individual lambs (ranging from 0.13 to 0.41 kg/day). Further analysis was conducted on serum amino acids, rumen fermentation characteristics, rumen metagenomics and transcriptome, and hepatic transcriptome of lambs with extremely high (HA; n = 6) and low (LA; n = 6) ADG. We observed significant increases in serum lysine, leucine, alanine, and phenylalanine in the HA group. The metagenome revealed that the HA group presented a higher rumen propionate molar proportion via increasing gene abundance in the succinate pathway for propionate synthesis. For the rumen transcriptome, higher expressed gene sets in the HA group were mainly related to rumen epithelial growth, including cytokine-cytokine receptor interaction, Jak-STAT signaling pathway, and adherens junction. For the liver transcriptome, the upregulated KEGG pathways in the HA group were primarily associated with fatty acid degradation, glyoxylate and dicarboxylate metabolism, cholesterol metabolism, and the immune system. This research suggests that preweaning lambs with high ADG may benefit from rumen development and enhanced liver metabolic and immune function.

IMPORTANCE: There is accumulating evidence indicating that the early-life rumen microbiome plays vital roles in rumen development and microbial fermentation, which subsequently affects the growth of young ruminants. The liver is also vital to regulate the metabolism and distribution of nutrients. Our results demonstrate that lambs with high average daily gain (ADG) enhanced microbial volatile fatty acid (VFA) metabolism toward rumen propionate and serum amino acid (AA) production to support host growth. The study highlights that high ADG in the preweaning period is beneficial for the rumen development and liver energy metabolism, leading to better growth later in life. Overall, this study explores the molecular mechanisms regulating the growth rate and the potential long-term effects of increased growth rate on the host metabolism, providing fundamental knowledge about nutrient manipulation in pre-weaning.}, } @article {pmid39162518, year = {2024}, author = {Hu, D and Zhang, T and He, S and Pu, T and Yin, Y and Hu, Y}, title = {Mining metagenomic data to gain a new insight into the gut microbial biosynthetic potential in placental mammals.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0086424}, pmid = {39162518}, issn = {2165-0497}, support = {32370552//MOST | National Natural Science Foundation of China (NSFC)/ ; 32070414,32325010//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Mammals/microbiology ; *Metagenome ; *Multigene Family ; Bacteria/genetics/classification/metabolism ; Polyketides/metabolism ; Data Mining ; Biological Products/metabolism ; Female ; Biosynthetic Pathways/genetics ; }, abstract = {Mammals host a remarkable diversity and abundance of gut microbes. Biosynthetic gene clusters (BGCs) in microbial genomes encode biologically active chemical products and play an important role in microbe-host interactions. Traditionally, the exploration of gut microbial metabolic functions has relied on the pure culture method. However, given the limited amounts of microbes being cultivated, insights into the metabolism of gut microbes in mammals continued to be very limited. In this study, we adopted a computational pipeline for mining the metagenomic data (named taxonomy-guided identification of biosynthetic gene clusters, TaxiBGC) to identify experimentally verified BGCs in 373 metagenomes across 53 mammalian species in an unbiased manner. We demonstrated that polyketides (PKs) and nonribosomal peptides (NRPs) are representative of mammals, and the products derived from them were associated with cell-cell communication and resistance to inflammation. Large carnivores had the highest number of BGCs, followed by large herbivores and small mammals. We also observed that the large mammals had more common BGCs that aid in the biosynthesis of a variety of natural products. However, small mammals not only had fewer BGCs but were also unique to each species. Our results provide novel insights into the mining of metagenomic data sets to identify active BGCs and their products across mammals.IMPORTANCEThe gut microbes host numerous biosynthetic gene clusters (BGCs) that biosynthesize natural products and impact the host's physiology. Historically, our understanding of BGCs in mammalian gut microbes was largely based on studies on cultured isolates; however, only a small fraction of mammal-associated microbes have been investigated. The biochemical diversity of the mammalian gut microbiota is poorly understood. Metagenomic sequencing contains data from a vast number of organisms and provides information on the total gene content of communities. Unfortunately, the existing BGC prediction tools are designed for individual microbial genomes. Recently, a BGC prediction tool called the taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC) that directly mine the metagenome was developed. To gain new insights into the microbial metabolism, we used TaxiBGC to predict BGCs from 373 metagenomes across 53 mammalian species representing seven orders. Our findings elucidate the functional activities of complex microbial communities in the gut.}, } @article {pmid39161223, year = {2024}, author = {Stokholm, J and Thorsen, J and Schoos, AM and Rasmussen, MA and Brandt, S and Sørensen, SJ and Vahman, N and Chawes, B and Bønnelykke, K}, title = {Infantile colic is associated with development of later constipation and atopic disorders.}, journal = {Allergy}, volume = {79}, number = {12}, pages = {3360-3372}, pmid = {39161223}, issn = {1398-9995}, support = {//Region Hovedstaden/ ; //Strategiske Forskningsråd/ ; //Lundbeck Foundation/ ; //Sundhed og Sygdom, Det Frie Forskningsråd/ ; }, mesh = {Humans ; *Constipation/epidemiology/etiology ; *Colic/epidemiology/etiology ; *Gastrointestinal Microbiome ; Male ; Female ; Infant ; Child, Preschool ; Dermatitis, Atopic/epidemiology/complications ; Child ; Prospective Studies ; Asthma/epidemiology/diagnosis/microbiology/etiology ; Hypersensitivity, Immediate/epidemiology/complications ; Risk Factors ; }, abstract = {BACKGROUND: Infantile colic is a common condition with limited knowledge about later clinical manifestations. We evaluated the role of the early life gut microbiome in infantile colic and later development of atopic and gastrointestinal disorders.

METHODS: Copenhagen Prospective Studies on Asthma in Childhood2010 cohort was followed with 6 years of extensive clinical phenotyping. The 1-month gut microbiome was analyzed by 16S rRNA sequencing. Infantile colic was evaluated at age 3 months by interviews. Clinical endpoints included constipation to age 3 years and prospectively diagnosed asthma and atopic dermatitis in the first 6 years of life, and allergic sensitization from skin prick tests, specific Immunoglobulin E, and component analyses.

RESULTS: Of 695 children, 55 children (7.9%) had infantile colic. Several factors were associated with colic including race, breastfeeding, and pets. The 1-month gut microbiome composition and taxa abundances were not associated with colic, however a sparse Partial Least Squares model including combined abundances of nine species was moderately predictive of colic: median, cross-validated AUC = 0.627, p = .003. Children with infantile colic had an increased risk of developing constipation (aOR, 2.88 [1.51-5.35], p = .001) later in life, but also asthma (aHR, 1.69 [1.02-2.79], p = .040), atopic dermatitis (aHR, 1.84 [1.20-2.81], p = .005) and had a higher number of positive allergic components (adjusted difference, 116% [14%-280%], p = .012) in the first 6 years. These associations were not mediated by gut microbiome differences.

CONCLUSIONS: We link infantile colic with risk of developing constipation and atopic disorders in the first 6 years of life, which was not mediated through an altered gut microbiome at age 1-month. These results suggest infantile colic to involve gastrointestinal and/or atopic mechanisms.}, } @article {pmid39160620, year = {2024}, author = {Yu, T and Luo, Y and Tan, X and Zhao, D and Bi, X and Li, C and Zheng, Y and Xiang, H and Hu, S}, title = {Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products.}, journal = {Genomics, proteomics & bioinformatics}, volume = {22}, number = {2}, pages = {}, doi = {10.1093/gpbjnl/qzad006}, pmid = {39160620}, issn = {2210-3244}, support = {//Center for Ocean Mega-Science, Chinese Academy of Sciences/ ; 2021QZKK0100//Second Tibetan Plateau Scientific Expedition and Research Program/ ; }, mesh = {*Metagenome/genetics ; *Archaea/genetics/metabolism/classification ; *Microbiota/genetics ; Bacteria/genetics/classification/metabolism ; Biological Products/metabolism ; Cold Temperature ; Phylogeny ; Seawater/microbiology ; Metagenomics/methods ; Biodiversity ; }, abstract = {Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change. The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life, showcasing an unparalleled reservoir of microbial genetic diversity. Here, by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types, we present a comprehensive Cold Seep Microbiomic Database (CSMD) to archive the genomic and functional diversity of cold seep microbiomes. The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes, which represent 1895 species spanning 105 phyla. In addition, beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community composition. Heterotrophic and anaerobic metabolisms are prevalent in microbial communities, accompanied by considerable mixotrophs and facultative anaerobes, highlighting the versatile metabolic potential in cold seeps. Furthermore, secondary metabolic gene cluster analysis indicates that at least 98.81% of the sequences potentially encode novel natural products, with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and bacteria. Overall, the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.}, } @article {pmid39160615, year = {2024}, author = {Hugerth, LW and Krog, MC and Vomstein, K and Du, J and Bashir, Z and Kaldhusdal, V and Fransson, E and Engstrand, L and Nielsen, HS and Schuppe-Koistinen, I}, title = {Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages, and bacterial genes.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {153}, pmid = {39160615}, issn = {2049-2618}, support = {KAW 2020.0239//Science for Life Laboratory/ ; E-22614-01, E-22614-02//Rigshospitalet/ ; 2021-01683//Vetenskapsrådet/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology ; *Bacteriophages/genetics/physiology ; *Microbiota/genetics ; *Menstruation ; *Bacteria/classification/genetics ; Adult ; *Dysbiosis/microbiology ; *Menstrual Cycle ; Young Adult ; Genes, Bacterial/genetics ; Metagenomics/methods ; }, abstract = {BACKGROUND: The composition of the vaginal microbiota during the menstrual cycle is dynamic, with some women remaining eu- or dysbiotic and others transitioning between these states. What defines these dynamics, and whether these differences are microbiome-intrinsic or mostly driven by the host is unknown. To address this, we characterized 49 healthy, young women by metagenomic sequencing of daily vaginal swabs during a menstrual cycle. We classified the dynamics of the vaginal microbiome and assessed the impact of host behavior as well as microbiome differences at the species, strain, gene, and phage levels.

RESULTS: Based on the daily shifts in community state types (CSTs) during a menstrual cycle, the vaginal microbiome was classified into four Vaginal Community Dynamics (VCDs) and reported in a classification tool, named VALODY: constant eubiotic, constant dysbiotic, menses-related, and unstable dysbiotic. The abundance of bacteria, phages, and bacterial gene content was compared between the four VCDs. Women with different VCDs showed significant differences in relative phage abundance and bacterial composition even when assigned to the same CST. Women with unstable VCDs had higher phage counts and were more likely dominated by L. iners. Their Gardnerella spp. strains were also more likely to harbor bacteriocin-coding genes.

CONCLUSIONS: The VCDs present a novel time series classification that highlights the complexity of varying degrees of vaginal dysbiosis. Knowing the differences in phage gene abundances and the genomic strains present allows a deeper understanding of the initiation and maintenance of permanent dysbiosis. Applying the VCDs to further characterize the different types of microbiome dynamics qualifies the investigation of disease and enables comparisons at individual and population levels. Based on our data, to be able to classify a dysbiotic sample into the accurate VCD, clinicians would need two to three mid-cycle samples and two samples during menses. In the future, it will be important to address whether transient VCDs pose a similar risk profile to persistent dysbiosis with similar clinical outcomes. This framework may aid interdisciplinary translational teams in deciphering the role of the vaginal microbiome in women's health and reproduction. Video Abstract.}, } @article {pmid39160043, year = {2024}, author = {Merino, N and Pagán, E and Berdejo, D and Worby, CJ and Young, M and Manson, AL and Pagán, R and Earl, AM and García-Gonzalo, D}, title = {Dynamics of microbiome and resistome in a poultry burger processing line.}, journal = {Food research international (Ottawa, Ont.)}, volume = {193}, number = {}, pages = {114842}, doi = {10.1016/j.foodres.2024.114842}, pmid = {39160043}, issn = {1873-7145}, mesh = {Animals ; *Microbiota/genetics ; *Food Microbiology ; *Bacteria/genetics/classification/isolation & purification/drug effects ; *Food Handling/methods ; Poultry/microbiology ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Drug Resistance, Bacterial/genetics ; Meat/microbiology ; Poultry Products/microbiology ; }, abstract = {Traditionally, surveillance programs for food products and food processing environments have focused on targeted pathogens and resistance genes. Recent advances in high throughput sequencing allow for more comprehensive and untargeted monitoring. This study assessed the microbiome and resistome in a poultry burger processing line using culturing techniques and whole metagenomic sequencing (WMS). Samples included meat, burgers, and expired burgers, and different work surfaces. Microbiome analysis revealed spoilage microorganisms as the main microbiota, with substantial shifts observed during the shelf-life period. Core microbiota of meat and burgers included Pseudomonas spp., Psychrobacter spp., Shewanella spp. and Brochothrix spp., while expired burgers were dominated by Latilactobacillus spp. and Leuconostoc spp. Cleaning and disinfection (C&D) procedures altered the microbial composition of work surfaces, which still harbored Hafnia spp. and Acinetobacter spp. after C&D. Resistome analysis showed a low overall abundance of resistance genes, suggesting that effective interventions during processing may mitigate their transmission. However, biocide resistance genes were frequently found, indicating potential biofilm formation or inefficient C&D protocols. This study demonstrates the utility of combining culturing techniques and WMS for comprehensive of the microbiome and resistome characterization in food processing lines.}, } @article {pmid39159777, year = {2024}, author = {Fang, XM and Li, J and Wang, NF and Zhang, T and Yu, LY}, title = {Metagenomics uncovers microbiome and resistome in soil and reindeer faeces from Ny-Ålesund (Svalbard, High Arctic).}, journal = {Environmental research}, volume = {262}, number = {Pt 1}, pages = {119788}, doi = {10.1016/j.envres.2024.119788}, pmid = {39159777}, issn = {1096-0953}, mesh = {Animals ; *Feces/microbiology ; *Reindeer/microbiology ; *Microbiota/drug effects/genetics ; *Soil Microbiology ; Svalbard ; *Metagenomics ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects/classification ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Arctic Regions ; Soil/chemistry ; Genes, Bacterial ; }, abstract = {Research on the microbiome and resistome in polar environments, such as the Arctic, is crucial for understanding the emergence and spread of antibiotic resistance genes (ARGs) in the environment. In this study, soil and reindeer faeces samples collected from Ny-Ålesund (Svalbard, High Arctic) were examined to analyze the microbiome, ARGs, and biocide/metal resistance genes (BMRGs). The dominant phyla in both soil and faeces were Pseudomonadota, Actinomycetota, and Bacteroidota. A total of 2618 predicted Open Reading Frames (ORFs) containing antibiotic resistance genes (ARGs) were detected. These ARGs belong to 162 different genes across 17 antibiotic classes, with rifamycin and multidrug resistance genes being the most prevalent. We focused on investigating antibiotic resistance mechanisms in the Ny-Ålesund environment by analyzing the resistance genes and their biological pathways. Procrustes analysis demonstrated a significant correlation between bacterial communities and ARG/BMRG profiles in soil and faeces samples. Correlation analysis revealed that Pseudomonadota contributed most to multidrug and triclosan resistance, while Actinomycetota were predominant contributors to rifamycin and aminoglycoside resistance. The geochemical factors, SiO4[2-] and NH4[+], were found to significantly influence the microbial composition and ARG distribution in the soil samples. Analysis of ARGs, BMRGs, virulence factors (VFs), and pathogens identified potential health risks associated with certain bacteria, such as Cryobacterium and Pseudomonas, due to the presence of different genetic elements. This study provided valuable insights into the molecular mechanisms and geochemical factors contributing to antibiotic resistance and enhanced our understanding of the evolution of antibiotic resistance genes in the environment.}, } @article {pmid39159729, year = {2024}, author = {Ma, J and Li, M and Bao, Y and Huang, W and He, X and Hong, Y and Wei, W and Liu, Z and Gao, X and Yang, Y and Cui, Z and Wang, W and Wang, J and Zhu, W and Zheng, N and Pan, L and Wang, D and Ke, Z and Zhou, B and Sheng, L and Li, H}, title = {Gut microbiota-brain bile acid axis orchestrates aging-related neuroinflammation and behavior impairment in mice.}, journal = {Pharmacological research}, volume = {208}, number = {}, pages = {107361}, doi = {10.1016/j.phrs.2024.107361}, pmid = {39159729}, issn = {1096-1186}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Aging/metabolism ; Male ; *Bile Acids and Salts/metabolism ; *Neuroinflammatory Diseases/metabolism ; Female ; *Brain-Gut Axis/physiology ; *Mice, Inbred C57BL ; Mice ; *Brain/metabolism ; *Behavior, Animal ; Caenorhabditis elegans/microbiology ; Microglia/metabolism ; }, abstract = {Emerging evidence shows that disrupted gut microbiota-bile acid (BA) axis is critically involved in the development of neurodegenerative diseases. However, the alterations in spatial distribution of BAs among different brain regions that command important functions during aging and their exact roles in aging-related neurodegenerative diseases are poorly understood. Here, we analyzed the BA profiles in cerebral cortex, hippocampus, and hypothalamus of young and natural aging mice of both sexes. The results showed that aging altered brain BA profiles sex- and region- dependently, in which TβMCA was consistently elevated in aging mice of both sexes, particularly in the hippocampus and hypothalamus. Furthermore, we found that aging accumulated-TβMCA stimulated microglia inflammation in vitro and shortened the lifespan of C. elegans, as well as behavioral impairment and neuroinflammation in mice. In addition, metagenomic analysis suggested that the accumulation of brain TβMCA during aging was partially attributed to reduction in BSH-carrying bacteria. Finally, rejuvenation of gut microbiota by co-housing aged mice with young mice restored brain BA homeostasis and improved neurological dysfunctions in natural aging mice. In conclusion, our current study highlighted the potential of improving aging-related neuro-impairment by targeting gut microbiota-brain BA axis.}, } @article {pmid39159726, year = {2024}, author = {Zhang, Y and Wang, N and Wan, J and Jousset, A and Jiang, G and Wang, X and Wei, Z and Xu, Y and Shen, Q}, title = {Exploring the antibiotic resistance genes removal dynamics in chicken manure by composting.}, journal = {Bioresource technology}, volume = {410}, number = {}, pages = {131309}, doi = {10.1016/j.biortech.2024.131309}, pmid = {39159726}, issn = {1873-2976}, mesh = {Animals ; *Manure/microbiology ; *Chickens ; *Composting ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Bacteria/genetics/drug effects ; Microbiota/drug effects ; Gene Transfer, Horizontal ; }, abstract = {Prolonged antibiotic usage in livestock farming leads to the accumulation of antibiotic resistance genes in animal manure. Composting has been shown as an effective way of removing antibiotic resistance from manures, but the specific mechanisms remain unclear. This study used time-series sampling and metagenomics to analyse the resistome types and their bacterial hosts in chicken manures. Composting significantly altered the physicochemical properties and microbiome composition, reduced antibiotic resistance genes by 65.71 %, mobile genetic elements by 68.15 % and horizontal gene transfer frequency. Source tracking revealed that Firmicutes, Actinobacteria, and Proteobacteria are the major bacterial hosts involved in the resistome and gene transfer events. Composting reduces the resistome risk by targeting pathogens such as Staphylococcus aureus. Structural equation modelling confirmed that composting reduces resistome risk by changing pH and pathogen abundance. This study demonstrates that composting is an effective strategy for mitigating resistome risk in chicken manure, thereby supporting the One Health initiative.}, } @article {pmid39159427, year = {2024}, author = {Yagi, K and Ethridge, AD and Falkowski, NR and Huang, YJ and Elesela, S and Huffnagle, GB and Lukacs, NW and Fonseca, W and Asai, N}, title = {Microbiome modifications by steroids during viral exacerbation of asthma and in healthy mice.}, journal = {American journal of physiology. Lung cellular and molecular physiology}, volume = {327}, number = {5}, pages = {L646-L660}, pmid = {39159427}, issn = {1522-1504}, support = {R01 AI138348/AI/NIAID NIH HHS/United States ; AI089473//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; HL150682//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; AI138348//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {Animals ; *Asthma/virology/microbiology/drug therapy ; *Respiratory Syncytial Virus Infections/virology/drug therapy/microbiology/immunology ; *Fluticasone/pharmacology ; Mice ; *Gastrointestinal Microbiome/drug effects ; Lung/virology/microbiology/metabolism/drug effects ; Female ; Mice, Inbred BALB C ; Microbiota/drug effects ; Respiratory Syncytial Viruses/drug effects ; }, abstract = {In the present studies, the assessment of how viral exacerbation of asthmatic responses with and without pulmonary steroid treatment alters the microbiome in conjunction with immune responses presents striking data. The overall findings identify that although steroid treatment of allergic animals diminished the severity of the respiratory syncytial virus (RSV)-induced exacerbation of airway function and mucus hypersecretion, there were local increases in IL-17 expression. Analysis of the lung and gut microbiome suggested that there are differences in RSV exacerbation that are further altered by fluticasone (FLUT) treatment. Using metagenomic inference software, PICRUSt2, we were able to predict that the metabolite profile produced by the changed gut microbiome was significantly different with multiple metabolic pathways and associated with specific treatments with or without FLUT. Importantly, measuring plasma metabolites in an unbiased manner, our data indicate that there are significant changes associated with chronic allergen exposure, RSV exacerbation, and FLUT treatment that are reflective of responses to the disease and treatment. In addition, the changes in metabolites appeared to have contributions from both host and microbial pathways. To understand if airway steroids on their own altered lung and gut microbiome along with host responses to RSV infection, naïve animals were treated with lung FLUT before RSV infection. The naïve animals treated with FLUT before RSV infection demonstrated enhanced disease that corresponded to an altered microbiome and the related PICRUSt2 metagenomic inference analysis. Altogether, these findings set the foundation for identifying important correlations of severe viral exacerbated allergic disease with microbiome changes and the relationship of host metabolome with a potential for early life pulmonary steroid influence on subsequent viral-induced disease.NEW & NOTEWORTHY These studies outline a novel finding that airway treatment with fluticasone, a commonly used inhaled steroid, has significant effects on not only the local lung environment but also on the mucosal microbiome, which may have significant disease implications. The findings further provide data to support that pulmonary viral exacerbations of asthma with or without steroid treatment alter the lung and gut microbiome, which have an impact on the circulating metabolome that likely alters the trajectory of disease progression.}, } @article {pmid39158287, year = {2024}, author = {Lui, LM and Nielsen, TN}, title = {Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses.}, journal = {mSystems}, volume = {9}, number = {9}, pages = {e0024224}, pmid = {39158287}, issn = {2379-5077}, support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; }, mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Estuaries ; San Francisco ; *Viruses/genetics/classification/isolation & purification ; Metagenome/genetics ; Bacteria/genetics/classification ; Archaea/genetics/virology ; Eukaryota/genetics ; Genome, Viral/genetics ; }, abstract = {UNLABELLED: Although long-read sequencing has enabled obtaining high-quality and complete genomes from metagenomes, many challenges still remain to completely decompose a metagenome into its constituent prokaryotic and viral genomes. This study focuses on decomposing an estuarine metagenome to obtain a more accurate estimate of microbial diversity. To achieve this, we developed a new bead-based DNA extraction method, a novel bin refinement method, and obtained 150 Gbp of Nanopore sequencing. We estimate that there are ~500 bacterial and archaeal species in our sample and obtained 68 high-quality bins (>90% complete, <5% contamination, ≤5 contigs, contig length of >100 kbp, and all ribosomal and tRNA genes). We also obtained many contigs of picoeukaryotes, environmental DNA of larger eukaryotes such as mammals, and complete mitochondrial and chloroplast genomes and detected ~40,000 viral populations. Our analysis indicates that there are only a few strains that comprise most of the species abundances.

IMPORTANCE: Ocean and estuarine microbiomes play critical roles in global element cycling and ecosystem function. Despite the importance of these microbial communities, many species still have not been cultured in the lab. Environmental sequencing is the primary way the function and population dynamics of these communities can be studied. Long-read sequencing provides an avenue to overcome limitations of short-read technologies to obtain complete microbial genomes but comes with its own technical challenges, such as needed sequencing depth and obtaining high-quality DNA. We present here new sampling and bioinformatics methods to attempt decomposing an estuarine microbiome into its constituent genomes. Our results suggest there are only a few strains that comprise most of the species abundances from viruses to picoeukaryotes, and to fully decompose a metagenome of this diversity requires 1 Tbp of long-read sequencing. We anticipate that as long-read sequencing technologies continue to improve, less sequencing will be needed.}, } @article {pmid39158107, year = {2024}, author = {Ming, Y and Abdullah Al, M and Zhang, D and Zhu, W and Liu, H and Cai, L and Yu, X and Wu, K and Niu, M and Zeng, Q and He, Z and Yan, Q}, title = {Insights into the evolutionary and ecological adaption strategies of nirS- and nirK-type denitrifying communities.}, journal = {Molecular ecology}, volume = {33}, number = {18}, pages = {e17507}, doi = {10.1111/mec.17507}, pmid = {39158107}, issn = {1365-294X}, support = {SML2020SP004//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2021SP203//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP205//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 42377111//National Natural Science Foundation of China/ ; //Ocean Negative Carbon Emissions (ONCE) Program/ ; }, mesh = {*Denitrification/genetics ; *Nitrite Reductases/genetics ; China ; *Phylogeny ; *Metagenome/genetics ; Lakes/microbiology ; Bioreactors/microbiology ; Gene Transfer, Horizontal ; Microbiota/genetics ; Metagenomics ; Geologic Sediments/microbiology ; Bacteria/genetics/classification/metabolism ; Nitrogen/metabolism ; Adaptation, Physiological/genetics ; }, abstract = {Denitrification is a crucial process in the global nitrogen cycle, in which two functionally equivalent genes, nirS and nirK, catalyse the critical reaction and are usually used as marker genes. The nirK gene can function independently, whereas nirS requires additional genes to encode nitrite reductase and is more sensitive to environmental factors than nirK. However, the ecological differentiation mechanisms of those denitrifying microbial communities and their adaptation strategies to environmental stresses remain unclear. Here, we conducted metagenomic analysis for sediments and bioreactor samples from Lake Donghu, China. We found that nirS-type denitrifying communities had a significantly lower horizontal gene transfer frequency than that of nirK-type denitrifying communities, and nirS gene phylogeny was more congruent with taxonomy than that of nirK gene. Metabolic reconstruction of metagenome-assembled genomes further revealed that nirS-type denitrifying communities have robust metabolic systems for energy conservation, enabling them to survive under environmental stresses. Nevertheless, nirK-type denitrifying communities seemed to adapt to oxygen-limited environments with the ability to utilize various carbon and nitrogen compounds. Thus, this study provides novel insights into the ecological differentiation mechanism of nirS and nirK-type denitrifying communities, as well as the regulation of the global nitrogen cycle and greenhouse gas emissions.}, } @article {pmid39157177, year = {2024}, author = {Huang, SS and Qiu, JY and Li, SP and Ma, YQ and He, J and Han, LN and Jiao, LL and Xu, C and Mao, YM and Zhang, YM}, title = {Microbial signatures predictive of short-term prognosis in severe pneumonia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1397717}, pmid = {39157177}, issn = {2235-2988}, mesh = {Humans ; Male ; Female ; Prognosis ; Retrospective Studies ; Middle Aged ; Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota ; Pneumonia/microbiology/mortality ; Bacteria/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Lung/microbiology/pathology ; Metagenomics ; Machine Learning ; }, abstract = {OBJECTIVE: This retrospective cohort study aimed to investigate the composition and diversity of lung microbiota in patients with severe pneumonia and explore its association with short-term prognosis.

METHODS: A total of 301 patients diagnosed with severe pneumonia underwent bronchoalveolar lavage fluid metagenomic next-generation sequencing (mNGS) testing from February 2022 to January 2024. After applying exclusion criteria, 236 patients were included in the study. Baseline demographic and clinical characteristics were compared between survival and non-survival groups. Microbial composition and diversity were analyzed using alpha and beta diversity metrics. Additionally, LEfSe analysis and machine learning methods were employed to identify key pathogenic microorganism associated with short-term mortality. Microbial interaction modes were assessed through network co-occurrence analysis.

RESULTS: The overall 28-day mortality rate was 37.7% in severe pneumonia. Non-survival patients had a higher prevalence of hypertension and exhibited higher APACHE II and SOFA scores, higher procalcitonin (PCT), and shorter hospitalization duration. Microbial α and β diversity analysis showed no significant differences between the two groups. However, distinct species diversity patterns were observed, with the non-survival group showing a higher abundance of Acinetobacter baumannii, Klebsiella pneumoniae, and Enterococcus faecium, while the survival group had a higher prevalence of Corynebacterium striatum and Enterobacter. LEfSe analysis identified 29 distinct terms, with 10 potential markers in the non-survival group, including Pseudomonas sp. and Enterococcus durans. Machine learning models selected 16 key pathogenic bacteria, such as Klebsiella pneumoniae, significantly contributing to predicting short-term mortality. Network co-occurrence analysis revealed greater complexity in the non-survival group compared to the survival group, with differences in central genera.

CONCLUSION: Our study highlights the potential significance of lung microbiota composition in predicting short-term prognosis in severe pneumonia patients. Differences in microbial diversity and composition, along with distinct microbial interaction modes, may contribute to variations in short-term outcomes. Further research is warranted to elucidate the clinical implications and underlying mechanisms of these findings.}, } @article {pmid39154602, year = {2024}, author = {García-Roldán, A and de la Haba, RR and Sánchez-Porro, C and Ventosa, A}, title = {'Altruistic' cooperation among the prokaryotic community of Atlantic salterns assessed by metagenomics.}, journal = {Microbiological research}, volume = {288}, number = {}, pages = {127869}, doi = {10.1016/j.micres.2024.127869}, pmid = {39154602}, issn = {1618-0623}, mesh = {*Metagenomics ; *Bacteria/genetics/classification ; *Salinity ; *Archaea/genetics/classification ; Spain ; Seawater/microbiology ; Phylogeny ; Atlantic Ocean ; Biodiversity ; Salts ; Microbiota/genetics ; Ecosystem ; Metagenome ; }, abstract = {Hypersaline environments are extreme habitats with a limited prokaryotic diversity, mainly restricted to halophilic or halotolerant archaeal and bacterial taxa adapted to highly saline conditions. This study attempts to analyze the taxonomic and functional diversity of the prokaryotes that inhabit a solar saltern located at the Atlantic Coast, in Isla Cristina (Huelva, Southwest Spain), and the influence of salinity on the diversity and metabolic potential of these prokaryotic communities, as well as the interactions and cooperation among the individuals within that community. Brine samples were obtained from different saltern ponds, with a salinity range between 19.5 % and 39 % (w/v). Total prokaryotic DNA was sequenced using the Illumina shotgun metagenomic strategy and the raw sequence data were analyzed using supercomputing services following the MetaWRAP and SqueezeMeta protocols. The most abundant phyla at moderate salinities (19.5-22 % [w/v]) were Methanobacteriota (formerly "Euryarchaeota"), Pseudomonadota and Bacteroidota, followed by Balneolota and Actinomycetota and Uroviricota in smaller proportions, while at high salinities (36-39 % [w/v]) the most abundant phylum was Methanobacteriota, followed by Bacteroidota. The most abundant genera at intermediate salinities were Halorubrum and the bacterial genus Spiribacter, while the haloarchaeal genera Halorubrum, Halonotius, and Haloquadratum were the main representatives at high salinities. A total of 65 MAGs were reconstructed from the metagenomic datasets and different functions and pathways were identified in them, allowing to find key taxa in the prokaryotic community able to synthesize and supply essential compounds, such as biotin, and precursors of other bioactive molecules, like β-carotene, and bacterioruberin, to other dwellers in this habitat, lacking the required enzymatic machinery to produce them. This work shed light on the ecology of aquatic hypersaline environments, such as the Atlantic Coast salterns, and on the dynamics and factors affecting the microbial populations under such extreme conditions.}, } @article {pmid39154578, year = {2024}, author = {Liang, T and Liu, Y and Guo, N and Li, Y and Niu, L and Liu, J and Ma, Q and Zhang, J and Shan, M}, title = {Jinhong decoction ameliorates injury in septic mice without disrupting the equilibrium of gut microbiota.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {251}, number = {}, pages = {116404}, doi = {10.1016/j.jpba.2024.116404}, pmid = {39154578}, issn = {1873-264X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Sepsis/drug therapy/microbiology ; *Drugs, Chinese Herbal/pharmacology ; Mice ; Male ; *Disease Models, Animal ; Anti-Bacterial Agents/pharmacology ; Chromatography, High Pressure Liquid/methods ; Cecum/microbiology ; Mice, Inbred C57BL ; }, abstract = {Sepsis is a life-threatening condition and usually be treated with antibiotics, which however often has severe side effects. This work proposed a novel Chinese traditional medicine JINHONG (JH) decoction for therapy of sepsis. We first identified the chemical constituents of JH decoction by using high-performance liquid chromatography and mass spectrometry (HPLC-MS). Then, we constructed a model mouse for sepsis by using cecal ligation and puncture (CLP). Metagenomic sequencing method was used to compare the diversity and abundance of the gut microbiota between normal, disease model, JH decoction-treatment and antibiotic-treatment mice. Many indices including the number of platelets, CD62p and CD63 content, AQP2 and AQP8 level, as well as the expression level of protein C confirmed that the sepsis resulted in serious pathological damage, while all of these indices could be reversed by JH decoction and antibiotics. The diversity and abundance of intestinal flora decreased in CLP mice, and the decrements aggravated after antibiotic treatment while can be recovered by JH decoction treatment. The abundance of anti-inflammatory Ruminococcaceae increased after JH decoction treatment, indicating that JH decoction could ameliorate pathology associated with sepsis in CLP model via modulating the intestinal flora. This study demonstrates that JH decoction could treat sepsis clinically without obvious adverse effects on gut microbiota.}, } @article {pmid39154041, year = {2024}, author = {Ma, T and Zhuang, Y and Lu, W and Tu, Y and Diao, Q and Fan, X and Zhang, N}, title = {Seven hundred and ninety-seven metagenome-assembled genomes from the goat rumen during early life.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {897}, pmid = {39154041}, issn = {2052-4463}, mesh = {Animals ; *Goats/microbiology ; *Rumen/microbiology ; *Metagenome ; Gastrointestinal Microbiome ; }, abstract = {The rumen microbiome plays an important role in providing energy and protein to the host. Manipulation of rumen microbiome during early life may have a long-term beneficial effect on the health, growth performance, and feed efficiency of ruminants. To better understand the profiles and functional potentials of rumen microbiome in young ruminants, metagenomic binning was performed to investigate the rumen microbiome of goat kids from one to 84 days of age. A total of 797 metagenome-assembled genomes (MAGs) were recovered from the rumen of 42 Laiwu black goat kids. Our findings provide fundamental knowledge of the rumen microbiome during early life based on metagenomic binning, which may provide insights into effective strategies to achieve long-term beneficial effects on animal health and production.}, } @article {pmid39153763, year = {2024}, author = {Cleminson, JS and Thomas, J and Stewart, CJ and Campbell, D and Gennery, A and Embleton, ND and Köglmeier, J and Wong, T and Spruce, M and Berrington, JE}, title = {Gut microbiota and intestinal rehabilitation: a prospective childhood cohort longitudinal study of short bowel syndrome (the MIRACLS study): study protocol.}, journal = {BMJ open gastroenterology}, volume = {11}, number = {1}, pages = {}, pmid = {39153763}, issn = {2054-4774}, mesh = {Humans ; *Short Bowel Syndrome/microbiology/epidemiology ; *Gastrointestinal Microbiome/physiology ; *Quality of Life/psychology ; Prospective Studies ; Child ; Child, Preschool ; Infant ; Longitudinal Studies ; Female ; Adolescent ; *Feces/microbiology ; Male ; *Parenteral Nutrition/methods/statistics & numerical data ; Infant, Newborn ; RNA, Ribosomal, 16S ; Intestines/microbiology ; }, abstract = {INTRODUCTION: Short bowel syndrome (SBS) is the predominant cause of paediatric intestinal failure. Although life-saving, parenteral nutrition (PN) is linked to complications and may impact quality of life (QoL). Most children will experience intestinal rehabilitation (IR), but the mechanisms underpinning this remain to be understood. SBS is characterised by abnormal microbiome patterns, which might serve as predictive indicators for IR. We aim to characterise the microbiome profiles of children with SBS during IR, concurrently exploring how parental perspectives of QoL relate to IR.

METHODS AND ANALYSIS: This study will enrol a minimum of 20 paediatric patients with SBS (0-18 years). Clinical data and biological samples will be collected over a 2-year study period. We will apply 16S rRNA gene sequencing to analyse the microbiome from faecal and gut tissue samples, with additional shotgun metagenomic sequencing specifically on samples obtained around the time of IR. Gas chromatography with flame ionisation detection will profile faecal short-chain fatty acids. Plasma citrulline and urinary intestinal fatty acid binding proteins will be measured annually. We will explore microbiome-clinical covariate interactions. Furthermore, we plan to assess parental perspectives on QoL during PN and post-IR by inviting parents to complete the Paediatric Quality of Life questionnaire at recruitment and after the completion of IR.

ETHICS AND DISSEMINATION: Ethical approval was obtained from the East Midlands-Nottingham 2 Research Ethics Committee (22/EM/0233; 28 November 2022). Recruitment began in February 2023. Outcomes of the study will be published in peer-reviewed scientific journals and presented at scientific meetings. A lay summary of the results will be made available to participants and the public.

TRIAL REGISTRATION NUMBER: ISRCTN90620576.}, } @article {pmid39153624, year = {2024}, author = {Barquero, MB and García-Díaz, C and Dobbler, PT and Jehmlich, N and Moreno, JL and López-Mondéjar, R and Bastida, F}, title = {Contrasting fertilization and phenological stages shape microbial-mediated phosphorus cycling in a maize agroecosystem.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175571}, doi = {10.1016/j.scitotenv.2024.175571}, pmid = {39153624}, issn = {1879-1026}, mesh = {*Zea mays ; *Phosphorus/metabolism ; *Fertilizers ; *Soil Microbiology ; Microbiota ; Bacteria/metabolism ; Agriculture/methods ; Archaea/physiology/metabolism ; Soil/chemistry ; }, abstract = {Phosphorus (P) is essential for plants but often limited in soils, with microbes playing a key role in its cycling. P deficiency in crops can be mitigated by applying by-products like sludge and struvite to enhance yield and sustainability. Here, we evaluated the contribution of four different types of fertilizers: i) conventional NPK; ii) sludge; iii) struvite; and iv) struvite+sludge in a semiarid maize plantation to the availability of P and the responses of the soil microbiome. We investigated the effects of these treatments on the relative abundance of bacterial and archaeal genes and proteins related to organic P mineralization, inorganic P solubilization, and the P starvation response regulation through a multi-omic approach. Moreover, we explored the impact of maize phenology by collecting samples at germination and flowering stages. Our findings suggest that the phenological stage has a notable impact on the abundance of P cycle genes within bacterial and archaeal communities, particularly regarding the solubilization of inorganic P. Furthermore, significant variations were observed in the relative abundance of genes associated with different P cycles in response to various fertilizer treatments. Sludge and struvite application improved P availability, which was related to an increase in the relative abundance of Sphingomonas (Proteobacteria) and Luteitalea (Acidobacteria) respectively, and genes related to inorganic P solubilization. Furthermore, we observed a substantial taxonomic clustering of functional processes associated with the P cycle. Among the dominant bacterial populations containing P-related genes, those microbes possessing genes linked to the solubilization of inorganic P typically did not harbor genes associated with the mineralization of organic P. This phenomenon was particularly evident among members of Actinobacteria. Overall, we reveal important shifts in bacterial and archaeal communities and associated molecular processes, stressing the intricate interplay between fertilization, phenology, and P cycling in agroecosystems.}, } @article {pmid39153565, year = {2024}, author = {Yang, C and Yan, S and Zhang, B and Yao, X and Mo, J and Rehman, F and Guo, J}, title = {Spatiotemporal distribution of the planktonic microbiome and antibiotic resistance genes in a typical urban river contaminated by macrolide antibiotics.}, journal = {Environmental research}, volume = {262}, number = {Pt 1}, pages = {119808}, doi = {10.1016/j.envres.2024.119808}, pmid = {39153565}, issn = {1096-0953}, mesh = {*Rivers/microbiology/chemistry ; *Microbiota/drug effects ; *Macrolides/analysis ; *Anti-Bacterial Agents/pharmacology/analysis ; *Plankton/drug effects/genetics ; *Drug Resistance, Microbial/genetics ; *Water Pollutants, Chemical/analysis ; Environmental Monitoring ; Genes, Bacterial ; Bacteria/genetics/drug effects/classification ; }, abstract = {The widespread application of macrolide antibiotics has caused antibiotic resistance pollution, threatening the river ecological health. In this study, five macrolide antibiotics (azithromycin, clarithromycin, roxithromycin, erythromycin, and anhydro erythromycin A) were monitored in the Zao River across three hydrological periods (April, July, and December). Simultaneously, the changes in antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and planktonic bacterial communities were determined using metagenomic sequencing. A clear pollution gradient was observed for azithromycin and roxithromycin, with the concentrations in the dry season surpassing those in other seasons. The highest concentration was observed for azithromycin (1.36 μg/L). The abundance of MLS resistance genes increased along the Zao River during the dry season, whereas the opposite trend was obtained during the wet season. A significant correlation between the levels of MLS resistance genes and macrolide antibiotics was identified during the dry season. Notably, compared with the reference site, the abundance of transposase in the effluent from wastewater treatment plants (WWTPs) was significantly elevated in both dry and wet seasons, whereas the abundance of insertion sequences (IS) and plasmids declined during the dry season. The exposure to wastewater containing macrolide antibiotics altered the diversity of planktonic bacterial communities. The bacterial host for ARGs appeared to be Pseudomonas, primarily associated with multidrug subtypes. Moreover, the ARG subtypes were highly correlated with MGEs (transposase and istA). The partial least-squares path model (PLS-PM) demonstrated a positive correlation between the abundance of MGEs and ARGs, indicating the significance of horizontal gene transfer (HGT) in the dissemination of ARGs within the Zao River. Environmental variables, such as TN and NO3[-]-N, were significantly correlated with the abundance of MGEs, ARGs, and bacteria. Collectively, our findings could provide insights into the shift patterns of the microbiome and ARGs across the contamination gradient of AZI and ROX in the river.}, } @article {pmid39152661, year = {2024}, author = {Leugger, F and Schmidlin, M and Lüthi, M and Kontarakis, Z and Pellissier, L}, title = {Scanning amplicons with CRISPR-Dx detects endangered amphibians in environmental DNA.}, journal = {Molecular ecology resources}, volume = {24}, number = {8}, pages = {e14009}, doi = {10.1111/1755-0998.14009}, pmid = {39152661}, issn = {1755-0998}, support = {//Swiss Federal Institute for Forest, Snow and Landscape Research/ ; 40B2-0_203550//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, mesh = {Animals ; *Amphibians/genetics/classification ; *DNA, Environmental/genetics ; *Endangered Species ; Switzerland ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; DNA Barcoding, Taxonomic/methods ; Ponds ; Biodiversity ; Metagenomics/methods ; }, abstract = {More efficient methods for extensive biodiversity monitoring are required to support rapid measures to address the biodiversity crisis. While environmental DNA (eDNA) metabarcoding and quantitative PCR (qPCR) methods offer advantages over traditional monitoring approaches, their large-scale application is limited by the time and labour required for developing assays and/or for analysis. CRISPR (clustered regularly interspaced short palindromic repeats) diagnostic technologies (Dx) may overcome some of these limitations, but they have been used solely with species-specific primers, restricting their versatility for biodiversity monitoring. Here, we demonstrate the feasibility of designing species-specific CRISPR-Dx assays in silico within a short metabarcoding fragment using a general primer set, a methodology we term 'ampliscanning', for 18 of the 22 amphibian species in Switzerland. We sub-selected nine species, including three classified as regionally endangered, to test the methodology using eDNA sampled from ponds at nine sites. We compared the ampliscanning detections to data from traditional monitoring at these sites. Ampliscanning was successful at detecting target species with different prevalences across the landscape. With only one visit, we detected more species per site than three traditional monitoring visits (visual and acoustic detections by trained experts), in particular more elusive species and previously undocumented but expected populations. Ampliscanning detected 25 species/site combinations compared to 12 with traditional monitoring. Sensitivity analyses showed that larger numbers of field visits and PCR replicates are more important for reliable detection than many technical replicates at the CRISPR-Dx assay level. Given the reduced sampling and analysis effort, our results highlight the benefits of eDNA and CRISPR-Dx combined with universal primers for large-scale monitoring of multiple endangered species across landscapes to inform conservation measures.}, } @article {pmid39152482, year = {2024}, author = {Luo, W and Zhao, M and Dwidar, M and Gao, Y and Xiang, L and Wu, X and Medema, MH and Xu, S and Li, X and Schäfer, H and Chen, M and Feng, R and Zhu, Y}, title = {Microbial assimilatory sulfate reduction-mediated H2S: an overlooked role in Crohn's disease development.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {152}, pmid = {39152482}, issn = {2049-2618}, support = {82370551//National Natural Science Foundation of China/ ; 82270579//National Natural Science Foundation of China/ ; 82100577//National Natural Science Foundation of China/ ; 2024GXNSFFA010009//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; }, mesh = {*Crohn Disease/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Hydrogen Sulfide/metabolism ; Animals ; Mice ; *Sulfates/metabolism ; Escherichia coli/genetics/metabolism ; Feces/microbiology ; Dysbiosis/microbiology ; Colon/microbiology ; Metagenomics ; Oxidation-Reduction ; Disease Models, Animal ; Female ; }, abstract = {BACKGROUND: H2S imbalances in the intestinal tract trigger Crohn's disease (CD), a chronic inflammatory gastrointestinal disorder characterized by microbiota dysbiosis and barrier dysfunction. However, a comprehensive understanding of H2S generation in the gut, and the contributions of both microbiota and host to systemic H2S levels in CD, remain to be elucidated. This investigation aimed to enhance comprehension regarding the sulfidogenic potential of both the human host and the gut microbiota.

RESULTS: Our analysis of a treatment-naive CD cohorts' fecal metagenomic and biopsy metatranscriptomic data revealed reduced expression of host endogenous H2S generation genes alongside increased abundance of microbial exogenous H2S production genes in correlation with CD. While prior studies focused on microbial H2S production via dissimilatory sulfite reductases, our metagenomic analysis suggests the assimilatory sulfate reduction (ASR) pathway is a more significant contributor in the human gut, given its high prevalence and abundance. Subsequently, we validated our hypothesis experimentally by generating ASR-deficient E. coli mutants ∆cysJ and ∆cysM through the deletion of sulfite reductase and L-cysteine synthase genes. This alteration significantly affected bacterial sulfidogenic capacity, colon epithelial cell viability, and colonic mucin sulfation, ultimately leading to colitis in murine model. Further study revealed that gut microbiota degrade sulfopolysaccharides and assimilate sulfate to produce H2S via the ASR pathway, highlighting the role of sulfopolysaccharides in colitis and cautioning against their use as food additives.

CONCLUSIONS: Our study significantly advances understanding of microbial sulfur metabolism in the human gut, elucidating the complex interplay between diet, gut microbiota, and host sulfur metabolism. We highlight the microbial ASR pathway as an overlooked endogenous H2S producer and a potential therapeutic target for managing CD. Video Abstract.}, } @article {pmid39152146, year = {2024}, author = {Mizsei, E and Radovics, D and Rák, G and Budai, M and Bancsik, B and Szabolcs, M and Sos, T and Lengyel, S}, title = {Alpine viper in changing climate: thermal ecology and prospects of a cold-adapted reptile in the warming Mediterranean.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {18988}, pmid = {39152146}, issn = {2045-2322}, support = {150510498//Mohamed bin Zayed Species Conservation Fund/ ; 15478-1//Rufford Foundation/ ; PD146621//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; K106133//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; K134391//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal,Hungary/ ; }, mesh = {Animals ; *Viperidae/physiology ; *Climate Change ; Male ; Female ; Ecosystem ; Body Temperature Regulation/physiology ; Greece ; Cold Temperature ; Adaptation, Physiological ; Mediterranean Region ; Acclimatization/physiology ; Phylogeny ; Body Temperature/physiology ; }, abstract = {In a rapidly changing thermal environment, reptiles are primarily dependent on in situ adaptation because of their limited ability to disperse and the restricted opportunity to shift their ranges. However, the rapid pace of climate change may surpass these adaptation capabilities or elevate energy expenditures. Therefore, understanding the variability in thermal traits at both individual and population scales is crucial, offering insights into reptiles' vulnerability to climate change. We studied the thermal ecology of the endangered Greek meadow viper (Vipera graeca), an endemic venomous snake of fragmented alpine-subalpine meadows above 1600 m of the Pindos mountain range in Greece and Albania, to assess its susceptibility to anticipated changes in the alpine thermal environment. We measured preferred body temperature in artificial thermal gradient, field body temperatures of 74 individuals in five populations encompassing the entire geographic range of the species, and collected data on the available of temperatures for thermoregulation. We found that the preferred body temperature (Tp) differed only between the northernmost and the southernmost populations and increased with female body size but did not depend on sex or the gravidity status of females. Tp increased with latitude but was unaffected by the phylogenetic position of the populations. We also found high accuracy of thermoregulation in V. graeca populations and variation in the thermal quality of habitats throughout the range. The overall effectiveness of thermoregulation was high, indicating that V. graeca successfully achieves its target temperatures and exploits the thermal landscape. Current climatic conditions limit the activity period by an estimated 1278 h per year, which is expected to increase considerably under future climate scenarios. Restricted time available for thermoregulation, foraging and reproduction will represent a serious threat to the fitness of individuals and the persistence of populations in addition to habitat loss due to mining, tourism or skiing and habitat degradation due to overgrazing in the shrinking mountaintop habitats of V. graeca.}, } @article {pmid39151634, year = {2024}, author = {Xu, WJ and Meng, L and Zhao, YK and Wu, J and Liu, HM and Wang, JQ and Zheng, N}, title = {Characteristics of psychrophilic bacterial communities and associated metabolism pathways in different environments by a metagenomic analysis.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {175496}, doi = {10.1016/j.scitotenv.2024.175496}, pmid = {39151634}, issn = {1879-1026}, mesh = {China ; *Bacteria/classification/metabolism/genetics ; *Metagenomics ; *Milk/microbiology ; Animals ; Microbiota ; }, abstract = {Psychrophilic bacteria, the dominant spoilage organisms in raw milk, secrete heat-stable extracellular proteases and lipases that lead to the decomposition of milk and dairy products. In this study, we investigated psychrophilic bacteria in 165 raw milk samples collected across four seasons and six regions in China using shotgun metagenomic sequencing and traditional culture methods. The isolated psychrophilic bacteria were classified into 40 genera and 185 species. Pseudomonas was the most prevalent, accounting for 51.13 % of the genera, while Lactococcus and Chryseobacterium were also notably abundant (> 6.0 %). Metagenomic sequencing revealed that Pseudomonas (47.9 %), Stenotrophomonas (9.75 %), Sphingomonas (6.73 %), Latilactobacillus (6.38 %) and Lactococcus (5.16 %) were the dominant genera in the raw milk samples. The diversity of psychrophilic bacteria in raw milk was strongly influenced by seasonal variations, with the sampling region being a less significant factor. KEGG annotation indicated that carbohydrate and amino acid metabolism were the primary metabolic pathways in these bacteria. Metagenomic sequencing not only accurately identifies species but also provides functional insights into psychrophilic bacteria in raw milk, aiding in understanding their activities, promoting their control on farms, and ultimately improving raw milk quality.}, } @article {pmid39151620, year = {2024}, author = {Zheng, Y and Wu, Z and Wang, P and Wei, Y and Jia, K and Zhang, M and Shi, X and Zhang, L and Li, J}, title = {Long-chain fatty acids facilitate acidogenic fermentation of food waste: Attention to the microbial response and the change of core metabolic pathway under saturated and unsaturated fatty acids loading.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175565}, doi = {10.1016/j.scitotenv.2024.175565}, pmid = {39151620}, issn = {1879-1026}, mesh = {*Fermentation ; *Fatty Acids/metabolism ; Metabolic Networks and Pathways ; Fatty Acids, Volatile/metabolism ; Fatty Acids, Unsaturated/metabolism ; Food Loss and Waste ; }, abstract = {Long-chain fatty acids (LCFAs) are recognized as a significant inhibitory factor in anaerobic digestion of food waste (FW), yet they are inevitably present in FW due to lipid hydrolysis. Given their distinct synthesis mechanism from traditional anaerobic digestion, little is known about the effect of LCFAs on FW acidogenic fermentation. This study reveals that total volatile fatty acids (VFAs) production increased by 9.98 % and 4.03 % under stearic acid and oleic acid loading, respectively. Acetic acid production increased by 20.66 % under stearic acid loading compared to the control group (CK). However, the LCFA stress restricted the degradation of solid organic matter, particularly under oleic acid stress. Analysis of microbial community structure and quorum sensing (QS) indicates that LCFA stress enhanced the relative abundance of Lactobacillus and Klebsiella. In QS system, the relative abundance of luxS declined from 0.157 % to 0.116 % and 0.125 % under oleic acid and stearic acid stress, respectively. LCFA stress limited the Autoinducer-2 (AI-2) biosynthesis, suggesting that microorganisms cannot use QS to resist the LCFA stress. Metagenomic sequencing showed that LCFA stress promoted acetic acid production via the conversion of pyruvate and acetyl-CoA to acetate. Direct conversion of pyruvate to acetic acid increased by 47.23 % compared to the CK group, accounting for the enhanced acetic acid production under stearic acid loading. The abundance of β-oxidation pathway under stearic acid loading was lower than under oleic acid loading. Overall, the stimulating direct conversion of pyruvate plays a pivotal role in enhancing acetic acid biosynthesis under stearic acid loading, providing insights into the effect of LCFA on mechanism of FW acidogenic fermentation.}, } @article {pmid39151617, year = {2024}, author = {Galisteo, C and Puente-Sánchez, F and de la Haba, RR and Bertilsson, S and Sánchez-Porro, C and Ventosa, A}, title = {Metagenomic insights into the prokaryotic communities of heavy metal-contaminated hypersaline soils.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175497}, doi = {10.1016/j.scitotenv.2024.175497}, pmid = {39151617}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Metals, Heavy/analysis ; *Soil Pollutants/analysis ; *Bacteria/metabolism/classification ; *Microbiota ; *Archaea/genetics ; Soil/chemistry ; Spain ; Salinity ; Metagenome ; Metagenomics ; }, abstract = {Saline soils and their microbial communities have recently been studied in response to ongoing desertification of agricultural soils caused by anthropogenic impacts and climate change. Here we describe the prokaryotic microbiota of hypersaline soils in the Odiel Saltmarshes Natural Area of Southwest Spain. This region has been strongly affected by mining and industrial activity and feature high levels of certain heavy metals. We sequenced 18 shotgun metagenomes through Illumina NovaSeq from samples obtained from three different areas in 2020 and 2021. Taxogenomic analyses demonstrate that these soils harbored equal proportions of archaea and bacteria, with Methanobacteriota, Pseudomonadota, Bacteroidota, Gemmatimonadota, and Balneolota as most abundant phyla. Functions related to the transport of heavy metal outside the cytoplasm are among the most relevant features of the community (i.e., ZntA and CopA enzymes). They seem to be indispensable to avoid the increase of zinc and copper concentration inside the cell. Besides, the archaeal phylum Methanobacteriota is the main arsenic detoxifier within the microbiota although arsenic related genes are widely distributed in the community. Regarding the osmoregulation strategies, "salt-out" mechanism was identified in part of the bacterial population, whereas "salt-in" mechanism was present in both domains, Bacteria and Archaea. De novo biosynthesis of two of the most universal compatible solutes was detected, with predominance of glycine betaine biosynthesis (betAB genes) over ectoine (ectABC genes). Furthermore, doeABCD gene cluster related to the use of ectoine as carbon and energy source was solely identified in Pseudomonadota and Methanobacteriota.}, } @article {pmid39150504, year = {2024}, author = {Sessa, R and Filardo, S and Viscardi, MF and Brandolino, G and Muzii, L and Di Pietro, M and Porpora, MG}, title = {Characterization of the vaginal microbiota in Italian women with endometriosis: preliminary study.}, journal = {Archives of gynecology and obstetrics}, volume = {310}, number = {4}, pages = {2141-2151}, pmid = {39150504}, issn = {1432-0711}, mesh = {Humans ; Female ; *Endometriosis/microbiology ; Adult ; *Vagina/microbiology ; Cross-Sectional Studies ; Italy ; *Microbiota ; Young Adult ; Dysbiosis/microbiology ; Bacteria/isolation & purification/classification/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {PURPOSE: This cross-sectional study aims to assess the interplay between the vaginal microbiota and endometriosis.

METHODS: 123 consecutive Italian fertile women, aged between 20 and 40 years old, were enrolled during a routine gynecological consultation; 24 were diagnosed with endometriosis and 99 did not complain of any gynecological disease. All women underwent a vaginal swab for the evaluation of the composition and diversity of vaginal microbiota by means of 16 s rDNA metagenomic sequencing.

RESULTS: Compared to women with no gynecological disease, the vaginal microbiota in women with endometriosis showed a similar abundance of Lactobacillus spp.; however, a statistically significant lower abundance in the genera Pseudomonas (p < 0.01), Bifidobacterium (p < 0.05), Novispirillum (p < 0.0000001) and Sphingomonas (p < 0.0000001), and a statistically significant increase in the abundance of the genera Escherichia (p < 0.00001), Megasphaera (p < 0.00001), and Sneathia (p < 0.0001) were observed.

CONCLUSIONS: There is a complex interplay between vaginal microbiota composition and endometriosis, showing a distinct microbial signature in the bacterial genera usually found in dysbiosis.}, } @article {pmid39150251, year = {2024}, author = {Lv, Y and Zhen, C and Liu, A and Hu, Y and Yang, G and Xu, C and Lou, Y and Cheng, Q and Luo, Y and Yu, J and Fang, Y and Zhao, H and Peng, K and Yu, Y and Lou, J and Chen, J and Ni, Y}, title = {Profiles and interactions of gut microbiome and intestinal microRNAs in pediatric Crohn's disease.}, journal = {mSystems}, volume = {9}, number = {9}, pages = {e0078324}, pmid = {39150251}, issn = {2379-5077}, mesh = {Humans ; *MicroRNAs/genetics/metabolism ; *Crohn Disease/microbiology/genetics/metabolism ; *Gastrointestinal Microbiome ; Child ; Male ; Female ; Adolescent ; Feces/microbiology ; Dysbiosis/genetics/microbiology ; Intestines/microbiology ; Bacteria/genetics/isolation & purification ; Intestinal Mucosa/microbiology/metabolism ; }, abstract = {UNLABELLED: Gut dysbiosis is closely related to dysregulated microRNAs (miRNAs) in the intestinal epithelial cells, which plays an important role in the pathogenesis of Crohn's disease (CD). We investigated the relationship between fecal gut microbiome (GM) and intestinal tissue miRNAs in different stages of pediatric CD. Metagenomic analysis and miRNA sequencing were conducted to examine the GM and intestinal miRNA profiles of CD patients before and after clinical induction therapy and the controls. Twenty-seven newly diagnosed, therapy-naïve pediatric patients with active CD and 11 non-inflammatory bowel disease (IBD) controls were recruited in this study. Among CD patients, 11 patients completed induction treatment and reached clinical remission. Both GM and miRNA profiles were significantly changed between CD patients and controls. Seven key bacteria were identified at species level including Defluviitalea raffinosedens, Thermotalea metallivorans, Roseburia intestinalis, Dorea sp. AGR2135, Escherichia coli, Shigella sonnei, and Salmonella enterica, the exact proportions of which were further validated by real-time quantitative PCR analysis. Eight key miRNAs were also identified including hsa-miR-215-5p, hsa-miR-194-5p, hsa-miR-12135, hsa-miR-509-3-5p, hsa-miR-212-5p, hsa-miR-4448, hsa-miR-501-3p, and hsa-miR-503-5p. The functional enrichment analysis of differential miRNAs indicated the significantly altered cyclin protein, cyclin-dependent protein, and cell cycle pathway. The close interactions between seven key bacteria and eight key miRNAs were further investigated by miRNA target prediction. The association between specific miRNA expressions and key gut bacteria at different stages of CD supported their important roles as potential molecular biomarkers. Understanding the relationship between them will help us to explore the molecular mechanisms of CD.

IMPORTANCE: Since previous studies have focused on the change of the fecal gut microbiome and intestinal tissue miRNA in pediatric Crohn's disease (CD), the relationship between them in different stages is still not clear. This is the first study to explore the gut microbiota and miRNA and their correlations with the Pediatric Crohn's Disease Activity Index (PCDAI). Crohn's Disease Endoscopic Index of Severity (CDEIS), and calprotectin, by applying two omics approach in three different groups (active CD, CD in remission with exclusive enteral nutrition or infliximab induction therapy, and the healthy controls). Both gut microbiome structure and the miRNA profiles were significantly changed in the different stage of CD. Seven key gut microbiome at species and eight key miRNAs were found, and their close interactions were further fully investigated by miRNA target prediction.}, } @article {pmid39149810, year = {2024}, author = {Liu, J and Wang, WJ and Xu, GF and Wang, YX and Lin, Y and Zheng, X and Yao, SH and Zheng, KH}, title = {Does Microbiome Contribute to Longevity? Compositional and Functional Differences in Gut Microbiota in Chinese Long-Living (>90 Years) and Elderly (65-74 Years) Adults.}, journal = {Omics : a journal of integrative biology}, volume = {28}, number = {9}, pages = {461-469}, doi = {10.1089/omi.2024.0120}, pmid = {39149810}, issn = {1557-8100}, mesh = {Humans ; Aged ; *Longevity ; *Gastrointestinal Microbiome/physiology ; Aged, 80 and over ; Male ; Female ; China ; Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; East Asian People ; }, abstract = {The study of longevity and its determinants has been revitalized with the rise of microbiome scholarship. The gut microbiota have been established to play essential protective, metabolic, and physiological roles in human health and disease. The gut dysbiosis has been identified as an important factor contributing to the development of multiple diseases. Accordingly, it is reasonable to hypothesize that the gut microbiota of long-living individuals have healthy antiaging-associated gut microbes, which, by extension, might provide specific molecular targets for antiaging treatments and interventions. In the present study, we compared the gut microbiota of Chinese individuals in two different age groups, long-living adults (aged over 90 years) and elderly adults (aged 65-74 years) who were free of major diseases. We found significantly lower relative abundances of bacteria in the genera Sutterella and Megamonas in the long-living individuals. Furthermore, we established that while biological processes such as autophagy (GO:0006914) and telomere maintenance through semiconservative replication (GO:0032201) were enhanced in the long-living group, response to lipopolysaccharide (GO:0032496), nicotinamide adenine dinucleotide oxidation (GO:0006116), and S-adenosyl methionine metabolism (GO:0046500) were weakened. Moreover, the two groups were found to differ with respect to amino acid metabolism. We suggest that these compositional and functional differences in the gut microbiota may potentially be associated with mechanisms that contribute to determining longevity or aging.}, } @article {pmid39147529, year = {2024}, author = {Xiang, L and Zhuo, S and Luo, W and Tian, C and Xu, S and Li, X and Zhu, Y and Feng, R and Chen, M}, title = {Decoding polyphenol metabolism in patients with Crohn's disease: Insights from diet, gut microbiota, and metabolites.}, journal = {Food research international (Ottawa, Ont.)}, volume = {192}, number = {}, pages = {114852}, doi = {10.1016/j.foodres.2024.114852}, pmid = {39147529}, issn = {1873-7145}, mesh = {Humans ; *Crohn Disease/microbiology/metabolism/drug therapy ; *Gastrointestinal Microbiome/physiology ; *Polyphenols/metabolism ; Female ; Male ; Adult ; *Diet ; Hippurates/metabolism ; Middle Aged ; Young Adult ; Bacteria/classification/metabolism/genetics ; Feces/microbiology ; }, abstract = {Crohn's disease (CD) is a chronic and progressive inflammatory disease that can involve any part of the gastrointestinal tract. The protective role of dietary polyphenols has been documented in preclinical models of CD. Gut microbiota mediates the metabolism of polyphenols and affects their bioactivity and physiological functions. However, it remains elusive the capacity of microbial polyphenol metabolism in CD patients and healthy controls (HCs) along with its correlation with polyphenols intake and polyphenol-derived metabolites. Thus, we aimed to decode polyphenol metabolism in CD patients through aspects of diet, gut microbiota, and metabolites. Dietary intake analysis revealed that CD patients exhibited decreased intake of polyphenols. Using metagenomic data from two independent clinical cohorts (FAH-SYSU and PRISM), we quantified abundance of polyphenol degradation associated bacteria and functional genes in CD and HCs and observed a lower capacity of flavonoids degradation in gut microbiota residing in CD patients. Furthermore, through analysis of serum metabolites and enterotypes in participants of FAH-SYSU cohort, we observed that CD patients exhibited reduced levels of serum hippuric acid (HA), one of polyphenol-derived metabolites. HA level was higher in healthier enterotypes (characterized by dominance of Ruminococcaceae and Prevotellaceae, dominant by HCs) and positively correlated with multiple polyphenols intake and abundance of bacteria engaged in flavonoids degradation as well as short-chain fatty acid production, which could serve as a biomarker for effective polyphenol metabolism by the gut microbiota and a healthier gut microbial community structure. Overall, our findings provide a foundation for future work exploring the polyphenol-based or microbiota-targeted therapeutic strategies in CD.}, } @article {pmid39147499, year = {2024}, author = {Magliulo, R and Valentino, V and Balivo, A and Esposito, A and Genovese, A and Ercolini, D and De Filippis, F}, title = {Microbiome signatures associated with flavor development differentiate Protected Designation of origin water Buffalo Mozzarella cheese from different production areas.}, journal = {Food research international (Ottawa, Ont.)}, volume = {192}, number = {}, pages = {114798}, doi = {10.1016/j.foodres.2024.114798}, pmid = {39147499}, issn = {1873-7145}, mesh = {*Cheese/microbiology/analysis ; Animals ; *Volatile Organic Compounds/analysis ; *Microbiota ; *Buffaloes ; Italy ; *Gas Chromatography-Mass Spectrometry ; *Taste ; Food Microbiology ; Lactobacillus helveticus ; Streptococcus thermophilus/classification ; }, abstract = {Water Buffalo Mozzarella (BM) is a typical cheese from Southern Italy with unique flavor profile and texture. It is produced following a traditional back-slopping procedure and received the Protected Designation of Origin (PDO) label. To better understand the link between the production area, the microbiome composition and the flavor profile of the products, we performed a multiomic characterization of PDO BM collected from 57 different dairies located in the two main PDO production area, i.e. Caserta (n = 35) and Salerno (n = 22). Thus, we assessed the microbiome by high-throughput shotgun metagenomic sequencing and the Volatile Organic Compounds (VOCs) by gas chromatography/mass spectrometry (GC/MS). Streptococcus thermophilus, Lactobacillus helveticus, and Lactobacillus delbrueckii subsp. delbrueckii were identified as the core microbiome present in all samples. However, the microbiome taxonomic profiles resulted in a clustering of the samples based on their geographical origin, also showing that BM from Caserta had a greater microbial diversity. Consistently, Caserta and Salerno samples also showed different VOC profiles. These results suggest that the microbiome and its specific metabolic activity are part of the terroir that shape BM specific features, linking this traditional product with the area of production, thus opening new clues for improving traceability and fraud protection of traditional products.}, } @article {pmid39147334, year = {2024}, author = {Hu, Z and Yao, Y and Chen, F and Feng, L and Yuan, Z and Deng, J and Huang, L and Yin, Y and Tang, X}, title = {Integrated analyses of the intestinal microbiome and transcriptome in Ningxiang piglets.}, journal = {Genomics}, volume = {116}, number = {5}, pages = {110919}, doi = {10.1016/j.ygeno.2024.110919}, pmid = {39147334}, issn = {1089-8646}, mesh = {Animals ; *Gastrointestinal Microbiome ; Swine ; *Transcriptome ; }, abstract = {Ningxiang (NX) pig has been recognized as one of the most famous Chinese indigenous breeds due to its characteristics in stress resistance. However, intestinal microbial feature and gene profiling in NX piglets have not been studied. Here, we compared the intestinal microbiome and transcriptome between NX and Duroc × Landrace × Large white (DLY) piglets and found the high enrichment of several colonic Bacteroides, Prevotella and Clostridium species in NX piglets. Further functional analyses revealed their predominant function in methane, glycolysis and gluconeogenesis metabolism. Our mRNA-sequencing data unraveled the distinct colonic gene expression between these two breeds. In particular, we showed that the improved intestinal function in NX piglets may be determined by enhanced intestinal barrier gene expression and varied immune gene expression through modulating the composition of the gut microbes. Together, our study revealed the intestinal characteristics of NX piglets, providing their potential application in improving breeding strategies and developing dietary interventions.}, } @article {pmid39147055, year = {2024}, author = {Lu, J and Qing, C and Huang, X and Zeng, J and Zheng, Y and Xia, P}, title = {Seasonal dynamics and driving mechanisms of microbial biogenic elements cycling function, assembly process, and co-occurrence network in plateau lake sediments.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175510}, doi = {10.1016/j.scitotenv.2024.175510}, pmid = {39147055}, issn = {1879-1026}, mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology ; *Seasons ; *Phosphorus/analysis ; *Microbiota ; *Nitrogen/analysis ; China ; Environmental Monitoring ; Bacteria/classification/genetics ; Carbon/analysis/metabolism ; }, abstract = {Microbial community diversity significantly varies with seasonality. However, little is known about seasonal variation of microbial community functions in lake sediments and their associated environmental influences. In this study, metagenomic sequencing of sediments collected from winter, summer, and autumn from Caohai Lake, Guizhou Plateau, were used to evaluate the composition and function of sediment microbial communities, the potential interactions of functional genes, key genes associated with seasons, and community assembly mechanisms. The average concentrations of nitrogen (TN) and phosphorus (TP) in lake sediments were higher, which were 6.136 and 0.501 g/kg, respectively. TN and organic matter (OM) were the primary factors associated with sediment community composition and functional profiles. The diversity and structure of the microbial communities varied with seasons, and Proteobacteria relative abundances were significantly lower in summer than in other seasons (58.43-44.12 %). Seasons were also associated with the relative abundances of functional genes, and in particular korA, metF, narC, nrfA, pstC/S, and soxB genes. Network complexity was highest in the summer and key genes in the network also varied across seasons. Neutral community model analysis revealed that the assembly mechanisms related to carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycle-related genes were primarily associated with random processes. In summary, diverse functional genes were identified in lake sediments and exhibited evidence for synergistic interactions (Positive proportion: 74.91-99.82 %), while seasonal factors influenced their distribution. The results of this study provide new insights into seasonal impacts on microbial-driven biogeochemical cycling in shallow lakes.}, } @article {pmid39146922, year = {2024}, author = {Yuan, Y and Mo, C and Huang, F and Liao, X and Yang, Y}, title = {Microbial metabolism affects the antibiotic resistome in the intestine of laying hens.}, journal = {Poultry science}, volume = {103}, number = {10}, pages = {104138}, pmid = {39146922}, issn = {1525-3171}, mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome/drug effects ; Female ; Anti-Bacterial Agents/pharmacology ; Escherichia coli/drug effects/genetics ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial ; Bacteria/drug effects/genetics/classification ; Intestines/microbiology/drug effects ; Cecum/microbiology ; }, abstract = {Intestinal microbial metabolism has an important impact on the health of laying hens, and microbes are also important hosts for ARGs. However, the relationship between intestinal microbes and antibiotic resistance in laying hens is unclear. In this study, a slaughtering experiment, an in vitro fermentation experiment and a single-bacteria culture experiment were carried out, and metagenomic and metabolomic analyses were used to investigate the relationships between microbial metabolism and the antibiotic resistome in the cecum of laying hens. The results showed that there were different types of ARGs in the intestines of laying hens, and the risk scores of the ARGs tended to decrease with growth stage. A total of 1142 metagenome-assembled genomes (MAGs) were obtained, and Escherichia coli was found to be the dominant ARG host, carrying 62 ARGs. Metabolomics revealed that indole and its derivatives, such as indole-3-lactic acid, were negatively correlated with a variety of ARGs. Moreover, in vitro fermentation experiment and single-bacteria culture experiment demonstrated that indole-3-lactic acid reduced the abundance and risk of multiple ARGs in the intestine and inhibited the growth of the ARG host Escherichia coli. In the context of high concern about intestinal microbial metabolism and antibiotic resistance, this is the first study to focus on the relationship between intestinal microbial metabolism and antibiotic resistance in laying hens. These findings have important implications for healthy farming and antibiotic resistance control.}, } @article {pmid39146704, year = {2024}, author = {Li, G and Wu, M and Xiao, Y and Tong, Y and Li, S and Qian, H and Zhao, T}, title = {Multi-omics reveals the ecological and biological functions of Enterococcus mundtii in the intestine of lepidopteran insects.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {52}, number = {}, pages = {101309}, doi = {10.1016/j.cbd.2024.101309}, pmid = {39146704}, issn = {1878-0407}, mesh = {Animals ; *Bombyx/microbiology/genetics ; *Enterococcus/genetics ; *Gastrointestinal Microbiome ; *Intestines/microbiology ; Proteomics ; Symbiosis ; Multiomics ; }, abstract = {Insect guts offer unique habitats for microbial colonization, with gut bacteria potentially offering numerous benefits to their hosts. Although Enterococcus has emerged as one of the predominant gut commensal bacteria in insects, its establishment in various niches within the gut has not been characterized well. In this study, Enterococcus mundtii was inoculated into the silkworm (Bombyx mori L.) to investigate its biological functions. Genome-based analysis revealed that its successful colonization is related to adherence genes (ebpA, ebpC, efaA, srtC, and scm). This bacterium did not alter the activities of related metabolic enzymes or the intestinal barrier function. However, significant changes in the gene expressions levels of Att2, CecA, and Lys suggest potential adaptive mechanisms of host immunity to symbiotic E. mundtii. Moreover, 16S metagenomics analysis revealed a significant increase in the relative abundance of E. mundtii in the intestines of silkworms following inoculation. The intestinal microbiome displayed marked heterogeneity, an elevated gut microbiome health index, a reduced microbial dysbiosis index, and low potential pathogenicity in the treatment group. Additionally, E. mundtii enhanced the breakdown of carbohydrates in host intestines. Overall, E. mundtii serves as a beneficial microbe for insects, promoting intestinal homeostasis by providing competitive advantage. This characteristic helps E. mundtii dominate complex microbial environments and remain prevalent across Lepidoptera, likely fostering long-term symbiosis between the both parties. The present study contributes to clarifying the niche of E. mundtii in the intestine of lepidopteran insects and further reveals its potential roles in their insect hosts.}, } @article {pmid39145585, year = {2024}, author = {Liu, B and Wang, G and Wang, L and Yan, J and Zhu, K and Liu, Q and Zhao, J and Jia, B and Fang, M and Rudich, Y and Morawska, L and Chen, J}, title = {Unraveling Cross-Organ Impacts of Airborne Pollutants: A Multiomics Study on Respiratory Exposure and Gastrointestinal Health.}, journal = {Environmental science & technology}, volume = {58}, number = {35}, pages = {15511-15521}, doi = {10.1021/acs.est.4c06035}, pmid = {39145585}, issn = {1520-5851}, mesh = {Mice ; Animals ; *Air Pollutants/toxicity ; Inhalation Exposure ; Gastrointestinal Microbiome/drug effects ; Gastrointestinal Tract/drug effects ; Multiomics ; }, abstract = {Poor air quality is increasingly linked to gastrointestinal diseases, suggesting a potential correlation with human intestine health. However, this relationship remains largely unexplored due to limited research. This study used a controlled mouse model exposed to cooking oil fumes (COFs) and metagenomics, transcriptomics, and metabolomics to elucidate interactions between intestine microbiota and host metabolism under environmental stress. Our findings reveal that short-term COF inhalation induces pulmonary inflammation within 3 days and leads to gastrointestinal disturbances, elucidating a pathway connecting respiratory exposure to intestinal dysfunction. The exposure intensity significantly correlates with changes in intestinal tissue integrity, microbial composition, and metabolic function. Extended exposure of 7 days disrupts intestine microbiota and alters tryptophan metabolism, with further changes observed after 14 days, highlighting an adaptive response. These results highlight the vulnerability of intestinal health to airborne pollutants and suggest a pathway through which inhaled pollutants may affect distant organ systems.}, } @article {pmid39143383, year = {2024}, author = {Vijayan, J and Ezhuthanikkunnel, AP and Punnorkodu, SAK and Poikayil, SS and Mohan, M and Ammanamveetil, MHA}, title = {Sediment microbial diversity, functional potentials, and antibiotic resistance pattern: a case study of Cochin Estuary core sediment.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {39}, pages = {52132-52146}, pmid = {39143383}, issn = {1614-7499}, mesh = {*Geologic Sediments/microbiology ; *Estuaries ; India ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Phylogeny ; Biodiversity ; }, abstract = {Marine sediments are an important part of the marine environment and the world's greatest organic carbon source. Sediment microorganisms are important regulators of major geochemical and eco-environmental processes in marine environments, especially nutrient dynamics and biogeochemical cycles. Despite their importance, core marine microorganisms are virtually unknown due to a lack of consensus on how to identify them. Most core microbiotas have been characterized thus far based on species abundance and occurrence. The combined effects of habitat and depth on benthic bacterial communities and ecological functions were studied using "Next-Generation sequencing (NGS) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predictive functional profiling" at the surface (0.2 cm) and bottom depth (250 cm) in a sediment core sample from Cochin Estuary, Kerala, India. The results showed that bacterial diversity and richness were significantly higher in the surface sediment sample with the most abundant phyla being Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidetes. The major metabolic functions were metabolism, followed by environmental information processing and genetic information processing. Antibiotic resistance genes between the surface and bottom samples help to understand the resistance pattern among multidrug resistance is the most prominent one. Among viruses, Siphoviridae is the dominant family, followed by Myoviridae. In the case of Archea, Crenarchaeota is dominant, whereas among eukaryotes phyla Streptophyta and Chordata were dominant in the surface and the bottom samples respectively.}, } @article {pmid39143364, year = {2024}, author = {Akhlaghi, E and Salari, E and Mansouri, M and Shafiei, M and Kalantar-Neyestanaki, D and Aghassi, H and Fasihi Harandi, M}, title = {Identification and comparison of intestinal microbial diversity in patients at different stages of hepatic cystic echinococcosis.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {18912}, pmid = {39143364}, issn = {2045-2322}, support = {400000473//Kerman University of Medical Sciences/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Echinococcosis, Hepatic/microbiology/parasitology ; Male ; Female ; *RNA, Ribosomal, 16S/genetics ; Adult ; Middle Aged ; Feces/microbiology/parasitology ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; High-Throughput Nucleotide Sequencing ; }, abstract = {There is a significant focus on the role of the host microbiome in different outcomes of human parasitic diseases, including cystic echinococcosis (CE). This study was conducted to identify the intestinal microbiome of patients with CE at different stages of hydatid cyst compared to healthy individuals. Stool samples from CE patients as well as healthy individuals were collected. The samples were divided into three groups representing various stages of hepatic hydatid cyst: active (CE1 and CE2), transitional (CE3), and inactive (CE4 and CE5). One family member from each group was selected to serve as a control. The gut microbiome of patients with different stages of hydatid cysts was investigated using metagenomic next-generation amplicon sequencing of the V3-V4 region of the 16S rRNA gene. In this study, we identified 4862 Operational Taxonomic Units from three stages of hydatid cysts in CE patients and healthy individuals with a combined frequency of 2,955,291. The most abundant genera observed in all the subjects were Blautia, Agathobacter, Faecalibacterium, Bacteroides, Bifidobacterium, and Prevotella. The highest microbial frequency was related to inactive forms of CE, and the lowest frequency was observed in the group with active forms. However, the lowest OTU diversity was found in patients with inactive cysts compared with those with active and transitional cyst stages. The genus Agatobacter had the highest OTU frequency. Pseudomonas, Gemella, and Ligilactobacillus showed significant differences among the patients with different stages of hydatid cysts. Additionally, Anaerostipes and Candidatus showed significantly different reads in CE patients compared to healthy individuals. Our findings indicate that several bacterial genera can play a role in the fate of hydatid cysts in patients at different stages of the disease.}, } @article {pmid39143178, year = {2024}, author = {Duru, IC and Lecomte, A and Shishido, TK and Laine, P and Suppula, J and Paulin, L and Scheperjans, F and Pereira, PAB and Auvinen, P}, title = {Metagenome-assembled microbial genomes from Parkinson's disease fecal samples.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {18906}, pmid = {39143178}, issn = {2045-2322}, support = {NNF22OC0080109//Novo Nordisk Foundation/ ; }, mesh = {*Parkinson Disease/genetics/microbiology ; Humans ; *Feces/microbiology ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Genome, Bacterial ; Male ; Aged ; Female ; Genome, Microbial ; Middle Aged ; High-Throughput Nucleotide Sequencing ; }, abstract = {The human gut microbiome composition has been linked to Parkinson's disease (PD). However, knowledge of the gut microbiota on the genome level is still limited. Here we performed deep metagenomic sequencing and binning to build metagenome-assembled genomes (MAGs) from 136 human fecal microbiomes (68 PD samples and 68 control samples). We constructed 952 non-redundant high-quality MAGs and compared them between PD and control groups. Among these MAGs, there were 22 different genomes of Collinsella and Prevotella, indicating high variability of those genera in the human gut environment. Microdiversity analysis indicated that Ruminococcus bromii was statistically significantly (p < 0.002) more diverse on the strain level in the control samples compared to the PD samples. In addition, by clustering all genes and performing presence-absence analysis between groups, we identified several control-specific (p < 0.05) related genes, such as speF and Fe-S oxidoreductase. We also report detailed annotation of MAGs, including Clusters of Orthologous Genes (COG), Cas operon type, antiviral gene, prophage, and secondary metabolites biosynthetic gene clusters, which can be useful for providing a reference for future studies.}, } @article {pmid39143108, year = {2024}, author = {Grahnemo, L and Kambur, O and Lahti, L and Jousilahti, P and Niiranen, T and Knight, R and Salomaa, V and Havulinna, AS and Ohlsson, C}, title = {Associations between gut microbiota and incident fractures in the FINRISK cohort.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {69}, pmid = {39143108}, issn = {2055-5008}, support = {NNF 190C0055250 and 22OC0078421//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 101096347/ERC_/European Research Council/International ; KAW 2015.0317//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; LU2021-0096//IngaBritt och Arne Lundbergs Forskningsstiftelse (Ingabritt and Arne Lundberg Research Foundation)/ ; 2020-01392//Vetenskapsrådet (Swedish Research Council)/ ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Male ; Female ; *Fractures, Bone/microbiology/epidemiology/etiology ; Middle Aged ; Finland/epidemiology ; Aged ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Cohort Studies ; Incidence ; Metagenomics/methods ; Proteobacteria/genetics/isolation & purification ; Risk Factors ; Adult ; }, abstract = {The gut microbiota (GM) can regulate bone mass, but its association with incident fractures is unknown. We used Cox regression models to determine whether the GM composition is associated with incident fractures in the large FINRISK 2002 cohort (n = 7043, 1092 incident fracture cases, median follow-up time 18 years) with information on GM composition and functionality from shotgun metagenome sequencing. Higher alpha diversity was associated with decreased fracture risk (hazard ratio [HR] 0.92 per standard deviation increase in Shannon index, 95% confidence interval 0.87-0.96). For beta diversity, the first principal component was associated with fracture risk (Aitchison distance, HR 0.90, 0.85-0.96). In predefined phyla analyses, we observed that the relative abundance of Proteobacteria was associated with increased fracture risk (HR 1.14, 1.07-1.20), while the relative abundance of Tenericutes was associated with decreased fracture risk (HR 0.90, 0.85-0.96). Explorative sub-analyses within the Proteobacteria phylum showed that higher relative abundance of Gammaproteobacteria was associated with increased fracture risk. Functionality analyses showed that pathways related to amino acid metabolism and lipopolysaccharide biosynthesis associated with fracture risk. The relative abundance of Proteobacteria correlated with pathways for amino acid metabolism, while the relative abundance of Tenericutes correlated with pathways for butyrate synthesis. In conclusion, the overall GM composition was associated with incident fractures. The relative abundance of Proteobacteria, especially Gammaproteobacteria, was associated with increased fracture risk, while the relative abundance of Tenericutes was associated with decreased fracture risk. Functionality analyses demonstrated that pathways known to regulate bone health may underlie these associations.}, } @article {pmid39143045, year = {2024}, author = {Baldi, A and Braat, S and Imrul Hasan, M and Bennett, C and Barrios, M and Jones, N and Moir-Meyer, G and Abdul Azeez, I and Wilcox, S and Saiful Alam Bhuiyan, M and Ataide, R and Clucas, D and Harrison, LC and Arifeen, SE and Bowden, R and Biggs, BA and Jex, A and Pasricha, SR}, title = {Community use of oral antibiotics transiently reprofiles the intestinal microbiome in young Bangladeshi children.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {6980}, pmid = {39143045}, issn = {2041-1723}, support = {GNT1103262//Department of Health | National Health and Medical Research Council (NHMRC)/ ; GNT1158696//Department of Health | National Health and Medical Research Council (NHMRC)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Bangladesh/epidemiology ; Infant ; *Anti-Bacterial Agents/administration & dosage/pharmacology ; *RNA, Ribosomal, 16S/genetics ; Male ; Female ; Administration, Oral ; Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Metagenomics/methods ; Bacteria/genetics/drug effects/classification/isolation & purification ; Cephalosporins/administration & dosage/pharmacology/therapeutic use ; Enterococcus/drug effects/genetics/isolation & purification ; Antimicrobial Stewardship ; }, abstract = {Antibiotics may alter the gut microbiome, and this is one of the mechanisms by which antimicrobial resistance may be promoted. Suboptimal antimicrobial stewardship in Asia has been linked to antimicrobial resistance. We aim to examine the relationship between oral antibiotic use and composition and antimicrobial resistance in the gut microbiome in 1093 Bangladeshi infants. We leverage a trial of 8-month-old infants in rural Bangladesh: 61% of children were cumulatively exposed to antibiotics (most commonly cephalosporins and macrolides) over the 12-month study period, including 47% in the first 3 months of the study, usually for fever or respiratory infection. 16S rRNA amplicon sequencing in 11-month-old infants reveals that alpha diversity of the intestinal microbiome is reduced in children who received antibiotics within the previous 7 days; these samples also exhibit enrichment for Enterococcus and Escherichia/Shigella genera. No effect is seen in children who received antibiotics earlier. Using shotgun metagenomics, overall abundance of antimicrobial resistance genes declines over time. Enrichment for an Enterococcus-related antimicrobial resistance gene is observed in children receiving antibiotics within the previous 7 days, but not earlier. Presence of antimicrobial resistance genes is correlated to microbiome composition. In Bangladeshi children, community use of antibiotics transiently reprofiles the gut microbiome.}, } @article {pmid39142773, year = {2024}, author = {Zaytsev, V and Tutukina, MN and Chetyrkina, MR and Shelyakin, PV and Ovchinnikov, G and Satybaldina, D and Kondrashov, VA and Bandurist, MS and Seilov, S and Gorin, DA and Fedorov, FS and Gelfand, MS and Nasibulin, AG}, title = {Monitoring of meat quality and change-point detection by a sensor array and profiling of bacterial communities.}, journal = {Analytica chimica acta}, volume = {1320}, number = {}, pages = {343022}, doi = {10.1016/j.aca.2024.343022}, pmid = {39142773}, issn = {1873-4324}, mesh = {*Electronic Nose ; *Bacteria/isolation & purification ; Meat/microbiology/analysis ; Microbiota ; Animals ; Food Quality ; Food Microbiology ; }, abstract = {BACKGROUND: Real-time monitoring of food consumer quality remains challenging due to diverse bio-chemical processes taking place in the food matrices, and hence it requires accurate analytical methods. Thresholds to determine spoiled food are often difficult to set. The existing analytical methods are too complicated for rapid in situ screening of foodstuff.

RESULTS: We have studied the dynamics of meat spoilage by electronic nose (e-nose) for digitizing the smell associated with volatile spoilage markers of meat, comparing the results with changes in the microbiome composition of the spoiling meat samples. We apply the time series analysis to follow dynamic changes in the gas profile extracted from the e-nose responses and to identify the change-point window of the meat state. The obtained e-nose features correlate with changes in the microbiome composition such as increase in the proportion of Brochothrix and Pseudomonas spp. and disappearance of Mycoplasma spp., and with representative gas sensors towards hydrogen, ammonia, and alcohol vapors with R[2] values of 0.98, 0.93, and 0.91, respectively. Integration of e-nose and computer vision into a single analytical panel improved the meat state identification accuracy up to 0.85, allowing for more reliable meat state assessment.

SIGNIFICANCE: Accurate identification of the change-point in the meat state achieved by digitalizing volatile spoilage markers from the e-nose unit holds promises for application of smart miniaturized devices in food industry.}, } @article {pmid39141729, year = {2024}, author = {Lai, S and Wang, H and Bork, P and Chen, WH and Zhao, XM}, title = {Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts.}, journal = {Science advances}, volume = {10}, number = {33}, pages = {eadn3316}, pmid = {39141729}, issn = {2375-2548}, mesh = {*Bacteriophages/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/virology/genetics ; *Gene Transfer, Horizontal ; Metagenomics/methods ; Genetic Variation ; Virome/genetics ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; }, abstract = {Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here, we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By using virome-enriched long-read metagenomic sequencing across 91 individuals, we identified a total of 14,438 nonredundant phage SVs and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Notably, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibit a higher frequency of genetic exchange with bacterial chromosomes and then virulent phages. Collectively, our findings provide insights into the genetic landscape of the human gut phageome.}, } @article {pmid39140734, year = {2024}, author = {Tian, Y and Rimal, B and Bisanz, JE and Gui, W and Wolfe, TM and Koo, I and Murray, IA and Nettleford, SK and Yokoyama, S and Dong, F and Koshkin, S and Prabhu, KS and Turnbaugh, PJ and Walk, ST and Perdew, GH and Patterson, AD}, title = {Effects of Early Life Exposures to the Aryl Hydrocarbon Receptor Ligand TCDF on Gut Microbiota and Host Metabolic Homeostasis in C57BL/6J Mice.}, journal = {Environmental health perspectives}, volume = {132}, number = {8}, pages = {87005}, pmid = {39140734}, issn = {1552-9924}, support = {R01 DK114034/DK/NIDDK NIH HHS/United States ; R35 ES028244/ES/NIEHS NIH HHS/United States ; R15 AI047165/AI/NIAID NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; R01 ES028288/ES/NIEHS NIH HHS/United States ; S10 OD021750/OD/NIH HHS/United States ; R35 GM151045/GM/NIGMS NIH HHS/United States ; R35 ES035027/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; *Receptors, Aryl Hydrocarbon/metabolism ; Mice ; *Mice, Inbred C57BL ; *Homeostasis/drug effects ; *Benzofurans ; Persistent Organic Pollutants ; Male ; Ligands ; }, abstract = {BACKGROUND: Exposure to persistent organic pollutants (POPs) and disruptions in the gastrointestinal microbiota have been positively correlated with a predisposition to factors such as obesity, metabolic syndrome, and type 2 diabetes; however, it is unclear how the microbiome contributes to this relationship.

OBJECTIVE: This study aimed to explore the association between early life exposure to a potent aryl hydrocarbon receptor (AHR) agonist and persistent disruptions in the microbiota, leading to impaired metabolic homeostasis later in life.

METHODS: This study used metagenomics, nuclear magnetic resonance (NMR)- and mass spectrometry (MS)-based metabolomics, and biochemical assays to analyze the gut microbiome composition and function, as well as the physiological and metabolic effects of early life exposure to 2,3,7,8-tetrachlorodibenzofuran (TCDF) in conventional, germ-free (GF), and Ahr-null mice. The impact of TCDF on Akkermansia muciniphila (A. muciniphila) in vitro was assessed using optical density (OD 600), flow cytometry, transcriptomics, and MS-based metabolomics.

RESULTS: TCDF-exposed mice exhibited lower abundances of A. muciniphila, lower levels of cecal short-chain fatty acids (SCFAs) and indole-3-lactic acid (ILA), as well as lower levels of the gut hormones glucagon-like peptide 1 (GLP-1) and peptide YY (PYY), findings suggestive of disruption in the gut microbiome community structure and function. Importantly, microbial and metabolic phenotypes associated with early life POP exposure were transferable to GF recipients in the absence of POP carry-over. In addition, AHR-independent interactions between POPs and the microbiota were observed, and they were significantly associated with growth, physiology, gene expression, and metabolic activity outcomes of A. muciniphila, supporting suppressed activity along the ILA pathway.

CONCLUSIONS: These data obtained in a mouse model point to the complex effects of POPs on the host and microbiota, providing strong evidence that early life, short-term, and self-limiting POP exposure can adversely impact the microbiome, with effects persisting into later life with associated health implications. https://doi.org/10.1289/EHP13356.}, } @article {pmid39140417, year = {2024}, author = {Hummel, G and Aagaard, K}, title = {Arthropods to Eutherians: A Historical and Contemporary Comparison of Sparse Prenatal Microbial Communities Among Animalia Species.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {92}, number = {2}, pages = {e13897}, doi = {10.1111/aji.13897}, pmid = {39140417}, issn = {1600-0897}, mesh = {Animals ; Humans ; *Microbiota ; Pregnancy ; Female ; }, abstract = {Since the advent of next-generation sequencing, investigators worldwide have sought to discern whether a functional and biologically or clinically relevant prenatal microbiome exists. One line of research has led to the hypothesis that microbial DNA detected in utero/in ovo or prior to birth/hatching is a result of contamination and does not belong to viable and functional microbes. Many of these preliminary evaluations have been conducted in humans, mice, and nonhuman primates due to sample and specimen availability. However, a comprehensive review of the literature across animal species suggests organisms that maintain an obligate relationship with microbes may act as better models for interrogating the selective pressures placed on vertical microbial transfer over traditional laboratory species. To date, studies in humans and viviparous laboratory species have failed to illustrate the clear presence and transfer of functional microbes in utero. Until a ground truth regarding the status and relevance of prenatal microbes can be ascertained, it is salient to conduct parallel investigations into the prevalence of a functional prenatal microbiome across the developmental lifespan of multiple organisms in the kingdom Animalia. This comprehensive understanding is necessary not only to determine the role of vertically transmitted microbes and their products in early human health but also to understand their full One Health impact. This review is among the first to compile such comprehensive primary conclusions from the original investigator's conclusions, and hence collectively illustrates that prenatal microbial transfer is supported by experimental evidence arising from over a long and rigorous scientific history encompassing a breadth of species from kingdom Animalia.}, } @article {pmid39138568, year = {2024}, author = {Belda, E and Capeau, J and Zucker, JD and Chatelier, EL and Pons, N and Oñate, FP and Quinquis, B and Alili, R and Fellahi, S and Katlama, C and Clément, K and Fève, B and Jaureguiberry, S and Goujard, C and Lambotte, O and Doré, J and Prifti, E and Bastard, JP}, title = {Major depletion of insulin sensitivity-associated taxa in the gut microbiome of persons living with HIV controlled by antiretroviral drugs.}, journal = {BMC medical genomics}, volume = {17}, number = {1}, pages = {209}, pmid = {39138568}, issn = {1755-8794}, support = {ANRS 157 study trial//Agence Nationale de Recherches sur le Sida et les Hépatites Virales/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *HIV Infections/drug therapy/microbiology ; Male ; Female ; Middle Aged ; *Insulin Resistance ; Adult ; Feces/microbiology ; Anti-Retroviral Agents/therapeutic use ; Metagenome ; }, abstract = {BACKGROUND: Persons living with HIV (PWH) harbor an altered gut microbiome (higher abundance of Prevotella and lower abundance of Bacillota and Ruminococcus lineages) compared to non-infected individuals. Some of these alterations are linked to sexual preference and others to the HIV infection. The relationship between these lineages and metabolic alterations, often present in aging PWH, has been poorly investigated.

METHODS: In this study, we compared fecal metagenomes of 25 antiretroviral-treatment (ART)-controlled PWH to three independent control groups of 25 non-infected matched individuals by means of univariate analyses and machine learning methods. Moreover, we used two external datasets to validate predictive models of PWH classification. Next, we searched for associations between clinical and biological metabolic parameters with taxonomic and functional microbiome profiles. Finally, we compare the gut microbiome in 7 PWH after a 17-week ART switch to raltegravir/maraviroc.

RESULTS: Three major enterotypes (Prevotella, Bacteroides and Ruminococcaceae) were present in all groups. The first Prevotella enterotype was enriched in PWH, with several of characteristic lineages associated with poor metabolic profiles (low HDL and adiponectin, high insulin resistance (HOMA-IR)). Conversely butyrate-producing lineages were markedly depleted in PWH independently of sexual preference and were associated with a better metabolic profile (higher HDL and adiponectin and lower HOMA-IR). Accordingly with the worst metabolic status of PWH, butyrate production and amino-acid degradation modules were associated with high HDL and adiponectin and low HOMA-IR. Random Forest models trained to classify PWH vs. control on taxonomic abundances displayed high generalization performance on two external holdout datasets (ROC AUC of 80-82%). Finally, no significant alterations in microbiome composition were observed after switching to raltegravir/maraviroc.

CONCLUSION: High resolution metagenomic analyses revealed major differences in the gut microbiome of ART-controlled PWH when compared with three independent matched cohorts of controls. The observed marked insulin resistance could result both from enrichment in Prevotella lineages, and from the depletion in species producing butyrate and involved into amino-acid degradation, which depletion is linked with the HIV infection.}, } @article {pmid39137550, year = {2024}, author = {Gao, SM and Wang, P and Li, Q and Shu, WS and Tang, LY and Lin, ZL and Li, JT and Huang, LN}, title = {Deciphering microbial metabolic interactions and their implications for community dynamics in acid mine drainage sediments.}, journal = {Journal of hazardous materials}, volume = {478}, number = {}, pages = {135478}, doi = {10.1016/j.jhazmat.2024.135478}, pmid = {39137550}, issn = {1873-3336}, mesh = {*Geologic Sediments/microbiology ; *Mining ; *Microbiota ; *Biodegradation, Environmental ; Bacteria/metabolism/genetics ; China ; Metagenomics ; Acids/metabolism ; Microbial Interactions ; }, abstract = {The microbially-mediated reduction processes have potential for the bioremediation of acid mine drainage (AMD), which represents a worldwide environment problem. However, we know little about the microbial interactions in anaerobic AMD sediments. Here we utilized genome-resolved metagenomics to uncover the nature of cooperative and competitive metabolic interactions in 90 AMD sediments across Southern China. Our analyses recovered well-represented prokaryotic communities through the reconstruction of 2625 population genomes. Functional analyses of these genomes revealed extensive metabolic handoffs which occurred more frequently in nitrogen metabolism than in sulfur metabolism, as well as stable functional redundancy across sediments resulting from populations with low genomic relatedness. Genome-scale metabolic modeling showed that metabolic competition promoted microbial co-occurrence relationships, suggesting that community assembly was dominated by habitat filtering in sediments. Notably, communities colonizing more extreme conditions tended to be highly competitive, which was typically accompanied with increased network complexity but decreased stability of the microbiome. Finally, our results demonstrated that heterotrophic Thermoplasmatota associated with ferric iron and sulfate reduction contributed most to the elevated levels of competition. Our study shed light on the cooperative and competitive metabolisms of microbiome in the hazardous AMD sediments, which may provide preliminary clues for the AMD bioremediation in the future.}, } @article {pmid39136455, year = {2024}, author = {Majzoub, ME and Luu, LDW and Haifer, C and Paramsothy, S and Borody, TJ and Leong, RW and Thomas, T and Kaakoush, NO}, title = {Refining microbial community metabolic models derived from metagenomics using reference-based taxonomic profiling.}, journal = {mSystems}, volume = {9}, number = {9}, pages = {e0074624}, pmid = {39136455}, issn = {2379-5077}, support = {988415//Crohn's and Colitis Foundation (CCF)/ ; 2011047//DHAC | National Health and Medical Research Council (NHMRC)/ ; //Bioplatforms Australia (Bioplatforms)/ ; //Integrated Marine Observing System (IMOS)/ ; Emerging leader grant//DHAC | National Health and Medical Research Council (NHMRC)/ ; Scientia fellowship//University of New South Wales (UNSW)/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Metabolomics/methods ; *Microbiota/genetics ; Metagenome/genetics ; }, abstract = {Characterization of microbial community metabolic output is crucial to understanding their functions. Construction of genome-scale metabolic models from metagenome-assembled genomes (MAG) has enabled prediction of metabolite production by microbial communities, yet little is known about their accuracy. Here, we examined the performance of two approaches for metabolite prediction from metagenomes, one that is MAG-guided and another that is taxonomic reference-guided. We applied both on shotgun metagenomics data from human and environmental samples, and validated findings in the human samples using untargeted metabolomics. We found that in human samples, where taxonomic profiling is optimized and reference genomes are readily available, when number of input taxa was normalized, the reference-guided approach predicted more metabolites than the MAG-guided approach. The two approaches showed significant overlap but each identified metabolites not predicted in the other. Pathway enrichment analyses identified significant differences in inferences derived from data based on the approach, highlighting the need for caution in interpretation. In environmental samples, when the number of input taxa was normalized, the reference-guided approach predicted more metabolites than the MAG-guided approach for total metabolites in both sample types and non-redundant metabolites in seawater samples. Nonetheless, as was observed for the human samples, the approaches overlapped substantially but also predicted metabolites not observed in the other. Our findings report on utility of a complementary input to genome-scale metabolic model construction that is less computationally intensive forgoing MAG assembly and refinement, and that can be applied on shallow shotgun sequencing where MAGs cannot be generated.IMPORTANCELittle is known about the accuracy of genome-scale metabolic models (GEMs) of microbial communities despite their influence on inferring community metabolic outputs and culture conditions. The performance of GEMs for metabolite prediction from metagenomes was assessed by applying two approaches on shotgun metagenomics data from human and environmental samples, and validating findings in the human samples using untargeted metabolomics. The performance of the approach was found to be dependent on sample type, but collectively, the reference-guided approach predicted more metabolites than the MAG-guided approach. Despite the differences, the predictions from the approaches overlapped substantially but each identified metabolites not predicted in the other. We found significant differences in biological inferences based on the approach, with some examples of uniquely enriched pathways in one group being invalidated when using the alternative approach, highlighting the need for caution in interpretation of GEMs.}, } @article {pmid39136189, year = {2024}, author = {Wang, J and Zhu, YG and Ge, Y}, title = {Global distribution pattern of soil phosphorus-cycling microbes under the influence of human activities.}, journal = {Global change biology}, volume = {30}, number = {8}, pages = {e17477}, doi = {10.1111/gcb.17477}, pmid = {39136189}, issn = {1365-2486}, support = {2023YFD1700803//National Key Research and Development Program of China/ ; 42177274//National Natural Science Foundation of China/ ; 42307162//National Natural Science Foundation of China/ ; 2019QZKK0306//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0308//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; }, mesh = {*Phosphorus/metabolism/analysis ; *Soil Microbiology ; Human Activities ; Humans ; Bacteria/genetics/metabolism ; Microbiota ; Soil/chemistry ; }, abstract = {Human activities have profoundly altered the Earth's phosphorus (P) cycling process and its associated microbial communities, yet their global distribution pattern and response to human influences remain unclear. Here, we estimated the abundances of P-cycling genes from 3321 global soil metagenomic samples and mapped the global distribution of five key P-cycling processes, that is, organic phosphoester hydrolysis, inorganic phosphorus solubilization, two-component system, phosphotransferase system, and transporters. Structural equation modeling and random forest analysis were employed to assess the impact of anthropogenic and environmental factors on the abundance of P-cycling genes. Our findings suggest that although less significant than the climate and soil profile, human-related factors, such as economic activities and population, are important drivers for the variations in P-cycling gene abundance. Notably, the gene abundances were increased parallel to the extent of human intervention, but generally at low and moderate levels of human activities. Furthermore, we identified critical genera, such as Pseudomonas and Lysobacter, which were sensitive to the changes in human activities. This study provides insights into the responses of P-cycling microbes to human activities at a global scale, enhancing our understanding of soil microbial P cycling and underscoring the importance of sustainable human activities in the Earth's biogeochemical cycle.}, } @article {pmid39134593, year = {2024}, author = {Trosvik, P and Noordzij, HT and de Muinck, EJ}, title = {Antibiotic resistance gene dynamics in the commensal infant gut microbiome over the first year of life.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {18701}, pmid = {39134593}, issn = {2045-2322}, support = {300948//Norges Forskningsråd/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Infant ; *Feces/microbiology ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Metagenomics/methods ; Metagenome ; Genes, Bacterial ; Bacteria/genetics/classification ; Infant, Newborn ; Female ; }, abstract = {Colonization of the infant gut is an important developmental process characterized by high carriage of antimicrobial resistance genes (ARGs) and high abundances of pathobionts. The horizontal transfer of ARGs to pathogenic bacteria represents a major public health concern. However, there is still a paucity of longitudinal studies surveilling ARGs in healthy infant guts at high temporal resolution. Furthermore, we do not yet have a clear view of how temporal variation in ARG carriage relates to the dynamics of specific bacterial populations, as well as community virulence potential. Here, we performed deep shotgun metagenomic sequencing of monthly fecal samples from a cohort of 12 infants, covering the first year of life to interrogate the infant gut microbiome for ARG content. We further relate ARG dynamics to the dynamics of taxa, virulence potential, as well as the potential for ARG mobilization. We identify a core resistome dominated by efflux systems typically associated with Enterobacteriaceae. Overall ARG carriage declined over the first year of life and showed strong contemporaneous correlation with the population dynamics of Proteobacteria. Furthermore, the majority of ARGs could be further mapped to metagenome-assembled genomes (MAGs) classified to this phylum. We were able to assign a large number of ARGs to E. coli by correlating the temporal dynamics of individual genes with species dynamics, and we show that the temporal dynamics of ARGs and virulence factors are highly correlated, suggesting close taxonomic associations between these two gene classes. Finally, we identify ARGs linked with various categories of mobile genetic elements, demonstrating preferential linkage among mobility categories and resistance to different drug classes. While individual variation in ARG carriage is substantial during infancy there is a clear reduction over the first year of life. With few exceptions, ARG abundances closely track the dynamics of pathobionts and community virulence potential. These findings emphasize the potential for development of resistant pathogens in the developing infant gut, and the importance of effective surveillance in order to detect such events.}, } @article {pmid39133323, year = {2024}, author = {Nehra, C and Harshini, V and Shukla, N and Chavda, P and Savaliya, K and Patil, S and Shah, T and Pandit, R and Patil, NV and Patel, AK and Kachhawaha, S and Kumawat, RN and Joshi, M and Joshi, CG}, title = {Moringa leaf meal exerts growth benefits in small ruminants through modulating the gastrointestinal microbiome.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {438}, pmid = {39133323}, issn = {1432-0614}, support = {Project Reference No: BT/AQ/1/SP41105/2020//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Animal Feed/analysis ; *Plant Leaves ; *Moringa/chemistry ; Sheep ; *Feces/microbiology ; *Goats ; Dietary Supplements ; Fatty Acids, Volatile/metabolism ; Rumen/microbiology ; Bacteria/classification/genetics/isolation & purification/metabolism ; Weight Gain/drug effects ; Diet/veterinary ; Metagenomics ; }, abstract = {This study investigated the impact of feeding 17% moringa leaf meal (MLM) on the ruminal and fecal microbial composition and body weight gain (BWG) performance of lambs (Ovis aries) and kids (Capra hircus). A total of n = 28 lambs (n = 14, no-moringa, n = 14, 17% moringa) and 24 kids (n = 12, no-moringa, n = 12, 17% moringa) were involved in the experiment and body weight was recorded fortnightly. Metagenomic shotgun sequencing was performed on 28, 22, and 26 ruminal solid, liquid fraction, and fecal samples from lambs, and 23, 22, and 23 samples from kids. Moringa supplementation significantly increased BWG in lambs (21.09 ± 0.78 to 26.12 ± 0.81 kg) and kids (14.60 ± 1.29 to 18.28 ± 1.09 kg) (p-value ≤ 0.01). Microbiome analysis revealed an elevated Firmicutes:Bacteroidetes ratio in the moringa diet group. Moringa-fed animals exhibited increased microbial genera associated with volatile fatty acids (VFAs) production (Prevotella, Anaerovibrio, Lachnospiraceae, Butyrivibrio, Christensenella) and starch and fiber digesters (Proteobacteria, Ruminococcus). The increase in the bacterial genus Sharpea suggested possible methane reduction and decreased proportion of pathogens, Aliarcobacter_ID28198, Campylobacter_ID194 and Campylobacter_ID1660076 suggest health benefits. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated significant alterations in microbial gene pool and metabolic pathways related to carbohydrate, protein, lipid and energy metabolism, indicating potential improvements in animal health. Overall, moringa feeding showed higher energy recovery, improved growth, and potential benefits in methane reduction and reduced pathogenic bacteria.}, } @article {pmid39128916, year = {2024}, author = {Osburn, ED and McBride, SG and Bahram, M and Strickland, MS}, title = {Global patterns in the growth potential of soil bacterial communities.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {6881}, pmid = {39128916}, issn = {2041-1723}, support = {2020-67034-41310//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; 2021-03724//Vetenskapsrådet (Swedish Research Council)/ ; 1845417//National Science Foundation (NSF)/ ; }, mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/growth & development/metabolism ; *Soil/chemistry ; *Ecosystem ; *Carbon/metabolism ; Nitrogen/metabolism ; Metagenome ; Forests ; Carbon Cycle ; Microbiota ; Codon Usage ; }, abstract = {Despite the growing catalogue of studies detailing the taxonomic and functional composition of soil bacterial communities, the life history traits of those communities remain largely unknown. This study analyzes a global dataset of soil metagenomes to explore environmental drivers of growth potential, a fundamental aspect of bacterial life history. We find that growth potential, estimated from codon usage statistics, was highest in forested biomes and lowest in arid latitudes. This indicates that bacterial productivity generally reflects ecosystem productivity globally. Accordingly, the strongest environmental predictors of growth potential were productivity indicators, such as distance to the equator, and soil properties that vary along productivity gradients, such as pH and carbon to nitrogen ratios. We also observe that growth potential was negatively correlated with the relative abundances of genes involved in carbohydrate metabolism, demonstrating tradeoffs between growth and resource acquisition in soil bacteria. Overall, we identify macroecological patterns in bacterial growth potential and link growth rates to soil carbon cycling.}, } @article {pmid39128520, year = {2024}, author = {Wang, C and Zhu, J and Wang, H and Zhang, L and Li, Y and Zhang, Y and Wu, Z and Zhou, Q}, title = {Sedimentary organic matter load influences the ecological effects of submerged macrophyte restoration through rhizosphere metabolites and microbial communities.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175419}, doi = {10.1016/j.scitotenv.2024.175419}, pmid = {39128520}, issn = {1879-1026}, mesh = {*Rhizosphere ; *Microbiota ; *Geologic Sediments/microbiology/chemistry ; Lakes ; Phosphorus/metabolism ; Nitrogen/metabolism ; Environmental Restoration and Remediation/methods ; }, abstract = {Organic matter (OM) accumulation in lake sediments has doubled owing to human activities over the past 100 years, which has negatively affected the restoration of submerged vegetation and ecological security. Changes in the pollution structure of sediments caused by plant recovery and rhizosphere chemical processes under different sediment OM levels are the theoretical basis for the rational application of plant rehabilitation technology in lake management. This study explored how Vallisneria natans mediates changes in sediment N and P through rhizospheric metabolites and microbial community and function under low (4.94 %) and high (17.35 %) sediment OM levels. V. natans promoted the accumulation of NH4-N in the high-OM sediment and the transformation of Fe/Al-P to Ca-P in the low-OM sediment. By analyzing 63 rhizospheric metabolites and the sediment microbial metagenome, the metabolites lactic acid and 3-hydroxybutyric acid and the genus Anammoximicrobium were found to mediate NH4-N accumulation in the high-OM sediment. Additionally, 3-hydroxy-decanoic acid, adipic acid, and the genus Bdellovibrionaceae mediated the transformation of Fe/Al-P to Ca-P in the low-OM sediment. The growth of V. natans enriched the abundance of functional genes mediating each step from nitrate to ammonia and the genes encoding urease in the high-OM sediment, and it up-regulated three genes related to microbial phosphorus uptake in the low-OM sediment. This study revealed the necessity of controlling endogenous pollution by recovering submerged macrophytes under high- and low-OM conditions from the perspective of the transformation of inorganic nitrogen and phosphorus.}, } @article {pmid39127908, year = {2024}, author = {Jabeen, MF and Sanderson, ND and Tinè, M and Donachie, G and Barber, C and Azim, A and Lau, LCK and Brown, T and Pavord, ID and Chauhan, A and Klenerman, P and Street, TL and Marchi, E and Howarth, PH and Hinks, TSC}, title = {Species-level, metagenomic and proteomic analysis of microbe-immune interactions in severe asthma.}, journal = {Allergy}, volume = {79}, number = {11}, pages = {2966-2980}, doi = {10.1111/all.16269}, pmid = {39127908}, issn = {1398-9995}, support = {//NIHR Primary Care Research Network/ ; //National Institute for Health Research Southampton Biomedical Research Centre/ ; //NIHR Oxford Biomedical Research Centre/ ; /WT_/Wellcome Trust/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Asthma/immunology/microbiology ; *Metagenomics/methods ; Female ; *Proteomics/methods ; *Microbiota/immunology ; Male ; Adult ; Middle Aged ; Sputum/microbiology/immunology ; Metagenome ; Cross-Sectional Studies ; Severity of Illness Index ; Cytokines/metabolism ; }, abstract = {BACKGROUND: The airway microbiome in severe asthma has not been characterised at species-level by metagenomic sequencing, nor have the relationships between specific species and mucosal immune responses in 'type-2 low', neutrophilic asthma been defined. We performed an integrated species-level metagenomic data with inflammatory mediators to characterise prevalence of dominant potentially pathogenic organisms and host immune responses.

METHODS: Sputum and nasal lavage samples were analysed using long-read metagenomic sequencing with Nanopore and qPCR in two cross-sectional adult severe asthma cohorts, Wessex (n = 66) and Oxford (n = 30). We integrated species-level data with clinical parameters and 39 selected airway proteins measured by immunoassay and O-link.

RESULTS: The sputum microbiome in health and mild asthma displayed comparable microbial diversity. By contrast, 23% (19/81) of severe asthma microbiomes were dominated by a single respiratory pathogen, namely H. influenzae (n = 10), M. catarrhalis (n = 4), S. pneumoniae (n = 4) and P. aeruginosa (n = 1). Neutrophilic asthma was associated with H. influenzae, M. catarrhalis, S. pneumoniae and T. whipplei with elevated type-1 cytokines and proteases; eosinophilic asthma with higher M. catarrhalis, but lower H. influenzae, and S. pneumoniae abundance. H. influenzae load correlated with Eosinophil Cationic Protein, elastase and IL-10. R. mucilaginosa associated positively with IL-6 and negatively with FGF. Bayesian network analysis also revealed close and distinct relationships of H. influenzae and M. catarrhalis with type-1 airway inflammation. The microbiomes and cytokine milieu were distinct between upper and lower airways.

CONCLUSIONS: This species-level integrated analysis reveals central, but distinct associations between potentially pathogenic bacteria and airways inflammation in severe asthma.}, } @article {pmid39127849, year = {2024}, author = {Vigil, BE and Ascue, F and Ayala, RY and Murúa, P and Calderon, MS and Bustamante, DE}, title = {Functional prediction based on 16S rRNA metagenome data from bacterial microbiota associated with macroalgae from the Peruvian coast.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {18577}, pmid = {39127849}, issn = {2045-2322}, support = {Project FitoAlga N° PE501079919-2022-PROCIENCIA//Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica/ ; }, mesh = {*Seaweed/microbiology ; *RNA, Ribosomal, 16S/genetics ; Peru ; *Metagenome ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Phylogeny ; Biodiversity ; }, abstract = {Macroalgae are vital reservoirs for essential epibiotic microorganisms. Among these are growth-promoting bacteria that support the growth and healthy development of their host macroalgae, and these macroalgae can be utilized in agriculture as biostimulants, offering an alternative to traditional agrochemicals. However, to date, no comparative studies have been conducted on the functional profile and bacterial diversity associated with coastal macroalgae of Peru. In this study, we employed amplicon sequencing of the V3-V4 region of 16S rRNA gene in twelve host macroalgae collected from two rocky shores in central Peru to compare their bacterial communities. The results revealed high bacterial diversity across both sites, but differences in microbial composition were noted. The phyla Bacteroidota and Pseudomonadota were predominant. The functional prediction highlighted 44 significant metabolic pathways associated with the bacterial microbiota when comparing host macroalgae. These active pathways are related to metabolism and genetic and cellular information processing. No direct association was detected between the macroalgal genera and the associated microbiota, suggesting that the bacterial community is largely influenced by their genetic functions than the taxonomic composition of their hosts. Furthermore, some species of Chlorophyta and Rhodophyta were observed to host growth-promoting bacteria, such as Maribacter sp. and Sulfitobacter sp.}, } @article {pmid39127718, year = {2024}, author = {Van Uffelen, A and Posadas, A and Roosens, NHC and Marchal, K and De Keersmaecker, SCJ and Vanneste, K}, title = {Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {864}, pmid = {39127718}, issn = {2052-4463}, mesh = {*Bacteria/genetics/classification ; Datasets as Topic ; *Metagenomics/methods ; Microbiota ; Nanopore Sequencing ; Nanopores ; }, abstract = {Taxonomic classification is crucial in identifying organisms within diverse microbial communities when using metagenomics shotgun sequencing. While second-generation Illumina sequencing still dominates, third-generation nanopore sequencing promises improved classification through longer reads. However, extensive benchmarking studies on nanopore data are lacking. We systematically evaluated performance of bacterial taxonomic classification for metagenomics nanopore sequencing data for several commonly used classifiers, using standardized reference sequence databases, on the largest collection of publicly available data for defined mock communities thus far (nine samples), representing different research domains and application scopes. Our results categorize classifiers into three categories: low precision/high recall; medium precision/medium recall, and high precision/medium recall. Most fall into the first group, although precision can be improved without excessively penalizing recall with suitable abundance filtering. No definitive 'best' classifier emerges, and classifier selection depends on application scope and practical requirements. Although few classifiers designed for long reads exist, they generally exhibit better performance. Our comprehensive benchmarking provides concrete recommendations, supported by publicly available code for reassessment and fine-tuning by other scientists.}, } @article {pmid39127363, year = {2024}, author = {Yun, Y and Lv, T and Gui, Z and Su, T and Cao, W and Tian, X and Chen, Y and Wang, S and Jia, Z and Li, G and Ma, T}, title = {Composition and metabolic flexibility of hydrocarbon-degrading consortia in oil reservoirs.}, journal = {Bioresource technology}, volume = {409}, number = {}, pages = {131244}, doi = {10.1016/j.biortech.2024.131244}, pmid = {39127363}, issn = {1873-2976}, mesh = {*Hydrocarbons/metabolism ; *Biodegradation, Environmental ; *Oil and Gas Fields/microbiology ; Microbial Consortia/physiology ; Bacteria/metabolism ; Petroleum/metabolism ; Phylogeny ; }, abstract = {Hydrocarbon-degrading consortia (HDC) play an important role in petroleum exploitation. However, the real composition and metabolic mechanism of HDC in the microbial enhanced oil recovery (MEOR) process remain unclear. By combining [13]C-DNA stable isotope probing microcosms with metagenomics, some newly reported phyla, including Chloroflexi, Synergistetes, Thermotogae, and Planctomycetes, dominated the HDC in the oil reservoirs. In the field trials, the HDC in the aerobic-facultative-anaerobic stage of oilfields jointly promoted the MEOR process, with monthly oil increments of up to 189 tons. Pseudomonas can improve oil recovery by producing rhamnolipid in the facultative condition. Roseovarius was the novel taxa potentially oxidizing alkane and producing acetate to improve oil porosity and permeability in the aerobic condition. Ca. Bacteroidia were the new members potentially degrading hydrocarbons by fumarate addition in the anaerobic environment. Comprehensive identification of the active HDC in oil reservoirs provides a novel theoretical basis for oilfield regulatory scheme.}, } @article {pmid39127317, year = {2024}, author = {Tang, W and Wang, Q and Sun, M and Liu, C and Huang, Y and Zhou, M and Zhang, X and Meng, Z and Zhang, J}, title = {The gut microbiota-oligodendrocyte axis: A promising pathway for modulating oligodendrocyte homeostasis and demyelination-associated disorders.}, journal = {Life sciences}, volume = {354}, number = {}, pages = {122952}, doi = {10.1016/j.lfs.2024.122952}, pmid = {39127317}, issn = {1879-0631}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Animals ; *Oligodendroglia/metabolism ; *Homeostasis/physiology ; *Demyelinating Diseases/metabolism/microbiology ; *Brain-Gut Axis/physiology ; Dysbiosis/microbiology ; Myelin Sheath/metabolism ; }, abstract = {The bidirectional regulation between the gut microbiota and brain, known as gut-brain axis, has received significant attention. The myelin sheath, produced by oligodendrocytes or Schwann cells, is essential for efficient nervous signal transmission and the maintenance of brain function. Growing evidence shows that both oligodendrogenesis and myelination are modulated by gut microbiota and its metabolites, and when dysbiosis occurs, changes in the microbiota composition and/or associated metabolites may impact developmental myelination and the occurrence of neurodevelopmental disabilities. Although the link between the microbiota and demyelinating disease such as multiple sclerosis has been extensively studied, our knowledge about the role of the microbiota in other myelin-related disorders, such as neurodegenerative diseases, is limited. Mechanistically, the microbiota-oligodendrocyte axis is primarily mediated by factors such as inflammation, the vagus nerve, endocrine hormones, and microbiota metabolites as evidenced by metagenomics, metabolomics, vagotomy, and morphological and molecular approaches. Treatments targeting this axis include probiotics, prebiotics, microbial metabolites, herbal bioactive compounds, and specific dietary management. In addition to the commonly used approaches, viral vector-mediated tracing and gene manipulation, integrated multiomics and multicenter clinical trials will greatly promote the mechanistic and interventional studies and ultimately, the development of new preventive and therapeutic strategies against gut-oligodendrocyte axis-mediated brain impairments. Interestingly, recent findings showed that microbiota dysbiosis can be induced by hippocampal myelin damage and is reversible by myelin-targeted drugs, which provides new insights into understanding how hippocampus-based functional impairment (such as in neurodegenerative Alzheimer's disease) regulates the peripheral homeostasis of microbiota and associated systemic disorders.}, } @article {pmid39125688, year = {2024}, author = {Ercolano, C and Iacono, R and Cafaro, V and Pizzo, E and Giovannelli, D and Feuerriegel, G and Streit, WR and Strazzulli, A and Moracci, M}, title = {Biochemical Characterisation of Sis: A Distinct Thermophilic PETase with Enhanced NanoPET Substrate Hydrolysis and Thermal Stability.}, journal = {International journal of molecular sciences}, volume = {25}, number = {15}, pages = {}, pmid = {39125688}, issn = {1422-0067}, support = {2020SBNHLH_003//Ministero dell'Università e della Ricerca (MUR)/ ; }, mesh = {*Polyethylene Terephthalates/chemistry/metabolism ; Hydrolysis ; *Enzyme Stability ; Phylogeny ; Temperature ; Substrate Specificity ; Kinetics ; Hydrolases/chemistry/metabolism ; Bacterial Proteins/chemistry/metabolism/genetics ; }, abstract = {Polyethylene terephthalate (PET) degradation by enzymatic hydrolysis is significant for addressing plastic pollution and fostering sustainable waste management practices. Identifying thermophilic and thermostable PET hydrolases is particularly crucial for industrial bioprocesses, where elevated temperatures may enhance enzymatic efficiency and process kinetics. In this study, we present the discovery of a novel thermophilic and thermostable PETase enzyme named Sis, obtained through metagenomic sequence-based analysis. Sis exhibits robust activity on nanoPET substrates, demonstrating effectiveness at temperatures up to 70 °C and displaying exceptional thermal stability with a melting temperature (Tm) of 82 °C. Phylogenetically distinct from previously characterised PET hydrolases, Sis represents a valuable addition to the repertoire of enzymes suitable for PET degradation.}, } @article {pmid39125621, year = {2024}, author = {Jelin-Uhlig, S and Weigel, M and Ott, B and Imirzalioglu, C and Howaldt, HP and Böttger, S and Hain, T}, title = {Bisphosphonate-Related Osteonecrosis of the Jaw and Oral Microbiome: Clinical Risk Factors, Pathophysiology and Treatment Options.}, journal = {International journal of molecular sciences}, volume = {25}, number = {15}, pages = {}, pmid = {39125621}, issn = {1422-0067}, support = {DZIF-MD / 80325MD058//German Center for Infection Research/ ; }, mesh = {Humans ; *Bisphosphonate-Associated Osteonecrosis of the Jaw/etiology/microbiology ; *Microbiota/drug effects ; Risk Factors ; *Diphosphonates/adverse effects/therapeutic use ; Mouth/microbiology ; }, abstract = {Bisphosphonate-related osteonecrosis of the jaw (BRONJ) represents a serious health condition, impacting the lives of many patients worldwide. The condition challenges clinical care due to its complex etiology and limited therapeutic options. A thorough understanding of the pathophysiological and patient-related factors that promote disease development is essential. Recently, the oral microbiome has been implicated as a potential driver and modulating factor of BRONJ by several studies. Modern genomic sequencing methods have provided a wealth of data on the microbial composition of BRONJ lesions; however, the role of individual species in the process of disease development remains elusive. A comprehensive PubMed search was conducted to identify relevant studies on the microbiome of BRONJ patients using the terms "microbiome", "osteonecrosis of the jaws", and "bisphosphonates". Studies focusing on symptoms, epidemiology, pathophysiology, risk factors, and treatment options were included. The principal risk factors for BRONJ are tooth extraction, surgical procedures, and the administration of high doses of bisphosphonates. Importantly, the oral microbiome plays a significant role in the progression of the disease. Several studies have identified alterations of microbial composition in BRONJ lesions. However, there is no consensus regarding bacterial species that are associated with BRONJ across studies. The bacterial genera typically found include Actinomyces, Fusobacterium, and Streptococcus. It is postulated that these microbes contribute to the pathogenesis of BRONJ by promoting inflammation and disrupting normal bone remodeling processes. Current therapeutic approaches are disease-stage-specific and the necessity for more effective treatment strategies remains. This review examines the potential causes of and therapeutic approaches to BRONJ, highlighting the link between microbial colonization and BRONJ development. Future research should seek to more thoroughly investigate the interactions between bisphosphonates, the oral microbiome, and the immune system in order to develop targeted therapies.}, } @article {pmid39125593, year = {2024}, author = {Kulecka, M and Czarnowski, P and Bałabas, A and Turkot, M and Kruczkowska-Tarantowicz, K and Żeber-Lubecka, N and Dąbrowska, M and Paszkiewicz-Kozik, E and Walewski, J and Ługowska, I and Koseła-Paterczyk, H and Rutkowski, P and Kluska, A and Piątkowska, M and Jagiełło-Gruszfeld, A and Tenderenda, M and Gawiński, C and Wyrwicz, L and Borucka, M and Krzakowski, M and Zając, L and Kamiński, M and Mikula, M and Ostrowski, J}, title = {Microbial and Metabolic Gut Profiling across Seven Malignancies Identifies Fecal Faecalibacillus intestinalis and Formic Acid as Commonly Altered in Cancer Patients.}, journal = {International journal of molecular sciences}, volume = {25}, number = {15}, pages = {}, pmid = {39125593}, issn = {1422-0067}, support = {2017/27/B/NZ5/01504//National Science Center/ ; 2018/31/B/NZ7/02675//National Science Center/ ; 2020/ABM/01/00004//The Medical Research Agency/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; *Feces/microbiology ; Male ; *Formates/metabolism ; Middle Aged ; Aged ; Neoplasms/metabolism/microbiology ; Adult ; Dysbiosis/microbiology ; Metabolomics/methods ; Metabolome ; Gas Chromatography-Mass Spectrometry ; Metagenomics/methods ; }, abstract = {The key association between gut dysbiosis and cancer is already known. Here, we used whole-genome shotgun sequencing (WGS) and gas chromatography/mass spectrometry (GC/MS) to conduct metagenomic and metabolomic analyses to identify common and distinct taxonomic configurations among 40, 45, 71, 34, 50, 60, and 40 patients with colorectal cancer, stomach cancer, breast cancer, lung cancer, melanoma, lymphoid neoplasms and acute myeloid leukemia (AML), respectively, and compared the data with those from sex- and age-matched healthy controls (HC). α-diversity differed only between the lymphoid neoplasm and AML groups and their respective HC, while β-diversity differed between all groups and their HC. Of 203 unique species, 179 and 24 were under- and over-represented, respectively, in the case groups compared with HC. Of these, Faecalibacillus intestinalis was under-represented in each of the seven groups studied, Anaerostipes hadrus was under-represented in all but the stomach cancer group, and 22 species were under-represented in the remaining five case groups. There was a marked reduction in the gut microbiome cancer index in all case groups except the AML group. Of the short-chain fatty acids and amino acids tested, the relative concentration of formic acid was significantly higher in each of the case groups than in HC, and the abundance of seven species of Faecalibacterium correlated negatively with most amino acids and formic acid, and positively with the levels of acetic, propanoic, and butanoic acid. We found more differences than similarities between the studied malignancy groups, with large variations in diversity, taxonomic/metabolomic profiles, and functional assignments. While the results obtained may demonstrate trends rather than objective differences that correlate with different types of malignancy, the newly developed gut microbiota cancer index did distinguish most of the cancer cases from HC. We believe that these data are a promising step forward in the search for new diagnostic and predictive tests to assess intestinal dysbiosis among cancer patients.}, } @article {pmid39123130, year = {2024}, author = {Bak, F and Keuschnig, C and Nybroe, O and Aamand, J and Jørgensen, PR and Nicolaisen, MH and Vogel, TM and Larose, C}, title = {Microbial life in preferential flow paths in subsurface clayey till revealed by metataxonomy and metagenomics.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {296}, pmid = {39123130}, issn = {1471-2180}, mesh = {*Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; *Archaea/genetics/classification/metabolism ; *Fungi/genetics/classification/isolation & purification ; *Geologic Sediments/microbiology ; *Soil Microbiology ; Microbiota/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Clay ; Sequence Analysis, DNA ; Ecosystem ; Soil/chemistry ; }, abstract = {BACKGROUND: Subsurface microorganisms contribute to important ecosystem services, yet little is known about how the composition of these communities is affected by small scale heterogeneity such as in preferential flow paths including biopores and fractures. This study aimed to provide a more complete characterization of microbial communities from preferential flow paths and matrix sediments of a clayey till to a depth of 400 cm by using 16S rRNA gene and fungal ITS2 amplicon sequencing of environmental DNA. Moreover, shotgun metagenomics was applied to samples from fractures located 150 cm below ground surface (bgs) to investigate the bacterial genomic adaptations resulting from fluctuating exposure to nutrients, oxygen and water.

RESULTS: The microbial communities changed significantly with depth. In addition, the bacterial/archaeal communities in preferential flow paths were significantly different from those in the adjacent matrix sediments, which was not the case for fungal communities. Preferential flow paths contained higher abundances of 16S rRNA and ITS gene copies than the corresponding matrix sediments and more aerobic bacterial taxa than adjacent matrix sediments at 75 and 150 cm bgs. These findings were linked to higher organic carbon and the connectivity of the flow paths to the topsoil as demonstrated by previous dye tracer experiments. Moreover, bacteria, which were differentially more abundant in the fractures than in the matrix sediment at 150 cm bgs, had higher abundances of carbohydrate active enzymes, and a greater potential for mixotrophic growth.

CONCLUSIONS: Our results demonstrate that the preferential flow paths in the subsurface are unique niches that are closely connected to water flow and the fluctuating ground water table. Although no difference in fungal communities were observed between these two niches, hydraulically active flow paths contained a significantly higher abundance in fungal, archaeal and bacterial taxa. Metagenomic analysis suggests that bacteria in tectonic fractures have the genetic potential to respond to fluctuating oxygen levels and can degrade organic carbon, which should result in their increased participation in subsurface carbon cycling. This increased microbial abundance and activity needs to be considered in future research and modelling efforts of the soil subsurface.}, } @article {pmid39122767, year = {2024}, author = {Zhang, B and Magnaye, KM and Stryker, E and Moltzau-Anderson, J and Porsche, CE and Hertz, S and McCauley, KE and Smith, BJ and Zydek, M and Pollard, KS and Ma, A and El-Nachef, N and Lynch, SV}, title = {Sustained mucosal colonization and fecal metabolic dysfunction by Bacteroides associates with fecal microbial transplant failure in ulcerative colitis patients.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {18558}, pmid = {39122767}, issn = {2045-2322}, support = {K12 GM081266/GM/NIGMS NIH HHS/United States ; T32 DK007007/DK/NIDDK NIH HHS/United States ; 1563159//National Science Foundation/ ; K12 GM081266-11/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Colitis, Ulcerative/microbiology/therapy/metabolism ; *Fecal Microbiota Transplantation ; Male ; Female ; *Feces/microbiology ; *Bacteroides/genetics ; Adult ; *Intestinal Mucosa/microbiology/metabolism ; Middle Aged ; Gastrointestinal Microbiome ; Treatment Failure ; RNA, Ribosomal, 16S/genetics ; Metabolome ; }, abstract = {Fecal microbial transplantation (FMT) offers promise for treating ulcerative colitis (UC), though the mechanisms underlying treatment failure are unknown. This study harnessed longitudinally collected colonic biopsies (n = 38) and fecal samples (n = 179) from 19 adults with mild-to-moderate UC undergoing serial FMT in which antimicrobial pre-treatment and delivery mode (capsules versus enema) were assessed for clinical response (≥ 3 points decrease from the pre-treatment Mayo score). Colonic biopsies underwent dual RNA-Seq; fecal samples underwent parallel 16S rRNA and shotgun metagenomic sequencing as well as untargeted metabolomic analyses. Pre-FMT, the colonic mucosa of non-responsive (NR) patients harbored an increased burden of bacteria, including Bacteroides, that expressed more antimicrobial resistance genes compared to responsive (R) patients. NR patients also exhibited muted mucosal expression of innate immune antimicrobial response genes. Post-FMT, NR and R fecal microbiomes and metabolomes exhibited significant divergence. NR metabolomes had elevated concentrations of immunostimulatory compounds including sphingomyelins, lysophospholipids and taurine. NR fecal microbiomes were enriched for Bacteroides fragilis and Bacteroides salyersiae strains that encoded genes capable of taurine production. These findings suggest that both effective mucosal microbial clearance and reintroduction of bacteria that reshape luminal metabolism associate with FMT success and that persistent mucosal and fecal colonization by antimicrobial-resistant Bacteroides species may contribute to FMT failure.}, } @article {pmid39122705, year = {2024}, author = {Neshat, SA and Santillan, E and Seshan, H and Wuertz, S}, title = {Non-redundant metagenome-assembled genomes of activated sludge reactors at different disturbances and scales.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {855}, pmid = {39122705}, issn = {2052-4463}, mesh = {*Sewage/microbiology ; *Metagenome ; *Bioreactors ; Metagenomics ; Microbiota ; }, abstract = {Metagenome-assembled genomes (MAGs) are microbial genomes reconstructed from metagenomic data and can be assigned to known taxa or lead to uncovering novel ones. MAGs can provide insights into how microbes interact with the environment. Here, we performed genome-resolved metagenomics on sequencing data from four studies using sequencing batch reactors at microcosm (~25 mL) and mesocosm (~4 L) scales inoculated with sludge from full-scale wastewater treatment plants. These studies investigated how microbial communities in such plants respond to two environmental disturbances: the presence of toxic 3-chloroaniline and changes in organic loading rate. We report 839 non-redundant MAGs with at least 50% completeness and 10% contamination (MIMAG medium-quality criteria). From these, 399 are of putative high-quality, while sixty-seven meet the MIMAG high-quality criteria. MAGs in this catalogue represent the microbial communities in sixty-eight laboratory-scale reactors used for the disturbance experiments, and in the full-scale wastewater treatment plant which provided the source sludge. This dataset can aid meta-studies aimed at understanding the responses of microbial communities to disturbances, particularly as ecosystems confront rapid environmental changes.}, } @article {pmid39122162, year = {2024}, author = {Liu, S and Hou, C and Dong, C and Zhao, D and Chen, Q and Terence Yang, JY and Tang, K}, title = {Integrated multi-omics analyses reveal microbial community resilience to fluctuating low oxygen in the East China sea.}, journal = {Environmental research}, volume = {261}, number = {}, pages = {119764}, doi = {10.1016/j.envres.2024.119764}, pmid = {39122162}, issn = {1096-0953}, mesh = {*Oxygen/metabolism/analysis ; China ; *Seawater/microbiology/chemistry ; *Microbiota ; Proteomics ; Bacteria/metabolism/genetics ; Metagenomics ; Oceans and Seas ; Multiomics ; }, abstract = {Climate change and eutrophication are accelerating ocean deoxygenation, leading to a global decline in oxygen levels. The East China Sea, frequently experiencing deoxygenation events, harbors diverse microbial communities. However, the response of these communities to the changing deoxygenation dynamics remains poorly understood. Here, we explored the composition and function of microbial communities inhabiting seawaters of the Changjiang Estuary and offshore areas. Our findings suggested that neutral processes significantly influenced the assembly of these communities. The overall bacterial composition demonstrated remarkable high stability across the oxygen gradient. Salinity exhibited a significantly stronger correlation with bacterial community structure than dissolved oxygen. Both metagenomics and metaproteomics revealed that all of the samples exhibited similar functional community structures. Heterotrophic metabolism dominated these sites, as evidenced by a diverse array of transporters and metabolic enzymes for organic matter uptake and utilization, which constituted a significant portion of the expressed proteins. O2 was the primary electron acceptor in bacteria even under hypoxic conditions, evidenced by expression of low- and high-affinity cytochrome oxidases. Proteins associated with anaerobic processes, such as dissimilatory sulfite reductases, were virtually undetectable. Untargeted liquid chromatography with tandem mass spectrometry analysis of seawater samples revealed a diverse range of dissolved organic matter (DOM) components in amino acids, lipids, organic acids, peptides, and carbohydrates, potentially fueling dominant taxa growth. Despite fluctuations in the abundance of specific genera, the remarkable similarity in community structure, function, and DOM suggests that this ecosystem possesses robust adaptive mechanisms that buffer against abrupt changes, even below the well-defined hypoxic threshold in marine ecosystem.}, } @article {pmid39122016, year = {2024}, author = {Fiorucci, S and Marchianò, S and Urbani, G and Di Giorgio, C and Distrutti, E and Zampella, A and Biagioli, M}, title = {Immunology of bile acids regulated receptors.}, journal = {Progress in lipid research}, volume = {95}, number = {}, pages = {101291}, doi = {10.1016/j.plipres.2024.101291}, pmid = {39122016}, issn = {1873-2194}, mesh = {Humans ; *Bile Acids and Salts/metabolism/immunology ; Animals ; Gastrointestinal Microbiome/immunology ; }, abstract = {Bile acids are steroids formed at the interface of host metabolism and intestinal microbiota. While primary bile acids are generated in the liver from cholesterol metabolism, secondary bile acids represent the products of microbial enzymes. Close to 100 different enzymatic modifications of bile acids structures occur in the human intestine and clinically guided metagenomic and metabolomic analyses have led to the identification of an extraordinary number of novel metabolites. These chemical mediators make an essential contribution to the composition and function of the postbiota, participating to the bidirectional communications of the intestinal microbiota with the host and contributing to the architecture of intestinal-liver and -brain and -endocrine axes. Bile acids exert their function by binding to a group of cell membrane and nuclear receptors collectively known as bile acid-regulated receptors (BARRs), expressed in monocytes, tissue-resident macrophages, CD4+ T effector cells, including Th17, T regulatory cells, dendritic cells and type 3 of intestinal lymphoid cells and NKT cells, highlighting their role in immune regulation. In this review we report on how bile acids and their metabolitesmodulate the immune system in inflammations and cancers and could be exploiting for developing novel therapeutic approaches in these disorders.}, } @article {pmid39120615, year = {2024}, author = {Li, X and Tao, Q and Hu, Q and Ma, N and Ma, G}, title = {In vitro gastrointestinal digestion and fecal fermentation of Pleurotus eryngii proteins extracted using different methods: insights for the utilization of edible mushroom-based proteins as novel nutritional and functional components.}, journal = {Food & function}, volume = {15}, number = {17}, pages = {8865-8877}, doi = {10.1039/d4fo02604g}, pmid = {39120615}, issn = {2042-650X}, mesh = {*Pleurotus/metabolism/chemistry ; *Digestion ; *Fermentation ; *Feces/microbiology ; *Fungal Proteins/metabolism ; Humans ; Gastrointestinal Tract/metabolism/microbiology ; Gastrointestinal Microbiome ; Hydrolysis ; }, abstract = {Pleurotus eryngii (P. eryngii) protein is considered a high-quality protein because it is rich in essential amino acids and displays multiple significant functional characterizations that vary with its fabrication processes. We aimed to investigate the differences in P. eryngii protein extracted via alkaline extraction and acid precipitation (AA), cellulase complex alkaline extraction and acid precipitation (CAA), ultrasound-assisted alkaline extraction and acid precipitation (UAA), and salt dissolution (S) in terms of gastrointestinal digestion and fecal fermentation consequences. Protein hydrolysis and structural analysis were performed after in vitro gastrointestinal digestion, and it was found that AA showed the highest hydrolysis degree, whereas CAA showed the lowest. The results of fluorescence chromatography and infrared chromatography indicated that the reasons for the digestion difference might be the unfolding degrees of the protein tertiary structure and polysaccharide content, which is the major component of crude proteins and can prevent protein hydrolysis. Metagenomic analysis suggested that compared with other groups, AA had excellent biological functions, including regulating obesity and insulin-related microbiota. This study could provide a new theoretical basis for the P. eryngii protein as a novel type of nutritional and functional component and contributes to the development of a diversified emerging food protein supply system.}, } @article {pmid39118488, year = {2024}, author = {Sanville, J and O'Toole, GA and Madan, J and Coker, M}, title = {Premodulator microbiome alterations associated with postmodulator growth outcomes in pediatric cystic fibrosis: Can we predict outcomes?.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {79}, number = {3}, pages = {695-704}, doi = {10.1002/jpn3.12350}, pmid = {39118488}, issn = {1536-4801}, support = {SANVIL19GEO//Cystic Fibrosis Foundation (CFF)/ ; MADAN22A0//Cystic Fibrosis Foundation (CFF)/ ; OTOOLE22G0//Cystic Fibrosis Foundation (CFF)/ ; P30-DK117469//National Institutes of Health (NIH)/ ; ES033988-01A1//National Institutes of Health (NIH)/ ; }, mesh = {Humans ; *Cystic Fibrosis/microbiology/complications ; Female ; Male ; *Gastrointestinal Microbiome ; Child, Preschool ; *Feces/microbiology ; Infant ; Longitudinal Studies ; Infant, Newborn ; Overweight/microbiology ; Body Mass Index ; }, abstract = {OBJECTIVES: The gut microbiota plays an important role in childhood growth. Our longitudinal cohort includes children with cystic fibrosis (CwCF) treated with highly effective modulator therapy. We aimed to elucidate early premodulator microbial signatures associated with postmodulator weight for CwCF later in childhood.

METHODS: Stool samples were collected from CwCF at 13 days to 60 months. Metagenomic sequencing determined differentially abundant taxa. Children with body mass index or weight for length Z-scores within 1 standard deviation of the mean (SD) were considered normal weight, those >1 SD were classified as risk of overweight while children <1 SD were considered undernourished, although no CwCF met this latter criterion here. Multivariate regression models were applied to identify significant associations between metadata and microbial taxonomic relative abundances.

RESULTS: One hundred and eighty-nine stool samples were analyzed from 39 CwCF. We identified statistically significant differences in early microbiome patterns among those at risk of being overweight compared to those who were normal weight when adjusted for age, sex, CF mutation, and early feeding method. Early microbiome was a stronger driver of growth status than current modulator use. Among those at risk of overweight, several taxa that were consistently in lower abundance included Eggerthella lentha, Ruminococcus, Bacteroides, with increase in abundance of Bacteroides stercoris.

CONCLUSIONS: The early microbiome strongly predicts growth in the setting of modulator use for CwCF and we identify microbiome signatures associated with risk of being overweight. We highlight the possibility for interventions or early alternations to nutritional guidance for prevention of comorbid complications.}, } @article {pmid39118486, year = {2024}, author = {Cui, S and Guo, R and Chen, C and Zhang, Y and Meng, J and Liu, L and Li, Y and Kang, Z and Li, S and Yan, Q and Ma, Y}, title = {Next-Generation Sequencing for Characterizing Respiratory Tract Virome and Improving Detection of Viral Pathogens in Children With Pneumonia.}, journal = {Influenza and other respiratory viruses}, volume = {18}, number = {8}, pages = {e13362}, pmid = {39118486}, issn = {1750-2659}, support = {81902037//National Natural Science Foundation of China/ ; 20180550075//Natural Science Foundation of Liaoning Province of China/ ; }, mesh = {Humans ; *Virome ; *High-Throughput Nucleotide Sequencing ; Child, Preschool ; *Nasopharynx/virology/microbiology ; *Bronchoalveolar Lavage Fluid/virology/microbiology ; Male ; Female ; Infant ; *Viruses/isolation & purification/genetics/classification ; Child ; Oropharynx/virology/microbiology ; Pneumonia/microbiology/virology/diagnosis ; Metagenomics/methods ; }, abstract = {BACKGROUND: Pneumonia is typically caused by a variety of pathogenic microorganisms. Traditional research often focuses on the infection of a few microorganisms, whereas metagenomic studies focus on the impact of the bacteriome and mycobiome on respiratory diseases. Reports on the virome characteristics of pediatric pneumonia remain relatively scarce.

METHODS: We employed de novo assembly and combined homology- and feature-based methods to characterize the respiratory virome in whole-genome DNA sequencing samples from oropharynx (OP) swabs, nasopharynx (NP) swabs, and bronchoalveolar lavage fluids (BALF) of children with pneumonia.

RESULTS: Significant differences were observed in the alpha and beta diversity indexes, as well as in the composition of the oropharyngeal virome, between pneumonia cases and controls. We identified 1137 viral operational taxonomic units (vOTUs) with significant differences, indicating a preference of pneumonia-reduced vOTUs for infecting Prevotella, Neisseria, and Veillonella, whereas pneumonia-enriched vOTUs included polyomavirus, human adenovirus, and phages targeting Staphylococcus, Streptococcus, Granulicatella, and Actinomyces. Comparative analysis revealed higher relative abundances and prevalence rates of pneumonia-enriched OP vOTUs in NP and BALF samples compared to pneumonia-reduced vOTUs. Additionally, virome analysis identified six pediatric patients with severe human adenovirus or polyomavirus infections, five of whom might have been undetected by targeted polymerase chain reaction (PCR)-based testing.

CONCLUSIONS: This study offers insights into pediatric pneumonia respiratory viromes, highlighting frequent transmission of potentially pathogenic viruses and demonstrating virome analysis as a valuable adjunct for pathogen detection.}, } @article {pmid39117774, year = {2024}, author = {Durand, K and Yainna, S and Nam, K}, title = {Population genomics unravels a lag phase during the global fall armyworm invasion.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {957}, pmid = {39117774}, issn = {2399-3642}, mesh = {Animals ; *Introduced Species ; *Spodoptera/genetics ; Genetic Variation ; Gene Flow ; Genetics, Population ; Metagenomics ; Genomics/methods ; }, abstract = {The time that elapsed between the initial introduction and the proliferation of an invasive species is referred to as the lag phase. The identification of the lag phase is critical for generating plans for pest management and for the prevention of biosecurity failure. However, lag phases have been identified mostly through retrospective searches of historical records. The agricultural pest fall armyworm (FAW; Spodoptera frugiperda) is native to the New World. FAW invasion was first reported from West Africa in 2016, then it spread quickly through Africa, Asia, and Oceania. Here, using population genomics approaches, we demonstrate that the FAW invasion involved an undocumented lag phase. Invasive FAW populations have negative signs of genomic Tajima's D, and invasive population-specific genetic variations have particularly decreased Tajima's D, supporting a substantial amount of time for the generation of new mutations in introduced FAW populations. Model-based diffusion approximations support the existence of a period with a cessation of gene flow between native and invasive FAW populations. Taken together, these results provide strong support for the presence of a lag phase during the FAW invasion. These results show the usefulness of using population genomics analyses to identify lag phases in biological invasions.}, } @article {pmid39117673, year = {2024}, author = {An, L and Liu, X and Wang, J and Xu, J and Chen, X and Liu, X and Hu, B and Nie, Y and Wu, XL}, title = {Global diversity and ecological functions of viruses inhabiting oil reservoirs.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {6789}, pmid = {39117673}, issn = {2041-1723}, support = {32130004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32161133023//National Natural Science Foundation of China (National Science Foundation of China)/ ; 91951204//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32170113//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Oil and Gas Fields/virology/microbiology ; *Viruses/genetics/classification/isolation & purification ; *Metagenome/genetics ; *Biodiversity ; Microbiota/genetics ; Genome, Viral/genetics ; Phylogeny ; Bacteria/genetics/classification/isolation & purification ; Metagenomics ; }, abstract = {Oil reservoirs, being one of the significant subsurface repositories of energy and carbon, host diverse microbial communities affecting energy production and carbon emissions. Viruses play crucial roles in the ecology of microbiomes, however, their distribution and ecological significance in oil reservoirs remain undetermined. Here, we assemble a catalogue encompassing viral and prokaryotic genomes sourced from oil reservoirs. The catalogue comprises 7229 prokaryotic genomes and 3,886 viral Operational Taxonomic Units (vOTUs) from 182 oil reservoir metagenomes. The results show that viruses are widely distributed in oil reservoirs, and 85% vOTUs in oil reservoir are detected in less than 10% of the samples, highlighting the heterogeneous nature of viral communities within oil reservoirs. Through combined microcosm enrichment experiments and bioinformatics analysis, we validate the ecological roles of viruses in regulating the community structure of sulfate reducing microorganisms, primarily through a virulent lifestyle. Taken together, this study uncovers a rich diversity of viruses and their ecological functions within oil reservoirs, offering a comprehensive understanding of the role of viral communities in the biogeochemical cycles of the deep biosphere.}, } @article {pmid39117653, year = {2024}, author = {Wu, Z and Liu, T and Chen, Q and Chen, T and Hu, J and Sun, L and Wang, B and Li, W and Ni, J}, title = {Unveiling the unknown viral world in groundwater.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {6788}, pmid = {39117653}, issn = {2041-1723}, support = {U2240205//National Natural Science Foundation of China (National Science Foundation of China)/ ; 51721006//National Natural Science Foundation of China (National Science Foundation of China)/ ; 423B2703//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Groundwater/microbiology/virology ; *Viruses/genetics/classification/isolation & purification ; *Virome/genetics ; *Bacteria/genetics/virology/metabolism/classification ; *Metagenomics ; China ; Archaea/virology/genetics/metabolism ; Phylogeny ; Water Microbiology ; Metagenome ; Genome, Viral/genetics ; }, abstract = {Viruses as the prevailing biological entities are poorly understood in underground realms. Here, we establish the first metagenomic Groundwater Virome Catalogue (GWVC) comprising 280,420 viral species (≥ 5 kb) detected from 607 monitored wells in seven geo-environmental zones throughout China. In expanding ~10-fold the global portfolio of known groundwater viruses, we uncover over 99% novel viruses and about 95% novel viral clusters. By linking viruses to hosts from 119 prokaryotic phyla, we double the number of microbial phyla known to be virus-infected in groundwater. As keystone ultrasmall symbionts in aquifers, CPR bacteria and DPANN archaea are susceptible to virulent viruses. Certain complete CPR viruses even likely infect non-CPR bacteria, while partial CPR/DPANN viruses harbor cell-surface modification genes that assist symbiont cell adhesion to free-living microbes. This study reveals the unknown viral world and auxiliary metabolism associated with methane, nitrogen, sulfur, and phosphorus cycling in groundwater, and highlights the importance of subsurface virosphere in viral ecology.}, } @article {pmid39117304, year = {2024}, author = {Mancin, L and Rollo, I and Golzato, D and Segata, N and Petri, C and Pengue, L and Vergani, L and Cassone, N and Corsini, A and Mota, JF and Sut, S and Dall'Acqua, S and Paoli, A}, title = {Short-Term Cocoa Supplementation Influences Microbiota Composition and Serum Markers of Lipid Metabolism in Elite Male Soccer Players.}, journal = {International journal of sport nutrition and exercise metabolism}, volume = {34}, number = {6}, pages = {349-361}, doi = {10.1123/ijsnem.2024-0012}, pmid = {39117304}, issn = {1543-2742}, mesh = {Humans ; Male ; *Soccer/physiology ; *Gastrointestinal Microbiome/drug effects ; Young Adult ; *Dietary Supplements ; *Lipid Metabolism/drug effects ; *Biomarkers/blood ; Polyphenols/administration & dosage/pharmacology ; Chocolate ; Cacao ; Arachidonic Acid/blood ; Adult ; Feces/microbiology/chemistry ; Eicosapentaenoic Acid/blood/administration & dosage ; Triglycerides/blood ; Sports Nutritional Physiological Phenomena ; Athletes ; }, abstract = {OBJECTIVES: Dietary strategies to improve arachidonic acid:eicosapentaenoic acid (AA:EPA) ratios are of interest due to potential reductions in inflammation and oxidative stress following exercise. The aim of this study was to investigate the impact of a novel dietary intervention, that is, the ingestion of 30 g of dark chocolate, on blood lipid profiles and gut microbiota composition in elite male soccer players.

METHODS: Professional male soccer players were randomly assigned to the experimental group (DC) provided with 30 g of dark chocolate or to the control group (WC), provided with 30 g of white chocolate, for 30 days. Before and after intervention, blood, fecal sample, and anthropometry data were collected. For each outcome, two-way repeated-measure analysis of variance was used to identify differences between baseline and endpoint (Week 4), considering treatment (dark chocolate, white chocolate) as intersubjects' factors. Metagenomic analysis was performed following the general guidelines, which relies on the bioBakery computational environment.

RESULTS: DC group showed increased plasma polyphenols (from 154.7 ± 18.6 μg gallic acid equivalents/ml to 185.11 ± 57.6 μg gallic acid equivalents/ml, Δ pre vs. post = +30.41 ± 21.50) and significant improvements in lipid profiles: total cholesterol (Δ -32.47 ± 17.18 mg/dl DC vs. Δ -2.84 ± 6.25 mg/dl WC, Time × Treatment interaction p < .001), triglycerides (Δ -6.32 ± 4.96 mg/dl DC vs. Δ -0.42 ± 6.47 mg/dl WC, Time × Treatment interaction p < .001), low-density lipoprotein (Δ -18.42 ± 17.13 mg/dl vs. Δ -2.05 ± 5.19 mg/dl WC, Time × Treatment interaction p < .001), AA/EPA ratio (Δ -5.26 ± 2.35; -54.1% DC vs. Δ -0.47 ± 0.73, -6.41% WC, Time × Treatment interaction p < .001) compared with WC group. In addition, 4 weeks of intervention showed a significant increase in high-density lipoprotein concentration in DC group (Δ + 3.26 ± 4.49 mg/dl DC vs. Δ -0.79 ± 5.12 mg/dl WC). Microbial communities in the DC group maintained a slightly higher microbial stability over time (exhibiting lower within-subject community dissimilarity).

CONCLUSION: Ingesting 30 g of dark chocolate over 4 weeks positively improved AA:EPA ratio and maintained gut microbial stability. Dark chocolate ingestion represents an effective nutritional strategy to improve blood lipid profiles in professional soccer players. What Are the Findings? Ingesting 30 g of dark chocolate for 4 weeks positively influences blood lipid AA: EPA ratio while maintaining gut microbial stability. What This Study Adds? Dietary intake of specific foods such as dark chocolate represents an alternative strategy to support the health and recovery of elite soccer players. What Impact Might This Have on Clinical Practice in the Future? From a clinical and translational perspective, dark chocolate ingestion positively modulates favorable blood lipid profiles and polyunsaturated fatty acid metabolism while maintaining gut microbial stability. Dark chocolate ingestion may be considered as an effective nutritional strategy in elite sport environments during periods of high-intensity training and congested competitions. Further research is required to determine functional outcomes associated with the observed improvements in blood lipid profiles.}, } @article {pmid39117202, year = {2024}, author = {Tariq, M and Liu, Y and Rizwan, A and Shoukat, CA and Aftab, Q and Lu, J and Zhang, Y}, title = {Impact of elevated CO2 on soil microbiota: A meta-analytical review of carbon and nitrogen metabolism.}, journal = {The Science of the total environment}, volume = {950}, number = {}, pages = {175354}, doi = {10.1016/j.scitotenv.2024.175354}, pmid = {39117202}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Nitrogen/metabolism ; *Carbon Dioxide/metabolism ; *Microbiota ; *Carbon/metabolism ; Climate Change ; Soil/chemistry ; Carbon Cycle ; }, abstract = {In the face of 21st-century challenges driven by population growth and resource depletion, understanding the intricacies of climate change is crucial for environmental sustainability. This review systematically explores the interaction between rising atmospheric CO2 concentrations and soil microbial populations, with possible feedback effects on climate change and terrestrial carbon (C) cycling through a meta-analytical approach. Furthermore, it investigates the enzymatic activities related to carbon acquisition, gene expression patterns governing carbon and nitrogen metabolism, and metagenomic and meta-transcriptomic dynamics in response to elevated CO2 levels. The study reveals that elevated CO2 levels substantially influence soil microbial communities, increasing microbial biomass C and respiration rate by 15 % and upregulating genes involved in carbon and nitrogen metabolism by 12 %. Despite a 14 % increase in C-acquiring enzyme activity, there is a 5 % decrease in N-acquiring enzyme activity, indicating complex microbial responses to CO2 changes. Additionally, fungal marker ratios increase by 14 % compared to bacterial markers, indicating potential ecosystem changes. However, the current inadequacy of data on metagenomic and meta-transcriptomic processes underscores the need for further research. Understanding soil microbial feedback mechanisms is crucial for elucidating the role of rising CO2 levels in carbon sequestration and climate regulation. Consequently, future research should prioritize a comprehensive elucidation of soil microbial carbon cycling, greenhouse gas emission dynamics, and their underlying drivers.}, } @article {pmid39117122, year = {2024}, author = {Wang, K and Lo, CH and Mehta, RS and Nguyen, LH and Wang, Y and Ma, W and Ugai, T and Kawamura, H and Ugai, S and Takashima, Y and Mima, K and Arima, K and Okadome, K and Giannakis, M and Sears, CL and Meyerhardt, JA and Ng, K and Segata, N and Izard, J and Rimm, EB and Garrett, WS and Huttenhower, C and Giovannucci, EL and Chan, AT and Ogino, S and Song, M}, title = {An Empirical Dietary Pattern Associated With the Gut Microbial Features in Relation to Colorectal Cancer Risk.}, journal = {Gastroenterology}, volume = {167}, number = {7}, pages = {1371-1383.e4}, pmid = {39117122}, issn = {1528-0012}, support = {R35 CA197735/CA/NCI NIH HHS/United States ; P01 CA087969/CA/NCI NIH HHS/United States ; U01 CA167552/CA/NCI NIH HHS/United States ; K99 CA283146/CA/NCI NIH HHS/United States ; UM1 CA186107/CA/NCI NIH HHS/United States ; R50 CA274122/CA/NCI NIH HHS/United States ; U01 CA176726/CA/NCI NIH HHS/United States ; U01 CA261961/CA/NCI NIH HHS/United States ; R01 CA263776/CA/NCI NIH HHS/United States ; R35 CA253185/CA/NCI NIH HHS/United States ; R01 CA243454/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Male ; *Colorectal Neoplasms/microbiology/epidemiology ; *Gastrointestinal Microbiome ; Female ; Middle Aged ; Risk Factors ; Aged ; *Diet/adverse effects ; *Bacteroides fragilis/isolation & purification ; Adult ; Feces/microbiology ; Risk Assessment ; Fusobacterium nucleatum/isolation & purification ; Incidence ; Escherichia coli/isolation & purification ; Prospective Studies ; Sex Factors ; Dietary Patterns ; }, abstract = {BACKGROUND & AIMS: Epidemiologic evidence for dietary influence on colorectal cancer (CRC) risk through the gut microbiome remains limited.

METHODS: Leveraging 307 men and 212 women with stool metagenomes and dietary data, we characterized and validated a sex-specific dietary pattern associated with the CRC-related gut microbial signature (CRC Microbial Dietary Score [CMDS]). We evaluated the associations of CMDS with CRC risk according to Fusobacterium nucleatum, pks[+]Escherichia coli, and enterotoxigenic Bacteroides fragilis status in tumor tissue using Cox proportional hazards regression in the Health Professionals Follow-Up Study (1986-2018), Nurses' Health Study (1984-2020), and Nurses' Health Study II (1991-2019).

RESULTS: The CMDS was characterized by high industrially processed food and low unprocessed fiber-rich food intakes. In 259,200 participants, we documented 3854 incident CRC cases over 6,467,378 person-years of follow-up. CMDS was associated with a higher risk of CRC (Ptrend < .001), with a multivariable hazard ratio (HRQ5 vs Q1) of 1.25 (95% CI, 1.13-1.39). The association remained after adjusting for previously established dietary patterns, for example, the Western and prudent diets. Notably, the association was stronger for tumoral F nucleatum-positive (HRQ5 vs Q1, 2.51; 95% CI, 1.68-3.75; Ptrend < .001; Pheterogeneity = .03, positivity vs negativity), pks[+]E coli-positive (HRQ5 vs Q1, 1.68; 95% CI, 0.84-3.38; Ptrend = .005; Pheterogeneity = .01, positivity vs negativity), and enterotoxigenic Bacteroides fragilis-positive CRC (HRQ5 vs Q1, 2.06; 95% CI, 1.10-3.88; Ptrend = .016; Pheterogeneity = .06, positivity vs negativity), compared with their negative counterparts.

CONCLUSIONS: CMDS was associated with increased CRC risk, especially for tumors with detectable F nucleatum, pks[+]E coli, and enterotoxigenic Bacteroides fragilis in tissue. Our findings support a potential role of the gut microbiome underlying the dietary effects on CRC.}, } @article {pmid39116926, year = {2024}, author = {Kong, D and Xu, L and Dai, M and Ye, Z and Ma, B and Tan, X}, title = {Deciphering the functional assembly of microbial communities driven by heavy metals in the tidal soils of Hangzhou Bay.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {360}, number = {}, pages = {124671}, doi = {10.1016/j.envpol.2024.124671}, pmid = {39116926}, issn = {1873-6424}, mesh = {*Metals, Heavy/analysis ; *Soil Pollutants/analysis ; *Soil Microbiology ; China ; *Microbiota ; *Bays ; *Soil/chemistry ; Environmental Monitoring ; Bacteria/genetics ; Arsenic/analysis ; }, abstract = {Understanding the interaction between heavy metals and soil microbiomes is essential for maintaining ecosystem health and functionality in the face of persistent human-induced challenges. This study investigated the complex relationships between heavy metal contamination and the functional characteristics of soil microbial communities in the tidal soils of Hangzhou Bay, a region experiencing substantial environmental pressure due to its proximity to densely populated and industrialized regions. The north-shore sampling site showed moderate contaminations (mg/kg) of total arsenic (16.61 ± 1.13), cadmium (0.3 ± 0.05), copper (31.28 ± 1.23), nickel (37.44 ± 2.74), lead (34.29 ± 5.99), and zinc (120.8 ± 5.96), which are 1.29-2.94 times higher than the geochemical background values in Hangzhou Bay and adjacent areas. In contrast, the south-shore sampling site showed slightly higher levels of total arsenic (13.76 ± 1.35) and cadmium (0.13 ± 0.02) than the background values. Utilizing metagenomic sequencing, we decoded microbial functional genes essential for nitrogen, phosphorus, sulfur, and methane biogeochemical cycles. Although soil available nickel content was relatively low at 1 mg/kg, it exhibited strong associations with diverse microbial genes and biogeochemical pathways. Four key genes-hxlB, glpX, opd, and phny-emerged as pivotal players in the interactions with available nickel, suggesting the adaptability of microbial metabolic responses to heavy metal. Additionally, microbial genera such as Gemmatimonas and Ilumatobacter, which harbored diverse functional genes, demonstrated potential interactions with soil nickel. These findings highlight the importance of understanding heavy metal-soil microbiome dynamics for effective environmental management strategies in the tidal soils of Hangzhou Bay, with the goal of preserving ecosystem health and functionality amidst ongoing anthropogenic challenges.}, } @article {pmid39116611, year = {2024}, author = {Huang, X and Toro, M and Reyes-Jara, A and Moreno-Switt, AI and Adell, AD and Oliveira, CJB and Bonelli, RR and Gutiérrez, S and Álvarez, FP and Rocha, ADL and Kraychete, GB and Chen, Z and Grim, C and Brown, E and Bell, R and Meng, J}, title = {Integrative genome-centric metagenomics for surface water surveillance: Elucidating microbiomes, antimicrobial resistance, and their associations.}, journal = {Water research}, volume = {264}, number = {}, pages = {122208}, doi = {10.1016/j.watres.2024.122208}, pmid = {39116611}, issn = {1879-2448}, mesh = {*Metagenomics ; *Microbiota ; Water Microbiology ; Brazil ; Bacteria/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Chile ; }, abstract = {Surface water ecosystems are intimately intertwined with anthropogenic activities and have significant public health implications as primary sources of irrigation water in agricultural production. Our extensive metagenomic analysis examined 404 surface water samples from four different geological regions in Chile and Brazil, spanning irrigation canals (n = 135), rivers (n = 121), creeks (n = 74), reservoirs (n = 66), and ponds (n = 8). Overall, 50.25 % of the surface water samples contained at least one of the pathogenic or contaminant bacterial genera (Salmonella: 29.21 %; Listeria: 6.19 %; Escherichia: 35.64 %). Furthermore, a total of 1,582 antimicrobial resistance (AMR) gene clusters encoding resistance to 25 antimicrobial classes were identified, with samples from Brazil exhibiting an elevated AMR burden. Samples from stagnant water sources were characterized by dominant Cyanobacteriota populations, resulting in significantly reduced biodiversity and more uniform community compositions. A significant association between taxonomic composition and the resistome was supported by a Procrustes analysis (p < 0.001). Notably, regional signatures were observed regarding the taxonomic and resistome profiles, as samples from the same region clustered together on both ordinates. Additionally, network analysis illuminated the intricate links between taxonomy and AMR at the contig level. Our deep sequencing efforts not only mapped the microbial landscape but also expanded the genomic catalog with newly characterized metagenome-assembled genomes (MAGs), boosting the classification of reads by 12.85 %. In conclusion, this study underscores the value of metagenomic approaches in surveillance of surface waters, enhancing our understanding of microbial and AMR dynamics with far-reaching public health and ecological ramifications.}, } @article {pmid39115410, year = {2024}, author = {Moncada, C and Arnosti, C and Brüwer, JD and de Beer, D and Amann, R and Knittel, K}, title = {Niche separation in bacterial communities and activities in porewater, loosely attached, and firmly attached fractions in permeable surface sediments.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39115410}, issn = {1751-7370}, support = {//Max Planck Society/ ; OCE-2022952//National Science Foundation/ ; }, mesh = {*Geologic Sediments/microbiology ; *Bacteria/classification/metabolism/isolation & purification/genetics ; *Microbiota ; Svalbard ; Heterotrophic Processes ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Heterotrophic microbes are central to organic matter degradation and transformation in marine sediments. Currently, most investigations of benthic microbiomes do not differentiate between processes in the porewater and on the grains and, hence, only show a generalized picture of the community. This limits our understanding of the structure and functions of sediment microbiomes. To address this problem, we fractionated sandy surface sediment microbial communities from a coastal site in Isfjorden, Svalbard, into cells associated with the porewater, loosely attached to grains, and firmly attached to grains; we found dissimilar bacterial communities and metabolic activities in these fractions. Most (84%-89%) of the cells were firmly attached, and this fraction comprised more anaerobes, such as sulfate reducers, than the other fractions. The porewater and loosely attached fractions (3% and 8%-13% of cells, respectively) had more aerobic heterotrophs. These two fractions generally showed a higher frequency of dividing cells, polysaccharide (laminarin) hydrolysis rates, and per-cell O2 consumption than the firmly attached cells. Thus, the different fractions occupy distinct niches within surface sediments: the firmly attached fraction is potentially made of cells colonizing areas on the grain that are protected from abrasion, but might be more diffusion-limited for organic matter and electron acceptors. In contrast, the porewater and loosely attached fractions are less resource-limited and have faster growth. Their cell numbers are kept low possibly through abrasion and exposure to grazers. Differences in community composition and activity of these cell fractions point to their distinct roles and contributions to carbon cycling within surface sediments.}, } @article {pmid39113216, year = {2024}, author = {Wakamori, C and De Velasco, MA and Sakai, K and Kura, Y and Matsushita, M and Fujimoto, S and Hatano, K and Nonomura, N and Fujita, K and Nishio, K and Uemura, H}, title = {A cross-species analysis of fecal microbiomes in humans and mice reveals similarities and dissimilarities associated with prostate cancer risk.}, journal = {The Prostate}, volume = {84}, number = {15}, pages = {1375-1386}, doi = {10.1002/pros.24776}, pmid = {39113216}, issn = {1097-0045}, support = {20K09570//Japan Society for the Promotion of Science/ ; }, mesh = {Male ; Animals ; *Prostatic Neoplasms/microbiology/pathology/metabolism ; Humans ; Mice ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Mice, Knockout ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; Middle Aged ; Aged ; }, abstract = {BACKGROUND: Prostate cancer is a complex disease that develops over time and is influenced by several lifestyle factors that also impact gut microbes. Gut dysbiosis is intricately linked to prostate carcinogenesis, but the precise mechanisms remain poorly understood. Mice are crucial for studying the relationships between gut microbes and prostate cancer, but discovering similarities between humans and mice may aid in elucidating new mechanisms.

METHODS: We used 16s rRNA sequencing data from stool samples of tumor-bearing prostate-specific conditional Pten-knockout mice, disease-free wildtype mice, and a human cohort suspected of having prostate cancer to conduct taxonomic and metagenomic profiling. Features were associated with prostate cancer status and low risk (a negative biopsy of Gleason grade <2) or high risk (Gleason grade ≥2) in humans.

RESULTS: In both humans and mice, community composition differed between individuals with and without prostate cancer. Odoribacter spp. and Desulfovibrio spp. were taxa associated with prostate cancer in mice and humans. Metabolic pathways associated with cofactor and vitamin synthesis were common in mouse and human prostate cancer, including bacterial synthesis of folate (vitamin B9), ubiquinone (CoQ10), phylloquinone (vitamin K1), menaquinone (vitamin K2), and tocopherol (vitamin E).

CONCLUSIONS: Our study provides valuable data that can help bridge the gap between human and mouse microbiomes. Our findings provide evidence to support the notion that certain bacterial-derived metabolites may promote prostate cancer, as well as a preclinical model that can be used to characterize biological mechanisms and develop preventive interventions.}, } @article {pmid39113195, year = {2024}, author = {Dong, T and Wang, Y and Qi, C and Fan, W and Xie, J and Chen, H and Zhou, H and Han, X}, title = {Sequencing Methods to Study the Microbiome with Antibiotic Resistance Genes in Patients with Pulmonary Infections.}, journal = {Journal of microbiology and biotechnology}, volume = {34}, number = {8}, pages = {1617-1626}, pmid = {39113195}, issn = {1738-8872}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Microbiota/genetics/drug effects ; Retrospective Studies ; *Drug Resistance, Bacterial/genetics ; Metagenomics/methods ; Microbial Sensitivity Tests ; Respiratory Tract Infections/microbiology/drug therapy ; Genes, Bacterial/genetics ; Male ; Female ; Middle Aged ; }, abstract = {Various antibiotic-resistant bacteria (ARB) are known to induce repeated pulmonary infections and increase morbidity and mortality. A thorough knowledge of antibiotic resistance is imperative for clinical practice to treat resistant pulmonary infections. In this study, we used a reads-based method and an assembly-based method according to the metagenomic next-generation sequencing (mNGS) data to reveal the spectra of ARB and corresponding antibiotic resistance genes (ARGs) in samples from patients with pulmonary infections. A total of 151 clinical samples from 144 patients with pulmonary infections were collected for retrospective analysis. The ARB and ARGs detection performance was compared by the reads-based method and assembly-based method with the culture method and antibiotic susceptibility testing (AST), respectively. In addition, ARGs and the attribution relationship of common ARB were analyzed by the two methods. The comparison results showed that the assembly-based method could assist in determining pathogens detected by the reads-based method as true ARB and improve the predictive capabilities (46% > 13%). ARG-ARB network analysis revealed that assembly-based method could promote determining clear ARG-bacteria attribution and 101 ARGs were detected both in two methods. 25 ARB were obtained by both methods, of which the most predominant ARB and its ARGs in the samples of pulmonary infections were Acinetobacter baumannii (ade), Pseudomonas aeruginosa (mex), Klebsiella pneumoniae (emr), and Stenotrophomonas maltophilia (sme). Collectively, our findings demonstrated that the assembly-based method could be a supplement to the reads-based method and uncovered pulmonary infection-associated ARB and ARGs as potential antibiotic treatment targets.}, } @article {pmid39113128, year = {2024}, author = {Robino, P and Galosi, L and Bellato, A and Vincenzetti, S and Gonella, E and Ferrocino, I and Serri, E and Biagini, L and Roncarati, A and Nebbia, P and Menzio, C and Rossi, G}, title = {Effects of a supplemented diet containing 7 probiotic strains (Honeybeeotic) on honeybee physiology and immune response: analysis of hemolymph cytology, phenoloxidase activity, and gut microbiome.}, journal = {Biological research}, volume = {57}, number = {1}, pages = {50}, pmid = {39113128}, issn = {0717-6287}, mesh = {Animals ; Bees/cytology/drug effects/enzymology/microbiology ; Dietary Supplements ; *Gastrointestinal Microbiome/drug effects/physiology ; Hemocytes ; *Hemolymph/cytology ; Immunity, Innate ; Italy ; *Monophenol Monooxygenase/metabolism ; *Probiotics/administration & dosage ; }, abstract = {BACKGROUND: In this study, a probiotic mixture (Honeybeeotic) consisting of seven bacterial strains isolated from a unique population of honeybees (Apis mellifera ligustica) was used. That honeybee population was located in the Roti Abbey locality of the Marche Region in Italy, an area isolated from human activities, and genetic contamination from other honeybee populations. The aim was to investigate the effects of this probiotic mixture on the innate immunity and intestinal microbiome of healthy common honeybees in two hives of the same apiary. Hive A received a diet of 50% glucose syrup, while hive B received the same syrup supplemented with the probiotics, both administered daily for 1 month. To determine whether the probiotic altered the immune response, phenoloxidase activity and hemolymph cellular subtype count were investigated. Additionally, metagenomic approaches were used to analyze the effects on gut microbiota composition and function, considering the critical role the gut microbiota plays in modulating host physiology.

RESULTS: The results revealed differences in hemocyte populations between the two hives, as hive A exhibited higher counts of oenocytoids and granulocytes. These findings indicated that the dietary supplementation with the probiotic mixture was safe and well-tolerated. Furthermore, phenoloxidase activity significantly decreased in hive B (1.75 ± 0.19 U/mg) compared to hive A (3.62 ± 0.44 U/mg, p < 0.005), suggesting an improved state of well-being in the honeybees, as they did not require activation of immune defense mechanisms. Regarding the microbiome composition, the probiotic modulated the gut microbiota in hive B compared to the control, retaining core microbiota components while causing both positive and negative variations. Notably, several genes, particularly KEGG genes involved in amino acid metabolism, carbohydrate metabolism, and branched-chain amino acid (BCAA) transport, were more abundant in the probiotic-fed group, suggesting an effective nutritional supplement for the host.

CONCLUSIONS: This study advocated that feeding with this probiotic mixture induces beneficial immunological effects and promoted a balanced gut microbiota with enhanced metabolic activities related to digestion. The use of highly selected probiotics was shown to contribute to the overall well-being of the honeybees, improving their immune response and gut health.}, } @article {pmid39113058, year = {2024}, author = {Valdes, AM and Louca, P and Visconti, A and Asnicar, F and Bermingham, K and Nogal, A and Wong, K and Michelotti, GA and Wolf, J and Segata, N and Spector, TD and Berry, SE and Falchi, M and Menni, C}, title = {Vitamin A carotenoids, but not retinoids, mediate the impact of a healthy diet on gut microbial diversity.}, journal = {BMC medicine}, volume = {22}, number = {1}, pages = {321}, pmid = {39113058}, issn = {1741-7015}, support = {MR/M016560/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Vitamin A/blood ; *Carotenoids/blood/metabolism ; Female ; Middle Aged ; Male ; *Retinoids/metabolism ; Aged ; Diet ; Feces/microbiology ; Adult ; }, abstract = {BACKGROUND: Vitamin A is essential for physiological processes like vision and immunity. Vitamin A's effect on gut microbiome composition, which affects absorption and metabolism of other vitamins, is still unknown. Here we examined the relationship between gut metagenome composition and six vitamin A-related metabolites (two retinoid: -retinol, 4 oxoretinoic acid (oxoRA) and four carotenoid metabolites, including beta-cryptoxanthin and three carotene diols).

METHODS: We included 1053 individuals from the TwinsUK cohort with vitamin A-related metabolites measured in serum and faeces, diet history, and gut microbiome composition assessed by shotgun metagenome sequencing. Results were replicated in 327 women from the ZOE PREDICT-1 study.

RESULTS: Five vitamin A-related serum metabolites were positively correlated with microbiome alpha diversity (r = 0.15 to r = 0.20, p < 4 × 10[-6]). Carotenoid compounds were positively correlated with the short-chain fatty-acid-producing bacteria Faecalibacterium prausnitzii and Coprococcus eutactus. Retinol was not associated with any microbial species. We found that gut microbiome composition could predict circulating levels of carotenoids and oxoretinoic acid with AUCs ranging from 0.66 to 0.74 using random forest models, but not retinol (AUC = 0.52). The healthy eating index (HEI) was strongly associated with gut microbiome diversity and with all carotenoid compounds, but not retinoids. We investigated the mediating role of carotenoid compounds on the effect of a healthy diet (HEI) on gut microbiome diversity, finding that carotenoids significantly mediated between 18 and 25% of the effect of HEI on gut microbiome alpha diversity.

CONCLUSIONS: Our results show strong links between circulating carotene compounds and gut microbiome composition and potential links to a healthy diet pattern.}, } @article {pmid39111416, year = {2024}, author = {Wang, HY and Yu, ZG and Zhou, FW and Hernandez, JC and Grandjean, A and Biester, H and Xiao, KQ and Knorr, KH}, title = {Microbial communities and functions are structured by vertical geochemical zones in a northern peatland.}, journal = {The Science of the total environment}, volume = {950}, number = {}, pages = {175273}, doi = {10.1016/j.scitotenv.2024.175273}, pmid = {39111416}, issn = {1879-1026}, mesh = {*Microbiota ; China ; *Soil Microbiology ; *Methane/metabolism/analysis ; RNA, Ribosomal, 16S ; Soil/chemistry ; Wetlands ; Carbon/analysis ; Nitrogen/analysis ; Bacteria/classification ; Sulfur/metabolism/analysis ; Archaea/classification ; }, abstract = {Northern peatlands are important carbon pools; however, differences in the structure and function of microbiomes inhabiting contrasting geochemical zones within these peatlands have rarely been emphasized. Using 16S rRNA gene sequencing, metagenomic profiling, and detailed geochemical analyses, we investigated the taxonomic composition and genetic potential across various geochemical zones of a typical northern peatland profile in the Changbai Mountains region (Northeastern China). Specifically, we focused on elucidating the turnover of organic carbon, sulfur (S), nitrogen (N), and methane (CH4). Three geochemical zones were identified and characterized according to porewater and solid-phase analyses: the redox interface (<10 cm), shallow peat (10-100 cm), and deep peat (>100 cm). The redox interface and upper shallow peat demonstrated a high availability of labile carbon, which decreased toward deeper peat. In deep peat, anaerobic respiration and methanogenesis were likely constrained by thermodynamics, rather than solely driven by available carbon, as the acetate concentrations reached 90 μmol·L[-1]. Both the microbial community composition and metabolic potentials were significantly different (p < 0.05) among the redox interface, shallow peat, and deep peat. The redox interface demonstrated a close interaction between N, S, and CH4 cycling, mainly driven by Thermodesulfovibrionia, Bradyrhizobium, and Syntrophorhabdia metagenome-assembled genomes (MAGs). The archaeal Bathyarchaeia were indicated to play a significant role in the organic carbon, N, and S cycling in shallow peat. Although constrained by anaerobic respiration and methanogenesis, deep peat exhibited a higher metabolic potential for organic carbon degradation, primarily mediated by Acidobacteriota. In terms of CH4 turnover, subsurface peat (10-20 cm) was a CH4 production hotspot, with a net turnover rate of ∼2.9 nmol·cm[-3]·d[-1], while the acetoclastic, hydrogenotrophic, and methylotrophic methanogenic pathways all potentially contributed to CH4 production. The results of this study improve our understanding of biogeochemical cycles and CH4 turnover along peatland profiles.}, } @article {pmid39111271, year = {2024}, author = {Zhang, Y and Chen, W and Yuan, Y and Liao, X and Mi, J}, title = {Decreasing light exposure increases the abundance of antibiotic resistance genes in the cecum and feces of laying hens.}, journal = {The Science of the total environment}, volume = {949}, number = {}, pages = {175275}, doi = {10.1016/j.scitotenv.2024.175275}, pmid = {39111271}, issn = {1879-1026}, mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Feces/microbiology ; *Drug Resistance, Microbial/genetics ; Light ; Female ; Bacteria/genetics ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The gut microbiome plays a crucial role in maintaining animal health and is influenced by various factors, including light exposure; however, the response in laying hens of the gut microbiome to intermittent light regimes and the related impact on antibiotic resistance genes (ARGs) remain poorly understood. In this study, we divided 20-week-old laying hens into two groups. These groups were exposed to either continuous normal light or intermittent light for 8 weeks. The feces and cecal contents of laying hens were collected for analysis. Metagenomic analysis of both feces and cecal content samples revealed significant shifts in the microbial composition and abundance of ARGs under intermittent light exposure compared to normal light exposure (P < 0.05). Furthermore, metabolomic analysis of the cecal contents revealed substantial alterations in the abundance and composition of ARGs and mobile genetic elements (MGEs) in response to intermittent light exposure (P < 0.05). Network analysis revealed intricate co-occurrence patterns among bacterial communities, metabolites, and ARGs, highlighting correlations between Bacteroidetes species, ARGs, and metabolites. Although certain bacterial species showed differential associations, the dominant bacteria carrying ARGs or MGEs had relatively low numbers, suggesting that other bacterial communities may have had a greater influence on ARG dissemination. Moreover, our observations highlight the crucial role of metabolites as mediators between bacterial communities and ARGs, providing novel insights into the dynamics of antibiotic resistance development. Our findings underscore the impact of intermittent light exposure on ARG proliferation in poultry farming and emphasize interconnections among ARGs, bacterial communities, and metabolic pathways. The results underscore the importance of considering both microbial communities and metabolic processes to understand antibiotic resistance in agricultural settings.}, } @article {pmid39110709, year = {2024}, author = {Lee, YM and Choi, KM and Mun, SH and Yoo, JW and Jung, JH}, title = {Gut microbiota composition of the isopod Ligia in South Korea exposed to expanded polystyrene pollution.}, journal = {PloS one}, volume = {19}, number = {8}, pages = {e0308246}, pmid = {39110709}, issn = {1932-6203}, mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Republic of Korea ; Animals ; *Isopoda/microbiology ; Water Pollutants, Chemical/toxicity/adverse effects ; Metagenomics/methods ; }, abstract = {Plastics pose a considerable challenge to aquatic ecosystems because of their increasing global usage and non-biodegradable properties. Coastal plastic debris can persist in ecosystems; however, its effects on resident organisms remain unclear. A metagenomic analysis of the isopoda Ligia, collected from clean (Nae-do, ND) and plastic-contaminated sites (Maemul-do, MD) in South Korea, was conducted to clarify the effects of microplastic contamination on the gut microbiota. Ligia gut microbiota's total operational taxonomic units were higher in ND than in MD. Alpha diversity did not differ significantly between the two Ligia gut microbial communities collected from ND and MD, although richness (Observed species) was lower in MD than in ND. Proteobacteria (67.47%, ND; 57.30%, MD) and Bacteroidetes (13.63%, ND; 20.76%, MD) were the most abundant phyla found at both sites. Significant different genera in Ligia from EPS-polluted sites were observed. Functional gene analysis revealed that 19 plastic degradation-related genes, including those encoding hydrogenase, esterase, and carboxylesterase, were present in the gut microbes of Ligia from MD, indicating the potential role of the Ligia gut microbiota in plastic degradation. This study provides the first comparative field evidence of the gut microbiota dynamics of plastic detritus consumers in marine ecosystems.}, } @article {pmid39110597, year = {2024}, author = {Fu, Y and Yu, S and Li, J and Lao, Z and Yang, X and Lin, Z}, title = {DeepMineLys: Deep mining of phage lysins from human microbiome.}, journal = {Cell reports}, volume = {43}, number = {8}, pages = {114583}, doi = {10.1016/j.celrep.2024.114583}, pmid = {39110597}, issn = {2211-1247}, mesh = {Humans ; *Microbiota ; *Bacteriophages/genetics/metabolism ; Data Mining ; Viral Proteins/metabolism ; Neural Networks, Computer ; Animals ; Muramidase/metabolism ; Escherichia coli/genetics/metabolism ; }, abstract = {Vast shotgun metagenomics data remain an underutilized resource for novel enzymes. Artificial intelligence (AI) has increasingly been applied to protein mining, but its conventional performance evaluation is interpolative in nature, and these trained models often struggle to extrapolate effectively when challenged with unknown data. In this study, we present a framework (DeepMineLys [deep mining of phage lysins from human microbiome]) based on the convolutional neural network (CNN) to identify phage lysins from three human microbiome datasets. When validated with an independent dataset, our method achieved an F1-score of 84.00%, surpassing existing methods by 20.84%. We expressed 16 lysin candidates from the top 100 sequences in E. coli, confirming 11 as active. The best one displayed an activity 6.2-fold that of lysozyme derived from hen egg white, establishing it as the most potent lysin from the human microbiome. Our study also underscores several important issues when applying AI to biology questions. This framework should be applicable for mining other proteins.}, } @article {pmid39109810, year = {2024}, author = {Tomar, SS and Khairnar, K}, title = {Detection of lumpy skin disease virus reads in the human upper respiratory tract microbiome requires further investigation.}, journal = {Journal of medical virology}, volume = {96}, number = {8}, pages = {e29829}, doi = {10.1002/jmv.29829}, pmid = {39109810}, issn = {1096-9071}, support = {//National Environmental Engineering Research Institute/ ; //Council of Scientific and Industrial Research, India/ ; //CSIR-NEERI/ ; }, mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; *Lumpy skin disease virus/isolation & purification/genetics/classification ; Oropharynx/virology/microbiology ; Animals ; India ; Genome, Viral/genetics ; Nasopharynx/virology/microbiology ; Respiratory System/microbiology/virology ; Male ; Whole Genome Sequencing ; SARS-CoV-2/genetics/isolation & purification/classification ; Female ; Adult ; COVID-19/diagnosis/virology ; Lumpy Skin Disease/virology ; }, abstract = {Lumpy skin disease virus (LSDV), a double-stranded DNA virus from the Capripoxvirus genus, primarily affects Bos indicus, Bos taurus breeds, and water buffalo. Arthropod vectors, including mosquitoes and biting flies, are the main LSDV transmitters. Although LSDV is not zoonotic, this study unexpectedly detected LSDV reads in the upper respiratory tract microbiome of humans from rural and urban areas in Maharashtra, India. Nasopharyngeal and oropharyngeal swab samples collected for SARS-CoV-2 surveillance underwent whole-genome metagenomics sequencing, revealing LSDV reads in 25% of samples. Split kmer analysis provided insights into sample relatedness despite the low coverage of LSDV reads with the reference genome. Our findings, which include the detection of LSDV contigs aligning to specific locations on the reference genome, suggest a common source for LSDV reads, potentially shared water sources, or milk/milk products. Further investigation is needed to ascertain the mode of transmission and reason for the detection of LSDV reads in human upper respiratory tract.}, } @article {pmid39104524, year = {2024}, author = {Han, L and Liu, X and Lan, Y and Hua, Y and Fan, Z and Li, Y}, title = {Metagenomic analysis demonstrates distinct changes in the gut microbiome of Kawasaki diseases children.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1416185}, pmid = {39104524}, issn = {1664-3224}, mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/microbiology/immunology ; *Gastrointestinal Microbiome/genetics ; Male ; *Metagenomics/methods ; Female ; Child, Preschool ; Infant ; *Feces/microbiology ; Immunoglobulins, Intravenous/therapeutic use ; Metagenome ; Child ; Bacteria/classification/genetics/isolation & purification ; Case-Control Studies ; }, abstract = {BACKGROUND: Kawasaki disease (KD) has been considered as the most common required pediatric cardiovascular diseases among the world. However, the molecular mechanisms of KD were not fully underlined, leading to a confused situation in disease management and providing precious prognosis prediction. The disorders of gut microbiome had been identified among several cardiovascular diseases and inflammation conditions. Therefore, it is urgent to elucidate the characteristics of gut microbiome in KD and demonstrate its potential role in regulating intravenous immunoglobulin (IVIG) resistance and coronary artery injuries.

METHODS: A total of 96 KD children and 62 controls were enrolled in the study. One hundred forty fecal samples had been harvested from KD patients, including individuals before or after IVIG treatment, with or without early coronary artery lesions and IVIG resistance. Fecal samples had been collected before and after IVIG administration and stored at -80°C. Then, metagenomic analysis had been done using Illumina NovaSeq 6000 platform. After that, the different strains and functional differences among comparisons were identified.

RESULTS: First, significant changes had been observed between KD and their controls. We found that the decrease of Akkermansia muciniphila, Faecalibacterium prausnitzii, Bacteroides uniformis, and Bacteroides ovatus and the increase of pathogenic bacteria Finegoldia magna, Abiotrophia defectiva, and Anaerococcus prevotii perhaps closely related to the incidence of KD. Then, metagenomic and responding functional analysis demonstrated that short-chain fatty acid pathways and related strains were associated with different outcomes of therapeutic efficacies. Among them, the reduction of Bacteroides thetaiotaomicron, the enrichment of Enterococcus faecalis and antibiotic resistance genes had been found to be involved in IVIG resistance of KD. Moreover, our data also revealed several potential pathogenetic microbiome of that KD patients with coronary artery lesions.

CONCLUSION: These results strongly proved that distinct changes in the gut microbiome of KD and the dysfunction of gut microbiomes should be responsible for the pathogenesis of KD and significantly impact the prognosis of KD.}, } @article {pmid39103543, year = {2024}, author = {Li, HZ and Peng, J and Yang, K and Zhang, Y and Chen, QL and Zhu, YG and Cui, L}, title = {Single-cell exploration of active phosphate-solubilizing bacteria across diverse soil matrices for sustainable phosphorus management.}, journal = {Nature food}, volume = {5}, number = {8}, pages = {673-683}, pmid = {39103543}, issn = {2662-1355}, support = {42021005//National Natural Science Foundation of China (National Science Foundation of China)/ ; 22241603//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Soil Microbiology ; *Phosphorus/metabolism ; *Bacteria/metabolism/genetics ; *Phosphates/metabolism ; *Soil/chemistry ; *Fertilizers/analysis ; Single-Cell Analysis ; Microbiota/physiology ; Solubility ; }, abstract = {Phosphate-solubilizing bacteria (PSB) are crucial for enhancing phosphorus bioavailability and regulating phosphorus transformation processes. However, the in situ phosphorus-solubilizing activity and the link between phenotypes and genotypes for PSB remain unidentified. Here we employed single-cell Raman spectroscopy combined with heavy water to discern and quantify soil active PSB. Our results reveal that PSB abundance and in situ activity differed significantly between soil types and fertilization treatments. Inorganic fertilizer input was the key driver for active PSB distribution. Targeted single-cell sorting and metagenomic sequencing of active PSB uncovered several low-abundance genera that are easily overlooked within bulk soil microbiota. We elucidate the underlying functional genes and metabolic pathway, and the interplay between phosphorus and carbon cycling involved in high phosphorus solubilization activity. Our study provides a single-cell approach to exploring PSB from native environments, enabling the development of a microbial solution for the efficient agronomic use of phosphorus and mitigating the phosphorus crisis.}, } @article {pmid39103408, year = {2024}, author = {Atencio, B and Geisler, E and Rubin-Blum, M and Bar-Zeev, E and Adar, EM and Ram, R and Ronen, Z}, title = {Metabolic adaptations underpin high productivity rates in relict subsurface water.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {18126}, pmid = {39103408}, issn = {2045-2322}, support = {1068/20//Israel Science Foundation/ ; 1068/20//Israel Science Foundation/ ; 1359/23//Israel Science Foundation/ ; 1068/20//Israel Science Foundation/ ; 1068/20//Israel Science Foundation/ ; 1068/20//Israel Science Foundation/ ; 1068/20//Israel Science Foundation/ ; 221-17-002//Ministry of Energy, Israel/ ; }, mesh = {*Groundwater/microbiology ; Israel ; Bacteria/metabolism/genetics/classification ; Adaptation, Physiological ; Water Microbiology ; Microbiota ; }, abstract = {Groundwater aquifers are ecological hotspots with diverse microbes essential for biogeochemical cycles. Their ecophysiology has seldom been studied on a basin scale. In particular, our knowledge of chemosynthesis in the deep aquifers where temperatures reach 60 °C, is limited. Here, we investigated the diversity, activity, and metabolic potential of microbial communities from nine wells reaching ancient groundwater beneath Israel's Negev Desert, spanning two significant, deep (up to 1.5 km) aquifers, the Judea Group carbonate and Kurnub Group Nubian sandstone that contain fresh to brackish, hypoxic to anoxic water. We estimated chemosynthetic productivity rates ranging from 0.55 ± 0.06 to 0.82 ± 0.07 µg C L[-1] d[-1] (mean ± SD), suggesting that aquifer productivity may be underestimated. We showed that 60% of MAGs harbored genes for autotrophic pathways, mainly the Calvin-Benson-Bassham cycle and the Wood-Ljungdahl pathway, indicating a substantial chemosynthetic capacity within these microbial communities. We emphasize the potential metabolic versatility in the deep subsurface, enabling efficient carbon and energy use. This study set a precedent for global aquifer exploration, like the Nubian Sandstone Aquifer System in the Arabian and Western Deserts, and reconsiders their role as carbon sinks.}, } @article {pmid39102225, year = {2024}, author = {Van Rossum, T and Haiß, A and Knoll, RL and Marißen, J and Podlesny, D and Pagel, J and Bleskina, M and Vens, M and Fortmann, I and Siller, B and Ricklefs, I and Klopp, J and Hilbert, K and Meyer, C and Thielemann, R and Goedicke-Fritz, S and Kuntz, M and Wieg, C and Teig, N and Körner, T and Kribs, A and Hudalla, H and Knuf, M and Stein, A and Gille, C and Bagci, S and Dohle, F and Proquitté, H and Olbertz, DM and Schmidt, E and Koch, L and Pirr, S and Rupp, J and Spiegler, J and Kopp, MV and Göpel, W and Herting, E and Forslund, SK and Viemann, D and Zemlin, M and Bork, P and Gehring, S and König, IR and Henneke, P and Härtel, C}, title = {Bifidobacterium and Lactobacillus Probiotics and Gut Dysbiosis in Preterm Infants: The PRIMAL Randomized Clinical Trial.}, journal = {JAMA pediatrics}, volume = {178}, number = {10}, pages = {985-995}, doi = {10.1001/jamapediatrics.2024.2626}, pmid = {39102225}, issn = {2168-6211}, mesh = {Humans ; *Probiotics/therapeutic use ; Infant, Newborn ; *Infant, Premature ; *Dysbiosis/prevention & control ; Double-Blind Method ; Male ; Female ; *Gastrointestinal Microbiome ; Bifidobacterium ; Lactobacillus ; Infant, Premature, Diseases/prevention & control/microbiology ; }, abstract = {IMPORTANCE: The effects of probiotic interventions on colonization with resistant bacteria and early microbiome development in preterm infants remain to be clarified.

OBJECTIVE: To examine the efficacy of Bifidobacterium longum subsp infantis, Bifidobacterium animalis subsp lactis (BB-12), and Lactobacillus acidophilus (La-5) probiotics to prevent colonization with multidrug-resistant organisms or highly epidemic bacteria (MDRO+) and to shape the microbiome of preterm infants toward the eubiotic state of healthy full-term infants.

The multicenter, double-blinded, placebo-controlled, group sequential, phase 3 Priming Immunity at the Beginning of Life (PRIMAL) randomized clinical trial, conducted from April 2018 to June 2020, included infants with gestational age of 28 to 32 weeks at 18 German neonatal units. Data analyses were conducted from March 2020 to August 2023.

INTERVENTION: A total of 28 days of multistrain probiotics diluted in human milk/formula starting within the first 72 hours of life.

MAIN OUTCOMES AND MEASURES: Colonization with MDRO+ at day 30 of life (primary end point), late-onset sepsis and severe gastrointestinal complication (safety end points), and gut dysbiosis, ie, deviations from the microbiome of healthy, term infants (eubiosis score) based on 16-subunit ribosomal RNA and metagenomic sequencing.

RESULTS: Among the 643 infants randomized until the stop of recruitment based on interim results, 618 (median [IQR] gestational age, 31.0 [29.7-32.1] weeks; 333 male [53.9%]; mean [SD] birth weight, 1502 [369] g) had follow-up at day 30. The interim analysis with all available data from 219 infants revealed MDRO+ colonization in 43 of 115 infants (37.4%) in the probiotics group and in 39 of 104 infants (37.5%) in the control group (adjusted risk ratio, 0.99; 95% CI, 0.54-1.81; P = .97). Safety outcomes were similar in both groups, ie, late-onset sepsis (probiotics group: 8 of 316 infants [2.5%]; control group: 12 of 322 infants [3.7%]) and severe gastrointestinal complications (probiotics group: 6 of 316 infants [1.9%]; control group: 7 of 322 infants [2.2%]). The probiotics group had higher eubiosis scores than the control group at the genus level (254 vs 258 infants; median scores, 0.47 vs 0.41; odds ratio [OR], 1.07; 95% CI, 1.02-1.13) and species level (96 vs 83 infants; median scores, 0.87 vs 0.59; OR, 1.28; 95% CI, 1.19-1.38). Environmental uptake of the B infantis probiotic strain in the control group was common (41 of 84 [49%]), which was highly variable across sites and particularly occurred in infants with a sibling who was treated with probiotics.

CONCLUSIONS AND RELEVANCE: Multistrain probiotics did not reduce the incidence of MDRO+ colonization at day 30 of life in preterm infants but modulated their microbiome toward eubiosis.

TRIAL REGISTRATION: German Clinical Trials Register: DRKS00013197.}, } @article {pmid39101654, year = {2024}, author = {Wang, XX and Liu, YT and Ren, JG and Liu, HM and Fu, Q and Yang, Y and Fu, QY and Chen, G}, title = {Salivary Microbiome Relates to Neoadjuvant Immunotherapy Response in OSCC.}, journal = {Journal of dental research}, volume = {103}, number = {10}, pages = {988-998}, doi = {10.1177/00220345241262759}, pmid = {39101654}, issn = {1544-0591}, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; *Carcinoma, Squamous Cell/therapy/immunology/microbiology ; *Immunotherapy/methods ; *Microbiota ; *Mouth Neoplasms/therapy/microbiology/immunology ; *Neoadjuvant Therapy ; *Saliva/microbiology/immunology ; Treatment Outcome ; }, abstract = {Most patients diagnosed with oral squamous cell carcinoma (OSCC) present with locally advanced stages, which are typically associated with poor outcomes. Although immunotherapy offers potential improvements in patient survival, its efficacy is hampered by low response rates. The microbiome is widely involved in tumor immunity and may play a role in immunotherapy. This study aimed to investigate the potential association between the oral (salivary) microbiome and immunotherapy response in patients with OSCC. Salivary metagenome sequencing was performed on 47 patients with OSCC undergoing neoadjuvant immunotherapy (NAIT) in a clinical trial (NCT04649476). Patients were divided into responders and nonresponders based on their pathological responses. The results showed that the species richness of the salivary microbiome was lower in the nonresponders before NAIT than in the responders. Differential analysis revealed that nonresponders exhibited a lower relative abundance of 34 bacterial species and a higher relative abundance of 4 bacterial species. Notably, low levels of Eubacterium infirmum, Actinobaculum, and Selenomas (EAS) in the saliva may be associated with the nonresponse of patients with OSCC to NAIT. A nomogram based on EAS was developed and validated to determine the efficacy of NAIT. The area under the curve for the training cohort was 0.81 (95% confidence interval, 0.66 to 0.81). Quantitative polymerase chain reaction confirmed that low levels of salivary EAS effectively identified nonresponders to NAIT. Furthermore, the low abundance of salivary EAS was closely correlated with a low density of intratumoral CD4[+], CD14[+], CD68[+], and FOXP3[+] cells. Metabolic functional annotation revealed numerous biosynthetic processes associated with EAS that were more active in responders. In summary, this study provides valuable data resources for the salivary microbiome and reveals that nonresponders have different salivary microbiome profiles than responders do before NAIT. Low salivary EAS levels can serve as potential biomarkers for distinguishing nonresponders from responders.}, } @article {pmid39099658, year = {2024}, author = {Talbot, BM and Clennon, JA and Rakotoarison, MFN and Rautman, L and Durry, S and Ragazzo, LJ and Wright, PC and Gillespie, TR and Read, TD}, title = {Metagenome-wide characterization of shared antimicrobial resistance genes in sympatric people and lemurs in rural Madagascar.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17805}, pmid = {39099658}, issn = {2167-8359}, mesh = {Animals ; Madagascar ; Humans ; *Metagenome/genetics ; *Gastrointestinal Microbiome/genetics ; Sympatry ; Rural Population ; Metagenomics ; Bacteria/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Cheirogaleidae/genetics/microbiology ; }, abstract = {BACKGROUND: Tracking the spread of antibiotic resistant bacteria is critical to reduce global morbidity and mortality associated with human and animal infections. There is a need to understand the role that wild animals in maintenance and transfer of antibiotic resistance genes (ARGs).

METHODS: This study used metagenomics to identify and compare the abundance of bacterial species and ARGs detected in the gut microbiomes from sympatric humans and wild mouse lemurs in a forest-dominated, roadless region of Madagascar near Ranomafana National Park. We examined the contribution of human geographic location toward differences in ARG abundance and compared the genomic similarity of ARGs between host source microbiomes.

RESULTS: Alpha and beta diversity of species and ARGs between host sources were distinct but maintained a similar number of detectable ARG alleles. Humans were differentially more abundant for four distinct tetracycline resistance-associated genes compared to lemurs. There was no significant difference in human ARG diversity from different locations. Human and lemur microbiomes shared 14 distinct ARGs with highly conserved in nucleotide identity. Synteny of ARG-associated assemblies revealed a distinct multidrug-resistant gene cassette carrying dfrA1 and aadA1 present in human and lemur microbiomes without evidence of geographic overlap, suggesting that these resistance genes could be widespread in this ecosystem. Further investigation into intermediary processes that maintain drug-resistant bacteria in wildlife settings is needed.}, } @article {pmid39098620, year = {2024}, author = {Padasas-Adalla, CS and Ortega-Kindica, RCMH and Lomelí-Ortega, CO and Tabugo, SRM and Balcázar, JL}, title = {A metagenomics-based approach to decipher the resistome and mobilome of two seahorse species, Hippocampus barbouri and Hippocampus comes.}, journal = {International journal of antimicrobial agents}, volume = {64}, number = {3}, pages = {107296}, doi = {10.1016/j.ijantimicag.2024.107296}, pmid = {39098620}, issn = {1872-7913}, mesh = {Animals ; *Smegmamorpha/microbiology ; *Metagenomics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects/classification ; Skin/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Microbiota/genetics/drug effects ; Interspersed Repetitive Sequences/genetics ; }, abstract = {OBJECTIVE: This study aimed to explore the abundance and diversity of antibiotic resistance genes (ARGs) in seahorses (Hippocampus barbouri and Hippocampus comes) and their surrounding environment.

METHODS: A combination of shotgun metagenomics and bioinformatics was used to investigate the resistome of both seahorse species.

RESULTS: The analyses demonstrated a higher abundance of ARGs in seahorse-associated microbiomes, particularly in skin and gut samples, compared to those from water and sediment. Interestingly, genes conferring multidrug resistance (e.g., acrB, acrF, cpxA, msbA, and oqxB) were highly prevalent in all samples, especially in skin and gut samples. High levels of genes conferring resistance to fluoroquinolones (e.g., mfd and emrB), β-lactam (e.g., blaCMY-71, blaOXA-55, and penA), aminocoumarin (e.g., mdtB and mdtC), and peptide antibiotics (arnA, pmrE, and rosA) were also observed in skin and gut samples. An enrichment of mobile genetic elements (MGEs) was also observed in the analysed samples, highlighting their potential role in facilitating the acquisition and spread of ARGs. In fact, the abundance of mobilisation (MOB) relaxases (e.g., MOBF, MOBP, MOBT, and MOBV) in gut and skin samples suggests a high potential for conjugation events.

CONCLUSIONS: The occurrence of ARGs and MGEs in seahorses and the surrounding environment raises concerns about their transmission to humans, either through direct contact or the consumption of contaminated seafood. To the best of our knowledge, this study represents the first comprehensive analysis of ARGs in seahorse-associated microbiomes, and its results emphasise the need for monitoring and controlling the spread of ARGs in environmental settings.}, } @article {pmid39098060, year = {2024}, author = {Cojkic, A and Niazi, A and Morrell, JM}, title = {Metagenomic identification of bull semen microbiota in different seasons.}, journal = {Animal reproduction science}, volume = {268}, number = {}, pages = {107569}, doi = {10.1016/j.anireprosci.2024.107569}, pmid = {39098060}, issn = {1873-2232}, mesh = {Male ; Animals ; *Seasons ; Cattle ; *Semen/microbiology ; *Microbiota ; *Semen Analysis/veterinary ; Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; Spermatozoa/microbiology ; RNA, Ribosomal, 16S/genetics/analysis ; }, abstract = {A seasonal effect on sperm quality parameters was observed previously. Although identification of the bull semen microbiota by 16S rRNA sequencing was performed previously, it has not been carried out in commercial semen samples from different seasons, and its connection with sperm quality parameters has not been evaluated yet. The objectives in this study were; (i) to evaluate diversity of bull semen microbiota and sperm quality parameters in different seasons, and (ii) to find if specific bacteria were associated with seasonal differences in specific sperm quality parameters. Bull semen microbiota was identified in 54 commercial bull semen samples from 3 seasons (winter, spring, summer). Sperm quality was analysed by Computer Assisted Sperm Analyses (CASA) and Flow Cytometry (FC). From 28 phyla in all samples, six phyla were identified in samples from all seasons, with observed seasonal differences in their distribution. At genus level, 388 genera were identified, of which 22 genera had a relative abundance over 1 % and showed seasonal differences in bacterial diversity, and 9 bacteria genera were present in all seasons. Differences between spring and summer (P < 0.05) were observed for live hydrogen peroxide positive sperm cells. A trend towards significance (0.10 > P > 0.05) was observed for some CASA kinematics (VCL and LIN) and FC parameters (High respiratory activity, and live hydrogen peroxide positive sperm cells) between seasons. Nevertheless, associations between sperm quality parameters and specific bacteria were observed in spring.}, } @article {pmid39096906, year = {2024}, author = {Giolai, M and Verweij, W and Martin, S and Pearson, N and Nicholson, P and Leggett, RM and Clark, MD}, title = {Measuring air metagenomic diversity in an agricultural ecosystem.}, journal = {Current biology : CB}, volume = {34}, number = {16}, pages = {3778-3791.e4}, doi = {10.1016/j.cub.2024.07.030}, pmid = {39096906}, issn = {1879-0445}, mesh = {*Biodiversity ; *Agriculture ; *Metagenomics/methods ; DNA, Environmental/analysis/genetics ; Air Microbiology ; Ecosystem ; Environmental Monitoring/methods ; Metagenome ; Crops, Agricultural/microbiology ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {All species shed DNA during life or in death, providing an opportunity to monitor biodiversity via environmental DNA (eDNA). In recent years, combining eDNA, high-throughput sequencing technologies, bioinformatics, and increasingly complete sequence databases has promised a non-invasive and non-destructive environmental monitoring tool. Modern agricultural systems are often large monocultures and so are highly vulnerable to disease outbreaks. Pest and pathogen monitoring in agricultural ecosystems is key for efficient and early disease prevention, lower pesticide use, and better food security. Although the air is rich in biodiversity, it has the lowest DNA concentration of all environmental media and yet is the route for windborne spread of many damaging crop pathogens. Our work suggests that ecosystems can be monitored efficiently using airborne nucleic acid information. Here, we show that the airborne DNA of microbes can be recovered, shotgun sequenced, and taxonomically classified, including down to the species level. We show that by monitoring a field growing key crops we can identify the presence of agriculturally significant pathogens and quantify their changing abundance over a period of 1.5 months, often correlating with weather variables. We add to the evidence that aerial eDNA can be used as a source for biomonitoring in terrestrial ecosystems, specifically highlighting agriculturally relevant species and how pathogen levels correlate with weather conditions. Our ability to detect dynamically changing levels of species and strains highlights the value of airborne eDNA in agriculture, monitoring biodiversity changes, and tracking taxa of interest.}, } @article {pmid39096506, year = {2024}, author = {Oggerin, M and Viver, T and Brüwer, J and Voß, D and García-Llorca, M and Zielinski, O and Orellana, LH and Fuchs, BM}, title = {Niche differentiation within bacterial key-taxa in stratified surface waters of the Southern Pacific Gyre.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39096506}, issn = {1751-7370}, support = {//Max Planck Society/ ; SO-245//UltraPac Expedition/ ; 03G0245A//Federal Ministry of Education and Research of Germany/ ; }, mesh = {*Seawater/microbiology ; Pacific Ocean ; Alphaproteobacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics ; In Situ Hybridization, Fluorescence ; Ecosystem ; Phylogeny ; Microbiota ; }, abstract = {One of the most hostile marine habitats on Earth is the surface of the South Pacific Gyre (SPG), characterized by high solar radiation, extreme nutrient depletion, and low productivity. During the SO-245 "UltraPac" cruise through the center of the ultra-oligotrophic SPG, the marine alphaproteobacterial group AEGEAN169 was detected by fluorescence in situ hybridization at relative abundances up to 6% of the total microbial community in the uppermost water layer, with two distinct populations (Candidatus Nemonibacter and Ca. Indicimonas). The high frequency of dividing cells combined with high transcript levels suggests that both clades may be highly metabolically active. Comparative metagenomic and metatranscriptomic analyses of AEGEAN169 revealed that they encoded subtle but distinct metabolic adaptions to this extreme environment in comparison to their competitors SAR11, SAR86, SAR116, and Prochlorococcus. Both AEGEAN169 clades had the highest percentage of transporters per predicted proteins (9.5% and 10.6%, respectively). In particular, the high expression of ABC transporters in combination with proteorhodopsins and the catabolic pathways detected suggest a potential scavenging lifestyle for both AEGEAN169 clades. Although both AEGEAN169 clades may share the genomic potential to utilize phosphonates as a phosphorus source, they differ in their metabolic pathways for carbon and nitrogen. Ca. Nemonibacter potentially use glycine-betaine, whereas Ca. Indicimonas may catabolize urea, creatine, and fucose. In conclusion, the different potential metabolic strategies of both clades suggest that both are well adapted to thrive resource-limited conditions and compete well with other dominant microbial clades in the uppermost layers of SPG surface waters.}, } @article {pmid39095404, year = {2024}, author = {De Filippis, F and Valentino, V and Yap, M and Cabrera-Rubio, R and Barcenilla, C and Carlino, N and Cobo-Díaz, JF and Quijada, NM and Calvete-Torre, I and Ruas-Madiedo, P and Sabater, C and Sequino, G and Pasolli, E and Wagner, M and Margolles, A and Segata, N and Álvarez-Ordóñez, A and Cotter, PD and Ercolini, D}, title = {Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {67}, pmid = {39095404}, issn = {2055-5008}, support = {818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {*Probiotics ; *Cheese/microbiology ; Metagenome ; Food Microbiology ; Microbiota ; Humans ; Dairying/methods ; Europe ; Metagenomics/methods ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {The resident microbiome in food industries may impact on food quality and safety. In particular, microbes residing on surfaces in dairy industries may actively participate in cheese fermentation and ripening and contribute to the typical flavor and texture. In this work, we carried out an extensive microbiome mapping in 73 cheese-making industries producing different types of cheeses (fresh, medium and long ripened) and located in 4 European countries. We sequenced and analyzed metagenomes from cheese samples, raw materials and environmental swabs collected from both food contact and non-food contact surfaces, as well as operators' hands and aprons. Dairy plants were shown to harbor a very complex microbiome, characterized by high prevalence of genes potentially involved in flavor development, probiotic activities, and resistance to gastro-intestinal transit, suggesting that these microbes may potentially be transferred to the human gut microbiome. More than 6100 high-quality Metagenome Assembled Genomes (MAGs) were reconstructed, including MAGs from several Lactic Acid Bacteria species and putative new species. Although microbial pathogens were not prevalent, we found several MAGs harboring genes related to antibiotic resistance, highlighting that dairy industry surfaces represent a potential hotspot for antimicrobial resistance (AR) spreading along the food chain. Finally, we identified facility-specific strains that can represent clear microbial signatures of different cheesemaking facilities, suggesting an interesting potential of microbiome tracking for the traceability of cheese origin.}, } @article {pmid39094895, year = {2024}, author = {Shi, Z and Zhang, C and Sun, M and Usman, M and Cui, Y and Zhang, S and Ni, B and Luo, G}, title = {Syntrophic propionate degradation in anaerobic digestion facilitated by hydrochar: Microbial insights as revealed by genome-centric metatranscriptomics.}, journal = {Environmental research}, volume = {261}, number = {}, pages = {119717}, doi = {10.1016/j.envres.2024.119717}, pmid = {39094895}, issn = {1096-0953}, mesh = {*Propionates/metabolism ; Anaerobiosis ; *Methane/metabolism ; Transcriptome ; Bacteria/metabolism/genetics ; Microbiota ; }, abstract = {Propionate is a model substrate for studying energy-limited syntrophic communities in anaerobic digestion, and syntrophic bacteria usually catalyze its degradation in syntrophy with methanogens. In the present study, metagenomics and metatranscriptomics were used to study the effect of the supportive material (e.g., hydrochar) on the key members of propionate degradation and their cooperation mechanism. The results showed that hydrochar increased the methane production rate (up to 57.1%) from propionate. The general transcriptional behavior of the microbiome showed that both interspecies H2 transfer (IHT) and direct interspecies electron transfer (DIET) played essential roles in the hydrochar-mediated methanation of propionate. Five highly active syntrophic propionate-oxidizing bacteria were identified by genome-centric metatranscriptomics. H85pel, a member of the family Pelotomaculaceae, was specifically enriched by hydrochar. Hydrochar enhanced the expression of the flagellum subunit, which interacted with methanogens and hydrogenases in H85pel, indicating that IHT was one of the essential factors promoting propionate degradation. Hydrochar also enriched H162tha belonging to the genus of Thauera. Hydrochar induced the expression of genes related to the complete propionate oxidation pathway, which did not produce acetate. Hydrochar and e-pili-mediated DIET were enhanced, which was another factor promoting propionate degradation. These findings improved the understanding of metabolic traits and cooperation between syntrophic propionate oxidizing bacteria (SPOB) and co-metabolizing partners and provided comprehensive transcriptional insights on function in propionate methanogenic systems.}, } @article {pmid39094704, year = {2024}, author = {Dang, S and Fan, W and Meng, F and Li, X and Hao, J and Wang, C}, title = {Decolorization and detoxification of direct blue 5B by a Marinobacter-dominated halo-thermoalkalophilic consortium.}, journal = {Chemosphere}, volume = {363}, number = {}, pages = {142957}, doi = {10.1016/j.chemosphere.2024.142957}, pmid = {39094704}, issn = {1879-1298}, mesh = {*Marinobacter/metabolism/genetics ; *Biodegradation, Environmental ; Azo Compounds/metabolism/chemistry ; Coloring Agents/metabolism/chemistry ; Microbial Consortia ; Salinity ; Sewage/microbiology ; Hydrogen-Ion Concentration ; Temperature ; Water Pollutants, Chemical/metabolism/analysis ; Oryza ; }, abstract = {Azo dye-containing sewage is commonly detected at high salinity, temperature and pH. In this study, a halo-thermoalkalophilic azo dye decolorization consortium was enriched and named "consortium HL". Consortium HL which was dominated by Marinobacter (84.30%), Desulfocurvibacter (1.89%), and Pseudomonas (1.85%), was able to completely decolorize Direct Blue 5B (DB5) during incubation with the material at 5% salinity, 50 °C, and pH 9 for 30 h. The decolorization mechanism was proposed based on combined metagenomic analysis, GC‒MS, and enzymatic activity detection. The action of the consortium HL showed great tolerance to variations in salinity, temperature and pH. A phytotoxicity study indicated that the metabolic intermediates showed no significant toxicity to the generation of Cucumis sativus and Oryza sativa seeds. This study, in which azo dye decolorization and degradation under high-salt, high-temperature and high-alkalinity conditions were investigated and deeply analyzed by metagenomic information, is the first report regarding the ability of Marinobacter to decolorize azo dyes at high temperatures.}, } @article {pmid39094546, year = {2024}, author = {Li, Q and Wang, J and Lv, J and Liu, D and Xiao, S and Mo, J and Lu, Z and Qiu, R and Li, C and Tang, L and He, S and Tang, Z and Cheng, Q and Zhan, T}, title = {Total flavonoids of litchi Seed alleviates schistosomiasis liver fibrosis in mice by suppressing hepatic stellate cells activation and modulating the gut microbiomes.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {178}, number = {}, pages = {117240}, doi = {10.1016/j.biopha.2024.117240}, pmid = {39094546}, issn = {1950-6007}, mesh = {Animals ; *Hepatic Stellate Cells/drug effects/metabolism/pathology ; *Liver Cirrhosis/drug therapy/parasitology/pathology ; *Gastrointestinal Microbiome/drug effects ; *Flavonoids/pharmacology ; Mice ; *Litchi/chemistry ; *Seeds/chemistry ; Schistosomiasis japonica/drug therapy/complications ; Cytokines/metabolism ; Schistosoma japonicum/drug effects/pathogenicity ; Male ; Liver/drug effects/pathology/parasitology ; }, abstract = {Infection with Schistosoma japonicum (S. japonicum) is an important zoonotic parasitic disease that causes liver fibrosis in both human and domestic animals. The activation of hepatic stellate cells (HSCs) is a crucial phase in the development of liver fibrosis, and inhibiting their activation can alleviate this progression. Total flavonoids of litchi seed (TFL) is a naturally extracted drug, and modern pharmacological studies have shown its anti-fibrotic and liver-protective effects. However, the role of TFL in schistosomiasis liver fibrosis is still unclear. This study investigated the therapeutic effects of TFL on liver fibrosis in S. japonicum infected mice and explored its potential mechanisms. Animal study results showed that TFL significantly reduced the levels of Interleukin-1β (IL-1β), Tumor Necrosis Factor-α (TNF-α), Interleukin-4 (IL-4), and Interleukin-6 (IL-6) in the serum of S. japonicum infected mice. TFL reduced the spleen index of mice and markedly improved the pathological changes in liver tissues induced by S. japonicum infection, decreasing the expression of alpha-smooth muscle actin (α-SMA), Collagen I and Collagen III protein in liver tissues. In vitro studies indicated that TFL also inhibited the activation of HCSs induced by Transforming Growth Factor-β1 (TGF-β1) and reduced the levels of α-SMA. Gut microbes metagenomics study revealed that the composition, abundance, and functions of the mice gut microbiomes changed significantly after S. japonicum infection, and TLF treatment reversed these changes. Therefore, our study indicated that TFL alleviated granulomatous lesions and improved S. japonicum induced liver fibrosis in mice by inhibiting the activation of HSCs and by improving the gut microbiomes.}, } @article {pmid39094393, year = {2024}, author = {Turco, S and Brugneti, F and Giubilei, I and Silvestri, C and Petrović, M and Drais, MI and Cristofori, V and Speranza, S and Mazzaglia, A and Contarini, M and Rossini, L}, title = {A bud's life: Metabarcoding analysis to characterise hazelnut big buds microbiome biodiversity.}, journal = {Microbiological research}, volume = {287}, number = {}, pages = {127851}, doi = {10.1016/j.micres.2024.127851}, pmid = {39094393}, issn = {1618-0623}, mesh = {*Corylus/microbiology ; *Microbiota ; Animals ; *DNA Barcoding, Taxonomic ; *Biodiversity ; *Bacteria/classification/genetics/isolation & purification ; Fungi/classification/genetics/isolation & purification ; Mites/microbiology ; Plant Tumors/microbiology ; Fusarium/genetics/classification/isolation & purification ; }, abstract = {Despite Corylus avellana L. being an economically important shrub species known for its resilience to adverse environmental conditions, it constantly faces attacks from a plethora of biotic entities. Among these, the mite pest Phytoptus avellanae is gaining importance, causing economic losses every year. This mite colonises the new generative and vegetative buds, leading them to become swollen and reddish, and drastically reducing hazelnut production. The biology behind gall formation is still poorly understood. This study provides a qualitative and quantitative description of the microbiome in both healthy and infested buds of two economically important hazelnut cultivars through metabarcoding of fungal ITS and bacterial 16 S. Potentially pathogenic genera such as Fusarium and Pseudomonas were predominant in the infested buds, along with the obligate intracellular bacterial genus Wolbachia. Akanthomyces muscarius was instead isolated from culture-based methods only from the infested buds. These findings could improve the understanding of gall ecology, supporting the management of mite populations, and they could also serve as a milestone for further studies on low-impact, monitoring-driven, and genetically targeted control strategies.}, } @article {pmid39094311, year = {2024}, author = {Wang, X and Qian, Y and Wang, Y and Wang, S and Bi, J and Shi, C and Han, Q and Wan-Yan, R and Yu, Q and Li, H}, title = {Metagenomics reveals the potential transmission risk of resistomes from urban park environment to human.}, journal = {Journal of hazardous materials}, volume = {477}, number = {}, pages = {135387}, doi = {10.1016/j.jhazmat.2024.135387}, pmid = {39094311}, issn = {1873-3336}, mesh = {Humans ; *Metagenomics ; Parks, Recreational ; Gastrointestinal Microbiome/drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; China ; Bacteria/genetics/drug effects/classification ; Soil Microbiology ; Cities ; Drug Resistance, Bacterial/genetics ; Water Microbiology ; Genes, Bacterial ; }, abstract = {Urban parks play a significant role in urban ecosystems and are strongly associated with human health. Nevertheless, the biological contamination of urban parks - opportunistic pathogens and antibiotic resistance genes (ARGs) - has been poorly reported. Here, metagenomic and 16 S rRNA sequencing methods were used to study the distribution and assembly of opportunistic pathogens and ARGs in soil and water from nine parks in Lanzhou city, and further compared them with local human gut microbiomes to investigate the potential transmission risk. Our results revealed that the most important type of drug resistance in urban parks was multidrug resistance, with various resistance mechanisms. Approximately half of ARGs were shared between human gut and park environment, and it was noteworthy that cross-species transmission might exist among some high-risk ARGs, such as mepA and mdtE, with a significant enrichment in human gut. Metagenomic binning uncovered several bacterial genomes carrying adjacent ARGs, MGEs, and virulence genes, indicating a possibility that these genes may jointly transfer among different environments, particularly from park environment to human. Our results provided a reference point for the management of environmental pollutants in urban parks.}, } @article {pmid39092808, year = {2024}, author = {Jokela, R and Pärnänen, KM and Ponsero, AJ and Lahti, L and Kolho, KL and de Vos, WM and Salonen, A}, title = {A cohort study in family triads: impact of gut microbiota composition and early life exposures on intestinal resistome during the first two years of life.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2383746}, pmid = {39092808}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Infant ; Female ; *Feces/microbiology ; Male ; Cohort Studies ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Infant, Newborn ; Bacteroides/genetics/drug effects/growth & development ; Child, Preschool ; Metagenome ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antibiotic resistance genes (ARGs) are prevalent in the infant gut microbiota and make up the intestinal resistome, representing a community ARG reservoir. This study focuses on the dynamics and persistence of ARGs in the early gut microbiota, and the effect of early exposures therein. We leveraged 2,328 stool metagenomes from 475 children in the HELMi cohort and the available parental samples to study the diversity, dynamics, and intra-familial sharing of the resistome during the first two years of life. We found higher within-family similarity of the gut resistome composition and ARG load in infant-mother pairs, and between spouses, but not in father-infant pairs. Early gut microbiota composition and development correlated with the ARG load; Bacteroides correlated positively and Bifidobacterium negatively with the load, reflecting the typical resistance levels in these taxa. Caesarean delivered infants harbored lower ARG loads, partly reflecting the scarcity of Bacteroides compared to vaginally delivered. Exposure to intrapartum or post-natal antibiotics showed only modest associations with the ARG load and composition, mainly before 12 months. Our results indicate that the resistome is strongly driven by the normal development of the microbiota in early life, and suggest importance of longer evolution of ARGs over effects of recent antibiotic exposure.}, } @article {pmid39091768, year = {2024}, author = {Quezada-Romegialli, C and Quiroga-Carmona, M and D'Elía, G and Harrod, C and Storz, JF}, title = {Diet of Andean leaf-eared mice (Phyllotis) living at extreme elevations on Atacama volcanoes: insights from metagenomics, DNA metabarcoding, and stable isotopes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39091768}, issn = {2692-8205}, support = {R01 HL159061/HL/NHLBI NIH HHS/United States ; }, abstract = {On the flanks of >6000 m Andean volcanoes that tower over the Atacama Desert, leaf-eared mice (Phyllotis vaccarum) live at extreme elevations that surpass known vegetation limits. What the mice eat in these barren, hyperarid environments has been the subject of much speculation. According to the arthropod fallout hypothesis, sustenance is provided by windblown insects that accumulate in snowdrifts ('aolian deposits'). It is also possible that mice feed on saxicolous lichen or forms of cryptic vegetation that have yet to be discovered at such high elevations. We tested hypotheses about the diet of mice living at extreme elevations on Atacama volcanoes by combining metagenomic and DNA metabarcoding analyses of gut contents with stable-isotope analyses of mouse tissues. Genomic analyses of contents of the gastrointestinal tract of a live-captured mouse from the 6739 m summit of Volcán Llullaillaco revealed evidence for an opportunistic but purely herbivorous diet, including lichens. Although we found no evidence of animal DNA in gut contents of the summit mouse, stable isotope data indicate that mice native to elevations at or near vegetation limits (~5100 m) include a larger fraction of animal prey in their diet than mice from lower elevations. Some plant species detected in the gut contents of the summit mouse are known to exist at lower elevations at the base of the volcano and in the surrounding Altiplano, suggesting that such plants may occur at higher elevations beneath the snowpack or in other cryptic microhabitats.}, } @article {pmid39091712, year = {2024}, author = {Qu, B and Li, Z}, title = {Exploring non-invasive diagnostics for metabolic dysfunction-associated fatty liver disease.}, journal = {World journal of gastroenterology}, volume = {30}, number = {28}, pages = {3447-3451}, pmid = {39091712}, issn = {2219-2840}, mesh = {Humans ; *Biomarkers/blood/analysis/metabolism ; *Non-alcoholic Fatty Liver Disease/diagnosis/blood/metabolism ; *Liver/pathology/metabolism ; Biopsy ; Liver Cirrhosis/diagnosis/blood/pathology ; Disease Progression ; Feces/chemistry ; Algorithms ; Gastrointestinal Microbiome ; Metagenome ; }, abstract = {The population with metabolic dysfunction-associated fatty liver disease (MAFLD) is increasingly common worldwide. Identification of people at risk of progression to advanced stages is necessary to timely offer interventions and appropriate care. Liver biopsy is currently considered the gold standard for the diagnosis and staging of MAFLD, but it has associated risks and limitations. This has spurred the exploration of non-invasive diagnostics for MAFLD, especially for steatohepatitis and fibrosis. These non-invasive approaches mostly include biomarkers and algorithms derived from anthropometric measurements, serum tests, imaging or stool metagenome profiling. However, they still need rigorous and widespread clinical validation for the diagnostic performance.}, } @article {pmid39091676, year = {2024}, author = {Li, Y and Mao, X and Shi, P and Wan, Z and Yang, D and Ma, T and Wang, B and Wang, J and Wang, J and Zhu, R}, title = {Microbiome-host interactions in the pathogenesis of acute exacerbation of chronic obstructive pulmonary disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1386201}, pmid = {39091676}, issn = {2235-2988}, mesh = {*Pulmonary Disease, Chronic Obstructive/microbiology ; Humans ; *Microbiota ; Female ; Male ; Aged ; *Sputum/microbiology ; Middle Aged ; Haemophilus influenzae/genetics ; Computational Biology ; Host Microbial Interactions ; Metagenomics ; Disease Progression ; Bacteria/classification/genetics/isolation & purification ; Signal Transduction ; Host-Pathogen Interactions ; }, abstract = {OBJECTIVE: To explore the underlying mechanisms the airway microbiome contributes to Acute Exacerbation of Chronic Obstructive Pulmonary Disease(AECOPD).

METHODS: We enrolled 31 AECOPD patients and 26 stable COPD patients, their sputum samples were collected for metagenomic and RNA sequencing, and then subjected to bioinformatic analyses. The expression of host genes was validated by Quantitative Real-time PCR(qPCR) using the same batch of specimens.

RESULTS: Our results indicated a higher expression of Rothia mucilaginosa(p=0.015) in the AECOPD group and Haemophilus influenzae(p=0.005) in the COPD group. The Different expressed genes(DEGs) detected were significantly enriched in "type I interferon signaling pathway"(p<0.001, q=0.001) in gene function annotation, and "Cytosolic DNA-sensing pathway"(p=0.002, q=0.024), "Toll-like receptor signaling pathway"(p=0.006, q=0.045), and "TNF signaling pathway"(p=0.006, q=0.045) in KEGG enrichment analysis. qPCR amplification experiment verified that the expression of OASL and IL6 increased significantly in the AECOPD group.

CONCLUSION: Pulmonary bacteria dysbiosis may regulate the pathogenesis of AECOPD through innate immune system pathways like type I interferon signaling pathway and Toll-like receptor signaling pathway.}, } @article {pmid39090708, year = {2024}, author = {Stiffler, AK and Hesketh-Best, PJ and Varona, NS and Zagame, A and Wallace, BA and Lapointe, BE and Silveira, CB}, title = {Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {143}, pmid = {39090708}, issn = {2049-2618}, support = {2023349872//National Science Foundation/ ; 2023353157//National Science Foundation Graduate Research Fellowship Program/ ; 80NSSC23K0676/NASA/NASA/United States ; }, mesh = {*Sargassum/microbiology ; *Symbiosis ; *Bacteriophages/genetics/physiology/classification/isolation & purification ; *Seawater/microbiology/virology ; Genome, Viral ; Metagenome ; Bacteria/virology/genetics/classification ; Genomics ; Microbiota ; Phylogeny ; Genome, Bacterial ; Synechococcus/virology/genetics ; }, abstract = {BACKGROUND: Symbioses between primary producers and bacteria are crucial for nutrient exchange that fosters host growth and niche adaptation. Yet, how viruses that infect bacteria (phages) influence these bacteria-eukaryote interactions is still largely unknown. Here, we investigate the role of viruses on the genomic diversity and functional adaptations of bacteria associated with pelagic sargassum. This brown alga has dramatically increased its distribution range in the Atlantic in the past decade and is predicted to continue expanding, imposing severe impacts on coastal ecosystems, economies, and human health.

RESULTS: We reconstructed 73 bacterial and 3963 viral metagenome-assembled genomes (bMAGs and vMAGs, respectively) from coastal Sargassum natans VIII and surrounding seawater. S. natans VIII bMAGs were enriched in prophages compared to seawater (28% and 0.02%, respectively). Rhodobacterales and Synechococcus bMAGs, abundant members of the S. natans VIII microbiome, were shared between the algae and seawater but were associated with distinct phages in each environment. Genes related to biofilm formation and quorum sensing were enriched in S. natans VIII phages, indicating their potential to influence algal association in their bacterial hosts. In-vitro assays with a bacterial community harvested from sargassum surface biofilms and depleted of free viruses demonstrated that these bacteria are protected from lytic infection by seawater viruses but contain intact and inducible prophages. These bacteria form thicker biofilms when growing on sargassum-supplemented seawater compared to seawater controls, and phage induction using mitomycin C was associated with a significant decrease in biofilm formation. The induced metagenomes were enriched in genomic sequences classified as temperate viruses compared to uninduced controls.

CONCLUSIONS: Our data shows that prophages contribute to the flexible genomes of S. natans VIII-associated bacteria. These prophages encode genes with symbiotic functions, and their induction decreases biofilm formation, an essential capacity for flexible symbioses between bacteria and the alga. These results indicate that prophage acquisition and induction contribute to genomic and functional diversification during sargassum-bacteria symbioses, with potential implications for algae growth. Video Abstract.}, } @article {pmid39090559, year = {2024}, author = {Sime, AM and Kifle, BA and Woldesemayat, AA and Gemeda, MT}, title = {Microbial carbohydrate active enzyme (CAZyme) genes and diversity from Menagesha Suba natural forest soils of Ethiopia as revealed by shotgun metagenomic sequencing.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {285}, pmid = {39090559}, issn = {1471-2180}, mesh = {*Soil Microbiology ; *Metagenomics/methods ; *Forests ; *Bacteria/genetics/enzymology/classification/isolation & purification ; Ethiopia ; *Phylogeny ; Glycoside Hydrolases/genetics/metabolism ; Microbiota/genetics ; Biodiversity ; Soil/chemistry ; Metagenome ; Biofuels ; Bacterial Proteins/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Carbohydrate Metabolism ; }, abstract = {BACKGROUND: The global over-reliance on non-renewable fossil fuels has led to the emission of greenhouse gases, creating a critical global environmental challenge. There is an urgent need for alternative solutions like biofuels. Advanced biofuel is a renewable sustainable energy generated from lignocellulosic plant materials, which can significantly contribute to mitigating CO2 emissions. Microbial Carbohydrate Active Enzymes (CAZymes) are the most crucial enzymes for the generation of sustainable biofuel energy. The present study designed shotgun metagenomics approaches to assemble, predict, and annotate, aiming to gain an insight into the taxonomic diversity, annotate CAZymes, and identify carbohydrate hydrolyzing CAZymes from microbiomes in Menagesha suba forest soil for the first time.

RESULTS: The microbial diversity based on small subunit (SSU) rRNA analysis revealed the dominance of the bacterial domain representing 81.82% and 92.31% in the studied samples. Furthermore, the phylum composition result indicated the dominance of the phyla Proteobacteria (23.08%, 27.27%), Actinobacteria (11.36%, 20.51%), and Acidobacteria (10.26%, 15.91%). The study also identified unassigned bacteria which might have a unique potential for biopolymer hydrolysis. The metagenomic study revealed that 100,244 and 65,356 genes were predicted from the two distinct samples. A total number of 1806 CAZyme genes were identified, among annotated CAZymes, 758 had a known enzyme assigned to CAZymes. Glycoside hydrolases (GHs) CAZyme family contained most of the CAZyme genes with known enzymes such as β-glucosidase, endo-β-1,4-mannanase, exo-β-1,4-glucanase, α-L-arabinofuranosidase and oligoxyloglucan reducing end-specific cellobiohydrolase. On the other hand, 1048 of the identified CAZyme genes were putative CAZyme genes with unknown enzymatical activity and the majority of which belong to the GHs family.

CONCLUSIONS: In general, the identified putative CAZymes genes open up an opportunity for the discovery of new enzymes responsible for hydrolyzing biopolymers utilized for biofuel energy generation. This finding is used as a first-hand piece of evidence to serve as a benchmark for further and comprehensive studies to unveil novel classes of bio-economically valuable genes and their encoded products.}, } @article {pmid39090215, year = {2024}, author = {Boscari, E and Palle, SD and Vitulo, N and Scapolatiello, A and Schiavon, L and Cariani, A and Papetti, C and Zane, L and Marino, IAM and Congiu, L}, title = {MIPs: multi-locus intron polymorphisms in species identification and population genomics.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {17870}, pmid = {39090215}, issn = {2045-2322}, support = {256475//FSBI Small Research Grants (Fishery Society of the Britisk Isles)/ ; 622320//European Marie Curie Project "Polarexpress"/ ; 164793//University of Padova BIRD/ ; 2016_00307//Italian National Programme of Antarctic Research (PNRA)/ ; CN00000033//NBFC to University of Padova/ ; }, mesh = {Animals ; *Introns/genetics ; *Fishes/genetics/classification ; Polymorphism, Single Nucleotide ; Genetics, Population ; Species Specificity ; Metagenomics/methods ; Genomics/methods ; }, abstract = {The study of species groups in which the presence of interspecific hybridization or introgression phenomena is known or suspected involves analysing shared bi-parentally inherited molecular markers. Current methods are based on different categories of markers among which the classical microsatellites or the more recent genome wide approaches for the analyses of thousands of SNPs or hundreds of microhaplotypes through high throughput sequencing. Our approach utilizes intron-targeted amplicon sequencing to characterise multi-locus intron polymorphisms (MIPs) and assess genetic diversity. These highly variable intron regions, combined with inter-specific transferable loci, serve as powerful multiple-SNP markers potentially suitable for various applications, from species and hybrid identification to population comparisons, without prior species knowledge. We developed the first panel of MIPs highly transferable across fish genomes, effectively distinguishing between species, even those closely related, and populations with different structures. MIPs offer versatile, hypervariable nuclear markers and promise to be especially useful when multiple nuclear loci must be genotyped across different species, such as for the monitoring of interspecific hybridization. Moreover, the relatively long sequences obtained ease the development of single-locus PCR-based diagnostic markers. This method, here demonstrated in teleost fishes, can be readily applied to other taxa, unlocking a new source of genetic variation.}, } @article {pmid39089643, year = {2024}, author = {Gautam, J and Aggarwal, H and Kumari, D and Gupta, SK and Kumar, Y and Dikshit, M}, title = {A methionine-choline-deficient diet induces nonalcoholic steatohepatitis and alters the lipidome, metabolome, and gut microbiome profile in the C57BL/6J mouse.}, journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids}, volume = {1869}, number = {8}, pages = {159545}, doi = {10.1016/j.bbalip.2024.159545}, pmid = {39089643}, issn = {1879-2618}, mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/metabolism/microbiology/etiology/pathology ; *Methionine/deficiency/metabolism ; *Gastrointestinal Microbiome ; Mice ; *Mice, Inbred C57BL ; Male ; *Metabolome ; Lipidomics ; Choline Deficiency/metabolism ; Liver/metabolism/pathology ; Choline/metabolism ; Lipid Metabolism ; Disease Models, Animal ; Diet/adverse effects ; }, abstract = {The methionine-choline-deficient (MCD) diet-induced non-alcoholic steatohepatitis (NASH) in mice is a well-established model. Our study aims to elucidate the factors influencing liver pathology in the MCD mouse model by examining physiological, biochemical, and molecular changes using histology, molecular techniques, and OMICS approaches (lipidomics, metabolomics, and metagenomics). Male C57BL/6J mice were fed a standard chow diet, a methionine-choline-sufficient (MCS) diet, or an MCD diet for 10 weeks. The MCD diet resulted in reduced body weight and fat mass, along with decreased plasma triglyceride, cholesterol, glucose, and insulin levels. However, it notably induced steatosis, inflammation, and alterations in gene expression associated with lipogenesis, inflammation, fibrosis, and the synthesis of apolipoproteins, sphingolipids, ceramides, and carboxylesterases. Lipid analysis revealed significant changes in plasma and tissues: most ceramide non-hydroxy-sphingosine lipids significantly decreased in the liver and plasma but increased in the adipose tissue of MCD diet-fed animals. Oxidized glycerophospholipids mostly increased in the liver but decreased in the adipose tissue of the MCD diet-fed group. The gut microbiome of the MCD diet-fed group showed an increase in Firmicutes and a decrease in Bacteroidetes and Actinobacteria. Metabolomic profiling demonstrated that the MCD diet significantly altered amino acid biosynthesis, metabolism, and nucleic acid metabolism pathways in plasma, liver, fecal, and cecal samples. LC-MS data indicated higher total plasma bile acid intensity and reduced fecal glycohyodeoxycholic acid intensity in the MCD diet group. This study demonstrates that although the MCD diet induces hepatic steatosis, the mechanisms underlying NASH in this model differ from those in human NASH pathology.}, } @article {pmid39089548, year = {2024}, author = {Zeng, X and Tang, S and Dong, X and Dong, M and Shao, R and Liu, R and Li, T and Zhang, X and Wong, YH and Xie, Q}, title = {Analysis of metagenome and metabolome disclosed the mechanisms of Dendrobium officinale polysaccharide on DSS-induced ulcerative colitis-affected mice.}, journal = {International journal of biological macromolecules}, volume = {277}, number = {Pt 2}, pages = {134229}, doi = {10.1016/j.ijbiomac.2024.134229}, pmid = {39089548}, issn = {1879-0003}, mesh = {Animals ; *Dendrobium/chemistry ; *Colitis, Ulcerative/chemically induced/drug therapy/metabolism ; *Polysaccharides/pharmacology/chemistry ; *Dextran Sulfate/adverse effects ; Mice ; *Metabolome/drug effects ; Male ; Gastrointestinal Microbiome/drug effects ; Cytokines/metabolism ; Antioxidants/pharmacology ; Disease Models, Animal ; }, abstract = {Currently, there is no known cause for ulcerative colitis (UC), an inflammatory bowel disease that is difficult to treat. This assay aimed to investigate the protective effects and mechanisms of Dendrobium officinale polysaccharide (DOP) in mice with acute UC induced by dextran sulphate sodium (DSS). We found that DOP could improve weight loss, decrease the disease activity index (DAI), and regulate the release of interleukin 2 (IL-2), IL-4, IL-6, and IL-10 in DSS-induced acute UC mice. Additionally, DOP preserved the integrity of the intestinal barrier in UC mice by increasing goblet cell density and maintaining tight junctions. DOP significantly enhanced total antioxidant capacity (T-AOC), and reduced glutathione (GSH), nitric oxide (NO), and malondialdehyde (MDA) levels in the bloodstream. In terms of serum biochemistry, DOP markedly elevated levels of bilirubin (BIL), alkaline phosphatase (ALP), total bile acid (TBA), creatinine (Crea), and creative kinase isoenzyme (CKMB). Furthermore, DOP increased the relative abundance of Lactobacillales. DOP also improved intestinal health and stimulated the synthesis of potent anti-inflammatory and antiviral substances by regulating the metabolism of purines, prostaglandins, and leukotrienes. Therefore, DOP can be considered a functional dietary supplement for the treatment of UC, as it improves the condition of DSS-induced UC mice.}, } @article {pmid39089095, year = {2024}, author = {Zhuang, M and Yan, W and Xiong, Y and Wu, Z and Cao, Y and Sanganyado, E and Siame, BA and Chen, L and Kashi, Y and Leung, KY}, title = {Horizontal plasmid transfer promotes antibiotic resistance in selected bacteria in Chinese frog farms.}, journal = {Environment international}, volume = {190}, number = {}, pages = {108905}, doi = {10.1016/j.envint.2024.108905}, pmid = {39089095}, issn = {1873-6750}, mesh = {Animals ; *Plasmids/genetics ; China ; *Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Farms ; Drug Resistance, Bacterial/genetics ; Rana catesbeiana/microbiology/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/genetics ; }, abstract = {The emergence and dissemination of antibiotic resistance genes (ARGs) in the ecosystem are global public health concerns. One Health emphasizes the interconnectivity between different habitats and seeks to optimize animal, human, and environmental health. However, information on the dissemination of antibiotic resistance genes (ARGs) within complex microbiomes in natural habitats is scarce. We investigated the prevalence of antibiotic resistant bacteria (ARB) and the spread of ARGs in intensive bullfrog (Rana catesbeiana) farms in the Shantou area of China. Antibiotic susceptibilities of 361 strains, combined with microbiome analyses, revealed Escherichia coli, Edwardsiella tarda, Citrobacter and Klebsiella sp. as prevalent multidrug resistant bacteria on these farms. Whole genome sequencing of 95 ARB identified 250 large plasmids that harbored a wide range of ARGs. Plasmid sequences and sediment metagenomes revealed an abundance of tetA, sul1, and aph(3″)-Ib ARGs. Notably, antibiotic resistance (against 15 antibiotics) highly correlated with plasmid-borne rather than chromosome-borne ARGs. Based on sequence similarities, most plasmids (62%) fell into 32 distinct groups, indicating a potential for horizontal plasmid transfer (HPT) within the frog farm microbiome. HPT was confirmed in inter- and intra-species conjugation experiments. Furthermore, identical mobile ARGs, flanked by mobile genetic elements (MGEs), were found in different locations on the same plasmid, or on different plasmids residing in the same or different hosts. Our results suggest a synergy between MGEs and HPT to facilitate ARGs dissemination in frog farms. Mining public databases retrieved similar plasmids from different bacterial species found in other environmental niches globally. Our findings underscore the importance of HPT in mediating the spread of ARGs in frog farms and other microbiomes of the ecosystem.}, } @article {pmid39089018, year = {2024}, author = {Cui, M and Wang, M and Liu, X and Sun, H and Su, Z and Zheng, Y and Shen, Y and Wang, M}, title = {Mining and characterization of novel antimicrobial peptides from the large-scale microbiome of Shanxi aged vinegar based on metagenomics, molecular dynamics simulations and mechanism validation.}, journal = {Food chemistry}, volume = {460}, number = {Pt 2}, pages = {140646}, doi = {10.1016/j.foodchem.2024.140646}, pmid = {39089018}, issn = {1873-7072}, mesh = {*Metagenomics ; *Molecular Dynamics Simulation ; *Staphylococcus aureus/drug effects ; *Acetic Acid/chemistry/pharmacology ; *Escherichia coli/drug effects/genetics/metabolism ; Antimicrobial Peptides/chemistry/pharmacology/metabolism/genetics ; Anti-Bacterial Agents/pharmacology/chemistry ; Microbiota ; Microbial Sensitivity Tests ; Humans ; Lactobacillus/chemistry/metabolism ; }, abstract = {The study aimed to mine and characterize novel antimicrobial peptides (AMPs) from the Shanxi aged vinegar microbiome. Utilizing machine learning techniques, AlphaFold2 structure prediction and molecular dynamics simulations, six novel AMPs were innovatively mined from 98,539 peptides based on metagenomic data, of which one peptide secreted by Lactobacillus (named La-AMP) was experimentally validated to have remarkable bactericidal effects against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) with high stability and no hemolytic activity. Scanning electron microscopy revealed that La-AMP caused irreversible damage to cell membranes of S. aureus and E. coli, a finding further confirmed by calcein-AM/propidium iodide staining. Additionally, La-AMP induced nucleic acid leakage and reactive oxygen species accumulation in bacterial cells. It was found to bind to DNA gyrase through salt bridges, hydrogen bonds, and hydrophobic interactions, ultimately inducing apoptosis. Thus, La-AMP exhibited encouraging promise as a valuable bioactive component for the development of natural preservatives.}, } @article {pmid39088249, year = {2024}, author = {Haring, VC and Litz, B and Jacob, J and Brecht, M and Bauswein, M and Sehl-Ewert, J and Heroldova, M and Wylezich, C and Hoffmann, D and Ulrich, RG and Beer, M and Pfaff, F}, title = {Detection of novel orthoparamyxoviruses, orthonairoviruses and an orthohepevirus in European white-toothed shrews.}, journal = {Microbial genomics}, volume = {10}, number = {8}, pages = {}, pmid = {39088249}, issn = {2057-5858}, mesh = {Animals ; *Shrews/virology ; *Phylogeny ; Genome, Viral ; Europe ; Paramyxoviridae/genetics/isolation & purification/classification ; Metagenomics ; Virome/genetics ; RNA, Viral/genetics ; Humans ; }, abstract = {While the viromes and immune systems of bats and rodents have been extensively studied, comprehensive data are lacking for insectivores (order Eulipotyphla) despite their wide geographic distribution. Anthropogenic land use and outdoor recreational activities, as well as changes in the range of shrews, may lead to an expansion of the human-shrew interface with the risk of spillover infections, as reported for Borna disease virus 1. We investigated the virome of 45 individuals of 4 white-toothed shrew species present in Europe, using metagenomic RNA sequencing of tissue and intestine pools. Moderate to high abundances of sequences related to the families Paramyxoviridae, Nairoviridae, Hepeviridae and Bornaviridae were detected. Whole genomes were determined for novel orthoparamyxoviruses (n=3), orthonairoviruses (n=2) and an orthohepevirus. The novel paramyxovirus, tentatively named Hasua virus, was phylogenetically related to the zoonotic Langya virus and Mòjiāng virus. The novel orthonairoviruses, along with the potentially zoonotic Erve virus, fall within the shrew-borne Thiafora virus genogroup. The highest viral RNA loads of orthoparamyxoviruses were detected in the kidneys, in well-perfused organs for orthonairoviruses and in the liver and intestine for orthohepevirus, indicating potential transmission routes. Notably, several shrews were found to be coinfected with viruses from different families. Our study highlights the virus diversity present in shrews, not only in biodiversity-rich regions but also in areas influenced by human activity. This study warrants further research to characterize and assess the clinical implications and risk of these viruses and the importance of shrews as reservoirs in European ecosystems.}, } @article {pmid39088170, year = {2024}, author = {Mukherjee, P and Sharma, RS and Mishra, V}, title = {Deciphering the ecological impact of azo dye pollution through microbial community analysis in water-sediment microcosms.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {39088170}, issn = {1614-7499}, abstract = {The uncontrolled release of untreated dyeing wastewater into aquatic ecosystems poses global environmental risks. It alters native microbial communities and associated ecological processes, often going unnoticed. Therefore, the influence of acid orange 7 dye (AO7) contamination on the natural microbial community was investigated using a water-sediment microcosm. Compared to sterile microcosms, complete dye decolourization in natural microcosms showed microbial communities' significance in combating xenobiotic contamination. Proteobacteria dominated the water community, whereas Firmicutes dominated the sediment. AO7 exposure induced notable shifts in the structural composition of the bacterial community in both water and sediment. Niveispirillum exhibited a marked decrease, and Pseudomonas demonstrated a notable increase. The - 9.0 log2FC in Niveispirillum, a nitrogen-fixing bacterium, from 24.4% in the control to 0.1% post-treatment, may disrupt nutrient balance, plant growth, and ecosystem productivity. Conversely, elevated levels of Pseudomonas sp. resulting from azo dye exposure demonstrate its ability to tolerate and bioremediate organic pollutants, highlighting its resilience. Functional profiling via KEGG pathway analysis revealed differential expression patterns under AO7 stress. Specifically, valine, leucine, and isoleucine degradation pathways in water decreased by 52.2%, and cysteine and methionine metabolism ceased expression entirely, indicating reduced protein metabolism and nutrient bioavailability under dye exposure. Furthermore, in sediment, glutathione metabolism ceased, indicating increased oxidative stress following AO7 infusion. However, C5-branched dibasic acid metabolism and limonene and pinene degradation were uniquely expressed in sediment. Decreased methane metabolism exacerbates the effects of global warming on aquatic ecosystems. Further, ceased-butanoate metabolic pathways reflect the textile dye wastewater-induced adverse impact on ecological processes, such as organic matter decomposition, energy flow, nutrient cycling, and community dynamics that help maintain self-purification and ecological balance in river ecosystems. These findings underscore the critical need for more comprehensive environmental monitoring and management strategies to mitigate ecological risks posed by textile dyes in aquatic ecosystems, which remain unnoticed.}, } @article {pmid39086173, year = {2024}, author = {Hu, A and Zhao, W and Wang, J and Qi, Q and Xiao, X and Jing, H}, title = {Microbial communities reveal niche partitioning across the slope and bottom zones of the challenger deep.}, journal = {Environmental microbiology reports}, volume = {16}, number = {4}, pages = {e13314}, pmid = {39086173}, issn = {1758-2229}, support = {SL2021PT103//Oceanic Interdisciplinary Program of Shanghai Jiao Tong University/ ; 91751116//Training Program of the Major Research Plan of the National Natural Science Foundation of China/ ; ZDKJ2021036//Hainan Province Science and Technology Special Fund/ ; 41921006//National Natural Science Foundation of China/ ; 42106087//National Natural Science Foundation of China/ ; }, mesh = {*Seawater/microbiology ; *Microbiota ; *Geologic Sediments/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *RNA, Ribosomal, 16S/genetics ; Phylogeny ; Metagenomics ; Metagenome ; Archaea/classification/genetics/isolation & purification/metabolism ; }, abstract = {Widespread marine microbiomes exhibit compositional and functional differentiation as a result of adaptation driven by environmental characteristics. We investigated the microbial communities in both seawater and sediments on the slope (7-9 km) and the bottom (9-11 km) of the Challenger Deep of the Mariana Trench to explore community differentiation. Both metagenome-assembled genomes (MAGs) and 16S rRNA amplicon sequence variants (ASVs) showed that the microbial composition in the seawater was similar to that of sediment on the slope, while distinct from that of sediment in the bottom. This scenario suggested a potentially stronger community interaction between seawater and sediment on the slope, which was further confirmed by community assembly and population movement analyses. The metagenomic analysis also indicates a specific stronger potential of nitrate reduction and sulphate assimilation in the bottom seawater, while more versatile nitrogen and sulphur cycling pathways occur on the slope, reflecting functional differentiations among communities in conjunction with environmental features. This work implies that microbial community differentiation occurred in the different hadal niches, and was likely an outcome of microbial adaptation to the extreme hadal trench environment, especially the associated hydrological and geological conditions, which should be considered and measured in situ in future studies.}, } @article {pmid39086104, year = {2024}, author = {Macher, JN and Martínez, A and Çakir, S and Cholley, PE and Christoforou, E and Curini Galletti, M and van Galen, L and García-Cobo, M and Jondelius, U and de Jong, D and Leasi, F and Lemke, M and Rubio Lopez, I and Sánchez, N and Sørensen, MV and Todaro, MA and Renema, W and Fontaneto, D}, title = {Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna.}, journal = {Molecular ecology resources}, volume = {24}, number = {7}, pages = {e13997}, doi = {10.1111/1755-0998.13997}, pmid = {39086104}, issn = {1755-0998}, support = {T0206/37197/2021/kg//Stemmler Foundation/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Electron Transport Complex IV/genetics ; Netherlands ; Biodiversity ; North Sea ; Invertebrates/genetics/classification ; Bathing Beaches ; Ecosystem ; Metagenomics/methods ; }, abstract = {Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack of reference DNA sequences available for taxonomic annotation. Our study explores the benefits of combining targeted DNA barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches are globally important ecosystems and are inhabited by meiofauna, microscopic animals living in the interstitial space between the sand grains, which play a key role in coastal biodiversity and ecosystem dynamics. However, research on meiofauna faces challenges due to limited taxonomic expertise and sparse sampling. We generated 775 new cytochrome c oxidase I DNA barcodes from meiofauna specimens collected along the Netherlands' west coast and combined them with the NCBI GenBank database. We analysed alpha and beta diversity in 561 metabarcoding samples from 24 North Sea beaches, a region extensively studied for meiofauna, using both the enriched reference database and the NCBI database without the additional reference barcodes. Our results show a 2.5-fold increase in sequence annotation and a doubling of species-level Operational Taxonomic Units (OTUs) identification when annotating the metabarcoding data with the enhanced database. Additionally, our analyses revealed a bell-shaped curve of OTU richness across the intertidal zone, aligning more closely with morphological analysis patterns, and more defined community dissimilarity patterns between supralittoral and intertidal sites. Our research highlights the importance of expanding molecular reference databases and combining morphological taxonomy with molecular techniques for biodiversity assessments, ultimately improving our understanding of coastal ecosystems.}, } @article {pmid39085298, year = {2024}, author = {Vidal-Verdú, À and Torrent, D and Iglesias, A and Latorre-Pérez, A and Abendroth, C and Corbín-Agustí, P and Peretó, J and Porcar, M}, title = {The highly differentiated gut of Pachnoda marginata hosts sequential microbiomes: microbial ecology and potential applications.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {65}, pmid = {39085298}, issn = {2055-5008}, support = {ACIF/2021/110//Generalitat Valenciana (Regional Government of Valencia)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification ; *Archaea/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; *Coleoptera/microbiology ; Metagenomics/methods ; Phylogeny ; Gastrointestinal Tract/microbiology ; Sequence Analysis, DNA/methods ; }, abstract = {Insect gut microbiomes play a crucial role in the insect development and are shaped, among other factors, by the specialized insect diet habits as well as the morphological structure of the gut. Rose chafers (Pachnoda spp.; Coleoptera: Scarabaeidae) have a highly differentiated gut characterized by a pronounced hindgut dilation which resembles a miniaturized rumen. Specifically, the species Pachnoda marginata has not been previously studied in detail in terms of microbial ecology. Here, we show a fine scale study of the highly compartmentalized gut of P. marginata by using amplicon and metagenomic sequencing to shed light on the bacterial, archaeal and fungal communities thriving in each section of the gut. We found a microbial gradient along the gut from aerobic (foregut) to strictly anaerobic communities (hindgut). In addition, we have characterized interesting biological activities and metabolic pathways of gut microbial communities related to cellulose degradation, methane production and sulfate reduction. Taken together, our results reveal the highly diverse microbial community and the potential of P. marginata gut as a source of industrially relevant microbial diversity.}, } @article {pmid39085233, year = {2024}, author = {Essex, M and Millet Pascual-Leone, B and Löber, U and Kuhring, M and Zhang, B and Brüning, U and Fritsche-Guenther, R and Krzanowski, M and Fiocca Vernengo, F and Brumhard, S and Röwekamp, I and Anna Bielecka, A and Lesker, TR and Wyler, E and Landthaler, M and Mantei, A and Meisel, C and Caesar, S and Thibeault, C and Corman, VM and Marko, L and Suttorp, N and Strowig, T and Kurth, F and Sander, LE and Li, Y and Kirwan, JA and Forslund, SK and Opitz, B}, title = {Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {66}, pmid = {39085233}, issn = {2055-5008}, support = {SFB-TR84 A1/A5//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 400667201//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB-TR84//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB-TR84//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB1365, SFB1470, KFO339//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Project 76251-99//Volkswagen Foundation (VolkswagenStiftung)/ ; Project 76251-99//Volkswagen Foundation (VolkswagenStiftung)/ ; KA1-Co-02 'COVIPA'//Helmholtz Association/ ; KA1-Co-02 'COVIPA'//Helmholtz Association/ ; }, mesh = {Humans ; *COVID-19/microbiology/immunology ; *Tryptophan/metabolism ; *Gastrointestinal Microbiome ; *Dysbiosis ; Male ; Female ; *SARS-CoV-2 ; Middle Aged ; *Cytokines/blood/metabolism ; Metabolome ; Inflammation ; Kynurenine/metabolism/blood ; Aged ; Adult ; }, abstract = {The clinical course of COVID-19 is variable and often unpredictable. To test the hypothesis that disease progression and inflammatory responses associate with alterations in the microbiome and metabolome, we analyzed metagenome, metabolome, cytokine, and transcriptome profiles of repeated samples from hospitalized COVID-19 patients and uninfected controls, and leveraged clinical information and post-hoc confounder analysis. Severe COVID-19 was associated with a depletion of beneficial intestinal microbes, whereas oropharyngeal microbiota disturbance was mainly linked to antibiotic use. COVID-19 severity was also associated with enhanced plasma concentrations of kynurenine and reduced levels of several other tryptophan metabolites, lysophosphatidylcholines, and secondary bile acids. Moreover, reduced concentrations of various tryptophan metabolites were associated with depletion of Faecalibacterium, and tryptophan decrease and kynurenine increase were linked to enhanced production of inflammatory cytokines. Collectively, our study identifies correlated microbiome and metabolome alterations as a potential contributor to inflammatory dysregulation in severe COVID-19.}, } @article {pmid39084885, year = {2024}, author = {Hu, F and Li, X and Liu, K and Li, Y and Xie, Y and Wei, C and Liu, S and Song, J and Wang, P and Shi, L and Li, C and Li, J and Xu, L and Xue, J and Zheng, X and Bai, M and Fang, X and Jin, X and Cao, L and Hao, P and He, J and Wang, J and Zhang, C and Li, Z}, title = {Rheumatoid arthritis patients harbour aberrant enteric bacteriophages with autoimmunity-provoking potential: a paired sibling study.}, journal = {Annals of the rheumatic diseases}, volume = {83}, number = {12}, pages = {1677-1690}, doi = {10.1136/ard-2024-225564}, pmid = {39084885}, issn = {1468-2060}, mesh = {Humans ; *Arthritis, Rheumatoid/immunology ; *Bacteriophages/immunology/genetics ; Female ; *Autoimmunity/immunology ; Male ; *Feces/virology ; Siblings ; Adult ; Middle Aged ; Virome/immunology ; CD4-Positive T-Lymphocytes/immunology ; Gastrointestinal Microbiome/immunology ; Case-Control Studies ; Prevotella/immunology ; Autoantibodies/immunology ; Molecular Mimicry/immunology ; B-Lymphocytes/immunology ; }, abstract = {OBJECTIVES: Viruses have been considered as important participants in the development of rheumatoid arthritis (RA). However, the profile of enteric virome and its role in RA remains elusive. This study aimed to investigate the atlas and involvement of virome in RA pathogenesis.

METHODS: Faecal samples from 30 pairs of RA and healthy siblings that minimise genetic interferences were collected for metagenomic sequencing. The α and β diversity of the virome and the virome-bacteriome interaction were analysed. The differential bacteriophages were identified, and their correlations with clinical and immunological features of RA were analysed. The potential involvement of these differential bacteriophages in RA pathogenesis was further investigated by auxiliary metabolic gene annotation and molecular mimicry study. The responses of CD4[+] T cells and B cells to the mimotopes derived from the differential bacteriophages were systemically studied.

RESULTS: The composition of the enteric bacteriophageome was distorted in RA. The differentially presented bacteriophages correlated with the immunological features of RA, including anti-CCP autoantibody and HLA-DR shared epitope. Intriguingly, the glycerolipid and purine metabolic genes were highly active in the bacteriophages from RA. Moreover, peptides of RA-enriched phages, in particular Prevotella phage and Oscillibacter phage could provoke the autoimmune responses in CD4[+] T cells and plasma cells via molecular mimicry of the disease-associated autoantigen epitopes, especially those of Bip.

CONCLUSIONS: This study provides new insights into enteric bacteriophageome in RA development. In particular, the aberrant bacteriophages demonstrated autoimmunity-provoking potential that would promote the occurrence of the disease.}, } @article {pmid39084687, year = {2024}, author = {Jiang, S and Cai, M and Li, D and Chen, X and Chen, X and Huang, Q and Zhong, C and Zheng, X and Zhou, D and Chen, Z and Zhang, L and Ching, JY and Chen, A and Lu, S and Zhang, L and Hu, L and Liao, Y and Li, Y and He, Z and Wu, J and Huo, H and Liang, Y and Li, W and Zou, Y and Luo, W and Ng, SC and Chan, FK and Chen, X and Deng, Y}, title = {Association of breast milk-derived arachidonic acid-induced infant gut dysbiosis with the onset of atopic dermatitis.}, journal = {Gut}, volume = {74}, number = {1}, pages = {45-57}, pmid = {39084687}, issn = {1468-3288}, mesh = {*Dermatitis, Atopic/microbiology/metabolism/etiology ; Humans ; *Milk, Human/chemistry ; *Dysbiosis/metabolism/microbiology ; *Gastrointestinal Microbiome ; Infant ; Female ; Animals ; *Arachidonic Acid/metabolism ; *Feces/microbiology ; Mice ; Infant, Newborn ; Male ; Breast Feeding ; }, abstract = {OBJECTIVE: The specific breast milk-derived metabolites that mediate host-microbiota interactions and contribute to the onset of atopic dermatitis (AD) remain unknown and require further investigation.

DESIGN: We enrolled 250 mother-infant pairs and collected 978 longitudinal faecal samples from infants from birth to 6 months of age, along with 243 maternal faecal samples for metagenomics. Concurrently, 239 corresponding breast milk samples were analysed for metabolomics. Animal and cellular experiments were conducted to validate the bioinformatics findings.

RESULTS: The clinical findings suggested that a decrease in daily breastfeeding duration was associated with a reduced incidence of AD. This observation inspired us to investigate the effects of breast milk-derived fatty acids. We found that high concentrations of arachidonic acid (AA), but not eicosapentaenoic acid (EPA) or docosahexaenoic acid, induced gut dysbiosis in infants. Further investigation revealed that four specific bacteria degraded mannan into mannose, consequently enhancing the mannan-dependent biosynthesis of O-antigen and lipopolysaccharide. Correlation analysis confirmed that in infants with AD, the abundance of Escherichia coli under high AA concentrations was positively correlated with some microbial pathways (eg, 'GDP-mannose-derived O-antigen and lipopolysaccharide biosynthesis'). These findings are consistent with those of the animal studies. Additionally, AA, but not EPA, disrupted the ratio of CD4/CD8 cells, increased skin lesion area and enhanced the proportion of peripheral Th2 cells. It also promoted IgE secretion and the biosynthesis of prostaglandins and leukotrienes in BALB/c mice fed AA following ovalbumin immunostimulation. Moreover, AA significantly increased IL-4 secretion in HaCaT cells costimulated with TNF-α and INF-γ.

CONCLUSIONS: This study demonstrates that AA is intimately linked to the onset of AD via gut dysbiosis.}, } @article {pmid39084575, year = {2024}, author = {Yadav, A and Shinde, PB and Mohan, H and Dhar, MS and Ponnusamy, K and Marwal, R and Radhakrishnan, VS and Goyal, S and Kedia, S and Ahuja, V and Sharma, KK}, title = {Gut colonization with antibiotic-resistant Escherichia coli pathobionts leads to disease severity in ulcerative colitis.}, journal = {International journal of antimicrobial agents}, volume = {64}, number = {4}, pages = {107289}, doi = {10.1016/j.ijantimicag.2024.107289}, pmid = {39084575}, issn = {1872-7913}, mesh = {Humans ; *Colitis, Ulcerative/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Escherichia coli/genetics/drug effects/pathogenicity ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Male ; Escherichia coli Infections/microbiology ; Adult ; Female ; Virulence Factors/genetics ; Microbial Sensitivity Tests ; Middle Aged ; Severity of Illness Index ; Metagenomics ; }, abstract = {BACKGROUND: Escherichia coli is a Gram-negative commensal of human gut. Surprisingly, the role of E. coli in the pathogenesis of ulcerative colitis (UC) has not been explored until now.

METHODS: Human gut microbiota composition and meta-gut resistome were evaluated using metagenomics. Antibiotic susceptibility of E. coli isolates against different class of antibiotics was investigated. Further, the genome sequence analysis of E. coli isolates was performed to gain insight into the antimicrobial resistance (AMR) mechanism and virulence factors. Gut proteome of UC and non-UC was examined to understand the effect of resistant bacteria on host physiology.

RESULTS: In UC patients, meta-gut resistome was found to be dominated by AMR genes (829) compared to healthy controls (HC) [518]. The metagenome study revealed a higher prevalence of AMR genes in the rural population (378 in HC; 607 in UC) compared to the urban (340 in HC; 578 in UC). Approximately, 40% of all E. coli isolates were multi-drug resistant (MDR), with higher prevalence in UC (43.75%) compared to HC (33.33%). Up-regulated expression of antimicrobial human proteins (lactotransferrin, azurocidin, cathepsin G, neutrophil elastase, and neutrophil defensin 3) and inflammatory mediator (Protein S100-A9 and Protein S100-A8) suggest microbial infection in UC gut.

CONCLUSIONS: In addition to the conventional culturomics method, a multi-omics strategy provides deeper insights into the disease etiology, emergence of MDR pathobionts, and their roles in the disruption of the healthy gut environment in UC patients.}, } @article {pmid39084558, year = {2024}, author = {Rodríguez-Fuentes, ME and Pérez-Sayáns, M and Barbeito-Castiñeiras, G and Molares-Vila, A and Prado-Pena, IB and Camolesi, GCV and López-López, R}, title = {Oral specimens as a tool for accurate metagenomic analysis: A pilot study.}, journal = {Journal of stomatology, oral and maxillofacial surgery}, volume = {125}, number = {5S2}, pages = {101991}, doi = {10.1016/j.jormas.2024.101991}, pmid = {39084558}, issn = {2468-7855}, mesh = {Humans ; Pilot Projects ; Adult ; Cross-Sectional Studies ; *Saliva/microbiology ; Male ; Female ; *Microbiota ; *Mouth Mucosa/microbiology/pathology ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics/analysis ; Mouth/microbiology ; Young Adult ; Biopsy ; DNA, Bacterial/analysis/genetics ; }, abstract = {OBJECTIVES: Acute oral mucosal damage, as well as other inflammatory processes seem to be related to dysbiosis of the oral microbiome. The need to study changes in the oral microbiome led us to hypothesize what type of sample would provide the most representative picture of the entire human oral microbiome.

MATERIALS AND METHODS: An observational, and cross-sectional study was carried out. Six healthy adult participants provided 3 different sample types each, that included saliva, oral rinse and mucosal biopsy tissue. We performed 16S rRNA sequencing of the V3-V4 region of the 18 samples using Illumina MiSeq technology.

RESULTS: Participants were 27 ± 6,3 years old. Bacterial alpha diversity was higher in oral rinse samples compared to whole unstimulated saliva and oral mucosa tissue (p = 0,005). However, saliva specimens showed a 56 % relative abundance of identified species followed by a 30 % in oral rinse and only 1 % in tissue samples.

CONCLUSIONS: This study found differences on oral microbiome composition for each type of sample. Oral rinse should be chosen when higher alpha diversity is needed, whereas whole unstimulated saliva should be more appropriate for larger amount of bacterial DNA.

CLINICAL RELEVANCE: The results obtained demonstrate the importance of a correct choice of the optimal type of oral sample for microbiome studies due to the differences found in its composition.}, } @article {pmid39084550, year = {2024}, author = {Kwon, M and Nilufar Zakhidovna, R and Boymaxmat Abdiazizovich, K and Jung, C and Kil, EJ}, title = {First metagenomic analysis of virome in Uzbekistan honey bee (Apis mellifera): Investigating basic information on honey bee viruses.}, journal = {Journal of invertebrate pathology}, volume = {206}, number = {}, pages = {108171}, doi = {10.1016/j.jip.2024.108171}, pmid = {39084550}, issn = {1096-0805}, mesh = {Bees/virology ; Animals ; *Virome ; Uzbekistan ; *Insect Viruses/genetics/classification/isolation & purification ; Metagenomics ; }, abstract = {Honey bees are economically important insects. However, they face multiple biotic and abiotic stresses, such as diseases, pesticides, climate change, and pests, which cause the loss of honey bee colonies worldwide. Among these factors, viruses have been identified as the major cause of colony loss. Research on honey bee viruses in Uzbekistan is limited. This study investigated the viruses affecting honey bees in Uzbekistan. Virome analysis was conducted for each sample using high-throughput sequencing and bioinformatics. Nine honey bee viruses have been identified: the acute bee paralysis virus, aphid lethal paralysis virus, Apis rhabdovirus 1 and 2, black queen cell virus, deformed wing virus, Lake Sinai virus 10, sacbrood virus, and Hubei partiti-like virus 34. Additionally, 15 plant viruses were identified, 7 of which were novel. This study is the first virome analysis of Uzbekistan honey bees and provides a foundation for understanding the viruses affecting honey bees and plants in Uzbekistan.}, } @article {pmid39084364, year = {2024}, author = {Kolenc, Ž and Kovač Viršek, M and Klančnik, A and Janecko, N}, title = {Microbial communities on microplastics from seawater and mussels: Insights from the northern Adriatic Sea.}, journal = {The Science of the total environment}, volume = {949}, number = {}, pages = {175130}, doi = {10.1016/j.scitotenv.2024.175130}, pmid = {39084364}, issn = {1879-1026}, mesh = {Animals ; *Seawater/microbiology ; *Microbiota ; *Water Pollutants, Chemical/analysis ; Slovenia ; *Microplastics/analysis ; *Environmental Monitoring ; Mytilus/microbiology ; Bacteria/classification/isolation & purification ; }, abstract = {Microplastics, synthetic solid particles of different sizes (< 5 mm), pose a major challenge to marine ecosystems. Introducing microplastics into the marine environment leads to the formation of complex microbial communities, a topic of growing interest in environmental research. For this study, we selected an area in the northern Adriatic Sea, less affected by human activities, to understand how pristine environmental conditions influence microbial colonization of microplastics. Samples of coastal seawater and Mediterranean mussels (Mytilus galloprovincialis) were collected in a mussel farm near Debeli rtič of the Slovenian coast. Microplastics were isolated, visually and chemically analyzed and DNA was extracted for metagenomics. In the marine water column, 12.7 microplastics per m[3] water column and 0.58 microplastics per individual mussel were found. Sufficient DNA was available to analyze six particles, five originating from seawater, and one from a mussel. This was the first-ever sequenced microplastic particle from a mussel. Genera of Pseudomonas and Serratia were identified in all samples. In one of the samples, the most abundant was a marine genus Pseudoalteromonas, while in another sample Campylobacter was present with >30 % abundance. The microbiomes of the mussel- and seawater-isolated particles were similar, suggesting a common microbial colonization pattern, which may have implications for the transfer of microplastic-associated microbes, including potential pathogens, through the food web to the consumers. Microplastic pollution is a complex issue requiring further research, especially regarding microbial biofilms, pathogen colonization and the potential of pathogen transmission via microplastic particles. Our findings enhance the understanding of microplastic pollution in the Adriatic Sea and stress the necessity for comprehensive strategies to mitigate the impact on marine ecosystems.}, } @article {pmid39082797, year = {2024}, author = {Roager, L and Kempen, PJ and Bentzon-Tilia, M and Sonnenschein, EC and Gram, L}, title = {Impact of host species on assembly, composition, and functional profiles of phycosphere microbiomes.}, journal = {mSystems}, volume = {9}, number = {8}, pages = {e0058324}, pmid = {39082797}, issn = {2379-5077}, support = {NNF20OC0064249,NNF19OC0055625//Novo Nordisk Fonden (NNF)/ ; }, mesh = {*Microbiota/physiology ; *Diatoms ; *Microalgae ; *RNA, Ribosomal, 16S/genetics ; *Haptophyta ; Chlorophyta/microbiology ; Seawater/microbiology ; }, abstract = {UNLABELLED: Microalgal microbiomes play vital roles in the growth and health of their host, however, their composition and functions remain only partially characterized, especially across microalgal phyla. In this study, a natural seawater microbiome was introduced to three distinct, axenic species of microalgae, the haptophyte Isochrysis galbana, the chlorophyte Tetraselmis suecica, and the diatom Conticribra weissflogii (previously Thalassiosira), and its divergence and assembly under constant illumination was monitored over 49 days using 16S rRNA amplicon and metagenomic analyses. The microbiomes had a high degree of host specificity in terms of taxonomic composition and potential functions, including CAZymes profiles. Rhodobacteraceae and Flavobacteriaceae families were abundant across all microalgal hosts, but I. galbana microbiomes diverged further from T. suecica and C. weissflogii microbiomes. I. galbana microbiomes had a much higher relative abundance of Flavobacteriaceae, whereas the two other algal microbiomes had higher relative abundances of Rhodobacteraceae. This could be due to the bacterivorous mixotrophic nature of I. galbana affecting the carbohydrate composition available to the microbiomes, which was supported by the CAZymes profile of I. galbana microbiomes diverging further from those of T. suecica and C. weissflogii microbiomes. Finally, the presence of denitrification and other anaerobic pathways was found exclusively in the microbiomes of C. weissflogii, which we speculate could be a result of anoxic microenvironments forming in aggregates formed by this diatom during the experiment. These results underline the significant role of the microalgal host species on microbiome composition and functional profiles along with other factors, such as the trophic mode of the microalgal host.

IMPORTANCE: As the main primary producers of the oceans, microalgae serve as cornerstones of the ecosystems they are part of. Additionally, they are increasingly used for biotechnological purposes such as the production of nutraceuticals, pigments, and antioxidants. Since the bacterial microbiomes of microalgae can affect their hosts in beneficial and detrimental ways, understanding these microbiomes is crucial to both the ecological and applied roles of microalgae. The present study advances the understanding of microalgal microbiome assembly, composition, and functionality across microalgal phyla, which may inform the modeling and engineering of microalgal microbiomes for biotechnological purposes.}, } @article {pmid39082382, year = {2024}, author = {Vidal-Villarejo, M and Dößelmann, B and Kogler, B and Hammerschmidt, M and Oppliger, B and Oppliger, H and Schmid, K}, title = {Regional diversity and leaf microbiome interactions of the fungal maize pathogen Exserohilum turcicum in Switzerland: A metagenomic analysis.}, journal = {Molecular ecology}, volume = {33}, number = {17}, pages = {e17482}, doi = {10.1111/mec.17482}, pmid = {39082382}, issn = {1365-294X}, support = {SCHM 1354-11/1//Deutsche Forschungsgemeinschaft/ ; 031B0731A//Bundesministerium für Bildung und Forschung/ ; PGRL-NN-0061//Swiss National Action Plan NAP-PGREL/ ; }, mesh = {*Zea mays/microbiology ; Switzerland ; *Ascomycota/genetics ; *Plant Leaves/microbiology ; *Plant Diseases/microbiology ; *Microbiota/genetics ; *Metagenomics ; }, abstract = {The spread and adaptation of fungal plant pathogens in agroecosystems are facilitated by environmental homogeneity. Metagenomic sequencing of infected tissues allowed us to monitor eco-evolutionary dynamics and interactions between host, pathogen and plant microbiome. Exserohilum turcicum, the causal agent of northern corn leaf blight (NCLB) in maize, is distributed in multiple clonal lineages throughout Europe. To characterize regional pathogen diversity, we conducted metagenomic DNA sequencing on 241 infected leaf samples from the highly susceptible Swiss maize landrace Rheintaler Ribelmais, collected over 3 years (2016-2018) from an average of 14 agricultural farms within the Swiss Rhine Valley. All major European clonal lineages of E. turcicum were identified. Lineages differ by their mating types which indicates potential for sexual recombination and rapid evolution of new pathogen strains, although we found no evidence of recent recombination. The associated eukaryotic and prokaryotic leaf microbiome exhibited variation in taxonomic diversity between years and locations and is likely influenced by local weather conditions. A network analysis revealed distinct clusters of eukaryotic and prokaryotic taxa that correlates with the frequency of E. turcicum sequencing reads, suggesting causal interactions. Notably, the yeast genus Metschnikowia exhibited a strongly negative association with E. turcicum, supporting its known potential as biological control agent against fungal pathogens. Our findings show that metagenomic sequencing is a useful tool for analysing the role of environmental factors and potential pathogen-microbiome interactions in shaping pathogen dynamics and evolution, suggesting their potential for effective pathogen management strategies.}, } @article {pmid39080854, year = {2024}, author = {Suárez-Moo, P and Haro-Moreno, JM and Rodriguez-Valera, F}, title = {Microdiversity in marine pelagic ammonia-oxidizing archaeal populations in a Mediterranean long-read metagenome.}, journal = {Environmental microbiology}, volume = {26}, number = {8}, pages = {e16684}, doi = {10.1111/1462-2920.16684}, pmid = {39080854}, issn = {1462-2920}, support = {PID2020-118052GB-I00//Ministerio de Economía, Industria y Competitividad/ ; }, mesh = {Mediterranean Sea ; *Archaea/genetics/metabolism/classification ; *Ammonia/metabolism ; *Metagenome ; *Oxidation-Reduction ; *Genome, Archaeal ; *Seawater/microbiology ; Metagenomics ; Phylogeny ; Genetic Variation ; Genomic Islands ; Biodiversity ; }, abstract = {The knowledge of the different population-level processes operating within a species, and the genetic variability of the individual prokaryotic genomes, is key to understanding the adaptability of microbial populations. Here, we characterized the flexible genome of ammonia-oxidizing archaeal (AOA) populations using a metagenomic recruitment approach and long-read (PacBio HiFi) metagenomic sequencing. In the lower photic zone of the western Mediterranean Sea (75 m deep), the genomes Nitrosopelagicus brevis CN25 and Nitrosopumilus catalinensis SPOT1 had the highest recruitment values among available complete AOA genomes. They were used to analyse the diversity of flexible genes (variable from strain to strain) by examining the long-reads located within the flexible genomic islands (fGIs) identified by their under-recruitment. Both AOA genomes had a large fGI involved in the glycosylation of exposed structures, highly variable, and rich in glycosyltransferases. N. brevis had two fGIs related to the transport of phosphorus and ammonium respectively. N. catalinensis had fGIs involved in phosphorus transportation and metal uptake. A fGI5 previously reported as 'unassigned function' in N. brevis could be associated with defense. These findings demonstrate that the microdiversity of marine microbe populations, including AOA, can be effectively characterized using an approach that incorporates third-generation sequencing metagenomics.}, } @article {pmid39080826, year = {2024}, author = {Lee, JY and Choi, M and Song, MJ and Kim, DD and Yun, T and Chang, J and Ho, A and Myung, J and Yoon, S}, title = {Selective Enrichment of Methylococcaceae versus Methylocystaceae Methanotrophs via Control of Methane Feeding Schemes.}, journal = {Environmental science & technology}, volume = {58}, number = {32}, pages = {14237-14248}, doi = {10.1021/acs.est.4c02655}, pmid = {39080826}, issn = {1520-5851}, mesh = {*Methane/metabolism ; *Methylococcaceae/metabolism ; *Methylocystaceae/metabolism ; Soil Microbiology ; Microbiota ; }, abstract = {Methanotrophs are crucial in keeping environmental CH4 emissions in check. However, the contributions of different groups of methanotrophs at terrestrial CH4-oxidation hotspots, such as the oxic-anoxic interface of rice paddies, have shown considerable inconsistency across observations. To address the knowledge gap regarding this inconsistency, methanotrophic microbiomes were enriched from paddy soils in well-mixed CH4-fed batch reactors under six different incubation conditions, prepared as combinations of two CH4 mixing ratios (0.5 and 10%) and three supplemented Cu[2+] concentrations (0, 2, and 10 μM). Monitoring of temporal community shifts in these cultures revealed a dominance of Methylocystis spp. in all 0.5%-CH4 cultures, while methanotrophs affiliated to Gammaproteobacteria dominated the 10%-CH4 cultures that were less consistent both temporally and across conditions. The shotgun metagenome analyses of the 0.5%-CH4 cultures corroborated the Methylocystis dominance and, interestingly, showed that copper deficiency did not select for mmoXYZ-possessing methanotrophs. Instead, a mbn cluster, accounting for approximately 5% of the Methylocystis population, was identified, suggesting the ecological significance of methanobactin in Cu-deficient methanotrophy. These findings underscore the important role of Methylocystis spp. in mitigating emissions from terrestrial CH4 hotspots and suggest the feasibility of directed enrichment and/or isolation of Methylocystis spp. for utilization in, for example, methanobactin and polyhydroxybutyrate production.}, } @article {pmid39080726, year = {2024}, author = {Li, X and Liu, S and Wu, H and Li, B and Li, Y and Li, R and Tang, D and Zhang, H}, title = {Viral metagenomics combined with non-targeted serum metabolomics reveals the role of enteroviruses in a mouse model of coronary heart disease.}, journal = {Virology journal}, volume = {21}, number = {1}, pages = {169}, pmid = {39080726}, issn = {1743-422X}, support = {NO. CI2021A00604//the Science and Technology Innovation Project of China Academy of Chinese Medical Sciences/ ; NO. CI2021A00604//the Science and Technology Innovation Project of China Academy of Chinese Medical Sciences/ ; NO. CI2021A00604//the Science and Technology Innovation Project of China Academy of Chinese Medical Sciences/ ; NO. CI2021A00604//the Science and Technology Innovation Project of China Academy of Chinese Medical Sciences/ ; NO. CI2021A00604//the Science and Technology Innovation Project of China Academy of Chinese Medical Sciences/ ; NO. CI2021A00604//the Science and Technology Innovation Project of China Academy of Chinese Medical Sciences/ ; NO. CI2021A00604//the Science and Technology Innovation Project of China Academy of Chinese Medical Sciences/ ; NO. 81973722//National Nature Science Foundation of China/ ; NO. 81973722//National Nature Science Foundation of China/ ; NO. 81973722//National Nature Science Foundation of China/ ; 82374182//National Nature Science Foundation of China/ ; NO. 81973722//National Nature Science Foundation of China/ ; NO. 81973722//National Nature Science Foundation of China/ ; NO. 81973722//National Nature Science Foundation of China/ ; NO. 81973722//National Nature Science Foundation of China/ ; }, mesh = {Animals ; *Disease Models, Animal ; Mice ; *Enterovirus/genetics/isolation & purification ; *Metagenomics ; *Metabolomics ; *Diet, High-Fat/adverse effects ; *Coronary Disease/virology/blood ; Male ; Mice, Inbred C57BL ; Enterovirus Infections/virology/blood ; Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: Coronary heart disease (CHD) is a common cardiovascular disease that is associated with altered gut microbiota. Enteroviruses, an essential component of the gut microbiome, may play an important role in disease progression. However, the relationship between enteroviruses and CHD remains unclear. The development of high-throughput sequencing technologies has facilitated research on the interconnections between viruses and disease-related metabolites.

METHODS AND RESULTS: Mice were fed a high-fat diet (CHD group) or chow diet (Sham group) for 12 weeks, and ligation of the left anterior descending coronary artery was performed at the end of week 8. After 4 weeks, all animals were euthanised. Subsequently, the animals were evaluated for basic haemato-biochemical parameters and cardiac function, and aorta staining was performed. Based on enteroviral metagenomics and serum UPLC-MS/MS metabolomics analyses, we evaluated the association between enteroviral groups and serum metabolites of CHD mouse model. A high-fat diet and coronary ligation enabled the establishment of the CHD mouse model. Notably, the enterovirus spectrum of the sham group was significantly different from that of the CHD group, with 24 viral communities of different family and species classification, such as Tsarbombavirus, Mingyongvirus, Claudivirus, and Firehammervirus, exhibiting significant differences. In addition, 731 Differential metabolites were detected in the serum of both groups of mice. Correlation network analysis revealed a close relationship between various metabolites related to lipid metabolism and different viruses, including Tsarbombavirus, Mingyongvirus, Claudivirus, and Firehammervirus.

CONCLUSIONS: An animal model of CHD, characterised by lipid disturbance and myocardial ischaemia, was established using a high-fat diet and ligation of the left anterior descending branch of the coronary artery. Tsarbombavirus, Firehammervirus, Mingyongvirus, and Claudivirus were associated with metabolites in the lipid metabolism pathway. The results indicate that Tsarbombavirus may be the main genus interacting with CHD-related metabolites in mice. Conclusively, the findings of our study provide novel insights into the potential relationship enterovirus groups and metabolites associated with CHD.}, } @article {pmid39080019, year = {2024}, author = {Gao, FZ and Yao, KS and Tan, LJ and He, LY and Liu, YS and Ying, GG}, title = {Single-/Co-Driving of Tetracycline, Triclocarban and Zinc on Microbial Community, Resistome and Function in the Cyanobacteria-Blooming Freshwater Ecosystem.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {113}, number = {2}, pages = {19}, pmid = {39080019}, issn = {1432-0800}, support = {42030703//National Natural Science Foundation of China/ ; U22A20604//National Natural Science Foundation of China/ ; U1701242//National Natural Science Foundation of China/ ; 2022M711215//Chinese Postdoctoral Science Foundation/ ; }, mesh = {*Cyanobacteria/drug effects/genetics ; *Zinc/toxicity ; *Carbanilides/toxicity ; *Fresh Water/microbiology ; *Water Pollutants, Chemical/toxicity ; *Ecosystem ; Anti-Bacterial Agents/toxicity/pharmacology ; Tetracycline/pharmacology/toxicity ; Microbiota/drug effects ; }, abstract = {Environmental concentrations of antimicrobials can inhibit Cyanobacteria, but little is known about their effects on Cyanobacteria-blooming freshwater ecosystem. Here, a 21 days' outdoor freshwater mesocosm experiment was established to study effects of single and combined tetracycline, triclocarban and zinc at environmental concentrations on microbial community, microbial function and antimicrobial resistance using amplicon- and metagenomic-based methods. Results showed that three chemicals reshaped the microbial community with magnified effects by chemical combinations. Relative abundance of Cyanobacteria was decreased in all chemical groups, especially from 74.5 to 0.9% in combination of three chemicals. Microbial community networks were more simplified after exposure. Proteobacteria and Bacteroidetes predominated in Cyanobacteria-degraded ecosystems, and their relative abundances were significantly correlated with antibiotic resistome, suggesting that they might host antibiotic resistance genes. Notably, relative abundance (copy per 16 S rRNA gene) of total antibiotic resistome reached five to nine folds higher than the initial abundance in chemical-combined groups. The affected antibiotic resistance genes referred to a wide range of antibiotic classes. However, weak effects were detected on biocide/metal resistance and microbial virulence. Three chemicals posed complicated effects on microbial function, some of which had consistent variations across the groups, while some varied greatly in chemical groups. The findings highlight sensitivity of Cyanobacteria-blooming ecosystem to antimicrobials.}, } @article {pmid39079980, year = {2024}, author = {Chen, YJ and Ho, HJ and Tseng, CH and Chen, YF and Wang, ST and Shieh, JJ and Wu, CY}, title = {Short-chain fatty acids ameliorate imiquimod-induced skin thickening and IL-17 levels and alter gut microbiota in mice: a metagenomic association analysis.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {17495}, pmid = {39079980}, issn = {2045-2322}, support = {NSTC 108-2314-B-075A-008//National Science and Technology Council/ ; NSTC 110-2314-B-075A-008//National Science and Technology Council/ ; TCVGH-1106801C//Taichung Veterans General Hospital/ ; TCVGH-1116801C//Taichung Veterans General Hospital/ ; TCVGH-1116802C//Taichung Veterans General Hospital/ ; }, mesh = {Animals ; *Imiquimod/adverse effects ; *Gastrointestinal Microbiome/drug effects ; *Interleukin-17/metabolism ; *Fatty Acids, Volatile/metabolism ; Mice ; *Skin/drug effects/pathology/microbiology/metabolism ; *Mice, Inbred C57BL ; Metagenomics/methods ; Psoriasis/drug therapy/chemically induced/microbiology ; Metagenome ; Feces/microbiology ; }, abstract = {Short-chain fatty acids (SCFAs) have been proposed to have anti-inflammatory effects and improve immune homeostasis. We aimed to examine the effects of SCFAs on skin phenotype, systemic inflammation, and gut microbiota in mice with psoriasis-like inflammation. Imiquimod (IMQ)-treated C57BL/6 mice served as the study model. We conducted a metagenomic association study of IMQ-mice treated with SCFAs or anti-IL-17 antibody using whole-genome shotgun sequencing. The associations among SCFA supplements, skin thickness, circulating inflammatory profiles, and fecal microbiota profiles were investigated. The microbiome study was performed using pipelines for phylogenetic analysis, functional gene analysis, and pathway analysis. In IMQ-treated mice, there were increases in skin thickness and splenic weight, as well as unique fecal microbial profiles. SCFAs ameliorated IMQ-induced skin thickening, splenic weight gain, and serum IL-17F levels, with results that were comparable with those receiving anti-IL-17 treatment. IMQ-treated mice receiving SCFAs had greater microbial diversity than mice treated with IMQ alone. SCFAs and anti-IL17 treatment were associated with alteration of gut microbiota, with increased prevalences of Oscillospiraceae and Lachnopiraceae and decreased prevalences of Muribaculaceae and Bacteroides, which have been predicted to be associated with increased glycan degradation, phenylalanine metabolism, and xylene degradation. SCFAs may mitigate IMQ-induced skin thickening and IL-17F levels and alter fecal microbiota profiles in IMQ-treated mice.}, } @article {pmid39078906, year = {2024}, author = {Fang, Q and Xie, J and Yin, S and Yin, H and Zhou, D}, title = {Analysis of blood microbiota in patients with adult-onset Still's disease and sepsis by metagenomic next-generation sequencing.}, journal = {British journal of hospital medicine (London, England : 2005)}, volume = {85}, number = {7}, pages = {1-16}, doi = {10.12968/hmed.2024.0121}, pmid = {39078906}, issn = {1750-8460}, mesh = {Humans ; *Sepsis/microbiology/blood/diagnosis ; Male ; Female ; *High-Throughput Nucleotide Sequencing ; *Still's Disease, Adult-Onset/blood/microbiology/diagnosis ; Adult ; Middle Aged ; *Metagenomics/methods ; Microbiota/genetics ; Diagnosis, Differential ; Biomarkers/blood ; }, abstract = {Aims/Background Adult-onset Still's disease (AOSD) shares similar clinical symptoms with sepsis. Thus, differentiating between AOSD and sepsis presents a great challenge while making diagnosis. This study aimed to analyse the changes in blood microbiota related to AOSD and sepsis using metagenomic next-generation sequencing (mNGS), identify potential biomarkers that distinguish AOSD from sepsis, and explore the diagnostic value of mNGS in differentiation between these two pathological conditions. Methods Clinical data of four AOSD patients and four sepsis patients treated in the Department of Rheumatology and Immunology, The Affiliated Hospital of Xuzhou Medical University between October 2021 and February 2022 were collected. The mNGS diagnostic records of these patients were analysed for microbial correlations in terms of species taxonomic structure and beta diversity by comparing blood microbiota between AOSD and sepsis. The biomarkers with the strongest capability in distinguishing the subgroups were screened using a random forest algorithm. Results There was no statistically significant differences between AOSD patients and sepsis controls in terms of gender and age (p > 0.05). A total of 91 operational taxonomic units (OTUs) were obtained. At the level of phylum, Proteobacteria, Ascomycota and Basidiomycota were present in high abundances in both groups (79.76%, 14.18% and 3.30% vs 54.03%, 32.77% and 5.81%). At the genus level, the abundances of Parainfluenzae, Aspergillus and Ralstonia were the top three highest in the AOSD group (73.88%, 10.92% and 5.48%), while Ralstonia, Aspergillus and Malassezia were ranked as the top three in the sepsis group in term of abundance (48.69%, 27.36% and 5.52%). In beta-diversity analysis, there were advances shown in visual principal coordinates analysis (PCoA) and non-metric multidimensional scaling (NMDS) between the AOSD group and sepsis group (p < 0.05), with little significant differences in the analysis of similarities (Anosim) (p > 0.05). Linear discriminant analysis effect size (LEfSe) showed that Mucoromycota, Saccharomycetes, Moraxellales, Mucorales, Xanthomonadales, Saccharomycetales, Acinetobacter, Stenotrophomonas, Yarrowia, Apophysomyces, Acinetobacter johnson, Yarrowia lipolytica, Apophysomyces variabilis and Stenotrophomonas maltophilia were more enriched in sepsis group (p < 0.05). The top five variables with the strongest capability in distinguishing between AOSD and sepsis were Acinetobacter johnsonii, Apophysomyces variabilis, Propionibacterium acnes, Stenotrophomonas maltophilia and Yarrowia lipolytica. Conclusion The blood microorganisms in AOSD were different from sepsis, and mNGS was potential to distinguish between AOSD and sepsis.}, } @article {pmid39078158, year = {2024}, author = {Jin, D-M and Morton, JT and Bonneau, R}, title = {Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases.}, journal = {mSystems}, volume = {9}, number = {8}, pages = {e0029524}, pmid = {39078158}, issn = {2379-5077}, support = {R01 AI130945/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Diabetes Mellitus, Type 2/microbiology ; Machine Learning ; Crohn Disease/microbiology ; Colorectal Neoplasms/microbiology ; Metagenomics/methods ; Colitis, Ulcerative/microbiology ; Parkinson Disease/microbiology ; Schizophrenia/microbiology ; Alzheimer Disease/microbiology ; }, abstract = {UNLABELLED: Microbiome studies have revealed gut microbiota's potential impact on complex diseases. However, many studies often focus on one disease per cohort. We developed a meta-analysis workflow for gut microbiome profiles and analyzed shotgun metagenomic data covering 11 diseases. Using interpretable machine learning and differential abundance analysis, our findings reinforce the generalization of binary classifiers for Crohn's disease (CD) and colorectal cancer (CRC) to hold-out cohorts and highlight the key microbes driving these classifications. We identified high microbial similarity in disease pairs like CD vs ulcerative colitis (UC), CD vs CRC, Parkinson's disease vs type 2 diabetes (T2D), and schizophrenia vs T2D. We also found strong inverse correlations in Alzheimer's disease vs CD and UC. These findings, detected by our pipeline, provide valuable insights into these diseases.

IMPORTANCE: Assessing disease similarity is an essential initial step preceding a disease-based approach for drug repositioning. Our study provides a modest first step in underscoring the potential of integrating microbiome insights into the disease similarity assessment. Recent microbiome research has predominantly focused on analyzing individual diseases to understand their unique characteristics, which by design excludes comorbidities in individuals. We analyzed shotgun metagenomic data from existing studies and identified previously unknown similarities between diseases. Our research represents a pioneering effort that utilizes both interpretable machine learning and differential abundance analysis to assess microbial similarity between diseases.}, } @article {pmid39078126, year = {2024}, author = {Ai, C and Cui, P and Liu, C and Wu, J and Xu, Y and Liang, X and Yang, Q and Tang, X and Zhou, S and Liao, H and Friman, V-P}, title = {Viral and thermal lysis facilitates transmission of antibiotic resistance genes during composting.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {8}, pages = {e0069524}, pmid = {39078126}, issn = {1098-5336}, mesh = {*Composting ; Gene Transfer, Horizontal ; Manure/microbiology/virology ; Soil Microbiology ; Bacteria/genetics/drug effects ; Animals ; Metagenome ; Cattle ; Hot Temperature ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; Microbiota ; Bacteriophages/genetics/physiology ; }, abstract = {UNLABELLED: While the distribution of extracellular ARGs (eARGs) in the environment has been widely reported, the factors governing their release remain poorly understood. Here, we combined multi-omics and direct experimentation to test whether the release and transmission of eARGs are associated with viral lysis and heat during cow manure composting. Our results reveal that the proportion of eARGs increased 2.7-fold during composting, despite a significant and concomitant reduction in intracellular ARG abundances. This relative increase of eARGs was driven by composting temperature and viral lysis of ARG-carrying bacteria based on metagenome-assembled genome (MAG) analysis. Notably, thermal lysis of mesophilic bacteria carrying ARGs was a key factor in releasing eARGs at the thermophilic phase, while viral lysis played a relatively stronger role during the non-thermal phase of composting. Furthermore, MAG-based tracking of ARGs in combination with direct transformation experiments demonstrated that eARGs released during composting pose a potential transmission risk. Our study provides bioinformatic and experimental evidence of the undiscovered role of temperature and viral lysis in co-driving the spread of ARGs in compost microbiomes via the horizontal transfer of environmentally released DNA.

IMPORTANCE: The spread of antibiotic resistance genes (ARGs) is a critical global health concern. Understanding the factors influencing the release of extracellular ARGs (eARGs) is essential for developing effective strategies. In this study, we investigated the association between viral lysis, heat, and eARG release during composting. Our findings revealed a substantial increase in eARGs despite reduced intracellular ARG abundance. Composting temperature and viral lysis were identified as key drivers, with thermal lysis predominant during the thermophilic phase and viral lysis during non-thermal phases. Moreover, eARGs released during composting posed a transmission risk through horizontal gene transfer. This study highlights the significance of temperature and phage lysis in ARG spread, providing valuable insights for mitigating antibiotic resistance threats.}, } @article {pmid39078043, year = {2024}, author = {Esparteiro, D and Fouquet, G and Courtois, A and Jedraszak, G and Marticho, L and Gourdel, M and Billon-Crossouard, S and Croyal, M and Naassila, M and Nguyen-Khac, E and Marcq, I}, title = {Serum bile acids profiles are altered without change of the gut microbiota composition following a seven-day prednisolone therapy in severe alcoholic hepatitis.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2382767}, pmid = {39078043}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Hepatitis, Alcoholic/drug therapy/blood ; Male ; *Feces/microbiology/chemistry ; *Bile Acids and Salts/blood/metabolism ; Middle Aged ; Female ; Retrospective Studies ; *Prednisolone/administration & dosage ; Adult ; Bacteria/classification/genetics/isolation & purification/drug effects ; Fatty Acids, Volatile/metabolism/blood ; Carrier Proteins/genetics/blood ; Acute-Phase Proteins/metabolism ; Membrane Glycoproteins/blood/genetics ; Aged ; Metagenomics ; }, abstract = {Severe Alcoholic Hepatitis (sAH) is an acute form of liver injury caused by chronic and heavy alcohol drinking. A one-month corticosteroids course is the only sAH reference treatment, and its interactions with the Gut Microbiota (GM), which is a key contributor to liver injury, remain unknown. To evaluate the evolution of the GM in sAH patients, we retrospectively investigated the composition of the GM of 27 sAH patients at the Amiens University Hospital before (D0) and after (D7) a 7-day corticotherapy course using fecal metagenomics sequencing. We also quantified fecal Short-Chain Fatty Acids (SCFA) and fecal and serum Bile Acids (BA), as well as serum Lipopolysaccharide-Binding Protein (LBP). Overall, the community and taxonomical analyses did not reveal any GM evolution between D0 and D7, nor did the SCFA profiles analysis. However, in serum but not fecal samples, the ratio of glyco-conjugated to tauro-conjugated BA was significantly reduced at D7, independently of the response to treatment, while two BA were enriched in non-responder patients. LBP concentration significantly diminished between D0 and D7, which may indicate an improvement of the gut barrier. The stability of the GM of sAH is interesting in the perspective of new treatments based on GM modulation.}, } @article {pmid39076360, year = {2024}, author = {Sandybayev, N and Beloussov, V and Strochkov, V and Solomadin, M and Granica, J and Yegorov, S}, title = {Metagenomic profiling of nasopharyngeal samples from adults with acute respiratory infection.}, journal = {Royal Society open science}, volume = {11}, number = {7}, pages = {240108}, pmid = {39076360}, issn = {2054-5703}, abstract = {Diagnosis of acute respiratory infections (ARIs) is challenging due to the broad diversity of potential microbial causes. We used metagenomic next-generation sequencing (mNGS) to analyze the nasopharyngeal virome of ARI patients, who had undergone testing with a clinical multiplex PCR panel (Amplisens ARVI-screen-FRT). We collected nasopharyngeal swabs from 49 outpatient adults, 32 of whom had ARI symptoms and were PCR-positive, and 4 asymptomatic controls in Kazakhstan during Spring 2021. We assessed the biodiversity of the mNGS-derived virome and concordance with PCR results. PCR identified common ARI viruses in 65% of the symptomatic cases. mNGS revealed viral taxa consisting of human, non-human eukaryotic and bacteriophage groups, comprising 15, 11 and 28 genera, respectively. Notable ARI-associated human viruses included rhinovirus (16.3%), betaherpesvirus 7 (14.3%) and Epstein-Barr virus (8.16%). The primary phage hosts were Streptococcus spp. (32.7%), Pseudomonas aeruginosa (24.5%) and Burkholderia spp. (20.4%). In total, 47% of ARIs were linked solely to bacterial pathogens, a third to viral-bacterial co-infections, and less than 10% to only viral infections by mNGS. PCR showed low concordance with mNGS, except for rhinovirus. These results underscore the importance of broad diagnostic methods and question the effectiveness of commonly used PCR panels in ARI diagnosis.}, } @article {pmid39075388, year = {2024}, author = {Bars-Cortina, D and Ramon, E and Rius-Sansalvador, B and Guinó, E and Garcia-Serrano, A and Mach, N and Khannous-Lleiffe, O and Saus, E and Gabaldón, T and Ibáñez-Sanz, G and Rodríguez-Alonso, L and Mata, A and García-Rodríguez, A and Obón-Santacana, M and Moreno, V}, title = {Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {730}, pmid = {39075388}, issn = {1471-2164}, support = {CD21/00094//Instituto de Salud Carlos III/ ; FI21/00056//Instituto de Salud Carlos III/ ; FI19/00221//Instituto de Salud Carlos III/ ; IMPACT Grant IMP/00019//Instituto de Salud Carlos III/ ; 874662//Horizon 2020/ ; ERC-2016-724173//Horizon 2020/ ; FPU2020-02907//Spanish Ministerio de Universidades/ ; PID2021-126067NB-I00//Spanish Ministry of Science and Innovation for grants/ ; PDC2022-133266-I00//Spanish Ministry of Science and Innovation/ ; SGR01551//Catalan Research Agency/ ; GBMF9742//Gordon and Betty Moore Foundation/ ; LCF/PR/HR21/00737//"La Caixa" foundation/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Metagenomics/methods ; Bacteria/genetics/classification ; Sequence Analysis, DNA/methods ; Male ; Metagenome ; Female ; }, abstract = {BACKGROUND: Gut dysbiosis has been associated with colorectal cancer (CRC), the third most prevalent cancer in the world. This study compares microbiota taxonomic and abundance results obtained by 16S rRNA gene sequencing (16S) and whole shotgun metagenomic sequencing to investigate their reliability for bacteria profiling. The experimental design included 156 human stool samples from healthy controls, advanced (high-risk) colorectal lesion patients (HRL), and CRC cases, with each sample sequenced using both 16S and shotgun methods. We thoroughly compared both sequencing technologies at the species, genus, and family annotation levels, the abundance differences in these taxa, sparsity, alpha and beta diversities, ability to train prediction models, and the similarity of the microbial signature derived from these models.

RESULTS: As expected, the results showed that 16S detects only part of the gut microbiota community revealed by shotgun, although some genera were only profiled by 16S. The 16S abundance data was sparser and exhibited lower alpha diversity. In lower taxonomic ranks, shotgun and 16S highly differed, partially due to a disagreement in reference databases. When considering only shared taxa, the abundance was positively correlated between the two strategies. We also found a moderate correlation between the shotgun and 16S alpha-diversity measures, as well as their PCoAs. Regarding the machine learning models, only some of the shotgun models showed some degree of predictive power in an independent test set, but we could not demonstrate a clear superiority of one technology over the other. Microbial signatures from both sequencing techniques revealed taxa previously associated with CRC development, e.g., Parvimonas micra.

CONCLUSIONS: Shotgun and 16S sequencing provide two different lenses to examine microbial communities. While we have demonstrated that they can unravel common patterns (including microbial signatures), shotgun often gives a more detailed snapshot than 16S, both in depth and breadth. Instead, 16S will tend to show only part of the picture, giving greater weight to dominant bacteria in a sample. Therefore, we recommend choosing one or another sequencing technique before launching a study. Specifically, shotgun sequencing is preferred for stool microbiome samples and in-depth analyses, while 16S is more suitable for tissue samples and studies with targeted aims.}, } @article {pmid39074770, year = {2024}, author = {Gao, T and Wang, Y and Lai, J and Wang, F and Yao, G and Bao, S and Liu, J and Wan, X and Chen, C and Zhang, Y and Jiang, H and Jiang, S and Han, P}, title = {Effects of nitrile compounds on the structure and function of soil microbial communities as revealed by metagenomes.}, journal = {Environmental research}, volume = {261}, number = {}, pages = {119700}, doi = {10.1016/j.envres.2024.119700}, pmid = {39074770}, issn = {1096-0953}, mesh = {*Soil Microbiology ; *Nitriles/toxicity ; *Soil Pollutants/toxicity ; *Metagenome/drug effects ; Microbiota/drug effects ; Bacteria/drug effects/genetics ; }, abstract = {The proliferation of nitrile mixtures has significantly exacerbated environmental pollution. This study employed metagenomic analysis to investigate the short-term effects of nitrile mixtures on soil microbial communities and their metabolic functions. It also examined the responses of indigenous microorganisms and their functional metabolic genes across various land use types to different nitrile stressors. The nitrile compound treatments in this study resulted in an increase in the abundance of Proteobacteria, Actinobacteria, and Firmicutes, while simultaneously reducing overall microbial diversity. The key genes involved in the denitrification process, namely, nirK, nosZ, and hao, were down-regulated, and NO3[-]-N, NO2[-]-N, and NH4[+]-N concentrations decreased by 7.7%-12.3%, 11.1%-21.3%, and 11.3%-30.9%, respectively. Notably, pond sludge samples exhibited a significant increase in the abundance of nitrogen fixation-related genes nifH, vnfK, vnfH, and vnfG following exposure to nitrile compounds. Furthermore, the fumarase gene fumD, which is responsible for catalyzing fumaric acid into malic acid in the tricarboxylic acid cycle, showed a substantial increase of 7.2-10.6-fold upon nitrile addition. Enzyme genes associated with the catechol pathway, including benB-xylY, dmpB, dmpC, dmpH, and mhpD, displayed increased abundance, whereas genes related to the benzoyl-coenzyme A pathway, such as bcrA, dch, had, oah, and gcdA, were notably reduced. In summary, complex nitrile compounds were found to significantly reduce the species diversity of soil microorganisms. Nitrile-tolerant microorganisms demonstrated the ability to degrade and adapt to nitrile pollutants by enhancing functional enzymes involved in the catechol pathway and fenugreek conversion pathway. This study offers insights into the specific responses of microorganisms to compound nitrile contamination, as well as valuable information for screening nitrile-degrading microorganisms and identifying nitrile metabolic enzymes.}, } @article {pmid39074691, year = {2024}, author = {Zhou, M and Liu, Z and Hu, B}, title = {Impact of arsenic and PAHs compound contamination on microorganisms in coking sites: From a community to individual perspective.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {360}, number = {}, pages = {124628}, doi = {10.1016/j.envpol.2024.124628}, pmid = {39074691}, issn = {1873-6424}, mesh = {*Polycyclic Aromatic Hydrocarbons/toxicity ; *Arsenic/toxicity ; *Soil Pollutants/toxicity ; *Soil Microbiology ; Coke ; Bacteria/drug effects/genetics ; Soil/chemistry ; Microbiota/drug effects ; }, abstract = {Arsenic (As) and polycyclic aromatic hydrocarbons (PAHs) are highly toxic, carcinogenic and teratogenic, and are commonly found in soils of industrial sites such as coking plants. They exert environmental stresses on soil microorganisms, but their compounding effects have not been systematically studied. Exploring the effects of compound contamination on microbial communities, species and genes is important for revealing the ecological damage caused by compound contamination and offering scientific insights into soil remediation strategies. In this study, we selected soil samples from 0 to 100 cm depth of a coking site with As, PAHs and compound contamination. We investigated the compound effects of As and PAHs on microbial communities by combining high-throughput sequencing, metagenomic sequencing and genome assembly. Compared with single contamination, compound contamination reduced the microbial community diversity by 10.68%-12.07% and reduced the community richness by 8.39%-18.61%. The compound contamination decreased 32.41%-46.02% of microbial PAHs metabolic gene abundance, 11.36%-19.25% of cell membrane transport gene abundance and 12.62%-57.77% of cell motility gene abundance. Xanthobacteraceae, the biomarker for compound contaminated soils, harbors arsenic reduction genes and PAHs degradation pathways of naphthalene, benzo [a]pyrene, fluorene, anthracene, and phenanthrene. Its broad metabolic capabilities, encompassing sulfur metabolism and quorum sensing, facilitate the acquisition of energy and nutrients, thereby conferring ecological niche advantages in compound contaminated environments. This study underscores the significant impacts of As and PAHs on the composition and function of microbial communities, thereby enriching our understanding of their combined effects and providing insights for the remediation of compound contaminated sites.}, } @article {pmid39073596, year = {2024}, author = {Shah, RR and Larrondo, J and Dawson, T and Mcmichael, A}, title = {Scalp microbiome: a guide to better understanding scalp diseases and treatments.}, journal = {Archives of dermatological research}, volume = {316}, number = {8}, pages = {495}, pmid = {39073596}, issn = {1432-069X}, support = {H17/01/a0/004//Agency for Science, Technology and Research/ ; }, mesh = {Humans ; *Microbiota/drug effects/immunology ; *Scalp/microbiology ; Scalp Dermatoses/microbiology/drug therapy/therapy ; Dysbiosis/microbiology/immunology ; Folliculitis/microbiology/diagnosis/drug therapy/therapy ; Psoriasis/microbiology/drug therapy/immunology/therapy ; Dermatitis, Seborrheic/microbiology/drug therapy/therapy ; Alopecia Areata/microbiology/immunology/therapy/drug therapy ; Dandruff/microbiology/drug therapy ; }, abstract = {The scalp microbiome represents an array of microorganisms important in maintaining scalp homeostasis and mediating inflammation. Scalp microbial dysregulation has been implicated in dermatologic conditions including alopecia areata (AA), dandruff/seborrheic dermatitis (D/SD), scalp psoriasis (SP) and folliculitis decalvans (FD). Understanding the impact of scalp microbial dysbiosis gives insight on disease pathophysiology and guides therapeutic decision making. Herein we review the scalp microbiome and its functional role in scalp conditions by analysis of metagenomic medical literature in alopecia, D/SD, SP, and other dermatologic disease.Increased abundance of Malassezia, Staphylococcus, and Brevibacterium was associated with SD compared to healthy controls. A higher proportion of Corynebacterium, actinobacteria, and firmicutes are present in AA patients, and lower proportions of Staphylococcus caprae are associated with worse clinical outcomes. Decreased prevalence of actinobacteria and Propionibacterium and increased firmicutes, staphylococcus, and streptococcus are associated with scalp psoriasis. Studies of central centrifugal cicatricial alopecia (CCCA) suggest scalp microbial composition contributes to CCCA's pro-inflammatory status. The most common organisms associated with FD include methicillin-resistant S. aureus and S. lugdunensis. Antifungals have been a mainstay treatment for these diseases, while other alternatives including coconut oils and shampoos with heat-killed probiotics have shown considerable potential efficacy by replenishing the scalp microbiome.}, } @article {pmid39069899, year = {2024}, author = {Ambat, A and Antony, L and Maji, A and Ghimire, S and Mattiello, S and Kashyap, PC and More, S and Sebastian, V and Scaria, J}, title = {Enhancing recovery from gut microbiome dysbiosis and alleviating DSS-induced colitis in mice with a consortium of rare short-chain fatty acid-producing bacteria.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2382324}, pmid = {39069899}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Fatty Acids, Volatile/metabolism ; Humans ; *Dysbiosis/microbiology ; Mice ; *Dextran Sulfate ; *Bacteria/classification/isolation & purification/genetics/metabolism ; *Colitis/microbiology/chemically induced ; Disease Models, Animal ; Mice, Inbred C57BL ; Microbial Consortia ; Male ; Female ; Colitis, Ulcerative/microbiology/metabolism ; Germ-Free Life ; }, abstract = {The human gut microbiota is a complex community comprising hundreds of species, with a few present in high abundance and the vast majority in low abundance. The biological functions and effects of these low-abundant species on their hosts are not yet fully understood. In this study, we assembled a bacterial consortium (SC-4) consisting of B. paravirosa, C. comes, M. indica, and A. butyriciproducens, which are low-abundant, short-chain fatty acid (SCFA)-producing bacteria isolated from healthy human gut, and tested its effect on host health using germ-free and human microbiota-associated colitis mouse models. The selection also favored these four bacteria being reduced in abundance in either Ulcerative Colitis (UC) or Crohn's disease (CD) metagenome samples. Our findings demonstrate that SC-4 can colonize germ-free (GF) mice, increasing mucin thickness by activating MUC-1 and MUC-2 genes, thereby protecting GF mice from Dextran Sodium Sulfate (DSS)-induced colitis. Moreover, SC-4 aided in the recovery of human microbiota-associated mice from DSS-induced colitis, and intriguingly, its administration enhanced the alpha diversity of the gut microbiome, shifting the community composition closer to control levels. The results showed enhanced phenotypes across all measures when the mice were supplemented with inulin as a dietary fiber source alongside SC-4 administration. We also showed a functional redundancy existing in the gut microbiome, resulting in the low abundant SCFA producers acting as a form of insurance, which in turn accelerates recovery from the dysbiotic state upon the administration of SC-4. SC-4 colonization also upregulated iNOS gene expression, further supporting its ability to produce an increasing number of goblet cells. Collectively, our results provide evidence that low-abundant SCFA-producing species in the gut may offer a novel therapeutic approach to IBD.}, } @article {pmid39069433, year = {2024}, author = {Tomiak, J and Stensvold, CR}, title = {Accelerating the paradigm shift in Blastocystis research.}, journal = {Trends in parasitology}, volume = {40}, number = {9}, pages = {775-776}, doi = {10.1016/j.pt.2024.07.006}, pmid = {39069433}, issn = {1471-5007}, mesh = {*Blastocystis/physiology ; *Blastocystis Infections/parasitology ; Humans ; Animals ; Gastrointestinal Microbiome/physiology ; }, abstract = {Blastocystis, once targeted as a harmful intestinal parasite, is now seen as potentially beneficial. Piperni et al. link its presence to improved gut health, higher microbial diversity, and favorable cardiometabolic outcomes, which suggests that Blastocystis might indicate a healthy diet and gut, possibly serving as a symbiont rather than a pathogen.}, } @article {pmid39069186, year = {2024}, author = {Zhu, S and Zhao, W and Sun, S and Yang, X and Mao, H and Sheng, L and Chen, Z}, title = {Community metagenomics reveals the processes of cadmium resistance regulated by microbial functions in soils with Oryza sativa root exudate input.}, journal = {The Science of the total environment}, volume = {949}, number = {}, pages = {175015}, doi = {10.1016/j.scitotenv.2024.175015}, pmid = {39069186}, issn = {1879-1026}, mesh = {*Oryza/microbiology/physiology ; *Soil Microbiology ; *Cadmium ; *Soil Pollutants ; *Plant Roots/microbiology ; *Rhizosphere ; *Microbiota/drug effects ; Metagenomics ; Soil/chemistry ; }, abstract = {Plants exert a profound influence on their rhizosphere microbiome through the secretion of root exudates, thereby imparting critical effects on their growth and overall health. The results unveil that japonica rice showcases a remarkable augmentation in its antioxidative stress mechanisms under Cd stress. This augmentation is characterized by the sequestration of heavy metal ions within the root system and the prodigious secretion of a spectrum of flavonoids, including Quercetin, Luteolin, Apigenin, Kaempferide, and Sakuranetin. These flavonoids operate as formidable guardians, shielding the plant from oxidative damage instigated by Cd-induced stress. Furthermore, the metagenomic analyses divulge the transformative potential of flavonoids, as they induce profound alterations in the composition and structural dynamics of plant rhizosphere microbial communities. These alterations manifest through the recruitment of plant growth-promoting bacteria, effectively engineering a conducive milieu for japonica rice. In addition, our symbiotic network analysis discerns that flavonoid compounds significantly improved the positive correlations among dominant species within the rhizosphere of japonica rice. This, in turn, bolsters the stability and intricacy of the microenvironmental ecological network. KEGG functional analyses reveal a notable upregulation in the expression of flavonoid functional genes, specifically cadA, cznA, nccC, and czrB, alongside an array of transporters, encompassing RND, ABC, MIT, and P-ATPase. These molecular orchestrations distinctly demarcated the rhizosphere microbiome of japonica rice, markedly enhancing its tolerance to Cd-induced stress. These findings not only shed light on the establishment of Cd-resistant bacterial consortia in rice but also herald a promising avenue for the precise modulation of plant rhizosphere microbiomes, thereby fortifying the safety and efficiency of crop production.}, } @article {pmid39069174, year = {2024}, author = {Shu, D and Banerjee, S and Mao, X and Zhang, J and Cui, W and Zhang, W and Zhang, B and Chen, S and Jiao, S and Wei, G}, title = {Conversion of monocropping to intercropping promotes rhizosphere microbiome functionality and soil nitrogen cycling.}, journal = {The Science of the total environment}, volume = {949}, number = {}, pages = {174953}, doi = {10.1016/j.scitotenv.2024.174953}, pmid = {39069174}, issn = {1879-1026}, mesh = {*Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Nitrogen Cycle ; *Soil/chemistry ; *Nitrogen/metabolism ; *Agriculture/methods ; Glycine max/growth & development ; Crop Production/methods ; }, abstract = {Intercropping can increase soil nutrient availability and provide greater crop yields for intensive agroecosystems. Despite its multiple benefits, how intercropping influences rhizosphere microbiome assemblages, functionality, and complex soil nitrogen cycling is not fully understood. Here, a three-year field experiment was carried out on different cropping system with five fertilization treatments at the main soybean production regions. We found that soybean yields in intercropped systems were on average 17 % greater than in monocropping system, regardless of fertilization treatments. We also found that intercropping systems significant increased network modularity (by 46 %) and functional diversity (by 11 %) than monocropping systems. Metagenomics analyses further indicated intercropping promotes microbiome functional adaptation, particularly enriching core functions related to nitrogen metabolism. Cropping patterns had a stronger influence on the functional genes associated with soil nitrogen cycling (R[2] = 0.499). Monocropping systems increased the abundance of functional genes related to organic nitrogen ammonification, nitrogen fixation, and denitrification, while functional guilds of nitrate assimilation (by 28 %), nitrification (by 31 %), and dissimilatory nitrate reduction (by 10.1 %) genes were enriched in intercropping systems. Furthermore, we found that abiotic factors (i.e. AP, pH, and Moisture) are important drivers in shaping soil microbial community assemblage and nitrogen cycling. The functional genes include hzsB, and nrfA, and nxrA that affected by these biotic and abiotic variables were strongly related to crop yield (R[2] = 0.076 ~ R[2] = 0.249), suggesting a key role for maintaining crop production. We demonstrated that land use conversion from maize monocropping to maize-soybean intercropping diversify rhizosphere microbiome and functionality signatures, and intercropping increased key gene abundance related to soil nitrogen cycling to maintain the advantage of crop yield. The results of this study significantly facilitate our understanding of the complex soil nitrogen cycling processes and lay the foundation for manipulating desired specific functional taxa for improved crop productivity under sustainable intensification.}, } @article {pmid39068883, year = {2024}, author = {Zhou, Z and Keiblinger, KM and Huang, Y and Bhople, P and Shi, X and Yang, S and Yu, F and Liu, D}, title = {Virome and metagenomic sequencing reveal the impact of microbial inoculants on suppressions of antibiotic resistome and viruses during co-composting.}, journal = {Journal of hazardous materials}, volume = {477}, number = {}, pages = {135355}, doi = {10.1016/j.jhazmat.2024.135355}, pmid = {39068883}, issn = {1873-3336}, mesh = {*Manure/microbiology/virology ; *Composting ; *Streptomyces/genetics ; *Drug Resistance, Microbial/genetics ; *Metagenomics ; Virome/genetics ; Bacteria/drug effects/genetics ; Viruses/drug effects/genetics ; Soil Microbiology ; Anti-Bacterial Agents/pharmacology ; Metagenome ; }, abstract = {Co-composting with exogenous microbial inoculant, presents an effective approach for the harmless utilization of livestock manure and agroforestry wastes. However, the impact of inoculant application on the variations of viral and antibiotic resistance genes (ARGs) remains poorly understood, particularly under varying manure quantity (low 10 % vs. high 20 % w/w). Thus, employing virome and metagenomic sequencing, we examined the influence of Streptomyces-Bacillus Inoculants (SBI) on viral communities, phytopathogen, ARGs, mobile genetic elements, and their interrelations. Our results indicate that SBI shifted dominant bacterial species from Phenylobacterium to thermotropic Bordetella, and the quantity of manure mediates the effect of SBI on whole bacterial community. Major ARGs and genetic elements experienced substantial changes with SBI addition. There was a higher ARGs elimination rate in the composts with low (∼76 %) than those with high manure (∼70 %) application. Virus emerged as a critical factor influencing ARG dynamics. We observed a significant variation in virus community, transitioning from Gemycircularvirus- (∼95 %) to Chlamydiamicrovirus-dominance. RDA analysis revealed that Gemycircularvirus was the most influential taxon in shaping ARGs, with its abundance decreased approximately 80 % after composting. Collectively, these findings underscore the role of microbial inoculants in modulating virus communities and ARGs during biowaste co-composting.}, } @article {pmid39068184, year = {2024}, author = {de Jonge, PA and van den Born, BH and Zwinderman, AH and Nieuwdorp, M and Dutilh, BE and Herrema, H}, title = {Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {6346}, pmid = {39068184}, issn = {2041-1723}, support = {955974//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 955974//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 0915018201002//ZonMw (Netherlands Organisation for Health Research and Development)/ ; 015.017.050//ZonMw (Netherlands Organisation for Health Research and Development)/ ; 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 2019.82.004//Diabetes Fonds (Dutch Diabetes Research Foundation)/ ; }, mesh = {Humans ; *Phylogeny ; *Bacteriophages/genetics/isolation & purification/classification ; *Gastrointestinal Microbiome/genetics ; Genome, Viral/genetics ; Metagenome/genetics ; Virome/genetics ; Inflammatory Bowel Diseases/virology ; Biodiversity ; Diabetes Mellitus, Type 2/virology ; Female ; Male ; Europe ; Netherlands ; Adult ; }, abstract = {Viruses are core components of the human microbiome, impacting health through interactions with gut bacteria and the immune system. Most human microbiome viruses are bacteriophages, which exclusively infect bacteria. Until recently, most gut virome studies focused on low taxonomic resolution (e.g., viral operational taxonomic units), hampering population-level analyses. We previously identified an expansive and widespread bacteriophage lineage in inhabitants of Amsterdam, the Netherlands. Here, we study their biodiversity and evolution in various human populations. Based on a phylogeny using sequences from six viral genome databases, we propose the Candidatus order Heliusvirales. We identify heliusviruses in 82% of 5441 individuals across 39 studies, and in nine metagenomes from humans that lived in Europe and North America between 1000 and 5000 years ago. We show that a large lineage started to diversify when Homo sapiens first appeared some 300,000 years ago. Ancient peoples and modern hunter-gatherers have distinct Ca. Heliusvirales populations with lower richness than modern urbanized people. Urbanized people suffering from type 1 and type 2 diabetes, as well as inflammatory bowel disease, have higher Ca. Heliusvirales richness than healthy controls. We thus conclude that these ancient core members of the human gut virome have thrived with increasingly westernized lifestyles.}, } @article {pmid39068001, year = {2024}, author = {Li, Y and Han, S}, title = {Metabolomic Applications in Gut Microbiota-Host Interactions in Human Diseases.}, journal = {Gastroenterology clinics of North America}, volume = {53}, number = {3}, pages = {383-397}, doi = {10.1016/j.gtc.2023.12.008}, pmid = {39068001}, issn = {1558-1942}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Metabolomics ; Host Microbial Interactions ; Biomarkers/metabolism ; Precision Medicine ; }, abstract = {The human gut microbiota, consisting of trillions of microorganisms, encodes diverse metabolic pathways that impact numerous aspects of host physiology. One key way in which gut bacteria interact with the host is through the production of small metabolites. Several of these microbiota-dependent metabolites, such as short-chain fatty acids, have been shown to modulate host diseases. In this review, we examine how disease-associated metabolic signatures are identified using metabolomic platforms, and where metabolomics is applied in gut microbiota-disease interactions. We further explore how integration of metagenomic and metabolomic data in human studies can facilitate biomarkers discoveries in precision medicine.}, } @article {pmid39067601, year = {2024}, author = {Roman, EKB and Ramos, MA and Tomazetto, G and Foltran, BB and Galvão, MH and Ciancaglini, I and Tramontina, R and de Almeida Rodrigues, F and da Silva, LS and Sandano, ALH and Fernandes, DGDS and Almeida, DV and Baldo, DA and de Oliveira Junior, JM and Garcia, W and Damasio, A and Squina, FM}, title = {Plastic-degrading microbial communities reveal novel microorganisms, pathways, and biocatalysts for polymer degradation and bioplastic production.}, journal = {The Science of the total environment}, volume = {949}, number = {}, pages = {174876}, doi = {10.1016/j.scitotenv.2024.174876}, pmid = {39067601}, issn = {1879-1026}, mesh = {*Biodegradation, Environmental ; *Microbiota ; *Plastics/metabolism ; Soil Microbiology ; Polyethylene Terephthalates/metabolism ; Soil Pollutants/metabolism ; Polymers/metabolism ; Bacteria/metabolism/genetics ; Biodegradable Plastics/metabolism ; Microbial Consortia ; Pseudomonas putida/metabolism/genetics ; }, abstract = {Plastics derived from fossil fuels are used ubiquitously owing to their exceptional physicochemical characteristics. However, the extensive and short-term use of plastics has caused environmental challenges. The biotechnological plastic conversion can help address the challenges related to plastic pollution, offering sustainable alternatives that can operate using bioeconomic concepts and promote socioeconomic benefits. In this context, using soil from a plastic-contaminated landfill, two consortia were established (ConsPlastic-A and -B) displaying versatility in developing and consuming polyethylene or polyethylene terephthalate as the carbon source of nutrition. The ConsPlastic-A and -B metagenomic sequencing, taxonomic profiling, and the reconstruction of 79 draft bacterial genomes significantly expanded the knowledge of plastic-degrading microorganisms and enzymes, disclosing novel taxonomic groups associated with polymer degradation. The microbial consortium was utilized to obtain a novel Pseudomonas putida strain (BR4), presenting a striking metabolic arsenal for aromatic compound degradation and assimilation, confirmed by genomic analyses. The BR4 displays the inherent capacity to degrade polyethylene terephthalate (PET) and produce polyhydroxybutyrate (PHB) containing hydroxyvalerate (HV) units that contribute to enhanced copolymer properties, such as increased flexibility and resistance to breakage, compared with pure PHB. Therefore, BR4 is a promising strain for developing a bioconsolidated plastic depolymerization and upcycling process. Collectively, our study provides insights that may extend beyond the artificial ecosystems established during our experiments and supports future strategies for effectively decomposing and valorizing plastic waste. Furthermore, the functional genomic analysis described herein serves as a valuable guide for elucidating the genetic potential of microbial communities and microorganisms in plastic deconstruction and upcycling.}, } @article {pmid39067396, year = {2024}, author = {Xie, XM and Feng, S and Liu, T and Feng, J and Xu, Y and Fan, ZJ and Wang, GY}, title = {Role of gut/liver metabolites and gut microbiota in liver fibrosis caused by cholestasis.}, journal = {International immunopharmacology}, volume = {139}, number = {}, pages = {112747}, doi = {10.1016/j.intimp.2024.112747}, pmid = {39067396}, issn = {1878-1705}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Cholestasis/metabolism/pathology/microbiology ; *Liver Cirrhosis/metabolism/microbiology/pathology ; Mice ; *Liver/metabolism/pathology ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Metabolomics ; }, abstract = {AIM OF THE STUDY: Cholestasis induces severe liver injury and subsequent liver fibrosis. However, a comprehensive understanding of the relationships between liver fibrosis and cholestasis-induced changes in metabolites in the gut and fibrotic liver tissue and in the gut microbiota is insufficient.

METHODS: Common bile duct ligation (BDL) was employed to establish a cholestatic liver fibrosis model in mice for 26 days. Fibrotic liver tissue and the gut contents were collected. Untargeted metabolomics was conducted for the determination of metabolites in the gut contents and liver tissues. Metagenomics was adopted to explore the gut microbiota.

RESULTS: The metabolites in the gut contents and liver tissues between normal and cholestatic liver fibrosis mice were highly distinct. Beta-alanine metabolism and glutathione metabolism were downregulated in the gut of the BDL group. Galactose metabolism, biosynthesis of unsaturated fatty acids, and ABC transporters were upregulated in the gut and downregulated in the liver of the BDL group. Arginine biosynthesis, taurine and hypotaurine metabolism, arginine and proline metabolism, and primary bile acid biosynthesis were downregulated in the gut and upregulated in the liver of the BDL group. Metagenomic analysis revealed that the alpha diversity of the microbiota in the BDL group decreased. The altered structure of the gut microbiota in the BDL group led to the hypofunction of important metabolic pathways (such as folate biosynthesis, histidine metabolism, thiamine metabolism, biotin metabolism, and phenylalanine, tyrosine and tryptophan biosynthesis) and enzymes (such as NADH, DNA helicase, and DNA-directed DNA polymerase). Correlation analyses indicated that certain gut microbes were associated with gut and liver metabolites.

CONCLUSIONS: Untargeted metabolomics and metagenomics provided comprehensive information on gut and liver metabolism and gut microbiota in mice with cholestatic liver fibrosis. Therefore, significantly altered bacteria and metabolites may help provide some targets against cholestatic liver fibrosis in the future.}, } @article {pmid39066857, year = {2024}, author = {de Matos, JP and Ribeiro, DF and da Silva, AK and de Paula, CH and Cordeiro, IF and Lemes, CGC and Sanchez, AB and Rocha, LCM and Garcia, CCM and Almeida, NF and Alves, RM and de Abreu, VAC and Varani, AM and Moreira, LM}, title = {Diversity and potential functional role of phyllosphere-associated actinomycetota isolated from cupuassu (Theobroma grandiflorum) leaves: implications for ecosystem dynamics and plant defense strategies.}, journal = {Molecular genetics and genomics : MGG}, volume = {299}, number = {1}, pages = {73}, pmid = {39066857}, issn = {1617-4623}, support = {#2019/25176-0//FAPESP/ ; 075/2020//FAPESPA/ ; 306039/2021-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 304367/2022-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; APQ-02357-17//FAPEMIG/ ; }, mesh = {*Plant Leaves/microbiology/genetics ; *Plant Diseases/microbiology/genetics ; Disease Resistance/genetics ; Microbiota/genetics ; Ecosystem ; Actinobacteria/genetics/isolation & purification ; Metagenomics/methods ; Metagenome/genetics ; Phylogeny ; Brassicaceae/microbiology/genetics ; }, abstract = {Exploring the intricate relationships between plants and their resident microorganisms is crucial not only for developing new methods to improve disease resistance and crop yields but also for understanding their co-evolutionary dynamics. Our research delves into the role of the phyllosphere-associated microbiome, especially Actinomycetota species, in enhancing pathogen resistance in Theobroma grandiflorum, or cupuassu, an agriculturally valuable Amazonian fruit tree vulnerable to witches' broom disease caused by Moniliophthora perniciosa. While breeding resistant cupuassu genotypes is a possible solution, the capacity of the Actinomycetota phylum to produce beneficial metabolites offers an alternative approach yet to be explored in this context. Utilizing advanced long-read sequencing and metagenomic analysis, we examined Actinomycetota from the phyllosphere of a disease-resistant cupuassu genotype, identifying 11 Metagenome-Assembled Genomes across eight genera. Our comparative genomic analysis uncovered 54 Biosynthetic Gene Clusters related to antitumor, antimicrobial, and plant growth-promoting activities, alongside cutinases and type VII secretion system-associated genes. These results indicate the potential of phyllosphere-associated Actinomycetota in cupuassu for inducing resistance or antagonism against pathogens. By integrating our genomic discoveries with the existing knowledge of cupuassu's defense mechanisms, we developed a model hypothesizing the synergistic or antagonistic interactions between plant and identified Actinomycetota during plant-pathogen interactions. This model offers a framework for understanding the intricate dynamics of microbial influence on plant health. In conclusion, this study underscores the significance of the phyllosphere microbiome, particularly Actinomycetota, in the broader context of harnessing microbial interactions for plant health. These findings offer valuable insights for enhancing agricultural productivity and sustainability.}, } @article {pmid39066334, year = {2024}, author = {Mbigha Donfack, KC and De Coninck, L and Ghogomu, SM and Matthijnssens, J}, title = {Aedes Mosquito Virome in Southwestern Cameroon: Lack of Core Virome, But a Very Rich and Diverse Virome in Ae. africanus Compared to Other Aedes Species.}, journal = {Viruses}, volume = {16}, number = {7}, pages = {}, pmid = {39066334}, issn = {1999-4915}, support = {BE2022GMUKULA101//Vlaamse Interuniversitaire Raad/ ; C14/20/108//KU Leuven/ ; 11L1323N//Research Foundation Flanders (FWO)/ ; }, mesh = {Animals ; *Aedes/virology ; Cameroon ; *Virome/genetics ; *Mosquito Vectors/virology ; Metagenomics ; Phylogeny ; Genome, Viral ; Arboviruses/genetics/classification/isolation & purification ; }, abstract = {In Cameroon, Aedes mosquitoes transmit various arboviruses, posing significant health risks. We aimed to characterize the Aedes virome in southwestern Cameroon and identify potential core viruses which might be associated with vector competence. A total of 398 Aedes mosquitoes were collected from four locations (Bafoussam, Buea, Edea, and Yaounde). Aedes albopictus dominated all sites except for Bafoussam, where Aedes africanus prevailed. Metagenomic analyses of the mosquitoes grouped per species into 54 pools revealed notable differences in the eukaryotic viromes between Ae. africanus and Ae. albopictus, with the former exhibiting greater richness and diversity. Thirty-seven eukaryotic virus species from 16 families were identified, including six novel viruses with near complete genome sequences. Seven viruses were further quantified in individual mosquitoes via qRT-PCR. Although none of them could be identified as core viruses, Guangzhou sobemo-like virus and Bafoussam mosquito solemovirus, were highly prevalent regionally in Ae. albopictus and Ae. africanus, respectively. This study highlights the diverse eukaryotic virome of Aedes species in southwestern Cameroon. Despite their shared genus, Aedes species exhibit limited viral sharing, with varying viral abundance and prevalence across locations. Ae. africanus, an understudied vector, harbors a rich and diverse virome, suggesting potential implications for arbovirus vector competence.}, } @article {pmid39066322, year = {2024}, author = {Laredo-Tiscareño, SV and Garza-Hernandez, JA and Tangudu, CS and Dankaona, W and Rodríguez-Alarcón, CA and Adame-Gallegos, JR and De Luna Santillana, EJ and Huerta, H and Gonzalez-Peña, R and Rivera-Martínez, A and Rubio-Tabares, E and Beristain-Ruiz, DM and Blitvich, BJ}, title = {Discovery of Novel Viruses in Culicoides Biting Midges in Chihuahua, Mexico.}, journal = {Viruses}, volume = {16}, number = {7}, pages = {}, pmid = {39066322}, issn = {1999-4915}, mesh = {Animals ; *Ceratopogonidae/virology ; Mexico ; *Phylogeny ; Female ; Metagenomics ; Virome ; High-Throughput Nucleotide Sequencing ; Insect Vectors/virology ; Genome, Viral ; }, abstract = {Biting midges (Culicoides) are vectors of many pathogens of medical and veterinary importance, but their viromes are poorly characterized compared to certain other hematophagous arthropods, e.g., mosquitoes and ticks. The goal of this study was to use metagenomics to identify viruses in Culicoides from Mexico. A total of 457 adult midges were collected in Chihuahua, northern Mexico, in 2020 and 2021, and all were identified as female Culicoides reevesi. The midges were sorted into five pools and homogenized. An aliquot of each homogenate was subjected to polyethylene glycol precipitation to enrich for virions, then total RNA was extracted and analyzed by unbiased high-throughput sequencing. We identified six novel viruses that are characteristic of viruses from five families (Nodaviridae, Partitiviridae, Solemoviridae, Tombusviridae, and Totiviridae) and one novel virus that is too divergent from all classified viruses to be assigned to an established family. The newly discovered viruses are phylogenetically distinct from their closest known relatives, and their minimal infection rates in female C. reevesi range from 0.22 to 1.09. No previously known viruses were detected, presumably because viral metagenomics had never before been used to study Culicoides from the Western Hemisphere. To conclude, we discovered multiple novel viruses in C. reevesi from Mexico, expanding our knowledge of arthropod viral diversity and evolution.}, } @article {pmid39066262, year = {2024}, author = {Paietta, EN and Kraberger, S and Lund, MC and Vargas, KL and Custer, JM and Ehmke, E and Yoder, AD and Varsani, A}, title = {Diverse Circular DNA Viral Communities in Blood, Oral, and Fecal Samples of Captive Lemurs.}, journal = {Viruses}, volume = {16}, number = {7}, pages = {}, pmid = {39066262}, issn = {1999-4915}, support = {internal//TriCEM (Triangle Center for Evolutionary Medicine), Duke Biology, Duke Lemur Center, Duke University/ ; }, mesh = {Animals ; *Feces/virology ; *Lemur/virology ; *Genome, Viral ; Phylogeny ; Virome ; DNA, Viral/genetics ; Mouth/virology ; Madagascar ; Blood/virology ; }, abstract = {Few studies have addressed viral diversity in lemurs despite their unique evolutionary history on the island of Madagascar and high risk of extinction. Further, while a large number of studies on animal viromes focus on fecal samples, understanding viral diversity across multiple sample types and seasons can reveal complex viral community structures within and across species. Groups of captive lemurs at the Duke Lemur Center (Durham, NC, USA), a conservation and research center, provide an opportunity to build foundational knowledge on lemur-associated viromes. We sampled individuals from seven lemur species, i.e., collared lemur (Eulemur collaris), crowned lemur (Eulemur coronatus), blue-eyed black lemur (Eulemur flavifrons), ring-tailed lemur (Lemur catta), Coquerel's sifaka (Propithecus coquereli), black-and-white ruffed lemur (Varecia variegata variegata), and red ruffed lemur (Varecia rubra), across two lemur families (Lemuridae, Indriidae). Fecal, blood, and saliva samples were collected from Coquerel's sifaka and black-and-white ruffed lemur individuals across two sampling seasons to diversify virome biogeography and temporal sampling. Using viral metagenomic workflows, the complete genomes of anelloviruses (n = 4), cressdnaviruses (n = 47), caudoviruses (n = 15), inoviruses (n = 34), and microviruses (n = 537) were determined from lemur blood, feces, and saliva. Many virus genomes, especially bacteriophages, identified in this study were present across multiple lemur species. Overall, the work presented here uses a viral metagenomics approach to investigate viral communities inhabiting the blood, oral cavity, and feces of healthy captive lemurs.}, } @article {pmid39066231, year = {2024}, author = {Liu, D and Zhang, Z and Wang, Z and Xue, L and Liu, F and Lu, Y and Yu, S and Li, S and Zheng, H and Zhang, Z and Tian, Z}, title = {Transposase-Assisted RNA/DNA Hybrid Co-Tagmentation for Target Meta-Virome of Foodborne Viruses.}, journal = {Viruses}, volume = {16}, number = {7}, pages = {}, pmid = {39066231}, issn = {1999-4915}, support = {2022YFC2302800//National Key Research and Development Program of China/ ; 2022M722152//China Postdoctoral Science Foundation/ ; 23YF1440400//Shanghai Rising-Star Program/ ; SKLAM007-2022//State Key Laboratory of Applied Microbiology Southern China/ ; RC2024-02//Innovation Promotion Program of NHC and Shanghai Key Labs SIBPT/ ; 2022HK136//General Administration of Customs Project/ ; }, mesh = {*Transposases/genetics/metabolism ; *Genome, Viral ; *Foodborne Diseases/virology ; Humans ; *Metagenomics/methods ; Virome/genetics ; RNA, Viral/genetics ; Norovirus/genetics/classification ; Gene Library ; DNA, Viral/genetics ; Viruses/genetics/classification ; }, abstract = {Foodborne diseases are major public health problems globally. Metagenomics has emerged as a widely used tool for pathogen screening. In this study, we conducted an updated Tn5 transposase-assisted RNA/DNA hybrid co-tagmentation (TRACE) library construction approach. To address the detection of prevalent known foodborne viruses and the discovery of unknown pathogens, we employed both specific primers and oligo-T primers during reverse transcription. The method was validated using clinical samples confirmed by RT-qPCR and compared with standard RNA-seq library construction methods. The mapping-based approach enabled the retrieval of nearly complete genomes (>95%) for the majority of virus genome segments (86 out of 88, 97.73%), with a mean coverage depth of 21,494.53× (ranging from 77.94× to 55,688.58×). Co-infection phenomena involving prevalent genotypes of Norovirus with Astrovirus and Human betaherpesvirus 6B were observed in two samples. The updated TRACE-seq exhibited superior performance in viral reads percentages compared to standard RNA-seq library preparation methods. This updated method has expanded its target pathogens beyond solely Norovirus to include other prevalent foodborne viruses. The feasibility and potential effectiveness of this approach were then evaluated as an alternative method for surveilling foodborne viruses, thus paving the way for further exploration into whole-genome sequencing of viruses.}, } @article {pmid39066202, year = {2024}, author = {McDonnell, B and Parlindungan, E and Vasiliauskaite, E and Bottacini, F and Coughlan, K and Krishnaswami, LP and Sassen, T and Lugli, GA and Ventura, M and Mastroleo, F and Mahony, J and van Sinderen, D}, title = {Viromic and Metagenomic Analyses of Commercial Spirulina Fermentations Reveal Remarkable Microbial Diversity.}, journal = {Viruses}, volume = {16}, number = {7}, pages = {}, pmid = {39066202}, issn = {1999-4915}, support = {15/SIRG/3430/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273-P1/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; MELiSSA POMP//European Space Agency/ ; }, mesh = {*Fermentation ; *Metagenomics/methods ; *Spirulina/genetics ; *Bacteriophages/genetics/isolation & purification/classification ; *Biodiversity ; Metagenome ; Virome ; Phylogeny ; Ponds/microbiology/virology ; Bacteria/virology/genetics/classification/isolation & purification ; }, abstract = {Commercially produced cyanobacteria preparations sold under the name spirulina are widely consumed, due to their traditional use as a nutrient-rich foodstuff and subsequent marketing as a superfood. Despite their popularity, the microbial composition of ponds used to cultivate these bacteria is understudied. A total of 19 pond samples were obtained from small-scale spirulina farms and subjected to metagenome and/or virome sequencing, and the results were analysed. A remarkable level of prokaryotic and viral diversity was found to be present in the ponds, with Limnospira sp. and Arthrospira sp. sometimes being notably scarce. A detailed breakdown of prokaryotic and viral components of 15 samples is presented. Twenty putative Limnospira sp.-infecting bacteriophage contigs were identified, though no correlation between the performance of these cultures and the presence of phages was found. The high diversity of these samples prevented the identification of clear trends in sample performance over time, between ponds or when comparing successful and failed fermentations.}, } @article {pmid39066183, year = {2024}, author = {Zell, R and Groth, M and Selinka, L and Selinka, HC}, title = {Diversity of Picorna-Like Viruses in the Teltow Canal, Berlin, Germany.}, journal = {Viruses}, volume = {16}, number = {7}, pages = {}, pmid = {39066183}, issn = {1999-4915}, mesh = {*Genome, Viral ; *Phylogeny ; *Picornaviridae/genetics/classification/isolation & purification ; Berlin ; Fresh Water/virology ; Virome/genetics ; RNA, Viral/genetics ; Germany ; Genetic Variation ; RNA Viruses/genetics/classification/isolation & purification ; }, abstract = {The viromes of freshwater bodies are underexplored. The Picornavirales order, with 371 acknowledged species, is one of the most expansive and diverse groups of eukaryotic RNA viruses. In this study, we add 513 picorna-like viruses to the assemblage of more than 2000 unassigned picorna-like viruses. Our set of the aquatic Picornavirales virome of the Teltow Canal in Berlin, Germany, consists of 239 complete and 274 partial genomes. This urban freshwater body is characterized by the predominance of marna-like viruses (30.8%) and dicistro-like viruses (19.1%), whereas picornaviruses, iflaviruses, solinvi-like viruses, polycipi-like viruses, and nora-like viruses are considerably less prevalent. Caliciviruses and secoviruses were absent in our sample. Although presenting characteristic domains of Picornavirales, more than 100 viruses (20.8%) could not be assigned to any of the 9 Picornavirales families. Thirty-three viruses of the Marnaviridae-mostly locarna-like viruses-exhibit a monocistronic genome layout. Besides a wealth of novel virus sequences, viruses with peculiar features are reported. Among these is a clade of untypeable marna-like viruses with dicistronic genomes, but with the capsid protein-encoding open reading frame located at the 5' part of their RNA. A virus with a similar genome layout but clustering with dicistroviruses was also observed. We further detected monocistronic viruses with a polymerase gene related to aparaviruses. The detection of Aichi virus and five novel posa-like viruses indicates a slight burden in municipal wastewater.}, } @article {pmid39065120, year = {2024}, author = {Li, F and Lyu, H and Li, H and Xi, K and Yi, Y and Zhang, Y}, title = {Domestication and Genetic Improvement Alter the Symbiotic Microbiome Structure and Function of Tomato Leaf and Fruit Pericarp.}, journal = {Microorganisms}, volume = {12}, number = {7}, pages = {}, pmid = {39065120}, issn = {2076-2607}, support = {Qiankehejichu-ZK[2022]Zhongdian 033//Natural Science Foundation of Guizhou Province/ ; 31960217,31902019, 32272022//National Natural Science Foundation of China/ ; }, abstract = {Many studies have attempted to explore the changes in the structure and function of symbiotic microbiomes, as well as the underlying genetic mechanism during crop domestication. However, most of these studies have focused on crop root microbiomes, while those on leaf and fruit are rare. In this study, we generated a comprehensive dataset including the metagenomic (leaf) and metatranscriptomic (fruit pericarp in the orange stage) data of hundreds of germplasms from three tomato clades: Solanum pimpinellifolium (PIM), cherry tomato (S. lycopersicum var. cerasiforme) (CER), and S. lycopersicum group (BIG). We investigated the effect of domestication and improvement processes on the structure of the symbiotic microbiome of tomato leaf and fruit pericarp, as well as its genetic basis. We were able to obtain the composition of the symbiotic microbiome of tomato leaf and fruit pericarp, based on which the tomato clade (PIM, CER, or BIG) was predicted with high accuracy through machine learning methods. In the processes of tomato domestication and improvement, changes were observed in the relative abundance of specific bacterial taxa, Bacillus for example, in the tomato leaf and fruit pericarp symbiotic microbiomes, as well as in the function of these symbiotic microbiomes. In addition, SNP loci that were significantly associated with microbial species that are characteristic of tomato leaf were identified. Our results show that domestication and genetic improvement processes alter the symbiotic microbiome structure and function of tomato leaf and fruit pericarp. We propose that leaf and fruit microbiomes are more suitable for revealing changes in symbiotic microbiomes during the domestication process and the underlying genetic basis for these changes due to the exclusion of the influence of environmental factors such as soil types on the microbiome structure.}, } @article {pmid39064618, year = {2024}, author = {Tsifintaris, M and Sitmalidis, M and Tokamani, M and Anastasiadi, C and Georganta, M and Tsochantaridis, I and Vlachakis, D and Tsikouras, P and Nikolettos, N and Chrousos, GP and Sandaltzopoulos, R and Giannakakis, A}, title = {Analysis of Human Milk Microbiota in Northern Greece by Comparative 16S rRNA Sequencing vs. Local Dairy Animals.}, journal = {Nutrients}, volume = {16}, number = {14}, pages = {}, pmid = {39064618}, issn = {2072-6643}, support = {05704//Hellenic Foundation for Research and Innovation/ ; }, mesh = {Animals ; Humans ; *Milk, Human/microbiology/chemistry ; *RNA, Ribosomal, 16S/genetics ; Greece ; *Microbiota ; Female ; Cattle ; *Goats ; *Colostrum/microbiology ; *Milk/microbiology ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Milk is a biological fluid with a dynamic composition of micronutrients and bioactive molecules that serves as a vital nutrient source for infants. Milk composition is affected by multiple factors, including genetics, geographical location, environmental conditions, lactation phase, and maternal nutrition, and plays a key role in dictating its microbiome. This study addresses a less-explored aspect, comparing the microbial communities in human breast milk with those in mature milk from species that are used for milk consumption. Since mature animal milk is used as a supplement for both the infant (formula) and the child/adolescent, our main aim was to identify shared microbial communities in colostrum and mature human milk. Using 16S rRNA metagenomic sequencing, we focused on characterizing the milk microbiota in the Northern Greek population by identifying shared microbial communities across samples and comparing the relative abundance of prevalent genera. We analyzed ten human milk samples (from five mothers), with five collected three days postpartum (colostrum) and five collected thirty to forty days postpartum (mature milk) from corresponding mothers. To perform an interspecies comparison of human milk microbiota, we analyzed five goat and five bovine milk samples from a local dairy industry, collected fifty to seventy days after birth. Alpha diversity analysis indicated moderate diversity and stability in bovine milk, high richness in goat milk, and constrained diversity in breast milk. Beta diversity analysis revealed significant distinctions among mammalian species, emphasizing both presence/absence and abundance-based clustering. Despite noticeable differences, shared microbial components underscore fundamental aspects across all mammalian species, highlighting the presence of a core microbiota predominantly comprising the Proteobacteria, Firmicutes, and Actinobacteriota phyla. At the genus level, Acinetobacter, Gemella, and Sphingobium exhibit significant higher abundance in human milk compared to bovine and goat milk, while Pseudomonas and Atopostipes are more prevalent in animal milk. Our comparative analysis revealed differences and commonalities in the microbial communities of various mammalian milks and unraveled the existence of a common fundamental milk core microbiome. We thus revealed both species-specific and conserved microbial communities in human, bovine, and goat milk. The existence of a common core microbiome with conserved differences between colostrum and mature human milk underscores fundamental similarities in the microbiota of milk across mammalian species, which could offer valuable implications for optimizing the nutritional quality and safety of dairy products as well as supplements for infant health.}, } @article {pmid39063072, year = {2024}, author = {Zhang, T and Yue, Y and Li, C and Wu, X and Park, S}, title = {Vagus Nerve Suppression in Ischemic Stroke by Carotid Artery Occlusion: Implications for Metabolic Regulation, Cognitive Function, and Gut Microbiome in a Gerbil Model.}, journal = {International journal of molecular sciences}, volume = {25}, number = {14}, pages = {}, pmid = {39063072}, issn = {1422-0067}, support = {RS-2023-00208567//National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Vagus Nerve/metabolism ; *Gerbillinae ; *Disease Models, Animal ; *Cognition ; Male ; Ischemic Stroke/metabolism ; Diet, High-Fat/adverse effects ; Brain-Gut Axis/physiology ; Vagotomy ; Hippocampus/metabolism ; Brain-Derived Neurotrophic Factor/metabolism ; }, abstract = {The vagus nerve regulates metabolic homeostasis and mediates gut-brain communication. We hypothesized that vagus nerve dysfunction, induced by truncated vagotomy (VGX) or carotid artery occlusion (AO), would disrupt gut-brain communication and exacerbate metabolic dysregulation, neuroinflammation, and cognitive impairment. This study aimed to test the hypothesis in gerbils fed a high-fat diet. The gerbils were divided into four groups: AO with VGX (AO_VGX), AO without VGX (AO_NVGX), no AO with VGX (NAO_VGX), and no AO without VGX (NAO_NVGX). After 5 weeks on a high-fat diet, the neuronal cell death, neurological severity, hippocampal lipids and inflammation, energy/glucose metabolism, intestinal morphology, and fecal microbiome composition were assessed. AO and VGX increased the neuronal cell death and neurological severity scores associated with increased hippocampal lipid profiles and lipid peroxidation, as well as changes in the inflammatory cytokine expression and brain-derived neurotrophic factor (BDNF) levels. AO and VGX also increased the body weight, visceral fat mass, and insulin resistance and decreased the skeletal muscle mass. The intestinal morphology and microbiome composition were altered, with an increase in the abundance of Bifidobacterium and a decrease in Akkermansia and Ruminococcus. Microbial metagenome functions were also impacted, including glutamatergic synaptic activity, glycogen synthesis, and amino acid biosynthesis. Interestingly, the effects of VGX were not significantly additive with AO, suggesting that AO inhibited the vagus nerve activity, partly offsetting the effects of VGX. In conclusion, AO and VGX exacerbated the dysregulation of energy, glucose, and lipid metabolism, neuroinflammation, and memory deficits, potentially through the modulation of the gut-brain axis. Targeting the gut-brain axis by inhibiting vagus nerve suppression represents a potential therapeutic strategy for ischemic stroke.}, } @article {pmid39062603, year = {2024}, author = {Mosca, A and Dimaria, G and Nicotra, D and Modica, F and Massimino, ME and Catara, AF and Scuderi, G and Russo, M and Catara, V}, title = {Soil Microbial Communities in Lemon Orchards Affected by Citrus Mal Secco Disease.}, journal = {Genes}, volume = {15}, number = {7}, pages = {}, pmid = {39062603}, issn = {2073-4425}, support = {08CT7211000254//PO FESR 2014-2020 Sicilia action 1.1.5/ ; }, mesh = {*Citrus/microbiology ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Microbiota/genetics ; Bacteria/genetics/classification/isolation & purification ; Fungi/genetics/classification/isolation & purification ; Ascomycota/genetics/pathogenicity ; }, abstract = {Mal secco is a vascular disease of citrus caused by the mitosporic fungus Plenodomus tracheiphilus. Soil containing infected plant material constitutes an inoculum source for root infections. In this study, the soil bacterial and fungal communities of five lemon orchards located in Syracuse Province (Sicily, Italy) affected by mal secco were analyzed. Soil samples were collected under lemon tree canopies and subjected to total genomic DNA extraction. The fungal DNA was detected through qPCR in all orchards, with variable concentrations. Bacterial and fungal communities were profiled using 16S and ITS amplicon-based high-throughput sequencing, respectively. According to our results, the relative abundances of the most represented bacterial phyla (e.g., Proteobacteria, Actinobacteriota, Acidobacteriota) changed across the orchards, while in the fungal community, the phylum Ascomycota was dominant, with Basidiomycota and Mortierellomycota abundances fluctuating. On the whole, β diversity analysis showed significant variation in the composition of the soil microbial communities across the orchards. This result was confirmed by the analysis of the core community (taxa present at ≥ 75% of total samples), where putative beneficial bacteria resulted in significantly enriched fungus-infected soil samples, suggesting complex microbial interactions. Our findings shed light on the composition and diversity of the soil microbiome in lemon orchards with the occurrence of mal secco infections.}, } @article {pmid39060894, year = {2024}, author = {Wu, J and Zhang, Y and Duan, J and Wei, Y and Miao, Y}, title = {A metagenomic next-generation sequencing (mNGS)-based analysis of bronchoalveolar lavage samples in patients with an acute exacerbation of chronic obstructive pulmonary disease.}, journal = {Journal of molecular histology}, volume = {55}, number = {5}, pages = {709-719}, pmid = {39060894}, issn = {1567-2387}, support = {MTP2022A008//China Primary Health Care Foundation/ ; }, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/diagnosis/virology/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Female ; *Metagenomics/methods ; Aged ; *Microbiota/genetics ; Middle Aged ; Metagenome ; Bacteria/genetics/isolation & purification/classification ; Disease Progression ; }, abstract = {The role of the bronchoalveolar lavage fluid (BALF) microbiome in acute exacerbations of chronic obstructive pulmonary disease (AECOPD) remains unclear. The advent of the metagenomic next-generation sequencing (mNGS) has made it possible to reveal the complex microbiome composition of the respiratory tract. This study aimed to explore whether there are differences in the BALF microbiome of AECOPD patients with different lung functions. We enrolled 55 AECOPD patients and divided them into a mild group (n = 31) and a severe group (n = 24) according to their lung function. We collected BALF and submitted it to mNGS and bioinformatics analysis. At the species level, mNGS identified 264 bacteria, 13 fungi and 12 viruses in the mild group, and 174 bacteria, 6 fungi and 6 viruses in the severe group. Mixed bacterial and viral infection occurred in both groups. At the genus level, Rothia and Veillonella were more abundant in the mild group, while Pseudomonas and Staphylococcus were more abundant in the severe group. At the species level, compared with the mild group, the relative abundance of Haemophilus influenzae and Pseudomonas aeruginosa was increased in the severe group. Besides, the BALF microbiome composition was similar between the two groups, and there was no significant difference in α and β diversity. Forced expiratory volume in 1 s/forced vital capacity (FEV1/FVC) (%) showed no significant correlation with the Shannon or Simpson index. The microbiome abundance was different between the mild and severe groups; however, microbiome diversity was similar between the two groups. Based on our findings, Haemophilus influenzae and Pseudomonas aeruginosa may be the pathogenic bacteria that cause the difference in lung function in patients with AECOPD.}, } @article {pmid39060733, year = {2024}, author = {Fasano, A and Matera, M}, title = {Probiotics to Prevent Celiac Disease and Inflammatory Bowel Diseases.}, journal = {Advances in experimental medicine and biology}, volume = {1449}, number = {}, pages = {95-111}, pmid = {39060733}, issn = {0065-2598}, mesh = {Humans ; *Celiac Disease/microbiology/genetics/prevention & control ; *Inflammatory Bowel Diseases/microbiology/genetics/prevention & control ; *Probiotics/therapeutic use ; *Gastrointestinal Microbiome ; }, abstract = {The incidence of chronic inflammatory diseases (CIDs) is dramatically increasing in the developed world, resulting in an increased burden of disease in childhood. Currently, there are limited effective strategies for treating or preventing these conditions. To date, myriads of cross-sectional studies have described alterations in the composition of the gut microbiota in a variety of disease states, after the disease has already occurred. We suggest that to mechanically link these microbiome changes with disease pathogenesis, a prospective cohort design is needed to capture changes that precede or coincide with disease onset and symptoms. In addition, these prospective studies must integrate microbiological, metagenomic, meta transcriptomic and metabolomic data with minimal and standardized clinical and environmental metadata that allow to correctly compare and interpret the results of the analysis of the human microbiota in order to build a system-level model of the interactions between the host and the development of the disease. The creation of new biological computational models thus constructed will allow us to finally move from the detection of simple elements of "association" to the identification of elements of real "causality" allowing to provide a mechanistic approach to the exploration of the development of CIDs.This can only be done when these diseases are studied as complex biological networks. In this chapter we discuss the current knowledge regarding the contribution of the microbiome to CID in childhood, focusing on celiac disease and inflammatory bowel disease, with the overall aim of identifying pathways to shift research from descriptive to mechanistic approaches. We then examine how some components of the microbiota, through epigenetic reprogramming, can start the march from genetic predisposition to clinical expression of CIDs, thus opening up new possibilities for intervention, through microbiota therapy targeting the manipulation of the composition and function of the microbiota, for future applications of precision medicine and primary prevention.}, } @article {pmid39060557, year = {2024}, author = {Hu, L and Wang, Z and Wang, Z and Wang, L and Fang, J and Liu, R}, title = {Community Composition and Functional Characterization of Microorganisms in Surface Sediment of the New Britain Trench.}, journal = {Current microbiology}, volume = {81}, number = {9}, pages = {282}, pmid = {39060557}, issn = {1432-0991}, support = {42276149//National Natural Science Foundation of China/ ; 92251303//National Natural Science Foundation of China/ ; }, mesh = {*Geologic Sediments/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Microbiota ; Archaea/classification/genetics/metabolism/isolation & purification ; Phylogeny ; Seawater/microbiology ; Metagenome ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Carbon/metabolism ; Biodiversity ; }, abstract = {The deep-sea harbors abundant prokaryotic biomass is a major site of organic carbon remineralization and long-term carbon burial in the ocean. Deep-sea trenches are the deepest part of the ocean, and their special geological and morphological features promoting the accumulation of organic matter and active organic carbon turnover. Despite the expanding reports about the organic matter inputs, limited information is known regarding microbial processes in deep-sea trenches. In this study, we investigated the species composition and metabolic potential in surface sediment of the New Britain Trench (NBT), using a metagenomic approach. The predominant microbial taxa in NBT sediment include Proteobacteria, Acidobacteria, Planctomycetes, Actinobacteria and Chloroflexota. The microbial communities showed highly diverse metabolic potentials. Particularly, genes encoding enzymes for degradation of aromatic compounds, as well as those encoding haloalkane dehalogenase and haloacetate dehalogenase were annotated in the NBT surface sediment, which indicate the potential of microorganisms to degrade different types of refractory organic matter. The functional genes encoding enzymes for dissimilatory nitrate reduction, denitrification, and nitrification were also represented in the NBT metagenome. Overall, the microbial communities show high diversity of heterotrophic lineages and metabolic features, supporting their potential contributions in organic carbon metabolism. Meanwhile, Nitrosopumilus, a dominant genus in the surface sediment of the NBT, is a typical ammonia-oxidizing archaea (AOA), with autotrophic CO2 fixation pathways including the 3-hydroxypropionate/4-hydroxybutylate (3HP/4HB) cycle, the reductive TCA (rTCA) cycle. The results demonstrate that autotrophic metabolic processes also play an important role in the surface sediment, by providing newly synthesized organic matter.}, } @article {pmid39060267, year = {2024}, author = {Gao, JM and Xia, SY and Hide, G and Li, BH and Liu, YY and Wei, ZY and Zhuang, XJ and Yan, Q and Wang, Y and Yang, W and Chen, JH and Rao, JH}, title = {Multiomics of parkinsonism cynomolgus monkeys highlights significance of metabolites in interaction between host and microbiota.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {61}, pmid = {39060267}, issn = {2055-5008}, support = {82200966//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31671311//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31671311//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Macaca fascicularis ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Disease Models, Animal ; Dysbiosis/microbiology ; Male ; Bacteria/classification/genetics/isolation & purification/metabolism ; Parkinsonian Disorders/microbiology/metabolism ; Metabolomics/methods ; Metabolome ; Host Microbial Interactions ; Multiomics ; }, abstract = {The gut microbiota has been demonstrated to play a significant role in the pathogenesis of Parkinson's disease (PD). However, conflicting findings regarding specific microbial species have been reported, possibly due to confounding factors within human populations. Herein, our current study investigated the interaction between the gut microbiota and host in a non-human primate (NHP) PD model induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) using a multi-omic approach and a self-controlled design. Our transcriptomic sequencing of peripheral blood leukocytes (PBL) identified key genes involved in pro-inflammatory cytokine dysregulation, mitochondrial function regulation, neuroprotection activation, and neurogenesis associated with PD, such as IL1B, ATP1A3, and SLC5A3. The metabolomic profiles in serum and feces consistently exhibited significant alterations, particularly those closely associated with inflammation, mitochondrial dysfunctions and neurodegeneration in PD, such as TUDCA, ethylmalonic acid, and L-homophenylalanine. Furthermore, fecal metagenome analysis revealed gut dysbiosis associated with PD, characterized by a significant decrease in alpha diversity and altered commensals, particularly species such as Streptococcus, Butyrivibrio, and Clostridium. Additionally, significant correlations were observed between PD-associated microbes and metabolites, such as sphingomyelin and phospholipids. Importantly, PDPC significantly reduced in both PD monkey feces and serum, exhibiting strong correlation with PD-associated genes and microbes, such as SLC5A3 and Butyrivibrio species. Moreover, such multi-omic differential biomarkers were linked to the clinical rating scales of PD monkeys. Our findings provided novel insights into understanding the potential role of key metabolites in the host-microbiota interaction involved in PD pathogenesis.}, } @article {pmid39059949, year = {2024}, author = {Zhang, P and Wang, H and Klima, C and Yang, X}, title = {Microbiota in lymph nodes of cattle harvested in a Canadian meat processing plant.}, journal = {Food research international (Ottawa, Ont.)}, volume = {191}, number = {}, pages = {114693}, doi = {10.1016/j.foodres.2024.114693}, pmid = {39059949}, issn = {1873-7145}, mesh = {Animals ; Cattle ; Canada ; *Lymph Nodes/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Abattoirs ; *Shiga-Toxigenic Escherichia coli/isolation & purification/genetics ; *Microbiota ; *Salmonella/isolation & purification/genetics/classification ; Red Meat/microbiology ; Food Microbiology ; }, abstract = {Lymph nodes (LN) harboring bacteria, when being incorporated into ground beef, may impact the microbial safety and quality of such products. We tested two main foodborne pathogens Salmonella and Shiga toxin-producing Escherichia coli (STEC) and profiled the microbiota in LNs (n = 160) of cattle harvested at a Canadian abattoir, by conventional plating methods, PCR, and high throughput sequencing. LNs at two anatomical locations, subiliac and popliteal from 80 cattle were included. All cattle had bacteria detected in popliteal and/or subiliac LNs with the maximum bacterial load of 5.4 and 2.8 log10CFU/g in popliteal and subiliac LNs, respectively. Neither Salmonella nor STEC was found in LNs although STEC was detected in a significant percentage of samples from beef hides (50.6 %) by plating and/or PCR. Both 16S rRNA gene amplicon and metagenome sequencing found the predominance of Escherichia (13-34.6 % among bacterial community), Clostridium (12.6-20.6 %) and Streptococcus (9.7-10 %) in popliteal LNs. Metagenomic sequencing was able to identify the predominant taxa at species level with E. coli (13 %), Clostridium perfringens (11.1 %) and Streptococcus uberis (6 %) predominant in LNs. Low prevalence/abundance of Salmonella was found by metagenomic sequencing. In conclusion, the relatively high bacterial load and diversity in LNs may affect the shelf life of ground beef and high relative abundance of E. coli would warrant further monitoring.}, } @article {pmid39059396, year = {2024}, author = {Kim, Y and Kim, G and Kim, S and Cho, B and Kim, SY and Do, EJ and Bae, DJ and Kim, S and Kweon, MN and Song, JS and Park, SH and Hwang, SW and Kim, MN and Kim, Y and Min, K and Kim, SH and Adams, MD and Lee, C and Park, H and Park, SR}, title = {Fecal microbiota transplantation improves anti-PD-1 inhibitor efficacy in unresectable or metastatic solid cancers refractory to anti-PD-1 inhibitor.}, journal = {Cell host & microbe}, volume = {32}, number = {8}, pages = {1380-1393.e9}, doi = {10.1016/j.chom.2024.06.010}, pmid = {39059396}, issn = {1934-6069}, mesh = {Animals ; Humans ; Mice ; Cytokines/metabolism ; *Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Neoplasms/immunology/therapy/microbiology ; *Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Male ; Female ; Adult ; Middle Aged ; }, abstract = {The gut microbiome significantly influences immune responses and the efficacy of immune checkpoint inhibitors. We conducted a clinical trial (NCT04264975) combining an anti-programmed death-1 (PD-1) inhibitor with fecal microbiota transplantation (FMT) from anti-PD-1 responder in 13 patients with anti-PD-1-refractory advanced solid cancers. FMT induced sustained microbiota changes and clinical benefits in 6 of 13 patients, with 1 partial response and 5 stable diseases, achieving an objective response rate of 7.7% and a disease control rate of 46.2%. The clinical response correlates with increased cytotoxic T cells and immune cytokines in blood and tumors. We isolated Prevotella merdae Immunoactis from a responder to FMT, which stimulates T cell activity and suppresses tumor growth in mice by enhancing cytotoxic T cell infiltration. Additionally, we found Lactobacillus salivarius and Bacteroides plebeius may inhibit anti-tumor immunity. Our findings suggest that FMT with beneficial microbiota can overcome resistance to anti-PD-1 inhibitors in advanced solid cancers, especially gastrointestinal cancers.}, } @article {pmid39056112, year = {2024}, author = {Dong, J and Zhang, J and Cheng, S and Qin, B and Jin, K and Chen, B and Zhang, Y and Lu, J}, title = {A high-fat diet induced depression-like phenotype via hypocretin-HCRTR1 mediated inflammation activation.}, journal = {Food & function}, volume = {15}, number = {17}, pages = {8661-8673}, doi = {10.1039/d4fo00210e}, pmid = {39056112}, issn = {2042-650X}, mesh = {Animals ; Male ; Mice ; Rats ; 3T3-L1 Cells ; Benzoxazoles ; *Depression/metabolism ; *Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome/drug effects ; Hippocampus/metabolism/drug effects ; *Inflammation/metabolism ; *Mice, Inbred C57BL ; Microglia/metabolism/drug effects ; Naphthyridines ; *Orexin Receptors/metabolism/genetics ; *Orexins/metabolism ; Phenotype ; *Rats, Sprague-Dawley ; Urea/analogs & derivatives ; }, abstract = {Background: A high-fat diet (HFD) is generally associated with an increased risk of mental disorders that constitute a sizeable worldwide health. A HFD results in the gut microbiota-brain axis being altered and linked to mental disorders. Hypocretin-1, which can promote appetite, has been previously confirmed to be associated with depression. However, no exact relationship has been found for hypocretin between depression and HFDs. Methods: Adult male SD rats were randomly assigned to either a HFD or a normal diet for eight weeks, followed by behavioral tests and plasma biochemical analyses. Then, we investigated the protein and mRNA levels of inflammation-related factors in the hippocampus. We also observed morphological changes in brain microglia and lipid accumulation. Additionally, metagenomic and metabolomic analyses of gut microbiomes were performed. 3T3-L1 cells were utilized in vitro to investigate the impact of hypocretin receptor 1 antagonists (SB334867) on lipid accumulation. To consider the connection between the brain and adipose tissue, we used a conditioned medium (CM) treated with 3T3-L1 cells to observe the activation and phagocytosis of BV2 cells. Following a 12-week period of feeding a HFD to C57BL/6 mice, a three-week intervention period was initiated during which the administration of SB334867 was observed. This was followed by a series of assessments, including monitoring of body weight changes and emotional problems, as well as attention to plasma biochemical levels and microglial cell phenotypes in the brain. Results: The HFD rats displayed anxiety and depressive-like behaviors. HFD rats exhibited increased plasma HDL, LDL, and TC levels. A HFD also causes an increase in hypocretin-1 and hypocretin-2 in the hypothalamus. Metagenomics and metabolomics revealed that the HFD caused an increase in the relative abundance of associated inflammatory bacteria and decreased the abundance of anti-inflammatory and bile acid metabolites. Compared with the CTR group, hippocampal microglia in the HFD group were significantly activated and accompanied by lipid deposition. At the same time, protein and mRNA expression levels of inflammation-related factors were increased. We found that SB334867 could significantly reduce lipid accumulation in 3T3-L1 cells after differentiation. The expression of inflammatory factors decreased in the SB334867 group. The administration of SB334867 was found to reverse the adverse effects of the HFD on body weight, depressive-like behaviour and anxiety-like mood. Furthermore, this treatment was associated with improvements in plasma biochemical levels and a reduction in the number of microglia in the brain. Conclusions: In summary, our results demonstrated that a HFD induced anxiety and depressive-like behaviors, which may be linked to the increased hypocretin-1 level and lipid accumulation. Supplementation with SB334867 improved the above. These observations highlight the possibility of hypocretin-1 inducing the risk of HFD-associated emotional dysfunctions.}, } @article {pmid39054479, year = {2024}, author = {Boldrini, L and Chiloiro, G and Di Franco, S and Romano, A and Smiljanic, L and Tran, EH and Bono, F and Charles Davies, D and Lopetuso, L and De Bonis, M and Minucci, A and Giacò, L and Cusumano, D and Placidi, L and Giannarelli, D and Sala, E and Gambacorta, MA}, title = {MOREOVER: multiomics MR-guided radiotherapy optimization in locally advanced rectal cancer.}, journal = {Radiation oncology (London, England)}, volume = {19}, number = {1}, pages = {94}, pmid = {39054479}, issn = {1748-717X}, support = {Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; }, mesh = {*Rectal Neoplasms/radiotherapy/pathology/therapy ; Humans ; Neoadjuvant Therapy/methods ; Gastrointestinal Microbiome ; Magnetic Resonance Imaging ; Radiotherapy, Image-Guided/methods ; Chemoradiotherapy/methods ; Circulating Tumor DNA/genetics ; Biomarkers, Tumor ; Genomics/methods ; Male ; Female ; Multiomics ; }, abstract = {BACKGROUND: Complete response prediction in locally advanced rectal cancer (LARC) patients is generally focused on the radiomics analysis of staging MRI. Until now, omics information extracted from gut microbiota and circulating tumor DNA (ctDNA) have not been integrated in composite biomarkers-based models, thereby omitting valuable information from the decision-making process. In this study, we aim to integrate radiomics with gut microbiota and ctDNA-based genomics tracking during neoadjuvant chemoradiotherapy (nCRT).

METHODS: The main hypothesis of the MOREOVER study is that the incorporation of composite biomarkers with radiomics-based models used in the THUNDER-2 trial will improve the pathological complete response (pCR) predictive power of such models, paving the way for more accurate and comprehensive personalized treatment approaches. This is due to the inclusion of actionable omics variables that may disclose previously unknown correlations with radiomics. Aims of this study are: - to generate longitudinal microbiome data linked to disease resistance to nCRT and postulate future therapeutic strategies in terms of both type of treatment and timing, such as fecal microbiota transplant in non-responding patients. - to describe the genomics pattern and ctDNA data evolution throughout the nCRT treatment in order to support the prediction outcome and identify new risk-category stratification agents. - to mine and combine collected data through integrated multi-omics approaches (radiomics, metagenomics, metabolomics, metatranscriptomics, human genomics, ctDNA) in order to increase the performance of the radiomics-based response predictive model for LARC patients undergoing nCRT on MR-Linac.

EXPERIMENTAL DESIGN: The objective of the MOREOVER project is to enrich the phase II THUNDER-2 trial (NCT04815694) with gut microbiota and ctDNA omics information, by exploring the possibility to enhance predictive performance of the developed model. Longitudinal ctDNA genomics, microbiome and genomics data will be analyzed on 7 timepoints: prior to nCRT, during nCRT on a weekly basis and prior to surgery. Specific modelling will be performed for data harvested, according to the TRIPOD statements.

DISCUSSION: We expect to find differences in fecal microbiome, ctDNA and radiomics profiles between the two groups of patients (pCR and not pCR). In addition, we expect to find a variability in the stability of the considered omics features over time. The identified profiles will be inserted into dedicated modelling solutions to set up a multiomics decision support system able to achieve personalized treatments.}, } @article {pmid39054372, year = {2024}, author = {Pu, Y and Sun, Z and Zhang, H and Huang, Q and Wang, Z and Mei, Z and Wang, P and Kong, M and Yang, W and Lin, C and Zhou, X and Lin, S and Huang, Q and Huang, L and Sun, L and Yuan, C and Xu, Q and Tang, H and Wang, X and Zheng, Y}, title = {Gut microbial features and circulating metabolomic signatures of frailty in older adults.}, journal = {Nature aging}, volume = {4}, number = {9}, pages = {1249-1262}, pmid = {39054372}, issn = {2662-8465}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; Aged ; Male ; *Frailty/blood/metabolism/microbiology ; Aged, 80 and over ; Middle Aged ; *Metabolomics ; Aging ; Frail Elderly ; Metabolome/physiology ; Clostridium/isolation & purification ; }, abstract = {Frailty, a multidimensional indicator of suboptimal aging, reflects cumulative declines across multiple physiological systems. Although age-related changes have been reported in gut microbiota, their role in healthy aging remains unclear. In this study, we calculated frailty index (FI) from 33 health-related items to reflect the overall health status of 1,821 older adults (62-96 years, 55% female) and conducted multi-omics analysis using gut metagenomic sequencing data and plasma metabolomic data. We identified 18 microbial species and 17 metabolites shifted along with frailty severity, with stronger links observed in females. The associations of nine species, including various Clostridium species and Faecalibacterium prausnitzii, with FI were reproducible in two external populations. Plasma glycerol levels, white blood cell count and kidney function partially mediated these associations. A composite microbial score derived from FI significantly predicted 2-year mortality (adjusted hazard ratio across extreme quartiles, 2.86; 95% confidence interval, 1.38-5.93), highlighting the potential of microbiota-based strategies for risk stratification in older adults.}, } @article {pmid39053208, year = {2024}, author = {Kong, Z and Wang, H and Wang, H and Man, S and Yan, Q}, title = {Magnetite-mediated shifts in denitrifying consortia in bioelectrochemical system: Insights into species selection and metabolic dynamics.}, journal = {Water research}, volume = {262}, number = {}, pages = {122132}, doi = {10.1016/j.watres.2024.122132}, pmid = {39053208}, issn = {1879-2448}, mesh = {*Denitrification ; *Ferrosoferric Oxide/metabolism ; Geobacter/metabolism ; Nitrates/metabolism ; Microbial Consortia ; Bioreactors/microbiology ; }, abstract = {Conductive materials, such as magnetite, are recognized for their ability to enhance electron transfer and stimulate microbial metabolic activities. This study aimed to elucidate the metabolic potential and species interactions of dominant microbial species within complex communities influenced by magnetite. It indicated that the optimal dosage of magnetite at 4.5 mg/cm[2], would significantly improve denitrification efficiency and then reduce the time for removing 50 mg/L nitrate by 24.33 %. This enhancement was attributed to the reduced charge transfer resistance and the promoted formation of extracellular polymeric substances (EPS) facilitated by magnetite. Metagenomic analysis revealed that magnetite addition mitigated the competition among truncated denitrifiers for downstream nitrogen species, diminished the contribution of bacteria with complete nitrogen metabolism pathways to denitrification, and fostered a transition towards co-denitrification through interspecies cooperation, consequently leading to decreased nitrite accumulation and increased tolerance to nitrate shock loads. Furthermore, an in-depth study on a key species, Geobacter anodireducens JN93 within the bioelectrochemical system revealed that while magnetite with varying Fe(II) and Fe(III) ratios improved denitrification performance, the metabolic potential of Geobacter sp. varied for different nitrogen metabolism pathways. Collectively, this research provides insights into the microecological effects of magnetite on denitrifying consortia by shifting interspecific interactions via enhanced electron transfer.}, } @article {pmid39052651, year = {2024}, author = {Fofanova, TY and Karandikar, UC and Auchtung, JM and Wilson, RL and Valentin, AJ and Britton, RA and Grande-Allen, KJ and Estes, MK and Hoffman, K and Ramani, S and Stewart, CJ and Petrosino, JF}, title = {A novel system to culture human intestinal organoids under physiological oxygen content to study microbial-host interaction.}, journal = {PloS one}, volume = {19}, number = {7}, pages = {e0300666}, pmid = {39052651}, issn = {1932-6203}, mesh = {Humans ; *Organoids/microbiology/metabolism ; *Oxygen/metabolism ; *Coculture Techniques/methods ; *Intestinal Mucosa/microbiology/metabolism/cytology ; Gastrointestinal Microbiome ; Host Microbial Interactions ; Bacteria, Anaerobic/growth & development/metabolism ; Intestines/microbiology/cytology ; Bacteroides thetaiotaomicron/metabolism ; }, abstract = {Mechanistic investigation of host-microbe interactions in the human gut are hindered by difficulty of co-culturing microbes with intestinal epithelial cells. On one hand the gut bacteria are a mix of facultative, aerotolerant or obligate anaerobes, while the intestinal epithelium requires oxygen for growth and function. Thus, a coculture system that can recreate these contrasting oxygen requirements is critical step towards our understanding microbial-host interactions in the human gut. Here, we demonstrate Intestinal Organoid Physoxic Coculture (IOPC) system, a simple and cost-effective method for coculturing anaerobic intestinal bacteria with human intestinal organoids (HIOs). Using commensal anaerobes with varying degrees of oxygen tolerance, such as nano-aerobe Bacteroides thetaiotaomicron and strict anaerobe Blautia sp., we demonstrate that IOPC can successfully support 24-48 hours HIO-microbe coculture. The IOPC recapitulates the contrasting oxygen conditions across the intestinal epithelium seen in vivo. The IOPC cultured HIOs showed increased barrier integrity, and induced expression of immunomodulatory genes. A transcriptomic analysis suggests that HIOs from different donors show differences in the magnitude of their response to coculture with anaerobic bacteria. Thus, the IOPC system provides a robust coculture setup for investigating host-microbe interactions in complex, patient-derived intestinal tissues, that can facilitate the study of mechanisms underlying the role of the microbiome in health and disease.}, } @article {pmid39052319, year = {2024}, author = {Liu, B and Qi, L and Zheng, Y and Zhang, C and Zhou, J and An, Z and Wang, B and Lin, Z and Yao, C and Wang, Y and Yin, G and Dong, H and Li, X and Liang, X and Han, P and Liu, M and Zhang, G and Cui, Y and Hou, L}, title = {Four years of climate warming reduced dark carbon fixation in coastal wetlands.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39052319}, issn = {1751-7370}, support = {YBNLTS2023-004//Fundamental Research Funds for the Central Universities/ ; 2023YFC3208404//National Key Research and Development Program of China/ ; 31800411//National Natural Science Foundation of China/ ; }, mesh = {*Wetlands ; *Carbon Cycle ; *Climate Change ; Soil Microbiology ; Carbon Sequestration ; Carbon/metabolism ; Biodiversity ; Soil/chemistry ; Metagenomics ; Temperature ; Bacteria/metabolism/classification/genetics/isolation & purification ; }, abstract = {Dark carbon fixation (DCF), conducted mainly by chemoautotrophs, contributes greatly to primary production and the global carbon budget. Understanding the response of DCF process to climate warming in coastal wetlands is of great significance for model optimization and climate change prediction. Here, based on a 4-yr field warming experiment (average annual temperature increase of 1.5°C), DCF rates were observed to be significantly inhibited by warming in coastal wetlands (average annual DCF decline of 21.6%, and estimated annual loss of 0.08-1.5 Tg C yr-1 in global coastal marshes), thus causing a positive climate feedback. Under climate warming, chemoautotrophic microbial abundance and biodiversity, which were jointly affected by environmental changes such as soil organic carbon and water content, were recognized as significant drivers directly affecting DCF rates. Metagenomic analysis further revealed that climate warming may alter the pattern of DCF carbon sequestration pathways in coastal wetlands, increasing the relative importance of the 3-hydroxypropionate/4-hydroxybutyrate cycle, whereas the relative importance of the dominant chemoautotrophic carbon fixation pathways (Calvin-Benson-Bassham cycle and W-L pathway) may decrease due to warming stress. Collectively, our work uncovers the feedback mechanism of microbially mediated DCF to climate warming in coastal wetlands, and emphasizes a decrease in carbon sequestration through DCF activities in this globally important ecosystem under a warming climate.}, } @article {pmid39051424, year = {2024}, author = {Ti, J and Ning, Z and Zhang, M and Wang, S and Gan, S and Xu, Z and Di, H and Kong, S and Sun, W and He, Z}, title = {Characterization the microbial diversity and functional genes in the multi-component contaminated groundwater in a petrochemical site.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {96}, number = {7}, pages = {e11085}, doi = {10.1002/wer.11085}, pmid = {39051424}, issn = {1554-7531}, support = {42330714//National Natural Science Foundation of China/ ; D2021504025//Natural Science Foundation of Hebei Province/ ; }, mesh = {*Groundwater/microbiology/chemistry ; *Water Pollutants, Chemical/metabolism ; *Petroleum ; Bacteria/classification/genetics/metabolism ; Hydrocarbons/metabolism ; RNA, Ribosomal, 16S/genetics ; Biodegradation, Environmental ; Biodiversity ; Water Microbiology ; }, abstract = {Microorganisms in groundwater at petroleum hydrocarbon (PHC)-contaminated sites are crucial for PHC natural attenuation. Studies mainly focused on the microbial communities and functions in groundwater contaminated by PHC only. However, due to diverse raw and auxiliary materials and the complex production processes, in some petrochemical sites, groundwater suffered multi-component contamination, but the microbial structure remains unclear. To solve the problem, in the study, a petrochemical enterprise site, where the groundwater suffered multi-component pollution by PHC and sulfates, was selected. Using hydrochemistry, 16S rRNA gene, and metagenomic sequencing analyses, the relationships among electron acceptors, microbial diversity, functional genes, and their interactions were investigated. Results showed that different production processes led to different microbial structures. Overall, pollution reduced species richness but increased the abundance of specific species. The multi-component contamination multiplied a considerable number of hydrocarbon-degrading and sulfate-reducing microorganisms, and the introduced sulfates might have promoted the biodegradation of PHC. PRACTITIONER POINTS: The compound pollution of the site changed the microbial community structure. Sulfate can promote the degradation of petroleum hydrocarbons by hydrocarbon-degrading microorganisms. The combined contamination of petroleum hydrocarbons and sulfates will decrease the species richness but increase the abundance of endemic species.}, } @article {pmid39048979, year = {2024}, author = {Jiang, C and Yang, J and Peng, X and Li, X}, title = {A permutable MLP-like architecture for disease prediction from gut metagenomic data.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {246}, pmid = {39048979}, issn = {1471-2105}, support = {82171526//National Natural Science Foundation of China/ ; 2020A38//Beijing Talents Fund/ ; SZU-BDSC-OF2024-19//National Engineering Laboratory for Big Data System Computing Technology/ ; }, mesh = {*Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Humans ; Neural Networks, Computer ; Phylogeny ; Machine Learning ; Deep Learning ; Metagenome/genetics ; }, abstract = {Metagenomic data plays a crucial role in analyzing the relationship between microbes and diseases. However, the limited number of samples, high dimensionality, and sparsity of metagenomic data pose significant challenges for the application of deep learning in data classification and prediction. Previous studies have shown that utilizing the phylogenetic tree structure to transform metagenomic abundance data into a 2D matrix input for convolutional neural networks (CNNs) improves classification performance. Inspired by the success of a Permutable MLP-like architecture in visual recognition, we propose Metagenomic Permutator (MetaP), which applied the Permutable MLP-like network structure to capture the phylogenetic information of microbes within the 2D matrix formed by phylogenetic tree. Our experiments demonstrate that our model achieved competitive performance compared to other deep neural networks and traditional machine learning, and has good prospects for multi-classification and large sample sizes. Furthermore, we utilize the SHAP (SHapley Additive exPlanations) method to interpret our model predictions, identifying the microbial features that are associated with diseases.}, } @article {pmid39048485, year = {2024}, author = {Pérez-Prieto, I and Plaza-Florido, A and Ubago-Guisado, E and Ortega, FB and Altmäe, S}, title = {Physical activity, sedentary behavior and microbiome: A systematic review and meta-analysis.}, journal = {Journal of science and medicine in sport}, volume = {27}, number = {11}, pages = {793-804}, doi = {10.1016/j.jsams.2024.07.003}, pmid = {39048485}, issn = {1878-1861}, mesh = {Humans ; *Exercise/physiology ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome/physiology ; *Sedentary Behavior ; }, abstract = {BACKGROUND: The effects of physical activity and sedentary behavior on human health are well known, however, the molecular mechanisms are poorly understood. Growing evidence points to physical activity as an important modulator of the composition and function of microbial communities, while evidence of sedentary behavior is scarce. We aimed to synthesize and meta-analyze the current evidence about the effects of physical activity and sedentary behavior on microbiome across different body sites and in different populations.

METHODS: A systematic search in PubMed, Web of Science, Scopus and Cochrane databases was conducted until September 2022. Random-effects meta-analyses including cross-sectional studies (active vs. inactive/athletes vs. non-athletes) or trials reporting the chronic effect of physical activity interventions on gut microbiome alpha-diversity in healthy individuals were performed.

RESULTS: Ninety-one studies were included in this systematic review. Our meta-analyses of 2632 participants indicated no consistent effect of physical activity on microbial alpha-diversity, although there seems to be a trend toward a higher microbial richness in athletes compared to non-athletes. Most of studies reported an increase in short-chain fatty acid-producing bacteria such as Akkermansia, Faecalibacterium, Veillonella or Roseburia in active individuals and after physical activity interventions.

CONCLUSIONS: Physical activity levels were positively associated with the relative abundance of short-chain fatty acid-producing bacteria. Athletes seem to have a richer microbiome compared to non-athletes. However, high heterogeneity between studies avoids obtaining conclusive information on the role of physical activity in microbial composition. Future multi-omics studies would enhance our understanding of the molecular effects of physical activity and sedentary behavior on the microbiome.}, } @article {pmid39047732, year = {2024}, author = {Yang, Z and Ma, J and Han, J and Li, A and Liu, G and Sun, Y and Zheng, J and Zhang, J and Chen, G and Xu, R and Sun, L and Meng, C and Gao, J and Bai, Z and Deng, W and Zhang, C and Su, J and Yao, H and Zhang, Z}, title = {Gut microbiome model predicts response to neoadjuvant immunotherapy plus chemoradiotherapy in rectal cancer.}, journal = {Med (New York, N.Y.)}, volume = {5}, number = {10}, pages = {1293-1306.e4}, doi = {10.1016/j.medj.2024.07.002}, pmid = {39047732}, issn = {2666-6340}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Rectal Neoplasms/therapy/microbiology/pathology ; Male ; Female ; Middle Aged ; *Neoadjuvant Therapy/methods ; Prospective Studies ; Aged ; *Immunotherapy/methods ; *Chemoradiotherapy/methods ; Adult ; Treatment Outcome ; Feces/microbiology ; }, abstract = {BACKGROUND: Accurate evaluation of the response to preoperative treatment enables the provision of a more appropriate personalized therapeutic schedule for locally advanced rectal cancer (LARC), which remains an enormous challenge, especially neoadjuvant immunotherapy plus chemoradiotherapy (nICRT).

METHODS: This prospective, multicenter cohort study enrolled patients with LARC from 6 centers who received nICRT. The dynamic variation in the gut microbiome during nICRT was evaluated. A species-level gut microbiome prediction (SPEED) model was developed and validated to predict the pathological complete response (pCR) to nICRT.

FINDINGS: A total of 50 patients were enrolled, 75 fecal samples were collected from 33 patients at different time points, and the pCR rate reached 42.4% (14/33). Lactobacillus and Eubacterium were observed to increase after nICRT. Additionally, significant differences in the gut microbiome were observed between responders and non-responders at baseline. Significantly higher abundances of Lachnospiraceae bacterium and Blautia wexlerae were found in responders, while Bacteroides, Prevotella, and Porphyromonas were found in non-responders. The SPEED model showcased a superior predictive performance with areas under the curve of 98.80% (95% confidence interval [CI]: 95.67%-100%) in the training cohort and 77.78% (95% CI: 65.42%-88.29%) in the validation cohort.

CONCLUSIONS: Programmed death 1 (PD-1) blockade plus concurrent long-course CRT showed a favorable pCR rate and is well tolerated in microsatellite-stable (MSS)/mismatch repair-proficient (pMMR) patients with LARC. The SPEED model can be used to predict the pCR to nICRT based on the baseline gut microbiome with high robustness and accuracy, thereby assisting clinical physicians in providing individualized management for patients with LARC.

FUNDING: This research was funded by the China National Natural Science Foundation (82202884).}, } @article {pmid39047022, year = {2024}, author = {Lekuya, HM and Kateete, DP and Olweny, G and Kigozi, E and Kamabu, LK and Mudekereza, SP and Nantambi, R and Mbiine, R and Makumbi, F and Cose, S and Vandersteene, J and Baert, E and Kalala, JO and Galukande, M}, title = {Metagenomic sequencing of the skin microbiota of the scalp predicting the risk of surgical site infections following surgery of traumatic brain injury in sub-Saharan Africa.}, journal = {PloS one}, volume = {19}, number = {7}, pages = {e0303483}, pmid = {39047022}, issn = {1932-6203}, mesh = {Humans ; Male ; *Surgical Wound Infection/microbiology/epidemiology ; Female ; *Scalp/microbiology ; Adult ; *Microbiota/genetics ; *Metagenomics/methods ; *Brain Injuries, Traumatic/microbiology ; Prospective Studies ; Africa South of the Sahara/epidemiology ; Skin/microbiology ; Young Adult ; Adolescent ; RNA, Ribosomal, 16S/genetics ; Uganda/epidemiology ; Middle Aged ; Risk Factors ; Metagenome ; }, abstract = {BACKGROUND: Surgical site infections (SSI) are a significant concern following traumatic brain injury (TBI) surgery and often stem from the skin's microbiota near the surgical site, allowing bacteria to penetrate deeper layers and potentially causing severe infections in the cranial cavity. This study investigated the relationship between scalp skin microbiota composition and the risk of SSI after TBI surgery in sub-Saharan Africa (SSA).

METHODS: This was a prospective cohort study, enrolling patients scheduled for TBI surgery. Sterile skin swabs were taken from the surrounding normal skin of the head and stored for analysis at -80°Celcius. Patients were monitored postoperatively for up to three months to detect any occurrences of SSI. 16S rRNA sequencing was used to analyze the skin microbiota composition, identifying different taxonomic microorganisms at the genus level. The analysis compared two groups: those who developed SSI and those who did not.

RESULTS: A total of 57 patients were included, mostly male (89.5%) with a mean age of 26.5 years, predominantly from urban areas in Uganda and victims of assault. Graphical visualization and metagenomic metrics analysis revealed differences in composition, richness, and evenness of skin microbiota within samples (α) or within the community (β), and showed specific taxa (phylum and genera) associated with either the group of SSI or the No SSI.

CONCLUSIONS: Metagenomic sequencing analysis uncovered several baseline findings and trends regarding the skin microbiome's relationship with SSI risk. There is an association between scalp microbiota composition (abundancy and diversity) and SSI occurrence following TBI surgery in SSA. We hypothesize under reserve that the scalp microbiota dysbiosis could potentially be an independent predictor of the occurrence of SSI; we advocate for further studies with larger cohorts.}, } @article {pmid39045787, year = {2024}, author = {Tayebwa, DS and Hyeroba, D and Dunn, CD and Dunay, E and Richard, JC and Biryomumaisho, S and Acai, JO and Goldberg, TL}, title = {Viruses of free-roaming and hunting dogs in Uganda show elevated prevalence, richness and abundance across a gradient of contact with wildlife.}, journal = {The Journal of general virology}, volume = {105}, number = {7}, pages = {}, pmid = {39045787}, issn = {1465-2099}, mesh = {Animals ; Dogs ; Uganda/epidemiology ; *Dog Diseases/virology/epidemiology/transmission ; Prevalence ; *Animals, Wild/virology ; Virome ; Viruses/classification/isolation & purification/genetics ; Metagenomics ; Anelloviridae/genetics/isolation & purification/classification ; Humans ; Virus Diseases/epidemiology/veterinary/transmission/virology ; }, abstract = {Domestic dogs (Canis lupus familiaris) live with humans, frequently contact other animals and may serve as intermediary hosts for the transmission of viruses. Free-roaming dogs, which account for over 70% of the world's domestic dog population, may pose a particularly high risk in this regard. We conducted an epidemiological study of dog viromes in three locations in Uganda, representing low, medium and high rates of contact with wildlife, ranging from dogs owned specifically for traditional hunting in a biodiversity and disease 'hotspot' to pets in an affluent suburb. We quantified rates of contact between dogs and wildlife through owner interviews and conducted canine veterinary health assessments. We then applied broad-spectrum viral metagenomics to blood plasma samples, from which we identified 46 viruses, 44 of which were previously undescribed, in three viral families, Sedoreoviridae, Parvoviridae and Anelloviridae. All 46 viruses (100 %) occurred in the high-contact population of dogs compared to 63 % and 39 % in the medium- and low-contact populations, respectively. Viral prevalence ranged from 2.1 % to 92.0 % among viruses and was highest, on average, in the high-contact population (22.3 %), followed by the medium-contact (12.3 %) and low-contact (4.8 %) populations. Viral richness (number of viruses per dog) ranged from 0 to 27 and was markedly higher, on average, in the high-contact population (10.2) than in the medium-contact (5.7) or low-contact (2.3) populations. Viral richness was strongly positively correlated with the number of times per year that a dog was fed wildlife and negatively correlated with the body condition score, body temperature and packed cell volume. Viral abundance (cumulative normalized metagenomic read density) varied 124-fold among dogs and was, on average, 4.1-fold higher and 2.4-fold higher in the high-contact population of dogs than in the low-contact or medium-contact populations, respectively. Viral abundance was also strongly positively correlated with the number of times per year that a dog was fed wildlife, negatively correlated with packed cell volume and positively correlated with white blood cell count. These trends were driven by nine viruses in the family Anelloviridae, genus Thetatorquevirus, and by one novel virus in the family Sedoreoviridae, genus Orbivirus. The genus Orbivirus contains zoonotic viruses and viruses that dogs can acquire through ingestion of infected meat. Overall, our findings show that viral prevalence, richness and abundance increased across a gradient of contact between dogs and wildlife and that the health status of the dog modified viral infection. Other ecological, geographic and social factors may also have contributed to these trends. Our finding of a novel orbivirus in dogs with high wildlife contact supports the idea that free-roaming dogs may serve as intermediary hosts for viruses of medical importance to humans and other animals.}, } @article {pmid39044909, year = {2024}, author = {Moumen, B and Samba-Louaka, C and Kimpamboudi, VAM and Boumba, AM and Ngoma, HS and Samba-Louaka, A}, title = {Metagenomic data from gutter water in the city of Pointe-Noire, Republic of Congo.}, journal = {Data in brief}, volume = {55}, number = {}, pages = {110655}, pmid = {39044909}, issn = {2352-3409}, abstract = {After Amazonia, the Congo Basin represents the second-largest tropical rainforest area in the world. This basin harbours remarkable biodiversity, yet much of its microbiological diversity within its waters, soils, and populations remains largely unexplored and undiscovered. While many initiatives to characterize global biodiversity are being undertaken, few are conducted in Africa and none of them concern the Congo Basin specifically in urban areas. In this context, we assessed the microbial diversity present in gutter water in the city of Pointe-Noire, Congo. This town has interesting characteristics as the population density is high and it is located between the Atlantic Ocean and the forest of Mayombe in Central Africa. The findings illuminate the microbial composition of surface water in Pointe-Noire. The dataset allows the identification of putative new bacteria through the assembly of 81 meta-genome-assembled genomes. It also serves as a valuable primary resource for assessing the presence of antibiotic-resistant genes, offering a useful tool for monitoring risks by public health authorities.}, } @article {pmid39044605, year = {2024}, author = {Xu, H and Zhang, J and Wang, F and Chen, Y and Chen, H and Feng, Y and Hou, G and Zi, J and Zhang, M and Zhou, J and Deng, L and Lin, L and Zhang, X and Liu, S}, title = {Integration of metagenomics and metaproteomics in the intestinal lavage fluids benefits construction of discriminative model and discovery of biomarkers for HBV liver diseases.}, journal = {Proteomics}, volume = {24}, number = {20}, pages = {e2400002}, doi = {10.1002/pmic.202400002}, pmid = {39044605}, issn = {1615-9861}, support = {2023YFC3402900//National Key Research and Development Program of China/ ; 2022YFA1304500//National Key Research and Development Program of China/ ; 2020YFE0202200//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Biomarkers/analysis/metabolism ; *Proteomics/methods ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Hepatitis B/virology/genetics/microbiology ; Female ; Adult ; Male ; Hepatitis B virus/genetics ; Machine Learning ; Middle Aged ; }, abstract = {Intestinal lavage fluid (IVF) containing the mucosa-associated microbiota instead of fecal samples was used to study the gut microbiota using different omics approaches. Focusing on the 63 IVF samples collected from healthy and hepatitis B virus-liver disease (HBV-LD), a question is prompted whether omics features could be extracted to distinguish these samples. The IVF-related microbiota derived from the omics data was classified into two enterotype sets, whereas the genomics-based enterotypes were poorly overlapped with the proteomics-based one in either distribution of microbiota or of IVFs. There is lack of molecular features in these enterotypes to specifically recognize healthy or HBV-LD. Running machine learning against the omics data sought the appropriate models to discriminate the healthy and HBV-LD IVFs based on selected genes or proteins. Although a single omics dataset is basically workable in such discrimination, integration of the two datasets enhances discrimination efficiency. The protein features with higher frequencies in the models are further compared between healthy and HBV-LD based on their abundance, bringing about three potential protein biomarkers. This study highlights that integration of metaomics data is beneficial for a molecular discriminator of healthy and HBV-LD, and reveals the IVF samples are valuable for microbiome in a small cohort.}, } @article {pmid39044261, year = {2024}, author = {Ma, S and Yin, Y and Guo, Y and Yao, C and Xu, S and Luo, Q and Yin, G and Wang, S and Wang, Q and Chen, H and Wang, R and Jin, L and Liang, G and Wang, H}, title = {The plasma viral communities associate with clinical profiles in a large-scale haematological patients cohort.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {137}, pmid = {39044261}, issn = {2049-2618}, mesh = {Humans ; Male ; Female ; *DNA Viruses/isolation & purification/genetics ; Middle Aged ; *Virus Diseases/blood/virology ; Adult ; *Hematologic Diseases/complications/blood ; *RNA Viruses/isolation & purification ; Virome ; Aged ; Torque teno virus/isolation & purification/genetics ; Cohort Studies ; Herpesvirus 4, Human/genetics/isolation & purification ; Young Adult ; }, abstract = {BACKGROUND: Haematological patients exhibit immune system abnormalities that make them susceptible to viral infections. Understanding the relationship between the virome in the blood plasma of haematological patients and their clinical characteristic is crucial for disease management. We aimed to explore the presence of viral pathogens and identify close associations between viral infections and various clinical features.

RESULTS: A total of 21 DNA viruses and 6 RNA viruses from 12 virus families were identified from 1383 patients. Patients with haematological diseases exhibited significantly higher diversity, prevalence, and co-detection rates of viral pathogens. During fever episodes, pathogen detection was notably higher, with Epstein-Barr virus (EBV) and Mucorales infections being the most probable culprits for fever symptoms in non-haematological patients. The detection rate of torque teno virus (TTV) significantly increases in haematological patients after transplantation and during primary lung infections. Additionally, TTV-positive patients demonstrate significantly higher absolute neutrophil counts, while C-reactive protein and procalcitonin levels are notably lower. Furthermore, TTV, cytomegalovirus, and parvovirus B19 (B19V) were found to be more prevalent in non-neutropenic patients, while non-viral pathogenic infections, such as Gram-negative bacteria and Mucorales, were more common in neutropenic patients. Pegivirus C (HPgV-C) infection often occurred post-transplantation, regardless of neutropenia. Additionally, some viruses such as TTV, B19V, EBV, and HPgV-C showed preferences for age and seasonal infections.

CONCLUSIONS: Analysis of the plasma virome revealed the susceptibility of haematological patients to plasma viral infections at specific disease stages, along with the occurrence of mixed infections with non-viral pathogens. Close associations were observed between the plasma virome and various clinical characteristics, as well as clinical detection parameters. Understanding plasma virome aids in auxiliary clinical diagnosis and treatment, enabling early prevention to reduce infection rates in patients and improve their quality of life. Video Abstract.}, } @article {pmid39044244, year = {2024}, author = {Glendinning, L and Jia, X and Kebede, A and Oyola, SO and Park, JE and Park, W and Assiri, A and Holm, JB and Kristiansen, K and Han, J and Hanotte, O}, title = {Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {138}, pmid = {39044244}, issn = {2049-2618}, mesh = {Animals ; *Chickens/microbiology ; Ethiopia ; *Altitude ; *Bacteria/classification/genetics/isolation & purification ; Gastrointestinal Microbiome/genetics ; Metagenome ; Cecum/microbiology ; Microbiota ; Biodiversity ; Phylogeny ; }, abstract = {BACKGROUND: Scavenging indigenous village chickens play a vital role in sub-Saharan Africa, sustaining the livelihood of millions of farmers. These chickens are exposed to vastly different environments and feeds compared to commercial chickens. In this study, we analysed the caecal microbiota of 243 Ethiopian village chickens living in different altitude-dependent agro-ecologies.

RESULTS: Differences in bacterial diversity were significantly correlated with differences in specific climate factors, topsoil characteristics, and supplemental diets provided by farmers. Microbiota clustered into three enterotypes, with one particularly enriched at high altitudes. We assembled 9977 taxonomically and functionally diverse metagenome-assembled genomes. The vast majority of these were not found in a dataset of previously published chicken microbes or in the Genome Taxonomy Database.

CONCLUSIONS: The wide functional and taxonomic diversity of these microbes highlights their importance in the local adaptation of indigenous poultry, and the significant impacts of environmental factors on the microbiota argue for further discoveries in other agro-ecologies. Video Abstract.}, } @article {pmid39043353, year = {2024}, author = {Thacharodi, A and Hassan, S and Ahmed, ZHT and Singh, P and Maqbool, M and Meenatchi, R and Pugazhendhi, A and Sharma, A}, title = {The ruminant gut microbiome vs enteric methane emission: The essential microbes may help to mitigate the global methane crisis.}, journal = {Environmental research}, volume = {261}, number = {}, pages = {119661}, doi = {10.1016/j.envres.2024.119661}, pmid = {39043353}, issn = {1096-0953}, mesh = {*Methane/metabolism ; Animals ; *Gastrointestinal Microbiome ; *Ruminants/microbiology ; Rumen/microbiology/metabolism ; Greenhouse Gases/metabolism ; Probiotics ; Cattle ; Fermentation ; Bacteria/metabolism ; }, abstract = {Ruminants release enteric methane into the atmosphere, significantly increasing greenhouse gas emissions and degrading the environment. A common focus of traditional mitigation efforts is on dietary management and manipulation, which may have limits in sustainability and efficacy, exploring the potential of essential microorganisms as a novel way to reduce intestinal methane emissions in ruminants; a topic that has garnered increased attention in recent years. Fermentation and feed digestion are significantly aided by essential microbes found in the rumen, such as bacteria, fungi, and archaea. The practical implications of the findings reported in various studies conducted on rumen gut concerning methane emissions may pave the way to understanding the mechanisms of CH4 production in the rumen to enhance cattle feed efficiency and mitigate CH4 emissions from livestock. This review discussed using essential bacteria to reduce intestinal methane emissions in ruminants. It investigates how particular microbial strains or consortia can alter rumen fermentation pathways to lower methane output while preserving the health and productivity of animals. We also describe the role of probiotics and prebiotics in managing methane emissions using microbial feed additives. Further, recent studies involving microbial interventions have been discussed. The use of new methods involving functional metagenomics and meta-transcriptomics for exploring the rumen microbiome structure has been highlighted. This review also emphasizes the challenges faced in altering the gut microbiome and future directions in this area.}, } @article {pmid39043311, year = {2024}, author = {Wang, X and Li, J and Wang, D and Sun, C and Zhang, X and Zhao, J and Teng, J and Wang, Q}, title = {Unveiling microplastic's role in nitrogen cycling: Metagenomic insights from estuarine sediment microcosms.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {359}, number = {}, pages = {124591}, doi = {10.1016/j.envpol.2024.124591}, pmid = {39043311}, issn = {1873-6424}, mesh = {*Geologic Sediments/chemistry/microbiology ; *Microplastics/toxicity ; *Nitrogen Cycle ; *Water Pollutants, Chemical/metabolism/analysis ; *Estuaries ; Metagenomics ; Nitrogen/metabolism ; Environmental Monitoring ; Microbiota/drug effects ; }, abstract = {Marine microplastics (MPs) pollution, with rivers as a major source, leads to MPs accumulation in estuarine sediments, which are also nitrogen cycling hotspots. However, the impact of MPs on nitrogen cycling in estuarine sediments has rarely been documented. In this study, we conducted microcosm experiment to investigate the effects of commonly encountered polyethylene (PE) and polystyrene (PS) MPs, with two MPs concentrations (0.3% and 3% wet sediment weight) based on environmental concentration considerations and dose-response effects, on sediment dissolved oxygen (DO) diffusion capacity and microbial communities using microelectrode system and metagenomic analysis respectively. The results indicated that high concentrations of PE-MPs inhibited DO diffusion during the mid-phase of the experiment, an effect that dissipated in the later stages. Metagenomic analysis revealed that MP treatments reduced the relative abundance of dominant microbial colonies in the sediments. The PCoA results demonstrated that MPs altered the microbial community structure, particularly evident under high concentration PE-MPs treatments. Functional analysis related to the nitrogen cycle suggested that PS-MPs promoted the nitrification, denitrification, and DNRA processes, but inhibited the ANRA process, while PE-MPs had an inhibitory effect on the nitrate reduction process and the ANRA process. Additionally, the high concentration of PE-MPs treatment significantly stimulated the abundance of genus (Bacillus) by 34.1% and genes (lip, pnbA) by 100-187.5% associated with plastic degradation, respectively. Overall, in terms of microbial community structure and the abundance of nitrogen cycling functional genes, PE- and PS- MPs exhibit both similarities and differences in their impact on nitrogen cycling. Our findings highlight the complexity of MP effects on nitrogen cycling in estuarine sediments and high concentrations of PE-MP stimulated plastic-degrading genus and genes.}, } @article {pmid39043054, year = {2024}, author = {Perdomo, A and Calle, A}, title = {Assessment of microbial communities in a dairy farm from a food safety perspective.}, journal = {International journal of food microbiology}, volume = {423}, number = {}, pages = {110827}, doi = {10.1016/j.ijfoodmicro.2024.110827}, pmid = {39043054}, issn = {1879-3460}, mesh = {Animals ; *Food Safety ; *Dairying ; Cattle ; *Farms ; *Milk/microbiology ; Bacteria/isolation & purification/classification/genetics ; Microbiota ; Food Microbiology ; Feces/microbiology ; Seasons ; Animal Feed/microbiology ; Staphylococcus aureus/isolation & purification/genetics ; }, abstract = {Microbial communities associated with dairy farm operations have a significant influence on food safety, dairy product quality, and animal health. This study aimed to create a microbial mapping at a dairy farm to learn about their bacterial diversity, distribution, and potential dissemination pathways. The investigation included the detection of key zoonotic pathogens, enumeration of Staphylococcus aureus and Escherichia coli as indicators of typical bacterial loads in a dairy production environment, and a microbiome analysis using metagenomics. A total of 160 samples (environmental, udder swabs, feed, feces, raw milk, and water) were collected during winter (N = 80) and spring (N = 80). In winter, Cronobacter spp. were detected in four feed and two water samples; L. monocytogenes was identified in two samples, one from feces and one from a cattle mat; E. coli O157:H7 was found in two feed samples. On the other hand, during spring, Cronobacter spp. were present in four feed samples and one hallway drain, with only one feed sample testing positive for E. coli O157:H7, while L. monocytogenes was absent during the spring season. Regarding microbial counts, there was no significant difference between the two seasons (p = 0.068) for S. aureus; however, a significant difference (p = 0.025) was observed for E. coli. Environmental microbiome analysis showed the presence of Proteobacteria (46.0 %) and Firmicutes (27.2 %) as the dominant phyla during both seasons. Moraxellaceae (11.8 %) and Pseudomonadaceae (10.62 %) were notable during winter, while Lactobacillaceae (13.0 %) and Enterobacteriaceae (12.6 %) were prominent during spring. These findings offer valuable insights into microbial distribution within a dairy farm and potential risks to animal and human health through environmental cross-contamination.}, } @article {pmid39042309, year = {2024}, author = {Hussan, H and Ali, MR and Lyo, V and Webb, A and Pietrzak, M and Zhu, J and Choueiry, F and Li, H and Cummings, BP and Marco, ML and Medici, V and Clinton, SK}, title = {Bariatric Surgery Is Associated with Lower Concentrations of Fecal Secondary Bile Acids and Their Metabolizing Microbial Enzymes: A Pilot Study.}, journal = {Obesity surgery}, volume = {34}, number = {9}, pages = {3420-3433}, pmid = {39042309}, issn = {1708-0428}, support = {R35GM133510/GM/NIGMS NIH HHS/United States ; R35GM133510/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Feces/microbiology ; Pilot Projects ; Male ; Female ; Cross-Sectional Studies ; Case-Control Studies ; Middle Aged ; *Bariatric Surgery ; *Bile Acids and Salts/metabolism ; Adult ; *Obesity, Morbid/surgery/microbiology ; Gastrointestinal Microbiome/physiology ; Weight Loss ; Lithocholic Acid/metabolism ; }, abstract = {INTRODUCTION: Excess body fat elevates colorectal cancer risk. While bariatric surgery (BRS) induces significant weight loss, its effects on the fecal stream and colon biology are poorly understood. Specifically, limited data exist on the impact of bariatric surgery (BRS) on fecal secondary bile acids (BA), including lithocholic acid (LCA), a putative promotor of colorectal carcinogenesis.

METHODS: This cross-sectional case-control study included 44 patients with obesity; 15 pre-BRS (controls) vs. 29 at a median of 24.1 months post-BRS. We examined the fecal concentrations of 11 BA by liquid chromatography and gene abundance of BA-metabolizing bacterial enzymes through fecal metagenomic sequencing. Differences were quantified using non-parametric tests for BA levels and linear discriminant analysis (LDA) effect size (LEfSe) for genes encoding BA-metabolizing enzymes.

RESULTS: Total fecal secondary BA concentrations trended towards lower levels post- vs. pre-BRS controls (p = 0.07). Individually, fecal LCA concentrations were significantly lower post- vs. pre-BRS (8477.0 vs. 11,914.0 uM/mg, p < 0.008). Consistent with this finding, fecal bacterial genes encoding BA-metabolizing enzymes, specifically 3-betahydroxycholanate-3-dehydrogenase (EC 1.1.1.391) and 3-alpha-hydroxycholanate dehydrogenase (EC 1.1.1.52), were also lower post- vs. pre-BRS controls (LDA of - 3.32 and - 2.64, respectively, adjusted p < 0.0001). Post-BRS fecal BA concentrations showed significant inverse correlations with weight loss, a healthy diet quality, and increased physical activity.

CONCLUSIONS: Concentrations of LCA, a secondary BA, and bacterial genes needed for BA metabolism are lower post-BRS. These changes can impact health and modulate the colorectal cancer cascade. Further research is warranted to examine how surgical alterations and the associated dietary changes impact bile acid metabolism.}, } @article {pmid39040604, year = {2024}, author = {Hasan, Z and Netherland, M and Hasan, NA and Begum, N and Yasmin, M and Ahmed, S}, title = {An insight into the vaginal microbiome of infertile women in Bangladesh using metagenomic approach.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1390088}, pmid = {39040604}, issn = {2235-2988}, mesh = {Humans ; Female ; *Vagina/microbiology ; *Metagenomics/methods ; *Infertility, Female/microbiology ; Adult ; *Microbiota/genetics ; Bangladesh ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Young Adult ; Lactobacillus/isolation & purification/genetics/classification ; Dysbiosis/microbiology ; Phylogeny ; }, abstract = {INTRODUCTION: The dysbiosis of vaginal microbiota is recognized as a potential underlying factor contributing to infertility in women. This study aimed to compare the vaginal microbiomes of infertile and fertile women to investigate their relationship with infertility.

METHODS: Metagenomic analysis was conducted on samples from 5 infertile and 5 fertile individuals using both amplicon 16S and metagenomics shotgun sequencing methods.

RESULTS AND DISCUSSION: In the infertile group, the bacterial community was primarily represented by three major bacterial genera: Lactobacillus (79.42%), Gardnerella (12.56%) and Prevotella (3.33%), whereas, the fertile group exhibited a more diverse composition with over 8 major bacterial genera, accompanied by significantly reduced abundance of Lactobacillus (48.79%) and Gardnerella (6.98%). At the species level, higher abundances of L. iners, L. gasseri and G. vaginalis were observed in the infertile group. Regarding the microbiome composition, only one fertile and two infertile subjects exhibited the healthiest Community State Types, CST-1, while CST-3 was observed among two infertile and one fertile subject, and CST-4 in three other fertile and one infertile subject. Overall, alpha diversity metrics indicated greater diversity and lower species richness in the control (fertile) group, while the infertile group displayed the opposite trend. However, beta-diversity analysis did not show distinct clustering of samples associated with any specific group; instead, it demonstrated CST-type specific clustering. Shotgun metagenomics further confirmed the dominance of Firmicutes, with a greater abundance of Lactobacillus species in the infertile group. Specifically, L. iners and G. vaginalis were identified as the most dominant and highly abundant in the infertile group. Fungi were only identified in the control group, dominated by Penicillium citrinum (62.5%). Metagenome-assembled genomes (MAGs) corroborated read-based taxonomic profiling, with the taxon L. johnsonii identified exclusively in disease samples. MAG identities shared by both groups include Shamonda orthobunyavirus, L. crispatus, Human endogenous retrovirus K113, L. iners, and G. vaginalis. Interestingly, the healthy microbiomes sequenced in this study contained two clusters, Penicillium and Staphylococcus haemolyticus, not found in the public dataset. In conclusion, this study suggests that lower species diversity with a higher abundance of L. iners, L. gasseri and G. vaginalis, may contribute to female infertility in our study datasets. However, larger sample sizes are necessary to further evaluate such association.}, } @article {pmid39039586, year = {2024}, author = {Liang, JL and Feng, SW and Jia, P and Lu, JL and Yi, X and Gao, SM and Wu, ZH and Liao, B and Shu, WS and Li, JT}, title = {Unraveling the habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses across China.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {136}, pmid = {39039586}, issn = {2049-2618}, support = {42177009//National Natural Science Foundation of China/ ; 41622106//National Natural Science Foundation of China/ ; 2023YFC3207300//National Key R&D Program of China/ ; }, mesh = {China ; *Soil Microbiology ; *Metagenome ; *Ecosystem ; *Giant Viruses/genetics/classification ; Soil/chemistry ; Phylogeny ; Genome, Viral/genetics ; Metagenomics ; }, abstract = {BACKGROUND: Soil giant viruses are increasingly believed to have profound effects on ecological functioning by infecting diverse eukaryotes. However, their biogeography and ecology remain poorly understood.

RESULTS: In this study, we analyzed 333 soil metagenomes from 5 habitat types (farmland, forest, grassland, Gobi desert, and mine wasteland) across China and identified 533 distinct giant virus phylotypes affiliated with nine families, thereby greatly expanding the diversity of soil giant viruses. Among the nine families, Pithoviridae were the most diverse. The majority of phylotypes exhibited a heterogeneous distribution among habitat types, with a remarkably high proportion of unique phylotypes in mine wasteland. The abundances of phylotypes were negatively correlated with their environmental ranges. A total of 76 phylotypes recovered in this study were detectable in a published global topsoil metagenome dataset. Among climatic, geographical, edaphic, and biotic characteristics, soil eukaryotes were identified as the most important driver of beta-diversity of giant viral communities across habitat types. Moreover, co-occurrence network analysis revealed some pairings between giant viral phylotypes and eukaryotes (protozoa, fungi, and algae). Analysis of 44 medium- to high-quality giant virus genomes recovered from our metagenomes uncovered not only their highly shared functions but also their novel auxiliary metabolic genes related to carbon, sulfur, and phosphorus cycling.

CONCLUSIONS: These findings extend our knowledge of diversity, habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses. Video Abstract.}, } @article {pmid39039555, year = {2024}, author = {Wang, D and Liu, L and Xu, X and Wang, C and Wang, Y and Deng, Y and Zhang, T}, title = {Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {134}, pmid = {39039555}, issn = {2049-2618}, mesh = {*Bacteriophages/genetics/classification/physiology/isolation & purification ; *Sewage/virology/microbiology ; *Wastewater/virology/microbiology ; *Bacteria/virology/genetics/classification ; Biofilms ; Metagenomics ; Water Purification/methods ; Microbiota ; }, abstract = {BACKGROUND: Understanding the interactions and dynamics of microbiotas within biological wastewater treatment systems is essential for ensuring their stability and long-term sustainability. In this study, we developed a systematic framework employing multi-omics and Hi-C sequencing to extensively investigate prokaryotic and phage communities within a hybrid biofilm and activated sludge system.

RESULTS: We uncovered distinct distribution patterns, metabolic capabilities, and activities of functional prokaryotes through the analysis of 454 reconstructed prokaryotic genomes. Additionally, we reconstructed a phage catalog comprising 18,645 viral operational taxonomic units (vOTUs) with high length and contiguity using hybrid assembly, and a distinct distribution of phages was depicted between activated sludge (AS) and biofilm. Importantly, 1340 host-phage pairs were established using Hi-C and conventional in silico methods, unveiling the host-determined phage prevalence. The majority of predicted hosts were found to be involved in various crucial metabolic processes, highlighting the potential vital roles of phages in influencing substance metabolism within this system. Moreover, auxiliary metabolic genes (AMGs) related to various categories (e.g., carbohydrate degradation, sulfur metabolism, transporter) were predicted. Subsequent activity analysis emphasized their potential ability to mediate host metabolism during infection. We also profiled the temporal dynamics of phages and their associated hosts using 13-month time-series metagenomic data, further demonstrating their tight interactions. Notably, we observed lineage-specific infection patterns, such as potentially host abundance- or phage/host ratio-driven phage population changes.

CONCLUSIONS: The insights gained from this research contribute to the growing body of knowledge surrounding interactions and dynamics of host-phage and pave the way for further exploration and potential applications in the field of microbial ecology. Video Abstract.}, } @article {pmid39039462, year = {2024}, author = {Yan, L and Ye, B and Yang, M and Shan, Y and Yan, D and Fang, D and Zhang, K and Yu, Y}, title = {Gut microbiota and metabolic changes in children with idiopathic short stature.}, journal = {BMC pediatrics}, volume = {24}, number = {1}, pages = {468}, pmid = {39039462}, issn = {1471-2431}, mesh = {Humans ; *Gastrointestinal Microbiome ; Child ; Male ; Female ; *Feces/microbiology ; Case-Control Studies ; Adolescent ; Body Height ; Growth Disorders/microbiology/metabolism ; Metabolomics/methods ; Metabolome ; }, abstract = {BACKGROUND: Idiopathic short stature (ISS) is characterized by short stature with unknown causes. Recent studies showed different gut microbiota flora and reduced fecal short-chain fatty acids in ISS children. However, the roles of the microbiome and metabolites in the pathogenesis of ISS remains largely unknown.

METHODS: We recruited 51 Chinese subjects, comprising 26 ISS children and 25 normal-height control individuals. Untargeted metabolomics was performed to explore the fecal metabolic profiles between groups. A shotgun metagenomic sequencing approach was used to investigate the microbiome at the strains level. Mediation analyses were done to reveal correlations between the height standard deviation (SD) value, the gut microbiome and metabolites.

RESULTS: We detected marked differences in the composition of fecal metabolites in the ISS group, particularly a significant increase in erucic acid and a decrease in spermidine, adenosine and L-5-Hydroxytryptophan, when compared to those of controls. We further identified specific groups of bacterial strains to be associated with the different metabolic profile. Through mediation analysis, 50 linkages were established. KEGG pathway analysis of microbiota and metabolites indicated nutritional disturbances. 13 selected features were able to accurately distinguish the ISS children from the controls (AUC = 0.933 [95%CI, 79.9-100%]) by receiver operating characteristic (ROC) analysis.

CONCLUSION: Our study suggests that the microbiome and the microbial-derived metabolites play certain roles in children's growth. These findings provide a new research direction for better understanding the mechanism(s) underlying ISS.}, } @article {pmid39039075, year = {2024}, author = {Stothart, MR and McLoughlin, PD and Medill, SA and Greuel, RJ and Wilson, AJ and Poissant, J}, title = {Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {6012}, pmid = {39039075}, issn = {2041-1723}, support = {2016-06459//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; 2019-04388//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; 25046//Canada Foundation for Innovation (Fondation canadienne pour l'innovation)/ ; D20EQ-05//Morris Animal Foundation (MAF)/ ; D20EQ-05//Morris Animal Foundation (MAF)/ ; D20EQ-05//Morris Animal Foundation (MAF)/ ; }, mesh = {Animals ; Horses/microbiology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; *Methane/metabolism ; Animals, Wild/microbiology ; Metagenome ; Fatty Acids, Volatile/metabolism ; Metagenomics/methods ; Male ; Female ; Canada ; }, abstract = {Gut microbiomes are widely hypothesised to influence host fitness and have been experimentally shown to affect host health and phenotypes under laboratory conditions. However, the extent to which they do so in free-living animal populations and the proximate mechanisms involved remain open questions. In this study, using long-term, individual-based life history and shallow shotgun metagenomic sequencing data (2394 fecal samples from 794 individuals collected between 2013-2019), we quantify relationships between gut microbiome variation and survival in a feral population of horses under natural food limitation (Sable Island, Canada), and test metagenome-derived predictions using short-chain fatty acid data. We report detailed evidence that variation in the gut microbiome is associated with a host fitness proxy in nature and outline hypotheses of pathogenesis and methanogenesis as key causal mechanisms which may underlie such patterns in feral horses, and perhaps, wild herbivores more generally.}, } @article {pmid39038938, year = {2024}, author = {Chuang, YF and Fan, KC and Su, YY and Wu, MF and Chiu, YL and Liu, YC and Lin, CC}, title = {Precision probiotics supplement strategy in aging population based on gut microbiome composition.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {4}, pages = {}, pmid = {39038938}, issn = {1477-4054}, support = {//Taiwan National Science and Technology Council/ ; MOST 110-2321-B-418//Ministry of Science and Technology/ ; MOHW111-TDU-B-221-114007//Ministry of Health and Welfare/ ; NYCU-FEMH 112DN11//FEMH-NYCU Joint Research Program/ ; }, mesh = {*Probiotics/therapeutic use/administration & dosage ; Humans ; *Gastrointestinal Microbiome ; Aged ; *Aging ; Female ; Male ; *Dietary Supplements ; Aged, 80 and over ; Middle Aged ; Lactobacillus/genetics ; Metagenomics/methods ; Bifidobacterium ; }, abstract = {With the increasing prevalence of age-related chronic diseases burdening healthcare systems, there is a pressing need for innovative management strategies. Our study focuses on the gut microbiota, essential for metabolic, nutritional, and immune functions, which undergoes significant changes with aging. These changes can impair intestinal function, leading to altered microbial diversity and composition that potentially influence health outcomes and disease progression. Using advanced metagenomic sequencing, we explore the potential of personalized probiotic supplements in 297 older adults by analyzing their gut microbiota. We identified distinctive Lactobacillus and Bifidobacterium signatures in the gut microbiota of older adults, revealing probiotic patterns associated with various population characteristics, microbial compositions, cognitive functions, and neuroimaging results. These insights suggest that tailored probiotic supplements, designed to match individual probiotic profile, could offer an innovative method for addressing age-related diseases and functional declines. Our findings enhance the existing evidence base for probiotic use among older adults, highlighting the opportunity to create more targeted and effective probiotic strategies. However, additional research is required to validate our results and further assess the impact of precision probiotics on aging populations. Future studies should employ longitudinal designs and larger cohorts to conclusively demonstrate the benefits of tailored probiotic treatments.}, } @article {pmid39038883, year = {2024}, author = {Han, PJ and Song, L and Wen, Z and Zhu, HY and Wei, YH and Wang, JW and Bai, M and Luo, LJ and Wang, JW and Chen, SX and You, XL and Han, DY and Bai, FY}, title = {Species-level understanding of the bacterial community in Daqu based on full-length 16S rRNA gene sequences.}, journal = {Food microbiology}, volume = {123}, number = {}, pages = {104566}, doi = {10.1016/j.fm.2024.104566}, pmid = {39038883}, issn = {1095-9998}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Fermentation ; China ; Microbiota ; Phylogeny ; DNA, Bacterial/genetics ; Biodiversity ; Alcoholic Beverages/microbiology/analysis ; Food Microbiology ; Metagenome ; Fermented Foods/microbiology ; }, abstract = {Daqu is used as the fermentation starter of Baijiu and contributes diversified functional microbes for saccharifying grains and converting sugars into ethanol and aroma components in Baijiu products. Daqu is mainly classified into three types, namely low (LTD), medium (MTD) and high (HTD) temperature Daqu, according to the highest temperatures reached in their fermentation processes. In this study, we used the PacBio small-molecule real-time (SMRT) sequencing technology to determine the full-length 16 S rRNA gene sequences from the metagenomes of 296 samples of different types of Daqu collected from ten provinces in China, and revealed the bacterial diversity at the species level in the Daqu samples. We totally identified 310 bacteria species, including 78 highly abundant species (with a relative abundance >0.1% each) which accounted for 91.90% of the reads from all the Daqu samples. We also recognized the differentially enriched bacterial species in different types of Daqu, and in the Daqu samples with the same type but from different provinces. Specifically, Lactobacillales, Enterobacterales and Bacillaceae were significantly enriched in the LTD, MTD and HTD groups, respectively. The potential co-existence and exclusion relationships among the bacteria species involved in all the Daqu samples and in the LTD, MTD and HTD samples from a specific region were also identified. These results provide a better understanding of the bacterial diversity in different types of Daqu at the species level.}, } @article {pmid39038849, year = {2024}, author = {Lee, S and Portlock, T and Le Chatelier, E and Garcia-Guevara, F and Clasen, F and Oñate, FP and Pons, N and Begum, N and Harzandi, A and Proffitt, C and Rosario, D and Vaga, S and Park, J and von Feilitzen, K and Johansson, F and Zhang, C and Edwards, LA and Lombard, V and Gauthier, F and Steves, CJ and Gomez-Cabrero, D and Henrissat, B and Lee, D and Engstrand, L and Shawcross, DL and Proctor, G and Almeida, M and Nielsen, J and Mardinoglu, A and Moyes, DL and Ehrlich, SD and Uhlen, M and Shoaie, S}, title = {Global compositional and functional states of the human gut microbiome in health and disease.}, journal = {Genome research}, volume = {34}, number = {6}, pages = {967-978}, pmid = {39038849}, issn = {1549-5469}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; *Metagenomics/methods ; Machine Learning ; Fusobacterium nucleatum/genetics ; Bacteria/classification/genetics ; }, abstract = {The human gut microbiota is of increasing interest, with metagenomics a key tool for analyzing bacterial diversity and functionality in health and disease. Despite increasing efforts to expand microbial gene catalogs and an increasing number of metagenome-assembled genomes, there have been few pan-metagenomic association studies and in-depth functional analyses across different geographies and diseases. Here, we explored 6014 human gut metagenome samples across 19 countries and 23 diseases by performing compositional, functional cluster, and integrative analyses. Using interpreted machine learning classification models and statistical methods, we identified Fusobacterium nucleatum and Anaerostipes hadrus with the highest frequencies, enriched and depleted, respectively, across different disease cohorts. Distinct functional distributions were observed in the gut microbiomes of both westernized and nonwesternized populations. These compositional and functional analyses are presented in the open-access Human Gut Microbiome Atlas, allowing for the exploration of the richness, disease, and regional signatures of the gut microbiota across different cohorts.}, } @article {pmid39037634, year = {2024}, author = {Elmagzoub, WA and Idris, SM and Elnaiem, MHE and Mukhtar, ME and Eltayeb, E and Bakhiet, SM and Okuni, JB and Ojok, L and El Sanousi, SM and El Wahed, AA and Gameel, AA and Eltom, KH}, title = {Faecal microbial diversity in a cattle herd infected by Mycobacterium avium subsp. paratuberculosis: a possible effect of production status.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {9}, pages = {276}, pmid = {39037634}, issn = {1573-0972}, support = {Project number 404935781//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; Cattle ; *Mycobacterium avium subsp. paratuberculosis/isolation & purification/genetics ; *Feces/microbiology ; *Paratuberculosis/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Cattle Diseases/microbiology ; *Milk/microbiology ; *DNA, Bacterial/genetics ; Gastrointestinal Microbiome ; Female ; Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; }, abstract = {Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease, or paratuberculosis (PTB) in ruminants, besides having zoonotic potential. It possibly changes the gut microbiome, but no conclusive data are available yet. This study aimed at investigating the influence of MAP on the faecal microbiome of cattle naturally infected with PTB. In a follow up period of 10 months, PTB status was investigated in a herd of dairy cattle with history of clinical cases. Each animal was tested for MAP infection using serum and milk ELISA for MAP anti-bodies and IS900 real-time PCR and recombinase polymerase amplification assays for MAP DNA in the faeces and milk monthly for 4 successive months, then a last one after 6 months. The faecal samples were subjected to 16S rDNA metagenomic analysis using Oxford Nanopore Sequencing Technology. The microbial content was compared between animal groups based on MAP positivity rate and production status. All animals were MAP positive by one or more tests, but two animals were consistently negative for MAP DNA in the faeces. In all animals, the phyla firmicutes and bacteroidetes were highly enriched with a small contribution of proteobacteria, and increased abundance of the families Oscillospiraceae, Planococcaceae, and Streptococcacaceae was noted. Animals with high MAP positivity rate showed comparable faecal microbial content, although MAP faecal positivity had no significant effect (p > 0.05) on the microbiome. Generally, richness and evenness indices decreased with increasing positivity rate. A significantly different microbial content was found between dry cows and heifers (p < 0.05). Particularly, Oscillospiraceae and Rikenellaceae were enriched in heifers, while Planococcaceae and Streptococcaceae were overrepresented in dry cows. Furthermore, abundance of 72 genera was significantly different between these two groups (p < 0.05). Changes in faecal microbiome composition were notably associated with increasing MAP shedding in the faeces. The present findings suggest a combined influence of the production status and MAP on the cattle faecal microbiome. This possibly correlates with the fate of the infection, the concern in disease control, again remains for further investigations.}, } @article {pmid39035870, year = {2024}, author = {Rabbachin, L and Nir, I and Waldherr, M and Vassallo, Y and Piñar, G and Graf, A and Kushmaro, A and Sterflinger, K}, title = {Diversity of fungi associated with petroglyph sites in the Negev Desert, Israel, and their potential role in bioweathering.}, journal = {Frontiers in fungal biology}, volume = {5}, number = {}, pages = {1400380}, pmid = {39035870}, issn = {2673-6128}, support = {I 4748/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {The petroglyphs of the Negev Desert, Israel, are famous and valuable archaeological remains. Previous studies have investigated the microbial communities associated with petroglyphs and their potential role in stone deterioration; nevertheless, the role of fungi remains unclear. In this study, the fungal communities present on the stone and, as a comparison, in the surrounding environment (soil and air) at Negev petroglyph sites were analyzed by means of culture-dependent and -independent (metagenomic) techniques. The metagenomic results showed a high fungal biodiversity in the soil, and both approaches highlighted the prevalence of species producing melanized, large, thick-walled spores (mainly Alternaria spp.). From the air sampling, mostly Cladosporium spp. were retrieved. On the other hand, on the rock, the results seem to indicate a low presence of fungi, but with a rock-specialized mycobiota consisting of extremotolerant microcolonial fungi (MCF) (e.g., Vermiconidia and Coniosporium) and lichens (Flavoplaca). In addition, low proportions of cosmopolitan fungi were detected on the stone, but the comparison of the data clearly indicates that they are transients from the surrounding environment. The ability of the isolated strains to dissolve CaCO3 and therefore be a potential threat to the petroglyphs (limestone substrate) was tested, but only one strain resulted in positive acid production under laboratory conditions. Nevertheless, both lichens and MCF detected in this study are well-known stone deteriogens, which may have a significant impact on the petroglyph's deterioration.}, } @article {pmid39034613, year = {2024}, author = {Krigul, KL and Feeney, RH and Wongkuna, S and Aasmets, O and Holmberg, SM and Andreson, R and Puértolas-Balint, F and Pantiukh, K and Sootak, L and Org, T and Tenson, T and Org, E and Schroeder, BO}, title = {A history of repeated antibiotic usage leads to microbiota-dependent mucus defects.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2377570}, pmid = {39034613}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Anti-Bacterial Agents/pharmacology ; Mice ; *Fecal Microbiota Transplantation ; *Mucus/metabolism/microbiology ; *Bacteria/classification/genetics/drug effects/isolation & purification/metabolism ; Intestinal Mucosa/microbiology/metabolism/drug effects ; Male ; Female ; Feces/microbiology ; Adult ; Middle Aged ; Akkermansia ; Mice, Inbred C57BL ; Colon/microbiology ; Bacteroides fragilis/drug effects ; }, abstract = {Recent evidence indicates that repeated antibiotic usage lowers microbial diversity and ultimately changes the gut microbiota community. However, the physiological effects of repeated - but not recent - antibiotic usage on microbiota-mediated mucosal barrier function are largely unknown. By selecting human individuals from the deeply phenotyped Estonian Microbiome Cohort (EstMB), we here utilized human-to-mouse fecal microbiota transplantation to explore long-term impacts of repeated antibiotic use on intestinal mucus function. While a healthy mucus layer protects the intestinal epithelium against infection and inflammation, using ex vivo mucus function analyses of viable colonic tissue explants, we show that microbiota from humans with a history of repeated antibiotic use causes reduced mucus growth rate and increased mucus penetrability compared to healthy controls in the transplanted mice. Moreover, shotgun metagenomic sequencing identified a significantly altered microbiota composition in the antibiotic-shaped microbial community, with known mucus-utilizing bacteria, including Akkermansia muciniphila and Bacteroides fragilis, dominating in the gut. The altered microbiota composition was further characterized by a distinct metabolite profile, which may be caused by differential mucus degradation capacity. Consequently, our proof-of-concept study suggests that long-term antibiotic use in humans can result in an altered microbial community that has reduced capacity to maintain proper mucus function in the gut.}, } @article {pmid39033825, year = {2024}, author = {Dong, Z and Han, K and Xie, Q and Lin, C and Shen, X and Hao, Y and Li, J and Xu, H and He, L and Yu, T and Kuang, W}, title = {Core antibiotic resistance genes mediate gut microbiota to intervene in the treatment of major depressive disorder.}, journal = {Journal of affective disorders}, volume = {363}, number = {}, pages = {507-519}, doi = {10.1016/j.jad.2024.07.106}, pmid = {39033825}, issn = {1573-2517}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Depressive Disorder, Major/drug therapy/genetics/microbiology ; Female ; Male ; Adult ; Middle Aged ; Drug Resistance, Microbial/genetics ; Case-Control Studies ; }, abstract = {INTRODUCTION: The relationship between depression and gut microbiota remains unclear, but an important role of gut microbiota has been verified. The relationship between gut microbiota and antibiotic resistance genes (ARGs) may be a potential new explanatory pathway.

METHODS: We collected samples from 63 depressed patients and 30 healthy controls for metagenomic sequencing. The two groups' microbiota characteristics, functional characteristics, and ARG differences were analyzed.

RESULTS: We obtained 30 differential KEGG orthologs (KOs) and their producers in 5 genera and 7 species by HUMAnN3. We found 6 KOs from Weissella_cibaria and Lactobacillus_plantaru are potentially coring functional mechanism of gut microbiota. Different metabolites including sphingolipids, pyrans, prenol lipids, and isoflavonoids also showed significance between MDD and HC. We detected 48 significantly different ARGs: 5 ARGs up-regulated and 43 ARGs down-regulated in MDD compared to HC. Based on Cox model results, Three ARGs significantly affected drug efficacy (ARG29, ARG105, and ARG111). Eggerthella, Weissella, and Lactobacillus were correlated with different core ARGs, which indicated different mechanisms in affecting MDD.

LIMITATIONS: The present study needs to be replicated in different ethnic groups. At the same time, a larger Chinese cohort study and detailed experimental verification are also the key to further discussion.

CONCLUSION: Our findings suggest that ARGs play a role in the interplay between major depressive disorder and gut microbiota. The role of ARGs should be taken into account when understanding the relationship between depression and gut microbiota.}, } @article {pmid39033688, year = {2024}, author = {Berryman, MA and Ilonen, J and Triplett, EW and Ludvigsson, J}, title = {Functional metagenomic analysis reveals potential inflammatory triggers associated with genetic risk for autoimmune disease.}, journal = {Journal of autoimmunity}, volume = {148}, number = {}, pages = {103290}, doi = {10.1016/j.jaut.2024.103290}, pmid = {39033688}, issn = {1095-9157}, mesh = {Humans ; *Autoimmune Diseases/immunology/etiology/genetics/microbiology ; *Metagenomics/methods ; *Genetic Predisposition to Disease ; Infant ; Female ; Sweden/epidemiology ; Male ; Feces/microbiology ; Haplotypes ; Inflammation/immunology/genetics ; Gastrointestinal Microbiome/immunology ; HLA-DQ Antigens/genetics/immunology ; Flagellin/immunology ; Prevotella/immunology/genetics ; Genotype ; }, abstract = {To assess functional differences between the microbiomes of individuals with autoimmune risk-associated human leukocyte antigen (HLA) genetics and autoimmune protection-associated HLA, we performed a metagenomic analysis of stool samples from 72 infants in the All Babies in Southeast Sweden general-population cohort and assessed haplotype-peptide binding affinities. Infants with risk-associated HLA DR3-DQ2.5 and DR4-DQ8 had a higher abundance of known pathogen-associated molecular patterns and virulence related genes than infants with protection-associated HLA DR15-DQ6.2. However, there was limited overlap in the type of inflammatory trigger between risk groups. Supported by a high Firmicutes/Bacteroides ratio and differentially abundant flagellated species, genes related to the synthesis of flagella were prominent in those with HLA DR3-DQ2.5. However, this haplotype had a significantly lower likelihood of binding affinity to flagellin peptides. O-antigen biosynthesis genes were significantly correlated with the risk genotypes and absent from protective genotype association, supported by the differential abundance of gram-negative bacteria seen in the risk-associated groups. Genes related to vitamin B biosynthesis stood out in higher abundance in infants with HLA DR3-DQ2.5/DR4-DQ8 heterozygosity compared to those with autoimmune-protective genetics. Prevotella species and genus were significantly abundant in all infant groups with high risk for autoimmune disease. The potential inflammatory triggers associated with genetic risk for autoimmunity have significant implications. These results suggest that certain HLA haplotypes may be creating the opportunity for dysbiosis and subsequent inflammation early in life by clearing beneficial microbes or not clearing proinflammatory microbes. This HLA gatekeeping may prevent genetically at-risk individuals from benefiting from probiotic therapies by restricting the colonization of those beneficial bacteria.}, } @article {pmid39033587, year = {2024}, author = {Pavon, JAR and da Silva Neves, NA and Pinho, JB and de Souza, VJ and Patroca da Silva, S and Ribeiro Cruz, AC and de Almeida Medeiros, DB and Teixeira Nunes, MR and Slhessarenko, RD}, title = {Disclosing the virome of Aedes, Anopheles and Culex female mosquitoes, Alto Pantanal of Mato Grosso, Brazil, 2019.}, journal = {Virology}, volume = {598}, number = {}, pages = {110182}, doi = {10.1016/j.virol.2024.110182}, pmid = {39033587}, issn = {1096-0341}, mesh = {Animals ; Brazil ; Female ; *Anopheles/virology ; *Virome/genetics ; *Phylogeny ; *Aedes/virology ; *Culex/virology ; *Genome, Viral ; Mosquito Vectors/virology ; High-Throughput Nucleotide Sequencing ; Insect Viruses/genetics/classification/isolation & purification ; }, abstract = {Using Illumina NextSeq sequencing and bioinformatics, we identified and characterized thirty-three viral sequences of unsegmented and multipartite viral families in Aedes spp., Culex sp. and Anopheles darlingi female mosquito pools from Porto São Luiz and Pirizal, Alto Pantanal. Seventeen sequences belong to unsegmented viral families, twelve represent putative novel insect-specific viruses (ISVs) within families Chuviridae (3/33; partial genomes) and coding-complete sequences of Xinmoviridae (1/33), Rhabdoviridae (2/33) and Metaviridae (6/33); and five coding-complete sequences of already-known ISVs. Notably, two putative novel rhabdoviruses, Corixo rhabdovirus 1 and 2, were phylogenetically related to Coxipo dielmovirus, but separated from other Alpharhabdovirinae genera, sharing Anopheles spp. as host. Regarding multipartite families, sixteen segments of different putative novel viruses were identified (13 coding-complete segments) within Durnavirales (4/33), Elliovirales (1/33), Hareavirales (3/33) and Reovirales (8/33) orders. Overall, this study describes twenty-eight (28/33) putative novel ISVs and five (5/33) already described viruses using metagenomics approach.}, } @article {pmid39033279, year = {2024}, author = {Trinh, P and Teichman, S and Roberts, MC and Rabinowitz, PM and Willis, AD}, title = {A cross-sectional comparison of gut metagenomes between dairy workers and community controls.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {708}, pmid = {39033279}, issn = {1471-2164}, support = {R21 AI168679/AI/NIAID NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; T32 ES015459/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; *Metagenome ; Female ; Dairying ; Metagenomics/methods ; Adult ; Animals ; Middle Aged ; Bacteria/genetics/classification ; Farmers ; Male ; Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens before a spillover event. In light of this, we aimed to characterize the microbiomes and resistomes of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases.

RESULTS: Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of 10 dairy farm workers and 6 community controls' gut metagenomes, contextualizing these samples with additional publicly available gut metagenomes. We found no significant differences in the prevalence of resistance genes, virulence factors, or taxonomic composition between the two groups. The lack of statistical significance may be attributed, in part, to the limited sample size of our study or the potential similarities in exposures between the dairy workers and community controls. We did, however, observe patterns warranting further investigation including greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes as well as lower average gene diversity (even after accounting for differential sequencing depth) in dairy workers' metagenomes. We also found evidence of commensal organism association with tetracycline resistance genes in both groups (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii).

CONCLUSIONS: This study highlights the utility of shotgun metagenomics in examining the microbiomes and resistomes of livestock workers, focusing on a cohort of dairy workers in the United States. While our study revealed no statistically significant differences between groups in taxonomy, diversity and gene presence, we observed patterns in antibiotic resistance gene abundance and prevalence that align with findings from previous studies of livestock workers in China and Europe. Our results lay the groundwork for future research involving larger cohorts of dairy and non-dairy workers to better understand the impact of occupational exposure to livestock farming on the microbiomes and resistomes of workers.}, } @article {pmid39032544, year = {2024}, author = {Ioannou, M and Borkent, J and Andreu-Sánchez, S and Wu, J and Fu, J and Sommer, IEC and Haarman, BCM}, title = {Reproducible gut microbial signatures in bipolar and schizophrenia spectrum disorders: A metagenome-wide study.}, journal = {Brain, behavior, and immunity}, volume = {121}, number = {}, pages = {165-175}, doi = {10.1016/j.bbi.2024.07.009}, pmid = {39032544}, issn = {1090-2139}, mesh = {Humans ; *Schizophrenia/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Bipolar Disorder/microbiology ; Adult ; Middle Aged ; *Metagenome ; Metagenomics/methods ; Antipsychotic Agents/therapeutic use/pharmacology ; Bacteria/genetics ; }, abstract = {BACKGROUND: Numerous studies report gut microbiome variations in bipolar disorder (BD) and schizophrenia spectrum disorders (SSD) compared to healthy individuals, though, there is limited consensus on which specific bacteria are associated with these disorders.

METHODS: In this study, we performed a comprehensive metagenomic shotgun sequencing analysis in 103 Dutch patients with BD/SSD and 128 healthy controls matched for age, sex, body mass index and income, while accounting for diet quality, transit time and technical confounders. To assess the replicability of the findings, we used two validation cohorts (total n = 203), including participants from a distinct population with a different metagenomic isolation protocol.

RESULTS: The gut microbiome of the patients had a significantly different β-diversity, but not α-diversity nor neuroactive potential compared to healthy controls. Initially, twenty-six bacterial taxa were identified as differentially abundant in patients. Among these, the previously reported genera Lachnoclostridium and Eggerthella were replicated in the validation cohorts. Employing the CoDaCoRe learning algorithm, we identified two bacterial balances specific to BD/SSD, which demonstrated an area under the receiver operating characteristic curve (AUC) of 0.77 in the test dataset. These balances were replicated in the validation cohorts and showed a positive association with the severity of psychiatric symptoms and antipsychotic use. Last, we showed a positive association between the relative abundance of Klebsiella and Klebsiella pneumoniae with antipsychotic use and between the Anaeromassilibacillus and lithium use.

CONCLUSIONS: Our findings suggest that microbial balances could be a reproducible method for identifying BD/SSD-specific microbial signatures, with potential diagnostic and prognostic applications. Notably, Lachnoclostridium and Eggerthella emerge as frequently occurring bacteria in BD/SSD. Last, our study reaffirms the previously established link between Klebsiella and antipsychotic medication use and identifies a novel association between Anaeromassilibacillus and lithium use.}, } @article {pmid39032335, year = {2024}, author = {Fan, Y and Zhou, Z and Liu, F and Qian, L and Yu, X and Huang, F and Hu, R and Su, H and Gu, H and Yan, Q and He, Z and Wang, C}, title = {The vertical partitioning between denitrification and dissimilatory nitrate reduction to ammonium of coastal mangrove sediment microbiomes.}, journal = {Water research}, volume = {262}, number = {}, pages = {122113}, doi = {10.1016/j.watres.2024.122113}, pmid = {39032335}, issn = {1879-2448}, mesh = {*Denitrification ; *Nitrates/metabolism ; *Geologic Sediments/microbiology ; *Microbiota ; *Ammonium Compounds/metabolism ; Wetlands ; }, abstract = {Mangrove aquatic ecosystems receive substantial nitrogen (N) inputs from both land and sea, playing critical roles in modulating coastal N fluxes. The microbially-mediated competition between denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in mangrove sediments significantly impacts the N fate and transformation processes. Despite their recognized role in N loss or retention in surface sediments, how these two processes vary with sediment depths and their influential factors remain elusive. Here, we employed a comprehensive approach combining [15]N isotope tracer, quantitative PCR (qPCR) and metagenomics to verify the vertical dynamics of denitrification and DNRA across five 100-cm mangrove sediment cores. Our results revealed a clear vertical partitioning, with denitrification dominated in 0-30 cm sediments, while DNRA played a greater role with increasing depths. Quantification of denitrification and DNRA functional genes further explained this phenomenon. Taxonomic analysis identified Pseudomonadota as the primary denitrification group, while Planctomycetota and Pseudomonadota exhibited high proportion in DNRA group. Furthermore, genome-resolved metagenomics revealed multiple salt-tolerance strategies and aromatic compound utilization potential in denitrification assemblages. This allowed denitrification to dominate in oxygen-fluctuating and higher-salinity surface sediments. However, the elevated C/N in anaerobic deep sediments favored DNRA, tending to generate biologically available NH4[+]. Together, our results uncover the depth-related variations in the microbially-mediated competition between denitrification and DNRA, regulating N dynamics in mangrove ecosystems.}, } @article {pmid39030898, year = {2024}, author = {Stevens, C and Norris, S and Arbeeva, L and Carter, S and Enomoto, M and Nelson, AE and Lascelles, BDX}, title = {Gut Microbiome and Osteoarthritis: Insights From the Naturally Occurring Canine Model of Osteoarthritis.}, journal = {Arthritis & rheumatology (Hoboken, N.J.)}, volume = {76}, number = {12}, pages = {1758-1763}, pmid = {39030898}, issn = {2326-5205}, mesh = {Dogs ; Animals ; *Gastrointestinal Microbiome ; *Osteoarthritis/microbiology ; *Disease Models, Animal ; *Feces/microbiology ; Male ; Female ; Firmicutes/isolation & purification ; Pain/microbiology ; Metagenomics ; }, abstract = {OBJECTIVE: The purpose of this study was to enhance the current knowledge of the relationship between the gut microbiome and osteoarthritis (OA) and associated pain using pet dogs as a clinically relevant translational model.

METHODS: Fecal samples were collected from 93 owned pet dogs. Dogs were designated as either clinically healthy or OA pain using validated methods. Metagenomic profiling was performed through shotgun sequencing using the Illumina NovaSeq platform. MetaPhlAn2 and HUMAnN2 were used to evaluate bacterial taxonomic and pathway relative abundance. Comparisons between healthy and OA-pain groups were performed individually for each taxa using nonparametric tests following Benjamini and Hochberg adjustment for multiple comparisons. Permutation analysis of variance was performed using Bray-Curtis distance matrices. All downstream analyses were completed in R.

RESULTS: No significant differences between healthy and OA-pain dogs were observed for alpha and beta diversity. We found 13 taxa with nominally significant (P < 0.05) associations with OA case status, but none of the associations remained significant after adjustment for multiple comparisons. No differences in alpha or beta diversities or the Firmicutes to Bacteroidetes ratio were found regarding pain severity, mobility or activity level, age, or body composition score.

CONCLUSION: Similar to recent studies in humans, the present study did not demonstrate a significant difference in the fecal microbial communities between dogs with OA pain and healthy control dogs. Future research in this naturally occurring model should expand on these data and relate the gut microbiome to gut permeability and circulating proinflammatory and anti-inflammatory molecules to better understand the influence of the gut microbiome on OA and OA pain.}, } @article {pmid39030686, year = {2024}, author = {Wallace, BA and Varona, NS and Hesketh-Best, PJ and Stiffler, AK and Silveira, CB}, title = {Globally distributed bacteriophage genomes reveal mechanisms of tripartite phage-bacteria-coral interactions.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39030686}, issn = {1751-7370}, support = {UM PRA 2022-2547//University of Miami Provost Research Award/ ; 2023353157//National Science Foundation Graduate Research Fellowship Program/ ; //University of Miami Holmes Fellowship/ ; //Kushlan Graduate Research Support Award/ ; 2023349872//NSF Graduate Research Fellowship Program/ ; //University of Miami Dean's Fellowship/ ; PG015171//Maytag Fellowship/ ; 80NSSC23K0676//National Aeronautics and Space Administration Exobiology Program/ ; }, mesh = {*Bacteriophages/genetics/isolation & purification/classification ; *Anthozoa/virology/microbiology ; *Genome, Viral ; Animals ; *Bacteria/virology/genetics/classification ; Metagenome ; Symbiosis ; Coral Reefs ; Virome/genetics ; Prophages/genetics ; }, abstract = {Reef-building corals depend on an intricate community of microorganisms for functioning and resilience. The infection of coral-associated bacteria by bacteriophages can modify bacterial ecological interactions, yet very little is known about phage functions in the holobiont. This gap stems from methodological limitations that have prevented the recovery of high-quality viral genomes and bacterial host assignment from coral samples. Here, we introduce a size fractionation approach that increased bacterial and viral recovery in coral metagenomes by 9-fold and 2-fold, respectively, and enabled the assembly and binning of bacterial and viral genomes at relatively low sequencing coverage. We combined these viral genomes with those derived from 677 publicly available metagenomes, viromes, and bacterial isolates from stony corals to build a global coral virus database of over 20,000 viral genomic sequences spanning four viral realms. The tailed bacteriophage families Kyanoviridae and Autographiviridae were the most abundant, replacing groups formerly referred to as Myoviridae and Podoviridae, respectively. Prophage and CRISPR spacer linkages between these viruses and 626 bacterial metagenome-assembled genomes and bacterial isolates showed that most viruses infected Alphaproteobacteria, the most abundant class, and less abundant taxa like Halanaerobiia and Bacteroidia. A host-phage-gene network identified keystone viruses with the genomic capacity to modulate bacterial metabolic pathways and direct molecular interactions with eukaryotic cells. This study reveals the genomic basis of nested symbioses between bacteriophage, bacteria, and the coral host and its endosymbiotic algae.}, } @article {pmid39030648, year = {2024}, author = {Moretti, LG and Crusciol, CAC and Leite, MFA and Momesso, L and Bossolani, JW and Costa, OYA and Hungria, M and Kuramae, EE}, title = {Diverse bacterial consortia: key drivers of rhizosoil fertility modulating microbiome functions, plant physiology, nutrition, and soybean grain yield.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {50}, pmid = {39030648}, issn = {2524-6372}, support = {2016/23699-8; 2018/14892-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 151120/2020-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Soybean cultivation in tropical regions relies on symbioses with nitrogen-fixing Bradyrhizobium and plant growth-promoting bacteria (PGPBs), reducing environmental impacts of N fertilizers and pesticides. We evaluate the effects of soybean inoculation with different bacterial consortia combined with PGPBs or microbial secondary metabolites (MSMs) on rhizosoil chemistry, plant physiology, plant nutrition, grain yield, and rhizosphere microbial functions under field conditions over three growing seasons with four treatments: standard inoculation of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens consortium (SI); SI plus foliar spraying with Bacillus subtilis (SI + Bs); SI plus foliar spraying with Azospirillum brasilense (SI + Az); and SI plus seed application of MSMs enriched in lipo-chitooligosaccharides extracted from B. diazoefficiens and Rhizobium tropici (SI + MSM). Rhizosphere microbial composition, diversity, and function was assessed by metagenomics. The relationships between rhizosoil chemistry, plant nutrition, grain yield, and the abundance of microbial taxa and functions were determined by generalized joint attribute modeling. The bacterial consortia had the most significant impact on rhizosphere soil fertility, which in turn affected the bacterial community, plant physiology, nutrient availability, and production. Cluster analysis identified microbial groups and functions correlated with shifts in rhizosoil chemistry and plant nutrition. Bacterial consortia positively modulated specific genera and functional pathways involved in biosynthesis of plant secondary metabolites, amino acids, lipopolysaccharides, photosynthesis, bacterial secretion systems, and sulfur metabolism. The effects of the bacterial consortia on the soybean holobiont, particularly the rhizomicrobiome and rhizosoil fertility, highlight the importance of selecting appropriate consortia for desired outcomes. These findings have implications for microbial-based agricultural practices that enhance crop productivity, quality, and sustainability.}, } @article {pmid39030599, year = {2024}, author = {Xu, SY and Feng, XR and Zhao, W and Bi, YL and Diao, QY and Tu, Y}, title = {Rumen and hindgut microbiome regulate average daily gain of preweaning Holstein heifer calves in different ways.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {131}, pmid = {39030599}, issn = {2049-2618}, mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Weaning ; Bacteria/classification/isolation & purification/metabolism/genetics ; Female ; Fermentation ; Metagenomics/methods ; Metabolomics ; Fatty Acids, Volatile/metabolism/analysis ; Weight Gain ; Butyrates/metabolism ; }, abstract = {BACKGROUND: The average daily gain (ADG) of preweaning calves significantly influences their adult productivity and reproductive performance. Gastrointestinal microbes are known to exert an impact on host phenotypes, including ADG. The aim of this study was to investigate the mechanisms by which gastrointestinal microbiome regulate ADG in preweaning calves and to further validate them by isolating ADG-associated rumen microbes in vitro.

RESULTS: Sixteen Holstein heifer calves were selected from a cohort with 106 calves and divided into higher ADG (HADG; n = 8) and lower ADG (LADG; n = 8) groups. On the day of weaning, samples of rumen contents, hindgut contents, and plasma were collected for rumen metagenomics, rumen metabolomics, hindgut metagenomics, hindgut metabolomics, and plasma metabolomics analyses. Subsequently, rumen contents of preweaning Holstein heifer calves from the same dairy farm were collected to isolate ADG-associated rumen microbes. The results showed that the rumen microbes, including Pyramidobacter sp. C12-8, Pyramidobacter sp. CG50-2, Pyramidobacter porci, unclassified_g_Pyramidobacter, Pyramidobacter piscolens, and Acidaminococcus fermentans, were enriched in the rumen of HADG calves (LDA > 2, P < 0.05). Enrichment of these microbes in HADG calves' rumen promoted carbohydrate degradation and volatile fatty acid production, increasing proportion of butyrate in the rumen and ultimately contributing to higher preweaning ADG in calves (P < 0.05). The presence of active carbohydrate degradation in the rumen was further suggested by the negative correlation of the rumen microbes P. piscolens, P. sp. C12-8 and unclassified_g_Pyramidobacter with the rumen metabolites D-fructose (R <  - 0.50, P < 0.05). Widespread positive correlations were observed between rumen microbes (such as P. piscolens, P. porci, and A. fermentans) and beneficial plasma metabolites (such as 1-pyrroline-5-carboxylic acid and 4-fluoro-L-phenylalanine), which were subsequently positively associated with the growth rate of HADG calves (R > 0.50, P < 0.05). We succeeded in isolating a strain of A. fermentans from the rumen contents of preweaning calves and named it Acidaminococcus fermentans P41. The in vitro cultivation revealed its capability to produce butyrate. In vitro fermentation experiments demonstrated that the addition of A. fermentans P41 significantly increased the proportion of butyrate in the rumen fluid (P < 0.05). These results further validated our findings. The relative abundance of Bifidobacterium pseudolongum in the hindgut of HADG calves was negatively correlated with hindgut 4-hydroxyglucobrassicin levels, which were positively correlated with plasma 4-hydroxyglucobrassicin levels, and plasma 4-hydroxyglucobrassicin levels were positively correlated with ADG (P < 0.05).

CONCLUSIONS: This study's findings unveil that rumen and hindgut microbes play distinctive roles in regulating the preweaning ADG of Holstein heifer calves. Additionally, the successful isolation of A. fermentans P41 not only validated our findings but also provided a valuable strain resource for modulating rumen microbes in preweaning calves. Video Abstract.}, } @article {pmid39029911, year = {2024}, author = {Tyagi, S and Katara, P}, title = {Metatranscriptomics: A Tool for Clinical Metagenomics.}, journal = {Omics : a journal of integrative biology}, volume = {28}, number = {8}, pages = {394-407}, doi = {10.1089/omi.2024.0130}, pmid = {39029911}, issn = {1557-8100}, mesh = {*Metagenomics/methods ; *Microbiota/genetics ; Humans ; *Computational Biology/methods ; *Transcriptome/genetics ; Gene Expression Profiling/methods ; RNA, Ribosomal, 16S/genetics ; Metagenome/genetics ; }, abstract = {In the field of bioinformatics, amplicon sequencing of 16S rRNA genes has long been used to investigate community membership and taxonomic abundance in microbiome studies. As we can observe, shotgun metagenomics has become the dominant method in this field. This is largely owing to advancements in sequencing technology, which now allow for random sequencing of the entire genetic content of a microbiome. Furthermore, this method allows profiling both genes and the microbiome's membership. Although these methods have provided extensive insights into various microbiomes, they solely assess the existence of organisms or genes, without determining their active role within the microbiome. Microbiome scholarship now includes metatranscriptomics to decipher how a community of microorganisms responds to changing environmental conditions over a period of time. Metagenomic studies identify the microbes that make up a community but metatranscriptomics explores the diversity of active genes within that community, understanding their expression profile and observing how these genes respond to changes in environmental conditions. This expert review article offers a critical examination of the computational metatranscriptomics tools for studying the transcriptomes of microbial communities. First, we unpack the reasons behind the need for community transcriptomics. Second, we explore the prospects and challenges of metatranscriptomic workflows, starting with isolation and sequencing of the RNA community, then moving on to bioinformatics approaches for quantifying RNA features, and statistical techniques for detecting differential expression in a community. Finally, we discuss strengths and shortcomings in relation to other microbiome analysis approaches, pipelines, use cases and limitations, and contextualize metatranscriptomics as a tool for clinical metagenomics.}, } @article {pmid39029427, year = {2024}, author = {Iacovacci, J and Serafini, MS and Avuzzi, B and Badenchini, F and Cicchetti, A and Devecchi, A and Dispinzieri, M and Doldi, V and Giandini, T and Gioscio, E and Mancinelli, E and Noris Chiorda, B and Orlandi, E and Palorini, F and Possenti, L and Reis Ferreira, M and Villa, S and Zaffaroni, N and De Cecco, L and Valdagni, R and Rancati, T}, title = {Intestinal microbiota composition is predictive of radiotherapy-induced acute gastrointestinal toxicity in prostate cancer patients.}, journal = {EBioMedicine}, volume = {106}, number = {}, pages = {105246}, pmid = {39029427}, issn = {2352-3964}, mesh = {Humans ; Male ; *Gastrointestinal Microbiome/radiation effects ; *Prostatic Neoplasms/radiotherapy ; Aged ; *Radiation Injuries/etiology/microbiology/diagnosis ; Middle Aged ; Metagenomics/methods ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Radiotherapy/adverse effects ; Bacteria/classification/genetics/radiation effects ; Gastrointestinal Diseases/etiology/microbiology ; Metagenome ; }, abstract = {BACKGROUND: The search for factors beyond the radiotherapy dose that could identify patients more at risk of developing radio-induced toxicity is essential to establish personalised treatment protocols for improving the quality-of-life of survivors. To investigate the role of the intestinal microbiota in the development of radiotherapy-induced gastrointestinal toxicity, the MicroLearner observational cohort study characterised the intestinal microbiota of 136 (discovery) and 79 (validation) consecutive prostate cancer patients at baseline radiotherapy.

METHODS: Gastrointestinal toxicity was assessed weekly during RT using CTCAE. An average grade >1.3 over time points was used to identify patients suffering from persistent acute toxicity (endpoint). The microbiota of patients was quantified from the baseline faecal samples using 16S rRNA gene sequencing technology and the Ion Reporter metagenomic pipeline. Statistical techniques and computational and machine learning tools were used to extract, functionally characterise, and predict core features of the bacterial communities of patients who developed acute gastrointestinal toxicity.

FINDINGS: Analysis of the core bacterial composition in the discovery cohort revealed a cluster of patients significantly enriched for toxicity, displaying a toxicity rate of 60%. Based on selected high-risk microbiota compositional features, we developed a clinical decision tree that could effectively predict the risk of toxicity based on the relative abundance of genera Faecalibacterium, Bacteroides, Parabacteroides, Alistipes, Prevotella and Phascolarctobacterium both in internal and external validation cohorts.

INTERPRETATION: We provide evidence showing that intestinal bacteria profiling from baseline faecal samples can be effectively used in the clinic to improve the pre-radiotherapy assessment of gastrointestinal toxicity risk in prostate cancer patients.

FUNDING: Italian Ministry of Health (Promotion of Institutional Research INT-year 2016, 5 × 1000, Ricerca Corrente funds). Fondazione Regionale per la Ricerca Biomedica (ID 2721017). AIRC (IG 21479).}, } @article {pmid39028528, year = {2024}, author = {Han, Y and Zhang, Y and Yang, Z and Zhang, Q and He, X and Song, Y and Tian, L and Wu, H}, title = {Improving Aerobic Digestion of Food Waste by Adding a Personalized Microbial Inoculum.}, journal = {Current microbiology}, volume = {81}, number = {9}, pages = {277}, pmid = {39028528}, issn = {1432-0991}, support = {236Z3301G//Natural Science Foundation of Hebei Province/ ; B2020203005//Natural Science Foundation of Hebei Province/ ; 2021LGQN027//Cultivation Project for Basic Research and Innovation of YanShan University/ ; 236Z3604G//National Science Founbdation of Hebei Province/ ; 2023GJJG396//Hebei Education Department/ ; ZD2022088//China Hebei Education Department/ ; ZC2023041//China Hebei Education Department/ ; 2021LGQN018//Cultivation Project for Basic Research and Innovation of YanShan University/ ; }, mesh = {Aerobiosis ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Microbial Consortia ; Garbage ; China ; Refuse Disposal/methods ; Hydrolysis ; Metagenomics ; Food Loss and Waste ; }, abstract = {In the context of China's garbage classification policy, on-site aerobic food waste (FW) digestion is crucial for reducing transportation and disposal costs. The efficiency of this process is largely determined by the microbial community structure and its functions. Therefore, this study aimed to analyze the impact of a personalized microbial consortium (MCM) on the efficiency of aerobic FW digestion and to reveal the underlying mechanisms. An MCM, sourced from naturally degrading FW, was selected to enrich degrading bacteria with relatively high hydrolyzing ability. The functionality of the MCM was evaluated by tracing the successions of microbial communities, and comparing the differences in the forms of organic compounds, metabolic functions, and hydrolase activities. X-ray photoelectron spectroscopy demonstrated that the MCM metabolized faster, and produced more acidic metabolites. Metagenomic analysis indicated that FW inoculated with the personalized MCM increased abundance of Bacillaceae producing hydrolysis enzymes and promoted glycolysis metabolic pathways, enhancing energy generation for metabolism, compared to the commercial effective bacterial agent. This paper provides both theoretical and practical evidence for the improvement of biochemical processor of FW with the personalized MCM, which has promising application prospects and economic value.}, } @article {pmid39026261, year = {2024}, author = {Lee, M and Kaul, A and Ward, JM and Zhu, Q and Richards, M and Wang, Z and González, A and Parks, CG and Beane Freeman, LE and Umbach, DM and Motsinger-Reif, AA and Knight, R and London, SJ}, title = {House dust metagenome and pulmonary function in a US farming population.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {129}, pmid = {39026261}, issn = {2049-2618}, support = {Z01-ES049030 and Z01-ES102385//National Institutes of Health, the National Institute of Environmental Health Sciences/ ; Z01-ES049030 and Z01-ES102385//National Institutes of Health, the National Institute of Environmental Health Sciences/ ; Z01-ES049030 and Z01-ES102385//National Institutes of Health, the National Institute of Environmental Health Sciences/ ; Z01-CP010119B/CA/NCI NIH HHS/United States ; }, mesh = {*Dust/analysis ; Humans ; *Metagenome ; Female ; Male ; United States ; *Microbiota/genetics ; Middle Aged ; Lung/microbiology ; Adult ; Bacteria/classification/genetics/isolation & purification ; Forced Expiratory Volume ; Agriculture ; Respiratory Function Tests ; Vital Capacity ; Metagenomics/methods ; }, abstract = {BACKGROUND: Chronic exposure to microorganisms inside homes can impact respiratory health. Few studies have used advanced sequencing methods to examine adult respiratory outcomes, especially continuous measures. We aimed to identify metagenomic profiles in house dust related to the quantitative traits of pulmonary function and airway inflammation in adults. Microbial communities, 1264 species (389 genera), in vacuumed bedroom dust from 779 homes in a US cohort were characterized by whole metagenome shotgun sequencing. We examined two overall microbial diversity measures: richness (the number of individual microbial species) and Shannon index (reflecting both richness and relative abundance). To identify specific differentially abundant genera, we applied the Lasso estimator with high-dimensional inference methods, a novel framework for analyzing microbiome data in relation to continuous traits after accounting for all taxa examined together.

RESULTS: Pulmonary function measures (forced expiratory volume in one second (FEV1), forced vital capacity (FVC), and FEV1/FVC ratio) were not associated with overall dust microbial diversity. However, many individual microbial genera were differentially abundant (p-value < 0.05 controlling for all other microbial taxa examined) in relation to FEV1, FVC, or FEV1/FVC. Similarly, fractional exhaled nitric oxide (FeNO), a marker of airway inflammation, was unrelated to overall microbial diversity but associated with differential abundance for many individual genera. Several genera, including Limosilactobacillus, were associated with a pulmonary function measure and FeNO, while others, including Moraxella to FEV1/FVC and Stenotrophomonas to FeNO, were associated with a single trait.

CONCLUSIONS: Using state-of-the-art metagenomic sequencing, we identified specific microorganisms in indoor dust related to pulmonary function and airway inflammation. Some were previously associated with respiratory conditions; others were novel, suggesting specific environmental microbial components contribute to various respiratory outcomes. The methods used are applicable to studying microbiome in relation to other continuous outcomes. Video Abstract.}, } @article {pmid39026166, year = {2024}, author = {Jing, Z and Zheng, W and Jianwen, S and Hong, S and Xiaojian, Y and Qiang, W and Yunfeng, Y and Xinyue, W and Shuwen, H and Feimin, Z}, title = {Gut microbes on the risk of advanced adenomas.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {264}, pmid = {39026166}, issn = {1471-2180}, support = {No.2023KY1178//Zhejiang Medical and Health Technology Project/ ; No.2023KY1178//Zhejiang Medical and Health Technology Project/ ; No.2023HT078//China University Industry University Research Innovation Fund/ ; No.2023HT078//China University Industry University Research Innovation Fund/ ; No. 2023GY18//PublicWelfare Technology Application Research Program of Huzhou/ ; No. 2023GY18//PublicWelfare Technology Application Research Program of Huzhou/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Adenoma/microbiology/virology ; *Feces/microbiology/virology ; *Colorectal Neoplasms/microbiology/virology ; Male ; Middle Aged ; Female ; Viruses/isolation & purification/classification/genetics/pathogenicity ; High-Throughput Nucleotide Sequencing ; Aged ; Machine Learning ; }, abstract = {BACKGROUND: More than 90% of colorectal cancer (CRC) arises from advanced adenomas (AA) and gut microbes are closely associated with the initiation and progression of both AA and CRC.

OBJECTIVE: To analyze the characteristic microbes in AA.

METHODS: Fecal samples were collected from 92 AA and 184 negative control (NC). Illumina HiSeq X sequencing platform was used for high-throughput sequencing of microbial populations. The sequencing results were annotated and compared with NCBI RefSeq database to find the microbial characteristics of AA. R-vegan package was used to analyze α diversity and β diversity. α diversity included box diagram, and β diversity included Principal Component Analysis (PCA), principal co-ordinates analysis (PCoA), and non-metric multidimensional scaling (NMDS). The AA risk prediction models were constructed based on six kinds of machine learning algorithms. In addition, unsupervised clustering methods were used to classify bacteria and viruses. Finally, the characteristics of bacteria and viruses in different subtypes were analyzed.

RESULTS: The abundance of Prevotella sp900557255, Alistipes putredinis, and Megamonas funiformis were higher in AA, while the abundance of Lilyvirus, Felixounavirus, and Drulisvirus were also higher in AA. The Catboost based model for predicting the risk of AA has the highest accuracy (bacteria test set: 87.27%; virus test set: 83.33%). In addition, 4 subtypes (B1V1, B1V2, B2V1, and B2V2) were distinguished based on the abundance of gut bacteria and enteroviruses (EVs). Escherichia coli D, Prevotella sp900557255, CAG-180 sp000432435, Phocaeicola plebeiuA, Teseptimavirus, Svunavirus, Felixounavirus, and Jiaodavirus are the characteristic bacteria and viruses of 4 subtypes. The results of Catboost model indicated that the accuracy of prediction improved after incorporating subtypes. The accuracy of discovery sets was 100%, 96.34%, 100%, and 98.46% in 4 subtypes, respectively.

CONCLUSION: Prevotella sp900557255 and Felixounavirus have high value in early warning of AA. As promising non-invasive biomarkers, gut microbes can become potential diagnostic targets for AA, and the accuracy of predicting AA can be improved by typing.}, } @article {pmid39024692, year = {2024}, author = {Chen, L and Bao, Y and Wang, D and Tian, Y and Zeng, T and Gu, T and Xu, W and Lu, L}, title = {Integrated omics analysis reveals the differentiation of intestinal microbiota and metabolites between Pekin ducks and Shaoxing ducks.}, journal = {Poultry science}, volume = {103}, number = {9}, pages = {103976}, pmid = {39024692}, issn = {1525-3171}, mesh = {Animals ; *Ducks ; *Gastrointestinal Microbiome ; Metabolome ; Metabolomics ; Metagenome ; Metagenomics ; Bacteria/classification/genetics/metabolism/isolation & purification ; }, abstract = {Pekin ducks and Shaoxing ducks are 2 Chinese local duck breeds, both domesticated from mallard, but after domestication and long-term artificial selection, the body weight of Pekin ducks is significantly higher than that of Shaoxing ducks. It is no debate that genetic factors are the main factors responsible for this difference, but whether intestinal microbiota contribute to this difference is yet unknown. Thus, we performed comparative intestinal metagenomics and metabolomics analysis between Pekin ducks and Shaoxing ducks. We found obvious differentiation of intestinal metagenome and metabolome between the 2 breeds. Four cecal microbial genera, including Fusobacterium, Methanobrevibacter, Butyricicoccus, and Anaerotignum showed higher abundance in Pekin ducks. Among them, Methanobrevibacter and Butyricicoccus may positively correlate with fat deposition and body weight. A total of 310 metabolites showed difference between the 2 breeds. Functions of these differential metabolites were mainly enriched in amino acid metabolism, including energy metabolism-related histidine metabolism. Integrated omics analysis showed that microbial changes were closely related to altered metabolites. Especially, Butyricicoccus showing higher abundance in Pekin ducks was significantly negatively correlated with D-glucosamine-6-phosphate, which has been reported to prevent body weight gains. These findings may contribute to further understand the difference in body weight between Pekin ducks and Shaoxing ducks.}, } @article {pmid39024228, year = {2024}, author = {Ravelo, AD and Ferm, P and Guo, Y and Omontese, BO and Morley, PS and Chen, C and Noyes, NR and Caixeta, LS}, title = {Using a multi-omics approach to explore potential associations with rumen content and serum of cows with different milk production levels based on genomic predicted transmitting ability for milk and phenotypic milk production.}, journal = {PloS one}, volume = {19}, number = {7}, pages = {e0305674}, pmid = {39024228}, issn = {1932-6203}, mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; Female ; *Milk/metabolism/microbiology ; *Lactation ; Phenotype ; Metabolome ; Microbiota ; Genomics/methods ; Metagenome ; Metabolomics/methods ; Multiomics ; }, abstract = {This study aims to compare rumen microbiome and metabolites between second lactation dairy cows in the 75th percentile (n = 12; 57.2 ± 5.08 kg/d) of production according to genomic predicted transmitting ability for milk (GPTAM) and their counterparts in the 25th percentile (n = 12; 47.2 ± 8.61 kg/d). It was hypothesized that the metagenome and metabolome would differ between production levels. Cows were matched by days in milk (DIM), sire, occurrence of disease, and days open in previous lactation. For an additional comparison, the cows were also divided by phenotype into high (n = 6; 61.3 ± 2.8 kg/d), medium (n = 10; 55 ± 1.2 kg/d), and low (n = 8; 41.9 ± 5.6 kg/d) based on their milk production. Samples were collected 65 ± 14 DIM. Rumen content was collected using an oro-gastric tube and serum samples were collected from the coccygeal vessels. High-resolution liquid chromatography-mass spectrometry (LC-MS) was used for rumen and serum metabolite profiling. Shotgun metagenomics was used for rumen microbiome profiling. Microbiome sample richness and diversity were used to determine alpha and Bray-Curtis dissimilarity index was used to estimate beta diversity. Differences in metabolites were determined using t-tests or ANOVA. Pearson correlations were used to consider associations between serum metabolites and milk production. There was no evidence of a difference in rumen metabolites or microbial communities by GPTAM or phenotype. Cows in the phenotypic low group had greater serum acetate to propionate ratio and acetate proportion compared to the cows in the phenotypic medium group. Likewise, serum propionate proportion was greater in the medium compared to the low phenotypic group. Serum acetate, butyrate, and propionate concentrations had a weak positive correlation with milk production. When investigating associations between rumen environment and milk production, future studies must consider the impact of the ruminal epithelium absorption and post-absorption processes in relation to milk production.}, } @article {pmid39023219, year = {2024}, author = {López-Beltrán, A and Botelho, J and Iranzo, J}, title = {Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39023219}, issn = {1751-7370}, support = {PRE2020-092935//Agencia Estatal de Investigación of Spain/ ; UP2021-035//Spanish Ministry of Universities/ ; CEX2020-000999-S//Severo Ochoa Program for Centres of Excellence in R&D of the Agencia Estatal de Investigación of Spain/ ; RYC-2017-22524//Ramón y Cajal Programme of the Spanish Ministry of Science/ ; PID2019-106618GA-I00//Agencia Estatal de Investigación of Spain/ ; SEV-2016-0672//Severo Ochoa Programme for Centres of Excellence in R&D of the Agencia Estatal de Investigación of Spain/ ; //Comunidad de Madrid/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *CRISPR-Cas Systems ; *Bacteriophages/genetics ; *Bacteria/genetics/classification/virology ; Metagenomics ; Plasmids/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Host Microbial Interactions ; Prophages/genetics/physiology ; }, abstract = {Arms races between mobile genetic elements and prokaryotic hosts are major drivers of ecological and evolutionary change in microbial communities. Prokaryotic defense systems such as CRISPR-Cas have the potential to regulate microbiome composition by modifying the interactions among bacteria, plasmids, and phages. Here, we used longitudinal metagenomic data from 130 healthy and diseased individuals to study how the interplay of genetic parasites and CRISPR-Cas immunity reflects on the dynamics and composition of the human gut microbiome. Based on the coordinated study of 80 000 CRISPR-Cas loci and their targets, we show that CRISPR-Cas immunity effectively modulates bacteriophage abundances in the gut. Acquisition of CRISPR-Cas immunity typically leads to a decrease in the abundance of lytic phages but does not necessarily cause their complete disappearance. Much smaller effects are observed for lysogenic phages and plasmids. Conversely, phage-CRISPR interactions shape bacterial microdiversity by producing weak selective sweeps that benefit immune host lineages. We also show that distal (and chronologically older) regions of CRISPR arrays are enriched in spacers that are potentially functional and target crass-like phages and local prophages. This suggests that exposure to reactivated prophages and other endemic viruses is a major selective pressure in the gut microbiome that drives the maintenance of long-lasting immune memory.}, } @article {pmid39023128, year = {2024}, author = {Li, L and Sun, H and Tan, L and Guo, H and He, L and Chen, J and Chen, S and Liu, D and Zhu, M and OuYang, Z}, title = {Miao sour soup alleviates DSS-induced colitis in mice: modulation of gut microbiota and intestinal barrier function.}, journal = {Food & function}, volume = {15}, number = {16}, pages = {8370-8385}, doi = {10.1039/d4fo01794c}, pmid = {39023128}, issn = {2042-650X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Colitis/chemically induced ; *Dextran Sulfate/adverse effects ; Male ; *Intestinal Mucosa/microbiology ; Mice, Inbred C57BL ; Fermented Foods ; Disease Models, Animal ; Colon/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/isolation & purification/genetics ; Intestinal Barrier Function ; }, abstract = {Miao sour soup (MSS), a daily fermented food in Guizhou, China, is rich in microorganisms with various beneficial activities, including anti-inflammatory and antioxidant activities. However, the therapeutic effects of MSS on IBD remain unexplored. This study aimed to investigate the protective effect of MSS against colitis in mice. In this study, we examined the microbial community structure of MSS by metagenomic sequencing and also explored the protective effect of MSS on DSS-induced colitis in mice. We investigated the effects of MSS on intestinal inflammatory response and intestinal barrier function in mice. Finally, the changes in intestinal flora were analyzed based on the 16S rRNA gene sequencing results. Significantly, the experiment result shows that MSS ameliorated the severity of DSS-induced disease in mice by mitigating colitis-associated weight loss, reducing the disease activity index of IBD, alleviating colonic hemorrhagic lesions, increasing colon length, and improving colonic tissue damage. Moreover, MSS preserved intestinal barrier integrity and restored intestinal epithelial function in mice. Additionally, MSS modulated the structure and composition of the intestinal flora. Furthermore, MSS downregulated pro-inflammatory factors and attenuated the NF-κB p65 expression, thereby mitigating the inflammatory response. These findings highlight the protective effect of MSS against DSS-induced colitis, providing substantial scientific support for potential applications of MSS as a functional food.}, } @article {pmid39023095, year = {2024}, author = {Zhang, P and Ma, S and Guo, R and Li, L and Guo, X and Chang, D and Li, S and Zhang, H and Fu, C and Yang, L and Zhang, Y and Jiang, J and Wang, T and Wang, J and Shi, H}, title = {Metagenomic analysis of the gut virome in patients with irritable bowel syndrome.}, journal = {Journal of medical virology}, volume = {96}, number = {7}, pages = {e29802}, doi = {10.1002/jmv.29802}, pmid = {39023095}, issn = {1096-9071}, mesh = {Humans ; *Irritable Bowel Syndrome/virology/microbiology ; *Virome ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Feces/virology/microbiology ; Viruses/classification/genetics/isolation & purification ; Adult ; Male ; Female ; Middle Aged ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; }, abstract = {Irritable bowel syndrome (IBS), a chronic functional gastrointestinal disorder, is recognized for its association with alterations in the gut microbiome and metabolome. This study delves into the largely unexplored domain of the gut virome in IBS patients. We conducted a comprehensive analysis of the fecal metagenomic data set from 277 IBS patients and 84 healthy controls to characterize the gut viral community. Our findings revealed a distinct gut virome in IBS patients compared to healthy individuals, marked by significant variances in between-sample diversity and altered abundances of 127 viral operational taxonomic units (vOTUs). Specifically, 111 vOTUs, predominantly belonging to crAss-like, Siphoviridae, Myoviridae, and Quimbyviridae families, were more abundant in IBS patients, whereas the healthy control group exhibited enrichment of 16 vOTUs from multiple families. We also investigated the interplay between the gut virome and bacteriome, identifying a correlation between IBS-enriched bacteria like Klebsiella pneumoniae, Fusobacterium varium, and Ruminococcus gnavus, and the IBS-associated vOTUs. Furthermore, we assessed the potential of gut viral signatures in predicting IBS, achieving a notable area under the receiver operator characteristic curve (AUC) of 0.834. These findings highlight significant shifts in the viral diversity, taxonomic distribution, and functional composition of the gut virome in IBS patients, suggesting the potential role of the gut virome in IBS pathogenesis and opening new avenues for diagnostic and therapeutic strategies targeting the gut virome in IBS management.}, } @article {pmid39022885, year = {2024}, author = {Piontek, J and Hassenrück, C and Zäncker, B and Jürgens, K}, title = {Environmental control and metabolic strategies of organic-matter-responsive bacterioplankton in the Weddell Sea (Antarctica).}, journal = {Environmental microbiology}, volume = {26}, number = {7}, pages = {e16675}, doi = {10.1111/1462-2920.16675}, pmid = {39022885}, issn = {1462-2920}, support = {PI 784/3-1//Deutsche Forschungsgemeinschaft/ ; PI 784/4-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Seawater/microbiology ; Antarctic Regions ; *Gammaproteobacteria/metabolism/genetics ; *Phytoplankton/metabolism/genetics ; Carbon/metabolism ; Microbiota ; Plankton/metabolism/genetics/growth & development ; Metagenome ; Ecosystem ; Bacteroidetes/genetics/metabolism/growth & development ; Temperature ; }, abstract = {Heterotrophic microbial communities play a significant role in driving carbon fluxes in marine ecosystems. Despite their importance, these communities remain understudied in remote polar oceans, which are known for their substantial contribution to the biological drawdown of atmospheric carbon dioxide. Our research focused on understanding the environmental factors and genetic makeup of key bacterial players involved in carbon remineralization in the Weddell Sea, including its coastal polynyas. Our experiments demonstrated that the combination of labile organic matter supply and temperature increase synergistically boosted bacterial growth. This suggests that, besides low seawater temperature, carbon limitation also hinders heterotrophic bacterial activity. Through the analysis of metagenome-assembled genomes, we discovered distinct genomic adaptation strategies in Bacteroidia and Gammaproteobacteria, both of which respond to organic matter. Both natural phytoplankton blooms and experimental addition of organic matter favoured Bacteroidia, which possess a large number of gene copies and a wide range of functional membrane transporters, glycoside hydrolases, and aminopeptidases. In contrast, the genomes of organic-matter-responsive Gammaproteobacteria were characterized by high densities of transcriptional regulators and transporters. Our findings suggest that bacterioplankton in the Weddell Sea, which respond to organic matter, employ metabolic strategies similar to those of their counterparts in temperate oceans. These strategies enable efficient growth at extremely low seawater temperatures, provided that organic carbon limitation is alleviated.}, } @article {pmid39020289, year = {2024}, author = {Pérez-Prieto, I and Vargas, E and Salas-Espejo, E and Lüll, K and Canha-Gouveia, A and Pérez, LA and Fontes, J and Salumets, A and Andreson, R and Aasmets, O and , and Whiteson, K and Org, E and Altmäe, S}, title = {Gut microbiome in endometriosis: a cohort study on 1000 individuals.}, journal = {BMC medicine}, volume = {22}, number = {1}, pages = {294}, pmid = {39020289}, issn = {1741-7015}, mesh = {Humans ; *Endometriosis/microbiology ; Female ; *Gastrointestinal Microbiome/physiology ; Adult ; Case-Control Studies ; Estonia/epidemiology ; Cohort Studies ; Middle Aged ; Metagenomics ; Dysbiosis/microbiology ; Young Adult ; }, abstract = {BACKGROUND: Endometriosis, defined as the presence of endometrial-like tissue outside of the uterus, is one of the most prevalent gynecological disorders. Although different theories have been proposed, its pathogenesis is not clear. Novel studies indicate that the gut microbiome may be involved in the etiology of endometriosis; nevertheless, the connection between microbes, their dysbiosis, and the development of endometriosis is understudied. This case-control study analyzed the gut microbiome in women with and without endometriosis to identify microbial targets involved in the disease.

METHODS: A subsample of 1000 women from the Estonian Microbiome cohort, including 136 women with endometriosis and 864 control women, was analyzed. Microbial composition was determined by shotgun metagenomics and microbial functional pathways were annotated using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Partitioning Around Medoids (PAM) algorithm was performed to cluster the microbial profile of the Estonian population. The alpha- and beta-diversity and differential abundance analyses were performed to assess the gut microbiome (species and KEGG orthologies (KO)) in both groups. Metagenomic reads were mapped to estrobolome-related enzymes' sequences to study potential microbiome-estrogen metabolism axis alterations in endometriosis.

RESULTS: Diversity analyses did not detect significant differences between women with and without endometriosis (alpha-diversity: all p-values > 0.05; beta-diversity: PERMANOVA, both R [2] < 0.0007, p-values > 0.05). No differential species or pathways were detected after multiple testing adjustment (all FDR p-values > 0.05). Sensitivity analysis excluding women at menopause (> 50 years) confirmed our results. Estrobolome-associated enzymes' sequence reads were not significantly different between groups (all FDR p-values > 0.05).

CONCLUSIONS: Our findings do not provide enough evidence to support the existence of a gut microbiome-dependent mechanism directly implicated in the pathogenesis of endometriosis. To the best of our knowledge, this is the largest metagenome study on endometriosis conducted to date.}, } @article {pmid39020259, year = {2024}, author = {Song, X and Fu, X and Niu, S and Wang, P and Qi, J and Shi, S and Chang, H and Bai, W}, title = {Exploring the effects of Saorilao-4 on the gut microbiota of pulmonary fibrosis model rats based on 16S rRNA sequencing.}, journal = {Journal of applied microbiology}, volume = {135}, number = {7}, pages = {}, doi = {10.1093/jambio/lxae178}, pmid = {39020259}, issn = {1365-2672}, support = {2024MS08025//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; 202202226//Inner Mongolia Health Science and Technology Project/ ; wskjjk2022065//Baotou Health Science and Technology Program/ ; BYJJ-DXK 2022047//Baotou Medical College Young Science and Technology Talent Development/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *RNA, Ribosomal, 16S/genetics ; Rats ; *Pulmonary Fibrosis/microbiology/genetics ; *Feces/microbiology ; *Disease Models, Animal ; *Bacteria/genetics/classification/isolation & purification ; Male ; Rats, Sprague-Dawley ; }, abstract = {AIMS: Pulmonary fibrosis (PF) is a progressive and incurable lung disease for which treatment options are limited. Here, we aimed to conduct an exploratory study on the effects of the Mongolian medicine Saorilao-4 (SRL) on the gut microbiota structure, species abundance, and diversity of a rat PF model as well as the mechanisms underlying such effects.

METHODS AND RESULTS: Rat fecal samples were analyzed using 16S rRNA sequencing technology. Bioinformatic and correlation analyses were performed on microbiota data to determine significant associations. SRL substantially attenuated the adverse effects exerted by PF on the structure and diversity of gut microbiota while regulating its alpha and beta diversities. Linear discriminant analysis effect size enabled the identification of 62 differentially abundant microbial taxa. Gut microbiota abundance analysis revealed that SRL significantly increased the relative abundance of bacterial phyla such as Firmicutes and Bacteroidetes. Moreover, SRL increased the proportion of beneficial bacteria, such as Lactobacillus and Bifidobacteriales, decreased the proportion of pathogenic bacteria, such as Rikenellaceae, and balanced the gut microbiota by regulating metabolic pathways.

CONCLUSIONS: SRL may attenuate PF by regulating gut microbiota. This exploratory study establishes the groundwork for investigating the metagenomics of PF.}, } @article {pmid39019914, year = {2024}, author = {Dong, Y and Chen, R and Graham, EB and Yu, B and Bao, Y and Li, X and You, X and Feng, Y}, title = {Eco-evolutionary strategies for relieving carbon limitation under salt stress differ across microbial clades.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {6013}, pmid = {39019914}, issn = {2041-1723}, support = {41977045//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Soil Microbiology ; *Carbon/metabolism ; *Archaea/genetics/metabolism ; *Bacteria/metabolism/genetics/classification ; *Salt Stress ; *Microbiota/genetics/drug effects ; *Climate Change ; Salinity ; Soil/chemistry ; Metagenomics ; Phylogeny ; Biological Evolution ; Genome, Bacterial ; Metagenome ; }, abstract = {With the continuous expansion of saline soils under climate change, understanding the eco-evolutionary tradeoff between the microbial mitigation of carbon limitation and the maintenance of functional traits in saline soils represents a significant knowledge gap in predicting future soil health and ecological function. Through shotgun metagenomic sequencing of coastal soils along a salinity gradient, we show contrasting eco-evolutionary directions of soil bacteria and archaea that manifest in changes to genome size and the functional potential of the soil microbiome. In salt environments with high carbon requirements, bacteria exhibit reduced genome sizes associated with a depletion of metabolic genes, while archaea display larger genomes and enrichment of salt-resistance, metabolic, and carbon-acquisition genes. This suggests that bacteria conserve energy through genome streamlining when facing salt stress, while archaea invest in carbon-acquisition pathways to broaden their resource usage. These findings suggest divergent directions in eco-evolutionary adaptations to soil saline stress amongst microbial clades and serve as a foundation for understanding the response of soil microbiomes to escalating climate change.}, } @article {pmid39019886, year = {2024}, author = {Dhariwal, A and Rajar, P and Salvadori, G and Åmdal, HA and Berild, D and Saugstad, OD and Fugelseth, D and Greisen, G and Dahle, U and Haaland, K and Petersen, FC}, title = {Prolonged hospitalization signature and early antibiotic effects on the nasopharyngeal resistome in preterm infants.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {6024}, pmid = {39019886}, issn = {2041-1723}, mesh = {Humans ; *Nasopharynx/microbiology ; *Infant, Premature ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Infant, Newborn ; Prospective Studies ; *Hospitalization ; Female ; Male ; Metagenomics/methods ; Infant ; Serratia marcescens/drug effects/genetics ; Microbiota/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics/drug effects ; }, abstract = {Respiratory pathogens, commonly colonizing nasopharynx, are among the leading causes of death due to antimicrobial resistance. Yet, antibiotic resistance determinants within nasopharyngeal microbial communities remain poorly understood. In this prospective cohort study, we investigate the nasopharynx resistome development in preterm infants, assess early antibiotic impact on its trajectory, and explore its association with clinical covariates using shotgun metagenomics. Our findings reveal widespread nasopharyngeal carriage of antibiotic resistance genes (ARGs) with resistomes undergoing transient changes, including increased ARG diversity, abundance, and composition alterations due to early antibiotic exposure. ARGs associated with the critical nosocomial pathogen Serratia marcescens persist up to 8-10 months of age, representing a long-lasting hospitalization signature. The nasopharyngeal resistome strongly correlates with microbiome composition, with inter-individual differences and postnatal age explaining most of the variation. Our report on the collateral effects of antibiotics and prolonged hospitalization underscores the urgency of further studies focused on this relatively unexplored reservoir of pathogens and ARGs.}, } @article {pmid39019308, year = {2024}, author = {Ewere, EE and White, S and Mauleon, R and Benkendorff, K}, title = {Soil microbial communities and degradation of pesticides in greenhouse effluent through a woodchip bioreactor.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {359}, number = {}, pages = {124561}, doi = {10.1016/j.envpol.2024.124561}, pmid = {39019308}, issn = {1873-6424}, mesh = {*Bioreactors/microbiology ; *Soil Microbiology ; *Biodegradation, Environmental ; *Pesticides/metabolism/analysis ; Soil Pollutants/analysis/metabolism ; Microbiota ; Agriculture ; Bacteria/metabolism/genetics/classification ; Soil/chemistry ; }, abstract = {Pesticides, including insecticides and fungicides, are major contaminants in the effluent from intensive agricultural systems, such as greenhouses. Because of their constant use and persistence, some pesticides can accumulate in soil and/or run off into adjacent waterways. Microbial communities in soil can degrade some pesticides, and bioreactors with enhanced microbial communities have the potential to facilitate decontamination before the effluent is released into the environment. In this study, we sampled the soil along a gradient from immediately below greenhouses, into, through and below a bioreactor. Multi-analyte pesticide screening was undertaken along with shotgun metagenomic sequencing, to assess microbial community taxonomic profiles and metabolic pathway responses for functional analysis. Two insecticides (imidacloprid and fipronil) and nine fungicides were identified in the soil samples, with a general decrease in most pesticides with increasing distance from the greenhouses. Diversity indexes of taxonomic profiles show changes in the microbial community along the gradient. In particular, microbial communities were significantly different in the bioreactor, with lower Shannon diversity compared to immediately below the greenhouses, in the channels leading into the bioreactor and further downstream. Metabolic pathway analysis revealed significant changes in a wide range of core housekeeping genes such as protein/amino acid synthesis and lipid/fatty acid biosynthesis among the sampling sites. The result demonstrates that the composition and potential functional pathways of the microbial community shifted towards an increased tendency for phytol and contaminant degradation in the bioreactor, facilitated by high organic matter content. This highlights the potential to use enhanced microbial communities within bioreactors to reduce contamination by some pesticides in sediment receiving run-off from greenhouses.}, } @article {pmid39019160, year = {2024}, author = {Zhu, Y and Yeo, EN and Smith, KM and Greenberg, AS and Rowan, S}, title = {Aging Modulates the Effect of Dietary Glycemic Index on Gut Microbiota Composition in Mice.}, journal = {The Journal of nutrition}, volume = {154}, number = {9}, pages = {2852-2861}, pmid = {39019160}, issn = {1541-6100}, support = {P30 DK046200/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Male ; *Mice, Inbred C57BL ; *Gastrointestinal Microbiome/drug effects ; *Aging ; *Glycemic Index ; Mice ; *Diet ; *Feces/microbiology/chemistry ; Bacteria/classification/genetics ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Gut microbiome composition profoundly impacts host physiology and is modulated by several environmental factors, most prominently diet. The composition of gut microbiota changes over the lifespan, particularly during the earliest and latest stages. However, we know less about diet-aging interactions on the gut microbiome. We previously showed that diets with different glycemic indices, based on the ratio of rapidly digested amylopectin to slowly digested amylose, led to altered composition of gut microbiota in male C57BL/6J mice.

OBJECTIVES: Here, we examined the role of aging in influencing dietary effects on gut microbiota composition and aimed to identify gut bacterial taxa that respond to diet and aging.

METHODS: We studied 3 age groups of male C57BL/6J wild-type mice: young (4 mo), middle-aged (13.5 mo), and old (22 mo), all fed either high glycemic (HG) or low glycemic (LG) diets matched for caloric content and macronutrient composition. Fecal microbiome composition was determined by 16S rDNA metagenomic sequencing and was evaluated for changes in α- and β-diversity and bacterial taxa that change by age, diet, or both.

RESULTS: Young mice displayed lower α-diversity scores than middle-aged counterparts but exhibited more pronounced differences in β-diversity between diets. In contrast, old mice had slightly lower α-diversity scores than middle-aged mice, with significantly higher β-diversity distances. Within-group variance was lowest in young, LG-fed mice and highest in old, HG-fed mice. Differential abundance analysis revealed taxa associated with both aging and diet. Most differential taxa demonstrated significant interactions between diet and aging. Notably, several members of the Lachnospiraceae family increased with aging and HG diet, whereas taxa from the Bacteroides_H genus increased with the LG diet. Akkermansia muciniphila decreased with aging.

CONCLUSIONS: These findings illustrate the complex interplay between diet and aging in shaping the gut microbiota, potentially contributing to age-related disease.}, } @article {pmid39017960, year = {2024}, author = {Daddy Gaoh, S and Alusta, P and Lee, YJ and LiPuma, JJ and Hussong, D and Marasa, B and Ahn, Y}, title = {A Comparative Metagenomic Analysis of Specified Microorganisms in Groundwater for Non-Sterilized Pharmaceutical Products.}, journal = {Current microbiology}, volume = {81}, number = {9}, pages = {273}, pmid = {39017960}, issn = {1432-0991}, mesh = {*Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; *Groundwater/microbiology ; Microbiota/genetics ; Pharmaceutical Preparations ; Metagenome ; Water Microbiology ; }, abstract = {In pharmaceutical manufacturing, ensuring product safety involves the detection and identification of microorganisms with human pathogenic potential, including Burkholderia cepacia complex (BCC), Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica, Staphylococcus aureus, Clostridium sporogenes, Candida albicans, and Mycoplasma spp., some of which may be missed or not identified by traditional culture-dependent methods. In this study, we employed a metagenomic approach to detect these taxa, avoiding the limitations of conventional cultivation methods. We assessed the groundwater microbiome's taxonomic and functional features from samples collected at two locations in the spring and summer. All datasets comprised 436-557 genera with Proteobacteria, Bacteroidota, Firmicutes, Actinobacteria, and Cyanobacteria accounting for > 95% of microbial DNA sequences. The aforementioned species constituted less than 18.3% of relative abundance. Escherichia and Salmonella were mainly detected in Hot Springs, relative to Jefferson, while Clostridium and Pseudomonas were mainly found in Jefferson relative to Hot Springs. Multidrug resistance efflux pumps and BlaR1 family regulatory sensor-transducer disambiguation dominated in Hot Springs and in Jefferson. These initial results provide insight into the detection of specified microorganisms and could constitute a framework for the establishment of comprehensive metagenomic analysis for the microbiological evaluation of pharmaceutical-grade water and other non-sterile pharmaceutical products, ensuring public safety.}, } @article {pmid39017661, year = {2024}, author = {Rashidi, A and Pidala, J and Hamilton, BK and Pavletic, SZ and Kim, K and Zevin, A and Mays, JW and Lee, SJ}, title = {Oral and Gut Microbiome Alterations in Oral Chronic GVHD Disease: Results from Close Assessment and Testing for Chronic GVHD (CATCH Study).}, journal = {Clinical cancer research : an official journal of the American Association for Cancer Research}, volume = {30}, number = {18}, pages = {4240-4250}, pmid = {39017661}, issn = {1557-3265}, support = {P30 CA015704/CA/NCI NIH HHS/United States ; U01 CA236229/CA/NCI NIH HHS/United States ; ZIA DE000747/ImNIH/Intramural NIH HHS/United States ; U01 CA118953/CA/NCI NIH HHS/United States ; CA118953//National Cancer Institute (NCI)/ ; CA236229//National Institute of Dental and Craniofacial Research (NIDCR)/ ; R01 CA118953/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Graft vs Host Disease/microbiology/diagnosis ; *Gastrointestinal Microbiome ; Female ; Male ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Middle Aged ; Adult ; Chronic Disease ; *Mouth/microbiology ; Transplantation, Homologous ; Aged ; Feces/microbiology ; Prospective Studies ; Metagenomics/methods ; Young Adult ; }, abstract = {PURPOSE: Whether and how the oral microbiome and its changes in allogeneic hematopoietic cell transplantation (alloHCT) recipients may contribute to oral chronic GVHD (cGVHD) pathogenesis is unknown. In addition, although the oral and colonic microbiota are distinct in healthy adults, whether oral microbes may ectopically colonize the gut in alloHCT patients is unknown.

EXPERIMENTAL DESIGN: To address these knowledge gaps, longitudinal oral and fecal samples were collected prospectively in the multicenter Close Assessment and Testing for Chronic GVHD study (NCT04188912). Through shotgun metagenomic sequencing of the samples collected at baseline, oral cGVHD onset, first post-cGVHD onset visit, and 1-year post-HCT time points in patients with oral cGVHD (cases; N = 29) or without any cGVHD (controls; N = 51), we examined whether (i) oral and/or gut microbiomes and their longitudinal trajectories differ between cases and controls and (ii) oral and gut microbiomes overlap in alloHCT recipients, especially those developing cGVHD.

RESULTS: A total of 195 samples were analyzed. The onset of oral cGVHD was characterized by an expansion of Streptococcus salivarius and Veillonella parvula in the oral microbiome. High levels of oral/gut microbiota overlap were observed, particularly in patients with oral cGVHD, suggesting ectopic colonization of the gut by oral bacteria.

CONCLUSIONS: The unusual coalescence of two distant niches in these patients may result in short- or long-term consequences for the host, a novel avenue for future research. In addition, this study suggests a contribution of the oral microbiome to oral cGVHD pathogenesis.}, } @article {pmid39016466, year = {2024}, author = {Zhang, P and Shi, H and Guo, R and Li, L and Guo, X and Yang, H and Chang, D and Cheng, Y and Zhao, G and Li, S and Zhong, Q and Zhang, H and Zhao, P and Fu, C and Song, Y and Yang, L and Wang, Y and Zhang, Y and Jiang, J and Wang, T and Zhao, J and Li, Y and Wang, B and Chen, F and Zhao, H and Wang, Y and Wang, J and Ma, S}, title = {Metagenomic analysis reveals altered gut virome and diagnostic potential in pancreatic cancer.}, journal = {Journal of medical virology}, volume = {96}, number = {7}, pages = {e29809}, doi = {10.1002/jmv.29809}, pmid = {39016466}, issn = {1096-9071}, mesh = {Humans ; *Pancreatic Neoplasms/virology/diagnosis/microbiology ; *Gastrointestinal Microbiome/genetics ; *Virome ; *Metagenomics/methods ; *Feces/virology/microbiology ; Viruses/isolation & purification/genetics/classification ; Metagenome ; Bacteria/isolation & purification/classification/genetics ; Middle Aged ; Male ; Female ; Aged ; Case-Control Studies ; }, abstract = {Pancreatic cancer (PC) is a highly aggressive malignancy with a poor prognosis, making early diagnosis crucial for improving patient outcomes. While the gut microbiome, including bacteria and viruses, is believed to be essential in cancer pathogenicity, the potential contribution of the gut virome to PC remains largely unexplored. In this study, we conducted a comparative analysis of the gut viral compositional and functional profiles between PC patients and healthy controls, based on fecal metagenomes from two publicly available data sets comprising a total of 101 patients and 82 healthy controls. Our results revealed a decreasing trend in the gut virome diversity of PC patients with disease severity. We identified significant alterations in the overall viral structure of PC patients, with a meta-analysis revealing 219 viral operational taxonomic units (vOTUs) showing significant differences in relative abundance between patients and healthy controls. Among these, 65 vOTUs were enriched in PC patients, and 154 were reduced. Host prediction revealed that PC-enriched vOTUs preferentially infected bacterial members of Veillonellaceae, Enterobacteriaceae, Fusobacteriaceae, and Streptococcaceae, while PC-reduced vOTUs were more likely to infect Ruminococcaceae, Lachnospiraceae, Clostridiaceae, Oscillospiraceae, and Peptostreptococcaceae. Furthermore, we constructed random forest models based on the PC-associated vOTUs, achieving an optimal average area under the curve (AUC) of up to 0.879 for distinguishing patients from controls. Through additional 10 public cohorts, we demonstrated the reproducibility and high specificity of these viral signatures. Our study suggests that the gut virome may play a role in PC development and could serve as a promising target for PC diagnosis and therapeutic intervention. Future studies should further explore the underlying mechanisms of gut virus-bacteria interactions and validate the diagnostic models in larger and more diverse populations.}, } @article {pmid39015337, year = {2024}, author = {Bashir, Z and Hugerth, LW and Krog, MC and Prast-Nielsen, S and Edfeldt, G and Boulund, F and Schacht, SR and Tetens, I and Engstrand, L and Schuppe-Koistinen, I and Fransson, E and Nielsen, HS}, title = {Investigations of microbiota composition and neuroactive pathways in association with symptoms of stress and depression in a cohort of healthy women.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1324794}, pmid = {39015337}, issn = {2235-2988}, mesh = {Humans ; Female ; Adult ; Young Adult ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Adolescent ; *Depression/microbiology ; *Vagina/microbiology ; *Feces/microbiology ; *Stress, Psychological/microbiology ; Microbiota ; Denmark ; Healthy Volunteers ; Brain-Gut Axis/physiology ; Surveys and Questionnaires ; Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {BACKGROUND: Despite mounting evidence of gut-brain involvement in psychiatric conditions, functional data remain limited, and analyses of other microbial niches, such as the vaginal microbiota, are lacking in relation to mental health. This aim of this study was to investigate if the connections between the gut microbiome and mental health observed in populations with a clinical diagnosis of mental illness extend to healthy women experiencing stress and depressive symptoms. Additionally, this study examined the functional pathways of the gut microbiota according to the levels of psychological symptoms. Furthermore, the study aimed to explore potential correlations between the vaginal microbiome and mental health parameters in young women without psychiatric diagnoses.

METHODS: In this cross-sectional study, 160 healthy Danish women (aged 18-40 years) filled out questionnaires with validated scales measuring symptoms of stress and depression and frequency of dietary intake. Fecal and vaginal microbiota samples were collected at the beginning of the menstrual cycle and vaginal samples were also collected at cycle day 8-12 and 18-22. Shotgun metagenomic profiling of the gut and vaginal microbiome was performed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) was used for functional profiling and 56 Gut Brain Modules were analyzed in the fecal samples.

RESULTS: The relative abundance in the gut of the genera Escherichia, Parabacteroides, and Shigella was higher in women with elevated depressive symptoms. Women with high perceived stress showed a tendency of increased abundance of Escherichia, Shigella, and Blautia. Amongst others, the potentially pathogenic genera, Escherichia and Shigella correlate with alterations in the neuroactive pathways such as the glutamatergic, GABAeric, dopaminergic, and Kynurenine pathways. Vaginosis symptoms were more prevalent in women reporting high levels of stress and depressive symptoms.

CONCLUSIONS: The findings of this study support the concept of a microbiota-associated effect on the neuroactive pathways even in healthy young women. This suggest, that targeting the gut microbiome could be a promising approach for future psychiatric interventions.}, } @article {pmid39014985, year = {2024}, author = {Duggan DiDominic, KL and Shapleigh, JP and Walter, MT and Wang, YS and Reid, MC and Regan, JM}, title = {Microbial diversity and gene abundance in denitrifying bioreactors: A comparison of the woodchip surface biofilm versus the interior wood matrix.}, journal = {Journal of environmental quality}, volume = {53}, number = {5}, pages = {565-576}, doi = {10.1002/jeq2.20600}, pmid = {39014985}, issn = {1537-2537}, support = {1922551//National Science Foundation Research Traineeship (NRT) Program/ ; 2019-67019-29461//U.S. Department of Agriculture/ ; }, mesh = {*Bioreactors ; *Wood ; *Biofilms ; *Denitrification ; Microbiota ; Nitrogen/analysis ; Bacteria/genetics/metabolism ; }, abstract = {Excessive amounts of nitrogen (N) and phosphorus (P) can lead to eutrophication in water sources. Woodchip bioreactors have shown success in removing N from agricultural runoff, but less is known regarding P removal. Woodchip bioreactors are subsurface basins filled with woodchips installed downgradient of agricultural land to collect and treat drainage runoff. Microorganisms use the woodchips as a carbon (C) source to transform N in the runoff, with unresolved biological impacts on P. This study aims to explore microbial communities present in the bioreactor and determine whether milling woodchips to probe the microbial communities within them reveals hidden microbial diversities or potential activities. Metagenomic sequencing and bioinformatic analyses were performed on six woodchip samples (i.e., three unmilled and three milled) collected from a 10-year-old woodchip bioreactor treating agricultural tile drainage. All samples had similar DNA purity, yield, quality, and microbial diversity regardless of milling. However, when sequences were aligned against various protein libraries, our results indicated greater relative abundance of denitrification and P transformation proteins on the outside of the woodchips (unmilled), while the interior of woodchips (milled) exhibited more functional gene abundance for carbohydrate breakdown. Thus, it may be important to characterize microbial communities both within woodchips, and on woodchip surfaces, to gain a more holistic understanding of coupled biogeochemical cycles on N, P, and C in woodchip bioreactors. Based on these findings, we advise that future microbial research on woodchips (and potentially other permeable organic materials) examine both the surface biofilm and the interior organic material during initial studies. Once researchers determine where specific proteins or enzymes of interest are most prevalent, subsequent studies may then focus on either one or both aspects, as needed.}, } @article {pmid39014300, year = {2024}, author = {Darabi, A and Sobhani, S and Aghdam, R and Eslahchi, C}, title = {AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {241}, pmid = {39014300}, issn = {1471-2105}, mesh = {*Metagenomics/methods ; *Algorithms ; Nucleotides/genetics ; High-Throughput Nucleotide Sequencing/methods ; Software ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Cluster Analysis ; Contig Mapping/methods ; Metagenome/genetics ; }, abstract = {BACKGROUND: Using next-generation sequencing technologies, scientists can sequence complex microbial communities directly from the environment. Significant insights into the structure, diversity, and ecology of microbial communities have resulted from the study of metagenomics. The assembly of reads into longer contigs, which are then binned into groups of contigs that correspond to different species in the metagenomic sample, is a crucial step in the analysis of metagenomics. It is necessary to organize these contigs into operational taxonomic units (OTUs) for further taxonomic profiling and functional analysis. For binning, which is synonymous with the clustering of OTUs, the tetra-nucleotide frequency (TNF) is typically utilized as a compositional feature for each OTU.

RESULTS: In this paper, we present AFIT, a new l-mer statistic vector for each contig, and AFITBin, a novel method for metagenomic binning based on AFIT and a matrix factorization method. To evaluate the performance of the AFIT vector, the t-SNE algorithm is used to compare species clustering based on AFIT and TNF information. In addition, the efficacy of AFITBin is demonstrated on both simulated and real datasets in comparison to state-of-the-art binning methods such as MetaBAT 2, MaxBin 2.0, CONCOT, MetaCon, SolidBin, BusyBee Web, and MetaBinner. To further analyze the performance of the purposed AFIT vector, we compare the barcodes of the AFIT vector and the TNF vector.

CONCLUSION: The results demonstrate that AFITBin shows superior performance in taxonomic identification compared to existing methods, leveraging the AFIT vector for improved results in metagenomic binning. This approach holds promise for advancing the analysis of metagenomic data, providing more reliable insights into microbial community composition and function.

AVAILABILITY: A python package is available at: https://github.com/SayehSobhani/AFITBin .}, } @article {pmid39012154, year = {2024}, author = {Salazar-Jaramillo, L and de la Cuesta-Zuluaga, J and Chica, LA and Cadavid, M and Ley, RE and Reyes, A and Escobar, JS}, title = {Gut microbiome diversity within Clostridia is negatively associated with human obesity.}, journal = {mSystems}, volume = {9}, number = {8}, pages = {e0062724}, pmid = {39012154}, issn = {2379-5077}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology ; Male ; Adult ; Female ; Cross-Sectional Studies ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Body Mass Index ; }, abstract = {UNLABELLED: Clostridia are abundant in the human gut and comprise families associated with host health such as Oscillospiraceae, which has been correlated with leanness. However, culturing bacteria within this family is challenging, leading to their detection primarily through 16S rRNA amplicon sequencing, which has a limited ability to unravel diversity at low taxonomic levels, or by shotgun metagenomics, which is hindered by its high costs and complexity. In this cross-sectional study involving 114 Colombian adults, we used an amplicon-based sequencing strategy with alternative markers-gyrase subunit B (gyrB) and DNA K chaperone heat protein 70 (dnaK)-that evolve faster than the 16S rRNA gene. Comparing the diversity and abundance observed with the three markers in our cohort, we found a reduction in the diversity of Clostridia, particularly within Lachnospiraceae and Oscillospiraceae among obese individuals [as measured by the body mass index (BMI)]. Within Lachnospiraceae, the diversity of Ruminococcus_A negatively correlated with BMI. Within Oscillospiraceae, the genera CAG-170 and Vescimonas also exhibited this negative correlation. In addition, the abundance of Vescimonas was negatively correlated with BMI. Leveraging shotgun metagenomic data, we conducted a phylogenetic and genomic characterization of 120 metagenome-assembled genomes from Vescimonas obtained from a larger sample of the same cohort. We identified 17 of the 72 reported species. The functional annotation of these genomes showed the presence of multiple carbohydrate-active enzymes, particularly glycosyl transferases and glycoside hydrolases, suggesting potential beneficial roles in fiber degradation, carbohydrate metabolism, and butyrate production.

IMPORTANCE: The gut microbiota is diverse across various taxonomic levels. At the intra-species level, it comprises multiple strains, some of which may be host-specific. However, our understanding of fine-grained diversity has been hindered by the use of the conserved 16S rRNA gene. While shotgun metagenomics offers higher resolution, it remains costly, may fail to identify specific microbes in complex samples, and requires extensive computational resources and expertise. To address this, we employed a simple and cost-effective analysis of alternative genetic markers to explore diversity within Clostridia, a crucial group within the human gut microbiota whose diversity may be underestimated. We found high intra-species diversity for certain groups and associations with obesity. Notably, we identified Vescimonas, an understudied group. Making use of metagenomic data, we inferred functionality, uncovering potential beneficial roles in dietary fiber and carbohydrate degradation, as well as in short-chain fatty acid production.}, } @article {pmid39012105, year = {2024}, author = {Wu, W-C and Pan, Y-F and Zhou, W-D and Liao, Y-Q and Peng, M-W and Luo, G-Y and Xin, G-Y and Peng, Y-N and An, T and Li, B and Luo, H and Barrs, VR and Beatty, JA and Holmes, EC and Zhao, W and Shi, M and Shu, Y}, title = {Meta-transcriptomic analysis of companion animal infectomes reveals their diversity and potential roles in animal and human disease.}, journal = {mSphere}, volume = {9}, number = {8}, pages = {e0043924}, pmid = {39012105}, issn = {2379-5042}, mesh = {Animals ; Cats ; Dogs ; *Pets/virology/microbiology ; Humans ; *Dog Diseases/microbiology/virology/transmission ; *Zoonoses/microbiology/virology/transmission ; *Cat Diseases/virology/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Microbiota/genetics ; China ; Viruses/classification/genetics/isolation & purification/pathogenicity ; Fungi/classification/genetics/isolation & purification/pathogenicity ; Gene Expression Profiling ; Transcriptome ; }, abstract = {UNLABELLED: Companion animals such as cats and dogs harbor diverse microbial communities that can potentially impact human health due to close and frequent contact. To better characterize their total infectomes and assess zoonotic risks, we characterized the overall infectomes of companion animals (cats and dogs) and evaluated their potential zoonotic risks. Meta-transcriptomic analyses were performed on 239 samples from cats and dogs collected across China, identifying 24 viral species, 270 bacterial genera, and two fungal genera. Differences in the overall microbiome and infectome composition were compared across different animal species (cats or dogs), sampling sites (rectal or oropharyngeal), and health status (healthy or diseased). Diversity analyses revealed that viral abundance was generally higher in diseased animals compared to healthy ones, while differences in microbial composition were mainly driven by sampling site, followed by animal species and health status. Disease association analyses validated the pathogenicity of known pathogens and suggested potential pathogenic roles of previously undescribed bacteria and newly discovered viruses. Cross-species transmission analyses identified seven pathogens shared between cats and dogs, such as alphacoronavirus 1, which was detected in both oropharyngeal and rectal swabs albeit with differential pathogenicity. Further analyses showed that some viruses, like alphacoronavirus 1, harbored multiple lineages exhibiting distinct pathogenicity, tissue, or host preferences. Ultimately, a systematic evolutionary screening identified 27 potential zoonotic pathogens in this sample set, with far more bacterial than viral species, implying potential health threats to humans. Overall, our meta-transcriptomic analysis reveals a landscape of actively transcribing microorganisms in major companion animals, highlighting key pathogens, those with the potential for cross-species transmission, and possible zoonotic threats.

IMPORTANCE: This study provides a comprehensive characterization of the entire community of infectious microbes (viruses, bacteria, and fungi) in companion animals like cats and dogs, termed the "infectome." By analyzing hundreds of samples from across China, the researchers identified numerous known and novel pathogens, including 27 potential zoonotic agents that could pose health risks to both animals and humans. Notably, some of these zoonotic pathogens were detected even in apparently healthy pets, highlighting the importance of surveillance. The study also revealed key microbial factors associated with respiratory and gastrointestinal diseases in pets, as well as potential cross-species transmission events between cats and dogs. Overall, this work sheds light on the complex microbial landscapes of companion animals and their potential impacts on animal and human health, underscoring the need for monitoring and management of these infectious agents.}, } @article {pmid39010331, year = {2025}, author = {Aydin, Ö and Wahlström, A and de Jonge, PA and Meijnikman, AS and Sjöland, W and Olsson, L and Henricsson, M and de Goffau, MC and Oonk, S and Bruin, SC and Acherman, YIZ and Marschall, HU and Gerdes, VEA and Nieuwdorp, M and Bäckhed, F and Groen, AK}, title = {An integrated analysis of bile acid metabolism in humans with severe obesity.}, journal = {Hepatology (Baltimore, Md.)}, volume = {81}, number = {1}, pages = {19-31}, doi = {10.1097/HEP.0000000000000938}, pmid = {39010331}, issn = {1527-3350}, mesh = {Humans ; *Bile Acids and Salts/metabolism ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Adult ; Middle Aged ; *Feces/microbiology/chemistry ; *Obesity, Morbid/metabolism/microbiology ; Fibroblast Growth Factors/metabolism ; }, abstract = {BACKGROUND AND AIMS: Bile acids (BA) are vital regulators of metabolism. BAs are AQ6 secreted in the small intestine, reabsorbed, and transported back to the liver, where they can modulate metabolic functions. There is a paucity of data regarding the portal BA composition in humans. This study aimed to address this knowledge gap by investigating portal BA composition and the relation with peripheral and fecal BA dynamics in conjunction with the gut microbiome.

APPROACH AND RESULTS: Thirty-three individuals from the BARIA cohort were included. Portal plasma, peripheral plasma, and feces were collected. BA and C4 levels were measured employing mass spectrometry. FGF19 was measured using ELISA. Gut microbiota composition was determined through metagenomics analysis on stool samples. Considerable diversity in the portal BA composition was observed. The majority (n = 26) of individuals had a 9-fold higher portal than peripheral BA concentration. In contrast, 8 individuals showed lower portal BA concentration compared with peripheral and had higher levels of unconjugated and secondary BA in this compartment, suggesting more distal origin. The altered portal BA profile was associated with altered gut microbiota composition. In particular, taxa within Bacteroides were reduced in abundance in the feces of these individuals.

CONCLUSIONS: Characterization of the portal BA composition in relation to peripheral and fecal BA increased insight into the dynamics of BA metabolism in individuals with obesity. Peripheral BA composition was much more diverse due to microbial metabolism. About 24% of the portal samples was surprisingly low in total BA; the underlying mechanism requires further exploration.}, } @article {pmid39010229, year = {2024}, author = {Chang, T and Gavelis, GS and Brown, JM and Stepanauskas, R}, title = {Genomic representativeness and chimerism in large collections of SAGs and MAGs of marine prokaryoplankton.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {126}, pmid = {39010229}, issn = {2049-2618}, support = {827839//Simons Foundation/ ; 827839//Simons Foundation/ ; 827839//Simons Foundation/ ; 827839//Simons Foundation/ ; OIA-1826734//National Science Foundation/ ; OIA-1826734//National Science Foundation/ ; OIA-1826734//National Science Foundation/ ; OIA-1826734//National Science Foundation/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Metagenome ; *Bacteria/genetics/classification ; *Plankton/genetics/classification/microbiology ; Phylogeny ; Seawater/microbiology ; Chimerism ; Genome, Bacterial ; Metagenomics/methods ; Microbiota/genetics ; Genomics ; }, abstract = {BACKGROUND: Single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are the predominant sources of information about the coding potential of uncultured microbial lineages, but their strengths and limitations remain poorly understood. Here, we performed a direct comparison of two previously published collections of thousands of SAGs and MAGs obtained from the same, global environment.

RESULTS: We found that SAGs were less prone to chimerism and more accurately reflected the relative abundance and the pangenome content of microbial lineages inhabiting the epipelagic of the tropical and subtropical ocean, as compared to MAGs. SAGs were also better suited to link genome information with taxa discovered through 16S rRNA amplicon analyses. Meanwhile, MAGs had the advantage of more readily recovering genomes of rare lineages.

CONCLUSIONS: Our analyses revealed the relative strengths and weaknesses of the two most commonly used genome recovery approaches in environmental microbiology. These considerations, as well as the need for better tools for genome quality assessment, should be taken into account when designing studies and interpreting data that involve SAGs or MAGs. Video Abstract.}, } @article {pmid39009515, year = {2024}, author = {Takeda, M and Doki, Y}, title = {[The Power of the Gut Microbiome: Exploring New Perspectives in Colorectal Cancer Therapy].}, journal = {Gan to kagaku ryoho. Cancer & chemotherapy}, volume = {51}, number = {6}, pages = {608-612}, pmid = {39009515}, issn = {0385-0684}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/therapy ; *Gastrointestinal Microbiome ; Animals ; Dysbiosis/microbiology ; }, abstract = {The gut microbiome is involved in host physiology, including nutrition, metabolism, and immunity. It was recently known that dysbiosis of the gut microbiome has been implicated in several human diseases such as inflammatory bowel disease. It is altered by environmental factors such as diet, habit and lifestyle and has been directly and indirectly linked to the development and progression of colorectal cancer(CRC). Fusobacterium(F.)nucleatum, which causes periodontal disease, has been shown to play an important role in the initiation and development of CRC, although not as clearly as Helicobacter(H.) pylori in gastric cancer. Therefore, gut bacteria hold promise as a potential therapeutic approach to prevent or treat CRC. Although its clinical usefulness has not yet been demonstrated, future research such as metagenomics may open new avenues for CRC treatment with gut bacteria. Here, we reviewed the role of the gut microbial community in the development, progression, and prevention of colorectal carcinogenesis.}, } @article {pmid39008123, year = {2024}, author = {Núñez-Muñoz, LA and Sánchez-García, ME and Calderón-Pérez, B and De la Torre-Almaraz, R and Ruiz-Medrano, R and Xoconostle-Cázares, B}, title = {Metagenomic Analysis of Rhizospheric Bacterial Community of Citrus Trees Expressing Phloem-Directed Antimicrobials.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {93}, pmid = {39008123}, issn = {1432-184X}, support = {SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; CF-2023-G-231//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; }, mesh = {*Rhizosphere ; *Phloem/microbiology/metabolism ; *Soil Microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Microbiota ; *Plant Diseases/microbiology ; *Citrus/microbiology ; Plants, Genetically Modified/microbiology/genetics ; Phylogeny ; Metagenomics ; Muramidase/metabolism/genetics ; Plant Proteins/genetics/metabolism ; beta-Defensins/genetics ; RNA, Ribosomal, 16S/genetics ; Anti-Infective Agents/pharmacology/metabolism ; Citrus sinensis/microbiology ; Plant Roots/microbiology ; }, abstract = {Huanglongbing, also known as citrus greening, is currently the most devastating citrus disease with limited success in prevention and mitigation. A promising strategy for Huanglongbing control is the use of antimicrobials fused to a carrier protein (phloem protein of 16 kDa or PP16) that targets vascular tissues. This study investigated the effects of genetically modified citrus trees expressing Citrus sinensis PP16 (CsPP16) fused to human lysozyme and β-defensin-2 on the soil microbiome diversity using 16S amplicon analysis. The results indicated that there were no significant alterations in alpha diversity, beta diversity, phylogenetic diversity, differential abundance, or functional prediction between the antimicrobial phloem-overexpressing plants and the control group, suggesting minimal impact on microbial community structure. However, microbiota diversity analysis revealed distinct bacterial assemblages between the rhizosphere soil and root environments. This study helps to understand the ecological implications of crops expressing phloem-targeted antimicrobials for vascular disease management, with minimal impact on soil microbiota.}, } @article {pmid39007947, year = {2024}, author = {Nilsen, M and Nygaard, UC and Brodin, P and Carlsen, KCL and Fredheim, C and Haugen, G and Hedlin, G and Jonassen, CM and Jonsmoen, ULA and Lakshmikanth, T and Nordlund, B and Olin, A and Rehbinder, EM and Skjerven, HO and Snipen, L and Staff, AC and Söderhäll, C and Vettukattil, R and Rudi, K}, title = {Gut bacteria at 6 months of age are associated with immune cell status in 1-year-old children.}, journal = {Scandinavian journal of immunology}, volume = {99}, number = {4}, pages = {e13346}, doi = {10.1111/sji.13346}, pmid = {39007947}, issn = {1365-3083}, support = {//Arne Ingel's legat/ ; //Barnestifteslen at Oslo University Hospital/ ; //Forte/ ; //Fürst Medical Laboratory, Oslo, Norway/ ; //Health and Rehabilitation Norway/ ; //Karolinska Institutet/ ; //Norges Forskningsråd/ ; //Norwegian Association of Asthma and Allergy/ ; //Norwegian Society of Dermatology and Venerology/ ; //Oslo University Hospital/ ; //Region Stockholm (ALF-project and individual grants)/ ; //Roche/ ; //SFO-V Karolinska Institutet/ ; //Swedish Asthma and Allergy Association's Research Foundation/ ; //Swedish Order of Freemasons Foundation Barnhuset/ ; //Swedish Research council/ ; //Sykehuset Østfold/ ; //The Cancer- and Allergy Foundation/ ; //Delegation of the European Union to Norway, University of Oslo/ ; //The Foundation for Healthcare and Allergy Research in Sweden - Vårdalstiftelsen/ ; //The Fridtjof Nansen Institute/ ; //The Hesselman foundation/ ; //The Initiative for Clinical Therapy Research/ ; //The King Gustaf V 80th Birthday Foundation/ ; //The Kloster foundation/ ; //The Konsul Th C Bergh's Foundation/ ; //The Magnus Bergwall foundation/ ; //The Pediatric Research Foundation at Astrid Lindgren Children's Hospital/ ; //The Samaritan Foundation for Pediatric research/ ; //The Sven Jerring Foundation/ ; //The Swedish Heart-Lung Foundation/ ; //The Swedish Society of Medicine/ ; //Thermo-Fisher Uppsala, Sweden/ ; //Universitetet i Oslo/ ; }, mesh = {Humans ; Infant ; *Gastrointestinal Microbiome/immunology ; Male ; Female ; *Feces/microbiology ; Infant, Newborn ; Bacteria/immunology/classification ; Fatty Acids, Volatile/metabolism ; Metagenome ; Prospective Studies ; }, abstract = {Age-related gut bacterial changes during infancy have been widely studied, but it remains still unknown how these changes are associated with immune cell composition. This study's aim was to explore if the temporal development of gut bacteria during infancy prospectively affects immune cell composition. Faecal bacteria and short-chain fatty acids were analysed from 67 PreventADALL study participants at four timepoints (birth to 12 months) using reduced metagenome sequencing and gas chromatography. Immune cell frequencies were assessed using mass cytometry in whole blood samples at 12 months. The infants clustered into four groups based on immune cell composition: clusters 1 and 2 showed a high relative abundance of naïve cells, cluster 3 exhibited increased abundance of classical- and non-classical monocytes and clusters 3 and 4 had elevated neutrophil levels. At all age groups, we did observe significant associations between the gut microbiota and immune cell clusters; however, these were generally from low abundant species. Only at 6 months of age we observed significant associations between abundant (>8%) species and immune cell clusters. Bifidobacterium adolescentis and Porphyromonadaceae are associated with cluster 1, while Bacteroides fragilis and Bifidobacterium longum are associated with clusters 3 and 4 respectively. These species have been linked to T-cell polarization and maturation. No significant correlations were found between short-chain fatty acids and immune cell composition. Our findings suggest that abundant gut bacteria at 6 months may influence immune cell frequencies at 12 months, highlighting the potential role of gut microbiota in shaping later immune cell composition.}, } @article {pmid39007592, year = {2024}, author = {Zhang, G and Wang, H and Zhang, Z and Zhang, L and Guo, G and Yang, J and Yuan, F and Ju, F}, title = {Highly accurate classification and discovery of microbial protein-coding gene functions using FunGeneTyper: an extensible deep learning framework.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {4}, pages = {}, pmid = {39007592}, issn = {1477-4054}, support = {WU2022A008//Center of Synthetic Biology and Integrated Bioengineering/ ; WU2022C030//Research Center for Industries of the Future/ ; 2024SSYS0032//'Pioneer' and 'Leading Goose' Key R&D Program of Zhejiang/ ; LR22D010001//Zhejiang Provincial Natural Science Foundation of China/ ; }, mesh = {*Deep Learning ; Humans ; Computational Biology/methods ; Microbiota/genetics ; Bacterial Proteins/genetics ; Drug Resistance, Microbial/genetics ; Software ; High-Throughput Nucleotide Sequencing/methods ; Virulence Factors/genetics ; }, abstract = {High-throughput DNA sequencing technologies decode tremendous amounts of microbial protein-coding gene sequences. However, accurately assigning protein functions to novel gene sequences remain a challenge. To this end, we developed FunGeneTyper, an extensible framework with two new deep learning models (i.e., FunTrans and FunRep), structured databases, and supporting resources for achieving highly accurate (Accuracy > 0.99, F1-score > 0.97) and fine-grained classification of antibiotic resistance genes (ARGs) and virulence factor genes. Using an experimentally confirmed dataset of ARGs comprising remote homologous sequences as the test set, our framework achieves by-far-the-best performance in the discovery of new ARGs from human gut (F1-score: 0.6948), wastewater (0.6072), and soil (0.5445) microbiomes, beating the state-of-the-art bioinformatics tools and sequence alignment-based (F1-score: 0.0556-0.5065) and domain-based (F1-score: 0.2630-0.5224) annotation approaches. Furthermore, our framework is implemented as a lightweight, privacy-preserving, and plug-and-play neural network module, facilitating its versatility and accessibility to developers and users worldwide. We anticipate widespread utilization of FunGeneTyper (https://github.com/emblab-westlake/FunGeneTyper) for precise classification of protein-coding gene functions and the discovery of numerous valuable enzymes. This advancement will have a significant impact on various fields, including microbiome research, biotechnology, metagenomics, and bioinformatics.}, } @article {pmid39006020, year = {2024}, author = {Enagbonma, BJ and Fadiji, AE and Babalola, OO}, title = {Anthropogenic fertilization influences a shift in barley rhizosphere microbial communities.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17303}, pmid = {39006020}, issn = {2167-8359}, mesh = {*Hordeum/microbiology ; *Rhizosphere ; *Soil Microbiology ; *Fertilizers/analysis ; Microbiota ; Bacteria/genetics/classification ; Soil/chemistry ; }, abstract = {BACKGROUND: Anthropogenic mediations contribute a significant role in stimulating positive reactions in soil-plant interactions; however, methodical reports on how anthropogenic activities impact soil microorganism-induced properties and soil health are still inadequate. In this study, we evaluated the influence of anthropogenic fertilization of farmland soil on barley rhizosphere microbial community structure and diversity, and the significant impacts on agro-ecosystem productivity. This will help validate the premise that soil amendment with prolonged synthetic fertilizers can lead to a significant reduction in bacterial abundance and diversity, while soils amended with organic fertilizers elicit the succession of the native soil microbial community and favor the growth of copiotrophic bacteria.

METHODS: The total metagenomic DNA was extracted from soils obtained from the barley rhizosphere under chemical fertilization (CB), organic fertilization (OB), and bulk soil (NB). Subsequently, these samples were sequenced using an amplicon-based sequencing approach, and the raw sequence dataset was examined using a metagenomic rast server (MG-RAST).

RESULTS: Our findings showed that all environments (CB, OB, and NB) shared numerous soil bacterial phyla but with different compositions. However, Bacteroidetes, Proteobacteria, and Actinobacteria predominated in the barley rhizosphere under chemical fertilization, organic fertilization, and bulk soils, respectively. Alpha and beta diversity analysis showed that the diversity of bacteria under organic barley rhizosphere was significantly higher and more evenly distributed than bacteria under chemical fertilization and bulk soil.

CONCLUSION: Understanding the impact of conventional and organic fertilizers on the structure, composition, and diversity of the rhizosphere microbiome will assist in soil engineering to enhance microbial diversity in the agroecosystem.}, } @article {pmid39005434, year = {2024}, author = {Kosch, TA and Torres-Sánchez, M and Liedtke, HC and Summers, K and Yun, MH and Crawford, AJ and Maddock, ST and Ahammed, MS and Araújo, VLN and Bertola, LV and Bucciarelli, GM and Carné, A and Carneiro, CM and Chan, KO and Chen, Y and Crottini, A and da Silva, JM and Denton, RD and Dittrich, C and Themudo, GE and Farquharson, KA and Forsdick, NJ and Gilbert, E and Che, J and Katzenback, BA and Kotharambath, R and Levis, NA and Márquez, R and Mazepa, G and Mulder, KP and Müller, H and O'Connell, MJ and Orozco-terWengel, P and Palomar, G and Petzold, A and Pfennig, DW and Pfennig, KS and Reichert, MS and Robert, J and Scherz, MD and Siu-Ting, K and Snead, AA and Stöck, M and Stuckert, AMM and Stynoski, JL and Tarvin, RD and Wollenberg Valero, KC and , }, title = {The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39005434}, issn = {2692-8205}, abstract = {Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, antipredator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to "leap" to the next level.}, } @article {pmid39005339, year = {2024}, author = {Kananen, K and Veseli, I and Quiles Pérez, CJ and Miller, S and Eren, AM and Bradley, PH}, title = {Adaptive adjustment of significance thresholds produces large gains in microbial gene annotations and metabolic insights.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39005339}, issn = {2692-8205}, support = {R35 GM151155/GM/NIGMS NIH HHS/United States ; }, abstract = {Gene function annotations enable microbial ecologists to make inferences about metabolic potential from genomes and metagenomes. However, even tools that use the same database and general approach can differ markedly in the annotations they recover. We compare three popular methods for identifying KEGG Orthologs, applying them to genomes drawn from a range of bacterial families that occupy different host-associated and free-living biomes. Our results show that by adaptively tuning sequence similarity thresholds, sensitivity can be substantially improved while maintaining accuracy. We observe the largest improvements when few reference sequences exist for a given protein family, and when annotating genomes from non-model organisms (such as gut-dwelling Lachnospiraceae). Our results suggest that straightforward heuristic adjustments can broadly improve microbial metabolic predictions.}, } @article {pmid39004662, year = {2024}, author = {Kang, L and Song, Y and Mackelprang, R and Zhang, D and Qin, S and Chen, L and Wu, L and Peng, Y and Yang, Y}, title = {Metagenomic insights into microbial community structure and metabolism in alpine permafrost on the Tibetan Plateau.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5920}, pmid = {39004662}, issn = {2041-1723}, support = {31988102 and 31825006//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Permafrost/microbiology ; Tibet ; *Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics ; *Microbiota/genetics ; Bacteria/genetics/classification/metabolism ; Soil/chemistry ; Metagenome ; Ecosystem ; Climate Change ; Biodiversity ; Phylogeny ; }, abstract = {Permafrost, characterized by its frozen soil, serves as a unique habitat for diverse microorganisms. Understanding these microbial communities is crucial for predicting the response of permafrost ecosystems to climate change. However, large-scale evidence regarding stratigraphic variations in microbial profiles remains limited. Here, we analyze microbial community structure and functional potential based on 16S rRNA gene amplicon sequencing and metagenomic data obtained from an ∼1000 km permafrost transect on the Tibetan Plateau. We find that microbial alpha diversity declines but beta diversity increases down the soil profile. Microbial assemblages are primarily governed by dispersal limitation and drift, with the importance of drift decreasing but that of dispersal limitation increasing with soil depth. Moreover, genes related to reduction reactions (e.g., ferric iron reduction, dissimilatory nitrate reduction, and denitrification) are enriched in the subsurface and permafrost layers. In addition, microbial groups involved in alternative electron accepting processes are more diverse and contribute highly to community-level metabolic profiles in the subsurface and permafrost layers, likely reflecting the lower redox potential and more complicated trophic strategies for microorganisms in deeper soils. Overall, these findings provide comprehensive insights into large-scale stratigraphic profiles of microbial community structure and functional potentials in permafrost regions.}, } @article {pmid39004260, year = {2024}, author = {Tischer, M and Bleidorn, C}, title = {Further evidence of low infection frequencies of Wolbachia in soil arthropod communities.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {123}, number = {}, pages = {105641}, doi = {10.1016/j.meegid.2024.105641}, pmid = {39004260}, issn = {1567-7257}, mesh = {*Wolbachia/genetics/classification ; Animals ; *Arthropods/microbiology ; *Phylogeny ; *Soil Microbiology ; Germany/epidemiology ; Multilocus Sequence Typing ; }, abstract = {Endosymbiotic Alphaproteobacteria of the genus Wolbachia are exclusively transferred maternally from mother to offspring, but horizontal transfer across species boundaries seems to be frequent as well. However, the (ecological) mechanisms of how these bacteria are transferred between distantly related arthropod hosts remain unclear. Based on the observation that species that are part of the same ecological community often also share similar Wolbachia strains, host ecology has been hypothesized as an important factor enabling transmission and a key factor in explaining the global distribution of Wolbachia lineages. In this study, we focus on the diversity and abundance of Wolbachia strains in soil arthropods, a so far rather neglected community. We screened 82 arthropod morphotypes collected in the beech forest (dominated by Fagus sp.) soil in the area of Göttingen in central Germany for the presence of Wolbachia. By performing a PCR screen with Wolbachia-MLST markers (coxA, dnaA, fbpA, ftsZ, gatB, and hcpA), we found a rather low infection frequency of 12,2%. Additionally, we performed metagenomic screening of pooled individuals from the same sampling site and could not find evidence that this low infection frequency is an artefact due to PCR-primer bias. Phylogenetic analyses of the recovered Wolbachia strains grouped them in three known supergroups (A, B, and E), with the first report of Wolbachia in Protura (Hexapoda). Moreover, Wolbachia sequences from the pseudoscorpion Neobisium carcinoides cluster outside the currently known supergroup diversity. Our screening supports results from previous studies that the prevalence of Wolbachia infections seems to be lower in soil habitats than in above-ground terrestrial habitats. The reasons for this pattern are not completely understood but might stem from the low opportunity of physical contact and the prevalence of supergroups that are less suited for horizontal transfer.}, } @article {pmid39003345, year = {2024}, author = {Das, BK and Chakraborty, HJ and Kumar, V and Rout, AK and Patra, B and Das, SK and Behera, BK}, title = {Comparative metagenomic analysis from Sundarbans ecosystems advances our understanding of microbial communities and their functional roles.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {16218}, pmid = {39003345}, issn = {2045-2322}, mesh = {*Metagenomics/methods ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Metagenome ; Wetlands ; Ecosystem ; Phylogeny ; Soil Microbiology ; India ; }, abstract = {The Sundarbans mangrove, located at the mouth of the Ganges and Brahmaputra Rivers, is the world's largest tidal mangrove forest. These mangroves are also one of the most striking sources of microbial diversity, essential in productivity, conservation, nutrient cycling, and rehabilitation. Hence, the main objective of this study was to use metagenome analysis and provide detailed insight into microbial communities and their functional roles in the Sundarbans mangrove ecosystem. A comparative analysis was also done with a non-mangrove region of the Sundarbans ecosystem to assess the capability of the environmental parameters to explain the variation in microbial community composition. The study found several dominant bacteria, viz., Alphaproteobacteria, Actinomycetota, Bacilli, Clostridia, Desulfobacterota, Gammaproteobacteria, and Nitrospira, from the mangrove region. The mangrove sampling site reports several salt-tolerant bacteria like Alkalibacillus haloalkaliphilus, Halomonas anticariensis, and Salinivibrio socompensis. We found some probiotic species, viz., Bacillus clausii, Lactobacillus curvatus, Vibrio mediterranei and Vibrio fluvialis, from the Sundarbans mangrove. Nitrifying bacteria in Sundarbans soils were Nitrococcus mobilis, Nitrosococcus oceani, Nitrosomonas halophila, Nitrospirade fluvii, and others. Methanogenic archaea, viz., Methanoculleus marisnigri, Methanobrevibacter gottschalkii, and Methanolacinia petrolearia, were highly abundant in the mangroves as compared to the non-mangrove soils. The identified methanotrophic bacterial species, viz., Methylobacter tundripaludum, Methylococcus capsulatus, Methylophaga thiooxydans, and Methylosarcina lacus are expected to play a significant role in the degradation of methane in mangrove soil. Among the bioremediation bacterial species identified, Pseudomonas alcaligenes, Pseudomonas mendocina, Paracoccus denitrificans, and Shewanella putrefaciens play a significant role in the remediation of environmental pollution. Overall, our study shows for the first time that the Sundarbans, the largest mangrove ecosystem in the world, has a wide range of methanogenic archaea, methanotrophs, pathogenic, salt-tolerant, probiotic, nitrifying, and bioremediation bacteria.}, } @article {pmid39003315, year = {2024}, author = {Knjaz, M and Baricevic, A and Tankovic, MS and Kuzat, N and Vlasicek, I and Grizancic, L and Podolsak, I and Pfannkuchen, M and Kogovsek, T and Pfannkuchen, DM}, title = {First regional reference database of northern Adriatic diatom transcriptomes.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {16209}, pmid = {39003315}, issn = {2045-2322}, support = {UIP -2020-02-7868//Hrvatska Zaklada za Znanost/ ; DOK-2021-02-5104//Hrvatska Zaklada za Znanost/ ; UIP-2014-09-6563//Hrvatska Zaklada za Znanost/ ; 871153//H2020 Excellent Science/ ; }, mesh = {*Diatoms/genetics/classification ; *Transcriptome ; Metagenomics/methods ; Gene Expression Profiling/methods ; Databases, Genetic ; }, abstract = {Marine microbial communities form the basis for the functioning of marine ecosystems and the conservation of biodiversity. With the application of metagenomics and metatranscriptomics in marine environmental studies, significant progress has been made in analysing the functioning of microbial communities as a whole. These molecular techniques are highly dependent on reliable, well-characterised, comprehensive and taxonomically diverse sequenced reference transcriptomes of microbial organisms. Here we present a set of 12 individual transcriptome assemblies derived from 6 representative diatom species from the northern Adriatic Sea grown under 2 environmentally relevant growth conditions (phosphate replete vs. phosphate deprived). After filtering the reads and assembly, an average number of 64,932 transcripts per assembly was obtained, of which an average of 8856 were assigned to functionally known proteins. Of all assigned transcripts, an average of 6483 proteins were taxonomically assigned to diatoms (Bacillariophyta). On average, a higher number of assigned proteins was detected in the transcriptome assemblies of diatoms grown under replete media condition. On average, 50% of the mapped proteins were shared between the two growth conditions. All recorded proteins in the dataset were classified into 24 COG categories, with approximately 25% belonging to the unknown function and the remaining 75% belonging to all other categories. The resulting diatom reference database for the northern Adriatic, focussing on the response to nutrient limitation as characteristic for the region and predicted for the future world oceans, provides a valuable resource for analysing environmental metatranscriptome and metagenome data. Each northern Adriatic transcriptome can also be used by itself as a reference database for the (meta)transcriptomes and gene expression studies of the associated species that will be generated in the future.}, } @article {pmid39002589, year = {2024}, author = {Bai, X and Zhong, H and Cui, X and Wang, T and Gu, Y and Li, M and Miao, X and Li, J and Lu, L and Xu, W and Li, D and Sun, J}, title = {Metagenomic profiling uncovers microbiota and antibiotic resistance patterns across human, chicken, pig fecal, and soil environments.}, journal = {The Science of the total environment}, volume = {947}, number = {}, pages = {174734}, doi = {10.1016/j.scitotenv.2024.174734}, pmid = {39002589}, issn = {1879-1026}, mesh = {Animals ; *Feces/microbiology ; *Chickens/microbiology ; Swine ; *Soil Microbiology ; Humans ; *Microbiota/drug effects ; *Drug Resistance, Microbial/genetics ; China ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {The ongoing and progressive evolution of antibiotic resistance presents escalating challenges for the clinical management and prevention of bacterial infections. Understanding the makeup of resistance genomes and accurately quantifying the current abundance of antibiotic resistance genes (ARGs) are crucial for assessing the threat of antimicrobial resistance (AMR) to public health. This comprehensive study investigated the distribution and diversity of bacterial community composition, ARGs, and virulence factors (VFs) across human, chicken, pig fecal, and soil microbiomes in various provinces of China. As a result, multidrug resistance was identified across all samples. Core ARGs primarily related to multidrug, MLS (Macrolides-Lincosamide-Streptogramins), and tetracycline resistance were characterized. A significant correlation between ARGs and bacterial taxa was observed, especially in soil samples. Probiotic strains such as Lactobacillus harbored ARGs, potentially contributing to the dissemination of antibiotic resistance. We screened subsets of ARGs from samples from different sources as indicators to assess the level of ARGs contamination in samples, with high accuracy. These results underline the complex relationship between microbial communities, resistance mechanisms, and environmental factors, emphasizing the importance of continued research and monitoring to better understand these dynamics.}, } @article {pmid39002480, year = {2024}, author = {Singh, DP and Kumar, A and Prajapati, J and Bijalwan, V and Kumar, J and Amin, P and Kandoriya, D and Vidhani, H and Patil, GP and Bishnoi, M and Rawal, R and Das, S}, title = {Sexual dimorphism in neurobehavioural phenotype and gut microbial composition upon long-term exposure to structural analogues of bisphenol-A.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {135178}, doi = {10.1016/j.jhazmat.2024.135178}, pmid = {39002480}, issn = {1873-3336}, mesh = {Animals ; *Phenols/toxicity ; Male ; *Gastrointestinal Microbiome/drug effects ; Female ; *Benzhydryl Compounds/toxicity ; *Sex Characteristics ; *Sulfones/toxicity ; *Endocrine Disruptors/toxicity ; *Behavior, Animal/drug effects ; Cytokines/metabolism ; Phenotype ; Mice ; Mice, Inbred C57BL ; Anxiety/chemically induced ; Depression/chemically induced ; Hippocampus/drug effects/metabolism ; Neurotransmitter Agents/metabolism ; Brain/drug effects/metabolism ; }, abstract = {Bisphenol S (BPS) and Bisphenol F (BPF), the analogues of the legacy endocrine disrupting chemical, Bisphenol A (BPA) are ubiquitous in the environment and present in various consumer goods, and potentially neurotoxic. Here, we studied sex-specific responses of bisphenols on behavioural phenotypes, including their association with pro-inflammatory biomarkers and altered neurotransmitters levels, and the key gut microbial abundances. Neurobehavioural changes, using standard test battery, biochemical and molecular estimations for inflammatory cytokines, neurotransmitters, and oxido-nitrosative stress markers, gene expression analysis using qRT-PCR, H&E based histological investigations, gut permeability assays and Oxford Nanopore-based 16S-rRNA metagenomics sequencing for the gut microbial abundance estimations were performed. Bisphenol(s) exposure induces anxiety and depression-like behaviours, particularly in the male mice, with heightened pro-inflammatory cytokines levels and systemic endotoxemia, altered monoamine neurotransmitters levels/turnovers and hippocampal neuronal degeneration and inflammatory responses in the brain. They also increased gut permeability and altered microbial diversity, particularly in males. Present study provides evidence for sex-specific discrepancies in neurobehavioural phenotypes and gut microbiota, which necessitate a nuanced understanding of sex-dependent responses to bisphenols. The study contributes to ongoing discussions on the multifaceted implications of bisphenols exposure and underscores the need for tailored regulatory measures to mitigate potential health risks associated with them.}, } @article {pmid39002479, year = {2024}, author = {Zeng, H and Wang, Y and Zhao, Z and Zhu, D and Xia, H and Wei, Y and Kuang, P and An, D and Chen, K and Li, R and Lei, Y and Sun, G}, title = {Travertine deposition rather than tourism activity is the primary contributor to the microplastic risks in alpine karst lakes.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {135192}, doi = {10.1016/j.jhazmat.2024.135192}, pmid = {39002479}, issn = {1873-3336}, mesh = {*Lakes/microbiology ; *Microplastics/toxicity ; China ; *Tourism ; *Water Pollutants, Chemical/analysis/toxicity ; Environmental Monitoring ; Microbiota/drug effects ; Drug Resistance, Microbial/genetics ; }, abstract = {Microplastics (MPs) are emerging as anthropogenic vectors to form plastisphere, facilitating microbiome colonization and pathogenic dissemination, thus contributing to environmental and health crises across various ecosystems. However, a knowledge gap persists regarding MPs risks and their driving factors in certain unique and vulnerable ecosystems, such as Karst travertine lakes, some of which are renowned World Natural Heritage Sites under ever-increasing tourism pressure. We hypothesized that tourism activities serve as the most important factor of MPs pollution, whereas intrinsic features, including travertine deposition can exacerbate potential environmental risks. Thus, metagenomic approaches were employed to investigate the geographical distribution of the microbiome, antibiotic resistance genes (ARGs), virulence factor genes (VFGs), and their combined environmental risks in Jiuzhaigou and Huanglong, two famous tourism destinations in Southwest China. The plastisphere risks were higher in Huanglong, contradicting our hypothesis that Jiuzhaigou would face more crucial antibiotic risks due to its higher tourist activities. Specifically, the levels of Lipopolysaccharide Lewis and fosD increased by sevenfold and 20-fold, respectively, from upstream to downstream in Huanglong, whereas in Jiuzhaigou, no significant accrual was observed. Structural equation modeling results showed that travertine deposition was the primary contributor to MPs risks in alpine karstic lakes. Our findings suggest that tourism has low impact on MPs risks, possibly because of proper management, and that travertine deposition might act as an MPs hotspot, emphasizing the importance of considering the unique aspects of travertine lakes in mitigating MPs pollution and promoting the sustainable development of World Natural Heritage Sites.}, } @article {pmid39002350, year = {2024}, author = {Lai, KP and Boncan, DAT and Qin, X and Chan, TF and Tse, WKF}, title = {Roles and occurrences of microbiota in the osmoregulatory organs, gills and gut, in marine medaka upon hypotonic stress.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {52}, number = {}, pages = {101285}, doi = {10.1016/j.cbd.2024.101285}, pmid = {39002350}, issn = {1878-0407}, mesh = {Animals ; *Gills/microbiology/metabolism ; *Osmoregulation ; *Oryzias/microbiology ; Osmotic Pressure ; Seawater/microbiology ; Gastrointestinal Microbiome ; Microbiota ; Fresh Water/microbiology ; }, abstract = {Gills and gut are the two primary osmoregulatory organs in fish. Recently, studies have expanded beyond the osmoregulatory mechanisms of these organs to explore the microbiota communities inhabiting them. It is now known that microbial communities in both organs shift in response to osmotic stress. However, there are limited studies identifying the major contributors and co-occurrence among these microbiota in both organs under seawater and freshwater transfer conditions. The current data mining report performed a bioinformatics analysis on two previous published datasets from our group, aiming to provide insights into host-bacteria relationships under osmotic stress. We divided the samples into four groups: control seawater gills (LSW); control seawater gut (TSW); freshwater transfer gills (LFW); and freshwater transfer gut (TFW). Our results showed that LSW had higher diversities, richness, and evenness compared to TSW. However, both the LFW and LSW did not show any significant differences after the freshwater transfer experiment. We further applied co-occurrence network analysis and, for the first time, reported on the interactions of taxa shaping the community structure in these two organs. Moreover, we identified enriched ectoine biosynthesis in seawater samples, suggesting its potential role in seawater environments. Increased mRNA expression levels of Na[+]/K[+]-atpase, and cftr, were observed in gills after 6 h of ectoine treatment. These findings provide a foundation for future studies on host-bacteria interactions under osmotic stress.}, } @article {pmid39000578, year = {2024}, author = {Min, M and Egli, C and Sivamani, RK}, title = {The Gut and Skin Microbiome and Its Association with Aging Clocks.}, journal = {International journal of molecular sciences}, volume = {25}, number = {13}, pages = {}, pmid = {39000578}, issn = {1422-0067}, mesh = {Humans ; *Skin/microbiology/metabolism ; *Aging ; *Gastrointestinal Microbiome/physiology ; *Microbiota ; Epigenesis, Genetic ; Animals ; Biological Clocks ; }, abstract = {Aging clocks are predictive models of biological age derived from age-related changes, such as epigenetic changes, blood biomarkers, and, more recently, the microbiome. Gut and skin microbiota regulate more than barrier and immune function. Recent studies have shown that human microbiomes may predict aging. In this narrative review, we aim to discuss how the gut and skin microbiomes influence aging clocks as well as clarify the distinction between chronological and biological age. A literature search was performed on PubMed/MEDLINE databases with the following keywords: "skin microbiome" OR "gut microbiome" AND "aging clock" OR "epigenetic". Gut and skin microbiomes may be utilized to create aging clocks based on taxonomy, biodiversity, and functionality. The top contributing microbiota or metabolic pathways in these aging clocks may influence aging clock predictions and biological age. Furthermore, gut and skin microbiota may directly and indirectly influence aging clocks through the regulation of clock genes and the production of metabolites that serve as substrates or enzymatic regulators. Microbiome-based aging clock models may have therapeutic potential. However, more research is needed to advance our understanding of the role of microbiota in aging clocks.}, } @article {pmid39000530, year = {2024}, author = {Liu, Y and Kou, C and Chen, J and Li, Y and Li, J}, title = {The Response of the Gut Physiological Function and Microbiome of a Wild Freshwater Fish (Megalobrama terminalis) to Alterations in Reproductive Behavior.}, journal = {International journal of molecular sciences}, volume = {25}, number = {13}, pages = {}, pmid = {39000530}, issn = {1422-0067}, support = {202201010762//Science and Technology Program of Guangzhou/ ; 2023TD10//Pearl river fishery resources investigation and evaluation innovation team project/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Reproduction ; Female ; Cyprinidae/microbiology/physiology/metabolism ; Fresh Water/microbiology ; Intestinal Mucosa/metabolism/microbiology ; }, abstract = {The fish gut microbiome is well known for its role in degrading nutrients to improve the host's digestion and absorption efficiency. In this study, we focused on the core physiological adaptability during the various reproductive stages of the black Amur bream (Megalobrama terminalis) to explore the interaction mechanisms among the fish host gut mucosal structure, gut enzyme activity, and gut microbial metabolism in the course of the host's reproductive cycle. Our findings showed that M. terminalis exhibited locomotion metabolic type (aids in sporting) in the reproductive stage, and a change to visceral metabolic type (aids in digestion) during non-reproductive and post-reproductive stage phases. The impact of metabolic type selection and energy demand during various reproductive stages on fish nutrition strategy and digestive function was substantial. Our resulted showed that mitochondria in intestinal epithelial cells of reproductive M. terminalis appeared autophagy phenomenon, and the digestive enzyme activities in the intestines of reproductive M. terminalis were lower than those in the non-reproductive and post-reproductive individuals. Moreover, these differences in nutrition strategy have a prominent impact on the gut microbiome of reproductive M. terminalis, compared to non-reproductive and post-reproductive samples. Our findings showed that reproductive females had lower levels of alpha diversity compared to non-reproductive and post-reproductive females. Our results also showed a greater functional variety and an increase in functional genes related to carbohydrate, lipid, amino acid, cofactors, and vitamin metabolic pathways in the NRS and PRS group. It is noteworthy that an enrichment of genes encoding putative enzymes implicated in the metabolism of taurine and hypotaurine was observed in the RS samples. Our findings illustrated that the stability and resilience of the gut bacterial community could be shaped in the wild fish host-microbiome interactions during reproductive life history.}, } @article {pmid38998029, year = {2024}, author = {Guo, Y and Garber, PA and Yang, Y and Wang, S and Zhou, J}, title = {The Conservation Implications of the Gut Microbiome for Protecting the Critically Endangered Gray Snub-Nosed Monkey (Rhinopithecus brelichi).}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {13}, pages = {}, pmid = {38998029}, issn = {2076-2615}, support = {(2018[2780])//Investigation into the conservation genetics of the gray snub-nosed monkey/ ; (32070523)//Population genetics analysis of the isolated gray snub-nosed monkey/ ; }, abstract = {The gut microbiota plays a crucial role in regulating energy metabolism, facilitating nutrient absorption, and supporting immune function, thereby assisting the host in adapting to seasonal dietary changes. Here, we compare the gut microbiome composition of wild gray snub-nosed monkeys during winter (from October to December) and spring (from January to March) to understand differences in seasonal nutrient intake patterns. Snub-nosed monkeys are foregut fermenters and consume difficult-to-digest carbohydrates and lichen. To examine the digestive adaptations of gray snub-nosed monkeys, we collected 14 fresh fecal samples for DNA analysis during the winter and spring. Based on 16S rRNA sequencing, metagenomic sequencing, and functional metagenomic analyses, we identified that Firmicutes, Actinobacteria, Verrucomicrobia, and Bacteroidetes constitute a keystone bacterial group in the gut microbiota during winter and spring and are responsible for degrading cellulose. Moreover, the transition in dietary composition from winter to spring was accompanied by changes in gut microbiota composition, demonstrating adaptive responses to varying food sources and availability. In winter, the bacterial species of the genera Streptococcus were found in higher abundance. At the functional level, these bacteria are involved in fructose and mannose metabolism and galactose metabolism c-related pathways, which facilitate the breakdown of glycogen, starch, and fiber found in fruits, seeds, and mature leaves. During spring, there was an increased abundance of bacteria species from the Prevotella and Lactobacillus genera, which aid the digestion of protein-rich buds. Combined, these findings reveal how the gut microbiota adjusts to fluctuations in energy balance and nutrient intake across different seasons in this critically endangered species. Moreover, we also identified Pseudomonas in two samples; the presence of potential pathogens within the gut could pose a risk to other troop members. Our findings highlight the necessity of a conservation plan that focuses on protecting vegetation and implementing measures to prevent disease transmission for this critically endangered species.}, } @article {pmid38997719, year = {2024}, author = {Sun, Y and Gan, Z and Wang, X and Liu, J and Zhong, W and Zhang, Z and Zuo, J and Zhong, H and Huang, X and Yan, Z and Cao, Q}, title = {Integrative metagenomic, transcriptomic, and proteomic analysis reveal the microbiota-host interplay in early-stage lung adenocarcinoma among non-smokers.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {652}, pmid = {38997719}, issn = {1479-5876}, support = {220904094208//The Fifth Affiliated Hospital of Sun Yat-sen University Qingdong Cao's talent-attracting fund/ ; }, mesh = {Humans ; *Proteomics ; *Adenocarcinoma of Lung/microbiology/genetics ; *Lung Neoplasms/microbiology/pathology/genetics ; *Metagenomics/methods ; Male ; Female ; *Transcriptome/genetics ; *Microbiota/genetics ; Middle Aged ; Neoplasm Staging ; Dysbiosis/microbiology ; Gene Expression Profiling ; Host Microbial Interactions/genetics ; Aged ; }, abstract = {BACKGROUND: The incidence of early-stage lung adenocarcinoma (ES-LUAD) is steadily increasing among non-smokers. Previous research has identified dysbiosis in the gut microbiota of patients with lung cancer. However, the local microbial profile of non-smokers with ES-LUAD remains largely unknown. In this study, we systematically characterized the local microbial community and its associated features to enable early intervention.

METHODS: A prospective collection of ES-LUAD samples (46 cases) and their corresponding normal tissues adjacent to the tumor (41 cases), along with normal lung tissue samples adjacent to pulmonary bullae in patients with spontaneous pneumothorax (42 cases), were subjected to ultra-deep metagenomic sequencing, host transcriptomic sequencing, and proteomic sequencing. The obtained omics data were subjected to both individual and integrated analysis using Spearman correlation coefficients.

RESULTS: We concurrently detected the presence of bacteria, fungi, and viruses in the lung tissues. The microbial profile of ES-LUAD exhibited similarities to NAT but demonstrated significant differences from the healthy controls (HCs), characterized by an overall reduction in species diversity. Patients with ES-LUAD exhibited local microbial dysbiosis, suggesting the potential pathogenicity of certain microbial species. Through multi-omics correlations, intricate local crosstalk between the host and local microbial communities was observed. Additionally, we identified a significant positive correlation (rho > 0.6) between Methyloversatilis discipulorum and GOLM1 at both the transcriptional and protein levels using multi-omics data. This correlated axis may be associated with prognosis. Finally, a diagnostic model composed of six bacterial markers successfully achieved precise differentiation between patients with ES-LUAD and HCs.

CONCLUSIONS: Our study depicts the microbial spectrum in patients with ES-LUAD and provides evidence of alterations in lung microbiota and their interplay with the host, enhancing comprehension of the pathogenic mechanisms that underlie ES-LUAD. The specific model incorporating lung microbiota can serve as a potential diagnostic tool for distinguishing between ES-LUAD and HCs.}, } @article {pmid38997445, year = {2024}, author = {He, C and Fucich, D and Sosa, A and Wang, H and Kan, J and Liu, J and Xu, Y and Jiao, N and Gonsior, M and Chen, F}, title = {Deep metagenomic sequencing unveils novel SAR202 lineages and their vertical adaptation in the ocean.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {853}, pmid = {38997445}, issn = {2399-3642}, support = {Award #1829888//Armenian National Science and Education Fund (Armenian National Science & Education Fund)/ ; }, mesh = {*Metagenomics/methods ; *High-Throughput Nucleotide Sequencing ; Oceans and Seas ; Metagenome ; Seawater/microbiology ; Phylogeny ; Genome, Bacterial ; Chloroflexi/genetics/classification ; Bermuda ; Adaptation, Physiological/genetics ; Microbiota/genetics ; }, abstract = {SAR202 bacteria in the Chloroflexota phylum are abundant and widely distributed in the ocean. Their genome coding capacities indicate their potential roles in degrading complex and recalcitrant organic compounds in the ocean. However, our understanding of their genomic diversity, vertical distribution, and depth-related metabolisms is still limited by the number of assembled SAR202 genomes. In this study, we apply deep metagenomic sequencing (180 Gb per sample) to investigate microbial communities collected from six representative depths at the Bermuda Atlantic Time Series (BATS) station. We obtain 173 SAR202 metagenome-assembled genomes (MAGs). Intriguingly, 154 new species and 104 new genera are found based on these 173 SAR202 genomes. We add 12 new subgroups to the current SAR202 lineages. The vertical distribution of 20 SAR202 subgroups shows their niche partitioning in the euphotic, mesopelagic, and bathypelagic oceans, respectively. Deep-ocean SAR202 bacteria contain more genes and exhibit more metabolic potential for degrading complex organic substrates than those from the euphotic zone. With deep metagenomic sequencing, we uncover many new lineages of SAR202 bacteria and their potential functions which greatly deepen our understanding of their diversity, vertical profile, and contribution to the ocean's carbon cycling, especially in the deep ocean.}, } @article {pmid38997249, year = {2024}, author = {Su, X and Huang, X and Zhang, Y and Yang, L and Wen, T and Yang, X and Zhu, G and Zhang, J and Tang, Y and Li, Z and Ding, J and Li, R and Pan, J and Chen, X and Huang, F and Rillig, MC and Zhu, YG}, title = {Nitrifying niche in estuaries is expanded by the plastisphere.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5866}, pmid = {38997249}, issn = {2041-1723}, support = {42021005//Science Fund for Creative Research Groups (Fund for Creative Research Groups)/ ; }, mesh = {*Nitrification ; *Estuaries ; *Seawater/microbiology ; *Bacteria/metabolism/genetics ; *Biofilms/growth & development ; Ecosystem ; Microbiota/physiology ; Metagenomics ; Phylogeny ; Nitrogen Cycle ; Nitrogen/metabolism ; Nitrogen Isotopes/metabolism ; }, abstract = {The estuarine plastisphere, a novel ecological habitat in the Anthropocene, has garnered global concerns. Recent geochemical evidence has pointed out its potential role in influencing nitrogen biogeochemistry. However, the biogeochemical significance of the plastisphere and its mechanisms regulating nitrogen cycling remain elusive. Using [15]N- and [13]C-labelling coupled with metagenomics and metatranscriptomics, here we unveil that the plastisphere likely acts as an underappreciated nitrifying niche in estuarine ecosystems, exhibiting a 0.9 ~ 12-fold higher activity of bacteria-mediated nitrification compared to surrounding seawater and other biofilms (stone, wood and glass biofilms). The shift of active nitrifiers from O2-sensitive nitrifiers in the seawater to nitrifiers with versatile metabolisms in the plastisphere, combined with the potential interspecific cooperation of nitrifying substrate exchange observed among the plastisphere nitrifiers, collectively results in the unique nitrifying niche. Our findings highlight the plastisphere as an emerging nitrifying niche in estuarine environment, and deepen the mechanistic understanding of its contribution to marine biogeochemistry.}, } @article {pmid38997032, year = {2024}, author = {Satta, A and Ghiotto, G and Santinello, D and Giangeri, G and Bergantino, E and Modesti, M and Raga, R and Treu, L and Campanaro, S and Zampieri, G}, title = {Synergistic functional activity of a landfill microbial consortium in a microplastic-enriched environment.}, journal = {The Science of the total environment}, volume = {947}, number = {}, pages = {174696}, doi = {10.1016/j.scitotenv.2024.174696}, pmid = {38997032}, issn = {1879-1026}, mesh = {*Microplastics ; *Soil Microbiology ; *Microbial Consortia ; *Waste Disposal Facilities ; Soil Pollutants/metabolism ; Microbiota ; Biodegradation, Environmental ; Metagenomics ; Plastics ; }, abstract = {Plastic pollution of the soil is a global issue of increasing concern, with far-reaching impact on the environment and human health. To fully understand the medium- and long-term impact of plastic dispersal in the environment, it is necessary to define its interaction with the residing microbial communities and the biochemical routes of its degradation and metabolization. However, despite recent attention on this problem, research has largely focussed on microbial functional potential, failing to clearly identify collective adaptation strategies of these communities. Our study combines genome-centric metagenomics and metatranscriptomics to characterise soil microbial communities adapting to high polyethylene and polyethylene terephthalate concentration. The microbiota were sampled from a landfill subject to decades-old plastic contamination and enriched through prolonged cultivation using these microplastics as the only carbon source. This approach aimed to select the microorganisms that best adapt to these specific substrates. As a result, we obtained simplified communities where multiple plastic metabolization pathways are widespread across abundant and rare microbial taxa. Major differences were found in terms of expression, which on average was higher in planktonic microbes than those firmly adhered to plastic, indicating complementary metabolic roles in potential microplastic assimilation. Moreover, metatranscriptomic patterns indicate a high transcriptional level of numerous genes in emerging taxa characterised by a marked accumulation of genomic variants, supporting the hypothesis that plastic metabolization requires an extensive rewiring in energy metabolism and thus provides a strong selective pressure. Altogether, our results provide an improved characterisation of the impact of microplastics derived from common plastics types on terrestrial microbial communities and suggest biotic responses investing contaminated sites as well as potential biotechnological targets for cooperative plastic upcycling.}, } @article {pmid38996548, year = {2024}, author = {Wu, C and Yang, F and Zhong, H and Hong, J and Lin, H and Zong, M and Ren, H and Zhao, S and Chen, Y and Shi, Z and Wang, X and Shen, J and Wang, Q and Ni, M and Chen, B and Cai, Z and Zhang, M and Cao, Z and Wu, K and Gao, A and Li, J and Liu, C and Xiao, M and Li, Y and Shi, J and Zhang, Y and Xu, X and Gu, W and Bi, Y and Ning, G and Wang, W and Wang, J and Liu, R}, title = {Obesity-enriched gut microbe degrades myo-inositol and promotes lipid absorption.}, journal = {Cell host & microbe}, volume = {32}, number = {8}, pages = {1301-1314.e9}, doi = {10.1016/j.chom.2024.06.012}, pmid = {38996548}, issn = {1934-6069}, mesh = {*Inositol/metabolism ; *Obesity/microbiology/metabolism ; *Gastrointestinal Microbiome ; Animals ; Humans ; Mice ; Male ; Lipid Metabolism ; Female ; Intestinal Absorption ; Mice, Inbred C57BL ; Metagenomics ; Middle Aged ; Adult ; Fatty Acids/metabolism ; Escherichia coli/genetics/metabolism ; }, abstract = {Numerous studies have reported critical roles for the gut microbiota in obesity. However, the specific microbes that causally contribute to obesity and the underlying mechanisms remain undetermined. Here, we conducted shotgun metagenomic sequencing in a Chinese cohort of 631 obese subjects and 374 normal-weight controls and identified a Megamonas-dominated, enterotype-like cluster enriched in obese subjects. Among this cohort, the presence of Megamonas and polygenic risk exhibited an additive impact on obesity. Megamonas rupellensis possessed genes for myo-inositol degradation, as demonstrated in vitro and in vivo, and the addition of myo-inositol effectively inhibited fatty acid absorption in intestinal organoids. Furthermore, mice colonized with M. rupellensis or E. coli heterologously expressing the myo-inositol-degrading iolG gene exhibited enhanced intestinal lipid absorption, thereby leading to obesity. Altogether, our findings uncover roles for M. rupellensis as a myo-inositol degrader that enhances lipid absorption and obesity, suggesting potential strategies for future obesity management.}, } @article {pmid38996003, year = {2024}, author = {Byndloss, M and Devkota, S and Duca, F and Hendrik Niess, J and Nieuwdorp, M and Orho-Melander, M and Sanz, Y and Tremaroli, V and Zhao, L}, title = {The Gut Microbiota and Diabetes: Research, Translation, and Clinical Applications-2023 Diabetes, Diabetes Care, and Diabetologia Expert Forum.}, journal = {Diabetes care}, volume = {47}, number = {9}, pages = {1491-1508}, pmid = {38996003}, issn = {1935-5548}, support = {//Novo Nordisk/ ; R01 DK123446/DK/NIDDK NIH HHS/United States ; DP1 DK130687/DK/NIDDK NIH HHS/United States ; R01 DK131104/DK/NIDDK NIH HHS/United States ; P30 ES006694/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetes Mellitus, Type 2/microbiology ; Diabetes Mellitus/microbiology ; }, abstract = {This article summarizes the state of the science on the role of the gut microbiota (GM) in diabetes from a recent international expert forum organized by Diabetes, Diabetes Care, and Diabetologia, which was held at the European Association for the Study of Diabetes 2023 Annual Meeting in Hamburg, Germany. Forum participants included clinicians and basic scientists who are leading investigators in the field of the intestinal microbiome and metabolism. Their conclusions were as follows: 1) the GM may be involved in the pathophysiology of type 2 diabetes, as microbially produced metabolites associate both positively and negatively with the disease, and mechanistic links of GM functions (e.g., genes for butyrate production) with glucose metabolism have recently emerged through the use of Mendelian randomization in humans; 2) the highly individualized nature of the GM poses a major research obstacle, and large cohorts and a deep-sequencing metagenomic approach are required for robust assessments of associations and causation; 3) because single-time point sampling misses intraindividual GM dynamics, future studies with repeated measures within individuals are needed; and 4) much future research will be required to determine the applicability of this expanding knowledge to diabetes diagnosis and treatment, and novel technologies and improved computational tools will be important to achieve this goal.}, } @article {pmid38995889, year = {2024}, author = {Melchior, PP and Reiss, E and Payne, Z and Vuong, N and Hovorka, K and Lindsay, HL and Diaz, GR and Gaire, T and Noyes, N}, title = {Analysis of the northern pitcher plant (Sarracenia purpurea L.) phytotelm bacteriome throughout a temperate region growing season.}, journal = {PloS one}, volume = {19}, number = {7}, pages = {e0306602}, pmid = {38995889}, issn = {1932-6203}, mesh = {*Seasons ; *Sarraceniaceae/microbiology ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Nitrogen/metabolism ; Bacteria/genetics/classification/isolation & purification ; Nitrogen Fixation ; Oxidoreductases/genetics/metabolism ; }, abstract = {The insectivorous Northern Pitcher Plant, Sarracenia purpurea, recruits a dynamic biotic community in the rainwater collected by its pitcher-shaped leaves. Insect capture and degradation within the pitcher fluid (phytotelma) has been well documented as a mechanism for supplementing the plant's nitrogen, phosphorous, and micronutrient requirements. Metagenomic studies have shown a diverse microbiome in this phytotelm environment, including taxa that contribute metabolically to prey digestion. In this investigation, we used high-throughput 16S rDNA sequencing and bioinformatics to analyze the S. purpurea phytotelm bacteriome as it changes through the growing season (May-September) in plants from the north-central region of the species' native range. Additionally, we used molecular techniques to detect and quantify bacterial nitrogenase genes (nifH) in all phytotelm samples to explore the hypothesis that diazotrophy is an additional mechanism of supplying biologically available nitrogen to S. purpurea. The results of this study indicate that while prokaryote diversity remains relatively stable in plants at different locations within our region, diversity changes significantly as the growing season progresses. Furthermore, nifH genes were detected at biologically significant concentrations in one hundred percent of samples, suggesting that nitrogen fixation may be an important contributor to the S. purpurea nutrient budget.}, } @article {pmid38995542, year = {2024}, author = {Van Den Bossche, T and Verschaffelt, P and Vande Moortele, T and Dawyndt, P and Martens, L and Mesuere, B}, title = {Biodiversity Analysis of Metaproteomics Samples with Unipept: A Comprehensive Tutorial.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2836}, number = {}, pages = {183-215}, pmid = {38995542}, issn = {1940-6029}, mesh = {*Proteomics/methods ; *Software ; *Microbiota/genetics ; *Biodiversity ; Humans ; Computational Biology/methods ; Metagenomics/methods ; }, abstract = {Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.be , has emerged as a valuable resource for analyzing metaproteomic data. It offers in-depth insights into both taxonomic distributions and functional characteristics of complex ecosystems. This tutorial explains essential concepts like Lowest Common Ancestor (LCA) determination and the handling of peptides with missed cleavages. It also provides a detailed, step-by-step guide on using the Unipept Web application and Unipept Desktop for thorough metaproteomics analyses. By integrating theoretical principles with practical methodologies, this tutorial empowers researchers with the essential knowledge and tools needed to fully utilize metaproteomics in their microbiome studies.}, } @article {pmid38995243, year = {2024}, author = {Leech, SM and Borg, DJ and Rae, KM and Kumar, S and Clifton, VL and Dekker Nitert, M}, title = {Delivery mode is a larger determinant of infant gut microbiome composition at 6 weeks than exposure to peripartum antibiotics.}, journal = {Microbial genomics}, volume = {10}, number = {7}, pages = {}, pmid = {38995243}, issn = {2057-5858}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; *Anti-Bacterial Agents/administration & dosage ; Pregnancy ; *Cesarean Section ; Adult ; Infant ; *Feces/microbiology ; *Delivery, Obstetric ; Peripartum Period ; Infant, Newborn ; Male ; Antibiotic Prophylaxis ; Longitudinal Studies ; }, abstract = {Background. Previous research has shown that delivery mode can shape infant gut microbiome composition. However, mothers delivering by caesarean section routinely receive prophylactic antibiotics prior to delivery, resulting in antibiotic exposure to the infant via the placenta. Previously, only a small number of studies have examined the effect of delivery mode versus antibiotic exposure on the infant gut microbiome with mixed findings.Objective. We aimed to determine the effect of delivery mode compared to antibiotic use during labour and delivery on the infant and maternal gut microbiome at 6 weeks post-partum.Methodology. Twenty-five mother-infant dyads were selected from the longitudinal Queensland Family Cohort Study. The selected dyads comprised nine vaginally delivered infants without antibiotics, seven vaginally delivered infants exposed to antibiotics and nine infants born by caesarean section with routine maternal prophylactic antibiotics. Shotgun-metagenomic sequencing of DNA from stool samples collected at 6 weeks post-partum from mother and infant was used to assess microbiome composition.Results. Caesarean section infants exhibited decreases in Bacteroidetes (ANCOM-BC q<0.0001, MaAsLin 2 q=0.041), changes to several functional pathways and altered beta diversity (R [2]=0.056, P=0.029), while minimal differences due to antibiotic exposure were detected. For mothers, caesarean delivery (P=0.0007) and antibiotic use (P=0.016) decreased the evenness of the gut microbiome at 6 weeks post-partum without changing beta diversity. Several taxa in the maternal microbiome were altered in association with antibiotic use, with few differentially abundant taxa associated with delivery mode.Conclusion. For infants, delivery mode appears to have a larger effect on gut microbiome composition at 6 weeks post-partum than intrapartum antibiotic exposure. For mothers, both delivery mode and intrapartum antibiotic use have a small effect on gut microbiome composition at 6 weeks post-partum.}, } @article {pmid38995144, year = {2024}, author = {Arikan, M and Muth, T}, title = {gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {38995144}, issn = {2047-217X}, support = {//Türkiye Bilimsel ve Teknolojik Araştirma Kurumu/ ; }, mesh = {*Microbiota ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; *Software ; *Computational Biology/methods ; *Proteomics/methods ; Humans ; Metagenome ; Multiomics ; }, abstract = {BACKGROUND: In recent years, omics technologies have offered an exceptional chance to gain a deeper insight into the structural and functional characteristics of microbial communities. As a result, there is a growing demand for user-friendly, reproducible, and versatile bioinformatic tools that can effectively harness multi-omics data to provide a holistic understanding of microbiomes. Previously, we introduced gNOMO, a bioinformatic pipeline tailored to analyze microbiome multi-omics data in an integrative manner. In response to the evolving demands within the microbiome field and the growing necessity for integrated multi-omics data analysis, we have implemented substantial enhancements to the gNOMO pipeline.

RESULTS: Here, we present gNOMO2, a comprehensive and modular pipeline that can seamlessly manage various omics combinations, ranging from 2 to 4 distinct omics data types, including 16S ribosomal RNA (rRNA) gene amplicon sequencing, metagenomics, metatranscriptomics, and metaproteomics. Furthermore, gNOMO2 features a specialized module for processing 16S rRNA gene amplicon sequencing data to create a protein database suitable for metaproteomics investigations. Moreover, it incorporates new differential abundance, integration, and visualization approaches, enhancing the toolkit for a more insightful analysis of microbiomes. The functionality of these new features is showcased through the use of 4 microbiome multi-omics datasets encompassing various ecosystems and omics combinations. gNOMO2 not only replicated most of the primary findings from these studies but also offered further valuable perspectives.

CONCLUSIONS: gNOMO2 enables the thorough integration of taxonomic and functional analyses in microbiome multi-omics data, offering novel insights in both host-associated and free-living microbiome research. gNOMO2 is available freely at https://github.com/muzafferarikan/gNOMO2.}, } @article {pmid38992765, year = {2024}, author = {Ng, DZW and Low, A and Tan, AJH and Ong, JH and Kwa, WT and Lee, JWJ and Chan, ECY}, title = {Ex vivo metabolism kinetics of primary to secondary bile acids via a physiologically relevant human faecal microbiota model.}, journal = {Chemico-biological interactions}, volume = {399}, number = {}, pages = {111140}, doi = {10.1016/j.cbi.2024.111140}, pmid = {38992765}, issn = {1872-7786}, mesh = {*Gastrointestinal Microbiome/physiology ; *Secondary Metabolism ; Humans ; *Chenodeoxycholic Acid/metabolism ; *Cholic Acid/metabolism ; Models, Biological ; *Deoxycholic Acid/metabolism ; }, abstract = {Bile acids (BA) are synthesized in the human liver and undergo metabolism by host gut bacteria. In diseased states, gut microbial dysbiosis may lead to high primary unconjugated BA concentrations and significant perturbations to secondary BA. Hence, it is important to understand the microbial-mediated formation kinetics of secondary bile acids using physiologically relevant ex vivo human faecal microbiota models. Here, we optimized an ex vivo human faecal microbiota model to recapitulate the metabolic kinetics of primary unconjugated BA and applied it to investigate the formation kinetics of novel secondary BA metabolites and their sequential pathways. We demonstrated (1) first-order depletion of primary BA, cholic acid (CA) and chenodeoxycholic acid (CDCA), under non-saturable conditions and (2) saturable Michaelis-Menten kinetics for secondary BA metabolite formation with increasing substrate concentration. Notably, relatively lower Michaelis constants (Km) were associated with the formation of deoxycholic acid (DCA, 14.3 μM) and lithocholic acid (LCA, 140 μM) versus 3-oxo CA (>1000 μM), 7-keto DCA (443 μM) and 7-keto LCA (>1000 μM), thereby recapitulating clinically observed saturation of 7α-dehydroxylation relative to oxidation of primary BA. Congruently, metagenomics revealed higher relative abundance of functional genes related to the oxidation pathway as compared to the 7α-dehydroxylation pathway. In addition, we demonstrated gut microbial-mediated hyocholic acid (HCA) and hyodeoxycholic acid (HDCA) formation from CDCA. In conclusion, we optimized a physiologically relevant ex vivo human faecal microbiota model to investigate gut microbial-mediated metabolism of primary BA and present a novel gut microbial-catalysed two-step pathway from CDCA to HCA and, subsequently, HDCA.}, } @article {pmid38990940, year = {2024}, author = {Zomer, A and Ingham, CJ and von Meijenfeldt, FAB and Escobar Doncel, Á and van de Kerkhof, GT and Hamidjaja, R and Schouten, S and Schertel, L and Müller, KH and Catón, L and Hahnke, RL and Bolhuis, H and Vignolini, S and Dutilh, BE}, title = {Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {29}, pages = {e2309757121}, pmid = {38990940}, issn = {1091-6490}, support = {40-43500-98-4102/435004516//ZonMw (Netherlands Organisation for Health Research and Development)/ ; 860125//EC | HORIZON EUROPE Framework Programme (Horizon Europe)/ ; 2110570//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 722842//EC | HORIZON EUROPE Framework Programme (Horizon Europe)/ ; P2ZHP2_183998/SNSF_/Swiss National Science Foundation/Switzerland ; SNSF3//Isaac Newton Trust/ ; SNSF 40B1-0_198708/SNSF_/Swiss National Science Foundation/Switzerland ; 865694//EC | European Research Council (ERC)/ ; 101001637//EC | European Research Council (ERC)/ ; BB/V00364X/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 390713860//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {*Genome, Bacterial ; Phenotype ; Color ; Bacteria/genetics/metabolism ; Proteobacteria/genetics/metabolism ; Phylogeny ; Metagenome ; Genome-Wide Association Study ; Bacteroidetes/genetics/metabolism ; }, abstract = {Structural color is an optical phenomenon resulting from light interacting with nanostructured materials. Although structural color (SC) is widespread in the tree of life, the underlying genetics and genomics are not well understood. Here, we collected and sequenced a set of 87 structurally colored bacterial isolates and 30 related strains lacking SC. Optical analysis of colonies indicated that diverse bacteria from at least two different phyla (Bacteroidetes and Proteobacteria) can create two-dimensional packing of cells capable of producing SC. A pan-genome-wide association approach was used to identify genes associated with SC. The biosynthesis of uroporphyrin and pterins, as well as carbohydrate utilization and metabolism, was found to be involved. Using this information, we constructed a classifier to predict SC directly from bacterial genome sequences and validated it by cultivating and scoring 100 strains that were not part of the training set. We predicted that SCr is widely distributed within gram-negative bacteria. Analysis of over 13,000 assembled metagenomes suggested that SC is nearly absent from most habitats associated with multicellular organisms except macroalgae and is abundant in marine waters and surface/air interfaces. This work provides a large-scale ecogenomics view of SC in bacteria and identifies microbial pathways and evolutionary relationships that underlie this optical phenomenon.}, } @article {pmid38990824, year = {2024}, author = {Schaible, GA and Jay, ZJ and Cliff, J and Schulz, F and Gauvin, C and Goudeau, D and Malmstrom, RR and Ruff, SE and Edgcomb, V and Hatzenpichler, R}, title = {Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells.}, journal = {PLoS biology}, volume = {22}, number = {7}, pages = {e3002638}, pmid = {38990824}, issn = {1545-7885}, support = {P30 GM140963/GM/NIGMS NIH HHS/United States ; }, mesh = {*In Situ Hybridization, Fluorescence ; Metagenome ; Microbial Consortia/genetics ; Genome, Bacterial ; Bacteria/genetics/metabolism ; Genetic Variation ; Phylogeny ; }, abstract = {Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single-cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing 8 new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nanoscale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal noncanonical amino acid tagging (BONCAT), we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.}, } @article {pmid38990271, year = {2024}, author = {Ulger, Y and Delik, A and Akkız, H}, title = {Gut Microbiome and colorectal cancer: discovery of bacterial changes with metagenomics application in Turkısh population.}, journal = {Genes & genomics}, volume = {46}, number = {9}, pages = {1059-1070}, pmid = {38990271}, issn = {2092-9293}, support = {148-TGD-2022//Turkish Gastroenterology Association/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics/pathology ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Female ; Male ; *Metagenomics/methods ; Aged ; Turkey ; Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is the 3rd most common cancer in the world and colonic carcinogenesis is a multifactorial disease that involves environmental and genetic factors. Gut microbiota plays a critical role in the regulation of intestinal homeostasis. Increasing evidence shows that the gut microbiome plays a role in CRC development and may be a biomarker for early diagnosis.

OBJECTIVE: This study aimed to determine the clinical prognostic significance of gut microbiota in CRC patients in the Turkish population by metagenomic analysis and to determine the microbial composition in tumor tissue biopsy samples.

METHODS: Tissue biopsies were taken from the participants with sterile forceps during colonoscopy and stored at -80 °C. Then, DNA isolation was performed from the tissue samples and the V3-V4 region of the 16 S rRNA gene was sequenced on the Illumina MiSeq platform. Quality control of the obtained sequence data was performed. Operational taxonomic units (OTUs) were classified according to the Greengenes database. Alpha diversity (Shannon index) and beta diversity (Bray-Curtis distance) analyses were performed. The most common bacterial species in CRC patients and healthy controls were determined and whether there were statistically significant differences between the groups was tested.

RESULTS: A total of 40 individuals, 13 CRC patients and 20 healthy control individuals were included in our metagenomic study. The mean age of the patients was 64.83 and BMI was 25.85. In CRC patients, the level of Bacteroidetes at the phylum taxonomy was significantly increased (p = 0.04), the level of Clostridia at the class taxonomy was increased (p = 0.23), and the level of Enterococcus at the genus taxonomy was significantly increased (p = 0.01). When CRC patients were compared with the control group, significant increases were detected in the species of Gemmiger formicilis (p = 0.15), Prevotella copri (p = 0.02) and Ruminococcus bromii (p = 0.001) at the species taxonomy.

CONCLUSIONS: Metagenomic analysis of intestinal microbiota composition in CRC patients provides important data for determining the treatment options for these patients. The results of this study suggest that it may be beneficial in terms of early diagnosis, poor prognosis and survival rates in CRC patients. In addition, this metagenomic study is the first study on the colon microbiome associated with CRC mucosa in the Turkish population.}, } @article {pmid38990071, year = {2024}, author = {Spirito, CM and Lucas, TN and Patz, S and Jeon, BS and Werner, JJ and Trondsen, LH and Guzman, JJ and Huson, DH and Angenent, LT}, title = {Variability in n-caprylate and n-caproate producing microbiomes in reactors with in-line product extraction.}, journal = {mSystems}, volume = {9}, number = {8}, pages = {e0041624}, pmid = {38990071}, issn = {2379-5077}, support = {STAR Fellowship//U.S. Environmental Protection Agency (EPA)/ ; Alexander von Humboldt Professorship//Alexander von Humboldt-Stiftung (AvH)/ ; EXC 2124 - 390838134//Deutsche Forschungsgemeinschaft (DFG)/ ; NNF21SA0072700//Novo Nordisk Fonden (NNF)/ ; W911NF-12-1-0555//DOD | USA | AFC | CCDC | Army Research Office (ARO)/ ; Collaboration between the University of Maryland and the University of Tübingen//Reinhard Frank Stiftung/ ; }, mesh = {*Bioreactors/microbiology ; *Microbiota ; Caprylates/metabolism ; Caproates/metabolism ; Bacteria/metabolism/genetics/classification/isolation & purification ; Liquid-Liquid Extraction/methods ; }, abstract = {Medium-chain carboxylates (MCCs) are used in various industrial applications. These chemicals are typically extracted from palm oil, which is deemed not sustainable. Recent research has focused on microbial chain elongation using reactors to produce MCCs, such as n-caproate (C6) and n-caprylate (C8), from organic substrates such as wastes. Even though the production of n-caproate is relatively well-characterized, bacteria and metabolic pathways that are responsible for n-caprylate production are not. Here, three 5 L reactors with continuous membrane-based liquid-liquid extraction (i.e., pertraction) were fed ethanol and acetate and operated for an operating period of 234 days with different operating conditions. Metagenomic and metaproteomic analyses were employed. n-Caprylate production rates and reactor microbiomes differed between reactors even when operated similarly due to differences in H2 and O2 between the reactors. The complete reverse β-oxidation (RBOX) pathway was present and expressed by several bacterial species in the Clostridia class. Several Oscillibacter spp., including Oscillibacter valericigenes, were positively correlated with n-caprylate production rates, while Clostridium kluyveri was positively correlated with n-caproate production. Pseudoclavibacter caeni, which is a strictly aerobic bacterium, was abundant across all the operating periods, regardless of n-caprylate production rates. This study provides insight into microbiota that are associated with n-caprylate production in open-culture reactors and provides ideas for further work.IMPORTANCEMicrobial chain elongation pathways in open-culture biotechnology systems can be utilized to convert organic waste and industrial side streams into valuable industrial chemicals. Here, we investigated the microbiota and metabolic pathways that produce medium-chain carboxylates (MCCs), including n-caproate (C6) and n-caprylate (C8), in reactors with in-line product extraction. Although the reactors in this study were operated similarly, different microbial communities dominated and were responsible for chain elongation. We found that different microbiota were responsible for n-caproate or n-caprylate production, and this can inform engineers on how to operate the systems better. We also observed which changes in operating conditions steered the production toward and away from n-caprylate, but more work is necessary to ascertain a mechanistic understanding that could be predictive. This study provides pertinent research questions for future work.}, } @article {pmid38989659, year = {2024}, author = {Zhou, L and Yan, Z and Yang, S and Lu, G and Nie, Y and Ren, Y and Xue, Y and Shi, JS and Xu, ZH and Geng, Y}, title = {High methionine intake alters gut microbiota and lipid profile and leads to liver steatosis in mice.}, journal = {Food & function}, volume = {15}, number = {15}, pages = {8053-8069}, doi = {10.1039/d4fo01613k}, pmid = {38989659}, issn = {2042-650X}, mesh = {Animals ; *Methionine/metabolism/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; Male ; *Mice, Inbred C57BL ; *Liver/metabolism ; Fatty Liver/metabolism ; Lipid Metabolism/drug effects ; Lipids ; }, abstract = {Methionine is an important sulfur-containing amino acid. Health effects of both methionine restriction (MR) and methionine supplementation (MS) have been studied. This study aimed to investigate the impact of a high-methionine diet (HMD) (1.64% methionine) on both the gut and liver functions in mice through multi-omic analyses. Hepatic steatosis and compromised gut barrier function were observed in mice fed the HMD. RNA-sequencing (RNA-seq) analysis of liver gene expression patterns revealed the upregulation of lipid synthesis and degradation pathways, cholesterol metabolism and inflammation-related nucleotide-binding oligomerization domain (NOD)-like receptor signaling pathway. Metagenomic sequencing of cecal content demonstrated a shift in gut microbial composition with an increased abundance of opportunistic pathogens and gut microbial functions with up-regulated lipopolysaccharide (LPS) biosynthesis in mice fed HMD. Metabolomic study of cecal content showed an altered gut lipid profile and the level of bioactive lipids, including docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), palmitoylethanolamide (PEA), linoleoyl ethanolamide (LEA) and arachidonoyl ethanolamide (AEA), that carry anti-inflammatory effects significantly reduced in the gut of mice fed the HMD. Correlation analysis demonstrated that gut microbiota was highly associated with liver and gut functions and gut bioactive lipid content. In conclusion, this study suggested that the HMD exerted negative impacts on both the gut and liver, and an adequate amount of methionine intake should be carefully determined to ensure normal physiological function without causing adverse effects.}, } @article {pmid38989650, year = {2024}, author = {Shi, Z and Long, X and Zhang, C and Chen, Z and Usman, M and Zhang, Y and Zhang, S and Luo, G}, title = {Viral and Bacterial Community Dynamics in Food Waste and Digestate from Full-Scale Biogas Plants.}, journal = {Environmental science & technology}, volume = {58}, number = {29}, pages = {13010-13022}, doi = {10.1021/acs.est.4c04109}, pmid = {38989650}, issn = {1520-5851}, mesh = {*Biofuels ; *Bacteria ; Food ; Microbiota ; Anaerobiosis ; Viruses ; Food Loss and Waste ; }, abstract = {Anaerobic digestion (AD) is commonly used in food waste treatment. Prokaryotic microbial communities in AD of food waste have been comprehensively studied. The role of viruses, known to affect microbial dynamics and metabolism, remains largely unexplored. This study employed metagenomic analysis and recovered 967 high-quality viral bins within food waste and digestate derived from 8 full-scale biogas plants. The diversity of viral communities was higher in digestate. In silico predictions linked 20.8% of viruses to microbial host populations, highlighting possible virus predators of key functional microbes. Lineage-specific virus-host ratio varied, indicating that viral infection dynamics might differentially affect microbial responses to the varying process parameters. Evidence for virus-mediated gene transfer was identified, emphasizing the potential role of viruses in controlling the microbiome. AD altered the specific process parameters, potentially promoting a shift in viral lifestyle from lysogenic to lytic. Viruses encoding auxiliary metabolic genes (AMGs) were involved in microbial carbon and nutrient cycling, and most AMGs were transcriptionally expressed in digestate, meaning that viruses with active functional states were likely actively involved in AD. These findings provided a comprehensive profile of viral and bacterial communities and expanded knowledge of the interactions between viruses and hosts in food waste and digestate.}, } @article {pmid38989465, year = {2024}, author = {Nanetti, E and Scicchitano, D and Palladino, G and Interino, N and Corlatti, L and Pedrotti, L and Zanetti, F and Pagani, E and Esposito, E and Brambilla, A and Grignolio, S and Marotti, I and Turroni, S and Fiori, J and Rampelli, S and Candela, M}, title = {The Alpine ibex (Capra ibex) gut microbiome, seasonal dynamics, and potential application in lignocellulose bioconversion.}, journal = {iScience}, volume = {27}, number = {7}, pages = {110194}, pmid = {38989465}, issn = {2589-0042}, abstract = {Aiming to shed light on the biology of wild ruminants, we investigated the gut microbiome seasonal dynamics of the Alpine ibex (Capra ibex) from the Central Italian Alps. Feces were collected in spring, summer, and autumn during non-invasive sampling campaigns. Samples were analyzed by 16S rRNA amplicon sequencing, shotgun metagenomics, as well as targeted and untargeted metabolomics. Our findings revealed season-specific compositional and functional profiles of the ibex gut microbiome that may allow the host to adapt to seasonal changes in available forage, by fine-tuning the holobiont catabolic layout to fully exploit the available food. Besides confirming the importance of the host-associated microbiome in providing the phenotypic plasticity needed to buffer dietary changes, we obtained species-level genome bins and identified minimal gut microbiome community modules of 11-14 interacting strains as a possible microbiome-based solution for the bioconversion of lignocellulose to high-value compounds, such as volatile fatty acids.}, } @article {pmid38988320, year = {2024}, author = {Kumar, M and Saini, HS}, title = {Deciphering Indigenous Bacterial Diversity of Co-Polluted Sites to Unravel Its Bioremediation Potential: A Metagenomic Approach.}, journal = {Journal of basic microbiology}, volume = {64}, number = {9}, pages = {e2400303}, doi = {10.1002/jobm.202400303}, pmid = {38988320}, issn = {1521-4028}, support = {//This study was funded by Department of Biotechnology (DBT), Ministry of Science and Technology, New Delhi (India) (Project number BT/PR7535/BCE/8/960/2013)./ ; }, mesh = {*Biodegradation, Environmental ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Soil Microbiology ; *Metagenomics ; Wastewater/microbiology ; Phylogeny ; Biodiversity ; Proteobacteria/genetics/classification/metabolism/isolation & purification ; DNA, Bacterial/genetics ; Metals, Heavy/metabolism/analysis ; Microbiota ; }, abstract = {Polluted drains across the globe are affected due to reckless disposal of untreated industrial effluents resulting in significant water pollution affecting microbial community structure/dynamics. To elucidate this, polluted samples were collected from Budha Nala (BN) drain, Tung Dhab (TD) drain, and wastewater treatment plant (WWTP) receiving an inflow of organic pollutants as well as heavy metals due to anthropogenic activities. The sample of unpolluted pristine soil (PS) was used as control, as there is no history of usage of organic chemicals at this site. The bacterial diversity of these samples was sequenced using the Illumina MiSeq platform by amplifying the V3/V4 region of 16S rRNA. The majority of operational taxonomic unit (OTUs) at polluted sites belonged to phyla Proteobacteria specifically Gammaproteobacteria class, followed by Actinobacteria, Bacteriodetes, Chloroflexi, Firmicutes, Planctomycetes, WS6, and TM7, whereas unpolluted site revealed the prevalence of Proteobacteria followed by Actinobacteria, Planctomycetes, Firmicutes, Acidobacteria, Chloroflexi, Bacteroidetes, Verrucomicrobia, and Nitrospirae. The data sets decode unclassified species of the phyla Proteobacteria, Bacteriodetes, Chloroflexi, Firmicutes, and WS6, along with some unclassified bacterial species. The study provided a comparative study of changed microbial community structure, their possible functions across diverse geographical locations, and identifying specific bacterial genera as pollution bio-indicators of aged polluted drains.}, } @article {pmid38987594, year = {2024}, author = {Fujimoto, K and Hayashi, T and Yamamoto, M and Sato, N and Shimohigoshi, M and Miyaoka, D and Yokota, C and Watanabe, M and Hisaki, Y and Kamei, Y and Yokoyama, Y and Yabuno, T and Hirose, A and Nakamae, M and Nakamae, H and Uematsu, M and Sato, S and Yamaguchi, K and Furukawa, Y and Akeda, Y and Hino, M and Imoto, S and Uematsu, S}, title = {An enterococcal phage-derived enzyme suppresses graft-versus-host disease.}, journal = {Nature}, volume = {632}, number = {8023}, pages = {174-181}, pmid = {38987594}, issn = {1476-4687}, mesh = {Adult ; Aged ; Animals ; Female ; Humans ; Male ; Mice ; Middle Aged ; Young Adult ; *Bacteriophages/enzymology/genetics ; Biofilms/drug effects/growth & development ; Dysbiosis/complications/microbiology ; *Enterococcus faecalis/drug effects/genetics/growth & development/metabolism/virology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Germ-Free Life ; *Graft vs Host Disease/complications/microbiology/prevention & control/therapy ; Hematopoietic Stem Cell Transplantation/adverse effects ; In Vitro Techniques ; Intestines/drug effects/microbiology ; Perforin/metabolism ; Risk Factors ; Transplantation, Homologous/adverse effects ; Whole Genome Sequencing ; Drug Resistance, Bacterial/drug effects ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Changes in the gut microbiome have pivotal roles in the pathogenesis of acute graft-versus-host disease (aGVHD) after allogenic haematopoietic cell transplantation (allo-HCT)[1-6]. However, effective methods for safely resolving gut dysbiosis have not yet been established. An expansion of the pathogen Enterococcus faecalis in the intestine, associated with dysbiosis, has been shown to be a risk factor for aGVHD[7-10]. Here we analyse the intestinal microbiome of patients with allo-HCT, and find that E. faecalis escapes elimination and proliferates in the intestine by forming biofilms, rather than by acquiring drug-resistance genes. We isolated cytolysin-positive highly pathogenic E. faecalis from faecal samples and identified an anti-E. faecalis enzyme derived from E. faecalis-specific bacteriophages by analysing bacterial whole-genome sequencing data. The antibacterial enzyme had lytic activity against the biofilm of E. faecalis in vitro and in vivo. Furthermore, in aGVHD-induced gnotobiotic mice that were colonized with E. faecalis or with patient faecal samples characterized by the domination of Enterococcus, levels of intestinal cytolysin-positive E. faecalis were decreased and survival was significantly increased in the group that was treated with the E. faecalis-specific enzyme, compared with controls. Thus, administration of a phage-derived antibacterial enzyme that is specific to biofilm-forming pathogenic E. faecalis-which is difficult to eliminate with existing antibiotics-might provide an approach to protect against aGVHD.}, } @article {pmid38986824, year = {2024}, author = {de Deus, DR and Siqueira, JAM and Maués, MAC and de Fátima Mesquita de Figueiredo, MJ and Júnior, ECS and da Silva Bandeira, R and da Costa Pinheiro, K and Teixeira, DM and da Silva, LD and de Fátima Dos Santos Guerra, S and da Silva Soares, L and Gabbay, YB}, title = {Analysis of viral diversity in dogs with acute gastroenteritis from Brazilian Amazon.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {123}, number = {}, pages = {105637}, doi = {10.1016/j.meegid.2024.105637}, pmid = {38986824}, issn = {1567-7257}, mesh = {Dogs ; Animals ; *Gastroenteritis/virology/veterinary/epidemiology ; Brazil/epidemiology ; *Dog Diseases/virology/epidemiology ; *Phylogeny ; Norovirus/genetics/classification/isolation & purification ; Feces/virology ; Genome, Viral ; Genetic Variation ; Metagenomics/methods ; Viruses/classification/genetics/isolation & purification ; Virome ; }, abstract = {Viral gastroenteritis is commonly reported in dogs and involves a great diversity of enteric viruses. In this research, viral diversity was investigated in dogs with diarrhea in Northern Brazil using shotgun metagenomics. Furthermore, the presence of norovirus (NoV) was investigated in 282 stool/rectal swabs of young/adult dogs with or without diarrhea from two public kennels, based on one-step reverse transcription polymerase chain reaction (RT-PCR) for genogroup VI and VII (GVI and GVII) and real-time RT-PCR for GI, GII, and GIV. Thirty-one viral families were identified, including bacteriophages. Phylogenetic analyses showed twelve complete or nearly complete genomes belonging to the species of Protoparvovirus carnivoran1, Mamastrovirus 5, Aichivirus A2, Alphacoronavirus 1, and Chipapillomavirus 1. This is the first description of the intestinal virome of dogs in Northern Brazil and the first detection of canine norovirus GVII in the country. These results are important for helping to understand the viral groups that circulate in the canine population.}, } @article {pmid38986711, year = {2024}, author = {Zhang, Y and Chen, J and Du, M and Ruan, Y and Wang, Y and Guo, J and Yang, Q and Shao, R and Wang, H}, title = {Metagenomic insights into microbial variation and carbon cycling function in crop rotation systems.}, journal = {The Science of the total environment}, volume = {947}, number = {}, pages = {174529}, doi = {10.1016/j.scitotenv.2024.174529}, pmid = {38986711}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Carbon Cycle ; *Crops, Agricultural ; Microbiota ; Soil/chemistry ; Carbon/metabolism ; Agriculture/methods ; Bacteria/metabolism ; Metagenomics ; Triticum ; }, abstract = {The decomposition and utilization of plant-derived carbon by microorganisms and carbon fixation are crucial pathways for enhancing soil organic carbon (SOC) storage. However, a gap remains in our understanding of the impact of microorganisms on the decomposition of plant-derived carbon and their capacity for carbon fixation in crop rotation systems. Based on a 12-year experiment with wheat-maize (WM), wheat-cotton (WC), and wheat-soybean (WS) rotations, the microbial communities and carbon cycle function were investigated. The results indicated that WS rotation significantly increased SOC content compared to WM and WC. In addition, a significant increase was observed in microbially available carbon and microbial biomass carbon in the WS soil compared with those in the others. Further analysis of the microbial community factors that influenced SOC content revealed that WS rotation, in contrast to WM rotation, enhanced the diversity and richness of bacteria and fungi. Analysis of microbial carbon decomposition functions revealed an increase in starch, lignin, and hemicellulose decomposition genes in the WS soil compared to the others. The changes in carbon decomposition genes were primarily attributed to six bacterial genera, namely Nocardioides, Agromyces, Microvirga, Skermanella, Anaeromyxobacter, and Arthrobacter, as well as four fungal genera, namely Dendryphion, Staphylotrichum, Apiotrichum, and Abortiporus, which were significantly influenced by the crop rotation systems. In addition, microbial carbon fixation-related genes such as ACAT, IDH1, GAPDH, rpiA, and rbcS were significantly enriched in WS. Species annotation of differential carbon fixation genes identified 18 genera that play a role in soil carbon fixation variation within the crop rotation systems. This study highlights the impact of crop rotation systems on SOC content and alterations in specific microbial communities on carbon cycle function.}, } @article {pmid38986696, year = {2024}, author = {Pellegrinetti, TA and Cotta, SR and Feitosa, YB and Melo, PLA and Bieluczyk, W and Silva, AMM and Mendes, LW and Sarmento, H and Camargo, PB and Tsai, SM and Fiore, MF}, title = {The role of microbial communities in biogeochemical cycles and greenhouse gas emissions within tropical soda lakes.}, journal = {The Science of the total environment}, volume = {947}, number = {}, pages = {174646}, doi = {10.1016/j.scitotenv.2024.174646}, pmid = {38986696}, issn = {1879-1026}, mesh = {*Lakes/chemistry/microbiology ; *Greenhouse Gases/analysis ; Brazil ; *Microbiota ; *Methane/analysis ; Environmental Monitoring ; Wetlands ; Eutrophication ; Air Pollutants/analysis ; }, abstract = {Although anthropogenic activities are the primary drivers of increased greenhouse gas (GHG) emissions, it is crucial to acknowledge that wetlands are a significant source of these gases. Brazil's Pantanal, the largest tropical inland wetland, includes numerous lacustrine systems with freshwater and soda lakes. This study focuses on soda lakes to explore potential biogeochemical cycling and the contribution of biogenic GHG emissions from the water column, particularly methane. Both seasonal variations and the eutrophic status of each examined lake significantly influenced GHG emissions. Eutrophic turbid lakes (ET) showed remarkable methane emissions, likely due to cyanobacterial blooms. The decomposition of cyanobacterial cells, along with the influx of organic carbon through photosynthesis, accelerated the degradation of high organic matter content in the water column by the heterotrophic community. This process released byproducts that were subsequently metabolized in the sediment leading to methane production, more pronounced during periods of increased drought. In contrast, oligotrophic turbid lakes (OT) avoided methane emissions due to high sulfate levels in the water, though they did emit CO2 and N2O. Clear vegetated oligotrophic turbid lakes (CVO) also emitted methane, possibly from organic matter input during plant detritus decomposition, albeit at lower levels than ET. Over the years, a concerning trend has emerged in the Nhecolândia subregion of Brazil's Pantanal, where the prevalence of lakes with cyanobacterial blooms is increasing. This indicates the potential for these areas to become significant GHG emitters in the future. The study highlights the critical role of microbial communities in regulating GHG emissions in soda lakes, emphasizing their broader implications for global GHG inventories. Thus, it advocates for sustained research efforts and conservation initiatives in this environmentally critical habitat.}, } @article {pmid38986687, year = {2024}, author = {Wang, J and Shen, C and Sun, J and Cheng, L and Zhao, G and Li, MM}, title = {Metagenomic analysis reveals a dynamic rumen microbiome with diversified adaptive functions in response to dietary protein restriction and re-alimentation.}, journal = {The Science of the total environment}, volume = {949}, number = {}, pages = {174618}, doi = {10.1016/j.scitotenv.2024.174618}, pmid = {38986687}, issn = {1879-1026}, mesh = {*Rumen/microbiology/metabolism ; Animals ; *Animal Feed/analysis ; Gastrointestinal Microbiome ; Cattle ; Dietary Proteins/metabolism ; Fermentation ; Metagenomics ; Diet, Protein-Restricted ; Male ; Microbiota ; }, abstract = {Understanding the dynamics of the rumen microbiome is crucial for optimizing ruminal fermentation to improve feed efficiency and addressing concerns regarding antibiotic resistance in the livestock production industry. This study aimed to investigate the adaptive effects of microbiome and the properties of carbohydrate-active enzymes (CAZy) and antibiotic resistance genes (ARGs) in response to dietary protein shifts. Twelve Charolais bulls were randomly divided into two groups based on initial body weight: 1) Treatment (REC), where the animals received a 7 % CP diet in a 4-week restriction period, followed by a 13 % CP diet in a 2-week re-alimentation period; 2) Control (CON), where the animals were fed the 13 % CP diet both in the restriction period and the re-alimentation period. Protein restriction decreased the concentrations of acetate, propionate, isovalerate, glutamine, glutamate, and isoleucine (P < 0.05), while protein re-alimentation increased the concentrations of arginine, methionine sulfoxide, lysine, and glutamate (P < 0.05). Protein restriction decreased the relative abundances of Bacteroidota but increased Proteobacteria, with no difference observed after re-alimentation. Protein restriction decreased relative abundances of the genera Bacteroides, Prevotella, and Bifidobacterium. Following protein recovery, Escherichia was enriched in CON, while Pusillibacter was enriched in REC, indicating that distinct microbial adaptations to protein shifts. Protein restriction increased GH97 while reducing GH94 and GT35 compared to CON. Protein restriction decreased abundances of KO genes involved in VFA production pathways, while they were recovered in the re-alimentation period. Protein restriction reduced tet(W/32/O) abundances but increased those of tet(X), nimJ, and rpoB2. Following protein re-alimentation, there was a decrease in ErmQ and tet(W/N/W), and an increase in Mef(En2) compared to CON, highlighting the impact of dietary protein on the distribution of antibiotic-resistant bacteria. Overall, comprehensive metagenomic analysis reveals the dynamic adaptability of the microbiome in response to dietary shifts, indicating its capacity to modulate carbohydrate metabolism and ARGs in response to protein availability.}, } @article {pmid38986506, year = {2024}, author = {Popov, IV and Koopmans, B and Venema, K}, title = {Modulation of human gut microbiota by linear and branched fructooligosaccharides in an in vitro colon model (TIM-2).}, journal = {Journal of applied microbiology}, volume = {135}, number = {7}, pages = {}, doi = {10.1093/jambio/lxae170}, pmid = {38986506}, issn = {1365-2672}, support = {//Grassa/ ; HEFI-1//Dutch Province of Limburg/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects ; *Oligosaccharides/pharmacology/metabolism ; Humans ; *Bacteria/genetics/classification/metabolism/isolation & purification/drug effects ; *Colon/microbiology/metabolism ; *RNA, Ribosomal, 16S/genetics ; Lolium/microbiology ; Cichorium intybus ; Feces/microbiology ; }, abstract = {AIMS: This study aimed to compare the effects of linear and branched fructooligosaccharides (FOS) extracted from chicory and grass (Lolium perenne), respectively on human microbiota composition, diversity, and metabolism.

METHODS AND RESULTS: To test the effects of linear and branched FOS on human microbiota we used the artificial in vitro human colon model (TIM-2). Microbiota composition and diversity were assessed by V3-V4 16S rRNA metagenomic sequencing, followed by differential taxa abundance and alpha/beta diversity analyses. SCFA/BCFA production was evaluated by gas chromatography-mass spectrometry. As a result, branched FOS had the most beneficial effects on microbial diversity and metabolite production. Also, branched FOS significantly increased the abundance of commensal bacteria associated with maintaining healthy gut functions and controlling inflammation, such as Butyricicoccus, Erysipelotrichaceae, Phascolarctobacterium, and Sutterella. Linear FOS also significantly increased the abundance of some other commensal gut bacteria (Anaerobutyricum, Lachnospiraceae, Faecalibacterium), but there were no differences in diversity metrics compared to the control.

CONCLUSIONS: The study revealed that branched FOS had the most beneficial effects compared to the linear FOS in vitro, concerning microbiota modulation, and metabolite production, making this a good candidate for further studies in food biotechnology.}, } @article {pmid38986408, year = {2024}, author = {Xie, ST and Zhu, D and Song, YQ and Zhu, YG and Ding, LJ}, title = {Unveiling potential roles of earthworms in mitigating the presence of virulence factor genes in terrestrial ecosystems.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {135133}, doi = {10.1016/j.jhazmat.2024.135133}, pmid = {38986408}, issn = {1873-3336}, mesh = {*Oligochaeta/microbiology ; Animals ; *Virulence Factors/genetics ; *Soil Microbiology ; *Ecosystem ; Microbiota ; Bacteria/genetics/metabolism/pathogenicity ; }, abstract = {Earthworms can redistribute soil microbiota, and thus might affect the profile of virulence factor genes (VFGs) which are carried by pathogens in soils. Nevertheless, the knowledge of VFG profile in the earthworm guts and its interaction with earthworm gut microbiome is still lacking. Herein, we characterized earthworm gut and soil microbiome and VFG profiles in natural and agricultural ecosystems at a national scale using metagenomics. VFG profiles in the earthworm guts significantly differed from those in the surrounding soils, which was mainly driven by variations of bacterial communities. Furthermore, the total abundance of different types of VFGs in the earthworm guts was about 20-fold lower than that in the soils due to the dramatic decline (also by approximately 20-fold) of VFG-carrying bacterial pathogens in the earthworm guts. Additionally, five VFGs related to nutritional/metabolic factors and stress survival were identified as keystones merely in the microbe-VFG network in the earthworm guts, implying their pivotal roles in facilitating pathogen colonization in earthworm gut microhabitats. These findings suggest the potential roles of earthworms in reducing risks related to the presence of VFGs in soils, providing novel insights into earthworm-based bioremediation of VFG contamination in terrestrial ecosystems.}, } @article {pmid38986403, year = {2024}, author = {Jiang, Y and Zhou, C and Khan, A and Zhang, X and Mamtimin, T and Fan, J and Hou, X and Liu, P and Han, H and Li, X}, title = {Environmental risks of mask wastes binding pollutants: Phytotoxicity, microbial community, nitrogen and carbon cycles.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {135058}, doi = {10.1016/j.jhazmat.2024.135058}, pmid = {38986403}, issn = {1873-3336}, mesh = {*Soil Microbiology ; *Soil Pollutants/toxicity ; Nitrogen ; Carbon Cycle ; Microbiota/drug effects ; Bacteria/drug effects/genetics/metabolism ; Medicago sativa/drug effects ; }, abstract = {The increasing contamination of mask wastes presents a significant global challenge to ecological health. However, there is a lack of comprehensive understanding regarding the environmental risks that mask wastes pose to soil. In this study, a total of 12 mask wastes were collected from landfills. Mask wastes exhibited negligible morphological changes, and bound eight metals and four types of organic pollutants. Masks combined with pollutants inhibited the growth of alfalfa and Elymus nutans, reducing underground biomass by 84.6 %. Mask wastes decreased the Chao1 index and the relative abundances (RAs) of functional bacteria (Micrococcales, Gemmatimonadales, and Sphingomonadales). Metagenomic analysis showed that mask wastes diminished the RAs of functional genes associated with nitrification (amoABC and HAO), denitrification (nirKS and nosZ), glycolysis (gap2), and TCA cycle (aclAB and mdh), thereby inhibiting the nitrogen transformation and ATP production. Furthermore, some pathogenic viruses (Herpesviridae and Tunggulvirus) were also found on the mask wastes. Structural equation models demonstrated that mask wastes restrained soil enzyme activities, ultimately affecting nitrogen and carbon cycles. Collectively, these evidences indicate that mask wastes contribute to soil health and metabolic function disturbances. This study offers a new perspective on the potential environmental risks associated with the improper disposal of masks.}, } @article {pmid38984661, year = {2024}, author = {Zhao, JT and Zhang, Y and Wang, XW and Zou, PY and Zhao, Z and Mei, H and Liu, YX and Su, NY and Zhu, YJ and Wang, B and Wei, YL and Chen, DF and Lan, CH}, title = {Long-term effects of fecal microbiota transplantation on gut microbiota after Helicobacter pylori eradication with bismuth quadruple therapy: A randomized controlled trial.}, journal = {Helicobacter}, volume = {29}, number = {4}, pages = {e13079}, doi = {10.1111/hel.13079}, pmid = {38984661}, issn = {1523-5378}, support = {82072253//National Natural Science Foundation of China/ ; 2022jstg020//Chongqing Appropriate Health Technology Promotion/ ; }, mesh = {Humans ; *Helicobacter Infections/therapy/microbiology/drug therapy ; *Gastrointestinal Microbiome/drug effects ; *Fecal Microbiota Transplantation/methods ; Male ; Female ; Middle Aged ; *Helicobacter pylori/drug effects ; Adult ; *Anti-Bacterial Agents/therapeutic use ; Prospective Studies ; *Bismuth/therapeutic use ; Drug Therapy, Combination ; China ; Amoxicillin/therapeutic use ; Clarithromycin/therapeutic use ; Treatment Outcome ; Aged ; Feces/microbiology ; }, abstract = {BACKGROUND: Eradicating Helicobacter pylori infection by bismuth quadruple therapy (BQT) is effective. However, the effect of BQT and subsequent fecal microbiota transplant (FMT) on the gut microbiota is less known.

MATERIALS AND METHODS: This prospective randomized controlled trial was conducted at a tertiary hospital in China from January 2019 to October 2020, with the primary endpoints the effect of BQT on the gut microbiota and the effect of FMT on the gut microbiota after bismuth quadruple therapy eradication therapy. A 14-day BQT with amoxicillin and clarithromycin was administered to H. pylori-positive subjects, and after eradication therapy, patients received a one-time FMT or placebo treatment. We then collected stool samples to assess the effects of 14-day BQT and FMT on the gut microbiota. 16 s rDNA and metagenomic sequencing were used to analyze the structure and function of intestinal flora. We also used Gastrointestinal Symptom Rating Scale (GSRS) to evaluate gastrointestinal symptom during treatment.

RESULTS: A total of 30 patients were recruited and 15 were assigned to either FMT or placebo groups. After eradication therapy, alpha-diversity was decreased in both groups. At the phylum level, the abundance of Bacteroidetes and Firmicutes decreased, while Proteobacteria increased. At the genus level, the abundance of beneficial bacteria decreased, while pathogenic bacteria increased. Eradication therapy reduced some resistance genes abundance while increased the resistance genes abundance linked to Escherichia coli. While they all returned to baseline by Week 10. Besides, the difference was observed in Week 10 by the diarrhea score between two groups. Compared to Week 2, the GSRS total score and diarrhea score decreased in Week 3 only in FMT group.

CONCLUSIONS: The balance of intestinal flora in patients can be considerably impacted by BQT in the short term, but it has reverted back to baseline by Week 10. FMT can alleviate gastrointestinal symptoms even if there was no evidence it promoted restoration of intestinal flora.}, } @article {pmid38983956, year = {2024}, author = {Jin, LX and Fang, YP and Xia, CM and Cai, TW and Li, QQ and Wang, YY and Yan, HF and Chen, X}, title = {Helicobacter pylori infection alters gastric microbiota structure and biological functions in patients with gastric ulcer or duodenal ulcer.}, journal = {World journal of gastroenterology}, volume = {30}, number = {24}, pages = {3076-3085}, pmid = {38983956}, issn = {2219-2840}, mesh = {Humans ; *Helicobacter Infections/microbiology ; *Helicobacter pylori/isolation & purification/genetics ; *Duodenal Ulcer/microbiology/diagnosis ; Male ; Female ; Middle Aged ; *Gastric Mucosa/microbiology/pathology ; *Gastrointestinal Microbiome ; *Stomach Ulcer/microbiology ; Adult ; Case-Control Studies ; Aged ; Metagenomics/methods ; Duodenum/microbiology ; Dysbiosis/microbiology ; }, abstract = {BACKGROUND: Helicobacter pylori (H. pylori) infection is closely associated with gastrointestinal diseases. Our preliminary studies have indicated that H. pylori infection had a significant impact on the mucosal microbiome structure in patients with gastric ulcer (GU) or duodenal ulcer (DU).

AIM: To investigate the contributions of H. pylori infection and the mucosal microbiome to the pathogenesis and progression of ulcerative diseases.

METHODS: Patients with H. pylori infection and either GU or DU, and healthy individuals without H. pylori infection were included. Gastric or duodenal mucosal samples was obtained and subjected to metagenomic sequencing. The compositions of the microbial communities and their metabolic functions in the mucosal tissues were analyzed.

RESULTS: Compared with that in the healthy individuals, the gastric mucosal microbiota in the H. pylori-positive patients with GU was dominated by H. pylori, with significantly reduced biodiversity. The intergroup differential functions, which were enriched in the H. pylori-positive GU patients, were all derived from H. pylori, particularly those concerning transfer RNA queuosine-modification and the synthesis of demethylmenaquinones or menaquinones. A significant enrichment of the uibE gene was detected in the synthesis pathway. There was no significant difference in microbial diversity between the H. pylori-positive DU patients and healthy controls.

CONCLUSION: H. pylori infection significantly alters the gastric microbiota structure, diversity, and biological functions, which may be important contributing factors for GU.}, } @article {pmid38982915, year = {2024}, author = {Wang, M and Li, H and Liu, C and Zhang, Y and Wu, Q and Yang, Y}, title = {Lingguizhugan Decoction Improved Obesity by Modulating the Gut Microbiota and its Metabolites in Mice.}, journal = {Current drug metabolism}, volume = {25}, number = {4}, pages = {276-287}, pmid = {38982915}, issn = {1875-5453}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Obesity/drug therapy/metabolism/microbiology ; *Drugs, Chinese Herbal/pharmacology ; Mice ; Male ; Mice, Inbred C57BL ; Anti-Obesity Agents/pharmacology ; Feces/microbiology ; Mice, Obese ; Metabolomics ; Plant Extracts ; }, abstract = {BACKGROUND: The global obese population is rapidly increasing, urgently requiring the development of effective and safe weight-loss medications. The classic Chinese medicine formulation Lingguizhugan Decoction has exerted a significant anti-obesity effect. However, the underlying mechanism is still unclear.

OBJECTIVE: This study aimed to explore the mechanism of LGZGD in the treatment of obesity based on the gut microbiota and its metabolites.

METHODS: Three different dosages of LGZGD were gavaged to ob/ob mice for 8 weeks. Body mass and visceral fat mass were evaluated. Additionally, the changes in gut microbiota, fecal and plasma metabolites in mice after LGZGD treatment were analyzed by metagenomics and non-targeted metabolomics.

RESULTS: The results demonstrated a significant anti-obesity effect of LGZGD treatment in ob/ob mice. Furthermore, the metagenomic analysis revealed that LGZGD reduced the ratio of Firmicutes / Bacteroidetes (F to B) in the gut, restored gut microbiota diversity, and identified 3 enriched KEGG pathways, including energy metabolism, lipid metabolism, and energy production and conversion pathways. Based on non-targeted metabolomics analysis, 20 key metabolites in the feces and 30 key metabolites in the plasma responding to LGZGD treatment were identified, and the levels of Eicosapentaenoic acid (EPA) and Myristoleic acid (MA) might be the metabolites related to gut microbiota after LGZGD treatment. Their biological functions were mainly related to the metabolism pathway.

CONCLUSIONS: These findings suggested that LGZGD had therapeutic potential for obesity. The mechanism of LGZGD alleviating obesity was associated with improving dysbiosis of the gut microbiota. LDZGD affected gut microbiota-derived metabolites of EPA and MA and may act on energy metabolism pathways.}, } @article {pmid38982403, year = {2024}, author = {Yao, G and Zhao, Z and Yang, C and Zuo, B and Sun, Z and Wang, J and Zhang, H}, title = {Evaluating the probiotic effects of spraying lactiplantibacillus plantarum P-8 in neonatal piglets.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {253}, pmid = {38982403}, issn = {1471-2180}, support = {2021ZD0014//Inner Mongolia Science and Technology Major Project/ ; 2019CG027//Inner Mongolia Autonomous Region Science and Technology Achievement Transformation Project/ ; }, mesh = {Animals ; *Probiotics/administration & dosage/pharmacology ; Swine ; *Animals, Newborn ; *Gastrointestinal Microbiome/drug effects ; Lactobacillus plantarum ; Fermentation ; Antioxidants/metabolism/administration & dosage/pharmacology ; Feces/microbiology ; }, abstract = {BACKGROUND: Gut microbes play an important role in the growth and health of neonatal piglets. Probiotics can promote the healthy growth of neonatal piglets by regulating their gut microbes. The study investigated the effects of spraying Lactiplantibacillus plantarum P-8 (L. plantarum P-8) fermentation broth on the growth performance and gut microbes of neonatal piglets.

RESULTS: The animals were randomly divided into probiotics groups (109 neonatal piglets) and control groups (113 neonatal piglets). The probiotics group was sprayed with L. plantarum P-8 fermented liquid from 3 day before the expected date of the sow to the 7-day-old of piglets, while the control group was sprayed with equal dose of PBS. Average daily gain (ADG), immune and antioxidant status and metagenome sequencing were used to assess the changes in growth performance and gut microbiota of neonatal piglets. The results showed that L. plantarum P-8 treatment significantly improved the average daily gain (P < 0.05) of neonatal piglets. L. plantarum P-8 increased the activities of CAT and SOD but reduced the levels of IL-2 and IL-6, effectively regulating the antioxidant capacity and immunity in neonatal piglets. L. plantarum P-8 adjusted the overall structure of gut microflora improving gut homeostasis to a certain extent, and significantly increased the relative abundance of gut beneficial bacteria such as L. mucosae and L. plantarum.

CONCLUSION: Spraying L. plantarum P-8 can be a feasible and effective probiotic intervention not only improving the growth of neonatal piglets, regulating the antioxidant capacity and immunity of neonatal piglets, but also improving the gut homeostasis to a certain extent.}, } @article {pmid38981836, year = {2024}, author = {Núñez-Montero, K and Leal, K and Rojas-Villalta, D and Castro, M and Larronde, C and Wagenknecht, L and Contreras, MJ}, title = {16s gene metagenomic characterization in healthy stallion semen.}, journal = {Research in veterinary science}, volume = {176}, number = {}, pages = {105354}, doi = {10.1016/j.rvsc.2024.105354}, pmid = {38981836}, issn = {1532-2661}, mesh = {Animals ; Horses/microbiology ; Male ; *Semen/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/isolation & purification ; Metagenomics ; Microbiota ; DNA, Bacterial/genetics ; }, abstract = {Studies on the bacterial composition of seminal samples have primarily focused on species isolated from semen and their effects on fertility and reproductive health. Culture-independent techniques, such as 16S rRNA gene sequencing and shotgun metagenomics, have revolutionized our ability to identify unculturable bacteria, which comprise >90% of the microbiome. These techniques allow for comprehensive analysis of microbial communities in seminal samples, shedding light on their interactions and roles. In this study, we characterized the taxonomic diversity of seminal microbial communities in healthy stallions using 16S rRNA gene sequencing. Semen samples were collected from four stallions during the reproductive season, and DNA was extracted for sequencing. The results revealed a diverse array of bacterial taxa, with Firmicutes, Bacteroidota, and Proteobacteria being predominant phyla. At the family and genus levels, significant variations were observed among individuals, with individual variability in microbial richness and diversity standing out. Moreover, each stallion showed a distinct microbial fingerprint, indicating the presence of a characteristic microbial core for each stallion. These results underscore the importance of considering individual microbial profiles in understanding reproductive health and fertility outcomes.}, } @article {pmid38981540, year = {2024}, author = {Funnicelli, MIG and de Carvalho, LAL and Teheran-Sierra, LG and Dibelli, SC and Lemos, EGM and Pinheiro, DG}, title = {Unveiling genomic features linked to traits of plant growth-promoting bacterial communities from sugarcane.}, journal = {The Science of the total environment}, volume = {947}, number = {}, pages = {174577}, doi = {10.1016/j.scitotenv.2024.174577}, pmid = {38981540}, issn = {1879-1026}, mesh = {*Saccharum/microbiology ; *Bacteria/genetics/classification ; Microbiota/genetics ; Metagenome ; Genome, Bacterial ; Plant Development ; }, abstract = {Microorganisms are ubiquitous, and those inhabiting plants have been the subject of several studies. Plant-associated bacteria exhibit various biological mechanisms that enable them to colonize host plants and, in some cases, enhance their fitness. In this study, we describe the genomic features predicted to be associated with plant growth-promoting traits in six bacterial communities isolated from sugarcane. The use of highly accurate single-molecule real-time sequencing technology for metagenomic samples from these bacterial communities allowed us to recover 17 genomes. The taxonomic assignments for the binned genomes were performed, revealing taxa distributed across three main phyla: Bacillota, Bacteroidota, and Pseudomonadota, with the latter being the most representative. Subsequently, we functionally annotated the metagenome-assembled genomes (MAGs) to characterize their metabolic pathways related to plant growth-promoting traits. Our study successfully identified the enrichment of important functions related to phosphate and potassium acquisition, modulation of phytohormones, and mechanisms for coping with abiotic stress. These findings could be linked to the robust colonization of these sugarcane endophytes.}, } @article {pmid38981480, year = {2024}, author = {Piperni, E and Nguyen, LH and Manghi, P and Kim, H and Pasolli, E and Andreu-Sánchez, S and Arrè, A and Bermingham, KM and Blanco-Míguez, A and Manara, S and Valles-Colomer, M and Bakker, E and Busonero, F and Davies, R and Fiorillo, E and Giordano, F and Hadjigeorgiou, G and Leeming, ER and Lobina, M and Masala, M and Maschio, A and McIver, LJ and Pala, M and Pitzalis, M and Wolf, J and Fu, J and Zhernakova, A and Cacciò, SM and Cucca, F and Berry, SE and Ercolini, D and Chan, AT and Huttenhower, C and Spector, TD and Segata, N and Asnicar, F}, title = {Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries.}, journal = {Cell}, volume = {187}, number = {17}, pages = {4554-4570.e18}, doi = {10.1016/j.cell.2024.06.018}, pmid = {38981480}, issn = {1097-4172}, mesh = {Humans ; *Blastocystis/metabolism ; *Gastrointestinal Microbiome ; *Diet ; Male ; *Obesity ; Female ; Blastocystis Infections ; Adult ; Middle Aged ; Intestines/parasitology/microbiology ; Cardiovascular Diseases/prevention & control ; Metagenome ; }, abstract = {Diet impacts human health, influencing body adiposity and the risk of developing cardiometabolic diseases. The gut microbiome is a key player in the diet-health axis, but while its bacterial fraction is widely studied, the role of micro-eukaryotes, including Blastocystis, is underexplored. We performed a global-scale analysis on 56,989 metagenomes and showed that human Blastocystis exhibits distinct prevalence patterns linked to geography, lifestyle, and dietary habits. Blastocystis presence defined a specific bacterial signature and was positively associated with more favorable cardiometabolic profiles and negatively with obesity (p < 1e-16) and disorders linked to altered gut ecology (p < 1e-8). In a diet intervention study involving 1,124 individuals, improvements in dietary quality were linked to weight loss and increases in Blastocystis prevalence (p = 0.003) and abundance (p < 1e-7). Our findings suggest a potentially beneficial role for Blastocystis, which may help explain personalized host responses to diet and downstream disease etiopathogenesis.}, } @article {pmid38981389, year = {2024}, author = {Li, W and Wang, Y and Gao, J and Wang, A}, title = {Antimicrobial resistance and its risks evaluation in wetlands on the Qinghai-Tibetan Plateau.}, journal = {Ecotoxicology and environmental safety}, volume = {282}, number = {}, pages = {116699}, doi = {10.1016/j.ecoenv.2024.116699}, pmid = {38981389}, issn = {1090-2414}, mesh = {*Wetlands ; Risk Assessment ; Tibet ; Drug Resistance, Microbial/genetics ; Microbiota/drug effects ; Drug Resistance, Bacterial/genetics ; China ; Bacteria/genetics/drug effects/classification ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Environmental Monitoring ; Interspersed Repetitive Sequences ; }, abstract = {Amidst the global antimicrobial resistance (AMR) crisis, antibiotic resistance has permeated even the most remote environments. To understand the dissemination and evolution of AMR in minimally impacted ecosystems, the resistome and mobilome of wetlands across the Qinghai-Tibetan Plateau and its marginal regions were scrutinized using metagenomic sequencing techniques. The composition of wetland microbiomes exhibits significant variability, with dominant phyla including Proteobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia. Notably, a substantial abundance of Antibiotic Resistance Genes (ARGs) and Mobile Genetic Elements (MGEs) was detected, encompassing 17 ARG types, 132 ARG subtypes, and 5 types of MGEs (Insertion Sequences, Insertions Sequences, Genomic Islands, Transposons, and Integrative Conjugative Elements). No significant variance was observed in the prevalence of resistome and mobilome across different wetland types (i.e., the Yellow River, other rivers, lakes, and marshes) (R=-0.5882, P=0.607). The co-occurrence of 74 ARG subtypes and 22 MGEs was identified, underscoring the pivotal role of MGEs in shaping ARG pools within the Qinghai-Tibetan Plateau wetlands. Metagenomic binning and analysis of assembled genomes (MAGs) revealed that 93 out of 206 MAGs harbored ARGs (45.15 %). Predominantly, Burkholderiales, Pseudomonadales, and Enterobacterales were identified as the primary hosts of these ARGs, many of which represent novel species. Notably, a substantial proportion of ARG-carrying MAGs also contained MGEs, reaffirming the significance of MGEs in AMR dissemination. Furthermore, utilizing the arg_ranker framework for risk assessment unveiled severe contamination of high-risk ARGs across most plateau wetlands. Moreover, some prevalent human pathogens were identified as potential hosts for these high-risk ARGs, posing substantial transmission risks. This study aims to investigate the prevalence of resistome and mobilome in wetlands, along with evaluating the risk posed by high-risk ARGs. Such insights are crucial for informing environmental protection strategies and facilitating the management of water resources on the Qinghai-Tibetan Plateau.}, } @article {pmid38981230, year = {2024}, author = {Tang, X and Chen, Y and Zheng, W and Chen, L and Liu, H and Li, M and Yang, Y}, title = {Enhancing neonicotinoid removal in recirculating constructed wetlands: The impact of Fe/Mn biochar and microbial interactions.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {135139}, doi = {10.1016/j.jhazmat.2024.135139}, pmid = {38981230}, issn = {1873-3336}, mesh = {*Wetlands ; *Charcoal/chemistry ; *Water Pollutants, Chemical/metabolism ; *Neonicotinoids/chemistry/metabolism ; *Biodegradation, Environmental ; *Iron/chemistry ; Manganese ; Wastewater/chemistry ; Nitrogen/metabolism ; Microbiota ; Phosphorus/chemistry ; Bacteria/genetics/metabolism ; Adsorption ; Insecticides/metabolism ; Waste Disposal, Fluid/methods ; Nitro Compounds ; }, abstract = {Neonicotinoids pose significant environmental risks due to their widespread use, persistence, and challenges in elimination. This study explores the effectiveness of Fe/Mn biochar in enhancing the removal efficiency of neonicotinoids in recirculating constructed wetlands (RCWs). Results demonstrated that incorporating Fe/Mn biochar into RCWs significantly improved the removal of COD, NH4[+]-N, TN, TP, imidacloprid (IMI), and acetamiprid (ACE). However, the simultaneous presence of IMI and ACE in the RCWs hindered the elimination of NH4[+]-N, TN, and TP from wastewater. The enhanced removal of nutrients and pollutants by Fe/Mn biochar was attributed to its promotion of carbon, nitrogen, and phosphorus cycling in RCWs, along with its facilitation of the adsorption and biodegradation of IMI and ACE. Metagenomics analysis demonstrated that Fe/Mn biochar altered the structure and diversity of microbial communities in RCWs. A total of 17 biodegradation genes (BDGs) and two pesticide degradation genes (PDGs) were identified within RCWs, with Fe/Mn biochar significantly increasing the abundance of BDGs such as cytochrome P450. The potential host genera for these BDGs/PDGs were identified as Betaproteobacteria, Acidobacteria, Nitrospiraceae, Gemmatimonadetes, and Bacillus. This study offers valuable insights into how Fe/Mn biochar enhances pesticide removal and its potential application in constructed wetland systems for treating pesticide-contaminated wastewater.}, } @article {pmid38980275, year = {2024}, author = {Li, Y and Peng, J and Meng, X}, title = {Gut bacteria, host immunity, and colorectal cancer: From pathogenesis to therapy.}, journal = {European journal of immunology}, volume = {54}, number = {10}, pages = {e2451022}, doi = {10.1002/eji.202451022}, pmid = {38980275}, issn = {1521-4141}, support = {81872419//National Natural Science Foundation of China/ ; 82102949//National Natural Science Foundation of China/ ; 82003167//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Colorectal Neoplasms/immunology/therapy/microbiology ; *Gastrointestinal Microbiome/immunology ; Animals ; *Dysbiosis/immunology ; Tumor Microenvironment/immunology ; Immunity, Innate ; Adaptive Immunity ; }, abstract = {The emergence of 16S rRNA and metagenomic sequencing has gradually revealed the close relationship between dysbiosis and colorectal cancer (CRC). Recent studies have confirmed that intestinal dysbiosis plays various roles in the occurrence, development, and therapeutic response of CRC. Perturbation of host immunity is one of the key mechanisms involved. The intestinal microbiota, or specific bacteria and their metabolites, can modulate the progression of CRC through pathogen recognition receptor signaling or via the recruitment, polarization, and activation of both innate and adaptive immune cells to reshape the protumor/antitumor microenvironment. Therefore, the administration of gut bacteria to enhance immune homeostasis represents a new strategy for the treatment of CRC. In this review, we cover recent studies that illuminate the role of gut bacteria in the progression and treatment of CRC through orchestrating the immune response, which potentially offers insights for subsequent transformative research.}, } @article {pmid38980075, year = {2024}, author = {Feng, Z and Zhu, J and Zhang, L and Li, C and Su, D and Wang, H and Yu, Y and Song, L}, title = {Microbiological and functional traits of peri-implant mucositis and correlation with disease severity.}, journal = {mSphere}, volume = {9}, number = {7}, pages = {e0005924}, pmid = {38980075}, issn = {2379-5042}, support = {82170990, 81870793//MOST | National Natural Science Foundation of China (NSFC)/ ; 2020MZYS08//high-level professional physician training program of Minhang District/ ; }, mesh = {Humans ; Male ; Middle Aged ; Female ; *Bacteria/classification/isolation & purification/genetics ; *Dental Implants/microbiology/adverse effects ; *Microbiota ; Adult ; *Dysbiosis/microbiology ; Severity of Illness Index ; Aged ; Gingivitis/microbiology ; Peri-Implantitis/microbiology ; Mucositis/microbiology ; Stomatitis/microbiology/etiology ; Metagenome ; Biofilms/growth & development ; }, abstract = {Osseointegrated dental implants replace missing teeth and create an artificial surface for biofilms of complex microbial communities to grow. These biofilms on implants and dental surfaces can trigger infection and inflammation in the surrounding tissue. This study investigated the microbial characteristics of peri-implant mucositis (PM) and explored the correlation between microbial ecological imbalance, community function, and disease severity by comparing the submucosal microflora from PM with those of healthy inter-subject implants and intra-subject gingivitis (G) within a group of 32 individuals. We analyzed submucosal plaques from PM, healthy implant (HI), and G sites using metagenome shotgun sequencing. The bacterial diversity of HIs was higher than that of PM, according to the Simpson index. Beta diversity revealed differences in taxonomic and functional compositions across the groups. Linear discriminant analysis of the effect size identified 15 genera and 37 species as biomarkers that distinguished PM from HIs. Pathways involving cell motility and protein processing in the endoplasmic reticulum were upregulated in PM, while pathways related to the metabolism of cofactors and vitamins were downregulated. Microbial dysbiosis correlated positively with the severity of clinical inflammation measured by the sulcus bleeding index (SBI) in PM. Prevotella and protein processing in the endoplasmic reticulum also correlated positively with the SBI. Our study revealed PM's microbiological and functional traits and suggested the importance of certain functions in disease severity.IMPORTANCEPeri-implant mucositis is an early stage in the progression of peri-implantitis. The high prevalence of it has been a threat to the widespread use of implant prosthodontics. The link between the submucosal microbiome and peri-implant mucositis was demonstrated previously. Nevertheless, the taxonomic and functional composition of the peri-implant mucositis microbiome remains controversial. In this study, we comprehensively characterize the microbial signature of peri-implant mucositis and for the first time, we investigate the correlations between microbial dysbiosis, functional potential, and disease severity. With the help of metagenomic sequencing, we find the positive correlations between microbial dysbiosis, genus Prevotella, pathway of protein processing in the endoplasmic reticulum, and more severe mucosal bleeding in the peri-implant mucositis. Our studies offer insight into the pathogenesis of peri-implant mucositis by providing information on the relationships between community function and disease severity.}, } @article {pmid38980054, year = {2024}, author = {Duller, S and Kumpitsch, C and Moissl-Eichinger, C and Wink, L and Koskinen Mora, K and Mahnert, A}, title = {In-hospital areas with distinct maintenance and staff/patient traffic have specific microbiome profiles, functions, and resistomes.}, journal = {mSystems}, volume = {9}, number = {8}, pages = {e0072624}, pmid = {38980054}, issn = {2379-5077}, support = {//Medizinische Universität Wien (MediUni Wien)/ ; }, mesh = {Humans ; *Microbiota/drug effects/genetics ; Hospitals ; Cross Infection/microbiology ; Bacteria/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Plasmids/genetics ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {UNLABELLED: Hospitals are subject to strict microbial control. Stringent cleaning and confinement measures in hospitals lead to a decrease in microbial diversity, but an increase in resistance genes. Given the rise of antimicrobial resistances and healthcare-associated infections, understanding the hospital microbiome and its resistome is crucial. This study compared the microbiome and resistome at different levels of confinement (CL) within a single hospital. Using amplicon sequencing, shotgun metagenomics, and genome/plasmid reconstruction, we demonstrate that microbial composition differs in a stable way between the CLs and that the most restrictive confinement level CL1 had the lowest microbial but the highest functional diversity. This CL also exhibited a greater abundance of functions related to virulence, disease, defense, and stress response. Comparison of antibiotic resistance also showed differences among CLs in terms of the selection process and specific mechanisms for antimicrobial/antibiotic resistance. The resistances found in the samples of CL1 were mostly mediated via antibiotic efflux pumps and were mainly located on chromosomes, whereas in the other, less restrictive CL antibiotic resistances were more present on plasmids. This could be of particular importance for patient-related areas (CL2), as the potential spread of antibiotic resistances could be a major concern in this area. Our results show that there are differences in the microbiome and resistome even within a single hospital, reflecting room utilization and confinement. Since restrictive confinement selects for resistant microorganisms, strategies are required to deepen our understanding of dynamic processes of microbiome and resistome within hospital environments.

IMPORTANCE: Effective measures to combat antibiotic resistances and healthcare-associated infections are urgently needed, including optimization of microbial control. However, previous studies have indicated that stringent control can lead to an increase in the resistance capacities of microbiomes on surfaces. This study adds to previous knowledge by focusing on the conditions in a single hospital, resolving the microbiomes and their resistomes in three different confinement levels (CL): operating room, patient-related areas, and non-patient-related areas. We were able to identify stable key taxa; profiled the capacities of taxa, functions, and antimicrobial resistances (AMR); and reconstruct genomes and plasmids in each CL. Our results show that the most restrictive CL indeed had the highest functional diversity, but that resistances were mostly encoded on chromosomes, indicating a lower possibility of resistance spread. However, clever strategies are still required to strike a balance between microbial control and selective pressures in environments where patients need protection.}, } @article {pmid38980053, year = {2024}, author = {Sanguineti, D and Zampieri, G and Treu, L and Campanaro, S}, title = {Metapresence: a tool for accurate species detection in metagenomics based on the genome-wide distribution of mapping reads.}, journal = {mSystems}, volume = {9}, number = {8}, pages = {e0021324}, pmid = {38980053}, issn = {2379-5077}, mesh = {*Metagenomics/methods ; Humans ; *Metagenome/genetics ; Gastrointestinal Microbiome/genetics ; Genome, Bacterial/genetics ; Software ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {Shotgun metagenomics allows comprehensive sampling of the genomic information of microbes in a given environment and is a tool of choice for studying complex microbial systems. Mapping sequencing reads against a set of reference or metagenome-assembled genomes is in principle a simple and powerful approach to define the species-level composition of the microbial community under investigation. However, despite the widespread use of this approach, there is no established way to properly interpret the alignment results, with arbitrary relative abundance thresholds being routinely used to discriminate between present and absent species. Such an approach can be affected by significant biases, especially in the identification of rare species. Therefore, it is important to develop new metrics to overcome these biases. Here, we present Metapresence, a new tool to perform reliable identification of the species in metagenomic samples based on the distribution of mapped reads on the reference genomes. The analysis is based on two metrics describing the breadth of coverage and the genomic distance between consecutive reads. We demonstrate the high precision and wide applicability of the tool using data from various synthetic communities, a real mock community, and the gut microbiome of healthy individuals and antibiotic-associated-diarrhea patients. Overall, our results suggest that the proposed approach has a robust performance in hard-to-analyze microbial communities containing contaminated or closely related genomes in low abundance.IMPORTANCEDespite the prevalent use of genome-centric alignment-based methods to characterize microbial community composition, there lacks a standardized approach for accurately identifying the species within a sample. Currently, arbitrary relative abundance thresholds are commonly employed for this purpose. However, due to the inherent complexity of genome structure and biases associated with genome-centric approaches, this practice tends to be imprecise. Notably, it introduces significant biases, particularly in the identification of rare species. The method presented here addresses these limitations and contributes significantly to overcoming inaccuracies in precisely defining community composition, especially when dealing with rare members.}, } @article {pmid38980052, year = {2024}, author = {Flinkstrom, Z and Bryson, S and Candry, P and Winkler, M-KH}, title = {Metagenomic clustering links specific metabolic functions to globally relevant ecosystems.}, journal = {mSystems}, volume = {9}, number = {8}, pages = {e0057324}, pmid = {38980052}, issn = {2379-5077}, support = {DE-SC0020356//U.S. Department of Energy (DOE)/ ; }, mesh = {*Metagenomics/methods ; *Metagenome/genetics ; Ecosystem ; Cluster Analysis ; Microbiota/genetics ; }, abstract = {UNLABELLED: Metagenomic sequencing has advanced our understanding of biogeochemical processes by providing an unprecedented view into the microbial composition of different ecosystems. While the amount of metagenomic data has grown rapidly, simple-to-use methods to analyze and compare across studies have lagged behind. Thus, tools expressing the metabolic traits of a community are needed to broaden the utility of existing data. Gene abundance profiles are a relatively low-dimensional embedding of a metagenome's functional potential and are, thus, tractable for comparison across many samples. Here, we compare the abundance of KEGG Ortholog Groups (KOs) from 6,539 metagenomes from the Joint Genome Institute's Integrated Microbial Genomes and Metagenomes (JGI IMG/M) database. We find that samples cluster into terrestrial, aquatic, and anaerobic ecosystems with marker KOs reflecting adaptations to these environments. For instance, functional clusters were differentiated by the metabolism of antibiotics, photosynthesis, methanogenesis, and surprisingly GC content. Using this functional gene approach, we reveal the broad-scale patterns shaping microbial communities and demonstrate the utility of ortholog abundance profiles for representing a rapidly expanding body of metagenomic data.

IMPORTANCE: Metagenomics, or the sequencing of DNA from complex microbiomes, provides a view into the microbial composition of different environments. Metagenome databases were created to compile sequencing data across studies, but it remains challenging to compare and gain insight from these large data sets. Consequently, there is a need to develop accessible approaches to extract knowledge across metagenomes. The abundance of different orthologs (i.e., genes that perform a similar function across species) provides a simplified representation of a metagenome's metabolic potential that can easily be compared with others. In this study, we cluster the ortholog abundance profiles of thousands of metagenomes from diverse environments and uncover the traits that distinguish them. This work provides a simple to use framework for functional comparison and advances our understanding of how the environment shapes microbial communities.}, } @article {pmid38980039, year = {2024}, author = {Su, L and Marshall, IPG and Teske, AP and Yao, H and Li, J}, title = {Genomic characterization of the bacterial phylum Candidatus Effluviviacota, a cosmopolitan member of the global seep microbiome.}, journal = {mBio}, volume = {15}, number = {8}, pages = {e0099224}, pmid = {38980039}, issn = {2150-7511}, support = {42072333//MOST | National Natural Science Foundation of China (NSFC)/ ; 2021YFF0501301//MOST | National Key Research and Development Program of China (NKPs)/ ; //Shanghai Pilot Program for Basic Research/ ; OCE-0647633//NSF-OCE/ ; }, mesh = {*Phylogeny ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Microbiota/genetics ; *Genome, Bacterial ; *Geologic Sediments/microbiology ; *Metagenome ; Seawater/microbiology ; Metagenomics ; }, abstract = {UNLABELLED: The microbial communities of marine seep sediments contain unexplored physiological and phylogenetic diversity. Here, we examined 30 bacterial metagenome-assembled genomes (MAGs) from cold seeps in the South China Sea, the Indian Ocean, the Scotian Basin, and the Gulf of Mexico, as well as from deep-sea hydrothermal sediments in the Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct phylum-level bacterial lineage, which we propose as a new phylum, Candidatus Effluviviacota, in reference to its preferential occurrence at diverse seep areas. Based on tightly clustered high-quality MAGs, we propose two new genus-level candidatus taxa, Candidatus Effluvivivax and Candidatus Effluvibates. Genomic content analyses indicate that Candidatus Effluviviacota are chemoheterotrophs that harbor the Embden-Meyerhof-Parnas glycolysis pathway. They gain energy by fermenting organic substrates. Additionally, they display potential capabilities for the degradation of cellulose, hemicellulose, starch, xylan, and various peptides. Extracellular anaerobic respiration appears to rely on metals as electron acceptors, with electron transfer primarily mediated by multiheme cytochromes and by a flavin-based extracellular electron transfer (EET) mechanism that involves NADH-quinone oxidoreductase-demethylmenaquinone-synthesizing enzymes, uncharacterized membrane proteins, and flavin-binding proteins, also known as the NUO-DMK-EET-FMN complex. The heterogeneity within the Ca. Effluviviacota phylum suggests varying roles in energy metabolism among different genera. While NUO-DMK-EET-FMN electron transfer has been reported predominantly in Gram-positive bacteria, it is now identified in Ca. Effluviviacota as well. We detected the presence of genes associated with bacterial microcompartments in Ca. Effluviviacota, which can promote specific metabolic processes and protect the cytosol from toxic intermediates.

IMPORTANCE: The newly discovered bacterial phylum Candidatus Effluviviacota is widespread across diverse seepage ecosystems, marine environments, and freshwater environments, with a notable preference for cold seeps. While maintaining an average abundance of approximately 1% in the global gene catalog of cold seep habitats, it has not hitherto been characterized. The metabolic versatility of Ca. Effluviviacota in anaerobic carbon, hydrogen, and metal cycling aligns with its prevalence in anoxic niches, with a preference for cold seep environments. Variations in metabolic potential between Ca. Effluvivivax and Ca. Effluvibates may contribute to shaping their respective habitat distributions.}, } @article {pmid38980017, year = {2024}, author = {Haghani, NB and Lampe, RH and Samuel, BS and Chalasani, SH and Matty, MA}, title = {Identification and characterization of a skin microbiome on Caenorhabditis elegans suggests environmental microbes confer cuticle protection.}, journal = {Microbiology spectrum}, volume = {12}, number = {8}, pages = {e0016924}, pmid = {38980017}, issn = {2165-0497}, support = {80NSSC22K0250//National Aeronautics and Space Administration (NASA)/ ; P40 OD010440/OD/NIH HHS/United States ; DP2DK116645//HHS | National Institutes of Health (NIH)/ ; R01 MH096881/MH/NIMH NIH HHS/United States ; R01MH096881//HHS | National Institutes of Health (NIH)/ ; CSP-503338//U.S. Department of Energy (DOE)/ ; DP2 DK116645/DK/NIDDK NIH HHS/United States ; 2011023//National Science Foundation (NSF)/ ; }, mesh = {Animals ; *Caenorhabditis elegans/microbiology ; *Microbiota/genetics ; *Skin/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; }, abstract = {UNLABELLED: In the wild, C. elegans are emersed in environments teeming with a veritable menagerie of microorganisms. The C. elegans cuticular surface serves as a barrier and first point of contact with their microbial environments. In this study, we identify microbes from C. elegans natural habitats that associate with its cuticle, constituting a simple "skin microbiome." We rear our animals on a modified CeMbio, mCeMbio, a consortium of ecologically relevant microbes. We first combine standard microbiological methods with an adapted micro skin-swabbing tool to describe the skin-resident bacteria on the C. elegans surface. Furthermore, we conduct 16S rRNA gene sequencing studies to identify relative shifts in the proportion of mCeMbio bacteria upon surface-sterilization, implying distinct skin- and gut-microbiomes. We find that some strains of bacteria, including Enterobacter sp. JUb101, are primarily found on the nematode skin, while others like Stenotrophomonas indicatrix JUb19 and Ochrobactrum vermis MYb71 are predominantly found in the animal's gut. Finally, we show that this skin microbiome promotes host cuticle integrity in harsh environments. Together, we identify a skin microbiome for the well-studied nematode model and propose its value in conferring host fitness advantages in naturalized contexts.

IMPORTANCE: The genetic model organism C. elegans has recently emerged as a tool for understanding host-microbiome interactions. Nearly all of these studies either focus on pathogenic or gut-resident microbes. Little is known about the existence of native, nonpathogenic skin microbes or their function. We demonstrate that members of a modified C. elegans model microbiome, mCeMbio, can adhere to the animal's cuticle and confer protection from noxious environments. We combine a novel micro-swab tool, the first 16S microbial sequencing data from relatively unperturbed C. elegans, and physiological assays to demonstrate microbially mediated protection of the skin. This work serves as a foundation to explore wild C. elegans skin microbiomes and use C. elegans as a model for skin research.}, } @article {pmid38977908, year = {2024}, author = {Crocker, K and Lee, KK and Chakraverti-Wuerthwein, M and Li, Z and Tikhonov, M and Mani, M and Gowda, K and Kuehn, S}, title = {Environmentally dependent interactions shape patterns in gene content across natural microbiomes.}, journal = {Nature microbiology}, volume = {9}, number = {8}, pages = {2022-2037}, pmid = {38977908}, issn = {2058-5276}, support = {EF 2025293//National Science Foundation (NSF)/ ; R01 GM151538/GM/NIGMS NIH HHS/United States ; R01GM151538//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; DGE 174604//National Science Foundation (NSF)/ ; 220020499//James S. McDonnell Foundation (McDonnell Foundation)/ ; EF 2025521//National Science Foundation (NSF)/ ; }, mesh = {*Soil Microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification/metabolism ; Hydrogen-Ion Concentration ; Denitrification ; Metagenomics ; Genotype ; Soil/chemistry ; }, abstract = {Sequencing surveys of microbial communities in hosts, oceans and soils have revealed ubiquitous patterns linking community composition to environmental conditions. While metabolic capabilities restrict the environments suitable for growth, the influence of ecological interactions on patterns observed in natural microbiomes remains uncertain. Here we use denitrification as a model system to demonstrate how metagenomic patterns in soil microbiomes can emerge from pH-dependent interactions. In an analysis of a global soil sequencing survey, we find that the abundances of two genotypes trade off with pH; nar gene abundances increase while nap abundances decrease with declining pH. We then show that in acidic conditions strains possessing nar fail to grow in isolation but are enriched in the community due to an ecological interaction with nap genotypes. Our study provides a road map for dissecting how associations between environmental variables and gene abundances arise from environmentally modulated community interactions.}, } @article {pmid38977906, year = {2024}, author = {Su, Q and Wong, OWH and Lu, W and Wan, Y and Zhang, L and Xu, W and Li, MKT and Liu, C and Cheung, CP and Ching, JYL and Cheong, PK and Leung, TF and Chan, S and Leung, P and Chan, FKL and Ng, SC}, title = {Multikingdom and functional gut microbiota markers for autism spectrum disorder.}, journal = {Nature microbiology}, volume = {9}, number = {9}, pages = {2344-2355}, pmid = {38977906}, issn = {2058-5276}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Autism Spectrum Disorder/microbiology/diagnosis ; Female ; Male ; Child ; Child, Preschool ; Adolescent ; *Feces/microbiology ; *Biomarkers/analysis ; Infant ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Metagenomics/methods ; Machine Learning ; Archaea/genetics/metabolism/classification/isolation & purification ; Fungi/genetics/classification/isolation & purification ; Viruses/genetics/isolation & purification/classification ; Metagenome ; }, abstract = {Associations between the gut microbiome and autism spectrum disorder (ASD) have been investigated although most studies have focused on the bacterial component of the microbiome. Whether gut archaea, fungi and viruses, or function of the gut microbiome, is altered in ASD is unclear. Here we performed metagenomic sequencing on faecal samples from 1,627 children (aged 1-13 years, 24.4% female) with or without ASD, with extensive phenotype data. Integrated analyses revealed that 14 archaea, 51 bacteria, 7 fungi, 18 viruses, 27 microbial genes and 12 metabolic pathways were altered in children with ASD. Machine learning using single-kingdom panels showed area under the curve (AUC) of 0.68 to 0.87 in differentiating children with ASD from those that are neurotypical. A panel of 31 multikingdom and functional markers showed a superior diagnostic accuracy with an AUC of 0.91, with comparable performance for males and females. Accuracy of the model was predominantly driven by the biosynthesis pathways of ubiquinol-7 or thiamine diphosphate, which were less abundant in children with ASD. Collectively, our findings highlight the potential application of multikingdom and functional gut microbiota markers as non-invasive diagnostic tools in ASD.}, } @article {pmid38977718, year = {2024}, author = {Wei, Y and Li, J and Zhu, B and Hu, Q and Lan, M and Zhou, J and Luo, J and Zhu, W and Lai, Y and Long, E and Zhou, L}, title = {Metagenomic comparison of intestinal microbiota between normal and liver fibrotic rhesus macaques (Macaca mulatta).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {15677}, pmid = {38977718}, issn = {2045-2322}, support = {2022JDZH0014//Science & Technology Department of Sichuan Province/ ; }, mesh = {Animals ; *Macaca mulatta/microbiology ; *Gastrointestinal Microbiome/genetics ; *Liver Cirrhosis/microbiology/genetics/pathology ; Male ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Feces/microbiology ; Metagenome ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {Liver fibrosis is an important pathological process in chronic liver disease and cirrhosis. Recent studies have found a close association between intestinal microbiota and the development of liver fibrosis. To determine whether there are differences in the intestinal microbiota between rhesus macaques with liver fibrosis (MG) and normal rhesus macaques (MN), fecal samples were collected from 8 male MG and 12 male MN. The biological composition of the intestinal microbiota was then detected using 16S rRNA gene sequencing. The results revealed statistically significant differences in ASVs and Chao1 in the alpha-diversity and the beta-diversity of intestinal microbiota between MG and MN. Both groups shared Prevotella and Lactobacillus as common dominant microbiota. However, beneficial bacteria such as Lactobacillus were significantly less abundant in MG (P = 0.02). Predictive functional analysis using PICRUSt2 gene prediction revealed that MG exhibited a higher relative abundance of functions related to substance transport and metabolic pathways. This study may provide insight into further exploration of the mechanisms by which intestinal microbiota affect liver fibrosis and its potential future use in treating liver fibrosis.}, } @article {pmid38977664, year = {2024}, author = {Zachariasen, T and Russel, J and Petersen, C and Vestergaard, GA and Shah, S and Atienza Lopez, P and Passali, M and Turvey, SE and Sørensen, SJ and Lund, O and Stokholm, J and Brejnrod, A and Thorsen, J}, title = {MAGinator enables accurate profiling of de novo MAGs with strain-level phylogenies.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5734}, pmid = {38977664}, issn = {2041-1723}, mesh = {*Phylogeny ; *Metagenomics/methods ; *Metagenome/genetics ; Humans ; *Microbiota/genetics ; Software ; Bacteria/genetics/classification ; Genome, Bacterial/genetics ; }, abstract = {Metagenomic sequencing has provided great advantages in the characterisation of microbiomes, but currently available analysis tools lack the ability to combine subspecies-level taxonomic resolution and accurate abundance estimation with functional profiling of assembled genomes. To define the microbiome and its associations with human health, improved tools are needed to enable comprehensive understanding of the microbial composition and elucidation of the phylogenetic and functional relationships between the microbes. Here, we present MAGinator, a freely available tool, tailored for profiling of shotgun metagenomics datasets. MAGinator provides de novo identification of subspecies-level microbes and accurate abundance estimates of metagenome-assembled genomes (MAGs). MAGinator utilises the information from both gene- and contig-based methods yielding insight into both taxonomic profiles and the origin of genes and genetic content, used for inference of functional content of each sample by host organism. Additionally, MAGinator facilitates the reconstruction of phylogenetic relationships between the MAGs, providing a framework to identify clade-level differences.}, } @article {pmid38977240, year = {2024}, author = {Chac, D and Slater, DM and Guillaume, Y and Dunmire, CN and Ternier, R and Vissières, K and Juin, S and Lucien, MAB and Boncy, J and Sanchez, VM and Dumayas, MG and Augustin, GC and Bhuiyan, TR and Qadri, F and Chowdhury, F and Khan, AI and Weil, AA and Ivers, LC and Harris, JB}, title = {Association between chlorine-treated drinking water, the gut microbiome, and enteric pathogen burden in young children in Haiti: An observational study.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {147}, number = {}, pages = {107165}, pmid = {38977240}, issn = {1878-3511}, support = {K08 AI123494/AI/NIAID NIH HHS/United States ; R01 AI099243/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Haiti/epidemiology ; *Chlorine/pharmacology ; *Drinking Water/microbiology ; Infant ; Child, Preschool ; *Gastrointestinal Microbiome/drug effects ; *Feces/microbiology ; Male ; Female ; Water Purification ; }, abstract = {OBJECTIVE: The effects of sanitation and hygiene interventions on the gut microbiome and enteric pathogen burden are not well understood. We measured the association between free chlorine residue (FCR) levels in drinking water, microbiome composition, and stool enteric pathogens in infants and young children in Haiti.

METHODS: FCR levels were measured in household drinking water and enteric pathogen burden was evaluated using multiplex RT-PCR of stool among 131 children from one month to five years of age living in Mirebalais, Haiti. Microbiome profiling was performed using metagenomic sequencing.

RESULTS: Most individuals lived in households with undetectable FCR measured in the drinking water (112/131, 86%). Detection of enteric pathogen DNA in stool was common and did not correlate with household water FCR. The infant microbiome in households with detectable FCR demonstrated reduced richness (fewer total number of species, P = 0.04 Kruskall-Wallis test) and less diversity by Inverse Simpson measures (P = 0.05) than households with undetectable FCR. Infants in households with a detectable FCR were more likely to have abundant Bifidobacterium. Using in vitro susceptibility testing, we found that some Bifidobacterium species were resistant to chlorine.

CONCLUSIONS: FCR in household drinking water did not correlate with enteric pathogen burden in our study.}, } @article {pmid38977109, year = {2024}, author = {Hu, L and Li, X and Li, C and Wang, L and Han, L and Ni, W and Zhou, P and Hu, S}, title = {Characterization of a novel multifunctional glycoside hydrolase family in the metagenome-assembled genomes of horse gut.}, journal = {Gene}, volume = {927}, number = {}, pages = {148758}, doi = {10.1016/j.gene.2024.148758}, pmid = {38977109}, issn = {1879-0038}, mesh = {Animals ; *Glycoside Hydrolases/genetics/metabolism/chemistry ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Horses ; Genome, Bacterial ; Bacterial Proteins/genetics/metabolism ; Substrate Specificity ; Phylogeny ; }, abstract = {The gut microbiota is a treasure trove of carbohydrate-active enzymes (CAZymes). To explore novel and efficient CAZymes, we analyzed the 4,142 metagenome-assembled genomes (MAGs) of the horse gut microbiota and found the MAG117.bin13 genome (Bacteroides fragilis) contains the highest number of polysaccharide utilisation loci sites (PULs), indicating its high capability for carbohydrate degradation. Bioinformatics analysis indicate that the PULs region of the MAG117.bin13 genome encodes many hypothetical proteins, which are important sources for exploring novel CAZymes. Interestingly, we discovered a hypothetical protein (595 amino acids). This protein exhibits potential CAZymes activity and has a lower similarity to CAZymes, we named it BfLac2275. We purified the protein using prokaryotic expression technology and studied its enzymatic function. The hydrolysis experiment of the polysaccharide substrate showed that the BfLac2275 protein has the ability to degrade α-lactose (156.94 U/mg), maltose (92.59 U/mg), raffinose (86.81 U/mg), and hyaluronic acid (5.71 U/mg). The enzyme activity is optimal at pH 5.0 and 30 ℃, indicating that the hypothetical protein BfLac2275 is a novel and multifunctional CAZymes in the glycoside hydrolases (GHs). These properties indicate that BfLac2275 has broad application prospects in many fields such as plant polysaccharide decomposition, food industry, animal feed additives and enzyme preparations. This study not only serves as a reference for exploring novel CAZymes encoded by gut microbiota but also provides an example for further studying the functional annotation of hypothetical genes in metagenomic assembly genomes.}, } @article {pmid38977080, year = {2024}, author = {Lichtenegger, AS and Posadas-Cantera, S and Badr, MT and Häcker, G}, title = {Comparison of the diversity of anaerobic-cultured gut bacterial communities on different culture media using 16S rDNA sequencing.}, journal = {Journal of microbiological methods}, volume = {224}, number = {}, pages = {106988}, doi = {10.1016/j.mimet.2024.106988}, pmid = {38977080}, issn = {1872-8359}, mesh = {Humans ; *Culture Media/chemistry ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Bacteria, Anaerobic/genetics/isolation & purification/classification/growth & development ; *Gastrointestinal Microbiome ; *DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Biodiversity ; Bacteria/genetics/classification/isolation & purification/drug effects/growth & development ; }, abstract = {The gut microbiome is a dense and diverse community of different microorganisms that deeply influence human physiology and that have important interactions with pathogens. For the correct antibiotic treatment of infections, with its twin goals of effective inhibition of the pathogen and limitation of collateral damage to the microbiome, the identification of infectious organisms is key. Microbiological culturing is still the mainstay of pathogen identification, and anaerobic species are among the most demanding bacterial communities to culture. This study aimed to evaluate the impact of growth media on the culture of an-aerobic bacteria from human stool samples. Stool samples from eight human subjects were cultured each on a yeast extract cysteine blood agar (HCB) and a modified peptone-yeast extract-glucose (MPYG) plate and subjected to Illumina NGS analysis after DNA extraction and amplification. The results showed tight clustering of sequencing samples belonging to the same human subject. Various differences in bacterial richness and evenness could be observed between the two media, with HCB plates supporting the growth of a more diverse microbial community, and MPYG plates improving the growth rates of certain taxa. No statistical significance was observed between the groups. This study highlights the importance of choosing the appropriate growth media for anaerobic bacterial culture and adjusting culture conditions to target specific pathological conditions. HCB plates are suitable for standard microbiological diagnostics, while MPYG plates may be more appropriate for targeting specific conditions. This work emphasizes the role of next-generation sequencing in supporting future research in clinical microbiology.}, } @article {pmid38977060, year = {2024}, author = {Liu, Q and Xu, Y and Lv, X and Guo, C and Zhu, H and Yang, L and Wang, Y}, title = {2', 3', 5'-tri-O-acetyl-N6-(3-hydroxyphenyl) adenosine alleviates diet-induced hyperlipidemia by modulating intestinal gene expression profiles and metabolic pathway.}, journal = {Life sciences}, volume = {352}, number = {}, pages = {122891}, doi = {10.1016/j.lfs.2024.122891}, pmid = {38977060}, issn = {1879-0631}, mesh = {Animals ; *Diet, High-Fat/adverse effects ; Male ; Cricetinae ; *Gastrointestinal Microbiome/drug effects ; *Lipid Metabolism/drug effects ; *Hyperlipidemias/drug therapy/metabolism ; *Adenosine/metabolism ; Metabolic Networks and Pathways/drug effects ; Mesocricetus ; Intestines/drug effects/microbiology ; Transcriptome/drug effects ; }, abstract = {There is a growing body of evidence suggesting that the composition of intestinal flora plays a significant role in regulating lipid metabolism. 2', 3', 5'-tri-O-acetyl-N6-(3-hydroxyphenyl) adenosine (IMMH007) is a new candidate compound for regulating blood cholesterol and other lipids. In this study, we conducted metagenomic and metabolomic analyses on samples from high-fat diet-fed (HFD) hamsters treated with IMMH007. Our findings revealed that IMM-H007 reversed the imbalance of gut microbiota caused by a high-fat diet. Additionally, it activated adiponectin receptor and pantothenate and CoA biosynthesis pathway-related genes, which are known to regulate lipid and glucose metabolism. Furthermore, IMM-H007 promotes cholesterol metabolism by reducing the abundance of genes and species associated with 7α-dehydroxylation and bile salt hydrolase (BSH). Metabolomics and pharmacological studies have shown that IMM-H007 effectively improved glucose and lipid metabolism disorders caused by HFD, reduced the aggregation of secondary bile acids (SBAs), significantly increased the content of hyodeoxycholic acid (HDCA), and also activated the expression of VDR in the small intestine. As a result, there was a reduction in the leakage of diamine oxidase (DAO) into the bloodstream in hamsters, accompanied by an upregulation of ZO-1 expression in the small intestine. The results suggested that IMM-H007 regulated glucose and lipid metabolism, promoted cholesterol metabolism through activating the expression of VDR, inhibiting inflammatory and improving the permeability of the intestinal barrier. Thus, our study provides new understanding of how IMM-H007 interacts with intestinal function, microbiota, and relevant targets, shedding light on its mechanism of action.}, } @article {pmid38976951, year = {2024}, author = {Islam, W and Zeng, F and Almoallim, HS and Ansari, MJ}, title = {Unveiling soil animal community dynamics beneath dominant shrub species in natural desert environment: Implications for ecosystem management and conservation.}, journal = {Journal of environmental management}, volume = {366}, number = {}, pages = {121697}, doi = {10.1016/j.jenvman.2024.121697}, pmid = {38976951}, issn = {1095-8630}, mesh = {*Soil ; *Ecosystem ; *Desert Climate ; Animals ; Conservation of Natural Resources ; Biodiversity ; }, abstract = {The Taklimakan Desert, known for extreme aridity and unique ecological challenges, maintains a delicate life balance beneath its harsh surface. This study investigates intricate dynamics of soil animal communities within this desert ecosystem, with a particular focus on vertical profile variations beneath four dominant shrub species (AS-Alhagi sparsifolia, KC-Karelinia caspia, TR- Tamarix ramosissima, CC- Calligonum caput-medusae). Utilizing comprehensive soil sampling and metagenomics techniques, we reveal the diversity and distribution patterns of soil animal communities from the soil surface down to deeper layers (0-100 cm). Our research outcomes have unveiled that Nematoda and Arthropoda emerge as the most predominant classes of soil animals across all studied shrubs. Specifically, Nematoda exhibited notably high abundance in the KC area, while Arthropoda thrived predominantly in the TR region. We also observed a linear decrease in Nematoda populations as soil depth increased, consistent among all shrub species. Moreover, the highest Shannon diversity within soil animal communities was recorded in the KC area, underscoring a trend of declining alpha diversity in the AS region and an increase in other shrub areas as soil depth increased. Notably, the zones dominated by CC and TR displayed the highest levels of beta diversity. Our correlation analysis of soil animals and environmental factors has pinpointed soil water content, available phosphorus, and available potassium as the most influential drivers of variations in the top-classified soil animal communities. This study provides insights into soil animals in deserts, supporting future research to preserve these fragile deserts and enhance our understanding of life below the surface in challenging ecosystems.}, } @article {pmid38975795, year = {2024}, author = {Padasas-Adalla, CS and Ortega-Kindica, RCM and Dalayap, R and Martinez, JG and Amparado, O and Moneva, CS and Lomelí-Ortega, CO and Tabugo, SR and Balcázar, JL}, title = {Deciphering taxonomic and functional patterns of microbial communities associated with the tiger tail seahorse (Hippocampus comes).}, journal = {Physiological genomics}, volume = {56}, number = {8}, pages = {590-595}, doi = {10.1152/physiolgenomics.00039.2024}, pmid = {38975795}, issn = {1531-2267}, mesh = {Animals ; *Smegmamorpha/microbiology/genetics ; *Skin/microbiology ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics/classification ; Metagenomics/methods ; }, abstract = {Gaining insight into the diversity, structure, and metabolic functions of microbial communities is essential for understanding their roles in host health and ecosystem dynamics. However, research on the seahorse-associated microbiome remains limited, despite these threatened fish facing increasing human pressures worldwide. Here, we explored the microbial diversity and metabolic functions of the skin and gut of the tiger tail seahorse (Hippocampus comes) and its surrounding environment using shotgun metagenomics and bioinformatics. Members of the Pseudomonadota phylum were dominant in the skin microbiome, whereas Bacteroidota was dominant in the gut. Bacillota, Actinomycetota, and Planctomycetota were also detected in the seahorse-associated microbiome. Statistical analysis revealed significant differences (P < 0.01) in species diversity between skin and gut microbiomes, with members belonging to the Moraxellaceae family being dominant on the skin and the Bacteroidaceae family in the gut. Moreover, the surrounding environment (water or sediment) did not have a direct effect on the seahorse microbiome composition. The skin microbiome exhibited a higher abundance of functional genes related to energy, lipid, and amino acid metabolism as well as terpenoids and polyketides metabolism, xenobiotics biodegradation, and metabolism compared with the gut. Despite differences among classes, the total abundance of bacteriocins was similar in both gut and skin microbiomes, which is significant in shaping microbial communities due to their antimicrobial properties. A better knowledge of seahorse microbiomes benefits conservation and sustainable aquaculture efforts, offering insights into habitat protection, disease management, and optimizing aquaculture environments, thereby promoting seahorse health and welfare while minimizing environmental impact and enhancing aquaculture sustainability.NEW & NOTEWORTHY To the best of our knowledge, this study represents the first comprehensive examination of the taxonomic and functional patterns of the skin and gut microbiome in the tiger tail seahorse. These findings have the potential to significantly enhance our understanding of the seahorse-associated microbiome, thereby contributing to the prediction and control of bacterial infections in seahorses, which are a leading cause of high mass mortality rates in seahorse aquaculture and other fish species.}, } @article {pmid38975760, year = {2024}, author = {Tang-Wing, C and Mohanty, I and Bryant, M and Makowski, K and Melendez, D and Dorrestein, PC and Knight, R and Caraballo-Rodríguez, AM and Allaband, C and Jenné, K}, title = {Impact of diet change on the gut microbiome of common marmosets (Callithrix jacchus).}, journal = {mSystems}, volume = {9}, number = {8}, pages = {e0010824}, pmid = {38975760}, issn = {2379-5077}, support = {R01 DK136117/DK/NIDDK NIH HHS/United States ; S10 OD026929/OD/NIH HHS/United States ; S10 OD026929/CD/ODCDC CDC HHS/United States ; }, mesh = {Animals ; *Callithrix/microbiology ; *Gastrointestinal Microbiome/physiology ; *Diet/veterinary ; Male ; Female ; Feces/microbiology ; Bifidobacterium/isolation & purification ; }, abstract = {UNLABELLED: Gastrointestinal diseases are the most frequently reported clinical problems in captive common marmosets (Callithrix jacchus), often affecting the health and welfare of the animal and ultimately their use as a research subject. The microbiome has been shown to be intimately connected to diet and gastrointestinal health. Here, we use shotgun metagenomics and untargeted metabolomics in fecal samples of common marmosets collected before, during, and after a dietary transition from a biscuit to a gel diet. The overall health of marmosets, measured as weight recovery and reproductive outcome, improved after the diet transition. Moreover, each marmoset pair had significant shifts in the microbiome and metabolome after the diet transition. In general, we saw a decrease in Escherichia coli and Prevotella species and an increase in Bifidobacterium species. Untargeted metabolic profiles indicated that polyamine levels, specifically cadaverine and putrescine, were high after diet transition, suggesting either an increase in excretion or a decrease in intestinal reabsorption at the intestinal level. In conclusion, our data suggest that Bifidobacterium species could potentially be useful as probiotic supplements to the laboratory marmoset diet. Future studies with a larger sample size will be beneficial to show that this is consistent with the diet change.

IMPORTANCE: Appropriate diet and health of the common marmoset in captivity are essential both for the welfare of the animal and to improve experimental outcomes. Our study shows that a gel diet compared to a biscuit diet improves the health of a marmoset colony, is linked to increases in Bifidobacterium species, and increases the removal of molecules associated with disease. The diet transition had an influence on the molecular changes at both the pair and time point group levels, but only at the pair level for the microbial changes. It appears to be more important which genes and functions present changed rather than specific microbes. Further studies are needed to identify specific components that should be considered when choosing an appropriate diet and additional supplementary foods, as well as to validate the benefits of providing probiotics. Probiotics containing Bifidobacterium species appear to be useful as probiotic supplements to the laboratory marmoset diet, but additional work is needed to validate these findings.}, } @article {pmid38972205, year = {2024}, author = {Jachimowicz, P and Mądzielewska, W and Cydzik-Kwiatkowska, A}, title = {Microplastics in granular sequencing batch reactors: Effects on pollutant removal dynamics and the microbial community.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {135061}, doi = {10.1016/j.jhazmat.2024.135061}, pmid = {38972205}, issn = {1873-3336}, mesh = {*Bioreactors ; *Water Pollutants, Chemical/metabolism ; *Microplastics/toxicity ; *Phosphorus/metabolism/chemistry ; *Nitrogen/metabolism ; Sewage/microbiology ; Polyethylene Terephthalates/metabolism/chemistry ; Polyethylene/metabolism/chemistry ; Microbiota ; Bacteria/metabolism/genetics ; Waste Disposal, Fluid/methods ; }, abstract = {This study investigated the relationship between microplastic (MP) presence and pollutant removal in granular sludge sequencing batch reactors (GSBRs). Two types of MPs, polyethylene (PE) and polyethylene terephthalate (PET), were introduced in varying concentrations to assess their effects on microbial community dynamics and rates of nitrogen, phosphorus, and organic compound removal. The study revealed type-dependent variations in the deposition of MPs within the biomass, with PET-MPs exhibiting a stronger affinity for accumulation in biomass. A 50 mg/L dose of PET-MP decreased COD removal efficiency by approximately 4 % while increasing P-PO4 removal efficiency by around 7 % compared to the control reactor. The rate of nitrogen compounds removal decreased with higher PET-MP dosages but increased with higher PE-MP dosages. An analysis of microbial activity and gene abundance highlighted the influence of MPs on the expression of the nosZ and ppk1 genes, which code enzymes responsible for nitrogen and phosphorus transformations. The study also explored shifts in microbial community structure, revealing alterations with changes in MP dose and type. This research contributes valuable insights into the complex interactions between MP, microbial communities, and pollutant removal processes in GSBR systems, with implications for the sustainable management of wastewater treatment in the presence of MP.}, } @article {pmid38972064, year = {2024}, author = {Lee, S and Lee, I}, title = {Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2375679}, pmid = {38972064}, issn = {1949-0984}, mesh = {Humans ; *Machine Learning ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; *Metagenome ; Case-Control Studies ; Crohn Disease/microbiology/diagnosis ; Colorectal Neoplasms/diagnosis/microbiology ; Bacteria/genetics/classification/isolation & purification ; Algorithms ; Gastrointestinal Diseases/diagnosis/microbiology ; }, abstract = {The gut microbiome, linked significantly to host diseases, offers potential for disease diagnosis through machine learning (ML) pipelines. These pipelines, crucial in modeling diseases using high-dimensional microbiome data, involve selecting profile modalities, data preprocessing techniques, and classification algorithms, each impacting the model accuracy and generalizability. Despite whole metagenome shotgun sequencing (WMS) gaining popularity for human gut microbiome profiling, a consensus on the optimal methods for ML pipelines in disease diagnosis using WMS data remains elusive. Addressing this gap, we comprehensively evaluated ML methods for diagnosing Crohn's disease and colorectal cancer, using 2,553 fecal WMS samples from 21 case-control studies. Our study uncovered crucial insights: gut-specific, species-level taxonomic features proved to be the most effective for profiling; batch correction was not consistently beneficial for model performance; compositional data transformations markedly improved the models; and while nonlinear ensemble classification algorithms typically offered superior performance, linear models with proper regularization were found to be more effective for diseases that are linearly separable based on microbiome data. An optimal ML pipeline, integrating the most effective methods, was validated for generalizability using holdout data. This research offers practical guidelines for constructing reliable disease diagnostic ML models with fecal WMS data.}, } @article {pmid38972056, year = {2024}, author = {Villani, A and Fontana, A and Panebianco, C and Ferro, C and Copetti, M and Pavlovic, R and Drago, D and Fiorentini, C and Terracciano, F and Bazzocchi, F and Canistro, G and Pisati, F and Maiello, E and Latiano, TP and Perri, F and Pazienza, V}, title = {A powerful machine learning approach to identify interactions of differentially abundant gut microbial subsets in patients with metastatic and non-metastatic pancreatic cancer.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2375483}, pmid = {38972056}, issn = {1949-0984}, mesh = {Humans ; *Pancreatic Neoplasms/microbiology/pathology ; *Gastrointestinal Microbiome ; *Machine Learning ; *Bacteria/classification/genetics/isolation & purification ; *Neoplasm Metastasis ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Feces/microbiology ; Aged ; Metagenomics ; }, abstract = {Pancreatic cancer has a dismal prognosis, as it is often diagnosed at stage IV of the disease and is characterized by metastatic spread. Gut microbiota and its metabolites have been suggested to influence the metastatic spread by modulating the host immune system or by promoting angiogenesis. To date, the gut microbial profiles of metastatic and non-metastatic patients need to be explored. Taking advantage of the 16S metagenomic sequencing and the PEnalized LOgistic Regression Analysis (PELORA) we identified clusters of bacteria with differential abundances between metastatic and non-metastatic patients. An overall increase in Gram-negative bacteria in metastatic patients compared to non-metastatic ones was identified using this method. Furthermore, to gain more insight into how gut microbes can predict metastases, a machine learning approach (iterative Random Forest) was performed. Iterative Random Forest analysis revealed which microorganisms were characterized by a different level of relative abundance between metastatic and non-metastatic patients and established a functional relationship between the relative abundance and the probability of having metastases. At the species level, the following bacteria were found to have the highest discriminatory power: Anaerostipes hadrus, Coprobacter secundus, Clostridium sp. 619, Roseburia inulinivorans, Porphyromonas and Odoribacter at the genus level, and Rhodospirillaceae, Clostridiaceae and Peptococcaceae at the family level. Finally, these data were intertwined with those from a metabolomics analysis on fecal samples of patients with or without metastasis to better understand the role of gut microbiota in the metastatic process. Artificial intelligence has been applied in different areas of the medical field. Translating its application in the field of gut microbiota analysis may help fully exploit the potential information contained in such a large amount of data aiming to open up new supportive areas of intervention in the management of cancer.}, } @article {pmid38971804, year = {2024}, author = {Huang, X and Zeng, J and Li, S and Chen, J and Wang, H and Li, C and Zhang, S}, title = {16S rRNA, metagenomics and 2bRAD-M sequencing to decode human thanatomicrobiome.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {736}, pmid = {38971804}, issn = {2052-4463}, support = {82371896//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82072123//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics ; *Microbiota ; *Cadaver ; }, abstract = {Microorganisms are essential in the decomposition of corpses and play a significant role in forensic science. However, previous studies have primarily focused on animal remains, specifically the gut, skin, and burial environment. Insufficient research has been conducted on the microbiota of human cadavers, especially in cases of advanced decomposition and additional tissues, resulting in a lack of relevant reference data. In this study, the microbiota of eight cadavers at different stages of decomposition were detected using 16S rRNA, metagenomic sequencing and 2bRAD-M sequencing. Nine different sites, including oral and nasal cavities, heart, liver, spleen, lung, kidney, muscle and gut, were analysed and the efficacy of these methods was evaluated. The results showed that 16S rRNA sequencing was the most cost-effective method for the study of cadavers in the early stages of decomposition, whereas for cadaveric tissues in the late stages of decomposition, 2bRAD-M could overcome host contamination more effectively than metagenomic sequencing. This paves the way for new opportunities in data retrieval and promotes in-depth investigations into the microbiota.}, } @article {pmid38971433, year = {2024}, author = {Favaron, A and Abdalla, Y and McCoubrey, LE and Nandiraju, LP and Shorthouse, D and Gaisford, S and Basit, AW and Orlu, M}, title = {Exploring the interactions of JAK inhibitor and S1P receptor modulator drugs with the human gut microbiome: Implications for colonic drug delivery and inflammatory bowel disease.}, journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences}, volume = {200}, number = {}, pages = {106845}, doi = {10.1016/j.ejps.2024.106845}, pmid = {38971433}, issn = {1879-0720}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Janus Kinase Inhibitors/pharmacology ; *Inflammatory Bowel Diseases/drug therapy/microbiology/metabolism ; *Sphingosine 1 Phosphate Receptor Modulators ; Pyrazoles/pharmacology ; Colon/microbiology/metabolism/drug effects ; Sulfonamides/pharmacology/administration & dosage ; Purines ; Azetidines/pharmacology/administration & dosage ; Benzyl Compounds/pharmacology/administration & dosage ; Piperidines/pharmacology/administration & dosage ; Pyrimidines/pharmacology/administration & dosage ; Drug Delivery Systems/methods ; Oxadiazoles/pharmacology/administration & dosage ; Sphingosine-1-Phosphate Receptors/metabolism/antagonists & inhibitors ; Pyrroles/pharmacology/administration & dosage ; Indans/pharmacology/administration & dosage ; Pyridines ; Triazoles ; }, abstract = {The gut microbiota is a complex ecosystem, home to hundreds of bacterial species and a vast repository of enzymes capable of metabolising a wide range of pharmaceuticals. Several drugs have been shown to affect negatively the composition and function of the gut microbial ecosystem. Janus Kinase (JAK) inhibitors and Sphingosine-1-phosphate (S1P) receptor modulators are drugs recently approved for inflammatory bowel disease through an immediate release formulation and would potentially benefit from colonic targeted delivery to enhance the local drug concentration at the diseased site. However, their impact on the human gut microbiota and susceptibility to bacterial metabolism remain unexplored. With the use of calorimetric, optical density measurements, and metagenomics next-generation sequencing, we show that JAK inhibitors (tofacitinib citrate, baricitinib, filgotinib) have a minor impact on the composition of the human gut microbiota, while ozanimod exerts a significant antimicrobial effect, leading to a prevalence of the Enterococcus genus and a markedly different metabolic landscape when compared to the untreated microbiota. Moreover, ozanimod, unlike the JAK inhibitors, is the only drug subject to enzymatic degradation by the human gut microbiota sourced from six healthy donors. Overall, given the crucial role of the gut microbiome in health, screening assays to investigate the interaction of drugs with the microbiota should be encouraged for the pharmaceutical industry as a standard in the drug discovery and development process.}, } @article {pmid38971241, year = {2024}, author = {Zhu, Y and Yan, S and Chen, X and Li, Y and Xie, S}, title = {Thallium spill shifts the structural and functional characteristics of viral communities with different lifestyles in river sediments.}, journal = {The Science of the total environment}, volume = {947}, number = {}, pages = {174531}, doi = {10.1016/j.scitotenv.2024.174531}, pmid = {38971241}, issn = {1879-1026}, mesh = {*Geologic Sediments/virology/chemistry ; *Thallium ; *Rivers/virology ; *Water Pollutants, Chemical/analysis ; Viruses ; China ; Environmental Monitoring ; Microbiota ; }, abstract = {Thallium (Tl), a highly toxic heavy metal, can affect microbial community, while little is known about its effect on viral community. The present study investigated the variation of viral communities, as well as their interactions with microbial hosts under Tl stress. Tl in sediments significantly altered the composition and diversity of the viral communities, but showed no significant links with the prokaryotic communities, which may reveal a potential discrepancy in the sensitivity of the viral and prokaryotic communities to heavy metal stress. Auxiliary metabolic genes (AMGs) involved in denitrification, methane oxidation and organic sulfur transformation were enriched at T1-contaminated sites, while the abundance of AMGs related to methanogenesis and sulfate reduction were higher at pristine sites. Specially, the enrichment of AMGs involved in assimilatory sulfate reduction in Tl-contaminated sites could possibly reduce Tl bioavailability by enhancing the microbially-driven sulfur cycling to generate sulfides that could be complexed with Tl. Moreover, there was a significantly positive correlation between virus-carrying metal resistant genes and the sedimentary Tl concentration, implying that Tl contamination might enhance the metal resistant potential of the viruses. Serving as the functional gene reservoir, the response of viral AMGs to Tl stress could represent a potential pathway for microorganisms to be adapted to the metal-polluted environments. Our study provided novel insights into the impact of Tl spill on viral communities, shedding light on functional characteristics and the links of virus-host interaction with Tl level.}, } @article {pmid38970783, year = {2024}, author = {Wang, X and Sun, J and Zhang, X and Chen, W and Cao, J and Hu, H}, title = {Metagenomics reveals unique gut mycobiome biomarkers in psoriasis.}, journal = {Skin research and technology : official journal of International Society for Bioengineering and the Skin (ISBS) [and] International Society for Digital Imaging of Skin (ISDIS) [and] International Society for Skin Imaging (ISSI)}, volume = {30}, number = {7}, pages = {e13822}, pmid = {38970783}, issn = {1600-0846}, mesh = {Humans ; *Psoriasis/microbiology/blood ; Female ; *Mycobiome ; Adult ; Male ; *Biomarkers/blood ; *Gastrointestinal Microbiome ; *Metagenomics/methods ; Middle Aged ; Machine Learning ; Feces/microbiology ; Young Adult ; Aspergillus ; }, abstract = {PURPOSE: In present, the diagnosis of psoriasis is mainly based on the patient's typical clinical manifestations, dermoscopy and skin biopsy, and unlike other immune diseases, psoriasis lacks specific indicators in the blood. Therefore, we are required to search novel biomarkers for the diagnosis of psoriasis.

METHODS: In this study, we analyzed the composition and the differences of intestinal fungal communities composition between psoriasis patients and healthy individuals in order to find the intestinal fungal communities associated with the diagnosis of psoriasis. We built a machine learning model and identified potential microbial markers for the diagnosis of psoriasis.

RESULTS: The results of AUROC (area under ROC) showed that Aspergillus puulaauensis (AUROC = 0.779), Kazachstania africana (AUROC = 0.750) and Torulaspora delbrueckii (AUROC = 0.745) had high predictive ability (AUROC > 0.7) for predicting psoriasis, While Fusarium keratoplasticum (AUROC = 0.670) was relatively lower (AUROC < 0.7).

CONCLUSION: The strategy based on the prediction of intestinal fungal communities provides a new idea for the diagnosis of psoriasis and is expected to become an auxiliary diagnostic method for psoriasis.}, } @article {pmid38970126, year = {2024}, author = {Zuppi, M and Vatanen, T and Wilson, BC and Golovina, E and Portlock, T and Cutfield, WS and Vickers, MH and O'Sullivan, JM}, title = {Fecal microbiota transplantation alters gut phage communities in a clinical trial for obesity.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {122}, pmid = {38970126}, issn = {2049-2618}, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; *Bacteriophages/physiology/classification/isolation & purification/genetics ; *Feces/microbiology/virology ; *Obesity/therapy/microbiology ; Double-Blind Method ; Female ; Adolescent ; Male ; Bacteria/classification/virology/genetics ; Metagenomics/methods ; Treatment Outcome ; }, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is a therapeutic intervention used to treat diseases associated with the gut microbiome. In the human gut microbiome, phages have been implicated in influencing human health, with successful engraftment of donor phages correlated with FMT treatment efficacy. The impact that gastrointestinal phages exert on human health has primarily been connected to their ability to modulate the bacterial communities in the gut. Nonetheless, how FMT affects recipients' phage populations, and in turn, how this influences the gut environment, is not yet fully understood. In this study, we investigated the effects of FMT on the phageome composition of participants within the Gut Bugs Trial (GBT), a double-blind, randomized, placebo-controlled trial that investigated the efficacy of FMT in treating obesity and comorbidities in adolescents. Stool samples collected from donors at the time of treatment and recipients at four time points (i.e., baseline and 6 weeks, 12 weeks, and 26 weeks post-intervention), underwent shotgun metagenomic sequencing. Phage sequences were identified and characterized in silico to examine evidence of phage engraftment and to assess the extent of FMT-induced alterations in the recipients' phageome composition.

RESULTS: Donor phages engrafted stably in recipients following FMT, composing a significant proportion of their phageome for the entire course of the study (33.8 ± 1.2% in females and 33.9 ± 3.7% in males). Phage engraftment varied between donors and donor engraftment efficacy was positively correlated with their phageome alpha diversity. FMT caused a shift in recipients' phageome toward the donors' composition and increased phageome alpha diversity and variability over time.

CONCLUSIONS: FMT significantly altered recipients' phage and, overall, microbial populations. The increase in microbial diversity and variability is consistent with a shift in microbial population dynamics. This proposes that phages play a critical role in modulating the gut environment and suggests novel approaches to understanding the efficacy of FMT in altering the recipient's microbiome.

TRIAL REGISTRATION: The Gut Bugs Trial was registered with the Australian New Zealand Clinical Trials Registry (ACTR N12615001351505). Trial protocol: the trial protocol is available at https://bmjopen.bmj.com/content/9/4/e026174 . Video Abstract.}, } @article {pmid38970122, year = {2024}, author = {Yan, W and Wang, D and Wang, Y and Wang, C and Chen, X and Liu, L and Wang, Y and Li, YY and Kamagata, Y and Nobu, MK and Zhang, T}, title = {Metatranscriptomics-guided genome-scale metabolic reconstruction reveals the carbon flux and trophic interaction in methanogenic communities.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {121}, pmid = {38970122}, issn = {2049-2618}, support = {T21-705/20-N//the Hong Kong Theme-based Research Scheme/ ; T21-705/20-N//the Hong Kong Theme-based Research Scheme/ ; T21-705/20-N//the Hong Kong Theme-based Research Scheme/ ; T21-705/20-N//the Hong Kong Theme-based Research Scheme/ ; T21-705/20-N//the Hong Kong Theme-based Research Scheme/ ; T21-705/20-N//the Hong Kong Theme-based Research Scheme/ ; T21-705/20-N//the Hong Kong Theme-based Research Scheme/ ; T21-705/20-N//the Hong Kong Theme-based Research Scheme/ ; }, mesh = {*Methane/metabolism ; *Carbon/metabolism ; *Metagenomics/methods ; Bioreactors/microbiology ; Metagenome ; Bacteria/genetics/metabolism/classification ; Phylogeny ; Anaerobiosis ; Transcriptome ; Genome, Bacterial ; Microbiota ; Gene Expression Profiling ; }, abstract = {BACKGROUND: Despite rapid advances in genomic-resolved metagenomics and remarkable explosion of metagenome-assembled genomes (MAGs), the function of uncultivated anaerobic lineages and their interactions in carbon mineralization remain largely uncertain, which has profound implications in biotechnology and biogeochemistry.

RESULTS: In this study, we combined long-read sequencing and metatranscriptomics-guided metabolic reconstruction to provide a genome-wide perspective of carbon mineralization flow from polymers to methane in an anaerobic bioreactor. Our results showed that incorporating long reads resulted in a substantial improvement in the quality of metagenomic assemblies, enabling the effective recovery of 132 high-quality genomes meeting stringent criteria of minimum information about a metagenome-assembled genome (MIMAG). In addition, hybrid assembly obtained 51% more prokaryotic genes in comparison to the short-read-only assembly. Metatranscriptomics-guided metabolic reconstruction unveiled the remarkable metabolic flexibility of several novel Bacteroidales-affiliated bacteria and populations from Mesotoga sp. in scavenging amino acids and sugars. In addition to recovering two circular genomes of previously known but fragmented syntrophic bacteria, two newly identified bacteria within Syntrophales were found to be highly engaged in fatty acid oxidation through syntrophic relationships with dominant methanogens Methanoregulaceae bin.74 and Methanothrix sp. bin.206. The activity of bin.206 preferring acetate as substrate exceeded that of bin.74 with increasing loading, reinforcing the substrate determinantal role.

CONCLUSION: Overall, our study uncovered some key active anaerobic lineages and their metabolic functions in this complex anaerobic ecosystem, offering a framework for understanding carbon transformations in anaerobic digestion. These findings advance the understanding of metabolic activities and trophic interactions between anaerobic guilds, providing foundational insights into carbon flux within both engineered and natural ecosystems. Video Abstract.}, } @article {pmid38969657, year = {2024}, author = {Łopucki, R and Sajnaga, E and Kalwasińska, A and Klich, D and Kitowski, I and Stępień-Pyśniak, D and Christensen, H}, title = {Green spaces contribute to structural resilience of the gut microbiota in urban mammals.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {15508}, pmid = {38969657}, issn = {2045-2322}, mesh = {Animals ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; Cities ; Murinae/microbiology ; Ecosystem ; Mammals/microbiology ; Bacteria/classification/genetics ; }, abstract = {The gut microbiome of wild animals is subject to various environmental influences, including those associated with human-induced alterations to the environment. We investigated how the gut microbiota of a synurbic rodent species, the striped field mouse (Apodemus agrarius), change in cities of varying sizes, seeking the urban microbiota signature for this species. Fecal samples for analysis were collected from animals living in non-urbanized areas and green spaces of different-sized cities (Poland). Metagenomic 16S rRNA gene sequencing and further bioinformatics analyses were conducted. Significant differences in the composition of gut microbiomes among the studied populations were found. However, the observed changes were dependent on local habitat conditions, without strong evidence of a correlation with the size of the urbanized area. The results suggest that ecological detachment from a more natural, non-urban environment does not automatically lead to the development of an "urban microbiome" model in the studied rodent. The exposure to the natural environment in green spaces may serve as a catalyst for microbiome transformations, providing a previously underestimated contribution to the maintenance of native gut microbial communities in urban mammals.}, } @article {pmid38969209, year = {2024}, author = {Snell, LB and Prossomariti, D and Alcolea-Medina, A and Sasson, M and Dibbens, M and Al-Yaakoubi, N and Humayun, G and Charalampous, T and Alder, C and Ward, D and Maldonado-Barrueco, A and Abadioru, O and Batra, R and Nebbia, G and Otter, JA and Edgeworth, JD and Goldenberg, SD}, title = {The drainome: longitudinal metagenomic characterization of wastewater from hospital ward sinks to characterize the microbiome and resistome and to assess the effects of decontamination interventions.}, journal = {The Journal of hospital infection}, volume = {153}, number = {}, pages = {55-62}, doi = {10.1016/j.jhin.2024.06.005}, pmid = {38969209}, issn = {1532-2939}, mesh = {Humans ; *Metagenomics/methods ; *Decontamination/methods ; *Wastewater/microbiology ; *Hospitals ; Fungi/genetics/isolation & purification/classification/drug effects ; Microbiota ; Bacteria/genetics/isolation & purification/classification/drug effects ; Longitudinal Studies ; Peracetic Acid/pharmacology ; Intensive Care Units ; Disinfectants/pharmacology ; }, abstract = {BACKGROUND: Hospital drains and water interfaces are implicated in nosocomial transmission of pathogens. Metagenomics can assess the microbial composition and presence of antimicrobial resistance genes in drains ('the drainome') but studies applying these methods longitudinally and to assess infection control interventions are lacking.

AIM: To apply long-read metagenomics coupled with microbiological measurements to investigate the drainome and assess the effects of a peracetic-acid-containing decontamination product.

METHODS: Twelve-week study in three phases: a baseline phase, an intervention phase of enhanced decontamination with peracetic acid, and a post-intervention phase. Five hospital sink drains on an intensive care unit were sampled twice weekly. Each sample had: (1) measurement of total viable count (TVC); (2) metagenomic analyses including (i) taxonomic classification of bacteria and fungi (ii), antibiotic resistance gene detection, (iii) plasmid identification; and (3) immunochromatographic detection of antimicrobial residues.

FINDINGS: Overall TVCs remain unchanged in the intervention phase (+386 cfu/mL, SE 705, P = 0.59). There was a small but significant increase in the microbial diversity in the intervention phase (-0.07 in Simpson's index, SE 0.03, P = 0.007), which was not sustained post-intervention (-0.05, SE 0.03, P = 0.08). The intervention was associated with increased relative abundance of the Pseudomonas genus (18.3% to 40.5% (+22.2%), SE 5.7%, P < 0.001). Extended spectrum β-lactamases were found in all samples, with NDM-carbapenemase found in three drains in six samples. Antimicrobial residues were detected in a large proportion of samples (31/115, 27%), suggesting use of sinks for non-handwashing activities.

CONCLUSION: Metagenomics and other measurements can determine the composition of the drainome and assess the effectiveness of decontamination interventions.}, } @article {pmid38968121, year = {2024}, author = {Lee, J and Wellenstein, K and Rahnavard, A and Nelson, AT and Holter, MM and Cummings, BP and Yeliseyev, V and Castoldi, A and Clish, CB and Bry, L and Siegel, D and Kahn, BB}, title = {Beneficial metabolic effects of PAHSAs depend on the gut microbiota in diet-induced obese mice but not in chow-fed mice.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {28}, pages = {e2318691121}, pmid = {38968121}, issn = {1091-6490}, support = {1K01DK114162-01A1//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; DK106210//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; R01 DK106210/DK/NIDDK NIH HHS/United States ; K01 DK114162/DK/NIDDK NIH HHS/United States ; P30DK57521//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; P30 DK057521/DK/NIDDK NIH HHS/United States ; n/a//JPB Foundation (JPBF)/ ; P30 DK034854/DK/NIDDK NIH HHS/United States ; 5P30DK057521-19//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; }, mesh = {Animals ; Male ; Female ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Obesity/metabolism/microbiology/etiology ; *Diet, High-Fat/adverse effects ; *Insulin Resistance ; Mice, Inbred C57BL ; Stearic Acids/metabolism ; Palmitic Acid/metabolism ; Feces/microbiology ; Mice, Obese ; }, abstract = {Dietary lipids play an essential role in regulating the function of the gut microbiota and gastrointestinal tract, and these luminal interactions contribute to mediating host metabolism. Palmitic Acid Hydroxy Stearic Acids (PAHSAs) are a family of lipids with antidiabetic and anti-inflammatory properties, but whether the gut microbiota contributes to their beneficial effects on host metabolism is unknown. Here, we report that treating chow-fed female and male germ-free (GF) mice with PAHSAs improves glucose tolerance, but these effects are lost upon high fat diet (HFD) feeding. However, transfer of feces from PAHSA-treated, but not vehicle-treated, chow-fed conventional mice increases insulin sensitivity in HFD-fed GF mice. Thus, the gut microbiota is necessary for, and can transmit, the insulin-sensitizing effects of PAHSAs in HFD-fed GF male mice. Analyses of the cecal metagenome and lipidome of PAHSA-treated mice identified multiple lipid species that associate with the gut commensal Bacteroides thetaiotaomicron (Bt) and with insulin sensitivity resulting from PAHSA treatment. Supplementing live, and to some degree, heat-killed Bt to HFD-fed female mice prevented weight gain, reduced adiposity, improved glucose tolerance, fortified the colonic mucus barrier and reduced systemic inflammation compared to HFD-fed controls. These effects were not observed in HFD-fed male mice. Furthermore, ovariectomy partially reversed the beneficial Bt effects on host metabolism, indicating a role for sex hormones in mediating the Bt probiotic effects. Altogether, these studies highlight the fact that PAHSAs can modulate the gut microbiota and that the microbiota is necessary for the beneficial metabolic effects of PAHSAs in HFD-fed mice.}, } @article {pmid38968070, year = {2024}, author = {Shridhar, SV and Beghini, F and Alexander, M and Singh, A and Juárez, RM and Brito, IL and Christakis, NA}, title = {Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages.}, journal = {Cell reports}, volume = {43}, number = {7}, pages = {114442}, pmid = {38968070}, issn = {2211-1247}, mesh = {Humans ; Honduras ; *Gastrointestinal Microbiome/genetics ; *Socioeconomic Factors ; Female ; Male ; Adult ; Bacteria/classification/genetics ; Phylogeny ; Middle Aged ; }, abstract = {Despite a growing interest in the gut microbiome of non-industrialized countries, data linking deeply sequenced microbiomes from such settings to diverse host phenotypes and situational factors remain uncommon. Using metagenomic data from a community-based cohort of 1,871 people from 19 isolated villages in the Mesoamerican highlands of western Honduras, we report associations between bacterial species and human phenotypes and factors. Among them, socioeconomic factors account for 51.44% of the total associations. Meta-analysis of species-level profiles across several datasets identified several species associated with body mass index, consistent with previous findings. Furthermore, the inclusion of strain-phylogenetic information modifies the overall relationship between the gut microbiome and the phenotypes, especially for some factors like household wealth (e.g., wealthier individuals harbor different strains of Eubacterium rectale). Our analysis suggests a role that gut microbiome surveillance can play in understanding broad features of individual and public health.}, } @article {pmid38966974, year = {2024}, author = {Wu, EH and Qiao, L}, title = {[Microbial metaproteomics--From sample processing to data acquisition and analysis].}, journal = {Se pu = Chinese journal of chromatography}, volume = {42}, number = {7}, pages = {658-668}, pmid = {38966974}, issn = {1872-2059}, mesh = {Databases, Protein ; Mass Spectrometry/methods ; Metagenomics/methods ; Microbiota ; *Proteomics/methods ; }, abstract = {Microorganisms are closely associated with human diseases and health. Understanding the composition and function of microbial communities requires extensive research. Metaproteomics has recently become an important method for throughout and in-depth study of microorganisms. However, major challenges in terms of sample processing, mass spectrometric data acquisition, and data analysis limit the development of metaproteomics owing to the complexity and high heterogeneity of microbial community samples. In metaproteomic analysis, optimizing the preprocessing method for different types of samples and adopting different microbial isolation, enrichment, extraction, and lysis schemes are often necessary. Similar to those for single-species proteomics, the mass spectrometric data acquisition modes for metaproteomics include data-dependent acquisition (DDA) and data-independent acquisition (DIA). DIA can collect comprehensive peptide information from a sample and holds great potential for future development. However, data analysis for DIA is challenged by the complexity of metaproteome samples, which hinders the deeper coverage of metaproteomes. The most important step in data analysis is the construction of a protein sequence database. The size and completeness of the database strongly influence not only the number of identifications, but also analyses at the species and functional levels. The current gold standard for metaproteome database construction is the metagenomic sequencing-based protein sequence database. A public database-filtering method based on an iterative database search has been proven to have strong practical value. The peptide-centric DIA data analysis method is a mainstream data analysis strategy. The development of deep learning and artificial intelligence will greatly promote the accuracy, coverage, and speed of metaproteomic analysis. In terms of downstream bioinformatics analysis, a series of annotation tools that can perform species annotation at the protein, peptide, and gene levels has been developed in recent years to determine the composition of microbial communities. The functional analysis of microbial communities is a unique feature of metaproteomics compared with other omics approaches. Metaproteomics has become an important component of the multi-omics analysis of microbial communities, and has great development potential in terms of depth of coverage, sensitivity of detection, and completeness of data analysis.}, } @article {pmid38965579, year = {2024}, author = {Dong, Y and Chen, WH and Zhao, XM}, title = {VirRep: a hybrid language representation learning framework for identifying viruses from human gut metagenomes.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {177}, pmid = {38965579}, issn = {1474-760X}, support = {T2225015//National Natural Science Foundation of China/ ; 61932008//National Natural Science Foundation of China/ ; 23JS1410100//Shanghai Science and Technology Commission Program/ ; ZDYF2024SHFZ058//Hainan Province Science and Technology Special Fund/ ; 2023YFF1204800//National Key R&D Program of China/ ; 2020YFA0712403//National Key R&D Program of China/ ; LG-TKN-202203-01//Lingang Laboratory & National Key Laboratory of Human Factors Engineering Joint Grant/ ; GZNL2024A01003//Major Project of Guangzhou National Laboratory/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Metagenome ; Viruses/genetics ; Feces/virology ; Metagenomics/methods ; Software ; Colorectal Neoplasms/virology/genetics ; }, abstract = {Identifying viruses from metagenomes is a common step to explore the virus composition in the human gut. Here, we introduce VirRep, a hybrid language representation learning framework, for identifying viruses from human gut metagenomes. VirRep combines a context-aware encoder and an evolution-aware encoder to improve sequence representation by incorporating k-mer patterns and sequence homologies. Benchmarking on both simulated and real datasets with varying viral proportions demonstrates that VirRep outperforms state-of-the-art methods. When applied to fecal metagenomes from a colorectal cancer cohort, VirRep identifies 39 high-quality viral species associated with the disease, many of which cannot be detected by existing methods.}, } @article {pmid38965317, year = {2024}, author = {de Freitas, STF and Silva, FG and Bessa, LA and de Souza, UJB and Augusto, DSS and de Faria, GS and Vitorino, LC}, title = {Low microbial diversity, yeast prevalence, and nematode-trapping fungal presence in fungal colonization and leaf microbiome of Serjania erecta.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {15456}, pmid = {38965317}, issn = {2045-2322}, mesh = {*Plant Leaves/microbiology/parasitology ; Animals ; *Nematoda/microbiology ; *Microbiota ; *Fungi/classification/genetics/isolation & purification ; Endophytes/genetics/isolation & purification ; Yeasts/classification/isolation & purification/genetics ; Metagenomics/methods ; Biodiversity ; }, abstract = {Medicinal plant microbiomes undergo selection due to secondary metabolite presence. Resident endophytic/epiphytic microorganisms directly influence plant's bioactive compound synthesis. Hypothesizing low microbial diversity in Serjania erecta leaves, we assessed leaf colonization by epiphytic and endophytic fungi. Given its traditional medicinal importance, we estimated diversity in the endophytic fungal microbiome. Analyses included scanning electron microscopy (SEM), isolation of cultivable species, and metagenomics. Epiphytic fungi interacted with S. erecta leaf tissues, horizontally transmitted via stomata/trichome bases, expressing traits for nematode trapping. Cultivable endophytic fungi, known for phytopathogenic habits, didn't induce dysbiosis symptoms. This study confirms low leaf microbiome diversity in S. erecta, with a tendency towards more fungal species, likely due to antibacterial secondary metabolite selection. The classification of Halicephalobus sp. sequence corroborated the presence of nematode eggs on the epidermal surface of S. erecta by SEM. In addition, we confirmed the presence of methanogenic archaea and a considerable number of methanotrophs of the genus Methylobacterium. The metagenomic study of endophytic fungi highlighted plant growth-promoting yeasts, mainly Malassezia, Leucosporidium, Meyerozyma, and Hannaella. Studying endophytic fungi and S. erecta microbiomes can elucidate their impact on beneficial bioactive compound production, on the other hand, it is possible that the bioactive compounds produced by this plant can recruit specific microorganisms, impacting the biological system.}, } @article {pmid38964747, year = {2024}, author = {Łukasik, J and Dierikx, T and Johnston, BC and de Meij, T and Szajewska, H}, title = {Systematic review: effect of probiotics on antibiotic-induced microbiome disruption.}, journal = {Beneficial microbes}, volume = {15}, number = {5}, pages = {431-447}, doi = {10.1163/18762891-bja00023}, pmid = {38964747}, issn = {1876-2891}, mesh = {*Probiotics/pharmacology/administration & dosage ; Humans ; *Anti-Bacterial Agents/pharmacology/adverse effects ; *Dysbiosis/microbiology ; Microbiota/drug effects ; Gastrointestinal Microbiome/drug effects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The effectiveness of probiotics in preventing or reversing antibiotic-induced microbiome disruption remains uncertain, and claims of microbiome restoration to its pre-antibiotic state may be overestimated. In this review, we aimed to assess the efficacy of probiotics in preventing or ameliorating disruptions in microbiome composition and function induced by antibiotic treatment. We searched Medline, Embase, and CENTRAL for randomised controlled and non-randomised trials. Participants were individuals of any age who were on systemic antibiotics with a low risk of baseline dysbiosis. The intervention consisted of probiotics during or after antibiotic treatment, compared to placebo, alternative interventions, or no intervention. Outcomes included microbiome composition and diversity analysed using high-throughput molecular methods, alongside microbial function and resistome assessments. Seven studies, reported in eight papers, were reviewed. One study showed probiotics counteracting antibiotic-induced diversity changes, another showed exacerbation of these changes, and four others showed no effect. Effects on taxa abundance ranged from mitigating dysbiosis to selective modulation, no effect, or delayed recovery. One study observed no impact on the resistome, while another reported an increase in antibiotic resistance genes. In conclusion, heterogeneous results preclude a definitive conclusion on the effectiveness of any specific probiotic in restoring antibiotic-exposed microbiomes. For a clearer understanding, future research should be more standardised and long-term, employing advanced methods, such as 16S rRNA gene sequencing and metagenomic sequencing. These studies should strive to include larger, diverse populations to enhance generalisability and clearly define what constitutes a healthy microbiome. Finally, linking changes in the microbiome to specific clinical outcomes is essential for clinical decision making. PROSPERO registration number: CRD42023446214.}, } @article {pmid38964511, year = {2024}, author = {Davido, B and Watson, AR and de Truchis, P and Galazzo, G and Dinh, A and Batista, R and Terveer, EM and Lawrence, C and Michelon, H and Jobard, M and Saleh-Mghir, A and Kuijper, EJ and Caballero, S}, title = {Bacterial diversity and specific taxa are associated with decolonization of carbapenemase-producing enterobacterales after fecal microbiota transplantation.}, journal = {The Journal of infection}, volume = {89}, number = {2}, pages = {106216}, doi = {10.1016/j.jinf.2024.106216}, pmid = {38964511}, issn = {1532-2742}, mesh = {Humans ; *Fecal Microbiota Transplantation ; Male ; Female ; Middle Aged ; Prospective Studies ; Adult ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Aged ; Bacterial Proteins/genetics/metabolism ; Enterobacteriaceae Infections/therapy/microbiology ; beta-Lactamases/genetics ; Carrier State/microbiology/therapy ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation & purification ; Biodiversity ; }, abstract = {OBJECTIVES: We evaluated the effect of fecal microbiota transplantation (FMT) on the clearance of carbapenemase-producing Enterobacterales (CPE) carriage.

METHODS: We performed a prospective, multi-center study, conducted among patients who received a single dose of FMT from one of four healthy donors. The primary endpoint was complete clearance of CPE carriage two weeks after FMT with a secondary endpoint at three months. Shotgun metagenomic sequencing was performed to assess gut microbiota composition of donors and recipients before and after FMT.

RESULTS: Twenty CPE-colonized patients were included in the study, where post-FMT 20% (n = 4/20) of patients met the primary endpoint and 40% (n = 8/20) of patients met the secondary endpoint. Kaplan-Meier curves between patients with FMT intervention and the control group (n = 82) revealed a similar rate of decolonization between groups. Microbiota composition analyses revealed that response to FMT was not donor-dependent. Responders had a significantly lower relative abundance of CPE species pre-FMT than non-responders, and 14 days post-FMT responders had significantly higher bacterial species richness and alpha diversity compared to non-responders (p < 0.05). Responder fecal samples were also enriched in specific species, with significantly higher relative abundances of Faecalibacterium prausnitzii, Parabacteroides distasonis, Collinsella aerofaciens, Alistipes finegoldii and Blautia_A sp900066335 (q<0.01) compared to non-responders.

CONCLUSION: FMT administration using the proposed regimen did not achieve statistical significance for complete CPE decolonization but was correlated with the relative abundance of specific bacterial taxa, including CPE species.}, } @article {pmid38961767, year = {2024}, author = {Xing, Y and Liu, Y and Sha, S and Zhang, Y and Dou, Y and Liu, C and Xu, M and Zhao, L and Wang, J and Wang, Y and Ma, X and Yan, Q and Kong, X}, title = {Multikingdom characterization of gut microbiota in patients with rheumatoid arthritis and rheumatoid arthritis-associated interstitial lung disease.}, journal = {Journal of medical virology}, volume = {96}, number = {7}, pages = {e29781}, doi = {10.1002/jmv.29781}, pmid = {38961767}, issn = {1096-9071}, support = {//Dalian Key Laboratory for Autoantibody Testing/ ; JCH22023017//Interdisciplinary Research Cooperation Project Team Funding of Dalian Medical University/ ; 82225048//National Natural Science Foundation of China/ ; XJ2023001102//The cultivating scientific research project of the Second Hopital of Dalian Medical University/ ; //Liaoning Province Key Clinical Specialized (Department of Rheumatology, the Second Affiliated Hospital of Dalian Medical University) Funds/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Lung Diseases, Interstitial/microbiology/virology ; *Arthritis, Rheumatoid/complications/microbiology ; *Feces/microbiology/virology ; Female ; Male ; Middle Aged ; *Bacteria/classification/isolation & purification/genetics ; Aged ; Virome ; Mycobiome ; Adult ; Viruses/classification/isolation & purification/genetics ; Fungi/isolation & purification/classification ; }, abstract = {Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is a serious and common extra-articular disease manifestation. Patients with RA-ILD experience reduced bacterial diversity and gut bacteriome alterations. However, the gut mycobiome and virome in these patients have been largely neglected. In this study, we performed whole-metagenome shotgun sequencing on fecal samples from 30 patients with RA-ILD, and 30 with RA-non-ILD, and 40 matched healthy controls. The gut bacteriome and mycobiome were explored using a reference-based approach, while the gut virome was profiled based on a nonredundant viral operational taxonomic unit (vOTU) catalog. The results revealed significant alterations in the gut microbiomes of both RA-ILD and RA-non-ILD groups compared with healthy controls. These alterations encompassed changes in the relative abundances of 351 bacterial species, 65 fungal species, and 4,367 vOTUs. Bacteria such as Bifidobacterium longum, Dorea formicigenerans, and Collinsella aerofaciens were enriched in both patient groups. Ruminococcus gnavus (RA-ILD), Gemmiger formicilis, and Ruminococcus bromii (RA-non-ILD) were uniquely enriched. Conversely, Faecalibacterium prausnitzii, Bacteroides spp., and Roseburia inulinivorans showed depletion in both patient groups. Mycobiome analysis revealed depletion of certain fungi, including Saccharomyces cerevisiae and Candida albicans, in patients with RA compared with healthy subjects. Notably, gut virome alterations were characterized by an increase in Siphoviridae and a decrease in Myoviridae, Microviridae, and Autographiviridae in both patient groups. Hence, multikingdom gut microbial signatures showed promise as diagnostic indicators for both RA-ILD and RA-non-ILD. Overall, this study provides comprehensive insights into the fecal virome, bacteriome, and mycobiome landscapes of RA-ILD and RA-non-ILD gut microbiota, thereby offering potential biomarkers for further mechanistic and clinical research.}, } @article {pmid38961596, year = {2024}, author = {Mehra, P and Kumar, A}, title = {Emerging importance of stool preservation methods in OMICS studies with special focus on cancer biology.}, journal = {Cell biochemistry and function}, volume = {42}, number = {5}, pages = {e4063}, doi = {10.1002/cbf.4063}, pmid = {38961596}, issn = {1099-0844}, support = {//National Institute of Immunology/ ; }, mesh = {Humans ; *Feces/microbiology/chemistry ; *Gastrointestinal Microbiome ; *Neoplasms/metabolism ; Metabolomics ; Metagenomics ; }, abstract = {The intricate consortium of microorganisms in the human gut plays a crucial role in different physiological functions. The complex known-unknown elements of the gut microbiome are perplexing and the absence of standardized procedures for collecting and preserving samples has hindered continuous research in comprehending it. The technological bias produced because of lack of standard protocols has affected the reproducibility of results. The complex nature of diseases like colorectal cancer, gastric cancer, hepatocellular carcinoma and breast cancer require a thorough understanding of its etiology for an efficient and timely diagnosis. The designated protocols for collection and preservation of stool specimens have great variance, hence generate inconsistencies in OMICS studies. Due to the complications associated to the nature of sample, it is important to preserve the sample to be studied later in a laboratory or to be used in the future research purpose. Stool preservation is gaining importance due to the increased use of treatment options like fecal microbiota transplantation to cure conditions like recurrent Clostridium difficile infections and for OMICS studies including metagenomics, metabolomics and culturomics. This review provides an insight into the importance of omics studies for the identification and development of novel biomarkers for quick and noninvasive diagnosis of various diseases.}, } @article {pmid38961134, year = {2024}, author = {Montgomery, TL and Wang, Q and Mirza, A and Dwyer, D and Wu, Q and Dowling, CA and Martens, JWS and Yang, J and Krementsov, DN and Mao-Draayer, Y}, title = {Identification of commensal gut microbiota signatures as predictors of clinical severity and disease progression in multiple sclerosis.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {15292}, pmid = {38961134}, issn = {2045-2322}, support = {UM1-AI144298-01//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; UM1-AI110557-05//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; UM1 AI110557/AI/NIAID NIH HHS/United States ; R01 NS097596/NS/NINDS NIH HHS/United States ; UM1 AI144298/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Multiple Sclerosis/microbiology/pathology ; *Disease Progression ; Male ; Female ; Adult ; Longitudinal Studies ; Feces/microbiology ; Middle Aged ; Severity of Illness Index ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system and a leading cause of neurological disability in young adults. Clinical presentation and disease course are highly heterogeneous. Typically, disease progression occurs over time and is characterized by the gradual accumulation of disability. The risk of developing MS is driven by complex interactions between genetic and environmental factors, including the gut microbiome. How the commensal gut microbiota impacts disease severity and progression over time remains unknown. In a longitudinal study, disability status and associated clinical features in 58 MS patients were tracked over 4.2 ± 0.98 years, and the baseline fecal gut microbiome was characterized via 16S amplicon sequencing. Progressor status, defined as patients with an increase in Expanded Disability Status Scale (EDSS), were correlated with features of the gut microbiome to determine candidate microbiota associated with risk of MS disease progression. We found no overt differences in microbial community diversity and overall structure between MS patients exhibiting disease progression and non-progressors. However, a total of 41 bacterial species were associated with worsening disease, including a marked depletion in Akkermansia, Lachnospiraceae, and Oscillospiraceae, with an expansion of Alloprevotella, Prevotella-9, and Rhodospirillales. Analysis of the metabolic potential of the inferred metagenome from taxa associated with progression revealed enrichment in oxidative stress-inducing aerobic respiration at the expense of microbial vitamin K2 production (linked to Akkermansia), and a depletion in SCFA metabolism (linked to Oscillospiraceae). Further, as a proof of principle, statistical modeling demonstrated that microbiota composition and clinical features were sufficient to predict disease progression. Additionally, we found that constipation, a frequent gastrointestinal comorbidity among MS patients, exhibited a divergent microbial signature compared with progressor status. These results demonstrate a proof of principle for the utility of the gut microbiome for predicting disease progression in MS in a small well-defined cohort. Further, analysis of the inferred metagenome suggested that oxidative stress, vitamin K2, and SCFAs are associated with progression, warranting future functional validation and mechanistic study.}, } @article {pmid38960872, year = {2024}, author = {Lee, H and Park, W and No, J and Hyung, NW and Lee, JY and Kim, S and Yang, H and Lee, P and Kim, E and Oh, KB and Yoo, JG and Lee, S}, title = {Comparing Gut Microbial Composition and Functional Adaptations between SPF and Non-SPF Pigs.}, journal = {Journal of microbiology and biotechnology}, volume = {34}, number = {7}, pages = {1484-1490}, pmid = {38960872}, issn = {1738-8872}, mesh = {Animals ; *Gastrointestinal Microbiome ; Swine/microbiology ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; Specific Pathogen-Free Organisms ; Metagenome ; Adaptation, Physiological ; }, abstract = {The gut microbiota is a key factor significantly impacting host health by influencing metabolism and immune function. Its composition can be altered by genetic factors, as well as environmental factors such as the host's surroundings, diet, and antibiotic usage. This study aims to examine how the characteristics of the gut microbiota in pigs, used as source animals for xenotransplantation, vary depending on their rearing environment. We compared the diversity and composition of gut microbiota in fecal samples from pigs raised in specific pathogen-free (SPF) and conventional (non-SPF) facilities. The 16S RNA metagenome sequencing results revealed that pigs raised in non-SPF facilities exhibited greater gut microbiota diversity compared to those in SPF facilities. Genera such as Streptococcus and Ruminococcus were more abundant in SPF pigs compared to non-SPF pigs, while Blautia, Bacteroides, and Roseburia were only observed in SPF pigs. Conversely, Prevotella was exclusively present in non-SPF pigs. It was predicted that SPF pigs would show higher levels of processes related to carbohydrate and nucleotide metabolism, and environmental information processing. On the other hand, energy and lipid metabolism, as well as processes associated with genetic information, cell communication, and diseases, were predicted to be more active in the gut microbiota of non-SPF pigs. This study provides insights into how the presence or absence of microorganisms, including pathogens, in pig-rearing facilities affects the composition and function of the pigs' gut microbiota. Furthermore, this serves as a reference for tracing whether xenotransplantation source pigs were maintained in a pathogen-controlled environment.}, } @article {pmid38960615, year = {2024}, author = {Mac Aogáin, M and Dicker, AJ and Mertsch, P and Chotirmall, SH}, title = {Infection and the microbiome in bronchiectasis.}, journal = {European respiratory review : an official journal of the European Respiratory Society}, volume = {33}, number = {173}, pages = {}, pmid = {38960615}, issn = {1600-0617}, mesh = {*Bronchiectasis/microbiology/immunology ; Humans ; *Microbiota ; *Dysbiosis ; *Host-Pathogen Interactions ; Lung/microbiology ; Animals ; Risk Factors ; Bacteria/genetics/classification ; Respiratory Tract Infections/microbiology/immunology ; Prognosis ; }, abstract = {Bronchiectasis is marked by bronchial dilatation, recurrent infections and significant morbidity, underpinned by a complex interplay between microbial dysbiosis and immune dysregulation. The identification of distinct endophenotypes have refined our understanding of its pathogenesis, including its heterogeneous disease mechanisms that influence treatment and prognosis responses. Next-generation sequencing (NGS) has revolutionised the way we view airway microbiology, allowing insights into the "unculturable". Understanding the bronchiectasis microbiome through targeted amplicon sequencing and/or shotgun metagenomics has provided key information on the interplay of the microbiome and host immunity, a central feature of disease progression. The rapid increase in translational and clinical studies in bronchiectasis now provides scope for the application of precision medicine and a better understanding of the efficacy of interventions aimed at restoring microbial balance and/or modulating immune responses. Holistic integration of these insights is driving an evolving paradigm shift in our understanding of bronchiectasis, which includes the critical role of the microbiome and its unique interplay with clinical, inflammatory, immunological and metabolic factors. Here, we review the current state of infection and the microbiome in bronchiectasis and provide views on the future directions in this field.}, } @article {pmid38960582, year = {2024}, author = {Sun, H and Sun, K and Tian, H and Chen, X and Su, S and Tu, Y and Chen, S and Wang, J and Peng, M and Zeng, M and Li, X and Luo, Y and Xie, Y and Feng, X and Li, Z and Zhang, X and Li, X and Liu, Y and Ye, W and Chen, Z and Zhu, Z and Li, Y and Xia, F and Zhou, H and Duan, C}, title = {Integrated metagenomic and metabolomic analysis reveals distinctive stage-specific gut-microbiome-derived metabolites in intracranial aneurysms.}, journal = {Gut}, volume = {73}, number = {10}, pages = {1662-1674}, doi = {10.1136/gutjnl-2024-332245}, pmid = {38960582}, issn = {1468-3288}, mesh = {*Intracranial Aneurysm/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Humans ; Animals ; Male ; Mice ; Female ; *Tryptophan/metabolism/blood ; *Metabolomics/methods ; *Metagenomics/methods ; Middle Aged ; Aneurysm, Ruptured/microbiology/metabolism ; Indican/metabolism/blood ; Biomarkers/blood/metabolism ; Feces/microbiology ; Disease Models, Animal ; Aged ; Disease Progression ; }, abstract = {OBJECTIVE: Our study aimed to explore the influence of gut microbiota and their metabolites on intracranial aneurysms (IA) progression and pinpoint-related metabolic biomarkers derived from the gut microbiome.

DESIGN: We recruited 358 patients with unruptured IA (UIA) and 161 with ruptured IA (RIA) from two distinct geographical regions for conducting an integrated analysis of plasma metabolomics and faecal metagenomics. Machine learning algorithms were employed to develop a classifier model, subsequently validated in an independent cohort. Mouse models of IA were established to verify the potential role of the specific metabolite identified.

RESULTS: Distinct shifts in taxonomic and functional profiles of gut microbiota and their related metabolites were observed in different IA stages. Notably, tryptophan metabolites, particularly indoxyl sulfate (IS), were significantly higher in plasma of RIA. Meanwhile, upregulated tryptophanase expression and indole-producing microbiota were observed in gut microbiome of RIA. A model harnessing gut-microbiome-derived tryptophan metabolites demonstrated remarkable efficacy in distinguishing RIA from UIA patients in the validation cohort (AUC=0.97). Gut microbiota depletion by antibiotics decreased plasma IS concentration, reduced IA formation and rupture in mice, and downregulated matrix metalloproteinase-9 expression in aneurysmal walls with elastin degradation reduction. Supplement of IS reversed the effect of gut microbiota depletion.

CONCLUSION: Our investigation highlights the potential of gut-microbiome-derived tryptophan metabolites as biomarkers for distinguishing RIA from UIA patients. The findings suggest a novel pathogenic role for gut-microbiome-derived IS in elastin degradation in the IA wall leading to the rupture of IA.}, } @article {pmid38960356, year = {2024}, author = {Zhang, W and Ye, J and Hu, F and Zhang, J and Chen, P and Yuan, Z and Xu, Z}, title = {Microbial community succession and responses to internal environmental drivers throughout the operation of constructed wetlands.}, journal = {Environmental research}, volume = {259}, number = {}, pages = {119522}, doi = {10.1016/j.envres.2024.119522}, pmid = {38960356}, issn = {1096-0953}, mesh = {*Wetlands ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Waste Disposal, Fluid/methods ; Bacteria/genetics/classification/isolation & purification/metabolism ; }, abstract = {Constructed wetlands (CWs) have been widely used to ensure effective domestic wastewater treatment. Microorganisms-derived CWs have received extensive attention as they play a crucial role. However, research on the succession patterns of microbial communities and the influencing mechanisms of internal environmental factors throughout entire CW operations remains limited. In this context, three parallel-operated CWs were established in this study to assess the microbial communities and their influencing environmental factors at different substrate depths throughout the operation process using 16S rRNA gene high-throughput sequencing and metagenomic sequencing. The results showed gradual reproduction and accumulation of the microbial communities throughout the CW operation. Although gradual increases in the richness and diversity of the microbial communities were found, there were decreases in the functional expression of the dominant microbial species. The excessive accumulation of microorganisms will decrease the oxidation-reduction potential (ORP) within CWs and attenuate their influence on effluent. Dissolved oxygen (DO) was the major factor influencing the microbial community succession over the CW operation. The main identified functional bacterial genera responsible for the ammonium oxidation, nitrification, and denitrification processes in the CWs were Nitrosospira, Nitrobacter, Nitrospira, Rhodanobacter, and Nakamurella. The narG gene was identified as a key functional gene linking various components of nitrogen cycling, while pH, electrical conductivity (EC), and ORP were the major environmental factors affecting the metabolism characteristics of nitrogen functional microorganisms. This study provides a theoretical basis for the effective regulation of related microbial communities to achieve long-term, efficient, and stable CW operations.}, } @article {pmid38959851, year = {2024}, author = {Hoetzinger, M and Hahn, MW and Andersson, LY and Buckley, N and Ramsin, C and Buck, M and Nuy, JK and Garcia, SL and Puente-Sánchez, F and Bertilsson, S}, title = {Geographic population structure and distinct intra-population dynamics of globally abundant freshwater bacteria.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38959851}, issn = {1751-7370}, support = {2017-04422//Swedish Research Council/ ; 2019-02336//Swedish Research Council Formas/ ; UNI-0404/2370//Tiroler Wissenschaftsförderung/ ; 27160-B22//Austrian Science Fund/ ; 300846//Research Council of Norway/ ; 311913//ERA-Net Cofund Project BlueBio/ ; 892961//European Union's Horizon 2020/ ; 2022-04801//Swedish Research Council/ ; }, mesh = {*Fresh Water/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Phylogeny ; Population Dynamics ; Ecosystem ; Biodiversity ; Genome, Bacterial ; Phylogeography ; }, abstract = {Implications of geographic separation and temporal dynamics on the evolution of free-living bacterial species are widely unclear. However, the vast amount of metagenome sequencing data generated during the last decades from various habitats around the world provides an unprecedented opportunity for such investigations. Here, we exploited publicly available and new freshwater metagenomes in combination with the genomes of abundant freshwater bacteria to reveal geographic and temporal population structure. We focused on species that were detected across broad geographic ranges at high enough sequence coverage for meaningful population genomic analyses, associated with the predominant freshwater taxa acI, LD12, Polynucleobacter, and Candidatus Methylopumilus. Despite the broad geographic ranges, each species appeared as a sequence-discrete cluster, in contrast to abundant marine taxa, for which continuous diversity structures were reported on a global scale. Population differentiation increased significantly with spatial distance in all species, but notable dispersal barriers (e.g. oceanic) were not apparent. Yet, the different species showed contrasting rates of geographic divergence and strikingly different intra-population dynamics in time series within individual habitats. The change in an LD12 population over 7 years was minor (FST = 0.04) compared to differentiation between lakes, whereas a Polynucleobacter population displayed strong changes within merely 2 months (FST up to 0.54), similar in scale to differentiation between populations separated by thousands of kilometers. The slowly and steadily evolving LD12 population showed high strain diversity, whereas the dynamic Polynucleobacter population exhibited alternating clonal expansions of mostly two strains only. Based on the contrasting population structures, we propose distinct models of speciation.}, } @article {pmid38959642, year = {2024}, author = {Cao, G and Yu, Y and Wang, H and Yang, H and Tao, F and Yang, S and Liu, J and Li, Z and Yang, C}, title = {Dietary Clostridium butyricum and 25-Hydroxyvitamin D3 modulate bone metabolism of broilers through the gut-brain axis.}, journal = {Poultry science}, volume = {103}, number = {8}, pages = {103966}, pmid = {38959642}, issn = {1525-3171}, mesh = {Animals ; *Chickens/physiology ; *Clostridium butyricum/physiology ; *Animal Feed/analysis ; *Diet/veterinary ; *Calcifediol/administration & dosage/pharmacology ; *Dietary Supplements/analysis ; Brain-Gut Axis/physiology/drug effects ; Probiotics/pharmacology/administration & dosage ; Male ; Bone and Bones/drug effects ; Random Allocation ; Gastrointestinal Microbiome/drug effects ; }, abstract = {Leg disorders have become increasingly common in broilers, leading to lower meat quality and major economic losses. This study evaluated the effects of dietary supplementation with Clostridium butyricum (C. butyricum) and 25-hydroxyvitamin D3 (25-OH-D3) on bone development by comparing growth performance, tibial parameters, Ca and P contents of tibial ash, bone development-related indicators' level, and cecal short-chain fatty acids in Cobb broilers. All birds were divided into four treatment groups, which birds fed either a basal diet (Con), basal diet + 75 mg chlortetracycline/kg (Anti), basal diet + C. butyricum at 10[9] CFU/kg (Cb), basal diet + C. butyricum at 10[9] CFU/kg and 25-OH-D3 at 25 μg/kg (CbD), or basal diet + 25-OH-D3 at 25 μg/kg (CD). Our results suggest that the dietary supplementation in Cb, CbD, and CD significantly increased the body weight (BW) and average daily gain (ADG), and reduced the feed-to-weight ratio (F/G) at different stages of growth (P < 0.05). Dietary supplementation in Cb, CbD, and CD prolonged (P < 0.05) the behavioral responses latency-to-lie (LTL) time, reduced (P < 0.05) the levels of osteocalcin (BGP) and peptide tyrosine (PYY), and increased (P < 0.05) serotonin (5-HT) and dopamine (DA). Treatment with Cb increased (P < 0.05) the levels of acetic acid, isobutyric acid, butyric acid, and isovaleric acid compared with those in Con group. The cecal metagenome showed that Alistipes spp. were significantly more abundant in Cb, CbD, and CD groups (P < 0.05). A total of 12 metabolic pathways were significantly affected by supplementation, including the signaling pathways of glucagon, insulin, and PI3K-AKT; primary and secondary bile acid biosynthesis; and P-type Ca 2+ transporters (P < 0.05). Hence, the CbD supplementation modulates bone metabolism by regulating the mediators of gut-brain axis, which may inform strategies to prevent leg diseases and improve meat quality in broilers.}, } @article {pmid38959253, year = {2024}, author = {Wang, Y and Bi, S and Li, X and Zhong, Y and Qi, D}, title = {Perturbations in gut microbiota composition in schizophrenia.}, journal = {PloS one}, volume = {19}, number = {7}, pages = {e0306582}, pmid = {38959253}, issn = {1932-6203}, mesh = {*Schizophrenia/microbiology ; Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Adult ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; Case-Control Studies ; Metagenomics/methods ; Metagenome ; }, abstract = {Schizophrenia is a severe, complex and long-term psychiatric disorder with unclear etiology. Gut microbes influence the central nervous system via the gut-brain axis. Consequently, investigations of the relationship between gut microbes and schizophrenia are warranted. This study involved 29 patients with schizophrenia and 30 age-matched normal controls. After 16S rRNA gene sequencing and whole-genome shotgun metagenomic sequencing, we analyzed microbial diversity, composition, and function. According to 16S rRNA and metagenomic gene sequencing results, patients with schizophrenia had higher abundances of Clostridium and Megasphaera. Functional analysis showed that sphingolipid, phosphonates and phosphinates, as well as glutamine metabolism were associated with the occurrence and development of schizophrenia. Our data suggest that the gut microbiota exerts an effect on patients with schizophrenia, providing valuable insights into the potential regulation of in the context of this disorder.}, } @article {pmid38957477, year = {2024}, author = {Bredon, M and Danne, C and Pham, HP and Ruffié, P and Bessede, A and Rolhion, N and Creusot, L and Brot, L and Alonso, I and Langella, P and Derosa, L and Cortot, AB and Routy, B and Zitvogel, L and Segata, N and Sokol, H}, title = {Faecalibaterium prausnitzii strain EXL01 boosts efficacy of immune checkpoint inhibitors.}, journal = {Oncoimmunology}, volume = {13}, number = {1}, pages = {2374954}, pmid = {38957477}, issn = {2162-402X}, mesh = {*Immune Checkpoint Inhibitors/pharmacology/therapeutic use ; Animals ; Humans ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Faecalibacterium prausnitzii/drug effects ; Female ; Carcinoma, Non-Small-Cell Lung/drug therapy/immunology/pathology ; Melanoma/drug therapy/immunology/pathology ; Feces/microbiology ; Male ; Lung Neoplasms/drug therapy/immunology/pathology ; Cell Line, Tumor ; Mice, Inbred C57BL ; }, abstract = {Gut microbiota impacts responses to immune checkpoint inhibitors (ICI). A high level of Faecalibacterium prausnitzii have been associated with a positive response to ICI in multiple cancer types. Here, based on fecal shotgun metagenomics data, we show in two independent cohorts of patients with non-small cell lung cancer and advanced melanoma that a high level of F. prausnitzii at baseline is positively associated with a better clinical response to ICI. In MCA205 tumor-bearing mice, administration of F. prausnitzii strain EXL01, already in clinical development for Inflammatory Bowel Disease, restores the anti-tumor response to ICI in the context of antibiotic-induced microbiota perturbation at clinical and tumor transcriptomics level. In vitro, EXL01 strain enhances T cell activation in the presence of ICI. Interestingly, oral administration of EXL01 strain did not induce any change in fecal microbiota diversity or composition, suggesting a direct effect on immune cells in the small intestine. F. prausnitzii strain EXL01 will be evaluated as an adjuvant to ICI in multiple cancers in the near future.}, } @article {pmid38956049, year = {2024}, author = {Kifle, BA and Sime, AM and Gemeda, MT and Woldesemayat, AA}, title = {Shotgun metagenomic insights into secondary metabolite biosynthetic gene clusters reveal taxonomic and functional profiles of microbiomes in natural farmland soil.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {15096}, pmid = {38956049}, issn = {2045-2322}, mesh = {*Soil Microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; *Multigene Family ; *Secondary Metabolism/genetics ; *Metagenome ; Farms ; Bacteria/genetics/classification/metabolism ; Ethiopia ; Phylogeny ; }, abstract = {Antibiotic resistance is a worldwide problem that imposes a devastating effect on developing countries and requires immediate interventions. Initially, most of the antibiotic drugs were identified by culturing soil microbes. However, this method is prone to discovering the same antibiotics repeatedly. The present study employed a shotgun metagenomics approach to investigate the taxonomic diversity, functional potential, and biosynthetic capacity of microbiomes from two natural agricultural farmlands located in Bekeka and Welmera Choke Kebelle in Ethiopia for the first time. Analysis of the small subunit rRNA revealed bacterial domain accounting for 83.33% and 87.24% in the two selected natural farmlands. Additionally, the analysis showed the dominance of Proteobacteria representing 27.27% and 28.79% followed by Actinobacteria making up 12.73% and 13.64% of the phyla composition. Furthermore, the analysis revealed the presence of unassigned bacteria in the studied samples. The metagenome functional analysis showed 176,961 and 104, 636 number of protein-coding sequences (pCDS) from the two samples found a match with 172,655 and 102, 275 numbers of InterPro entries, respectively. The Genome ontology annotation suggests the presence of 5517 and 3293 pCDS assigned to the "biosynthesis process". Numerous Kyoto Encyclopedia of Genes and Genomes modules (KEGG modules) involved in the biosynthesis of terpenoids and polyketides were identified. Furthermore, both known and novel Biosynthetic gene clusters, responsible for the production of secondary metabolites, such as polyketide synthases, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptides (Ripp), and Terpene, were discovered. Generally, from the results it can be concluded that the microbiomes in the selected sampling sites have a hidden functional potential for the biosynthesis of secondary metabolites. Overall, this study can serve as a strong preliminary step in the long journey of bringing new antibiotics to the market.}, } @article {pmid38955825, year = {2024}, author = {Pan, H and Wattiez, R and Gillan, D}, title = {Soil Metaproteomics for Microbial Community Profiling: Methodologies and Challenges.}, journal = {Current microbiology}, volume = {81}, number = {8}, pages = {257}, pmid = {38955825}, issn = {1432-0991}, support = {No.2023-BSBA-024//Joint Funds of the Natural Science Foundation of Liaoning Province of China/ ; }, mesh = {*Soil Microbiology ; *Proteomics/methods ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Microbiota ; Fungi/classification/genetics/metabolism/isolation & purification ; Soil/chemistry ; Computational Biology/methods ; }, abstract = {Soil represents a complex and dynamic ecosystem, hosting a myriad of microorganisms that coexist and play vital roles in nutrient cycling and organic matter transformation. Among these microorganisms, bacteria and fungi are key members of the microbial community, profoundly influencing the fate of nitrogen, sulfur, and carbon in terrestrial environments. Understanding the intricacies of soil ecosystems and the biological processes orchestrated by microbial communities necessitates a deep dive into their composition and metabolic activities. The advent of next-generation sequencing and 'omics' techniques, such as metagenomics and metaproteomics, has revolutionized our understanding of microbial ecology and the functional dynamics of soil microbial communities. Metagenomics enables the identification of microbial community composition in soil, while metaproteomics sheds light on the current biological functions performed by these communities. However, metaproteomics presents several challenges, both technical and computational. Factors such as the presence of humic acids and variations in extraction methods can influence protein yield, while the absence of high-resolution mass spectrometry and comprehensive protein databases limits the depth of protein identification. Notwithstanding these limitations, metaproteomics remains a potent tool for unraveling the intricate biological processes and functions of soil microbial communities. In this review, we delve into the methodologies and challenges of metaproteomics in soil research, covering aspects such as protein extraction, identification, and bioinformatics analysis. Furthermore, we explore the applications of metaproteomics in soil bioremediation, highlighting its potential in addressing environmental challenges.}, } @article {pmid38955400, year = {2024}, author = {Swarte, JC and Zhang, S and Nieuwenhuis, LM and Gacesa, R and Knobbe, TJ and , and De Meijer, VE and Damman, K and Verschuuren, EAM and Gan, TC and Fu, J and Zhernakova, A and Harmsen, HJM and Blokzijl, H and Bakker, SJL and Björk, JR and Weersma, RK and , }, title = {Multiple indicators of gut dysbiosis predict all-cause and cause-specific mortality in solid organ transplant recipients.}, journal = {Gut}, volume = {73}, number = {10}, pages = {1650-1661}, doi = {10.1136/gutjnl-2023-331441}, pmid = {38955400}, issn = {1468-3288}, mesh = {Humans ; *Dysbiosis/mortality ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; *Organ Transplantation/adverse effects ; Prospective Studies ; Cause of Death ; Transplant Recipients/statistics & numerical data ; Adult ; Feces/microbiology ; Netherlands/epidemiology ; Metagenome ; Aged ; }, abstract = {OBJECTIVE: Gut microbiome composition is associated with multiple diseases, but relatively little is known about its relationship with long-term outcome measures. While gut dysbiosis has been linked to mortality risk in the general population, the relationship with overall survival in specific diseases has not been extensively studied. In the current study, we present results from an in-depth analysis of the relationship between gut dysbiosis and all-cause and cause-specific mortality in the setting of solid organ transplant recipients (SOTR).

DESIGN: We analysed 1337 metagenomes derived from faecal samples of 766 kidney, 334 liver, 170 lung and 67 heart transplant recipients part of the TransplantLines Biobank and Cohort-a prospective cohort study including extensive phenotype data with 6.5 years of follow-up. To analyze gut dysbiosis, we included an additional 8208 metagenomes from the general population of the same geographical area (northern Netherlands). Multivariable Cox regression and a machine learning algorithm were used to analyse the association between multiple indicators of gut dysbiosis, including individual species abundances, and all-cause and cause-specific mortality.

RESULTS: We identified two patterns representing overall microbiome community variation that were associated with both all-cause and cause-specific mortality. The gut microbiome distance between each transplantation recipient to the average of the general population was associated with all-cause mortality and death from infection, malignancy and cardiovascular disease. A multivariable Cox regression on individual species abundances identified 23 bacterial species that were associated with all-cause mortality, and by applying a machine learning algorithm, we identified a balance (a type of log-ratio) consisting of 19 out of the 23 species that were associated with all-cause mortality.

CONCLUSION: Gut dysbiosis is consistently associated with mortality in SOTR. Our results support the observations that gut dysbiosis is associated with long-term survival. Since our data do not allow us to infer causality, more preclinical research is needed to understand mechanisms before we can determine whether gut microbiome-directed therapies may be designed to improve long-term outcomes.}, } @article {pmid38955276, year = {2024}, author = {Gaire, TN and Odland, C and Zhang, B and Slizovskiy, I and Jorgenson, B and Wehri, T and Meneguzzi, M and Wass, B and Schuld, J and Hanson, D and Doster, E and Singer, J and Cannon, J and Asmus, A and Ray, T and Dee, S and Nerem, J and Davies, P and Noyes, NR}, title = {Slaughtering processes impact microbial communities and antimicrobial resistance genes of pig carcasses.}, journal = {The Science of the total environment}, volume = {946}, number = {}, pages = {174394}, doi = {10.1016/j.scitotenv.2024.174394}, pmid = {38955276}, issn = {1879-1026}, mesh = {Animals ; *Abattoirs ; Swine ; *Microbiota/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; }, abstract = {Several steps in the abattoir can influence the presence of microbes and associated resistance genes (ARGs) on the animal carcasses used for further meat processing. We investigated how these processes influence the resistome-microbiome of groups of pigs with different on-farm antimicrobial exposure status, from the moment they entered the abattoir until the end of carcass processing. Using a targeted enrichment metagenomic approach, we identified 672 unique ARGs conferring resistance to 43 distinct AMR classes from pooled skin (N = 42) and carcass swabs (N = 63) collected sequentially before, during, and after the slaughter process and food safety interventions. We observed significant variations in the resistome and microbial profiles of pigs before and after slaughter, as well as a significant decline in ARG counts, diversity, and microbial DNA load during slaughter and carcass processing, irrespective of prior antimicrobial treatments on the farm. These results suggest that existing interventions in the abattoir are effective in reducing not only the pathogen load but also the overall bacterial burden, including ARGs on pork carcasses. Concomitant with reductions in microbial and ARG counts, we observed an increase in the relative abundance of non-drug-specific ARGs, such as those conferring resistance to metals and biocides, and in particular mercury. Using a strict colocalization procedure, we found that most mercury ARGs were associated with genomes from the Pseudomonadaceae and Enterobacteriaceae families. Collectively, these findings demonstrate that slaughter and processing practices within the abattoir can shape the microbial and ARG profiles of pork carcasses during the transition from living muscle to meat.}, } @article {pmid38955186, year = {2024}, author = {Wang, S and Liu, Y and Tam, WH and Ching, JYL and Xu, W and Yan, S and Qin, B and Lin, L and Peng, Y and Zhu, J and Cheung, CP and Ip, KL and Wong, YM and Cheong, PK and Yeung, YL and Kan, WHB and Leung, TF and Leung, TY and Chang, EB and Rubin, DT and Claud, EC and Wu, WKK and Tun, HM and Chan, FKL and Ng, SC and Zhang, L}, title = {Maternal gestational diabetes mellitus associates with altered gut microbiome composition and head circumference abnormalities in male offspring.}, journal = {Cell host & microbe}, volume = {32}, number = {7}, pages = {1192-1206.e5}, doi = {10.1016/j.chom.2024.06.005}, pmid = {38955186}, issn = {1934-6069}, mesh = {*Gastrointestinal Microbiome ; Female ; Humans ; *Diabetes, Gestational/microbiology ; Pregnancy ; Male ; Infant ; *Feces/microbiology ; Head/microbiology ; Adult ; Infant, Newborn ; Clostridium/growth & development ; Prenatal Exposure Delayed Effects/microbiology ; }, abstract = {The impact of gestational diabetes mellitus (GDM) on maternal or infant microbiome trajectory remains poorly understood. Utilizing large-scale longitudinal fecal samples from 264 mother-baby dyads, we present the gut microbiome trajectory of the mothers throughout pregnancy and infants during the first year of life. GDM mothers had a distinct microbiome diversity and composition during the gestation period. GDM leaves fingerprints on the infant's gut microbiome, which are confounded by delivery mode. Further, Clostridium species positively correlate with a larger head circumference at month 12 in male offspring but not females. The gut microbiome of GDM mothers with male fetuses displays depleted gut-brain modules, including acetate synthesis I and degradation and glutamate synthesis II. The gut microbiome of female infants of GDM mothers has higher histamine degradation and dopamine degradation. Together, our integrative analysis indicates that GDM affects maternal and infant gut composition, which is associated with sexually dimorphic infant head growth.}, } @article {pmid38954855, year = {2024}, author = {Nie, C and Chen, L and Zhao, B and Wu, Z and Zhang, M and Yan, Y and Li, B and Xia, Y}, title = {Deciphering the adaptation mechanism of anammox consortia under sulfamethoxazole stress: A model coupling resistance accumulation and interspecies-cooperation.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {135074}, doi = {10.1016/j.jhazmat.2024.135074}, pmid = {38954855}, issn = {1873-3336}, mesh = {*Sulfamethoxazole/metabolism ; Microbial Consortia ; Adaptation, Physiological ; Wastewater/microbiology ; Water Pollutants, Chemical/metabolism ; Bacteria/metabolism/genetics ; Oxidation-Reduction ; Ammonia/metabolism ; Anti-Bacterial Agents/metabolism ; Drug Resistance, Microbial/genetics ; Anaerobiosis ; }, abstract = {Sulfamethoxazole (SMX) is frequently detected in wastewater where anammox applications are promising. While it has been demonstrated that anammox consortia can adapt to SMX stress, the underlying community adaptation strategy has not yet been fully addressed. Therefore, in this study, we initially ascertained anammox consortia's ability to co-metabolize SMX in batch tests. Then, a 200-day domestication process of anammox consortia under SMX stress was carried out with community variations and transcriptional activities monitored by metagenomic and metatranscriptomic sequencing techniques. Despite the initial drop to 41.88 %, the nitrogen removal efficiency of the anammox consortia rebounded to 84.64 % post-domestication under 5 mg/L SMX. Meanwhile, a 4.85-fold accumulation of antibiotic resistance genes (ARGs) under SMX stress was observed as compared to the control group. Interestingly, the anammox consortia may unlock the SMX-inhibited folate synthesis pathway through a novel interspecies cooperation triangle among Nitrospira (NAA), Desulfobacillus denitrificans (DSS1), and the core anammox population Candidatus Brocadia sinica (AMX1), in which the modified dihydropteroate synthase (encoded by sul1) of NAA reconnected the symbiotic cooperation between AMX1 and DSS1. Overall, this study provides a new model for the adaptation strategies of anammox consortia to SMX stress.}, } @article {pmid38954516, year = {2024}, author = {Banerjee, G and Papri, SR and Banerjee, P}, title = {Protocol for the construction and functional profiling of metagenome-assembled genomes for microbiome analyses.}, journal = {STAR protocols}, volume = {5}, number = {3}, pages = {103167}, pmid = {38954516}, issn = {2666-1667}, mesh = {*Metagenome/genetics ; *Microbiota/genetics ; Humans ; *Metagenomics/methods ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Constructing metagenome-assembled genomes (MAGs) from complex metagenomic samples involves a series of bioinformatics operations, each requiring deep bioinformatics knowledge. Here, we present a protocol for constructing MAGs and conducting functional profiling to address biological questions. We describe steps for system configuration, data downloads, read processing, removal of human DNA contamination, metagenomic assembly, and statistical quality assessment of the final assembly. Additionally, we detail procedures for the construction and refinement of MAGs, as well as the functional profiling of MAGs.}, } @article {pmid38952337, year = {2024}, author = {Sardar, P and Almeida, A and Pedicord, VA}, title = {Integrating functional metagenomics to decipher microbiome-immune interactions.}, journal = {Immunology and cell biology}, volume = {102}, number = {8}, pages = {680-691}, doi = {10.1111/imcb.12798}, pmid = {38952337}, issn = {1440-1711}, support = {MR/W016184/1/MRC_/Medical Research Council/United Kingdom ; MR/W016184/1//Career Development Award by the Medical Research Council/ ; PGS22/100116//Rosetrees Trust/ ; 206245/Z/17/Z//Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society/ ; }, mesh = {*Metagenomics/methods ; Humans ; Animals ; *Gastrointestinal Microbiome/immunology/genetics ; Microbiota/immunology/genetics ; Metagenome ; Bacteria/genetics/immunology/classification ; }, abstract = {Microbial metabolites can be viewed as the cytokines of the microbiome, transmitting information about the microbial and metabolic environment of the gut to orchestrate and modulate local and systemic immune responses. Still, many immunology studies focus solely on the taxonomy and community structure of the gut microbiota rather than its functions. Early sequencing-based microbiota profiling approaches relied on PCR amplification of small regions of bacterial and fungal genomes to facilitate identification of the microbes present. However, recent microbiome analysis methods, particularly shotgun metagenomic sequencing, now enable culture-independent profiling of microbiome functions and metabolites in addition to taxonomic characterization. In this review, we showcase recent advances in functional metagenomics methods and applications and discuss the current limitations and potential avenues for future development. Importantly, we highlight a few examples of key areas of opportunity in immunology research where integrating functional metagenomic analyses of the microbiome can substantially enhance a mechanistic understanding of microbiome-immune interactions and their contributions to health and disease states.}, } @article {pmid38951915, year = {2024}, author = {Koci, O and Russell, RK and Shaikh, MG and Edwards, C and Gerasimidis, K and Ijaz, UZ}, title = {CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {117}, pmid = {38951915}, issn = {2049-2618}, support = {NE/L011956/1//NERC Environmental Bioinformatics Centre/ ; BB/T010657/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; EP/V030515/1//Engineering and Physical Sciences Research Council/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Software ; Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Computational Biology/methods ; Metagenome ; Crohn Disease/microbiology/genetics ; }, abstract = {BACKGROUND: Shotgun metagenomics for microbial community survey recovers enormous amount of information for microbial genomes that include their abundances, taxonomic, and phylogenetic information, as well as their genomic makeup, the latter of which then helps retrieve their function based on annotated gene products, mRNA, protein, and metabolites. Within the context of a specific hypothesis, additional modalities are often included, to give host-microbiome interaction. For example, in human-associated microbiome projects, it has become increasingly common to include host immunology through flow cytometry. Whilst there are plenty of software approaches available, some that utilize marker-based and assembly-based approaches, for downstream statistical analyses, there is still a dearth of statistical tools that help consolidate all such information in a single platform. By virtue of stringent computational requirements, the statistical workflow is often passive with limited visual exploration.

RESULTS: In this study, we have developed a Java-based statistical framework (https://github.com/KociOrges/cviewer) to explore shotgun metagenomics data, which integrates seamlessly with conventional pipelines and offers exploratory as well as hypothesis-driven analyses. The end product is a highly interactive toolkit with a multiple document interface, which makes it easier for a person without specialized knowledge to perform analysis of multiomics datasets and unravel biologically relevant patterns. We have designed algorithms based on frequently used numerical ecology and machine learning principles, with value-driven from integrated omics tools which not only find correlations amongst different datasets but also provide discrimination based on case-control relationships.

CONCLUSIONS: CViewer was used to analyse two distinct metagenomic datasets with varying complexities. These include a dietary intervention study to understand Crohn's disease changes during a dietary treatment to include remission, as well as a gut microbiome profile for an obesity dataset comparing subjects who suffer from obesity of different aetiologies and against controls who were lean. Complete analyses of both studies in CViewer then provide very powerful mechanistic insights that corroborate with the published literature and demonstrate its full potential. Video Abstract.}, } @article {pmid38951816, year = {2024}, author = {Qiu, H and Kan, C and Han, F and Luo, Y and Qu, N and Zhang, K and Ma, Y and Hou, N and Wu, D and Sun, X and Shi, J}, title = {Metagenomic and metabolomic analysis showing the adverse risk-benefit trade-off of the ketogenic diet.}, journal = {Lipids in health and disease}, volume = {23}, number = {1}, pages = {207}, pmid = {38951816}, issn = {1476-511X}, support = {ZR2022QH013//Natural Science Foundation of Shandong Province of China/ ; ZR2021QD132//Natural Science Foundation of Shandong Province of China/ ; 202003060400//Shandong Province Medical and Health Science and Technology Development Project/ ; 82170865//National Natural Science Foundation of China/ ; tsqn202211365//Taishan Scholars Project of Shandong Province/ ; 2022YB033//Education, Teaching and Research Projects of Weifang Medical University/ ; }, mesh = {*Diet, Ketogenic/adverse effects ; Animals ; *Gastrointestinal Microbiome ; Male ; Mice ; *Obesity/metabolism/microbiology/etiology ; *Diet, High-Fat/adverse effects ; *Metagenomics/methods ; Metabolomics/methods ; Dysbiosis/microbiology/metabolism ; Mice, Inbred C57BL ; Metabolome ; Body Weight ; }, abstract = {BACKGROUND: Ketogenic diets are increasingly popular for addressing obesity, but their impacts on the gut microbiota and metabolome remain unclear. This paper aimed to investigate how a ketogenic diet affects intestinal microorganisms and metabolites in obesity.

METHODS: Male mice were provided with one of the following dietary regimens: normal chow, high-fat diet, ketogenic diet, or high-fat diet converted to ketogenic diet. Body weight and fat mass were measured weekly using high-precision electronic balances and minispec body composition analyzers. Metagenomics and non-targeted metabolomics data were used to analyze differences in intestinal contents.

RESULTS: Obese mice on the ketogenic diet exhibited notable improvements in weight and body fat. However, these were accompanied by a significant decrease in intestinal microbial diversity, as well as an increase in Firmicutes abundance and a 247% increase in the Firmicutes/Bacteroidetes ratio. The ketogenic diet also altered multiple metabolic pathways in the gut, including glucose, lipid, energy, carbohydrate, amino acid, ketone body, butanoate, and methane pathways, as well as bacterial secretion and colonization pathways. These changes were associated with increased intestinal inflammation and dysbiosis in obese mice. Furthermore, the ketogenic diet enhanced the secretion of bile and the synthesis of aminoglycoside antibiotics in obese mice, which may impair the gut microbiota and be associated with intestinal inflammation and immunity.

CONCLUSIONS: The study suggest that the ketogenic diet had an unfavorable risk-benefit trade-off and may compromise metabolic homeostasis in obese mice.}, } @article {pmid38951807, year = {2024}, author = {Li, W and Cheng, L and He, X and He, G and Liu, Y and Sang, Z and Wang, Y and Shao, M and Xiong, T and Xu, H and Zhao, J}, title = {Gut fungi of black-necked cranes (Grus nigricollis) respond to dietary changes during wintering.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {232}, pmid = {38951807}, issn = {1471-2180}, support = {NO. 202101BA070001-060//Special Basic Cooperative Research Programs of Yunnan Provincial Undergraduate Universities Association/ ; }, mesh = {Animals ; *Seasons ; *Fungi/classification/genetics/isolation & purification ; *Diet ; *Gastrointestinal Microbiome ; *Birds/microbiology ; Gastrointestinal Tract/microbiology ; DNA, Fungal/genetics ; Phylogeny ; }, abstract = {BACKGROUND: Migratory birds exhibit heterogeneity in foraging strategies during wintering to cope with environmental and migratory pressures, and gut bacteria respond to changes in host diet. However, less is known about the dynamics of diet and gut fungi during the wintering period in black-necked cranes (Grus nigricollis).

RESULTS: In this work, we performed amplicon sequencing of the trnL-P6 loop and ITS1 regions to characterize the dietary composition and gut fungal composition of black-necked cranes during wintering. Results indicated that during the wintering period, the plant-based diet of black-necked cranes mainly consisted of families Poaceae, Solanaceae, and Polygonaceae. Among them, the abundance of Solanaceae, Polygonaceae, Fabaceae, and Caryophyllaceae was significantly higher in the late wintering period, which also led to a more even consumption of various food types by black-necked cranes during this period. The diversity of gut fungal communities and the abundance of core fungi were more conserved during the wintering period, primarily dominated by Ascomycota and Basidiomycota. LEfSe analysis (P < 0.05, LDA > 2) found that Pyxidiophora, Pseudopeziza, Sporormiella, Geotrichum, and Papiliotrema were significantly enriched in early winter, Ramularia and Dendryphion were significantly enriched in mid-winter, Barnettozyma was significantly abundant in late winter, and Pleuroascus was significantly abundant in late winter. Finally, mantel test revealed a significant correlation between winter diet and gut fungal.

CONCLUSIONS: This study revealed the dynamic changes in the food composition and gut fungal community of black-necked cranes during wintering in Dashanbao. In the late wintering period, their response to environmental and migratory pressures was to broaden their diet, increase the intake of non-preferred foods, and promote a more balanced consumption ratio of various foods. Balanced food composition played an important role in stabilizing the structure of the gut fungal community. While gut fungal effectively enhanced the host's food utilization rate, they may also faced potential risks of introducing pathogenic fungi. Additionally, we recongnized the limitations of fecal testing in studying the composition of animal gut fungal, as it cannot effectively distinguished between fungal taxa from food or soil inadvertently ingested and intestines. Future research on functions such as cultivation and metagenomics may further elucidate the role of fungi in the gut ecosystem.}, } @article {pmid38949882, year = {2024}, author = {Aparna, KG and Ravindra, J and Chakraborty, G and Ballamoole, KK and Vinaya Kumar, JR and Chakraborty, A}, title = {16S rRNA based metagenomic analysis unveils unique oral microbial signatures in oral squamous cell carcinoma cases from Coastal Karnataka, India.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {71}, number = {3}, pages = {253-262}, doi = {10.1556/030.2024.02307}, pmid = {38949882}, issn = {1588-2640}, mesh = {Humans ; *Mouth Neoplasms/microbiology/genetics ; India ; *RNA, Ribosomal, 16S/genetics ; *Carcinoma, Squamous Cell/microbiology/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics ; *Microbiota ; Male ; Female ; Mouth/microbiology ; Middle Aged ; Adult ; Aged ; }, abstract = {Oral Squamous cell carcinoma (OSCC) is the 14th most frequent cancer with 300,000 new cases and 100,000 deaths reported annually. Even with advanced therapy, the treatment outcomes are poor at advanced stages of the disease. The diagnosis of early OSCC is of paramount clinical value given the high mortality rate associated with the late stages of the disease. Recently, the role of microbiome in the disease manifestation, including oral cancer, has garnered considerable attention. But, to establish the role of bacteria in oral cancer, it is important to determine the differences in the colonization pattern in non-tumour and tumour tissues. In this study, 16S rRNA based metagenomic analyses of 13 tumorous and contralateral anatomically matched normal tissue biopsies, obtained from patients with advanced stage of OSCC were evaluated to understand the correlation between OSCC and oral microbiome. In this study we identified Fusobacterium, Prevotella, Capnocytophaga, Leptotrichia, Peptostreptococcus, Parvimonas and Bacteroidetes as the most significantly enriched taxa in OSCC lesions compared to the non-cancerous tissues. Further, PICRUSt2 analysis unveiled enhanced expression of metabolic pathways associated with L-lysine fermentation, pyruvate fermentation, and isoleucine biosynthesis in those microbes associated with OSCC tissues. These findings provide valuable insights into the distinctive microbial signatures associated with OSCC, offering potential biomarkers and metabolic pathways underlying OSCC pathogenesis. While our focus has primarily centred on microbial signatures, it is essential to recognize the pivotal role of host factors such as immune responses, genetic predisposition, and the oral microenvironment in shaping OSCC development and microbiome composition.}, } @article {pmid38948211, year = {2024}, author = {Kallapura, G and Prakash, AS and Sankaran, K and Manjappa, P and Chaudhary, P and Ambhore, S and Dhar, D}, title = {Microbiota based personalized nutrition improves hyperglycaemia and hypertension parameters and reduces inflammation: a prospective, open label, controlled, randomized, comparative, proof of concept study.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17583}, pmid = {38948211}, issn = {2167-8359}, mesh = {Humans ; Male ; *Hypertension/diet therapy/microbiology ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Prospective Studies ; *Diabetes Mellitus, Type 2/diet therapy/microbiology ; *Hyperglycemia/diet therapy/microbiology ; *Precision Medicine/methods ; Inflammation/diet therapy ; Proof of Concept Study ; Glycated Hemoglobin/metabolism/analysis ; Aged ; Hyperlipidemias/diet therapy/blood/microbiology ; Adult ; C-Reactive Protein/analysis/metabolism ; }, abstract = {BACKGROUND: Recent studies suggest that gut microbiota composition, abundance and diversity can influence many chronic diseases such as type 2 diabetes. Modulating gut microbiota through targeted nutrition can provide beneficial effects leading to the concept of personalized nutrition for health improvement. In this prospective clinical trial, we evaluated the impact of a microbiome-based targeted personalized diet on hyperglycaemic and hyperlipidaemic individuals. Specifically, BugSpeaks[®]-a microbiome profile test that profiles microbiota using next generation sequencing and provides personalized nutritional recommendation based on the individual microbiota profile was evaluated.

METHODS: A total of 30 participants with type 2 diabetes and hyperlipidaemia were recruited for this study. The microbiome profile of the 15 participants (test arm) was evaluated using whole genome shotgun metagenomics and personalized nutritional recommendations based on their microbiota profile were provided. The remaining 15 participants (control arm) were provided with diabetic nutritional guidance for 3 months. Clinical and anthropometric parameters such as HbA1c, systolic/diastolic pressure, c-reactive protein levels and microbiota composition were measured and compared during the study.

RESULTS: The test arm (microbiome-based nutrition) showed a statistically significant decrease in HbA1c level from 8.30 (95% confidence interval (CI), [7.74-8.85]) to 6.67 (95% CI [6.2-7.05]), p < 0.001 after 90 days. The test arm also showed a 5% decline in the systolic pressure whereas the control arm showed a 7% increase. Incidentally, a sub-cohort of the test arm of patients with >130 mm Hg systolic pressure showed a statistically significant decrease of systolic pressure by 14%. Interestingly, CRP level was also found to drop by 19.5%. Alpha diversity measures showed a significant increase in Shannon diversity measure (p < 0.05), after the microbiome-based personalized dietary intervention. The intervention led to a minimum two-fold (Log2 fold change increase in species like Phascolarctobacterium succinatutens, Bifidobacterium angulatum, and Levilactobacillus brevis which might have a beneficial role in the current context and a similar decrease in species like Alistipes finegoldii, and Sutterella faecalis which have been earlier shown to have some negative effects in the host. Overall, the study indicated a net positive impact of the microbiota based personalized dietary regime on the gut microbiome and correlated clinical parameters.}, } @article {pmid38947127, year = {2024}, author = {Li, Y and Qi, X and Wang, Q and He, Y and Li, Z and Cen, X and Wei, L}, title = {Comprehensive analysis of key host gene-microbe networks in the cecum tissues of the obese rabbits induced by a high-fat diet.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1407051}, pmid = {38947127}, issn = {2235-2988}, mesh = {Animals ; Rabbits ; *Diet, High-Fat/adverse effects ; *Cecum/microbiology/metabolism ; *Obesity/metabolism/microbiology ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; Metagenomics ; Bacteria/classification/genetics/metabolism/isolation & purification ; Gene Regulatory Networks ; Male ; Gene Expression Profiling ; }, abstract = {The Cecum is a key site for cellulose digestion in nutrient metabolism of intestine, but its mechanisms of microbial and gene interactions has not been fully elucidated during pathogenesis of obesity. Therefore, the cecum tissues of the New Zealand rabbits and their contents between the high-fat diet-induced group (Ob) and control group (Co) were collected and analyzed using multi-omics. The metagenomic analysis indicated that the relative abundances of Corallococcus_sp._CAG:1435 and Flavobacteriales bacterium species were significantly lower, while those of Akkermansia glycaniphila, Clostridium_sp._CAG:793, Mycoplasma_sp._CAG:776, Mycoplasma_sp._CAG:472, Clostridium_sp._CAG:609, Akkermansia_sp._KLE1605, Clostridium_sp._CAG:508, and Firmicutes_bacterium_CAG:460 species were significantly higher in the Ob as compared to those in Co. Transcriptomic sequencing results showed that the differentially upregulated genes were mainly enriched in pathways, including calcium signaling pathway, PI3K-Akt signaling pathway, and Wnt signaling pathway, while the differentially downregulated genes were mainly enriched in pathways of NF-kappaB signaling pathway and T cell receptor signaling pathway. The comparative analysis of metabolites showed that the glycine, serine, and threonine metabolism and cysteine and methionine metabolism were the important metabolic pathways between the two groups. The combined analysis showed that CAMK1, IGFBP6, and IGFBP4 genes were highly correlated with Clostridium_sp._CAG:793, and Akkermansia_glycaniphila species. Thus, the preliminary study elucidated the microbial and gene interactions in cecum of obese rabbit and provided a basis for further studies in intestinal intervention for human obesity.}, } @article {pmid38945961, year = {2024}, author = {Kim, N and Ma, J and Kim, W and Kim, J and Belenky, P and Lee, I}, title = {Genome-resolved metagenomics: a game changer for microbiome medicine.}, journal = {Experimental & molecular medicine}, volume = {56}, number = {7}, pages = {1501-1512}, pmid = {38945961}, issn = {2092-6413}, support = {R01 DK125382/DK/NIDDK NIH HHS/United States ; HI19C1344//Korea Health Industry Development Institute (KHIDI)/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; Bacteria/genetics/classification ; Animals ; Genome, Bacterial ; Gastrointestinal Microbiome/genetics ; }, abstract = {Recent substantial evidence implicating commensal bacteria in human diseases has given rise to a new domain in biomedical research: microbiome medicine. This emerging field aims to understand and leverage the human microbiota and derivative molecules for disease prevention and treatment. Despite the complex and hierarchical organization of this ecosystem, most research over the years has relied on 16S amplicon sequencing, a legacy of bacterial phylogeny and taxonomy. Although advanced sequencing technologies have enabled cost-effective analysis of entire microbiota, translating the relatively short nucleotide information into the functional and taxonomic organization of the microbiome has posed challenges until recently. In the last decade, genome-resolved metagenomics, which aims to reconstruct microbial genomes directly from whole-metagenome sequencing data, has made significant strides and continues to unveil the mysteries of various human-associated microbial communities. There has been a rapid increase in the volume of whole metagenome sequencing data and in the compilation of novel metagenome-assembled genomes and protein sequences in public depositories. This review provides an overview of the capabilities and methods of genome-resolved metagenomics for studying the human microbiome, with a focus on investigating the prokaryotic microbiota of the human gut. Just as decoding the human genome and its variations marked the beginning of the genomic medicine era, unraveling the genomes of commensal microbes and their sequence variations is ushering us into the era of microbiome medicine. Genome-resolved metagenomics stands as a pivotal tool in this transition and can accelerate our journey toward achieving these scientific and medical milestones.}, } @article {pmid38945213, year = {2024}, author = {Si, HR and Wu, K and Su, J and Dong, TY and Zhu, Y and Li, B and Chen, Y and Li, Y and Shi, ZL and Zhou, P}, title = {Individual virome analysis reveals the general co-infection of mammal-associated viruses with SARS-related coronaviruses in bats.}, journal = {Virologica Sinica}, volume = {39}, number = {4}, pages = {565-573}, pmid = {38945213}, issn = {1995-820X}, mesh = {*Chiroptera/virology ; Animals ; *Virome ; China ; *Coinfection/virology/veterinary/microbiology ; *Metagenomics ; *Severe acute respiratory syndrome-related coronavirus/genetics/isolation & purification/classification ; Phylogeny ; Genome, Viral/genetics ; Disease Reservoirs/virology ; }, abstract = {Bats are the natural reservoir hosts for SARS-related coronavirus (SARSr-CoV) and other highly pathogenic microorganisms. Therefore, it is conceivable that an individual bat may harbor multiple microbes. However, there is limited knowledge on the overall co-circulation of microorganisms in bats. Here, we conducted a 16-year monitoring of bat viruses in south and central China and identified 238 SARSr-CoV positive samples across nine bat species from ten provinces or administrative districts. Among these, 76 individual samples were selected for further metagenomics analysis. We found a complex microenvironment characterized by the general co-circulation of microbes from two different sources: mammal-associated viruses or environment-associated microbes. The later includes commensal bacteria, enterobacteria-related phages, and insect or fungal viruses of food origin. Results showed that 25% (19/76) of the samples contained at least one another mammal-associated virus, notably alphacoronaviruses (13/76) such as AlphaCoV/YN2012, HKU2-related CoV and AlphaCoV/Rf-HuB2013, along with viruses from other families. Notably, we observed three viruses co-circulating within a single bat, comprising two coronavirus species and one picornavirus. Our analysis also revealed the potential presence of pathogenic bacteria or fungi in bats. Furthermore, we obtained 25 viral genomes from the 76 bat SARSr-CoV positive samples, some of which formed new evolutionary lineages. Collectively, our study reveals the complex microenvironment of bat microbiome, facilitating deeper investigations into their pathogenic potential and the likelihood of cross-species transmission.}, } @article {pmid38945001, year = {2024}, author = {Schäfer, L and Grundmann, SM and Rühl, M and Zorn, H and Seel, W and Simon, MC and Schuchardt, S and Most, E and Ringseis, R and Eder, K}, title = {Effects of a biotechnologically produced Pleurotus sapidus mycelium on gut microbiome, liver transcriptome and plasma metabolome of broilers.}, journal = {Poultry science}, volume = {103}, number = {9}, pages = {103975}, pmid = {38945001}, issn = {1525-3171}, mesh = {Animals ; *Chickens ; *Gastrointestinal Microbiome ; *Pleurotus ; *Animal Feed/analysis ; Male ; *Transcriptome ; *Liver/metabolism ; *Diet/veterinary ; *Metabolome ; *Mycelium ; *Dietary Supplements/analysis ; Random Allocation ; }, abstract = {Submerged cultivation using low-value agro-industrial side streams allows large-scale and efficient production of fungal mycelia, which has a high nutritional value. As the dietary properties of fungal mycelia in poultry are largely unknown, the present study aimed to investigate the effect of feeding a Pleurotus sapidus (PSA) mycelium as a feed supplement on growth performance, composition of the cecal microbiota and several physiological traits including gut integrity, nutrient digestibility, liver lipids, liver transcriptome and plasma metabolome in broilers. 72 males, 1-day-old Cobb 500 broilers were randomly assigned to 3 different groups and fed 3 different adequate diets containing either 0% (PSA-0), 2.5% (PSA-2.5) and 5% (PSA-5.0) P. sapidus mycelium in a 3-phase feeding system for 35 d. Each group consisted of 6 cages (replicates) with 4 broilers/cage. Body weight gain, feed intake and feed:gain ratio and apparent ileal digestibility of crude protein, ether extract and amino acids were not different between groups. Metagenomic analysis of the cecal microbiota revealed no differences between groups, except that one α-diversity metric (Shannon index) and the abundance of 2 low-abundance bacterial taxa (Clostridia UCG 014, Eubacteriales) differed between groups (P < 0.05). Concentrations of total and individual short-chain fatty acids in the cecal digesta and concentrations of plasma lipopolysaccharide and mRNA levels of proinflammatory genes, tight-junction proteins, and mucins in the cecum mucosa did not differ between groups. None of the plasma metabolites analyzed using targeted-metabolomics differed across the groups. Hepatic transcript profiling revealed a total of 144 transcripts to be differentially expressed between group PSA-5.0 and group PSA-0 but none of these genes was regulated greater 2-fold. Considering either the lack of effects or the very weak effects of feeding the P. sapidus mycelium in the broilers it can be concluded that inclusion of a sustainably produced fungal mycelium in broiler diets at the expense of other feed components has no negative consequences on broilers´ performance and metabolism.}, } @article {pmid38944892, year = {2024}, author = {Bhat, AH and Tak, H and Ganai, BA and Malik, IM and Bambou, JC}, title = {Beyond parasitism: Exploring the microbial profile of Haemonchus contortus and its predilection site (abomasum) in Kashmir Merino sheep.}, journal = {Veterinary parasitology}, volume = {330}, number = {}, pages = {110243}, doi = {10.1016/j.vetpar.2024.110243}, pmid = {38944892}, issn = {1873-2550}, mesh = {Animals ; Sheep ; *Haemonchus/physiology ; *Sheep Diseases/parasitology/microbiology ; *Haemonchiasis/veterinary/parasitology ; *Abomasum/parasitology/microbiology ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Host-Parasite Interactions ; India ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Gastrointestinal helminth infection, particularly by Haemonchus contortus, poses significant challenges to sheep farming worldwide. While anthelmintic drugs have been traditional control measures, the emergence of resistance calls for alternative strategies. Understanding the interaction between parasites, host, and their microbiome is crucial for management of helminth infection. This study intricately explores the interactions between microbial communities in Kashmir Merino sheep infected with H. contortus, to understand the complex interplay between host, parasite, and their microbiome. Sheep abomasal contents and H. contortus were collected from infected and control groups, processed for DNA extraction, and subjected to metagenomic sequencing of the 16 S rRNA gene. Downstream analysis unveils distinct microbial patterns, where Proteobacteria were dominant in H. contortus, while Bacteroidota and Firmicutes prevailed in the sheep abomasum. The revelation of unique genera and shifts in diversity indices underscored helminth-induced disruptions in the host. Beta diversity analysis further showed significant variations in bacterial profiles, providing insights into the intricate host, parasite, and microbiome dynamics. Additionally, this study elucidated the presence of pathogenic bacteria within H. contortus, accentuating their potential role in exacerbating sheep health issues. This finding underscores the complexity of the host-parasite-microbiome interaction showing helminth-induced microbiome alterations of the host.}, } @article {pmid38943887, year = {2024}, author = {Zhou, Y and Wang, Y and Yao, S and Zhao, X and Kong, Q and Cui, L and Zhang, H}, title = {Driving mechanisms for the adaptation and degradation of petroleum hydrocarbons by native microbiota from seas prone to oil spills.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {135060}, doi = {10.1016/j.jhazmat.2024.135060}, pmid = {38943887}, issn = {1873-3336}, mesh = {*Biodegradation, Environmental ; *Petroleum Pollution ; *Microbiota ; *Petroleum/metabolism ; *Seawater/microbiology ; *Water Pollutants, Chemical/metabolism ; *Hydrocarbons/metabolism ; Bacteria/metabolism/genetics/classification ; Oceans and Seas ; Adaptation, Physiological ; Gas Chromatography-Mass Spectrometry ; }, abstract = {Offshore waters have a high incidence of oil pollution, which poses an elevated risk of ecological damage. The microbial community composition and metabolic mechanisms influenced by petroleum hydrocarbons vary across different marine regions. However, research on metabolic strategies for in-situ petroleum degradation and pollution adaptation remains in its nascent stages. This study combines metagenomic techniques with gas chromatography-mass spectrometry (GC-MS) analysis. The data show that the genera Pseudoalteromonas, Hellea, Lentisphaera, and Polaribacter exhibit significant oil-degradation capacity, and that the exertion of their degradation capacity is correlated with nutrient and oil pollution stimuli. Furthermore, tmoA, badA, phdF, nahAc, and fadA were found to be the key genes involved in the degradation of benzene, polycyclic aromatic hydrocarbons, and their intermediates. Key genes (INSR, SLC2A1, and ORC1) regulate microbial adaptation to oil-contaminated seawater, activating oil degradation processes. This process enhances the biological activity of microbial communities and accounts for the geographical variation in their compositional structure. Our results enrich the gene pool for oil pollution adaptation and degradation and provide an application basis for optimizing bioremediation intervention strategies.}, } @article {pmid38943206, year = {2024}, author = {Larzul, C and Estellé, J and Borey, M and Blanc, F and Lemonnier, G and Billon, Y and Thiam, MG and Quinquis, B and Galleron, N and Jardet, D and Lecardonnel, J and Plaza Oñate, F and Rogel-Gaillard, C}, title = {Driving gut microbiota enterotypes through host genetics.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {116}, pmid = {38943206}, issn = {2049-2618}, support = {Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Swine/microbiology ; *Feces/microbiology ; Bacteria/classification/genetics ; Metagenomics/methods ; Prevotella/genetics/classification ; Ruminococcus/genetics ; Treponema/genetics ; }, abstract = {BACKGROUND: Population stratification based on interindividual variability in gut microbiota composition has revealed the existence of several ecotypes named enterotypes in humans and various animal species. Enterotypes are often associated with environmental factors including diet, but knowledge of the role of host genetics remains scarce. Moreover, enterotypes harbor functionalities likely associated with varying abilities and susceptibilities of their host. Previously, we showed that under controlled conditions, 60-day-old pig populations consistently split into two enterotypes with either Prevotella and Mitsuokella (PM enterotype) or Ruminococcus and Treponema (RT enterotype) as keystone taxa. Here, our aim was to rely on pig as a model to study the influence of host genetics to assemble enterotypes, and to provide clues on enterotype functional differences and their links with growth traits.

RESULTS: We established two pig lines contrasted for abundances of the genera pairs specifying each enterotype at 60 days of age and assessed them for fecal microbiota composition and growth throughout three consecutive generations. Response to selection across three generations revealed, per line, an increase in the prevalence of the selected enterotype and in the average relative abundances of directly and indirectly selected bacterial genera. The PM enterotype was found less diverse than the RT enterotype but more efficient for piglet growth during the post-weaning period. Shotgun metagenomics revealed differentially abundant bacterial species between the two enterotypes. By using the KEGG Orthology database, we show that functions related to starch degradation and polysaccharide metabolism are enriched in the PM enterotype, whereas functions related to general nucleoside transport and peptide/nickel transport are enriched in the RT enterotype. Our results also suggest that the PM and RT enterotypes might differ in the metabolism of valine, leucin, and isoleucine, favoring their biosynthesis and degradation, respectively.

CONCLUSION: We experimentally demonstrated that enterotypes are functional ecosystems that can be selected as a whole by exerting pressure on the host genetics. We also highlight that holobionts should be considered as units of selection in breeding programs. These results pave the way for a holistic use of host genetics, microbiota diversity, and enterotype functionalities to understand holobiont shaping and adaptation. Video Abstract.}, } @article {pmid38943070, year = {2024}, author = {Laux, M and Ciapina, LP and de Carvalho, FM and Gerber, AL and Guimarães, APC and Apolinário, M and Paes, JES and Jonck, CR and de Vasconcelos, ATR}, title = {Living in mangroves: a syntrophic scenario unveiling a resourceful microbiome.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {228}, pmid = {38943070}, issn = {1471-2180}, support = {Process number: 2018/00190-8//Petrobras/ ; 307145/2021-2//CNPq/ ; E-26/210.012/ 2020 and E-26/201.046/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; }, mesh = {*Microbiota/genetics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Wetlands ; Phylogeny ; Heterotrophic Processes ; Carbon Cycle ; Carbon/metabolism ; Methane/metabolism ; Autotrophic Processes ; Metabolic Networks and Pathways/genetics ; }, abstract = {BACKGROUND: Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The frequent variation in organic matter concentration, nutrients, and oxygen availability, among other factors, drives the microbial community composition, favoring syntrophic populations harboring a rich and diverse, stress-driven metabolism. Mangroves are known for their carbon sequestration capability, and their complex and integrated metabolic activity is essential to global biogeochemical cycling. Here, we present a metabolic reconstruction based on the genomic functional capability and flux profile between sympatric MAGs co-assembled from a tropical restored mangrove.

RESULTS: Eleven MAGs were assigned to six Bacteria phyla, all distantly related to the available reference genomes. The metabolic reconstruction showed several potential coupling points and shortcuts between complementary routes and predicted syntrophic interactions. Two metabolic scenarios were drawn: a heterotrophic scenario with plenty of carbon sources and an autotrophic scenario with limited carbon sources or under inhibitory conditions. The sulfur cycle was dominant over methane and the major pathways identified were acetate oxidation coupled to sulfate reduction, heterotrophic acetogenesis coupled to carbohydrate catabolism, ethanol production and carbon fixation. Interestingly, several gene sets and metabolic routes similar to those described for wastewater and organic effluent treatment processes were identified.

CONCLUSION: The mangrove microbial community metabolic reconstruction reflected the flexibility required to survive in fluctuating environments as the microhabitats created by the tidal regime in mangrove sediments. The metabolic components related to wastewater and organic effluent treatment processes identified strongly suggest that mangrove microbial communities could represent a resourceful microbial model for biotechnological applications that occur naturally in the environment.}, } @article {pmid38942995, year = {2024}, author = {Ebrahimi, H and Dizman, N and Meza, L and Malhotra, J and Li, X and Dorff, T and Frankel, P and Llamas-Quitiquit, M and Hsu, J and Zengin, ZB and Alcantara, M and Castro, D and Mercier, B and Chawla, N and Chehrazi-Raffle, A and Barragan-Carrillo, R and Jaime-Casas, S and Govindarajan, A and Gillece, J and Trent, J and Lee, PP and Parks, TP and Takahashi, M and Hayashi, A and Kortylewski, M and Caporaso, JG and Lee, K and Tripathi, A and Pal, SK}, title = {Cabozantinib and nivolumab with or without live bacterial supplementation in metastatic renal cell carcinoma: a randomized phase 1 trial.}, journal = {Nature medicine}, volume = {30}, number = {9}, pages = {2576-2585}, pmid = {38942995}, issn = {1546-170X}, mesh = {Humans ; *Nivolumab/therapeutic use/adverse effects ; *Carcinoma, Renal Cell/drug therapy/pathology ; *Anilides/therapeutic use/administration & dosage ; *Pyridines/therapeutic use ; Male ; Female ; Middle Aged ; *Kidney Neoplasms/drug therapy/pathology ; Aged ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use/adverse effects ; Adult ; Gastrointestinal Microbiome/drug effects ; Neoplasm Metastasis ; Progression-Free Survival ; }, abstract = {Supplementation with CBM588, a bifidogenic live bacterial product, has been associated with improved clinical outcomes in persons with metastatic renal cell carcinoma (mRCC) receiving nivolumab and ipilimumab. However, its effect on those receiving tyrosine kinase inhibitor-based combinations is unknown. In this open-label, randomized, investigator-initiated, phase 1 study, 30 participants with locally advanced or mRCC with histological confirmation of clear cell, papillary or sarcomatoid component were randomized in a 2:1 fashion to receive cabozantinib (an inhibitor of vascular endothelial growth factor receptor, MET and AXL) and nivolumab (anti-programmed cell death protein 1) with or without CBM588 as first-line treatment. Metagenomic sequencing was performed on stool samples to characterize their gut microbiome at baseline and 13 weeks into treatment. The primary endpoint was a change in the relative abundance of Bifidobacterium spp.; secondary endpoints included objective response rate (ORR), progression-free survival (PFS) and toxicity profile. The primary endpoint of the study was not met and the addition of CBM588 to cabozantinib and nivolumab did not result in a difference in the relative abundance of Bifidobacterium spp. or alpha diversity (as measured by the Shannon index). However, ORR was significantly higher in participants treated with CBM588 compared to those in the control arm (14 of 19, 74% versus 2 of 10, 20%; P = 0.01). PFS at 6 months was 84% (16 of 19) and 60% (6 of 10) in the experimental and control arms, respectively. No significant difference in toxicity profile was seen between the study arms. Our results provide a preliminary signal of improved clinical activity with CBM588 in treatment-naive participants with mRCC receiving cabozantinib and nivolumab. Further investigation is needed to confirm these findings and better characterize the underlying mechanism driving this effect.ClinicalTrials.gov identifier: NCT05122546.}, } @article {pmid38942886, year = {2024}, author = {Fo, X and Pei, ML and Liu, PJ and Zhu, F and Zhang, Y and Mu, X}, title = {Metagenomic analysis revealed the association between gut microbiota and different ovary responses to controlled ovarian stimulation.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {14930}, pmid = {38942886}, issn = {2045-2322}, support = {2022SF-471//Shaanxi Science and Technology/ ; }, mesh = {Female ; *Gastrointestinal Microbiome ; Animals ; Humans ; *Metagenomics/methods ; Adult ; Mice ; *Ovulation Induction/methods ; Ovary/microbiology ; Pregnancy ; Feces/microbiology ; Fertilization in Vitro/methods ; }, abstract = {The aim of this study was to assess the correlation between gut microbial taxonomy and various ovarian responses to controlled ovarian stimulation. A total of 22 IVF cycles with a follicle-to-oocyte index (FOI) < 0.5 and 25 IVF cycles with FOI ≥ 0.5 were included in this study. Baseline demographic characteristics were compared between the two groups. Metagenomic sequencing was performed to analyze fecal microbial community profiles. Mice were used to evaluate the effect of Bifidobacterium_longum on ovarian response to stimulation. Compared with FOI < 0.5 group, women in group with FOI ≥ 0.5 had significant more oocytes retrieved (p < 0.01). Prevotella_copri, Bateroides_vulgatus, Escherichia_coli and Bateroides_stercoris were more abundant in FOI < 0.5 group while Bifidobacterium_longum, Faecalibacterium_prausnitzii, Ruminococcus_gnavus and Bifidobacterium_pseudocatenula were more abundant in FOI ≥ 0.5 group. After adjusting for women's age and BMI, Pearson correlation analysis indicated alteration of gut microbiome was related with serum E2, FSH, number of oocytes retrieved and clinical pregnancy rate. Animal study showed ovarian response will be improved after Bifidobacterium_longum applied. An increased abundance of Bacteroidetes and Prevotella copri, as well as a decreased abundance of Bifidobacterium longum, have been found to be associated with poor ovarian responsiveness. Changes in gut microbiomes have been observed to be correlated with certain clinical characteristics. The potential enhancement of ovarian response may be facilitated by the integration of Bifidobacterium longum.}, } @article {pmid38942318, year = {2024}, author = {Ogola, HJO and Ijoma, GN and Edokpayi, JN}, title = {Exploring the dichotomy: Shotgun metagenomics reveals diversity of beneficial and pathogenic protist community in arid wetlands of northeastern South Africa.}, journal = {The Science of the total environment}, volume = {946}, number = {}, pages = {174306}, doi = {10.1016/j.scitotenv.2024.174306}, pmid = {38942318}, issn = {1879-1026}, mesh = {*Wetlands ; South Africa ; *Biodiversity ; Metagenomics ; Eukaryota/genetics ; Metagenome ; Microbiota ; }, abstract = {Arid regions harbor seasonal and permanent wetlands, as biodiversity hotspots crucial for ecosystem services despite harsh conditions. These wetlands, typically dependent on episodic intense rainfall, are understudied compared to their humid counterparts. While the diversity of plants and animals in these wetlands is well-known, the microbial communities remain largely unexplored. To address this knowledge gap, we employed metagenome sequencing technologies to profile protist communities, including pathogenic protozoa, and their associated functional pathways, in sediment of permanent and seasonal arid freshwater wetlands across northern South Africa. Results revealed a core community of protists dominated by phylum Apicomplexa (66.73 %), Euglenazoa (19.03 %), Bacillariophyta (5.44 %), Metamonada (4.65 %), Cryptophyta (1.90 %), and Amoebazoa (1.21 %). Seasonal wetlands showed significantly higher protist diversity compared to permanent wetlands (Shannon index, p = 0.019; Chao1, p = 0.0095). A high abundance and diversity of human and zoonotic pathogenic protists (87.67 %) was observed, with lower levels of photoautotrophs (6.69 %) and limited diversity of phagotrophs (5.64 %). Key photoautotrophs identified included diatoms (Thalassiosiraceae and Phaeodactylaceae) and cryptophytes (genus Hemiselmis and Cryptophyta), with consumers/phagotrophs exhibited a correlation with the bacterial community abundance (r[2] = 0.218, p < 0.001). Pathogenic protozoans identified, include malaria-causing Plasmodium, kinetoplastids (genus Besnoita, Theilleria, Neospora, Toxoplasma, Encephalitozoon, and Babesia) and waterborne protozoans of public health importance (such as Cryptosporidium parvum and Giardia lamblia). Furthermore, the enrichment of pathogenesis-associated pathways (amino acid biosynthesis, peptidoglycan maturation, heme biosynthesis and degradation, and the Calvin-Benson-Bassham cycle), along with virulence gene families identified, highlighted these wetlands as potential reservoirs for infectious diseases. Our results unveil a baseline protist taxonomic and functional composition within arid wetlands, including beneficial and pathogenic protozoa. The close proximity of these wetlands to human activity raises concern for local and transboundary spread of these pathogens. Thus, continued monitoring is vital for disease control and preserving these unique ecosystems.}, } @article {pmid38941664, year = {2024}, author = {Parab, AS and Manohar, CS}, title = {Insights into the seasonal changes in the taxonomic and functional diversity of bacteria in the eastern Arabian Sea: Shotgun metagenomics approach.}, journal = {Marine environmental research}, volume = {199}, number = {}, pages = {106616}, doi = {10.1016/j.marenvres.2024.106616}, pmid = {38941664}, issn = {1879-0291}, mesh = {*Seasons ; *Bacteria/genetics/classification ; *Metagenomics ; *Seawater/microbiology ; Biodiversity ; Oceans and Seas ; }, abstract = {The eastern Arabian Sea (EAS) is known for its unique oceanographic features such as the seasonal monsoonal winds, upwelling of nutrient-rich waters and a significant increase in primary productivity during the monsoon season. In this study, we utilised the shotgun metagenomics approach to determine the seasonal variations in bacterial taxonomic and functional profiles during the non-monsoon and monsoon seasons in the EAS. Significant seasonal variations in the bacterial community structure were observed at the phylum and genera levels. These findings also correspond with seasonal shifts in the functional profiles of the bacterial communities based on the variations of genes encoding enzymes associated with different metabolic pathways. Pronounced seasonal variation of bacterial taxa was evident with an increased abundance of Idiomarina, Marinobacter, Psychrobacter and Alteromonas of Proteobacteria, Bacillus and Staphylococcus of Firmicutes during the non-monsoon season. These taxa were linked to elevated nucleotide and amino acid biosynthesis, amino acid and lipid degradation. Conversely, during the monsoon, the taxa composition changed with Alteromonas, Candidatus Pelagibacter of Proteobacteria and Cyanobacteria Synechococcus; contributing largely to the amino acid and lipid biosynthesis, fermentation and inorganic nutrient metabolism which was evident from functional analysis. Regression analysis confirmed that increased seasonal primary productivity significantly influenced the abundance of genes associated with carbohydrate, protein and lipid metabolism. These highlight the pivotal role of seasonal changes in primary productivity in shaping the bacterial communities, their functional profiles and driving the biogeochemical cycling in the EAS.}, } @article {pmid38941024, year = {2024}, author = {Holstein, T and Muth, T}, title = {Bioinformatic Workflows for Metaproteomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2820}, number = {}, pages = {187-213}, pmid = {38941024}, issn = {1940-6029}, mesh = {*Proteomics/methods ; *Computational Biology/methods ; *Workflow ; *Software ; *Microbiota/genetics ; Humans ; Databases, Protein ; Metagenomics/methods ; }, abstract = {The strong influence of microbiomes on areas such as ecology and human health has become widely recognized in the past years. Accordingly, various techniques for the investigation of the composition and function of microbial community samples have been developed. Metaproteomics, the comprehensive analysis of the proteins from microbial communities, allows for the investigation of not only the taxonomy but also the functional and quantitative composition of microbiome samples. Due to the complexity of the investigated communities, methods developed for single organism proteomics cannot be readily applied to metaproteomic samples. For this purpose, methods specifically tailored to metaproteomics are required. In this work, a detailed overview of current bioinformatic solutions and protocols in metaproteomics is given. After an introduction to the proteomic database search, the metaproteomic post-processing steps are explained in detail. Ten specific bioinformatic software solutions are focused on, covering various steps including database-driven identification and quantification as well as taxonomic and functional assignment.}, } @article {pmid38940525, year = {2024}, author = {Huang, Y and Zhang, X and Xin, Y and Tian, J and Li, M}, title = {Distinct microbial nitrogen cycling processes in the deepest part of the ocean.}, journal = {mSystems}, volume = {9}, number = {7}, pages = {e0024324}, pmid = {38940525}, issn = {2379-5077}, support = {91951102//MOST | National Natural Science Foundation of China (NSFC)/ ; 92251306, 32070108, 32225003//MOST | National Natural Science Foundation of China (NSFC)/ ; 2023B0303000017//Guangdong Major Project of Basic and Applied Basic Research/ ; SML2023SP218//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 2022B002//Shenzhen University 2035 Program for Excellent Research/ ; //Synthetic Biology Research Center of Shenzhen University/ ; }, mesh = {*Seawater/microbiology/chemistry ; *Nitrogen Cycle ; *Geologic Sediments/microbiology ; *Bacteria/metabolism/genetics ; *Oceans and Seas ; Nitrogen/metabolism ; Microbiota/physiology ; Phylogeny ; }, abstract = {UNLABELLED: The Mariana Trench (MT) is the deepest part of the ocean on Earth. Previous studies have described the microbial community structures and functional potential in the seawater and surface sediment of MT. Still, the metabolic features and adaptation strategies of the microorganisms involved in nitrogen cycling processes are poorly understood. In this study, comparative metagenomic approaches were used to study microbial nitrogen cycling in three MT habitats, including hadal seawater [9,600-10,500 m below sea level (mbsl)], surface sediments [0-46 cm below seafloor (cmbsf) at a water depth between 7,143 and 8,638 mbsl], and deep sediments (200-306 cmbsf at a water depth of 8,300 mbsl). We identified five new nitrite-oxidizing bacteria (NOB) lineages that had adapted to the oligotrophic MT slope sediment, via their CO2 fixation capability through the reductive tricarboxylic acid (rTCA) or Calvin-Benson-Bassham (CBB) cycle; an anammox bacterium might perform aerobic respiration and utilize sedimentary carbohydrates for energy generation because it contains genes encoding type A cytochrome c oxidase and complete glycolysis pathway. In seawater, abundant alkane-oxidizing Ketobacter species can fix inert N2 released from other denitrifying and/or anammox bacteria. This study further expands our understanding of microbial life in the largely unexplored deepest part of the ocean.

IMPORTANCE: The metabolic features and adaptation strategies of the nitrogen cycling microorganisms in the deepest part of the ocean are largely unknown. This study revealed that anammox bacteria might perform aerobic respiration in response to nutrient limitation or O2 fluctuations in the Mariana Trench sediments. Meanwhile, an abundant alkane-oxidizing Ketobacter species could fix N2 in hadal seawater. This study provides new insights into the roles of hadal microorganisms in global nitrogen biogeochemical cycles. It substantially expands our understanding of the microbial life in the largely unexplored deepest part of the ocean.}, } @article {pmid38940510, year = {2024}, author = {Finnegan, PM and Garber, PA and McKenney, AC and Bicca-Marques, JC and De la Fuente, MF and Abreu, F and Souto, A and Schiel, N and Amato, KR and Mallott, EK}, title = {Group membership, not diet, structures the composition and functional potential of the gut microbiome in a wild primate.}, journal = {mSphere}, volume = {9}, number = {7}, pages = {e0023324}, pmid = {38940510}, issn = {2379-5042}, support = {PVE 88881.064998/2014-01//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; APQ 03126/2016-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; PQ-1C 303306/2013-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Callithrix/microbiology ; *Diet ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; Brazil ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Male ; Female ; Animals, Wild/microbiology ; }, abstract = {UNLABELLED: The gut microbiome has the potential to buffer temporal variations in resource availability and consumption, which may play a key role in the ability of animals to adapt to a broad range of habitats. We investigated the temporal composition and function of the gut microbiomes of wild common marmosets (Callithrix jacchus) exploiting a hot, dry environment-Caatinga-in northeastern Brazil. We collected fecal samples during two time periods (July-August and February-March) for 2 years from marmosets belonging to eight social groups. We used 16S rRNA gene amplicon sequencing, metagenomic sequencing, and butyrate RT-qPCR to assess changes in the composition and potential function of their gut microbiomes. Additionally, we identified the plant, invertebrate, and vertebrate components of the marmosets' diet via DNA metabarcoding. Invertebrate, but not plant or vertebrate, consumption varied across the year. However, gut microbiome composition and potential function did not markedly vary across study periods or as a function of diet composition. Instead, the gut microbiome differed markedly in both composition and potential function across marmosets residing in different social groups. We highlight the likely role of factors, such as behavior, residence, and environmental heterogeneity, in modulating the structure of the gut microbiome.

IMPORTANCE: In a highly socially cohesive and cooperative primate, group membership more strongly predicts gut microbiome composition and function than diet.}, } @article {pmid38940462, year = {2024}, author = {Zeng, Y and Fan, N and Gu, X and Zhang, Y and Min, W and Mao, Q and Qian, Q}, title = {Characteristics of gut microbiota and serum metabolism in patients with atopic dermatitis.}, journal = {Skin research and technology : official journal of International Society for Bioengineering and the Skin (ISBS) [and] International Society for Digital Imaging of Skin (ISDIS) [and] International Society for Skin Imaging (ISSI)}, volume = {30}, number = {7}, pages = {e13792}, pmid = {38940462}, issn = {1600-0846}, support = {YJXK-2021-14//Minhang District Central Hospital of Shanghai Municipal/ ; }, mesh = {Humans ; *Dermatitis, Atopic/microbiology/blood ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Adult ; *Feces/microbiology ; Child ; Young Adult ; Middle Aged ; Adolescent ; Metabolome/physiology ; Bacteroidetes ; }, abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin disease that affects 15%-30% of children and 10% of adults globally, with its incidence being influenced by genetic, environmental, and various other factors. While the immune plays a crucial role in the development, the composition of gut microbiota and serum metabolites also contribute to its pathogenesis.

SUBJECT: Study the characteristics of gut microbiota and serum metabolites in patients with atopic dermatitis METHOD: In this study, we collected stool and serum samples from 28 AD patients and 23 healthy individuals (NC) for metagenomic sequencing of gut microbiota and non-targeted metabolomic sequencing of serum.

RESULT: Our results revealed a lower diversity of gut microbiota in the AD group compared to the NC group. The predominant Phylum in AD patients were Bacteroidetes, Pseudomonas, and Verrucomicrobia, with the most dominant bacterial genus being Faecalibacterium. At the species level, Prevotella copri and Faecalibacterium prausnitzii were found to be the most abundant bacteria. Significant differences in serum metabolite profiles were observed between NC and AD patients, with noticeable variations in metabolite expression levels. The majority of metabolites in the serum of AD patients exhibited low expression, while a few showed high expression levels. Notably, metabolites such as Cholesterol glucuronide, Styrene, Lutein, Betaine, Phosphorylcholine, Taurine, and Creatinine displayed the most pronounced alterations.

CONCLUSION: These findings contribute to a further understanding of the complexities underlying this disease.}, } @article {pmid38940183, year = {2024}, author = {Shaw, J and Gounot, JS and Chen, H and Nagarajan, N and Yu, YW}, title = {Floria: fast and accurate strain haplotyping in metagenomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {Suppl 1}, pages = {i30-i38}, pmid = {38940183}, issn = {1367-4811}, support = {//A*STAR Computational Resource Centre/ ; RGPIN-2022-03074//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Metagenome ; *Metagenomics/methods ; Haplotypes ; Software ; Humans ; Genome, Bacterial ; Microbiota/genetics ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; }, abstract = {SUMMARY: Shotgun metagenomics allows for direct analysis of microbial community genetics, but scalable computational methods for the recovery of bacterial strain genomes from microbiomes remains a key challenge. We introduce Floria, a novel method designed for rapid and accurate recovery of strain haplotypes from short and long-read metagenome sequencing data, based on minimum error correction (MEC) read clustering and a strain-preserving network flow model. Floria can function as a standalone haplotyping method, outputting alleles and reads that co-occur on the same strain, as well as an end-to-end read-to-assembly pipeline (Floria-PL) for strain-level assembly. Benchmarking evaluations on synthetic metagenomes show that Floria is > 3× faster and recovers 21% more strain content than base-level assembly methods (Strainberry) while being over an order of magnitude faster when only phasing is required. Applying Floria to a set of 109 deeply sequenced nanopore metagenomes took <20 min on average per sample and identified several species that have consistent strain heterogeneity. Applying Floria's short-read haplotyping to a longitudinal gut metagenomics dataset revealed a dynamic multi-strain Anaerostipes hadrus community with frequent strain loss and emergence events over 636 days. With Floria, accurate haplotyping of metagenomic datasets takes mere minutes on standard workstations, paving the way for extensive strain-level metagenomic analyses.

Floria is available at https://github.com/bluenote-1577/floria, and the Floria-PL pipeline is available at https://github.com/jsgounot/Floria_analysis_workflow along with code for reproducing the benchmarks.}, } @article {pmid38940156, year = {2024}, author = {Curry, KD and Yu, FB and Vance, SE and Segarra, S and Bhaya, D and Chikhi, R and Rocha, EPC and Treangen, TJ}, title = {Reference-free structural variant detection in microbiomes via long-read co-assembly graphs.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {Suppl 1}, pages = {i58-i67}, pmid = {38940156}, issn = {1367-4811}, support = {//Department of Energy Joint Genome Institute/ ; P01 AI152999/AI/NIAID NIH HHS/United States ; //National Institute of Allergy and Infectious Diseases/ ; //Department of Energy/ ; P01-AI152999/GF/NIH HHS/United States ; //European Union's Horizon 2020/ ; 2023333162//NSF/ ; //Office of Science/ ; //Carnegie Institution for Science/ ; //Ken Kennedy Institute Recruiting/ ; EF-2126387//MIM Universal Rules of Live/ ; //Rice University Wagoner Foreign Study Scholarship/ ; IIS-2239114//NSF/ ; 872539//Marie Skłodowska-Curie/ ; //NSF/ ; }, mesh = {*Microbiota/genetics ; *Metagenome ; *Genome, Bacterial ; Metagenomics/methods ; Gene Transfer, Horizontal ; Bacteria/genetics ; Algorithms ; }, abstract = {MOTIVATION: The study of bacterial genome dynamics is vital for understanding the mechanisms underlying microbial adaptation, growth, and their impact on host phenotype. Structural variants (SVs), genomic alterations of 50 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to the absence of clear reference genomes and the presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing all metagenomic samples in a series (time or other metric) into a single co-assembly graph. The log fold change in graph coverage between successive samples is then calculated to call SVs that are thriving or declining.

RESULTS: We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, particularly as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between successive time and temperature samples, suggesting host advantage. Our approach leverages previous work in assembly graph structural and coverage patterns to provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial gene flux.

rhea is open source and available at: https://github.com/treangenlab/rhea.}, } @article {pmid38938117, year = {2024}, author = {Tansirichaiya, S and Songsomboon, K and Chaianant, N and Lertsivawinyu, W and Al-Haroni, M}, title = {Impact of cell lysis treatment before saliva metagenomic DNA extraction on the oral microbiome and the associated resistome.}, journal = {Clinical and experimental dental research}, volume = {10}, number = {4}, pages = {e905}, pmid = {38938117}, issn = {2057-4347}, support = {//Department of Clinical Dentistry, Faculty of Health Sciences, UiT The Arctic University of Norway/ ; RGNS 65-156//The Office of the Permanent Secretary, Ministry of Higher Education, Science, Research and Innovation (OPS MHESI)/ ; }, mesh = {*Saliva/microbiology ; Humans ; *Microbiota/drug effects/genetics ; *DNA, Bacterial/isolation & purification/genetics ; Metagenomics/methods ; Metagenome ; Drug Resistance, Bacterial/genetics ; Mouth/microbiology ; Adult ; Anti-Bacterial Agents/pharmacology ; Male ; Female ; Healthy Volunteers ; }, abstract = {OBJECTIVES: The human oral microbiome, a complex ecosystem linked to oral and systemic health, harbors a diverse array of microbial populations, including antimicrobial resistance genes (ARGs). As a critical component of the One Health approach to tackle antibiotic resistance, comprehending the oral resistome's composition and diversity is imperative. The objective of this study was to investigate the impact of chemical cell lysis treatment using MetaPolyzyme on the detectability of the oral microbiome, resistome, and DNA quality and quantity.

MATERIALS AND METHODS: Saliva samples were collected from five healthy individuals, and each of the samples was subjected to DNA extraction with and without the treatment with MetaPolyzyme. Through metagenomic sequencing, we analyzed, assessed, and compared the microbial composition, resistome, and DNA characteristics between both groups of extracted DNA.

RESULTS: Our study revealed that MetaPolyzyme treatment led to significant shifts in the detectability of microbial composition, favoring Gram-positive bacteria, notably Streptococcus, over Gram-negative counterparts. Moreover, the MetaPolyzyme treatment also resulted in a distinct change in ARG distribution. This shift was characterized by an elevated proportion of ARGs linked to fluoroquinolones and efflux pumps, coupled with a reduction in the prevalence of tetracycline and β-lactam resistance genes when compared with the nontreated group. Alpha diversity analysis demonstrated altered species and ARG distribution without affecting overall diversity, while beta diversity analysis confirmed significant differences in the taxonomical composition and oral resistome between treated and nontreated groups.

CONCLUSIONS: These findings underscore the critical role of cell lysis treatment in optimizing oral metagenomic studies and enhance our understanding of the oral resistome's dynamics in the context of antimicrobial resistance.}, } @article {pmid38936492, year = {2024}, author = {Rodriguez-Ruiz, JP and Lin, Q and Van Heirstraeten, L and Lammens, C and Stewardson, AJ and Godycki-Cwirko, M and Coenen, S and Goossens, H and Harbarth, S and Malhotra-Kumar, S and , }, title = {Long-term effects of ciprofloxacin treatment on the gastrointestinal and oropharyngeal microbiome are more pronounced after longer antibiotic courses.}, journal = {International journal of antimicrobial agents}, volume = {64}, number = {3}, pages = {107259}, doi = {10.1016/j.ijantimicag.2024.107259}, pmid = {38936492}, issn = {1872-7913}, mesh = {Humans ; *Ciprofloxacin/therapeutic use/pharmacology ; *Oropharynx/microbiology ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Female ; Male ; Middle Aged ; *Gastrointestinal Microbiome/drug effects/genetics ; *Urinary Tract Infections/microbiology/drug therapy ; Aged ; Adult ; Switzerland ; Belgium ; Poland ; Drug Resistance, Bacterial ; Feces/microbiology ; Microbiota/drug effects/genetics ; Metagenomics ; }, abstract = {BACKGROUND: Urinary tract infections (UTIs) are one of the main reasons for antibiotic prescriptions in primary care. Recent studies demonstrate similar clinical outcomes with short vs. long antibiotics courses. The aim of this study was to investigate the differential collateral effect of ciprofloxacin treatment duration on the gastrointestinal and oropharyngeal microbiome in patients presenting with uncomplicated UTI to primary care practices in Switzerland, Belgium and Poland.

METHODS: Stool and oropharyngeal samples were obtained from 36 treated patients and 14 controls at the beginning of antibiotic therapy, end of therapy and one month after the end of therapy. Samples underwent shotgun metagenomics.

RESULTS: At the end of therapy, patients treated with both short (≤7 days) and long (>7 days) ciprofloxacin courses showed similar changes in the gastrointestinal microbiome compared to non-treated controls. After one month, most changes in patients receiving short courses were reversed; however, long courses led to increased abundance of the genera Roseburia, Faecalicatena and Escherichia. Changes in the oropharynx were minor and reversed to baseline levels within one month. Ciprofloxacin resistance encoding mutations in gyrA/B and parC/E reads were observed in both short and long treatment groups but decreased to baseline levels after one month. An increased abundance of resistance genes was observed in the gastrointestinal microbiome after longer treatment, and correlated to increased prevalence of aminoglycoside, β-lactam, sulphonamide, and tetracycline resistance genes.

CONCLUSION: Collateral effects on the gastrointestinal community, including an increased prevalence of antimicrobial resistance genes, persists for up to at least one month following longer ciprofloxacin therapy. These data support the use of shorter antimicrobial treatment duration.}, } @article {pmid38934645, year = {2024}, author = {Liébana, R and Viver, T and Ramos-Barbero, MD and Bustos-Caparros, E and Urdiain, M and López, C and Amoozegar, MA and Antón, J and Rossello-Mora, R}, title = {Extremely halophilic brine community manipulation shows higher robustness of microbiomes inhabiting human-driven solar saltern than naturally driven lake.}, journal = {mSystems}, volume = {9}, number = {7}, pages = {e0053824}, pmid = {38934645}, issn = {2379-5077}, support = {PGC2018-096956-B-C41, PGC2018-096956-B-C43, RTC-2017-6405-1, PID2021-126114NB-C42, PID2021-126114NB-C44//Ministerio de Ciencia e Innovación (MCIN)/ ; }, mesh = {*Lakes/microbiology/virology ; *Microbiota ; Spain ; Humans ; Salts/chemistry ; Salinity ; Iran ; Metagenome ; Bacteria/genetics/isolation & purification/classification ; }, abstract = {UNLABELLED: Hypersaline ecosystems display taxonomically similar assemblages with low diversities and highly dense accompanying viromes. The ecological implications of viral infection on natural microbial populations remain poorly understood, especially at finer scales of diversity. Here, we sought to investigate the influence of changes in environmental physicochemical conditions and viral predation pressure by autochthonous and allochthonous viruses on host dynamics. For this purpose, we transplanted two microbiomes coming from distant hypersaline systems (solar salterns of Es Trenc in Spain and the thalassohaline lake of Aran-Bidgol lake in Iran), by exchanging the cellular fractions with the sterile-filtered accompanying brines with and without the free extracellular virus fraction. The midterm exposure (1 month) of the microbiomes to the new conditions showed that at the supraspecific taxonomic range, the assemblies from the solar saltern brine more strongly resisted the environmental changes and viral predation than that of the lake. The metagenome-assembled genomes (MAGs) analysis revealed an intraspecific transition at the ecotype level, mainly driven by changes in viral predation pressure, by both autochthonous and allochthonous viruses.

IMPORTANCE: Viruses greatly influence succession and diversification of their hosts, yet the effects of viral infection on the ecological dynamics of natural microbial populations remain poorly understood, especially at finer scales of diversity. By manipulating the viral predation pressure by autochthonous and allochthonous viruses, we uncovered potential phage-host interaction, and their important role in structuring the prokaryote community at an ecotype level.}, } @article {pmid38934598, year = {2024}, author = {Kruk, ME and Mehta, S and Murray, K and Higgins, L and Do, K and Johnson, JE and Wagner, R and Wendt, CH and O'Connor, JB and Harris, JK and Laguna, TA and Jagtap, PD and Griffin, TJ}, title = {An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease.}, journal = {mSystems}, volume = {9}, number = {7}, pages = {e0092923}, pmid = {38934598}, issn = {2379-5077}, support = {R01 HL136499/HL/NHLBI NIH HHS/United States ; S10 OD028717/OD/NIH HHS/United States ; R01HL136499//HHS | National Institutes of Health (NIH)/ ; S10OD028717//HHS | National Institutes of Health (NIH)/ ; }, mesh = {Humans ; *Cystic Fibrosis/microbiology ; *Proteomics/methods ; *Bronchoalveolar Lavage Fluid/microbiology/chemistry ; *Workflow ; *Tandem Mass Spectrometry ; Host Microbial Interactions/genetics ; Microbiota/genetics ; Bronchoalveolar Lavage ; Computational Biology/methods ; Male ; }, abstract = {Airway microbiota are known to contribute to lung diseases, such as cystic fibrosis (CF), but their contributions to pathogenesis are still unclear. To improve our understanding of host-microbe interactions, we have developed an integrated analytical and bioinformatic mass spectrometry (MS)-based metaproteomics workflow to analyze clinical bronchoalveolar lavage (BAL) samples from people with airway disease. Proteins from BAL cellular pellets were processed and pooled together in groups categorized by disease status (CF vs. non-CF) and bacterial diversity, based on previously performed small subunit rRNA sequencing data. Proteins from each pooled sample group were digested and subjected to liquid chromatography tandem mass spectrometry (MS/MS). MS/MS spectra were matched to human and bacterial peptide sequences leveraging a bioinformatic workflow using a metagenomics-guided protein sequence database and rigorous evaluation. Label-free quantification revealed differentially abundant human peptides from proteins with known roles in CF, like neutrophil elastase and collagenase, and proteins with lesser-known roles in CF, including apolipoproteins. Differentially abundant bacterial peptides were identified from known CF pathogens (e.g., Pseudomonas), as well as other taxa with potentially novel roles in CF. We used this host-microbe peptide panel for targeted parallel-reaction monitoring validation, demonstrating for the first time an MS-based assay effective for quantifying host-microbe protein dynamics within BAL cells from individual CF patients. Our integrated bioinformatic and analytical workflow combining discovery, verification, and validation should prove useful for diverse studies to characterize microbial contributors in airway diseases. Furthermore, we describe a promising preliminary panel of differentially abundant microbe and host peptide sequences for further study as potential markers of host-microbe relationships in CF disease pathogenesis.IMPORTANCEIdentifying microbial pathogenic contributors and dysregulated human responses in airway disease, such as CF, is critical to understanding disease progression and developing more effective treatments. To this end, characterizing the proteins expressed from bacterial microbes and human host cells during disease progression can provide valuable new insights. We describe here a new method to confidently detect and monitor abundance changes of both microbe and host proteins from challenging BAL samples commonly collected from CF patients. Our method uses both state-of-the art mass spectrometry-based instrumentation to detect proteins present in these samples and customized bioinformatic software tools to analyze the data and characterize detected proteins and their association with CF. We demonstrate the use of this method to characterize microbe and host proteins from individual BAL samples, paving the way for a new approach to understand molecular contributors to CF and other diseases of the airway.}, } @article {pmid38934548, year = {2024}, author = {Yang, C and Lan, R and Zhao, L and Pu, J and Hu, D and Yang, J and Zhou, H and Han, L and Ye, L and Jin, D and Xu, J and Liu, L}, title = {Prevotella copri alleviates hyperglycemia and regulates gut microbiota and metabolic profiles in mice.}, journal = {mSystems}, volume = {9}, number = {7}, pages = {e0053224}, pmid = {38934548}, issn = {2379-5077}, support = {2018RU010//Research Unit of Discovery of Unknown Bacteria and Function/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Hyperglycemia/metabolism ; Mice ; *Prevotella ; *Metabolome/drug effects ; Male ; Probiotics/pharmacology/administration & dosage/therapeutic use ; Mice, Inbred C57BL ; Humans ; Glucagon-Like Peptide 1/metabolism ; }, abstract = {UNLABELLED: Prevotella copri is the dominant species of the Prevotella genus in the gut, which is genomically heterogeneous and difficult to isolate; hence, scarce research was carried out for this species. This study aimed to investigate the effect of P. copri on hyperglycemia. Thirty-nine strains were isolated from healthy individuals, and three strains (HF2123, HF1478, and HF2130) that had the highest glucose consumption were selected to evaluate the effects of P. copri supplementation on hyperglycemia. Microbiomics and non-target metabolomics were used to uncover the underlying mechanisms. Oral administration of P. copri in diabetic db/db mice increased the expression and secretion of glucagon-like peptide-1 (GLP-1), significantly improved hyperglycemia, insulin resistance, and lipid accumulation, and alleviated the pathological morphology in the pancreas, liver, and colon. P. copri changed the composition of the gut microbiota of diabetic db/db mice, which was characterized by increasing the ratio of Bacteroidetes to Firmicutes and increasing the relative abundance of genera Bacteroides, Akkermansia, and Faecalibacterium. After intervention with P. copri, fecal metabolic profiling showed that fumaric acid and homocysteine contents decreased, and glutamine contents increased. Furthermore, amino acid metabolism and cAMP/PKA signaling pathways were enriched. Our findings indicate that P. copri improved glucose metabolism abnormalities in diabetic db/db mice. Especially, one of the P. copri strains, HF2130, has shown superior performance in improving hyperglycemia, which may have the potential as a probiotic against hyperglycemia.

IMPORTANCE: As a core member of the human intestinal ecosystem, Prevotelal copri has been associated with glucose metabolic homeostasis in previous studies. However, these results have often been derived from metagenomic studies, and the experimental studies have been based solely on the type of strain DSM 18205[T]. Therefore, more experimental evidence from additional isolates is needed to validate the results according to their high genomic heterogeneity. In this study, we isolated different branches of strains and demonstrated that P. copri could improve the metabolic profile of hyperglycemic mice by modulating microbial activity. This finding supports the causal contribution of P. copri in host glucose metabolism.}, } @article {pmid38934052, year = {2024}, author = {Liu, C and Tang, Z and Li, L and Kang, Y and Teng, Y and Yu, Y}, title = {Enhancing antimicrobial resistance detection with MetaGeneMiner: Targeted gene extraction from metagenomes.}, journal = {Chinese medical journal}, volume = {137}, number = {17}, pages = {2092-2098}, pmid = {38934052}, issn = {2542-5641}, mesh = {*Metagenome/genetics ; Humans ; Acinetobacter baumannii/genetics/drug effects/isolation & purification ; Metagenomics/methods ; Drug Resistance, Bacterial/genetics ; Software ; Drug Resistance, Microbial/genetics ; }, abstract = {BACKGROUND: Accurately and efficiently extracting microbial genomic sequences from complex metagenomic data is crucial for advancing our understanding in fields such as clinical diagnostics, environmental microbiology, and biodiversity. As sequencing technologies evolve, this task becomes increasingly challenging due to the intricate nature of microbial communities and the vast amount of data generated. Especially in intensive care units (ICUs), infections caused by antibiotic-resistant bacteria are increasingly prevalent among critically ill patients, significantly impacting the effectiveness of treatments and patient prognoses. Therefore, obtaining timely and accurate information about infectious pathogens is of paramount importance for the treatment of patients with severe infections, which enables precisely targeted anti-infection therapies, and a tool that can extract microbial genomic sequences from metagenomic dataset would be of help.

METHODS: We developed MetaGeneMiner to help with retrieving specific microbial genomic sequences from metagenomes using a k-mer-based approach. It facilitates the rapid and accurate identification and analysis of pathogens. The tool is designed to be user-friendly and efficient on standard personal computers, allowing its use across a wide variety of settings. We validated MetaGeneMiner using eight metagenomic samples from ICU patients, which demonstrated its efficiency and accuracy.

RESULTS: The software extensively retrieved coding sequences of pathogens Acinetobacter baumannii and herpes simplex virus type 1 and detected a variety of resistance genes. All documentation and source codes for MetaGeneMiner are freely available at https://gitee.com/sculab/MetaGeneMiner .

CONCLUSIONS: It is foreseeable that MetaGeneMiner possesses the potential for applications across multiple domains, including clinical diagnostics, environmental microbiology, gut microbiome research, as well as biodiversity and conservation biology. Particularly in ICU settings, MetaGeneMiner introduces a novel, rapid, and precise method for diagnosing and treating infections in critically ill patients. This tool is capable of efficiently identifying infectious pathogens, guiding personalized and precise treatment strategies, and monitoring the development of antibiotic resistance, significantly impacting the diagnosis and treatment of severe infections.}, } @article {pmid38932245, year = {2024}, author = {Conradie, T and Caparros-Martin, JA and Egan, S and Kicic, A and Koks, S and Stick, SM and Agudelo-Romero, P}, title = {Exploring the Complexity of the Human Respiratory Virome through an In Silico Analysis of Shotgun Metagenomic Data Retrieved from Public Repositories.}, journal = {Viruses}, volume = {16}, number = {6}, pages = {}, pmid = {38932245}, issn = {1999-4915}, support = {NHMRC115648//National Health and Medical Research Council/ ; Synergy grant APP118364//National Health and Medical Research Council/ ; Theme Collaboration Award 2023//Telethon Kids Institute/ ; N/A//Google cloud education program/ ; Investigator grant 2021/GR000216//National Health and Medical Research Council/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Virome ; *Genome, Viral ; *Respiratory System/virology ; *Viruses/genetics/classification/isolation & purification ; Metagenome ; Computer Simulation ; Phylogeny ; Computational Biology/methods ; Microbiota ; Bacteriophages/genetics/classification/isolation & purification ; }, abstract = {BACKGROUND: Respiratory viruses significantly impact global morbidity and mortality, causing more disease in humans than any other infectious agent. Beyond pathogens, various viruses and bacteria colonize the respiratory tract without causing disease, potentially influencing respiratory diseases' pathogenesis. Nevertheless, our understanding of respiratory microbiota is limited by technical constraints, predominantly focusing on bacteria and neglecting crucial populations like viruses. Despite recent efforts to improve our understanding of viral diversity in the human body, our knowledge of viral diversity associated with the human respiratory tract remains limited.

METHODS: Following a comprehensive search in bibliographic and sequencing data repositories using keyword terms, we retrieved shotgun metagenomic data from public repositories (n = 85). After manual curation, sequencing data files from 43 studies were analyzed using EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion). Complete and high-quality contigs were further assessed for genomic and taxonomic characterization.

RESULTS: Viral contigs were obtained from 194 out of the 868 FASTQ files processed through EVEREST. Of the 1842 contigs that were quality assessed, 8% (n = 146) were classified as complete/high-quality genomes. Most of the identified viral contigs were taxonomically classified as bacteriophages, with taxonomic resolution ranging from the superkingdom level down to the species level. Captured contigs were spread across 25 putative families and varied between RNA and DNA viruses, including previously uncharacterized viral genomes. Of note, airway samples also contained virus(es) characteristic of the human gastrointestinal tract, which have not been previously described as part of the lung virome. Additionally, by performing a meta-analysis of the integrated datasets, ecological trends within viral populations linked to human disease states and their biogeographical distribution along the respiratory tract were observed.

CONCLUSION: By leveraging publicly available repositories of shotgun metagenomic data, the present study provides new insights into viral genomes associated with specimens from the human respiratory tract across different disease spectra. Further studies are required to validate our findings and evaluate the potential impact of these viral communities on respiratory tract physiology.}, } @article {pmid38932211, year = {2024}, author = {Jiao, G and Ye, Z and Feng, K and Zhang, C and Chen, J and Li, J and He, Y}, title = {Discovery of Two Novel Viruses of the Willow-Carrot Aphid, Cavariella aegopodii.}, journal = {Viruses}, volume = {16}, number = {6}, pages = {}, pmid = {38932211}, issn = {1999-4915}, support = {32270146//National Natural Science Foundation of China/ ; U20A2036//National Natural Science Foundation of China/ ; 2023M741836//National Postdoctoral Foundation Project/ ; ZCLQ24C1401//the Natural Science Foundation of Zhejiang Province/ ; }, mesh = {Animals ; *Aphids/virology ; *Phylogeny ; *Genome, Viral ; *RNA Viruses/genetics/classification/isolation & purification ; Virome/genetics ; RNA, Viral/genetics ; Metagenomics ; Plant Diseases/virology ; }, abstract = {The advancement of bioinformatics and sequencing technology has resulted in the identification of an increasing number of new RNA viruses. This study systematically identified the RNA virome of the willow-carrot aphid, Cavariella aegopodii (Hemiptera: Aphididae), using metagenomic sequencing and rapid amplification of cDNA ends (RACE) approaches. C. aegopodii is a sap-sucking insect widely distributed in Europe, Asia, North America, and Australia. The deleterious effects of C. aegopodii on crop growth primarily stem from its feeding activities and its role as a vector for transmitting plant viruses. The virome includes Cavariella aegopodii virga-like virus 1 (CAVLV1) and Cavariella aegopodii iflavirus 1 (CAIV1). Furthermore, the complete genome sequence of CAVLV1 was obtained. Phylogenetically, CAVLV1 is associated with an unclassified branch of the Virgaviridae family and is susceptible to host antiviral RNA interference (RNAi), resulting in the accumulation of a significant number of 22nt virus-derived small interfering RNAs (vsiRNAs). CAIV1, on the other hand, belongs to the Iflaviridae family, with vsiRNAs ranging from 18 to 22 nt. Our findings present a comprehensive analysis of the RNA virome of C. aegopodii for the first time, offering insights that could potentially aid in the future control of the willow-carrot aphid.}, } @article {pmid38931324, year = {2024}, author = {Faraj, S and Sequeira-Bisson, IR and Lu, L and Miles-Chan, JL and Hoggard, M and Barnett, D and Parry-Strong, A and Foster, M and Krebs, JD and Poppitt, SD and Taylor, MW and Mathrani, A}, title = {Effect of a Higher-Protein Nut versus Higher-Carbohydrate Cereal Enriched Diet on the Gut Microbiomes of Chinese Participants with Overweight and Normoglycaemia or Prediabetes in the Tū Ora Study.}, journal = {Nutrients}, volume = {16}, number = {12}, pages = {}, pmid = {38931324}, issn = {2072-6643}, support = {3710040//Ministry for Business, Innovation and Employment (MBIE)/ ; 3713851//Maurice Wilkins Centre/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Prediabetic State/diet therapy/microbiology ; Male ; *Overweight/microbiology ; Female ; *Nuts ; *Dietary Carbohydrates/administration & dosage ; *Edible Grain ; Middle Aged ; New Zealand ; Adult ; Feces/microbiology ; China ; RNA, Ribosomal, 16S/genetics ; Diabetes Mellitus, Type 2/microbiology ; Diet, High-Protein ; Dietary Proteins/administration & dosage ; East Asian People ; }, abstract = {Global increases in metabolic disorders such as type 2 diabetes (T2D), especially within Asian populations, highlight the need for novel approaches to dietary intervention. The Tū Ora study previously evaluated the effects on metabolic health of including a nut product into the diet of a New Zealand cohort of Chinese participants with overweight and normoglycaemia or prediabetes through a 12-week randomised, parallel-group clinical trial. In this current study, we compared the impact of this higher-protein nut bar (HP-NB) versus a higher-carbohydrate cereal bar (HC-CB) on the faecal microbiome by employing both 16S rRNA gene amplicon and shotgun metagenomic sequencing of pre- and post-intervention pairs from 84 participants. Despite the higher fibre, protein, and unsaturated fat content of nuts, there was little difference between dietary groups in gut microbiome composition or functional potential, with the bacterial phylum Firmicutes dominating irrespective of diet. The lack of observed change suggests the dietary impact of the bars may have been insufficient to affect the gut microbiome. Manipulating the interplay between the diet, microbiome, and metabolic health may require a more substantial and/or prolonged dietary perturbation to generate an impactful modification of the gut ecosystem and its functional potential to aid in T2D risk reduction.}, } @article {pmid38930811, year = {2024}, author = {Zhang, Y and Yu, P and Tao, F}, title = {Dynamic Interplay between Microbiota Shifts and Differential Metabolites during Dairy Processing and Storage.}, journal = {Molecules (Basel, Switzerland)}, volume = {29}, number = {12}, pages = {}, pmid = {38930811}, issn = {1420-3049}, support = {2022-45//SCIENCE and TECHNOLOGY PROJECT of SHANGHAI MUNICIPAL MARKET SUPERVISION ADMINISTRATION/ ; 2022YFD2100705//NATIONAL KEY RESEARCH and DEVELOPMENT PROGRAM of CHINA/ ; }, mesh = {*Microbiota ; Animals ; *Milk/microbiology/metabolism ; Food Storage/methods ; Pasteurization ; High-Throughput Nucleotide Sequencing ; Dairy Products/microbiology ; Metagenomics/methods ; Gas Chromatography-Mass Spectrometry ; Food Handling/methods ; Bacteria/metabolism/classification/genetics ; Metabolome ; }, abstract = {Due to the intricate complexity of the original microbiota, residual heat-resistant enzymes, and chemical components, identifying the essential factors that affect dairy quality using traditional methods is challenging. In this study, raw milk, pasteurized milk, and ultra-heat-treated (UHT) milk samples were collectively analyzed using metagenomic next-generation sequencing (mNGS), high-throughput liquid chromatography-mass spectrometry (LC-MS), and gas chromatography-mass spectrometry (GC-MS). The results revealed that raw milk and its corresponding heated dairy products exhibited different trends in terms of microbiota shifts and metabolite changes during storage. Via the analysis of differences in microbiota and correlation analysis of the microorganisms present in differential metabolites in refrigerated pasteurized milk, the top three differential microorganisms with increased abundance, Microbacterium (p < 0.01), unclassified Actinomycetia class (p < 0.05), and Micrococcus (p < 0.01), were detected; these were highly correlated with certain metabolites in pasteurized milk (r > 0.8). This indicated that these genera were the main proliferating microorganisms and were the primary genera involved in the metabolism of pasteurized milk during refrigeration-based storage. Microorganisms with decreased abundance were classified into two categories based on correlation analysis with certain metabolites. It was speculated that the heat-resistant enzyme system of a group of microorganisms with high correlation (r > 0.8), such as Pseudomonas and Acinetobacter, was the main factor causing milk spoilage and that the group with lower correlation (r < 0.3) had a lower impact on the storage process of pasteurized dairy products. By comparing the metabolic pathway results based on metagenomic and metabolite annotation, it was proposed that protein degradation may be associated with microbial growth, whereas lipid degradation may be linked to raw milk's initial heat-resistant enzymes. By leveraging the synergy of metagenomics and metabolomics, the interacting factors determining the quality evolution of dairy products were systematically investigated, providing a novel perspective for controlling dairy processing and storage effectively.}, } @article {pmid38929370, year = {2024}, author = {Khan, I and Bu, R and Ali, Z and Iqbal, MS and Shi, H and Ding, L and Hong, M}, title = {Metagenomics Analysis Reveals the Composition and Functional Differences of Fecal Microbiota in Wild, Farm, and Released Chinese Three-Keeled Pond Turtles (Mauremys reevesii).}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {12}, pages = {}, pmid = {38929370}, issn = {2076-2615}, support = {32160251，32271577, 32300415//National Natural Science Foundation of China/ ; }, abstract = {The intestine of living organisms harbors different microbiota associated with the biological functioning and health of the host and influences the process of ecological adaptation. Here, we studied the intestinal microbiota's composition and functional differences using 16S rRNA and metagenomic analysis in the wild, farm, and released Chinese three-keeled pond turtle (Mauremys reevesii). At the phylum level, Bacteroidota dominated, followed by Firmicutes, Fusobacteriota, and Actinobacteriota in the wild group, but Chloroflexi was more abundant in the farm and released groups. Moreover, Chryseobacterium, Acinetobacter, Comamonas, Sphingobacterium, and Rhodobacter were abundant in the released and farm cohorts, respectively. Cetobacterium, Paraclostridium, Lysobacter, and Leucobacter showed an abundance in the wild group. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed that the relative abundance of most pathways was significantly higher in the wild turtles (carbohydrate metabolism, lipid metabolism, metabolism of cofactors, and vitamins). The comprehensive antibiotic resistance database (CARD) showed that the antibiotic resistance gene (ARG) subtype macB was the most abundant in the farm turtle group, while tetA was higher in the wild turtles, and srpYmcr was higher in the released group. Our findings shed light on the association between the intestinal microbiota of M. reevesii and its habitats and could be useful for tracking habitats to protect and conserve this endangered species.}, } @article {pmid38928411, year = {2024}, author = {De Sales-Millán, A and Reyes-Ferreira, P and Aguirre-Garrido, JF and Corral-Guillé, I and Barrientos-Ríos, R and Velázquez-Aragón, JA}, title = {Comprehensive Analysis of Gut Microbiota Composition and Functional Metabolism in Children with Autism Spectrum Disorder and Neurotypical Children: Implications for Sex-Based Differences and Metabolic Dysregulation.}, journal = {International journal of molecular sciences}, volume = {25}, number = {12}, pages = {}, pmid = {38928411}, issn = {1422-0067}, support = {Recursos Fiscales 2022, 2023, 2024 Programa E022 Investigación y Desarrollo Tecnológico en Salud//Instituto Nacional de Pediatria/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Autism Spectrum Disorder/microbiology/metabolism ; Female ; Male ; Child ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/metabolism/isolation & purification ; Feces/microbiology ; Child, Preschool ; Sex Factors ; Sex Characteristics ; Metabolic Networks and Pathways ; }, abstract = {This study aimed to investigate the gut microbiota composition in children with autism spectrum disorder (ASD) compared to neurotypical (NT) children, with a focus on identifying potential differences in gut bacteria between these groups. The microbiota was analyzed through the massive sequencing of region V3-V4 of the 16S RNA gene, utilizing DNA extracted from stool samples of participants. Our findings revealed no significant differences in the dominant bacterial phyla (Firmicutes, Bacteroidota, Actinobacteria, Proteobacteria, Verrucomicrobiota) between the ASD and NT groups. However, at the genus level, notable disparities were observed in the abundance of Blautia, Prevotella, Clostridium XI, and Clostridium XVIII, all of which have been previously associated with ASD. Furthermore, a sex-based analysis unveiled additional discrepancies in gut microbiota composition. Specifically, three genera (Megamonas, Oscilibacter, Acidaminococcus) exhibited variations between male and female groups in both ASD and NT cohorts. Particularly noteworthy was the exclusive presence of Megamonas in females with ASD. Analysis of predicted metabolic pathways suggested an enrichment of pathways related to amine and polyamine degradation, as well as amino acid degradation in the ASD group. Conversely, pathways implicated in carbohydrate biosynthesis, degradation, and fermentation were found to be underrepresented. Despite the limitations of our study, including a relatively small sample size (30 ASD and 31 NT children) and the utilization of predicted metabolic pathways derived from 16S RNA gene analysis rather than metagenome sequencing, our findings contribute to the growing body of evidence suggesting a potential association between gut microbiota composition and ASD. Future research endeavors should focus on validating these findings with larger sample sizes and exploring the functional significance of these microbial differences in ASD. Additionally, there is a critical need for further investigations to elucidate sex differences in gut microbiota composition and their potential implications for ASD pathology and treatment.}, } @article {pmid38927134, year = {2024}, author = {Martins, D and Silva, C and Ferreira, AC and Dourado, S and Albuquerque, A and Saraiva, F and Batista, AB and Castro, P and Leite-Moreira, A and Barros, AS and Miranda, IM}, title = {Unravelling the Gut Microbiome Role in Cardiovascular Disease: A Systematic Review and a Meta-Analysis.}, journal = {Biomolecules}, volume = {14}, number = {6}, pages = {}, pmid = {38927134}, issn = {2218-273X}, support = {UIDB/00051/2020//Fundação para a Ciência e Tecnologia/ ; UIDP/00051/2020//Fundação para a Ciência e Tecnologia/ ; 2021.06947.BD//Fundação para a Ciência e Tecnologia/ ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; *Cardiovascular Diseases/microbiology/metabolism ; Bacteria/metabolism/classification/genetics ; Methylamines/metabolism/blood ; }, abstract = {A notable shift in understanding the human microbiome's influence on cardiovascular disease (CVD) is underway, although the causal association remains elusive. A systematic review and meta-analysis were conducted to synthesise current knowledge on microbial taxonomy and metabolite variations between healthy controls (HCs) and those with CVD. An extensive search encompassing three databases identified 67 relevant studies (2012-2023) covering CVD pathologies from 4707 reports. Metagenomic and metabolomic data, both qualitative and quantitative, were obtained. Analysis revealed substantial variability in microbial alpha and beta diversities. Moreover, specific changes in bacterial populations were shown, including increased Streptococcus and Proteobacteria and decreased Faecalibacterium in patients with CVD compared with HC. Additionally, elevated trimethylamine N-oxide levels were reported in CVD cases. Biochemical parameter analysis indicated increased fasting glucose and triglycerides and decreased total cholesterol and low- and high-density lipoprotein cholesterol levels in diseased individuals. This study revealed a significant relationship between certain bacterial species and CVD. Additionally, it has become clear that there are substantial inconsistencies in the methodologies employed and the reporting standards adhered to in various studies. Undoubtedly, standardising research methodologies and developing extensive guidelines for microbiome studies are crucial for advancing the field.}, } @article {pmid38927027, year = {2024}, author = {Huang, JK and Wu, PH and Chen, ZF and Liu, PY and Kuo, CC and Chuang, YS and Lu, MZ and Kuo, MC and Chiu, YW and Lin, YT}, title = {Identification of Gut Microbiome Signatures Associated with Indole Pathway in Tryptophan Metabolism in Patients Undergoing Hemodialysis.}, journal = {Biomolecules}, volume = {14}, number = {6}, pages = {}, pmid = {38927027}, issn = {2218-273X}, support = {MOST 111-2314-B-037-032-MY3//Ministry of Science and Technology, Taiwan/ ; MOST 111-2314-B-037 -083 -MY3//Ministry of Science and Technology, Taiwan/ ; KMUH-DK(C)113003//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH-DK(B)110003-4//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2M08//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2R21//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2R76//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH111-1M60//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH111-1R73//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH110-0M73//Kaohsiung Medical University Hospital, Taiwan/ ; NHRIKMU-111-I003-2//Kaohsiung Medical University, Taiwan/ ; NHRIKMU-113-I005//Kaohsiung Medical University, Taiwan/ ; NYCUKMU-112-I006//Kaohsiung Medical University, Taiwan/ ; KT112P012//Kaohsiung Medical University, Taiwan/ ; KT113P006//Kaohsiung Medical University, Taiwan/ ; S11209//Kaohsiung Medical University, Taiwan/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Tryptophan/metabolism ; *Renal Dialysis ; *Indoles/metabolism ; Male ; Female ; Middle Aged ; Aged ; Kidney Failure, Chronic/therapy/metabolism/microbiology ; Feces/microbiology ; Metabolic Networks and Pathways ; Adult ; Metagenome ; }, abstract = {Microbiota tryptophan metabolism and the biosynthesis of indole derivatives play an important role in homeostasis and pathogenesis in the human body and can be affected by the gut microbiota. However, studies on the interplay between gut microbiota and tryptophan metabolites in patients undergoing dialysis are lacking. This study aimed to identify the gut microbiota, the indole pathway in tryptophan metabolism, and significant functional differences in ESRD patients with regular hemodialysis. We performed the shotgun metagenome sequencing of stool samples from 85 hemodialysis patients. Using the linear discriminant analysis effect size (LEfSe), we examined the composition of the gut microbiota and metabolic features across varying concentrations of tryptophan and indole metabolites. Higher tryptophan levels promoted tyrosine degradation I and pectin degradation I metabolic modules; lower tryptophan levels were associated with glutamate degradation I, fructose degradation, and valine degradation modules. Higher 3-indoxyl sulfate concentrations were characterized by alanine degradation I, anaerobic fatty acid beta-oxidation, sulfate reduction, and acetyl-CoA to crotonyl-CoA. Contrarily, lower 3-indoxyl sulfate levels were related to propionate production III, arabinoxylan degradation, the Entner-Doudoroff pathway, and glutamate degradation II. The present study provides a better understanding of the interaction between tryptophan, indole metabolites, and the gut microbiota as well as their gut metabolic modules in ESRD patients with regular hemodialysis.}, } @article {pmid38926602, year = {2024}, author = {Sané, S and Diouara, AAM and Coundoul, S and Tene, SD and Kane, A and Wade, SF and Tamba, A and Diop, M and Mbaye, MN and Thiam, F and Dieng, M and Mbengue, M and Nguer, CM and Sarr, AD and Ndao, AS and Touré Kane, C}, title = {A metagenomic assessment of bacterial community in spices sold open-air markets in Saint-Louis, Senegal.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {14709}, pmid = {38926602}, issn = {2045-2322}, support = {N°0001292MESRI/SG/DC/DAGE/DGRI/DFRSDT/ng//This research was funded by the Ministry of Higher Education, Research and Innovation (MESRI) of Senegal govment through his FIRST (Fonds d'Impulsion de la Recherche Scientifique et Technique) program/ ; }, mesh = {*Spices/microbiology ; Senegal ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/isolation & purification ; Humans ; Metagenome ; Microbiota/genetics ; Curcuma/genetics/microbiology ; }, abstract = {Natural spices play an essential role in human nutrition and well-being. However, their processing on different scales can expose them to potential sources of contamination. This study aimed to describe the bacterial community genomic footprint in spices sold in Senegal. Spice samples were collected in August 2022 in Saint-Louis, Senegal. The genomic region coding bacterial 16S rRNA was then amplified and sequenced using Oxford Nanopore Technology (ONT). Sequencing was carried out on two batches of samples, one containing part of the "Local Spices or Herbs" (n = 10), and the other, a mixture of 7 spices, Curcuma, Thyme and the other part of the "Local Spices or Herbs" (n = 39). Results showed high bacterial diversity and the predominance of Escherichia coli and Salmonella enterica in samples, with total reads of 65,744 and 165,325 for the two batches, respectively. The sample category "Homemade mixture of food condiments ", which includes all "Local Spices or Herbs" samples, showed remarkable bacterial diversity. These were followed by Curcuma, a blend of 7 spices and thyme. Also, the different categories of spices studied show similarities in their bacterial composition. These results highlight the microbial community's highly diverse genomic profile, including pathogenic bacteria, in spice samples.}, } @article {pmid38926449, year = {2024}, author = {Mo, J and Song, Z and Che, Y and Li, J and Liu, T and Feng, J and Wang, Z and Rong, J and Gu, S}, title = {Effects of aeolian deposition on soil properties and microbial carbon metabolism function in farmland of Songnen Plain, China.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {14791}, pmid = {38926449}, issn = {2045-2322}, support = {2021YFD1500801//National Key Research and Development Program of China/ ; }, mesh = {*Soil Microbiology ; *Carbon/metabolism/analysis ; China ; *Soil/chemistry ; Ecosystem ; Farms ; Microbiota ; Sand/microbiology ; Bacteria/genetics/metabolism/classification ; Wind ; }, abstract = {The effects of wind erosion, one of the crucial causes of soil desertification in the world, on the terrestrial ecosystem are well known. However, ecosystem responses regarding soil microbial carbon metabolism to sand deposition caused by wind erosion, a crucial driver of biogeochemical cycles, remain largely unclear. In this study, we collected soil samples from typical aeolian deposition farmland in the Songnen Plain of China to evaluate the effects of sand deposition on soil properties, microbial communities, and carbon metabolism function. We also determined the reads number of carbon metabolism-related genes by high-throughput sequencing technologies and evaluated the association between sand deposition and them. The results showed that long-term sand deposition resulted in soil infertile, roughness, and dryness. The impacts of sand deposition on topsoil were more severe than on deep soil. The diversity of soil microbial communities was significantly reduced due to sand deposition. The relative abundances of Nitrobacteraceae, Burkholderiaceae, and Rhodanobacteraceae belonging to α-Proteobacteria significantly decreased, while the relative abundances of Streptomycetaceae and Geodermatophilaceae belonging to Actinobacteria increased. The results of the metagenomic analysis showed that the gene abundances of carbohydrate metabolism and carbohydrate-activity enzyme (GH and CBM) significantly decreased with the increase of sand deposition amount. The changes in soil microbial community structure and carbon metabolism decreased soil carbon emissions and carbon cycling in aeolian deposition farmland, which may be the essential reasons for land degradation in aeolian deposition farmland.}, } @article {pmid38925382, year = {2024}, author = {Ramos, B and Lourenço, AB and Monteiro, S and Santos, R and Cunha, MV}, title = {Metagenomic profiling of raw wastewater in Portugal highlights microbiota and resistome signatures of public health interest beyond the usual suspects.}, journal = {The Science of the total environment}, volume = {946}, number = {}, pages = {174272}, doi = {10.1016/j.scitotenv.2024.174272}, pmid = {38925382}, issn = {1879-1026}, mesh = {*Wastewater/microbiology ; Portugal ; *Microbiota/drug effects/genetics ; Metagenomics ; Public Health ; Bacteria/genetics/drug effects ; Environmental Monitoring ; Drug Resistance, Bacterial/genetics ; COVID-19 ; Waste Disposal, Fluid ; }, abstract = {In response to the rapid emergence and dissemination of antimicrobial resistant bacteria (ARB) and genes (ARGs), integrated surveillance systems are needed to address antimicrobial resistance (AMR) within the One Health Era. Wastewater analyses enable biomarker monitoring at the sewershed level, offering timely insights into pathogen circulation and ARB/ARGs trends originating from different compartments. During two consecutive epidemic waves of the COVID-19 pandemic in Portugal, taxonomic and functional composition of raw urban wastewater from two wastewater treatment plants (WWTPs) representing one million in equivalent population, located in the main urban areas of the country, were profiled by shotgun metagenomics. Hospital wastewater from two central hospitals located in the WWTPs catchment areas were also sequenced. The resistome and virulome were profiled using metagenomic assemblies without taxonomic constraint, and then specifically characterized for ESKAPE pathogens. Urban and hospital wastewater exhibited specific microbiota signatures, Pseudomonadota dominated in the first and Bacteroidota in the latter. Correlation network analyses highlighted 85 (out of top 100) genera co-occurring across samples. The most frequent ARGs were classified in the multidrug, tetracyclines, and Macrolides, Lincosamides, Streptogramins (MLS) classes. Links established between AMR determinants and bacterial hosts evidenced that the diversity and abundance of ARGs is not restricted to ESKAPE, being also highly predominant among emergent enteropathogens, like Aeromonas and Aliarcobacter, or in the iron (II) oxidizer Acidovorax. The Aliarcobacter genus accumulated high abundance of sulphonamides and polymyxins ARGs, while Acinetobacter and Aeromonas hosted the highest abundance of ARGs against beta-lactams. Other bacteria (e.g. Clostridioides, Francisella, Vibrio cholerae) and genes (e.g. vanA-type vancomycin resistance) of public health interest were detected, with targeted monitoring efforts being needed to establish informative baseline data. Altogether, results highlight that wastewater monitoring is a valuable component of pathogen and AMR surveillance in healthy populations, providing a community-representative snapshot of public health trends beyond priority pathogens.}, } @article {pmid38925301, year = {2024}, author = {Rajasekaran, S and Vasudevan, G and Tangavel, C and Ramachandran, K and Nayagam, SM and Muthurajan, R and Gopalakrishnan, C and Anand, SV and Shetty, AP and Kanna, RM}, title = {Does the gut microbiome influence disc health and disease? The interplay between dysbiosis, pathobionts, and disc inflammation: a pilot study.}, journal = {The spine journal : official journal of the North American Spine Society}, volume = {24}, number = {10}, pages = {1952-1963}, doi = {10.1016/j.spinee.2024.06.020}, pmid = {38925301}, issn = {1878-1632}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology/immunology ; *Intervertebral Disc Degeneration/microbiology ; Adult ; Middle Aged ; Pilot Projects ; Male ; Female ; Case-Control Studies ; Intervertebral Disc Displacement/microbiology/surgery ; Discitis/microbiology ; }, abstract = {BACKGROUND CONTEXT: Gut microbiome alterations resulting in inflammatory responses have been implicated in many distant effects on different organs. However, its influence on disc health is still not fully investigated.

PURPOSE: Our objective was to document the gut biome in healthy volunteers and patients with disc degeneration and to understand the role of gut dysbiosis on human disc health.

STUDY DESIGN: Experimental case-control study.

PATIENT SAMPLE: We included 40 patients with disc degeneration (DG) and 20 healthy volunteers (HV). HV comprised of age groups 30 to 60 years with no known record of back pain and no clinical comorbidities, with normal MRI. Diseased group (DG) were patients in the same age group undergoing surgery for disc disease (disc herniation-25; discogenic stenosis-15) and without instability (with Modic-20; and non-Modic-20).

OUTCOME MEASURES: N/A.

METHODS: We analyzed 16S V3-V4 rDNA gut metagenome from 20 healthy volunteers (HV) and compared the top signature genera from 40 patients with disc degeneration (DG) across Modic and non-Modic groups. Norgen Stool DNA Kit was used for DNA extraction from ∼200 mg of each faecal sample collected using the Norgen Stool Collection Kit.16S V3-V4 rDNA amplicons were generated with universal bacterial primers 341F and 806R and amplified with Q5 High-Fidelity DNA Polymerase. Libraries were sequenced with 250×2 PE to an average of 0.1 million raw reads per sample (Illumina Novaseq 6000). Demultiplexed raw data was assessed with FastQC, and adapter trimmed reads >Q30 reads were processed in the QIME2 pipeline. Serum C-reactive protein (CRP) was measured by the immunoturbimetry method and Fatty acid-binding protein 5 (FABP5) was measured in albumin-globulin-depleted plasma through global proteome analysis.

RESULTS: We observed significant gut dysbiosis between HV and DG and also between the Modic and non-Modic groups. In the Modic group, commensals Bifidobacterium and Ruminococcus were significantly depleted, while pathobionts Streptococcus, Prevotella, and Butryvibrio were enriched. Firmicutes/Bacteroidetes ratio was decreased in DG (Modic-0.62, non-Modic-0.43) compared to HV (0.70). Bacteria-producing beneficial short-chain fatty acids were also depleted in DG. Elevated serum CRP and increased FABP5 were observed in DG.

CONCLUSION: The study revealed gut dysbiosis, an altered Firmicutes/Bacteroidetes ratio, reduced SCFA-producing bacteria, and increased systemic and local inflammation in association with disc disease, especially in Modic changes. The findings have considerable importance for our understanding and prevention of disc degeneration.}, } @article {pmid38924840, year = {2024}, author = {Yang, Y and Olah, P and Radai, Z and Maia, G and Salava, A and Salo, V and Barker, J and Lauerma, A and Andersson, B and Homey, B and Fyhrquist, N and Alenius, H}, title = {Exploratory multi-omics analysis reveals host-microbe interactions associated with disease severity in psoriatic skin.}, journal = {EBioMedicine}, volume = {105}, number = {}, pages = {105222}, pmid = {38924840}, issn = {2352-3964}, mesh = {Humans ; *Psoriasis/microbiology/genetics/metabolism ; *Metagenomics/methods ; *Skin/microbiology/metabolism/pathology ; Female ; Male ; Adult ; *Severity of Illness Index ; *Host Microbial Interactions/genetics ; *Microbiota ; Middle Aged ; Cross-Sectional Studies ; Metagenome ; Gene Expression Profiling ; Transcriptome ; Gene Regulatory Networks ; Host-Pathogen Interactions/genetics ; Computational Biology/methods ; Multiomics ; }, abstract = {BACKGROUND: Psoriasis (Pso) is a chronic inflammatory skin disease that poses both physical and psychological challenges. Dysbiosis of the skin microbiome has been implicated in Pso, yet a comprehensive multi-omics analysis of host-microbe interactions is still lacking. To bridge this gap, we conducted an exploratory study by adopting the integrated approach that combines whole metagenomic shotgun sequencing with skin transcriptomics.

METHODS: This was a cross-sectional study, adult patients with plaque-type Psoriasis (Pso) and healthy volunteers were included. Skin microbiota samples and biopsies were collected from both lesional and non-lesional skin areas on the lower back. Weighted Gene Correlation Network Analysis (WGCNA) was employed for co-expression network analysis, and cell deconvolution was conducted to estimate cell fractions. Taxonomic and functional features of the microbiome were identified using whole metagenomic shotgun sequencing. Association between host genes and microbes was analyzed using Spearman correlation.

FINDINGS: Host anti-viral responses and interferon-related networks were identified and correlated with the severity of psoriasis. The skin microbiome showed a greater prevalence of Corynebacterium simulans in the PASI severe-moderate groups, which correlated with interferon-induced host genes. Two distinct psoriatic clusters with varying disease severities were identified. Variations in the expression of cell apoptosis-associated antimicrobial peptides (AMPs) and microbial aerobic respiration I pathway may partly account for these differences in disease severity.

INTERPRETATION: Our multi-omics analysis revealed for the first time anti-viral responses and the presence of C. simulans associated with psoriasis severity. It also identified two psoriatic subtypes with distinct AMP and metabolic pathway expression. Our study provides new insights into understanding the host-microbe interaction in psoriasis and lays the groundwork for developing subtype-specific strategies for managing this chronic skin disease.

FUNDING: The research has received funding from the FP7 (MAARS-Grant 261366) and the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 821511 (BIOMAP). The JU receives support from the European Union's Horizon 2020 research and innovation programme and EFPIA. This publication reflects only the author's view and the JU is not responsible for any use that may be made of the information it contains. GAM was supported by a scholarship provided by CAPES-PRINT, financed by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES (Brazilian Government Agency). The authors thank all patients who participated in our study.}, } @article {pmid38923598, year = {2024}, author = {du Preez, LL and van der Walt, E and Valverde, A and Rothmann, C and Neser, FWC and Cason, ED}, title = {A metagenomic survey of the fecal microbiome of the African savanna elephant (Loxodonta africana).}, journal = {Animal genetics}, volume = {55}, number = {4}, pages = {621-643}, doi = {10.1111/age.13458}, pmid = {38923598}, issn = {1365-2052}, mesh = {Animals ; *Elephants/genetics/microbiology ; *Feces/microbiology ; *Gastrointestinal Microbiome ; *Metagenome ; *Bacteria/genetics/classification/isolation & purification ; Archaea/genetics/classification ; Metagenomics ; Fungi/genetics/classification ; }, abstract = {The African savanna elephant (Loxodonta africana) is the largest terrestrial animal on Earth and is found primarily in Southern and Eastern Africa. It is a hindgut, colonic fermenter and subsists on a diet of raw plant materials found in its grazing area. In this study the bacterial, archaeal and fungal populations of seven African savanna elephant fecal metagenomes were first characterized using amplicon sequencing. On the genus level it was observed that the p-1088-a5 gut group in the bacteriome, Methanocorpusulum and Methanobrevibacter in the archaeome and Alternaria, Aurobasidium, Didymella and Preussia in the mycome, predominated. Subsequently, metagenomic shotgun sequencing was employed to identify possible functional pathways and carbohydrate-active enzymes (CAZymes). Carbohydrate catabolic pathways represented the main degradation pathways, and the fecal metagenome was enriched in the glycohydroside (GH) class of CAZymes. Additionally, the top GH families identified - GH43, GH2, GH13 and GH3 - are known to be associated with cellulytic, hemicellulytic and pectolytic activities. Finally, the CAZymes families identified in the African savanna elephant were compared with those found in the Asian elephant and it was demonstrated that there is a unique repository of CAZymes that could be leveraged in the biotechnological context such as the degradation of lignocellulose for the production of second-generation biofuels and energy.}, } @article {pmid38922785, year = {2024}, author = {Bomberg, M and Miettinen, H and Kinnunen, P}, title = {Seasonal variation in metabolic profiles and microbial communities in a subarctic ore processing plant.}, journal = {Environmental microbiology reports}, volume = {16}, number = {3}, pages = {e13284}, pmid = {38922785}, issn = {1758-2229}, support = {730480//Horizon Europe Framework/ ; }, mesh = {*Seasons ; *Mining ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Finland ; Microbiota ; Water Microbiology ; Metagenomics ; }, abstract = {The mining industry strives to reduce its water footprint by recycling water in ore processing. This leads to build-up of ions, flotation chemicals and microbial biomass, which may affect the process. The Boliden Kevitsa mine in Northern Finland is exposed to seasonal change and recycles up to 90% of the process water. We studied the variation in size, composition and putative functions of microbial communities in summer and winter in the ore processing plant. The raw water, Cu and Ni thickener overflow waters had statistically significantly higher bacterial numbers in winter compared to summer, and specific summer and winter communities were identified. Metagenomic analysis indicated that Cu and Hg resistance genes, sulphate/thiosulphate, molybdate, iron(III) and zinc ABC transporters, nitrate reduction, denitrification, thiosulphate oxidation and methylotrophy were more common in winter than in summer. Raw water drawn from the nearby river did not affect the microbial communities in the process samples, indicating that the microbial communities and metabolic capacities develop within the process over time in response to the conditions in the processing plant, water chemistry, used chemicals, ore properties and seasonal variation. We propose that the microbial community structures are unique to the Boliden Kevitsa mine and processing plant.}, } @article {pmid38922750, year = {2024}, author = {Lawruk-Desjardins, C and Storck, V and Ponton, DE and Amyot, M and Walsh, DA}, title = {A genome catalogue of mercury-methylating bacteria and archaea from sediments of a boreal river facing human disturbances.}, journal = {Environmental microbiology}, volume = {26}, number = {6}, pages = {e16669}, doi = {10.1111/1462-2920.16669}, pmid = {38922750}, issn = {1462-2920}, support = {ALLRP 560330 - 20//Natural Sciences and Engineering Research Council of Canada/ ; RDCPJ493474-15//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Geologic Sediments/microbiology ; *Rivers/microbiology ; *Archaea/genetics/metabolism/classification ; *Bacteria/genetics/classification/metabolism ; *Mercury/metabolism ; *Methylmercury Compounds/metabolism ; Metagenomics ; Humans ; Genome, Bacterial ; Genome, Archaeal ; Ecosystem ; Microbiota ; }, abstract = {Methyl mercury, a toxic compound, is produced by anaerobic microbes and magnifies in aquatic food webs, affecting the health of animals and humans. The exploration of mercury methylators based on genomes is still limited, especially in the context of river ecosystems. To address this knowledge gap, we developed a genome catalogue of potential mercury-methylating microorganisms. This was based on the presence of hgcAB from the sediments of a river affected by two run-of-river hydroelectric dams, logging activities and a wildfire. Through the use of genome-resolved metagenomics, we discovered a unique and diverse group of mercury methylators. These were dominated by members of the metabolically versatile Bacteroidota and were particularly rich in microbes that ferment butyrate. By comparing the diversity and abundance of mercury methylators between sites subjected to different disturbances, we found that ongoing disturbances, such as the input of organic matter related to logging activities, were particularly conducive to the establishment of a mercury-methylating niche. Finally, to gain a deeper understanding of the environmental factors that shape the diversity of mercury methylators, we compared the mercury-methylating genome catalogue with the broader microbial community. The results suggest that mercury methylators respond to environmental conditions in a manner similar to the overall microbial community. Therefore, it is crucial to interpret the diversity and abundance of mercury methylators within their specific ecological context.}, } @article {pmid38922447, year = {2024}, author = {Yan, Z and Hao, T and Yan, Y and Zhao, Y and Wu, Y and Tan, Y and Bi, Y and Cui, Y and Yang, R and Zhao, Y}, title = {Quantitative and dynamic profiling of human gut core microbiota by real-time PCR.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {396}, pmid = {38922447}, issn = {1432-0614}, mesh = {Humans ; *Real-Time Polymerase Chain Reaction/methods ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; DNA Primers/genetics ; DNA, Bacterial/genetics ; }, abstract = {The human gut microbiota refers to a diverse community of microorganisms that symbiotically exist in the human intestinal system. Altered microbial communities have been linked to many human pathologies. However, there is a lack of rapid and efficient methods to assess gut microbiota signatures in practice. To address this, we established an appraisal system containing 45 quantitative real-time polymerase chain reaction (qPCR) assays targeting gut core microbes with high prevalence and/or abundance in the population. Through comparative genomic analysis, we selected novel species-specific genetic markers and primers for 31 of the 45 core microbes with no previously reported specific primers or whose primers needed improvement in specificity. We comprehensively evaluated the performance of the qPCR assays and demonstrated that they showed good sensitivity, selectivity, and quantitative linearity for each target. The limit of detection ranged from 0.1 to 1.0 pg/µL for the genomic DNA of these targets. We also demonstrated the high consistency (Pearson's r = 0.8688, P < 0.0001) between the qPCR method and metagenomics next-generation sequencing (mNGS) method in analyzing the abundance of selected bacteria in 22 human fecal samples. Moreover, we quantified the dynamic changes (over 8 weeks) of these core microbes in 14 individuals using qPCR, and considerable stability was demonstrated in most participants, albeit with significant individual differences. Overall, this study enables the simple and rapid quantification of 45 core microbes in the human gut, providing a promising tool to understand the role of gut core microbiota in human health and disease. KEY POINTS: • A panel of original qPCR assays was developed to quantify human gut core microbes. • The qPCR assays were evaluated and compared with mNGS using real fecal samples. • This method was used to dynamically profile the gut core microbiota in individuals.}, } @article {pmid38922379, year = {2024}, author = {Mikó, E and Sipos, A and Tóth, E and Lehoczki, A and Fekete, M and Sebő, É and Kardos, G and Bai, P}, title = {Guideline for designing microbiome studies in neoplastic diseases.}, journal = {GeroScience}, volume = {46}, number = {5}, pages = {4037-4057}, pmid = {38922379}, issn = {2509-2723}, support = {K142141//NKFIH/ ; FK128387//NKFIH/ ; FK146852//NKFIH/ ; TKP2021-EGA-20//NKFIH/ ; TKP2021-EGA-19//NFKIH/ ; POST-COVID2021-33//Magyar Tudományos Akadémia/ ; NKM2022-30//Magyar Tudományos Akadémia/ ; }, mesh = {Humans ; *Neoplasms/microbiology ; *Microbiota ; Research Design ; }, abstract = {Oncobiosis has emerged as a key contributor to the development, and modulator of the treatment efficacy of cancer. Hereby, we review the modalities through which the oncobiome can support the progression of tumors, and the emerging therapeutic opportunities they present. The review highlights the inherent challenges and limitations faced in sampling and accurately characterizing oncobiome. Additionally, the review underscores the critical need for the standardization of microbial analysis techniques and the consistent reporting of microbiome data. We provide a suggested metadata set that should accompany microbiome datasets from oncological settings so that studies remain comparable and decipherable.}, } @article {pmid38920000, year = {2024}, author = {Chen, P and Wang, R and Lei, J and Feng, L and Zhou, B}, title = {Urolithin B protects mice from diet-induced obesity, insulin resistance, and intestinal inflammation by regulating gut microbiota composition.}, journal = {Food & function}, volume = {15}, number = {14}, pages = {7518-7533}, doi = {10.1039/d4fo02545h}, pmid = {38920000}, issn = {2042-650X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Insulin Resistance ; *Obesity/metabolism ; *Mice, Inbred C57BL ; Mice ; Male ; *Diet, High-Fat/adverse effects ; *Coumarins/pharmacology/administration & dosage ; Inflammation ; Oxidative Stress/drug effects ; }, abstract = {The increasing prevalence of obesity and type 2 diabetes (T2D) signifies the failure of conventional treatments for these diseases. The gut microbiota has been proposed as a key player in the pathophysiology of diet-induced T2D. Urolithin B (Uro B), a gut microbiota-derived polyphenol metabolite, exerts several beneficial health effects. In this study, we investigated the metabolic effects of Uro B on high-fat/high-sucrose (HFHS)-fed mice and determined whether its antidiabetic effects are related to the modulation of the gut microbiota. C57BL/6J mice were fed either a chow or HFHS diet. HFHS-fed mice were administered daily with either a vehicle (water) or different doses of Uro B (100 or 200 mg kg[-1]) for eight weeks. The composition of the gut microbiota was assessed by 16S rRNA sequencing. The results showed that Uro B treatment reduced HFHS-induced weight gain and visceral obesity and decreased liver weight and triglyceride accumulation associated with blunted hepatic oxidative stress and inflammation. Furthermore, Uro B administration improved insulin sensitivity as revealed by improved insulin tolerance, a lower homeostasis model assessment of insulin resistance, and decreased glucose-induced hyperinsulinemia during the oral glucose tolerance test. Uro B treatment was found to lower the intestinal triglyceride content and alleviate intestinal inflammation and oxidative stress. Remarkably, Uro B treatment markedly increased the proportion of the mucin-degrading bacterium Akkermansia in metagenomic samples. In conclusion, Uro B exerts beneficial metabolic effects by alleviating HFHS diet-induced features of metabolic syndrome, which is associated with a proportional increase in the population of Akkermansia spp.}, } @article {pmid38918932, year = {2024}, author = {Tian, B and Xu, LL and Jiang, LD and Lin, X and Shen, J and Shen, H and Su, KJ and Gong, R and Qiu, C and Luo, Z and Yao, JH and Wang, ZQ and Xiao, HM and Zhang, LS and Deng, HW}, title = {Identification of the serum metabolites associated with cow milk consumption in Chinese Peri-/Postmenopausal women.}, journal = {International journal of food sciences and nutrition}, volume = {75}, number = {6}, pages = {537-549}, doi = {10.1080/09637486.2024.2366223}, pmid = {38918932}, issn = {1465-3478}, mesh = {Humans ; Female ; *Milk ; Animals ; Middle Aged ; *Postmenopause/blood ; China ; *Gastrointestinal Microbiome ; Cattle ; Citrulline/blood ; Aged ; Diet ; Metabolome ; Bacteroides ; East Asian People ; }, abstract = {Cow milk consumption (CMC) and downstream alterations of serum metabolites are commonly considered important factors regulating human health status. Foods may lead to metabolic changes directly or indirectly through remodelling gut microbiota (GM). We sought to identify the metabolic alterations in Chinese Peri-/Postmenopausal women with habitual CMC and explore if the GM mediates the CMC-metabolite associations. 346 Chinese Peri-/Postmenopausal women participants were recruited in this study. Fixed effects regression and partial least squares discriminant analysis (PLS-DA) were applied to reveal alterations of serum metabolic features in different CMC groups. Spearman correlation coefficient was computed to detect metabolome-metagenome association. 36 CMC-associated metabolites including palmitic acid (FA(16:0)), 7alpha-hydroxy-4-cholesterin-3-one (7alphaC4), citrulline were identified by both fixed effects regression (FDR < 0.05) and PLS-DA (VIP score > 2). Some significant metabolite-GM associations were observed, including FA(16:0) with gut species Bacteroides ovatus, Bacteroides sp.D2. These findings would further prompt our understanding of the effect of cow milk on human health.}, } @article {pmid38918820, year = {2024}, author = {Wu, Z and Li, M and Qu, L and Zhang, C and Xie, W}, title = {Metagenomic insights into microbial adaptation to the salinity gradient of a typical short residence-time estuary.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {115}, pmid = {38918820}, issn = {2049-2618}, support = {SML2023SP218//Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 92051117//National Natural Science Foundation of China/ ; 2022YFC2805505//National Key Basic Research Program of China/ ; 2021B1515120080//Guangdong Basic and Applied Basic Research Foundation/ ; }, mesh = {*Estuaries ; *Salinity ; *Metagenomics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Archaea/genetics/classification/metabolism ; *Metagenome ; Adaptation, Physiological ; Microbiota/genetics ; Seawater/microbiology ; Water Microbiology ; }, abstract = {BACKGROUND: Microbial adaptation to salinity has been a classic inquiry in the field of microbiology. It has been demonstrated that microorganisms can endure salinity stress via either the "salt-in" strategy, involving inorganic ion uptake, or the "salt-out" strategy, relying on compatible solutes. While these insights are mostly based on laboratory-cultured isolates, exploring the adaptive mechanisms of microorganisms within natural salinity gradient is crucial for gaining a deeper understanding of microbial adaptation in the estuarine ecosystem.

RESULTS: Here, we conducted metagenomic analyses on filtered surface water samples collected from a typical subtropical short residence-time estuary and categorized them by salinity into low-, intermediate-, and high-salinity metagenomes. Our findings highlighted salinity-driven variations in microbial community composition and function, as revealed through taxonomic and Clusters of Orthologous Group (COG) functional annotations. Through metagenomic binning, 127 bacterial and archaeal metagenome-assembled genomes (MAGs) were reconstructed. These MAGs were categorized as stenohaline-specific to low-, intermediate-, or high-salinity-based on the average relative abundance in one salinity category significantly exceeding those in the other two categories by an order of magnitude. Those that did not meet this criterion were classified as euryhaline, indicating a broader range of salinity tolerance. Applying the Boruta algorithm, a machine learning-based feature selection method, we discerned important genomic features from the stenohaline bacterial MAGs. Of the total 12,162 COGs obtained, 40 were identified as important features, with the "inorganic ion transport and metabolism" COG category emerging as the most prominent. Furthermore, eight COGs were implicated in microbial osmoregulation, of which four were related to the "salt-in" strategy, three to the "salt-out" strategy, and one to the regulation of water channel activity. COG0168, annotated as the Trk-type K[+] transporter related to the "salt-in" strategy, was ranked as the most important feature. The relative abundance of COG0168 was observed to increase with rising salinity across metagenomes, the stenohaline strains, and the dominant Actinobacteriota and Proteobacteria phyla.

CONCLUSIONS: We demonstrated that salinity exerts influences on both the taxonomic and functional profiles of the microbial communities inhabiting the estuarine ecosystem. Our findings shed light on diverse salinity adaptation strategies employed by the estuarine microbial communities, highlighting the crucial role of the "salt-in" strategy mediated by Trk-type K[+] transporters for microorganisms thriving under osmotic stress in the short residence-time estuary. Video Abstract.}, } @article {pmid38918632, year = {2024}, author = {Mei, Z and Wang, F and Bhosle, A and Dong, D and Mehta, R and Ghazi, A and Zhang, Y and Liu, Y and Rinott, E and Ma, S and Rimm, EB and Daviglus, M and Willett, WC and Knight, R and Hu, FB and Qi, Q and Chan, AT and Burk, RD and Stampfer, MJ and Shai, I and Kaplan, RC and Huttenhower, C and Wang, DD}, title = {Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes.}, journal = {Nature medicine}, volume = {30}, number = {8}, pages = {2265-2276}, pmid = {38918632}, issn = {1546-170X}, support = {K99 DK119412/DK/NIDDK NIH HHS/United States ; R01NR01999//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01 MD011389/MD/NIMHD NIH HHS/United States ; U01 CA152904/CA/NCI NIH HHS/United States ; N01HC65235/HL/NHLBI NIH HHS/United States ; R01AG077489//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; N01HC65234/HL/NHLBI NIH HHS/United States ; R01 NR019992/NR/NINR NIH HHS/United States ; P30 DK046200/DK/NIDDK NIH HHS/United States ; N01HC65237/HL/NHLBI NIH HHS/United States ; R01 AG077489/AG/NIA NIH HHS/United States ; RF1 AG083764/AG/NIA NIH HHS/United States ; R01 HL035464/HL/NHLBI NIH HHS/United States ; P30DK046200//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R00DK119412//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R24 DK110499/DK/NIDDK NIH HHS/United States ; R00 DK119412/DK/NIDDK NIH HHS/United States ; R24DK110499//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01 CA202704/CA/NCI NIH HHS/United States ; P01 CA055075/CA/NCI NIH HHS/United States ; 209933838//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 897161//American Heart Association (American Heart Association, Inc.)/ ; U01 CA176726/CA/NCI NIH HHS/United States ; U01 CA167552/CA/NCI NIH HHS/United States ; N01HC65236/HL/NHLBI NIH HHS/United States ; P30 DK111022/DK/NIDDK NIH HHS/United States ; N01HC65233/HL/NHLBI NIH HHS/United States ; R35 CA253185/CA/NCI NIH HHS/United States ; R01 HL060712/HL/NHLBI NIH HHS/United States ; }, mesh = {*Diabetes Mellitus, Type 2/microbiology/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; *Phylogeny ; Cohort Studies ; Male ; Middle Aged ; Female ; China/epidemiology ; Dysbiosis/microbiology ; United States/epidemiology ; Israel/epidemiology ; Europe/epidemiology ; }, abstract = {The association of gut microbial features with type 2 diabetes (T2D) has been inconsistent due in part to the complexity of this disease and variation in study design. Even in cases in which individual microbial species have been associated with T2D, mechanisms have been unable to be attributed to these associations based on specific microbial strains. We conducted a comprehensive study of the T2D microbiome, analyzing 8,117 shotgun metagenomes from 10 cohorts of individuals with T2D, prediabetes, and normoglycemic status in the United States, Europe, Israel and China. Dysbiosis in 19 phylogenetically diverse species was associated with T2D (false discovery rate < 0.10), for example, enriched Clostridium bolteae and depleted Butyrivibrio crossotus. These microorganisms also contributed to community-level functional changes potentially underlying T2D pathogenesis, for example, perturbations in glucose metabolism. Our study identifies within-species phylogenetic diversity for strains of 27 species that explain inter-individual differences in T2D risk, such as Eubacterium rectale. In some cases, these were explained by strain-specific gene carriage, including loci involved in various mechanisms of horizontal gene transfer and novel biological processes underlying metabolic risk, for example, quorum sensing. In summary, our study provides robust cross-cohort microbial signatures in a strain-resolved manner and offers new mechanistic insights into T2D.}, } @article {pmid38918238, year = {2024}, author = {Sajid, M and Sharma, U and Srivastava, S and Yadav, RK and Bharadwaj, M}, title = {Microbial community and functions involved in smokeless tobacco product: a metagenomic approach.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {395}, pmid = {38918238}, issn = {1432-0614}, mesh = {*Tobacco, Smokeless ; *Metagenomics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Microbiota ; *Nitrosamines/metabolism ; India ; Nicotine/metabolism ; Humans ; }, abstract = {Smokeless tobacco products (STPs) are attributed to oral cancer and oral pathologies in their users. STP-associated cancer induction is driven by carcinogenic compounds including tobacco-specific nitrosamines (TSNAs). The TSNAs synthesis could enhanced due to the metabolic activity (nitrate metabolism) of the microbial populations residing in STPs, but identifying microbial functions linked to the TSNAs synthesis remains unexplored. Here, we rendered the first report of shotgun metagenomic sequencing to comprehensively determine the genes of all microorganisms residing in the Indian STPs belonging to two commercial (Moist-snuff and Qiwam) and three loose (Mainpuri Kapoori, Dohra, and Gudakhu) STPs, specifically consumed in India. Further, the level of nicotine, TSNAs, mycotoxins, and toxic metals were determined to relate their presence with microbial activity. The microbial population majorly belongs to bacteria with three dominant phyla including Actinobacteria, Proteobacteria, and Firmicutes. Furthermore, the STP-linked microbiome displayed several functional genes associated with nitrogen metabolism and antibiotic resistance. The chemical analysis revealed that the Mainpuri Kapoori product contained a high concentration of ochratoxins-A whereas TSNAs and Zink (Zn) quantities were high in the Moist-snuff, Mainpuri Kapoori, and Gudakhu products. Hence, our observations will help in attributing the functional potential of STP-associated microbiome and in the implementation of cessation strategies against STPs. KEY POINTS: •Smokeless tobacco contains microbes that can assist TSNA synthesis. •Antibiotic resistance genes present in smokeless tobacco-associated bacteria. •Pathogens in STPs can cause infections in smokeless tobacco users.}, } @article {pmid38917808, year = {2024}, author = {Kumbhari, A and Cheng, TNH and Ananthakrishnan, AN and Kochar, B and Burke, KE and Shannon, K and Lau, H and Xavier, RJ and Smillie, CS}, title = {Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases.}, journal = {Cell host & microbe}, volume = {32}, number = {7}, pages = {1147-1162.e12}, pmid = {38917808}, issn = {1934-6069}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AI172147/AI/NIAID NIH HHS/United States ; R01 DK127171/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Phylogeny ; Genotype ; }, abstract = {Gut bacteria are implicated in inflammatory bowel disease (IBD), but the strains driving these associations are unknown. Large-scale studies of microbiome evolution could reveal the imprint of disease on gut bacteria, thus pinpointing the strains and genes that may underlie inflammation. Here, we use stool metagenomes of thousands of IBD patients and healthy controls to reconstruct 140,000 strain genotypes, revealing hundreds of lineages enriched in IBD. We demonstrate that these strains are ancient, taxonomically diverse, and ubiquitous in humans. Moreover, disease-associated strains outcompete their healthy counterparts during inflammation, implying long-term adaptation to disease. Strain genetic differences map onto known axes of inflammation, including oxidative stress, nutrient biosynthesis, and immune evasion. Lastly, the loss of health-associated strains of Eggerthella lenta was predictive of fecal calprotectin, a biomarker of disease severity. Our work identifies reservoirs of strain diversity that may impact inflammatory disease and can be extended to other microbiome-associated diseases.}, } @article {pmid38917500, year = {2024}, author = {Zhang, D and Calmanovici, B and Marican, H and Reisser, J and Summers, S}, title = {The assembly and ecological roles of biofilms attached to plastic debris of Ashmore reef.}, journal = {Marine pollution bulletin}, volume = {205}, number = {}, pages = {116651}, doi = {10.1016/j.marpolbul.2024.116651}, pmid = {38917500}, issn = {1879-3363}, mesh = {*Biofilms ; *Plastics ; Australia ; Microbiota ; Seawater/microbiology ; Coral Reefs ; Bacteria ; Waste Products ; }, abstract = {Plastic pollution in the ocean is a global environmental hazard aggravated by poor management of plastic waste and growth of annual plastic consumption. Microbial communities colonizing the plastic's surface, the plastisphere, has gained global interest resulting in numerous efforts to characterize the plastisphere. However, there are insufficient studies deciphering the underlying metabolic processes governing the function of the plastisphere and the plastic they reside upon. Here, we collected plastic and seawater samples from Ashmore Reef in Australia to examine the planktonic microbes and plastic associated biofilm (PAB) to investigate the ecological impact, pathogenic potential, and plastic degradation capabilities of PAB in Ashmore Reef, as well as the role and impact of bacteriophages on PAB. Using high-throughput metagenomic sequencing, we demonstrated distinct microbial communities between seawater and PAB. Similar numbers of pathogenic bacteria were found in both sample types, yet plastic and seawater select for different pathogen populations. Virulence Factor analysis further illustrated stronger pathogenic potential in PAB, highlighting the pathogenicity of environmental PAB. Furthermore, functional analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed xenobiotic degradation and fatty acid degradation to be enriched in PABs. In addition, construction of metagenome-assembled genomes (MAG) and functional analysis further demonstrated the presence of a complete Polyethylene (PE) degradation pathway in multiple Proteobacteria MAGs, especially in Rhodobacteriaceae sp. Additionally, we identified viral population presence in PAB, revealing the key role of bacteriophages in shaping these communities within the PAB. Our result provides a comprehensive overview of the various ecological processes shaping microbial community on marine plastic debris.}, } @article {pmid38916949, year = {2024}, author = {Goussarov, G and Mysara, M and Cleenwerck, I and Claesen, J and Leys, N and Vandamme, P and Van Houdt, R}, title = {Benchmarking short-, long- and hybrid-read assemblers for metagenome sequencing of complex microbial communities.}, journal = {Microbiology (Reading, England)}, volume = {170}, number = {6}, pages = {}, pmid = {38916949}, issn = {1465-2080}, mesh = {*Metagenome ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; *Sequence Analysis, DNA/methods ; Genome, Bacterial/genetics ; Microbiota/genetics ; }, abstract = {Metagenome community analyses, driven by the continued development in sequencing technology, is rapidly providing insights in many aspects of microbiology and becoming a cornerstone tool. Illumina, Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) are the leading technologies, each with their own advantages and drawbacks. Illumina provides accurate reads at a low cost, but their length is too short to close bacterial genomes. Long reads overcome this limitation, but these technologies produce reads with lower accuracy (ONT) or with lower throughput (PacBio high-fidelity reads). In a critical first analysis step, reads are assembled to reconstruct genomes or individual genes within the community. However, to date, the performance of existing assemblers has never been challenged with a complex mock metagenome. Here, we evaluate the performance of current assemblers that use short, long or both read types on a complex mock metagenome consisting of 227 bacterial strains with varying degrees of relatedness. We show that many of the current assemblers are not suited to handle such a complex metagenome. In addition, hybrid assemblies do not fulfil their potential. We conclude that ONT reads assembled with CANU and Illumina reads assembled with SPAdes offer the best value for reconstructing genomes and individual genes of complex metagenomes, respectively.}, } @article {pmid38916350, year = {2024}, author = {Sankaranarayanan, G and Kodiveri Muthukaliannan, G}, title = {Exploring antimicrobial resistance determinants in the Neanderthal microbiome.}, journal = {Microbiology spectrum}, volume = {12}, number = {8}, pages = {e0266223}, pmid = {38916350}, issn = {2165-0497}, support = {20/2022-ECR-II//Indian Council of Medical Research (ICMR)/ ; }, mesh = {Animals ; *Microbiota/genetics/drug effects ; *Neanderthals/genetics/microbiology ; *DNA, Ancient/analysis ; *Metagenomics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Humans ; Feces/microbiology ; Metagenome ; Drug Resistance, Microbial/genetics ; Europe ; Fossils/microbiology ; }, abstract = {UNLABELLED: This study aimed to investigate the presence of antimicrobial resistance determinants (ARDs) in the Neanderthal microbiome through meticulous analysis of metagenomic data derived directly from dental calculus and fecal sediments across diverse Neanderthal sites in Europe. Employing a targeted locus mapping approach followed by a consensus strategy instead of an assembly-first approach, we aimed to identify and characterize ARDs within these ancient microbial communities. A comprehensive and redundant ARD database was constructed by amalgamating data from various antibiotic resistance gene repositories. Our results highlighted the efficacy of the KMA tool in providing a robust alignment of ancient metagenomic reads to the antibiotic resistance gene database. Notably, the KMA tool identified a limited number of ARDs, with only the 23S ribosomal gene from the dental calculus sample of Neanderthal remains at Goyet Troisieme Caverne exhibiting ancient DNA (aDNA) characteristics. Despite not identifying ARDs with typical ancient DNA damage patterns or negative distance proportions, our findings suggest a nuanced identification of putative antimicrobial resistance determinants in the Neanderthal microbiome's genetic repertoire based on the taxonomy-habitat correlation. Nevertheless, our findings are limited by factors such as environmental DNA contamination, DNA fragmentation, and cytosine deamination of aDNA. The study underscores the necessity for refined methodologies to unlock the genomic assets of prehistoric populations, fostering a comprehensive understanding of the intricate dynamics shaping the microbial landscape across history.

IMPORTANCE: The results of our analysis demonstrate the challenges in identifying determinants of antibiotic resistance within the endogenous microbiome of Neanderthals. Despite the comprehensive investigation of multiple studies and the utilization of advanced analytical techniques, the detection of antibiotic resistance determinants in the ancient microbial communities proved to be particularly difficult. However, our analysis did reveal the presence of some authentic ancient conservative genes, indicating the preservation of certain genetic elements over time. These findings raise intriguing questions about the factors influencing the presence or absence of antibiotic resistance in ancient microbial communities. It could be speculated that the spread of current antibiotic resistance, which has reached alarming levels in modern times, is primarily driven by anthropogenic factors such as the widespread use and misuse of antibiotics in medical and agricultural practices.}, } @article {pmid38916335, year = {2024}, author = {Yin, X-F and Ye, T and Chen, H-L and Liu, J and Mu, X-F and Li, H and Wang, J and Hu, Y-J and Cao, H and Kang, W-Q}, title = {The microbiome compositional and functional differences between rectal mucosa and feces.}, journal = {Microbiology spectrum}, volume = {12}, number = {8}, pages = {e0354923}, pmid = {38916335}, issn = {2165-0497}, support = {2020001//Shenzhen Nanshan District Scientific Research program of the People's Republic of China/ ; 006/2023/SKL//The Science and Tchnology Development Fund, Macau SAR/ ; }, mesh = {Humans ; *Feces/microbiology ; Male ; *Intestinal Mucosa/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; *Rectum/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Adult ; Colonic Polyps/microbiology ; Metagenomics ; Colorectal Neoplasms/microbiology ; }, abstract = {UNLABELLED: In recent years, most studies on the gut microbiome have primarily focused on feces samples, leaving the microbial communities in the intestinal mucosa relatively unexplored. To address this gap, our study employed shotgun metagenomics to analyze the microbial compositions in normal rectal mucosa and matched feces from 20 patients with colonic polyps. Our findings revealed a pronounced distinction of the microbial communities between these two sample sets. Compared with feces, the mucosal microbiome contains fewer genera, with Burkholderia being the most discriminating genus between feces and mucosa, highlighting its significant influence on the mucosa. Furthermore, based on the microbial classification and KEGG Orthology (KO) annotation results, we explored the association between rectal mucosal microbiota and factors such as age, gender, BMI, and polyp risk level. Notably, we identified novel biomarkers for these phenotypes, such as Clostridium ramosum and Enterobacter cloacae in age. The mucosal microbiota showed an enrichment of KO pathways related to sugar transport and short chain fatty acid metabolism. Our comprehensive approach not only bridges the knowledge gap regarding the microbial community in the rectal mucosa but also underscores the complexity and specificity of microbial interactions within the human gut, particularly in the Chinese population.

IMPORTANCE: This study presents a system-level map of the differences between feces and rectal mucosal microbial communities in samples with colorectal cancer risk. It reveals the unique microecological characteristics of rectal mucosa and its potential influence on health. Additionally, it provides novel insights into the role of the gut microbiome in the pathogenesis of colorectal cancer and paves the way for the development of new prevention and treatment strategies.}, } @article {pmid38916334, year = {2024}, author = {Du, L and Wang, J and Qiu, X and Wang, Q and Peng, H and Huang, J and Yang, F and Liu, Z and Qi, R}, title = {Clostridium sporogenes increases fat accumulation in mice by enhancing energy absorption and adipogenesis.}, journal = {Microbiology spectrum}, volume = {12}, number = {8}, pages = {e0411623}, pmid = {38916334}, issn = {2165-0497}, support = {U21A20245, 32272830//MOST | National Natural Science Foundation of China (NSFC)/ ; 23509J//Financial Resourced Program of Chongqing/ ; }, mesh = {Animals ; Mice ; *Adipogenesis ; *Energy Metabolism ; *Gastrointestinal Microbiome/physiology ; *Clostridium/metabolism/genetics ; Male ; Adipose Tissue/metabolism ; Mice, Inbred C57BL ; Liver/metabolism ; Lipid Metabolism ; Triglycerides/metabolism ; }, abstract = {UNLABELLED: Gut bacteria belonging to the Clostridium family play a pivotal role in regulating host energy balance and metabolic homeostasis. As a commensal bacterium, Clostridium sporogenes has been implicated in modulating host energy homeostasis, albeit the underlying mechanism remains elusive. Therefore, this study aimed to investigate the impact of C. sporogenes supplementation on various physiological parameters, intestinal morphology, particularly adipose tissue accumulation, and glucolipid metabolism in mice. The findings reveal that mice supplemented with C. sporogenes for 6 weeks exhibited a notable increase in body weight, fat mass, adipocyte size, and serum triglyceride (TG) levels. Notably, the increased fat accumulation is observed despite consistent feed intake in treated mice. Mechanistically, C. sporogenes supplementation significantly improved the structure integrity of intestinal villi and enhanced energy absorption efficiency while reducing excretion of carbohydrates and fatty acids in feces. This was accompanied by upregulation of glucose and fatty acid transporter expression. Furthermore, supplementation with C. sporogenes promoted adipogenesis in both liver and adipose tissues, as evidenced by increased levels of hepatic pyruvate, acetyl-CoA, and TG, along with elevated expression levels of genes associated with lipid synthesis. Regarding the microbiological aspect, C. sporogenes supplementation correlated with an increased abundance of Clostridium genus bacteria and enhanced carbohydrate enzyme activity. In summary, C. sporogenes supplementation significantly promotes fat accumulation in mice by augmenting energy absorption and adipogenesis, possibly mediated by the expansion of Clostridium bacteria population with robust glycolipid metabolic ability.

IMPORTANCE: The Clostridia clusters have been implicated in energy metabolism, the specific species and underlying mechanisms remain unclear. This present study is the first to report Clostridium sporogenes is able to affect fat accumulation and glycolipid metabolism. We indicated that gavage of C. sporogenes promoted the adipogenesis and fat accumulation in mice by not only increasing the abundance of Clostridium bacteria but by also enhancing the metabolic absorption of carbohydrates and fatty acids significantly. Obviously, changes of gut microbiota caused by the C. sporogenes, especially the significant increase of Clostridium bacteria, contributed to the fat accumulation of mice. In addition, the enhancement of Clostridium genus bacteria remarkably improved the synthesis of hepatic pyruvate, acetyl-CoA, and triglyceride levels, as well as reduced the excretion of fecal carbohydrates, short-chain fatty acids, and free fatty acids remarkably. These findings will help us to understand the relationship of specific bacteria and host energy homeostasis.}, } @article {pmid38916313, year = {2024}, author = {Maqsood, R and Wu, LI and Brennan, DC and Lim, ES}, title = {Longitudinal alterations in the urinary virome of kidney transplant recipients are influenced by BK viremia and patient sex.}, journal = {Microbiology spectrum}, volume = {12}, number = {8}, pages = {e0405523}, pmid = {38916313}, issn = {2165-0497}, support = {R00 DK107923/DK/NIDDK NIH HHS/United States ; R00DK107923//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; }, mesh = {Humans ; *Kidney Transplantation/adverse effects ; *BK Virus/isolation & purification/genetics ; Male ; Female ; *Polyomavirus Infections/urine/virology ; *Virome ; *Viremia/urine ; Middle Aged ; Adult ; *Transplant Recipients ; Longitudinal Studies ; Tumor Virus Infections/urine/virology ; Aged ; Sex Factors ; Urine/virology ; }, abstract = {UNLABELLED: Little is known about the urinary virome and how it interacts with the host, particularly in renal transplant diseases. Using metagenomic sequencing, we characterized the urinary virome of 23 kidney transplant recipients longitudinally (11 BKV+ patients and 12 BKV- patients). We applied linear mixed effects models, PERMANOVA, k-means clustering, and MaAsLin2 algorithms to determine virome signatures associated with post-transplant time, BK viremia status, and patient sex. We found that the richness and alpha diversity of urinary virome were significantly different in renal transplant recipients with BKV+ over time in comparison to BKV- (richness P = 0.012, alpha P < 0.0001). Female BKV- patients had significantly higher virome richness than males (P = 0.0063). Virome beta diversity was significantly different between patients by BKV status (P < 0.001). Additionally, we identified underlying interactions between patient sex and BKV status, in terms of virome beta diversity (P = 0.008). BK polyomavirus infections were primarily of subtypes IA, IB1, and IB2. The non-BK dominant samples clustered into six urinary virome community states. BKV- samples had more anelloviruses than BKV+ samples though this difference was not statistically significant. Lastly, we identified specific viruses, associated with BKV+ and time in our samples. Our results indicate that dynamic alterations in the urinary virome over the post-transplant period in kidney transplant recipients can be shaped by BK viremia and patient sex. These findings advance our fundamental understanding of the urinary virome and support a new line of investigation in renal disease and transplantation.

IMPORTANCE: The urinary microbiome is increasingly implicated in renal health and disease. While most research focuses on bacteria communities of the microbiome, factors that influence the urinary virome are not understood. Here, we investigated the urinary virome of 23 adult kidney transplant recipients longitudinally over 14 weeks post-transplant. We show that alterations in the urinary virome are associated with kidney transplant recipients with BK polyomavirus viremia that can lead to BK nephropathy and allograft rejection. By modeling the temporal dynamics post-transplant, we delineated specific profiles of the urinary virome associated with patient sex and urinary community states. These findings reveal fundamental aspects of the urinary virome that can be leveraged to better manage kidney diseases.}, } @article {pmid38915450, year = {2024}, author = {Trouche, B and Schrieke, H and Duron, O and Eren, AM and Reveillaud, J}, title = {Wolbachia populations across organs of individual Culex pipiens: highly conserved intra-individual core pangenome with inter-individual polymorphisms.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae078}, pmid = {38915450}, issn = {2730-6151}, abstract = {Wolbachia is a maternally inherited intracellular bacterium that infects a wide range of arthropods including mosquitoes. The endosymbiont is widely used in biocontrol strategies due to its capacity to modulate arthropod reproduction and limit pathogen transmission. Wolbachia infections in Culex spp. are generally assumed to be monoclonal but the potential presence of genetically distinct Wolbachia subpopulations within and between individual organs has not been investigated using whole genome sequencing. Here we reconstructed Wolbachia genomes from ovary and midgut metagenomes of single naturally infected Culex pipiens mosquitoes from Southern France to investigate patterns of intra- and inter-individual differences across mosquito organs. Our analyses revealed a remarkable degree of intra-individual conservancy among Wolbachia genomes from distinct organs of the same mosquito both at the level of gene presence-absence signal and single-nucleotide polymorphisms (SNPs). Yet, we identified several synonymous and non-synonymous substitutions between individuals, demonstrating the presence of some level of genomic heterogeneity among Wolbachia that infect the same C. pipiens field population. Overall, the absence of genetic heterogeneity within Wolbachia populations in a single individual confirms the presence of a dominant Wolbachia that is maintained under strong purifying forces of evolution.}, } @article {pmid38915068, year = {2024}, author = {Yan, J and Zhou, G and Ren, R and Zhang, X and Zhang, N and Wang, Z and Peng, L and Yang, Y}, title = {Siderophore-harboring gut bacteria and fecal siderophore genes for predicting the responsiveness of fecal microbiota transplantation for active ulcerative colitis.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {589}, pmid = {38915068}, issn = {1479-5876}, support = {2015AA020701//National High-tech Research and Development Program/ ; 82200609//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Colitis, Ulcerative/therapy/microbiology/genetics ; Male ; Female ; *Feces/microbiology ; *Fecal Microbiota Transplantation ; Adult ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; *Siderophores/metabolism ; Treatment Outcome ; Bacteria/genetics ; Genes, Bacterial ; Gene Dosage ; ROC Curve ; }, abstract = {BACKGROUND: Predictive markers for fecal microbiota transplantation (FMT) outcomes in patients with active ulcerative colitis (UC) are poorly defined. We aimed to investigate changes in gut microbiota pre- and post-FMT and to assess the potential value in determining the total copy number of fecal bacterial siderophore genes in predicting FMT responsiveness.

METHODS: Patients with active UC (Mayo score ≥ 3) who had undergone two FMT procedures were enrolled. Fecal samples were collected before and 8 weeks after each FMT session. Patients were classified into clinical response and non-response groups, based on their Mayo scores. The fecal microbiota profile was accessed using metagenomic sequencing, and the total siderophore genes copy number via quantitative real-time polymerase chain reaction. Additionally, we examined the association between the total siderophore genes copy number and FMT efficacy.

RESULTS: Seventy patients with UC had undergone FMT. The clinical response and remission rates were 50% and 10% after the first FMT procedure, increasing to 72.41% and 27.59% after the second FMT. The cumulative clinical response and clinical remission rates were 72.86% and 25.71%. Compared with baseline, the response group showed a significant increase in Faecalibacterium, and decrease in Enterobacteriaceae, consisted with the changes of the total bacterial siderophore genes copy number after the second FMT (1889.14 vs. 98.73 copies/ng, P < 0.01). Virulence factor analysis showed an enriched iron uptake system, especially bacterial siderophores, in the pre-FMT response group, with a greater contribution from Escherichia coli. The total baseline copy number was significantly higher in the response group than non-response group (1889.14 vs. 94.86 copies/ng, P < 0.01). A total baseline copy number cutoff value of 755.88 copies/ng showed 94.7% specificity and 72.5% sensitivity in predicting FMT responsiveness.

CONCLUSIONS: A significant increase in Faecalibacterium, and decrease in Enterobacteriaceae and the total fecal siderophore genes copy number were observed in responders after FMT. The siderophore genes and its encoding bacteria may be of predictive value for the clinical responsiveness of FMT to active ulcerative colitis.}, } @article {pmid38914944, year = {2024}, author = {Nwokorogu, VC and Pillai, S and San, JE and Pillay, C and Nyaga, MM and Sabiu, S}, title = {A metagenomic investigation of the faecal RNA virome structure of asymptomatic chickens obtained from a commercial farm in Durban, KwaZulu-Natal province, South Africa.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {629}, pmid = {38914944}, issn = {1471-2164}, support = {Directorate of Research and Postgraduate Support, Master's Scholarship Scheme//Durban University of Technology/ ; Grant number INV-046917//Bill and Melinda Gates Foundation/ ; Grant number 120433//National Research Foundation (NRF) Research Development Grant for Rated Researchers/ ; }, mesh = {Animals ; *Chickens/virology ; South Africa/epidemiology ; *Feces/virology ; *Virome/genetics ; *Metagenomics/methods ; *RNA, Viral/genetics ; RNA Viruses/genetics/classification/isolation & purification ; Farms ; Metagenome ; Seasons ; }, abstract = {BACKGROUND: Virome studies on birds, including chickens are relatively scarce, particularly from the African continent. Despite the continuous evolution of RNA viruses and severe losses recorded in poultry from seasonal viral outbreaks, the information on RNA virome composition is even scantier as a result of their highly unstable nature, genetic diversity, and difficulties associated with characterization. Also, information on factors that may modulate the occurrence of some viruses in birds is limited, particularly for domesticated birds. Viral metagenomics through advancements in sequencing technologies, has enabled the characterization of the entire virome of diverse host species using various samples.

METHODS: The complex RNA viral constituents present in 27 faecal samples of asymptomatic chickens from a South African farm collected at 3-time points from two independent seasons were determined, and the impact of the chicken's age and collection season on viral abundance and diversity was further investigated. The study utilized the non-invasive faecal sampling method, mRNA viral targeted enrichment steps, a whole transcriptome amplification strategy, Illumina sequencing, and bioinformatics tools.

RESULTS: The results obtained revealed a total of 48 viral species spanning across 11 orders, 15 families and 21 genera. Viral RNA families such as Coronaviridae, Picornaviridae, Reoviridae, Astroviridae, Caliciviridae, Picorbirnaviridae and Retroviridae were abundant, among which picornaviruses, demonstrated a 100% prevalence across the three age groups (2, 4 and 7 weeks) and two seasons (summer and winter) of the 27 faecal samples investigated. A further probe into the extent of variation between the different chicken groups investigated indicated that viral diversity and abundance were significantly influenced by age (P = 0.01099) and season (P = 0.00099) between chicken groups, while there was no effect on viral shedding within samples in a group (alpha diversity) for age (P = 0.146) and season (P = 0.242).

CONCLUSION: The presence of an exceedingly varied chicken RNA virome, encompassing avian, mammalian, fungal, and dietary-associated viruses, underscores the complexities inherent in comprehending the causation, dynamics, and interspecies transmission of RNA viruses within the investigated chicken population. Hence, chickens, even in the absence of discernible symptoms, can harbour viruses that may exhibit opportunistic, commensal, or pathogenic characteristics.}, } @article {pmid38914932, year = {2024}, author = {Phumiphanjarphak, W and Aiewsakun, P}, title = {Entourage: all-in-one sequence analysis software for genome assembly, virus detection, virus discovery, and intrasample variation profiling.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {222}, pmid = {38914932}, issn = {1471-2105}, support = {JRA-CO-2563-12568-TH//National Science and Technology Development Agency/ ; HSRI. 66-142//Health Systems Research Institute/ ; }, mesh = {*Software ; *Genome, Viral/genetics ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *SARS-CoV-2/genetics ; Metagenomics/methods ; Viruses/genetics ; COVID-19/virology ; Virome/genetics ; HeLa Cells ; }, abstract = {BACKGROUND: Pan-virus detection, and virome investigation in general, can be challenging, mainly due to the lack of universally conserved genetic elements in viruses. Metagenomic next-generation sequencing can offer a promising solution to this problem by providing an unbiased overview of the microbial community, enabling detection of any viruses without prior target selection. However, a major challenge in utilising metagenomic next-generation sequencing for virome investigation is that data analysis can be highly complex, involving numerous data processing steps.

RESULTS: Here, we present Entourage to address this challenge. Entourage enables short-read sequence assembly, viral sequence search with or without reference virus targets using contig-based approaches, and intrasample sequence variation quantification. Several workflows are implemented in Entourage to facilitate end-to-end virus sequence detection analysis through a single command line, from read cleaning, sequence assembly, to virus sequence searching. The results generated are comprehensive, allowing for thorough quality control, reliability assessment, and interpretation. We illustrate Entourage's utility as a streamlined workflow for virus detection by employing it to comprehensively search for target virus sequences and beyond in raw sequence read data generated from HeLa cell culture samples spiked with viruses. Furthermore, we showcase its flexibility and performance on a real-world dataset by analysing a preassembled Tara Oceans dataset. Overall, our results show that Entourage performs well even with low virus sequencing depth in single digits, and it can be used to discover novel viruses effectively. Additionally, by using sequence data generated from a patient with chronic SARS-CoV-2 infection, we demonstrate Entourage's capability to quantify virus intrasample genetic variations, and generate publication-quality figures illustrating the results.

CONCLUSIONS: Entourage is an all-in-one, versatile, and streamlined bioinformatics software for virome investigation, developed with a focus on ease of use. Entourage is available at https://codeberg.org/CENMIG/Entourage under the MIT license.}, } @article {pmid38914648, year = {2024}, author = {Rana, S and Canfield, JR and Ward, CS and Sprague, JE}, title = {Bile acids and the gut microbiome are involved in the hyperthermia mediated by 3,4-methylenedioxymethamphetamine (MDMA).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {14485}, pmid = {38914648}, issn = {2045-2322}, mesh = {*Gastrointestinal Microbiome/drug effects ; *N-Methyl-3,4-methylenedioxyamphetamine/pharmacology ; Animals ; Rats ; Male ; *Hyperthermia ; *Bile Acids and Salts/metabolism ; Anti-Bacterial Agents/pharmacology/adverse effects ; Rats, Sprague-Dawley ; RNA, Ribosomal, 16S/genetics ; Deoxycholic Acid/metabolism ; }, abstract = {Hyperthermia induced by phenethylamines, such as 3,4-methylenedioxymethamphetamine (MDMA), can lead to life-threatening complications and death. Activation of the sympathetic nervous system and subsequent release of norepinephrine and activation of uncoupling proteins have been demonstrated to be the key mediators of phenethylamine-induced hyperthermia (PIH). Recently, the gut microbiome was shown to also play a contributing role in PIH. Here, the hypothesis that bile acids (BAs) produced by the gut microbiome are essential to PIH was tested. Changes in the serum concentrations of unconjugated primary BAs cholic acid (CA) and chenodeoxycholic acid (CDCA) and secondary BA deoxycholic acid (DCA) were measured following MDMA (20 mg/kg, sc) treatment in antibiotic treated and control rats. MDMA-induced a significant hyperthermic response and reduced the serum concentrations of three BAs 60 min post-treatment. Pretreatment with antibiotics (vancomycin, bacitracin and neomycin) in the drinking water for five days resulted in the depletion of BAs and a hypothermic response to MDMA. Gut bacterial communities in the antibiotic-treated group were distinct from the MDMA or saline treatment groups, with decreased microbiome diversity and alteration in taxa. Metagenomic functions inferred using the bioinformatic tool PICRUSt2 on 16S rRNA gene sequences indicated that bacterial genes associated to BA metabolism are less abundant in the antibiotic-MDMA treated group. Overall, these findings suggest that gut bacterial produced BAs might play an important role in MDMA-induced hyperthermia.}, } @article {pmid38914350, year = {2024}, author = {Akram, J and Song, C and El Mashad, HM and Chen, C and Zhang, R and Liu, G}, title = {Advances in microbial community, mechanisms and stimulation effects of direct interspecies electron transfer in anaerobic digestion.}, journal = {Biotechnology advances}, volume = {76}, number = {}, pages = {108398}, doi = {10.1016/j.biotechadv.2024.108398}, pmid = {38914350}, issn = {1873-1899}, mesh = {Electron Transport ; Anaerobiosis ; *Microbiota/physiology ; Bioreactors/microbiology ; Bacteria/metabolism/genetics ; Methane/metabolism ; }, abstract = {Anaerobic digestion (AD) has been proven to be an effective green technology for producing biomethane while reducing environmental pollution. The interspecies electron transfer (IET) processes in AD are critical for acetogenesis and methanogenesis, and these IET processes are carried out via mediated interspecies electron transfer (MIET) and direct interspecies electron transfer (DIET). The latter has recently become a topic of significant interest, considering its potential to allow diffusion-free electron transfer during the AD process steps. To date, different multi-heme c-type cytochromes, electrically conductive pili (e-pili), and other relevant accessories during DIET between microorganisms of different natures have been reported. Additionally, several studies have been carried out on metagenomics and metatranscriptomics for better detection of DIET, the role of DIET's stimulation in alleviating stressed conditions, such as high organic loading rates (OLR) and low pH, and the stimulation mechanisms of DIET in mixed cultures and co-cultures by various conductive materials. Keeping in view this significant research progress, this study provides in-depth insights into the DIET-active microbial community, DIET mechanisms of different species, utilization of various approaches for stimulating DIET, characterization approaches for effectively detecting DIET, and potential future research directions. This study can help accelerate the field's research progress, enable a better understanding of DIET in complex microbial communities, and allow its utilization to alleviate various inhibitions in complex AD processes.}, } @article {pmid38913582, year = {2024}, author = {Xiao, BL and Hu, XQ and Li, M}, title = {Dysbiosis and Staphylococcus species over representation in the exit site skin microbiota of hemodialysis patients carrying tunneled cuffed central venous catheter.}, journal = {Renal failure}, volume = {46}, number = {2}, pages = {2363417}, pmid = {38913582}, issn = {1525-6049}, mesh = {Humans ; Middle Aged ; Male ; *Renal Dialysis/adverse effects/instrumentation ; Female ; *Skin/microbiology ; *Kidney Failure, Chronic/therapy/complications ; *Dysbiosis/microbiology/etiology ; *Microbiota ; Aged ; *Staphylococcus/isolation & purification ; Catheter-Related Infections/microbiology ; Central Venous Catheters/adverse effects/microbiology ; Adult ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVES: Hemodialysis patients with end-stage renal disease (ESRD) are susceptible to infections and dysbiosis. Catheter-related infections are typically caused by opportunistic skin pathogens. This study aims to compare the skin microbiota changes around the exit site of tunneled cuffed catheters (peri-catheter group) and the contralateral site (control group).

METHODS: ESRD patients on hemodialysis were recruited. The skin microbiota were collected with moist skin swabs and analyzed using high-throughput sequencing of the 16S rDNA V3-V4 region. After denoising, de-replication, and removal of chimeras, the reads were assigned to zero-radius operational taxonomic units (ZOTU).

RESULTS: We found significantly reduced alpha diversity in the peri-catheter group compared to the control group, as indicated by the Shannon, Jost, and equitability indexes, but not by the Chao1 or richness indexes. Beta diversity analysis revealed significant deviation of the peri-catheter microbiota from its corresponding control group. There was an overrepresentation of Firmicutes and an underrepresentation of Actinobacteria, Proteobacteria, and Acidobacteria at the phylum level in the peri-catheter group. The most abundant ZOTU (Staphylococcus spp.) drastically increased, while Cutibacterium, a commensal bacterium, decreased in the peri-catheter group. Network analysis revealed that the skin microbiota demonstrated covariance with both local and biochemical factors.

CONCLUSIONS: In conclusion, there was significant skin microbiota dysbiosis at the exit sites compared to the control sites in ESRD dialysis patients. Managing skin dysbiosis represents a promising target in the prevention of catheter-related bacterial infections.}, } @article {pmid38912690, year = {2024}, author = {Byndloss, M and Devkota, S and Duca, F and Niess, JH and Nieuwdorp, M and Orho-Melander, M and Sanz, Y and Tremaroli, V and Zhao, L}, title = {The Gut Microbiota and Diabetes: Research, Translation, and Clinical Applications-2023 Diabetes, Diabetes Care, and Diabetologia Expert Forum.}, journal = {Diabetes}, volume = {73}, number = {9}, pages = {1391-1410}, pmid = {38912690}, issn = {1939-327X}, support = {PID2020-119536RB-I00//Spanish Ministry of Science, Innovation and Universities MICIU/AEI/ ; 2020 (09150182010020)//ZONMW-VICI/ ; //Novo Nordisk Foundation/ ; DP1 DK130687/DK/NIDDK NIH HHS/United States ; CEX2021-001189-S/10.13039/501100011033//Severo Ochoa Center of Excellence/ ; 1DP1 DK130687/DK/NIDDK NIH HHS/United States ; 310030_219210//Swiss National Science Foundation (SNSF)/ ; R01 DK123446/DK/NIDDK NIH HHS/United States ; 875534//European Union’s Innovative Medicine Initiative/ ; R01 DK131104/DK/NIDDK NIH HHS/United States ; 2020 (2020.10.002)//DFN-DON/ ; }, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Diabetes Mellitus, Type 2/microbiology/metabolism/therapy ; Translational Research, Biomedical ; }, abstract = {This article summarizes the state of the science on the role of the gut microbiota (GM) in diabetes from a recent international expert forum organized by Diabetes, Diabetes Care, and Diabetologia, which was held at the European Association for the Study of Diabetes 2023 Annual Meeting in Hamburg, Germany. Forum participants included clinicians and basic scientists who are leading investigators in the field of the intestinal microbiome and metabolism. Their conclusions were as follows: 1) the GM may be involved in the pathophysiology of type 2 diabetes, as microbially produced metabolites associate both positively and negatively with the disease, and mechanistic links of GM functions (e.g., genes for butyrate production) with glucose metabolism have recently emerged through the use of Mendelian randomization in humans; 2) the highly individualized nature of the GM poses a major research obstacle, and large cohorts and a deep-sequencing metagenomic approach are required for robust assessments of associations and causation; 3) because single-time point sampling misses intraindividual GM dynamics, future studies with repeated measures within individuals are needed; and 4) much future research will be required to determine the applicability of this expanding knowledge to diabetes diagnosis and treatment, and novel technologies and improved computational tools will be important to achieve this goal.}, } @article {pmid38910513, year = {2024}, author = {You, HS and Park, JY and Seo, H and Kim, BJ and Kim, JG}, title = {Increasing correlation between oral and gastric microbiota during gastric carcinogenesis.}, journal = {The Korean journal of internal medicine}, volume = {39}, number = {4}, pages = {590-602}, pmid = {38910513}, issn = {2005-6648}, support = {2021R1G1A1091400//National Research Foundation of Korea/ ; //Ministry of Science and ICT/ ; //Chung-Ang University/ ; }, mesh = {Humans ; *Stomach Neoplasms/microbiology ; Middle Aged ; Male ; Female ; *Gastric Juice/microbiology ; *Gastrointestinal Microbiome ; Aged ; *Saliva/microbiology ; Bacteria/genetics/classification/isolation & purification ; Ribotyping ; RNA, Ribosomal, 16S/genetics ; Mouth/microbiology ; Adult ; Case-Control Studies ; Gastric Mucosa/microbiology ; Carcinogenesis ; Stomach/microbiology ; Metagenomics ; }, abstract = {BACKGROUND/AIMS: Recent research has increasingly focused on the role of the gastric microbiome in the development of gastric cancer. We aimed to investigate the changes in the microbiome during gastric carcinogenesis in structural and functional aspects, with a specific focus on the association between oral and gastric microbiomes.

METHODS: We collected saliva, gastric juice, and gastric tissue samples from 141 patients at different stages of gastric carcinogenesis and processed them for microbiome analysis using 16S rRNA gene profiling. The alpha and beta diversities were analyzed, and the differences in microbiome composition and function profiles were analyzed among the groups, as well as the correlation between changes in the oral and gastric microbiomes during carcinogenesis.

RESULTS: We observed significant differences in microbial diversity and composition between the disease and control groups, primarily in the gastric juice. Specific bacterial strains, including Schaalia odontolytica, Streptococcus cristatus, and Peptostreptococcus stomatis, showed a significant increase in abundance in the gastric juice in the low-grade dysplasia and gastric cancer groups. Notably, the correlation between the oral and gastric microbiota compositions, increased as the disease progressed. Predictive analysis of the metagenomic functional profiles revealed changes in functional pathways that may be associated with carcinogenesis (ABC transport and two-component systems).

CONCLUSION: During gastric carcinogenesis, the abundance of oral commensals associated with cancer increased in the stomach. The similarity in microbial composition between the stomach and oral cavity also increased, implying a potential role of oral-gastric bacterial interactions in gastric cancer development.}, } @article {pmid38910254, year = {2024}, author = {Stege, PB and Schokker, D and Harders, F and Kar, SK and Stockhofe, N and Perricone, V and Rebel, JMJ and de Jong, IC and Bossers, A}, title = {Diet-induced changes in the jejunal microbiota of developing broilers reduce the abundance of Enterococcus hirae and Enterococcus faecium.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {627}, pmid = {38910254}, issn = {1471-2164}, support = {2019-2022 KB34 Towards a Circular and Climate Neutral Society//Wageningen University and Research/ ; 2019-2022 KB34 Towards a Circular and Climate Neutral Society//Wageningen University and Research/ ; 2019-2022 KB34 Towards a Circular and Climate Neutral Society//Wageningen University and Research/ ; 2019-2022 KB34 Towards a Circular and Climate Neutral Society//Wageningen University and Research/ ; 2019-2022 KB34 Towards a Circular and Climate Neutral Society//Wageningen University and Research/ ; 2019-2022 KB34 Towards a Circular and Climate Neutral Society//Wageningen University and Research/ ; 2019-2022 KB34 Towards a Circular and Climate Neutral Society//Wageningen University and Research/ ; 2019-2022 KB34 Towards a Circular and Climate Neutral Society//Wageningen University and Research/ ; 2019-2022 KB34 Towards a Circular and Climate Neutral Society//Wageningen University and Research/ ; WOT-01-003-085/KB-37-003-013 Bioinformatics and sequencing applications//Ministry of Agriculture, the Netherlands/ ; WOT-01-003-085/KB-37-003-013 Bioinformatics and sequencing applications//Ministry of Agriculture, the Netherlands/ ; WOT-01-003-085/KB-37-003-013 Bioinformatics and sequencing applications//Ministry of Agriculture, the Netherlands/ ; WOT-01-003-085/KB-37-003-013 Bioinformatics and sequencing applications//Ministry of Agriculture, the Netherlands/ ; }, mesh = {Animals ; *Chickens/microbiology/growth & development ; *Enterococcus faecium/genetics ; *Gastrointestinal Microbiome/drug effects ; *Jejunum/microbiology ; *Enterococcus hirae ; *Animal Feed ; Diet/veterinary ; Metagenomics/methods ; Dietary Supplements ; }, abstract = {Modern broiler breeds allow for high feed efficiency and rapid growth, which come at a cost of increased susceptibility to pathogens and disease. Broiler growth rate, feed efficiency, and health are affected by the composition of the gut microbiota, which in turn is influenced by diet. In this study, we therefore assessed how diet composition can affect the broiler jejunal gut microbiota. A total of 96 broiler chickens were divided into four diet groups: control, coated butyrate supplementation, medium-chain fatty acid supplementation, or a high-fibre low-protein content. Diet groups were sub-divided into age groups (4, 12 and 33 days of age) resulting in groups of 8 broilers per diet per age. The jejunum content was used for metagenomic shotgun sequencing to determine the microbiota taxonomic composition at species level. The composed diets resulted in a total of 104 differentially abundant bacterial species. Most notably were the butyrate-induced changes in the jejunal microbiota of broilers 4 days post-hatch, resulting in the reduced relative abundance of mainly Enterococcus faecium (-1.8 l2fc, Padj = 9.9E-05) and the opportunistic pathogen Enterococcus hirae (-2.9 l2fc, Padj = 2.7E-08), when compared to the control diet. This effect takes place during early broiler development, which is critical for broiler health, thus exemplifying the importance of how diet can influence the microbiota composition in relation to broiler health. Future studies should therefore elucidate how diet can be used to promote a beneficial microbiota in the early stages of broiler development.}, } @article {pmid38910152, year = {2024}, author = {Byndloss, M and Devkota, S and Duca, F and Niess, JH and Nieuwdorp, M and Orho-Melander, M and Sanz, Y and Tremaroli, V and Zhao, L}, title = {The gut microbiota and diabetes: research, translation, and clinical applications - 2023 Diabetes, Diabetes Care, and Diabetologia Expert Forum.}, journal = {Diabetologia}, volume = {67}, number = {9}, pages = {1760-1782}, pmid = {38910152}, issn = {1432-0428}, support = {R01 DK131104/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetes Mellitus, Type 2/microbiology/metabolism ; Translational Research, Biomedical ; }, abstract = {This article summarises the state of the science on the role of the gut microbiota (GM) in diabetes from a recent international expert forum organised by Diabetes, Diabetes Care, and Diabetologia, which was held at the European Association for the Study of Diabetes 2023 Annual Meeting in Hamburg, Germany. Forum participants included clinicians and basic scientists who are leading investigators in the field of the intestinal microbiome and metabolism. Their conclusions were as follows: (1) the GM may be involved in the pathophysiology of type 2 diabetes, as microbially produced metabolites associate both positively and negatively with the disease, and mechanistic links of GM functions (e.g. genes for butyrate production) with glucose metabolism have recently emerged through the use of Mendelian randomisation in humans; (2) the highly individualised nature of the GM poses a major research obstacle, and large cohorts and a deep-sequencing metagenomic approach are required for robust assessments of associations and causation; (3) because single time point sampling misses intraindividual GM dynamics, future studies with repeated measures within individuals are needed; and (4) much future research will be required to determine the applicability of this expanding knowledge to diabetes diagnosis and treatment, and novel technologies and improved computational tools will be important to achieve this goal.}, } @article {pmid38909792, year = {2024}, author = {Zhu, J and Chen, G and Tang, S and Cheng, K and Wu, K and Cai, Z and Zhou, J}, title = {The micro-ecological feature of colonies is a potential strategy for Phaeocystis globosa bloom formation.}, journal = {The Science of the total environment}, volume = {946}, number = {}, pages = {174134}, doi = {10.1016/j.scitotenv.2024.174134}, pmid = {38909792}, issn = {1879-1026}, mesh = {*Haptophyta/growth & development ; *Harmful Algal Bloom ; *Microbiota ; Microalgae ; Bacteria/classification ; Biodiversity ; }, abstract = {Phaeocystis globosa is among the dominant microalgae associated with harmful algal blooms. P. globosa has a polymorphic life cycle and its ecological success has been attributed to algal colony formation, however, few studies have assessed differences in microbial communities and their functional profiles between intra- and extra-colonies during P. globosa blooms. To address this, environmental and metagenomics tools were used to conduct a time-series analysis of the bacterial composition and metabolic characteristics of intra- and extra-colonies during a natural P. globosa bloom. The results show that bacterial composition, biodiversity, and network interactions differed significantly between intra- and extra-colonies. Dominant extra-colonial bacteria were Bacteroidia and Saccharimonadis, while dominant intra-colonial bacteria included Alphaproteobacteria and Gammaproteobacteria. Despite the lower richness and diversity observed in the intra-colonial bacterial community, relative to extra-colonies, the complexity and interconnectedness of the intra-colonial networks were higher. Regarding bacterial function, more functional genes were enriched in substance metabolism (polysaccharides, iron element and dimethylsulfoniopropionate) and signal communication (quorum sensing, indoleacetic acid-IAA) pathways in intra- than in extra-colonies. Conceptual model construction showed that microbial cooperative synthesis of ammonium, vitamin B12, IAA, and siderophores were strongly related to the P. globosa bloom, particularly in the intra-colonial environment. Overall, our data highlight the differences in bacterial structure and functions within and outside the colony during P. globosa blooms. These findings represent fundamental information indicating that phenotypic heterogeneity is a selective strategy that improves microbial population competitiveness and environmental adaptation, benefiting P. globosa bloom formation and persistence.}, } @article {pmid38909766, year = {2024}, author = {Heil, BA and van Heule, M and Thompson, SK and Kearns, TA and Beckers, KF and Oberhaus, EL and King, G and Daels, P and Dini, P and Sones, JL}, title = {Metagenomic characterization of the equine endometrial microbiome during anestrus.}, journal = {Journal of equine veterinary science}, volume = {140}, number = {}, pages = {105134}, doi = {10.1016/j.jevs.2024.105134}, pmid = {38909766}, issn = {0737-0806}, mesh = {Animals ; Horses/microbiology ; Female ; *Endometrium/microbiology ; *Microbiota/genetics ; *Anestrus ; Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Estrus/physiology ; RNA, Bacterial/genetics/analysis ; }, abstract = {The equine uterus is highly interrogated during estrus prior to breeding and establishing pregnancy. Many studies in mares have been performed during estrus under the influence of high estrogen concentrations, including the equine estrual microbiome. To date, it is unknown how the uterine microbiome of the mare is influenced by cyclicity; while, the equine vaginal microbiome is stable throughout the estrous cycle. We hypothesized that differences would exist between the equine endometrial microbiome of mares in estrus and anestrus. The aim of this study was two-fold: to characterize the resident endometrial microbiome of healthy mares during anestrus and to compare this with estrus. Double-guarded endometrial swabs were taken from healthy mares during estrus (n = 16) and in the following non-breeding season during anestrus (n = 8). Microbial population was identified using 16S rRNA sequencing. Our results suggest that the equine uterine microbiome in estrus has a low diversity and low richness, while during anestrus, a higher diversity and higher richness were seen compared to estrus. Despite this difference, both the estrus and anestrus endometrial microbiome were dominated by Proteobacteria, Firmicutes, and Bacteroidota. The composition of the microbial community between anestrus and estrus was significantly different. This may be explained by the difference in the composition of the endometrial immune milieu based on the stage of the cycle. Further research investigating the function of the equine endometrial microbiome and dynamics changes within the uterine environment is required.}, } @article {pmid38909053, year = {2024}, author = {de Oliveira Lino, FS and Garg, S and Li, SS and Misiakou, MA and Kang, K and Vale da Costa, BL and Beyer-Pedersen, TS and Giacon, TG and Basso, TO and Panagiotou, G and Sommer, MOA}, title = {Strain dynamics of contaminating bacteria modulate the yield of ethanol biorefineries.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5323}, pmid = {38909053}, issn = {2041-1723}, support = {NNF10CC1016517//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; ALTF 137-2018//European Molecular Biology Organization (EMBO)/ ; APP1166180//Department of Health | National Health and Medical Research Council (NHMRC)/ ; 406564/2022-1//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Científico e Tecnológico (National Council for Scientific and Technological Development)/ ; }, mesh = {*Ethanol/metabolism ; *Fermentation ; *Bacteria/metabolism/genetics/classification ; Microbiota/physiology ; Biofuels ; Metagenomics ; Industrial Microbiology/methods ; Temperature ; }, abstract = {Bioethanol is a sustainable energy alternative and can contribute to global greenhouse-gas emission reductions by over 60%. Its industrial production faces various bottlenecks, including sub-optimal efficiency resulting from bacteria. Broad-spectrum removal of these contaminants results in negligible gains, suggesting that the process is shaped by ecological interactions within the microbial community. Here, we survey the microbiome across all process steps at two biorefineries, over three timepoints in a production season. Leveraging shotgun metagenomics and cultivation-based approaches, we identify beneficial bacteria and find improved outcome when yeast-to-bacteria ratios increase during fermentation. We provide a microbial gene catalogue which reveals bacteria-specific pathways associated with performance. We also show that Limosilactobacillus fermentum overgrowth lowers production, with one strain reducing yield by ~5% in laboratory fermentations, potentially due to its metabolite profile. Temperature is found to be a major driver for strain-level dynamics. Improved microbial management strategies could unlock environmental and economic gains in this US $ 60 billion industry enabling its wider adoption.}, } @article {pmid38908906, year = {2024}, author = {González, A and Fullaondo, A and Odriozola, A}, title = {Techniques, procedures, and applications in microbiome analysis.}, journal = {Advances in genetics}, volume = {111}, number = {}, pages = {81-115}, doi = {10.1016/bs.adgen.2024.01.003}, pmid = {38908906}, issn = {0065-2660}, mesh = {*Microbiota ; Humans ; *Computational Biology/methods ; Metagenomics/methods ; Animals ; Sequence Analysis, DNA/methods ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing ; }, abstract = {Microbiota is a complex community of microorganisms living in a defined environment. Until the 20th century, knowledge of microbiota was partial, as the techniques available for their characterization were primarily based on bacteriological culture. In the last twenty years, the development of DNA sequencing technologies, multi-omics, and bioinformatics has expanded our understanding of microorganisms. We have moved from mainly considering them isolated disease-causing agents to recognizing the microbiota as an essential component of host biology. These techniques have shown that the microbiome plays essential roles in various host phenotypes, influencing development, physiology, reproduction, and evolution. This chapter provides researchers with a summary of the primary concepts, sample collection, experimental techniques, and bioinformatics analysis commonly used in microbiome research. The main features, applications in microbiome studies, and their advantages and limitations are included in each section.}, } @article {pmid38908733, year = {2024}, author = {Lau, RI and Su, Q and Ching, JYL and Lui, RN and Chan, TT and Wong, MTL and Lau, LHS and Wing, YK and Chan, RNY and Kwok, HYH and Ho, AHY and Tse, YK and Cheung, CP and Li, MKT and Siu, WY and Liu, C and Lu, W and Wang, Y and Chiu, EOL and Cheong, PK and Chan, FKL and Ng, SC}, title = {Fecal Microbiota Transplantation for Sleep Disturbance in Post-acute COVID-19 Syndrome.}, journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association}, volume = {22}, number = {12}, pages = {2487-2496.e6}, doi = {10.1016/j.cgh.2024.06.004}, pmid = {38908733}, issn = {1542-7714}, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; *COVID-19/complications/therapy ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; *Post-Acute COVID-19 Syndrome ; Prospective Studies ; SARS-CoV-2 ; Sleep Initiation and Maintenance Disorders/therapy ; Treatment Outcome ; }, abstract = {BACKGROUND & AIMS: Post-acute COVID-19 syndrome (PACS) is associated with sleep disturbance, but treatment options are limited. The etiology of PACS may be secondary to alterations in the gut microbiome. Here, we report the efficacy of fecal microbiota transplantation (FMT) in alleviating post-COVID insomnia symptoms in a nonrandomized, open-label prospective interventional study.

METHODS: Between September 22, 2022, and May 22, 2023, we recruited 60 PACS patients with insomnia defined as Insomnia Severity Index (ISI) ≥8 and assigned them to the FMT group (FMT at weeks 0, 2, 4, and 8; n = 30) or the control group (n = 30). The primary outcome was clinical remission defined by an ISI of <8 at 12 weeks. Secondary outcomes included changes in the Pittsburgh Sleep Quality Index, Generalized Anxiety Disorder-7 scale, Epworth Sleepiness Scale, Multidimensional Fatigue Inventory, blood cortisol and melatonin, and gut microbiome analysis on metagenomic sequencing.

RESULTS: At week 12, more patients in the FMT than the control group had insomnia remission (37.9% vs 10.0%; P = .018). The FMT group showed a decrease in ISI score (P < .0001), Pittsburgh Sleep Quality Index (P < .0001), Generalized Anxiety Disorder-7 scale (P = .0019), Epworth Sleepiness Scale (P = .0057), and blood cortisol concentration (P = .035) from baseline to week 12, but there was no significant change in the control group. There was enrichment of bacteria such as Gemmiger formicilis and depletion of microbial pathways producing menaquinol derivatives after FMT. The gut microbiome profile resembled that of the donor in FMT responders but not in nonresponders at week 12. There was no serious adverse event.

CONCLUSIONS: This pilot study showed that FMT could be effective and safe in alleviating post-COVID insomnia, and further clinical trials are warranted.

CLINICALTRIALS: gov, Number: NCT05556733.}, } @article {pmid38908613, year = {2024}, author = {Xu, Q and Gao, J and Zhao, R and Li, H and Cui, H and Yuan, Z and Ren, H and Cao, B and Wei, B}, title = {Akkermansia muciniphila-derived pentadecanoic acid enhances oxaliplatin sensitivity in gastric cancer by modulating glycolysis.}, journal = {Pharmacological research}, volume = {206}, number = {}, pages = {107278}, doi = {10.1016/j.phrs.2024.107278}, pmid = {38908613}, issn = {1096-1186}, mesh = {*Stomach Neoplasms/drug therapy/metabolism ; *Oxaliplatin/pharmacology/therapeutic use ; Animals ; *Akkermansia/drug effects ; *Gastrointestinal Microbiome/drug effects ; Humans ; Cell Line, Tumor ; *Antineoplastic Agents/pharmacology/therapeutic use ; *Glycolysis/drug effects ; Mice ; Male ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Anti-Bacterial Agents/pharmacology/therapeutic use ; }, abstract = {Accumulating evidence has proved the close association between alterations in gut microbiota and resistance to chemotherapeutic drugs. However, the potential roles of gut microbiota in regulating oxaliplatin sensitivity in gastric cancer (GC) have not been investigated before. We first found that antibiotic treatment diminished the therapeutic efficacy of oxaliplatin in a GC mouse model. Importantly, this effect could be transmitted to germ-free mice via fecal microbiota transplantation, indicating a potential role of gut microbiota modulation in oxaliplatin efficacy. Further, metagenomics data showed that Akkermansia muciniphila (A. muciniphila) ranked first among the bacterial species with decreased relative abundances after antibiotic treatment. Metabolically active A. muciniphila promotes oxaliplatin efficacy. As shown by metabolomics analysis, the metabolic pattern of gut microbiota was disrupted with significantly downregulated levels of pentadecanoic acid (PEA), and the use of PEA significantly promoted oxaliplatin efficacy. Mechanistically, FUBP1 positively regulated aerobic glycolysis of GC cells to hinder the therapeutic efficacy of oxaliplatin. A. muciniphila-derived PEA functioned as an inhibitory factor of glycolysis by directly antagonizing the activity of FUBP1, which potentiated GC responses to oxaliplatin. Our research suggested a key role for intestinal A. muciniphila and its metabolite PEA in promoting oxaliplatin efficacy, thus providing a new perspective for probiotic and prebiotic intervention in GC patients during chemotherapy.}, } @article {pmid38908447, year = {2024}, author = {Gao, H and Guo, Z and He, X and Yang, J and Jiang, L and Yang, A and Xiao, X and Xu, R}, title = {Stress mitigation mechanism of rice leaf microbiota amid atmospheric deposition of heavy metals.}, journal = {Chemosphere}, volume = {362}, number = {}, pages = {142680}, doi = {10.1016/j.chemosphere.2024.142680}, pmid = {38908447}, issn = {1879-1298}, mesh = {*Oryza/microbiology ; *Metals, Heavy/metabolism ; *Plant Leaves/metabolism ; *Microbiota/drug effects ; Stress, Physiological ; Air Pollutants/toxicity ; Pantoea/physiology ; }, abstract = {Leaf microbiota have been extensively applied in the biological control of plant diseases, but their crucial roles in mitigating atmospheric heavy metal (HM) deposition and promoting plant growth remain poorly understood. This study demonstrates that elevated atmospheric HM deposition on rice leaves significantly shapes distinct epiphytic and endophytic microbiota across all growth stages. HM stress consistently leads to the dominance of epiphytic Pantoea and endophytic Microbacterium in rice leaves, particularly during the booting and filling stages. Leaf-bound HMs stimulate the differentiation of specialized microbial communities in both endophytic and epiphytic compartments, thereby regulating leaf microbial interactions. Metagenomic binning retrieved high-quality genomes of keystone leaf microorganisms, indicating their potential for essential metabolic functions. Notably, Pantoea and Microbacterium show significant HM resistance, plant growth-promoting capabilities, and diverse element cycling functions. They possess genes associated with metal(loid) resistance, such as ars and czc, suggesting their ability to detoxify arsenic(As) and cadmium(Cd). They also support carbon, nitrogen, and sulfur cycling, with genes linked to carbon fixation, nitrogen fixation, and sulfur reduction. Additionally, these bacteria may enhance plant stress resistance and growth by producing antioxidants, phytohormones, and other beneficial compounds, potentially improving HM stress tolerance and nutrient availability in rice plants. This study shows that atmospheric HMs affect rice leaf microbial communities, prompting plants to seek microbial help to combat stress. The unique composition and metabolic potential of rice leaf microbiota offer a novel perspective for mitigating adverse stress induced by atmospheric HM deposition. This contributes to the utilization of leaf microbiota to alleviate the negative impact of heavy metal deposition on rice development and food security.}, } @article {pmid38908099, year = {2024}, author = {Ling, CW and Deng, K and Yang, Y and Lin, HR and Liu, CY and Li, BY and Hu, W and Liang, X and Zhao, H and Tang, XY and Zheng, JS and Chen, YM}, title = {Mapping the gut microecological multi-omics signatures to serum metabolome and their impact on cardiometabolic health in elderly adults.}, journal = {EBioMedicine}, volume = {105}, number = {}, pages = {105209}, pmid = {38908099}, issn = {2352-3964}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Aged ; *Metabolome ; *Metabolomics/methods ; *Metabolic Syndrome/blood/epidemiology ; Proteomics/methods ; Metagenomics/methods ; Middle Aged ; Biomarkers/blood ; Feces/microbiology ; Multiomics ; }, abstract = {BACKGROUND: Mapping gut microecological features to serum metabolites (SMs) will help identify functional links between gut microbiome and cardiometabolic health.

METHODS: This study encompassed 836-1021 adults over 9.7 year in a cohort, assessing metabolic syndrome (MS), carotid atherosclerotic plaque (CAP), and other metadata triennially. We analyzed mid-term microbial metagenomics, targeted fecal and serum metabolomics, host genetics, and serum proteomics.

FINDINGS: Gut microbiota and metabolites (GMM) accounted for 15.1% overall variance in 168 SMs, with individual GMM factors explaining 5.65%-10.1%, host genetics 3.23%, and sociodemographic factors 5.95%. Specifically, GMM elucidated 5.5%-49.6% variance in the top 32 GMM-explained SMs. Each 20% increase in the 32 metabolite score (derived from the 32 SMs) correlated with 73% (95% confidence interval [CI]: 53%-95%) and 19% (95% CI: 11%-27%) increases in MS and CAP incidences, respectively. Among the 32 GMM-explained SMs, sebacic acid, indoleacetic acid, and eicosapentaenoic acid were linked to MS or CAP incidence. Serum proteomics revealed certain proteins, particularly the apolipoprotein family, mediated the relationship between GMM-SMs and cardiometabolic risks.

INTERPRETATION: This study reveals the significant influence of GMM on SM profiles and illustrates the intricate connections between GMM-explained SMs, serum proteins, and the incidence of MS and CAP, providing insights into the roles of gut dysbiosis in cardiometabolic health via regulating blood metabolites.

FUNDING: This study was jointly supported by the National Natural Science Foundation of China, Key Research and Development Program of Guangzhou, 5010 Program for Clinical Research of Sun Yat-sen University, and the 'Pioneer' and 'Leading goose' R&D Program of Zhejiang.}, } @article {pmid38907008, year = {2024}, author = {Huang, L and Guo, R and Li, S and Wu, X and Zhang, Y and Guo, S and Lv, Y and Xiao, Z and Kang, J and Meng, J and Zhou, P and Ma, J and You, W and Zhang, Y and Yu, H and Zhao, J and Huang, G and Duan, Z and Yan, Q and Sun, W}, title = {A multi-kingdom collection of 33,804 reference genomes for the human vaginal microbiome.}, journal = {Nature microbiology}, volume = {9}, number = {8}, pages = {2185-2200}, pmid = {38907008}, issn = {2058-5276}, mesh = {Humans ; Female ; *Vagina/microbiology/virology ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Metagenomics/methods ; Fungi/genetics/classification/isolation & purification ; Phylogeny ; Genome, Microbial ; Metagenome ; Viruses/genetics/classification/isolation & purification ; Vaginosis, Bacterial/microbiology ; }, abstract = {The human vagina harbours diverse microorganisms-bacteria, viruses and fungi-with profound implications for women's health. Genome-level analysis of the vaginal microbiome across multiple kingdoms remains limited. Here we utilize metagenomic sequencing data and fungal cultivation to establish the Vaginal Microbial Genome Collection (VMGC), comprising 33,804 microbial genomes spanning 786 prokaryotic species, 11 fungal species and 4,263 viral operational taxonomic units. Notably, over 25% of prokaryotic species and 85% of viral operational taxonomic units remain uncultured. This collection significantly enriches genomic diversity, especially for prevalent vaginal pathogens such as BVAB1 (an uncultured bacterial vaginosis-associated bacterium) and Amygdalobacter spp. (BVAB2 and related species). Leveraging VMGC, we characterize functional traits of prokaryotes, notably Saccharofermentanales (an underexplored yet prevalent order), along with prokaryotic and eukaryotic viruses, offering insights into their niche adaptation and potential roles in the vagina. VMGC serves as a valuable resource for studying vaginal microbiota and its impact on vaginal health.}, } @article {pmid38906446, year = {2024}, author = {Ran, Z and Yang, J and Liu, L and Wu, S and An, Y and Hou, W and Cheng, T and Zhang, Y and Zhang, Y and Huang, Y and Zhang, Q and Wan, J and Li, X and Xing, B and Ye, Y and Xu, P and Chen, Z and Zhao, J and Li, R}, title = {Chronic PM2.5 exposure disrupts intestinal barrier integrity via microbial dysbiosis-triggered TLR2/5-MyD88-NLRP3 inflammasome activation.}, journal = {Environmental research}, volume = {258}, number = {}, pages = {119415}, doi = {10.1016/j.envres.2024.119415}, pmid = {38906446}, issn = {1096-0953}, mesh = {Animals ; *NLR Family, Pyrin Domain-Containing 3 Protein/metabolism/genetics ; *Dysbiosis/chemically induced ; *Inflammasomes/metabolism/drug effects ; *Mice, Inbred C57BL ; *Particulate Matter/toxicity ; *Myeloid Differentiation Factor 88/metabolism/genetics ; *Toll-Like Receptor 2/metabolism ; Mice ; *Toll-Like Receptor 5/metabolism ; Air Pollutants/toxicity ; Male ; Gastrointestinal Microbiome/drug effects ; Intestinal Mucosa/metabolism/drug effects ; Intestines/drug effects/microbiology ; }, abstract = {BACKGROUND: PM2.5, a known public health risk, is increasingly linked to intestinal disorders, however, the mechanisms of its impact are not fully understood.

PURPOSE: This study aimed to explore the impact of chronic PM2.5 exposure on intestinal barrier integrity and to uncover the underlying molecular mechanisms.

METHODS: C57BL/6 J mice were exposed to either concentrated ambient PM2.5 (CPM) or filtered air (FA) for six months to simulate urban pollution conditions. We evaluated intestinal barrier damage, microbial shifts, and metabolic changes through histopathology, metagenomics, and metabolomics. Analysis of the TLR signaling pathway was also conducted.

RESULTS: The mean concentration of PM2.5 in the CPM exposure chamber was consistently measured at 70.9 ± 26.8 μg/m³ throughout the study period. Our findings show that chronic CPM exposure significantly compromises intestinal barrier integrity, as indicated by reduced expression of the key tight junction proteins Occludin and Tjp1/Zo-1. Metagenomic sequencing revealed significant shifts in the microbial landscape, identifying 35 differentially abundant species. Notably, there was an increase in pro-inflammatory nongastric Helicobacter species and a decrease in beneficial bacteria, such as Lactobacillus intestinalis, Lactobacillus sp. ASF360, and Eubacterium rectale. Metabolomic analysis further identified 26 significantly altered metabolites commonly associated with intestinal diseases. A strong correlation between altered bacterial species and metabolites was also observed. For example, 4 Helicobacter species all showed positive correlations with 13 metabolites, including Lactate, Bile acids, Pyruvate and Glutamate. Additionally, increased expression levels of TLR2, TLR5, Myd88, and NLRP3 proteins were noted, and their expression patterns showed a strong correlation, suggesting a possible involvement of the TLR2/5-MyD88-NLRP3 signaling pathway.

CONCLUSIONS: Chronic CPM exposure induces intestinal barrier dysfunction, microbial dysbiosis, metabolic imbalance, and activation of the TLR2/5-MyD88-NLRP3 inflammasome. These findings highlight the urgent need for intervention strategies to mitigate the detrimental effects of air pollution on intestinal health and identify potential therapeutic targets.}, } @article {pmid38906444, year = {2024}, author = {Asif, A and Koner, S and Chen, JS and Hussain, A and Huang, SW and Hussain, B and Hsu, BM}, title = {Uncovering the microbial community structure and physiological profiles of terrestrial mud volcanoes: A comprehensive metagenomic insight towards their trichloroethylene biodegradation potentiality.}, journal = {Environmental research}, volume = {258}, number = {}, pages = {119457}, doi = {10.1016/j.envres.2024.119457}, pmid = {38906444}, issn = {1096-0953}, mesh = {*Trichloroethylene/metabolism ; *Biodegradation, Environmental ; *Microbiota ; Volcanic Eruptions ; Bacteria/genetics/metabolism/classification ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Mud volcanoes are dynamic geological features releasing methane (CH4), carbon dioxide (CO2), and hydrocarbons, harboring diverse methane and hydrocarbon-degrading microbes. However, the potential application of these microbial communities in chlorinated hydrocarbons bioremediation purposes such as trichloroethylene (TCE) has not yet been explored. Hence, this study investigated the mud volcano's microbial diversity functional potentiality in TCE degradation as well as their eco-physiological profiling using metabolic activity. Geochemical analysis of the mud volcano samples revealed variations in pH, temperature, and oxidation-reduction potential, indicating diverse environmental conditions. The Biolog Ecoplate™ carbon substrates utilization pattern showed that the Tween 80 was highly consumed by mud volcanic microbial community. Similarly, MicroResp® analysis results demonstrated that presence of additive C-substrates condition might enhanced the cellular respiration process within mud-volcanic microbial community. Full-length 16 S rRNA sequencing identified Proteobacteria as the dominant phylum, with genera like Pseudomonas and Hydrogenophaga associated with chloroalkane degradation, and methanotrophic bacteria such as Methylomicrobium and Methylophaga linked to methane oxidation. Functional analysis uncovered diverse metabolic functions, including sulfur and methane metabolism and hydrocarbon degradation, with specific genes involved in methane oxidation and sulfur metabolism. These findings provide insights into the microbial diversity and metabolic capabilities of mud volcano ecosystems, which could facilitate their effective application in the bioremediation of chlorinated compounds.}, } @article {pmid38906102, year = {2024}, author = {Derosa, L and Iebba, V and Silva, CAC and Piccinno, G and Wu, G and Lordello, L and Routy, B and Zhao, N and Thelemaque, C and Birebent, R and Marmorino, F and Fidelle, M and Messaoudene, M and Thomas, AM and Zalcman, G and Friard, S and Mazieres, J and Audigier-Valette, C and Sibilot, DM and Goldwasser, F and Scherpereel, A and Pegliasco, H and Ghiringhelli, F and Bouchard, N and Sow, C and Darik, I and Zoppi, S and Ly, P and Reni, A and Daillère, R and Deutsch, E and Lee, KA and Bolte, LA and Björk, JR and Weersma, RK and Barlesi, F and Padilha, L and Finzel, A and Isaksen, ML and Escudier, B and Albiges, L and Planchard, D and André, F and Cremolini, C and Martinez, S and Besse, B and Zhao, L and Segata, N and Wojcik, J and Kroemer, G and Zitvogel, L}, title = {Custom scoring based on ecological topology of gut microbiota associated with cancer immunotherapy outcome.}, journal = {Cell}, volume = {187}, number = {13}, pages = {3373-3389.e16}, doi = {10.1016/j.cell.2024.05.029}, pmid = {38906102}, issn = {1097-4172}, mesh = {Female ; Humans ; Male ; Akkermansia ; *Carcinoma, Non-Small-Cell Lung/microbiology/drug therapy/immunology ; Dysbiosis/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Immunotherapy/methods ; *Lung Neoplasms/microbiology/drug therapy ; Metagenomics/methods ; *Neoplasms/microbiology ; Treatment Outcome ; }, abstract = {The gut microbiota influences the clinical responses of cancer patients to immunecheckpoint inhibitors (ICIs). However, there is no consensus definition of detrimental dysbiosis. Based on metagenomics (MG) sequencing of 245 non-small cell lung cancer (NSCLC) patient feces, we constructed species-level co-abundance networks that were clustered into species-interacting groups (SIGs) correlating with overall survival. Thirty-seven and forty-five MG species (MGSs) were associated with resistance (SIG1) and response (SIG2) to ICIs, respectively. When combined with the quantification of Akkermansia species, this procedure allowed a person-based calculation of a topological score (TOPOSCORE) that was validated in an additional 254 NSCLC patients and in 216 genitourinary cancer patients. Finally, this TOPOSCORE was translated into a 21-bacterial probe set-based qPCR scoring that was validated in a prospective cohort of NSCLC patients as well as in colorectal and melanoma patients. This approach could represent a dynamic diagnosis tool for intestinal dysbiosis to guide personalized microbiota-centered interventions.}, } @article {pmid38904365, year = {2024}, author = {Dandachi, I and Alrezaihi, A and Amin, D and AlRagi, N and Alhatlani, B and Binjomah, A and Aleisa, K and Dong, X and Hiscox, JA and Aljabr, W}, title = {Molecular surveillance of influenza A virus in Saudi Arabia: whole-genome sequencing and metagenomic approaches.}, journal = {Microbiology spectrum}, volume = {12}, number = {8}, pages = {e0066524}, pmid = {38904365}, issn = {2165-0497}, support = {019-034//King Fahad Medical City (KFMC)/ ; }, mesh = {Humans ; Saudi Arabia/epidemiology ; *Influenza, Human/virology/epidemiology/microbiology ; *Phylogeny ; Male ; *Nasopharynx/virology/microbiology ; *Whole Genome Sequencing ; Female ; Adult ; *Metagenomics ; Middle Aged ; *Influenza A virus/genetics/classification/isolation & purification ; *Genome, Viral/genetics ; Adolescent ; Aged ; Young Adult ; Child ; Child, Preschool ; Molecular Epidemiology ; Infant ; Microbiota/genetics ; Antiviral Agents/pharmacology/therapeutic use ; }, abstract = {Outbreaks of influenza A viruses are generally seasonal and cause annual epidemics worldwide. Due to their frequent reassortment and evolution, annual surveillance is of paramount importance to guide vaccine strategies. The aim of this study was to explore the molecular epidemiology of influenza A virus and nasopharyngeal microbiota composition in infected patients in Saudi Arabia. A total of 103 nasopharyngeal samples from 2015 and 12 samples from 2022 were collected from patients positive for influenza A. Sequencing of influenza A as well as metatranscriptomic analysis of the nasopharyngeal microbiota was conducted using Oxford Nanopore sequencing. Phylogenetic analysis of hemagglutinin, neuraminidase segments, and concatenated influenza A genomes was performed using MEGA7. Whole-genome sequencing analysis revealed changing clades of influenza A virus: from 6B.1 in 2015 to 5a.2a in 2022. One sample containing the antiviral resistance-mediating mutation S247N toward oseltamivir and zanamivir was found. Phylogenetic analysis showed the clustering of influenza A strains with the corresponding vaccine strains in each period, thus suggesting vaccine effectiveness. Principal component analysis and alpha diversity revealed the absence of a relationship between hospital admission status, age, or gender of infected patients and the nasopharyngeal microbial composition, except for the infecting clade 5a.2a. The opportunistic pathogens Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis were the most common species detected. The molecular epidemiology appears to be changing in Saudi Arabia after the COVID-19 pandemic. Antiviral resistance should be carefully monitored in future studies. In addition, the disease severity of patients as well as the composition of the nasopharyngeal microbiota in patients infected with different clades should also be assessed.IMPORTANCEIn this work, we have found that the clade of influenza A virus circulating in Riyadh, KSA, has changed over the last few years from 6B.1 to 5a.2a. Influenza strains clustered with the corresponding vaccine strains in our population, thus emphasizing vaccine effectiveness. Metatranscriptomic analysis showed no correlation between the nasopharyngeal microbiome and the clinical and/or demographic characteristics of infected patients. This is except for the 5a.2a strains isolated post-COVID-19 pandemic. The influenza virus is among the continuously evolving viruses that can cause severe respiratory infections. Continuous surveillance of its molecular diversity and the monitoring of anti-viral-resistant strains are thus of vital importance. Furthermore, exploring potential microbial markers and/or dysbiosis of the nasopharyngeal microbiota during infection could assist in the better management of patients in severe cases.}, } @article {pmid38902796, year = {2024}, author = {Chaudhari, NM and Pérez-Carrascal, OM and Overholt, WA and Totsche, KU and Küsel, K}, title = {Genome streamlining in Parcubacteria transitioning from soil to groundwater.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {41}, pmid = {38902796}, issn = {2524-6372}, abstract = {BACKGROUND: To better understand the influence of habitat on the genetic content of bacteria, with a focus on members of Candidate Phyla Radiation (CPR) bacteria, we studied the effects of transitioning from soil via seepage waters to groundwater on genomic composition of ultra-small Parcubacteria, the dominating CPR class in seepage waters, using genome resolved metagenomics.

RESULTS: Bacterial metagenome-assembled genomes (MAGs), (318 total, 32 of Parcubacteria) were generated from seepage waters and compared directly to groundwater counterparts. The estimated average genome sizes of members of major phyla Proteobacteria, Bacteroidota and Cand. Patescibacteria (Candidate Phyla Radiation - CPR bacteria) were significantly higher in soil-seepage water as compared to their groundwater counterparts. Seepage water Parcubacteria (Paceibacteria) exhibited 1.18-fold greater mean genome size and 2-fold lower mean proportion of pseudogenes than those in groundwater. Bacteroidota and Proteobacteria also showed a similar trend of reduced genomes in groundwater compared to seepage. While exploring gene loss and adaptive gains in closely related CPR lineages in groundwater, we identified a membrane protein, and a lipoglycopeptide resistance gene unique to a seepage Parcubacterium genome. A nitrite reductase gene was also identified and was unique to the groundwater Parcubacteria genomes, likely acquired from other planktonic microbes via horizontal gene transfer.

CONCLUSIONS: Overall, our data suggest that bacteria in seepage waters, including ultra-small Parcubacteria, have significantly larger genomes and higher metabolic enrichment than their groundwater counterparts, highlighting possible genome streamlining of the latter in response to habitat selection in an oligotrophic environment.}, } @article {pmid38902374, year = {2024}, author = {Graham, EB and Camargo, AP and Wu, R and Neches, RY and Nolan, M and Paez-Espino, D and Kyrpides, NC and Jansson, JK and McDermott, JE and Hofmockel, KS and , }, title = {A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts.}, journal = {Nature microbiology}, volume = {9}, number = {7}, pages = {1873-1883}, pmid = {38902374}, issn = {2058-5276}, mesh = {*Soil Microbiology ; *Viruses/genetics/classification/isolation & purification ; *Biodiversity ; *Metagenome ; *Soil/chemistry ; *Genome, Viral/genetics ; *Microbiota/genetics ; Carbon/metabolism ; Metagenomics ; Phylogeny ; Virome/genetics ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.}, } @article {pmid38902263, year = {2024}, author = {Na, HH and Kim, S and Kim, JS and Lee, S and Kim, Y and Kim, SH and Lee, CH and Kim, D and Yoon, SH and Jeong, H and Kweon, D and Seo, HW and Ryu, CM}, title = {Facemask acne attenuation through modulation of indirect microbiome interactions.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {50}, pmid = {38902263}, issn = {2055-5008}, support = {KRIBB initiative program//Korea Research Institute of Bioscience and Biotechnology (KRIBB)/ ; 2021087000//National Research Council of Science and Technology (National Research Council of Science & Technology)/ ; RS-2023-00219213//National Research Foundation of Korea (NRF)/ ; }, mesh = {Animals ; Mice ; *Masks ; *Microbiota ; Humans ; *COVID-19/microbiology/virology ; *Skin/microbiology ; Acne Vulgaris/microbiology ; SARS-CoV-2 ; Female ; Metagenomics/methods ; Disease Models, Animal ; Bacteria/classification/genetics/isolation & purification ; Microbial Interactions ; Dermatitis, Contact/etiology ; }, abstract = {During the COVID-19 pandemic, facemasks played a pivotal role in preventing person-person droplet transmission of viral particles. However, prolonged facemask wearing causes skin irritations colloquially referred to as 'maskne' (mask + acne), which manifests as acne and contact dermatitis and is mostly caused by pathogenic skin microbes. Previous studies revealed that the putative causal microbes were anaerobic bacteria, but the pathogenesis of facemask-associated skin conditions remains poorly defined. We therefore characterized the role of the facemask-associated skin microbiota in the development of maskne using culture-dependent and -independent methodologies. Metagenomic analysis revealed that the majority of the facemask microbiota were anaerobic bacteria that originated from the skin rather than saliva. Previous work demonstrated direct interaction between pathogenic bacteria and antagonistic strains in the microbiome. We expanded this analysis to include indirect interaction between pathogenic bacteria and other indigenous bacteria classified as either 'pathogen helper (PH)' or 'pathogen inhibitor (PIn)' strains. In vitro screening of bacteria isolated from facemasks identified both strains that antagonized and promoted pathogen growth. These data were validated using a mouse skin infection model, where we observed attenuation of symptoms following pathogen infection. Moreover, the inhibitor of pathogen helper (IPH) strain, which did not directly attenuate pathogen growth in vitro and in vivo, functioned to suppress symptom development and pathogen growth indirectly through PH inhibitory antibacterial products such as phenyl lactic acid. Taken together, our study is the first to define a mechanism by which indirect microbiota interactions under facemasks can control symptoms of maskne by suppressing a skin pathogen.}, } @article {pmid38901747, year = {2024}, author = {Li, YQ and Zhang, CM and Wang, Q and Jiao, XR}, title = {Metagenomic insights into effects of carbon/nitrogen ratio on microbial community and antibiotic resistance in moving bed biofilm reactor.}, journal = {Bioresource technology}, volume = {406}, number = {}, pages = {131007}, doi = {10.1016/j.biortech.2024.131007}, pmid = {38901747}, issn = {1873-2976}, mesh = {*Biofilms/drug effects ; *Carbon/pharmacology ; *Nitrogen ; *Bioreactors/microbiology ; *Metagenomics/methods ; Drug Resistance, Microbial/genetics ; Microbiota/drug effects ; Bacteria/drug effects/genetics ; }, abstract = {This study investigated the effects of carbon/nitrogen (C/N) ratio on microbial community in moving bed biofilm reactor (MBBR) using metagenomic analysis, and the dynamic changes of relevant antibiotic resistance genes (ARGs) were also analyzed. The results showed that under low C/N ratio, MBBR exhibited average removal rates of 98.41 % for ammonia nitrogen and 75.79 % for total nitrogen. Metagenomic analysis showed low C/N ratio altered the structure of biofilm and water microbiota, resulting in the detachment of bacteria such as Actinobacteria from biofilm into water. Furthermore, sulfamethazine (SMZ)-resistant bacteria and related ARGs were released into water under low C/N ratio, which lead to the increase of SMZ resistance rate to 90%. Moreover, most dominant genera are potential hosts for both nitrogen cycle related genes and ARGs. Specifically, Nitrosomonas that carried gene sul2 might be released from biofilm into water. These findings implied the risks of antibiotic resistance dissemination in MBBR under low C/N ratio.}, } @article {pmid38901353, year = {2024}, author = {Wei, G and Zhang, Z and Zhao, F and Sang, Y and Regenstein, JM and Zhou, P}, title = {Characteristic aroma compounds during the fermentation of Chinese steamed bread fermented with different starters.}, journal = {Food chemistry}, volume = {457}, number = {}, pages = {140151}, doi = {10.1016/j.foodchem.2024.140151}, pmid = {38901353}, issn = {1873-7072}, mesh = {Bacteria/metabolism/genetics/classification/isolation & purification ; *Bread/analysis/microbiology ; *Fermentation ; Flavoring Agents/metabolism/chemistry ; Gas Chromatography-Mass Spectrometry ; Microbiota ; *Odorants/analysis ; *Saccharomyces cerevisiae/metabolism ; *Volatile Organic Compounds/metabolism/chemistry/analysis ; }, abstract = {The characteristic aroma compounds of Chinese steamed bread (CSB) fermented with different starters were studied using HS-SPME-GC/MS, aroma recombination and omission experiments. The dynamic changes of the microbiota and their function and metabolites during fermentation were analyzed using metagenomics and non-targeted metabolomics. Forty-nine volatile flavor compounds were identified, while 5 characteristic aroma-active compounds were investigated in CSB fermented with commercial dry yeast (AQ-CSB), and 10 were investigated in CSB fermented with traditional starter (NY-CSB). Microbial structure and function analysis showed that Saccharomyces cerevisiae dominated during AQ-CSB fermentation and contributed >95% to its KEGG pathways, while Pediococcus pentosaceus, unclassified Pediococcus, Lactobacillus plantarum, Lactobacillus brevis and unclassified Lactobacillus were predominant in NY-CSB and together had an ~96% contribution to these pathways. NY-CSB showed higher metabolic activity during fermentation, and the characteristic metabolites were mainly involved in carbohydrate, amino acid and lipid metabolism. The characteristic aroma compounds were identified and increased the understanding of the contributions of the microbiota. This may be useful for designing starter cultures that produce CSB with desirable aroma properties.}, } @article {pmid38900914, year = {2024}, author = {Heinz, JM and Lu, J and Huebner, LK and Salzberg, SL and Sommer, M and Rosales, SM}, title = {Novel metagenomics analysis of stony coral tissue loss disease.}, journal = {G3 (Bethesda, Md.)}, volume = {14}, number = {8}, pages = {}, pmid = {38900914}, issn = {2160-1836}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; R35-GM130151/GF/NIH HHS/United States ; }, mesh = {*Anthozoa/microbiology ; Animals ; *Metagenomics/methods ; Metagenome ; Computational Biology/methods ; Microbiota/genetics ; Coral Reefs ; }, abstract = {Stony coral tissue loss disease (SCTLD) has devastated coral reefs off the coast of Florida and continues to spread throughout the Caribbean. Although a number of bacterial taxa have consistently been associated with SCTLD, no pathogen has been definitively implicated in the etiology of SCTLD. Previous studies have predominantly focused on the prokaryotic community through 16S rRNA sequencing of healthy and affected tissues. Here, we provide a different analytical approach by applying a bioinformatics pipeline to publicly available metagenomic sequencing samples of SCTLD lesions and healthy tissues from 4 stony coral species. To compensate for the lack of coral reference genomes, we used data from apparently healthy coral samples to approximate a host genome and healthy microbiome reference. These reads were then used as a reference to which we matched and removed reads from diseased lesion tissue samples, and the remaining reads associated only with disease lesions were taxonomically classified at the DNA and protein levels. For DNA classifications, we used a pathogen identification protocol originally designed to identify pathogens in human tissue samples, and for protein classifications, we used a fast protein sequence aligner. To assess the utility of our pipeline, a species-level analysis of a candidate genus, Vibrio, was used to demonstrate the pipeline's effectiveness. Our approach revealed both complementary and unique coral microbiome members compared with a prior metagenome analysis of the same dataset.}, } @article {pmid38900289, year = {2024}, author = {Seethalakshmi, PS and Kumaresan, TN and Vishnu Prasad Nair, RU and Prathiviraj, R and Seghal Kiran, G and Selvin, J}, title = {Comparative analysis of commercially available kits for optimal DNA extraction from bovine fecal samples.}, journal = {Archives of microbiology}, volume = {206}, number = {7}, pages = {314}, pmid = {38900289}, issn = {1432-072X}, support = {BT/IN/Indo-UK/AMR-Env/02/JS/2020-21//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {Animals ; Cattle ; *Feces/microbiology ; *RNA, Ribosomal, 16S/genetics ; *DNA, Bacterial/genetics/isolation & purification ; Bacteria/genetics/isolation & purification/classification ; Metagenomics ; Sequence Analysis, DNA ; Reagent Kits, Diagnostic/standards ; Microbiota/genetics ; }, abstract = {In the field of metagenomic research, the choice of DNA extraction methods plays a pivotal yet often underestimated role in shaping the reliability and interpretability of microbial community data. This study delves into the impact of five commercially available DNA extraction kits on the analysis of bovine fecal microbiota. Recognizing the importance of accurate DNA extraction in elucidating microbial community dynamics, we systematically assessed DNA yield, quality, and microbial composition across these kits using 16S rRNA gene sequencing. Notably, the FastDNA spin soil kit yielded the highest DNA concentration, while significant variations in quality were observed across kits. Furthermore, differential abundance analysis revealed kit-specific biases that impacted taxa representation. Microbial richness and diversity were significantly influenced by the choice of extraction kit, with QIAamp DNA stool minikit, QIAamp Power Pro, and DNeasy PowerSoil outperforming the Stool DNA Kit. Principal-coordinate analysis revealed distinct clustering based on DNA isolation procedures, particularly highlighting the unique microbial community composition derived from the Stool DNA Kit. This study also addressed practical implications, demonstrating how kit selection influences the concentration of Gram-positive and Gram-negative bacterial taxa in samples. This research highlights the need for consideration of DNA extraction kits in metagenomic studies, offering valuable insights for researchers striving to advance the precision and depth of microbiota analyses in ruminants.}, } @article {pmid38899956, year = {2024}, author = {Zhan, H and Wan, Y and Sun, Y and Xu, Z and Zhang, F and Yang, K and Zhu, W and Cheung, CP and Tang, W and Ng, EK and Wong, SK and Yeoh, YK and Kl Chan, F and Miao, Y and Zuo, T and Zeng, Z and Ng, SC}, title = {Gut mycobiome alterations in obesity in geographically different regions.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2367297}, pmid = {38899956}, issn = {1949-0984}, mesh = {*Obesity/microbiology ; Humans ; Animals ; *Gastrointestinal Microbiome ; *Fungi/classification/isolation & purification/genetics ; Male ; Mice ; China ; Female ; *Mycobiome ; *Feces/microbiology ; Adult ; Bacteria/classification/isolation & purification/genetics ; Middle Aged ; Mice, Inbred C57BL ; Body Mass Index ; }, abstract = {The gut fungi play important roles in human health and are involved in energy metabolism. This study aimed to examine gut mycobiome composition in obese subjects in two geographically different regions in China and to identify specific gut fungi associated with obesity. A total of 217 subjects from two regions with different urbanization levels [Hong Kong (HK): obese, n = 59; lean, n = 59; Kunming (KM): obese, n = 50; lean, n = 49. Mean body mass index (BMI) for obesity = 33.7] were recruited. We performed deep shotgun metagenomic sequencing on fecal samples to compare gut mycobiome composition and trophic functions in lean and obese subjects across these two regions. The gut mycobiome of obese subjects in both HK and KM were altered compared to those of lean subjects, characterized by a decrease in the relative abundance of Nakaseomyces, Schizosaccharomyces pombe, Candida dubliniensis and an increase in the abundance of Lanchanceathermotolerans, Saccharomyces paradox, Parastagonospora nodorum and Myceliophthorathermophila. Reduced fungal - bacterial and fungal - fungal correlations as well as increased negative fungal-bacterial correlations were observed in the gut of obese subjects. Furthermore, the anti-obesity effect of fungus S. pombe was further validated using a mouse model. Supplementing high-fat diet-induced obese mice with the fungus for 12 weeks led to a significant reduction in body weight gain (p < 0.001), and an improvement in lipid and glucose metabolism compared to mice without intervention. In conclusion, the gut mycobiome composition and functionalities of obese subjects were altered. These data shed light on the potential of utilizing fungus-based therapeutics for the treatment of obesity. S. pombe may serve as a potential fungal probiotic in the prevention of diet-induced obesity and future human trials are needed.}, } @article {pmid38899609, year = {2024}, author = {Behera, PR and Behera, KK and Sethi, G and Prabina, BJ and Bai, AT and Sipra, BS and Adarsh, V and Das, S and Behera, KC and Singh, L and Mishra, MK and Behera, M}, title = {Enhancing Agricultural Sustainability Through Rhizomicrobiome: A Review.}, journal = {Journal of basic microbiology}, volume = {64}, number = {11}, pages = {e2400100}, doi = {10.1002/jobm.202400100}, pmid = {38899609}, issn = {1521-4028}, mesh = {*Rhizosphere ; *Agriculture/methods ; *Soil Microbiology ; *Microbiota ; *Plant Development ; Symbiosis ; Sustainable Development ; Plant Roots/microbiology ; Bacteria/genetics/metabolism/classification/growth & development ; Crops, Agricultural/microbiology/growth & development ; Metagenomics ; Plants/microbiology ; }, abstract = {Sustainable agriculture represents the responsible utilization of natural resources while safeguarding the well-being of the natural environment. It encompasses the objectives of preserving the environment, fostering economic growth, and promoting socioeconomic equality. To achieve sustainable development for humanity, it is imperative to prioritize sustainable agriculture. One significant approach to achieving this transition is the extensive utilization of microbes, which play a crucial role due to the genetic reliance of plants on the beneficial functions provided by symbiotic microbes. This review focuses on the significance of rhizospheric microbial communities, also known as the rhizomicrobiome (RM). It is a complex community of microorganisms that live in the rhizosphere and influence the plant's growth and health. It provides its host plant with various benefits related to plant growth, including biocontrol, biofertilization, phytostimulation, rhizoremediation, stress resistance, and other advantageous properties. Yet, the mechanisms by which the RM contributes to sustainable agriculture remain largely unknown. Investigating this microbial population presents a significant opportunity to advance toward sustainable agriculture. Hence, this study aims to provide an overview of the diversity and applications of RM in sustainable agriculture practices. Lately, there has been growing momentum in various areas related to rhizobiome research and its application in agriculture. This includes rhizosphere engineering, synthetic microbiome application, agent-based modeling of the rhizobiome, and metagenomic studies. So, developing bioformulations of these beneficial microorganisms that support plant growth could serve as a promising solution for future strategies aimed at achieving a new green revolution.}, } @article {pmid38898980, year = {2024}, author = {Zhang, J and Tang, A and Jin, T and Sun, D and Guo, F and Lei, H and Lin, L and Shu, W and Yu, P and Li, X and Li, B}, title = {A panoramic view of the virosphere in three wastewater treatment plants by integrating viral-like particle-concentrated and traditional non-concentrated metagenomic approaches.}, journal = {iMeta}, volume = {3}, number = {3}, pages = {e188}, pmid = {38898980}, issn = {2770-596X}, abstract = {Wastewater biotreatment systems harbor a rich diversity of microorganisms, and the effectiveness of biotreatment systems largely depends on the activity of these microorganisms. Specifically, viruses play a crucial role in altering microbial behavior and metabolic processes throughout their infection phases, an aspect that has recently attracted considerable interest. Two metagenomic approaches, viral-like particle-concentrated (VPC, representing free viral-like particles) and non-concentrated (NC, representing the cellular fraction), were employed to assess their efficacy in revealing virome characteristics, including taxonomy, diversity, host interactions, lifestyle, dynamics, and functional genes across processing units of three wastewater treatment plants (WWTPs). Our findings indicate that each approach offers unique insights into the viral community and functional composition. Their combined use proved effective in elucidating WWTP viromes. We identified nearly 50,000 viral contigs, with Cressdnaviricota and Uroviricota being the predominant phyla in the VPC and NC fractions, respectively. Notably, two pathogenic viral families, Asfarviridae and Adenoviridae, were commonly found in these WWTPs. We also observed significant differences in the viromes of WWTPs processing different types of wastewater. Additionally, various phage-derived auxiliary metabolic genes (AMGs) were active at the RNA level, contributing to the metabolism of the microbial community, particularly in carbon, sulfur, and phosphorus cycling. Moreover, we identified 29 virus-carried antibiotic resistance genes (ARGs) with potential for host transfer, highlighting the role of viruses in spreading ARGs in the environment. Overall, this study provides a detailed and integrated view of the virosphere in three WWTPs through the application of VPC and NC metagenomic approaches. Our findings enhance the understanding of viral communities, offering valuable insights for optimizing the operation and regulation of wastewater treatment systems.}, } @article {pmid38898276, year = {2024}, author = {Nasseri, SA and Lazarski, AC and Lemmer, IL and Zhang, CY and Brencher, E and Chen, HM and Sim, L and Panwar, D and Betschart, L and Worrall, LJ and Brumer, H and Strynadka, NCJ and Withers, SG}, title = {An alternative broad-specificity pathway for glycan breakdown in bacteria.}, journal = {Nature}, volume = {631}, number = {8019}, pages = {199-206}, pmid = {38898276}, issn = {1476-4687}, mesh = {Humans ; Acarbose/chemistry/metabolism ; *Bacteria/enzymology/genetics/isolation & purification/metabolism ; Biocatalysis ; *Gastrointestinal Microbiome ; Glucosinolates/metabolism/chemistry ; *Glycoside Hydrolases/metabolism/chemistry ; Hydrolysis ; Metagenome ; Oxidation-Reduction ; Plants/chemistry ; *Polysaccharides/metabolism/chemistry ; Seawater/microbiology ; Soil Microbiology ; Substrate Specificity ; Male ; }, abstract = {The vast majority of glycosidases characterized to date follow one of the variations of the 'Koshland' mechanisms[1] to hydrolyse glycosidic bonds through substitution reactions. Here we describe a large-scale screen of a human gut microbiome metagenomic library using an assay that selectively identifies non-Koshland glycosidase activities[2]. Using this, we identify a cluster of enzymes with extremely broad substrate specificities and thoroughly characterize these, mechanistically and structurally. These enzymes not only break glycosidic linkages of both α and β stereochemistry and multiple connectivities, but also cleave substrates that are not hydrolysed by standard glycosidases. These include thioglycosides, such as the glucosinolates from plants, and pseudoglycosidic bonds of pharmaceuticals such as acarbose. This is achieved through a distinct mechanism of hydrolysis that involves oxidation/reduction and elimination/hydration steps, each catalysed by enzyme modules that are in many cases interchangeable between organisms and substrate classes. Homologues of these enzymes occur in both Gram-positive and Gram-negative bacteria associated with the gut microbiome and other body parts, as well as other environments, such as soil and sea. Such alternative step-wise mechanisms appear to constitute largely unrecognized but abundant pathways for glycan degradation as part of the metabolism of carbohydrates in bacteria.}, } @article {pmid38898104, year = {2024}, author = {Ji, M and Li, Y and Zhou, J and Song, W and Zhou, Y and Ma, K and Wang, M and Liu, X and Li, Y and Gong, X and Tu, Q}, title = {Temporal turnover of viral biodiversity and functional potential in intertidal wetlands.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {48}, pmid = {38898104}, issn = {2055-5008}, support = {32371598//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92051110//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Wetlands ; *Biodiversity ; *Viruses/genetics/classification/isolation & purification ; *Metagenome ; Seasons ; Microbiota ; Genome, Viral ; Metagenomics/methods ; Virome/genetics ; Phylogeny ; }, abstract = {As the central members of the microbiome networks, viruses regulate the composition of microbial communities and drive the nutrient cycles of ecosystems by lysing host cells. Therefore, uncovering the dynamic patterns and the underlying ecological mechanisms mediating the tiniest viral communities across space and through time in natural ecosystems is of crucial importance for better understanding the complex microbial world. Here, the temporal dynamics of intertidal viral communities were investigated via a time-series sampling effort. A total of 1911 viral operational taxonomic units were recovered from 36 bimonthly collected shotgun metagenomes. Functionally important auxiliary metabolic genes involved in carbohydrate, sulfur, and phosphorus metabolism were detected, some of which (e.g., cysH gene) were stably present within viral genomes over time. Over the sampling period, strong and comparable temporal turnovers were observed for intertidal viromes and their host microbes. Winter was determined as the pivotal point for the shifts in viral diversity patterns. Notably, the viral micro-diversity covaried with the macro-diversity, following similar temporal patterns. The relative abundances of viral taxa also covaried with their host prokaryotes. Meanwhile, the virus-host relationships at the whole community level were relatively stable. Further statistical analyses demonstrated that the dynamic patterns of viral communities were highly deterministic, for which temperature was the major driver. This study provided valuable mechanistic insights into the temporal turnover of viral communities in complex ecosystems such as intertidal wetlands.}, } @article {pmid38898025, year = {2024}, author = {Bogdanov, A and Salib, MN and Chase, AB and Hammerlindl, H and Muskat, MN and Luedtke, S and da Silva, EB and O'Donoghue, AJ and Wu, LF and Altschuler, SJ and Molinski, TF and Jensen, PR}, title = {Small molecule in situ resin capture provides a compound first approach to natural product discovery.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5230}, pmid = {38898025}, issn = {2041-1723}, support = {R21AT010493//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01 AI158612/AI/NIAID NIH HHS/United States ; R01AI158612//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R21AI171824//DH | NIHR | Efficacy and Mechanism Evaluation Programme (NIHR Efficacy and Mechanism Evaluation Programme)/ ; R01 GM085770/GM/NIGMS NIH HHS/United States ; R01CA184984//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; R01 CA184984/CA/NCI NIH HHS/United States ; R21 AT010493/AT/NCCIH NIH HHS/United States ; R21 AI171824/AI/NIAID NIH HHS/United States ; }, mesh = {*Biological Products/chemistry/metabolism ; *Drug Discovery/methods ; Metabolomics/methods ; Microbiota ; Metagenomics/methods ; Magnetic Resonance Spectroscopy ; Small Molecule Libraries/chemistry ; }, abstract = {Culture-based microbial natural product discovery strategies fail to realize the extraordinary biosynthetic potential detected across earth's microbiomes. Here we introduce Small Molecule In situ Resin Capture (SMIRC), a culture-independent method to obtain natural products directly from the environments in which they are produced. We use SMIRC to capture numerous compounds including two new carbon skeletons that were characterized using NMR and contain structural features that are, to the best of our knowledge, unprecedented among natural products. Applications across diverse marine habitats reveal biome-specific metabolomic signatures and levels of chemical diversity in concordance with sequence-based predictions. Expanded deployments, in situ cultivation, and metagenomics facilitate compound discovery, enhance yields, and link compounds to candidate producing organisms, although microbial community complexity creates challenges for the later. This compound-first approach to natural product discovery provides access to poorly explored chemical space and has implications for drug discovery and the detection of chemically mediated biotic interactions.}, } @article {pmid38897777, year = {2024}, author = {Guo, XW and Xiang, GQ and Zhang, FC and Jiang, S and Min, W}, title = {[Effects of Biochar and Straw Return on Soil Microbial Community Characteristics and Functional Differences in Saline Water Drip Irrigation Cotton Fields].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {45}, number = {6}, pages = {3571-3583}, doi = {10.13227/j.hjkx.202308051}, pmid = {38897777}, issn = {0250-3301}, mesh = {*Charcoal ; *Soil Microbiology ; *Agricultural Irrigation/methods ; *Soil/chemistry ; *Gossypium/growth & development ; *Plant Stems/chemistry ; Saline Waters ; Microbiota ; Bacteria/classification/growth & development ; }, abstract = {In arid areas, fresh water resources are insufficient, and agricultural water mainly depends on shallow saline groundwater. However, long-term saline irrigation will cause soil salt accumulation and soil environment deterioration, which is not conducive to crop growth. In this study, based on the long-term irrigation of fresh water (0.35 dS·m[-1], FW) and saline water (8.04 dS·m[-1], SW), biochar (3.7 t·hm[-2], BC) and straw (6 t·hm[-2], ST) were added to the soil by an equal-carbon design. The aim was to clarify the effects of biochar and straw returning on the physical and chemical properties and microbial community structure of salinized soil. The results showed that saline irrigation significantly increased soil water content, electrical conductivity, available phosphorus, and total carbon content but significantly decreased pH value and available potassium content. The contents of available phosphorus, available potassium, and total carbon in soil were significantly increased by biochar and straw returning, but the conductivity value of soil irrigated with saline water was significantly decreased. The dominant bacteria in each treatment were Proteobacteria, Actinomycetes, Acidobacteria, Chloromycetes, and Blastomonas. Saline water irrigation significantly increased the relative abundance of Blastomonas and Proteobacteria but significantly decreased the relative abundance of Acidobacteria and Actinobacteria. Under the condition of fresh water irrigation, the relative abundance of Chlorocurvula was significantly reduced by the return of biochar. Straw returning significantly increased the relative abundance of Proteobacteria but significantly decreased the relative abundance of Acidobacteria, Actinomyces, Chloromyces, and Blastomonas. Under saline irrigation, the relative abundance of Chlorocurvula and Blastomonas were significantly reduced by biochar return to field. Straw returning significantly increased the relative abundance of Proteobacteria but significantly decreased the relative abundance of Acidobacteria, Actinomyces, Chloromyces, and Blastomonas. LEfSe analysis showed that saline irrigation decreased the potential markers and functional numbers of soil microorganisms.Under saline irrigation, biochar returning increased the number of potential markers and functions of soil microorganisms. Straw returning to field increases the number of potential markers of soil microorganisms. RDA results showed that soil microbial community and functional structure were significantly correlated with EC1:5, SWC, and pH. Saline water irrigation will deteriorate the soil environment, which is not conducive to agricultural production, among which EC1:5, SWC, and pH are important factors driving changes in soil microbial community and functional structure. Using biochar and straw to return to the field can reduce the harm of salt to soil and crops, laying a foundation for improving agricultural productivity.}, } @article {pmid38897586, year = {2024}, author = {Kortman, GAM and Hester, ER and Schaafsma, A and Mulder, J and Mallee, L and Nauta, A}, title = {Gut microbiome composition and functionality impact the responsiveness to a dairy-based product containing galacto-oligosaccharides for improving sleep quality in adults.}, journal = {Beneficial microbes}, volume = {15}, number = {4}, pages = {373-385}, doi = {10.1163/18762891-bja00017}, pmid = {38897586}, issn = {1876-2891}, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Oligosaccharides/pharmacology/administration & dosage ; Adult ; *Feces/microbiology ; Female ; Male ; *Dairy Products/microbiology ; *Sleep Quality ; Middle Aged ; Bacteria/classification/genetics/drug effects/isolation & purification ; Metagenomics ; Young Adult ; Whey Proteins/pharmacology ; Brain-Gut Axis/drug effects ; }, abstract = {Sleep quality and duration can be impacted by diet, and has been linked to gut microbiota composition and function as the result of communication via the microbiota-gut-brain axis. As one strategy to improve sleep quality could be through the modulation of the gut microbiome, we assessed the effects of a dairy-based product containing whey protein, galacto-oligosaccharides, tryptophan, vitamins and minerals after a 3 weeks intervention on gut microbiota composition and (gut-brain related) functions on basis of 67 healthy subjects with moderate sleep disturbances. Associations of the gut microbiota with sleep quality and with response/non-response to the treatment were revealed by shotgun metagenomics sequencing of faecal DNA samples, and subsequent analyses of microbiota taxonomy and generic functionality. A database of manually curated Gut-Brain Modules (GBMs) was applied to analyse specific microbial functions/pathways that have the potential to interact with the brain. A moderate discriminating effect of the DP treatment on gut microbiota composition was revealed which could be mainly attributed to a decrease in Pseudomonas resinovorans, Flintibacter sp. KGM00164, Intestinimonas butyriciproducens, and Flavonifractor plautii. As interindividual variance in microbiota composition could have given rise to a heterogenous responsiveness of the subjects in the intervention group, we zoomed in on the differences between responders and non-responders. A significant difference in baseline microbiota composition between responders and non-responders was apparent, showing lower Bifidobacterium longum and Bifidobacterium adolescentis, and higher Faecalibacterium prausnitzii relative abundances in responders. The findings provide leads with respect to the effectiveness and potential underlying mechanisms of mode of action in sleep improvement that could support future nutritional interventions to aid sleep improvement.}, } @article {pmid38896886, year = {2024}, author = {Yan, P and Zhuang, S and Li, M and Zhang, J and Wu, S and Xie, H and Wu, H}, title = {Combined environmental pressure induces unique assembly patterns of micro-plastisphere biofilm microbial communities in constructed wetlands.}, journal = {Water research}, volume = {260}, number = {}, pages = {121958}, doi = {10.1016/j.watres.2024.121958}, pmid = {38896886}, issn = {1879-2448}, mesh = {*Wetlands ; *Biofilms ; Microbiota ; Wastewater/microbiology ; Humic Substances ; Sulfamethoxazole ; Microplastics ; }, abstract = {The characteristics and dynamics of micro-plastisphere biofilm on the surface of microplastics (MPs) within artificial ecosystems, such as constructed wetlands (CWs), remain unclear, despite these ecosystems' potential to serve as sinks for MPs. This study investigates the dynamic evolution of micro-plastisphere biofilm in CWs, utilizing simulated wastewater containing sulfamethoxazole and humic acid, through physicochemical characterization and metagenomic analysis. Two different types of commercial plastics, including non-degradable polyethylene and degradable polylactic acid, were shredded into MPs and studied. The findings reveal that the types, shape and incubation time of MPs, along with humic acid content in wastewater, affected the quantity and quality of biofilms, such as the biofilm composition, spatial structure and microbial communities. After just 15 days into incubation, numerous microbials were observed on MP samples, with increases in biofilms content and enhanced humification of extracellular polymeric substances over time. Additionally, microbial communities on polylactic acid MPs, or those incubated for longer time, exhibit higher diversity, connectivity and stability, along with reduced vulnerability. Conversely, biofilms on polyethylene MPs were thicker, with higher potential for greenhouse gas emission and increased risk of antibiotic resistance genes. The addition of humic acid demonstrated opposite effects on biofilms across environmental interfaces, possibly due to its dual potential to produce light-induced free radicals and serve as a carbon source. Binning analysis further uncovered a unique assembly pattern of nutrients cycle genes and antibiotic resistance genes, significantly correlated within micro-plastisphere microbial communities, under the combined stress of nutrition and sulfamethoxazole. These results emphasize the shaping of micro-plastisphere biofilm characteristics by unique environmental conditions in artificial ecosystems, and the need to understand how DOM and other pollutants covary with MP pollution.}, } @article {pmid38892546, year = {2024}, author = {Garrison, EC and Brown, AMV and Salazar, MM and Barr, B and Moustaid-Moussa, N and Gollahon, LS}, title = {Microbiome Taxonomic and Functional Differences in C3H/HeJ Mice Fed a Long-Term High-Fat Diet with Beef Protein ± Ammonium Hydroxide Supplementation.}, journal = {Nutrients}, volume = {16}, number = {11}, pages = {}, pmid = {38892546}, issn = {2072-6643}, support = {A18-0187-001//Empirical Foods Inc./ ; }, mesh = {Animals ; *Diet, High-Fat/adverse effects ; Female ; Male ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Dietary Supplements ; *Ammonium Hydroxide ; Feces/microbiology ; Red Meat/microbiology ; Dietary Proteins/administration & dosage ; Bacteria/classification/drug effects/genetics ; Cattle ; }, abstract = {Studies have suggested that alkalinized foods may reduce the effects of the acidogenic Western diet in promoting obesity, metabolic syndrome, type 2 diabetes, cancer, and coronary heart disease. Indeed, a recent study in mice fed a high-fat diet containing dietary beef supplemented with ammonium hydroxide showed improvement in a suite of metabolic outcomes. However, the effects of dietary protein ammonium supplementation on the microbiome remain unknown. In this study, the effects of ammonium supplementation on beef protein towards microbiome taxa and function in a high-fat diet were analyzed. Fecal microbiomes were characterized using a shotgun metagenomic approach for 16-month-old male and female mice after long-term diet treatments. The results for ammoniated diets showed that several bacteria known to be associated with health benefits increased significantly, including Romboutsia, Oscillospiraceae, and Lactococcus cremoris. The beneficial mucin-degrader Akkermansia was especially abundant, with a high prevalence (~86%) in females. Concurrently, the phyla Actinomycetota (Actinobacteria) and Bacteroidota (Bacteroidetes) were significantly reduced. While sex was a confounding factor affecting microbiome responses to ammonium supplementation in dietary protein, it is worth noting that several putatively beneficial microbiome functions increased with ammonium supplementation, such as glycine betaine transport, xenobiotic detoxification, enhanced defense, and others. Conversely, many disease-associated microbiome functions reduced. Importantly, modifying protein pH alone via ammonium supplementation induced beneficial microbiota changes. Taken together, these results suggest that ammonium-supplemented proteins may mediate some negative microbiome-associated effects of high-fat/Western diets.}, } @article {pmid38892444, year = {2024}, author = {Spörri, L and Uldry, AC and Kreuzer, M and Herzog, EL and Zinkernagel, MS and Unterlauft, JD and Zysset-Burri, DC}, title = {Exploring the Ocular Surface Microbiome and Tear Proteome in Glaucoma.}, journal = {International journal of molecular sciences}, volume = {25}, number = {11}, pages = {}, pmid = {38892444}, issn = {1422-0067}, support = {CF10000044-EPFL SCR0237812//This research was funded by the Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; }, mesh = {Humans ; *Glaucoma/metabolism/microbiology ; *Proteome/metabolism ; Male ; Female ; *Microbiota ; *Tears/metabolism ; Middle Aged ; Eye Proteins/metabolism/genetics ; Aged ; Conjunctiva/metabolism/microbiology ; Metagenome ; Adult ; }, abstract = {Although glaucoma is a leading cause of irreversible blindness worldwide, its pathogenesis is incompletely understood, and intraocular pressure (IOP) is the only modifiable risk factor to target the disease. Several associations between the gut microbiome and glaucoma, including the IOP, have been suggested. There is growing evidence that interactions between microbes on the ocular surface, termed the ocular surface microbiome (OSM), and tear proteins, collectively called the tear proteome, may also play a role in ocular diseases such as glaucoma. This study aimed to find characteristic features of the OSM and tear proteins in patients with glaucoma. The whole-metagenome shotgun sequencing of 32 conjunctival swabs identified Actinobacteria, Firmicutes, and Proteobacteria as the dominant phyla in the cohort. The species Corynebacterium mastitidis was only found in healthy controls, and their conjunctival microbiomes may be enriched in genes of the phospholipase pathway compared to glaucoma patients. Despite these minor differences in the OSM, patients showed an enrichment of many tear proteins associated with the immune system compared to controls. In contrast to the OSM, this emphasizes the role of the proteome, with a potential involvement of immunological processes in glaucoma. These findings may contribute to the design of new therapeutic approaches targeting glaucoma and other associated diseases.}, } @article {pmid38891970, year = {2024}, author = {Averina, OV and Poluektova, EU and Zorkina, YA and Kovtun, AS and Danilenko, VN}, title = {Human Gut Microbiota for Diagnosis and Treatment of Depression.}, journal = {International journal of molecular sciences}, volume = {25}, number = {11}, pages = {}, pmid = {38891970}, issn = {1422-0067}, support = {20-14-00132//Russian Science Foundation/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Depression/therapy/microbiology/diagnosis ; *Probiotics/therapeutic use ; Biomarkers ; Fecal Microbiota Transplantation ; Brain-Gut Axis ; Prebiotics/administration & dosage ; }, abstract = {Nowadays, depressive disorder is spreading rapidly all over the world. Therefore, attention to the studies of the pathogenesis of the disease in order to find novel ways of early diagnosis and treatment is increasing among the scientific and medical communities. Special attention is drawn to a biomarker and therapeutic strategy through the microbiota-gut-brain axis. It is known that the symbiotic interactions between the gut microbes and the host can affect mental health. The review analyzes the mechanisms and ways of action of the gut microbiota on the pathophysiology of depression. The possibility of using knowledge about the taxonomic composition and metabolic profile of the microbiota of patients with depression to select gene compositions (metagenomic signature) as biomarkers of the disease is evaluated. The use of in silico technologies (machine learning) for the diagnosis of depression based on the biomarkers of the gut microbiota is given. Alternative approaches to the treatment of depression are being considered by balancing the microbial composition through dietary modifications and the use of additives, namely probiotics, postbiotics (including vesicles) and prebiotics as psychobiotics, and fecal transplantation. The bacterium Faecalibacterium prausnitzii is under consideration as a promising new-generation probiotic and auxiliary diagnostic biomarker of depression. The analysis conducted in this review may be useful for clinical practice and pharmacology.}, } @article {pmid38888585, year = {2024}, author = {Chalita, M and Kim, YO and Park, S and Oh, HS and Cho, JH and Moon, J and Baek, N and Moon, C and Lee, K and Yang, J and Nam, GG and Jung, Y and Na, SI and Bailey, MJ and Chun, J}, title = {EzBioCloud: a genome-driven database and platform for microbiome identification and discovery.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {6}, pages = {}, pmid = {38888585}, issn = {1466-5034}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota ; *Archaea/genetics/classification ; *Genome, Bacterial ; Phylogeny ; Databases, Genetic ; Genome, Archaeal ; Sequence Analysis, DNA ; Computational Biology/methods ; }, abstract = {With the continued evolution of DNA sequencing technologies, the role of genome sequence data has become more integral in the classification and identification of Bacteria and Archaea. Six years after introducing EzBioCloud, an integrated platform representing the taxonomic hierarchy of Bacteria and Archaea through quality-controlled 16S rRNA gene and genome sequences, we present an updated version, that further refines and expands its capabilities. The current update recognizes the growing need for accurate taxonomic information as defining a species increasingly relies on genome sequence comparisons. We also incorporated an advanced strategy for addressing underrepresented or less studied lineages, bolstering the comprehensiveness and accuracy of our database. Our rigorous quality control protocols remain, where whole-genome assemblies from the NCBI Assembly Database undergo stringent screening to remove low-quality sequence data. These are then passed through our enhanced identification bioinformatics pipeline which initiates a 16S rRNA gene similarity search and then calculates the average nucleotide identity (ANI). For genome sequences lacking a 16S rRNA sequence and without a closely related genomic representative for ANI calculation, we apply a different ANI approach using bacterial core genes for improved taxonomic placement (core gene ANI, cgANI). Because of the increase in genome sequences available in NCBI and our newly introduced cgANI method, EzBioCloud now encompasses a total of 109 835 species, of which 21 964 have validly published names. 47 896 are candidate species identified either through 16S rRNA sequence similarity (phylotypes) or through whole genome ANI (genomospecies), and the remaining 39 975 were positioned in the taxonomic tree by cgANI (species clusters). Our EzBioCloud database is accessible at www.ezbiocloud.net/db.}, } @article {pmid38887493, year = {2024}, author = {Xu, Y and Xu, J and Zhu, Y and Mao, H and Li, J and Kong, X and Zhu, X and Zhang, J}, title = {Investigating gut microbiota-blood and urine metabolite correlations in early sepsis-induced acute kidney injury: insights from targeted KEGG analyses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1375874}, pmid = {38887493}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Acute Kidney Injury/metabolism ; *Sepsis/microbiology/urine ; Male ; Prospective Studies ; *Metabolomics/methods ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; Bacteria/classification/genetics/isolation & purification/metabolism ; Metabolome ; Urine/microbiology/chemistry ; }, abstract = {BACKGROUND: The interplay between gut microbiota and metabolites in the early stages of sepsis-induced acute kidney injury (SA-AKI) is not yet clearly understood. This study explores the characteristics and interactions of gut microbiota, and blood and urinary metabolites in patients with SA-AKI.

METHODS: Utilizing a prospective observational approach, we conducted comparative analyses of gut microbiota and metabolites via metabolomics and metagenomics in individuals diagnosed with SA-AKI compared to those without AKI (NCT06197828). Pearson correlations were used to identify associations between microbiota, metabolites, and clinical indicators. The Comprehensive Antibiotic Resistance Database was employed to detect antibiotic resistance genes (ARGs), while Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways informed on metabolic processes and microbial resistance patterns.

RESULTS: Our study included analysis of four patients with SA-AKI and five without AKI. Significant disparities in bacterial composition were observed, illustrated by diversity indices (Shannon index: 2.0 ± 0.4 vs. 1.4 ± 0.6, P = 0.230; Simpson index: 0.8 ± 0.1 vs. 0.6 ± 0.2, P = 0.494) between the SA-AKI group and the non-AKI group. N6, N6, N6-Trimethyl-L-lysine was detected in both blood and urine metabolites, and also showed significant correlations with specific gut microbiota (Campylobacter hominis and Bacteroides caccae, R > 0, P < 0.05). Both blood and urine metabolites were enriched in the lysine degradation pathway. We also identified the citrate cycle (TCA cycle) as a KEGG pathway enriched in sets of differentially expressed ARGs in the gut microbiota, which exhibits an association with lysine degradation.

CONCLUSIONS: Significant differences in gut microbiota and metabolites were observed between the SA-AKI and non-AKI groups, uncovering potential biomarkers and metabolic changes linked to SA-AKI. The lysine degradation pathway may serve as a crucial link connecting gut microbiota and metabolites.}, } @article {pmid38886729, year = {2024}, author = {Wang, Y and Wang, T and Yan, D and Zhao, H and Wang, M and Liu, T and Fan, X and Xu, X}, title = {Vaginal microbial profile of cervical cancer patients receiving chemoradiotherapy: the potential involvement of Lactobacillus iners in recurrence.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {575}, pmid = {38886729}, issn = {1479-5876}, support = {2021KY570,2022KY667,2023KY591, 2024KY933, 2021KY540//Medical Science and Technology Project of Zhejiang Province/ ; 2022ZB053//Zhejiang Traditional Chinese Medicine Administration/ ; }, mesh = {Humans ; Female ; *Uterine Cervical Neoplasms/microbiology/therapy/pathology ; *Vagina/microbiology ; *Chemoradiotherapy ; *Lactobacillus ; *Neoplasm Recurrence, Local/microbiology ; Middle Aged ; *Microbiota ; Adult ; Aged ; Machine Learning ; }, abstract = {The vaginal microbiome is an immune defense against reproductive diseases and can serve as an important biomarker for cervical cancer. However, the intrinsic relationship between the recurrence and the vaginal microbiome in patients with cervical cancer before and after concurrent chemoradiotherapy is poorly understood. Here, we analyzed 125 vaginal microbial profiles from a patient cohort of stage IB-IVB cervical cancer using 16S metagenomic sequencing and deciphered the microbial composition and functional characteristics of the recurrent and non-recurrent both before and after chemoradiotherapy. We demonstrated that the abundance of beneficial bacteria and stability of the microbial community in the vagina decreased in the recurrence group, implying the unique characteristics of the vaginal microbiome for recurrent cervical cancer. Moreover, using machine learning, we identified Lactobacillus iners as the most important biomarker, combined with age and other biomarkers (such as Ndongobacter massiliensis, Corynebacterium pyruviciproducens ATCC BAA-1742, and Prevotella buccalis), and could predict cancer recurrence phenotype before chemoradiotherapy. This study prospectively employed rigorous bioinformatics analysis and highlights the critical role of vaginal microbiota in post-treatment cervical cancer recurrence, identifying promising biomarkers with prognostic significance in the context of concurrent chemoradiotherapy for cervical cancer. The role of L. iners in determining chemoradiation resistance in cervical cancer warrants further detailed investigation. Our results expand our understanding of cervical cancer recurrence and help develop better strategies for prognosis prediction and personalized therapy.}, } @article {pmid38886447, year = {2024}, author = {Liu, ZT and Ma, RA and Zhu, D and Konstantinidis, KT and Zhu, YG and Zhang, SY}, title = {Organic fertilization co-selects genetically linked antibiotic and metal(loid) resistance genes in global soil microbiome.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5168}, pmid = {38886447}, issn = {2041-1723}, support = {52270198//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Soil Microbiology ; *Microbiota/genetics/drug effects ; *Fertilizers ; Metagenome/genetics ; Drug Resistance, Microbial/genetics ; Soil/chemistry ; Genes, Bacterial ; Metals ; Anti-Bacterial Agents/pharmacology ; Agriculture ; }, abstract = {Antibiotic resistance genes (ARGs) and metal(loid) resistance genes (MRGs) coexist in organic fertilized agroecosystems based on their correlations in abundance, yet evidence for the genetic linkage of ARG-MRGs co-selected by organic fertilization remains elusive. Here, an analysis of 511 global agricultural soil metagenomes reveals that organic fertilization correlates with a threefold increase in the number of diverse types of ARG-MRG-carrying contigs (AMCCs) in the microbiome (63 types) compared to non-organic fertilized soils (22 types). Metatranscriptomic data indicates increased expression of AMCCs under higher arsenic stress, with co-regulation of the ARG-MRG pairs. Organic fertilization heightens the coexistence of ARG-MRG in genomic elements through impacting soil properties and ARG and MRG abundances. Accordingly, a comprehensive global map was constructed to delineate the distribution of coexistent ARG-MRGs with virulence factors and mobile genes in metagenome-assembled genomes from agricultural lands. The map unveils a heightened relative abundance and potential pathogenicity risks (range of 4-6) for the spread of coexistent ARG-MRGs in Central North America, Eastern Europe, Western Asia, and Northeast China compared to other regions, which acquire a risk range of 1-3. Our findings highlight that organic fertilization co-selects genetically linked ARGs and MRGs in the global soil microbiome, and underscore the need to mitigate the spread of these co-resistant genes to safeguard public health.}, } @article {pmid38885765, year = {2024}, author = {Di Gregorio, S and Niccolini, L and Seggiani, M and Strangis, G and Barbani, N and Vitiello, V and Becarelli, S and Petroni, G and Yan, X and Buttino, I}, title = {Marine copepod culture as a potential source of bioplastic-degrading microbiome: The case of poly(butylene succinate-co-adipate).}, journal = {Chemosphere}, volume = {362}, number = {}, pages = {142603}, doi = {10.1016/j.chemosphere.2024.142603}, pmid = {38885765}, issn = {1879-1298}, mesh = {Animals ; *Copepoda ; *Biodegradation, Environmental ; *Microbiota ; Bacteria/metabolism/classification/genetics/isolation & purification ; Polyesters/metabolism ; Adipates/metabolism ; Polymers/metabolism ; RNA, Ribosomal, 16S/genetics ; Plankton/metabolism ; Butylene Glycols ; }, abstract = {The poly(butylene succinate-co-adipate) (PBSA) is emerging as environmentally sustainable polyester for applications in marine environment. In this work the capacity of microbiome associated with marine plankton culture to degrade PBSA, was tested. A taxonomic and functional characterization of the microbiome associated with the copepod Acartia tonsa, reared in controlled conditions, was analysed by 16S rDNA metabarcoding, in newly-formed adult stages and after 7 d of incubation. A predictive functional metagenomic profile was inferred for hydrolytic activities involved in bioplastic degradation with a particular focus on PBSA. The copepod-microbiome was also characterized in newly-formed carcasses of A. tonsa, and after 7 and 33 d of incubation in the plankton culture medium. Copepod-microbiome showed hydrolytic activities at all developmental stages of the alive copepods and their carcasses, however, the evenness of the hydrolytic bacterial community significantly increased with the time of incubation in carcasses. Microbial genera, never described in association with copepods: Devosia, Kordia, Lentibacter, Methylotenera, Rheinheimera, Marinagarivorans, Paraglaciecola, Pseudophaeobacter, Gaiella, Streptomyces and Kribbella sps., were retrieved. Kribbella sp. showed carboxylesterase activity and Streptomyces sp. showed carboxylesterase, triacylglycerol lipase and cutinase activities, that might be involved in PBSA degradation. A culturomic approach, adopted to isolate bacterial specimen from carcasses, led to the isolation of the bacterial strain, Vibrio sp. 01 tested for the capacity to promote the hydrolysis of the ester bonds. Granules of PBSA, incubated 82 d at 20 °C with Vibrio sp. 01, were characterized by scanning electron microscopy, infrared spectroscopy, thermogravimetric analysis, and differential scanning calorimetry, showing fractures compared to the control sample, and hydrolysis of ester bonds. These preliminary results are encouraging for further investigation on the ability of the microbiome associated with plankton to biodegrade polyesters, such as PBSA, and increasing knowledge on microorganisms involved in bioplastic degradation in marine environment.}, } @article {pmid38885604, year = {2024}, author = {Balasundaram, D and Veerasamy, V and Sylvia Singarayar, M and Neethirajan, V and Ananth Devanesan, A and Thilagar, S}, title = {Therapeutic potential of probiotics in gut microbial homeostasis and Rheumatoid arthritis.}, journal = {International immunopharmacology}, volume = {137}, number = {}, pages = {112501}, doi = {10.1016/j.intimp.2024.112501}, pmid = {38885604}, issn = {1878-1705}, mesh = {Humans ; *Arthritis, Rheumatoid/therapy/immunology/microbiology/drug therapy ; *Probiotics/therapeutic use ; *Gastrointestinal Microbiome ; Animals ; *Dysbiosis/therapy ; *Homeostasis ; Fecal Microbiota Transplantation ; }, abstract = {Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by inflammation and joint damage. Existing treatment options primarily focus on managing symptoms and slowing disease progression, often with side effects and limitations. The gut microbiome, a vast community of microorganisms present in the gastrointestinal tract, plays a crucial role in health and disease. Recent research suggests a bidirectional relationship between the gut microbiome and RA, highlighting its potential as a therapeutic option. This review focuses on the interaction between the gut microbiome and RA development, by discussing how dysbiosis, an imbalance in gut bacteria, can contribute to RA through multiple mechanisms such as molecular mimicry, leaky gut, and metabolic dysregulation. Probiotics, live microorganisms with health benefits, are emerging as promising tools for managing RA. They can prevent the negative effects of dysbiosis by displacing harmful bacteria, producing anti-inflammatory metabolites like short-chain fatty acids (SCFA), Directly influencing immune cells, and modifying host metabolism. animal and clinical studies demonstrate the potential of probiotics in improving RA symptoms and disease outcomes. However, further research is needed to optimize probiotic strains, dosages, and treatment protocols for personalized and effective management of RA. This review summarizes the current understanding of the gut microbiome and its role in RA and discusses future research directions. In addition to the established role of gut dysbiosis in RA, emerging strategies like fecal microbiota transplantation, prebiotics, and postbiotics offer exciting possibilities. However, individual variations in gut composition necessitate personalized treatment plans. Long-term effects and clear regulations need to be established. Future research focusing on metagenomic analysis, combination therapies, and mechanistic understanding will unlock the full potential of gut microbiome modulation for effective RA management.}, } @article {pmid38884260, year = {2024}, author = {Wang, S and Jiang, Y and Che, L and Wang, RH and Li, SC}, title = {Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome.}, journal = {Nucleic acids research}, volume = {52}, number = {14}, pages = {e61}, pmid = {38884260}, issn = {1362-4962}, support = {20220814183301001//Shenzhen Science and Technology Program/ ; 9667242//Applied Research/ ; 9440262//Hong Kong Innovation and Technology Fund/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Gene Transfer, Horizontal ; *Metagenomics/methods ; Colorectal Neoplasms/genetics/microbiology ; Diarrhea/microbiology/genetics ; Bacteria/genetics/classification ; }, abstract = {Horizontal gene transfer (HGT) phenomena pervade the gut microbiome and significantly impact human health. Yet, no current method can accurately identify complete HGT events, including the transferred sequence and the associated deletion and insertion breakpoints from shotgun metagenomic data. Here, we develop LocalHGT, which facilitates the reliable and swift detection of complete HGT events from shotgun metagenomic data, delivering an accuracy of 99.4%-verified by Nanopore data-across 200 gut microbiome samples, and achieving an average F1 score of 0.99 on 100 simulated data. LocalHGT enables a systematic characterization of HGT events within the human gut microbiome across 2098 samples, revealing that multiple recipient genome sites can become targets of a transferred sequence, microhomology is enriched in HGT breakpoint junctions (P-value = 3.3e-58), and HGTs can function as host-specific fingerprints indicated by the significantly higher HGT similarity of intra-personal temporal samples than inter-personal samples (P-value = 4.3e-303). Crucially, HGTs showed potential contributions to colorectal cancer (CRC) and acute diarrhoea, as evidenced by the enrichment of the butyrate metabolism pathway (P-value = 3.8e-17) and the shigellosis pathway (P-value = 5.9e-13) in the respective associated HGTs. Furthermore, differential HGTs demonstrated promise as biomarkers for predicting various diseases. Integrating HGTs into a CRC prediction model achieved an AUC of 0.87.}, } @article {pmid38882194, year = {2024}, author = {Saleem, F and Ameer, A and Star-Shirko, B and Keating, C and Gundogdu, O and Ijaz, UZ and Javed, S}, title = {Dataset of 569 metagenome-assembled genomes from the caeca of multiple chicken breeds from commercial and backyard farming setups of Pakistan.}, journal = {Data in brief}, volume = {54}, number = {}, pages = {110552}, pmid = {38882194}, issn = {2352-3409}, abstract = {This article focuses the recovery of prokaryotic organisms including bacteria and archaea from 9 different groups of chicken raised in different farm setups in Pakistan. The groups comprise of three different breeds (Broilers, White Layers, and Black Australorp) of chicken raised in different farming setups that include antibiotic-free control, commercial (open and controlled shed), and backyard farms. We have recovered 569 Metagenomics-Assembled Genomes (MAGs) with a completeness of ≥50 % and contamination of ≤10 %. For each MAG, functional annotations were obtained that include KEGG modules, carbohydrate active enzymes (CAZymes), peptidases, geochemical cycles, antibiotic resistance genes, stress genes, and virulence genes. Furthermore, two different sets of Single Copy Genes (SCGs) were used to construct the phylogenetic trees. Based on the reconstructed phylogeny, phylogenetic gain of each MAG is calculated to give an account of novelty.}, } @article {pmid38881655, year = {2024}, author = {Xu, Y and Feng, T and Ding, Z and Li, L and Li, Z and Cui, K and Chen, W and Pan, H and Zhu, P and Liu, Q}, title = {Age-related compositional and functional changes in the adult and breastfed buffalo rumen microbiome.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1342804}, pmid = {38881655}, issn = {1664-302X}, abstract = {INTRODUCTION: The buffalo is an important domestic animal globally, providing milk, meat, and labor to more than 2 billion people in 67 countries. The rumen microorganisms of buffaloes play an indispensable role in enabling the healthy functionality and digestive function of buffalo organisms. Currently, there is a lack of clarity regarding the differences in the composition and function of rumen microorganisms among buffaloes at different growth stages.

METHODS: In this study, metagenomics sequencing technology was applied to examine the compositional and functional differences of rumen microorganisms in adult and breastfed buffaloes.

RESULTS: The results revealed that the rumen of adult buffaloes had significantly higher levels of the following dominant genera: Prevotella, UBA1711, RF16, Saccharofermentans, F23-D06, UBA1777, RUG472, and Methanobrevibacter_A. Interestingly, the dominant genera specific to the rumen of adult buffaloes showed a significant positive correlation (correlation>0.5, p-value<0.05) with both lignocellulose degradation-related carbohydrate-active enzymes (CAZymes) and immune signaling pathways activated by antigenic stimulation. The rumen of breastfed buffaloes had significantly higher levels of the following dominant genera: UBA629, CAG- 791, Selenomonas_C, Treponema_D, Succinivibrio, and RC9. Simultaneously, the rumen-dominant genera specific to breastfed buffaloes were significantly positively correlated (correlation>0.5, p-value<0.05) with CAZymes associated with lactose degradation, amino acid synthesis pathways, and antibiotic-producing pathways.

DISCUSSION: This indicates that rumen microorganisms in adult buffaloes are more engaged in lignocellulose degradation, whereas rumen microorganisms in breastfed buffaloes are more involved in lactose and amino acid degradation, as well as antibiotic production. In conclusion, these findings suggest a close relationship between differences in rumen microbes and the survival needs of buffaloes at different growth stages.}, } @article {pmid38881319, year = {2024}, author = {Shah, M and Bornemann, TLV and Nuy, JK and Hahn, MW and Probst, AJ and Beisser, D and Boenigk, J}, title = {Genome-resolved metagenomics reveals the effect of nutrient availability on bacterial genomic properties across 44 European freshwater lakes.}, journal = {Environmental microbiology}, volume = {26}, number = {6}, pages = {e16634}, doi = {10.1111/1462-2920.16634}, pmid = {38881319}, issn = {1462-2920}, support = {//Stemmler-Stiftung/ ; //Bauer-Stiftung zur Förderung von Wissenschaft und Forschung/ ; }, mesh = {*Bacteria/genetics/classification/metabolism ; *Genome, Bacterial ; *Metagenomics/methods ; *Phosphorus/metabolism ; *Nutrients/metabolism ; *Nitrogen/metabolism ; *Lakes/microbiology ; Europe ; Base Composition ; Carbon/metabolism ; Genome Size ; Microbiota/genetics ; Phylogeny ; }, abstract = {Understanding intricate microbial interactions in the environment is crucial. This is especially true for the relationships between nutrients and bacteria, as phosphorus, nitrogen and organic carbon availability are known to influence bacterial population dynamics. It has been suggested that low nutrient conditions prompt the evolutionary process of genome streamlining. This process helps conserve scarce nutrients and allows for proliferation. Genome streamlining is associated with genomic properties such as %GC content, genes encoding sigma factors, percent coding regions, gene redundancy, and functional shifts in processes like cell motility and ATP binding cassette transporters, among others. The current study aims to unveil the impact of nutrition on the genome size, %GC content, and functional properties of pelagic freshwater bacteria. We do this at finer taxonomic resolutions for many metagenomically characterized communities. Our study confirms the interplay of trophic level and genomic properties. It also highlights that different nutrient types, particularly phosphorus and nitrogen, impact these properties differently. We observed a covariation of functional traits with genome size. Larger genomes exhibit enriched pathways for motility, environmental interaction, and regulatory genes. ABC transporter genes reflect the availability of nutrients in the environment, with small genomes presumably relying more on metabolites from other organisms. We also discuss the distinct strategies different phyla adopt to adapt to oligotrophic environments. The findings contribute to our understanding of genomic adaptations within complex microbial communities.}, } @article {pmid38881311, year = {2024}, author = {Blair, EM and Brown, JL and Li, D and Holden, PA and O'Malley, MA}, title = {Metagenomics analysis yields assembled genomes from prokaryotic anaerobes with polymer-degrading potential.}, journal = {Biotechnology progress}, volume = {40}, number = {6}, pages = {e3484}, pmid = {38881311}, issn = {1520-6033}, support = {CNS-1725797//National Science Foundation/ ; //California NanoSystems Institute/ ; NSF DMR 2308708//Materials Research Laboratory, University of California, Santa Barbara, CA/ ; }, mesh = {*Metagenomics ; Animals ; Metagenome/genetics ; Anaerobiosis ; Feces/microbiology ; Goats ; Polymers/metabolism/chemistry ; Genome, Bacterial/genetics ; Bacteria, Anaerobic/genetics/metabolism/classification ; Microbial Consortia/genetics ; Biodegradation, Environmental ; Sewage/microbiology ; }, abstract = {Anaerobic microbial communities are often highly degradative, such as those found in the herbivore rumen and large-scale anaerobic digesters. Since the microbial communities in these systems degrade recalcitrant organic polymers, we hypothesize that some microbes in anaerobic environments may be involved in man-made plastic association, deformation, or even breakdown. While efforts have been put toward characterizing microbial communities, many microbes remain unidentified until they can be sufficiently cultivated to generate enough genetic material to assemble high-quality metagenome assemblies and reference genomes. In this study, microbial consortia from goat fecal pellets and anaerobic digester sludge were cultivated for over 6 weeks to assemble metagenomes from novel anaerobic taxa with potential degradative activity. To select for microbes with potential plastic-degrading abilities, plastic strips were included in culture, though the presence of plastic did not appear to enrich for particularly degradative consortia, yet it did select for novel species that otherwise may not have been characterized. Whole-genome shotgun sequencing enabled assembly of 72 prokaryotic metagenome-assembled genomes (MAGs) with >90% completion, <5% contamination, and an N50 >10,000 bp; 17 of these MAGs are classified as novel species given their lack of similarity to publicly available genomes and MAGs. These 72 MAGs vary in predicted carbohydrate-degrading abilities, with genes predicted to encode fewer than 10 or up to nearly 400 carbohydrate-active enzymes. Overall, this enrichment strategy enables characterization of less abundant MAGs in a community, and the MAGs identified here can be further mined to advance understanding of degradative anaerobic microbial consortia.}, } @article {pmid38881221, year = {2024}, author = {Greco, C and Andersen, DT and Yallop, ML and Barker, G and Jungblut, AD}, title = {Genome-resolved metagenomics reveals diverse taxa and metabolic complexity in Antarctic lake microbial structures.}, journal = {Environmental microbiology}, volume = {26}, number = {6}, pages = {e16663}, doi = {10.1111/1462-2920.16663}, pmid = {38881221}, issn = {1462-2920}, support = {//The Arctic and Antarctic Research Institute/ ; //The Trottier Family Foundation/ ; 80NSSC18K1094/NASA/NASA/United States ; NE/L002434/1//UK Research and Innovation/ ; //TAWANI Foundation of Chicago/ ; }, mesh = {Antarctic Regions ; *Lakes/microbiology ; *Metagenomics ; *Bacteria/genetics/classification/metabolism ; *Cyanobacteria/genetics/classification/metabolism ; Microbiota/genetics ; Phylogeny ; Geologic Sediments/microbiology ; Metagenome ; Genome, Bacterial ; Archaea/genetics/classification/metabolism ; }, abstract = {Lake Untersee, a lake in Antarctica that is perennially covered with ice, is home to unique microbial structures that are not lithified. We have evaluated the structure of the community and its metabolic potential across the pigmented upper layers and the sediment-enriched deeper layers in these pinnacle and cone-shaped microbial structures using metagenomics. These microbial structures are inhabited by distinct communities. The upper layers of the cone-shaped structures have a higher abundance of the cyanobacterial MAG Microcoleus, while the pinnacle-shaped structures have a higher abundance of Elainellacea MAG. This suggests that cyanobacteria influence the morphologies of the mats. We identified stark contrasts in the composition of the community and its metabolic potential between the upper and lower layers of the mat. The upper layers of the mat, which receive light, have an increased abundance of photosynthetic pathways. In contrast, the lower layer has an increased abundance of heterotrophic pathways. Our results also showed that Lake Untersee is the first Antarctic lake with a substantial presence of ammonia-oxidizing Nitrospiracea and amoA genes. The genomic capacity for recycling biological molecules was prevalent across metagenome-assembled genomes (MAGs) that cover 19 phyla. This highlights the importance of nutrient scavenging in ultra-oligotrophic environments. Overall, our study provides new insights into the formation of microbial structures and the potential metabolic complexity of Antarctic laminated microbial mats. These mats are important environments for biodiversity that drives biogeochemical cycling in polar deserts.}, } @article {pmid38879636, year = {2024}, author = {Wang, Q and Zhan, PC and Han, XL and Lu, T}, title = {Metagenomic and culture-dependent analysis of Rhinopithecius bieti gut microbiota and characterization of a novel genus of Sphingobacteriaceae.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {13819}, pmid = {38879636}, issn = {2045-2322}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Phylogeny ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; Bacteroidetes/genetics/isolation & purification/classification ; }, abstract = {Culture-dependent and metagenomic binning techniques were employed to gain an insight into the diversification of gut bacteria in Rhinopithecius bieti, a highly endangered primate endemic to China. Our analyses revealed that Bacillota_A and Bacteroidota were the dominant phyla. These two phyla species are rich in carbohydrate active enzymes, which could provide nutrients and energy for their own or hosts' survival under different circumstances. Among the culturable bacteria, one novel bacterium, designated as WQ 2009[T], formed a distinct branch that had a low similarity to the known species in the family Sphingobacteriaceae, based on the phylogenetic analysis of its 16S rRNA gene sequence or phylogenomic analysis. The ANI, dDDH and AAI values between WQ 2009[T] and its most closely related strains S. kitahiroshimense 10C[T], S. pakistanense NCCP-246[T] and S. faecium DSM 11690[T] were significantly lower than the accepted cut-off values for microbial species delineation. All results demonstrated that WQ 2009[T] represent a novel genus, for which names Rhinopithecimicrobium gen. nov. and Rhinopithecimicrobium faecis sp. nov. (Type strain WQ 2009[T] = CCTCC AA 2021153[T] = KCTC 82941[T]) are proposed.}, } @article {pmid38879542, year = {2024}, author = {Lo, WS and Sommer, RJ and Han, Z}, title = {Microbiota succession influences nematode physiology in a beetle microcosm ecosystem.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5137}, pmid = {38879542}, issn = {2041-1723}, support = {32200495//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32370458//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Coleoptera/microbiology/physiology ; *Microbiota/physiology ; *Ecosystem ; *Nematoda/microbiology/physiology ; Metagenomics ; Bacteria/genetics/classification/metabolism ; Cellulases/metabolism/genetics ; }, abstract = {Unravelling the multifaceted and bidirectional interactions between microbiota and host physiology represents a major scientific challenge. Here, we utilise the nematode model, Pristionchus pacificus, coupled to a laboratory-simulated decay process of its insect host, to mimic natural microbiota succession and investigate associated tripartite interactions. Metagenomics reveal that during initial decay stages, the population of vitamin B-producing bacteria diminishes, potentially due to a preferential selection by nematodes. As decay progresses to nutrient-depleted stages, bacteria with smaller genomes producing less nutrients become more prevalent. Lipid utilisation and dauer formation, representing key nematode survival strategies, are influenced by microbiota changes. Additionally, horizontally acquired cellulases extend the nematodes' reproductive phase due to more efficient foraging. Lastly, the expressions of Pristionchus species-specific genes are more responsive to natural microbiota compared to conserved genes, suggesting their importance in the organisms' adaptation to its ecological niche. In summary, we show the importance of microbial successions and their reciprocal interaction with nematodes for insect decay in semi-artificial ecosystems.}, } @article {pmid38879505, year = {2024}, author = {Wang, H and Zhang, Y and Zhou, Q and Yu, L and Fu, J and Lin, D and Huang, L and Lai, X and Wu, L and Zhang, J and Zi, J and Liao, X and Huang, S and Xie, Y and He, Y and Yang, L}, title = {Microbial metagenomic shifts in children with acute lymphoblastic leukaemia during induction therapy and predictive biomarkers for infection.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {23}, number = {1}, pages = {52}, pmid = {38879505}, issn = {1476-0711}, support = {2019YFA0802300//National Key Research and Development Program of China/ ; 82022044//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy ; *Gastrointestinal Microbiome/drug effects ; Female ; Male ; *Feces/microbiology ; Child ; Child, Preschool ; *Metagenomics ; Induction Chemotherapy ; Biomarkers ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Escherichia coli/genetics ; Klebsiella pneumoniae/genetics/drug effects ; }, abstract = {BACKGROUND: Emerging evidence has indicated a link between the gut microbiota and acute lymphoblastic leukaemia (ALL). However, the acute changes in gut microbiota during chemotherapy and the predictive value of baseline gut microbiota in infectious complication remain largely unknown.

METHODS: Faecal samples (n = 126) from children with ALL (n = 49) undergoing induction chemotherapy were collected at three timepoints, i.e., initiation of chemotherapy (baseline, T0), 7 days (T1) and 33 days (T2) after initiation of chemotherapy. Gut microbiome profile was performed via metagenomic shotgun sequencing. The bioBakery3 pipeline (Kneaddata, Metaphlan 3 and HUMAnN) was performed to assign taxonomy and functional annotations. Gut microbiome at T0 were used to predict infection during chemotherapy.

RESULTS: The microbial diversities and composition changed significantly during chemotherapy, with Escherichia coli, Klebsiella pneumoniae and Bifidobacterium longum being the most prominent species. The microbial metabolic pathways were also significantly altered during chemotherapy, including the pathway of pyruvate fermentation to acetate and lactate, and assimilatory sulfate reduction pathway. The receiver operating characteristic (ROC) models based on Bifidobacterium longum at T0 could predict infectious complications during the first month of chemotherapy with the area under the curve (AUC) of 0.720.

CONCLUSIONS: Our study provides new insights into the acute changes in microbial and functional characteristics in children with ALL during chemotherapy. The baseline gut microbiota could be potential biomarkers for infections during chemotherapy.

TRIAL REGISTRATION: The study was approved by the Ethics Committee of Zhujiang Hospital, Southern Medical University (2021-KY-171-01) and registered on http://www.chictr.org.cn (ChiCTR2200065406, Registration Date: November 4, 2022).}, } @article {pmid38879123, year = {2024}, author = {Jiang, X and Wang, X and Zhang, M and Yu, L and He, J and Wu, S and Yan, J and Zheng, Y and Zhou, Y and Chen, Y}, title = {Associations between specific dietary patterns, gut microbiome composition, and incident subthreshold depression in Chinese young adults.}, journal = {Journal of advanced research}, volume = {65}, number = {}, pages = {183-195}, pmid = {38879123}, issn = {2090-1224}, mesh = {Adolescent ; Adult ; Female ; Humans ; Male ; Young Adult ; China ; Cross-Sectional Studies ; *Depression/microbiology ; *Diet/methods ; East Asian People ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Incidence ; }, abstract = {INTRODUCTION: The interplay between influential factors and the incidence of subthreshold depression (SD) in young adults remains poorly understood.

OBJECTIVES: This study sought to understand the dietary habits, gut microbiota composition, etc. among individuals with SD in young adults and to investigate their association with SD occurrence.

METHODS: Employing a cross-sectional approach, 178 individuals with SD, aged 18-32 years, were matched with 114 healthy counterparts. SD status was evaluated using the Zung Self-rating Depression Scale (SDS), Zung Self-rating Anxiety Scale (SAS), Beck Depression Inventory 2nd version (BDI-II), the 17-item Hamilton Rating Scales of Depression (HAMD-17), and Pittsburgh Sleep Quality Index (PSQI). Metagenomic sequencing was utilized to identify fecal microbial profiles. Dietary patterns were discerned via factor analysis of a 25-item food frequency questionnaire (FFQ). Logistic regression analysis and mediation analysis were performed to explore the potential links between gut microbiota, dietary patterns, and incident SD.

RESULTS: Data on dietary habits were available for 292 participants (mean [SD] age, 22.1 [2.9] years; 216 [73.9 %] female). Logistic regression analysis revealed that dietary patterns Ⅰ (odds ratio [OR], 0.34; 95 % CI, 0.15-0.75) and IV (OR, 0.39; 95 % CI, 0.17-0.86 and OR, 0.39; 95 % CI, 0.18-0.84) were associated with reduced risk of SD. Distinct microbial profiles were observed in young adults with SD, marked by increased microbial diversity and taxonomic alterations. Moreover, mediation analysis suggested Veillonella atypica as a potential mediator linking SDS or BDI-II scores with a healthy dietary pattern rich in bean products, coarse grains, nuts, fruits, mushrooms, and potatoes (β = 0.25, 95 % CI: 0.02-0.78 and β = 0.18, 95 % CI: 0.01-0.54).

CONCLUSIONS: Our findings highlight the complex interplay between dietary patterns, gut microbiota, and the risk of developing SD in young adults, underscoring the potential for dietary interventions and microbiome modulation in mental health promotion.}, } @article {pmid38876593, year = {2024}, author = {Salamandane, A and Leech, J and Almeida, R and Silva, C and Crispie, F and Cotter, PD and Malfeito-Ferreira, M and Brito, L}, title = {Metagenomic analysis of the bacterial microbiome, resistome and virulome distinguishes Portuguese Serra da Estrela PDO cheeses from similar non-PDO cheeses: An exploratory approach.}, journal = {Food research international (Ottawa, Ont.)}, volume = {189}, number = {}, pages = {114556}, doi = {10.1016/j.foodres.2024.114556}, pmid = {38876593}, issn = {1873-7145}, mesh = {*Cheese/microbiology ; *Microbiota/genetics ; Portugal ; *Food Microbiology ; Animals ; Metagenomics ; Bacteria/genetics/isolation & purification/classification ; RNA, Ribosomal, 16S/genetics ; Drug Resistance, Bacterial/genetics ; Sheep ; High-Throughput Nucleotide Sequencing ; Milk/microbiology ; Enterococcus/genetics/isolation & purification ; }, abstract = {This study aimed to evaluate the microbiome, resistome and virulome of two types of Portuguese cheese using high throughput sequencing (HTS). Culture-dependent chromogenic methods were also used for certain groups/microorganisms. Eight samples of raw ewe's milk cheese were obtained from four producers: two producers with cheeses with a PDO (Protected Designation of Origin) label and the other two producers with cheeses without a PDO label. Agar-based culture methods were used to quantify total mesophiles, Enterobacteriaceae, Escherichia coli, Staphylococcus, Enterococcus and lactic acid bacteria. The presence of Listeria monocytogenes and Salmonella was also investigated. The selected isolates were identified by 16S rRNA gene sequencing and evaluated to determine antibiotic resistance and the presence of virulence genes. The eight cheese samples analyzed broadly complied with EC regulations in terms of the microbiological safety criteria. The HTS results demonstrated that Leuconostoc mesenteroides, Lactococcus lactis, Lactobacillus plantarum, Lacticaseibacillus rhamnosus, Enterococcus durans and Lactobacillus coryniformis were the most prevalent bacterial species in cheeses. The composition of the bacterial community varied, not only between PDO and non-PDO cheeses, but also between producers, particularly between the two non-PDO cheeses. Alpha-diversity analyses showed that PDO cheeses had greater bacterial diversity than non-PDO cheeses, demonstrating that the diversity of spontaneously fermented foods is significantly higher in cheeses produced without the addition of food preservatives and dairy ferments. Despite complying with microbiological regulations, both PDO and non-PDO cheeses harbored potential virulence genes as well as antibiotic resistance genes. However, PDO cheeses exhibited fewer of these virulence and antibiotic resistance genes compared to non-PDO cheeses. Therefore, the combination of conventional microbiological methods and the metagenomic approach could contribute to improving the attribution of the PDO label to this type of cheese.}, } @article {pmid38876584, year = {2024}, author = {Kothe, CI and Carøe, C and Mazel, F and Zilber, D and Cruz-Morales, P and Mohellibi, N and Evans, JD}, title = {Novel misos shape distinct microbial ecologies: opportunities for flavourful sustainable food innovation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {189}, number = {}, pages = {114490}, doi = {10.1016/j.foodres.2024.114490}, pmid = {38876584}, issn = {1873-7145}, mesh = {*Fermentation ; *Bacteria/classification/genetics/metabolism ; *Food Microbiology ; Taste ; Fermented Foods/microbiology ; Microbiota ; Japan ; Metagenomics ; }, abstract = {Fermentation is resurgent around the world as people seek healthier, more sustainable, and tasty food options. This study explores the microbial ecology of miso, a traditional Japanese fermented paste, made with novel regional substrates to develop new plant-based foods. Eight novel miso varieties were developed using different protein-rich substrates: yellow peas, Gotland lentils, and fava beans (each with two treatments: standard and nixtamalisation), as well as rye bread and soybeans. The misos were produced at Noma, a restaurant in Copenhagen, Denmark. Samples were analysed with biological and technical triplicates at the beginning and end of fermentation. We also incorporated in this study six samples of novel misos produced following the same recipe at Inua, a former affiliate restaurant of Noma in Tokyo, Japan. To analyse microbial community structure and diversity, metabarcoding (16S and ITS) and shotgun metagenomic analyses were performed. The misos contain a greater range of microbes than is currently described for miso in the literature. The composition of the novel yellow pea misos was notably similar to the traditional soybean ones, suggesting they are a good alternative, which supports our culinary collaborators' sensory conclusions. For bacteria, we found that overall substrate had the strongest effect, followed by time, treatment (nixtamalisation), and geography. For fungi, there was a slightly stronger effect of geography and a mild effect of substrate, and no significant effects for treatment or time. Based on an analysis of metagenome-assembled genomes (MAGs), strains of Staphylococccus epidermidis differentiated according to substrate. Carotenoid biosynthesis genes in these MAGs appeared in strains from Japan but not from Denmark, suggesting a possible gene-level geographical effect. The benign and possibly functional presence of S. epidermidis in these misos, a species typically associated with the human skin microbiome, suggests possible adaptation to the miso niche, and the flow of microbes between bodies and foods in certain fermentation as more common than is currently recognised. This study improves our understanding of miso ecology, highlights the potential for developing novel misos using diverse local ingredients, and suggests how fermentation innovation can contribute to studies of microbial ecology and evolution.}, } @article {pmid38876338, year = {2024}, author = {Qian, L and Yan, B and Zhou, J and Fan, Y and Tao, M and Zhu, W and Wang, C and Tu, Q and Tian, Y and He, Q and Wu, K and Niu, M and Yan, Q and Nikoloski, Z and Liu, G and Yu, X and He, Z}, title = {Comprehensive profiles of sulfur cycling microbial communities along a mangrove sediment depth.}, journal = {The Science of the total environment}, volume = {944}, number = {}, pages = {173961}, doi = {10.1016/j.scitotenv.2024.173961}, pmid = {38876338}, issn = {1879-1026}, mesh = {*Geologic Sediments/microbiology/chemistry ; *Sulfur/metabolism ; *Microbiota ; *Wetlands ; Bacteria/metabolism/classification/genetics ; }, abstract = {The sulfur (S) cycle is an important biogeochemical cycle with profound implications for both cellular- and ecosystem-level processes by diverse microorganisms. Mangrove sediments are a hotspot of biogeochemical cycling, especially for the S cycle with high concentrations of S compounds. Previous studies have mainly focused on some specific inorganic S cycling processes without paying specific attention to the overall S-cycling communities and processes as well as organic S metabolism. In this study, we comprehensively analyzed the distribution, ecological network and assembly mechanisms of S cycling microbial communities and their changes with sediment depths using metagenome sequencing data. The results showed that the abundance of gene families involved in sulfur oxidation, assimilatory sulfate reduction, and dimethylsulfoniopropionate (DMSP) cleavage and demethylation decreased with sediment depths, while those involved in S reduction and dimethyl sulfide (DMS) transformation showed an opposite trend. Specifically, glpE, responsible for converting S2O3[2-] to SO3[2-], showed the highest abundance in the surface sediment and decreased with sediment depths; in contrast, high abundances of dmsA, responsible for converting dimethyl sulfoxide (DMSO) to DMS, were identified and increased with sediment depths. We identified Pseudomonas and Streptomyces as the main S-cycling microorganisms, while Thermococcus could play an import role in microbial network connections in the S-cycling microbial community. Our statistical analysis showed that both taxonomical and functional compositions were generally shaped by stochastic processes, while the functional composition of organic S metabolism showed a transition from stochastic to deterministic processes. This study provides a novel perspective of diversity distribution of S-cycling functions and taxa as well as their potential assembly mechanisms, which has important implications for maintaining mangrove ecosystem functions.}, } @article {pmid38876324, year = {2024}, author = {Wen, M and Zhang, Q and Li, Y and Cui, Y and Shao, J and Liu, Y}, title = {Influence of dissolved organic matter on the anaerobic biotransformation of roxarsone accompanying microbial community response.}, journal = {Chemosphere}, volume = {362}, number = {}, pages = {142606}, doi = {10.1016/j.chemosphere.2024.142606}, pmid = {38876324}, issn = {1879-1298}, mesh = {*Biotransformation ; *Roxarsone/metabolism ; Anaerobiosis ; *Microbiota/drug effects ; *Biodegradation, Environmental ; Bacteria/metabolism/genetics/classification ; }, abstract = {Roxarsone (ROX), commonly employed as a livestock feed additive, largely remains unmetabolized and is subsequently excreted via feces. ROX could cause serious environmental risks due to its rapid transformation and high mobility in the anaerobic subsurface environment. Dissolved organic matter (DOM) is an important constituent of fecal organics in livestock waste and could affect the ROX biotransformation. Nonetheless, the underlying mechanisms governing the interaction between DOM and ROX biotransformation have not yet been elucidated in the anaerobic environment. In this study, the changes of ROX, metabolites, and microbial biomass in the solutions with varying DOM concentrations (0, 50, 100, 200, and 400 mg/L) under anaerobic environments were investigated during the ROX (200 mg/L) degradation. EEM-PARAFAC and metagenomic sequencing were combined to identify the dynamic shifts of DOM components and the functional microbial populations responsible for ROX degradation. Results indicated that DOM facilitated the anaerobic biotransformation of ROX and 200 mg/L ROX could be degraded completely in 28 h. The tryptophan-like within DOM functioned as a carbon source to promote the growth of microorganisms, thus accelerating the degradation of ROX. The mixed microflora involved in ROX anaerobic degrading contained genes associated with arsenic metabolism (arsR, arsC, acr3, arsA, nfnB, and arsB), and arsR, arsC, acr3 exhibited high microbial diversity. Variations in DOM concentrations significantly impacted the population dynamics of microorganisms involved in arsenic metabolism (Proteiniclasticum, Exiguobacterium, Clostridium, Proteiniphilum, Alkaliphilus, and Corynebacterium spp.), which in turn affected the transformation of ROX and its derivatives. This study reveals the mechanism of ROX degradation influenced by the varying concentrations of DOM under anaerobic environments, which is important for the prevention of arsenic contamination with elevated levels of organic matter.}, } @article {pmid38876022, year = {2024}, author = {Sivalingam, P and Sabatino, R and Sbaffi, T and Corno, G and Fontaneto, D and Borgomaneiro, G and Rogora, M and Crotti, E and Mapelli, F and Borin, S and Pilar, AL and Eckert, EM and Di Cesare, A}, title = {Anthropogenic pollution may enhance natural transformation in water, favouring the spread of antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {475}, number = {}, pages = {134885}, doi = {10.1016/j.jhazmat.2024.134885}, pmid = {38876022}, issn = {1873-3336}, mesh = {*Wastewater/microbiology ; Drug Resistance, Microbial/genetics ; Lakes/microbiology ; Genes, Bacterial/drug effects ; Water Pollution ; Water Microbiology ; Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; Drug Resistance, Bacterial/genetics ; Bacteria/drug effects/genetics/classification ; }, abstract = {Aquatic ecosystems are crucial in the antimicrobial resistance cycle. While intracellular DNA has been extensively studied to understand human activity's impact on antimicrobial resistance gene (ARG) dissemination, extracellular DNA is frequently overlooked. This study examines the effect of anthropogenic water pollution on microbial community diversity, the resistome, and ARG dissemination. We analyzed intracellular and extracellular DNA from wastewater treatment plant effluents and lake surface water by shotgun sequencing. We also conducted experiments to evaluate anthropogenic pollution's effect on transforming extracellular DNA (using Gfp-plasmids carrying ARGs) within a natural microbial community. Chemical analysis showed treated wastewater had higher anthropogenic pollution-related parameters than lake water. The richness of microbial community, antimicrobial resistome, and high-risk ARGs was greater in treated wastewaters than in lake waters both for intracellular and extracellular DNA. Except for the high-risk ARGs, richness was significantly higher in intracellular than in extracellular DNA. Several ARGs were associated with mobile genetic elements and located on plasmids. Furthermore, Gfp-plasmid transformation within a natural microbial community was enhanced by anthropogenic pollution levels. Our findings underscore anthropogenic pollution's pivotal role in shaping microbial communities and their antimicrobial resistome. Additionally, it may facilitate ARG dissemination through extracellular DNA plasmid uptake.}, } @article {pmid38874746, year = {2024}, author = {Kumari, S and Choudhary, G and Anu, K and Devi, S}, title = {Metagenomics insight into Puga geothermal geyser located in Himalayan Geothermal Belt (Trans-Himalayan Plateau) Ladakh, India.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {55}, number = {3}, pages = {2321-2334}, pmid = {38874746}, issn = {1678-4405}, mesh = {India ; *Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; *Archaea/genetics/classification/isolation & purification ; *Hot Springs/microbiology ; Phylogeny ; Microbiota ; Metagenome ; }, abstract = {Puga geothermal geyser and surrounding area, located in the Himalayan Geothermal Belt of the Trans-Himalayan Plateau in Ladakh, India, are very geographically isolated and considered pristine and free of anthropogenic activities. In this study, we have conducted the first metagenomic investigation of the microbes in and around the geyser. The whole genome sequencing analysis showed the presence of a total of 44.8%, 39.7% and 41.4% bacterial phyla in the PugW, PugS, and PugSo samples respectively, 8.6% of archaeal phyla (in all the samples), unclassified (derived from other sequences, PugW: 27.6%, PugS: 27.6%, and PugSo: 15.5%) and unclassified (derived from bacteria, PugW: 12%, PugS: 13.8%, and PugSo: 13.8%). The majority of archaeal sequences were linked to Euryarchaeota (2.84%) while the majority of the bacterial communities that predominated in most geothermal locations were linked to Pseudomonadota (67.14%) and Bacteroidota (12.52%). The abundant bacterial strains at the species level included Dechloromonas aromatica, Acinetobacter baumannii, and Arcobacter butzleri, in all the samples while the most abundant archaeal species were Methanosaeta thermophile, Methanoregula boonei, and Methanosarcina berkeri. Further, this geothermal geyser metagenome has a large number of unique sequences linked to unidentified and unclassified lineages, suggesting a potential source for novel species of microbes and their products. The present study which only examined one of the many geothermal geysers and springs in the Puga geothermal area, should be regarded as a preliminary investigation of the microbiota that live in the geothermal springs on these remote areas. These findings suggest that further investigations should be undertaken to characterize the ecosystems of the Puga geothermal area, which serve as a repository for unidentified microbial lineages.}, } @article {pmid38873612, year = {2024}, author = {Pulvirenti, F and Giufrè, M and Pentimalli, TM and Camilli, R and Milito, C and Villa, A and Sculco, E and Cerquetti, M and Pantosti, A and Quinti, I}, title = {Oropharyngeal microbial ecosystem perturbations influence the risk for acute respiratory infections in common variable immunodeficiency.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1371118}, pmid = {38873612}, issn = {1664-3224}, mesh = {Humans ; *Common Variable Immunodeficiency/microbiology/immunology/complications ; *Oropharynx/microbiology ; Male ; Female ; Middle Aged ; Adult ; *Respiratory Tract Infections/microbiology/immunology ; *Dysbiosis ; Microbiota ; Prospective Studies ; Aged ; RNA, Ribosomal, 16S/genetics ; Acute Disease ; Bacteria/classification/genetics ; Case-Control Studies ; }, abstract = {BACKGROUND: The respiratory tract microbiome is essential for human health and well-being and is determined by genetic, lifestyle, and environmental factors. Patients with Common Variable Immunodeficiency (CVID) suffer from respiratory and intestinal tract infections, leading to chronic diseases and increased mortality rates. While CVID patients' gut microbiota have been analyzed, data on the respiratory microbiome ecosystem are limited.

OBJECTIVE: This study aims to analyze the bacterial composition of the oropharynx of adults with CVID and its link with clinical and immunological features and risk for respiratory acute infections.

METHODS: Oropharyngeal samples from 72 CVID adults and 26 controls were collected in a 12-month prospective study. The samples were analyzed by metagenomic bacterial 16S ribosomal RNA sequencing and processed using the Quantitative Insights Into Microbial Ecology (QIME) pipeline. Differentially abundant species were identified and used to build a dysbiosis index. A machine learning model trained on microbial abundance data was used to test the power of microbiome alterations to distinguish between healthy individuals and CVID patients.

RESULTS: Compared to controls, the oropharyngeal microbiome of CVID patients showed lower alpha- and beta-diversity, with a relatively increased abundance of the order Lactobacillales, including the family Streptococcaceae. Intra-CVID analysis identified age >45 years, COPD, lack of IgA, and low residual IgM as associated with a reduced alpha diversity. Expansion of Haemophilus and Streptococcus genera was observed in patients with undetectable IgA and COPD, independent from recent antibiotic use. Patients receiving azithromycin as antibiotic prophylaxis had a higher dysbiosis score. Expansion of Haemophilus and Anoxybacillus was associated with acute respiratory infections within six months.

CONCLUSIONS: CVID patients showed a perturbed oropharynx microbiota enriched with potentially pathogenic bacteria and decreased protective species. Low residual levels of IgA/IgM, chronic lung damage, anti antibiotic prophylaxis contributed to respiratory dysbiosis.}, } @article {pmid38872164, year = {2024}, author = {Chen, CM and Yan, QL and Guo, RC and Tang, F and Wang, MH and Yi, HZ and Huang, CX and Liu, C and Wang, QY and Lan, WY and Jiang, Z and Yang, YZ and Wang, GY and Zhang, AQ and Ma, J and Zhang, Y and You, W and Ullah, H and Zhang, Y and Li, SH and Yao, XM and Sun, W and Ma, WK}, title = {Distinct characteristics of the gut virome in patients with osteoarthritis and gouty arthritis.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {564}, pmid = {38872164}, issn = {1479-5876}, support = {[2020]2202//Guizhou Provincial Platform and Talent Program/ ; [2021]general006//Guizhou Provincial Key Technology R&D Program/ ; ZK[2021]general515//Natural Science Research Project of Guizhou Province/ ; ZK[2023]general436//Natural Science Research Project of Guizhou Province/ ; 82260894//National Natural Science Foundation of China/ ; 82160917//National Natural Science Foundation of China/ ; Guizhou Education Technology [2023] No.017//the Key Laboratory of Guizhou Provincial Education Department/ ; GZUTCM-TD[2022]004//Collaborative Innovation Center for Modern Science and Technology and Industrial Development of Jiangxi Traditional Medicine/ ; }, mesh = {Humans ; *Virome ; *Arthritis, Gouty/virology/microbiology ; *Gastrointestinal Microbiome ; Male ; *Osteoarthritis/virology/microbiology ; Female ; Middle Aged ; Case-Control Studies ; Aged ; Metagenomics ; Feces/virology/microbiology ; }, abstract = {BACKGROUND/PURPOSE(S): The gut microbiota and its metabolites play crucial roles in pathogenesis of arthritis, highlighting gut microbiota as a promising avenue for modulating autoimmunity. However, the characterization of the gut virome in arthritis patients, including osteoarthritis (OA) and gouty arthritis (GA), requires further investigation.

METHODS: We employed virus-like particle (VLP)-based metagenomic sequencing to analyze gut viral community in 20 OA patients, 26 GA patients, and 31 healthy controls, encompassing a total of 77 fecal samples.

RESULTS: Our analysis generated 6819 vOTUs, with a considerable proportion of viral genomes differing from existing catalogs. The gut virome in OA and GA patients differed significantly from healthy controls, showing variations in diversity and viral family abundances. We identified 157 OA-associated and 94 GA-associated vOTUs, achieving high accuracy in patient-control discrimination with random forest models. OA-associated viruses were predicted to infect pro-inflammatory bacteria or bacteria associated with immunoglobulin A production, while GA-associated viruses were linked to Bacteroidaceae or Lachnospiraceae phages. Furthermore, several viral functional orthologs displayed significant differences in frequency between OA-enriched and GA-enriched vOTUs, suggesting potential functional roles of these viruses. Additionally, we trained classification models based on gut viral signatures to effectively discriminate OA or GA patients from healthy controls, yielding AUC values up to 0.97, indicating the clinical utility of the gut virome in diagnosing OA or GA.

CONCLUSION: Our study highlights distinctive alterations in viral diversity and taxonomy within gut virome of OA and GA patients, offering insights into arthritis etiology and potential treatment and prevention strategies.}, } @article {pmid38871865, year = {2024}, author = {Faial, T}, title = {Metagenomics of the human gut mycobiome.}, journal = {Nature genetics}, volume = {56}, number = {6}, pages = {1038}, doi = {10.1038/s41588-024-01817-4}, pmid = {38871865}, issn = {1546-1718}, mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Mycobiome/genetics ; Fungi/genetics ; Metagenome ; }, } @article {pmid38871078, year = {2024}, author = {Rosell-Díaz, M and Petit-Gay, A and Molas-Prat, C and Gallardo-Nuell, L and Ramió-Torrentà, L and Garre-Olmo, J and Pérez-Brocal, V and Moya, A and Jové, M and Pamplona, R and Puig, J and Ramos, R and Bäckhed, F and Mayneris-Perxachs, J and Fernández-Real, JM}, title = {Metformin-induced changes in the gut microbiome and plasma metabolome are associated with cognition in men.}, journal = {Metabolism: clinical and experimental}, volume = {157}, number = {}, pages = {155941}, doi = {10.1016/j.metabol.2024.155941}, pmid = {38871078}, issn = {1532-8600}, mesh = {Humans ; *Metformin/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; *Metabolome/drug effects ; Female ; Aged ; *Diabetes Mellitus, Type 2/microbiology/metabolism/drug therapy ; *Hypoglycemic Agents/therapeutic use/pharmacology ; *Cognition/drug effects ; Double-Blind Method ; Middle Aged ; Pilot Projects ; }, abstract = {BACKGROUND: An altered gut microbiome characterized by reduced abundance of butyrate producing bacteria and reduced gene richness is associated with type 2 diabetes (T2D). An important complication of T2D is increased risk of cognitive impairment and dementia. The biguanide metformin is a commonly prescribed medication for the control of T2D and metformin treatment has been associated with a significant reduction in the risk of dementia and improved cognition, particularly in people with T2D.

AIM: To investigate the associations of metformin use with cognition exploring potential mechanisms by analyzing the gut microbiome and plasma metabolome using shotgun metagenomics and HPLC-ESI-MS/MS, respectively.

METHODS: We explored two independent cohorts: an observational study (Aging Imageomics) and a phase IV, randomized, double-blind, parallel-group, randomized pilot study (MEIFLO). From the two studies, we analyzed four study groups: (1) individuals with no documented medical history or medical treatment (n = 172); (2) people with long-term T2D on metformin monotherapy (n = 134); (3) people with long-term T2D treated with oral hypoglycemic agents other than metformin (n = 45); (4) a newly diagnosed T2D subjects on metformin monotherapy (n = 22). Analyses were also performed stratifying by sex.

RESULTS: Several bacterial species belonging to the Proteobacteria (Escherichia coli) and Verrucomicrobia (Akkermansia muciniphila) phyla were positively associated with metformin treatment, while bacterial species belonging to the Firmicutes phylum (Romboutsia timonensis, Romboutsia ilealis) were negatively associated. Due to the consistent increase in A. muciniphila and decrease in R.ilealis in people with T2D subjects treated with metformin, we investigated the association between this ratio and cognition. In the entire cohort of metformin-treated T2D subjects, the A.muciniphila/R.ilealis ratio was not significantly associated with cognitive test scores. However, after stratifying by sex, the A.muciniphila/R. ilealis ratio was significantly and positively associated with higher memory scores and improved memory in men. Metformin treatment was associated with an enrichment of microbial pathways involved in the TCA cycle, and butanoate, arginine, and proline metabolism in both cohorts. The bacterial genes involved in arginine metabolism, especially in production of glutamate (astA, astB, astC, astD, astE, putA), were enriched following metformin intake. In agreement, in the metabolomics analysis, metformin treatment was strongly associated with the amino acid proline, a metabolite involved in the metabolism of glutamate.

CONCLUSIONS: The beneficial effects of metformin may be mediated by changes in the composition of the gut microbiota and microbial-host-derived co-metabolites.}, } @article {pmid38870905, year = {2024}, author = {Shama, S and Asbury, MR and O'Connor, DL}, title = {From parent to progeny.}, journal = {Cell host & microbe}, volume = {32}, number = {6}, pages = {947-949}, doi = {10.1016/j.chom.2024.05.012}, pmid = {38870905}, issn = {1934-6069}, mesh = {Humans ; *Gastrointestinal Microbiome ; Metagenomics ; Infant ; }, abstract = {How infants acquire their gut microbial communities and the various factors influencing these dynamics remain unclear. In this issue of Cell Host & Microbe, Selma-Royo et al. and Dubois et al. use shotgun metagenomic sequencing to understand the transmission of microbes from parents to infants and delve into factors modifying this process.}, } @article {pmid38870892, year = {2024}, author = {Dubois, L and Valles-Colomer, M and Ponsero, A and Helve, O and Andersson, S and Kolho, KL and Asnicar, F and Korpela, K and Salonen, A and Segata, N and de Vos, WM}, title = {Paternal and induced gut microbiota seeding complement mother-to-infant transmission.}, journal = {Cell host & microbe}, volume = {32}, number = {6}, pages = {1011-1024.e4}, doi = {10.1016/j.chom.2024.05.004}, pmid = {38870892}, issn = {1934-6069}, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; *Fecal Microbiota Transplantation ; Male ; Infant, Newborn ; Infant ; Fathers ; Mothers ; Feces/microbiology ; Cesarean Section ; Pregnancy ; Infectious Disease Transmission, Vertical ; Bacteria/genetics ; }, abstract = {Microbial colonization of the neonatal gut involves maternal seeding, which is partially disrupted in cesarean-born infants and after intrapartum antibiotic prophylaxis. However, other physically close individuals could complement such seeding. To assess the role of both parents and of induced seeding, we analyzed two longitudinal metagenomic datasets (health and early life microbiota [HELMi]: N = 74 infants, 398 samples, and SECFLOR: N = 7 infants, 35 samples) with cesarean-born infants who received maternal fecal microbiota transplantation (FMT). We found that the father constitutes a stable source of strains for the infant independently of the delivery mode, with the cumulative contribution becoming comparable to that of the mother after 1 year. Maternal FMT increased mother-infant strain sharing in cesarean-born infants, raising the average bacterial empirical growth rate while reducing pathogen colonization. Overall, our results indicate that maternal seeding is partly complemented by that of the father and support the potential of induced seeding to restore potential deviations in this process.}, } @article {pmid38870614, year = {2024}, author = {Xiong, X and Lan, Y and Wang, Z and Xu, J and Gong, J and Chai, X}, title = {Bacteroidales reduces growth rate through serum metabolites and cytokines in Chinese Ningdu yellow chickens.}, journal = {Poultry science}, volume = {103}, number = {8}, pages = {103905}, pmid = {38870614}, issn = {1525-3171}, mesh = {Animals ; Male ; Bacteroidetes ; *Cecum/microbiology ; *Chickens/growth & development/blood ; *Cytokines/metabolism/genetics/blood ; *Gastrointestinal Microbiome ; Metabolome ; }, abstract = {Increasing evidence has indicated that the gut microbiome plays an important role in chicken growth traits. However, the cecal microbial taxa associated with the growth rates of the Chinese Ningdu yellow chickens are unknown. In this study, shotgun metagenomic sequencing was used to identify cecal bacterial species associated with the growth rate of the Chinese Ningdu yellow chickens. We found that nine cecal bacterial species differed significantly between high and low growth rate chickens, including three species (Succinatimonas hippei, Phocaeicola massiliensis, and Parabacteroides sp. ZJ-118) that were significantly enriched in high growth rate chickens. We identified six Bacteroidales that were significantly enriched in low growth rate chickens, including Barnesiella sp. An22, Barnesiella sp. ET7, and Bacteroidales bacterium which were key biomarkers in differentiating high and low growth rate chickens and were associated with alterations in the functional taxa of the cecal microbiome. Untargeted serum metabolome analysis revealed that 8 metabolites showing distinct enrichment patterns between high and low growth rate chickens, including triacetate lactone and N-acetyl-a-neuraminic acid, which were at higher concentrations in low growth rate chickens and were positively and significantly correlated with Barnesiella sp. An22, Barnesiella sp. ET7, and Bacteroidales bacterium. Furthermore, the results suggest that serum cytokines, such as IL-5, may reduce growth rate and are related to changes in serum metabolites and gut microbes (e.g., Barnesiella sp. An22 and Barnesiella sp. ET7). These results provide important insights into the effects of the cecal microbiome, serum metabolism and cytokines in Ningdu yellow chickens.}, } @article {pmid38868903, year = {2024}, author = {Elbere, I and Orlovskis, Z and Ansone, L and Silamikelis, I and Jagare, L and Birzniece, L and Megnis, K and Leskovskis, K and Vaska, A and Turks, M and Klavins, K and Pirags, V and Briviba, M and Klovins, J}, title = {Gut microbiome encoded purine and amino acid pathways present prospective biomarkers for predicting metformin therapy efficacy in newly diagnosed T2D patients.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2361491}, pmid = {38868903}, issn = {1949-0984}, mesh = {Humans ; *Metformin/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Diabetes Mellitus, Type 2/drug therapy/microbiology/metabolism ; *Amino Acids/metabolism ; Male ; Middle Aged ; Female ; *Purines/metabolism ; *Bacteria/classification/metabolism/genetics/drug effects/isolation & purification ; *Biomarkers/metabolism ; *Hypoglycemic Agents/therapeutic use/pharmacology ; Aged ; Adult ; Treatment Outcome ; Metabolomics ; }, abstract = {Metformin is widely used for treating type 2 diabetes mellitus (T2D). However, the efficacy of metformin monotherapy is highly variable within the human population. Understanding the potential indirect or synergistic effects of metformin on gut microbiota composition and encoded functions could potentially offer new insights into predicting treatment efficacy and designing more personalized treatments in the future. We combined targeted metabolomics and metagenomic profiling of gut microbiomes in newly diagnosed T2D patients before and after metformin therapy to identify potential pre-treatment biomarkers and functional signatures for metformin efficacy and induced changes in metformin therapy responders. Our sequencing data were largely corroborated by our metabolic profiling and identified that pre-treatment enrichment of gut microbial functions encoding purine degradation and glutamate biosynthesis was associated with good therapy response. Furthermore, we identified changes in glutamine-associated amino acid (arginine, ornithine, putrescine) metabolism that characterize differences in metformin efficacy before and after the therapy. Moreover, metformin Responders' microbiota displayed a shifted balance between bacterial lipidA synthesis and degradation as well as alterations in glutamate-dependent metabolism of N-acetyl-galactosamine and its derivatives (e.g. CMP-pseudaminate) which suggest potential modulation of bacterial cell walls and human gut barrier, thus mediating changes in microbiome composition. Together, our data suggest that glutamine and associated amino acid metabolism as well as purine degradation products may potentially condition metformin activity via its multiple effects on microbiome functional composition and therefore serve as important biomarkers for predicting metformin efficacy.}, } @article {pmid38867204, year = {2024}, author = {Wang, B and Tan, M and Li, W and Xu, Q and Jin, L and Xie, S and Wang, C}, title = {Exploring the microbiota difference of bronchoalveolar lavage fluid between community-acquired pneumonia with or without COPD based on metagenomic sequencing: a retrospective study.}, journal = {BMC pulmonary medicine}, volume = {24}, number = {1}, pages = {278}, pmid = {38867204}, issn = {1471-2466}, support = {18410720900//Shanghai Science and Technology/ ; }, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology ; *Bronchoalveolar Lavage Fluid/microbiology ; *Community-Acquired Infections/microbiology ; Male ; Retrospective Studies ; Aged ; Female ; *Microbiota/genetics ; Middle Aged ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Pneumonia/microbiology ; Aged, 80 and over ; }, abstract = {BACKGROUND: Community-acquired pneumonia (CAP) patients with chronic obstructive pulmonary disease (COPD) have higher disease severity and mortality compared to those without COPD. However, deep investigation into microbiome distribution of lower respiratory tract of CAP with or without COPD was unknown.

METHODS: So we used metagenomic next generation sequencing (mNGS) to explore the microbiome differences between the two groups.

RESULTS: Thirty-six CAP without COPD and 11 CAP with COPD cases were retrieved. Bronchoalveolar lavage fluid (BALF) was collected and analyzed using untargeted mNGS and bioinformatic analysis. mNGS revealed that CAP with COPD group was abundant with Streptococcus, Prevotella, Bordetella at genus level and Cutibacterium acnes, Rothia mucilaginosa, Bordetella genomosp. 6 at species level. While CAP without COPD group was abundant with Ralstonia, Prevotella, Streptococcus at genus level and Ralstonia pickettii, Rothia mucilaginosa, Prevotella melaninogenica at species level. Meanwhile, both alpha and beta microbiome diversity was similar between groups. Linear discriminant analysis found that pa-raburkholderia, corynebacterium tuberculostearicum and staphylococcus hominis were more enriched in CAP without COPD group while the abundance of streptococcus intermedius, streptococcus constellatus, streptococcus milleri, fusarium was higher in CAP with COPD group.

CONCLUSIONS: These findings revealed that concomitant COPD have an mild impact on lower airway microbiome of CAP patients.}, } @article {pmid38866993, year = {2024}, author = {Rubio-Noguez, D and Breton-Deval, L and Salinas-Peralta, I and Juárez, K and Galicia, L}, title = {Pollution pressure drives microbial assemblages that improve the phytoremediation potential of heavy metals by Ricinus communis.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {8}, pages = {241}, pmid = {38866993}, issn = {1573-0972}, support = {FOINS 4785//National Council of Science and Technology of Mexico/ ; }, mesh = {*Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Metals, Heavy/metabolism ; *Cadmium/metabolism ; *Ricinus/microbiology/metabolism ; *Plant Roots/microbiology/metabolism ; *Microbiota ; Lead/metabolism ; Soil Microbiology ; Bacteria/classification/metabolism/genetics/isolation & purification ; Metagenomics ; Rivers/microbiology ; }, abstract = {Due to the rapid expansion of industrial activity, soil pollution has intensified. Plants growing in these polluted areas have developed a rhizobiome uniquely and specially adapted to thrive in such environments. However, it remains uncertain whether pollution acts as a sufficiently selective force to shape the rhizobiome, and whether these adaptations endure over time, potentially aiding in long-term phytoremediation. Therefore, in the present study, we aimed to compare whether the microbiome associated with roots from plants germinated in polluted riverbanks will improve the phytoremediation of Cd and Pb under mesocosm experiments compared with plants germinating in a greenhouse. The experimental design was a factorial 2 × 2, i.e., the origin of the plant and the presence or absence of 100 mg/L of Cd and 1000 mg/L of Pb. Our results showed that plants germinated in polluted riverbanks have the capacity to accumulate twice the amount of Pb and Cd during mesocosm experiments. The metagenomic analysis showed that plants from the river exposed to heavy metals at the end of mesocosm experiments were rich in Rhizobium sp. AC44/96 and Enterobacter sp. EA-1, Enterobacter soli, Pantoea rwandensis, Pantoea endophytica. In addition, those plants were uniquely associated with Rhizobium grahamii, which likely contributed to the differences in the levels of phytoremediation achieved. Furthermore, the functional analysis revealed an augmented functional potential related to hormones, metallothioneins, dismutases, and reductases; meanwhile, the plants germinated in the greenhouse showed an unspecific strategy to exceed heavy metal stress. In conclusion, pollution pressure drives stable microbial assemblages, which could be used in future phytostabilization and phytoremediation experiments.}, } @article {pmid38866340, year = {2024}, author = {Kim, M and Cha, IT and Li, M and Park, SJ}, title = {Unraveling interspecies cross-feeding during anaerobic lignin degradation for bioenergy applications.}, journal = {Chemosphere}, volume = {361}, number = {}, pages = {142588}, doi = {10.1016/j.chemosphere.2024.142588}, pmid = {38866340}, issn = {1879-1298}, mesh = {*Lignin/metabolism ; Anaerobiosis ; *Biodegradation, Environmental ; *Biofuels ; *Archaea/metabolism/genetics ; *Bacteria/metabolism/classification/genetics ; Methane/metabolism ; Microbiota ; Metagenome ; }, abstract = {Lignin, a major component of plant biomass, remains underutilized for renewable biofuels due to its complex and heterogeneous structure. Although investigations into depolymerizing lignin using fungi are well-established, studies of microbial pathways that enable anaerobic lignin breakdown linked with methanogenesis are limited. Through an enrichment cultivation approach with inoculation of freshwater sediment, we enriched a microbial community capable of producing methane during anaerobic lignin degradation. We reconstructed the near-complete population genomes of key lignin degraders and methanogens using metagenome-assembled genomes finally selected in this study (MAGs; 92 bacterial and 4 archaeal MAGs affiliated into 45 and 2 taxonomic groups, respectively). This study provides genetic evidence of microbial interdependence in conversion of lignin to methane in a syntrophic community. Metagenomic analysis revealed metabolic linkages, with lignin-hydrolyzing and/or fermentative bacteria such as the genera Alkalibaculum and Propionispora transforming lignin breakdown products into compounds such as acetate to feed methanogens (two archaeal MAGs classified into the genus Methanosarcina or UBA6 of the family Methanomassiliicoccaceae). Understanding the synergistic relationships between microbes that convert lignin could inform strategies for producing renewable bioenergy and treating aromatic-contaminated environments through anaerobic biodegradation processes. Overall, this study offers fundamental insights into complex community-level anaerobic lignin metabolism, highlighting hitherto unknown players, interactions, and pathways in this biotechnologically valuable process.}, } @article {pmid38865893, year = {2024}, author = {Wu, Z and Ji, Y and Liu, G and Yu, X and Shi, K and Liang, B and Freilich, S and Jiang, J}, title = {Electro-stimulation modulates syntrophic interactions in methanogenic toluene-degrading microbiota for enhanced functionality.}, journal = {Water research}, volume = {260}, number = {}, pages = {121898}, doi = {10.1016/j.watres.2024.121898}, pmid = {38865893}, issn = {1879-2448}, mesh = {*Microbiota ; *Methane/metabolism ; *Toluene/metabolism ; Biodegradation, Environmental ; }, abstract = {Syntrophy achieved via microbial cooperation is vital for anaerobic hydrocarbon degradation and methanogenesis. However, limited understanding of the metabolic division of labor and electronic interactions in electro-stimulated microbiota has impeded the development of enhanced biotechnologies for degrading hydrocarbons to methane. Here, compared to the non-electro-stimulated methanogenic toluene-degrading microbiota, electro-stimulation at 800 mV promoted toluene degradation and methane production efficiencies by 11.49 %-14.76 % and 75.58 %-290.11 %, respectively. Hydrocarbon-degrading gene bamA amplification and metagenomic sequencing analyses revealed that f_Syntrophobacteraceae MAG116 may act as a toluene degrader in the non-electro-stimulated microbiota, which was proposed to establish electron syntrophy with the acetoclastic methanogen Methanosarcina spp. (or Methanothrix sp.) through e-pili or shared acetate. In the electro-stimulated microbiota, 37.22 ± 4.33 % of Desulfoprunum sp. (affiliated f_Desulfurivibrionaceae MAG10) and 58.82 ± 3.74 % of the hydrogenotrophic methanogen Methanobacterium sp. MAG74 were specifically recruited to the anode and cathode, respectively. The potential electrogen f_Desulfurivibrionaceae MAG10 engaged in interspecies electron transfer with both syntroph f_Syntrophobacteraceae MAG116 and the anode, which might be facilitated by c-type cytochromes (e.g., ImcH, OmcT, and PilZ). Moreover, upon capturing electrons from the external circuit, the hydrogen-producing electrotroph Aminidesulfovibrio sp. MAG60 could share electrons and hydrogen with the methanogen Methanobacterium sp. MAG74, which uniquely harbored hydrogenase genes ehaA-R and ehbA-P. This study elucidates the microbial interaction mechanisms underlying the enhanced metabolic efficiency of the electro-stimulated methanogenic toluene-degrading microbiota, and emphasizes the significance of metabolic and electron syntrophic interactions in maintaining the stability of microbial community functionality.}, } @article {pmid38865431, year = {2024}, author = {Tedersoo, L and Hosseyni Moghaddam, MS and Mikryukov, V and Hakimzadeh, A and Bahram, M and Nilsson, RH and Yatsiuk, I and Geisen, S and Schwelm, A and Piwosz, K and Prous, M and Sildever, S and Chmolowska, D and Rueckert, S and Skaloud, P and Laas, P and Tines, M and Jung, JH and Choi, JH and Alkahtani, S and Anslan, S}, title = {EUKARYOME: the rRNA gene reference database for identification of all eukaryotes.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {38865431}, issn = {1758-0463}, support = {Distinguished Scientist Fellowship Programme//King Saud University/ ; MOBERC66 MOBTP198//European Regional Development Fund/ ; //LOEWE Zentrum AdRIA/ ; Distinguished Scientist Fellowship Programme//King Saud University/ ; MOBERC66 MOBTP198//European Regional Development Fund/ ; //LOEWE Zentrum AdRIA/ ; }, mesh = {*Eukaryota/genetics ; RNA, Ribosomal, 18S/genetics ; Databases, Genetic ; Databases, Nucleic Acid ; Animals ; Genes, rRNA/genetics ; Phylogeny ; }, abstract = {Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers-ITS1, ITS2, 18S V4-V5 and 28S D1-D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding-a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.}, } @article {pmid38864956, year = {2024}, author = {Barac, A and Vujovic, A and Peric, J and Tulic, I and Stojanovic, M and Stjepanovic, M}, title = {Rethinking Aspergillosis in the Era of Microbiota and Mycobiota.}, journal = {Mycopathologia}, volume = {189}, number = {4}, pages = {49}, pmid = {38864956}, issn = {1573-0832}, mesh = {Humans ; *Aspergillosis/microbiology/diagnosis/immunology ; *Mycobiome ; Aspergillus fumigatus/pathogenicity/genetics/immunology ; Aspergillus/genetics/pathogenicity ; Virulence Factors/genetics ; Microbiota ; Virulence ; Metagenomics ; Host-Pathogen Interactions/immunology ; }, abstract = {Aspergillosis encompasses a wide range of clinical conditions based on the interaction between Aspergillus and the host. It ranges from colonization to invasive aspergillosis. The human lung provides an entry door for Aspergillus. Aspergillus has virulence characteristics such as conidia, rapid growth at body temperature, and the production of specific proteins, carbohydrates, and secondary metabolites that allow A. fumigatus to infiltrate the lung's alveoli and cause invasive aspergillosis. Alveolar epithelial cells play an important role in both fungus clearance and immune cell recruitment via cytokine release. Although the innate immune system quickly clears conidia in immunocompetent hosts, A. fumigatus has evolved multiple virulence factors in order to escape immune response such as ROS detoxifying enzymes, the rodlet layer, DHN-melanin and toxins. Bacterial co-infections or interactions can alter the immune response, impact Aspergillus growth and virulence, enhance biofilm formation, confound diagnosis, and reduce treatment efficacy. The gut microbiome's makeup influences pulmonary immune responses generated by A. fumigatus infection and vice versa. The real-time PCR for Aspergillus DNA detection might be a particularly useful tool to diagnose pulmonary aspergillosis. Metagenomics analyses allow quick and easy detection and identification of a great variety of fungi in different clinical samples, although optimization is still required particularly for the use of NGS techniques. This review will analyze the current state of aspergillosis in light of recent discoveries in the microbiota and mycobiota.}, } @article {pmid38864950, year = {2024}, author = {Ortega-Kindica, RCMH and Padasas-Adalla, CS and Tabugo, SRM and Martinez, JGT and Amparado, OA and Moneva, CSO and Dalayap, R and Lomeli-Ortega, CO and Balcazar, JL}, title = {Shotgun Metagenomics Reveals Taxonomic and Functional Patterns of the Microbiome Associated with Barbour's Seahorse (Hippocampus barbouri).}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {26}, number = {4}, pages = {835-841}, pmid = {38864950}, issn = {1436-2236}, mesh = {Animals ; *Smegmamorpha/microbiology ; *Metagenomics ; *Skin/microbiology/metabolism ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/metabolism ; *Microbiota/genetics ; }, abstract = {This study aimed to investigate the taxonomic and functional patterns of the microbiome associated with Barbour's seahorse (Hippocampus barbouri) using a combination of shotgun metagenomics and bioinformatics. The analyses revealed that Pseudomonadota and Bacillota were the dominant phyla in the seahorse skin microbiome, whereas Pseudomonadota and, to a lesser extent, Bacillota and Bacteroidota were the dominant phyla in the seahorse gut microbiome. Several metabolic pathway categories were found to be enriched in the skin microbiome, including amino acid metabolism, carbohydrate metabolism, cofactor and vitamin metabolism, energy metabolism, nucleotide metabolism, as well as membrane transport, signal transduction, and cellular community-prokaryotes. In contrast, the gut microbiome exhibited enrichment in metabolic pathways associated with the metabolism of terpenoids and polyketides, biosynthesis of other secondary metabolites, xenobiotics biodegradation and metabolism, and quorum sensing. Additionally, although the relative abundance of bacteriocins in the skin and gut was slightly similar, notable differences were observed at the class level. Specifically, class I bacteriocins were found to be more abundant in the skin microbiome, whereas class III bacteriocins were more abundant in the gut microbiome. To the best of our knowledge, this study represents the first comprehensive examination of the taxonomic and functional patterns of the skin and gut microbiome in Barbour's seahorse. These findings can greatly contribute to a deeper understanding of the seahorse-associated microbiome, which can play a pivotal role in predicting and controlling bacterial infections, thereby contributing to the success of aquaculture and health-promoting initiatives.}, } @article {pmid38863033, year = {2024}, author = {Hu, M and Yang, W and Yan, R and Chi, J and Xia, Q and Yang, Y and Wang, Y and Sun, L and Li, P}, title = {Co-evolution of vaginal microbiome and cervical cancer.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {559}, pmid = {38863033}, issn = {1479-5876}, support = {SKY2023093，KJXW2019064//Suzhou science and technology plan project/ ; Grant No.2023T160328, Grant No.2023M731765//China Postdoctoral Science Foundation/ ; Grant No.23KJB320002//Major Basic Research Project of the Natural Science Foundation of the Jiangsu Higher Education Institutions/ ; }, mesh = {Humans ; Female ; *Uterine Cervical Neoplasms/microbiology/virology/genetics ; *Vagina/microbiology ; *Microbiota/genetics ; Mutation/genetics ; Middle Aged ; Adult ; Polymorphism, Single Nucleotide/genetics ; Case-Control Studies ; Disease Progression ; }, abstract = {BACKGROUND: Exploration of adaptive evolutionary changes at the genetic level in vaginal microbial communities during different stages of cervical cancer remains limited. This study aimed to elucidate the mutational profile of the vaginal microbiota throughout the progression of cervical disease and subsequently establish diagnostic models.

METHODS: This study utilized a metagenomic dataset consisting of 151 subjects classified into four categories: invasive cervical cancer (CC) (n = 42), cervical intraepithelial neoplasia (CIN) (n = 43), HPV-infected (HPVi) patients without cervical lesions (n = 34), and healthy controls (n = 32). The analysis focused on changes in microbiome abundance and extracted information on genetic variation. Consequently, comprehensive multimodal microbial signatures associated with CC, encompassing taxonomic alterations, mutation signatures, and enriched metabolic functional pathways, were identified. Diagnostic models for predicting CC were established considering gene characteristics based on single nucleotide variants (SNVs).

RESULTS: In this study, we screened and analyzed the abundances of 18 key microbial strains during CC progression. Additionally, 71,6358 non-redundant mutations were identified, predominantly consisting of SNVs that were further annotated into 25,773 genes. Altered abundances of SNVs and mutation types were observed across the four groups. Specifically, there were 9847 SNVs in the HPV-infected group and 14,892 in the CC group. Furthermore, two distinct mutation signatures corresponding to the benign and malignant groups were identified. The enriched metabolic pathways showed limited similarity with only two overlapping pathways among the four groups. HPVi patients exhibited active nucleotide biosynthesis, whereas patients with CC demonstrated a significantly higher abundance of signaling and cellular-associated protein families. In contrast, healthy controls showed a distinct enrichment in sugar metabolism. Moreover, biomarkers based on microbial SNV abundance displayed stronger diagnostic capability (cc.AUC = 0.87) than the species-level biomarkers (cc.AUC = 0.78). Ultimately, the integration of multimodal biomarkers demonstrated optimal performance for accurately identifying different cervical statuses (cc.AUC = 0.86), with an acceptable performance (AUC = 0.79) in the external testing set.

CONCLUSIONS: The vaginal microbiome exhibits specific SNV evolution in conjunction with the progression of CC, and serves as a specific biomarker for distinguishing between different statuses of cervical disease.}, } @article {pmid38862604, year = {2024}, author = {Tierney, BT and Kim, J and Overbey, EG and Ryon, KA and Foox, J and Sierra, MA and Bhattacharya, C and Damle, N and Najjar, D and Park, J and Garcia Medina, JS and Houerbi, N and Meydan, C and Wain Hirschberg, J and Qiu, J and Kleinman, AS and Al-Ghalith, GA and MacKay, M and Afshin, EE and Dhir, R and Borg, J and Gatt, C and Brereton, N and Readhead, BP and Beyaz, S and Venkateswaran, KJ and Wiseman, K and Moreno, J and Boddicker, AM and Zhao, J and Lajoie, BR and Scott, RT and Altomare, A and Kruglyak, S and Levy, S and Church, GM and Mason, CE}, title = {Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight.}, journal = {Nature microbiology}, volume = {9}, number = {7}, pages = {1661-1675}, pmid = {38862604}, issn = {2058-5276}, support = {R01 CA249054/CA/NCI NIH HHS/United States ; R01 MH117406/MH/NIMH NIH HHS/United States ; NNX14AH50G//NASA | Johnson Space Center (JSC)/ ; NNX16AO69A//NASA | Johnson Space Center (JSC)/ ; R01MH117406//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01 ES032638/ES/NIEHS NIH HHS/United States ; R01 AI151059/AI/NIAID NIH HHS/United States ; }, mesh = {*Space Flight ; Humans ; Longitudinal Studies ; *Microbiota/immunology ; *Metagenomics ; *Astronauts ; *Bacteria/classification/genetics/immunology ; Male ; Gene Expression Profiling ; Adult ; Middle Aged ; Female ; Transcriptome ; Multiomics ; }, abstract = {Maintenance of astronaut health during spaceflight will require monitoring and potentially modulating their microbiomes. However, documenting microbial shifts during spaceflight has been difficult due to mission constraints that lead to limited sampling and profiling. Here we executed a six-month longitudinal study to quantify the high-resolution human microbiome response to three days in orbit for four individuals. Using paired metagenomics and metatranscriptomics alongside single-nuclei immune cell profiling, we characterized time-dependent, multikingdom microbiome changes across 750 samples and 10 body sites before, during and after spaceflight at eight timepoints. We found that most alterations were transient across body sites; for example, viruses increased in skin sites mostly during flight. However, longer-term shifts were observed in the oral microbiome, including increased plaque-associated bacteria (for example, Fusobacteriota), which correlated with immune cell gene expression. Further, microbial genes associated with phage activity, toxin-antitoxin systems and stress response were enriched across multiple body sites. In total, this study reveals in-depth characterization of microbiome and immune response shifts experienced by astronauts during short-term spaceflight and the associated changes to the living environment, which can help guide future missions, spacecraft design and space habitat planning.}, } @article {pmid38862509, year = {2024}, author = {Overbey, EG and Ryon, K and Kim, J and Tierney, BT and Klotz, R and Ortiz, V and Mullane, S and Schmidt, JC and MacKay, M and Damle, N and Najjar, D and Matei, I and Patras, L and Garcia Medina, JS and Kleinman, AS and Wain Hirschberg, J and Proszynski, J and Narayanan, SA and Schmidt, CM and Afshin, EE and Innes, L and Saldarriaga, MM and Schmidt, MA and Granstein, RD and Shirah, B and Yu, M and Lyden, D and Mateus, J and Mason, CE}, title = {Collection of biospecimens from the inspiration4 mission establishes the standards for the space omics and medical atlas (SOMA).}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4964}, pmid = {38862509}, issn = {2041-1723}, support = {R01 ES032638/ES/NIEHS NIH HHS/United States ; R01 MH117406/MH/NIMH NIH HHS/United States ; }, mesh = {*Specimen Handling/standards ; Humans ; *Space Flight ; *Biological Specimen Banks/standards ; Exobiology ; *Preservation, Biological/standards ; Metagenomics/standards ; }, abstract = {The SpaceX Inspiration4 mission provided a unique opportunity to study the impact of spaceflight on the human body. Biospecimen samples were collected from four crew members longitudinally before (Launch: L-92, L-44, L-3 days), during (Flight Day: FD1, FD2, FD3), and after (Return: R + 1, R + 45, R + 82, R + 194 days) spaceflight, spanning a total of 289 days across 2021-2022. The collection process included venous whole blood, capillary dried blood spot cards, saliva, urine, stool, body swabs, capsule swabs, SpaceX Dragon capsule HEPA filter, and skin biopsies. Venous whole blood was further processed to obtain aliquots of serum, plasma, extracellular vesicles and particles, and peripheral blood mononuclear cells. In total, 2,911 sample aliquots were shipped to our central lab at Weill Cornell Medicine for downstream assays and biobanking. This paper provides an overview of the extensive biospecimen collection and highlights their processing procedures and long-term biobanking techniques, facilitating future molecular tests and evaluations.As such, this study details a robust framework for obtaining and preserving high-quality human, microbial, and environmental samples for aerospace medicine in the Space Omics and Medical Atlas (SOMA) initiative, which can aid future human spaceflight and space biology experiments.}, } @article {pmid38862069, year = {2024}, author = {Ni, H and Chan, BK and Ye, L and Wu, H and Heng, H and Xu, Q and Chen, K and Cheung, RY and Wang, H and Chan, EW and Li, F and Chen, S}, title = {Lowering mortality risk in CR-HvKP infection in intestinal immunohistological and microbiota restoration.}, journal = {Pharmacological research}, volume = {206}, number = {}, pages = {107254}, doi = {10.1016/j.phrs.2024.107254}, pmid = {38862069}, issn = {1096-1186}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Klebsiella Infections/drug therapy/immunology/mortality/microbiology ; *Klebsiella pneumoniae/drug effects ; *Rifampin/therapeutic use/pharmacology ; Male ; Zidovudine/therapeutic use ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Intestines/microbiology/pathology/drug effects/immunology ; Mice, Inbred C57BL ; Sepsis/drug therapy/microbiology/immunology/mortality ; Mice ; Immunity, Innate/drug effects ; }, abstract = {Gut damage during carbapenem-resistant and hypervirulent Klebsiella pneumoniae (CR-HvKP) infection is associated with a death risk. Understanding the mechanisms by which CR-HvKP causes intestinal damage and gut microbiota alteration, and the impact on immunity, is crucial for developing therapeutic strategies. This study investigated if gastrointestinal tract damage and disruption of gut microbiota induced by CR-HvKP infection undermined host immunity and facilitated multi-organ invasion of CR-HvKP; whether the therapeutic value of the rifampicin (RIF) and zidovudine (ZDV) combination was attributed to their ability to repair damages and restore host immunity was determined. A sepsis model was utilized to assess the intestinal pathological changes. Metagenomic analysis was performed to characterize the alteration of gut microbiota. The effects of the RIF and ZDV on suppressing inflammatory responses and improving immune functions and gut microbiota were evaluated by immunopathological and transcriptomic analyses. Rapid colonic damage occurred upon activation of the inflammation signaling pathways during lethal infections. Gut inflammation compromised host innate immunity and led to a significant decrease in probiotics abundance, including Bifidobacterium and Lactobacillus. Treatment with combination drugs significantly attenuated the inflammatory response, up-regulated immune cell differentiation signaling pathways, and promoted the abundance of Bifidobacterium (33.40 %). Consistently, supplementation of Bifidobacterium alone delayed the death in sepsis model. Gut inflammation and disrupted microbiota are key disease features of CR-HvKP infection but can be reversed by the RIF and ZDV drug combination. The finding that these drugs can restore host immunity through multiple mechanisms is novel and deserves further investigation of their clinical application potential.}, } @article {pmid38860825, year = {2024}, author = {Paillet, T and Lamy-Besnier, Q and Figueroa, C and Petit, M-A and Dugat-Bony, E}, title = {Dynamics of the viral community on the surface of a French smear-ripened cheese during maturation and persistence across production years.}, journal = {mSystems}, volume = {9}, number = {7}, pages = {e0020124}, pmid = {38860825}, issn = {2379-5077}, mesh = {*Cheese/microbiology/virology ; *Bacteriophages/genetics/isolation & purification ; Bacteria/virology/genetics/isolation & purification ; Microbiota ; Food Microbiology ; France ; Metagenomics ; Virome ; }, abstract = {The surface of smear-ripened cheeses constitutes a dynamic microbial ecosystem resulting from the successive development of different microbial groups such as lactic acid bacteria, fungi, and ripening bacteria. Recent studies indicate that a viral community, mainly composed of bacteriophages, also represents a common and substantial part of the cheese microbiome. However, the composition of this community, its temporal variations, and associations between bacteriophages and their hosts remain poorly characterized. Here, we studied a French smear-ripened cheese by both viral metagenomics and 16S metabarcoding approaches to assess both the succession of phages and bacterial communities on the cheese surface during cheese ripening and their temporal variations in ready-to-eat cheeses over the years of production. We observed a clear transition of the phage community structure during ripening with a decreased relative abundance of viral species (vOTUs) associated with Lactococcus phages, which were replaced by vOTUs associated with phages infecting ripening bacteria such as Brevibacterium, Glutamicibacter, Pseudoalteromonas, and Vibrio. The dynamics of the phage community was strongly associated with bacterial successions observed on the cheese surface. Finally, while some variations in the distribution of phages were observed in ready-to-eat cheeses produced at different dates spanning more than 4 years of production, the most abundant phages were detected throughout. This result revealed the long-term persistence of the dominant phages in the cheese production environment. Together, these findings offer novel perspectives on the ecology of bacteriophages in smear-ripened cheese and emphasize the significance of incorporating bacteriophages in the microbial ecology studies of fermented foods.IMPORTANCEThe succession of diverse microbial populations is critical for ensuring the production of high-quality cheese. We observed a temporal succession of phages on the surface of a smear-ripened cheese, with new phage communities showing up when ripening bacteria start covering this surface. Interestingly, the final phage community of this cheese is also consistent over large periods of time, as the same bacteriophages were found in cheese products from the same manufacturer made over 4 years. This research highlights the importance of considering these bacteriophages when studying the microbial life of fermented foods like cheese.}, } @article {pmid38860762, year = {2024}, author = {Li, Y and Xue, Y and Roy Chowdhury, T and Graham, DE and Tringe, SG and Jansson, JK and Taş, N}, title = {Genomic insights into redox-driven microbial processes for carbon decomposition in thawing Arctic soils and permafrost.}, journal = {mSphere}, volume = {9}, number = {7}, pages = {e0025924}, pmid = {38860762}, issn = {2379-5042}, support = {NGEE Arctic//U.S. Department of Energy (DOE)/ ; DE-AC0205CH11231//U.S. Department of Energy (DOE)/ ; 41871067//MOST | National Natural Science Foundation of China (NSFC)/ ; //China Scholarship Council (CSC)/ ; //U.S. Department of Energy (DOE)/ ; DE-AC06-76RL01830//DOE | SC | Pacific Northwest National Laboratory (PNNL)/ ; }, mesh = {*Permafrost/microbiology ; *Soil Microbiology ; Arctic Regions ; *Carbon/metabolism ; *Oxidation-Reduction ; *Soil/chemistry ; *Microbiota ; Climate Change ; Bacteria/genetics/metabolism/classification ; Metagenome ; Methane/metabolism ; Freezing ; }, abstract = {UNLABELLED: Climate change is rapidly transforming Arctic landscapes where increasing soil temperatures speed up permafrost thaw. This exposes large carbon stocks to microbial decomposition, possibly worsening climate change by releasing more greenhouse gases. Understanding how microbes break down soil carbon, especially under the anaerobic conditions of thawing permafrost, is important to determine future changes. Here, we studied the microbial community dynamics and soil carbon decomposition potential in permafrost and active layer soils under anaerobic laboratory conditions that simulated an Arctic summer thaw. The microbial and viral compositions in the samples were analyzed based on metagenomes, metagenome-assembled genomes, and metagenomic viral contigs (mVCs). Following the thawing of permafrost, there was a notable shift in microbial community structure, with fermentative Firmicutes and Bacteroidota taking over from Actinobacteria and Proteobacteria over the 60-day incubation period. The increase in iron and sulfate-reducing microbes had a significant role in limiting methane production from thawed permafrost, underscoring the competition within microbial communities. We explored the growth strategies of microbial communities and found that slow growth was the major strategy in both the active layer and permafrost. Our findings challenge the assumption that fast-growing microbes mainly respond to environmental changes like permafrost thaw. Instead, they indicate a common strategy of slow growth among microbial communities, likely due to the thermodynamic constraints of soil substrates and electron acceptors, and the need for microbes to adjust to post-thaw conditions. The mVCs harbored a wide range of auxiliary metabolic genes that may support cell protection from ice formation in virus-infected cells.

IMPORTANCE: As the Arctic warms, thawing permafrost unlocks carbon, potentially accelerating climate change by releasing greenhouse gases. Our research delves into the underlying biogeochemical processes likely mediated by the soil microbial community in response to the wet and anaerobic conditions, akin to an Arctic summer thaw. We observed a significant shift in the microbial community post-thaw, with fermentative bacteria like Firmicutes and Bacteroidota taking over and switching to different fermentation pathways. The dominance of iron and sulfate-reducing bacteria likely constrained methane production in the thawing permafrost. Slow-growing microbes outweighed fast-growing ones, even after thaw, upending the expectation that rapid microbial responses to dominate after permafrost thaws. This research highlights the nuanced and complex interactions within Arctic soil microbial communities and underscores the challenges in predicting microbial response to environmental change.}, } @article {pmid38857812, year = {2024}, author = {Yi, Y and Liang, L and de Jong, A and Kuipers, OP}, title = {A systematic comparison of natural product potential, with an emphasis on RiPPs, by mining of bacteria of three large ecosystems.}, journal = {Genomics}, volume = {116}, number = {4}, pages = {110880}, doi = {10.1016/j.ygeno.2024.110880}, pmid = {38857812}, issn = {1089-8646}, mesh = {*Bacteria/metabolism/genetics/classification ; *Multigene Family ; *Biological Products/metabolism ; Peptides/metabolism/genetics ; Protein Processing, Post-Translational ; Metagenome ; Bacterial Proteins/genetics/metabolism ; Ecosystem ; Genome, Bacterial ; Microbiota ; Polyketides/metabolism ; }, abstract = {The implementation of several global microbiome studies has yielded extensive insights into the biosynthetic potential of natural microbial communities. However, studies on the distribution of several classes of ribosomally synthesized and post-translationally modified peptides (RiPPs), non-ribosomal peptides (NRPs) and polyketides (PKs) in different large microbial ecosystems have been very limited. Here, we collected a large set of metagenome-assembled bacterial genomes from marine, freshwater and terrestrial ecosystems to investigate the biosynthetic potential of these bacteria. We demonstrate the utility of public dataset collections for revealing the different secondary metabolite biosynthetic potentials among these different living environments. We show that there is a higher occurrence of RiPPs in terrestrial systems, while in marine systems, we found relatively more terpene-, NRP-, and PK encoding gene clusters. Among the many new biosynthetic gene clusters (BGCs) identified, we analyzed various Nif-11-like and nitrile hydratase leader peptide (NHLP) containing gene clusters that would merit further study, including promising products, such as mersacidin-, LAP- and proteusin analogs. This research highlights the significance of public datasets in elucidating the biosynthetic potential of microbes in different living environments and underscores the wide bioengineering opportunities within the RiPP family.}, } @article {pmid38857786, year = {2024}, author = {Zhou, Y and Guo, L and Xiao, T and Chen, Y and Lv, T and Wang, Y and Zhang, S and Cai, H and Chi, X and Kong, X and Zhou, K and Shen, P and Xiao, Y}, title = {Characterization and dynamics of intestinal microbiota in patients with Clostridioides difficile colonization and infection.}, journal = {Microbes and infection}, volume = {26}, number = {8}, pages = {105373}, doi = {10.1016/j.micinf.2024.105373}, pmid = {38857786}, issn = {1769-714X}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Clostridium Infections/microbiology ; *Clostridioides difficile ; Female ; Male ; Middle Aged ; Dysbiosis/microbiology ; Aged ; Bacteria/classification/isolation & purification/genetics/metabolism ; Adult ; Metagenomics ; Feces/microbiology ; Fatty Acids, Volatile/metabolism ; Bacteroidetes/isolation & purification ; Aged, 80 and over ; }, abstract = {Gut microbiota dysbiosis increases the susceptibility to Clostridioides difficile infection (CDI). In this study, we monitored C. difficile colonization (CDC) patients from no CDC status (CDN) to CDC status (CDCp) and CDI patients from asymptomatic status before CDI (PRECDI), CDI status (ONCDI), to asymptomatic status after CDI (POSTCDI). Based on metagenomic sequencing, we aimed to investigate the interaction pattern between gut microbiota and C. difficile. There was no significant difference of microbiota diversity between CDN and CDCp. In CDCp, Bacteroidetes and short-chain fatty acid (SCFA)-producing bacteria increased, with a positive correlation between SCFA-producing bacteria and C. difficile colonization. Compared with PRECDI, ONCDI and POSTCDI showed a significant decrease in microbiota diversity, particularly in Bacteroidetes and SCFA-producing bacteria, with a positive correlation between opportunistic pathogen and C. difficile. Fatty acid metabolism, and amino acid biosynthesis were enriched in CDN, CDCp, and PRECDI, while bile secretion was enriched in ONCDI and POSTCDI. Microbiota and metabolic pathways interaction networks in CDN and CDCp were more complex, particularly pathways in fatty acid and bile acid metabolism. Increasing of Bacteroidetes and SCFA-producing bacteria, affecting amino acid and fatty acid metabolism, is associated with colonization resistance to C. difficile and inhibiting the development of CDI.}, } @article {pmid38856205, year = {2024}, author = {Krausfeldt, LE and Shmakova, E and Lee, HW and Mazzei, V and Loftin, KA and Smith, RP and Karwacki, E and Fortman, PE and Rosen, BH and Urakawa, H and Dadlani, M and Colwell, RR and Lopez, JV}, title = {Microbial diversity, genomics, and phage-host interactions of cyanobacterial harmful algal blooms.}, journal = {mSystems}, volume = {9}, number = {7}, pages = {e0070923}, pmid = {38856205}, issn = {2379-5077}, support = {W912HZ-19-2-0014//DOD | USA | U.S. Army Corps of Engineers (USACE)/ ; //USGS Environmental Health Program/ ; }, mesh = {*Cyanobacteria/virology/genetics ; *Harmful Algal Bloom ; *Bacteriophages/genetics ; RNA, Ribosomal, 16S/genetics ; Microbiota/genetics ; Metagenome ; Lakes/microbiology/virology ; Genomics ; Biodiversity ; }, abstract = {UNLABELLED: The occurrence of cyanobacterial harmful algal blooms (cyanoHABs) is related to their physical and chemical environment. However, less is known about their associated microbial interactions and processes. In this study, cyanoHABs were analyzed as a microbial ecosystem, using 1 year of 16S rRNA sequencing and 70 metagenomes collected during the bloom season from Lake Okeechobee (Florida, USA). Biogeographical patterns observed in microbial community composition and function reflected ecological zones distinct in their physical and chemical parameters that resulted in bloom "hotspots" near major lake inflows. Changes in relative abundances of taxa within multiple phyla followed increasing bloom severity. Functional pathways that correlated with increasing bloom severity encoded organic nitrogen and phosphorus utilization, storage of nutrients, exchange of genetic material, phage defense, and protection against oxidative stress, suggesting that microbial interactions may promote cyanoHAB resilience. Cyanobacterial communities were highly diverse, with picocyanobacteria ubiquitous and oftentimes most abundant, especially in the absence of blooms. The identification of novel bloom-forming cyanobacteria and genomic comparisons indicated a functionally diverse cyanobacterial community with differences in its capability to store nitrogen using cyanophycin and to defend against phage using CRISPR and restriction-modification systems. Considering blooms in the context of a microbial ecosystem and their interactions in nature, physiologies and interactions supporting the proliferation and stability of cyanoHABs are proposed, including a role for phage infection of picocyanobacteria. This study displayed the power of "-omics" to reveal important biological processes that could support the effective management and prediction of cyanoHABs.

IMPORTANCE: Cyanobacterial harmful algal blooms pose a significant threat to aquatic ecosystems and human health. Although physical and chemical conditions in aquatic systems that facilitate bloom development are well studied, there are fundamental gaps in the biological understanding of the microbial ecosystem that makes a cyanobacterial bloom. High-throughput sequencing was used to determine the drivers of cyanobacteria blooms in nature. Multiple functions and interactions important to consider in cyanobacterial bloom ecology were identified. The microbial biodiversity of blooms revealed microbial functions, genomic characteristics, and interactions between cyanobacterial populations that could be involved in bloom stability and more coherently define cyanobacteria blooms. Our results highlight the importance of considering cyanobacterial blooms as a microbial ecosystem to predict, prevent, and mitigate them.}, } @article {pmid38854849, year = {2024}, author = {Mahar, JE and Wille, M and Harvey, E and Moritz, CC and Holmes, EC}, title = {The diverse liver viromes of Australian geckos and skinks are dominated by hepaciviruses and picornaviruses and reflect host taxonomy and habitat.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {veae044}, pmid = {38854849}, issn = {2057-1577}, abstract = {Lizards have diverse ecologies and evolutionary histories, and represent a promising group to explore how hosts shape virome structure and virus evolution. Yet, little is known about the viromes of these animals. In Australia, squamates (lizards and snakes) comprise the most diverse order of vertebrates, and Australia hosts the highest diversity of lizards globally, with the greatest breadth of habitat use. We used meta-transcriptomic sequencing to determine the virome of nine co-distributed, tropical lizard species from three taxonomic families in Australia and analyzed these data to identify host traits associated with viral abundance and diversity. We show that lizards carry a large diversity of viruses, identifying more than thirty novel, highly divergent vertebrate-associated viruses. These viruses were from nine viral families, including several that contain well known pathogens, such as the Flaviviridae, Picornaviridae, Bornaviridae, Iridoviridae, and Rhabdoviridae. Members of the Flaviviridae were particularly abundant across species sampled here, largely belonging to the genus Hepacivirus: fourteen novel hepaciviruses were identified, broadening the known diversity of this group and better defining its evolution by uncovering new reptilian clades. The evolutionary histories of the viruses studied here frequently aligned with the biogeographic and phylogenetic histories of the hosts, indicating that exogenous viruses may help infer host evolutionary history if sampling is strategic and sampling density high enough. Notably, analysis of alpha and beta diversity revealed that virome composition and richness in the animals sampled here was shaped by host taxonomy and habitat. In sum, we identified a diverse range of reptile viruses that broadly contributes to our understanding of virus-host ecology and evolution.}, } @article {pmid38852447, year = {2024}, author = {Dong, S and Wu, S and Li, L and Hao, F and Wu, J and Liao, Z and Wang, J and Zhong, R and Wei, H and Fang, X}, title = {Alleviation of lipid metabolic dysfunction through regulation of intestinal bacteriophages and bacteria by green tea polyphenols in Ob/Ob mice.}, journal = {Food chemistry}, volume = {456}, number = {}, pages = {139988}, doi = {10.1016/j.foodchem.2024.139988}, pmid = {38852447}, issn = {1873-7072}, mesh = {Animals ; Mice ; *Polyphenols/pharmacology/administration & dosage/metabolism/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Bacteriophages/metabolism ; *Tea/chemistry ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Male ; *Lipid Metabolism/drug effects ; Humans ; Mice, Obese ; Obesity/metabolism/drug therapy/physiopathology/therapy/microbiology ; Mice, Inbred C57BL ; Intestines/microbiology ; Plant Extracts/pharmacology/administration & dosage ; Diet, High-Fat/adverse effects ; }, abstract = {Green tea polyphenols (GTP) have been shown to ameliorate lipid metabolic disorders by regulating intestinal bacteria. Given the significant role of intestinal bacteriophages in shaping the gut microbiota, this study investigates GTP's influence on gut bacteriophage-bacteria interactions and lipid metabolism using metagenomics and metabonomics. The research results indicated that GTP significantly reduced body weight, serum triglycerides, leptin, insulin resistance, interleukin-6, and TNF-α levels while increasing adiponectin in ob/ob mice fed high-fat diet, aiding intestinal repair. GTP improved gut health by decreasing Enterobacter, Siphoviridae and Enterobacteria_phage_sfv, increasing Bifidobacterium and intestinal metabolites SCFA and hippuric acid. Correlation analysis showed negative correlations between Enterobacter sp. 50,588,862 and Enterobacteria_phages, Shigella_phages with 4-hydroxyphenylpyruvate and hippuric acid. Bifidobacterium choerinum and Bifidobacterium sp. AGR2158 were positively correlated with fatty acids and bile acids. In conclusion, GTP reduced fat accumulation and inflammation, enhanced gut barrier function in obese mice, closely associated with changes in the gut bacteriophage community.}, } @article {pmid38852299, year = {2024}, author = {Herruzo-Ruiz, AM and Trombini, C and Moreno-Garrido, I and Blasco, J and Alhama, J and Michán, C}, title = {Ions and nanoparticles of Ag and/or Cd metals in a model aquatic microcosm: Effects on the abundance, diversity and functionality of the sediment bacteriome.}, journal = {Marine pollution bulletin}, volume = {204}, number = {}, pages = {116525}, doi = {10.1016/j.marpolbul.2024.116525}, pmid = {38852299}, issn = {1879-3363}, mesh = {*Silver/toxicity ; *Geologic Sediments/chemistry/microbiology ; *Water Pollutants, Chemical/analysis ; *Cadmium/analysis ; *Microbiota/drug effects ; *Metal Nanoparticles/toxicity ; Bacteria ; Ions ; RNA, Ribosomal, 16S ; Biodiversity ; }, abstract = {Metals can be adsorbed on particulate matter, settle in sediments and cause alterations in aquatic environments. This study assesses the effect of Ag and/or Cd, both in ionic and nanoparticle (NP) forms, on the microbiome of sediments. For that purpose, aquatic controlled-microcosm experiments were exposed to an environmentally relevant and at tenfold higher doses of each form of the metals. Changes in the bacteriome were inferred by 16S rDNA sequencing. Ionic Ag caused a significant decrease of several bacterial families, whereas the effect was opposite when mixed with Cd, e.g., Desulfuromonadaceae family; in both cases, the bacteriome functionalities were greatly affected, particularly the nitrogen and sulfur metabolism. Compared to ionic forms, metallic NPs produced hardly any change in the abundance of microbial families, although the α-biodiversity of the bacteriome was reduced, and the functionality altered, when exposed to the NPs´ mixture. Our goal is to understand how metals, in different forms and combinations, released into the environment may endanger the health of aquatic ecosystems. This work may help to understand how aquatic metal pollution alters the structure and functionality of the microbiome and biogeochemical cycles, and how these changes can be addressed.}, } @article {pmid38851693, year = {2024}, author = {Rubio Garcia, E and Casadellà, M and Parera, M and Vila, J and Paredes, R and Noguera-Julian, M}, title = {Gut resistome linked to sexual preference and HIV infection.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {201}, pmid = {38851693}, issn = {1471-2180}, support = {847943 (MISTRAL)//European Union's Horizon 2020 Research and Innovation/ ; 847943 (MISTRAL)//European Union's Horizon 2020 Research and Innovation/ ; 847943 (MISTRAL)//European Union's Horizon 2020 Research and Innovation/ ; 847943 (MISTRAL)//European Union's Horizon 2020 Research and Innovation/ ; 847943 (MISTRAL)//European Union's Horizon 2020 Research and Innovation/ ; 847943 (MISTRAL)//European Union's Horizon 2020 Research and Innovation/ ; }, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; Bacteria/genetics/classification/drug effects/isolation & purification ; Dysbiosis/microbiology ; Feces/microbiology/virology ; *Gastrointestinal Microbiome/genetics ; *HIV Infections/microbiology/virology/complications ; HIV-1/genetics/drug effects ; Homosexuality, Male ; Metagenomics ; Prevotella/genetics/isolation & purification ; Sexual Behavior ; Spain ; }, abstract = {BACKGROUND: People living with HIV (PLWH) are at increased risk of acquisition of multidrug resistant organisms due to higher rates of predisposing factors. The gut microbiome is the main reservoir of the collection of antimicrobial resistance determinants known as the gut resistome. In PLWH, changes in gut microbiome have been linked to immune activation and HIV-1 associated complications. Specifically, gut dysbiosis defined by low microbial gene richness has been linked to low Nadir CD4 + T-cell counts. Additionally, sexual preference has been shown to strongly influence gut microbiome composition in PLWH resulting in different Prevotella or Bacteroides enriched enterotypes, in MSM (men-who-have-sex-with-men) or no-MSM, respectively. To date, little is known about gut resistome composition in PLWH due to the scarcity of studies using shotgun metagenomics. The present study aimed to detect associations between different microbiome features linked to HIV-1 infection and gut resistome composition.

RESULTS: Using shotgun metagenomics we characterized the gut resistome composition of 129 HIV-1 infected subjects showing different HIV clinical profiles and 27 HIV-1 negative controls from a cross-sectional observational study conducted in Barcelona, Spain. Most no-MSM showed a Bacteroides-enriched enterotype and low microbial gene richness microbiomes. We did not identify differences in resistome diversity and composition according to HIV-1 infection or immune status. However, gut resistome was more diverse in MSM group, Prevotella-enriched enterotype and gut micorbiomes with high microbial gene richness compared to no-MSM group, Bacteroides-enriched enterotype and gut microbiomes with low microbial gene richness. Additionally, gut resistome beta-diversity was different according to the defined groups and we identified a set of differentially abundant antimicrobial resistance determinants based on the established categories.

CONCLUSIONS: Our findings reveal a significant correlation between gut resistome composition and various host variables commonly associated with gut microbiome, including microbiome enterotype, microbial gene richness, and sexual preference. These host variables have been previously linked to immune activation and lower Nadir CD4 + T-Cell counts, which are prognostic factors of HIV-related comorbidities. This study provides new insights into the relationship between antibiotic resistance and clinical characteristics of PLWH.}, } @article {pmid38851338, year = {2024}, author = {Liu, Y and Wang, Y and Wei, F and Chai, L and Wang, H}, title = {Gut microbiota-bile acid crosstalk contributes to intestinal damage after nitrate exposure in Bufo gargarizans tadpoles.}, journal = {The Science of the total environment}, volume = {943}, number = {}, pages = {173795}, doi = {10.1016/j.scitotenv.2024.173795}, pmid = {38851338}, issn = {1879-1026}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Larva/drug effects ; *Nitrates/toxicity ; *Water Pollutants, Chemical/toxicity ; *Bile Acids and Salts/metabolism ; *Bufonidae ; Intestines/drug effects/microbiology ; }, abstract = {Bile acids (BAs) are amphipathic steroid acids whose production and diversity depend on both host and microbial metabolism. Nitrate (NO3[-]) is a widespread pollutant in aquatic ecosystems, which can cause rapid changes in microbial community structure and function. However, the effect of gut microbiota reshaped by nitrate‑nitrogen (NO3-N) on BAs profiles remains unclarified. To test this, intestinal targeted BAs metabolomics and fecal metagenomic sequencing were performed on Bufo gargarizans tadpoles treated with different concentrations of NO3-N. NO3-N exposure induced a reduction in the abundance of microbiota with bile acid-inducible enzymes (BAIs) and/or hydroxysteroid dehydrogenases (HSDHs), thus inhibiting the conversion of primary BAs to secondary BAs. Inhibition of BAs biotransformation decreased protective hydrophilic BAs (UDCA) and increased toxic hydrophobic BAs (CA and CDCA), which may contribute to intestinal histopathological damage. Moreover, we found that NO3-N treatment increased microbial virulence factors and decreased Glycoside hydrolases, further highlighting the deleterious risk of NO3-N. Overall, this study shed light on the complex interactions of NO3-N, gut microbiota, and BAs, and emphasized the hazardous effects of NO3-N pollution on the health of amphibians.}, } @article {pmid38851232, year = {2024}, author = {Alemu, BK and Lee, MW and Leung, MBW and Lee, WF and Wang, Y and Wang, CC and Lau, SL}, title = {Preventive effect of prenatal maternal oral probiotic supplementation on neonatal jaundice (POPS Study): A protocol for the randomised double-blind placebo-controlled clinical trial.}, journal = {BMJ open}, volume = {14}, number = {6}, pages = {e083641}, pmid = {38851232}, issn = {2044-6055}, mesh = {Adult ; Female ; Humans ; Infant, Newborn ; Pregnancy ; Bilirubin/blood ; Dietary Supplements ; Double-Blind Method ; Gastrointestinal Microbiome/drug effects ; Hong Kong ; *Jaundice, Neonatal/prevention & control ; Prenatal Care/methods ; *Probiotics/administration & dosage/therapeutic use ; Randomized Controlled Trials as Topic ; }, abstract = {INTRODUCTION: Neonatal jaundice is a common and life-threatening health problem in neonates due to overaccumulation of circulating unconjugated bilirubin. Gut flora has a potential influence on bilirubin metabolism. The infant gut microbiome is commonly copied from the maternal gut. During pregnancy, due to changes in dietary habits, hormones and body weight, maternal gut dysbiosis is common, which can be stabilised by probiotics supplementation. However, whether probiotic supplements can reach the baby through the mother and reduce the incidence of neonatal jaundice has not been studied yet. Therefore, we aim to evaluate the effect of prenatal maternal probiotic supplementation on the incidence of neonatal jaundice.

METHODS AND ANALYSIS: This is a randomised double-blind placebo-controlled clinical trial among 94 pregnant women (47 in each group) in a tertiary hospital in Hong Kong. Voluntary eligible participants will be recruited between 28 and 35 weeks of gestation. Computer-generated randomisation and allocation to either the intervention or control group will be carried out. Participants will take either one sachet of Vivomixx (450 billion colony-forming units per sachet) or a placebo per day until 1 week post partum. Neither the study participants nor researchers will know the randomisation and allocation. The intervention will be initiated at 36 weeks of gestation. Neonatal bilirubin level will be measured to determine the primary outcome (hyperbilirubinaemia) while the metagenomic microbiome profile of breast milk and maternal and infant stool samples as well as pregnancy outcomes will be secondary outcomes. Binary logistic and linear regressions will be carried out to assess the association of the microbiome data with different clinical outcomes.

ETHICS AND DISSEMINATION: Ethics approval is obtained from the Joint CUHK-NTEC Clinical Research Ethics Committee, Hong Kong (CREC Ref: 2023.100-T). Findings will be published in peer-reviewed journals and presented at international conferences.

TRIAL REGISTRATION NUMBER: NCT06087874.}, } @article {pmid38851175, year = {2024}, author = {Li, L and Flores, M and Salvador, A and Belloch, C}, title = {Impact of paprika and dextrose addition on dry cured loins microbiota and its effect on aroma development.}, journal = {International journal of food microbiology}, volume = {421}, number = {}, pages = {110782}, doi = {10.1016/j.ijfoodmicro.2024.110782}, pmid = {38851175}, issn = {1879-3460}, mesh = {*Volatile Organic Compounds/analysis/pharmacology ; *Odorants/analysis ; *Glucose/metabolism ; *Bacteria/classification/drug effects/genetics/growth & development ; *Microbiota/drug effects ; Humans ; Fungi/classification/drug effects/growth & development ; Amino Acids/metabolism ; Food Microbiology ; }, abstract = {The impact of paprika and dextrose addition on the surface of dry cured loins was analysed attending to differences in microbiota composition and aroma profile. Three different types of loins containing either dextrose (D), paprika (P) or a mixture of dextrose and paprika (DP) were manufactured. The loins were characterized using physic-chemical parameters, free amino acids, volatile compounds and aroma sensorial analysis, as well as applying microbiological counts and metagenomics of the 16S rRNA gene and its rDNA region. The analysis of volatile compounds clearly distinguished all loins, whereas the total content of free amino acids only separated P from D and DP loins. The main sensory differences were linked to paprika addition, which increased the perception of paprika and smoky odors as well as cured, savoury and cheesy notes. Microbial counts analysis could not differentiate between the three loin types; however, metagenomics analysis revealed clear differences in key bacterial and fungal genera among the three loins. Paprika addition favoured dominance of Latilactobacillus in the microbiota of P loins. On the contrary, dextrose addition caused the dominance of Staphylococcus in the microbiota of D loins. In DP loins, both genera were similarly represented in the bacterial community. Regarding fungi, large differences could be observed within the P and D loins, whereas the proportion of Debaryomyces in DP loins increased. The microbiota composition of DP loins controlled the lipid oxidation phenomenon, reducing the generation of derived volatiles producing rancid notes and increase the volatile compounds derived from amino acids such as branched aldehydes, pyrazines and pyrroles, providing particular aroma notes to the loins.}, } @article {pmid38850944, year = {2024}, author = {Han, H and Song, P and Jiang, Y and Fan, J and Khan, A and Liu, P and Mašek, O and Li, X}, title = {Biochar immobilized hydrolase degrades PET microplastics and alleviates the disturbance of soil microbial function via modulating nitrogen and phosphorus cycles.}, journal = {Journal of hazardous materials}, volume = {474}, number = {}, pages = {134838}, doi = {10.1016/j.jhazmat.2024.134838}, pmid = {38850944}, issn = {1873-3336}, mesh = {*Hydrolases/metabolism ; *Polyethylene Terephthalates/chemistry/metabolism ; *Soil Microbiology ; *Soil Pollutants/metabolism ; *Charcoal/chemistry ; *Phosphorus/metabolism/chemistry ; Microplastics/toxicity ; Biodegradation, Environmental ; Enzymes, Immobilized/metabolism/chemistry ; Nitrogen/metabolism ; Nitrogen Cycle ; Microbiota/drug effects ; Bacteria/genetics/metabolism/drug effects ; }, abstract = {Microplastics (MPs) pose an emerging threat to soil ecological function, yet effective solutions remain limited. This study introduces a novel approach using magnetic biochar immobilized PET hydrolase (MB-LCC-FDS) to degrade soil polyethylene terephthalate microplastics (PET-MPs). MB-LCC-FDS exhibited a 1.68-fold increase in relative activity in aquatic solutions and maintained 58.5 % residual activity after five consecutive cycles. Soil microcosm experiment amended with MB-LCC-FDS observed a 29.6 % weight loss of PET-MPs, converting PET into mono(2-hydroxyethyl) terephthalate (MHET). The generated MHET can subsequently be metabolized by soil microbiota to release terephthalic acid. The introduction of MB-LCC-FDS shifted the functional composition of soil microbiota, increasing the relative abundances of Microbacteriaceae and Skermanella while reducing Arthobacter and Vicinamibacteraceae. Metagenomic analysis revealed that MB-LCC-FDS enhanced nitrogen fixation, P-uptake and transport, and organic-P mineralization in PET-MPs contaminated soil, while weakening the denitrification and nitrification. Structural equation model indicated that changes in soil total carbon and Simpson index, induced by MB-LCC-FDS, were the driving factors for soil carbon and nitrogen transformation. Overall, this study highlights the synergistic role of magnetic biochar-immobilized PET hydrolase and soil microbiota in degrading soil PET-MPs, and enhances our understanding of the microbiome and functional gene responses to PET-MPs and MB-LCC-FDS in soil systems.}, } @article {pmid38850443, year = {2024}, author = {Korneev, A and Peshkova, M and Koteneva, P and Gundogdu, A and Timashev, P}, title = {Modulation of the skin and gut microbiome by psoriasis treatment: a comprehensive systematic review.}, journal = {Archives of dermatological research}, volume = {316}, number = {7}, pages = {374}, pmid = {38850443}, issn = {1432-069X}, support = {075-15-2021-951 (13.2251.21.0022)//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-951 (13.2251.21.0022)//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-951 (13.2251.21.0022)//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-951 (13.2251.21.0022)//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {*Psoriasis/microbiology/immunology/therapy ; Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Skin/microbiology ; *Probiotics/administration & dosage ; Phototherapy/methods ; Biological Products/therapeutic use ; Treatment Outcome ; Dermatologic Agents/therapeutic use/administration & dosage ; }, abstract = {The microbiome is intricately linked to the development of psoriasis, serving as both a potential cause and consequence of the psoriatic process. In recent years, there has been growing interest among psoriasis researchers in exploring how psoriasis treatments affect the skin and gut microbiome. However, a comprehensive evaluation of the impact of modern treatment approaches on the microbiome has yet to be conducted. In this systematic review, we analyze studies investigating alterations in the skin and gut microbiome resulting from psoriasis treatment, aiming to understand how current therapies influence the role of the microbiome in psoriasis development. The systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. PubMed and Scopus databases were searched for eligible studies from the inception dates until July 5, 2023. Study selection, data extraction, and risk of bias assessment were carried out by three overlapping pairs of reviewers, resolving any disagreements through consensus. Our analysis of various treatments, including biologics, conventional medications, phototherapy, and probiotics, reveals significant shifts in microbial diversity and abundance. Importantly, favorable treatment outcomes are associated with microbiota alterations that approach those observed in healthy individuals. While the studies reviewed exhibit varying degrees of bias, underscoring the need for further research, this review supports the potential of microbiome modulation as both a preventive and therapeutic strategy for psoriasis patients. The findings underscore the importance of personalized therapeutic approaches, recognizing the profound impact of treatment on the microbiome. They also highlight the promise of probiotics, prebiotics, and dietary interventions in psoriasis management.}, } @article {pmid38850348, year = {2025}, author = {Qian, SX and Bao, YF and Li, XY and Dong, Y and Zhang, XL and Wu, ZY}, title = {Multi-omics Analysis Reveals Key Gut Microbiota and Metabolites Closely Associated with Huntington's Disease.}, journal = {Molecular neurobiology}, volume = {62}, number = {1}, pages = {351-365}, pmid = {38850348}, issn = {1559-1182}, support = {2022KY1249//the Medical and Health Science and Technology Plan of Zhejiang Provincial Health Commission/ ; 2019C03039//Key Research and Development project of Zhejiang Province/ ; }, mesh = {Humans ; *Huntington Disease/microbiology/metabolism ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Metabolomics ; *Feces/microbiology ; Adult ; Metagenomics/methods ; Metabolome ; Aged ; Multiomics ; }, abstract = {Dysbiosis of the gut microbiota is closely associated with neurodegenerative diseases, including Huntington's disease (HD). Gut microbiome-derived metabolites are key factors in host-microbiome interactions. This study aimed to investigate the crucial gut microbiome and metabolites in HD and their correlations. Fecal and serum samples from 11 to 26 patients with HD, respectively, and 16 and 23 healthy controls, respectively, were collected. The fecal samples were used for shotgun metagenomics while the serum samples for metabolomics analysis. Integrated analysis of the metagenomics and metabolomics data was also conducted. Firmicutes, Bacteroidota, Proteobacteria, Uroviricota, Actinobacteria, and Verrucomicrobia were the dominant phyla. At the genus level, the presence of Bacteroides, Faecalibacterium, Parabacteroides, Alistipes, Dialister, and Christensenella was higher in HD patients, while the abundance of Lachnospira, Roseburia, Clostridium, Ruminococcus, Blautia, Butyricicoccus, Agathobaculum, Phocaeicola, Coprococcus, and Fusicatenibacter decreased. A total of 244 differential metabolites were identified and found to be enriched in the glycerophospholipid, nucleotide, biotin, galactose, and alpha-linolenic acid metabolic pathways. The AUC value from the integrated analysis (1) was higher than that from the analysis of the gut microbiota (0.8632). No significant differences were found in the ACE, Simpson, Shannon, Sobs, and Chao indexes between HD patients and controls. Our study determined crucial functional gut microbiota and potential biomarkers associated with HD pathogenesis, providing new insights into the role of the gut microbiota-brain axis in HD occurrence and development.}, } @article {pmid38849107, year = {2024}, author = {Sutanti, S and Sukenda, S and Widanarni, W and Alimuddin, A and Siti Aliah, R}, title = {Novel indigenous probiotic isolated from the healthy Pacific white shrimp Litopenaeus vannamei intestine in differing stages based on metagenomic and screening approaches.}, journal = {Fish & shellfish immunology}, volume = {151}, number = {}, pages = {109678}, doi = {10.1016/j.fsi.2024.109678}, pmid = {38849107}, issn = {1095-9947}, mesh = {Animals ; *Probiotics/pharmacology ; *Penaeidae/immunology/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Intestines/microbiology ; }, abstract = {The healthy intestinal microbiota of shrimp can be used as an indicator sustainable shrimp production. In this study, the integrated of metagenomic and screening probiotic approach from healthy Litopenaeus vannamei intestines in differing stages was studied to find novel indigenous probiotics. The microbiota from intestine of naupli, post larva (PL-10), juvenile (40 days), and adult (80 days) of Pacific white shrimp were characterized using a high-quality sequence of V3-V4 of 16S rRNA gene as the hypervariable region. The classifiable sequence number was detected in 54 phyla. Several core intestine bacteria, 35 of these 557 genera, have a prevalence >10 sequences across all samples. We found microbiota were different taxa in the difference stages, such as Proteobacteria, Firmicutes, and Bacteriodetes. The top 10 most abundant genera were Vibrio, Pseudoalteromonas, Spingomonas, Marinibacterium, Klebsiella, Alteromonas, Aestuaribacter, Shimia, Stenotrophomonas, and Ruegeria. Microbiota profiling based on a metagenomic approach was integrated with screening assessment for pathogenicity, antagonistic activity with Vibrio parahaemolyticus Vp5, antibiotic resistance, and digestive enzyme activities. As their assessment activity, several screened culturable bacteria were 19 of these 84 isolates. Three isolates with high activities (P < 0.05) found as novel indigenous probiotics were Shewanella algae A1, Shewanella algae A3, and Vibrio diabolicus UB3. Integrating metagenomic and screening methods was a new signature for the isolating novel indigenous probiotics in Pacific white shrimp.}, } @article {pmid38846353, year = {2024}, author = {Li, J and Xiong, A and Wang, J and Wu, X and Bai, L and Zhang, L and He, X and Li, G}, title = {Deciphering the microbial landscape of lower respiratory tract infections: insights from metagenomics and machine learning.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1385562}, pmid = {38846353}, issn = {2235-2988}, mesh = {Humans ; *Machine Learning ; *Metagenomics/methods ; Middle Aged ; *Respiratory Tract Infections/microbiology/virology ; Aged ; Male ; Female ; Adult ; *Bacteria/classification/genetics/isolation & purification ; *Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *High-Throughput Nucleotide Sequencing ; Young Adult ; Bronchiectasis/microbiology ; Aged, 80 and over ; Metagenome ; Adolescent ; Lung/microbiology/virology ; Hospitalization ; }, abstract = {BACKGROUND: Lower respiratory tract infections represent prevalent ailments. Nonetheless, current comprehension of the microbial ecosystems within the lower respiratory tract remains incomplete and necessitates further comprehensive assessment. Leveraging the advancements in metagenomic next-generation sequencing (mNGS) technology alongside the emergence of machine learning, it is now viable to compare the attributes of lower respiratory tract microbial communities among patients across diverse age groups, diseases, and infection types.

METHOD: We collected bronchoalveolar lavage fluid samples from 138 patients diagnosed with lower respiratory tract infections and conducted mNGS to characterize the lung microbiota. Employing various machine learning algorithms, we investigated the correlation of key bacteria in patients with concurrent bronchiectasis and developed a predictive model for hospitalization duration based on these identified key bacteria.

RESULT: We observed variations in microbial communities across different age groups, diseases, and infection types. In the elderly group, Pseudomonas aeruginosa exhibited the highest relative abundance, followed by Corynebacterium striatum and Acinetobacter baumannii. Methylobacterium and Prevotella emerged as the dominant genera at the genus level in the younger group, while Mycobacterium tuberculosis and Haemophilus influenzae were prevalent species. Within the bronchiectasis group, dominant bacteria included Pseudomonas aeruginosa, Haemophilus influenzae, and Klebsiella pneumoniae. Significant differences in the presence of Pseudomonas phage JBD93 were noted between the bronchiectasis group and the control group. In the group with concomitant fungal infections, the most abundant genera were Acinetobacter and Pseudomonas, with Acinetobacter baumannii and Pseudomonas aeruginosa as the predominant species. Notable differences were observed in the presence of Human gammaherpesvirus 4, Human betaherpesvirus 5, Candida albicans, Aspergillus oryzae, and Aspergillus fumigatus between the group with concomitant fungal infections and the bacterial group. Machine learning algorithms were utilized to select bacteria and clinical indicators associated with hospitalization duration, confirming the excellent performance of bacteria in predicting hospitalization time.

CONCLUSION: Our study provided a comprehensive description of the microbial characteristics among patients with lower respiratory tract infections, offering insights from various perspectives. Additionally, we investigated the advanced predictive capability of microbial community features in determining the hospitalization duration of these patients.}, } @article {pmid38845533, year = {2024}, author = {Shukla, R and Tsuchiya, Y and Behari, A and Ikoma, T and Nakamura, K and Kapoor, VK}, title = {Metagenomic Analysis of Biliary Microbial Flora in Patients with Gallbladder Cancer or Gallstones-Associated Chronic Cholecystitis.}, journal = {Cancer investigation}, volume = {42}, number = {6}, pages = {478-490}, doi = {10.1080/07357907.2024.2361305}, pmid = {38845533}, issn = {1532-4192}, mesh = {Humans ; *Gallbladder Neoplasms/microbiology ; *Cholecystitis/microbiology ; *Gallstones/microbiology ; Female ; Male ; *Metagenomics/methods ; Middle Aged ; Aged ; RNA, Ribosomal, 16S/genetics ; Chronic Disease ; Bacteria/genetics/classification/isolation & purification ; Microbiota ; Adult ; Dysbiosis/microbiology ; }, abstract = {Biliary dysbiosis is associated with gallbladder cancer (GBC). We aimed to look for biliary bacteria specifically detected in GBC patients. We used 16S rRNA-based metagenomic analysis to elucidate biliary microbiota in 30 GBC and 30 gallstones-associated chronic cholecystitis patients. Relative abundance of five genera, Streptococcus, Enterococcus, Halomonas, Escherichia and Caulobacter was significantly associated with GBC. Of 15-species, 7 were detected significantly higher in GBC, Streptococcus anginosus, Streptococcus constellatus, Streptococcus intermedius, Actinomyces bowdenii, Actinomyces israelii, Actinomyces gerencseriae, and Escherichia fergusonii were biosafety level-2 infectious bacteria; other 8 species were biosafety level-1 bacteria. These bacterial species may be involved in pathogenesis of GBC.}, } @article {pmid38845047, year = {2024}, author = {Zhang, K and He, C and Wang, L and Suo, L and Guo, M and Guo, J and Zhang, T and Xu, Y and Lei, Y and Liu, G and Qian, Q and Mao, Y and Kalds, P and Wu, Y and Cuoji, A and Yang, Y and Brugger, D and Gan, S and Wang, M and Wang, X and Zhao, F and Chen, Y}, title = {Compendium of 5810 genomes of sheep and goat gut microbiomes provides new insights into the glycan and mucin utilization.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {104}, pmid = {38845047}, issn = {2049-2618}, support = {2023-6-2-1//Young Talent Fund of Association for Science and Technology in Shaanxi, China/ ; 2022GD-TSLD-46//"Double-chain" project on livestock breeding/ ; XZ202101ZD0001N//Science and Technology Plan Projects of Tibet Autonomous Region/ ; CARS-39//Agriculture Research System of China/ ; CARS-39//Agriculture Research System of China/ ; 2022YFD1300203//National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Goats/microbiology ; Sheep/microbiology ; *Gastrointestinal Microbiome ; *Mucins/metabolism ; *Polysaccharides/metabolism ; *Bacteria/classification/genetics/metabolism ; *Feces/microbiology ; Metagenome ; Genome, Bacterial ; Metagenomics/methods ; Phylogeny ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Ruminant gut microbiota are critical in ecological adaptation, evolution, and nutrition utilization because it regulates energy metabolism, promotes nutrient absorption, and improves immune function. To study the functional roles of key gut microbiota in sheep and goats, it is essential to construct reference microbial gene catalogs and high-quality microbial genomes database.

RESULTS: A total of 320 fecal samples were collected from 21 different sheep and goat breeds, originating from 32 distinct farms. Metagenomic deep sequencing and binning assembly were utilized to construct a comprehensive microbial genome information database for the gut microbiota. We successfully generated the largest reference gene catalogs for gut microbiota in sheep and goats, containing over 162 million and 82 million nonredundant predicted genes, respectively, with 49 million shared nonredundant predicted genes and 1138 shared species. We found that the rearing environment has a greater impact on microbial composition and function than the host's species effect. Through subsequent assembly, we obtained 5810 medium- and high-quality metagenome-assembled genomes (MAGs), out of which 2661 were yet unidentified species. Among these MAGs, we identified 91 bacterial taxa that specifically colonize the sheep gut, which encode polysaccharide utilization loci for glycan and mucin degradation.

CONCLUSIONS: By shedding light on the co-symbiotic microbial communities in the gut of small ruminants, our study significantly enhances the understanding of their nutrient degradation and disease susceptibility. Our findings emphasize the vast potential of untapped resources in functional bacterial species within ruminants, further expanding our knowledge of how the ruminant gut microbiota recognizes and processes glycan and mucins. Video Abstract.}, } @article {pmid38844795, year = {2024}, author = {Wang, T and Shi, Z and Ren, H and Xu, M and Lu, J and Yang, F and Ye, C and Wu, K and Chen, M and Xu, X and Liu, D and Kong, L and Zheng, R and Zheng, J and Li, M and Xu, Y and Zhao, Z and Chen, Y and Yang, H and Wang, J and Ning, G and Li, J and Zhong, H and Bi, Y and Wang, W}, title = {Divergent age-associated and metabolism-associated gut microbiome signatures modulate cardiovascular disease risk.}, journal = {Nature medicine}, volume = {30}, number = {6}, pages = {1722-1731}, pmid = {38844795}, issn = {1546-170X}, support = {82370820//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82088102//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Middle Aged ; Aged ; *Cardiovascular Diseases/microbiology/epidemiology ; Female ; Male ; Adult ; Aged, 80 and over ; Aging ; Risk Factors ; Feces/microbiology ; Cohort Studies ; Age Factors ; Metagenome ; }, abstract = {Insight into associations between the gut microbiome with metabolism and aging is crucial for tailoring interventions to promote healthy longevity. In a discovery cohort of 10,207 individuals aged 40-93 years, we used 21 metabolic parameters to classify individuals into five clusters, termed metabolic multimorbidity clusters (MCs), that represent different metabolic subphenotypes. Compared to the cluster classified as metabolically healthy (MC1), clusters classified as 'obesity-related mixed' (MC4) and 'hyperglycemia' (MC5) exhibited an increased 11.1-year cardiovascular disease (CVD) risk by 75% (multivariable-adjusted hazard ratio (HR): 1.75, 95% confidence interval (CI): 1.43-2.14) and by 117% (2.17, 1.72-2.74), respectively. These associations were replicated in a second cohort of 9,061 individuals with a 10.0-year follow-up. Based on analysis of 4,491 shotgun fecal metagenomes from the discovery cohort, we found that gut microbial composition was associated with both MCs and age. Next, using 55 age-specific microbial species to capture biological age, we developed a gut microbial age (MA) metric, which was validated in four external cohorts comprising 4,425 metagenomic samples. Among individuals aged 60 years or older, the increased CVD risk associated with MC4 or MC5, as compared to MC1, MC2 or MC3, was exacerbated in individuals with high MA but diminished in individuals with low MA, independent of age, sex and other lifestyle and dietary factors. This pattern, in which younger MA appears to counteract the CVD risk attributable to metabolic dysfunction, implies a modulating role of MA in cardiovascular health for metabolically unhealthy older people.}, } @article {pmid38844487, year = {2024}, author = {Faleiros, CA and Nunes, AT and Gonçalves, OS and Alexandre, PA and Poleti, MD and Mattos, EC and Perna-Junior, F and Rodrigues, PHM and Fukumasu, H}, title = {Exploration of mobile genetic elements in the ruminal microbiome of Nellore cattle.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {13056}, pmid = {38844487}, issn = {2045-2322}, support = {2022/05541-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, mesh = {Animals ; Cattle ; *Rumen/microbiology ; *Interspersed Repetitive Sequences/genetics ; Metagenomics/methods ; Metagenome ; Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Bacteria/genetics/classification ; Genome, Bacterial ; Phylogeny ; }, abstract = {Metagenomics has made it feasible to elucidate the intricacies of the ruminal microbiome and its role in the differentiation of animal production phenotypes of significance. The search for mobile genetic elements (MGEs) has taken on great importance, as they play a critical role in the transfer of genetic material between organisms. Furthermore, these elements serve a dual purpose by controlling populations through lytic bacteriophages, thereby maintaining ecological equilibrium and driving the evolutionary progress of host microorganisms. In this study, we aimed to identify the association between ruminal bacteria and their MGEs in Nellore cattle using physical chromosomal links through the Hi-C method. Shotgun metagenomic sequencing and the proximity ligation method ProxiMeta were used to analyze DNA, getting 1,713,111,307 bp, which gave rise to 107 metagenome-assembled genomes from rumen samples of four Nellore cows maintained on pasture. Taxonomic analysis revealed that most of the bacterial genomes belonged to the families Lachnospiraceae, Bacteroidaceae, Ruminococcaceae, Saccharofermentanaceae, and Treponemataceae and mostly encoded pathways for central carbon and other carbohydrate metabolisms. A total of 31 associations between host bacteria and MGE were identified, including 17 links to viruses and 14 links to plasmids. Additionally, we found 12 antibiotic resistance genes. To our knowledge, this is the first study in Brazilian cattle that connect MGEs with their microbial hosts. It identifies MGEs present in the rumen of pasture-raised Nellore cattle, offering insights that could advance biotechnology for food digestion and improve ruminant performance in production systems.}, } @article {pmid38844407, year = {2024}, author = {Zhu, C and Zhang, C and Wang, S and Xun, Z and Zhang, D and Lan, Z and Zhang, L and Chao, J and Liang, Y and Pu, Z and Ning, C and Sang, X and Yang, X and Wang, H and Jiang, X and Zhao, H}, title = {Characterizations of multi-kingdom gut microbiota in immune checkpoint inhibitor-treated hepatocellular carcinoma.}, journal = {Journal for immunotherapy of cancer}, volume = {12}, number = {6}, pages = {}, pmid = {38844407}, issn = {2051-1426}, mesh = {Humans ; *Carcinoma, Hepatocellular/drug therapy/microbiology/immunology ; *Gastrointestinal Microbiome/drug effects ; *Liver Neoplasms/drug therapy/immunology/microbiology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Male ; Female ; Middle Aged ; Aged ; Bacteria/drug effects/classification ; Prospective Studies ; }, abstract = {BACKGROUND: The association between gut bacteria and the response to immune checkpoint inhibitors (ICI) in hepatocellular carcinoma (HCC) has been studied; however, multi-kingdom gut microbiome alterations and interactions in ICI-treated HCC cohorts are not fully understood.

METHODS: From November 2018 to April 2022, patients receiving ICI treatment for advanced HCC were prospectively enrolled. Herein, we investigated the multi-kingdom microbiota characterization of the gut microbiome, mycobiome, and metabolome using metagenomic, ITS2, and metabolomic data sets of 80 patients with ICI-treated HCC.

RESULTS: Our findings demonstrated that bacteria and metabolites differed significantly between the durable clinical benefit (DCB) and non-durable clinical benefit (NDB) groups, whereas the differences were smaller for fungi. The overall diversity of bacteria and fungi before treatment was higher in the DCB group than in the NDB group, and the difference in diversity began to change with the use of immunotherapy after 6-8 weeks. We also explored the alterations of gut microbes in the DCB and NDB groups, established 18 bacterial species models as predictive biomarkers for predicting whether immunotherapy is of sustained benefit (area under the curve=75.63%), and screened two species of bacteria (Actinomyces_sp_ICM47, and Senegalimassilia_anaerobia) and one metabolite (galanthaminone) as prognostic biomarkers for predicting survival in patients with HCC treated with ICI.

CONCLUSIONS: In this study, the status and characterization of the multi-kingdom microbiota, including gut bacteria, fungi, and their metabolites, were described by multiomics sequencing for the first time in patients with HCC treated with ICI. Our findings demonstrate the potential of bacterial taxa as predictive biomarkers of ICI clinical efficacy, and bacteria and their metabolites as prognostic biomarkers.}, } @article {pmid38844031, year = {2024}, author = {Zhuo, T and Yu, K and Chai, B and Tang, Q and Gao, X and Wang, J and He, L and Lei, X and Li, Y and Meng, Y and Wu, L and Chen, B}, title = {Microplastics increase the microbial functional potential of greenhouse gas emissions and water pollution in a freshwater lake: A metagenomic study.}, journal = {Environmental research}, volume = {257}, number = {}, pages = {119250}, doi = {10.1016/j.envres.2024.119250}, pmid = {38844031}, issn = {1096-0953}, mesh = {*Lakes/microbiology/chemistry ; *Metagenomics ; *Greenhouse Gases/analysis ; *Microplastics/toxicity ; *Water Pollutants, Chemical/analysis/toxicity ; Water Pollution/analysis ; Microbiota/drug effects ; Bacteria/genetics/drug effects/classification/metabolism ; }, abstract = {Aquatic ecosystems are being increasingly polluted by microplastics (MPs), which calls for an understanding of how MPs affect microbially driven biogenic element cycling in water environments. A 28-day incubation experiment was conducted using freshwater lake water added with three polymer types of MPs (i.e., polyethylene, polypropylene, polystyrene) separately or in combination at a concentration of 1 items/L. The effects of various MPs on microbial communities and functional genes related to carbon, nitrogen, phosphorus, and sulfur cycling were analyzed using metagenomics. Results showed that Sphingomonas and Novosphingobium, which were indicator taxa (genus level) in the polyethylene treatment group, made the largest functional contribution to biogenic element cycling. Following the addition of MPs, the relative abundances of genes related to methane oxidation (e.g., hdrD, frhB, accAB) and denitrification (napABC, nirK, norB) increased. These changes were accompanied by increased relative abundances of genes involved in organic phosphorus mineralization (e.g., phoAD) and sulfate reduction (cysHIJ), as well as decreased relative abundances of genes involved in phosphate transport (phnCDE) and the SOX system. Findings of this study underscore that MPs, especially polyethylene, increase the potential of greenhouse gas emissions (CO2, N2O) and water pollution (PO4[3-], H2S) in freshwater lakes at the functional gene level.}, } @article {pmid38843834, year = {2024}, author = {Santos-Júnior, CD and Torres, MDT and Duan, Y and Rodríguez Del Río, Á and Schmidt, TSB and Chong, H and Fullam, A and Kuhn, M and Zhu, C and Houseman, A and Somborski, J and Vines, A and Zhao, XM and Bork, P and Huerta-Cepas, J and de la Fuente-Nunez, C and Coelho, LP}, title = {Discovery of antimicrobial peptides in the global microbiome with machine learning.}, journal = {Cell}, volume = {187}, number = {14}, pages = {3761-3778.e16}, pmid = {38843834}, issn = {1097-4172}, support = {R35 GM138201/GM/NIGMS NIH HHS/United States ; }, mesh = {*Machine Learning ; *Antimicrobial Peptides/pharmacology/chemistry/genetics ; Humans ; *Microbiota ; Animals ; Anti-Bacterial Agents/pharmacology ; Mice ; Metagenome ; Bacteria/drug effects/genetics ; Gastrointestinal Microbiome/drug effects ; }, abstract = {Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machine-learning-based approach to predict antimicrobial peptides (AMPs) within the global microbiome and leverage a vast dataset of 63,410 metagenomes and 87,920 prokaryotic genomes from environmental and host-associated habitats to create the AMPSphere, a comprehensive catalog comprising 863,498 non-redundant peptides, few of which match existing databases. AMPSphere provides insights into the evolutionary origins of peptides, including by duplication or gene truncation of longer sequences, and we observed that AMP production varies by habitat. To validate our predictions, we synthesized and tested 100 AMPs against clinically relevant drug-resistant pathogens and human gut commensals both in vitro and in vivo. A total of 79 peptides were active, with 63 targeting pathogens. These active AMPs exhibited antibacterial activity by disrupting bacterial membranes. In conclusion, our approach identified nearly one million prokaryotic AMP sequences, an open-access resource for antibiotic discovery.}, } @article {pmid38841888, year = {2024}, author = {Bank, NC and Singh, V and McCourt, B and Burberry, A and Roberts, KD and Grubb, B and Rodriguez-Palacios, A}, title = {Antigenic operon fragmentation and diversification mechanism in Bacteroidota impacts gut metagenomics and pathobionts in Crohn's disease microlesions.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2350150}, pmid = {38841888}, issn = {1949-0984}, support = {R21 DK118373/DK/NIDDK NIH HHS/United States ; }, mesh = {*Operon ; Mice ; *Gastrointestinal Microbiome ; Animals ; Humans ; *Metagenomics ; *Crohn Disease/microbiology/genetics ; Bacteroidetes/genetics/classification ; Antigens, Bacterial/genetics ; Genome, Bacterial ; Enterobacteriaceae/genetics/classification ; }, abstract = {Comensal Bacteroidota (Bacteroidota) and Enterobacteriacea are often linked to gut inflammation. However, the causes for variability of pro-inflammatory surface antigens that affect gut commensal/opportunistic dualism in Bacteroidota remain unclear. By using the classical lipopolysaccharide/O-antigen 'rfb operon' in Enterobacteriaceae as a surface antigen model (5-rfb-gene-cluster rfbABCDX), and a recent rfbA-typing strategy for strain classification, we characterized the integrity and conservancy of the entire rfb operon in Bacteroidota. Through exploratory analysis of complete genomes and metagenomes, we discovered that most Bacteroidota have the rfb operon fragmented into nonrandom patterns of gene-singlets and doublets/triplets, termed 'rfb-gene-clusters', or rfb-'minioperons' if predicted as transcriptional. To reflect global operon integrity, contiguity, duplication, and fragmentation principles, we propose a six-category (infra/supra-numerary) cataloging system and a Global Operon Profiling System for bacteria. Mechanistically, genomic sequence analyses revealed that operon fragmentation is driven by intra-operon insertions of predominantly Bacteroides-DNA (thetaiotaomicron/fragilis) and likely natural selection in gut-wall specific micro-niches or micropathologies. Bacteroides-insertions, also detected in other antigenic operons (fimbriae), but not in operons deemed essential (ribosomal), could explain why Bacteroidota have fewer KEGG-pathways despite large genomes. DNA insertions, overrepresenting DNA-exchange-avid (Bacteroides) species, impact our interpretation of functional metagenomics data by inflating by inflating gene-based pathway inference and by overestimating 'extra-species' abundance. Of disease relevance, Bacteroidota species isolated from cavitating/cavernous fistulous tract (CavFT) microlesions in Crohn's Disease have supra-numerary fragmented operons, stimulate TNF-alpha from macrophages with low potency, and do not induce hyperacute peritonitis in mice compared to CavFT Enterobacteriaceae. The impact of 'foreign-DNA' insertions on pro-inflammatory operons, metagenomics, and commensalism/opportunism requires further studies to elucidate their potential for novel diagnostics and therapeutics, and to elucidate the role of co-existing pathobionts in Crohn's disease microlesions.}, } @article {pmid38840247, year = {2024}, author = {Hu, J and Chen, J and Nie, Y and Zhou, C and Hou, Q and Yan, X}, title = {Characterizing the gut phageome and phage-borne antimicrobial resistance genes in pigs.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {102}, pmid = {38840247}, issn = {2049-2618}, support = {32102499//National Natural Science Foundation of China/ ; 31925037//National Natural Science Foundation of China/ ; BX20190133//National Postdoctoral Program for Innovative Talents/ ; 2019M662671//Postdoctoral Science Foundation of China/ ; 2022CFB358//Natural Science Foundation of Hubei Province/ ; }, mesh = {Animals ; Swine ; *Bacteriophages/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Genome, Viral ; Bacteria/virology/genetics/classification ; Metagenome ; Virome/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: Mammalian intestine harbors a mass of phages that play important roles in maintaining gut microbial ecosystem and host health. Pig has become a common model for biomedical research and provides a large amount of meat for human consumption. However, the knowledge of gut phages in pigs is still limited.

RESULTS: Here, we investigated the gut phageome in 112 pigs from seven pig breeds using PhaBOX strategy based on the metagenomic data. A total of 174,897 non-redundant gut phage genomes were assembled from 112 metagenomes. A total of 33,487 gut phage genomes were classified and these phages mainly belonged to phage families such as Ackermannviridae, Straboviridae, Peduoviridae, Zierdtviridae, Drexlerviridae, and Herelleviridae. The gut phages in seven pig breeds exhibited distinct communities and the gut phage communities changed with the age of pig. These gut phages were predicted to infect a broad range of 212 genera of prokaryotes, such as Candidatus Hamiltonella, Mycoplasma, Colwellia, and Lactobacillus. The data indicated that broad KEGG and CAZy functions were also enriched in gut phages of pigs. The gut phages also carried the antimicrobial resistance genes (ARGs) and the most abundant antimicrobial resistance genotype was diaminopyrimidine resistance.

CONCLUSIONS: Our research delineates a landscape for gut phages in seven pig breeds and reveals that gut phages serve as a key reservoir of ARGs in pigs. Video Abstract.}, } @article {pmid38840214, year = {2024}, author = {Qiao, Y and Wang, Z and Sun, H and Guo, H and Song, Y and Zhang, H and Ruan, Y and Xu, Q and Huang, Q and Shen, Q and Ling, N}, title = {Synthetic community derived from grafted watermelon rhizosphere provides protection for ungrafted watermelon against Fusarium oxysporum via microbial synergistic effects.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {101}, pmid = {38840214}, issn = {2049-2618}, support = {31972506//National Natural Science Foundation of China/ ; 32302670//National Natural Science Foundation of China/ ; }, mesh = {*Citrullus/microbiology ; *Rhizosphere ; *Fusarium/genetics ; *Soil Microbiology ; *Plant Diseases/microbiology/prevention & control ; *Pseudomonas/genetics ; *Microbiota ; Disease Resistance ; Bacteria/classification/genetics/isolation & purification ; Plant Roots/microbiology ; }, abstract = {BACKGROUND: Plant microbiota contributes to plant growth and health, including enhancing plant resistance to various diseases. Despite remarkable progress in understanding diseases resistance in plants, the precise role of rhizosphere microbiota in enhancing watermelon resistance against soil-borne diseases remains unclear. Here, we constructed a synthetic community (SynCom) of 16 core bacterial strains obtained from the rhizosphere of grafted watermelon plants. We further simplified SynCom and investigated the role of bacteria with synergistic interactions in promoting plant growth through a simple synthetic community.

RESULTS: Our results demonstrated that the SynCom significantly enhanced the growth and disease resistance of ungrafted watermelon grown in non-sterile soil. Furthermore, analysis of the amplicon and metagenome data revealed the pivotal role of Pseudomonas in enhancing plant health, as evidenced by a significant increase in the relative abundance and biofilm-forming pathways of Pseudomonas post-SynCom inoculation. Based on in vitro co-culture experiments and bacterial metabolomic analysis, we selected Pseudomonas along with seven other members of the SynCom that exhibited synergistic effects with Pseudomonas. It enabled us to further refine the initially constructed SynCom into a simplified SynCom comprising the eight selected bacterial species. Notably, the plant-promoting effects of simplified SynCom were similar to those of the initial SynCom. Furthermore, the simplified SynCom protected plants through synergistic effects of bacteria.

CONCLUSIONS: Our findings suggest that the SynCom proliferate in the rhizosphere and mitigate soil-borne diseases through microbial synergistic interactions, highlighting the potential of synergistic effects between microorganisms in enhancing plant health. This study provides a novel insight into using the functional SynCom as a promising solution for sustainable agriculture. Video Abstract.}, } @article {pmid38840170, year = {2024}, author = {Liu, Z and Zhang, Q and Zhang, H and Yi, Z and Ma, H and Wang, X and Wang, J and Liu, Y and Zheng, Y and Fang, W and Huang, P and Liu, X}, title = {Colorectal cancer microbiome programs DNA methylation of host cells by affecting methyl donor metabolism.}, journal = {Genome medicine}, volume = {16}, number = {1}, pages = {77}, pmid = {38840170}, issn = {1756-994X}, support = {2022YFA1303900//National key research and development program/ ; 82172288//National Natural Science Foundation of China/ ; BE2021721//Key society development project of Jiangsu Province/ ; 23KJB310006//The Natural Science Foundation of the Jiangsu Higher Education Institutions of China/ ; 2023C03061//The Major Scientific Project of Zhejiang Province/ ; }, mesh = {*DNA Methylation ; Humans ; *Colorectal Neoplasms/genetics/microbiology ; Gastrointestinal Microbiome/genetics ; Female ; Male ; Middle Aged ; Epigenesis, Genetic ; Aged ; CpG Islands ; Metagenomics/methods ; Metagenome ; Microbiota/genetics ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) arises from complex interactions between host and environment, which include the gut and tissue microbiome. It is hypothesized that epigenetic regulation by gut microbiota is a fundamental interface by which commensal microbes dynamically influence intestinal biology. The aim of this study is to explore the interplay between gut and tissue microbiota and host DNA methylation in CRC.

METHODS: Metagenomic sequencing of fecal samples was performed on matched CRC patients (n = 18) and healthy controls (n = 18). Additionally, tissue microbiome was profiled with 16S rRNA gene sequencing on tumor (n = 24) and tumor-adjacent normal (n = 24) tissues of CRC patients, while host DNA methylation was assessed through whole-genome bisulfite sequencing (WGBS) in a subset of 13 individuals.

RESULTS: Our analysis revealed substantial alterations in the DNA methylome of CRC tissues compared to adjacent normal tissues. An extensive meta-analysis, incorporating publicly available and in-house data, identified significant shifts in microbial-derived methyl donor-related pathways between tumor and adjacent normal tissues. Of note, we observed a pronounced enrichment of microbial-associated CpGs within the promoter regions of genes in adjacent normal tissues, a phenomenon notably absent in tumor tissues. Furthermore, we established consistent and recurring associations between methylation patterns of tumor-related genes and specific bacterial taxa.

CONCLUSIONS: This study emphasizes the pivotal role of the gut microbiota and pathogenic bacteria in dynamically shaping DNA methylation patterns, impacting physiological homeostasis, and contributing to CRC tumorigenesis. These findings provide valuable insights into the intricate host-environment interactions in CRC development and offer potential avenues for therapeutic interventions in this disease.}, } @article {pmid38839228, year = {2024}, author = {Luo, Y and Zhang, C and Liao, H and Luo, Y and Huang, X and Wang, Z and Xiaole, X}, title = {Integrative metagenomics, volatilomics and chemometrics for deciphering the microbial structure and core metabolic network during Chinese rice wine (Huangjiu) fermentation in different regions.}, journal = {Food microbiology}, volume = {122}, number = {}, pages = {104569}, doi = {10.1016/j.fm.2024.104569}, pmid = {38839228}, issn = {1095-9998}, mesh = {*Bacteria/classification/metabolism/genetics/isolation & purification ; Biogenic Amines/analysis/metabolism ; China ; *Fermentation ; Flavoring Agents/metabolism/chemistry ; *Gas Chromatography-Mass Spectrometry ; *Metabolic Networks and Pathways ; Metabolomics/methods ; *Metagenomics ; Microbiota ; Odorants/analysis ; *Oryza/microbiology/chemistry/metabolism ; Solid Phase Microextraction ; Taste ; *Volatile Organic Compounds/metabolism/analysis ; *Wine/analysis/microbiology ; }, abstract = {Huangjiu is a spontaneously fermented alcoholic beverage, that undergoes intricate microbial compositional changes. This study aimed to unravel the flavor and quality formation mechanisms based on the microbial metabolism of Huangjiu. Here, metagenome techniques, chemometrics analysis, and headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) metabolomics combined with microbial metabolic network were employed to investigate the distinctions and relationship between the microbial profiles and the quality characteristics, flavor metabolites, functional metabolic patterns of Huangjiu across three regions. Significant variations (P < 0.05) were observed in metabolic rate of physicochemical parameters and biogenic amine concentration among three regions. 8 aroma compounds (phenethyl acetate, phenylethyl alcohol, isobutyl alcohol, ethyl octanoate, ethyl acetate, ethyl hexanoate, isoamyl alcohol, and diethyl succinate) out of 448 volatile compounds were identified as the regional chemical markers. 25 dominant microbial genera were observed through metagenomic analysis, and 13 species were confirmed as microbial markers in three regions. A metabolic network analysis revealed that Saccharomycetales (Saccharomyces), Lactobacillales (Lactobacillus, Weissella, and Leuconostoc), and Eurotiales (Aspergillus) were the predominant populations responsible for substrate, flavor (mainly esters and phenylethyl alcohol) metabolism, Lactobacillales and Enterobacterales were closely linked with biogenic amine. These findings provide scientific evidence for regional microbial contributions to geographical characteristics of Huangjiu, and perspectives for optimizing microbial function to promote Huangjiu quality.}, } @article {pmid38839073, year = {2024}, author = {Davies, JM and Teh, JJ and Ewais, T and Begun, J}, title = {Does Improving Depression Symptoms in Young Adults With Inflammatory Bowel Disease Alter Their Microbiome?.}, journal = {Inflammatory bowel diseases}, volume = {30}, number = {12}, pages = {2428-2439}, pmid = {38839073}, issn = {1536-4844}, mesh = {Humans ; Male ; Female ; Young Adult ; *Depression/microbiology/therapy ; *Feces/microbiology ; Adolescent ; *Inflammatory Bowel Diseases/microbiology/psychology/therapy ; *Gastrointestinal Microbiome ; Adult ; Cross-Sectional Studies ; Cognitive Behavioral Therapy/methods ; Anxiety/microbiology/etiology/therapy ; Longitudinal Studies ; }, abstract = {BACKGROUND: Patients with inflammatory bowel diseases (IBDs) are more likely to have depression and anxiety symptoms compared with healthy individuals and those with other chronic illnesses. Previous studies have shown a link between the microbiome composition and depression symptoms; however, many antidepressant medications have antibacterial activity confounding cross-sectional studies of these populations. Therefore, we aimed to determine whether we could detect longitudinal changes in the microbiome of a subset of patients who participated in a previously published mindfulness-based cognitive therapy (MBCT) study to improve depression symptoms in adolescents and young adults with IBD.

METHODS: Stool samples were collected at baseline and 8 weeks (n = 24 participants, 37 total samples, 13 paired samples). During this time, some participants achieved a 50% reduction in their depression symptoms either through MBCT or treatment as usual with their mental health team (responders). The microbiome composition and function of responders were compared with participants who did not improve their depression scores (nonresponders). Depression scores were determined using the depression, anxiety, and stress score (DASS-21), and metagenomic sequencing of stool samples was performed.

RESULTS: No difference in alpha diversity was found between responders and nonresponders. Beta diversity measures were similarly unchanged. Clinical features including fecal calprotectin, C-reactive protein, and serum IL-6 levels were unchanged.

CONCLUSIONS: In this small longitudinal study, we were not able to detect longitudinal changes in the microbiome associated with improvement in depression scores. Follow-up studies that are sufficiently powered to detect changes in the microbiome are required to confirm our results.}, } @article {pmid38838481, year = {2024}, author = {Wang, J and Ju, F and Yu, P and Lou, J and Jiang, M and Zhang, H and Lu, H}, title = {Metabolomics-based estimation of activated sludge microbial composition and prediction of filamentous bulking.}, journal = {Water research}, volume = {259}, number = {}, pages = {121805}, doi = {10.1016/j.watres.2024.121805}, pmid = {38838481}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; *Metabolomics ; Microbiota ; Waste Disposal, Fluid/methods ; Machine Learning ; }, abstract = {Understanding the structure and activity of activated sludge (AS) microbiome is key to ensuring optimal operation of wastewater treatment processes. While high-throughput metagenomics offers a comprehensive view of AS microbiome, its cost and time demands warrant alternative approaches. This study employed machine learning methods to integrate metabolomic and metagenomic data, enabling predictions of selected microbial abundances from metabolite profiling. Model training relied on rich microbial and metabolite abundance data collected in an intensively sampled AS system, including a period of filamentous bulking, as well as a few other AS systems. Multiple linear regression out-competed other three algorithms in achieving relatively high prediction accuracy (R[2] = 0.70±0.02) for the abundances of 10 selected, either keystone or core metagenome-assembled genomes (MAGs). The model predicted the abundances of filamentous Microtrichaceae and Thiotrichaceae during bulking with an error range of 14-17.8 %. This predictive power extends beyond the specific system studied, showcasing potentials for broader applications across other AS systems. Aspartate, glycine, and folate were the most influential metabolite features contributing to model performance, which were also effective indicators for filamentous bulking, with up to one week of early warning potential. This study pioneers the application of metabolomics for fast, relatively accurate and cost-effective prediction of AS community composition, enabling proactive management of AS systems towards improved efficiency and stability.}, } @article {pmid38838470, year = {2024}, author = {Matharu, D and Ponsero, AJ and Lengyel, M and Meszaros-Matwiejuk, A and Kolho, KL and de Vos, WM and Molnar-Gabor, D and Salonen, A}, title = {Human milk oligosaccharide composition is affected by season and parity and associates with infant gut microbiota in a birth mode dependent manner in a Finnish birth cohort.}, journal = {EBioMedicine}, volume = {104}, number = {}, pages = {105182}, pmid = {38838470}, issn = {2352-3964}, mesh = {Humans ; *Milk, Human/chemistry/metabolism ; *Gastrointestinal Microbiome ; *Oligosaccharides/metabolism/analysis ; Female ; Finland ; Infant ; *Parity ; *Seasons ; Birth Cohort ; Metagenomics/methods ; Pregnancy ; Infant, Newborn ; Adult ; Metagenome ; Male ; Feces/microbiology ; }, abstract = {BACKGROUND: Human milk oligosaccharides (HMOs), their determinants, infant gut microbiota and health are under extensive research; however, seldom jointly addressed. Leveraging data from the HELMi birth cohort, we investigated them collectively, considering maternal and infant secretor status.

METHODS: HMO composition in breastmilk collected 3 months postpartum (n = 350 mothers) was profiled using high-performance liquid chromatography. Infant gut microbiota taxonomic and functional development was studied at 3, 6, and 12 months (n = 823 stool samples) via shotgun metagenomic sequencing, focusing on HMO metabolism via glycoside hydrolase (GH) analysis. Maternal and infant secretor statuses were identified through phenotyping and genotyping, respectively. Child health, emphasizing allergies and antibiotics as proxies for infectious diseases, was recorded until 2 years.

FINDINGS: Mother's parity, irritable bowel syndrome, gestational diabetes, and season of milk collection associated with HMO composition. Neither maternal nor infant secretor status associated with infant gut microbiota, except for a few taxa linked to individual HMOs. Analysis stratified for birth mode revealed distinct patterns between the infant gut microbiota and HMOs. Child health parameters were not associated to infant or maternal secretor status.

INTERPRETATION: This comprehensive exploration unveils intricate links between secretor genotype, maternal factors, HMO composition, infant microbiota, and child health. Understanding these nuanced relationships is paramount for refining strategies to optimize early life nutrition and its enduring impact on long-term health.

FUNDING: Sweet Crosstalk EU H2020 MSCA ITN, Academy of Finland, Mary and Georg C. Ehrnrooth Foundation, Päivikki and Sakari Sohlberg Foundation, and Tekes.}, } @article {pmid38837014, year = {2024}, author = {Florjan, A and Rupnik, M and Mahnic, A}, title = {Gut microbiota composition in recurrent acute otitis media: a cross-sectional observational study.}, journal = {Folia microbiologica}, volume = {69}, number = {6}, pages = {1363-1368}, pmid = {38837014}, issn = {1874-9356}, support = {ARIS SF Infrastructure core activity//Javna Agencija za Raziskovalno Dejavnost RS/ ; }, mesh = {Humans ; Cross-Sectional Studies ; Child, Preschool ; *Otitis Media/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; Child ; Infant ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Prospective Studies ; Feces/microbiology ; Recurrence ; Nasopharynx/microbiology ; Acute Disease ; }, abstract = {Recurrent acute otitis media (rAOM) poses a significant challenge in children aged 1 to 6 years, characterized by frequent and treatment-resistant ear infections. While existing studies predominantly focus on alterations in the nasopharyngeal microbiome associated with rAOM, our research explores the understudied association with the gut microbiome. In this cross-sectional observational prospective study, we enrolled 35 children aged 1 to 6 years during the 2021/2022 cold season. The test group comprised children with rAOM (n = 16), and the control group consisted of generally healthy children (n = 19). Samples (stool and nasopharyngeal swabs) were collected in late spring to ensure an antibiotic-free period. Detailed metadata was gathered through a questionnaire examining factors potentially influencing microbiota. Microbiota composition was assessed through amplicon sequencing of the V3-V4 region of the 16S rRNA gene. Our findings revealed limited alterations in gut microbiota composition among children with rAOM compared to healthy controls. Six bacterial taxa (Veillonella, Lachnospiraceae, Ruminococcaceae, Lachnospiraceae, Bacteroides and Blautia) were differentially represented with weak statistical significance. However, several bacterial taxa displayed correlations with multiple consecutive infections, with Turicibacter showing the most significant association. Additionally, day care centre attendance emerged as a potent gut microbiota modifier, independent of rAOM. Although our study identified limited differences in gut microbiota composition between children with rAOM and healthy controls, the observed correlations between the number of infections and specific bacterial taxa suggest a potential link between rAOM and the gut microbiota, warranting further investigation.}, } @article {pmid38836628, year = {2024}, author = {Tamburini, FB and Tripathi, A and Gold, MP and Yang, JC and Biancalani, T and McBride, JM and Keir, ME and Gardenia Study Group, }, title = {Gut Microbial Species and Endotypes Associate with Remission in Ulcerative Colitis Patients Treated with Anti-TNF or Anti-integrin Therapy.}, journal = {Journal of Crohn's & colitis}, volume = {18}, number = {11}, pages = {1819-1831}, pmid = {38836628}, issn = {1876-4479}, support = {//Genentech/ ; }, mesh = {*Colitis, Ulcerative/drug therapy/microbiology ; Humans ; *Infliximab/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Remission Induction/methods ; Male ; Female ; *Antibodies, Monoclonal, Humanized/therapeutic use ; Adult ; Feces/microbiology ; Middle Aged ; Gastrointestinal Agents/therapeutic use ; Tumor Necrosis Factor Inhibitors/therapeutic use ; }, abstract = {BACKGROUND AND AIMS: The gut microbiota contributes to aberrant inflammation in inflammatory bowel disease, but the bacterial factors causing or exacerbating inflammation are not fully understood. Further, the predictive or prognostic value of gut microbial biomarkers for remission in response to biologic therapy is unclear.

METHODS: We perform whole metagenomic sequencing of 550 stool samples from 287 ulcerative colitis patients from a large, phase 3, head-to-head study of infliximab and etrolizumab.

RESULTS: We identify several bacterial species in baseline and/or post-treatment samples that associate with clinical remission. These include previously described associations [Faecalibacterium prausnitzii_F] as well as new associations with remission to biologic therapy [Flavonifractor plautii]. We build multivariate models and find that gut microbial species are better predictors for remission than clinical variables alone. Finally, we describe patient groups that differ in microbiome composition and remission rate after induction therapy, suggesting the potential utility of microbiome-based endotyping.

CONCLUSIONS: In this large study of ulcerative colitis patients, we show that few individual species associate strongly with clinical remission, but multivariate models including microbiome can predict clinical remission and have better predictive power compared with clinical data alone.}, } @article {pmid38836500, year = {2024}, author = {Zhang, B and Jiang, X and Yu, Y and Cui, Y and Wang, W and Luo, H and Stergiadis, S and Wang, B}, title = {Rumen microbiome-driven insight into bile acid metabolism and host metabolic regulation.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38836500}, issn = {1751-7370}, support = {2022YFD1301400//National Key Research and Development Program of China/ ; CARS-38//China Agriculture Research System/ ; }, mesh = {*Rumen/microbiology ; Animals ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome ; Bacteria/classification/metabolism/genetics/isolation & purification ; Metagenome ; Cattle ; Ruminants/microbiology ; Lipid Metabolism ; }, abstract = {Gut microbes play a crucial role in transforming primary bile acids (BAs) into secondary forms, which influence systemic metabolic processes. The rumen, a distinctive and critical microbial habitat in ruminants, boasts a diverse array of microbial species with multifaceted metabolic capabilities. There remains a gap in our understanding of BA metabolism within this ecosystem. Herein, through the analysis of 9371 metagenome-assembled genomes and 329 cultured organisms from the rumen, we identified two enzymes integral to BA metabolism: 3-dehydro-bile acid delta4,6-reductase (baiN) and the bile acid:Na + symporter family (BASS). Both in vitro and in vivo experiments were employed by introducing exogenous BAs. We revealed a transformation of BAs in rumen and found an enzyme cluster, including L-ribulose-5-phosphate 3-epimerase and dihydroorotate dehydrogenase. This cluster, distinct from the previously known BA-inducible operon responsible for 7α-dehydroxylation, suggests a previously unrecognized pathway potentially converting primary BAs into secondary BAs. Moreover, our in vivo experiments indicated that microbial BA administration in the rumen can modulate amino acid and lipid metabolism, with systemic impacts underscored by core secondary BAs and their metabolites. Our study provides insights into the rumen microbiome's role in BA metabolism, revealing a complex microbial pathway for BA biotransformation and its subsequent effect on host metabolic pathways, including those for glucose, amino acids, and lipids. This research not only advances our understanding of microbial BA metabolism but also underscores its wider implications for metabolic regulation, offering opportunities for improving animal and potentially human health.}, } @article {pmid38833839, year = {2024}, author = {Mostafa, I and Hibberd, MC and Hartman, SJ and Hafizur Rahman, MH and Mahfuz, M and Hasan, SMT and Ashorn, P and Barratt, MJ and Ahmed, T and Gordon, JI}, title = {A microbiota-directed complementary food intervention in 12-18-month-old Bangladeshi children improves linear growth.}, journal = {EBioMedicine}, volume = {104}, number = {}, pages = {105166}, pmid = {38833839}, issn = {2352-3964}, mesh = {Humans ; Infant ; Female ; Male ; Bangladesh/epidemiology ; *Gastrointestinal Microbiome ; Feces/microbiology ; Metagenome ; Growth Disorders/etiology ; }, abstract = {BACKGROUND: Globally, stunting affects ∼150 million children under five, while wasting affects nearly 50 million. Current interventions have had limited effectiveness in ameliorating long-term sequelae of undernutrition including stunting, cognitive deficits and immune dysfunction. Disrupted development of the gut microbiota has been linked to the pathogenesis of undernutrition, providing potentially new treatment approaches.

METHODS: 124 Bangladeshi children with moderate acute malnutrition (MAM) enrolled (at 12-18 months) in a previously reported 3-month RCT of a microbiota-directed complementary food (MDCF-2) were followed for two years. Weight and length were monitored by anthropometry, the abundances of bacterial strains were assessed by quantifying metagenome-assembled genomes (MAGs) in serially collected fecal samples and levels of growth-associated proteins were measured in plasma.

FINDINGS: Children who had received MDCF-2 were significantly less stunted during follow-up than those who received a standard ready-to-use supplementary food (RUSF) [linear mixed-effects model, βtreatment group x study week (95% CI) = 0.002 (0.001, 0.003); P = 0.004]. They also had elevated fecal abundances of Agathobacter faecis, Blautia massiliensis, Lachnospira and Dialister, plus increased levels of a group of 37 plasma proteins (linear model; FDR-adjusted P < 0.1), including IGF-1, neurotrophin receptor NTRK2 and multiple proteins linked to musculoskeletal and CNS development, that persisted for 6-months post-intervention.

INTERPRETATION: MDCF-2 treatment of Bangladeshi children with MAM, which produced significant improvements in wasting during intervention, also reduced stunting during follow-up. These results suggest that the effectiveness of supplementary foods for undernutrition may be improved by including ingredients that sponsor healthy microbiota-host co-development.

FUNDING: This work was supported by the BMGF (Grants OPP1134649/INV-000247).}, } @article {pmid38833830, year = {2024}, author = {Ma, B and Wang, D and Chen, X and Wang, Q and Zhang, T and Wen, R and Yang, M and Li, C and Lei, C and Wang, H}, title = {Dietary α-linolenic acid supplementation enhances resistance to Salmonella Typhimurium challenge in chickens by altering the intestinal mucosal barrier integrity and cecal microbes.}, journal = {Microbiological research}, volume = {285}, number = {}, pages = {127773}, doi = {10.1016/j.micres.2024.127773}, pmid = {38833830}, issn = {1618-0623}, mesh = {Animals ; *Chickens/microbiology ; *Salmonella typhimurium/drug effects ; *Dietary Supplements ; *Gastrointestinal Microbiome/drug effects ; *alpha-Linolenic Acid/pharmacology/administration & dosage ; *Salmonella Infections, Animal/prevention & control/microbiology ; *Poultry Diseases/microbiology/prevention & control ; *Intestinal Mucosa/microbiology ; *Cecum/microbiology ; Animal Feed ; Fecal Microbiota Transplantation ; }, abstract = {Salmonella is an important foodborne pathogen. Given the ban on the use of antibiotics during the egg-laying period in China, finding safe and effective alternatives to antibiotics to reduce Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) infections in chickens is essential for the prevention and control of this pathogen and the protection of human health. Numerous studies have shown that unsaturated fatty acids have a positive effect on intestinal inflammation and resistance to infection by intestinal pathogens. Here we investigated the protective effect of α-linolenic acid (ALA) against S. Typhimurium infection in chickens and further explored its mechanism of action. We added different proportions of ALA to the feed and observed the effect of ALA on S. Typhimurium colonization using metagenomic sequencing technology and physiological index measurements. The role of gut flora on S. Typhimurium colonization was subsequently verified by fecal microbiota transplantation (FMT). We found that ALA protects chickens from S. Typhimurium infection by reducing intestinal inflammation through remodeling the gut microbiota, up-regulating the expression of ileocecal barrier-related genes, and maintaining the integrity of the intestinal epithelium. Our data suggest that supplementation of feed with ALA may be an effective strategy to alleviate S. Typhimurium infection in chickens.}, } @article {pmid38833520, year = {2024}, author = {Laumen, JGE and Van Dijck, C and Manoharan-Basil, SS and de Block, T and Abdellati, S and Xavier, BB and Malhotra-Kumar, S and Kenyon, C}, title = {The effect of daily usage of Listerine Cool Mint mouthwash on the oropharyngeal microbiome: a substudy of the PReGo trial.}, journal = {Journal of medical microbiology}, volume = {73}, number = {6}, pages = {}, doi = {10.1099/jmm.0.001830}, pmid = {38833520}, issn = {1473-5644}, mesh = {Humans ; *Mouthwashes/administration & dosage/pharmacology ; Male ; *Salicylates/pharmacology/therapeutic use/administration & dosage ; *Microbiota/drug effects ; *Cross-Over Studies ; Double-Blind Method ; Adult ; *Oropharynx/microbiology ; *Terpenes/administration & dosage/pharmacology ; Drug Combinations ; Homosexuality, Male ; Gonorrhea/microbiology/prevention & control ; HIV Infections/prevention & control ; Pre-Exposure Prophylaxis/methods ; Syphilis/prevention & control/microbiology ; Bacteria/classification/drug effects/genetics/isolation & purification ; }, abstract = {Introduction. Listerine[Ò] is a bactericidal mouthwash widely used to prevent oral health problems such as dental plaque and gingivitis. However, whether it promotes or undermines a healthy oral microbiome is unclear.Hypothesis/Gap Statement. We hypothesized that the daily use of Listerine Cool Mint would have a significant impact on the oropharyngeal microbiome.Aim. We aimed to assess if daily usage of Listerine Cool Mint influenced the composition of the pharyngeal microbiome.Methodology. The current microbiome substudy is part of the Preventing Resistance in Gonorrhoea trial. This was a double-blind single-centre, crossover, randomized controlled trial of antibacterial versus placebo mouthwash to reduce the incidence of gonorrhoea/chlamydia/syphilis in men who have sex with men (MSM) taking HIV pre-exposure prophylaxis (PrEP). Fifty-nine MSM taking HIV PrEP were enrolled. In this crossover trial, participants received 3 months of daily Listerine followed by 3 months of placebo mouthwash or vice versa. Oropharyngeal swabs were taken at baseline and after 3 months use of each mouthwash. DNA was extracted for shotgun metagenomic sequencing (Illumina Inc.). Non-host reads were taxonomically classified with MiniKraken and Bracken. The alpha and beta diversity indices were compared between baseline and after each mouthwash use. Differentially abundant bacterial taxa were identified using ANOVA-like differential expression analysis.Results. Streptococcus was the most abundant genus in most samples (n = 103, 61.7 %) with a median relative abundance of 31.5% (IQR 20.6-44.8), followed by Prevotella [13.5% (IQR 4.8-22.6)] and Veillonella [10.0% (IQR 4.0-16.8)]. Compared to baseline, the composition of the oral microbiome at the genus level (beta diversity) was significantly different after 3 months of Listerine (P = 0.006, pseudo-F = 2.29) or placebo (P = 0.003, pseudo-F = 2.49, permutational multivariate analysis of variance) use. Fusobacterium nucleatum and Streptococcus anginosus were significantly more abundant after Listerine use compared to baseline.Conclusion. Listerine use was associated with an increased abundance of common oral opportunistic bacteria previously reported to be enriched in periodontal diseases, oesophageal and colorectal cancer, and systemic diseases. These findings suggest that the regular use of Listerine mouthwash should be carefully considered.}, } @article {pmid38832971, year = {2024}, author = {Vatanen, T and de Beaufort, C and Marcovecchio, ML and Overbergh, L and Brunak, S and Peakman, M and Mathieu, C and Knip, M and , }, title = {Gut microbiome shifts in people with type 1 diabetes are associated with glycaemic control: an INNODIA study.}, journal = {Diabetologia}, volume = {67}, number = {9}, pages = {1930-1942}, pmid = {38832971}, issn = {1432-0428}, support = {Innovative Medicines Initiative 2 Joint Undertakin//European Commission/ ; }, mesh = {Humans ; *Diabetes Mellitus, Type 1/microbiology/immunology ; *Gastrointestinal Microbiome ; Female ; Male ; Adult ; *Glycemic Control ; C-Peptide/blood/metabolism ; Feces/microbiology ; Glycated Hemoglobin/metabolism ; Young Adult ; Autoantibodies/blood/immunology ; Adolescent ; Blood Glucose/metabolism ; Longitudinal Studies ; Middle Aged ; }, abstract = {AIMS/HYPOTHESIS: The gut microbiome is implicated in the disease process leading to clinical type 1 diabetes, but less is known about potential changes in the gut microbiome after the diagnosis of type 1 diabetes and implications in glucose homeostasis. We aimed to analyse potential associations between the gut microbiome composition and clinical and laboratory data during a 2 year follow-up of people with newly diagnosed type 1 diabetes, recruited to the Innovative approaches to understanding and arresting type 1 diabetes (INNODIA) study. In addition, we analysed the microbiome composition in initially unaffected family members, who progressed to clinical type 1 diabetes during or after their follow-up for 4 years.

METHODS: We characterised the gut microbiome composition of 98 individuals with newly diagnosed type 1 diabetes (ND cohort) and 194 autoantibody-positive unaffected family members (UFM cohort), representing a subgroup of the INNODIA Natural History Study, using metagenomic sequencing. Participants from the ND cohort attended study visits within 6 weeks from the diagnosis and 3, 6, 12 and 24 months later for stool sample collection and laboratory tests (HbA1c, C-peptide, diabetes-associated autoantibodies). Participants from the UFM cohort were assessed at baseline and 6, 12, 18, 24 and 36 months later.

RESULTS: We observed a longitudinal increase in 21 bacterial species in the ND cohort but not in the UFM cohort. The relative abundance of Faecalibacterium prausnitzii was inversely associated with the HbA1c levels at diagnosis (p=0.0019). The rate of the subsequent disease progression in the ND cohort, as assessed by change in HbA1c, C-peptide levels and insulin dose, was associated with the abundance of several bacterial species. Individuals with rapid decrease in C-peptide levels in the ND cohort had the lowest gut microbiome diversity. Nineteen individuals who were diagnosed with type 1 diabetes in the UFM cohort had increased abundance of Sutterella sp. KLE1602 compared with the undiagnosed UFM individuals (p=1.2 × 10[-4]).

CONCLUSIONS/INTERPRETATION: Our data revealed associations between the gut microbiome composition and the disease progression in individuals with recent-onset type 1 diabetes. Future mechanistic studies as well as animal studies and human trials are needed to further validate the significance and causality of these associations.}, } @article {pmid38832759, year = {2024}, author = {Deek, RA and Ma, S and Lewis, J and Li, H}, title = {Statistical and computational methods for integrating microbiome, host genomics, and metabolomics data.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {38832759}, issn = {2050-084X}, support = {GM123056/GM/NIGMS NIH HHS/United States ; GM129781/GM/NIGMS NIH HHS/United States ; P30DK050306/DK/NIDDK NIH HHS/United States ; PPRND-1507-31465//Patient Centered Outcomes Research Institute/ ; }, mesh = {*Metabolomics/methods ; *Microbiota/genetics ; *Computational Biology/methods ; *Metagenomics/methods ; *Genomics/methods ; Humans ; }, abstract = {Large-scale microbiome studies are progressively utilizing multiomics designs, which include the collection of microbiome samples together with host genomics and metabolomics data. Despite the increasing number of data sources, there remains a bottleneck in understanding the relationships between different data modalities due to the limited number of statistical and computational methods for analyzing such data. Furthermore, little is known about the portability of general methods to the metagenomic setting and few specialized techniques have been developed. In this review, we summarize and implement some of the commonly used methods. We apply these methods to real data sets where shotgun metagenomic sequencing and metabolomics data are available for microbiome multiomics data integration analysis. We compare results across methods, highlight strengths and limitations of each, and discuss areas where statistical and computational innovation is needed.}, } @article {pmid38832716, year = {2024}, author = {Hallberg, ZF and Nicolas, AM and Alvarez-Aponte, ZI and Mok, KC and Sieradzki, ET and Pett-Ridge, J and Banfield, JF and Carlson, HK and Firestone, MK and Taga, ME}, title = {Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38832716}, issn = {1751-7370}, support = {SCW1632//Genomic Science Program LLNL "Microbes Persist" Scientific Focus Area/ ; //Office of Biological and Environmental Research/ ; K99 GM143653/GM/NIGMS NIH HHS/United States ; //DOE/ ; //Office of Science/ ; 5K99GM143653-02/NH/NIH HHS/United States ; DE-SC0020155//Genomic Science Program/ ; //U.S. Department of Energy/ ; }, mesh = {*Soil Microbiology ; *Corrinoids/metabolism ; *Vitamin B 12/metabolism ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Archaea/classification/genetics/metabolism/isolation & purification ; *Microbiota ; Metagenome ; Soil/chemistry ; Grassland ; }, abstract = {Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests that corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community- and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.}, } @article {pmid38832467, year = {2024}, author = {Roach, MJ and Beecroft, SJ and Mihindukulasuriya, KA and Wang, L and Paredes, A and Cárdenas, LAC and Henry-Cocks, K and Lima, LFO and Dinsdale, EA and Edwards, RA and Handley, SA}, title = {Hecatomb: an integrated software platform for viral metagenomics.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {38832467}, issn = {2047-217X}, support = {U01 AI151810/AI/NIAID NIH HHS/United States ; RC2 DK116713/NH/NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; *Software ; Virome/genetics ; Viruses/genetics/classification ; Animals ; Computational Biology/methods ; Genome, Viral ; Metagenome ; }, abstract = {BACKGROUND: Modern sequencing technologies offer extraordinary opportunities for virus discovery and virome analysis. Annotation of viral sequences from metagenomic data requires a complex series of steps to ensure accurate annotation of individual reads and assembled contigs. In addition, varying study designs will require project-specific statistical analyses.

FINDINGS: Here we introduce Hecatomb, a bioinformatic platform coordinating commonly used tasks required for virome analysis. Hecatomb means "a great sacrifice." In this setting, Hecatomb is "sacrificing" false-positive viral annotations using extensive quality control and tiered-database searches. Hecatomb processes metagenomic data obtained from both short- and long-read sequencing technologies, providing annotations to individual sequences and assembled contigs. Results are provided in commonly used data formats useful for downstream analysis. Here we demonstrate the functionality of Hecatomb through the reanalysis of a primate enteric and a novel coral reef virome.

CONCLUSION: Hecatomb provides an integrated platform to manage many commonly used steps for virome characterization, including rigorous quality control, host removal, and both read- and contig-based analysis. Each step is managed using the Snakemake workflow manager with dependency management using Conda. Hecatomb outputs several tables properly formatted for immediate use within popular data analysis and visualization tools, enabling effective data interpretation for a variety of study designs. Hecatomb is hosted on GitHub (github.com/shandley/hecatomb) and is available for installation from Bioconda and PyPI.}, } @article {pmid38830853, year = {2024}, author = {Kitsios, GD and Sayed, K and Fitch, A and Yang, H and Britton, N and Shah, F and Bain, W and Evankovich, JW and Qin, S and Wang, X and Li, K and Patel, A and Zhang, Y and Radder, J and Dela Cruz, C and Okin, DA and Huang, CY and Van Tyne, D and Benos, PV and Methé, B and Lai, P and Morris, A and McVerry, BJ}, title = {Longitudinal multicompartment characterization of host-microbiota interactions in patients with acute respiratory failure.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4708}, pmid = {38830853}, issn = {2041-1723}, support = {COVID-19 Respiratory Virus Research//American Lung Association (Lung Association)/ ; IK2 BX004886/BX/BLRD VA/United States ; IK2BX004886//U.S. Department of Veterans Affairs (Department of Veterans Affairs)/ ; P01 HL114453/HL/NHLBI NIH HHS/United States ; T32 HL116275/HL/NHLBI NIH HHS/United States ; R03 HL162655/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; Female ; Male ; *Dysbiosis/microbiology ; Middle Aged ; *Lung/microbiology ; *COVID-19/microbiology/virology ; Aged ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Host Microbial Interactions/genetics ; Longitudinal Studies ; RNA, Ribosomal, 16S/genetics ; Respiratory Insufficiency/microbiology ; SARS-CoV-2/genetics/isolation & purification ; Adult ; Respiration, Artificial ; Bacteria/genetics/classification/isolation & purification ; Critical Illness ; Metagenomics/methods ; }, abstract = {Critical illness can significantly alter the composition and function of the human microbiome, but few studies have examined these changes over time. Here, we conduct a comprehensive analysis of the oral, lung, and gut microbiota in 479 mechanically ventilated patients (223 females, 256 males) with acute respiratory failure. We use advanced DNA sequencing technologies, including Illumina amplicon sequencing (utilizing 16S and ITS rRNA genes for bacteria and fungi, respectively, in all sample types) and Nanopore metagenomics for lung microbiota. Our results reveal a progressive dysbiosis in all three body compartments, characterized by a reduction in microbial diversity, a decrease in beneficial anaerobes, and an increase in pathogens. We find that clinical factors, such as chronic obstructive pulmonary disease, immunosuppression, and antibiotic exposure, are associated with specific patterns of dysbiosis. Interestingly, unsupervised clustering of lung microbiota diversity and composition by 16S independently predicted survival and performed better than traditional clinical and host-response predictors. These observations are validated in two separate cohorts of COVID-19 patients, highlighting the potential of lung microbiota as valuable prognostic biomarkers in critical care. Understanding these microbiome changes during critical illness points to new opportunities for microbiota-targeted precision medicine interventions.}, } @article {pmid38828760, year = {2024}, author = {Maccaro, JJ and Figueroa, LL and McFrederick, QS}, title = {From pollen to putrid: Comparative metagenomics reveals how microbiomes support dietary specialization in vulture bees.}, journal = {Molecular ecology}, volume = {33}, number = {13}, pages = {e17421}, doi = {10.1111/mec.17421}, pmid = {38828760}, issn = {1365-294X}, support = {3120//Organization for Tropical Studies/ ; CA-R-ENT-5109-H//U.S. Department of Agriculture/ ; 1929572//National Science Foundation/ ; NSF-2010615//National Science Foundation Postdoctoral Research Fellowship in Biology Program/ ; DGE -1840991//National Science Foundation Graduate Research Fellowship Program/ ; DGE-1650441//National Science Foundation Graduate Research Fellowship Program/ ; }, mesh = {Animals ; Bees/microbiology ; *Pollen/microbiology ; *Metagenomics ; *Microbiota/genetics ; *Diet ; Pollination ; }, abstract = {For most animals, the microbiome is key for nutrition and pathogen defence, and is often shaped by diet. Corbiculate bees, including honey bees, bumble bees, and stingless bees, share a core microbiome that has been shaped, at least in part, by the challenges associated with pollen digestion. However, three species of stingless bees deviate from the general rule of bees obtaining their protein exclusively from pollen (obligate pollinivores) and instead consume carrion as their sole protein source (obligate necrophages) or consume both pollen and carrion (facultative necrophages). These three life histories can provide missing insights into microbiome evolution associated with extreme dietary transitions. Here, we investigate, via shotgun metagenomics, the functionality of the microbiome across three bee diet types: obligate pollinivory, obligate necrophagy, and facultative necrophagy. We find distinct differences in microbiome composition and gene functional profiles between the diet types. Obligate necrophages and pollinivores have more specialized microbes, whereas facultative necrophages have a diversity of environmental microbes associated with several dietary niches. Our study suggests that necrophagous bee microbiomes may have evolved to overcome cellular stress and microbial competition associated with carrion. We hypothesize that the microbiome evolved social phenotypes, such as biofilms, that protect the bees from opportunistic pathogens present on carcasses, allowing them to overcome novel nutritional challenges. Whether specific microbes enabled diet shifts or diet shifts occurred first and microbial evolution followed requires further research to disentangle. Nonetheless, we find that necrophagous microbiomes, vertebrate and invertebrate alike, have functional commonalities regardless of their taxonomy.}, } @article {pmid38827283, year = {2024}, author = {Viladomat Jasso, M and García-Ulloa, M and Zapata-Peñasco, I and Eguiarte, LE and Souza, V}, title = {Metagenomic insight into taxonomic composition, environmental filtering and functional redundancy for shaping worldwide modern non-lithifying microbial mats.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17412}, pmid = {38827283}, issn = {2167-8359}, mesh = {*Metagenomics ; Archaea/genetics/classification ; Mexico ; Bacteria/genetics/classification ; Ecosystem ; Microbiota/genetics ; Metagenome ; Geologic Sediments/microbiology ; }, abstract = {Modern microbial mats are relictual communities mostly found in extreme environments worldwide. Despite their significance as representatives of the ancestral Earth and their important roles in biogeochemical cycling, research on microbial mats has largely been localized, focusing on site-specific descriptions and environmental change experiments. Here, we present a global comparative analysis of non-lithifying microbial mats, integrating environmental measurements with metagenomic data from 62 samples across eight sites, including two new samples from the recently discovered Archaean Domes from Cuatro Ciénegas, Mexico. Our results revealed a notable influence of environmental filtering on both taxonomic and functional compositions of microbial mats. Functional redundancy appears to confer resilience to mats, with essential metabolic pathways conserved across diverse and highly contrasting habitats. We identified six highly correlated clusters of taxa performing similar ecological functions, suggesting niche partitioning and functional specialization as key mechanisms shaping community structure. Our findings provide insights into the ecological principles governing microbial mats, and lay the foundation for future research elucidating the intricate interplay between environmental factors and microbial community dynamics.}, } @article {pmid38825930, year = {2024}, author = {Yan, W and Li, XQ and Liu, BB and Sun, XY and Wu, WY and Shen, N}, title = {[Exploratory analysis of gut microbiota differences in patients with bronchial asthma of different inflammatory types].}, journal = {Zhonghua nei ke za zhi}, volume = {63}, number = {6}, pages = {605-612}, doi = {10.3760/cma.j.cn112138-20240207-00103}, pmid = {38825930}, issn = {0578-1426}, mesh = {Humans ; *Asthma/microbiology ; *Gastrointestinal Microbiome ; *Feces/microbiology ; *Inflammation/microbiology ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Adult ; }, abstract = {Objective: To observe the characteristics and differences of gut microbiota in asthma patients with different inflammatory types through metagenomic analysis. Methods: Adults aged ≥18 years who visited the Respiratory Clinic of Peking University Third Hospital from August 1, 2021 to August 31, 2022 and were primarily diagnosed with asthma were selected as the study subjects. Finally, 29 patients with stable asthma were included. Fresh fecal samples were collected and the fecal DNA was extracted for high-throughput 16sRNA sequencing of gut microbiota. The diversity and community structure of gut microbiota in different groups of asthma patients were compared, and the species differences were analyzed through random forest and LEfSe analysis. Results: There were sex-based differences in asthma patients with different types of inflammation, and the proportion of female patients was higher in neutrophilic asthma patients (χ[2]=4.14, P=0.042). There was no significant intergroup difference in the alpha diversity of gut microbiota among asthma patients with different inflammatory types, but there were significant differences in the microbiome. Patients with neutrophilic asthma had higher relative abundance of Bacillales (P=0.029) and Oscillospiraceae (P=0.015). In species LEfSe analysis, patients with eosinophilic asthma had a higher relative abundance of fungi. Conclusion: There are intergroup differences in the gut microbiota of asthma patients with different inflammation types, and fungi are biomarkers that distinguish the differences in gut microbiota between patients with eosinophilic asthma and neutrophilic asthma.}, } @article {pmid38825103, year = {2024}, author = {You, L and Yang, C and Jin, H and Kwok, LY and Lv, R and Ma, T and Zhao, Z and Zhang, H and Sun, Z}, title = {Shotgun metagenomic analysis of microbiota dynamics during long-term backslopping fermentation of traditional fermented milk in a controlled laboratory environment.}, journal = {Journal of dairy science}, volume = {107}, number = {10}, pages = {7619-7630}, doi = {10.3168/jds.2023-23710}, pmid = {38825103}, issn = {1525-3198}, mesh = {*Fermentation ; *Microbiota ; Animals ; *Milk/microbiology ; Metagenomics ; }, abstract = {Traditional fermented milks are produced through an inoculation process that involves the deliberate introduction of microorganisms that have been adapted and perpetuated across successive generations. However, the changes in the microbiota of traditional fermented milk during long-term inoculation fermentation in a laboratory environment remain unclear. In this study, we collected 5 samples of traditional fermented milk samples from 5 different counties in Tibet (3 kurut products) and Xinjiang (2 tarag products) of China, which served as starter cultures for a 9-mo continuous inoculation fermentation experiment. We analyzed the inter- and intrapopulation variations in the microbial communities of the collected samples, representing their macrodiversity and microdiversity, using shotgun metagenomic sequencing. Across all samples, we obtained a total of 186 high-quality metagenomic-assembled genomes, including 7 genera and 13 species with a relative abundance of more than 1%. The majority of these genomes were annotated as Lactobacillus helveticus (60.46%), Enterococcus durans (9.52%), and Limosilactobacillus fermentum (6.23%). We observed significant differences in species composition and abundance among the 5 initial inoculants. During the long-term inoculation fermentation, we found an overall increasing trend in species diversity, composition, and abundances of carbohydrate metabolism module-encoding genes in the fermented milk bacterial metagenome, while the fermented milk virome exhibited a relatively narrow range of variation. Lactobacillus helveticus, a dominant species in traditional fermented milk, displayed high stability during the long-term inoculation fermentation. Our study provides valuable insights for the industrial production of traditional fermented milk.}, } @article {pmid38824761, year = {2024}, author = {Alqawasmeh, OAM and Jiang, XT and Cong, L and Wu, W and Leung, MBW and Chung, JPW and Yim, HCH and Fok, EKL and Chan, DYL}, title = {Vertical transmission of microbiomes into embryo culture media and its association with assisted reproductive outcomes.}, journal = {Reproductive biomedicine online}, volume = {49}, number = {2}, pages = {103977}, doi = {10.1016/j.rbmo.2024.103977}, pmid = {38824761}, issn = {1472-6491}, mesh = {Humans ; Female ; Male ; *Microbiota ; Adult ; *Culture Media ; Pregnancy ; *Follicular Fluid/microbiology ; *Reproductive Techniques, Assisted ; *Semen/microbiology ; Embryo Culture Techniques ; Fertilization in Vitro ; Infertility, Female/microbiology/therapy ; }, abstract = {RESEARCH QUESTION: Can microbes vertically transmit from semen and follicular fluid to embryo culture media during assisted reproductive technology (ART) treatment?

DESIGN: Spent embryo culture media (SECM), seminal fluid and follicular fluid samples were collected from 61 couples with infertility undergoing ART treatment at the Prince of Wales Hospital, Hong Kong SAR, China. Metagenomic analysis was conducted using 16s rRNA sequencing to identify the source of microbes in SECM, correlation between the semen microbiome and male infertility, and correlation between the follicular fluid microbiome and female infertility.

RESULTS: Microbial vertical transmission into SECM was reported in 82.5% of cases, and semen was the main source of contamination in conventional IVF cases. The increased abundances of Staphylococcus spp. and Streptococcus anginosus in semen had negative impacts on total motility and sperm count, respectively (P < 0.001). Significant increases in abundance of the genera Prophyromonas, Neisseria and Facklamia were observed in follicular fluid in women with anovulation, uterine factor infertility and unexplained infertility, respectively (P < 0.01). No significant correlation was found between the bacteria identified in all sample types and ART outcomes, including fertilization rate, embryo development, number of available embryos, and clinical pregnancy rate.

CONCLUSION: Embryo culture media can be contaminated during ART treatment, not only by seminal microbes but also by follicular fluid and other sources of microbes. Strong correlations were found between specific microbial taxa in semen and sperm quality, and between the follicular fluid microbiome and the aetiology of female infertility. However, no significant association was found between the microbiomes of SECM, semen and follicular fluid and ART outcomes.}, } @article {pmid38823882, year = {2024}, author = {Chen, C and Yang, H and Zhang, K and Ye, G and Luo, H and Zou, W}, title = {Revealing microbiota characteristics and predicting flavor-producing sub-communities in Nongxiangxing baijiu pit mud through metagenomic analysis and metabolic modeling.}, journal = {Food research international (Ottawa, Ont.)}, volume = {188}, number = {}, pages = {114507}, doi = {10.1016/j.foodres.2024.114507}, pmid = {38823882}, issn = {1873-7145}, mesh = {*Metagenomics ; *Microbiota ; *Bacteria/genetics/metabolism/classification ; Archaea/genetics/metabolism/classification ; Flavoring Agents/metabolism ; Metagenome ; }, abstract = {The microorganisms of the pit mud (PM) of Nongxiangxing baijiu (NXXB) have an important role in the synthesis of flavor substances, and they determine attributes and quality of baijiu. Herein, we utilize metagenomics and genome-scale metabolic models (GSMMs) to investigate the microbial composition, metabolic functions in PM microbiota, as well as to identify microorganisms and communities linked to flavor compounds. Metagenomic data revealed that the most prevalent assembly of bacteria and archaea was Proteiniphilum, Caproicibacterium, Petrimonas, Lactobacillus, Clostridium, Aminobacterium, Syntrophomonas, Methanobacterium, Methanoculleus, and Methanosarcina. The important enzymes ofPMwere in bothGH and GT familymetabolism. A total of 38 high-quality metagenome-assembled genomes (MAGs) were obtained, including those at the family level (n = 13), genus level (n = 17), and species level (n = 8). GSMMs of the 38 MAGs were then constructed. From the GSMMs, individual and community capabilities respectively were predicted to be able to produce 111 metabolites and 598 metabolites. Twenty-three predicted metabolites were consistent with the metabonomics detected flavors and served as targets. Twelve sub-community of were screened by cross-feeding of 38 GSMMs. Of them, Methanobacterium, Sphaerochaeta, Muricomes intestini, Methanobacteriaceae, Synergistaceae, and Caloramator were core microorganisms for targets in each sub-community. Overall, this study of metagenomic and target-community screening could help our understanding of the metabolite-microbiome association and further bioregulation of baijiu.}, } @article {pmid38823616, year = {2024}, author = {Peng, J and Wang, D and He, P and Wei, P and Zhang, L and Lan, W and Zhang, X and Guan, J and Chen, Y and Li, W and Zheng, Y and Li, Y and Chen, W and Zhao, Z and Jiang, L and Zhou, L}, title = {Seasonal dynamics of antibiotic resistance genes and mobile genetic elements in a subtropical coastal ecosystem: Implications for environmental health risks.}, journal = {Environmental research}, volume = {257}, number = {}, pages = {119298}, doi = {10.1016/j.envres.2024.119298}, pmid = {38823616}, issn = {1096-0953}, mesh = {*Seasons ; China ; *Ecosystem ; *Drug Resistance, Microbial/genetics ; Interspersed Repetitive Sequences ; Environmental Health ; Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antibiotic resistance poses a considerable global public health concern, leading to heightened rates of illness and mortality. However, the impact of seasonal variations and environmental factors on the health risks associated with antibiotic resistance genes (ARGs) and their assembly mechanisms is not fully understood. Based on metagenomic sequencing, this study investigated the antibiotic resistome, mobile genetic elements (MGEs), and microbiomes in a subtropical coastal ecosystem of the Beibu Gulf, China, over autumn and winter, and explored the factors influencing seasonal changes in ARG and MGE abundance and diversity. Results indicated that ARG abundance and diversity were higher in winter than in autumn, with beta-lactam and multidrug resistance genes being the most diverse and abundant, respectively. Similarly, MGE abundance and diversity increased in winter and were strongly correlated with ARGs. In contrast, more pronounced associations between microbial communities, especially archaea, and the antibiotic resistome were observed in autumn than in winter. The co-occurrence network identified multiple interactions between MGEs and various multidrug efflux pumps in winter, suggesting a potential for ARG dissemination. Multivariate correlation analyses and path modeling indicated that environmental factors driving microbial community changes predominantly influenced antibiotic resistome assembly in autumn, while the relative importance of MGEs increased significantly in winter. These findings suggest an elevated health risk associated with antimicrobial resistance in the Beibu Gulf during winter, attributed to the dissemination of ARGs by horizontal gene transfer. The observed seasonal variations highlight the dynamic nature of antibiotic resistance dissemination in coastal ecosystems, emphasizing the need for comprehensive surveillance and management measures to address the growing threat of antimicrobial resistance in vulnerable environments.}, } @article {pmid38821971, year = {2024}, author = {Zhang, Z and Xiao, J and Wang, H and Yang, C and Huang, Y and Yue, Z and Chen, Y and Han, L and Yin, K and Lyu, A and Fang, X and Zhang, L}, title = {Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4631}, pmid = {38821971}, issn = {2041-1723}, mesh = {Humans ; *Metagenome/genetics ; *Algorithms ; *Genome, Microbial ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Deep Learning ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Genome, Bacterial ; }, abstract = {Although long-read sequencing enables the generation of complete genomes for unculturable microbes, its high cost limits the widespread adoption of long-read sequencing in large-scale metagenomic studies. An alternative method is to assemble short-reads with long-range connectivity, which can be a cost-effective way to generate high-quality microbial genomes. Here, we develop Pangaea, a bioinformatic approach designed to enhance metagenome assembly using short-reads with long-range connectivity. Pangaea leverages connectivity derived from physical barcodes of linked-reads or virtual barcodes by aligning short-reads to long-reads. Pangaea utilizes a deep learning-based read binning algorithm to assemble co-barcoded reads exhibiting similar sequence contexts and abundances, thereby improving the assembly of high- and medium-abundance microbial genomes. Pangaea also leverages a multi-thresholding algorithm strategy to refine assembly for low-abundance microbes. We benchmark Pangaea on linked-reads and a combination of short- and long-reads from simulation data, mock communities and human gut metagenomes. Pangaea achieves significantly higher contig continuity as well as more near-complete metagenome-assembled genomes (NCMAGs) than the existing assemblers. Pangaea also generates three complete and circular NCMAGs on the human gut microbiomes.}, } @article {pmid38821514, year = {2024}, author = {Corrêa, PS and Fernandes, MA and Jimenez, CR and Mendes, LW and Lima, PMT and Abdalla, AL and Louvandini, H}, title = {Interaction between methanotrophy and gastrointestinal nematodes infection on the rumen microbiome of lambs.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {6}, pages = {}, pmid = {38821514}, issn = {1574-6941}, support = {403541/2021-2//National Council for Scientific and Technological Development/ ; 2017/50451-0//FAPESP/ ; }, mesh = {Animals ; *Rumen/microbiology/parasitology ; Sheep/microbiology ; *Methane/metabolism ; *Gastrointestinal Microbiome ; *Sheep Diseases/microbiology/parasitology ; Bacteria/classification/genetics/isolation & purification ; Archaea/genetics/classification ; Haemonchus/genetics ; Trichostrongylus ; Microbiota ; Nematode Infections/microbiology/veterinary ; }, abstract = {Complex cross-talk occurs between gastrointestinal nematodes and gut symbiotic microbiota, with consequences for animal metabolism. To investigate the connection between methane production and endoparasites, this study evaluated the effect of mixed infection with Haemonchus contortus and Trichostrongylus colubriformis on methanogenic and methanotrophic community in rumen microbiota of lambs using shotgun metagenomic and real-time quantitative PCR (qPCR). The rumen content was collected from six Santa Inês lambs, (7 months old) before and after 42 days infection by esophageal tube. The metagenomic analysis showed that the infection affected the microbial community structure leading to decreased abundance of methanotrophs bacteria, i.e. α-proteobacteria and β-proteobacteria, anaerobic methanotrophic archaea (ANME), protozoa, sulfate-reducing bacteria, syntrophic bacteria with methanogens, geobacter, and genes related to pyruvate, fatty acid, nitrogen, and sulfur metabolisms, ribulose monophosphate cycle, and Entner-Doudoroff Pathway. Additionally, the abundance of methanogenic archaea and the mcrA gene did not change. The co-occurrence networks enabled us to identify the interactions between each taxon in microbial communities and to determine the reshaping of rumen microbiome associations by gastrointestinal nematode infection. Besides, the correlation between ANMEs was lower in the animal's postinfection. Our findings suggest that gastrointestinal parasites potentially lead to decreased methanotrophic metabolism-related microorganisms and genes.}, } @article {pmid38821286, year = {2024}, author = {Liddicoat, C and Edwards, RA and Roach, M and Robinson, JM and Wallace, KJ and Barnes, AD and Brame, J and Heintz-Buschart, A and Cavagnaro, TR and Dinsdale, EA and Doane, MP and Eisenhauer, N and Mitchell, G and Rai, B and Ramesh, SA and Breed, MF}, title = {Bioenergetic mapping of 'healthy microbiomes' via compound processing potential imprinted in gut and soil metagenomes.}, journal = {The Science of the total environment}, volume = {940}, number = {}, pages = {173543}, doi = {10.1016/j.scitotenv.2024.173543}, pmid = {38821286}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Gastrointestinal Microbiome ; *Metagenome ; Humans ; Microbiota ; Energy Metabolism ; Soil/chemistry ; }, abstract = {Despite mounting evidence of their importance in human health and ecosystem functioning, the definition and measurement of 'healthy microbiomes' remain unclear. More advanced knowledge exists on health associations for compounds used or produced by microbes. Environmental microbiome exposures (especially via soils) also help shape, and may supplement, the functional capacity of human microbiomes. Given the synchronous interaction between microbes, their feedstocks, and micro-environments, with functional genes facilitating chemical transformations, our objective was to examine microbiomes in terms of their capacity to process compounds relevant to human health. Here we integrate functional genomics and biochemistry frameworks to derive new quantitative measures of in silico potential for human gut and environmental soil metagenomes to process a panel of major compound classes (e.g., lipids, carbohydrates) and selected biomolecules (e.g., vitamins, short-chain fatty acids) linked to human health. Metagenome functional potential profile data were translated into a universal compound mapping 'landscape' based on bioenergetic van Krevelen mapping of function-level meta-compounds and corresponding functional relative abundances, reflecting imprinted genetic capacity of microbiomes to metabolize an array of different compounds. We show that measures of 'compound processing potential' associated with human health and disease (examining atherosclerotic cardiovascular disease, colorectal cancer, type 2 diabetes and anxious-depressive behavior case studies), and displayed seemingly predictable shifts along gradients of ecological disturbance in plant-soil ecosystems (three case studies). Ecosystem quality explained 60-92 % of variation in soil metagenome compound processing potential measures in a post-mining restoration case study dataset. With growing knowledge of the varying proficiency of environmental microbiota to process human health associated compounds, we might design environmental interventions or nature prescriptions to modulate our exposures, thereby advancing microbiota-oriented approaches to human health. Compound processing potential offers a simplified, integrative approach for applying metagenomics in ongoing efforts to understand and quantify the role of microbiota in environmental- and human-health.}, } @article {pmid38821186, year = {2024}, author = {Xu, Q and Mei, Z and Zha, Q and Chen, J and Qin, H and Liu, B and Jie, Z and Wu, X}, title = {Characterization of bronchoalveolar lavage fluid microbiota in acute exacerbations of bronchiectasis with non-tuberculous mycobacterial detection.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {146}, number = {}, pages = {107120}, doi = {10.1016/j.ijid.2024.107120}, pmid = {38821186}, issn = {1878-3511}, mesh = {Humans ; *Bronchiectasis/microbiology ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Female ; Middle Aged ; Aged ; *Microbiota ; *Nontuberculous Mycobacteria/isolation & purification/genetics ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; High-Throughput Nucleotide Sequencing ; Community-Acquired Infections/microbiology/diagnosis ; }, abstract = {OBJECTIVES: Non-tuberculous mycobacteria (NTM) frequently colonize the airways of patients with bronchiectasis; however, there has been limited research into airway microbiota composition and predisposing factors for NTM detection during acute bronchiectasis exacerbations.

METHODS: This study enrolled 34 patients with bronchiectasis experiencing acute exacerbations. Metagenomic next-generation sequencing was used to detect microbiota in bronchoalveolar lavage fluid (BALF), and bioinformatics methods were used for the comparative analysis of meaningful microbiota in the BALF of patients with acute exacerbations of bronchiectasis. A correlation analysis was conducted to identify susceptibility factors for NTM in patients with bronchiectasis.

RESULTS: Compared with patients with community-acquired pneumonia, patients with bronchiectasis had higher detection rates of NTM (38.2%), Pseudomonas aeruginosa, and Haemophilus influenzae. Patients with NTM-positive bronchiectasis had lower body mass index and lipid profiles than patients who were NTM-negative. Metagenomic next-generation sequencing of BALF revealed patients who were NTM-positive had increased relative abundance of Rothia and other anaerobic genera compared with patients who were NTM-negative. Patients who were NTM-positive also showed higher levels of Streptococcus parasanguinis at the species level. Elevated Rothia mucilaginosa and S. parasanguinis correlated with decreased percentages of clusters of differentiation 3+ T lymphocytes and clusters of differentiation 3+ T-cell subgroups in peripheral blood.

CONCLUSIONS: NTM colonization increases the risk of acute bronchiectasis exacerbations. Low body mass index, lipid levels, and isolation of R. mucilaginosa and S. parasanguinis in BALF are susceptibility factors for NTM colonization in patients with bronchiectasis.}, } @article {pmid38820878, year = {2024}, author = {Huang, B and Zhang, N and Wang, J and Gao, Y and Wu, W and Jiang, M and Han, M}, title = {Maternal Di-(2-ethylhexyl)-Phthalate exposure during pregnancy altered energy metabolism in immature offspring and caused hyperglycemia.}, journal = {Ecotoxicology and environmental safety}, volume = {279}, number = {}, pages = {116494}, doi = {10.1016/j.ecoenv.2024.116494}, pmid = {38820878}, issn = {1090-2414}, mesh = {Female ; Animals ; Pregnancy ; *Diethylhexyl Phthalate/toxicity ; Mice ; *Hyperglycemia/chemically induced ; *Energy Metabolism/drug effects ; *Maternal Exposure/adverse effects ; Endocrine Disruptors/toxicity ; Prenatal Exposure Delayed Effects/chemically induced ; Gastrointestinal Microbiome/drug effects ; Environmental Pollutants/toxicity ; Placenta/drug effects ; Liver/drug effects ; }, abstract = {Di-(2-ethylhexyl)-phthalate (DEHP), as distinctive endocrine disrupting chemicals, has become a global environmental pollutant harmful to human and animal health. However, the impacts on offspring and mothers with maternal DEHP exposure are largely unknown and the mechanism remains elusive. We established DEHP-exposed maternal mice to investigate the impacts on mother and offspring and illustrate the mechanism from multiple perspectives. Pregnant mice were administered with different doses of DEHP, respectively. Metagenomic sequencing used fecal and transcriptome sequencing using placentas and livers from offspring have been performed, respectively. The results of the histopathology perspective demonstrated that DEHP exposure could disrupt the function of islets impact placentas and fetus development for maternal mice, and cause the disorder of glucose and lipid metabolism for immature offspring mice, resulting in hyperglycemia. The results of the metagenome of gut microbial communities indicated that the dysbiosis of gut microbiota in mother and offspring mice and the dominant phyla transformed through vertical transmission. Transcriptome analysis found DEHP exposure induced mutations of Ahcy and Gstp3, which can damage liver cells and affect the metabolism of the host. DEHP exposure harms pregnant mice and offspring by affecting gene expression and altering metabolism. Our results suggested that exposure of pregnant mice to DEHP during pregnancy and lactation increased the risk of metabolic disorders by altering key genes in liver and gut microbiota, and these results provided new insights into the potential long-term harms of DEHP.}, } @article {pmid38820703, year = {2024}, author = {Díaz-Sánchez, S and Vaz-Rodrigues, R and Contreras, M and Rafael, M and Villar, M and González-García, A and Artigas-Jerónimo, S and Gortázar, C and de la Fuente, J}, title = {Zebrafish gut microbiota composition in response to tick saliva biomolecules correlates with allergic reactions to mammalian meat consumption.}, journal = {Microbiological research}, volume = {285}, number = {}, pages = {127786}, doi = {10.1016/j.micres.2024.127786}, pmid = {38820703}, issn = {1618-0623}, mesh = {Animals ; *Saliva/microbiology/immunology ; *Gastrointestinal Microbiome ; *Zebrafish/microbiology ; *Food Hypersensitivity/microbiology/immunology ; RNA, Ribosomal, 16S/genetics ; Meat ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Salivary Proteins and Peptides/immunology/metabolism ; Ixodes/microbiology ; Disease Models, Animal ; }, abstract = {The α-Gal syndrome (AGS) is an IgE-mediated tick borne-allergy that results in delayed anaphylaxis to the consumption of mammalian meat and products containing α-Gal. Considering that α-Gal-containing microbiota modulates natural antibody production to this glycan, this study aimed to evaluate the influence on tick salivary compounds on the gut microbiota composition in the zebrafish (Danio rerio) animal model. Sequencing of 16 S rDNA was performed in a total of 75 zebrafish intestine samples, representing different treatment groups: PBS control, Ixodes ricinus tick saliva, tick saliva non-protein fraction (NPF), tick saliva protein fraction (PF), and tick saliva protein fractions 1-5 with NPF (F1-5). The results revealed that treatment with tick saliva and different tick salivary fractions, combined with α-Gal-positive dog food feeding, resulted in specific variations in zebrafish gut microbiota composition at various taxonomic levels and affected commensal microbial alpha and beta diversities. Metagenomics results were corroborated by qPCR, supporting the overrepresentation of phylum Firmicutes in the tick saliva group, phylum Fusobacteriota in group F1, and phylum Cyanobacteria in F2 and F5 compared to the PBS-control. qPCRs results at genus level sustained significant enrichment of Plesiomonas spp. in groups F3 and F5, Rhizobium spp. in NPF and F4, and Cloacibacterium spp. dominance in the PBS control group. This study provides new results on the role of gut microbiota in allergic reactions to tick saliva components using a zebrafish model of AGS. Overall, gut microbiota composition in response to tick saliva biomolecules may be associated with allergic reactions to mammalian meat consumption in AGS.}, } @article {pmid38819818, year = {2024}, author = {Zhao, J and Zhou, X and Qiu, Y and Jia, R}, title = {Characterization of the gut butyrate-producing bacteria and lipid metabolism in African green monkey as a natural host of simian immunodeficiency virus infection.}, journal = {AIDS (London, England)}, volume = {38}, number = {11}, pages = {1617-1626}, doi = {10.1097/QAD.0000000000003944}, pmid = {38819818}, issn = {1473-5571}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Butyrates/metabolism ; *Simian Acquired Immunodeficiency Syndrome/metabolism/virology ; *Lipid Metabolism ; *Feces/microbiology ; Chlorocebus aethiops ; *Macaca mulatta ; Bacteria/classification/isolation & purification/metabolism ; Simian Immunodeficiency Virus ; Metagenomics ; Metabolomics ; Macaca fascicularis ; }, abstract = {OBJECTIVE: Natural hosts of simian immunodeficiency virus (SIV), such as the African green monkey (AGM), possess the ability to avoid acquired immune deficiency syndrome (AIDS) despite lifelong infection. The underlying mechanisms are not completely understood. This study aimed to characterize the gut microbiome and metabolite profiles of different nonhuman primates (NHPs) to provide potential insight into AIDS resistance.

DESIGN AND METHODS: Fresh feces from Cynomolgus macaques (CMs), and Rhesus macaques (RMs), SIV- AGMs (AGM_N), and SIV+ AGMs (AGM_P) were collected and used for metagenomic sequencing and metabonomic analysis.

RESULTS: Compared with CMs and RMs, significant decreases in the abundances of Streptococcus , Alistipes , Treponema , Bacteroides , and Methanobrevibacter (P  < 0.01), and significant increases in the abundances of Clostridium , Eubacterium , Blautia , Roseburia , Faecalibacterium , and Dialister (P  < 0.01) were detected in AGM_N. Compared with AGM_N, a trend toward increased abundances of Streptococcus and Roseburia were found in AGM_P. The levels of metabolites involved in lipid metabolism and butanoate metabolism significantly differed among AGM_P, AGM_N and CM (P  < 0.05).

CONCLUSIONS: Our data, for the first time, demonstrated distinguishing features in the abundances of butyrate-producing bacteria and lipid metabolism capacities between different NHP hosts of SIV infection. These findings may correlate with the different characteristics observed among these hosts in the maintenance of intestinal epithelial barrier integrity, regulation of inflammation, and provide insights into AIDS resistance in AGMs.}, } @article {pmid38819499, year = {2024}, author = {Li, M and Shao, D and Fan, Z and Qin, J and Xu, J and Huang, Q and Li, X and Hua, Z and Li, J and Hao, C and Wei, W and Abnet, CC}, title = {Non-invasive early detection on esophageal squamous cell carcinoma and precancerous lesions by microbial biomarkers combining epidemiological factors in China.}, journal = {Journal of gastroenterology}, volume = {59}, number = {7}, pages = {531-542}, pmid = {38819499}, issn = {1435-5922}, support = {81974493//National Natural Science Fund/ ; 2016YFC0901404//National Key R&D Program of China/ ; 2019FY101101//National Science & Technology Fundamental Resources Investigation Program of China/ ; }, mesh = {Humans ; *Esophageal Neoplasms/diagnosis/epidemiology/microbiology ; Male ; Female ; Middle Aged ; *Precancerous Conditions/diagnosis/microbiology ; China/epidemiology ; *Esophageal Squamous Cell Carcinoma/diagnosis/epidemiology/microbiology ; *Early Detection of Cancer/methods ; Aged ; Saliva/microbiology ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Biomarkers, Tumor ; Adult ; Metagenomics/methods ; Predictive Value of Tests ; }, abstract = {BACKGROUND: Microbiota may be associated with esophageal squamous cell carcinoma (ESCC) development. However, it is not known the predictive value of microbial biomarkers combining epidemiological factors for the early detection of ESCC and precancerous lesions.

METHODS: A total of 449 specimens (esophageal swabs and saliva) were collected from 349 participants with different esophageal statuses in China to explore and validate ESCC-associated microbial biomarkers from genes level to species level by 16S rRNA sequencing, metagenomic sequencing and real-time quantitative polymerase chain reaction.

RESULTS: A bacterial biomarker panel including Actinomyces graevenitzii (A.g_1, A.g_2, A.g_3, A.g_4), Fusobacteria nucleatum (F.n_1, F.n_2, F.n_3), Haemophilus haemolyticus (H.h_1), Porphyromonas gingivalis (P.g_1, P.g_2, P.g_3) and Streptococcus australis (S.a_1) was explored by metagenomic sequencing to early detect the participants in Need group (low-grade intraepithelial neoplasia, high-grade intraepithelial neoplasia and ESCC) vs participants without these lesions as the Noneed group. Significant quantitative differences existed for each microbial target in which the detection efficiency rate was higher in saliva than esophageal swab. In saliva, the area under the curve (AUC) based on the microbial biomarkers (A.g_4 ∩ P.g_3 ∩ H.h_1 ∩ S.a_1 ∩ F.n_2) was 0.722 (95% CI 0.621-0.823) in the exploration cohort. Combining epidemiological factors (age, smoking, drinking, intake of high-temperature food and toothache), the AUC improved to 0.869 (95% CI 0.802-0.937) in the exploration cohort, which was validated with AUC of 0.757 (95% CI 0.663-0.852) in the validation cohort.

CONCLUSIONS: It is feasible to combine microbial biomarkers in saliva and epidemiological factors to early detect ESCC and precancerous lesions in China.}, } @article {pmid38819146, year = {2024}, author = {Tang, S and Wu, G and Liu, Y and Xue, B and Zhang, S and Zhang, W and Jia, Y and Xie, Q and Liang, C and Wang, L and Heng, H and Wei, W and Shi, X and Hu, Y and Yang, J and Zhao, L and Wang, X and Zhao, L and Yuan, H}, title = {Guild-level signature of gut microbiome for diabetic kidney disease.}, journal = {mBio}, volume = {15}, number = {7}, pages = {e0073524}, pmid = {38819146}, issn = {2150-7511}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetic Nephropathies/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Male ; Female ; *Feces/microbiology ; Middle Aged ; *Metagenomics ; Adult ; Aged ; *Metagenome ; }, abstract = {UNLABELLED: Current microbiome signatures for chronic diseases such as diabetic kidney disease (DKD) are mainly based on low-resolution taxa such as genus or phyla and are often inconsistent among studies. In microbial ecosystems, bacterial functions are strain specific, and taxonomically different bacteria tend to form co-abundance functional groups called guilds. Here, we identified guild-level signatures for DKD by performing in-depth metagenomic sequencing and conducting genome-centric and guild-based analysis on fecal samples from 116 DKD patients and 91 healthy subjects. Redundancy analysis on 1,543 high-quality metagenome-assembled genomes (HQMAGs) identified 54 HQMAGs that were differentially distributed among the young healthy control group, elderly healthy control group, early-stage DKD patients (EDG), and late-stage DKD patients (LDG). Co-abundance network analysis classified the 54 HQMAGs into two guilds. Compared to guild 2, guild 1 contained more short-chain fatty acid biosynthesis genes and fewer genes encoding uremic toxin indole biosynthesis, antibiotic resistance, and virulence factors. Guild indices, derived from the total abundance of guild members and their diversity, delineated DKD patients from healthy subjects and between different severities of DKD. Age-adjusted partial Spearman correlation analysis showed that the guild indices were correlated with DKD disease progression and with risk indicators of poor prognosis. We further validated that the random forest classification model established with the 54 HQMAGs was also applicable for classifying patients with end-stage renal disease and healthy subjects in an independent data set. Therefore, this genome-level, guild-based microbial analysis strategy may identify DKD patients with different severity at an earlier stage to guide clinical interventions.

IMPORTANCE: Traditionally, microbiome research has been constrained by the reliance on taxonomic classifications that may not reflect the functional dynamics or the ecological interactions within microbial communities. By transcending these limitations with a genome-centric and guild-based analysis, our study sheds light on the intricate and specific interactions between microbial strains and diabetic kidney disease (DKD). We have unveiled two distinct microbial guilds with opposite influences on host health, which may redefine our understanding of microbial contributions to disease progression. The implications of our findings extend beyond mere association, providing potential pathways for intervention and opening new avenues for patient stratification in clinical settings. This work paves the way for a paradigm shift in microbiome research in DKD and potentially other chronic kidney diseases, from a focus on taxonomy to a more nuanced view of microbial ecology and function that is more closely aligned with clinical outcomes.}, } @article {pmid38819127, year = {2024}, author = {Bulka, O and Picott, K and Mahadevan, R and Edwards, EA}, title = {From mec cassette to rdhA: a key Dehalobacter genomic neighborhood in a chloroform and dichloromethane-transforming microbial consortium.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {6}, pages = {e0073224}, pmid = {38819127}, issn = {1098-5336}, support = {BCB 285MPR//Genome Canada (GC)/ ; CGS-D//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; OGS//Government of Ontario (Ontario Government)/ ; Discovery//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; }, mesh = {*Chloroform/metabolism ; *Methylene Chloride/metabolism ; *Microbial Consortia/genetics ; *Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Groundwater/microbiology ; Metagenomics ; Water Pollutants, Chemical/metabolism ; }, abstract = {UNLABELLED: Chloroform (CF) and dichloromethane (DCM) are groundwater contaminants of concern due to their high toxicity and inhibition of important biogeochemical processes such as methanogenesis. Anaerobic biotransformation of CF and DCM has been well documented but typically independently of one another. CF is the electron acceptor for certain organohalide-respiring bacteria that use reductive dehalogenases (RDases) to dechlorinate CF to DCM. In contrast, known DCM degraders use DCM as their electron donor, which is oxidized using a series of methyltransferases and associated proteins encoded by the mec cassette to facilitate the entry of DCM to the Wood-Ljungdahl pathway. The SC05 culture is an enrichment culture sold commercially for bioaugmentation, which transforms CF via DCM to CO2. This culture has the unique ability to dechlorinate CF to DCM using electron equivalents provided by the oxidation of DCM to CO2. Here, we use metagenomic and metaproteomic analyses to identify the functional genes involved in each of these transformations. Though 91 metagenome-assembled genomes were assembled, the genes for an RDase-named acdA-and a complete mec cassette were found to be encoded on a single contig belonging to Dehalobacter. AcdA and critical Mec proteins were also highly expressed by the culture. Heterologously expressed AcdA dechlorinated CF and other chloroalkanes but had 100-fold lower activity on DCM. Overall, the high expression of Mec proteins and the activity of AcdA suggest a Dehalobacter capable of dechlorination of CF to DCM and subsequent mineralization of DCM using the mec cassette.

IMPORTANCE: Chloroform (CF) and dichloromethane (DCM) are regulated groundwater contaminants. A cost-effective approach to remove these pollutants from contaminated groundwater is to employ microbes that transform CF and DCM as part of their metabolism, thus depleting the contamination as the microbes continue to grow. In this work, we investigate bioaugmentation culture SC05, a mixed microbial consortium that effectively and simultaneously degrades both CF and DCM coupled to the growth of Dehalobacter. We identified the functional genes responsible for the transformation of CF and DCM in SC05. These genetic biomarkers provide a means to monitor the remediation process in the field.}, } @article {pmid38817668, year = {2024}, author = {Gupta, P and Hiller, A and Chowdhury, J and Lim, D and Lim, DY and Saeij, JPJ and Babaian, A and Rodriguez, F and Pereira, L and Morales-Tapia, A}, title = {A parasite odyssey: An RNA virus concealed in Toxoplasma gondii.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {veae040}, pmid = {38817668}, issn = {2057-1577}, abstract = {We are entering a 'Platinum Age of Virus Discovery', an era marked by exponential growth in the discovery of virus biodiversity, and driven by advances in metagenomics and computational analysis. In the ecosystem of a human (or any animal) there are more species of viruses than simply those directly infecting the animal cells. Viruses can infect all organisms constituting the microbiome, including bacteria, fungi, and unicellular parasites. Thus the complexity of possible interactions between host, microbe, and viruses is unfathomable. To understand this interaction network we must employ computationally assisted virology as a means of analyzing and interpreting the millions of available samples to make inferences about the ways in which viruses may intersect human health. From a computational viral screen of human neuronal datasets, we identified a novel narnavirus Apocryptovirus odysseus (Ao) which likely infects the neurotropic parasite Toxoplasma gondii. Previously, several parasitic protozoan viruses (PPVs) have been mechanistically established as triggers of host innate responses, and here we present in silico evidence that Ao is a plausible pro-inflammatory factor in human and mouse cells infected by T. gondii. T. gondii infects billions of people worldwide, yet the prognosis of toxoplasmosis disease is highly variable, and PPVs like Ao could function as a hitherto undescribed hypervirulence factor. In a broader screen of over 7.6 million samples, we explored phylogenetically proximal viruses to Ao and discovered nineteen Apocryptovirus species, all found in libraries annotated as vertebrate transcriptome or metatranscriptomes. While samples containing this genus of narnaviruses are derived from sheep, goat, bat, rabbit, chicken, and pigeon samples, the presence of virus is strongly predictive of parasitic Apicomplexa nucleic acid co-occurrence, supporting the fact that Apocryptovirus is a genus of parasite-infecting viruses. This is a computational proof-of-concept study in which we rapidly analyze millions of datasets from which we distilled a mechanistically, ecologically, and phylogenetically refined hypothesis. We predict that this highly diverged Ao RNA virus is biologically a T. gondii infection, and that Ao, and other viruses like it, will modulate this disease which afflicts billions worldwide.}, } @article {pmid38815878, year = {2024}, author = {Olbrich, M and Hartmann, AM and Künzel, S and Aherrahrou, Z and Schilf, P and Baines, JF and Ibrahim, SM and Hirose, M}, title = {Mitochondrial DNA variants and microbiota: An experimental strategy to identify novel therapeutic potential in chronic inflammatory diseases.}, journal = {Pharmacological research}, volume = {205}, number = {}, pages = {107231}, doi = {10.1016/j.phrs.2024.107231}, pmid = {38815878}, issn = {1096-1186}, mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Mice, Inbred C57BL ; Gastrointestinal Microbiome ; Mice ; Skin/metabolism/microbiology/pathology ; Dermatitis/immunology/microbiology/genetics/drug therapy/metabolism ; Inflammation/genetics/immunology ; Disease Models, Animal ; Male ; Germ-Free Life ; Psoriasis/drug therapy/immunology/genetics ; Cecum/microbiology ; Chronic Disease ; Female ; }, abstract = {We previously demonstrated that mice carrying natural mtDNA variants of the FVB/NJ strain (m.7778 G>T in the mt-Atp8 gene in mitochondrial complex V), namely C57BL/6 J-mt[FVB/NJ] (B6-mtFVB), exhibited (i) partial protection from experimental skin inflammatory diseases in an anti-murine type VII collagen antibody-induced skin inflammation model and psoriasiform dermatitis model; (ii) significantly altered metabolites, including short-chain fatty acids, according to targeted metabolomics of liver, skin and lymph node samples; and (iii) a differential composition of the gut microbiota according to bacterial 16 S rRNA gene sequencing of stool samples compared to wild-type C57BL/6 J (B6) mice. To further dissect these disease-contributing factors, we induced an experimental antibody-induced skin inflammatory disease in gnotobiotic mice. We performed shotgun metagenomic sequencing of caecum contents and untargeted metabolomics of liver, CD4+ T cell, and caecum content samples from conventional B6-mtFVB and B6 mice. We identified D-glucosamine as a candidate mediator that ameliorated disease severity in experimental antibody-induced skin inflammation by modulating immune cell function in T cells, neutrophils and macrophages. Because mice carrying mtDNA variants of the FVB/NJ strain show differential disease susceptibility to a wide range of experimental diseases, including diet-induced atherosclerosis in low-density lipoprotein receptor knockout mice and collagen antibody-induced arthritis in DBA/1 J mice, this experimental approach is valuable for identifying novel therapeutic options for skin inflammatory conditions and other chronic inflammatory diseases to which mice carrying specific mtDNA variants show differential susceptibility.}, } @article {pmid38815393, year = {2024}, author = {Foysal, MJ and Kawser, AQMR and Paul, SI and Chaklader, MR and Gupta, SK and Tay, A and Neilan, BA and Gagnon, MM and Fotedar, R and Rahman, MM and Timms, VJ}, title = {Prevalence of opportunistic pathogens and anti-microbial resistance in urban aquaculture ponds.}, journal = {Journal of hazardous materials}, volume = {474}, number = {}, pages = {134661}, doi = {10.1016/j.jhazmat.2024.134661}, pmid = {38815393}, issn = {1873-3336}, mesh = {*Ponds/microbiology ; *Aquaculture ; *Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial ; Bangladesh ; Anti-Bacterial Agents/pharmacology ; Cities ; Water Microbiology ; Microbiota/drug effects ; }, abstract = {Bacterial antimicrobial resistance (AMR) has emerged as a significant concern worldwide. The microbial community profile and potential AMR level in aquaculture ponds are often undervalued and attract less attention than other aquatic environments. We used amplicon and metagenomic shotgun sequencing to study microbial communities and AMR in six freshwater polyculture ponds in rural and urban areas of Bangladesh. Amplicon sequencing revealed different community structures between rural and urban ponds, with urban ponds having a higher bacterial diversity and opportunistic pathogens including Streptococcus, Staphylococcus, and Corynebacterium. Despite proteobacterial dominance, Firmicutes was the most interactive in the community network, especially in the urban ponds. Metagenomes showed that drug resistance was the most common type of AMR found, while metal resistance was only observed in urban ponds. AMR and metal resistance genes were found mainly in beta and gamma-proteobacteria in urban ponds, while AMR was found primarily in alpha-proteobacteria in rural ponds. We identified potential pathogens with a high profile of AMR and metal resistance in urban aquaculture ponds. As these ponds provide a significant source of protein for humans, our results raise significant concerns for the environmental sustainability of this food source and the dissemination of AMR into the food chain.}, } @article {pmid38814931, year = {2024}, author = {Tunbenjasiri, K and Pongking, T and Sitthirach, C and Kongsintaweesuk, S and Roytrakul, S and Charoenlappanit, S and Klungsaeng, S and Anutrakulchai, S and Chalermwat, C and Pairojkul, C and Pinlaor, S and Pinlaor, P}, title = {Metagenomics and metaproteomics alterations are associated with kidney disease in opisthorchiasis hamsters fed a high-fat and high-fructose diet.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0301907}, pmid = {38814931}, issn = {1932-6203}, mesh = {Animals ; *Fructose ; *Opisthorchiasis/complications/parasitology/pathology/metabolism ; *Diet, High-Fat/adverse effects ; *Metagenomics/methods ; Cricetinae ; *Proteomics/methods ; *Gastrointestinal Microbiome ; Kidney Diseases/metabolism/parasitology/microbiology/pathology/etiology ; Opisthorchis ; Male ; Proteome ; Kidney/pathology/metabolism/microbiology ; Mesocricetus ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Opisthorchis viverrini (O. viverrini, Ov) infection and consumption of high-fat and high-fructose (HFF) diet exacerbate liver and kidney disease. Here, we investigated the effects of a combination of O. viverrini infection and HFF diet on kidney pathology via changes in the gut microbiome and host proteome in hamsters.

Twenty animals were divided into four groups; 1) fed a normal diet not infected with O. viverrini (normal group), 2) fed an HFF diet and not infected with O. viverrini (HFF), 3) fed a normal diet and infected with O. viverrini (Ov), and 4) fed an HFF diet and infected with O. viverrini (HFFOv). DNA was extracted from fecal samples and the V3-V4 region of the bacterial 16S rRNA gene sequenced on an Illumina MiSeq sequencing platform. In addition, LC/MS-MS analysis was done. Histopathological studies and biochemical assays were also conducted. The results indicated that the HFFOv group exhibited the most severe kidney injury, manifested as elevated KIM-1 expression and accumulation of fibrosis in kidney tissue. The microbiome of the HFFOv group was more diverse than in the HFF group: there were increased numbers of Ruminococcaceae, Lachnospiraceae, Desulfovibrionaceae and Akkermansiaceae, but fewer Eggerthellaceae. In total, 243 host proteins were identified across all groups. Analysis using STITCH predicted that host proteome changes may lead to leaking of the gut, allowing molecules such as soluble CD14 and p-cresol to pass through to promote kidney disease. In addition, differential expression of TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 (Tab2, involving renal inflammation and injury) are predicted to be associated with kidney disease.

CONCLUSIONS/SIGNIFICANCE: The combination of HFF diet and O. viverrini infection may promote kidney injury through alterations in the gut microbiome and host proteome. This knowledge may suggest an effective strategy to prevent kidney disease beyond the early stages.}, } @article {pmid38813004, year = {2023}, author = {Al-Kebsi, BLA and Kars, G and Özer, H and Güner, ŞN}, title = {Unraveling the impact of primary immunodeficiency disorders on the microbiota of dental caries in children through 16S rRNA gene-based metagenomic analysis.}, journal = {Turkish journal of medical sciences}, volume = {53}, number = {5}, pages = {1512-1522}, pmid = {38813004}, issn = {1303-6165}, mesh = {Humans ; *Dental Caries/microbiology ; Child ; *RNA, Ribosomal, 16S/genetics ; Female ; Male ; *Metagenomics/methods ; *Microbiota/genetics ; Primary Immunodeficiency Diseases/genetics ; Child, Preschool ; Saliva/microbiology ; Case-Control Studies ; }, abstract = {BACKGROUND/AIM: Dental caries is a frequently occurring and multifactorial chronic disease in children resulting from the interaction of cariogenic bacteria and host susceptibility. The aim of this study was to elucidate the impacts of primary immunodeficiency disorders (PIDs) on microbiota of dental caries in children by 16S rRNA gene-based metagenomic analysis.

MATERIALS AND METHODS: Enrolled in this study were 15 children with primary PID with caries (PID group) and 15 healthy children with caries as a control (CG). The DMFT index, saliva flow rate, and buffering capacity of each participant were assessed before the metagenomic analyses were conducted. For taxonomic profiling, the reads were obtained by high-throughput sequencing of the V3-V4 hypervariable region of 16S rRNA.

RESULTS: The DMFT score, saliva flow rate, and buffering capacity of the groups were similar. The flow rate and buffering capacity had no correlation with the number of species with 95% confidence. The metagenomic analysis resulted in the identification of 2440 bacterial species in all of the samples. Among the 50 most prevalent species present at ≥1% relative abundance, Prevotella melaninogenica and Prevotella salivae were differentially more abundant in the PID group. The PID group and CG showed similar species richness and evenness, but 4 of the 5 samples with the highest Shannon-Weiner and Inverse Simpson indices belonged to the PID group. The Spearman test results for correlation of the species in the PID subgroups showed that Prevotella oris had a positively correlated relationship with both Scardovia wiggsiae and Saccharibacteria genera incertae sedis.

CONCLUSION: This study provided insight into the caries microbiota of children with immunodeficiency diseases. Differentially abundant species, novel bacterial associations, and unique bacterial species were disclosed in the PID samples, indicating the role of the immune system in altering the caries microbiota. The prominent bacterial species and associations in the PID group should be suspected in regard to their link with present or future diseases.}, } @article {pmid38812066, year = {2024}, author = {Du, P and Cao, Y and Li, J and Zhou, S and Li, Z and Zhang, X and Xu, J and Liang, B}, title = {Dopamine Alleviates Phloridzin Toxicity in Apple by Modifying Rhizosphere Bacterial Community Structure and Function.}, journal = {Journal of agricultural and food chemistry}, volume = {72}, number = {23}, pages = {13001-13014}, doi = {10.1021/acs.jafc.4c02276}, pmid = {38812066}, issn = {1520-5118}, mesh = {*Malus/microbiology/metabolism/drug effects ; *Rhizosphere ; *Soil Microbiology ; *Bacteria/genetics/metabolism/classification/drug effects/isolation & purification ; *Dopamine/metabolism ; *Plant Roots/microbiology/metabolism/drug effects/growth & development ; *Phlorhizin/pharmacology ; Microbiota/drug effects ; Nitrogen/metabolism ; Reactive Oxygen Species/metabolism ; Photosynthesis/drug effects ; }, abstract = {Phloridzin significantly influences apple plant growth, development, and resistance to environmental stresses by engaging in various metabolic processes. Its excessive accumulation in soil, attributed to continuous monoculture practices, not only inhibits plant growth but also disrupts the rhizosphere microbial community. This study aims to explore the remedial effects of dopamine, a known antioxidant and stress resistance modulator in plants, on the adverse impacts of phloridzin stress in apple. Through hydroponic and pot experiments, it was demonstrated that dopamine significantly mitigates the growth inhibition caused by phloridzin stress in apple by reducing reactive oxygen species levels and enhancing photosynthesis and nitrogen transport. Additionally, dopamine reduced phloridzin concentrations in both the rhizosphere and roots. Furthermore, dopamine positively influences the structure of the rhizosphere microbial community, enriching beneficial microbes associated with nitrogen cycling. It increases the potential for soil nitrogen degradation and fixation by upregulating the abundance of ureC, GDH, and nifH, as revealed by metagenomic analysis. This aids in alleviating phloridzin stress. The study reveals dopamine's pivotal roles in modulating rhizosphere ecology under phloridzin stress and suggests its potential in sustainable apple cultivation practices to counter ARD and enhance productivity.}, } @article {pmid38810936, year = {2024}, author = {Cho, Y and Park, K and Park, J and An, J and Myung, H and Yoon, H}, title = {Exploring the therapeutic potential of endolysin CD27L_EAD against Clostridioides difficile infection.}, journal = {International journal of antimicrobial agents}, volume = {64}, number = {2}, pages = {107222}, doi = {10.1016/j.ijantimicag.2024.107222}, pmid = {38810936}, issn = {1872-7913}, mesh = {*Clostridioides difficile/drug effects/genetics ; *Endopeptidases/pharmacology/genetics/therapeutic use ; *Clostridium Infections/drug therapy/microbiology ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Gastrointestinal Microbiome/drug effects ; Bacteriophages/genetics ; Bacteriolysis/drug effects ; }, abstract = {OBJECTIVES: Clostridioides difficile has emerged as a major cause of life-threatening diarrheal disease. Conventional antibiotics used in current standards of care exacerbate the emergence of antibiotic-resistant strains and pose a risk of recurrent C. difficile infection (CDI). Thus, there is an urgent need for alternative therapeutics that selectively eliminate C. difficile without disturbing the commensal microbiota. This study aimed to explore the potential of endolysins as an alternative therapeutic agent to antibiotics. Endolysin is a bacteriophage-derived peptidoglycan hydrolase that aids in the release of phage progeny during the final stage of infection.

METHODS: In order to exploit endolysin as a therapeutic agent against CDI, the bactericidal activity of 23 putative endolysins was compared and ΦCD27 endolysin CD27L was selected and modified to CD27L_EAD by cleaving the cell-wall binding domain of CD27L.

RESULTS: CD27L_EAD exhibited greater bacteriolytic activity than CD27L and its activity was stable over a wide range of salt concentrations and pH conditions. CD27L_EAD was added to a co-culture of human gut microbiota with C. difficile and the bacterial community structure was analyzed. CD27L_EAD did not impair the richness and diversity of the bacterial population but remarkably attenuated the abundance of C. difficile. Furthermore, the co-administration of vancomycin exerted synergistic bactericidal activity against C. difficile. β-diversity analysis revealed that CD27L_EAD did not significantly disturb the composition of the microbial community, whereas the abundance of some species belonging to the family Lachnospiraceae decreased after CD27L_EAD treatment.

CONCLUSIONS: This study provides insights into endolysin as a prospective therapeutic agent for the treatment of CDI without damaging the normal gut microbiota.}, } @article {pmid38810746, year = {2024}, author = {Fernández-Triana, I and Rubilar, O and Parada, J and Fincheira, P and Benavides-Mendoza, A and Durán, P and Fernández-Baldo, M and Seabra, AB and Tortella, GR}, title = {Metal nanoparticles and pesticides under global climate change: Assessing the combined effects of multiple abiotic stressors on soil microbial ecosystems.}, journal = {The Science of the total environment}, volume = {942}, number = {}, pages = {173494}, doi = {10.1016/j.scitotenv.2024.173494}, pmid = {38810746}, issn = {1879-1026}, mesh = {*Climate Change ; *Soil Microbiology ; *Metal Nanoparticles/toxicity ; *Pesticides ; Soil Pollutants ; Soil/chemistry ; Ecosystem ; Microbiota/drug effects ; Agriculture/methods ; }, abstract = {The soil is a vital resource that hosts many microorganisms crucial in biogeochemical cycles and ecosystem health. However, human activities such as the use of metal nanoparticles (MNPs), pesticides and the impacts of global climate change (GCCh) can significantly affect soil microbial communities (SMC). For many years, pesticides and, more recently, nanoparticles have contributed to sustainable agriculture to ensure continuous food production to sustain the significant growth of the world population and, therefore, the demand for food. Pesticides have a recognized pest control capacity. On the other hand, nanoparticles have demonstrated a high ability to improve water and nutrient retention, promote plant growth, and control pests. However, it has been reported that their accumulation in agricultural soils can also adversely affect the environment and soil microbial health. In addition, climate change, with its variations in temperature and extreme water conditions, can lead to drought and increased soil salinity, modifying both soil conditions and the composition and function of microbial communities. Abiotic stressors can interact and synergistically or additively affect soil microorganisms, significantly impacting soil functioning and the capacity to provide ecosystem services. Therefore, this work reviewed the current scientific literature to understand how multiple stressors interact and affect the SMC. In addition, the importance of molecular tools such as metagenomics, metatranscriptomics, proteomics, or metabolomics in the study of the responses of SMC to exposure to multiple abiotic stressors was examined. Future research directions were also proposed, focusing on exploring the complex interactions between stressors and their long-term effects and developing strategies for sustainable soil management. These efforts will contribute to the preservation of soil health and the promotion of sustainable agricultural practices.}, } @article {pmid38810582, year = {2024}, author = {Li, J and Jong, MC and Hu, H and Gin, KY and He, Y}, title = {Size-dependent effects of microplastics on intestinal microbiome for Perna viridis.}, journal = {Journal of hazardous materials}, volume = {474}, number = {}, pages = {134658}, doi = {10.1016/j.jhazmat.2024.134658}, pmid = {38810582}, issn = {1873-3336}, mesh = {Animals ; *Microplastics/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Water Pollutants, Chemical/toxicity ; *Perna/drug effects ; Particle Size ; Polystyrenes/toxicity ; Bacteria/drug effects/metabolism/genetics/classification ; Aquaculture ; }, abstract = {Microplastics pollution threatens to marine organisms, particularly bivalves that actively ingest and accumulate microplastics of certain sizes, potentially disrupting intestinal homeostasis. This study investigated the microplastic abundance in wild and farmed mussels around Singapore, and examined the size-dependent effects of nano- to micro-scale polystyrene (0.5 µm/5 µm/50 µm) on the mussel intestinal microbiome in the laboratory. The field investigation revealed higher microplastic abundance in farmed mussels compared to wild ones. Experimentally, mussels exposed to 0.6 mg/L of microplastics for 7 days, followed by a 7-day depuration period, showed substantial impacts on Spirochaetes and Proteobacteria, facilitating the proliferation of pathogenic species and differentially affecting their pathogenic contributions. Metagenomics analysis revealed that microplastic exposure reduced Spirochaeta's contribution to virulence and pathogenicity loss, did not affect Vibrio and Oceanispirochaeta's pathogenicity, and increased Treponema and Oceanispirochaeta's contributions to pathogenicity loss. Moreover, microplastics increased transmembrane transporters and impacted oxidative phosphorylation enzymes, impairing energy metabolism. These effects persisted after depuration, indicating lack of resilience in the microbiome. Nano- and micro-scale plastics perturbed the mussel microbiome composition and functions in a size-dependent manner, with nano-plastics being the most disruptive. The increasing use and sale of aquaculture equipment of plastic may exacerbate the intestinal dysbiosis in bivalves, which threatens consumers' health.}, } @article {pmid38808521, year = {2024}, author = {Park, JS and Kim, E and Kwon, SJ and Heo, JS and Ahn, KH}, title = {Differences in maternal subgingival microbiome between preterm and term births: The MOHEPI study.}, journal = {Journal of periodontal research}, volume = {59}, number = {5}, pages = {939-950}, doi = {10.1111/jre.13292}, pmid = {38808521}, issn = {1600-0765}, support = {//Korea University Medicine/ ; //Korea University Anam Hospital/ ; //National Research Foundation of Korea/ ; //Korea University/ ; //Ministry of Trade, Industry and Energy/ ; }, mesh = {Humans ; Female ; *Premature Birth/microbiology ; Adult ; *Microbiota ; Pregnancy ; *Term Birth ; Prospective Studies ; *Gingiva/microbiology ; Periodontal Index ; Periodontitis/microbiology ; Dental Plaque/microbiology ; RNA, Ribosomal, 16S/analysis ; }, abstract = {AIM: Periodontitis is a potential risk factor for preterm birth (PTB) in women; however, the causal relationship or the exact mechanism remain unknown. This study aimed to compare the oral microbiome features of mothers with full-term birth (FTB) with those who had preterm delivery.

METHODS: This study prospectively enrolled 60 women (30 mothers with PTB and 30 mothers with FTB), and subgingival plaque samples were collected and analysed by metagenomic 16S rDNA sequencing. Clinical measurements, including periodontal probing depth, clinical attachment level, modified gingival index (mGI) and plaque index, were performed to determine the periodontal state of the participants. Medical and obstetric data were collected as well.

RESULTS: Among the periodontal measurements, mGI score, reflecting the level of gingival inflammation, exhibited a statistically significant association with PTB (adjusted odds ratio 2.705, 95% confidence interval 1.074-6.811, p = .035). When subgroup analysis was conducted based on mean mGI scores (mGI ≥ 2, high inflammation [HI] versus mGI < 2, low inflammation [LI]), microbiome analysis revealed clear distinctions in microbial compositions between PTB and FTB mothers in both the HI and LI groups. Especially in the HI group, alpha diversity exhibited a decreasing trend in PTB mothers compared to FTB mothers. Beta diversity also revealed significant differences between the two groups. In Linear Discriminant Analysis Effect Size analysis, certain anaerobic taxa, including the genera Spirochaetes, Treponema and Porphyromonas, were relatively abundant in the FTB/HI group, whereas the PTB/HI group showed a high abundance of the order Actinomycetales. Network analysis showed that the FTB/HI had relatively stronger connectivity in microbial composition than the PTB/HI group. Dysbiosis ratio of plaque microbiome, in terms of periodontitis, was significantly lower in PTB/HI group compared to FTB/HI group.

CONCLUSION: The compositions of maternal subgingival microbiomes differed between PTB and FTB mothers in both the high and low levels of gingival inflammation groups. In the presence of high level of gingival inflammation, dysbiosis in plaque microbiome, in terms of periodontitis, was decreased in PTB mothers compared to FTB mothers.}, } @article {pmid38807549, year = {2024}, author = {Bae, WY and Jung, WH and Shin, SL and Kim, TR and Sohn, M and Suk, J and Jung, I and Lee, YI and Lee, JH}, title = {Heat-treated Limosilactobacillus fermentum LM1020 with menthol, salicylic acid, and panthenol promotes hair growth and regulates hair scalp microbiome balance in androgenetic alopecia: A double-blind, randomized and placebo-controlled clinical trial.}, journal = {Journal of cosmetic dermatology}, volume = {23}, number = {9}, pages = {2943-2955}, doi = {10.1111/jocd.16357}, pmid = {38807549}, issn = {1473-2165}, support = {S3003957//Ministry of SMEs and Startups/ ; }, mesh = {Humans ; *Alopecia/therapy/microbiology/drug therapy ; Double-Blind Method ; *Scalp/microbiology ; *Microbiota/drug effects ; Adult ; *Limosilactobacillus fermentum/physiology/isolation & purification ; Male ; Female ; Hair/microbiology/growth & development ; Middle Aged ; Hair Follicle/microbiology ; Hot Temperature ; Cell Proliferation/drug effects ; }, abstract = {BACKGROUND: Androgenetic alopecia (AGA) is a common and chronic problem characterized by hair follicle miniaturization.

AIMS: In this study, heat-treated Limosilactobacillus fermentum LM1020 (HT-LM1020) was investigated in human follicle dermal papilla cell (HFDPC), scalp tissue, and clinical trials for patients with AGA.

PATIENTS/METHODS: Cell proliferation and the expression of cyclins and cyclin-dependent kinases (CDKs) were measured in HFDPC. The relative gene expression of 5α-reductase and growth factors were investigated in hair scalp. This double-blind, randomized, placebo-controlled clinical trial was conducted over 24 weeks. Primary efficacy was evaluated by measuring hair density, and secondary efficacy was assessed by experts and self-assessment. Changes in the microbiota of the hair scalps were analyzed using 16S metagenome amplicon sequencing.

RESULTS: HT-LM1020 promoted cell growth (p < 0.001) and cyclin B1 expression, and it reduced 5α-reductase and induced fibroblast growth factor 7 (FGF7), FGF10, and epithelial growth factor7 (EGF7) (p < 0.001). In the clinical trial, the experimental group demonstrated an increase in hair density from 133.70 to 148.87 n/cm[2] at Week 24 (p < 0.001), while also expressing satisfaction with their hair density, reduced hair loss, and hairline. At Week 24, the total ratio of lactic acid bacteria operational taxonomic unit (OTU) in the scalp increased from 6.65% to 26.19%. At the same period, placebo-controlled group decreased Staphylococcus caprae OTU from 77.95% to 14.57% while experimental group decreased from 65.80% to 41.02%.

CONCLUSIONS: These present results showed that HT-LM1020 was a co-effector of ingredients for anti-hair loss contributing to cell proliferation and the expression of CDKs.}, } @article {pmid38806322, year = {2024}, author = {Zhang, S and Fang, X and Xu, B and Zhou, Y and Li, F and Gao, Y and Luo, Y and Yao, X and Liu, X}, title = {Comprehensive analysis of phenotypes and transcriptome characteristics reveal the best atopic dermatitis mouse model induced by MC903.}, journal = {Journal of dermatological science}, volume = {114}, number = {3}, pages = {104-114}, doi = {10.1016/j.jdermsci.2024.05.003}, pmid = {38806322}, issn = {1873-569X}, mesh = {Animals ; *Dermatitis, Atopic/immunology/microbiology/chemically induced ; *Disease Models, Animal ; Female ; Mice ; *Mice, Inbred BALB C ; *Ovalbumin/immunology ; *Phenotype ; *Staphylococcus aureus/immunology ; Humans ; *Transcriptome ; *Dinitrofluorobenzene ; Skin/immunology/pathology/microbiology ; Immunoglobulin E/blood/immunology ; Gastrointestinal Microbiome/immunology ; Severity of Illness Index ; Gene Expression Profiling ; Calcitriol/analogs & derivatives ; }, abstract = {BACKGROUND: Although several mouse models of exogenous-agent-induced atopic dermatitis (AD) are currently available, the lack of certainty regarding their similarity with human AD has limited their scientific value. Thus, comprehensive evaluation of the characteristics of mouse models and their similarity with human AD is essential.

OBJECTIVE: To compare six different exogenous-agent-induced AD mouse models and find out the optimum models for study.

METHODS: Female BALB/c mice underwent induction of AD-like dermatitis by MC903 alone or in combination with ovalbumin (OVA), dinitrofluorobenzene (DNFB) alone or in combination with OVA, OVA alone, or Staphylococcus aureus. Gross phenotype, total immunoglobulin E (IgE) level, histopathological manifestations, and skin lesion transcriptome were analyzed, and metagenomic sequencing of the gut microbiome was performed.

RESULTS: The DNFB plus OVA model showed the highest disease severity, while the OVA model showed the lowest severity. The MC903 and MC903 plus OVA models showed high expression of T-helper (Th)2- and Th17-related genes; the DNFB and DNFB plus OVA models showed upregulation of Th1-, Th2-, and Th17-related genes; while the S. aureus inoculation model showed more enhanced Th1 and Th17 immune responses. In contrast to the other models, the OVA-induced model showed the lowest expression levels of inflammation-related genes, while the MC903 model shared the largest overlap with human AD profiles. The intestinal microbiota of all groups showed significant differences after modeling.

CONCLUSION: Each AD mouse model exhibited different characteristics. The MC903 model was the best to recapitulate most features of human AD among these exogenous-agent-induced AD models.}, } @article {pmid38805978, year = {2024}, author = {Jagadesh, M and Dash, M and Kumari, A and Singh, SK and Verma, KK and Kumar, P and Bhatt, R and Sharma, SK}, title = {Revealing the hidden world of soil microbes: Metagenomic insights into plant, bacteria, and fungi interactions for sustainable agriculture and ecosystem restoration.}, journal = {Microbiological research}, volume = {285}, number = {}, pages = {127764}, doi = {10.1016/j.micres.2024.127764}, pmid = {38805978}, issn = {1618-0623}, mesh = {*Soil Microbiology ; *Fungi/genetics/classification/metabolism ; *Metagenomics ; *Agriculture/methods ; *Bacteria/genetics/classification/metabolism ; *Ecosystem ; *Climate Change ; *Plants/microbiology ; Microbiota/genetics ; Soil/chemistry ; }, abstract = {The future of agriculture is questionable under the current climate change scenario. Climate change and climate-related calamities directly influence biotic and abiotic factors that control agroecosystems, endangering the safety of the world's food supply. The intricate interactions between soil microorganisms, including plants, bacteria, and fungi, play a pivotal role in promoting sustainable agriculture and ecosystem restoration. Soil microbes play a major part in nutrient cycling, including soil organic carbon (SOC), and play a pivotal function in the emission and depletion of greenhouse gases, including CH4, CO2, and N2O, which can impact the climate. At this juncture, developing a triumphant metagenomics approach has greatly increased our knowledge of the makeup, functionality, and dynamics of the soil microbiome. Currently, the involvement of plants in climate change indicates that they can interact with the microbial communities in their environment to relieve various stresses through the innate microbiome assortment of focused strains, a phenomenon dubbed "Cry for Help." The metagenomics method has lately appeared as a new platform to adjust and encourage beneficial communications between plants and microbes and improve plant fitness. The metagenomics of soil microbes can provide a powerful tool for designing and evaluating ecosystem restoration strategies that promote sustainable agriculture under a changing climate. By identifying the specific functions and activities of soil microbes, we can develop restoration programs that support these critical components of healthy ecosystems while providing economic benefits through ecosystem services. In the current review, we highlight the innate functions of microbiomes to maintain the sustainability of agriculture and ecosystem restoration. Through this insight study of soil microbe metagenomics, we pave the way for innovative strategies to address the pressing challenges of food security and environmental conservation. The present article elucidates the mechanisms through which plants and microbes communicate to enhance plant resilience and ecosystem restoration and to leverage metagenomics to identify and promote beneficial plant-microbe interactions. Key findings reveal that soil microbes are pivotal in nutrient cycling, greenhouse gas modulation, and overall ecosystem health, offering novel insights into designing ecosystem restoration strategies that bolster sustainable agriculture. As this is a topic many are grappling with, hope these musings will provide people alike with some food for thought.}, } @article {pmid38805323, year = {2024}, author = {Ravinath, R and Usha, T and Das, AJ and Sarangi, AN and Sarvashiva Kiran, N and Kumar Goyal, A and Krishnareddy Prasannakumar, M and Ramesh, N and Middha, SK}, title = {Pomegranate Rhizosphere Microbial Diversity Revealed by Metagenomics: Toward Organic Farming, Plant Growth Promotion and Biocontrol?.}, journal = {Omics : a journal of integrative biology}, volume = {28}, number = {6}, pages = {303-318}, doi = {10.1089/omi.2023.0272}, pmid = {38805323}, issn = {1557-8100}, mesh = {*Rhizosphere ; *Soil Microbiology ; *Metagenomics/methods ; *Organic Agriculture/methods ; *Pomegranate/microbiology/genetics/growth & development ; Metagenome ; Plant Development ; Indoleacetic Acids/metabolism ; Microbiota/genetics ; }, abstract = {Food production must undergo systems change to meet the sustainable development goals (SDGs). For example, organic farming can be empowered by soil microorganisms with plant growth promotion (PGP) and biocontrol features. In this context, there have been limited studies on pomegranate. We investigated microbial diversity in rhizosphere of the pomegranate "Bhagwa" variety and its potential role in PGP and biocontrol. Both bulk and rhizosphere soil samples were analyzed for their physicochemical properties. Whole metagenome sequencing was conducted using the Illumina NovaSeq6000 platform. Surprisingly, we found that bulk and rhizosphere soil samples had comparable microbial diversity. Metagenome sequencing revealed the abundance of Streptomyces indicus, Bradyrhizobium kalamazoonesis, and Pseudomonas cellulosum in the rhizosphere that are reported here for the first time in agricultural literature. Pathway prediction analysis using KEGG (Kyoto Encyclopedia for Genes and Genomes) and COG (clusters of orthologous genes) databases identified metabolic pathways associated with biocontrol properties against pathogens. We confirmed the metagenome data in vitro, which demonstrated their PGP potential and antimicrobial properties. For instance, S. indicus produced high concentration of indole-3-acetic acid, a PGP phytohormone, that can stimulate plant growth. In addition, an antimicrobial susceptibility assay suggested that bacterial extracts displayed activity against Xanthomonas, a primary pathogen causing the pomegranate wilt disease. In conclusion, this study suggests that S. indicus, B. kalamazoonesis, and P. cellulosum can potentially be PGP and biocontrol agents that may contribute to increased crop productivity in pomegranate cultivation. These agents and their combinations warrant future research with an eye on SDGs and so as to enable and innovate organic farming and pomegranate agricultural practices.}, } @article {pmid38804464, year = {2024}, author = {Lappan, R and Thakar, J and Molares Moncayo, L and Besser, A and Bradley, JA and Goordial, J and Trembath-Reichert, E and Greening, C}, title = {The atmosphere: a transport medium or an active microbial ecosystem?.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38804464}, issn = {1751-7370}, support = {RGY0058/2022//Human Frontier Science Program/ ; }, mesh = {*Atmosphere ; *Ecosystem ; Microbiota ; Air Microbiology ; Biodiversity ; Bacteria/metabolism/classification/growth & development ; }, abstract = {The atmosphere may be Earth's largest microbial ecosystem. It is connected to all of Earth's surface ecosystems and plays an important role in microbial dispersal on local to global scales. Despite this grand scale, surprisingly little is understood about the atmosphere itself as a habitat. A key question remains unresolved: does the atmosphere simply transport microorganisms from one location to another, or does it harbour adapted, resident, and active microbial communities that overcome the physiological stressors and selection pressures the atmosphere poses to life? Advances in extreme microbiology and astrobiology continue to push our understanding of the limits of life towards ever greater extremes of temperature, pressure, salinity, irradiance, pH, and water availability. Earth's atmosphere stands as a challenging, but potentially surmountable, extreme environment to harbour living, active, resident microorganisms. Here, we confront the current understanding of the atmosphere as a microbial habitat, highlighting key advances and limitations. We pose major ecological and mechanistic questions about microbial life in the atmosphere that remain unresolved and frame the problems and technical pitfalls that have largely hindered recent developments in this space, providing evidence-based insights to drive future research in this field. New innovations supported by rigorous technical standards are needed to enable progress in understanding atmospheric microorganisms and their influence on global processes of weather, climate, nutrient cycling, biodiversity, and microbial connectivity, especially in the context of rapid global change.}, } @article {pmid38802370, year = {2024}, author = {De Filippis, F and Valentino, V and Sequino, G and Borriello, G and Riccardi, MG and Pierri, B and Cerino, P and Pizzolante, A and Pasolli, E and Esposito, M and Limone, A and Ercolini, D}, title = {Exposure to environmental pollutants selects for xenobiotic-degrading functions in the human gut microbiome.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4482}, pmid = {38802370}, issn = {2041-1723}, support = {GR-2016-02362975//Ministero della Salute (Ministry of Health, Italy)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Xenobiotics/metabolism ; *Environmental Pollutants/metabolism/toxicity ; Female ; Male ; *Feces/microbiology ; Italy ; Adult ; Middle Aged ; Environmental Exposure/adverse effects ; Metagenomics/methods ; Bacteria/genetics/classification/metabolism/drug effects/isolation & purification ; Cohort Studies ; Metals, Heavy/toxicity/metabolism ; Aged ; Environmental Pollution/adverse effects ; Biodegradation, Environmental ; }, abstract = {Environmental pollutants from different chemical families may reach the gut microbiome, where they can be metabolized and transformed. However, how our gut symbionts respond to the exposure to environmental pollution is still underexplored. In this observational, cohort study, we aim to investigate the influence of environmental pollution on the gut microbiome composition and potential activity by shotgun metagenomics. We select as a case study a population living in a highly polluted area in Campania region (Southern Italy), proposed as an ideal field for exposomic studies and we compare the fecal microbiome of 359 subjects living in areas with high, medium and low environmental pollution. We highlight changes in gut microbiome composition and functionality that were driven by pollution exposure. Subjects from highly polluted areas show higher blood concentrations of dioxin and heavy metals, as well as an increase in microbial genes related to degradation and/or resistance to these molecules. Here we demonstrate the dramatic effect that environmental xenobiotics have on gut microbial communities, shaping their composition and boosting the selection of strains with degrading capacity. The gut microbiome can be considered as a pivotal player in the environment-health interaction that may contribute to detoxifying toxic compounds and should be taken into account when developing risk assessment models. The study was registered at ClinicalTrials.gov with the identifier NCT05976126.}, } @article {pmid38801952, year = {2024}, author = {Gan, Y and Ji, X and Yang, R}, title = {Metagenomic profiling of antibiotic resistance genes/bacteria removal in urban water: Algal-bacterial consortium treatment system.}, journal = {Bioresource technology}, volume = {404}, number = {}, pages = {130905}, doi = {10.1016/j.biortech.2024.130905}, pmid = {38801952}, issn = {1873-2976}, mesh = {*Chlorella vulgaris/genetics ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects ; Metagenomics/methods ; Water Purification/methods ; Genes, Bacterial ; Microbial Consortia/genetics ; Bacillus licheniformis/genetics ; Water Microbiology ; Cities ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antibiotic resistance genes (ARGs) have exhibited significant ecological concerns, especially in the urban water that are closely associated with human health. In this study, with presence of exogenous Chlorella vulgaris-Bacillus licheniformis consortium, most of the typical ARGs and MGEs were removed. Furthermore, the relative abundance of potential ARGs hosts has generally decreased by 1-4 orders of magnitude, revealing the role of algal-bacterial consortium in cutting the spread of ARGs in urban water. While some of ARGs such as macB increased, which may be due to the negative impact of algicidal bacteria and algal viruses in urban water on exogenous C. vulgaris and the suppression of exogenous B. licheniformis by indigenous microorganisms. A new algal-bacterial interaction might form between C. vulgaris and indigenous microorganisms. The interplay between C. vulgaris and bacteria has a significant impact on the fate of ARGs removal in urban water.}, } @article {pmid38801939, year = {2024}, author = {Chen, X and Zou, T and Zeng, Q and Chen, Y and Zhang, C and Jiang, S and Ding, G}, title = {Metagenomic analysis reveals ecological and functional signatures of oral phageome associated with severe early childhood caries.}, journal = {Journal of dentistry}, volume = {146}, number = {}, pages = {105059}, doi = {10.1016/j.jdent.2024.105059}, pmid = {38801939}, issn = {1879-176X}, mesh = {Humans ; *Dental Caries/microbiology/virology ; *Saliva/virology/microbiology ; *Metagenomics/methods ; *Bacteriophages/genetics/classification/isolation & purification ; Child, Preschool ; Female ; Male ; Mouth/microbiology/virology ; Microbiota ; Metagenome ; Child ; }, abstract = {OBJECTIVES: Severe early childhood caries (S-ECC) is highly prevalent, affecting children's oral health. S-ECC development is closely associated with the complex oral microbial microbiome and its microorganism interactions, such as the imbalance of bacteriophages and bacteria. Till now, little is known about oral phageome on S-ECC. Therefore, this study aimed to investigate the potential role of the oral phageome in the pathogenesis of S-ECC.

METHODS: Unstimulated saliva (2 mL) was collected from 20 children with and without S-ECC for metagenomics analysis. Metagenomics sequencing and bioinformatic analysis were performed to determine the two groups' phageome diversity, taxonomic and functional annotations. Statistical analysis and visualization were performed with R and SPSS Statistics software.

RESULTS: 85.7 % of the extracted viral sequences were predicted from phages, in which most phages were classified into Myoviridae, Siphoviridae, and Podoviridae. Alpha diversity decreased, and Beta diversity increased in the S-ECC phageome compared to the healthy group. The abundance of Podoviridae phages increased, and the abundance of Inoviridae, Herelleviridae, and Streptococcus phages decreased in the S-ECC group. Functional annotation revealed increased annotation on glycoside hydrolases and nucleotide metabolism, decreased glycosyl transferases, carbohydrate-binding modules, and biogenic metabolism in the S-ECC phageome.

CONCLUSIONS: Metagenomic analysis revealed reduced Streptococcus phages and significant changes in functional annotations within the S-ECC phageome. These findings suggest a potential weakening of the regulatory influence of oral bacteria, which may indicate the development of innovative prevention and treatment strategies for S-ECC. These implications deserve further investigation and hold promise for advancing our understanding and management of S-ECC.

CLINICAL SIGNIFICANCE: The findings of this study indicate that oral phageomes are associated with bacterial genomes and metabolic processes, affecting the development of S-ECC. The reduced modulatory effect of the oral phageome in counteracting S-ECC's cariogenic activity suggests a new avenue for the prevention and treatment of S-ECC.}, } @article {pmid38801259, year = {2024}, author = {Naithani, H and Rios-Galicia, B and Camarinha Silva, A and Seifert, J}, title = {Strategies to Enhance Cultivation of Anaerobic Bacteria from Gastrointestinal Tract of Chicken.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {207}, pages = {}, doi = {10.3791/66570}, pmid = {38801259}, issn = {1940-087X}, mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Tract/microbiology ; *Bacteria, Anaerobic/isolation & purification ; Bacteriological Techniques/methods ; Gastrointestinal Microbiome/physiology ; }, abstract = {The gastrointestinal tract (GIT) of chicken is a complex ecosystem harboring trillions of microbes that play a pivotal role in the host's physiology, digestion, nutrient absorption, immune system maturation, and prevention of pathogen intrusion. For optimal animal health and productivity, it is imperative to characterize these microorganisms and comprehend their role. While the GIT of poultry holds a reservoir of microorganisms with potential probiotic applications, most of the diversity remains unexplored. To enhance our understanding of uncultured microbial diversity, concerted efforts are required to bring these microorganisms into culture. Isolation and cultivation of GIT-colonizing microorganisms yield reproducible material, including cells, DNA, and metabolites, offering new insights into metabolic processes in the environment. Without cultivation, the role of these organisms in their natural settings remains unclear and limited to a descriptive level. Our objective is to implement cultivation strategies aimed at improving the isolation of a diverse range of anaerobic microbes from the chicken's GIT, leveraging multidisciplinary knowledge from animal physiology, animal nutrition, metagenomics, feed biochemistry, and modern cultivation strategies. Additionally, we aim to implement the use of proper practices for sampling, transportation, and media preparation, which are known to influence isolation success. Appropriate methodologies should ensure a consistent oxygen-free environment, optimal atmospheric conditions, appropriate host incubation temperature, and provision for specific nutritional requirements in alignment with their distinctive needs. By following these methodologies, cultivation will not only yield reproducible results for isolation but will also facilitate isolation procedures, thus fostering a comprehensive understanding of the intricate microbial ecosystem within the chicken's GIT.}, } @article {pmid38799799, year = {2024}, author = {Liu, S and Yang, D and Li, W and Chen, Q and Lu, D and Xiong, L and Wu, J and Ao, H and Huang, L}, title = {Magnolia Officinalis Alcohol Extract Alleviates the Intestinal Injury Induced by Polygala Tenuifolia Through Regulating the PI3K/AKT/NF-κB Signaling Pathway and Intestinal Flora.}, journal = {Drug design, development and therapy}, volume = {18}, number = {}, pages = {1695-1710}, pmid = {38799799}, issn = {1177-8881}, mesh = {*Magnolia/chemistry ; *Polygala/chemistry ; Animals ; *Gastrointestinal Microbiome/drug effects ; *NF-kappa B/metabolism ; *Signal Transduction/drug effects ; *Proto-Oncogene Proteins c-akt/metabolism ; *Phosphatidylinositol 3-Kinases/metabolism ; *Zebrafish ; Plant Extracts/pharmacology/chemistry/isolation & purification ; Intestines/drug effects/pathology ; }, abstract = {PURPOSE: Polygala tenuifolia Willd. (PT), a traditional Chinese medicinal plant extensively employed in managing Alzheimer's disease, exhibits notable gastrointestinal side effects as highlighted by prior investigations. In contrast, Magnolia officinalis Rehd. et Wils (MO), a traditional remedy for gastrointestinal ailments, shows promising potential for ameliorating this adverse effect of PT. The objective of this study is to examine the underlying mechanism of MO in alleviating the side effects of PT.

METHODS: Hematoxylin-eosin (H&E) staining was used to observe the structural damage of zebrafish intestine, and enzyme-linked immunosorbent assay (ELISA) was used to detect the levels of inflammatory factors and oxidative stress. The integrity of the intestinal tight junctions was examined using transmission electron microscope (TEM). Moreover, the expression of intestinal barrier genes and PI3K/AKT/NF-κB signaling pathway-related genes was determined through quantitative real-time PCR. The changes in intestinal microbial composition were analyzed using 16S rRNA and metagenomic techniques.

RESULTS: MO effectively ameliorated intestinal pathological damage and barrier gene expression, and significantly alleviated intestinal injury by reducing the expression of inflammatory cytokines IL-1β, IL-6, TNF-α, and inhibiting the activation of PI3K/AKT/NF-κB pathway. Furthermore, MO could significantly increase the relative abundance of beneficial microorganisms (Lactobacillus, Blautia and Saccharomyces cerevisiae), and reduce the relative abundance of pathogenic bacteria (Plesiomonas and Aeromonas).

CONCLUSION: MO alleviated PT-induced intestinal injury, and its mechanism may be related to the inhibition of PI3K/AKT/NF-κB pathway activation and regulation of intestinal flora.}, } @article {pmid38797888, year = {2024}, author = {Manoil, D and Parga, A and Bostanci, N and Belibasakis, GN}, title = {Microbial diagnostics in periodontal diseases.}, journal = {Periodontology 2000}, volume = {95}, number = {1}, pages = {176-193}, doi = {10.1111/prd.12571}, pmid = {38797888}, issn = {1600-0757}, support = {//University of Geneva/ ; ED6481B-2023/117//Regional Government of Galicia, Spain/ ; 2021-03528//Swedish Research Council/ ; 2022-01014//Swedish Research Council/ ; FoUI-966140//Steering Group for Odontological Research (SOF)/ ; FoUI-978687//Steering Group for Odontological Research (SOF)/ ; }, mesh = {Humans ; *Periodontal Diseases/microbiology/diagnosis ; *Dysbiosis/microbiology ; Microbiota ; Biomarkers ; }, abstract = {Microbial analytical methods have been instrumental in elucidating the complex microbial etiology of periodontal diseases, by shaping our understanding of subgingival community dynamics. Certain pathobionts can orchestrate the establishment of dysbiotic communities that can subvert the host immune system, triggering inflammation and tissue destruction. Yet, diagnosis and management of periodontal conditions still rely on clinical and radiographic examinations, overlooking the well-established microbial etiology. This review summarizes the chronological emergence of periodontal etiological models and the co-evolution with technological advances in microbial detection. We additionally review the microbial analytical approaches currently accessible to clinicians, highlighting their value in broadening the periodontal assessment. The epidemiological importance of obtaining culture-based antimicrobial susceptibility profiles of periodontal taxa for antibiotic resistance surveillance is also underscored, together with clinically relevant analytical approaches to guide antibiotherapy choices, when necessary. Furthermore, the importance of 16S-based community and shotgun metagenomic profiling is discussed in outlining dysbiotic microbial signatures. Because dysbiosis precedes periodontal damage, biomarker identification offers early diagnostic possibilities to forestall disease relapses during maintenance. Altogether, this review highlights the underutilized potential of clinical microbiology in periodontology, spotlighting the clinical areas most conductive to its diagnostic implementation for enhancing prevention, treatment predictability, and addressing global antibiotic resistance.}, } @article {pmid38796418, year = {2024}, author = {Kok, CR and Rose, DJ and Cui, J and Whisenhunt, L and Hutkins, R}, title = {Identification of carbohydrate gene clusters obtained from in vitro fermentations as predictive biomarkers of prebiotic responses.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {183}, pmid = {38796418}, issn = {1471-2180}, mesh = {*Prebiotics/analysis ; Humans ; *Fermentation ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Adult ; *Fatty Acids, Volatile/metabolism ; Multigene Family ; Machine Learning ; Metagenomics/methods ; Biomarkers/metabolism ; Bacteria/genetics/metabolism/classification ; Female ; Male ; Inulin/metabolism ; Young Adult ; Carbohydrate Metabolism ; }, abstract = {BACKGROUND: Prebiotic fibers are non-digestible substrates that modulate the gut microbiome by promoting expansion of microbes having the genetic and physiological potential to utilize those molecules. Although several prebiotic substrates have been consistently shown to provide health benefits in human clinical trials, responder and non-responder phenotypes are often reported. These observations had led to interest in identifying, a priori, prebiotic responders and non-responders as a basis for personalized nutrition. In this study, we conducted in vitro fecal enrichments and applied shotgun metagenomics and machine learning tools to identify microbial gene signatures from adult subjects that could be used to predict prebiotic responders and non-responders.

RESULTS: Using short chain fatty acids as a targeted response, we identified genetic features, consisting of carbohydrate active enzymes, transcription factors and sugar transporters, from metagenomic sequencing of in vitro fermentations for three prebiotic substrates: xylooligosacharides, fructooligosacharides, and inulin. A machine learning approach was then used to select substrate-specific gene signatures as predictive features. These features were found to be predictive for XOS responders with respect to SCFA production in an in vivo trial.

CONCLUSIONS: Our results confirm the bifidogenic effect of commonly used prebiotic substrates along with inter-individual microbial responses towards these substrates. We successfully trained classifiers for the prediction of prebiotic responders towards XOS and inulin with robust accuracy (≥ AUC 0.9) and demonstrated its utility in a human feeding trial. Overall, the findings from this study highlight the practical implementation of pre-intervention targeted profiling of individual microbiomes to stratify responders and non-responders.}, } @article {pmid38796259, year = {2024}, author = {Shenoy, BD and Khandeparker, RDS and Fernandes, P and Amberkar, U}, title = {Fungal diversity associated with Goa's tarballs: Insights from ITS region amplicon sequencing.}, journal = {Fungal biology}, volume = {128}, number = {3}, pages = {1751-1757}, doi = {10.1016/j.funbio.2024.03.001}, pmid = {38796259}, issn = {1878-6146}, mesh = {India ; *DNA, Fungal/genetics ; *Fungi/genetics/classification/isolation & purification ; *Biodiversity ; Sequence Analysis, DNA ; DNA, Ribosomal Spacer/genetics ; Phylogeny ; Petroleum/microbiology ; }, abstract = {This study explores the fungal diversity associated with tarballs, weathered crude oil deposits, on Goa's tourist beaches. Despite tarball pollution being a longstanding issue in Goa state in India, comprehensive studies on associated fungi are scarce. Our research based on amplicon sequence analysis of fungal ITS region fills this gap, revealing a dominance of Aspergillus, particularly Aspergillus penicillioides, associated with tarballs from Vagator and Morjim beaches. Other notable species, including Aspergillus sydowii, Aspergillus carbonarius, and Trichoderma species, were identified, all with potential public health and ecosystem implications. A FUNGuild analysis was conducted to investigate the potential ecological roles of these fungi, revealing a diverse range of roles, including nutrient cycling, disease propagation, and symbiotic relationships. The study underscores the need for further research and monitoring, given the potential health risks and contribution of tarball-associated fungi to the bioremediation of crude oil-contaminated beaches.}, } @article {pmid38795190, year = {2024}, author = {Bøifot, KO and Skogan, G and Dybwad, M}, title = {Sampling efficiency and nucleic acid stability during long-term sampling with different bioaerosol samplers.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {6}, pages = {577}, pmid = {38795190}, issn = {1573-2959}, mesh = {*Aerosols/analysis ; *Environmental Monitoring/methods/instrumentation ; *Air Microbiology ; *Nucleic Acids/analysis ; Particle Size ; Microbiota ; Air Pollutants/analysis ; }, abstract = {Aerosol microbiome studies have received increased attention as technological advancements have made it possible to dive deeper into the microbial diversity. To enhance biomass collection for metagenomic sequencing, long-term sampling is a common strategy. While the impact of prolonged sampling times on microorganisms' culturability and viability is well-established, its effect on nucleic acid stability remains less understood but is essential to ensure representative sample collection. This study evaluated four air samplers (SKC BioSampler, SASS3100, Coriolis μ, BioSpot-VIVAS 300-P) against a reference sampler (isopore membrane filters) to identify nucleic acid stability during long-term sampling. Physical sampling efficiencies determined with a fluorescent tracer for three particle sizes (0.8, 1, and 3 μm), revealed high efficiencies (> 80% relative to reference) for BioSampler, SASS3100, and BioSpot-VIVAS for all particle sizes, and for Coriolis with 3 μm particles. Coriolis exhibited lower efficiency for 0.8 μm (7%) and 1 μm (50%) particles. During 2-h sampling with MS2 and Pantoea agglomerans, liquid-based collection with Coriolis and BioSampler showed a decrease in nucleic acid yields for all test conditions. BioSpot-VIVAS displayed reduced sampling efficiency for P. agglomerans compared to MS2 and the other air samplers, while filter-based collection with SASS3100 and isopore membrane filters, showed indications of DNA degradation for 1 μm particles of P. agglomerans after long-term sampling. These findings show that long-term air sampling affects nucleic acid stability in both liquid- and filter-based collection methods. These results highlight bias produced by bioaerosol collection and should be considered when selecting an air sampler and interpreting aerosol microbiome data.}, } @article {pmid38794698, year = {2024}, author = {Chi, R and Li, M and Zhang, M and Zhang, N and Zhang, G and Cui, L and Ma, G}, title = {Exploring the Association between Anxiety, Depression, and Gut Microbiota during Pregnancy: Findings from a Pregnancy Cohort Study in Shijiazhuang, Hebei Province, China.}, journal = {Nutrients}, volume = {16}, number = {10}, pages = {}, pmid = {38794698}, issn = {2072-6643}, support = {DIC2019-06//Danone Nutrition Center Food Nutrition Research and Education Fund/ ; 2019-03//Friesland Campina Trading (Shanghai) Co., Ltd/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Pregnancy ; *Anxiety/microbiology ; *Depression/microbiology/epidemiology ; China/epidemiology ; Adult ; Cohort Studies ; Pregnancy Complications/microbiology/psychology ; Bacteria/classification/isolation & purification/genetics ; }, abstract = {Negative emotions and gut microbiota during pregnancy both bear significant public health implications. However, the relationship between them has not been fully elucidated. This study, utilizing data from a pregnancy cohort, employed metagenomic sequencing to elucidate the relationship between anxiety, depression, and gut microbiota's diversity, composition, species, and functional pathways. Data from 87 subjects, spanning 225 time points across early, mid, and late pregnancy, were analyzed. The results revealed that anxiety and depression significantly corresponded to lower alpha diversity (including the Shannon entropy and the Simpson index). Anxiety and depression scores, along with categorical distinctions of anxiety/non-anxiety and depression/non-depression, were found to account for 0.723%, 0.731%, 0.651%, and 0.810% of the variance in gut-microbiota composition (p = 0.001), respectively. Increased anxiety was significantly positively associated with the abundance of Oscillibacter sp. KLE 1745, Oscillibacter sp. PEA192, Oscillibacter sp. KLE 1728, Oscillospiraceae bacterium VE202 24, and Treponema socranskii. A similar association was significantly noted for Oscillibacter sp. KLE 1745 with elevated depression scores. While EC.3.5.3.1: arginase appeared to be higher in the anxious group than in the non-anxious group, vitamin B12-related enzymes appeared to be lower in the depression group than in the non-depression group. The changes were found to be not statistically significant after post-multiple comparison adjustment.}, } @article {pmid38793605, year = {2024}, author = {Anantharam, R and Duchen, D and Cox, AL and Timp, W and Thomas, DL and Clipman, SJ and Kandathil, AJ}, title = {Long-Read Nanopore-Based Sequencing of Anelloviruses.}, journal = {Viruses}, volume = {16}, number = {5}, pages = {}, pmid = {38793605}, issn = {1999-4915}, support = {R01DA058567/DA/NIDA NIH HHS/United States ; R21 DA053145/DA/NIDA NIH HHS/United States ; R01 DA058567/DA/NIDA NIH HHS/United States ; R21DA053145/DA/NIDA NIH HHS/United States ; DP2DA056130/DA/NIDA NIH HHS/United States ; }, mesh = {*Anelloviridae/genetics/isolation & purification/classification ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Genome, Viral ; *Nanopore Sequencing/methods ; Nanopores ; DNA, Viral/genetics ; Virome/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Routinely used metagenomic next-generation sequencing (mNGS) techniques often fail to detect low-level viremia (<10[4] copies/mL) and appear biased towards viruses with linear genomes. These limitations hinder the capacity to comprehensively characterize viral infections, such as those attributed to the Anelloviridae family. These near ubiquitous non-pathogenic components of the human virome have circular single-stranded DNA genomes that vary in size from 2.0 to 3.9 kb and exhibit high genetic diversity. Hence, species identification using short reads can be challenging. Here, we introduce a rolling circle amplification (RCA)-based metagenomic sequencing protocol tailored for circular single-stranded DNA genomes, utilizing the long-read Oxford Nanopore platform. The approach was assessed by sequencing anelloviruses in plasma drawn from people who inject drugs (PWID) in two geographically distinct cohorts. We detail the methodological adjustments implemented to overcome difficulties inherent in sequencing circular genomes and describe a computational pipeline focused on anellovirus detection. We assessed our protocol across various sample dilutions and successfully differentiated anellovirus sequences in conditions simulating mixed infections. This method provides a robust framework for the comprehensive characterization of circular viruses within the human virome using the Oxford Nanopore.}, } @article {pmid38791490, year = {2024}, author = {De Caro, C and Spagnuolo, R and Quirino, A and Mazza, E and Carrabetta, F and Maurotti, S and Cosco, C and Bennardo, F and Roberti, R and Russo, E and Giudice, A and Pujia, A and Doldo, P and Matera, G and Marascio, N}, title = {Gut Microbiota Profile Changes in Patients with Inflammatory Bowel Disease and Non-Alcoholic Fatty Liver Disease: A Metagenomic Study.}, journal = {International journal of molecular sciences}, volume = {25}, number = {10}, pages = {}, pmid = {38791490}, issn = {1422-0067}, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; Female ; Male ; Middle Aged ; Adult ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/isolation & purification ; Metagenome ; }, abstract = {Gut microbiota imbalances have a significant role in the pathogenesis of Inflammatory Bowel Disease (IBD) and Non-Alcoholic Fatty Liver Disease (NAFLD). Herein, we compared gut microbial composition in patients diagnosed with either IBD or NAFLD or a combination of both. Seventy-four participants were stratified into four groups: IBD-NAFLD, IBD-only, NAFLD-only patients, and healthy controls (CTRLs). The 16S rRNA was sequenced by Next-Generation Sequencing. Bioinformatics and statistical analysis were performed. Bacterial α-diversity showed a significant lower value when the IBD-only group was compared to the other groups and particularly against the IBD-NAFLD group. β-diversity also showed a significant difference among groups. The higher Bacteroidetes/Firmicutes ratio was found only when comparing IBD groups and CTRLs. Comparing the IBD-only group with the IBD-NAFLD group, a decrease in differential abundance of Subdoligranulum, Parabacteroides, and Fusicatenibacter was found. Comparing the NAFLD-only with the IBD-NAFLD groups, there was a higher abundance of Alistipes, Odoribacter, Sutterella, and Lachnospira. An inverse relationship in the comparison between the IBD-only group and the other groups was shown. For the first time, the singularity of the gut microbial composition in IBD and NAFLD patients has been shown, implying a potential microbial signature mainly influenced by gut inflammation.}, } @article {pmid38791249, year = {2024}, author = {Kim, S and Cho, M and Jung, ES and Sim, I and Woo, YR}, title = {Investigating Distinct Skin Microbial Communities and Skin Metabolome Profiles in Atopic Dermatitis.}, journal = {International journal of molecular sciences}, volume = {25}, number = {10}, pages = {}, pmid = {38791249}, issn = {1422-0067}, support = {NRF-2021R1I1A1A01052146//National Research Foundation of Korea/ ; }, mesh = {*Dermatitis, Atopic/microbiology/metabolism ; Humans ; *Skin/microbiology/metabolism ; *Metabolome ; Female ; Male ; *Microbiota ; Adult ; RNA, Ribosomal, 16S/genetics ; Metabolomics/methods ; Young Adult ; Middle Aged ; Case-Control Studies ; }, abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disorder influenced by genetic predisposition, environmental factors, immune dysregulation, and skin barrier dysfunction. The skin microbiome and metabolome play crucial roles in modulating the skin's immune environment and integrity. However, their specific contributions to AD remain unclear. We aimed to investigate the distinct skin microbial communities and skin metabolic compounds in AD patients compared to healthy controls (HCs). Seven patients with AD patients and seven HCs were enrolled, from whom skin samples were obtained for examination. The study involved 16S rRNA metagenomic sequencing and bioinformatics analysis as well as the use of gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) to detect metabolites associated with AD in the skin. We observed significant differences in microbial diversity between lesional and non-lesional skin of AD patients and HCs. Staphylococcus overgrowth was prominent in AD lesions, while Cutibacterium levels were decreased. Metabolomic analysis revealed elevated levels of several metabolites, including hypoxanthine and glycerol-3-phosphate in AD lesions, indicating perturbations in purine metabolism and energy production pathways. Moreover, we found a positive correlation between hypoxanthine and glycerol-3-phosphate and clinical severity of AD and Staphylococcus overgrowth. These findings suggest potential biomarkers for monitoring AD severity. Further research is needed to elucidate the causal relationships between microbial dysbiosis, metabolic alterations, and AD progression, paving the way for targeted therapeutic interventions.}, } @article {pmid38790239, year = {2024}, author = {Lei, Y and Ding, D and Duan, J and Luo, Y and Huang, F and Kang, Y and Chen, Y and Li, S}, title = {Soil Microbial Community Characteristics and Their Effect on Tea Quality under Different Fertilization Treatments in Two Tea Plantations.}, journal = {Genes}, volume = {15}, number = {5}, pages = {}, pmid = {38790239}, issn = {2073-4425}, support = {2022YFD1600801//the National Key R&D Program of China/ ; }, mesh = {*Soil Microbiology ; *Fertilizers/analysis ; *Tea/microbiology ; *Microbiota ; *Camellia sinensis/microbiology/genetics ; Soil/chemistry ; Bacteria/genetics/classification ; Nitrogen/metabolism/analysis ; Phosphorus/analysis/metabolism ; Fungi/genetics/classification ; }, abstract = {Fertilization is an essential aspect of tea plantation management that supports a sustainable tea production and drastically influences soil microbial communities. However, few research studies have focused on the differences of microbial communities and the variation in tea quality in response to different fertilization treatments. In this work, the soil fertility, tea quality, and soil microbial communities were investigated in two domestic tea plantations following the application of chemical and organic fertilizers. We determined the content of mineral elements in the soil, including nitrogen, phosphorus, and potassium, and found that the supplementation of chemical fertilizer directly increased the content of mineral elements. However, the application of organic fertilizer significantly improved the accumulation of tea polyphenols and reduced the content of caffeine. Furthermore, amplicon sequencing results showed that the different ways of applying fertilizer have limited effect on the alpha diversity of the microbial community in the soil while the beta diversity was remarkably influenced. This work also suggests that the bacterial community structure and abundance were also relatively constant while the fungal community structure and abundance were dramatically influenced; for example, Chaetomiaceae at the family level, Hypocreaceae at the order level, Trichoderma at the genus level, and Fusarium oxysporum at the species level were predominantly enriched in the tea plantation applying organic fertilizer. Moreover, the bacterial and fungal biomarkers were also analyzed and it was found that Proteobacteria and Gammaproteobacteria (bacteria) and Tremellomycetes (fungi) were potentially characterized as biomarkers in the plantation under organic fertilization. These results provide a valuable basis for the application of organic fertilizer to improve the soil of tea plantations in the future.}, } @article {pmid38790063, year = {2024}, author = {Zhang, B and Xiao, L and Lyu, L and Zhao, F and Miao, M}, title = {Exploring the landscape of symbiotic diversity and distribution in unicellular ciliated protists.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {96}, pmid = {38790063}, issn = {2049-2618}, mesh = {*Symbiosis ; *Ciliophora/genetics/classification/physiology ; *Bacteria/genetics/classification ; Archaea/genetics/classification ; Phylogeny ; Metagenome ; Biodiversity ; }, abstract = {BACKGROUND: The eukaryotic-bacterial symbiotic system plays an important role in various physiological, developmental, and evolutionary processes. However, our current understanding is largely limited to multicellular eukaryotes without adequate consideration of diverse unicellular protists, including ciliates.

RESULTS: To investigate the bacterial profiles associated with unicellular organisms, we collected 246 ciliate samples spanning the entire Ciliophora phylum and conducted single-cell based metagenome sequencing. This effort has yielded the most extensive collection of bacteria linked to unicellular protists to date. From this dataset, we identified 883 bacterial species capable of cohabiting with ciliates, unveiling the genomes of 116 novel bacterial cohabitants along with 7 novel archaeal cohabitants. Highlighting the intimate relationship between ciliates and their cohabitants, our study unveiled that over 90% of ciliates coexist with bacteria, with individual hosts fostering symbiotic relationships with multiple bacteria concurrently, resulting in the observation of seven distinct symbiotic patterns among bacteria. Our exploration of symbiotic mechanisms revealed the impact of host digestion on the intracellular diversity of cohabitants. Additionally, we identified the presence of eukaryotic-like proteins in bacteria as a potential contributing factor to their resistance against host digestion, thereby expanding their potential host range.

CONCLUSIONS: As the first large-scale analysis of prokaryotic associations with ciliate protists, this study provides a valuable resource for future research on eukaryotic-bacterial symbioses. Video Abstract.}, } @article {pmid38790062, year = {2024}, author = {Joannard, B and Sanchez-Cid, C}, title = {Bacterial dynamics of the plastisphere microbiome exposed to sub-lethal antibiotic pollution.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {97}, pmid = {38790062}, issn = {2049-2618}, support = {2022-52//Agence Regionale de Santé Île-de-France/ ; SARA//JPIAMR, Agence Nationale de la Recherche/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Microbiota/drug effects/genetics ; *RNA, Ribosomal, 16S/genetics ; Integrons/genetics ; Drug Resistance, Bacterial/genetics ; Water Pollutants, Chemical ; Microplastics ; High-Throughput Nucleotide Sequencing ; Metagenome ; Plasmids/genetics ; Water Microbiology ; Drug Resistance, Microbial/genetics ; }, abstract = {BACKGROUND: Antibiotics and microplastics are two major aquatic pollutants that have been associated to antibiotic resistance selection in the environment and are considered a risk to human health. However, little is known about the interaction of these pollutants at environmental concentrations and the response of the microbial communities in the plastisphere to sub-lethal antibiotic pollution. Here, we describe the bacterial dynamics underlying this response in surface water bacteria at the community, resistome and mobilome level using a combination of methods (next-generation sequencing and qPCR), sequencing targets (16S rRNA gene, pre-clinical and clinical class 1 integron cassettes and metagenomes), technologies (short and long read sequencing), and assembly approaches (non-assembled reads, genome assembly, bacteriophage and plasmid assembly).

RESULTS: Our results show a shift in the microbial community response to antibiotics in the plastisphere microbiome compared to surface water communities and describe the bacterial subpopulations that respond differently to antibiotic and microplastic pollution. The plastisphere showed an increased tolerance to antibiotics and selected different antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs). Several metagenome assembled genomes (MAGs) derived from the antibiotic-exposed plastisphere contained ARGs, virulence factors, and genes involved in plasmid conjugation. These include Comamonas, Chryseobacterium, the opportunistic pathogen Stenotrophomonas maltophilia, and other MAGs belonging to genera that have been associated to human infections, such as Achromobacter. The abundance of the integron-associated ciprofloxacin resistance gene aac(6')-Ib-cr increased under ciprofloxacin exposure in both freshwater microbial communities and in the plastisphere. Regarding the antibiotic mobilome, although no significant changes in ARG load in class 1 integrons and plasmids were observed in polluted samples, we identified three ARG-containing viral contigs that were integrated into MAGs as prophages.

CONCLUSIONS: This study illustrates how the selective nature of the plastisphere influences bacterial response to antibiotics at sub-lethal selective pressure. The microbial changes identified here help define the selective role of the plastisphere and its impact on the maintenance of environmental antibiotic resistance in combination with other anthropogenic pollutants. This research highlights the need to evaluate the impact of aquatic pollutants in environmental microbial communities using complex scenarios with combined stresses. Video Abstract.}, } @article {pmid38790049, year = {2024}, author = {Masuda, Y and Mise, K and Xu, Z and Zhang, Z and Shiratori, Y and Senoo, K and Itoh, H}, title = {Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {95}, pmid = {38790049}, issn = {2049-2618}, mesh = {*Soil Microbiology ; *Nitrogen Fixation/genetics ; *Metagenomics/methods ; *Microbiota/genetics ; *Deltaproteobacteria/genetics/classification/metabolism ; Soil/chemistry ; Phylogeny ; Nitrogen/metabolism ; Metagenome ; }, abstract = {BACKGROUND: Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome.

RESULTS: After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments).

CONCLUSION: Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.}, } @article {pmid38790030, year = {2024}, author = {Gao, Y and Zhong, Z and Zhang, D and Zhang, J and Li, YX}, title = {Exploring the roles of ribosomal peptides in prokaryote-phage interactions through deep learning-enabled metagenome mining.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {94}, pmid = {38790030}, issn = {2049-2618}, support = {(27107320, 17115322, and C6012-22GF)//Research Grants Council of Hong Kong/ ; }, mesh = {*Metagenome ; *Peptides/metabolism/genetics ; *Bacteriophages/genetics ; *Deep Learning ; *Metagenomics/methods ; *Ribosomes/metabolism/genetics ; *Bacteria/genetics/metabolism/virology/classification ; Microbiota/genetics ; Protein Processing, Post-Translational ; Seawater/microbiology/virology ; Oceans and Seas ; }, abstract = {BACKGROUND: Microbial secondary metabolites play a crucial role in the intricate interactions within the natural environment. Among these metabolites, ribosomally synthesized and post-translationally modified peptides (RiPPs) are becoming a promising source of therapeutic agents due to their structural diversity and functional versatility. However, their biosynthetic capacity and ecological functions remain largely underexplored.

RESULTS: Here, we aim to explore the biosynthetic profile of RiPPs and their potential roles in the interactions between microbes and viruses in the ocean, which encompasses a vast diversity of unique biomes that are rich in interactions and remains chemically underexplored. We first developed TrRiPP to identify RiPPs from ocean metagenomes, a deep learning method that detects RiPP precursors in a hallmark gene-independent manner to overcome the limitations of classic methods in processing highly fragmented metagenomic data. Applying this method to metagenomes from the global ocean microbiome, we uncover a diverse array of previously uncharacterized putative RiPP families with great novelty and diversity. Through correlation analysis based on metatranscriptomic data, we observed a high prevalence of antiphage defense-related and phage-related protein families that were co-expressed with RiPP families. Based on this putative association between RiPPs and phage infection, we constructed an Ocean Virus Database (OVD) and established a RiPP-involving host-phage interaction network through host prediction and co-expression analysis, revealing complex connectivities linking RiPP-encoding prokaryotes, RiPP families, viral protein families, and phages. These findings highlight the potential of RiPP families involved in prokaryote-phage interactions and coevolution, providing insights into their ecological functions in the ocean microbiome.

CONCLUSIONS: This study provides a systematic investigation of the biosynthetic potential of RiPPs from the ocean microbiome at a global scale, shedding light on the essential insights into the ecological functions of RiPPs in prokaryote-phage interactions through the integration of deep learning approaches, metatranscriptomic data, and host-phage connectivity. This study serves as a valuable example of exploring the ecological functions of bacterial secondary metabolites, particularly their associations with unexplored microbial interactions. Video Abstract.}, } @article {pmid38789907, year = {2024}, author = {Vishal, V and Das, T and Lal, S and Rahaman, S}, title = {Endophytic bacterial diversity in the latex-bearing caulosphere of Hevea brasiliensis Müll. Arg.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {55}, number = {3}, pages = {2473-2481}, pmid = {38789907}, issn = {1678-4405}, mesh = {*Hevea/microbiology ; *Latex/metabolism ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Endophytes/genetics/classification/isolation & purification/metabolism ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; India ; }, abstract = {Rubber trees are a commercial cash crop, and the milky latex or polyisoprene they produce is the natural source of rubber. Little is known about the bacterial populations found in active zone of latex-bearing caulosphere. We employed a tailored cloud microbial bioinformatic approach for the identification and potential hypothetical ecological roles of an uncultured endophytic hidden bacterial community in the active zone of the latex-bearing caulosphere of Hevea brasiliensis. Small pieces of slivers were collected from healthy plant from the village: Belonia, South Tripura, rubber plantation in Northeastern India. These uncultured bacteria were identified using the V3-V4 hypervariable amplicon region of the 16 S rDNA gene. A total of 209,586 contigs have been generated. EasyMAP Version 1.0, a cloud-based microbial bioinformatics tool with an integrated QIIME2 pipeline, was used to analyze contigs. We detected 15 phyla and 91 OTUs (operational taxonomic units). Proteobacteria (73.5%) was the most enriched phylum, followed by Firmicutes (13.8%), Bacteroidetes (5.2%), and Actinobacteria (3.2%). Ammonia oxidizers, sulfate reducers, dehalogenation, chitin degradation, nitrite reducers, and aromatic hydrocarbon degraders were the most prevalent functional categories in the active zones of caulosphere. Furthermore, Gammaproteobacteria (49.2%) and Erwinia (29.19%) were the most abundant classes and genera of endophytic bacterial communities. Thus, the presence of a substantial amount of phosphate-solubilizing Gammaproteobacteria (PSB) may stimulate growth, increase plant resilience, suppress disease, and aid in the rubber and sugar breakdown. This is the first report of microbial endophytes associated with Hevea caulosphere.}, } @article {pmid38788953, year = {2024}, author = {Osman, JR and Castillo, J and Sanhueza, V and Miller, AZ and Novoselov, A and Cotoras, D and Morales, D}, title = {Key energy metabolisms in modern living microbialites from hypersaline Andean lagoons of the Salar de Atacama, Chile.}, journal = {The Science of the total environment}, volume = {937}, number = {}, pages = {173469}, doi = {10.1016/j.scitotenv.2024.173469}, pmid = {38788953}, issn = {1879-1026}, mesh = {Chile ; *Energy Metabolism ; Salinity ; Microbiota ; Bacteria/metabolism ; Minerals/metabolism ; Cyanobacteria/metabolism/genetics ; Geologic Sediments/microbiology ; Oxidation-Reduction ; }, abstract = {Microbialites are organosedimentary structures formed mainly due to the precipitation of carbonate minerals, although they can also incorporate siliceous, phosphate, ferric, and sulfate minerals. The minerals' precipitation occurs because of local chemical changes triggered by changes in pH and redox transformations catalyzed by the microbial energy metabolisms. Here, geochemistry, metagenomics, and bioinformatics tools reveal the key energy metabolisms of microbial mats, stromatolites and an endoevaporite distributed across four hypersaline lagoons from the Salar de Atacama. Chemoautotrophic and chemoheterotrophic microorganisms seem to coexist and influence microbialite formation. The microbialite types of each lagoon host unique microbial communities and metabolisms that influence their geochemistry. Among them, photosynthetic, carbon- and nitrogen- fixing and sulfate-reducing microorganisms appear to control the main biogeochemical cycles. Genes associated with non-conventional energy pathways identified in MAGs, such as hydrogen production/consumption, arsenic oxidation/reduction, manganese oxidation and selenium reduction, also contribute to support life in microbialites. The presence of genes encoding for enzymes associated with ureolytic processes in the Cyanobacteria phylum and Gammaproteobacteria class might induce carbonate precipitation in hypersaline environments, contributing to the microbialites formation. To the best of our knowledge, this is the first study characterizing metagenomically microbialites enriched in manganese and identifying metabolic pathways associated with manganese oxidation, selenium reduction, and ureolysis in this ecosystem, which suggests that the geochemistry and bioavailability of energy sources (As, Mn and Se) shapes the microbial metabolisms in the microbialites.}, } @article {pmid38788173, year = {2024}, author = {Nguyen, CB and Vaishampayan, UN}, title = {Clinical Applications of the Gut Microbiome in Genitourinary Cancers.}, journal = {American Society of Clinical Oncology educational book. American Society of Clinical Oncology. Annual Meeting}, volume = {44}, number = {3}, pages = {e100041}, doi = {10.1200/EDBK_100041}, pmid = {38788173}, issn = {1548-8756}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Urogenital Neoplasms/microbiology ; Immunotherapy/methods ; Probiotics/therapeutic use ; }, abstract = {Recently recognized as one of the hallmarks of cancer, the microbiome consists of symbiotic microorganisms that play pivotal roles in carcinogenesis, the tumor microenvironment, and responses to therapy. With recent advances in microbiome metagenomic sequencing, a growing body of work has demonstrated that changes in gut microbiome composition are associated with differential responses to immune checkpoint inhibitors (ICIs) because of alterations in cytokine signaling and cytotoxic T-cell recruitment. Therefore, strategies to shape the gut microbiome into a more favorable, immunogenic profile may lead to improved responses with ICIs. Immunotherapy is commonly used in genitourinary (GU) cancers such as renal cell carcinoma, urothelial cancer, and to a limited extent, prostate cancer. However, a subset of patients do not derive clinical benefit with ICIs. Gut microbiome-based interventions are of particular interest given the potential to boost responses to ICIs in preclinical and early-phase prospective studies. Novel approaches using probiotic therapy (live bacterial supplementation) and fecal microbiota transplantation in patients with GU cancers are currently under investigation.}, } @article {pmid38785444, year = {2024}, author = {Liu, Y and Huang, Q and Zhuang, Z and Yang, H and Gou, X and Xu, T and Liu, K and Wang, J and Liu, B and Gao, P and Cao, F and Yang, B and Zhang, C and Chen, M and Fan, G}, title = {Gut virome alterations in patients with chronic obstructive pulmonary disease.}, journal = {Microbiology spectrum}, volume = {12}, number = {7}, pages = {e0428723}, pmid = {38785444}, issn = {2165-0497}, mesh = {*Pulmonary Disease, Chronic Obstructive/virology ; Humans ; *Virome ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Male ; Female ; Aged ; *Feces/virology/microbiology ; *Bacteriophages/genetics/classification/isolation & purification ; Bacteria/classification/genetics/isolation & purification/virology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; China ; }, abstract = {UNLABELLED: Chronic obstructive pulmonary disease (COPD) is one of the primary causes of mortality and morbidity worldwide. The gut microbiome, particularly the bacteriome, has been demonstrated to contribute to the progression of COPD. However, the influence of gut virome on the pathogenesis of COPD is rarely studied. Recent advances in viral metagenomics have enabled the rapid discovery of its remarkable role in COPD. In this study, deep metagenomics sequencing of fecal virus-like particles and bacterial 16S rRNA sequencing was performed on 92 subjects from China to characterize alterations of the gut virome in COPD. Lower richness and diversity of the gut virome were observed in the COPD subjects compared with the healthy individuals. Sixty-four viral species, including Clostridium phage, Myoviridae sp., and Synechococcus phage, showed positive relationships with pulmonary ventilation functions and had markedly declined population in COPD subjects. Multiple viral functions, mainly involved in bacterial susceptibility and the interaction between bacteriophages and bacterial hosts, were significantly declined in COPD. In addition, COPD was characterized by weakened viral-bacterial interactions compared with those in the healthy cohort. The gut virome showed diagnostic performance with an area under the curve (AUC) of 88.7%, which indicates the potential diagnostic value of the gut virome for COPD. These results suggest that gut virome may play an important role in the development of COPD. The information can provide a reference for the future investigation of diagnosis, treatment, and in-depth mechanism research of COPD.

IMPORTANCE: Previous studies showed that the bacteriome plays an important role in the progression of chronic obstructive pulmonary disease (COPD). However, little is known about the involvement of the gut virome in COPD. Our study explored the disease-specific virome signatures of patients with COPD. We found the diversity and compositions altered of the gut virome in COPD subjects compared with healthy individuals, especially those viral species positively correlated with pulmonary ventilation functions. Additionally, the declined bacterial susceptibility, the interaction between bacteriophages and bacterial hosts, and the weakened viral-bacterial interactions in COPD were observed. The findings also suggested the potential diagnostic value of the gut virome for COPD. The results highlight the significance of gut virome in COPD. The novel strategies for gut virome rectifications may help to restore the balance of gut microecology and represent promising therapeutics for COPD.}, } @article {pmid38785422, year = {2024}, author = {Costa, VA and Holmes, EC}, title = {Diversity, evolution, and emergence of fish viruses.}, journal = {Journal of virology}, volume = {98}, number = {6}, pages = {e0011824}, pmid = {38785422}, issn = {1098-5514}, support = {DP200102351//Department of Education and Training | Australian Research Council (ARC)/ ; GNT2017197//DHAC | National Health and Medical Research Council (NHMRC)/ ; }, mesh = {Animals ; Aquaculture/trends ; *Evolution, Molecular ; *Fish Diseases/transmission/virology ; *Fishes/classification/virology ; Genetic Variation ; Metagenomics ; Phylogeny ; Virome/genetics ; Virus Diseases/transmission/veterinary/virology ; *Viruses/genetics/classification ; }, abstract = {The production of aquatic animals has more than doubled over the last 50 years and is anticipated to continually increase. While fish are recognized as a valuable and sustainable source of nutrition, particularly in the context of human population growth and climate change, the rapid expansion of aquaculture coincides with the emergence of highly pathogenic viruses that often spread globally through aquacultural practices. Here, we provide an overview of the fish virome and its relevance for disease emergence, with a focus on the insights gained through metagenomic sequencing, noting potential areas for future study. In particular, we describe the diversity and evolution of fish viruses, for which the majority have no known disease associations, and demonstrate how viruses emerge in fish populations, most notably at an expanding domestic-wild interface. We also show how wild fish are a powerful and tractable model system to study virus ecology and evolution more broadly and can be used to identify the major factors that shape vertebrate viromes. Central to this is a process of virus-host co-divergence that proceeds over many millions of years, combined with ongoing cross-species virus transmission.}, } @article {pmid38785231, year = {2024}, author = {Goris, T and Braune, A}, title = {Genomics and physiology of Catenibacillus, human gut bacteria capable of polyphenol C-deglycosylation and flavonoid degradation.}, journal = {Microbial genomics}, volume = {10}, number = {5}, pages = {}, pmid = {38785231}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Polyphenols/metabolism ; *Flavonoids/metabolism ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Genomics ; Flavones/metabolism ; Glycosides/metabolism ; Phylogeny ; Feces/microbiology ; Glycosylation ; Xanthones/metabolism ; }, abstract = {The genus Catenibacillus (family Lachnospiraceae, phylum Bacillota) includes only one cultivated species so far, Catenibacillus scindens, isolated from human faeces and capable of deglycosylating dietary polyphenols and degrading flavonoid aglycones. Another human intestinal Catenibacillus strain not taxonomically resolved at that time was recently genome-sequenced. We analysed the genome of this novel isolate, designated Catenibacillus decagia, and showed its ability to deglycosylate C-coupled flavone and xanthone glucosides and O-coupled flavonoid glycosides. Most of the resulting aglycones were further degraded to the corresponding phenolic acids. Including the recently sequenced genome of C. scindens and ten faecal metagenome-assembled genomes assigned to the genus Catenibacillus, we performed a comparative genome analysis and searched for genes encoding potential C-glycosidases and other polyphenol-converting enzymes. According to genome data and physiological characterization, the core metabolism of Catenibacillus strains is based on a fermentative lifestyle with butyrate production and hydrogen evolution. Both C. scindens and C. decagia encode a flavonoid O-glycosidase, a flavone reductase, a flavanone/flavanonol-cleaving reductase and a phloretin hydrolase. Several gene clusters encode enzymes similar to those of the flavonoid C-deglycosylation system of Dorea strain PUE (DgpBC), while separately located genes encode putative polyphenol-glucoside oxidases (DgpA) required for C-deglycosylation. The diversity of dgpA and dgpBC gene clusters might explain the broad C-glycoside substrate spectrum of C. scindens and C. decagia. The other Catenibacillus genomes encode only a few potential flavonoid-converting enzymes. Our results indicate that several Catenibacillus species are well-equipped to deglycosylate and degrade dietary plant polyphenols and might inhabit a corresponding, specific niche in the gut.}, } @article {pmid38785049, year = {2023}, author = {Yanushevich, OO and Maev, IV and Krikheli, NI and Levchenko, OV and Galeeva, JS and Starikova, EV and Andreev, DN and Sokolov, PS and Fomenko, AK and Devkota, MK and Andreev, NG and Zaborovsky, AV and Evdokimov, VV and Tsaregorodtsev, SV and Ilina, EN and Govorun, VM and Bely, PA and Sabelnikova, EA and Solodov, AA and Cheremushkin, SV and Shaburov, RI and Kebina, AL}, title = {[Study of the resistome of human microbial communities using a targeted panel of antibiotic resistance genes in COVID-19 patients].}, journal = {Terapevticheskii arkhiv}, volume = {95}, number = {12}, pages = {1103-1111}, doi = {10.26442/00403660.2023.12.202490}, pmid = {38785049}, issn = {0040-3660}, mesh = {Humans ; *COVID-19/epidemiology ; Female ; Male ; Retrospective Studies ; Middle Aged ; *SARS-CoV-2/genetics ; Gastrointestinal Microbiome/drug effects/genetics ; Adult ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Microbial/genetics ; Severity of Illness Index ; Drug Resistance, Bacterial/genetics ; COVID-19 Drug Treatment ; }, abstract = {AIM: To study overall drug resistance genes (resistome) in the human gut microbiome and the changes in these genes during COVID-19 in-hospital therapy.

MATERIALS AND METHODS: A single-center retrospective cohort study was conducted. Only cases with laboratory-confirmed SARS-CoV-2 RNA using polymerase chain reaction in oro-/nasopharyngeal swab samples were subject to analysis. The patients with a documented history of or current comorbidities of the hepatobiliary system, malignant neoplasms of any localization, systemic and autoimmune diseases, as well as pregnant women were excluded. Feces were collected from all study subjects for subsequent metagenomic sequencing. The final cohort was divided into two groups depending on the disease severity: mild (group 1) and severe (group 2). Within group 2, five subgroups were formed, depending on the use of antibacterial drugs (ABD): group 2A (receiving ABD), group 2AC (receiving ABD before hospitalization), group 2AD (receiving ABD during hospitalization), group 2AE (receiving ABD during and before hospitalization), group 2B (not receiving ABD).

RESULTS: The median number of antibiotic resistance (ABR) genes (cumulative at all time points) was significantly higher in the group of patients treated with ABD: 81.0 (95% CI 73.8-84.5) vs. 51.0 (95% CI 31.1-68.4). In the group of patients treated with ABD (2A), the average number of multidrug resistance genes (efflux systems) was significantly higher than in controls (group 2B): 47.0 (95% CI 46.0-51.2) vs. 21.5 (95% CI 7.0-43.9). Patients with severe coronavirus infection tended to have a higher median number of ABR genes but without statistical significance. Patients in the severe COVID-19 group who did not receive ABD before and during hospitalization also had more resistance genes than the patients in the comparison group.

CONCLUSION: This study demonstrated that fewer ABR genes were identified in the group with a milder disease than in the group with a more severe disease associated with more ABR genes, with the following five being the most common: SULI, MSRC, ACRE, EFMA, SAT.}, } @article {pmid38783719, year = {2024}, author = {Liu, Y and Pang, H and Li, N and Jiao, Y and Zhang, Z and Zhu, Q}, title = {The Metabolic Functional Feature of Gut Microbiota in Mongolian Patients with Type 2 Diabetes.}, journal = {Journal of microbiology and biotechnology}, volume = {34}, number = {6}, pages = {1214-1221}, pmid = {38783719}, issn = {1738-8872}, mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Middle Aged ; Male ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Mongolia ; Female ; China ; Adult ; Metabolomics ; Firmicutes/isolation & purification ; Metagenomics ; Bacteroidetes/isolation & purification/metabolism/genetics ; Metabolic Networks and Pathways ; Aged ; }, abstract = {The accumulating evidence substantiates the indispensable role of gut microbiota in modulating the pathogenesis of type 2 diabetes. Uncovering the intricacies of the mechanism is imperative in aiding disease control efforts. Revealing key bacterial species, their metabolites and/or metabolic pathways from the vast array of gut microorganisms can significantly contribute to precise treatment of the disease. With a high prevalence of type 2 diabetes in Inner Mongolia, China, we recruited volunteers from among the Mongolian population to investigate the relationship between gut microbiota and the disease. Fecal samples were collected from the Volunteers of Mongolia with Type 2 Diabetes group and a Control group, and detected by metagenomic analysis and untargeted metabolomics analysis. The findings suggest that Firmicutes and Bacteroidetes phyla are the predominant gut microorganisms that exert significant influence on the pathogenesis of type 2 diabetes in the Mongolian population. In the disease group, despite an increase in the quantity of most gut microbial metabolic enzymes, there was a concomitant weakening of gut metabolic function, suggesting that the gut microbiota may be in a compensatory state during the disease stage. β-Tocotrienol may serve as a pivotal gut metabolite produced by gut microorganisms and a potential biomarker for type 2 diabetes. The metabolic biosynthesis pathways of ubiquinone and other terpenoid quinones could be the crucial mechanism through which the gut microbiota regulates type 2 diabetes. Additionally, certain Clostridium gut species may play a pivotal role in the progression of the disease.}, } @article {pmid38783065, year = {2024}, author = {Hsieh, YE and Tandon, K and Verbruggen, H and Nikoloski, Z}, title = {Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches.}, journal = {NPJ systems biology and applications}, volume = {10}, number = {1}, pages = {54}, pmid = {38783065}, issn = {2056-7189}, mesh = {*Metagenomics/methods ; *Bacteria/genetics/metabolism ; *Models, Biological ; Microbiota/genetics/physiology ; Metabolic Networks and Pathways/genetics ; Computational Biology/methods ; Computer Simulation ; }, abstract = {Genome-scale metabolic models (GEMs) of microbial communities offer valuable insights into the functional capabilities of their members and facilitate the exploration of microbial interactions. These models are generated using different automated reconstruction tools, each relying on different biochemical databases that may affect the conclusions drawn from the in silico analysis. One way to address this problem is to employ a consensus reconstruction method that combines the outcomes of different reconstruction tools. Here, we conducted a comparative analysis of community models reconstructed from three automated tools, i.e. CarveMe, gapseq, and KBase, alongside a consensus approach, utilizing metagenomics data from two marine bacterial communities. Our analysis revealed that these reconstruction approaches, while based on the same genomes, resulted in GEMs with varying numbers of genes and reactions as well as metabolic functionalities, attributed to the different databases employed. Further, our results indicated that the set of exchanged metabolites was more influenced by the reconstruction approach rather than the specific bacterial community investigated. This observation suggests a potential bias in predicting metabolite interactions using community GEMs. We also showed that consensus models encompassed a larger number of reactions and metabolites while concurrently reducing the presence of dead-end metabolites. Therefore, the usage of consensus models allows making full and unbiased use from aggregating genes from the different reconstructions in assessing the functional potential of microbial communities.}, } @article {pmid38782729, year = {2024}, author = {Alessandri, G and Fontana, F and Mancabelli, L and Tarracchini, C and Lugli, GA and Argentini, C and Longhi, G and Rizzo, SM and Vergna, LM and Anzalone, R and Viappiani, A and Turroni, F and Ossiprandi, MC and Milani, C and Ventura, M}, title = {Species-level characterization of saliva and dental plaque microbiota reveals putative bacterial and functional biomarkers of periodontal diseases in dogs.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {6}, pages = {}, pmid = {38782729}, issn = {1574-6941}, support = {//Fondazione Cariparma/ ; }, mesh = {Animals ; Dogs ; *Saliva/microbiology ; *Biomarkers ; *Dental Plaque/microbiology ; *Periodontal Diseases/microbiology/veterinary ; *Microbiota ; *Dog Diseases/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Porphyromonas/genetics/isolation & purification ; Metagenomics ; Mouth/microbiology ; Male ; }, abstract = {Periodontal diseases are among the most common bacterial-related pathologies affecting the oral cavity of dogs. Nevertheless, the canine oral ecosystem and its correlations with oral disease development are still far from being fully characterized. In this study, the species-level taxonomic composition of saliva and dental plaque microbiota of 30 healthy dogs was investigated through a shallow shotgun metagenomics approach. The obtained data allowed not only to define the most abundant and prevalent bacterial species of the oral microbiota in healthy dogs, including members of the genera Corynebacterium and Porphyromonas, but also to identify the presence of distinct compositional motifs in the two oral microniches as well as taxonomical differences between dental plaques collected from anterior and posterior teeth. Subsequently, the salivary and dental plaque microbiota of 18 dogs affected by chronic gingival inflammation and 18 dogs with periodontitis were compared to those obtained from the healthy dogs. This analysis allowed the identification of bacterial and metabolic biomarkers correlated with a specific clinical status, including members of the genera Porphyromonas and Fusobacterium as microbial biomarkers of a healthy and diseased oral status, respectively, and genes predicted to encode for metabolites with anti-inflammatory properties as metabolic biomarkers of a healthy status.}, } @article {pmid38780806, year = {2024}, author = {Islam, MM and Jana, SK and Sengupta, S and Mandal, S}, title = {Impact of Rhizospheric Microbiome on Rice Cultivation.}, journal = {Current microbiology}, volume = {81}, number = {7}, pages = {188}, pmid = {38780806}, issn = {1432-0991}, mesh = {*Oryza/microbiology/growth & development ; *Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Bacteria/classification/metabolism/genetics ; Agriculture/methods ; }, abstract = {The rhizosphere niche is extremely important for the overall growth and development of plants. Evidently, it is necessary to understand the complete mechanism of plant microbe interactions of the rhizosphere for sustainable and low input productivity. To meet the increasing global food demand, rice (Oryza sativa L.) agriculture seeks optimal conditions. The unique oxic-anoxic interface of rice-growing soil has invited divergent microbes with dynamic biogeochemical cycles. This review provides the systematic analysis of microbes associated with the major biogeochemical cycles with the aim to generate better management strategies of rhizospheric microbiome in the field of rice agriculture. For instance, several methanogenic and methanotrophic bacteria in the rice rhizosphere make an equilibrium for methane concentration in the environment. The carbon sequestration in paddy soil is again done through many rhizospheric microorganisms that can directly assimilate CO2 with their photoautotrophic mode of nutrition. Also the phosphate solubilizing microbes remain to be the most important keys for the PGPR activity of the paddy ecosystem. In addition, rhizospheric microbiome remain crucial in degradation and solubilization of organo-sulfur and insoluble inorganic sulfides which can be taken by the plants. Further, this review elucidates on the advantages of using metagenomic and metaproteomic approaches as an alternative of traditional approaches to understand the overall metabolic pathways operational in paddy-field. These knowledges are expected to open new possibilities for designing the balanced microbiome used as inoculum for intensive farming and will eventually lead to exert positive impacts on rice cultivation.}, } @article {pmid38780313, year = {2024}, author = {Güven Gülhan, Ü and Nikerel, E and Çakır, T and Erdoğan Sevilgen, F and Durmuş, S}, title = {Species-level identification of enterotype-specific microbial markers for colorectal cancer and adenoma.}, journal = {Molecular omics}, volume = {20}, number = {6}, pages = {397-416}, doi = {10.1039/d4mo00016a}, pmid = {38780313}, issn = {2515-4184}, mesh = {Humans ; *Adenoma/microbiology ; Biomarkers, Tumor ; *Colorectal Neoplasms/microbiology ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics/methods ; }, abstract = {Enterotypes have been shown to be an important factor for population stratification based on gut microbiota composition, leading to a better understanding of human health and disease states. Classifications based on compositional patterns will have implications for personalized microbiota-based solutions. There have been limited enterotype based studies on colorectal adenoma and cancer. Here, an enterotype-based meta-analysis of fecal shotgun metagenomic studies was performed, including 1579 samples of healthy controls (CTR), colorectal adenoma (ADN) and colorectal cancer (CRC) in total. Gut microbiota of healthy people were clustered into three enterotypes (Ruminococcus-, Bacteroides- and Prevotella-dominated enterotypes). Reference-based enterotype assignments were performed for CRC and ADN samples, using the supervised machine learning algorithm, K-nearest neighbors. Differential abundance analyses and random forest classification were conducted on each enterotype between healthy controls and CRC-ADN groups, revealing novel enterotype-specific microbial markers for non-invasive CRC screening strategies. Furthermore, we identified microbial species unique to each enterotype that play a role in the production of secondary bile acids and short-chain fatty acids, unveiling the correlation between cancer-associated gut microbes and dietary patterns. The enterotype-based approach in this study is promising in elucidating the mechanisms of differential gut microbiome profiles, thereby improving the efficacy of personalized microbiota-based solutions.}, } @article {pmid38780275, year = {2024}, author = {Cai, L and Wang, X and Zhu, X and Xu, Y and Qin, W and Ren, J and Jiang, Q and Yan, X}, title = {Lactobacillus-derived protoporphyrin IX and SCFAs regulate the fiber size via glucose metabolism in the skeletal muscle of chickens.}, journal = {mSystems}, volume = {9}, number = {6}, pages = {e0021424}, pmid = {38780275}, issn = {2379-5077}, support = {2023YFD1301304//the National Key Research and Development Project/ ; Project 2662023DKPY002//MOE | Fundamental Research Funds for the Central Universities (Fundamental Research Fund for the Central Universities)/ ; 2019TQ0108//China Postdoctoral Science Foundation (China Postdoctoral Foundation Project)/ ; }, mesh = {Animals ; *Chickens/metabolism/microbiology ; *Glucose/metabolism ; *Gastrointestinal Microbiome/physiology ; *Fatty Acids, Volatile/metabolism ; *Lactobacillus/metabolism ; Muscle, Skeletal/metabolism ; Muscle Fibers, Skeletal/metabolism ; Energy Metabolism ; Fecal Microbiota Transplantation ; }, abstract = {The gut microbiota contributes to skeletal muscle energy metabolism and is an indirect factor affecting meat quality. However, the role of specific gut microbes in energy metabolism and fiber size of skeletal muscle in chickens remains largely unknown. In this study, we first performed cecal microbiota transplantation from Chinese indigenous Jingyuan chickens (JY) to Arbor Acres chickens (AA), to determine the effects of microbiota on skeletal muscle fiber and energy metabolism. Then, we used metagenomics, gas chromatography, and metabolomics analysis to identify functional microbes. Finally, we validated the role of these functional microbes in regulating the fiber size via glucose metabolism in the skeletal muscle of chickens through feeding experiments. The results showed that the skeletal muscle characteristics of AA after microbiota transplantation tended to be consistent with that of JY, as the fiber diameter was significantly increased, and glucose metabolism level was significantly enhanced in the pectoralis muscle. L. plantarum, L. ingluviei, L. salivarius, and their mixture could increase the production of the microbial metabolites protoporphyrin IX and short-chain fatty acids, therefore increasing the expression levels of genes related to the oxidative fiber type (MyHC SM and MyHC FRM), mitochondrial function (Tfam and CoxVa), and glucose metabolism (PFK, PK, PDH, IDH, and SDH), thereby increasing the fiber diameter and density. These three Lactobacillus species could be promising probiotics to improve the meat quality of chicken.IMPORTANCEThis study revealed that the L. plantarum, L. ingluviei, and L. salivarius could enhance the production of protoporphyrin IX and short-chain fatty acids in the cecum of chickens, improving glucose metabolism, and finally cause the increase in fiber diameter and density of skeletal muscle. These three microbes could be potential probiotic candidates to regulate glucose metabolism in skeletal muscle to improve the meat quality of chicken in broiler production.}, } @article {pmid38780265, year = {2024}, author = {Zheng, L and Jiao, Y and Zhong, H and Tan, Y and Yin, Y and Liu, Y and Liu, D and Wu, M and Wang, G and Huang, J and Wang, P and Qin, M and Wang, M and Xiao, Y and Lv, T and Luo, Y and Hu, H and Hou, S-T and Kui, L}, title = {Human-derived fecal microbiota transplantation alleviates social deficits of the BTBR mouse model of autism through a potential mechanism involving vitamin B6 metabolism.}, journal = {mSystems}, volume = {9}, number = {6}, pages = {e0025724}, pmid = {38780265}, issn = {2379-5077}, support = {SZSM202103007//The Sanming Project of Medicine in Shenzhen Nanshan/ ; NSZD2023046//Major Program of Shenzhen Nanshan/ ; 81871026//MOST | National Natural Science Foundation of China (NSFC)/ ; 32371029//MOST | National Natural Science Foundation of China (NSFC)/ ; 2023SHIBS0002//the Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions/ ; B2301001//Shenzhen Medical Research Fund/ ; }, mesh = {Animals ; *Fecal Microbiota Transplantation ; Mice ; Humans ; *Disease Models, Animal ; *Vitamin B 6/metabolism ; Gastrointestinal Microbiome ; Male ; Social Behavior ; Autism Spectrum Disorder/therapy/metabolism/microbiology ; Autistic Disorder/therapy/metabolism/microbiology ; }, abstract = {Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition characterized by social communication deficiencies and stereotypic behaviors influenced by hereditary and/or environmental risk factors. There are currently no approved medications for treating the core symptoms of ASD. Human fecal microbiota transplantation (FMT) has emerged as a potential intervention to improve autistic symptoms, but the underlying mechanisms are not fully understood. In this study, we evaluated the effects of human-derived FMT on behavioral and multi-omics profiles of the BTBR mice, an established model for ASD. FMT effectively alleviated the social deficits in the BTBR mice and normalized their distinct plasma metabolic profile, notably reducing the elevated long-chain acylcarnitines. Integrative analysis linked these phenotypic changes to specific Bacteroides species and vitamin B6 metabolism. Indeed, vitamin B6 supplementation improved the social behaviors in BTBR mice. Collectively, these findings shed new light on the interplay between FMT and vitamin B6 metabolism and revealed a potential mechanism underlying the therapeutic role of FMT in ASD.IMPORTANCEAccumulating evidence supports the beneficial effects of human fecal microbiota transplantation (FMT) on symptoms associated with autism spectrum disorder (ASD). However, the precise mechanism by which FMT induces a shift in the microbiota and leads to symptom improvement remains incompletely understood. This study integrated data from colon-content metagenomics, colon-content metabolomics, and plasma metabolomics to investigate the effects of FMT treatment on the BTBR mouse model for ASD. The analysis linked the amelioration of social deficits following FMT treatment to the restoration of mitochondrial function and the modulation of vitamin B6 metabolism. Bacterial species and compounds with beneficial roles in vitamin B6 metabolism and mitochondrial function may further contribute to improving FMT products and designing novel therapies for ASD treatment.}, } @article {pmid38779561, year = {2024}, author = {Guo, Y and Wang, W and Yu, Y and Sun, X and Zhang, B and Wang, Y and Cao, J and Wen, S and Wang, X and Li, Y and Cai, S and Wu, R and Duan, W and Xia, W and Wei, F and Duan, J and Dong, H and Guo, S and Zhang, F and Sun, Z and Huang, X}, title = {Crosstalk between human immunodeficiency virus infection and salivary bacterial function in men who have sex with men.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1341545}, pmid = {38779561}, issn = {2235-2988}, mesh = {Humans ; Male ; *Saliva/microbiology/virology ; *HIV Infections/microbiology ; *Homosexuality, Male ; *RNA, Ribosomal, 16S/genetics ; Adult ; Bacteria/classification/genetics/isolation & purification ; Microbiota ; Metagenomics ; CD4 Lymphocyte Count ; Middle Aged ; Young Adult ; Sexual and Gender Minorities ; }, abstract = {BACKGROUND: Engaging in anal sexual intercourse markedly increases the risk of developing HIV among men who have sex with men (MSM); oral sexual activities tend to uniquely introduce gut-derived microbes to salivary microbiota, which, combined with an individual's positive HIV status, may greatly perturb oral microecology. However, till date, only a few published studies have addressed this aspect.

METHODS: Based on 16S rRNA sequencing data of bacterial taxa, MicroPITA picks representative samples for metagenomic analysis, effectively revealing how the development and progression of the HIV disease influences oral microbiota in MSM. Therefore, we collected samples from 11 HIV-negative and 44 HIV-positive MSM subjects (stage 0 was defined by HIV RNA positivity, but negative or indeterminate antibody status; stages 1, 2, and 3 were defined by CD4[+] T lymphocyte counts ≥ 500, 200-499, and ≤ 200 or opportunistic infection) and selected 25 representative saliva samples (5 cases/stage) using MicroPITA. Metagenomic sequencing analysis were performed to explore whether positive HIV status changes salivary bacterial KEGG function and metabolic pathway in MSM.

RESULTS: The core functions of oral microbiota were maintained across each of the five groups, including metabolism, genetic and environmental information processing. All HIV-positive groups displayed KEGG functions of abnormal proliferation, most prominently at stage 0, and others related to metabolism. Clustering relationship analysis tentatively identified functional relationships between groups, with bacterial function being more similar between stage 0-control groups and stage 1-2 groups, whereas the stage 3 group exhibited large functional changes. Although we identified most metabolic pathways as being common to all five groups, several unique pathways formed clusters for certain groups; the stage 0 group had several, while the stage 2 and 3 groups had few, such clusters. The abundance of K03046 was positively correlated with CD4 counts.

CONCLUSION: As HIV progresses, salivary bacterial function and metabolic pathways in MSM progressively changes, which may be related to HIV promoting abnormal energy metabolism and exacerbate pathogen virulence. Further, infection and drug resistance of acute stage and immune cell destruction of AIDS stage were abnormally increased, predicting an increased risk for MSM individuals to develop systemic and oral diseases.}, } @article {pmid38779558, year = {2024}, author = {Hansen, ZA and Schilmiller, AL and Guzior, DV and Rudrik, JT and Quinn, RA and Vasco, KA and Manning, SD}, title = {Shifts in the functional capacity and metabolite composition of the gut microbiome during recovery from enteric infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1359576}, pmid = {38779558}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Feces/microbiology/chemistry ; *Metabolome ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Metabolic Networks and Pathways ; Adult ; Metabolomics ; Aged ; Bacteria/classification/metabolism/genetics/isolation & purification ; Young Adult ; }, abstract = {While enteric pathogens have been widely studied for their roles in causing foodborne infection, their impacts on the gut microbial community have yet to be fully characterized. Previous work has identified notable changes in the gut microbiome related to pathogen invasion, both taxonomically and genetically. Characterization of the metabolic landscape during and after enteric infection, however, has not been explored. Consequently, we investigated the metabolome of paired stools recovered from 60 patients (cases) during and after recovery from enteric bacterial infections (follow-ups). Shotgun metagenomics was applied to predict functional microbial pathways combined with untargeted metametabolomics classified by Liquid Chromatography Mass Spectrometry. Notably, cases had a greater overall metabolic capacity with significantly higher pathway richness and evenness relative to the follow-ups (p<0.05). Metabolic pathways related to central carbon metabolism, amino acid metabolism, and lipid and fatty acid biosynthesis were more highly represented in cases and distinct signatures for menaquinone production were detected. By contrast, the follow-up samples had a more diverse metabolic landscape with enhanced richness of polar metabolites (p<0.0001) and significantly greater richness, evenness, and overall diversity of nonpolar metabolites (p<0.0001). Although many metabolites could not be annotated with existing databases, a marked increase in certain clusters of metabolites was observed in the follow-up samples when compared to the case samples and vice versa. These findings suggest the importance of key metabolites in gut health and recovery and enhance understanding of metabolic fluctuations during enteric infections.}, } @article {pmid38778483, year = {2024}, author = {Yan, J and Chen, H and Zhang, Y and Peng, L and Wang, Z and Lan, X and Yu, S and Yang, Y}, title = {Fecal microbiota transplantation significantly improved respiratory failure of amyotrophic lateral sclerosis.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2353396}, pmid = {38778483}, issn = {1949-0984}, mesh = {Humans ; *Amyotrophic Lateral Sclerosis/therapy/microbiology ; Bacteroides ; Faecalibacterium prausnitzii ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Gastrointestinal Microbiome ; Respiration, Artificial ; *Respiratory Insufficiency/therapy/microbiology ; Treatment Outcome ; }, abstract = {Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease that leads to respiratory failure, and eventually death. However, there is a lack of effective treatments for ALS. Here we report the results of fecal microbiota transplantation (FMT) in two patients with late-onset classic ALS with a Japan ALS severity classification of grade 5 who required tracheostomy and mechanical ventilation. In both patients, significant improvements in respiratory function were observed following two rounds of FMT, leading to weaning off mechanical ventilation. Their muscle strength improved, allowing for assisted standing and mobility. Other notable treatment responses included improved swallowing function and reduced muscle fasciculations. Metagenomic and metabolomic analysis revealed an increase in beneficial Bacteroides species (Bacteroides stercoris, Bacteroides uniformis, Bacteroides vulgatus), and Faecalibacterium prausnitzii after FMT, as well as elevated levels of metabolites involved in arginine biosynthesis and decreased levels of metabolites involved in branched-chain amino acid biosynthesis. These findings offer a potential rescue therapy for ALS with respiratory failure and provide new insights into ALS in general.}, } @article {pmid38778276, year = {2024}, author = {Alsharif, SM and Ismaeil, M and Saeed, AM and El-Sayed, WS}, title = {Metagenomic 16S rRNA analysis and predictive functional profiling revealed intrinsic organohalides respiration and bioremediation potential in mangrove sediment.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {176}, pmid = {38778276}, issn = {1471-2180}, mesh = {*Geologic Sediments/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Biodegradation, Environmental ; *Phylogeny ; *Microbiota/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Indian Ocean ; Metagenomics ; DNA, Bacterial/genetics ; Wetlands ; Metagenome ; }, abstract = {BACKGROUND: Mangrove sediment microbes are increasingly attracting scientific attention due to their demonstrated capacity for diverse bioremediation activities, encompassing a wide range of environmental contaminants.

MATERIALS AND METHODS: The microbial communities of five Avicennia marina mangrove sediment samples collected from Al Rayyis White Head, Red Sea (KSA), were characterized using Illumina amplicon sequencing of the 16S rRNA genes.

RESULTS: Our study investigated the microbial composition and potential for organohalide bioremediation in five mangrove sediments from the Red Sea. While Proteobacteria dominated four microbiomes, Bacteroidetes dominated the fifth. Given the environmental concerns surrounding organohalides, their bioremediation is crucial. Encouragingly, we identified phylogenetically diverse organohalide-respiring bacteria (OHRB) across all samples, including Dehalogenimonas, Dehalococcoides, Anaeromyxobacter, Desulfuromonas, Geobacter, Desulfomonile, Desulfovibrio, Shewanella and Desulfitobacterium. These bacteria are known for their ability to dechlorinate organohalides through reductive dehalogenation. PICRUSt analysis further supported this potential, predicting the presence of functional biomarkers for organohalide respiration (OHR), including reductive dehalogenases targeting tetrachloroethene (PCE) and 3-chloro-4-hydroxyphenylacetate in most sediments. Enrichment cultures studies confirmed this prediction, demonstrating PCE dechlorination by the resident microbial community. PICRUSt also revealed a dominance of anaerobic metabolic processes, suggesting the microbiome's adaptation to the oxygen-limited environment of the sediments.

CONCLUSION: This study provided insights into the bacterial community composition of five mangrove sediments from the Red Sea. Notably, diverse OHRB were detected across all samples, which possess the metabolic potential for organohalide bioremediation through reductive dehalogenation pathways. Furthermore, PICRUSt analysis predicted the presence of functional biomarkers for OHR in most sediments, suggesting potential intrinsic OHR activity by the enclosed microbial community.}, } @article {pmid38777200, year = {2024}, author = {Peng, L and Hou, J and Zhang, Y and Wang, B and Zhang, Y and Zhao, K and Wang, Q and Christie, P and Liu, W and Luo, Y}, title = {Metagenomic analysis of a thermophilic bacterial consortium and its use in the bioremediation of a petroleum-contaminated soil.}, journal = {Chemosphere}, volume = {360}, number = {}, pages = {142379}, doi = {10.1016/j.chemosphere.2024.142379}, pmid = {38777200}, issn = {1879-1298}, mesh = {*Biodegradation, Environmental ; *Petroleum/metabolism ; *Soil Pollutants/metabolism/analysis ; *Soil Microbiology ; *Metagenomics ; *Bacteria/metabolism/genetics/classification ; Microbial Consortia ; Hydrocarbons/metabolism ; Petroleum Pollution ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; Alkanes/metabolism ; }, abstract = {Biodegradation is difficult at high temperatures due to the limited capacity of microorganisms to survive and function outside their optimum temperature range. Here, a thermophilic petroleum-degrading consortium was enriched from compost at a temperature of 55 °C. 16S rDNA and metagenomic techniques were used to analyze the composition of the consortium and the mechanisms of degradation. The consortium degraded 17000 mg total petroleum hydrocarbons (TPHs) L[-1] with a degradation efficiency of 81.5% in 14 days. The consortium utilized a range of substrates such as n-hexadecane, n-docosane, naphthalene and pyrene and grew well over a wide range of pH (4-10) and salinity (0-90 g L[-1]). The hydrocarbon-degrading extremophilic consortium contained, inter alia, (relative abundance >1%) Caldibacillus, Geobacillus, Mycolicibacterium, Bacillus, Chelatococcus, and Aeribacillus spp. Metagenomic analysis was conducted to discover the degradation and environmental tolerance functional genes of the consortium. Two alkane hydroxylase genes, alkB and ladA, were found. A microcosm study shows that the consortium promoted the bioremediation of soil TPHs. The results indicate that the consortium may be a good candidate for the high-temperature bioremediation of petroleum-contaminated soils.}, } @article {pmid38776984, year = {2024}, author = {Mogotsi, MT and Ogunbayo, AE and Bester, PA and O'Neill, HG and Nyaga, MM}, title = {Longitudinal analysis of the enteric virome in paediatric subjects from the Free State Province, South Africa, reveals early gut colonisation and temporal dynamics.}, journal = {Virus research}, volume = {346}, number = {}, pages = {199403}, pmid = {38776984}, issn = {1872-7492}, mesh = {Humans ; *Virome ; South Africa ; Infant ; Longitudinal Studies ; *Feces/virology ; Infant, Newborn ; Gastrointestinal Microbiome ; Male ; Female ; Viruses/classification/isolation & purification/genetics ; Metagenomics ; Gastrointestinal Tract/virology ; Gastroenteritis/virology ; Sapovirus/genetics/isolation & purification/classification ; Norovirus/genetics/isolation & purification/classification ; Picornaviridae/genetics/classification/isolation & purification ; Caliciviridae/genetics/isolation & purification/classification ; Metagenome ; }, abstract = {The gut of healthy neonates is devoid of viruses at birth, but rapidly becomes colonised by normal viral commensals that aid in important physiological functions like metabolism but can, in some instances, result in gastrointestinal illnesses. However, little is known about how this colonisation begins, its variability and factors shaping the gut virome composition. Thus, understanding the development, assembly, and progression of enteric viral communities over time is key. To explore early-life virome development, metagenomic sequencing was employed in faecal samples collected longitudinally from a cohort of 17 infants during their first six months of life. The gut virome analysis revealed a diverse and dynamic viral community, formed by a richness of different viruses infecting humans, non-human mammals, bacteria, and plants. Eukaryotic viruses were detected as early as one week of life, increasing in abundance and diversity over time. Most of the viruses detected are commonly associated with gastroenteritis and include members of the Caliciviridae, Picornaviridae, Astroviridae, Adenoviridae, and Sedoreoviridae families. The most common co-occurrences involved asymptomatic norovirus-parechovirus, norovirus-sapovirus, sapovirus-parechovirus, observed in at least 40 % of the samples. Majority of the plant-derived viruses detected in the infants' gut were from the Virgaviridae family. This study demonstrates the first longitudinal characterisation of the gastrointestinal virome in infants, from birth up to 6 months of age, in sub-Saharan Africa. Overall, the findings from this study delineate the composition and variability of the healthy infants' gut virome over time, which is a significant step towards understanding the dynamics and biogeography of viral communities in the infant gut.}, } @article {pmid38776961, year = {2024}, author = {Remaks, JD and Vientos-Plotts, AI and Rindt, H and McAdams, Z and Ericsson, AC and Reinero, CR}, title = {Multistrain probiotics fail to modulate the asthmatic phenotype, respiratory microbiota, and immune responses in cats.}, journal = {American journal of veterinary research}, volume = {85}, number = {8}, pages = {}, doi = {10.2460/ajvr.23.12.0271}, pmid = {38776961}, issn = {1943-5681}, mesh = {Animals ; Cats ; *Asthma/veterinary/immunology ; *Probiotics/pharmacology/administration & dosage/therapeutic use ; *Cat Diseases/immunology/microbiology ; Female ; Male ; Microbiota/drug effects ; Bronchoalveolar Lavage Fluid/cytology ; Glucocorticoids/therapeutic use ; Phenotype ; }, abstract = {OBJECTIVE: To determine if multistrain probiotics administered to asthmatic cats treated with anti-inflammatory glucocorticoids would attenuate the asthmatic phenotype and beneficially alter respiratory, blood, and oropharyngeal (OP) microbial communities and immune parameters versus placebo.

ANIMALS: 13 client-owned asthmatic cats.

METHODS: A randomized, blinded, placebo-controlled clinical trial of asthmatic cats receiving anti-inflammatory glucocorticoids with oral multistrain probiotics or placebo assessed owner-perceived improvement and airway eosinophilia at baseline and after 2 weeks of treatment. Bronchoalveolar lavage fluid (BALF), blood, OP, and rectal microbial communities were compared using 16S rRNA amplicon sequencing. Real-time PCR for transcription factors, activation markers and cytokines, and IgA ELISAs were evaluated. Statistical analyses used 2-way repeated-measures ANOVA or permutational ANOVA (significance, P < .05).

RESULTS: After treatment, there were no significant differences in owner-perceived clinical signs or mean ± SEM BALF eosinophils between groups. There was a significant decrease in rectal α-diversity but not in α- or β-diversity in BALF, blood, or OP between groups or over time. There were no significant differences in CD25, FoxP3, GATA, Helios, IL-4, IL-5, IL-10, IL-13, IL-17, IFN-γ mRNA, or serum or BALF IgA between groups or over time.

CLINICAL RELEVANCE: In asthmatic cats, oral multistrain probiotics failed to improve owner-perceived signs, reduce airway eosinophilia, modify microbial community composition, or alter assessed immune responses versus placebo or over time. Longer treatment, different probiotic composition or delivery (eg, aerosolized), or larger number of cats would represent the next stages of study.}, } @article {pmid38776919, year = {2024}, author = {Yan, Q and Li, S and Yan, Q and Huo, X and Wang, C and Wang, X and Sun, Y and Zhao, W and Yu, Z and Zhang, Y and Guo, R and Lv, Q and He, X and Yao, C and Li, Z and Chen, F and Ji, Q and Zhang, A and Jin, H and Wang, G and Feng, X and Feng, L and Wu, F and Ning, J and Deng, S and An, Y and Guo, DA and Martin, FM and Ma, X}, title = {A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases.}, journal = {Cell}, volume = {187}, number = {12}, pages = {2969-2989.e24}, doi = {10.1016/j.cell.2024.04.043}, pmid = {38776919}, issn = {1097-4172}, mesh = {Animals ; Humans ; Male ; Mice ; Feces/microbiology ; *Fungi/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome ; Genome, Fungal/genetics ; Genomics ; Inflammatory Bowel Diseases/microbiology/genetics ; Metagenome ; *Mycobiome ; Phylogeny ; Female ; Adult ; Middle Aged ; }, abstract = {The gut fungal community represents an essential element of human health, yet its functional and metabolic potential remains insufficiently elucidated, largely due to the limited availability of reference genomes. To address this gap, we presented the cultivated gut fungi (CGF) catalog, encompassing 760 fungal genomes derived from the feces of healthy individuals. This catalog comprises 206 species spanning 48 families, including 69 species previously unidentified. We explored the functional and metabolic attributes of the CGF species and utilized this catalog to construct a phylogenetic representation of the gut mycobiome by analyzing over 11,000 fecal metagenomes from Chinese and non-Chinese populations. Moreover, we identified significant common disease-related variations in gut mycobiome composition and corroborated the associations between fungal signatures and inflammatory bowel disease (IBD) through animal experimentation. These resources and findings substantially enrich our understanding of the biological diversity and disease relevance of the human gut mycobiome.}, } @article {pmid38776859, year = {2024}, author = {Yang, C and Dong, B and Chen, A and Jiang, Y and Bai, H and Chen, G and Chang, G and Wang, Z}, title = {Metagenomic insights into the relationship between intestinal flora and residual feed intake of meat ducks.}, journal = {Poultry science}, volume = {103}, number = {7}, pages = {103836}, pmid = {38776859}, issn = {1525-3171}, mesh = {Animals ; *Ducks/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/analysis ; Animal Feed/analysis ; Male ; Cecum/microbiology ; Eating ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {In this study, we sought to determine the effects of intestinal flora on the feed efficiency of meat ducks by evaluating the correlation between intestinal flora and residual feed intake. The F2 generation of Cherry Valley ducks × Runzhou Crested White ducks was used as the study subjects, and feed consumption being recorded from d 21 to 42. RFI was calculated based on growth performance, and 20 low RFI and 20 high RFI ducks were randomly selected to characterize the effect of RFI on growth performance. To analyze the intestinal flora affecting RFI, 16s rDNA sequencing was performed on the contents of 5 intestinal segments from the HR and LR groups, and macrogenomic sequencing was performed on the cecal contents. Feed intake, average daily feed intake, feed conversion ratio, and residual feed intake were lower in low RFI. Analysis of the intestinal flora revealed the cecum to be more highly enriched in the carbohydrate metabolism pathway and less enriched with potentially pathogenic taxa than the other assessed intestinal regions. Further analysis of the cecal microbiota identified nine significantly differentially enriched intestinal flora. In this study, we accordingly identified a basis for the mechanisms underlying the effects of the intestinal flora on meat duck feed efficiency.}, } @article {pmid38775898, year = {2024}, author = {Ferrarezi, JVS and Owatari, MS and Martins, MA and de Souza Sá, L and Dutra, SAP and de Oliveira, HM and Soligo, T and Martins, ML and Mouriño, JLP}, title = {Effects of a multi-strain Bacillus probiotic on the intestinal microbiome, haemato-immunology, and growth performance of Nile tilapia.}, journal = {Veterinary research communications}, volume = {48}, number = {4}, pages = {2357-2368}, pmid = {38775898}, issn = {1573-7446}, support = {001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 301524/2017-3; 306635/2018-6 and 155524/2018-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; *Cichlids/immunology/growth & development/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Bacillus ; *Animal Feed/analysis ; *Diet/veterinary ; Dietary Supplements/analysis ; }, abstract = {The study evaluated dietary supplementation with a feed additive composed of multi-strain Bacillus for Nile tilapia Oreochromis niloticus. In vitro and in vivo assays employing culture-based microbiological methods and metagenomics were performed. Additionally, the study assessed the haemato-immunology, intestinal microbiome, and growth performance of the animals. For this, 30 juvenile Nile tilapia were used in the in vitro assay and 180 (60 + 120) in the in vivo assays. In the in vitro assay, we found evidence of adhesion of the probiotic bacteria to the intestinal mucus of fish, corroborated in the 15-day in vivo assay, in which the count of B. licheniformis was significantly higher in fish fed with probiotic when compared to fish of the control group. Furthermore, in the 50-day in vivo trial, a metagenomic analysis provided evidence for the modulation of the intestine microbiome of Nile tilapia by dietary supplementation of the probiotic. In addition, there was an increase in species richness, higher abundance of potentially probiotic autochthonous species and a lower abundance of Aeromonas sp. when the animals were fed the supplemented diet. Finally, no significant differences were observed in growth performance and haemato-immunological analyses, suggesting no harm to fish health when the product was supplemented for 15 and 50 days. The in vitro results indicate that the multi-strain probiotics were able to adhere to the intestinal mucus of Nile tilapia. Additionally, a modulation of the intestinal microbiome was evidenced in the in vivo assay.}, } @article {pmid38775858, year = {2024}, author = {Starevich, VA and Madueño, L and Festa, S and Agnello, AC and Cecotti, M and Layún, MF and Oneto, ME and Del Panno, MT and Morelli, IS}, title = {Microbial community structure and metabolic profile of anthropized freshwater tributary channels from La Plata River, Argentina, to develop sustainable remediation strategies.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {6}, pages = {566}, pmid = {38775858}, issn = {1573-2959}, support = {PICT 2018-1887//Agencia Nacional de Promoción Científica y Tecnológica/ ; }, mesh = {*Rivers/microbiology/chemistry ; *Microbiota ; *Water Pollutants, Chemical/metabolism/analysis ; Argentina ; *Environmental Monitoring ; RNA, Ribosomal, 16S/genetics ; Biodegradation, Environmental ; Hydrocarbons/metabolism ; Geologic Sediments/microbiology/chemistry ; Bacteria/metabolism/classification/genetics ; Environmental Restoration and Remediation/methods ; }, abstract = {Microbial communities from freshwater sediments are involved in biogeochemical cycles and they can be modified by physical and chemical changes in the environment. Linking the microbial community structure (MCS) with physicochemistry of freshwater courses allows a better understanding of its ecology and can be useful to assess the ecological impact generated by human activity. The MCS of tributary channels from La Plata River affected by oil refinery (C, D, and E) and one also by urban discharges (C) was studied. For this purpose, 16S rRNA metabarcoding analysis, in silico metagenome functional prediction, and the hydrocarbon degradation potential (in silico predictions of hydrocarbon-degrading genes and their quantification by qPCR) of the MCS were studied. Principal coordinate analysis revealed that the MCS was different between sites, and it was not structured by the hydrocarbon content. Site C showed physicochemical characteristics, bacterial taxa, and an in silico functional prediction related to fermentative/heterotrophic metabolism. Site D, despite having higher concentration of hydrocarbon, presented autotrophic, syntrophic, and methanogenic pathways commonly involved in natural processes in anoxic sediments. Site E showed and intermediate autotrophic/heterotrophic behavior. The hydrocarbon degradation potential showed no positive correlation between the hydrocarbon-degrading genes quantified and predicted. The results suggest that the hydrocarbon concentration in the sites was not enough selection pressure to structure the bacterial community composition. Understanding which is the variable that structures the bacterial community composition is essential for monitoring and designing of sustainable management strategies for contaminated freshwater ecosystems.}, } @article {pmid38775706, year = {2024}, author = {Zhuo, LB and Yang, Y and Xiao, C and Li, F and Lin, L and Xi, Y and Fu, Y and Zheng, JS and Chen, YM}, title = {Gut microbiota-bile acid axis mediated the beneficial associations between dietary lignans and hyperuricemia: a prospective study.}, journal = {Food & function}, volume = {15}, number = {12}, pages = {6438-6449}, doi = {10.1039/d4fo00961d}, pmid = {38775706}, issn = {2042-650X}, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Lignans/administration & dosage ; Middle Aged ; Male ; *Hyperuricemia ; Female ; Prospective Studies ; Aged ; *Bile Acids and Salts/metabolism ; Longitudinal Studies ; Feces/microbiology ; Diet ; Bacteria/classification/genetics/isolation & purification/metabolism ; China ; Adult ; }, abstract = {Background: The escalating prevalence of hyperuricemia is emerging as a significant public health concern. The association between dietary lignans and hyperuricemia is yet to be fully elucidated. Our study aims to evaluate the relationships between dietary lignan intake and hyperuricemia among middle-aged and elderly Chinese individuals, with an additional focus on investigating the underlying mechanisms. Methods: Dietary lignan intake was measured using a validated Food Frequency Questionnaire in 3801 participants at the baseline. Among them, 2552 participants were included in the longitudinal study with a median follow-up of 10.5 years. The gut microbiota was analyzed by shotgun metagenome sequencing in 1789 participants, and the targeted fecal metabolome was determined in 987 participants using UPLC-MS/MS at the midpoint of follow-up. Results: The multivariable-adjusted HRs (95% CIs) for hyperuricemia incidence in the highest quartile (vs. the lowest quartile) of dietary intake of total lignans, matairesinol, pinoresinol, and secoisolariciresinol were 0.93 (0.78-1.10), 0.77 (0.66-0.90), 0.83 (0.70-0.97), and 0.85 (0.73-1.00), respectively. The gut microbial and fecal metabolic compositions were significantly different across the dietary lignan groups and the hyperuricemia groups. The beneficial associations between dietary lignans and hyperuricemia might be mediated by several gut microbes (e.g., Fusobacterium mortiferum and Blautia sp. CAG-257) and the downstream bile acid products (e.g., NorCA, glycochenodeoxycholic acid, and glycoursodeoxycholic acid). Conclusion: We found that dietary lignans were inversely associated with hyperuricemia incidence, and the gut microbiota-bile acid axis might mediate this association. Our findings provide new perspectives on precise therapeutic targets and underlying mechanisms for conditions associated with elevated uric acid.}, } @article {pmid38774631, year = {2024}, author = {Dorst, M and Zeevenhooven, N and Wilding, R and Mende, D and Brandt, BW and Zaura, E and Hoekstra, A and Sheraton, VM}, title = {FAIR compliant database development for human microbiome data samples.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1384809}, pmid = {38774631}, issn = {2235-2988}, mesh = {Humans ; *Microbiota/genetics ; Databases, Factual ; Metadata ; Metagenome ; Information Dissemination ; Computational Biology/methods ; Metagenomics/methods ; Databases, Genetic ; }, abstract = {INTRODUCTION: Sharing microbiome data among researchers fosters new innovations and reduces cost for research. Practically, this means that the (meta)data will have to be standardized, transparent and readily available for researchers. The microbiome data and associated metadata will then be described with regards to composition and origin, in order to maximize the possibilities for application in various contexts of research. Here, we propose a set of tools and protocols to develop a real-time FAIR (Findable. Accessible, Interoperable and Reusable) compliant database for the handling and storage of human microbiome and host-associated data.

METHODS: The conflicts arising from privacy laws with respect to metadata, possible human genome sequences in the metagenome shotgun data and FAIR implementations are discussed. Alternate pathways for achieving compliance in such conflicts are analyzed. Sample traceable and sensitive microbiome data, such as DNA sequences or geolocalized metadata are identified, and the role of the GDPR (General Data Protection Regulation) data regulations are considered. For the construction of the database, procedures have been realized to make data FAIR compliant, while preserving privacy of the participants providing the data.

RESULTS AND DISCUSSION: An open-source development platform, Supabase, was used to implement the microbiome database. Researchers can deploy this real-time database to access, upload, download and interact with human microbiome data in a FAIR complaint manner. In addition, a large language model (LLM) powered by ChatGPT is developed and deployed to enable knowledge dissemination and non-expert usage of the database.}, } @article {pmid38773202, year = {2024}, author = {Pfingstl, T and Hiruta, SF and Shimano, S}, title = {Mitochondrial metagenomics reveal the independent colonization of the world's coasts by intertidal oribatid mites (Acari, Oribatida, Ameronothroidea).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {11634}, pmid = {38773202}, issn = {2045-2322}, support = {I 3815//Austrian Science Fund/ ; }, mesh = {Animals ; *Mites/genetics/classification ; *Phylogeny ; *Metagenomics/methods ; Genome, Mitochondrial ; Mitochondria/genetics ; Metagenome ; Evolution, Molecular ; Ecosystem ; }, abstract = {Oribatid mites are an ancient group that already roamed terrestrial ecosystems in the early and middle Devonian. The superfamily of Ameronothroidea, a supposedly monophyletic lineage, represents the only group of oribatid mites that has successfully invaded the marine coastal environment. By using mitogenome data and nucleic ribosomal RNA genes (18S, 5.8S, 28S), we show that Ameronothroidea are a paraphyletic assemblage and that the land-to-sea transition happened three times independently. Common ancestors of the tropical Fortuyniidae and Selenoribatidae were the first to colonize the coasts and molecular calibration of our phylogeny dates this event to a period in the Triassic and Jurassic era (225-146 mya), whereas present-day distribution indicates that this event might have happened early in this period during the Triassic, when the supercontinent Pangaea still existed. The cold temperate northern hemispheric Ameronothridae colonized the marine littoral later in the late Jurassic-Early Cretaceous and had an ancient distribution on Laurasian coasts. The third and final land-to-sea transition happened in the same geological period, but approx. 30 my later when ancestors of Podacaridae invaded coastal marine environments of the Gondwanan landmasses.}, } @article {pmid38773139, year = {2024}, author = {Zhao, Y and Deng, S and Zhang, Z and Chen, J and Teng, L and Liu, Z}, title = {Exploring Alashan Ground Squirrel (Spermophilus alashanicus) Diversity: Metagenomic and Transcriptomic Datasets from the Helan Mountains.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {517}, pmid = {38773139}, issn = {2052-4463}, mesh = {Animals ; Bacteria/genetics/classification ; Ecosystem ; Metagenome ; *Metagenomics ; Microbiota ; *Sciuridae/genetics ; *Transcriptome ; Mongolia ; }, abstract = {This study investigates the adaptive strategies of the Alashan Ground Squirrel (Spermophilus alashanicus) in response to habitat changes, as rodents are sensitive indicators of ecosystem changes. Despite its ecological importance, the genome and microbiome of this species have not been thoroughly studied. This research fills this gap by presenting the first comprehensive metagenomic and transcriptomic datasets of the species. Transcriptomic data was collected from five tissue types, including heart, liver, cecum, muscle, and blood, resulting in the assembly of 72,156 unigenes. Metagenomic sequencing identified predominant bacterial groups such as Firmicutes, Bacteroidetes, Verrucomicrobia, Urovircota, and Proteobacteria. Our workflow involved RNA and DNA extraction, library preparation, assembly, and annotation, yielding valuable insights into gene discovery, microbial composition, and further genome and microbial function studies. In conclusion, our findings have significant implications for understanding the adaptive mechanisms of this species in response to environmental changes.}, } @article {pmid38772522, year = {2024}, author = {Guo, X and Wang, R and Chen, R and Zhang, Z and Wang, J and Liu, X}, title = {Gut microbiota and serum metabolite signatures along the colorectal adenoma-carcinoma sequence: Implications for early detection and intervention.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {560}, number = {}, pages = {119732}, doi = {10.1016/j.cca.2024.119732}, pmid = {38772522}, issn = {1873-3492}, mesh = {Humans ; *Colorectal Neoplasms/blood/diagnosis/metabolism ; *Gastrointestinal Microbiome ; *Adenoma/metabolism/blood/diagnosis ; Male ; Female ; Middle Aged ; *Early Detection of Cancer ; Adult ; Aged ; Feces/microbiology/chemistry ; Biomarkers, Tumor/blood ; Carcinoma/metabolism/blood/diagnosis ; }, abstract = {AIM: Our study focuses on the microbial and metabolomic profile changes during the adenoma stage, as adenomas can be considered potential precursors to colorectal cancer through the adenoma-carcinoma sequence. Identifying possible intervention targets at this stage may aid in preventing the progression of colorectal adenoma (CRA) to malignant lesions. Furthermore, we evaluate the efficacy of combined microbial and metabolite biomarkers in detecting CRA.

METHODS: Fecal metagenomic and serum metabolomic analyses were performed for the discovery of alterations of gut microbiome and metabolites in CRA patients (n = 26), Colorectal cancer (CRC) patients (n = 19), Familial Adenomatous Polyposis (FAP) patients (n = 10), and healthy controls (n = 20). Finally, analyzing the associations between gut microbes and metabolites was performed by a Receiver Operating Characteristic (ROC) curve.

RESULTS: Our analysis present that CRA patients differ significantly in gut microflora and serum metabolites compared with healthy controls, especially for Lachnospiraceae and Parasutterella. Its main metabolite, butyric acid, concentrations were raised in CRA patients compared with the healthy controls, indicating its role as a promoter of colorectal tumorigenesis. α-Linolenic acid and lysophosphatidylcholine represented the other healthy metabolite for CRA. Combining five microbial and five metabolite biomarkers, we differentiated CRA from CRC with an Area Under the Curve (AUC) of 0.85 out of this performance vastly superior to the specificity recorded by traditional markers CEA and CA199 in such differentiation of these conditions.

CONCLUSIONS: The study underlines significant microbial and metabolic alterations in CRA with a novel insight into screening and early intervention of its tumorigenesis.}, } @article {pmid38771858, year = {2024}, author = {Maleki-Ravasan, N and Ghafari, SM and Najafzadeh, N and Karimian, F and Darzi, F and Davoudian, R and Farshbaf Pourabad, R and Parvizi, P}, title = {Characterization of bacteria expectorated during forced salivation of the Phlebotomus papatasi: A neglected component of sand fly infectious inoculums.}, journal = {PLoS neglected tropical diseases}, volume = {18}, number = {5}, pages = {e0012165}, pmid = {38771858}, issn = {1935-2735}, mesh = {Animals ; *Phlebotomus/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Saliva/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Iran ; Insect Vectors/microbiology/physiology ; Female ; Microbiota ; Leishmaniasis, Cutaneous/transmission/microbiology/parasitology ; Male ; }, abstract = {The infectious inoculum of a sand fly, apart from its metacyclic promastigotes, is composed of factors derived from both the parasite and the vector. Vector-derived factors, including salivary proteins and the gut microbiota, are essential for the establishment and enhancement of infection. However, the type and the number of bacteria egested during salivation is unclear. In the present study, sand flies of Phlebotomus papatasi were gathered from three locations in hyperendemic focus of zoonotic cutaneous leishmaniasis (ZCL) in Isfahan Province, Iran. By using the forced salivation assay and targeting the 16S rRNA barcode gene, egested bacteria were characterized in 99 (44%) out of 224 sand flies. Culture-dependent and culture-independent methods identified the members of Enterobacter cloacae and Spiroplasma species as dominant taxa, respectively. Ten top genera of Spiroplasma, Ralstonia, Acinetobacter, Reyranella, Undibacterium, Bryobacter, Corynebacterium, Cutibacterium, Psychrobacter, and Wolbachia constituted >80% of the saliva microbiome. Phylogenetic analysis displayed the presence of only one bacterial species for the Spiroplasma, Ralstonia, Reyranella, Bryobacter and Wolbachia, two distinct species for Cutibacterium, three for Undibacterium and Psychrobacter, 16 for Acinetobacter, and 27 for Corynebacterium, in the saliva. The abundance of microbes in P. papatasi saliva was determined by incorporating the data on the read counts and the copy number of 16S rRNA gene, about 9,000 bacterial cells, per sand fly. Both microbiological and metagenomic data indicate that bacteria are constant companions of Leishmania, from the intestine of the vector to the vertebrate host. This is the first forced salivation experiment in a sand fly, addressing key questions on infectious bite and competent vectors.}, } @article {pmid38771555, year = {2024}, author = {Rethinavelu, G and Dharshini, RS and Manickam, R and Balakrishnan, A and Ramya, M and Maddela, NR and Prasad, R}, title = {Unveiling the microbial diversity of biofilms on titanium surfaces in full-scale water-cooling plants using metagenomics approach.}, journal = {Folia microbiologica}, volume = {69}, number = {6}, pages = {1331-1341}, pmid = {38771555}, issn = {1874-9356}, mesh = {*Biofilms/growth & development ; *Titanium/chemistry ; *Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; Microbiota ; Copper/pharmacology ; Water Microbiology ; }, abstract = {Microbial colonization on the titanium condenser material (TCM) used in the cooling system leads to biofouling and corrosion and influences the water supply. The primary investigation of the titanium condenser was infrequently studied on characterizing biofilm-forming bacterial communities. Different treatment methods like electropotential charge, ultrasonication, and copper coating of titanium condenser material may influence the microbial population over the surface of the titanium condensers. The present study aimed to catalog the primary colonizers and the effect of different treatment methods on the microbial community. CFU (1.7 × 10[9] CFU/mL) and ATP count (< 5000 × 10[-7] relative luminescence units) showed a minimal microbial population in copper-coated surface biofilm as compared with the other treatments. Live and dead cell result also showed consistency with colony count. The biofilm sample on the copper-coated surface showed an increased dead cell count and decreased live cells. In the metagenomic approach, the microbiome coverage was 10.06 Mb in samples derived from copper-coated TCM than in other treated samples (electropotential charge-17.94 Mb; ultrasonication-20.01 Mb), including control (10.18 Mb). Firmicutes preponderate the communities in the biofilm samples, and Proteobacteria stand next in the population in all the treated condenser materials. At the genus level, Lactobacillaceae and Azospirillaceae dominated the biofilm community. The metagenome data suggested that the attached community is different from those biofilm samples based on the environment that influences the bacterial community. The outcome of the present study depicts that copper coating was effective against biofouling and corrosion resistance of titanium condenser material for designing long-term durability.}, } @article {pmid38771321, year = {2024}, author = {Moya-Gonzálvez, EM and Zeuner, B and Thorhallsson, AT and Holck, J and Palomino-Schätzlein, M and Rodríguez-Díaz, J and Meyer, AS and Yebra, MJ}, title = {Synthesis of fucosyllactose using α-L-fucosidases GH29 from infant gut microbial metagenome.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {338}, pmid = {38771321}, issn = {1432-0614}, support = {PID2020-115403RB (C21 and C22)//Ministerio de Ciencia e Innovación/ ; AICO/2021/033//Conselleria de Cultura, Educación y Ciencia, Generalitat Valenciana/ ; }, mesh = {Humans ; Infant ; *alpha-L-Fucosidase/genetics/metabolism ; Fucose/metabolism ; *Gastrointestinal Microbiome ; Lactose/metabolism ; *Metagenome ; *Milk, Human/chemistry ; Mutagenesis, Site-Directed ; Oligosaccharides/metabolism ; *Trisaccharides/metabolism ; }, abstract = {Fucosyl-oligosaccharides (FUS) provide many health benefits to breastfed infants, but they are almost completely absent from bovine milk, which is the basis of infant formula. Therefore, there is a growing interest in the development of enzymatic transfucosylation strategies for the production of FUS. In this work, the α-L-fucosidases Fuc2358 and Fuc5372, previously isolated from the intestinal bacterial metagenome of breastfed infants, were used to synthesize fucosyllactose (FL) by transfucosylation reactions using p-nitrophenyl-α-L-fucopyranoside (pNP-Fuc) as donor and lactose as acceptor. Fuc2358 efficiently synthesized the major fucosylated human milk oligosaccharide (HMO) 2'-fucosyllactose (2'FL) with a 35% yield. Fuc2358 also produced the non-HMO FL isomer 3'-fucosyllactose (3'FL) and traces of non-reducing 1-fucosyllactose (1FL). Fuc5372 showed a lower transfucosylation activity compared to Fuc2358, producing several FL isomers, including 2'FL, 3'FL, and 1FL, with a higher proportion of 3'FL. Site-directed mutagenesis using rational design was performed to increase FUS yields in both α-L-fucosidases, based on structural models and sequence identity analysis. Mutants Fuc2358-F184H, Fuc2358-K286R, and Fuc5372-R230K showed a significantly higher ratio between 2'FL yields and hydrolyzed pNP-Fuc than their respective wild-type enzymes after 4 h of transfucosylation. The results with the Fuc2358-F184W and Fuc5372-W151F mutants showed that the residues F184 of Fuc2358 and W151 of Fuc5372 could have an effect on transfucosylation regioselectivity. Interestingly, phenylalanine increases the selectivity for α-1,2 linkages and tryptophan for α-1,3 linkages. These results give insight into the functionality of the active site amino acids in the transfucosylation activity of the GH29 α-L-fucosidases Fuc2358 and Fuc5372. KEY POINTS: Two α-L-fucosidases from infant gut bacterial microbiomes can fucosylate glycans Transfucosylation efficacy improved by tailored point-mutations in the active site F184 of Fuc2358 and W151 of Fuc5372 seem to steer transglycosylation regioselectivity.}, } @article {pmid38768195, year = {2024}, author = {Gorman, ED and Lladser, ME}, title = {Interpretable metric learning in comparative metagenomics: The adaptive Haar-like distance.}, journal = {PLoS computational biology}, volume = {20}, number = {5}, pages = {e1011543}, pmid = {38768195}, issn = {1553-7358}, mesh = {*Metagenomics/methods ; *Phylogeny ; *Computational Biology/methods ; *Algorithms ; Microbiota/genetics ; Machine Learning ; Metagenome/genetics ; }, abstract = {Random forests have emerged as a promising tool in comparative metagenomics because they can predict environmental characteristics based on microbial composition in datasets where β-diversity metrics fall short of revealing meaningful relationships between samples. Nevertheless, despite this efficacy, they lack biological insight in tandem with their predictions, potentially hindering scientific advancement. To overcome this limitation, we leverage a geometric characterization of random forests to introduce a data-driven phylogenetic β-diversity metric, the adaptive Haar-like distance. This new metric assigns a weight to each internal node (i.e., split or bifurcation) of a reference phylogeny, indicating the relative importance of that node in discerning environmental samples based on their microbial composition. Alongside this, a weighted nearest-neighbors classifier, constructed using the adaptive metric, can be used as a proxy for the random forest while maintaining accuracy on par with that of the original forest and another state-of-the-art classifier, CoDaCoRe. As shown in datasets from diverse microbial environments, however, the new metric and classifier significantly enhance the biological interpretability and visualization of high-dimensional metagenomic samples.}, } @article {pmid38767350, year = {2024}, author = {Van Syoc, E and Nixon, MP and Silverman, JD and Luo, Y and Gonzalez, FJ and Elbere, I and Klovins, J and Patterson, AD and Rogers, CJ and Ganda, E}, title = {Changes in the type 2 diabetes gut mycobiome associate with metformin treatment across populations.}, journal = {mBio}, volume = {15}, number = {6}, pages = {e0016924}, pmid = {38767350}, issn = {2150-7511}, support = {//Penn State College of Agriculture Graduate Student Competitive Grant/ ; 2022-67011-36461//USDA NIFA AFRI Predoctoral Fellowship/ ; Project #PEN04752 Accession #1023328//USDA NIFA and Hatch Appropriation/ ; R01 GM148972/GM/NIGMS NIH HHS/United States ; 1R01GM148972-01//HHS | National Institutes of Health (NIH)/ ; //Intramural Research Program of the National Cancer Institute/ ; T32 DK120509/DK/NIDDK NIH HHS/United States ; T32DK120509//PSU/NIDDK Integrative Analysis of Metabolic Phenotypes (IAMP) Predoctoral Training Program/ ; }, mesh = {*Metformin/pharmacology/therapeutic use ; *Diabetes Mellitus, Type 2/microbiology/drug therapy ; *Gastrointestinal Microbiome/drug effects ; Animals ; Humans ; *Mycobiome/drug effects ; Mice ; *Fungi/drug effects/classification/isolation & purification/genetics ; *Hypoglycemic Agents/pharmacology/therapeutic use ; Male ; Female ; Middle Aged ; Mice, Inbred C57BL ; Cohort Studies ; }, abstract = {UNLABELLED: The human gut teems with a diverse ecosystem of microbes, yet non-bacterial portions of that community are overlooked in studies of metabolic diseases firmly linked to gut bacteria. Type 2 diabetes mellitus (T2D) is associated with compositional shifts in the gut bacterial microbiome and the mycobiome, the fungal portion of the microbiome. However, whether T2D and/or metformin treatment underpins fungal community changes is unresolved. To differentiate these effects, we curated a gut mycobiome cohort spanning 1,000 human samples across five countries and validated our findings in a murine experimental model. We use Bayesian multinomial logistic normal models to show that T2D and metformin both associate with shifts in the relative abundance of distinct gut fungi. T2D is associated with shifts in the Saccharomycetes and Sordariomycetes fungal classes, while the genera Fusarium and Tetrapisipora most consistently associate with metformin treatment. We confirmed the impact of metformin on individual gut fungi by administering metformin to healthy mice. Thus, metformin and T2D account for subtle, but significant and distinct variation in the gut mycobiome across human populations. This work highlights for the first time that metformin can confound associations of gut fungi with T2D and warrants the need to consider pharmaceutical interventions in investigations of linkages between metabolic diseases and gut microbial inhabitants.

IMPORTANCE: This is the largest to-date multi-country cohort characterizing the human gut mycobiome, and the first to investigate potential perturbations in gut fungi from oral pharmaceutical treatment. We demonstrate the reproducible effects of metformin treatment on the human and murine gut mycobiome and highlight a need to consider metformin as a confounding factor in investigations between type 2 diabetes mellitus and the gut microbial ecosystem.}, } @article {pmid38765606, year = {2024}, author = {Aplakidou, E and Vergoulidis, N and Chasapi, M and Venetsianou, NK and Kokoli, M and Panagiotopoulou, E and Iliopoulos, I and Karatzas, E and Pafilis, E and Georgakopoulos-Soares, I and Kyrpides, NC and Pavlopoulos, GA and Baltoumas, FA}, title = {Visualizing metagenomic and metatranscriptomic data: A comprehensive review.}, journal = {Computational and structural biotechnology journal}, volume = {23}, number = {}, pages = {2011-2033}, pmid = {38765606}, issn = {2001-0370}, abstract = {The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.}, } @article {pmid38764451, year = {2024}, author = {Ameer, A and Saleem, F and Keating, C and Gundogdu, O and Ijaz, UZ and Javed, S}, title = {Dataset of 130 metagenome-assembled genomes of healthy and diseased broiler chicken caeca from Pakistan.}, journal = {Data in brief}, volume = {54}, number = {}, pages = {110487}, pmid = {38764451}, issn = {2352-3409}, abstract = {This article presents metagenomic-assembled genomes (MAGs) of prokaryotic organisms originating from chicken caeca. The samples originate from broiler chickens, one group was infected with Newcastle Disease Virus (NDV) and one uninfected control group. There were four birds per group. Both groups were raised on commercially available antibiotic free feed under a semi-controlled setup. The binning step of the samples identified 130 MAGs with ≥50 % completion, and ≤10 % contamination. The data presented includes sequences in FASTA format, tables of functional annotation of genes, and data from two different approaches for phylogenetic tree construction using these MAGs. Major geochemical cycles at community level including carbon, sulfur, and nitrogen cycles are also presented.}, } @article {pmid38763204, year = {2024}, author = {Liu, H and Xu, Y and Dai, X}, title = {Electron-transfer-driven spatial optimisation of anaerobic consortia for efficient methanogenesis: Neglected inductive effect of conductive materials.}, journal = {Bioresource technology}, volume = {403}, number = {}, pages = {130856}, doi = {10.1016/j.biortech.2024.130856}, pmid = {38763204}, issn = {1873-2976}, mesh = {*Methane/metabolism ; Electron Transport ; Anaerobiosis ; *Microbial Consortia/physiology ; Electrons ; Extracellular Polymeric Substance Matrix/metabolism ; Biofuels ; Electric Conductivity ; Lewis Acids ; }, abstract = {The inductive effect of conductive materials (CMs) on enhancing methanogenesis metabolism has been overlooked. Herein, we highlight role of CMs in inducing the spatial optimisation of methanogenic consortia by altering the Lewis acid-base (AB) interactions within microbial aggregates. In the presence of CMs and after their removal, the methane production and methane proportion in biogas significantly increase, with no significant difference between the two situations. Analyses of interactions between CMs and extracellular polymer substances (EPSs) with and without D2O reveal that CMs promote release and transfer potential of electron in EPSs, which induce and enhance the role of water molecules being primarily as proton acceptors in the hydrogen bonding between EPSs and water, thereby changing the electron-donor- and electron-acceptor-based AB interactions. Investigations of succession dynamics of microbial communities, co-occurrence networks, and metagenomics further indicate that electron transfer drives the microbial spatial optimisation for efficient methanogenesis through intensive interspecies interactions.}, } @article {pmid38763016, year = {2024}, author = {Herrera, G and Castañeda, S and Arboleda, JC and Pérez-Jaramillo, JE and Patarroyo, MA and Ramírez, JD and Muñoz, M}, title = {Metagenome-assembled genomes (MAGs) suggest an acetate-driven protective role in gut microbiota disrupted by Clostridioides difficile.}, journal = {Microbiological research}, volume = {285}, number = {}, pages = {127739}, doi = {10.1016/j.micres.2024.127739}, pmid = {38763016}, issn = {1618-0623}, mesh = {*Clostridioides difficile/genetics ; *Acetates/metabolism ; *Gastrointestinal Microbiome ; *Metagenome ; Humans ; *Metagenomics ; *Clostridium Infections/microbiology ; Fatty Acids, Volatile/metabolism ; Genome, Bacterial ; Butyrates/metabolism ; Metabolic Networks and Pathways/genetics ; Feces/microbiology ; Diarrhea/microbiology ; }, abstract = {Clostridioides difficile may have a negative impact on gut microbiota composition in terms of diversity and abundance, thereby triggering functional changes supported by the differential presence of genes involved in significant metabolic pathways, such as short-chain fatty acids (SCFA). This work has evaluated shotgun metagenomics data regarding 48 samples from four groups classified according to diarrhea acquisition site (community- and healthcare facility-onset) and positive or negative Clostridioides difficile infection (CDI) result. The metagenomic-assembled genomes (MAGs) obtained from each sample were taxonomically assigned for preliminary comparative analysis concerning differences in composition among groups. The predicted genes involved in metabolism, transport, and signaling remained constant in microbiota members; characteristic patterns were observed in MAGs and genes involved in SCFA butyrate and acetate metabolic pathways for each study group. A decrease in genera and species, as well as relative MAG abundance with the presence of the acetate metabolism-related gene, was evident in the HCFO/- group. Increased antibiotic resistance markers (ARM) were observed in MAGs along with the genes involved in acetate metabolism. The results highlight the need to explore the role of acetate in greater depth as a potential protector of the imbalances produced by CDI, as occurs in other inflammatory intestinal diseases.}, } @article {pmid38763011, year = {2024}, author = {Xie, DY and Lin, M and Luo, YM and Dong, L and Wei, Y and Gao, JM and Zhu, YZ and Gong, QH}, title = {Trilobatin suppresses aging-induced cognitive impairment by targeting SIRT2: Involvement of remodeling gut microbiota to mediate the brain-gut axis.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {130}, number = {}, pages = {155744}, doi = {10.1016/j.phymed.2024.155744}, pmid = {38763011}, issn = {1618-095X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Cognitive Dysfunction/drug therapy ; Mice ; *Aging/drug effects ; *Sirtuin 2/metabolism ; Male ; *Brain-Gut Axis/drug effects ; Blood-Brain Barrier/drug effects/metabolism ; Molecular Docking Simulation ; Hippocampus/drug effects/metabolism ; Disease Models, Animal ; }, abstract = {BACKGROUND: Aging is associated with learning and memory disorder, affecting multiple brain areas, especially the hippocampus. Previous studies have demonstrated trilobatin (TLB), as a natural food additive, can extend the life of Caenorhabditis elegans and exhibit neuroprotection in Alzheimer's disease mice. However, the possible significance of TLB in anti-aging remains elusive.

PURPOSE: This study aimed to delve into the physiological mechanism by which TLB ameliorated aging-induced cognitive impairment in senescence-accelerated mouse prone 8 (SAMP8) mice.

METHODS: 6-month-old SAMP8 mice were administrated with TLB (5, 10, 20 mg/kg/day, i.g.) for 3 months. The therapeutic effect of TLB on aging-induced cognitive impairment was assessed in mice using behavioral tests and aging score. The gut microbiota composition in fecal samples was analyzed by metagenomic analysis. The protective effects of TLB on blood-brain barrier (BBB) and intestinal barrier were detected by transmission electron microscope, H&E staining and western blot (WB) assay. The inhibitive effects of TLB on inflammation in brain and intestine were assessed using immunofluorescence, WB and ELISA assay. Molecular docking and surface plasma resonance (SPR) assay were utilized to investigate interaction between TLB and sirtuin 2 (SIRT2).

RESULTS: Herein, the findings exhibited TLB mitigated aging-induced cognitive impairment, neuron injury and neuroinflammation in hippocampus of aged SAMP8 mice. Moreover, TLB treatment repaired imbalance of gut microbiota in aged SAMP8 mice. Furthermore, TLB alleviated the damage to BBB and intestinal barrier, concomitant with reducing the expression of SIRT2, phosphorylated levels of c-Jun NH2 terminal kinases (JNK) and c-Jun, and expression of MMP9 protein in aged SAMP8 mice. Molecular docking and SPR unveiled TLB combined with SIRT2 and down-regulated SIRT2 protein expression. Mechanistically, the potential mechanism of SIRT2 in TLB that exerted anti-aging effect was validated in vitro. As expected, SIRT2 deficiency attenuated phosphorylated level of JNK in HT22 cells treated with d-galactose.

CONCLUSION: These findings reveal, for the first time, SIRT2-mediated brain-gut barriers contribute to aging and aging-related diseases, and TLB can rescue aging-induced cognitive impairment by targeting SIRT2 and restoring gut microbiota disturbance to mediate the brain-gut axis. Overall, this work extends the potential application of TLB as a natural food additive in aging-related diseases.}, } @article {pmid38762482, year = {2024}, author = {Min, K and Glowacki, AJ and Bosma, ML and McGuire, JA and Tian, S and McAdoo, K and DelSasso, A and Fourre, T and Gambogi, RJ and Milleman, J and Milleman, KR}, title = {Quantitative analysis of the effects of essential oil mouthrinses on clinical plaque microbiome: a parallel-group, randomized trial.}, journal = {BMC oral health}, volume = {24}, number = {1}, pages = {578}, pmid = {38762482}, issn = {1472-6831}, mesh = {Humans ; *Mouthwashes/therapeutic use ; *Oils, Volatile/therapeutic use/pharmacology ; *Dental Plaque/microbiology ; *Microbiota/drug effects ; Adult ; *Gingivitis/microbiology/prevention & control ; Male ; Female ; Anti-Infective Agents, Local/therapeutic use ; Salicylates/therapeutic use ; Young Adult ; Middle Aged ; Drug Combinations ; Terpenes ; }, abstract = {BACKGROUND: The rich diversity of microorganisms in the oral cavity plays an important role in the maintenance of oral health and development of detrimental oral health conditions. Beyond commonly used qualitative microbiome metrics, such as relative proportions or diversity, both the species-level identification and quantification of bacteria are key to understanding clinical disease associations. This study reports the first-time application of an absolute quantitative microbiome analysis using spiked DNA standards and shotgun metagenome sequencing to assess the efficacy and safety of product intervention on dental plaque microbiome.

METHODS: In this parallel-group, randomized clinical trial, essential oil mouthrinses, including LISTERINE® Cool Mint Antiseptic (LCM), an alcohol-containing prototype mouthrinse (ACPM), and an alcohol-free prototype mouthrinse (AFPM), were compared against a hydroalcohol control rinse on clinical parameters and the oral microbiome of subjects with moderate gingivitis. To enable a sensitive and clinically meaningful measure of bacterial abundances, species were categorized according to their associations with oral conditions based on published literature and quantified using known amounts of spiked DNA standards.

RESULTS: Multivariate analysis showed that both LCM and ACPM shifted the dysbiotic microbiome composition of subjects with gingivitis to a healthier state after 4 weeks of twice-daily use, resembling the composition of subjects with clinically healthy oral conditions recruited for observational reference comparison at baseline. The essential oil-containing mouthrinses evaluated in this study showed statistically significant reductions in clinical gingivitis and plaque measurements when compared to the hydroalcohol control rinse after 6 weeks of use.

CONCLUSIONS: By establishing a novel quantitative method for microbiome analysis, this study sheds light on the mechanisms of LCM mouthrinse efficacy on oral microbial ecology, demonstrating that repeated usage non-selectively resets a gingivitis-like oral microbiome toward that of a healthy oral cavity.

TRIAL REGISTRATION: The trial was registered on ClinicalTrials.gov on 10/06/2021. The registration number is NCT04921371.}, } @article {pmid38760994, year = {2024}, author = {Nebauer, DJ and Pearson, LA and Neilan, BA}, title = {Critical steps in an environmental metaproteomics workflow.}, journal = {Environmental microbiology}, volume = {26}, number = {5}, pages = {e16637}, doi = {10.1111/1462-2920.16637}, pmid = {38760994}, issn = {1462-2920}, support = {2018/RD/0068//NSW Environmental Trust/ ; CE200100029//Australian Research Council Centre of Excellence in Synthetic Biology/ ; LP180100835//Australian Research Council's Linkage Projects/ ; }, mesh = {*Proteomics/methods ; *Workflow ; Environmental Microbiology ; Microbiota ; Metagenomics/methods ; Mass Spectrometry ; Bacteria/metabolism/genetics/classification ; }, abstract = {Environmental metaproteomics is a rapidly advancing field that provides insights into the structure, dynamics, and metabolic activity of microbial communities. As the field is still maturing, it lacks consistent workflows, making it challenging for non-expert researchers to navigate. This review aims to introduce the workflow of environmental metaproteomics. It outlines the standard practices for sample collection, processing, and analysis, and offers strategies to overcome the unique challenges presented by common environmental matrices such as soil, freshwater, marine environments, biofilms, sludge, and symbionts. The review also highlights the bottlenecks in data analysis that are specific to metaproteomics samples and provides suggestions for researchers to obtain high-quality datasets. It includes recent benchmarking studies and descriptions of software packages specifically built for metaproteomics analysis. The article is written without assuming the reader's familiarity with single-organism proteomic workflows, making it accessible to those new to proteomics or mass spectrometry in general. This primer for environmental metaproteomics aims to improve accessibility to this exciting technology and empower researchers to tackle challenging and ambitious research questions. While it is primarily a resource for those new to the field, it should also be useful for established researchers looking to streamline or troubleshoot their metaproteomics experiments.}, } @article {pmid38760865, year = {2024}, author = {Laue, HE and Bonham, KS and Coker, MO and Moroishi, Y and Pathmasiri, W and McRitchie, S and Sumner, S and Hoen, AG and Karagas, MR and Klepac-Ceraj, V and Madan, JC and , }, title = {Prospective association of the infant gut microbiome with social behaviors in the ECHO consortium.}, journal = {Molecular autism}, volume = {15}, number = {1}, pages = {21}, pmid = {38760865}, issn = {2040-2392}, support = {UG3OD023313/NH/NIH HHS/United States ; U24OD023319/NH/NIH HHS/United States ; P42ES007373/NH/NIH HHS/United States ; U24DK097193/NH/NIH HHS/United States ; U24OD023382/NH/NIH HHS/United States ; K99 ES034086/ES/NIEHS NIH HHS/United States ; RD-83544201//U.S. Environmental Protection Agency/ ; U2COD023375/NH/NIH HHS/United States ; P20GM104416/NH/NIH HHS/United States ; U24 DK097193/DK/NIDDK NIH HHS/United States ; P20ES018175/NH/NIH HHS/United States ; P01ES022832/NH/NIH HHS/United States ; UH3OD023275/NH/NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; Infant ; *Feces/microbiology ; *Social Behavior ; Prospective Studies ; Child, Preschool ; Autism Spectrum Disorder/microbiology ; }, abstract = {BACKGROUND: Identifying modifiable risk factors of autism spectrum disorders (ASDs) may inform interventions to reduce financial burden. The infant/toddler gut microbiome is one such feature that has been associated with social behaviors, but results vary between cohorts. We aimed to identify consistent overall and sex-specific associations between the early-life gut microbiome and autism-related behaviors.

METHODS: Utilizing the Environmental influences on Children Health Outcomes (ECHO) consortium of United States (U.S.) pediatric cohorts, we gathered data on 304 participants with fecal metagenomic sequencing between 6-weeks to 2-years postpartum (481 samples). ASD-related social development was assessed with the Social Responsiveness Scale (SRS-2). Linear regression, PERMANOVA, and Microbiome Multivariable Association with Linear Models (MaAsLin2) were adjusted for sociodemographic factors. Stratified models estimated sex-specific effects.

RESULTS: Genes encoding pathways for synthesis of short-chain fatty acids were associated with higher SRS-2 scores, indicative of ASDs. Fecal concentrations of butyrate were also positively associated with ASD-related SRS-2 scores, some of which may be explained by formula use.

LIMITATIONS: The distribution of age at outcome assessment differed in the cohorts included, potentially limiting comparability between cohorts. Stool sample collection methods also differed between cohorts. Our study population reflects the general U.S. population, and thus includes few participants who met the criteria for being at high risk of developing ASD.

CONCLUSIONS: Our study is among the first multicenter studies in the U.S. to describe prospective microbiome development from infancy in relation to neurodevelopment associated with ASDs. Our work contributes to clarifying which microbial features associate with subsequent diagnosis of neuropsychiatric outcomes. This will allow for future interventional research targeting the microbiome to change neurodevelopmental trajectories.}, } @article {pmid38760758, year = {2024}, author = {Min, K and Bosma, ML and John, G and McGuire, JA and DelSasso, A and Milleman, J and Milleman, KR}, title = {Quantitative analysis of the effects of brushing, flossing, and mouthrinsing on supragingival and subgingival plaque microbiota: 12-week clinical trial.}, journal = {BMC oral health}, volume = {24}, number = {1}, pages = {575}, pmid = {38760758}, issn = {1472-6831}, mesh = {Humans ; *Dental Plaque/microbiology ; *Gingivitis/microbiology ; *Mouthwashes/therapeutic use ; Female ; *Microbiota/drug effects ; Adult ; *Toothbrushing/methods ; Male ; *Dental Devices, Home Care ; Single-Blind Method ; Middle Aged ; Salicylates/therapeutic use ; Drug Combinations ; Terpenes/therapeutic use/pharmacology ; Bacterial Load/drug effects ; Anti-Infective Agents, Local/therapeutic use ; Young Adult ; }, abstract = {BACKGROUND: Translational microbiome research using next-generation DNA sequencing is challenging due to the semi-qualitative nature of relative abundance data. A novel method for quantitative analysis was applied in this 12-week clinical trial to understand the mechanical vs. chemotherapeutic actions of brushing, flossing, and mouthrinsing against the supragingival dental plaque microbiome. Enumeration of viable bacteria using vPCR was also applied on supragingival plaque for validation and on subgingival plaque to evaluate interventional effects below the gingival margin.

METHODS: Subjects with gingivitis were enrolled in a single center, examiner-blind, virtually supervised, parallel group controlled clinical trial. Subjects with gingivitis were randomized into brushing only (B); brushing and flossing (BF); brushing and rinsing with Listerine® Cool Mint® Antiseptic (BA); brushing and rinsing with Listerine® Cool Mint® Zero (BZ); or brushing, flossing, and rinsing with Listerine® Cool Mint® Zero (BFZ). All subjects brushed twice daily for 1 min with a sodium monofluorophosphate toothpaste and a soft-bristled toothbrush. Subjects who flossed used unflavored waxed dental floss once daily. Subjects assigned to mouthrinses rinsed twice daily. Plaque specimens were collected at the baseline visit and after 4 and 12 weeks of intervention. Bacterial cell number quantification was achieved by adding reference amounts of DNA controls to plaque samples prior to DNA extraction, followed by shallow shotgun metagenome sequencing.

RESULTS: 286 subjects completed the trial. The metagenomic data for supragingival plaque showed significant reductions in Shannon-Weaver diversity, species richness, and total and categorical bacterial abundances (commensal, gingivitis, and malodor) after 4 and 12 weeks for the BA, BZ, and BFZ groups compared to the B group, while no significant differences were observed between the B and BF groups. Supragingival plaque vPCR further validated these results, and subgingival plaque vPCR demonstrated significant efficacy for the BFZ intervention only.

CONCLUSIONS: This publication reports on a successful application of a quantitative method of microbiome analysis in a clinical trial demonstrating the sustained and superior efficacy of essential oil mouthrinses at controlling dental plaque compared to mechanical methods. The quantitative microbiological data in this trial also reinforce the safety and mechanism of action of EO mouthrinses against plaque microbial ecology and highlights the importance of elevating EO mouthrinsing as an integral part of an oral hygiene regimen.

TRIAL REGISTRATION: The trial was registered on ClinicalTrials.gov on 31/10/2022. The registration number is NCT05600231.}, } @article {pmid38760736, year = {2024}, author = {Li, S and Li, X and Ye, Y and Chen, M and Chen, H and Yang, D and Li, M and Jiang, F and Zhang, X and Zhang, C}, title = {The rhizosphere microbiome and its influence on the accumulation of metabolites in Bletilla striata (Thunb.) Reichb. f.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {409}, pmid = {38760736}, issn = {1471-2229}, support = {2021ZX008//Zhejiang Province Traditional Chinese Medicine Science and Technology Project/ ; 2021ZX008//Zhejiang Province Traditional Chinese Medicine Science and Technology Project/ ; }, mesh = {*Rhizosphere ; *Orchidaceae/microbiology/metabolism ; *Microbiota ; *Soil Microbiology ; China ; Plant Tubers/microbiology/metabolism ; }, abstract = {BACKGROUND: Bletilla striata (Thunb.) Reichb. f. (B. striata) is a perennial herbaceous plant in the Orchidaceae family known for its diverse pharmacological activities, such as promoting wound healing, hemostasis, anti-inflammatory effects, antioxidant properties, and immune regulation. Nevertheless, the microbe-plant-metabolite regulation patterns for B. striata remain largely undetermined, especially in the field of rhizosphere microbes. To elucidate the interrelationships between soil physics and chemistry and rhizosphere microbes and metabolites, a comprehensive approach combining metagenome analysis and targeted metabolomics was employed to investigate the rhizosphere soil and tubers from four provinces and eight production areas in China.

RESULTS: Our study reveals that the core rhizosphere microbiome of B. striata is predominantly comprised of Paraburkholderia, Methylibium, Bradyrhizobium, Chitinophaga, and Mycobacterium. These microbial species are recognized as potentially beneficial for plants health. Comprehensive analysis revealed a significant association between the accumulation of metabolites, such as militarine and polysaccharides in B. striata and the composition of rhizosphere microbes at the genus level. Furthermore, we found that the soil environment indirectly influenced the metabolite profile of B. striata by affecting the composition of rhizosphere microbes. Notably, our research identifies soil organic carbon as a primary driving factor influencing metabolite accumulation in B. striata.

CONCLUSION: Our fndings contribute to an enhanced understanding of the comprehensive regulatory mechanism involving microbe-plant-metabolite interactions. This research provides a theoretical basis for the cultivation of high-quality traditional Chinese medicine B. striata.}, } @article {pmid38760487, year = {2024}, author = {Zhao, J and Guan, G and Li, D and Yu, X and Shentu, X}, title = {Study on the gut symbiotic microbiota in long- and short-winged brown planthopper, Nilaparvata lugens (Stål).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {11306}, pmid = {38760487}, issn = {2045-2322}, support = {U21A20223//National Natural Science Foundation of China/ ; 2019C02015//Zhejiang Provincial Programs for Science and Technology Development/ ; }, mesh = {Animals ; *Hemiptera/microbiology/physiology ; *Gastrointestinal Microbiome ; *Symbiosis ; *Wings, Animal/microbiology ; Female ; *RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics ; }, abstract = {The brown planthopper (BPH), Nilaparvata lugens (Stål), is one of the most important rice pests in Asia rice regions. BPH has monophagy, migration, rapid reproduction and strong environmental adaptability, and its control is a major problem in pest management. Adult BPH exhibit wing dimorphism, and the symbiotic microbiota enriched in the gut can provide energy for wing flight muscles as a source of nutrition. In order to study the diversity of symbiotic microbiota in different winged BPHs, this paper takes female BPH as the research object. It was found that the number of symbiotic microbiota of different winged BPHs would change at different development stages. Then, based on the 16S rRNA and ITS sequences, a metagenomic library was constructed, combined with fluorescent quantitative PCR and high-throughput sequencing, the dominant symbiotic microbiota flora in the gut of different winged BPHs was found, and the community structure and composition of symbiotic microbiota in different winged BPHs were further determined. Together, our results preliminarily revealed that symbiotic microbiota in the gut of BPHs have certain effects on wing morphology, and understanding the mechanisms underlying wing morph differentiation will clarify how nutritional factors or environmental cues alter or regulate physiological and metabolic pathways. These findings also establish a theoretical basis for subsequent explorations into BPH-symbiont interplay.}, } @article {pmid38759465, year = {2024}, author = {Di Cesare, A and Sathicq, MB and Sbaffi, T and Sabatino, R and Manca, D and Breider, F and Coudret, S and Pinnell, LJ and Turner, JW and Corno, G}, title = {Parity in bacterial communities and resistomes: Microplastic and natural organic particles in the Tyrrhenian Sea.}, journal = {Marine pollution bulletin}, volume = {203}, number = {}, pages = {116495}, doi = {10.1016/j.marpolbul.2024.116495}, pmid = {38759465}, issn = {1879-3363}, mesh = {*Bacteria/genetics/drug effects ; *Microplastics/toxicity ; Water Pollutants, Chemical/analysis ; Microbiota/drug effects ; Drug Resistance, Bacterial/genetics ; Environmental Monitoring ; Seawater/microbiology/chemistry ; }, abstract = {Petroleum-based microplastic particles (MPs) are carriers of antimicrobial resistance genes (ARGs) in aquatic environments, influencing the selection and spread of antimicrobial resistance. This research characterized MP and natural organic particle (NOP) bacterial communities and resistomes in the Tyrrhenian Sea, a region impacted by plastic pollution and climate change. MP and NOP bacterial communities were similar but different from the free-living planktonic communities. Likewise, MP and NOP ARG abundances were similar but different (higher) from the planktonic communities. MP and NOP metagenome-assembled genomes contained ARGs associated with mobile genetic elements and exhibited co-occurrence with metal resistance genes. Overall, these findings show that MPs and NOPs harbor potential pathogenic and antimicrobial resistant bacteria, which can aid in the spread of antimicrobial resistance. Further, petroleum-based MPs do not represent novel ecological niches for allochthonous bacteria; rather, they synergize with NOPs, collectively facilitating the spread of antimicrobial resistance in marine ecosystems.}, } @article {pmid38757981, year = {2024}, author = {Mourik, K and Sidorov, I and Carbo, EC and van der Meer, D and Boot, A and Kroes, ACM and Claas, ECJ and Boers, SA and de Vries, JJC}, title = {Comparison of the performance of two targeted metagenomic virus capture probe-based methods using reference control materials and clinical samples.}, journal = {Journal of clinical microbiology}, volume = {62}, number = {6}, pages = {e0034524}, pmid = {38757981}, issn = {1098-660X}, support = {//Corona accelerated R&D in Europe/ ; }, mesh = {Humans ; *Metagenomics/methods/standards ; *Viruses/genetics/isolation & purification/classification ; *Sensitivity and Specificity ; Virus Diseases/diagnosis/virology ; Reference Standards ; Molecular Diagnostic Techniques/methods/standards ; Limit of Detection ; Nucleic Acid Hybridization/methods ; Virome ; }, abstract = {UNLABELLED: Viral enrichment by probe hybridization has been reported to significantly increase the sensitivity of viral metagenomics. This study compares the analytical performance of two targeted metagenomic virus capture probe-based methods: (i) SeqCap EZ HyperCap by Roche (ViroCap) and (ii) Twist Comprehensive Viral Research Panel workflow, for diagnostic use. Sensitivity, specificity, and limit of detection were analyzed using 25 synthetic viral sequences spiked in increasing proportions of human background DNA, eight clinical samples, and American Type Culture Collection (ATCC) Virome Virus Mix. Sensitivity and specificity were 95% and higher for both methods using the synthetic and reference controls as gold standard. Combining thresholds for viral sequence read counts and genome coverage [respectively 500 reads per million (RPM) and 10% coverage] resulted in optimal prediction of true positive results. Limits of detection were approximately 50-500 copies/mL for both methods as determined by ddPCR. Increasing proportions of spike-in cell-free human background sequences up to 99.999% (50 ng/mL) did not negatively affect viral detection, suggesting effective capture of viral sequences. These data show analytical performances in ranges applicable to clinical samples, for both probe hybridization metagenomic approaches. This study supports further steps toward more widespread use of viral metagenomics for pathogen detection, in clinical and surveillance settings using low biomass samples.

IMPORTANCE: Viral metagenomics has been gradually applied for broad-spectrum pathogen detection of infectious diseases, surveillance of emerging diseases, and pathogen discovery. Viral enrichment by probe hybridization methods has been reported to significantly increase the sensitivity of viral metagenomics. During the past years, a specific hybridization panel distributed by Roche has been adopted in a broad range of different clinical and zoonotic settings. Recently, Twist Bioscience has released a new hybridization panel targeting human and animal viruses. This is the first report comparing the performance of viral metagenomic hybridization panels.}, } @article {pmid38757952, year = {2024}, author = {Ross, PA and Xu, W and Jalomo-Khayrova, E and Bange, G and Gumerov, VM and Bradley, PH and Sourjik, V and Zhulin, IB}, title = {Framework for exploring the sensory repertoire of the human gut microbiota.}, journal = {mBio}, volume = {15}, number = {6}, pages = {e0103924}, pmid = {38757952}, issn = {2150-7511}, support = {//Chinese Scholarship Council/ ; //Peterson Group Charity Foundation/ ; 464366151//Deutsche Forschungsgemeinschaft (DFG)/ ; R35GM131760//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; //Hessian Ministry of Higher Education, Research and the Arts/ ; R35 GM131760/GM/NIGMS NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Bacteria/genetics/classification/metabolism ; *Genome, Bacterial ; Signal Transduction ; Metagenome ; }, abstract = {Bacteria sense changes in their environment and transduce signals to adjust their cellular functions accordingly. For this purpose, bacteria employ various sensors feeding into multiple signal transduction pathways. Signal recognition by bacterial sensors is studied mainly in a few model organisms, but advances in genome sequencing and analysis offer new ways of exploring the sensory repertoire of many understudied organisms. The human gut is a natural target of this line of study: it is a nutrient-rich and dynamic environment and is home to thousands of bacterial species whose activities impact human health. Many gut commensals are also poorly studied compared to model organisms and are mainly known through their genome sequences. To begin exploring the signals human gut commensals sense and respond to, we have designed a framework that enables the identification of sensory domains, prediction of signals that they recognize, and experimental verification of these predictions. We validate this framework's functionality by systematically identifying amino acid sensors in selected bacterial genomes and metagenomes, characterizing their amino acid binding properties, and demonstrating their signal transduction potential.IMPORTANCESignal transduction is a central process governing how bacteria sense and respond to their environment. The human gut is a complex environment with many living organisms and fluctuating streams of nutrients. One gut inhabitant, Escherichia coli, is a model organism for studying signal transduction. However, E. coli is not representative of most gut microbes, and signaling pathways in the thousands of other organisms comprising the human gut microbiota remain poorly understood. This work provides a foundation for how to explore signals recognized by these organisms.}, } @article {pmid38757812, year = {2024}, author = {Salsinha, AS and Cima, A and Araújo-Rodrigues, H and Viana, S and Reis, F and Coscueta, ER and Rodríguez-Alcalá, LM and Relvas, JB and Pintado, M}, title = {The use of an in vitro fecal fermentation model to uncover the beneficial role of omega-3 and punicic acid in gut microbiota alterations induced by a Western diet.}, journal = {Food & function}, volume = {15}, number = {11}, pages = {6095-6117}, doi = {10.1039/d4fo00727a}, pmid = {38757812}, issn = {2042-650X}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Feces/microbiology ; Rats ; *Fermentation ; Male ; *Diet, Western/adverse effects ; *Bacteria/classification/genetics/isolation & purification/metabolism/drug effects ; *Fatty Acids, Omega-3/pharmacology ; Linolenic Acids/pharmacology ; Rats, Wistar ; Fish Oils/pharmacology ; Pomegranate/chemistry ; Plant Oils/pharmacology ; Cecum/microbiology/metabolism ; }, abstract = {The influence of gut microbiota in the onset and development of several metabolic diseases has gained attention over the last few years. Diet plays an essential role in gut microbiota modulation. Western diet (WD), characterized by high-sugar and high-fat consumption, alters gut microbiome composition, diversity index, microbial relative levels, and functional pathways. Despite the promising health effects demonstrated by polyunsaturated fatty acids, their impact on gut microbiota is still overlooked. The effect of Fish oil (omega-3 source) and Pomegranate oil (punicic acid source), and a mixture of both oils in gut microbiota modulation were determined by subjecting the oil samples to in vitro fecal fermentations. Cecal samples from rats from two different dietary groups: a control diet (CD) and a high-fat high-sugar diet (WD), were used as fecal inoculum. 16S amplicon metagenomics sequencing showed that Fish oil + Pomegranate oil from the WD group increased α-diversity. This sample can also increase the relative abundance of the Firmicutes and Bacteroidetes phylum as well as Akkermansia and Blautia, which were affected by the WD consumption. All samples were able to increase butyrate and acetate concentration in the WD group. Moreover, tyrosine concentrations, a precursor for dopamine and norepinephrine, increase in the Fish oil + Pomegranate oil WD sample. GABA, an important neurotransmitter, was also increased in WD samples. These results suggest a potential positive impact of these oils' mixture on gut-brain axis modulation. It was demonstrated, for the first time, the great potential of using a mixture of both Fish and Pomegranate oil to restore the gut microbiota changes associated with WD consumption.}, } @article {pmid38755302, year = {2024}, author = {Elbakary, M and Hammad, SF and Youseif, SH and Soliman, HSM}, title = {Revealing the diversity of Jojoba-associated fungi using amplicon metagenome approach and assessing the in vitro biocontrol activity of its cultivable community.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {7}, pages = {205}, pmid = {38755302}, issn = {1573-0972}, mesh = {*Fungi/genetics/classification/isolation & purification ; *Alternaria/genetics/growth & development ; *Soil Microbiology ; Metagenome ; Rhizoctonia/growth & development ; Phylogeny ; Plant Diseases/microbiology/prevention & control ; Fusarium/genetics/growth & development ; Antibiosis ; Plant Roots/microbiology ; Biodiversity ; Biological Control Agents ; Ascomycota/growth & development/genetics ; Plant Development ; }, abstract = {Jojoba shrubs are wild plants cultivated in arid and semiarid lands and characterized by tolerance to drought, salinity, and high temperatures. Fungi associated with such plants may be attributed to the tolerance of host plants against biotic stress in addition to the promotion of plant growth. Previous studies showed the importance of jojoba as jojoba oil in the agricultural field; however, no prior study discussed the role of jojoba-associated fungi (JAF) in reflecting plant health and the possibility of using JAF in biocontrol. Here, the culture-independent and culture-dependent approaches were performed to study the diversity of the jojoba-associated fungi. Then, the cultivable fungi were evaluated for in-vitro antagonistic activity and in vitro plant growth promotion assays. The metagenome analysis revealed the existence of four fungal phyla: Ascomycota, Aphelidiomycota, Basidiomycota, and Mortierellomycota. The phylum Ascomycota was the most common and had the highest relative abundance in soil, root, branch, and fruit samples (59.7%, 50.7%, 49.8%, and 52.4%, respectively). Alternaria was the most abundant genus in aboveground tissues: branch (43.7%) and fruit (32.1%), while the genus Discosia had the highest abundance in the underground samples: soil (24%) and root (30.7%). For the culture-dependent method, a total of 14 fungi were isolated, identified, and screened for their chitinolytic and antagonist activity against three phytopathogenic fungi (Fusarium oxysporum, Alternaria alternata and Rhizoctonia solani) as well as their in vitro plant growth promotion (PGP) activity. Based on ITS sequence analysis, the selected potent isolates were identified as Aspergillus stellatusEJ-JFF3, Aspergillus flavus EJ-JFF4, Stilbocrea sp. EJ-JLF1, Fusarium solani EJ-JRF3, and Amesia atrobrunneaEJ-JSF4. The endophyte strain A. flavus EJ-JFF4 exhibited the highest chitinolytic activity (9 Enzyme Index) and antagonistic potential against Fusarium oxysporum, Alternaria alternata, and Rhizoctonia solani phytopathogens with inhibitory percentages of 72, 70, and 80 respectively. Also, A. flavus EJ-JFF4 had significant multiple PGP properties, including siderophore production (69.3%), phosphate solubilization (95.4 µg ml[-1]). The greatest production of Indol-3-Acetic Acid was belonged to A. atrobrunnea EJ-JSF4 (114.5 µg ml[-1]). The analysis of FUNGuild revealed the abundance of symbiotrophs over other trophic modes, and the guild of endophytes was commonly assigned in all samples. For the first time, this study uncovered fungal diversity associated with jojoba plants using a culture-independent approach and in-vitro assessed the roles of cultivable fungal strains in promoting plant growth and biocontrol. The present study indicated the significance of jojoba shrubs as a potential source of diverse fungi with high biocontrol and PGP activities.}, } @article {pmid38755259, year = {2024}, author = {Norenhag, J and Edfeldt, G and Stålberg, K and Garcia, F and Hugerth, LW and Engstrand, L and Fransson, E and Du, J and Schuppe-Koistinen, I and Olovsson, M}, title = {Compositional and functional differences of the vaginal microbiota of women with and without cervical dysplasia.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {11183}, pmid = {38755259}, issn = {2045-2322}, support = {KAW 2020.0239//SciLifeLab & Wallenberg Data Driven Life Science Program/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology ; *Microbiota ; Adult ; *Uterine Cervical Dysplasia/microbiology/pathology ; Middle Aged ; Case-Control Studies ; Metagenomics/methods ; Bacteria/genetics/classification ; }, abstract = {Alterations in the vaginal microbiota, including both species composition and functional pathways, have been associated with HPV infection and progression of dysplasia to cervical cancer. To further explore this, shotgun metagenomic sequencing was used to taxonomically and functionally characterize the vaginal microbiota of women with and without cervical dysplasia. Women with histologically verified dysplasia (n = 177; low grade dysplasia (LSIL) n = 81, high-grade dysplasia (HSIL) n = 94, cancer n = 2) were compared with healthy controls recruited from the cervical screening programme (n = 177). Women with dysplasia had a higher vaginal microbial diversity, and higher abundances of Gardnerella vaginalis, Aerococcus christensenii, Peptoniphilus lacrimalis and Fannyhessea vaginae, while healthy controls had higher relative abundance of Lactobacillus crispatus. Genes involved in e.g. nucleotide biosynthesis and peptidoglycan biosynthesis were more abundant in women with dysplasia. Healthy controls showed higher abundance of genes important for e.g. amino acid biosynthesis, (especially L-lysine) and sugar degradation. These findings suggest that the microbiota may have a role in creating a pro-oncogenic environment in women with dysplasia. Its role and potential interactions with other components in the microenvironment deserve further exploration.}, } @article {pmid38755047, year = {2024}, author = {Wang, Y and Yao, J and Zhu, Y and Yin, Z and Zhao, X}, title = {Combination of Simo Decoction and Golden Bifid alleviates functional dyspepsia through a mechanism involving intestinal microbiota and short-chain fatty acids.}, journal = {Arab journal of gastroenterology : the official publication of the Pan-Arab Association of Gastroenterology}, volume = {25}, number = {3}, pages = {239-249}, doi = {10.1016/j.ajg.2023.12.009}, pmid = {38755047}, issn = {2090-2387}, mesh = {Animals ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Drugs, Chinese Herbal/pharmacology ; *Dyspepsia/drug therapy/metabolism/microbiology ; *Disease Models, Animal ; Male ; Duodenum/metabolism/microbiology ; Intestinal Mucosa/metabolism/drug effects ; Colon/metabolism ; Drug Therapy, Combination ; }, abstract = {BACKGROUND AND STUDY AIMS: The integration of traditional Chinese medicine and Western medicine holds promise for the treatment of gastrointestinal disorders, which are influenced by intestinal microbiota and metabolites. This study reports a possible mechanism for the combination of Simo Decoction and Golden Bifid in functional dyspepsia (FD) by regulating intestinal microbiota and short-chain fatty acids (SCFAs).

PATIENTS AND METHODS: A mouse model of food stagnation was constructed and treated with Simo Decoction combined with different concentrations of Golden Bifid. Meta-genomics sequencing was conducted to analyze the cecum contents of the mice. Following analyses of the composition and abundance of intestinal microbiota, gas chromatography-mass spectrometry was performed to measure SCFAs in the colonic content of mice. Finally, ELISA was utilized to determine the levels of pro-inflammatory factors in the duodenal mucosa of mice and the infiltration of eosinophils in the duodenum was observed by immunohistochemical staining.

RESULTS: Combination of Simo Decoction and Golden Bifid more significantly alleviated dyspepsia in mice with food stagnation compared with Simo Decoction alone. The optimal ratio of combined treatment was 0.0075 mL/g (body weight) Simo Decoction and 0.0032 mg/g (body weight) Golden Bifid. The combined treatment increased the abundance of Bifidobacterium and Bacteroides in the intestine. The levels of SCFAs in the colonic contents of mice were increased after the combined treatment, contributing to diminished pro-inflammatory factors in the duodenal mucosa and reduced eosinophil infiltration.

CONCLUSION: Combination of Simo Decoction and Golden Bifid increases the abundance of Bacteroides and Bifidobacterium and promotes the production of SCFAs, which is instrumental for alleviation of FD.}, } @article {pmid38754482, year = {2024}, author = {Bombaywala, S and Bajaj, A and Dafale, NA}, title = {Meta-analysis of wastewater microbiome for antibiotic resistance profiling.}, journal = {Journal of microbiological methods}, volume = {223}, number = {}, pages = {106953}, doi = {10.1016/j.mimet.2024.106953}, pmid = {38754482}, issn = {1872-8359}, mesh = {*Wastewater/microbiology ; *Microbiota/drug effects/genetics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Sewage/microbiology ; Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Drug Resistance, Bacterial/genetics ; Hospitals ; Metagenomics/methods ; Genes, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Pseudomonas/genetics/drug effects/isolation & purification/classification ; }, abstract = {The microbial composition and stress molecules are main drivers influencing the development and spread of antibiotic resistance bacteria (ARBs) and genes (ARGs) in the environment. A reliable and rapid method for identifying associations between microbiome composition and resistome remains challenging. In the present study, secondary metagenome data of sewage and hospital wastewaters were assessed for differential taxonomic and ARG profiling. Subsequently, Random Forest (RF)-based ML models were used to predict ARG profiles based on taxonomic composition and model validation on hospital wastewaters. Total ARG abundance was significantly higher in hospital wastewaters (15 ppm) than sewage (5 ppm), while the resistance towards methicillin, carbapenem, and fluoroquinolone were predominant. Although, Pseudomonas constituted major fraction, Streptomyces, Enterobacter, and Klebsiella were characteristic of hospital wastewaters. Prediction modeling showed that the relative abundance of pathogenic genera Escherichia, Vibrio, and Pseudomonas contributed most towards variations in total ARG count. Moreover, the model was able to identify host-specific patterns for contributing taxa and related ARGs with >90% accuracy in predicting the ARG subtype abundance. More than >80% accuracy was obtained for hospital wastewaters, demonstrating that the model can be validly extrapolated to different types of wastewater systems. Findings from the study showed that the ML approach could identify ARG profile based on bacterial composition including 16S rDNA amplicon data, and can serve as a viable alternative to metagenomic binning for identification of potential hosts of ARGs. Overall, this study demonstrates the promising application of ML techniques for predicting the spread of ARGs and provides guidance for early warning of ARBs emergence.}, } @article {pmid38754417, year = {2024}, author = {Simpson, JB and Walker, ME and Sekela, JJ and Ivey, SM and Jariwala, PB and Storch, CM and Kowalewski, ME and Graboski, AL and Lietzan, AD and Walton, WG and Davis, KA and Cloer, EW and Borlandelli, V and Hsiao, YC and Roberts, LR and Perlman, DH and Liang, X and Overkleeft, HS and Bhatt, AP and Lu, K and Redinbo, MR}, title = {Gut microbial β-glucuronidases influence endobiotic homeostasis and are modulated by diverse therapeutics.}, journal = {Cell host & microbe}, volume = {32}, number = {6}, pages = {925-944.e10}, pmid = {38754417}, issn = {1934-6069}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 GM135218/GM/NIGMS NIH HHS/United States ; P30 CA016086/CA/NCI NIH HHS/United States ; UL1 TR002489/TR/NCATS NIH HHS/United States ; R01 GM137286/GM/NIGMS NIH HHS/United States ; R35 GM152079/GM/NIGMS NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; P42 ES031007/ES/NIEHS NIH HHS/United States ; UM1 TR004406/TR/NCATS NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Homeostasis ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Glucuronidase/metabolism ; Mice, Inbred C57BL ; Serotonin/metabolism ; Glucuronides/metabolism ; Humans ; Intestines/microbiology ; Male ; Germ-Free Life ; }, abstract = {Hormones and neurotransmitters are essential to homeostasis, and their disruptions are connected to diseases ranging from cancer to anxiety. The differential reactivation of endobiotic glucuronides by gut microbial β-glucuronidase (GUS) enzymes may influence interindividual differences in the onset and treatment of disease. Using multi-omic, in vitro, and in vivo approaches, we show that germ-free mice have reduced levels of active endobiotics and that distinct gut microbial Loop 1 and FMN GUS enzymes drive hormone and neurotransmitter reactivation. We demonstrate that a range of FDA-approved drugs prevent this reactivation by intercepting the catalytic cycle of the enzymes in a conserved fashion. Finally, we find that inhibiting GUS in conventional mice reduces free serotonin and increases its inactive glucuronide in the serum and intestines. Our results illuminate the indispensability of gut microbial enzymes in sustaining endobiotic homeostasis and indicate that therapeutic disruptions of this metabolism promote interindividual response variabilities.}, } @article {pmid38752784, year = {2024}, author = {Berman, HL and Goltsman, DSA and Anderson, M and Relman, DA and Callahan, BJ}, title = {Gardnerella diversity and ecology in pregnancy and preterm birth.}, journal = {mSystems}, volume = {9}, number = {6}, pages = {e0133923}, pmid = {38752784}, issn = {2379-5077}, support = {R35GM133745//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; K99 HD090290/HD/NICHD NIH HHS/United States ; F31 HD104353/HD/NICHD NIH HHS/United States ; F31HD104353//HHS | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; //March of Dimes Prematurity Research Center/ ; K99HD090290//HHS | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; //Triangle Center for Evolutionary Medicine/ ; R35 GM133745/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Female ; Pregnancy ; *Premature Birth/microbiology ; *Vagina/microbiology ; *Microbiota/genetics ; *Gardnerella/genetics/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; Adult ; Genetic Variation ; }, abstract = {The vaginal microbiome has been linked to negative health outcomes including preterm birth. Specific taxa, including Gardnerella spp., have been identified as risk factors for these conditions. Historically, microbiome analysis methods have treated all Gardnerella spp. as one species, but the broad diversity of Gardnerella has become more apparent. We explore the diversity of Gardnerella clades and genomic species in the vaginal microbiome of pregnant women and their associations with microbiome composition and preterm birth. Relative abundance of Gardnerella clades and genomic species and other taxa was quantified in shotgun metagenomic sequencing data from three distinct cohorts of pregnant women. We also assessed the diversity and abundance of Gardnerella variants in 16S rRNA gene amplicon sequencing data from seven previously conducted studies in differing populations. Individual microbiomes often contained multiple Gardnerella variants, and the number of clades was associated with increased microbial load, or the ratio of non-human reads to human reads. Taxon co-occurrence patterns were largely consistent across Gardnerella clades and among cohorts. Some variants previously described as rare were prevalent in other cohorts, highlighting the importance of surveying a diverse set of populations to fully capture the diversity of Gardnerella. The diversity of Gardnerella both across populations and within individual vaginal microbiomes has long been unappreciated, as has been the intra-species diversity of many other members of the vaginal microbiome. The broad genomic diversity of Gardnerella has led to its reclassification as multiple species; here we demonstrate the diversity of Gardnerella found within and between vaginal microbiomes.IMPORTANCEThe present study shows that single microbiomes can contain all currently known species of Gardnerella and that multiple similar species can exist within the same environment. Furthermore, surveys of demographically distinct populations suggest that some species appear more commonly in certain populations. Further studies in broad and diverse populations will be necessary to fully understand the ecological roles of each Gardnerella sp., how they can co-exist, and their distinct impacts on microbial communities, preterm birth, and other health outcomes.}, } @article {pmid38752697, year = {2024}, author = {Chen, X and Wei, J and Li, Z and Zhang, Y and Zhang, X and Zhang, L and Wang, X and Zhang, Y and Zhang, T}, title = {Dysregulation of Gut Microbiota-Derived Neuromodulatory Amino Acid Metabolism in Human Immunodeficiency Virus-Associated Neurocognitive Disorder: An Integrative Metagenomic and Metabolomic Analysis.}, journal = {Annals of neurology}, volume = {96}, number = {2}, pages = {306-320}, doi = {10.1002/ana.26963}, pmid = {38752697}, issn = {1531-8249}, support = {7222091//Natural Science Foundation of Beijing Municipality/ ; 7222095//Natural Science Foundation of Beijing Municipality/ ; 82072271//National Natural Science Foundation of China/ ; 82241072//National Natural Science Foundation of China/ ; Z221100007422055//Research and application of characteristic clinical diagnosis and treatment technology in Beijing/ ; DFL20191701//Climbing the Peak (Deng feng) Talent Training Program of the Beijing Hospitals Authority/ ; BHTPP2020//Beijing Health Technologies Promotion Program/ ; BZ0089//Beijing Key Laboratory for HIV/AIDS Research/ ; BJRID2024-001//Beijing research center for respiratory infectious diseases project/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Middle Aged ; Female ; *Metabolomics/methods ; *Amino Acids/metabolism/blood ; Adult ; *Metagenomics ; HIV Infections/complications ; AIDS Dementia Complex/metabolism/microbiology ; Feces/microbiology ; Dysbiosis ; }, abstract = {OBJECTIVE: Although accumulating evidence implicating altered gut microbiota in human immunodeficiency virus (HIV) infection and neurodegenerative disorders; however, the association between dysbiosis of the gut microbiota and metabolites in the pathogenesis of HIV-associated neurocognitive disorder (HAND) remains unclear.

METHODS: Fecal and plasma samples were obtained from 3 cohorts (HAND, HIV-non-HAND, and healthy controls), metagenomic analysis and metabolomic profiling were performed to investigate alterations in the gut microbial composition and circulating metabolites in HAND.

RESULTS: The gut microbiota of people living with HIV (PLWH) had an increased relative abundance of Prevotella and a decreased relative abundance of Bacteroides. In contrast, Prevotella and Megamonas were substantially decreased, and Bacteroides and Phocaeicola were increased in HAND patients. Moreover, untargeted metabolomics identified several neurotransmitters and certain amino acids associated with neuromodulation, and the differential metabolic pathways of amino acids associated with neurocognition were depleted in HAND patients. Notably, most neuromodulatory metabolites are associated with an altered abundance of specific gut bacteria.

INTERPRETATION: Our findings provide new insights into the intricate interplay between the gut and microbiome-brain axis in the pathogenesis of HAND, highlighting the potential for developing novel therapeutic strategies that specifically target the gut microbiota. ANN NEUROL 2024;96:306-320.}, } @article {pmid38751720, year = {2024}, author = {Singh, P and Singh, SM and Segawa, T and Singh, PK}, title = {Bacterial diversity and biopotentials of Hamtah glacier cryoconites, Himalaya.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1362678}, pmid = {38751720}, issn = {1664-302X}, abstract = {Cryoconite is a granular structure present on the glaciers and ice sheets found in polar regions including the Himalayas. It is composed of organic and inorganic matter which absorb solar radiations and reduce ice surface albedo, therefore impacting the melting and retreat of glaciers. Though climate warming has a serious impact on Himalayan glaciers, the biodiversity of sub-glacier ecosystems is poorly understood. Moreover, cryoconite holes are unique habitats for psychrophile biodiversity hotspots in the NW Himalayas, but unfortunately, studies on the microbial diversity of such habitats remain elusive. Therefore, the current study was designed to explore the bacterial diversity of the Hamtah Glacier Himalaya using both culturable and non-culturable approaches. The culturable bacterial count ranged from 2.0 × 10[3] to 8.8 × 10[5] colony-forming units (CFUs)/g at the different locations of the glacier. A total of 88 bacterial isolates were isolated using the culturable approach. Based on the 16S ribosomal RNA gene (16S rRNA), the identified species belong to seven genera, namely, Cryobacterium, Duganella, Janthinobacterium, Pseudomonas, Peribacillus, Psychrobacter, and Sphingomonas. In the non-culturable approach, high-throughput sequencing of 16S rRNA genes (using MiSeq) showed unique bacterial community profiles and represented 440 genera belonging to 20 phyla, namely, Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Acidobacteria, Planctomycetes, Cyanobacteria, Verrucomicrobia, Spirochaetes, Elusimicrobia, Armatimonadetes, Gemmatimonadetes, Deinococcus-Thermus, Nitrospirae, Chlamydiae, Chlorobi, Deferribacteres, Fusobacteria, Lentisphaerae, and others. High relative abundances of Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes were observed in the samples. Phototrophic (Cyanobacteria and Chloroflexi) and nitrifier (Nitrospirae) in bacterial populations indicated sustenance of the micro-ecosystem in the oligotrophic glacier environment. The isolates varied in their phenotypic characteristics, enzyme activities, and antibiotic sensitivity. Furthermore, the fatty acid profiles of bacterial isolates indicate the predominance of branched fatty acids. Iso-, anteiso-, unsaturated and saturated fatty acids together constituted a major proportion of the total fatty acid composition. High cold-adapted enzyme activities such as lipase and cellulase expressed by Cryobacterium arcticum (KY783365) and protease and cellulase activities by Pseudomonas sp. strains (KY783373, KY783377-79, KY783382) provide evidence of the possible applications of these organisms. Additionally, antibiotic tests indicated that most isolates were sensitive to antibiotics. In conclusion, the present study contributed for the first time to bacterial diversity and biopotentials of cryoconites of Hamtah Glacier, Himalayas. Furthermore, the cold-adapted enzymes and polyunsaturated fatty acids (PUFAs) may provide an opportunity for biotechnology in the Himalayas. Inductively coupled plasma mass spectrometry (ICPMS) analyses showed the presence of several elements in cryoconites, providing a clue for the accelerating melting and retreating of the Hamtah glacier.}, } @article {pmid38750900, year = {2024}, author = {Lewis, JD and Daniel, SG and Li, H and Hao, F and Patterson, AD and Hecht, AL and Brensinger, CM and Wu, GD and Bittinger, K and , and , }, title = {Surgery for Crohn's Disease Is Associated With a Dysbiotic Microbiome and Metabolome: Results From Two Prospective Cohorts.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {18}, number = {3}, pages = {101357}, pmid = {38750900}, issn = {2352-345X}, mesh = {Humans ; *Crohn Disease/microbiology/surgery/pathology/metabolism ; *Gastrointestinal Microbiome ; Female ; Male ; Adult ; *Metabolome ; Prospective Studies ; *Feces/microbiology ; *Dysbiosis/microbiology ; Middle Aged ; Bile Acids and Salts/metabolism ; Butyrates/metabolism ; Metagenomics/methods ; Cholestenones/metabolism ; Ileum/microbiology/surgery/metabolism/pathology ; Young Adult ; Bacteria/isolation & purification/classification/metabolism/genetics ; }, abstract = {BACKGROUND & AIMS: Crohn's disease is associated with alterations in the gut microbiome and metabolome described as dysbiosis. We characterized the microbial and metabolic consequences of ileal resection, the most common Crohn's disease surgery.

METHODS: Patients with and without intestinal resection were identified from the Diet to Induce Remission in Crohn's Disease and Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease studies. Stool samples were analyzed with shotgun metagenomics sequencing. Fecal butyrate was measured with [1]H nuclear magnetic resonance spectroscopy. Fecal bile acids and plasma 7α-hydroxy-4-cholesten-3-one (C4) was measured with mass spectrometry.

RESULTS: Intestinal resection was associated with reduced alpha diversity and altered beta diversity with increased Proteobacteria and reduced Bacteroidetes and Firmicutes. Surgery was associated with higher representation of genes in the KEGG pathway for ABC transporters and reduction in genes related to bacterial metabolism. Surgery was associated with reduced concentration of the But gene but this did not translate to reduced fecal butyrate concentration. Surgery was associated with decreased abundance of bai operon genes, with increased plasma C4 concentration, increased primary bile acids and reduced secondary bile acids, including isoLCA. Additionally, Egerthella lenta, Adlercreutzia equalofaciens, and Gordonibacter pamelaeae were lower in abundance among patients with prior surgery in both cohorts.

CONCLUSIONS: In 2 different populations, prior surgery in Crohn's disease is associated with altered fecal microbiome. Patients who had undergone ileal resection had reduction in the potentially beneficial bacteria E lenta and related actinobacteria and secondary bile acids, including isoLCA, suggesting that these could be biomarkers of patients at higher risk for disease progression.}, } @article {pmid38750777, year = {2024}, author = {Xiang, Y and Wang, S and Huang, H and Li, X and Wei, Y and Li, H and Ji, X}, title = {A novel endolysin from an Enterococcus faecalis phage and application.}, journal = {Microbial pathogenesis}, volume = {192}, number = {}, pages = {106689}, doi = {10.1016/j.micpath.2024.106689}, pmid = {38750777}, issn = {1096-1208}, mesh = {*Enterococcus faecalis/drug effects ; *Endopeptidases/pharmacology/genetics/metabolism ; Animals ; *Biofilms/drug effects/growth & development ; *Bacteriophages/genetics ; *Gram-Positive Bacterial Infections/microbiology/drug therapy ; *Rats, Sprague-Dawley ; *Anti-Bacterial Agents/pharmacology ; Rats ; *Disease Models, Animal ; RNA, Ribosomal, 16S/genetics ; Gastrointestinal Microbiome/drug effects ; Microbial Sensitivity Tests ; Recombinant Proteins/genetics/pharmacology ; Male ; }, abstract = {Enterococcus faecalis is the primary species detected in cases of secondary persistent infection resulting from root canal therapy failure. Due to the overuse of antibacterial agents, E. faecalis has developed resistance to these drugs, making it challenging to treat clinical diseases caused by E. faecalis infection. Therefore, there is an urgent need to explore new alternative drugs for treating E. faecalis infections. We aimed to clone and express the genes of phage endolysins, purify the recombinant proteins, and analyze their antibacterial activity, lysis profile, and ability to remove biofilm. The crude enzyme of phage endolysin pEF51 (0.715 mg/mL), derived from phage PEf771 infecting E. faecalis, exhibited superior bacterial inhibitory activity and a broader bactericidal spectrum than its parental phage PEf771. Furthermore, pEF51 demonstrated high efficacy in eliminating E. faecalis biofilm. Therapeutic results of the infected Sprague-Dawley (SD) rat model indicated that among 10 SD rats, only one developed a thoracic peritoneal abscess and splenic peritoneal abscess after 72 h of treatment with pEF51. This suggests that pEF51 could provide protection against E. faecalis infection in SD rats. Based on the 16S rDNA metagenomic data of the intestinal microbial community of SD rats, endolysin pEF51 exerted a certain influence on the diversity of intestinal microorganisms at the genus level. Thus, pEF51 may serve as a promising alternative to antibiotics in the management of E. faecalis infection.}, } @article {pmid38750737, year = {2024}, author = {Kaijser, W and Lorenz, AW and Brauer, VS and Burfeid-Castellanos, A and David, GM and Nuy, JK and Baikova, D and Beszteri, B and Gillmann, SM and Kiesel, J and Mayombo, NAS and Peters, K and Rettig, K and Rolauffs, P and Haase, P and Hering, D}, title = {Differential associations of five riverine organism groups with multiple stressors.}, journal = {The Science of the total environment}, volume = {934}, number = {}, pages = {173105}, doi = {10.1016/j.scitotenv.2024.173105}, pmid = {38750737}, issn = {1879-1026}, mesh = {*Rivers/microbiology ; *Environmental Monitoring ; Animals ; *Biodiversity ; Fungi ; Diatoms/physiology ; Invertebrates/physiology ; Fishes ; Bacteria/classification ; Water Pollutants, Chemical/analysis ; }, abstract = {The decline of river and stream biodiversity results from multiple simultaneous occuring stressors, yet few studies explore responses explore responses across various taxonomic groups at the same locations. In this study, we address this shortcoming by using a coherent data set to study the association of nine commonly occurring stressors (five chemical, one morphological and three hydraulic) with five taxonomic groups (bacteria, fungi, diatoms, macro-invertebrates and fish). According to studies on single taxonomic groups, we hypothesise that gradients of chemical stressors structure community composition of all taxonomic groups, while gradients of hydraulic and morphological stressors are mainly related to larger organisms such as benthic macro-invertebrates and fish. Organisms were sampled over two years at 20 sites in two catchments: a recently restored urban lowland catchment (Boye) and a moderately disturbed rural mountainous catchment (Kinzig). Dissimilarity matrices were computed for each taxonomic group within a catchment. Taxonomic dissimilarities between sites were linked to stressor dissimilarities using multivariable Generalized Linear Mixed Models. Stressor gradients were longer in the Boye, but did in contrast to the Kinzig not cover low stress intensities. Accordingly, responses of the taxonomic groups were stronger in the Kinzig catchment than in the recently restored Boye catchment. The discrepancy between catchments underlines that associations to stressors strongly depend on which part of the stressor gradient is covered in a catchment. All taxonomic groups were related to conductivity. Bacteria, fungi and macro-invertebrates change with dissolved oxygen, and bacteria and fungi with total nitrogen. Morphological and hydraulic stressors had minor correlations with bacteria, fungi and diatoms, while macro-invertebrates were strongly related to fine sediment and discharge, and fish to high flow peaks. The results partly support our hypotheses about the differential associations of the different taxonomic groups with the stressors.}, } @article {pmid38750423, year = {2024}, author = {Kuster, R and Staton, M}, title = {Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {191}, pmid = {38750423}, issn = {1471-2105}, mesh = {*Metagenome/genetics ; *Metagenomics/methods ; *Software ; Humans ; Sequence Analysis, DNA/methods ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {BACKGROUND: The application of reduced metagenomic sequencing approaches holds promise as a middle ground between targeted amplicon sequencing and whole metagenome sequencing approaches but has not been widely adopted as a technique. A major barrier to adoption is the lack of read simulation software built to handle characteristic features of these novel approaches. Reduced metagenomic sequencing (RMS) produces unique patterns of fragmentation per genome that are sensitive to restriction enzyme choice, and the non-uniform size selection of these fragments may introduce novel challenges to taxonomic assignment as well as relative abundance estimates.

RESULTS: Through the development and application of simulation software, readsynth, we compare simulated metagenomic sequencing libraries with existing RMS data to assess the influence of multiple library preparation and sequencing steps on downstream analytical results. Based on read depth per position, readsynth achieved 0.79 Pearson's correlation and 0.94 Spearman's correlation to these benchmarks. Application of a novel estimation approach, fixed length taxonomic ratios, improved quantification accuracy of simulated human gut microbial communities when compared to estimates of mean or median coverage.

CONCLUSIONS: We investigate the possible strengths and weaknesses of applying the RMS technique to profiling microbial communities via simulations with readsynth. The choice of restriction enzymes and size selection steps in library prep are non-trivial decisions that bias downstream profiling and quantification. The simulations investigated in this study illustrate the possible limits of preparing metagenomic libraries with a reduced representation sequencing approach, but also allow for the development of strategies for producing and handling the sequence data produced by this promising application.}, } @article {pmid38749545, year = {2024}, author = {Sato, Y}, title = {Transcriptome analysis: a powerful tool to understand individual microbial behaviors and interactions in ecosystems.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {88}, number = {8}, pages = {850-856}, doi = {10.1093/bbb/zbae064}, pmid = {38749545}, issn = {1347-6947}, support = {17H04716//Japan Society for the Promotion of Science/ ; JPMJFR2174//Japan Science and Technology Agency/ ; }, mesh = {*Ecosystem ; *Gene Expression Profiling/methods ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; Transcriptome ; Microbiota/genetics ; Bacteria/genetics/metabolism/classification ; Microbial Interactions/genetics ; Metagenome ; }, abstract = {Transcriptome analysis is a powerful tool for studying microbial ecology, especially individual microbial functions in an ecosystem and their interactions. With the development of high-throughput sequencing technology, great progress has been made in analytical methods for microbial communities in natural environments. 16S rRNA gene amplicon sequencing (ie microbial community structure analysis) and shotgun metagenome analysis have been widely used to determine the composition and potential metabolic capability of microorganisms in target environments without requiring culture. However, even if the types of microorganisms present and their genes are known, it is difficult to determine what they are doing in an ecosystem. Gene expression analysis (transcriptome analysis; RNA-seq) is a powerful tool to address these issues. The history and basic information of gene expression analysis, as well as examples of studies using this method to analyze microbial ecosystems, are presented.}, } @article {pmid38748395, year = {2024}, author = {Jiya, N and Ghosh, R and Shede, P and Sharma, A}, title = {Comparative analysis of bacterial diversity in accumulated snow and exposed sediments across Antarctic Islands.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {55}, number = {3}, pages = {2355-2362}, pmid = {38748395}, issn = {1678-4405}, support = {SRG/2022/000126//Science and Engineering Research Board (SERB), Department of Science and Technology, India/ ; }, mesh = {Antarctic Regions ; *Geologic Sediments/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Snow/microbiology ; *Biodiversity ; Phylogeny ; Islands ; DNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Microbiota ; }, abstract = {The Antarctic continent hosts exceptional niches, making it an ideal environment for studying polyextremophilic microorganisms. These organisms are uniquely shaped by the geographic niches and variations in soil types. Here we present, a culture-independent approach using DNA metabarcoding to assess the bacterial communities associated with accumulated snow and exposed sediments across different Antarctic islands situated in the Larsemann Hills, Antarctica. The exposed sediments (ES) were found to be more diverse than the accumulated snow (AS) sediments as represented by the alpha diversity metrics. Out of the total 303 amplicon sequence variants (ASVs) found at the genus level, 93 were unique to accumulated snow sediments and 97 were unique to exposed sediments. The bacterial community composition in accumulated snow was dominated by the phylum Actinobacteriota (24.7%). However, Pseudonocardia (11.9%), Crossiella (11%), and Rhodanobacter (9.1%) were the predominant genera. In contrast, in the exposed sediments, Bacteroidota (24.6%) was the most prevalent phylum, with Crossiella (17.1%), Rhodanobacter (11.1%), and Blastocatella (10%) as the most abundant genera. Metagenomic imputations revealed the abundance of gene families responsible for carbon metabolism, coping with environmental stresses through DNA repair mechanisms, and carbon fixation.}, } @article {pmid38747864, year = {2024}, author = {Naliukhin, AN and Kozlov, AV and Eregin, AV and Guseva, YE and Kuzina, NI}, title = {Responses of soil physico-chemical properties, structure of the microbial community and crop yields to different fertilization practices in Russia's conventional farming system.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {84}, number = {}, pages = {e282493}, doi = {10.1590/1519-6984.282493}, pmid = {38747864}, issn = {1678-4375}, mesh = {*Fertilizers/analysis ; *Soil Microbiology ; *Soil/chemistry ; *Crops, Agricultural/microbiology ; Russia ; Agriculture/methods ; RNA, Ribosomal, 16S/genetics/analysis ; Animals ; Cattle ; Microbiota ; Manure/microbiology ; }, abstract = {The use of fertilizers affects not only the soil fertility and crop yield, but also significantly changes the taxonomic structure of the soil microbiocenosis. Here, based on stationary field experiment, we studied the influence of organo-mineral fertilizer (ОМF), modified by bacteria Bacillus subtilis, H-13 in comparison with different fertilizer systems (organic, mineral, organo-mineral) on (i) crop yield, (ii) physical and chemical properties, and (iii) alpha and beta diversity of the microbial community Albic Retisol (Loamic, Aric, Cutanic, Differentic, Ochric). The studies were carried out against the background of liming (рНКCl - 5.9) and without it (рНКCl - 5.1). The use of only one cattle farmyard manure was less effective than its co-application with mineral fertilizers in half doses. A similar effect was obtained when applying ОМF. In addition, the use of OMF contributes to a significant increase in the reserves of soil organic carbon in the soil layer 0-20 cm by 18%-32%. Using high-throughput sequencing of the 16S rRNA variable V4 gene sequence libraries, 10.759 taxa from 456 genera were identified, assigned to 34 fila (31 bacterial and 3 archaeotic. Unilateral application of mineral fertilizers leads to a significant decrease in the alpha diversity of the structure of soil microbial communities (OTE (other things equal) and Shannon index). A clear clustering of the microbiota was found in the variants with and without the introduction of сattle farmyard manure. It is revealed that the taxonomic structure of the microbiocenosis is formed under the influence of two main factors: crop rotation culture and applied fertilizers. The type of cultivated crop determines the dynamics of the microbiota at the level of larger taxa, such as domains, and fertilizers affect the structure of the microbial community at a lower taxonomic level (phyla, orders, bloodlines). On the basis of the Deseq analysis, marker taxa were identified, according to the share participation of which it is possible to determine the type of cultivated crop and fertilizers used in the experiment. Understanding the dynamics of taxa association and other influential factors can lead to the creation of universal systems of metagenomic indication, where tracking the dynamics of microbial communities will allow for a comprehensive assessment of the agroecological state of soils and timely decisions to prevent their degradation.}, } @article {pmid38747631, year = {2024}, author = {Medeiros, W and Hidalgo, K and Leão, T and de Carvalho, LM and Ziemert, N and Oliveira, V}, title = {Unlocking the biosynthetic potential and taxonomy of the Antarctic microbiome along temporal and spatial gradients.}, journal = {Microbiology spectrum}, volume = {12}, number = {6}, pages = {e0024424}, pmid = {38747631}, issn = {2165-0497}, support = {2020/11534-0, 2022/15112-8//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2019/12914-3//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; }, mesh = {Antarctic Regions ; *Microbiota/genetics ; *Metagenome ; Bacteria/genetics/classification/metabolism ; Multigene Family ; Biofilms ; Phylogeny ; Proteobacteria/genetics/metabolism/classification ; Terpenes/metabolism ; Bacteroidetes/genetics/metabolism/classification ; }, abstract = {Extreme environments, such as Antarctica, select microbial communities that display a range of evolutionary strategies to survive and thrive under harsh environmental conditions. These include a diversity of specialized metabolites, which have the potential to be a source for new natural product discovery. Efforts using (meta)genome mining approaches to identify and understand biosynthetic gene clusters in Antarctica are still scarce, and the extent of their diversity and distribution patterns in the environment have yet to be discovered. Herein, we investigated the biosynthetic gene diversity of the biofilm microbial community of Whalers Bay, Deception Island, in the Antarctic Peninsula and revealed its distribution patterns along spatial and temporal gradients by applying metagenome mining approaches and multivariable analysis. The results showed that the Whalers Bay microbial community harbors a great diversity of biosynthetic gene clusters distributed into seven classes, with terpene being the most abundant. The phyla Proteobacteria and Bacteroidota were the most abundant in the microbial community and contributed significantly to the biosynthetic gene abundances in Whalers Bay. Furthermore, the results highlighted a significant correlation between the distribution of biosynthetic genes and taxonomic diversity, emphasizing the intricate interplay between microbial taxonomy and their potential for specialized metabolite production.IMPORTANCEThis research on antarctic microbial biosynthetic diversity in Whalers Bay, Deception Island, unveils the hidden potential of extreme environments for natural product discovery. By employing metagenomic techniques, the research highlights the extensive diversity of biosynthetic gene clusters and identifies key microbial phyla, Proteobacteria and Bacteroidota, as significant contributors. The correlation between taxonomic diversity and biosynthetic gene distribution underscores the intricate interplay governing specialized metabolite production. These findings are crucial for understanding microbial adaptation in extreme environments and hold significant implications for bioprospecting initiatives. The study opens avenues for discovering novel bioactive compounds with potential applications in medicine and industry, emphasizing the importance of preserving and exploring these polyextreme ecosystems to advance biotechnological and pharmaceutical research.}, } @article {pmid38747599, year = {2024}, author = {Wang, Y and Zhou, Y and Huang, Y and Li, X and Zhang, J and Gao, Y and Qin, F and Fu, H and Wang, S and Niu, A and Guo, R}, title = {Analyzing the characteristics of respiratory microbiota after the placement of an airway stent for malignant central airway obstruction.}, journal = {Microbiology spectrum}, volume = {12}, number = {6}, pages = {e0347223}, pmid = {38747599}, issn = {2165-0497}, mesh = {Humans ; *Stents/microbiology ; Female ; Male ; *Microbiota ; Middle Aged ; Aged ; *Bacteria/classification/isolation & purification/genetics ; *Airway Obstruction/microbiology ; Respiratory System/microbiology ; Granulation Tissue/microbiology/pathology ; Adult ; Aged, 80 and over ; Tracheoesophageal Fistula/microbiology ; }, abstract = {UNLABELLED: Malignant central airway stenosis is treated with airway stent placement, but post-placement microbial characteristics remain unclear. We studied microbial features in 60 patients post-stent placement, focusing on changes during granulation tissue proliferation. Samples were collected before stent (N = 29), after stent on day 3 (N = 20), and after granulation tissue formation (AS-GTF, N = 43). Metagenomic sequencing showed significant respiratory tract microbiota changes with granulation tissue. The microbiota composition, dominated by Actinobacteria, Firmicutes, and Proteobacteria, was similar among the groups. At the species level, the AS-GTF group exhibited significant differences, with Peptostreptococcus stomatis and Achromobacter xylosoxidans enriched. Analysis based on tracheoesophageal fistula presence identified Tannerella forsythia and Stenotrophomonas maltophilia as the main differential species, enriched in the fistula subgroup. Viral and fungal detection showed Human gammaherpesvirus 4 and Candida albicans as the main species, respectively. These findings highlight microbiota changes after stent placement, potentially associated with granulation tissue proliferation, informing stent placement therapy and anti-infective treatment optimization.

IMPORTANCE: Malignant central airway stenosis is a life-threatening condition that can be effectively treated with airway stent placement. However, despite its clinical importance, the microbial characteristics of the respiratory tract following stent insertion remain poorly understood. This study addresses this gap by investigating the microbial features in patients with malignant central airway stenosis after stent placement, with a specific focus on microbial changes during granulation tissue proliferation. The findings reveal significant alterations in the diversity and structure of the respiratory tract microbiota following the placement of malignant central airway stents. Notably, certain bacterial species, including Peptostreptococcus stomatis and Achromobacter xylosoxidans, exhibit distinct patterns in the after-stent granulation tissue formation group. Additionally, the presence of tracheoesophageal fistula further influences the microbial composition. These insights provide valuable references for optimizing stent placement therapy and enhancing clinical anti-infective strategies.}, } @article {pmid38744885, year = {2024}, author = {Qi, YL and Chen, YT and Xie, YG and Li, YX and Rao, YZ and Li, MM and Xie, QJ and Cao, XR and Chen, L and Qu, YN and Yuan, ZX and Xiao, ZC and Lu, L and Jiao, JY and Shu, WS and Li, WJ and Hedlund, BP and Hua, ZS}, title = {Analysis of nearly 3000 archaeal genomes from terrestrial geothermal springs sheds light on interconnected biogeochemical processes.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4066}, pmid = {38744885}, issn = {2041-1723}, support = {32170014//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Hot Springs/microbiology ; *Archaea/genetics/classification ; *Genome, Archaeal ; China ; *Metagenome ; *Phylogeny ; *Metagenomics/methods ; Biodiversity ; Hydrogen-Ion Concentration ; Sulfur/metabolism ; Temperature ; Ecosystem ; }, abstract = {Terrestrial geothermal springs are physicochemically diverse and host abundant populations of Archaea. However, the diversity, functionality, and geological influences of these Archaea are not well understood. Here we explore the genomic diversity of Archaea in 152 metagenomes from 48 geothermal springs in Tengchong, China, collected from 2016 to 2021. Our dataset is comprised of 2949 archaeal metagenome-assembled genomes spanning 12 phyla and 392 newly identified species, which increases the known species diversity of Archaea by ~48.6%. The structures and potential functions of the archaeal communities are strongly influenced by temperature and pH, with high-temperature acidic and alkaline springs favoring archaeal abundance over Bacteria. Genome-resolved metagenomics and metatranscriptomics provide insights into the potential ecological niches of these Archaea and their potential roles in carbon, sulfur, nitrogen, and hydrogen metabolism. Furthermore, our findings illustrate the interplay of competition and cooperation among Archaea in biogeochemical cycles, possibly arising from overlapping functional niches and metabolic handoffs. Taken together, our study expands the genomic diversity of Archaea inhabiting geothermal springs and provides a foundation for more incisive study of biogeochemical processes mediated by Archaea in geothermal ecosystems.}, } @article {pmid38744831, year = {2024}, author = {Warwick-Dugdale, J and Tian, F and Michelsen, ML and Cronin, DR and Moore, K and Farbos, A and Chittick, L and Bell, A and Zayed, AA and Buchholz, HH and Bolanos, LM and Parsons, RJ and Allen, MJ and Sullivan, MB and Temperton, B}, title = {Long-read powered viral metagenomics in the oligotrophic Sargasso Sea.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4089}, pmid = {38744831}, issn = {2041-1723}, support = {NE/L002434/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/P008534/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/R010935/1//RCUK | Natural Environment Research Council (NERC)/ ; 3790//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 5488//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; OCE#1829831//National Science Foundation (NSF)/ ; ABI#1759874//National Science Foundation (NSF)/ ; OCE#1829640//National Science Foundation (NSF)/ ; OCE#2019589//National Science Foundation (NSF)/ ; }, mesh = {*Metagenomics/methods ; *Bacteriophages/genetics/isolation & purification/classification ; *Seawater/virology/microbiology ; *Metagenome/genetics ; *Oceans and Seas ; Genome, Viral/genetics ; Phylogeny ; Prochlorococcus/virology/genetics ; Microbiota/genetics ; Bacteria/genetics/virology/classification/isolation & purification ; }, abstract = {Dominant microorganisms of the Sargasso Sea are key drivers of the global carbon cycle. However, associated viruses that shape microbial community structure and function are not well characterised. Here, we combined short and long read sequencing to survey Sargasso Sea phage communities in virus- and cellular fractions at viral maximum (80 m) and mesopelagic (200 m) depths. We identified 2,301 Sargasso Sea phage populations from 186 genera. Over half of the phage populations identified here lacked representation in global ocean viral metagenomes, whilst 177 of the 186 identified genera lacked representation in genomic databases of phage isolates. Viral fraction and cell-associated viral communities were decoupled, indicating viral turnover occurred across periods longer than the sampling period of three days. Inclusion of long-read data was critical for capturing the breadth of viral diversity. Phage isolates that infect the dominant bacterial taxa Prochlorococcus and Pelagibacter, usually regarded as cosmopolitan and abundant, were poorly represented.}, } @article {pmid38744663, year = {2024}, author = {Hartmann, A and Binder, T and Rothballer, M}, title = {Quorum sensing-related activities of beneficial and pathogenic bacteria have important implications for plant and human health.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {6}, pages = {}, pmid = {38744663}, issn = {1574-6941}, support = {//Helmholtz Zentrum München/ ; }, mesh = {*Quorum Sensing ; Humans ; *Bacteria/genetics/metabolism/classification ; *Plants/microbiology ; Acyl-Butyrolactones/metabolism ; Bacterial Physiological Phenomena ; Soil Microbiology ; Microbiota ; Symbiosis ; Rhizosphere ; }, abstract = {Eukaryotic organisms coevolved with microbes from the environment forming holobiotic meta-genomic units. Members of host-associated microbiomes have commensalic, beneficial/symbiotic, or pathogenic phenotypes. More than 100 years ago, Lorenz Hiltner, pioneer of soil microbiology, introduced the term 'Rhizosphere' to characterize the observation that a high density of saprophytic, beneficial, and pathogenic microbes are attracted by root exudates. The balance between these types of microbes decide about the health of the host. Nowadays we know, that for the interaction of microbes with all eukaryotic hosts similar principles and processes of cooperative and competitive functions are in action. Small diffusible molecules like (phyto)hormones, volatiles and quorum sensing signals are examples for mediators of interspecies and cross-kingdom interactions. Quorum sensing of bacteria is mediated by different autoinducible metabolites in a density-dependent manner. In this perspective publication, the role of QS-related activities for the health of hosts will be discussed focussing mostly on N-acyl-homoserine lactones (AHL). It is also considered that in some cases very close phylogenetic relations exist between plant beneficial and opportunistic human pathogenic bacteria. Based on a genome and system-targeted new understanding, sociomicrobiological solutions are possible for the biocontrol of diseases and the health improvement of eukaryotic hosts.}, } @article {pmid38744390, year = {2024}, author = {Hu, W and Zheng, N and Zhang, Y and Li, S and Bartlam, M and Wang, Y}, title = {Metagenomics analysis reveals effects of salinity fluctuation on diversity and ecological functions of high and low nucleic acid content bacteria.}, journal = {The Science of the total environment}, volume = {933}, number = {}, pages = {173186}, doi = {10.1016/j.scitotenv.2024.173186}, pmid = {38744390}, issn = {1879-1026}, mesh = {*Salinity ; *Bacteria/genetics/classification ; *Metagenomics ; *RNA, Ribosomal, 16S ; Nucleic Acids ; Seawater/microbiology ; Biodiversity ; Microbiota ; Ecosystem ; }, abstract = {Salinity is a critical environmental factor in marine ecosystems and has complex and wide-ranging biological effects. However, the effects of changing salinity on diversity and ecological functions of high nucleic acid (HNA) and low nucleic acid (LNA) bacteria are not well understood. In this study, we used 16S rRNA sequencing and metagenomic sequencing analysis to reveal the response of HNA and LNA bacterial communities and their ecological functions to salinity, which was decreased from 26 ‰ to 16 ‰. The results showed that salinity changes had significant effects on the community composition of HNA and LNA bacteria. Among LNA bacteria, 14 classes showed a significant correlation between relative abundance and salinity. Salinity changes can lead to the transfer of some bacteria from HNA bacteria to LNA bacteria. In the network topology relationship, the complexity of the network between HNA and LNA bacterial communities gradually decreased with decreased salinity. The abundance of some carbon and nitrogen cycling genes in HNA and LNA bacteria varied with salinity. Overall, this study demonstrates the effects of salinity on diversity and ecological functions and suggests the importance of salinity in regulating HNA and LNA bacterial communities and functions.}, } @article {pmid38743658, year = {2024}, author = {Yue, J and Zhang, D and Cao, M and Li, Y and Liang, Q and Liu, F and Dong, Y}, title = {Response of microbial community composition and function to land use in mining soils of Xikuang Mountain in Hunan.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0299550}, pmid = {38743658}, issn = {1932-6203}, mesh = {*Soil Microbiology ; *Mining ; China ; *Bacteria/genetics/classification ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Soil/chemistry ; Ecosystem ; Biodiversity ; High-Throughput Nucleotide Sequencing ; }, abstract = {Nine land types in the northern mining area (BKQ) (mining land, smelting land, living area), the old mining area (LKQ) (whole-ore heap, wasteland, grassland), and southern mining area (NKQ) (grassland, shrubs, farmland) of Xikuang Mountain were chosen to explore the composition and functions of soil bacterial communities under different habitats around mining areas. The composition and functions of soil bacterial communities were compared among the sampling sites using 16S rRNA high-throughput sequencing and metagenomic sequencing. α diversity analysis showed the soil bacterial diversity and abundance in the old mining area were significantly higher than those in the northern mining area. β diversity analysis demonstrated that the soil bacterial community composition was highly similar among different vegetation coverages in the southern mining area. Microbial community function analysis showed the annotated KEGG function pathways and eggNOG function composition were consistent between the grassland of the old mining area and the grassland of the southern mining area. This study uncovers the soil bacterial community composition and functions among different habitats in the mining areas of Xikuang Mountain and will underlie soil ecosystem restoration in different habitats under heavy metal pollution around the mining areas there.}, } @article {pmid38743428, year = {2024}, author = {Mac Aogáin, M and Tiew, PY and Jaggi, TK and Narayana, JK and Singh, S and Hansbro, PM and Segal, LN and Chotirmall, SH}, title = {Targeting respiratory microbiomes in COPD and bronchiectasis.}, journal = {Expert review of respiratory medicine}, volume = {18}, number = {3-4}, pages = {111-125}, doi = {10.1080/17476348.2024.2355155}, pmid = {38743428}, issn = {1747-6356}, mesh = {Humans ; *Bronchiectasis/microbiology/immunology/therapy ; *Pulmonary Disease, Chronic Obstructive/microbiology/immunology/therapy/physiopathology ; *Microbiota ; Disease Progression ; Treatment Outcome ; Animals ; Immunotherapy ; }, abstract = {INTRODUCTION: This review summarizes our current understanding of the respiratory microbiome in COPD and Bronchiectasis. We explore the interplay between microbial communities, host immune responses, disease pathology, and treatment outcomes.

AREAS COVERED: We detail the dynamics of the airway microbiome, its influence on chronic respiratory diseases, and analytical challenges. Relevant articles from PubMed and Medline (January 2010-March 2024) were retrieved and summarized. We examine clinical correlations of the microbiome in COPD and bronchiectasis, assessing how current therapies impact upon it. The potential of emerging immunotherapies, antiinflammatories and antimicrobial strategies is discussed, with focus on the pivotal role of commensal taxa in maintaining respiratory health and the promising avenue of microbiome remodeling for disease management.

EXPERT OPINION: Given the heterogeneity in microbiome composition and its pivotal role in disease development and progression, a shift toward microbiome-directed therapeutics is appealing. This transition, from traditional 'pathogencentric' diagnostic and treatment modalities to those acknowledging the microbiome, can be enabled by evolving crossdisciplinary platforms which have the potential to accelerate microbiome-based interventions into routine clinical practice. Bridging the gap between comprehensive microbiome analysis and clinical application, however, remains challenging, necessitating continued innovation in research, diagnostics, trials, and therapeutic development pipelines.}, } @article {pmid38743050, year = {2024}, author = {Aguilar, C and Alwali, A and Mair, M and Rodriguez-Orduña, L and Contreras-Peruyero, H and Modi, R and Roberts, C and Sélem-Mojica, N and Licona-Cassani, C and Parkinson, EI}, title = {Actinomycetota bioprospecting from ore-forming environments.}, journal = {Microbial genomics}, volume = {10}, number = {5}, pages = {}, pmid = {38743050}, issn = {2057-5858}, support = {R35 GM138002/GM/NIGMS NIH HHS/United States ; }, mesh = {*Actinobacteria/genetics/metabolism ; Metagenomics ; Fluorides/metabolism ; Biological Products/metabolism ; Bioprospecting ; Metabolomics ; Biodiversity ; Genome, Bacterial ; Phylogeny ; Hydrogen-Ion Concentration ; Salinity ; }, abstract = {Natural products from Actinomycetota have served as inspiration for many clinically relevant therapeutics. Despite early triumphs in natural product discovery, the rate of unearthing new compounds has decreased, necessitating inventive approaches. One promising strategy is to explore environments where survival is challenging. These harsh environments are hypothesized to lead to bacteria developing chemical adaptations (e.g. natural products) to enable their survival. This investigation focuses on ore-forming environments, particularly fluoride mines, which typically have extreme pH, salinity and nutrient scarcity. Herein, we have utilized metagenomics, metabolomics and evolutionary genome mining to dissect the biodiversity and metabolism in these harsh environments. This work has unveiled the promising biosynthetic potential of these bacteria and has demonstrated their ability to produce bioactive secondary metabolites. This research constitutes a pioneering endeavour in bioprospection within fluoride mining regions, providing insights into uncharted microbial ecosystems and their previously unexplored natural products.}, } @article {pmid38742910, year = {2024}, author = {Shi, Z and Lan, Y and Wang, Y and Yan, X and Ma, X and Hassan, F-u and Rushdi, HE and Xu, Z and Wang, W and Deng, T}, title = {Multi-omics strategy reveals potential role of antimicrobial resistance and virulence factor genes responsible for Simmental diarrheic calves caused by Escherichia coli.}, journal = {mSystems}, volume = {9}, number = {6}, pages = {e0134823}, pmid = {38742910}, issn = {2379-5077}, mesh = {Cattle ; Animals ; *Virulence Factors/genetics ; *Diarrhea/veterinary/microbiology/genetics ; *Escherichia coli/genetics/pathogenicity/drug effects ; *Escherichia coli Infections/veterinary/microbiology/genetics/drug therapy ; *Cattle Diseases/microbiology/genetics ; *Gastrointestinal Microbiome/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Metabolomics ; Multiomics ; }, abstract = {Escherichia coli (E. coli) is reported to be an important pathogen associated with calf diarrhea. Antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) pose a considerable threat to both animal and human health. However, little is known about the characterization of ARGs and VFGs presented in the gut microbiota of diarrheic calves caused by E. coli. In this study, we used multi-omics strategy to analyze the ARG and VFG profiles of Simmental calves with diarrhea caused by E. coli K99. We found that gut bacterial composition and their microbiome metabolic functions varied greatly in diarrheic calves compared to healthy calves. In total, 175 ARGs were identified, and diarrheal calves showed a significantly higher diversity and abundance of ARGs than healthy calves. Simmental calves with diarrhea showed higher association of VFGs with pili function, curli assembly, and ferrienterobactin transport of E. coli. Co-occurrence patterns based on Pearson correlation analysis revealed that E. coli had a highly significant (P < 0.0001) correlation coefficient (>0.8) with 16 ARGs and 7 VFGs. Metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Phylotype analysis of E. coli genomes showed that the predominant phylogroup B1 in diarrheic Simmental calves was associated with 10 ARGs and 3 VFGs. These findings provide an overview of the diversity and abundance of the gut microbiota in diarrheic calves caused by E. coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the calves affected with diarrhea.IMPORTANCESimmental is a well-recognized beef cattle breed worldwide. They also suffer significant economic losses due to diarrhea. In this study, fecal metagenomic analysis was applied to characterize the antibiotic resistance gene (ARG) and virulence factor gene (VFG) profiles of diarrheic Simmental calves. We identified key ARGs and VFGs correlated with Escherichia coli isolated from Simmental calves. Additionally, metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Our findings provide an insight into the diversity and abundance of the gut microbiota in diarrheic calves caused by Escherichia coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the diarrheal calves from cattle hosts.}, } @article {pmid38742892, year = {2024}, author = {Martyn, C and Hayes, BM and Lauko, D and Midthun, E and Castaneda, G and Bosco-Lauth, A and Salkeld, DJ and Kistler, A and Pollard, KS and Chou, S}, title = {Metatranscriptomic investigation of single Ixodes pacificus ticks reveals diverse microbes, viruses, and novel mRNA-like endogenous viral elements.}, journal = {mSystems}, volume = {9}, number = {6}, pages = {e0032124}, pmid = {38742892}, issn = {2379-5077}, support = {//Chan Zuckerberg Biohub/ ; R01 AI32851//HHS | National Institutes of Health (NIH)/ ; //Gladstone Institutes (J. David Gladstone Institutes)/ ; //Pew Charitable Trusts (PCT)/ ; R01 AI032851/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Ixodes/virology/microbiology ; Transcriptome ; RNA, Messenger/genetics ; Microbiota/genetics ; Genome, Viral/genetics ; RNA Viruses/genetics/isolation & purification ; Bacteria/genetics/virology/isolation & purification ; }, abstract = {UNLABELLED: Ticks are increasingly important vectors of human and agricultural diseases. While many studies have focused on tick-borne bacteria, far less is known about tick-associated viruses and their roles in public health or tick physiology. To address this, we investigated patterns of bacterial and viral communities across two field populations of western black-legged ticks (Ixodes pacificus). Through metatranscriptomic analysis of 100 individual ticks, we quantified taxon prevalence, abundance, and co-occurrence with other members of the tick microbiome. In addition to commonly found tick-associated microbes, we assembled 11 novel RNA virus genomes from Rhabdoviridae, Chuviridae, Picornaviridae, Phenuiviridae, Reoviridae, Solemovidiae, Narnaviridae and two highly divergent RNA virus genomes lacking sequence similarity to any known viral families. We experimentally verified the presence of these in I. pacificus ticks across several life stages. We also unexpectedly identified numerous virus-like transcripts that are likely encoded by tick genomic DNA, and which are distinct from known endogenous viral element-mediated immunity pathways in invertebrates. Taken together, our work reveals that I. pacificus ticks carry a greater diversity of viruses than previously appreciated, in some cases resulting in evolutionarily acquired virus-like transcripts. Our findings highlight how pervasive and intimate tick-virus interactions are, with major implications for both the fundamental biology and vectorial capacity of I. pacificus ticks.

IMPORTANCE: Ticks are increasingly important vectors of disease, particularly in the United States where expanding tick ranges and intrusion into previously wild areas has resulted in increasing human exposure to ticks. Emerging human pathogens have been identified in ticks at an increasing rate, and yet little is known about the full community of microbes circulating in various tick species, a crucial first step to understanding how they interact with each and their tick host, as well as their ability to cause disease in humans. We investigated the bacterial and viral communities of the Western blacklegged tick in California and found 11 previously uncharacterized viruses circulating in this population.}, } @article {pmid38742878, year = {2024}, author = {Mies, US and Hervé, V and Kropp, T and Platt, K and Sillam-Dussès, D and Šobotník, J and Brune, A}, title = {Genome reduction and horizontal gene transfer in the evolution of Endomicrobia-rise and fall of an intracellular symbiosis with termite gut flagellates.}, journal = {mBio}, volume = {15}, number = {6}, pages = {e0082624}, pmid = {38742878}, issn = {2150-7511}, support = {//Max-Planck-Institut für Terrestrische Mikrobiologie (MPI for Terrestrial Microbiology)/ ; SFB 987//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {Animals ; *Isoptera/microbiology/parasitology ; *Symbiosis ; *Gene Transfer, Horizontal ; *Gastrointestinal Microbiome ; *Phylogeny ; *Genome, Bacterial ; *Bacteria/genetics/classification ; Evolution, Molecular ; Metagenome ; }, abstract = {Bacterial endosymbionts of eukaryotic hosts typically experience massive genome reduction, but the underlying evolutionary processes are often obscured by the lack of free-living relatives. Endomicrobia, a family-level lineage of host-associated bacteria in the phylum Elusimicrobiota that comprises both free-living representatives and endosymbionts of termite gut flagellates, are an excellent model to study evolution of intracellular symbionts. We reconstructed 67 metagenome-assembled genomes (MAGs) of Endomicrobiaceae among more than 1,700 MAGs from the gut microbiota of a wide range of termites. Phylogenomic analysis confirmed a sister position of representatives from termites and ruminants, and allowed to propose eight new genera in the radiation of Endomicrobiaceae. Comparative genome analysis documented progressive genome erosion in the new genus Endomicrobiellum, which comprises all flagellate endosymbionts characterized to date. Massive gene losses were accompanied by the acquisition of new functions by horizontal gene transfer, which led to a shift from a glucose-based energy metabolism to one based on sugar phosphates. The breakdown of glycolysis and many anabolic pathways for amino acids and cofactors in several subgroups was compensated by the independent acquisition of new uptake systems, including an ATP/ADP antiporter, from other gut microbiota. The putative donors are mostly flagellate endosymbionts from other bacterial phyla, including several, hitherto unknown lineages of uncultured Alphaproteobacteria, documenting the importance of horizontal gene transfer in the convergent evolution of these intracellular symbioses. The loss of almost all biosynthetic capacities in some lineages of Endomicrobiellum suggests that their originally mutualistic relationship with flagellates is on its decline.IMPORTANCEUnicellular eukaryotes are frequently colonized by bacterial and archaeal symbionts. A prominent example are the cellulolytic gut flagellates of termites, which harbor diverse but host-specific bacterial symbionts that occur exclusively in termite guts. One of these lineages, the so-called Endomicrobia, comprises both free-living and endosymbiotic representatives, which offers the unique opportunity to study the evolutionary processes underpinning the transition from a free-living to an intracellular lifestyle. Our results revealed a progressive gene loss in energy metabolism and biosynthetic pathways, compensated by the acquisition of new functions via horizontal gene transfer from other gut bacteria, and suggest the eventual breakdown of an initially mutualistic symbiosis. Evidence for convergent evolution of unrelated endosymbionts reflects adaptations to the intracellular environment of termite gut flagellates.}, } @article {pmid38742876, year = {2024}, author = {De Coninck, L and Soto, A and Wang, L and De Wolf, K and Smitz, N and Deblauwe, I and Mbigha Donfack, KC and Müller, R and Delang, L and Matthijnssens, J}, title = {Lack of abundant core virome in Culex mosquitoes from a temperate climate region despite a mosquito species-specific virome.}, journal = {mSystems}, volume = {9}, number = {6}, pages = {e0001224}, pmid = {38742876}, issn = {2379-5077}, support = {11L1323N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; C14/20/108//KU Leuven/ ; }, mesh = {Animals ; *Culex/virology/microbiology ; *Virome/genetics ; *Wolbachia/genetics/isolation & purification ; Belgium ; Species Specificity ; Mosquito Vectors/virology/microbiology ; Metagenomics ; Insect Viruses/genetics/isolation & purification ; Climate ; }, abstract = {In arthropod-associated microbial communities, insect-specific viruses (ISVs) are prevalent yet understudied due to limited infectivity outside their natural hosts. However, ISVs might play a crucial role in regulating mosquito populations and influencing arthropod-borne virus transmission. Some studies have indicated a core virome in mosquitoes consisting of mostly ISVs. Employing single mosquito metagenomics, we comprehensively profiled the virome of native and invasive mosquito species in Belgium. This approach allowed for accurate host species determination, prevalence assessment of viruses and Wolbachia, and the identification of novel viruses. Contrary to our expectations, no abundant core virome was observed in Culex mosquitoes from Belgium. In that regard, we caution against rigidly defining mosquito core viromes and encourage nuanced interpretations of other studies. Nonetheless, our study identified 45 viruses of which 28 were novel, enriching our understanding of the mosquito virome and ISVs. We showed that the mosquito virome in this study is species-specific and less dependent on the location where mosquitoes from the same species reside. In addition, because Wolbachia has previously been observed to influence arbovirus transmission, we report the prevalence of Wolbachia in Belgian mosquitoes and the detection of several Wolbachia mobile genetic elements. The observed prevalence ranged from 83% to 92% in members from the Culex pipiens complex.IMPORTANCECulex pipiens mosquitoes are important vectors for arboviruses like West Nile virus and Usutu virus. Virome studies on individual Culex pipiens, and on individual mosquitoes in general, have been lacking. To mitigate this, we sequenced the virome of 190 individual Culex and 8 individual Aedes japonicus mosquitoes. We report the lack of a core virome in these mosquitoes from Belgium and caution the interpretation of other studies in this light. The discovery of new viruses in this study will aid our comprehension of insect-specific viruses and the mosquito virome in general in relation to mosquito physiology and mosquito population dynamics.}, } @article {pmid38742714, year = {2024}, author = {Bei, Q and Reitz, T and Schädler, M and Hodgskiss, LH and Peng, J and Schnabel, B and Buscot, F and Eisenhauer, N and Schleper, C and Heintz-Buschart, A}, title = {Metabolic potential of Nitrososphaera-associated clades.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38742714}, issn = {1751-7370}, support = {//German Centre for Integrative Biodiversity Research/ ; FZT 118//Halle-Jena-Leipzig of the German Research Foundation/ ; HE 8266/4-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Soil Microbiology ; *Archaea/metabolism/genetics/classification ; *Ammonia/metabolism ; *Oxidation-Reduction ; Germany ; Metagenome ; Phylogeny ; Genome, Archaeal ; Soil/chemistry ; }, abstract = {Soil ammonia-oxidizing archaea (AOA) play a crucial role in converting ammonia to nitrite, thereby mobilizing reactive nitrogen species into their soluble form, with a significant impact on nitrogen losses from terrestrial soils. Yet, our knowledge regarding their diversity and functions remains limited. In this study, we reconstructed 97 high-quality AOA metagenome-assembled genomes (MAGs) from 180 soil samples collected in Central Germany during 2014-2019 summers. These MAGs were affiliated with the order Nitrososphaerales and clustered into four family-level clades (NS-α/γ/δ/ε). Among these MAGs, 75 belonged to the most abundant but least understood δ-clade. Within the δ-clade, the amoA genes in three MAGs from neutral soils showed a 99.5% similarity to the fosmid clone 54d9, which has served as representative of the δ-clade for the past two decades since even today no cultivated representatives are available. Seventy-two MAGs constituted a distinct δ sub-clade, and their abundance and expression activity were more than twice that of other MAGs in slightly acidic soils. Unlike the less abundant clades (α, γ, and ε), the δ-MAGs possessed multiple highly expressed intracellular and extracellular carbohydrate-active enzymes responsible for carbohydrate binding (CBM32) and degradation (GH5), along with highly expressed genes involved in ammonia oxidation. Together, these results suggest metabolic versatility of uncultured soil AOA and a potential mixotrophic or chemolithoheterotrophic lifestyle among 54d9-like AOA.}, } @article {pmid38742695, year = {2024}, author = {Yang, L and Canarini, A and Zhang, W and Lang, M and Chen, Y and Cui, Z and Kuzyakov, Y and Richter, A and Chen, X and Zhang, F and Tian, J}, title = {Microbial life-history strategies mediate microbial carbon pump efficacy in response to N management depending on stoichiometry of microbial demand.}, journal = {Global change biology}, volume = {30}, number = {5}, pages = {e17311}, doi = {10.1111/gcb.17311}, pmid = {38742695}, issn = {1365-2486}, support = {32102490//National Natural Science Foundation of China/ ; 32071629//National Natural Science Foundation of China/ ; 2023YFD1901500//National Key Research and Development Program of China/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism/analysis ; *Nitrogen/metabolism/analysis ; *Fertilizers/analysis ; Carbon Cycle ; Microbiota ; }, abstract = {The soil microbial carbon pump (MCP) is increasingly acknowledged as being directly linked to soil organic carbon (SOC) accumulation and stability. Given the close coupling of carbon (C) and nitrogen (N) cycles and the constraints imposed by their stoichiometry on microbial growth, N addition might affect microbial growth strategies with potential consequences for necromass formation and carbon stability. However, this topic remains largely unexplored. Based on two multi-level N fertilizer experiments over 10 years in two soils with contrasting soil fertility located in the North (Cambisol, carbon-poor) and Southwest (Luvisol, carbon-rich), we hypothesized that different resource demands of microorganism elicit a trade-off in microbial growth potential (Y-strategy) and resource-acquisition (A-strategy) in response to N addition, and consequently on necromass formation and soil carbon stability. We combined measurements of necromass metrics (MCP efficacy) and soil carbon stability (chemical composition and mineral associated organic carbon) with potential changes in microbial life history strategies (assessed via soil metagenomes and enzymatic activity analyses). The contribution of microbial necromass to SOC decreased with N addition in the Cambisol, but increased in the Luvisol. Soil microbial life strategies displayed two distinct responses in two soils after N amendment: shift toward A-strategy (Cambisol) or Y-strategy (Luvisol). These divergent responses are owing to the stoichiometric imbalance between microbial demands and resource availability for C and N, which presented very distinct patterns in the two soils. The partial correlation analysis further confirmed that high N addition aggravated stoichiometric carbon demand, shifting the microbial community strategy toward resource-acquisition which reduced carbon stability in Cambisol. In contrast, the microbial Y-strategy had the positive direct effect on MCP efficacy in Luvisol, which greatly enhanced carbon stability. Such findings provide mechanistic insights into the stoichiometric regulation of MCP efficacy, and how this is mediated by site-specific trade-offs in microbial life strategies, which contribute to improving our comprehension of soil microbial C sequestration and potential optimization of agricultural N management.}, } @article {pmid38742484, year = {2024}, author = {Makri, N and Ring, N and Shaw, DJ and Athinodorou, A and Robinson, V and Paterson, GK and Richardson, J and Gow, D and Nuttall, T}, title = {Cytological evaluation, culture and genomics to evaluate the microbiome in healthy rabbit external ear canals.}, journal = {Veterinary dermatology}, volume = {35}, number = {5}, pages = {479-491}, pmid = {38742484}, issn = {1365-3164}, support = {//R(D)SVS Hospital for Small Animals/ ; }, mesh = {Animals ; Rabbits/microbiology ; *Ear Canal/microbiology ; *Microbiota ; Female ; Male ; Otoscopy ; Bacteria/genetics/classification/isolation & purification ; Genomics ; Fungi/genetics/classification/isolation & purification ; }, abstract = {BACKGROUND: Lop-eared rabbits may be predisposed to otitis externa (OE) as a consequence of their ear conformation. Although otoscopy, otic cytological evaluation and culture are valuable tools in dogs and cats, published data on rabbits remain lacking.

HYPOTHESIS/OBJECTIVES: This study aimed to assess the utility of otoscopy and cytological results in evaluating healthy rabbit external ear canals (EECs) and to characterise ear cytological and microbiological findings through culture techniques and metagenomic sequencing.

ANIMALS: Sixty-three otitis-free client-owned rabbits.

MATERIALS AND METHODS: All rabbits underwent otoscopy and ear cytological evaluation. In a subset of 12 rabbits, further bacterial and fungal culture, fungal DNA assessment and metagenomic sequencing were performed.

RESULTS: Otic cytological results revealed yeast in 73%, cocci in 42.9% and rods in 28.6% of healthy rabbit EECs. Compared to upright-eared rabbits, lop-eared rabbits had more discharge and more bacteria per oil immersion field. Culture isolated eight different species yet metagenomic sequencing identified 36, belonging to the Bacillota (Firmicutes), Pseudomonadota and Actinomycetota phyla. Staphylococcus were the most commonly observed species with both methods. Ten of 12 rabbits were yeast-positive on cytological evaluation with only three yielding fungal growth identified as Yarrowia (Candida) lipolytica, Eurotium echinulatum and Cystofilobasidium infirmominiatum.

Healthy rabbit EECs lack inflammatory cells yet can host yeast and bacteria, emphasising the need to evaluate cytological results alongside the clinical signs. Lop-ear anatomy may predispose to bacterial overgrowth and OE. Notably, yeasts may be present despite a negative culture.}, } @article {pmid38741135, year = {2024}, author = {Cai, H and McLimans, CJ and Jiang, H and Chen, F and Krumholz, LR and Hambright, KD}, title = {Aerobic anoxygenic phototrophs play important roles in nutrient cycling within cyanobacterial Microcystis bloom microbiomes.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {88}, pmid = {38741135}, issn = {2049-2618}, support = {Grant 2018YFA0903000//National Key Research and Development Program of China/ ; DEB-1831061//National Science Foundation/ ; DEB-1831061//National Science Foundation/ ; DEB-1831061//National Science Foundation/ ; DEB-1831061//National Science Foundation/ ; BK20191508//Natural Science Foundation of Jiangsu Province of China/ ; }, mesh = {*Microcystis/genetics/metabolism/growth & development ; *Microbiota ; China ; *Lakes/microbiology ; Nutrients/metabolism ; Phototrophic Processes ; Aerobiosis ; Eutrophication ; Bacteria/classification/metabolism/genetics/isolation & purification ; Nitrogen/metabolism ; Carbon/metabolism ; }, abstract = {BACKGROUND: During the bloom season, the colonial cyanobacterium Microcystis forms complex aggregates which include a diverse microbiome within an exopolymer matrix. Early research postulated a simple mutualism existing with bacteria benefitting from the rich source of fixed carbon and Microcystis receiving recycled nutrients. Researchers have since hypothesized that Microcystis aggregates represent a community of synergistic and interacting species, an interactome, each with unique metabolic capabilities that are critical to the growth, maintenance, and demise of Microcystis blooms. Research has also shown that aggregate-associated bacteria are taxonomically different from free-living bacteria in the surrounding water. Moreover, research has identified little overlap in functional potential between Microcystis and members of its microbiome, further supporting the interactome concept. However, we still lack verification of general interaction and know little about the taxa and metabolic pathways supporting nutrient and metabolite cycling within Microcystis aggregates.

RESULTS: During a 7-month study of bacterial communities comparing free-living and aggregate-associated bacteria in Lake Taihu, China, we found that aerobic anoxygenic phototrophic (AAP) bacteria were significantly more abundant within Microcystis aggregates than in free-living samples, suggesting a possible functional role for AAP bacteria in overall aggregate community function. We then analyzed gene composition in 102 high-quality metagenome-assembled genomes (MAGs) of bloom-microbiome bacteria from 10 lakes spanning four continents, compared with 12 complete Microcystis genomes which revealed that microbiome bacteria and Microcystis possessed complementary biochemical pathways that could serve in C, N, S, and P cycling. Mapping published transcripts from Microcystis blooms onto a comprehensive AAP and non-AAP bacteria MAG database (226 MAGs) indicated that observed high levels of expression of genes involved in nutrient cycling pathways were in AAP bacteria.

CONCLUSIONS: Our results provide strong corroboration of the hypothesized Microcystis interactome and the first evidence that AAP bacteria may play an important role in nutrient cycling within Microcystis aggregate microbiomes. Video Abstract.}, } @article {pmid38740930, year = {2024}, author = {Piton, G and Allison, SD and Bahram, M and Hildebrand, F and Martiny, JBH and Treseder, KK and Martiny, AC}, title = {Reply to: Microbial dark matter could add uncertainties to metagenomic trait estimations.}, journal = {Nature microbiology}, volume = {9}, number = {6}, pages = {1431-1433}, pmid = {38740930}, issn = {2058-5276}, support = {DE-SC0020382//U.S. Department of Energy (DOE)/ ; DE-SC0016410//U.S. Department of Energy (DOE)/ ; erc-stg-948219, EPYC//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; BB/X011054/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {*Metagenomics ; Bacteria/genetics/classification ; Metagenome ; Microbiota/genetics ; Uncertainty ; }, } @article {pmid38740929, year = {2024}, author = {Osburn, ED and McBride, SG and Strickland, MS}, title = {Microbial dark matter could add uncertainties to metagenomic trait estimations.}, journal = {Nature microbiology}, volume = {9}, number = {6}, pages = {1427-1430}, pmid = {38740929}, issn = {2058-5276}, mesh = {*Metagenomics ; Bacteria/genetics/classification ; Metagenome ; Microbiota/genetics ; }, } @article {pmid38740275, year = {2024}, author = {Long, AR and Mortara, EL and Mendoza, BN and Fink, EC and Sacco, FX and Ciesla, MJ and Stack, TMM}, title = {Sequence similarity network analysis of drug- and dye-modifying azoreductase enzymes found in the human gut microbiome.}, journal = {Archives of biochemistry and biophysics}, volume = {757}, number = {}, pages = {110025}, pmid = {38740275}, issn = {1096-0384}, support = {P20 GM103430/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Nitroreductases/metabolism/genetics ; *Gastrointestinal Microbiome ; *NADH, NADPH Oxidoreductases/metabolism/genetics/chemistry ; Coloring Agents/metabolism ; Molecular Docking Simulation ; Substrate Specificity ; Sulfasalazine ; Bacterial Proteins/metabolism/genetics/chemistry ; Kinetics ; Clostridiales/enzymology/genetics ; Azo Compounds/metabolism/chemistry ; }, abstract = {Drug metabolism by human gut microbes is often exemplified by azo bond reduction in the anticolitic prodrug sulfasalazine. Azoreductase activity is often found in incubations with cell cultures or ex vivo gut microbiome samples and contributes to the xenobiotic metabolism of drugs and food additives. Applying metagenomic studies to personalized medicine requires knowledge of the genes responsible for sulfasalazine and other drug metabolism, and candidate genes and proteins for drug modifications are understudied. A representative gut-abundant azoreductase from Anaerotignum lactatifermentan DSM 14214 efficiently reduces sulfasalazine and another drug, phenazopyridine, but could not reduce all azo-bonded drugs in this class. We used enzyme kinetics to characterize this enzyme for its NADH-dependent reduction of these drugs and food additives and performed computational docking to provide the groundwork for understanding substrate specificity in this family. We performed an analysis of the Flavodoxin-like fold InterPro family (IPR003680) by computing a sequence similarity network to classify distinct subgroups of the family and then performed chemically-guided functional profiling to identify proteins that are abundant in the NIH Human Microbiome Project dataset. This strategy aims to reduce the number of unique azoreductases needed to characterize one protein family in the diverse set of potential drug- and dye-modifying activities found in the human gut microbiome.}, } @article {pmid38740246, year = {2024}, author = {Torres, MC and Breyer, GM and Riveros Escalona, MA and Mayer, FQ and Muterle Varela, AP and Ariston de Carvalho Azevedo, V and Matiuzzi da Costa, M and Aburjaile, FF and Dorn, M and Brenig, B and Ribeiro de Itapema Cardoso, M and Siqueira, FM}, title = {Exploring bacterial diversity and antimicrobial resistance gene on a southern Brazilian swine farm.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {352}, number = {}, pages = {124146}, doi = {10.1016/j.envpol.2024.124146}, pmid = {38740246}, issn = {1873-6424}, mesh = {Animals ; Swine ; Brazil ; *Farms ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Wastewater/microbiology ; Manure/microbiology ; Microbiota/drug effects/genetics ; }, abstract = {The bacterial composition of and the circulation of antimicrobial resistance genes (ARGs) in waste from Brazilian swine farms are still poorly understood. Considering that antimicrobial resistance (AMR) is one of the main threats to human, animal, and environmental health, the need to accurately assess the load of ARGs released into the environment is urgent. Therefore, this study aimed to characterize the microbiota in a swine farm in southern Brazil and the resistome in swine farm wastewater treated in a series of waste stabilization ponds (WSPs). Samples were collected from farm facilities and the surrounding environment, representing all levels of swine manure within the treatment system. Total metagenomic sequencing was performed on samples from WSPs, and 16S-rDNA sequencing was performed on all the collected samples. The results showed increased bacterial diversity in WSPs, characterized by the presence of Caldatribacteriota, Cloacimonadota, Desulfobacterota, Spirochaetota, Synergistota, and Verrucomicrobiota. Furthermore, resistance genes to tetracyclines, lincosamides, macrolides, rifamycin, phenicol, and genes conferring multidrug resistance were detected in WSPs samples. Interestingly, the most abundant ARG was linG, which confers resistance to the lincosamides. Notably, genes conferring macrolide (mphG and mefC) and rifamycin (rpoB_RIF) resistance appeared in greater numbers in the late WSPs. These drugs are among the high-priority antibiotic classes for human health. Moreover, certain mobile genetic elements (MGEs) were identified in the samples, notably tnpA, which was found in high abundance. These elements are of particular concern due to their potential to facilitate the dissemination of ARGs among bacteria. In summary, the results indicate that, in the studied farm, the swine manure treatment system could not eliminate ARGs and MGEs. Our results validate concerns about Brazil's swine production system. The misuse and overuse of antimicrobials during animal production must be avoided to mitigate AMR.}, } @article {pmid38740021, year = {2024}, author = {Huang, P and Dong, Q and Wang, Y and Tian, Y and Wang, S and Zhang, C and Yu, L and Tian, F and Gao, X and Guo, H and Yi, S and Li, M and Liu, Y and Zhang, Q and Lu, W and Wang, G and Yang, B and Cui, S and Hua, D and Wang, X and Jiao, Y and Liu, L and Deng, Q and Ma, B and Wu, T and Zou, H and Shi, J and Zhang, H and Fan, D and Sheng, Y and Zhao, J and Tang, L and Zhang, H and Sun, W and , and Chen, W and Kong, X and Chen, L and Zhai, Q}, title = {Gut microbial genomes with paired isolates from China illustrate probiotic and cardiometabolic effects.}, journal = {Cell genomics}, volume = {4}, number = {6}, pages = {100559}, pmid = {38740021}, issn = {2666-979X}, mesh = {*Probiotics ; *Gastrointestinal Microbiome/genetics ; China ; Animals ; Humans ; Mice ; Male ; Female ; Genome, Bacterial/genetics ; Genome, Microbial ; Feces/microbiology ; Obesity/microbiology ; Adult ; Mice, Inbred C57BL ; }, abstract = {The gut microbiome displays genetic differences among populations, and characterization of the genomic landscape of the gut microbiome in China remains limited. Here, we present the Chinese Gut Microbial Reference (CGMR) set, comprising 101,060 high-quality metagenomic assembled genomes (MAGs) of 3,707 nonredundant species from 3,234 fecal samples across primarily rural Chinese locations, 1,376 live isolates mainly from lactic acid bacteria, and 987 novel species relative to worldwide databases. We observed region-specific coexisting MAGs and MAGs with probiotic and cardiometabolic functionalities. Preliminary mouse experiments suggest a probiotic effect of two Faecalibacillus intestinalis isolates in alleviating constipation, cardiometabolic influences of three Bacteroides fragilis_A isolates in obesity, and isolates from the genera Parabacteroides and Lactobacillus in host lipid metabolism. Our study expands the current microbial genomes with paired isolates and demonstrates potential host effects, contributing to the mechanistic understanding of host-microbe interactions.}, } @article {pmid38735188, year = {2024}, author = {Ningthoujam, R and Pinyakong, O}, title = {Exploring di (2-ethylhexyl) phthalate degradation by a synthetic marine bacterial consortium: Genomic insights, pathway and interaction prediction, and application in sediment microcosms.}, journal = {Journal of hazardous materials}, volume = {472}, number = {}, pages = {134557}, doi = {10.1016/j.jhazmat.2024.134557}, pmid = {38735188}, issn = {1873-3336}, mesh = {*Geologic Sediments/microbiology ; *Diethylhexyl Phthalate/metabolism ; *Biodegradation, Environmental ; *Bacteria/metabolism/genetics ; *Microbial Consortia/genetics ; *Water Pollutants, Chemical/metabolism ; Plasticizers/metabolism ; Genome, Bacterial ; }, abstract = {Di (2-ethylhexyl) phthalate (DEHP), a toxic phthalate ester (PAE) plasticizer, is often detected in marine sediment and biota. Our understanding of DEHP-degrading marine bacteria and the associated genetic mechanisms is limited. This study established a synthetic bacterial consortium (A02) consisting of three marine bacteria (OR05, OR16, and OR21). Consortium A02 outperformed the individual strains in DEHP degradation. Investigations into the degradation of DEHP intermediates revealed that OR05 and OR16 likely contributed to enhanced DEHP degradation by Consortium A02 via the utilization of DEHP intermediates, such as protocatechuic acid and mono (ethylhexyl) phthalate, with OR21 as the key DEHP degrader. A pathway of DEHP degradation by Consortium A02 was predicted based on genome analysis and experimental degradation. Bioaugmentation with Consortium A02 led to 80% DEHP degradation in 26 days in saline sediment (100 mg/kg), surpassing the 53% degradation by indigenous microbes, indicating the potential of A02 for treating DEHP-contaminated sediments. Meanwhile, bioaugmentation notably changed the bacterial community, with the exclusive presence of certain bacterial genera in the A02 bioaugmented microcosms, and was predicted to result in a more dynamic and active sediment bacterial community. This study contributes to the limited literature on DEHP degradation by marine bacteria and their associated genes.}, } @article {pmid38735183, year = {2024}, author = {Wijaya, J and Park, J and Yang, Y and Siddiqui, SI and Oh, S}, title = {A metagenome-derived artificial intelligence modeling framework advances the predictive diagnosis and interpretation of petroleum-polluted groundwater.}, journal = {Journal of hazardous materials}, volume = {472}, number = {}, pages = {134513}, doi = {10.1016/j.jhazmat.2024.134513}, pmid = {38735183}, issn = {1873-3336}, mesh = {*Water Pollutants, Chemical/analysis ; *Metagenome ; *Groundwater/microbiology ; *Petroleum ; Artificial Intelligence ; Environmental Monitoring/methods ; Machine Learning ; Biodegradation, Environmental ; Petroleum Pollution ; Metagenomics/methods ; Microbiota ; }, abstract = {Groundwater (GW) quality monitoring is vital for sustainable water resource management. The present study introduced a metagenome-derived machine learning (ML) model aimed at enhancing the predictive understanding and diagnostic interpretation of GW pollution associated with petroleum. In this framework, taxonomic and metabolic profiles derived from GW metagenomes were combined for use as the input dataset. By employing strategies that optimized data integration, model selection, and parameter tuning, we achieved a significant increase in diagnostic accuracy for petroleum-polluted GW. Explanatory artificial intelligence techniques identified petroleum degradation pathways and Rhodocyclaceae as strong predictors of a pollution diagnosis. Metagenomic analysis corroborated the presence of gene operons encoding aminobenzoate and xylene biodegradation within the de novo assembled genome of Rhodocyclaceae. Our genome-centric metagenomic analysis thus clarified the ecological interactions associated with microbiomes in breaking down petroleum contaminants, validating the ML-based diagnostic results. This metagenome-derived ML framework not only enhances the predictive diagnosis of petroleum pollution but also offers interpretable insights into the interaction between microbiomes and petroleum. The proposed ML framework demonstrates great promise for use as a science-based strategy for the on-site monitoring and remediation of GW pollution.}, } @article {pmid38734682, year = {2024}, author = {Buysse, M and Koual, R and Binetruy, F and de Thoisy, B and Baudrimont, X and Garnier, S and Douine, M and Chevillon, C and Delsuc, F and Catzeflis, F and Bouchon, D and Duron, O}, title = {Detection of Anaplasma and Ehrlichia bacteria in humans, wildlife, and ticks in the Amazon rainforest.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3988}, pmid = {38734682}, issn = {2041-1723}, support = {ANR-21-CE02-0002//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-LABX-25-01//Agence Nationale de la Recherche (French National Research Agency)/ ; }, mesh = {*Anaplasma/genetics/isolation & purification/pathogenicity/classification ; *Ehrlichia/genetics/isolation & purification/classification ; Humans ; Animals ; *Rainforest ; *Ticks/microbiology ; *Animals, Wild/microbiology ; *Phylogeny ; Anaplasmosis/microbiology/epidemiology/transmission ; French Guiana ; Ehrlichiosis/microbiology/epidemiology/veterinary/transmission ; Metagenomics/methods ; Genome, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Tick-borne bacteria of the genera Ehrlichia and Anaplasma cause several emerging human infectious diseases worldwide. In this study, we conduct an extensive survey for Ehrlichia and Anaplasma infections in the rainforests of the Amazon biome of French Guiana. Through molecular genetics and metagenomics reconstruction, we observe a high indigenous biodiversity of infections circulating among humans, wildlife, and ticks inhabiting these ecosystems. Molecular typing identifies these infections as highly endemic, with a majority of new strains and putative species specific to French Guiana. They are detected in unusual rainforest wild animals, suggesting they have distinctive sylvatic transmission cycles. They also present potential health hazards, as revealed by the detection of Candidatus Anaplasma sparouinense in human red blood cells and that of a new close relative of the human pathogen Ehrlichia ewingii, Candidatus Ehrlichia cajennense, in the tick species that most frequently bite humans in South America. The genome assembly of three new putative species obtained from human, sloth, and tick metagenomes further reveals the presence of major homologs of Ehrlichia and Anaplasma virulence factors. These observations converge to classify health hazards associated with Ehrlichia and Anaplasma infections in the Amazon biome as distinct from those in the Northern Hemisphere.}, } @article {pmid38734193, year = {2024}, author = {Ballanti, M and Antonetti, L and Mavilio, M and Casagrande, V and Moscatelli, A and Pietrucci, D and Teofani, A and Internò, C and Cardellini, M and Paoluzi, O and Monteleone, G and Lefebvre, P and Staels, B and Mingrone, G and Menghini, R and Federici, M}, title = {Decreased circulating IPA levels identify subjects with metabolic comorbidities: A multi-omics study.}, journal = {Pharmacological research}, volume = {204}, number = {}, pages = {107207}, doi = {10.1016/j.phrs.2024.107207}, pmid = {38734193}, issn = {1096-1186}, mesh = {Humans ; Male ; Animals ; *Gastrointestinal Microbiome ; Female ; Middle Aged ; Insulin Resistance ; Indoles ; Mice, Inbred C57BL ; Metabolomics ; Mice ; Adult ; Metabolic Syndrome/blood/metabolism/microbiology ; Comorbidity ; Muscle, Skeletal/metabolism/microbiology ; Multiomics ; }, abstract = {In recent years several experimental observations demonstrated that the gut microbiome plays a role in regulating positively or negatively metabolic homeostasis. Indole-3-propionic acid (IPA), a Tryptophan catabolic product mainly produced by C. Sporogenes, has been recently shown to exert either favorable or unfavorable effects in the context of metabolic and cardiovascular diseases. We performed a study to delineate clinical and multiomics characteristics of human subjects characterized by low and high IPA levels. Subjects with low IPA blood levels showed insulin resistance, overweight, low-grade inflammation, and features of metabolic syndrome compared to those with high IPA. Metabolomics analysis revealed that IPA was negatively correlated with leucine, isoleucine, and valine metabolism. Transcriptomics analysis in colon tissue revealed the enrichment of several signaling, regulatory, and metabolic processes. Metagenomics revealed several OTU of ruminococcus, alistipes, blautia, butyrivibrio and akkermansia were significantly enriched in [high]IPA group while in [low]IPA group Escherichia-Shigella, megasphera, and Desulfovibrio genus were more abundant. Next, we tested the hypothesis that treatment with IPA in a mouse model may recapitulate the observations of human subjects, at least in part. We found that a short treatment with IPA (4 days at 20/mg/kg) improved glucose tolerance and Akt phosphorylation in the skeletal muscle level, while regulating blood BCAA levels and gene expression in colon tissue, all consistent with results observed in human subjects stratified for IPA levels. Our results suggest that treatment with IPA may be considered a potential strategy to improve insulin resistance in subjects with dysbiosis.}, } @article {pmid38733121, year = {2024}, author = {Mady, EA and Osuga, H and Toyama, H and El-Husseiny, HM and Inoue, R and Murase, H and Yamamoto, Y and Nagaoka, K}, title = {Relationship between the components of mare breast milk and foal gut microbiome: shaping gut microbiome development after birth.}, journal = {The veterinary quarterly}, volume = {44}, number = {1}, pages = {1-9}, pmid = {38733121}, issn = {1875-5941}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Horses ; Female ; *Milk/chemistry/microbiology ; *Feces/microbiology/chemistry ; *Animals, Newborn/microbiology ; *RNA, Ribosomal, 16S/genetics/analysis ; *Lactation ; }, abstract = {The gut microbiota (GM) is essential for mammalian health. Although the association between infant GM and breast milk (BM) composition has been well established in humans, such a relationship has not been investigated in horses. Hence, this study was conducted to analyze the GM formation of foals during lactation and determine the presence of low-molecular-weight metabolites in mares' BM and their role in shaping foals' GM. The fecal and BM samples from six pairs of foals and mares were subjected to 16S ribosomal RNA metagenomic and metabolomic analyses, respectively. The composition of foal GM changed during lactation time; hierarchical cluster analysis divided the fetal GM into three groups corresponding to different time points in foal development. The level of most metabolites in milk decreased over time with increasing milk yield, while threonic acid and ascorbic acid increased. Further analyses revealed gut bacteria that correlated with changes in milk metabolites; for instance, there was a positive correlation between Bacteroidaceae in the foal's gut microbiota and serine/glycine in the mother's milk. These findings help improve the rearing environment of lactating horses and establish artificial feeding methods for foals.}, } @article {pmid38732540, year = {2024}, author = {Chai, X and Chen, X and Yan, T and Zhao, Q and Hu, B and Jiang, Z and Guo, W and Zhang, Y}, title = {Intestinal Barrier Impairment Induced by Gut Microbiome and Its Metabolites in School-Age Children with Zinc Deficiency.}, journal = {Nutrients}, volume = {16}, number = {9}, pages = {}, pmid = {38732540}, issn = {2072-6643}, support = {CNS-ZD2019008//Chinese Nutrition Society/ ; 82173497//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Zinc/deficiency/blood ; Child ; Male ; Female ; *Feces/microbiology ; Bacteria/classification/metabolism ; Intestinal Mucosa/metabolism/microbiology ; Metabolome ; Intestines/microbiology ; }, abstract = {Zinc deficiency affects the physical and intellectual development of school-age children, while studies on the effects on intestinal microbes and metabolites in school-age children have not been reported. School-age children were enrolled to conduct anthropometric measurements and serum zinc and serum inflammatory factors detection, and children were divided into a zinc deficiency group (ZD) and control group (CK) based on the results of serum zinc. Stool samples were collected to conduct metagenome, metabolome, and diversity analysis, and species composition analysis, functional annotation, and correlation analysis were conducted to further explore the function and composition of the gut flora and metabolites of children with zinc deficiency. Beta-diversity analysis revealed a significantly different gut microbial community composition between ZD and CK groups. For instance, the relative abundances of Phocaeicola vulgatus, Alistipes putredinis, Bacteroides uniformis, Phocaeicola sp000434735, and Coprococcus eutactus were more enriched in the ZD group, while probiotic bacteria Bifidobacterium kashiwanohense showed the reverse trend. The functional profile of intestinal flora was also under the influence of zinc deficiency, as reflected by higher levels of various glycoside hydrolases in the ZD group. In addition, saccharin, the pro-inflammatory metabolites, and taurocholic acid, the potential factor inducing intestinal leakage, were higher in the ZD group. In conclusion, zinc deficiency may disturb the gut microbiome community and metabolic function profile of school-age children, potentially affecting human health.}, } @article {pmid38731876, year = {2024}, author = {Park, G and Kim, S and Lee, W and Kim, G and Shin, H}, title = {Deciphering the Impact of Defecation Frequency on Gut Microbiome Composition and Diversity.}, journal = {International journal of molecular sciences}, volume = {25}, number = {9}, pages = {}, pmid = {38731876}, issn = {1422-0067}, support = {2021R1A2C1095215//Korea Basic Science Institute/ ; 2023R1A6C101A045//Korea Basic Science Institute/ ; OTTOGI Corporation through Research and Publication Projects//OTTOGI Corporation/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; Male ; Adult ; *Defecation ; Female ; Metabolome ; Biodiversity ; Amino Acids, Branched-Chain/metabolism ; Metabolomics/methods ; Bacteria/classification/genetics/metabolism ; Bacteroides/genetics ; Metagenome ; }, abstract = {This study explores the impact of defecation frequency on the gut microbiome structure by analyzing fecal samples from individuals categorized by defecation frequency: infrequent (1-3 times/week, n = 4), mid-frequent (4-6 times/week, n = 7), and frequent (daily, n = 9). Utilizing 16S rRNA gene-based sequencing and LC-MS/MS metabolome profiling, significant differences in microbial diversity and community structures among the groups were observed. The infrequent group showed higher microbial diversity, with community structures significantly varying with defecation frequency, a pattern consistent across all sampling time points. The Ruminococcus genus was predominant in the infrequent group, but decreased with more frequent defecation, while the Bacteroides genus was more common in the frequent group, decreasing as defecation frequency lessened. The infrequent group demonstrated enriched biosynthesis genes for aromatic amino acids and branched-chain amino acids (BCAAs), in contrast to the frequent group, which had a higher prevalence of genes for BCAA catabolism. Metabolome analysis revealed higher levels of metabolites derived from aromatic amino acids and BCAA metabolism in the infrequent group, and lower levels of BCAA-derived metabolites in the frequent group, consistent with their predicted metagenomic functions. These findings underscore the importance of considering stool consistency/frequency in understanding the factors influencing the gut microbiome.}, } @article {pmid38730339, year = {2024}, author = {Rekadwad, BN and Shouche, YS and Jangid, K}, title = {A culture-independent approach, supervised machine learning, and the characterization of the microbial community composition of coastal areas across the Bay of Bengal and the Arabian Sea.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {162}, pmid = {38730339}, issn = {1471-2180}, support = {PDFSS-2013-14-ST-MAH-4350//University Grants Commission/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota/genetics ; *Seawater/microbiology ; India ; *Phylogeny ; *Supervised Machine Learning ; *Bays/microbiology ; Biodiversity ; DNA, Bacterial/genetics ; Salinity ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Coastal areas are subject to various anthropogenic and natural influences. In this study, we investigated and compared the characteristics of two coastal regions, Andhra Pradesh (AP) and Goa (GA), focusing on pollution, anthropogenic activities, and recreational impacts. We explored three main factors influencing the differences between these coastlines: The Bay of Bengal's shallower depth and lower salinity; upwelling phenomena due to the thermocline in the Arabian Sea; and high tides that can cause strong currents that transport pollutants and debris.

RESULTS: The microbial diversity in GA was significantly higher than that in AP, which might be attributed to differences in temperature, soil type, and vegetation cover. 16S rRNA amplicon sequencing and bioinformatics analysis indicated the presence of diverse microbial phyla, including candidate phyla radiation (CPR). Statistical analysis, random forest regression, and supervised machine learning models classification confirm the diversity of the microbiome accurately. Furthermore, we have identified 450 cultures of heterotrophic, biotechnologically important bacteria. Some strains were identified as novel taxa based on 16S rRNA gene sequencing, showing promising potential for further study.

CONCLUSION: Thus, our study provides valuable insights into the microbial diversity and pollution levels of coastal areas in AP and GA. These findings contribute to a better understanding of the impact of anthropogenic activities and climate variations on biology of coastal ecosystems and biodiversity.}, } @article {pmid38730321, year = {2024}, author = {Li, X and Brejnrod, A and Trivedi, U and Russel, J and Thorsen, J and Shah, SA and Vestergaard, GA and Rasmussen, MA and Nesme, J and Bisgaard, H and Stokholm, J and Sørensen, SJ}, title = {Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {87}, pmid = {38730321}, issn = {2049-2618}, support = {BIOCODEX INTERNATIONAL GRANT 2022//BIOCODEX INTERNATIONAL GRANT/ ; NNF17OC0025014//The Novo Nordisk Foundation/ ; NNF17OC0025014//The Novo Nordisk Foundation/ ; NNF17OC0025014//The Novo Nordisk Foundation/ ; NNF17OC0025014//The Novo Nordisk Foundation/ ; NNF17OC0025014//The Novo Nordisk Foundation/ ; NNF17OC0025014//The Novo Nordisk Foundation/ ; NNF17OC0025014//The Novo Nordisk Foundation/ ; NNF17OC0025014//The Novo Nordisk Foundation/ ; NNF17OC0025014//The Novo Nordisk Foundation/ ; }, mesh = {*Gastrointestinal Microbiome/genetics/drug effects ; Humans ; Infant ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Denmark ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial/genetics ; Female ; Feces/microbiology ; Drug Resistance, Microbial/genetics ; Male ; Cohort Studies ; Infant, Newborn ; }, abstract = {BACKGROUND: In environmental bacteria, the selective advantage of antibiotic resistance genes (ARGs) can be increased through co-localization with genes such as other ARGs, biocide resistance genes, metal resistance genes, and virulence genes (VGs). The gut microbiome of infants has been shown to contain numerous ARGs, however, co-localization related to ARGs is unknown during early life despite frequent exposures to biocides and metals from an early age.

RESULTS: We conducted a comprehensive analysis of genetic co-localization of resistance genes in a cohort of 662 Danish children and examined the association between such co-localization and environmental factors as well as gut microbial maturation. Our study showed that co-localization of ARGs with other resistance and virulence genes is common in the early gut microbiome and is associated with gut bacteria that are indicative of low maturity. Statistical models showed that co-localization occurred mainly in the phylum Proteobacteria independent of high ARG content and contig length. We evaluated the stochasticity of co-localization occurrence using enrichment scores. The most common forms of co-localization involved tetracycline and fluoroquinolone resistance genes, and, on plasmids, co-localization predominantly occurred in the form of class 1 integrons. Antibiotic use caused a short-term increase in mobile ARGs, while non-mobile ARGs showed no significant change. Finally, we found that a high abundance of VGs was associated with low gut microbial maturity and that VGs showed even higher potential for mobility than ARGs.

CONCLUSIONS: We found that the phenomenon of co-localization between ARGs and other resistance and VGs was prevalent in the gut at the beginning of life. It reveals the diversity that sustains antibiotic resistance and therefore indirectly emphasizes the need to apply caution in the use of antimicrobial agents in clinical practice, animal husbandry, and daily life to mitigate the escalation of resistance. Video Abstract.}, } @article {pmid38730026, year = {2024}, author = {Tshisekedi, KA and De Maayer, P and Botes, A}, title = {Metagenomic sequencing and reconstruction of 82 microbial genomes from barley seed communities.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {484}, pmid = {38730026}, issn = {2052-4463}, mesh = {*Hordeum/microbiology/genetics ; *Seeds/microbiology ; Metagenome ; Microbiota ; Metagenomics ; Genome, Microbial ; Genome, Bacterial ; Bacteria/genetics/classification ; }, abstract = {Barley (Hordeum vulgare) is essential to global food systems and the brewing industry. Its physiological traits and microbial communities determine malt quality. Although microbes influence barley from seed health to fermentation, there is a gap in metagenomic insights during seed storage. Crucially, elucidating the changes in microbial composition associated with barley seeds is imperative for understanding how these fluctuations can impact seed health and ultimately, influence both agricultural yield and quality of barley-derived products. Whole metagenomes were sequenced from eight barley seed samples obtained at different storage time points from harvest to nine months. After binning, 82 metagenome-assembled genomes (MAGs) belonging to 26 distinct bacterial genera were assembled, with a substantial proportion of potential novel species. Most of our MAG dataset (61%) showed over 90% genome completeness. This pioneering barley seed microbial genome retrieval provides insights into species diversity and structure, laying the groundwork for understanding barley seed microbiome interactions at the genome level.}, } @article {pmid38729711, year = {2024}, author = {Sequino, G and Cobo-Diaz, JF and Valentino, V and Tassou, C and Volpe, S and Torrieri, E and Nychas, GJ and Álvarez Ordóñez, A and Ercolini, D and De Filippis, F}, title = {Microbiome mapping in beef processing reveals safety-relevant variations in microbial diversity and genomic features.}, journal = {Food research international (Ottawa, Ont.)}, volume = {186}, number = {}, pages = {114318}, doi = {10.1016/j.foodres.2024.114318}, pmid = {38729711}, issn = {1873-7145}, mesh = {*Microbiota/genetics ; *Red Meat/microbiology ; Animals ; Cattle ; *Food Microbiology ; Food Handling/methods ; Bacteria/genetics/classification ; Metagenomics/methods ; Drug Resistance, Bacterial/genetics ; Abattoirs ; Anti-Bacterial Agents/pharmacology ; Food Contamination/analysis ; Drug Resistance, Microbial/genetics ; Food Packaging ; }, abstract = {The microbiome of surfaces along the beef processing chain represents a critical nexus where microbial ecosystems play a pivotal role in meat quality and safety of end products. This study offers a comprehensive analysis of the microbiome along beef processing using whole metagenomics with a particular focus on antimicrobial resistance and virulence-associated genes distribution. Our findings highlighted that microbial communities change dynamically in the different steps along beef processing chain, influenced by the specific conditions of each micro-environment. Brochothrix thermosphacta, Carnobacterium maltaromaticum, Pseudomonas fragi, Psychrobacter cryohalolentis and Psychrobacter immobilis were identified as the key species that characterize beef processing environments. Carcass samples and slaughterhouse surfaces exhibited a high abundance of antibiotic resistance genes (ARGs), mainly belonging to aminoglycosides, β-lactams, amphenicols, sulfonamides and tetracyclines antibiotic classes, also localized on mobile elements, suggesting the possibility to be transmitted to human pathogens. We also evaluated how the initial microbial contamination of raw beef changes in response to storage conditions, showing different species prevailing according to the type of packaging employed. We identified several genes leading to the production of spoilage-associated compounds, and highlighted the different genomic potential selected by the storage conditions. Our results suggested that surfaces in beef processing environments represent a hotspot for beef contamination and evidenced that mapping the resident microbiome in these environments may help in reducing meat microbial contamination, increasing shelf-life, and finally contributing to food waste restraint.}, } @article {pmid38729361, year = {2024}, author = {Liao, Q and Zhao, Y and Wang, Z and Yu, L and Su, Q and Li, J and Yuan, A and Wang, J and Tian, D and Lin, C and Huang, X and Li, W and Sun, Z and Wang, Q and Liu, J}, title = {Kiwifruit resistance to gray mold is enhanced by yeast-induced modulation of the endophytic microbiome.}, journal = {The Science of the total environment}, volume = {932}, number = {}, pages = {173109}, doi = {10.1016/j.scitotenv.2024.173109}, pmid = {38729361}, issn = {1879-1026}, mesh = {*Microbiota ; *Endophytes/physiology ; *Botrytis/physiology ; *Actinidia/microbiology ; *Plant Diseases/microbiology/prevention & control ; Fruit/microbiology ; Disease Resistance ; Debaryomyces/physiology ; Ascomycota/physiology ; }, abstract = {The influence of endophytic microbial community on plant growth and disease resistance is of considerable importance. Prior research indicates that pre-treatment of kiwifruit with the biocontrol yeast Debaryomyces hansenii suppresses gray mold disease induced by Botrytis cinerea. However, the specific underlying mechanisms remain unclear. In this study, Metagenomic sequencing was utilized to analyze the composition of the endophytic microbiome of kiwifruit under three distinct conditions: the healthy state, kiwifruit inoculated with B. cinerea, and kiwifruit treated with D. hansenii prior to inoculation with B. cinerea. Results revealed a dominance of Proteobacteria in all treatment groups, accompanied by a notable increase in the relative abundance of Actinobacteria and Firmicutes. Ascomycota emerged as the major dominant group within the fungal community. Treatment with D. hansenii induced significant alterations in microbial community diversity, specifically enhancing the relative abundance of yeast and exerting an inhibitory effect on B. cinerea. The introduction of D. hansenii also enriched genes associated with energy metabolism and signal transduction, positively influencing the overall structure and function of the microbial community. Our findings highlight the potential of D. hansenii to modulate microbial dynamics, inhibit pathogenic organisms, and positively influence functional attributes of the microbial community.}, } @article {pmid38728837, year = {2024}, author = {Zhou, S and Liu, L and Ye, B and Xu, Y and You, Y and Zhu, S and Ju, J and Yang, J and Li, W and Xia, M and Liu, Y}, title = {Gut microbial metabolism is linked to variations in circulating non-high density lipoprotein cholesterol.}, journal = {EBioMedicine}, volume = {104}, number = {}, pages = {105150}, pmid = {38728837}, issn = {2352-3964}, mesh = {*Gastrointestinal Microbiome ; Humans ; Female ; Male ; Middle Aged ; *Metabolomics/methods ; Metagenomics/methods ; Feces/microbiology ; Aged ; Biomarkers ; Risk Factors ; Mendelian Randomization Analysis ; Metagenome ; Cholesterol/metabolism/blood ; Metabolome ; Cardiovascular Diseases/etiology/metabolism/microbiology/blood ; }, abstract = {BACKGROUND: Non-high-density lipoprotein cholesterol (non-HDL-c) was a strong risk factor for incident cardiovascular diseases and proved to be a better target of lipid-lowering therapies. Recently, gut microbiota has been implicated in the regulation of host metabolism. However, its causal role in the variation of non-HDL-c remains unclear.

METHODS: Microbial species and metabolic capacities were assessed with fecal metagenomics, and their associations with non-HDL-c were evaluated by Spearman correlation, followed by LASSO and linear regression adjusted for established cardiovascular risk factors. Moreover, integrative analysis with plasma metabolomics were performed to determine the key molecules linking microbial metabolism and variation of non-HDL-c. Furthermore, bi-directional mendelian randomization analysis was performed to determine the potential causal associations of selected species and metabolites with non-HDL-c.

FINDINGS: Decreased Eubacterium rectale but increased Clostridium sp CAG_299 were causally linked to a higher level of non-HDL-c. A total of 16 microbial capacities were found to be independently associated with non-HDL-c after correcting for age, sex, demographics, lifestyles and comorbidities, with the strongest association observed for tricarboxylic acid (TCA) cycle. Furthermore, decreased 3-indolepropionic acid and N-methyltryptamine, resulting from suppressed capacities for microbial reductive TCA cycle, functioned as major microbial effectors to the elevation of circulating non-HDL-c.

INTERPRETATION: Overall, our findings provided insight into the causal effects of gut microbes on non-HDL-c and uncovered a novel link between non-HDL-c and microbial metabolism, highlighting the possibility of regulating non-HDL-c by microbiota-modifying interventions.

FUNDING: A full list of funding bodies can be found in the Sources of funding section.}, } @article {pmid38727605, year = {2024}, author = {Farooq, S and Talat, A and Khan, AU}, title = {Letter to the Editor: Identification of Mcr-9.1 and Mcr-10.1 Colistin Resistance Genes in Neonates from Publicly Available Gut Metagenomic Data.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {30}, number = {7}, pages = {314-316}, doi = {10.1089/mdr.2024.0006}, pmid = {38727605}, issn = {1931-8448}, mesh = {*Colistin/pharmacology ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Infant, Newborn ; *Metagenomics/methods ; Gastrointestinal Microbiome/drug effects/genetics ; Escherichia coli Proteins/genetics ; Microbial Sensitivity Tests ; Escherichia coli/genetics/drug effects ; }, } @article {pmid38727215, year = {2024}, author = {Abdallah, RZ and Elbehery, AHA and Ahmed, SF and Ouf, A and Malash, MN and Liesack, W and Siam, R}, title = {Deciphering the functional and structural complexity of the Solar Lake flat mat microbial benthic communities.}, journal = {mSystems}, volume = {9}, number = {6}, pages = {e0009524}, pmid = {38727215}, issn = {2379-5077}, support = {EA19/1215//British Ecological Society (BES)/ ; }, mesh = {*Lakes/microbiology ; *Microbiota/physiology ; *RNA, Ribosomal, 16S/genetics ; Egypt ; Bacteria/genetics/classification ; Archaea/genetics ; Metagenome ; Phylogeny ; Geologic Sediments/microbiology ; Sunlight ; }, abstract = {UNLABELLED: The Solar Lake in Taba, Egypt, encompasses one of the few modern-day microbial mats' systems metabolically analogous to Precambrian stromatolites. Solar Lake benthic communities and their adaptation to the Lake's unique limnological cycle have not been described for over two decades. In this study, we revisit the flat mat and describe the summer's shallow water versus exposed microbial community; the latter occurs in response to the seasonal partial receding of water. We employed metagenomic NovaSeq-6000 shotgun sequencing and 16S rRNA, mcrA, and dsrB quantitative PCR. A total of 292 medium-to-high-quality metagenome-assembled genomes (MAGs) were reconstructed. At the structural level, Candidatus Aenigmatarchaeota, Micrarchaeota, and Omnitrophota MAGs were exclusively detected in the shallow-water mats, whereas Halobacteria and Myxococcota MAGs were specific to the exposed microbial mat. Functionally, genes involved in reactive oxygen species (ROS) detoxification and osmotic pressure were more abundant in the exposed than in the shallow-water microbial mats, whereas genes involved in sulfate reduction/oxidation and nitrogen fixation were ubiquitously detected. Genes involved in the utilization of methylated amines for methane production were predominant when compared with genes associated with alternative methanogenesis pathways. Solar Lake methanogen MAGs belonged to Methanosarcinia, Bathyarchaeia, Candidatus Methanofastidiosales, and Archaeoglobales. The latter had the genetic capacity for anaerobic methane oxidation. Moreover, Coleofasciculus chthonoplastes, previously reported to dominate the winter shallow-water flat mat, had a substantial presence in the summer. These findings reveal the taxonomic and biochemical microbial zonation of the exposed and shallow-water Solar Lake flat mat benthic community and their capacity to ecologically adapt to the summer water recession.

IMPORTANCE: Fifty-five years ago, the extremophilic "Solar Lake" was discovered on the Red Sea shores, garnering microbiologists' interest worldwide from the 1970s to 1990s. Nevertheless, research on the lake paused at the turn of the millennium. In our study, we revisited the Solar Lake benthic community using a genome-centric approach and described the distinct microbial communities in the exposed versus shallow-water mat unveiling microbial zonation in the benthic communities surrounding the Solar Lake. Our findings highlighted the unique structural and functional adaptations employed by these microbial mat communities. Moreover, we report new methanogens and phototrophs, including an intriguing methanogen from the Archaeoglobales family. We describe how the Solar Lake's flat mat microbial community adapts to stressors like oxygen intrusion and drought due to summer water level changes, which provides insights into the genomic strategies of microbial communities to cope with altered and extreme environmental conditions.}, } @article {pmid38727176, year = {2024}, author = {He, Q and Zhang, T and Zhang, W and Feng, C and Kwok, LY and Zhang, H and Sun, Z}, title = {Administering Lactiplantibacillus fermentum F6 decreases intestinal Akkermansia muciniphila in a dextran sulfate sodium-induced rat colitis model.}, journal = {Food & function}, volume = {15}, number = {11}, pages = {5882-5894}, doi = {10.1039/d4fo00462k}, pmid = {38727176}, issn = {2042-650X}, mesh = {Animals ; Male ; Rats ; *Akkermansia ; *Colitis/chemically induced ; Cytokines/metabolism ; Dextran Sulfate/adverse effects ; Disease Models, Animal ; Dysbiosis/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Limosilactobacillus fermentum/physiology ; *Probiotics/pharmacology/administration & dosage ; Rats, Sprague-Dawley ; }, abstract = {Probiotics are increasingly used to manage gut dysbiosis-related conditions due to their robust ability to manipulate the gut microbial community. However, few studies have reported that probiotics can specifically modulate individual gut microbes. This study demonstrated that administering the probiotic, Lactiplantibacillus fermentum F6, could ameliorate dextran sulfate sodium-induced colitis in a rat model, evidenced by the decreases in the disease activity index score, histopathology grading, and serum pro-inflammatory cytokine levels, as well as the increase in the serum anti-inflammatory cytokine levels. Shotgun metagenomics revealed that the fecal metagenomic of colitis rats receiving the probiotic intervention contained substantially fewer Akkermansia muciniphila than the dextran sulfate sodium group. Thus, the probiotic mechanism might be exerted by reducing specific gut microbial species associated with disease pathogenesis. A new paradigm for designing probiotics that manage diseases through direct and precise manipulation of gut microbes has been provided through this study.}, } @article {pmid38725064, year = {2024}, author = {Yan, M and Yu, Z}, title = {Viruses contribute to microbial diversification in the rumen ecosystem and are associated with certain animal production traits.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {82}, pmid = {38725064}, issn = {2049-2618}, support = {2021-67015-33393//USDA National Institute of Food and Agriculture/ ; 2021-67015-33393//USDA National Institute of Food and Agriculture/ ; }, mesh = {*Rumen/microbiology/virology ; Animals ; *Viruses/classification/genetics ; *Metagenome ; Gastrointestinal Microbiome ; Virome ; Ruminants/microbiology/virology ; Methane/metabolism ; Animal Feed ; Bacteria/classification/genetics ; }, abstract = {BACKGROUND: The rumen microbiome enables ruminants to digest otherwise indigestible feedstuffs, thereby facilitating the production of high-quality protein, albeit with suboptimal efficiency and producing methane. Despite extensive research delineating associations between the rumen microbiome and ruminant production traits, the functional roles of the pervasive and diverse rumen virome remain to be determined.

RESULTS: Leveraging a recent comprehensive rumen virome database, this study analyzes virus-microbe linkages, at both species and strain levels, across 551 rumen metagenomes, elucidating patterns of microbial and viral diversity, co-occurrence, and virus-microbe interactions. Additionally, this study assesses the potential role of rumen viruses in microbial diversification by analyzing prophages found in rumen metagenome-assembled genomes. Employing CRISPR-Cas spacer-based matching and virus-microbe co-occurrence network analysis, this study suggests that the viruses in the rumen may regulate microbes at strain and community levels through both antagonistic and mutualistic interactions. Moreover, this study establishes that the rumen virome demonstrates responsiveness to dietary shifts and associations with key animal production traits, including feed efficiency, lactation performance, weight gain, and methane emissions.

CONCLUSIONS: These findings provide a substantive framework for further investigations to unravel the functional roles of the virome in the rumen in shaping the microbiome and influencing overall animal production performance. Video Abstract.}, } @article {pmid38723976, year = {2024}, author = {Bute, TF and Wyness, A and Wasserman, RJ and Dondofema, F and Keates, C and Dalu, T}, title = {Microbial community and extracellular polymeric substance dynamics in arid-zone temporary pan ecosystems.}, journal = {The Science of the total environment}, volume = {932}, number = {}, pages = {173059}, doi = {10.1016/j.scitotenv.2024.173059}, pmid = {38723976}, issn = {1879-1026}, mesh = {*Extracellular Polymeric Substance Matrix ; *Microbiota ; *Ecosystem ; Geologic Sediments/microbiology/chemistry ; Bacteria/classification/genetics ; Seasons ; Environmental Monitoring ; }, abstract = {Microbial extracellular polymeric substances (EPS) are an important component in sediment ecology. However, most research is highly skewed towards the northern hemisphere and in more permanent systems. This paper investigates EPS (i.e., carbohydrates and proteins) dynamics in arid Austral zone temporary pans sediments. Colorimetric methods and sequence-based metagenomics techniques were employed in a series of small temporary pan ecosystems characterised by alternating wet and dry hydroperiods. Microbial community patterns of distribution were evaluated between seasons (hot-wet and cool-dry) and across depths (and inferred inundation period) based on estimated elevation. Carbohydrates generally occurred in relatively higher proportions than proteins; the carbohydrate:protein ratio was 2.8:1 and 1.6:1 for the dry and wet season respectively, suggesting that EPS found in these systems was largely diatom produced. The wet- hydroperiods (Carbohydrate mean 102 μg g[-1]; Protein mean 65 μg g[-1]) supported more EPS production as compared to the dry- hydroperiods (Carbohydrate mean 73 μg g[-1]; Protein mean 26 μg g[-1]). A total of 15,042 Unique Amplicon Sequence Variants (ASVs) were allocated to 51 bacterial phyla and 1127 genera. The most abundant genera had commonality in high temperature tolerance, with Firmicutes, Actinobacteria and Proteobacteria in high abundances. Microbial communities were more distinct between seasons compared to within seasons which further suggested that the observed metagenome functions could be seasonally driven. This study's findings implied that there were high levels of denitrification by mostly nitric oxide reductase and nitrite reductase enzymes. EPS production was high in the hot-wet season as compared to relatively lower rates of nitrification in the cool-dry season by ammonia monooxygenases. Both EPS quantities and metagenome functions were highly associated with availability of water, with high rates being mainly associated with wet- hydroperiods compared to dry- hydroperiods. These data suggest that extended dry periods threaten microbially mediated processes in temporary wetlands, with implications to loss of biodiversity by desiccation.}, } @article {pmid38723876, year = {2024}, author = {Wan, B and Lei, Y and Yuan, Z and Wang, W}, title = {Metagenomic dissection of the intestinal microbiome in the giant river prawn Macrobrachium rosenbergii infected with Decapod iridescent virus 1.}, journal = {Fish & shellfish immunology}, volume = {149}, number = {}, pages = {109617}, doi = {10.1016/j.fsi.2024.109617}, pmid = {38723876}, issn = {1095-9947}, mesh = {Animals ; *Palaemonidae/immunology/virology/microbiology/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; Metagenome ; Iridoviridae/physiology ; }, abstract = {Microbiome in the intestines of aquatic invertebrates plays pivotal roles in maintaining intestinal homeostasis, especially when the host is exposed to pathogen invasion. Decapod iridescent virus 1 (DIV1) is a devastating virus seriously affecting the productivity and success of crustacean aquaculture. In this study, a metagenomic analysis was conducted to investigate the genomic sequences, community structure and functional characteristics of the intestinal microbiome in the giant river prawn Macrobrachiumrosenbergii infected with DIV1. The results showed that DIV1 infection could significantly reduce the diversity and richness of intestinal microbiome. Proteobacteria represented the largest taxon at the phylum level, and at the species level, the abundance of Gonapodya prolifera and Solemya velum gill symbiont increased significantly following DIV1 infection. In the infected prawns, four metabolic pathways related to purine metabolism, pyrimidine metabolism, glycerophospholipid metabolism, and pentose phosphate pathway, and five pathways related to nucleotide excision repair, homologous recombination, mismatch repair, base excision repair, and DNA replication were significantly enriched. Moreover, several immune response related pathways, such as shigellosis, bacterial invasion of epithelial cells, Salmonella infection, and Vibrio cholerae infection were repressed, indicating that secondary infection in M. rosenbergii may be inhibited via the suppression of these immune related pathways. DIV1 infection led to the induction of microbial carbohydrate enzymes such as the glycoside hydrolases (GHs), and reduced the abundance and number of antibiotic-resistant ontologies (AROs). A variety of AROs were identified from the microbiota, and mdtF and lrfA appeared as the dominant genes in the detected AROs. In addition, antibiotic efflux, antibiotic inactivation, and antibiotic target alteration were the main antibiotic resistance mechanisms. Collectively, the data would enable a deeper understanding of the molecular response of intestinal microbiota to DIV1, and offer more insights into its roles in prawn resistance to DIVI infection.}, } @article {pmid38723528, year = {2024}, author = {Luo, Y and Lin, B and Yu, P and Zhang, D and Hu, Y and Meng, X and Xiang, L}, title = {Scutellaria baicalensis water decoction ameliorates lower respiratory tract infection by modulating respiratory microbiota.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {129}, number = {}, pages = {155706}, doi = {10.1016/j.phymed.2024.155706}, pmid = {38723528}, issn = {1618-095X}, mesh = {Animals ; *Scutellaria baicalensis/chemistry ; *Lung/drug effects/microbiology ; Mice ; Klebsiella pneumoniae/drug effects ; Microbiota/drug effects ; Respiratory Tract Infections/drug therapy/microbiology ; Plant Extracts/pharmacology ; Male ; Streptococcus pneumoniae/drug effects ; Cytokines/metabolism/blood ; Disease Models, Animal ; Drugs, Chinese Herbal/pharmacology ; Flavanones/pharmacology ; Mice, Inbred C57BL ; Klebsiella Infections/drug therapy/microbiology ; Flavonoids/pharmacology ; Pneumococcal Infections/drug therapy/microbiology ; Apigenin/pharmacology ; Dysbiosis/drug therapy/microbiology ; }, abstract = {BACKGROUND: The pathogenesis of lower respiratory tract infections (LRTIs) has been demonstrated to be strongly associated with dysbiosis of respiratory microbiota. Scutellaria baicalensis, a traditional Chinese medicine, is widely used to treat respiratory infections. However, whether the therapeutic effect of S. baicalensis on LRTIs depends upon respiratory microbiota regulation is largely unclear.

PURPOSE: To investigate the potential effect and mechanism of S. baicalensis on the respiratory microbiota of LRTI mice.

METHODS: A mouse model of LRTI was established using Klebsiella pneumoniae or Streptococcus pneumoniae. Antibiotic treatment was administered, and transplantation of respiratory microbiota was performed to deplete the respiratory microbiota of mice and recover the destroyed microbial community, respectively. High-performance liquid chromatography (HPLC) was used to determine and quantify the chemical components of S. baicalensis water decoction (SBWD). Pathological changes in lung tissues and the expressions of serum inflammatory cytokines, including interleukin-17A (IL-17A), granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α), were determined by hematoxylin and eosin (H&E) staining and enzyme-linked immunosorbent assay (ELISA), respectively. Quantitative real-time PCR (qRT-PCR) analysis was performed to detect the mRNA expression of GM-CSF. Metagenomic sequencing was performed to evaluate the effect of SBWD on the composition and function of the respiratory microbiota in LRTI mice.

RESULTS: Seven main components, including scutellarin, baicalin, oroxylin A-7-O-β-d-glucuronide, wogonoside, baicalein, wogonin, and oroxylin A, were identified and their levels in SBWD were quantified. SBWD ameliorated pulmonary pathological injury and inflammatory responses in K. pneumoniae and S. pneumoniae-induced LRTI mice, as evidenced by the dose-dependent reductions in the levels of serum inflammatory cytokines, IL-6 and TNF-α. SBWD may exert a bidirectional regulatory effect on the host innate immune responses in LRTI mice and regulate the expressions of IL-17A and GM-CSF in a microbiota-dependent manner. K. pneumoniae infection but not S. pneumoniae infection led to dysbiosis in the respiratory microbiota, evident through disturbances in the taxonomic composition characterized by bacterial enrichment, including Proteobacteria, Enterobacteriaceae, and Klebsiella. K. pneumoniae and S. pneumoniae infection altered the bacterial functional profile of the respiratory microbiota, as indicated by increases in lipopolysaccharide biosynthesis, metabolic pathways, and carbohydrate metabolism. SBWD had a certain trend on the regulation of compositional disorders in the respiratory flora and modulated partial microbial functions embracing carbohydrate metabolism in K. pneumoniae-induced LRTI mice.

CONCLUSION: SBWD may exert an anti-infection effect on LRTI by targeting IL-17A and GM-CSF through respiratory microbiota regulation. The mechanism of S. baicalensis action on respiratory microbiota in LRTI treatment merits further investigation.}, } @article {pmid38722174, year = {2024}, author = {Graham, EB and Garayburu-Caruso, VA and Wu, R and Zheng, J and McClure, R and Jones, GD}, title = {Genomic fingerprints of the world's soil ecosystems.}, journal = {mSystems}, volume = {9}, number = {6}, pages = {e0111223}, pmid = {38722174}, issn = {2379-5077}, support = {//DOE | SC | Pacific Northwest National Laboratory (PNNL)/ ; }, mesh = {*Soil Microbiology ; *Microbiota/genetics ; *Metagenome ; Soil/chemistry ; Ecosystem ; Metagenomics/methods ; Phylogeny ; Fungi/genetics/classification ; Bacteria/genetics/classification ; }, abstract = {Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes-more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.IMPORTANCEWe address a critical gap in our understanding of soil microorganisms and their functions, which have a profound impact on our environment. We analyzed 1,512 global soils with advanced analytics to create detailed genetic profiles (fingerprints) of soil microbiomes. Our work reveals novel patterns in how microorganisms are distributed across different soil environments. For instance, we discovered shifts in microbial potential to acquire nutrients in relation to soil acidity, as well as changes in stress responses and potential greenhouse gas emissions linked to soil structure. We also identified soils with putative high activity that had unique genomic characteristics surrounding resource acquisition, plant-microbe interactions, and fungal activity. Finally, we observed that closely related microorganisms tend to respond in similar ways to changes in their surroundings. Our work is a significant step toward comprehending the intricate world of soil microorganisms and its role in the global climate.}, } @article {pmid38720628, year = {2024}, author = {Leibovitzh, H and Sarbagili Shabat, C and Hirsch, A and Zittan, E and Mentella, MC and Petito, V and Cohen, NA and Ron, Y and Fliss Isakov, N and Pfeffer, J and Yaakov, M and Fanali, C and Turchini, L and Masucci, L and Quaranta, G and Kolonimos, N and Godneva, A and Weinberger, A and Scaldaferri, F and Maharshak, N}, title = {Faecal Transplantation for Ulcerative Colitis From Diet Conditioned Donors Followed by Dietary Intervention Results in Favourable Gut Microbial Profile Compared to Faecal Transplantation Alone.}, journal = {Journal of Crohn's & colitis}, volume = {18}, number = {10}, pages = {1606-1614}, doi = {10.1093/ecco-jcc/jjae062}, pmid = {38720628}, issn = {1876-4479}, support = {//Pinkerton Foundation/ ; //Azrieli Foundation/ ; }, mesh = {Humans ; *Colitis, Ulcerative/therapy/microbiology/diet therapy ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Adult ; Middle Aged ; *Feces/microbiology ; Colonoscopy/methods ; Diet/methods ; Enema/methods ; }, abstract = {BACKGROUND AND AIMS: Several faecal microbial transplantation [FMT] approaches for ulcerative colitis [UC] have been investigated with conflicting results. We have recently published the clinical outcomes from the CRAFT UC Trial using FMT with the UC Exclusion Diet [UCED], compared with FMT alone. Here we aimed to compare the two FMT strategies in terms of microbial profile and function.

METHODS: Subjects recruited to the CRAFT UC study with available pre- and post-intervention faecal samples were included. Donors received diet conditioning for 14 days based on the UCED principles. Group 1 received single FMT by colonoscopy [Day 1] and enemas [Days 2 and 14] without donors' dietary conditioning [N = 11]. Group 2 received FMT but with donors' dietary pre-conditioning and UCED for the patients [N = 10]. Faecal samples were assessed by DNA shotgun metagenomic sequencing.

RESULTS: Following diet conditioning, donors showed depletion in metabolic pathways involved in biosynthesis of sulphur-containing amino acids. Only Group 2 showed significant shifts towards the donors' microbial composition [ADONIS: R2 = 0.15, p = 0.008] and significantly increased Eubacterium_sp_AF228LB post-intervention [β-coefficient 2.66, 95% confidence interval 2.1-3.3, q < 0.05] which was inversely correlated with faecal calprotectin [rho = -0.52, p = 0.035]. Moreover, pathways involved in gut inflammation and barrier function including branched chain amino acids were enriched post-intervention in Group 2 and were significantly inversely correlated with faecal calprotectin.

CONCLUSION: FMT from diet conditioned donors followed by the UCED led to microbial alterations associated with favourable microbial profiles which correlated with decreased faecal calprotectin. Our findings support further exploration of the additive benefit of dietary intervention for both donors and patients undergoing FMT as a potential treatment of UC.}, } @article {pmid38720071, year = {2024}, author = {Wienhausen, G and Moraru, C and Bruns, S and Tran, DQ and Sultana, S and Wilkes, H and Dlugosch, L and Azam, F and Simon, M}, title = {Ligand cross-feeding resolves bacterial vitamin B12 auxotrophies.}, journal = {Nature}, volume = {629}, number = {8013}, pages = {886-892}, pmid = {38720071}, issn = {1476-4687}, mesh = {Atlantic Ocean ; Coculture Techniques ; *Ligands ; Microbial Interactions ; Prophages/genetics/growth & development/metabolism ; *Vitamin B 12/biosynthesis/chemistry/metabolism ; *Alteromonadaceae/growth & development/metabolism ; *Rhodobacteraceae/cytology/metabolism/virology ; Ribonucleosides/metabolism ; Cobamides/metabolism ; Ecosystem ; }, abstract = {Cobalamin (vitamin B12, herein referred to as B12) is an essential cofactor for most marine prokaryotes and eukaryotes[1,2]. Synthesized by a limited number of prokaryotes, its scarcity affects microbial interactions and community dynamics[2-4]. Here we show that two bacterial B12 auxotrophs can salvage different B12 building blocks and cooperate to synthesize B12. A Colwellia sp. synthesizes and releases the activated lower ligand α-ribazole, which is used by another B12 auxotroph, a Roseovarius sp., to produce the corrin ring and synthesize B12. Release of B12 by Roseovarius sp. happens only in co-culture with Colwellia sp. and only coincidently with the induction of a prophage encoded in Roseovarius sp. Subsequent growth of Colwellia sp. in these conditions may be due to the provision of B12 by lysed cells of Roseovarius sp. Further evidence is required to support a causative role for prophage induction in the release of B12. These complex microbial interactions of ligand cross-feeding and joint B12 biosynthesis seem to be widespread in marine pelagic ecosystems. In the western and northern tropical Atlantic Ocean, bacteria predicted to be capable of salvaging cobinamide and synthesizing only the activated lower ligand outnumber B12 producers. These findings add new players to our understanding of B12 supply to auxotrophic microorganisms in the ocean and possibly in other ecosystems.}, } @article {pmid38720057, year = {2024}, author = {Hirpara, KR and Hinsu, AT and Kothari, RK}, title = {Metagenomic evaluation of peanut rhizosphere microbiome from the farms of Saurashtra regions of Gujarat, India.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {10525}, pmid = {38720057}, issn = {2045-2322}, mesh = {*Rhizosphere ; *Arachis/microbiology ; India ; *Soil Microbiology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Farms ; Plant Roots/microbiology ; Phylogeny ; Metagenome ; Biodiversity ; }, abstract = {The narrow zone of soil around the plant roots with maximum microbial activity termed as rhizosphere. Rhizospheric bacteria promote the plant growth directly or indirectly by providing the nutrients and producing antimicrobial compounds. In this study, the rhizospheric microbiota of peanut plants was characterized from different farms using an Illumina-based partial 16S rRNA gene sequencing to evaluate microbial diversity and identify the core microbiome through culture-independent (CI) approach. Further, all rhizospheric bacteria that could grow on various nutrient media were identified, and the diversity of those microbes through culture-dependent method (CD) was then directly compared with their CI counterparts. The microbial population profiles showed a significant correlation with organic carbon and concentration of phosphate, manganese, and potassium in the rhizospheric soil. Genera like Sphingomicrobium, Actinoplanes, Aureimonas _A, Chryseobacterium, members from Sphingomonadaceae, Burkholderiaceae, Pseudomonadaceae, Enterobacteriaceae family, and Bacilli class were found in the core microbiome of peanut plants. As expected, the current study demonstrated more bacterial diversity in the CI method. However, a higher number of sequence variants were exclusively present in the CD approach compared to the number of sequence variants shared between both approaches. These CD-exclusive variants belonged to organisms that are more typically found in soil. Overall, this study portrayed the changes in the rhizospheric microbiota of peanuts in different rhizospheric soil and environmental conditions and gave an idea about core microbiome of peanut plant and comparative bacterial diversity identified through both approaches.}, } @article {pmid38719945, year = {2024}, author = {Zhang, Y and Chen, H and Lian, C and Cao, L and Guo, Y and Wang, M and Zhong, Z and Li, M and Zhang, H and Li, C}, title = {Insights into phage-bacteria interaction in cold seep Gigantidas platifrons through metagenomics and transcriptome analyses.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {10540}, pmid = {38719945}, issn = {2045-2322}, support = {42030407//National Natural Science Foundation of China/ ; 2022QNLM030004//Laoshan Laboratory/ ; ZDBS-LY-DQC032//the Key Research Program of Frontier Sciences/ ; XDA22050303//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, mesh = {Animals ; *Metagenomics/methods ; *Bacteriophages/genetics/isolation & purification ; *Gills/microbiology/virology/metabolism ; *Bivalvia/microbiology/virology/genetics ; Gene Expression Profiling ; Transcriptome ; Virome/genetics ; Bacteria/genetics/classification ; Symbiosis/genetics ; Metagenome ; }, abstract = {Viruses are crucial for regulating deep-sea microbial communities and biogeochemical cycles. However, their roles are still less characterized in deep-sea holobionts. Bathymodioline mussels are endemic species inhabiting cold seeps and harboring endosymbionts in gill epithelial cells for nutrition. This study unveiled a diverse array of viruses in the gill tissues of Gigantidas platifrons mussels and analyzed the viral metagenome and transcriptome from the gill tissues of Gigantidas platifrons mussels collected from a cold seep in the South Sea. The mussel gills contained various viruses including Baculoviridae, Rountreeviridae, Myoviridae and Siphovirdae, but the active viromes were Myoviridae, Siphoviridae, and Podoviridae belonging to the order Caudovirales. The overall viral community structure showed significant variation among environments with different methane concentrations. Transcriptome analysis indicated high expression of viral structural genes, integrase, and restriction endonuclease genes in a high methane concentration environment, suggesting frequent virus infection and replication. Furthermore, two viruses (GP-phage-contig14 and GP-phage-contig72) interacted with Gigantidas platifrons methanotrophic gill symbionts (bathymodiolin mussels host intracellular methanotrophic Gammaproteobacteria in their gills), showing high expression levels, and have huge different expression in different methane concentrations. Additionally, single-stranded DNA viruses may play a potential auxiliary role in the virus-host interaction using indirect bioinformatics methods. Moreover, the Cro and DNA methylase genes had phylogenetic similarity between the virus and Gigantidas platifrons methanotrophic gill symbionts. This study also explored a variety of viruses in the gill tissues of Gigantidas platifrons and revealed that bacteria interacted with the viruses during the symbiosis with Gigantidas platifrons. This study provides fundamental insights into the interplay of microorganisms within Gigantidas platifrons mussels in deep sea.}, } @article {pmid38718521, year = {2024}, author = {Ye, T and He, S and Li, J and Luo, J and Yang, S and Wang, P and Li, C}, title = {Metagenomic and transcriptomic analysis revealing the impact of oxytetracycline and ciprofloxacin on gut microbiota and gene expression in the Chinese giant salamander (Andrias davidianus).}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {271}, number = {}, pages = {106925}, doi = {10.1016/j.aquatox.2024.106925}, pmid = {38718521}, issn = {1879-1514}, mesh = {Animals ; *Oxytetracycline/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Ciprofloxacin/pharmacology/toxicity ; *Urodela/genetics/microbiology ; *Anti-Bacterial Agents/toxicity/pharmacology ; Transcriptome/drug effects ; Metagenome ; Metagenomics ; Gene Expression Profiling ; Water Pollutants, Chemical/toxicity ; Aeromonas hydrophila/drug effects ; Gene Expression Regulation/drug effects ; }, abstract = {Excessive antibiotic use has led to the spread of antibiotic resistance genes (ARGs), impacting gut microbiota and host health. However, the effects of antibiotics on amphibian populations remain unclear. We investigated the impact of oxytetracycline (OTC) and ciprofloxacin (CIP) on Chinese giant salamanders (Andrias davidianus), focusing on gut microbiota, ARGs, and gene expression by performing metagenome and transcriptome sequencing. A. davidianus were given OTC (20 or 40 mg/kg) or CIP (50 or 100 mg/kg) orally for 7 days. The results revealed that oral administration of OTC and CIP led to distinct changes in microbial composition and functional potential, with CIP treatment having a greater impact than OTC. Antibiotic treatment also influenced the abundance of ARGs, with an increase in fluoroquinolone and multi-drug resistance genes observed post-treatment. The construction of metagenome-assembled genomes (MAGs) accurately validated that CIP intervention enriched fish-associated potential pathogens Aeromonas hydrophila carrying an increased number of ARGs. Additionally, mobile genetic elements (MGEs), such as phages and plasmids, were implicated in the dissemination of ARGs. Transcriptomic analysis of the gut revealed significant alterations in gene expression, particularly in immune-related pathways, with differential effects observed between OTC and CIP treatments. Integration of metagenomic and transcriptomic data highlighted potential correlations between gut gene expression and microbial composition, suggesting complex interactions between the host gut and its gut microbiota in response to antibiotic exposure. These findings underscore the importance of understanding the impact of antibiotic intervention on the gut microbiome and host health in amphibians, particularly in the context of antibiotic resistance and immune function.}, } @article {pmid38718148, year = {2024}, author = {Li, W and Baliu-Rodriguez, D and Premathilaka, SH and Thenuwara, SI and Kimbrel, JA and Samo, TJ and Ramon, C and Kiledal, EA and Rivera, SR and Kharbush, J and Isailovic, D and Weber, PK and Dick, GJ and Mayali, X}, title = {Microbiome processing of organic nitrogen input supports growth and cyanotoxin production of Microcystis aeruginosa cultures.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38718148}, issn = {1751-7370}, support = {20-ERD-061//Lawrence Livermore National Laboratory's (LLNL) Laboratory Directed Research Development/ ; DE-AC52-07NA27344//US Department of Energy/ ; DURIP 14RT0605//Air Force Office of Scientific Research/ ; //Cooperative Institute for Great Lakes Research/ ; //NOAA/ ; NA17OAR4320152//University of Michigan/ ; NO_0086//NOAA/OAR 'Omics/ ; }, mesh = {*Microcystis/metabolism/growth & development ; *Microbiota ; *Microcystins/metabolism ; *Nitrogen/metabolism ; Amino Acids/metabolism ; }, abstract = {Nutrient-induced blooms of the globally abundant freshwater toxic cyanobacterium Microcystis cause worldwide public and ecosystem health concerns. The response of Microcystis growth and toxin production to new and recycled nitrogen (N) inputs and the impact of heterotrophic bacteria in the Microcystis phycosphere on these processes are not well understood. Here, using microbiome transplant experiments, cyanotoxin analysis, and nanometer-scale stable isotope probing to measure N incorporation and exchange at single cell resolution, we monitored the growth, cyanotoxin production, and microbiome community structure of several Microcystis strains grown on amino acids or proteins as the sole N source. We demonstrate that the type of organic N available shaped the microbial community associated with Microcystis, and external organic N input led to decreased bacterial colonization of Microcystis colonies. Our data also suggest that certain Microcystis strains could directly uptake amino acids, but with lower rates than heterotrophic bacteria. Toxin analysis showed that biomass-specific microcystin production was not impacted by N source (i.e. nitrate, amino acids, or protein) but rather by total N availability. Single-cell isotope incorporation revealed that some bacterial communities competed with Microcystis for organic N, but other communities promoted increased N uptake by Microcystis, likely through ammonification or organic N modification. Our laboratory culture data suggest that organic N input could support Microcystis blooms and toxin production in nature, and Microcystis-associated microbial communities likely play critical roles in this process by influencing cyanobacterial succession through either decreasing (via competition) or increasing (via biotransformation) N availability, especially under inorganic N scarcity.}, } @article {pmid38717124, year = {2024}, author = {Yadegar, A and Bar-Yoseph, H and Monaghan, TM and Pakpour, S and Severino, A and Kuijper, EJ and Smits, WK and Terveer, EM and Neupane, S and Nabavi-Rad, A and Sadeghi, J and Cammarota, G and Ianiro, G and Nap-Hill, E and Leung, D and Wong, K and Kao, D}, title = {Fecal microbiota transplantation: current challenges and future landscapes.}, journal = {Clinical microbiology reviews}, volume = {37}, number = {2}, pages = {e0006022}, pmid = {38717124}, issn = {1098-6618}, support = {PJT168954//Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; //NIHR | NIHR Nottingham Biomedical Research Centre (BRC)/ ; }, mesh = {*Fecal Microbiota Transplantation/methods ; Humans ; *Gastrointestinal Microbiome ; Clostridium Infections/therapy/microbiology ; Inflammatory Bowel Diseases/therapy/microbiology ; Animals ; }, abstract = {SUMMARYGiven the importance of gut microbial homeostasis in maintaining health, there has been considerable interest in developing innovative therapeutic strategies for restoring gut microbiota. One such approach, fecal microbiota transplantation (FMT), is the main "whole gut microbiome replacement" strategy and has been integrated into clinical practice guidelines for treating recurrent Clostridioides difficile infection (rCDI). Furthermore, the potential application of FMT in other indications such as inflammatory bowel disease (IBD), metabolic syndrome, and solid tumor malignancies is an area of intense interest and active research. However, the complex and variable nature of FMT makes it challenging to address its precise functionality and to assess clinical efficacy and safety in different disease contexts. In this review, we outline clinical applications, efficacy, durability, and safety of FMT and provide a comprehensive assessment of its procedural and administration aspects. The clinical applications of FMT in children and cancer immunotherapy are also described. We focus on data from human studies in IBD in contrast with rCDI to delineate the putative mechanisms of this treatment in IBD as a model, including colonization resistance and functional restoration through bacterial engraftment, modulating effects of virome/phageome, gut metabolome and host interactions, and immunoregulatory actions of FMT. Furthermore, we comprehensively review omics technologies, metagenomic approaches, and bioinformatics pipelines to characterize complex microbial communities and discuss their limitations. FMT regulatory challenges, ethical considerations, and pharmacomicrobiomics are also highlighted to shed light on future development of tailored microbiome-based therapeutics.}, } @article {pmid38716863, year = {2024}, author = {Hirsch, P and Molano, LG and Engel, A and Zentgraf, J and Rahmann, S and Hannig, M and Müller, R and Kern, F and Keller, A and Schmartz, GP}, title = {Mibianto: ultra-efficient online microbiome analysis through k-mer based metagenomics.}, journal = {Nucleic acids research}, volume = {52}, number = {W1}, pages = {W407-W414}, pmid = {38716863}, issn = {1362-4962}, support = {469073465//DFG/ ; 101057548-EPIVINF//European Health and Digital Executive Agency/ ; //Marie Skłodowska-Curie COFUND-Action of the European Commission/ ; }, mesh = {*Metagenomics/methods ; *Microbiota/genetics ; *Software ; Humans ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Internet ; Workflow ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; }, abstract = {Quantifying microbiome species and composition from metagenomic assays is often challenging due to its time-consuming nature and computational complexity. In Bioinformatics, k-mer-based approaches were long established to expedite the analysis of large sequencing data and are now widely used to annotate metagenomic data. We make use of k-mer counting techniques for efficient and accurate compositional analysis of microbiota from whole metagenome sequencing. Mibianto solves this problem by operating directly on read files, without manual preprocessing or complete data exchange. It handles diverse sequencing platforms, including short single-end, paired-end, and long read technologies. Our sketch-based workflow significantly reduces the data volume transferred from the user to the server (up to 99.59% size reduction) to subsequently perform taxonomic profiling with enhanced efficiency and privacy. Mibianto offers functionality beyond k-mer quantification; it supports advanced community composition estimation, including diversity, ordination, and differential abundance analysis. Our tool aids in the standardization of computational workflows, thus supporting reproducibility of scientific sequencing studies. It is adaptable to small- and large-scale experimental designs and offers a user-friendly interface, thus making it an invaluable tool for both clinical and research-oriented metagenomic studies. Mibianto is freely available without the need for a login at: https://www.ccb.uni-saarland.de/mibianto.}, } @article {pmid38715137, year = {2024}, author = {Hong, Y and Li, H and Chen, L and Su, H and Zhang, B and Luo, Y and Li, C and Zhao, Z and Shao, Y and Guo, L}, title = {Short-term exposure to antibiotics begets long-term disturbance in gut microbial metabolism and molecular ecological networks.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {80}, pmid = {38715137}, issn = {2049-2618}, support = {2022ZDZX4116//Special Project in Key Areas of Ordinary Higher University of Guangdong Province/ ; 126//Science and Technology Planning Project of Basic and Theoretical Scientific Research of Jiangmen City/ ; 2023B1515020106//the Natural Science Foundation of Guangdong Province/ ; 82273757//National Natural Science Foundation of China/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Anti-Bacterial Agents/pharmacology/adverse effects ; Mice ; *RNA, Ribosomal, 16S/genetics ; *Mice, Inbred C57BL ; *Bacteria/genetics/classification/metabolism/drug effects ; Ceftriaxone/pharmacology ; Metagenomics/methods ; Male ; Metabolomics ; Feces/microbiology ; }, abstract = {BACKGROUND: Antibiotic exposure can occur in medical settings and from environmental sources. Long-term effects of brief antibiotic exposure in early life are largely unknown.

RESULTS: Post a short-term treatment by ceftriaxone to C57BL/6 mice in early life, a 14-month observation was performed using 16S rRNA gene-sequencing technique, metabolomics analysis, and metagenomics analysis on the effects of ceftriaxone exposure. Firstly, the results showed that antibiotic pre-treatment significantly disturbed gut microbial α and β diversities (P < 0.05). Both Chao1 indices and Shannon indices manifested recovery trends over time, but they didn't entirely recover to the baseline of control throughout the experiment. Secondly, antibiotic pre-treatment reduced the complexity of gut molecular ecological networks (MENs). Various network parameters were affected and manifested recovery trends over time with different degrees, such as nodes (P < 0.001, R[2] = 0.6563), links (P < 0.01, R[2] = 0.4543), number of modules (P = 0.0672, R[2] = 0.2523), relative modularity (P = 0.6714, R[2] = 0.0155), number of keystones (P = 0.1003, R[2] = 0.2090), robustness_random (P = 0.79, R[2] = 0.0063), and vulnerability (P = 0.0528, R[2] = 0.28). The network parameters didn't entirely recover. Antibiotic exposure obviously reduced the number of key species in gut MENs. Interestingly, new keystones appeared during the recovery process of network complexity. Changes in network stability might be caused by variations in network complexity, which supports the ecological theory that complexity begets stability. Besides, the metabolism profiles of the antibiotic group and control were significantly different. Correlation analysis showed that antibiotic-induced differences in gut microbial metabolism were related to MEN changes. Antibiotic exposure also caused long-term effects on gut microbial functional networks in mice.

CONCLUSIONS: These results suggest that short-term antibiotic exposure in early life will cause long-term negative impacts on gut microbial diversity, MENs, and microbial metabolism. Therefore, great concern should be raised about children's brief exposure to antibiotics if the results observed in mice are applicable to humans. Video Abstract.}, } @article {pmid38715051, year = {2024}, author = {Morandi, SC and Herzog, EL and Munk, M and Kreuzer, M and Largiadèr, CR and Wolf, S and Zinkernagel, M and Zysset-Burri, DC}, title = {The gut microbiome and HLA-B27-associated anterior uveitis: a case-control study.}, journal = {Journal of neuroinflammation}, volume = {21}, number = {1}, pages = {120}, pmid = {38715051}, issn = {1742-2094}, support = {YTCR 24/22//Gottfried und Julia Bangerter-Rhyner-Stiftung/ ; }, mesh = {Humans ; *HLA-B27 Antigen/genetics/immunology ; Female ; Male ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; *Uveitis, Anterior/microbiology/immunology ; Adult ; Case-Control Studies ; Aged ; }, abstract = {BACKGROUND: The human gut microbiome (GM) is involved in inflammation and immune response regulation. Dysbiosis, an imbalance in this ecosystem, facilitates pathogenic invasion, disrupts immune equilibrium, and potentially triggers diseases including various human leucocyte antigen (HLA)-B27-associated autoinflammatory and autoimmune diseases such as inflammatory bowel disease (IBD) and spondyloarthropathy (SpA). This study assesses compositional and functional alterations of the GM in patients with HLA-B27-associated non-infectious anterior uveitis (AU) compared to healthy controls.

METHODS: The gut metagenomes of 20 patients with HLA-B27-associated non-infectious AU, 21 age- and sex-matched HLA-B27-negative controls, and 6 HLA-B27-positive healthy controls without a history of AU were sequenced using the Illumina NovaSeq 6000 platform for whole metagenome shotgun sequencing. To identify taxonomic and functional features with significantly different relative abundances between groups and to identify associations with clinical metadata, the multivariate association by linear models (MaAsLin) R package was applied.

RESULTS: Significantly higher levels of the Eubacterium ramulus species were found in HLA-B27-negative controls (p = 0.0085, Mann-Whitney U-test). No significant differences in microbial composition were observed at all other taxonomic levels. Functionally, the lipid IVA biosynthesis pathway was upregulated in patients (p < 0.0001, Mann-Whitney U-test). A subgroup analysis comparing patients with an active non-infectious AU to their age- and sex-matched HLA-B27-negative controls, showed an increase of the species Phocaeicola vulgatus in active AU (p = 0.0530, Mann-Whitney U-test). An additional analysis comparing AU patients to age- and sex-matched HLA-B27-positive controls, showed an increase of the species Bacteroides caccae in controls (p = 0.0022, Mann-Whitney U-test).

CONCLUSION: In our cohort, non-infectious AU development is associated with compositional and functional alterations of the GM. Further research is needed to assess the causality of these associations, offering potentially novel therapeutic strategies.}, } @article {pmid38714759, year = {2024}, author = {Lee, KS and Landry, Z and Athar, A and Alcolombri, U and Pramoj Na Ayutthaya, P and Berry, D and de Bettignies, P and Cheng, JX and Csucs, G and Cui, L and Deckert, V and Dieing, T and Dionne, J and Doskocil, O and D'Souza, G and García-Timermans, C and Gierlinger, N and Goda, K and Hatzenpichler, R and Henshaw, RJ and Huang, WE and Iermak, I and Ivleva, NP and Kneipp, J and Kubryk, P and Küsel, K and Lee, TK and Lee, SS and Ma, B and Martínez-Pérez, C and Matousek, P and Meckenstock, RU and Min, W and Mojzeš, P and Müller, O and Kumar, N and Nielsen, PH and Notingher, I and Palatinszky, M and Pereira, FC and Pezzotti, G and Pilat, Z and Plesinger, F and Popp, J and Probst, AJ and Riva, A and Saleh, AAE and Samek, O and Sapers, HM and Schubert, OT and Stubbusch, AKM and Tadesse, LF and Taylor, GT and Wagner, M and Wang, J and Yin, H and Yue, Y and Zenobi, R and Zini, J and Sarkans, U and Stocker, R}, title = {MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data.}, journal = {Nature microbiology}, volume = {9}, number = {5}, pages = {1152-1156}, pmid = {38714759}, issn = {2058-5276}, support = {GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 542395//Simons Foundation/ ; }, mesh = {*Spectrum Analysis, Raman/methods ; *Internet ; Humans ; Databases, Factual ; }, } @article {pmid38714217, year = {2024}, author = {Martínez-Fajardo, C and Navarro-Simarro, P and Morote, L and Rubio-Moraga, Á and Mondéjar-López, M and Niza, E and Argandoña, J and Ahrazem, O and Gómez-Gómez, L and López-Jiménez, AJ}, title = {Exploring the viral landscape of saffron through metatranscriptomic analysis.}, journal = {Virus research}, volume = {345}, number = {}, pages = {199389}, pmid = {38714217}, issn = {1872-7492}, mesh = {*Crocus/genetics ; *Plant Diseases/virology ; Plant Viruses/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing ; Virome/genetics ; Gene Expression Profiling ; Transcriptome ; Phylogeny ; Genome, Viral ; Potyviridae/genetics/isolation & purification ; Flexiviridae/genetics/classification/isolation & purification ; }, abstract = {Saffron (Crocus sativus L.), a historically significant crop valued for its nutraceutical properties, has been poorly explored from a phytosanitary perspective. This study conducted a thorough examination of viruses affecting saffron samples from Spanish cultivars, using high-throughput sequencing alongside a systematic survey of transcriptomic datasets from Crocus sativus at the Sequence Read Archive. Our analysis unveiled a broad diversity and abundance, identifying 17 viruses across the 52 analyzed libraries, some of which were highly prevalent. This includes known saffron-infecting viruses and previously unreported ones. In addition, we discovered 7 novel viruses from the Alphaflexiviridae, Betaflexiviridae, Potyviridae, Solemoviridae, and Geminiviridae families, with some present in libraries from various locations. These findings indicate that the saffron-associated virome is more complex than previously reported, emphasizing the potential of phytosanitary analysis to enhance saffron productivity.}, } @article {pmid38714055, year = {2024}, author = {Li, Z and Wang, J and Yue, H and Rehman, A and Yousaf, M and Du, M and Zhang, X}, title = {Applying metabolic modeling and multi-omics to elucidate the biotransformation mechanisms of marine algal toxin domoic acid (DA) in sediments.}, journal = {Journal of hazardous materials}, volume = {472}, number = {}, pages = {134541}, doi = {10.1016/j.jhazmat.2024.134541}, pmid = {38714055}, issn = {1873-3336}, mesh = {*Kainic Acid/analogs & derivatives/metabolism ; *Geologic Sediments/microbiology ; *Biotransformation ; *Marine Toxins/metabolism ; Microbiota ; Metabolome ; Biodegradation, Environmental ; Metagenome ; Water Pollutants, Chemical/metabolism ; Multiomics ; }, abstract = {Domoic acid (DA)-producing algal blooms are a global marine environmental issue. However, there has been no previous research addressing the question regarding the fate of DA in marine benthic environments. In this work, we investigated the DA fate in the water-sediment microcosm via the integrative analysis of a top-down metabolic model, metagenome, and metabolome. Results demonstrated that biodegradation is the leading mechanism for the nonconservative attenuation of DA. Specifically, DA degradation was prominently completed by the sediment aerobic community, with a degradation rate of 0.0681 ± 0.00954 d[-1]. The DA degradation pathway included hydration, dehydrogenation, hydrolysis, decarboxylation, automatic ring opening of hydration, and β oxidation reactions. Moreover, the reverse ecological analysis demonstrated that the microbial community transitioned from nutrient competition to metabolic cross-feeding during DA degradation, further enhancing the cooperation between DA degraders and other taxa. Finally, we reconstructed the metabolic process of microbial communities during DA degradation and confirmed that the metabolism of amino acid and organic acid drove the degradation of DA. Overall, our work not only elucidated the fate of DA in marine environments but also provided crucial insights for applying metabolic models and multi-omics to investigate the biotransformation of other contaminants.}, } @article {pmid38712927, year = {2024}, author = {Zhang, S and Swarte, JC and Gacesa, R and Knobbe, TJ and Kremer, D and Jansen, BH and de Borst, MH and , and Harmsen, HJM and Erasmus, ME and Verschuuren, EAM and Bakker, SJL and Gan, CT and Weersma, RK and Björk, JR}, title = {The gut microbiome in end-stage lung disease and lung transplantation.}, journal = {mSystems}, volume = {9}, number = {6}, pages = {e0131223}, pmid = {38712927}, issn = {2379-5077}, mesh = {Humans ; *Lung Transplantation/adverse effects ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; Adult ; *Dysbiosis/microbiology ; Lung Diseases/microbiology/surgery ; Immunosuppressive Agents/therapeutic use/adverse effects ; Feces/microbiology ; Aged ; }, abstract = {Gut dysbiosis has been associated with impaired outcomes in liver and kidney transplant recipients, but the gut microbiome of lung transplant recipients has not been extensively explored. We assessed the gut microbiome in 64 fecal samples from end-stage lung disease patients before transplantation and 219 samples from lung transplant recipients after transplantation using metagenomic sequencing. To identify dysbiotic microbial signatures, we analyzed 243 fecal samples from age-, sex-, and BMI-matched healthy controls. By unsupervised clustering, we identified five groups of lung transplant recipients using different combinations of immunosuppressants and antibiotics and analyzed them in relation to the gut microbiome. Finally, we investigated the gut microbiome of lung transplant recipients in different chronic lung allograft dysfunction (CLAD) stages and longitudinal gut microbiome changes after transplantation. We found 108 species (58.1%) in end-stage lung disease patients and 139 species (74.7%) in lung transplant recipients that were differentially abundant compared with healthy controls, with several species exhibiting sharp longitudinal increases from before to after transplantation. Different combinations of immunosuppressants and antibiotics were associated with specific gut microbial signatures. We found that the gut microbiome of lung transplant recipients in CLAD stage 0 was more similar to healthy controls compared to those in CLAD stage 1. Finally, the gut microbial diversity of lung transplant recipients remained lower than the average gut microbial diversity of healthy controls up to more than 20 years post-transplantation. Gut dysbiosis, already present before lung transplantation was exacerbated following lung transplantation.IMPORTANCEThis study provides extensive insights into the gut microbiome of end-stage lung disease patients and lung transplant recipients, which warrants further investigation before the gut microbiome can be used for microbiome-targeted interventions that could improve the outcome of lung transplantation.}, } @article {pmid38712467, year = {2024}, author = {Cao, Y and Du, P and Li, Z and Xu, J and Ma, C and Liang, B}, title = {Melatonin promotes the recovery of apple plants after waterlogging by shaping the structure and function of the rhizosphere microbiome.}, journal = {Plant, cell & environment}, volume = {47}, number = {7}, pages = {2614-2630}, doi = {10.1111/pce.14903}, pmid = {38712467}, issn = {1365-3040}, support = {C2021204158//Natural Science Foundation of Hebei/ ; 31901964//National Natural Science Foundation of China/ ; CXZZBS2024076//Innovation Ability Training Project for Graduate Student of Hebei Province/ ; HBCT2024150205//Earmarked Fund for Hebei Apple Innovation Team of Modern Agroindustry Technology Research System/ ; CARS-27//Earmarked fund for the China Agricultural Research System/ ; }, mesh = {*Melatonin/pharmacology/metabolism ; *Malus/drug effects/genetics/microbiology/physiology/metabolism ; *Rhizosphere ; *Microbiota/drug effects ; Soil Microbiology ; Nitrogen/metabolism ; Photosynthesis/drug effects ; Bacteria/metabolism/genetics/drug effects ; }, abstract = {The dynamics of the physiological adaptability of plants and the rhizosphere soil environment after waterlogging remain unclear. Here we investigated the mechanisms regulating plant condition and shaping of the rhizosphere microbiome in a pot experiment. In the experiment, we added melatonin to waterlogged plants, which promoted waterlogging relief. The treatment significantly enhanced photosynthesis and the antioxidant capacity of apple plants, and significantly promoted nitrogen (N) utilization efficiency by upregulating genes related to N transport and metabolism. Multiperiod soil microbiome analysis showed the dynamic effects of melatonin on the diversity of the microbial community during waterlogging recovery. Random forest and linear regression analyses were used to screen for potential beneficial bacteria (e.g., Azoarcus, Pseudomonas and Nocardioides) specifically regulated by melatonin and revealed a positive correlation with soil nutrient levels and plant growth. Furthermore, metagenomic analyses revealed the regulatory effects of melatonin on genes involved in N cycling in soil. Melatonin positively contributed to the accumulation of plant dry weight by upregulating the expression of nifD and nifK (N fixation). In summary, melatonin positively regulates physiological functions in plants and the structure and function of the microbial community; it promoted the recovery of apple plants after waterlogging stress.}, } @article {pmid38711505, year = {2024}, author = {Lai, Y and Tang, W and Luo, X and Zheng, H and Zhang, Y and Wang, M and Yu, G and Yang, M}, title = {Gut microbiome and metabolome to discover pathogenic bacteria and probiotics in ankylosing spondylitis.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1369116}, pmid = {38711505}, issn = {1664-3224}, mesh = {Humans ; *Spondylitis, Ankylosing/microbiology/metabolism/immunology ; *Gastrointestinal Microbiome ; *Probiotics ; Male ; Female ; *Metabolome ; Adult ; *Feces/microbiology ; Metagenomics/methods ; Middle Aged ; Prospective Studies ; Metabolomics ; Bacteria/metabolism/classification/isolation & purification ; Tumor Necrosis Factor Inhibitors/therapeutic use/pharmacology ; }, abstract = {OBJECTIVE: Previous research has partially revealed distinct gut microbiota in ankylosing spondylitis (AS). In this study, we performed non-targeted fecal metabolomics in AS in order to discover the microbiome-metabolome interface in AS. Based on prospective cohort studies, we further explored the impact of the tumor necrosis factor inhibitor (TNFi) on the gut microbiota and metabolites in AS.

METHODS: To further understand the gut microbiota and metabolites in AS, along with the influence of TNFi, we initiated a prospective cohort study. Fecal samples were collected from 29 patients with AS before and after TNFi therapy and 31 healthy controls. Metagenomic and metabolomic experiments were performed on the fecal samples; moreover, validation experiments were conducted based on the association between the microbiota and metabolites.

RESULTS: A total of 7,703 species were annotated using the metagenomic sequencing system and by profiling the microbial community taxonomic composition, while 50,046 metabolites were identified using metabolite profiling. Differential microbials and metabolites were discovered between patients with AS and healthy controls. Moreover, TNFi was confirmed to partially restore the gut microbiota and the metabolites. Multi-omics analysis of the microbiota and metabolites was performed to determine the associations between the differential microbes and metabolites, identifying compounds such as oxypurinol and biotin, which were correlated with the inhibition of the pathogenic bacteria Ruminococcus gnavus and the promotion of the probiotic bacteria Bacteroides uniformis. Through experimental studies, the relationship between microbes and metabolites was further confirmed, and the impact of these two types of microbes on the enterocytes and the inflammatory cytokine interleukin-18 (IL-18) was explored.

CONCLUSION: In summary, multi-omics exploration elucidated the impact of TNFi on the gut microbiota and metabolites and proposed a novel therapeutic perspective: supplementation of compounds to inhibit potential pathogenic bacteria and to promote potential probiotics, therefore controlling inflammation in AS.}, } @article {pmid38710918, year = {2024}, author = {Liu, L and Zhao, M and Lang, X and Jia, S and Kang, X and Liu, Y and Liu, J}, title = {Modified Lichong decoction intervenes in colorectal cancer by modulating the intestinal flora and the Wnt/β-catenin signaling pathway.}, journal = {Journal of cancer research and clinical oncology}, volume = {150}, number = {5}, pages = {234}, pmid = {38710918}, issn = {1432-1335}, mesh = {*Wnt Signaling Pathway/drug effects ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Colorectal Neoplasms/drug therapy/pathology/metabolism ; *Drugs, Chinese Herbal/pharmacology ; Mice ; Humans ; Male ; Apoptosis/drug effects ; Epithelial-Mesenchymal Transition/drug effects ; Cell Proliferation/drug effects ; Dextran Sulfate ; beta Catenin/metabolism ; Disease Models, Animal ; }, abstract = {BACKGROUND: The pathogenesis and treatment of colorectal cancer (CRC) continue to be areas of ongoing research, especially the benefits of traditional Chinese medicine (TCM) in slowing the progression of CRC. This study was conducted to investigate the effectiveness and mechanism of action of modified Lichong decoction (MLCD) in inhibiting CRC progression.

METHODS: We established CRC animal models using azoxymethane/dextran sodium sulfate (AOM/DSS) and administered high, medium, or low doses of MLCD or mesalazine (MS) for 9 weeks to observe MLCD alleviation of CRC. The optimal MLCD dose group was then subjected to metagenomic and RNA sequencing (RNA-seq) to explore the differentially abundant flora and genes in the control, model and MLCD groups. Finally, the mechanism of action was verified using WB, qRT‒PCR, immunohistochemistry and TUNEL staining.

RESULTS: MLCD inhibited the progression of CRC, and the optimal effect was observed at high doses. MLCD regulated the structure and function of the intestinal flora by decreasing the abundance of harmful bacteria and increasing that of beneficial bacteria. The differentially expressed genes were mainly associated with the Wnt/β-catenin pathway and the cell cycle. Molecular biology analysis indicated that MLCD suppressed the Wnt/β-catenin pathway and the epithelial-mesenchymal transition (EMT), inhibited abnormal cell proliferation and promoted intestinal epithelial cell apoptosis.

CONCLUSION: MLCD mitigated the abnormal growth of intestinal epithelial cells and promoted apoptosis, thereby inhibiting the progression of CRC. This inhibition was accomplished by modifying the intestinal microbiota and disrupting the Wnt/β-catenin pathway and the EMT. Therefore, MLCD could serve as a potential component of TCM prescriptions for CRC treatment.}, } @article {pmid38709876, year = {2024}, author = {Zhao, J and Nair, S and Zhang, Z and Wang, Z and Jiao, N and Zhang, Y}, title = {Macroalgal virosphere assists with host-microbiome equilibrium regulation and affects prokaryotes in surrounding marine environments.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38709876}, issn = {1751-7370}, support = {U1906216//Natural Science Foundation of China/ ; GZC20232809//Postdoctoral Fellowship Program of CPSF/ ; SDBX2022030//Shandong Province Postdoctoral Fund Project/ ; QN2022025001L//Ministry of Science and Technology Foreign Youth Expert Talent Project/ ; QDBSH20240102185//Qingdao Postdoctoral Fund Project/ ; //Ocean Negative Carbon Emissions (ONCE) Program/ ; }, mesh = {*Microbiota ; *Kelp/microbiology ; *Seawater/microbiology/virology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics ; Seaweed/microbiology/virology ; Geologic Sediments/microbiology/virology ; Prokaryotic Cells/virology/metabolism ; Bacteriophages/genetics/physiology/isolation & purification ; Virome ; }, abstract = {The microbiomes in macroalgal holobionts play vital roles in regulating macroalgal growth and ocean carbon cycling. However, the virospheres in macroalgal holobionts remain largely underexplored, representing a critical knowledge gap. Here we unveil that the holobiont of kelp (Saccharina japonica) harbors highly specific and unique epiphytic/endophytic viral species, with novelty (99.7% unknown) surpassing even extreme marine habitats (e.g. deep-sea and hadal zones), indicating that macroalgal virospheres, despite being closest to us, are among the least understood. These viruses potentially maintain microbiome equilibrium critical for kelp health via lytic-lysogenic infections and the expression of folate biosynthesis genes. In-situ kelp mesocosm cultivation and metagenomic mining revealed that kelp holobiont profoundly reshaped surrounding seawater and sediment virus-prokaryote pairings through changing surrounding environmental conditions and virus-host migrations. Some kelp epiphytic viruses could even infect sediment autochthonous bacteria after deposition. Moreover, the presence of ample viral auxiliary metabolic genes for kelp polysaccharide (e.g. laminarin) degradation underscores the underappreciated viral metabolic influence on macroalgal carbon cycling. This study provides key insights into understanding the previously overlooked ecological significance of viruses within macroalgal holobionts and the macroalgae-prokaryotes-virus tripartite relationship.}, } @article {pmid38709734, year = {2024}, author = {Yahara, H and Yanamoto, S and Takahashi, M and Hamada, Y and Asaka, T and Kitagawa, Y and Moridera, K and Noguchi, K and Maruoka, Y and Yahara, K}, title = {Shotgun metagenomic analysis of saliva microbiome suggests Mogibacterium as a factor associated with chronic bacterial osteomyelitis.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0302569}, pmid = {38709734}, issn = {1932-6203}, mesh = {Humans ; *Saliva/microbiology ; *Osteomyelitis/microbiology ; Female ; *Microbiota/genetics ; Male ; Middle Aged ; *Metagenomics/methods ; Chronic Disease ; Adult ; Metagenome ; Aged ; }, abstract = {Osteomyelitis of the jaw is a severe inflammatory disorder that affects bones, and it is categorized into two main types: chronic bacterial and nonbacterial osteomyelitis. Although previous studies have investigated the association between these diseases and the oral microbiome, the specific taxa associated with each disease remain unknown. In this study, we conducted shotgun metagenome sequencing (≥10 Gb from ≥66,395,670 reads per sample) of bulk DNA extracted from saliva obtained from patients with chronic bacterial osteomyelitis (N = 5) and chronic nonbacterial osteomyelitis (N = 10). We then compared the taxonomic composition of the metagenome in terms of both taxonomic and sequence abundances with that of healthy controls (N = 5). Taxonomic profiling revealed a statistically significant increase in both the taxonomic and sequence abundance of Mogibacterium in cases of chronic bacterial osteomyelitis; however, such enrichment was not observed in chronic nonbacterial osteomyelitis. We also compared a previously reported core saliva microbiome (59 genera) with our data and found that out of the 74 genera detected in this study, 47 (including Mogibacterium) were not included in the previous meta-analysis. Additionally, we analyzed a core-genome tree of Mogibacterium from chronic bacterial osteomyelitis and healthy control samples along with a reference complete genome and found that Mogibacterium from both groups was indistinguishable at the core-genome and pan-genome levels. Although limited by the small sample size, our study provides novel evidence of a significant increase in Mogibacterium abundance in the chronic bacterial osteomyelitis group. Moreover, our study presents a comparative analysis of the taxonomic and sequence abundances of all genera detected using deep salivary shotgun metagenome data. The distinct enrichment of Mogibacterium suggests its potential as a marker to distinguish between patients with chronic nonbacterial osteomyelitis and chronic bacterial osteomyelitis, particularly at the early stages when differences are unclear.}, } @article {pmid38709303, year = {2024}, author = {Veschetti, L and Paiella, S and Carelli, M and Zotti, F and Secchettin, E and Malleo, G and Signoretto, C and Zulianello, G and Nocini, R and Crovetto, A and Salvia, R and Bassi, C and Malerba, G}, title = {Dental plaque microbiota sequence counts for microbial profiling and resistance genes detection.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {319}, pmid = {38709303}, issn = {1432-0614}, mesh = {Humans ; *Metagenomics/methods ; *Dental Plaque/microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Drug Resistance, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Metagenome ; }, abstract = {Shotgun metagenomics sequencing experiments are finding a wide range of applications. Nonetheless, there are still limited guidelines regarding the number of sequences needed to acquire meaningful information for taxonomic profiling and antimicrobial resistance gene (ARG) identification. In this study, we explored this issue in the context of oral microbiota by sequencing with a very high number of sequences (~ 100 million), four human plaque samples, and one microbial community standard and by evaluating the performance of microbial identification and ARGs detection through a downsampling procedure. When investigating the impact of a decreasing number of sequences on quantitative taxonomic profiling in the microbial community standard datasets, we found some discrepancies in the identified microbial species and their abundances when compared to the expected ones. Such differences were consistent throughout downsampling, suggesting their link to taxonomic profiling methods limitations. Overall, results showed that the number of sequences has a great impact on metagenomic samples at the qualitative (i.e., presence/absence) level in terms of loss of information, especially in experiments having less than 40 million reads, whereas abundance estimation was minimally affected, with only slight variations observed in low-abundance species. The presence of ARGs was also assessed: a total of 133 ARGs were identified. Notably, 23% of them inconsistently resulted as present or absent across downsampling datasets of the same sample. Moreover, over half of ARGs were lost in datasets having less than 20 million reads. This study highlights the importance of carefully considering sequencing aspects and suggests some guidelines for designing shotgun metagenomics experiments with the final goal of maximizing oral microbiome analyses. Our findings suggest varying optimized sequence numbers according to different study aims: 40 million for microbiota profiling, 50 million for low-abundance species detection, and 20 million for ARG identification. KEY POINTS: • Forty million sequences are a cost-efficient solution for microbiota profiling • Fifty million sequences allow low-abundance species detection • Twenty million sequences are recommended for ARG identification.}, } @article {pmid38708883, year = {2025}, author = {El Mouzan, M and Al Mofarreh, M and Alsaleem, B and Al Sarkhy, A and Alanazi, A and Khormi, M and Almasoud, A and Assiri, A}, title = {Bacterial dysbiosis in newly diagnosed treatment naïve pediatric ulcerative colitis in Saudi Arabia.}, journal = {Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association}, volume = {31}, number = {1}, pages = {14-21}, doi = {10.4103/sjg.sjg_66_24}, pmid = {38708883}, issn = {1998-4049}, mesh = {Humans ; *Colitis, Ulcerative/microbiology/epidemiology/diagnosis ; Saudi Arabia/epidemiology ; Male ; *Dysbiosis/microbiology/epidemiology ; Female ; Child ; *Feces/microbiology ; Gastrointestinal Microbiome ; Adolescent ; Case-Control Studies ; Child, Preschool ; Intestinal Mucosa/microbiology/pathology ; }, abstract = {BACKGROUND: The role of microbiota in the pathogenesis of ulcerative colitis (UC) has been increasingly recognized. However, most of the reports are from Western populations. In Middle Eastern countries, including Saudi Arabia, little is known about the role of microbiota. Therefore, our aim was to describe the bacterial microbiota profile and signature in pediatric UC in Saudi Arabia.

METHODS: Twenty children with UC and 20 healthy controls enrolled in the study gave stool samples. Twenty rectal mucosal samples were taken from UC and 20 from non-UC controls. Inclusion criteria included newly diagnosed and untreated children and lack of antibiotic exposure for at least 6 months before stool collection was required for children with UC and controls. Bacterial deoxyribonucleic acid was extracted and sequenced using shotgun metagenomic analysis. Statistical analysis included Shannon alpha diversity metrics, Bray-Curtis dissimilarity, DESeq2, and biomarker discovery.

RESULTS: The demographic characteristics were similar in children with UC and controls. There was a significant reduction in alpha diversity (P = 0.037) and beta diversity in samples from children with UC (P = 0.001). Many taxa were identified with log2 abundance analysis, revealing 110 and 102 species significantly depleted and enriched in UC, respectively. Eleven bacterial species' signatures were identified.

CONCLUSIONS: In Saudi Arabian children with UC, we demonstrate a dysbiosis similar to reports from Western populations, possibly related to changes of lifestyle. Microbial signature discovery in this report is an important contribution to research, leading to the development of adjunctive non-invasive diagnostic options in unusual cases of UC.}, } @article {pmid38705650, year = {2024}, author = {Powell, AM and Khan, FZA and Ravel, J and Elovitz, MA}, title = {Untangling Associations of Microbiomes of Pregnancy and Preterm Birth.}, journal = {Clinics in perinatology}, volume = {51}, number = {2}, pages = {425-439}, pmid = {38705650}, issn = {1557-9840}, support = {K23 AI155296/AI/NIAID NIH HHS/United States ; R01 NR014784/NR/NINR NIH HHS/United States ; }, mesh = {Humans ; Female ; Pregnancy ; *Premature Birth/microbiology/epidemiology ; *Vagina/microbiology ; *Microbiota ; Infant, Newborn ; *Placenta/microbiology ; *Gastrointestinal Microbiome/physiology ; Lactobacillus ; Mouth/microbiology ; }, abstract = {This review illuminates the complex interplay between various maternal microbiomes and their influence on preterm birth (PTB), a driving and persistent contributor to neonatal morbidity and mortality. Here, we examine the dynamics of oral, gastrointestinal (gut), placental, and vaginal microbiomes, dissecting their roles in the pathogenesis of PTB. Importantly, focusing on the vaginal microbiome and PTB, the review highlights (1) a protective role of Lactobacillus species; (2) an increased risk with select anaerobes; and (3) the influence of social health determinants on the composition of vaginal microbial communities.}, } @article {pmid38703845, year = {2024}, author = {Han, B and He, Y and Chen, J and Wang, Y and Shi, L and Lin, Z and Yu, L and Wei, X and Zhang, W and Geng, Y and Shao, X and Jia, S}, title = {Different microbial functional traits drive bulk and rhizosphere soil phosphorus mobilization in an alpine meadow after nitrogen input.}, journal = {The Science of the total environment}, volume = {931}, number = {}, pages = {172904}, doi = {10.1016/j.scitotenv.2024.172904}, pmid = {38703845}, issn = {1879-1026}, mesh = {*Phosphorus/analysis ; *Soil Microbiology ; *Rhizosphere ; *Nitrogen/metabolism/analysis ; *Grassland ; *Soil/chemistry ; Microbiota ; }, abstract = {Enhanced nitrogen (N) input is expected to influence the soil phosphorus (P) cycling through biotic and abiotic factors. Among these factors, soil microorganisms play a vital role in regulating soil P availability. However, the divergent contribution of functional microorganisms to soil P availability in the rhizosphere and bulk soil under N addition remains unclear. We conducted an N addition experiment with four N input rates (0, 5, 10, and 15 g N m[-2] year[-1]) in an alpine meadow over three years. Metagenomics was employed to investigate the functional microbial traits in the rhizosphere and bulk soil. We showed that N addition had positive effects on microbial functional traits related to P-cycling in the bulk and rhizosphere soil. Specifically, high N addition significantly increased the abundance of most microbial genes in the bulk soil but only enhanced the abundance of five genes in the rhizosphere soil. The soil compartment, rather than the N addition treatment, was the dominant factor explaining the changes in the diversity and network of functional microorganisms. Furthermore, the abundance of functional microbial genes had a profound effect on soil available P, particularly in bulk soil P availability driven by the ppa and ppx genes, as well as rhizosphere soil P availability driven by the ugpE gene. Our results highlight that N addition stimulates the microbial potential for soil P mobilization in alpine meadows. Distinct microbial genes play vital roles in soil P availability in bulk and rhizosphere soil respectively. This indicates the necessity for models to further our knowledge of P mobilization processes from the bulk soil to the rhizosphere soil, allowing for more precise predictions of the effects of N enrichment on soil P cycling.}, } @article {pmid38703606, year = {2024}, author = {An, K and Jia, Y and Xie, B and Gao, J and Chen, Y and Yuan, W and Zhong, J and Su, P and Liu, X}, title = {Alterations in the gut mycobiome with coronary artery disease severity.}, journal = {EBioMedicine}, volume = {103}, number = {}, pages = {105137}, pmid = {38703606}, issn = {2352-3964}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Coronary Artery Disease/microbiology ; Male ; Female ; Middle Aged ; *Mycobiome ; Aged ; Cross-Sectional Studies ; Feces/microbiology ; Metagenomics/methods ; Fungi/genetics/classification/isolation & purification ; Severity of Illness Index ; Dysbiosis/microbiology ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; Adult ; }, abstract = {BACKGROUND: Coronary artery disease (CAD) is a prevalent cardiovascular condition, and numerous studies have linked gut bacterial imbalance to CAD. However, the relationship of gut fungi, another essential component of the intestinal microbiota, with CAD remains poorly understood.

METHODS: In this cross-sectional study, we analyzed fecal samples from 132 participants, split into 31 healthy controls and 101 CAD patients, further categorized into stable CAD (38), unstable angina (41), and acute myocardial infarction (22) groups. We conducted internal transcribed spacer 1 (ITS1) and 16S sequencing to examine gut fungal and bacterial communities.

FINDINGS: Based on ITS1 analyses, Ascomycota and Basidiomycota were the dominant fungal phyla in all the groups. The α diversity of gut mycobiome remained unaltered among the control group and CAD subgroups; however, the structure and composition of the mycobiota differed significantly with the progression of CAD. The abundances of 15 taxa gradually changed with the occurrence and progression of the disease and were significantly correlated with major CAD risk factor indicators. The mycobiome changes were closely linked to gut microbiome dysbiosis in patients with CAD. Furthermore, disease classifiers based on gut fungi effectively identified subgroups with different degrees of CAD. Finally, the FUNGuild analysis further categorized these fungi into distinct ecological guilds.

INTERPRETATION: In conclusion, the structure and composition of the gut fungal community differed from healthy controls to various subtypes of CAD, revealing key fungi taxa alterations linked to the onset and progression of CAD. Our study highlights the potential role of gut fungi in CAD and may facilitate the development of novel biomarkers and therapeutic targets for CAD.

FUNDING: This work was supported by the grants from the National Natural Science Foundation of China (No. 82170302, 92168117, 82370432), National clinical key specialty construction project- Cardiovascular Surgery, the Reform and Development Program of Beijing Institute of Respiratory Medicine (No. Ggyfz202417, Ggyfz202308), the Beijing Natural Science Foundation (No. 7222068); and the Clinical Research Incubation Program of Beijing Chaoyang Hospital Affiliated to Capital Medical University (No. CYFH202209).}, } @article {pmid38703502, year = {2024}, author = {Kandathil, AJ and Thomas, DL}, title = {The Blood Virome: A new frontier in biomedical science.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {175}, number = {}, pages = {116608}, pmid = {38703502}, issn = {1950-6007}, support = {R01 DA048063/DA/NIDA NIH HHS/United States ; R01 DA058567/DA/NIDA NIH HHS/United States ; R21 DA053145/DA/NIDA NIH HHS/United States ; }, mesh = {Humans ; *Virome/genetics ; Animals ; Viruses/genetics/isolation & purification ; Metagenomics/methods ; Virus Diseases/virology/blood ; }, abstract = {Recent advances in metagenomic testing opened a new window into the mammalian blood virome. Comprised of well-known viruses like human immunodeficiency virus, hepatitis C virus, and hepatitis B virus, the virome also includes many other eukaryotic viruses and phages whose medical significance, lifecycle, epidemiology, and impact on human health are less well known and thus regarded as commensals. This review synthesizes available information for the so-called commensal virome members that circulate in the blood of humans considering their restriction to and interaction with the human host, their natural history, and their impact on human health and physiology.}, } @article {pmid38702796, year = {2024}, author = {Morsli, M and Salipante, F and Magnan, C and Dunyach-Remy, C and Sotto, A and Lavigne, JP}, title = {Direct metagenomics investigation of non-surgical hard-to-heal wounds: a review.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {23}, number = {1}, pages = {39}, pmid = {38702796}, issn = {1476-0711}, mesh = {Humans ; *Metagenomics/methods ; *Bacteria/genetics/isolation & purification/classification ; *High-Throughput Nucleotide Sequencing ; Wound Healing ; Microbiota/genetics ; Pressure Ulcer/microbiology ; Diabetic Foot/microbiology ; Wound Infection/microbiology ; Varicose Ulcer/microbiology ; }, abstract = {BACKGROUND: Non-surgical chronic wounds, including diabetes-related foot diseases (DRFD), pressure injuries (PIs) and venous leg ulcers (VLU), are common hard-to-heal wounds. Wound evolution partly depends on microbial colonisation or infection, which is often confused by clinicians, thereby hampering proper management. Current routine microbiology investigation of these wounds is based on in vitro culture, focusing only on a limited panel of the most frequently isolated bacteria, leaving a large part of the wound microbiome undocumented.

METHODS: A literature search was conducted on original studies published through October 2022 reporting metagenomic next generation sequencing (mNGS) of chronic wound samples. Studies were eligible for inclusion if they applied 16 S rRNA metagenomics or shotgun metagenomics for microbiome analysis or diagnosis. Case reports, prospective, or retrospective studies were included. However, review articles, animal studies, in vitro model optimisation, benchmarking, treatment optimisation studies, and non-clinical studies were excluded. Articles were identified in PubMed, Google Scholar, Web of Science, Microsoft Academic, Crossref and Semantic Scholar databases.

RESULTS: Of the 3,202 articles found in the initial search, 2,336 articles were removed after deduplication and 834 articles following title and abstract screening. A further 14 were removed after full text reading, with 18 articles finally included. Data were provided for 3,628 patients, including 1,535 DRFDs, 956 VLUs, and 791 PIs, with 164 microbial genera and 116 species identified using mNGS approaches. A high microbial diversity was observed depending on the geographical location and wound evolution. Clinically infected wounds were the most diverse, possibly due to a widespread colonisation by pathogenic bacteria from body and environmental microbiota. mNGS data identified the presence of virus (EBV) and fungi (Candida and Aspergillus species), as well as Staphylococcus and Pseudomonas bacteriophages.

CONCLUSION: This study highlighted the benefit of mNGS for time-effective pathogen genome detection. Despite the majority of the included studies investigating only 16 S rDNA, ignoring a part of viral, fungal and parasite colonisation, mNGS detected a large number of bacteria through the included studies. Such technology could be implemented in routine microbiology for hard-to-heal wound microbiota investigation and post-treatment wound colonisation surveillance.}, } @article {pmid38702505, year = {2024}, author = {Macdonald, JFH and Pérez-García, P and Schneider, YK and Blümke, P and Indenbirken, D and Andersen, JH and Krohn, I and Streit, WR}, title = {Community dynamics and metagenomic analyses reveal Bacteroidota's role in widespread enzymatic Fucus vesiculosus cell wall degradation.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {10237}, pmid = {38702505}, issn = {2045-2322}, support = {AquaHealth FKZ 031B0945C//Bundesministerium für Bildung und Forschung/ ; SuReMetS FKZ 031B0944A//Bundesministerium für Bildung und Forschung/ ; PlastiSea FKZ 031B0867F//Bundesministerium für Bildung und Forschung/ ; SuReMetS FKZ 031B0944A//Bundesministerium für Bildung und Forschung/ ; }, mesh = {*Cell Wall/metabolism ; *Fucus/metabolism/genetics/microbiology ; *Metagenomics/methods ; Bacteroidetes/genetics/enzymology ; Metagenome ; Microbiota ; Phylogeny ; }, abstract = {Enzymatic degradation of algae cell wall carbohydrates by microorganisms is under increasing investigation as marine organic matter gains more value as a sustainable resource. The fate of carbon in the marine ecosystem is in part driven by these degradation processes. In this study, we observe the microbiome dynamics of the macroalga Fucus vesiculosus in 25-day-enrichment cultures resulting in partial degradation of the brown algae. Microbial community analyses revealed the phylum Pseudomonadota as the main bacterial fraction dominated by the genera Marinomonas and Vibrio. More importantly, a metagenome-based Hidden Markov model for specific glycosyl hydrolyses and sulphatases identified Bacteroidota as the phylum with the highest potential for cell wall degradation, contrary to their low abundance. For experimental verification, we cloned, expressed, and biochemically characterised two α-L-fucosidases, FUJM18 and FUJM20. While protein structure predictions suggest the highest similarity to a Bacillota origin, protein-protein blasts solely showed weak similarities to defined Bacteroidota proteins. Both enzymes were remarkably active at elevated temperatures and are the basis for a potential synthetic enzyme cocktail for large-scale algal destruction.}, } @article {pmid38701628, year = {2024}, author = {Marková, K and Kreisinger, J and Vinkler, M}, title = {Are there consistent effects of gut microbiota composition on performance, productivity and condition in poultry?.}, journal = {Poultry science}, volume = {103}, number = {6}, pages = {103752}, pmid = {38701628}, issn = {1525-3171}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Chickens/microbiology/physiology ; Probiotics/pharmacology/administration & dosage ; Animal Husbandry/methods ; }, abstract = {Microbiome of the gastrointestinal tract (GIT) has been identified as one of the crucial factors influencing the health and condition of domestic animals. The global poultry industry faces the challenge of understanding the complex relationship between gut microbiota composition and performance-related traits in birds. Considerable variation exists in the results of correlational studies using either 16S rRNA profiling or metagenomics to identify bacterial taxa associated with performance, productivity, or condition in poultry (e.g., body weight, growth rate, feeding efficiency, or egg yield). In this review, we survey the existing reports, discuss variation in research approaches, and identify bacterial taxa consistently linked to improved or deteriorated performance across individual poultry-focused studies. Our survey revealed high methodological heterogeneity, which was in contrast with vastly uniform focus of the research mainly on the domestic chicken (Gallus gallus) as a model. We also show that the bacterial taxa most frequently used in manipulative experiments and commercial probiotics intended for use in poultry (e.g., species of Lactobacillus, Bacillus, Enterococcus, or Bifidobacterium) do not overlap with the bacteria consistently correlated with their improved performance (Candidatus Arthromitus, Methanobrevibacter). Our conclusions urge for increased methodological standardization of the veterinary research in this field. We highlight the need to bridge the gap between correlational results and experimental applications in animal science. To better understand causality in the observed relationships, future research should involve a broader range of host species that includes both agricultural and wild models, as well as a broader range of age groups.}, } @article {pmid38700829, year = {2024}, author = {Jang, CS and Kim, H and Kim, D and Han, B}, title = {MicroPredict: predicting species-level taxonomic abundance of whole-shotgun metagenomic data using only 16S amplicon sequencing data.}, journal = {Genes & genomics}, volume = {46}, number = {6}, pages = {701-712}, pmid = {38700829}, issn = {2092-9293}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Humans ; *Microbiota/genetics ; Machine Learning ; Whole Genome Sequencing/methods ; Metagenome/genetics ; Bacteria/genetics/classification ; }, abstract = {BACKGROUND: The importance of the human microbiome in the analysis of various diseases is emerging. The two main methods used to profile the human microbiome are 16S rRNA gene sequencing (16S sequencing) and whole-genome shotgun sequencing (WGS). Owing to the full coverage of the genome in sequencing, WGS has multiple advantages over 16S sequencing, including higher taxonomic profiling resolution at the species-level and functional profiling analysis. However, 16S sequencing remains widely used because of its relatively low cost. Although WGS is the standard method for obtaining accurate species-level data, we found that 16S sequencing data contained rich information to predict high-resolution species-level abundances with reasonable accuracy.

OBJECTIVE: In this study, we proposed MicroPredict, a method for accurately predicting WGS-comparable species-level abundance data using 16S taxonomic profile data.

METHODS: We employed a mixed model using two key strategies: (1) modeling both sample- and species-specific information for predicting WGS abundances, and (2) accounting for the possible correlations among different species.

RESULTS: We found that MicroPredict outperformed the other machine learning methods.

CONCLUSION: We expect that our approach will help researchers accurately approximate the species-level abundances of microbiome profiles in datasets for which only cost-effective 16S sequencing has been applied.}, } @article {pmid38697527, year = {2024}, author = {Zhu, W and Zhao, H and Ke, J and Zhang, J and Liu, X and Zhou, Y and Chen, R and Wang, A and Li, X}, title = {Deciphering the environmental adaptation and functional trait of core and noncore bacterial communities in impacted coral reef seawater.}, journal = {The Science of the total environment}, volume = {931}, number = {}, pages = {172897}, doi = {10.1016/j.scitotenv.2024.172897}, pmid = {38697527}, issn = {1879-1026}, mesh = {*Coral Reefs ; *Seawater/microbiology ; *Bacteria/classification/genetics ; *Microbiota ; Phosphorus/analysis ; RNA, Ribosomal, 16S ; Nitrogen/analysis ; Environmental Monitoring ; Eutrophication ; }, abstract = {Microorganisms play pivotal roles in different biogeochemical cycles within coral reef waters. Nevertheless, our comprehension of the microbially mediated processes following environmental perturbation is still limited. To gain a deeper insight into the environmental adaptation and nutrient cycling, particularly within core and noncore bacterial communities, it is crucial to understand reef ecosystem functioning. In this study, we delved into the microbial community structure and function of seawater in a coral reef under different degrees of anthropogenic disturbance. To achieve this, we harnessed the power of 16S rRNA gene high-throughput sequencing and metagenomics techniques. The results showed that a continuous temporal succession but little spatial heterogeneity in the bacterial communities of core and noncore taxa and functional profiles involved in nitrogen (N) and phosphorus (P) cycling. Eutrophication state (i.e., nutrient concentration and turbidity) and temperature played pivotal roles in shaping both the microbial community composition and functional traits of coral reef seawater. Within this context, the core subcommunity exhibited a remarkably broader habitat niche breadth, stronger phylogenetic signal and lower environmental sensitivity when compared to the noncore taxa. Null model analysis further revealed that the core subcommunity was governed primarily by stochastic processes, while deterministic processes played a more significant role in shaping the noncore subcommunity. Furthermore, our observations indicated that changes in function related to N cycling were correlated to the variations in noncore taxa, while core taxa played a more substantial role in critical processes such as P cycling. Collectively, these findings facilitated our knowledge about environmental adaptability of core and noncore bacterial taxa and shed light on their respective roles in maintaining diverse nutrient cycling within coral reef ecosystems.}, } @article {pmid38697408, year = {2024}, author = {Dong, B and Peng, Y and Wang, M and Peng, C and Li, X}, title = {Multi-omics integrated analyses indicated that non-polysaccharides of Sijunzi decoction ameliorated spleen deficiency syndrome via regulating microbiota-gut-metabolites axis and exerted synergistic compatibility.}, journal = {Journal of ethnopharmacology}, volume = {331}, number = {}, pages = {118276}, doi = {10.1016/j.jep.2024.118276}, pmid = {38697408}, issn = {1872-7573}, mesh = {Animals ; *Drugs, Chinese Herbal/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; Rats ; *Splenic Diseases/drug therapy ; Rats, Sprague-Dawley ; Metabolomics ; Molecular Docking Simulation ; Spleen/drug effects/metabolism ; Drug Synergism ; Disease Models, Animal ; Multiomics ; }, abstract = {As a classical traditional Chinese medicine formula to invigorating spleen and replenishing qi, Sijunzi decoction (SJZD) is composed of four herbs, which is applied to cure spleen deficiency syndrome (SDS) clinically. The non-polysaccharides (NPSs) of SJZD (SJZD_NPS) are important pharmacodynamic material basis. However, the amelioration mechanism of SJZD_NPS on SDS has not been fully elaborated. Additionally, the contribution of herbs compatibility to efficacy of this formula remains unclear.

AIM OF THE STUDY: The aim was to explore the underlying mechanisms of SJZD_NPS on improving SDS, and uncover the scientific connotation in SJZD compatibility.

MATERIALS AND METHODS: A strategy integrating incomplete formulae (called "Chai-fang" in Chinese) comparison, pharmacodynamics, gut microbiome, and metabolome was employed to reveal the role of each herb to SJZD compatibility against SDS. Additionally, the underlying mechanism harbored by SJZD_NPS was further explored through targeted metabolomics, network pharmacology, molecular docking, pseudo-sterile model, and metagenomics.

RESULTS: SJZD_NPS significantly alleviated diarrhea, disordered secretion of gastrointestinal hormones and neurotransmitters, damage of ileal morphology and intestinal barrier in SDS rats, which was superior to the NPSs of Chai-fang. 16S rRNA gene sequencing and metabolomics analyses revealed that SJZD_NPS effectively restored the disturbed gut microbiota community and abnormal metabolism caused by SDS, showing the most evident recovery. Moreover, SJZD_NPS recalled the levels of partial amino acids, short chain fatty acids and bile acids, which possessed strong binding affinity towards potential targets. The depletion of gut microbiota confirmed that the SDS-amelioration efficacy of SJZD_NPS is dependent on the intact gut microbiome, with the relative abundance of potential probiotics such as Lactobacillus_johnsonii and Lactobacillus_taiwanensis been enriched.

CONCLUSION: NPSs in SJZD can improve SDS-induced gastrointestinal-nervous system dysfunction through regulating microbiota-gut-metabolites axis, with four herbs exerting synergistic effects, which indicated the compatibility rationality of SJZD.}, } @article {pmid38696985, year = {2024}, author = {da Silva Duarte, V and de Paula Dias Moreira, L and Skeie, SB and Svalestad, F and Øyaas, J and Porcellato, D}, title = {Database selection for shotgun metaproteomic of low-diversity dairy microbiomes.}, journal = {International journal of food microbiology}, volume = {418}, number = {}, pages = {110706}, doi = {10.1016/j.ijfoodmicro.2024.110706}, pmid = {38696985}, issn = {1879-3460}, mesh = {*Microbiota/genetics ; *Proteomics/methods ; Bacteria/classification/genetics/isolation & purification ; Tandem Mass Spectrometry ; Metagenomics/methods ; Cheese/microbiology ; Dairy Products/microbiology ; Databases, Protein ; Chromatography, Liquid ; }, abstract = {The metaproteomics field has recently gained more and more interest as a valuable tool for studying both the taxonomy and function of microbiomes, including those used in food fermentations. One crucial step in the metaproteomics pipeline is selecting a database to obtain high-quality taxonomical and functional information from microbial communities. One of the best strategies described for building protein databases is using sample-specific or study-specific protein databases obtained from metagenomic sequencing. While this is true for high-diversity microbiomes (such as gut and soil), there is still a lack of validation for different database construction strategies in low-diversity microbiomes, such as those found in fermented dairy products where starter cultures containing few species are used. In this study, we assessed the performance of various database construction strategies applied to metaproteomics on two low-diversity microbiomes obtained from cheese production using commercial starter cultures and analyzed by LC-MS/MS. Substantial differences were detected between the strategies, and the best performance in terms of the number of peptides and proteins identified from the spectra was achieved by metagenomic-derived databases. However, extensive databases constructed from a high number of available online genomes obtained a similar taxonomical and functional annotation of the metaproteome compared to the metagenomic-derived databases. Our results indicate that, in the case of low-diversity dairy microbiomes, the use of publically available genomes to construct protein databases can be considered as an alternative to metagenome-derived databases.}, } @article {pmid38692845, year = {2024}, author = {Guadalupe, JJ and Pazmiño-Vela, M and Pozo, G and Vernaza, W and Ochoa-Herrera, V and Torres, ML and Torres, AF}, title = {Metagenomic analysis of microbial consortia native to the Amazon, Highlands, and Galapagos regions of Ecuador with potential for wastewater remediation.}, journal = {Environmental microbiology reports}, volume = {16}, number = {3}, pages = {e13272}, pmid = {38692845}, issn = {1758-2229}, support = {//Universidad San Francisco de Quito Collaboration Grant/ ; }, mesh = {Ecuador ; *Wastewater/microbiology ; *Microbial Consortia/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Metagenomics ; Microalgae/classification/metabolism ; Water Purification ; Biodegradation, Environmental ; Metagenome ; }, abstract = {Native microbial consortia have been proposed for biological wastewater treatment, but their diversity and function remain poorly understood. This study investigated three native microalgae-bacteria consortia collected from the Amazon, Highlands, and Galapagos regions of Ecuador to assess their metagenomes and wastewater remediation potential. The consortia were evaluated for 12 days under light (LC) and continuous dark conditions (CDC) to measure their capacity for nutrient and organic matter removal from synthetic wastewater (SWW). Overall, all three consortia demonstrated higher nutrient removal efficiencies under LC than CDC, with the Amazon and Galapagos consortia outperforming the Highlands consortium in nutrient removal capabilities. Despite differences in α- and β-diversity, microbial species diversity within and between consortia did not directly correlate with their nutrient removal capabilities. However, all three consortia were enriched with core taxonomic groups associated with wastewater remediation activities. Our analyses further revealed higher abundances for nutrient removing microorganisms in the Amazon and Galapagos consortia compared with the Highland consortium. Finally, this study also uncovered the contribution of novel microbial groups that enhance wastewater bioremediation processes. These groups have not previously been reported as part of the core microbial groups commonly found in wastewater communities, thereby highlighting the potential of investigating microbial consortia isolated from ecosystems of megadiverse countries like Ecuador.}, } @article {pmid38692373, year = {2024}, author = {Yin, W and Li, Y and Xu, W and Bao, Y and Zhu, J and Su, X and Han, J and Chen, C and Lin, H and Sun, F}, title = {Unveiling long-term combined effect of salinity and Lead(II) on anammox activity and microbial community dynamics in saline wastewater treatment.}, journal = {Bioresource technology}, volume = {402}, number = {}, pages = {130767}, doi = {10.1016/j.biortech.2024.130767}, pmid = {38692373}, issn = {1873-2976}, mesh = {*Salinity ; *Wastewater/chemistry ; *Lead/metabolism ; *Nitrogen/metabolism ; Water Purification/methods ; Oxidation-Reduction ; Sewage/microbiology ; Anaerobiosis/drug effects ; Bacteria/metabolism/drug effects ; Bioreactors ; Microbiota/drug effects ; Denitrification/drug effects ; }, abstract = {The study assessed the effect of salinity and lead (Pb(II)) on the anammox sludge for nitrogen removal from saline wastewater. Results showed decreased nitrogen removal and specific anammox activity (SAA) with elevated salinity and Pb(II). SAA reduced from 541.3 ± 4.3 mg N g[-1] VSS d[-1] at 0.5 mg/L Pb(II) to 436.0 ± 0.2 mg N g[-1] VSS d[-1] at 30 g/L NaCl, further to 303.6 ± 7.1 mg N g[-1] VSS d[-1] under 30 g/L NaCl + 0.5 mg/L Pb(II). Notably, the combined inhibition at salinity (15-20 g/L NaCl) and Pb(II) (0.3-0.4 mg/L) exhibited synergistic effect, while higher salinity and Pb(II) aligned with independent inhibition models. Combined inhibition decreased protein/polysaccharides ratio, indicating more severe negative effect on anammox aggregation capacity. Metagenomics confirmed decreased Candidatus Kuenenia, and enhanced denitrification under elevated salinity and Pb(II) conditions. This study offers insights into anammox operation for treating saline wastewater with heavy metals.}, } @article {pmid38691556, year = {2024}, author = {Kawser, AQMR and Hoque, MN and Rahman, MS and Sakif, TI and Coffey, TJ and Islam, T}, title = {Unveiling the gut bacteriome diversity and distribution in the national fish hilsa (Tenualosa ilisha) of Bangladesh.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0303047}, pmid = {38691556}, issn = {1932-6203}, mesh = {Animals ; Bangladesh ; *Gastrointestinal Microbiome/genetics ; *Fishes/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/isolation & purification ; Biodiversity ; Phylogeny ; }, abstract = {The field of fish microbiome research has rapidly been advancing, primarily focusing on farmed or laboratory fish species rather than natural or marine fish populations. This study sought to reveal the distinctive gut bacteriome composition and diversity within the anadromous fish species Tenualosa ilisha (hilsa), which holds the status of being the national fish of Bangladesh. We conducted an analysis on 15 gut samples obtained from 15 individual hilsa fishes collected from three primary habitats (e.g., freshwater = 5, brackish water = 5 and marine water = 5) in Bangladesh. The analysis utilized metagenomics based on 16S rRNA gene sequencing targeting the V3-V4 regions. Our comprehensive identification revealed a total of 258 operational taxonomic units (OTUs). The observed OTUs were represented by six phyla, nine classes, 19 orders, 26 families and 40 genera of bacteria. Our analysis unveiled considerable taxonomic differences among the habitats (freshwater, brackish water, and marine water) of hilsa fishes, as denoted by a higher level of shared microbiota (p = 0.007, Kruskal-Wallis test). Among the identified genera in the gut of hilsa fishes, including Vagococcus, Morganella, Enterobacter, Plesiomonas, Shigella, Clostridium, Klebsiella, Serratia, Aeromonas, Macrococcus, Staphylococcus, Proteus, and Hafnia, several are recognized as fish probiotics. Importantly, some bacterial genera such as Sinobaca, Synechococcus, Gemmata, Serinicoccus, Saccharopolyspora, and Paulinella identified in the gut of hilsa identified in this study have not been reported in any aquatic or marine fish species. Significantly, we observed that 67.50% (27/40) of bacterial genera were found to be common among hilsa fishes across all three habitats. Our findings offer compelling evidence for the presence of both exclusive and communal bacteriomes within the gut of hilsa fishes, exhibiting potential probiotic properties. These observations could be crucial for guiding future microbiome investigations in this economically significant fish species.}, } @article {pmid38690990, year = {2024}, author = {Chen, P and Chen, H and Liu, Z and Pan, X and Liu, Q and Yang, X}, title = {Fungal-bacteria interactions provide shelter for bacteria in Caesarean section scar diverticulum.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {38690990}, issn = {2050-084X}, support = {2023A1515012940//Natural Science Foundation of Guangdong Province/ ; 2023A1515110325//Guangdong Basic and Applied Basic Research Foundation/ ; GZC20233216//Postdoctoral Fellowship Program of CPSF/ ; }, mesh = {Female ; *Cesarean Section/adverse effects ; Humans ; *Diverticulum/microbiology/metabolism ; *Bacteria/metabolism/genetics ; *Cicatrix/microbiology/metabolism ; Dysbiosis/microbiology ; Fungi/metabolism/genetics/physiology ; Microbial Interactions ; Microbiota ; }, abstract = {Caesarean section scar diverticulum (CSD) is a significant cause of infertility among women who have previously had a Caesarean section, primarily due to persistent inflammatory exudation associated with this condition. Even though abnormal bacterial composition is identified as a critical factor leading to this chronic inflammation, clinical data suggest that a long-term cure is often unattainable with antibiotic treatment alone. In our study, we employed metagenomic analysis and mass spectrometry techniques to investigate the fungal composition in CSD and its interaction with bacteria. We discovered that local fungal abnormalities in CSD can disrupt the stability of the bacterial population and the entire microbial community by altering bacterial abundance via specific metabolites. For instance, Lachnellula suecica reduces the abundance of several Lactobacillus spp., such as Lactobacillus jensenii, by diminishing the production of metabolites like Goyaglycoside A and Janthitrem E. Concurrently, Clavispora lusitaniae and Ophiocordyceps australis can synergistically impact the abundance of Lactobacillus spp. by modulating metabolite abundance. Our findings underscore that abnormal fungal composition and activity are key drivers of local bacterial dysbiosis in CSD.}, } @article {pmid38690913, year = {2024}, author = {Chen, Y and Dong, X and Sun, Z and Xu, C and Zhang, X and Qin, S and Geng, W and Cao, H and Zhai, B and Li, X and Wu, N}, title = {Potential coupling of microbial methane, nitrogen, and sulphur cycling in the Okinawa Trough cold seep sediments.}, journal = {Microbiology spectrum}, volume = {12}, number = {6}, pages = {e0349023}, pmid = {38690913}, issn = {2165-0497}, support = {LSKJ202203500//Laoshan Laboratory/ ; 42106137//MOST | National Natural Science Foundation of China (NSFC)/ ; 42176057//MOST | National Natural Science Foundation of China (NSFC)/ ; HY202301//Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources/ ; DD20230402//Marine Geological Survey Program of China Geological Survey/ ; }, mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Sulfur/metabolism ; *Nitrogen/metabolism ; *Bacteria/metabolism/genetics/classification ; *Nitrogen Fixation ; *Archaea/metabolism/genetics/classification ; Microbiota/genetics ; Seawater/microbiology ; Japan ; Phylogeny ; }, abstract = {The Okinawa Trough (OT) is a back-arc basin with a wide distribution of active cold seep systems. However, our understanding of the metabolic function of microbial communities in the cold seep sediments of the OT remains limited. In this study, we investigated the vertical profiles of functional genes involved in methane, nitrogen, and sulphur cycling in the cold seep sediments of the OT. Furthermore, we explored the possible coupling mechanisms between these biogeochemical cycles. The study revealed that the majority of genes associated with the nitrogen and sulphur cycles were most abundant in the surface sediment layers. However, only the key genes responsible for sulphur disproportionation (sor), nitrogen fixation (nifDKH), and methane metabolism (mcrABG) were more prevalent within sulfate-methane transition zone (SMTZ). Significant positive correlations (P < 0.05) were observed between functional genes involved in sulphur oxidation, thiosulphate disproportionation with denitrification, and dissimilatory nitrate reduction to ammonium (DNRA), as well as between AOM/methanogenesis and nitrogen fixation, and between sulphur disproportionation and AOM. A genome of Filomicrobium (class Alphaproteobacteria) has demonstrated potential in chemoautotrophic activities, particularly in coupling DNRA and denitrification with sulphur oxidation. Additionally, the characterized sulfate reducers such as Syntrophobacterales have been found to be capable of utilizing nitrate as an electron acceptor. The predominant methanogenic/methanotrophic groups in the OT sediments were identified as H2-dependent methylotrophic methanogens (Methanomassiliicoccales and Methanofastidiosales) and ANME-1a. This study offered a thorough understanding of microbial ecosystems in the OT cold seep sediments, emphasizing their contribution to nutrient cycling.IMPORTANCEThe Okinawa Trough (OT) is a back-arc basin formed by extension within the continental lithosphere behind the Ryukyu Trench arc system. Cold seeps are widespread in the OT. While some studies have explored microbial communities in OT cold seep sediments, their metabolic potential remains largely unknown. In this study, we used metagenomic analysis to enhance comprehension of the microbial community's role in nutrient cycling and proposed hypotheses on the coupling process and mechanisms involved in biogeochemical cycles. It was revealed that multiple metabolic pathways can be performed by a single organism or microbes that interact with each other to carry out various biogeochemical cycling. This data set provided a genomic road map on microbial nutrient cycling in OT sediment microbial communities.}, } @article {pmid38689099, year = {2024}, author = {Agustinho, DP and Fu, Y and Menon, VK and Metcalf, GA and Treangen, TJ and Sedlazeck, FJ}, title = {Unveiling microbial diversity: harnessing long-read sequencing technology.}, journal = {Nature methods}, volume = {21}, number = {6}, pages = {954-966}, pmid = {38689099}, issn = {1548-7105}, support = {1U19AI144297//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; P01-AI152999//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; III-2239114//National Science Foundation (NSF)/ ; EF-2126387//National Science Foundation (NSF)/ ; }, mesh = {*Metagenomics/methods ; *Metagenome/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; Humans ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; }, abstract = {Long-read sequencing has recently transformed metagenomics, enhancing strain-level pathogen characterization, enabling accurate and complete metagenome-assembled genomes, and improving microbiome taxonomic classification and profiling. These advancements are not only due to improvements in sequencing accuracy, but also happening across rapidly changing analysis methods. In this Review, we explore long-read sequencing's profound impact on metagenomics, focusing on computational pipelines for genome assembly, taxonomic characterization and variant detection, to summarize recent advancements in the field and provide an overview of available analytical methods to fully leverage long reads. We provide insights into the advantages and disadvantages of long reads over short reads and their evolution from the early days of long-read sequencing to their recent impact on metagenomics and clinical diagnostics. We further point out remaining challenges for the field such as the integration of methylation signals in sub-strain analysis and the lack of benchmarks.}, } @article {pmid38687787, year = {2024}, author = {Kobayashi, D and Inoue, Y and Suzuki, R and Matsuda, M and Shimoda, H and Faizah, AN and Kaku, Y and Ishijima, K and Kuroda, Y and Tatemoto, K and Virhuez-Mendoza, M and Harada, M and Nishino, A and Inumaru, M and Yonemitsu, K and Kuwata, R and Takano, A and Watanabe, M and Higa, Y and Sawabe, K and Maeda, K and Isawa, H}, title = {Identification and epidemiological study of an uncultured flavivirus from ticks using viral metagenomics and pseudoinfectious viral particles.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {19}, pages = {e2319400121}, pmid = {38687787}, issn = {1091-6490}, support = {JP18fk0108067//Japan Agency for Medical Research and Development (AMED)/ ; JP19fk0108097//Japan Agency for Medical Research and Development (AMED)/ ; JP20wm0225009//Japan Agency for Medical Research and Development (AMED)/ ; JP21fk0108613//Japan Agency for Medical Research and Development (AMED)/ ; JP22fk0108123//Japan Agency for Medical Research and Development (AMED)/ ; JP22fk0108634//Japan Agency for Medical Research and Development (AMED)/ ; JP23fk0108625//Japan Agency for Medical Research and Development (AMED)/ ; JP23fk0108656//Japan Agency for Medical Research and Development (AMED)/ ; Strategic International Collaborative Research Program (SICORP)//MEXT | Japan Science and Technology Agency (JST)/ ; 20KC1001//Regulatory Science Research from Ministry of Health, Labor and Welfare/ ; 21KA1003//Regulatory Science Research from Ministry of Health, Labor and Welfare/ ; JP18H02856//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP20K15671//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {Animals ; *Metagenomics/methods ; Japan/epidemiology ; *Deer/virology ; *Flavivirus/genetics/isolation & purification/classification ; *Ticks/virology ; Phylogeny ; Virome/genetics ; Virion/genetics ; Sus scrofa/virology ; High-Throughput Nucleotide Sequencing ; Humans ; Seroepidemiologic Studies ; Genome, Viral ; }, abstract = {During their blood-feeding process, ticks are known to transmit various viruses to vertebrates, including humans. Recent viral metagenomic analyses using next-generation sequencing (NGS) have revealed that blood-feeding arthropods like ticks harbor a large diversity of viruses. However, many of these viruses have not been isolated or cultured, and their basic characteristics remain unknown. This study aimed to present the identification of a difficult-to-culture virus in ticks using NGS and to understand its epidemic dynamics using molecular biology techniques. During routine tick-borne virus surveillance in Japan, an unknown flaviviral sequence was detected via virome analysis of host-questing ticks. Similar viral sequences have been detected in the sera of sika deer and wild boars in Japan, and this virus was tentatively named the Saruyama virus (SAYAV). Because SAYAV did not propagate in any cultured cells tested, single-round infectious virus particles (SRIP) were generated based on its structural protein gene sequence utilizing a yellow fever virus-based replicon system to understand its nationwide endemic status. Seroepidemiological studies using SRIP as antigens have demonstrated the presence of neutralizing antibodies against SAYAV in sika deer and wild boar captured at several locations in Japan, suggesting that SAYAV is endemic throughout Japan. Phylogenetic analyses have revealed that SAYAV forms a sister clade with the Orthoflavivirus genus, which includes important mosquito- and tick-borne pathogenic viruses. This shows that SAYAV evolved into a lineage independent of the known orthoflaviviruses. This study demonstrates a unique approach for understanding the epidemiology of uncultured viruses by combining viral metagenomics and pseudoinfectious viral particles.}, } @article {pmid38687069, year = {2024}, author = {Ma, G and Yan, H and Tye, KD and Tang, X and Luo, H and Li, Z and Xiao, X}, title = {Effect of probiotic administration during pregnancy on the functional diversity of the gut microbiota in healthy pregnant women.}, journal = {Microbiology spectrum}, volume = {12}, number = {6}, pages = {e0041324}, pmid = {38687069}, issn = {2165-0497}, support = {81771664//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; 2022B1212010004//Guangdong Provincial Key Laboratory of Human Digital Twin/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/administration & dosage ; Pregnancy ; Adult ; *RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification/metabolism/drug effects ; Feces/microbiology ; Streptococcus thermophilus/genetics ; Bifidobacterium longum ; Young Adult ; Lactobacillus delbrueckii/genetics ; }, abstract = {UNLABELLED: Our study aims to investigate the impact of probiotic consumption during pregnancy on gut microbiota functional diversity in healthy pregnant women. Thirty-two pregnant women were randomly assigned to two groups. The probiotic group (PG) consisted of pregnant women who consumed triple viable Bifidobacterium longum, Lactobacillus delbrueckii bulgaricus, and Streptococcus thermophilus tablets from the 32nd week of pregnancy until delivery. The functional profiles of the gut microbiota were predicted through high-throughput 16S rRNA sequencing results using PICRUSt software and referencing the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. In the gut microbiota of the PG, the genera Blautia and Ruminococcus, as well as the species Subdoligranulum, showed significantly higher relative abundances compared to the control group (CG) (P < 0.05). At Level 1 of the KEGG signaling pathways, there was a significant reduction in the functional genes of the gut microbiota involved in Organismal Systems in the PG (P < 0.05). In Level 2 of the KEGG signaling pathways, there was a significant reduction in the functional genes of the gut microbiota involved in Infectious Disease in the PG (P < 0.05). In Level 3 of the KEGG signaling pathways, the PG exhibited a significant increase in the functional genes of the gut microbiota involved in ABC transporters, Oxidative phosphorylation, Folate biosynthesis, and Biotin metabolism (P < 0.05). The CG showed a significant increase in the functional genes related to Cysteine and methionine metabolism, Vitamin B6 metabolism, Tuberculosis, and Vibrio cholerae pathogenic cycle (P < 0.05). In conclusion, our findings suggest that probiotic supplementation during pregnancy has a significant impact on functional metabolism in healthy pregnant women.

IMPORTANCE: Probiotics are considered beneficial to human health. There is limited understanding of how probiotic consumption during pregnancy affects the functional diversity of the gut microbiota. The aim of our study is to investigate the impact of probiotic consumption during pregnancy on the functional diversity of the gut microbiota. Our findings suggest that probiotic supplementation during pregnancy has a significant impact on functional metabolism. This could potentially open up new avenues for preventing various pregnancy-related complications. This also provides new insights into the effects of probiotic consumption during pregnancy on the gut microbiota and offers a convenient method for exploring the potential mechanisms underlying the impact of probiotics on the gut microbiota of pregnant women.}, } @article {pmid38686914, year = {2025}, author = {Spatola Rossi, T and Gallia, M and Erijman, L and Figuerola, E}, title = {Biotic and abiotic factors acting on community assembly in parallel anaerobic digestion systems from a brewery wastewater treatment plant.}, journal = {Environmental technology}, volume = {46}, number = {1}, pages = {135-150}, doi = {10.1080/09593330.2024.2343797}, pmid = {38686914}, issn = {1479-487X}, mesh = {*Bioreactors/microbiology ; Anaerobiosis ; *Archaea/metabolism/genetics ; *Wastewater/microbiology ; *Bacteria/metabolism/genetics/classification ; Waste Disposal, Fluid/methods ; Sewage/microbiology ; Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Anaerobic digestion is a complex microbial process that mediates the transformation of organic waste into biogas. The performance and stability of anaerobic digesters relies on the structure and function of the microbial community. In this study, we asked whether the deterministic effect of wastewater composition outweighs the effect of reactor configuration on the structure and dynamics of anaerobic digester archaeal and bacterial communities. Biotic and abiotic factors acting on microbial community assembly in two parallel anaerobic digestion systems, an upflow anaerobic sludge blanket digestor (UASB) and a closed digester tank with a solid recycling system (CDSR), from a brewery WWTP were analysed utilizing 16S rDNA and mcrA amplicon sequencing and genome-centric metagenomics. This study confirmed the deterministic effect of the wastewater composition on bacterial community structure, while the archaeal community composition resulted better explained by organic loading rate (ORL) and volatile free acids (VFA). According to the functions assigned to the differentially abundant metagenome-assembled genomes (MAGs) between reactors, CDSR was enriched in genes related to methanol and methylamines methanogenesis, protein degradation, and sulphate and alcohol utilization. Conversely, the UASB reactor was enriched in genes associated with carbohydrate and lipid degradation, as well as amino acid, fatty acid, and propionate fermentation. By comparing interactions derived from the co-occurrence network with predicted metabolic interactions of the prokaryotic communities in both anaerobic digesters, we conclude that the overall community structure is mainly determined by habitat filtering.}, } @article {pmid38685762, year = {2024}, author = {Ishnaiwer, M and Le Bastard, Q and Naour, M and Zeman, M and Dailly, E and Montassier, E and Batard, E and Dion, M}, title = {Efficacy of an inulin-based treatment on intestinal colonization by multidrug-resistant E. coli: insight into the mechanism of action.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2347021}, pmid = {38685762}, issn = {1949-0984}, mesh = {Animals ; *Inulin/pharmacology/metabolism ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Escherichia coli/drug effects/genetics ; *Feces/microbiology ; *Amoxicillin/pharmacology ; *Pantoprazole/pharmacology ; *Drug Resistance, Multiple, Bacterial ; beta-Lactamases/metabolism/genetics ; Dysbiosis/microbiology/drug therapy ; Anti-Bacterial Agents/pharmacology ; Escherichia coli Infections/drug therapy/microbiology ; Female ; Prebiotics/administration & dosage ; }, abstract = {Inulin, an increasingly studied dietary fiber, alters intestinal microbiota. The aim of this study was to assess whether inulin decreases intestinal colonization by multidrug resistant E. coli and to investigate its potential mechanisms of action. Mice with amoxicillin-induced intestinal dysbiosis mice were inoculated with extended spectrum beta-lactamase producing E. coli (ESBL-E. coli). The combination of inulin and pantoprazole (IP) significantly reduced ESBL-E. coli fecal titers, whereas pantoprazole alone did not and inulin had a delayed and limited effect. Fecal microbiome was assessed using shotgun metagenomic sequencing and qPCR. The efficacy of IP was predicted by increased abundance of 74 taxa, including two species of Adlercreutzia. Preventive treatments with A. caecimuris or A. muris also reduced ESBL-E. coli fecal titers. Fecal microbiota of mice effectively treated by IP was enriched in genes involved in inulin catabolism, production of propionate and expression of beta-lactamases. They also had increased beta-lactamase activity and decreased amoxicillin concentration. These results suggest that IP act through production of propionate and degradation of amoxicillin by the microbiota. The combination of pantoprazole and inulin is a potential treatment of intestinal colonization by multidrug-resistant E. coli. The ability of prebiotics to promote propionate and/or beta-lactamase producing bacteria may be used as a screening tool to identify potential treatments of intestinal colonization by multidrug resistant Enterobacterales.}, } @article {pmid38684965, year = {2024}, author = {Shi, J and Li, Z and Jia, L and Ma, Y and Huang, Y and He, P and Ran, T and Liu, W and Zhang, W and Cheng, Q and Zhang, Z and Lei, Z}, title = {Castration alters the ileum microbiota of Holstein bulls and promotes beef flavor compounds.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {426}, pmid = {38684965}, issn = {1471-2164}, support = {GSA-XMLZ-2021-01//Gansu beef cattle quality fattening project/ ; GAU-XKTD-2022-22//Discipline Team Project of Gansu Agricultural University/ ; 2020C-08//the Application of Pingliang Red Bull Planting and Breeding Combined with High-efficiency Circular Production System Construction Technology Application/ ; }, mesh = {Animals ; Cattle ; Male ; *Red Meat/microbiology ; *Ileum/microbiology/metabolism ; *Gastrointestinal Microbiome ; Metabolomics ; }, abstract = {BACKGROUND: In the beef industry, bull calves are usually castrated to improve flavor and meat quality; however, this can reduce their growth and slaughter performance. The gut microbiota is known to exert a significant influence on growth and slaughter performance. However, there is a paucity of research investigating the impact of castration on gut microbiota composition and its subsequent effects on slaughter performance and meat flavor.

RESULT: The objective of this study was to examine the processes via which castration hinders slaughter productivity and enhances meat quality. Bull and castrated calves were maintained under the same management conditions, and at slaughter, meat quality was assessed, and ileum and epithelial tissue samples were obtained. The research employed metagenomic sequencing and non-targeted metabolomics techniques to investigate the makeup of the microbiota and identify differential metabolites. The findings of this study revealed the Carcass weight and eye muscle area /carcass weight in the bull group were significantly higher than those in the steer group. There were no significant differences in the length, width, and crypt depth of the ileum villi between the two groups. A total of 53 flavor compounds were identified in the two groups of beef, of which 16 were significantly higher in the steer group than in the bull group, and 5 were significantly higher in the bull group than in the steer group. In addition, bacteria, Eukaryota, and virus species were significantly separated between the two groups. The lipid metabolism pathways of α-linolenic acid, linoleic acid, and unsaturated fatty acids were significantly enriched in the Steers group. Compared with the steer group, the organic system pathway is significantly enriched in the bull group. The study also found that five metabolites (LPC (0:0/20:3), LPC (20:3/0:0), LPE (0:0/22:5), LPE (22:5/0:0), D-Mannosamine), and three species (s_Cloning_vector_Hsp70_LexA-HP1, s_Bacteroides_Coprophilus_CAG: 333, and s_Clostridium_nexile-CAG: 348) interfere with each other and collectively have a positive impact on the flavor compounds of beef.

CONCLUSIONS: These findings provide a basic understanding that under the same management conditions, castration does indeed reduce the slaughter performance of bulls and improve the flavor of beef. Microorganisms and metabolites contribute to these changes through interactions.}, } @article {pmid38684791, year = {2024}, author = {Forry, SP and Servetas, SL and Kralj, JG and Soh, K and Hadjithomas, M and Cano, R and Carlin, M and Amorim, MG and Auch, B and Bakker, MG and Bartelli, TF and Bustamante, JP and Cassol, I and Chalita, M and Dias-Neto, E and Duca, AD and Gohl, DM and Kazantseva, J and Haruna, MT and Menzel, P and Moda, BS and Neuberger-Castillo, L and Nunes, DN and Patel, IR and Peralta, RD and Saliou, A and Schwarzer, R and Sevilla, S and Takenaka, IKTM and Wang, JR and Knight, R and Gevers, D and Jackson, SA}, title = {Variability and bias in microbiome metagenomic sequencing: an interlaboratory study comparing experimental protocols.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {9785}, pmid = {38684791}, issn = {2045-2322}, support = {K01 DK119582/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Metagenomics/methods/standards ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Microbiota/genetics ; Bias ; Metagenome ; Gastrointestinal Microbiome/genetics ; Sequence Analysis, DNA/methods ; Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Several studies have documented the significant impact of methodological choices in microbiome analyses. The myriad of methodological options available complicate the replication of results and generally limit the comparability of findings between independent studies that use differing techniques and measurement pipelines. Here we describe the Mosaic Standards Challenge (MSC), an international interlaboratory study designed to assess the impact of methodological variables on the results. The MSC did not prescribe methods but rather asked participating labs to analyze 7 shared reference samples (5 × human stool samples and 2 × mock communities) using their standard laboratory methods. To capture the array of methodological variables, each participating lab completed a metadata reporting sheet that included 100 different questions regarding the details of their protocol. The goal of this study was to survey the methodological landscape for microbiome metagenomic sequencing (MGS) analyses and the impact of methodological decisions on metagenomic sequencing results. A total of 44 labs participated in the MSC by submitting results (16S or WGS) along with accompanying metadata; thirty 16S rRNA gene amplicon datasets and 14 WGS datasets were collected. The inclusion of two types of reference materials (human stool and mock communities) enabled analysis of both MGS measurement variability between different protocols using the biologically-relevant stool samples, and MGS bias with respect to ground truth values using the DNA mixtures. Owing to the compositional nature of MGS measurements, analyses were conducted on the ratio of Firmicutes: Bacteroidetes allowing us to directly apply common statistical methods. The resulting analysis demonstrated that protocol choices have significant effects, including both bias of the MGS measurement associated with a particular methodological choices, as well as effects on measurement robustness as observed through the spread of results between labs making similar methodological choices. In the analysis of the DNA mock communities, MGS measurement bias was observed even when there was general consensus among the participating laboratories. This study was the result of a collaborative effort that included academic, commercial, and government labs. In addition to highlighting the impact of different methodological decisions on MGS result comparability, this work also provides insights for consideration in future microbiome measurement study design.}, } @article {pmid38684664, year = {2024}, author = {Ma, W and Wang, Y and Nguyen, LH and Mehta, RS and Ha, J and Bhosle, A and Mclver, LJ and Song, M and Clish, CB and Strate, LL and Huttenhower, C and Chan, AT}, title = {Gut microbiome composition and metabolic activity in women with diverticulitis.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3612}, pmid = {38684664}, issn = {2041-1723}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; K23 DK125838/DK/NIDDK NIH HHS/United States ; R01 DK101495/DK/NIDDK NIH HHS/United States ; U01 CA176726/CA/NCI NIH HHS/United States ; K01 DK135854/DK/NIDDK NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; *Diverticulitis/metabolism/microbiology ; *Feces/microbiology ; Aged ; Prospective Studies ; Bilophila/metabolism ; Metabolomics ; Case-Control Studies ; Clostridiales/metabolism/isolation & purification ; Bile Acids and Salts/metabolism ; Adult ; Dietary Fiber/metabolism ; Metabolome ; Metagenomics/methods ; }, abstract = {The etiopathogenesis of diverticulitis, among the most common gastrointestinal diagnoses, remains largely unknown. By leveraging stool collected within a large prospective cohort, we performed shotgun metagenomic sequencing and untargeted metabolomics profiling among 121 women diagnosed with diverticulitis requiring antibiotics or hospitalizations (cases), matched to 121 women without diverticulitis (controls) according to age and race. Overall microbial community structure and metabolomic profiles differed in diverticulitis cases compared to controls, including enrichment of pro-inflammatory Ruminococcus gnavus, 1,7-dimethyluric acid, and histidine-related metabolites, and depletion of butyrate-producing bacteria and anti-inflammatory ceramides. Through integrated multi-omic analysis, we detected covarying microbial and metabolic features, such as Bilophila wadsworthia and bile acids, specific to diverticulitis. Additionally, we observed that microbial composition modulated the protective association between a prudent fiber-rich diet and diverticulitis. Our findings offer insights into the perturbations in inflammation-related microbial and metabolic signatures associated with diverticulitis, supporting the potential of microbial-based diagnostics and therapeutic targets.}, } @article {pmid38684473, year = {2024}, author = {Díaz, L and Castellá, G and Bragulat, MR and Paytuví-Gallart, A and Sanseverino, W and Cabañes, FJ}, title = {Mycobiome of the external ear canal of healthy cows.}, journal = {Medical mycology}, volume = {62}, number = {5}, pages = {}, doi = {10.1093/mmy/myae049}, pmid = {38684473}, issn = {1460-2709}, support = {//UAB/ ; }, mesh = {Animals ; Cattle ; *Ear Canal/microbiology ; *Mycobiome ; *Malassezia/isolation & purification/classification/genetics ; High-Throughput Nucleotide Sequencing ; Female ; Metagenomics ; Polymerase Chain Reaction ; }, abstract = {Malassezia yeasts belong to the normal skin microbiota of a wide range of warm-blooded animals. However, their significance in cattle is still poorly understood. In the present study, the mycobiota of the external ear canal of 20 healthy dairy Holstein cows was assessed by cytology, culture, PCR, and next-generation sequencing. The presence of Malassezia was detected in 15 cows by cytology and PCR. The metagenomic analysis revealed that Ascomycota was the predominant phylum but M. pachydermatis the main species. The Malassezia phylotype 131 was detected in low abundance. Nor M. nana nor M. equina were detected in the samples.}, } @article {pmid38683843, year = {2024}, author = {Hernández, AM and Alcaraz, LD and Hernández-Álvarez, C and Romero, MF and Jara-Servín, A and Barajas, H and Ramírez, CM and Peimbert, M}, title = {Revealing the microbiome diversity and biocontrol potential of field Aedes ssp.: Implications for disease vector management.}, journal = {PloS one}, volume = {19}, number = {4}, pages = {e0302328}, pmid = {38683843}, issn = {1932-6203}, mesh = {*Aedes/microbiology ; Animals ; *Microbiota ; *Mosquito Vectors/microbiology ; *RNA, Ribosomal, 16S/genetics ; Wolbachia/genetics/physiology/isolation & purification ; Larva/microbiology ; Metagenomics/methods ; Mexico ; Mosquito Control/methods ; }, abstract = {The mosquito Aedes spp. holds important relevance for human and animal health, as it serves as a vector for transmitting multiple diseases, including dengue and Zika virus. The microbiome's impact on its host's health and fitness is well known. However, most studies on mosquito microbiomes have been conducted in laboratory settings. We explored the mixed microbial communities within Aedes spp., utilizing the 16S rRNA gene for diversity analysis and shotgun metagenomics for functional genomics. Our samples, which included Ae. aegypti and Ae. albopictus, spanned various developmental stages-eggs, larvae, and adults-gathered from five semiurban areas in Mexico. Our findings revealed a substantial diversity of 8,346 operational taxonomic units (OTUs), representing 967 bacterial genera and 126,366 annotated proteins. The host developmental stage was identified as the primary factor associated with variations in the microbiome composition. Subsequently, we searched for genes and species involved in mosquito biocontrol. Wolbachia accounted for 9.6% of the 16S gene sequences. We observed a high diversity (203 OTUs) of Wolbachia strains commonly associated with mosquitoes, such as wAlb, with a noticeable increase in abundance during the adult stages. Notably, we detected the presence of the cifA and cifB genes, which are associated with Wolbachia's cytoplasmic incompatibility, a biocontrol mechanism. Additionally, we identified 221 OTUs related to Bacillus, including strains linked to B. thuringiensis. Furthermore, we discovered multiple genes encoding insecticidal toxins, such as Cry, Mcf, Vip, and Vpp. Overall, our study contributes to the understanding of mosquito microbiome biodiversity and metabolic capabilities, which are essential for developing effective biocontrol strategies against this disease vector.}, } @article {pmid38683195, year = {2024}, author = {Cook, R and Telatin, A and Hsieh, SY and Newberry, F and Tariq, MA and Baker, DJ and Carding, SR and Adriaenssens, EM}, title = {Nanopore and Illumina sequencing reveal different viral populations from human gut samples.}, journal = {Microbial genomics}, volume = {10}, number = {4}, pages = {}, pmid = {38683195}, issn = {2057-5858}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Genome, Viral ; *Gastrointestinal Microbiome/genetics ; *Feces/virology/microbiology ; Nanopores ; Nanopore Sequencing/methods ; Viruses/genetics/classification/isolation & purification ; Virome/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The advent of viral metagenomics, or viromics, has improved our knowledge and understanding of global viral diversity. High-throughput sequencing technologies enable explorations of the ecological roles, contributions to host metabolism, and the influence of viruses in various environments, including the human intestinal microbiome. However, bacterial metagenomic studies frequently have the advantage. The adoption of advanced technologies like long-read sequencing has the potential to be transformative in refining viromics and metagenomics. Here, we examined the effectiveness of long-read and hybrid sequencing by comparing Illumina short-read and Oxford Nanopore Technology (ONT) long-read sequencing technologies and different assembly strategies on recovering viral genomes from human faecal samples. Our findings showed that if a single sequencing technology is to be chosen for virome analysis, Illumina is preferable due to its superior ability to recover fully resolved viral genomes and minimise erroneous genomes. While ONT assemblies were effective in recovering viral diversity, the challenges related to input requirements and the necessity for amplification made it less ideal as a standalone solution. However, using a combined, hybrid approach enabled a more authentic representation of viral diversity to be obtained within samples.}, } @article {pmid38682956, year = {2024}, author = {Pol, S and Kallonen, T and Mäklin, T and Sar, P and Hopkins, J and Soeng, S and Miliya, T and Ling, CL and Bentley, SD and Corander, J and Turner, P}, title = {Exploring the pediatric nasopharyngeal bacterial microbiota with culture-based MALDI-TOF mass spectrometry and targeted metagenomic sequencing.}, journal = {mBio}, volume = {15}, number = {6}, pages = {e0078424}, pmid = {38682956}, issn = {2150-7511}, support = {742154//EC | European Research Council (ERC)/ ; 299941//Norwegian Research Council/ ; /WT_/Wellcome Trust/United Kingdom ; 220211/WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; *Nasopharynx/microbiology ; *Microbiota/genetics ; Child, Preschool ; *Bacteria/classification/genetics/isolation & purification ; Female ; *Metagenomics/methods ; Child ; Infant ; Male ; Cambodia ; Haemophilus influenzae/genetics/isolation & purification/classification ; }, abstract = {UNLABELLED: The nasopharynx is an important reservoir of disease-associated and antimicrobial-resistant bacterial species. This proof-of-concept study assessed the utility of a combined culture, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and targeted metagenomic sequencing workflow for the study of the pediatric nasopharyngeal bacterial microbiota. Nasopharyngeal swabs and clinical metadata were collected from Cambodian children during a hospital outpatient visit and then biweekly for 12 weeks. Swabs were cultured on chocolate and blood-gentamicin agar, and all colony morphotypes were identified by MALDI-TOF MS. Metagenomic sequencing was done on a scrape of all colonies from a chocolate agar culture and processed using the mSWEEP pipeline. One hundred one children were enrolled, yielding 620 swabs. MALDI-TOF MS identified 106 bacterial species/40 genera: 20 species accounted for 88.5% (2,190/2,474) of isolates. Colonization by Moraxella catarrhalis (92.1% of children on ≥1 swab), Haemophilus influenzae (87.1%), and Streptococcus pneumoniae (83.2%) was particularly common. In S. pneumoniae-colonized children, a median of two serotypes [inter-quartile range (IQR) 1-2, range 1-4] was detected. For the 21 bacterial species included in the mSWEEP database and identifiable by MALDI-TOF, detection by culture + MALDI-TOF MS and culture + mSWEEP was highly concordant with a median species-level agreement of 96.9% (IQR 86.8%-98.8%). mSWEEP revealed highly dynamic lineage-level colonization patterns for S. pneumoniae which were quite different to those for S. aureus. A combined culture, MALDI-TOF MS, targeted metagenomic sequencing approach for the exploration of the young child nasopharyngeal microbiome was technically feasible, and each component yielded complementary data.

IMPORTANCE: The human upper respiratory tract is an important source of disease-causing and antibiotic-resistant bacteria. However, understanding the interactions and stability of these bacterial populations is technically challenging. We used a combination of approaches to determine colonization patterns over a 3-month period in 101 Cambodian children. The combined approach was feasible to implement, and each component gave complementary data to enable a better understanding of the complex patterns of bacterial colonization.}, } @article {pmid38680886, year = {2024}, author = {Nimnoi, P and Pirankham, P and Srimuang, K and Ruanpanun, P}, title = {Insights into soil nematode diversity and bacterial community of Thai jasmine rice rhizosphere from different paddy fields in Thailand.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17289}, pmid = {38680886}, issn = {2167-8359}, mesh = {Animals ; Bacteria/classification/isolation & purification/genetics ; Biodiversity ; Microbiota ; *Nematoda/microbiology ; *Oryza/microbiology/parasitology ; *Rhizosphere ; Soil/parasitology/chemistry ; *Soil Microbiology ; Thailand ; }, abstract = {Globally, phytonematodes cause significant crop losses. Understanding the functions played by the plant rhizosphere soil microbiome during phytonematodes infection is crucial. This study examined the distribution of phytonematodes in the paddy fields of five provinces in Thailand, as well as determining the keystone microbial taxa in response to environmental factors that could be considered in the development of efficient biocontrol tactics in agriculture. The results demonstrated that Meloidogyne graminicola and Hirschmanniella spp. were the major and dominant phytonematodes distributed across the paddy fields of Thailand. Soil parameters (total P, Cu, Mg, and Zn) were the important factors affecting the abundance of both nematodes. Illumina next-generation sequencing demonstrated that the levels of bacterial diversity among all locations were not significantly different. The Acidobacteriota, Proteobacteria, Firmicutes, Actinobacteriota, Myxococcota, Chloroflexi, Verrucomicrobiota, Bacteroidota, Gemmatimonadota, and Desulfobacterota were the most abundant bacterial phyla observed at all sites. The number of classes of the Acidobacteriae, Clostridia, Bacilli, and Bacteroidia influenced the proportions of Hirschmanniella spp., Tylenchorhynchus spp., and free-living nematodes in the sampling dirt, whereas the number of classes of the Polyangia and Actinobacteria affected the amounts of Pratylenchus spp. in both roots and soils. Soil organic matter, N, and Mn were the main factors that influenced the structure of the bacterial community. Correlations among rhizosphere microbiota, soil nematodes, and soil properties will be informative data in considering phytonematode management in a rice production system.}, } @article {pmid38679334, year = {2024}, author = {Fang, Y and Wang, J and Sun, J and Su, Z and Chen, S and Xiao, J and Ni, J and Hu, Z and He, Y and Shen, S and Deng, F}, title = {RNA viromes of Dermacentor nuttalli ticks reveal a novel uukuvirus in Qīnghăi Province, China.}, journal = {Virologica Sinica}, volume = {39}, number = {4}, pages = {537-545}, pmid = {38679334}, issn = {1995-820X}, mesh = {Animals ; *Dermacentor/virology ; China ; *Phylogeny ; *Virome/genetics ; *Genome, Viral/genetics ; RNA, Viral/genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics ; RNA Viruses/genetics/classification/isolation & purification ; Bunyaviridae/genetics/classification/isolation & purification ; }, abstract = {Ticks are a major parasite on the Qīnghăi-Tibet Plateau, western China, and represent an economic burden to agriculture and animal husbandry. Despite research on tick-borne pathogens that threaten humans and animals, the viromes of dominant tick species in this area remain unknown. In this study, we collected Dermacentor nuttalli ticks near Qīnghăi Lake and identified 13 viruses belonging to at least six families through metagenomic sequencing. Four viruses were of high abundance in pools, including Xīnjiāng tick-associated virus 1 (XJTAV1), and three novel viruses: Qīnghăi Lake virus 1, Qīnghăi Lake virus 2 (QHLV1, and QHLV2, unclassified), and Qīnghăi Lake virus 3 (QHLV3, genus Uukuvirus of family Phenuiviridae in order Bunyavirales), which lacks the M segment. The minimum infection rates of the four viruses in the tick groups were 8.2%, 49.5%, 6.2%, and 24.7%, respectively, suggesting the prevalence of these viruses in D. nuttalli ticks. A putative M segment of QHLV3 was identified from the next-generation sequencing data and further characterized for its signal peptide cleavage site, N-glycosylation, and transmembrane region. Furthermore, we probed the L, M, and S segments of other viruses from sequencing data of other tick pools by using the putative M segment sequence of QHLV3. By revealing the viromes of D. nuttalli ticks, this study enhances our understanding of tick-borne viral communities in highland regions. The putative M segment identified in a novel uukuvirus suggests that previously identified uukuviruses without M segments should have had the same genome organization as typical bunyaviruses. These findings will facilitate virus discovery and our understanding of the phylogeny of tick-borne uukuviruses.}, } @article {pmid38679240, year = {2024}, author = {Chen, C and Gong, H and Wei, Y and Xu, T and Li, J and Ding, GC}, title = {Promoting agricultural waste-driven denitrification and nitrogen sequestration with nano-enabled strategy.}, journal = {Bioresource technology}, volume = {401}, number = {}, pages = {130746}, doi = {10.1016/j.biortech.2024.130746}, pmid = {38679240}, issn = {1873-2976}, mesh = {*Nitrogen ; *Denitrification ; *Agriculture/methods ; *Soil/chemistry ; Nitrates ; Soil Microbiology ; Soil Pollutants/metabolism ; }, abstract = {Nanotechnology and biotechnology offer promising avenues for bolstering food security through the facilitation of soil nitrogen (N) sequestration and the reduction of nitrate leaching. Nonetheless, a comprehensive and mechanistic evaluation of their effectiveness and safety remains unclear. In this study, a soil remediation strategy employing nano-Fe3O4 and straw in N-contaminated soil was developed to elucidate N retention mechanisms via diverse metagenomics techniques. The findings revealed that subsoil amended with straw, particularly in conjunction with nano-Fe3O4, significantly increased subsoil N content (53.2%) and decreased nitrate concentration (74.6%) in leachate. Furthermore, the enrichment of functional genes associated with N-cycling, sulfate, nitrate, and iron uptake, along with chemotaxis, and responses to environmental stimuli or microbial collaboration, effectively mitigates nitrate leaching while enhancing soil N sequestration. This study introduces a pioneering approach utilizing nanomaterials in soil remediation, thereby offering the potential for the cultivation of safe vegetables in high N input greenhouse agriculture.}, } @article {pmid38678973, year = {2024}, author = {Hoepers, PG and Nunes, PLF and Almeida-Souza, HO and Martins, MM and Carvalho, RDO and Dreyer, CT and Aburjaile, FF and Sommerfeld, S and Azevedo, V and Fonseca, BB}, title = {Harnessing probiotics capability to combat Salmonella Heidelberg and improve intestinal health in broilers.}, journal = {Poultry science}, volume = {103}, number = {7}, pages = {103739}, pmid = {38678973}, issn = {1525-3171}, mesh = {Animals ; *Chickens/physiology ; *Probiotics/pharmacology/administration & dosage ; *Poultry Diseases/prevention & control/microbiology ; *Salmonella Infections, Animal/prevention & control/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Saccharomyces boulardii/physiology ; Salmonella enterica/physiology ; Animal Feed/analysis ; Lactobacillales/physiology ; Feces/microbiology/chemistry ; Diet/veterinary ; Male ; }, abstract = {The poultry industry faces significant challenges in controlling Salmonella contamination while reducing antibiotic use, particularly with the emergence of Salmonella Heidelberg (SH) strains posing risks to food safety and public health. Probiotics, notably lactic acid bacteria (LAB) and Saccharomyces boulardii (SB) offer promising alternatives for mitigating Salmonella colonization in broilers. Understanding the efficacy of probiotics in combating SH and their impact on gut health and metabolism is crucial for improving poultry production practices and ensuring food safety standards. This study aimed to assess the inhibitory effects of LAB and SB against SH both in vitro and in vivo broilers, while also investigating their impact on fecal metabolites and caecal microbiome composition. In vitro analysis demonstrated strong inhibition of SH by certain probiotic strains, such as Lactiplantibacillus plantarum (LP) and Lacticaseibacillus acidophilus (LA), while others like SB and Lactobacillus delbrueckii (LD) did not exhibit significant inhibition. In vivo testing revealed that broilers receiving probiotics had significantly lower SH concentrations in cecal content compared to the positive control (PC) at all ages, indicating a protective effect of probiotics against SH colonization. Metagenomic analysis of cecal-content microbiota identified predominant bacterial families and genera, highlighting changes in microbiota composition with age and probiotic supplementation. Additionally, fecal metabolomics profiling showed alterations in metabolite concentrations, suggesting reduced oxidative stress, intestinal inflammation, and improved gut health in probiotic-supplemented birds. These findings underscore the potential of probiotics to mitigate SH colonization and improve broiler health while reducing reliance on antibiotics.}, } @article {pmid38678728, year = {2024}, author = {Tyagi, S and Katara, P}, title = {A metagenome-wide association study of gut microbiome in patients with AMD, ASD, RA, T2D & VKH diseases.}, journal = {Computational biology and chemistry}, volume = {110}, number = {}, pages = {108076}, doi = {10.1016/j.compbiolchem.2024.108076}, pmid = {38678728}, issn = {1476-928X}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Arthritis, Rheumatoid/microbiology ; *Autism Spectrum Disorder/microbiology ; *Diabetes Mellitus, Type 2/microbiology ; *Macular Degeneration/microbiology/genetics ; Metagenome ; Metagenomics ; }, abstract = {Clinical studies have already illustrated the associations between gut microbes and diseases, yet fundamental questions remain unclear that how we can universalize this knowledge. Considering the important role of human gut microbial composition in maintaining overall health, it is important to understand the microbial diversity and altered disease conditions of the human gut. Metagenomics provides a way to analyze and understand the microbes and their role in a community manner. It provides qualitative as well as quantitative measurements, in terms of relative abundance. Various studies are already going on to find out the association between microbes and diseases; still, the mined knowledge is limited. Considering the current scenario, using the targeted metagenomics approach, we analyzed the gut microbiome of 99 samples from healthy and diseased individuals. Our metagenomic analysis mainly targeted five diseased microbiomes (i.e., Age-related macular degeneration, Autism spectrum disorder, Rheumatoid arthritis, Type 2 diabetes and Vogt-Koyanagi harada), with compare to healthy microbiome, and reported disease-associated microbiome shift in different conditions.}, } @article {pmid38678707, year = {2024}, author = {Guruge, KS and Goswami, P and Kanda, K and Abeynayaka, A and Kumagai, M and Watanabe, M and Tamamura-Andoh, Y}, title = {Plastiome: Plastisphere-enriched mobile resistome in aquatic environments.}, journal = {Journal of hazardous materials}, volume = {471}, number = {}, pages = {134353}, doi = {10.1016/j.jhazmat.2024.134353}, pmid = {38678707}, issn = {1873-3336}, mesh = {*Rivers/microbiology/chemistry ; *Microplastics/toxicity ; Anti-Bacterial Agents/pharmacology ; Water Pollutants, Chemical/toxicity ; Bacteria/genetics/drug effects ; Water Microbiology ; Interspersed Repetitive Sequences ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Disinfectants/pharmacology ; Microbiota/drug effects ; Drug Resistance, Microbial/genetics ; }, abstract = {Aquatic microplastics (MPs) act as reservoirs for microbial communities, fostering the formation of a mobile resistome encompassing diverse antibiotic (ARGs) and biocide/metal resistance genes (BMRGs), and mobile genetic elements (MGEs). This collective genetic repertoire, referred to as the "plastiome," can potentially perpetuate environmental antimicrobial resistance (AMR). Our study examining two Japanese rivers near Tokyo revealed that waterborne MPs are primarily composed of polyethylene and polypropylene fibers and sheets of diverse origin. Clinically important genera like Exiguobacterium and Eubacterium were notably enriched on MPs. Metagenomic analysis uncovered a 3.46-fold higher enrichment of ARGs on MPs than those in water, with multidrug resistance genes (MDRGs) and BMRGs prevailing, particularly within MPs. Specific ARG and BMRG subtypes linked to resistance to vancomycin, beta-lactams, biocides, arsenic, and mercury showed selective enrichment on MPs. Network analysis revealed intense associations between host genera with ARGs, BMRGs, and MGEs on MPs, emphasizing their role in coselection. In contrast, river water exhibited weaker associations. This study underscores the complex interactions shaping the mobile plastiome in aquatic environments and emphasizes the global imperative for research to comprehend and effectively control AMR within the One Health framework.}, } @article {pmid38678226, year = {2024}, author = {Alexa, EA and Cobo-Díaz, JF and Renes, E and O Callaghan, TF and Kilcawley, K and Mannion, D and Skibinska, I and Ruiz, L and Margolles, A and Fernández-Gómez, P and Alvarez-Molina, A and Puente-Gómez, P and Crispie, F and López, M and Prieto, M and Cotter, PD and Alvarez-Ordóñez, A}, title = {The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {78}, pmid = {38678226}, issn = {2049-2618}, support = {818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; }, mesh = {*Cheese/microbiology/standards ; *Food Microbiology ; *Microbiota/physiology ; Gene Transfer, Horizontal/genetics ; Metagenome/genetics ; Drug Resistance, Microbial/genetics ; }, abstract = {BACKGROUND: Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe a detailed longitudinal study assessing the impact of ripening in three natural caves on the microbiome and resistome succession across three different producers of Cabrales blue-veined cheese.

RESULTS: Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome. Lactococcus and the former Lactobacillus genus, among other taxa, showed high abundance in cheeses at initial stages of ripening, either coming from the raw material, starter culture used, and/or the environment of processing plants. Along cheese ripening in caves, these taxa were displaced by other bacteria, such as Tetragenococcus, Corynebacterium, Brevibacterium, Yaniella, and Staphylococcus, predominantly originating from cave environments (mainly food contact surfaces), as demonstrated by source-tracking analysis, strain analysis at read level, and the characterization of 613 metagenome-assembled genomes. The high abundance of Tetragenococcus koreensis and Tetragenococcus halophilus detected in cheese has not been found previously in cheese metagenomes. Furthermore, Tetragenococcus showed a high level of horizontal gene transfer with other members of the cheese microbiome, mainly with Lactococcus and Staphylococcus, involving genes related to carbohydrate metabolism functions. The resistome analysis revealed that raw milk and the associated processing environments are a rich reservoir of antimicrobial resistance determinants, mainly associated with resistance to aminoglycosides, tetracyclines, and β-lactam antibiotics and harbored by aerobic gram-negative bacteria of high relevance from a safety point of view, such as Escherichia coli, Salmonella enterica, Acinetobacter, and Klebsiella pneumoniae, and that the displacement of most raw milk-associated taxa by cave-associated taxa during ripening gave rise to a significant decrease in the load of ARGs and, therefore, to a safer end product.

CONCLUSION: Overall, the cave environments represented an important source of non-starter microorganisms which may play a relevant role in the quality and safety of the end products. Among them, we have identified novel taxa and taxa not previously regarded as being dominant components of the cheese microbiome (Tetragenococcus spp.), providing very valuable information for the authentication of this protected designation of origin artisanal cheese. Video Abstract.}, } @article {pmid38677439, year = {2024}, author = {Luo, X and Hounmanou, YMG and Ndayisenga, F and Yu, Z}, title = {Spontaneous fermentation mitigates the frequency of genes encoding antimicrobial resistance spreading from the phyllosphere reservoir to the diet.}, journal = {The Science of the total environment}, volume = {931}, number = {}, pages = {172712}, doi = {10.1016/j.scitotenv.2024.172712}, pmid = {38677439}, issn = {1879-1026}, mesh = {*Fermentation ; *Microbiota/drug effects ; Bacteria/genetics ; Genes, Bacterial ; Metagenome ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Vegetables/microbiology ; Humans ; Diet ; }, abstract = {The phyllosphere microbiome of vegetable products constitutes an important reservoir for multidrug resistant bacteria and Antibiotic Resistance Genes (ARG). Vegetable products including fermented products such as Paocai therefore may serve as a shuttle for extrinsic microorganisms with ARGs into the gut of consumers. Here we study the effect of fermentation on Paocai ARG dissemination by metagenomic analysis. Microbial abundance and diversity of the Paocai microbiome were diminished during fermentation, which correlated with the reduction of abundance in ARGs. Specifically, as fermentation progressed, Enterobacterales overtook Pseudomonadales as the predominant ARG carriers, and Lactobacillales and Enterobacteriales became the determinants of Paocai resistome variation. Moreover, the dual effect of microbes and metal resistance genes (MRGs) was the major contributor driving Paocai resistome dynamics. We recovered several metagenome-assembled genomes (MAGs) carrying acquired ARGs in the phyllosphere microbiome. ARGs of potential clinical and epidemiological relevance such as tet M and emrB-qacA, were mainly hosted by non-dominant bacterial genera. Overall, our study provides evidence that changes in microbial community composition by fermentation aid in constraining ARG dispersal from raw ingredients to the human microbiome but does not eliminate them.}, } @article {pmid38677385, year = {2024}, author = {Wang, YC and Fu, HM and Shen, Y and Wang, J and Wang, N and Chen, YP and Yan, P}, title = {Biosynthetic potential of uncultured anammox community bacteria revealed through multi-omics analysis.}, journal = {Bioresource technology}, volume = {401}, number = {}, pages = {130740}, doi = {10.1016/j.biortech.2024.130740}, pmid = {38677385}, issn = {1873-2976}, mesh = {*Oxidation-Reduction ; Bacteria/metabolism/genetics ; Ammonium Compounds/metabolism ; Microbiota ; Multigene Family ; Phylogeny ; Proteomics/methods ; Metagenomics/methods ; Anaerobiosis ; Multiomics ; }, abstract = {Microbial secondary metabolites (SMs) and their derivatives have been widely used in medicine, agriculture, and energy. Growing needs for renewable energy and the challenges posed by antibiotic resistance, cancer, and pesticides emphasize the crucial hunt for new SMs. Anaerobic ammonium-oxidation (anammox) systems harbor many uncultured or underexplored bacteria, representing potential resources for discovering novel SMs. Leveraging HiFi long-read metagenomic sequencing, 1,040 biosynthetic gene clusters (BGCs) were unearthed from the anammox microbiome with 58% being complete and showcasing rich diversity. Most of them showed distant relations to known BGCs, implying novelty. Members of the underexplored lineages (Chloroflexota and Planctomycetota) and Proteobacteria contained lots of BGCs, showcasing substantial biosynthetic potential. Metaproteomic results indicated that Planctomycetota members harbored the most active BGCs, particularly those involved in producing potential biofuel-ladderane. Overall, these findings underscore that anammox microbiomes could serve as valuable resources for mining novel BGCs and discovering new SMs for practical application.}, } @article {pmid38676863, year = {2024}, author = {Xiang, F and Han, L and Jiang, S and Xu, X and Zhang, Z}, title = {Black soldier fly larvae mitigate greenhouse gas emissions from domestic biodegradable waste by recycling carbon and nitrogen and reconstructing microbial communities.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {23}, pages = {33347-33359}, pmid = {38676863}, issn = {1614-7499}, support = {42377002//Major Research Plan/ ; 32171466//Major Research Plan/ ; }, mesh = {Animals ; *Greenhouse Gases ; *Nitrogen ; *Larva ; *Carbon/metabolism ; *Microbiota ; Diptera ; Bioreactors ; RNA, Ribosomal, 16S ; Methane/metabolism ; }, abstract = {Black soldier fly larvae have been proven to reduce greenhouse gas emissions in the treatment of organic waste. However, the microbial mechanisms involved have not been fully understood. The current study mainly examined the dynamic changes of carbon and nitrogen, greenhouse gas emissions, the succession of microbial community structure, and changes in functional gene abundance in organic waste under larvae treatment and non-aeration composting. Thirty percent carbon and 55% nitrogen in the organic waste supplied were stored in larvae biomass. Compared to the non-aeration composting, the larvae bioreactor reduced the proportion of carbon and nitrogen converted into greenhouse gases (CO2, CH4, and N2O decreased by 62%, 87%, and 95%, respectively). 16S rRNA sequencing analysis indicated that the larvae bioreactor increased the relative abundance of Methanophaga, Marinobacter, and Campylobacter during the bioprocess, enhancing the consumption of CH4 and N2O. The metagenomic data showed that the intervention of larvae reduced the ratio of (nirK + nirS + nor)/nosZ in the residues, thereby reducing the emission of N2O. Larvae also increased the functional gene abundance of nirA, nirB, nirD, and nrfA in the residues, making nitrite more inclined to be reduced to ammonia instead of N2O. The larvae bioreactor mitigated greenhouse gas emissions by redistributing carbon and nitrogen and remodeling microbiomes during waste bioconversion, giving related enterprises a relative advantage in carbon trading.}, } @article {pmid38676557, year = {2024}, author = {Glasl, B and Luter, HM and Damjanovic, K and Kitzinger, K and Mueller, AJ and Mahler, L and Engelberts, JP and Rix, L and Osvatic, JT and Hausmann, B and Séneca, J and Daims, H and Pjevac, P and Wagner, M}, title = {Co-occurring nitrifying symbiont lineages are vertically inherited and widespread in marine sponges.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, doi = {10.1093/ismejo/wrae069}, pmid = {38676557}, issn = {1751-7370}, support = {T 1218//Austrian Science Fund/ ; }, mesh = {Animals ; *Porifera/microbiology ; *Symbiosis ; *Nitrification ; *Archaea/genetics/classification/metabolism/isolation & purification ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Phylogeny ; *Ammonia/metabolism ; Nitrites/metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Metagenome ; }, abstract = {Ammonia-oxidizing archaea and nitrite-oxidizing bacteria are common members of marine sponge microbiomes. They derive energy for carbon fixation and growth from nitrification-the aerobic oxidation of ammonia to nitrite and further to nitrate-and are proposed to play essential roles in the carbon and nitrogen cycling of sponge holobionts. In this study, we characterize two novel nitrifying symbiont lineages, Candidatus Nitrosokoinonia and Candidatus Nitrosymbion in the marine sponge Coscinoderma matthewsi using a combination of molecular tools, in situ visualization, and physiological rate measurements. Both represent a new genus in the ammonia-oxidizing archaeal class Nitrososphaeria and the nitrite-oxidizing bacterial order Nitrospirales, respectively. Furthermore, we show that larvae of this viviparous sponge are densely colonized by representatives of Ca. Nitrosokoinonia and Ca. Nitrosymbion indicating vertical transmission. In adults, the representatives of both symbiont genera are located extracellularly in the mesohyl. Comparative metagenome analyses and physiological data suggest that ammonia-oxidizing archaeal symbionts of the genus Ca. Nitrosokoinonia strongly rely on endogenously produced nitrogenous compounds (i.e. ammonium, urea, nitriles/cyanides, and creatinine) rather than on exogenous ammonium sources taken up by the sponge. Additionally, the nitrite-oxidizing bacterial symbionts of the genus Ca. Nitrosymbion may reciprocally support the ammonia-oxidizers with ammonia via the utilization of sponge-derived urea and cyanate. Comparative analyses of published environmental 16S rRNA gene amplicon data revealed that Ca. Nitrosokoinonia and Ca. Nitrosymbion are widely distributed and predominantly associated with marine sponges and corals, suggesting a broad relevance of our findings.}, } @article {pmid38675947, year = {2024}, author = {Luo, R and Guan, A and Ma, B and Gao, Y and Peng, Y and He, Y and Xu, Q and Li, K and Zhong, Y and Luo, R and Cao, R and Jin, H and Lin, Y and Shang, P}, title = {Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups.}, journal = {Viruses}, volume = {16}, number = {4}, pages = {}, pmid = {38675947}, issn = {1999-4915}, mesh = {Animals ; *Altitude ; Swine ; *Virome/genetics ; *Metagenomics ; *Gastrointestinal Microbiome/genetics ; Tibet ; Viruses/genetics/classification ; Metagenome ; Female ; Genome, Viral ; }, abstract = {Tibetan pig is a geographically isolated pig breed that inhabits high-altitude areas of the Qinghai-Tibetan plateau. At present, there is limited research on viral diseases in Tibetan pigs. This study provides a novel metagenomic exploration of the gut virome in Tibetan pigs (altitude ≈ 3000 m) across three critical developmental stages, including lactation, nursery, and fattening. The composition of viral communities in the Tibetan pig intestine, with a dominant presence of Microviridae phages observed across all stages of development, in combination with the previous literature, suggest that it may be associated with geographical locations with high altitude. Functional annotation of viral operational taxonomic units (vOTUs) highlights that, among the constantly increasing vOTUs groups, the adaptability of viruses to environmental stressors such as salt and heat indicates an evolutionary response to high-altitude conditions. It shows that the lactation group has more abundant viral auxiliary metabolic genes (vAMGs) than the nursery and fattening groups. During the nursery and fattening stages, this leaves only DNMT1 at a high level. which may be a contributing factor in promoting gut health. The study found that viruses preferentially adopt lytic lifestyles at all three developmental stages. These findings not only elucidate the dynamic interplay between the gut virome and host development, offering novel insights into the virome ecology of Tibetan pigs and their adaptation to high-altitude environments, but also provide a theoretical basis for further studies on pig production and epidemic prevention under extreme environmental conditions.}, } @article {pmid38675877, year = {2024}, author = {Zhao, H and Yang, M and Fan, X and Gui, Q and Yi, H and Tong, Y and Xiao, W}, title = {A Metagenomic Investigation of Potential Health Risks and Element Cycling Functions of Bacteria and Viruses in Wastewater Treatment Plants.}, journal = {Viruses}, volume = {16}, number = {4}, pages = {}, pmid = {38675877}, issn = {1999-4915}, support = {32071570//National Natural Science Foundation of China/ ; 202303AP140004//the Science and Technology Planning Project in Key Areas of Yunnan Province/ ; }, mesh = {*Metagenomics ; *Wastewater/virology/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Sewage/virology/microbiology ; Humans ; *Viruses/genetics/classification/isolation & purification ; Metagenome ; Bacteriophages/genetics/isolation & purification/classification ; Virome/genetics ; Water Purification ; Animals ; }, abstract = {The concentration of viruses in sewage sludge is significantly higher (10-1000-fold) than that found in natural environments, posing a potential risk for human and animal health. However, the composition of these viruses and their role in the transfer of pathogenic factors, as well as their role in the carbon, nitrogen, and phosphorus cycles remain poorly understood. In this study, we employed a shotgun metagenomic approach to investigate the pathogenic bacteria and viral composition and function in two wastewater treatment plants located on a campus. Our analysis revealed the presence of 1334 amplicon sequence variants (ASVs) across six sludge samples, with 242 ASVs (41.22% of total reads) identified as pathogenic bacteria. Arcobacter was found to be the most dominant pathogen accounting for 6.79% of total reads. The virome analysis identified 613 viral genera with Aorunvirus being the most abundant genus at 41.85%. Approximately 0.66% of these viruses were associated with human and animal diseases. More than 60% of the virome consisted of lytic phages. Host prediction analysis revealed that the phages primarily infected Lactobacillus (37.11%), Streptococcus (21.11%), and Staphylococcus (7.11%). Furthermore, our investigation revealed an abundance of auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and phosphorus cycling within the virome. We also detected a total of 113 antibiotic resistance genes (ARGs), covering major classes of antibiotics across all samples analyzed. Additionally, our findings indicated the presence of virulence factors including the clpP gene accounting for approximately 4.78%, along with toxin genes such as the RecT gene representing approximately 73.48% of all detected virulence factors and toxin genes among all samples analyzed. This study expands our understanding regarding both pathogenic bacteria and viruses present within sewage sludge while providing valuable insights into their ecological functions.}, } @article {pmid38675716, year = {2024}, author = {Chudan, S and Kurakawa, T and Nishikawa, M and Nagai, Y and Tabuchi, Y and Ikushiro, S and Furusawa, Y}, title = {Beneficial Effects of Dietary Fiber in Young Barley Leaf on Gut Microbiota and Immunity in Mice.}, journal = {Molecules (Basel, Switzerland)}, volume = {29}, number = {8}, pages = {}, pmid = {38675716}, issn = {1420-3049}, support = {20K05929//Japan Society for the Promotion of Science/ ; n/a//Takeda Science Foundation/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Hordeum/chemistry ; *Dietary Fiber/pharmacology ; *Plant Leaves/chemistry ; Mice ; Retinal Dehydrogenase/metabolism ; Butyrates/metabolism ; Feces/microbiology ; }, abstract = {The health benefits of young barley leaves, rich in dietary fiber, have been studied for several decades; however, their beneficial effects on the intestinal microenvironment remain to be elucidated. To investigate the effects of young barley leaf-derived dietary fiber (YB) on the gut microbiota and immunity, mice were fed an AIN-93G diet containing cellulose or YB and subjected to subsequent analysis. The population of MHC-II-positive conventional dendritic cells (cDCs) and CD86 expression in the cDCs of Peyer's patches were elevated in the YB-fed mice. MHC-II and CD86 expression was also elevated in the bone marrow-derived DCs treated with YB. 16S-based metagenomic analysis revealed that the gut microbiota composition was markedly altered by YB feeding. Among the gut microbiota, Lachnospiraceae, mainly comprising butyrate-producing NK4A136 spp., were overrepresented in the YB-fed mice. In fact, fecal butyrate concentration was also augmented in the YB-fed mice, which coincided with increased retinaldehyde dehydrogenase (RALDH) activity in the CD103[+] cDCs of the mesenteric lymph nodes. Consistent with elevated RALDH activity, the population of colonic IgA[+] plasma cells was higher in the YB-fed mice than in the parental control mice. In conclusion, YB has beneficial effects on the gut microbiota and intestinal immune system.}, } @article {pmid38674803, year = {2024}, author = {Arteaga-Muller, GY and Flores-Treviño, S and Bocanegra-Ibarias, P and Robles-Espino, D and Garza-González, E and Fabela-Valdez, GC and Camacho-Ortiz, A}, title = {Changes in the Progression of Chronic Kidney Disease in Patients Undergoing Fecal Microbiota Transplantation.}, journal = {Nutrients}, volume = {16}, number = {8}, pages = {}, pmid = {38674803}, issn = {2072-6643}, mesh = {Humans ; *Renal Insufficiency, Chronic/therapy/microbiology ; *Fecal Microbiota Transplantation ; Male ; Female ; *Disease Progression ; Middle Aged ; Double-Blind Method ; *Gastrointestinal Microbiome ; Aged ; *Feces/microbiology ; Dysbiosis/therapy ; Treatment Outcome ; Adult ; Creatinine/blood ; }, abstract = {Chronic kidney disease (CKD) is a progressive loss of renal function in which gut dysbiosis is involved. Fecal microbiota transplantation (FMT) may be a promising alternative for restoring gut microbiota and treating CKD. This study evaluated the changes in CKD progression in patients treated with FMT. Patients with diabetes and/or hypertension with CKD clinical stages 2, 3, and 4 in this single-center, double-blind, randomized, placebo-controlled clinical trial (NCT04361097) were randomly assigned to receive either FMT or placebo capsules for 6 months. Laboratory and stool metagenomic analyses were performed. A total of 28 patients were included (15 FMT and 13 placebo). Regardless of CKD stages, patients responded similarly to FMT treatment. More patients (53.8%) from the placebo group progressed to CKD than the FMT group (13.3%). The FMT group maintained stable renal function parameters (serum creatinine and urea nitrogen) compared to the placebo group. Adverse events after FMT treatment were mild or moderate gastrointestinal symptoms. The abundance of Firmicutes and Actinobacteria decreased whereas Bacteroidetes, Proteobacteria and Roseburia spp. increased in the FMT group. CKD patients showed less disease progression after FMT administration. The administration of oral FMT in patients with CKD is a safe strategy, does not represent a risk, and has potential benefits.}, } @article {pmid38674796, year = {2024}, author = {Chang, WL and Chen, YE and Tseng, HT and Cheng, CF and Wu, JH and Hou, YC}, title = {Gut Microbiota in Patients with Prediabetes.}, journal = {Nutrients}, volume = {16}, number = {8}, pages = {}, pmid = {38674796}, issn = {2072-6643}, support = {TCRD-TPE-109-RT-10//Taipei Tzu Chi Hospital/ ; TCRD-TPE-111-65//Taipei Tzu Chi Hospital/ ; TCRD-TPE-112-RT-9//Taipei Tzu Chi Hospital/ ; TCRD-TPE-108-38//Taipei Tzu Chi Hospital/ ; }, mesh = {Humans ; *Prediabetic State/microbiology ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; Male ; Female ; *Feces/microbiology ; Aged ; Young Adult ; Adolescent ; RNA, Ribosomal, 16S/genetics ; Blood Glucose/metabolism ; Diabetes Mellitus, Type 2/microbiology ; Bacteria/classification/genetics/isolation & purification ; Dietary Fiber/administration & dosage ; }, abstract = {Prediabetes is characterized by abnormal glycemic levels below the type 2 diabetes threshold, and effective control of blood glucose may prevent the progression to type 2 diabetes. While the association between the gut microbiota, glucose metabolism, and insulin resistance in diabetic patients has been established in previous studies, there is a lack of research regarding these aspects in prediabetic patients in Asia. We aim to investigate the composition of the gut microbiota in prediabetic patients and their differences compared to healthy individuals. In total, 57 prediabetic patients and 60 healthy adult individuals aged 18 to 65 years old were included in this study. Biochemistry data, fecal samples, and 3 days of food records were collected. Deoxyribonucleic acid extraction and next-generation sequencing via 16S ribosomal ribonucleic acid metagenomic sequencing were conducted to analyze the relationship between the gut microbiota and dietary habits. Prediabetic patients showed a lower microbial diversity than healthy individuals, with 9 bacterial genera being less abundant and 14 others more abundant. Prediabetic patients who consumed a low-carbohydrate (LC) diet exhibited higher diversity in the gut microbiota than those who consumed a high-carbohydrate diet. A higher abundance of Coprococcus was observed in the prediabetic patients on an LC diet. Compared to healthy individuals, the gut microbiota of prediabetic patients was significantly different, and adopting an LC diet with high dietary fiber consumption may positively impact the gut microbiota. Future studies should aim to understand the relationship between the gut microbiota and glycemic control in the Asian population.}, } @article {pmid38674771, year = {2024}, author = {Gómez, F and Rodríguez, N and Rodríguez-Manfredi, JA and Escudero, C and Carrasco-Ropero, I and Martínez, JM and Ferrari, M and De Angelis, S and Frigeri, A and Fernández-Sampedro, M and Amils, R}, title = {Association of Acidotolerant Cyanobacteria to Microbial Mats below pH 1 in Acidic Mineral Precipitates in Río Tinto River in Spain.}, journal = {Microorganisms}, volume = {12}, number = {4}, pages = {}, pmid = {38674771}, issn = {2076-2607}, abstract = {This report describes acidic microbial mats containing cyanobacteria that are strongly associated to precipitated minerals in the source area of Río Tinto. Río Tinto (Huelva, Southwestern Spain) is an extreme acidic environment where iron and sulfur cycles play a fundamental role in sustaining the extremely low pH and the high concentration of heavy metals, while maintaining a high level of microbial diversity. These multi-layered mineral deposits are stable all year round and are characterized by a succession of thick greenish-blue and brownish layers mainly composed of natrojarosite. The temperature and absorbance above and below the mineral precipitates were followed and stable conditions were detected inside the mineral precipitates. Different methodologies, scanning and transmission electron microscopy, immunological detection, fluorescence in situ hybridization, and metagenomic analysis were used to describe the biodiversity existing in these microbial mats, demonstrating, for the first time, the existence of acid-tolerant cyanobacteria in a hyperacidic environment of below pH 1. Up to 0.46% of the classified sequences belong to cyanobacterial microorganisms, and 1.47% of the aligned DNA reads belong to the Cyanobacteria clade.}, } @article {pmid38674691, year = {2024}, author = {Deryabin, D and Lazebnik, C and Vlasenko, L and Karimov, I and Kosyan, D and Zatevalov, A and Duskaev, G}, title = {Broiler Chicken Cecal Microbiome and Poultry Farming Productivity: A Meta-Analysis.}, journal = {Microorganisms}, volume = {12}, number = {4}, pages = {}, pmid = {38674691}, issn = {2076-2607}, support = {22-16-00036//Russian Science Foundation/ ; FNWZ-2022-0010//research project/ ; }, abstract = {The cecal microbial community plays an important role in chicken growth and development via effective feed conversion and essential metabolite production. The aim of this study was to define the microbial community's variants in chickens' ceca and to explore the most significant association between the microbiome compositions and poultry farming productivity. The meta-analysis included original data from 8 control broiler chicken groups fed with a standard basic diet and 32 experimental groups supplemented with various feed additives. Standard Illumina 16S-RNA gene sequencing technology was used to characterize the chicken cecal microbiome. Zootechnical data sets integrated with the European Production Effectiveness Factor (EPEF) were collected. Analysis of the bacterial taxa abundance and co-occurrence in chicken cecal microbiomes revealed two alternative patterns: Bacteroidota-dominated with decreased alpha biodiversity; and Bacillota-enriched, which included the Actinomycetota, Cyanobacteriota and Thermodesulfobacteriota phyla members, with increased biodiversity indices. Bacillota-enriched microbiome groups showed elevated total feed intake (especially due to the starter feed intake) and final body weight, and high EPEF values, while Bacteroidota-dominated microbiomes were negatively associated with poultry farming productivity. The meta-analysis results lay the basis for the development of chicken growth-promoting feed supplementations, aimed at the stimulation of beneficial and inhibition of harmful bacterial patterns, where relevant metagenomic data can be a tool for their control and selection.}, } @article {pmid38674632, year = {2024}, author = {Couto, RDS and Abreu, WU and Rodrigues, LRR and Marinho, LF and Morais, VDS and Villanova, F and Pandey, RP and Deng, X and Delwart, E and da Costa, AC and Leal, E}, title = {Genomoviruses in Liver Samples of Molossus molossus Bats.}, journal = {Microorganisms}, volume = {12}, number = {4}, pages = {}, pmid = {38674632}, issn = {2076-2607}, abstract = {CRESS-DNA encompasses a broad spectrum of viruses documented across diverse organisms such as animals, plants, diatoms, fungi, and marine invertebrates. Despite this prevalence, the full extent of these viruses' impact on the environment and their respective hosts remains incompletely understood. Furthermore, an increasing number of viruses within this category lack detailed characterization. This investigation focuses on unveiling and characterizing viruses affiliated with the Genomoviridae family identified in liver samples from the bat Molossus molossus. Leveraging viral metagenomics, we identified seven sequences (MmGmV-PA) featuring a circular DNA genome housing two ORFs encoding replication-associated protein (Rep) and capsid protein (Cap). Predictions based on conserved domains typical of the Genomoviridae family were established. Phylogenetic analysis revealed the segregation of these sequences into two clades aligning with the genera Gemycirculavirus (MmGmV-06-PA and MmGmV-07-PA) and Gemykibivirus (MmGmV-01-PA, MmGmV-02-PA, MmGmV-03-PA, MmGmV-05-PA, and MmGmV-09-PA). At the species level, pairwise comparisons based on complete nucleotide sequences indicated the potential existence of three novel species. In summary, our study significantly contributes to an enhanced understanding of the diversity of Genomoviridae within bat samples, shedding light on previously undiscovered viral entities and their potential ecological implications.}, } @article {pmid38672421, year = {2024}, author = {Zhang, L and Tang, X and Fan, C and Ren, S and Cheng, Q and Zhou, H and Liu, K and Jia, S and Zhang, Y}, title = {Dysbiosis of Gut Microbiome Aggravated Male Infertility in Captivity of Plateau Pika.}, journal = {Biomolecules}, volume = {14}, number = {4}, pages = {}, pmid = {38672421}, issn = {2218-273X}, support = {LHZX-2023-02//Sanjiangyuan National Park Collaborative Research Special Fund/ ; 31670394, U21A20186//National Natural Science Foundation of China/ ; 2021-ZJ-Y01//Qinghai innovation platform construction project by Chinese Academy of Sciences/ ; }, mesh = {Animals ; Male ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/metabolism ; *Infertility, Male/microbiology/metabolism ; *Testosterone/metabolism ; *Lagomorpha/microbiology ; Testis/microbiology/metabolism ; Fatty Acids, Volatile/metabolism ; }, abstract = {Captivity is an important and efficient technique for rescuing endangered species. However, it induces infertility, and the underlying mechanism remains obscure. This study used the plateau pika (Ochotona curzoniae) as a model to integrate physiological, metagenomic, metabolomic, and transcriptome analyses and explore whether dysbiosis of the gut microbiota induced by artificial food exacerbates infertility in captive wild animals. Results revealed that captivity significantly decreased testosterone levels and the testicle weight/body weight ratio. RNA sequencing revealed abnormal gene expression profiles in the testicles of captive animals. The microbial α-diversity and Firmicutes/Bacteroidetes ratio were drastically decreased in the captivity group. Bacteroidetes and Muribaculaceae abundance notably increased in captive pikas. Metagenomic analysis revealed that the alteration of flora increased the capacity for carbohydrate degradation in captivity. The levels of microbe metabolites' short-chain fatty acids (SCFAs) were significantly high in the captive group. Increasing SCFAs influenced the immune response of captivity plateau pikas; pro-inflammatory cytokines were upregulated in captivity. The inflammation ultimately contributed to male infertility. In addition, a positive correlation was observed between Gastranaerophilales family abundance and testosterone concentration. Our results provide evidence for the interactions between artificial food, the gut microbiota, and male infertility in pikas and benefit the application of gut microbiota interference in threatened and endangered species.}, } @article {pmid38672407, year = {2024}, author = {Schiano-Lomoriello, D and Abicca, I and Contento, L and Gabrielli, F and Alfonsi, C and Di Pietro, F and Papa, FT and Ballesteros-Sánchez, A and Sánchez-González, JM and Rocha-De-Lossada, C and Mazzotta, C and Giannaccare, G and Bonzano, C and Borroni, D}, title = {Infectious Keratitis: Characterization of Microbial Diversity through Species Richness and Shannon Diversity Index.}, journal = {Biomolecules}, volume = {14}, number = {4}, pages = {}, pmid = {38672407}, issn = {2218-273X}, mesh = {*Keratitis/microbiology ; Humans ; *Biodiversity ; Bacteria/genetics/classification/isolation & purification ; DNA, Bacterial/genetics ; Microbiota/genetics ; }, abstract = {Purpose: To characterize microbial keratitis diversity utilizing species richness and Shannon Diversity Index. Methods: Corneal impression membrane was used to collect samples. All swabs were processed and analyzed by Biolab Laboratory (level V-SSN Excellence: ISO 9001:2015), Biolab Srl (Ascoli Piceno, Italy). DNA extraction, library preparation, and sequencing were performed in all samples. After sequencing, low-quality and polyclonal sequences were filtered out by the Ion software. At this point, we employed Kraken2 for microbial community analysis in keratitis samples. Nuclease-free water and all the reagents included in the experiment were used as a negative control. The primary outcome was the reduction in bacterial DNA (microbial load) at T1, expressed as a percentage of the baseline value (T0). Richness and Shannon alpha diversity metrics, along with Bray-Curtis beta diversity values, were calculated using the phyloseq package in R. Principal coordinate analysis was also conducted to interpret these metrics. Results: 19 samples were included in the study. The results exhibited a motley species richness, with the highest recorded value surpassing 800 species. Most of the samples displayed richness values ranging broadly from under 200 to around 600, indicating considerable variability in species count among the keratitis samples. Conclusions: A significant presence of both typical and atypical bacterial phyla in keratitis infections, underlining the complexity of the disease's microbial etiology.}, } @article {pmid38670644, year = {2024}, author = {Akinsuyi, OS and Xhumari, J and Ojeda, A and Roesch, LFW}, title = {Gut permeability among Astronauts during Space missions.}, journal = {Life sciences in space research}, volume = {41}, number = {}, pages = {171-180}, doi = {10.1016/j.lssr.2024.03.003}, pmid = {38670644}, issn = {2214-5532}, mesh = {*Space Flight ; *Astronauts ; Humans ; Animals ; *Permeability ; *Gastrointestinal Microbiome ; Mice ; Transcriptome ; Gastrointestinal Tract/microbiology ; }, abstract = {The space environment poses substantial challenges to human physiology, including potential disruptions in gastrointestinal health. Gut permeability has only recently become widely acknowledged for its potential to cause adverse effects on a systemic level, rendering it a critical factor to investigate in the context of spaceflight. Here, we propose that astronauts experience the onset of leaky gut during space missions supported by transcriptomic and metagenomic analysis of human and murine samples. A genetic map contributing to intestinal permeability was constructed from a systematic review of current literature. This was referenced against our re-analysis of three independent transcriptomic datasets which revealed significant changes in gene expression patterns associated with the gut barrier. Specifically, in astronauts during flight, we observed a substantial reduction in the expression genes that are crucial for intestinal barrier function, goblet cell development, gut microbiota modulation, and immune responses. Among rodent spaceflight studies, differential expression of cytokines, chemokines, and genes which regulate mucin production and post-translational modifications suggest a similar dysfunction of intestinal permeability. Metagenomic analysis of feces from two murine studies revealed a notable reduction probiotic, short chain fatty acid-producing bacteria and an increase in the Gram-negative pathogens, including Citrobacter rodentium, Enterobacter cloacea, Klebsiella aerogenes, and Proteus hauseri which promote LPS circulation, a recipe for barrier disruption and systemic inflammatory activation. These findings emphasize the critical need to understand the underlying mechanisms and develop interventions to maintain gastrointestinal health in space.}, } @article {pmid38670293, year = {2024}, author = {Clagnan, E and Petrini, S and Pioli, S and Piergiacomo, F and Chowdhury, AA and Brusetti, L and Foladori, P}, title = {Conventional activated sludge vs. photo-sequencing batch reactor for enhanced nitrogen removal in municipal wastewater: Microalgal-bacterial consortium and pathogenic load insights.}, journal = {Bioresource technology}, volume = {401}, number = {}, pages = {130735}, doi = {10.1016/j.biortech.2024.130735}, pmid = {38670293}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Nitrogen ; *Microalgae/metabolism ; *Wastewater/microbiology/chemistry ; *Bioreactors/microbiology ; *Bacteria/metabolism ; Microbial Consortia/physiology ; Water Purification/methods ; Denitrification ; Waste Disposal, Fluid/methods ; Nitrification ; }, abstract = {Municipal wastewater treatment plants are mostly based on traditional activated sludge (AS) processes. These systems are characterised by major drawbacks: high energy consumption, large amount of excess sludge and high greenhouse gases emissions. Treatment through microalgal-bacterial consortia (MBC) is an alternative and promising solution thanks to lower energy consumption and emissions, biomass production and water sanitation. Here, microbial difference between a traditional anaerobic sludge (AS) and a consortium-based system (photo-sequencing batch reactor (PSBR)) with the same wastewater inlet were characterised through shotgun metagenomics. Stable nitrification was achieved in the PSBR ensuring ammonium removal > 95 % and significant total nitrogen removal thanks to larger flocs enhancing denitrification. The new system showed enhanced pathogen removal, a higher abundance of photosynthetic and denitrifying microorganisms with a reduced emissions potential identifying this novel PSBR as an effective alternative to AS.}, } @article {pmid38669328, year = {2024}, author = {Dong, X and Zhang, T and Wu, W and Peng, Y and Liu, X and Han, Y and Chen, X and Gao, Z and Xia, J and Shao, Z and Greening, C}, title = {A vast repertoire of secondary metabolites potentially influences community dynamics and biogeochemical processes in cold seeps.}, journal = {Science advances}, volume = {10}, number = {17}, pages = {eadl2281}, pmid = {38669328}, issn = {2375-2548}, mesh = {*Geologic Sediments/microbiology ; *Microbiota ; *Metagenome ; Bacteria/metabolism/genetics ; Metabolome ; Ecosystem ; Secondary Metabolism ; Archaea/metabolism/genetics ; Multigene Family ; Cold Temperature ; Metabolomics/methods ; Phylogeny ; Metagenomics/methods ; }, abstract = {In deep-sea cold seeps, microbial communities thrive on the geological seepage of hydrocarbons and inorganic compounds, differing from photosynthetically driven ecosystems. However, their biosynthetic capabilities remain largely unexplored. Here, we analyzed 81 metagenomes, 33 metatranscriptomes, and 7 metabolomes derived from nine different cold seep areas to investigate their secondary metabolites. Cold seep microbiomes encode diverse and abundant biosynthetic gene clusters (BGCs). Most BGCs are affiliated with understudied bacteria and archaea, including key mediators of methane and sulfur cycling. The BGCs encode diverse antimicrobial compounds that potentially shape community dynamics and various metabolites predicted to influence biogeochemical cycling. BGCs from key players are widely distributed and highly expressed, with their abundance and expression levels varying with sediment depth. Sediment metabolomics reveals unique natural products, highlighting uncharted chemical potential and confirming BGC activity in these sediments. Overall, these results demonstrate that cold seep sediments serve as a reservoir of hidden natural products and sheds light on microbial adaptation in chemosynthetically driven ecosystems.}, } @article {pmid38668783, year = {2024}, author = {Shamjana, U and Vasu, DA and Hembrom, PS and Nayak, K and Grace, T}, title = {The role of insect gut microbiota in host fitness, detoxification and nutrient supplementation.}, journal = {Antonie van Leeuwenhoek}, volume = {117}, number = {1}, pages = {71}, pmid = {38668783}, issn = {1572-9699}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Insecta/microbiology ; *Symbiosis ; Nutrients/metabolism ; Metagenomics ; Host Microbial Interactions ; Inactivation, Metabolic ; Bacteria/classification/genetics/metabolism ; }, abstract = {Insects are incredibly diverse, ubiquitous and have successfully flourished out of the dynamic and often unpredictable nature of evolutionary processes. The resident microbiome has accompanied the physical and biological adaptations that enable their continued survival and proliferation in a wide array of environments. The host insect and microbiome's bidirectional relationship exhibits their capability to influence each other's physiology, behavior and characteristics. Insects are reported to rely directly on the microbial community to break down complex food, adapt to nutrient-deficit environments, protect themselves from natural adversaries and control the expression of social behavior. High-throughput metagenomic approaches have enhanced the potential for determining the abundance, composition, diversity and functional activities of microbial fauna associated with insect hosts, enabling in-depth investigation into insect-microbe interactions. We undertook a review of some of the major advances in the field of metagenomics, focusing on insect-microbe interaction, diversity and composition of resident microbiota, the functional capability of endosymbionts and discussions on different symbiotic relationships. The review aims to be a valuable resource on insect gut symbiotic microbiota by providing a comprehensive understanding of how insect gut symbionts systematically perform a range of functions, viz., insecticide degradation, nutritional support and immune fitness. A thorough understanding of manipulating specific gut symbionts may aid in developing advanced insect-associated research to attain health and design strategies for pest management.}, } @article {pmid38668594, year = {2024}, author = {Bishop, SL and Solonenka, JT and Giebelhaus, RT and Bakker, DTR and Li, ITS and Murch, SJ}, title = {Microbial Diversity Impacts Non-Protein Amino Acid Production in Cyanobacterial Bloom Cultures Collected from Lake Winnipeg.}, journal = {Toxins}, volume = {16}, number = {4}, pages = {}, pmid = {38668594}, issn = {2072-6651}, support = {Unknown//Natural Sciences and Engineering Research Council/ ; Unknown//Canadian Foundation for Innovation/ ; }, mesh = {*Lakes/microbiology ; *Cyanobacteria/metabolism/genetics/isolation & purification ; Manitoba ; Harmful Algal Bloom ; Amino Acids/analysis/metabolism ; Tandem Mass Spectrometry ; Biodiversity ; Microbiota ; Cyanobacteria Toxins ; }, abstract = {Lake Winnipeg in Manitoba, Canada is heavily impacted by harmful algal blooms that contain non-protein amino acids (NPAAs) produced by cyanobacteria: N-(2-aminoethyl)glycine (AEG), β-aminomethyl-L-alanine (BAMA), β-N-methylamino-L-alanine (BMAA), and 2,4-diaminobutyric acid (DAB). Our objective was to investigate the impact of microbial diversity on NPAA production by cyanobacteria using semi-purified crude cyanobacterial cultures established from field samples collected by the Lake Winnipeg Research Consortium between 2016 and 2021. NPAAs were detected and quantified by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) using validated analytical methods, while Shannon and Simpson alpha diversity scores were determined from 16S rRNA metagenomic sequences. Alpha diversity in isolate cultures was significantly decreased compared to crude cyanobacterial cultures (p < 0.001), indicating successful semi-purification. BMAA and AEG concentrations were higher in crude compared to isolate cultures (p < 0.0001), and AEG concentrations were correlated to the alpha diversity in cultures (r = 0.554; p < 0.0001). BAMA concentrations were increased in isolate cultures (p < 0.05), while DAB concentrations were similar in crude and isolate cultures. These results demonstrate that microbial community complexity impacts NPAA production by cyanobacteria and related organisms.}, } @article {pmid38666797, year = {2024}, author = {Llorenç-Vicedo, A and Lluesma Gomez, M and Zeising, O and Kleiner, T and Freitag, J and Martinez-Hernandez, F and Wilhelms, F and Martinez-Garcia, M}, title = {New avenues for potentially seeking microbial responses to climate change beneath Antarctic ice shelves.}, journal = {mSphere}, volume = {9}, number = {5}, pages = {e0007324}, pmid = {38666797}, issn = {2379-5042}, mesh = {Antarctic Regions ; *Climate Change ; *Ice Cover/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification ; *Seawater/microbiology ; Archaea/genetics/classification ; Ecosystem ; Single-Cell Analysis ; Phylogeny ; }, abstract = {UNLABELLED: The signs of climate change are undeniable, and the impact of these changes on ecosystem function heavily depends on the response of microbes that underpin the food web. Antarctic ice shelf is a massive mass of floating ice that extends from the continent into the ocean, exerting a profound influence on global carbon cycles. Beneath Antarctic ice shelves, marine ice stores valuable genetic information, where marine microbial communities before the industrial revolution are archived. Here, in this proof-of-concept, by employing a combination of single-cell technologiesand metagenomics, we have been able to sequence frozen microbial DNA (≈300 years old) stored in the marine ice core B15 collected from the Filchnner-Ronne Ice Shelf. Metagenomic data indicated that Proteobacteria and Thaumarchaeota (e.g., Nitrosopumilus spp.), followed by Actinobacteria (e.g., Actinomarinales), were abundant. Remarkably, our data allow us to "travel to the past" and calibrate genomic and genetic evolutionary changes for ecologically relevant microbes and functions, such as Nitrosopumilus spp., preserved in the marine ice (≈300 years old) with those collected recently in seawater under an ice shelf (year 2017). The evolutionary divergence for the ammonia monooxygenase gene amoA involved in chemolithoautotrophy was about 0.88 amino acid and 2.8 nucleotide substitution rate per 100 sites in a century, while the accumulated rate of genomic SNPs was 2,467 per 1 Mb of genome and 100 years. Whether these evolutionary changes remained constant over the last 300 years or accelerated during post-industrial periods remains an open question that will be further elucidated.

IMPORTANCE: Several efforts have been undertaken to predict the response of microbes under climate change, mainly based on short-term microcosm experiments under forced conditions. A common concern is that manipulative experiments cannot properly simulate the response of microbes to climate change, which is a long-term evolutionary process. In this proof-of-concept study with a limited sample size, we demonstrate a novel approach yet to be fully explored in science for accessing genetic information from putative past marine microbes preserved under Antarctic ice shelves before the industrial revolution. This potentially allows us estimating evolutionary changes as exemplified in our study. We advocate for gathering a more comprehensive Antarctic marine ice core data sets across various periods and sites. Such a data set would enable the establishment of a robust baseline, facilitating a better assessment of the potential effects of climate change on key genetic signatures of microbes.}, } @article {pmid38664929, year = {2024}, author = {Fu, Q and Ma, X and Li, S and Shi, M and Song, T and Cui, J}, title = {New insights into the interactions between the gut microbiota and the inflammatory response to ulcerative colitis in a mouse model of dextran sodium sulfate and possible mechanisms of action for treatment with PE&AFWE.}, journal = {Animal models and experimental medicine}, volume = {7}, number = {2}, pages = {83-97}, pmid = {38664929}, issn = {2576-2095}, support = {81774449//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Colitis, Ulcerative/microbiology/drug therapy/pathology ; *Disease Models, Animal ; *Dextran Sulfate/pharmacology ; *Mice, Inbred C57BL ; Mice ; Dysbiosis ; Male ; Inflammation ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD), comprising Crohn's disease (CD) and ulcerative colitis (UC), is a heterogeneous state of chronic intestinal inflammation. Intestinal innate immunity, including innate immune cells, defends against pathogens and excessive entry of gut microbiota, while preserving immune tolerance to resident intestinal microbiota, and may be characterized by its capacity to produce a rapid and nonspecific reaction. The association between microbiota dysbiosis and the pathogenesis of IBD is complex and dynamic. When the intestinal ecosystem is in dysbiosis, the reduced abundance and diversity of intestinal gut microbiota make the host more vulnerable to the attack of exogenous and endogenous pathogenic gut microbiota. The aim of our study was to comprehensively assess the relationship between microbial populations within UC, the signaling pathways of pathogenic gut microbe therein and the inflammatory response, as well as to understand the effects of using PE&AFWE (poppy extract [Papaver nudicaule L.] and Artemisia frigida Willd. extract) on UC modulation.

METHODS: A UC mouse model was established by inducing SPF-grade C57BL/6 mice using dextrose sodium sulfate (DSS). Based on metagenomic sequencing to characterize the gut microbiome, the relationship between gut microbiota dysbiosis and gut microbiota was further studied using random forest and Bayesian network analysis methods, as well as histopathological analysis.

RESULTS: (1) We found that the 5 gut microbiota with the highest relative abundance of inflammatory bowel disease UC model gut microbiota were consistent with the top 5 ranked natural bacteria. There were three types of abundance changes in the model groups: increases (Chlamydiae/Proteobacteria and Deferribacteres), decreases (Firmicutes), and no significant changes (Bacteroidetes). The UC model group was significantly different from the control group, with 1308 differentially expressed species with abundance changes greater than or equal to 2-fold. (2) The proportion of the fecal flora in the UC group decreased by 37.5% in the Firmicutes and increased by 14.29% in the proportion of Proteobacteria compared to the control group before treatment. (3) The significantly enriched and increased signaling pathways screened were the 'arachidonic acid metabolic pathway' and the 'phagosomal pathway', which both showed a decreasing trend after drug administration. (4) Based on the causal relationship between different OTUs and the UC model/PE&AFWE administration, screening for directly relevant OTU networks, the UC group was found to directly affect OTU69, followed by a cascade of effects on OTU12, OTU121, OTU93, and OTU7, which may be the pathway of action that initiated the pathological changes in normal mice. (5) We identified a causal relationship between common differentially expressed OTUs and PE&AFWE and UC in the pre- and post-PE&AFWE-treated groups. Thereby, we learned that PE&AFWE can directly affect OTU90, after which it inhibits UC, inhibiting the activity of arachidonic acid metabolic pathway by affecting OTU118, which in turn inhibits the colonization of gut microbiota by OTU93 and OTU7. (6) Histopathological observation and scoring (HS) of the colon showed that there was a significant difference between the model group and the control group (p < 0.001), and that there was a significant recovery in both the sulfasalazine (SASP)and the PE&AFWE groups after the administration of the drug (p < 0.0001).

CONCLUSION: We demonstrated causal effects and inflammatory metabolic pathways in gut microbiota dysbiosis and IBD, with five opportunistic pathogens directly contributing to IBD. PE&AFWE reduced the abundance of proteobacteria in the gut microbiota, and histopathology showed significant improvement.}, } @article {pmid38664737, year = {2024}, author = {Dang, YR and Cha, QQ and Liu, SS and Wang, SY and Li, PY and Li, CY and Wang, P and Chen, XL and Tian, JW and Xin, Y and Chen, Y and Zhang, YZ and Qin, QL}, title = {Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {77}, pmid = {38664737}, issn = {2049-2618}, mesh = {*Polysaccharides/metabolism ; *Seawater/microbiology ; *Phytoplankton/metabolism/genetics ; *Nutrients/metabolism ; *Peptidoglycan/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Metagenomics ; Microbiota ; }, abstract = {BACKGROUND: The deep sea represents the largest marine ecosystem, driving global-scale biogeochemical cycles. Microorganisms are the most abundant biological entities and play a vital role in the cycling of organic matter in such ecosystems. The primary food source for abyssal biota is the sedimentation of particulate organic polymers. However, our knowledge of the specific biopolymers available to deep-sea microbes remains largely incomplete. One crucial rate-limiting step in organic matter cycling is the depolymerization of particulate organic polymers facilitated by extracellular enzymes (EEs). Therefore, the investigation of active EEs and the microbes responsible for their production is a top priority to better understand the key nutrient sources for deep-sea microbes.

RESULTS: In this study, we conducted analyses of extracellular enzymatic activities (EEAs), metagenomics, and metatranscriptomics from seawater samples of 50-9305 m from the Mariana Trench. While a diverse array of microbial groups was identified throughout the water column, only a few exhibited high levels of transcriptional activities. Notably, microbial populations actively transcribing EE genes involved in biopolymer processing in the abyssopelagic (4700 m) and hadopelagic zones (9305 m) were primarily associated with the class Actinobacteria. These microbes actively transcribed genes coding for enzymes such as cutinase, laccase, and xyloglucanase which are capable of degrading phytoplankton polysaccharides as well as GH23 peptidoglycan lyases and M23 peptidases which have the capacity to break down peptidoglycan. Consequently, corresponding enzyme activities including glycosidases, esterase, and peptidases can be detected in the deep ocean. Furthermore, cell-specific EEAs increased at 9305 m compared to 4700 m, indicating extracellular enzymes play a more significant role in nutrient cycling in the deeper regions of the Mariana Trench.

CONCLUSIONS: Transcriptomic analyses have shed light on the predominant microbial population actively participating in organic matter cycling in the deep-sea environment of the Mariana Trench. The categories of active EEs suggest that the complex phytoplankton polysaccharides (e.g., cutin, lignin, and hemicellulose) and microbial peptidoglycans serve as the primary nutrient sources available to deep-sea microbes. The high cell-specific EEA observed in the hadal zone underscores the robust polymer-degrading capacities of hadal microbes even in the face of the challenging conditions they encounter in this extreme environment. These findings provide valuable new insights into the sources of nutrition, the key microbes, and the EEs crucial for biopolymer degradation in the deep seawater of the Mariana Trench. Video Abstract.}, } @article {pmid38664402, year = {2024}, author = {Zheng, Y and Cao, X and Zhou, Y and Ma, S and Wang, Y and Li, Z and Zhao, D and Yang, Y and Zhang, H and Meng, C and Xie, Z and Sui, X and Xu, K and Li, Y and Zhang, CS}, title = {Purines enrich root-associated Pseudomonas and improve wild soybean growth under salt stress.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3520}, pmid = {38664402}, issn = {2041-1723}, support = {32101289//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32171948//National Natural Science Foundation of China (National Science Foundation of China)/ ; ZR2021QD026//Natural Science Foundation of Shandong Province (Shandong Provincial Natural Science Foundation)/ ; }, mesh = {*Pseudomonas/genetics/metabolism ; *Glycine max/microbiology/metabolism/genetics ; *Plant Roots/microbiology/metabolism ; *Rhizosphere ; Microbiota/drug effects ; Purines/metabolism/pharmacology ; Salt Stress/genetics ; Chemotaxis/genetics ; Salt Tolerance/genetics ; Soil Microbiology ; Xanthine/metabolism ; Bacterial Proteins/metabolism/genetics ; }, abstract = {The root-associated microbiota plays an important role in the response to environmental stress. However, the underlying mechanisms controlling the interaction between salt-stressed plants and microbiota are poorly understood. Here, by focusing on a salt-tolerant plant wild soybean (Glycine soja), we demonstrate that highly conserved microbes dominated by Pseudomonas are enriched in the root and rhizosphere microbiota of salt-stressed plant. Two corresponding Pseudomonas isolates are confirmed to enhance the salt tolerance of wild soybean. Shotgun metagenomic and metatranscriptomic sequencing reveal that motility-associated genes, mainly chemotaxis and flagellar assembly, are significantly enriched and expressed in salt-treated samples. We further find that roots of salt stressed plants secreted purines, especially xanthine, which induce motility of the Pseudomonas isolates. Moreover, exogenous application for xanthine to non-stressed plants results in Pseudomonas enrichment, reproducing the microbiota shift in salt-stressed root. Finally, Pseudomonas mutant analysis shows that the motility related gene cheW is required for chemotaxis toward xanthine and for enhancing plant salt tolerance. Our study proposes that wild soybean recruits beneficial Pseudomonas species by exudating key metabolites (i.e., purine) against salt stress.}, } @article {pmid38664270, year = {2024}, author = {Cadena, S and Cerqueda-García, D and Uribe-Flores, MM and Ramírez, SI}, title = {Metagenomic profiling of halites from the Atacama Desert: an extreme environment with natural perchlorate does not promote high diversity of perchlorate reducing microorganisms.}, journal = {Extremophiles : life under extreme conditions}, volume = {28}, number = {2}, pages = {25}, pmid = {38664270}, issn = {1433-4909}, support = {377887//Consejo Nacional de Humanidades Ciencias y Tecnologías/ ; 570049-2022-2023//Consejo Nacional de Humanidades Ciencias y Tecnologías/ ; 88//Consejo de Ciencia y Tecnología del Estado de Morelos/ ; }, mesh = {*Perchlorates/metabolism ; *Oxidation-Reduction ; *Desert Climate ; *Extreme Environments ; Metagenome ; Microbiota ; }, abstract = {We surveyed the presence of perchlorate-reducing microorganisms in available metagenomic data of halite environments from the Atacama Desert, an extreme environment characterized by high perchlorate concentrations, intense ultraviolet radiation, saline and oxidizing soils, and severe desiccation. While the presence of perchlorate might suggest a broad community of perchlorate reducers or a high abundance of a dominant taxa, our search reveals a scarce presence. In fact, we identified only one halophilic species, Salinibacter sp003022435, carrying the pcrA and pcrC genes, represented in low abundance. Moreover, we also discovered some napA genes and organisms carrying the nitrate reductase nasB gene, which hints at the possibility of cryptic perchlorate reduction occurring in these ecosystems. Our findings contribute with the knowledge of perchlorate reduction metabolism potentially occurring in halites from Atacama Desert and point towards promising future research into the perchlorate-reducing mechanism in Salinibacter, a common halophilic bacterium found in hypersaline ecosystems, whose metabolic potential remains largely unknown.}, } @article {pmid38664180, year = {2024}, author = {Knorr, J and Lone, Z and Werneburg, G and Adler, A and Agudelo, J and Suryavanshi, M and Campbell, RA and Ericson, K and Qiu, H and Bajic, P and Haber, GP and Weight, CJ and Ahern, PP and Almassi, N and Miller, AW and Lee, BH}, title = {An exploratory study investigating the impact of the bladder tumor microbiome on Bacillus Calmette Guerin (BCG) response in non-muscle invasive bladder cancer.}, journal = {Urologic oncology}, volume = {42}, number = {9}, pages = {291.e1-291.e11}, doi = {10.1016/j.urolonc.2024.04.011}, pmid = {38664180}, issn = {1873-2496}, mesh = {Humans ; *Urinary Bladder Neoplasms/microbiology/pathology/drug therapy ; *BCG Vaccine/therapeutic use ; Male ; Female ; *Microbiota ; Aged ; Retrospective Studies ; Middle Aged ; Neoplasm Invasiveness ; Adjuvants, Immunologic/therapeutic use ; Treatment Outcome ; Administration, Intravesical ; Non-Muscle Invasive Bladder Neoplasms ; }, abstract = {PURPOSE: Intravesical Bacillus Calmette-Guerin (BCG) is standard of care for intermediate- and high-risk non-muscle invasive bladder cancer (NMIBC). The effect of the bladder microbiome on response to BCG is unclear. We sought to characterize the microbiome of bladder tumors in BCG-responders and non-responders and identify potential mechanisms that drive treatment response.

MATERIALS AND METHODS: Patients with archival pre-treatment biopsy samples (2012-2018) were identified retrospectively. Prospectively, urine and fresh tumor samples were collected from individuals with high-risk NMIBC (2020-2023). BCG response was defined as tumor-free 2 years from induction therapy. Extracted DNA was sequenced for 16S rRNA and shotgun metagenomics. Primary outcomes were species richness (α-diversity) and microbial composition (β-diversity). Paired t-tests were performed for α-diversity (Observed species/Margalef). Statistical analysis for β-diversity (weighted and unweighted UniFrac distances, weighted Bray-Curtis dissimilarity) were conducted through Permanova, with 999 permutations.

RESULTS: Microbial species richness (P < 0.001) and composition (P = 0.001) differed between BCG responders and non-responders. Lactobacillus spp. were significantly enriched in BCG-responders. Shotgun metagenomics identified possible mechanistic pathways such as assimilatory sulfate reduction.

CONCLUSION: A compositional difference exists in the tumor microbiome of BCG responders and non-responders with Lactobacillus having increased abundance in BCG responders.}, } @article {pmid38663623, year = {2024}, author = {Liang, X and Zhu, Y and Liu, H and Xie, Z and Li, G and Li, D and Liang, Y and Peng, C}, title = {Nitrogen-fixing cyanobacteria enhance microbial carbon utilization by modulating the microbial community composition in paddy soils of the Mollisols region.}, journal = {The Science of the total environment}, volume = {929}, number = {}, pages = {172609}, doi = {10.1016/j.scitotenv.2024.172609}, pmid = {38663623}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Carbon/metabolism ; *Cyanobacteria/metabolism ; *Microbiota ; China ; *Oryza ; *Soil/chemistry ; Fertilizers ; Nitrogen Fixation ; Nitrogen/metabolism ; Agriculture/methods ; }, abstract = {Nitrogen-fixing cyanobacteria (NFC) are photosynthetic prokaryotic microorganisms capable of nitrogen fixation. They can be used as biofertilizers in paddy fields, thereby improving the rice tillering capacity and yield. To reveal the microbiological mechanisms by which nitrogen-fixing cyanobacteria alter soil carbon storage, we conducted a field experiment using NFC as a partial substitute for nitrogen fertilizer in paddy fields in the Sanjiang Plain of Northeast China's Mollisols region. Using metagenomic sequencing technology and Biolog Ecoplate™ carbon matrix metabolism measurements, we explored the changes in the soil microbial community structure and carbon utilization in paddy fields. The results indicated that the replacement of nitrogen fertilizer with NFC predisposed the soil microbial community to host a great number of copiotrophic bacterial taxa, and Proteobacteria and Actinobacteria were closely associated with the metabolism of soil carbon sources. Moreover, through co-occurrence network analysis, we found that copiotrophic bacteria clustered in modules that were positively correlated with the metabolic level of carbon sources. The addition of NFC promoted the growth of copiotrophic bacteria, which increased the carbon utilization level of soil microorganisms, improved the diversity of the microbial communities, and had a potential impact on the soil carbon stock. The findings of this study are helpful for assessing the impact of NFC on the ecological function of soil microbial communities in paddy fields in the black soil area of Northeast China, which is highly important for promoting sustainable agricultural development and providing scientific reference for promoting the use of algal-derived nitrogen fertilizers.}, } @article {pmid38663298, year = {2024}, author = {Rout, AK and Dixit, S and Tripathy, PS and Rout, SS and Parida, SN and Parida, PK and Sarkar, DJ and Kumar Das, B and Singh, AK and Behera, BK}, title = {Metagenomic landscape of sediments of river Ganga reveals microbial diversity, potential plastic and xenobiotic degradation enzymes.}, journal = {Journal of hazardous materials}, volume = {471}, number = {}, pages = {134377}, doi = {10.1016/j.jhazmat.2024.134377}, pmid = {38663298}, issn = {1873-3336}, mesh = {*Geologic Sediments/microbiology ; *Rivers/microbiology/chemistry ; *Biodegradation, Environmental ; *Bacteria/genetics/enzymology ; Biodiversity ; Xenobiotics/metabolism ; Water Pollutants, Chemical/analysis ; India ; Plastics ; Metagenome ; Metagenomics ; Benzhydryl Compounds ; }, abstract = {The Ganga is the largest river in India, serves as a lifeline for agriculture, drinking water, and religious rites. However, it became highly polluted due to the influx of industrial wastes and untreated sewages, leading to the decline of aquatic biodiversity. This study investigated the microbial diversity and plastic-xenobiotic degrading enzymes of six sediment metagenomes of river Ganga at Prayagraj (RDG, TSG, SDG) and Devprayag (KRG, BNG, BRG). The water quality parameters, higher values of BOD (1.8-3.7 ppm), COD (23-29.2 ppm) and organic carbon (0.18-0.51%) were recorded at Prayagraj. Comparative analysis of microbial community structure between Prayagraj and Devprayag revealed significant differences between Bacteroidetes and Firmicutes, which emerging as the predominant bacterial phyla across six sediment samples. Notably, their prevalence was highest in the BRG samples. Furthermore, 25 OTUs at genus level were consistent across all six samples. Alpha diversity exhibited minimal variation among samples, while beta diversity indicated an inverse relationship between species richness and diversity. Co-occurrence network analysis established that genera from the same and different groups of phyla show positive co-relations with each other. Thirteen plastic degrading enzymes, including Laccase, Alkane-1 monooxygenase and Alkane monooxygenase, were identified from six sediment metagenomes of river Ganga, which can degrade non-biodegradable plastic viz. Polyethylene, Polystyrene and Low-density Polyethelene. Further, 18 xenobiotic degradation enzymes were identified for the degradation of Bisphenol, Xylene, Toluene, Polycyclic aromatic hydrocarbon, Styrene, Atrazene and Dioxin etc. This is the first report on the identification of non-biodegradable plastic degrading enzymes from sediment metagenomes of river Ganga, India. The findings of this study would help in pollution abatement and sustainable management of riverine ecosystem.}, } @article {pmid38662518, year = {2024}, author = {Lages da Silva, DH and Marques da Silva, RL and Rios, DL and de Souza, DDG and Aburjaile, F and de Freitas Neto, OC and Camargos Lara, LJ and Dias Araújo, M and Ecco, R}, title = {Intestinal microbiota diversity from broilers with runting and stunting syndrome performed by metagenomics.}, journal = {Avian pathology : journal of the W.V.P.A}, volume = {53}, number = {5}, pages = {408-418}, doi = {10.1080/03079457.2024.2348509}, pmid = {38662518}, issn = {1465-3338}, mesh = {Animals ; *Chickens/microbiology/virology ; *Gastrointestinal Microbiome ; *Poultry Diseases/microbiology/virology ; *Metagenomics ; Brazil/epidemiology ; Dysbiosis/veterinary/microbiology ; Ileum/microbiology ; High-Throughput Nucleotide Sequencing/veterinary ; Growth Disorders/veterinary/microbiology ; Bacteria/isolation & purification/classification/genetics ; }, abstract = {Runting and stunting syndrome (RSS) is an enteric viral disease in commercial poultry that directly affects gut health; however, its influence on gut microbiota remains unknown. This study aimed to investigate the compositional changes in the bacterial community of the ileum of 7-day-old broiler chicks naturally affected or not affected by RSS, using next-generation sequencing (NGS) technology. Twenty-one samples were obtained from the ileal contents and mucosa of 11 chicks with RSS and 10 healthy chicks, raised in a dark house system located on a farm in the state of Minas Gerais, Brazil. The results revealed overall changes in the gut microbiota of the chicks with RSS, including a decrease in microbial richness and diversity. In particular, there was a decrease in Lactobacillus and an increase in Candidatus Arthromitus and Clostridium sensu stricto 1. These results indicate a relationship between viral infection and the gut microbial composition, which can cause gut dysbiosis and may influence inflammation in this organ.RESEARCH HIGHLIGHTS RSS causes dysbiosis of the gut microbiota of the ilea of chicks.A difference was found in gut microbiota between chicks with or without RSS.Candidatus Arthromitus was predominant in chicks with RSS.Clostridium sensu stricto 1 was strictly associated with chicks with RSS.}, } @article {pmid38662153, year = {2024}, author = {Choudhary, G and Kumari, S and Anu, K and Devi, S}, title = {Deciphering the microbial communities of alkaline hot spring in Panamik, Ladakh, India using a high-throughput sequencing approach.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {55}, number = {2}, pages = {1465-1476}, pmid = {38662153}, issn = {1678-4405}, mesh = {*Hot Springs/microbiology ; India ; *Bacteria/genetics/classification/isolation & purification ; *High-Throughput Nucleotide Sequencing ; *Microbiota ; *Archaea/genetics/classification/isolation & purification ; *Metagenomics ; Phylogeny ; Biodiversity ; }, abstract = {Due to their distinctive physicochemical characteristics, hot springs are extremely important. The whole genome metagenomic sequencing technology can be utilized to analyze the diverse microbial community that thrives in this habitat due to the particular selection pressure that prevails there. The current investigation emphasizes on culture-independent metagenomic study of the Panamik hot spring and its nearby areas from Ladakh, India. Based on different diversity indices, sequence analysis of the soil reservoir showed higher species richness and diversity in comparison to water and sediment samples. The mineral content and various physicochemical pameters like temperature, pH had an impact on the composition of the microbial community of the geothermal springs. The phyla Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacter, Firmicutes, and Verrucomicrobia in bacterial domain dominate the thermos-alkaline spring at Panamik in different concentrations. Economically significant microbes from the genera Actinobacter, Thermosynechoccus, Candidatus Solibacter, Chthoniobacter, Synechoccus, Pseudomonas and Sphingomonas, were prevalent in hot spring. In the archaeal domain, the most dominant phylum and genera were Euryarchaeota and Thermococcus in all the samples. Further, the most abundant species were Methanosarcina barkeri, Nitrospumilus maritimus and Methanosarcina acetivorans. The present study which only examined one of the several thermal springs present in the Himalayan geothermal area, should be regarded as a preliminary investigation of the microbiota that live in the hot springs on these remote areas. These findings suggest that further investigations should be undertaken to characterize the ecosystems of the Panamik hot spring, which serve as a repository for unidentified microbial lineages.}, } @article {pmid38661445, year = {2024}, author = {Sánchez-Terrón, G and Martínez, R and Morcuende, D and Caballero, V and Estévez, M}, title = {Pomegranate supplementation alleviates dyslipidemia and the onset of non-alcoholic fatty liver disease in Wistar rats by shifting microbiota and producing urolithin-like microbial metabolites.}, journal = {Food & function}, volume = {15}, number = {14}, pages = {7348-7363}, doi = {10.1039/d4fo00688g}, pmid = {38661445}, issn = {2042-650X}, mesh = {Animals ; *Pomegranate/chemistry ; *Non-alcoholic Fatty Liver Disease/drug therapy/metabolism ; *Rats, Wistar ; Rats ; Male ; *Dietary Supplements ; *Dyslipidemias/drug therapy ; *Fructose ; *Coumarins/pharmacology ; Gastrointestinal Microbiome/drug effects ; Hydrolyzable Tannins/pharmacology ; Liver/metabolism/drug effects ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD), obesity and related chronic diseases are major non-communicable diseases with high mortality rates worldwide. While dietary sugars are known to be responsible for insulin resistance and metabolic syndrome (MetS), the underlying pathophysiological effects of sustained fructose consumption require further elucidation. We hypothesize that certain bioactive compounds (i.e. punicalagin and ellagic acid) from dietary pomegranate could counteract the harmful effects of sustained fructose consumption in terms of obesity and liver damage. The present study aimed to elucidate both the molecular mechanisms involved in the pathophysiology associated with fructose intake and the effect of a punicalagin-rich commercial pomegranate dietary supplement (P) used as a nutritional strategy to alleviate fructose-induced metabolic impairments. Thus, nineteen Wistar rats fed on a basal commercial feed were supplemented with either 30% (w/v) fructose in drinking water (F; n = 7) or 30% (w/v) fructose solution plus 0.2% (w/v) P (F + P; n = 6) for 10 weeks. The results were compared to those from a control group fed on the basal diet and provided with drinking water (C; n = 6). Body weight and energy intake were registered weekly. P supplementation decreased fat depots, counteracted the dyslipidemia caused by F and improved markers of liver injury including steatosis. The study of the microbiota by metagenomics and urine by untargeted MS-based metabolomics revealed microbial metabolites from P that may be responsible for these health benefits.}, } @article {pmid38661357, year = {2023}, author = {Chen, XX and Zeng, MX and Cai, D and Zhou, HH and Wang, YJ and Liu, Z}, title = {Correlation between APOE4 gene and gut microbiota in Alzheimer's disease.}, journal = {Beneficial microbes}, volume = {14}, number = {4}, pages = {349-360}, doi = {10.1163/18762891-20220116}, pmid = {38661357}, issn = {1876-2891}, mesh = {Aged ; Aged, 80 and over ; Female ; Humans ; Male ; Middle Aged ; *Alzheimer Disease/microbiology/genetics ; *Apolipoprotein E4/genetics ; *Bacteria/genetics/classification/isolation & purification ; Case-Control Studies ; China ; Dysbiosis/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; United States ; }, abstract = {Gut microbiota (GM) dysbiosis has been increasingly associated with Alzheimer's disease (AD). However, the association between APOE4, the most common genetic risk factor for sporadic AD, and GM in AD remains unclear. In this study, we conducted a comparative analysis of the GM of participants from China and the USA, with and without APOE4 genes and with or without AD (67 AD cases, 67 control cases). Our results revealed that the GM alpha diversity was not different between groups (AD_APOE4, Control_APOE4, AD_non-APOE4, and Control_non-APOE4) (419.031 ± 143.631 vs 391.091 ± 126.081, 351.086 ± 169.174 and 386.089 ± 177.200, respectively. P > 0.05). Interestingly, individuals in the AD_APOE4 group had different bacterial compositions and bacterial biomarkers. The Kruskal-Wallis rank sum test indicated that the abundances of many bacterial species in the AD_APOE4 patients differed from those in control individuals, including decreases in unclassified_g__Escherichia-Shigella (1.763 ± 6.73, 4.429 ± 11.13, 8.245 ± 16.55, and 5.69 ± 13.91 in four groups, respectively; P < 0.05), and unclassified_g_Clostridium_sensu_stricto_1 (0.1519 ± 0.348, 2.502 ± 5.913, 0.5146 ± 0.9487, 1.063 ± 3.428 in four groups, respectively; P < 0.05), and increases in gut_metagenome_g_Faecalibacterium (2.885 ± 4.47, 2.174 ± 3.957, 0.5765 ± 1.784, 1.582 ± 2.92 in four groups, respectively. P < 0.01) and unclassified_g_Bacteroides (3.875 ± 3.738, 2.47 ± 2.748, 2.046 ± 3.674, 3.206 ± 3.446 in four groups, respectively; P < 0.05). In the KEGG pathway level 2 analysis, we identified three significant differences in relative abundances of predicted functions between AD_APOE4 and AD_non-APOE4_carrier groups: neurodegenerative diseases (0.0007 ± 0.0005 vs 0.0009 ± 0.0004; P < 0.01), metabolism (0.0240 ± 0.0003 vs 0.0250 ± 0.0003; P < 0.05), and biosynthesis of other secondary metabolites (0.0094 ± 0.0002 vs 0.0090 ± 0.0002; P < 0.05). Receiver operating characteristic curves further demonstrated an area under the curve (AUC) of 0.74 for the discrimination of AD_APOE4_carrier and AD_non-APOE4_carrier individuals.}, } @article {pmid38661344, year = {2024}, author = {Phan, J and Calvo, DC and Nair, D and Jain, S and Montagne, T and Dietsche, S and Blanchard, K and Treadwell, S and Adams, J and Krajmalnik-Brown, R}, title = {Precision synbiotics increase gut microbiome diversity and improve gastrointestinal symptoms in a pilot open-label study for autism spectrum disorder.}, journal = {mSystems}, volume = {9}, number = {5}, pages = {e0050324}, pmid = {38661344}, issn = {2379-5077}, mesh = {Humans ; *Autism Spectrum Disorder/microbiology/diet therapy ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; Pilot Projects ; Child ; *Synbiotics/administration & dosage ; Adult ; Adolescent ; Child, Preschool ; Young Adult ; Probiotics/administration & dosage/therapeutic use/pharmacology ; }, abstract = {UNLABELLED: The efficacy of prebiotics and probiotics (synbiotics when combined) to improve symptoms associated with autism spectrum disorder (ASD) has shown considerable inter-study variation, likely due to the complex, heterogeneous nature of the disorder and its associated behavioral, developmental, and gastrointestinal symptoms. Here, we present a precision synbiotic supplementation study in 296 children and adults diagnosed with ASD versus 123 age-matched neurotypical controls. One hundred seventy ASD participants completed the study. Baseline and post-synbiotic assessment of ASD and gastrointestinal (GI) symptoms and deep metagenomic sequencing were performed. Within the ASD cohort, there were significant differences in microbes between subpopulations based on the social responsiveness scale (SRS2) survey (Prevotella spp., Bacteroides, Fusicatenibacter, and others) and gluten and dairy-free diets (Bifidobacterium spp., Lactococcus, Streptococcus spp., and others). At the baseline, the ASD cohort maintained a lower taxonomic alpha diversity and significant differences in taxonomic composition, metabolic pathways, and gene families, with a greater proportion of potential pathogens, including Shigella, Klebsiella, and Clostridium, and lower proportions of beneficial microbes, including Faecalibacterium compared to controls. Following the 3-month synbiotic supplementation, the ASD cohort showed increased taxonomic alpha diversity, shifts in taxonomy and metabolic pathway potential, and improvements in some ASD-related symptoms, including a significant reduction in GI discomfort and overall improved language, comprehension, cognition, thinking, and speech. However, the open-label study design may include some placebo effects. In summary, we found that precision synbiotics modulated the gut microbiome and could be used as supplementation to improve gastrointestinal and ASD-related symptoms.

IMPORTANCE: Autism spectrum disorder (ASD) is prevalent in 1 out of 36 children in the United States and contributes to health, financial, and psychological burdens. Attempts to identify a gut microbiome signature of ASD have produced varied results. The limited pre-clinical and clinical population sizes have hampered the success of these trials. To understand the microbiome associated with ASD, we employed whole metagenomic shotgun sequencing to classify microbial composition and genetic functional potential. Despite being one of the most extensive ASD post-synbiotic assessment studies, the results highlight the complexity of performing such a case-control supplementation study in this population and the potential for a future therapeutic approach in ASD.}, } @article {pmid38659188, year = {2024}, author = {Pérez-Castillo, ÍM and Sabag-Daigle, A and López-Chicharro, J and Mihic, N and Rueda, R and Bouzamondo, H}, title = {The athlete gut microbiota: state of the art and practical guidance.}, journal = {Beneficial microbes}, volume = {15}, number = {2}, pages = {97-126}, doi = {10.1163/18762891-bja00007}, pmid = {38659188}, issn = {1876-2891}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Athletes ; *Diet ; Exercise/physiology ; Bacteria/classification/metabolism/genetics/isolation & purification ; Fatty Acids, Volatile/metabolism ; }, abstract = {The gut microbiota has been proposed to grant the athlete a metabolic advantage that might be key when optimising performance. While a taxonomic core set of microorganisms characterising the athlete's gut microbiota has not been delineated, some compositional features might be associated with improved metabolic efficiency, which appears to be driven by the production of bacterial metabolites, such as short-chain fatty acids. Not only long-term exercise but also dietary patterns associated with high-level sports practice contribute to this microbial environment, yet isolating the impact of individual dietary components is challenging. The present review synthetises the available evidence on the compositional aspects of the athlete's gut microbiota, discusses mechanisms involved in the bidirectional association between exercise and the gut environment, and evaluates the role of athletes' diet in this interplay. Additionally, a practical approach to indicators commonly reported in metagenomic and metabolomic analyses is provided to explore how these insights can translate to support dietary protocols.}, } @article {pmid38658858, year = {2024}, author = {Liu, C and Liu, F and Nie, D and Xiao, Y and Wu, W and Jia, Y and Jin, L and Qiao, N and Cai, K and Ru, S and Liu, X and Song, Y and Xu, J and Cao, L and Gui, S}, title = {Gut microbiota composition and metabolic characteristics in patients with Craniopharyngioma.}, journal = {BMC cancer}, volume = {24}, number = {1}, pages = {521}, pmid = {38658858}, issn = {1471-2407}, mesh = {Humans ; *Craniopharyngioma/metabolism ; *Gastrointestinal Microbiome ; Male ; Female ; Adult ; *Pituitary Neoplasms/metabolism/microbiology ; *Feces/microbiology ; Middle Aged ; Case-Control Studies ; Young Adult ; Adolescent ; Metabolomics/methods ; Metagenomics/methods ; Metabolome ; }, abstract = {BACKGROUND: Emerging evidence suggests that the gut microbiota is associated with various intracranial neoplastic diseases. It has been observed that alterations in the gut microbiota are present in gliomas, meningiomas, and pituitary neuroendocrine tumors (Pit-NETs). However, the correlation between gut microbiota and craniopharyngioma (CP), a rare embryonic malformation tumor in the sellar region, has not been previously mentioned. Consequently, this study aimed to investigate the gut microbiota composition and metabolic patterns in CP patients, with the goal of identifying potential therapeutic approaches.

METHODS: We enrolled 15 medication-free and non-operated patients with CP and 15 healthy controls (HCs), conducting sequential metagenomic and metabolomic analyses on fecal samples to investigate changes in the gut microbiota of CP patients.

RESULTS: The composition of gut microbiota in patients with CP compared to HCs show significant discrepancies at both the genus and species levels. The CP group exhibits greater species diversity. And the metabolic patterns between the two groups vary markedly.

CONCLUSIONS: The gut microbiota composition and metabolic patterns in patients with CP differ significantly from the healthy population, presenting potential new therapeutic opportunities.}, } @article {pmid38658841, year = {2024}, author = {Jeong, S and Liao, YT and Tsai, MH and Wang, YK and Wu, IC and Liu, CJ and Wu, MS and Chan, TS and Chen, MY and Hu, PJ and Kao, WY and Liu, HC and Tsai, MJ and Liu, CY and Chang, CC and Wu, DC and Hsu, YH}, title = {Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {139}, pmid = {38658841}, issn = {1471-2180}, mesh = {Humans ; *Stomach Neoplasms/microbiology ; Male ; Female ; Middle Aged ; *Gastritis/microbiology ; *Feces/microbiology ; *Metagenome ; *Bacteria/genetics/classification/isolation & purification ; Aged ; Gastrointestinal Microbiome/genetics ; Adult ; }, abstract = {BACKGROUND: Gastric cancer is one of the global health concerns. A series of studies on the stomach have confirmed the role of the microbiome in shaping gastrointestinal diseases. Delineation of microbiome signatures to distinguish chronic gastritis from gastric cancer will provide a non-invasive preventative and treatment strategy. In this study, we performed whole metagenome shotgun sequencing of fecal samples to enhance the detection of rare bacterial species and increase genome sequence coverage. Additionally, we employed multiple bioinformatics approaches to investigate the potential targets of the microbiome as an indicator of differentiating gastric cancer from chronic gastritis.

RESULTS: A total of 65 patients were enrolled, comprising 33 individuals with chronic gastritis and 32 with gastric cancer. Within each group, the chronic gastritis group was sub-grouped into intestinal metaplasia (n = 15) and non-intestinal metaplasia (n = 18); the gastric cancer group, early stage (stages 1 and 2, n = 13) and late stage (stages 3 and 4, n = 19) cancer. No significant differences in alpha and beta diversities were detected among the patient groups. However, in a two-group univariate comparison, higher Fusobacteria abundance was identified in phylum; Fusobacteria presented higher abundance in gastric cancer (LDA scored 4.27, q = 0.041 in LEfSe). Age and sex-adjusted MaAsLin and Random Forest variable of importance (VIMP) analysis in species provided meaningful features; Bacteria_caccae was the most contributing species toward gastric cancer and late-stage cancer (beta:2.43, se:0.891, p:0.008, VIMP score:2.543). In contrast, Bifidobacterium_longum significantly contributed to chronic gastritis (beta:-1.8, se:0.699, p:0.009, VIMP score:1.988). Age, sex, and BMI-adjusted MasAsLin on metabolic pathway analysis showed that GLCMANNANAUT-PWY degradation was higher in gastric cancer and one of the contributing species was Fusobacterium_varium.

CONCLUSION: Microbiomes belonging to the pathogenic phylum Fusobacteria and species Bacteroides_caccae and Streptococcus_anginosus can be significant targets for monitoring the progression of gastric cancer. Whereas Bifidobacterium_longum and Lachnospiraceae_bacterium_5_1_63FAA might be protection biomarkers against gastric cancer.}, } @article {pmid38658654, year = {2024}, author = {Han, G and Huang, T and Liu, X and Liu, R}, title = {Bacteriophage EPP-1, a potential antibiotic alternative for controlling edwardsiellosis caused by Edwardsiella piscicida while mitigating drug-resistant gene dissemination.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {9399}, pmid = {38658654}, issn = {2045-2322}, support = {42377120//the National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Zebrafish/microbiology ; *Edwardsiella/genetics ; *Enterobacteriaceae Infections/microbiology/veterinary/therapy ; *Bacteriophages/genetics/physiology ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Gastrointestinal Microbiome ; Phage Therapy/methods ; RNA, Ribosomal, 16S/genetics ; Fish Diseases/microbiology/therapy/prevention & control ; Thiamphenicol/*analogs & derivatives/pharmacology ; Aquaculture/methods ; }, abstract = {Edwardsiella piscicida causes significant economic losses to the aquaculture industry worldwide. Phage-based biocontrol methods are experiencing a renaissance because of the spread of drug-resistant genes and bacteria resulting from the heavy use of antibiotics. Here, we showed that the novel Edwardsiella phage EPP-1 could achieve comparable efficacy to florfenicol using a zebrafish model of Edwardsiella piscicida infection and could reduce the content of the floR resistance gene in zebrafish excreta. Specifically, phage EPP-1 inhibited bacterial growth in vitro and significantly improved the zebrafish survival rate in vivo (P = 0.0035), achieving an efficacy comparable to that of florfenicol (P = 0.2304). Notably, integrating the results of 16S rRNA sequencing, metagenomic sequencing, and qPCR, although the effects of phage EPP-1 converged with those of florfenicol in terms of the community composition and potential function of the zebrafish gut microbiota, it reduced the floR gene content in zebrafish excreta and aquaculture water. Overall, our study highlights the feasibility and safety of phage therapy for edwardsiellosis control, which has profound implications for the development of antibiotic alternatives to address the antibiotic crisis.}, } @article {pmid38658578, year = {2024}, author = {Pedrazzoli, E and Demozzi, M and Visentin, E and Ciciani, M and Bonuzzi, I and Pezzè, L and Lucchetta, L and Maule, G and Amistadi, S and Esposito, F and Lupo, M and Miccio, A and Auricchio, A and Casini, A and Segata, N and Cereseto, A}, title = {CoCas9 is a compact nuclease from the human microbiome for efficient and precise genome editing.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3478}, pmid = {38658578}, issn = {2041-1723}, support = {R01 CA230551/CA/NCI NIH HHS/United States ; U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {*Gene Editing/methods ; Humans ; *CRISPR-Cas Systems ; Animals ; Mice ; *Microbiota/genetics ; Dependovirus/genetics ; CRISPR-Associated Protein 9/metabolism/genetics ; RNA, Guide, CRISPR-Cas Systems/genetics/metabolism ; Retina/metabolism ; Clostridiales/genetics/enzymology ; HEK293 Cells ; Genetic Vectors/metabolism/genetics ; }, abstract = {The expansion of the CRISPR-Cas toolbox is highly needed to accelerate the development of therapies for genetic diseases. Here, through the interrogation of a massively expanded repository of metagenome-assembled genomes, mostly from human microbiomes, we uncover a large variety (n = 17,173) of type II CRISPR-Cas loci. Among these we identify CoCas9, a strongly active and high-fidelity nuclease with reduced molecular size (1004 amino acids) isolated from an uncultivated Collinsella species. CoCas9 is efficiently co-delivered with its sgRNA through adeno associated viral (AAV) vectors, obtaining efficient in vivo editing in the mouse retina. With this study we uncover a collection of previously uncharacterized Cas9 nucleases, including CoCas9, which enriches the genome editing toolbox.}, } @article {pmid38657605, year = {2024}, author = {Su, Q and Lau, RI and Liu, Q and Li, MKT and Yan Mak, JW and Lu, W and Lau, ISF and Lau, LHS and Yeung, GTY and Cheung, CP and Tang, W and Liu, C and Ching, JYL and Cheong, PK and Chan, FKL and Ng, SC}, title = {The gut microbiome associates with phenotypic manifestations of post-acute COVID-19 syndrome.}, journal = {Cell host & microbe}, volume = {32}, number = {5}, pages = {651-660.e4}, doi = {10.1016/j.chom.2024.04.005}, pmid = {38657605}, issn = {1934-6069}, mesh = {Humans ; *Gastrointestinal Microbiome ; *COVID-19/microbiology ; *Post-Acute COVID-19 Syndrome ; Male ; *Phenotype ; Female ; *Machine Learning ; *SARS-CoV-2 ; Middle Aged ; Adult ; Bacteria/classification/isolation & purification/genetics ; Aged ; Feces/microbiology/virology ; Cohort Studies ; Longitudinal Studies ; }, abstract = {The mechanisms underlying the many phenotypic manifestations of post-acute COVID-19 syndrome (PACS) are poorly understood. Herein, we characterized the gut microbiome in heterogeneous cohorts of subjects with PACS and developed a multi-label machine learning model for using the microbiome to predict specific symptoms. Our processed data covered 585 bacterial species and 500 microbial pathways, explaining 12.7% of the inter-individual variability in PACS. Three gut-microbiome-based enterotypes were identified in subjects with PACS and associated with different phenotypic manifestations. The trained model showed an accuracy of 0.89 in predicting individual symptoms of PACS in the test set and maintained a sensitivity of 86% and a specificity of 82% in predicting upcoming symptoms in an independent longitudinal cohort of subjects before they developed PACS. This study demonstrates that the gut microbiome is associated with phenotypic manifestations of PACS, which has potential clinical utility for the prediction and diagnosis of PACS.}, } @article {pmid38656971, year = {2024}, author = {Alahdal, H and Almuneef, G and Alkhulaifi, MM and Aldibasi, O and Aljouie, A and Alharbi, O and Almohawes, ZN and Basingab, F and Rejili, M}, title = {Gut microbiota composition in patients with Crohn's disease in Saudi Arabia.}, journal = {PloS one}, volume = {19}, number = {4}, pages = {e0299749}, pmid = {38656971}, issn = {1932-6203}, mesh = {Humans ; *Crohn Disease/microbiology ; *Gastrointestinal Microbiome ; Saudi Arabia/epidemiology ; Male ; Female ; Adult ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; Dysbiosis/microbiology ; Young Adult ; Bacteria/genetics/classification/isolation & purification ; Case-Control Studies ; Quality of Life ; }, abstract = {Crohn's disease (CD) entails intricate interactions with gut microbiome diversity, richness, and composition. The relationship between CD and gut microbiome is not clearly understood and has not been previously characterized in Saudi Arabia. We performed statistical analysis about various factors influencing CD activity and microbiota dysbiosis, including diagnosis, treatment, and its impact on their quality of life as well as high-throughput metagenomic V3-V4 16S rRNA encoding gene hypervariable region of a total of eighty patients with CD, both in its active and inactive state with healthy controls. The results were correlated with the demographic and lifestyle information, which the participants provided via a questionnaire. α-diversity measures indicated lower bacterial diversity and richness in the active and inactive CD groups compared to the control group. Greater dysbiosis was observed in the active CD patients compared to the inactive form of the disease, showed by a reduction in microbial diversity. Specific pathogenic bacteria such as Filifactor, Peptoniphilus, and Sellimonas were identified as characteristic of CD groups. In contrast, anti-inflammatory bacteria like Defluviitalea, Papillibacter, and Petroclostridium were associated with the control group. Among the various factors influencing disease activity and microbiota dysbiosis, smoking emerged as the most significant, with reduced α-diversity and richness for the smokers in all groups, and proinflammatory Fusobacteria was more present (p<0.05). Opposite to the control group, microbial diversity and richness were lower in CD participants of older age compared to younger ones, and male CD participants showed less diversity compared to women participants from the same groups. Our results describe the first report on the relationship between microbiota and Crohn's disease progress in Saudi Arabia, which may provide a theoretical basis for the application of therapeutic methods to regulate gut microbes in CD.}, } @article {pmid38655082, year = {2024}, author = {Thøgersen, MS and Zervas, A and Stougaard, P and Ellegaard-Jensen, L}, title = {Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1358787}, pmid = {38655082}, issn = {1664-302X}, abstract = {The ikaite columns in the Ikka Fjord, SW Greenland, represent a permanently cold and alkaline environment known to contain a rich bacterial diversity. 16S and 18S rRNA gene amplicon and metagenomic sequencing was used to investigate the microbial diversity in the columns and for the first time, the eukaryotic and archaeal diversity in ikaite columns were analyzed. The results showed a rich prokaryotic diversity that varied across columns as well as within each column. Seven different archaeal phyla were documented in multiple locations inside the columns. The columns also contained a rich eukaryotic diversity with 27 phyla representing microalgae, protists, fungi, and small animals. Based on metagenomic sequencing, 25 high-quality MAGs were assembled and analyzed for the presence of genes involved in cycling of nitrogen, sulfur, and phosphorous as well as genes encoding carbohydrate-active enzymes (CAZymes), showing a potentially very bioactive microbial community.}, } @article {pmid38652444, year = {2024}, author = {Li, D and Wang, H and Chen, N and Jiang, H and Chen, N}, title = {Metagenomic analysis of soil microbial communities associated with Poa alpigena Lindm in Haixin Mountain, Qinghai Lake.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {55}, number = {3}, pages = {2423-2435}, pmid = {38652444}, issn = {1678-4405}, support = {WXBSH2021001//Postdoctoral Science Foundation of West Anhui University/ ; WGKQ2021021//The High-level Talent Project of West Anhui University/ ; GXYQ2020127//the Provincial Level Nature Science Foundation of Anhui Education Department/ ; 2022AH010090//Anhui Scientific Research and Innovation Team of Quality Evaluation and Improvement of Traditional Chinese Medicine/ ; KJ2021A0924//Natural Science Research Project of Anhui Provincial Colleges and Universities/ ; }, mesh = {*Soil Microbiology ; *Metagenomics ; *Bacteria/genetics/classification/isolation & purification/metabolism/enzymology ; *Lakes/microbiology ; China ; *Rhizosphere ; Phylogeny ; Microbiota ; Biodiversity ; Metagenome ; }, abstract = {To investigate the impact of Poa alpigena Lindm on rhizosphere and bulk soil microorganisms in Haixin Mountain, Qinghai Lake, this study employed metagenomics technology to analyze the microbial communities of the samples. Results showed that 65 phyla, 139 classes, 278 orders, 596 families, 2376 genera, and 5545 species of soil microorganisms were identified from rhizosphere and bulk soil samples. Additionally, a microbial gene library specific to Poa alpigena Lindm was established for Qinghai Lake. Through α-diversity analysis, the richness and diversity of bulk microorganisms both significantly had a higher value than that in rhizosphere soil. The indicator microorganisms of rhizosphere and bulk soil at class level were Actinobacteria and Alphaproteobacteria, respectively. KEGG pathway analysis indicated that Carotenoid biosynthesis, Starch and sucrose metabolism, Bacterial chemotaxis, MAPK signaling pathway, Terpenoid backbone biosynthesis, and vancomycin resistance were the key differential metabolic pathways of rhizosphere soil microorganisms; in contrast, in bulk soil, the key differential metabolic were Benzoate degradation, Glycolysis gluconeogenesis, Aminobenzoate degradation, ABC transporters, Glyoxylate and dicarboxylate metabolism, oxidative phosphorylation, Degradation of aromatic compounds, Methane metabolism, Pyruvate metabolism and Microbial metabolism diverse environments. Our results indicated that Poa alpigena Lindm rhizosphere soil possessed selectivity for microorganisms in Qinghai Lake Haixin Mountain, and the rhizosphere soil also provided a suitable survival environment for microorganisms.}, } @article {pmid38651930, year = {2024}, author = {Reygner, J and Delannoy, J and Barba-Goudiaby, M-T and Gasc, C and Levast, B and Gaschet, E and Ferraris, L and Paul, S and Kapel, N and Waligora-Dupriet, A-J and Barbut, F and Thomas, M and Schwintner, C and Laperrousaz, B and Corvaïa, N}, title = {Reduction of product composition variability using pooled microbiome ecosystem therapy and consequence in two infectious murine models.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {5}, pages = {e0001624}, pmid = {38651930}, issn = {1098-5336}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Clostridioides difficile ; *Clostridium Infections/therapy/microbiology ; *Disease Models, Animal ; *Fecal Microbiota Transplantation ; *Feces/microbiology ; Bacteria/classification/genetics ; Humans ; Mice, Inbred C57BL ; Female ; }, abstract = {Growing evidence demonstrates the key role of the gut microbiota in human health and disease. The recent success of microbiotherapy products to treat recurrent Clostridioides difficile infection has shed light on its potential in conditions associated with gut dysbiosis, such as acute graft-versus-host disease, intestinal bowel diseases, neurodegenerative diseases, or even cancer. However, the difficulty in defining a "good" donor as well as the intrinsic variability of donor-derived products' taxonomic composition limits the translatability and reproducibility of these studies. Thus, the pooling of donors' feces has been proposed to homogenize product composition and achieve higher taxonomic richness and diversity. In this study, we compared the metagenomic profile of pooled products to corresponding single donor-derived products. We demonstrated that pooled products are more homogeneous, diverse, and enriched in beneficial bacteria known to produce anti-inflammatory short chain fatty acids compared to single donor-derived products. We then evaluated pooled products' efficacy compared to corresponding single donor-derived products in Salmonella and C. difficile infectious mouse models. We were able to demonstrate that pooled products decreased pathogenicity by inducing a structural change in the intestinal microbiota composition. Single donor-derived product efficacy was variable, with some products failing to control disease progression. We further performed in vitro growth inhibition assays of two extremely drug-resistant bacteria, Enterococcus faecium vanA and Klebsiella pneumoniae oxa48, supporting the use of pooled microbiotherapies. Altogether, these results demonstrate that the heterogeneity of donor-derived products is corrected by pooled fecal microbiotherapies in several infectious preclinical models.IMPORTANCEGrowing evidence demonstrates the key role of the gut microbiota in human health and disease. Recent Food and Drug Administration approval of fecal microbiotherapy products to treat recurrent Clostridioides difficile infection has shed light on their potential to treat pathological conditions associated with gut dysbiosis. In this study, we combined metagenomic analysis with in vitro and in vivo studies to compare the efficacy of pooled microbiotherapy products to corresponding single donor-derived products. We demonstrate that pooled products are more homogeneous, diverse, and enriched in beneficial bacteria compared to single donor-derived products. We further reveal that pooled products decreased Salmonella and Clostridioides difficile pathogenicity in mice, while single donor-derived product efficacy was variable, with some products failing to control disease progression. Altogether, these findings support the development of pooled microbiotherapies to overcome donor-dependent treatment efficacy.}, } @article {pmid38651859, year = {2024}, author = {Cai, X and Yi, P and Chen, X and Wu, J and Lan, G and Li, S and Luo, S and Huang, F and Huang, J and Shen, P}, title = {Intake of compound probiotics accelerates the construction of immune function and gut microbiome in Holstein calves.}, journal = {Microbiology spectrum}, volume = {12}, number = {6}, pages = {e0190923}, pmid = {38651859}, issn = {2165-0497}, support = {20220620-5//Science Research and Technology Development Project of Jiangnan District of Nanning/ ; Guike-AA18118051//Special Project on Innovation Driven Development of Guangxi/ ; nycytxgxcxtd-15-01//National modern agricultural industrial technology system/ ; Guike-AA18118041//Special Project on Innovation Driven Development/ ; }, mesh = {Animals ; Cattle ; *Probiotics/administration & dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Diarrhea/veterinary/microbiology/immunology/prevention & control ; Animals, Newborn ; Cattle Diseases/microbiology/prevention & control/immunology ; Saccharomyces cerevisiae ; Lactobacillus plantarum ; Enterococcus faecium/immunology ; }, abstract = {UNLABELLED: Acquired immunity is an important way to construct the intestinal immune barrier in mammals, which is almost dependent on suckling. To develop a new strategy for accelerating the construction of gut microbiome, newborn Holstein calves were continuously fed with 40 mL of compound probiotics (containing Lactobacillus plantarum T-14, Enterococcus faecium T-11, Saccharomyces cerevisiae T-209, and Bacillus licheniformis T-231) per day for 60 days. Through diarrhea rate monitoring, immune index testing, antioxidant capacity detection, and metagenome sequencing, the changes in diarrhea incidence, average daily gain, immune index, and gut microbiome of newborn calves within 60 days were investigated. Results indicated that feeding the compound probiotics reduced the average diarrhea rate of calves by 42.90%, increased the average daily gain by 43.40%, raised the antioxidant indexes of catalase, superoxide dismutase, total antioxidant capacity, and Glutathione peroxidase by 22.81%, 6.49%, 8.33%, and 13.67%, respectively, and increased the immune indexes of IgA, IgG, and IgM by 10.44%, 4.85%, and 6.12%, respectively. Moreover, metagenome sequencing data showed that feeding the compound probiotics increased the abundance of beneficial strains (e.g., Lactococcus lactis and Bacillus massionigeriensis) and decreased the abundance of some harmful strains (e.g., Escherichia sp. MOD1-EC5189 and Mycobacterium brisbane) in the gut microbiome of calves, thus contributing to accelerating the construction of healthy gut microbiome in newborn Holstein calves.

IMPORTANCE: The unstable gut microbiome and incomplete intestinal function of newborn calves are important factors for the high incidence of early diarrhea. This study presents an effective strategy to improve the overall immunity and gut microbiome in calves and provides new insights into the application of compound probiotics in mammals.}, } @article {pmid38650647, year = {2024}, author = {Tunsakul, N and Wongsaroj, L and Janchot, K and Pongpirul, K and Somboonna, N}, title = {Non-significant influence between aerobic and anaerobic sample transport materials on gut (fecal) microbiota in healthy and fat-metabolic disorder Thai adults.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17270}, pmid = {38650647}, issn = {2167-8359}, mesh = {Humans ; Adult ; *Gastrointestinal Microbiome/physiology/genetics ; *Feces/microbiology ; Thailand ; Male ; *RNA, Ribosomal, 16S/genetics ; Female ; Young Adult ; Specimen Handling/methods ; Anaerobiosis/physiology ; Aerobiosis ; Metagenomics ; Southeast Asian People ; }, abstract = {BACKGROUND: The appropriate sample handling for human fecal microbiota studies is essential to prevent changes in bacterial composition and quantities that could lead to misinterpretation of the data.

METHODS: This study firstly identified the potential effect of aerobic and anaerobic fecal sample collection and transport materials on microbiota and quantitative microbiota in healthy and fat-metabolic disorder Thai adults aged 23-43 years. We employed metagenomics followed by 16S rRNA gene sequencing and 16S rRNA gene qPCR, to analyze taxonomic composition, alpha diversity, beta diversity, bacterial quantification, Pearson's correlation with clinical factors for fat-metabolic disorder, and the microbial community and species potential metabolic functions.

RESULTS: Our study successfully obtained microbiota results in percent and quantitative compositions. Each sample exhibited quality sequences with a >99% Good's coverage index, and a relatively plateau rarefaction curve. Alpha diversity indices showed no statistical difference in percent and quantitative microbiota OTU richness and evenness, between aerobic and anaerobic sample transport materials. Obligate and facultative anaerobic species were analyzed and no statistical difference was observed. Supportively, the beta diversity analysis by non-metric multidimensional scale (NMDS) constructed using various beta diversity coefficients showed resembling microbiota community structures between aerobic and anaerobic sample transport groups (P = 0.86). On the other hand, the beta diversity could distinguish microbiota community structures between healthy and fat-metabolic disorder groups (P = 0.02), along with Pearson's correlated clinical parameters (i.e., age, liver stiffness, GGT, BMI, and TC), the significantly associated bacterial species and their microbial metabolic functions. For example, genera such as Ruminococcus and Bifidobacterium in healthy human gut provide functions in metabolisms of cofactors and vitamins, biosynthesis of secondary metabolites against gut pathogens, energy metabolisms, digestive system, and carbohydrate metabolism. These microbial functional characteristics were also predicted as healthy individual biomarkers by LEfSe scores. In conclusion, this study demonstrated that aerobic sample collection and transport (<48 h) did not statistically affect the microbiota and quantitative microbiota analyses in alpha and beta diversity measurements. The study also showed that the short-term aerobic sample collection and transport still allowed fecal microbiota differentiation between healthy and fat-metabolic disorder subjects, similar to anaerobic sample collection and transport. The core microbiota were analyzed, and the findings were consistent. Moreover, the microbiota-related metabolic potentials and bacterial species biomarkers in healthy and fat-metabolic disorder were suggested with statistical bioinformatics (i.e., Bacteroides plebeius).}, } @article {pmid38650065, year = {2024}, author = {Kharey, GS and Palace, V and Whyte, L and Greer, CW}, title = {Influence of heavy Canadian crude oil on pristine freshwater boreal lake ecosystems in an experimental oil spill.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {5}, pages = {}, pmid = {38650065}, issn = {1574-6941}, support = {CRDPJ-532225//Natural Sciences and Engineering Research Council of Canada/ ; //University of Manitoba/ ; //Genome Canada/ ; }, mesh = {*Petroleum/metabolism ; *Petroleum Pollution ; *Lakes/microbiology ; *Polycyclic Aromatic Hydrocarbons/metabolism ; Canada ; *Water Pollutants, Chemical/metabolism ; *Ecosystem ; Biodegradation, Environmental ; Geologic Sediments/microbiology ; Microbiota/drug effects ; Bacteria/genetics/drug effects/metabolism/classification ; Fresh Water/microbiology ; }, abstract = {The overall impact of a crude oil spill into a pristine freshwater environment in Canada is largely unknown. To evaluate the impact on the native microbial community, a large-scale in situ model experimental spill was conducted to assess the potential role of the natural community to attenuate hydrocarbons. A small volume of conventional heavy crude oil (CHV) was introduced within contained mesocosm enclosures deployed on the shoreline of a freshwater lake. The oil was left to interact with the shoreline for 72 h and then free-floating oil was recovered using common oil spill response methods (i.e. freshwater flushing and capture on oleophilic absorptive media). Residual polycyclic aromatic hydrocarbon (PAH) concentrations returned to near preoiling concentrations within 2 months, while the microbial community composition across the water, soil, and sediment matrices of the enclosed oligotrophic freshwater ecosystems did not shift significantly over this period. Metagenomic analysis revealed key polycyclic aromatic and alkane degradation mechanisms also did not change in their relative abundance over the monitoring period. These trends suggest that for small spills (<2 l of oil per 15 m2 of surface freshwater), physical oil recovery reduces polycyclic aromatic hydrocarbon concentrations to levels tolerated by the native microbial community. Additionally, the native microbial community present in the monitored pristine freshwater ecosystem possesses the appropriate hydrocarbon degradation mechanisms without prior challenge by hydrocarbon substrates. This study corroborated trends found previously (Kharey et al. 2024) toward freshwater hydrocarbon degradation in an environmentally relevant scale and conditions on the tolerance of residual hydrocarbons in situ.}, } @article {pmid38650064, year = {2024}, author = {Kharey, GS and Palace, V and Whyte, L and Greer, CW}, title = {Native freshwater lake microbial community response to an in situ experimental dilbit spill.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {5}, pages = {}, pmid = {38650064}, issn = {1574-6941}, support = {#CRDPJ-532225//NSERC/ ; //University of Manitoba/ ; }, mesh = {*Lakes/microbiology ; *Biodegradation, Environmental ; Canada ; *Hydrocarbons/metabolism ; *Petroleum Pollution ; Microbiota ; Water Pollutants, Chemical/metabolism ; Bacteria/genetics/metabolism/classification ; Polycyclic Aromatic Hydrocarbons/metabolism ; Geologic Sediments/microbiology ; Fresh Water/microbiology ; Metagenomics ; }, abstract = {With the increase in crude oil transport throughout Canada, the potential for spills into freshwater ecosystems has increased and additional research is needed in these sensitive environments. Large enclosures erected in a lake were used as mesocosms for this controlled experimental dilbit (diluted bitumen) spill under ambient environmental conditions. The microbial response to dilbit, the efficacy of standard remediation protocols on different shoreline types commonly found in Canadian freshwater lakes, including a testing of a shoreline washing agent were all evaluated. We found that the native microbial community did not undergo any significant shifts in composition after exposure to dilbit or the ensuing remediation treatments. Regardless of the treatment, sample type (soil, sediment, or water), or type of associated shoreline, the community remained relatively consistent over a 3-month monitoring period. Following this, metagenomic analysis of polycyclic aromatic and alkane hydrocarbon degradation mechanisms also showed that while many key genes identified in PAH and alkane biodegradation were present, their abundance did not change significantly over the course of the experiment. These results showed that the native microbial community present in a pristine freshwater lake has the prerequisite mechanisms for hydrocarbon degradation in place, and combined with standard remediation practices in use in Canada, has the genetic potential and resilience to potentially undertake bioremediation.}, } @article {pmid38649355, year = {2024}, author = {Qin, Y and Tong, X and Mei, WJ and Cheng, Y and Zou, Y and Han, K and Yu, J and Jie, Z and Zhang, T and Zhu, S and Jin, X and Wang, J and Yang, H and Xu, X and Zhong, H and Xiao, L and Ding, PR}, title = {Consistent signatures in the human gut microbiome of old- and young-onset colorectal cancer.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3396}, pmid = {38649355}, issn = {2041-1723}, support = {82073159//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/microbiology ; Adult ; *Age of Onset ; Male ; Female ; Middle Aged ; Aged ; Metagenome ; Metagenomics/methods ; Bacteria/classification/isolation & purification/genetics ; Young Adult ; Feces/microbiology ; Cohort Studies ; }, abstract = {The incidence of young-onset colorectal cancer (yCRC) has been increasing in recent decades, but little is known about the gut microbiome of these patients. Most studies have focused on old-onset CRC (oCRC), and it remains unclear whether CRC signatures derived from old patients are valid in young patients. To address this, we assembled the largest yCRC gut metagenomes to date from two independent cohorts and found that the CRC microbiome had limited association with age across adulthood. Differential analysis revealed that well-known CRC-associated taxa, such as Clostridium symbiosum, Peptostreptococcus stomatis, Parvimonas micra and Hungatella hathewayi were significantly enriched (false discovery rate <0.05) in both old- and young-onset patients. Similar strain-level patterns of Fusobacterium nucleatum, Bacteroides fragilis and Escherichia coli were observed for oCRC and yCRC. Almost all oCRC-associated metagenomic pathways had directionally concordant changes in young patients. Importantly, CRC-associated virulence factors (fadA, bft) were enriched in both oCRC and yCRC compared to their respective controls. Moreover, the microbiome-based classification model had similar predication accuracy for CRC status in old- and young-onset patients, underscoring the consistency of microbial signatures across different age groups.}, } @article {pmid38647870, year = {2024}, author = {Yang, F and Li, Q and Yin, X}, title = {Metagenomic analysis of the effects of salinity on microbial community and functional gene diversity in glacial meltwater estuary, Ny-Alesund, Arctic.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {55}, number = {2}, pages = {1587-1599}, pmid = {38647870}, issn = {1678-4405}, support = {ZR2020KC036//Natural Science Foundation of Shandong Province/ ; }, mesh = {*Salinity ; *Estuaries ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Metagenomics ; Arctic Regions ; Microbiota ; Ice Cover/microbiology ; Genetic Variation ; Biodiversity ; Metagenome ; Sulfur/metabolism ; Nitrogen/metabolism ; Phylogeny ; }, abstract = {Due to the inflow of meltwater from the Midre Lovénbreen glacier upstream of Kongsfjorden, the nutrient concentration of Kongsfjorden change from the estuary to the interior of the fjord. Our objective was to explore the changes in bacterial community structure and metabolism-related genes from the estuary to fjord by metagenomic analysis. Our data indicate that glacial meltwater input has altered the physicochemical properties of the fjords, with a significant effect, in particular, on fjords salinity, thus altering the relative abundance of some specific bacterial groups. In addition, we suggest that the salinity of a fjord is an important factor affecting the abundance of genes associated with the nitrogen and sulfur cycles in the fjord. Changes in salinity may affect the relative abundance of microbial populations that carry metabolic genes, thus affecting the relative abundance of genes associated with the nitrogen and sulfur cycles.}, } @article {pmid38647315, year = {2024}, author = {Chen, L-p and Zhang, L-f and Liu, S and Hua, H and Zhang, L and Liu, B-c and Wang, R-r}, title = {Ling-Gui-Zhu-Gan decoction ameliorates nonalcoholic fatty liver disease via modulating the gut microbiota.}, journal = {Microbiology spectrum}, volume = {12}, number = {6}, pages = {e0197923}, pmid = {38647315}, issn = {2165-0497}, support = {82004149//MOST | National Natural Science Foundation of China (NSFC)/ ; 82274213//MOST | National Natural Science Foundation of China (NSFC)/ ; 81973730//MOST | National Natural Science Foundation of China (NSFC)/ ; 2021 Science and Technology 02-37//Shanghai Collaborative Innovation Center for Chronic Disease Prevention and Health Services/ ; 22010504300//Local Colleges Faculty Constitution of Shanghai MSTC/ ; 202204051001030//Science and Technology Innovation Teams of Shanxi Province/ ; }, mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/drug therapy/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Mice ; Male ; *Disease Models, Animal ; *Diet, High-Fat/adverse effects ; Dysbiosis/drug therapy/microbiology ; Liver/drug effects/metabolism ; Mice, Inbred C57BL ; Bile Acids and Salts/metabolism ; Fatty Acids, Volatile/metabolism ; Lipid Metabolism/drug effects ; Signal Transduction/drug effects ; Plant Extracts ; }, abstract = {UNLABELLED: Numerous studies have supported that nonalcoholic fatty liver disease (NAFLD) is highly associated with gut microbiota dysbiosis. Ling-Gui-Zhu-Gan decoction (LG) has been clinically used to treat NAFLD, but the underlying mechanism remains unknown. This study investigated the therapeutic effect and mechanisms of LG in mice with NAFLD induced by a high-fat diet (HD). An HD-induced NAFLD mice model was established to evaluate the efficacy of LG followed by biochemical and histopathological analysis. Metagenomics, metabolomics, and transcriptomics were used to explore the structure and metabolism of the gut microbiota. LG significantly improved hepatic function and decreased lipid droplet accumulation in HD-induced NAFLD mice. LG reversed the structure of the gut microbiota that is damaged by HD and improved intestinal barrier function. Meanwhile, the LG group showed a lower total blood bile acids (BAs) concentration, a shifted BAs composition, and a higher fecal short-chain fatty acids (SCFAs) concentration. Furthermore, LG could regulate the hepatic expression of genes associated with the primary BAs biosynthesis pathway and peroxisome proliferator-activated receptor (PPAR) signaling pathway. Our study suggested that LG could ameliorate NAFLD by altering the structure and metabolism of gut microbiota, while BAs and SCFAs are considered possible mediating substances.

IMPORTANCE: Until now, there has still been no study on the gut microbiota and metabolomics of Ling-Gui-Zhu-Gan decoction (LG) in nonalcoholic fatty liver disease (NAFLD) mouse models. Our study is the first to report on the reshaping of the structure and metabolism of the gut microbiota by LG, as well as explore the potential mechanism underlying the improvement of NAFLD. Specifically, our study demonstrates the potential of gut microbial-derived short-chain fatty acids (SCFAs) and blood bile acids (BAs) as mediators of LG therapy for NAFLD in animal models. Based on the results of transcriptomics, we further verified that LG attenuates NAFLD by restoring the metabolic disorder of BAs via the up-regulation of Fgf15/FXR in the ileum and down-regulation of CYP7A1/FXR in the liver. LG also reduces lipogenesis in NAFLD mice by mediating the peroxisome proliferator-activated receptor (PPAR) signaling pathway, which then contributes to reducing hepatic inflammation and improving intestinal barrier function to treat NAFLD.}, } @article {pmid38646932, year = {2024}, author = {Saranholi, BH and França, FM and Vogler, AP and Barlow, J and Vaz de Mello, FZ and Maldaner, ME and Carvalho, E and Gestich, CC and Howes, B and Banks-Leite, C and Galetti, PM}, title = {Testing and optimizing metabarcoding of iDNA from dung beetles to sample mammals in the hyperdiverse Neotropics.}, journal = {Molecular ecology resources}, volume = {24}, number = {5}, pages = {e13961}, doi = {10.1111/1755-0998.13961}, pmid = {38646932}, issn = {1755-0998}, support = {1989427//University of Bristol (PolicyBristol, SYNPAM)/ ; ProjectBIOCLIMATE//BNP Paribas Foundation (Climate and Biodiversity Initiative)/ ; 2258319//Cabot Seedcorn 2023 (Voices of Amazonia)/ ; 303524/2019-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 406767/2022-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 420254/2018-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 441257/2023-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 441573/2020-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 441659/2016-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 1777136//University of Bristol (Liv Sidse Jansen Memorial Foundation, FOR-TRAITS)/ ; NE/S011811/1//Natural Environment Research Council/ ; 170839//Climate and Net Zero Impact Awards (Scaling-up TAOCA)/ ; MR/X032949/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Coleoptera/genetics/classification ; *Mammals/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA/methods ; Biodiversity ; Metagenomics/methods ; DNA/genetics ; Feces/chemistry ; }, abstract = {Over the past few years, insects have been used as samplers of vertebrate diversity by assessing the ingested-derived DNA (iDNA), and dung beetles have been shown to be a good mammal sampler given their broad feeding preference, wide distribution and easy sampling. Here, we tested and optimized the use of iDNA from dung beetles to assess the mammal community by evaluating if some biological and methodological aspects affect the use of dung beetles as mammal species samplers. We collected 403 dung beetles from 60 pitfall traps. iDNA from each dung beetle was sequenced by metabarcoding using two mini-barcodes (12SrRNA and 16SrRNA). We assessed whether dung beetles with different traits related to feeding, nesting and body size differed in the number of mammal species found in their iDNA. We also tested differences among four killing solutions in preserving the iDNA and compared the effectiveness of each mini barcode to recover mammals. We identified a total of 50 mammal OTUs (operational taxonomic unit), including terrestrial and arboreal species from 10 different orders. We found that at least one mammal-matching sequence was obtained from 70% of the dung beetle specimens. The number of mammal OTUs obtained did not vary with dung beetle traits as well as between the killing solutions. The 16SrRNA mini-barcode recovered a higher number of mammal OTUs than 12SrRNA, although both sets were partly non-overlapping. Thus, the complete mammal diversity may not be achieved by using only one of them. This study refines the methodology for routine assessment of tropical mammal communities via dung beetle 'samplers' and its universal applicability independently of the species traits of local beetle communities.}, } @article {pmid38646847, year = {2024}, author = {Fontana, F and Longhi, G and Carli, E and Alessandri, G and Mancabelli, L and Lugli, GA and Tarracchini, C and Viappiani, A and Anzalone, R and Turroni, F and Milani, C and Ventura, M}, title = {Revealing the genetic traits of the foodborne microbial genus hafnia: Implications for the human gut microbiome.}, journal = {Environmental microbiology}, volume = {26}, number = {4}, pages = {e16626}, doi = {10.1111/1462-2920.16626}, pmid = {38646847}, issn = {1462-2920}, support = {//Cariparma/ ; //GenProbio Srl/ ; CUP D93C22000890001//Concession Decree No.1550 of 11 October 2022, Italian Ministry of University and Research/ ; PE00000003//Mission 4 Component 2 Investment 1.3 - Call for tender No. 341 of 15 March 2022, Italian Ministry of University and Research funded by the European Union-NextGenerationEU/ ; //the National Recovery and Resilience Plan (NRRP)/ ; //ON Foods - Research and innovation network on food and nutrition Sustainability, Safety and Security -Working ON Foods/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Animals ; Bees/microbiology ; Fatty Acids, Volatile/metabolism ; Genome, Bacterial ; Food Microbiology ; Metagenomics ; Vitamins/metabolism ; Phylogeny ; }, abstract = {The bacterial genus Hafnia has recently attracted attention due to its complex metabolic features and host-interaction capabilities, which are associated with health benefits, primarily weight loss. However, significant gaps remain in our understanding of the genomic characteristics of this emerging microbial group. In this study, we utilized all available high-quality genomes of Hafnia alvei and Hafnia paralvei to uncover the broad distribution of Hafnia in human and honeybee guts, as well as in dairy products, by analysing 1068 metagenomic datasets. We then investigated the genetic traits related to Hafnia's production of vitamins and short-chain fatty acids (SCFAs) through a comparative genomics analysis that included all dominant bacterial species in the three environments under study. Our findings underscore the extensive metabolic capabilities of Hafnia, particularly in the production of vitamins such as thiamine (B1), nicotinate (B3), pyridoxine (B6), biotin (B7), folate (B9), cobalamin (B12), and menaquinone (K2). Additionally, Hafnia demonstrated a conserved genetic makeup associated with SCFA production, including acetate, propanoate, and butanoate. These metabolic traits were further confirmed using RNAseq analyses of a newly isolated H. paralvei strain T10. Overall, our study illuminates the ecological distribution and genetic attributes of this bacterial genus, which is of increasing scientific and industrial relevance.}, } @article {pmid38644048, year = {2024}, author = {Wielkopolan, B and Szabelska-Beręsewicz, A and Gawor, J and Obrępalska-Stęplowska, A}, title = {Cereal leaf beetle-associated bacteria enhance the survival of their host upon insecticide treatments and respond differently to insecticides with different modes of action.}, journal = {Environmental microbiology reports}, volume = {16}, number = {2}, pages = {e13247}, pmid = {38644048}, issn = {1758-2229}, support = {UMO-2020/37/N/NZ9/02577//Polish National Science Centre/ ; }, mesh = {Animals ; *Insecticides/pharmacology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Larva/microbiology/drug effects ; *Coleoptera/microbiology/drug effects ; RNA, Ribosomal, 16S/genetics ; Microbiota/drug effects ; Metagenomics ; Pyrethrins/pharmacology ; Chlorpyrifos ; Pantoea/genetics/drug effects ; }, abstract = {The cereal leaf beetle (CLB, Oulema melanopus) is one of the major cereal pests. The effect of insecticides belonging to different chemical classes, with different mechanisms of action and the active substances' concentrations on the CLB bacterial microbiome, was investigated. Targeted metagenomic analysis of the V3-V4 regions of the 16S ribosomal gene was used to determine the composition of the CLB bacterial microbiome. Each of the insecticides caused a decrease in the abundance of bacteria of the genus Pantoea, and an increase in the abundance of bacteria of the genus Stenotrophomonas, Acinetobacter, compared to untreated insects. After cypermethrin application, a decrease in the relative abundance of bacteria of the genus Pseudomonas was noted. The dominant bacterial genera in cypermethrin-treated larvae were Lactococcus, Pantoea, while in insects exposed to chlorpyrifos or flonicamid it was Pseudomonas. Insecticide-treated larvae were characterized, on average, by higher biodiversity and richness of bacterial genera, compared to untreated insects. The depletion of CLB-associated bacteria resulted in a decrease in larval survival, especially after cypermethrin and chlorpyrifos treatments. The use of a metagenome-based functional prediction approach revealed a higher predicted function of bacterial acetyl-CoA C-acetyltransferase in flonicamid and chlorpyrifos-treated larvae and tRNA dimethyltransferase in cypermethrin-treated insects than in untreated insects.}, } @article {pmid38643745, year = {2024}, author = {Mang, Q and Gao, J and Li, Q and Sun, Y and Xu, G and Xu, P}, title = {Integrative analysis of metagenome and metabolome provides new insights into intestinal health protection in Coilia nasus larvae via probiotic intervention.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {50}, number = {}, pages = {101230}, doi = {10.1016/j.cbd.2024.101230}, pmid = {38643745}, issn = {1878-0407}, mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; *Metabolome ; *Gastrointestinal Microbiome ; *Larva/microbiology/growth & development ; Metagenome ; Fishes/microbiology ; Intestines/microbiology ; }, abstract = {With the development of large-scale intensive feeding, growth performance and animal welfare have attracted more and more attention. Exogenous probiotics can promote the growth performance of fish through improving intestinal microbiota; however, it remains unclear whether intestinal microbiota influence physiological biomarkers. Therefore, we performed metagenomic and metabolomic analysis to investigate the effects of a 90-day Lactiplantibacillus plantarum supplementation to a basal diet (1.0 × 10[8] CFU/g) on the growth performance, intestinal microbiota and their metabolites, and physiological biomarkers in Coilia nasus larvae. The results showed that the probiotic supplementation could significantly increase weight and body length. Moreover, it could also enhance digestive enzymes and tight junctions, and inhibit oxidative stress and inflammation. The metagenomic analysis showed that L. plantarum supplementation could significantly decrease the relative abundance of Proteobacteria and increase the relative abundance of Firmicutes. Additionally, pathogenic bacteria (Aeromonadaceae, Aeromonas, and Enterobacterales) were inhibited and beneficial bacteria (Bacillales) were promoted. The metabolome analysis showed that acetic acid and propanoic acid were significantly elevated, and were associated with Kitasatospora, Seonamhaeicola, and Thauera. A correlation analysis demonstrated that the digestive enzymes, tight junction, oxidative stress, and inflammation effects were significantly associated with the increased acetic acid and propanoic acid levels. These results indicated that L. plantarum supplementation could improve intestinal microbial community structure and function, which could raise acetic acid and propanoic acid levels to protect intestinal health and improve growth performance in C. nasus larvae.}, } @article {pmid38643524, year = {2024}, author = {Mishra, S and Zhang, X and Yang, X}, title = {Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition.}, journal = {Microbiological research}, volume = {284}, number = {}, pages = {127726}, doi = {10.1016/j.micres.2024.127726}, pmid = {38643524}, issn = {1618-0623}, mesh = {Bacteria/genetics/classification/metabolism ; Metagenomics ; Microbiota/physiology ; *Plant Development ; *Plant Roots/microbiology ; *Plants/microbiology ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.}, } @article {pmid38643272, year = {2024}, author = {Hauptfeld, E and Pappas, N and van Iwaarden, S and Snoek, BL and Aldas-Vargas, A and Dutilh, BE and von Meijenfeldt, FAB}, title = {Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3373}, pmid = {38643272}, issn = {2041-1723}, mesh = {*Metagenome/genetics ; Software ; Algorithms ; *Microbiota/genetics ; Metagenomics ; }, abstract = {Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, RAT annotates a large fraction of the metagenomic reads, calling novel taxa at the appropriate, sometimes high taxonomic ranks. Thus, RAT integrative profiling provides an accurate and comprehensive view of the microbiome from shotgun metagenomics data. The package of Contig Annotation Tool (CAT), Bin Annotation Tool (BAT), and RAT is available at https://github.com/MGXlab/CAT_pack (from CAT pack v6.0). The CAT pack now also supports Genome Taxonomy Database (GTDB) annotations.}, } @article {pmid38643098, year = {2024}, author = {Wang, Z and Wu, Y and Li, X and Ji, X and Liu, W}, title = {The gut microbiota facilitate their host tolerance to extreme temperatures.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {131}, pmid = {38643098}, issn = {1471-2180}, support = {31501175//National Natural Science Foundation of China/ ; RC342201//Talents in Anhui Agricultural University/ ; }, mesh = {Animals ; Mice ; Temperature ; *Hot Temperature ; *Gastrointestinal Microbiome/physiology ; Cold Temperature ; Adaptation, Physiological/physiology ; }, abstract = {BACKGROUND: Exposure to extreme cold or heat temperature is one leading cause of weather-associated mortality and morbidity in animals. Emerging studies demonstrate that the microbiota residing in guts act as an integral factor required to modulate host tolerance to cold or heat exposure, but common and unique patterns of animal-temperature associations between cold and heat have not been simultaneously examined. Therefore, we attempted to investigate the roles of gut microbiota in modulating tolerance to cold or heat exposure in mice.

RESULTS: The results showed that both cold and heat acutely change the body temperature of mice, but mice efficiently maintain their body temperature at conditions of chronic extreme temperatures. Mice adapt to extreme temperatures by adjusting body weight gain, food intake and energy harvest. Fascinatingly, 16 S rRNA sequencing shows that extreme temperatures result in a differential shift in the gut microbiota. Moreover, transplantation of the extreme-temperature microbiota is sufficient to enhance host tolerance to cold and heat, respectively. Metagenomic sequencing shows that the microbiota assists their hosts in resisting extreme temperatures through regulating the host insulin pathway.

CONCLUSIONS: Our findings highlight that the microbiota is a key factor orchestrating the overall energy homeostasis under extreme temperatures, providing an insight into the interaction and coevolution of hosts and gut microbiota.}, } @article {pmid38642657, year = {2024}, author = {Vacca, M and Celano, G and Serale, N and Costantino, G and Calabrese, FM and Calasso, M and De Angelis, M}, title = {Dynamic microbial and metabolic changes during Apulian Caciocavallo cheesemaking and ripening produced according to a standardized protocol.}, journal = {Journal of dairy science}, volume = {107}, number = {9}, pages = {6541-6557}, doi = {10.3168/jds.2023-24049}, pmid = {38642657}, issn = {1525-3198}, mesh = {*Cheese/microbiology ; Animals ; Milk/microbiology/chemistry ; Food Microbiology ; }, abstract = {The microbiota of a cheese play a critical role in influencing its sensory and physicochemical properties. In this study, traditional Apulian Caciocavallo cheeses coming from 4 different dairies in the same area and produced following standardized procedures were examined, as well as the different bulk milks and natural whey starter (NWS) cultures used. Moreover, considering the cheese wheels as the blocks of Caciocavallo cheeses as whole, these were characterized at different layers (i.e., core, under-rind, and rind) of the block using a multi-omics approach. In addition to physical-chemical characterization, culturomics, quantitative PCR, metagenomics, and metabolomics analysis were carried out after salting and throughout the ripening time (2 mo) to investigate major shifts in the succession of the microbiota and flavor development. Culture-dependent and 16S rRNA metataxonomics results clearly clustered samples based on microbiota biodiversity related to the production dairy plant as a result of the use of different NWS or the intrinsic conditions of each production site. At the beginning of the ripening, cheeses were dominated by Lactobacillus, and in 2 dairies (Art and SdC), Streptococcus genera were associated with the NWS. The analysis allowed us to show that although the diversity of identified genera did not change significantly between the rind, under-rind, and core fractions of the same samples, there was an evolution in the relative abundance and absolute quantification, modifying and differentiating profiles during ripening. The real-time PCR, also known as quantitative or qPCR, mainly differentiated the temporal adaptation of those species originating from bulk milks and those provided by NWS. The primary starters detected in NWS and cheeses contributed to the high relative concentration of 1-butanol, 2-butanol, 2-heptanol, 2-butanone, acetoin, delta-dodecalactone, hexanoic acid ethyl ester, octanoic acid ethyl ester, and volatile free fatty acids during ripening, whereas cheeses displaying low abundances of Streptococcus and Lactococcus (dairy Del) had a lower total concentration of acetoin compared with Art and SdC. However, the subdominant strains and nonstarter lactic acid bacteria present in cheeses are responsible for the production of secondary metabolites belonging to the chemical classes of ketones, alcohols, and organic acids, reaffirming the importance and relevance of autochthonous strains of each dairy plant although only considering a delimited production area.}, } @article {pmid38641693, year = {2024}, author = {Chen, X and Yang, Y and Wang, J and Pan, C and Zhang, Z and Chen, S and Xie, S}, title = {Impacts of o-cresol spill on composition and function of river sediment and soil microbial communities.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {22}, pages = {31978-31988}, pmid = {38641693}, issn = {1614-7499}, mesh = {*Soil Microbiology ; *Cresols ; *Rivers/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S ; Microbiota/drug effects ; }, abstract = {o-Cresol is a toxic substance with strong irritating and corrosive effects on skin and mucous membranes. To date, information on the effects of o-cresol on microbial communities in the natural environment is very limited. In the present study, 16S rRNA sequencing and metagenomic technique were carried out to elucidate the effects of the o-cresol spill on microbial communities in river sediments and nearby soils. o-Cresol spill induced the increase in the relative abundance of phyla Planctomycetes and Gemmatimonadetes, suggesting their resilience to o-cresol-induced stress. Uncultured Gemmatimonadetes genera and the MND1 genus exhibited enrichment, while the Pseudomonas genus dominated across all samples, indicating their potential pivotal roles in adapting to the o-cresol spill. Moreover, o-cresol spill impaired the metabolic functions of microbes but triggered their defense mechanisms. Under o-cresol pressure, microbial functions related to carbon fixation were upregulated and functions associated with sulfur metabolism were downregulated. In addition, the o-cresol spill led to an increase in functional genes related to the conversion of o-cresol to 3-methylcatechol. Several genes involved in the degradation of aromatic compounds were also identified, potentially contributing to the biodegradation of o-cresol. This study provides fresh insights into the repercussions of an abrupt o-cresol spill on microbial communities in natural environments, shedding light on their adaptability, defense mechanisms, and biodegradation potential.}, } @article {pmid38641105, year = {2024}, author = {Lin, L and Xiong, J and Yue, T and Xu, W and Liu, L and Wang, F and Yang, S and Cao, W}, title = {Phosphorus starvation response genes and function coupling: A mechanism to regulate phosphorus availability in a subtropical estuary.}, journal = {The Science of the total environment}, volume = {928}, number = {}, pages = {172575}, doi = {10.1016/j.scitotenv.2024.172575}, pmid = {38641105}, issn = {1879-1026}, mesh = {*Phosphorus/metabolism/analysis ; *Estuaries ; Salinity ; Environmental Monitoring ; Microbiota ; Water Pollutants, Chemical/analysis ; China ; }, abstract = {Phosphorus (P) plays an important role in regulating primary production in estuarine environments. However, knowledge of the P-functional gene composition of microbial communities and the mechanisms of microbial adaptation to changes in available P in estuaries remain limited. This study coupling 16 s rDNA and metagenomics sequencing was conducted to reveal the relationship between P cycling functional genes, microbial interactions, and P availability in the Jiulong River Estuary. The results showed that the relative abundance of P cycling functions genes was highest in winter, and lowest in summer. Spatially, the total relative abundance of P cycling functions genes was higher in the riverward than that in the seaward. P cycling functional microbial interactions and P cycling gene coupling were strongest in summer and in the seaward. Changes in both temperature and salinity had significant direct and indirect effects on P cycling function, and the influence of salinity on P cycling function was greater than that on the microbial community in the estuary. Salinity had significant direct negative effects on inorganic P-solubilization (IP), organic P-mineralization (OP), and P uptake and transport functions (PT). Whereas, salinity had a significant positive effect on P-starvation response regulation (PR) function. Thus, salinity and microbial communities regulate the soluble reactive phosphate concentrations in estuarine environments by strengthening internal coupling among P cycling functions, promoting PR function, and facilitating PT gene expression. PR is the most important predictors, PR, PT, and PR-PT together explained 38.56 % of the overall soluble reactive phosphorus (SRP) variation. Over 66 % of the explained SRP variations can be predicted by the PR, PT, and PR-PT functional genes. This finding improves the knowledge base of the microbial processes for P cycling and provides a foundation for eutrophication management strategies in the estuary.}, } @article {pmid38640860, year = {2024}, author = {Dai, L and Liu, Z and Zhou, W and Zhang, L and Miao, M and Wang, L and Hua, H and Wang, B and Ji, G}, title = {Sijunzi decoction, a classical Chinese herbal formula, improves fatigue symptoms with changes in gut microbiota in chronic fatigue syndrome: A randomized, double-blind, placebo-controlled, multi-center clinical trial.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {129}, number = {}, pages = {155636}, doi = {10.1016/j.phymed.2024.155636}, pmid = {38640860}, issn = {1618-095X}, mesh = {Humans ; *Fatigue Syndrome, Chronic/drug therapy ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Female ; Double-Blind Method ; Male ; Adult ; Middle Aged ; Quality of Life ; Fatigue/drug therapy ; Treatment Outcome ; Surveys and Questionnaires ; }, abstract = {BACKGROUD: Chronic fatigue syndrome (CFS) severely impact patients' quality of life and lacks well-acknowledged drug therapy. Sijunzi decoction (SJZD), a classical Chinese herbal formula, has been widely used for spleen deficiency syndrome like fatigue in China. However, there is a lack of evidence on the efficacy of SJZD in treating CFS.

PURPOSE: To evaluate the efficacy and safety of SJZD for CFS.

STUDY DESIGN: A multi-center, double-blinded, randomized controlled trial.

METHODS: Participants with definite diagnoses of CFS and spleen deficiency syndrome were randomly assigned in 1:1 ratio to receive SJZD or placebo granules for 2 months. The primary outcome was the change of Chalder fatigue questionnaire (CFQ) scoring after treatment. Other outcomes included changes in short form-36 physical function (SF36-PF) score, spleen deficiency scale score, Euroqol Questionnaire-Visual Analogue Scale (ED-VAS) score, and clinical global impression (CGI) evaluating by corresponding questionnaires. Fecal metagenome sequencing was conducted to explore the potential mechanism of SJZD effect.

RESULTS: From June 2020 to July 2021, 105 of 127 participants completed the study at four hospitals in China. After a 2-month treatment, intention-to-treat (ITT) analysis found participants who received SJZD had larger reduction than placebo control (mean change 6.65 [standard deviation (SD) 6.11] points vs. 5.31 [SD 5.19] points; difference 1.34, 95 % confidence interval [CI] -0.65 to 3.33). Per-protocol (PP) analysis reported confirmative results with a significant difference between SJZD and placebo groups (2.24, 95 % CI 0.10 to 4.39). SJZD also significantly improved overall health status compared with placebo in per-protocol population (p = 0.009). No significant difference was found between groups in changes of SF36-PF, spleen deficiency scale scoring, and CGI. Fecal metagenome sequencing and correlation analyses indicated that the beneficial effect of SJZD may be related to the abundance change of Pediococcus acidilactici. No serious adverse event or abnormal laboratory test was found during the whole study.

CONCLUSION: Our results indicated that SJZD can improve fatigue symptom and overall health status in patients with CFS under good medication adherence. Potential therapeutic effects may be related to the regulation of gut microbiota. Large-scale trials with longer intervention period are encouraged to further support SJZD's application.

CLINICAL TRIAL REGISTRATION: (ID, ISRCTN23930966, URL = https://www.isrctn.com/ISRCTN23930966).}, } @article {pmid38640816, year = {2024}, author = {Yi, S and Song, H and Kim, WH and Lee, S and Guk, JH and Woo, J and Cho, S}, title = {Dynamics of microbiota and antimicrobial resistance in on-farm dairy processing plants using metagenomic and culture-dependent approaches.}, journal = {International journal of food microbiology}, volume = {417}, number = {}, pages = {110704}, doi = {10.1016/j.ijfoodmicro.2024.110704}, pmid = {38640816}, issn = {1879-3460}, mesh = {*Metagenomics ; *Dairying ; *Microbiota ; *Bacteria/genetics/drug effects/isolation & purification/classification ; *Drug Resistance, Bacterial/genetics ; Farms ; Anti-Bacterial Agents/pharmacology ; Dairy Products/microbiology ; Pasteurization ; Food Microbiology ; Animals ; Food Handling/methods ; Humans ; Cattle ; Metagenome ; }, abstract = {On-farm dairy processing plants, which are situated close to farms and larger dairy processing facilities, face unique challenges in maintaining environmental hygiene. This can impact various stages of dairy processing. These plants operate on smaller scales and use Low-Temperature-Long-Time (LTLT) pasteurization, making them more susceptible to microbial contamination through direct and indirect contact. Antimicrobial-resistant bacteria found on dairy farms pose risks to human health by potentially transferring resistance via dairy products. Our study aimed to investigate microbial distribution and antimicrobial resistance at four key stages: the farm, pre-pasteurization, post-pasteurization, and processing environments. We assessed microbial distribution by quantifying indicator bacteria and conducting metagenomic analysis. Antimicrobial resistance was examined by identifying resistance phenotypes and detecting resistance genes in bacterial isolates and metagenomes. Our results showed that the indicator bacteria were detected at all stages of on-farm dairy processing. We observed a significant reduction in aerobic microbes and coliforms post-pasteurization. However, contamination of the final dairy products increased, suggesting potential cross-contamination during post-pasteurization. Metagenomic analysis revealed that Pseudomonas, a representative psychrotrophic bacterium, was predominant in both the farm (24.1 %) and pre-pasteurization (65.9 %) stages, indicating microbial transfer from the farms to the processing plants. Post-pasteurization, Pseudomonas and other psychrotrophs like Acinetobacter and Enterobacteriaceae remained dominant. Core microbiota analysis identified 74 genera in total, including 13 psychrotrophic bacteria, across all stages. Of the 59 strains isolated from these plants, 49 were psychrotrophic. Antimicrobial resistance analysis showed that 74.6 % (44/59) of isolates were resistant to at least one antibiotic, with cefoxitin-, ampicillin-, amoxicillin-, and ticarcillin-resistant bacteria present at all stages. Identical antimicrobial resistance patterns were observed in isolates from serial stages of the same farm and season, suggesting bacterial transmission across stages. Additionally, 27.1 % (16/59) of isolates carried plasmid-mediated resistance genes, which were also detected in the metagenomes of non-isolated samples, indicating potential antimicrobial resistance gene transmission and their presence in uncultured bacteria. These findings reveal the persistence of antimicrobial-resistant psychrotrophic bacteria in on-farm dairy processing plants, which pose potential health risks via dairy consumption. Our study underscores the importance of both culture-dependent and culture-independent methods to fully understand their distribution and impact.}, } @article {pmid38640749, year = {2024}, author = {Gago, JF and Viver, T and Urdiain, M and Ferreira, E and Robledo, P and Rossello-Mora, R}, title = {Metagenomics of two aquifers with thermal anomalies in Mallorca Island, and proposal of new uncultivated taxa named following the rules of SeqCode.}, journal = {Systematic and applied microbiology}, volume = {47}, number = {2-3}, pages = {126506}, doi = {10.1016/j.syapm.2024.126506}, pmid = {38640749}, issn = {1618-0984}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Groundwater/microbiology ; *Phylogeny ; *Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; Islands ; Sequence Analysis, DNA ; Spain ; Metagenome ; Genome, Bacterial/genetics ; Temperature ; }, abstract = {Groundwater offers an intriguing blend of distinctive physical and chemical conditions, constituting a challenge for microbial life. In Mallorca, the largest island of Balearic archipelago, harbours a variety of thermal anomalies (i.e., geothermal manifestation where surface aquifers exhibiting temperatures exceeding the regional average). The metagenomes of two aquifers in the centre and southern of the island showed Pseudomonadota to be the most represented phylum when using extracted 16S rRNA gene sequences. However, the microbial structures within and between aquifers were remarkably diverse but similar in their metabolic profiles as revealed by the metagenome-assembled genomes (MAGs) pointing to a prevalence of aerobic chemolithoautotrophic and heterotrophic metabolisms, especially in the Llucmajor aquifer. Also, some evidences of anaerobic lifestyles were detected, which would indicate that these environments either could suffer episodes of oxygen depletion or the anaerobes had been transported from deeper waters. We believe that the local environmental factors (temperature, external inputs or chemistry) seem to be more relevant than the connection and, eventually, transport of microbial cells within the aquifer in determining the highly divergent structures. Notably, most of the reconstructed genomes belonged to undescribed bacterial lineages and from them two high-quality MAGs could be classified as novel taxa named following the rules of the Code for Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Accordingly, we propose the new species and genus Costitxia debesea gen. nov., sp. nov., affiliated with the novel family Costitxiaceae fam. nov., order Costitxiales ord. nov. and class Costitxiia class. nov.; and the new new species and genus Lloretia debesea gen. nov. sp. nov. affiliated with the novel family Lloretiaceae fam. nov.}, } @article {pmid38640440, year = {2024}, author = {Bosch, J and Dobbler, PT and Větrovský, T and Tláskal, V and Baldrian, P and Brabcová, V}, title = {Decomposition of Fomes fomentatius fruiting bodies - transition of healthy living fungus into a decayed bacteria-rich habitat is primarily driven by Arthropoda.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {5}, pages = {}, pmid = {38640440}, issn = {1574-6941}, support = {21-09334 J//Czech Science Foundation/ ; }, mesh = {Animals ; *Arthropods ; *Coriolaceae ; *Microbiota/genetics ; *Ascomycota ; Fruiting Bodies, Fungal ; Bacteria/genetics ; }, abstract = {Fomes fomentarius is a widespread, wood-rotting fungus of temperate, broadleaved forests. Although the fruiting bodies of F. fomentarius persist for multiple years, little is known about its associated microbiome or how these recalcitrant structures are ultimately decomposed. Here we used metagenomics and metatranscriptomics to analyse the microbial community associated with healthy living and decomposing F. fomentarius fruiting bodies to assess the functional potential of the fruiting body-associated microbiome and to determine the main players involved in fruiting body decomposition. F. fomentarius sequences in the metagenomes were replaced by bacterial sequences as the fruiting body decomposed. Most CAZymes expressed in decomposing fruiting bodies targeted components of the fungal cell wall with almost all chitin-targeting sequences, plus a high proportion of beta-glucan-targeting sequences, belonging to Arthropoda. We suggest that decomposing fruiting bodies of F. fomentarius represent a habitat rich in bacteria, while its decomposition is primarily driven by Arthropoda. Decomposing fruiting bodies thus represent a specific habitat supporting both microorganisms and microfauna.}, } @article {pmid38640403, year = {2024}, author = {Ekpruke, CD and Alford, R and Parker, E and Silveyra, P}, title = {Gonadal sex and chromosome complement influence the gut microbiome in a mouse model of allergic airway inflammation.}, journal = {Physiological genomics}, volume = {56}, number = {6}, pages = {417-425}, pmid = {38640403}, issn = {1531-2267}, support = {R01 HL159764/HL/NHLBI NIH HHS/United States ; R03 HL141618/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Mice ; *Disease Models, Animal ; Sex Chromosomes/genetics ; Asthma/immunology/microbiology/genetics ; Pyroglyphidae/immunology ; Inflammation/genetics/immunology/microbiology ; Genotype ; Gonads/microbiology ; Hypersensitivity/immunology/microbiology/genetics ; Sex Characteristics ; }, abstract = {Evidence abounds that gut microbiome components are associated with sex disparities in the immune system. However, it remains unclear whether the observed sex disparity in asthma incidence is associated with sex-dependent differences in immune-modulating gut microbiota, and/or its influence on allergic airway inflammatory processes. Using a mouse model of house dust mite (HDM)-induced allergic inflammation and the four core genotypes (FCGs) model, we have previously reported sex differences in lung inflammatory phenotypes. Here, we investigated associations of gut microbiomes with these phenotypes by challenging FCG mice [mouse with female sex chromosome and male gonad (XXM), mouse with female sex chromosome and female gonad (XXF), mouse with male sex chromosome and male gonad (XYM), and mouse with male sex chromosome and female gonad (XYF); n = 7/group] with HDM (25 μg) or PBS intranasally for 5 wk and collecting fecal samples. We extracted fecal DNA and analyzed the 16S microbiome via Targeted Metagenomic Sequencing. We compared α and β diversity across genotypes and assessed the Firmicutes/Bacteroidetes (F/B) ratio. When comparing baseline and after exposure for the FCG, we found that the gut F/B ratio was only increased in the XXM genotype. We also found that α diversity was significantly increased in all FCG mice upon HDM challenge, with the highest increase in the XXF, and the lowest in the XXM genotypes. Similarly, β diversity of the microbial community was also affected by challenge in a gonad- and chromosome-dependent manner. In summary, our results indicated that HDM treatment, gonads, and sex chromosomes significantly influence the gut microbial community composition. We concluded that allergic lung inflammation may be affected by the gut microbiome in a sex-dependent manner involving both hormonal and genetic influences.NEW & NOTEWORTHY Recently, the gut microbiome and its role in chronic respiratory disease have been the subject of extensive research and the establishment of its involvement in immune functions. Using the FCG mouse model, our findings revealed the influence of gonads and sex chromosomes on the microbial community structure before and after exposure to HDM. Our data provide a potential new avenue to better understand mediators of sex disparities associated with allergic airway inflammation.}, } @article {pmid38638832, year = {2024}, author = {Filardo, S and Di Pietro, M and Sessa, R}, title = {Current progresses and challenges for microbiome research in human health: a perspective.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1377012}, pmid = {38638832}, issn = {2235-2988}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenome ; Metagenomics ; }, abstract = {It is becoming increasingly clear that the human microbiota, also known as "the hidden organ", possesses a pivotal role in numerous processes involved in maintaining the physiological functions of the host, such as nutrient extraction, biosynthesis of bioactive molecules, interplay with the immune, endocrine, and nervous systems, as well as resistance to the colonization of potential invading pathogens. In the last decade, the development of metagenomic approaches based on the sequencing of the bacterial 16s rRNA gene via Next Generation Sequencing, followed by whole genome sequencing via third generation sequencing technologies, has been one of the great advances in molecular biology, allowing a better profiling of the human microbiota composition and, hence, a deeper understanding of the importance of microbiota in the etiopathogenesis of different pathologies. In this scenario, it is of the utmost importance to comprehensively characterize the human microbiota in relation to disease pathogenesis, in order to develop novel potential treatment or preventive strategies by manipulating the microbiota. Therefore, this perspective will focus on the progress, challenges, and promises of the current and future technological approaches for microbiome profiling and analysis.}, } @article {pmid38638830, year = {2024}, author = {Narrowe, AB and Lemons, JMS and Mahalak, KK and Firrman, J and den Abbeele, PV and Baudot, A and Deyaert, S and Li, Y and Yu, LL and Liu, L}, title = {Targeted remodeling of the human gut microbiome using Juemingzi (Senna seed extracts).}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1296619}, pmid = {38638830}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; Senna Extract/analysis/pharmacology ; *Microbiota ; Bacteria ; Feces/microbiology ; Seeds ; Sennosides/analysis/pharmacology ; *Anti-Infective Agents/pharmacology ; *Drugs, Chinese Herbal ; }, abstract = {The genus Senna contains globally distributed plant species of which the leaves, roots, and seeds have multiple traditional medicinal and nutritional uses. Notable chemical compounds derived from Senna spp. include sennosides and emodin which have been tested for antimicrobial effects in addition to their known laxative functions. However, studies of the effects of the combined chemical components on intact human gut microbiome communities are lacking. This study evaluated the effects of Juemingzi (Senna sp.) extract on the human gut microbiome using SIFR[®] (Systemic Intestinal Fermentation Research) technology. After a 48-hour human fecal incubation, we measured total bacterial cell density and fermentation products including pH, gas production and concentrations of short chain fatty acids (SCFAs). The initial and post-incubation microbial community structure and functional potential were characterized using shotgun metagenomic sequencing. Juemingzi (Senna seed) extracts displayed strong, taxon-specific anti-microbial effects as indicated by significant reductions in cell density (40%) and intra-sample community diversity. Members of the Bacteroidota were nearly eliminated over the 48-hour incubation. While generally part of a healthy gut microbiome, specific species of Bacteroides can be pathogenic. The active persistence of the members of the Enterobacteriaceae and selected Actinomycetota despite the reduction in overall cell numbers was demonstrated by increased fermentative outputs including high concentrations of gas and acetate with correspondingly reduced pH. These large-scale shifts in microbial community structure indicate the need for further evaluation of dosages and potential administration with prebiotic or synbiotic supplements. Overall, the very specific effects of these extracts may offer the potential for targeted antimicrobial uses or as a tool in the targeted remodeling of the gut microbiome.}, } @article {pmid38636860, year = {2024}, author = {Zhou, ZZ and Zhu, J and Yin, Y and Ding, LJ}, title = {Seasonal variations of profiles of antibiotic resistance genes and virulence factor genes in household dust from Beijing, China revealed by the metagenomics.}, journal = {The Science of the total environment}, volume = {928}, number = {}, pages = {172542}, doi = {10.1016/j.scitotenv.2024.172542}, pmid = {38636860}, issn = {1879-1026}, mesh = {*Metagenomics ; *Seasons ; *Dust/analysis ; *Virulence Factors/genetics ; *Drug Resistance, Microbial/genetics ; Beijing ; Environmental Monitoring ; Bacteria/genetics ; Microbiota/drug effects/genetics ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; }, abstract = {Household-related microbiome is closely related with human health. However, the knowledge about profiles of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) which are carried by microbes inside homes and their temporal dynamics are rather limited. Here we monitored the seasonal changes of bacterial community (especially pathogenic bacteria), ARGs, and VFGs in household dust samples during two years. Based on metagenomic sequencing, the dust-related bacterial pathogenic community, ARGs, and VFGs all harbored the lowest richness in spring among four seasons. Their structure (except that of VFGs) also exhibited remarkable differences among the seasons. The structural variations of ARGs and VFGs were almost explained by mobile genetic elements (MGEs), bacterial pathogens, and particulate matter-related factors, with MGEs explaining the most. Moreover, the total normalized abundance of ARGs or VFGs showed no significant change across the seasons. Results of metagenomic binning and microbial network both showed that several pathogenic taxa (e.g., Ralstonia pickettii) were strongly linked with numerous ARGs (mainly resistant to multidrug) and VFGs (mainly encoding motility) simultaneously. Overall, these findings underline the significance of MGEs in structuring ARGs and VFGs inside homes along with seasonal variations, suggesting that household dust is a neglected reservoir for ARGs and VFGs.}, } @article {pmid38636385, year = {2024}, author = {Xu, L and Mao, T and Xia, M and Wu, W and Chen, J and Jiang, C and Zeng, T and Tian, Y and Lu, L and Cai, Z}, title = {New evidence for gut-muscle axis: Lactic acid bacteria-induced gut microbiota regulates duck meat flavor.}, journal = {Food chemistry}, volume = {450}, number = {}, pages = {139354}, doi = {10.1016/j.foodchem.2024.139354}, pmid = {38636385}, issn = {1873-7072}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Ducks/microbiology ; *Meat/analysis/microbiology ; *Lactobacillales/metabolism/genetics ; *Taste ; Volatile Organic Compounds/metabolism/chemistry ; Fatty Acids/metabolism ; Flavoring Agents/metabolism/chemistry ; }, abstract = {The interaction between gut microbiota and muscles through the gut-muscle axis has received increasing attention. This study attempted to address existing research gaps by investigating the effects of gut microbiota on meat flavor. Specifically, lactic acid bacteria were administered to ducks, and the results of e-nose and e-tongue showed significantly enhanced meat flavor in the treatment group. Further analyses using GC-MS revealed an increase in 6 characteristic volatile flavor compounds, including pentanal, hexanal, heptanal, 1-octen-3-ol, 2,3-octanedione, and 2-pentylfuran. Linoleic acid was identified as the key fatty acid that influences meat flavor. Metagenomic and transcriptomic results further confirmed that cecal microbiota affects the duck meat flavor by regulating the metabolic pathways of fatty acids and amino acids, especially ACACB was related to fatty acid biosynthesis and ACAT2, ALDH1A1 with fatty acid degradation. This study sheds light on a novel approach to improving the flavor of animal-derived food.}, } @article {pmid38635882, year = {2024}, author = {Al Radi, ZMA and Prins, FM and Collij, V and Vich Vila, A and Festen, EAM and Dijkstra, G and Weersma, RK and Klaassen, MAY and Gacesa, R}, title = {Exploring the Predictive Value of Gut Microbiome Signatures for Therapy Intensification in Patients With Inflammatory Bowel Disease: A 10-Year Follow-up Study.}, journal = {Inflammatory bowel diseases}, volume = {30}, number = {10}, pages = {1642-1653}, pmid = {38635882}, issn = {1536-4844}, support = {//Netherlands Organization for Scientific Research/ ; MLDS D16-14//Dutch Digestive Foundation/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Follow-Up Studies ; Male ; Adult ; Retrospective Studies ; *Inflammatory Bowel Diseases/microbiology/therapy ; *Feces/microbiology ; Middle Aged ; *Metagenomics/methods ; Prognosis ; Predictive Value of Tests ; Biomarkers/analysis ; Young Adult ; }, abstract = {BACKGROUND: Inflammatory bowel diseases (IBDs) pose a significant challenge due to their diverse, often debilitating, and unpredictable clinical manifestations. The absence of prognostic tools to anticipate the future complications that require therapy intensification presents a substantial burden to patient private life and health. We aimed to explore whether the gut microbiome is a potential biomarker for future therapy intensification in a cohort of 90 IBD patients.

METHODS: We conducted whole-genome metagenomics sequencing on fecal samples from these patients, allowing us to profile the taxonomic and functional composition of their gut microbiomes. Additionally, we conducted a retrospective analysis of patients' electronic records over a period of 10 years following the sample collection and classified patients into (1) those requiring and (2) not requiring therapy intensification. Therapy intensification included medication escalation, intestinal resections, or a loss of response to a biological treatment. We applied gut microbiome diversity analysis, dissimilarity assessment, differential abundance analysis, and random forest modeling to establish associations between baseline microbiome profiles and future therapy intensification.

RESULTS: We identified 12 microbial species (eg, Roseburia hominis and Dialister invisus) and 16 functional pathways (eg, biosynthesis of L-citrulline and L-threonine) with significant correlations to future therapy intensifications. Random forest models using microbial species and pathways achieved areas under the curve of 0.75 and 0.72 for predicting therapy intensification.

CONCLUSIONS: The gut microbiome is a potential biomarker for therapy intensification in IBD patients and personalized management strategies. Further research should validate our findings in other cohorts to enhance the generalizability of these results.}, } @article {pmid38635629, year = {2024}, author = {Wang, T and Weiss, A and You, L}, title = {A generic approach to infer community-level fitness of microbial genes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {17}, pages = {e2318380121}, pmid = {38635629}, issn = {1091-6490}, support = {R01 AI125604/AI/NIAID NIH HHS/United States ; R01 GM098642/GM/NIGMS NIH HHS/United States ; R01 EB031869/EB/NIBIB NIH HHS/United States ; }, mesh = {*Microbiota/genetics ; Metagenome/genetics ; Selection, Genetic ; Genes, Microbial ; }, abstract = {The gene content in a metagenomic pool defines the function potential of a microbial community. Natural selection, operating on the level of genomes or genes, shapes the evolution of community functions by enriching some genes while depriving the others. Despite the importance of microbiomes in the environment and health, a general metric to evaluate the community-wide fitness of microbial genes remains lacking. In this work, we adapt the classic neutral model of species and use it to predict how the abundances of different genes will be shaped by selection, regardless of at which level the selection acts. We establish a simple metric that quantitatively infers the average survival capability of each gene in a microbiome. We then experimentally validate the predictions using synthetic communities of barcoded Escherichia coli strains undergoing neutral assembly and competition. We further show that this approach can be applied to publicly available metagenomic datasets to gain insights into the environment-function interplay of natural microbiomes.}, } @article {pmid38635587, year = {2024}, author = {Ohdera, AH and Mansbridge, M and Wang, M and Naydenkov, P and Kamel, B and Goentoro, L}, title = {The microbiome of a Pacific moon jellyfish Aurelia coerulea.}, journal = {PloS one}, volume = {19}, number = {4}, pages = {e0298002}, pmid = {38635587}, issn = {1932-6203}, mesh = {Animals ; *Scyphozoa/physiology ; *Microbiota ; Metagenome ; Bacteria/genetics ; Pacific Ocean ; }, abstract = {The impact of microbiome in animal physiology is well appreciated, but characterization of animal-microbe symbiosis in marine environments remains a growing need. This study characterizes the microbial communities associated with the moon jellyfish Aurelia coerulea, first isolated from the East Pacific Ocean and has since been utilized as an experimental system. We find that the microbiome of this Pacific Aurelia culture is dominated by two taxa, a Mollicutes and Rickettsiales. The microbiome is stable across life stages, although composition varies. Mining the host sequencing data, we assembled the bacterial metagenome-assembled genomes (MAGs). The bacterial MAGs are highly reduced, and predict a high metabolic dependence on the host. Analysis using multiple metrics suggest that both bacteria are likely new species. We therefore propose the names Ca. Mariplasma lunae (Mollicutes) and Ca. Marinirickettsia aquamalans (Rickettsiales). Finally, comparison with studies of Aurelia from other geographical populations suggests the association with Ca. Mariplasma lunae occurs in Aurelia from multiple geographical locations. The low-diversity microbiome of Aurelia provides a relatively simple system to study host-microbe interactions.}, } @article {pmid38635321, year = {2024}, author = {Wang, M and Lkhagva, E and Kim, S and Zhai, C and Islam, MM and Kim, HJ and Hong, ST}, title = {The gut microbe pair of Oribacterium sp. GMB0313 and Ruminococcus sp. GMB0270 confers complete protection against SARS-CoV-2 infection by activating CD8+ T cell-mediated immunity.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2342497}, pmid = {38635321}, issn = {1949-0984}, mesh = {Animals ; Cricetinae ; Ruminococcus ; *Gastrointestinal Microbiome ; *COVID-19 ; SARS-CoV-2 ; Clostridiales ; CD8-Positive T-Lymphocytes ; Immunity, Cellular ; }, abstract = {Despite the potential protective role of the gut microbiome against COVID-19, specific microbes conferring resistance to COVID-19 have not yet been identified. In this work, we aimed to identify and validate gut microbes at the species level that provide protection against SARS-CoV-2 infection. To identify gut microbes conferring protection against COVID-19, we conducted a fecal microbiota transplantation (FMT) from an individual with no history of COVID-19 infection or immunization into a lethal COVID-19 hamster model. FMT from this COVID-19-resistant donor resulted in significant phenotypic changes related to COVID-19 sensitivity in the hamsters. Metagenomic analysis revealed distinct differences in the gut microbiome composition among the hamster groups, leading to the identification of two previously unknown bacterial species: Oribacterium sp. GMB0313 and Ruminococcus sp. GMB0270, both associated with COVID-19 resistance. Subsequently, we conducted a proof-of-concept confirmation animal experiment adhering to Koch's postulates. Oral administration of this gut microbe pair, Oribacterium sp. GMB0313 and Ruminococcus sp. GMB0270, to the hamsters provided complete protection against SARS-CoV-2 infection through the activation of CD8+ T cell mediated immunity. The prophylactic efficacy of the gut microbe pair against SARS-CoV-2 infection was comparable to, or even superior to, current mRNA vaccines. This strong prophylactic efficacy suggests that the gut microbe pair could be developed as a host-directed universal vaccine for all betacoronaviruses, including potential future emerging viruses.}, } @article {pmid38634770, year = {2024}, author = {Lee, I and Jo, JW and Woo, HJ and Suk, KT and Lee, SS and Kim, BS}, title = {Proton pump inhibitors increase the risk of carbapenem-resistant Enterobacteriaceae colonization by facilitating the transfer of antibiotic resistance genes among bacteria in the gut microbiome.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2341635}, pmid = {38634770}, issn = {1949-0984}, mesh = {Humans ; Proton Pump Inhibitors ; *Gastrointestinal Microbiome ; *Carbapenem-Resistant Enterobacteriaceae ; Case-Control Studies ; Bacteria ; Anti-Bacterial Agents ; Drug Resistance, Microbial ; }, abstract = {Carbapenem-resistant Enterobacteriaceae (CRE) pose a global health threat; however, there is still limited understanding of the risk factors and underlying mechanisms of CRE colonization in the gut microbiome. We conducted a matched case-control study involving 282 intensive care unit patients to analyze influencing covariates on CRE colonization. Subsequently, their effects on the gut microbiome were analyzed in a subset of 98 patients (47 CRE carriers and 51 non-CRE carriers) using whole metagenome sequences. The concomitant use of proton pump inhibitors (PPIs) and antibiotics was a significant risk factor for CRE colonization. The gut microbiome differed according to PPI administration, even within the CRE and non-CRE groups. Moreover, the transfer of mobile genetic elements (MGEs) harboring carbapenem resistance genes (CRGs) between bacteria was higher in the PPI-treated group than in the PPI-not-treated group among CRE carriers. The concomitant use of PPIs and antibiotics significantly alters the gut microbiome and increases the risk of CRE colonization by facilitating the transfer of CRGs among bacteria of the gut microbiome. Based on these findings, improved stewardship of PPIs as well as antibiotics can provide strategies to reduce the risk of CRE colonization, thereby potentially improving patient prognosis.}, } @article {pmid38632606, year = {2024}, author = {Liu, X and Zeng, X and Li, X and Xin, S and Zhang, F and Liu, F and Zeng, Y and Wu, J and Zou, Y and Xiong, X}, title = {Landscapes of gut bacterial and fecal metabolic signatures and their relationship in severe preeclampsia.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {360}, pmid = {38632606}, issn = {1479-5876}, support = {82160298//National Natural Science Foundation of China/ ; }, mesh = {Female ; Pregnancy ; Humans ; *Gastrointestinal Microbiome/genetics ; *Pre-Eclampsia ; *Agmatine ; Reproducibility of Results ; Feces/microbiology ; Metabolome ; Inflammation ; *Pregnancy Complications ; Bacteria ; *Hypertension ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Preeclampsia is a pregnancy-specific disease leading to maternal and perinatal morbidity. Hypertension and inflammation are the main characteristics of preeclampsia. Many factors can lead to hypertension and inflammation, including gut microbiota which plays an important role in hypertension and inflammation in humans. However, alterations to the gut microbiome and fecal metabolome, and their relationships in severe preeclampsia are not well known. This study aims to identify biomarkers significantly associated with severe preeclampsia and provide a knowledge base for treatments regulating the gut microbiome.

METHODS: In this study, fecal samples were collected from individuals with severe preeclampsia and healthy controls for shotgun metagenomic sequencing to evaluate changes in gut microbiota composition. Quantitative polymerase chain reaction analysis was used to validate the reliability of our shotgun metagenomic sequencing results. Additionally, untargeted metabolomics analysis was performed to measure fecal metabolome concentrations.

RESULTS: We identified several Lactobacillaceae that were significantly enriched in the gut of healthy controls, including Limosilactobacillus fermentum, the key biomarker distinguishing severe preeclampsia from healthy controls. Limosilactobacillus fermentum was significantly associated with shifts in KEGG Orthology (KO) genes and KEGG pathways of the gut microbiome in severe preeclampsia, such as flagellar assembly. Untargeted fecal metabolome analysis found that severe preeclampsia had higher concentrations of Phenylpropanoate and Agmatine. Increased concentrations of Phenylpropanoate and Agmatine were associated with the abundance of Limosilactobacillus fermentum. Furthermore, all metabolites with higher abundances in healthy controls were enriched in the arginine and proline metabolism pathway.

CONCLUSION: Our research indicates that changes in metabolites, possibly due to the gut microbe Limosilactobacillus fermentum, can contribute to the development of severe preeclampsia. This study provides insights into the interaction between gut microbiome and fecal metabolites and offers a basis for improving severe preeclampsia by modulating the gut microbiome.}, } @article {pmid38632506, year = {2024}, author = {Alkathiry, HA and Alghamdi, SQ and Sinha, A and Margos, G and Stekolnikov, AA and Alagaili, AN and Darby, AC and Makepeace, BL and Khoo, JJ}, title = {Microbiome and mitogenomics of the chigger mite Pentidionis agamae: potential role as an Orientia vector and associations with divergent clades of Wolbachia and Borrelia.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {380}, pmid = {38632506}, issn = {1471-2164}, mesh = {Animals ; *Borrelia/genetics ; DNA ; *Microbiota ; Multilocus Sequence Typing ; Orientia ; *Orientia tsutsugamushi/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rodentia/genetics ; Saudi Arabia ; *Scrub Typhus/epidemiology/microbiology ; *Trombiculidae/genetics/microbiology ; *Wolbachia/genetics ; }, abstract = {BACKGROUND: Trombiculid mites are globally distributed, highly diverse arachnids that largely lack molecular resources such as whole mitogenomes for the elucidation of taxonomic relationships. Trombiculid larvae (chiggers) parasitise vertebrates and can transmit bacteria (Orientia spp.) responsible for scrub typhus, a zoonotic febrile illness. Orientia tsutsugamushi causes most cases of scrub typhus and is endemic to the Asia-Pacific Region, where it is transmitted by Leptotrombidium spp. chiggers. However, in Dubai, Candidatus Orientia chuto was isolated from a case of scrub typhus and is also known to circulate among rodents in Saudi Arabia and Kenya, although its vectors remain poorly defined. In addition to Orientia, chiggers are often infected with other potential pathogens or arthropod-specific endosymbionts, but their significance for trombiculid biology and public health is unclear.

RESULTS: Ten chigger species were collected from rodents in southwestern Saudi Arabia. Chiggers were pooled according to species and screened for Orientia DNA by PCR. Two species (Microtrombicula muhaylensis and Pentidionis agamae) produced positive results for the htrA gene, although Ca. Orientia chuto DNA was confirmed by Sanger sequencing only in P. agamae. Metagenomic sequencing of three pools of P. agamae provided evidence for two other bacterial associates: a spirochaete and a Wolbachia symbiont. Phylogenetic analysis of 16S rRNA and multi-locus sequence typing genes placed the spirochaete in a clade of micromammal-associated Borrelia spp. that are widely-distributed globally with no known vector. For the Wolbachia symbiont, a genome assembly was obtained that allowed phylogenetic localisation in a novel, divergent clade. Cytochrome c oxidase I (COI) barcodes for Saudi Arabian chiggers enabled comparisons with global chigger diversity, revealing several cases of discordance with classical taxonomy. Complete mitogenome assemblies were obtained for the three P. agamae pools and almost 50 SNPs were identified, despite a common geographic origin.

CONCLUSIONS: P. agamae was identified as a potential vector of Ca. Orientia chuto on the Arabian Peninsula. The detection of an unusual Borrelia sp. and a divergent Wolbachia symbiont in P. agamae indicated links with chigger microbiomes in other parts of the world, while COI barcoding and mitogenomic analyses greatly extended our understanding of inter- and intraspecific relationships in trombiculid mites.}, } @article {pmid38632042, year = {2024}, author = {Coskun, ÖK and Gomez-Saez, GV and Beren, M and Özcan, D and Günay, SD and Elkin, V and Hoşgörmez, H and Einsiedl, F and Eisenreich, W and Orsi, WD}, title = {Quantifying genome-specific carbon fixation in a 750-meter deep subsurface hydrothermal microbial community.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {5}, pages = {}, pmid = {38632042}, issn = {1574-6941}, support = {364653263//Deutsche Forschungsgemeinschaft/ ; GO 3267/2-1//DFG/ ; }, mesh = {*Carbon Cycle ; *Bicarbonates/metabolism ; *Microbiota ; *Carbon Isotopes/metabolism ; *Metagenome ; Bacteria/genetics/metabolism/classification ; Carbon/metabolism ; Hydrothermal Vents/microbiology ; Groundwater/microbiology ; Chemoautotrophic Growth ; Archaea/genetics/metabolism ; }, abstract = {Dissolved inorganic carbon has been hypothesized to stimulate microbial chemoautotrophic activity as a biological sink in the carbon cycle of deep subsurface environments. Here, we tested this hypothesis using quantitative DNA stable isotope probing of metagenome-assembled genomes (MAGs) at multiple 13C-labeled bicarbonate concentrations in hydrothermal fluids from a 750-m deep subsurface aquifer in the Biga Peninsula (Turkey). The diversity of microbial populations assimilating 13C-labeled bicarbonate was significantly different at higher bicarbonate concentrations, and could be linked to four separate carbon-fixation pathways encoded within 13C-labeled MAGs. Microbial populations encoding the Calvin-Benson-Bassham cycle had the highest contribution to carbon fixation across all bicarbonate concentrations tested, spanning 1-10 mM. However, out of all the active carbon-fixation pathways detected, MAGs affiliated with the phylum Aquificae encoding the reverse tricarboxylic acid (rTCA) pathway were the only microbial populations that exhibited an increased 13C-bicarbonate assimilation under increasing bicarbonate concentrations. Our study provides the first experimental data supporting predictions that increased bicarbonate concentrations may promote chemoautotrophy via the rTCA cycle and its biological sink for deep subsurface inorganic carbon.}, } @article {pmid38631646, year = {2024}, author = {Muscarella, SM and Alduina, R and Badalucco, L and Capri, FC and Di Leto, Y and Gallo, G and Laudicina, VA and Paliaga, S and Mannina, G}, title = {Water reuse of treated domestic wastewater in agriculture: Effects on tomato plants, soil nutrient availability and microbial community structure.}, journal = {The Science of the total environment}, volume = {928}, number = {}, pages = {172259}, doi = {10.1016/j.scitotenv.2024.172259}, pmid = {38631646}, issn = {1879-1026}, mesh = {*Solanum lycopersicum ; *Wastewater ; *Soil Microbiology ; *Soil/chemistry ; *Agricultural Irrigation/methods ; *Microbiota ; *Waste Disposal, Fluid/methods ; Nitrogen/analysis ; Agriculture/methods ; }, abstract = {The reuse of treated wastewater (TWW) in agriculture for crop irrigation is desirable. Crop responses to irrigation with TWW depend on the characteristics of TWW and on intrinsic and extrinsic soil properties. The aim of this study was to assess the response of tomato (Solanum lycopersicum L.) cultivated in five different soils to irrigation with TWW, compared to tap water (TAP) and an inorganic NPK solution (IFW). In addition, since soil microbiota play many important roles in plant growth, a metataxonomic analysis was performed to reveal the prokaryotic community structures of TAP, TWW and IFW treated soil, respectively. A 56-days pot experiment was carried out. Plant biometric parameters, and chemical, biochemical and microbiological properties of different soils were investigated. Shoot and root dry and fresh weights, as well as plant height, were the highest in plants irrigated with IFW followed by those irrigated with TWW, and finally with TAP water. Plant biometric parameters were positively affected by soil total organic carbon (TOC) and nitrogen (TN). Electrical conductivity was increased by TWW and IFW, being such an increase proportional to clay and TOC. Soil available P was not affected by TWW, whereas mineral N increased following their application. Total microbial biomass, as well as, main microbial groups were positively affected by TOC and TN, and increased according to the following order: IFW > TWW > TAP. However, the fungi-to-bacteria ratio was lowered in soil irrigated with TWW because of its adverse effect on fungi. The germicidal effect of sodium hypochlorite on soil microorganisms was affected by soil pH. Nutrients supplied by TWW are not sufficient to meet the whole nutrients requirement of tomato, thus integration by fertilization is required. Bacteria were more stimulated than fungi by TWW, thus leading to a lower fungi-to-bacteria ratio. Interestingly, IFW and TWW treatment led to an increased abundance of Proteobacteria and Acidobacteria phyla and Balneimonas, Rubrobacter, and Steroidobacter genera. This soil microbiota structure modulation paralleled a general decrement of fungi versus bacteria abundance ratio, the increment of electrical conductivity and nitrogen content of soil and an improvement of tomato growth. Finally, the potential adverse effect of TWW added with sodium chloride on soil microorganisms depends on soil pH.}, } @article {pmid38631637, year = {2024}, author = {Zhang, D and Liu, F and Al, MA and Yang, Y and Yu, H and Li, M and Wu, K and Niu, M and Wang, C and He, Z and Yan, Q}, title = {Nitrogen and sulfur cycling and their coupling mechanisms in eutrophic lake sediment microbiomes.}, journal = {The Science of the total environment}, volume = {928}, number = {}, pages = {172518}, doi = {10.1016/j.scitotenv.2024.172518}, pmid = {38631637}, issn = {1879-1026}, mesh = {*Lakes/microbiology ; *Sulfur/metabolism ; *Geologic Sediments/microbiology ; *Microbiota ; *Nitrogen/metabolism ; Eutrophication ; Nitrogen Cycle ; Denitrification ; }, abstract = {Microorganisms play important roles in the biogeochemical cycles of lake sediment. However, the integrated metabolic mechanisms governing nitrogen (N) and sulfur (S) cycling in eutrophic lakes remain poorly understood. Here, metagenomic analysis of field and bioreactor enriched sediment samples from a typical eutrophic lake were applied to elucidate the metabolic coupling of N and S cycling. Our results showed significant diverse genes involved in the pathways of dissimilatory sulfur metabolism, denitrification and dissimilatory nitrate reduction to ammonium (DNRA). The N and S associated functional genes and microbial groups generally showed significant correlation with the concentrations of NH4[+], NO2[-] and SO4[2], while with relatively low effects from other environmental factors. The gene-based co-occurrence network indicated clear cooperative interactions between N and S cycling in the sediment. Additionally, our analysis identified key metabolic processes, including the coupled dissimilatory sulfur oxidation (DSO) and DNRA as well as the association of thiosulfate oxidation complex (SOX systems) with denitrification pathway. However, the enriched N removal microorganisms in the bioreactor ecosystem demonstrated an additional electron donor, incorporating both the SOX systems and DSO processes. Metagenome-assembled genomes-based ecological model indicated that carbohydrate metabolism is the key linking factor for the coupling of N and S cycling. Our findings uncover the coupling mechanisms of microbial N and S metabolism, involving both inorganic and organic respiration pathways in lake sediment. This study will enhance our understanding of coupled biogeochemical cycles in lake ecosystems.}, } @article {pmid38631413, year = {2024}, author = {Ravichandran, A and Sivapackiam, J and Periasamy, S}, title = {Oral bacterial insights from a comparative study between healthy and comorbid diseased human individuals.}, journal = {Microbial pathogenesis}, volume = {191}, number = {}, pages = {106643}, doi = {10.1016/j.micpath.2024.106643}, pmid = {38631413}, issn = {1096-1208}, mesh = {Humans ; *Mouth/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; India/epidemiology ; DNA, Bacterial/genetics ; Microbiota/genetics ; Metagenomics ; Adult ; Male ; Female ; Dysbiosis/microbiology ; Young Adult ; Middle Aged ; Comorbidity ; }, abstract = {The human oral cavity is colonized by a diverse microbial community, which includes both native and transient colonizers. The microbial composition is crucial for maintaining oral homeostasis, but due to overgrowth or imbalances of these microbial communities, dysbiosis can occur. There is a lack of understanding of the research of native and transient colonizers in the oral cavity of the Indian subpopulation Therefore, in our present study, we explored the role and prevalence of transient and native colonizers between healthy and comorbid oral diseased human individuals. Culture-dependent techniques and culture-independent 16S r DNA metagenomic analyses were employed to isolate and study the interactions of native and transient colonizers from human oral samples. Among the 66 human individuals of both healthy and comorbid individuals, the most abundant isolate was found to be Bacillus amyloliquefaciens MCC 4424. In addition, the more prevalent culturable isolate from the healthy samples was Streptococcus salivarius MTCC 13009, whereas in comorbid samples Staphylococcus pasteuri MTCC 13076, Rothia dentocariosa MTCC 13010 and Pseudomonas aeruginosa MTCC 13077 were prevalent to a greater extent. 16S rDNA metagenomic analyses revealed the prevalence and abundance of genera such as Bacteroidetes and Proteobacteria in healthy individuals; consequently, Fusobacteria and Firmicutes were observed mostly in comorbid individuals. The significant differences in bacterial population density were observed in terms of the Shannon index (p = 0.5145) and Simpson index (p = 0.9061) between the healthy and comorbid groups. B. amyloliquefaciens MCC 4424 exhibits antagonistic behavior when grown as a dual-species with native and transient colonizers. This result is very consistent with the findings of antibiofilm studies using confocal laser scanning microscopy, which revealed a significant reduction in biofilm biovolume (73 %) and maximum thickness (80 %) and an increase in the rough coefficient of biofilms (30 %). Our data suggested that B. amyloliquefaciens MCC 4424 can be a native colonizer of Indian sub-populations. It may act as a novel candidate for oral healthcare applications and greatly aids in the regulation of transient species in the oral cavity.}, } @article {pmid38631226, year = {2024}, author = {Rubin-Blum, M and Makovsky, Y and Rahav, E and Belkin, N and Antler, G and Sisma-Ventura, G and Herut, B}, title = {Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea.}, journal = {Marine environmental research}, volume = {198}, number = {}, pages = {106497}, doi = {10.1016/j.marenvres.2024.106497}, pmid = {38631226}, issn = {1879-0291}, mesh = {Mediterranean Sea ; *Archaea/genetics/metabolism ; *Seawater/microbiology ; *Bacteria/metabolism/genetics/classification ; *Microbiota ; Carbon/metabolism ; Salts ; Methane/metabolism ; }, abstract = {Discharge of gas-rich brines fuels productive chemosynthetic ecosystems in the deep sea. In these salty, methanic and sulfidic brines, microbial communities adapt to specific niches along the physicochemical gradients. However, the molecular mechanisms that underpin these adaptations are not fully known. Using metagenomics, we investigated the dense (∼10[6] cell ml[-1]) microbial communities that occupy small deep-sea brine pools found in the Southeastern Mediterranean Sea (1150 m water depth, ∼22 °C, ∼60 PSU salinity, sulfide, methane, ammonia reaching millimolar levels, and oxygen usually depleted), reaching high productivity rates of 685 μg C L[-1] d[-1] ex-situ. We curated 266 metagenome-assembled genomes of bacteria and archaea from the several pools and adjacent sediment-water interface, highlighting the dominance of a single Sulfurimonas, which likely fuels its autotrophy using sulfide oxidation or inorganic sulfur disproportionation. This lineage may be dominant in its niche due to genome streamlining, limiting its metabolic repertoire, particularly by using a single variant of sulfide: quinone oxidoreductase. These primary producers co-exist with ANME-2c archaea that catalyze the anaerobic oxidation of methane. Other lineages can degrade the necromass aerobically (Halomonas and Alcanivorax), or anaerobically through fermentation of macromolecules (e.g., Caldatribacteriota, Bipolaricaulia, Chloroflexota, etc). These low-abundance organisms likely support the autotrophs, providing energy-rich H2, and vital organics such as vitamin B12.}, } @article {pmid38630611, year = {2024}, author = {Roy, G and Prifti, E and Belda, E and Zucker, JD}, title = {Deep learning methods in metagenomics: a review.}, journal = {Microbial genomics}, volume = {10}, number = {4}, pages = {}, pmid = {38630611}, issn = {2057-5858}, support = {U01 AI069470/AI/NIAID NIH HHS/United States ; UM1 AI069470/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Deep Learning ; *Microbiota ; Metagenome ; *Gastrointestinal Microbiome ; Metagenomics/methods ; }, abstract = {The ever-decreasing cost of sequencing and the growing potential applications of metagenomics have led to an unprecedented surge in data generation. One of the most prevalent applications of metagenomics is the study of microbial environments, such as the human gut. The gut microbiome plays a crucial role in human health, providing vital information for patient diagnosis and prognosis. However, analysing metagenomic data remains challenging due to several factors, including reference catalogues, sparsity and compositionality. Deep learning (DL) enables novel and promising approaches that complement state-of-the-art microbiome pipelines. DL-based methods can address almost all aspects of microbiome analysis, including novel pathogen detection, sequence classification, patient stratification and disease prediction. Beyond generating predictive models, a key aspect of these methods is also their interpretability. This article reviews DL approaches in metagenomics, including convolutional networks, autoencoders and attention-based models. These methods aggregate contextualized data and pave the way for improved patient care and a better understanding of the microbiome's key role in our health.}, } @article {pmid38630153, year = {2024}, author = {Salam, LB}, title = {Metagenomic investigations into the microbial consortia, degradation pathways, and enzyme systems involved in the biodegradation of plastics in a tropical lentic pond sediment.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {6}, pages = {172}, pmid = {38630153}, issn = {1573-0972}, mesh = {*Microbial Consortia/genetics ; *Ecosystem ; Ponds ; Lipase ; Adipates ; Polymers ; *Phthalic Acids ; }, abstract = {The exploitation of exciting features of plastics for diverse applications has resulted in significant plastic waste generation, which negatively impacts environmental compartments, metabolic processes, and the well-being of aquatic ecosystems biota. A shotgun metagenomic approach was deployed to investigate the microbial consortia, degradation pathways, and enzyme systems involved in the degradation of plastics in a tropical lentic pond sediment (APS). Functional annotation of the APS proteome (ORFs) using the PlasticDB database revealed annotation of 1015 proteins of enzymes such as depolymerase, esterase, lipase, hydrolase, nitrobenzylesterase, chitinase, carboxylesterase, polyesterase, oxidoreductase, polyamidase, PETase, MHETase, laccase, alkane monooxygenase, among others involved in the depolymerization of the plastic polymers. It also revealed that polyethylene glycol (PEG), polyhydroxyalkanoates (PHA), polyhydroxybutyrate (PHB), polylactic acid (PLA), polybutylene adipate terephthalate (PBAT), polyethylene terephthalate (PET), and nylon have the highest number of annotated enzymes. Further annotation using the KEGG GhostKOALA revealed that except for terephthalate, all the other degradation products of the plastic polymers depolymerization such as glyoxylate, adipate, succinate, 1,4-butanediol, ethylene glycol, lactate, and acetaldehyde were further metabolized to intermediates of the tricarboxylic acid cycle. Taxonomic characterization of the annotated proteins using the AAI Profiler and BLASTP revealed that Pseudomonadota members dominate most plastic types, followed by Actinomycetota and Acidobacteriota. The study reveals novel plastic degraders from diverse phyla hitherto not reported to be involved in plastic degradation. This suggests that plastic pollution in aquatic environments is prevalent with well-adapted degrading communities and could be the silver lining in mitigating the impacts of plastic pollution in aquatic environments.}, } @article {pmid38627868, year = {2024}, author = {Ho, M and Nguyen, HN and Van Hoang, M and Bui, TTT and Vu, BQ and Dinh, THT and Vo, HTM and Blaydon, DC and Eldirany, SA and Bunick, CG and Bui, CB}, title = {Altered skin microbiome, inflammation, and JAK/STAT signaling in Southeast Asian ichthyosis patients.}, journal = {Human genomics}, volume = {18}, number = {1}, pages = {38}, pmid = {38627868}, issn = {1479-7364}, support = {K08 AR070290/AR/NIAMS NIH HHS/United States ; K08AR070290/AR/NIAMS NIH HHS/United States ; R03 AR076484/AR/NIAMS NIH HHS/United States ; R01 AR079428/AR/NIAMS NIH HHS/United States ; }, mesh = {Humans ; Case-Control Studies ; Leukocytes, Mononuclear ; Southeast Asian People ; Inflammation/genetics ; *Microbiota/genetics ; *Ichthyosis/genetics ; }, abstract = {BACKGROUND: Congenital ichthyosis (CI) is a collective group of rare hereditary skin disorders. Patients present with epidermal scaling, fissuring, chronic inflammation, and increased susceptibility to infections. Recently, there is increased interest in the skin microbiome; therefore, we hypothesized that CI patients likely exhibit an abnormal profile of epidermal microbes because of their various underlying skin barrier defects. Among recruited individuals of Southeast Asian ethnicity, we performed skin meta-genomics (i.e., whole-exome sequencing to capture the entire multi-kingdom profile, including fungi, protists, archaea, bacteria, and viruses), comparing 36 CI patients (representing seven subtypes) with that of 15 CI age-and gender-matched controls who had no family history of CI.

RESULTS: This case-control study revealed 20 novel and 31 recurrent pathogenic variants. Microbiome meta-analysis showed distinct microbial populations, decreases in commensal microbiota, and higher colonization by pathogenic species associated with CI; these were correlated with increased production of inflammatory cytokines and Th17- and JAK/STAT-signaling pathways in peripheral blood mononuclear cells. In the wounds of CI patients, we identified specific changes in microbiota and alterations in inflammatory pathways, which are likely responsible for impaired wound healing.

CONCLUSIONS: Together, this research enhances our understanding of the microbiological, immunological, and molecular properties of CI and should provide critical information for improving therapeutic management of CI patients.}, } @article {pmid38627687, year = {2024}, author = {Zhang, K and Paul, K and Jacobs, JP and Cockburn, MG and Bronstein, JM and Del Rosario, I and Ritz, B}, title = {Ambient long-term exposure to organophosphorus pesticides and the human gut microbiome: an observational study.}, journal = {Environmental health : a global access science source}, volume = {23}, number = {1}, pages = {41}, pmid = {38627687}, issn = {1476-069X}, support = {P30 ES007048/ES/NIEHS NIH HHS/United States ; R01 ES031106/ES/NIEHS NIH HHS/United States ; K01AG07204401/AG/NIA NIH HHS/United States ; R01ES031106/ES/NIEHS NIH HHS/United States ; R01 ES010544/ES/NIEHS NIH HHS/United States ; IK2 CX001717/CX/CSRD VA/United States ; }, mesh = {Aged ; Humans ; Bacteria ; *Gastrointestinal Microbiome ; *Microbiota ; Organophosphorus Compounds ; *Parkinson Disease ; *Pesticides/adverse effects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Organophosphorus pesticides (OP) have been associated with various human health conditions. Animal experiments and in-vitro models suggested that OP may also affect the gut microbiota. We examined associations between ambient chronic exposure to OP and gut microbial changes in humans.

METHODS: We recruited 190 participants from a community-based epidemiologic study of Parkinson's disease living in a region known for heavy agricultural pesticide use in California. Of these, 61% of participants had Parkinson's disease and their mean age was 72 years. Microbiome and predicted metagenome data were generated by 16S rRNA gene sequencing of fecal samples. Ambient long-term OP exposures were assessed using pesticide application records combined with residential addresses in a geographic information system. We examined gut microbiome differences due to OP exposures, specifically differences in microbial diversity based on the Shannon index and Bray-Curtis dissimilarities, and differential taxa abundance and predicted Metacyc pathway expression relying on regression models and adjusting for potential confounders.

RESULTS: OP exposure was not associated with alpha or beta diversity of the gut microbiome. However, the predicted metagenome was sparser and less evenly expressed among those highly exposed to OP (p = 0.04). Additionally, we found that the abundance of two bacterial families, 22 genera, and the predicted expression of 34 Metacyc pathways were associated with long-term OP exposure. These pathways included perturbed processes related to cellular respiration, increased biosynthesis and degradation of compounds related to bacterial wall structure, increased biosynthesis of RNA/DNA precursors, and decreased synthesis of Vitamin B1 and B6.

CONCLUSION: In support of previous animal studies and in-vitro findings, our results suggest that ambient chronic OP pesticide exposure alters gut microbiome composition and its predicted metabolism in humans.}, } @article {pmid38626494, year = {2024}, author = {Zhu, Y and Ke, M and Yu, Z and Lei, C and Liu, M and Yang, Y and Lu, T and Zhou, NY and Peijnenburg, WJGM and Tang, T and Qian, H}, title = {Combined effects of azoxystrobin and oxytetracycline on rhizosphere microbiota of Arabidopsis thaliana.}, journal = {Environment international}, volume = {186}, number = {}, pages = {108655}, doi = {10.1016/j.envint.2024.108655}, pmid = {38626494}, issn = {1873-6750}, mesh = {*Rhizosphere ; *Arabidopsis/microbiology/drug effects ; *Oxytetracycline/toxicity ; *Microbiota/drug effects ; *Soil Microbiology ; *Strobilurins ; *Pyrimidines ; Soil Pollutants/toxicity ; Pesticides/toxicity ; Biodegradation, Environmental ; }, abstract = {The rhizosphere is one of the key determinants of plant health and productivity. Mixtures of pesticides are commonly used in intensified agriculture. However, the combined mechanisms underlying their impacts on soil microbiota remain unknown. The present study revealed that the rhizosphere microbiota was more sensitive to azoxystrobin and oxytetracycline, two commonly used pesticides, than was the microbiota present in bulk soil. Moreover, the rhizosphere microbiota enhanced network complexity and stability and increased carbohydrate metabolism and xenobiotic biodegradation as well as the expression of metabolic genes involved in defence against pesticide stress. Co-exposure to azoxystrobin and oxytetracycline had antagonistic effects on Arabidopsis thaliana growth and soil microbial variation by recruiting organic-degrading bacteria and regulating ABC transporters to reduce pesticide uptake. Our study explored the composition and function of soil microorganisms through amplicon sequencing and metagenomic approaches, providing comprehensive insights into the synergistic effect of plants and rhizosphere microbiota on pesticides and contributing to our understanding of the ecological risks associated with pesticide use.}, } @article {pmid38626236, year = {2024}, author = {Remenyik, J and Csige, L and Dávid, P and Fauszt, P and Szilágyi-Rácz, AA and Szőllősi, E and Bacsó, ZR and Szepsy Jnr, I and Molnár, K and Rácz, C and Fidler, G and Kállai, Z and Stündl, L and Dobos, AC and Paholcsek, M}, title = {Exploring the interplay between the core microbiota, physicochemical factors, agrobiochemical cycles in the soil of the historic tokaj mád wine region.}, journal = {PloS one}, volume = {19}, number = {4}, pages = {e0300563}, pmid = {38626236}, issn = {1932-6203}, mesh = {Humans ; Soil/chemistry ; *Wine ; *Microbiota/genetics ; Bacteria ; *Ascomycota ; Steroids/metabolism ; Soil Microbiology ; }, abstract = {A Hungarian survey of Tokaj-Mád vineyards was conducted. Shotgun metabarcoding was applied to decipher the microbial-terroir. The results of 60 soil samples showed that there were three dominant fungal phyla, Ascomycota 66.36% ± 15.26%, Basidiomycota 18.78% ± 14.90%, Mucoromycota 11.89% ± 8.99%, representing 97% of operational taxonomic units (OTUs). Mutual interactions between microbiota diversity and soil physicochemical parameters were revealed. Principal component analysis showed descriptive clustering patterns of microbial taxonomy and resistance gene profiles in the case of the four historic vineyards (Szent Tamás, Király, Betsek, Nyúlászó). Linear discriminant analysis effect size was performed, revealing pronounced shifts in community taxonomy based on soil physicochemical properties. Twelve clades exhibited the most significant shifts (LDA > 4.0), including the phyla Verrucomicrobia, Bacteroidetes, Chloroflexi, and Rokubacteria, the classes Acidobacteria, Deltaproteobacteria, Gemmatimonadetes, and Betaproteobacteria, the order Sphingomonadales, Hypomicrobiales, as well as the family Sphingomonadaceae and the genus Sphingomonas. Three out of the four historic vineyards exhibited the highest occurrences of the bacterial genus Bradyrhizobium, known for its positive influence on plant development and physiology through the secretion of steroid phytohormones. During ripening, the taxonomical composition of the soil fungal microbiota clustered into distinct groups depending on altitude, differences that were not reflected in bacteriomes. Network analyses were performed to unravel changes in fungal interactiomes when comparing postveraison and preharvest samples. In addition to the arbuscular mycorrhiza Glomeraceae, the families Mycosphaerellacae and Rhyzopodaceae and the class Agaricomycetes were found to have important roles in maintaining soil microbial community resilience. Functional metagenomics showed that the soil Na content stimulated several of the microbiota-related agrobiogeochemical cycles, such as nitrogen and sulphur metabolism; steroid, bisphenol, toluene, dioxin and atrazine degradation and the synthesis of folate.}, } @article {pmid38625103, year = {2024}, author = {Zhao, Z and Li, C and Huang, J and Yuan, X and Cui, Y and Liu, Y and Zhou, Y and Zhu, Z and Zhang, Z}, title = {Phlorizin Limits Bovine Viral Diarrhea Virus Infection in Mice via Regulating Gut Microbiota Composition.}, journal = {Journal of agricultural and food chemistry}, volume = {72}, number = {17}, pages = {9906-9914}, doi = {10.1021/acs.jafc.4c01228}, pmid = {38625103}, issn = {1520-5118}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; Cattle ; *Bacteria/classification/isolation & purification/genetics/drug effects ; *Bovine Virus Diarrhea-Mucosal Disease ; *Diarrhea Viruses, Bovine Viral/drug effects ; Antiviral Agents/pharmacology/administration & dosage ; Feces/microbiology/virology ; Female ; Mice, Inbred BALB C ; Male ; }, abstract = {Phlorizin (PHZ) is one of the main pharmacologically active ingredients in Lithocarpus polystachyus. We have previously shown that PHZ inhibits the replication of bovine viral diarrhea virus (BVDV), but the exact antiviral mechanism, especially in vivo, is still unknown. Here, we further confirm that PHZ has good protective effects in BVDV-infected mice. We analyzed BVDV-induced CD3[+], CD4[+], and CD8[+] T cells among peripheral blood lymphocytes and found that PHZ significantly restored their percentage. Metagenomic analyses revealed that PHZ markedly improved the richness and diversity of intestinal microbiota and increased the abundance of potentially health-related microbes (families Lachnosipiraceae, Ruminococcaceae, and Oscillospiraceae). Specifically, the relative abundance of short chain fatty acid (SCFA)-producing bacteria, including Lachnospiraceae_UCG-006, unclassified_f_Ruminococcaceae, Oscillibacter, Intestinimonas, Blautia, and Lachnoclostridium increased significantly after PHZ treatment. Interestingly, BVDV-infected mice that received fecal microbiota from PHZ-treated mice (PHZ-FMT) had a significantly lower viral load in the duodenum and jejunum than untreated mice. Pathological lesions of duodenum and jejunum were also greatly reduced in the PHZ-FMT group, confirming a significant antiviral effect. These findings show that gut microbiota play an important role in PHZ's antiviral activity and suggest that their targeted intervention might be a promising endogenous strategy to prevent and control BVDV.}, } @article {pmid38625060, year = {2024}, author = {Garvin, ZK and Abades, SR and Trefault, N and Alfaro, FD and Sipes, K and Lloyd, KG and Onstott, TC}, title = {Prevalence of trace gas-oxidizing soil bacteria increases with radial distance from Polloquere hot spring within a high-elevation Andean cold desert.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38625060}, issn = {1751-7370}, support = {/NASA/NASA/United States ; //Astrobiology Early Career Collaboration Award/ ; //High Meadows Environmental Institute at Princeton University/ ; //Walbridge Fund Graduate Award/ ; G110-21-W8189//W.M. Keck Foundation/ ; 1170995//National Fund for Scientific and Technological Development/ ; //National Science Foundation/ ; 2121637//Frontier Research in Earth Sciences/ ; 2151015//Division of Ocean Sciences/ ; }, mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Desert Climate ; *Hot Springs/microbiology ; *Oxidation-Reduction ; Carbon Monoxide/metabolism ; Hydrogen/metabolism ; Microbiota ; Altitude ; Soil/chemistry ; }, abstract = {High-elevation arid regions harbor microbial communities reliant on metabolic niches and flexibility to survive under biologically stressful conditions, including nutrient limitation that necessitates the utilization of atmospheric trace gases as electron donors. Geothermal springs present "oases" of microbial activity, diversity, and abundance by delivering water and substrates, including reduced gases. However, it is unknown whether these springs exhibit a gradient of effects, increasing their impact on trace gas-oxidizers in the surrounding soils. We assessed whether proximity to Polloquere, a high-altitude geothermal spring in an Andean salt flat, alters the diversity and metabolic structure of nearby soil bacterial populations compared to the surrounding cold desert. Recovered DNA and metagenomic analyses indicate that the spring represents an oasis for microbes in this challenging environment, supporting greater biomass with more diverse metabolic functions in proximal soils that declines sharply with radial distance from the spring. Despite the sharp decrease in biomass, potential rates of atmospheric hydrogen (H2) and carbon monoxide (CO) uptake increase away from the spring. Kinetic estimates suggest this activity is due to high-affinity trace gas consumption, likely as a survival strategy for energy/carbon acquisition. These results demonstrate that Polloquere regulates a gradient of diverse microbial communities and metabolisms, culminating in increased activity of trace gas-oxidizers as the influence of the spring yields to that of the regional salt flat environment. This suggests the spring holds local importance within the context of the broader salt flat and potentially represents a model ecosystem for other geothermal systems in high-altitude desert environments.}, } @article {pmid38624222, year = {2024}, author = {Ali, R and Chaluvadi, SR and Wang, X and Hazzouri, KM and Sudalaimuthuasari, N and Rafi, M and Al-Nuaimi, M and Sasi, S and Antepenko, E and Bennetzen, JL and Amiri, KMA}, title = {Microbiome properties in the root nodules of Prosopis cineraria, a leguminous desert tree.}, journal = {Microbiology spectrum}, volume = {12}, number = {6}, pages = {e0361723}, pmid = {38624222}, issn = {2165-0497}, support = {//KCGEB/ ; }, mesh = {*Microbiota ; *Root Nodules, Plant/microbiology ; *Soil Microbiology ; *Prosopis/microbiology/growth & development ; *Desert Climate ; *Rhizosphere ; Plant Roots/microbiology ; Bacteria/classification/genetics/isolation & purification ; Symbiosis ; Trees/microbiology ; Nitrogen Fixation ; Phylogeny ; }, abstract = {We conducted a comprehensive analysis of the total microbiome and transcriptionally active microbiome communities in the roots and root nodules of Prosopis cineraria, an important leguminous tree in arid regions of many Asian countries. Mature P. cineraria trees growing in the desert did not exhibit any detected root nodules. However, we observed root nodules on the roots of P. cineraria growing on a desert farm and on young plants growing in a growth chamber, when inoculated with rhizosphere soil, including with rhizosphere soil from near desert tree roots that had no nodules. Compared to nearby soil, non-nodulated roots were enriched with Actinobacteria (e.g., Actinophytocola sp.), whereas root nodules sampled from the desert farm and growth chamber had abundant Alphaproteobacteria (e.g., Ensifer sp.). These nodules yielded many microbes in addition to such nitrogen-fixing bacteria as Ensifer and Sinorhizobium species. Significant differences exist in the composition and abundance of microbial isolates between the nodule surface and the nodule endosphere. Shotgun metagenome analysis of nodule endospheres revealed that the root nodules comprised over 90% bacterial DNA, whereas metatranscriptome analysis showed that the plant produces vastly more transcripts than the microbes in these nodules. Control inoculations demonstrated that four out of six Rhizobium, Agrobacterium, or Ensifer isolates purified from P. cineraria nodules produced nodules in the roots of P. cineraria seedlings under greenhouse conditions. The best nodulation was achieved when seedlings were inoculated with a mixture of those bacterial strains. Though root nodulation could be achieved under water stress conditions, nodule number and nodule biomass increased with copious water availability. .IMPORTANCEMicrobial communities were investigated in roots and root nodules of Prosopis cineraria, a leguminous tree species in arid Asian regions that is responsible for exceptionally important contributions to soil fertility in these dramatically dry locations. Soil removed from regions near nodule-free roots on these mature plants contained an abundance of bacteria with the genetic ability to generate nodules and fix nitrogen but did not normally nodulate in their native rhizosphere environment, suggesting a very different co-evolved relationship than that observed for herbaceous legumes. The relative over-expression of the low-gene-density plant DNA compared to the bacterial DNA in the nodules was also unexpected, indicating a very powerful induction of host genetic contributions within the nodule. Finally, the water dependence of nodulation in inoculated seedlings suggested a possible link between early seedling growth (before a deep root system can be developed) and the early development of nitrogen-fixing capability.}, } @article {pmid38623900, year = {2024}, author = {Zhang, Y and Lo, KL and Liman, AN and Feng, XP and Ye, W}, title = {Tongue-Coating Microbial and Metabolic Characteristics in Halitosis.}, journal = {Journal of dental research}, volume = {103}, number = {5}, pages = {484-493}, doi = {10.1177/00220345241230067}, pmid = {38623900}, issn = {1544-0591}, mesh = {Humans ; *Halitosis/microbiology/metabolism ; *Tongue/microbiology ; Male ; *Microbiota ; Female ; Adult ; Metabolome ; Metabolomics/methods ; Middle Aged ; Metagenomics/methods ; Young Adult ; Actinomyces/metabolism ; }, abstract = {Halitosis is a common oral condition, which leads to social embarrassment and affects quality of life. Cumulative evidence has suggested the association of tongue-coating microbiome with the development of intraoral halitosis. The dynamic variations of tongue-coating microbiota and metabolites in halitosis have not been fully elucidated. Therefore, the present study aimed to determine the tongue-coating microbial and metabolic characteristics in halitosis subjects without other oral diseases using metagenomics and metabolomics analysis. The participants underwent oral examination, halitosis assessment, and tongue-coating sample collection for the microbiome and metabolome analysis. It was found that the microbiota richness and diversity were significantly elevated in the halitosis group. Furthermore, species from Actinomyces, Prevotella, Veillonella, and Solobacterium were significantly more abundant in the halitosis group. However, the Rothia and Streptococcus species exhibited opposite tendencies. Eleven Kyoto Encyclopedia of Genes and Genomes pathways were significantly enriched in the halitosis tongue coatings, including cysteine and methionine metabolism. Functional genes related to sulfur, indole, skatole, and cadaverine metabolic processes (such as serA, metH, metK and dsrAB) were identified to be more abundant in the halitosis samples. The metabolome analysis revealed that indole-3-acetic, ornithine, and L-tryptophan were significantly elevated in the halitosis samples. Furthermore, it was observed that the values of volatile sulfur compounds and indole-3-acetic abundances were positively correlated. The multiomics analysis identified the metagenomic and metabolomic characteristics to differentiate halitosis from healthy individuals using the least absolute shrinkage and selection operator logistic regression and random forest classifier. A total of 19 species and 39 metabolites were identified as features in halitosis patients, which included indole-3-acetic acid, Bacillus altitudinis, Candidatus Saccharibacteria, and Actinomyces species. In conclusion, an evident shift in microbiome and metabolome characteristics was observed in the halitosis tongue coating, which may have a potential etiological significance and provide novel insights into the mechanism for halitosis.}, } @article {pmid38622738, year = {2024}, author = {Wu, LY and Wijesekara, Y and Piedade, GJ and Pappas, N and Brussaard, CPD and Dutilh, BE}, title = {Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {97}, pmid = {38622738}, issn = {1474-760X}, support = {Consolidator grant 865694//H2020 European Research Council/ ; Consolidator grant 865694//H2020 European Research Council/ ; 955974//H2020 Marie Skłodowska-Curie Actions/ ; grant ALWPP.2016.019//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; grant ALWPP.2016.019//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; 865694/ERC_/European Research Council/International ; }, mesh = {Metagenome ; Ecosystem ; Metagenomics/methods ; Computational Biology/methods ; Databases, Genetic ; *Viruses/genetics ; }, abstract = {BACKGROUND: As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identification tools have been developed for this task, making it challenging to choose the right tools, parameters, and cutoffs. As all these tools measure different biological signals, and use different algorithms and training and reference databases, it is imperative to conduct an independent benchmarking to give users objective guidance.

RESULTS: We compare the performance of nine state-of-the-art virus identification tools in thirteen modes on eight paired viral and microbial datasets from three distinct biomes, including a new complex dataset from Antarctic coastal waters. The tools have highly variable true positive rates (0-97%) and false positive rates (0-30%). PPR-Meta best distinguishes viral from microbial contigs, followed by DeepVirFinder, VirSorter2, and VIBRANT. Different tools identify different subsets of the benchmarking data and all tools, except for Sourmash, find unique viral contigs. Performance of tools improved with adjusted parameter cutoffs, indicating that adjustment of parameter cutoffs before usage should be considered.

CONCLUSIONS: Together, our independent benchmarking facilitates selecting choices of bioinformatic virus identification tools and gives suggestions for parameter adjustments to viromics researchers.}, } @article {pmid38622589, year = {2024}, author = {Gao, J and Yang, Y and Xiang, X and Zheng, H and Yi, X and Wang, F and Liang, Z and Chen, D and Shi, W and Wang, L and Wu, D and Feng, S and Huang, Q and Li, X and Shu, W and Chen, R and Zhong, N and Wang, Z}, title = {Human genetic associations of the airway microbiome in chronic obstructive pulmonary disease.}, journal = {Respiratory research}, volume = {25}, number = {1}, pages = {165}, pmid = {38622589}, issn = {1465-993X}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/diagnosis/genetics/complications ; *Microbiota/genetics ; Sputum ; Transcriptome ; Human Genetics ; Adaptor Proteins, Signal Transducing/genetics ; }, abstract = {Little is known about the relationships between human genetics and the airway microbiome. Deeply sequenced airway metagenomics, by simultaneously characterizing the microbiome and host genetics, provide a unique opportunity to assess the microbiome-host genetic associations. Here we performed a co-profiling of microbiome and host genetics with the identification of over 5 million single nucleotide polymorphisms (SNPs) through deep metagenomic sequencing in sputum of 99 chronic obstructive pulmonary disease (COPD) and 36 healthy individuals. Host genetic variation was the most significant factor associated with the microbiome except for geography and disease status, with its top 5 principal components accounting for 12.11% of the microbiome variability. Within COPD individuals, 113 SNPs mapped to candidate genes reported as genetically associated with COPD exhibited associations with 29 microbial species and 48 functional modules (P < 1 × 10[-5]), where Streptococcus salivarius exhibits the strongest association to SNP rs6917641 in TBC1D32 (P = 9.54 × 10[-8]). Integration of concurrent host transcriptomic data identified correlations between the expression of host genes and their genetically-linked microbiome features, including NUDT1, MAD1L1 and Veillonella parvula, TTLL9 and Stenotrophomonas maltophilia, and LTA4H and Haemophilus influenzae. Mendelian randomization analyses revealed a potential causal link between PARK7 expression and microbial type III secretion system, and a genetically-mediated association between COPD and increased relative abundance of airway Streptococcus intermedius. These results suggest a previously underappreciated role of host genetics in shaping the airway microbiome and provide fresh hypotheses for genetic-based host-microbiome interactions in COPD.}, } @article {pmid38621967, year = {2024}, author = {Wang, ZH and Liu, S and Yang, G and Lu, ZY and Zhu, RQ and Li, Y and Shen, Y and Kang, LP and Chen, ML}, title = {[Effects of organic fertilizer from traditional Chinese medicine residues on growth and soil microbial community of Salvia miltiorrhiza by metagenomic technique].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {49}, number = {5}, pages = {1206-1216}, doi = {10.19540/j.cnki.cjcmm.20231213.101}, pmid = {38621967}, issn = {1001-5302}, mesh = {Soil/chemistry ; *Salvia miltiorrhiza/chemistry ; Fertilizers ; Medicine, Chinese Traditional ; Bacteria/genetics ; *Mycobiome ; Soil Microbiology ; }, abstract = {Soil microbiome is a key evaluation index of soil health. Previous studies have shown that organic fertilizer from traditional Chinese medicine(TCM)residues can improve the yield and quality of cultivated traditional Chinese medicinal materials. However, there are few reports on the effects of organic fertilizer from TCM residues on soil microbiome. Therefore, on the basis of evaluating the effects of organic fertilizer from TCM residues on the yield and quality of cultivated Salvia miltiorrhiza, the metagenomic sequencing technique was used to study the effects of organic fertilizer from TCM residues on rhizosphere microbiome community and function of cultivated S. miltiorrhiza. The results showed that:(1) the application of organic fertilizer from TCM residues promoted the growth of S. miltiorrhiza and the accumulation of active components, and the above-ground and underground dry weight and fresh weight of S. miltiorrhiza increased by 371.4%, 288.3%, 313.4%, and 151.9%. The increases of rosmarinic acid and salvianolic acid B were 887.0% and 183.0%.(2)The application of organic fertilizer from TCM residues significantly changed the rhizosphere bacterial and fungal community structures, and the microbial community composition was significantly different.(3)The relative abundance of soil-beneficial bacteria, such as Nitrosospira multiformis, Bacillus subtilis, Lysobacter enzymogenes, and Trichoderma was significantly increased by the application of organic fertilizer from TCM residues.(4)KEGG function prediction analysis showed that metabolism-related microorganisms were more easily enriched in the soil environment after organic fertilizer application. The abundance of functional genes related to nitrification and denitrification could also be increased after the application of organic fertilizer from TCM residues. The results of this study provide guidance for the future application of organic fertilizer from TCM residues in the cultivation of traditio-nal Chinese medicinal materials and enrich the content of green cultivation technology of traditional Chinese medicinal materials.}, } @article {pmid38618705, year = {2024}, author = {Sarkar, S and Anyaso-Samuel, S and Qiu, P and Datta, S}, title = {Multiblock partial least squares and rank aggregation: Applications to detection of bacteriophages associated with antimicrobial resistance in the presence of potential confounding factors.}, journal = {Statistics in medicine}, volume = {43}, number = {13}, pages = {2527-2546}, doi = {10.1002/sim.10058}, pmid = {38618705}, issn = {1097-0258}, mesh = {*Bacteriophages/genetics ; Humans ; Least-Squares Analysis ; Metagenomics/methods ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Confounding Factors, Epidemiologic ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Microbiota/drug effects ; }, abstract = {Urban environments, characterized by bustling mass transit systems and high population density, host a complex web of microorganisms that impact microbial interactions. These urban microbiomes, influenced by diverse demographics and constant human movement, are vital for understanding microbial dynamics. We explore urban metagenomics, utilizing an extensive dataset from the Metagenomics & Metadesign of Subways & Urban Biomes (MetaSUB) consortium, and investigate antimicrobial resistance (AMR) patterns. In this pioneering research, we delve into the role of bacteriophages, or "phages"-viruses that prey on bacteria and can facilitate the exchange of antibiotic resistance genes (ARGs) through mechanisms like horizontal gene transfer (HGT). Despite their potential significance, existing literature lacks a consensus on their significance in ARG dissemination. We argue that they are an important consideration. We uncover that environmental variables, such as those on climate, demographics, and landscape, can obscure phage-resistome relationships. We adjust for these potential confounders and clarify these relationships across specific and overall antibiotic classes with precision, identifying several key phages. Leveraging machine learning tools and validating findings through clinical literature, we uncover novel associations, adding valuable insights to our comprehension of AMR development.}, } @article {pmid38617453, year = {2024}, author = {Chen, SJ and Zhang, DY and Wu, X and Zhang, FM and Cui, BT and Huang, YH and Zhang, ZL and Wang, R and Bai, FH}, title = {Washed microbiota transplantation for Crohn's disease: A metagenomic, metatranscriptomic, and metabolomic-based study.}, journal = {World journal of gastroenterology}, volume = {30}, number = {11}, pages = {1572-1587}, pmid = {38617453}, issn = {2219-2840}, mesh = {Humans ; Amino Acids ; *Antifibrinolytic Agents ; *Crohn Disease/diagnosis/therapy ; Escherichia coli ; Metagenome ; *Microbiota ; Prospective Studies ; }, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is a promising therapeutic approach for treating Crohn's disease (CD). The new method of FMT, based on the automatic washing process, was named as washed microbiota transplantation (WMT). Most existing studies have focused on observing the clinical phenomena. However, the mechanism of action of FMT for the effective management of CD-particularly in-depth multi-omics analysis involving the metagenome, metatranscriptome, and metabolome-has not yet been reported.

AIM: To assess the efficacy of WMT for CD and explore alterations in the microbiome and metabolome in response to WMT.

METHODS: We conducted a prospective, open-label, single-center clinical study. Eleven CD patients underwent WMT. Their clinical responses (defined as a decrease in their CD Activity Index score of > 100 points) and their microbiome (metagenome, metatranscriptome) and metabolome profiles were evaluated three months after the procedure.

RESULTS: Seven of the 11 patients (63.6%) showed an optimal clinical response three months post-WMT. Gut microbiome diversity significantly increased after WMT, consistent with improved clinical symptoms. Comparison of the metagenome and metatranscriptome analyses revealed consistent alterations in certain strains, such as Faecalibacterium prausnitzii, Roseburia intestinalis, and Escherichia coli. In addition, metabolomics analyses demonstrated that CD patients had elevated levels of various amino acids before treatment compared to the donors. However, levels of vital amino acids that may be associated with disease progression (e.g., L-glutamic acid, gamma-glutamyl-leucine, and prolyl-glutamine) were reduced after WMT.

CONCLUSION: WMT demonstrated therapeutic efficacy in CD treatment, likely due to the effective reconstruction of the patient's microbiome. Multi-omics techniques can effectively help decipher the potential mechanisms of WMT in treating CD.}, } @article {pmid38614455, year = {2024}, author = {Li, X and Kurahara, LH and Zhao, Z and Zhao, F and Ishikawa, R and Ohmichi, K and Li, G and Yamashita, T and Hashimoto, T and Hirano, M and Sun, Z and Hirano, K}, title = {Therapeutic Effect of Proteinase-Activated Receptor-1 Antagonist on Colitis-Associated Carcinogenesis.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {18}, number = {1}, pages = {105-131}, pmid = {38614455}, issn = {2352-345X}, mesh = {Animals ; *Receptor, PAR-1/metabolism/antagonists & inhibitors ; Humans ; Mice ; Caco-2 Cells ; *Dextran Sulfate/toxicity ; *Azoxymethane/toxicity ; *Disease Models, Animal ; *Gastrointestinal Microbiome/drug effects ; Male ; Colitis/complications/chemically induced/pathology/drug therapy ; Carcinogenesis/drug effects/pathology ; STAT3 Transcription Factor/metabolism ; Myofibroblasts/metabolism/pathology/drug effects ; Colitis-Associated Neoplasms/pathology/microbiology/drug therapy/immunology ; Thrombin/metabolism ; Mice, Inbred C57BL ; Crohn Disease/pathology/drug therapy/microbiology/chemically induced ; }, abstract = {BACKGROUND & AIMS: Inflammatory bowel disease is associated with carcinogenesis, which limits the prognosis of the patients. The local expression of proteinases and proteinase-activated receptor 1 (PAR1) increases in inflammatory bowel disease. The present study investigated the therapeutic effects of PAR1 antagonism on colitis-associated carcinogenesis.

METHODS: A colitis-associated carcinogenesis model was prepared in mice by treatment with azoxymethane (AOM) and dextran sulfate sodium (DSS). PAR1 antagonist E5555 was administered in long- and short-term protocol, starting on the day of AOM injection and 1 week after completing AOM/DSS treatment, respectively. The fecal samples were collected for metagenome analysis of gut microbiota. The intestinal myofibroblasts of the Crohn's disease patients were used to elucidate underlying cellular mechanisms. Caco-2 cells were used to investigate a possible source of PAR1 agonist proteinases.

RESULTS: AOM/DSS model showed weight loss, diarrhea, tumor development, inflammation, fibrosis, and increased production of inflammatory cytokines. The β-diversity, but not α-diversity, of microbiota significantly differed between AOM/DSS and control mice. E5555 alleviated these pathological changes and altered the microbiota β-diversity in AOM/DSS mice. The thrombin expression was up-regulated in tumor and non-tumor areas, whereas PAR1 mRNA expression was higher in tumor areas compared with non-tumor areas. E5555 inhibited thrombin-triggered elevation of cytosolic Ca[2+] concentration and ERK1/2 phosphorylation, as well as IL6-induced signal transducer and activator of transcription 3 (STAT3) phosphorylation in intestinal myofibroblasts. Caco-2 cell-conditioned medium contained immunoreactive thrombin, which cleaved the recombinant protein containing the extracellular domain of PAR1 at the thrombin cleavage site.

CONCLUSIONS: PAR1 antagonism is proposed to be a novel therapeutic strategy for treatment of inflammatory bowel disease and its associated carcinogenesis.}, } @article {pmid38614128, year = {2024}, author = {Li, C and Guo, X and He, Y and Wang, J and Hao, J and Liu, X}, title = {Cohabiting with ulcerative colitis patients decreases differences of gut microbiome between healthy individuals and the patients.}, journal = {Annals of medicine}, volume = {56}, number = {1}, pages = {2337712}, pmid = {38614128}, issn = {1365-2060}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colitis, Ulcerative/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Inflammation ; }, abstract = {Background: Ulcerative colitis (UC), which is characterized by chronic relapsing inflammation of the colon, results from a complex interaction of factors involving the host, environment, and microbiome. The present study aimed to investigate the gut microbial composition and metabolic variations in patients with UC and their spouses. Materials and Methods: Fecal samples were collected from 13 healthy spouses and couples with UC. 16S rRNA gene amplicon sequencing and metagenomics sequencing were used to analyze gut microbiota composition, pathways, gene expression, and enzyme activity, followed by the Kyoto Encyclopedia of Genes and Genomes. Results: We found that the microbiome diversity of couples with UC decreased, especially that of UC patients. Bacterial composition, such as Firmicutes, was altered between UC patients and healthy controls, but was not significantly different between UC patients and their spouses. This has also been observed in pathways, such as metabolism, genetic information processing, organismal systems, and human diseases. However, the genes and enzymes of spouses with UC were not significantly different from those of healthy individuals. Furthermore, the presence of Faecalibacterium correlated with oxidative phosphorylation, starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, and the bacterial secretion system, showed a marked decline in the UC group compared with their spouses, but did not vary between healthy couples. Conclusion: Our study revealed that cohabitation with UC patients decreased differences in the gut microbiome between healthy individuals and patients. Not only was the composition and diversity of the microbiota diminished, but active pathways also showed some decline. Furthermore, Firmicutes, Faecalibacterium, and the four related pathways may be associated with the pathological state of the host rather than with human behavior.}, } @article {pmid38613799, year = {2024}, author = {Zhanbo, Q and Jing, Z and Shugao, H and Yinhang, W and Jian, C and Xiang, Y and Feimin, Z and Jian, L and Xinyue, W and Wei, W and Shuwen, H}, title = {Age and aging process alter the gut microbes.}, journal = {Aging}, volume = {16}, number = {8}, pages = {6839-6851}, pmid = {38613799}, issn = {1945-4589}, mesh = {Humans ; *Gastrointestinal Microbiome ; Middle Aged ; *Aging/physiology ; Aged ; Male ; Female ; *Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; Age Factors ; Aged, 80 and over ; }, abstract = {BACKGROUND: Gut microbes and age are both factors that influence the development of disease. The community structure of gut microbes is affected by age.

OBJECTIVE: To plot time-dependent gut microbe profiles in individuals over 45 years old and explore the correlation between age and gut microbes.

METHODS: Fecal samples were collected from 510 healthy individuals over 45 years old. Shannon index, Simpson index, Ace index, etc. were used to analyze the diversity of gut microbes. The beta diversity analysis, including non-metric multidimensional scaling (NMDS), was used to analyze community distribution. Linear discriminant analysis (LDA) and random forest (RF) algorithm were used to analyze the differences of gut microbes. Trend analysis was used to plot the abundances of characteristic gut microbes in different ages.

RESULTS: The individuals aged 45-49 had the highest richness of gut bacteria. Fifteen characteristic gut microbes, including Siphoviridae and Bifidobacterium breve, were screened by RF algorithm. The abundance of Ligiactobacillus and Microviridae were higher in individuals older than 65 years. Moreover, the abundance of Blautia_A massiliensis, Lubbockvirus and Enterocloster clostridioformis decreased with age and the abundance of Klebsiella variicola and Prevotella increased with age. The functional genes, such as human diseases and aging, were significantly different among different aged individuals.

CONCLUSIONS: The individuals in different ages have characteristic gut microbes. The changes in community structure of gut microbes may be related to age-induced diseases.}, } @article {pmid38613781, year = {2024}, author = {Gheorghe, CE and Leigh, SJ and Tofani, GSS and Bastiaanssen, TFS and Lyte, JM and Gardellin, E and Govindan, A and Strain, C and Martinez-Herrero, S and Goodson, MS and Kelley-Loughnane, N and Cryan, JF and Clarke, G}, title = {The microbiota drives diurnal rhythms in tryptophan metabolism in the stressed gut.}, journal = {Cell reports}, volume = {43}, number = {4}, pages = {114079}, doi = {10.1016/j.celrep.2024.114079}, pmid = {38613781}, issn = {2211-1247}, mesh = {*Tryptophan/metabolism ; Animals ; *Circadian Rhythm/physiology ; *Gastrointestinal Microbiome/physiology ; Mice ; Male ; Mice, Inbred C57BL ; Stress, Physiological ; }, abstract = {Chronic stress disrupts microbiota-gut-brain axis function and is associated with altered tryptophan metabolism, impaired gut barrier function, and disrupted diurnal rhythms. However, little is known about the effects of acute stress on the gut and how it is influenced by diurnal physiology. Here, we used germ-free and antibiotic-depleted mice to understand how microbiota-dependent oscillations in tryptophan metabolism would alter gut barrier function at baseline and in response to an acute stressor. Cecal metabolomics identified tryptophan metabolism as most responsive to a 15-min acute stressor, while shotgun metagenomics revealed that most bacterial species exhibiting rhythmicity metabolize tryptophan. Our findings highlight that the gastrointestinal response to acute stress is dependent on the time of day and the microbiome, with a signature of stress-induced functional alterations in the ileum and altered tryptophan metabolism in the colon.}, } @article {pmid38613509, year = {2024}, author = {Ucak, S}, title = {Determination of Bacterial Community Structure of Table Olive via Metagenomic Approach in Şarköy.}, journal = {Chemistry & biodiversity}, volume = {21}, number = {6}, pages = {e202302120}, doi = {10.1002/cbdv.202302120}, pmid = {38613509}, issn = {1612-1880}, mesh = {*Bacteria/genetics/isolation & purification/classification ; *Metagenomics ; *Olea/microbiology ; Turkey ; RNA, Ribosomal, 16S/genetics ; Microbiota ; High-Throughput Nucleotide Sequencing ; }, abstract = {One of the most popular pickled foods created worldwide is table olives. The aim was to identify the bacterial microbiota of table olive samples collected from Şarköy, Tekirdağ-Türkiye using next generation sequencing and 16S metagenomic analysis. Samples were studied as non-pre-enriched (n : 10) and after pre-enrichment (n : 10) to compare the effects of the enrichment process on the bacterial diversity. In non-pre-enriched, the most common genus found was Sphingomonas, followed by Altererythrobacter and Lysobacter. The most common phylum found was Proteobacteria, followed by Bacteroidota and Actinobacteria. In pre-enriched, Bacillus was the most commonly detected genus, followed by Pantoea and Staphylococcus. The most frequently found phylum was Firmicutes, followed by Proteobacteria and Cyanobacteria. This study is the first study for Şarköy, which is the only table olive production place in the Tekirdağ region due to its microclimate feature. Further studies are needed in more table olive samples from different geographical areas to confirm and develop current findings.}, } @article {pmid38613119, year = {2024}, author = {Zhou, Y and Zeng, Y and Wang, R and Pang, J and Wang, X and Pan, Z and Jin, Y and Chen, Y and Yang, Y and Ling, W}, title = {Resveratrol Improves Hyperuricemia and Ameliorates Renal Injury by Modulating the Gut Microbiota.}, journal = {Nutrients}, volume = {16}, number = {7}, pages = {}, pmid = {38613119}, issn = {2072-6643}, support = {81730090//National Natural Science Foundation of China/ ; 81973022//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Mice ; *Hyperuricemia/drug therapy ; *Gastrointestinal Microbiome ; Resveratrol/pharmacology ; Uric Acid ; Kidney Tubules ; Inflammation ; }, abstract = {Resveratrol (RES) has been reported to prevent hyperuricemia (HUA); however, its effect on intestinal uric acid metabolism remains unclear. This study evaluated the impact of RES on intestinal uric acid metabolism in mice with HUA induced by a high-fat diet (HFD). Moreover, we revealed the underlying mechanism through metagenomics, fecal microbiota transplantation (FMT), and 16S ribosomal RNA analysis. We demonstrated that RES reduced the serum uric acid, creatinine, urea nitrogen, and urinary protein levels, and improved the glomerular atrophy, unclear renal tubule structure, fibrosis, and renal inflammation. The results also showed that RES increased intestinal uric acid degradation. RES significantly changed the intestinal flora composition of HFD-fed mice by enriching the beneficial bacteria that degrade uric acid, reducing harmful bacteria that promote inflammation, and improving microbial function via the upregulation of purine metabolism. The FMT results further showed that the intestinal microbiota is essential for the effect of RES on HUA, and that Lactobacillus may play a key role in this process. The present study demonstrated that RES alleviates HFD-induced HUA and renal injury by regulating the gut microbiota composition and the metabolism of uric acid.}, } @article {pmid38613058, year = {2024}, author = {Lombardi, M and Troisi, J and Motta, BM and Torre, P and Masarone, M and Persico, M}, title = {Gut-Liver Axis Dysregulation in Portal Hypertension: Emerging Frontiers.}, journal = {Nutrients}, volume = {16}, number = {7}, pages = {}, pmid = {38613058}, issn = {2072-6643}, mesh = {Humans ; *Hypertension, Portal/metabolism/physiopathology/etiology ; *Gastrointestinal Microbiome/physiology ; *Liver/metabolism ; *Dysbiosis ; Bacterial Translocation ; Animals ; Fecal Microbiota Transplantation ; }, abstract = {Portal hypertension (PH) is a complex clinical challenge with severe complications, including variceal bleeding, ascites, hepatic encephalopathy, and hepatorenal syndrome. The gut microbiota (GM) and its interconnectedness with human health have emerged as a captivating field of research. This review explores the intricate connections between the gut and the liver, aiming to elucidate how alterations in GM, intestinal barrier function, and gut-derived molecules impact the development and progression of PH. A systematic literature search, following PRISMA guidelines, identified 12 original articles that suggest a relationship between GM, the gut-liver axis, and PH. Mechanisms such as dysbiosis, bacterial translocation, altered microbial structure, and inflammation appear to orchestrate this relationship. One notable study highlights the pivotal role of the farnesoid X receptor axis in regulating the interplay between the gut and liver and proposes it as a promising therapeutic target. Fecal transplantation experiments further emphasize the pathogenic significance of the GM in modulating liver maladies, including PH. Recent advancements in metagenomics and metabolomics have expanded our understanding of the GM's role in human ailments. The review suggests that addressing the unmet need of identifying gut-liver axis-related metabolic and molecular pathways holds potential for elucidating pathogenesis and directing novel therapeutic interventions.}, } @article {pmid38612976, year = {2024}, author = {Fagunwa, O and Davies, K and Bradbury, J}, title = {The Human Gut and Dietary Salt: The Bacteroides/Prevotella Ratio as a Potential Marker of Sodium Intake and Beyond.}, journal = {Nutrients}, volume = {16}, number = {7}, pages = {}, pmid = {38612976}, issn = {2072-6643}, support = {FMoH/PTDF//Federal Government of Nigeria/ ; NA//University of Huddersfield/ ; publishing//Queen's University Belfast/ ; }, mesh = {Humans ; *Sodium Chloride, Dietary ; *Microbiota ; Bacteroides ; Bacteroidetes ; Firmicutes ; Prevotella ; Sodium ; }, abstract = {The gut microbiota is a dynamic ecosystem that plays a pivotal role in maintaining host health. The perturbation of these microbes has been linked to several health conditions. Hence, they have emerged as promising targets for understanding and promoting good health. Despite the growing body of research on the role of sodium in health, its effects on the human gut microbiome remain under-explored. Here, using nutrition and metagenomics methods, we investigate the influence of dietary sodium intake and alterations of the human gut microbiota. We found that a high-sodium diet (HSD) altered the gut microbiota composition with a significant reduction in Bacteroides and inverse increase in Prevotella compared to a low-sodium diet (LSD). However, there is no clear distinction in the Firmicutes/Bacteroidetes (F/B) ratio between the two diet types. Metabolic pathway reconstruction revealed the presence of sodium reabsorption genes in the HSD, but not LSD. Since it is currently difficult in microbiome studies to confidently associate the F/B ratio with what is considered healthy (e.g., low sodium) or unhealthy (e.g., high sodium), we suggest that the use of a genus-based ratio such as the Bacteroides/Prevotella (B/P) ratio may be more beneficial for the application of microbiome studies in health.}, } @article {pmid38612702, year = {2024}, author = {McDermott, G and Walsh, A and Crispie, F and Frost, S and Greally, P and Cotter, PD and O'Sullivan, O and Renwick, J}, title = {Insights into the Adolescent Cystic Fibrosis Airway Microbiome Using Shotgun Metagenomics.}, journal = {International journal of molecular sciences}, volume = {25}, number = {7}, pages = {}, pmid = {38612702}, issn = {1422-0067}, support = {/WT_/Wellcome Trust/United Kingdom ; 204814/Z/16/A/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Child ; Humans ; Adolescent ; *Cystic Fibrosis ; Staphylococcus aureus ; Biological Assay ; DNA, Ribosomal ; *Microbiota/genetics ; }, abstract = {Cystic fibrosis (CF) is an inherited genetic disorder which manifests primarily in airway disease. Recent advances in molecular technologies have unearthed the diverse polymicrobial nature of the CF airway. Numerous studies have characterised the genus-level composition of this airway community using targeted 16S rDNA sequencing. Here, we employed whole-genome shotgun metagenomics to provide a more comprehensive understanding of the early CF airway microbiome. We collected 48 sputum samples from 11 adolescents and children with CF over a 12-month period and performed shotgun metagenomics on the Illumina NextSeq platform. We carried out functional and taxonomic analysis of the lung microbiome at the species and strain levels. Correlations between microbial diversity measures and independent demographic and clinical variables were performed. Shotgun metagenomics detected a greater diversity of bacteria than culture-based methods. A large proportion of the top 25 most-dominant species were anaerobes. Samples dominated by Staphylococcus aureus and Prevotella melaninogenica had significantly higher microbiome diversity, while no CF pathogen was associated with reduced microbial diversity. There was a diverse resistome present in all samples in this study, with 57.8% agreement between shotgun metagenomics and culture-based methods for detection of resistance. Pathogenic sequence types (STs) of S. aureus, Pseudomonas aeruginosa, Haemophilus influenzae and Stenotrophomonas maltophilia were observed to persist in young CF patients, while STs of S. aureus were both persistent and shared between patients. This study provides new insight into the temporal changes in strain level composition of the microbiome and the landscape of the resistome in young people with CF. Shotgun metagenomics could provide a very useful one-stop assay for detecting pathogens, emergence of resistance and conversion to persistent colonisation in early CF disease.}, } @article {pmid38612577, year = {2024}, author = {Feng, C and Li, N and Gao, G and He, Q and Kwok, LY and Zhang, H}, title = {Dynamic Changes of the Gut Microbiota and Its Functional Metagenomic Potential during the Development of Non-Small Cell Lung Cancer.}, journal = {International journal of molecular sciences}, volume = {25}, number = {7}, pages = {}, pmid = {38612577}, issn = {1422-0067}, support = {NDYB2022-41//Research Initiation Project for Introducing Excellent Doctoral Talents from Inner Mongolia Agricultural University/ ; 2022YFD2100700//Research Fund for the National Key R&D Program of China/ ; U22A20540//National Natural Science Foundation of China/ ; 2021ZD0014//Inner Mongolia Science and Technology Major Projects/ ; CARS36//earmarked fund/ ; }, mesh = {Humans ; Animals ; Mice ; *Carcinoma, Non-Small-Cell Lung ; *Lung Neoplasms ; *Gastrointestinal Microbiome ; Biomarkers, Tumor ; Clostridiales ; }, abstract = {The gut microbiota plays a significant role in tumor pathogenesis by regulating the host metabolism and immune response, and there are few studies focused on tracking changes in the gut microbiota from the onset of lung cancer. Therefore, the aim of our study is combining preclinical and clinical research to thoroughly analyze the signatures of fecal microbiota in lung cancer, which will be useful for early diagnosis and predicting the therapeutic efficacy of lung cancer. The first part of this study analyzed the fecal metagenomic differences between patients with non-small cell lung cancer and healthy subjects, and the second part of this work constructed a murine lung cancer model to monitor changes in mouse fecal metagenomics and T cell immunology during lung cancer progression. We found that the fecal microbiota was altered in both humans and mice with lung cancer, characterized by a significantly reduced microbial diversity and number of beneficial microbes, with increases in potential pathogens. The fecal level of Akkermansia muciniphila and the gut metabolic module of the secondary bile acid metabolism were diminished in both humans and mice with lung cancer compared with healthy subjects. Splenomegaly was observed in the lung cancer mice. Flow cytometer analysis of the splenocytes revealed substantial alterations in the proportions of T cell subsets in the lung cancer mice, characterized by significant increases in CD4[+]Foxp3[+]CD25[+] T regulatory cells (p < 0.05) while significant decreases in CD3[+] T cells (p < 0.001), CD4[+] T cells (p < 0.001), and the CD4[+]/CD8[+] ratio (p < 0.01). Vertical and longitudinal analyses of the fecal microbiota of the two mouse groups identified some lung cancer biomarkers (including Acutalibacter timonensis, Lachnospiraceae bacterium NSJ-38 sp014337195, etc.). The fecal microbiota of the lung cancer mice had a reduced metagenomic potential for neurotransmitters (melatonin, γ-aminobutyric acid, and histamine) compared with healthy mice. In summary, this study found that the diversity, structure, and composition of gut microbiota vary between cancer and healthy conditions, ultimately leading to changes in the potential for functional metagenomics.}, } @article {pmid38611776, year = {2024}, author = {Szulc, J and Okrasa, M and Nowak, A and Ryngajłło, M and Nizioł, J and Kuźniar, A and Ruman, T and Gutarowska, B}, title = {Uncontrolled Post-Industrial Landfill-Source of Metals, Potential Toxic Compounds, Dust, and Pathogens in Environment-A Case Study.}, journal = {Molecules (Basel, Switzerland)}, volume = {29}, number = {7}, pages = {}, pmid = {38611776}, issn = {1420-3049}, support = {Phase IV of the National Program "Safety and working conditions improvement"//Ministry of Science and Higher Education and the National Centre for Research and Development/ ; 726/BN/D/2019-2021//Regional Found for Environmental Protection and Water Management in Lodz/ ; }, mesh = {Humans ; *Dust ; Caco-2 Cells ; Metals ; *Mercury ; Soil ; }, abstract = {The aim of this case study was the evaluation of the selected metals' concentration, potential toxic compound identification, cytotoxicity analysis, estimation of the airborne dust concentration, biodiversity, and number of microorganisms in the environment (leachate, soil, air) of the biggest uncontrolled post-industrial landfills in Poland. Based on the results obtained, preliminary solutions for the future management of post-industrial objects that have become an uncontrolled landfill were indicated. In the air, the PM1 fraction dominated, constituting 78.1-98.2% of the particulate matter. Bacterial counts were in the ranges of 9.33 × 10[1]-3.21 × 10[3] CFU m[-3] (air), 1.87 × 10[5]-2.30 × 10[6] CFU mL[-1] (leachates), and 8.33 × 10[4]-2.69 × 10[6] CFU g[-1] (soil). In the air, the predominant bacteria were Cellulosimicrobium and Stenotrophomonas. The predominant fungi were Mycosphaerella, Cladosporium, and Chalastospora. The main bacteria in the leachates and soils were Acinetobacter, Mortierella, Proteiniclasticum, Caloramator, and Shewanella. The main fungi in the leachates and soils were Lindtneria. Elevated concentrations of Pb, Zn, and Hg were detected. The soil showed the most pronounced cytotoxic potential, with rates of 36.55%, 63.08%, and 100% for the A-549, Caco-2, and A-549 cell lines. Nine compounds were identified which may be responsible for this cytotoxic effect, including 2,4,8-trimethylquinoline, benzo(f)quinoline, and 1-(m-tolyl)isoquinoline. The microbiome included bacteria and fungi potentially metabolizing toxic compounds and pathogenic species.}, } @article {pmid38609443, year = {2024}, author = {Kholousi Adab, F and Mehdi Yaghoobi, M and Gharechahi, J}, title = {Enhanced crystalline cellulose degradation by a novel metagenome-derived cellulase enzyme.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {8560}, pmid = {38609443}, issn = {2045-2322}, mesh = {Animals ; Metagenome ; Camelus ; *Microbiota ; *Cellulase/genetics ; Cellulose ; }, abstract = {Metagenomics has revolutionized access to genomic information of microorganisms inhabiting the gut of herbivorous animals, circumventing the need for their isolation and cultivation. Exploring these microorganisms for novel hydrolytic enzymes becomes unattainable without utilizing metagenome sequencing. In this study, we harnessed a suite of bioinformatic analyses to discover a novel cellulase-degrading enzyme from the camel rumen metagenome. Among the protein-coding sequences containing cellulase-encoding domains, we identified and subsequently cloned and purified a promising candidate cellulase enzyme, Celcm05-2, to a state of homogeneity. The enzyme belonged to GH5 subfamily 4 and exhibited robust enzymatic activity under acidic pH conditions. It maintained hydrolytic activity under various environmental conditions, including the presence of metal ions, non-ionic surfactant Triton X-100, organic solvents, and varying temperatures. With an optimal temperature of 40 °C, Celcm05-2 showcased remarkable efficiency when deployed on crystalline cellulose (> 3.6 IU/mL), specifically Avicel, thereby positioning it as an attractive candidate for a myriad of biotechnological applications spanning biofuel production, paper and pulp processing, and textile manufacturing. Efficient biodegradation of waste paper pulp residues and the evidence of biopolishing suggested that Celcm05-2 can be used in the bioprocessing of cellulosic craft fabrics in the textile industry. Our findings suggest that the camel rumen microbiome can be mined for novel cellulase enzymes that can find potential applications across diverse biotechnological processes.}, } @article {pmid38609235, year = {2024}, author = {Hou, Q and Wang, Y and Qu, D and Zhao, H and Tian, L and Zhou, J and Liu, J and Guo, Z}, title = {Microbial communities, functional, and flavor differences among three different-colored high-temperature Daqu: A comprehensive metagenomic, physicochemical, and electronic sensory analysis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {184}, number = {}, pages = {114257}, doi = {10.1016/j.foodres.2024.114257}, pmid = {38609235}, issn = {1873-7145}, mesh = {Temperature ; *Metagenome ; *Microbiota ; Cluster Analysis ; Electronics ; }, abstract = {High-temperature Daqu (HTD) is the starter for producing sauce-flavor Baijiu, with different-colored Daqu (white, yellow, and black) reflecting variations in fermentation chamber conditions, chemical reactions, and associated microbiota. Understanding the relationship between Daqu characteristics and flavor/taste is challenging yet vital for improving Baijiu fermentation. This study utilized metagenomic sequencing, physicochemical analysis, and electronic sensory evaluation to compare three different-colored HTD and their roles in fermentation. Fungi and bacteria dominated the HTD-associated microbiota, with fungi increasing as the fermentation temperature rose. The major fungal genera were Aspergillus (40.17%) and Kroppenstedtia (21.16%), with Aspergillus chevalieri (25.65%) and Kroppenstedtia eburnean (21.07%) as prevalent species. Microbial communities, functionality, and physicochemical properties, particularly taste and flavor, were color-specific in HTD. Interestingly, the microbial communities in different-colored HTDs demonstrated robust functional complementarity. White Daqu exhibited non-significantly higher α-diversity compared to the other two Daqu. It played a crucial role in breaking down substrates such as starch, proteins, hyaluronic acid, and glucan, contributing to flavor precursor synthesis. Yellow Daqu, which experienced intermediate temperature and humidity, demonstrated good esterification capacity and a milder taste profile. Black Daqu efficiently broke down raw materials, especially complex polysaccharides, but had inferior flavor and taste. Notably, large within-group variations in physicochemical quality and microbial composition were observed, highlighting limitations in color-based HTD quality assessment. Water content in HTD was associated with Daqu flavor, implicating its crucial role. This study revealed the complementary roles of the three HTD types in sauce-flavor Baijiu fermentation, providing valuable insights for product enhancement.}, } @article {pmid38609223, year = {2024}, author = {Ma, J and Qian, C and Hu, Q and Zhang, J and Gu, G and Liang, X and Zhang, L}, title = {The bacteriome-coupled phage communities continuously contract and shift to orchestrate the traditional rice vinegar fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {184}, number = {}, pages = {114244}, doi = {10.1016/j.foodres.2024.114244}, pmid = {38609223}, issn = {1873-7145}, mesh = {Humans ; *Oryza ; Acetic Acid ; Fermentation ; *Bacteriophages/genetics ; *Microbiota/genetics ; }, abstract = {Amounts of microbiome studies have uncovered the microbial communities of traditional food fermentations, while in which the phageome development with time is poorly understood. Here, we conducted a study to decipher both phageome and bacteriome of the traditional rice vinegar fermentation. The vinegar phageomes showed significant differences in the alpha diversity, network density and clustering coefficient over time. Peduoviridae had the highest relative abundance. Moreover, the phageome negatively correlated to the cognate bacteriome in alpha diversity, and undergone constantly contracting and shifting across the temporal scale. Nevertheless, 257 core virial clusters (VCs) persistently occurred with time whatever the significant impacts imposed by the varied physiochemical properties. Glycoside hydrolase (GH) and glycosyltransferase (GT) families genes displayed the higher abundances across all samples. Intriguingly, diversely structuring of toxin-antitoxin systems (TAs) and CRISPR-Cas arrays were frequently harbored by phage genomes. Their divergent organization and encoding attributes underlie the multiple biological roles in modulation of network and/or contest of phage community as well as bacterial host community. This phageome-wide mapping will fuel the current insights of phage community ecology in other traditional fermented ecosystems that are challenging to decipher.}, } @article {pmid38608842, year = {2024}, author = {Sun, Z and Ning, Z and Figeys, D}, title = {The Landscape and Perspectives of the Human Gut Metaproteomics.}, journal = {Molecular & cellular proteomics : MCP}, volume = {23}, number = {5}, pages = {100763}, pmid = {38608842}, issn = {1535-9484}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Proteomics/methods ; *Metagenomics/methods ; Proteome/metabolism ; Tandem Mass Spectrometry ; Chromatography, Liquid ; }, abstract = {The human gut microbiome is closely associated with human health and diseases. Metaproteomics has emerged as a valuable tool for studying the functionality of the gut microbiome by analyzing the entire proteins present in microbial communities. Recent advancements in liquid chromatography and tandem mass spectrometry (LC-MS/MS) techniques have expanded the detection range of metaproteomics. However, the overall coverage of the proteome in metaproteomics is still limited. While metagenomics studies have revealed substantial microbial diversity and functional potential of the human gut microbiome, few studies have summarized and studied the human gut microbiome landscape revealed with metaproteomics. In this article, we present the current landscape of human gut metaproteomics studies by re-analyzing the identification results from 15 published studies. We quantified the limited proteome coverage in metaproteomics and revealed a high proportion of annotation coverage of metaproteomics-identified proteins. We conducted a preliminary comparison between the metaproteomics view and the metagenomics view of the human gut microbiome, identifying key areas of consistency and divergence. Based on the current landscape of human gut metaproteomics, we discuss the feasibility of using metaproteomics to study functionally unknown proteins and propose a whole workflow peptide-centric analysis. Additionally, we suggest enhancing metaproteomics analysis by refining taxonomic classification and calculating confidence scores, as well as developing tools for analyzing the interaction between taxonomy and function.}, } @article {pmid38608741, year = {2024}, author = {Kebede, V and Ravizza, T and Balosso, S and Di Sapia, R and Canali, L and Soldi, S and Galletti, S and Papazlatani, C and Karas, PA and Vasileiadis, S and Sforzini, A and Pasetto, L and Bonetto, V and Vezzani, A and Vesci, L}, title = {Early treatment with rifaximin during epileptogenesis reverses gut alterations and reduces seizure duration in a mouse model of acquired epilepsy.}, journal = {Brain, behavior, and immunity}, volume = {119}, number = {}, pages = {363-380}, doi = {10.1016/j.bbi.2024.04.007}, pmid = {38608741}, issn = {1090-2139}, mesh = {Animals ; *Rifaximin/therapeutic use/pharmacology ; Mice ; Male ; *Gastrointestinal Microbiome/drug effects ; *Disease Models, Animal ; *Mice, Inbred C57BL ; *Seizures/drug therapy ; *Epilepsy, Temporal Lobe/drug therapy ; Status Epilepticus/drug therapy ; Brain/drug effects/metabolism ; Hippocampus/drug effects/metabolism/pathology ; Epilepsy/drug therapy ; }, abstract = {The gut microbiota is altered in epilepsy and is emerging as a potential target for new therapies. We studied the effects of rifaximin, a gastrointestinal tract-specific antibiotic, on seizures and neuropathology and on alterations in the gut and its microbiota in a mouse model of temporal lobe epilepsy (TLE). Epilepsy was induced by intra-amygdala kainate injection causing status epilepticus (SE) in C57Bl6 adult male mice. Sham mice were injected with vehicle. Two cohorts of SE mice were fed a rifaximin-supplemented diet for 21 days, starting either at 24 h post-SE (early disease stage) or at day 51 post-SE (chronic disease stage). Corresponding groups of SE mice (one each disease stage) were fed a standard (control) diet. Cortical ECoG recording was done at each disease stage (24/7) for 21 days in all SE mice to measure the number and duration of spontaneous seizures during either rifaximin treatment or control diet. Then, epileptic mice ± rifaximin and respective sham mice were sacrificed and brain, gut and feces collected. Biospecimens were used for: (i) quantitative histological analysis of the gut structural and cellular components; (ii) markers of gut inflammation and intestinal barrier integrity by RTqPCR; (iii) 16S rRNA metagenomics analysis in feces. Hippocampal neuronal cell loss was assessed in epileptic mice killed in the early disease phase. Rifaximin administered for 21 days post-SE (early disease stage) reduced seizure duration (p < 0.01) and prevented hilar mossy cells loss in the hippocampus compared to epileptic mice fed a control diet. Epileptic mice fed a control diet showed a reduction of both villus height and villus height/crypt depth ratio (p < 0.01) and a decreased number of goblet cells (p < 0.01) in the duodenum, as well as increased macrophage (Iba1)-immunostaining in the jejunum (p < 0.05), compared to respective sham mice. Rifaximin's effect on seizures was associated with a reversal of gut structural and cellular changes, except for goblet cells which remained reduced. Seizure duration in epileptic mice was negatively correlated with the number of mossy cells (p < 0.01) and with villus height/crypt depth ratio (p < 0.05). Rifaximin-treated epileptic mice also showed increased tight junctions (occludin and ZO-1, p < 0.01) and decreased TNF mRNA expression (p < 0.01) in the duodenum compared to epileptic mice fed a control diet. Rifaximin administered for 21 days in chronic epileptic mice (chronic disease stage) did not change the number or duration of seizures compared to epileptic mice fed a control diet. Chronic epileptic mice fed a control diet showed an increased crypt depth (p < 0.05) and reduced villus height/crypt depth ratio (p < 0.01) compared to respective sham mice. Rifaximin treatment did not affect these intestinal changes. At both disease stages, rifaximin modified α- and β-diversity in epileptic and sham mice compared to respective mice fed a control diet. The microbiota composition in epileptic mice, as well as the effects of rifaximin at the phylum, family and genus levels, depended on the stage of the disease. During the early disease phase, the abundance of specific taxa was positively correlated with seizure duration in epileptic mice. In conclusion, gut-related alterations reflecting a dysfunctional state, occur during epilepsy development in a TLE mouse model. A short-term treatment with rifaximin during the early phase of the disease, reduced seizure duration and neuropathology, and reversed some intestinal changes, strengthening the therapeutic effects of gut-based therapies in epilepsy.}, } @article {pmid38606341, year = {2024}, author = {Eitel, M and Osigus, HJ and Brenzinger, B and Wörheide, G}, title = {Beauty in the beast - Placozoan biodiversity explored through molluscan predator genomics.}, journal = {Ecology and evolution}, volume = {14}, number = {4}, pages = {e11220}, pmid = {38606341}, issn = {2045-7758}, abstract = {The marine animal phylum Placozoa is characterized by a poorly explored cryptic biodiversity combined with very limited knowledge of their ecology. While placozoans are typically found as part of the epibenthos of coastal waters, known placozoan predators, namely small, shell-less sea slugs belonging to the family Rhodopidae (Mollusca: Gastropoda: Heterobranchia), inhabit the interstitium of seafloor sediment. In order to gain further insights into this predator-prey relationship and to expand our understanding of placozoan ecological niches, we screened publicly available whole-body metagenomic data from two rhodopid specimens collected from coastal sediments. Our analysis not only revealed the signatures of three previously unknown placozoan lineages in these sea slug samples but also enabled the assembly of three complete and two partial mitochondrial chromosomes belonging to four previously described placozoan genera, substantially extending the picture of placozoan biodiversity. Our findings further refine the molecular phylogeny of the Placozoa, corroborate the recently established taxonomic ranks in this phylum, and provide molecular support that known placozoan clades should be referred to as genera. We finally discuss the main finding of our study - the presence of placozoans in the sea floor sediment interstitium - in the context of their ecological, biological, and natural history implications.}, } @article {pmid38605646, year = {2024}, author = {Heston, SM and Hurst, JH and Kelly, MS}, title = {Understanding the influence of the microbiome on childhood infections.}, journal = {Expert review of anti-infective therapy}, volume = {22}, number = {7}, pages = {529-545}, pmid = {38605646}, issn = {1744-8336}, support = {K01 AI173398/AI/NIAID NIH HHS/United States ; K12 HD105253/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; Child ; *Microbiota/physiology ; *Gastrointestinal Microbiome/physiology ; Adolescent ; Communicable Diseases/microbiology/immunology ; Vaccines/administration & dosage/immunology ; Respiratory Tract Infections/microbiology/immunology ; Disease Susceptibility ; Animals ; Immune System/microbiology ; }, abstract = {INTRODUCTION: The microbiome is known to have a substantial impact on human health and disease. However, the impacts of the microbiome on immune system development, susceptibility to infectious diseases, and vaccine-elicited immune responses are emerging areas of interest.

AREAS COVERED: In this review, we provide an overview of development of the microbiome during childhood. We highlight available data suggesting that the microbiome is critical to maturation of the immune system and modifies susceptibility to a variety of infections during childhood and adolescence, including respiratory tract infections, Clostridioides difficile infection, and sexually transmitted infections. We discuss currently available and investigational therapeutics that have the potential to modify the microbiome to prevent or treat infections among children. Finally, we review the accumulating evidence that the gut microbiome influences vaccine-elicited immune responses among children.

EXPERT OPINION: Recent advances in sequencing technologies have led to an explosion of studies associating the human microbiome with the risk and severity of infectious diseases. As our knowledge of the extent to which the microbiome influences childhood infections continues to grow, microbiome-based diagnostics and therapeutics will increasingly be incorporated into clinical practice to improve the prevention, diagnosis, and treatment of infectious diseases among children.}, } @article {pmid38605401, year = {2024}, author = {Feng, X and Li, H}, title = {Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {92}, pmid = {38605401}, issn = {1474-760X}, support = {R01 HG010040/HG/NHGRI NIH HHS/United States ; U01 HG010961/HG/NHGRI NIH HHS/United States ; U01HG010961/HG/NHGRI NIH HHS/United States ; R01HG010040/HG/NHGRI NIH HHS/United States ; }, mesh = {*Metagenome ; *Microbiota/genetics ; Algorithms ; Bacteria/genetics ; Metagenomics/methods ; }, abstract = {BACKGROUND: In the metagenomic assembly of a microbial community, abundant species are often thought to assemble well given their deeper sequencing coverage. This conjuncture is rarely tested or evaluated in practice. We often do not know how many abundant species are missing and do not have an approach to recover them.

RESULTS: Here, we propose k-mer based and 16S RNA based methods to measure the completeness of metagenome assembly. We show that even with PacBio high-fidelity (HiFi) reads, abundant species are often not assembled, as high strain diversity may lead to fragmented contigs. We develop a novel reference-free algorithm to recover abundant metagenome-assembled genomes (MAGs) by identifying circular assembly subgraphs. Complemented with a reference-free genome binning heuristics based on dimension reduction, the proposed method rescues many abundant species that would be missing with existing methods and produces competitive results compared to those state-of-the-art binners in terms of total number of near-complete genome bins.

CONCLUSIONS: Our work emphasizes the importance of metagenome completeness, which has often been overlooked. Our algorithm generates more circular MAGs and moves a step closer to the complete representation of microbial communities.}, } @article {pmid38604355, year = {2024}, author = {Yin, Z and Liang, J and Zhang, M and Chen, B and Yu, Z and Tian, X and Deng, X and Peng, L}, title = {Pan-genome insights into adaptive evolution of bacterial symbionts in mixed host-microbe symbioses represented by human gut microbiota Bacteroides cellulosilyticus.}, journal = {The Science of the total environment}, volume = {927}, number = {}, pages = {172251}, doi = {10.1016/j.scitotenv.2024.172251}, pmid = {38604355}, issn = {1879-1026}, mesh = {*Symbiosis ; *Gastrointestinal Microbiome/genetics ; *Bacteroides/genetics/physiology ; Humans ; *Genome, Bacterial ; Evolution, Molecular ; Gene Transfer, Horizontal ; }, abstract = {Animal hosts harbor diverse assemblages of microbial symbionts that play crucial roles in the host's lifestyle. The link between microbial symbiosis and host development remains poorly understood. In particular, little is known about the adaptive evolution of gut bacteria in host-microbe symbioses. Recently, symbiotic relationships have been categorized as open, closed, or mixed, reflecting their modes of inter-host transmission and resulting in distinct genomic features. Members of the genus Bacteroides are the most abundant human gut microbiota and possess both probiotic and pathogenic potential, providing an excellent model for studying pan-genome evolution in symbiotic systems. Here, we determined the complete genome of an novel clinical strain PL2022, which was isolated from a blood sample and performed pan-genome analyses on a representative set of Bacteroides cellulosilyticus strains to quantify the influence of the symbiotic relationship on the evolutionary dynamics. B. cellulosilyticus exhibited correlated genomic features with both open and closed symbioses, suggesting a mixed symbiosis. An open pan-genome is characterized by abundant accessory gene families, potential horizontal gene transfer (HGT), and diverse mobile genetic elements (MGEs), indicating an innovative gene pool, mainly associated with genomic islands and plasmids. However, massive parallel gene loss, weak purifying selection, and accumulation of positively selected mutations were the main drivers of genome reduction in B. cellulosilyticus. Metagenomic read recruitment analyses showed that B. cellulosilyticus members are globally distributed and active in human gut habitats, in line with predominant vertical transmission in the human gut. However, existence and/or high abundance were also detected in non-intestinal tissues, other animal hosts, and non-host environments, indicating occasional horizontal transmission to new niches, thereby creating arenas for the acquisition of novel genes. This case study of adaptive evolution under a mixed host-microbe symbiosis advances our understanding of symbiotic pan-genome evolution. Our results highlight the complexity of genetic evolution in this unusual intestinal symbiont.}, } @article {pmid38603815, year = {2024}, author = {Bai, H and He, LY and Gao, FZ and Yao, KS and Zhang, M and Qiao, LK and Chen, ZY and He, LX and Liu, YS and Zhao, JL and Ying, GG}, title = {Airborne antibiotic resistome and microbiome in pharmaceutical factories.}, journal = {Environment international}, volume = {186}, number = {}, pages = {108639}, doi = {10.1016/j.envint.2024.108639}, pmid = {38603815}, issn = {1873-6750}, mesh = {*Microbiota/genetics/drug effects ; China ; *Air Microbiology ; *Anti-Bacterial Agents/pharmacology ; *Wastewater/microbiology ; Bacteria/genetics/drug effects ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antimicrobial resistance is considered to be one of the biggest public health problems, and airborne transmission is an important but under-appreciated pathway for the spread of antibiotic resistance genes (ARGs) in the environment. Previous research has shown pharmaceutical factories to be a major source of ARGs and antibiotic resistant bacteria (ARB) in the surrounding receiving water and soil environments. Pharmaceutical factories are hotspots of antibiotic resistance, but the atmospheric transmission and its environmental risk remain more concerns. Here, we conducted a metagenomic investigation into the airborne microbiome and resistome in three pharmaceutical factories in China. Soil (average: 38.45%) and wastewater (average: 28.53%) were major contributors of airborne resistome. ARGs (vanR/vanS, blaOXA, and CfxA) conferring resistance to critically important clinically used antibiotics were identified in the air samples. The wastewater treatment area had significantly higher relative abundances of ARGs (average: 0.64 copies/16S rRNA). Approximately 28.2% of the detected airborne ARGs were found to be associated with plasmids, and this increased to about 50% in the wastewater treatment area. We have compiled a list of high-risk airborne ARGs found in pharmaceutical factories. Moreover, A total of 1,043 viral operational taxonomic units were identified and linked to 47 family-group taxa. Different CRISPR-Cas immune systems have been identified in bacterial hosts in response to phage infection. Similarly, higher phage abundance (average: 2451.70 PPM) was found in the air of the wastewater treatment area. Our data provide insights into the antibiotic resistance gene profiles and microbiome (bacterial and non-bacterial) in pharmaceutical factories and reveal the potential role of horizontal transfer in the spread of airborne ARGs, with implications for human and animal health.}, } @article {pmid38600293, year = {2024}, author = {Jiang, MZ and Liu, C and Xu, C and Jiang, H and Wang, Y and Liu, SJ}, title = {Gut microbial interactions based on network construction and bacterial pairwise cultivation.}, journal = {Science China. Life sciences}, volume = {67}, number = {8}, pages = {1751-1762}, pmid = {38600293}, issn = {1869-1889}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Bacteria/genetics/classification/metabolism ; *Feces/microbiology ; *Coculture Techniques ; Metagenome ; Microbial Interactions ; Metagenomics/methods ; }, abstract = {Association networks are widely applied for the prediction of bacterial interactions in studies of human gut microbiomes. However, the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated bacteria. In this study, we addressed this challenge by integrating in vitro time series network (TSN) associations and co-cultivation of TSN taxon pairs. Fecal samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 days. Enriched cells were harvested for DNA extraction and metagenomic sequencing. A total of 198 metagenome-assembled genomes (MAGs) were recovered. Temporal dynamics of bacteria growing on the YCFA agar were used to infer microbial association networks. To experimentally validate the interactions of taxon pairs in networks, we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank, respectively, for pairwise co-cultures. The co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism (51.67%), followed by commensalism (21.67%), amensalism (18.33%), competition (5%) and exploitation (3.33%). Genome-centric analysis further revealed that the commensal gut bacteria (helpers and beneficiaries) might interact with each other via the exchanges of amino acids with high biosynthetic costs, short-chain fatty acids, and/or vitamins. We also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7% of these strains was significantly promoted. This approach provides new insights into the gut microbiome complexity and microbial interactions in association networks. Our work highlights that the positive relationships in gut microbial communities tend to be overestimated, and that amino acids, short-chain fatty acids, and vitamins are contributed to the positive relationships.}, } @article {pmid38600101, year = {2024}, author = {Ma, X and Wen, G and Zhao, Z and Lu, L and Li, T and Gao, N and Han, G}, title = {Alternations in the human skin, gut and vaginal microbiomes in perimenopausal or postmenopausal Vulvar lichen sclerosus.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {8429}, pmid = {38600101}, issn = {2045-2322}, support = {YN2021QX02//Peking University International Hospital/ ; }, mesh = {Female ; Humans ; *Vulvar Lichen Sclerosus/pathology ; Postmenopause ; Perimenopause ; Quality of Life ; *Microbiota ; Arrhythmias, Cardiac ; Vagina/pathology ; }, abstract = {Vulvar lichen sclerosus (VLS) is a chronic and progressive dermatologic condition that can cause physical dysfunction, disfigurement, and impaired quality of life. However, the etiology of VLS remains unknown. The vulvar skin, intestinal and vaginal microbiomes have been postulated to play important roles in the pathogenesis of this disease. The aim of this study was to compare the compositional characteristics of the vulvar skin, vagina, and gut microbiota between perimenopausal or postmenopausal VLS patients and healthy controls. The study involved six perimenopausal or postmenopausal VLS patients which were based on characteristic clinical manifestations and histologic confirmation and five healthy controls. The pruritus severity of each patient was evaluated using the NRS scale, and the dermatology-specific health-related quality of life was assessed using the Skindex-16. Metagenomic sequencing was performed, and the results were analyzed for alpha and beta diversity. LEfSe analysis were used to investigate the microbial alterations in vulvar skin, gut and vagina. KEGG databases were used to analyze differences in functional abundance. The study found significant differences in alpha diversity between the two groups in stool and vaginal samples (P < 0.05). Patients with VLS had a higher abundance of Enterobacter cloacae, Flavobacterium_branchiophilum, Mediterranea_sp._An20, Parabacteroides_johnsoniiand Streptococcus_bovimastitidis on the vulvar skin, while Corynebacterium_sp._zg-913 was less abundant compared to the control group. The relative abundance of Sphingomonas_sp._SCN_67_18, Sphingobium_sp._Ant17, and Pontibacter_sp_BT213 was significantly higher in the gut samples of patients with VLS.Paenibacillus_popilliae,Gemella_asaccharolytica, and Coriobacteriales_bacterium_DNF00809 compared to the control group. Additionally, the vaginal samples of patients with VLS exhibited a significantly lower relative abundance of Bacteroidales_bacterium_43_8, Bacteroides_sp._CAG:20, Blautia_sp._AM28-10, Fibrobacter_sp._UWB16, Lachnospiraceae_bacterium_AM25-39, Holdemania_filiformis, Lachnospiraceae_bacterium_GAM79, and Tolumonas_sp. Additionally, the butyrate-producing bacterium SS3/4 showed a significant difference compared to the controls. The study found a negative relationship between Sphingobium_sp._Ant17 in stool and Skindex-16 (P < 0.05), while Mediterranea_sp._An20 had a positive correlation with Skindex-16 (P < 0.05) in the skin. Additionally, our functional analysis revealed alterations in Aminoacyl_tRNA_biosynthesis, Glutathione_metabolism, the pentose phosphate pathway, and Alanine__aspartate_and_glutamate_metabolism in the VLS patient group. The study suggests that perimenopausal or postmenopausal patients with VLS have a modified microbiome in the vulvar skin, gut, and vagina. This modification is linked to abnormal energy metabolism, increased oxidative stress, and abnormal amino acid metabolism.}, } @article {pmid38599786, year = {2024}, author = {Su, ACY and Ding, X and Lau, HCH and Kang, X and Li, Q and Wang, X and Liu, Y and Jiang, L and Lu, Y and Liu, W and Ding, Y and Cheung, AH and To, KF and Yu, J}, title = {Lactococcus lactis HkyuLL 10 suppresses colorectal tumourigenesis and restores gut microbiota through its generated alpha-mannosidase.}, journal = {Gut}, volume = {73}, number = {9}, pages = {1478-1488}, pmid = {38599786}, issn = {1468-3288}, mesh = {Animals ; *Colorectal Neoplasms/microbiology/pathology/prevention & control ; *Gastrointestinal Microbiome/physiology ; Humans ; Mice ; *Probiotics/therapeutic use ; *Lactococcus lactis ; *Feces/microbiology ; *alpha-Mannosidase/metabolism ; *Carcinogenesis ; Mice, Transgenic ; Female ; Male ; }, abstract = {OBJECTIVE: Probiotic Lactococcus lactis is known to confer health benefits to humans. Here, we aimed to investigate the role of L. lactis in colorectal cancer (CRC).

DESIGN: L. lactis abundance was evaluated in patients with CRC (n=489) and healthy individuals (n=536). L. lactis was isolated from healthy human stools with verification by whole genome sequencing. The effect of L. lactis on CRC tumourigenesis was assessed in transgenic Apc [Min/+] mice and carcinogen-induced CRC mice. Faecal microbiota was profiled by metagenomic sequencing. Candidate proteins were characterised by nano liquid chromatography-mass spectrometry. Biological function of L. lactis conditioned medium (HkyuLL 10-CM) and functional protein was studied in human CRC cells, patient-derived organoids and xenograft mice.

RESULTS: Faecal L. lactis was depleted in patients with CRC. A new L. lactis strain was isolated from human stools and nomenclated as HkyuLL 10. HkyuLL 10 supplementation suppressed CRC tumourigenesis in Apc [Min/+] mice, and this tumour-suppressing effect was confirmed in mice with carcinogen-induced CRC. Microbiota profiling revealed probiotic enrichment including Lactobacillus johnsonii in HkyuLL 10-treated mice. HkyuLL 10-CM significantly abrogated the growth of human CRC cells and patient-derived organoids. Such protective effect was attributed to HkyuLL 10-secreted proteins, and we identified that α-mannosidase was the functional protein. The antitumourigenic effect of α-mannosidase was demonstrated in human CRC cells and organoids, and its supplementation significantly reduced tumour growth in xenograft mice.

CONCLUSION: HkyuLL 10 suppresses CRC tumourigenesis in mice through restoring gut microbiota and secreting functional protein α-mannosidase. HkyuLL 10 administration may serve as a prophylactic measure against CRC.}, } @article {pmid38599211, year = {2024}, author = {Battaglia, TW and Mimpen, IL and Traets, JJH and van Hoeck, A and Zeverijn, LJ and Geurts, BS and de Wit, GF and Noë, M and Hofland, I and Vos, JL and Cornelissen, S and Alkemade, M and Broeks, A and Zuur, CL and Cuppen, E and Wessels, L and van de Haar, J and Voest, E}, title = {A pan-cancer analysis of the microbiome in metastatic cancer.}, journal = {Cell}, volume = {187}, number = {9}, pages = {2324-2335.e19}, doi = {10.1016/j.cell.2024.03.021}, pmid = {38599211}, issn = {1097-4172}, mesh = {Humans ; *Microbiota ; *Neoplasm Metastasis ; *Neoplasms/microbiology/pathology ; Metagenomics/methods ; Lung Neoplasms/microbiology/pathology ; Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Neutrophils/immunology ; Tumor Microenvironment ; Bacteria/genetics/classification ; }, abstract = {Microbial communities are resident to multiple niches of the human body and are important modulators of the host immune system and responses to anticancer therapies. Recent studies have shown that complex microbial communities are present within primary tumors. To investigate the presence and relevance of the microbiome in metastases, we integrated mapping and assembly-based metagenomics, genomics, transcriptomics, and clinical data of 4,160 metastatic tumor biopsies. We identified organ-specific tropisms of microbes, enrichments of anaerobic bacteria in hypoxic tumors, associations between microbial diversity and tumor-infiltrating neutrophils, and the association of Fusobacterium with resistance to immune checkpoint blockade (ICB) in lung cancer. Furthermore, longitudinal tumor sampling revealed temporal evolution of the microbial communities and identified bacteria depleted upon ICB. Together, we generated a pan-cancer resource of the metastatic tumor microbiome that may contribute to advancing treatment strategies.}, } @article {pmid38599113, year = {2024}, author = {Pilkington, LI and Kerner, W and Bertoldi, D and Larcher, R and Lee, SA and Goddard, MR and Albanese, D and Franceschi, P and Fedrizzi, B}, title = {Integration and holistic analysis of multiple multidimensional soil data sets.}, journal = {Talanta}, volume = {274}, number = {}, pages = {125954}, doi = {10.1016/j.talanta.2024.125954}, pmid = {38599113}, issn = {1873-3573}, mesh = {*Soil/chemistry ; Soil Microbiology ; Fungi ; Biodiversity ; New Zealand ; }, abstract = {Complex matrices such as soil have a range of measurable characteristics, and thus data to describe them can be considered multidimensional. These characteristics can be strongly influenced by factors that introduce confounding effects that hinder analyses. Traditional statistical approaches lack the flexibility and granularity required to adequately evaluate such matrices, particularly those with large dataset of varying data types (i.e. quantitative non-compositional, quantitative compositional). We present a statistical workflow designed to effectively analyse complex, multidimensional systems, even in the presence of confounding variables. The developed methodology involves exploratory analysis to identify the presence of confounding variables, followed by data decomposition (including strategies for both compositional and non-compositional quantitative data) to minimise the influence of these confounding factors such as sampling site/location. These data processing methods then allow for common patterns to be highlighted in the data, including the identification of biomarkers and determination of non-trivial associations between variables. We demonstrate the utility of this statistical workflow by jointly analysing the chemical composition and fungal biodiversity of New Zealand vineyard soils that have been managed with either organic low-input or conventional input approaches. By applying this pipeline, we were able to identify biomarkers that distinguish viticultural soil from both approaches and also unearth links and associations between the chemical and metagenomic profiles. While soil is an example of a system that can require this type of statistical methodology, there are a range of biological and ecological systems that are challenging to analyse due to the complex interplay of global and local effects. Utilising our developed pipeline will greatly enhance the way that these systems can be studied and the quality and impact of insight gained from their analysis.}, } @article {pmid38598617, year = {2024}, author = {Gilbert, JA and Alverdy, J}, title = {Where do the pathogens that cause surgical site infections come from?.}, journal = {Science translational medicine}, volume = {16}, number = {742}, pages = {eado1449}, doi = {10.1126/scitranslmed.ado1449}, pmid = {38598617}, issn = {1946-6242}, mesh = {Humans ; *Surgical Wound Infection/drug therapy ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Microbiota ; }, abstract = {A study from Long et al. shows that many pathogens that cause surgical site infections during spine surgery come from the patient's own microbiome, suggesting a paradigm shift in the understanding of surgical site infections that questions the effectiveness of current enhanced sterility and antibiotic protocols.}, } @article {pmid38597375, year = {2024}, author = {Arunan, B and Talukdar, D and Swain, S and Varadarajan, A and Sarda, R and Singh, G and Nischal, N and Soneja, M and Bakshi, S and Jana, P and Tanwar, S and Sikka, K and Verma, H and Subramanian, A and Xess, I and Wig, N and Das, B and Ray, A}, title = {Metagenomic insights into fungal community composition of the nasopharyngeal region of COVID-19 associated mucormycosis patients from India.}, journal = {Journal of medical virology}, volume = {96}, number = {4}, pages = {e29601}, doi = {10.1002/jmv.29601}, pmid = {38597375}, issn = {1096-9071}, support = {//All-India Institute of Medical Sciences Intramural Grant/ ; RAD-22017/19/2022-KGD-DBT//Department of Biotechnology (DBT), Govt. of India/ ; }, mesh = {Humans ; *Mucormycosis/epidemiology ; *Mycobiome ; *COVID-19 ; Nose ; India/epidemiology ; }, abstract = {Coronavirus disease 2019 (COVID-19) associated mucormycosis (CAM) was reported predominantly from India during the second wave of COVID-19 and has a high mortality rate. The present study aims to understand the fungal community composition of the nasopharyngeal region of CAM-infected individuals and compare it with severe COVID-19 patients and healthy controls. The fungal community composition was decoded by analyzing the sequence homology of the internal transcribed spacer-2-(ITS-2) region of metagenomic DNA extracted from the upper respiratory samples. The alpha-diversity indices were found to be significantly altered in CAM patients (p < 0.05). Interestingly, a higher abundance of Candida africana, Candida haemuloni, Starmerella floris, and Starmerella lactiscondensi was observed exclusively in CAM patients. The interindividual changes in mycobiome composition were well supported by beta-diversity analysis (p < 0.05). The current study provides insights into the dysbiosis of the nasal mycobiome during CAM infection. In conclusion, our study shows that severe COVID-19 and CAM are associated with alteration in mycobiome as compared to healthy controls. However, the sequential alteration in the fungal flora which ultimately leads to the development of CAM needs to be addressed by future studies.}, } @article {pmid38594499, year = {2024}, author = {Franceschetti, L and Lodetti, G and Blandino, A and Amadasi, A and Bugelli, V}, title = {Exploring the role of the human microbiome in forensic identification: opportunities and challenges.}, journal = {International journal of legal medicine}, volume = {138}, number = {5}, pages = {1891-1905}, pmid = {38594499}, issn = {1437-1596}, mesh = {Humans ; *Microbiota ; *Skin/microbiology ; RNA, Ribosomal, 16S/genetics ; DNA Fingerprinting ; Metagenomics/methods ; }, abstract = {Forensic microbiology is rapidly emerging as a novel tool for human identification. The human microbiome, comprising diverse microbial communities including fungi, bacteria, protozoa, and viruses, is unique to each individual, offering a new dimension to forensic investigations. While traditional identification methods primarily rely on DNA profiling and fingerprint analysis, they face limitations when complete DNA or fingerprints profiles are unattainable or degraded. In this context, the microbial signatures of the human skin microbiome present a promising alternative due to their resilience to environmental stresses and individual-specific composition. This review explores the potential of microbiome analysis in forensic human identification, evaluating its applications, advantages, limitations, and future prospects. The uniqueness of an individual's microbial community, particularly the skin microbiota, can provide distinctive biological markers for identification purposes, while technological advancements like 16 S rRNA sequencing and metagenomic shotgun sequencing are enhancing the specificity of microbial identification, enabling detailed analysis of these complex ecological communities. Despite these promising findings, current research has not yet achieved a level of identification probability that could establish microbial analysis as a stand-alone evidence tool. Therefore, it is presently considered ancillary to traditional methods, contributing to a more comprehensive biological profile of individuals.}, } @article {pmid38594375, year = {2024}, author = {Poulsen, CS and Hesse, D and Fernandes, GR and Hansen, TH and Kern, T and Linneberg, A and Van Espen, L and Jørgensen, T and Nielsen, T and Alibegovic, AC and Matthijnssens, J and Pedersen, O and Vestergaard, H and Hansen, T and Andersen, MK}, title = {Characterization of the gut bacterial and viral microbiota in latent autoimmune diabetes in adults.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {8315}, pmid = {38594375}, issn = {2045-2322}, support = {1S25720N//Fonds voor Wetenschappelijk Onderzoek/ ; po0115//The Danish Diabetes Academy/ ; DFF-5053-00159//Danish Council for Independent Research/ ; }, mesh = {Adult ; Humans ; *Diabetes Mellitus, Type 1/genetics ; *Diabetes Mellitus, Type 2/genetics ; *Latent Autoimmune Diabetes in Adults/genetics ; *Gastrointestinal Microbiome/genetics ; Adenosine Deaminase ; RNA, Ribosomal, 16S/genetics ; Intercellular Signaling Peptides and Proteins ; Insulin ; *Glucose Intolerance ; }, abstract = {Latent autoimmune diabetes in adults (LADA) is a heterogeneous disease characterized by autoantibodies against insulin producing pancreatic beta cells and initial lack of need for insulin treatment. The aim of the present study was to investigate if individuals with LADA have an altered gut microbiota relative to non-diabetic control subjects, individuals with type 1 diabetes (T1D), and individuals with type 2 diabetes (T2D). Bacterial community profiling was performed with primers targeting the variable region 4 of the 16S rRNA gene and sequenced. Amplicon sequence variants (ASVs) were generated with DADA2 and annotated to the SILVA database. The gut virome was sequenced, using a viral particle enrichment and metagenomics approach, assembled, and quantified to describe the composition of the viral community. Comparison of the bacterial alpha- and beta-diversity measures revealed that the gut bacteriome of individuals with LADA resembled that of individuals with T2D. Yet, specific genera were found to differ in abundance in individuals with LADA compared with T1D and T2D, indicating that LADA has unique taxonomical features. The virome composition reflected the stability of the most dominant order Caudovirales and the families Siphoviridae, Podoviridae, and Inoviridae, and the dominant family Microviridae. Further studies are needed to confirm these findings.}, } @article {pmid38594362, year = {2024}, author = {Lateef, AA and Azeez, AA and Ren, W and Hamisu, HS and Oke, OA and Asiegbu, FO}, title = {Bacterial biota associated with the invasive insect pest Tuta absoluta (Meyrick).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {8268}, pmid = {38594362}, issn = {2045-2322}, support = {Grant number 4400T-2002//Maa- ja MetsätalousministeriÖ/ ; }, mesh = {Animals ; *Moths/physiology ; RNA, Ribosomal, 16S/genetics ; Insecta ; Larva/physiology ; *Microbiota ; *Solanum lycopersicum ; Bacteria/genetics ; }, abstract = {Tuta absoluta (the tomato pinworm) is an invasive insect pest with a highly damaging effect on tomatoes causing between 80 and 100% yield losses if left uncontrolled. Resistance to chemical pesticides have been reported in some T. absoluta populations. Insect microbiome plays an important role in the behavior, physiology, and survivability of their host. In a bid to explore and develop an alternative control method, the associated microbiome of this insect was studied. In this study, we unraveled the bacterial biota of T. absoluta larvae and adults by sequencing and analyzing the 16S rRNA V3-V4 gene regions using Illumina NovaSeq PE250. Out of 2,092,015 amplicon sequence variants (ASVs) recovered from 30 samples (15 larvae and 15 adults), 1,268,810 and 823,205 ASVs were obtained from the larvae and adults, respectively. A total of 433 bacterial genera were shared between the adults and larval samples while 264 and 139 genera were unique to the larvae and adults, respectively. Amplicon metagenomic analyses of the sequences showed the dominance of the phylum Proteobacteria in the adult samples while Firmicutes and Proteobacteria dominated in the larval samples. Linear discriminant analysis effect size (LEfSe) comparison revealed the genera Pseudomonas, Delftia and Ralstonia to be differentially enriched in the adult samples while Enterococcus, Enterobacter, Lactococcus, Klebsiella and Wiessella were differentially abundant in the larvae. The diversity indices showed that the bacterial communities were not different between the insect samples collected from different geographical regions. However, the bacterial communities significantly differed based on the sample type between larvae and adults. A co-occurrence network of significantly correlated taxa revealed a strong interaction between the microbial communities. The functional analysis of the microbiome using FAPROTAX showed that denitrification, arsenite oxidation, methylotrophy and methanotrophy as the active functional groups of the adult and larvae microbiomes. Our results have revealed the core taxonomic, functional, and interacting microbiota of T. absoluta and these indicate that the larvae and adults harbor a similar but transitory set of bacteria. The results provide a novel insight and a basis for exploring microbiome-based biocontrol strategy for this invasive insect pest as well as the ecological significance of some of the identified microbiota is discussed.}, } @article {pmid38593340, year = {2024}, author = {Suárez-Moo, P and Prieto-Davó, A}, title = {Biosynthetic potential of the sediment microbial subcommunities of an unexplored karst ecosystem and its ecological implications.}, journal = {MicrobiologyOpen}, volume = {13}, number = {2}, pages = {e1407}, pmid = {38593340}, issn = {2045-8827}, support = {//Consejo Nacional de Humanidades Ciencias y Tecnologías (CONAHCYT), México project A1-S-10785 (APD) and postdoctoral fellowship (362331) (PSM)/ ; }, mesh = {Bacteria/genetics ; Metagenome ; *Microbiota ; Multigene Family ; *Bacillaceae/genetics ; *Biological Products ; Biosynthetic Pathways/genetics ; }, abstract = {Microbial communities from various environments have been studied in the quest for new natural products with a broad range of applications in medicine and biotechnology. We employed an enrichment method and genome mining tools to examine the biosynthetic potential of microbial communities in the sediments of a coastal sinkhole within the karst ecosystem of the Yucatán Peninsula, Mexico. Our investigation led to the detection of 203 biosynthetic gene clusters (BGCs) and 55 secondary metabolites (SMs) within 35 high-quality metagenome-assembled genomes (MAGs) derived from these subcommunities. The most abundant types of BGCs were Terpene, Nonribosomal peptide-synthetase, and Type III polyketide synthase. Some of the in silico identified BGCs and SMs have been previously reported to exhibit biological activities against pathogenic bacteria and fungi. Others could play significant roles in the sinkhole ecosystem, such as iron solubilization and osmotic stress protection. Interestingly, 75% of the BGCs showed no sequence homology with bacterial BGCs previously reported in the MiBIG database. This suggests that the microbial communities in this environment could be an untapped source of genes encoding novel specialized compounds. The majority of the BGCs were identified in pathways found in the genus Virgibacillus, followed by Sporosarcina, Siminovitchia, Rhodococcus, and Halomonas. The latter, along with Paraclostridium and Lysinibacillus, had the highest number of identified BGC types. This study offers fresh insights into the potential ecological role of SMs from sediment microbial communities in an unexplored environment, underscoring their value as a source of novel natural products.}, } @article {pmid38589361, year = {2024}, author = {Barker-Tejeda, TC and Zubeldia-Varela, E and Macías-Camero, A and Alonso, L and Martín-Antoniano, IA and Rey-Stolle, MF and Mera-Berriatua, L and Bazire, R and Cabrera-Freitag, P and Shanmuganathan, M and Britz-McKibbin, P and Ubeda, C and Francino, MP and Barber, D and Ibáñez-Sandín, MD and Barbas, C and Pérez-Gordo, M and Villaseñor, A}, title = {Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3004}, pmid = {38589361}, issn = {2041-1723}, support = {PI17/01087//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PI19/00044//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PI20/01366//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PCI2018-092930//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; }, mesh = {Infant ; Male ; Adult ; Female ; Humans ; Child ; Aged ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics/metabolism ; Multiomics ; Metabolome ; Feces/microbiology ; Mothers ; }, abstract = {The human gut microbiome establishes and matures during infancy, and dysregulation at this stage may lead to pathologies later in life. We conducted a multi-omics study comprising three generations of family members to investigate the early development of the gut microbiota. Fecal samples from 200 individuals, including infants (0-12 months old; 55% females, 45% males) and their respective mothers and grandmothers, were analyzed using two independent metabolomics platforms and metagenomics. For metabolomics, gas chromatography and capillary electrophoresis coupled to mass spectrometry were applied. For metagenomics, both 16S rRNA gene and shotgun sequencing were performed. Here we show that infants greatly vary from their elders in fecal microbiota populations, function, and metabolome. Infants have a less diverse microbiota than adults and present differences in several metabolite classes, such as short- and branched-chain fatty acids, which are associated with shifts in bacterial populations. These findings provide innovative biochemical insights into the shaping of the gut microbiome within the same generational line that could be beneficial in improving childhood health outcomes.}, } @article {pmid38587642, year = {2024}, author = {Srinivasan, S and Jnana, A and Murali, TS}, title = {Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {56}, pmid = {38587642}, issn = {1432-184X}, support = {CRG/2022/003227//Science and Engineering Research Board/ ; }, mesh = {Humans ; *Microbial Interactions ; *Microbiota ; Microbial Consortia ; Coculture Techniques ; Community Networks ; }, abstract = {Microbial interactions function as a fundamental unit in complex ecosystems. By characterizing the type of interaction (positive, negative, neutral) occurring in these dynamic systems, one can begin to unravel the role played by the microbial species. Towards this, various methods have been developed to decipher the function of the microbial communities. The current review focuses on the various qualitative and quantitative methods that currently exist to study microbial interactions. Qualitative methods such as co-culturing experiments are visualized using microscopy-based techniques and are combined with data obtained from multi-omics technologies (metagenomics, metabolomics, metatranscriptomics). Quantitative methods include the construction of networks and network inference, computational models, and development of synthetic microbial consortia. These methods provide a valuable clue on various roles played by interacting partners, as well as possible solutions to overcome pathogenic microbes that can cause life-threatening infections in susceptible hosts. Studying the microbial interactions will further our understanding of complex less-studied ecosystems and enable design of effective frameworks for treatment of infectious diseases.}, } @article {pmid38585649, year = {2024}, author = {Yang, Y and Chen, J and Gao, H and Cui, M and Zhu, M and Xiang, X and Wang, Q}, title = {Characterization of the gut microbiota and fecal and blood metabolomes under various factors in urban children from Northwest China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1374544}, pmid = {38585649}, issn = {2235-2988}, mesh = {Pregnancy ; Child ; Humans ; Female ; *Gastrointestinal Microbiome ; Caffeine ; Cesarean Section ; Urban Population ; Metabolome ; Amino Acids ; }, abstract = {INTRODUCTION: Children have regional dynamics in the gut microbiota development trajectory. Hitherto, the features and influencing factors of the gut microbiota and fecal and plasma metabolites in children from Northwest China remain unclear.

METHODS: Shotgun metagenomic sequencing and untargeted metabolomics were performed on 100 healthy volunteers aged 2-12 years.

RESULTS: Age, body mass index (BMI), regular physical exercise (RPE), and delivery mode (DM) significantly affect gut microbiota and metabolites. Lactobacillus, Butyricimonas, Prevotella, Alistipes, and predicted pathway propanoate production were significantly increased with age while Bifidobacterium breve, B. animalis, B. pseudocatenulatum, Streptococcus infantis, and carbohydrate degradation were decreased. Fecal metabolome revealed that the metabolism of caffeine, amino acids, and lipid significantly increased with age while galactose metabolism decreased. Noticeably, BMI was positively associated with pathogens including Erysipelatoclostridium ramosum, Parabacteroides distasonis, Ruminococcus gnavus, and amino acid metabolism but negatively associated with beneficial Akkermansia muciniphila, Alistipes finegoldii, Eubacterium ramulus, and caffeine metabolism. RPE has increased probiotic Faecalibacterium prausnitzii and Anaerostipes hadrus, acetate and lactate production, and major nutrient metabolism in gut and plasma, but decreased pathobiont Bilophila wadsworthia, taurine degradation, and pentose phosphate pathway. Interestingly, DM affects the gut microbiota and metabolites throughout the whole childhood. Bifidobacterium animalis, Lactobacillus mucosae, L. ruminis, primary bile acid, and neomycin biosynthesis were enriched in eutocia, while anti-inflammatory Anaerofustis stercorihominis, Agathobaculum butyriciproducens, Collinsella intestinalis, and pathogenic Streptococcus salivarius, Catabacter hongkongensis, and amino acid metabolism were enriched in Cesarean section children.

DISCUSSION: Our results provided theoretical and data foundation for the gut microbiota and metabolites in preadolescent children's growth and development in Northwest China.}, } @article {pmid38584937, year = {2024}, author = {Tang, H and Huang, Y and Yuan, D and Liu, J}, title = {Atherosclerosis, gut microbiome, and exercise in a meta-omics perspective: a literature review.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17185}, pmid = {38584937}, issn = {2167-8359}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Cardiovascular Diseases/metabolism ; Metabolomics/methods ; Metabolome ; *Atherosclerosis ; }, abstract = {BACKGROUND: Cardiovascular diseases are the leading cause of death worldwide, significantly impacting public health. Atherosclerotic cardiovascular diseases account for the majority of these deaths, with atherosclerosis marking the initial and most critical phase of their pathophysiological progression. There is a complex relationship between atherosclerosis, the gut microbiome's composition and function, and the potential mediating role of exercise. The adaptability of the gut microbiome and the feasibility of exercise interventions present novel opportunities for therapeutic and preventative approaches.

METHODOLOGY: We conducted a comprehensive literature review using professional databases such as PubMed and Web of Science. This review focuses on the application of meta-omics techniques, particularly metagenomics and metabolomics, in studying the effects of exercise interventions on the gut microbiome and atherosclerosis.

RESULTS: Meta-omics technologies offer unparalleled capabilities to explore the intricate connections between exercise, the microbiome, the metabolome, and cardiometabolic health. This review highlights the advancements in metagenomics and metabolomics, their applications in research, and examines how exercise influences the gut microbiome. We delve into the mechanisms connecting these elements from a metabolic perspective. Metagenomics provides insight into changes in microbial strains post-exercise, while metabolomics sheds light on the shifts in metabolites. Together, these approaches offer a comprehensive understanding of how exercise impacts atherosclerosis through specific mechanisms.

CONCLUSIONS: Exercise significantly influences atherosclerosis, with the gut microbiome serving as a critical intermediary. Meta-omics technology holds substantial promise for investigating the gut microbiome; however, its methodologies require further refinement. Additionally, there is a pressing need for more extensive cohort studies to enhance our comprehension of the connection among these element.}, } @article {pmid38583688, year = {2024}, author = {Thorman, AW and Morrow, AL and Groeneveld, A and Nauta, A and Newburg, DS}, title = {Validation of collection and anaerobic fermentation techniques for measuring prebiotic impact on gut microbiota.}, journal = {Pharmacological research}, volume = {203}, number = {}, pages = {107169}, doi = {10.1016/j.phrs.2024.107169}, pmid = {38583688}, issn = {1096-1186}, mesh = {Humans ; *Prebiotics/analysis ; *Fermentation ; *Gastrointestinal Microbiome ; *Feces/microbiology/chemistry ; Infant ; Adult ; Anaerobiosis ; Male ; Female ; Specimen Handling/methods ; Metabolomics/methods ; }, abstract = {BACKGROUND: Defining the ability of prebiotic dietary carbohydrates to influence the composition and metabolism of the gut microbiota is central to defining their health impact in diverse individuals. Many clinical trials are using indirect methods. This study aimed to validate collection and fermentation methods enabling their use in the context of clinical studies.

METHODS AND RESULTS: Parameters tested included stool sample acquisition, storage, and growth conditions. Stool from 3 infants and 3 adults was collected and stored under varying conditions. Samples were cultured anaerobically for two days in the presence of prebiotics, whereupon optical density and pH were measured across time. Whole genome shotgun sequencing and NMR metabolomics were performed. Neither the type of collection vial (standard vial and two different BD anaerobic collection vials) nor cryopreservation (-80 °C or 4 °C) significantly influenced either microbial composition at 16 h of anaerobic culture or the principal components of the metabolome at 8 or 16 h. Metagenomic differences were driven primarily by subject, while metabolomic differences were driven by fermentation sugar (2'-fucosyllactose or dextrose).

CONCLUSIONS: These data identified a feasible and valid approach for prebiotic fermentation analysis of individual samples in large clinical studies: collection of stool microbiota using standard vials; cryopreservation prior to testing; and collecting fermentation read-out at 8 and 16 hr. Thus, fermentation analysis can be a valid technique for testing the effects of prebiotics on human fecal microbiota.}, } @article {pmid38583259, year = {2024}, author = {Zhang, S and Chau, HT and Tun, HM and Huang, FY and Wong, DK and Mak, LY and Yuen, MF and Seto, WK}, title = {Virological response to nucleos(t)ide analogues treatment in chronic hepatitis B patients is associated with Bacteroides-dominant gut microbiome.}, journal = {EBioMedicine}, volume = {103}, number = {}, pages = {105101}, pmid = {38583259}, issn = {2352-3964}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Hepatitis B, Chronic/drug therapy/virology/microbiology ; Male ; Female ; Middle Aged ; Adult ; *Hepatitis B virus/genetics ; Bacteroides ; Antiviral Agents/therapeutic use ; Metabolome ; Treatment Outcome ; Liver Cirrhosis/drug therapy/etiology/microbiology/virology ; Viral Load ; Bile Acids and Salts/metabolism/blood ; Metagenomics/methods ; Nucleosides/therapeutic use/analogs & derivatives ; }, abstract = {BACKGROUND: Gut dysbiosis is present in chronic hepatitis B virus (HBV) infection. In this study, we integrated microbiome and metabolome analysis to investigate the role of gut microbiome in virological response to nucleos(t)ide analogues (NAs) treatment.

METHODS: Chronic HBV patients were prospectively recruited for steatosis and fibrosis assessments via liver elastography, with full-length 16S sequencing performed to identify the compositional gut microbiota differences. Fasting plasma bile acids were quantified by liquid chromatography-tandem mass spectrometry.

FINDINGS: All patients (n = 110) were characterized into three distinct microbial clusters by their dominant genus: c-Bacteroides, c-Blautia, and c-Prevotella. Patients with c-Bacteroides had a higher plasma ursodeoxycholic acids (UDCA) level and an increase in 7-alpha-hydroxysteroid dehydrogenase (secondary bile acid biotransformation) than other clusters. In NAs-treated patients (n = 84), c-Bacteroides was associated with higher odds of plasma HBV-DNA undetectability when compared with non-c-Bacteroides clusters (OR 3.49, 95% CI 1.43-8.96, p = 0.01). c-Blautia was positively associated with advanced fibrosis (OR 2.74, 95% CI 1.09-7.31, p = 0.04). No such associations were found in treatment-naïve patients. Increased Escherichia coli relative abundance (0.21% vs. 0.03%, p = 0.035) was found in on-treatment patients (median treatment duration 98.1 months) with advanced fibrosis despite HBV DNA undetectability. An enrichment in l-tryptophan biosynthesis was observed in patients with advanced fibrosis, which exhibited a positive correlation with Escherichia coli.

INTERPRETATION: Collectively, unique bacterial signatures, including c-Bacteroides and c-Blautia, were associated with virological undetectability and fibrosis evolution during NAs therapy in chronic HBV, setting up intriguing possibilities in optimizing HBV treatment.

FUNDING: This study was supported by the Guangdong Natural Science Fund (2019A1515012003).}, } @article {pmid38582109, year = {2024}, author = {Chen, Q and Lyu, W and Pan, C and Ma, L and Sun, Y and Yang, H and Wang, W and Xiao, Y}, title = {Tracking investigation of archaeal composition and methanogenesis function from parental to offspring pigs.}, journal = {The Science of the total environment}, volume = {927}, number = {}, pages = {172078}, doi = {10.1016/j.scitotenv.2024.172078}, pmid = {38582109}, issn = {1879-1026}, mesh = {Animals ; *Methane/metabolism ; *Archaea/genetics ; Swine ; Feces/microbiology ; Gastrointestinal Microbiome ; Animal Feed/analysis ; Diet/veterinary ; Female ; Metagenome ; }, abstract = {Archaea play a crucial role in microbial systems, including driving biochemical reactions and affecting host health by producing methane through hydrogen. The study of swine gut archaea has a positive significance in reducing methane emissions and improving feed utilization efficiency. However, the development and functional changes of archaea in the pig intestines have been overlooked for a long time. In this study, 54 fecal samples were collected from 36 parental pigs (18 boars and 18 pregnant/lactating sows), and 108 fecal samples from 18 offspring pigs during lactation, nursery, growing, and finishing stages were tracked and collected for metagenomic sequencing. We obtained 14 archaeal non-redundant metagenome-assembled genomes (MAGs). These archaea were classified as Methanobacteriota and Thermoplasmatota at the phylum level, and Methanobrevibacter, Methanosphaera, MX-02, and UBA71 at the genus level, involving hydrogenotrophic, methylotrophic, and acetoclastic pathways. The hydrogenotrophic pathway dominated the methanogenesis function, and the vast majority of archaea participated in it. Dietary changes profoundly affected the archaeal composition and methanogenesis function in pigs. The abundance of hydrogen-producing bacteria in parental pigs fed high-fiber diets was higher than that in offspring pigs fed low-fiber diets. The methanogenesis function was positively correlated with fiber decomposition functions and negatively correlated with the starch decomposition function. Increased abundance of sulfate reductase and fumarate reductase, as well as decreased acetate/propionate ratio, indicated that the upregulation of alternative hydrogen uptake pathways competing with methanogens may be the reason for the reduced methanogenesis function. These findings contribute to providing information and direction in the pig industry for the development of strategies to reduce methane emissions, improve feed efficiency, and maintain intestinal health.}, } @article {pmid38581039, year = {2024}, author = {Li, Y and Liu, Y and Cui, J and Zhu, M and Wang, W and Chen, K and Huang, L and Liu, Y}, title = {Oral-gut microbial transmission promotes diabetic coronary heart disease.}, journal = {Cardiovascular diabetology}, volume = {23}, number = {1}, pages = {123}, pmid = {38581039}, issn = {1475-2840}, support = {82022076//National Outstanding Youth Foundation of China/ ; }, mesh = {Humans ; Animals ; Mice ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Fusobacterium nucleatum/physiology ; *Coronary Artery Disease/etiology ; *Diabetes Mellitus ; }, abstract = {BACKGROUND: Diabetes is a predominant driver of coronary artery disease worldwide. This study aims to unravel the distinct characteristics of oral and gut microbiota in diabetic coronary heart disease (DCHD). Simultaneously, we aim to establish a causal link between the diabetes-driven oral-gut microbiota axis and increased susceptibility to diabetic myocardial ischemia-reperfusion injury (MIRI).

METHODS: We comprehensively investigated the microbial landscape in the oral and gut microbiota in DCHD using a discovery cohort (n = 183) and a validation chohort (n = 68). Systematically obtained oral (tongue-coating) and fecal specimens were subjected to metagenomic sequencing and qPCR analysis, respectively, to holistically characterize the microbial consortia. Next, we induced diabetic MIRI by administering streptozotocin to C57BL/6 mice and subsequently investigated the potential mechanisms of the oral-gut microbiota axis through antibiotic pre-treatment followed by gavage with specific bacterial strains (Fusobacterium nucleatum or fecal microbiota from DCHD patients) to C57BL/6 mice.

RESULTS: Specific microbial signatures such as oral Fusobacterium nucleatum and gut Lactobacillus, Eubacterium, and Roseburia faecis, were identified as potential microbial biomarkers in DCHD. We further validated that oral Fusobacterium nucleatum and gut Lactobacillus are increased in DCHD patients, with a positive correlation between the two. Experimental evidence revealed that in hyperglycemic mice, augmented Fusobacterium nucleatum levels in the oral cavity were accompanied by an imbalance in the oral-gut axis, characterized by an increased coexistence of Fusobacterium nucleatum and Lactobacillus, along with elevated cardiac miRNA-21 and a greater extent of myocardial damage indicated by TTC, HE, TUNEL staining, all of which contributed to exacerbated MIRI.

CONCLUSION: Our findings not only uncover dysregulation of the oral-gut microbiota axis in diabetes patients but also highlight the pivotal intermediary role of the increased abundance of oral F. nucleatum and gut Lactobacillus in exacerbating MIRI. Targeting the oral-gut microbiota axis emerges as a potent strategy for preventing and treating DCHD. Oral-gut microbial transmission constitutes an intermediate mechanism by which diabetes influences myocardial injury, offering new insights into preventing acute events in diabetic patients with coronary heart disease.}, } @article {pmid38580930, year = {2024}, author = {Hu, X and Yu, C and He, Y and Zhu, S and Wang, S and Xu, Z and You, S and Jiao, Y and Liu, SL and Bao, H}, title = {Integrative metagenomic analysis reveals distinct gut microbial signatures related to obesity.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {119}, pmid = {38580930}, issn = {1471-2180}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Obesity/microbiology ; Bacteria/genetics ; Feces/microbiology ; *Clostridiales ; Akkermansia ; }, abstract = {Obesity is a metabolic disorder closely associated with profound alterations in gut microbial composition. However, the dynamics of species composition and functional changes in the gut microbiome in obesity remain to be comprehensively investigated. In this study, we conducted a meta-analysis of metagenomic sequencing data from both obese and non-obese individuals across multiple cohorts, totaling 1351 fecal metagenomes. Our results demonstrate a significant decrease in both the richness and diversity of the gut bacteriome and virome in obese patients. We identified 38 bacterial species including Eubacterium sp. CAG:274, Ruminococcus gnavus, Eubacterium eligens and Akkermansia muciniphila, and 1 archaeal species, Methanobrevibacter smithii, that were significantly altered in obesity. Additionally, we observed altered abundance of five viral families: Mesyanzhinovviridae, Chaseviridae, Salasmaviridae, Drexlerviridae, and Casjensviridae. Functional analysis of the gut microbiome indicated distinct signatures associated to obesity and identified Ruminococcus gnavus as the primary driver for function enrichment in obesity, and Methanobrevibacter smithii, Akkermansia muciniphila, Ruminococcus bicirculans, and Eubacterium siraeum as functional drivers in the healthy control group. Additionally, our results suggest that antibiotic resistance genes and bacterial virulence factors may influence the development of obesity. Finally, we demonstrated that gut vOTUs achieved a diagnostic accuracy with an optimal area under the curve of 0.766 for distinguishing obesity from healthy controls. Our findings offer comprehensive and generalizable insights into the gut bacteriome and virome features associated with obesity, with the potential to guide the development of microbiome-based diagnostics.}, } @article {pmid38580669, year = {2024}, author = {Schadt, C and Martin, S and Carrell, A and Fortner, A and Hopp, D and Jacobson, D and Klingeman, D and Kristy, B and Phillips, J and Piatkowski, B and Miller, MA and Smith, M and Patil, S and Flynn, M and Canon, S and Clum, A and Mungall, CJ and Pennacchio, C and Bowen, B and Louie, K and Northen, T and Eloe-Fadrosh, EA and Mayes, MA and Muchero, W and Weston, DJ and Mitchell, J and Doktycz, M}, title = {An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {339}, pmid = {38580669}, issn = {2052-4463}, mesh = {Fungi/genetics ; Gene Expression Profiling ; Genotype ; *Metagenome ; *Microbiota ; *Populus/genetics ; Soil ; *Transcriptome ; }, abstract = {Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa. Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P. trichocarpa genotypes grown in two different environments leading to an integrated dataset of 318 metagenomes, 98 plant transcriptomes, and 314 metabolomic profiles that are supported by diverse soil measurements. This expansive dataset will provide insights into causal linkages that relate genomic features and molecular level events to system-level properties and their environmental influences.}, } @article {pmid38579997, year = {2024}, author = {Cao, Y and Li, Y and Jia, L and Wang, Q and Niu, T and Yang, Q and Wang, Q and Zeng, X and Wang, R and Yue, L}, title = {Long-term and combined heavy-metal contamination forms a unique microbiome and resistome: A case study in a Yellow River tributary sediments.}, journal = {Environmental research}, volume = {252}, number = {Pt 1}, pages = {118861}, doi = {10.1016/j.envres.2024.118861}, pmid = {38579997}, issn = {1096-0953}, mesh = {*Metals, Heavy/toxicity/analysis ; *Geologic Sediments/microbiology/chemistry ; *Rivers/microbiology/chemistry ; *Microbiota/drug effects ; *Water Pollutants, Chemical/analysis/toxicity ; China ; Environmental Monitoring ; Bacteria/genetics/drug effects ; }, abstract = {Microorganisms have developed mechanisms to adapt to environmental stress, but how microbial communities adapt to long-term and combined heavy-metal contamination under natural environmental conditions remains unclear. Specifically, this study analyzed the characteristics of heavy metal composition, microbial community, and heavy metal resistance genes (MRGs) in sediments along Mang River, a tributary of the Yellow River, which has been heavily polluted by industrial production for more than 40 years. The results showed that the concentrations of Cr, Zn, Pb, Cu and As in most sediments were higher than the ambient background values. Bringing the heavy metals speciation and concentration into the risk evaluation method, two-thirds of the sediment samples were at or above the moderate risk level, and the ecological risk of combined heavy metals in the sediments decreased along the river stream. The high ecological risk of heavy metals affected the microbial community structure, metabolic pathways and MRG distribution. The formation of a HM-resistant microbiome possibly occurred through the spread of insertion sequences (ISs) carrying multiple MRGs, the types of ISs carrying MRGs outnumber those of plasmids, and the quantity of MRGs on ISs is also higher than that on plasmids. These findings could improve our understanding of the adaptation mechanism of microbial communities to long-term combined heavy metal contamination.}, } @article {pmid38579995, year = {2024}, author = {Zeng, Z and Lv, B and Tang, YE and Sun, H and Li, S and He, Y and Wang, J and Wang, Z}, title = {Effects of dietary selenized glucose on intestinal microbiota and tryptophan metabolism in rats: Assessing skatole reduction potential.}, journal = {Environmental research}, volume = {252}, number = {Pt 3}, pages = {118874}, doi = {10.1016/j.envres.2024.118874}, pmid = {38579995}, issn = {1096-0953}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Skatole/metabolism ; Male ; *Tryptophan/metabolism ; *Rats, Sprague-Dawley ; Rats ; *Glucose/metabolism ; Selenium/pharmacology ; Diet ; }, abstract = {3-Methylindole (Skatole), a degradation product of tryptophan produced by intestinal microbial activity, significantly contributes to odor nuisance. Its adverse effects on animal welfare, human health, and environmental pollution have been noted. However, it is still unclear whether the intestinal microbiota mediates the impact of selenium (Se) on skatole production and what the underlying mechanisms remain elusive. A selenized glucose (SeGlu) derivative is a novel organic selenium compound. In this study, a diverse range of dietary SeGlu-treated levels, including SeGlu-deficient (CK), SeGlu-adequate (0.15 mg Se per L), and SeGlu-supranutritional (0.4 mg Se per L) conditions, were used to investigate the complex interaction of SeGlu on intestinal microbiome and serum metabolome changes in male Sprague-Dawley (SD) rats. The study showed that SeGlu supplementation enhanced the antioxidant ability in rats, significantly manifested in the increases of the activity of catalase (CAT) and glutathione peroxidase (GSH-Px), while no change in the level of malonaldehyde (MDA). Metagenomic sequencing analysis verified that the SeGlu treatment group significantly increased the abundance of beneficial microorganisms such as Clostridium, Ruminococcus, Faecalibacterium, Lactobacillus, and Alloprevotella while reducing the abundance of opportunistic pathogens such as Bacteroides and Alistipes significantly. Further metabolomic analysis revealed phenylalanine, tyrosine, and tryptophan biosynthesis changes in the SeGlu treatment group. Notably, the biosynthesis of indole, a critical pathway, was affected by SeGlu treatment, with several crucial enzymes implicated. Correlation analysis demonstrated strong associations between specific bacterial species - Treponema, Bacteroides, and Ruminococcus, and changes in indole and derivative concentrations. Moreover, the efficacy of SeGlu-treated fecal microbiota was confirmed through fecal microbiota transplantation, leading to a decrease in the concentration of skatole in rats. Collectively, the analysis of microbiota and metabolome response to diverse SeGlu levels suggests that SeGlu is a promising dietary additive in modulating intestinal microbiota and reducing odor nuisance in the livestock and poultry industry.}, } @article {pmid38579579, year = {2024}, author = {Lavilla-Lerma, ML and Aibar-Almazán, A and Martínez-Amat, A and Jiménez-García, JD and Hita-Contreras, F}, title = {Moderate-intensity continuous training and high-intensity interval training modulate the composition of the oral microbiota of elderly adults: Randomized controlled trial.}, journal = {Maturitas}, volume = {185}, number = {}, pages = {107973}, doi = {10.1016/j.maturitas.2024.107973}, pmid = {38579579}, issn = {1873-4111}, mesh = {Humans ; Aged ; *High-Intensity Interval Training/methods ; Middle Aged ; Female ; Male ; *Saliva/microbiology ; *Mouth/microbiology ; *Microbiota ; Exercise/physiology ; Bacteroidetes ; }, abstract = {OBJECTIVE: We investigates the effects of 16-week high-intensity interval training and moderate-intensity continuous training on the composition of the oral microbiota. To the best of our knowledge, at the time of writing this paper no other scholars had described the oral metagenomic changes associated with prescribed exercise in older adults.

METHODS: Forty-three participants aged 60-74 years were randomized 1:1:1 to a control group, high-intensity interval training or moderate-intensity continuous training twice weekly for 16 weeks. Saliva samples were sequenced at baseline, week 8 and week 16 of intervention.

RESULTS: High-intensity interval training produced significant differences over time in Richness and a clear trend to decreased Simpson and Shannon diversity indices. In contrast, Simpson and Shannon indices showed an upward trend over time with moderate-intensity continuous training, which also decreased Firmicutes and increased Bacteroidetes levels. Significant differences in the abundance of pathogenic species were also observed after the participants completed the exercise interventions of either type.

CONCLUSIONS: Both types of exercise promoted subtle changes in the oral microbiota, confirming the modulatory effect of high-intensity interval training and moderate-intensity continuous training on the oral microbiome. Clinical trial registration NCT05220670.}, } @article {pmid38579536, year = {2024}, author = {Yang, Y and Huang, S and Liao, Y and Wu, X and Zhang, C and Wang, X and Yang, Z}, title = {Hippuric acid alleviates dextran sulfate sodium-induced colitis via suppressing inflammatory activity and modulating gut microbiota.}, journal = {Biochemical and biophysical research communications}, volume = {710}, number = {}, pages = {149879}, doi = {10.1016/j.bbrc.2024.149879}, pmid = {38579536}, issn = {1090-2104}, mesh = {Humans ; Animals ; Mice ; Dextran Sulfate ; *Gastrointestinal Microbiome ; Molecular Docking Simulation ; *Colitis/chemically induced/drug therapy ; *Inflammatory Bowel Diseases/chemically induced/drug therapy ; Benzoic Acid ; Disease Models, Animal ; Mice, Inbred C57BL ; Colon ; *Hippurates ; }, abstract = {Inflammatory bowel disease (IBD) is a chronic inflammatory disease associated with metabolic disorder and gut dysbiosis. Decreased abundance of hippuric acid (HA) was found in patients with IBD. HA, metabolized directly from benzoic acid in the intestine and indirectly from polyphenols, serves as a marker of polyphenol catabolism. While polyphenols and benzoic acid have been shown to alleviate intestinal inflammation, the role of HA in this context remains unknown. Herein, we investigated the effects and mechanism of HA on DSS-induced colitis mice. The results revealed that HA alleviated clinical activity and intestinal barrier damage, decreased pro-inflammatory cytokine production. Metagenomic sequencing suggested that HA treatment restored the gut microbiota, including an increase in beneficial gut bacteria such as Adlercreutzia, Eubacterium, Schaedlerella and Bifidobacterium_pseudolongum. Furthermore, we identified 113 candidate genes associated with IBD that are potentially under HA regulation through network pharmacological analyses. 10 hub genes including ALB, IL-6, HSP90AA1, and others were identified using PPI analysis and validated using molecular docking and mRNA expression analysis. Additionally, KEGG analysis suggested that the renin-angiotensin system (RAS), NF-κB signaling and Rap1 signaling pathways were important pathways in the response of HA to colitis. Thus, HA may provide novel biotherapy options for IBD.}, } @article {pmid38575861, year = {2024}, author = {Murtaza, N and Nawaz, M and Yaqub, T and Mehmood, AK}, title = {Impact of Limosilactobacillus fermentum probiotic treatment on gut microbiota composition in sahiwal calves with rotavirus diarrhea: A 16S metagenomic analysis study".}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {114}, pmid = {38575861}, issn = {1471-2180}, mesh = {Animals ; Cattle ; *Rotavirus/genetics ; *Rotavirus Infections/drug therapy/veterinary ; *Gastrointestinal Microbiome/genetics ; *Limosilactobacillus fermentum ; Dysbiosis ; Diarrhea/drug therapy/veterinary ; Feces/microbiology ; *Probiotics/therapeutic use ; *Cattle Diseases/drug therapy/microbiology ; }, abstract = {BACKGROUND: Diarrhea poses a major threat to bovine calves leading to mortality and economic losses. Among the causes of calf diarrhea, bovine rotavirus is a major etiological agent and may result in dysbiosis of gut microbiota. The current study was designed to investigate the effect of probiotic Limosilactobacillus fermentum (Accession No.OR504458) on the microbial composition of rotavirus-infected calves using 16S metagenomic analysis technique. Screening of rotavirus infection in calves below one month of age was done through clinical signs and Reverse Transcriptase PCR. The healthy calves (n = 10) were taken as control while the infected calves (n = 10) before treatment was designated as diarrheal group were treated with Probiotic for 5 days. All the calves were screened for the presence of rotavirus infection on each day and fecal scoring was done to assess the fecal consistency. Infected calves after treatment were designated as recovered group. Fecal samples from healthy, recovered and diarrheal (infected calves before sampling) were processed for DNA extraction while four samples from each group were processed for 16S metagenomic analysis using Illumina sequencing technique and analyzed via QIIME 2.

RESULTS: The results show that Firmicutes were more abundant in the healthy and recovered group than in the diarrheal group. At the same time Proteobacteria was higher in abundance in the diarrheal group. Order Oscillospirales dominated healthy and recovered calves and Enterobacterials dominated the diarrheal group. Alpha diversity indices show that diversity indices based on richness were higher in the healthy group and lower in the diarrheal group while a mixed pattern of clustering between diarrheal and recovered groups samples in PCA plots based on beta diversity indices was observed.

CONCLUSION: It is concluded that probiotic Limosilactobacillus Fermentum N-30 ameliorate the dysbiosis caused by rotavirus diarrhea and may be used to prevent diarrhea in pre-weaned calves after further exploration.}, } @article {pmid38575625, year = {2024}, author = {Flores, VS and Amgarten, DE and Iha, BKV and Ryon, KA and Danko, D and Tierney, BT and Mason, C and da Silva, AM and Setubal, JC}, title = {Discovery and description of novel phage genomes from urban microbiomes sampled by the MetaSUB consortium.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {7913}, pmid = {38575625}, issn = {2045-2322}, mesh = {*Bacteriophages/genetics ; *Railroads ; *Microbiota/genetics ; Metagenome/genetics ; Bacteria/genetics ; }, abstract = {Bacteriophages are recognized as the most abundant members of microbiomes and have therefore a profound impact on microbial communities through the interactions with their bacterial hosts. The International Metagenomics and Metadesign of Subways and Urban Biomes Consortium (MetaSUB) has sampled mass-transit systems in 60 cities over 3 years using metagenomics, throwing light into these hitherto largely unexplored urban environments. MetaSUB focused primarily on the bacterial community. In this work, we explored MetaSUB metagenomic data in order to recover and analyze bacteriophage genomes. We recovered and analyzed 1714 phage genomes with size at least 40 kbp, from the class Caudoviricetes, the vast majority of which (80%) are novel. The recovered genomes were predicted to belong to temperate (69%) and lytic (31%) phages. Thirty-three of these genomes have more than 200 kbp, and one of them reaches 572 kbp, placing it among the largest phage genomes ever found. In general, the phages tended to be site-specific or nearly so, but 194 genomes could be identified in every city from which phage genomes were retrieved. We predicted hosts for 48% of the phages and observed general agreement between phage abundance and the respective bacterial host abundance, which include the most common nosocomial multidrug-resistant pathogens. A small fraction of the phage genomes are carriers of antibiotic resistance genes, and such genomes tended to be particularly abundant in the sites where they were found. We also detected CRISPR-Cas systems in five phage genomes. This study expands the previously reported MetaSUB results and is a contribution to the knowledge about phage diversity, global distribution, and phage genome content.}, } @article {pmid38575584, year = {2024}, author = {Messer, LF and Bourne, DG and Robbins, SJ and Clay, M and Bell, SC and McIlroy, SJ and Tyson, GW}, title = {A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2902}, pmid = {38575584}, issn = {2041-1723}, mesh = {Animals ; *Anthozoa/genetics/microbiology ; *Resilience, Psychological ; *Microbiota/genetics ; Metagenome/genetics ; Nitrogen ; Coral Reefs ; Symbiosis/genetics ; }, abstract = {Microbial diversity has been extensively explored in reef-building corals. However, the functional roles of coral-associated microorganisms remain poorly elucidated. Here, we recover 191 bacterial and 10 archaeal metagenome-assembled genomes (MAGs) from the coral Acropora kenti (formerly A. tenuis) and adjacent seawater, to identify microbial functions and metabolic interactions within the holobiont. We show that 82 MAGs were specific to the A. kenti holobiont, including members of the Pseudomonadota, Bacteroidota, and Desulfobacterota. A. kenti-specific MAGs displayed significant differences in their genomic features and functional potential relative to seawater-specific MAGs, with a higher prevalence of genes involved in host immune system evasion, nitrogen and carbon fixation, and synthesis of five essential B-vitamins. We find a diversity of A. kenti-specific MAGs encode the biosynthesis of essential amino acids, such as tryptophan, histidine, and lysine, which cannot be de novo synthesised by the host or Symbiodiniaceae. Across a water quality gradient spanning 2° of latitude, A. kenti microbial community composition is correlated to increased temperature and dissolved inorganic nitrogen, with corresponding enrichment in molecular chaperones, nitrate reductases, and a heat-shock protein. We reveal mechanisms of A. kenti-microbiome-symbiosis on the Great Barrier Reef, highlighting the interactions underpinning the health of this keystone holobiont.}, } @article {pmid38575441, year = {2024}, author = {Tarzi, C and Zampieri, G and Sullivan, N and Angione, C}, title = {Emerging methods for genome-scale metabolic modeling of microbial communities.}, journal = {Trends in endocrinology and metabolism: TEM}, volume = {35}, number = {6}, pages = {533-548}, doi = {10.1016/j.tem.2024.02.018}, pmid = {38575441}, issn = {1879-3061}, mesh = {*Models, Biological ; Microbiota/physiology ; Humans ; }, abstract = {Genome-scale metabolic models (GEMs) are consolidating as platforms for studying mixed microbial populations, by combining biological data and knowledge with mathematical rigor. However, deploying these models to answer research questions can be challenging due to the increasing number of available computational tools, the lack of universal standards, and their inherent limitations. Here, we present a comprehensive overview of foundational concepts for building and evaluating genome-scale models of microbial communities. We then compare tools in terms of requirements, capabilities, and applications. Next, we highlight the current pitfalls and open challenges to consider when adopting existing tools and developing new ones. Our compendium can be relevant for the expanding community of modelers, both at the entry and experienced levels.}, } @article {pmid38572990, year = {2024}, author = {Sorouri, B and Scales, NC and Gaut, BS and Allison, SD}, title = {Sphingomonas clade and functional distribution with simulated climate change.}, journal = {Microbiology spectrum}, volume = {12}, number = {5}, pages = {e0023624}, pmid = {38572990}, issn = {2165-0497}, support = {DEB-1457160//National Science Foundation (NSF)/ ; DE-SC0020382//US Department of Energy, Office of Science, Biological and Environmental Research/ ; DBI-2305844//National Science Foundation Postdoctoral Research Fellowship in Biology/ ; }, mesh = {*Sphingomonas/genetics/classification/metabolism/isolation & purification ; *Climate Change ; California ; *Soil Microbiology ; Ecosystem ; Phylogeny ; Microbiota/genetics ; Metagenomics ; Grassland ; }, abstract = {Microbes are essential for the functioning of all ecosystems, and as global warming and anthropogenic pollution threaten ecosystems, it is critical to understand how microbes respond to these changes. We investigated the climate response of Sphingomonas, a widespread gram-negative bacterial genus, during an 18-month microbial community reciprocal transplant experiment across a Southern California climate gradient. We hypothesized that after 18 months, the transplanted Sphingomonas clade and functional composition would correspond with site conditions and reflect the Sphingomonas composition of native communities. We extracted Sphingomonas sequences from metagenomic data across the gradient and assessed their clade and functional composition. Representatives of at least 12 major Sphingomonas clades were found at varying relative abundances along the climate gradient, and transplanted Sphingomonas clade composition shifted after 18 months. Site had a significant effect (PERMANOVA; P < 0.001) on the distribution of both Sphingomonas functional (R[2] = 0.465) and clade composition (R[2] = 0.400), suggesting that Sphingomonas composition depends on climate parameters. Additionally, for both Sphingomonas clade and functional composition, ordinations revealed that the transplanted communities shifted closer to the native Sphingomonas composition of the grassland site compared with the site they were transplanted into. Overall, our results indicate that climate and substrate collectively determine Sphingomonas clade and functional composition.IMPORTANCESphingomonas is the most abundant gram-negative bacterial genus in litter-degrading microbial communities of desert, grassland, shrubland, and forest ecosystems in Southern California. We aimed to determine whether Sphingomonas responds to climate change in the same way as gram-positive bacteria and whole bacterial communities in these ecosystems. Within Sphingomonas, both clade composition and functional genes shifted in response to climate and litter chemistry, supporting the idea that bacteria respond similarly to climate at different scales of genetic variation. This understanding of how microbes respond to perturbation across scales may aid in future predictions of microbial responses to climate change.}, } @article {pmid38572865, year = {2024}, author = {Dunham, SJB and Avelar-Barragan, J and Rothman, JA and Adams, ED and Faraci, G and Forner, S and Kawauchi, S and Tenner, AJ and Green, KN and LaFerla, FM and MacGregor, GR and Mapstone, M and Whiteson, KL}, title = {Sex-specific associations between AD genotype and the microbiome of human amyloid beta knock-in (hAβ-KI) mice.}, journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association}, volume = {20}, number = {7}, pages = {4935-4950}, pmid = {38572865}, issn = {1552-5279}, support = {T32 AG00096-38/AG/NIA NIH HHS/United States ; U54 AG054349/AG/NIA NIH HHS/United States ; P30CA062203//National Cancer Institute of the National Institutes of Health/ ; T32 AG000096/AG/NIA NIH HHS/United States ; P30 CA062203/CA/NCI NIH HHS/United States ; //Hewitt Foundation for Biomedical Research/ ; }, mesh = {Animals ; Female ; Humans ; Male ; Mice ; *Alzheimer Disease/microbiology/genetics ; *Amyloid beta-Peptides/metabolism ; *Disease Models, Animal ; Gastrointestinal Microbiome ; Gene Knock-In Techniques ; *Genotype ; Metabolomics ; *Mice, Transgenic ; Microbiota ; Sex Characteristics ; }, abstract = {INTRODUCTION: Emerging evidence links changes in the gut microbiome to late-onset Alzheimer's disease (LOAD), necessitating examination of AD mouse models with consideration of the microbiome.

METHODS: We used shotgun metagenomics and untargeted metabolomics to study the human amyloid beta knock-in (hAβ-KI) murine model for LOAD compared to both wild-type (WT) mice and a model for early-onset AD (3xTg-AD).

RESULTS: Eighteen-month female (but not male) hAβ-KI microbiomes were distinct from WT microbiomes, with AD genotype accounting for 18% of the variance by permutational multivariate analysis of variance (PERMANOVA). Metabolomic diversity differences were observed in females, however no individual metabolites were differentially abundant. hAβ-KI mice microbiomes were distinguishable from 3xTg-AD animals (81% accuracy by random forest modeling), with separation primarily driven by Romboutsia ilealis and Turicibacter species. Microbiomes were highly cage specific, with cage assignment accounting for more than 40% of the PERMANOVA variance between the groups.

DISCUSSION: These findings highlight a sex-dependent variation in the microbiomes of hAβ-KI mice and underscore the importance of considering the microbiome when designing studies that use murine models for AD.

HIGHLIGHTS: Microbial diversity and the abundance of several species differed in human amyloid beta knock-in (hAβ-KI) females but not males. Correlations to Alzheimer's disease (AD) genotype were stronger for the microbiome than the metabolome. Microbiomes from hAβ-KI mice were distinct from 3xTg-AD mice. Cage effects accounted for most of the variance in the microbiome and metabolome.}, } @article {pmid38570378, year = {2024}, author = {Ślusarczyk, A and Ismail, H and Zapała, Ł and Piecha, T and Zapała, P and Radziszewski, P}, title = {Changes in the Urinary Microbiome After Transurethral Resection of Non-muscle-Invasive Bladder Cancer: Insights from a Prospective Observational Study.}, journal = {Annals of surgical oncology}, volume = {31}, number = {7}, pages = {4773-4786}, pmid = {38570378}, issn = {1534-4681}, support = {M/MB/07/22//Warszawski Uniwersytet Medyczny/ ; }, mesh = {Humans ; *Urinary Bladder Neoplasms/microbiology/surgery/pathology/urine ; Prospective Studies ; Male ; Female ; *Microbiota ; Aged ; Middle Aged ; Follow-Up Studies ; Prognosis ; Cystectomy ; Neoplasm Invasiveness ; RNA, Ribosomal, 16S/genetics/analysis ; Bacteria/isolation & purification/genetics/classification ; Phylogeny ; Non-Muscle Invasive Bladder Neoplasms ; }, abstract = {BACKGROUND: This study aimed to characterize the urinary and tumor microbiomes in patients with non-muscle-invasive bladder cancer (NMIBC) before and after transurethral resection of the bladder tumor (TURBT).

METHODS: This single-center prospective study included 26 samples from 11 patients with low-grade Ta papillary NMIBC. Urine samples were collected at the index TURBT and at a 1-year follow-up cystoscopy. The metagenomic analysis of bacterial and archaeal populations was performed based on the highly variable V3-V4 region of the 16S rRNA gene.

RESULTS: Phylogenetic alpha diversity of the bladder microbiome detected in urine was found to be lower at the 1-year follow-up cystoscopy compared to the time of the index TURBT (p < 0.01). Actinomyces, Candidatus cloacimonas, Sphingobacterium, Sellimonas, Fusobacterium, and Roseobacter were more differentially enriched taxa in urine at the follow-up cystoscopy than at the index TURBT. Beta diversity of urine microbiome significantly changed over time (p < 0.05). Phylogenetic alpha diversity of the microbiome was greater in tumor tissues than in paired urine samples (p<0.01). Sphingomonas, Acinetobacter, Candidatus, and Kocuria were more differentially overrepresented in tumor tissues than in urine. The enrichment of the abundance of Corynebacterium and Anaerococcus species in urine collected at TURBT was observed in patients who experienced recurrence within the follow-up period.

CONCLUSIONS: In patients with low-grade NMIBC, the urine microbiome undergoes changes over time after removal of the tumor. The microbiome detected in tumor tissues is more phylogenetically diverse than in paired urine samples collected at TURBT. The interplay between bladder microbiome, tumor microbiome, and their alterations requires further studies to elucidate their predictive value and perhaps therapeutic implications.}, } @article {pmid38569543, year = {2024}, author = {Li, C and Stražar, M and Mohamed, AMT and Pacheco, JA and Walker, RL and Lebar, T and Zhao, S and Lockart, J and Dame, A and Thurimella, K and Jeanfavre, S and Brown, EM and Ang, QY and Berdy, B and Sergio, D and Invernizzi, R and Tinoco, A and Pishchany, G and Vasan, RS and Balskus, E and Huttenhower, C and Vlamakis, H and Clish, C and Shaw, SY and Plichta, DR and Xavier, RJ}, title = {Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria.}, journal = {Cell}, volume = {187}, number = {8}, pages = {1834-1852.e19}, pmid = {38569543}, issn = {1097-4172}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 HL157717/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Bacteria/metabolism ; *Cardiovascular Diseases/metabolism ; *Cholesterol/analysis/blood/metabolism ; Feces/chemistry ; *Gastrointestinal Microbiome ; Longitudinal Studies ; Metabolome ; Metabolomics ; RNA, Ribosomal, 16S/metabolism ; }, abstract = {Accumulating evidence suggests that cardiovascular disease (CVD) is associated with an altered gut microbiome. Our understanding of the underlying mechanisms has been hindered by lack of matched multi-omic data with diagnostic biomarkers. To comprehensively profile gut microbiome contributions to CVD, we generated stool metagenomics and metabolomics from 1,429 Framingham Heart Study participants. We identified blood lipids and cardiovascular health measurements associated with microbiome and metabolome composition. Integrated analysis revealed microbial pathways implicated in CVD, including flavonoid, γ-butyrobetaine, and cholesterol metabolism. Species from the Oscillibacter genus were associated with decreased fecal and plasma cholesterol levels. Using functional prediction and in vitro characterization of multiple representative human gut Oscillibacter isolates, we uncovered conserved cholesterol-metabolizing capabilities, including glycosylation and dehydrogenation. These findings suggest that cholesterol metabolism is a broad property of phylogenetically diverse Oscillibacter spp., with potential benefits for lipid homeostasis and cardiovascular health.}, } @article {pmid38568776, year = {2024}, author = {Hu, ZQ and Hung, YM and Chen, LH and Lai, LC and Pan, MH and Chuang, EY and Tsai, MH}, title = {NURECON: A Novel Online System for Determining Nutrition Requirements Based on Microbial Composition.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {21}, number = {2}, pages = {254-264}, doi = {10.1109/TCBB.2024.3349572}, pmid = {38568776}, issn = {1557-9964}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Diet ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Nutritional Requirements ; }, abstract = {Dietary habits have been proven to have an impact on the microbial composition and health of the human gut. Over the past decade, researchers have discovered that gut microbiota can use nutrients to produce metabolites that have major implications for human physiology. However, there is no comprehensive system that specifically focuses on identifying nutrient deficiencies based on gut microbiota, making it difficult to interpret and compare gut microbiome data in the literature. This study proposes an analytical platform, NURECON, that can predict nutrient deficiency information in individuals by comparing their metagenomic information to a reference baseline. NURECON integrates a next-generation bacterial 16S rRNA analytical pipeline (QIIME2), metabolic pathway prediction tools (PICRUSt2 and KEGG), and a food compound database (FooDB) to enable the identification of missing nutrients and provide personalized dietary suggestions. Metagenomic information from total number of 287 healthy subjects was used to establish baseline microbial composition and metabolic profiles. The uploaded data is analyzed and compared to the baseline for nutrient deficiency assessment. Visualization results include gut microbial composition, related enzymes, pathways, and nutrient abundance. NURECON is a user-friendly online platform that provides nutritional advice to support dietitians' research or menu design.}, } @article {pmid38567644, year = {2024}, author = {Chen, J and Lin, L and Tu, Q and Peng, Q and Wang, X and Liang, C and Zhou, J and Yu, X}, title = {Metagenomic-based discovery and comparison of the lignin degrading potential of microbiomes in aquatic and terrestrial ecosystems via the LCdb database.}, journal = {Molecular ecology resources}, volume = {24}, number = {5}, pages = {e13950}, doi = {10.1111/1755-0998.13950}, pmid = {38567644}, issn = {1755-0998}, support = {2019YFA0606704//National Key Research and Development Program of China/ ; 32370115//National Natural Science Foundation of China/ ; }, mesh = {*Lignin/metabolism ; *Microbiota/genetics/physiology ; *Metagenomics/methods ; *Ecosystem ; Archaea/genetics/classification/metabolism ; Bacteria/classification/genetics/metabolism/isolation & purification ; Microbial Consortia/genetics/physiology ; Metagenome ; }, abstract = {Lignin, as an abundant organic carbon, plays a vital role in the global carbon cycle. However, our understanding of the global lignin-degrading microbiome remains elusive. The greatest barrier has been absence of a comprehensive and accurate functional gene database. Here, we first developed a curated functional gene database (LCdb) for metagenomic profiling of lignin degrading microbial consortia. Via the LCdb, we draw a clear picture describing the global biogeography of communities with lignin-degrading potential. They exhibit clear niche differentiation at the levels of taxonomy and functional traits. The terrestrial microbiomes showed the highest diversity, yet the lowest correlations. In particular, there were few correlations between genes involved in aerobic and anaerobic degradation pathways, showing a clear functional redundancy property. In contrast, enhanced correlations, especially closer inter-connections between anaerobic and aerobic groups, were observed in aquatic consortia in response to the lower diversity. Specifically, dypB and dypA, are widespread on Earth, indicating their essential roles in lignin depolymerization. Estuarine and marine consortia featured the laccase and mnsod genes, respectively. Notably, the roles of archaea in lignin degradation were revealed in marine ecosystems. Environmental factors strongly influenced functional traits, but weakly shaped taxonomic groups. Null mode analysis further verified that composition of functional traits was deterministic, while taxonomic composition was highly stochastic, demonstrating that the environment selects functional genes rather than taxonomic groups. Our study not only develops a useful tool to study lignin degrading microbial communities via metagenome sequencing but also advances our understanding of ecological traits of these global microbiomes.}, } @article {pmid38566975, year = {2024}, author = {Moubset, O and Filloux, D and Fontes, H and Julian, C and Fernandez, E and Galzi, S and Blondin, L and Chehida, SB and Lett, JM and Mesléard, F and Kraberger, S and Custer, JM and Salywon, A and Makings, E and Marais, A and Chiroleu, F and Lefeuvre, P and Martin, DP and Candresse, T and Varsani, A and Ravigné, V and Roumagnac, P}, title = {Virome release of an invasive exotic plant species in southern France.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {veae025}, pmid = {38566975}, issn = {2057-1577}, abstract = {The increase in human-mediated introduction of plant species to new regions has resulted in a rise of invasive exotic plant species (IEPS) that has had significant effects on biodiversity and ecosystem processes. One commonly accepted mechanism of invasions is that proposed by the enemy release hypothesis (ERH), which states that IEPS free from their native herbivores and natural enemies in new environments can outcompete indigenous species and become invasive. We here propose the virome release hypothesis (VRH) as a virus-centered variant of the conventional ERH that is only focused on enemies. The VRH predicts that vertically transmitted plant-associated viruses (PAV, encompassing phytoviruses and mycoviruses) should be co-introduced during the dissemination of the IEPS, while horizontally transmitted PAV of IEPS should be left behind or should not be locally transmitted in the introduced area due to a maladaptation of local vectors. To document the VRH, virome richness and composition as well as PAV prevalence, co-infection, host range, and transmission modes were compared between indigenous plant species and an invasive grass, cane bluestem (Bothriochloa barbinodis), in both its introduced range (southern France) and one area of its native range (Sonoran Desert, Arizona, USA). Contrary to the VRH, we show that invasive populations of B. barbinodis in France were not associated with a lower PAV prevalence or richness than native populations of B. barbinodis from the USA. However, comparison of virome compositions and network analyses further revealed more diverse and complex plant-virus interactions in the French ecosystem, with a significant richness of mycoviruses. Setting mycoviruses apart, only one putatively vertically transmitted phytovirus (belonging to the Amalgaviridae family) and one putatively horizontally transmitted phytovirus (belonging to the Geminiviridae family) were identified from B. barbinodis plants in the introduced area. Collectively, these characteristics of the B. barbinodis-associated PAV community in southern France suggest that a virome release phase may have immediately followed the introduction of B. barbinodis to France in the 1960s or 1970s, and that, since then, the invasive populations of this IEPS have already transitioned out of this virome release phase, and have started interacting with several local mycoviruses and a few local plant viruses.}, } @article {pmid38566380, year = {2024}, author = {Syafarina, I and Mazaya, M and Indrawati, A and Akbar, SZ and Sukowati, C and Sadikin, R}, title = {Skin Microbial Composition and Genetic Mutation Analysis in Precision Medicine for Epidermolysis Bullosa.}, journal = {Current drug targets}, volume = {25}, number = {6}, pages = {404-415}, pmid = {38566380}, issn = {1873-5592}, mesh = {Humans ; *Epidermolysis Bullosa/genetics/therapy ; *Precision Medicine/methods ; *Skin/microbiology/pathology ; *Mutation ; Metagenomics/methods ; Microbiota/genetics ; }, abstract = {Epidermolysis bullosa (EB) is an inherited skin disease representing a spectrum of rare genetic disorders. These conditions share the common trait that causes fragile skin, resulting in the development of blisters and erosions. The inheritance follows an autosomal pattern, and the array of clinical presentations leads to significant physical suffering, considerable morbidity, and mortality. Despite EB having no cure, effectively managing EB remains an exceptional challenge due to its rarity and complexity, occasionally casting a profound impact on the lives of affected individuals. Considering that EB management requires a multidisciplinary approach, this sometimes worsens the condition of patients with EB due to inappropriate handling. Thus, more appropriate and precise treatment management of EB is essentially needed. Advanced technology in medicine and health comes into the bioinformatics era. Including treatment for skin diseases, omics-based approaches aim to evaluate and handle better disease management and treatment. In this work, we review several approaches regarding the implementation of omics-based technology, including genetics, pathogenic mutation, skin microbiomics, and metagenomics analysis for EB. In addition, we highlight recent updates on the potential of metagenomics analysis in precision medicine for EB.}, } @article {pmid38566102, year = {2024}, author = {Luo, WC and Mei, SQ and Huang, ZJ and Chen, ZH and Zhang, YC and Yang, MY and Liu, JQ and Xu, JY and Yang, XR and Zhong, RW and Tang, LB and Yin, LX and Deng, Y and Peng, YL and Lu, C and Chen, BL and Ke, DX and Tu, HY and Yang, JJ and Xu, CR and Wu, YL and Zhou, Q}, title = {Correlation of distribution characteristics and dynamic changes of gut microbiota with the efficacy of immunotherapy in EGFR-mutated non-small cell lung cancer.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {326}, pmid = {38566102}, issn = {1479-5876}, support = {82102808//National Natural Science Foundation of China/ ; 82373349//National Natural Science Foundation of China/ ; G623281109//The Southern Medical University's Young Talents Climbing Program for Science and Technology Development/ ; 2017B030314120//Guangdong Provincial Key Lab of Translational Medicine in Lung Cancer/ ; KY0120220136//Guangdong Provincial People's Hospital Young Talent Project/ ; }, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/therapy/drug therapy ; *Lung Neoplasms/therapy/drug therapy ; *Gastrointestinal Microbiome ; Immunotherapy ; ErbB Receptors/genetics ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {BACKGROUND: The effects of gut microbiota and metabolites on the responses to immune checkpoint inhibitors (ICIs) in advanced epidermal growth factor receptor (EGFR) wild-type non-small cell lung cancer (NSCLC) have been studied. However, their effects on EGFR-mutated (EGFR +) NSCLC remain unknown.

METHODS: We prospectively recorded the clinicopathological characteristics of patients with advanced EGFR + NSCLC and assessed potential associations between the use of antibiotics or probiotics and immunotherapy efficacy. Fecal samples were collected at baseline, early on-treatment, response and progression status and were subjected to metagenomic next-generation sequencing and ultra-high-performance liquid chromatography-mass spectrometry analyses to assess the effects of gut microbiota and metabolites on immunotherapy efficacy.

RESULTS: The clinical data of 74 advanced EGFR + NSCLC patients were complete and 18 patients' fecal samples were dynamically collected. Patients that used antibiotics had shorter progression-free survival (PFS) (mPFS, 4.8 vs. 6.7 months; P = 0.037); probiotics had no impact on PFS. Two dynamic types of gut microbiota during immunotherapy were identified: one type showed the lowest relative abundance at the response time point, whereas the other type showed the highest abundance at the response time point. Metabolomics revealed significant differences in metabolites distribution between responders and non-responders. Deoxycholic acid, glycerol, and quinolinic acid were enriched in responders, whereas L-citrulline was enriched in non-responders. There was a significant correlation between gut microbiota and metabolites.

CONCLUSIONS: The use of antibiotics weakens immunotherapy efficacy in patients with advanced EGFR + NSCLC. The distribution characteristics and dynamic changes of gut microbiota and metabolites may indicate the efficacy of immunotherapy in advanced EGFR + NSCLC.}, } @article {pmid38565843, year = {2024}, author = {Brar, NK and Dhariwal, A and Åmdal, HA and Junges, R and Salvadori, G and Baker, JL and Edlund, A and Petersen, FC}, title = {Exploring ex vivo biofilm dynamics: consequences of low ampicillin concentrations on the human oral microbiome.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {37}, pmid = {38565843}, issn = {2055-5008}, support = {K99 DE029228/DE/NIDCR NIH HHS/United States ; R00 DE029228/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Ampicillin/pharmacology ; *Microbiota ; Bacteria/genetics ; Biofilms ; }, abstract = {Prolonged exposure to antibiotics at low concentration can promote processes associated with bacterial biofilm formation, virulence and antibiotic resistance. This can be of high relevance in microbial communities like the oral microbiome, where commensals and pathogens share a common habitat and where the total abundance of antibiotic resistance genes surpasses the abundance in the gut. Here, we used an ex vivo model of human oral biofilms to investigate the impact of ampicillin on biofilm viability. The ecological impact on the microbiome and resistome was investigated using shotgun metagenomics. The results showed that low concentrations promoted significant shifts in microbial taxonomic profile and could enhance biofilm viability by up to 1 to 2-log. For the resistome, low concentrations had no significant impact on antibiotic resistance gene (ARG) diversity, while ARG abundance decreased by up to 84%. A positive correlation was observed between reduced microbial diversity and reduced ARG abundance. The WHO priority pathogens Streptococcus pneumoniae and Staphylococcus aureus were identified in some of the samples, but their abundance was not significantly altered by ampicillin. Most of the antibiotic resistance genes that increased in abundance in the ampicillin group were associated with streptococci, including Streptococcus mitis, a well-known potential donor of ARGs to S. pneumoniae. Overall, the results highlight the potential of using the model to further our understanding of ecological and evolutionary forces driving antimicrobial resistance in oral microbiomes.}, } @article {pmid38565528, year = {2024}, author = {Liang, JL and Feng, SW and Lu, JL and Wang, XN and Li, FL and Guo, YQ and Liu, SY and Zhuang, YY and Zhong, SJ and Zheng, J and Wen, P and Yi, X and Jia, P and Liao, B and Shu, WS and Li, JT}, title = {Hidden diversity and potential ecological function of phosphorus acquisition genes in widespread terrestrial bacteriophages.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2827}, pmid = {38565528}, issn = {2041-1723}, support = {41622106//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42177009//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Bacteriophages/genetics ; Ecosystem ; Phosphorus ; Metagenome/genetics ; Soil ; }, abstract = {Phosphorus (P) limitation of ecosystem processes is widespread in terrestrial habitats. While a few auxiliary metabolic genes (AMGs) in bacteriophages from aquatic habitats are reported to have the potential to enhance P-acquisition ability of their hosts, little is known about the diversity and potential ecological function of P-acquisition genes encoded by terrestrial bacteriophages. Here, we analyze 333 soil metagenomes from five terrestrial habitat types across China and identify 75 viral operational taxonomic units (vOTUs) that encode 105 P-acquisition AMGs. These AMGs span 17 distinct functional genes involved in four primary processes of microbial P-acquisition. Among them, over 60% (11/17) have not been reported previously. We experimentally verify in-vitro enzymatic activities of two pyrophosphatases and one alkaline phosphatase encoded by P-acquisition vOTUs. Thirty-six percent of the 75 P-acquisition vOTUs are detectable in a published global topsoil metagenome dataset. Further analyses reveal that, under certain circumstances, the identified P-acquisition AMGs have a greater influence on soil P availability and are more dominant in soil metatranscriptomes than their corresponding bacterial genes. Overall, our results reinforce the necessity of incorporating viral contributions into biogeochemical P cycling.}, } @article {pmid38565493, year = {2024}, author = {Fonnes, S and Mollerup, S and Paulsen, SJ and Holzknecht, BJ and Westh, H and Rosenberg, J}, title = {The microbiome of the appendix differs in patients with and without appendicitis: A prospective cohort study.}, journal = {Surgery}, volume = {175}, number = {6}, pages = {1482-1488}, doi = {10.1016/j.surg.2024.02.020}, pmid = {38565493}, issn = {1532-7361}, mesh = {Humans ; *Appendicitis/microbiology/surgery ; Prospective Studies ; Adult ; Female ; Male ; *Appendix/microbiology/surgery/pathology ; Middle Aged ; *Appendectomy ; Microbiota ; Laparoscopy ; Young Adult ; Aged ; }, abstract = {BACKGROUND: Appendicitis seems to be a disease of infectious origin, but the detailed pathogenesis is unknown. We aimed to investigate the microbiome of the appendix lumen in patients with and without appendicitis, including a comparison of the subgroups of complicated versus uncomplicated appendicitis.

METHODS: This prospective observational cohort study included adult patients undergoing laparoscopic appendectomy for suspected appendicitis. According to histopathologic findings, the investigated groups consisted of patients with and without appendicitis, including subgroups of complicated versus uncomplicated appendicitis based on the surgical report. A swab of the appendix lumen was analyzed for genetic material from bacteria with shotgun metagenomics, and outcomes included analyses of microbiome diversity and differential abundance of bacteria.

RESULTS: A total of 53 swabs from patients with suspected appendicitis were analyzed: 42 with appendicitis (16 complicated) and 11 without appendicitis. When comparing patients with and without appendicitis, they were equally rich in bacteria (alpha diversity), but the microbiome composition was dissimilar between these groups (beta diversity) (P < .01). No consistent bacterial species were detected in all patients with appendicitis, but a least 3 genera (Blautia, Faecalibacterium, and Fusicatenibacter) and 2 species, Blautia faecis and Blautia wexlerae, were more abundant in patients without appendicitis. For the subgroups complicated versus uncomplicated appendicitis, both measures for microbiome diversity were similar.

CONCLUSION: The appendix microbiome composition of genetic material from bacteria in adult patients with and without appendicitis differed, but the microbiome was similar for patients with complicated versus uncomplicated appendicitis. Trial registration NCT03349814.}, } @article {pmid38565143, year = {2024}, author = {Kirsch, JM and Hryckowian, AJ and Duerkop, BA}, title = {A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota.}, journal = {Cell host & microbe}, volume = {32}, number = {5}, pages = {739-754.e4}, pmid = {38565143}, issn = {1934-6069}, support = {F31 AI169976/AI/NIAID NIH HHS/United States ; R01 AI141479/AI/NIAID NIH HHS/United States ; R35 GM150996/GM/NIGMS NIH HHS/United States ; T32 AI052066/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Metagenomics/methods ; *DNA Transposable Elements/genetics ; Bacteroides/genetics ; Evolution, Molecular ; Genome, Bacterial ; Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Bacteria/genetics/classification ; }, abstract = {Insertion sequence (IS) elements are mobile genetic elements in bacterial genomes that support adaptation. We developed a database of IS elements coupled to a computational pipeline that identifies IS element insertions in the microbiota. We discovered that diverse IS elements insert into the genomes of intestinal bacteria regardless of human host lifestyle. These insertions target bacterial accessory genes that aid in their adaptation to unique environmental conditions. Using IS expansion in Bacteroides, we show that IS activity leads to the insertion of "hot spots" in accessory genes. We show that IS insertions are stable and can be transferred between humans. Extreme environmental perturbations force IS elements to fall out of the microbiota, and many fail to rebound following homeostasis. Our work shows that IS elements drive bacterial genome diversification within the microbiota and establishes a framework for understanding how strain-level variation within the microbiota impacts human health.}, } @article {pmid38565017, year = {2024}, author = {Zhang, P and Lu, G and Sun, Y and Yan, Z and Zhang, L and Liu, J}, title = {Effect of microplastics on oxytetracycline trophic transfer: Immune, gut microbiota and antibiotic resistance gene responses.}, journal = {Journal of hazardous materials}, volume = {470}, number = {}, pages = {134147}, doi = {10.1016/j.jhazmat.2024.134147}, pmid = {38565017}, issn = {1873-3336}, mesh = {Animals ; *Oxytetracycline/toxicity ; *Microplastics/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Water Pollutants, Chemical/toxicity ; *Food Chain ; *Anti-Bacterial Agents/toxicity/pharmacology ; Drug Resistance, Microbial/genetics ; Polypropylenes ; Goldfish/genetics/metabolism ; Penaeidae/microbiology/drug effects ; Muramidase/metabolism ; }, abstract = {Microplastics and antibiotics are prevalent and emerging pollutants in aquatic ecosystems, but their interactions in aquatic food chains remain largely unexplored. This study investigated the impact of polypropylene microplastics (PP-MPs) on oxytetracycline (OTC) trophic transfer from the shrimp (Neocaridina denticulate) to crucian carp (Carassius auratus) by metagenomic sequencing. The carrier effects of PP-MPs promoted OTC bioaccumulation and trophic transfer, which exacerbated enterocyte vacuolation and hepatocyte eosinophilic necrosis. PP-MPs enhanced the inhibitory effect of OTC on intestinal lysozyme activities and complement C3 levels in shrimp and fish, and hepatic immunoglobulin M levels in fish (p < 0.05). Co-exposure of MPs and OTC markedly increased the abundance of Actinobacteria in shrimp and Firmicutes in fish, which caused disturbances in carbohydrate, amino acid, and energy metabolism. Moreover, OTC exacerbated the enrichment of antibiotic resistance genes (ARGs) in aquatic animals, and PP-MPs significantly increased the diversity and abundance of ARGs and facilitated the trophic transfer of teta and tetm. Our findings disclosed the impacts of PP-MPs on the mechanism of antibiotic toxicity in aquatic food chains and emphasized the importance of gut microbiota for ARGs trophic transfer, which contributed to a deeper understanding of potential risks posed by complex pollutants on aquatic ecosystems.}, } @article {pmid38563656, year = {2024}, author = {Zhu, J and Yin, J and Chen, J and Hu, M and Lu, W and Wang, H and Zhang, H and Chen, W}, title = {Integrative analysis with microbial modelling and machine learning uncovers potential alleviators for ulcerative colitis.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2336877}, pmid = {38563656}, issn = {1949-0984}, mesh = {Animals ; Mice ; Humans ; *Colitis, Ulcerative ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases ; *Colitis ; Machine Learning ; }, abstract = {Ulcerative colitis (UC) is a challenging form of inflammatory bowel disease, and its etiology is intricately linked to disturbances in the gut microbiome. To identify the potential alleviators of UC, we employed an integrative analysis combining microbial community modeling with advanced machine learning techniques. Using metagenomics data sourced from the Integrated Human Microbiome Project, we constructed individualized microbiome community models for each participant. Our analysis highlighted a significant decline in both α and β-diversity of strain-level microbial populations in UC subjects compared to controls. Distinct differences were also observed in the predicted fecal metabolite profiles and strain-to-metabolite contributions between the two groups. Using tree-based machine learning models, we successfully identified specific microbial strains and their associated metabolites as potential alleviators of UC. Notably, our experimental validation using a dextran sulfate sodium-induced UC mouse model demonstrated that the administration of Parabacteroides merdae ATCC 43,184 and N-acetyl-D-mannosamine provided notable relief from colitis symptoms. In summary, our study underscores the potential of an integrative approach to identify novel therapeutic avenues for UC, paving the way for future targeted interventions.}, } @article {pmid38562473, year = {2024}, author = {Seth, N and Vats, S and Lakhanpaul, S and Arafat, Y and Mazumdar-Leighton, S and Bansal, M and Babu, CR}, title = {Microbial community diversity of an integrated constructed wetland used for treatment of sewage.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1355718}, pmid = {38562473}, issn = {1664-302X}, abstract = {The microbial community diversity in Constructed Wetland System (CWS) plays a key role in the removal of pollutants from waste water. An integrated functional CWS developed at Neela Hauz Biodiversity Park, Delhi was selected to assess the diversity in composition and structure of microbial community diversity of sludge and sediment of CWS, based on metagenomic approach using 16S rRNA genes. The sediment showed higher diversity than sludge and both formed distinct clusters. The taxonomic structure of the microbial community of CWS is represented by 6,731 OTUs distributed among 2 kingdoms, 103 phyla, 227 classes, 337 orders, 320 families, 295 identified genera, and 84 identified species. The relative abundance of top 5 dominant phyla of sludge and sediment varied from 3.77% (Acidobacteria) to 35.33% (Proteobacteria) and 4.07% (Firmicutes) to 28.20% (Proteobacteria), respectively. The range of variation in relative abundance of top 5 dominant genera of sludge and sediment was 2.58% (Hyphomicrobium) to 6.61% (Planctomyces) and 2.47% (Clostridium) to 4.22% (Syntrophobacter), respectively. The rich microbial diversity of CWS makes it perform better in pollutants removal (59.91-95.76%) than other CWs. Based on the abundance values of taxa, the taxa are grouped under four frequency distribution classes-abundant (>20), common (10-19), rare (5-9), and very rare (1-4). The unique structure of microbial communities of integrated CWS is that the number of abundant taxa decreases in descending order of taxonomic hierarchy, while the number of rare and very rare taxa increases. For example, the number of abundant phyla was 14 and 21 in sludge and sediment, respectively and both communities have only 3 abundant genera each. This is in contrast to 4 and 17 very rare phyla in sludge and sediment, respectively and both the communities have 114 and 91 very rare genera, respectively. The outcomes of the study is that the integrated CWS has much higher microbial community diversity than the diversity reported for other CWs, and the rich diversity can be used for optimizing the performance efficiency of CWS in the removal of pollutants from waste water. Such structural diversity might be an adaptation to heterogeneous environment of CWS.}, } @article {pmid38561814, year = {2024}, author = {Logares, R}, title = {Decoding populations in the ocean microbiome.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {67}, pmid = {38561814}, issn = {2049-2618}, support = {PID2019-105775RB-I00//Agencia Estatal de Investigación/ ; }, mesh = {Animals ; *Ecosystem ; *Microbiota/genetics ; Oceans and Seas ; Metagenomics ; }, abstract = {Understanding the characteristics and structure of populations is fundamental to comprehending ecosystem processes and evolutionary adaptations. While the study of animal and plant populations has spanned a few centuries, microbial populations have been under scientific scrutiny for a considerably shorter period. In the ocean, analyzing the genetic composition of microbial populations and their adaptations to multiple niches can yield important insights into ecosystem function and the microbiome's response to global change. However, microbial populations have remained elusive to the scientific community due to the challenges associated with isolating microorganisms in the laboratory. Today, advancements in large-scale metagenomics and metatranscriptomics facilitate the investigation of populations from many uncultured microbial species directly from their habitats. The knowledge acquired thus far reveals substantial genetic diversity among various microbial species, showcasing distinct patterns of population differentiation and adaptations, and highlighting the significant role of selection in structuring populations. In the coming years, population genomics is expected to significantly increase our understanding of the architecture and functioning of the ocean microbiome, providing insights into its vulnerability or resilience in the face of ongoing global change. Video Abstract.}, } @article {pmid38561516, year = {2024}, author = {Lu, G and Gao, D and Jiang, W and Yu, X and Tong, J and Liu, X and Qiao, T and Wang, R and Zhang, M and Wang, S and Yang, J and Li, D and Lv, Z}, title = {Disrupted gut microecology after high-dose [131]I therapy and radioprotective effects of arachidonic acid supplementation.}, journal = {European journal of nuclear medicine and molecular imaging}, volume = {51}, number = {8}, pages = {2395-2408}, pmid = {38561516}, issn = {1619-7089}, support = {21ZR1449600//Natural Science Foundation of Shanghai/ ; 82071964//National Natural Science Foundation of China/ ; 22YF1433600//Science and Technology Commission of Shanghai Municipality/ ; 2019//Shanghai Leading Talent Program sponsored by Shanghai Human Resources and Social Security Bureau/ ; GWVI-11.2-YQ51//Shanghai Municipal Health Commission/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/radiation effects ; *Iodine Radioisotopes/adverse effects ; Mice ; *Radiation-Protective Agents/pharmacology ; Humans ; *Arachidonic Acid/metabolism ; Male ; Female ; Adult ; Thyroid Neoplasms/radiotherapy ; Middle Aged ; Dietary Supplements ; Whole-Body Irradiation/adverse effects ; }, abstract = {BACKGROUND: Despite the potential radiotoxicity in differentiated thyroid cancer (DTC) patients with high-dose [131]I therapy, the alterations and regulatory mechanisms dependent on intestinal microecology remain poorly understood. We aimed to identify the characteristics of the gut microbiota and metabolites in DTC patients suffering from high-dose [131]I therapy and explore the radioprotective mechanisms underlying arachidonic acid (ARA) treatment.

METHODS: A total of 102 patients with DTC were recruited, with fecal samples collected before and after [131]I therapy for microbiome and untargeted and targeted metabolomic analyses. Mice were exposed to total body irradiation with ARA replenishment and antibiotic pretreatment and were subjected to metagenomic, metabolomic, and proteomic analyses.

RESULTS: [131]I therapy significantly changed the structure of gut microbiota and metabolite composition in patients with DTC. Lachnospiraceae were the most dominant bacteria after [131]I treatment, and metabolites with decreased levels and pathways related to ARA and linoleic acid were observed. In an irradiation mouse model, ARA supplementation not only improved quality of life and recovered hematopoietic and gastrointestinal systems but also ameliorated oxidative stress and inflammation and preserved enteric microecology composition. Additionally, antibiotic intervention eliminated the radioprotective effects of ARA. Proteomic analysis and ursolic acid pretreatment showed that ARA therapy greatly influenced intestinal lipid metabolism in mice subjected to irradiation by upregulating the expression of hydroxy-3-methylglutaryl-coenzyme A synthase 1.

CONCLUSION: These findings highlight that ARA, as a key metabolite, substantially contributes to radioprotection. Our study provides novel insights into the pivotal role that the microbiota-metabolite axis plays in radionuclide protection and offers effective biological targets for treating radiation-induced adverse effects.}, } @article {pmid38561312, year = {2024}, author = {Hong, L and Huang, Y and Han, J and Li, S and Zhang, L and Zhou, Q and Cao, X and Yu, W and Guo, X and Yang, Y and Zhou, Y and Yan, W and Hong, S and Jiang, S and Cao, Y}, title = {Pathogen-specific alterations in intestinal microbiota precede urinary tract infections in preterm infants: a longitudinal case-control study.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2333413}, pmid = {38561312}, issn = {1949-0984}, mesh = {Infant ; Child ; Humans ; Infant, Newborn ; Adolescent ; Case-Control Studies ; *Gastrointestinal Microbiome ; Escherichia coli ; Infant, Premature ; Anti-Bacterial Agents/therapeutic use ; *Urinary Tract Infections ; Enterobacteriaceae ; Leukocyte L1 Antigen Complex ; }, abstract = {Urinary tract infections (UTIs) are among the most common late-onset infections in preterm infants, characterized by nonspecific symptoms and a pathogenic spectrum that diverges from that of term infants and older children, which present unique diagnostic and therapeutic challenges. Existing data on the role of gut microbiota in UTI pathogenesis in this demographic are limited. This study aims to investigate alterations in gut microbiota and fecal calprotectin levels and their association with the development of UTIs in hospitalized preterm infants. A longitudinal case-control study was conducted involving preterm infants admitted between January 2018 and October 2020. Fecal samples were collected weekly and analyzed for microbial profiles and calprotectin levels. Propensity score matching, accounting for key perinatal factors including age and antibiotic use, was utilized to match samples from UTI-diagnosed infants to those from non-UTI counterparts. Among the 151 preterm infants studied, 53 were diagnosed with a UTI, predominantly caused by Enterobacteriaceae (79.3%) and Enterococcaceae (19.0%). Infants with UTIs showed a significantly higher abundance of these families compared to non-UTI infants, for both Gram-negative and positive pathogens, respectively. Notably, there was a significant pre-UTI increase in the abundance of pathogen-specific taxa in infants later diagnosed with UTIs, offering high predictive value for early detection. Shotgun metagenomic sequencing further confirmed the dominance of specific pathogenic species pre-UTI and revealed altered virulence factor profiles associated with Klebsiella aerogenes and Escherichia coli infections. Additionally, a decline in fecal calprotectin levels was observed preceding UTI onset, particularly in cases involving Enterobacteriaceae. The observed pathogen-specific alterations in the gut microbiota preceding UTI onset offer novel insight into the UTI pathogenesis and promising early biomarkers for UTIs in preterm infants, potentially enhancing the timely management of this common infection. However, further validation in larger cohorts is essential to confirm these findings.}, } @article {pmid38561162, year = {2024}, author = {Ozsefil, IC and Miraloglu, IH and Ozbayram, EG and Ince, B and Ince, O}, title = {Bioaugmentation of anaerobic digesters with the enriched lignin-degrading microbial consortia through a metagenomic approach.}, journal = {Chemosphere}, volume = {355}, number = {}, pages = {141831}, doi = {10.1016/j.chemosphere.2024.141831}, pmid = {38561162}, issn = {1879-1298}, mesh = {*Lignin/metabolism ; Microbial Consortia ; Bioreactors ; Anaerobiosis ; *Microbiota ; Methane/metabolism ; Biofuels ; }, abstract = {The recalcitrance of lignin impedes the efficient utilization of lignocellulosic biomass, hindering the efficient production of biogas and value-added materials. Despite the emergence of anaerobic digestion as a superior alternative to the aerobic method for lignin processing, achieving its feasibility requires thorough characterization of lignin-degrading anaerobic microorganisms, assessment of their biomethane production potential, and a comprehensive understanding of the degradation pathway. This study aimed to address the aforementioned necessities by bioaugmenting seed sludge with three distinct enriched lignin-degrading microbial consortia at both 25 °C and 37 °C. Enhanced biomethane yields was detected in the bioaugmented digesters, while the highest production was observed as 188 mLN CH4 gVS[-1] in digesters operated at 37 °C. Moreover, methane yield showed a significant improvement in the samples at 37 °C ranging from 110% to 141% compared to the control, demonstrating the efficiency of the enriched lignin-degrading microbial community. Temperature and substrate were identified as key factors influencing microbial community dynamics. The observation that microbial communities tended to revert to the initial state after lignin depletion, indicating the stability of the overall microbiota composition in the digesters, is a promising finding for large-scale studies. Noteworthy candidates for lignin degradation, including Sporosarcina psychrophila, Comamonas aquatica, Shewanella baltica, Pseudomonas sp. C27, and Brevefilum fermentans were identified in the bioaugmented samples. PICRUSt2 predictions suggest that the pathway and specific proteins involved in anaerobic lignin degradation might share similarities with those engaged in the degradation of aromatic compounds.}, } @article {pmid38561038, year = {2024}, author = {Lim, TW and Huang, S and Zhang, Y and Burrow, MF and McGrath, C}, title = {A comparison of the prevalence of respiratory pathogens and opportunistic respiratory pathogenic profile of 'clean' and 'unclean' removable dental prostheses.}, journal = {Journal of dentistry}, volume = {145}, number = {}, pages = {104968}, doi = {10.1016/j.jdent.2024.104968}, pmid = {38561038}, issn = {1879-176X}, mesh = {Humans ; Cross-Sectional Studies ; Female ; Male ; Aged ; Middle Aged ; Prevalence ; *Dental Plaque/microbiology ; *Respiratory Tract Infections/microbiology/epidemiology ; Opportunistic Infections/microbiology/epidemiology ; Oral Hygiene ; Microbiota ; Bacteria/classification/isolation & purification ; Aged, 80 and over ; Prosthesis-Related Infections/microbiology/epidemiology ; Denture, Partial, Removable/microbiology ; }, abstract = {OBJECTIVES: To determine and compare the opportunistic respiratory pathogenic index (ORPI) and prevalence of respiratory pathogens between clean and unclean removable prostheses.

METHODS: A cross-sectional study was conducted among 97 removable prosthesis wearers at a teaching dental hospital. Participants' prosthesis hygiene was grouped into clean and unclean. After prosthesis plaque samples were sequenced using the Type IIB Restriction-site Associated DNA Sequencing for Microbiome method, the prevalence was assessed for the presence of respiratory pathogens on each sample. The ORPIs for clean and unclean prostheses were quantified based on the sum of the relative abundance of respiratory pathogenic bacteria in a microbiome using a reference database that contains opportunistic respiratory pathogens and disease-associated information.

RESULTS: A total of 30 opportunistic respiratory pathogens were identified on the removable prostheses. Eighty-one (83.5 %) removable prostheses harboured respiratory pathogenic bacteria. Stenotrophomonas maltophilia (34.0 %), Pseudomonas aeruginosa (27.8 %), and Streptococcus agalactiae (27.8 %) were the top three prevalent respiratory pathogens detected in plaque samples. There was a significantly higher prevalence of respiratory pathogens residing on unclean than clean prostheses (P = 0.046). However, the ORPIs in both groups showed no statistically significant difference (P = 0.516).

CONCLUSIONS: The ORPIs for both clean and unclean prostheses demonstrated a similar abundance of respiratory pathogens. However, the high prevalence of respiratory pathogens residing on unclean prostheses should not be underestimated. Therefore, maintaining good prosthesis hygiene is still important for overall oral and systemic health, even though the direct link between prosthesis cleanliness and reduced abundance of respiratory pathogens has not been established.

CLINICAL SIGNIFICANCE: The association between the prevalence of respiratory pathogens and unclean removable prostheses has been demonstrated and might increase the theoretical risk of respiratory disease development.}, } @article {pmid38558411, year = {2024}, author = {Lee, D and Braly, K and Nuding, M and Braly, I and Hopp, C and Twible, H and Pope, C and Hayden, HS and Hoffman, L and Zheng, H and Wahbeh, G and Suskind, DL}, title = {Reverse-engineered exclusive enteral nutrition in pediatric Crohn's disease: A pilot trial.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {78}, number = {5}, pages = {1135-1142}, doi = {10.1002/jpn3.12196}, pmid = {38558411}, issn = {1536-4801}, support = {//Wendy and John Evans/ ; //Richards Family Foundation/ ; //Marco Agenti/ ; //Nanyang Li/ ; }, mesh = {Humans ; *Crohn Disease/therapy/diet therapy ; *Enteral Nutrition/methods ; Pilot Projects ; Female ; Male ; Adolescent ; Prospective Studies ; *Gastrointestinal Microbiome ; Child ; Feces/microbiology ; Remission Induction/methods ; Food, Formulated ; Treatment Outcome ; Leukocyte L1 Antigen Complex/analysis ; }, abstract = {BACKGROUND: In pediatric Crohn's disease (CD), commercial formulas used as exclusive enteral nutrition (EEN) are effective at inducing remission. This study aims to assess the impact of a whole-food blended smoothie as EEN on CD activity and the intestinal microbiome.

METHODS: A 4-week prospective trial assessed the impact of EEN with a whole-food smoothie on newly diagnosed mild-to-moderate active pediatric CD. The smoothie with a multivitamin were developed to meet age-appropriate nutritional requirements. Assessment over 4 weeks included Pediatric Crohn's Disease Activity Index (PCDAI), serum laboratories, fecal calprotectin (FCP), and stool collection for metagenomic shotgun sequencing and microbiota composition analysis. Clinical remission was defined as PCDAI ≤ 10 at week 4.

RESULTS: Ten participants were enrolled with median age 14.5 years, and 8 completed the trial. Baseline mean PCDAI was 26.3 ± 9.1 and mean FCP 1149 ± 718 µg/g. At week 4, 80% of participants achieved clinical remission. FCP decreased by over half in 60% of participants, with FCP below 250 µg/g in 60% and below 100 µg/g in 40%. Microbiome analysis showed a significant increase in species richness over 4 weeks (p = 0.01). Compared to baseline, the relative abundance at week 2 and at week 4 was significantly increased for Bifidobacterium and Streptococcus and decreased for Blautia (p < 0.05 for all).

CONCLUSION: A whole-food blended smoothie was effective for inducing clinical remission and decreasing FCP in pediatric CD similar to commercial EEN formulas. Further research may give insight into data-driven whole-food dietary approaches for CD management.

CLINICALTRIALS: gov NCT03508193.}, } @article {pmid38558277, year = {2024}, author = {Ye, S and Lu, Y and Li, G and Li, D and Wu, Y and Yao, Y}, title = {Stenotrophomonas maltophilia Isolated from the Gut Symbiotic Community of the Plastic-Eating Tenebrio molitor.}, journal = {Applied biochemistry and biotechnology}, volume = {196}, number = {11}, pages = {7805-7815}, pmid = {38558277}, issn = {1559-0291}, support = {02020200-K02013008//Zhejiang University/ ; }, mesh = {Animals ; *Stenotrophomonas maltophilia/isolation & purification/genetics ; *Tenebrio/microbiology ; *Symbiosis ; Gastrointestinal Microbiome ; Plastics ; }, abstract = {Polyvinyl chloride (PVC) waste is a major environmental challenge. In this study, we found that a PVC-eating insect, Tenebrio molitor, could survive by consuming PVC as a dietary supplement. To understand the gut symbiotic community, metagenomic analysis was performed to reveal the biodiversity of a symbiotic community in the midgut of Tenebrio molitor. Among them, seven genera were enriched from the midgut of the insect under culture conditions with PVC as carbon source. A strain of Stenotrophomonas maltophilia was isolated from the midgut symbiotic community of the plastic-eating Tenebrio molitor. To unravel the functional gene for the biodegradation enzyme, we sequenced the whole genome of Stenotrophomonas maltophilia and found that orf00390, annotated as a hydrolase, was highly expressed in the PVC culture niche.}, } @article {pmid38558266, year = {2024}, author = {Rassner, SME and Cook, JM and Mitchell, AC and Stevens, IT and Irvine-Fynn, TDL and Hodson, AJ and Edwards, A}, title = {The distinctive weathering crust habitat of a High Arctic glacier comprises discrete microbial micro-habitats.}, journal = {Environmental microbiology}, volume = {26}, number = {4}, pages = {e16617}, doi = {10.1111/1462-2920.16617}, pmid = {38558266}, issn = {1462-2920}, support = {//The Rolex Foundation/ ; NE/S001034/1//Natural Environment Research Council/ ; NE/V012991/1//Natural Environment Research Council/ ; RF-2018-584/4//Leverhulme Trust/ ; 288402//Norges Forskningsråd/ ; }, mesh = {*Ice Cover/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Arctic Regions ; }, abstract = {Sunlight penetrates the ice surfaces of glaciers and ice sheets, forming a water-bearing porous ice matrix known as the weathering crust. This crust is home to a significant microbial community. Despite the potential implications of microbial processes in the weathering crust for glacial melting, biogeochemical cycles, and downstream ecosystems, there have been few explorations of its microbial communities. In our study, we used 16S rRNA gene sequencing and shotgun metagenomics of a Svalbard glacier surface catchment to characterise the microbial communities within the weathering crust, their origins and destinies, and the functional potential of the weathering crust metagenome. Our findings reveal that the bacterial community in the weathering crust is distinct from those in upstream and downstream habitats. However, it comprises two separate micro-habitats, each with different taxa and functional categories. The interstitial porewater is dominated by Polaromonas, influenced by the transfer of snowmelt, and exported via meltwater channels. In contrast, the ice matrix is dominated by Hymenobacter, and its metagenome exhibits a diverse range of functional adaptations. Given that the global weathering crust area and the subsequent release of microbes from it are strongly responsive to climate projections for the rest of the century, our results underscore the pressing need to integrate the microbiome of the weathering crust with other communities and processes in glacial ecosystems.}, } @article {pmid38557867, year = {2024}, author = {Bar Ziv, O and Cahn, A and Jansen, T and Istomin, V and Kedem, E and Olshtain-Pops, K and Israel, S and Oster, Y and Orenbuch-Harroch, E and Korem, M and Strahilevitz, J and Levy, I and Valdés-Mas, R and Ivanova, V and Elinav, E and Shahar, E and Elinav, H}, title = {Diagnosis and Risk Factors of Prediabetes and Diabetes in People Living With Human Immunodeficiency Virus: Evaluation of Clinical and Microbiome Parameters.}, journal = {The Journal of infectious diseases}, volume = {230}, number = {2}, pages = {411-420}, doi = {10.1093/infdis/jiae167}, pmid = {38557867}, issn = {1537-6613}, support = {//D-cure/ ; //Novo Nordisk/ ; //Israeli HIV Association/ ; }, mesh = {Humans ; *Prediabetic State/diagnosis ; *HIV Infections/complications ; Female ; Male ; Middle Aged ; Risk Factors ; Prospective Studies ; Adult ; *Blood Glucose/analysis ; *Glycated Hemoglobin/analysis/metabolism ; *Microbiota ; *Diabetes Mellitus/epidemiology ; Glucose Tolerance Test ; }, abstract = {Diabetes mellitus (DM) is more common among people living with human immunodeficiency virus (PLWH) compared with healthy individuals. In a prospective multicenter study (N = 248), we identified normoglycemic (48.7%), prediabetic (44.4%), and diabetic (6.9%) PLWH. Glycosylated hemoglobin (HbA1c) and fasting blood glucose (FBG) sensitivity in defining dysglycemia was 96.8%, while addition of oral glucose tolerance test led to reclassification of only 4 patients. Inclusion of 93 additional PLWH with known DM enabled identification of multiple independent predictors of dysglycemia or diabetes: older age, higher body mass index, Ethiopian origin, HIV duration, lower integrase inhibitor exposure, and advanced disease at diagnosis. Shotgun metagenomic microbiome analysis revealed 4 species that were significantly expanded with hyperglycemia/hyperinsulinemia, and 2 species that were differentially more prevalent in prediabetic/diabetic PLWH. Collectively, we uncover multiple potential host and microbiome predictors of altered glycemic status in PLWH, while demonstrating that FBG and HbA1c likely suffice for diabetes screening. These potential diabetic predictors merit future prospective validation.}, } @article {pmid38557102, year = {2024}, author = {Aljabr, W and Dandachi, I and Abbas, B and Karkashan, A and Al-Amari, A and AlShahrani, D}, title = {Metagenomic next-generation sequencing of nasopharyngeal microbiota in COVID-19 patients with different disease severities.}, journal = {Microbiology spectrum}, volume = {12}, number = {5}, pages = {e0416623}, pmid = {38557102}, issn = {2165-0497}, support = {021-017//King Fahad Medical City (KFMC)/ ; 75F40120C00085//HHS | U.S. Food and Drug Administration (FDA)/ ; }, mesh = {Humans ; *COVID-19/microbiology/virology/epidemiology/diagnosis ; *Nasopharynx/microbiology/virology ; *Microbiota/genetics ; *SARS-CoV-2/genetics/isolation & purification ; Male ; Female ; *High-Throughput Nucleotide Sequencing ; Middle Aged ; Adult ; Metagenomics/methods ; Metagenome ; Aged ; Bacteria/classification/genetics/isolation & purification ; Severity of Illness Index ; Streptococcus pneumoniae/genetics/isolation & purification/classification ; }, abstract = {Throughout the COVID-19 pandemic, extensive research has been conducted on SARS-COV-2 to elucidate its genome, prognosis, and possible treatments. However, few looked at the microbial markers that could be explored in infected patients and that could predict possible disease severity. The aim of this study is to compare the nasopharyngeal microbiota of healthy subjects, moderate, under medication, and recovered SARS-COV-2 patients. In 2020, 38 nasopharyngeal swabs were collected from 6 healthy subjects, 14 moderates, 10 under medication and 8 recovered SARS-COV-2 patients at the Prince Mohammed Bin Abdulaziz Hospital Riyadh. Metatranscriptomic sequencing was performed using Minion Oxford nanopore sequencing. No significant difference in alpha as well as beta diversity was observed among all four categories. Nevertheless, we have found that Streptococcus spp including Streptococcus pneumoniae and Streptococcus thermophilus were among the top 15 most abundant species detected in COVID-19 patients but not in healthy subjects. The genus Staphylococcus was found to be associated with COVID-19 patients compared to healthy subjects. Furthermore, the abundance of Leptotrichia was significantly higher in healthy subjects compared to recovered patients. Corynebacterium on the other hand, was associated with under-medication patients. Taken together, our study revealed no differences in the overall microbial composition between healthy subjects and COVID-19 patients. Significant differences were seen only at specific taxonomic level. Future studies should explore the nasopharyngeal microbiota between controls and COVID-19 patients while controlling for confounders including age, gender, and comorbidities; since these latter could affect the results and accordingly the interpretation.IMPORTANCEIn this work, no significant difference in the microbial diversity was seen between healthy subjects and COVID-19 patients. Changes in specific taxa including Leptotrichia, Staphylococcus, and Corynebacterium were only observed. Leptotrichia was significantly higher in healthy subjects, whereas Staphylococcus and Corynebacterium were mostly associated with COVID-19, and specifically with under-medication SARS-COV-2 patients, respectively. Although the COVID-19 pandemic has ended, the SARS-COV-2 virus is continuously evolving and the emergence of new variants causing more severe disease should be always kept in mind. Microbial markers in SARS-COV-2 infected patients can be useful in the early suspicion of the disease, predicting clinical outcomes, framing hospital and intensive care unit admission as well as, risk stratification. Data on which microbial marker to tackle is still controversial and more work is needed, hence the importance of this study.}, } @article {pmid38557040, year = {2024}, author = {Li, C and Lü, F and Peng, W and He, PJ and Zhang, H}, title = {Functional Redundant Microbiome Enhanced Anaerobic Digestion Efficiency under Ammonium Inhibition Conditions.}, journal = {Environmental science & technology}, volume = {58}, number = {15}, pages = {6659-6669}, doi = {10.1021/acs.est.4c01227}, pmid = {38557040}, issn = {1520-5851}, mesh = {Anaerobiosis ; *Ammonium Compounds ; Bioreactors ; *Microbiota ; Metagenome ; Methane ; }, abstract = {Revealing the role of functional redundancy is of great importance considering its key role in maintaining the stability of microbial ecosystems in response to various disturbances. However, experimental evidence on this point is still lacking due to the difficulty in "manipulating" and depicting the degree of redundancy. In this study, manipulative experiments of functional redundancy were conducted by adopting the mixed inoculation strategy to evaluate its role in engineered anaerobic digestion systems under ammonium inhibition conditions. The results indicated that the functional redundancy gradient was successfully constructed and confirmed by evidence from pathway levels. All mixed inoculation groups exhibited higher methane production regardless of the ammonium level, indicating that functional redundancy is crucial in maintaining the system's efficiency. Further analysis of the metagenome-assembled genomes within different functional guilds revealed that the extent of redundancy decreased along the direction of the anaerobic digestion flow, and the role of functional redundancy appeared to be related to the stress level. The study also found that microbial diversity of key functional populations might play a more important role than their abundance on the system's performance under stress. The findings provide direct evidence and highlight the critical role of functional redundancy in enhancing the efficiency and stability of anaerobic digestion.}, } @article {pmid38556024, year = {2024}, author = {Chen, T and Liu, S and Zhang, S and Song, H and Zhuang, Y and Ma, J and Xiao, J and Wang, J and Ma, Y and Wang, Y and Wang, W and Li, S and Cao, Z}, title = {Initial diet shapes resistance-gene composition and fecal microbiome dynamics in young ruminants during nursing.}, journal = {The Science of the total environment}, volume = {926}, number = {}, pages = {172103}, doi = {10.1016/j.scitotenv.2024.172103}, pmid = {38556024}, issn = {1879-1026}, mesh = {Animals ; Cattle ; Female ; Pregnancy ; Aminoglycosides ; Animal Feed/analysis ; Animals, Newborn ; Anti-Bacterial Agents/analysis ; Colostrum/chemistry ; *Diet/veterinary ; Feces/microbiology ; *Microbiota ; Milk/chemistry ; Ruminants ; }, abstract = {This study was conducted to examine how colostrum pasteurization affects resistance genes and microbial communities in calf feces. Forty female Holstein calves were randomly assigned to either the control (CON) group, which received unheated colostrum, or the pasteurized colostrum (PAT) group. The calves body weight was measured weekly before morning feeding. Calf starter intake were measured and recorded daily before morning feeding. Samples of colostrum were collected before feeding. Blood was collected on d 1 and 70 before morning feeding. Ten calves were randomly selected from each group (n = 20 calves total) for fecal sampling on d 3, 28, 56 and 70 for subsequent DNA extraction and metagenomic sequencing. Total bacterial counts in the colostrum were markedly higher in the CON group than in the PAT group. Pasteurized colostrum administration substantially reduced the ARO diversity and diminishes the abundance of Enterobacteriaceae, thereby decreasing their contribution to resistance genes. Pasteurization also reduced glucoside hydrolase-66 activity in 3-day-old calves which led to an increase in the activity of aminoglycoside antibiotics, resulting in 52.63 % of PAT-enriched bacteria acquiring aminoglycoside resistance genes. However, from the perspective of overall microbial community, the proportion of aminoglycoside, beta-lactam and tetracycline resistance genes carried by microbial community in PAT group was lower than CON group (P < 0.05). Fecal samples from the PAT group contained greater abundances of Subdoligranulum (P < 0.05) and Lachnospiraceae_NK4A136_group (P < 0.05) on days 28 and 70 compared to CON. Network analysis and abundance variations of the different bacteria obtained by linear discriminant analysis effect size analysis showed that pasteurized colostrum feeding reduced the interactions among related bacteria and maintained stability of the hind-gut microbiome. In conclusion, these findings underscore the intricate interactions between early diet, calf resistance-gene transmission and microbial dynamics, which should be carefully considered in calf-rearing practices.}, } @article {pmid38555499, year = {2024}, author = {Heston, SM and Young, RR and Jenkins, K and Martin, PL and Stokhuyzen, A and Ward, DV and Bhattarai, SK and Bucci, V and Arshad, M and Chao, NJ and Seed, PC and Kelly, MS}, title = {The effects of antibiotic exposures on the gut resistome during hematopoietic cell transplantation in children.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2333748}, pmid = {38555499}, issn = {1949-0984}, support = {K12 HD105253/HD/NICHD NIH HHS/United States ; UM1 AI104681/AI/NIAID NIH HHS/United States ; T32 HG008955/HG/NHGRI NIH HHS/United States ; K23 AI135090/AI/NIAID NIH HHS/United States ; T32 HD094671/HD/NICHD NIH HHS/United States ; }, mesh = {Child ; Humans ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/genetics ; Fluoroquinolones/pharmacology ; *Gastrointestinal Microbiome/genetics ; *Hematopoietic Stem Cell Transplantation ; }, abstract = {Antibiotic resistance is a global threat driven primarily by antibiotic use. We evaluated the effects of antibiotic exposures on the gut microbiomes and resistomes of children at high risk of colonization by antibiotic-resistant bacteria. We performed shotgun metagenomic sequencing of 691 serially collected fecal samples from 80 children (<18 years) undergoing hematopoietic cell transplantation. We evaluated the effects of aerobic (cefepime, vancomycin, fluoroquinolones, aminoglycosides, macrolides, and trimethoprim-sulfamethoxazole) and anaerobic (piperacillin-tazobactam, carbapenems, metronidazole, and clindamycin) antibiotic exposures on the diversity and composition of the gut microbiome and resistome. We identified 372 unique antibiotic resistance genes (ARGs); the most frequent ARGs identified encode resistance to tetracyclines (n = 88), beta-lactams (n = 84), and fluoroquinolones (n = 79). Both aerobic and anaerobic antibiotic exposures were associated with a decrease in the number of bacterial species (aerobic, β = 0.71, 95% CI: 0.64, 0.79; anaerobic, β = 0.66, 95% CI: 0.53, 0.82) and the number of unique ARGs (aerobic, β = 0.81, 95% CI: 0.74, 0.90; anaerobic, β = 0.73, 95% CI: 0.61, 0.88) within the gut metagenome. However, only antibiotic regimens that included anaerobic activity were associated with an increase in acquisition of new ARGs (anaerobic, β = 1.50; 95% CI: 1.12, 2.01) and an increase in the relative abundance of ARGs in the gut resistome (anaerobic, β = 1.62; 95% CI: 1.15, 2.27). Specific antibiotic exposures were associated with distinct changes in the number and abundance of ARGs for individual antibiotic classes. Our findings detail the impact of antibiotics on the gut microbiome and resistome and demonstrate that anaerobic antibiotics are particularly likely to promote acquisition and expansion of antibiotic-resistant bacteria.}, } @article {pmid38555322, year = {2024}, author = {Nagy, NA and Tóth, GE and Kurucz, K and Kemenesi, G and Laczkó, L}, title = {The updated genome of the Hungarian population of Aedes koreicus.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {7545}, pmid = {38555322}, issn = {2045-2322}, support = {OTKA PD142602//National Research, Development and Innovation Office/ ; FK-138563//National Research, Development and Innovation Office/ ; }, mesh = {Animals ; Humans ; *Aedes/genetics ; Mosquito Vectors/genetics ; Hungary ; Europe/epidemiology ; Introduced Species ; }, abstract = {Vector-borne diseases pose a potential risk to human and animal welfare, and understanding their spread requires genomic resources. The mosquito Aedes koreicus is an emerging vector that has been introduced into Europe more than 15 years ago but only a low quality, fragmented genome was available. In this study, we carried out additional sequencing and assembled and characterized the genome of the species to provide a background for understanding its evolution and biology. The updated genome was 1.1 Gbp long and consisted of 6099 contigs with an N50 value of 329,610 bp and a BUSCO score of 84%. We identified 22,580 genes that could be functionally annotated and paid particular attention to the identification of potential insecticide resistance genes. The assessment of the orthology of the genes indicates a high turnover at the terminal branches of the species tree of mosquitoes with complete genomes, which could contribute to the adaptation and evolutionary success of the species. These results could form the basis for numerous downstream analyzes to develop targets for the control of mosquito populations.}, } @article {pmid38554650, year = {2024}, author = {Zhao, M and Liu, H and Liu, M and Yue, Z and Li, C and Liu, L and Li, F}, title = {Metagenomics and metabolomics reveal that gut microbiome adapts to the diet transition in Hyla rabbits.}, journal = {Microbiological research}, volume = {283}, number = {}, pages = {127705}, doi = {10.1016/j.micres.2024.127705}, pmid = {38554650}, issn = {1618-0623}, mesh = {Humans ; Animals ; Female ; Rabbits ; *Gastrointestinal Microbiome/genetics ; Metabolomics ; *Microbiota ; Diet ; Intestines ; Metagenomics ; }, abstract = {There is still a lack of longitudinal dynamic studies on the taxonomic features, functional reserves, and metabolites of the rabbit gut microbiome. An experiment was conducted to characterize the bacterial community of rabbits. By combining metagenomics and metabolomics, we have comprehensively analyzed the longitudinal dynamics of the rabbit gut microbiota and its effect on host adaptability. Our data reveal an overall increasing trend in microbial community and functional gene diversity and richness during the pre-harvest lifespan of rabbits. The introduction of solid feed is an important driving factor affecting rabbit gut microbiological compositions. Clostridium and Ruminococcus had significantly higher relative abundances in the solid feed stage. Further, the starch and fiber in solid feed promote the secretion of carbohydrate-degrading enzymes, which helps the host adapt to dietary changes. The rabbit gut microbiota can synthesize lysine, and the synthase is gradually enriched during the diet transformation. The gut microbiota of newborn rabbits has a higher abundance of lipid metabolism, which helps the host obtain more energy from breast milk lipids. The rabbit gut microbiota can also synthesize a variety of secondary bile acids after the introduction of solid feed. These findings provide a novel understanding of how the gut microbiota mediates adaptability to environment and diet in rabbits and provide multiple potential strategies for regulating intestinal health and promoting higher feed efficiency.}, } @article {pmid38553666, year = {2024}, author = {Ma, ZS}, title = {Towards a unified medical microbiome ecology of the OMU for metagenomes and the OTU for microbes.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {137}, pmid = {38553666}, issn = {1471-2105}, mesh = {Animals ; Humans ; Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome ; Biodiversity ; Sequence Analysis, DNA ; Metagenomics/methods ; }, abstract = {BACKGROUND: Metagenomic sequencing technologies offered unprecedented opportunities and also challenges to microbiology and microbial ecology particularly. The technology has revolutionized the studies of microbes and enabled the high-profile human microbiome and earth microbiome projects. The terminology-change from microbes to microbiomes signals that our capability to count and classify microbes (microbiomes) has achieved the same or similar level as we can for the biomes (macrobiomes) of plants and animals (macrobes). While the traditional investigations of macrobiomes have usually been conducted through naturalists' (Linnaeus & Darwin) naked eyes, and aerial and satellite images (remote-sensing), the large-scale investigations of microbiomes have been made possible by DNA-sequencing-based metagenomic technologies. Two major types of metagenomic sequencing technologies-amplicon sequencing and whole-genome (shotgun sequencing)-respectively generate two contrastingly different categories of metagenomic reads (data)-OTU (operational taxonomic unit) tables representing microorganisms and OMU (operational metagenomic unit), a new term coined in this article to represent various cluster units of metagenomic genes.

RESULTS: The ecological science of microbiomes based on the OTU representing microbes has been unified with the classic ecology of macrobes (macrobiomes), but the unification based on OMU representing metagenomes has been rather limited. In a previous series of studies, we have demonstrated the applications of several classic ecological theories (diversity, composition, heterogeneity, and biogeography) to the studies of metagenomes. Here I push the envelope for the unification of OTU and OMU again by demonstrating the applications of metacommunity assembly and ecological networks to the metagenomes of human gut microbiomes. Specifically, the neutral theory of biodiversity (Sloan's near neutral model), Ning et al.stochasticity framework, core-periphery network, high-salience skeleton network, special trio-motif, and positive-to-negative ratio are applied to analyze the OMU tables from whole-genome sequencing technologies, and demonstrated with seven human gut metagenome datasets from the human microbiome project.

CONCLUSIONS: All of the ecological theories demonstrated previously and in this article, including diversity, composition, heterogeneity, stochasticity, and complex network analyses, are equally applicable to OMU metagenomic analyses, just as to OTU analyses. Consequently, I strongly advocate the unification of OTU/OMU (microbiomes) with classic ecology of plants and animals (macrobiomes) in the context of medical ecology.}, } @article {pmid38553222, year = {2024}, author = {Hafeez, R and Guo, J and Ahmed, T and Jiang, H and Raza, M and Shahid, M and Ibrahim, E and Wang, Y and Wang, J and Yan, C and An, Q and White, JC and Li, B}, title = {Bio-formulated chitosan nanoparticles enhance disease resistance against rice blast by physiomorphic, transcriptional, and microbiome modulation of rice (Oryza sativa L.).}, journal = {Carbohydrate polymers}, volume = {334}, number = {}, pages = {122023}, doi = {10.1016/j.carbpol.2024.122023}, pmid = {38553222}, issn = {1879-1344}, mesh = {Disease Resistance ; *Oryza/genetics ; *Chitosan/pharmacology ; Bacteria ; *Microbiota ; Plant Diseases/prevention & control ; }, abstract = {Rice blast disease (RBD) caused by Magnaporthe oryzae, threaten food security by cutting agricultural output. Nano agrochemicals are now perceived as sustainable, cost-effective alternatives to traditional pesticides. This study investigated bioformulation of moringa chitosan nanoparticles (M-CsNPs) and their mechanisms for suppressing RBD while minimizing toxic effects on the microenvironment. M-CsNPs, sized 46 nm with semi-spherical morphology, significantly suppressed pathogen growth, integrity, and colonization at 200 mg L[-1]in vitro. Greenhouse tests with foliar exposure to the same concentration resulted in a substantial 77.7 % reduction in RBD, enhancing antioxidant enzyme activity and plant health. Furthermore, M-CsNPs improved photosynthesis, gas exchange, and the nutritional profile of diseased rice plants. RNA-seq analysis highlighted upregulated defense-related genes in treated rice plants. Metagenomic study showcased reshaping of the rice microbiome, reducing Magnaporthe abundance by 93.5 %. Both healthy and diseased rice plants showed increased microbial diversity, particularly favoring specific beneficial species Thiobacillus, Nitrospira, Nocardioides, and Sphingomicrobium in the rhizosphere and Azonexus, Agarivorans, and Bradyrhizobium in the phyllosphere. This comprehensive study unravels the diverse mechanisms by which M-CsNPs interact with plants and pathogens, curbing M. oryzae damage, promoting plant growth, and modulating the rice microbiome. It underscores the significant potential for effective plant disease management.}, } @article {pmid38548676, year = {2024}, author = {Jiao, B and Ouyang, Z and Liu, Q and Xu, T and Wan, M and Ma, G and Zhou, L and Guo, J and Wang, J and Tang, B and Zhao, Z and Shen, L}, title = {Integrated analysis of gut metabolome, microbiome, and brain function reveal the role of gut-brain axis in longevity.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2331434}, pmid = {38548676}, issn = {1949-0984}, mesh = {Aged, 80 and over ; Humans ; Brain-Gut Axis ; *Gastrointestinal Microbiome ; Metabolome ; *Microbiota ; Brain ; }, abstract = {The role of microbiota-gut-brain axis in modulating longevity remains undetermined. Here, we performed a multiomics analysis of gut metagenomics, gut metabolomics, and brain functional near-infrared spectroscopy (fNIRS) in a cohort of 164 participants, including 83 nonagenarians (NAs) and 81 non-nonagenarians (NNAs) matched with their spouses and offspring. We found that 438 metabolites were significantly different between the two groups; among them, neuroactive compounds and anti-inflammatory substances were enriched in NAs. In addition, increased levels of neuroactive metabolites in NAs were significantly associated with NA-enriched species that had three corresponding biosynthetic potentials: Enterocloster asparagiformis, Hungatella hathewayi and Oxalobacter formigenes. Further analysis showed that the altered gut microbes and metabolites were linked to the enhanced brain connectivity in NAs, including the left dorsolateral prefrontal cortex (DLPFC)-left premotor cortex (PMC), left DLPFC-right primary motor area (M1), and right inferior frontal gyrus (IFG)-right M1. Finally, we found that neuroactive metabolites, altered microbe and enhanced brain connectivity contributed to the cognitive preservation in NAs. Our findings provide a comprehensive understanding of the microbiota-gut-brain axis in a long-lived population and insights into the establishment of a microbiome and metabolite homeostasis that can benefit human longevity and cognition by enhancing functional brain connectivity.}, } @article {pmid38548661, year = {2024}, author = {Aya, JV and Vega, LC and Muñoz, E and Muñoz, M and López, DF and Guzmán, MP and Martínez, DF and Cruz-Saavedra, LB and Castillo, AK and Quintero, KJ and Gónzalez Soltero, R and Cala, MP and Ramírez, JD}, title = {Divergent Gut Microbiota: Archaeal and Bacterial Signatures Unveil Unique Patterns in Colombian Cyclists Compared to Weightlifters and Non-Athletes.}, journal = {Advanced biology}, volume = {8}, number = {6}, pages = {e2400069}, doi = {10.1002/adbi.202400069}, pmid = {38548661}, issn = {2701-0198}, support = {//Research and Innovation Directorate of Universidad del Rosario/ ; //Universidad del Rosario/ ; //Universidad Europea de Madrid/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Colombia ; *Bicycling ; Adult ; *Athletes/statistics & numerical data ; *Archaea/isolation & purification ; Young Adult ; *Bacteria/classification/isolation & purification/genetics ; Weight Lifting/physiology ; Feces/microbiology ; }, abstract = {Engagement in physical activity, across various sports, promotes a diverse microbiota in active individuals. This study examines the gut microbiota of Colombian athletes, specifically weightlifters (n = 16) and road cyclists (n = 13), compared to non-athletes (n = 15). Using Kruskal-Wallis tests, the physical activity level of a group of non-athletic individuals and the sports experience of a group of professional athletes is analyzed. The median age of participants is 24 years, comprising 25 men and 19 women. The microbiota is collected using fecal samples. Participants provided these samples during their pre-competitive stage, specifically during the concentration phase occurring two weeks prior to national competitions. This timing is chosen to capture the microbial composition during a period of heightened physical preparation. Questionnaire responses and microbial composition assessments identify disparities among groups. Microbial composition analysis explores core microbiome, abundance, and taxonomy using Pavian, MicrobiomeAnalyst 2.0, and GraPhlAn. ANCOM-BC2 reveals differentially abundant species. Road cyclists exhibit decreased Bacteria and increased Archaea abundance. Phylum-level variations included Planctomycetes, Acidobacteria, and Proteobacteria, while Bacteroidetes prevailed. Key families influencing gut microbiota are Bacteroidaceae, Muribaculaceae, and Selenomonadaceae. Weightlifters exhibit unique viral and archaeal community connections, while cyclists showed specialized microbial interplay influenced by endurance exercise. Correlation network analysis emphasizes distinctive microbial interactions within athlete groups, shedding light on the impact of physical activities on gut microbiota and athlete health.}, } @article {pmid38547246, year = {2024}, author = {Wang, Z and Peters, BA and Yu, B and Grove, ML and Wang, T and Xue, X and Thyagarajan, B and Daviglus, ML and Boerwinkle, E and Hu, G and Mossavar-Rahmani, Y and Isasi, CR and Knight, R and Burk, RD and Kaplan, RC and Qi, Q}, title = {Gut Microbiota and Blood Metabolites Related to Fiber Intake and Type 2 Diabetes.}, journal = {Circulation research}, volume = {134}, number = {7}, pages = {842-854}, pmid = {38547246}, issn = {1524-4571}, support = {R01 DK120870/DK/NIDDK NIH HHS/United States ; R01 DK119268/DK/NIDDK NIH HHS/United States ; N01HC65236/HL/NHLBI NIH HHS/United States ; N01HC65235/HL/NHLBI NIH HHS/United States ; N01HC65234/HL/NHLBI NIH HHS/United States ; K01 HL169019/HL/NHLBI NIH HHS/United States ; R01 DK134672/DK/NIDDK NIH HHS/United States ; N01HC65237/HL/NHLBI NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; R01 HL136266/HL/NHLBI NIH HHS/United States ; R01 DK126698/DK/NIDDK NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; R01 HL170904/HL/NHLBI NIH HHS/United States ; N01HC65233/HL/NHLBI NIH HHS/United States ; K01 HL129892/HL/NHLBI NIH HHS/United States ; P30 DK111022/DK/NIDDK NIH HHS/United States ; R01 HL060712/HL/NHLBI NIH HHS/United States ; UM1 HG008898/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2/diagnosis/microbiology ; Diet ; Bacteria ; Dietary Fiber ; }, abstract = {BACKGROUND: Consistent evidence suggests diabetes-protective effects of dietary fiber intake. However, the underlying mechanisms, particularly the role of gut microbiota and host circulating metabolites, are not fully understood. We aimed to investigate gut microbiota and circulating metabolites associated with dietary fiber intake and their relationships with type 2 diabetes (T2D).

METHODS: This study included up to 11 394 participants from the HCHS/SOL (Hispanic Community Health Study/Study of Latinos). Diet was assessed with two 24-hour dietary recalls at baseline. We examined associations of dietary fiber intake with gut microbiome measured by shotgun metagenomics (350 species/85 genera and 1958 enzymes; n=2992 at visit 2), serum metabolome measured by untargeted metabolomics (624 metabolites; n=6198 at baseline), and associations between fiber-related gut bacteria and metabolites (n=804 at visit 2). We examined prospective associations of serum microbial-associated metabolites (n=3579 at baseline) with incident T2D over 6 years.

RESULTS: We identified multiple bacterial genera, species, and related enzymes associated with fiber intake. Several bacteria (eg, Butyrivibrio, Faecalibacterium) and enzymes involved in fiber degradation (eg, xylanase EC3.2.1.156) were positively associated with fiber intake, inversely associated with prevalent T2D, and favorably associated with T2D-related metabolic traits. We identified 159 metabolites associated with fiber intake, 47 of which were associated with incident T2D. We identified 18 of these 47 metabolites associated with the identified fiber-related bacteria, including several microbial metabolites (eg, indolepropionate and 3-phenylpropionate) inversely associated with the risk of T2D. Both Butyrivibrio and Faecalibacterium were associated with these favorable metabolites. The associations of fiber-related bacteria, especially Faecalibacterium and Butyrivibrio, with T2D were attenuated after further adjustment for these microbial metabolites.

CONCLUSIONS: Among United States Hispanics/Latinos, dietary fiber intake was associated with favorable profiles of gut microbiota and circulating metabolites for T2D. These findings advance our understanding of the role of gut microbiota and microbial metabolites in the relationship between diet and T2D.}, } @article {pmid38546675, year = {2024}, author = {Pötgens, SA and Havelange, V and Lecop, S and Li, F and Neyrinck, AM and Bindels, F and Neveux, N and Demoulin, JB and Moors, I and Kerre, T and Maertens, J and Walter, J and Schoemans, H and Delzenne, NM and Bindels, LB}, title = {Gut microbiome alterations at acute myeloid leukemia diagnosis are associated with muscle weakness and anorexia.}, journal = {Haematologica}, volume = {109}, number = {10}, pages = {3194-3208}, pmid = {38546675}, issn = {1592-8721}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Leukemia, Myeloid, Acute/microbiology/diagnosis/complications ; Male ; *Muscle Weakness/diagnosis/microbiology/etiology ; Female ; Middle Aged ; *Anorexia/microbiology/etiology/diagnosis ; Aged ; Adult ; Prospective Studies ; Feces/microbiology ; Cross-Sectional Studies ; Metabolomics/methods ; Metabolome ; }, abstract = {The gut microbiota makes critical contributions to host homeostasis, and its role in the treatment of acute myeloid leukemia (AML) has attracted attention. We investigated whether the gut microbiome is affected by AML, and whether such changes are associated with hallmarks of cachexia. Biological samples and clinical data were collected from 30 antibiotic- free AML patients at diagnosis and matched volunteers (1:1) in a multicenter, cross-sectional, prospective study. The composition and functional potential of the fecal microbiota were analyzed using shotgun metagenomics. Fecal, blood, and urinary metabolomics analyses were performed. AML patients displayed muscle weakness, anorexia, signs of altered gut function, and glycemic disorders. The composition of the fecal microbiota differed between patients with AML and control subjects, with an increase in oral bacteria. Alterations in bacterial functions and fecal metabolome support an altered redox status in the gut microbiota, which may contribute to the altered redox status observed in patients with AML. Eubacterium eligens, reduced 3-fold in AML patients, was strongly correlated with muscle strength and citrulline, a marker of enterocyte mass and function. Blautia and Parabacteroides, increased in patients with AML, were correlated with anorexia. Several bacterial taxa and metabolites (e.g., Blautia, Prevotella, phenylacetate, and hippurate) previously associated with glycemic disorders were altered. Our work revealed important perturbations in the gut microbiome of AML patients at diagnosis, which are associated with muscle strength, altered redox status, and anorexia. These findings pave the way for future mechanistic work to explore the function and therapeutic potential of the bacteria identified in this study.}, } @article {pmid38546528, year = {2024}, author = {Wang, Z and Zhang, J and Yuan, J and Min, F and Gao, J and Liu, W and Huang, M and Wu, Y and Chen, H}, title = {Oral administration of egg ovalbumin allergen induces dysregulation of tryptophan metabolism in sensitized BALB/c mice.}, journal = {Food & function}, volume = {15}, number = {8}, pages = {4375-4388}, doi = {10.1039/d3fo05300h}, pmid = {38546528}, issn = {2042-650X}, mesh = {Animals ; *Mice, Inbred BALB C ; *Tryptophan/metabolism ; *Ovalbumin/immunology ; Mice ; *Allergens/immunology ; Administration, Oral ; *Gastrointestinal Microbiome/drug effects ; Female ; Food Hypersensitivity/immunology ; Cytokines/metabolism ; Immunoglobulin E/immunology ; Egg Hypersensitivity/immunology ; Indoles/pharmacology ; Chymases/metabolism ; Th2 Cells/immunology ; }, abstract = {Food allergy (FA), triggered by specific dietary allergens, has emerged as a substantial global concern for food safety and public health. While studies have elucidated changes in immune cells and cytokines associated with allergen exposure, a comprehensive analysis of the host's metabolic features and the interaction between metabolites and the gut microbiota has not been conducted. In this study, egg allergen ovalbumin (OVA) was administered by the oral route to sensitized BALB/c mice to faithfully replicate key aspects of human FA, including severe allergic diarrhea, mast cell infiltration, and elevated levels of serum IgE, mMCPT-1, and Th2 cell hallmark cytokines (such as IL-4, IL-5, and IL-13). Furthermore, the untargeted and targeted metabolomic analyses indicated that FA in mice precipitated a substantial decrease in the tryptophan metabolites indole-3-acrylic acid (IA) and indole-3-lactic acid (ILA). The integration of shotgun metagenome and metabolome data further unveiled that the dysregulation of indole metabolism is related to a decline in the abundance of beneficial bacteria such as Lactobacillus and Bifidobacterium. Additionally, disruption of the tryptophan indole derivative pathway compromises the maintenance of intestinal mucosal function through the AHR signaling pathway, manifested by decreased expression of Reg3g and IL22. Taken together, this study demonstrated that the anaphylaxis triggered by oral ingestion of food allergens can lead to disruptions in tryptophan metabolism, consequently impairing intestinal immune homeostasis.}, } @article {pmid38545984, year = {2024}, author = {Liu, W and Liu, G and Zhang, R and Zheng, L and Lu, Z and Zhang, X and Wang, S and Shen, C and Shi, J and Xu, Z and Chai, L}, title = {[Metagenomics unveils the differences in the functions of microbial community of medium-temperature Daqu before and after maturation].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {40}, number = {3}, pages = {877-894}, doi = {10.13345/j.cjb.230340}, pmid = {38545984}, issn = {1872-2075}, mesh = {*Bacteria/genetics ; Temperature ; Acetoin Dehydrogenase ; Alcohol Dehydrogenase ; *Microbiota/physiology ; Fermentation ; Pyrazines ; }, abstract = {Daqu is the saccharifying, fermenting, and aroma-producing agent used in Baijiu brewing, and its maturation is crucial for obtaining high-quality Daqu. Previous studies have explored the microbial community composition and diversity before and after maturation. However, little is known about the changes in the functions of microbial community. In this study, based on the analyses of enzyme activities and volatile compounds of medium-temperature Daqu before and after maturation, metagenomics was used to analyze the differences in the composition of microbial community and the potential functions, with the aim to explore the microorganisms involved in changes in enzyme activities and important volatiles. The results showed that the moisture (P≤0.05), starch content, liquefying activity, saccharifying activity (P≤0.05), and fermentative activity decreased, while the acidity and esterifying activity (P≤0.05) increased after Daqu maturation. In the meantime, the composition of volatile compounds changed significantly (P=0.001), with significant decreases in the contents of aromatic alcohols and esters as well as significant increases in the contents of pyrazines, ketones, and higher fatty alcohols. The relative abundances of Mucorales (34.8%-23.0%) and Eurotiales (34.3%-20.1%) decreased in matured Daqu, and functional predictions showed these changes decreased the gene abundances of α-amylase, α-glucosidase, alcohol dehydrogenase, and alcohol dehydrogenase (NADP[+]) (P > 0.05), resulting in lower levels of liquefying activity (P > 0.05), saccharifying activity (P≤0.05), fermentative activity (P > 0.05), as well as aromatic alcohols such as phenylethyl alcohol (P≤0.05). In addition, higher relative abundances of Saccharomycetales (2.9%-16.6%), Lactobacillales (14.9%-23.6%), and Bacillales (0.8%-3.8%) were observed after maturation, and they were conducive to improving the gene abundances of alcohol O-acetyltransferase, carboxylesterase, acetolactate decarboxylase, (R)-acetoin dehydrogenase, and (S)-acetoin dehydrogenase (P≤0.05), resulting in significantly higher levels of esterifying activity and pyrazines (P≤0.05). The microorganisms involved in the changes in enzyme activities and important volatiles before and after Daqu maturation were studied at the gene level in this work, which may facilitate further rational regulation for Daqu production.}, } @article {pmid38543762, year = {2024}, author = {Liu, J and Li, X and Song, W and Zeng, X and Li, H and Yang, L and Wang, D}, title = {The Multi-Kingdom Microbiome of Wintering Migratory Birds in Poyang Lake, China.}, journal = {Viruses}, volume = {16}, number = {3}, pages = {}, pmid = {38543762}, issn = {1999-4915}, support = {2022YFC2303800//National Key Research and Development Program of China/ ; 81961128002//National Nature Science Foundation of China/ ; }, mesh = {Humans ; Animals ; Phylogeny ; *Lakes ; Birds ; Animals, Wild ; *Microbiota ; Biomarkers ; China ; }, abstract = {Wild birds are a natural reservoir for zoonotic viruses. To clarify the role of migratory birds in viruses spread in Poyang Lake, we investigated the microbiome of 250 wild bird samples from 19 species in seven orders. The bacterial and viral content abundance and diversity were preliminarily evaluated by Kraken2 and Bracken. After de novo assembly by Megahit and Vamb, viral contigs were identified by CheckV. The reads remapped to viral contigs were quantified using Bowtie2. The bacterial microbiome composition of the samples covers 1526 genera belonging to 175 bacterial orders, while the composition of viruses covers 214 species belonging to 22 viral families. Several taxonomic biomarkers associated with avian carnivory, oral sampling, and raptor migration were identified. Additionally, 17 complete viral genomes belonging to Astroviridae, Caliciviridae, Dicistroviridae, Picornaviridae, and Tombusviridae were characterized, and their phylogenetic relationships were analyzed. This pioneering metagenomic study of migratory birds in Poyang Lake, China illuminates the diverse microbial landscape within these birds. It identifies potential pathogens, and uncovers taxonomic biomarkers relevant to varied bird habitats, feeding habits, ecological classifications, and sample types, underscoring the public health risks associated with wintering migratory birds.}, } @article {pmid38543568, year = {2024}, author = {Li, J and Cheng, H and Yin, F and Liu, J and Zhang, XH and Yu, M}, title = {Deciphering Microbial Communities and Distinct Metabolic Pathways in the Tangyin Hydrothermal Fields of Okinawa Trough through Metagenomic and Genomic Analyses.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, pmid = {38543568}, issn = {2076-2607}, support = {42376145 and 41976137//National Natural Science Foundation of China/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Deep-sea hydrothermal vents have been extensively explored around the globe in the past decades, and the diversity of microbial communities and their ecological functions related to hydrothermal vents have become hotspots in the study of microbial biogeochemistry. However, knowledge of dominant microbial communities and their unique metabolic characteristics adapting to hydrothermal vents is still limited. In our study, the sediment sample near the Tangyin hydrothermal vent in the southern part of the Okinawa Trough was collected, and the most abundant phyla are Proteobacteria and Desulfobacterota based on the 16S rRNA genes and metagenome sequencing. Metagenomic analysis revealed that methane metabolism, sulfur reduction, and Fe[2+] uptake were abundantly distributed in hydrothermal sediment. In addition, most of the metagenomic assembly genomes (MAGs), belonging to Chloroflexota, Desulfobacterota, and Gammaproteobacteria, were found to be involved in methanogenesis, sulfur oxidation/reduction, and ferrous/ferric iron metabolisms. Among these MAGs, the two representative groups (Bathyarchaeia and Thioglobaceae) also showed distinct metabolic characteristics related to carbon, sulfur, and iron to adapt to hydrothermal environments. Our results reveal the dominant microbial populations and their metabolic features in the sediment near the Tangyin hydrothermal fields, providing a better understanding of microbial survival strategies in the extreme environment.}, } @article {pmid38543562, year = {2024}, author = {Masenya, K and Manganyi, MC and Dikobe, TB}, title = {Exploring Cereal Metagenomics: Unravelling Microbial Communities for Improved Food Security.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, pmid = {38543562}, issn = {2076-2607}, abstract = {Food security is an urgent global challenge, with cereals playing a crucial role in meeting the nutritional requirements of populations worldwide. In recent years, the field of metagenomics has emerged as a powerful tool for studying the microbial communities associated with cereal crops and their impact on plant health and growth. This chapter aims to provide a comprehensive overview of cereal metagenomics and its role in enhancing food security through the exploration of beneficial and pathogenic microbial interactions. Furthermore, we will examine how the integration of metagenomics with other tools can effectively address the adverse effects on food security. For this purpose, we discuss the integration of metagenomic data and machine learning in providing novel insights into the dynamic interactions shaping plant-microbe relationships. We also shed light on the potential applications of leveraging microbial diversity and epigenetic modifications in improving crop resilience and yield sustainability. Ultimately, cereal metagenomics has revolutionized the field of food security by harnessing the potential of beneficial interactions between cereals and their microbiota, paving the way for sustainable agricultural practices.}, } @article {pmid38542697, year = {2024}, author = {Shearer, J and Shah, S and MacInnis, MJ and Shen-Tu, G and Mu, C}, title = {Dose-Responsive Effects of Iron Supplementation on the Gut Microbiota in Middle-Aged Women.}, journal = {Nutrients}, volume = {16}, number = {6}, pages = {}, pmid = {38542697}, issn = {2072-6643}, support = {150364/CAPMC/CIHR/Canada ; }, mesh = {Middle Aged ; Humans ; Female ; *Gastrointestinal Microbiome ; Iron ; RNA, Ribosomal, 16S/genetics ; Retrospective Studies ; Dietary Supplements ; }, abstract = {Oral iron supplementation is the first-line treatment for addressing iron deficiency, a concern particularly relevant to women who are susceptible to sub-optimal iron levels. Nevertheless, the impact of iron supplementation on the gut microbiota of middle-aged women remains unclear. To investigate the association between iron supplementation and the gut microbiota, healthy females aged 40-65 years (n = 56, BMI = 23 ± 2.6 kg/m[2]) were retrospectively analyzed from the Alberta's Tomorrow Project. Fecal samples along with various lifestyle, diet, and health questionnaires were obtained. The gut microbiota was assessed by 16S rRNA sequencing. Individuals were matched by age and BMI and classified as either taking no iron supplement, a low-dose iron supplement (6-10 mg iron/day), or high-dose iron (>100 mg/day). Compositional and functional analyses of microbiome data in relation to iron supplementation were investigated using various bioinformatics tools. Results revealed that iron supplementation had a dose-dependent effect on microbial communities. Elevated iron intake (>100 mg) was associated with an augmentation of Proteobacteria and a reduction in various taxa, including Akkermansia, Butyricicoccus, Verrucomicrobia, Ruminococcus, Alistipes, and Faecalibacterium. Metagenomic prediction further suggested the upregulation of iron acquisition and siderophore biosynthesis following high iron intake. In conclusion, adequate iron levels are essential for the overall health and wellbeing of women through their various life stages. Our findings offer insights into the complex relationships between iron supplementation and the gut microbiota in middle-aged women and underscore the significance of iron dosage in maintaining optimal gut health.}, } @article {pmid38542271, year = {2024}, author = {Park, W and Park, J}, title = {A Comparative Investigation of the Bile Microbiome in Patients with Choledocholithiasis and Cholecystolithiasis through Metagenomic Analysis.}, journal = {International journal of molecular sciences}, volume = {25}, number = {6}, pages = {}, pmid = {38542271}, issn = {1422-0067}, support = {0//Biomedical Research Institute, Jeonbuk National University Hospital./ ; }, mesh = {Humans ; *Choledocholithiasis/genetics ; *Gallstones ; Bile ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; }, abstract = {While the precise triggers of gallstone formation remain incompletely understood, it is believed to arise from a complex interplay of genetic and environmental factors. The bile microbiome is being increasingly recognized as a possible contributor to the onset of gallstone disease. The primary objective of this study was to investigate distinctions in the microbial communities within bile specimens from patients with choledocholithiasis (common bile duct stones) and cholecystolithiasis (gallbladder stones). We employed massively parallel sequencing of the 16S rRNA gene to examine the microbial communities within bile samples obtained from 28 patients with choledocholithiasis (group DS) and cholecystolithiasis (group GS). The taxonomic composition of the bile microbial communities displayed significant disparities between the group DS and the group GS. Within the 16 prevalent genera, only Streptococcus, Ralstonia, Lactobacillus, and Enterococcus were predominantly found in the group GS. In contrast, the group DS displayed a more diverse range of genera. The alpha diversity of bile specimens was also notably lower in the group GS compared to the group DS (p = 0.041). Principal coordinate analysis unveiled distinct clustering of bile microbial communities depending on the location of the gallstone. Linear discriminant analysis effect size analysis, with a score threshold of >3 and the Kruskall-Wallis test (α < 0.05), recognized Bacilli and Lactobacillales as potential taxonomic markers for distinguishing patients with cholecystolithiasis limited to the gallbladder. Significant variations were found in the distribution and diversity of bile microbial communities between patients with choledocholithiasis and cholecystolithiasis. This observation suggests that alterations in the bile microbiome may contribute to the development of gallstones in these patients.}, } @article {pmid38541334, year = {2024}, author = {Kataržytė, M and Rapolienė, L and Kalvaitienė, G and Picazo-Espinosa, R}, title = {Microbial Composition Dynamics in Peloids Used for Spa Procedures in Lithuania: Pilot Study.}, journal = {International journal of environmental research and public health}, volume = {21}, number = {3}, pages = {}, pmid = {38541334}, issn = {1660-4601}, support = {S-REP-22-6//Lithuanian Science Council/ ; S-A-UEI-23-9//Lithuanian Science Council (LMT) and Ministry of Education, Science and Sports of the Republic of Lithuania/ ; }, mesh = {Humans ; Pilot Projects ; Lithuania ; *Mud Therapy/methods ; Soil ; *Microbiota ; Bacteria/genetics ; }, abstract = {Despite peloids' acknowledged therapeutic and cosmetic potential, there remains a limited understanding of their microbial diversity and dynamics, especially concerning beneficial and non-beneficial microorganisms under different heating conditions. Our study employs both cultivation and metagenomic methods to assess the microbiota of peloids, focusing on lake sapropel and peat under heating conditions recommended for external application and safety assurance. By applying microbial indicators specified in national regulatory documents, we found that all peloids reached thresholds for sulphite-reducing clostridia and colony-forming units. Each peloid exhibited a distinctive bacterial composition based on metagenomic analysis, and temperature-induced changes were observed in microbial diversity. We identified beneficial bacteria potentially contributing to the therapeutic properties of peloids. However, the same peloids indicated the presence of bacteria of human faecal origin, with a notably higher abundance of Escherichia coli, pointing to a potential source of contamination. Unfortunately, it remains unclear at which stage this contamination entered the peloids. The findings underscore the importance of monitoring and controlling microbial aspects in peloid applications, emphasising the need for measures to prevent and address contamination during their preparation and application processes.}, } @article {pmid38540015, year = {2024}, author = {Zuo, C and Ma, P and Ma, X and Zhu, Y and Yan, S and Zhang, Z}, title = {Integrated Metagenomic and Metabolomic Analysis on Two Competing Mussels, Mytella strigata and Perna viridis, in China.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {6}, pages = {}, pmid = {38540015}, issn = {2076-2615}, support = {2022YFD2401204//National Key R&D Program of China/ ; 42006080//National Natural Science Foundation of China/ ; }, abstract = {Biological invasion is a primary direct driver of biodiversity loss. Recently, owing to exploitation competition with an invasive mussel, Mytella strigata (Hanley, 1843), there has been a drastic decrease in the population of native Perna viridis (Linnaeus, 1758) in several western Pacific regions. In the present study, intestinal microbiota, metabolome, and key digestive enzyme activities were compared between the two competing mussels, M. strigata and P. viridis, to elucidate the differences in intestinal microbiota and metabolic points. We observed that Proteobacteria, Firmicutes, and Bacteroidota were the three predominant bacterial phyla in the two species. The relative abundance of Bacteroidota related to carbohydrate-degrading ability was significantly higher in M. strigata than in P. viridis. Compared to P. viridis, different metabolites including maltose and trehalose were enriched in M. strigata. Lastly, higher carbohydrases activities of alpha-amylase, cellulase, and xylanase were observed in M. strigata than in P. viridis. These differences might play an important role in the adaptation process of M. strigata to the new environment. This study provides important basic knowledge for investigating the competition between M. strigata and P. viridis in terms of food resources utilization.}, } @article {pmid38538803, year = {2024}, author = {Masuda, S and Gan, P and Kiguchi, Y and Anda, M and Sasaki, K and Shibata, A and Iwasaki, W and Suda, W and Shirasu, K}, title = {Uncovering microbiomes of the rice phyllosphere using long-read metagenomic sequencing.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {357}, pmid = {38538803}, issn = {2399-3642}, mesh = {*Oryza/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenome ; Plasmids ; }, abstract = {The plant microbiome is crucial for plant growth, yet many important questions remain, such as the identification of specific bacterial species in plants, their genetic content, and location of these genes on chromosomes or plasmids. To gain insights into the genetic makeup of the rice-phyllosphere, we perform a metagenomic analysis using long-read sequences. Here, 1.8 Gb reads are assembled into 26,067 contigs including 142 circular sequences. Within these contigs, 669 complete 16S rRNA genes are clustered into 166 bacterial species, 121 of which show low identity (<97%) to defined sequences, suggesting novel species. The circular contigs contain novel chromosomes and a megaplasmid, and most of the smaller circular contigs are defined as novel plasmids or bacteriophages. One circular contig represents the complete chromosome of a difficult-to-culture bacterium Candidatus Saccharibacteria. Our findings demonstrate the efficacy of long-read-based metagenomics for profiling microbial communities and discovering novel sequences in plant-microbiome studies.}, } @article {pmid38534158, year = {2024}, author = {Oliver, A and Podell, S and Wegley Kelly, L and Sparagon, WJ and Plominsky, AM and Nelson, RS and Laurens, LML and Augyte, S and Sims, NA and Nelson, CE and Allen, EE}, title = {Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish.}, journal = {mBio}, volume = {15}, number = {5}, pages = {e0049624}, pmid = {38534158}, issn = {2150-7511}, support = {S10 OD026929/OD/NIH HHS/United States ; R01 ES030316/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; *Polysaccharides/metabolism ; *Seaweed/microbiology ; *Symbiosis ; *Gastrointestinal Microbiome ; Microbial Consortia ; Bacteria/metabolism/classification/genetics/isolation & purification ; Metagenome ; Fishes/microbiology ; Phylogeny ; }, abstract = {Coastal herbivorous fishes consume macroalgae, which is then degraded by microbes along their digestive tract. However, there is scarce genomic information about the microbiota that perform this degradation. This study explores the potential of Kyphosus gastrointestinal microbial symbionts to collaboratively degrade and ferment polysaccharides from red, green, and brown macroalgae through in silico study of carbohydrate-active enzyme and sulfatase sequences. Recovery of metagenome-assembled genomes (MAGs) from previously described Kyphosus gut metagenomes and newly sequenced bioreactor enrichments reveals differences in enzymatic capabilities between the major microbial taxa in Kyphosus guts. The most versatile of the recovered MAGs were from the Bacteroidota phylum, whose MAGs house enzyme collections able to decompose a variety of algal polysaccharides. Unique enzymes and predicted degradative capacities of genomes from the Bacillota (genus Vallitalea) and Verrucomicrobiota (order Kiritimatiellales) highlight the importance of metabolic contributions from multiple phyla to broaden polysaccharide degradation capabilities. Few genomes contain the required enzymes to fully degrade any complex sulfated algal polysaccharide alone. The distribution of suitable enzymes between MAGs originating from different taxa, along with the widespread detection of signal peptides in candidate enzymes, is consistent with cooperative extracellular degradation of these carbohydrates. This study leverages genomic evidence to reveal an untapped diversity at the enzyme and strain level among Kyphosus symbionts and their contributions to macroalgae decomposition. Bioreactor enrichments provide a genomic foundation for degradative and fermentative processes central to translating the knowledge gained from this system to the aquaculture and bioenergy sectors.IMPORTANCESeaweed has long been considered a promising source of sustainable biomass for bioenergy and aquaculture feed, but scalable industrial methods for decomposing terrestrial compounds can struggle to break down seaweed polysaccharides efficiently due to their unique sulfated structures. Fish of the genus Kyphosus feed on seaweed by leveraging gastrointestinal bacteria to degrade algal polysaccharides into simple sugars. This study reconstructs metagenome-assembled genomes for these gastrointestinal bacteria to enhance our understanding of herbivorous fish digestion and fermentation of algal sugars. Investigations at the gene level identify Kyphosus guts as an untapped source of seaweed-degrading enzymes ripe for further characterization. These discoveries set the stage for future work incorporating marine enzymes and microbial communities in the industrial degradation of algal polysaccharides.}, } @article {pmid38533900, year = {2024}, author = {Jackson, I and Woodman, P and Dowd, M and Fibiger, L and Cassidy, LM}, title = {Ancient Genomes From Bronze Age Remains Reveal Deep Diversity and Recent Adaptive Episodes for Human Oral Pathobionts.}, journal = {Molecular biology and evolution}, volume = {41}, number = {3}, pages = {}, pmid = {38533900}, issn = {1537-1719}, support = {/WT_/Wellcome Trust/United Kingdom ; IRCLA/2022/126//Wellcome Trust Institutional Strategic Support Fund/ ; 18/CRT/6214//Science Foundation Ireland Centre for Research Training in Genomics Data Science/ ; }, mesh = {Humans ; Phylogeny ; *Streptococcus mutans/genetics ; Genomics ; Metagenome ; *Microbiota ; }, abstract = {Ancient microbial genomes can illuminate pathobiont evolution across millenia, with teeth providing a rich substrate. However, the characterization of prehistoric oral pathobiont diversity is limited. In Europe, only preagricultural genomes have been subject to phylogenetic analysis, with none compared to more recent archaeological periods. Here, we report well-preserved microbiomes from two 4,000-year-old teeth from an Irish limestone cave. These contained bacteria implicated in periodontitis, as well as Streptococcus mutans, the major cause of caries and rare in the ancient genomic record. Despite deriving from the same individual, these teeth produced divergent Tannerella forsythia genomes, indicating higher levels of strain diversity in prehistoric populations. We find evidence of microbiome dysbiosis, with a disproportionate quantity of S. mutans sequences relative to other oral streptococci. This high abundance allowed for metagenomic assembly, resulting in its first reported ancient genome. Phylogenetic analysis indicates major postmedieval population expansions for both species, highlighting the inordinate impact of recent dietary changes. In T. forsythia, this expansion is associated with the replacement of older lineages, possibly reflecting a genome-wide selective sweep. Accordingly, we see dramatic changes in T. forsythia's virulence repertoire across this period. S. mutans shows a contrasting pattern, with deeply divergent lineages persisting in modern populations. This may be due to its highly recombining nature, allowing for maintenance of diversity through selective episodes. Nonetheless, an explosion in recent coalescences and significantly shorter branch lengths separating bacteriocin-carrying strains indicate major changes in S. mutans demography and function coinciding with sugar popularization during the industrial period.}, } @article {pmid38532703, year = {2024}, author = {Sheikh, IA and Bianchi-Smak, J and Laubitz, D and Schiro, G and Midura-Kiela, MT and Besselsen, DG and Vedantam, G and Jarmakiewicz, S and Filip, R and Ghishan, FK and Gao, N and Kiela, PR}, title = {Transplant of microbiota from Crohn's disease patients to germ-free mice results in colitis.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2333483}, pmid = {38532703}, issn = {1949-0984}, support = {R01 DK136240/DK/NIDDK NIH HHS/United States ; R01 DK119198/DK/NIDDK NIH HHS/United States ; R01 AT010243/AT/NCCIH NIH HHS/United States ; R01 DK139790/DK/NIDDK NIH HHS/United States ; R01 DK132885/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Mice ; Animals ; *Crohn Disease/microbiology ; *Clostridioides difficile ; *Gastrointestinal Microbiome ; *Colitis ; *Microbiota ; Fecal Microbiota Transplantation ; Dysbiosis/microbiology ; }, abstract = {Although the role of the intestinal microbiota in the pathogenesis of inflammatory bowel disease (IBD) is beyond debate, attempts to verify the causative role of IBD-associated dysbiosis have been limited to reports of promoting the disease in genetically susceptible mice or in chemically induced colitis. We aimed to further test the host response to fecal microbiome transplantation (FMT) from Crohn's disease patients on mucosal homeostasis in ex-germ-free (xGF) mice. We characterized and transferred fecal microbiota from healthy patients and patients with defined Crohn's ileocolitis (CD_L3) to germ-free mice and analyzed the resulting microbial and mucosal homeostasis by 16S profiling, shotgun metagenomics, histology, immunofluorescence (IF) and RNAseq analysis. We observed a markedly reduced engraftment of CD_L3 microbiome compared to healthy control microbiota. FMT from CD_L3 patients did not lead to ileitis but resulted in colitis with features consistent with CD: a discontinued pattern of colitis, more proximal colonic localization, enlarged isolated lymphoid follicles and/or tertiary lymphoid organ neogenesis, and a transcriptomic pattern consistent with epithelial reprograming and promotion of the Paneth cell-like signature in the proximal colon and immune dysregulation characteristic of CD. The observed inflammatory response was associated with persistently increased abundance of Ruminococcus gnavus, Erysipelatoclostridium ramosum, Faecalimonas umbilicate, Blautia hominis, Clostridium butyricum, and C. paraputrificum and unexpected growth of toxigenic C. difficile, which was below the detection level in the community used for inoculation. Our study provides the first evidence that the transfer of a dysbiotic community from CD patients can lead to spontaneous inflammatory changes in the colon of xGF mice and identifies a signature microbial community capable of promoting colonization of pathogenic and conditionally pathogenic bacteria.}, } @article {pmid38532461, year = {2024}, author = {Pax, K and Buduneli, N and Alan, M and Meric, P and Gurlek, O and Dabdoub, SM and Kumar, PS}, title = {Placental TLR recognition of salivary and subgingival microbiota is associated with pregnancy complications.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {64}, pmid = {38532461}, issn = {2049-2618}, support = {1F30DE029676-01A1/DE/NIDCR NIH HHS/United States ; R01DE027857/DE/NIDCR NIH HHS/United States ; R01DE027857/DE/NIDCR NIH HHS/United States ; }, mesh = {Infant, Newborn ; Pregnancy ; Female ; Humans ; Placenta/microbiology ; Cross-Sectional Studies ; *Pregnancy Complications ; *Periodontal Diseases ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Pre-term birth, the leading cause of neonatal mortality, has been associated with maternal periodontal disease and the presence of oral pathogens in the placenta. However, the mechanisms that underpin this link are not known. This investigation aimed to identify the origins of placental microbiota and to interrogate the association between parturition complications and immune recognition of placental microbial motifs. Video Abstract METHODS: Saliva, plaque, serum, and placenta were collected during 130 full-term (FT), pre-term (PT), or pre-term complicated by pre-eclampsia (PTPE) deliveries and subjected to whole-genome shotgun sequencing. Real-time quantitative PCR was used to measure toll-like receptors (TLR) 1-10 expression in placental samples. Source tracking was employed to trace the origins of the placental microbiota.

RESULTS: We discovered 10,007 functionally annotated genes representing 420 taxa in the placenta that could not be attributed to contamination. Placental microbial composition was the biggest discriminator of pregnancy complications, outweighing hypertension, BMI, smoking, and maternal age. A machine-learning algorithm trained on this microbial dataset predicted PTPE and PT with error rates of 4.05% and 8.6% (taxonomy) and 6.21% and 7.38% (function). Logistic regression revealed 32% higher odds of parturition complication (95% CI 2.8%, 81%) for every IQR increase in the Shannon diversity index after adjusting for maternal smoking status, maternal age, and gravida. We also discovered distinct expression patterns of TLRs that detect RNA- and DNA-containing antigens in the three groups, with significant upregulation of TLR9, and concomitant downregulation of TLR7 in PTPE and PT groups, and dense correlation networks between microbial genes and these TLRs. 70-82% of placental microbiota were traced to serum and thence to the salivary and subgingival microbiomes. The oral and serum microbiomes of PTPE and PT groups displayed significant enrichment of genes encoding iron transport, exosome, adhesion, quorum sensing, lipopolysaccharide, biofilm, and steroid degradation.

CONCLUSIONS: Within the limits of cross-sectional analysis, we find evidence to suggest that oral bacteria might translocate to the placenta via serum and trigger immune signaling pathways capable of inducing placental vascular pathology. This might explain, in part, the higher incidence of obstetric syndromes in women with periodontal disease.}, } @article {pmid38531781, year = {2024}, author = {Jiang, X and Li, H and Ma, J and Li, H and Ma, X and Tang, Y and Li, J and Chi, X and Deng, Y and Zeng, S and Liu, Z}, title = {Role of Type VI secretion system in pathogenic remodeling of host gut microbiota during Aeromonas veronii infection.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38531781}, issn = {1751-7370}, support = {32160038//National Natural Science Foundation of China/ ; 2020WNLOKF019//Open Project Program of Wuhan National Laboratory for Optoelectronics/ ; }, mesh = {*Type VI Secretion Systems/genetics ; *Gastrointestinal Microbiome/physiology ; Aeromonas veronii/genetics ; Symbiosis ; Ecosystem ; Bacterial Proteins/genetics ; }, abstract = {Intestinal microbial disturbance is a direct cause of host disease. The bacterial Type VI secretion system (T6SS) often plays a crucial role in the fitness of pathogenic bacteria by delivering toxic effectors into target cells. However, its impact on the gut microbiota and host pathogenesis is poorly understood. To address this question, we characterized a new T6SS in the pathogenic Aeromonas veronii C4. First, we validated the secretion function of the core machinery of A. veronii C4 T6SS. Second, we found that the pathogenesis and colonization of A. veronii C4 is largely dependent on its T6SS. The effector secretion activity of A. veronii C4 T6SS not only provides an advantage in competition among bacteria in vitro, but also contributes to occupation of an ecological niche in the nutritionally deficient and anaerobic environment of the host intestine. Metagenomic analysis showed that the T6SS directly inhibits or eliminates symbiotic strains from the intestine, resulting in dysregulated gut microbiome homeostasis. In addition, we identified three unknown effectors, Tse1, Tse2, and Tse3, in the T6SS, which contribute to T6SS-mediated bacterial competition and pathogenesis by impairing targeted cell integrity. Our findings highlight that T6SS can remodel the host gut microbiota by intricate interplay between T6SS-mediated bacterial competition and altered host immune responses, which synergistically promote pathogenesis of A. veronii C4. Therefore, this newly characterized T6SS could represent a general interaction mechanism between the host and pathogen, and may offer a potential therapeutic target for controlling bacterial pathogens.}, } @article {pmid38528097, year = {2024}, author = {Wang, B and Sun, F and Luan, Y}, title = {Comparison of the effectiveness of different normalization methods for metagenomic cross-study phenotype prediction under heterogeneity.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {7024}, pmid = {38528097}, issn = {2045-2322}, support = {2018YFA0703900//National Key Research and Development Program of China/ ; 2018YFA0703900//National Key Research and Development Program of China/ ; 11971264//National Science Foundation of China/ ; 11971264//National Science Foundation of China/ ; }, mesh = {Humans ; *Microbiota/genetics ; Metagenome ; Metagenomics ; Research Design ; Phenotype ; }, abstract = {The human microbiome, comprising microorganisms residing within and on the human body, plays a crucial role in various physiological processes and has been linked to numerous diseases. To analyze microbiome data, it is essential to account for inherent heterogeneity and variability across samples. Normalization methods have been proposed to mitigate these variations and enhance comparability. However, the performance of these methods in predicting binary phenotypes remains understudied. This study systematically evaluates different normalization methods in microbiome data analysis and their impact on disease prediction. Our findings highlight the strengths and limitations of scaling, compositional data analysis, transformation, and batch correction methods. Scaling methods like TMM show consistent performance, while compositional data analysis methods exhibit mixed results. Transformation methods, such as Blom and NPN, demonstrate promise in capturing complex associations. Batch correction methods, including BMC and Limma, consistently outperform other approaches. However, the influence of normalization methods is constrained by population effects, disease effects, and batch effects. These results provide insights for selecting appropriate normalization approaches in microbiome research, improving predictive models, and advancing personalized medicine. Future research should explore larger and more diverse datasets and develop tailored normalization strategies for microbiome data analysis.}, } @article {pmid38527398, year = {2024}, author = {Xue, YX and Huang, LJ and Wang, HY and Peng, JJ and Jin, MK and Hu, SL and Li, HB and Xue, XM and Zhu, YG}, title = {Interaction of tetracycline and copper co-intake in inducing antibiotic resistance genes and potential pathogens in mouse gut.}, journal = {Environment international}, volume = {186}, number = {}, pages = {108594}, doi = {10.1016/j.envint.2024.108594}, pmid = {38527398}, issn = {1873-6750}, mesh = {Animals ; *Copper/toxicity ; *Tetracycline/pharmacology ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria/drug effects/genetics ; Feces/microbiology ; }, abstract = {The widespread use of copper and tetracycline as growth promoters in the breeding industry poses a potential threat to environmental health. Nevertheless, to the best of our knowledge, the potential adverse effects of copper and tetracycline on the gut microbiota remain unknown. Herein, mice were fed different concentrations of copper and/or tetracycline for 6 weeks to simulate real life-like exposure in the breeding industry. Following the exposure, antibiotic resistance genes (ARGs), potential pathogens, and other pathogenic factors were analyzed in mouse feces. The co-exposure of copper with tetracycline significantly increased the abundance of ARGs and enriched more potential pathogens in the gut of the co-treated mice. Copper and/or tetracycline exposure increased the abundance of bacteria carrying either ARGs, metal resistance genes, or virulence factors, contributing to the widespread dissemination of potentially harmful genes posing a severe risk to public health. Our study provides insights into the effects of copper and tetracycline exposure on the gut resistome and potential pathogens, and our findings can help reduce the risks associated with antibiotic resistance under the One Health framework.}, } @article {pmid38524178, year = {2024}, author = {Tu, JB and Liao, WJ and Long, SP and Li, MP and Gao, XH}, title = {Construction and validation of a machine learning model for the diagnosis of juvenile idiopathic arthritis based on fecal microbiota.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1371371}, pmid = {38524178}, issn = {2235-2988}, mesh = {Humans ; *Arthritis, Juvenile/diagnosis/genetics ; Biomarkers ; ROC Curve ; Machine Learning ; *Microbiota ; }, abstract = {PURPOSE: Human gut microbiota has been shown to be significantly associated with various inflammatory diseases. Therefore, this study aimed to develop an excellent auxiliary tool for the diagnosis of juvenile idiopathic arthritis (JIA) based on fecal microbial biomarkers.

METHOD: The fecal metagenomic sequencing data associated with JIA were extracted from NCBI, and the sequencing data were transformed into the relative abundance of microorganisms by professional data cleaning (KneadData, Trimmomatic and Bowtie2) and comparison software (Kraken2 and Bracken). After that, the fecal microbes with high abundance were extracted for subsequent analysis. The extracted fecal microbes were further screened by least absolute shrinkage and selection operator (LASSO) regression, and the selected fecal microbe biomarkers were used for model training. In this study, we constructed six different machine learning (ML) models, and then selected the best model for constructing a JIA diagnostic tool by comparing the performance of the models based on a combined consideration of area under receiver operating characteristic curve (AUC), accuracy, specificity, F1 score, calibration curves and clinical decision curves. In addition, to further explain the model, Permutation Importance analysis and Shapley Additive Explanations (SHAP) were performed to understand the contribution of each biomarker in the prediction process.

RESULT: A total of 231 individuals were included in this study, including 203 JIA patients and Non-JIA individuals. In the analysis of diversity at the genus level, the alpha diversity represented by Shannon value was not significantly different between the two groups, while the belt diversity was slightly different. After selection by LASSO regression, 10 fecal microbe biomarkers were selected for model training. By comparing six different models, the XGB model showed the best performance, which average AUC, accuracy and F1 score were 0.976, 0.914 and 0.952, respectively, thus being used to construct the final JIA diagnosis model.

CONCLUSION: A JIA diagnosis model based on XGB algorithm was constructed with excellent performance, which may assist physicians in early detection of JIA patients and improve the prognosis of JIA patients.}, } @article {pmid38521963, year = {2024}, author = {Sengupta, P and Muthamilselvi Sivabalan, SK and Singh, NK and Raman, K and Venkateswaran, K}, title = {Genomic, functional, and metabolic enhancements in multidrug-resistant Enterobacter bugandensis facilitating its persistence and succession in the International Space Station.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {62}, pmid = {38521963}, issn = {2049-2618}, support = {19-12829-26//2012 Space Biology NNH12ZTT001N/ ; 19-12829-26//2012 Space Biology NNH12ZTT001N/ ; MTR/2020/000490//Science and Engineering Board (SERB) MATRICS/ ; }, mesh = {Humans ; *Anti-Infective Agents ; *Enterobacter ; Genomics ; *Microbiota/genetics ; *Space Flight ; Spacecraft ; }, abstract = {BACKGROUND: The International Space Station (ISS) stands as a testament to human achievement in space exploration. Despite its highly controlled environment, characterised by microgravity, increased CO 2 levels, and elevated solar radiation, microorganisms occupy a unique niche. These microbial inhabitants play a significant role in influencing the health and well-being of astronauts on board. One microorganism of particular interest in our study is Enterobacter bugandensis, primarily found in clinical specimens including the human gastrointestinal tract, and also reported to possess pathogenic traits, leading to a plethora of infections.

RESULTS: Distinct from their Earth counterparts, ISS E. bugandensis strains have exhibited resistance mechanisms that categorise them within the ESKAPE pathogen group, a collection of pathogens recognised for their formidable resistance to antimicrobial treatments. During the 2-year Microbial Tracking 1 mission, 13 strains of multidrug-resistant E. bugandensis were isolated from various locations within the ISS. We have carried out a comprehensive study to understand the genomic intricacies of ISS-derived E. bugandensis in comparison to terrestrial strains, with a keen focus on those associated with clinical infections. We unravel the evolutionary trajectories of pivotal genes, especially those contributing to functional adaptations and potential antimicrobial resistance. A hypothesis central to our study was that the singular nature of the stresses of the space environment, distinct from any on Earth, could be driving these genomic adaptations. Extending our investigation, we meticulously mapped the prevalence and distribution of E. bugandensis across the ISS over time. This temporal analysis provided insights into the persistence, succession, and potential patterns of colonisation of E. bugandensis in space. Furthermore, by leveraging advanced analytical techniques, including metabolic modelling, we delved into the coexisting microbial communities alongside E. bugandensis in the ISS across multiple missions and spatial locations. This exploration revealed intricate microbial interactions, offering a window into the microbial ecosystem dynamics within the ISS.

CONCLUSIONS: Our comprehensive analysis illuminated not only the ways these interactions sculpt microbial diversity but also the factors that might contribute to the potential dominance and succession of E. bugandensis within the ISS environment. The implications of these findings are twofold. Firstly, they shed light on microbial behaviour, adaptation, and evolution in extreme, isolated environments. Secondly, they underscore the need for robust preventive measures, ensuring the health and safety of astronauts by mitigating risks associated with potential pathogenic threats. Video Abstract.}, } @article {pmid38521945, year = {2024}, author = {Bemmelen, JV and Smyth, DS and Baaijens, JA}, title = {Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {126}, pmid = {38521945}, issn = {1471-2105}, mesh = {*Metagenome ; *Microbiota ; DNA Primers/genetics ; Algorithms ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Metagenomic profiling algorithms commonly rely on genomic differences between lineages, strains, or species to infer the relative abundances of sequences present in a sample. This observation plays an important role in the analysis of diverse microbial communities, where targeted sequencing of 16S and 18S rRNA, both well-known hypervariable genomic regions, have led to insights into microbial diversity and the discovery of novel organisms. However, the variable nature of discriminatory regions can also act as a double-edged sword, as the sought-after variability can make it difficult to design primers for their amplification through PCR. Moreover, the most variable regions are not necessarily the most informative regions for the purpose of differentiation; one should focus on regions that maximize the number of lineages that can be distinguished.

RESULTS: Here we present AmpliDiff, a computational tool that simultaneously finds highly discriminatory genomic regions in viral genomes of a single species, as well as primers allowing for the amplification of these regions. We show that regions and primers found by AmpliDiff can be used to accurately estimate relative abundances of SARS-CoV-2 lineages, for example in wastewater sequencing data. We obtain errors that are comparable with using whole genome information to estimate relative abundances. Furthermore, our results show that AmpliDiff is robust against incomplete input data and that primers designed by AmpliDiff also bind to genomes sampled months after the primers were selected.

CONCLUSIONS: With AmpliDiff we provide an effective, cost-efficient alternative to whole genome sequencing for estimating lineage abundances in viral metagenomes.}, } @article {pmid38520323, year = {2024}, author = {Cao, S and Ren, X and Zhang, G and Wang, H and Wei, B and Niu, C}, title = {Gut microbiota metagenomics and mediation of phenol degradation in Bactrocera minax (Diptera, Tephritidae).}, journal = {Pest management science}, volume = {80}, number = {8}, pages = {3935-3944}, doi = {10.1002/ps.8096}, pmid = {38520323}, issn = {1526-4998}, support = {2023YFD1400700//National Key Research and Development Program of China/ ; 32272529//National Natural Science Foundation of China/ ; 31972270//National Natural Science Foundation of China/ ; 31661143045//National Natural Science Foundation of China/ ; 2482/16//Joint programme of the Israel Science Foundation and the Science Foundation of China/ ; }, mesh = {Animals ; *Tephritidae/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Larva/microbiology/growth & development/metabolism ; *Metagenomics ; *Phenol/metabolism ; Phenols/metabolism ; Bacteria/genetics/metabolism/classification/isolation & purification ; Citrus/microbiology ; }, abstract = {BACKGROUND: Gut microbiota mediating insect-plant interactions have many manifestations, either by provisioning missing nutrients, or by overcoming plant defensive reactions. However, the mechanism by which gut microbiota empower insects to survive by overcoming a variety of plant secondary metabolites remains largely unknown. Bactrocera minax larvae develop in immature citrus fruits, which present numerous phenolic compounds that challenge the larvae. To explore the role of gut microbes in host use and adaptability, we uncovered the mechanisms of phenol degradation by gut microbes using metagenomic and metatranscriptomic analyses, and verified the degradation ability of isolated and cultured bacteria. Research on this subject can help develop potential strain for the environmental friendly pest management operations.

RESULTS: We demonstrated the ability of gut microbes in B. minax larvae to degrade phenols in unripe citrus. After antibiotic treatment, coniferyl alcohol and coumaric aldehyde significantly reduced the survival rate, body length and body weight of the larvae. The metagenomic and metatranscriptomic analyses in B. minax provided evidence for the presence of genes in bacteria and the related pathway involved in phenol degradation. Among them, Enterococcus faecalis and Serratia marcescens, isolated from the gut of B. minax larvae, played critical roles in phenol degradation. Furthermore, supplementation of E. faecalis and S. marcescens in artificial diets containing coniferyl alcohol and coumaric aldehyde increased the survival rate of larvae.

CONCLUSION: In summary, our results provided the first comprehensive analysis of gut bacterial communities by high-throughput sequencing and elucidated the role of bacteria in phenol degradation in B. minax, which shed light on the mechanism underlying specialist insect adaption to host secondary metabolites via gut bacteria. © 2024 Society of Chemical Industry.}, } @article {pmid38519631, year = {2024}, author = {Pan, YF and Zhao, H and Gou, QY and Shi, PB and Tian, JH and Feng, Y and Li, K and Yang, WH and Wu, D and Tang, G and Zhang, B and Ren, Z and Peng, S and Luo, GY and Le, SJ and Xin, GY and Wang, J and Hou, X and Peng, MW and Kong, JB and Chen, XX and Yang, CH and Mei, SQ and Liao, YQ and Cheng, JX and Wang, J and Chaolemen, and Wu, YH and Wang, JB and An, T and Huang, X and Eden, JS and Li, J and Guo, D and Liang, G and Jin, X and Holmes, EC and Li, B and Wang, D and Li, J and Wu, WC and Shi, M}, title = {Metagenomic analysis of individual mosquito viromes reveals the geographical patterns and drivers of viral diversity.}, journal = {Nature ecology & evolution}, volume = {8}, number = {5}, pages = {947-959}, pmid = {38519631}, issn = {2397-334X}, mesh = {Animals ; *Culicidae/virology ; China ; *Virome ; *Mosquito Vectors/virology ; Metagenomics ; Arboviruses/genetics/classification ; Phylogeny ; Biodiversity ; }, abstract = {Mosquito transmitted viruses are responsible for an increasing burden of human disease. Despite this, little is known about the diversity and ecology of viruses within individual mosquito hosts. Here, using a meta-transcriptomic approach, we determined the viromes of 2,438 individual mosquitoes (81 species), spanning ~4,000 km along latitudes and longitudes in China. From these data we identified 393 viral species associated with mosquitoes, including 7 (putative) species of arthropod-borne viruses (that is, arboviruses). We identified potential mosquito species and geographic hotspots of viral diversity and arbovirus occurrence, and demonstrated that the composition of individual mosquito viromes was strongly associated with host phylogeny. Our data revealed a large number of viruses shared among mosquito species or genera, enhancing our understanding of the host specificity of insect-associated viruses. We also detected multiple virus species that were widespread throughout the country, perhaps reflecting long-distance mosquito dispersal. Together, these results greatly expand the known mosquito virome, linked viral diversity at the scale of individual insects to that at a country-wide scale, and offered unique insights into the biogeography and diversity of viruses in insect vectors.}, } @article {pmid38519592, year = {2024}, author = {Kunasegaran, T and Balasubramaniam, VRMT and Thirunavuk Arasoo, VJ and Palanisamy, UD and Tan, YK and Ramadas, A}, title = {Diet, lifestyle and gut microbiota composition among Malaysian women with gestational diabetes mellitus: a prospective cohort study.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6891}, pmid = {38519592}, issn = {2045-2322}, support = {SCH SEED/2020/005//Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia/ ; }, mesh = {Pregnancy ; Humans ; Female ; *Diabetes, Gestational/diagnosis ; *Gastrointestinal Microbiome/genetics ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Diet ; Life Style ; }, abstract = {The study addressed a significant gap in the profiling and understanding of the gut microbiota's influence on Malaysian Malay women with gestational diabetes mellitus (GDM). This prospective cohort study aimed to explore the intricate relationship between gut microbiota, dietary choices, and lifestyle factors among Malay women, both with and without GDM. The research specifically focused on participants during the second (T0) and third (T1) trimesters of pregnancy in Johor Bahru, Malaysia. In Part 1 of the study, a diverse pool of pregnant women at T0 was categorized into two groups: those diagnosed with GDM and those without GDM, with a total sample size of 105 individuals. The assessments encompassed demographic, clinical, lifestyle, and dietary factors at the T0 and T1 trimesters. Part 2 of the study delved into microbiome analysis, targeting a better understanding of the gut microbiota among the participants. Stool samples were randomly collected from 50% of the individuals in each group (GDM and non-GDM) at T0 and T1. The collected samples underwent processing, and 16s rRNA metagenomic analysis was employed to study the microbial composition. The results suggested an association between elevated body weight and glucose levels, poor sleep quality, lack of physical activity, greater intake of iron and meat, and reduced fruit consumption among women with GDM compared to non-GDM groups. The microbiome analysis revealed changes in microbial composition over time, with reduced diversity observed in the GDM group during the third trimester. The genera Lactiplantibacillus, Parvibacter, Prevotellaceae UCG001, and Vagococcus positively correlated with physical activity levels in GDM women in the second trimester. Similarly, the genus Victivallis exhibited a strong positive correlation with gravida and parity. On the contrary, the genus Bacteroides and Roseburia showed a negative correlation with omega-3 polyunsaturated fatty acids (PUFAs) in women without GDM in the third trimester. The study highlighted the multifaceted nature of GDM, involving a combination of lifestyle factors, dietary choices, and changes in gut microbiota composition. The findings emphasized the importance of considering these interconnected elements in understanding and managing gestational diabetes among Malaysian Malay women. Further exploration is essential to comprehend the mechanisms underlying this relationship and develop targeted interventions for effective GDM management.}, } @article {pmid38519112, year = {2024}, author = {Deng, Y and Yang, S and Zhang, L and Chen, C and Cheng, X and Hou, C}, title = {Chronic bee paralysis virus exploits host antimicrobial peptides and alters gut microbiota composition to facilitate viral infection.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38519112}, issn = {1751-7370}, support = {31811530276//National Natural Science Foundation of China/ ; CAAS-ASTIP-2023//Agricultural Science, Technology Innovation Program of CAAS/ ; Y2021YJ25//Central Public-interest Scientific Institution Basal Research Fund/ ; }, mesh = {Bees ; Animals ; *RNA Viruses/physiology ; *Gastrointestinal Microbiome ; Antimicrobial Peptides ; *Insect Viruses/physiology ; *Viruses ; *Virus Diseases ; Paralysis ; }, abstract = {The significance of gut microbiota in regulating animal immune response to viral infection is increasingly recognized. However, how chronic bee paralysis virus (CBPV) exploits host immune to disturb microbiota for its proliferation remains elusive. Through histopathological examination, we discovered that the hindgut harbored the highest level of CBPV, and displayed visible signs of damages. The metagenomic analysis showed that a notable reduction in the levels of Snodgrassella alvi and Lactobacillus apis, and a significant increase in the abundance of the opportunistic pathogens such as Enterobacter hormaechei and Enterobacter cloacae following CBPV infection. Subsequent co-inoculation experiments showed that these opportunistic pathogens facilitated the CBPV proliferation, leading to accelerated mortality in bees and exacerbation of bloated abdomen symptoms after CBPV infection. The expression level of antimicrobial peptide (AMP) was found to be significantly up-regulated by over 1000 times in response to CBPV infection, as demonstrated by subsequent transcriptome and quantitative real-time PCR investigations. In particular, through correlation analysis and a bacteriostatic test revealed that the AMPs did not exhibit any inhibitory effect against the two opportunistic pathogens. However, they did demonstrate inhibitory activity against S. alvi and L. apis. Our findings provide different evidence that the virus infection may stimulate and utilize the host's AMPs to eradicate probiotic species and facilitate the proliferation of opportunistic bacteria. This process weakens the intestinal barrier and ultimately resulting in the typical bloated abdomen.}, } @article {pmid38519004, year = {2024}, author = {Sepulveda, M and Rasic, M and Lei, YM and Kwan, M and Chen, L and Chen, Y and Perkins, D and Alegre, ML}, title = {Coordinated elimination of bacterial taxa optimally attenuates alloimmunity and prolongs allograft survival.}, journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons}, volume = {24}, number = {9}, pages = {1573-1582}, pmid = {38519004}, issn = {1600-6143}, support = {R25 GM109439/GM/NIGMS NIH HHS/United States ; T32 AI007090/AI/NIAID NIH HHS/United States ; TL1 DK132769/DK/NIDDK NIH HHS/United States ; U01 AI132898/AI/NIAID NIH HHS/United States ; R01 AI115716/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Graft Survival/immunology/drug effects ; *Graft Rejection/immunology/prevention & control ; *Gastrointestinal Microbiome/immunology ; *Skin Transplantation ; *Mice, Inbred BALB C ; *Mice, Inbred C57BL ; Anti-Bacterial Agents/pharmacology ; Allografts ; Male ; }, abstract = {This study aimed to dissect the relationship between specific gut commensal bacterial subgroups, their functional metabolic pathways, and their impact on skin allograft outcome and alloimmunity. We previously showed that oral broad-spectrum antibiotic (Abx) pretreatment in mice delayed skin, heart, and lung allograft rejection and dampened alloimmune responses. Here, rationally designed Abx combinations targeting major bacterial groups were used to elucidate their individual contribution to modulating alloimmune responses. Abx cocktails targeting intestinal gram-negative, gram-positive, or anaerobic/gram-positive bacteria by oral gavage, all delayed skin allograft rejection, and reduced alloreactive T cell priming to different extents. Notably, the most pronounced extension of skin allograft survival and attenuation of alloimmunity were achieved when all gut bacterial groups were simultaneously targeted. These results suggest a model in which the strength of the alloimmune response is additively tuned up by gut microbial diversity. Shotgun metagenomic sequencing enabled strain-level resolution and identified a shared commensal, Parabacteroides distasonis, as the most enriched following all Abx treatments. Oral administration of P.distasonis to mice harboring a diverse microbiota significantly prolonged skin allograft survival, identifying a probiotic with therapeutic benefit in transplantation.}, } @article {pmid38515324, year = {2024}, author = {Zou, S and Chen, Z and Tan, Y and Tan, M and Guo, W and Wu, S and Liu, J and Song, S and Peng, Y and Wang, M and Liang, K}, title = {Microbiomes detected by cerebrospinal fluid metagenomic next-generation sequencing among patients with and without HIV with suspected central nervous system infection.}, journal = {HIV medicine}, volume = {25}, number = {7}, pages = {794-804}, doi = {10.1111/hiv.13634}, pmid = {38515324}, issn = {1468-1293}, support = {PTXM2020008//Medical Science Advancement Program (Basic Medical Sciences) of Wuhan University/ ; //Science and Technology Innovation Cultivation Fund of Zhongnan Hospital/ ; 2020-PT320-004//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; //Medical Science and Technology Innovation Platform Support Project of Zhongnan Hospital, Wuhan University/ ; ZNXKPY2021027//Discipline Cultivation Funding, Zhongnan Hospital of Wuhan University/ ; }, mesh = {Humans ; Male ; Retrospective Studies ; Female ; *High-Throughput Nucleotide Sequencing/methods ; Adult ; Middle Aged ; *Central Nervous System Infections/cerebrospinal fluid/microbiology/diagnosis/virology ; *HIV Infections/complications/cerebrospinal fluid ; *Metagenomics/methods ; *Cerebrospinal Fluid/microbiology/virology ; Microbiota/genetics ; AIDS-Related Opportunistic Infections/cerebrospinal fluid/microbiology/diagnosis ; }, abstract = {BACKGROUND: Opportunistic infections in the central nervous system (CNS) can be a serious threat to people living with HIV. Early aetiological diagnosis and targeted treatment are crucial but difficult. Metagenomic next-generation sequencing (mNGS) has significant advantages over traditional detection methods. However, differences in the cerebrospinal fluid (CSF) microbiome profiles of patients living with and without HIV with suspected CNS infections using mNGS and conventional testing methods have not yet been adequately evaluated.

METHODS: We conducted a retrospective cohort study in the first hospital of Changsha between January 2019 and June 2022 to investigate the microbiomes detected using mNGS of the CSF of patients living with and without HIV with suspected CNS infections. The pathogens causing CNS infections were concurrently identified using both mNGS and traditional detection methods. The spectrum of pathogens identified was compared between the two groups.

RESULTS: Overall, 173 patients (140 with and 33 without HIV) with suspected CNS infection were enrolled in our study. In total, 106 (75.7%) patients with and 16 (48.5%) patients without HIV tested positive with mNGS (p = 0.002). Among the enrolled patients, 71 (50.7%) with HIV and five (15.2%) without HIV tested positive for two or more pathogens (p < 0.001). Patients with HIV had significantly higher proportions of fungus (20.7% vs. 3.0%, p = 0.016) and DNA virus (59.3% vs. 21.2%, p < 0.001) than those without HIV. Epstein-Barr virus (33.6%) was the most commonly identified potential pathogen in the CSF of patients living with HIV using mNGS, followed by cytomegalovirus (20.7%) and torque teno virus (13.8%). The top three causative pathogens identified in patients without HIV were Streptococcus (18.2%), Epstein-Barr virus (12.1%), and Mycobacterium tuberculosis (9.1%). In total, 113 patients living with HIV were diagnosed as having CNS infections. The rate of pathogen detection in people living with HIV with a CNS infection was significantly higher with mNGS than with conventional methods (93.8% vs. 15.0%, p < 0.001).

CONCLUSION: CSF microbiome profiles differ between patients living with and without HIV with suspected CNS infection. mNGS is a powerful tool for the diagnosis of CNS infection among people living with HIV, especially in those with mixed infections.}, } @article {pmid38514648, year = {2024}, author = {Liu, J and Yan, Q and Li, S and Jiao, J and Hao, Y and Zhang, G and Zhang, Q and Luo, F and Zhang, Y and Lv, Q and Zhang, W and Zhang, A and Song, H and Xin, Y and Ma, Y and Owusu, L and Ma, X and Yin, P and Shang, D}, title = {Integrative metagenomic and metabolomic analyses reveal the potential of gut microbiota to exacerbate acute pancreatitis.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {29}, pmid = {38514648}, issn = {2055-5008}, support = {81873156//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82004152//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Mice ; Humans ; *Gastrointestinal Microbiome ; Metagenome ; Acute Disease ; *Pancreatitis/etiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Early dysbiosis in the gut microbiota may contribute to the severity of acute pancreatitis (AP), however, a comprehensive understanding of the gut microbiome, potential pathobionts, and host metabolome in individuals with AP remains elusive. Hence, we employed fecal whole-metagenome shotgun sequencing in 82 AP patients and 115 matched healthy controls, complemented by untargeted serum metabolome and lipidome profiling in a subset of participants. Analyses of the gut microbiome in AP patients revealed reduced diversity, disrupted microbial functions, and altered abundance of 77 species, influenced by both etiology and severity. AP-enriched species, mostly potential pathobionts, correlated positively with host liver function and serum lipid indicators. Conversely, many AP-depleted species were short-chain fatty acid producers. Gut microflora changes were accompanied by shifts in the serum metabolome and lipidome. Specifically, certain gut species, like enriched Bilophila wadsworthia and depleted Bifidobacterium spp., appeared to contribute to elevated triglyceride levels in biliary or hyperlipidemic AP patients. Through culturing and whole-genome sequencing of bacterial isolates, we identified virulence factors and clinically relevant antibiotic resistance in patient-derived strains, suggesting a predisposition to opportunistic infections. Finally, our study demonstrated that gavage of specific pathobionts could exacerbate pancreatitis in a caerulein-treated mouse model. In conclusion, our comprehensive analysis sheds light on the gut microbiome and serum metabolome in AP, elucidating the role of pathobionts in disease progression. These insights offer valuable perspectives for etiologic diagnosis, prevention, and intervention in AP and related conditions.}, } @article {pmid38511953, year = {2024}, author = {Zhao, Z and Baltar, F and Herndl, GJ}, title = {Decoupling between the genetic potential and the metabolic regulation and expression in microbial organic matter cleavage across microbiomes.}, journal = {Microbiology spectrum}, volume = {12}, number = {5}, pages = {e0303623}, pmid = {38511953}, issn = {2165-0497}, support = {P28781-B21, I4978-B//Austrian Science Fund (FWF)/ ; }, mesh = {*Microbiota/genetics/physiology ; *Bacteria/genetics/metabolism/classification/enzymology ; *Metagenomics ; Humans ; Proteomics ; Soil Microbiology ; Bacterial Proteins/genetics/metabolism ; Peptide Hydrolases/metabolism/genetics ; Ecosystem ; Gastrointestinal Microbiome/genetics ; Seawater/microbiology ; }, abstract = {UNLABELLED: Metagenomics, metatranscriptomics, and metaproteomics are used to explore the microbial capability of enzyme secretion, but the links between protein-encoding genes and corresponding transcripts/proteins across ecosystems are underexplored. By conducting a multi-omics comparison focusing on key enzymes (carbohydrate-active enzymes [CAZymes] and peptidases) cleaving the main biomolecules across distinct microbiomes living in the ocean, soil, and human gut, we show that the community structure, functional diversity, and secretion mechanisms of microbial secretory CAZymes and peptidases vary drastically between microbiomes at metagenomic, metatranscriptomic, and metaproteomic levels. Such variations lead to decoupled relationships between CAZymes and peptidases from genetic potentials to protein expressions due to the different responses of key players toward organic matter sources and concentrations. Our results highlight the need for systematic analysis of the factors shaping patterns of microbial cleavage on organic matter to better link omics data to ecosystem processes.

IMPORTANCE: Omics tools are used to explore adaptive mechanism of microbes in diverse systems, but the advantages and limitations of different omics tools remain skeptical. Here, we reported distinct profiles in microbial secretory enzyme composition revealed by different omics methods. In general, the predicted function from metagenomic analysis decoupled from the expression of corresponding transcripts/proteins. Linking omics results to taxonomic origin, functional capability, substrate specificity, secretion preference, and enzymatic activity measurement suggested the substrate's source, concentration and stoichiometry impose strong filtering on the expression of extracellular enzymes, which may overwrite the genetic potentials. Our results present an integrated perspective on the need for multi-dimensional characterization of microbial adaptation in a changing environment.}, } @article {pmid38511950, year = {2024}, author = {Blais, M-A and Vincent, WF and Vigneron, A and Labarre, A and Matveev, A and Coelho, LF and Lovejoy, C}, title = {Diverse winter communities and biogeochemical cycling potential in the under-ice microbial plankton of a subarctic river-to-sea continuum.}, journal = {Microbiology spectrum}, volume = {12}, number = {5}, pages = {e0416023}, pmid = {38511950}, issn = {2165-0497}, support = {//Canada First Research Excellence Fund (CFREF)/ ; //Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; //ArcticNet/ ; //Canada Research Chairs (Chaires de recherche du Canada)/ ; //UL | Sentinelle Nord, Université Laval (Sentinel North)/ ; }, mesh = {*Rivers/microbiology ; *Seasons ; *Plankton/classification/genetics/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota/genetics ; Canada ; Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; RNA, Ribosomal, 18S/genetics ; }, abstract = {UNLABELLED: Winter conditions greatly alter the limnological properties of lotic ecosystems and the availability of nutrients, carbon, and energy resources for microbial processes. However, the composition and metabolic capabilities of winter microbial communities are still largely uncharacterized. Here, we sampled the winter under-ice microbiome of the Great Whale River (Nunavik, Canada) and its discharge plume into Hudson Bay. We used a combination of 16S and 18S rRNA gene amplicon analysis and metagenomic sequencing to evaluate the size-fractionated composition and functional potential of the microbial plankton. These under-ice communities were diverse in taxonomic composition and metabolically versatile in terms of energy and carbon acquisition, including the capacity to carry out phototrophic processes and degrade aromatic organic matter. Limnological properties, community composition, and metabolic potential differed between shallow and deeper sites in the river, and between fresh and brackish water in the vertical profile of the plume. Community composition also varied by size fraction, with a greater richness of prokaryotes in the larger size fraction (>3 µm) and of microbial eukaryotes in the smaller size fraction (0.22-3 µm). The freshwater communities included cosmopolitan bacterial genera that were previously detected in the summer, indicating their persistence over time in a wide range of physico-chemical conditions. These observations imply that the microbial communities of subarctic rivers and their associated discharge plumes retain a broad taxonomic and functional diversity throughout the year and that microbial processing of complex terrestrial materials persists beneath the ice during the long winter season.

IMPORTANCE: Microbiomes vary over multiple timescales, with short- and long-term changes in the physico-chemical environment. However, there is a scarcity of data and understanding about the structure and functioning of aquatic ecosystems during winter relative to summer. This is especially the case for seasonally ice-covered rivers, limiting our understanding of these ecosystems that are common throughout the boreal, subpolar, and polar regions. Here, we examined the winter under-ice microbiome of a Canadian subarctic river and its entry to the sea to characterize the taxonomic and functional features of the microbial community. We found substantial diversity in both composition and functional capabilities, including the capacity to degrade complex terrestrial compounds, despite the constraints imposed by a prolonged seasonal ice-cover and near-freezing water temperatures. This study indicates the ecological complexity and importance of winter microbiomes in ice-covered rivers and the coastal marine environment that they discharge into.}, } @article {pmid38510442, year = {2024}, author = {Mousa, WK and Abu-Izneid, T and Salah-Tantawy, A}, title = {High-throughput sequencing reveals the structure and metabolic resilience of desert microbiome confronting climate change.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1294173}, pmid = {38510442}, issn = {1664-462X}, abstract = {INTRODUCTION: Desert ecosystems harbor a unique microbial diversity that is crucial for ecological stability and biogeochemical cycles. An in-depth understanding of the biodiversity, compositions, and functions of these microbial communities is imperative to navigate global changes and confront potential threats and opportunities applicable to agricultural ecosystems amid climate change.

METHODS: This study explores microbial communities in the rhizosphere and endosphere of desert plants native to the Arabian Peninsula using next-generation sequencing of the 16S rRNA gene (V3-V4 hypervariable region).

RESULTS: Our results reveal that each microbial community has a diverse and unique microbial composition. Based on alpha and beta diversity indices, the rhizosphere microbiome is significantly diverse and richer in microbial taxa compared to the endosphere. The data reveals a shift towards fast-growing microbes with active metabolism, involvement in nutrient cycling, nitrogen fixation, and defense pathways. Our data reveals the presence of habitat-specific microbial communities in the desert, highlighting their remarkable resilience and adaptability to extreme environmental conditions. Notably, we observed the existence of radiation-resistant microbes such as Deinococcus radiotolerans, Kocuria sp., and Rubrobacter radiotolerans which can tolerate high levels of ionizing radiation. Additionally, examples of microbes exhibiting tolerance to challenging conditions include Nocardioides halotolerans, thriving in high-salinity environments, and hyperthermophilic microbes such as Quasibacillus thermotolerans. Moreover, functional analysis reveals enrichment in chaperon biosynthesis pathways associated with correct protein folding under heat stress conditions.

DISCUSSION: Our research sheds light on the unique diversity of desert microbes and underscores their potential applications to increase the resilience of agriculture ecosystems, offering a promising strategy to fortify crops against the challenges posed by climate change, ultimately supporting sustainable food production for our ever-expanding global population.}, } @article {pmid38508263, year = {2024}, author = {Sánchez-Marañón, M and Ortega, R and Pulido-Fernández, M and Barrena-González, J and Lavado-Contador, F and Miralles, I and García-Salcedo, JA and Soriano, M}, title = {Compositional and functional analysis of the bacterial community of Mediterranean Leptosols under livestock grazing.}, journal = {The Science of the total environment}, volume = {925}, number = {}, pages = {171811}, doi = {10.1016/j.scitotenv.2024.171811}, pmid = {38508263}, issn = {1879-1026}, mesh = {Animals ; *Ecosystem ; Livestock ; Soil Microbiology ; Bacteria/genetics ; *Microbiota ; Acidobacteria ; Soil/chemistry ; }, abstract = {The composition and functioning of soil bacterial communities, as well as their responses to multiple perturbations, are not well understood in the terrestrial ecosystems. Our study focuses on the bacterial community of erosive and poorly developed soils (Haplic Leptosols) in Mediterranean rangelands of Extremadura (W Spain) with different grazing intensities. Leptosols from similar natural conditions were selected and sampled at two depths to determine the soil properties as well as the structure and activity of bacterial communities. As grazing intensified, the soil C and N content increased, as did the number and diversity of bacteria, mainly of fast-growing lineages. Aridibacter, Acidobacteria Gp6 and Gp10, Gemmatimonas, and Segetibacter increased their abundance along the grazing-intensity gradient. Firmicutes such as Romboutsia and Turicibacter from livestock microbiome also increased. In functional terms, the KEGG pathways enriched in the soils with moderate and high grazing intensity were ABC transporters, DNA repair and recombination proteins, the two-component system, and the degradation of xenobiotics. All of these proved to be related to stronger cell division and response mechanisms to environmental stressors such as drought, warming, toxic substances, and nutrient deprivation. Consequently, the bacterial community was affected by grazing, but appeared to adapt and counteract the effects of a high grazing intensity. Therefore, a clearly detrimental effect of grazing was not detected in the bacterial community of the soils studied.}, } @article {pmid38506520, year = {2024}, author = {Lv, L-J and Wen, J-Y and Zhang, Y and Guo, R-C and Li, H and Yi, Z-T and He, T-W and Chen, M-C and Chen, Y and Wu, X-Y and Li, S-h and Kang, J and Hou, Y-P and Yan, Q-l and Yin, A-H}, title = {Deep metagenomic characterization of the gut virome in pregnant women with preeclampsia.}, journal = {mSphere}, volume = {9}, number = {4}, pages = {e0067623}, pmid = {38506520}, issn = {2379-5042}, support = {2019A1515110389//Guangdong Basic and Applied Basic Research Foundation/ ; 2019A1515111000//Guangdong Basic and Applied Baisc Research Foundation/ ; }, mesh = {Humans ; Female ; *Pre-Eclampsia/virology/microbiology ; Pregnancy ; *Gastrointestinal Microbiome/genetics ; *Virome/genetics ; Adult ; *Metagenomics ; *Feces/virology/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Viruses/genetics/classification/isolation & purification ; Metagenome ; }, abstract = {Preeclampsia (PE), a pregnancy-specific syndrome, has been associated with the gut bacteriome. Here, to investigate the impact of the gut virome on the development of PE, we identified over 8,000 nonredundant viruses from the fecal metagenomes of 40 early-onset PE and 37 healthy pregnant women and profiled their abundances. Comparison and correlation analysis showed that PE-enriched viruses frequently connected to Blautia species enriched in PE. By contrast, bacteria linked to PE-depleted viruses were often the Bacteroidaceae members such as Bacteroides spp., Phocaeicola spp., Parabacteroides spp., and Alistipes shahii. In terms of viral function, PE-depleted viruses had auxiliary metabolic genes that participated in the metabolism of simple and complex polysaccharides, sulfur metabolism, lipopolysaccharide biosynthesis, and peptidoglycan biosynthesis, while PE-enriched viruses had a gene encoding cyclic pyranopterin monophosphate synthase, which seemed to be special, that participates in the biosynthesis of the molybdenum cofactor. Furthermore, the classification model based on gut viral signatures was developed to discriminate PE patients from healthy controls and showed an area under the receiver operating characteristic curve of 0.922 that was better than that of the bacterium-based model. This study opens up new avenues for further research, providing valuable insights into the PE gut virome and offering potential directions for future mechanistic and therapeutic investigations, with the ultimate goal of improving the diagnosis and management of PE.IMPORTANCEThe importance of this study lies in its exploration of the previously overlooked but potentially critical role of the gut virome in preeclampsia (PE). While the association between PE and the gut bacteriome has been recognized, this research takes a pioneering step into understanding how the gut virome, represented by over 8,000 nonredundant viruses, contributes to this condition. The findings reveal intriguing connections between PE-enriched viruses and specific gut bacteria, such as the prevalence of Blautia species in individuals with PE, contrasting with bacteria linked to PE-depleted viruses, including members of the Bacteroidaceae family. These viral interactions and associations provide a deeper understanding of the complex dynamics at play in PE.}, } @article {pmid38505550, year = {2024}, author = {Yang, S and Zhang, W and Yang, B and Feng, X and Li, Y and Li, X and Liu, Q}, title = {Metagenomic evidence for antibiotic-associated actinomycetes in the Karamay Gobi region.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1330880}, pmid = {38505550}, issn = {1664-302X}, abstract = {Due to the misuse of antibiotics, there is an increasing emergence and spread of multidrug-resistant (MDR) bacteria, leading to a human health crisis. To address clinical antibiotic resistance and prevent/control pathogenic microorganisms, the development of novel antibiotics is essential. This also offers a new approach to discovering valuable actinobacterial flora capable of producing natural bioactive products. In this study, we employed bioinformatics and macro-genome sequencing to collect 15 soil samples from three different locations in the Karamay Gobi region. First, we assessed the diversity of microorganisms in soil samples from different locations, analyzing the content of bacteria, archaea, actinomycetes, and fungi. The biodiversity of soil samples from outside the Gobi was found to be higher than that of soil samples from within and in the center of the Gobi. Second, through microbial interaction network analysis, we identified actinomycetes as the dominant group in the system. We have identified the top four antibiotic genes, such as Ecol_fabG_TRC, Efac_liaR_DAP, tetA (58), and macB, by CARD. These genes are associated with peptide antibiotics, disinfecting agents and antiseptics, tetracycline antibiotics, and macrolide antibiotics. In addition, we also obtained 40 other antibiotic-related genes through CARD alignment. Through in-depth analysis of desert soil samples, we identified several unstudied microbial species belonging to different families, including Erythrobacteriaceae, Solirubrobacterales, Thermoleophilaceae, Gaiellaceae, Nocardioidaceae, Actinomycetia, Egibacteraceae, and Acidimicrobiales. These species have the capability to produce peptide antibiotics, macrolide antibiotics, and tetracycline antibiotics, as well as disinfectants and preservatives. This study provides valuable theoretical support for future in-depth research.}, } @article {pmid38504332, year = {2024}, author = {Wu, E and Mallawaarachchi, V and Zhao, J and Yang, Y and Liu, H and Wang, X and Shen, C and Lin, Y and Qiao, L}, title = {Contigs directed gene annotation (ConDiGA) for accurate protein sequence database construction in metaproteomics.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {58}, pmid = {38504332}, issn = {2049-2618}, support = {22022401//National Natural Science Foundation of China/ ; M-0614//Chinesisch-Deutsche Zentrum für Wissenschaftsförderung/ ; 2020YFF0304502//Ministry of Science and Technology of the People's Republic of China/ ; }, mesh = {Humans ; Databases, Protein ; Molecular Sequence Annotation ; Reproducibility of Results ; *Microbiota/genetics ; Metagenome/genetics ; Bacteria/genetics ; Metagenomics/methods ; }, abstract = {BACKGROUND: Microbiota are closely associated with human health and disease. Metaproteomics can provide a direct means to identify microbial proteins in microbiota for compositional and functional characterization. However, in-depth and accurate metaproteomics is still limited due to the extreme complexity and high diversity of microbiota samples. It is generally recommended to use metagenomic data from the same samples to construct the protein sequence database for metaproteomic data analysis. Although different metagenomics-based database construction strategies have been developed, an optimization of gene taxonomic annotation has not been reported, which, however, is extremely important for accurate metaproteomic analysis.

RESULTS: Herein, we proposed an accurate taxonomic annotation pipeline for genes from metagenomic data, namely contigs directed gene annotation (ConDiGA), and used the method to build a protein sequence database for metaproteomic analysis. We compared our pipeline (ConDiGA or MD3) with two other popular annotation pipelines (MD1 and MD2). In MD1, genes were directly annotated against the whole bacterial genome database; in MD2, contigs were annotated against the whole bacterial genome database and the taxonomic information of contigs was assigned to the genes; in MD3, the most confident species from the contigs annotation results were taken as reference to annotate genes. Annotation tools, including BLAST, Kaiju, and Kraken2, were compared. Based on a synthetic microbial community of 12 species, it was found that Kaiju with the MD3 pipeline outperformed the others in the construction of protein sequence database from metagenomic data. Similar performance was also observed with a fecal sample, as well as in silico mixed datasets of the simulated microbial community and the fecal sample.

CONCLUSIONS: Overall, we developed an optimized pipeline for gene taxonomic annotation to construct protein sequence databases. Our study can tackle the current taxonomic annotation reliability problem in metagenomics-derived protein sequence database and can promote the in-depth metaproteomic analysis of microbiome. The unique metagenomic and metaproteomic datasets of the 12 bacterial species are publicly available as a standard benchmarking sample for evaluating various analysis pipelines. The code of ConDiGA is open access at GitHub for the analysis of microbiota samples. Video Abstract.}, } @article {pmid38503977, year = {2024}, author = {Chang, HW and Lee, EM and Wang, Y and Zhou, C and Pruss, KM and Henrissat, S and Chen, RY and Kao, C and Hibberd, MC and Lynn, HM and Webber, DM and Crane, M and Cheng, J and Rodionov, DA and Arzamasov, AA and Castillo, JJ and Couture, G and Chen, Y and Balcazo, NP and Lebrilla, CB and Terrapon, N and Henrissat, B and Ilkayeva, O and Muehlbauer, MJ and Newgard, CB and Mostafa, I and Das, S and Mahfuz, M and Osterman, AL and Barratt, MJ and Ahmed, T and Gordon, JI}, title = {Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition.}, journal = {Nature microbiology}, volume = {9}, number = {4}, pages = {922-937}, pmid = {38503977}, issn = {2058-5276}, support = {F30 DK131866/DK/NIDDK NIH HHS/United States ; R01 DK030292/DK/NIDDK NIH HHS/United States ; K01 DK134840/DK/NIDDK NIH HHS/United States ; T32 GM007200/GM/NIGMS NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; F30 DK123838/DK/NIDDK NIH HHS/United States ; T32 DK007120/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Malnutrition ; *Microbiota ; *Prevotella ; Weight Gain ; }, abstract = {Microbiota-directed complementary food (MDCF) formulations have been designed to repair the gut communities of malnourished children. A randomized controlled trial demonstrated that one formulation, MDCF-2, improved weight gain in malnourished Bangladeshi children compared to a more calorically dense standard nutritional intervention. Metagenome-assembled genomes from study participants revealed a correlation between ponderal growth and expression of MDCF-2 glycan utilization pathways by Prevotella copri strains. To test this correlation, here we use gnotobiotic mice colonized with defined consortia of age- and ponderal growth-associated gut bacterial strains, with or without P. copri isolates closely matching the metagenome-assembled genomes. Combining gut metagenomics and metatranscriptomics with host single-nucleus RNA sequencing and gut metabolomic analyses, we identify a key role of P. copri in metabolizing MDCF-2 glycans and uncover its interactions with other microbes including Bifidobacterium infantis. P. copri-containing consortia mediated weight gain and modulated energy metabolism within intestinal epithelial cells. Our results reveal structure-function relationships between MDCF-2 and members of the gut microbiota of malnourished children with potential implications for future therapies.}, } @article {pmid38502869, year = {2024}, author = {Nelson, AR and Fegel, TS and Danczak, RE and Caiafa, MV and Roth, HK and Dunn, OI and Turvold, CA and Borch, T and Glassman, SI and Barnes, RT and Rhoades, CC and Wilkins, MJ}, title = {Soil microbiome feedbacks during disturbance-driven forest ecosystem conversion.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38502869}, issn = {1751-7370}, support = {DEB-2114868//National Science Foundation/ ; 2021-67019-34608//US Department of Agriculture National Institute of Food and Agriculture/ ; 21-1-01-49//US Bureau of Land Management Joint Fire Science Program Graduate Research Innovation/ ; //CSU Agricultural Experiment Station/ ; //Facilities Integrating Collaborations for User Science/ ; 504279//Joint Genome Institute/ ; //US Department of Energy Office of Science User Facility/ ; DE-AC02-05CH11231//Office of Biological and Environmental Research/ ; }, mesh = {Ecosystem ; Feedback ; Forests ; *Microbiota ; Soil/chemistry ; }, abstract = {Disturbances cause rapid changes to forests, with different disturbance types and severities creating unique ecosystem trajectories that can impact the underlying soil microbiome. Pile burning-the combustion of logging residue on the forest floor-is a common fuel reduction practice that can have impacts on forest soils analogous to those following high-severity wildfire. Further, pile burning following clear-cut harvesting can create persistent openings dominated by nonwoody plants surrounded by dense regenerating conifer forest. A paired 60-year chronosequence of burn scar openings and surrounding regenerating forest after clear-cut harvesting provides a unique opportunity to assess whether belowground microbial processes mirror aboveground vegetation during disturbance-induced ecosystem shifts. Soil ectomycorrhizal fungal diversity was reduced the first decade after pile burning, which could explain poor tree seedling establishment and subsequent persistence of herbaceous species within the openings. Fine-scale changes in the soil microbiome mirrored aboveground shifts in vegetation, with short-term changes to microbial carbon cycling functions resembling a postfire microbiome (e.g. enrichment of aromatic degradation genes) and respiration in burn scars decoupled from substrate quantity and quality. Broadly, however, soil microbiome composition and function within burn scar soils converged with that of the surrounding regenerating forest six decades after the disturbances, indicating potential microbial resilience that was disconnected from aboveground vegetation shifts. This work begins to unravel the belowground microbial processes that underlie disturbance-induced ecosystem changes, which are increasing in frequency tied to climate change.}, } @article {pmid38502690, year = {2024}, author = {Rosay, T and Jimenez, AG and Sperandio, V}, title = {Glucuronic acid confers colonization advantage to enteric pathogens.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {13}, pages = {e2400226121}, pmid = {38502690}, issn = {1091-6490}, support = {R01 AI053067/AI/NIAID NIH HHS/United States ; R01 AI154597/AI/NIAID NIH HHS/United States ; R01 AI155398/AI/NIAID NIH HHS/United States ; R37 AI053067/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Mice ; Escherichia coli/genetics ; Glucuronic Acid ; *Escherichia coli Infections/drug therapy/microbiology ; Virulence/physiology ; *Microbiota ; }, abstract = {Glucuronidation is a detoxification process to eliminate endo- and xeno-biotics and neurotransmitters from the host circulation. Glucuronosyltransferase binds these compounds to glucuronic acid (GlcA), deactivating them and allowing their elimination through the gastrointestinal (GI) tract. However, the microbiota produces β-glucuronidases that release GlcA and reactivate these compounds. Enteric pathogens such as enterohemorrhagic Escherichia coli (EHEC) and Citrobacter rodentium sense and utilize galacturonic acid (GalA), an isomer of GlcA, to outcompete the microbiota promoting gut colonization. However, the role of GlcA in pathogen colonization has not been explored. Here, we show that treatment of mice with a microbial β-glucuronidase inhibitor (GUSi) decreased C. rodentium's colonization of the GI tract, without modulating bacterial virulence or host inflammation. Metagenomic studies indicated that GUSi did not change the composition of the intestinal microbiota in these animals. GlcA confers an advantage for pathogen expansion through its utilization as a carbon source. Congruently mutants unable to catabolize GlcA depict lower GI colonization compared to wild type and are not sensitive to GUSi. Germfree mice colonized with a commensal E. coli deficient for β-glucuronidase production led to a decrease of C. rodentium tissue colonization, compared to animals monocolonized with an E. coli proficient for production of this enzyme. GlcA is not sensed as a signal and doesn't activate virulence expression but is used as a metabolite. Because pathogens can use GlcA to promote their colonization, inhibitors of microbial β-glucuronidases could be a unique therapeutic against enteric infections without disturbing the host or microbiota physiology.}, } @article {pmid38501864, year = {2024}, author = {Xiong, C and K Singh, B and Zhu, Y-G and Hu, H-W and Li, P-P and Han, Y-L and Han, L-L and Zhang, Q-B and Wang, J-T and Liu, S-Y and Wu, C-F and Ge, A-H and Zhang, L-M and He, J-Z}, title = {Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development.}, journal = {mSystems}, volume = {9}, number = {4}, pages = {e0105523}, pmid = {38501864}, issn = {2379-5077}, support = {XDA28020101//Chinese Academy of Sciences (CAS)/ ; 42277289//National Natural Science Foundation of China (NSFC)/ ; 42207142//National Natural Science Foundation of China (NSFC)/ ; DP210102081//Australian Research Council (ARC)/ ; }, mesh = {*Microbiota/genetics ; Agriculture ; Soil/chemistry ; Nitrogen/analysis ; Crops, Agricultural/metabolism ; Plant Development ; }, abstract = {Plant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N metabolism in plant microbiomes is largely limited. Here we examined the assembly and temporal dynamics of diazotrophic communities across multiple compartments (soils, epiphytic and endophytic niches of root and leaf, and grain) of three cereal crops (maize, wheat, and barley) and identified the potential N-cycling pathways in phylloplane microbiomes. Our results demonstrated that the microbial species pool, influenced by site-specific environmental factors (e.g., edaphic factors), had a stronger effect than host selection (i.e., plant species and developmental stage) in shaping diazotrophic communities across the soil-plant continuum. Crop diazotrophic communities were dominated by a few taxa (~0.7% of diazotrophic phylotypes) which were mainly affiliated with Methylobacterium, Azospirillum, Bradyrhizobium, and Rhizobium. Furthermore, eight dominant taxa belonging to Azospirillum and Methylobacterium were identified as keystone diazotrophic taxa for three crops and were potentially associated with microbial network stability and crop yields. Metagenomic binning recovered 58 metagenome-assembled genomes (MAGs) from the phylloplane, and the majority of them were identified as novel species (37 MAGs) and harbored genes potentially related to multiple N metabolism processes (e.g., nitrate reduction). Notably, for the first time, a high-quality MAG harboring genes involved in the complete denitrification process was recovered in the phylloplane and showed high identity to Pseudomonas mendocina. Overall, these findings significantly expand our understanding of ecological drivers of crop diazotrophs and provide new insights into the potential microbial N metabolism in the phyllosphere.IMPORTANCEPlants harbor diverse nitrogen-fixing microorganisms (i.e., diazotrophic communities) in both belowground and aboveground tissues, which play a vital role in plant nitrogen supply and growth promotion. Understanding the assembly and temporal dynamics of crop diazotrophic communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the site-specific microbial species pool largely shapes the structure of diazotrophic communities in the leaves and roots of three cereal crops. We further identify keystone diazotrophic taxa in crop microbiomes and characterize potential microbial N metabolism pathways in the phyllosphere, which provides essential information for developing microbiome-based tools in future sustainable agricultural production.}, } @article {pmid38499445, year = {2024}, author = {Russ, L and Andreo Jimenez, B and Nijhuis, E and Postma, J}, title = {Rhizoctonia solani disease suppression: addition of keratin-rich soil amendment leads to functional shifts in soil microbial communities.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {4}, pages = {}, pmid = {38499445}, issn = {1574-6941}, support = {TKI-AF-15261//Top Sector Agri and Food/ ; }, mesh = {Humans ; *Soil ; Keratins/pharmacology ; Soil Microbiology ; Plant Diseases/prevention & control/microbiology ; *Microbiota ; Anti-Bacterial Agents/pharmacology ; *Rhizoctonia ; }, abstract = {Promoting soil suppressiveness against soil borne pathogens could be a promising strategy to manage crop diseases. One way to increase the suppression potential in agricultural soils is via the addition of organic amendments. This microbe-mediated phenomenon, although not fully understood, prompted our study to explore the microbial taxa and functional properties associated with Rhizoctonia solani disease suppression in sugar beet seedlings after amending soil with a keratin-rich waste stream. Soil samples were analyzed using shotgun metagenomics sequencing. Results showed that both amended soils were enriched in bacterial families found in disease suppressive soils before, indicating that the amendment of keratin-rich material can support the transformation into a suppressive soil. On a functional level, genes encoding keratinolytic enzymes were found to be abundant in the keratin-amended samples. Proteins enriched in amended soils were those potentially involved in the production of secondary metabolites/antibiotics, motility, keratin-degradation, and contractile secretion system proteins. We hypothesize these taxa contribute to the amendment-induced suppression effect due to their genomic potential to produce antibiotics, secrete effectors via the contractile secretion system, and degrade oxalate-a potential virulence factor of R. solani-while simultaneously possessing the ability to metabolize keratin.}, } @article {pmid38499102, year = {2024}, author = {Gao, Y and Tariq, A and Zeng, F and Sardans, J and Graciano, C and Li, X and Wang, W and Peñuelas, J}, title = {Soil microbial functional profiles of P-cycling reveal drought-induced constraints on P-transformation in a hyper-arid desert ecosystem.}, journal = {The Science of the total environment}, volume = {925}, number = {}, pages = {171767}, doi = {10.1016/j.scitotenv.2024.171767}, pmid = {38499102}, issn = {1879-1026}, mesh = {*Ecosystem ; Soil ; Droughts ; Soil Microbiology ; *Microbiota ; Plants ; }, abstract = {Soil water conditions are known to influence soil nutrient availability, but the specific impact of different conditions on soil phosphorus (P) availability through the modulation of P-cycling functional microbial communities in hyper-arid desert ecosystems remains largely unexplored. To address this knowledge gap, we conducted a 3-year pot experiment using a typical desert plant species (Alhagi sparsifolia Shap.) subjected to two water supply levels (25 %-35 % and 65 %-75 % of maximum field capacity, MFC) and four P-supply levels (0, 1, 3, and 5 g P m[-2] y[-1]). Our investigation focused on the soil Hedley-P pool and the four major microbial groups involved in the critical phases of soil microbial P-cycling. The results revealed that the drought (25 %-35 % MFC) and no P-supply treatments reduced soil resin-P and NaHCO3-Pi concentrations by 87.03 % and 93.22 %, respectively, compared to the well-watered (65 %-75 % MFC) and high P-supply (5 g P m[-2] y[-1]) treatments. However, the P-supply treatment resulted in a 12 %-22 % decrease in the soil NH4[+]-N concentration preferred by microbes compared to the no P-supply treatment. Moreover, the abundance of genes engaged in microbial P-cycling (e.g. gcd and phoD) increased under the drought and no P-supply treatments (p < 0.05), suggesting that increased NH4[+]-N accumulation under these conditions may stimulate P-solubilizing microbes, thereby promoting the microbial community's investment in resources to enhance the P-cycling potential. Furthermore, the communities of Steroidobacter cummioxidans, Mesorhizobium alhagi, Devosia geojensis, and Ensifer sojae, associated with the major P-cycling genes, were enriched in drought and no or low-P soils. Overall, the drought and no or low-P treatments stimulated microbial communities and gene abundances involved in P-cycling. However, this increase was insufficient to maintain soil P-bioavailability. These findings shed light on the responses and feedback of microbial-mediated P-cycling behaviors in desert ecosystems under three-year drought and soil P-deficiency.}, } @article {pmid38497819, year = {2024}, author = {Sekeresova Kralova, J and Donic, C and Dassa, B and Livyatan, I and Jansen, PM and Ben-Dor, S and Fidel, L and Trzebanski, S and Narunsky-Haziza, L and Asraf, O and Brenner, O and Dafni, H and Jona, G and Boura-Halfon, S and Stettner, N and Segal, E and Brunke, S and Pilpel, Y and Straussman, R and Zeevi, D and Bacher, P and Hube, B and Shlezinger, N and Jung, S}, title = {Competitive fungal commensalism mitigates candidiasis pathology.}, journal = {The Journal of experimental medicine}, volume = {221}, number = {5}, pages = {}, pmid = {38497819}, issn = {1540-9538}, support = {696/21//Israeli Science Foundation/ ; //Weizmann Institute/ ; //Morris Kahn Institute for Human Immunology/ ; //Henry H. Drake Professorial Chair of Immunology/ ; 390713860//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; Animals ; Mice ; Symbiosis ; *Candidiasis ; *Gastrointestinal Microbiome ; Immunosuppression Therapy ; }, abstract = {The mycobiota are a critical part of the gut microbiome, but host-fungal interactions and specific functional contributions of commensal fungi to host fitness remain incompletely understood. Here, we report the identification of a new fungal commensal, Kazachstania heterogenica var. weizmannii, isolated from murine intestines. K. weizmannii exposure prevented Candida albicans colonization and significantly reduced the commensal C. albicans burden in colonized animals. Following immunosuppression of C. albicans colonized mice, competitive fungal commensalism thereby mitigated fatal candidiasis. Metagenome analysis revealed K. heterogenica or K. weizmannii presence among human commensals. Our results reveal competitive fungal commensalism within the intestinal microbiota, independent of bacteria and immune responses, that could bear potential therapeutic value for the management of C. albicans-mediated diseases.}, } @article {pmid38497257, year = {2024}, author = {Maritan, E and Quagliariello, A and Frago, E and Patarnello, T and Martino, ME}, title = {The role of animal hosts in shaping gut microbiome variation.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1901}, pages = {20230071}, pmid = {38497257}, issn = {1471-2970}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Microbiota ; Host Microbial Interactions ; Metagenomics ; }, abstract = {Millions of years of co-evolution between animals and their associated microbial communities have shaped and diversified the nature of their relationship. Studies continue to reveal new layers of complexity in host-microbe interactions, the fate of which depends on a variety of different factors, ranging from neutral processes and environmental factors to local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics and mathematical modelling to disentangle the individual contribution of ecological factors to microbiome evolution. Within this framework, host factors are known to be among the dominant drivers of microbiome composition in different animal species. However, the extent to which they shape microbiome assembly and evolution remains unclear. In this review, we summarize our understanding of how host factors drive microbial communities and how these dynamics are conserved and vary across taxa. We conclude by outlining key avenues for research and highlight the need for implementation of and key modifications to existing theory to fully capture the dynamics of host-associated microbiomes. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.}, } @article {pmid38493845, year = {2024}, author = {Sun, J and Zhang, X and Gong, X and Sun, Y and Zhang, S and Wang, F}, title = {Metagenomic analysis reveals gene taxonomic and functional diversity response to microplastics and cadmium in an agricultural soil.}, journal = {Environmental research}, volume = {251}, number = {Pt 2}, pages = {118673}, doi = {10.1016/j.envres.2024.118673}, pmid = {38493845}, issn = {1096-0953}, mesh = {*Soil Microbiology ; *Cadmium/toxicity/analysis ; *Soil Pollutants/toxicity/analysis ; *Microplastics/toxicity ; *Metagenomics ; Agriculture ; Microbiota/drug effects ; Soil/chemistry ; Bacteria/genetics/classification/drug effects ; }, abstract = {Both microplastics (MPs) and heavy metals are common soil pollutants and can interact to generate combined toxicity to soil ecosystems, but their impact on soil microbial communities (e.g., archaea and viruses) remains poorly studied. Here, metagenomic analysis was used to explore the response of soil microbiome in an agricultural soil exposed to MPs [i.e., polyethylene (PE), polystyrene (PS), and polylactic acid (PLA)] and/or Cd. Results showed that MPs had more profound effects on microbial community composition, diversity, and gene abundances when compared to Cd or their combination. Metagenomic analysis indicated that the gene taxonomic diversity and functional diversity of microbial communities varied with MPs type and dose. MPs affected the relative abundance of major microbial phyla and genera, while their coexistence with Cd influenced dominant fungi and viruses. Nitrogen-transforming and pathogenic genera, which were more sensitive to MPs variations, could serve as the indicative taxa for MPs contamination. High-dose PLA treatments (10%, w/w) not only elevated nitrogen metabolism and pathogenic genes, but also enriched copiotrophic microbes from the Proteobacteria phylum. Overall, MPs and Cd showed minimal interactions on soil microbial communities. This study highlights the microbial shifts due to co-occurring MPs and Cd, providing evidence for understanding their environmental risks.}, } @article {pmid38493232, year = {2024}, author = {Moreno-Pino, M and Manrique-de-la-Cuba, MF and López-Rodríguez, M and Parada-Pozo, G and Rodríguez-Marconi, S and Ribeiro, CG and Flores-Herrera, P and Guajardo, M and Trefault, N}, title = {Unveiling microbial guilds and symbiotic relationships in Antarctic sponge microbiomes.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6371}, pmid = {38493232}, issn = {2045-2322}, support = {3210656//ANID FONDECYT Postdoctoral Grant/ ; 21211164//ANID Doctoral Fellowships/ ; 21192150//ANID Doctoral Fellowships/ ; 21190286//ANID Doctoral Fellowships/ ; DG_02-22//INACH Grants/ ; DG_15-20//INACH Grants/ ; DG_12-20//INACH Grants/ ; RT_34-17//INACH Grants/ ; 1230758//ANID FONDECYT Grant/ ; }, mesh = {Animals ; *Porifera/microbiology ; Antarctic Regions ; Ammonia ; Archaea/genetics ; Bacteria/genetics ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Marine sponges host diverse microbial communities. Although we know many of its ecological patterns, a deeper understanding of the polar sponge holobiont is still needed. We combine high-throughput sequencing of ribosomal genes, including the largest taxonomic repertoire of Antarctic sponge species analyzed to date, functional metagenomics, and metagenome-assembled genomes (MAGs). Our findings show that sponges harbor more exclusive bacterial and archaeal communities than seawater, while microbial eukaryotes are mostly shared. Furthermore, bacteria in Antarctic sponge holobionts establish more cooperative interactions than in sponge holobionts from other environments. The bacterial classes that established more positive relations were Bacteroidia, Gamma- and Alphaproteobacteria. Antarctic sponge microbiomes contain microbial guilds that encompass ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and sulfur-oxidizing bacteria. The retrieved MAGs showed a high level of novelty and streamlining signals and belong to the most abundant members of the main microbial guilds in the Antarctic sponge holobiont. Moreover, the genomes of these symbiotic bacteria contain highly abundant functions related to their adaptation to the cold environment, vitamin production, and symbiotic lifestyle, helping the holobiont survive in this extreme environment.}, } @article {pmid38492594, year = {2024}, author = {Lienhart, PH and Rohra, V and Clement, C and Toppen, LC and DeCola, AC and Rizzo, DM and Scarborough, MJ}, title = {Landfill intermediate cover soil microbiomes and their potential for mitigating greenhouse gas emissions revealed through metagenomics.}, journal = {The Science of the total environment}, volume = {925}, number = {}, pages = {171697}, doi = {10.1016/j.scitotenv.2024.171697}, pmid = {38492594}, issn = {1879-1026}, mesh = {*Greenhouse Gases ; Nitrous Oxide/analysis ; Ammonia ; Soil ; Waste Disposal Facilities ; *Microbiota ; Methane/analysis ; Soil Microbiology ; }, abstract = {Landfills are a major source of anthropogenic methane emissions and have been found to produce nitrous oxide, an even more potent greenhouse gas than methane. Intermediate cover soil (ICS) plays a key role in reducing methane emissions but may also result in nitrous oxide production. To assess the potential for microbial methane oxidation and nitrous oxide production, long sequencing reads were generated from ICS microbiome DNA and reads were functionally annotated for 24 samples across ICS at a large landfill in New York. Further, incubation experiments were performed to assess methane consumption and nitrous oxide production with varying amounts of ammonia supplemented. Methane was readily consumed by microbes in the composite ICS and all incubations with methane produced small amounts of nitrous oxide even when ammonia was not supplemented. Incubations without methane produced significantly less nitrous oxide than those incubated with methane. In incubations with methane added, the observed specific rate of methane consumption was 0.776 +/- 0.055 μg CH4 g dry weight (DW) soil[-1] h[-1] and the specific rate of nitrous oxide production was 3.64 × 10[-5] +/- 1.30 × 10[-5] μg N2O g DW soil[-1] h[-1]. The methanotrophs Methylobacter and an unclassified genus within the family Methlyococcaceae were present in the original ICS samples and the incubation samples, and their abundance increased during incubations with methane. Genes encoding particulate methane monooxygenase/ ammonia monooxygenase (pMMO) were much more abundant than genes encoding soluble methane monooxygenase (sMMO) across the landfill ICS. Genes encoding proteins that convert hydroxylamine to nitrous oxide were not highly abundant in the ICS or incubation metagenomes. In total, these results suggest that although ammonia oxidation via methanotrophs may result in low levels of nitrous oxide production, ICS microbial communities have the potential to greatly reduce the overall global warming potential of landfill emissions.}, } @article {pmid38491814, year = {2024}, author = {Malakar, S and Sutaoney, P and Madhyastha, H and Shah, K and Chauhan, NS and Banerjee, P}, title = {Understanding gut microbiome-based machine learning platforms: A review on therapeutic approaches using deep learning.}, journal = {Chemical biology & drug design}, volume = {103}, number = {3}, pages = {e14505}, doi = {10.1111/cbdd.14505}, pmid = {38491814}, issn = {1747-0285}, mesh = {Humans ; *Gastrointestinal Microbiome ; Artificial Intelligence ; *Deep Learning ; *Microbiota/genetics ; Machine Learning ; }, abstract = {Human beings possess trillions of microbial cells in a symbiotic relationship. This relationship benefits both partners for a long time. The gut microbiota helps in many bodily functions from harvesting energy from digested food to strengthening biochemical barriers of the gut and intestine. But the changes in microbiota composition and bacteria that can enter the gastrointestinal tract can cause infection. Several approaches like culture-independent techniques such as high-throughput and meta-omics projects targeting 16S ribosomal RNA (rRNA) sequencing are popular methods to investigate the composition of the human gastrointestinal tract microbiota and taxonomically characterizing microbial communities. The microbiota conformation and diversity should be provided by whole-genome shotgun metagenomic sequencing of site-specific community DNA associating genome mapping, gene inventory, and metabolic remodelling and reformation, to ease the functional study of human microbiota. Preliminary examination of the therapeutic potency for dysbiosis-associated diseases permits investigation of pharmacokinetic-pharmacodynamic changes in microbial communities for escalation of treatment and dosage plan. Gut microbiome study is an integration of metagenomics which has influenced the field in the last two decades. And the incorporation of artificial intelligence and deep learning through "omics-based" methods and microfluidic evaluation enhanced the capability of identification of thousands of microbes.}, } @article {pmid38491422, year = {2024}, author = {Martínez-Álvaro, M and Mattock, J and González-Recio, Ó and Saborío-Montero, A and Weng, Z and Lima, J and Duthie, CA and Dewhurst, R and Cleveland, MA and Watson, M and Roehe, R}, title = {Including microbiome information in a multi-trait genomic evaluation: a case study on longitudinal growth performance in beef cattle.}, journal = {Genetics, selection, evolution : GSE}, volume = {56}, number = {1}, pages = {19}, pmid = {38491422}, issn = {1297-9686}, support = {BBSRC BB/N01720X/1//BBRSC/ ; BB/N016742/1//UKRI/ ; BB/S006567/1//UKRI/ ; BB/S006680/1//UKRI/ ; }, mesh = {Cattle/genetics ; Animals ; Phenotype ; *Genomics ; Body Weight ; Metagenome ; *Microbiota ; Animal Feed ; }, abstract = {BACKGROUND: Growth rate is an important component of feed conversion efficiency in cattle and varies across the different stages of the finishing period. The metabolic effect of the rumen microbiome is essential for cattle growth, and investigating the genomic and microbial factors that underlie this temporal variation can help maximize feed conversion efficiency at each growth stage.

RESULTS: By analysing longitudinal body weights during the finishing period and genomic and metagenomic data from 359 beef cattle, our study demonstrates that the influence of the host genome on the functional rumen microbiome contributes to the temporal variation in average daily gain (ADG) in different months (ADG1, ADG2, ADG3, ADG4). Five hundred and thirty-three additive log-ratio transformed microbial genes (alr-MG) had non-zero genomic correlations (rg) with at least one ADG-trait (ranging from |0.21| to |0.42|). Only a few alr-MG correlated with more than one ADG-trait, which suggests that a differential host-microbiome determinism underlies ADG at different stages. These alr-MG were involved in ribosomal biosynthesis, energy processes, sulphur and aminoacid metabolism and transport, or lipopolysaccharide signalling, among others. We selected two alternative subsets of 32 alr-MG that had a non-uniform or a uniform rg sign with all the ADG-traits, regardless of the rg magnitude, and used them to develop a microbiome-driven breeding strategy based on alr-MG only, or combined with ADG-traits, which was aimed at shaping the rumen microbiome towards increased ADG at all finishing stages. Combining alr-MG information with ADG records increased prediction accuracy of genomic estimated breeding values (GEBV) by 11 to 22% relative to the direct breeding strategy (using ADG-traits only), whereas using microbiome information, only, achieved lower accuracies (from 7 to 41%). Predicted selection responses varied consistently with accuracies. Restricting alr-MG based on their rg sign (uniform subset) did not yield a gain in the predicted response compared to the non-uniform subset, which is explained by the absence of alr-MG showing non-zero rg at least with more than one of the ADG-traits.

CONCLUSIONS: Our work sheds light on the role of the microbial metabolism in the growth trajectory of beef cattle at the genomic level and provides insights into the potential benefits of using microbiome information in future genomic breeding programs to accurately estimate GEBV and increase ADG at each finishing stage in beef cattle.}, } @article {pmid38490631, year = {2024}, author = {Hu, M and Sardans, J and Sun, D and Yan, R and Wu, H and Ni, R and Peñuelas, J}, title = {Microbial diversity and keystone species drive soil nutrient cycling and multifunctionality following mangrove restoration.}, journal = {Environmental research}, volume = {251}, number = {Pt 2}, pages = {118715}, doi = {10.1016/j.envres.2024.118715}, pmid = {38490631}, issn = {1096-0953}, mesh = {*Wetlands ; *Soil Microbiology ; Soil/chemistry ; Microbiota ; Nitrogen Cycle ; Phosphorus/metabolism ; Biodiversity ; Nitrogen/metabolism ; Environmental Restoration and Remediation/methods ; Bacteria/classification/metabolism/genetics ; }, abstract = {Vegetation restoration exerts transformative effects on nutrient cycling, microbial communities, and ecosystem functions. While extensive research has been conducted on the significance of mangroves and their restoration efforts, the effectiveness of mangrove restoration in enhancing soil multifunctionality in degraded coastal wetlands remains unclear. Herein, we carried out a field experiment to explore the impacts of mangrove restoration and its chronosequence on soil microbial communities, keystone species, and soil multifunctionality, using unrestored aquaculture ponds as controls. The results revealed that mangrove restoration enhanced soil multifunctionality, with these positive effects progressively amplifying over the restoration chronosequence. Furthermore, mangrove restoration led to a substantial increase in microbial diversity and a reshaping of microbial community composition, increasing the relative abundance of dominant phyla such as Nitrospirae, Deferribacteres, and Fusobacteria. Soil multifunctionality exhibited positive correlations with microbial diversity, suggesting a link between variations in microbial diversity and soil multifunctionality. Metagenomic screening demonstrated that mangrove restoration resulted in a simultaneous increase in the abundance of nitrogen (N) related genes, such as N fixation (nirD/H/K), nitrification (pmoA-amoA/B/C), and denitrification (nirK, norB/C, narG/H, napA/B), as well as phosphorus (P)-related genes, including organic P mineralization (phnX/W, phoA/D/G, phnJ/N/P), inorganic P solubilization (gcd, ppx-gppA), and transporters (phnC/D/E, pstA/B/C/S)). The relationship between the abundance of keystone species (such as phnC/D/E) and restoration-induced changes in soil multifunctionality indicates that mangrove restoration enhances soil multifunctionality through an increase in the abundance of keystone species associated with N and P cycles. Additionally, it was observed that changes in microbial community and multifunctionality were largely associated with shifts in soil salinity. These findings demonstrate that mangrove restoration positively influences soil multifunctionality and shapes nutrient dynamics, microbial communities, and overall ecosystem resilience. As global efforts continue to focus on ecosystem restoration, understanding the complexity of mangrove-soil interactions is critical for effective nutrient management and mangrove conservation.}, } @article {pmid38489588, year = {2024}, author = {David, G and Bertolotti, A and Layer, R and Scofield, D and Hayward, A and Baril, T and Burnett, HA and Gudmunds, E and Jensen, H and Husby, A}, title = {Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations.}, journal = {Genome biology and evolution}, volume = {16}, number = {4}, pages = {}, pmid = {38489588}, issn = {1759-6653}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Genomics ; *Genome ; Metagenomics ; Polymorphism, Single Nucleotide ; }, abstract = {Comprehensive characterization of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation, reproducible and high-confidence structural variation callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus). To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of structural variants is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analyzing short-read-discovered structural variation data sets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence structural variation callsets.}, } @article {pmid38488837, year = {2024}, author = {Wang, F and Liu, X and Huang, F and Zhou, Y and Wang, X and Song, Z and Wang, S and Wang, X and Shi, D and Ruan, G and Ji, X and Zhang, E and Tan, Z and Ye, Y and Wang, C and Zhu, J and Wang, W}, title = {Gut microbiota-derived gamma-aminobutyric acid from metformin treatment reduces hepatic ischemia/reperfusion injury through inhibiting ferroptosis.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {38488837}, issn = {2050-084X}, support = {2022R413C074//Zhejiang University Student Science and Technology Innovation Activity Plan/ ; LGF22H030011//Zhejiang Province Public Welfare Technology Application Research Project/ ; KJHX2212//Suzhou Inhale Pharma Co, Ltd/ ; KJHX2202//Zhejiang Xiaolun Intelligent Manufacturing Co, Ltd/ ; }, mesh = {Humans ; Mice ; Animals ; *Metformin/pharmacology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; *Ferroptosis ; *Reperfusion Injury/drug therapy/metabolism ; Ischemia ; gamma-Aminobutyric Acid/pharmacology ; }, abstract = {Hepatic ischemia/reperfusion injury (HIRI) is a common and inevitable factor leading to poor prognosis in various liver diseases, making the outcomes of current treatments in clinic unsatisfactory. Metformin has been demonstrated to be beneficial to alleviate HIRI in recent studies, however, the underpinning mechanism remains unclear. In this study, we found metformin mitigates HIRI-induced ferroptosis through reshaped gut microbiota in mice, which was confirmed by the results of fecal microbiota transplantation treatment but showed the elimination of the beneficial effects when gut bacteria were depleted using antibiotics. Detailedly, through 16S rRNA and metagenomic sequencing, we identified that the metformin-reshaped microbiota was characterized by the increase of gamma-aminobutyric acid (GABA) producing bacteria. This increase was further confirmed by the elevation of GABA synthesis key enzymes, glutamic acid decarboxylase and putrescine aminotransferase, in gut microbes of metformin-treated mice and healthy volunteers. Furthermore, the benefit of GABA against HIRI-induced ferroptosis was demonstrated in GABA-treated mice. Collectively, our data indicate that metformin can mitigate HIRI-induced ferroptosis by reshaped gut microbiota, with GABA identified as a key metabolite.}, } @article {pmid38486264, year = {2024}, author = {Lian, Q and Song, X and Yang, J and Wang, L and Xu, P and Wang, X and Xu, X and Yang, B and He, J and Ju, C}, title = {Alterations of lung microbiota in lung transplant recipients with pneumocystis jirovecii pneumonia.}, journal = {Respiratory research}, volume = {25}, number = {1}, pages = {125}, pmid = {38486264}, issn = {1465-993X}, support = {ZNSA-2020013//Zhongnanshan Medical Foundation of Guangdong Province/ ; SKLRHQN20205//State Key Laboratory of Respiratory Disease/Guangzhou Institute of Respiratory Health/National Center for Respiratory Medicine/ ; 2023C-TS10//Specific Clinical Technology Project of Guangzhou City/ ; 2022A1515012216//Natural Science Foundation of Guangdong Province/ ; 202201020371//Basic Research Program of Guangzhou Institute of Respiratory Health/ ; }, mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis/complications ; Transplant Recipients ; CD8-Positive T-Lymphocytes ; *Pneumocystis carinii/genetics ; *Microbiota ; Lung ; }, abstract = {BACKGROUND: Increasing evidence revealed that lung microbiota dysbiosis was associated with pulmonary infection in lung transplant recipients (LTRs). Pneumocystis jirovecii (P. jirovecii) is an opportunistic fungal pathogen that frequently causes lethal pneumonia in LTRs. However, the lung microbiota in LTRs with P. jirovecii pneumonia (PJP) remains unknow.

METHODS: In this prospective observational study, we performed metagenomic next-generation sequencing (mNGS) on 72 bronchoalveolar lavage fluid (BALF) samples from 61 LTRs (20 with PJP, 22 with PJC, 19 time-matched stable LTRs, and 11 from LTRs after PJP recovery). We compared the lung microbiota composition of LTRs with and without P. jirovecii, and analyzed the related clinical variables.

RESULTS: BALFs collected at the episode of PJP showed a more discrete distribution with a lower species diversity, and microbiota composition differed significantly compared to P. jirovecii colonization (PJC) and control group. Human gammaherpesvirus 4, Phreatobacter oligotrophus, and Pseudomonas balearica were the differential microbiota species between the PJP and the other two groups. The network analysis revealed that most species had a positive correlation, while P. jirovecii was correlated negatively with 10 species including Acinetobacter venetianus, Pseudomonas guariconensis, Paracandidimonas soli, Acinetobacter colistiniresistens, and Castellaniella defragrans, which were enriched in the control group. The microbiota composition and diversity of BALF after PJP recovery were also different from the PJP and control groups, while the main components of the PJP recovery similar to control group. Clinical variables including age, creatinine, total protein, albumin, IgG, neutrophil, lymphocyte, CD3[+]CD45[+], CD3[+]CD4[+] and CD3[+]CD8[+] T cells were deeply implicated in the alterations of lung microbiota in LTRs.

CONCLUSIONS: This study suggests that LTRs with PJP had altered lung microbiota compared to PJC, control, and after recovery groups. Furthermore, lung microbiota is related to age, renal function, nutritional and immune status in LTRs.}, } @article {pmid38485151, year = {2024}, author = {Frayman, KB and Macowan, M and Caparros-Martin, J and Ranganathan, SC and Marsland, BJ and , }, title = {The longitudinal microbial and metabolic landscape of infant cystic fibrosis: the gut-lung axis.}, journal = {The European respiratory journal}, volume = {63}, number = {5}, pages = {}, doi = {10.1183/13993003.02290-2023}, pmid = {38485151}, issn = {1399-3003}, mesh = {Humans ; *Cystic Fibrosis/microbiology/metabolism ; Infant ; *Bronchoalveolar Lavage Fluid/microbiology ; *Feces/microbiology ; Male ; Female ; *RNA, Ribosomal, 16S/genetics ; *Lung/microbiology/metabolism ; Infant, Newborn ; *Gastrointestinal Microbiome ; Longitudinal Studies ; Case-Control Studies ; Metabolome ; Metabolomics ; Anti-Bacterial Agents/therapeutic use ; Child, Preschool ; }, abstract = {BACKGROUND AND AIM: In cystic fibrosis, gastrointestinal dysfunction and lower airway infection occur early and are independently associated with poorer outcomes in childhood. This study aimed to define the relationship between the microbiota at each niche during the first 2 years of life, its association with growth and airway inflammation, and explanatory features in the metabolome.

MATERIALS AND METHODS: 67 bronchoalveolar lavage fluid (BALF), 62 plasma and 105 stool samples were collected from 39 infants with cystic fibrosis between 0 and 24 months who were treated with prophylactic antibiotics. 16S rRNA amplicon and shotgun metagenomic sequencing were performed on BALF and stool samples, respectively; metabolomic analyses were performed on all sample types. Sequencing data from healthy age-matched infants were used as controls.

RESULTS: Bacterial diversity increased over the first 2 years in both BALF and stool, and microbial maturation was delayed in comparison to healthy controls from the RESONANCE cohort. Correlations between their respective abundance in both sites suggest stool may serve as a noninvasive alternative for detecting BALF Pseudomonas and Veillonella. Multisite metabolomic analyses revealed age- and growth-related changes, associations with neutrophilic airway inflammation, and a set of core systemic metabolites. BALF Pseudomonas abundance was correlated with altered stool microbiome composition and systemic metabolite alterations, highlighting a complex gut-plasma-lung interplay and new targets with therapeutic potential.

CONCLUSION: Exploration of the gut-lung microbiome and metabolome reveals diverse multisite interactions in cystic fibrosis that emerge in early life. Gut-lung metabolomic links with airway inflammation and Pseudomonas abundance warrant further investigation for clinical utility, particularly in non-expectorating patients.}, } @article {pmid38485093, year = {2024}, author = {Riva, A and Sahin, E and Volpedo, G and Petretto, A and Lavarello, C and Di Sapia, R and Barbarossa, D and Zaniani, NR and Craparotta, I and Barbera, MC and Sezerman, U and Vezzani, A and Striano, P and Ravizza, T}, title = {Identification of an epilepsy-linked gut microbiota signature in a pediatric rat model of acquired epilepsy.}, journal = {Neurobiology of disease}, volume = {194}, number = {}, pages = {106469}, doi = {10.1016/j.nbd.2024.106469}, pmid = {38485093}, issn = {1095-953X}, mesh = {Humans ; Child ; Rats ; Animals ; *Gastrointestinal Microbiome ; *Epilepsy ; *Status Epilepticus ; Seizures ; Inflammation ; }, abstract = {A dysfunctional gut microbiota-brain axis is emerging as a potential pathogenic mechanism in epilepsy, particularly in pediatric forms of epilepsy. To add new insights into gut-related changes in acquired epilepsy that develops early in life, we used a multi-omics approach in a rat model with a 56% incidence of epilepsy. The presence of spontaneous seizures was assessed in adult rats (n = 46) 5 months after status epilepticus induced by intra-amygdala kainate at postnatal day 13, by 2 weeks (24/7) ECoG monitoring. Twenty-six rats developed epilepsy (Epi) while the remaining 20 rats (No-Epi) did not show spontaneous seizures. At the end of ECoG monitoring, all rats and their sham controls (n = 20) were sacrificed for quantitative histopathological and immunohistochemical analyses of the gut structure, glia and macrophages, as well as RTqPCR analysis of inflammation/oxidative stress markers. By comparing Epi, No-Epi rats, and sham controls, we found structural, cellular, and molecular alterations reflecting a dysfunctional gut, which were specifically associated with epilepsy. In particular, the villus height-to-crypt depth ratio and number of Goblet cells were reduced in the duodenum of Epi rats vs both No-Epi rats and sham controls (p < 0.01). Villus height and crypt depth in the duodenum and jejunum (p < 0.01) were increased in No-Epi vs both Epi and sham controls. We also detected enhanced Iba1-positive macrophages, together with increased IL1b and NFE2L2 transcripts and TNF protein, in the small intestine of Epi vs both No-Epi and sham control rats (p < 0.01), denoting the presence of inflammation and oxidative stress. Astroglial GFAP-immunostaining was similar in all experimental groups. Metagenomic analysis in the feces collected 5 months after status epilepticus showed that the ratio of two dominant phyla (Bacteroidota-to-Firmicutes) was similarly increased in Epi and No-Epi rats vs sham control rats. Notably, the relative abundance of families, genera, and species associated with SCFA production differed in Epi vs No-Epi rats, describing a bacterial imprint associated with epilepsy. Furthermore, Epi rats showed a blood metabolic signature characterized by changes in lipid metabolism compared to both No-Epi and sham control rats. Our study provides new evidence of long-term gut alterations, along with microbiota-related metabolic changes, occurring specifically in rats that develop epilepsy after brain injury early in life.}, } @article {pmid38485002, year = {2024}, author = {Zhao, T and Huang, S and Zhang, Y and Chow, AT and Chen, P and Wang, Y and Lu, Y and Xiong, J}, title = {Removal of sulfur and nitrogen pollutants in a sediment microbial fuel cell coupled with Vallisneria natans: Efficiency, microbial community structure, and functional genes.}, journal = {Chemosphere}, volume = {354}, number = {}, pages = {141667}, doi = {10.1016/j.chemosphere.2024.141667}, pmid = {38485002}, issn = {1879-1298}, mesh = {*Bioelectric Energy Sources ; Nitrogen/metabolism ; Geologic Sediments/chemistry ; Water/chemistry ; *Microbiota ; Sulfur ; Denitrification ; }, abstract = {The rapid development of the economy has led to an increase in the sulfur and nitrogen load in surface water, which has the potential to cause river eutrophication and the emission of malodorous gases. A lab-scale sediment microbial fuel cell coupled with Vallisneria natans (P-SMFC) was designed for surface water remediation. The enhancement of pollutant removal performance of P-SMFC was evaluated in contrast to the SMFC system without plants (SMFC), the open-circuit control system with plants (C-P), and the open-circuit control system without plants (C-S), while illustrating the mechanisms of the sulfur and nitrogen transformation process. The results demonstrated that the effluent and sediment of P-SMFC had lower concentrations of sulfide compared to other systems. Furthermore, P-SMFC exhibited higher removal efficiency for COD (73.1 ± 8.7%), NH4[+]-N (80.5 ± 19.8%), and NO3[-]-N (88.5 ± 11.8%) compared to other systems. The closed-circuit conditions and growth of Vallisneria natans create a favorable ecological niche for functional microorganisms involved in power generation, sulfur oxidation, and nitrogen transformation. Additionally, metagenomic analysis revealed that multifunctional bacteria possessing both denitrification and sulfur oxidation genes, such as Thiobacillus, Dechloromonas, and Bacillus, may play simultaneous roles in metabolizing sulfur and nitrogen, thus serving as integral factors in maintaining the performance of P-SMFC. In summary, these findings provide a theoretical reference for the concurrent enhancement of sulfur and nitrogen pollutants removal in P-SMFC and will facilitate its practical application in the remediation of contaminated surface water.}, } @article {pmid38484575, year = {2024}, author = {Deepa, N and Chauhan, S and Singh, A}, title = {Unraveling the functional characteristics of endophytic bacterial diversity for plant growth promotion and enhanced secondary metabolite production in Pelargonium graveolens.}, journal = {Microbiological research}, volume = {283}, number = {}, pages = {127673}, doi = {10.1016/j.micres.2024.127673}, pmid = {38484575}, issn = {1618-0623}, mesh = {*Pelargonium ; Bacteria ; Endophytes ; Firmicutes ; Plants ; *Microbiota ; Plant Roots/microbiology ; }, abstract = {The rich diversity of microbial endophytic communities associated with plants, often referred to as the second genome, serves as a compelling illustration of efficient co-evolution. This noteworthy partnership plays a pivotal role in sustaining plant well-being and enhancing plant adaptability across diverse habitats. Therefore, examining the diversity of endophytic microbes associated with their particular host plant is valuable for gaining insights into the vast spectrum of plant-microbe interactions. The present experiments aimed at investigating the bacterial endophytic diversity in both root and shoot tissues of Pelargonium graveolens, employing culture dependent and culture independent high-throughput metagenomics approach. A total of 614 and 620 operational taxonomic units (OTUs), encompassing 291 and 229 genera, were identified in the shoot and root tissues of P. graveolens, respectively. Furthermore, the subsequent classification of OTUs revealed 15 highly abundant phyla, with Proteobacteria dominating both root and shoot tissues. Notably, an exceptionally high abundance of Firmicutes phyla was observed in the shoot compared to the root. Additionally, 30 bacterial endophytes from the root, stem, petiole, and leaves were isolated and molecularly characterized, unveiling a consistent pattern of diversity distribution between the root and shoot of P. graveolens. Upon screening all isolates for plant growth promoting traits, Pseudomonas oryzihabitans was found to be positive for major biochemical test like nitrogen fixation, phosphate solubilization etc. and on inoculation resulted in about two-fold increase in content of essential oil accompanied by a significant rise in the geraniol and citronellol content. Diving deep into the genetic constitution of P. oryzihabitans unveiled a substantial number of genes directly and indirectly contributing to the endophyte's capability in colonizing host plants effectively. In summary, data obtained from metagenomics and culture dependent approaches including glass house trials suggest potential bacterial endophytes suitable for field applications for yield enhancement and in planta secondary metabolite enhancement investigations.}, } @article {pmid38483744, year = {2024}, author = {Bharathi Rathinam, R and Tripathi, G and Das, BK and Jain, R and Acharya, A}, title = {Comparative analysis of gut microbiome in Pangasionodon hypopthalmus and Labeo catla during health and disease.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {27}, number = {5}, pages = {1557-1571}, pmid = {38483744}, issn = {1618-1905}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; *Catfishes/microbiology ; *Fish Diseases/microbiology ; Phylogeny ; Aeromonas hydrophila/isolation & purification/genetics/classification/pathogenicity ; Gram-Negative Bacterial Infections/veterinary/microbiology ; Metagenomics ; DNA, Bacterial/genetics ; }, abstract = {The present study was conducted to study the composition of gut microbiome in the advanced fingerling and fingerling stage of striped pangasius catfish and catla during healthy and diseased conditions. Healthy pangasius and catla fishes were obtained from commercial farms and injected with the LD50 dose of A. hydrophila. The intestinal samples from the control and injected group were collected and pooled for 16 s metagenomic analysis. Community analysis was performed by targeting the 16 s rRNA gene to explore and compare the gut microbiota composition of these fishes. The operational taxonomic units (OTUs) consisted of four major phyla: Bacteroidia, Proteobacteria, Firmicutes, and Actinobacteria. Alpha and beta diversity indices were carried out to understand the diversity of microbes within and between a sample. While comparing the advanced fingerling and fingerling stage gut microbiome of Pangasius catfish, the dominance of Proteobacteria was found in fingerlings, whereas Firmicutes and Bacteroides were found in advanced fingerlings. In catla, Proteobacteria and Bacteroides were predominant. Taxonomic abundance of the microbiota in control and diseased Pangasius and catla fishes at phylum, class, order, family, genus, and species levels were also depicted. The present study is the first of its kind, and it will help to identify the diversity of novel potential bacterial species involved in disease protection of fishes. It can lead to the development of sustainable prophylactic measures against (re-)emerging bacterial diseases in aquaculture.}, } @article {pmid38482731, year = {2024}, author = {Jiang, S and Du, L and Zhao, Q and Su, S and Huang, S and Zhang, J}, title = {Tropical postbiotics alleviate the disorders in the gut microbiota and kidney damage induced by ochratoxin A exposure.}, journal = {Food & function}, volume = {15}, number = {8}, pages = {3980-3992}, doi = {10.1039/d3fo05213c}, pmid = {38482731}, issn = {2042-650X}, mesh = {*Ochratoxins/toxicity ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Kidney/drug effects/metabolism ; Mice ; Male ; Kidney Diseases/chemically induced/metabolism ; NF-E2-Related Factor 2/metabolism ; Mice, Inbred C57BL ; Humans ; Reactive Oxygen Species/metabolism ; }, abstract = {Ochratoxin A (OTA), commonly found in various foods, significantly impacts the health of humans and animals, especially their kidneys. Our study explores OTA's effects on the gut microbiota and kidney damage while examining how postbiotics offer protection. Using metagenomic sequencing, we observed that OTA increased the potential gut pathogens such as Alistipes, elevating detrimental metabolites and inflammation. Also, OTA inhibited the Nrf2/HO-1 pathway, reducing kidney ROS elimination and leading to cellular ferroptosis and subsequent kidney damage. Postbiotics mitigate OTA's effects by downregulating the abundance of the assimilatory sulfate reduction IV pathway and virulence factors associated with iron uptake and relieving the inhibition of OTA on Nrf2/HO-1, restoring ROS-clearing capabilities and thereby alleviating chronic OTA-induced kidney damage. Understanding the OTA-gut-kidney link provides new approaches for preventing kidney damage, with postbiotics showing promise as a preventive treatment.}, } @article {pmid38480867, year = {2024}, author = {Fronton, F and Villemur, R and Robert, D and St-Pierre, Y}, title = {Divergent bacterial landscapes: unraveling geographically driven microbiomes in Atlantic cod.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6088}, pmid = {38480867}, issn = {2045-2322}, mesh = {Animals ; *Gadus morhua/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics ; *Gadiformes/genetics ; }, abstract = {Establishing microbiome signatures is now recognized as a critical step toward identifying genetic and environmental factors shaping animal-associated microbiomes and informing the health status of a given host. In the present work, we prospectively collected 63 blood samples of the Atlantic cod population of the Southern Gulf of Saint Lawrence (GSL) and characterized their 16S rRNA circulating microbiome signature. Our results revealed that the blood microbiome signature was dominated at the phylum level by Proteobacteria, Bacteroidetes, Acidobacteria and Actinobacteria, a typical signature for fish populations inhabiting the GSL and other marine ecosystems. At the genus level, however, we identified two distinct cod groups. While the microbiome signature of the first group was dominated by Pseudoalteromonas, a genus we previously found in the microbiome signature of Greenland and Atlantic halibut populations of the GSL, the second group had a microbiome signature dominated by Nitrobacter and Sediminibacterium (approximately 75% of the circulating microbiome). Cods harboring a Nitrobacter/Sediminibacterium-rich microbiome signature were localized in the most southern part of the GSL, just along the northern coast of Cape Breton Island. Atlantic cod microbiome signatures did not correlate with the weight, length, relative condition, depth, temperature, sex, and salinity, as previously observed in the halibut populations. Our study provides, for the first time, a unique snapshot of the circulating microbiome signature of Atlantic cod populations and the potential existence of dysbiotic signatures associated with the geographical distribution of the population, probably linked with the presence of nitrite in the environment.}, } @article {pmid38480864, year = {2024}, author = {Sato, Y and Sato, R and Fukui, E and Yoshizawa, F}, title = {Impact of rumen microbiome on cattle carcass traits.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6064}, pmid = {38480864}, issn = {2045-2322}, support = {22K20608//Japan Society for the Promotion of Science/ ; }, mesh = {Cattle ; Animals ; RNA, Ribosomal, 16S/genetics/metabolism ; *Rumen/microbiology ; *Microbiota/genetics ; Fermentation ; Polysaccharides/metabolism ; Methane/metabolism ; Diet/veterinary ; Animal Feed ; }, abstract = {Rumen microbes are crucial in the anaerobic fermentation of plant polysaccharides to produce volatile fatty acids. However, limited information exists about the specific microbial species and strains in the rumen that affect carcass traits, and it is unclear whether there is a relationship between rumen metabolic functions and these traits. This study investigated the relationship between the rumen microbiome and carcass traits in beef cattle using 16S rRNA amplicon and shotgun sequencing. Metagenomic sequencing was used to compare the rumen microbiome between high-carcass weight (HW) and low-carcass weight (LW) cattle, and high-marbling (HM) and low-marbling (LM) cattle. Prokaryotic communities in the rumen of HW vs. LW and HM vs. LM were separated using 16S rRNA amplicon sequencing. Notably, shotgun metagenomic sequencing revealed that HW cattle had more methane-producing bacteria and ciliate protozoa, suggesting higher methane emissions. Additionally, variations were observed in the abundances of certain glycoside hydrolases and polysaccharide lyases involved in the ruminal degradation of plant polysaccharides between HW and LW. From our metagenome dataset, 807 non-redundant metagenome-assembled genomes (MAGs) of medium to high quality were obtained. Among these, 309 and 113 MAGs were associated with carcass weight and marbling, respectively.}, } @article {pmid38476164, year = {2024}, author = {Kumar, V and Roy, S and Parida, SN and Bisai, K and Dhar, S and Jana, AK and Das, BK}, title = {Deciphering the impact of endoparasitic infection on immune response and gut microbial composition of Channa punctata.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1296769}, pmid = {38476164}, issn = {2235-2988}, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/physiology ; Channa punctatus ; *Nematoda ; *Intestinal Diseases, Parasitic ; *Parasites ; *Helminths ; Bacteria ; Fishes ; Immunity ; }, abstract = {Intestinal parasitic infections caused by helminths are globally distributed and are a major cause of morbidity worldwide. Parasites may modulate the virulence, gut microbiota diversity and host responses during infection. Despite numerous works, little is known about the complex interaction between parasites and the gut microbiota. In the present study, the complex interplay between parasites and the gut microbiota was investigated. A total of 12 bacterial strains across four major families, including Enterobacteriaceae, Morganellaceae, Flavobacteriaceae, and Pseudomonadaceae, were isolated from Channa punctata, infected with the nematode species Aporcella sp., Axonchium sp., Tylencholaimus mirabilis, and Dioctophyme renale. The findings revealed that nematode infection shaped the fish gut bacterial microbiota and significantly affected their virulence levels. Nematode-infected fish bacterial isolates are more likely to be pathogenic, with elevated hemolytic activity and biofilm formation, causing high fish mortality. In contrast, isolates recovered further from non-parasitised C. punctata were observed to be non-pathogenic and had negligible hemolytic activity and biofilm formation. Antibiogram analysis of the bacterial isolates revealed a disproportionately high percentage of bacteria that were either marginally or multidrug resistant, suggesting that parasitic infection-induced stress modulates the gut microenvironment and enables colonization by antibiotic-resistant strains. This isolation-based study provides an avenue to unravel the influence of parasitic infection on gut bacterial characteristics, which is valuable for understanding the infection mechanism and designing further studies aimed at optimizing treatment strategies. In addition, the cultured isolates can supplement future gut microbiome studies by providing wet lab specimens to compare (meta)genomic information discovered within the gut microenvironment of fish.}, } @article {pmid38474789, year = {2024}, author = {Fernandez-Sanjurjo, M and Fernandez, J and Martinez-Camblor, P and Rodriguez-Alonso, M and Ortolano-Rios, R and Pinto-Hernandez, P and Castilla-Silgado, J and Coto-Vilcapoma, A and Ruiz, L and Villar, CJ and Tomas-Zapico, C and Margolles, A and Fernandez-Garcia, B and Iglesias-Gutierrez, E and Lombó, F}, title = {Dynamics of Gut Microbiota and Short-Chain Fatty Acids during a Cycling Grand Tour Are Related to Exercise Performance and Modulated by Dietary Intake.}, journal = {Nutrients}, volume = {16}, number = {5}, pages = {}, pmid = {38474789}, issn = {2072-6643}, support = {AYUD/2021/51347//Foundation for the Promotion of Applied Scientific Research and Technology in Asturias/ ; PID2021-127812OB-I00//Ministerio de Ciencia e Innovación/ ; RTI2018-095021-J-I00//Agencia Estatal de Investigación/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Eating ; Exercise ; Carbohydrates/analysis ; }, abstract = {BACKGROUND: Regular exercise has been described to modify both the diversity and the relative abundance of certain bacterial taxa. To our knowledge, the effect of a cycling stage race, which entails extreme physiological and metabolic demands, on the gut microbiota composition and its metabolic activity has not been analysed.

OBJECTIVE: The aim of this cohort study was to analyse the dynamics of faecal microbiota composition and short-chain fatty acids (SCFAs) content of professional cyclists over a Grand Tour and their relationship with performance and dietary intake.

METHODS: 16 professional cyclists competing in La Vuelta 2019 were recruited. Faecal samples were collected at four time points: the day before the first stage (A); after 9 stages (B); after 15 stages (C); and on the last stage (D). Faecal microbiota populations and SCFA content were analysed using 16S rRNA sequencing and gas chromatography, respectively. A principal component analysis (PCA) followed by Generalised Estimating Equation (GEE) models were carried out to explore the dynamics of microbiota and SCFAs and their relationship with performance.

RESULTS: Bifidobacteriaceae, Coriobacteriaceae, Erysipelotrichaceae, and Sutterellaceae dynamics showed a strong final performance predictive value (r = 0.83, ranking, and r = 0.81, accumulated time). Positive correlations were observed between Coriobacteriaceae with acetate (r = 0.530) and isovalerate (r = 0.664) and between Bifidobacteriaceae with isobutyrate (r = 0.682). No relationship was observed between SCFAs and performance. The abundance of Erysipelotrichaceae at the beginning of La Vuelta was directly related to the previous intake of complex-carbohydrate-rich foods (r = 0.956), while during the competition, the abundance of Bifidobacteriaceae was negatively affected by the intake of simple carbohydrates from supplements (r = -0.650).

CONCLUSIONS: An ecological perspective represents more realistically the relationship between gut microbiota composition and performance compared to single-taxon approaches. The composition and periodisation of diet and supplementation during a Grand Tour, particularly carbohydrates, could be designed to modulate gut microbiota composition to allow better performance.}, } @article {pmid38473829, year = {2024}, author = {Ng, HY and Liao, Y and Zhang, R and Chan, KH and To, WP and Hui, CH and Seto, WK and Leung, WK and Hung, IFN and Lam, TTY and Cheung, KS}, title = {The Predictive Value of Gut Microbiota Composition for Sustained Immunogenicity following Two Doses of CoronaVac.}, journal = {International journal of molecular sciences}, volume = {25}, number = {5}, pages = {}, pmid = {38473829}, issn = {1422-0067}, support = {COVID1903010, Project 16//Health and Medical Research Fund, Food and Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; D24H, C2i//InnoHK funding from the Innovation and Technology Commission/ ; }, mesh = {Humans ; Male ; Middle Aged ; *Gastrointestinal Microbiome ; Prospective Studies ; Adenosine ; Antibodies, Neutralizing ; Antibodies, Viral ; *COVID-19 Vaccines ; *Vaccines, Inactivated ; }, abstract = {CoronaVac immunogenicity decreases with time, and we aimed to investigate whether gut microbiota associate with longer-term immunogenicity of CoronaVac. This was a prospective cohort study recruiting two-dose CoronaVac recipients from three centres in Hong Kong. We collected blood samples at baseline and day 180 after the first dose and used chemiluminescence immunoassay to test for neutralizing antibodies (NAbs) against the receptor-binding domain (RBD) of wild-type SARS-CoV-2 virus. We performed shotgun metagenomic sequencing performed on baseline stool samples. The primary outcome was the NAb seroconversion rate (seropositivity defined as NAb ≥ 15AU/mL) at day 180. Linear discriminant analysis [LDA] effect size analysis was used to identify putative bacterial species and metabolic pathways. A univariate logistic regression model was used to derive the odds ratio (OR) of seropositivity with bacterial species. Of 119 CoronaVac recipients (median age: 53.4 years [IQR: 47.8-61.3]; male: 39 [32.8%]), only 8 (6.7%) remained seropositive at 6 months after vaccination. Bacteroides uniformis (log10LDA score = 4.39) and Bacteroides eggerthii (log10LDA score = 3.89) were significantly enriched in seropositive than seronegative participants. Seropositivity was associated with B. eggerthii (OR: 5.73; 95% CI: 1.32-29.55; p = 0.022) and B. uniformis with borderline significance (OR: 3.27; 95% CI: 0.73-14.72; p = 0.110). Additionally, B. uniformis was positively correlated with most enriched metabolic pathways in seropositive vaccinees, including the superpathway of adenosine nucleotide de novo biosynthesis I (log10LDA score = 2.88) and II (log10LDA score = 2.91), as well as pathways related to vitamin B biosynthesis, all of which are known to promote immune functions. In conclusion, certain gut bacterial species (B. eggerthii and B. uniformis) and metabolic pathways were associated with longer-term CoronaVac immunogenicity.}, } @article {pmid38471893, year = {2024}, author = {Li, CL and Zhang, F and Wang, LD and Zhao, HR and Zhao, XC and Zhang, HP}, title = {[Soil Microbial Community Structure and Functional Diversity Character of Abandoned Farmland in Minqin Oasis].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {45}, number = {3}, pages = {1821-1829}, doi = {10.13227/j.hjkx.202305174}, pmid = {38471893}, issn = {0250-3301}, mesh = {*Soil/chemistry ; Farms ; Soil Microbiology ; *Microbiota ; Bacteria ; }, abstract = {To clarify the impact of the structure and function of soil microbial communities in the stage of abandoned farmland, three different stages of land abandoned in desert oasis areas were selected as the research objects. We used metagenomic sequencing technology to research soil microbial community structure and functional diversity characteristics of different stages of abandoned farmland. The results showed that there were significant differences in the relative abundance of the dominant phyla Actinobacteria, Proteobacteria, and Gemmatimonadetes in the soil of the three stages of returning farmland. Compared with that in the early stage of abandoned farmland, the later stage of abandoned farmland restoration increased the gene proportion involved in Quorum sensing, porphyrin and chlorophyll metabolism, pantothenate and CoA biosynthesis, and styrene degradation, and there was a significant difference in relative abundance (P<0.05), which indicated that different stages of abandoned farmland had changed the functional potential of the nutrient cycle and energy metabolism in soil microbial communities. The RDA results showed that EC, AK, and TN had a significant impact on the functional composition of soil microbes, and soil EC had the greatest impact on microbial functional composition. The results showed that different stages of abandoned farmland had a significant impact on the soil microbial community structure and functional composition. In the ecological restoration of abandoned farmland in Minqin Oasis, the sensitivity of microbial community structure and functional composition to soil restoration at different stages should be considered using comprehensive relevant indicators.}, } @article {pmid38471380, year = {2024}, author = {Meng, S and Peng, T and Liu, Y and Zhang, S and Qian, Z and Huang, T and Xie, Q and Gu, JD and Hu, Z}, title = {Novel insights into the synergetic degradation of pyrene by microbial communities from mangroves in China.}, journal = {Journal of hazardous materials}, volume = {469}, number = {}, pages = {133907}, doi = {10.1016/j.jhazmat.2024.133907}, pmid = {38471380}, issn = {1873-3336}, mesh = {Pyrenes/metabolism ; *Polycyclic Aromatic Hydrocarbons/analysis ; Bacteria/metabolism ; *Microbiota ; Biodegradation, Environmental ; }, abstract = {Pyrene is a high molecular weight polycyclic aromatic hydrocarbon (HMW-PAHs). It is a ubiquitous, persistent, and carcinogenic environmental contaminant that has raised concern worldwide. This research explored synergistic bacterial communities for efficient pyrene degradation in seven typical Southern China mangroves. The bacterial communities of seven typical mangroves were enriched by pyrene, and enriched bacterial communities showed an excellent pyrene degradation capacity of > 95% (except for HK mangrove and ZJ mangrove). Devosia, Hyphomicrobium, Flavobacterium, Marinobacter, Algoriphahus, and Youhaiella all have significant positive correlations with pyrene (R>0, p < 0.05) by 16SrRNA gene sequencing and metagenomics analysis, indicated that these genera play a vital role in pyrene metabolism. Meanwhile, the functional genes were involved in pyrene degradation that was enriched in the bacterial communities, including the genes of nagAa, ndoR, pcaG, etc. Furthermore, the analyses of functional genes and binning genomes demonstrated that some bacterial communities as a unique teamwork to cooperatively participate in pyrene degradation. Interestingly, the genes related to biogeochemical cycles were enriched, such as narG , soxA, and cyxJ, suggested that bacterial communities were also helpful in maintaining the stability of the ecological environment. In addition, some novel species with pyrene-degradation potential were identified in the pyrene-degrading bacterial communities, which can enrich the resource pool of pyrene-degrading strains. Overall, this study will help develop further research strategies for pollutant removal.}, } @article {pmid38471337, year = {2024}, author = {Conco-Biyela, T and Malla, MA and Olatunji Awolusi, O and Allam, M and Ismail, A and Stenström, TA and Bux, F and Kumari, S}, title = {Metagenomics insights into microbiome and antibiotic resistance genes from free living amoeba in chlorinated wastewater effluents.}, journal = {International journal of hygiene and environmental health}, volume = {258}, number = {}, pages = {114345}, doi = {10.1016/j.ijheh.2024.114345}, pmid = {38471337}, issn = {1618-131X}, mesh = {Wastewater ; Anti-Bacterial Agents/pharmacology ; *Amoeba/microbiology ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; *Microbiota/genetics ; Bacteria ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Cephalosporins ; }, abstract = {Free living amoeba (FLA) are among the organisms commonly found in wastewater and are well-established hosts for diverse microbial communities. Despite its clinical significance, there is little knowledge on the FLA microbiome and resistome, with previous studies relying mostly on conventional approaches. In this study we comprehensively analyzed the microbiome, antibiotic resistome and virulence factors (VFs) within FLA isolated from final treated effluents of two wastewater treatment plants (WWTPs) using shotgun metagenomics. Acanthamoeba has been identified as the most common FLA, followed by Entamoeba. The bacterial diversity showed no significant difference (p > 0.05) in FLA microbiomes obtained from the two WWTPs. At phylum level, the most dominant taxa were Proteobacteria, followed by Firmicutes and Actinobacteria. The most abundant genera identified were Enterobacter followed by Citrobacter, Paenibacillus, and Cupriavidus. The latter three genera are reported here for the first time in Acanthamoeba. In total, we identified 43 types of ARG conferring resistance to cephalosporins, phenicol, streptomycin, trimethoprim, quinolones, cephalosporins, tigecycline, rifamycin, and kanamycin. Similarly, a variety of VFs in FLA metagenomes were detected which included flagellar proteins, Type IV pili twitching motility proteins (pilH and rpoN), alginate biosynthesis genes AlgI, AlgG, AlgD and AlgW and Type VI secretion system proteins and general secretion pathway proteins (tssM, tssA, tssL, tssK, tssJ, fha, tssG, tssF, tssC and tssB, gspC, gspE, gspD, gspF, gspG, gspH, gspI, gspJ, gspK, and gspM). To the best of our knowledge, this is the first study of its kind to examine both the microbiomes and resistome in FLA, as well as their potential pathogenicity in treated effluents. Additionally, this study showed that FLA can host a variety of potentially pathogenic bacteria including Paenibacillus, and Cupriavidus that had not previously been reported, indicating that their relationship may play a role in the spread and persistence of antibiotic resistant bacteria (ARBs) and antibiotic resistance genes (ARGs) as well as the evolution of novel pathogens.}, } @article {pmid38470313, year = {2024}, author = {Yu, J and Lee, JYY and Tang, SN and Lee, PKH}, title = {Niche differentiation in microbial communities with stable genomic traits over time in engineered systems.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38470313}, issn = {1751-7370}, support = {9231297//TAL Apparel Limited to the City University of Hong Kong/ ; }, mesh = {*Sewage ; Bacteria/genetics ; *Microbiota/genetics ; Metagenome ; Genomics ; }, abstract = {Microbial communities in full-scale engineered systems undergo dynamic compositional changes. However, mechanisms governing assembly of such microbes and succession of their functioning and genomic traits under various environmental conditions are unclear. In this study, we used the activated sludge and anaerobic treatment systems of four full-scale industrial wastewater treatment plants as models to investigate the niches of microbes in communities and the temporal succession patterns of community compositions. High-quality representative metagenome-assembled genomes revealed that taxonomic, functional, and trait-based compositions were strongly shaped by environmental selection, with replacement processes primarily driving variations in taxonomic and functional compositions. Plant-specific indicators were associated with system environmental conditions and exhibited strong determinism and trajectory directionality over time. The partitioning of microbes in a co-abundance network according to groups of plant-specific indicators, together with significant between-group differences in genomic traits, indicated the occurrence of niche differentiation. The indicators of the treatment plant with rich nutrient input and high substrate removal efficiency exhibited a faster predicted growth rate, lower guanine-cytosine content, smaller genome size, and higher codon usage bias than the indicators of the other plants. In individual plants, taxonomic composition displayed a more rapid temporal succession than functional and trait-based compositions. The succession of taxonomic, functional, and trait-based compositions was correlated with the kinetics of treatment processes in the activated sludge systems. This study provides insights into ecological niches of microbes in engineered systems and succession patterns of their functions and traits, which will aid microbial community management to improve treatment performance.}, } @article {pmid38470142, year = {2024}, author = {Zhang, Z and Zhang, L and Zhang, L and Chu, H and Zhou, J and Ju, F}, title = {Diversity and distribution of biosynthetic gene clusters in agricultural soil microbiomes.}, journal = {mSystems}, volume = {9}, number = {4}, pages = {e0126323}, pmid = {38470142}, issn = {2379-5077}, support = {2024SSYS0032//The "Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; LR22D010001//Zhejiang Provincial Natural Science Foundation of China/ ; 22241603//National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Soil/chemistry ; Phylogeny ; Soil Microbiology ; *Microbiota/genetics ; Bacteria/genetics ; Multigene Family/genetics ; }, abstract = {Bacterial secondary metabolites serve as an important source of molecules for drug discovery. They also play an important function in mediating the interactions of microbial producers with their living environment and surrounding organisms. However, little is known about the genetic novelty, distribution, and community-level impacts of soil bacterial biosynthetic potential on a large geographic scale. Here, we constructed the first catalog of 11,149 biosynthetic gene clusters (BGCs) from agricultural soils across China and unearthed hidden biosynthetic potential for new natural product discovery from the not-yet-cultivated soil bacteria. Notably, we revealed soil pH as the strongest environmental driver of BGC biogeography and predicted that soil acidification and global climate change could damage the biosynthetic potential of the soil microbiome. The co-occurrence network of bacterial genomes revealed two BGC-rich species, i.e., Nocardia niigatensis from Actinobacteriota and PSRF01 from Acidobacteriota, as the module hub and connector, respectively, indicating their keystone positions in the soil microbial communities. We also uncovered a dominant role of BGC-inferred biotic interactions over environmental drivers in structuring the soil microbiome. Overall, this study achieved novel insights into the BGC landscape in agricultural soils of China, substantially expanding our understanding of the diversity and novelty of bacterial secondary metabolism and the potential role of secondary metabolites in microbiota assembly.IMPORTANCEBacterial secondary metabolites not only serve as the foundation for numerous therapeutics (e.g., antibiotics and anticancer drugs), but they also play critical ecological roles in mediating microbial interactions (e.g., competition and communication). However, our knowledge of bacterial secondary metabolism is limited to only a small fraction of cultured strains, thus restricting our comprehensive understanding of their diversity, novelty, and potential ecological roles in soil ecosystems. Here, we used culture-independent metagenomics to explore biosynthetic potentials in agricultural soils of China. Our analyses revealed a high degree of genetic diversity and novelty within biosynthetic gene clusters in agricultural soil environments, offering valuable insights for biochemists seeking to synthesize novel bioactive products. Furthermore, we uncovered the pivotal role of BGC-rich species in microbial communities and the significant relationship between BGC richness and microbial phylogenetic turnover. This information emphasizes the importance of biosynthetic potential in the assembly of microbial communities.}, } @article {pmid38469667, year = {2024}, author = {Alemasi, A and Gu, L and Zhou, Y}, title = {Gut microbiota in the association between obesity and kidney function decline: a metagenomics-based study in a rat model.}, journal = {Renal failure}, volume = {46}, number = {1}, pages = {2328320}, pmid = {38469667}, issn = {1525-6049}, mesh = {Rats ; Animals ; Mice ; *Gastrointestinal Microbiome/physiology ; Rats, Sprague-Dawley ; Obesity/complications ; Diet, High-Fat/adverse effects ; *Kidney Diseases/complications ; Kidney ; Mice, Inbred C57BL ; }, abstract = {OBJECTIVES: Obesity can induce dysbiosis in the gut microbiota and is considered a separate risk factor for kidney function decline. Nonetheless, the precise function of intestinal microorganisms in facilitating the connection between obesity and kidney function decline remains uncertain. Hence, the objective of this study was to investigate the alterations in the gut microbiota composition that take place during obesity and their correlations with renal function utilizing a rat model.

METHODS: For 20 weeks, 25 Sprague-Dawley rats were fed either a high-fat diet (HFD) or a normal-fat normal diet (ND). Physiological indices, peripheral plasma, kidney tissue, and colon contents were collected for comparison between groups. Metagenomic analysis of intestinal flora was performed.

RESULTS: The HFD group demonstrated significantly increased levels of creatinine and urea nitrogen in the peripheral blood. Additionally, the HFD rats exhibited a significantly larger glomerular diameter compared to the ND group, accompanied by the presence of glomerulosclerosis, tubular vacuolar transformation, and other pathological changes in certain glomeruli. Metagenomics analysis revealed a notable rise in the prevalence of the Firmicutes phylum within the HFD group, primarily comprising the Rumenococcus genus. Functional analysis indicated that the gut microbiota in the HFD group primarily correlated with infectious diseases, signal transduction, and signaling molecules and interactions.

CONCLUSIONS: This study provides evidence that the consumption of a HFD induces modifications in the composition and functionality of the gut microbiome in rats, which may serve as a potential mechanism underlying the relationship between obesity and the progression of kidney function decline.}, } @article {pmid38468305, year = {2024}, author = {d'Humières, C and Delavy, M and Alla, L and Ichou, F and Gauliard, E and Ghozlane, A and Levenez, F and Galleron, N and Quinquis, B and Pons, N and Mullaert, J and Bridier-Nahmias, A and Condamine, B and Touchon, M and Rainteau, D and Lamazière, A and Lesnik, P and Ponnaiah, M and Lhomme, M and Sertour, N and Devente, S and Docquier, JD and Bougnoux, ME and Tenaillon, O and Magnan, M and Ruppé, E and Grall, N and Duval, X and Ehrlich, D and Mentré, F and Denamur, E and Rocha, EPC and Le Chatelier, E and Burdet, C and , }, title = {Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {50}, pmid = {38468305}, issn = {2049-2618}, mesh = {Adult ; Humans ; *Gastrointestinal Microbiome/genetics ; beta-Lactamases/genetics ; beta-Lactams/pharmacology ; Healthy Volunteers ; *Resilience, Psychological ; Anti-Bacterial Agents ; Bacteria/genetics ; Feces/microbiology ; }, abstract = {BACKGROUND: Antibiotics notoriously perturb the gut microbiota. We treated healthy volunteers either with cefotaxime or ceftriaxone for 3 days, and collected in each subject 12 faecal samples up to day 90. Using untargeted and targeted phenotypic and genotypic approaches, we studied the changes in the bacterial, phage and fungal components of the microbiota as well as the metabolome and the β-lactamase activity of the stools. This allowed assessing their degrees of perturbation and resilience.

RESULTS: While only two subjects had detectable concentrations of antibiotics in their faeces, suggesting important antibiotic degradation in the gut, the intravenous treatment perturbed very significantly the bacterial and phage microbiota, as well as the composition of the metabolome. In contrast, treatment impact was relatively low on the fungal microbiota. At the end of the surveillance period, we found evidence of resilience across the gut system since most components returned to a state like the initial one, even if the structure of the bacterial microbiota changed and the dynamics of the different components over time were rarely correlated. The observed richness of the antibiotic resistance genes repertoire was significantly reduced up to day 30, while a significant increase in the relative abundance of β-lactamase encoding genes was observed up to day 10, consistent with a concomitant increase in the β-lactamase activity of the microbiota. The level of β-lactamase activity at baseline was positively associated with the resilience of the metabolome content of the stools.

CONCLUSIONS: In healthy adults, antibiotics perturb many components of the microbiota, which return close to the baseline state within 30 days. These data suggest an important role of endogenous β-lactamase-producing anaerobes in protecting the functions of the microbiota by de-activating the antibiotics reaching the colon. Video Abstract.}, } @article {pmid38468206, year = {2024}, author = {Watai, K and Suda, W and Kurokawa, R and Sekiya, K and Hayashi, H and Iwata, M and Nagayama, K and Nakamura, Y and Hamada, Y and Kamide, Y and Fukutomi, Y and Nakabayashi, T and Tanaka, K and Kamita, M and Taniguchi, M and Hattori, M}, title = {Metagenomic gut microbiome analysis of Japanese patients with multiple chemical sensitivity/idiopathic environmental intolerance.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {84}, pmid = {38468206}, issn = {1471-2180}, support = {2015-EBM-02//Grant-in-Aid for Evidence-Based Medicine Research from the National Hospital Organization, Japan/ ; 2015-EBM-02//Grant-in-Aid for Evidence-Based Medicine Research from the National Hospital Organization, Japan/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; *Multiple Chemical Sensitivity ; Japan ; Feces/microbiology ; Amino Acids ; }, abstract = {BACKGROUND: Although the pathology of multiple chemical sensitivity (MCS) is unknown, the central nervous system is reportedly involved. The gut microbiota is important in modifying central nervous system diseases. However, the relationship between the gut microbiota and MCS remains unclear. This study aimed to identify gut microbiota variations associated with MCS using shotgun metagenomic sequencing of fecal samples.

METHODS: We prospectively recruited 30 consecutive Japanese female patients with MCS and analyzed their gut microbiomes using shotgun metagenomic sequencing. The data were compared with metagenomic data obtained from 24 age- and sex-matched Japanese healthy controls (HC).

RESULTS: We observed no significant difference in alpha and beta diversity of the gut microbiota between the MCS patients and HC. Focusing on the important changes in the literatures, at the genus level, Streptococcus, Veillonella, and Akkermansia were significantly more abundant in MCS patients than in HC (p < 0.01, p < 0.01, p = 0.01, respectively, fold change = 4.03, 1.53, 2.86, respectively). At the species level, Akkermansia muciniphila was significantly more abundant (p = 0.02, fold change = 3.3) and Faecalibacterium prausnitzii significantly less abundant in MCS patients than in HC (p = 0.03, fold change = 0.53). Functional analysis revealed that xylene and dioxin degradation pathways were significantly enriched (p < 0.01, p = 0.01, respectively, fold change = 1.54, 1.46, respectively), whereas pathways involved in amino acid metabolism and synthesis were significantly depleted in MCS (p < 0.01, fold change = 0.96). Pathways related to antimicrobial resistance, including the two-component system and cationic antimicrobial peptide resistance, were also significantly enriched in MCS (p < 0.01, p < 0.01, respectively, fold change = 1.1, 1.2, respectively).

CONCLUSIONS: The gut microbiota of patients with MCS shows dysbiosis and alterations in bacterial functions related to exogenous chemicals and amino acid metabolism and synthesis. These findings may contribute to the further development of treatment for MCS.

TRIAL REGISTRATION: This study was registered with the University Hospital Medical Information Clinical Trials Registry as UMIN000031031. The date of first trial registration: 28/01/2018.}, } @article {pmid38468006, year = {2024}, author = {Ma, J and Yao, Z and Zhang, M and Gao, J and Li, W and Yang, W}, title = {Microbial and environmental medium-driven responses to phosphorus fraction changes in the sediments of different lake types during the freezing period.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {17}, pages = {25147-25162}, pmid = {38468006}, issn = {1614-7499}, support = {42167018//the National Natural Science Foundation of China/ ; 2023YXXS026//the Fundamental Research Funds for Inner Mongolia University of Science & Technology/ ; }, mesh = {*Lakes ; *Water Pollutants, Chemical/analysis ; Ecosystem ; Phosphorus/analysis ; Freezing ; Sodium Hydroxide ; Environmental Monitoring ; Geologic Sediments ; Eutrophication ; China ; }, abstract = {The comparative study of the transformation among sediment phosphorus (P) fractions in different lake types is a global issue in lake ecosystems. However, interactions between sediment P fractions, environmental factors, and microorganisms vary with the nutrient status of lakes. In this study, we combine sequential extraction and metagenomics sequencing to assess the characteristics of P fractions and transformation in sediments from different lake types in the Inner Mongolian section of the Yellow River Basin. We then further explore the response of relevant microbial and environmental drivers to P fraction transformation and bioavailability in sediments. The sediments of all three lakes exhibited strong exogenous pollution input characteristics, and higher nutritional conditions led to enhanced sediment P fraction transformation ability. The transformation capacity of the sediment P fractions also differed among the different lake types at the same latitudes, which is affected by many factors such as lake environmental factors and microorganisms. Different drivers reflected the mutual control of weakly adsorbed phosphorus (WA-P), potential active phosphorus (PA-P), Fe/Al-bound phosphorus (NaOH-P), and Ca-bound phosphorus (HCl-P) with the bio-directly available phosphorus (Bio-P). The transformation of NaOH-P in reducing environments can improve P bioavailability, while HCl-P is not easily bioavailable in weakly alkaline environments. There were significant differences in the bacterial community diversity and composition between the different lake types at the same latitude (p < 0.05), and the role of P fractions was stronger in the sediments of lakes with rich biodiversity than in poor biodiversity. Lake eutrophication recovery was somewhat hindered by the microbial interactions of P cycling and P fractions within the sediment. This study provides data and theoretical support for exploring the commonalities and differences among different lake types in the Inner Mongolian section of the Yellow River Basin. Besides, it is representative and typical for promoting the optimization of ecological security patterns in ecologically fragile watersheds.}, } @article {pmid38466428, year = {2024}, author = {Sonthiphand, P and Rueangmongkolrat, N and Uthaipaisanwong, P and Kusonmano, K and Mhuantong, W and Termsaithong, T and Limthamprasert, C and Chotpantarat, S and Luepromchai, E}, title = {Soil Microbiomes and their Arsenic Functional Genes in Chronically High-Arsenic Contaminated Soils.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {112}, number = {3}, pages = {49}, pmid = {38466428}, issn = {1432-0800}, support = {RGNS 63- 173//Office of the Permanent Secretary, Ministry of Higher Education, Science, Research and Innovation (OPS MHESI), Thailand Science Research and Innovation (TSRI) and Mahidol University/ ; Faculty of Science, Mahidol University//Faculty of Science, Mahidol University/ ; }, mesh = {*Arsenic/toxicity/analysis ; Soil ; Bacteria/genetics ; Genes, Bacterial ; *Microbiota ; Soil Microbiology ; *Soil Pollutants/toxicity/analysis ; }, abstract = {Microbial arsenic transformations play essential roles in controlling pollution and ameliorating risk. This study combined high-throughput sequencing and PCR-based approaches targeting both the 16 S rRNA and arsenic functional genes to investigate the temporal and spatial dynamics of the soil microbiomes impacted by high arsenic contamination (9.13 to 911.88 mg/kg) and to investigate the diversity and abundance of arsenic functional genes in soils influenced by an arsenic gradient. The results showed that the soil microbiomes were relatively consistent and mainly composed of Actinobacteria (uncultured Gaiellales and an unknown_67 - 14 bacterium), Proteobacteria, Firmicutes (particularly, Bacillus), Chloroflexi, and Acidobacteria (unknown_Subgroup_6). Although a range of arsenic functional genes (e.g., arsM, arsC, arrA, and aioA) were identified by shotgun metagenomics, only the arsM gene was detected by the PCR-based method. The relative abundance of the arsM gene accounted for 0.20%-1.57% of the total microbial abundance. Combining all analyses, arsenic methylation mediated by the arsM gene was proposed to be a key process involved in the arsenic biogeochemical cycle and mitigation of arsenic toxicity. This study advances our knowledge about arsenic mechanisms over the long-term in highly contaminated soils.}, } @article {pmid38466097, year = {2024}, author = {Möller, L and Vainshtein, Y and Meyer, B and Neidhardt, J and Eren, AM and Sohn, K and Rabus, R}, title = {Rich microbial and depolymerising diversity in Antarctic krill gut.}, journal = {Microbiology spectrum}, volume = {12}, number = {4}, pages = {e0403523}, pmid = {38466097}, issn = {2165-0497}, support = {KiGuMi//Bundesministerium für Bildung und Forschung (BMBF)/ ; }, mesh = {Humans ; Animals ; *Euphausiacea/metabolism ; Ecosystem ; Seasons ; Hydrolases/genetics/metabolism ; Biopolymers/metabolism ; }, abstract = {With almost a quadrillion individuals, the Antarctic krill processes five million tons of organic carbon every day during austral summer. This high carbon flux requires a broad range of hydrolytic enzymes to decompose the diverse food-derived biopolymers. While krill itself possesses numerous such enzymes, it is unclear, to what extent the endogenous microbiota contribute to the hydrolytic potential of the gut environment. Here we applied amplicon sequencing, shotgun metagenomics, cultivation, and physiological assays to characterize the krill gut microbiota. The broad bacterial diversity (273 families, 919 genera, and 2,309 species) also included a complex potentially anaerobic sub-community. Plate-based assays with 198 isolated pure cultures revealed widespread capacities to utilize lipids (e.g., tributyrin), followed by proteins (casein) and to a lesser extent by polysaccharides (e.g., alginate and chitin). While most isolates affiliated with the genera Pseudoalteromonas and Psychrobacter, also Rubritalea spp. (Verrucomicrobia) were observed. The krill gut microbiota growing on marine broth agar plates possess 13,012 predicted hydrolyses; 15-fold more than previously predicted from a transcriptome-proteome compendium of krill. Cultivation-independent and -dependent approaches indicated members of the families Flavobacteriaceae and Pseudoalteromonadaceae to dominate the capacities for lipid/protein hydrolysis and to provide a plethora of carbohydrate-active enzymes, sulfatases, and laminarin- or porphyrin-depolymerizing hydrolases. Notably, also the potential to hydrolyze plastics such as polyethylene terephthalate and polylactatide was observed, affiliating mostly with Moraxellaceae. Overall, this study shows extensive microbial diversity in the krill gut, and suggests that the microbiota likely play a significant role in the nutrient acquisition of the krill by enriching its hydrolytic enzyme repertoire.IMPORTANCEThe Antarctic krill (Euphausia superba) is a keystone species of the Antarctic marine food web, connecting the productivity of phyto- and zooplankton with the nutrition of the higher trophic levels. Accordingly, krill significantly contributes to biomass turnover, requiring the decomposition of seasonally varying plankton-derived biopolymers. This study highlights the likely role of the krill gut microbiota in this ecosystem function by revealing the great number of diverse hydrolases that microbes contribute to the krill gut environment. The here resolved repertoire of hydrolytic enzymes could contribute to the overall nutritional resilience of krill and to the general organic matter cycling under changing environmental conditions in the Antarctic sea water. Furthermore, the krill gut microbiome could serve as a valuable resource of cold-adapted hydrolytic enzymes for diverse biotechnological applications.}, } @article {pmid38462069, year = {2024}, author = {Rossi, A and Marroni, F and Renoldi, N and Di Filippo, G and Gover, E and Marino, M and Innocente, N}, title = {An integrated approach to explore the microbial biodiversity of natural milk cultures for cheesemaking.}, journal = {Journal of dairy science}, volume = {107}, number = {7}, pages = {4288-4297}, doi = {10.3168/jds.2024-24463}, pmid = {38462069}, issn = {1525-3198}, mesh = {*Milk/microbiology ; *Cheese/microbiology ; Animals ; *Biodiversity ; }, abstract = {The use of natural milk culture (NMC) represents a key factor in Protected Designation of Origin (PDO) Montasio cheese, contributing to its distinctive sensory profile. The complex microbial ecosystem of NMC is the result of heat treatment and incubation conditions, which can vary considerably among different production plants. In this study, the microbiota of NMC collected from 10 PDO Montasio cheese dairies was investigated by employing colony counts and metagenomic analysis. Furthermore, residual sugars, organic acids, and volatile profiles were quantitatively investigated. Results showed that Streptococcus thermophilus was the dominant species in all NMC, and a subdominant population made of other streptococci and Ligilactobacillus salivarius was also present. The incubation temperature appeared to be the main driver of biodiversity in NMC. Metagenomics allowed us to evidence the presence of minor species involving safety (e.g., Staphylococcus aureus) as well as possible functional aspects (Next Generation Probiotics). Statistical analysis based on residual sugars, organic acids, and volatiles' content allowed to correlate the presence of specific microbial groups with metabolites of great technological and sensory relevance, which can contribute to giving value to the artisanal production procedures of NMC and clarify their role in the creation of the characteristics of PDO Montasio cheese.}, } @article {pmid38461607, year = {2024}, author = {Wang, S and Zhang, C and Zhang, K and Zhang, L and Bi, R and Zhang, Y and Hu, Z}, title = {One-step bioremediation of hypersaline and nutrient-rich food industry process water with a domestic microbial community containing diatom Halamphora coffeaeformis.}, journal = {Water research}, volume = {254}, number = {}, pages = {121430}, doi = {10.1016/j.watres.2024.121430}, pmid = {38461607}, issn = {1879-2448}, mesh = {Wastewater ; Biodegradation, Environmental ; Water/analysis ; *Diatoms ; Phosphorus/analysis ; Bacteria/genetics/metabolism ; Food Industry ; Nutrients/analysis ; *Microbiota ; Biomass ; *Microalgae/metabolism ; Nitrogen/metabolism ; }, abstract = {Proper treatment of hypersaline and nutrient-rich food industry process water (FIPW) is challenging in conventional wastewater plants. Insufficient treatment leads to serious environmental hazards. However, bioremediation of FIPW with an indigenous microbial community can not only recover nutrients but generate biomass of diverse applications. In this study, monoculture of Halamphora coffeaeformis, together with synthetic bacteria isolated from a local wastewater plant, successfully recovered 91% of NH4[+]-N, 78% of total nitrogen, 95% of total phosphorus as well as 82% of total organic carbon from medium enriched with 10% FIPW. All identified organic acids and amino acids, except oxalic acid, were completely removed after 14 days treatment. A significantly higher biomass concentration (1.74 g L[-1]) was achieved after 14 days treatment in the medium with 10% FIPW than that in a nutrient-replete lab medium as control. The harvested biomass could be a potential feedstock for high-value biochemicals and fertilizer production, due to fucoxanthin accumulation (3 mg g[-1]) and a fantastic performance in P assimilation. Metagenomic analysis revealed that bacteria community in the algal system, dominated by Psychrobacter and Halomonas, also contributed to the biomass accumulation and uptake of nutrients. Transcriptomic analysis further disclosed that multiple pathways, involved in translation, folding, sorting and degradation as well as transport and catabolism, were depressed in H. coffeaeformis grown in FIPW-enriched medium, as compared to the control. Collectively, the proposed one-step strategy in this work offers an opportunity to achieve sustainable wastewater management and a way towards circular economy.}, } @article {pmid38461372, year = {2024}, author = {Ali, MJ}, title = {Alterations of Lacrimal Sac Microbiota in Failed Dacryocystorhinostomy: The Lacriome Paper 6.}, journal = {Seminars in ophthalmology}, volume = {39}, number = {4}, pages = {324-329}, doi = {10.1080/08820538.2024.2327481}, pmid = {38461372}, issn = {1744-5205}, mesh = {Humans ; *Dacryocystorhinostomy/methods ; *Nasolacrimal Duct/surgery ; *Lacrimal Duct Obstruction ; Prospective Studies ; Phylogeny ; *Microbiota ; Treatment Outcome ; }, abstract = {PURPOSE: To study the metagenomics of the microbes isolated from the lacrimal sac in patients with failed dacryocystorhinostomy (DCR).

METHODS: A prospective study was performed on 10 consecutive patients with failed DCR. Lacrimal sac samples were obtained for metagenomic analysis during the revision endoscopic DCR. The samples were collected intraoperatively after a full-length lacrimal sac marsupialization and immediately transported on ice to the laboratory. A whole shotgun metagenome sequencing was performed on the Illumina[TM] platform following DNA extraction and library preparation. The downstream analysis of the samples was performed using various software packaged in the Squeeze Metapipeline v1.3.0 and marker gene-based metagenomic phylogenetic analysis using MetaPhlAn4.

RESULTS: The five major phyla identified across the samples of failed DCR include Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Fusobacteria (Figure 1). The prevalent species include Stenotrophomonas maltophilia, Pseudomonas juntendi, Streptococcus pneumoniae, Acinetobacter ursingii, Citrobacter koseri, and Cutibacterium acnes (Figure 2). Among the other organisms identified, few were from genera candida and mezorhizobium. Among the viruses, the most abundant was the BeAn 58058 virus. It was interesting to note the occasional presence of plasmodium and toxoplasma species. The functional category distribution of KEGG (Kyoto encyclopedia of genes and genomes) data showed microbial metabolism to be the most involved function, followed by cellular processes.

CONCLUSION: This is the first whole metagenome sequencing of the lacrimal sac contents from failed DCR patients. The organisms identified varied significantly from those isolated from patients with primary acquired nasolacrimal duct obstruction (PANDO) using similar techniques and reflect altered lacrimal microbiota in surgically unsuccessful DCRs.}, } @article {pmid38461199, year = {2024}, author = {Papp, M and Tóth, AG and Békési, L and Farkas, R and Makrai, L and Maróti, G and Solymosi, N}, title = {Apis mellifera filamentous virus from a honey bee gut microbiome survey in Hungary.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {5803}, pmid = {38461199}, issn = {2045-2322}, support = {874735//European Union's Horizon 2020/ ; 874735//European Union's Horizon 2020/ ; 874735//European Union's Horizon 2020/ ; ÚNKP-22-3-II//Ministry for Culture and Innovation/ ; LP2020-5/2020//Hungarian Academy of Sciences/ ; }, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome/genetics ; Hungary ; Phylogeny ; *Honey ; High-Throughput Nucleotide Sequencing ; }, abstract = {In Hungary, as part of a nationwide, climatically balanced survey for a next-generation sequencing-based study of the honey bee (Apis mellifera) gut microbiome, repeated sampling was carried out during the honey production season (March and May 2019). Among other findings, the presence of Apis mellifera filamentous virus (AmFV) was detected in all samples, some at very high levels. AmFV-derived reads were more abundant in the March samples than in the May samples. In March, a higher abundance of AmFV-originated reads was identified in samples collected from warmer areas compared to those collected from cooler areas. A lower proportion of AmFV-derived reads were identified in samples collected in March from the wetter areas than those collected from the drier areas. AmFV-read abundance in samples collected in May showed no significant differences between groups based on either environmental temperature or precipitation. The AmFV abundance correlated negatively with Bartonella apihabitans, Bartonella choladocola, and positively with Frischella perrara, Gilliamella apicola, Gilliamella sp. ESL0443, Lactobacillus apis, Lactobacillus kullabergensis, Lactobacillus sp. IBH004. De novo metagenome assembly of four samples resulted in almost the complete AmFV genome. According to phylogenetic analysis based on DNA polymerase, the Hungarian strains are closest to the strain CH-05 isolated in Switzerland.}, } @article {pmid38460685, year = {2024}, author = {Zhang, Y and Ren, Y and Zhou, S and Ning, X and Wang, X and Yang, Y and Sun, S and Vinay, N and Bahn, M and Han, J and Liu, Y and Xiong, Y and Liao, Y and Mo, F}, title = {Spatio-temporal microbial regulation of aggregate-associated priming effects under contrasting tillage practices.}, journal = {The Science of the total environment}, volume = {925}, number = {}, pages = {171564}, doi = {10.1016/j.scitotenv.2024.171564}, pmid = {38460685}, issn = {1879-1026}, mesh = {*Carbon ; Soil/chemistry ; *Microbiota ; Soil Microbiology ; Biomass ; Agriculture/methods ; }, abstract = {Tillage intensity significantly influences the heterogeneous distribution and dynamic changes of soil microorganisms, consequently shaping spatio-temporal patterns of SOC decomposition. However, little is known about the microbial mechanisms by which tillage intensity regulates the priming effect (PE) dynamics in heterogeneous spatial environments such as aggregates. Herein, a microcosm experiment was established by adding [13]C-labeled straw residue to three distinct aggregate-size classes (i.e., mega-, macro-, and micro-aggregates) from two long-term contrasting tillage histories (no-till [NT] and conventional plow tillage [CT]) for 160 days to observe the spatio-temporal variations in PE. Metagenomic sequencing and Fourier transform mid-infrared techniques were used to assess the relative importance of C-degrading functional genes, microbial community succession, and SOC chemical composition in the aggregate-associated PE dynamics during straw decomposition. Spatially, straw addition induced a positive PE for all aggregates, with stronger PE occurring in larger aggregates, especially in CT soil compared to NT soil. Larger aggregates have more unique microbial communities enriched in genes for simple C degradation (e.g., E5.1.3.6, E2.4.1.7, pmm-pgm, and KduD in Nitrosospeera and Burkholderia), contributing to the higher short-term PE; however, CT soils harbored more genes for complex C degradation (e.g., TSTA3, fcl, pmm-pgm, and K06871 in Gammaproteobacteria and Phycicoccus), supporting a stronger long-term PE. Temporally, soil aggregates played a significant role in the early-stage PEs (i.e., < 59 days after residue addition) through co-metabolism and nitrogen (N) mining, as evidenced by the increased microbial biomass C and dissolved organic C (DOC) and reduced inorganic N with increasing aggregate-size class. At a later stage, however, the legacy effect of tillage histories controlled the PEs via microbial stoichiometry decomposition, as suggested by the higher DOC-to-inorganic N and DOC-to-available P stoichiometries in CT than NT. Our study underscores the importance of incorporating both spatial and temporal microbial dynamics for a comprehensive understanding of the mechanisms underlying SOC priming, especially in the context of long-term contrasting tillage practices.}, } @article {pmid38460218, year = {2024}, author = {Zhang, X and Chen, Y and Lv, Z and Zhou, L and Guo, Y}, title = {Analysis of the effects of β-mannanase on immune function and intestinal flora in broilers fed the low energy diet based on 16S rRNA sequencing and metagenomic sequencing.}, journal = {Poultry science}, volume = {103}, number = {5}, pages = {103581}, pmid = {38460218}, issn = {1525-3171}, mesh = {Animals ; *Chickens/immunology/microbiology ; *Animal Feed/analysis ; *Diet/veterinary ; *Gastrointestinal Microbiome/drug effects ; *beta-Mannosidase/metabolism/genetics ; *RNA, Ribosomal, 16S/analysis ; *Random Allocation ; Dietary Supplements/analysis ; Male ; Animal Nutritional Physiological Phenomena/drug effects ; Metagenomics ; }, abstract = {As an enzyme, β-mannanase (BM) can be widely used as feed additive to improve the growth performance of animals. This experiment aimed to determine the effect of the addition of BM to low-energy diet on the immune function and intestinal microflora of broiler chickens. In this study, 384 one-day-old Arbor Acres broilers were randomly divided into 3 groups (8 replicates per group): positive control (PC, received a corn-soybean meal basal diet), negative control (NC, received a low-energy diet with Metabolizable Energy (ME) reduced by 50 kcal/kg) and NC + BM group (NC birds + 100 mg/kg BM). All birds were raised for 42 d. The results showed that BM mitigated the damage of immune function in peripheral blood of broilers caused by the decrease of dietary energy level by increasing the Concanavalin A (Con A) index of stimulation (SI) and macrophages phagocytic activity in the peripheral blood of broilers at 42 d (P < 0.05). The analysis of cecum flora showed that the low-energy diet significantly reduced the observed_species index (P < 0.01), Chao1 index and ACE index (P < 0.05), which reduced the abundance and evenness of species in the cecum of broilers at 21 d. It also significantly reduced the relative abundance of Candidatus_Arthromitus and significantly increased the relative abundance of Pseudomonas in the cecum of broilers at 21 d, while also significantly increasing the relative abundance of Monoglobus at 42 d. BM significantly increased the relative abundance of Lachnospiraceae_UCG-001 and Lachnospiraceae_bacterium_615 in the cecum of broilers at 21 d. In addition, BM inhibited microbial Fatty acid degradation by decreasing the activity of glutaryl-CoA dehydrogenase. Collectively, BM could improve intestinal health by enhancing the immune function of broilers, promoting the proliferation of beneficial bacteria and reducing the number of harmful bacteria, regulating intestinal flora, thereby alleviating the adverse effects of lower dietary energy levels.}, } @article {pmid38458994, year = {2024}, author = {Coelho, LP and Santos-Júnior, CD and de la Fuente-Nunez, C}, title = {Challenges in computational discovery of bioactive peptides in 'omics data.}, journal = {Proteomics}, volume = {24}, number = {12-13}, pages = {e2300105}, pmid = {38458994}, issn = {1615-9861}, support = {HDTRA1-23-1-0001//Defense Threat Reduction Agency/ ; R35 GM138201/GM/NIGMS NIH HHS/United States ; //Langer Prize (AIChE Foundation)/ ; //Procter & Gamble Company, United Therapeutics/ ; //BBRF Young Investigator Grant/ ; FT230100724//Australian Research Council/ ; //Penn Health-Tech Accelerator Award/ ; DTRA//Defense Threat Reduction Agency/ ; HDTRA1-21-1-0014//Defense Threat Reduction Agency/ ; //Dean's Innovation Fund from the Perelman School of Medicine at the University of Pennsylvania/ ; R35GM138201//National Institute of General Medical Sciences of the National Institutes of Health/ ; //Nemirovsky Prize/ ; HDTRA11810041//Defense Threat Reduction Agency/ ; }, mesh = {*Peptides ; *Proteomics ; Metagenome ; Prokaryotic Cells/chemistry ; *Computational Biology/methods ; }, abstract = {Peptides have a plethora of activities in biological systems that can potentially be exploited biotechnologically. Several peptides are used clinically, as well as in industry and agriculture. The increase in available 'omics data has recently provided a large opportunity for mining novel enzymes, biosynthetic gene clusters, and molecules. While these data primarily consist of DNA sequences, other types of data provide important complementary information. Due to their size, the approaches proven successful at discovering novel proteins of canonical size cannot be naïvely applied to the discovery of peptides. Peptides can be encoded directly in the genome as short open reading frames (smORFs), or they can be derived from larger proteins by proteolysis. Both of these peptide classes pose challenges as simple methods for their prediction result in large numbers of false positives. Similarly, functional annotation of larger proteins, traditionally based on sequence similarity to infer orthology and then transferring functions between characterized proteins and uncharacterized ones, cannot be applied for short sequences. The use of these techniques is much more limited and alternative approaches based on machine learning are used instead. Here, we review the limitations of traditional methods as well as the alternative methods that have recently been developed for discovering novel bioactive peptides with a focus on prokaryotic genomes and metagenomes.}, } @article {pmid38457496, year = {2024}, author = {Pigani, E and Mele, BH and Campese, L and Ser-Giacomi, E and Ribera, M and Iudicone, D and Suweis, S}, title = {Deviation from neutral species abundance distributions unveils geographical differences in the structure of diatom communities.}, journal = {Science advances}, volume = {10}, number = {10}, pages = {eadh0477}, pmid = {38457496}, issn = {2375-2548}, mesh = {*Diatoms ; Plankton ; Biodiversity ; Oceans and Seas ; Ecosystem ; }, abstract = {In recent years, the application of metagenomics techniques has advanced our understanding of plankton communities and their global distribution. Despite this progress, the relationship between the abundance distribution of diatom species and varying marine environmental conditions remains poorly understood. This study, leveraging data from the Tara Oceans expedition, tests the hypothesis that diatoms in sampled stations display a consistent species abundance distribution structure, as though they were sampled from a single ocean-wide metacommunity. Using a neutral sampling theory, we thus develop a framework to estimate the structure and diversity of diatom communities at each sampling station given the shape of the species abundance distribution of the metacommunity and the information of a reference station. Our analysis reveals a substantial temperature gradient in the discrepancies between predicted and observed biodiversity across the sampled stations. These findings challenge the hypothesis of a single neutral metacommunity, indicating that environmental differences substantially influence both the composition and structure of diatom communities.}, } @article {pmid38455081, year = {2024}, author = {Renzi, S and Nenciarini, S and Bacci, G and Cavalieri, D}, title = {Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome.}, journal = {Microbiome research reports}, volume = {3}, number = {1}, pages = {2}, pmid = {38455081}, issn = {2771-5965}, abstract = {Even if their impact is often underestimated, yeasts and yeast-like fungi represent the most prevalent eukaryotic members of microbial communities on Earth. They play numerous roles in natural ecosystems and in association with their hosts. They are involved in the food industry and pharmaceutical production, but they can also cause diseases in other organisms, making the understanding of their biology mandatory. The ongoing loss of biodiversity due to overexploitation of environmental resources is a growing concern in many countries. Therefore, it becomes crucial to understand the ecology and evolutionary history of these organisms to systematically classify them. To achieve this, it is essential that our knowledge of the mycobiota reaches a level similar to that of the bacterial communities. To overcome the existing challenges in the study of fungal communities, the first step should be the establishment of standardized techniques for the correct identification of species, even from complex matrices, both in wet lab practices and in bioinformatic tools.}, } @article {pmid38454513, year = {2024}, author = {Lavecchia, A and Fosso, B and Engelen, AH and Borin, S and Manzari, C and Picardi, E and Pesole, G and Placido, A}, title = {Macroalgal microbiomes unveil a valuable genetic resource for halogen metabolism.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {47}, pmid = {38454513}, issn = {2049-2618}, support = {UIDB/04326/2020//Portuguese national funds from FCT/ ; 634486//European Commission/ ; 634486//European Commission/ ; 634486//European Commission/ ; }, mesh = {*Rhodophyta/genetics/metabolism ; *Microbiota/genetics ; Bacteria/genetics/metabolism ; *Seaweed/genetics/metabolism ; Metagenome ; *Anti-Infective Agents ; Halogens/metabolism ; }, abstract = {BACKGROUND: Macroalgae, especially reds (Rhodophyta Division) and browns (Phaeophyta Division), are known for producing various halogenated compounds. Yet, the reasons underlying their production and the fate of these metabolites remain largely unknown. Some theories suggest their potential antimicrobial activity and involvement in interactions between macroalgae and prokaryotes. However, detailed investigations are currently missing on how the genetic information of prokaryotic communities associated with macroalgae may influence the fate of organohalogenated molecules.

RESULTS: To address this challenge, we created a specialized dataset containing 161 enzymes, each with a complete enzyme commission number, known to be involved in halogen metabolism. This dataset served as a reference to annotate the corresponding genes encoded in both the metagenomic contigs and 98 metagenome-assembled genomes (MAGs) obtained from the microbiome of 2 red (Sphaerococcus coronopifolius and Asparagopsis taxiformis) and 1 brown (Halopteris scoparia) macroalgae. We detected many dehalogenation-related genes, particularly those with hydrolytic functions, suggesting their potential involvement in the degradation of a wide spectrum of halocarbons and haloaromatic molecules, including anthropogenic compounds. We uncovered an array of degradative gene functions within MAGs, spanning various bacterial orders such as Rhodobacterales, Rhizobiales, Caulobacterales, Geminicoccales, Sphingomonadales, Granulosicoccales, Microtrichales, and Pseudomonadales. Less abundant than degradative functions, we also uncovered genes associated with the biosynthesis of halogenated antimicrobial compounds and metabolites.

CONCLUSION: The functional data provided here contribute to understanding the still largely unexplored role of unknown prokaryotes. These findings support the hypothesis that macroalgae function as holobionts, where the metabolism of halogenated compounds might play a role in symbiogenesis and act as a possible defense mechanism against environmental chemical stressors. Furthermore, bacterial groups, previously never connected with organohalogen metabolism, e.g., Caulobacterales, Geminicoccales, Granulosicoccales, and Microtrichales, functionally characterized through MAGs reconstruction, revealed a biotechnologically relevant gene content, useful in synthetic biology, and bioprospecting applications. Video Abstract.}, } @article {pmid38454476, year = {2024}, author = {Li, C and Jin, S and Lv, O and Wang, G and Zhang, Y and Li, S and Zhang, W and Long, F and Shen, Z and Bai, S and Zhaxi, D and Kong, F and Yan, Q and Xiao, Z}, title = {Comparative analysis of the vaginal bacteriome and virome in healthy women living in high-altitude and sea-level areas.}, journal = {European journal of medical research}, volume = {29}, number = {1}, pages = {157}, pmid = {38454476}, issn = {2047-783X}, mesh = {Pregnancy ; Female ; Humans ; Virome/genetics ; Altitude ; Vagina/microbiology ; *Microbiota ; *Sexually Transmitted Diseases ; *Viruses ; }, abstract = {The vaginal microbiota plays an important role in the health of the female reproductive tract and is closely associated with various pregnancy outcomes and sexually transmitted diseases. Plenty of internal and external factors have strong influence on the changes in a woman's vaginal microbiome. However, the effect of a high-altitude on female vaginal microbiota has not been described. In this study, we characterized the vaginal bacteriome and virome of 13 and 34 healthy women living in high-altitude and sea-level areas, using whole-metagenome shotgun sequencing of their vaginal mucus samples. The results revealed that the vaginal bacteriomes of high-altitude individuals are featured by a significant increase of species diversity, depletion of Lactobacillus crispatus, and more abundant of some anaerobic bacteria, such as Chlamydia trachomatis, Mageeibacillus indolicus, Dialister micraerophilus, and Sneathia amnii). In addition, the vagina samples of sea-level subjects harbor more Lactobacillus strains, whereas the anaerobic bacteroidetes strains mostly appeared in high-altitude subjects. Identified and assembled 191 virus operational taxonomic units (vOTUs), there were significant differences in the abundance of 107 vOTUs between the two groups. Together, the results of this study raised the understanding of bacteriome and virome in the vagina of women at different elevations, and demonstrated that the vaginal microbiome is related to the high-altitude geographic adaptation.}, } @article {pmid38454103, year = {2024}, author = {Vázquez, X and Lumbreras-Iglesias, P and Rodicio, MR and Fernández, J and Bernal, T and Moreno, AF and de Ugarriza, PL and Fernández-Verdugo, A and Margolles, A and Sabater, C}, title = {Study of the intestinal microbiota composition and the effect of treatment with intensive chemotherapy in patients recovered from acute leukemia.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {5585}, pmid = {38454103}, issn = {2045-2322}, support = {FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Bacteria/genetics ; *Microbiota ; *Leukemia, Myeloid, Acute ; Bacteroidetes ; }, abstract = {A dataset comprising metagenomes of outpatients (n = 28) with acute leukemia (AL) and healthy controls (n = 14) was analysed to investigate the associations between gut microbiota composition and metabolic activity and AL. According to the results obtained, no significant differences in the microbial diversity between AL outpatients and healthy controls were found. However, significant differences in the abundance of specific microbial clades of healthy controls and AL outpatients were found. We found some differences at taxa level. The relative abundance of Enterobacteriaceae, Prevotellaceae and Rikenellaceae was increased in AL outpatients, while Bacteirodaceae, Bifidobacteriaceae and Lachnospiraceae was decreased. Interestingly, the abundances of several taxa including Bacteroides and Faecalibacterium species showed variations based on recovery time from the last cycle of chemotherapy. Functional annotation of metagenome-assembled genomes (MAGs) revealed the presence of functional domains corresponding to therapeutic enzymes including L-asparaginase in a wide range of genera including Prevotella, Ruminococcus, Faecalibacterium, Alistipes, Akkermansia. Metabolic network modelling revealed potential symbiotic relationships between Veillonella parvula and Levyella massiliensis and several species found in the microbiota of AL outpatients. These results may contribute to develop strategies for the recovery of microbiota composition profiles in the treatment of patients with AL.}, } @article {pmid38453993, year = {2024}, author = {Bergfeldt, N and Kırdök, E and Oskolkov, N and Mirabello, C and Unneberg, P and Malmström, H and Fraser, M and Sanchez-Quinto, F and Jorgensen, R and Skar, B and Lidén, K and Jakobsson, M and Storå, J and Götherström, A}, title = {Identification of microbial pathogens in Neolithic Scandinavian humans.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {5630}, pmid = {38453993}, issn = {2045-2322}, support = {2017-02503//Vetenskapsrådet/ ; 2019-00849//Vetenskapsrådet/ ; P21-0266//Riksbankens Jubileumsfond/ ; P19.0740:1//Riksbankens Jubileumsfond/ ; }, mesh = {Humans ; Agriculture ; *DNA, Mitochondrial/genetics ; Europe ; History, Ancient ; *Yersinia/classification/isolation & purification ; *Microbiota ; }, abstract = {With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.}, } @article {pmid38452204, year = {2024}, author = {Gios, E and Mosley, OE and Hoggard, M and Handley, KM}, title = {High niche specificity and host genetic diversity of groundwater viruses.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38452204}, issn = {1751-7370}, support = {UOAX1720//MBIE Smart Ideas/ ; 2101//Genomics Aotearoa for M. Hoggard/ ; //New Zealand eScience Infrastructure/ ; }, mesh = {Bacteria/genetics/metabolism ; *Microbiota ; *Groundwater/microbiology ; *Viruses/genetics ; Genetic Variation ; }, abstract = {Viruses are key members of microbial communities that exert control over host abundance and metabolism, thereby influencing ecosystem processes and biogeochemical cycles. Aquifers are known to host taxonomically diverse microbial life, yet little is known about viruses infecting groundwater microbial communities. Here, we analysed 16 metagenomes from a broad range of groundwater physicochemistries. We recovered 1571 viral genomes that clustered into 468 high-quality viral operational taxonomic units. At least 15% were observed to be transcriptionally active, although lysis was likely constrained by the resource-limited groundwater environment. Most were unclassified (95%), and the remaining 5% were Caudoviricetes. Comparisons with viruses inhabiting other aquifers revealed no shared species, indicating substantial unexplored viral diversity. In silico predictions linked 22.4% of the viruses to microbial host populations, including to ultra-small prokaryotes, such as Patescibacteria and Nanoarchaeota. Many predicted hosts were associated with the biogeochemical cycling of carbon, nitrogen, and sulfur. Metabolic predictions revealed the presence of 205 putative auxiliary metabolic genes, involved in diverse processes associated with the utilization of the host's intracellular resources for biosynthesis and transformation reactions, including those involved in nucleotide sugar, glycan, cofactor, and vitamin metabolism. Viruses, prokaryotes overall, and predicted prokaryotic hosts exhibited narrow spatial distributions, and relative abundance correlations with the same groundwater parameters (e.g. dissolved oxygen, nitrate, and iron), consistent with host control over viral distributions. Results provide insights into underexplored groundwater viruses, and indicate the large extent to which viruses may manipulate microbial communities and biogeochemistry in the terrestrial subsurface.}, } @article {pmid38452018, year = {2024}, author = {Du, Z and Behrens, SF}, title = {Effect of target gene sequence evenness and dominance on real-time PCR quantification of artificial sulfate-reducing microbial communities.}, journal = {PloS one}, volume = {19}, number = {3}, pages = {e0299930}, pmid = {38452018}, issn = {1932-6203}, mesh = {Real-Time Polymerase Chain Reaction/methods ; Phylogeny ; Reproducibility of Results ; *Sulfates ; *Microbiota/genetics ; }, abstract = {Quantitative real-time PCR of phylogenetic and functional marker genes is among the most commonly used techniques to quantify the abundance of microbial taxa in environmental samples. However, in most environmental applications, the approach is a rough assessment of population abundance rather than an exact absolute quantification method because of PCR-based estimation biases caused by multiple factors. Previous studies on these technical issues have focused on primer or template sequence features or PCR reaction conditions. However, how target gene sequence characteristics (e.g., evenness and dominance) in environmental samples affect qPCR quantifications has not been well studied. Here, we compared three primer sets targeting the beta subunit of the dissimilatory sulfite reductase (dsrB) to investigate qPCR quantification performance under different target gene sequence evenness and dominance conditions using artificial gBlock template mixtures designed accordingly. Our results suggested that the qPCR quantification performance of all tested primer sets was determined by the comprehensive effect of the target gene sequence evenness and dominance in environmental samples. Generally, highly degenerate primer sets have equivalent or better qPCR quantification results than a more target-specific primer set. Low template concentration in this study (~105 copies/L) will exaggerate the qPCR quantification results difference among tested primer sets. Improvements to the accuracy and reproducibility of qPCR assays for gene copy number quantification in environmental microbiology and microbial ecology studies should be based on prior knowledge of target gene sequence information acquired by metagenomic analysis or other approaches, careful selection of primer sets, and proper reaction conditions optimization.}, } @article {pmid38451250, year = {2024}, author = {Bustos-Diaz, ED and Cruz-Perez, A and Garfias-Gallegos, D and D'Agostino, PM and Gehringer, MM and Cibrian-Jaramillo, A and Barona-Gomez, F}, title = {Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals.}, journal = {Microbial genomics}, volume = {10}, number = {3}, pages = {}, pmid = {38451250}, issn = {2057-5858}, mesh = {Phylogeny ; *Symbiosis ; Australia ; Coculture Techniques ; *Genomics ; }, abstract = {Cycads are known to host symbiotic cyanobacteria, including Nostocales species, as well as other sympatric bacterial taxa within their specialized coralloid roots. Yet, it is unknown if these bacteria share a phylogenetic origin and/or common genomic functions that allow them to engage in facultative symbiosis with cycad roots. To address this, we obtained metagenomic sequences from 39 coralloid roots sampled from diverse cycad species and origins in Australia and Mexico. Culture-independent shotgun metagenomic sequencing was used to validate sub-community co-cultures as an efficient approach for functional and taxonomic analysis. Our metanalysis shows a host-independent microbiome core consisting of seven bacterial orders with high species diversity within the identified taxa. Moreover, we recovered 43 cyanobacterial metagenome-assembled genomes, and in addition to Nostoc spp., symbiotic cyanobacteria of the genus Aulosira were identified for the first time. Using this robust dataset, we used phylometagenomic analysis to reveal three monophyletic cyanobiont clades, two host-generalist and one cycad-specific that includes Aulosira spp. Although the symbiotic clades have independently arisen, they are enriched in certain functional genes, such as those related to secondary metabolism. Furthermore, the taxonomic composition of associated sympatric bacterial taxa remained constant. Our research quadruples the number of cycad cyanobiont genomes and provides a robust framework to decipher cyanobacterial symbioses, with the potential of improving our understanding of symbiotic communities. This study lays a solid foundation to harness cyanobionts for agriculture and bioprospection, and assist in conservation of critically endangered cycads.}, } @article {pmid38451230, year = {2024}, author = {Eisenhofer, R and Nesme, J and Santos-Bay, L and Koziol, A and Sørensen, SJ and Alberdi, A and Aizpurua, O}, title = {A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics.}, journal = {Microbiology spectrum}, volume = {12}, number = {4}, pages = {e0359023}, pmid = {38451230}, issn = {2165-0497}, support = {DNRF143//Danish National Research Foundation award/ ; CF20-0460//The Carlsberg Foundation/ ; }, mesh = {Animals ; Mice ; Sequence Analysis, DNA/methods ; *Genome, Bacterial ; *Microbiota/genetics ; Metagenomics/methods ; DNA ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level of detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well as a combination of both. To assess the pros and cons of these different approaches, we used 22 fecal DNA extracts collected weekly for 11 weeks from two respective lab mice to study seven performance metrics over four combinations of sequencing depth and technology: (i) 20 Gbp of Illumina short-read data, (ii) 40 Gbp of short-read data, (iii) 20 Gbp of PacBio HiFi long-read data, and (iv) 40 Gbp of hybrid (20 Gbp of short-read +20 Gbp of long-read) data. No strategy was best for all metrics; instead, each one excelled across different metrics. The long-read approach yielded the best assembly statistics, with the highest N50 and lowest number of contigs. The 40 Gbp short-read approach yielded the highest number of refined bins. Finally, the hybrid approach yielded the longest assemblies and the highest mapping rate to the bacterial genomes. Our results suggest that while long-read sequencing significantly improves the quality of reconstructed bacterial genomes, it is more expensive and requires deeper sequencing than short-read approaches to recover a comparable amount of reconstructed genomes. The most optimal strategy is study-specific and depends on how researchers assess the trade-off between the quantity and quality of recovered genomes.IMPORTANCEMice are an important model organism for understanding the gut microbiome. When studying these gut microbiomes using DNA techniques, researchers can choose from technologies that use short or long DNA reads. In this study, we perform an extensive benchmark between short- and long-read DNA sequencing for studying mice gut microbiomes. We find that no one approach was best for all metrics and provide information that can help guide researchers in planning their experiments.}, } @article {pmid38448281, year = {2024}, author = {Duong, JT and Pope, CE and Hayden, HS and Miller, C and Salipante, SJ and Rowe, SM and Solomon, GM and Nichols, D and Hoffman, LR and Narkewicz, MR and Green, N}, title = {Alterations in the fecal microbiota in patients with advanced cystic fibrosis liver disease after 6 months of elexacaftor/tezacaftor/ivacaftor.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {23}, number = {3}, pages = {490-498}, pmid = {38448281}, issn = {1873-5010}, support = {K24 HL141669/HL/NHLBI NIH HHS/United States ; P30 DK089507/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Female ; Humans ; Male ; Young Adult ; *Aminophenols/therapeutic use ; *Benzodioxoles/therapeutic use ; Chloride Channel Agonists/therapeutic use ; *Cystic Fibrosis/microbiology/drug therapy ; Drug Combinations ; Dysbiosis/microbiology/etiology ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Indoles/therapeutic use ; Liver Diseases/microbiology/etiology ; Pyrazoles/therapeutic use ; Pyridines ; Pyrroles/administration & dosage ; Pyrrolidines ; *Quinolones/therapeutic use ; }, abstract = {BACKGROUND: Cystic fibrosis associated liver disease (CFLD) carries a significant disease burden with no effective preventive therapies. According to the gut-liver axis hypothesis for CFLD pathogenesis, dysbiosis and increased intestinal inflammation and permeability permit pathogenic bacterial translocation into the portal circulation, leading to hepatic inflammation and fibrosis. Evaluating the effect of CFTR (cystic fibrosis transmembrane conductance regulator) modulation with elexacaftor/tezacaftor/ivacaftor (ETI) may help determine the role of CFTR in CFLD and increase understanding of CFLD pathogenesis, which is critical for developing therapies. We aimed to characterize the fecal microbiota in participants with CF with and without advanced CFLD (aCFLD) before and after ETI.

METHODS: This is an ancillary analysis of stool samples from participants ages ≥12 y/o enrolled in PROMISE (NCT04038047). Included participants had aCFLD (cirrhosis with or without portal hypertension, or non-cirrhotic portal hypertension) or CF without liver disease (CFnoLD). Fecal microbiota were defined by shotgun metagenomic sequencing at baseline and 1 and 6 months post-ETI.

RESULTS: We analyzed 93 samples from 34 participants (11 aCFLD and 23 CFnoLD). Compared to CFnoLD, aCFLD had significantly higher baseline relative abundances of potential pathogens Streptococcus salivarius and Veillonella parvula. Four of 11 aCFLD participants had an initially abnormal fecal calprotectin that normalized 6 months post-ETI, correlating with a significant decrease in S. salivarius and a trend towards decreasing V. parvula.

CONCLUSIONS: These results support an association between dysbiosis and intestinal inflammation in CFLD with improvements in both post-ETI, lending further support to the gut-liver axis in aCFLD.}, } @article {pmid38448159, year = {2024}, author = {Zakharevich, NV and Morozov, MD and Kanaeva, VA and Filippov, MS and Zyubko, TI and Ivanov, AB and Ulyantsev, VI and Klimina, KM and Olekhnovich, EI}, title = {Systemic metabolic depletion of gut microbiome undermines responsiveness to melanoma immunotherapy.}, journal = {Life science alliance}, volume = {7}, number = {5}, pages = {}, pmid = {38448159}, issn = {2575-1077}, mesh = {Animals ; Humans ; *Gastrointestinal Microbiome/genetics ; *Melanoma/therapy ; Quality of Life ; Immunotherapy ; Vitamin B 12 ; }, abstract = {Immunotherapy has proven to be a boon for patients battling metastatic melanoma, significantly improving their clinical condition and overall quality of life. A compelling link between the composition of the gut microbiome and the efficacy of immunotherapy has been established in both animal models and human patients. However, the precise biological mechanisms by which gut microbes influence treatment outcomes remain poorly understood. Using a robust dataset of 680 fecal metagenomes from melanoma patients, a detailed catalog of metagenome-assembled genomes (MAGs) was constructed to explore the compositional and functional properties of the gut microbiome. Our study uncovered significant findings that deepen the understanding of the intricate relationship between gut microbes and the efficacy of melanoma immunotherapy. In particular, we discovered the specific metagenomic profile of patients with favorable treatment outcomes, characterized by a prevalence of MAGs with increased overall metabolic potential and proficiency in polysaccharide utilization, along with those responsible for cobalamin and amino acid production. Furthermore, our investigation of the biosynthetic pathways of short-chain fatty acids, known for their immunomodulatory role, revealed a differential abundance of these pathways among the specific MAGs. Among others, the cobalamin-dependent Wood-Ljungdahl pathway of acetate synthesis was directly associated with responsiveness to melanoma immunotherapy.}, } @article {pmid38447371, year = {2024}, author = {Wang, Y and Zhang, Z and Kang, J and Chen, B and Hong, W and Lv, B and Wang, T and Qian, H}, title = {Phages in different habitats and their ability to carry antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {469}, number = {}, pages = {133941}, doi = {10.1016/j.jhazmat.2024.133941}, pmid = {38447371}, issn = {1873-3336}, mesh = {Humans ; *Bacteriophages/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Ecosystem ; Biodiversity ; Genes, Bacterial ; }, abstract = {As the most abundant organisms on Earth, phages play a key role in the evolution of bacterial antibiotic resistance. Although previous studies have demonstrated the molecular mechanisms of horizontal gene transfer mediated by mobile genetic elements, our understanding of the intertwined relationships between antibiotic resistance genes (ARGs) and phages is limited. In this study, we analysed 2781 metagenomic samples to reveal the composition and species interactions of phage communities in different habitats as well as their capacity to carry ARGs with health risks. The composition of phage communities varies in different habitats and mainly depends on environmental conditions. Terrestrial habitats display more complex and robust interactions between phages than aquatic and human-associated habitats, resulting in the highest biodiversity of phages. Several types of phages in certain taxa (4.95-7.67%, mainly belonging to Caudoviricetes) have the capacity to carry specific ARGs and display a high potential risk to human health, especially in human-associated habitats. Overall, our results provide insights into the assembly mechanisms of phage communities and their effects on the dissemination of antibiotic resistance.}, } @article {pmid38446011, year = {2024}, author = {Ni, Y and Chu, T and Yan, S and Wang, Y}, title = {Forty-nine metagenomic-assembled genomes from an aquatic virome expand Caudoviricetes by 45 potential new families and the newly uncovered Gossevirus of Bamfordvirae.}, journal = {The Journal of general virology}, volume = {105}, number = {3}, pages = {}, doi = {10.1099/jgv.0.001967}, pmid = {38446011}, issn = {1465-2099}, mesh = {Humans ; *Virome ; Metagenome ; Flavobacterium/genetics ; Metagenomics ; *Viruses ; }, abstract = {Twenty complete genomes (29-63 kb) and 29 genomes with an estimated completeness of over 90 % (30-90 kb) were identified for novel dsDNA viruses in the Yangshan Harbor metavirome. These newly discovered viruses contribute to the expansion of viral taxonomy by introducing 46 potential new families. Except for one virus, all others belong to the class Caudoviricetes. The exception is a novel member of the recently characterized viral group known as Gossevirus. Fifteen viruses were predicted to be temperate. The predicted hosts for the viruses appear to be involved in various aspects of the nitrogen cycle, including nitrogen fixation, oxidation and denitrification. Two viruses were identified to have a host of Flavobacterium and Tepidimonas fonticaldi, respectively, by matching CRISPR spacers with viral protospacers. Our findings provide an overview for characterizing and identifying specific viruses from Yangshan Harbor. The Gossevirus-like virus uncovered emphasizes the need for further comprehensive isolation and investigation of polinton-like viruses.}, } @article {pmid38445871, year = {2024}, author = {Cai, M and Zhang, C and Ndungu, CN and Liu, G and Liu, W and Zhang, Q}, title = {Linking ecosystem multifunctionality to microbial community features in rivers along a latitudinal gradient.}, journal = {mSystems}, volume = {9}, number = {4}, pages = {e0014724}, pmid = {38445871}, issn = {2379-5077}, support = {32022051//MOST | National Natural Science Foundation of China (NSFC)/ ; 32201387//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Rivers ; Rhizosphere ; Plants ; *Microbiota ; Soil/chemistry ; Nitrogen ; }, abstract = {Microorganisms regulate numerous ecosystem functions and show considerable differences along a latitudinal gradient. Although studies have revealed the latitudinal patterns of microbial community structure and single ecosystem function, the latitudinal patterns of ecosystem multifunctionality (EMF) and how microbial communities affect EMF along a latitudinal gradient remain unclear. Here, we collected channel sediments, riparian rhizosphere soils, and riparian bulk soils from 30 rivers across China and calculated EMF using 18 variables related to nitrogen cycling, nutrient pool, plant productivity, and water quality. We also determined microbial diversity (taxonomic and functional) and microbial network complexity using metagenomic sequencing. The results showed that EMF significantly decreased with increasing latitude in riparian rhizosphere and bulk soils but not in channel sediments. Microbial taxonomic and functional richness (observed species) in channel sediments were significantly higher in the low-latitude group than in the high-latitude group. However, microbial co-occurrence networks were more complex in the high-latitude group compared with the low-latitude group. Abiotic factors, primarily geographic and climatic factors, contributed more to EMF than microbial diversity and network complexity parameters in which only betweenness centralization had a significant relationship with EMF. Together, this study provides insight into the latitudinal pattern of EMF in rivers and highlights the importance of large-scale factors in explaining such latitudinal patterns.IMPORTANCEEcosystem multifunctionality (EMF) is the capacity of an ecosystem to provide multiple functions simultaneously. Microorganisms, as dominant drivers of belowground processes, have a profound effect on ecosystem functions. Although studies have revealed the latitudinal patterns of microbial community structure and single ecosystem function, the latitudinal patterns of EMF and how microbial communities affect EMF along a latitudinal gradient remain unclear. We collected channel sediments, riparian rhizosphere soils, and riparian bulk soils from 30 rivers along a latitudinal gradient across China and calculated EMF using 18 variables related to nitrogen cycling, nutrient pool, plant productivity, and water quality. This study fills a critical knowledge gap regarding the latitudinal patterns and drivers of EMF in river ecosystems and gives new insights into how microbial diversity and network complexity affect EMF from a metagenomic perspective.}, } @article {pmid38445870, year = {2024}, author = {Yap, M and O'Sullivan, O and O'Toole, PW and Sheehan, JJ and Fenelon, MA and Cotter, PD}, title = {Seasonal and geographical impact on the Irish raw milk microbiota correlates with chemical composition and climatic variables.}, journal = {mSystems}, volume = {9}, number = {4}, pages = {e0129023}, pmid = {38445870}, issn = {2379-5077}, support = {16/RC/3835//Science Foundation Ireland (SFI)/ ; TC 2020 0028//Enterprise Ireland/ ; }, mesh = {Female ; Animals ; *Milk ; Seasons ; Bacteria ; *Microbiota ; Metagenome ; }, abstract = {UNLABELLED: Season and location have previously been shown to be associated with differences in the microbiota of raw milk, especially in milk from pasture-based systems. Here, we further advance research in this area by examining differences in the raw milk microbiota from several locations across Ireland over 12 months, and by investigating microbiota associations with climatic variables and chemical composition. Shotgun metagenomic sequencing was used to investigate the microbiota of raw milk collected from nine locations (n = 241). Concurrent chemical analysis of the protein, fat, lactose, total solids, nonprotein nitrogen contents, and titratable acidity (TA) of the same raw milk were performed. Although the raw milk microbiota was highly diverse, a core microbiota was found, with Pseudomonas_E, Lactococcus, Acinetobacter, and Leuconostoc present in all samples. Microbiota diversity significantly differed by season and location, with differences in seasonality and geography corresponding to 11.8% and 10.5% of the variation in the microbiota. Functional and antibiotic resistance profiles also varied across season and location. The analysis of other metadata revealed additional interactions, such as an association between mean daily air and grass temperatures with the abundance of spoilage taxa like Pseudomonas species. Correlations were identified between pathogenic, mastitis-related species, fat content, and the number of sun hours, suggesting a seasonal effect. Ultimately, this study expands our understanding of the interconnected nature of the microbiota, environment/climate variables, and chemical composition of raw milk and provides evidence of a season- and location-specific microbiota.

IMPORTANCE: The microbiota of raw milk is influenced by many factors that encourage or prevent the introduction and growth of both beneficial and undesirable microorganisms. The seasonal and geographical impacts on the microbial communities of raw milk have been previously seen, but the relationships with environmental factors and the chemical composition has yet to be investigated. In this year-long study, we found that while raw milk is highly diverse, a core microbiota was detected for Irish raw milk, with strong evidence of seasonal and geographical influence. We also found associations between groups of microorganisms, environmental factors, and milk composition, which expand current knowledge on the relationships between microbial and chemical composition and the climate. These results provide evidence for the development of a tool to allow for the prediction of raw milk quality and safety.}, } @article {pmid38445660, year = {2024}, author = {Heumel, S and de Rezende Rodovalho, V and Urien, C and Specque, F and Brito Rodrigues, P and Robil, C and Delval, L and Sencio, V and Descat, A and Deruyter, L and Ferreira, S and Gomes Machado, M and Barthelemy, A and Angulo, FS and Haas, JT and Goosens, JF and Wolowczuk, I and Grangette, C and Rouillé, Y and Grimaud, G and Lenski, M and Hennart, B and Ramirez Vinolo, MA and Trottein, F}, title = {Shotgun metagenomics and systemic targeted metabolomics highlight indole-3-propionic acid as a protective gut microbial metabolite against influenza infection.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2325067}, pmid = {38445660}, issn = {1949-0984}, mesh = {Humans ; Animals ; Mice ; Propionates ; *Influenza, Human ; *Gastrointestinal Microbiome ; Tryptophan ; *Actinobacteria ; Inflammation ; Polyamines ; }, abstract = {The gut-to-lung axis is critical during respiratory infections, including influenza A virus (IAV) infection. In the present study, we used high-resolution shotgun metagenomics and targeted metabolomic analysis to characterize influenza-associated changes in the composition and metabolism of the mouse gut microbiota. We observed several taxonomic-level changes on day (D)7 post-infection, including a marked reduction in the abundance of members of the Lactobacillaceae and Bifidobacteriaceae families, and an increase in the abundance of Akkermansia muciniphila. On D14, perturbation persisted in some species. Functional scale analysis of metagenomic data revealed transient changes in several metabolic pathways, particularly those leading to the production of short-chain fatty acids (SCFAs), polyamines, and tryptophan metabolites. Quantitative targeted metabolomics analysis of the serum revealed changes in specific classes of gut microbiota metabolites, including SCFAs, trimethylamine, polyamines, and indole-containing tryptophan metabolites. A marked decrease in indole-3-propionic acid (IPA) blood level was observed on D7. Changes in microbiota-associated metabolites correlated with changes in taxon abundance and disease marker levels. In particular, IPA was positively correlated with some Lactobacillaceae and Bifidobacteriaceae species (Limosilactobacillus reuteri, Lactobacillus animalis) and negatively correlated with Bacteroidales bacterium M7, viral load, and inflammation markers. IPA supplementation in diseased animals reduced viral load and lowered local (lung) and systemic inflammation. Treatment of mice with antibiotics targeting IPA-producing bacteria before infection enhanced viral load and lung inflammation, an effect inhibited by IPA supplementation. The results of this integrated metagenomic-metabolomic analysis highlighted IPA as an important contributor to influenza outcomes and a potential biomarker of disease severity.}, } @article {pmid38445567, year = {2024}, author = {Gottscho, AD and Mulcahy, DG and Leaché, AD and de Queiroz, K and Lovich, RE}, title = {Population genomics of flat-tailed horned lizards (Phrynosoma mcallii) informs conservation and management across a fragmented Colorado Desert landscape.}, journal = {Molecular ecology}, volume = {33}, number = {7}, pages = {e17308}, doi = {10.1111/mec.17308}, pmid = {38445567}, issn = {1365-294X}, support = {//Smithsonian Institution, L.A.B./ ; //Smithsonian Institution, Peter Buck Postdoctoral Fellowship/ ; 16-824//Department of Defense Legacy Resource Management Program/ ; }, mesh = {Animals ; Phylogeny ; *Metagenomics ; Colorado ; Ecosystem ; *Lizards/genetics ; Genetic Variation/genetics ; DNA, Mitochondrial/genetics ; Phylogeography ; }, abstract = {Phrynosoma mcallii (flat-tailed horned lizards) is a species of conservation concern in the Colorado Desert of the United States and Mexico. We analysed ddRADseq data from 45 lizards to estimate population structure, infer phylogeny, identify migration barriers, map genetic diversity hotspots, and model demography. We identified the Colorado River as the main geographic feature contributing to population structure, with the populations west of this barrier further subdivided by the Salton Sea. Phylogenetic analysis confirms that northwestern populations are nested within southeastern populations. The best-fit demographic model indicates Pleistocene divergence across the Colorado River, with significant bidirectional gene flow, and a severe Holocene population bottleneck. These patterns suggest that management strategies should focus on maintaining genetic diversity on both sides of the Colorado River and the Salton Sea. We recommend additional lands in the United States and Mexico that should be considered for similar conservation goals as those in the Rangewide Management Strategy. We also recommend periodic rangewide genomic sampling to monitor ongoing attrition of diversity, hybridization, and changing structure due to habitat fragmentation, climate change, and other long-term impacts.}, } @article {pmid38444804, year = {2024}, author = {Suo, B and Castro, MP and Sreenivasa, MY}, title = {Editorial: Microbiota biodiversity of traditional fermented products.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1380205}, doi = {10.3389/fmicb.2024.1380205}, pmid = {38444804}, issn = {1664-302X}, } @article {pmid38443997, year = {2024}, author = {Yerke, A and Fry Brumit, D and Fodor, AA}, title = {Proportion-based normalizations outperform compositional data transformations in machine learning applications.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {45}, pmid = {38443997}, issn = {2049-2618}, mesh = {*Algorithms ; Machine Learning ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Normalization, as a pre-processing step, can significantly affect the resolution of machine learning analysis for microbiome studies. There are countless options for normalization scheme selection. In this study, we examined compositionally aware algorithms including the additive log ratio (alr), the centered log ratio (clr), and a recent evolution of the isometric log ratio (ilr) in the form of balance trees made with the PhILR R package. We also looked at compositionally naïve transformations such as raw counts tables and several transformations that are based on relative abundance, such as proportions, the Hellinger transformation, and a transformation based on the logarithm of proportions (which we call "lognorm").

RESULTS: In our evaluation, we used 65 metadata variables culled from four publicly available datasets at the amplicon sequence variant (ASV) level with a random forest machine learning algorithm. We found that different common pre-processing steps in the creation of the balance trees made very little difference in overall performance. Overall, we found that the compositionally aware data transformations such as alr, clr, and ilr (PhILR) performed generally slightly worse or only as well as compositionally naïve transformations. However, relative abundance-based transformations outperformed most other transformations by a small but reliably statistically significant margin.

CONCLUSIONS: Our results suggest that minimizing the complexity of transformations while correcting for read depth may be a generally preferable strategy in preparing data for machine learning compared to more sophisticated, but more complex, transformations that attempt to better correct for compositionality. Video Abstract.}, } @article {pmid38443576, year = {2024}, author = {Yu, MK and Fogarty, EC and Eren, AM}, title = {Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess.}, journal = {Nature microbiology}, volume = {9}, number = {3}, pages = {830-847}, pmid = {38443576}, issn = {2058-5276}, support = {RC2 DK122394/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Metagenome ; *Algorithms ; Life Style ; Machine Learning ; Plasmids/genetics ; }, abstract = {Plasmids alter microbial evolution and lifestyles by mobilizing genes that often confer fitness in changing environments across clades. Yet our ecological and evolutionary understanding of naturally occurring plasmids is far from complete. Here we developed a machine-learning model, PlasX, which identified 68,350 non-redundant plasmids across human gut metagenomes and organized them into 1,169 evolutionarily cohesive 'plasmid systems' using our sequence containment-aware network-partitioning algorithm, MobMess. Individual plasmids were often country specific, yet most plasmid systems spanned across geographically distinct human populations. Cargo genes in plasmid systems included well-known determinants of fitness, such as antibiotic resistance, but also many others including enzymes involved in the biosynthesis of essential nutrients and modification of transfer RNAs, revealing a wide repertoire of likely fitness determinants in complex environments. Our study introduces computational tools to recognize and organize plasmids, and uncovers the ecological and evolutionary patterns of diverse plasmids in naturally occurring habitats through plasmid systems.}, } @article {pmid38443405, year = {2024}, author = {Ho, CW and Chen, PY and Liao, YT and Cheng, YF and Tsou, HH and Liu, TY and Liang, KH}, title = {Uncovering the microbiome landscape in sashimi delicacies.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {5454}, pmid = {38443405}, issn = {2045-2322}, support = {V113E-002-4//Taipei Veterans General Hospital/ ; }, mesh = {Animals ; Phylogeny ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Salmon ; Tuna/genetics ; Seafood ; Photobacterium ; Pseudomonas ; }, abstract = {It is widely believed that a significant portion of the gut microbiota, which play crucial roles in overall health and disease, originates from the food we consume. Sashimi is a type of popular raw seafood cuisine. Its microbiome, however, remained to be thoroughly explored. The objective of this study is to explore the microbiome composition in sashimi at the time when it is served and ready to be eaten. Specifically, our tasks include investigating the diversity and characteristics of microbial profiles in sashimi with respect to the fish types. We utilized the Sanger-sequencing based DNA barcoding technology for fish species authentication and next-generation sequencing for sashimi microbiome profiling. We investigated the microbiome profiles of amberjack, cobia, salmon, tuna and tilapia sashimi, which were all identified using the MT-CO1 DNA sequences regardless of their menu offering names. Chao1 and Shannon indexes, as well as Bray-Curtis dissimilarity index were used to evaluate the alpha and beta diversities of sashimi microbiome. We successfully validated our previous observation that tilapia sashimi has a significantly higher proportions of Pseudomonas compared to other fish sashimi, using independent samples (P = 0.0010). Salmon sashimi exhibited a notably higher Chao1 index in its microbiome in contrast to other fish species (P = 0.0031), indicating a richer and more diverse microbial ecosystem. Non-Metric Multidimensional Scaling (NMDS) based on Bray-Curtis dissimilarity index revealed distinct clusters of microbiome profiles with respect to fish types. Microbiome similarity was notably observed between amberjack and tuna, as well as cobia and salmon. The relationship of microbiome similarity can be depicted as a tree which resembles partly the phylogenetic tree of host species, emphasizing the close relationship between host evolution and microbial composition. Moreover, salmon exhibited a pronounced relative abundance of the Photobacterium genus, significantly surpassing tuna (P = 0.0079), observed consistently across various restaurant sources. In conclusion, microbiome composition of Pseudomonas is significantly higher in tilapia sashimi than in other fish sashimi. Salmon sashimi has the highest diversity of microbiome among all fish sashimi that we analyzed. The level of Photobacterium is significantly higher in salmon than in tuna across all the restaurants we surveyed. These findings provide critical insights into the intricate relationship between the host evolution and the microbial composition. These discoveries deepen our understanding of sashimi microbiota, facilitating our decision in selecting raw seafood.}, } @article {pmid38443373, year = {2024}, author = {Dzofou Ngoumelah, D and Heggeset, TMB and Haugen, T and Sulheim, S and Wentzel, A and Harnisch, F and Kretzschmar, J}, title = {Effect of model methanogens on the electrochemical activity, stability, and microbial community structure of Geobacter spp. dominated biofilm anodes.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {17}, pmid = {38443373}, issn = {2055-5008}, support = {57381414//Deutscher Akademischer Austauschdienst (German Academic Exchange Service)/ ; 731101//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {*Geobacter/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Biofilms ; Electrodes ; }, abstract = {Combining anaerobic digestion (AD) and microbial electrochemical technologies (MET) in AD-MET holds great potential. Methanogens have been identified as one cause of decreased electrochemical activity and deterioration of Geobacter spp. biofilm anodes. A better understanding of the different interactions between methanogenic genera/species and Geobacter spp. biofilms is needed to shed light on the observed reduction in electrochemical activity and stability of Geobacter spp. dominated biofilms as well as observed changes in microbial communities of AD-MET. Here, we have analyzed electrochemical parameters and changes in the microbial community of Geobacter spp. biofilm anodes when exposed to three representative methanogens with different metabolic pathways, i.e., Methanosarcina barkeri, Methanobacterium formicicum, and Methanothrix soehngenii. M. barkeri negatively affected the performance and stability of Geobacter spp. biofilm anodes only in the initial batches. In contrast, M. formicicum did not affect the stability of Geobacter spp. biofilm anodes but caused a decrease in maximum current density of ~37%. M. soehngenii induced a coloration change of Geobacter spp. biofilm anodes and a decrease in the total transferred charge by ~40%. Characterization of biofilm samples after each experiment by 16S rRNA metabarcoding, whole metagenome nanopore sequencing, and shotgun sequencing showed a higher relative abundance of Geobacter spp. after exposure to M. barkeri as opposed to M. formicicum or M. soehngenii, despite the massive biofilm dispersal observed during initial exposure to M. barkeri.}, } @article {pmid38443364, year = {2024}, author = {Xie, P and Zhou, X and Li, Y and Wu, J and Zhang, H and Huang, Y and Tan, X and Wen, L and Olasunkanmi, OI and Zhou, J and Sun, Z and Liu, M and Zhang, G and Wang, Y and Xie, P and Yang, J and Zheng, P}, title = {Gut microbial CAZymes markers for depression.}, journal = {Translational psychiatry}, volume = {14}, number = {1}, pages = {135}, pmid = {38443364}, issn = {2158-3188}, support = {cstc2021jcyj-msxmX0096//Chongqing Science and Technology Commission (Chongqing Science and Technology Commission, Chongqing People's Municipal Government)/ ; }, mesh = {Humans ; *Depressive Disorder, Major/diagnosis ; Depression ; *Gastrointestinal Microbiome ; }, abstract = {Major depressive disorder (MDD) is a serious mental illness, characterized by disturbances of gut microbiome, it is required to further explore how the carbohydrate-active enzymes (CAZymes) were changed in MDD. Here, using the metagenomic data from patients with MDD (n = 118) and heath controls (HC, n = 118), we found that the whole CAZymes signatures of MDD were significantly discriminated from that in HC. α-diversity indexes of the two groups were also significantly different. The patients with MDD were characterized by enriched Glycoside Hydrolases (GHs) and Polysaccharide Lyases (PLs) relative to HC. A panel of makers composed of 9 CAZymes mainly belonging to GHs enabled to discriminate the patients with MDD and HC with AUC of 0.824. In addition, this marker panel could classify blinded test samples from the two groups with an AUC of 0.736. Moreover, we found that baseline 4 CAZymes levels also could predict the antidepressant efficacy after adjusted confounding factors and times of depressive episode. Our findings showed that MDD was associated with disturbances of gut CAZymes, which may help to develop diagnostic and predictive tools for depression.}, } @article {pmid38442360, year = {2024}, author = {Yang, Y and Xu, N and Zhang, Z and Lei, C and Chen, B and Qin, G and Qiu, D and Lu, T and Qian, H}, title = {Deciphering Microbial Community and Nitrogen Fixation in the Legume Rhizosphere.}, journal = {Journal of agricultural and food chemistry}, volume = {72}, number = {11}, pages = {5659-5670}, doi = {10.1021/acs.jafc.3c09160}, pmid = {38442360}, issn = {1520-5118}, mesh = {*Fabaceae/genetics ; Rhizosphere ; Nitrogen Fixation ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Vegetables/genetics ; Bacteria/genetics ; Nitrogen ; Soil Microbiology ; }, abstract = {Nitrogen is the most limiting factor in crop production. Legumes establish a symbiotic relationship with rhizobia and enhance nitrogen fixation. We analyzed 1,624 rhizosphere 16S rRNA gene samples and 113 rhizosphere metagenomic samples from three typical legumes and three non-legumes. The rhizosphere microbial community of the legumes had low diversity and was enriched with nitrogen-cycling bacteria (Sphingomonadaceae, Xanthobacteraceae, Rhizobiaceae, and Bacillaceae). Furthermore, the rhizosphere microbiota of legumes exhibited a high abundance of nitrogen-fixing genes, reflecting a stronger nitrogen-fixing potential, and Streptomycetaceae and Nocardioidaceae were the predominant nitrogen-fixing bacteria. We also identified helper bacteria and confirmed through metadata analysis and a pot experiment that the synthesis of riboflavin by helper bacteria is the key factor in promoting nitrogen fixation. Our study emphasizes that the construction of synthetic communities of nitrogen-fixing bacteria and helper bacteria is crucial for the development of efficient nitrogen-fixing microbial fertilizers.}, } @article {pmid38441977, year = {2024}, author = {Chen, H and Huang, S and Zhao, Y and Sun, R and Wang, J and Yao, S and Huang, J and Yu, Z}, title = {Metagenomic analysis of the intestinal microbiome reveals the potential mechanism involved in Bacillus amyloliquefaciens in treating schistosomiasis japonica in mice.}, journal = {Microbiology spectrum}, volume = {12}, number = {4}, pages = {e0373523}, pmid = {38441977}, issn = {2165-0497}, support = {32300051//MOST | National Natural Science Foundation of China (NSFC)/ ; 32170071//MOST | National Natural Science Foundation of China (NSFC)/ ; 82102428//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022JJ40663//HSTD | Natural Science Foundation of Hunan Province ()/ ; }, mesh = {Animals ; Mice ; *Schistosomiasis japonica/drug therapy ; *Gastrointestinal Microbiome ; *Bacillus amyloliquefaciens ; Urease ; *Schistosoma japonicum/genetics ; Bacteria/genetics ; }, abstract = {UNLABELLED: Schistosomiasis japonica is one of the neglected tropical diseases characterized by chronic hepatic, intestinal granulomatous inflammation and fibrosis, as well as dysbiosis of intestinal microbiome. Previously, the probiotic Bacillus amyloliquefaciens has been shown to alleviate the pathological injuries in mice infected with Schistosoma japonicum by improving the disturbance of the intestinal microbiota. However, the underlying mechanisms involved in this process remain unclear. In this study, metagenomics sequencing and functional analysis were employed to investigate the differential changes in taxonomic composition and functional genes of the intestinal microbiome in S. japonicum-infected mice treated with B. amyloliquefaciens. The results revealed that intervention with B. amyloliquefaciens altered the taxonomic composition of the intestinal microbiota at the species level in infected mice and significantly increased the abundance of beneficial bacteria. Moreover, the abundance of predicted genes in the intestinal microbiome was also significantly changed, and the abundance of xfp/xpk and genes translated to urease was significantly restored. Further analysis showed that Limosilactobacillus reuteri was positively correlated with several KEGG Orthology (KO) genes and metabolic reactions, which might play important roles in alleviating the pathological symptoms caused by S. japonicum infection, indicating that it has the potential to function as another effective therapeutic agent for schistosomiasis. These data suggested that treatment of murine schistosomiasis japonica by B. amyloliquefaciens might be induced by alterations in the taxonomic composition and functional gene of the intestinal microbiome in mice. We hope this study will provide adjuvant strategies and methods for the early prevention and treatment of schistosomiasis japonica.

IMPORTANCE: Targeted interventions of probiotics on gut microbiome were used to explore the mechanism of alleviating schistosomiasis japonica. Through metagenomic analysis, there were significant changes in the composition of gut microbiota in mice infected with Schistosoma japonicum and significant increase in the abundance of beneficial bacteria after the intervention of Bacillus amyloliquefaciens. At the same time, the abundance of functional genes was found to change significantly. The abundance of genes related to urease metabolism and xfp/xpk related to D-erythrose 4-phosphate production was significantly restored, highlighting the importance of Limosilactobacillus reuteri in the recovery and abundance of predicted genes of the gut microbiome. These results indicated potential regulatory mechanism between the gene function of gut microbiome and host immune response. Our research lays the foundation for elucidating the regulatory mechanism of probiotic intervention in alleviating schistosomiasis japonica, and provides potential adjuvant treatment strategies for early prevention and treatment of schistosomiasis japonica.}, } @article {pmid38441971, year = {2024}, author = {Kadlečková, D and Saláková, M and Erban, T and Tachezy, R}, title = {Discovery and characterization of novel DNA viruses in Apis mellifera: expanding the honey bee virome through metagenomic analysis.}, journal = {mSystems}, volume = {9}, number = {4}, pages = {e0008824}, pmid = {38441971}, issn = {2379-5077}, support = {QK1910018; MZE-RO0423//Ministerstvo Zemědělství (Ministry of Agriculture)/ ; LX22NPO5103//Ministerstvo Školství, Mládeže a Tělovýchovy (MŠMT)/ ; SVV 260679//Charles University/ ; 101102733//EU4H Project No.101102733 (DURABLE)/ ; }, mesh = {Bees ; Animals ; Virome/genetics ; Ecosystem ; DNA Viruses/genetics ; *Viruses ; Metagenome/genetics ; *Nudiviridae ; }, abstract = {To date, many viruses have been discovered to infect honey bees. In this study, we used high-throughput sequencing to expand the known virome of the honey bee, Apis mellifera, by identifying several novel DNA viruses. While the majority of previously identified bee viruses are RNA, our study reveals nine new genomes from the Parvoviridae family, tentatively named Bee densoviruses 1 to 9. In addition, we characterized a large DNA virus, Apis mellifera filamentous-like virus (AmFLV), which shares limited protein identities with the known Apis mellifera filamentous virus. The complete sequence of AmFLV, obtained by a combination of laboratory techniques and bioinformatics, spans 152,678 bp. Linear dsDNA genome encodes for 112 proteins, of which 49 are annotated. Another large virus we discovered is Apis mellifera nudivirus, which belongs to a group of Alphanudivirus. The virus has a length of 129,467 bp and a circular dsDNA genome, and has 106 protein encoding genes. The virus contains most of the core genes of the family Nudiviridae. This research demonstrates the effectiveness of viral binning in identifying viruses in honey bee virology, showcasing its initial application in this field.IMPORTANCEHoney bees contribute significantly to food security by providing pollination services. Understanding the virome of honey bees is crucial for the health and conservation of bee populations and also for the stability of the ecosystems and economies for which they are indispensable. This study unveils previously unknown DNA viruses in the honey bee virome, expanding our knowledge of potential threats to bee health. The use of the viral binning approach we employed in this study offers a promising method to uncovering and understanding the vast viral diversity in these essential pollinators.}, } @article {pmid38441468, year = {2024}, author = {Xiao, Y and Wang, Y and Tong, B and Gu, Y and Zhou, X and Zhu, N and Xu, X and Yin, X and Kou, Y and Tan, Y and Wang, J and Li, W}, title = {Eubacterium rectale is a potential marker of altered gut microbiota in psoriasis and psoriatic arthritis.}, journal = {Microbiology spectrum}, volume = {12}, number = {4}, pages = {e0115423}, pmid = {38441468}, issn = {2165-0497}, support = {ZYJC21050//The 1.3.5 project for disciplines of excellence, West China Hospital, Sichuan University/ ; }, mesh = {Humans ; *Arthritis, Psoriatic/diagnosis/drug therapy/metabolism ; Eubacterium ; *Gastrointestinal Microbiome ; *Psoriasis/diagnosis/drug therapy/metabolism ; Feces ; }, abstract = {UNLABELLED: Previous studies have profiled the gut microbiota among psoriatic patients compared to that among healthy individuals. However, a comprehensive understanding of the magnitude, direction, and detailed compositional and functional profiles remains limited. Additionally, research exploring the gut microbiota in the context of both plaque psoriasis (PsO) and psoriatic arthritis (PsA) is lacking. To assess the taxonomic and functional characteristics of the gut microbiota in PsO and PsA patients and investigate potential links between the gut microbiota and disease pathogenesis. We collected fecal samples from 70 psoriatic patients (44 PsO and 26 PsA) and 25 age- and gender-matched healthy controls (HC) and employed deep metagenomic sequencing to characterize their gut microbiota. We noted significant alternations in the gut microbiota compositions of both PsO and PsA patients compared to those of HC. Despite limited effect sizes in alpha diversity (12.3% reduction of microbial richness but unchanged evenness in psoriatic patients) and beta diversity (disease accounts for 3.5% of total variations), we consistently observed substantial reductions of Eubacterium rectale in both PsO and PsA patients, with PsA patients exhibiting even lower levels of E. rectale than PsO patients. Additionally, two Alistipes species were also depleted in psoriatic patients. These microorganisms are known to play crucial roles in carbohydrate metabolism pathways, mainly producing short-chain fatty acids with anti-inflammatory effects. Overall, our observations supplemented the profiling of altered gut microbiota in patients with PsO and PsA at the species level and described a link between the dominant short-chain fatty acid-producing bacterial species and systemic immunity in psoriatic patients.

IMPORTANCE: In this observational clinical study with sufficient sample size and metagenomic sequencing to profile the gut microbiota, we identified consistent signals of the depleted abundance of Eubacterium rectale and related functional genes among psoriatic patients, including those with psoriatic arthritis. E. rectale may serve as an ecologically important functional unit in the gut microbiota, holding potential as a diagnostic marker and target for therapeutic interventions to achieve lasting effects. Our findings provide comprehensive gut microbiota profiling in psoriasis, resolving previous contradictions and generating new hypotheses for further investigation. These insights may significantly impact psoriasis management and related conditions.}, } @article {pmid38441032, year = {2024}, author = {Mancabelli, L and Milani, C and De Biase, R and Bocchio, F and Fontana, F and Lugli, GA and Alessandri, G and Tarracchini, C and Viappiani, A and De Conto, F and Nouvenne, A and Ticinesi, A and Bussolati, O and Meschi, T and Cecchi, R and Turroni, F and Ventura, M}, title = {Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation.}, journal = {mSystems}, volume = {9}, number = {4}, pages = {e0129423}, pmid = {38441032}, issn = {2379-5077}, support = {GR-2018-12365988//Ministero della Salute (Italy Ministry of Health)/ ; 20229LEB99//Ministero della Ricerca e dell'Universita/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Metagenome/genetics ; Bacteria/genetics ; Vitamins ; }, abstract = {UNLABELLED: The human gut microbiota is a dynamic community of microorganisms that undergo variable changes over the entire life span. To thoroughly investigate the possible fluctuations of the microbiota throughout human life, we performed a pooled analysis of healthy fecal samples across different age groups covering the entire human life span. Our study integrated data from 79 publicly available studies and new stool samples from an Italian cohort, i.e., the Parma Microbiota project, resulting in 6,653 samples processed through the shotgun metagenomic approach. This approach has allowed species-level taxonomic reconstruction of the gut microbiota and investigation of its metabolic potential across the human life span. From a taxonomic point of view, our findings confirmed and detailed at species-level accuracy that the microbial richness of the gut microbiota gradually increases in the first stage of life, becoming relatively stable during adolescence. Moreover, the analysis identified the potential core microbiota representative of distinct age groups, revealing age-related bacterial patterns and the continuous rearrangement of the microbiota in terms of relative abundances across the life span rather than the acquisition and loss of taxa. Furthermore, the shotgun approach provided insights into the functional contribution of the human gut microbiome. The metagenomic analysis revealed functional age-related differences, particularly in carbohydrate and fiber metabolism, suggesting a co-evolution of the microbiome assembly with diet. Additionally, we identified correlations between vitamin synthesis, such as thiamine and niacin, and early life, suggesting a potential role of the microbiome in human physiology, in particular in the functions of the host's nervous and immune systems.

IMPORTANCE: In this study, we provided comprehensive insights into the dynamic nature of the human gut microbiota across the human life span. In detail, we analyzed a large data set based on a shotgun metagenomic approach, combining public data sets and new samples from the Parma Microbiota project and obtaining a detailed overview of the possible relationship between gut microbiota development and aging. Our findings confirmed the main stages in microbial richness development and revealed specific core microbiota associated with different age stages. Moreover, the shotgun metagenomic approach allowed the disentangling of the functional changes in the microbiome across the human life span, particularly in diet-related metabolism, which is probably correlated to bacterial co-evolution with dietary habits. Notably, our study also uncovered positive correlations with vitamin synthesis in early life, suggesting a possible impact of the microbiota on human physiology.}, } @article {pmid38440408, year = {2024}, author = {Eisenhofer, R and Wright, S and Weyrich, L}, title = {Benchmarking a targeted 16S ribosomal RNA gene enrichment approach to reconstruct ancient microbial communities.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e16770}, pmid = {38440408}, issn = {2167-8359}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Benchmarking ; Genes, rRNA ; Dental Calculus ; *Microbiota ; DNA, Ancient ; }, abstract = {The taxonomic characterization of ancient microbiomes is a key step in the rapidly growing field of paleomicrobiology. While PCR amplification of the 16S ribosomal RNA (rRNA) gene is a widely used technique in modern microbiota studies, this method has systematic biases when applied to ancient microbial DNA. Shotgun metagenomic sequencing has proven to be the most effective method in reconstructing taxonomic profiles of ancient dental calculus samples. Nevertheless, shotgun sequencing approaches come with inherent limitations that could be addressed through hybridization enrichment capture. When employed together, shotgun sequencing and hybridization capture have the potential to enhance the characterization of ancient microbial communities. Here, we develop, test, and apply a hybridization enrichment capture technique to selectively target 16S rRNA gene fragments from the libraries of ancient dental calculus samples generated with shotgun techniques. We simulated data sets generated from hybridization enrichment capture, indicating that taxonomic identification of fragmented and damaged 16S rRNA gene sequences was feasible. Applying this enrichment approach to 15 previously published ancient calculus samples, we observed a 334-fold increase of ancient 16S rRNA gene fragments in the enriched samples when compared to unenriched libraries. Our results suggest that 16S hybridization capture is less prone to the effects of background contamination than 16S rRNA amplification, yielding a higher percentage of on-target recovery. While our enrichment technique detected low abundant and rare taxa within a given sample, these assignments may not achieve the same level of specificity as those achieved by unenriched methods.}, } @article {pmid38439546, year = {2024}, author = {Madhav, A and Bousfield, R and Pereira-Dias, J and Cormie, C and Forrest, S and Keane, J and Kermack, L and Higginson, E and Dougan, G and Spiers, H and Massey, D and Sharkey, L and Rutter, C and Woodward, J and Russell, N and Amin, I and Butler, A and Atkinson, K and Dymond, T and Bartholdson Scott, J and Baker, S and Gkrania-Klotsas, E}, title = {A metagenomic prospective cohort study on gut microbiome composition and clinical infection in small bowel transplantation.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2323232}, pmid = {38439546}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Prospective Studies ; *Sepsis ; *Microbiota ; }, abstract = {Two-thirds of small-bowel transplantation (SBT) recipients develop bacteremia, with the majority of infections occurring within 3 months post-transplant. Sepsis-related mortality occurs in 31% of patients and is commonly caused by bacteria of gut origin, which are thought to translocate across the implanted organ. Serial post-transplant surveillance endoscopies provide an opportunity to study whether the composition of the ileal and colonic microbiota can predict the emergence as well as the pathogen of subsequent clinical infections in the SBT patient population. Five participants serially underwent aspiration of ileal and colonic bowel effluents at transplantation and during follow-up endoscopy either until death or for up to 3 months post-SBT. We performed whole-metagenome sequencing (WMS) of 40 bowel effluent samples and compared the results with clinical infection episodes. Microbiome composition was concordant between participants and timepoint-matched ileal and colonic samples. Four out of five (4/5) participants had clinically significant infections thought to be of gut origin. Bacterial translocation from the gut was observed in 3/5 patients with bacterial infectious etiologies. In all three cases, the pathogens had demonstrably colonized the gut between 1-10 days prior to invasive clinical infection. Recipients with better outcomes received donor grafts with higher alpha diversity. There was an increase in the number of antimicrobial resistance genes associated with longer hospital stay for all participants. This metagenomic study provides preliminary evidence to support the pathogen translocation hypothesis of gut-origin sepsis in the SBT cohort. Ileal and colonic microbiome compositions were concordant; therefore, fecal metagenomic analysis could be a useful surveillance tool for impeding infection with specific gut-residing pathogens.}, } @article {pmid38438919, year = {2024}, author = {Sun, D and Bian, G and Zhang, K and Liu, N and Yin, Y and Hou, Y and Xie, F and Zhu, W and Mao, S and Liu, J}, title = {Early-life ruminal microbiome-derived indole-3-carboxaldehyde and prostaglandin D2 are effective promoters of rumen development.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {64}, pmid = {38438919}, issn = {1474-760X}, support = {2021YFF1000703//National Key Research and Development Program of China/ ; 2021YFA1301300//National Key Research and Development Program of China/ ; 32172752//National Natural Science Foundation of China/ ; }, mesh = {Sheep ; Animals ; *Prostaglandin D2 ; Rumen ; *Microbiota ; Metagenome ; *Indoles ; }, abstract = {BACKGROUND: The function of diverse ruminal microbes is tightly linked to rumen development and host physiology. The system of ruminal microbes is an excellent model to clarify the fundamental ecological relationships among complex nutrient-microbiome-host interactions. Here, neonatal lambs are introduced to different dietary regimes to investigate the influences of early-life crosstalk between nutrients and microbiome on rumen development.

RESULTS: We find starchy corn-soybean starter-fed lambs exhibit the thickest ruminal epithelia and fiber-rich alfalfa hay-fed lambs have the thickest rumen muscle. Metabolome and metagenome data reveal that indole-3-carboxaldehyde (3-IAld) and prostaglandin D2 (PGD2) are the top characteristic ruminal metabolites associated with ruminal epithelial and muscular development, which depend on the enhanced ruminal microbial synthesis potential of 3-IAld and PGD2. Moreover, microbial culture experiment first demonstrates that Bifidobacterium pseudolongum is able to convert tryptophan into 3-IAld and Candida albicans is a key producer for PGD2. Transcriptome sequencing of the ruminal epithelia and smooth muscle shows that ruminal epithelial and muscular development is accompanied by Wnt and Ca[2+] signaling pathway activation. Primary cell cultures further confirm that 3-IAld promotes ruminal epithelial cell proliferation depending on AhR-wnt/β-catenin signaling pathway and PGD2 accelerates ruminal smooth muscle cell proliferation via Ca[2+] signaling pathway. Furthermore, we find that 3-IAld and PGD2 infusion promote ruminal epithelial and musculature development in lambs.

CONCLUSIONS: This study demonstrates that early-life ruminal microbiome-derived 3-IAld and PGD2 are effective promoters of rumen development, which enhances our understanding of nutrient-microbiome-host interactions in early life.}, } @article {pmid38438326, year = {2024}, author = {Pinto, GR and Carvalho Filho, PC and Carvalho, RDO and Conceição, RR and Fortuna, V and Gomes-Filho, IS and Trindade, SC and Sarmento, VA}, title = {Subgingival biofilm microbiome in individuals with asthma and periodontitis: Metagenomic analysis.}, journal = {Oral diseases}, volume = {30}, number = {7}, pages = {4721-4730}, doi = {10.1111/odi.14913}, pmid = {38438326}, issn = {1601-0825}, support = {SUS0054/2018//PPSUS (Programa Pesquisa para o SUS) / FAPESB/ ; }, mesh = {Humans ; *Asthma/microbiology ; *Biofilms ; *Periodontitis/microbiology ; Adult ; *Microbiota ; Female ; Male ; Middle Aged ; Metagenomics/methods ; RNA, Ribosomal, 16S/analysis ; Gingiva/microbiology ; Dysbiosis/microbiology ; Young Adult ; }, abstract = {OBJECTIVE: This observational study aimed to explore the metagenomics of subgingival biofilms in individuals with varying degrees of asthma, from severe to none, to elucidate the association between the subgingival microbiome and asthma.

MATERIALS AND METHODS: Subgingival biofilm samples were collected from thirty participants at the Asthma Control Program Outpatient Clinic in Bahia (ProAR). These samples were categorized into six groups based on the severity of asthma and the presence or absence of periodontitis. We employed next-generation sequencing (Illumina MiSeq), targeting the 16S rRNA gene, to characterize the microbial communities present. Our analysis included descriptive statistics and sequencing data, evaluated using multivariate statistical methods such as the Shannon index, principal coordinate analysis, and the Bray-Curtis dissimilarity.

RESULTS: Our findings indicate a higher prevalence of periodontally detrimental bacterial genera in individuals with severe asthma and periodontitis. Additionally, individuals with asthma, but without periodontitis, exhibited a tendency toward dysbiosis, particularly in cases of severe asthma.

CONCLUSION: This research provides new insights into the composition of the subgingival microbiome in individuals with varying severities of asthma and periodontitis. The genera identified in this study underscore the need for further investigations to build upon these findings.}, } @article {pmid38437464, year = {2024}, author = {Shen, D and Lv, X and Zhang, H and Fei, C and Feng, J and Zhou, J and Cao, L and Ying, Y and Li, N and Ma, X}, title = {Association between Clinical Characteristics and Microbiota in Bronchiectasis Patients Based on Metagenomic Next-Generation Sequencing Technology.}, journal = {Polish journal of microbiology}, volume = {73}, number = {1}, pages = {59-68}, pmid = {38437464}, issn = {2544-4646}, mesh = {Humans ; Retrospective Studies ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; *Aspergillosis ; *Bronchiectasis/diagnosis ; }, abstract = {This study aimed to investigate the disparities between metagenomic next-generation sequencing (mNGS) and conventional culture results in patients with bronchiectasis. Additionally, we sought to investigate the correlation between the clinical characteristics of patients and their microbiome profiles. The overarching goal was to enhance the effective management and treatment of bronchiectasis patients, providing a theoretical foundation for healthcare professionals. A retrospective survey was conducted on 67 bronchiectasis patients admitted to The First Hospital of Jiaxing from October 2019 to March 2023. Clinical baseline information, inflammatory indicators, and pathogen detection reports, including mNGS, conventional blood culture, bronchoalveolar lavage fluid (BALF) culture, and sputum culture results, were collected. By comparing the results of mNGS and conventional culture, the differences in pathogen detection rate and pathogen types were explored, and the diagnostic performance of mNGS compared to conventional culture was evaluated. Based on the various pathogens detected by mNGS, the association between clinical characteristics of bronchiectasis patients and mNGS microbiota results was analyzed. The number and types of pathogens detected by mNGS were significantly larger than those detected by conventional culture. The diagnostic efficacy of mNGS was significantly superior to conventional culture for all types of pathogens, particularly in viral detection (p < 0.01). Regarding pathogen detection rate, the bacteria with the highest detection rate were Pseudomonas aeruginosa (17/58) and Haemophilus influenzae (11/58); the fungus with the highest detection rate was Aspergillus fumigatus (10/21), and the virus with the highest detection rate was human herpes virus 4 (4/11). Differences were observed between the positive and negative groups for P. aeruginosa in terms of common scoring systems for bronchiectasis and whether the main symptom of bronchiectasis manifested as thick sputum (p < 0.05). Significant distinctions were also noted between the positive and negative groups for A. fumigatus regarding Reiff score, neutrophil percentage, bronchiectasis etiology, and alterations in treatment plans following mNGS results reporting (p < 0.05). Notably, 70% of patients with positive A. fumigatus infection opted to change their treatment plans. The correlation study between clinical characteristics of bronchiectasis patients and mNGS microbiological results revealed that bacteria, such as P. aeruginosa, and fungi, such as A. fumigatus, were associated with specific clinical features of patients. This underscored the significance of mNGS in guiding personalized treatment approaches. mNGS could identify multiple pathogens in different types of bronchiectasis samples and was a rapid and effective diagnostic tool for pathogen identification. Its use was recommended for diagnosing the causes of infections in bronchiectasis patients.}, } @article {pmid38433960, year = {2024}, author = {Banchi, E and Corre, E and Del Negro, P and Celussi, M and Malfatti, F}, title = {Genome-resolved metagenomics of Venice Lagoon surface sediment bacteria reveals high biosynthetic potential and metabolic plasticity as successful strategies in an impacted environment.}, journal = {Marine life science & technology}, volume = {6}, number = {1}, pages = {126-142}, pmid = {38433960}, issn = {2662-1746}, abstract = {UNLABELLED: Bacteria living in sediments play essential roles in marine ecosystems and deeper insights into the ecology and biogeochemistry of these largely unexplored organisms can be obtained from 'omics' approaches. Here, we characterized metagenome-assembled-genomes (MAGs) from the surface sediment microbes of the Venice Lagoon (northern Adriatic Sea) in distinct sub-basins exposed to various natural and anthropogenic pressures. MAGs were explored for biodiversity, major marine metabolic processes, anthropogenic activity-related functions, adaptations at the microscale, and biosynthetic gene clusters. Starting from 126 MAGs, a non-redundant dataset of 58 was compiled, the majority of which (35) belonged to (Alpha- and Gamma-) Proteobacteria. Within the broad microbial metabolic repertoire (including C, N, and S metabolisms) the potential to live without oxygen emerged as one of the most important features. Mixotrophy was also found as a successful lifestyle. Cluster analysis showed that different MAGs encoded the same metabolic patterns (e.g., C fixation, sulfate oxidation) thus suggesting metabolic redundancy. Antibiotic and toxic compounds resistance genes were coupled, a condition that could promote the spreading of these genetic traits. MAGs showed a high biosynthetic potential related to antimicrobial and biotechnological classes and to organism defense and interactions as well as adaptive strategies for micronutrient uptake and cellular detoxification. Our results highlighted that bacteria living in an impacted environment, such as the surface sediments of the Venice Lagoon, may benefit from metabolic plasticity as well as from the synthesis of a wide array of secondary metabolites, promoting ecosystem resilience and stability toward environmental pressures.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-023-00192-z.}, } @article {pmid38433907, year = {2024}, author = {Rampelli, S and Gallois, S and D'Amico, F and Turroni, S and Fabbrini, M and Scicchitano, D and Candela, M and Henry, A}, title = {The gut microbiome of Baka forager-horticulturalists from Cameroon is optimized for wild plant foods.}, journal = {iScience}, volume = {27}, number = {3}, pages = {109211}, pmid = {38433907}, issn = {2589-0042}, abstract = {The human gut microbiome is losing biodiversity, due to the "microbiome modernization process" that occurs with urbanization. To keep track of it, here we applied shotgun metagenomics to the gut microbiome of the Baka, a group of forager-horticulturalists from Cameroon, who combine hunting and gathering with growing a few crops and working for neighboring Bantu-speaking farmers. We analyzed the gut microbiome of individuals with different access to and use of wild plant and processed foods, to explore the variation of their gut microbiome along the cline from hunter-gatherer to agricultural subsistence patterns. We found that 26 species-level genome bins from our cohort were pivotal for the degradation of the wild plant food substrates. These microbes include Old Friend species and are encoded for genes that are no longer present in industrialized gut microbiome. Our results highlight the potential relevance of these genes to human biology and health, in relation to lifestyle.}, } @article {pmid38431663, year = {2024}, author = {Garmaeva, S and Sinha, T and Gulyaeva, A and Kuzub, N and Spreckels, JE and Andreu-Sánchez, S and Gacesa, R and Vich Vila, A and Brushett, S and Kruk, M and , and Dekens, J and Sikkema, J and Kuipers, F and Shkoporov, AN and Hill, C and Scherjon, S and Wijmenga, C and Fu, J and Kurilshikov, A and Zhernakova, A}, title = {Transmission and dynamics of mother-infant gut viruses during pregnancy and early life.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1945}, pmid = {38431663}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Infant ; Humans ; Female ; Pregnancy ; Mothers ; *Viruses ; *Bacteriophages/genetics ; *Microbiota ; *Gastrointestinal Microbiome ; Bacteria/genetics ; }, abstract = {Early development of the gut ecosystem is crucial for lifelong health. While infant gut bacterial communities have been studied extensively, the infant gut virome remains under-explored. To study the development of the infant gut virome over time and the factors that shape it, we longitudinally assess the composition of gut viruses and their bacterial hosts in 30 women during and after pregnancy and in their 32 infants during their first year of life. Using shotgun metagenomic sequencing applied to dsDNA extracted from Virus-Like Particles (VLPs) and bacteria, we generate 205 VLP metaviromes and 322 total metagenomes. With this data, we show that while the maternal gut virome composition remains stable during late pregnancy and after birth, the infant gut virome is dynamic in the first year of life. Notably, infant gut viromes contain a higher abundance of active temperate phages compared to maternal gut viromes, which decreases over the first year of life. Moreover, we show that the feeding mode and place of delivery influence the gut virome composition of infants. Lastly, we provide evidence of co-transmission of viral and bacterial strains from mothers to infants, demonstrating that infants acquire some of their virome from their mother's gut.}, } @article {pmid38431030, year = {2024}, author = {Shahzad, M and Saeed, M and Amin, H and Binmadi, N and Ullah, Z and Bibi, S and Andrew, SC}, title = {The oral microbiome of newly diagnosed tuberculosis patients; a pilot study.}, journal = {Genomics}, volume = {116}, number = {2}, pages = {110816}, doi = {10.1016/j.ygeno.2024.110816}, pmid = {38431030}, issn = {1089-8646}, mesh = {Humans ; Pilot Projects ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria/genetics ; *Tuberculosis ; }, abstract = {BACKGROUND: Changes in oral microbiota composition (dysbiosis) have long been known to play a key role in the pathogenesis of oral and systemic diseases including respiratory diseases. However, till now, no study has assessed changes in oral microbiota following tuberculosis (TB) infection in humans.

AIMS: This is the first study of its kind that aimed to investigate oral microbial dysbiosis in newly diagnosed, treatment naïve, TB patients.

METHODS: Oral swab samples were collected from newly diagnosed TB patients (n = 20) and age, gender and ethnicity matched healthy controls (n = 10). DNA was extracted and microbiota analyzed by sequencing the hypervariable (V3-V4) region of the bacterial 16S rRNA gene using Illumina MiSeq platform. Bioinformatics and statistical analyses were performed using QIIME and R.

RESULTS: Bacterial richness, diversity and community composition were significantly different between TB patients and healthy controls. The two groups also exhibit differential abundance at phylum, class, genus and species levels. LEfSe analysis revealed enrichment (LDA scores (log10) >2, P < 0.05) of Firmicutes (especially Streptococcus) and Actinobacteriota (especially Rothia) in TB patients relative to healthy controls. Gene function prediction analysis showed upregulation of metabolic pathways related to carbohydrates (butanoate, galactose) and fatty acids metabolism, antibiotics biosynthesis, proteosome and immune system signaling.

CONCLUSION: These observations suggest significant variations in diversity, relative abundance and functional potential of oral microbiota of TB patients compared to healthy controls thereby suggesting potential role of oral bacterial dysbiosis in TB pathogenesis. However, longitudinal studies using powerful metagenomic and transcriptomic approaches are crucial to more fully understand and confrim these findings.}, } @article {pmid38429524, year = {2024}, author = {Gunjur, A and Shao, Y and Rozday, T and Klein, O and Mu, A and Haak, BW and Markman, B and Kee, D and Carlino, MS and Underhill, C and Frentzas, S and Michael, M and Gao, B and Palmer, J and Cebon, J and Behren, A and Adams, DJ and Lawley, TD}, title = {A gut microbial signature for combination immune checkpoint blockade across cancer types.}, journal = {Nature medicine}, volume = {30}, number = {3}, pages = {797-809}, pmid = {38429524}, issn = {1546-170X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Immune Checkpoint Inhibitors/therapeutic use ; *Gastrointestinal Microbiome/genetics ; *Neoplasms/drug therapy/genetics ; }, abstract = {Immune checkpoint blockade (ICB) targeting programmed cell death protein 1 (PD-1) and cytotoxic T lymphocyte protein 4 (CTLA-4) can induce remarkable, yet unpredictable, responses across a variety of cancers. Studies suggest that there is a relationship between a cancer patient's gut microbiota composition and clinical response to ICB; however, defining microbiome-based biomarkers that generalize across cohorts has been challenging. This may relate to previous efforts quantifying microbiota to species (or higher taxonomic rank) abundances, whereas microbial functions are often strain specific. Here, we performed deep shotgun metagenomic sequencing of baseline fecal samples from a unique, richly annotated phase 2 trial cohort of patients with diverse rare cancers treated with combination ICB (n = 106 discovery cohort). We demonstrate that strain-resolved microbial abundances improve machine learning predictions of ICB response and 12-month progression-free survival relative to models built using species-rank quantifications or comprehensive pretreatment clinical factors. Through a meta-analysis of gut metagenomes from a further six comparable studies (n = 364 validation cohort), we found cross-cancer (and cross-country) validity of strain-response signatures, but only when the training and test cohorts used concordant ICB regimens (anti-PD-1 monotherapy or combination anti-PD-1 plus anti-CTLA-4). This suggests that future development of gut microbiome diagnostics or therapeutics should be tailored according to ICB treatment regimen rather than according to cancer type.}, } @article {pmid38428395, year = {2024}, author = {Fogarty, EC and Schechter, MS and Lolans, K and Sheahan, ML and Veseli, I and Moore, RM and Kiefl, E and Moody, T and Rice, PA and Yu, MK and Mimee, M and Chang, EB and Ruscheweyh, HJ and Sunagawa, S and Mclellan, SL and Willis, AD and Comstock, LE and Eren, AM}, title = {A cryptic plasmid is among the most numerous genetic elements in the human gut.}, journal = {Cell}, volume = {187}, number = {5}, pages = {1206-1222.e16}, pmid = {38428395}, issn = {1097-4172}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; RC2 DK122394/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Bacteria/genetics ; Bacteroidetes/genetics ; Feces/microbiology ; *Metagenome ; *Plasmids/genetics ; *Gastrointestinal Tract ; }, abstract = {Plasmids are extrachromosomal genetic elements that often encode fitness-enhancing features. However, many bacteria carry "cryptic" plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes and is 14 times as numerous as crAssphage, currently established as the most abundant extrachromosomal genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales, and although it does not appear to impact bacterial host fitness in vivo, it can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an alternative approach to track human colonic inflammatory states.}, } @article {pmid38427084, year = {2024}, author = {Tamang, A and Kaur, A and Thakur, D and Thakur, A and Thakur, BK and Shivani, and Swarnkar, M and Pal, PK and Hallan, V and Pandey, SS}, title = {Unraveling endophytic diversity in dioecious Siraitia grosvenorii: implications for mogroside production.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {247}, pmid = {38427084}, issn = {1432-0614}, support = {MLP-0171//Council of Scientific and Industrial Research, India/ ; GAP-0269 (SRG/2020/001524)//Science and Engineering Research Board/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria/genetics ; Firmicutes/genetics ; Endophytes/genetics ; Crops, Agricultural/genetics ; }, abstract = {Host and tissue-specificity of endophytes are important attributes that limit the endophyte application on multiple crops. Therefore, understanding the endophytic composition of the targeted crop is essential, especially for the dioecious plants where the male and female plants are different. Here, efforts were made to understand the endophytic bacterial composition of the dioecious Siraitia grosvenorii plant using 16S rRNA amplicon sequencing. The present study revealed the association of distinct endophytic bacterial communities with different parts of male and female plants. Roots of male and female plants had a higher bacterial diversity than other parts of plants, and the roots of male plants had more bacterial diversity than the roots of female plants. Endophytes belonging to the phylum Proteobacteria were abundant in all parts of male and female plants except male stems and fruit pulp, where the Firmicutes were most abundant. Class Gammaproteobacteria predominated in both male and female plants, with the genus Acinetobacter as the most dominant and part of the core microbiome of the plant (present in all parts of both, male and female plants). The presence of distinct taxa specific to male and female plants was also identified. Macrococcus, Facklamia, and Propionibacterium were the distinct genera found only in fruit pulp, the edible part of S. grosvenorii. Predictive functional analysis revealed the abundance of enzymes of secondary metabolite (especially mogroside) biosynthesis in the associated endophytic community with predominance in roots. The present study revealed bacterial endophytic communities of male and female S. grosvenorii plants that can be further explored for monk fruit cultivation, mogroside production, and early-stage identification of male and female plants. KEY POINTS: • Male and female Siraitia grosvenorii plants had distinct endophytic communities • The diversity of endophytic communities was specific to different parts of plants • S. grosvenorii-associated endophytes may be valuable for mogroside biosynthesis and monk fruit cultivation.}, } @article {pmid38426620, year = {2024}, author = {Zhang, L and Yuan, L and Wen, Y and Zhang, M and Huang, S and Wang, S and Zhao, Y and Hao, X and Li, L and Gao, Q and Wang, Y and Zhang, S and Huang, S and Liu, K and Yu, X and Li, D and Xu, J and Zhao, B and Zhang, L and Zhang, H and Zhou, W and Ai, C}, title = {Maize functional requirements drive the selection of rhizobacteria under long-term fertilization practices.}, journal = {The New phytologist}, volume = {242}, number = {3}, pages = {1275-1288}, doi = {10.1111/nph.19653}, pmid = {38426620}, issn = {1469-8137}, support = {2022YFD1900900//National Key Research and Development Program of China/ ; 32322076//National Natural Science Foundation of China/ ; 32272817//National Natural Science Foundation of China/ ; 05//Smart Fertilization Project/ ; BX20230425//Postdoctoral Innovation Talents Support Program/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; }, mesh = {Zea mays/microbiology ; Soil Microbiology ; Soil/chemistry ; *Microbiota ; *Alphaproteobacteria ; Rhizosphere ; Fertilization ; }, abstract = {Rhizosphere microbiomes are pivotal for crop fitness, but the principles underlying microbial assembly during root-soil interactions across soils with different nutrient statuses remain elusive. We examined the microbiomes in the rhizosphere and bulk soils of maize plants grown under six long-term (≥ 29 yr) fertilization experiments in three soil types across middle temperate to subtropical zones. The assembly of rhizosphere microbial communities was primarily driven by deterministic processes. Plant selection interacted with soil types and fertilization regimes to shape the structure and function of rhizosphere microbiomes. Predictive functional profiling showed that, to adapt to nutrient-deficient conditions, maize recruited more rhizobacteria involved in nutrient availability from bulk soil, although these functions were performed by different species. Metagenomic analyses confirmed that the number of significantly enriched Kyoto Encyclopedia of Genes and Genomes Orthology functional categories in the rhizosphere microbial community was significantly higher without fertilization than with fertilization. Notably, some key genes involved in carbon, nitrogen, and phosphorus cycling and purine metabolism were dominantly enriched in the rhizosphere soil without fertilizer input. In conclusion, our results show that maize selects microbes at the root-soil interface based on microbial functional traits beneficial to its own performance, rather than selecting particular species.}, } @article {pmid38425025, year = {2024}, author = {Pereira-Marques, J and Ferreira, RM and Figueiredo, C}, title = {A metatranscriptomics strategy for efficient characterization of the microbiome in human tissues with low microbial biomass.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2323235}, pmid = {38425025}, issn = {1949-0984}, mesh = {Humans ; Biomass ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; *Microbiota/genetics ; Bacteria/genetics ; }, abstract = {The high background of host RNA poses a major challenge to metatranscriptome analysis of human samples. Hence, metatranscriptomics has been mainly applied to microbe-rich samples, while its application in human tissues with low ratio of microbial to host cells has yet to be explored. Since there is no computational workflow specifically designed for the taxonomic and functional analysis of this type of samples, we propose an effective metatranscriptomics strategy to accurately characterize the microbiome in human tissues with a low ratio of microbial to host content. We experimentally generated synthetic samples with well-characterized bacterial and host cell compositions, and mimicking human samples with high and low microbial loads. These synthetic samples were used for optimizing and establishing the workflow in a controlled setting. Our results show that the integration of the taxonomic analysis of optimized Kraken 2/Bracken with the functional analysis of HUMAnN 3 in samples with low microbial content, enables the accurate identification of a large number of microbial species with a low false-positive rate, while improving the detection of microbial functions. The effectiveness of our metatranscriptomics workflow was demonstrated in synthetic samples, simulated datasets, and most importantly, human gastric tissue specimens, thus providing a proof of concept for its applicability on mucosal tissues of the gastrointestinal tract. The use of an accurate and reliable metatranscriptomics approach for human tissues with low microbial content will expand our understanding of the functional activity of the mucosal microbiome, uncovering critical interactions between the microbiome and the host in health and disease.}, } @article {pmid38424077, year = {2024}, author = {Zeng, S and Almeida, A and Li, S and Ying, J and Wang, H and Qu, Y and Paul Ross, R and Stanton, C and Zhou, Z and Niu, X and Mu, D and Wang, S}, title = {A metagenomic catalog of the early-life human gut virome.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1864}, pmid = {38424077}, issn = {2041-1723}, support = {82100590//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82241036//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Adult ; Infant ; Child ; Humans ; Metagenome/genetics ; Virome/genetics ; *Viruses/genetics ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; }, abstract = {Early-life human gut microbiome is a pivotal driver of gut homeostasis and infant health. However, the viral component (known as "virome") remains mostly unexplored. Here, we establish the Early-Life Gut Virome (ELGV), a catalog of 160,478 non-redundant DNA and RNA viral sequences from 8130 gut virus-like particles (VLPs) enriched or bulk metagenomes in the first three years of life. By clustering, 82,141 viral species are identified, 68.3% of which are absent in existing databases built mainly from adults, and 64 and 8 viral species based on VLPs-enriched and bulk metagenomes, respectively, exhibit potentials as biomarkers to distinguish infants from adults. With the largest longitudinal population of infants profiled by either VLPs-enriched or bulk metagenomic sequencing, we track the inherent instability and temporal development of the early-life human gut virome, and identify differential viruses associated with multiple clinical factors. The mother-infant shared virome and interactions between gut virome and bacteriome early in life are further expanded. Together, the ELGV catalog provides the most comprehensive and complete metagenomic blueprint of the early-life human gut virome, facilitating the discovery of pediatric disease-virome associations in future.}, } @article {pmid38424056, year = {2024}, author = {Istvan, P and Birkeland, E and Avershina, E and Kværner, AS and Bemanian, V and Pardini, B and Tarallo, S and de Vos, WM and Rognes, T and Berstad, P and Rounge, TB}, title = {Exploring the gut DNA virome in fecal immunochemical test stool samples reveals associations with lifestyle in a large population-based study.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1791}, pmid = {38424056}, issn = {2041-1723}, support = {198048//Kreftforeningen (Norwegian Cancer Society)/ ; 190179//Kreftforeningen (Norwegian Cancer Society)/ ; 2022067//Ministry of Health and Care Services | Helse Sør-Øst RHF (Southern and Eastern Norway Regional Health Authority)/ ; }, mesh = {Humans ; Virome ; DNA Viruses/genetics ; *Viruses/genetics ; DNA ; *Colorectal Neoplasms/diagnosis/genetics ; }, abstract = {Stool samples for fecal immunochemical tests (FIT) are collected in large numbers worldwide as part of colorectal cancer screening programs. Employing FIT samples from 1034 CRCbiome participants, recruited from a Norwegian colorectal cancer screening study, we identify, annotate and characterize more than 18000 DNA viruses, using shotgun metagenome sequencing. Only six percent of them are assigned to a known taxonomic family, with Microviridae being the most prevalent viral family. Linking individual profiles to comprehensive lifestyle and demographic data shows 17/25 of the variables to be associated with the gut virome. Physical activity, smoking, and dietary fiber consumption exhibit strong and consistent associations with both diversity and relative abundance of individual viruses, as well as with enrichment for auxiliary metabolic genes. We demonstrate the suitability of FIT samples for virome analysis, opening an opportunity for large-scale studies of this enigmatic part of the gut microbiome. The diverse viral populations and their connections to the individual lifestyle uncovered herein paves the way for further exploration of the role of the gut virome in health and disease.}, } @article {pmid38423316, year = {2024}, author = {Xiang, Y and Yu, Y and Wang, J and Li, W and Rong, Y and Ling, H and Chen, Z and Qian, Y and Han, X and Sun, J and Yang, Y and Chen, L and Zhao, C and Li, J and Chen, K}, title = {Neural network establishes co-occurrence links between transformation products of the contaminant and the soil microbiome.}, journal = {The Science of the total environment}, volume = {924}, number = {}, pages = {171287}, doi = {10.1016/j.scitotenv.2024.171287}, pmid = {38423316}, issn = {1879-1026}, mesh = {*Soil/chemistry ; RNA, Ribosomal, 16S ; *Microbiota ; Isotopes/analysis ; DNA ; Pyrenes ; Neural Networks, Computer ; Soil Microbiology ; }, abstract = {It remains challenging to establish reliable links between transformation products (TPs) of contaminants and corresponding microbes. This challenge arises due to the sophisticated experimental regime required for TP discovery and the compositional nature of 16S rRNA gene amplicon sequencing and mass spectrometry datasets, which can potentially confound statistical inference. In this study, we present a new strategy by combining the use of [2]H-labeled Stable Isotope-Assisted Metabolomics ([2]H-SIAM) with a neural network-based algorithm (i.e., MMvec) to explore links between TPs of pyrene and the soil microbiome. The links established by this novel strategy were further validated using different approaches. Briefly, a metagenomic study provided indirect evidence for the established links, while the identification of pyrene degraders from soils, and a DNA-based stable isotope probing (DNA-SIP) study offered direct evidence. The comparison among different approaches, including Pearson's and Spearman's correlations, further confirmed the superior performance of our strategy. In conclusion, we summarize the unique features of the combined use of [2]H-SIAM and MMvec. This study not only addresses the challenges in linking TPs to microbes but also introduces an innovative and effective approach for such investigations. Environmental Implication: Taxonomically diverse bacteria performing successive metabolic steps of the contaminant were firstly depicted in the environmental matrix.}, } @article {pmid38423015, year = {2024}, author = {Carasso, S and Zaatry, R and Hajjo, H and Kadosh-Kariti, D and Ben-Assa, N and Naddaf, R and Mandelbaum, N and Pressman, S and Chowers, Y and Gefen, T and Jeffrey, KL and Jofre, J and Coyne, MJ and Comstock, LE and Sharon, I and Geva-Zatorsky, N}, title = {Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota.}, journal = {Cell host & microbe}, volume = {32}, number = {3}, pages = {322-334.e9}, pmid = {38423015}, issn = {1934-6069}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; *Gastrointestinal Microbiome ; *Colitis ; *Inflammatory Bowel Diseases/microbiology ; Inflammation ; DNA ; }, abstract = {Reversible genomic DNA inversions control the expression of numerous gut bacterial molecules, but how this impacts disease remains uncertain. By analyzing metagenomic samples from inflammatory bowel disease (IBD) cohorts, we identified multiple invertible regions where a particular orientation correlated with disease. These include the promoter of polysaccharide A (PSA) of Bacteroides fragilis, which induces regulatory T cells (Tregs) and ameliorates experimental colitis. The PSA promoter was mostly oriented "OFF" in IBD patients, which correlated with increased B. fragilis-associated bacteriophages. Similarly, in mice colonized with a healthy human microbiota and B. fragilis, induction of colitis caused a decline of PSA in the "ON" orientation that reversed as inflammation resolved. Monocolonization of mice with B. fragilis revealed that bacteriophage infection increased the frequency of PSA in the "OFF" orientation, causing reduced PSA expression and decreased Treg cells. Altogether, we reveal dynamic bacterial phase variations driven by bacteriophages and host inflammation, signifying bacterial functional plasticity during disease.}, } @article {pmid38421596, year = {2024}, author = {Anu, K and Kumari, S and Choudhary, G and Devi, S}, title = {Microbial diversity analysis of Chumathang geothermal spring, Ladakh, India.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {55}, number = {2}, pages = {1545-1555}, pmid = {38421596}, issn = {1678-4405}, mesh = {*Hot Springs/microbiology ; India ; *Bacteria/classification/genetics/isolation & purification ; *Archaea/classification/genetics/isolation & purification ; *Biodiversity ; *Soil Microbiology ; *Phylogeny ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Water Microbiology ; }, abstract = {In light of their unique and challenging environment, the high-altitude Chumathang geothermal springs in Ladakh, India, are undeniably intriguing for microbiological study. The purpose of this study was to employ a culture-independent sequencing approach to give a comprehensive characterization of the unknown bacterial and archaeal community structure, composition and networks in water and soil from the Chumathang geothermal spring. A total of 50%, and 42.86% bacterial phyla were found in the water, and soil samples respectively and this analysis also showed a total of 9.62% and 7.94% of archaeal phyla in both the samples, respectively. Further, the presence of unclassified (derived from other sequences, water: 17.31%, and soil: 19.05%) and unclassified (derived from bacteria, water: 13.46%, and soil: 12.70%) were also observed in the current metagenomics investigation. Firmicutes and Proteobacteria were the most abundant bacterial phyla in water, whereas Proteobacteria and Bacteroidetes were the most abundant bacterial phyla in geothermal soil. Crenarchaeota and Euryarchaeota dominated archeal communities in soil and water, respectively. This metagenomic study gave a detailed insight into the microbial diversity found in Chumathang geothermal spring and surrounding area, located in Ladakh, India. Surprisingly, this finding indicated the existence of geographically distinct microbial communities that were suited to various geothermal water habitats along the Himalayan Geothermal Belt. Future studies must take into account the metabolic pathways of these microbial communities that exist in these extreme environments. This will allow us to obtain a better knowledge of the microbial metabolisms that are common at these geothermal locations, which have a lot of potential for biotechnological applications. They will also enable us to establish links between the microbial community composition and the physicochemical environment of geothermal water and area.}, } @article {pmid38421266, year = {2024}, author = {Matchado, MS and Rühlemann, M and Reitmeier, S and Kacprowski, T and Frost, F and Haller, D and Baumbach, J and List, M}, title = {On the limits of 16S rRNA gene-based metagenome prediction and functional profiling.}, journal = {Microbial genomics}, volume = {10}, number = {2}, pages = {}, pmid = {38421266}, issn = {2057-5858}, mesh = {Humans ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; *Microbiota/genetics ; Algorithms ; }, abstract = {Molecular profiling techniques such as metagenomics, metatranscriptomics or metabolomics offer important insights into the functional diversity of the microbiome. In contrast, 16S rRNA gene sequencing, a widespread and cost-effective technique to measure microbial diversity, only allows for indirect estimation of microbial function. To mitigate this, tools such as PICRUSt2, Tax4Fun2, PanFP and MetGEM infer functional profiles from 16S rRNA gene sequencing data using different algorithms. Prior studies have cast doubts on the quality of these predictions, motivating us to systematically evaluate these tools using matched 16S rRNA gene sequencing, metagenomic datasets, and simulated data. Our contribution is threefold: (i) using simulated data, we investigate if technical biases could explain the discordance between inferred and expected results; (ii) considering human cohorts for type two diabetes, colorectal cancer and obesity, we test if health-related differential abundance measures of functional categories are concordant between 16S rRNA gene-inferred and metagenome-derived profiles and; (iii) since 16S rRNA gene copy number is an important confounder in functional profiles inference, we investigate if a customised copy number normalisation with the rrnDB database could improve the results. Our results show that 16S rRNA gene-based functional inference tools generally do not have the necessary sensitivity to delineate health-related functional changes in the microbiome and should thus be used with care. Furthermore, we outline important differences in the individual tools tested and offer recommendations for tool selection.}, } @article {pmid38421192, year = {2024}, author = {Zhang, N and Gao, X and Li, D and Xu, L and Zhou, G and Xu, M and Peng, L and Sun, G and Pan, F and Li, Y and Ren, R and Huang, R and Yang, Y and Wang, Z}, title = {Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites.}, journal = {Microbiology spectrum}, volume = {12}, number = {4}, pages = {e0143723}, pmid = {38421192}, issn = {2165-0497}, mesh = {Rats ; Animals ; *Gastrointestinal Microbiome/physiology ; Sleep Deprivation/complications ; Lipopolysaccharides ; Anxiety/metabolism ; Inflammation/metabolism ; }, abstract = {UNLABELLED: The present study aimed to characterize the gut microbiota and serum metabolome changes associated with sleep deprivation (SD) as well as to explore the potential benefits of multi-probiotic supplementation in alleviating SD-related mental health disorders. Rats were subjected to 7 days of SD, followed by 14 days of multi-probiotics or saline administration. Open-field tests were conducted at baseline, end of SD (day 7), and after 14 days of saline or multi-probiotic gavage (day 21). Metagenomic sequencing was conducted on fecal samples, and serum metabolites were measured by untargeted liquid chromatography tandem-mass spectrometry. At day 7, anxiety-like behaviors, including significant decreases in total movement distance (P = 0.0002) and staying time in the central zone (P = 0.021), were observed. In addition, increased levels of lipopolysaccharide (LPS; P = 0.028) and decreased levels of uridine (P = 0.018) and tryptophan (P = 0.01) were detected in rats after 7 days of SD. After SD, the richness of the gut bacterial community increased, and the levels of Akkermansia muciniphila, Muribaculum intestinale, and Bacteroides caecimuris decreased. The changes in the host metabolism and gut microbiota composition were strongly associated with the anxiety-like behaviors caused by SD. In addition, multi-probiotic supplementation for 14 days modestly improved the anxiety-like behaviors in SD rats but significantly reduced the serum level of LPS (P = 0.045). In conclusion, SD induces changes in the gut microbiota and serum metabolites, which may contribute to the development of chronic inflammatory responses and affect the gut-brain axis, causing anxiety-like behaviors. Probiotic supplementation significantly reduces serum LPS, which may alleviate the influence of chronic inflammation.

IMPORTANCE: The disturbance in the gut microbiome and serum metabolome induced by SD may be involved in anxiety-like behaviors. Probiotic supplementation decreases serum levels of LPS, but this reduction may be insufficient for alleviating SD-induced anxiety-like behaviors.}, } @article {pmid38420723, year = {2024}, author = {Zhu, K and Jin, Y and Zhao, Y and He, A and Wang, R and Cao, C}, title = {Proteomic scrutiny of nasal microbiomes: implications for the clinic.}, journal = {Expert review of proteomics}, volume = {21}, number = {4}, pages = {169-179}, doi = {10.1080/14789450.2024.2323983}, pmid = {38420723}, issn = {1744-8387}, mesh = {Humans ; *Microbiota/genetics ; *Proteomics/methods ; Nasal Cavity/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {INTRODUCTION: The nasal cavity is the initial site of the human respiratory tract and is one of the habitats where microorganisms colonize. The findings from a growing number of studies have shown that the nasal microbiome is an important factor for human disease and health. 16S rRNA sequencing and metagenomic next-generation sequencing (mNGS) are the most commonly used means of microbiome evaluation. Among them, 16S rRNA sequencing is the primary method used in previous studies of nasal microbiomes. However, neither 16S rRNA sequencing nor mNGS can be used to analyze the genes specifically expressed by nasal microorganisms and their functions. This problem can be addressed by proteomic analysis of the nasal microbiome.

AREAS COVERED: In this review, we summarize current advances in research on the nasal microbiome, introduce the methods for proteomic evaluation of the nasal microbiome, and focus on the important roles of proteomic evaluation of the nasal microbiome in the diagnosis and treatment of related diseases.

EXPERT OPINION: The detection method for microbiome-expressed proteins is known as metaproteomics. Metaproteomic analysis can help us dig deeper into the nasal microbiomes and provide new targets and ideas for clinical diagnosis and treatment of many nasal dysbiosis-related diseases.}, } @article {pmid38420673, year = {2024}, author = {Lu, Y and Zhang, L and Liu, X and Lan, Y and Wu, L and Wang, J and Wu, K and Yang, C and Lv, R and Yi, D and Zhuo, G and Li, Y and Shen, F and Hou, R and Yue, B and Fan, Z}, title = {Red pandas with different diets and environments exhibit different gut microbial functional composition and capacity.}, journal = {Integrative zoology}, volume = {19}, number = {4}, pages = {662-682}, doi = {10.1111/1749-4877.12813}, pmid = {38420673}, issn = {1749-4877}, support = {2022NSFSC0126//Natural Science Foundation of Sichuan Province/ ; 2020CPB-B06//Foundation of Chengdu Research Base of Giant Panda Breeding/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Diet/veterinary ; *Ailuridae/microbiology ; *Feces/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacteria/classification ; Animal Feed/analysis ; Environment ; }, abstract = {The red panda (Ailurus fulgens) is a distinctive mammal known for its reliance on a diet primarily consisting of bamboo. The gut microbiota and overall health of animals are strongly influenced by diets and environments. Therefore, conducting research to explore the taxonomical and functional variances within the gut microbiota of red pandas exposed to various dietary and environmental conditions could shed light on the dynamic complexities of their microbial communities. In this study, normal fecal samples were obtained from red pandas residing in captive and semi-free environments under different dietary regimes and used for metabolomic, 16S rRNA, and metagenomic sequencing analysis, with the pandas classified into four distinct cohorts according to diet and environment. In addition, metagenomic sequencing was conducted on mucus fecal samples to elucidate potential etiological agents of disease. Results revealed an increased risk of gastrointestinal diseases in red pandas consuming bamboo shoots due to the heightened presence of pathogenic bacteria, although an increased presence of microbiota-derived tryptophan metabolites appeared to facilitate intestinal balance. The red pandas fed bamboo leaves also exhibited a decrease in gut microbial diversity, which may be attributed to the antibacterial flavonoids and lower protein levels in leaves. Notably, red pandas residing in semi-free environments demonstrated an enriched gut microbial diversity. Moreover, the occurrence of mucus secretion may be due to an increased presence of species associated with diarrhea and a reduced level of microbiota-derived tryptophan metabolites. In summary, our findings substantiate the influential role of diet and environment in modulating the gut microbiota of red pandas, offering potential implications for improved captive breeding practices.}, } @article {pmid38419010, year = {2024}, author = {Nooij, S and Vendrik, KEW and Zwittink, RD and Ducarmon, QR and Keller, JJ and Kuijper, EJ and Terveer, EM and , }, title = {Long-term beneficial effect of faecal microbiota transplantation on colonisation of multidrug-resistant bacteria and resistome abundance in patients with recurrent Clostridioides difficile infection.}, journal = {Genome medicine}, volume = {16}, number = {1}, pages = {37}, pmid = {38419010}, issn = {1756-994X}, mesh = {Humans ; Fecal Microbiota Transplantation/methods ; *Clostridioides difficile/genetics ; Feces/microbiology ; *Microbiota ; *Clostridium Infections/therapy/microbiology ; Treatment Outcome ; }, abstract = {BACKGROUND: Multidrug-resistant (MDR) bacteria are a growing global threat, especially in healthcare facilities. Faecal microbiota transplantation (FMT) is an effective prevention strategy for recurrences of Clostridioides difficile infections and can also be useful for other microbiota-related diseases.

METHODS: We study the effect of FMT in patients with multiple recurrent C. difficile infections on colonisation with MDR bacteria and antibiotic resistance genes (ARG) on the short (3 weeks) and long term (1-3 years), combining culture methods and faecal metagenomics.

RESULTS: Based on MDR culture (n = 87 patients), we notice a decrease of 11.5% in the colonisation rate of MDR bacteria after FMT (20/87 before FMT = 23%, 10/87 3 weeks after FMT). Metagenomic sequencing of patient stool samples (n = 63) shows a reduction in relative abundances of ARGs in faeces, while the number of different resistance genes in patients remained higher compared to stools of their corresponding healthy donors (n = 11). Furthermore, plasmid predictions in metagenomic data indicate that patients harboured increased levels of resistance plasmids, which appear unaffected by FMT. In the long term (n = 22 patients), the recipients' resistomes are still donor-like, suggesting the effect of FMT may last for years.

CONCLUSIONS: Taken together, we hypothesise that FMT restores the gut microbiota to a composition that is closer to the composition of healthy donors, and potential pathogens are either lost or decreased to very low abundances. This process, however, does not end in the days following FMT. It may take months for the gut microbiome to re-establish a balanced state. Even though a reservoir of resistance genes remains, a notable part of which on plasmids, FMT decreases the total load of resistance genes.}, } @article {pmid38418677, year = {2024}, author = {Halleran, J and Sylvester, H and Jacob, M and Callahan, B and Baynes, R and Foster, D}, title = {Impact of florfenicol dosing regimen on the phenotypic and genotypic resistance of enteric bacteria in steers.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {4920}, pmid = {38418677}, issn = {2045-2322}, support = {USDA Grants 2020-41480-32520//Food Animal Residue Avoidance Databank (FARAD)/ ; USDA Grants 2021-41480-35270//Food Animal Residue Avoidance Databank (FARAD)/ ; }, mesh = {Animals ; Humans ; Escherichia coli/genetics ; *Gastrointestinal Microbiome/genetics ; *Thiamphenicol/pharmacology/*analogs & derivatives ; Anti-Bacterial Agents/pharmacology ; Enterobacteriaceae ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; }, abstract = {The food animal sector's use of antimicrobials is heavily critiqued for its role in allowing resistance to develop against critically important antimicrobials in human health. The WHO recommends using lower tier antimicrobials such as florfenicol for disease treatment. The primary objective of this study was to assess the differences in resistance profiles of enteric microbes following administration of florfenicol to steers using both FDA-approved dosing regimens and two different detection methods. Our hypothesis was that we would identify an increased prevalence of resistance in the steers administered the repeated, lower dose of florfenicol; additionally, we hypothesized resistance profiles would be similar between both detection methods. Twelve steers were administered either two intramuscular (20 mg/kg q 48 h; n = 6) or a single subcutaneous dose (40 mg/kg, n = 6). Fecal samples were collected for 38 days, and E. coli and Enterococcus were isolated and tested for resistance. Fecal samples were submitted for metagenomic sequencing analysis. Metagenomics revealed genes conferring resistance to aminoglycosides as the most abundant drug class. Most multidrug resistance genes contained phenicols. The genotypic and phenotypic patterns of resistance were not similar between drug classes. Observed increases in resistant isolates and relative abundance of resistance genes peaked after drug administration and returned to baseline by the end of the sampling period. The use of a "lower tier" antimicrobial, such as florfenicol, may cause an increased amount of resistance to critically important antimicrobials for a brief period, but these changes largely resolve by the end of the drug withdrawal period.}, } @article {pmid38417224, year = {2024}, author = {Xie, Z and Huang, J and Sun, G and He, S and Luo, Z and Zhang, L and Li, L and Yao, M and Du, C and Yu, W and Feng, Y and Yang, D and Zhang, J and Ge, C and Li, H and Geng, M}, title = {Integrated multi-omics analysis reveals gut microbiota dysbiosis and systemic disturbance in major depressive disorder.}, journal = {Psychiatry research}, volume = {334}, number = {}, pages = {115804}, doi = {10.1016/j.psychres.2024.115804}, pmid = {38417224}, issn = {1872-7123}, mesh = {Humans ; *Depressive Disorder, Major ; *Gastrointestinal Microbiome ; Dysbiosis/complications ; Multiomics ; RNA, Ribosomal, 16S ; }, abstract = {Major depressive disorder (MDD) involves systemic changes in peripheral blood and gut microbiota, but the current understanding is incomplete. Herein, we conducted a multi-omics analysis of fecal and blood samples obtained from an observational cohort including MDD patients (n = 99) and healthy control (HC, n = 50). 16S rRNA sequencing of gut microbiota showed structural alterations in MDD, as characterized by increased Enterococcus. Metagenomics sequencing of gut microbiota showed substantial functional alterations including upregulation in the superpathway of the glyoxylate cycle and fatty acid degradation and downregulation in various metabolic pathways in MDD. Plasma metabolomics revealed decreased amino acids and bile acids, together with increased sphingolipids and cholesterol esters in MDD. Notably, metabolites involved in arginine and proline metabolism were decreased while sphingolipid metabolic pathway were increased. Mass cytometry analysis of blood immune cell subtypes showed rises in proinflammatory immune subsets and declines in anti-inflammatory immune subsets in MDD. Furthermore, our findings revealed disease severity-related factors of MDD. Interestingly, we classified MDD into two immune subtypes that were highly correlated with disease relapse. Moreover, we established discriminative signatures that differentiate MDD from HC. These findings contribute to a comprehensive understanding of the MDD pathogenesis and provide valuable resources for the discovery of biomarkers.}, } @article {pmid38417116, year = {2024}, author = {Zheng, R and Wang, C and Sun, C}, title = {Deep-sea in situ and laboratory multi-omics provide insights into the sulfur assimilation of a deep-sea Chloroflexota bacterium.}, journal = {mBio}, volume = {15}, number = {4}, pages = {e0000424}, pmid = {38417116}, issn = {2150-7511}, support = {LSKJ202203103//Science and Technology Innovation Project of Laoshan Laboratory/ ; }, mesh = {Proteomics ; Multiomics ; Thiosulfates/metabolism ; Oxidation-Reduction ; Bacteria/genetics ; *Chloroflexi/genetics ; *Microbiota ; Sulfur/metabolism ; Phylogeny ; }, abstract = {UNLABELLED: Chloroflexota bacteria are abundant and globally distributed in various deep-sea ecosystems. It has been reported based on metagenomics data that two deep-sea Chloroflexota lineages (the SAR202 group and Dehalococcoidia class) have the potential to drive sulfur cycling. However, the absence of cultured Chloroflexota representatives is a significant bottleneck toward understanding their contribution to the deep-sea sulfur cycling. In this study, we find that Phototrophicus methaneseepsis ZRK33 isolated from deep-sea sediment has a heterotrophic lifestyle and can assimilate sulfate and thiosulfate. Using combined physiological, genomic, proteomic, and in situ transcriptomic methods, we find that strain ZRK33 can perform assimilatory sulfate reduction in both laboratory and deep-sea conditions. Metabolism of sulfate or thiosulfate by strain ZRK33 significantly promotes the transport and degradation of various macromolecules and thereby stimulates the energy production. In addition, metagenomic results show that genes associated with assimilatory and dissimilatory sulfate reduction are ubiquitously distributed in the metagenome-assembled genomes of Chloroflexota members derived from deep-sea sediments. Metatranscriptomic results also show that the expression levels of related genes are upregulated, strongly suggesting that Chloroflexota bacteria may play undocumented roles in deep-sea sulfur cycling.

IMPORTANCE: The cycling of sulfur is one of Earth's major biogeochemical processes and is closely related to the energy metabolism of microorganisms living in the deep-sea cold seep and hydrothermal vents. To date, some of the members of Chloroflexota are proposed to play a previously unrecognized role in sulfur cycling. However, the sulfur metabolic characteristics of deep-sea Chloroflexota bacteria have never been reported, and remain to be verified in cultured deep-sea representatives. Here, we show that the deep-sea Chloroflexota bacterium ZRK33 can perform sulfate assimilation in both laboratory and deep-sea conditions, which expands our knowledge of the sulfur metabolic potential of deep-sea Chloroflexota bacteria. We also show that the genes associated with assimilatory and dissimilatory sulfate reduction ubiquitously distribute in the deep-sea Chloroflexota members, providing hints to the roles of Chloroflexota bacteria in deep-sea sulfur biogeochemical cycling.}, } @article {pmid38415986, year = {2024}, author = {Genitsaris, S and Stefanidou, N and Hatzinikolaou, D and Kourkoutmani, P and Michaloudi, E and Voutsa, D and Gros, M and García-Gómez, E and Petrović, M and Ntziachristos, L and Moustaka-Gouni, M}, title = {Marine Microbiota Responses to Shipping Scrubber Effluent Assessed at Community Structure and Function Endpoints.}, journal = {Environmental toxicology and chemistry}, volume = {43}, number = {5}, pages = {1012-1029}, doi = {10.1002/etc.5834}, pmid = {38415986}, issn = {1552-8618}, support = {874990//Horizon 2020 Framework Programme/ ; }, mesh = {*Microbiota/drug effects ; *Water Pollutants, Chemical/toxicity ; Polycyclic Aromatic Hydrocarbons ; Bacteria/genetics ; Biodegradation, Environmental ; Seawater/microbiology ; Petroleum ; Plankton/genetics ; }, abstract = {The use of novel high-throughput sequencing (HTS) technologies to examine the responses of natural multidomain microbial communities to scrubber effluent discharges to the marine environment is still limited. Thus, we applied metabarcoding sequencing targeting the planktonic unicellular eukaryotic and prokaryotic fraction (phytoplankton, bacterioplankton, and protozooplankton) in mesocosm experiments with natural microbial communities from a polluted and an unpolluted site. Furthermore, metagenomic analysis revealed changes in the taxonomic and functional dominance of multidomain marine microbial communities after scrubber effluent additions. The results indicated a clear shift in the microbial communities after such additions, which favored bacterial taxa with known oil and polycyclic aromatic hydrocarbons (PAHs) biodegradation capacities. These bacteria exhibited high connectedness with planktonic unicellular eukaryotes employing variable trophic strategies, suggesting that environmentally relevant bacteria can influence eukaryotic community structure. Furthermore, Clusters of Orthologous Genes associated with pathways of PAHs and monocyclic hydrocarbon degradation increased in numbers at treatments with high scrubber effluent additions acutely. These genes are known to express enzymes acting at various substrates including PAHs. These indications, in combination with the abrupt decrease in the most abundant PAHs in the scrubber effluent below the limit of detection-much faster than their known half-lives-could point toward a bacterioplankton-initiated rapid ultimate biodegradation of the most abundant toxic contaminants of the scrubber effluent. The implementation of HTS could be a valuable tool to develop multilevel biodiversity indicators of the scrubber effluent impacts on the marine environment, which could lead to improved impact assessment. Environ Toxicol Chem 2024;43:1012-1029. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.}, } @article {pmid38414315, year = {2024}, author = {Torma, F and Kerepesi, C and Jókai, M and Babszki, G and Koltai, E and Ligeti, B and Kalcsevszki, R and McGreevy, KM and Horvath, S and Radák, Z}, title = {Alterations of the gut microbiome are associated with epigenetic age acceleration and physical fitness.}, journal = {Aging cell}, volume = {23}, number = {4}, pages = {e14101}, pmid = {38414315}, issn = {1474-9726}, support = {RRF-2.3.1-21-2022-00004//European Union/ ; 126823//Ministry of Innovation and Technology National Excellence Program/ ; OTKA142192//National Research, Development and Innovation Office/ ; OTKA146113//National Research, Development and Innovation Office/ ; TKP2021-EGA-37//Hungarian University Sport Science, Innovation and Technology Ministry, Hungary/ ; 2021-28//National Academy of Science, Hungary/ ; }, mesh = {Humans ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; Physical Fitness ; *Microbiota/genetics ; Acceleration ; Aging/genetics ; Epigenesis, Genetic ; DNA Methylation ; }, abstract = {Epigenetic clocks can measure aging and predict the incidence of diseases and mortality. Higher levels of physical fitness are associated with a slower aging process and a healthier lifespan. Microbiome alterations occur in various diseases and during the aging process, yet their relation to epigenetic clocks is not explored. To fill this gap, we collected metagenomic (from stool), epigenetic (from blood), and exercise-related data from physically active individuals and, by applying epigenetic clocks, we examined the relationship between gut flora, blood-based epigenetic age acceleration, and physical fitness. We revealed that an increased entropy in the gut microbiome of physically active middle-aged/old individuals is associated with accelerated epigenetic aging, decreased fitness, or impaired health status. We also observed that a slower epigenetic aging and higher fitness level can be linked to altered abundance of some bacterial species often linked to anti-inflammatory effects. Overall our data suggest that alterations in the microbiome can be associated with epigenetic age acceleration and physical fitness.}, } @article {pmid38413544, year = {2024}, author = {Remesh, AT and Viswanathan, R}, title = {CrAss-Like Phages: From Discovery in Human Fecal Metagenome to Application as a Microbial Source Tracking Marker.}, journal = {Food and environmental virology}, volume = {16}, number = {2}, pages = {121-135}, pmid = {38413544}, issn = {1867-0342}, mesh = {Humans ; *Feces/virology/microbiology ; *Bacteriophages/genetics/isolation & purification/classification ; *Gastrointestinal Microbiome ; *Metagenome ; Bacteria/virology/genetics/classification/isolation & purification ; Metagenomics ; }, abstract = {CrAss-like phages are a diverse group of bacteriophages genetically similar to the prototypical crAssphage (p-crAssphage), which was discovered in the human gut microbiome through a metagenomics approach. It was identified as a ubiquitous and highly abundant bacteriophage group in the gut microbiome. Initial co-occurrence analysis postulated Bacteroides spp. as the prospective bacterial host. Subsequent studies have confirmed multiple host species under Phylum Bacteroidetes and some Firmicutes. Detection of crAss-like phages in sewage-contaminated environmental water and robust correlation with enteric viruses and bacteria has culminated in their adoption as a microbial source tracking (MST) marker. Polymerase chain reaction (PCR) and real-time PCR assays have been developed utilizing the conserved genes in the p-crAssphage genome to detect human fecal contamination of different water sources, with high specificity. Numerous investigations have examined the implications of crAss-like phages in diverse disease conditions, including ulcerative colitis, obesity and metabolic syndrome, autism spectrum disorders, rheumatoid arthritis, atopic eczema, and other autoimmune disorders. These studies have unveiled associations between certain diseases and diminished abundance and diversity of crAss-like phages. This review offers insights into the diverse aspects of research on crAss-like phages, including their discovery, genomic characteristics, structure, taxonomy, isolation, molecular detection, application as an MST marker, and role as a gut microbiome modulator with consequential health implications.}, } @article {pmid38413462, year = {2024}, author = {Choy, WH and Adler, A and Morgan-Lang, C and Gough, EK and Hallam, SJ and Manges, AR and Chew, BH and Penniston, K and Miller, A and Lange, D}, title = {Deficient butyrate metabolism in the intestinal microbiome is a potential risk factor for recurrent kidney stone disease.}, journal = {Urolithiasis}, volume = {52}, number = {1}, pages = {38}, pmid = {38413462}, issn = {2194-7236}, mesh = {Humans ; *Gastrointestinal Microbiome ; Oxalates/metabolism ; Risk Factors ; Bacteria/genetics ; Butyrates ; *Kidney Calculi/microbiology ; }, abstract = {Intestinal microbiome dysbiosis is a known risk factor for recurrent kidney stone disease (KSD) with prior data suggesting a role for dysfunctional metabolic pathways other than those directly utilizing oxalate. To identify alternative mechanisms, the current study analyzed differences in the metabolic potential of intestinal microbiomes of patients (n = 17) and live-in controls (n = 17) and determined their relevance to increased risk for KSD using shotgun metagenomic sequencing. We found no differences in the abundance of genes associated with known oxalate degradation pathways, supporting the notion that dysfunction in other metabolic pathways plays a role in KSD. Further analysis showed decreased abundance of key enzymes involved in butyrate biosynthesis in patient intestinal microbiomes. Furthermore, de novo construction of microbial genomes showed that the majority of genes significantly enriched in non-stone formers are affiliated with Faecalibacterium prausnitzii, a major butyrate producer. Specifically pertaining to butyrate metabolism, the majority of abundant genes mapped back to F. prausnitzii, Alistipes spp., and Akkermansia muciniphila. No differences were observed in ascorbate or glyoxylate metabolic pathways. Collectively, these data suggest that impaired bacterial-associated butyrate metabolism may be an oxalate-independent mechanism that contributes to an increased risk for recurrent KSD. This indicates that the role of the intestinal microbiome in recurrent KSD is multi-factorial, which is representative of the highly intertwined metabolic nature of this complex environment. Future bacteria-based treatments must not be restricted to targeting only oxalate metabolism.}, } @article {pmid38412016, year = {2024}, author = {Ding, Y and Yanagi, K and Yang, F and Callaway, E and Cheng, C and Hensel, ME and Menon, R and Alaniz, RC and Lee, K and Jayaraman, A}, title = {Oral supplementation of gut microbial metabolite indole-3-acetate alleviates diet-induced steatosis and inflammation in mice.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {38412016}, issn = {2050-084X}, support = {Ray B. Nesbitt Endowed Chair//Texas A and M University/ ; Karol Family Professorship//Tufts University/ ; }, mesh = {Animals ; Mice ; *Non-alcoholic Fatty Liver Disease/drug therapy ; *Gastrointestinal Microbiome ; Inflammation ; Diet, Western/adverse effects ; Cytokines ; Dietary Supplements ; Acetates ; Indoles/pharmacology ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease in Western countries. There is growing evidence that dysbiosis of the intestinal microbiota and disruption of microbiota-host interactions contribute to the pathology of NAFLD. We previously demonstrated that gut microbiota-derived tryptophan metabolite indole-3-acetate (I3A) was decreased in both cecum and liver of high-fat diet-fed mice and attenuated the expression of inflammatory cytokines in macrophages and Tnfa and fatty acid-induced inflammatory responses in an aryl-hydrocarbon receptor (AhR)-dependent manner in hepatocytes. In this study, we investigated the effect of orally administered I3A in a mouse model of diet-induced NAFLD. Western diet (WD)-fed mice given sugar water (SW) with I3A showed dramatically decreased serum ALT, hepatic triglycerides (TG), liver steatosis, hepatocyte ballooning, lobular inflammation, and hepatic production of inflammatory cytokines, compared to WD-fed mice given only SW. Metagenomic analysis show that I3A administration did not significantly modify the intestinal microbiome, suggesting that I3A's beneficial effects likely reflect the metabolite's direct actions on the liver. Administration of I3A partially reversed WD-induced alterations of liver metabolome and proteome, notably, decreasing expression of several enzymes in hepatic lipogenesis and β-oxidation. Mechanistically, we also show that AMP-activated protein kinase (AMPK) mediates the anti-inflammatory effects of I3A in macrophages. The potency of I3A in alleviating liver steatosis and inflammation clearly demonstrates its potential as a therapeutic modality for preventing the progression of steatosis to non-alcoholic steatohepatitis (NASH).}, } @article {pmid38410449, year = {2024}, author = {Seitz, VA and McGivem, BB and Borton, MA and Chaparro, JM and Schipanski, ME and Prenni, JE and Wrighton, KC}, title = {Cover Crop Root Exudates Impact Soil Microbiome Functional Trajectories in Agricultural Soils.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {38410449}, issn = {2693-5015}, support = {P30 CA046934/CA/NCI NIH HHS/United States ; }, abstract = {BACKGROUND: Cover cropping is an agricultural practice that uses secondary crops to support the growth of primary crops through various mechanisms including erosion control, weed suppression, nutrient management, and enhanced biodiversity. Cover crops may elicit some of these ecosystem services through chemical interactions with the soil microbiome via root exudation, or the release of plant metabolites from roots. Phytohormones are one metabolite type exuded by plants that activate the rhizosphere microbiome, yet managing this chemical interaction remains an untapped mechanism for optimizing plant-soil microbiome interactions. Currently, there is limited understanding on the diversity of cover crop phytohormone root exudation patterns and how these chemical messages selectively enrich specific microbial taxa and functionalities in agricultural soils.

RESULTS: Here, we link variability in cover crop root exudate composition to changes in soil microbiome functionality. Exudate chemical profiles from 4 cover crop species (Sorghum bicolor, Vicia villosa, Brassica napus, and Secale cereal) were used as the chemical inputs to decipher microbial responses. These distinct exudate profiles, along with a no exudate control, were amended to agricultural soil microcosms with microbial responses tracked over time using metabolomes and genome-resolved metatranscriptomes. Our findings illustrated microbial metabolic patterns were unique in response to cover crop exudate inputs over time, particularly by sorghum and cereal rye amended microcosms where we identify novel microbial members (at the genera and family level) who produced IAA and GA4 over time. We also identify broad changes in microbial nitrogen cycling in response chemical inputs.

CONCLUSIONS: We highlight that root exudate amendments alter microbial community function and phytohormone metabolisms, particularly in response to root exudates isolated from cereal rye and sorghum plants. Additionally, we constructed a soil microbial genomic catalog of microorganisms responding to commonly used cover crops, a public resource for agriculturally-relevant microbes. Many of our exudate-stimulated microorganisms are representatives from poorly characterized or novel taxa, highlighting the yet to be discovered metabolic reservoir harbored in agricultural soils. Our findings emphasize the tractability of high-resolution multiomics approaches to investigate processes relevant for agricultural soils, opening the possibility of targeting specific soil biogeochemical outcomes through biological precision agricultural practices that use cover crops and the microbiome as levers for enhanced crop production.}, } @article {pmid38406876, year = {2024}, author = {Li, A and Liu, A and Wang, J and Song, H and Luo, P and Zhan, M and Zhou, X and Chen, L and Zhang, L}, title = {The prophylaxis functions of Lactobacillus fermentum GLF-217 and Lactobacillus plantarum FLP-215 on ulcerative colitis via modulating gut microbiota of mice.}, journal = {Journal of the science of food and agriculture}, volume = {104}, number = {10}, pages = {5816-5825}, doi = {10.1002/jsfa.13410}, pmid = {38406876}, issn = {1097-0010}, support = {322QN259//Hainan Provincial Natural Science Foundation of China/ ; 2022YFD2100702//National Key Research and Development Program of China/ ; KYQD(ZR)-21122//Scientific Research Foundation of Hainan University/ ; }, mesh = {Animals ; *Limosilactobacillus fermentum ; *Colitis, Ulcerative/microbiology/prevention & control/chemically induced/immunology ; *Gastrointestinal Microbiome ; *Lactobacillus plantarum ; Mice ; *Probiotics/administration & dosage/pharmacology ; Male ; Humans ; Dextran Sulfate/adverse effects ; Colon/microbiology/immunology/pathology ; Intestinal Mucosa/microbiology/immunology/metabolism ; Mice, Inbred C57BL ; Interleukin-10/genetics/metabolism ; Interleukin-1beta/genetics/metabolism/immunology ; Bacteria/classification/genetics/isolation & purification ; Mucin-2/metabolism/genetics ; Interleukin-6/genetics/metabolism/immunology ; Tumor Necrosis Factor-alpha/metabolism/genetics/immunology ; Interferon-gamma/metabolism/genetics/immunology ; Zonula Occludens-1 Protein/metabolism/genetics ; Disease Models, Animal ; }, abstract = {BACKGROUND: The strong connection between gut microbes and human health has been confirmed by an increasing number of studies. Although probiotics have been found to relieve ulcerative colitis, the mechanism varies by the species involved. In this study, the physiological, immune and pathological factors of mice were measured and shotgun metagenomic sequencing was conducted to investigate the potential mechanisms in preventing ulcerative colitis.

RESULTS: The results demonstrated that ingestion of Lactobacillus fermentum GLF-217 and Lactobacillus plantarum FLP-215 significantly alleviated ulcerative colitis induced by dextran sulfate sodium (DSS), as evidenced by the increase in body weight, food intake, water intake and colon length as well as the decrease in disease activity index, histopathological score and inflammatory factor. Both strains not only improved intestinal mucosa by increasing mucin-2 and zonula occludens-1, but also improved the immune system response by elevating interleukin-10 levels and decreasing the levels of interleukin-1β, interleukin-6, tumor necrosis factor-α and interferon-γ. Moreover, L. fermentum GLF-217 and L. plantarum FLP-215 play a role in preventing DSS-induced colitis by regulating the structure of gut microbiota and promoting the formation of short-chain fatty acids.

CONCLUSIONS: This study may provide a reference for the prevention strategy of ulcerative colitis. © 2024 Society of Chemical Industry.}, } @article {pmid38406289, year = {2024}, author = {Banar, M and Rokaya, D and Azizian, R and Khurshid, Z and Banakar, M}, title = {Oral bacteriophages: metagenomic clues to interpret microbiomes.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e16947}, pmid = {38406289}, issn = {2167-8359}, mesh = {*Bacteriophages/genetics ; *Microbiota/genetics ; Metagenome ; Prophages/genetics ; Mouth/microbiology ; Bacteria/genetics ; }, abstract = {Bacteriophages are bacterial viruses that are distributed throughout the environment. Lytic phages and prophages in saliva, oral mucosa, and dental plaque interact with the oral microbiota and can change biofilm formation. The interactions between phages and bacteria can be considered a portion of oral metagenomics. The metagenomic profile of the oral microbiome indicates various bacteria. Indeed, there are various phages against these bacteria in the oral cavity. However, some other phages, like phages against Absconditabacteria, Chlamydiae, or Chloroflexi, have not been identified in the oral cavity. This review gives an overview of oral bacteriophage and used for metagenomics. Metagenomics of these phages deals with multi-drug-resistant bacterial plaques (biofilms) in oral cavities and oral infection. Hence, dentists and pharmacologists should know this metagenomic profile to cope with predental and dental infectious diseases.}, } @article {pmid38404111, year = {2024}, author = {Conrad, MA and Bittinger, K and Ren, Y and Kachelries, K and Vales, J and Li, H and Wu, GD and Bushman, FD and Devoto, M and Baldassano, RN and Kelsen, JR}, title = {The intestinal microbiome of inflammatory bowel disease across the pediatric age range.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2317932}, pmid = {38404111}, issn = {1949-0984}, support = {R01 HL113252/HL/NHLBI NIH HHS/United States ; P30 DK050306/DK/NIDDK NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; R61 HL137063/HL/NHLBI NIH HHS/United States ; K23 DK119585/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Humans ; Child ; Infant ; *Gastrointestinal Microbiome ; Dysbiosis ; *Inflammatory Bowel Diseases/epidemiology ; Inflammation ; *Microbiota ; }, abstract = {Dysbiosis is associated with pediatric and adult-onset inflammatory bowel disease (IBD), but the role of dysbiosis and the microbiome in very early onset IBD (VEO-IBD) has not yet been described. Here, we aimed to demonstrate the impact of age and inflammation on microbial community structure using shotgun metagenomic sequencing in children with VEO-IBD, pediatric-onset IBD, and age-matched pediatric healthy controls (HC) observed longitudinally over the course of 8 weeks. We found disease-related differences in alpha and beta diversity between HC and children with IBD or VEO-IBD. Using a healthy microbial maturity index modeled from HC across the age range to characterize their gut microbiota, we found that children with pediatric-onset IBD and VEO-IBD had lower maturity than their age-matched HC groups, suggesting a disease effect on the microbial community. In addition, patients with pediatric IBD had significantly lower maturity than those with VEO-IBD, who had more heterogeneity at the youngest ages, highlighting differences in these two cohorts that were not captured in standard comparisons of alpha and beta diversity. These results demonstrate that young age and inflammation independently impact microbial community structure. However, the effect is not additive in the youngest patients, likely because of the heterogeneous and dynamic stool microbiome in this population.}, } @article {pmid38403655, year = {2024}, author = {Ren, Y and Chen, L and Guo, R and Ma, S and Li, S and Zhang, Y and Jiang, H and Shi, H and Zhang, P}, title = {Altered gut mycobiome in patients with end-stage renal disease and its correlations with serum and fecal metabolomes.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {202}, pmid = {38403655}, issn = {1479-5876}, support = {Program No. 2023-ZDLSF-45//Key Research and Development Projects of Shaanxi Province/ ; }, mesh = {Humans ; *Mycobiome ; Saccharomyces cerevisiae ; *Gastrointestinal Microbiome ; Feces/microbiology ; Metabolome ; *Kidney Failure, Chronic ; }, abstract = {BACKGROUND: The relationship between the gut mycobiome and end-stage renal disease (ESRD) remains largely unexplored.

METHODS: In this study, we compared the gut fungal populations of 223 ESRD patients and 69 healthy controls (HCs) based on shotgun metagenomic sequencing data, and analyzed their associations with host serum and fecal metabolites.

RESULTS: Our findings revealed that ESRD patients had a higher diversity in the gut mycobiome compared to HCs. Dysbiosis of the gut mycobiome in ESRD patients was characterized by a decrease of Saccharomyces cerevisiae and an increase in various opportunistic pathogens, such as Aspergillus fumigatus, Cladophialophora immunda, Exophiala spinifera, Hortaea werneckii, Trichophyton rubrum, and others. Through multi-omics analysis, we observed a substantial contribution of the gut mycobiome to host serum and fecal metabolomes. The opportunistic pathogens enriched in ESRD patients were frequently and positively correlated with the levels of creatinine, homocysteine, and phenylacetylglycine in the serum. The populations of Saccharomyces, including the HC-enriched Saccharomyces cerevisiae, were frequently and negatively correlated with the levels of various toxic metabolites in the feces.

CONCLUSIONS: Our results provided a comprehensive understanding of the associations between the gut mycobiome and the development of ESRD, which had important implications for guiding future therapeutic studies in this field.}, } @article {pmid38403443, year = {2024}, author = {Román-Camacho, JJ and Mauricio, JC and Santos-Dueñas, IM and García-Martínez, T and García-García, I}, title = {Recent advances in applying omic technologies for studying acetic acid bacteria in industrial vinegar production: A comprehensive review.}, journal = {Biotechnology journal}, volume = {19}, number = {2}, pages = {e2300566}, doi = {10.1002/biot.202300566}, pmid = {38403443}, issn = {1860-7314}, support = {//Universidad de Córdoba/ ; PID2021-127766OB-I00//Ministry of Science and Innovation/ ; PY20_00590//Junta de Andalucía/ ; }, mesh = {*Acetic Acid/metabolism ; Fermentation ; Biodiversity ; *Microbiota ; Asia ; }, abstract = {Vinegar and related bioproducts containing acetic acid as the main component are among the most appreciated fermented foodstuffs in numerous European and Asian countries because of their exceptional organoleptic and bio-healthy properties. Regarding the acetification process and obtaining of final products, there is still a lack of knowledge on fundamental aspects, especially those related to the study of biodiversity and metabolism of the present microbiota. In this context, omic technologies currently allow for the massive analysis of macromolecules and metabolites for the identification and characterization of these microorganisms working in their natural media without the need for isolation. This review approaches comprehensive research on the application of omic tools for the identification of vinegar microbiota, mainly acetic acid bacteria, with subsequent emphasis on the study of the microbial diversity, behavior, and key molecular strategies used by the predominant groups throughout acetification. The current omics tools are enabling both the finding of new vinegar microbiota members and exploring underlying strategies during the elaboration process. The species Komagataeibacter europaeus may be a model organism for present and future research in this industry; moreover, the development of integrated meta-omic analysis may facilitate the achievement of numerous of the proposed milestones. This work might provide useful guidance for the vinegar industry establishing the first steps towards the improvement of the acetification conditions and the development of new products with sensory and bio-healthy profiles adapted to the agri-food market.}, } @article {pmid38402921, year = {2024}, author = {Molina-Hoyos, K and Montoya-Ruíz, C and Aguilar, PV and Pérez-Doria, A and Díaz, FJ and Rodas, JD}, title = {Virome analyses of Amblyomma cajennense and Rhipicephalus microplus ticks collected in Colombia.}, journal = {Acta tropica}, volume = {253}, number = {}, pages = {107158}, doi = {10.1016/j.actatropica.2024.107158}, pmid = {38402921}, issn = {1873-6254}, support = {D43 TW010331/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Humans ; Horses ; *Rhipicephalus/genetics ; Amblyomma ; Colombia ; Virome/genetics ; *RNA Viruses ; }, abstract = {Tick-borne viruses (TBV) have gained public health relevance in recent years due to the recognition of human-associated fatal cases and the increase in tick-borne disease and transmission. However, many tick species have not been studied for their potential to transmit pathogenic viruses, especially those found in Latin America. To gain better understanding of the tick virome, we conducted targeted amplification using broadly-reactive consensus-degenerate pan-viral targeting viruses from the genera Flavivirus, Bandavirus, Uukuvirus, and Orthonairovirus genus. Additionally, we conducted unbiased metagenomic analyses to investigate the presence of viral RNA sequences in Amblyomma cajennense, A. patinoi and Rhipicephalus microplus ticks collected from a horse slaughter plant in Medellín, Colombia. While no viral products were detected by PCR, results of the metagenomic analyses revealed the presence of viral genomes belonging to the genera Phlebovirus, Bandavirus, and Uukuvirus, including Lihan Tick Virus (LTV), which was previously reported in Rhipicephalus microplus from Colombia. Overall, the results emphasized the enormous utility of the next-generation sequencing in identifying virus genetic diversity presents in ticks and other species of vectors and reservoirs.}, } @article {pmid38402727, year = {2024}, author = {Wang, R and Li, X and Lv, F and He, J and Lv, R and Wei, L}, title = {Sesame bacterial wilt significantly alters rhizosphere soil bacterial community structure, function, and metabolites in continuous cropping systems.}, journal = {Microbiological research}, volume = {282}, number = {}, pages = {127649}, doi = {10.1016/j.micres.2024.127649}, pmid = {38402727}, issn = {1618-0623}, mesh = {*Soil/chemistry ; *Sesamum ; Rhizosphere ; Soil Microbiology ; Biodiversity ; Bacteria/genetics ; }, abstract = {Bacterial wilt is the leading disease of sesame and alters the bacterial community composition, function, and metabolism of sesame rhizosphere soil. However, its pattern of change is unclear. Here, the purpose of this study was to investigate how these communities respond to three differing severities of bacterial wilt in mature continuously cropped sesame plants by metagenomic and metabolomic techniques, namely, absence (WH), moderate (WD5), and severe (WD9) wilt. The results indicated that bacterial wilt could significantly change the bacterial community structure in the rhizosphere soil of continuously cropped sesame plants. The biomarker species with significant differences will also change with increasing disease severity. In particular, the gene expression levels of Ralstonia solanacearum in the WD9 and WD5 treatments increased by 25.29% and 33.61%, respectively, compared to those in the WH treatment (4.35 log10 copies g-1). The occurrence of bacterial wilt significantly altered the functions of the bacterial community in rhizosphere soil. KEEG and CAZy functional annotations revealed that the number of significantly different functions in WH was greater than that in WD5 and WD9. Bacterial wilt significantly affected the relative content of metabolites, especially acids, in the rhizosphere soil, and compared with those in the rhizosphere soil from WH, 10 acids (including S-adenosylmethionine, N-acetylleucine, and desaminotyrosine, etc.) in the rhizosphere soil from WD5 or WD9 significantly increased. In comparison, the changes in the other 10 acids (including hypotaurine, erucic acid, and 6-hydroxynicotinic acid, etc.) were reversed. The occurrence of bacterial wilt also significantly inhibited metabolic pathways such as ABC transporter and amino acid biosynthesis pathways in rhizosphere soil and had a significant impact on two key enzymes (1.1.1.11 and 2.6.1.44). In conclusion, sesame bacterial wilt significantly alters the rhizosphere soil bacterial community structure, function, and metabolites. This study enhances the understanding of sesame bacterial wilt mechanisms and lays the groundwork for future prevention and control strategies against this disease.}, } @article {pmid38400721, year = {2024}, author = {Liu, X and Fang, H and Pan, L and Zhang, P and Lin, H and Gao, H and Ye, C and Mao, D and Luo, Y}, title = {S-amlodipine induces liver inflammation and dysfunction through the alteration of intestinal microbiome in a rat model.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2316923}, pmid = {38400721}, issn = {1949-0984}, mesh = {Rats ; Male ; Animals ; *Amlodipine/adverse effects ; *Gastrointestinal Microbiome ; Lipopolysaccharides ; Escherichia coli ; Liver ; Bacteria ; Inflammation ; }, abstract = {S-amlodipine, a commonly prescribed antihypertensive agent, is widely used in clinical settings to treat hypertension. However, the potential adverse effects of long-term S-amlodipine treatment on the liver remain uncertain, given the cautionary recommendations from clinicians regarding its administration in individuals with impaired liver function. To address this, we conducted a study using an eight-week-old male rat model and administered a daily dose of 0.6 ~ 5 mg/kg of S-amlodipine for 7 weeks. Our findings demonstrated that 1.2 ~ 5 mg/kg of S-amlodipine treatment induced liver inflammation and associated dysfunction in rats, further in vitro experiments revealed that the observed liver inflammation and dysfunction were not attributable to direct effects of S-amlodipine on the liver. Metagenome sequencing analysis revealed that S-amlodipine treatment led to alterations in the gut microbiome of rats, with the bloom of E. coli (4.5 ~ 6.6-fold increase) and a decrease in A. muciniphila (1,613.4 ~ 2,000-fold decrease) and B. uniformis (20.6 ~ 202.7-fold decrease), subsequently causing an increase in the gut bacterial lipopolysaccharide (LPS) content (1.4 ~ 1.5-fold increase in feces). S-amlodipine treatment also induced damage to the intestinal barrier and increased intestinal permeability, as confirmed by elevated levels of fecal albumin; furthermore, the flux of gut bacterial LPS into the bloodstream through the portal vein resulted in an increase in serum LPS content (3.3 ~ 4-fold increase). LPS induces liver inflammation and subsequent dysfunction in rats by activating the TLR4 pathway. This study is the first to show that S-amlodipine induces liver inflammation and dysfunction by perturbing the rat gut microbiome. These results indicate the adverse effects of S-amlodipine on the liver and provide a rich understanding of the safety of long-term S-amlodipine administration.}, } @article {pmid38400004, year = {2024}, author = {Zhu, P and Liu, C and Liu, GF and Liu, H and Xie, KM and Zhang, HS and Xu, X and Xiao, J and Jiang, JZ}, title = {Unveiling CRESS DNA Virus Diversity in Oysters by Virome.}, journal = {Viruses}, volume = {16}, number = {2}, pages = {}, pmid = {38400004}, issn = {1999-4915}, support = {2022B1111030001//Key-Area Research and Development Program of Guangdong Province/ ; 31972847//National Natural Science Foundation of China/ ; 2023TD44//Central Public-Interest Scientific Institution Basal Research Fund, CAFS/ ; 2021SD05//Central Public-Interest Scientific Institution Basal Research Fund, CAFS/ ; }, mesh = {DNA, Viral/genetics ; *Brassicaceae ; Virome ; DNA Viruses/genetics ; *Viruses/genetics ; Phylogeny ; Genome, Viral ; }, abstract = {Oysters that filter feed can accumulate numerous pathogens, including viruses, which can serve as a valuable viral repository. As oyster farming becomes more prevalent, concerns are mounting about diseases that can harm both cultivated and wild oysters. Unfortunately, there is a lack of research on the viruses and other factors that can cause illness in shellfish. This means that it is harder to find ways to prevent these diseases and protect the oysters. This is part of a previously started project, the Dataset of Oyster Virome, in which we further study 30 almost complete genomes of oyster-associated CRESS DNA viruses. The replication-associated proteins and capsid proteins found in CRESS DNA viruses display varying evolutionary rates and frequently undergo recombination. Additionally, some CRESS DNA viruses have the capability for cross-species transmission. A plethora of unclassified CRESS DNA viruses are detectable in transcriptome libraries, exhibiting higher levels of transcriptional activity than those found in metagenome libraries. The study significantly enhances our understanding of the diversity of oyster-associated CRESS DNA viruses, emphasizing the widespread presence of CRESS DNA viruses in the natural environment and the substantial portion of CRESS DNA viruses that remain unidentified. This study's findings provide a basis for further research on the biological and ecological roles of viruses in oysters and their environment.}, } @article {pmid38399658, year = {2024}, author = {Ishola, OA and Kublik, S and Durai Raj, AC and Ohnmacht, C and Schulz, S and Foesel, BU and Schloter, M}, title = {Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models.}, journal = {Microorganisms}, volume = {12}, number = {2}, pages = {}, pmid = {38399658}, issn = {2076-2607}, support = {Helmholtz Munich Allergy Program//Helmholtz Munich Allergy Program/ ; }, abstract = {Gnotobiotic murine models are important to understand microbiota-host interactions. Despite the role of bacteriophages as drivers for microbiome structure and function, there is no information about the structure and function of the gut virome in gnotobiotic models and the link between bacterial and bacteriophage/prophage diversity. We studied the virome of gnotobiotic murine Oligo-MM12 (12 bacterial species) and reduced Altered Schaedler Flora (ASF, three bacterial species). As reference, the virome of Specific Pathogen-Free (SPF) mice was investigated. A metagenomic approach was used to assess prophages and bacteriophages in the guts of 6-week-old female mice. We identified a positive correlation between bacteria diversity, and bacteriophages and prophages. Caudoviricetes (82.4%) were the most prominent class of phages in all samples with differing relative abundance. However, the host specificity of bacteriophages belonging to class Caudoviricetes differed depending on model bacterial diversity. We further studied the role of bacteriophages in horizontal gene transfer and microbial adaptation to the host's environment. Analysis of mobile genetic elements showed the contribution of bacteriophages to the adaptation of bacterial amino acid metabolism. Overall, our results implicate virome "dark matter" and interactions with the host system as factors for microbial community structure and function which determine host health. Taking the importance of the virome in the microbiome diversity and horizontal gene transfer, reductions in the virome might be an important factor driving losses of microbial biodiversity and the subsequent dysbiosis of the gut microbiome.}, } @article {pmid38399650, year = {2024}, author = {Muter, O and Gudrā, D and Daumova, G and Idrisheva, Z and Rakhymberdina, M and Tabors, G and Dirnēna, B and Dobkeviča, L and Petrova, O and Apshikur, B and Luņģe, M and Fridmanis, D and Denissov, I and Bekishev, Y and Kasparinskis, R and Mukulysova, Z and Polezhayev, S}, title = {Impact of Anthropogenic Activities on Microbial Community Structure in Riverbed Sediments of East Kazakhstan.}, journal = {Microorganisms}, volume = {12}, number = {2}, pages = {}, pmid = {38399650}, issn = {2076-2607}, support = {IRN BR21881921//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; Contract for the provision of services (O.Muter), Ust-Kamenogorsk, No 13-12, 23.06.2023//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, abstract = {Heavy metal (HMe) pollution in regions with mining and metallurgy activities is known to be a serious environmental problem worldwide. Hydrological processes contribute to the dissemination of HMes (drainage, precipitation, flow rate). The aim of the present study is to investigate the microbial community structure in ten river sediments sampled in different regions of East Kazakhstan, which are contaminated with HMes. The overall degree of sediment contamination with HMes (Cr, Cu, Zn, Pb, and Cd) was assessed using the pollution index Zc, which ranged from 0.43 to 21.6, with the highest in Ridder City (Zc = 21.6) and Ust-Kamenogorsk City, 0.8 km below the dam of the hydroelectric power station (Zc = 19.6). The tested samples considerably differed in organic matter, total carbon, nitrogen, and phosphorus content, as well as in the abundance of HMe-related functional gene families and antibiotic resistance genes. Metagenomic analysis of benthic microorganisms showed the prevalence of Proteobacteria (88.84-97.61%) and Actinobacteria (1.21-5.98%) at the phylum level in all samples. At the class level, Actinobacteria (21.68-57.48%), Betaproteobacteria (19.38-41.17%), and Alphaproteobacteria (10.0-39.78%) were the most common among the classified reads. To the best of our knowledge, this is the first study on the metagenomic characteristics of benthic microbial communities exposed to chronic HMe pressure in different regions of East Kazakhstan.}, } @article {pmid38397160, year = {2024}, author = {da Fonseca, RR and Campos, PF and Rey-Iglesia, A and Barroso, GV and Bergeron, LA and Nande, M and Tuya, F and Abidli, S and Pérez, M and Riveiro, I and Carrera, P and Jurado-Ruzafa, A and G Santamaría, MT and Faria, R and Machado, AM and Fonseca, MM and Froufe, E and C Castro, LF}, title = {Population Genomics Reveals the Underlying Structure of the Small Pelagic European Sardine and Suggests Low Connectivity within Macaronesia.}, journal = {Genes}, volume = {15}, number = {2}, pages = {}, pmid = {38397160}, issn = {2073-4425}, support = {VKR023446//Villum Fonden/ ; CEECIND/00627/2017//Fundação para a Ciência e Tecnologia/ ; CEECIND/01799/2017//Fundação para a Ciência e Tecnologia/ ; 25925//Villum Fonden/ ; IN607B 2018/14//Axencia Galega de Innovacion/ ; IN607-A 2018/4//Axencia Galega de Innovacion/ ; RTI2018-099868-B-I00//Ministerio de Ciencia e Innovación/ ; PTDC/BIA-EVL/30628/2017//Programa Operacional Temático Factores de Competitividade/ ; POCI-01-0145-FEDER-030628//Programa Operacional Temático Factores de Competitividade/ ; 24517//Programa Operacional Temático Factores de Competitividade/ ; UIDB/04423/2020//European Regional Development Fund/ ; }, mesh = {Humans ; Animals ; *Metagenomics ; *Fishes/genetics ; Portugal ; Genome/genetics ; Spain ; }, abstract = {The European sardine (Sardina pilchardus, Walbaum 1792) is indisputably a commercially important species. Previous studies using uneven sampling or a limited number of makers have presented sometimes conflicting evidence of the genetic structure of S. pilchardus populations. Here, we show that whole genome data from 108 individuals from 16 sampling areas across 5000 km of the species' distribution range (from the Eastern Mediterranean to the archipelago of Azores) support at least three genetic clusters. One includes individuals from Azores and Madeira, with evidence of substructure separating these two archipelagos in the Atlantic. Another cluster broadly corresponds to the center of the distribution, including the sampling sites around Iberia, separated by the Almeria-Oran front from the third cluster that includes all of the Mediterranean samples, except those from the Alboran Sea. Individuals from the Canary Islands appear to belong to the Mediterranean cluster. This suggests at least two important geographical barriers to gene flow, even though these do not seem complete, with many individuals from around Iberia and the Mediterranean showing some patterns compatible with admixture with other genetic clusters. Genomic regions corresponding to the top outliers of genetic differentiation are located in areas of low recombination indicative that genetic architecture also has a role in shaping population structure. These regions include genes related to otolith formation, a calcium carbonate structure in the inner ear previously used to distinguish S. pilchardus populations. Our results provide a baseline for further characterization of physical and genetic barriers that divide European sardine populations, and information for transnational stock management of this highly exploited species towards sustainable fisheries.}, } @article {pmid38396840, year = {2024}, author = {Blondeaux, A and Valibouze, C and Speca, S and Rousseaux, C and Dubuquoy, C and Blanquart, H and Zerbib, P and Desreumaux, P and Foligné, B and Titécat, M}, title = {Changes in HLA-B27 Transgenic Rat Fecal Microbiota Following Tofacitinib Treatment and Ileocecal Resection Surgery: Implications for Crohn's Disease Management.}, journal = {International journal of molecular sciences}, volume = {25}, number = {4}, pages = {}, pmid = {38396840}, issn = {1422-0067}, support = {59223519//Pfizer (France)/ ; }, mesh = {Rats ; Animals ; *Crohn Disease/drug therapy/surgery/complications ; Rats, Transgenic ; HLA-B27 Antigen ; *Inflammatory Bowel Diseases/drug therapy/complications ; *Microbiota ; Disease Management ; *Piperidines ; *Pyrimidines ; }, abstract = {The therapeutic management of Crohn's disease (CD), a chronic relapsing-remitting inflammatory bowel disease (IBD), is highly challenging. Surgical resection is sometimes a necessary procedure even though it is often associated with postoperative recurrences (PORs). Tofacitinib, an orally active small molecule Janus kinase inhibitor, is an anti-inflammatory drug meant to limit PORs in CD. Whereas bidirectional interactions between the gut microbiota and the relevant IBD drug are crucial, little is known about the impact of tofacitinib on the gut microbiota. The HLA-B27 transgenic rat is a good preclinical model used in IBD research, including for PORs after ileocecal resection (ICR). In the present study, we used shotgun metagenomics to first delineate the baseline composition and determinants of the fecal microbiome of HLA-B27 rats and then to evaluate the distinct impact of either tofacitinib treatment, ileocecal resection or the cumulative effect of both interventions on the gut microbiota in these HLA-B27 rats. The results confirmed that the microbiome of the HLA-B27 rats was fairly different from their wild-type littermates. We demonstrated here that oral treatment with tofacitinib does not affect the gut microbial composition of HLA-B27 rats. Of note, we showed that ICR induced an intense loss of bacterial diversity together with dramatic changes in taxa relative abundances. However, the oral treatment with tofacitinib neither modified the alpha-diversity nor exacerbated significant modifications in bacterial taxa induced by ICR. Collectively, these preclinical data are rather favorable for the use of tofacitinib in combination with ICR to address Crohn's disease management when considering microbiota.}, } @article {pmid38395948, year = {2024}, author = {Alves Costa Silva, C and Piccinno, G and Suissa, D and Bourgin, M and Schreibelt, G and Durand, S and Birebent, R and Fidelle, M and Sow, C and Aprahamian, F and Manghi, P and Punčochář, M and Asnicar, F and Pinto, F and Armanini, F and Terrisse, S and Routy, B and Drubay, D and Eggermont, AMM and Kroemer, G and Segata, N and Zitvogel, L and Derosa, L and Bol, KF and de Vries, IJM}, title = {Influence of microbiota-associated metabolic reprogramming on clinical outcome in patients with melanoma from the randomized adjuvant dendritic cell-based MIND-DC trial.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1633}, pmid = {38395948}, issn = {2041-1723}, mesh = {Humans ; *Melanoma ; Metabolic Reprogramming ; *Microbiota/genetics ; Dendritic Cells ; }, abstract = {Tumor immunosurveillance plays a major role in melanoma, prompting the development of immunotherapy strategies. The gut microbiota composition, influencing peripheral and tumoral immune tonus, earned its credentials among predictors of survival in melanoma. The MIND-DC phase III trial (NCT02993315) randomized (2:1 ratio) 148 patients with stage IIIB/C melanoma to adjuvant treatment with autologous natural dendritic cell (nDC) or placebo (PL). Overall, 144 patients collected serum and stool samples before and after 2 bimonthly injections to perform metabolomics (MB) and metagenomics (MG) as prespecified exploratory analysis. Clinical outcomes are reported separately. Here we show that different microbes were associated with prognosis, with the health-related Faecalibacterium prausnitzii standing out as the main beneficial taxon for no recurrence at 2 years (p = 0.008 at baseline, nDC arm). Therapy coincided with major MB perturbations (acylcarnitines, carboxylic and fatty acids). Despite randomization, nDC arm exhibited MG and MB bias at baseline: relative under-representation of F. prausnitzii, and perturbations of primary biliary acids (BA). F. prausnitzii anticorrelated with BA, medium- and long-chain acylcarnitines. Combined, these MG and MB biomarkers markedly determined prognosis. Altogether, the host-microbial interaction may play a role in localized melanoma. We value systematic MG and MB profiling in randomized trials to avoid baseline differences attributed to host-microbe interactions.}, } @article {pmid38395946, year = {2024}, author = {Jin, C and Wu, S and Liang, Z and Zhang, J and Lei, X and Bai, H and Liang, G and Su, X and Chen, X and Wang, P and Wang, Y and Guan, L and Yao, J}, title = {Multi-omics reveal mechanisms of high enteral starch diet mediated colonic dysbiosis via microbiome-host interactions in young ruminant.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {38}, pmid = {38395946}, issn = {2049-2618}, support = {2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 32272829//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Multiomics ; Dysbiosis ; Ruminants/metabolism/microbiology ; *Microbiota ; Goats ; Cytokines ; Diet/veterinary ; Starch/chemistry/metabolism ; }, abstract = {BACKGROUND: Although rumen development is crucial, hindgut undertakes a significant role in young ruminants' physiological development. High-starch diet is usually used to accelerate rumen development for young ruminants, but always leading to the enteral starch overload and hindgut dysbiosis. However, the mechanism behind remains unclear. The combination of colonic transcriptome, colonic luminal metabolome, and metagenome together with histological analysis was conducted using a goat model, with the aim to identify the potential molecular mechanisms behind the disrupted hindgut homeostasis by overload starch in young ruminants.

RESULT: Compared with low enteral starch diet (LES), high enteral starch diet (HES)-fed goats had significantly higher colonic pathology scores, and serum diamine oxidase activity, and meanwhile significantly decreased colonic mucosal Mucin-2 (MUC2) protein expression and fecal scores, evidencing the HES-triggered colonic systemic inflammation. The bacterial taxa Prevotella sp. P4-67, Prevotella sp. PINT, and Bacteroides sp. CAG:927, together with fungal taxa Fusarium vanettenii, Neocallimastix californiae, Fusarium sp. AF-8, Hypoxylon sp. EC38, and Fusarium pseudograminearum, and the involved microbial immune pathways including the "T cell receptor signaling pathway" were higher in the colon of HES goats. The integrated metagenome and host transcriptome analysis revealed that these taxa were associated with enhanced pathogenic ability, antigen processing and presentation, and stimulated T helper 2 cell (TH2)-mediated cytokine secretion functions in the colon of HES goats. Further luminal metabolomics analysis showed increased relative content of chenodeoxycholic acid (CDCA) and deoxycholic acid (DCA), and decreased the relative content of hypoxanthine in colonic digesta of HES goats. These altered metabolites contributed to enhancing the expression of TH2-mediated inflammatory-related cytokine secretion including GATA Binding Protein 3 (GATA3), IL-5, and IL-13. Using the linear mixed effect model, the variation of MUC2 biosynthesis explained by the colonic bacteria, bacterial functions, fungi, fungal functions, and metabolites were 21.92, 20.76, 19.43, 12.08, and 44.22%, respectively. The variation of pathology scores explained by the colonic bacterial functions, fungal functions, and metabolites were 15.35, 17.61, and 57.06%.

CONCLUSIONS: Our findings revealed that enteral starch overload can trigger interrupted hindgut host-microbiome homeostasis that led to impaired mucosal, destroyed colonic water absorption, and TH2-mediated inflammatory process. Except for the colonic metabolites mostly contribute to the impaired mucosa, the nonnegligible contribution from fungi deserves more future studies focused on the fungal functions in hindgut dysbiosis of young ruminants. Video Abstract.}, } @article {pmid38394893, year = {2024}, author = {Chen, T and Mo, C and Yuan, Y and Li, S and Wu, Y and Liao, X and Yang, Y}, title = {Short-, long-read metagenome and virome reveal the profile of phage-mediated ARGs in anoxic-oxic processes for swine wastewater treatment.}, journal = {Journal of hazardous materials}, volume = {468}, number = {}, pages = {133789}, doi = {10.1016/j.jhazmat.2024.133789}, pmid = {38394893}, issn = {1873-3336}, mesh = {Animals ; Swine ; *Anti-Bacterial Agents/pharmacology ; Metagenome ; Wastewater ; *Bacteriophages/genetics ; Virome ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Genes, Bacterial ; }, abstract = {Phages are among the most widely spread viruses, but their profiles and the antibiotic resistance genes (ARGs) they carry in swine wastewater remain underexplored. The present study investigated the distribution characteristics of phages and their ARG risk in anoxic/oxic (A/O) wastewater treatment processes of swine farms using short- and long-read metagenome and virome. The results demonstrated that the virome could extract more phage sequences than the total metagenome; thus, it was more suited for studying phages in wastewater settings. Intriguingly, phages had significantly lower abundance of ARG than ARGs harbored by total microorganisms (P < 0.01). Eleven ARGs co-occurred with phages and bacteria (R > 0.6 and P < 0.05), with Siphoviridae being the phage co-occurring with the most ARGs (5). Horizontal gene transfer (HGT) events were observed between Proteobacteria and the major phyla except for Bacteroidota. Furthermore, there were prophage sequences and ARGs on the same contig in bacterial MAGs. These data strongly demonstrate that phages promote horizontal transfer of ARG between bacterial hosts in A/O processes for swine wastewater treatment. Therefore, the risk of phage-mediated horizontal transfer of ARGs cannot be overlooked despite the low abundance of phage ARGs (pARG).}, } @article {pmid38394797, year = {2024}, author = {Patel, ZZ and Joshi, H and Puvar, A and Pandit, R and Joshi, C and Joshi, M and Tipre, DR}, title = {A study into the diversity of coral-associated bacteria using culture-dependent and culture-independent approaches in coral Dipsastraea favus from the Gulf of Kutch.}, journal = {Marine pollution bulletin}, volume = {201}, number = {}, pages = {116172}, doi = {10.1016/j.marpolbul.2024.116172}, pmid = {38394797}, issn = {1879-3363}, mesh = {Animals ; *Anthozoa/microbiology ; Ecosystem ; *Tinea Favosa ; Phylogeny ; RNA, Ribosomal, 16S ; Bacteria/genetics ; Coral Reefs ; Biodiversity ; }, abstract = {Corals harbour ~25 % of the marine diversity referring to biodiversity hotspots in marine ecosystems. Global efforts to find ways to restore the coral reef ecosystem from various threats can be complemented by studying coral-associated bacteria. Coral-associated bacteria are vital components of overall coral wellbeing. We explored the bacterial diversity associated with coral Dipsastraea favus (D. favus) collected from the Gulf of Kutch, India, using both culture-dependent and metagenomic approaches. In both approaches, phylum Proteobacteria, Firmicutes, and Actinobacteria predominated, comprising the genera Vibrio, Bacillus, Shewanella, Pseudoalteromonas, Exiguobacterium and Streptomyces. Moreover, the majority of culturable isolates showed multiple antibiotic resistance index ≥0.2. In this study, specific bacterial diversity associated with coral sp. D. favus and its possible role in managing coral health was established. Almost 43 strains from the samples were successfully cultured, creating a base for exploring these microbes for their potential use in coral conservation methods.}, } @article {pmid38393009, year = {2024}, author = {Zulfiqar, M and Crusoe, MR and König-Ries, B and Steinbeck, C and Peters, K and Gadelha, L}, title = {Implementation of FAIR Practices in Computational Metabolomics Workflows-A Case Study.}, journal = {Metabolites}, volume = {14}, number = {2}, pages = {}, pmid = {38393009}, issn = {2218-1989}, support = {390713860//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Scientific workflows facilitate the automation of data analysis tasks by integrating various software and tools executed in a particular order. To enable transparency and reusability in workflows, it is essential to implement the FAIR principles. Here, we describe our experiences implementing the FAIR principles for metabolomics workflows using the Metabolome Annotation Workflow (MAW) as a case study. MAW is specified using the Common Workflow Language (CWL), allowing for the subsequent execution of the workflow on different workflow engines. MAW is registered using a CWL description on WorkflowHub. During the submission process on WorkflowHub, a CWL description is used for packaging MAW using the Workflow RO-Crate profile, which includes metadata in Bioschemas. Researchers can use this narrative discussion as a guideline to commence using FAIR practices for their bioinformatics or cheminformatics workflows while incorporating necessary amendments specific to their research area.}, } @article {pmid38388811, year = {2024}, author = {de Carvalho, FM and Laux, M and Ciapina, LP and Gerber, AL and Guimarães, APC and Kloh, VP and Apolinário, M and Paes, JES and Jonck, CR and de Vasconcelos, ATR}, title = {Finding microbial composition and biological processes as predictive signature to access the ongoing status of mangrove preservation.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {27}, number = {5}, pages = {1485-1500}, pmid = {38388811}, issn = {1618-1905}, support = {2018/00190-8//Petrobras/ ; E-26/201.046/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Brazil ; *Microbiota ; *Wetlands ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics/methods ; Soil Microbiology ; Phylogeny ; }, abstract = {Mangroves are complex land-sea transition ecosystems whose microbiota are essential for their nutrient recycling and conservation. Brazil is the third-largest estuarine area in the world and "Baía de Todos os Santos" (BTS) is one of the largest bays of the country, with wide anthropogenic exploration. Using a metagenomic approach, we investigated composition and functional adaptability as signatures of the microbiome of pristine and anthropized areas of BTS, including those under petroleum refinery influence. The taxonomic analysis showed dominance of sulfate-reducing Desulfobacteraceae, Rhodobacteraceae, and Flavobacteriaceae. Taxa were significantly diverse between pristine and disturbed areas. Disturbed mangroves showed a notary increase in abundance of halophilic, sulfur-related, and hydrocarbon-degrading genera and a decrease in diatoms compared to pristine area. The metabolic profile of BTS mangroves was correlated with the differentially abundant microbiota. Two ecological scenarios were observed: one marked by functions of central metabolism associated with biomass degradation and another by mechanisms of microbial adaptability to pollution conditions and environmental degradation. Part of the microbiome was distinct and not abundant in Brazilian estuarine soils. The microbiome signature observed in each BTS mangrove reflects how human actions impact the diversity of these ecosystems and also emphasize their role in attempting to restore disturbed mangroves. The microbiome may act as a potential biological indicator of the preservation status of these soils, despite the limitation of soil property conditions. Additionally, our data pointed to metagenomics as an additional tool for environmental assessment and reinforced the need for protective measures for the mangroves under study.}, } @article {pmid38388732, year = {2024}, author = {Maruyama, R and Yasumoto, K and Mizusawa, N and Iijima, M and Yasumoto-Hirose, M and Iguchi, A and Hermawan, OR and Hosono, T and Takada, R and Song, KH and Shinjo, R and Watabe, S and Yasumoto, J}, title = {Metagenomic analysis of the microbial communities and associated network of nitrogen metabolism genes in the Ryukyu limestone aquifer.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {4356}, pmid = {38388732}, issn = {2045-2322}, support = {20H03077//Grants-in-Aid from the Japan Society for the Promotion of Science/ ; 19K12310//Grants-in-Aid from the Japan Society for the Promotion of Science/ ; JPMEERF20194007//Environment Research and Technology Development Fund/ ; RIHN14200145//Research Institute for Humanity and Nature/ ; JPMJRX19IA//Solution-Driven Co-creative R&D Program for SDGs Program/ ; }, mesh = {Calcium Carbonate/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; Bacteria ; *Microbiota ; *Groundwater/chemistry ; Nitrogen/metabolism ; Denitrification ; Nitrates/metabolism ; }, abstract = {While microbial biogeochemical activities such as those involving denitrification and sulfate reduction have been considered to play important roles in material cycling in various aquatic ecosystems, our current understanding of the microbial community in groundwater ecosystems is remarkably insufficient. To assess the groundwater in the Ryukyu limestone aquifer of Okinawa Island, which is located in the southernmost region of Japan, we performed metagenomic analysis on the microbial communities at the three sites and screened for functional genes associated with nitrogen metabolism. 16S rRNA amplicon analysis showed that bacteria accounted for 94-98% of the microbial communities, which included archaea at all three sites. The bacterial communities associated with nitrogen metabolism shifted by month at each site, indicating that this metabolism was accomplished by the bacterial community as a whole. Interestingly, site 3 contained much higher levels of the denitrification genes such as narG and napA than the other two sites. This site was thought to have undergone denitrification that was driven by high quantities of dissolved organic carbon (DOC). In contrast, site 2 was characterized by a high nitrate-nitrogen (NO3-N) content and a low amount of DOC, and this site yielded a moderate amount of denitrification genes. Site 1 showed markedly low amounts of all nitrogen metabolism genes. Overall, nitrogen metabolism in the Ryukyu limestone aquifer was found to change based on environmental factors.}, } @article {pmid38388542, year = {2024}, author = {Jia, L and Jiang, Y and Wu, L and Fu, J and Du, J and Luo, Z and Guo, L and Xu, J and Liu, Y}, title = {Porphyromonas gingivalis aggravates colitis via a gut microbiota-linoleic acid metabolism-Th17/Treg cell balance axis.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1617}, pmid = {38388542}, issn = {2041-1723}, support = {81991504//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81974149//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82101009//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82122015//National Natural Science Foundation of China (National Science Foundation of China)/ ; ZYLX202121//Beijing Municipal Administration of Hospitals Clinical Medicine Development of Special Funding Support/ ; }, mesh = {Humans ; Mice ; Animals ; T-Lymphocytes, Regulatory ; Porphyromonas gingivalis ; *Gastrointestinal Microbiome ; Linoleic Acid/metabolism ; Mice, Inbred C57BL ; *Colitis ; *Inflammatory Bowel Diseases ; *Periodontitis ; Inflammation/metabolism ; Th17 Cells ; }, abstract = {Periodontitis is closely related to inflammatory bowel disease (IBD). An excessive and non-self-limiting immune response to the dysbiotic microbiome characterizes the two. However, the underlying mechanisms that overlap still need to be clarified. We demonstrate that the critical periodontal pathogen Porphyromonas gingivalis (Pg) aggravates intestinal inflammation and Th17/Treg cell imbalance in a gut microbiota-dependent manner. Specifically, metagenomic and metabolomic analyses shows that oral administration of Pg increases levels of the Bacteroides phylum but decreases levels of the Firmicutes, Verrucomicrobia, and Actinobacteria phyla. Nevertheless, it suppresses the linoleic acid (LA) pathway in the gut microbiota, which was the target metabolite that determines the degree of inflammation and functions as an aryl hydrocarbon receptor (AHR) ligand to suppress Th17 differentiation while promoting Treg cell differentiation via the phosphorylation of Stat1 at Ser727. Therapeutically restoring LA levels in colitis mice challenged with Pg exerts anti-colitis effects by decreasing the Th17/Treg cell ratio in an AHR-dependent manner. Our study suggests that Pg aggravates colitis via a gut microbiota-LA metabolism-Th17/Treg cell balance axis, providing a potential therapeutically modifiable target for IBD patients with periodontitis.}, } @article {pmid38387264, year = {2024}, author = {Wang, G and Feng, Z and Yin, X and Chen, D and Zhao, N and Yuan, Y and Chen, C and Liu, C and Ao, M and Chen, L and Chen, Z and Yang, W and Li, D and Morel, JL and Chao, Y and Wang, P and Tang, Y and Qiu, R and Wang, S}, title = {Biogenic manganese oxides promote metal(loid) remediation by shaping microbial communities in biological aqua crust.}, journal = {Water research}, volume = {253}, number = {}, pages = {121287}, doi = {10.1016/j.watres.2024.121287}, pmid = {38387264}, issn = {1879-2448}, mesh = {Manganese ; Lead ; Bacteria/genetics ; Oxides ; Minerals ; *Microbiota ; *Metals, Heavy ; *Manganese Compounds ; }, abstract = {Biological aqua crust (biogenic aqua crust-BAC) is a potentially sustainable solution for metal(loid) bioremediation in global water using solar energy. However, the key geochemical factors and underlying mechanisms shaping microbial communities in BAC remain poorly understood. The current study aimed at determining the in situ metal(loid) distribution and the key geochemical factors related to microbial community structure and metal(loid)-related genes in BAC of a representative Pb/Zn tailing pond. Here we showed that abundant metal(loid)s (e.g. Pb, As) were co-distributed with Mn/Fe-rich minerals (e.g. biogenic Mn oxide, FeOOH) in BAC. Biogenic Mn oxide (i.e. Mn) was the most dominant factor in shaping microbial community structure in BAC and source tailings. Along with the fact that keystone species (e.g. Burkholderiales, Haliscomenobacter) have the potential to promote Mn ion oxidization and particle agglomeration, as well as Mn is highly associated with metal(loid)-related genes, especially genes related to As redox (e.g. arsC, aoxA), and Cd transport (e.g. zipB), biogenic Mn oxides thus effectively enhance metal(loid) remediation by accelerating the formation of organo-mineral aggregates in biofilm-rich BAC system. Our study indicated that biogenic Mn oxides may play essential roles in facilitating in situ metal(loid) bioremediation in BAC of mine drainage.}, } @article {pmid38387163, year = {2024}, author = {Cotes-Perdomo, AP and Sánchez-Vialas, A and Thomas, R and Jenkins, A and Uribe, JE}, title = {New insights into the systematics of the afrotropical Amblyomma marmoreum complex (Acari: Ixodidae) and the genome of a novel Rickettsia africae strain using morphological and metagenomic approaches.}, journal = {Ticks and tick-borne diseases}, volume = {15}, number = {3}, pages = {102323}, doi = {10.1016/j.ttbdis.2024.102323}, pmid = {38387163}, issn = {1877-9603}, mesh = {Male ; Animals ; *Ixodidae/microbiology ; Amblyomma ; *Rickettsia/genetics ; *Ticks/microbiology ; Mammals ; }, abstract = {The Amblyomma marmoreum complex includes afrotropical species, such as Amblyomma sparsum, a three-host tick that parasitizes reptiles, birds, and mammals, and is a recognized vector of Ehrlichia ruminantium. However, the lack of morphological, genetic and ecological data on A. sparsum has caused considerable confusion in its identification. In this study, we used microscopy and metagenomic approaches to analyze A. sparsum ticks collected from a puff adder snake (Bitis arietans) in southwest Senegal (an endemic rickettsioses area) in order to supplement previous morphological descriptions, provide novel genomic data for the A. marmoreum complex, and describe the genome of a novel spotted fever group Rickettsia strain. Based on stereoscope and scanning electron microscopy (SEM) morphological evaluations, we provide high-quality images and new insights about punctation and enameling in the adult male of A. sparsum to facilitate identification for future studies. The metagenomic approach allowed us assembly the complete mitochondrial genome of A. sparsum, as well as the nearly entire chromosome and complete plasmid sequences of a novel Rickettsia africae strain. Phylogenomic analyses demonstrated a close relationship between A. sparsum and Amblyomma nuttalli for the first time and confirmed the position of A. sparsum within the A. marmoreum complex. Our results provide new insights into the systematics of A. sparsum and A. marmoreum complex, as well as the genetic diversity of R. africae in the Afrotropical region. Future studies should consider the possibility that A. sparsum may be a vector for R. africae.}, } @article {pmid38385739, year = {2024}, author = {Hong, J-C and Chen, J-S and Jiang, Z-J and Chen, Z-C and Ruan, N and Yao, X-P}, title = {Microbiota in adult perianal abscess revealed by metagenomic next-generation sequencing.}, journal = {Microbiology spectrum}, volume = {12}, number = {4}, pages = {e0347423}, pmid = {38385739}, issn = {2165-0497}, support = {2019QH1079//Startup Fund for Scientific Research, Fujian Medical University/ ; 82171841//MOST | National Natural Science Foundation of China (NSFC)/ ; 2020Y9118//Joint Funds for the Innovation of Science and Technology, Fujian Province/ ; }, mesh = {Adult ; Humans ; Abscess/diagnosis ; Escherichia coli/genetics ; Retrospective Studies ; *Microbiota ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents ; Bacteroides fragilis/genetics ; Metagenomics ; *Skin Diseases ; Biomarkers ; }, abstract = {The microbiota of perianal abscesses is scarcely investigated. Identifying causative bacteria is essential to develop antibiotic therapy. However, culture-based methods and molecular diagnostics through 16S PCR technology are often hampered by the polymicrobial nature of perianal abscesses. We sought to characterize the microbiota composition of perianal abscesses via metagenomic next-generation sequencing (mNGS). Fourteen patients suffering from perianal abscesses between March 2023 and August 2023 underwent retrospective assessment. Information from medical records was used, including clinical information, laboratory data, and culture and mNGS results. Forty bacterial taxa were identified from perianal abscesses through mNGS, with Bilophila wadsworthia (71.4%), Bacteroides fragilis (57.1%), and Escherichia coli (50.0%) representing the most prevalent species. mNGS identified an increased number of bacterial taxa, with an average of 6.1 compared to a traditional culture-based method which only detected an average of 1.1 in culture-positive perianal abscess patients, predominantly E. coli (75.0%), revealing the polymicrobial nature of perianal abscesses. Our study demonstrates that a more diverse bacterial profile is detected by mNGS in perianal abscesses, and that Bilophila wadsworthia is the most prevalent microorganism, potentially serving as a potential biomarker for perianal abscess.IMPORTANCEAccurately, identifying the bacteria causing perianal abscesses is crucial for effective antibiotic therapy. However, traditional culture-based methods and 16S PCR technology often struggle with the polymicrobial nature of these abscesses. This study employed metagenomic next-generation sequencing (mNGS) to comprehensively analyze the microbiota composition. Results revealed 40 bacterial taxa, with Bilophila wadsworthia (71.4%), Bacteroides fragilis (57.1%), and Escherichia coli (50.0%) being the most prevalent species. Compared to the culture-based approach, mNGS detected a significantly higher number of bacterial taxa (average 6.1 vs 1.1), highlighting the complex nature of perianal abscesses. Notably, Bilophila wadsworthia emerged as a potential biomarker for these abscesses. This research emphasizes the importance of mNGS in understanding perianal abscesses and suggests its potential for improving diagnostic accuracy and guiding targeted antibiotic therapy in the future.}, } @article {pmid38385646, year = {2024}, author = {Hou, Z and Zhang, T and Ding, Z and Qian, T and Wang, P and Wu, B and Pan, X and Li, X}, title = {Analysis on the change of gut microbiota and metabolome in lung transplant patients.}, journal = {Microbiology spectrum}, volume = {12}, number = {4}, pages = {e0314223}, pmid = {38385646}, issn = {2165-0497}, support = {32070623//MOST | National Natural Science Foundation of China (NSFC)/ ; LHGJ20190027 and LHGJ20190109//Henan Province medical science and technology research plan joint construction projects/ ; SBGJ202002015 Wjlx2020080//Joint construction by provinces and the Ministry of Education/ ; 20211013//Engineering Laboratory of Henan Province/ ; XKZDQY202006//The advanced medical research center of Zhengzhou University/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Metabolome ; Enterococcus ; *Lung Transplantation ; Tretinoin ; Immunoglobulin A ; RNA, Ribosomal, 16S ; }, abstract = {UNLABELLED: Previous studies have shown that the gut microbiota and its metabolites are associated with the success of organ transplantation. However, the specific changes in the gut microbiota of lung transplant patients remain unclear. Hence, this study aimed to elucidate the interplay between the gut microbiota, metabolome, and lung transplantation outcomes. Using 16S metagenomics sequencing and untargeted metabolic profiling, we conducted a comprehensive analysis of gut microbial and metabolic alterations in lung transplant recipients relative to non-transplant group. Our findings revealed the predominance of Enterococcus and Streptococcus genera within the lung transplant cohort, accompanied by the significant reduction in Bacteroides, Epulopiscium, Faecalibacterium, and Prevotella abundance. In addition, a significant reduction in ATRA (all-trans retinoic acid) levels and suppression of IgA production were observed in lung transplant recipients, which were found to be closely associated with the Enterococcus genus. It was speculated that the association might have implications for the prognosis of lung transplant patients. Notably, the differences in gut microbial composition and metabolomic profiles between successful transplant recipients and those experiencing chronic rejection were not statistically significant. These novel insights shed light on the putative implications of the gut microbiota and metabolome in shaping lung transplantation outcomes, and provide a foundation for future investigations and targeted therapeutic interventions.

IMPORTANCE: This study has profound implications for lung transplantation as it uncovers the important role of gut microbiota and metabolome in shaping transplantation outcomes. The identification of dominant bacterial genera, such as Enterococcus and Streptococcus, within the lung transplant cohort, along with the significant decrease in Bacteroides, Epulopiscium, Faecalibacterium, and Prevotella abundance, reveals potential microbial imbalances associated with lung transplantation. In addition, a significant reduction in ATRA (all-trans retinoic acid) levels and suppression of IgA production were observed in lung transplant recipients, which were found to be closely associated with the Enterococcus genus. It was speculated that the association might have implications for the prognosis of lung transplant patients. These findings hold immense clinical significance as they lay the groundwork for future research and targeted therapeutic interventions. Understanding the impact of the gut microbiota and metabolome on lung transplantation outcomes offers promising avenues for improving transplantation patient prognosis.}, } @article {pmid38384305, year = {2024}, author = {Liu, X and Li, K and Yang, Y and Cao, D and Xu, X and He, Z and Wu, W}, title = {Gut resistome profiling reveals high diversity and fluctuations in pancreatic cancer cohorts.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1354234}, pmid = {38384305}, issn = {2235-2988}, mesh = {Humans ; Cross-Sectional Studies ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Microbial ; *Microbiota/genetics ; *Pancreatic Neoplasms/genetics ; Metagenomics ; }, abstract = {BACKGROUND: Pancreatic cancer is one of the deadliest cancer, with a 5-year overall survival rate of 11%. Unfortunately, most patients are diagnosed with advanced stage by the time they present with symptoms. In the past decade, microbiome studies have explored the association of pancreatic cancer with the human oral and gut microbiomes. However, the gut microbial antibiotic resistance genes profiling of pancreatic cancer patients was never reported compared to that of the healthy cohort.

RESULTS: In this study, we addressed the gut microbial antibiotic resistance genes profile using the metagenomic data from two online public pancreatic cancer cohorts. We found a high degree of data concordance between the two cohorts, which can therefore be used for cross-sectional comparisons. Meanwhile, we used two strategies to predict antibiotic resistance genes and compared the advantages and disadvantages of these two approaches. We also constructed microbe-antibiotic resistance gene networks and found that most of the hub nodes in the networks were antibiotic resistance genes.

CONCLUSIONS: In summary, we describe the panorama of antibiotic resistance genes in the gut microbes of patients with pancreatic cancer. We hope that our study will provide new perspectives on treatment options for the disease.}, } @article {pmid38384302, year = {2024}, author = {Ortiz Sanjuán, JM and Manzanilla, EG and Cabrera-Rubio, R and Crispie, F and Cotter, PD and Garrido, JJ and Ekhlas, D and O'Neill, L and Argüello, H}, title = {Fine-tuning of post-weaning pig microbiome structure and functionality by in-feed zinc oxide and antibiotics use.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1354449}, pmid = {38384302}, issn = {2235-2988}, mesh = {Swine ; Animals ; Escherichia coli ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Zinc Oxide/pharmacology/therapeutic use ; Diarrhea/microbiology ; *Microbiota ; }, abstract = {INTRODUCTION: Post-weaning diarrhoea (PWD) is a multifactorial disease that affects piglets after weaning, contributing to productive and economic losses. Its control includes the use of in-feed prophylactic antibiotics and therapeutic zinc oxide (ZnO), treatments that, since 2022, are no longer permitted in the European Union due to spread of antimicrobial resistance genes and pollution of soil with heavy metals. A dysbiosis in the microbiota has been suggested as a potential risk factor of PWD onset. Understanding pig's microbiota development around weaning and its changes in response to ZnO and antibiotics is crucial to develop feasible alternatives to prophylactic and metaphylactic antimicrobial use.

METHODS: This study used shotgun metagenomic sequencing to investigate the environmental and faecal microbiota on 10 farms using (Treated) or not using (ZnO-free) in-feed antibiotics and ZnO during the first 14 days post-weaning (dpw). Environmental samples from clean pens were collected at weaning day (0dpw), and faecal samples at 0, 7 and 14dpw. Diarrhoeic faecal samples were collected at 7dpw when available.

RESULTS: The analysis of data revealed that the faecal microbiota composition and its functionality was impacted by the sampling time point (microbiota maturation after weaning) but not by the farm environment. Treatment with antibiotics and ZnO showed no effects on diversity indices while the analyses of microbiota taxonomic and functional profiles revealed increased abundance of taxa and metabolic functions associated with Phascolarctobacterium succinatutens or different species of Prevotella spp. on the Treated farms, and with Megasphaera elsdenii and Escherichia coli on the ZnO-free farms. The analysis of diarrhoea samples revealed that the treatment favoured the microbiota transition or maturation from 0dpw to 14dpw in Treated farms, resembling the composition of healthy animals, when compared to diarrhoea from ZnO-free farms, which were linked in composition to 0dpw samples.

DISCUSSION: The results provide a comprehensive overview of the beneficial effects of ZnO and antibiotics in PWD in the microbiota transition after weaning, preventing the overgrowth of pathogens such as pathogenic E. coli and revealing the key aspects in microbiota maturation that antibiotics or ZnO alternatives should fulfil.}, } @article {pmid38383853, year = {2024}, author = {Ma, B and Wang, Y and Zhao, K and Stirling, E and Lv, X and Yu, Y and Hu, L and Tang, C and Wu, C and Dong, B and Xue, R and Dahlgren, RA and Tan, X and Dai, H and Zhu, YG and Chu, H and Xu, J}, title = {Biogeographic patterns and drivers of soil viromes.}, journal = {Nature ecology & evolution}, volume = {8}, number = {4}, pages = {717-728}, pmid = {38383853}, issn = {2397-334X}, support = {41721007//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42090060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42277283//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41991334//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Soil/chemistry ; Ecosystem ; Virome ; Soil Microbiology ; Ecology ; *Viruses/genetics ; }, abstract = {Viruses are crucial in shaping soil microbial functions and ecosystems. However, studies on soil viromes have been limited in both spatial scale and biome coverage. Here we present a comprehensive synthesis of soil virome biogeographic patterns using the Global Soil Virome dataset (GSV) wherein we analysed 1,824 soil metagenomes worldwide, uncovering 80,750 partial genomes of DNA viruses, 96.7% of which are taxonomically unassigned. The biogeography of soil viral diversity and community structure varies across different biomes. Interestingly, the diversity of viruses does not align with microbial diversity and contrasts with it by showing low diversity in forest and shrubland soils. Soil texture and moisture conditions are further corroborated as key factors affecting diversity by our predicted soil viral diversity atlas, revealing higher diversity in humid and subhumid regions. In addition, the binomial degree distribution pattern suggests a random co-occurrence pattern of soil viruses. These findings are essential for elucidating soil viral ecology and for the comprehensive incorporation of viruses into soil ecosystem models.}, } @article {pmid38383537, year = {2024}, author = {Haeussermann, I and Hasselmann, M}, title = {Complex European invasion history of Anoplophora glabripennis (Motschulsky): new insights in its population genomic differentiation using genotype-by-sequencing.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {4263}, pmid = {38383537}, issn = {2045-2322}, support = {2814905615//Federal Office for Agriculture and Food Germany (BLE)/ ; }, mesh = {Animals ; Phylogeny ; *Metagenomics ; Europe ; *Coleoptera/genetics ; Genotype ; }, abstract = {Anthropogenic activities like trade facilitate increasing rates of biological invasions. Asian long-horned beetle (ALB), which is naturally distributed in eastern Asia (China, Korean peninsula), was introduced via wood packing materials (WPM) used in trade to North America (1996) and Europe (2001). We used 7810 single nucleotide polymorphisms (SNPs) derived by a genotype-by-sequencing (GBS) approach to decipher the introduction patterns into Europe. This is applied for the first time on European ALB outbreaks from Germany, Switzerland, and Italy, both from still active and already eradicated infestations. The genome-wide SNPs detected signs of small and highly structured populations within Europe, showing clear founder effects. The very high population differentiation is presumably derived from multiple independent introductions to Europe, which are spatially restricted in mating. By admixture and phylogenetic analyses, some cases of secondary dispersal were observed. Furthermore, some populations suggest admixture, which might have been originated by either multiple introductions from different sources into the new sites or recurrent introductions from an admixed source population. Our results confirmed a complex invasion history of the ALB into Europe and the usability of GBS obtained SNPs in invasion science even without source populations.}, } @article {pmid38382662, year = {2024}, author = {Yang, S and Sun, J and Wang, C and Li, S and Li, Z and Luo, W and Wei, G and Chen, W}, title = {Residue quality drives SOC sequestration by altering microbial taxonomic composition and ecophysiological function in desert ecosystem.}, journal = {Environmental research}, volume = {250}, number = {}, pages = {118518}, doi = {10.1016/j.envres.2024.118518}, pmid = {38382662}, issn = {1096-0953}, mesh = {*Desert Climate ; *Soil Microbiology ; Ecosystem ; Carbon/analysis/metabolism ; Soil/chemistry ; Carbon Sequestration ; Microbiota ; Bacteria/classification/genetics ; }, abstract = {Plant residues are important sources of soil organic carbon in terrestrial ecosystems. The degradation of plant residue by microbes can influence the soil carbon cycle and sequestration. However, little is known about the microbial composition and function, as well as the accumulation of soil organic carbon (SOC) in response to the inputs of different quality plant residues in the desert environment. The present study evaluated the effects of plant residue addition from Pinus sylvestris var. mongolica (Pi), Artemisia desertorum (Ar) and Amorpha fruticosa (Am) on desert soil microbial community composition and function in a field experiment in the Mu Us Desert. The results showed that the addition of the three plant residues with different C/N ratios induced significant variation in soil microbial communities. The Am treatment (low C/N ratio) improved microbial diversity compared with the Ar and Pi treatments (medium and high C/N ratios). The variations in the taxonomic and functional compositions of the dominant phyla Actinobacteria and Proteobacteria were higher than those of the other phyla among the different treatments. Moreover, the network links between Proteobacteria and other phyla and the CAZyme genes abundances from Proteobacteria increased with increasing residue C/N, whereas those decreased for Actinobacteria. The SOC content of the Am, Ar and Pi treatments increased by 45.73%, 66.54% and 107.99%, respectively, as compared to the original soil. The net SOC accumulation was positively correlated with Proteobacteria abundance and negatively correlated with Actinobacteria abundance. These findings showed that changing the initial quality of plant residue from low C/N to high C/N can result in shifts in taxonomic and functional composition from Actinobacteria to Proteobacteria, which favors SOC accumulation. This study elucidates the ecophysiological roles of Actinobacteria and Proteobacteria in the desert carbon cycle, expands our understanding of the potential microbial-mediated mechanisms by which plant residue inputs affect SOC sequestration in desert soils, and provides valuable guidance for species selection in desert vegetation reconstruction.}, } @article {pmid38382601, year = {2024}, author = {Moreno, Y and Moreno-Mesonero, L and Soler, P and Zornoza, A and Soriano, A}, title = {Influence of drinking water biofilm microbiome on water quality: Insights from a real-scale distribution system.}, journal = {The Science of the total environment}, volume = {921}, number = {}, pages = {171086}, doi = {10.1016/j.scitotenv.2024.171086}, pmid = {38382601}, issn = {1879-1026}, mesh = {Water Quality ; *Drinking Water ; *Microbiota ; Bacteria ; Biofilms ; Water Supply ; Water Microbiology ; }, abstract = {Biofilms, constituting over 95 % of the biomass in drinking water distribution systems, form an ecosystem impacting both the aesthetic and microbiological quality of water. This study investigates the microbiome of biofilms within a real-scale drinking water distribution system in eastern Spain, utilizing amplicon-based metagenomics. Forty-one biofilm samples underwent processing and sequencing to analyze both bacterial and eukaryotic microbiomes, with an assessment of active biomass. Genus-level analysis revealed considerable heterogeneity, with Desulfovibrio, Ralstonia, Bradyrhizobium, Methylocystis, and Bacillus identified as predominant genera. Notably, bacteria associated with corrosion processes, including Desulfovibrio, Sulfuricella, Hyphomicrobium, and Methylobacterium, were prevalent. Potentially pathogenic bacteria such as Helicobacter, Pseudomonas, and Legionella were also detected. Among protozoa, Opisthokonta and Archaeplastida were the most abundant groups in biofilm samples, with potential pathogenic eukaryotes (Acanthamoeba, Naegleria, Blastocystis) identified. Interestingly, no direct correlation between microbiota composition and pipe materials was observed. The study suggests that the usual concentration of free chlorine in bulk water proved insufficient to prevent the presence of undesirable bacteria and protozoa in biofilms, which exhibited a high concentration of active biomass.}, } @article {pmid38380943, year = {2024}, author = {Zhang, IH and Borer, B and Zhao, R and Wilbert, S and Newman, DK and Babbin, AR}, title = {Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential.}, journal = {mBio}, volume = {15}, number = {3}, pages = {e0291823}, pmid = {38380943}, issn = {2150-7511}, support = {R01 HL152190/HL/NHLBI NIH HHS/United States ; }, mesh = {*Archaea/genetics ; Nitrous Oxide/metabolism ; Phylogeny ; Metagenome ; *Microbiota ; Methane/metabolism ; Oxygen/metabolism ; Carbon/metabolism ; Nitrogen/metabolism ; Sulfur/metabolism ; Water/metabolism ; }, abstract = {UNLABELLED: Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%-50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.

IMPORTANCE: Archaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.}, } @article {pmid38380923, year = {2024}, author = {Zhong, J and Osborn, T and Del Rosario Hernández, T and Kyrysyuk, O and Tully, BJ and Anderson, RE}, title = {Increasing transposase abundance with ocean depth correlates with a particle-associated lifestyle.}, journal = {mSystems}, volume = {9}, number = {3}, pages = {e0006724}, pmid = {38380923}, issn = {2379-5077}, support = {//Towsley Endowment, Carleton College/ ; //Rosenow Fund, Carleton College/ ; //Summer Science Fellows Program, Carleton College/ ; }, mesh = {*Transposases/genetics ; Oceans and Seas ; Metagenome/genetics ; *Microbiota/genetics ; }, abstract = {Transposases are mobile genetic elements that move within and between genomes, promoting genomic plasticity in microorganisms. In marine microbial communities, the abundance of transposases increases with depth, but the reasons behind this trend remain unclear. Our analysis of metagenomes from the Tara Oceans and Malaspina Expeditions suggests that a particle-associated lifestyle is the main covariate for the high occurrence of transposases in the deep ocean, and this trend holds true for individual genomes as well as in a community-wide sense. We observed a strong and depth-independent correlation between transposase abundance and the presence of biofilm-associated genes, as well as the prevalence of secretory enzymes. This suggests that mobile genetic elements readily propagate among microbial communities within crowded biofilms. Furthermore, we show that particle association positively correlates with larger genome size, which is in turn associated with higher transposase abundance. Cassette sequences associated with transposons are enriched with genes related to defense mechanisms, which are more highly expressed in the deep sea. Thus, while transposons spread at the expense of their microbial hosts, they also introduce novel genes and potentially benefit the hosts in helping to compete for limited resources. Overall, our results suggest a new understanding of deep ocean particles as highways for gene sharing among defensively oriented microbial genomes.IMPORTANCEGenes can move within and between microbial genomes via mobile genetic elements, which include transposases and transposons. In the oceans, there is a puzzling increase in transposase abundance in microbial genomes as depth increases. To gain insight into this trend, we conducted an extensive analysis of marine microbial metagenomes and metatranscriptomes. We found a significant correlation between transposase abundance and a particle-associated lifestyle among marine microbes at both the metagenome and genome-resolved levels. We also observed a link between transposase abundance and genes related to defense mechanisms. These results suggest that as microbes become densely packed into crowded particles, mobile genes are more likely to spread and carry genetic material that provides a competitive advantage in crowded habitats. This may enable deep sea microbes to effectively compete in such environments.}, } @article {pmid38380878, year = {2024}, author = {Galli, BD}, title = {Sustainability implications and relevance of using omics sciences to investigate cheeses with protected designation of origin.}, journal = {Journal of the science of food and agriculture}, volume = {104}, number = {11}, pages = {6388-6396}, doi = {10.1002/jsfa.13403}, pmid = {38380878}, issn = {1097-0010}, mesh = {*Cheese/analysis/microbiology ; *Metabolomics ; *Proteomics ; Humans ; *Metagenomics ; Animals ; Biodiversity ; }, abstract = {Cheese, a fundamental component of the human diet and a cornerstone of the global food economy, has a significance beyond its role as a commodity, playing a crucial part in the cultural identity of various communities. The intricate natural aging process known as maturation involves a series of reactions that induce changes in the cheese's physical, biochemical, microbiological, and particularly sensory characteristics, making it a complex aspect of cheese production. Recently, the adoption of omics sciences (e.g., metagenomics, metabolomics, proteomics) has emerged as a new trend in studies related to protected designation of origin (PDO) cheese. This mini-summary aims to outline the relationship between omics studies in these food matrices and all the sustainability facets of the production chain in general, and to discuss and recognize that the importance of these studies goes beyond comprehending the cheese biome and extends to fostering and ensuring the sustainability of the production chain. In this context, numerous studies in recent years have linked the identification of intrinsic characteristics of PDO cheeses through omics sciences to crucial sustainability themes such as territoriality, biodiversity, and the preservation of product authenticity. The trajectory suggests that, increasingly, multidisciplinary studies spanning various omics sciences will not only contribute to the characterization of these products but will also address sustainability aspects directly related to the production chain (e.g., authenticity, microbial biodiversity, functionality). This expansion underscores the multidisciplinary nature of these studies, broadening their social impact beyond the academic realm. Consequently, these pivotal studies play a crucial role in advancing discussions on PDO products and sustainability. © 2024 Society of Chemical Industry.}, } @article {pmid38378443, year = {2024}, author = {Li, J and Li, Y and Zhou, L and Li, H and Wan, T and Tang, J and Zhou, L and Xie, H and Wang, L}, title = {Microbiome analysis reveals the inducing effect of Pseudomonas on prostatic hyperplasia via activating NF-κB signalling.}, journal = {Virulence}, volume = {15}, number = {1}, pages = {2313410}, pmid = {38378443}, issn = {2150-5608}, mesh = {Male ; Middle Aged ; Aged ; Humans ; *Prostatic Hyperplasia/pathology ; NF-kappa B/genetics ; Pseudomonas ; Dysbiosis ; In Situ Hybridization, Fluorescence ; Lipopolysaccharides ; *Microbiota ; }, abstract = {Benign prostatic hyperplasia (BPH) is a prevalent disease among middle-aged and elderly males, but its pathogenesis remains unclear. Dysbiosis of the microbiome is increasingly recognized as a significant factor in various human diseases. Prostate tissue also contains a unique microbiome, and its dysbiosis has been proposed to contribute to prostate diseases. Here, we obtained prostate tissues and preoperative catheterized urine from 24 BPH individuals, and 8 normal prostate samples as controls, which followed strict aseptic measures. Using metagenomic next-generation sequencing (mNGS), we found the disparities in the microbiome composition between normal and BPH tissues, with Pseudomonas significantly enriched in BPH tissues, as confirmed by fluorescence in situ hybridization (FISH). Additionally, we showed that the prostate microbiome differed from the urine microbiome. In vitro experiments revealed that lipopolysaccharide (LPS) of Pseudomonas activated NF-κB signalling, leading to inflammation, proliferation, and EMT processes, while inhibiting apoptosis in prostatic cells. Overall, our research determines the presence of microbiome dysbiosis in BPH, and suggests that Pseudomonas, as the dominant microflora, may promote the progression of BPH through LPS activation of NF-κB signalling.}, } @article {pmid38378003, year = {2024}, author = {Li, J and Chen, Z and Wang, Q and Du, L and Yang, Y and Guo, F and Li, X and Chao, Y and Ma, Y}, title = {Microbial and metabolic profiles unveil mutualistic microbe-microbe interaction in obesity-related colorectal cancer.}, journal = {Cell reports. Medicine}, volume = {5}, number = {3}, pages = {101429}, pmid = {38378003}, issn = {2666-3791}, mesh = {Humans ; Metabolome ; *Microbiota ; Obesity/metabolism ; *Colorectal Neoplasms/microbiology ; Microbial Interactions ; }, abstract = {Obesity is a risk factor for colorectal cancer (CRC), and the involvement of gut microbiota in the pathogenesis of obesity and CRC is widely recognized. However, the landscape of fecal microbiome and metabolome distinguishing patients with obesity-related CRC from obesity remains unknown. Here, we utilize metagenomic sequencing and metabolomics from 522 patients with CRC and healthy controls to identify the characteristics of obese CRC. Our integrated analysis reveals that obesity-related CRC is characterized by elevated Peptostreptococcus stomatis, dysregulated fatty acids and phospholipids, and altered Kyoto Encyclopedia of Genes and Genomes pathways involving glycerophospholipid metabolism and lipopolysaccharide synthesis. Correlation analysis unveils microbial interactions in obesity, where the probiotic Faecalibacterium prausnitzii and the tumor-promoting species P. stomatis may engage in cross-feeding, thereby promoting tumorigenesis. In vitro experiments affirm enhanced growth under cross-feeding conditions. The mutualistic microbe-microbe interaction may contribute to the association between obesity and elevated CRC risk. Additionally, diagnostic models incorporating BMI-specific microbial biomarkers display promise for precise CRC screening.}, } @article {pmid38377278, year = {2024}, author = {Dindhoria, K and Kumar, R and Bhargava, B and Kumar, R}, title = {Metagenomic assembled genomes indicated the potential application of hypersaline microbiome for plant growth promotion and stress alleviation in salinized soils.}, journal = {mSystems}, volume = {9}, number = {3}, pages = {e0105023}, pmid = {38377278}, issn = {2379-5077}, mesh = {Soil ; Metagenome ; *Microbiota/genetics ; Agriculture ; *Metals, Heavy ; }, abstract = {UNLABELLED: Climate change is causing unpredictable seasonal variations globally. Due to the continuously increasing earth's surface temperature, the rate of water evaporation is enhanced, conceiving a problem of soil salinization, especially in arid and semi-arid regions. The accumulation of salt degrades soil quality, impairs plant growth, and reduces agricultural yields. Salt-tolerant, plant-growth-promoting microorganisms may offer a solution, enhancing crop productivity and soil fertility in salinized areas. In the current study, genome-resolved metagenomic analysis has been performed to investigate the salt-tolerating and plant growth-promoting potential of two hypersaline ecosystems, Sambhar Lake and Drang Mine. The samples were co-assembled independently by Megahit, MetaSpades, and IDBA-UD tools. A total of 67 metagenomic assembled genomes (MAGs) were reconstructed following the binning process, including 15 from Megahit, 26 from MetaSpades, and 26 from IDBA_UD assembly tools. As compared to other assemblers, the MAGs obtained by MetaSpades were of superior quality, with a completeness range of 12.95%-96.56% and a contamination range of 0%-8.65%. The medium and high-quality MAGs from MetaSpades, upon functional annotation, revealed properties such as salt tolerance (91.3%), heavy metal tolerance (95.6%), exopolysaccharide (95.6%), and antioxidant (60.86%) biosynthesis. Several plant growth-promoting attributes, including phosphate solubilization and indole-3-acetic acid (IAA) production, were consistently identified across all obtained MAGs. Conversely, characteristics such as iron acquisition and potassium solubilization were observed in a substantial majority, specifically 91.3%, of the MAGs. The present study indicates that hypersaline microflora can be used as bio-fertilizing agents for agricultural practices in salinized areas by alleviating prevalent stresses.

IMPORTANCE: The strategic implementation of metagenomic assembled genomes (MAGs) in exploring the properties and harnessing microorganisms from ecosystems like hypersaline niches has transformative potential in agriculture. This approach promises to redefine our comprehension of microbial diversity and its ecosystem roles. Recovery and decoding of MAGs unlock genetic resources, enabling the development of new solutions for agricultural challenges. Enhanced understanding of these microbial communities can lead to more efficient nutrient cycling, pest control, and soil health maintenance. Consequently, traditional agricultural practices can be improved, resulting in increased yields, reduced environmental impacts, and heightened sustainability. MAGs offer a promising avenue for sustainable agriculture, bridging the gap between cutting-edge genomics and practical field applications.}, } @article {pmid38376627, year = {2024}, author = {Isali, I and Helstrom, EK and Uzzo, N and Lakshmanan, A and Nandwana, D and Valentine, H and Sindhani, M and Abbosh, P and Bukavina, L}, title = {Current Trends and Challenges of Microbiome Research in Bladder Cancer.}, journal = {Current oncology reports}, volume = {26}, number = {3}, pages = {292-298}, pmid = {38376627}, issn = {1534-6269}, mesh = {Humans ; Mice ; Animals ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Urinary Bladder Neoplasms ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {PURPOSE OF THE REVIEW: Microbiome research has provided valuable insights into the associations between microbial communities and bladder cancer. However, this field faces significant challenges that hinder the interpretation, generalization, and translation of findings into clinical practice. This review aims to elucidate these challenges and highlight the importance of addressing them for the advancement of microbiome research in bladder cancer.

RECENT FINDINGS: Recent findings underscore the complexities involved in microbiome research, particularly in the context of bladder cancer. Challenges include low microbial biomass in urine samples, potential contamination issues during collection and processing, variability in sequencing methods and primer selection, and the difficulty of establishing causality between microbiota and bladder cancer. Studies have shown the impact of sample storage conditions and DNA isolation kits on microbiome analysis, emphasizing the need for standardization. Additionally, variations in urine collection methods can introduce contamination and affect results. The choice of 16S rRNA gene amplicon sequencing or shotgun metagenomic sequencing introduces technical challenges, including primer selection and sequencing read length. Establishing causality between the microbiota and bladder cancer requires experimental methods like fecal microbiota transplantation and human microbiota-associated murine models, which face their own set of challenges. Translating microbiome research into therapeutic applications is hindered by methodological variability, incomplete understanding of bioactive molecules, imperfect animal models, and the inherent heterogeneity of microbiome communities among individuals. Microbiome research in bladder cancer presents significant challenges stemming from technical and conceptual complexities. Addressing these challenges through standardization, improved experimental models, and advanced analytical approaches is essential for advancing our understanding of the microbiome's role in bladder cancer and its potential clinical applications. Achieving this goal can lead to improved patient outcomes and novel therapeutic strategies in the future.}, } @article {pmid38376378, year = {2024}, author = {Kitamura, N and Kajihara, T and Volpiano, CG and Naung, M and Méric, G and Hirabayashi, A and Yano, H and Yamamoto, M and Yoshida, F and Kobayashi, T and Yamanashi, S and Kawamura, T and Matsunaga, N and Okochi, J and Sugai, M and Yahara, K}, title = {Exploring the effects of antimicrobial treatment on the gut and oral microbiomes and resistomes from elderly long-term care facility residents via shotgun DNA sequencing.}, journal = {Microbial genomics}, volume = {10}, number = {2}, pages = {}, pmid = {38376378}, issn = {2057-5858}, mesh = {Aged ; Humans ; Angiotensin Receptor Antagonists ; Cross-Sectional Studies ; Long-Term Care ; Angiotensin-Converting Enzyme Inhibitors ; DNA ; Sequence Analysis, DNA ; *Microbiota ; *Anti-Infective Agents ; }, abstract = {Monitoring antibiotic-resistant bacteria (ARB) and understanding the effects of antimicrobial drugs on the human microbiome and resistome are crucial for public health. However, no study has investigated the association between antimicrobial treatment and the microbiome-resistome relationship in long-term care facilities, where residents act as reservoirs of ARB but are not included in the national surveillance for ARB. We conducted shotgun metagenome sequencing of oral and stool samples from long-term care facility residents and explored the effects of antimicrobial treatment on the human microbiome and resistome using two types of comparisons: cross-sectional comparisons based on antimicrobial treatment history in the past 6 months and within-subject comparisons between stool samples before, during and 2-4 weeks after treatment using a single antimicrobial drug. Cross-sectional analysis revealed two characteristics in the group with a history of antimicrobial treatment: the archaeon Methanobrevibacter was the only taxon that significantly increased in abundance, and the total abundance of antimicrobial resistance genes (ARGs) was also significantly higher. Within-subject comparisons showed that taxonomic diversity did not decrease during treatment, suggesting that the effect of the prescription of a single antimicrobial drug in usual clinical treatment on the gut microbiota is likely to be smaller than previously thought, even among very elderly people. Additional analysis of the detection limit of ARGs revealed that they could not be detected when contig coverage was <2.0. This study is the first to report the effects of usual antimicrobial treatments on the microbiome and resistome of long-term care facility residents.}, } @article {pmid38376235, year = {2024}, author = {Huang, J and Wu, Y and Gao, Q and Li, X and Zeng, Y and Guo, Y and Zhang, H and Qin, Z}, title = {Metagenomic exploration of the rhizosphere soil microbial community and their significance in facilitating the development of wild-simulated ginseng.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {3}, pages = {e0233523}, pmid = {38376235}, issn = {1098-5336}, support = {32170079//National Natural Science Foundation of China (NSFC)/ ; 32200035//National Natural Science Foundation of China (NSFC)/ ; 2021A1515012026//Natural Science Foundation of Guangdong Province/ ; 2021QN020100//Guangdong Talent Scheme/ ; }, mesh = {Humans ; Child ; *Panax/microbiology ; Soil/chemistry ; Rhizosphere ; Metagenome ; *Hypocreales ; *Microbiota ; *Streptomyces ; Soil Microbiology ; }, abstract = {Panax ginseng, a prized medicinal herb, has faced increasingly challenging field production due to soil degradation and fungal diseases in Northeast China. Wild-simulated cultivation has prevailed because of its sustainable soil management and low disease incidence. Despite the recognized benefits of rhizosphere microorganisms in ginseng cultivation, their genomic and functional diversity remain largely unexplored. In this work, we utilized shotgun metagenomic analysis to reveal that Pseudomonadota, Actinomycetota, and Acidobacteriota were dominant in the ginseng rhizobiome and recovered 14 reliable metagenome-assembled genomes. Functional analysis indicated an enrichment of denitrification-associated genes, potentially contributing to the observed decline in soil fertility, while genes associated with aromatic carbon degradation may be linked to allelochemical degradation. Further analysis demonstrated enrichment of Actinomycetota in 9-year-old wild-simulated ginseng (WSG), suggesting the need for targeted isolation of Actinomycetota bacteria. Among these, at least three different actinomycete strains were found to play a crucial role in fungal disease resistance, with Streptomyces spp. WY144 standing out for its production of actinomycin natural products active against the pathogenic fungus Ilyonectria robusta. These findings not only enhance our understanding of the rhizobiome of WSG but also present promising avenues for combating detrimental fungal pathogens, underscoring the importance of ginseng in both medicinal and agricultural contexts.IMPORTANCEWild-simulated ginseng, growing naturally without human interference, is influenced by its soil microbiome. Using shotgun metagenomics, we analyzed the rhizospheric soil microbiome of 7- and 9-year-old wild-simulated ginseng. The study aimed to reveal its composition and functions, exploring the microbiome's key roles in ginseng growth. Enrichment analysis identified Streptomycetes in ginseng soil, with three strains inhibiting plant pathogenic fungi. Notably, one strain produced actinomycins, suppressing the ginseng pathogenic fungus Ilyonectria robusta. This research accelerates microbiome application in wild-simulated ginseng cultivation, offering insights into pathogen protection and supporting microbiome utilization in agriculture.}, } @article {pmid38376207, year = {2024}, author = {Xu, Q and Li, L and Guo, J and Guo, H and Liu, M and Guo, S and Kuzyakov, Y and Ling, N and Shen, Q}, title = {Active microbial population dynamics and life strategies drive the enhanced carbon use efficiency in high-organic matter soils.}, journal = {mBio}, volume = {15}, number = {3}, pages = {e0017724}, pmid = {38376207}, issn = {2150-7511}, support = {2021YFD1900300//MOST | National Key Research and Development Program of China (NKPs)/ ; XUEKEN2023039//Nanjing Agricultural University (NAU)/ ; 2022M711656//China Postdoctoral Science Foundation (China Postdoctoral Foundation Project)/ ; BK20221004//JST | Natural Science Foundation of Jiangsu Province (Jiangsu Natural Science Foundation)/ ; 2022ZB323//Jiangsu Excellent Postdoctoral Program/ ; 42307174//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Carbon/chemistry ; Soil/chemistry ; Soil Microbiology ; *Microbiota ; Climate Change ; }, abstract = {Microbial carbon use efficiency (CUE) is a critical parameter that controls carbon storage in soil, but many uncertainties remain concerning adaptations of microbial communities to long-term fertilization that impact CUE. Based on H2[18]O quantitative stable isotope probing coupled with metagenomic sequencing, we disentangled the roles of active microbial population dynamics and life strategies for CUE in soils after a long-term (35 years) mineral or organic fertilization. We found that the soils rich in organic matter supported high microbial CUE, indicating a more efficient microbial biomass formation and a greater carbon sequestration potential. Organic fertilizers supported active microbial communities characterized by high diversity and a relative increase in net growth rate, as well as an anabolic-biased carbon cycling, which likely explains the observed enhanced CUE. Overall, these results highlight the role of population dynamics and life strategies in understanding and predicting microbial CUE and sequestration in soil.IMPORTANCEMicrobial CUE is a major determinant of global soil organic carbon storage. Understanding the microbial processes underlying CUE can help to maintain soil sustainable productivity and mitigate climate change. Our findings indicated that active microbial communities, adapted to long-term organic fertilization, exhibited a relative increase in net growth rate and a preference for anabolic carbon cycling when compared to those subjected to chemical fertilization. These shifts in population dynamics and life strategies led the active microbes to allocate more carbon to biomass production rather than cellular respiration. Consequently, the more fertile soils may harbor a greater microbially mediated carbon sequestration potential. This finding is of great importance for manipulating microorganisms to increase soil C sequestration.}, } @article {pmid38376180, year = {2024}, author = {Schaan, AP and Vidal, A and Zhang, A-N and Poyet, M and Alm, EJ and Groussin, M and Ribeiro-Dos-Santos, Â}, title = {Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia.}, journal = {mSystems}, volume = {9}, number = {3}, pages = {e0070723}, pmid = {38376180}, issn = {2379-5077}, support = {88882.160155/2017-01//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; 304413/2015-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Brazil ; *Microbiota ; Bacteria ; Urbanization ; }, abstract = {Increasing levels of industrialization have been associated with changes in gut microbiome structure and loss of features thought to be crucial for maintaining gut ecological balance. The stability of gut microbial communities over time within individuals seems to be largely affected by these changes but has been overlooked among transitioning populations from low- to middle-income countries. Here, we used metagenomic sequencing to characterize the temporal dynamics in gut microbiomes of 24 individuals living an urban non-industrialized lifestyle in the Brazilian Amazon. We further contextualized our data with 165 matching longitudinal samples from an urban industrialized and a rural non-industrialized population. We show that gut microbiome composition and diversity have greater variability over time among non-industrialized individuals when compared to industrialized counterparts and that taxa may present diverse temporal dynamics across human populations. Enterotype classifications show that community types are generally stable over time despite shifts in microbiome structure. Furthermore, by tracking genomes over time, we show that levels of bacterial population replacements are more frequent among Amazonian individuals and that non-synonymous variants accumulate in genes associated with degradation of host dietary polysaccharides. Taken together, our results suggest that the stability of gut microbiomes is influenced by levels of industrialization and that tracking microbial population dynamics is important to understand how the microbiome will adapt to these transitions.IMPORTANCEThe transition from a rural or non-industrialized lifestyle to urbanization and industrialization has been linked to changes in the structure and function of the human gut microbiome. Understanding how the gut microbiomes changes over time is crucial to define healthy states and to grasp how the gut microbiome interacts with the host environment. Here, we investigate the temporal dynamics of gut microbiomes from an urban and non-industrialized population in the Amazon, as well as metagenomic data sets from urban United States and rural Tanzania. We showed that healthy non-industrialized microbiomes experience greater compositional shifts over time compared to industrialized individuals. Furthermore, bacterial strain populations are more frequently replaced in non-industrialized microbiomes, and most non-synonymous mutations accumulate in genes associated with the degradation of host dietary components. This indicates that microbiome stability is affected by transitions to industrialization, and that strain tracking can elucidate the ecological dynamics behind such transitions.}, } @article {pmid38375831, year = {2024}, author = {Reuter, MA and Tucker, M and Marfori, Z and Shishani, R and Bustamante, JM and Moreno, R and Goodson, ML and Ehrlich, A and Taha, AY and Lein, PJ and Joshi, N and Brito, I and Durbin-Johnson, B and Nandakumar, R and Cummings, BP}, title = {Dietary resistant starch supplementation increases gut luminal deoxycholic acid abundance in mice.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2315632}, pmid = {38375831}, issn = {1949-0984}, support = {R21 AT010956/AT/NCCIH NIH HHS/United States ; T32 ES007059/ES/NIEHS NIH HHS/United States ; T32 GM135741/GM/NIGMS NIH HHS/United States ; UL1 TR001873/TR/NCATS NIH HHS/United States ; }, mesh = {Mice ; Male ; Female ; Animals ; *Resistant Starch ; *Gastrointestinal Microbiome/physiology ; Bile Acids and Salts ; Dietary Supplements ; Bacteria/genetics ; Deoxycholic Acid ; }, abstract = {Bile acids (BA) are among the most abundant metabolites produced by the gut microbiome. Primary BAs produced in the liver are converted by gut bacterial 7-α-dehydroxylation into secondary BAs, which can differentially regulate host health via signaling based on their varying affinity for BA receptors. Despite the importance of secondary BAs in host health, the regulation of 7-α-dehydroxylation and the role of diet in modulating this process is incompletely defined. Understanding this process could lead to dietary guidelines that beneficially shift BA metabolism. Dietary fiber regulates gut microbial composition and metabolite production. We tested the hypothesis that feeding mice a diet rich in a fermentable dietary fiber, resistant starch (RS), would alter gut bacterial BA metabolism. Male and female wild-type mice were fed a diet supplemented with RS or an isocaloric control diet (IC). Metabolic parameters were similar between groups. RS supplementation increased gut luminal deoxycholic acid (DCA) abundance. However, gut luminal cholic acid (CA) abundance, the substrate for 7-α-dehydroxylation in DCA production, was unaltered by RS. Further, RS supplementation did not change the mRNA expression of hepatic BA producing enzymes or ileal BA transporters. Metagenomic assessment of gut bacterial composition revealed no change in the relative abundance of bacteria known to perform 7-α-dehydroxylation. P. ginsenosidimutans and P. multiformis were positively correlated with gut luminal DCA abundance and increased in response to RS supplementation. These data demonstrate that RS supplementation enriches gut luminal DCA abundance without increasing the relative abundance of bacteria known to perform 7-α-dehydroxylation.}, } @article {pmid38375198, year = {2024}, author = {Liu, C and Xu, Q and Dong, S and Ding, H and Li, B and Zhang, D and Liang, Y and Li, L and Liu, Q and Cheng, Y and Wu, J and Zhu, J and Zhong, M and Cao, Y and Zhang, G}, title = {New mechanistic insights of anti-obesity by sleeve gastrectomy-altered gut microbiota and lipid metabolism.}, journal = {Frontiers in endocrinology}, volume = {15}, number = {}, pages = {1338147}, pmid = {38375198}, issn = {1664-2392}, mesh = {Humans ; *Gastrointestinal Microbiome ; Lipid Metabolism ; Obesity/surgery ; *Bariatric Surgery/methods ; Gastrectomy/methods ; }, abstract = {BACKGROUND: The obesity epidemic has been on the rise due to changes in living standards and lifestyles. To combat this issue, sleeve gastrectomy (SG) has emerged as a prominent bariatric surgery technique, offering substantial weight reduction. Nevertheless, the mechanisms that underlie SG-related bodyweight loss are not fully understood.

METHODS: In this study, we conducted a collection of preoperative and 3-month postoperative serum and fecal samples from patients who underwent laparoscopic SG at the First Affiliated Hospital of Shandong First Medical University (Jinan, China). Here, we took an unbiased approach of multi-omics to investigate the role of SG-altered gut microbiota in anti-obesity of these patients. Non-target metabolome sequencing was performed using the fecal and serum samples.

RESULTS: Our data show that SG markedly increased microbiota diversity and Rikenellaceae, Alistipes, Parabacteroides, Bactreoidales, and Enterobacteraies robustly increased. These compositional changes were positively correlated with lipid metabolites, including sphingolipids, glycerophospholipids, and unsaturated fatty acids. Increases of Rikenellaceae, Alistipes, and Parabacteroide were reversely correlated with body mass index (BMI).

CONCLUSION: In conclusion, our findings provide evidence that SG induces significant alterations in the abundances of Rikenellaceae, Alistipes, Parabacteroides, and Bacteroidales, as well as changes in lipid metabolism-related metabolites. Importantly, these changes were found to be closely linked to the alleviation of obesity. On the basis of these findings, we have identified a number of microbiotas that could be potential targets for treatment of obesity.}, } @article {pmid38374282, year = {2024}, author = {Spohr, P and Scharf, S and Rommerskirchen, A and Henrich, B and Jäger, P and Klau, GW and Haas, R and Dilthey, A and Pfeffer, K}, title = {Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {4068}, pmid = {38374282}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; *Hematopoietic Stem Cell Transplantation ; Bacteria/genetics ; Anti-Bacterial Agents ; Fungi/genetics ; DNA, Ribosomal ; Metagenomics/methods ; }, abstract = {The gut microbiome is a diverse ecosystem, dominated by bacteria; however, fungi, phages/viruses, archaea, and protozoa are also important members of the gut microbiota. Exploration of taxonomic compositions beyond bacteria as well as an understanding of the interaction between the bacteriome with the other members is limited using 16S rDNA sequencing. Here, we developed a pipeline enabling the simultaneous interrogation of the gut microbiome (bacteriome, mycobiome, archaeome, eukaryome, DNA virome) and of antibiotic resistance genes based on optimized long-read shotgun metagenomics protocols and custom bioinformatics. Using our pipeline we investigated the longitudinal composition of the gut microbiome in an exploratory clinical study in patients undergoing allogeneic hematopoietic stem cell transplantation (alloHSCT; n = 31). Pre-transplantation microbiomes exhibited a 3-cluster structure, characterized by Bacteroides spp. /Phocaeicola spp., mixed composition and Enterococcus abundances. We revealed substantial inter-individual and temporal variabilities of microbial domain compositions, human DNA, and antibiotic resistance genes during the course of alloHSCT. Interestingly, viruses and fungi accounted for substantial proportions of microbiome content in individual samples. In the course of HSCT, bacterial strains were stable or newly acquired. Our results demonstrate the disruptive potential of alloHSCTon the gut microbiome and pave the way for future comprehensive microbiome studies based on long-read metagenomics.}, } @article {pmid38374154, year = {2024}, author = {Wang, FQ and Bartosik, D and Sidhu, C and Siebers, R and Lu, DC and Trautwein-Schult, A and Becher, D and Huettel, B and Rick, J and Kirstein, IV and Wiltshire, KH and Schweder, T and Fuchs, BM and Bengtsson, MM and Teeling, H and Amann, RI}, title = {Particle-attached bacteria act as gatekeepers in the decomposition of complex phytoplankton polysaccharides.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {32}, pmid = {38374154}, issn = {2049-2618}, support = {AM 73/9-3//Deutsche Forschungsgemeinschaft,Germany/ ; SCHW 595/10-3//Deutsche Forschungsgemeinschaft,Germany/ ; TE 813/2-3//Deutsche Forschungsgemeinschaft,Germany/ ; RI 969/9-2//Deutsche Forschungsgemeinschaft,Germany/ ; BE 3869/4-3//Deutsche Forschungsgemeinschaft,Germany/ ; SCHW 595/11-3//Deutsche Forschungsgemeinschaft,Germany/ ; FU 627/2-3//Deutsche Forschungsgemeinschaft,Germany/ ; RI 969/9-2//Deutsche Forschungsgemeinschaft,Germany/ ; TE 813/2-3//Deutsche Forschungsgemeinschaft,Germany/ ; AM 73/9-3//Deutsche Forschungsgemeinschaft,Germany/ ; AWI_BAH_o 1//Biological Station Helgoland, Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research/ ; AWI_BAH_o 1//Biological Station Helgoland, Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research/ ; }, mesh = {Phytoplankton/genetics/metabolism ; Eutrophication ; Polysaccharides/metabolism ; *Flavobacteriaceae/metabolism ; *Microalgae/metabolism ; }, abstract = {BACKGROUND: Marine microalgae (phytoplankton) mediate almost half of the worldwide photosynthetic carbon dioxide fixation and therefore play a pivotal role in global carbon cycling, most prominently during massive phytoplankton blooms. Phytoplankton biomass consists of considerable proportions of polysaccharides, substantial parts of which are rapidly remineralized by heterotrophic bacteria. We analyzed the diversity, activity, and functional potential of such polysaccharide-degrading bacteria in different size fractions during a diverse spring phytoplankton bloom at Helgoland Roads (southern North Sea) at high temporal resolution using microscopic, physicochemical, biodiversity, metagenome, and metaproteome analyses.

RESULTS: Prominent active 0.2-3 µm free-living clades comprised Aurantivirga, "Formosa", Cd. Prosiliicoccus, NS4, NS5, Amylibacter, Planktomarina, SAR11 Ia, SAR92, and SAR86, whereas BD1-7, Stappiaceae, Nitrincolaceae, Methylophagaceae, Sulfitobacter, NS9, Polaribacter, Lentimonas, CL500-3, Algibacter, and Glaciecola dominated 3-10 µm and > 10 µm particles. Particle-attached bacteria were more diverse and exhibited more dynamic adaptive shifts over time in terms of taxonomic composition and repertoires of encoded polysaccharide-targeting enzymes. In total, 305 species-level metagenome-assembled genomes were obtained, including 152 particle-attached bacteria, 100 of which were novel for the sampling site with 76 representing new species. Compared to free-living bacteria, they featured on average larger metagenome-assembled genomes with higher proportions of polysaccharide utilization loci. The latter were predicted to target a broader spectrum of polysaccharide substrates, ranging from readily soluble, simple structured storage polysaccharides (e.g., laminarin, α-glucans) to less soluble, complex structural, or secreted polysaccharides (e.g., xylans, cellulose, pectins). In particular, the potential to target poorly soluble or complex polysaccharides was more widespread among abundant and active particle-attached bacteria.

CONCLUSIONS: Particle-attached bacteria represented only 1% of all bloom-associated bacteria, yet our data suggest that many abundant active clades played a pivotal gatekeeping role in the solubilization and subsequent degradation of numerous important classes of algal glycans. The high diversity of polysaccharide niches among the most active particle-attached clades therefore is a determining factor for the proportion of algal polysaccharides that can be rapidly remineralized during generally short-lived phytoplankton bloom events. Video Abstract.}, } @article {pmid38374114, year = {2024}, author = {Bazzani, D and Heidrich, V and Manghi, P and Blanco-Miguez, A and Asnicar, F and Armanini, F and Cavaliere, S and Bertelle, A and Dell'Acqua, F and Dellasega, E and Waldner, R and Vicentini, D and Bolzan, M and Tomasi, C and Segata, N and Pasolli, E and Ghensi, P}, title = {Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {12}, pmid = {38374114}, issn = {2055-5008}, mesh = {Humans ; *Peri-Implantitis/therapy ; *Microbiota ; }, abstract = {We performed a longitudinal shotgun metagenomic investigation of the plaque microbiome associated with peri-implant diseases in a cohort of 91 subjects with 320 quality-controlled metagenomes. Through recently improved taxonomic profiling methods, we identified the most discriminative species between healthy and diseased subjects at baseline, evaluated their change over time, and provided evidence that clinical treatment had a positive effect on plaque microbiome composition in patients affected by mucositis and peri-implantitis.}, } @article {pmid38373261, year = {2024}, author = {Dumonteil, E and Tu, W and Jiménez, FA and Herrera, C}, title = {Ecological interactions of Triatoma sanguisuga (Hemiptera: Reduviidae) and risk for human infection with Trypanosoma cruzi (Kinetoplastida: Trypanosomatidae) in Illinois and Louisiana.}, journal = {Journal of medical entomology}, volume = {61}, number = {6}, pages = {1282-1289}, doi = {10.1093/jme/tjae017}, pmid = {38373261}, issn = {1938-2928}, mesh = {Animals ; Louisiana ; Illinois ; *Chagas Disease/transmission/epidemiology ; *Trypanosoma cruzi/physiology ; *Triatoma/parasitology/physiology ; *Insect Vectors/physiology/parasitology/microbiology ; Humans ; Feeding Behavior ; Gastrointestinal Microbiome ; }, abstract = {Triatoma sanguisuga (Leconte) is one of the most widely distributed kissing bugs in the United States, associated with an extensive zoonotic circulation of Trypanosoma cruzi, the agent of Chagas disease, in a large part of the country. However, the actual risk for human infection in the United States is poorly understood. Here, we further assessed the ecology of T. sanguisuga bugs collected in residents' houses in Illinois and Louisiana, using a metagenomic approach to identify their blood-feeding sources, T. cruzi parasites and gut microbiota. Blood meal analysis revealed feeding on domestic animals (dogs, cats, pigs, goats, and turkeys), synanthropic species (raccoons, opossums, and squirrels), as well as the more sylvatic white-tail deer. Human blood was identified in 11/14 (78%) of bugs, highlighting a frequent vector-human contact. The infection rate with T. cruzi was 53% (8/15), and most infected bugs (6/8) had fed on humans. A total of 41 bacterial families were identified, with significant differences in microbiota alpha and beta diversity between bugs from Louisiana and Illinois. However, predicted metabolic functions remained highly conserved, suggesting important constraints to fulfill their role in bug biology. These results confirmed a significant risk for vector-borne transmission of T. cruzi to humans in Louisiana and Illinois, which warrants more active screening for human infections. Also, while there is broad plasticity in the bacterial composition of T. sanguisuga microbiota, there are strong constraints to preserve metabolic profile and function, making it a good target for novel vector control strategies.}, } @article {pmid38371901, year = {2024}, author = {Nandakumar, K and Anto, PV and Antony, I}, title = {Diversity of soil fungi from sacred groves of Kerala, India revealed by comparative metagenomics analysis using illumina sequencing.}, journal = {3 Biotech}, volume = {14}, number = {3}, pages = {79}, pmid = {38371901}, issn = {2190-572X}, abstract = {The diversity, composition, and abundance of soil fungi from three sacred groves in Kerala, namely Iringole kavu of Ernakulam District, Kollakal Thapovanam of Alappuzha District, and Poyilkavu of Kozhikode District were analysed using Metagenomics analysis and Illumina sequencing. A total of 30,584, 78,323, and 55,640 reads were obtained from these groves, respectively. Ascomycota constitutes over 96% of the total fungi, making it the most abundant phylum, followed by Mortierellomycota, Basidiomycota, Chytridiomycota, and Rozellomycota. These phyla were subdivided into 20 classes, 40 orders, 83 families, 119 genera, and 135 species, while 1269 OTUs remained unidentified at the species level. Eurotiomycetes predominates the class, while the genus Talaromyces from the family Trichomaceae dominates the genera. Neocarmospora falciformis, Trichoderma lixii, and Candida ethanolic are the most abundant fungal species. Diversity analysis shows that Kollakal Thapovanam is rich in fungal species, while Poyilkavu is rich in biodiversity, with a high degree of dominance. Several species were found only in a particular grove and were absent in others and vice-versa, indicating high fungal specificity. Therefore, fungi have to be preserved in their original habitat. The Principal Coordinate Analysis revealed that each grove is distinct highlighting the importance of preserving the unique diversity of each sacred grove. In conclusion, this research provides valuable information about the soil fungal genera in their natural habitat. It emphasizes the need for more systematic research to understand the actual diversity and ecological role of fungi in sacred groves. This study is the first of its kind to analyse and compare soil fungal diversity in sacred groves using the metagenomics approach.}, } @article {pmid38371896, year = {2023}, author = {Gregorczyk-Maga, I and Kania, M and Dąbrowska, M and Samborowska, E and Żeber-Lubecka, N and Kulecka, M and Klupa, T}, title = {The interplay between gingival crevicular fluid microbiome and metabolomic profile in intensively treated people with type 1 diabetes - a combined metagenomic/metabolomic approach cross-sectional study.}, journal = {Frontiers in endocrinology}, volume = {14}, number = {}, pages = {1332406}, pmid = {38371896}, issn = {1664-2392}, mesh = {Adult ; Humans ; Young Adult ; *Diabetes Mellitus, Type 1/drug therapy ; Cross-Sectional Studies ; Gingival Crevicular Fluid ; *Gingivitis ; *Microbiota ; }, abstract = {AIMS: This study aimed to assess the gingival crevicular fluid (GCF) microbiome and metabolome of adults with type 1 diabetes (T1D) treated with continuous subcutaneous insulin infusion (CSII).

METHODS: In this cross-sectional study, the GCF of adults with T1D treated with CSII and non-diabetic controls were sampled, and metagenomic/metabolomic analyses were performed.

RESULTS: In total, 65 participants with T1D and 45 healthy controls with a mean age of 27.05 ± 5.95 years were investigated. There were 22 cases of mild gingivitis (G) in the T1D group. There were no differences considering the Shannon and Chao indices and β-diversity between people with T1D and G, with T1D without G, and healthy controls. Differential taxa were identified, which were mainly enriched in people with T1D and G. Acetic acid concentration was higher in people with T1D, regardless of the presence of G, than in healthy controls. Propionic acid was higher in people with T1D and G than in healthy controls. Isobutyric and isovaleric acid levels were higher in individuals with T1D and G than in the other two subgroups. The concentration of valeric acid was lower and that of caproic acid was higher in people with T1D (regardless of gingival status) than in healthy controls.

CONCLUSIONS: The identification of early changes in periodontal tissues by targeting the microbiome and metabolome could potentially enable effective prevention and initial treatment of periodontal disease in people with T1D.}, } @article {pmid38370893, year = {2023}, author = {Marlida, Y and Susalam, MK and Harnentis, H and Jamsari, J and Huda, N and Noordin, WNM and Anggraini, L and Ardani, LR}, title = {Metagenomic analysis and biodiversity of bacteria in traditional fermented fish or Budu from West Sumatera, Indonesia.}, journal = {Journal of advanced veterinary and animal research}, volume = {10}, number = {4}, pages = {801-808}, pmid = {38370893}, issn = {2311-7710}, abstract = {OBJECTIVE: This research aims to investigate the microbial diversity of Budu prepared from fresh and frozen fish from the Pariaman and Pasaman districts in West Sumatra Province, Indonesia, as well as provide basic information about Budu quality.

MATERIALS AND METHODS: To obtain the bacterial microbial composition, deoxyribonucleic acid extraction was carried out using amplicon-sequencing of the 16S-rRNA gene in the V3-V4 region from two types of Budu and carried out in duplicate.

RESULTS: Budu prepared with fresh (Pariaman) or frozen (Pasaman) fish was dominated by Firmicutes (78.455%-92.37%) and Proteobacteria (6.477%-7.23%) phyla. The total microbial species in Budu from Pariaman were higher (227 species) than in Pasaman (153 species). The bacterial species found are Lentibacillus kimchi (1.878%-2.21%), Staphylococcus cohnii (0.597%-0.70%), Peptostreptococcus russeli (0.00%-0.002%), Clostridium disporicum (0.073%-0.09%), Clostridium novyi (0.00%-0.01%), Nioella sediminis (0.00%-0.001%), and Shewanella baltica (0.00%-0.003%). Lentibacillus kimchi, S. cohnii, and C. disporicum are found in both Budu. Nioella sediminis and S. baltica are found in Budu Pariaman. Peptostreptococcus russeli and C. novyi were found in Budu Pasaman.

CONCLUSION: Metagenomic analysis of Budu from different fish, Pariaman (fresh fish) and Pasaman (frozen fish) showed that the biodiversity of bacteria was barely different. Both Budu found lactic acid bacteria from the Enterococcaceae family, genus Vagococcus, and pathogenic bacteria, such as S. cohnii, P. russeli, C. disporicum, and S. baltica. The discovery of various species of pathogenic bacteria indicates that development is still needed in the Budu production process to improve Budu quality.}, } @article {pmid38369656, year = {2024}, author = {Chang, X and Zhang, Y and Chen, X and Li, S and Mei, H and Xiao, H and Ma, X and Liu, Z and Li, R}, title = {Gut microbiome and serum amino acid metabolome alterations in autism spectrum disorder.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {4037}, pmid = {38369656}, issn = {2045-2322}, support = {the Knowledge Innovation Program of Wuhan-Shugung Project//the Knowledge Innovation Program of Wuhan-Shugung Project/ ; 2022DCC020//the Hubei Provincial Science and Technology Plan Project for Clinical Research Center of Neurodevelopmental Disorders in Children/ ; 2019ZYYD051//the Special Projects for the Central Government to Guide the Development of Local Science and Technology/ ; }, mesh = {Child ; Humans ; *Gastrointestinal Microbiome/physiology ; *Autism Spectrum Disorder ; Nickel ; Metabolome ; Amino Acids/metabolism ; }, abstract = {Gut microbiota and their metabolic products might play important roles in regulating the pathogenesis of autism spectrum disorder (ASD). The purpose of this study was to characterize gut microbiota and serum amino acid metabolome profiles in children with ASD. A non-randomized controlled study was carried out to analyze the alterations in the intestinal microbiota and their metabolites in patients with ASD (n = 30) compared with neurotypical controls (NC) (n = 30) by metagenomic sequencing to define the gut microbiota community and liquid chromatography/mass spectrometry (LC/MS) analysis to characterize the metabolite profiles. Compared with children in the NC group, those in the ASD group showed lower richness, higher evenness, and an altered microbial community structure. At the class level, Deinococci and Holophagae were significantly lower in children with ASD compared with TD. At the phylum level, Deinococcus-Thermus was significantly lower in children with ASD compared with TD. In addition, the functional properties (such as galactose metabolism) displayed significant differences between the ASD and NC groups. Five dominant altered species were identified and analyzed (LDA score > 2.0, P < 0.05), including Subdoligranulum, Faecalibacterium_praushitzii, Faecalibacterium, Veillonellaceae, and Rumminococcaceae. The peptides/nickel transport system was the main metabolic pathway involved in the differential species in the ASD group. Decreased ornithine levels and elevated valine levels may increase the risk of ASD through a metabolic pathway known as the nickel transport system. The microbial metabolism in diverse environments was negatively correlated with phascolarctobacterium succinatutens. Our study provides novel insights into compositional and functional alterations in the gut microbiome and metabolite profiles in ASD and the underlying mechanisms between metabolite and ASD.}, } @article {pmid38369542, year = {2024}, author = {Zou, S and Yang, C and Zhang, J and Zhong, D and Meng, M and Zhang, L and Chen, H and Fang, L}, title = {Multi-omic profiling reveals associations between the gut microbiome, host genome and transcriptome in patients with colorectal cancer.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {175}, pmid = {38369542}, issn = {1479-5876}, support = {82373512//National Natural Science Foundation of China/ ; 82222056//National Natural Science Foundation of China/ ; 82302910//National Natural Science Foundation of China/ ; 2022A1515012316//Natural Science Foundation of Guangdong Province/ ; 2021B1212010004//Natural Science Foundation of Guangdong Province/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Transcriptome/genetics ; *Colorectal Neoplasms/diagnosis ; Multiomics ; *Microbiota ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is the leading cancer worldwide. Microbial agents have been considered to contribute to the pathogenesis of different disease. But the underlying relevance between CRC and microbiota remain unclear.

METHODS: We dissected the fecal microbiome structure and genomic and transcriptomic profiles of matched tumor and normal mucosa tissues from 41 CRC patients. Of which, the relationship between CRC-associated bacterial taxa and their significantly correlated somatic mutated gene was investigated by exome sequencing technology. Differentially expressed functional genes in CRC were clustered according to their correlation with differentially abundant species, following by annotation with DAVID. The composition of immune and stromal cell types was identified by XCELL.

RESULTS: We identified a set of 22 microbial gut species associated with CRC and estimate the relative abundance of KEGG ontology categories. Next, the interactions between CRC-related gut microbes and clinical phenotypes were evaluated. 4 significantly mutated gene: TP53, APC, KRAS, SMAD4 were pointed out and the associations with cancer related microbes were identified. Among them, Fusobacterium nucleatum positively corelated with different host metabolic pathways. Finally, we revealed that Fusobacterium nucleatum modified the tumor immune environment by TNFSF9 gene expression.

CONCLUSION: Collectively, our multi-omics data could help identify novel biomarkers to inform clinical decision-making in the detection and diagnosis of CRC.}, } @article {pmid38369136, year = {2024}, author = {Singh, JP and Bottos, EM and Van Hamme, JD and Fraser, LH}, title = {Microbial composition and function in reclaimed mine sites along a reclamation chronosequence become increasingly similar to undisturbed reference sites.}, journal = {The Science of the total environment}, volume = {920}, number = {}, pages = {170996}, doi = {10.1016/j.scitotenv.2024.170996}, pmid = {38369136}, issn = {1879-1026}, mesh = {Soil Microbiology ; Mining ; *Microbiota ; *Mycobiome ; Plants ; Soil ; Bacteria/genetics ; }, abstract = {Mine reclamation historically focuses on enhancing plant coverage to improve below and aboveground ecology. However, there is a great need to study the role of soil microorganisms in mine reclamation, particularly long-term studies that track the succession of microbial communities. Here, we investigate the trajectory of microbial communities of mining sites reclaimed between three and 26 years. We used high-throughput amplicon sequencing to characterize the bacterial and fungal communities. We quantified how similar the reclaimed sites were to unmined, undisturbed reference sites and explored the trajectory of microbial communities along the reclamation chronosequence. We also examined the ecological processes that shape the assembly of bacterial communities. Finally, we investigated the functional potential of the microbial communities through metagenomic sequencing. Our results reveal that the reclamation age significantly impacted the community compositions of bacterial and fungal communities. As the reclamation age increases, bacterial and fungal communities become similar to the unmined, undisturbed reference site, suggesting a favorable succession in microbial communities. The bacterial community assembly was also significantly impacted by reclamation age and was primarily driven by stochastic processes, indicating a lesser influence of environmental properties on the bacterial community. Furthermore, our read-based metagenomic analysis showed that the microbial communities' functional potential increasingly became similar to the reference sites. Additionally, we found that the plant richness increased with the reclamation age. Overall, our study shows that both above- and belowground ecological properties of reclaimed mine sites trend towards undisturbed sites with increasing reclamation age. Further, it demonstrates the importance of microbial genomics in tracking the trajectory of ecosystem reclamation.}, } @article {pmid38369119, year = {2024}, author = {McGovern, CJ and González-Orozco, BD and Jiménez-Flores, R}, title = {Evaluation of kefir grain microbiota, grain viability, and bioactivity from fermenting dairy processing by-products.}, journal = {Journal of dairy science}, volume = {107}, number = {7}, pages = {4259-4276}, doi = {10.3168/jds.2023-24364}, pmid = {38369119}, issn = {1525-3198}, mesh = {*Kefir/microbiology ; *Fermentation ; Animals ; Whey/chemistry ; Microbiota ; Humans ; Caco-2 Cells ; Antioxidants/pharmacology ; }, abstract = {Four dairy foods processing by-products (acid whey permeate [AWP], buttermilk [BM], sweet whey permeate [SWP], and sweet whey permeate with added milk fat globule ingredient [SWP+MFGM]) were fermented for 4 wk and compared with traditional kefir milks for production of novel kefir-like dairy products. Sweet whey permeates and SWP supplemented with 1.5% milk fat globule membrane (MFGM) proved to be the most viable by-products for kefir grain fermentation, exhibiting diverse abundance of traditional kefir microorganisms and positive indicators of bioactive properties. Grain viability was assessed with shotgun metagenomics, texture profile analysis, live cell counts, and scanning electron microscopy. Assessed bioactivities of the kefir-like products included antibacterial, antioxidant, potential anticancerogenic properties, and membrane barrier effects on human colorectal adenocarcinoma Caco-2 cells. All kefir grains were most abundant in Lactobacillus kefiranofaciens when analyzed with shotgun metagenomics. When analyzed with live cell counts on selective media, AWP kefir-like product had no countable Lactococcus spp., indicating suboptimal conditions for kefir grain microbiota survival and application for fermented dairy starter culture bacterium. Live cell counts were affirmed with kefir grain surface scanning electron microscopy images. The SWP treatment had the most adhesive kefir grain surface, and SWP+MFGM had the largest exopolysaccharide yield from grain extraction. All kefir and kefir-like products were able to achieve a 6-log reduction against Listeria innocua and Escherichia coli. Traditional milk kefirs had the highest antioxidant capacity for 2,2-diphenyl-1-picrylhydrazyl (DPPH) and the 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid; ABTS) assay. The AWP formulation had a significantly higher DPPH antioxidant activity compared with the other kefir and kefir-like products, and SWP had the lowest Trolox equivalence concentration in the ABTS assay. Sweet whey and supplemented milk fat sweet whey had upregulation of Cldn-1 and Ocln-1 gene expression, which correspond with a significant increase in transepithelial electrical resistance.}, } @article {pmid38368734, year = {2024}, author = {Deng, C and Chen, T and Qiu, Z and Zhou, H and Li, B and Zhang, Y and Xu, X and Lian, C and Qiao, X and Yu, K}, title = {A mixed blessing of influent leachate microbes in downstream biotreatment systems of a full-scale landfill leachate treatment plant.}, journal = {Water research}, volume = {253}, number = {}, pages = {121310}, doi = {10.1016/j.watres.2024.121310}, pmid = {38368734}, issn = {1879-2448}, mesh = {Humans ; *Water Pollutants, Chemical/analysis ; Sewage ; Metagenome ; *Microbiota ; }, abstract = {In landfill leachate treatment plants (LLTPs), the microbiome plays a pivotal role in the decomposition of organic compounds, reduction in nutrient levels, and elimination of toxins. However, the effects of microbes in landfill leachate influents on downstream treatment systems remain poorly understood. To address this knowledge gap, we collected 23 metagenomic and 12 metatranscriptomic samples from landfill leachate and activated sludge from various treatment units in a full-scale LLTP. We successfully recovered 1,152 non-redundant metagenome-assembled genomes (MAGs), encompassing a wide taxonomic range, including 48 phyla, 95 classes, 166 orders, 247 families, 238 genera, and 1,152 species. More diverse microbes were observed in the influent leachate than in the downstream biotreatment systems, among which, an unprecedented ∼30 % of microbes with transcriptional expression migrated from the influent to the biological treatment units. Network analysis revealed that 399 shared MAGs across the four units exhibited high node centrality and degree, thus supporting enhanced interactions and increased stability of microbial communities. Functional reconstruction and genome characterization of MAGs indicated that these shared MAGs possessed greater capabilities for carbon, nitrogen, sulfur, and arsenic metabolism compared to non-shared MAGs. We further identified a novel species of Zixibacteria in the leachate influent with discrete lineages from those in other environments that accounted for up to 17 % of the abundance of the shared microbial community and exhibited notable metabolic versatility. Meanwhile, we presented groundbreaking evidence of the involvement of Zixibacteria-encoded genes in the production of harmful gas emissions, such as N2O and H2S, at the transcriptional level, thus suggesting that influent microbes may pose safety risks to downstream treatment systems. In summary, this study revealed the complex impact of the influent microbiome on LLTP and emphasizes the need to consider these microbial characteristics when designing treatment technologies and strategies for landfill leachate management.}, } @article {pmid38368431, year = {2024}, author = {Laczkó, L and Jordán, S and Póliska, S and Rácz, HV and Nagy, NA and Molnár V, A and Sramkó, G}, title = {The draft genome of Spiraea crenata L. (Rosaceae) - the first complete genome in tribe Spiraeeae.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {219}, pmid = {38368431}, issn = {2052-4463}, mesh = {Genomics ; *Spiraea ; Whole Genome Sequencing ; *Genome, Plant ; }, abstract = {Spiraea crenata L. is a deciduous shrub distributed across the Eurasian steppe zone. The species is of cultural and horticultural importance and occurs in scattered populations throughout its westernmost range. Currently, there is no genomic information on the tribe of Spiraeeae. Therefore we sequenced and assembled the whole genome of S. crenata using second- and third-generation sequencing and a hybrid assembly approach to expand genomic resources for conservation and support research on this horticulturally important lineage. In addition to the organellar genomes (the plastome and the mitochondrion), we present the first draft genome of the species with an estimated size of 220 Mbp, an N50 value of 7.7 Mbp, and a BUSCO score of 96.0%. Being the first complete genome in tribe Spiraeeae, this may not only be the first step in the genomic study of a rare plant but also a contribution to genomic resources supporting the study of biodiversity and evolutionary history of Rosaceae.}, } @article {pmid38367621, year = {2024}, author = {Chen, Q and Wu, C and Xu, J and Ye, C and Chen, X and Tian, H and Zong, N and Zhang, S and Li, L and Gao, Y and Zhao, D and Lv, X and Yang, Q and Wang, L and Cui, J and Lin, Z and Lu, J and Yang, R and Yin, F and Qin, N and Li, N and Xu, Q and Qin, H}, title = {Donor-recipient intermicrobial interactions impact transfer of subspecies and fecal microbiota transplantation outcome.}, journal = {Cell host & microbe}, volume = {32}, number = {3}, pages = {349-365.e4}, doi = {10.1016/j.chom.2024.01.013}, pmid = {38367621}, issn = {1934-6069}, mesh = {Feces ; *Autism Spectrum Disorder ; East Asian People ; Humans ; Gastrointestinal Tract ; *Gastrointestinal Microbiome/genetics ; Treatment Outcome ; Clostridium Infections ; Fecal Microbiota Transplantation ; }, abstract = {Studies on fecal microbiota transplantation (FMT) have reported inconsistent connections between clinical outcomes and donor strain engraftment. Analyses of subspecies-level crosstalk and its influences on lineage transfer in metagenomic FMT datasets have proved challenging, as single-nucleotide polymorphisms (SNPs) are generally not linked and are often absent. Here, we utilized species genome bin (SGB), which employs co-abundance binning, to investigate subspecies-level microbiome dynamics in patients with autism spectrum disorder (ASD) who had gastrointestinal comorbidities and underwent encapsulated FMT (Chinese Clinical Trial: 2100043906). We found that interactions between donor and recipient microbes, which were overwhelmingly phylogenetically divergent, were important for subspecies transfer and positive clinical outcomes. Additionally, a donor-recipient SGB match was indicative of a high likelihood of strain transfer. Importantly, these ecodynamics were shared across FMT datasets encompassing multiple diseases. Collectively, these findings provide detailed insight into specific microbial interactions and dynamics that determine FMT success.}, } @article {pmid38367110, year = {2024}, author = {Yadav, R and Dharne, M}, title = {Utility of metagenomics for bioremediation: a comprehensive review on bioremediation mechanisms and microbial dynamics of river ecosystem.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {12}, pages = {18422-18434}, pmid = {38367110}, issn = {1614-7499}, mesh = {Biodegradation, Environmental ; Ecosystem ; Rivers ; *Microbiota ; *Environmental Pollutants/analysis ; Metagenome ; Metagenomics ; }, abstract = {Global industrialization has contributed substantial amounts of chemical pollutants in rivers, resulting in an uninhabitable state and impacting different life forms. Moreover, water macrophytes, such as water hyacinths, are abundantly present in polluted rivers, significantly affecting the overall water biogeochemistry. Bioremediation involves utilizing microbial metabolic machinery and is one of the most viable approaches for removing toxic pollutants. Conventional techniques generate limited information on the indigenous microbial population and their xenobiotic metabolism, failing the bioremediation process. Metagenomics can overcome these limitations by providing in-depth details of microbial taxa and functionality-related information required for successful biostimulation and augmentation. An in-depth summary of the findings related to pollutant metabolizing genes and enzymes in rivers still needs to be collated. The present study details bioremediation genes and enzymes functionally mined from polluted river ecosystems worldwide using a metagenomic approach. Several studies reported a wide variety of pollutant-degrading enzymes involved in the metabolism of dyes, plastics, persistent organic pollutants, and aromatic hydrocarbons. Additionally, few studies also noted a shift in the microbiome of the rivers upon exposure to contaminants, crucially affecting the ecological determinant processes. Furthermore, minimal studies have focused on the role of water-hyacinth-associated microbes in the bioremediation potentials, suggesting the need for the bioprospecting of these lesser-studied microbes. Overall, our study summarizes the prospects and utilities of the metagenomic approach and proposes the need to employ it for efficient bioremediation.}, } @article {pmid38367105, year = {2024}, author = {Domínguez-Maldonado, JA and Solís-Pereira, SE and Valle-Gough, RE and Álvarez, AAM and Olguín-Maciel, E and Alzate-Gaviria, L and Tapia-Tussell, R}, title = {Microbial communities present in Sargassum spp. leachates from the Mexican Caribbean which are involved in their degradation in the environment, a tool to tackle the problem.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {13}, pages = {19904-19916}, pmid = {38367105}, issn = {1614-7499}, support = {305292.//Consejo Nacional de Ciencia y Tecnología/ ; }, mesh = {*Sargassum ; Caribbean Region ; *Microbiota ; Bacteria, Anaerobic ; Mexico ; }, abstract = {The Sargassum phenomenon is currently affecting the Caribbean in several ways; one of them is the increase of greenhouse gases due to the decomposition process of this macroalgae; these processes also produce large amounts of pollutant leachates, in which several microbial communities are involved. To understand these processes, we conducted a 150-day study on the Sargassum spp environmental degradation under outdoor conditions, during which leachates were collected at 0, 30, 90, and 150 days. Subsequently, a metagenomic study of the microorganisms found in the leachates was carried out, in which changes in the microbial community were observed over time. The results showed that anaerobic bacterial genera such as Thermofilum and Methanopyrus were predominant at the beginning of this study (0 and 30 days), degrading sugars of sulfur polymers such as fucoidan, but throughout the experiment, the microbial communities were changed also, with the genera Fischerella and Dolichospermum being the most predominant at days 90 and 150, respectively. A principal component analysis (PCA) indicated, with 94% variance, that genera were positively correlated at 30 and 90 days, but not with initial populations, indicating changes in community structure due to sargassum degradation were present. Finally, at 150 days, the leachate volume decreased by almost 50% and there was a higher abundance of the genera Desulfobacter and Dolichospemum. This is the first work carried out to understand the degradation of Sargassum spp, which will serve, together with other works, to understand and provide a solution to this serious environmental problem in the Caribbean.}, } @article {pmid38366600, year = {2024}, author = {Huang, KD and Amend, L and Gálvez, EJC and Lesker, TR and de Oliveira, R and Bielecka, A and Blanco-Míguez, A and Valles-Colomer, M and Ruf, I and Pasolli, E and Buer, J and Segata, N and Esser, S and Strowig, T and Kehrmann, J}, title = {Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices.}, journal = {Cell reports. Medicine}, volume = {5}, number = {3}, pages = {101426}, pmid = {38366600}, issn = {2666-3791}, mesh = {Male ; Humans ; *Gastrointestinal Microbiome ; Homosexuality, Male ; *Sexual and Gender Minorities ; Sexual Behavior ; *Microbiota ; }, abstract = {The human gut microbiota is influenced by various factors, including health status and environmental conditions, yet considerable inter-individual differences remain unexplained. Previous studies identified that the gut microbiota of men who have sex with men (MSM) is distinct from that of non-MSM. Here, we reveal through species-level microbiota analysis using shotgun metagenomics that the gut microbiota of many MSM with Western origin resembles gut microbial communities of non-Westernized populations. Specifically, MSM gut microbiomes are frequently dominated by members of the Prevotellaceae family, including co-colonization of species from the Segatella copri complex and unknown Prevotellaceae members. Questionnaire-based analysis exploring inter-individual differences in MSM links specific sexual practices to microbiota composition. Moreover, machine learning identifies microbial features associated with sexual activities in MSM. Together, this study shows associations of sexual activities with gut microbiome alterations in MSM, which may have a large impact on population-based microbiota studies.}, } @article {pmid38366262, year = {2024}, author = {Wang, J and Zhu, YG and Tiedje, JM and Ge, Y}, title = {Global biogeography and ecological implications of cobamide-producing prokaryotes.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38366262}, issn = {1751-7370}, support = {42307162//National Natural Science Foundation of China/ ; 2019QZKK0308//Second Tibetan Plateau Scientific Expedition and Research Program/ ; DBI-1759892//US National Science Foundation/ ; //Institute for Cyber-Enabled Research at Michigan State University/ ; }, mesh = {*Cobamides ; Metagenome ; *Microbiota ; Soil ; }, abstract = {Cobamides, a class of essential coenzymes synthesized only by a subset of prokaryotes, are model nutrients in microbial interaction studies and play significant roles in global ecosystems. Yet, their spatial patterns and functional roles remain poorly understood. Herein, we present an in-depth examination of cobamide-producing microorganisms, drawn from a comprehensive analysis of 2862 marine and 2979 soil metagenomic samples. A total of 1934 nonredundant metagenome-assembled genomes (MAGs) potentially capable of producing cobamides de novo were identified. The cobamide-producing MAGs are taxonomically diverse but habitat specific. They constituted only a fraction of all the recovered MAGs, with the majority of MAGs being potential cobamide users. By mapping the distribution of cobamide producers in marine and soil environments, distinct latitudinal gradients were observed: the marine environment showed peak abundance at the equator, whereas soil environments peaked at mid-latitudes. Importantly, significant and positive links between the abundance of cobamide producers and the diversity and functions of microbial communities were observed, as well as their promotional roles in essential biogeochemical cycles. These associations were more pronounced in marine samples than in soil samples, which suggests a heightened propensity for microorganisms to engage in cobamide sharing in fluid environments relative to the more spatially restricted soil environment. These findings shed light on the global patterns and potential ecological roles of cobamide-producing microorganisms in marine and soil ecosystems, enhancing our understanding of large-scale microbial interactions.}, } @article {pmid38366194, year = {2024}, author = {Hu, J and Chen, J and Ma, L and Hou, Q and Zhang, Y and Kong, X and Huang, X and Tang, Z and Wei, H and Wang, X and Yan, X}, title = {Characterizing core microbiota and regulatory functions of the pig gut microbiome.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38366194}, issn = {1751-7370}, support = {31925037//National Natural Science Foundation of China/ ; 2021hszd018//Hubei Hongshan Laboratory/ ; 2662023DKPY002//Fundamental Research Funds for the Central Universities/ ; 32102499//National Natural Science Foundation of China/ ; BX20190133//National Postdoctoral Program for Innovative Talents/ ; 2019 M662671//Postdoctoral Science Foundation of China/ ; 2022CFB358//Natural Science Foundation of Hubei Province/ ; //Hubei Provincial Postdoctoral Innovative Post Project of China/ ; }, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Gastrointestinal Tract ; Metagenomics ; Phenylalanine ; }, abstract = {Domestic pigs (Sus scrofa) are the leading terrestrial animals used for meat production. The gut microbiota significantly affect host nutrition, metabolism, and immunity. Hence, characterization of the gut microbial structure and function will improve our understanding of gut microbial resources and the mechanisms underlying host-microbe interactions. Here, we investigated the gut microbiomes of seven pig breeds using metagenomics and 16S rRNA gene amplicon sequencing. We established an expanded gut microbial reference catalog comprising 17 020 160 genes and identified 4910 metagenome-assembled genomes. We also analyzed the gut resistome to provide an overview of the profiles of the antimicrobial resistance genes in pigs. By analyzing the relative abundances of microbes, we identified three core-predominant gut microbes (Phascolarctobacterium succinatutens, Prevotella copri, and Oscillibacter valericigenes) in pigs used in this study. Oral administration of the three core-predominant gut microbes significantly increased the organ indexes (including the heart, spleen, and thymus), but decreased the gastrointestinal lengths in germ-free mice. The three core microbes significantly enhanced intestinal epithelial barrier function and altered the intestinal mucosal morphology, as was evident from the increase in crypt depths in the duodenum and ileum. Furthermore, the three core microbes significantly affected several metabolic pathways (such as "steroid hormone biosynthesis," "primary bile acid biosynthesis," "phenylalanine, tyrosine and tryptophan biosynthesis," and "phenylalanine metabolism") in germ-free mice. These findings provide a panoramic view of the pig gut microbiome and insights into the functional contributions of the core-predominant gut microbes to the host.}, } @article {pmid38366085, year = {2024}, author = {Fernández-Pato, A and Sinha, T and Gacesa, R and Andreu-Sánchez, S and Gois, MFB and Gelderloos-Arends, J and Jansen, DBH and Kruk, M and Jaeger, M and Joosten, LAB and Netea, MG and Weersma, RK and Wijmenga, C and Harmsen, HJM and Fu, J and Zhernakova, A and Kurilshikov, A}, title = {Choice of DNA extraction method affects stool microbiome recovery and subsequent phenotypic association analyses.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {3911}, pmid = {38366085}, issn = {2045-2322}, support = {LSHM18057-SGF//TIMID project/ ; 2018-27//Netherlands Heart Foundation CVON grant/ ; 16-14//Seerave Foundation and the Dutch Digestive Foundation/ ; 024.003.001//NWO Gravitation grant Netherlands Organ-on-Chip Initiative/ ; SPI 92-266//NWO Spinoza Prize/ ; 101001678//ERC Consolidator grant/ ; VI.C.202.022//NWO VICI grant/ ; 715772//European Research Council (ERC) Starting Grant/ ; 016.178.056//Netherlands Organization for Scientific Research (NWO) VIDI grant/ ; 024.004.017//NWO Gravitation grant ExposomeNL/ ; 101094099//EU Horizon Europe Program grant INITIALISE/ ; }, mesh = {Humans ; DNA, Bacterial/genetics/analysis ; RNA, Ribosomal, 16S/genetics ; DNA ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Sequence Analysis, DNA ; Feces/microbiology ; Metagenomics/methods ; }, abstract = {The lack of standardization in the methods of DNA extraction from fecal samples represents the major source of experimental variation in the microbiome research field. In this study, we aimed to compare the metagenomic profiles and microbiome-phenotype associations obtained by applying two commercially available DNA extraction kits: the AllPrep DNA/RNA Mini Kit (APK) and the QIAamp Fast DNA Stool Mini Kit (FSK). Using metagenomic sequencing data available from 745 paired fecal samples from two independent population cohorts, Lifelines-DEEP (LLD, n = 292) and the 500 Functional Genomics project (500FG, n = 453), we confirmed significant differences in DNA yield and the recovered microbial communities between protocols, with the APK method resulting in a higher DNA concentration and microbial diversity. Further, we observed a massive difference in bacterial relative abundances at species-level between the APK and the FSK protocols, with > 75% of species differentially abundant between protocols in both cohorts. Specifically, comparison with a standard mock community revealed that the APK method provided higher accuracy in the recovery of microbial relative abundances, with the absence of a bead-beating step in the FSK protocol causing an underrepresentation of gram-positive bacteria. This heterogeneity in the recovered microbial composition led to remarkable differences in the association with anthropometric and lifestyle phenotypes. The results of this study further reinforce that the choice of DNA extraction method impacts the metagenomic profile of human gut microbiota and highlight the importance of harmonizing protocols in microbiome studies.}, } @article {pmid38365827, year = {2024}, author = {Bosch, ME and Dodiya, HB and Michalkiewicz, J and Lee, C and Shaik, SM and Weigle, IQ and Zhang, C and Osborn, J and Nambiar, A and Patel, P and Parhizkar, S and Zhang, X and Laury, ML and Mondal, P and Gomm, A and Schipma, MJ and Mallah, D and Butovsky, O and Chang, EB and Tanzi, RE and Gilbert, JA and Holtzman, DM and Sisodia, SS}, title = {Sodium oligomannate alters gut microbiota, reduces cerebral amyloidosis and reactive microglia in a sex-specific manner.}, journal = {Molecular neurodegeneration}, volume = {19}, number = {1}, pages = {18}, pmid = {38365827}, issn = {1750-1326}, support = {P30 CA091842/CA/NCI NIH HHS/United States ; P30 DK042086/DK/NIDDK NIH HHS/United States ; UL1 TR002345/TR/NCATS NIH HHS/United States ; T32AG05851804/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Mice ; Male ; Female ; Animals ; *Alzheimer Disease/metabolism ; *Gastrointestinal Microbiome ; Microglia/metabolism ; Mice, Transgenic ; *Amyloidosis/metabolism ; Amyloid beta-Peptides/metabolism ; Plaque, Amyloid/pathology ; Amyloid/metabolism ; Amyloidogenic Proteins/metabolism ; Disease Models, Animal ; }, abstract = {It has recently become well-established that there is a connection between Alzheimer's disease pathology and gut microbiome dysbiosis. We have previously demonstrated that antibiotic-mediated gut microbiota perturbations lead to attenuation of Aβ deposition, phosphorylated tau accumulation, and disease-associated glial cell phenotypes in a sex-dependent manner. In this regard, we were intrigued by the finding that a marine-derived oligosaccharide, GV-971, was reported to alter gut microbiota and reduce Aβ amyloidosis in the 5XFAD mouse model that were treated at a point when Aβ burden was near plateau levels. Utilizing comparable methodologies, but with distinct technical and temporal features, we now report on the impact of GV-971 on gut microbiota, Aβ amyloidosis and microglial phenotypes in the APPPS1-21 model, studies performed at the University of Chicago, and independently in the 5X FAD model, studies performed at Washington University, St. Louis.Methods To comprehensively characterize the effects of GV-971 on the microbiota-microglia-amyloid axis, we conducted two separate investigations at independent institutions. There was no coordination of the experimental design or execution between the two laboratories. Indeed, the two laboratories were not aware of each other's experiments until the studies were completed. Male and female APPPS1-21 mice were treated daily with 40, 80, or 160 mg/kg of GV-971 from 8, when Aβ burden was detectable upto 12 weeks of age when Aβ burden was near maximal levels. In parallel, and to corroborate existing published studies and further investigate sex-related differences, male and female 5XFAD mice were treated daily with 100 mg/kg of GV-971 from 7 to 9 months of age when Aβ burden was near peak levels. Subsequently, the two laboratories independently assessed amyloid-β deposition, metagenomic, and neuroinflammatory profiles. Finally, studies were initiated at the University of Chicago to evaluate the metabolites in cecal tissue from vehicle and GV-971-treated 5XFAD mice.Results These studies showed that independent of the procedural differences (dosage, timing and duration of treatment) between the two laboratories, cerebral amyloidosis was reduced primarily in male mice, independent of strain. We also observed sex-specific microbiota differences following GV-971 treatment. Interestingly, GV-971 significantly altered multiple overlapping bacterial species at both institutions. Moreover, we discovered that GV-971 significantly impacted microbiome metabolism, particularly by elevating amino acid production and influencing the tryptophan pathway. The metagenomics and metabolomics changes correspond with notable reductions in peripheral pro-inflammatory cytokine and chemokine profiles. Furthermore, GV-971 treatment dampened astrocyte and microglia activation, significantly decreasing plaque-associated reactive microglia while concurrently increasing homeostatic microglia only in male mice. Bulk RNAseq analysis unveiled sex-specific changes in cerebral cortex transcriptome profiles, but most importantly, the transcriptome changes in the GV-971-treated male group revealed the involvement of microglia and inflammatory responses.Conclusions In conclusion, these studies demonstrate the connection between the gut microbiome, neuroinflammation, and Alzheimer's disease pathology while highlighting the potential therapeutic effect of GV-971. GV-971 targets the microbiota-microglia-amyloid axis, leading to the lowering of plaque pathology and neuroinflammatory signatures in a sex-dependent manner when given at the onset of Aβ deposition or when given after Aβ deposition is already at higher levels.}, } @article {pmid38365793, year = {2024}, author = {Cheng, M and Luo, S and Zhang, P and Xiong, G and Chen, K and Jiang, C and Yang, F and Huang, H and Yang, P and Liu, G and Zhang, Y and Ba, S and Yin, P and Xiong, J and Miao, W and Ning, K}, title = {A genome and gene catalog of the aquatic microbiomes of the Tibetan Plateau.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1438}, pmid = {38365793}, issn = {2041-1723}, mesh = {Humans ; Tibet ; *Microbiota/genetics ; Lakes ; Rivers ; Water ; }, abstract = {The Tibetan Plateau supplies water to nearly 2 billion people in Asia, but climate change poses threats to its aquatic microbial resources. Here, we construct the Tibetan Plateau Microbial Catalog by sequencing 498 metagenomes from six water ecosystems (saline lakes, freshwater lakes, rivers, hot springs, wetlands and glaciers). Our catalog expands knowledge of regional genomic diversity by presenting 32,355 metagenome-assembled genomes that de-replicated into 10,723 representative genome-based species, of which 88% were unannotated. The catalog contains nearly 300 million non-redundant gene clusters, of which 15% novel, and 73,864 biosynthetic gene clusters, of which 50% novel, thus expanding known functional diversity. Using these data, we investigate the Tibetan Plateau aquatic microbiome's biogeography along a distance of 2,500 km and >5 km in altitude. Microbial compositional similarity and the shared gene count with the Tibetan Plateau microbiome decline along with distance and altitude difference, suggesting a dispersal pattern. The Tibetan Plateau Microbial Catalog stands as a substantial repository for high-altitude aquatic microbiome resources, providing potential for discovering novel lineages and functions, and bridging knowledge gaps in microbiome biogeography.}, } @article {pmid38365259, year = {2024}, author = {Jiao, J and Wu, J and Zhou, C and He, Z and Tan, Z and Wang, M}, title = {Ecological niches and assembly dynamics of diverse microbial consortia in the gastrointestine of goat kids.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365259}, issn = {1751-7370}, support = {31972992//National Natural Science Foundation of China/ ; 161343KYSB20200015//International Partnership Program of Chinese Academy of Sciences/ ; 2023JJ10047//Hunan Provincial Natural Science Foundation of China/ ; U22A20512//National Natural Science Foundation of China/ ; 2023382//Youth Innovation Promotion Association CAS/ ; }, mesh = {Animals ; *Goats ; *Microbial Consortia ; Bacteria ; Ruminants ; Carbohydrates ; }, abstract = {Goats are globally invaluable ruminants that balance food security and environmental impacts, and their commensal microbiome residing in the gastrointestinal tract (GIT) is associated with animal health and productivity. However, the reference genomes and functional repertoires of GIT microbes in goat kids have not been fully elucidated. Herein, we performed a comprehensive landscape survey of the GIT microbiome of goat kids using metagenomic sequencing and binning, spanning a dense sampling regime covering three gastrointestinal compartments spatially and five developmental ages temporally. We recovered 1002 high-quality metagenome-assembled genomes (termed the goat kid GIT microbial catalog [GKGMC]), 618 of which were novel. They encode more than 2.3 million nonredundant proteins, and represent a variety of carbohydrate-degrading enzymes and metabolic gene clusters. The GKGMC-enriched microbial taxa, particularly Sodaliphilus, expanded the microbial tree of life in goat kids. Using this GKGMC, we first deciphered the prevalence of fiber-degrading bacteria for carbohydrate decomposition in the rumen and colon, while the ileal microbiota specialized in the uptake and conversion of simple sugars. Moreover, GIT microorganisms were rapidly assembled after birth, and their carbohydrate metabolic adaptation occurred in three phases of progression. Finally, phytobiotics modified the metabolic cascades of the ileal microbiome, underpinned by the enrichment of Sharpea azabuensis and Olsenella spp. implicated in lactate formation and utilization. This GKGMC reference provides novel insights into the early-life microbial developmental dynamics in distinct compartments, and offers expanded resources for GIT microbiota-related research in goat kids.}, } @article {pmid38365257, year = {2024}, author = {Dong, Q and Hua, D and Wang, X and Jiao, Y and Liu, L and Deng, Q and Wu, T and Zou, H and Zhao, C and Wang, C and Reng, J and Ding, L and Hu, S and Shi, J and Wang, Y and Zhang, H and Sheng, Y and Sun, W and Shen, Y and Tang, L and Kong, X and Chen, L}, title = {Temporal colonization and metabolic regulation of the gut microbiome in neonatal oxen at single nucleotide resolution.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365257}, issn = {1751-7370}, support = {32394052//National Natural Science Foundation of China/ ; JSSCBS20221815//Jiangsu Shuangchuang Project/ ; BK20220709//Natural Science Foundation of Jiangsu/ ; C2022204247//Natural Science Foundation of Hebei/ ; CMCM202204//Nanjing Medical University/ ; //Development of Jiangsu Higher Education Institutions Priority Academic Program/ ; }, mesh = {Infant, Newborn ; Humans ; Female ; *Gastrointestinal Microbiome/physiology ; Nucleotides ; Levodopa ; *Microbiota ; Feces ; Metagenomics/methods ; }, abstract = {The colonization of microbes in the gut is key to establishing a healthy host-microbiome symbiosis for newborns. We longitudinally profiled the gut microbiome in a model consisting of 36 neonatal oxen from birth up to 2 months postpartum and carried out microbial transplantation to reshape their gut microbiome. Genomic reconstruction of deeply sequenced fecal samples resulted in a total of 3931 metagenomic-assembled genomes from 472 representative species, of which 184 were identified as new species when compared with existing databases of oxen. Single nucleotide level metagenomic profiling shows a rapid influx of microbes after birth, followed by dynamic shifts during the first few weeks of life. Microbial transplantation was found to reshape the genetic makeup of 33 metagenomic-assembled genomes (FDR < 0.05), mainly from Prevotella and Bacteroides species. We further linked over 20 million microbial single nucleotide variations to 736 plasma metabolites, which enabled us to characterize 24 study-wide significant associations (P < 4.4 × 10-9) that identify the potential microbial genetic regulation of host immune and neuro-related metabolites, including glutathione and L-dopa. Our integration analyses further revealed that microbial genetic variations may influence the health status and growth performance by modulating metabolites via structural regulation of their encoded proteins. For instance, we found that the albumin levels and total antioxidant capacity were correlated with L-dopa, which was determined by single nucleotide variations via structural regulations of metabolic enzymes. The current results indicate that temporal colonization and transplantation-driven strain replacement are crucial for newborn gut development, offering insights for enhancing newborn health and growth.}, } @article {pmid38365241, year = {2024}, author = {Luo, ZH and Li, Q and Xie, YG and Lv, AP and Qi, YL and Li, MM and Qu, YN and Liu, ZT and Li, YX and Rao, YZ and Jiao, JY and Liu, L and Narsing Rao, MP and Hedlund, BP and Evans, PN and Fang, Y and Shu, WS and Huang, LN and Li, WJ and Hua, ZS}, title = {Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365241}, issn = {1751-7370}, support = {32300001//National Natural Science Foundation of China/ ; 2021A1515012468//National Science Foundation of Guangdong Province/ ; 2021M703757//China Postdoctoral Science Foundation/ ; }, mesh = {*Ammonia/metabolism ; Temperature ; *Archaea/genetics/metabolism ; Oxidation-Reduction ; Nitrogen/metabolism ; Sulfur/metabolism ; Hydrogen-Ion Concentration ; Phylogeny ; }, abstract = {Ammonia-oxidizing Nitrososphaeria are among the most abundant archaea on Earth and have profound impacts on the biogeochemical cycles of carbon and nitrogen. In contrast to these well-studied ammonia-oxidizing archaea (AOA), deep-branching non-AOA within this class remain poorly characterized because of a low number of genome representatives. Here, we reconstructed 128 Nitrososphaeria metagenome-assembled genomes from acid mine drainage and hot spring sediment metagenomes. Comparative genomics revealed that extant non-AOA are functionally diverse, with capacity for carbon fixation, carbon monoxide oxidation, methanogenesis, and respiratory pathways including oxygen, nitrate, sulfur, or sulfate, as potential terminal electron acceptors. Despite their diverse anaerobic pathways, evolutionary history inference suggested that the common ancestor of Nitrososphaeria was likely an aerobic thermophile. We further surmise that the functional differentiation of Nitrososphaeria was primarily shaped by oxygen, pH, and temperature, with the acquisition of pathways for carbon, nitrogen, and sulfur metabolism. Our study provides a more holistic and less biased understanding of the diversity, ecology, and deep evolution of the globally abundant Nitrososphaeria.}, } @article {pmid38365235, year = {2024}, author = {Zhu, W and Chang, L and Shi, S and Lu, N and Du, S and Li, J and Jiang, J and Wang, B}, title = {Gut microbiota reflect adaptation of cave-dwelling tadpoles to resource scarcity.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365235}, issn = {1751-7370}, support = {2019QZKK05010203//Second Tibetan Plateau Scientific Expedition and Research Program/ ; 31900327//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome ; Larva ; Caves ; }, abstract = {Gut microbiota are significant to the host's nutrition and provide a flexible way for the host to adapt to extreme environments. However, whether gut microbiota help the host to colonize caves, a resource-limited environment, remains unknown. The nonobligate cave frog Oreolalax rhodostigmatus completes its metamorphosis within caves for 3-5 years before foraging outside. Their tadpoles are occasionally removed from the caves by floods and utilize outside resources, providing a contrast to the cave-dwelling population. For both cave and outside tadpoles, the development-related reduction in their growth rate and gut length during prometamorphosis coincided with a shift in their gut microbiota, which was characterized by decreased Lactobacillus and Cellulosilyticum and Proteocatella in the cave and outside individuals, respectively. The proportion of these three genera was significantly higher in the gut microbiota of cave-dwelling individuals compared with those outside. The cave-dwellers' gut microbiota harbored more abundant fibrolytic, glycolytic, and fermentative enzymes and yielded more short-chain fatty acids, potentially benefitting the host's nutrition. Experimentally depriving the animals of food resulted in gut atrophy for the individuals collected outside the cave, but not for those from inside the cave. Imitating food scarcity reproduced some major microbial features (e.g. abundant Proteocatella and fermentative genes) of the field-collected cave individuals, indicating an association between the cave-associated gut microbiota and resource scarcity. Overall, the gut microbiota may reflect the adaptation of O. rhodostigmatus tadpoles to resource-limited environments. This extends our understanding of the role of gut microbiota in the adaptation of animals to extreme environments.}, } @article {pmid38365233, year = {2024}, author = {Stephens, BM and Durkin, CA and Sharpe, G and Nguyen, TTH and Albers, J and Estapa, ML and Steinberg, DK and Levine, NM and Gifford, SM and Carlson, CA and Boyd, PW and Santoro, AE}, title = {Direct observations of microbial community succession on sinking marine particles.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365233}, issn = {1751-7370}, support = {80NSSC17K0662/NASA/NASA/United States ; }, mesh = {*Seawater ; *Microbiota ; Carbon ; Carbon Sequestration ; }, abstract = {Microbial community dynamics on sinking particles control the amount of carbon that reaches the deep ocean and the length of time that carbon is stored, with potentially profound impacts on Earth's climate. A mechanistic understanding of the controls on sinking particle distributions has been hindered by limited depth- and time-resolved sampling and methods that cannot distinguish individual particles. Here, we analyze microbial communities on nearly 400 individual sinking particles in conjunction with more conventional composite particle samples to determine how particle colonization and community assembly might control carbon sequestration in the deep ocean. We observed community succession with corresponding changes in microbial metabolic potential on the larger sinking particles transporting a significant fraction of carbon to the deep sea. Microbial community richness decreased as particles aged and sank; however, richness increased with particle size and the attenuation of carbon export. This suggests that the theory of island biogeography applies to sinking marine particles. Changes in POC flux attenuation with time and microbial community composition with depth were reproduced in a mechanistic ecosystem model that reflected a range of POC labilities and microbial growth rates. Our results highlight microbial community dynamics and processes on individual sinking particles, the isolation of which is necessary to improve mechanistic models of ocean carbon uptake.}, } @article {pmid38365229, year = {2024}, author = {Miksch, S and Orellana, LH and Oggerin de Orube, M and Vidal-Melgosa, S and Solanki, V and Hehemann, JH and Amann, R and Knittel, K}, title = {Taxonomic and functional stability overrules seasonality in polar benthic microbiomes.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365229}, issn = {1751-7370}, support = {//Max Planck Society/ ; //MARUM Center for Marine Environmental Science/ ; //Andreas Rühl foundation/ ; 2077//DFG Exzellenzcluster/ ; HE 7217/5-1//DFG Heisenberg program/ ; HE 7217/1-1//DFG Emmy Noether program/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; Bacteria/genetics ; *Microbiota ; Glucose ; Geologic Sediments/microbiology ; }, abstract = {Coastal shelf sediments are hot spots of organic matter mineralization. They receive up to 50% of primary production, which, in higher latitudes, is strongly seasonal. Polar and temperate benthic bacterial communities, however, show a stable composition based on comparative 16S rRNA gene sequencing despite different microbial activity levels. Here, we aimed to resolve this contradiction by identifying seasonal changes at the functional level, in particular with respect to algal polysaccharide degradation genes, by combining metagenomics, metatranscriptomics, and glycan analysis in sandy surface sediments from Isfjorden, Svalbard. Gene expressions of diverse carbohydrate-active enzymes changed between winter and spring. For example, β-1,3-glucosidases (e.g. GH30, GH17, GH16) degrading laminarin, an energy storage molecule of algae, were elevated in spring, while enzymes related to α-glucan degradation were expressed in both seasons with maxima in winter (e.g. GH63, GH13_18, and GH15). Also, the expression of GH23 involved in peptidoglycan degradation was prevalent, which is in line with recycling of bacterial biomass. Sugar extractions from bulk sediments were low in concentrations during winter but higher in spring samples, with glucose constituting the largest fraction of measured monosaccharides (84% ± 14%). In porewater, glycan concentrations were ~18-fold higher than in overlying seawater (1107 ± 484 vs. 62 ± 101 μg C l-1) and were depleted in glucose. Our data indicate that microbial communities in sandy sediments digest and transform labile parts of photosynthesis-derived particulate organic matter and likely release more stable, glucose-depleted residual glycans of unknown structures, quantities, and residence times into the ocean, thus modulating the glycan composition of marine coastal waters.}, } @article {pmid38363349, year = {2024}, author = {Yang, W and Cui, H and Liu, Q and Wang, F and Liao, H and Lu, P and Qin, S}, title = {Effect of nitrogen reduction by chemical fertilization with green manure (Vicia sativa L.) on soil microbial community, nitrogen metabolism and and yield of Uncaria rhynchophylla by metagenomics.}, journal = {Archives of microbiology}, volume = {206}, number = {3}, pages = {106}, pmid = {38363349}, issn = {1432-072X}, support = {[2020]4Y100 and [2018]5768-06//Department of Science and Technology of Guizhou Province and Guizhou Academy of Agricultural Sciences/ ; CARS-22//China Agriculture Research System-Green Manure/ ; }, mesh = {Soil ; Agriculture/methods ; Manure ; Fertilizers/analysis ; *Vicia sativa ; Nitrogen/metabolism ; Urease ; *Microbiota/genetics ; Soil Microbiology ; Fertilization ; *Uncaria ; }, abstract = {Uncaria rhynchophylla is an important herbal medicine, and the predominant issues affecting its cultivation include a single method of fertilizer application and inappropriate chemical fertilizer application. To reduce the use of inorganic nitrogen fertilization and increase the yield of Uncaria rhynchophylla, field experiments in 2020-2021 were conducted. The experimental treatments included the following categories: S1, no fertilization; S2, application of chemical NPK fertilizer; and S3-S6, application of chemical fertilizers and green manures, featuring nitrogen fertilizers reductions of 0%, 15%, 30%, and 45%, respectively. The results showed that a moderate application of nitrogen fertilizer when combined with green manure, can help alleviate soil acidification and increase urease activity. Specifically, the treatment with green manure provided in a 14.71-66.67% increase in urease activity compared to S2. Metagenomics sequencing results showed a decrease in diversity in S3, S4, S5, and S6 compared to S2, but the application of chemical fertilizer with green manure promoted an increase in the relative abundance of Acidobacteria and Chloroflexi. In addition, the nitrification pathway displayed a progressive augmentation in tandem with the reduction in nitrogen fertilizer and application of green manure, reaching its zenith at S5. Conversely, other nitrogen metabolism pathways showed a decline in correlation with diminishing nitrogen fertilizer dosages. The rest of the treatments showed an increase in yield in comparison to S1, S5 showing significant differences (p < 0.05). In summary, although S2 demonstrate the ability to enhance soil microbial diversity, it is important to consider the long-term ecological impacts, and S5 may be a better choice.}, } @article {pmid38359904, year = {2024}, author = {Parvin, N and Mandal, S and Rath, J}, title = {Microbiome of seventh-century old Parsurameswara stone monument of India and role of desiccation-tolerant cyanobacterium Lyngbya corticicola on its biodeterioration.}, journal = {Biofouling}, volume = {40}, number = {1}, pages = {40-53}, doi = {10.1080/08927014.2024.2305381}, pmid = {38359904}, issn = {1029-2454}, mesh = {Lyngbya ; Desiccation ; Biofilms ; *Cyanobacteria/genetics ; *Microbiota/genetics ; Carotenoids/analysis/metabolism ; }, abstract = {The Parsurameswara stone monument, built in the seventh century, is one of the oldest stone monuments in Odisha, India. Metagenomic analysis of the biological crust samples collected from the stone monument revealed 17 phyla in the microbiome, with Proteobacteria being the most dominant phylum, followed by cyanobacteria. Eight cyanobacteria were isolated. Lyngbya corticicola was the dominant cyanobacterium in all crust samples and could tolerate six months of desiccation in vitro. With six months of desiccation, chlorophyll-a decreased; however, carotenoid and cellular carbohydrate contents of this organism increased in the desiccated state. Resistance to desiccation, high carotenoid content, and effective trehalose biosynthesis in this cyanobacterium provide a distinct advantage over other microbiomes. Comparative metabolic profiles of the biological crust and L. corticicola show strongly corrosive organic acids such as dichloroacetic acid, which might be responsible for the biocorrosion of stone monuments.}, } @article {pmid38359595, year = {2024}, author = {Cha, G and Zhu, KJ and Fischer, JM and Flores, CI and Brown, J and Pinto, A and Hatt, JK and Konstantinidis, KT and Graham, KE}, title = {Metagenomic evaluation of the performance of passive Moore swabs for sewage monitoring relative to composite sampling over time resolved deployments.}, journal = {Water research}, volume = {253}, number = {}, pages = {121269}, doi = {10.1016/j.watres.2024.121269}, pmid = {38359595}, issn = {1879-2448}, mesh = {Humans ; Pandemics ; Sewage ; Metagenome ; *Microbiota ; *COVID-19 ; }, abstract = {Moore swabs have re-emerged as a versatile tool in the field of wastewater-based epidemiology during the COVID-19 pandemic and offer unique advantages for monitoring pathogens in sewer systems, especially at the neighborhood-level. However, whether Moore swabs provide comparable results to more commonly used composite samples remains to be rigorously tested including the optimal duration of Moore swab deployment. This study provides new insights into these issues by comparing the results from Moore swab samples to those of paired composite samples collected from the same sewer lines continuously over six to seventy-two hours post-deployment, during low COVID-19 prevalence periods. Our results show that Moore swabs accumulated approximately 10-fold higher PMMoV concentrations (on a basis of mL of Moore swab squeezed filtrate to mL of composite sewage) and showed comparable trends in terms of bacterial species abundance when compared to composite samples. Moore swabs also generally captured higher SARS-CoV-2 N1/N2 RNA concentrations than composite samples. Moore swabs showed comparable trends in terms of abundance dynamics of the sewage microbiome to composite samples and variable signs of saturation over time that were site and/or microbial population-specific. Based on our dual ddRT-PCR and shotgun metagenomic approach, we find that Moore swabs at our sites were optimally deployed for 6 h at a time at two sites.}, } @article {pmid38359370, year = {2024}, author = {Nguyen, SM and Tran, HTT and Long, J and Shrubsole, MJ and Cai, H and Yang, Y and Nguyen, LM and Nguyen, GH and Nguyen, CV and Ta, TV and Wu, J and Cai, Q and Zheng, W and Tran, TV and Shu, XO}, title = {Gut Microbiome of Patients With Breast Cancer in Vietnam.}, journal = {JCO global oncology}, volume = {10}, number = {}, pages = {e2300234}, pmid = {38359370}, issn = {2687-8941}, support = {D43 TW009337/TW/FIC NIH HHS/United States ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Vietnam/epidemiology ; *Breast Neoplasms ; Feces/microbiology ; Metagenome ; }, abstract = {PURPOSE: Gut microbiota play an important role in human health, including cancer. Cancer and its treatment, in turn, may alter the gut microbiome. To understand this complex relationship, we profiled the gut microbiome of 356 Vietnamese patients with breast cancer.

MATERIALS AND METHODS: Stool samples were collected before chemotherapy, with 162 pre- and 194 postsurgery. The gut microbiome was measured by shotgun metagenomic sequencing. Associations of gut microbial diversity, taxa abundance, and gut microbiome health index (GMHI) with sociodemographic, clinical factors, and tumor characteristics were evaluated.

RESULTS: Postsurgery samples were associated with significantly lower α- and β-diversities (P < .001) and showed significant differences in the abundance of 15% of 2,864 investigated taxa (false discovery rate [FDR] <0.1) compared with presurgery samples. An unhealthy gut microbiome was prevalent among patients with breast cancer, with a mean GMHI of -0.79 and -2.81 in pre- and postsurgery stool samples, respectively. In an analysis of 162 presurgery stool samples, diagnosis delay was significantly associated with lower α-diversity, variation in β-diversity, an increased abundance of species Enorma massiliensis, and a decreased abundance of Faecalicoccus pleomorphus. High intake of fiber was significantly associated with lower α-diversity and a higher abundance of species belonging to Bifidobacterium, Prevotella, and Bacteroides gena (FDR < 0.1). We did not find that cancer stage and subtype, menopausal status, comorbidity, antibiotic use during 3 months before stool collection, or physical activity was significantly associated with α- and β-diversities or GMHI although a few significant differences were observed in taxa abundance.

CONCLUSION: Our study revealed that diagnosis delay, high fiber intake, and breast cancer surgery, which is always followed by antibiotic prophylaxis in Vietnam, led to a less diverse and unhealthy gut microbiome among patients with breast cancer.}, } @article {pmid38358269, year = {2024}, author = {Carter, KA and France, MT and Rutt, L and Bilski, L and Martinez-Greiwe, S and Regan, M and Brotman, RM and Ravel, J}, title = {Sexual transmission of urogenital bacteria: whole metagenome sequencing evidence from a sexual network study.}, journal = {mSphere}, volume = {9}, number = {3}, pages = {e0003024}, pmid = {38358269}, issn = {2379-5042}, support = {T32 AI162579/AI/NIAID NIH HHS/United States ; U19 AI084044/AI/NIAID NIH HHS/United States ; }, mesh = {Infant, Newborn ; Child ; Humans ; Male ; Female ; Metagenome ; Gardnerella vaginalis/genetics ; *Vaginosis, Bacterial/microbiology ; Vagina/microbiology ; *Microbiota ; }, abstract = {Sexual transmission of the urogenital microbiota may contribute to adverse sexual and reproductive health outcomes. The extent of sexual transmission of the urogenital microbiota is unclear as prior studies largely investigated specific pathogens. We used epidemiologic data and whole metagenome sequencing to characterize urogenital microbiota strain concordance between participants of a sexual network study. Individuals who screened positive for genital Chlamydia trachomatis were enrolled and referred their sexual contacts from the prior 60-180 days. Snowball recruitment of sexual contacts continued for up to four waves. Vaginal swabs and penile urethral swabs were collected for whole metagenome sequencing. We evaluated bacterial strain concordance using inStrain and network analysis. We defined concordance as ≥99.99% average nucleotide identity over ≥50% shared coverage; we defined putative sexual transmission as concordance between sexual contacts with <5 single-nucleotide polymorphisms per megabase. Of 138 participants, 74 (54%) were female; 120 (87%) had genital chlamydia; and 43 (31%) were recruited contacts. We identified 115 strain-concordance events among 54 participants representing 25 bacterial species. Seven events (6%) were between sexual contacts including putative heterosexual transmission of Fannyhessea vaginae, Gardnerella leopoldii, Prevotella amnii, Sneathia sanguinegens, and Sneathia vaginalis (one strain each), and putative sexual transmission of Lactobacillus iners between female contacts. Most concordance events (108, 94%) were between non-contacts, including eight female participants connected through 18 Lactobacillus crispatus and 3 Lactobacillus jensenii concordant strains, and 14 female and 2 male participants densely interconnected through 52 Gardnerella swidsinskii concordance events.IMPORTANCEEpidemiologic evidence consistently indicates bacterial vaginosis (BV) is sexually associated and may be sexually transmitted, though sexual transmission remains subject to debate. This study is not capable of demonstrating BV sexual transmission; however, we do provide strain-level metagenomic evidence that strongly supports heterosexual transmission of BV-associated species. These findings strengthen the evidence base that supports ongoing investigations of concurrent male partner treatment for reducing BV recurrence. Our data suggest that measuring the impact of male partner treatment on F. vaginae, G. leopoldii, P. amnii, S. sanguinegens, and S. vaginalis may provide insight into why a regimen does or does not perform well. We also observed a high degree of strain concordance between non-sexual-contact female participants. We posit that this may reflect limited dispersal capacity of vaginal bacteria coupled with individuals' comembership in regional transmission networks where transmission may occur between parent and child at birth, cohabiting individuals, or sexual contacts.}, } @article {pmid38357732, year = {2024}, author = {Virendra, A and Gulavane, SU and Ahmed, ZA and Reddy, R and Chaudhari, RJ and Gaikwad, SM and Shelar, RR and Ingole, SD and Thorat, VD and Khanam, A and Khan, FA}, title = {Metagenomic analysis unravels novel taxonomic differences in the uterine microbiome between healthy mares and mares with endometritis.}, journal = {Veterinary medicine and science}, volume = {10}, number = {2}, pages = {e1369}, pmid = {38357732}, issn = {2053-1095}, mesh = {Horses ; Animals ; Female ; *Endometritis/veterinary ; Proteomics ; RNA, Ribosomal, 16S ; Uterus ; *Microbiota ; }, abstract = {BACKGROUND: The application of high throughput technologies has enabled unravelling of unique differences between healthy mares and mares with endometritis at transcriptomic and proteomic levels. However, differences in the uterine microbiome are yet to be investigated.

OBJECTIVES: The present study was aimed at evaluating the differences in uterine microbiome between healthy mares and mares with endometritis.

METHODS: Low-volume lavage (LVL) samples were collected from the uterus of 30 mares classified into healthy (n = 15) and endometritis (n = 15) based on their reproductive history, intrauterine fluid accumulation, gross appearance of LVL samples, endometrial cytology and bacterial culture. The samples were subjected to 16S rRNA sequencing.

RESULTS: Notable differences in the uterine microbiome were observed between healthy mares and mares with endometritis at various taxonomic levels. In healthy mares, the most abundant phylum, class, order and family were Firmicutes, Bacilli, Bacillales and Paenibacillaceae, respectively. In contrast, the most abundant corresponding taxonomic levels in mares with endometritis were Proteobacteria, Gammaproteobacteria, Enterobacterales and Enterobacteriaceae, respectively. At the genus level, Brevibacillus and Paenibacillus were more abundant in healthy mares, whereas Escherichia, Salmonella and Klebsiella were more abundant in mares with endometritis. In healthy mares, Brevibacillus brevis was the most abundant species, followed by Brevibacillus choshinensis and Paenibacillus sp JDR-2. However, in mares with endometritis, Escherichia coli was the most abundant species, followed by Salmonella enterica and Klebsiella pneumoniae.

CONCLUSIONS: These results confirmed the previously reported presence of a uterine microbiome in healthy mares and helped unravel some alterations that occur in mares with endometritis. The findings can potentially help formulate new approaches to prevent or treat equine endometritis.}, } @article {pmid38357351, year = {2024}, author = {Antunes, A and de la Haba, RR and Jebbar, M and Hedlund, BP}, title = {Editorial: Community series-extremophiles: microbial genomics and taxogenomics, volume II.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1371210}, pmid = {38357351}, issn = {1664-302X}, } @article {pmid38356108, year = {2024}, author = {Nweze, JE and Schweichhart, JS and Angel, R}, title = {Viral communities in millipede guts: Insights into the diversity and potential role in modulating the microbiome.}, journal = {Environmental microbiology}, volume = {26}, number = {2}, pages = {e16586}, doi = {10.1111/1462-2920.16586}, pmid = {38356108}, issn = {1462-2920}, support = {21-04987S//Czech Science Foundation (GA ČR)/ ; 19-24309Y//Grantová Agentura České Republiky/ ; }, mesh = {*Viruses/genetics ; *Microbiota/genetics ; DNA Viruses/genetics ; *Gastrointestinal Microbiome/genetics ; DNA ; *RNA Viruses/genetics ; }, abstract = {Millipedes are important detritivores harbouring a diverse microbiome. Previous research focused on bacterial and archaeal diversity, while the virome remained neglected. We elucidated the DNA and RNA viral diversity in the hindguts of two model millipede species with distinct microbiomes: the tropical Epibolus pulchripes (methanogenic, dominated by Bacillota) and the temperate Glomeris connexa (non-methanogenic, dominated by Pseudomonadota). Based on metagenomic and metatranscriptomic assembled viral genomes, the viral communities differed markedly and preferentially infected the most abundant prokaryotic taxa. The majority of DNA viruses were Caudoviricetes (dsDNA), Cirlivirales (ssDNA) and Microviridae (ssDNA), while RNA viruses consisted of Leviviricetes (ssRNA), Potyviridae (ssRNA) and Eukaryotic viruses. A high abundance of subtypes I-C, I-B and II-C CRISPR-Cas systems was found, primarily from Pseudomonadota, Bacteroidota and Bacillota. In addition, auxiliary metabolic genes that modulate chitin degradation, vitamins and amino acid biosynthesis and sulphur metabolism were also detected. Lastly, we found low virus-to-microbe-ratios and a prevalence of lysogenic viruses, supporting a Piggyback-the-Winner dynamic in both hosts.}, } @article {pmid38354633, year = {2024}, author = {Ma, C and Huang, Z and Feng, X and Memon, FU and Cui, Y and Duan, X and Zhu, J and Tettamanti, G and Hu, W and Tian, L}, title = {Selective breeding of cold-tolerant black soldier fly (Hermetia illucens) larvae: Gut microbial shifts and transcriptional patterns.}, journal = {Waste management (New York, N.Y.)}, volume = {177}, number = {}, pages = {252-265}, doi = {10.1016/j.wasman.2024.02.007}, pmid = {38354633}, issn = {1879-2456}, mesh = {Animals ; Humans ; Larva/genetics ; Selective Breeding ; *Gastrointestinal Microbiome ; Amino Acids ; *Diptera/genetics ; }, abstract = {The larvae of black soldier fly (BSFL) convert organic waste into insect proteins used as feedstuff for livestock and aquaculture. BSFL production performance is considerably reduced during winter season. Herein, the intraspecific diversity of ten commercial BSF colonies collected in China was evaluated. The Bioforte colony was subjected to selective breeding at 12 °C and 16 °C to develop cold-tolerant BSF with improved production performance. After breeding for nine generations, the weight of larvae, survival rate, and the dry matter conversion rate significantly increased. Subsequently, intestinal microbiota in the cold-tolerant strain showed that bacteria belonging to Morganella, Dysgonomonas, Salmonella, Pseudochrobactrum, and Klebsiella genera were highly represented in the 12 °C bred, while those of Acinetobacter, Pseudochrobactrum, Enterococcus, Comamonas, and Leucobacter genera were significantly represented in the 16 °C bred group. Metagenomic revealed that several animal probiotics of the Enterococcus and Vagococcus genera were greatly enriched in the gut of larvae bred at 16 °C. Moreover, bacterial metabolic pathways including carbohydrate, lipid, amino acids, and cofactors and vitamins, were significantly increased, while organismal systems and human diseases was decreased in the 16 °C bred group. Transcriptomic analysis revealed that the upregulated differentially expressed genes in the 16 °C bred groups mainly participated in Autophagy-animal, AMPK signaling pathway, mTOR signaling pathway, Wnt signaling pathway, FoxO signaling pathway, Hippo signaling pathway at day 34 under 16 °C conditions, suggesting their significant role in the survival of BSFL. Taken together, these results shed lights on the role of intestinal microflora and gene pathways in the adaptation of BSF larvae to cold stress.}, } @article {pmid38353022, year = {2024}, author = {Schwenger, KJP and Sharma, D and Ghorbani, Y and Xu, W and Lou, W and Comelli, EM and Fischer, SE and Jackson, TD and Okrainec, A and Allard, JP}, title = {Links between gut microbiome, metabolome, clinical variables and non-alcoholic fatty liver disease severity in bariatric patients.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {44}, number = {5}, pages = {1176-1188}, doi = {10.1111/liv.15864}, pmid = {38353022}, issn = {1478-3231}, support = {//CIHR/Canada ; //CIHR/Canada ; }, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/complications ; *Gastrointestinal Microbiome ; Escherichia coli ; Liver/pathology ; Fibrosis ; *Bariatric Surgery ; Metabolome ; Glycerophospholipids/metabolism ; Glucose/metabolism ; *Obesity, Morbid/complications ; }, abstract = {BACKGROUND AND AIMS: Bacterial species and microbial pathways along with metabolites and clinical parameters may interact to contribute to non-alcoholic fatty liver disease (NAFLD) and disease severity. We used integrated machine learning models and a cross-validation approach to assess this interaction in bariatric patients.

METHODS: 113 patients undergoing bariatric surgery had clinical and biochemical parameters, blood and stool metabolite measurements as well as faecal shotgun metagenome sequencing to profile the intestinal microbiome. Liver histology was classified as normal liver obese (NLO; n = 30), simple steatosis (SS; n = 41) or non-alcoholic steatohepatitis (NASH; n = 42); fibrosis was graded F0 to F4.

RESULTS: We found that those with NASH versus NLO had an increase in potentially harmful E. coli, a reduction of potentially beneficial Alistipes putredinis and an increase in ALT and AST. There was higher serum glucose, faecal 3-(3-hydroxyphenyl)-3-hydroxypropionic acid and faecal cholic acid and lower serum glycerophospholipids. In NAFLD, those with severe fibrosis (F3-F4) versus F0 had lower abundance of anti-inflammatory species (Eubacterium ventriosum, Alistipes finegoldii and Bacteroides dorei) and higher AST, serum glucose, faecal acylcarnitines, serum isoleucine and homocysteine as well as lower serum glycerophospholipids. Pathways involved with amino acid biosynthesis and degradation were significantly more represented in those with NASH compared to NLO, with severe fibrosis having an overall stronger significant association with Superpathway of menaquinol-10 biosynthesis and Peptidoglycan biosynthesis IV.

CONCLUSIONS: In bariatric patients, NASH and severe fibrosis were associated with specific bacterial species, metabolic pathways and metabolites that may contribute to NAFLD pathogenesis and disease severity.}, } @article {pmid38351104, year = {2024}, author = {Xu, S and Huang, H and Chen, S and Muhammad, ZUA and Wei, W and Xie, W and Jiang, H and Hou, S}, title = {Recovery of 1887 metagenome-assembled genomes from the South China Sea.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {197}, pmid = {38351104}, issn = {2052-4463}, support = {42276163//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92051117//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32170108//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42188102//National Natural Science Foundation of China (National Science Foundation of China)/ ; JCYJ20220530115401003//Shenzhen Science and Technology Innovation Commission/ ; }, mesh = {China ; Genomics ; *Metagenome ; Metagenomics ; *Microbiota ; Oceans and Seas ; *Water Microbiology ; }, abstract = {The South China Sea (SCS) is a marginal sea characterized by strong land-sea biogeochemical interactions. SCS has a distinctive landscape with a multitude of seamounts in its basin. Seamounts create "seamount effects" that influence the diversity and distribution of planktonic microorganisms in the surrounding oligotrophic waters. Although the vertical distribution and community structure of marine microorganisms have been explored in certain regions of the global ocean, there is a lack of comprehensive microbial genomic surveys for uncultured microorganisms in SCS, particularly in the seamount regions. Here, we employed a metagenomic approach to study the uncultured microbial communities sampled from the Xianbei seamount region to the North Coast waters of SCS. A total of 1887 non-redundant prokaryotic metagenome-assembled genomes (MAGs) were reconstructed, of which, 153 MAGs were classified as high-quality MAGs based on the MIMAG standards. The community structure and genomic information provided by this dataset could be used to analyze microbial distribution and metabolism in the SCS.}, } @article {pmid38350856, year = {2024}, author = {Hui, TKL and Lo, ICN and Wong, KKW and Tsang, CTT and Tsang, LM}, title = {Metagenomic analysis of gut microbiome illuminates the mechanisms and evolution of lignocellulose degradation in mangrove herbivorous crabs.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {57}, pmid = {38350856}, issn = {1471-2180}, support = {CUHK14119419//Research Grants Council, University Grants Committee/ ; }, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome ; Herbivory ; *Brachyura/physiology ; *Microbiota/genetics ; *Cellulase/genetics ; Nitrogen ; *Lignin ; }, abstract = {BACKGROUND: Sesarmid crabs dominate mangrove habitats as the major primary consumers, which facilitates the trophic link and nutrient recycling in the ecosystem. Therefore, the adaptations and mechanisms of sesarmid crabs to herbivory are not only crucial to terrestrialization and its evolutionary success, but also to the healthy functioning of mangrove ecosystems. Although endogenous cellulase expressions were reported in crabs, it remains unknown if endogenous enzymes alone can complete the whole lignocellulolytic pathway, or if they also depend on the contribution from the intestinal microbiome. We attempt to investigate the role of gut symbiotic microbes of mangrove-feeding sesarmid crabs in plant digestion using a comparative metagenomic approach.

RESULTS: Metagenomics analyses on 43 crab gut samples from 23 species of mangrove crabs with different dietary preferences revealed a wide coverage of 127 CAZy families and nine KOs targeting lignocellulose and their derivatives in all species analyzed, including predominantly carnivorous species, suggesting the crab gut microbiomes have lignocellulolytic capacity regardless of dietary preference. Microbial cellulase, hemicellulase and pectinase genes in herbivorous and detritivorous crabs were differentially more abundant when compared to omnivorous and carnivorous crabs, indicating the importance of gut symbionts in lignocellulose degradation and the enrichment of lignocellulolytic microbes in response to diet with higher lignocellulose content. Herbivorous and detritivorous crabs showed highly similar CAZyme composition despite dissimilarities in taxonomic profiles observed in both groups, suggesting a stronger selection force on gut microbiota by functional capacity than by taxonomy. The gut microbiota in herbivorous sesarmid crabs were also enriched with nitrogen reduction and fixation genes, implying possible roles of gut microbiota in supplementing nitrogen that is deficient in plant diet.

CONCLUSIONS: Endosymbiotic microbes play an important role in lignocellulose degradation in most crab species. Their abundance is strongly correlated with dietary preference, and they are highly enriched in herbivorous sesarmids, thus enhancing their capacity in digesting mangrove leaves. Dietary preference is a stronger driver in determining the microbial CAZyme composition and taxonomic profile in the crab microbiome, resulting in functional redundancy of endosymbiotic microbes. Our results showed that crabs implement a mixed mode of digestion utilizing both endogenous and microbial enzymes in lignocellulose degradation, as observed in most of the more advanced herbivorous invertebrates.}, } @article {pmid38350567, year = {2024}, author = {Ge, Y and Chen, J and Xue, Y and Xing, W and Zhang, L and Lu, X and Liu, J and Li, F and Yang, Q}, title = {Elimination of inhibitory effects of dodecyl dimethyl benzyl ammonium chloride on microalgae in wastewater by cocultivation with a newly screened microbial consortium.}, journal = {The Science of the total environment}, volume = {919}, number = {}, pages = {170676}, doi = {10.1016/j.scitotenv.2024.170676}, pmid = {38350567}, issn = {1879-1026}, mesh = {Wastewater ; *Microalgae ; Ammonium Chloride/metabolism ; Microbial Consortia ; *Chlorella/metabolism ; Coculture Techniques ; Biomass ; }, abstract = {As one of the most commonly used biocidal cationic surfactants, benzalkonium chlorides (BACs) have been an increasing concern as emerging contaminants. Wastewater has been claimed the main point for BACs to enter into the environment, but to date, it is still largely unknown how the BACs affect the microbes (especially microalgae) in the practical wastewater and how to cost-effectively remove them. In this study, the inhibitory effects of a typical BACs, dodecyl dimethyl benzyl ammonium chloride (DDBAC), on a green microalga Chlorella sp. in oxidation pond wastewater were investigated. The results showed that though a hermetic effect at the first 2 days was observed with the DDBAC at low concentration (<6 mg/L), the algal growth and photosynthesis were significantly inhibited by the DDBAC at all the tested concentrations (3 to 48 mg/L). Fortunately, a new microbial consortium (MC) capable of degrading DDBAC was screened through a gradient domestication method. The MC mainly composed of Wickerhamomyces sp., Purpureocillium sp., and Achromobacter sp., and its maximum removal efficiency and removal rate of DDBAC (48 mg/L) respectively reached 98.1 % and 46.32 mg/L/d. Interestingly, a microbial-microalgal system (MMS) was constructed using the MC and Chlorella sp., and a synergetic effect between the two kinds of microorganisms was proposed: microalga provided oxygen and extracellular polysaccharides as co-metabolic substrates to help the MC to degrade DDBAC, while the MC helped to eliminate the DDBAC-induced inhibition on the alga. Further, by observing the seven kinds of degradation products (mainly including CH5O3P, C6H5CH2-, and C8H11N), two possible chemical pathways of the DDBAC degradation were proposed. In addition, the metagenomic sequencing results showed that the main functional genes of the MMS included antibiotic-resistant genes, ABC transporter genes, quorum sensing genes, two-component regulatory system genes, etc. This study provided some theoretical and application findings for the cost-effective pollution prevention of BACs in wastewater.}, } @article {pmid38350466, year = {2023}, author = {Nguyen, TT and Bui, ATP and Le, NTH and Vo, HTN and Nguyen, AH and Pham, TD and Hara, T and Yokota, K and Matsutani, M and Takatsuka, Y and Nguyen, ATV}, title = {Heat-stable spores of carotenoid-producing Bacillus marisflavi and non-pigmented Bacillus subtilis cooperatively promote growth, quality, and gut microbiota of white-leg shrimp.}, journal = {Beneficial microbes}, volume = {14}, number = {6}, pages = {623-640}, doi = {10.1163/18762891-20230041}, pmid = {38350466}, issn = {1876-2891}, mesh = {Animals ; Bacillus subtilis ; *Gastrointestinal Microbiome ; Hot Temperature ; RNA, Ribosomal, 16S/genetics ; Spores, Bacterial ; *Probiotics/analysis ; *Bacillus ; Carotenoids ; *Penaeidae/genetics/microbiology ; Immunity, Innate ; Animal Feed/analysis ; Diet ; }, abstract = {We evaluated the benefits of heat-stable carotenoid-producing Bacillus marisflavi SH8 spores individually and in combination with non-pigmented Bacillus subtilis SH23 spores on growth, colour change, nutritional content, innate immunity, and gut microbiota of white-leg shrimp. White-leg shrimp (Litopenaeus vannamei; n = 30 per tank; 2 tanks per group) were provided feed without (control group) or with SH8, SH23, or mixed spores (total, 1 × 106 cfu/g pellet) for 28 d. The SH8 and SH8-23 combination groups had significantly higher specific growth rates (9.6 and 11.0%), improved red-colour score (4 scores), astaxanthin concentration (1.8- and 2.3-fold), lipid contents (30 and 50%), and superoxidase dismutase activity (8.5 and 12.3%) than that of the control group. Analysis of shrimp's gut microbiome using 16S rRNA metagenome sequencing revealed increased abundance of four useful species and reduced abundance of four harmful species in the combination group than in the control group. Heat-stable Bacillus spore combination improved growth parameters, nutrient content, red-colour score, live counts, and abundance of useful bacteria in the gut of L. vannamei. This is the first study to show the benefits of combining highly heat-stable pigmented and non-pigmented Bacillus spores and their possible mechanisms in a shrimp model.}, } @article {pmid38349445, year = {2024}, author = {López-Sánchez, R and Rebollar, EA and Gutiérrez-Ríos, RM and Garciarrubio, A and Juarez, K and Segovia, L}, title = {Metagenomic analysis of carbohydrate-active enzymes and their contribution to marine sediment biodiversity.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {3}, pages = {95}, pmid = {38349445}, issn = {1573-0972}, support = {756092//Consejo Nacional de Ciencia y Tecnología/ ; 269435//Consejo Nacional de Ciencia y Tecnología/ ; IN209921//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; }, mesh = {Metagenome ; *Alphaproteobacteria ; Bacteroidetes ; Biodiversity ; Carbon ; *Gammaproteobacteria ; Geologic Sediments ; Oxygen ; Soil ; }, abstract = {Marine sediments constitute the world's most substantial long-term carbon repository. The microorganisms dwelling in these sediments mediate the transformation of fixed oceanic carbon, but their contribution to the carbon cycle is not fully understood. Previous culture-independent investigations into sedimentary microorganisms have underscored the significance of carbohydrates in the carbon cycle. In this study, we employ a metagenomic methodology to investigate the distribution and abundance of carbohydrate-active enzymes (CAZymes) in 37 marine sediments sites. These sediments exhibit varying oxygen availability and were isolated in diverse regions worldwide. Our comparative analysis is based on the metabolic potential for oxygen utilisation, derived from genes present in both oxic and anoxic environments. We found that extracellular CAZyme modules targeting the degradation of plant and algal detritus, necromass, and host glycans were abundant across all metagenomic samples. The analysis of these results indicates that the oxic/anoxic conditions not only influence the taxonomic composition of the microbial communities, but also affect the occurrence of CAZyme modules involved in the transformation of necromass, algae and plant detritus. To gain insight into the sediment microbial taxa, we reconstructed metagenome assembled genomes (MAG) and examined the presence of primary extracellular carbohydrate active enzyme (CAZyme) modules. Our findings reveal that the primary CAZyme modules and the CAZyme gene clusters discovered in our metagenomes were prevalent in the Bacteroidia, Gammaproteobacteria, and Alphaproteobacteria classes. We compared those MAGs to organisms from the same taxonomic classes found in soil, and we found that they were similar in its CAZyme repertoire, but the soil MAG contained a more abundant and diverse CAZyme content. Furthermore, the data indicate that abundant classes in our metagenomic samples, namely Alphaproteobacteria, Bacteroidia and Gammaproteobacteria, play a pivotal role in carbohydrate transformation within the initial few metres of the sediments.}, } @article {pmid38349437, year = {2024}, author = {Gu, L and Alemasi, A and Chen, Y and Li, X and Mei, Y and Zhou, J and He, D and Zeng, J}, title = {Gut Microbiota Disorders in Obesity-Associated Benign Prostatic Hyperplasia in Rats.}, journal = {Biochemical genetics}, volume = {62}, number = {6}, pages = {4639-4653}, pmid = {38349437}, issn = {1573-4927}, support = {82172684//National Natural Science Foundation of China/ ; 82073304//National Natural Science Foundation of China/ ; 2019YFC0121501//National Key Research and Development Program of China/ ; }, mesh = {Animals ; Male ; *Prostatic Hyperplasia/microbiology/pathology ; *Gastrointestinal Microbiome ; *Obesity/microbiology ; *Rats, Sprague-Dawley ; Rats ; *Diet, High-Fat/adverse effects ; Prostate/microbiology/pathology/metabolism ; }, abstract = {UNLABELLED: Benign prostatic hyperplasia (BPH), commonly seen in older men, can cause symptoms of discomfort, and may even need surgical intervention. Studies have shown the potential link between gut microbes and BPH, but the molecular association is not fully understood.

METHODS: Four-week-old male Sprague-Dawley rats (n = 16) were randomly allocated to normal control diet (ND, 10% fat) and high-fat diet-induced BPH (HFD, 45% fat) groups. Metagenomic analysis was used to examine the abundance and discrepancies in gut microbiota within the two groups after 24 weeks of feeding. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was conducted to assess the biological functions of the differentially expressed genes.

RESULTS: Rats with HFD-induced obesity exhibited morphological abnormalities in their prostate tissues. Metagenomic analysis of the gut revealed that Firmicutes were the dominant phyla in the HFD group, whereas the ND group had a higher abundance of Spirochaetes. At the genus level, Ruminococcus spp exhibited greater abundance in the HFD group, whereas Treponema spp were more abundant in the ND group. KEGG analysis demonstrated that the differentially expressed genes were mainly enriched in the NOD-like receptor (NLR) signaling, PI3K-Akt signaling, estrogen-signaling, signalings associated with GABAergic synapses, pantothenate and CoA biosynthesis.

CONCLUSION: The findings of our study indicated that there was a notable variation in the microbiota abundance within the intestinal tract of obese rats suffering from prostate hyperplasia. It is plausible that these differentially abundant bacteria played a role in the development of pathological alterations in the prostate through the facilitation of inflammatory responses; however, additional research is required to validate the findings.}, } @article {pmid38349151, year = {2024}, author = {Zhang, Y and Si, L and Gao, J and Shu, X and Qiu, C and Zhang, Y and Zu, S and Hu, H}, title = {Serial passage of PDCoV in cell culture reduces its pathogenicity and its damage of gut microbiota homeostasis in piglets.}, journal = {mSystems}, volume = {9}, number = {3}, pages = {e0134623}, pmid = {38349151}, issn = {2379-5077}, support = {2021YFD1801103-4//MOST | National Key Research and Development Program of China (NKPs)/ ; U22A20520//MOST | National Natural Science Foundation of China (NSFC)/ ; 32130106//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; Swine ; Virulence ; *Gastrointestinal Microbiome ; Serial Passage ; *Swine Diseases ; Cell Culture Techniques ; Diarrhea/veterinary ; *Vaccines ; Homeostasis ; }, abstract = {Porcine deltacoronavirus (PDCoV) is an enteropathogenic coronavirus that mainly causes diarrhea in suckling piglets, and also has the potential for cross-species transmission. However, there are still no commercial vaccines available to prevent and control PDCoV infection. In this study, PDCoV strain HNZK-02 was serially propagated in vitro for up to 150 passages and the amino acid changes have mainly occurred in the S protein during serial passage which caused structure change. PDCoV HNZK-02-passage 5 (P5)-infected piglets exhibited acute and severe watery diarrhea, an obvious intestinal damage, while the piglets infected with PDCoV HNZK-02-P150 showed no obvious clinical signs, weak intestinal lesions, and lower viral loads in rectal swabs and various tissues. Compared with the PDCoV HNZK-02-P5 infection, HNZK-02-P150 infection resulted in a decrease in intestinal mucosal permeability and pro-inflammatory cytokines. Moreover, PDCoV HNZK-02-P5 infection had significantly reduced bacterial diversity and increased relative abundance of opportunistic pathogens, while PDCoV HNZK-02-P150 infection did not significantly affect the bacterial diversity, and the relative abundance of probiotics increased. Furthermore, the alterations of gut microbiota were closely related to the change of pro-inflammatory factor. Metagenomics prediction analysis demonstrated that HNZK-02-P150 modulated the tyrosine metabolism, Nucleotide-binding and oligomerization domain (NOD)-like receptor signaling pathway, and lipopolysaccharide biosynthesis, which coincided with lower inflammatory response and intestinal permeability in the piglets infected with HNZK-02-P150. In conclusion, the PDCoV HNZK-02 was successfully attenuated by serial passage in vitro, and the changes of S gene, metabolic function, and gut microbiota may contribute to the attenuation. The PDCoV HNZK-02-P150 may have the potential for developing live-attenuated vaccine.IMPORTANCEPorcine deltacoronavirus (PDCoV) is an enteropathogen causing severe diarrhea, dehydration, and death in nursing piglets, devastating great economic losses for the global swine industry, and has cross-species transmission and zoonotic potential. There are currently no approved treatments or vaccines available for PDCoV. In addition, gut microbiota has an important relationship with the development of many diseases. Here, the PDCoV virulent HNZK-02 strain was successfully attenuated by serial passage on cell cultures, and the pathogenesis and effects on the gut microbiota composition and metabolic function of the PDCoV HNZK-02-P5 and P150 strains were investigated in piglets. We also found the genetic changes in the S protein during passage in vitro and the gut microbiota may contribute to the pathogenesis of PDCoV, while their interaction molecular mechanism would need to be explored further.}, } @article {pmid38347627, year = {2024}, author = {Behling, AH and Wilson, BC and Ho, D and Cutfield, WS and Vatanen, T and O'Sullivan, JM}, title = {Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {26}, pmid = {38347627}, issn = {2049-2618}, mesh = {Adolescent ; Humans ; Fecal Microbiota Transplantation/methods ; Gene Transfer, Horizontal ; *Pediatric Obesity ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; Feces/microbiology ; Treatment Outcome ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) describes the transmission of DNA outside of direct ancestral lineages. The process is best characterised within the bacterial kingdom and can enable the acquisition of genetic traits that support bacterial adaptation to novel niches. The adaptation of bacteria to novel niches has particular relevance for faecal microbiota transplantation (FMT), a therapeutic procedure which aims to resolve gut-related health conditions of individuals, through transplanted gut microbiota from healthy donors.

RESULTS: Three hundred eighty-one stool metagenomic samples from a placebo-controlled FMT trial for obese adolescents (the Gut Bugs Trial) were analysed for HGT, using two complementary methodologies. First, all putative HGT events, including historical HGT signatures, were quantified using the bioinformatics application WAAFLE. Second, metagenomic assembly and gene clustering were used to assess and quantify donor-specific genes transferred to recipients following the intervention. Both methodologies found no difference between the level of putative HGT events in the gut microbiomes of FMT and placebo recipients, post-intervention. HGT events facilitated by engrafted donor species in the FMT recipient gut at 6 weeks post-intervention were identified and characterised. Bacterial strains contributing to this subset of HGT events predominantly belonged to the phylum Bacteroidetes. Engraftment-dependent horizontally transferred genes were retained within recipient microbiomes at 12 and 26 weeks post-intervention.

CONCLUSION: Our study suggests that novel microorganisms introduced into the recipient gut following FMT have no impact on the basal rate of HGT within the human gut microbiome. Analyses of further FMT studies are required to assess the generalisability of this conclusion across different FMT study designs and for the treatment of different gut-related conditions. Video Abstract.}, } @article {pmid38347598, year = {2024}, author = {Shen, H and Wang, T and Dong, W and Sun, G and Liu, J and Peng, N and Zhao, S}, title = {Metagenome-assembled genome reveals species and functional composition of Jianghan chicken gut microbiota and isolation of Pediococcus acidilactic with probiotic properties.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {25}, pmid = {38347598}, issn = {2049-2618}, support = {2021hszd022//Foundation of Hubei Hongshan Laboratory/ ; 2020BBA054//Key Research and Development Program of Hubei Province/ ; }, mesh = {Animals ; Chickens/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Pediococcus/genetics ; Anti-Bacterial Agents/pharmacology ; *Probiotics ; Bacteroidetes/genetics ; }, abstract = {BACKGROUND: Chickens are one of the most widely farmed animals worldwide and play a crucial role in meat and egg production. Gut microbiota is essential for chickens' health, disease, growth, and egg production. However, native chickens such as Jianghan chickens have better meat and egg production quality than centralized chickens, their intestinal microbial diversity is richer, and the potential gut microbial resources may bring health benefits to the host.

RESULTS: The bacterial species composition in the gut microbiota of Jianghan chickens is similar to that of other chicken breeds, with Phocaeicola and Bacteroides being the most abundant bacterial genera. The LEfSe analysis revealed significant differences in species composition and functional profiles between samples from Jingzhou and the other three groups. Functional annotation indicated that the gut microbiota of Jianghan chickens were dominated by metabolic genes, with the highest number of genes related to carbohydrate metabolism. Several antibiotic resistance genes (ARGs) were found, and the composition of ARGs was similar to that of factory-farmed chickens, suggesting that antibiotics were widely present in the gut microbiota of Jianghan chickens. The resistance genes of Jianghan chickens are mainly carried by microorganisms of the Bacteroidota and Bacillota phylum. In addition, more than 829 isolates were selected from the microbiota of Jianghan chickens. Following three rounds of acid and bile tolerance experiments performed on all the isolated strains, it was determined that six strains of Pediococcus acidilactici exhibited consistent tolerance. Further experiments confirmed that three of these strains (A4, B9, and C2) held substantial probiotic potential, with P. acidilactici B9 displaying the highest probiotic potential.

CONCLUSIONS: This study elucidates the composition of the intestinal microbiota and functional gene repertoire in Jianghan chickens. Despite the absence of antibiotic supplementation, the intestinal microbial community of Jianghan chickens still demonstrates a profile of antibiotic resistance genes similar to that of intensively reared chickens, suggesting resistance genes are prevalent in free-ranging poultry. Moreover, Jianghan and intensively reared chickens host major resistance genes differently, an aspect seldom explored between free-range and pastured chickens. Furthermore, among the 829 isolates, three strains of P. acidilatici exhibited strong probiotic potential. These findings provide insights into the unique gut microbiota of Jianghan chickens and highlight potential probiotic strains offering benefits to the host. Video Abstract.}, } @article {pmid38347104, year = {2024}, author = {Burcham, ZM and Belk, AD and McGivern, BB and Bouslimani, A and Ghadermazi, P and Martino, C and Shenhav, L and Zhang, AR and Shi, P and Emmons, A and Deel, HL and Xu, ZZ and Nieciecki, V and Zhu, Q and Shaffer, M and Panitchpakdi, M and Weldon, KC and Cantrell, K and Ben-Hur, A and Reed, SC and Humphry, GC and Ackermann, G and McDonald, D and Chan, SHJ and Connor, M and Boyd, D and Smith, J and Watson, JMS and Vidoli, G and Steadman, D and Lynne, AM and Bucheli, S and Dorrestein, PC and Wrighton, KC and Carter, DO and Knight, R and Metcalf, JL}, title = {A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables.}, journal = {Nature microbiology}, volume = {9}, number = {3}, pages = {595-613}, pmid = {38347104}, issn = {2058-5276}, support = {T32 GM132057/GM/NIGMS NIH HHS/United States ; I01 BX000194/BX/BLRD VA/United States ; }, mesh = {Mice ; Humans ; Animals ; Swine ; Cattle ; Cadaver ; *Microbial Consortia ; *Soil Microbiology ; Metagenome ; Bacteria ; }, abstract = {Microbial breakdown of organic matter is one of the most important processes on Earth, yet the controls of decomposition are poorly understood. Here we track 36 terrestrial human cadavers in three locations and show that a phylogenetically distinct, interdomain microbial network assembles during decomposition despite selection effects of location, climate and season. We generated a metagenome-assembled genome library from cadaver-associated soils and integrated it with metabolomics data to identify links between taxonomy and function. This universal network of microbial decomposers is characterized by cross-feeding to metabolize labile decomposition products. The key bacterial and fungal decomposers are rare across non-decomposition environments and appear unique to the breakdown of terrestrial decaying flesh, including humans, swine, mice and cattle, with insects as likely important vectors for dispersal. The observed lockstep of microbial interactions further underlies a robust microbial forensic tool with the potential to aid predictions of the time since death.}, } @article {pmid38346660, year = {2024}, author = {Durán-Viseras, A and Lindner, BG and Hatt, JK and Lai, A and Wallace, R and Ginn, O and Brown, J and Konstantinidis, KT}, title = {Metagenomic insights into the impact of litter from poultry Concentrated Animal Feeding Operations (CAFOs) to adjacent soil and water microbial communities.}, journal = {The Science of the total environment}, volume = {920}, number = {}, pages = {170772}, doi = {10.1016/j.scitotenv.2024.170772}, pmid = {38346660}, issn = {1879-1026}, mesh = {Humans ; Animals ; Poultry ; Soil ; Metagenome ; Chickens ; Water ; *Microbiota ; *Anti-Infective Agents ; Anti-Bacterial Agents ; Metagenomics ; }, abstract = {In recent decades, human food consumption has led to an increased demand for animal-based foods, particularly chicken meat production. The state of Georgia, USA is one of the top broiler chicken producers in the United States, where animals are raised in Concentrated Animal Feeding Operations (CAFOs). Without proper management, CAFOs could negatively impact the environment and become a public health risk as a source of water and air pollution and/or by spreading antimicrobial resistance genes. In this study, we used metagenome sequencing to investigate the impact of the application of the CAFO's litter on adjacent soils and downstream creek waters in terms of microbial diversity and antimicrobial resistance profile changes. Our data indicate that while a few microbial groups increased in abundance within a short period of time after litter application, these populations subsequently decreased to levels similar to those found prior to the litter application or to below the detection limit of our metagenome sequencing effort. Microbial taxonomic composition analyses, relative abundance of Metagenome-Assembled Genomes (MAGs) and detection of Antimicrobial Resistance Genes (ARGs) allow us to conclude that this practice of litter application had a negligible effect on the microbiome or resistome profile of these soils and nearby waterways, likely due to its dilution in the field and/or outcompetition by indigenous microbes, revealing a minimal impact of these poultry facilities on the natural microbial communities.}, } @article {pmid38345311, year = {2024}, author = {Guimond, AJ and Ke, S and Tworoger, SS and Huang, T and Chan, AT and Kubzansky, LD and Liu, YY}, title = {Fulfilled Mind, Healthy Gut? Relationships of Eudaimonic Psychological Well-Being With the Gut Microbiome in Postmenopausal Women.}, journal = {Psychosomatic medicine}, volume = {86}, number = {5}, pages = {398-409}, pmid = {38345311}, issn = {1534-7796}, support = {R01 CA067262/CA/NCI NIH HHS/United States ; R01 CA163451/CA/NCI NIH HHS/United States ; R01 CA202704/CA/NCI NIH HHS/United States ; U01 CA176726/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; Middle Aged ; *Postmenopause/psychology/physiology ; Aged ; Personal Satisfaction ; Healthy Aging/physiology/psychology ; Psychological Well-Being ; }, abstract = {OBJECTIVE: Eudaimonic facets of psychological well-being (PWB), like purpose in life and sense of mastery, are associated with healthy aging. Variation in the gut microbiome may be one pathway by which mental health influences age-related health outcomes. However, associations between eudaimonic PWB and the gut microbiome are understudied. We examined whether purpose in life and sense of mastery, separately, were associated with features of the gut microbiome in older women.

METHODS: Participants were from the Mind-Body Study (N = 206, mean age = 61 years), a substudy of the Nurses' Health Study II cohort. In 2013, participants completed the Life Engagement Test and the Pearlin Mastery Scale. Three months later, up to two pairs of stool samples were collected, 6 months apart. Covariates included sociodemographics, depression, health status, and health behaviors. Analyses examined associations of PWB with gut microbiome taxonomic diversity, overall community structure, and specific species/pathways. To account for multiple testing, statistical significance was established using Benjamini-Hochberg adjusted p values (i.e., q values ≤0.25).

RESULTS: We found no evidence of an association between PWB and gut microbiome alpha diversity. In multivariate analysis, higher purpose levels were significantly associated with lower abundance of species previously linked with poorer health outcomes, notably Blautia hydrogenotrophica and Eubacterium ventriosum (q values ≤0.25). No significant associations were found between PWB and metabolic pathways.

CONCLUSIONS: These findings offer early evidence suggesting that eudaimonic PWB is linked with variation in the gut microbiome, and this might be one pathway by which PWB promotes healthy aging.}, } @article {pmid38345108, year = {2024}, author = {Shih, KC and Tong, L}, title = {The Conjunctival Microbiome and Dry Eye: What We Know and Controversies.}, journal = {Eye & contact lens}, volume = {50}, number = {5}, pages = {208-211}, doi = {10.1097/ICL.0000000000001077}, pmid = {38345108}, issn = {1542-233X}, mesh = {Humans ; *Conjunctiva/microbiology ; *Dry Eye Syndromes/microbiology ; *Microbiota/physiology ; }, abstract = {Dry eye disease is a common multifactorial condition that may be idiopathic or associated with autoimmune conditions, such as Sjogren syndrome. Commensal microorganisms modify immune responses, so it is relevant to understand how they modify such immune-mediated diseases. Microbiota in the gut regulate inflammation in the eye, and conversely, severe inflammation of the ocular surface results in alteration of gut microbiome. The conjunctiva microbiome can be analyzed using 16S or shotgun metagenomics. The amount of microbial DNA in ocular surface mucosa relative to human DNA is limited compared with the case of the intestinal microbiome. There are challenges in defining, harvesting, processing, and analyzing the microbiome in the ocular surface mucosa. Recent studies have shown that the conjunctiva microbiome depends on age, presence of local and systemic inflammation, and environmental factors. Microbiome-based therapy, such as the use of oral probiotics to manage dry eye disease, has initial promising results. Further longitudinal studies are required to investigate the alteration of the conjunctival microbiome after local therapy and surgery.}, } @article {pmid38343326, year = {2024}, author = {Miao, Y and Sun, Z and Ma, C and Lin, C and Wang, G and Yang, C}, title = {VirGrapher: a graph-based viral identifier for long sequences from metagenomes.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {2}, pages = {}, pmid = {38343326}, issn = {1477-4054}, support = {62301139//Fundamental Research Funds for the Central Universities/ ; 62225109//National Natural Science Foundation of China/ ; }, mesh = {*Metagenome ; *Microbiota/genetics ; }, abstract = {Viruses are the most abundant biological entities on earth and are important components of microbial communities. A metagenome contains all microorganisms from an environmental sample. Correctly identifying viruses from these mixed sequences is critical in viral analyses. It is common to identify long viral sequences, which has already been passed thought pipelines of assembly and binning. Existing deep learning-based methods divide these long sequences into short subsequences and identify them separately. This makes the relationships between them be omitted, leading to poor performance on identifying long viral sequences. In this paper, VirGrapher is proposed to improve the identification performance of long viral sequences by constructing relationships among short subsequences from long ones. VirGrapher see a long sequence as a graph and uses a Graph Convolutional Network (GCN) model to learn multilayer connections between nodes from sequences after a GCN-based node embedding model. VirGrapher achieves a better AUC value and accuracy on validation set, which is better than three benchmark methods.}, } @article {pmid38341971, year = {2024}, author = {Zhu, Z and Ding, J and Du, R and Zhang, Z and Guo, J and Li, X and Jiang, L and Chen, G and Bu, Q and Tang, N and Lu, L and Gao, X and Li, W and Li, S and Zeng, G and Liang, J}, title = {Systematic tracking of nitrogen sources in complex river catchments: Machine learning approach based on microbial metagenomics.}, journal = {Water research}, volume = {253}, number = {}, pages = {121255}, doi = {10.1016/j.watres.2024.121255}, pmid = {38341971}, issn = {1879-2448}, mesh = {Nitrogen/analysis ; Rivers/chemistry ; RNA, Ribosomal, 16S ; Water Pollution/analysis ; *Microbiota ; Environmental Monitoring ; China ; *Water Pollutants, Chemical/analysis ; }, abstract = {Tracking nitrogen pollution sources is crucial for the effective management of water quality; however, it is a challenging task due to the complex contaminative scenarios in the freshwater systems. The contaminative pattern variations can induce quick responses of aquatic microorganisms, making them sensitive indicators of pollution origins. In this study, the soil and water assessment tool, accompanied by a detailed pollution source database, was used to detect the main nitrogen pollution sources in each sub-basin of the Liuyang River watershed. Thus, each sub-basin was assigned to a known class according to SWAT outputs, including point source pollution-dominated area, crop cultivation pollution-dominated area, and the septic tank pollution-dominated area. Based on these outputs, the random forest (RF) model was developed to predict the main pollution sources from different river ecosystems using a series of input variable groups (e.g., natural macroscopic characteristics, river physicochemical properties, 16S rRNA microbial taxonomic composition, microbial metagenomic data containing taxonomic and functional information, and their combination). The accuracy and the Kappa coefficient were used as the performance metrics for the RF model. Compared with the prediction performance among all the input variable groups, the prediction performance of the RF model was significantly improved using metagenomic indices as inputs. Among the metagenomic data-based models, the combination of the taxonomic information with functional information of all the species achieved the highest accuracy (0.84) and increased median Kappa coefficient (0.70). Feature importance analysis was used to identify key features that could serve as indicators for sudden pollution accidents and contribute to the overall function of the river system. The bacteria Rhabdochromatium marinum, Frankia, Actinomycetia, and Competibacteraceae were the most important species, whose mean decrease Gini indices were 0.0023, 0.0021, 0.0019, and 0.0018, respectively, although their relative abundances ranged only from 0.0004 to 0.1 %. Among the top 30 important variables, functional variables constituted more than half, demonstrating the remarkable variation in the microbial functions among sites with distinct pollution sources and the key role of functionality in predicting pollution sources. Many functional indicators related to the metabolism of Mycobacterium tuberculosis, such as K24693, K25621, K16048, and K14952, emerged as significant important factors in distinguishing nitrogen pollution origins. With the shortage of pollution source data in developing regions, this suggested approach offers an economical, quick, and accurate solution to locate the origins of water nitrogen pollution using the metagenomic data of microbial communities.}, } @article {pmid38341424, year = {2024}, author = {Gao, SM and Fei, HL and Li, Q and Lan, LY and Huang, LN and Fan, PF}, title = {Eco-evolutionary dynamics of gut phageome in wild gibbons (Hoolock tianxing) with seasonal diet variations.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1254}, pmid = {38341424}, issn = {2041-1723}, support = {2022YFF1301500//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 31822049//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31770421//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32201269//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2021A1515110523//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; 2023A1515010695//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; 2021M703754//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; *Hylobates ; Seasons ; Ecosystem ; Virome ; Diet ; *Bacteriophages/genetics ; Fruit ; *Hylobatidae ; }, abstract = {It has been extensively studied that the gut microbiome provides animals flexibility to adapt to food variability. Yet, how gut phageome responds to diet variation of wild animals remains unexplored. Here, we analyze the eco-evolutionary dynamics of gut phageome in six wild gibbons (Hoolock tianxing) by collecting individually-resolved fresh fecal samples and parallel feeding behavior data for 15 consecutive months. Application of complementary viral and microbial metagenomics recovers 39,198 virulent and temperate phage genomes from the feces. Hierarchical cluster analyses show remarkable seasonal diet variations in gibbons. From high-fruit to high-leaf feeding period, the abundances of phage populations are seasonally fluctuated, especially driven by the increased abundance of virulent phages that kill the Lachnospiraceae hosts, and a decreased abundance of temperate phages that piggyback the Bacteroidaceae hosts. Functional profiling reveals an enrichment through horizontal gene transfers of toxin-antitoxin genes on temperate phage genomes in high-leaf season, potentially conferring benefits to their prokaryotic hosts. The phage-host ecological dynamics are driven by the coevolutionary processes which select for tail fiber and DNA primase genes on virulent and temperate phage genomes, respectively. Our results highlight complex phageome-microbiome interactions as a key feature of the gibbon gut microbial ecosystem responding to the seasonal diet.}, } @article {pmid38340561, year = {2024}, author = {Jing, Z and Tu, S and Yuan, P and Liu, X and Wang, S and Dong, B and Li, Q and Gao, H}, title = {The ecological role of microbiome at community-, taxonomic - and genome-levels in black-odorous waters.}, journal = {Journal of hazardous materials}, volume = {467}, number = {}, pages = {133673}, doi = {10.1016/j.jhazmat.2024.133673}, pmid = {38340561}, issn = {1873-3336}, mesh = {*Microbiota/genetics ; Nitrification ; Water Microbiology ; Water Pollution ; Water ; }, abstract = {Black-odorous waters (BOWs) are heavily polluted waters where microbial information remains elusive mechanistically. Based on gene amplicon and metagenomics sequencing, a comprehensive study was conducted to investigate the microbial communities in urban and rural BOWs. The results revealed that microbial communities' assembly in urban and rural BOWs was predominantly governed by stochastic factors at the community level. At the taxonomic level, there were 62 core species (58.48%) in water and 207 core species (44.56%) in sediment across urban and rural areas. Notably, significant differences were observed in the functional genetic composition of BOWs between urban and rural areas. Specifically, rural areas exhibited an enhanced abundance of genes involved in nitrogen fixation, Fe[2+] transport, and sulfate reduction. Conversely, urban areas showed higher abundances of some genes associated with carbon fixation, nitrification and denitrification. A sulfur-centered ecological model of microbial communities was constructed by integrating data from the three levels of analysis, and 14 near-complete draft genomes were generated, representing a substantial portion of the microbial community (35.04% in rural BOWs and 29.97% in urban BOWs). This research provides significant insights into the sustainable management and preservation of aquatic ecosystems affected by BOWs.}, } @article {pmid38339197, year = {2024}, author = {Laske, C and Müller, S and Munk, MHJ and Honold, I and Willmann, M and Peter, S and Schoppmeier, U}, title = {Prognostic Value of Gut Microbiome for Conversion from Mild Cognitive Impairment to Alzheimer's Disease Dementia within 4 Years: Results from the AlzBiom Study.}, journal = {International journal of molecular sciences}, volume = {25}, number = {3}, pages = {}, pmid = {38339197}, issn = {1422-0067}, support = {374-1-0//University of Tübingen/ ; 32-5400/58/3//Forum Gesundheitsstandort BW/ ; D3030814//Faber Foundation/ ; }, mesh = {Humans ; *Alzheimer Disease/genetics ; *Gastrointestinal Microbiome/genetics ; Longitudinal Studies ; Prognosis ; *Cognitive Dysfunction/etiology ; Disease Progression ; Biomarkers ; }, abstract = {Alterations in the gut microbiome are associated with the pathogenesis of Alzheimer's disease (AD) and can be used as a diagnostic measure. However, longitudinal data of the gut microbiome and knowledge about its prognostic significance for the development and progression of AD are limited. The aim of the present study was to develop a reliable predictive model based on gut microbiome data for AD development. In this longitudinal study, we investigated the intestinal microbiome in 49 mild cognitive impairment (MCI) patients over a mean (SD) follow-up of 3.7 (0.6) years, using shotgun metagenomics. At the end of the 4-year follow-up (4yFU), 27 MCI patients converted to AD dementia and 22 MCI patients remained stable. The best taxonomic model for the discrimination of AD dementia converters from stable MCI patients included 24 genera, yielding an area under the receiver operating characteristic curve (AUROC) of 0.87 at BL, 0.92 at 1yFU and 0.95 at 4yFU. The best models with functional data were obtained via analyzing 25 GO (Gene Ontology) features with an AUROC of 0.87 at BL, 0.85 at 1yFU and 0.81 at 4yFU and 33 KO [Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog] features with an AUROC of 0.79 at BL, 0.88 at 1yFU and 0.82 at 4yFU. Using ensemble learning for these three models, including a clinical model with the four parameters of age, gender, body mass index (BMI) and Apolipoprotein E (ApoE) genotype, yielded an AUROC of 0.96 at BL, 0.96 at 1yFU and 0.97 at 4yFU. In conclusion, we identified novel and timely stable gut microbiome algorithms that accurately predict progression to AD dementia in individuals with MCI over a 4yFU period.}, } @article {pmid38337180, year = {2024}, author = {Finn, DR}, title = {A metagenomic alpha-diversity index for microbial functional biodiversity.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {3}, pages = {}, pmid = {38337180}, issn = {1574-6941}, support = {522758166//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Metagenome ; *Biodiversity ; RNA, Ribosomal ; Ecosystem ; }, abstract = {Alpha-diversity indices are an essential tool for describing and comparing biodiversity. Microbial ecologists apply indices originally intended for, or adopted by, macroecology to address questions relating to taxonomy (conserved marker) and function (metagenome-based data). In this Perspective piece, I begin by discussing the nature and mathematical quirks important for interpreting routinely employed alpha-diversity indices. Secondly, I propose a metagenomic alpha-diversity index (MD) that measures the (dis)similarity of protein-encoding genes within a community. MD has defined limits, whereby a community comprised mostly of similar, poorly diverse protein-encoding genes pulls the index to the lower limit, while a community rich in divergent homologs and unique genes drives it toward the upper limit. With data acquired from an in silico and three in situ metagenome studies, I derive MD and typical alpha-diversity indices applied to taxonomic (ribosomal rRNA) and functional (all protein-encoding) genes, and discuss their relationships with each other. Not all alpha-diversity indices detect biological trends, and taxonomic does not necessarily follow functional biodiversity. Throughout, I explain that protein Richness and MD provide complementary and easily interpreted information, while probability-based indices do not. Finally, considerations regarding the unique nature of microbial metagenomic data and its relevance for describing functional biodiversity are discussed.}, } @article {pmid38336233, year = {2024}, author = {Osadchiy, V and Belarmino, A and Kianian, R and Sigalos, JT and Furtado, TP and Ancira, JS and Kanie, T and Mangum, SF and Tipton, CD and Hsieh, TM and Mills, JN and Eleswarapu, SV}, title = {Urine microbes and predictive metagenomic profiles associate with abnormalities in sperm parameters: implications for male subfertility.}, journal = {F&S science}, volume = {5}, number = {2}, pages = {163-173}, doi = {10.1016/j.xfss.2024.01.002}, pmid = {38336233}, issn = {2666-335X}, mesh = {Humans ; Male ; *Infertility, Male/microbiology/urine/genetics ; Adult ; *Sperm Motility ; Cross-Sectional Studies ; *Semen Analysis/methods ; Spermatozoa/microbiology ; Microbiota/genetics ; Urine/microbiology ; }, abstract = {OBJECTIVE: To explore the taxonomic and predicted functional relationship between the urine microbiome and alterations of semen analysis (SA) parameters.

DESIGN: Cross-sectional study.

SETTING: Academic medical center.

PATIENT(S): Men presenting for fertility evaluation or men presenting for vasectomy consultation with proven biological paternity were recruited and stratified on the basis of alterations, or lack thereof, in SA parameters.

MAIN OUTCOME MEASURE: Changes in the functional and taxonomic urine microbiome profiles of participants with or without alterations in SA parameters.

RESULTS: Seventy-three participants were included in our study. Men with abnormal sperm motility (N = 27) showed a nearly 50-fold higher abundance of Dialister micraerophilus compared with those with normal sperm motility (N = 46). This relationship persisted on canonical correlational analysis (r = 0.439). Men with abnormal sperm concentration (N = 20) showed a lower abundance of Enterococcus faecalis and Staphylococcus aureus, compared with those with normal sperm concentration (N = 53). The urine of participants with impaired sperm motility demonstrated dramatic differences in predictive functional profiles in pathways involved in oxidation-reduction balance and cell longevity.

CONCLUSIONS: Our findings underscore differences in the urinary microbiome and abnormalities in semen parameters, especially sperm motility. By incorporating predictive functional profiling, we also highlight possible mechanisms that may drive the observed differences in sperm parameters.}, } @article {pmid38334873, year = {2024}, author = {Gao, Q and Li, D and Wang, Y and Zhao, C and Li, M and Xiao, J and Kang, Y and Lin, H and Wang, N}, title = {Analysis of intestinal flora and cognitive function in maintenance hemodialysis patients using combined 16S ribosome DNA and shotgun metagenome sequencing.}, journal = {Aging clinical and experimental research}, volume = {36}, number = {1}, pages = {28}, pmid = {38334873}, issn = {1720-8319}, support = {LJKZZ20220099//Key research project of basic scientific research projects of the educational department of Liaoning province/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome ; DNA, Ribosomal ; Quality of Life ; RNA, Ribosomal, 16S/genetics ; Ribosomes ; Cognition ; }, abstract = {BACKGROUND: Cognitive impairment is widely prevalent in maintenance hemodialysis (MHD) patients, and seriously affects their quality of life. The intestinal flora likely regulates cognitive function, but studies on cognitive impairment and intestinal flora in MHD patients are lacking.

METHODS: MHD patients (36) and healthy volunteers (18) were evaluated using the Montreal Cognitive Function Scale, basic clinical data, and 16S ribosome DNA (rDNA) sequencing. Twenty MHD patients and ten healthy volunteers were randomly selected for shotgun metagenomic analysis to explore potential metabolic pathways of intestinal flora. Both16S rDNA sequencing and shotgun metagenomic sequencing were conducted on fecal samples.

RESULTS: Roseburia were significantly reduced in the MHD group based on both 16S rDNA and shotgun metagenomic sequencing analyses. Faecalibacterium, Megamonas, Bifidobacterium, Parabacteroides, Collinsella, Tyzzerella, and Phascolarctobacterium were positively correlated with cognitive function or cognitive domains. Enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways included oxidative phosphorylation, photosynthesis, retrograde endocannabinoid signaling, flagellar assembly, and riboflavin metabolism.

CONCLUSION: Among the microbiota, Roseburia may be important in MHD patients. We demonstrated a correlation between bacterial genera and cognitive function, and propose possible mechanisms.}, } @article {pmid38332701, year = {2024}, author = {Li, P and Zhang, R and Zhou, J and Guo, P and Liu, Y and Shi, S}, title = {Vancomycin relieves tacrolimus-induced hyperglycemia by eliminating gut bacterial beta-glucuronidase enzyme activity.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2310277}, pmid = {38332701}, issn = {1949-0984}, mesh = {Mice ; Animals ; Tacrolimus/pharmacology/therapeutic use ; Vancomycin/pharmacology ; Immunosuppressive Agents/therapeutic use ; *Gastrointestinal Microbiome ; *Hyperglycemia/chemically induced/drug therapy ; *Diabetes Mellitus ; Bacteria/genetics/metabolism ; Glucuronidase/metabolism/pharmacology ; Bile Acids and Salts/pharmacology ; Glucagon-Like Peptide 1 ; }, abstract = {Up to 40% of transplant recipients treated long-term with tacrolimus (TAC) develop post-transplant diabetes mellitus (PTDM). TAC is an important risk factor for PTDM, but is also essential for immunosuppression after transplantation. Long-term TAC treatment alters the gut microbiome, but the mechanisms of TAC-induced gut microbiota in the pathogenesis of PTDM are poorly characterized. Here, we showed that vancomycin, an inhibitor of bacterial beta-glucuronidase (GUS), prevents TAC-induced glucose disorder and insulin resistance in mice. Metagenomics shows that GUS-producing bacteria are predominant and flourish in the TAC-induced hyperglycemia mouse model, with upregulation of intestinal GUS activity. Targeted metabolomics analysis revealed that in the presence of high GUS activity, the hydrolysis of bile acid (BAs)-glucuronic conjugates is increased and most BAs are overproduced in the serum and liver, which, in turn, activates the ileal farnesoid X receptor (FXR) and suppresses GLP-1 secretion by L-cells. The GUS inhibitor vancomycin significantly eliminated GUS-producing bacteria and inhibited bacterial GUS activity and BAs levels, thereby enhancing L-cell GLP-1 secretion and preventing hyperglycemia. Our results propose a novel clinical strategy for inhibiting the bacterial GUS enzyme to prevent hyperglycemia without requiring withdrawal of TAC treatment. This strategy exerted its effect through the ileal bile acid-FXR-GLP-1 pathway.}, } @article {pmid38330645, year = {2024}, author = {Liu, F and Ding, J and Zeng, J and Wang, C and Wu, B and Yan, Q and He, Z and Shu, L}, title = {Mangrove sediments are environmental hotspots for pathogenic protists.}, journal = {Journal of hazardous materials}, volume = {467}, number = {}, pages = {133643}, doi = {10.1016/j.jhazmat.2024.133643}, pmid = {38330645}, issn = {1873-3336}, mesh = {Humans ; *Archaea ; Metagenome ; *Microbiota ; Salinity ; Sulfates ; }, abstract = {Mangrove sediments are unique ecosystems providing habitats for diverse organisms, especially microbial communities. However, little is known about the diversity and environmental risk of a critical group of microorganisms, the protists. To address this gap, we employed metagenome sequencing technologies to provide the first comprehensive view of the protistan community in the mangrove sediment. Our results surprisingly showed that parasitic protists dominated the protistan community in mangrove sediments, with an average abundance of 59.67%, one of the highest in all ecosystems on Earth. We also found that the relative abundance of protists decreased significantly (R = -0.21, p = 0.045) with latitude but increased with depths (R = 0.7099, p < 0.001). The parasitic communities were positively influenced by microbial (bacteria, fungi, and archaea) communities, including horizontal-scale and vertical-scale. In addition, sulfate and salinity had the most significant influence on the protistan community. Our findings provide new insights into our understanding of protistan variation in mangrove sediments, including abundance, composition, and possible functions, and indicate that mangrove sediments are hotspots for environmental pathogens, posing a potential risk to human health.}, } @article {pmid38329942, year = {2024}, author = {Zhan, K and Wu, H and Xu, Y and Rao, K and Zheng, H and Qin, S and Yang, Y and Jia, R and Chen, W and Huang, S}, title = {The function of the gut microbiota-bile acid-TGR5 axis in diarrhea-predominant irritable bowel syndrome.}, journal = {mSystems}, volume = {9}, number = {3}, pages = {e0129923}, pmid = {38329942}, issn = {2379-5077}, support = {81974563, 81703992, 81904148//MOST | National Natural Science Foundation of China (NSFC)/ ; No.SZ2022QN08//Guangdong Provincial Academy of Chinese Medical Sciences/ ; 202102010226, 202102010207, 2023A03J0733, 2023A03J0735//Bureau of Science and Information Technology of Guangzhou Municipality | Guangzhou Municipal Science and Technology Project (Guangzhou Science and Technology Plan)/ ; }, mesh = {Humans ; Rats ; Animals ; *Irritable Bowel Syndrome/metabolism ; Bile Acids and Salts ; *Gastrointestinal Microbiome ; Diarrhea/etiology ; Intestinal Mucosa/metabolism ; Chenodeoxycholic Acid/pharmacology ; *Hypersensitivity/complications ; *Bacteroides ; }, abstract = {UNLABELLED: Imbalanced gut microbiota (GM) and abnormal fecal bile acid (BA) are thought to be the key factors for diarrhea-predominant irritable bowel syndrome (IBS-D), but the underlying mechanism remains unclear. Herein, we explore the influence of the GM-BA-Takeda G-protein-coupled receptor 5 (TGR5) axis on IBS-D. Twenty-five IBS-D patients and fifteen healthy controls were recruited to perform BA-related metabolic and metagenomic analyses. Further, the microbiota-humanized IBS-D rat model was established by fecal microbial transplantation (FMT) to investigate the GM-BA-TGR5 axis effects on the colonic barrier and visceral hypersensitivity (VH) in IBS-D. Finally, we used chenodeoxycholic acid (CDCA), an important BA screened out by metabolome, to evaluate whether it affected diarrhea and VH via the TGR5 pathway. Clinical research showed that GM associated with bile salt hydrolase (BSH) activity such as Bacteroides ovatus was markedly reduced in the GM of IBS-D, accompanied by elevated total and primary BA levels. Moreover, we found that CDCA not only was increased as the most important primary BA in IBS-D patients but also could induce VH through upregulating TGR5 in the colon and ileum of normal rats. TGR5 inhibitor could reverse the phenotype, depression-like behaviors, pathological change, and level of fecal BSH in a microbiota-humanized IBS-D rat model. Our findings proved that human-associated FMT could successfully induce the IBS-D rat model, and the imbalanced GM-BA-TGR5 axis may promote colonic mucosal barrier dysfunction and enhance VH in IBS-D.

IMPORTANCE: Visceral hypersensitivity and intestinal mucosal barrier damage are important factors that cause abnormal brain-gut interaction in diarrhea-predominant irritable bowel syndrome (IBS-D). Recently, it was found that the imbalance of the gut microbiota-bile acid axis is closely related to them. Therefore, understanding the structure and function of the gut microbiota and bile acids and the underlying mechanisms by which they shape visceral hypersensitivity and mucosal barrier damage in IBS-D is critical. An examination of intestinal feces from IBS-D patients revealed that alterations in gut microbiota and bile acid metabolism underlie IBS-D and symptom onset. We also expanded beyond existing knowledge of well-studied gut microbiota and bile acid and found that Bacteroides ovatus and chenodeoxycholic acid may be potential bacteria and bile acid involved in the pathogenesis of IBS-D. Moreover, our data integration reveals the influence of the microbiota-bile acid-TGR5 axis on barrier function and visceral hypersensitivity.}, } @article {pmid38329355, year = {2024}, author = {Nguyen, TM and Pombubpa, N and Huntemann, M and Clum, A and Foster, B and Foster, B and Roux, S and Palaniappan, K and Varghese, N and Mukherjee, S and Reddy, TBK and Daum, C and Copeland, A and Chen, I-MA and Ivanova, NN and Kyrpides, NC and Harmon-Smith, M and Eloe-Fadrosh, EA and Pietrasiak, N and Stajich, JE and Hom, EFY}, title = {Whole community shotgun metagenomes of two biological soil crust types from the Mojave Desert.}, journal = {Microbiology resource announcements}, volume = {13}, number = {3}, pages = {e0098023}, pmid = {38329355}, issn = {2576-098X}, support = {DEB-1541538, DEB-1846376//National Science Foundation (NSF)/ ; FICUS-50356//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//Joint Genome Institute (JGI)/ ; DE-AC02-05CH11231//National Energy Research Scientific Computing Center (NERSC)/ ; CA-R-PPA-211-5062-H//U.S. Department of Agriculture (USDA)/ ; Scholarship//Royal Thai Government/ ; }, abstract = {We present six whole community shotgun metagenomic sequencing data sets of two types of biological soil crusts sampled at the ecotone of the Mojave Desert and Colorado Desert in California. These data will help us understand the diversity and function of biocrust microbial communities, which are essential for desert ecosystems.}, } @article {pmid38329353, year = {2024}, author = {Dong, J-H and Xu, X and Ren, Z-X and Zhao, Y-H and Zhang, Y and Chen, L and Wu, Y and Chen, G and Cao, R and Wu, Q and Wang, H}, title = {The adaptation of bumblebees to extremely high elevation associated with their gut microbiota.}, journal = {mSystems}, volume = {9}, number = {3}, pages = {e0121923}, pmid = {38329353}, issn = {2379-5077}, support = {XDB31000000//CAS | Bureau of Frontier Sciences and Education, Chinese Academy of Sciences (BFSE)/ ; YLXL20170001//Scholarship for Academic Leader of Yunnan Province/ ; }, mesh = {Bees/genetics ; Animals ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; *Neisseriaceae/genetics ; Metagenome ; Biological Evolution ; }, abstract = {Bumblebees are among the most abundant and important pollinators for sub-alpine and alpine flowering plant species in the Northern Hemisphere, but little is known about their adaptations to high elevations. In this article, we focused on two bumblebee species, Bombus friseanus and Bombus prshewalskyi, and their respective gut microbiota. The two species, distributed through the Hengduan Mountains of southwestern China, show species replacement at different elevations. We performed genome sequencing based on 20 worker bee samples of each species. Applying evolutionary population genetics and metagenomic approaches, we detected genes under selection and analyzed functional pathways between bumblebees and their gut microbes. We found clear genetic differentiation between the two host species and significant differences in their microbiota. Species replacement occurred in both hosts and their bacteria (Snodgrassella) with an increase in elevation. These extremely high-elevation bumblebees show evidence of positive selection related to diverse biological processes. Positively selected genes involved in host immune systems probably contributed to gut microbiota changes, while the butyrate generated by gut microbiota may influence both host energy metabolism and immune systems. This suggests a close association between the genomes of the host species and their microbiomes based on some degree of natural selection.IMPORTANCETwo closely related and dominant bumblebee species, distributed at different elevations through the Hengduan Mountains of southwestern China, showed a clear genomic signature of adaptation to elevation at the molecular level and significant differences in their respective microbiota. Species replacement occurred in both hosts and their bacteria (Snodgrassella) with an increase in elevation. Bumblebees' adaptations to higher elevations are closely associated with their gut microbiota through two biological processes: energy metabolism and immune response. Information allowing us to understand the adaptive mechanisms of species to extreme conditions is implicit if we are to conserve them as their environments change.}, } @article {pmid38329258, year = {2024}, author = {Euzen, V and Ghelfenstein-Ferreira, T and Le Goff, J and Salmona, M}, title = {[Interests of clinical metagenomic in infectious diseases].}, journal = {La Revue du praticien}, volume = {74}, number = {1}, pages = {63-68}, pmid = {38329258}, issn = {2101-017X}, mesh = {Humans ; *Communicable Diseases/diagnosis ; *Microbiota/genetics ; *Anti-Infective Agents ; *Sepsis ; Metagenomics/methods ; }, abstract = {INTERESTS OF CLINICAL METAGENOMICS IN INFECTIOUS DISEASES. Clinical metagenomics (CM) is a cutting-edge molecular biology technique that is now a valuable diagnostic tool for microbiologists. It enables the detection of all microorganisms present in a sample, without any prior assumption or bias. The CM approach can be applied to various types of samples and involves multiple steps, such as extraction, library preparation, Next Generation Sequencing, and bioinformatics analysis. CM has been implemented in the diagnosis of various conditions, including infections of the central nervous system, respiratory, digestive, ocular, skin infection, and sepsis. Moreover, CM provides a comprehensive analysis of the microbiome present in the sample, microbial transcripts, and the host response in a single analysis. However, further studies are necessary to determine its place in the diagnostic algorithm. Besides diagnosis, CM has proven useful in identifying resistance to antimicrobial treatments and in epidemiology. Although the cost of CM is still higher than conventional methods, the emergence of more affordable sequencers and commercial tests will enable its implementation in a larger number of laboratories in the future.}, } @article {pmid38327077, year = {2024}, author = {Wang, N and Wang, H and Bai, Y and Zhao, Y and Zheng, X and Gao, X and Zhang, Z and Yang, L}, title = {Metagenomic Analysis Reveals Difference of Gut Microbiota in ADHD.}, journal = {Journal of attention disorders}, volume = {28}, number = {5}, pages = {872-879}, doi = {10.1177/10870547231225491}, pmid = {38327077}, issn = {1557-1246}, mesh = {Adolescent ; Child ; Humans ; *Gastrointestinal Microbiome/genetics ; *Attention Deficit Disorder with Hyperactivity ; }, abstract = {OBJECTIVE: Although ADHD is highly heritable, some environmental factors contribute to its development. Given the growing evidence that gut microbiota was involved in psychiatric disorders, we aimed to identify the characteristic composition of the gut microbiota in ADHD.

METHODS: We recruited 47 medication-naive children and adolescents with ADHD, and 60 healthy controls (HCs). We used shotgun metagenomics to measure the structure of the gut microbiota and analyzed the difference in bacterial taxa between ADHD and HCs.

RESULTS: Significant differences were found between the ADHD and HC groups in both alpha diversity indices (Simpson index, p = .025 and Shannon index, p = .049) and beta diversity indices (Euclidean distance, Bray-Curtis distance, and JSD distance, p < 2.2e-16). Nine representative species best explain the difference.

CONCLUSION: Patients with ADHD showed significant differences in the composition of the gut microbiota compared with HCs. These results may help identify potential biomarkers of ADHD.}, } @article {pmid38326388, year = {2024}, author = {Chan, OM and Xu, W and Cheng, NS and Leung, ASY and Ching, JYL and Fong, BLY and Cheong, PK and Zhang, L and Chan, FKL and Ng, SC and Leung, TF}, title = {A novel infant microbiome formula (SIM03) improved eczema severity and quality of life in preschool children.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {3168}, pmid = {38326388}, issn = {2045-2322}, mesh = {Humans ; Infant ; Child, Preschool ; Child ; Quality of Life ; Pilot Projects ; *Dermatitis, Atopic/therapy/microbiology ; *Bifidobacterium bifidum ; *Gastrointestinal Microbiome/genetics ; *Eczema/therapy ; }, abstract = {Altered gut microbiome composition has been reported in children with eczema and interventions that restore beneficial bacteria in the gut may improve eczema. This open-label pilot study aimed to investigate the efficacy of a novel infant microbiome formula (SIM03) in young children with eczema. Pre-school Chinese children aged 1-5 years old with eczema received SIM03 twice daily for three months. The novelty of SIM03 consists of both the use of a patented microencapsulation technology to protect the viability of unique Bifidobacterium bifidum and Bifidobacterium breve strains identified through big data analysis of large metagenomic datasets of young Chinese children. Paired stool samples at baseline and following SIM03 were analyzed by metagenomics sequencing. Generalized estimating equation was used to analyze changes in eczema severity, skin biophysical parameters, quality of life and stool microbiome. Twenty children aged 3.0 ± 1.6 years (10 with severe eczema) were recruited. Treatment compliance was ≥ 98%. SCORing Atopic Dermatitis score decreased significantly at two months (P = 0.008) and three months (P < 0.001), while quality of life improved significantly at 1, 2, and 3 months. The relative abundance of B. breve and microbial pathways on acetate and acetyl-CoA synthesis were enriched in stool samples at one month (P = 0.0014). Children who demonstrated increased B. bifidum after SIM03 showed improvement in sleep loss (P = 0.045). Relative abundance of B. breve correlated inversely with eczema extent (P = 0.023) and intensity (P = 0.019) only among patients with increased B. breve at Month 3. No serious adverse event was observed. In conclusion, SIM03 is well tolerated. This patented microbiome formula improves disease severity and quality of life in young eczematous children by enhancing the delivery of B. bifidum and B. breve in the gut. SIM03 is a potential treatment option for childhood eczema.}, } @article {pmid38325494, year = {2024}, author = {Forsmark, B and Bizjak, T and Nordin, A and Rosenstock, NP and Wallander, H and Gundale, MJ}, title = {Shifts in microbial community composition and metabolism correspond with rapid soil carbon accumulation in response to 20 years of simulated nitrogen deposition.}, journal = {The Science of the total environment}, volume = {918}, number = {}, pages = {170741}, doi = {10.1016/j.scitotenv.2024.170741}, pmid = {38325494}, issn = {1879-1026}, mesh = {*Nitrogen/analysis ; Soil ; Carbon ; Forests ; *Microbiota ; Soil Microbiology ; }, abstract = {Anthropogenic nitrogen (N) deposition and fertilization in boreal forests frequently reduces decomposition and soil respiration and enhances C storage in the topsoil. This enhancement of the C sink can be as strong as the aboveground biomass response to N additions and has implications for the global C cycle, but the mechanisms remain elusive. We hypothesized that this effect would be associated with a shift in the microbial community and its activity, and particularly by fungal taxa reported to be capable of lignin degradation and organic N acquisition. We sampled the organic layer below the intact litter of a Norway spruce (Picea abies (L.) Karst) forest in northern Sweden after 20 years of annual N additions at low (12.5 kg N ha[-1] yr[-1]) and high (50 kg N ha[-1] yr[-1]) rates. We measured microbial biomass using phospholipid fatty-acid analysis (PLFA) and ergosterol measurements and used ITS metagenomics to profile the fungal community of soil and fine-roots. We probed the metabolic activity of the soil community by measuring the activity of extracellular enzymes and evaluated its relationships with the most N responsive soil fungal species. Nitrogen addition decreased the abundance of fungal PLFA markers and changed the fungal community in humus and fine-roots. Specifically, the humus community changed in part due to a shift from Oidiodendron pilicola, Cenococcum geophilum, and Cortinarius caperatus to Tylospora fibrillosa and Russula griseascens. These microbial community changes were associated with decreased activity of Mn-peroxidase and peptidase, and an increase in the activity of C acquiring enzymes. Our results show that the rapid accumulation of C in the humus layer frequently observed in areas with high N deposition is consistent with a shift in microbial metabolism, where decomposition associated with organic N acquisition is downregulated when inorganic N forms are readily available.}, } @article {pmid38325450, year = {2024}, author = {Lin, W and Cao, S and Wu, Q and Xu, F and Li, R and Cui, L}, title = {Size effects of microplastics on antibiotic resistome and core microbiome in an urban river.}, journal = {The Science of the total environment}, volume = {919}, number = {}, pages = {170716}, doi = {10.1016/j.scitotenv.2024.170716}, pmid = {38325450}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Microbiota ; *Microplastics ; Plastics ; Rivers ; Polystyrenes/chemistry ; Polypropylenes/chemistry ; }, abstract = {Microplastics (MPs) in aquatic environments provide a new ecological niche that facilitates the attachment of antibiotic-resistance genes (ARGs) and pathogens. However, the effect of particle size on the colonization of antibiotic resistomes and pathogens remains poorly understood. To address this knowledge gap, this study explored the antibiotic resistome and core microbiome on three distinct types of MPs including polyethylene, polypropylene, and polystyrene (PS), with varying sizes of 30, 200, and 3000 μm by metagenomic sequencing. Our finding showed that the ARG abundances of the PS type increased by 4-folds with increasing particle size from 30 to 3000 μm, and significant differences in ARG profiles were found across the three MP types. In addition, the concentrations of ARGs and mobile genetic elements (MGEs) were markedly higher in the MPs than in the surrounding water, indicating their enrichment at these artificial interfaces. Notably, several pathogens such as Pseudomonas aeruginosa, Mycobacterium tuberculosis, and Legionella pneumophila were enriched in MP biofilms, and the co-occurrence of ARGs and virulence factor genes (VFGs)/MGEs suggested the presence of pathogenic antibiotic-resistant microbes with potential mobility. Both redundancy analysis (RDA) and structural equation modeling (SEM) demonstrated that physicochemical properties such as zeta potential, MP size, and contact angle were the most significant contributors to the antibiotic resistome. Strikingly, no significant differences were observed in the health risk scores of the ARG profiles among different sizes and types of MPs. This study expands our knowledge on the impact of MP size on microbial risks, thus enhancing our understanding of the potential health hazards they pose.}, } @article {pmid38325080, year = {2024}, author = {Yu, X and Gu, C and Guo, X and Guo, R and Zhu, L and Qiu, X and Chai, J and Liu, F and Feng, Z}, title = {Dynamic changes of microbiota and metabolite of traditional Hainan dregs vinegar during fermentation based on metagenomics and metabolomics.}, journal = {Food chemistry}, volume = {444}, number = {}, pages = {138641}, doi = {10.1016/j.foodchem.2024.138641}, pmid = {38325080}, issn = {1873-7072}, mesh = {*Acetic Acid/metabolism ; Fermentation ; *Microbiota ; Lactobacillus/metabolism ; Metagenomics/methods ; }, abstract = {Hainan dregs vinegar (HNDV) is a traditional fermented food in China that is renowned for its unique flavor. HNDV is one of the most popular vinegars in Southeast Asia. However, research on the microorganisms and characteristic metabolites specific to HNDV is lacking. This study investigated the changes in microbial succession, volatile flavor compounds and characteristic non-volatile flavor compounds during HNDV fermentation based on metagenomics and metabolomics. The predominant microbial genera were Lactococcus, Limosilactobacillus, Lactiplantibacillus, and Saccharomyces. Unlike traditional vinegar, l-lactic acid was identified as the primary organic acid in HNDV. Noteworthy flavor compounds specific to HNDV included 3-methylthiopropanol and dl-phenylalanine. Significant associations were observed between six predominant microorganisms and six characteristic volatile flavor compounds, as well as seven characteristic non-volatile flavor compounds. The present results contribute to the development of starter cultures and the enhancement of HNDV quality.}, } @article {pmid38320576, year = {2023}, author = {Salas-Espejo, E and Terrón-Camero, LC and Ruiz, JL and Molina, NM and Andrés-León, E}, title = {Exploring the Microbiome in Human Reproductive Tract: High-Throughput Methods for the Taxonomic Characterization of Microorganisms.}, journal = {Seminars in reproductive medicine}, volume = {41}, number = {5}, pages = {125-143}, doi = {10.1055/s-0044-1779025}, pmid = {38320576}, issn = {1526-4564}, mesh = {Pregnancy ; Female ; Humans ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; *Microbiota/genetics ; Vagina ; Pregnancy Outcome ; }, abstract = {Microorganisms are important due to their widespread presence and multifaceted roles across various domains of life, ecology, and industries. In humans, they underlie the proper functioning of multiple systems crucial to well-being, including immunological and metabolic functions. Emerging research addressing the presence and roles of microorganisms within human reproduction is increasingly relevant. Studies implementing new methodologies (e.g., to investigate vaginal, uterine, and semen microenvironments) can now provide relevant insights into fertility, reproductive health, or pregnancy outcomes. In that sense, cutting-edge sequencing techniques, as well as others such as meta-metabolomics, culturomics, and meta-proteomics, are becoming more popular and accessible worldwide, allowing the characterization of microbiomes at unprecedented resolution. However, they frequently involve rather complex laboratory protocols and bioinformatics analyses, for which researchers may lack the required expertise. A suitable pipeline would successfully enable both taxonomic classification and functional profiling of the microbiome, providing easy-to-understand biological interpretations. However, the selection of an appropriate methodology would be crucial, as it directly impacts the reproducibility, accuracy, and quality of the results and observations. This review focuses on the different current microbiome-related techniques in the context of human reproduction, encompassing niches like vagina, endometrium, and seminal fluid. The most standard and reliable methods are 16S rRNA gene sequencing, metagenomics, and meta-transcriptomics, together with complementary approaches including meta-proteomics, meta-metabolomics, and culturomics. Finally, we also offer case examples and general recommendations about the most appropriate methods and workflows and discuss strengths and shortcomings for each technique.}, } @article {pmid38320392, year = {2024}, author = {Lyte, JM and Eckenberger, J and Keane, J and Robinson, K and Bacon, T and Assumpcao, ALFV and Donoghue, AM and Liyanage, R and Daniels, KM and Caputi, V and Lyte, M}, title = {Cold stress initiates catecholaminergic and serotonergic responses in the chicken gut that are associated with functional shifts in the microbiome.}, journal = {Poultry science}, volume = {103}, number = {3}, pages = {103393}, pmid = {38320392}, issn = {1525-3171}, support = {P30 GM103450/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Chickens ; Cold-Shock Response ; RNA, Ribosomal, 16S ; *Microbiota ; Metagenome ; Mammals ; }, abstract = {Climate change is one of the most significant challenges facing the sustainability of global poultry production. Stress resulting from extreme temperature swings, including cold snaps, is a major concern for food production birds. Despite being well-documented in mammals, the effect of environmental stress on enteric neurophysiology and concomitant impact on host-microbiome interactions remains poorly understood in birds. As early life stressors may imprint long-term adaptive changes in the host, the present study sought to determine whether cold temperature stress, a prominent form of early life stress in chickens, elicits changes in enteric stress-related neurochemical concentrations that coincide with compositional and functional changes in the microbiome that persist into the later life of the bird. Chicks were, or were not, subjected to cold ambient temperature stress during the first week post-hatch and then remained at normal temperature for the remainder of the study. 16S rRNA gene and shallow shotgun metagenomic analyses demonstrated taxonomic and functional divergence between the cecal microbiomes of control and cold stressed chickens that persisted for weeks following cessation of the stressor. Enteric concentrations of serotonin, norepinephrine, and other monoamine neurochemicals were elevated (P < 0.05) in both cecal tissue and luminal content of cold stressed chickens. Significant (P < 0.05) associations were identified between cecal neurochemical concentrations and microbial taxa, suggesting host enteric neurochemical responses to environmental stress may shape the cecal microbiome. These findings demonstrate for the first time that early life exposure to environmental temperature stress can change the developmental trajectory of both the chicken cecal microbiome and host neuroendocrine enteric physiology. As many neurochemicals serve as interkingdom signaling molecules, the relationships identified here could be exploited to control the impact of climate change-driven stress on avian enteric host-microbe interactions.}, } @article {pmid38319284, year = {2024}, author = {Nguyen, SM and Tran, HTT and Long, J and Shrubsole, MJ and Cai, H and Yang, Y and Cai, Q and Tran, TV and Zheng, W and Shu, XO}, title = {Gut microbiome in association with chemotherapy-induced toxicities among patients with breast cancer.}, journal = {Cancer}, volume = {130}, number = {11}, pages = {2014-2030}, doi = {10.1002/cncr.35229}, pmid = {38319284}, issn = {1097-0142}, support = {OISE-19-66185//Foundation for the National Institutes of Health/ ; D43 TW009337/TW/FIC NIH HHS/United States ; /GH/CGH CDC HHS/United States ; P20 CA210300/CA/NCI NIH HHS/United States ; /CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Breast Neoplasms/drug therapy ; *Gastrointestinal Microbiome/drug effects ; Female ; Middle Aged ; Prospective Studies ; Aged ; Adult ; Neutropenia/chemically induced/microbiology ; Metagenomics/methods ; Feces/microbiology ; Antineoplastic Combined Chemotherapy Protocols/adverse effects/therapeutic use ; Antineoplastic Agents/adverse effects ; }, abstract = {BACKGROUND: Little research has focused on the relationship between gut microbiome and chemotherapy-induced toxicity.

METHODS: This prospective study involves 301 patients with breast cancer who had prechemotherapy stool samples collected. Gut microbiome was sequenced by shotgun metagenomics; associations with chemotherapy-induced toxicities during first-line treatment by gut microbial diversity, composition, and metabolic pathways with severe (i.e., grade ≥3) hematological and gastrointestinal toxicities were evaluated via multivariable logistic regression.

RESULTS: High prechemotherapy α-diversity was associated with a significantly reduced risk of both severe hematological toxicity (odds ratio [OR] = 0.94; 95% CI, 0.89-0.99; p = .048) and neutropenia (OR = 0.94; 95% CI, 0.89-0.99; p = .016). A high abundance of phylum Synergistota, class Synergistia, and order Synergistales were significantly associated with a reduced risk of severe neutropenia; conversely, enrichment of phylum Firmicutes C, class Negativicutes, phylum Firmicutes I, and class Bacilli A, order Paenibacillales were significantly associated with an increased risk of severe neutropenia (p range: 0.012-2.32 × 10[-3]; false discovery rate <0.1). Significant positive associations were also observed between severe nausea/vomiting and high Chao1 indexes, β-diversity (p < .05), 20 species belonging to the family Lachnospiraceae, Oscillospiraceae, and Ruminococcaceae (p value range: 6.14 × 10[-3] to 1.33 × 10[-5]; false discovery rate <0.1), and three metabolic pathways involved in reductive tricarboxylic acid cycle I and cycle II, and an incomplete reductive tricarboxylic acid cycle (p < .01). Conversely, a high abundance of species Odoribacter laneus and the pathway related to the L-proline biosynthesis II were inversely associated with severe nausea/vomiting.

CONCLUSIONS: Our study suggests that gut microbiota may be a potential preventive target to reduce chemotherapy-induced toxicity.}, } @article {pmid38318812, year = {2024}, author = {Li, Z and Feng, C and Lei, J and He, X and Wang, Q and Zhao, Y and Qian, Y and Zhan, X and Shen, Z}, title = {Farmland Microhabitat Mediated by a Residual Microplastic Film: Microbial Communities and Function.}, journal = {Environmental science & technology}, volume = {58}, number = {8}, pages = {3654-3664}, doi = {10.1021/acs.est.3c07717}, pmid = {38318812}, issn = {1520-5851}, mesh = {Farms ; *Microplastics ; Plastics ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Nitrogen ; Soil ; Sulfur ; }, abstract = {How the plastisphere mediated by the residual microplastic film in farmlands affects microhabitat systems is unclear. Here, microbial structure, assembly, and biogeochemical cycling in the plastisphere and soil in 33 typical farmland sites were analyzed by amplicon sequencing of 16S rRNA genes and ITS and metagenome analysis. The results indicated that residual microplastic film was colonized by microbes, forming a unique niche called the plastisphere. Notable differences in the microbial community structure and function were observed between soil and plastisphere. Residual microplastic film altered the microbial symbiosis and assembly processes. Stochastic processes significantly dominated the assembly of the bacterial community in the plastisphere and soil but only in the plastisphere for the fungal community. Deterministic processes significantly dominated the assembly of fungal communities only in soil. Moreover, the plastisphere mediated by the residual microplastic film acted as a preferred vector for pathogens and microorganisms associated with plastic degradation and the nitrogen and sulfur cycle. The abundance of genes associated with denitrification and sulfate reduction activity in the plastisphere was pronouncedly higher than that of soil, which increase the potential risk of nitrogen and sulfur loss. The results will offer a scientific understanding of the harm caused by the residual microplastic film in farmlands.}, } @article {pmid38318164, year = {2024}, author = {Piazzesi, A and Pane, S and Del Chierico, F and Romani, L and Campana, A and Palma, P and Putignani, L}, title = {The pediatric gut bacteriome and virome in response to SARS-CoV-2 infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1335450}, pmid = {38318164}, issn = {2235-2988}, mesh = {Adult ; Humans ; Child ; *COVID-19 ; Virome ; SARS-CoV-2/genetics ; *Microbiota ; Anti-Bacterial Agents/pharmacology/therapeutic use ; }, abstract = {INTRODUCTION: Since the beginning of the SARS-CoV-2 pandemic in early 2020, it has been apparent that children were partially protected from both infection and the more severe forms of the disease. Many different mechanisms have been proposed to explain this phenomenon, including children's frequent exposure to other upper respiratory infections and vaccines, and which inflammatory cytokines they are more likely to produce in response to infection. Furthermore, given the presence of SARS-CoV-2 in the intestine and its ability to infect enterocytes, combined with the well described immunomodulatory capabilities of the microbiome, another potential contributing factor may be the presence of certain protective microbial members of the gut microbiota (GM).

METHODS: We performed shotgun metagenomic sequencing and profiled both the bacteriome and virome of the GM of pediatric SARS-CoV-2 patients compared to healthy, age-matched subjects.

RESULTS: We found that, while pediatric patients do share some pro-inflammatory microbial signatures with adult patients, they also possess a distinct microbial signature of protective bacteria previously found to be negatively correlated with SARS-CoV-2 infectivity and COVID-19 severity. COVID-19 was also associated with higher fecal Cytomegalovirus load, and with shifts in the relative abundances of bacteriophages in the GM. Furthermore, we address how the preventative treatment of COVID-19 patients with antibiotics, a common practice especially in the early days of the pandemic, affected the bacteriome and virome, as well as the abundances of antimicrobial resistance and virulence genes in these patients.

DISCUSSION: To our knowledge, this is the first study to address the bacteriome, virome, and resistome of pediatric patients in response to COVID-19 and to preventative antibiotics use.}, } @article {pmid38317217, year = {2024}, author = {Xing, JH and Niu, TM and Zou, BS and Yang, GL and Shi, CW and Yan, QS and Sun, MJ and Yu, T and Zhang, SM and Feng, XZ and Fan, SH and Huang, HB and Wang, JH and Li, MH and Jiang, YL and Wang, JZ and Cao, X and Wang, N and Zeng, Y and Hu, JT and Zhang, D and Sun, WS and Yang, WT and Wang, CF}, title = {Gut microbiota-derived LCA mediates the protective effect of PEDV infection in piglets.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {20}, pmid = {38317217}, issn = {2049-2618}, support = {U21A20261， 721 32202819, 31941018, 31972696 and 32072888//National Natural Science Foundation of China/ ; CARS-35//China Agriculture Research System of MOF 722 and MARA/ ; 20190301042NY, YDZJ202102CXJD029, and 20210202102NC//Science and Technology Development Program of Jilin Province/ ; }, mesh = {Animals ; Swine ; *Gastrointestinal Microbiome ; *Porcine epidemic diarrhea virus ; *Coronavirus Infections/prevention & control/veterinary ; *Swine Diseases/prevention & control ; Disease Resistance ; }, abstract = {BACKGROUND: The gut microbiota is a critical factor in the regulation of host health, but the relationship between the differential resistance of hosts to pathogens and the interaction of gut microbes is not yet clear. Herein, we investigated the potential correlation between the gut microbiota of piglets and their disease resistance using single-cell transcriptomics, 16S amplicon sequencing, metagenomics, and untargeted metabolomics.

RESULTS: Porcine epidemic diarrhea virus (PEDV) infection leads to significant changes in the gut microbiota of piglets. Notably, Landrace pigs lose their resistance quickly after being infected with PEDV, but transplanting the fecal microbiota of Min pigs to Landrace pigs alleviated the infection status. Macrogenomic and animal protection models identified Lactobacillus reuteri and Lactobacillus amylovorus in the gut microbiota as playing an anti-infective role. Moreover, metabolomic screening of the secondary bile acids' deoxycholic acid (DCA) and lithocholic acid (LCA) correlated significantly with Lactobacillus reuteri and Lactobacillus amylovorus, but only LCA exerted a protective function in the animal model. In addition, LCA supplementation altered the distribution of intestinal T-cell populations and resulted in significantly enriched CD8[+] CTLs, and in vivo and in vitro experiments showed that LCA increased SLA-I expression in porcine intestinal epithelial cells via FXR receptors, thereby recruiting CD8[+] CTLs to exert antiviral effects.

CONCLUSIONS: Overall, our findings indicate that the diversity of gut microbiota influences the development of the disease, and manipulating Lactobacillus reuteri and Lactobacillus amylovorus, as well as LCA, represents a promising strategy to improve PEDV infection in piglets. Video Abstract.}, } @article {pmid38316929, year = {2024}, author = {Ritz, NL and Draper, LA and Bastiaanssen, TFS and Turkington, CJR and Peterson, VL and van de Wouw, M and Vlckova, K and Fülling, C and Guzzetta, KE and Burokas, A and Harris, H and Dalmasso, M and Crispie, F and Cotter, PD and Shkoporov, AN and Moloney, GM and Dinan, TG and Hill, C and Cryan, JF}, title = {The gut virome is associated with stress-induced changes in behaviour and immune responses in mice.}, journal = {Nature microbiology}, volume = {9}, number = {2}, pages = {359-376}, pmid = {38316929}, issn = {2058-5276}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Mice ; Virome ; RNA, Ribosomal, 16S/genetics ; *Viruses/genetics ; *Microbiota ; *Bacteriophages/genetics ; Immunity ; }, abstract = {The microbiota-gut-brain axis has been shown to play an important role in the stress response, but previous work has focused primarily on the role of the bacteriome. The gut virome constitutes a major portion of the microbiome, with bacteriophages having the potential to remodel bacteriome structure and activity. Here we use a mouse model of chronic social stress, and employ 16S rRNA and whole metagenomic sequencing on faecal pellets to determine how the virome is modulated by and contributes to the effects of stress. We found that chronic stress led to behavioural, immune and bacteriome alterations in mice that were associated with changes in the bacteriophage class Caudoviricetes and unassigned viral taxa. To determine whether these changes were causally related to stress-associated behavioural or physiological outcomes, we conducted a faecal virome transplant from mice before stress and autochthonously transferred it to mice undergoing chronic social stress. The transfer of the faecal virome protected against stress-associated behaviour sequelae and restored stress-induced changes in select circulating immune cell populations, cytokine release, bacteriome alterations and gene expression in the amygdala. These data provide evidence that the virome plays a role in the modulation of the microbiota-gut-brain axis during stress, indicating that these viral populations should be considered when designing future microbiome-directed therapies.}, } @article {pmid38316105, year = {2024}, author = {Benvenuti, E and Ferriani, R and Gianella, P and Ruggiero, P and Cagnasso, F and Borrelli, A and Benvenuto, G and Bertoldi, L and Bottero, E}, title = {The fecal bacterial microbiota is not useful for discriminating between lymphoplasmacytic enteritis and low-grade intestinal T-cell lymphoma in cats nor for predicting therapeutic response.}, journal = {American journal of veterinary research}, volume = {85}, number = {4}, pages = {}, doi = {10.2460/ajvr.23.11.0251}, pmid = {38316105}, issn = {1943-5681}, mesh = {Humans ; Cats ; Animals ; RNA, Ribosomal, 16S/genetics ; *Enteritis/diagnosis/veterinary ; Feces/microbiology ; Bacteria ; *Microbiota ; *Lymphoma, T-Cell/veterinary ; *Cat Diseases/diagnosis ; }, abstract = {OBJECTIVE: To evaluate the fecal bacterial microbiota at the time of diagnosis (T0) and after 1 month of therapy (T1) in cats diagnosed with lymphoplasmacytic enteritis (LPE) or cats with low-grade intestinal T-cell lymphoma (LGITL) and to compare these findings with those of healthy cats.

ANIMALS: 5 healthy cats, 13 cats with LPE, and 7 cats with LGITL were prospectively enrolled between June 2020 and June 2021.

METHODS: Fecal samples were collected at T0 and T1, and DNA was extracted for 16S ribosomal amplicon sequencing. Alpha diversity and beta diversity were computed. The taxonomic assignment was performed using sequences from the Silva v138 formatted reference database. Differential abundant taxa were selected in each taxonomic level, with the P value adjusted < .05, as the cut-off.

RESULTS: No significant differences in alpha and beta diversity were found either at T0 or T1 between healthy and diseased cats or between cats with LPE and LGITL. Beta-diversity analysis showed an increase in the Fusobacteriaceae family in cats with LGITL at T0, compared to cats with LPE. Regardless of histological diagnosis, several microbiota differences were found at T0 based on serum cobalamin levels.

CLINICAL RELEVANCE: Fecal samples were successfully used to characterize the bacteriome of the intestinal tract in cats by 16S rRNA gene sequencing. However, results highlighted that the metagenomic evaluation was not useful to discriminate between LPE and LGITL nor to predict the therapeutic response in this study population.}, } @article {pmid38315959, year = {2024}, author = {Meldrum, OW and Donaldson, GC and Narayana, JK and Ivan, FX and Jaggi, TK and Mac Aogáin, M and Finney, LJ and Allinson, JP and Wedzicha, JA and Chotirmall, SH}, title = {Accelerated Lung Function Decline and Mucus-Microbe Evolution in Chronic Obstructive Pulmonary Disease.}, journal = {American journal of respiratory and critical care medicine}, volume = {210}, number = {3}, pages = {298-310}, pmid = {38315959}, issn = {1535-4970}, support = {020458-00001//LKCMedicine-ICL Fellowship/ ; LEARN008//LKCMedicine LEARN Grant/ ; SGL026/1079//National Heart and Lung Institute (NHLI) Lectureship/ ; MOH-000141//National Medical Research Council/ ; MOH-001356//National Medical Research Council/ ; MOH-000710//National Medical Research Council/ ; RT1/22//Singapore Ministry of Education under its AcRF Tier 1 Grant/ ; //National Institute of Health Research (NIHR) Biomedical Research Centre to Imperial College London/ ; //National Institute of Health Research (NIHR) Biomedical Research Centre to Royal Brompton Hospital/ ; }, mesh = {*Pulmonary Disease, Chronic Obstructive/microbiology ; *Sputum/microbiology ; Disease Progression ; Respiratory Function Tests ; *Microbiota ; *Mucus/microbiology ; Humans ; Male ; Female ; Prospective Studies ; Achromobacter ; Klebsiella ; Mucin 5AC/metabolism ; Mucin-5B/metabolism ; Longitudinal Studies ; Forced Expiratory Volume ; Middle Aged ; Aged ; Aged, 80 and over ; }, abstract = {Rationale: Progressive lung function loss is recognized in chronic obstructive pulmonary disease (COPD); however, no study concurrently evaluates how accelerated lung function decline relates to mucus properties and the microbiome in COPD. Objectives: Longitudinal assessment of mucus and microbiome changes accompanying accelerated lung function decline in patients COPD. Methods: This was a prospective, longitudinal assessment of the London COPD cohort exhibiting the greatest FEV1 decline (n = 30; accelerated decline; 156 ml/yr FEV1 loss) and with no FEV1 decline (n = 28; nondecline; 49 ml/yr FEV1 gain) over time. Lung microbiomes from paired sputum (total 116 specimens) were assessed by shotgun metagenomics and corresponding mucus profiles evaluated for biochemical and biophysical properties. Measurements and Main Results: Biochemical and biophysical mucus properties are significantly altered in the accelerated decline group. Unsupervised principal component analysis showed clear separation, with mucus biochemistry associated with accelerated decline, whereas biophysical mucus characteristics contributed to interindividual variability. When mucus and microbes are considered together, an accelerated decline mucus-microbiome association emerges, characterized by increased mucin (MUC5AC [mucin 5AC] and MUC5B [mucin 5B]) concentration and the presence of Achromobacter and Klebsiella. As COPD progresses, mucus-microbiome shifts occur, initially characterized by low mucin concentration and transition from viscous to elastic dominance accompanied by the commensals Veillonella, Gemella, Rothia, and Prevotella (Global Initiative for Chronic Obstructive Lung Disease [GOLD] A and B) before transition to increased mucus viscosity, mucins, and DNA concentration together with the emergence of pathogenic microorganisms including Haemophilus, Moraxella, and Pseudomonas (GOLD E). Conclusions: Mucus-microbiome associations evolve over time with accelerated lung function decline, symptom progression, and exacerbations affording fresh therapeutic opportunities for early intervention.}, } @article {pmid38315309, year = {2024}, author = {Macharoen, P and Mhuantong, W and Wannawong, T and Leesutthiphonchai, W and Tanasupawat, S and Suwannarach, N and Kuncharoen, N}, title = {Bacterial diversity, community structure and function in association of potato scabby tubers during storage in northern Thailand.}, journal = {Folia microbiologica}, volume = {69}, number = {4}, pages = {941-952}, pmid = {38315309}, issn = {1874-9356}, support = {N42A650203//National Research Council of Thailand/ ; }, mesh = {*Solanum tuberosum/microbiology ; Thailand ; *Plant Tubers/microbiology ; *Plant Diseases/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; *Food Storage ; Biodiversity ; Temperature ; Phylogeny ; Microbiota ; DNA, Bacterial/genetics ; Metagenomics ; }, abstract = {Potato scab is a common potato tuber disease that affects quality and cost in the marketplace, shortening storage, and increasing the chance for secondary infection. The tubers with disease severity of 1 to 4 are accepted and stored in potato storage for cheap selling in Thailand. However, there are few studies of the bacterial community of the scabby tuber during storage. Thus, we aim to elucidate the diversity, structure, and function of the bacterial community of 30-day storage potato scabby tubers stored in different temperatures using 16S amplicon metagenomic sequencing. Bacterial communities of storage potato scabby tubers (Spunta cultivar) collected from different storage temperatures, 4 °C (MEP1) and 6 °C (MEP2), were characterized using 16S rRNA amplicon metagenomic sequencing. The alpha-diversity abundance in the bacteriome of the scabby tubers stored at 6 °C was higher than in those stored at 4 °C. Actinobacteria (34.7%) was a dominant phylum in MEP1, while Proteobacteria (39.9%) was predominant in MEP2. The top 10 genera of both communities were Rhizobium group, Streptomyces, Pectobacterium, Ruminococcus, Cellulomonas, Promicromonospora, Prevotella, Enterobacter, Pedobacter, and Paenarthrobacter. Moreover, functional profile prediction of both communities reveals essential genes in the pathosystem: nos, bglA, and cebEFG-msiK for potato scab disease and phc and peh operons for rot disease. Our findings are the first study to explore details of the bacteriome of the accepted potato scabby tubers for selling during storage in Thailand and strongly indicate that although potatoes were stored at low temperatures, diseases still occur by secondary pathogens.}, } @article {pmid38312103, year = {2024}, author = {Han, B and Tang, D and Lv, X and Fan, J and Li, S and Zhu, H and Zhang, J and Xu, S and Xu, X and Huang, Z and Huang, Z and Lin, G and Zhan, L and Lv, X}, title = {Integrated multi-omics reveal gut microbiota-mediated bile acid metabolism alteration regulating immunotherapy responses to anti-α4β7-integrin in Crohn's disease.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2310894}, pmid = {38312103}, issn = {1949-0984}, mesh = {Animals ; Mice ; *Crohn Disease/drug therapy ; *Gastrointestinal Microbiome ; Multiomics ; Integrins/genetics/therapeutic use ; *Colitis/chemically induced/therapy ; Bile Acids and Salts/therapeutic use ; Immunotherapy ; }, abstract = {Gut microbiota and related metabolites are both crucial factors that significantly influence how individuals with Crohn's disease respond to immunotherapy. However, little is known about the interplay among gut microbiota, metabolites, Crohn's disease, and the response to anti-α4β7-integrin in current studies. Our research utilized 2,4,6-trinitrobenzene sulfonic acid to induce colitis based on the humanized immune system mouse model and employed a combination of whole-genome shotgun metagenomics and non-targeted metabolomics to investigate immunotherapy responses. Additionally, clinical cases with Crohn's disease initiating anti-α4β7-integrin therapy were evaluated comprehensively. Particularly, 16S-rDNA gene high-throughput sequencing and targeted bile acid metabolomics were conducted at weeks 0, 14, and 54. We found that anti-α4β7-integrin therapy has shown significant potential for mitigating disease phenotypes in remission-achieving colitis mice. Microbial profiles demonstrated that not only microbial composition but also microbially encoded metabolic pathways could predict immunotherapy responses. Metabonomic signatures revealed that bile acid metabolism alteration, especially elevated secondary bile acids, was a determinant of immunotherapy responses. Especially, the remission mice significantly enriched the proportion of the beneficial Lactobacillus and Clostridium genera, which were correlated with increased gastrointestinal levels of BAs involving lithocholic acid and deoxycholic acid. Moreover, most of the omics features observed in colitis mice were replicated in clinical cases. Notably, anti-α4β7 integrin provided sustained therapeutic benefits in clinical remitters during follow-up, and long-lasting remission was linked to persistent changes in the microbial-related bile acids. In conclusion, gut microbiota-mediated bile acid metabolism alteration could play a crucial role in regulating immunotherapy responses to anti-α4β7-integrin in Crohn's disease. Therefore, the identification of prognostic microbial signals facilitates the advancement of targeted probiotics that activate anti-inflammatory bile acid metabolic pathways, thereby improving immunotherapy responses. The integrated multi-omics established in our research provide valuable insights into potential mechanisms that impact treatment responses in complex diseases.}, } @article {pmid38310089, year = {2024}, author = {Mercado-Evans, V and Mejia, ME and Zulk, JJ and Ottinger, S and Hameed, ZA and Serchejian, C and Marunde, MG and Robertson, CM and Ballard, MB and Ruano, SH and Korotkova, N and Flores, AR and Pennington, KA and Patras, KA}, title = {Gestational diabetes augments group B Streptococcus infection by disrupting maternal immunity and the vaginal microbiota.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1035}, pmid = {38310089}, issn = {2041-1723}, support = {R21 AI149366/AI/NIAID NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; R25 GM056929/GM/NIGMS NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; T32 GM152777/GM/NIGMS NIH HHS/United States ; R21 AI173448/AI/NIAID NIH HHS/United States ; T32 GM136554/GM/NIGMS NIH HHS/United States ; R01 DK128053/DK/NIDDK NIH HHS/United States ; F31 AI167547/AI/NIAID NIH HHS/United States ; F31 HD111236/HD/NICHD NIH HHS/United States ; F31 AI167538/AI/NIAID NIH HHS/United States ; }, mesh = {Pregnancy ; Female ; Humans ; Animals ; Mice ; *Diabetes, Gestational ; Infectious Disease Transmission, Vertical ; *Microbiota ; Cytokines ; Vagina/microbiology ; Streptococcus ; Streptococcus agalactiae ; *Streptococcal Infections/microbiology ; }, abstract = {Group B Streptococcus (GBS) is a pervasive perinatal pathogen, yet factors driving GBS dissemination in utero are poorly defined. Gestational diabetes mellitus (GDM), a complication marked by dysregulated immunity and maternal microbial dysbiosis, increases risk for GBS perinatal disease. Using a murine GDM model of GBS colonization and perinatal transmission, we find that GDM mice display greater GBS in utero dissemination and subsequently worse neonatal outcomes. Dual-RNA sequencing reveals differential GBS adaptation to the GDM reproductive tract, including a putative glycosyltransferase (yfhO), and altered host responses. GDM immune disruptions include reduced uterine natural killer cell activation, impaired recruitment to placentae, and altered maternofetal cytokines. Lastly, we observe distinct vaginal microbial taxa associated with GDM status and GBS invasive disease status. Here, we show a model of GBS dissemination in GDM hosts that recapitulates several clinical aspects and identifies multiple host and bacterial drivers of GBS perinatal disease.}, } @article {pmid38309691, year = {2025}, author = {Yuan, Q and Liu, W and Hao, W and Chen, Y and Xiao, Y and Li, H and Shui, M and Wu, DT and Wang, S}, title = {Glycosidic linkages of fungus polysaccharides influence the anti-inflammatory activity in mice.}, journal = {Journal of advanced research}, volume = {67}, number = {}, pages = {161-172}, doi = {10.1016/j.jare.2024.01.037}, pmid = {38309691}, issn = {2090-1224}, mesh = {Animals ; Mice ; *Anti-Inflammatory Agents/pharmacology/chemistry ; *Colitis/drug therapy/metabolism/chemically induced ; *Dextran Sulfate ; *Fungal Polysaccharides/chemistry/pharmacology ; Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Glycosides/pharmacology/chemistry ; Male ; Mice, Inbred C57BL ; Basidiomycota/chemistry ; Polysaccharides/chemistry/pharmacology ; Cytokines/metabolism ; }, abstract = {INTRODUCTION: Over decades, the source-function relationships of bioactive polysaccharides have been progressively investigated, however, it is still unclear how a defined structure may conduce to the bioactivities of polysaccharides.

OBJECTIVES: To explore the structure-function relationship of fungus polysaccharides, we employed a dextran sulfate sodium (DSS)-induced colitis mouse model to compare the anti-inflammatory activity of two fungus polysaccharides from Dictyophora indusiata (DIP) and Tremella fuciformis (TFP), which exhibit distinct glycosidic linkages.

METHODS: The structures of DIP and TFP were characterized through molecular weight detection, molecular morphology analysis, methylation analysis, and NMR analysis. Subsequently, we employed a DSS-induced colitis model to assess the anti-inflammatory efficacy of DIP and TFP. The colitis symptoms, histological morphology, intestinal inflammatory cytokines, and the composition and function of gut microbiota before and after polysaccharides treatment in colitis mice were also investigated.

RESULTS: DIP, l,3-β-D-glucan with 1,4-β and 1,6-β-D-Glcp as branched chains, exhibited superior therapeutic effect than that of TFP consisted of a linear 1,3-α-D-mannose backbone with D-xylose and L-fucose in the side chains. Both DIP and TFP relieved DSS-induced colitis in a gut microbiota-dependent manner. Furthermore, metagenomics showed that DIP and TFP could partially reverse the bacterial function in colitis mice. Glycoside Hydrolase 1 (GH1) and GH3 were identified as being involved in hydrolyzing the glucose linkages in DIP, while GH92 and GH29 were predicted to be active in cleaving the α-1,3-linked mannose linkages and the glycosidic bonds of L-fucose residues in TFP.

CONCLUSION: Our findings highlight the pivotal role of glycosidic linkages in anti-inflammatory activities of fungus polysaccharides and would promote the design and discovery of polysaccharides with designated activity to be used as functional foods and/or therapeutics.}, } @article {pmid38309618, year = {2024}, author = {Bouzid, F and Gtif, I and Charfeddine, S and Abid, L and Kharrat, N}, title = {Polyphasic molecular approach to the characterization of methanogens in the saliva of Tunisian adults.}, journal = {Anaerobe}, volume = {85}, number = {}, pages = {102820}, doi = {10.1016/j.anaerobe.2024.102820}, pmid = {38309618}, issn = {1095-8274}, mesh = {Adult ; Humans ; *Saliva ; RNA, Ribosomal, 16S/genetics ; Methanobrevibacter/genetics ; Archaea/genetics ; *Microbiota ; }, abstract = {OBJECTIVES: Methanogenic archaea are a minor component of human oral microbiota. Due to their relatively low abundance, the detection of these neglected microorganisms is challenging. This study concerns the presence of methanogens in salivary samples collected from Tunisian adults to evaluate their prevalence and burden using a polyphasic molecular approach.

METHODS: A total of 43 saliva samples were included. Metagenomic and standard 16S rRNA sequencing were performed as an initial screening to detect the presence of methanogens in the oral microbiota of Tunisian adults. Further investigations were performed using specific quantitative real-time PCR targeting Methanobrevibacter oralis and Methanobrevibacter smithii.

RESULTS: Methanobrevibacter was detected in 5/43 (11.62 %) saliva samples after metagenomic 16S rRNA data analysis. The presence of M. oralis was confirmed in 6/43 samples by standard 16S rRNA sequencing. Using real-time PCR, methanogens were detected in 35/43 (81.39 %) samples, including 62.79 % positive for M. oralis and 76.74 % positive for M. smithii. These findings reflect the high prevalence of both methanogens, revealed by the high sensitivity of the real-time PCR approach. Interestingly, we also noted a significant statistical association between the detection of M. smithii and poor adherence to a Mediterranean diet, indicating the impact of diet on M. smithii prevalence.

CONCLUSION: Our study showed the presence of methanogens in the oral microbiota of Tunisian adults with an unprecedented relatively high prevalence. Choice of methodology is also central to picturing the real prevalence and diversity of such minor taxa in the oral microbiota.}, } @article {pmid38309340, year = {2024}, author = {Yu, K and Song, Y and Wang, N and Yu, X and Sun, T and Yu, H and Ruan, Z and Qiu, Y}, title = {Exposure of Danio rerio to environmental sulfamethoxazole may contribute to neurobehavioral abnormalities via gut microbiome disturbance.}, journal = {The Science of the total environment}, volume = {918}, number = {}, pages = {170546}, doi = {10.1016/j.scitotenv.2024.170546}, pmid = {38309340}, issn = {1879-1026}, mesh = {Animals ; *Gastrointestinal Microbiome ; Zebrafish/genetics ; Sulfamethoxazole/toxicity ; *Microbiota ; Metagenome ; }, abstract = {The neurotoxic effects and mechanisms of low-dose and long-term sulfamethoxazole (SMZ) exposure remain unknown. This study exposed zebrafish to environmental SMZ concentrations and observed behavioral outcomes. SMZ exposure increased hyperactivity and altered the transcript levels of 17 genes associated with neurological function. It impaired intestinal function by reducing the number of intestinal goblet cells and lipid content. Metabolomic results indicated that the contents of several lipids and amino acids in the gut were altered, which might affect the expression levels of neurological function-related genes. Metagenomic results demonstrated that SMZ exposure substantially altered the composition of the gut microbiome. Zebrafish receiving a transplanted fecal microbiome from the SMZ group were also found to exhibit abnormal behavior, suggesting that the gut microbiome is an important target for SMZ exposure-induced neurobehavioral abnormalities. Multi-omics correlation analysis revealed that gut micrometabolic function was related to differential gut metabolite levels, which may affect neurological function through the gut-brain-axis. Reduced abundance of Lefsonia and Microbacterium was strongly correlated with intestinal metabolic function and may be the key bacterial genera in neurobehavioral changes. This study confirms for the first time that SMZ-induced neurotoxicity in zebrafish is closely mediated by alterations in the gut microbiome.}, } @article {pmid38309231, year = {2024}, author = {Xu, J and Dong, Y}, title = {Analysis of the gut microbiome associated to PVC biodegradation in yellow mealworms.}, journal = {Ecotoxicology and environmental safety}, volume = {272}, number = {}, pages = {116046}, doi = {10.1016/j.ecoenv.2024.116046}, pmid = {38309231}, issn = {1090-2414}, mesh = {Animals ; *Tenebrio ; Polystyrenes/metabolism ; *Gastrointestinal Microbiome/physiology ; Plastics/metabolism ; Larva/metabolism ; Biodegradation, Environmental ; Esters ; }, abstract = {The potential of invertebrates in the biodegradation of plastic polymers such as polyvinyl chloride (PVC) is receiving increasing attention. The present study is aimed to identify the gut microbiome involved in this degradation in yellow mealworms, i.e., the larvae of Tenebrio molitor Linnaeus. The egested PVC polymer experienced a dramatic reduction in both number average molecular weight (Mn) and weight average molecular weight (Mw) of 99.3% and 99.6%, respectively, whereas FTIR analysis revealed chemical alterations. Mass spectrometry analysis identified two potential degradation products: phthalic acid, di(2-propylpentyl) ester and 2-Propenoic acid, tridecyl ester. Further, we used metagenomic sequencing to elucidate the response of the gut microbiome when transitioning from bran to PVC as a food source, identifying four microorganisms actively involved in PVC degradation. Additionally, metagenomic functional analysis of the gut microbiome identified 111 key gene modules that were significantly enriched. In summary, our findings suggest that yellow mealworms adapt to PVC degradation by modifying their gut microbiome both structurally and functionally.}, } @article {pmid38307921, year = {2024}, author = {Ho, SX and Law, JH and Png, CW and Alberts, R and Zhang, Y and Chu, JJH and Tan, KK}, title = {Alterations in colorectal cancer virome and its persistence after surgery.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {2819}, pmid = {38307921}, issn = {2045-2322}, support = {NUHSRO/2020/142/RO5+6/Seed-Sep/02//National University Health System/ ; }, mesh = {Humans ; Virome ; Dysbiosis/microbiology ; *Viruses ; *Microbiota ; *Colorectal Neoplasms/surgery/microbiology ; }, abstract = {Viruses are a key component of the colon microbiome, but the relationship between virome and colorectal cancer (CRC) remains poorly understood. We seek to identify alterations in the viral community that is characteristic of CRC and examine if they persist after surgery. Forty-nine fecal samples from 25 non-cancer (NC) individuals and 12 CRC patients, before and 6-months after surgery, were collected for metagenomic analysis. The fecal virome of CRC patients demonstrated an increased network connectivity as compared to NC individuals. Co-exclusion of influential viruses to bacterial species associated with healthy gut status was observed in CRC, suggesting an altered virome induced a change in the healthy gut bacteriome. Network analysis revealed lower connectivity within the virome and trans-kingdom interactions in NC. After surgery, the number of strong correlations decreased for trans-kingdom and within the bacteria and virome networks, indicating lower connectivity within the microbiome. Some co-occurrence patterns between dominant viruses and bacteria were also lost after surgery, suggesting a possible return to the healthy state of gut microbiome. Microbial signatures characteristic of CRC include an altered virome besides an altered bacterial composition. Elevated viral correlations and network connectivity were observed in CRC patients relative to healthy individuals, alongside distinct changes in the cross-kingdom correlation network unique to CRC patients. Some patterns of dysbiosis persist after surgery. Future studies should seek to verify if dysbiosis truly persists after surgery in a larger sample size with microbiome data collected at various time points after surgery to explore if there is field-change in the remaining colon, as well as to examine if persistent dysbiosis correlates with patient outcomes.}, } @article {pmid38307295, year = {2024}, author = {Ding, X and Lan, W and Li, J and Deng, M and Li, Y and Katayama, Y and Gu, JD}, title = {Metagenomic insight into the pathogenic-related characteristics and resistome profiles within microbiome residing on the Angkor sandstone monuments in Cambodia.}, journal = {The Science of the total environment}, volume = {918}, number = {}, pages = {170402}, doi = {10.1016/j.scitotenv.2024.170402}, pmid = {38307295}, issn = {1879-1026}, mesh = {Cambodia ; *Bacteria/genetics ; *Microbiota/genetics ; Metagenome ; Genes, Bacterial ; Anti-Bacterial Agents ; }, abstract = {To reveal the characteristics of indigenous microbiome including the pathogenic-related ones on Angkor monuments in Cambodia and the distribution pattern of resistome at different locations, several sites, namely Angkor Wat, Bayon of Angkor Thom, and Prasat Preah Vihear with different exposure levels to tourists were selected to conduct the metagenomic analysis in this study. The general characteristics of the microbiome on these monuments were revealed, and the association between the environmental geo-ecological feature and the indigenous microbiome was delineated. The most common microbial groups included 6 phyla, namely Acidobacteria, Actinobacteria, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia on the monuments, but Firmicutes and Chlamydiae were the most dominant phyla found in bats droppings. The taxonomic family of Chitinophagaceae could serve as a signature microbial group for Preah Vihear, the less visited site. More importantly, the pathogenic-related characteristics of the microbiome residing on Angkor monuments were uncovered. A set of specific antibiotic resistance genes (ARGs) with cross-niches dispersal capacity (between the environmental microbiome and the microbiome within warm blood fauna) was identified to be high by the source tracking analysis based on ARGs profile varies in this study. Among the 10 ARG-types detected in this study, 6 of them are confined to resistance mechanism of antibiotic efflux-pump. The findings of this study provide new a new direction on public health management and implication globally at archaeological sites for tourism.}, } @article {pmid38307030, year = {2024}, author = {Wan, Y and Zhang, L and Xu, Z and Su, Q and Leung, TF and Chan, D and Wong, OWH and Chan, S and Chan, FKL and Tun, HM and Ng, SC}, title = {Alterations in fecal virome and bacteriome virome interplay in children with autism spectrum disorder.}, journal = {Cell reports. Medicine}, volume = {5}, number = {2}, pages = {101409}, pmid = {38307030}, issn = {2666-3791}, mesh = {Child ; Humans ; *Autism Spectrum Disorder/therapy/microbiology ; Virome ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Microbiota ; *Bacteriophages/genetics ; Bacteria/genetics ; }, abstract = {Emerging evidence suggests autism spectrum disorder (ASD) is associated with altered gut bacteria. However, less is known about the gut viral community and its role in shaping microbiota in neurodevelopmental disorders. Herein, we perform a metagenomic analysis of gut-DNA viruses in 60 children with ASD and 64 age- and gender-matched typically developing children to investigate the effect of the gut virome on host bacteria in children with ASD. ASD is associated with altered gut virome composition accompanied by the enrichment of Clostridium phage, Bacillus phage, and Enterobacteria phage. These ASD-enriched phages are largely associated with disrupted viral ecology in ASD. Importantly, changes in the interplay between the gut bacteriome and virome seen in ASD may influence the encoding capacity of microbial pathways for neuroactive metabolite biosynthesis. These findings suggest an impaired bacteriome-virome ecology in ASD, which sheds light on the importance of bacteriophages in pathogenesis and the development of microbial therapeutics in ASD.}, } @article {pmid38306774, year = {2024}, author = {Li, X and Wang, H and Abdelrahman, H and Kelly, A and Roy, L and Wang, L}, title = {Profiling and source tracking of the microbial populations and resistome present in fish products.}, journal = {International journal of food microbiology}, volume = {413}, number = {}, pages = {110591}, doi = {10.1016/j.ijfoodmicro.2024.110591}, pmid = {38306774}, issn = {1879-3460}, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Anti-Bacterial Agents/pharmacology ; Fish Products ; *Microbiota/genetics ; Genes, Bacterial ; Fishes ; }, abstract = {Microorganisms in processing environments significantly impact the quality and safety of food products and can serve as potential reservoirs for antibiotic-resistant genes, contributing to public health concerns about antimicrobial resistance (AMR). Fish processing plants represent an understudied environment for microbiome mapping. This study investigated the microbial composition, prevalence of Listeria spp., and resistome structures in three catfish processing facilities in the southeastern United States. The 16S rRNA gene sequencing revealed that the observed richness and Shannon diversity index increased significantly from fish to fillet. Beta diversity analysis showed distinct clustering of microbial communities between fish, environment, and fillet samples. Fast expectation-maximization microbial source tracking (FEAST) algorithm demonstrated that the microbiota presents in the processing environment contributed 48.2 %, 62.4 %, and 53.7 % to the microbiota present on fillet in Facility 1 (F1), F2, and F3, respectively. Food contact surfaces made larger contributions compared to the non-food contact surfaces. The linear discriminant analysis of effect size (LEfSe) identified specific microbial genera (e.g., Plesiomohas, Brochothrix, Chryseobacterium and Cetobacterium) that significantly varied between Listeria spp. positive and negative samples in all three processing plants. The metagenomic sequencing results identified 212 antimicrobial resistance genes (ARGs) belonging to 72 groups from the raw fish and fish fillet samples collected from three processing plants. Although there was a significant decrease in the overall diversity of ARGs from fish to fillet samples, the total abundance of ARGs did not change significantly (P > 0.05). ARGs associated with resistance to macrolide-lincosamide-streptogramin (MLS), cationic antimicrobial peptides, aminoglycosides, and beta-lactams were found to be enriched in the fillet samples when compared to fish samples. Results of this study highlight the profound impact of processing environment on shaping the microbial populations present on the final fish product and the need for additional strategies to mitigate AMR in fish products.}, } @article {pmid38306257, year = {2024}, author = {Song, J and Zheng, C and Qiu, M and Zhan, XP and Zhang, Z and Zhang, H and Shi, N and Zhang, L and Yu, Y and Nicolaisen, M and Xu, L and Fang, H}, title = {Mechanisms Underlying the Overlooked Chiral Fungicide-Driven Enantioselective Proliferation of Antibiotic Resistance in Earthworm Intestinal Microbiome.}, journal = {Environmental science & technology}, volume = {58}, number = {6}, pages = {2931-2943}, doi = {10.1021/acs.est.3c07761}, pmid = {38306257}, issn = {1520-5851}, mesh = {Animals ; *Oligochaeta/genetics ; *Fungicides, Industrial/pharmacology/analysis ; Genes, Bacterial ; Ecosystem ; *Gastrointestinal Microbiome ; Stereoisomerism ; Drug Resistance, Microbial/genetics ; Soil ; Anti-Bacterial Agents/pharmacology ; Cell Proliferation ; }, abstract = {From a "One Health" perspective, the global threat of antibiotic resistance genes (ARGs) is associated with modern agriculture practices including agrochemicals application. Chiral fungicides account for a considerable proportion of wildly used agrochemicals; however, whether and how their enantiomers lead to differential proliferation of antibiotic resistance in agricultural environments remain overlooked. Focused on the soil-earthworm ecosystem, we for the first time deciphered the mechanisms underlying the enantioselective proliferation of antibiotic resistance driven by the enantiomers of a typical chiral fungicide mandipropamid (i.e., R-MDP and S-MDP) utilizing a multiomic approach. Time-series metagenomic analysis revealed that R-MDP led to a significant enhancement of ARGs with potential mobility (particularly the plasmid-borne ARGs) in the earthworm intestinal microbiome. We further demonstrated that R-MDP induced a concentration-dependent facilitation of plasmid-mediated ARG transfer among microbes. In addition, transcriptomic analysis with verification identified the key aspects involved, where R-MDP enhanced cell membrane permeability, transfer ability, biofilm formation and quorum sensing, rebalanced energy production, and decreased cell mobility versus S-MDP. Overall, the findings provide novel insights into the enantioselective disruption of microbiome and resistome in earthworm gut by chiral fungicides and offer significant contributions to the comprehensive risk assessment of chiral agrochemicals in agroecosystems.}, } @article {pmid38305171, year = {2024}, author = {Ning, R and Li, C and Xia, M and Zhang, Y and Gan, Y and Huang, Y and Zhang, T and Song, H and Zhang, S and Guo, W}, title = {Pseudomonas-associated bacteria play a key role in obtaining nutrition from bamboo for the giant panda (Ailuropoda melanoleuca).}, journal = {Microbiology spectrum}, volume = {12}, number = {3}, pages = {e0381923}, pmid = {38305171}, issn = {2165-0497}, support = {31900307//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Lignin/metabolism ; *Ursidae/metabolism/microbiology ; Acetyl Coenzyme A ; Pseudomonas/genetics/metabolism ; Bacteria ; *Adipates ; }, abstract = {UNLABELLED: Gut microbiota plays a vital role in obtaining nutrition from bamboo for giant pandas. However, low cellulase activity has been observed in the panda's gut. Besides, no specific pathway has been implicated in lignin digestion by gut microbiota of pandas. Therefore, the mechanism by which they obtain nutrients is still controversial. It is necessary to elucidate the precise pathways employed by gut microbiota of pandas to degrade lignin. Here, the metabolic pathways for lignin degradation in pandas were explored by comparing 209 metagenomic sequencing data from wild species with different feeding habits. Lignin degradation central pathways, including beta-ketoadipate and homogentisate pathway, were enriched in the gut of wild bamboo-eating pandas. The gut microbiome of wild bamboo-eating specialists was enriched with genes from pathways implicated in degrading ferulate and p-coumarate into acetyl-CoA and succinyl-CoA, which can potentially provide the raw materials for metabolism in pandas. Specifically, Pseudomonas, as the most dominant gut bacteria genus, was found to be the main bacteria to provide genes involved in lignin or lignin derivative degradation. Herein, three Pseudomonas-associated strains isolated from the feces of wild pandas showed the laccase, lignin peroxidase, and manganese peroxidase activity and extracellular lignin degradation ability in vitro. A potential mechanism for pandas to obtain nutrition from bamboo was proposed based on the results. This study provides novel insights into the adaptive evolution of pandas from the perspective of lignin metabolism.

IMPORTANCE: Although giant pandas only feed on bamboo, the mechanism of lignin digestion in pandas is unclear. Here, the metabolic pathways for lignin degradation in wild pandas were explored by comparing gut metagenomic from species with different feeding habits. Results showed that lignin degradation central pathways, including beta-ketoadipate and homogentisate pathway, were enriched in the gut of wild bamboo-eating pandas. Genes from pathways involved in degrading ferulate and p-coumarate via beta-ketoadipate pathway were also enriched in bamboo-eating pandas. The final products of the above process, such as acetyl-CoA, can potentially provide the raw materials for metabolism in pandas. Specifically, Pseudomonas, as the most dominant gut bacteria genus, mainly provides genes involved in lignin degradation. Herein, Pseudomonas-associated strains isolated from the feces of pandas could degrade extracellular lignin. These findings suggest that gut microbiome of pandas is crucial in obtaining nutrition from lignin via Pseudomonas, as the main lignin-degrading bacteria.}, } @article {pmid38305149, year = {2024}, author = {Mukhia, S and Kumar, A and Kumar, R}, title = {Bacterial community distribution and functional potentials provide key insights into their role in the ecosystem functioning of a retreating Eastern Himalayan glacier.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {3}, pages = {}, pmid = {38305149}, issn = {1574-6941}, support = {45/17/2020-/BIO/BMS//Indian Council of Medical Research/ ; DBT/JRF/BET-17/I/2017/AL/367//Department of Biotechnology/ ; DST/INSPIRE/04/2014/001280//Department of Science and Technology/ ; SRG/2019/001071//Science and Engineering Research Board/ ; }, mesh = {*Ecosystem ; Ice Cover ; Metagenomics ; Bacteria ; Metagenome ; *Microbiota ; Proteobacteria/genetics ; Sulfur/metabolism ; }, abstract = {Himalayan glaciers are receding at an exceptional rate, perturbing the local biome and ecosystem processes. Understanding the microbial ecology of an exclusively microbe-driven biome provides insights into their contributions to the ecosystem functioning through biogeochemical fluxes. Here, we investigated the bacterial communities and their functional potential in the retreating East Rathong Glacier (ERG) of Sikkim Himalaya. Amplicon-based taxonomic classification revealed the dominance of the phyla Proteobacteria, Bacteroidota, and candidate Patescibacteria in the glacial sites. Further, eight good-quality metagenome-assembled genomes (MAGs) of Proteobacteria, Patescibacteria, Acidobacteriota, and Choloflexota retrieved from the metagenomes elucidated the microbial contributions to nutrient cycling. The ERG MAGs showed aerobic respiration as a primary metabolic feature, accompanied by carbon fixation and complex carbon degradation potentials. Pathways for nitrogen metabolism, chiefly dissimilatory nitrate reduction and denitrification, and a complete sulphur oxidation enzyme complex for sulphur metabolism were identified in the MAGs. We observed that DNA repair and oxidative stress response genes complemented with osmotic and periplasmic stress and protein chaperones were vital for adaptation against the intense radiation and stress conditions of the extreme Himalayan niche. Current findings elucidate the microbiome and associated functional potentials of a vulnerable glacier, emphasizing their significant ecological roles in a changing glacial ecosystem.}, } @article {pmid38305096, year = {2024}, author = {Linnehan, BK and Kodera, SM and Allard, SM and Brodie, EC and Allaband, C and Knight, R and Lutz, HL and Carroll, MC and Meegan, JM and Jensen, ED and Gilbert, JA}, title = {Evaluation of the safety and efficacy of fecal microbiota transplantations in bottlenose dolphins (Tursiops truncatus) using metagenomic sequencing.}, journal = {Journal of applied microbiology}, volume = {135}, number = {2}, pages = {}, pmid = {38305096}, issn = {1365-2672}, support = {S10 OD026929/OD/NIH HHS/United States ; #S10 OD026929/NH/NIH HHS/United States ; }, mesh = {Animals ; Fecal Microbiota Transplantation/methods ; *Bottle-Nosed Dolphin ; Prospective Studies ; Feces ; *Gastrointestinal Microbiome ; Treatment Outcome ; }, abstract = {AIMS: Gastrointestinal disease is a leading cause of morbidity in bottlenose dolphins (Tursiops truncatus) under managed care. Fecal microbiota transplantation (FMT) holds promise as a therapeutic tool to restore gut microbiota without antibiotic use. This prospective clinical study aimed to develop a screening protocol for FMT donors to ensure safety, determine an effective FMT administration protocol for managed dolphins, and evaluate the efficacy of FMTs in four recipient dolphins.

METHODS AND RESULTS: Comprehensive health monitoring was performed on donor and recipient dolphins. Fecal samples were collected before, during, and after FMT therapy. Screening of donor and recipient fecal samples was accomplished by in-house and reference lab diagnostic tests. Shotgun metagenomics was used for sequencing. Following FMT treatment, all four recipient communities experienced engraftment of novel microbial species from donor communities. Engraftment coincided with resolution of clinical signs and a sustained increase in alpha diversity.

CONCLUSION: The donor screening protocol proved to be safe in this study and no adverse effects were observed in four recipient dolphins. Treatment coincided with improvement in clinical signs.}, } @article {pmid38303501, year = {2024}, author = {Oliphant, K and Cruz Ayala, W and Ilyumzhinova, R and Mbayiwa, K and Sroka, A and Xie, B and Andrews, B and Keenan, K and Claud, EC}, title = {Microbiome function and neurodevelopment in Black infants: vitamin B12 emerges as a key factor.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2298697}, pmid = {38303501}, issn = {1949-0984}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; R01 HD084586/HD/NICHD NIH HHS/United States ; R01 HD105234/HD/NICHD NIH HHS/United States ; }, mesh = {Infant ; Child ; Pregnancy ; Female ; Adolescent ; Humans ; Male ; *Vitamin B 12 ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; Brain ; Vitamins ; }, abstract = {The early life gut microbiome affects the developing brain, and therefore may serve as a target to support neurodevelopment of children living in stressful and under-resourced environments, such as Black youth living on the South Side of Chicago, for whom we observe racial disparities in health. Microbiome compositions/functions key to multiple neurodevelopmental facets have not been studied in Black children, a vulnerable population due to racial disparities in health; thus, a subsample of Black infants living in urban, low-income neighborhoods whose mothers participated in a prenatal nutrition study were recruited for testing associations between composition and function of the gut microbiome (16S rRNA gene sequencing, shotgun metagenomics, and targeted metabolomics of fecal samples) and neurodevelopment (developmental testing, maternal report of temperament, and observed stress regulation). Two microbiome community types, defined by high Lachnospiraceae or Enterobacteriaceae abundance, were discovered in this cohort from 16S rRNA gene sequencing analysis; the Enterobacteriaceae-dominant community type was significantly negatively associated with cognition and language scores, specifically in male children. Vitamin B12 biosynthesis emerged as a key microbiome function from shotgun metagenomics sequencing analysis, showing positive associations with all measured developmental skills (i.e., cognition, language, motor, surgency, effortful control, and observed stress regulation). Blautia spp. also were identified as substantial contributors of important microbiome functions, including vitamin B12 biosynthesis and related vitamin B12-dependent microbiome functions, anti-inflammatory microbial surface antigens, competitive mechanisms against pathobionts, and production of antioxidants. The results are promising with respect to the potential for exploring therapeutic candidates, such as vitamin B12 nutritional or Blautia spp. probiotic supplementation, to support the neurodevelopment of infants at risk for experiencing racial disparities in health.}, } @article {pmid38303006, year = {2024}, author = {Asher, EE and Bashan, A}, title = {Model-free prediction of microbiome compositions.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {17}, pmid = {38303006}, issn = {2049-2618}, support = {1258/21//Israel Science Foundation/ ; I-1523-500.15/2021//German-Israeli Foundation for Scientific Research and Development/ ; }, mesh = {Humans ; *Microbiota/genetics ; Metagenome ; }, abstract = {BACKGROUND: The recent recognition of the importance of the microbiome to the host's health and well-being has yielded efforts to develop therapies that aim to shift the microbiome from a disease-associated state to a healthier one. Direct manipulation techniques of the species' assemblage are currently available, e.g., using probiotics or narrow-spectrum antibiotics to introduce or eliminate specific taxa. However, predicting the species' abundances at the new state remains a challenge, mainly due to the difficulties of deciphering the delicate underlying network of ecological interactions or constructing a predictive model for such complex ecosystems.

RESULTS: Here, we propose a model-free method to predict the species' abundances at the new steady state based on their presence/absence configuration by utilizing a multi-dimensional k-nearest-neighbors (kNN) regression algorithm. By analyzing data from numeric simulations of ecological dynamics, we show that our predictions, which consider the presence/absence of all species holistically, outperform both the null model that uses the statistics of each species independently and a predictive neural network model. We analyze real metagenomic data of human-associated microbial communities and find that by relying on a small number of "neighboring" samples, i.e., samples with similar species assemblage, the kNN predicts the species abundance better than the whole-cohort average. By studying both real metagenomic and simulated data, we show that the predictability of our method is tightly related to the dissimilarity-overlap relationship of the training data.

CONCLUSIONS: Our results demonstrate how model-free methods can prove useful in predicting microbial communities and may facilitate the development of microbial-based therapies. Video Abstract.}, } @article {pmid38302952, year = {2024}, author = {Kim, HY and Jung, YS and Park, W and Choi, YJ and Kim, JY}, title = {Can medication-related osteonecrosis of the jaw be attributed to specific microorganisms through oral microbiota analyses? A preliminary study.}, journal = {BMC oral health}, volume = {24}, number = {1}, pages = {160}, pmid = {38302952}, issn = {1472-6831}, mesh = {Humans ; Aged ; Aged, 80 and over ; *Bisphosphonate-Associated Osteonecrosis of the Jaw/surgery ; *Bone Density Conservation Agents ; Prospective Studies ; *Periodontitis/complications ; *Microbiota ; Diphosphonates ; }, abstract = {BACKGROUND: Medication-related osteonecrosis of the jaw (MRONJ) can cause significant pain and loss of aesthetics and function if not treated properly. However, diagnosis still relies on detailed intraoral examinations and imaging. Prognosis varies even among patients with similar stages or conditions of MRONJ, emphasizing the need for a deeper understanding of its complex mechanisms. Thus, this study aimed to identify the oral microbiota of patients with MRONJ.

METHODS: This single-center prospective cohort study included patients with confirmed MRONJ who visited the Department of Oral and Maxillofacial Surgery at Yonsei University Dental Hospital between 2021 and 2022. Oral swab samples were collected from the affected and unaffected sides of each patient. The composition and enumeration of the microbial communities were analyzed, and the diversity was compared to verify ecological changes in the groups using a next-generation sequencing-based 16S metagenomic analysis. A statistical analysis was performed using Wilcoxon signed-rank test with SPSS version 22, and values of P less than 0.05 were considered statistically significant.

RESULTS: The final study sample included 12 patients. The mean age was 82.67 ± 5.73 (range, 72-90) years. Changes in microbial composition were observed at different taxonomic levels (phylum, genus, and species). The identified microorganisms were commonly associated with periodontitis, gingival disease, and endodontic infection, suggesting a multifactorial etiology of MRONJ.

CONCLUSIONS: Although this study is based on a small number of cases, it shows that MRONJ is not caused by a specific microorganism but can rather be caused by a variety of factors. By addressing these findings in large-scale studies, the significance of oral microbiome in pathogenesis can be further elucidated and can facilitate the development of effective therapeutic interventions for patients with MRONJ.}, } @article {pmid38302666, year = {2024}, author = {Gose, MA and Humble, E and Brownlow, A and Wall, D and Rogan, E and Sigurðsson, GM and Kiszka, JJ and Thøstesen, CB and IJsseldijk, LL and Ten Doeschate, M and Davison, NJ and Øien, N and Deaville, R and Siebert, U and Ogden, R}, title = {Population genomics of the white-beaked dolphin (Lagenorhynchus albirostris): Implications for conservation amid climate-driven range shifts.}, journal = {Heredity}, volume = {132}, number = {4}, pages = {192-201}, pmid = {38302666}, issn = {1365-2540}, mesh = {Animals ; *Dolphins/genetics ; Metagenomics ; Climate Change ; Temperature ; }, abstract = {Climate change is rapidly affecting species distributions across the globe, particularly in the North Atlantic. For highly mobile and elusive cetaceans, the genetic data needed to understand population dynamics are often scarce. Cold-water obligate species such as the white-beaked dolphin (Lagenorhynchus albirostris) face pressures from habitat shifts due to rising sea surface temperatures in addition to other direct anthropogenic threats. Unravelling the genetic connectivity between white-beaked dolphins across their range is needed to understand the extent to which climate change and anthropogenic pressures may impact species-wide genetic diversity and identify ways to protect remaining habitat. We address this by performing a population genomic assessment of white-beaked dolphins using samples from much of their contemporary range. We show that the species displays significant population structure across the North Atlantic at multiple scales. Analysis of contemporary migration rates suggests a remarkably high connectivity between populations in the western North Atlantic, Iceland and the Barents Sea, while two regional populations in the North Sea and adjacent UK and Irish waters are highly differentiated from all other clades. Our results have important implications for the conservation of white-beaked dolphins by providing guidance for the delineation of more appropriate management units and highlighting the risk that local extirpation may have on species-wide genetic diversity. In a broader context, this study highlights the importance of understanding genetic structure of all species threatened with climate change-driven range shifts to assess the risk of loss of species-wide genetic diversity.}, } @article {pmid38302544, year = {2024}, author = {Prasoodanan P K, V and Kumar, S and Dhakan, DB and Waiker, P and Saxena, R and Sharma, VK}, title = {Metagenomic exploration of Andaman region of the Indian Ocean.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {2717}, pmid = {38302544}, issn = {2045-2322}, mesh = {Indian Ocean ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; Metagenome ; *Microbiota/genetics ; Water ; Seawater ; }, abstract = {Ocean microbiome is crucial for global biogeochemical cycles and primary productivity. Despite numerous studies investigating the global ocean microbiomes, the microbiome composition of the Andaman region of the Indian Ocean remains largely unexplored. While this region harbors pristine biological diversity, the escalating anthropogenic activities along coastal habitats exert an influence on the microbial ecology and impact the aquatic ecosystems. We investigated the microbiome composition in the coastal waters of the Andaman Islands by 16S rRNA gene amplicon and metagenomic shotgun sequencing approaches and compared it with the Tara Oceans Consortium. In the coastal waters of the Andaman Islands, a significantly higher abundance and diversity of Synechococcus species was observed with a higher abundance of photosynthesis pigment-related genes to adapt to variable light conditions and nutrition. In contrast, Prochlorococcus species showed higher abundance in open ocean water samples of the Indian Ocean region, with a relatively limited functional diversity. A higher abundance of antibiotic-resistance genes was also noted in the coastal waters region. We also updated the ocean microbiome gene catalog with 93,172 unique genes from the Andaman coastal water microbiome. This study provides valuable insights into the Indian Ocean microbiome and supplements the global marine microbial ecosystem studies.}, } @article {pmid38302438, year = {2024}, author = {Eberhart, T and Stanley, FU and Ricci, L and Chirico, T and Ferrarese, R and Sisti, S and Scagliola, A and Baj, A and Badurek, S and Sommer, A and Culp-Hill, R and Dzieciatkowska, M and Shokry, E and Sumpton, D and D'Alessandro, A and Clementi, N and Mancini, N and Cardaci, S}, title = {ACOD1 deficiency offers protection in a mouse model of diet-induced obesity by maintaining a healthy gut microbiota.}, journal = {Cell death & disease}, volume = {15}, number = {2}, pages = {105}, pmid = {38302438}, issn = {2041-4889}, support = {Start-Up 2017 - ID. 20464 project//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; GR-2018-12365954//Ministero della Salute (Ministry of Health, Italy)/ ; }, mesh = {Animals ; Mice ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Obesity/metabolism ; *Succinates ; }, abstract = {Aconitate decarboxylase 1 (ACOD1) is the enzyme synthesizing itaconate, an immuno-regulatory metabolite tuning host-pathogen interactions. Such functions are achieved by affecting metabolic pathways regulating inflammation and microbe survival. However, at the whole-body level, metabolic roles of itaconate remain largely unresolved. By using multiomics-integrated approaches, here we show that ACOD1 responds to high-fat diet consumption in mice by promoting gut microbiota alterations supporting metabolic disease. Genetic disruption of itaconate biosynthesis protects mice against obesity, alterations in glucose homeostasis and liver metabolic dysfunctions by decreasing meta-inflammatory responses to dietary lipid overload. Mechanistically, fecal metagenomics and microbiota transplantation experiments demonstrate such effects are dependent on an amelioration of the intestinal ecosystem composition, skewed by high-fat diet feeding towards obesogenic phenotype. In particular, unbiased fecal microbiota profiling and axenic culture experiments point towards a primary role for itaconate in inhibiting growth of Bacteroidaceae and Bacteroides, family and genus of Bacteroidetes phylum, the major gut microbial taxon associated with metabolic health. Specularly to the effects imposed by Acod1 deficiency on fecal microbiota, oral itaconate consumption enhances diet-induced gut dysbiosis and associated obesogenic responses in mice. Unveiling an unrecognized role of itaconate, either endogenously produced or exogenously administered, in supporting microbiota alterations underlying diet-induced obesity in mice, our study points ACOD1 as a target against inflammatory consequences of overnutrition.}, } @article {pmid38301483, year = {2024}, author = {Baldanzi, G and Sayols-Baixeras, S and Ekblom-Bak, E and Ekblom, Ö and Dekkers, KF and Hammar, U and Nguyen, D and Ahmad, S and Ericson, U and Arvidsson, D and Börjesson, M and Johanson, PJ and Smith, JG and Bergström, G and Lind, L and Engström, G and Ärnlöv, J and Kennedy, B and Orho-Melander, M and Fall, T}, title = {Accelerometer-based physical activity is associated with the gut microbiota in 8416 individuals in SCAPIS.}, journal = {EBioMedicine}, volume = {100}, number = {}, pages = {104989}, pmid = {38301483}, issn = {2352-3964}, mesh = {Humans ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Exercise ; Life Style ; Accelerometry ; }, abstract = {BACKGROUND: Previous population-based studies investigating the relationship between physical activity and the gut microbiota have relied on self-reported activity, prone to reporting bias. Here, we investigated the associations of accelerometer-based sedentary (SED), moderate-intensity (MPA), and vigorous-intensity (VPA) physical activity with the gut microbiota using cross-sectional data from the Swedish CArdioPulmonary bioImage Study.

METHODS: In 8416 participants aged 50-65, time in SED, MPA, and VPA were estimated with hip-worn accelerometer. Gut microbiota was profiled using shotgun metagenomics of faecal samples. We applied multivariable regression models, adjusting for sociodemographic, lifestyle, and technical covariates, and accounted for multiple testing.

FINDINGS: Overall, associations between time in SED and microbiota species abundance were in opposite direction to those for MPA or VPA. For example, MPA was associated with lower, while SED with higher abundance of Escherichia coli. MPA and VPA were associated with higher abundance of the butyrate-producers Faecalibacterium prausnitzii and Roseburia spp. We observed discrepancies between specific VPA and MPA associations, such as a positive association between MPA and Prevotella copri, while no association was detected for VPA. Additionally, SED, MPA and VPA were associated with the functional potential of the microbiome. For instance, MPA was associated with higher capacity for acetate synthesis and SED with lower carbohydrate degradation capacity.

INTERPRETATION: Our findings suggest that sedentary and physical activity are associated with a similar set of gut microbiota species but in opposite directions. Furthermore, the intensity of physical activity may have specific effects on certain gut microbiota species.

FUNDING: European Research Council, Swedish Heart-Lung Foundation, Swedish Research Council, Knut and Alice Wallenberg Foundation.}, } @article {pmid38299854, year = {2024}, author = {Podar, NA and Carrell, AA and Cassidy, KA and Klingeman, DM and Yang, Z and Stahler, EA and Smith, DW and Stahler, DR and Podar, M}, title = {From wolves to humans: oral microbiome resistance to transfer across mammalian hosts.}, journal = {mBio}, volume = {15}, number = {3}, pages = {e0334223}, pmid = {38299854}, issn = {2150-7511}, support = {R01 DE024463/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; Animals ; Dogs ; *Wolves ; *Microbiota ; Mammals/microbiology ; *Gastrointestinal Microbiome ; Bacteria ; *Hominidae ; }, abstract = {The mammalian mouth is colonized by complex microbial communities, adapted to specific niches, and in homeostasis with the host. Individual microbes interact metabolically and rely primarily on nutrients provided by the host, with which they have potentially co-evolved along the mammalian lineages. The oral environment is similar across mammals, but the diversity, specificity, and evolution of community structure in related or interacting mammals are little understood. Here, we compared the oral microbiomes of dogs with those of wild wolves and humans. In dogs, we found an increased microbial diversity relative to wolves, possibly related to the transition to omnivorous nutrition following domestication. This includes a larger diversity of Patescibacteria than previously reported in any other oral microbiota. The oral microbes are most distinct at bacterial species or strain levels, with few if any shared between humans and canids, while the close evolutionary relationship between wolves and dogs is reflected by numerous shared taxa. More taxa are shared at higher taxonomic levels including with humans, supporting their more ancestral common mammalian colonization followed by diversification. Phylogenies of selected oral bacterial lineages do not support stable human-dog microbial transfers but suggest diversification along mammalian lineages (apes and canids). Therefore, despite millennia of cohabitation and close interaction, the host and its native community controls and limits the assimilation of new microbes, even if closely related. Higher resolution metagenomic and microbial physiological studies, covering a larger mammalian diversity, should help understand how oral communities assemble, adapt, and interact with their hosts.IMPORTANCENumerous types of microbes colonize the mouth after birth and play important roles in maintaining oral health. When the microbiota-host homeostasis is perturbed, proliferation of some bacteria leads to diseases such as caries and periodontitis. Unlike the gut microbiome, the diversity of oral microbes across the mammalian evolutionary space is not understood. Our study compared the oral microbiomes of wild wolves, dogs, and apes (humans, chimpanzees, and bonobos), with the aim of identifying if microbes have been potentially exchanged between humans and dogs as a result of domestication and cohabitation. We found little if any evidence for such exchanges. The significance of our research is in finding that the oral microbiota and/or the host limit the acquisition of exogenous microbes, which is important in the context of natural exclusion of potential novel pathogens. We provide a framework for expanded higher-resolution studies across domestic and wild animals to understand resistance/resilience.}, } @article {pmid38297006, year = {2024}, author = {Maza-Márquez, P and Lee, MD and Bebout, BM}, title = {Community ecology and functional potential of bacteria, archaea, eukarya and viruses in Guerrero Negro microbial mat.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {2561}, pmid = {38297006}, issn = {2045-2322}, mesh = {Archaea/genetics ; Bacteria/genetics ; Eukaryota/genetics ; Phylogeny ; Viruses/genetics ; *Microbiota ; }, abstract = {In this study, the microbial ecology, potential environmental adaptive mechanisms, and the potential evolutionary interlinking of genes between bacterial, archaeal and viral lineages in Guerrero Negro (GN) microbial mat were investigated using metagenomic sequencing across a vertical transect at millimeter scale. The community composition based on unique genes comprised bacteria (98.01%), archaea (1.81%), eukarya (0.07%) and viruses (0.11%). A gene-focused analysis of bacteria archaea, eukarya and viruses showed a vertical partition of the community. The greatest coverages of genes of bacteria and eukarya were detected in first layers, while the highest coverages of genes of archaea and viruses were found in deeper layers. Many genes potentially related to adaptation to the local environment were detected, such as UV radiation, multidrug resistance, oxidative stress, heavy metals, salinity and desiccation. Those genes were found in bacterial, archaeal and viral lineages with 6477, 44, and 1 genes, respectively. The evolutionary histories of those genes were studied using phylogenetic analysis, showing an interlinking between domains in GN mat.}, } @article {pmid38295455, year = {2024}, author = {Liu, L and Wang, H and Guo, Y and Yan, Q and Chen, J}, title = {Human-induced homogenization of microbial taxa and function in a subtropical river and its impacts on community stability.}, journal = {Water research}, volume = {252}, number = {}, pages = {121198}, doi = {10.1016/j.watres.2024.121198}, pmid = {38295455}, issn = {1879-2448}, mesh = {Humans ; *Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Metagenome ; *Microbiota/genetics ; Rivers ; }, abstract = {Combination of taxa and function can provide a more comprehensive picture on human-induced microbial homogenization. Here, we obtained 2.58 billion high-throughput sequencing reads and 479 high-quality metagenome-assembled genomes (MAGs) of planktonic microbial communities in a subtropical river for 5 years. We found the microbial taxa homogenization and functional homogenization were uncoupled. Although human activities in downstream sites significantly decreased the taxonomic diversity of non-abundant ASV communities (16S rRNA gene amplicon sequence variants), they did not significantly decrease the taxonomic diversity of abundant ASV and total observed MAG communities. However, the total observed MAG communities in downstream sites tended to homogenize into some specific taxa which encode human-activity-related functional genes, such as nutrient cycles, greenhouse gas emission, antibiotic and arsenic resistance. Those specific MAGs with high taxonomic diversity caused the weak heterogenization of total observed MAG communities in downstream sites. Moreover, functional homogenization promoted the synchrony among downstream MAGs, and these MAGs constructed some specific network modules might to synergistically execute or resist the human-activity-related functions. High synchrony also led to the tandem effects among MAGs and thus decreased community stability. Overall, our findings revealed the links of microbial taxa, functions and stability under human activity impacts, and provided a strong evidence to encourage us re-thinking biotic homogenization based on microbial taxa and their functional attributes.}, } @article {pmid38294805, year = {2024}, author = {Vasileva, SS and Yang, Y and Baker, A and Siskind, D and Gratten, J and Eyles, D}, title = {Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia.}, journal = {JAMA psychiatry}, volume = {81}, number = {3}, pages = {292-302}, pmid = {38294805}, issn = {2168-6238}, mesh = {Adult ; Male ; Humans ; Female ; *Schizophrenia/drug therapy/chemically induced ; *Clozapine/therapeutic use ; *Gastrointestinal Microbiome ; Case-Control Studies ; *Antipsychotic Agents/adverse effects ; *Drug-Related Side Effects and Adverse Reactions ; }, abstract = {IMPORTANCE: There is growing interest in the role of gut microbiome composition in schizophrenia. However, lifestyle factors are often neglected, and few studies have investigated microbiome composition in treatment-resistant schizophrenia.

OBJECTIVE: To explore associations between the gut microbiome and schizophrenia diagnosis, treatment resistance, clozapine response, and treatment-related adverse effects while adjusting for demographic and lifestyle factors.

In this case-control study of adults aged 20 to 63 years, stool samples and data on demographic characteristics, lifestyle, and medication use were collected and gut microbiome measures obtained using shotgun metagenomics. Participants with a schizophrenia diagnosis were referred through psychiatric inpatient units and outpatient clinics. Data were collected for 4 distinct groups: control individuals without a psychiatric diagnosis (past or present), individuals with treatment-responsive schizophrenia taking nonclozapine antipsychotic medications, clozapine-responsive individuals with treatment-resistant schizophrenia, and clozapine-nonresponsive individuals with treatment-resistant schizophrenia. Participants were recruited between November 2020 and November 2021. Control individuals were recruited in parallel through posters and online advertisements and matched for age, sex, and body mass index (BMI) to the individuals with schizophrenia. Participants were excluded if taking antibiotics in the past 2 months, if unable to communicate in English or otherwise follow study instructions, were pregnant or planning to become pregnant, or had any concomitant disease or condition making them unsuited to the study per investigator assessment. Data were analyzed from January 2022 to March 2023.

MAIN OUTCOMES AND MEASURES: Omics relationship matrices, α and β diversity, and relative abundance of microbiome features.

RESULTS: Data were collected for 97 individuals (71 [74%] male; mean [SD] age, 40.4 [10.3] years; mean [SD] BMI, 32.8 [7.4], calculated as weight in kilograms divided by height in meters squared). Significant microbiome associations with schizophrenia were observed at multiple taxonomic and functional levels (eg, common species: b2, 30%; SE, 13%; adjusted P = .002) and treatment resistance (eg, common species: b2, 27%; SE, 16%; adjusted P = .03). In contrast, limited evidence was found for microbiome associations with clozapine response, constipation, or metabolic syndrome. Significantly decreased microbial richness was found in individuals with schizophrenia compared to control individuals (t95 = 4.25; P < .001; mean [SD] for control individuals, 151.8 [32.31]; mean [SD] for individuals with schizophrenia, 117.00 [36.2]; 95% CI, 18.6-51.0), which remained significant after a covariate and multiple comparison correction. However, limited evidence was found for differences in β diversity (weighted UniFrac) for schizophrenia diagnosis (permutational multivariate analysis of variance [PERMANOVA]: R2, 0.03; P = .02), treatment resistance (R2, 0.02; P = .18), or clozapine response (R2, 0.04; P = .08). Multiple differentially abundant bacterial species (19) and metabolic pathways (162) were found in individuals with schizophrenia, which were primarily associated with treatment resistance and clozapine exposure.

CONCLUSIONS AND RELEVANCE: The findings in this study are consistent with the idea that clozapine induces alterations to gut microbiome composition, although the possibility that preexisting microbiome differences contribute to treatment resistance cannot be ruled out. These findings suggest that prior reports of microbiome alterations in individuals with chronic schizophrenia may be due to medication or lifestyle factors and that future studies should incorporate these variables in their design and interpretation.}, } @article {pmid38294254, year = {2024}, author = {Brealey, JC and Kodama, M and Rasmussen, JA and Hansen, SB and Santos-Bay, L and Lecaudey, LA and Hansen, M and Fjære, E and Myrmel, LS and Madsen, L and Bernhard, A and Sveier, H and Kristiansen, K and Gilbert, MTP and Martin, MD and Limborg, MT}, title = {Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon.}, journal = {mSystems}, volume = {9}, number = {2}, pages = {e0104323}, pmid = {38294254}, issn = {2379-5077}, support = {901436//Fiskeri - og havbruksnæringens forskningsfond (FHF)/ ; CEH-DNRF143//Danmarks Grundforskningsfond (DNRF)/ ; 817729//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; 311913//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; CF21-0356//Carlsbergfondet (Carlsberg Foundation)/ ; 325589//Norges Forskningsråd (Forskningsrådet)/ ; }, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/genetics ; *Salmo salar ; Aquaculture ; Dysbiosis/veterinary ; *Parasitic Diseases ; *Cestode Infections ; }, abstract = {Animals and their associated microbiota share long evolutionary histories. However, it is not always clear how host genotype and microbiota interact to affect phenotype. We applied a hologenomic approach to explore how host-microbiota interactions shape lifetime growth and parasite infection in farmed Atlantic salmon (Salmo salar). Multi-omics data sets were generated from the guts of 460 salmon, 82% of which were naturally infected with an intestinal cestode. A single Mycoplasma bacterial strain, MAG01, dominated the gut metagenome of large, non-parasitized fish, consistent with previous studies showing high levels of Mycoplasma in the gut microbiota of healthy salmon. While small and/or parasitized salmon also had high abundance of MAG01, we observed increased alpha diversity in these individuals, driven by increased frequency of low-abundance Vibrionaceae and other Mycoplasma species that carried known virulence genes. Colonization by one of these cestode-associated Mycoplasma strains was associated with host individual genomic variation in long non-coding RNAs. Integrating the multi-omic data sets revealed coordinated changes in the salmon gut mRNA transcriptome and metabolome that correlated with shifts in the microbiota of smaller, parasitized fish. Our results suggest that the gut microbiota of small and/or parasitized fish is in a state of dysbiosis that partly depends on the host genotype, highlighting the value of using a hologenomic approach to incorporate the microbiota into the study of host-parasite dynamics.IMPORTANCEStudying host-microbiota interactions through the perspective of the hologenome is gaining interest across all life sciences. Intestinal parasite infections are a huge burden on human and animal health; however, there are few studies investigating the role of the hologenome during parasite infections. We address this gap in the largest multi-omics fish microbiota study to date using natural cestode infection of farmed Atlantic salmon. We find a clear association between cestode infection, salmon lifetime growth, and perturbation of the salmon gut microbiota. Furthermore, we provide the first evidence that the genetic background of the host may partly determine how the gut microbiota changes during parasite-associated dysbiosis. Our study therefore highlights the value of a hologenomic approach for gaining a more in-depth understanding of parasitism.}, } @article {pmid38294252, year = {2024}, author = {Argentini, C and Lugli, GA and Tarracchini, C and Fontana, F and Mancabelli, L and Viappiani, A and Anzalone, R and Angelini, L and Alessandri, G and Bianchi, MG and Taurino, G and Bussolati, O and Milani, C and van Sinderen, D and Turroni, F and Ventura, M}, title = {Ecology- and genome-based identification of the Bifidobacterium adolescentis prototype of the healthy human gut microbiota.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {2}, pages = {e0201423}, pmid = {38294252}, issn = {1098-5336}, support = {//Fondazione Cariparma (Fondazione Cassa di Risparmio di Parma)/ ; SFI/12/RC/2273a, SFI/12/RC/2273b//UCC | APC Microbiome Institute/ ; GR-2018-12365988//Ministero della Salute (Italy Ministry of Health)/ ; }, mesh = {Adult ; Humans ; *Bifidobacterium adolescentis/genetics/metabolism ; *Gastrointestinal Microbiome/genetics ; Bifidobacterium/genetics/metabolism ; *Probiotics ; Phylogeny ; }, abstract = {Bifidobacteria are among the first microbial colonizers of the human gut, being frequently associated with human health-promoting activities. In the current study, an in silico methodology based on an ecological and phylogenomic-driven approach allowed the selection of a Bifidobacterium adolescentis prototype strain, i.e., B. adolescentis PRL2023, which best represents the overall genetic content and functional features of the B. adolescentis taxon. Such features were confirmed by in vitro experiments aimed at evaluating the ability of this strain to survive in the gastrointestinal tract of the host and its ability to interact with human intestinal cells and other microbial gut commensals. In this context, co-cultivation of B. adolescentis PRL2023 and several gut commensals revealed various microbe-microbe interactions and indicated co-metabolism of particular plant-derived glycans, such as xylan.IMPORTANCEThe use of appropriate bacterial strains in experimental research becomes imperative in order to investigate bacterial behavior while mimicking the natural environment. In the current study, through in silico and in vitro methodologies, we were able to identify the most representative strain of the Bifidobacterium adolescentis species. The ability of this strain, B. adolescentis PRL2023, to cope with the environmental challenges imposed by the gastrointestinal tract, together with its ability to switch its carbohydrate metabolism to compete with other gut microorganisms, makes it an ideal choice as a B. adolescentis prototype and a member of the healthy microbiota of adults. This strain possesses a genetic blueprint appropriate for its exploitation as a candidate for next-generation probiotics.}, } @article {pmid38800117, year = {2023}, author = {Ryan, MJ and Mauchline, TH and Malone, JG and Jones, S and Thompson, CMA and Bonnin, JM and Stewart, H and Yau, PTO and Taketani, RG and Clark, IM and Holden, N}, title = {The UK Crop Microbiome Cryobank: a utility and model for supporting Phytobiomes research.}, journal = {CABI agriculture and bioscience}, volume = {4}, number = {1}, pages = {53}, pmid = {38800117}, issn = {2662-4044}, abstract = {Plant microbiomes are the microbial communities essential to the functioning of the phytobiome-the system that consist of plants, their environment, and their associated communities of organisms. A healthy, functional phytobiome is critical to crop health, improved yields and quality food. However, crop microbiomes are relatively under-researched, and this is associated with a fundamental need to underpin phytobiome research through the provision of a supporting infrastructure. The UK Crop Microbiome Cryobank (UKCMC) project is developing a unique, integrated and open-access resource to enable the development of solutions to improve soil and crop health. Six economically important crops (Barley, Fava Bean, Oats, Oil Seed Rape, Sugar Beet and Wheat) are targeted, and the methods as well as data outputs will underpin research activity both in the UK and internationally. This manuscript describes the approaches being taken, from characterisation, cryopreservation and analysis of the crop microbiome through to potential applications. We believe that the model research framework proposed is transferable to different crop and soil systems, acting not only as a mechanism to conserve biodiversity, but as a potential facilitator of sustainable agriculture systems.}, } @article {pmid38294243, year = {2024}, author = {Omondi, VO and Bosire, GO and Onyari, JM and Kibet, C and Mwasya, S and Onyonyi, VN and Getahun, MN}, title = {Multi-omics analyses reveal rumen microbes and secondary metabolites that are unique to livestock species.}, journal = {mSystems}, volume = {9}, number = {2}, pages = {e0122823}, pmid = {38294243}, issn = {2379-5077}, support = {B1126A-185//Max Planck Institute for Chemical Ecology/ ; B1126A-185//International Centre of Insect Physiology and Ecology (ICIPE)/ ; }, mesh = {Cattle ; Humans ; Sheep ; Animals ; *Livestock/microbiology ; Rumen/metabolism ; Camelus ; Multiomics ; Ruminants/microbiology ; *Microbiota/genetics ; Goats/physiology ; Animal Feed/analysis ; }, abstract = {Ruminant livestock, including cattle, sheep, goats, and camels, possess a distinctive digestive system with complex microbiota communities critical for feed conversion and secondary metabolite production, including greenhouse gases. Yet, there is limited knowledge regarding the diversity of rumen microbes and metabolites benefiting livestock physiology, productivity, climate impact, and defense mechanisms across ruminant species. In this study, we utilized metataxonomics and metabolomics data from four evolutionarily distinct livestock species, which had fed on diverse plant materials like grass, shrubs, and acacia trees, to uncover the unique signature microbes and secondary metabolites. We established the presence of a distinctive anaerobic fungus called Oontomyces in camels, while cattle exhibited a higher prevalence of unique microbes like Psychrobacter, Anaeromyces, Cyllamyces, and Orpinomyces. Goats hosted Cleistothelebolus, and Liebetanzomyces was unique to sheep. Furthermore, we identified a set of conserved core microbes, including Prevotella, Rickenellaceae, Cladosporium, and Pecoramyces, present in all the ruminants, irrespective of host genetics and dietary composition. This underscores their indispensable role in maintaining crucial physiological functions. Regarding secondary metabolites, camel's rumen is rich in organic acids, goat's rumen is rich in alcohols and hydrocarbons, sheep's rumen is rich in indoles, and cattle's rumen is rich in sesquiterpenes. Additionally, linalool propionate and terpinolene were uniquely found in sheep rumen, while valencene was exclusive to cattle. This may suggest the existence of species-specific microbes and metabolites that require host rumen-microbes' environment balance. These results have implications for manipulating the rumen environment to target specific microbes and secondary metabolite networks, thereby enhancing livestock productivity, resilience, reducing susceptibility to vectors, and environmentally preferred livestock husbandry.IMPORTANCERumen fermentation, which depends on feed components and rumen microbes, plays a crucial role in feed conversion and the production of various metabolites important for the physiological functions, health, and environmental smartness of ruminant livestock, in addition to providing food for humans. However, given the complexity and variation of the rumen ecosystem and feed of these various livestock species, combined with inter-individual differences between gut microbial communities, how they influence the rumen secondary metabolites remains elusive. Using metagenomics and metabolomics approaches, we show that each livestock species has a signature microbe(s) and secondary metabolites. These findings may contribute toward understanding the rumen ecosystem, microbiome and metabolite networks, which may provide a gateway to manipulating rumen ecosystem pathways toward making livestock production efficient, sustainable, and environmentally friendly.}, } @article {pmid38291185, year = {2024}, author = {Liu, X and Tong, X and Zou, L and Ju, Y and Liu, M and Han, M and Lu, H and Yang, H and Wang, J and Zong, Y and Liu, W and Xu, X and Jin, X and Xiao, L and Jia, H and Guo, R and Zhang, T}, title = {A genome-wide association study reveals the relationship between human genetic variation and the nasal microbiome.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {139}, pmid = {38291185}, issn = {2399-3642}, support = {32200548//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; Genome-Wide Association Study ; Nose ; *Microbiota/genetics ; Genetic Variation ; *Cardiovascular Diseases ; }, abstract = {The nasal cavity harbors diverse microbiota that contributes to human health and respiratory diseases. However, whether and to what extent the host genome shapes the nasal microbiome remains largely unknown. Here, by dissecting the human genome and nasal metagenome data from 1401 healthy individuals, we demonstrated that the top three host genetic principal components strongly correlated with the nasal microbiota diversity and composition. The genetic association analyses identified 63 genome-wide significant loci affecting the nasal microbial taxa and functions, of which 2 loci reached study-wide significance (p < 1.7 × 10[-10]): rs73268759 within CAMK2A associated with genus Actinomyces and family Actinomycetaceae; and rs35211877 near POM121L12 with Gemella asaccharolytica. In addition to respiratory-related diseases, the associated loci are mainly implicated in cardiometabolic or neuropsychiatric diseases. Functional analysis showed the associated genes were most significantly expressed in the nasal airway epithelium tissue and enriched in the calcium signaling and hippo signaling pathway. Further observational correlation and Mendelian randomization analyses consistently suggested the causal effects of Serratia grimesii and Yokenella regensburgei on cardiometabolic biomarkers (cystine, glutamic acid, and creatine). This study suggested that the host genome plays an important role in shaping the nasal microbiome.}, } @article {pmid38289284, year = {2024}, author = {Wang, H and Chen, Y and Feng, L and Lu, S and Zhu, J and Zhao, J and Zhang, H and Chen, W and Lu, W}, title = {A gut aging clock using microbiome multi-view profiles is associated with health and frail risk.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2297852}, pmid = {38289284}, issn = {1949-0984}, mesh = {Aged ; Humans ; *Gastrointestinal Microbiome ; Frail Elderly ; *Frailty ; *Microbiota ; Aging ; }, abstract = {Age-related changes in the microbiome have been reported in previous studies; however, direct evidence for their association with frailty is lacking. Here, we introduce biological age based on gut microbiota (gAge), an integrated prediction model that integrates gut microbiota data from different perspectives with potential background factors for aging assessment. Simulation results show that, compared with a single model, the ensemble model can not only significantly improve the prediction accuracy, but also make full use of the data in unpaired samples. From this, we identified markers associated with age development and grouped markers into accelerated aging and mitigated aging according to their effect on the prediction. Importantly, the application of gAge to an elderly cohort with different frailty levels confirmed that gAge and its predictive residuals are closely related to the individual's health status and frailty stage, and age-related markers overlap significantly with disease and frailty characteristics. Furthermore, we applied the gAge prediction model to another independent cohort of the elderly population for aging assessment and found that gAge could effectively represent the aging population. Overall, our study explains the association between the gut microbiota and frailty, providing potential targets for the development of gut microbiota-based targeted intervention strategies for aging.}, } @article {pmid38289113, year = {2024}, author = {Abdulkadir, N and Saraiva, JP and Zhang, J and Stolte, S and Gillor, O and Harms, H and Rocha, U}, title = {Genome-centric analyses of 165 metagenomes show that mobile genetic elements are crucial for the transmission of antimicrobial resistance genes to pathogens in activated sludge and wastewater.}, journal = {Microbiology spectrum}, volume = {12}, number = {3}, pages = {e0291823}, pmid = {38289113}, issn = {2165-0497}, support = {VH-NG-1248 Micro' Big Data'//Helmholtz Association ()/ ; 460129525//Deutsche Forschungsgemeinschaft (DFG)/ ; 91717355//German Academic Exchange Service (DAAD)/ ; }, mesh = {Animals ; Humans ; *Wastewater ; Sewage/microbiology ; Anti-Bacterial Agents/pharmacology ; Metagenome ; Genes, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Bacteria ; *Microbiota ; Interspersed Repetitive Sequences ; }, abstract = {UNLABELLED: Wastewater is considered a reservoir of antimicrobial resistance genes (ARGs), where the abundant antimicrobial-resistant bacteria and mobile genetic elements facilitate horizontal gene transfer. However, the prevalence and extent of these phenomena in different taxonomic groups that inhabit wastewater are still not fully understood. Here, we determined the presence of ARGs in metagenome-assembled genomes (MAGs) and evaluated the risks of MAG-carrying ARGs in potential human pathogens. The potential of these ARGs to be transmitted horizontally or vertically was also determined. A total of 5,916 MAGs (completeness >50%, contamination <10%) were recovered, covering 68 phyla and 279 genera. MAGs were dereplicated into 1,204 genome operational taxonomic units (gOTUs) as a proxy for species (average nucleotide identity >0.95). The dominant ARG classes detected were bacitracin, multi-drug, macrolide-lincosamide-streptogramin (MLS), glycopeptide, and aminoglycoside, and 10.26% of them were located on plasmids. The main hosts of ARGs belonged to Escherichia, Klebsiella, Acinetobacter, Gresbergeria, Mycobacterium, and Thauera. Our data showed that 253 MAGs carried virulence factor genes (VFGs) divided into 44 gOTUs, of which 45 MAGs were carriers of ARGs, indicating that potential human pathogens carried ARGs. Alarmingly, the MAG assigned as Escherichia coli contained 159 VFGs, of which 95 were located on chromosomes and 10 on plasmids. In addition to shedding light on the prevalence of ARGs in individual genomes recovered from activated sludge and wastewater, our study demonstrates a workflow that can identify antimicrobial-resistant pathogens in complex microbial communities.

IMPORTANCE: Antimicrobial resistance (AMR) threatens the health of humans, animals, and natural ecosystems. In our study, an analysis of 165 metagenomes from wastewater revealed antibiotic-targeted alteration, efflux, and inactivation as the most prevalent AMR mechanisms. We identified several genera correlated with multiple ARGs, including Klebsiella, Escherichia, Acinetobacter, Nitrospira, Ottowia, Pseudomonas, and Thauera, which could have significant implications for AMR transmission. The abundance of bacA, mexL, and aph(3")-I in the genomes calls for their urgent management in wastewater. Our approach could be applied to different ecosystems to assess the risk of potential pathogens containing ARGs. Our findings highlight the importance of managing AMR in wastewater and can help design measures to reduce the transmission and evolution of AMR in these systems.}, } @article {pmid38289047, year = {2024}, author = {Romani, L and Del Chierico, F and Pane, S and Ristori, MV and Pirona, I and Guarrasi, V and Cotugno, N and Bernardi, S and Lancella, L and Perno, CF and Rossi, P and Villani, A and Campana, A and Palma, P and Putignani, L and , }, title = {Exploring nasopharyngeal microbiota profile in children affected by SARS-CoV-2 infection.}, journal = {Microbiology spectrum}, volume = {12}, number = {3}, pages = {e0300923}, pmid = {38289047}, issn = {2165-0497}, support = {//Ministero della Salute (Italy Ministry of Health)/ ; 202003_Bioarte_Putignani//The BioArte Limited/ ; Current Research funds//Italian Ministry of Health/ ; }, mesh = {Adult ; Humans ; Child ; *COVID-19 ; RNA, Ribosomal, 16S/genetics ; SARS-CoV-2/genetics ; *Microbiota/genetics ; Nasopharynx ; Streptococcus/genetics ; }, abstract = {UNLABELLED: The relationship between COVID-19 and nasopharyngeal (NP) microbiota has been investigated mainly in the adult population. We explored the NP profile of children affected by COVID-19, compared to healthy controls (CTRLs). NP swabs of children with COVID-19, collected between March and September 2020, were investigated at the admission (T0), 72 h to 7 days (T1), and at the discharge (T2) of the patients. NP microbiota was analyzed by 16S rRNA targeted-metagenomics. Data from sequencing were investigated by QIIME 2.0 and PICRUSt 2. Multiple machine learning (ML) models were exploited to classify patients compared to CTRLs. The NP microbiota of COVID-19 patients (N = 71) was characterized by reduction of α-diversity compared to CTRLs (N = 59). The NP microbiota of COVID-19 cohort appeared significantly enriched in Streptococcus, Haemophilus, Staphylococcus, Veillonella, Enterococcus, Neisseria, Moraxella, Enterobacteriaceae, Gemella, Bacillus, and reduced in Faecalibacterium, Akkermansia, Blautia, Bifidobacterium, Ruminococcus, and Bacteroides, compared to CTRLs (FDR < 0.001). Exploiting ML models, Enterococcus, Pseudomonas, Streptococcus, Capnocytopagha, Tepidiphilus, Porphyromonas, Staphylococcus, and Veillonella resulted as NP microbiota biomarkers, in COVID-19 patients. No statistically significant differences were found comparing the NP microbiota profile of COVID-19 patients during the time-points or grouping patients on the basis of high, medium, and low viral load (VL). This evidence provides specific pathobiont signatures of the NP microbiota in pediatric COVID-19 patients, and the reduction of anaerobic protective commensals. Our data suggest that the NP microbiota may have a specific disease-related signature since infection onset without changes during disease progression, regardless of the SARS-CoV-2 VL.

IMPORTANCE: Since the beginning of pandemic, we know that children are less susceptible to severe COVID-19 disease. A potential role of the nasopharyngeal (NP) microbiota has been hypothesized but to date, most of the studies have been focused on adults. We studied the NP microbiota modifications in children affected by SARS-CoV-2 infection showing a specific NP microbiome profile, mainly composed by pathobionts and almost missing protective anaerobic commensals. Moreover, in our study, specific microbial signatures appear since the first days of infection independently from SARS-CoV-2 viral load.}, } @article {pmid38287457, year = {2024}, author = {Nweze, JE and Šustr, V and Brune, A and Angel, R}, title = {Functional similarity, despite taxonomical divergence in the millipede gut microbiota, points to a common trophic strategy.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {16}, pmid = {38287457}, issn = {2049-2618}, support = {19-24309Y//Grantová Agentura České Republiky/ ; 19-24309Y//Grantová Agentura České Republiky/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; Bacteria ; *Arthropods/genetics ; Metagenome ; Bacteroidetes/genetics ; Proteobacteria/genetics ; Metagenomics ; Carbohydrates ; Nitrogen/metabolism ; Sulfates/metabolism ; }, abstract = {BACKGROUND: Many arthropods rely on their gut microbiome to digest plant material, which is often low in nitrogen but high in complex polysaccharides. Detritivores, such as millipedes, live on a particularly poor diet, but the identity and nutritional contribution of their microbiome are largely unknown. In this study, the hindgut microbiota of the tropical millipede Epibolus pulchripes (large, methane emitting) and the temperate millipede Glomeris connexa (small, non-methane emitting), fed on an identical diet, were studied using comparative metagenomics and metatranscriptomics.

RESULTS: The results showed that the microbial load in E. pulchripes is much higher and more diverse than in G. connexa. The microbial communities of the two species differed significantly, with Bacteroidota dominating the hindguts of E. pulchripes and Proteobacteria (Pseudomonadota) in G. connexa. Despite equal sequencing effort, de novo assembly and binning recovered 282 metagenome-assembled genomes (MAGs) from E. pulchripes and 33 from G. connexa, including 90 novel bacterial taxa (81 in E. pulchripes and 9 in G. connexa). However, despite this taxonomic divergence, most of the functions, including carbohydrate hydrolysis, sulfate reduction, and nitrogen cycling, were common to the two species. Members of the Bacteroidota (Bacteroidetes) were the primary agents of complex carbon degradation in E. pulchripes, while members of Proteobacteria dominated in G. connexa. Members of Desulfobacterota were the potential sulfate-reducing bacteria in E. pulchripes. The capacity for dissimilatory nitrate reduction was found in Actinobacteriota (E. pulchripes) and Proteobacteria (both species), but only Proteobacteria possessed the capacity for denitrification (both species). In contrast, some functions were only found in E. pulchripes. These include reductive acetogenesis, found in members of Desulfobacterota and Firmicutes (Bacillota) in E. pulchripes. Also, diazotrophs were only found in E. pulchripes, with a few members of the Firmicutes and Proteobacteria expressing the nifH gene. Interestingly, fungal-cell-wall-degrading glycoside hydrolases (GHs) were among the most abundant carbohydrate-active enzymes (CAZymes) expressed in both millipede species, suggesting that fungal biomass plays an important role in the millipede diet.

CONCLUSIONS: Overall, these results provide detailed insights into the genomic capabilities of the microbial community in the hindgut of millipedes and shed light on the ecophysiology of these essential detritivores. Video Abstract.}, } @article {pmid38287146, year = {2024}, author = {Achberger, AM and Jones, R and Jamieson, J and Holmes, CP and Schubotz, F and Meyer, NR and Dekas, AE and Moriarty, S and Reeves, EP and Manthey, A and Brünjes, J and Fornari, DJ and Tivey, MK and Toner, BM and Sylvan, JB}, title = {Inactive hydrothermal vent microbial communities are important contributors to deep ocean primary productivity.}, journal = {Nature microbiology}, volume = {9}, number = {3}, pages = {657-668}, pmid = {38287146}, issn = {2058-5276}, support = {OCE 1756339//National Science Foundation (NSF)/ ; OCE 1756558//National Science Foundation (NSF)/ ; ECCS-2026822//National Science Foundation (NSF)/ ; OCE-1949485//National Science Foundation (NSF)/ ; OCE-1756419//National Science Foundation (NSF)/ ; OCE-1756558//National Science Foundation (NSF)/ ; OCE-1756339//National Science Foundation (NSF)/ ; CRC-2020-001165//Canada Research Chairs (Chaires de recherche du Canada)/ ; EXC 2077 - 390741603//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Hydrothermal Vents/microbiology ; Phylogeny ; *Microbiota ; Carbon/metabolism ; Oceans and Seas ; }, abstract = {Active hydrothermal vents are oases for productivity in the deep ocean, but the flow of dissolved substrates that fuel such abundant life ultimately ceases, leaving behind inactive mineral deposits. The rates of microbial activity on these deposits are largely unconstrained. Here we show primary production occurs on inactive hydrothermal deposits and quantify its contribution to new organic carbon production in the deep ocean. Measured incorporation of [14]C-bicarbonate shows that microbial communities on inactive deposits fix inorganic carbon at rates comparable to those on actively venting deposits. Single-cell uptake experiments and nanoscale secondary ion mass spectrometry showed chemoautotrophs comprise a large fraction (>30%) of the active microbial cells. Metagenomic and lipidomic surveys of inactive deposits further revealed that the microbial communities are dominated by Alphaproteobacteria and Gammaproteobacteria using the Calvin-Benson-Bassham pathway for carbon fixation. These findings establish inactive vent deposits as important sites for microbial activity and organic carbon production on the seafloor.}, } @article {pmid38286361, year = {2024}, author = {Pourafshar, S and Sharma, B and Allen, J and Hoang, M and Lee, H and Dressman, H and Tyson, CC and Mallawaarachchi, I and Kumar, P and Ma, JZ and Lin, PH and Scialla, JJ}, title = {Longitudinal Pilot Evaluation of the Gut Microbiota Comparing Patients With and Without Chronic Kidney Disease.}, journal = {Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation}, volume = {34}, number = {4}, pages = {302-312}, doi = {10.1053/j.jrn.2024.01.003}, pmid = {38286361}, issn = {1532-8503}, mesh = {Humans ; *Renal Insufficiency, Chronic/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; *RNA, Ribosomal, 16S/genetics ; Longitudinal Studies ; Pilot Projects ; *Feces/microbiology ; Aged ; Adult ; Glomerular Filtration Rate ; }, abstract = {OBJECTIVE: The gut microbiota contributes to metabolic diseases, such as diabetes and hypertension, but is poorly characterized in chronic kidney disease (CKD).

DESIGN AND METHODS: We enrolled 24 adults within household pairs, in which at least one member had self-reported kidney disease, diabetes, or hypertension. CKD was classified based on estimated glomerular filtration rate < 60 mL/min/1.73 m[2] or urine-albumin-to-creatinine ratio of ≥ 30 mg/g. Participants collected stool and dietary recalls seasonally over a year. Gut microbiota was characterized using 16s rRNA and metagenomic sequencing.

RESULTS: Ten participants had CKD (42%) with a median (interquartile range) estimated glomerular filtration rate of 49 (44, 54) mL/min/1.73 m[2]. By 16s rRNA sequencing, there was moderate to high intraclass correlation (ICC = 0.63) for seasonal alpha diversity (Shannon index) within individuals and modest differences by season (P < .01). ICC was lower with metagenomics, which has resolution at the species level (ICC = 0.26). There were no differences in alpha or beta diversity by CKD with either method. Among 79 genera, Frisingicoccus, Tuzzerella, Faecalitalea, and Lachnoclostridium had lower abundance in CKD, while Collinsella, Lachnospiraceae_ND3007, Veillonella, and Erysipelotrichaceae_UCG_003 were more abundant in CKD (each nominal P < .05) using 16s rRNA sequencing. Higher Collinsella and Veillonella and lower Lachnoclostridium in CKD were also identified by metagenomics. By metagenomics, Coprococcus catus and Bacteroides stercoris were more and less abundant in CKD, respectively, at false discovery rate corrected P = .02.

CONCLUSIONS: We identified candidate taxa in the gut microbiota associated with CKD. High ICC in individuals with modest seasonal impacts implies that follow-up studies may use less frequent sampling.}, } @article {pmid38285123, year = {2024}, author = {Rana, S and Singh, P and Bhardwaj, T and Somvanshi, P}, title = {A Comprehensive Metagenome Study Identifies Distinct Biological Pathways in Asthma Patients: An In-Silico Approach.}, journal = {Biochemical genetics}, volume = {62}, number = {6}, pages = {4264-4279}, pmid = {38285123}, issn = {1573-4927}, mesh = {*Asthma/microbiology/genetics ; Humans ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Computer Simulation ; Gastrointestinal Microbiome ; Female ; Metabolic Networks and Pathways ; Male ; Adult ; }, abstract = {Asthma is a multifactorial disease with phenotypes and several clinical and pathophysiological characteristics. Besides innate and adaptive immune responses, the gut microbiome generates Treg cells, mediating the allergic response to environmental factors and exposure to allergens. Because of the complexity of asthma, microbiome analysis and other precision medicine methods are now widely regarded as essential elements of efficient disease therapy. An in-silico pipeline enables the comparative taxonomic profiling of 16S rRNA metagenomic profiles of 20 asthmatic patients and 15 healthy controls utilizing QIIME2. Further, PICRUSt supports downstream gene enrichment and pathway analysis, inferring the enriched pathways in a diseased state. A significant abundance of the phylum Proteobacteria, Sutterella, and Megamonas is identified in asthma patients and a diminished genus Akkermansia. Nasal samples reveal a high relative abundance of Mycoplasma in the nasal samples. Further, differential functional profiling identifies the metabolic pathways related to cofactors and amino acids, secondary metabolism, and signaling pathways. These findings support that a combination of bacterial communities is involved in mediating the responses involved in chronic respiratory conditions like asthma by exerting their influence on various metabolic pathways.}, } @article {pmid38283642, year = {2023}, author = {Teh, HE and Pung, CK and Arasoo, VJT and Yap, PSX}, title = {A Landscape View of the Female Genital Tract Microbiome in Healthy Controls and Women With Reproductive Health Conditions Associated With Ectopic Pregnancy.}, journal = {British journal of biomedical science}, volume = {80}, number = {}, pages = {12098}, pmid = {38283642}, issn = {2474-0896}, mesh = {Pregnancy ; Infant, Newborn ; Female ; Humans ; Reproductive Health ; *Microbiota/genetics ; *Pregnancy, Ectopic ; Vagina ; Lactobacillus/genetics ; RNA, Ribosomal, 16S ; }, abstract = {Disruption of the female genital microbiome is associated with several pregnancy complications, including miscarriage, preterm onset of labour, and tubal pregnancy. Ectopic pregnancy is a known cause of maternal morbidity and mortality, but early diagnosis and treatment of ectopic pregnancy remain a challenge. Despite growing established associations between genital microbiome and female reproductive health, few studies have specifically focused on its link with ectopic pregnancy. Therefore, the current review aims to provide a comprehensive account of the female genital microbiome in healthy and fertile women compared to those in ectopic pregnancy and its associated risk factors. The microbial diversity from various sites of the female genital tract was explored for a reliable proxy of female reproductive health in sequencing-based ectopic pregnancy research. Our report confirmed the predominance of Lactobacillus in the vagina and the cervix among healthy women. The relative abundance decreased in the vaginal and cervical microbiome in the disease state. In contrast, there were inconsistent findings on the uterine microbiome across studies. Additionally, we explore a spectrum of opportunities to enhance our understanding of the female genital tract microbiome and reproductive conditions. In conclusion, this study identifies gaps within the field and emphasises the need for visionary solutions in metagenomic tools for the early detection of ectopic pregnancy and other gynaecological diseases.}, } @article {pmid38281639, year = {2024}, author = {Sharma, A and Taubert, M and Pérez-Carrascal, OM and Lehmann, R and Ritschel, T and Totsche, KU and Lazar, CS and Küsel, K}, title = {Iron coatings on carbonate rocks shape the attached bacterial aquifer community.}, journal = {The Science of the total environment}, volume = {917}, number = {}, pages = {170384}, doi = {10.1016/j.scitotenv.2024.170384}, pmid = {38281639}, issn = {1879-1026}, mesh = {*Iron ; Ecosystem ; Bacteria ; Carbonates ; *Groundwater/microbiology ; }, abstract = {Most studies of groundwater ecosystems target planktonic microbes, which are easily obtained via water samples. In contrast, little is known about the diversity and function of microbes adhering to rock surfaces, particularly to consolidated rocks. To investigate microbial attachment to rock surfaces, we incubated rock chips from fractured aquifers in limestone-mudstone alternations in bioreactors fed with groundwater from two wells representing oxic and anoxic conditions. Half of the chips were coated with iron oxides, representing common secondary mineralization in fractured rock. Our time-series analysis showed bacteria colonizing the chips within two days, reaching cell numbers up to 4.16 × 10[5] cells/mm[2] after 44 days. Scanning electron microscopy analyses revealed extensive colonization but no multi-layered biofilms, with chips from oxic bioreactors more densely colonized than from anoxic ones. Estimated attached-to-planktonic cell ratios yielded values of up to 10[6]: 1 and 10[3]: 1, for oxic and anoxic aquifers, respectively. We identified distinct attached and planktonic communities with an overlap between 17 % and 42 %. Oxic bioreactors were dominated by proteobacterial genera Aquabacterium and Rhodoferax, while Rheinheimera and Simplicispira were the key players of anoxic bioreactors. Motility, attachment, and biofilm formation traits were predicted in major genera based on groundwater metagenome-assembled genomes and reference genomes. Early rock colonizers appeared to be facultative autotrophs, capable of fixing CO2 to synthesize biomass and a biofilm matrix. Late colonizers were predicted to possess biofilm degrading enzymes such as beta-glucosidase, beta-galactosidase, amylases. Fe-coated chips of both bioreactors featured more potential iron reducers and oxidizers than bare rock chips. As secondary minerals can also serve as energy source, they might favor primary production and thus contribute to subsurface ecosystem services like carbon fixation. Since most subsurface microbes seem to be attached, their contribution to ecosystem services should be considered in future studies.}, } @article {pmid38281336, year = {2024}, author = {Wang, L and Wang, Z and Li, Y and Cai, W and Zou, Y and Hui, C}, title = {Deciphering solute transport, microbiota assembly patterns and metabolic functions in the hyporheic zone of an effluent-dominated river.}, journal = {Water research}, volume = {251}, number = {}, pages = {121190}, doi = {10.1016/j.watres.2024.121190}, pmid = {38281336}, issn = {1879-2448}, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota ; Oxidation-Reduction ; Rivers/chemistry ; }, abstract = {We lack a clear understanding of how anthropogenic pressures, exemplified by effluent discharge from wastewater treatment plants, destabilize microbial communities in the hyporheic zone (HZ) of receiving rivers. In this study, the spatiotemporal characteristics of hydrological parameters, and the physicochemical properties of surface and subsurface water in a representative effluent-dominated river were monitored. Sequencing of 16S rRNA amplicons and metagenomes revealed the microbial community structure in the HZ of both effluent discharge area and downstream region. The keystone taxa (taxa vital in determining the composition of each microbial cluster) and the keystone functions they controlled were subsequently identified. Effluent discharge amplified the depth of the oxic/suboxic zone and the hyporheic exchange fluxes in the effluent discharge area, which was 50-120% and 40-300% higher than in the downstream region, respectively. Microbial community structure pattern analysis demonstrated an enhancement in the rate of dispersal, an increase in microbial diversity, and an improved community network complexity in the effluent discharge area. By contrast, the number of keystone taxa in the effluent discharge area was 50-70% lower than that of the downstream region, resulting in reduced community network stability and functionality. The keystone taxa controlling metabolic functions in the networks categorized to effluent discharge area were comprised of more genera related to nitrogen and sulfur cycling, e.g., Dechloromonas, Desulfobacter, Flavobacterium, Nitrosomonas, etc., highlighting a research need in monitoring species associated with nutrient element cycling in the HZ of receiving waterbodies. The results showed that the keystone taxa could contribute positively to network stability, which was negatively correlated to hyporheic exchange fluxes and redox gradients. This study provides valuable insights that will improve our understanding of how river ecosystems respond to changes in anthropogenic pressures.}, } @article {pmid38280535, year = {2024}, author = {Stiernborg, M and Prast-Nielsen, S and Melas, PA and Skott, M and Millischer, V and Boulund, F and Forsell, Y and Lavebratt, C}, title = {Differences in the gut microbiome of young adults with schizophrenia spectrum disorder: using machine learning to distinguish cases from controls.}, journal = {Brain, behavior, and immunity}, volume = {117}, number = {}, pages = {298-309}, doi = {10.1016/j.bbi.2024.01.218}, pmid = {38280535}, issn = {1090-2139}, mesh = {Humans ; Young Adult ; *Gastrointestinal Microbiome/genetics ; *Schizophrenia/genetics ; Feces/microbiology ; Metagenome ; Bacteria/genetics ; }, abstract = {While an association between the gut microbiome and schizophrenia spectrum disorders (SSD) has been suggested, the existing evidence is still inconclusive. To this end, we analyzed bacteria and bacterial genes in feces from 52 young adult SSD patients and 52 controls using fecal shotgun metagenomic sequencing. Compared to controls, young SSD patients were found to have significantly lower α-diversity and different β-diversity both regarding bacterial species (i.e., taxonomic diversity) and bacterial genes (i.e., functional diversity). Furthermore, the α-diversity measures 'Pielou's evenness' and 'Shannon' were significantly higher for both bacterial species, bacterial genes encoding enzymes and gut brain modules in young SSD patients on antipsychotic treatment (young SSD not on antipsychotics=9 patients, young SSD on antipsychotics=43 patients). We also applied machine learning classifiers to distinguish between young SSD patients and healthy controls based on their gut microbiome. Results showed that taxonomic and functional data classified young SSD individuals with an accuracy of ≥ 70% and with an area under the receiver operating characteristic curve (AUROC) of ≥ 0.75. Differential abundance analysis on the most important features in the classifier models revealed that most of the species with higher abundance in young SSD patients had their natural habitat in the oral cavity. In addition, many of the modules with higher abundance in young SSD patients were amino acid biosynthesis modules. Moreover, the abundances of gut-brain modules of butyrate synthesis and acetate degradation were lower in the SSD patients compared to controls. Collectively, our findings continue to support the presence of gut microbiome alterations in SSD and provide support for the use of machine learning algorithms to distinguish patients from controls based on gut microbiome profiles.}, } @article {pmid38280177, year = {2024}, author = {Liberato, MV and Paixao, DAA and Tomazetto, G and Ndeh, D and Bolam, DN and Squina, FM}, title = {Discovery, structural characterization, and functional insights into a novel apiosidase from the GH140 family, isolated from a lignocellulolytic-enriched mangrove microbial community.}, journal = {Biotechnology letters}, volume = {46}, number = {2}, pages = {201-211}, pmid = {38280177}, issn = {1573-6776}, support = {2022/08958-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 306279/2020-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {*Polysaccharides ; Oligosaccharides/chemistry ; Glycoside Hydrolases/genetics/chemistry ; Monosaccharides ; *Microbiota ; }, abstract = {OBJECTIVES: Apiosidases are enzymes that cleave the glycosidic bond between the monosaccharides linked to apiose, a branched chain furanose found in the cell walls of vascular plants and aquatic monocots. There is biotechnological interest in this enzyme group because apiose is the flavor-active compound of grapes, fruit juice, and wine, and the monosaccharide is found to be a plant secondary metabolite with pharmaceutical properties. However, functional and structural studies of this enzyme family are scarce. Recently, a glycoside hydrolase family member GH140 was isolated from Bacteroides thetaiotaomicron and identified as an endo-apiosidase.

RESULTS: The structural characterization and functional identification of a second GH140 family enzyme, termed MmApi, discovered through mangrove soil metagenomic approach, are described. Among the various substrates tested, MmApi exhibited activity on an apiose-containing oligosaccharide derived from the pectic polysaccharide rhamnogalacturonan-II. While the crystallographic model of MmApi was similar to the endo-apiosidase from Bacteroides thetaiotaomicron, differences in the shape of the binding sites indicated that MmApi could cleave apioses within oligosaccharides of different compositions.

CONCLUSION: This enzyme represents a novel tool for researchers interested in studying the physiology and structure of plant cell walls and developing biocatalytic strategies for drug and flavor production.}, } @article {pmid38280093, year = {2024}, author = {Jasmin, MY and Isa, NM and Kamarudin, MS and Lim, KC and Karim, M}, title = {Evaluating Bacillus flexus as bioremediators for ammonia removal in shrimp culture water and wastewater and characterizing microbial communities in shrimp pond sludge.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {55}, number = {1}, pages = {529-536}, pmid = {38280093}, issn = {1678-4405}, mesh = {*Wastewater ; Sewage/microbiology ; Ammonia ; Ponds ; Bacteria/genetics ; *Microbiota ; Nitrogen ; *Bacillus ; }, abstract = {The accumulation of nitrogen compounds in shrimp farming water and effluent presents a major challenge. Ammonia is a form of nitrogen that limits shrimp growth due to its potential toxicity and effects on shrimp health and water quality. This study is aimed at identifying promising bioremediators from shrimp pond sludge to mitigate ammonia levels in both culture water and wastewater and at determining major bacterial communities in sludge using metagenomic analysis. A sludge sample was collected from a shrimp pond in Selangor, Malaysia, to isolate potential ammonia-removing bacteria. Out of 64 isolated strains, Bacillus flexus SS2 showed the highest growth in synthetic basal media (SBM) containing ammonium sulfate at a concentration of 70 mg/L as the sole nitrogen source. The strain was then incubated in SBM with varying pH levels and showed optimal growth at pH 6.5-7. After 24 h of incubation, B. flexus SS2 reduced the ammonia concentration from an initial concentration of 5 to 0.01 mg/L, indicating a 99.61% reduction rate, which was highest in SBM at pH 7. Moreover, the strain showed ammonia removal ability at concentrations ranging from 5 to 70 mg/L. Metagenomic analysis revealed that Proteobacteria was the most abundant phylum in the sludge, followed by Cyanobacteria, Actinobacteria, Chloraflexi, Firmicutes, and Campilobacterota. Bacillus flexus SS2 belongs to the Bacillota phylum and has the potential to serve as a bioremediator for removing ammonia from shrimp culture water and wastewater.}, } @article {pmid38280026, year = {2024}, author = {Otsuka, K and Isobe, J and Asai, Y and Nakano, T and Hattori, K and Ariyoshi, T and Yamashita, T and Motegi, K and Saito, A and Kohmoto, M and Hosonuma, M and Kuramasu, A and Baba, Y and Murayama, M and Narikawa, Y and Toyoda, H and Funayama, E and Tajima, K and Shida, M and Hirasawa, Y and Tsurui, T and Ariizumi, H and Ishiguro, T and Suzuki, R and Ohkuma, R and Kubota, Y and Sambe, T and Tsuji, M and Wada, S and Kiuchi, Y and Kobayashi, S and Horiike, A and Goto, S and Murakami, M and Kim, YG and Tsunoda, T and Yoshimura, K}, title = {Butyricimonas is a key gut microbiome component for predicting postoperative recurrence of esophageal cancer.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {73}, number = {2}, pages = {23}, pmid = {38280026}, issn = {1432-0851}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Neoplasm Recurrence, Local ; Bacteria/genetics ; *Esophageal Neoplasms/surgery ; Biomarkers ; }, abstract = {BACKGROUND: Recently, intestinal bacteria have attracted attention as factors affecting the prognosis of patients with cancer. However, the intestinal microbiome is composed of several hundred types of bacteria, necessitating the development of an analytical method that can allow the use of this information as a highly accurate biomarker. In this study, we investigated whether the preoperative intestinal bacterial profile in patients with esophageal cancer who underwent surgery after preoperative chemotherapy could be used as a biomarker of postoperative recurrence of esophageal cancer.

METHODS: We determined the gut microbiome of the patients using 16S rRNA metagenome sequencing, followed by statistical analysis. Simultaneously, we performed a machine learning analysis using a random forest model with hyperparameter tuning and compared the data obtained.

RESULTS: Statistical and machine learning analyses revealed two common bacterial genera, Butyricimonas and Actinomyces, which were abundant in cases with recurrent esophageal cancer. Butyricimonas primarily produces butyrate, whereas Actinomyces are oral bacteria whose function in the gut is unknown.

CONCLUSION: Our results indicate that Butyricimonas spp. may be a biomarker of postoperative recurrence of esophageal cancer. Although the extent of the involvement of these bacteria in immune regulation remains unknown, future research should investigate their presence in other pathological conditions. Such research could potentially lead to a better understanding of the immunological impact of these bacteria on patients with cancer and their application as biomarkers.}, } @article {pmid38278977, year = {2024}, author = {Cho, EJ and Kim, B and Yu, SJ and Hong, SK and Choi, Y and Yi, NJ and Lee, KW and Suh, KS and Yoon, JH and Park, T}, title = {Urinary microbiome-based metagenomic signature for the noninvasive diagnosis of hepatocellular carcinoma.}, journal = {British journal of cancer}, volume = {130}, number = {6}, pages = {970-975}, pmid = {38278977}, issn = {1532-1827}, support = {NRF-2020R1C1C1012749//National Research Foundation of Korea (NRF)/ ; 05-2021-0010//Seoul National University Hospital (SNUH)/ ; HI16C2037//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; }, mesh = {Humans ; *Carcinoma, Hepatocellular/pathology ; *Liver Neoplasms/diagnosis/genetics/pathology ; Prospective Studies ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Gut microbial dysbiosis is implicated in chronic liver disease and hepatocellular carcinoma (HCC), but the role of microbiomes from various body sites remains unexplored. We assessed disease-specific alterations in the urinary microbiome in HCC patients, investigating their potential as diagnostic biomarkers.

METHODS: We performed cross-sectional analyses of urine samples from 471 HCC patients and 397 healthy controls and validated the results in an independent cohort of 164 HCC patients and 164 healthy controls. Urinary microbiomes were analyzed by 16S rRNA gene sequencing. A microbial marker-based model distinguishing HCC from controls was built based on logistic regression, and its performance was tested.

RESULTS: Microbial diversity was significantly reduced in the HCC patients compared with the controls. There were significant differences in the abundances of various bacteria correlated with HCC, thus defining a urinary microbiome-derived signature of HCC. We developed nine HCC-associated genera-based models with robust diagnostic accuracy (area under the curve [AUC], 0.89; balanced accuracy, 81.2%). In the validation, this model detected HCC with an AUC of 0.94 and an accuracy of 88.4%.

CONCLUSIONS: The urinary microbiome might be a potential biomarker for the detection of HCC. Further clinical testing and validation of these results are needed in prospective studies.}, } @article {pmid38278245, year = {2024}, author = {Midya, V and Nagdeo, K and Lane, JM and Torres-Olascoaga, LA and Torres-Calapiz, M and Gennings, C and Horton, MK and Téllez-Rojo, MM and Wright, RO and Arora, M and Eggers, S}, title = {Prenatal metal exposures and childhood gut microbial signatures are associated with depression score in late childhood.}, journal = {The Science of the total environment}, volume = {916}, number = {}, pages = {170361}, pmid = {38278245}, issn = {1879-1026}, support = {U2C ES026555/ES/NIEHS NIH HHS/United States ; R00 ES032884/ES/NIEHS NIH HHS/United States ; S10 OD026880/OD/NIH HHS/United States ; R01 ES013744/ES/NIEHS NIH HHS/United States ; P30 ES023515/ES/NIEHS NIH HHS/United States ; UL1 TR004419/TR/NCATS NIH HHS/United States ; S10 OD030463/OD/NIH HHS/United States ; R35 ES030435/ES/NIEHS NIH HHS/United States ; }, mesh = {Pregnancy ; Female ; Humans ; Child ; *Gastrointestinal Microbiome ; Depression/epidemiology ; Metals ; Pregnancy Trimester, Third ; Pregnancy Trimester, Second ; *Prenatal Exposure Delayed Effects/epidemiology ; }, abstract = {BACKGROUND: Childhood depression is a major public health issue worldwide. Previous studies have linked both prenatal metal exposures and the gut microbiome to depression in children. However, few, if any, have studied their interacting effect in specific subgroups of children.

OBJECTIVES: Using an interpretable machine-learning method, this study investigates whether children with specific combinations of prenatal metals and childhood microbial signatures (cliques or groups of metals and microbes) were more likely to have higher depression scores at 9-11 years of age.

METHODS: We leveraged data from a well-characterized pediatric longitudinal birth cohort in Mexico City and its microbiome substudy (n = 112). Eleven metal exposures were measured in maternal whole blood samples in the second and third trimesters of pregnancy. The gut microbial abundances were measured at 9-11-year-olds using shotgun metagenomic sequencing. Depression symptoms were assessed using the Child Depression Index (CDI) t-scores at 9-11 years of age. We used Microbial and Chemical Exposure Analysis (MiCxA), which combines interpretable machine-learning into a regression framework to identify and estimate joint associations of metal-microbial cliques in specific subgroups. Analyses were adjusted for relevant covariates.

RESULTS: We identified a subgroup of children (11.6 % of the sample) characterized by a four-component metal-microbial clique that had a significantly high depression score (15.4 % higher than the rest) in late childhood. This metal-microbial clique consisted of high Zinc in the second trimester, low Cobalt in the third trimester, a high abundance of Bacteroides fragilis, a high abundance of Faecalibacterium prausnitzii. All combinations of cliques (two-, three-, and four-components) were significantly associated with increased log-transformed t-scored CDI (β = 0.14, 95%CI = [0.05,0.23], P < 0.01 for the four-component clique).

SIGNIFICANCE: This study offers a new approach to chemical-microbial analysis and a novel demonstration that children with specific gut microbiome cliques and metal exposures during pregnancy may have a higher likelihood of elevated depression scores.}, } @article {pmid38277936, year = {2024}, author = {Liu, M and Deng, N and Hou, X and Zhang, B and Li, H and Wang, J}, title = {Characterisation of flavour profiles and microbial communities of fermented peppers with different fermentation years by combining flavouromics and metagenomics.}, journal = {Food chemistry}, volume = {443}, number = {}, pages = {138550}, doi = {10.1016/j.foodchem.2024.138550}, pmid = {38277936}, issn = {1873-7072}, mesh = {Fermentation ; *Microbiota/genetics ; Bacteria/genetics/metabolism ; Fungi/genetics ; Food ; }, abstract = {The changes in flavours, volatile aromas and microbial communities of fermented peppers with different fermentation years and their relationships were investigated in this study. Results indicated a gradual increase in organic acids during fermentation, whereas free amino acids and capsaicinoids reached stability after 1 year of fermentation. Overall, the analysis detected 340 volatile compounds in fermented peppers and regarded 69 of them as differential compounds. Peppers fermented for 2 (FY2) and 4 years (FY4) possessed a greater number of differential volatiles with large odour activity values, thus endowing them with more favourable flavours. Hence, metagenomic analysis compared their microbial communities and functional annotations. Results revealed that Lactiplantibacillus plantarum and Zygosaccharomyces rouxii were the dominant bacterium and fungus, and metabolism was the main Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway in FY2. Correlation analysis demonstrated that Hyphopichia, Kazachstania and Clavispora were highly positively correlated with 12 key aroma flavours.}, } @article {pmid38276191, year = {2024}, author = {Couto, RDS and Ramos, EDSF and Abreu, WU and Rodrigues, LRR and Marinho, LF and Morais, VDS and Villanova, F and Pandey, RP and Deng, X and Delwart, E and Costa, ACD and Leal, E}, title = {Metagenomic of Liver Tissue Identified at Least Two Genera of Totivirus-like Viruses in Molossus molossus Bats.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, pmid = {38276191}, issn = {2076-2607}, abstract = {The Totiviridae family of viruses has a unique genome consisting of double-stranded RNA with two open reading frames that encode the capsid protein (Cap) and the RNA-dependent RNA polymerase (RdRpol). Most virions in this family are isometric in shape, approximately 40 nm in diameter, and lack an envelope. There are five genera within this family, including Totivirus, Victorivirus, Giardiavirus, Leishmaniavirus, and Trichomonasvirus. While Totivirus and Victorivirus primarily infect fungi, Giardiavirus, Leishmaniavirus, and Trichomonasvirus infect diverse hosts, including protists, insects, and vertebrates. Recently, new totivirus-like species have been discovered in fish and plant hosts, and through metagenomic analysis, a novel totivirus-like virus (named Tianjin totivirus) has been isolated from bat guano. Interestingly, Tianjin totivirus causes cytopathic effects in insect cells but cannot grow in mammalian cells, suggesting that it infects insects consumed by insectivorous bats. In this study, we used next-generation sequencing and identified totivirus-like viruses in liver tissue from Molossus molossus bats in the Amazon region of Brazil. Comparative phylogenetic analysis based on the RNA-dependent RNA polymerase region revealed that the viruses identified in Molossus bats belong to two distinct phylogenetic clades, possibly comprising different genera within the Totiviridae family. Notably, the mean similarity between the Tianjin totivirus and the totiviruses identified in Molossus bats is less than 18%. These findings suggest that the diversity of totiviruses in bats is more extensive than previously recognized and highlight the potential for bats to serve as reservoirs for novel toti-like viruses.}, } @article {pmid38275746, year = {2023}, author = {Seppi, M and Pasqualini, J and Facchin, S and Savarino, EV and Suweis, S}, title = {Emergent Functional Organization of Gut Microbiomes in Health and Diseases.}, journal = {Biomolecules}, volume = {14}, number = {1}, pages = {}, pmid = {38275746}, issn = {2218-273X}, mesh = {Humans ; *Gastrointestinal Microbiome ; Dysbiosis ; *Microbiota ; Metagenome ; Metagenomics ; }, abstract = {Continuous and significant progress in sequencing technologies and bioinformatics pipelines has revolutionized our comprehension of microbial communities, especially for human microbiomes. However, most studies have focused on studying the taxonomic composition of the microbiomes and we are still not able to characterize dysbiosis and unveil the underlying ecological consequences. This study explores the emergent organization of functional abundances and correlations of gut microbiomes in health and disease. Leveraging metagenomic sequences, taxonomic and functional tables are constructed, enabling comparative analysis. First, we show that emergent taxonomic and functional patterns are not useful to characterize dysbiosis. Then, through differential abundance analyses applied to functions, we reveal distinct functional compositions in healthy versus unhealthy microbiomes. In addition, we inquire into the functional correlation structure, revealing significant differences between the healthy and unhealthy groups, which may significantly contribute to understanding dysbiosis. Our study demonstrates that scrutinizing the functional organization in the microbiome provides novel insights into the underlying state of the microbiome. The shared data structure underlying the functional and taxonomic compositions allows for a comprehensive macroecological examination. Our findings not only shed light on dysbiosis, but also underscore the importance of studying functional interrelationships for a nuanced understanding of the dynamics of the microbial community. This research proposes a novel approach, bridging the gap between microbial ecology and functional analyses, promising a deeper understanding of the intricate world of the gut microbiota and its implications for human health.}, } @article {pmid38275294, year = {2024}, author = {Reasoner, SA and Bernard, R and Waalkes, A and Penewit, K and Lewis, J and Sokolow, AG and Brown, RF and Edwards, KM and Salipante, SJ and Hadjifrangiskou, M and Nicholson, MR}, title = {Longitudinal profiling of the intestinal microbiome in children with cystic fibrosis treated with elexacaftor-tezacaftor-ivacaftor.}, journal = {mBio}, volume = {15}, number = {2}, pages = {e0193523}, pmid = {38275294}, issn = {2150-7511}, support = {T32 DK007673/DK/NIDDK NIH HHS/United States ; L30 AI140315/AI/NIAID NIH HHS/United States ; K23 AI156132/AI/NIAID NIH HHS/United States ; P30 DK089507/DK/NIDDK NIH HHS/United States ; T32 GM007347/GM/NIGMS NIH HHS/United States ; F30 AI169748/AI/NIAID NIH HHS/United States ; }, mesh = {Child ; Humans ; *Cystic Fibrosis/drug therapy ; Cystic Fibrosis Transmembrane Conductance Regulator/genetics ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents/therapeutic use ; Inflammation ; Mutation ; *Benzodioxoles ; *Indoles ; *Aminophenols ; *Pyrazoles ; *Pyridines ; *Pyrrolidines ; *Quinolones ; }, abstract = {The intestinal microbiome influences growth and disease progression in children with cystic fibrosis (CF). Elexacaftor-tezacaftor-ivacaftor (ELX/TEZ/IVA), the newest pharmaceutical modulator for CF, restores the function of the pathogenic mutated CF transmembrane conductance regulator (CFTR) channel. We performed a single-center longitudinal analysis of the effect of ELX/TEZ/IVA on the intestinal microbiome, intestinal inflammation, and clinical parameters in children with CF. Following ELX/TEZ/IVA, children with CF had significant improvements in body mass index and percent predicted forced expiratory volume in one second, and required fewer antibiotics for respiratory infections. Intestinal microbiome diversity increased following ELX/TEZ/IVA coupled with a decrease in the intestinal carriage of Staphylococcus aureus, the predominant respiratory pathogen in children with CF. There was a reduced abundance of microbiome-encoded antibiotic resistance genes. Microbial pathways for aerobic respiration were reduced after ELX/TEZ/IVA. The abundance of microbial acid tolerance genes was reduced, indicating microbial adaptation to increased CFTR function. In all, this study represents the first comprehensive analysis of the intestinal microbiome in children with CF receiving ELX/TEZ/IVA.IMPORTANCECystic fibrosis (CF) is an autosomal recessive disease with significant gastrointestinal symptoms in addition to pulmonary complications. Recently approved treatments for CF, CF transmembrane conductance regulator (CFTR) modulators, are anticipated to substantially improve the care of people with CF and extend their lifespans. Prior work has shown that the intestinal microbiome correlates with health outcomes in CF, particularly in children. Here, we study the intestinal microbiome of children with CF before and after the CFTR modulator, ELX/TEZ/IVA. We identify promising improvements in microbiome diversity, reduced measures of intestinal inflammation, and reduced antibiotic resistance genes. We present specific bacterial taxa and protein groups which change following ELX/TEZ/IVA. These results will inform future mechanistic studies to understand the microbial improvements associated with CFTR modulator treatment. This study demonstrates how the microbiome can change in response to a targeted medication that corrects a genetic disease.}, } @article {pmid38274799, year = {2023}, author = {Nguyen, WQ and Chrisman, LP and Enriquez, GL and Hooper, MJ and Griffin, TL and Ahmad, M and Rahman, S and Green, SJ and Seed, PC and Guitart, J and Burns, MB and Zhou, XA}, title = {Gut microbiota analyses of cutaneous T-cell lymphoma patients undergoing narrowband ultraviolet B therapy reveal alterations associated with disease treatment.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1280205}, pmid = {38274799}, issn = {1664-3224}, support = {KL2 TR001424/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Dysbiosis ; Phylogeny ; RNA, Ribosomal, 16S ; *Lymphoma, T-Cell, Cutaneous/pathology ; Bacteria/genetics ; *Skin Neoplasms/pathology ; }, abstract = {Recent studies have shown a close relationship between cutaneous T-cell lymphoma (CTCL) and its microbiome. CTCL disease progression is associated with gut dysbiosis and alterations in bacterial taxa parallel those observed in immunologically similar atopic dermatitis. Moreover, the microbial profile of lesional skin may predict response to narrowband ultraviolet B (nbUVB), a common skin-directed therapy. However, the relationship between the gut microbiome, an immunologically vital niche, and nbUVB remains unexplored in CTCL. Herein, we performed 16S rRNA sequencing and PICRUSt2 predictive metagenomics on DNA extracted from stool swabs of 13 CTCL patients treated with nbUVB, 8 non-treated patients, and 13 healthy controls. Disease response was assessed with modified Severity Weighted Assessment Tool (mSWAT); of nbUVB-treated patients, 6 improved (decreased mSWAT), 2 remained stable, and 5 worsened (increased mSWAT). Protective commensal bacteria including Lactobacillaceae and Erysipelatoclostridiaceae were significantly less abundant in CTCL patients compared to controls. With treatment, the CTCL gut microbiome exhibited decreased phylogenetic diversity and lower relative abundance of pro-inflammatory Sutterellaceae. Sutterellaceae was also significantly more abundant in patients who worsened, and Eggerthellaceae and Erysipelotrichaceae trended higher in patients who improved. Finally, PICRUSt2 functional predictions based on shifts in abundance of bacterial sequences repeatedly identified alterations in inositol degradation, which plays a key role in host immunomodulation, including inositol phospholipid signaling relevant to T-cell survival and proliferation. Our results bolster the paradigm of gut dysbiosis in CTCL and its functional implications in disease pathogenesis, and further delineate bacterial taxa associated with nbUVB response and with nbUVB treatment itself.}, } @article {pmid38274751, year = {2023}, author = {Barba, M and Toquet, M and García-Roselló, E and Gomis, J and Quereda, JJ and González-Torres, P and Carbonetto, B and Gómez-Martín, Á}, title = {Description of the vaginal microbiota in nulliparous ewes during natural mating and pregnancy: preliminary signs of the male preputial microbiota modulation.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1224910}, pmid = {38274751}, issn = {1664-302X}, abstract = {The vaginal microbiota plays a key role in animals' health. Understanding its diversity and composition and associated changes occurring through the reproductive cycle represents valuable knowledge to disclose the mechanisms leading to dysbiosis and eventually to infection. Even if the human vaginal microbiota has been thoroughly studied, scarce research has been conducted on the vaginal microbiota of livestock. In this study, 16S rRNA gene-based sequencing was performed on vaginal samples of ten nulliparous ewes at three different sampling points: before the estrus synchronization protocol (T0), at the time of estrus before mating (Testrus), and the day of the pregnancy diagnosis (Tpreg). Preputial samples from the three males collected pre and post-mating were also analyzed. Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria were the most abundant phyla in vaginal samples. The most abundant genera were Porphyromonas, Anaerococcus, and Peptinophilius. Vaginal microbiota biodiversity decreased during pregnancy. Tenericutes (Ureaplasma spp.) increased significantly at Tpreg in both pregnant and non-pregnant ewes. Differences were observed between pregnant and non-pregnant ewes at Tpreg where pregnant ewes had a significantly higher abundance of Actinobacillus spp. and Ureaplasma spp. Ewes that were diagnosed with pregnancy at Tpreg showed a decreased abundance of gram-negative bacteria such as Bacteroidales, Campylobacterales, and Enterobacteriales. In addition, a significant decrease in the relative abundances of genera within Firmicutes, such as Alloicoccus (Lactobacillales), Atopostipes (Lactobacillales), and an uncultured bacteria W5053 from Family XI (Firmicutes, Clostridiales) was observed in non-pregnant ewes at Tpreg. The four most abundant phyla in the rams' prepuce were the same as in the ewes' vagina. The most abundant genus was Corynebacterium. No major differences were observed in the ram's preputial microbiota between pre and post-mating samples. Nevertheless, the differences in the taxonomic composition of ewes' vaginal microbiota between Testrus and Tpreg could be explained by the exposure to the preputial microbiota. This study offers new insights into the effects of several key steps of the ewe's reproductive cycle such as estrus-synchronization protocol, mating, and pregnancy on ovine vaginal microbiota. The knowledge of the microbiota dynamics during the reproductive cycle can help improve the reproductive outcomes of dams by identifying biomarkers and putative probiotics.}, } @article {pmid38273486, year = {2024}, author = {Benham, PM and Walsh, J and Bowie, RCK}, title = {Spatial variation in population genomic responses to over a century of anthropogenic change within a tidal marsh songbird.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17126}, doi = {10.1111/gcb.17126}, pmid = {38273486}, issn = {1365-2486}, support = {PRFB 1812282//Division of Environmental Biology/ ; }, mesh = {Animals ; Humans ; *Wetlands ; Metagenomics ; Ecosystem ; *Sparrows/genetics ; Fresh Water ; Genetic Variation ; }, abstract = {Combating the current biodiversity crisis requires the accurate documentation of population responses to human-induced ecological change. However, our ability to pinpoint population responses to human activities is often limited to the analysis of populations studied well after the fact. Museum collections preserve a record of population responses to anthropogenic change that can provide critical baseline data on patterns of genetic diversity, connectivity, and population structure prior to the onset of human perturbation. Here, we leverage a spatially replicated time series of specimens to document population genomic responses to the destruction of nearly 90% of coastal habitats occupied by the Savannah sparrow (Passerculus sandwichensis) in California. We sequenced 219 sparrows collected from 1889 to 2017 across the state of California using an exome capture approach. Spatial-temporal analyses of genetic diversity found that the amount of habitat lost was not predictive of genetic diversity loss. Sparrow populations from southern California historically exhibited lower levels of genetic diversity and experienced the most significant temporal declines in genetic diversity. Despite experiencing the greatest levels of habitat loss, we found that genetic diversity in the San Francisco Bay area remained relatively high. This was potentially related to an observed increase in gene flow into the Bay Area from other populations. While gene flow may have minimized genetic diversity declines, we also found that immigration from inland freshwater-adapted populations into tidal marsh populations led to the erosion of divergence at loci associated with tidal marsh adaptation. Shifting patterns of gene flow through time in response to habitat loss may thus contribute to negative fitness consequences and outbreeding depression. Together, our results underscore the importance of tracing the genomic trajectories of multiple populations over time to address issues of fundamental conservation concern.}, } @article {pmid38272816, year = {2024}, author = {Morsli, M and Salipante, F and Gelis, A and Magnan, C and Guigon, G and Lavigne, JP and Sotto, A and Dunyach-Remy, C}, title = {Evolution of the urinary microbiota in spinal cord injury patients with decubitus ulcer: A snapshot study.}, journal = {International wound journal}, volume = {21}, number = {1}, pages = {e14626}, pmid = {38272816}, issn = {1742-481X}, support = {//Centre Hospitalier Universitaire de Nîmes/ ; //French Society of Pressure Ulcer/ ; }, mesh = {Humans ; *Pressure Ulcer/complications ; Prospective Studies ; *Spinal Cord Injuries/complications ; *Microbiota ; }, abstract = {Current microbiome investigations of patients with pressure ulcers (PU) are mainly based on wound swabs and/or biopsy sequencing, leaving the colonization scenario unclear. Urinary microbiota has been never studied. As a part of the prospective ESCAFLOR study, we studied urinary microbiota of spinal cord injury (SCI) patients with PU without any urinary tract infection at the inclusion, collected at two times (at admission [D0] and after 28 days [D28]) during the patient's care, investigated by 16S rDNA metagenomics next generation sequencing. Subgroup analyses were carried out between patients with wounds showing improved evolution versus stagnated/worsened wounds at D28. Analysis was done using EPISEQ® 16S and R software. Among the 12 studied patients, the urinary microbiota of patients with improved wound evolution at D28 (n = 6) presented a significant decrease of microbial diversity. This modification was associated with the presence of Proteobacteria phylum and an increase of Escherichia-Shigella (p = 0.005), as well as the presence of probiotic anaerobic bacteria Lactobacillus and Bifidobacterium. In contrast, Proteus abundance was significantly increased in urine of patients with stagnated/worsened wound evolution (n = 6) (p = 0.003). This study proposes urinary microbiota as a complementary factor indirectly associated with the wound evolution and patient cure. It opens new perspectives for further investigations based on multiple body microbiome comparison to describe the complete scenario of the transmission dynamics of wound-colonizing microorganisms.}, } @article {pmid38272730, year = {2024}, author = {Rodríguez, MA and Fernández, LA and Díaz, ML and Gallo, CA and Corona, M and Evans, JD and Reynaldi, FJ}, title = {Bacterial diversity using metagenomics of 16s rDNA in water kefir, an innovative source of probiotics for bee nutrition.}, journal = {Revista Argentina de microbiologia}, volume = {56}, number = {2}, pages = {191-197}, doi = {10.1016/j.ram.2023.12.002}, pmid = {38272730}, issn = {0325-7541}, mesh = {*Probiotics ; Animals ; Bees/microbiology ; *Kefir/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Bacteria/isolation & purification/genetics/classification ; DNA, Bacterial/analysis ; Biodiversity ; DNA, Ribosomal/genetics ; Animal Feed/microbiology ; }, abstract = {Water kefir is a sparkling, slightly acidic fermented beverage made from sugar, water, and water kefir grains, which are a mixture of yeast and bacteria. These grains produce a variety of fermentation compounds such as lactic acid, acetaldehyde, acetoin, ethanol and carbon dioxide. In this study, a high-throughput sequencing technique was used to characterize the bacterial composition of the original water kefir from which potential probiotics were obtained. We studied the bacterial diversity of both water kefir grains and beverages. DNA was extracted from three replicate samples of both grains and beverages using the Powerlyzer Microbial Kit. The hypervariable V1-V2 region of the bacterial 16S ribosomal RNA gene was amplified to prepare six DNA libraries. Between 1.4M and 2.4M base-pairs were sequenced for the library. In total, 28721971 raw reads were obtained from all the samples. Estimated species richness was higher in kefir beverage samples compared to grain samples. Moreover, a higher level of microbial alpha diversity was observed in the beverage samples. Particularly, the predominant bacteria in beverages were Anaerocolumna and Ralstonia, while in grains Liquorilactobacillus dominated, with lower levels of Leuconostoc and Oenococcus. Although the bacterial diversity in kefir grains was low because only three genera were the most represented, all of them are LAB bacteria with the potential to serve as probiotics in the artificial feeding of bees.}, } @article {pmid38271608, year = {2024}, author = {Mac Aogáin, M and Ivan, FX and Jaggi, TK and Richardson, H and Shoemark, A and Narayana, JK and Dicker, AJ and Koh, MS and Lee, KCH and Thun How, O and Poh, ME and Chin, KK and Hou, ALY and Ser Hon, P and Low, TB and Abisheganaden, JA and Dimakou, K and Digalaki, A and Kosti, C and Gkousiou, A and Hansbro, PM and Blasi, F and Aliberti, S and Chalmers, JD and Chotirmall, SH}, title = {Airway "Resistotypes" and Clinical Outcomes in Bronchiectasis.}, journal = {American journal of respiratory and critical care medicine}, volume = {210}, number = {1}, pages = {47-62}, pmid = {38271608}, issn = {1535-4970}, support = {MOH-000141//National Medical Research Council/ ; MOH-001356//National Medical Research Council/ ; MOH-000710//National Medical Research Council/ ; RT1/22//Singapore Ministry of Education under its AcRF Tier 1 Grant/ ; 1059238//National Health and Medical Research Council/ ; 1175134//National Health and Medical Research Council/ ; 2010287//National Health and Medical Research Council/ ; 260/01/2022//Ministero della Salute, Ricerca Corrente Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico/ ; //European Respiratory Society/ ; }, mesh = {*Bronchiectasis/physiopathology/microbiology/drug therapy ; Humans ; Male ; Female ; Middle Aged ; Aged ; Cross-Sectional Studies ; Longitudinal Studies ; Anti-Bacterial Agents/therapeutic use ; Prospective Studies ; Microbiota/genetics ; Pseudomonas aeruginosa/genetics ; Sputum/microbiology ; Metagenomics/methods ; Adult ; Pseudomonas Infections/drug therapy/complications ; }, abstract = {Rationale: Chronic infection and inflammation shapes the airway microbiome in bronchiectasis. Utilizing whole-genome shotgun metagenomics to analyze the airway resistome provides insight into interplay between microbes, resistance genes, and clinical outcomes. Objectives: To apply whole-genome shotgun metagenomics to the airway microbiome in bronchiectasis to highlight a diverse pool of antimicrobial resistance genes: the "resistome," the clinical significance of which remains unclear. Methods: Individuals with bronchiectasis were prospectively recruited into cross-sectional and longitudinal cohorts (n = 280), including the international multicenter cross-sectional Cohort of Asian and Matched European Bronchiectasis 2 (CAMEB 2) study (n = 251) and two independent cohorts, one describing patients experiencing acute exacerbation and a further cohort of patients undergoing Pseudomonas aeruginosa eradication treatment. Sputum was subjected to metagenomic sequencing, and the bronchiectasis resistome was evaluated in association with clinical outcomes and underlying host microbiomes. Measurements and Main Results: The bronchiectasis resistome features a unique resistance gene profile and increased counts of aminoglycoside, bicyclomycin, phenicol, triclosan, and multidrug resistance genes. Longitudinally, it exhibits within-patient stability over time and during exacerbations despite between-patient heterogeneity. Proportional differences in baseline resistome profiles, including increased macrolide and multidrug resistance genes, associate with shorter intervals to the next exacerbation, whereas distinct resistome archetypes associate with frequent exacerbations, poorer lung function, geographic origin, and the host microbiome. Unsupervised analysis of resistome profiles identified two clinically relevant "resistotypes," RT1 and RT2, the latter characterized by poor clinical outcomes, increased multidrug resistance, and P. aeruginosa. Successful targeted eradication in P. aeruginosa-colonized individuals mediated reversion from RT2 to RT1, a more clinically favorable resistome profile demonstrating reduced resistance gene diversity. Conclusions: The bronchiectasis resistome associates with clinical outcomes, geographic origin, and the underlying host microbiome. Bronchiectasis resistotypes link to clinical disease and are modifiable through targeted antimicrobial therapy.}, } @article {pmid38271603, year = {2024}, author = {Wicaksono, WA and Mora, M and Bickel, S and Berg, C and Kühn, I and Cernava, T and Berg, G}, title = {Rhizosphere assembly alters along a chronosequence in the Hallstätter glacier forefield (Dachstein, Austria).}, journal = {FEMS microbiology ecology}, volume = {100}, number = {2}, pages = {}, pmid = {38271603}, issn = {1574-6941}, mesh = {*Rhizosphere ; Ice Cover/microbiology ; Austria ; Soil Microbiology ; Bacteria/genetics ; Soil ; *Microbiota ; Plants ; }, abstract = {Rhizosphere microbiome assembly is essential for plant health, but the temporal dimension of this process remains unexplored. We used a chronosequence of 150 years of the retreating Hallstätter glacier (Dachstein, Austria) to disentangle this exemplarily for the rhizosphere of three pioneer alpine plants. Time of deglaciation was an important factor shaping the rhizosphere microbiome. Microbiome functions, i.e. nutrient uptake and stress protection, were carried out by ubiquitous and cosmopolitan bacteria. The rhizosphere succession along the chronosequence was characterized by decreasing microbial richness but increasing specificity of the plant-associated bacterial community. Environmental selection is a critical factor in shaping the ecosystem, particularly in terms of plant-driven recruitment from the available edaphic pool. A higher rhizosphere microbial richness during early succession compared to late succession can be explained by the occurrence of cold-acclimated bacteria recruited from the surrounding soils. These taxa might be sensitive to changing habitat conditions that occurred at the later stages. A stronger influence of the plant host on the rhizosphere microbiome assembly was observed with increased time since deglaciation. Overall, this study indicated that well-adapted, ubiquitous microbes potentially support pioneer plants to colonize new ecosystems, while plant-specific microbes may be associated with the long-term establishment of their hosts.}, } @article {pmid38268451, year = {2024}, author = {Koslicki, D and White, S and Ma, C and Novikov, A}, title = {YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {2}, pages = {}, pmid = {38268451}, issn = {1367-4811}, support = {R01 GM146462/GM/NIGMS NIH HHS/United States ; 5R01GM146462-02/GF/NIH HHS/United States ; }, mesh = {*Metagenome ; *Microbiota/genetics ; Algorithms ; Software ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; }, abstract = {MOTIVATION: In metagenomics, the study of environmentally associated microbial communities from their sampled DNA, one of the most fundamental computational tasks is that of determining which genomes from a reference database are present or absent in a given sample metagenome. Existing tools generally return point estimates, with no associated confidence or uncertainty associated with it. This has led to practitioners experiencing difficulty when interpreting the results from these tools, particularly for low-abundance organisms as these often reside in the "noisy tail" of incorrect predictions. Furthermore, few tools account for the fact that reference databases are often incomplete and rarely, if ever, contain exact replicas of genomes present in an environmentally derived metagenome.

RESULTS: We present solutions for these issues by introducing the algorithm YACHT: Yes/No Answers to Community membership via Hypothesis Testing. This approach introduces a statistical framework that accounts for sequence divergence between the reference and sample genomes, in terms of ANI, as well as incomplete sequencing depth, thus providing a hypothesis test for determining the presence or absence of a reference genome in a sample. After introducing our approach, we quantify its statistical power and how this changes with varying parameters. Subsequently, we perform extensive experiments using both simulated and real data to confirm the accuracy and scalability of this approach.

The source code implementing this approach is available via Conda and at https://github.com/KoslickiLab/YACHT. We also provide the code for reproducing experiments at https://github.com/KoslickiLab/YACHT-reproducibles.}, } @article {pmid38268397, year = {2024}, author = {Wietz, M and Engel, A and Ramondenc, S and Niwano, M and von Appen, WJ and Priest, T and von Jackowski, A and Metfies, K and Bienhold, C and Boetius, A}, title = {The Arctic summer microbiome across Fram Strait: Depth, longitude, and substrate concentrations structure microbial diversity in the euphotic zone.}, journal = {Environmental microbiology}, volume = {26}, number = {2}, pages = {e16568}, doi = {10.1111/1462-2920.16568}, pmid = {38268397}, issn = {1462-2920}, support = {//Max-Planck-Gesellschaft/ ; //Natural Environment Research Council/ ; 03F0802A//Bundesministerium für Bildung, Wissenschaft und Kultur/ ; //Helmholtz Association; Helmholtz Program-Oriented Funding (POF-IV)/ ; //AWI program "International Science Program for Integrative Research in Earth Systems" (INSPIRES)/ ; 294757//European Research Council; (FP7/2007-2013) research project ABYSS/ ; }, mesh = {*Ecosystem ; *Microbiota ; Chlorophyll ; Metagenome ; Arctic Regions ; Water ; }, abstract = {The long-term dynamics of microbial communities across geographic, hydrographic, and biogeochemical gradients in the Arctic Ocean are largely unknown. To address this, we annually sampled polar, mixed, and Atlantic water masses of the Fram Strait (2015-2019; 5-100 m depth) to assess microbiome composition, substrate concentrations, and oceanographic parameters. Longitude and water depth were the major determinants (~30%) of microbial community variability. Bacterial alpha diversity was highest in lower-photic polar waters. Community composition shifted from west to east, with the prevalence of, for example, Dadabacteriales and Thiotrichales in Arctic- and Atlantic-influenced waters, respectively. Concentrations of dissolved organic carbon peaked in the western, compared to carbohydrates in the chlorophyll-maximum of eastern Fram Strait. Interannual differences due to the time of sampling, which varied between early (June 2016/2018) and late (September 2019) phytoplankton bloom stages, illustrated that phytoplankton composition and resulting availability of labile substrates influence bacterial dynamics. We identified 10 species clusters with stable environmental correlations, representing signature populations of distinct ecosystem states. In context with published metagenomic evidence, our microbial-biogeochemical inventory of a key Arctic region establishes a benchmark to assess ecosystem dynamics and the imprint of climate change.}, } @article {pmid38267717, year = {2024}, author = {Barcenilla, C and Cobo-Díaz, JF and De Filippis, F and Valentino, V and Cabrera Rubio, R and O'Neil, D and Mahler de Sanchez, L and Armanini, F and Carlino, N and Blanco-Míguez, A and Pinto, F and Calvete-Torre, I and Sabater, C and Delgado, S and Ruas-Madiedo, P and Quijada, NM and Dzieciol, M and Skírnisdóttir, S and Knobloch, S and Puente, A and López, M and Prieto, M and Marteinsson, VT and Wagner, M and Margolles, A and Segata, N and Cotter, PD and Ercolini, D and Alvarez-Ordóñez, A}, title = {Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments.}, journal = {Nature protocols}, volume = {19}, number = {5}, pages = {1291-1310}, pmid = {38267717}, issn = {1750-2799}, support = {818368//European Commission (EC)/ ; }, mesh = {DNA/isolation & purification ; DNA, Bacterial/genetics/isolation & purification ; Food Handling/methods ; Food Microbiology/methods ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Deep investigation of the microbiome of food-production and food-processing environments through whole-metagenome sequencing (WMS) can provide detailed information on the taxonomic composition and functional potential of the microbial communities that inhabit them, with huge potential benefits for environmental monitoring programs. However, certain technical challenges jeopardize the application of WMS technologies with this aim, with the most relevant one being the recovery of a sufficient amount of DNA from the frequently low-biomass samples collected from the equipment, tools and surfaces of food-processing plants. Here, we present the first complete workflow, with optimized DNA-purification methodology, to obtain high-quality WMS sequencing results from samples taken from food-production and food-processing environments and reconstruct metagenome assembled genomes (MAGs). The protocol can yield DNA loads >10 ng in >98% of samples and >500 ng in 57.1% of samples and allows the collection of, on average, 12.2 MAGs per sample (with up to 62 MAGs in a single sample) in ~1 week, including both laboratory and computational work. This markedly improves on results previously obtained in studies performing WMS of processing environments and using other protocols not specifically developed to sequence these types of sample, in which <2 MAGs per sample were obtained. The full protocol has been developed and applied in the framework of the European Union project MASTER (Microbiome applications for sustainable food systems through technologies and enterprise) in 114 food-processing facilities from different production sectors.}, } @article {pmid38267279, year = {2024}, author = {Koh, C and Saleh, MC}, title = {Mosquito core viromes: do they exist?.}, journal = {Trends in parasitology}, volume = {40}, number = {3}, pages = {203-204}, doi = {10.1016/j.pt.2024.01.003}, pmid = {38267279}, issn = {1471-5007}, mesh = {Animals ; *Culicidae ; Virome ; Phylogeny ; Mosquito Vectors ; }, } @article {pmid38266788, year = {2024}, author = {Jiang, Q and Feng, L and Luo, J and Wu, Y and Dong, H and Mustafa, AM and Su, Y and Zhao, Y and Chen, Y}, title = {Simultaneous volatile fatty acids promotion and antibiotic resistance genes reduction in fluoranthene-induced sludge alkaline fermentation: Regulation of microbial consortia and cell functions.}, journal = {Bioresource technology}, volume = {395}, number = {}, pages = {130367}, doi = {10.1016/j.biortech.2024.130367}, pmid = {38266788}, issn = {1873-2976}, mesh = {Fermentation ; *Sewage/chemistry ; *Anti-Bacterial Agents ; Microbial Consortia ; Fatty Acids, Volatile ; Drug Resistance, Microbial ; Hydrogen-Ion Concentration ; *Fluorenes ; }, abstract = {The impact and mechanism of fluoranthene (Flr), a typical polycyclic aromatic hydrocarbon highly detected in sludge, on alkaline fermentation for volatile fatty acids (VFAs) recovery and antibiotic resistance genes (ARGs) transfer were studied. The results demonstrated that VFAs production increased from 2189 to 4272 mg COD/L with a simultaneous reduction of ARGs with Flr. The hydrolytic enzymes and genes related to glucose and amino acid metabolism were provoked. Also, Flr benefited for the enrichment of hydrolytic-acidifying consortia (i.e., Parabacteroides and Alkalibaculum) while reduced VFAs consumers (i.e., Rubrivivax) and ARGs potential hosts (i.e., Rubrivivax and Pseudomonas). Metagenomic analysis indicated that the genes related to cell wall synthesis, biofilm formation and substrate transporters to maintain high VFAs-producer activities were upregulated. Moreover, cell functions of efflux pump and Type IV secretion system were suppressed to inhibit ARGs proliferation. This study provided intrinsic mechanisms of Flr-induced VFAs promotion and ARGs reduction during alkaline fermentation.}, } @article {pmid38266051, year = {2024}, author = {Camacho-Mateu, J and Lampo, A and Sireci, M and Muñoz, MA and Cuesta, JA}, title = {Sparse species interactions reproduce abundance correlation patterns in microbial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {5}, pages = {e2309575121}, pmid = {38266051}, issn = {1091-6490}, support = {PGC2018-098186-B-I00//Ministerio de Ciencia e Innovación (MCIN)/ ; PID2021-128966NB-I00//Ministerio de Ciencia e Innovación (MCIN)/ ; PID2020-113681GB-I00//Ministerio de Ciencia e Innovación (MCIN)/ ; B-FQM-366-UGR20//Consejería de Conocimiento, Investigación y Universidad, Junta de Andalucía (Ministry of Knowledge, Research and University, Andalusia)/ ; PGC2022-141802NB-I00//Ministerio de Ciencia e Innovación (MCIN)/ ; }, mesh = {Bayes Theorem ; *Microbiota ; Metagenome ; Algorithms ; Metagenomics ; }, abstract = {During the last decades, macroecology has identified broad-scale patterns of abundances and diversity of microbial communities and put forward some potential explanations for them. However, these advances are not paralleled by a full understanding of the dynamical processes behind them. In particular, abundance fluctuations of different species are found to be correlated, both across time and across communities in metagenomic samples. Reproducing such correlations through appropriate population models remains an open challenge. The present paper tackles this problem and points to sparse species interactions as a necessary mechanism to account for them. Specifically, we discuss several possibilities to include interactions in population models and recognize Lotka-Volterra constants as a successful ansatz. For this, we design a Bayesian inference algorithm to extract sets of interaction constants able to reproduce empirical probability distributions of pairwise correlations for diverse biomes. Importantly, the inferred models still reproduce well-known single-species macroecological patterns concerning abundance fluctuations across both species and communities. Endorsed by the agreement with the empirically observed phenomenology, our analyses provide insights into the properties of the networks of microbial interactions, revealing that sparsity is a crucial feature.}, } @article {pmid38265338, year = {2024}, author = {Chanda, D and De, D}, title = {Meta-analysis reveals obesity associated gut microbial alteration patterns and reproducible contributors of functional shift.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2304900}, pmid = {38265338}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; Amino Acids ; Bacteroides ; Obesity ; }, abstract = {The majority of cohort-specific studies associating gut microbiota with obesity are often contradictory; thus, the replicability of the signature remains questionable. Moreover, the species that drive obesity-associated functional shifts and their replicability remain unexplored. Thus, we aimed to address these questions by analyzing gut microbial metagenome sequencing data to develop an in-depth understanding of obese host-gut microbiota interactions using 3329 samples (Obese, n = 1494; Control, n = 1835) from 17 different countries, including both 16S rRNA gene and metagenomic sequence data. Fecal metagenomic data from diverse geographical locations were curated, profiled, and pooled using a machine learning-based approach to identify robust global signatures of obesity. Furthermore, gut microbial species and pathways were systematically integrated through the genomic content of the species to identify contributors to obesity-associated functional shifts. The community structure of the obese gut microbiome was evaluated, and a reproducible depletion of diversity was observed in the obese compared to the lean gut. From this, we infer that the loss of diversity in the obese gut is responsible for perturbations in the healthy microbial functional repertoire. We identified 25 highly predictive species and 37 pathway associations as signatures of obesity, which were validated with remarkably high accuracy (AUC, Species: 0.85, and pathway: 0.80) with an independent validation dataset. We observed a reduction in short-chain fatty acid (SCFA) producers (several Alistipes species, Odoribacter splanchnicus, etc.) and depletion of promoters of gut barrier integrity (Akkermansia muciniphila and Bifidobacterium longum) in obese guts. Our analysis underlines SCFAs and purine/pyrimidine biosynthesis, carbohydrate metabolism pathways in control individuals, and amino acid, enzyme cofactor, and peptidoglycan biosynthesis pathway enrichment in obese individuals. We also mapped the contributors to important obesity-associated functional shifts and observed that these are both dataset-specific and shared across the datasets. In summary, a comprehensive analysis of diverse datasets unveils species specifically contributing to functional shifts and consistent gut microbial patterns associated to obesity.}, } @article {pmid38263937, year = {2024}, author = {Arıkan, M and Kahraman Demir, T and Yıldız, Z and Helvacı Yılmaz, N and Şen, A and Hanoğlu, L and Yıldırım, S}, title = {[Investigation of the Relationship Between Akkermansia Genomic Diversity in Gut Microbiota and Parkinson's Disease Dementia].}, journal = {Mikrobiyoloji bulteni}, volume = {58}, number = {1}, pages = {13-28}, doi = {10.5578/mb.20249951}, pmid = {38263937}, issn = {0374-9096}, mesh = {Humans ; *Parkinson Disease ; Akkermansia ; *Gastrointestinal Microbiome ; *Dementia ; Genomics ; }, abstract = {Although it is known that the relative abundance of Akkermansia, a bacterial genus commonly associated with health, increases in the gut microbiota of Parkinson's disease (PD) patients, the exact reason for this increase remains unclear. This study was aimed to identify potential changes in Akkermansia within the gut microbiota of PD patients in Türkiye. For this purpose, shotgun metagenomics and a novel Akkermansia genus-specific amplicon sequencing technique was used to investigate the presence of specific Akkermansia strains associated with cognitive impairment (CI) stages in PD and to examine potential genes within these strains. In this context, four gut microbiota samples from Türkiye -three PD with dementia (PDD) and one healthy control without CI (HC)- were analyzed by shotgun metagenomics and metagenome-assembled genomes assigned to Akkermansia genus were reconstructed. Then, a custom database was created by combining these genomes with the Akkermansia genomes in public databases and next generation sequencing (NGS) compatible primers specific to the genus Akkermansia were designed using this database. After optimization of amplification and library preparation steps for genus-specific next generation sequencing, gut microbiota samples from 64 PD patients [32 PDD and 32 PD with mild CI (PD-MCI)] and 26 HCs were analyzed by genus-specific amplicon sequencing. The results revealed the presence of seven strains assigned to Akkermansia muciniphila in gut microbiota samples, two of which showed significant distribution differences (p< 0.05) between demented (PDD) and non-demented groups (PD-MCI, HC). When gene contents of the detected Akkermansia genomes were examined through comparative genomic analysis, the presence of 12 genes only in Akkermansia genomes specific to non-demented groups were predicted. The annotations of these genes showed that they were not reported before with unknown functions. In this study, for the first time, gut microbiota samples from PD patients in Türkiye were analyzed using shotgun metagenomics, a novel genus-specific amplicon sequencing method was developed specifically for the analysis of Akkermansia genus, and then Akkermansia strains and genes potentially associated with CI stages in PD were identified using this method. The results underscore that investigating the species or strain level differences could help better understanding of the changes associated with PD in the human gut microbiota.}, } @article {pmid38262490, year = {2024}, author = {Parida, D and Katare, K and Ganguly, A and Chakraborty, D and Konar, O and Nogueira, R and Bala, K}, title = {Molecular docking and metagenomics assisted mitigation of microplastic pollution.}, journal = {Chemosphere}, volume = {351}, number = {}, pages = {141271}, doi = {10.1016/j.chemosphere.2024.141271}, pmid = {38262490}, issn = {1879-1298}, mesh = {Animals ; Humans ; *Microplastics/toxicity ; Plastics ; Molecular Docking Simulation ; Ecosystem ; Prospective Studies ; Polymers ; *Microbiota ; Biodegradation, Environmental ; }, abstract = {Microplastics, tiny, flimsy, and direct progenitors of principal and subsidiary plastics, cause environmental degradation in aquatic and terrestrial entities. Contamination concerns include irrevocable impacts, potential cytotoxicity, and negative health effects on mortals. The detection, recovery, and degradation strategies of these pollutants in various biota and ecosystems, as well as their impact on plants, animals, and humans, have been a topic of significant interest. But the natural environment is infested with several types of plastics, all having different chemical makeup, structure, shape, and origin. Plastic trash acts as a substrate for microbial growth, creating biofilms on the plastisphere surface. This colonizing microbial diversity can be glimpsed with meta-genomics, a culture-independent approach. Owing to its comprehensive description of microbial communities, genealogical evidence on unconventional biocatalysts or enzymes, genomic correlations, evolutionary profile, and function, it is being touted as one of the promising tools in identifying novel enzymes for the degradation of polymers. Additionally, computational tools such as molecular docking can predict the binding of these novel enzymes to the polymer substrate, which can be validated through in vitro conditions for its environmentally feasible applications. This review mainly deals with the exploration of metagenomics along with computational tools to provide a clearer perspective into the microbial potential in the biodegradation of microplastics. The computational tools due to their polymathic nature will be quintessential in identifying the enzyme structure, binding affinities of the prospective enzymes to the substrates, and foretelling of degradation pathways involved which can be quite instrumental in the furtherance of the plastic degradation studies.}, } @article {pmid38259106, year = {2024}, author = {Wei, W and Li, J and Tang, B and Deng, Y and Li, Y and Chen, Q}, title = {Metabolomics and metagenomics reveal the impact of γδ T inhibition on gut microbiota and metabolism in periodontitis-promoting OSCC.}, journal = {mSystems}, volume = {9}, number = {2}, pages = {e0077723}, pmid = {38259106}, issn = {2379-5077}, support = {81991500, 81991502//MOST | National Natural Science Foundation of China (NSFC)/ ; 2020YFSY0008//Key Projects of Sichuan Provincial Department of Science and Technology/ ; YSP202314//Young Scientist Program of Beijing Stomatologocal Hospital, Capital Medical University/ ; 81771085//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Carcinoma, Squamous Cell ; Squamous Cell Carcinoma of Head and Neck ; RNA, Ribosomal, 16S/genetics ; *Mouth Neoplasms ; *Head and Neck Neoplasms ; *Periodontitis ; }, abstract = {During the process of periodontitis-promoting oral squamous cell carcinoma (OSCC), the periodontitis microbiota can facilitate OSCC development by activating γδ T cells. Inhibiting γδ T cells through immunotherapy has been shown to significantly alleviate various types of cancer. However, the underlying mechanism by which inhibiting γδ T cells influenced cancer treatment has not been fully elucidated. In this study, a mouse model of OSCC with periodontitis was established, and γδ T cells were inhibited by antibodies. Gut samples from the mice were collected and analyzed by metabolomics, metagenomics, and 16S rRNA. Integrative analysis of the gut metabolome and microbiome revealed that targeting γδ T resulted in changes in the levels of metabolites associated with cancer in the gut. Although there was no difference in the α diversity of microbiota, β diversity was significantly different, with a more heterogeneous community structure in the mice receiving targeted γδ T immunotherapy. Statistical analysis of the gut microbiota at the species level revealed a significant enrichment of Lactobacillus murinus, which was significantly correlated with γδ T abundance. The functional analysis revealed that inhibiting γδ T could impact the functional gene. A comprehensive analysis revealed that L. murinus is especially associated with changes in adenine, which also had connection with the concentration of IL-17 and the abundance of γδ T.IMPORTANCEThis study revealed the effect of γδ T cells on gut microbial dysbiosis and identify potential links between gut microbiota and metabolism, providing new insights into the role of γδ T during the process of periodontitis-induced OSCC, and identifying relevant biomarkers for future research and clinical monitoring protocol development.}, } @article {pmid38259104, year = {2024}, author = {Fadeev, E and Hennenfeind, JH and Amano, C and Zhao, Z and Klun, K and Herndl, GJ and Tinta, T}, title = {Bacterial degradation of ctenophore Mnemiopsis leidyi organic matter.}, journal = {mSystems}, volume = {9}, number = {2}, pages = {e0126423}, pmid = {38259104}, issn = {2379-5077}, support = {793778//EC | European Research Council (ERC)/ ; J7-2599//Javna Agencija za Raziskovalno Dejavnost RS (ARRS)/ ; I04978//Austrian Science Fund (FWF)/ ; }, mesh = {Animals ; *Ctenophora/microbiology ; *Pseudoalteromonas ; Biomass ; *Microbiota ; *Scyphozoa/metabolism ; Zooplankton/metabolism ; }, abstract = {Blooms of gelatinous zooplankton, an important source of protein-rich biomass in coastal waters, often collapse rapidly, releasing large amounts of labile detrital organic matter (OM) into the surrounding water. Although these blooms have the potential to cause major perturbations in the marine ecosystem, their effects on the microbial community and hence on the biogeochemical cycles have yet to be elucidated. We conducted microcosm experiments simulating the scenario experienced by coastal bacterial communities after the decay of a ctenophore (Mnemiopsis leidyi) bloom in the northern Adriatic Sea. Within 24 h, a rapid response of bacterial communities to the M. leidyi OM was observed, characterized by elevated bacterial biomass production and respiration rates. However, compared to our previous microcosm study of jellyfish (Aurelia aurita s.l.), M. leidyi OM degradation was characterized by significantly lower bacterial growth efficiency, meaning that the carbon stored in the OM was mostly respired. Combined metagenomic and metaproteomic analysis indicated that the degradation activity was mainly performed by Pseudoalteromonas, producing a large amount of proteolytic extracellular enzymes and exhibiting high metabolic activity. Interestingly, the reconstructed metagenome-assembled genome (MAG) of Pseudoalteromonas phenolica was almost identical (average nucleotide identity >99%) to the MAG previously reconstructed in our A. aurita microcosm study, despite the fundamental genetic and biochemical differences of the two gelatinous zooplankton species. Taken together, our data suggest that blooms of different gelatinous zooplankton are likely triggering a consistent response from natural bacterial communities, with specific bacterial lineages driving the remineralization of the gelatinous OM.IMPORTANCEJellyfish blooms are increasingly becoming a recurring seasonal event in marine ecosystems, characterized by a rapid build-up of gelatinous biomass that collapses rapidly. Although these blooms have the potential to cause major perturbations, their impact on marine microbial communities is largely unknown. We conducted an incubation experiment simulating a bloom of the ctenophore Mnemiopsis leidyi in the Northern Adriatic, where we investigated the bacterial response to the gelatinous biomass. We found that the bacterial communities actively degraded the gelatinous organic matter, and overall showed a striking similarity to the dynamics previously observed after a simulated bloom of the jellyfish Aurelia aurita s.l. In both cases, we found that a single bacterial species, Pseudoalteromonas phenolica, was responsible for most of the degradation activity. This suggests that blooms of different jellyfish are likely to trigger a consistent response from natural bacterial communities, with specific bacterial species driving the remineralization of gelatinous biomass.}, } @article {pmid38259099, year = {2024}, author = {Caesar, L and Rice, DW and McAfee, A and Underwood, R and Ganote, C and Tarpy, DR and Foster, LJ and Newton, ILG}, title = {Metagenomic analysis of the honey bee queen microbiome reveals low bacterial diversity and Caudoviricetes phages.}, journal = {mSystems}, volume = {9}, number = {2}, pages = {e0118223}, pmid = {38259099}, issn = {2379-5077}, support = {2005306//National Science Foundation (NSF)/ ; 2022049//National Science Foundation (NSF)/ ; //L'Oreal USA (L'Oréal)/ ; //Project Apis m. (PAm)/ ; 2017-51300-26814//U.S. Department of Agriculture (USDA)/ ; }, mesh = {Bees ; Female ; Animals ; *Bacteriophages/genetics ; *Microbiota/genetics ; Reproduction ; Metagenome ; }, abstract = {In eusocial insects, the health of the queens-the colony founders and sole reproductive females-is a primary determinant for colony success. Queen failure in the honey bee Apis mellifera, for example, is a major concern of beekeepers who annually suffer colony losses, necessitating a greater knowledge of queen health. Several studies on the microbiome of honey bees have characterized its diversity and shown its importance for the health of worker bees, the female non-reproductive caste. However, the microbiome of workers differs from that of queens, which, in comparison, is still poorly studied. Thus, direct investigations of the queen microbiome are required to understand colony-level microbiome assembly, functional roles, and evolution. Here, we used metagenomics to comprehensively characterize the honey bee queen microbiome. Comparing samples from different geographic locations and breeder sources, we show that the microbiome of queens is mostly shaped by the environment experienced since early life and is predicted to play roles in the breakdown of the diet and protection from pathogens and xenobiotics. We also reveal that the microbiome of queens comprises only four candidate core bacterial species, Apilactobacillus kunkeei, Lactobacillus apis, Bombella apis, and Commensalibacter sp. Interestingly, in addition to bacteria, we show that bacteriophages infect the queen microbiome, for which Lactobacillaceae are predicted to be the main reservoirs. Together, our results provide the basis to understand the honey bee colony microbiome assemblage, can guide improvements in queen-rearing processes, and highlight the importance of considering bacteriophages for queen microbiome health and microbiome homeostasis in eusocial insects.IMPORTANCEThe queen caste plays a central role in colony success in eusocial insects, as queens lay eggs and regulate colony behavior and development. Queen failure can cause colonies to collapse, which is one of the major concerns of beekeepers. Thus, understanding the biology behind the queen's health is a pressing issue. Previous studies have shown that the bee microbiome plays an important role in worker bee health, but little is known about the queen microbiome and its function in vivo. Here, we characterized the queen microbiome, identifying for the first time the present species and their putative functions. We show that the queen microbiome has predicted nutritional and protective roles in queen association and comprises only four consistently present bacterial species. Additionally, we bring to attention the spread of phages in the queen microbiome, which increased in abundance in failing queens and may impact the fate of the colony.}, } @article {pmid38259074, year = {2024}, author = {Zhang, Y-S and Zhang, Y-Q and Zhao, X-M and Liu, X-L and Qin, Q-L and Liu, N-H and Xu, F and Chen, X-L and Zhang, Y-Z and Li, P-Y}, title = {Metagenomic insights into the dynamic degradation of brown algal polysaccharides by kelp-associated microbiota.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {2}, pages = {e0202523}, pmid = {38259074}, issn = {1098-5336}, support = {42176229, 42376106//MOST | National Natural Science Foundation of China (NSFC)/ ; 32270047//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022QNLM030004-3//Marine S&T Fund of Shandong Province for Qingdao Marine Science and Technology Center/ ; 2022YFC2807503//National Key R&D Program of China/ ; 2021CXGC010502//Key R&D Program of Shandong Province/ ; }, mesh = {Humans ; Metagenome ; *Kelp/metabolism ; Polysaccharides/metabolism ; *Microbiota ; Alginates/metabolism ; *Phaeophyceae ; *Flavobacteriaceae/genetics/metabolism ; Carbon/metabolism ; *Edible Seaweeds ; *Laminaria ; }, abstract = {Marine bacteria play important roles in the degradation and cycling of algal polysaccharides. However, the dynamics of epiphytic bacterial communities and their roles in algal polysaccharide degradation during kelp decay are still unclear. Here, we performed metagenomic analyses to investigate the identities and predicted metabolic abilities of epiphytic bacterial communities during the early and late decay stages of the kelp Saccharina japonica. During kelp decay, the dominant epiphytic bacterial communities shifted from Gammaproteobacteria to Verrucomicrobia and Bacteroidetes. In the early decay stage of S. japonica, epiphytic bacteria primarily targeted kelp-derived labile alginate for degradation, among which the gammaproteobacterial Vibrionaceae (particularly Vibrio) and Psychromonadaceae (particularly Psychromonas), abundant in alginate lyases belonging to the polysaccharide lyase (PL) families PL6, PL7, and PL17, were key alginate degraders. More complex fucoidan was preferred to be degraded in the late decay stage of S. japonica by epiphytic bacteria, predominantly from Verrucomicrobia (particularly Lentimonas), Pirellulaceae of Planctomycetes (particularly Rhodopirellula), Pontiellaceae of Kiritimatiellota, and Flavobacteriaceae of Bacteroidetes, which depended on using glycoside hydrolases (GHs) from the GH29, GH95, and GH141 families and sulfatases from the S1_15, S1_16, S1_17, and S1_25 families to depolymerize fucoidan. The pathways for algal polysaccharide degradation in dominant epiphytic bacterial groups were reconstructed based on analyses of metagenome-assembled genomes. This study sheds light on the roles of different epiphytic bacteria in the degradation of brown algal polysaccharides.IMPORTANCEKelps are important primary producers in coastal marine ecosystems. Polysaccharides, as major components of brown algal biomass, constitute a large fraction of organic carbon in the ocean. However, knowledge of the identities and pathways of epiphytic bacteria involved in the degradation process of brown algal polysaccharides during kelp decay is still elusive. Here, based on metagenomic analyses, the succession of epiphytic bacterial communities and their metabolic potential were investigated during the early and late decay stages of Saccharina japonica. Our study revealed a transition in algal polysaccharide-degrading bacteria during kelp decay, shifting from alginate-degrading Gammaproteobacteria to fucoidan-degrading Verrucomicrobia, Planctomycetes, Kiritimatiellota, and Bacteroidetes. A model for the dynamic degradation of algal cell wall polysaccharides, a complex organic carbon, by epiphytic microbiota during kelp decay was proposed. This study deepens our understanding of the role of epiphytic bacteria in marine algal carbon cycling as well as pathogen control in algal culture.}, } @article {pmid38257834, year = {2024}, author = {Veldsman, WP and Yang, C and Zhang, Z and Huang, Y and Chowdhury, D and Zhang, L}, title = {Structural and Functional Disparities within the Human Gut Virome in Terms of Genome Topology and Representative Genome Selection.}, journal = {Viruses}, volume = {16}, number = {1}, pages = {}, pmid = {38257834}, issn = {1999-4915}, support = {BGIRSZ20220014//BGI Group (China)/ ; HKBU 22201419//Hong Kong Research Grant Council Early Career Scheme/ ; RC-SGT2/19-20/SCI/007//HKBU Start-up Grant Tier 2/ ; IRCMS/19-20/D02//HKBU IRCMS/ ; 2021A1515012226//Guangdong Basic and Applied Basic Research Foundation/ ; }, mesh = {Humans ; *Virome/genetics ; Genome, Viral ; *Bacteriophages/genetics ; Metagenome ; Biological Assay ; }, abstract = {Circularity confers protection to viral genomes where linearity falls short, thereby fulfilling the form follows function aphorism. However, a shift away from morphology-based classification toward the molecular and ecological classification of viruses is currently underway within the field of virology. Recent years have seen drastic changes in the International Committee on Taxonomy of Viruses' operational definitions of viruses, particularly for the tailed phages that inhabit the human gut. After the abolition of the order Caudovirales, these tailed phages are best defined as members of the class Caudoviricetes. To determine the epistemological value of genome topology in the context of the human gut virome, we designed a set of seven experiments to assay the impact of genome topology and representative viral selection on biological interpretation. Using Oxford Nanopore long reads for viral genome assembly coupled with Illumina short-read polishing, we showed that circular and linear virus genomes differ remarkably in terms of genome quality, GC skew, transfer RNA gene frequency, structural variant frequency, cross-reference functional annotation (COG, KEGG, Pfam, and TIGRfam), state-of-the-art marker-based classification, and phage-host interaction. Furthermore, the disparity profile changes during dereplication. In particular, our phage-host interaction results demonstrated that proportional abundances cannot be meaningfully compared without due regard for genome topology and dereplication threshold, which necessitates the need for standardized reporting. As a best practice guideline, we recommend that comparative studies of the human gut virome always report the ratio of circular to linear viral genomes along with the dereplication threshold so that structural and functional metrics can be placed into context when assessing biologically relevant metagenomic properties such as proportional abundance.}, } @article {pmid38257809, year = {2024}, author = {Gangopadhayya, A and Lole, K and Ghuge, O and Ramdasi, A and Kamble, A and Roy, D and Thakar, S and Nath, A and Sudeep, AB and Cherian, S}, title = {Metagenomic Analysis of Viromes of Aedes Mosquitoes across India.}, journal = {Viruses}, volume = {16}, number = {1}, pages = {}, pmid = {38257809}, issn = {1999-4915}, support = {6/9-7(209)/2019-ECD-II//Indian Council of Medical Research/ ; }, mesh = {Animals ; Swine ; Humans ; *Aedes ; *African Swine Fever Virus ; Virome ; India ; *Bacteriophages ; *Arenaviridae ; *Granulovirus ; }, abstract = {Metagenomic analysis of Aedes aegypti and Ae. albopictus mosquitoes from diverse geographical regions of India revealed the presence of several insect viruses of human interest. Most abundant reads found in Ae. aegypti mosquitoes were of Phasi Charoen-like virus (PCLV), Choristoneura fumiferana granulovirus (CfGV), Cell fusing agent virus (CFAV), and Wenzhou sobemo-like virus 4 (WSLV4), whereas WSLV4 and CfGV constituted the highest percentage of reads in Ae. albopictus viromes. Other reads that were of low percentage included Hubei mosquito virus 2 (HMV2), Porcine astrovirus 4 (PAstV4), and Wild Boar astrovirus (WBAstV). PCLV and CFAV, which were found to be abundant in Ae. aegypti viromes were absent in Ae. albopictus viromes. Among the viromes analyzed, Ae. aegypti sampled from Pune showed the highest percentage (79.82%) of viral reads, while Ae. aegypti mosquitoes sampled from Dibrugarh showed the lowest percentage (3.47%). Shamonda orthobunyavirus (SHAV), African swine fever virus (ASFV), Aroa virus (AROAV), and Ilheus virus (ILHV), having the potential to infect vertebrates, including humans, were also detected in both mosquito species, albeit with low read numbers. Reads of gemykibivirus, avian retrovirus, bacteriophages, herpesviruses, and viruses infecting protozoans, algae, etc., were also detected in the mosquitoes. A high percentage of reads in the Ae. albopictus mosquito samples belonged to unclassified viruses and warrant further investigation. The data generated in the present work may not only lead to studies to explain the influence of these viruses on the replication and transmission of viruses of clinical importance but also to find applications as biocontrol agents against pathogenic viruses.}, } @article {pmid38256252, year = {2024}, author = {Ramon, E and Obón-Santacana, M and Khannous-Lleiffe, O and Saus, E and Gabaldón, T and Guinó, E and Bars-Cortina, D and Ibáñez-Sanz, G and Rodríguez-Alonso, L and Mata, A and García-Rodríguez, A and Moreno, V}, title = {Performance of a Shotgun Prediction Model for Colorectal Cancer When Using 16S rRNA Sequencing Data.}, journal = {International journal of molecular sciences}, volume = {25}, number = {2}, pages = {}, pmid = {38256252}, issn = {1422-0067}, support = {PI17-00092 and PI20-01439//Instituto de Salud Carlos III/ ; GCTRA18022MORE//Spanish Association Against Cancer (AECC) Scientific Foundation/ ; action Genrisk//Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP)/ ; A18131 Ml4Microbiome//COST action/ ; PID2021-126067NB-I00, CPP2021-008552, PCI2022-135066-2 and PDC2022-133266-I00//Spanish Ministry of Science and Innovation, cofounded by ERDF "A way of making Europe"/ ; SGR01551//Catalan Research Agency (AGAUR)/ ; ERC-2016-724173//European Union's Horizon 2020 research and innovation programme/ ; GBMF9742//Gordon and Betty Moore Foundation/ ; LCF/PR/HR21/00737//"La Caixa" foundation/ ; IMPACT Grant IMP/00019 and CIBERINFEC CB21/13/00061- ISCIII-SGEFI/ERDF//Instituto de Salud Carlos III/ ; 875/C/2021//Fundació Marató TV3/ ; CD21/00094//Instituto de Salud Carlos III Sara Borrell/ ; FPU2020-02907//Spanish Ministerio de Universidades/ ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; Algorithms ; *Gastrointestinal Microbiome/genetics ; Health Personnel ; *Colorectal Neoplasms/genetics ; }, abstract = {Colorectal cancer (CRC), the third most common cancer globally, has shown links to disturbed gut microbiota. While significant efforts have been made to establish a microbial signature indicative of CRC using shotgun metagenomic sequencing, the challenge lies in validating this signature with 16S ribosomal RNA (16S) gene sequencing. The primary obstacle is reconciling the differing outputs of these two methodologies, which often lead to divergent statistical models and conclusions. In this study, we introduce an algorithm designed to bridge this gap by mapping shotgun-derived taxa to their 16S counterparts. This mapping enables us to assess the predictive performance of a shotgun-based microbiome signature using 16S data. Our results demonstrate a reduction in performance when applying the 16S-mapped taxa in the shotgun prediction model, though it retains statistical significance. This suggests that while an exact match between shotgun and 16S data may not yet be feasible, our approach provides a viable method for comparative analysis and validation in the context of CRC-associated microbiome research.}, } @article {pmid38256164, year = {2024}, author = {Bombardi, L and Salini, A and Aulitto, M and Zuliani, L and Andreolli, M and Bordoli, P and Coltro, A and Vitulo, N and Zaccone, C and Lampis, S and Fusco, S}, title = {Lignocellulolytic Potential of Microbial Consortia Isolated from a Local Biogas Plant: The Case of Thermostable Xylanases Secreted by Mesophilic Bacteria.}, journal = {International journal of molecular sciences}, volume = {25}, number = {2}, pages = {}, pmid = {38256164}, issn = {1422-0067}, support = {CUP B31I18000230006//MUR - Italian Ministry of University and Research/ ; CUP B33C22000660001//NextGenerationEU - European Union/ ; }, mesh = {Microbial Consortia ; Biofuels ; *Microbiota ; Substrate Specificity ; *Agaricales ; Bacteria/genetics ; }, abstract = {Lignocellulose biomasses (LCB), including spent mushroom substrate (SMS), pose environmental challenges if not properly managed. At the same time, these renewable resources hold immense potential for biofuel and chemicals production. With the mushroom market growth expected to amplify SMS quantities, repurposing or disposal strategies are critical. This study explores the use of SMS for cultivating microbial communities to produce carbohydrate-active enzymes (CAZymes). Addressing a research gap in using anaerobic digesters for enriching microbiomes feeding on SMS, this study investigates microbial diversity and secreted CAZymes under varied temperatures (37 °C, 50 °C, and 70 °C) and substrates (SMS as well as pure carboxymethylcellulose, and xylan). Enriched microbiomes demonstrated temperature-dependent preferences for cellulose, hemicellulose, and lignin degradation, supported by thermal and elemental analyses. Enzyme assays confirmed lignocellulolytic enzyme secretion correlating with substrate degradation trends. Notably, thermogravimetric analysis (TGA), coupled with differential scanning calorimetry (TGA-DSC), emerged as a rapid approach for saccharification potential determination of LCB. Microbiomes isolated at mesophilic temperature secreted thermophilic hemicellulases exhibiting robust stability and superior enzymatic activity compared to commercial enzymes, aligning with biorefinery conditions. PCR-DGGE and metagenomic analyses showcased dynamic shifts in microbiome composition and functional potential based on environmental conditions, impacting CAZyme abundance and diversity. The meta-functional analysis emphasised the role of CAZymes in biomass transformation, indicating microbial strategies for lignocellulose degradation. Temperature and substrate specificity influenced the degradative potential, highlighting the complexity of environmental-microbial interactions. This study demonstrates a temperature-driven microbial selection for lignocellulose degradation, unveiling thermophilic xylanases with industrial promise. Insights gained contribute to optimizing enzyme production and formulating efficient biomass conversion strategies. Understanding microbial consortia responses to temperature and substrate variations elucidates bioconversion dynamics, emphasizing tailored strategies for harnessing their biotechnological potential.}, } @article {pmid38255816, year = {2024}, author = {Smutin, D and Taldaev, A and Lebedev, E and Adonin, L}, title = {Shotgun Metagenomics Reveals Minor Micro"bee"omes Diversity Defining Differences between Larvae and Pupae Brood Combs.}, journal = {International journal of molecular sciences}, volume = {25}, number = {2}, pages = {}, pmid = {38255816}, issn = {1422-0067}, support = {agreement №075-15-2021-1345, unique identifier RF-193021X0012//the Ministry of Science and Higher Education of the Russian Federation within the framework of the Federal Scientific and Technical Program for the Development of Genetic Technologies for 2019-2027./ ; }, mesh = {Bees/genetics ; Animals ; Larva/genetics ; Pupa/genetics ; Metagenome ; *Microbiota/genetics ; *Actinobacteria ; }, abstract = {Bees represent not only a valuable asset in agriculture, but also serve as a model organism within contemporary microbiology. The metagenomic composition of the bee superorganism has been substantially characterized. Nevertheless, traditional cultural methods served as the approach to studying brood combs in the past. Indeed, the comb microbiome may contribute to determining larval caste differentiation and hive immunity. To further this understanding, we conducted a shotgun sequencing analysis of the brood comb microbiome. While we found certain similarities regarding species diversity, it exhibits significant differentiation from all previously described hive metagenomes. Many microbiome members maintain a relatively constant ratio, yet taxa with the highest abundance level tend to be ephemeral. More than 90% of classified metagenomes were Gammaproteobacteria, Bacilli and Actinobacteria genetic signatures. Jaccard dissimilarity between samples based on bacteria genus classifications hesitate from 0.63 to 0.77, which for shotgun sequencing indicates a high consistency in bacterial composition. Concurrently, we identified antagonistic relationships between certain bacterial clusters. The presence of genes related to antibiotic synthesis and antibiotic resistance suggests potential mechanisms underlying the stability of comb microbiomes. Differences between pupal and larval combs emerge in the total metagenome, while taxa with the highest abundance remained consistent. All this suggests that a key role in the functioning of the comb microbiome is played by minor biodiversity, the function of which remains to be established experimentally.}, } @article {pmid38254996, year = {2024}, author = {Silva, I and Alves, M and Malheiro, C and Silva, ARR and Loureiro, S and Henriques, I and González-Alcaraz, MN}, title = {Structural and Functional Shifts in the Microbial Community of a Heavy Metal-Contaminated Soil Exposed to Short-Term Changes in Air Temperature, Soil Moisture and UV Radiation.}, journal = {Genes}, volume = {15}, number = {1}, pages = {}, pmid = {38254996}, issn = {2073-4425}, support = {PTDC/CTA-AMB/29557/2017//Fundação para a Ciência e Tecnologia/ ; UIDP/50017/2020+UIDB/50017/2020 + LA/P/0094/2020//Fundação para a Ciência e Tecnologia/ ; UIDB/04004/2020//Fundação para a Ciência e Tecnologia/ ; BI/CESAM/0063/METOXCLIM/2018//Fundação para a Ciência e Tecnologia/ ; BI/CESAM/00060/METOXCLIM/2018//Fundação para a Ciência e Tecnologia/ ; PD/BD/135577/2018//Fundação para a Ciência e Tecnologia/ ; RYC2020-029322-I//Government of Spain/ ; MICROCLIM//Analyses et Expérimentations pour les Ecosystèmes/ ; }, mesh = {Ultraviolet Rays ; Temperature ; *Metals, Heavy/toxicity ; *Microbiota ; Soil ; }, abstract = {The interplay between metal contamination and climate change may exacerbate the negative impact on the soil microbiome and, consequently, on soil health and ecosystem services. We assessed the response of the microbial community of a heavy metal-contaminated soil when exposed to short-term (48 h) variations in air temperature, soil humidity or ultraviolet (UV) radiation in the absence and presence of Enchytraeus crypticus (soil invertebrate). Each of the climate scenarios simulated significantly altered at least one of the microbial parameters measured. Irrespective of the presence or absence of invertebrates, the effects were particularly marked upon exposure to increased air temperature and alterations in soil moisture levels (drought and flood scenarios). The observed effects can be partly explained by significant alterations in soil properties such as pH, dissolved organic carbon, and water-extractable heavy metals, which were observed for all scenarios in comparison to standard conditions. The occurrence of invertebrates mitigated some of the impacts observed on the soil microbial community, particularly in bacterial abundance, richness, diversity, and metabolic activity. Our findings emphasize the importance of considering the interplay between climate change, anthropogenic pressures, and soil biotic components to assess the impact of climate change on terrestrial ecosystems and to develop and implement effective management strategies.}, } @article {pmid38254181, year = {2024}, author = {Chai, J and Zhuang, Y and Cui, K and Bi, Y and Zhang, N}, title = {Metagenomics reveals the temporal dynamics of the rumen resistome and microbiome in goat kids.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {14}, pmid = {38254181}, issn = {2049-2618}, support = {31872385//National Natural Science Foundation of China/ ; 31872385//National Natural Science Foundation of China/ ; 2021SZD0014//Inner Mongolia Science and Technology Key Project/ ; 2018YFD0501902//National Key R&D Program Projects/ ; }, mesh = {Animals ; Humans ; Goats ; Rumen ; *Microbiota/genetics ; Animals, Domestic ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {BACKGROUND: The gut microbiome of domestic animals carries antibiotic resistance genes (ARGs) which can be transmitted to the environment and humans, resulting in challenges of antibiotic resistance. Although it has been reported that the rumen microbiome of ruminants may be a reservoir of ARGs, the factors affecting the temporal dynamics of the rumen resistome are still unclear. Here, we collected rumen content samples of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days of age, analyzed their microbiome and resistome profiles using metagenomics, and assessed the temporal dynamics of the rumen resistome in goats at the early stage of life under a conventional feeding system.

RESULTS: In our results, the rumen resistome of goat kids contained ARGs to 41 classes, and the richness of ARGs decreased with age. Four antibiotic compound types of ARGs, including drugs, biocides, metals, and multi-compounds, were found during milk feeding, while only drug types of ARGs were observed after supplementation with starter feed. The specific ARGs for each age and their temporal dynamics were characterized, and the network inference model revealed that the interactions among ARGs were related to age. A strong correlation between the profiles of rumen resistome and microbiome was found using Procrustes analysis. Ruminal Escherichia coli within Proteobacteria phylum was the main carrier of ARGs in goats consuming colostrum, while Prevotella ruminicola and Fibrobacter succinogenes associated with cellulose degradation were the carriers of ARGs after starter supplementation. Milk consumption was likely a source of rumen ARGs, and the changes in the rumen resistome with age were correlated with the microbiome modulation by starter supplementation.

CONCLUSIONS: Our data revealed that the temporal dynamics of the rumen resistome are associated with the microbiome, and the reservoir of ARGs in the rumen during early life is likely related to age and diet. It may be a feasible strategy to reduce the rumen and its downstream dissemination of ARGs in ruminants through early-life dietary intervention. Video Abstract.}, } @article {pmid38253478, year = {2024}, author = {Kean, IRL and Clark, JA and Zhang, Z and Daubney, E and White, D and Ferrando-Vivas, P and Milla, G and Cuthbertson, B and Pappachan, J and Klein, N and Mouncey, P and Rowan, K and Myburgh, J and Gouliouris, T and Baker, S and Parkhill, J and Pathan, N and Arctic Research Team, }, title = {Short-duration selective decontamination of the digestive tract infection control does not contribute to increased antimicrobial resistance burden in a pilot cluster randomised trial (the ARCTIC Study).}, journal = {Gut}, volume = {73}, number = {6}, pages = {910-921}, pmid = {38253478}, issn = {1468-3288}, support = {/WT_/Wellcome Trust/United Kingdom ; GN2751//Medical Research UK/ ; 215515/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Pilot Projects ; *Critical Illness/therapy ; Male ; Female ; Child, Preschool ; *Feces/microbiology ; *Decontamination/methods ; Child ; Gastrointestinal Microbiome/drug effects ; Infection Control/methods ; Respiration, Artificial ; Infant ; Anti-Bacterial Agents/therapeutic use/administration & dosage ; Drug Resistance, Bacterial/genetics ; Gastrointestinal Tract/microbiology ; Oropharynx/microbiology ; }, abstract = {OBJECTIVE: Selective decontamination of the digestive tract (SDD) is a well-studied but hotly contested medical intervention of enhanced infection control. Here, we aim to characterise the changes to the microbiome and antimicrobial resistance (AMR) gene profiles in critically ill children treated with SDD-enhanced infection control compared with conventional infection control.

DESIGN: We conducted shotgun metagenomic microbiome and resistome analysis on serial oropharyngeal and faecal samples collected from critically ill, mechanically ventilated patients in a pilot multicentre cluster randomised trial of SDD. The microbiome and AMR profiles were compared for longitudinal and intergroup changes. Of consented patients, faecal microbiome baseline samples were obtained in 89 critically ill children. Additionally, samples collected during and after critical illness were collected in 17 children treated with SDD-enhanced infection control and 19 children who received standard care.

RESULTS: SDD affected the alpha and beta diversity of critically ill children to a greater degree than standard care. At cessation of treatment, the microbiome of SDD patients was dominated by Actinomycetota, specifically Bifidobacterium, at the end of mechanical ventilation. Altered gut microbiota was evident in a subset of SDD-treated children who returned late longitudinal samples compared with children receiving standard care. Clinically relevant AMR gene burden was unaffected by the administration of SDD-enhanced infection control compared with standard care. SDD did not affect the composition of the oral microbiome compared with standard treatment.

CONCLUSION: Short interventions of SDD caused a shift in the microbiome but not of the AMR gene pool in critically ill children at the end mechanical ventilation, compared with standard antimicrobial therapy.}, } @article {pmid38253195, year = {2024}, author = {Wang, H and Wang, Z and Yu, J and Ma, C and Liu, L and Xu, D and Zhang, J}, title = {The function and keystone microbiota in typical habitats under the influence of anthropogenic activities in Baiyangdian Lake.}, journal = {Environmental research}, volume = {247}, number = {}, pages = {118196}, doi = {10.1016/j.envres.2024.118196}, pmid = {38253195}, issn = {1096-0953}, mesh = {Animals ; Humans ; *Lakes/chemistry ; Anthropogenic Effects ; *Microbiota ; Oxidation-Reduction ; Fishes ; Water ; }, abstract = {Microbe is an essential driver in regulating the biochemical cycles of carbon, nitrogen, and sulfur. In freshwater lake, microbial communities and functions are influenced by multiple factors, especially anthropogenic activities. Baiyangdian Lake consisted of various habitats, and was frequently interfered with human activities. In this study, 16 S rRNA sequencing and metagenomic sequencing were performed to characterize the microbial communities, determine keystone taxa and reveal dominated metabolic functions in typical habitats in Baiyangdian Lake. The results showed that the diversity of microbial community was significantly higher in sediment compared with corresponding water sample. Microbial community showed strong spatial heterogeneity in sediment, and temporal heterogeneity in water. As for different habitats, significantly higher alpha diversity was observed in ecotone, where the interference of human activities was relatively weak. The shared OTUs were distinguished from the keystone taxa, which indicated the uniqueness of microbiota in different ecological habitat. Moreover, the interactions of microbial in ecological restoration area (abandoned fish pond) were relatively simple, suggesting that this ecosystem was relatively fragile compared with others. Based on the metagenomic sequencing, we recognized that the canal, open water, and abandoned fish pond were beneficial for methanogenic and the ecotone might be a hot zone for the oxidation of methane. Notably, most of the microbes that participated in these predominant metabolisms were unclassified, which indicated the hug potential for exploring functional microorganisms in Baiyangdian Lake. This study provided a comprehensive understanding of the ecology characteristics of microbiota in habitats undergoing various human interference in Baiyangdian Lake.}, } @article {pmid38247211, year = {2024}, author = {Jo, E and Lee, H and Song, Y and Cha, J}, title = {Taxonomic Variations of Bacterial and Fungal Communities depending on Fermentation Temperature in Traditional Korean Fermented Soybean Food, Doenjang.}, journal = {Journal of microbiology and biotechnology}, volume = {34}, number = {4}, pages = {863-870}, pmid = {38247211}, issn = {1738-8872}, mesh = {*Fermentation ; *Fungi/classification/genetics/isolation & purification/metabolism ; *Temperature ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Soy Foods/microbiology ; *Glycine max/microbiology ; *Food Microbiology ; Fermented Foods/microbiology ; High-Throughput Nucleotide Sequencing ; Microbiota ; Republic of Korea ; Metagenomics ; }, abstract = {Meju, a fermented soybean brick, is a key component in soybean foods like doenjang and ganjang, harboring a variety of microorganisms, including bacteria and fungi. These microorganisms significantly contribute to the nutritional and sensory characteristics of doenjang and ganjang. Amplicon-based next-generation sequencing was applied to investigate how the microbial communities of meju fermented at low and high temperatures differ and how this variation affects the microbial communities of doenjang, a subsequently fermented soybean food. Our metagenomic data showed distinct patterns depending on the fermentation temperature. The microbial abundance in the bacterial community was increased under both temperatures during the fermentation of meju and doenjang. Weissella was the most abundant genus before the fermentation of meju, however, it was replaced by Bacillus at high temperature-fermented meju and lactic acid bacteria such as Weissella and Latilactobacillus at low temperature-fermented meju. Leuconostoc, Logiolactobacillus, and Tetragenococcus gradually took over the dominant role during the fermentation process of doenjang, replacing the previous dominant microorganisms. Mucor was dominant in the fungal community before and after meju fermentation, whereas Debaryomyces was dominant under both temperatures during doenjang fermentation. The dominant fungal genus of doenjang was not affected regardless of the fermentation temperature of meju. Strong correlations were shown for specific bacteria and fungi linked to specific fermentation temperatures. This study helps our understanding of meju fermentation process at different fermentation temperatures and highlights different bacteria and fungi associated with specific fermentation periods which may influence the nutritional and organoleptic properties of the final fermented soybean foods doenjang.}, } @article {pmid38246848, year = {2024}, author = {Liu, Y and Fachrul, M and Inouye, M and Méric, G}, title = {Harnessing human microbiomes for disease prediction.}, journal = {Trends in microbiology}, volume = {32}, number = {7}, pages = {707-719}, doi = {10.1016/j.tim.2023.12.004}, pmid = {38246848}, issn = {1878-4380}, support = {RG/18/13/33946/BHF_/British Heart Foundation/United Kingdom ; }, mesh = {Humans ; *Microbiota ; Risk Factors ; Cardiovascular Diseases/microbiology ; }, abstract = {The human microbiome has been increasingly recognized as having potential use for disease prediction. Predicting the risk, progression, and severity of diseases holds promise to transform clinical practice, empower patient decisions, and reduce the burden of various common diseases, as has been demonstrated for cardiovascular disease or breast cancer. Combining multiple modifiable and non-modifiable risk factors, including high-dimensional genomic data, has been traditionally favored, but few studies have incorporated the human microbiome into models for predicting the prospective risk of disease. Here, we review research into the use of the human microbiome for disease prediction with a particular focus on prospective studies as well as the modulation and engineering of the microbiome as a therapeutic strategy.}, } @article {pmid38246133, year = {2024}, author = {Chulenbayeva, L and Ganzhula, Y and Kozhakhmetov, S and Jarmukhanov, Z and Nurgaziyev, M and Nurgozhina, A and Muhanbetzhanov, N and Sergazy, S and Zhetkenev, S and Borykbay, Z and Tkachev, V and Urazova, S and Vinogradova, E and Kushugulova, A}, title = {The Trajectory of Successful Aging: Insights from Metagenome and Cytokine Profiling.}, journal = {Gerontology}, volume = {70}, number = {4}, pages = {390-407}, pmid = {38246133}, issn = {1423-0003}, mesh = {Aged, 80 and over ; Humans ; *Metagenome ; Aging ; *Microbiota ; Longevity ; Cytokines ; }, abstract = {INTRODUCTION: The longevity is influenced by genetic, environmental, and lifestyle factors. The specific changes that occur in the gut microbiome during the aging process, and their relationship to longevity and immune function, have not yet been fully understood. The ongoing research of other microbiome based on longevity cohort in Kazakhstan provides preliminary information on longevity-related aging, where cytokine expression is associated with specific microbial communities and microbial functions.

METHODS: Metagenomic shotgun sequencing study of 40 long-lived individuals aged 90 years and over was carried out, who were conditionally healthy and active, able to serve themselves, without a history of serious infection and cancer, who had not taken any antimicrobials, including probiotics. Blood serum was analyzed for clinical and laboratory characteristics. The cytokine and chemokine profile in serum and stool samples was assessed using multiplex analysis.

RESULTS: We found a significant increase in the expression of pro-inflammatory cytokines IL-1a, IL-6, 12p70, IP-10, IFNα2, IL-15, TNFa, as well as chemokines MIP-1a/CCL3 and MIP-1b/CCL4, chemokine motif ligands MCP-3/CCL7 and MDC/CCL22(1c). Nonagenerians and centenarians demonstrated a greater diversity of core microbiota genera and showed an elevated prevalence of the genera Bacteroides, Clostridium, Escherichia, and Alistipes. Conversely, there was a decrease in the abundance of the genera Ruminococcus, Fusicatenibacter, Dorea, as well as the species Fusicatenibacter saccharivorans. Furthermore, functional analysis revealed that the microbiome in long-lived group has a high capacity for lipid metabolism, amino acid degradation, and potential signs of chronic inflammatory status.

CONCLUSION: Long-lived individuals exhibit an immune system imbalance and observed changes in the composition of the gut microbiota at the genus level between to the two age-groups. Age-related changes in the gut microbiome, metabolic functions of the microbial community, and chronic inflammation all contribute to immunosenescence. In turn, the inflammatory state and microbial composition of the gut is related to nutritional status.}, } @article {pmid38246125, year = {2024}, author = {Mahony, J}, title = {Biological and bioinformatic tools for the discovery of unknown phage-host combinations.}, journal = {Current opinion in microbiology}, volume = {77}, number = {}, pages = {102426}, doi = {10.1016/j.mib.2024.102426}, pmid = {38246125}, issn = {1879-0364}, mesh = {*Bacteriophages/genetics ; Artificial Intelligence ; Computational Biology ; *Microbiota ; Metagenomics ; }, abstract = {The field of microbial ecology has been transformed by metagenomics in recent decades and has culminated in vast datasets that facilitate the bioinformatic dissection of complex microbial communities. Recently, attention has turned from defining the microbiota composition to the interactions and relationships that occur between members of the microbiota. Within complex microbiota, the identification of bacteriophage-host combinations has been a major challenge. Recent developments in artificial intelligence tools to predict protein structure and function as well as the relationships between bacteria and their infecting bacteriophages allow a strategic approach to identifying and validating phage-host relationships. However, biological validation of these predictions remains essential and will serve to improve the existing predictive tools. In this review, I provide an overview of the most recent developments in both bioinformatic and experimental approaches to predicting and experimentally validating unknown phage-host combinations.}, } @article {pmid38246077, year = {2024}, author = {Tang, M and Chen, Q and Zhong, H and Liu, S and Sun, W}, title = {CPR bacteria and DPANN archaea play pivotal roles in response of microbial community to antibiotic stress in groundwater.}, journal = {Water research}, volume = {251}, number = {}, pages = {121137}, doi = {10.1016/j.watres.2024.121137}, pmid = {38246077}, issn = {1879-2448}, mesh = {Archaea/genetics/metabolism ; Anti-Bacterial Agents/pharmacology/metabolism ; Bacteria/genetics/metabolism ; *Microbiota ; *Groundwater/microbiology ; Phylogeny ; }, abstract = {The accumulation of antibiotics in the natural environment can disrupt microbial population dynamics. However, our understanding of how microbial communities adapt to the antibiotic stress in groundwater ecosystems remains limited. By recovering 2675 metagenome-assembled genomes (MAGs) from 66 groundwater samples, we explored the effect of antibiotics on bacterial, archaeal, and fungal communities, and revealed the pivotal microbes and their mechanisms in coping with antibiotic stress. The results indicated that antibiotics had the most significant influence on bacterial and archaeal communities, while the impact on the fungal community was minimal. Analysis of co-occurrence networks between antibiotics and microbes revealed the critical roles of Candidate Phyla Radiation (CPR) bacteria and DPANN archaea, two representative microbial groups in groundwater ecosystem, in coping with antibiotic resistance and enhancing network connectivity and complexity. Further genomic analysis demonstrated that CPR bacteria carried approximately 6 % of the identified antibiotic resistance genes (ARGs), indicating their potential to withstand antibiotics on their own. Meanwhile, the genomes of CPR bacteria and DPANN archaea were found to encode diverse biosynthetic gene clusters (BGCs) responsible for producing antimicrobial metabolites, which could not only assist CPR and DPANN organisms but also benefit the surrounding microbes in combating antibiotic stress. These findings underscore the significant impact of antibiotics on prokaryotic microbial communities in groundwater, and highlight the importance of CPR bacteria and DPANN archaea in enhancing the overall resilience and functionality of the microbial community in the face of antibiotic stress.}, } @article {pmid38246038, year = {2024}, author = {Phulpoto, IA and Qi, Z and Qazi, MA and Yu, Z}, title = {Biosurfactants-based mixed polycyclic aromatic hydrocarbon degradation: From microbial community structure toward non-targeted metabolomic profile determination.}, journal = {Environment international}, volume = {184}, number = {}, pages = {108448}, doi = {10.1016/j.envint.2024.108448}, pmid = {38246038}, issn = {1873-6750}, mesh = {*Polycyclic Aromatic Hydrocarbons/metabolism ; Tandem Mass Spectrometry ; *Soil Pollutants/metabolism ; Biodegradation, Environmental ; *Microbiota ; *Environmental Pollutants ; Lipopeptides ; Soil Microbiology ; }, abstract = {Biosurfactants-based bioremediation is considered an efficient technology to eliminate environmental pollutants including polycyclic aromatic hydrocarbons (PAHs). However, the precise role of rhamnolipids or lipopeptide-biosurfactants in mixed PAH dissipation, shaping microbial community structure, and influencing metabolomic profile remained unclear. In this study, results showed that the maximum PAH degradation was achieved in lipopeptide-assisted treatment (SPS), where the pyrene and phenanthrene were substantially degraded up to 74.28 % and 63.05 % respectively, as compared to rhamnolipids (SPR) and un-aided biosurfactants (SP). Furthermore, the high throughput sequencing analysis revealed a significant change in the PAH-degrading microbial community, with Proteobacteria being the predominant phylum (>98 %) followed by Bacteroidota and Firmicutes in all the treatments. Moreover, Pseudomonas and Pannonibacter were found as highly potent bacterial genera for mixed PAH degradation in SPR, SPS, and SP treatments, nevertheless, the abundance of the genus Pseudomonas was significantly enhanced (>97 %) in SPR treatment groups. On the other hand, the non-targeted metabolomic profile through UHPLC-MS/MS exhibited a remarkable change in the metabolites of amino acids, carbohydrates, and lipid metabolisms by the input of rhamnolipids or lipopeptide-biosurfactants whereas, the maximum intensities of metabolites (more than two-fold) were observed in SPR treatment. The findings of this study suggested that the aforementioned biosurfactants can play an indispensable role in mixed PAH degradation as well as seek to offer new insights into shifts in PAH-degrading microbial communities and their metabolic function, which can guide the development of more efficient and targeted strategies for complete removal of organic pollutants such as PAH from the contaminated environment.}, } @article {pmid38246037, year = {2024}, author = {Adhikari, BN and Paskey, AC and Frey, KG and Bennett, AJ and Long, KA and Kuhn, JH and Hamilton, T and Glang, L and Cer, RZ and Goldberg, TL and Bishop-Lilly, KA}, title = {Virome profiling of fig wasps (Ceratosolen spp.) reveals virus diversity spanning four realms.}, journal = {Virology}, volume = {591}, number = {}, pages = {109992}, pmid = {38246037}, issn = {1096-0341}, support = {HHSN272201800013C/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Animals ; *Wasps ; *Ficus ; Virome ; Pollination ; Fruit ; Symbiosis ; }, abstract = {We investigated the virome of agaonid fig wasps (Ceratosolen spp.) inside syconia ("fruits") of various Ficus trees fed upon by frugivores such as pteropodid bats in Sub-Saharan Africa. This virome includes representatives of viral families spanning four realms and includes near-complete genome sequences of three novel viruses and fragments of five additional potentially novel viruses evolutionarily associated with insects, fungi, plants, and vertebrates. Our study provides evidence that frugivorous animals are exposed to a plethora of viruses by coincidental consumption of fig wasps, which are obligate pollinators of figs worldwide.}, } @article {pmid38245554, year = {2024}, author = {Tang, Q and Huang, H and Xu, H and Xia, H and Zhang, C and Ye, D and Bi, F}, title = {Endogenous Coriobacteriaceae enriched by a high-fat diet promotes colorectal tumorigenesis through the CPT1A-ERK axis.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {5}, pmid = {38245554}, issn = {2055-5008}, mesh = {Mice ; Animals ; Diet, High-Fat/adverse effects ; RNA, Ribosomal, 16S/genetics ; Carcinogenesis ; *Gastrointestinal Microbiome/physiology ; *Colorectal Neoplasms/etiology ; }, abstract = {A high-fat diet (HFD) may be linked to an increased colorectal cancer (CRC) risk. Stem cell proliferation and adipokine release under inflammatory and obese conditions are the main factors regulating CRC progression. Furthermore, alterations in intestinal flora have been linked to tumorigenesis and tumour progression. However, whether a HFD can promote CRC occurrence by altering intestinal flora remains unclear. The objective of this study was to identify bacterial strains enriched by a HFD and investigate the association and mechanism by which a HFD and bacterial enrichment promote CRC occurrence and development. In this study, the intestinal microbiota of mice was assessed using 16S rRNA and metagenomic sequencing. Serum metabolites of HFD-fed mice were assessed using tandem liquid chromatography-mass spectrometry. CRC cell lines and organoids were co-cultured with Coriobacteriaceae to evaluate the effect of these bacteria on the CPT1A-ERK signalling pathway. We found that Coriobacteriaceae were enriched in the colons of HFD-fed mice. An endogenous Coriobacteriaceae strain, designated as Cori.ST1911, was successfully isolated and cultured from the stools of HFD-fed mice, and the tumorigenic potential of Cori.ST1911 in CRC was validated in several CRC mouse models. Furthermore, Cori.ST1911 increased acylcarnitine levels by activating CPT1A, demonstrating the involvement of the CPT1A-ERK axis. We also found that the endogenous Lactobacillus strain La.mu730 can interfere with Cori.ST1911 colonisation and restore gut barrier function. In conclusion, we identified a novel endogenous intestinal Coriobacteriaceae, Cori.ST1911, which might lead to a new gut microbiota intervention strategy for the prevention and treatment of CRC.}, } @article {pmid38245349, year = {2024}, author = {Shama, S and Ranade, AV and Qaisar, R and Khan, NA and Tauseef, I and Elmoselhi, A and Siddiqui, R}, title = {Enhancing microbial diversity as well as multi-organ health in hind-limb unloaded mice.}, journal = {Life sciences in space research}, volume = {40}, number = {}, pages = {62-71}, doi = {10.1016/j.lssr.2023.08.006}, pmid = {38245349}, issn = {2214-5532}, mesh = {Mice ; Male ; Animals ; RNA, Ribosomal, 16S/genetics ; Culture Media, Conditioned ; Prospective Studies ; *Gastrointestinal Microbiome/genetics ; *Cyanobacteria ; }, abstract = {During space travel, the gut microbiota is changed which can lead to health-related issues. Previously, we utilized the hind-limb unloaded (HU) mouse, which is an established ground-based in-vivo model of microgravity and observed altered gut microbiota. In this study, we evaluated the beneficial effects of novel bacterial conditioned media in HU mice to understand if they can offset the effects of unloading in the HU mouse model. We aimed to explore the influence of bacterial conditioned media on diversity and quantity of intestinal microbes in HU mice, and investigated the microarchitecture of mice retinas and kidneys to evaluate the potential systemic effects of bacterial conditioned media in HU mice. Four-month-old, male C57/Bl6 mice were separated into groups: including the ground-based control group, the HU group mice fed with vehicle as placebo (HU-placebo mice), and the HU group fed with bacterial conditioned media (HU-CP mice) and kept under controlled environmental conditions for three weeks. Next, mice were sacrificed; gut dissections were conducted, and metagenomic analysis of bacterial species was performed via DNA extraction and 16S rRNA analysis. The results revealed an HU-induced reduction in intestinal microbial diversity, and an increase in pathogenic bacteria dominated by Firmicutes (45%). In contrast, supplementation with bacterial conditioned media for three weeks led to a significant increase in gut microbial diversity with noticeable changes in the OTUs abundance in the HU mice. Additionally, HU-induced muscle weakness and structural abnormalities in the retina and kidney were partially prevented with bacterial conditioned media. Moreover, a greater diversity of several bacteria in the HU-CP was observed including, Bacteriodota, Firmicutes, Proteobacteria, Actionobacteriota, Verrucomicorbiota, Cyanobacteria, Gemmatimonadota, Acidobacteriota, Chloroflexi, Myxococcota, and others. Prospective research involving molecular mechanistic studies are needed to comprehend the systemic effects of bacterial metabolites conditioned media on experimental animal models under chronic stress.}, } @article {pmid38244622, year = {2024}, author = {Coleine, C and Albanese, D and Ray, AE and Delgado-Baquerizo, M and Stajich, JE and Williams, TJ and Larsen, S and Tringe, S and Pennacchio, C and Ferrari, BC and Donati, C and Selbmann, L}, title = {Metagenomics untangles potential adaptations of Antarctic endolithic bacteria at the fringe of habitability.}, journal = {The Science of the total environment}, volume = {917}, number = {}, pages = {170290}, doi = {10.1016/j.scitotenv.2024.170290}, pmid = {38244622}, issn = {1879-1026}, mesh = {Antarctic Regions ; *Bacteria/genetics/metabolism ; Metagenome ; *Microbiota ; Metagenomics ; }, abstract = {Survival and growth strategies of Antarctic endolithic microbes residing in Earth's driest and coldest desert remain virtually unknown. From 109 endolithic microbiomes, 4539 metagenome-assembled genomes were generated, 49.3 % of which were novel candidate bacterial species. We present evidence that trace gas oxidation and atmospheric chemosynthesis may be the prevalent strategies supporting metabolic activity and persistence of these ecosystems at the fringe of life and the limits of habitability.}, } @article {pmid38244232, year = {2024}, author = {Wu, IW and Chang, LC and Wu, YL and Yang, HY and Twu, YC and Tsai, PY and Paulus, S and Resnick, R and Chung, WH and Yang, CW and Hsieh, WP and Su, SC}, title = {Gut flora metagenomic analysis coupled with metabolic and deep immune profiling in chronic kidney disease.}, journal = {Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association}, volume = {39}, number = {8}, pages = {1333-1343}, doi = {10.1093/ndt/gfae013}, pmid = {38244232}, issn = {1460-2385}, support = {MOST-110-2320-B-182A-012 -MY3//Ministry of Science and Technology/ ; BMRPE97//Chang Gung Memorial Hospital/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Renal Insufficiency, Chronic/microbiology/immunology ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Case-Control Studies ; Aged ; Metabolome ; }, abstract = {BACKGROUND: Perturbation of gut microbiota has been linked to chronic kidney disease (CKD), which was correlated with a sophisticated milieu of metabolic and immune dysregulation.

METHODS: To clarify the underlying host-microbe interaction in CKD, we performed multi-omics measurements, including systems-level gut microbiome, targeted serum metabolome and deep immunotyping, in a cohort of patients and non-CKD controls.

RESULTS: Our analyses on functional profiles of the gut microbiome showed a decrease in the diversity and abundance of carbohydrate-active enzyme (CAZyme) genes but an increase in the abundance of antibiotic resistance, nitrogen cycling enzyme and virulence factor genes in CKD. Moreover, models generated using measurements of serum metabolites (amino acids, bile acids and short-chain fatty acids) or immunotypes were predictive of renal impairment but less so than many of the functional profiles derived from gut microbiota, with the CAZyme genes being the top-performing model to accurately predict the early stage of diseases. In addition, co-occurrence analyses revealed coordinated host-microbe relationships in CKD. Specifically, the highest fractions of significant correlations were identified with circulating metabolites by several taxonomic and functional profiles of gut microbiome, while immunotype features were moderately associated with the abundance of microbiome-encoded metabolic pathways and serum levels of amino acids (e.g. B cell cluster tryptophan and B cell cluster tryptophan metabolism).

CONCLUSION: Overall, our multi-omics integration revealed several signatures of systems-level gut microbiome in robust associations with host-microbe co-metabolites and renal function, which may have aetiological and diagnostic implications in CKD.}, } @article {pmid38243750, year = {2024}, author = {Cerk, K and Ugalde-Salas, P and Nedjad, CG and Lecomte, M and Muller, C and Sherman, DJ and Hildebrand, F and Labarthe, S and Frioux, C}, title = {Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing.}, journal = {Microbial biotechnology}, volume = {17}, number = {1}, pages = {e14396}, pmid = {38243750}, issn = {1751-7915}, support = {BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Metagenome ; *Microbiota ; Metagenomics ; Sequence Analysis, DNA ; Computational Biology ; }, abstract = {Building models is essential for understanding the functions and dynamics of microbial communities. Metabolic models built on genome-scale metabolic network reconstructions (GENREs) are especially relevant as a means to decipher the complex interactions occurring among species. Model reconstruction increasingly relies on metagenomics, which permits direct characterisation of naturally occurring communities that may contain organisms that cannot be isolated or cultured. In this review, we provide an overview of the field of metabolic modelling and its increasing reliance on and synergy with metagenomics and bioinformatics. We survey the means of assigning functions and reconstructing metabolic networks from (meta-)genomes, and present the variety and mathematical fundamentals of metabolic models that foster the understanding of microbial dynamics. We emphasise the characterisation of interactions and the scaling of model construction to large communities, two important bottlenecks in the applicability of these models. We give an overview of the current state of the art in metagenome sequencing and bioinformatics analysis, focusing on the reconstruction of genomes in microbial communities. Metagenomics benefits tremendously from third-generation sequencing, and we discuss the opportunities of long-read sequencing, strain-level characterisation and eukaryotic metagenomics. We aim at providing algorithmic and mathematical support, together with tool and application resources, that permit bridging the gap between metagenomics and metabolic modelling.}, } @article {pmid38243343, year = {2024}, author = {Hu, M and Lin, X and Sun, T and Shao, X and Huang, X and Du, W and Guo, M and Zhu, X and Zhou, Y and Tong, T and Guo, F and Han, T and Wu, X and Shi, Y and Xiao, X and Zhang, Y and Hong, J and Chen, H}, title = {Gut microbiome for predicting immune checkpoint blockade-associated adverse events.}, journal = {Genome medicine}, volume = {16}, number = {1}, pages = {16}, pmid = {38243343}, issn = {1756-994X}, support = {82073115//National Natural Science Foundation of China/ ; 82002487//National Natural Science Foundation of China/ ; 81973346//National Natural Science Foundation of China/ ; 2022YFE0125300//Key Technologies Research and Development Program/ ; 2019M660142//China Postdoctoral Science Foundation/ ; }, mesh = {Humans ; *Neoplasms/drug therapy ; Immune Checkpoint Inhibitors/therapeutic use ; *Gastrointestinal Microbiome ; *Antineoplastic Agents, Immunological/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Vitamin K 2/therapeutic use ; *Drug-Related Side Effects and Adverse Reactions ; Immunotherapy/adverse effects ; Programmed Cell Death 1 Receptor ; *Immune System Diseases ; Retrospective Studies ; *Lung Neoplasms/drug therapy ; }, abstract = {BACKGROUND: The impact of the gut microbiome on the initiation and intensity of immune-related adverse events (irAEs) prompted by immune checkpoint inhibitors (ICIs) is widely acknowledged. Nevertheless, there is inconsistency in the gut microbial associations with irAEs reported across various studies.

METHODS: We performed a comprehensive analysis leveraging a dataset that included published microbiome data (n = 317) and in-house generated data from 16S rRNA and shotgun metagenome samples of irAEs (n = 115). We utilized a machine learning-based approach, specifically the Random Forest (RF) algorithm, to construct a microbiome-based classifier capable of distinguishing between non-irAEs and irAEs. Additionally, we conducted a comprehensive analysis, integrating transcriptome and metagenome profiling, to explore potential underlying mechanisms.

RESULTS: We identified specific microbial species capable of distinguishing between patients experiencing irAEs and non-irAEs. The RF classifier, developed using 14 microbial features, demonstrated robust discriminatory power between non-irAEs and irAEs (AUC = 0.88). Moreover, the predictive score from our classifier exhibited significant discriminative capability for identifying non-irAEs in two independent cohorts. Our functional analysis revealed that the altered microbiome in non-irAEs was characterized by an increased menaquinone biosynthesis, accompanied by elevated expression of rate-limiting enzymes menH and menC. Targeted metabolomics analysis further highlighted a notably higher abundance of menaquinone in the serum of patients who did not develop irAEs compared to the irAEs group.

CONCLUSIONS: Our study underscores the potential of microbial biomarkers for predicting the onset of irAEs and highlights menaquinone, a metabolite derived from the microbiome community, as a possible selective therapeutic agent for modulating the occurrence of irAEs.}, } @article {pmid38243314, year = {2024}, author = {Yang, HT and Jiang, ZH and Yang, Y and Wu, TT and Zheng, YY and Ma, YT and Xie, X}, title = {Faecalibacterium prausnitzii as a potential Antiatherosclerotic microbe.}, journal = {Cell communication and signaling : CCS}, volume = {22}, number = {1}, pages = {54}, pmid = {38243314}, issn = {1478-811X}, mesh = {Humans ; Animals ; Mice ; Faecalibacterium prausnitzii/metabolism ; Lipopolysaccharides ; *Gastrointestinal Microbiome ; *Atherosclerosis ; }, abstract = {BACKGROUND: The gut microbiota plays a crucial role in coronary artery disease (CAD) development, but limited attention has been given to the role of the microbiota in preventing this disease. This study aimed to identify key biomarkers using metagenomics and untargeted metabolomics and verify their associations with atherosclerosis.

METHODS: A total of 371 participants, including individuals with various CAD types and CAD-free controls, were enrolled. Subsequently, significant markers were identified in the stool samples through gut metagenomic sequencing and untargeted metabolomics. In vivo and in vitro experiments were performed to investigate the mechanisms underlying the association between these markers and atherosclerosis.

RESULTS: Faecal omics sequencing revealed that individuals with a substantial presence of Faecalibacterium prausnitzii had the lowest incidence of CAD across diverse CAD groups and control subjects. A random forest model confirmed the significant relationship between F. prausnitzii and CAD incidence. Notably, F. prausnitzii emerged as a robust, independent CAD predictor. Furthermore, our findings indicated the potential of the gut microbiota and gut metabolites to predict CAD occurrence and progression, potentially impacting amino acid and vitamin metabolism. F. prausnitzii mitigated inflammation and exhibited an antiatherosclerotic effect on ApoE[-/-] mice after gavage. This effect was attributed to reduced intestinal LPS synthesis and reinforced mechanical and mucosal barriers, leading to decreased plasma LPS levels and an antiatherosclerotic outcome.

CONCLUSIONS: Sequencing of the samples revealed a previously unknown link between specific gut microbiota and atherosclerosis. Treatment with F. prausnitzii may help prevent CAD by inhibiting atherosclerosis.}, } @article {pmid38243297, year = {2024}, author = {Garcia-Fernandez, H and Arenas-de Larriva, AP and Lopez-Moreno, J and Gutierrez-Mariscal, FM and Romero-Cabrera, JL and Molina-Abril, H and Torres-Peña, JD and Rodriguez-Cano, D and Malagon, MM and Ordovas, JM and Delgado-Lista, J and Perez-Martinez, P and Lopez-Miranda, J and Camargo, A}, title = {Sex-specific differences in intestinal microbiota associated with cardiovascular diseases.}, journal = {Biology of sex differences}, volume = {15}, number = {1}, pages = {7}, pmid = {38243297}, issn = {2042-6410}, support = {Cordioprev-CEAS, 1/2016//the Fundacion Patrimonio Comunal Olivarero/ ; AGL2015-67896-P//Secretaría de Estado de Investigación, Desarrollo e Innovación/ ; AGL2012/39615//Ministerio de Ciencia e Innovación/ ; PID2019-104362RB-Ioo//Ministerio de Ciencia e Innovación/ ; PIE14/00005//Instituto de Salud Carlos III/ ; PIE14/00031//Instituto de Salud Carlos III/ ; CP14/00114//Instituto de Salud Carlos III/ ; DTS19/00007//Instituto de Salud Carlos III/ ; PI22/00925//Instituto de Salud Carlos III/ ; CPII19/00007//Instituto de Salud Carlos III/ ; PI-0055-2021//Consejería de Salud y Familias, Junta de Andalucía/ ; C1-0001-2022//Servicio Andaluz de Salud/ ; }, mesh = {Male ; Humans ; Female ; *Cardiovascular Diseases/epidemiology ; *Gastrointestinal Microbiome ; Sex Characteristics ; Bacteria ; Incidence ; }, abstract = {BACKGROUND: Cardiovascular diseases (CVD), including coronary heart disease (CHD), display a higher prevalence in men than women. This study aims to evaluate the variations in the intestinal microbiota between men and women afflicted with CHD and delineate these against a non-CVD control group for each sex.

METHODS: Our research was conducted in the framework of the CORDIOPREV study, a clinical trial which involved 837 men and 165 women with CHD. We contrasted our findings with a reference group of 375 individuals (270 men, 105 women) without CVD. The intestinal microbiota was examined through 16S metagenomics on the Illumina MiSeq platform and the data processed with Quiime2 software.

RESULTS: Our results showed a sex-specific variation (beta diversity) in the intestinal microbiota, while alpha-biodiversity remained consistent across both sexes. Linear discriminant analysis effect size (LEfSe) analysis revealed sex-centric alterations in the intestinal microbiota linked to CVD. Moreover, using random forest (RF) methodology, we identified seven bacterial taxa-g_UBA1819 (Ruminococcaceae), g_Bilophila, g_Subdoligranulum, g_Phascolarctobacterium, f_Barnesiellaceae, g_Ruminococcus, and an unknown genus from the Ruminococcaceae family (Ruminococcaceae incertae sedis)-as key discriminators between men and women diagnosed with CHD. The same taxa also emerged as critical discriminators between CHD-afflicted and non-CVD individuals, when analyzed separately by sex.

CONCLUSION: Our findings suggest a sex-specific dysbiosis in the intestinal microbiota linked to CHD, potentially contributing to the sex disparity observed in CVD incidence. Trial registration Clinical Trials.gov.Identifier NCT00924937.}, } @article {pmid38242997, year = {2024}, author = {Abe, S and Masuda, A and Matsumoto, T and Inoue, J and Toyama, H and Sakai, A and Kobayashi, T and Tanaka, T and Tsujimae, M and Yamakawa, K and Gonda, M and Masuda, S and Uemura, H and Kohashi, S and Inomata, N and Nagao, K and Harada, Y and Miki, M and Irie, Y and Juri, N and Ko, T and Yokotani, Y and Oka, Y and Ota, S and Kanzawa, M and Itoh, T and Imai, T and Fukumoto, T and Hara, E and Kodama, Y}, title = {Impact of intratumoral microbiome on tumor immunity and prognosis in human pancreatic ductal adenocarcinoma.}, journal = {Journal of gastroenterology}, volume = {59}, number = {3}, pages = {250-262}, pmid = {38242997}, issn = {1435-5922}, mesh = {Humans ; RNA, Ribosomal, 16S ; *Pancreatic Neoplasms/pathology ; *Carcinoma, Pancreatic Ductal/pathology ; Prognosis ; *Microbiota ; }, abstract = {BACKGROUND: Recent evidence suggests that the presence of microbiome within human pancreatic ductal adenocarcinoma (PDAC) tissue potentially influences cancer progression and prognosis. However, the significance of tumor-resident microbiome remains unclear. We aimed to elucidate the impact of intratumoral bacteria on the pathophysiology and prognosis of human PDAC.

METHODS: The presence of intratumoral bacteria was assessed in 162 surgically resected PDACs using quantitative polymerase chain reaction (qPCR) and in situ hybridization (ISH) targeting 16S rRNA. The intratumoral microbiome was explored by 16S metagenome sequencing using DNA extracted from formalin-fixed paraffin-embedded tissues. The profile of intratumoral bacteria was compared with clinical information, pathological findings including tumor-infiltrating T cells, tumor-associated macrophage, fibrosis, and alterations in four main driver genes (KRAS, TP53, CDKN2A/p16, SMAD4) in tumor genomes.

RESULTS: The presence of intratumoral bacteria was confirmed in 52 tumors (32%) using both qPCR and ISH. The 16S metagenome sequencing revealed characteristic bacterial profiles within these tumors, including phyla such as Proteobacteria and Firmicutes. Comparison of bacterial profiles between cases with good and poor prognosis revealed a significant positive correlation between a shorter survival time and the presence of anaerobic bacteria such as Bacteroides, Lactobacillus, and Peptoniphilus. The abundance of these bacteria was correlated with a decrease in the number of tumor-infiltrating T cells positive for CD4, CD8, and CD45RO.

CONCLUSIONS: Intratumoral infection of anaerobic bacteria such as Bacteroides, Lactobacillus, and Peptoniphilus is correlated with the suppressed anti-PDAC immunity and poor prognosis.}, } @article {pmid38242941, year = {2024}, author = {Kim, G and Park, C and Yoon, YK and Park, D and Lee, JE and Lee, D and Sun, P and Park, S and Yun, C and Kang, DH and Chung, C}, title = {Prediction of lung cancer using novel biomarkers based on microbiome profiling of bronchoalveolar lavage fluid.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {1691}, pmid = {38242941}, issn = {2045-2322}, support = {NRF-2022R1C1C1007301//The Basic Science Research Program of the National Research Foundation of Korea (NRF), funded by the Ministry of Science and Technology/ ; HR22C1734//The Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea/ ; HR20C0025//The Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea/ ; }, mesh = {Humans ; *Lung Neoplasms/diagnosis/pathology ; Bronchoalveolar Lavage Fluid ; RNA, Ribosomal, 16S/genetics ; Biomarkers ; Lung/pathology ; *Lung Diseases ; *Microbiota/genetics ; }, abstract = {There is an unmet need for biomarkers for the diagnosis of lung cancer and decision criteria for lung biopsy. We comparatively investigated the lung microbiomes of patients with lung cancer and benign lung diseases. Patients who underwent bronchoscopy at Chungnam National University Hospital between June 2021 and June 2022 were enrolled. Bronchoalveolar lavage fluid (BALF) was collected from 24 patients each with lung cancer and benign lung diseases. The samples were analyzed using 16S rRNA-based metagenomic sequencing. We found that alpha diversity and the beta diversity distribution (P = 0.001) differed significantly between patients with benign lung diseases and those with lung cancer. Firmicutes was the most abundant phylum in patients with lung cancer (33.39% ± 17.439), whereas Bacteroidota was the most abundant phylum in patients with benign lung disease (31.132% ± 22.505), respectively. In differential abundance analysis, the most differentially abundant microbiota taxon was unclassified_SAR202_clade, belonging to the phylum Chloroflexi. The established prediction model distinguished patients with benign lung disease from those with lung cancer with a high accuracy (micro area under the curve [AUC] = 0.98 and macro AUC = 0.99). The BALF microbiome may be a novel biomarker for the detection of lung cancer.}, } @article {pmid38240649, year = {2024}, author = {Martínez-Ugalde, E and Ávila-Akerberg, V and González Martínez, TM and Rebollar, EA}, title = {Gene functions of the Ambystoma altamirani skin microbiome vary across space and time but potential antifungal genes are widespread and prevalent.}, journal = {Microbial genomics}, volume = {10}, number = {1}, pages = {}, pmid = {38240649}, issn = {2057-5858}, mesh = {Animals ; *Antifungal Agents ; Bacteria/genetics ; Ambystoma/genetics ; *Microbiota/genetics ; Metagenome ; }, abstract = {Amphibian skin microbiomes can play a critical role in host survival against emerging diseases by protecting their host against pathogens. While a plethora of biotic and abiotic factors have been shown to influence the taxonomic diversity of amphibian skin microbiomes it remains unclear whether functional genomic diversity varies in response to temporal and environmental factors. Here we applied a metagenomic approach to evaluate whether seasonality, distinct elevations/sites, and pathogen presence influenced the functional genomic diversity of the A. altamirani skin microbiome. We obtained a gene catalogue of 92 107 nonredundant annotated genes and a set of 50 unique metagenome assembled genomes (MAGs). Our analysis showed that genes linked to general and potential antifungal traits significantly differed across seasons and sampling locations at different elevations. Moreover, we found that the functional genomic diversity of A. altamirani skin microbiome differed between B. dendrobatidis infected and not infected axolotls only during winter, suggesting an interaction between seasonality and pathogen infection. In addition, we identified the presence of genes and biosynthetic gene clusters (BGCs) linked to potential antifungal functions such as biofilm formation, quorum sensing, secretion systems, secondary metabolite biosynthesis, and chitin degradation. Interestingly genes linked to these potential antifungal traits were mainly identified in Burkholderiales and Chitinophagales MAGs. Overall, our results identified functional traits linked to potential antifungal functions in the A. altamirani skin microbiome regardless of variation in the functional diversity across seasons, elevations/sites, and pathogen presence. Our findings suggest that potential antifungal traits found in Burkholderiales and Chitinophagales taxa could be related to the capacity of A. altamirani to survive in the presence of Bd, although further experimental analyses are required to test this hypothesis.}, } @article {pmid38239028, year = {2023}, author = {Dominguez-Lafage, C and Laganà, M and Gesbert, F and Marin-Esteban, V and Schlecht-Louf, G and Bachelerie, F and Deback, C}, title = {[The cutaneous virome: from virology to personalized medicine].}, journal = {Virologie (Montrouge, France)}, volume = {27}, number = {6}, pages = {333-354}, doi = {10.1684/vir.2023.1028}, pmid = {38239028}, issn = {1267-8694}, mesh = {Humans ; Virome ; Precision Medicine ; *Viruses/genetics ; *Bacteriophages/genetics ; Skin/microbiology ; }, abstract = {The virome of the skin, defined as all viruses detected in the skin, represents a significant part of the microbiota. A much more recent discovery than the bacterial flora, the existence of the cutaneous virome has been revealed by recent metagenomic studies. The normal human skin virome is dominated by bacteriophages, Papillomaviridae, whose genomic diversity has proved extraordinary, and Polyomaviridae. Many yet unknown viral genomes within this virome await identification. The composition of the virome of the skin has been shown to be strictly individual and relatively stable over time, resulting from adaptation to everyone's genetics, lifestyle and mechanisms of immunological tolerance finely selected over the course of evolution. Yet little studied, the virome of the skin and all its interactions with other microbiota and the host are attracting growing interest. Indeed, constitutional or acquired alterations in the homeostasis between the commensal virome and the skin, ranging from sub-clinical viral dysbiosis to severe transformation of keratinocytes or adnexal cells, have been observed. These recent observations are stimulating the search for innovative solutions aimed at measuring or even modulating its pathological expression, with a view to personalized medicine.}, } @article {pmid38238372, year = {2024}, author = {Kırdök, E and Kashuba, N and Damlien, H and Manninen, MA and Nordqvist, B and Kjellström, A and Jakobsson, M and Lindberg, AM and Storå, J and Persson, P and Andersson, B and Aravena, A and Götherström, A}, title = {Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22125}, pmid = {38238372}, issn = {2045-2322}, support = {2019-3-AP3-3729//Mersin University BAP project/ ; The Research Council of Norway project no. 231305//Pioneers of NW Europe/ ; The Research Council of Norway project no. 231305//Pioneers of NW Europe/ ; The Research Council of Norway project no. 231305//Pioneers of NW Europe/ ; The Research Council of Norway project no. 231305//Pioneers of NW Europe/ ; project no. 2019-00849//The Swedish Research Council/ ; }, mesh = {Animals ; Humans ; Dysbiosis/genetics ; Metagenome ; *Microbiota/genetics ; Oral Health ; *Periodontitis/genetics ; }, abstract = {Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890-9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70-80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.}, } @article {pmid38237031, year = {2024}, author = {Khan, R and Di Gesù, CM and Lee, J and McCullough, LD}, title = {The contribution of age-related changes in the gut-brain axis to neurological disorders.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2302801}, pmid = {38237031}, issn = {1949-0984}, support = {R01 NS094543/NS/NINDS NIH HHS/United States ; R01 NS103592/NS/NINDS NIH HHS/United States ; R35 NS132265/NS/NINDS NIH HHS/United States ; 857947/AHA/American Heart Association-American Stroke Association/United States ; }, mesh = {Humans ; Brain-Gut Axis ; *Gastrointestinal Microbiome/physiology ; *Nervous System Diseases ; Brain/metabolism ; *Parkinson Disease ; }, abstract = {Trillions of microbes live symbiotically in the host, specifically in mucosal tissues such as the gut. Recent advances in metagenomics and metabolomics have revealed that the gut microbiota plays a critical role in the regulation of host immunity and metabolism, communicating through bidirectional interactions in the microbiota-gut-brain axis (MGBA). The gut microbiota regulates both gut and systemic immunity and contributes to the neurodevelopment and behaviors of the host. With aging, the composition of the microbiota changes, and emerging studies have linked these shifts in microbial populations to age-related neurological diseases (NDs). Preclinical studies have demonstrated that gut microbiota-targeted therapies can improve behavioral outcomes in the host by modulating microbial, metabolomic, and immunological profiles. In this review, we discuss the pathways of brain-to-gut or gut-to-brain signaling and summarize the role of gut microbiota and microbial metabolites across the lifespan and in disease. We highlight recent studies investigating 1) microbial changes with aging; 2) how aging of the maternal microbiome can affect offspring health; and 3) the contribution of the microbiome to both chronic age-related diseases (e.g., Parkinson's disease, Alzheimer's disease and cerebral amyloidosis), and acute brain injury, including ischemic stroke and traumatic brain injury.}, } @article {pmid38233815, year = {2024}, author = {Song, L and Feng, Z and Zhou, Q and Wu, X and Zhang, L and Sun, Y and Li, R and Chen, H and Yang, F and Yu, Y}, title = {Metagenomic analysis of healthy and diseased peri-implant microbiome under different periodontal conditions: a cross-sectional study.}, journal = {BMC oral health}, volume = {24}, number = {1}, pages = {105}, pmid = {38233815}, issn = {1472-6831}, support = {2020MZYS08//high-level professional physician training program of Minhang District/ ; 201940382//Shanghai Municipal Planning Commission of Science and Research Fund/ ; 82170990//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Peri-Implantitis/microbiology ; *Dental Implants/microbiology ; Cross-Sectional Studies ; *Periodontitis ; *Microbiota ; *Dental Plaque/microbiology ; *Periodontal Diseases ; }, abstract = {BACKGROUND: Peri-implantitis is a polybacterial infection that can lead to the failure of dental implant rehabilitation. This study aimed to profile the microbiome of the peri-implant plaque and estimate the effect of periodontitis on it among 40 Chinese participants with dental implant prostheses and presenting with varying peri-implant and periodontal health states.

METHODS: Submucosal plaque samples were collected from four distinct clinical categories based on both their implant and periodontal health status at sampling point. Clinical examinations of dental implant and remaining teeth were carried out. Metagenomic analysis was then performed.

RESULTS: The microbiome of the peri-implantitis sites differed from that of healthy implant sites, both taxonomically and functionally. Moreover, the predominant species in peri-implantitis sites were slightly affected by the presence of periodontitis. T. forsythia, P. gingivalis, T. denticola, and P. endodontalis were consistently associated with peri-implantitis and inflammatory clinical parameters regardless of the presence of periodontitis. Prevotella spp. and P. endodontalis showed significant differences in the peri-implantitis cohorts under different periodontal conditions. The most distinguishing function between diseased and healthy implants is related to flagellar assembly, which plays an important role in epithelial cell invasion.

CONCLUSIONS: The composition of the peri-implant microbiome varied in the diseased and healthy states of implants and is affected by individual periodontal conditions. Based on their correlations with clinical parameters, certain species are associated with disease and healthy implants. Flagellar assembly may play a vital role in the process of peri-implantitis.}, } @article {pmid38233502, year = {2024}, author = {Chopra, A and Franco-Duarte, R and Rajagopal, A and Choowong, P and Soares, P and Rito, T and Eberhard, J and Jayasinghe, TN}, title = {Exploring the presence of oral bacteria in non-oral sites of patients with cardiovascular diseases using whole metagenomic data.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {1476}, pmid = {38233502}, issn = {2045-2322}, support = {2022.00340.CEECIND//Fundação para a Ciência e a Tecnologia/ ; "Contrato-Programa" UIDB/04050/2020//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {Humans ; *Cardiovascular Diseases ; *Microbiota/genetics ; Bacteria/genetics ; Metagenome ; *Plaque, Atherosclerotic ; }, abstract = {Cardiovascular diseases (CVDs) encompass various conditions affecting the heart and its blood vessels and are often linked with oral microbes. Our data analysis aimed to identify oral bacteria from other non-oral sites (i.e., gut, arterial plaque and cultured blood) that could be linked with CVDs. Taxonomic profiling identified bacteria to the species level and compared with the Human Oral Microbiome Database (HOMD). The oral bacteria in the gut, cultured blood and arterial plaque samples were catalogued, with their average frequency calculated for each sample. Additionally, data were filtered by comparison with the Human Microbiome Project (HMP) database. We identified 17,243 microbial species, of which 410 were present in the HOMD database and further denominated as "oral", and were found in at least one gut sample, but only 221 and 169 species were identified in the cultured blood and plaque samples, respectively. Of the 410 species, 153 were present solely in oral-associated environments after comparison with the HMP database, irrespective of their presence in other body sites. Our results suggest a potential connection between the presence of specific species of oral bacterial and occurrence of CVDs. Detecting these oral bacterial species in non-oral sites of patients with CVDs could help uncover the link between oral health and general health, including cardiovascular conditions via bacterial translocation.}, } @article {pmid38233447, year = {2024}, author = {Valencia, EM and Maki, KA and Dootz, JN and Barb, JJ}, title = {Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {81}, pmid = {38233447}, issn = {2052-4463}, mesh = {Bacteria/genetics ; *Gastrointestinal Microbiome ; *Metagenome ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Shotgun metagenomic sequencing comprehensively samples the DNA of a microbial sample. Choosing the best bioinformatics processing package can be daunting due to the wide variety of tools available. Here, we assessed publicly available shotgun metagenomics processing packages/pipelines including bioBakery, Just a Microbiology System (JAMS), Whole metaGenome Sequence Assembly V2 (WGSA2), and Woltka using 19 publicly available mock community samples and a set of five constructed pathogenic gut microbiome samples. Also included is a workflow for labelling bacterial scientific names with NCBI taxonomy identifiers for better resolution in assessing results. The Aitchison distance, a sensitivity metric, and total False Positive Relative Abundance were used for accuracy assessments for all pipelines and mock samples. Overall, bioBakery4 performed the best with most of the accuracy metrics, while JAMS and WGSA2, had the highest sensitivities. Furthermore, bioBakery is commonly used and only requires a basic knowledge of command line usage. This work provides an unbiased assessment of shotgun metagenomics packages and presents results assessing the performance of the packages using mock community sequence data.}, } @article {pmid38231673, year = {2024}, author = {Sung, C and Park, CG and Maienschein-Cline, M and Chlipala, G and Green, S and Doorenbos, A and Fink, A and Bronas, U and Lockwood, M}, title = {Associations Between Gut Microbial Features and Sickness Symptoms in Kidney Transplant Recipients.}, journal = {Biological research for nursing}, volume = {26}, number = {3}, pages = {368-379}, doi = {10.1177/10998004241227560}, pmid = {38231673}, issn = {1552-4175}, mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Gastrointestinal Microbiome ; Male ; Female ; Prospective Studies ; Middle Aged ; Longitudinal Studies ; Adult ; Cross-Sectional Studies ; Transplant Recipients/statistics & numerical data ; Feces/microbiology ; }, abstract = {PURPOSE: The study investigated the relationship of gut microbiome features and sickness symptoms in kidney transplant recipients.

METHODS: Employing a prospective, longitudinal design, we collected data from 19 participants who had undergone living-donor kidney transplant at three timepoints (pre-transplant and 1 week and 3 months post-transplant). Sickness symptom data and fecal specimens were collected at each timepoint. Participants were grouped either as high or low sickness symptom severity at baseline. Shotgun metagenomics sequencing characterized gut microbial structure and functional gene content. Fecal microbial features, including alpha (evenness and richness within samples) and beta (dissimilarities between samples) diversity and relative abundances, were analyzed using R statistical packages. Cross-sectional and longitudinal analyses examined relationships between gut microbial features and sickness symptoms.

RESULTS: Although our exploratory findings revealed no significant differences in alpha and beta diversity between groups, the high-severity group showed lower microbial richness and evenness than the low-severity group. The high-severity group had enriched relative abundance of bacteria from the genera Citrobacter and Enterobacter and reduced relative abundance of bacteria from the genus Akkermansia across timepoints. No functional genes differed significantly between groups or timepoints.

CONCLUSIONS: Kidney transplant recipients with high symptom burden displayed increased putative proinflammatory bacteria and decreased beneficial bacteria. This study provides an effect size that future large cohort studies can employ to confirm associations between gut microbial features and sickness symptom experiences in the kidney transplant population. The study findings also have implications for future interventional studies aiming to alleviate the sickness symptom burden in this population.}, } @article {pmid38231265, year = {2024}, author = {Yu, SJ and Morris, A and Kayal, A and Milošević, I and Van, TTH and Bajagai, YS and Stanley, D}, title = {Pioneering gut health improvements in piglets with phytogenic feed additives.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {142}, pmid = {38231265}, issn = {1432-0614}, mesh = {Animals ; Swine ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; *Microbiota ; Anti-Bacterial Agents ; *Fluorocarbons ; }, abstract = {This research investigates the effects of phytogenic feed additives (PFAs) on the growth performance, gut microbial community, and microbial metabolic functions in weaned piglets via a combined 16S rRNA gene amplicon and shotgun metagenomics approach. A controlled trial was conducted using 200 pigs to highlight the significant influence of PFAs on gut microbiota dynamics. Notably, the treatment group revealed an increased gut microbiota diversity, as measured with the Shannon and Simpson indices. The increase in diversity is accompanied by an increase in beneficial bacterial taxa, such as Roseburia, Faecalibacterium, and Prevotella, and a decline in potential pathogens like Clostridium sensu stricto 1 and Campylobacter. Shotgun sequencing at the species level confirmed these findings. This modification in microbial profile was coupled with an altered profile of microbial metabolic pathways, suggesting a reconfiguration of microbial function under PFA influence. Significant shifts in overall microbial community structure by week 8 demonstrate PFA treatment's temporal impact. Histomorphological examination unveiled improved gut structure in PFA-treated piglets. The results of this study indicate that the use of PFAs as dietary supplements can be an effective strategy, augmenting gut microbiota diversity, reshaping microbial function, enhancing gut structure, and optimising intestinal health of weaned piglets providing valuable implications for swine production. KEY POINTS: • PFAs significantly diversify the gut microbiota in weaned piglets, aiding balance. • Changes in gut structure due to PFAs indicate improved resistance to weaning stress. • PFAs show potential to ease weaning stress, offering a substitute for antibiotics in piglet diets.}, } @article {pmid38230938, year = {2024}, author = {Marinos, G and Hamerich, IK and Debray, R and Obeng, N and Petersen, C and Taubenheim, J and Zimmermann, J and Blackburn, D and Samuel, BS and Dierking, K and Franke, A and Laudes, M and Waschina, S and Schulenburg, H and Kaleta, C}, title = {Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics.}, journal = {Microbiology spectrum}, volume = {12}, number = {2}, pages = {e0114423}, pmid = {38230938}, issn = {2165-0497}, support = {P40 OD010440/OD/NIH HHS/United States ; DP2 DK116645/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Prebiotics ; Caenorhabditis elegans ; *Microbiota ; Serine ; *Pseudomonas ; }, abstract = {While numerous health-beneficial interactions between host and microbiota have been identified, there is still a lack of targeted approaches for modulating these interactions. Thus, we here identify precision prebiotics that specifically modulate the abundance of a microbiome member species of interest. In the first step, we show that defining precision prebiotics by compounds that are only taken up by the target species but no other species in a community is usually not possible due to overlapping metabolic niches. Subsequently, we use metabolic modeling to identify precision prebiotics for a two-member Caenorhabditis elegans microbiome community comprising the immune-protective target species Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71. We experimentally confirm four of the predicted precision prebiotics, L-serine, L-threonine, D-mannitol, and γ-aminobutyric acid, to specifically increase the abundance of MYb11. L-serine was further assessed in vivo, leading to an increase in MYb11 abundance also in the worm host. Overall, our findings demonstrate that metabolic modeling is an effective tool for the design of precision prebiotics as an important cornerstone for future microbiome-targeted therapies.IMPORTANCEWhile various mechanisms through which the microbiome influences disease processes in the host have been identified, there are still only few approaches that allow for targeted manipulation of microbiome composition as a first step toward microbiome-based therapies. Here, we propose the concept of precision prebiotics that allow to boost the abundance of already resident health-beneficial microbial species in a microbiome. We present a constraint-based modeling pipeline to predict precision prebiotics for a minimal microbial community in the worm Caenorhabditis elegans comprising the host-beneficial Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71 with the aim to boost the growth of MYb11. Experimentally testing four of the predicted precision prebiotics, we confirm that they are specifically able to increase the abundance of MYb11 in vitro and in vivo. These results demonstrate that constraint-based modeling could be an important tool for the development of targeted microbiome-based therapies against human diseases.}, } @article {pmid38230927, year = {2024}, author = {Wang, Q and Wang, B-Y and Pratap, S and Xie, H}, title = {Oral microbiome associated with differential ratios of Porphyromonas gingivalis and Streptococcus cristatus.}, journal = {Microbiology spectrum}, volume = {12}, number = {2}, pages = {e0348223}, pmid = {38230927}, issn = {2165-0497}, support = {R16 GM149359/GM/NIGMS NIH HHS/United States ; U54 MD007586/MD/NIMHD NIH HHS/United States ; }, mesh = {Humans ; Porphyromonas gingivalis/genetics ; *Dental Plaque ; *Periodontitis ; *Microbiota ; *Streptococcus ; }, abstract = {Periodontitis has recently been defined as a dysbiotic disease caused by an imbalanced oral microbiota. The transition from commensal microbial communities to periodontitis-associated ones requires colonization by specific pathogens, including Porphyromonas gingivalis. We previously reported an antagonistic relationship between Streptococcus cristatus and P. gingivalis. To determine the role of S. cristatus in altering the interactions of P. gingivalis with other oral bacteria in a complex context, we collected dental plaque samples from patients with periodontitis and assigned them to two groups based on the ratios of S. cristatus and P. gingivalis. We then characterized the microbial profiles of the dental plaque samples using shotgun metagenomic sequencing and compared the oral microbial composition and functional capabilities of the group with high S. cristatus-P. gingivalis ratios with the low ratio group. Taxonomic annotation revealed significant differences in the microbial composition at both the genus and species levels between the low and high S. cristatus-P. gingivalis ratio groups. Notably, a higher microbial diversity was observed in the samples with low S. cristatus-P. gingivalis ratios. Furthermore, the antibiotic resistance gene profiles of the two groups were also distinct, with a significantly increased abundance of the genes in the dental plaque samples with low S. cristatus-P. gingivalis ratios. It, therefore, indicates that the S. cristatus-P. gingivalis ratios influenced the virulence potential of the oral microbiome. Our work shows that enhancing the S. cristatus-P. gingivalis ratio in oral microbial communities can be an attractive approach for revising the dysbiotic oral microbiome.IMPORTANCEPeriodontitis, one of the most common chronic diseases, is linked to several systemic diseases, such as cardiovascular disease and diabetes. Although Porphyromonas gingivalis is a keystone pathogen that causes periodontitis, its levels, interactions with accessory bacteria and pathobionts in the oral microbiome, and its association with the pathogenic potential of the microbial communities are still not well understood. In this study, we revealed the role of Streptococcus cristatus and the ratios of S. cristatus and P. gingivalis in modulating the oral microbiome to facilitate a deeper understanding of periodontitis and its progression. The study has important clinical implications as it laid a foundation for developing novel non-antibiotic therapies against P. gingivalis and improving the efficiency of periodontal treatments.}, } @article {pmid38230544, year = {2024}, author = {Yegin, Z and Mamatova, Z and Yurt, MNZ and Tasbasi, BB and Acar, EE and Ucak, S and Süleymanoğlu, AA and Aydin, A and Ozalp, VC and Sudagidan, M}, title = {A metagenomic survey of bacterial communities from kurut: The fermented cow milk in Kyrgyzstan.}, journal = {Chemistry & biodiversity}, volume = {21}, number = {2}, pages = {e202301374}, doi = {10.1002/cbdv.202301374}, pmid = {38230544}, issn = {1612-1880}, mesh = {Animals ; Cattle ; Female ; *Milk/microbiology ; Kyrgyzstan ; *Bacteria ; Lactobacillus ; Streptococcus ; }, abstract = {Kurut is a traditional dry dairy product mostly consumed in Central Asia. In this study, the distribution of the dominant bacteria present in kurut samples (n=84) originated from seven (Chuy, Issyk-Kul, Talas, Naryn, Jalal-Abad, Osh, and Batken) regions in Kyrgyzstan were analyzed with Illumina iSeq100 platform. The dominant phylum detected was Firmicutes followed by Proteobacteria, Actinobacteria, Cyanobacteria/Chloroplast, and Tenericutes. The most abundant family detected was Lactobacillaceae followed by Streptococcaceae, Enterococcaceae, Chloroplast, and Leuconostocaceae. At the genus level, Lactobacillus was the predominant one in samples and Streptococcus, Enterococcus, Lactococcus, and Streptophyta followed this. Further comprehensive characterization analyses in kurut samples may have potential applications both in industrial starter culture developments and also future therapeutic approaches based on potential strains with probiotic properties.}, } @article {pmid38229335, year = {2024}, author = {Venkatachalam, S and Jabir, T and Vipindas, PV and Krishnan, KP}, title = {Ecological significance of Candidatus ARS69 and Gemmatimonadota in the Arctic glacier foreland ecosystems.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {128}, pmid = {38229335}, issn = {1432-0614}, mesh = {Phylogeny ; *Ice Cover ; Bacteria/genetics ; Metagenome ; *Microbiota ; }, abstract = {The Gemmatimonadota phylum has been widely detected in diverse natural environments, yet their specific ecological roles in many habitats remain poorly investigated. Similarly, the Candidatus ARS69 phylum has been identified only in a few habitats, and literature on their metabolic functions is relatively scarce. In the present study, we investigated the ecological significance of phyla Ca. ARS69 and Gemmatimonadota in the Arctic glacier foreland (GF) ecosystems through genome-resolved metagenomics. We have reconstructed the first high-quality metagenome-assembled genome (MAG) belonging to Ca. ARS69 and 12 other MAGs belonging to phylum Gemmatimonadota from the three different Arctic GF samples. We further elucidated these two groups phylogenetic lineage and their metabolic function through phylogenomic and pangenomic analysis. The analysis showed that all the reconstructed MAGs potentially belonged to novel species. The MAGs belonged to Ca. ARS69 consist about 8296 gene clusters, of which only about 8% of single-copy core genes (n = 980) were shared among them. The study also revealed the potential ecological role of Ca. ARS69 is associated with carbon fixation, denitrification, sulfite oxidation, and reduction biochemical processes in the GF ecosystems. Similarly, the study demonstrates the widespread distribution of different classes of Gemmatimonadota across wide ranges of ecosystems and their metabolic functions, including in the polar region. KEY POINTS: • Glacier foreland ecosystems act as a natural laboratory to study microbial community structure. • We have reconstructed 13 metagenome-assembled genomes from the soil samples. • All the reconstructed MAGs belonged to novel species with different metabolic processes. • Ca. ARS69 and Gemmatimonadota MAGs were found to participate in carbon fixation and denitrification processes.}, } @article {pmid38229330, year = {2024}, author = {Zhang, Z and Bao, C and Li, Z and He, C and Jin, W and Li, C and Chen, Y}, title = {Integrated omics analysis reveals the alteration of gut microbiota and fecal metabolites in Cervus elaphus kansuensis.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {125}, pmid = {38229330}, issn = {1432-0614}, support = {2021-JS-02//Science and Technology Innovation Project of Three RiverSource First-class Discipline, College of Eco-Environment Engineering, Qinghai University/ ; 2021-BS-093//Doctoral Scientific Research Start-up Foundation of Qinghai University/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Chromatography, Liquid ; *Deer ; Tandem Mass Spectrometry ; *Bacillus/genetics ; DNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {The gut microbiota is the largest and most complex microecosystem in animals. It is influenced by the host's dietary habits and living environment, and its composition and diversity play irreplaceable roles in animal nutrient metabolism, immunity, and adaptation to the environment. Although the gut microbiota of red deer has been studied, the composition and function of the gut microbiota in Gansu red deer (Cervus elaphus kansuensis), an endemic subspecies of red deer in China, has not been reported. In this study, the composition and diversity of the gut microbiome and fecal metabolomics of C. elaphus kansuensis were identified and compared for the first time by using 16S rDNA sequencing, metagenomic sequencing, and LC-MS/MS. There were significant differences in gut microbiota structure and diversity between wild and farmed C. elaphus kansuensis. The 16S rDNA sequencing results showed that the genus UCRD-005 was dominant in both captive red deer (CRD) and wild red deer (WRD). Metagenomic sequencing showed similar results to those of 16S rDNA sequencing for gut microbiota in CRD and WRD at the phylum and genus levels. 16S rDNA and metagenomics sequencing data suggested that Bacteroides and Bacillus might serve as marker genera for CRD and WRD, respectively. Fecal metabolomics results showed that 520 metabolites with significant differences were detected between CRD and WRD and most differential metabolites were involved in lipid metabolism. The results suggested that large differences in gut microbiota composition and fecal metabolites between CRD and WRD, indicating that different dietary habits and living environments over time have led to the development of stable gut microbiome characteristics for CRD and WRD to meet their respective survival and reproduction needs. KEY POINTS: • Environment and food affected the gut microbiota and fecal metabolites in red deer • Genera Bacteroides and Bacillus may play important roles in CRD and WRD, respectively • Flavonoids and ascorbic acid in fecal metabolites may influence health of red deer.}, } @article {pmid38228744, year = {2024}, author = {Adeniyi-Ipadeola, GO and Hoffman, KL and Yang, H and Javornik Cregeen, SJ and Preidis, GA and Ramani, S and Hair, AB}, title = {Human milk cream alters intestinal microbiome of preterm infants: a prospective cohort study.}, journal = {Pediatric research}, volume = {95}, number = {6}, pages = {1564-1571}, pmid = {38228744}, issn = {1530-0447}, support = {R25 GM056929/GM/NIGMS NIH HHS/United States ; T32 GM152777/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Milk, Human ; Infant, Newborn ; Prospective Studies ; *Infant, Premature ; *Infant, Very Low Birth Weight ; Female ; Male ; Food, Fortified ; Feces/microbiology ; Proteobacteria ; Dietary Supplements ; Infant Nutritional Physiological Phenomena ; }, abstract = {BACKGROUND: In very low birth weight (VLBW) infants, human milk cream added to standard human milk fortification is used to improve growth. This study aimed to evaluate the impact of cream supplement on the intestinal microbiome of VLBW infants.

METHODS: Whole genome shotgun sequencing was performed on stool (n = 57) collected from a cohort of 23 infants weighing 500-1250 grams (control = 12, cream = 11). Both groups received an exclusive human milk diet (mother's own milk, donor human milk, and donor human milk-derived fortifier) with the cream group receiving an additional 2 kcal/oz cream at 100 mL/kg/day of fortified feeds and then 4 kcal/oz if poor growth.

RESULTS: While there were no significant differences in alpha diversity, infants receiving cream significantly differed from infants in the control group in beta diversity. Cream group samples had significantly higher prevalence of Proteobacteria and significantly lower Firmicutes compared to control group. Klebsiella species dominated the microbiota of cream-exposed infants, along with bacterial pathways involved in lipid metabolism and metabolism of cofactors and amino acids.

CONCLUSIONS: Cream supplementation significantly altered composition of the intestinal microbiome of VLBW infants to favor increased prevalence of Proteobacteria and functional gene content associated with these bacteria.

IMPACT: We report changes to the intestinal microbiome associated with administration of human milk cream; a novel supplement used to improve growth rates of preterm very low birth weight infants. Since little is known about the impact of cream on intestinal microbiota composition of very low birth weight infants, our study provides valuable insight on the effects of diet on the microbiome of this population. Dietary supplements administered to preterm infants in neonatal intensive care units have the potential to influence the intestinal microbiome composition which may affect overall health status of the infant.}, } @article {pmid38228614, year = {2024}, author = {Rashidi, A and Gem, H and McLean, JS and Kerns, K and Dean, DR and Dey, N and Minot, S}, title = {Multi-cohort shotgun metagenomic analysis of oral and gut microbiota overlap in healthy adults.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {75}, pmid = {38228614}, issn = {2052-4463}, mesh = {Adult ; Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Microbiota/genetics ; Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The multitude of barriers between the mouth and colon may eliminate swallowed oral bacteria. Ascertaining the presence of the same bacteria in the mouth and colon is methodologically challenging partly because 16S rRNA gene sequencing - the most commonly used method to characterize the human microbiota - has low confidence in taxonomic assignments deeper than genus for most bacteria. As different species of the same genus can have low-level variation across the same 16S rRNA gene region, shotgun sequencing is needed to identify a true overlap. We analyzed a curated, multi-cohort, shotgun metagenomic database with species-level taxonomy and clade-specific marker genes to fill this knowledge gap. Using 500 paired fecal/oral (4 oral sites) samples from 4 healthy adult cohorts, we found a minute overlap between the two niches. Comparing marker genes between paired oral and fecal samples with species-level overlap, the pattern of overlap in only 7 individuals was consistent with same-strain colonization. These findings argue against ectopic colonization of oral bacteria in the distal gut in healthy adults.}, } @article {pmid38228587, year = {2024}, author = {Viver, T and Conrad, RE and Rodriguez-R, LM and Ramírez, AS and Venter, SN and Rocha-Cárdenas, J and Llabrés, M and Amann, R and Konstantinidis, KT and Rossello-Mora, R}, title = {Towards estimating the number of strains that make up a natural bacterial population.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {544}, pmid = {38228587}, issn = {2041-1723}, support = {1831582//National Science Foundation (NSF)/ ; 2129823//National Science Foundation (NSF)/ ; PGC2018-096956-B-C41//Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)/ ; PID2021-126114NB-C42//Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)/ ; }, mesh = {*Bacteria/genetics ; *Bacteroidetes/genetics ; Metagenomics/methods ; Metagenome/genetics ; Phylogeny ; Genome, Bacterial/genetics ; }, abstract = {What a strain is and how many strains make up a natural bacterial population remain elusive concepts despite their apparent importance for assessing the role of intra-population diversity in disease emergence or response to environmental perturbations. To advance these concepts, we sequenced 138 randomly selected Salinibacter ruber isolates from two solar salterns and assessed these genomes against companion short-read metagenomes from the same samples. The distribution of genome-aggregate average nucleotide identity (ANI) values among these isolates revealed a bimodal distribution, with four-fold lower occurrence of values between 99.2% and 99.8% relative to ANI >99.8% or <99.2%, revealing a natural "gap" in the sequence space within species. Accordingly, we used this ANI gap to define genomovars and a higher ANI value of >99.99% and shared gene-content >99.0% to define strains. Using these thresholds and extrapolating from how many metagenomic reads each genomovar uniquely recruited, we estimated that -although our 138 isolates represented about 80% of the Sal. ruber population- the total population in one saltern pond is composed of 5,500 to 11,000 genomovars, the great majority of which appear to be rare in-situ. These data also revealed that the most frequently recovered isolate in lab media was often not the most abundant genomovar in-situ, suggesting that cultivation biases are significant, even in cases that cultivation procedures are thought to be robust. The methodology and ANI thresholds outlined here should represent a useful guide for future microdiversity surveys of additional microbial species.}, } @article {pmid38228159, year = {2024}, author = {Nenciarini, S and Renzi, S and di Paola, M and Meriggi, N and Cavalieri, D}, title = {Ascomycetes yeasts: The hidden part of human microbiome.}, journal = {WIREs mechanisms of disease}, volume = {16}, number = {3}, pages = {e1641}, doi = {10.1002/wsbm.1641}, pmid = {38228159}, issn = {2692-9368}, support = {G84I18000160002//Regione Toscana/ ; 36954/7303/18//Ministero delle Politiche Agricole Alimentari e Forestali/ ; 529051018//Joint Programming Initiative A healthy diet for a healthy life/ ; JTC-2017-7//Joint Programming Initiative A healthy diet for a healthy life/ ; }, mesh = {Humans ; *Ascomycota/genetics ; Mycobiome/genetics ; Microbiota ; Metagenomics/methods ; Candida/genetics/isolation & purification ; Gastrointestinal Microbiome ; }, abstract = {The fungal component of the microbiota, the mycobiota, has been neglected for a long time due to its poor richness compared to bacteria. Limitations in fungal detection and taxonomic identification arise from using metagenomic approaches, often borrowed from bacteriome analyses. However, the relatively recent discoveries of the ability of fungi to modulate the host immune response and their involvement in human diseases have made mycobiota a fundamental component of the microbial communities inhabiting the human host, deserving some consideration in host-microbe interaction studies and in metagenomics. Here, we reviewed recent data on the identification of yeasts of the Ascomycota phylum across human body districts, focusing on the most representative genera, that is, Saccharomyces and Candida. Then, we explored the key factors involved in shaping the human mycobiota across the lifespan, ranging from host genetics to environment, diet, and lifestyle habits. Finally, we discussed the strengths and weaknesses of culture-dependent and independent methods for mycobiota characterization. Overall, there is still room for some improvements, especially regarding fungal-specific methodological approaches and bioinformatics challenges, which are still critical steps in mycobiota analysis, and to advance our knowledge on the role of the gut mycobiota in human health and disease. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Environmental Factors Infectious Diseases > Environmental Factors.}, } @article {pmid38227799, year = {2024}, author = {Kai, N and Qingsong, C and Kejia, M and Weiwei, L and Xing, W and Xuejie, C and Lixia, C and Minzi, D and Yuanyuan, Y and Xiaoyan, W}, title = {An Inflammatory Bowel Diseases Integrated Resources Portal (IBDIRP).}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {38227799}, issn = {1758-0463}, support = {82300636//National Natural Science Foundation of China/ ; 2023JJ40898//Young Hunan Natural Science Foundation (HNSF)/ ; 82300636//National Natural Science Foundation of China/ ; 2023JJ40898//Young Hunan Natural Science Foundation (HNSF)/ ; }, mesh = {Humans ; *Inflammatory Bowel Diseases/genetics ; *Crohn Disease/genetics ; *Colitis, Ulcerative/genetics ; *Microbiota ; Gene Expression Profiling ; }, abstract = {IBD, including ulcerative colitis and Crohn's disease, is a chronic and debilitating gastrointestinal disorder that affects millions of people worldwide. Research on IBD has generated massive amounts of data, including literature, metagenomics, metabolomics, bioresources and databases. We aim to create an IBD Integrated Resources Portal (IBDIRP) that provides the most comprehensive resources for IBD. An integrated platform was developed that provides information on different aspects of IBD research resources, such as single-nucleotide polymorphisms (SNPs), genes, transcriptome, microbiota, metabolomics, single cells and other resources. Valuable and comprehensive IBD-related data were collected from PubMed, Google, GMrepo, gutMega, gutMDisorder, Single Cell Portal and other sources. Then, the data were systematically sorted, and these resources were manually curated. We systematically sorted and cataloged more than 320 unique risk SNPs associated with IBD in the SNP section. We presented over 289 IBD-related genes based on the database collection in the gene section. We also obtained 153 manually curated IBD transcriptomics data, including 12 388 samples, on the Gene Expression Omnibus database. The sorted IBD-related microbiota data from three primary microbiome databases (GMrepo, gutMega and gutMDisorder) were available for download. We selected 23 149 IBD-related taxonomic records from these databases. Additionally, we collected 24 IBD metabolomics studies with 2896 participants in the metabolomics section. We introduced two interactive single-cell data plug-in units that provided data visualization based on cells and genes. Finally, we listed 18 significant IBD web resources, such as the official European Crohn's and Colitis Organisation and International Organization for the Study of IBD websites, IBD scoring tools, IBD genetic and multi-omics resources, IBD biobanks and other useful research resources. The IBDIRP website is the first integrated resource for global IBD researchers. This portal will help researchers by providing comprehensive knowledge and enabling them to reinforce the multidimensional impression of IBD. The IBDIRP website is accessible via www.ibdirp.com Database URL: www.ibdirp.com.}, } @article {pmid38225124, year = {2024}, author = {Chang, H and Gu, C and Wang, M and Chang, Z and Zhou, J and Yue, M and Chen, J and Qin, X and Feng, Z}, title = {Integrating shotgun metagenomics and metabolomics to elucidate the dynamics of microbial communities and metabolites in fine flavor cocoa fermentation in Hainan.}, journal = {Food research international (Ottawa, Ont.)}, volume = {177}, number = {}, pages = {113849}, doi = {10.1016/j.foodres.2023.113849}, pmid = {38225124}, issn = {1873-7145}, mesh = {Fermentation ; Bacteria ; *Chocolate ; *Cacao/metabolism ; *Microbiota ; }, abstract = {The aim of this study was to investigate the dynamic profile of microorganisms and metabolites in Hainan Trinitario cocoa during a six-day spontaneous box fermentation process. Shotgun metagenomic and metabolomic approaches were employed for this investigation. The potential metabolic functions of microorganisms in cocoa fermentation were revealed through a joint analysis of microbes, functional genes, and metabolites. During the anaerobic fermentation phase, Hanseniaspora emerged as the most prevalent yeast genus, implicated in pectin decomposition and potentially involved in glycolysis and starch and sucrose metabolism. Tatumella, possessing potential for pyruvate kinase, and Fructobacillus with a preference for fructose, constituted the primary bacteria during the pre-turning fermentation stage. Upon the introduction of oxygen into the fermentation mass, acetic acid bacteria ascended to dominant within the microflora. The exponential proliferation of Acetobacter resulted in a decline in taxonomic richness and abundance. Moreover, the identification of novel species within the Komagataeibacter genus suggests that Hainan cocoa may serve as a valuable reservoir for the discovery of unique cocoa fermentation bacteria. The KEGG annotation of metabolites and enzymes also highlighted the significant involvement of phenylalanine metabolism in cocoa fermentation. This research will offer a new perspective for the selection of starter strains and the formulation of mixed starter cultures.}, } @article {pmid38225117, year = {2024}, author = {Xiang, Y and Zhou, B and Jiang, C and Tang, Z and Liu, P and Ding, W and Lin, H and Tang, J}, title = {Revealing the formation mechanisms of key flavors in fermented broad bean paste.}, journal = {Food research international (Ottawa, Ont.)}, volume = {177}, number = {}, pages = {113880}, doi = {10.1016/j.foodres.2023.113880}, pmid = {38225117}, issn = {1873-7145}, mesh = {*Fabaceae/genetics ; *Vicia faba ; *Microbiota/genetics ; Metagenome ; Fermentation ; Aspergillus flavus/genetics ; *Lactobacillus ; }, abstract = {Pixian Douban (PXDB) is a popular Chinese condiment for its distinctive flavor. Broad bean fermentation (Meju) is the most important process in the formation of flavor substances. Key flavors were analyzed qualitatively and quantitatively, and metagenomic technology was applied to study the microbial diversity during broad bean fermentation. In addition, the main metabolic pathways of key flavors were explored. Results indicated that Staphylococcus_gallinarum was the main microorganism in the microbial community, accounting for 39.13%, followed by Lactobacillus_agilis, accounting for 13.76%. Aspergillus_flavus was the fungus with the highest species abundance, accounting for 3.02%. The KEGG Pathway enrichment analysis showed that carbohydrate metabolism and amino acid metabolism were the main metabolic pathways. Glycoside hydrolase and glycosyltransferase genes were the most abundant, accounting for more than 70% of the total number of active enzyme genes. A total of 113 enzymes related to key flavors and 39 microorganisms corresponding to enzymes were annotated. And Staphylococcus_gallinarum, Lactobacillus_agilis, Weissella_confusa, Pediococcus_acidilactici, Staphylococcus_kloosii, Aspergillus_oryzae, and Aspergillus_flavus played a key role in the metabolic pathway. This study reveals the formation mechanism of key flavors in fermented broad bean, it is important for guiding the industrial production of PXDB and improving product quality.}, } @article {pmid38220540, year = {2024}, author = {Russo, AE and Memon, A and Ahmed, S}, title = {Bladder Cancer and the Urinary Microbiome-New Insights and Future Directions: A Review.}, journal = {Clinical genitourinary cancer}, volume = {22}, number = {2}, pages = {434-444}, doi = {10.1016/j.clgc.2023.12.015}, pmid = {38220540}, issn = {1938-0682}, mesh = {Humans ; *Urinary Bladder Neoplasms/therapy ; *Carcinoma, Transitional Cell ; *Urinary Tract/microbiology ; *Microbiota/genetics ; Carcinogenesis ; }, abstract = {The presence of a microbiome in the urinary system has been established through recent advancements in technology and investigation of microbial communities in the human body. The study of the taxonomic and genomic ecology of microbial communities has been greatly improved by the use of metagenomics. The research in this area has expanded our understanding of microbial ecosystems and shows that the urinary tract contains over 100 species from over 50 genera, with Lactobacillus, Gardnerella, and Streptococcus being the most common. Previous studies have suggested that the microbiota in the urinary tract may play a role in carcinogenesis by causing chronic inflammation and genotoxicity, but more research is needed to reach a definite conclusion. This is a narrative review. We conducted a search for relevant publications by using the databases Medline/PubMed and Google Scholar. The search was based on keywords such as "urinary microbiome," "bladder cancer," "carcinogenesis," "urothelial carcinoma," and "next-generation sequencing." The retrieved publications were then reviewed to study the contribution of the urinary microbiome in the development of bladder cancer. The results have been categorized into four sections to enhance understanding of the urinary microbiome and to highlight its role in the emergence of bladder cancer through alterations in the immune response that involve T-cells and antibodies. The immune system and microbiome play crucial roles in maintaining health and preventing disease. Manipulating the immune system is a key aspect of various cancer treatments, and certain gut bacteria have been linked to positive responses to immunotherapies. However, the impact of these treatments on the urinary microbiome, and how diet and lifestyle affect it, are not well understood. Research in this area could have significant implications for improving bladder cancer treatment and patient outcomes.}, } @article {pmid38220146, year = {2024}, author = {Pan, SY and Zhou, CB and Deng, JW and Zhou, YL and Liu, ZH and Fang, JY}, title = {The effects of pks[+] Escherichia coli and bile acid in colorectal tumorigenesis among people with cholelithiasis or cholecystectomy.}, journal = {Journal of gastroenterology and hepatology}, volume = {39}, number = {5}, pages = {868-879}, doi = {10.1111/jgh.16462}, pmid = {38220146}, issn = {1440-1746}, support = {2016YFC0906002//National Key R&D Program of China/ ; 2020YFA0509200//National Key R&D Program of China/ ; 31970718//National Natural Science Foundation of China/ ; 81830081//National Natural Science Foundation of China/ ; 81972203//National Natural Science Foundation of China/ ; 82070570//National Natural Science Foundation of China/ ; 82203224//National Natural Science Foundation of China/ ; 2019CXJQ02//Shanghai Municipal Health Commission, Collaborative Innovation Cluster Project/ ; 21YF1425600//Shanghai Sailing Program/ ; 2022M712124//China Postdoctoral Science Foundation/ ; }, mesh = {Humans ; *Escherichia coli ; *Bile Acids and Salts/metabolism/blood ; *Colorectal Neoplasms/microbiology/etiology ; Retrospective Studies ; Male ; Female ; Middle Aged ; *Cholelithiasis/microbiology/etiology/surgery ; *Cholecystectomy ; Gastrointestinal Microbiome ; Adult ; Carcinogenesis ; RNA, Ribosomal, 16S/genetics ; Aged ; }, abstract = {BACKGROUND AND AIM: Patients with cholelithiasis (CL) or cholecystectomy (CE) would have more chances of getting colorectal adenoma (CRA) or cancer (CRC). We aimed to figure out the effects of gut microbiota and bile acid on colorectal neoplasm in CL and CE patients.

METHODS: This was a retrospective observational study that recruited 514 volunteers, including 199 people with normal gallbladders (normal), 152 CL, and 163 CE patients. Discovery cohort was established to explore the difference in gut microbiota through 16S rRNA and metagenomics sequencing. Validation cohort aimed to verify the results through quantitative polymerase chain reaction (qPCR).

RESULTS: Significant enrichment of Escherichia coli was found in patients with cholelithiasis or cholecystectomy both in the discovery cohort (16S rRNA sequencing, PNormal-CL = 0.013, PNormal-CE = 0.042; metagenomics sequencing, PNormal-CE = 0.026) and validation cohort (PNormal-CL < 0.0001, PNormal-CE < 0.0001). Pks[+] E. coli was found enriched in CL and CE patients through qPCR (in discovery cohort: PNormal-CE = 0.018; in validation cohort: PNormal-CL < 0.0001, PNormal-CE < 0.0001). The differences in bile acid metabolism were found both through Tax4Fun analysis of 16S rRNA sequencing (Ko00120, primary bile acid biosynthesis, PNormal-CE = 0.014; Ko00121, secondary bile acid biosynthesis, PNormal-CE = 0.010) and through metagenomics sequencing (map 00121, PNormal-CE = 0.026). The elevation of serum total bile acid of CE patients was also found in validation cohort (PNormal-CE < 0.0001). The level of serum total bile acid was associated with the relative abundance of pks[+] E. coli (r = 0.1895, P = 0.0012).

CONCLUSIONS: E. coli, especially pks[+] species, was enriched in CL and CE patients. Pks[+] E. coli and bile acid metabolism were found associated with CRA and CRC in people after cholecystectomy.}, } @article {pmid38219994, year = {2024}, author = {Koloti, LE and Nkuna, R and Matambo, TS}, title = {Impact of current anthropogenic activities on Blesbokspruit wetland microbiome and functions.}, journal = {The Science of the total environment}, volume = {915}, number = {}, pages = {170010}, doi = {10.1016/j.scitotenv.2024.170010}, pmid = {38219994}, issn = {1879-1026}, mesh = {Humans ; Wetlands ; Anthropogenic Effects ; *Metals, Heavy/analysis ; *Microbiota ; Water/analysis ; Geologic Sediments/chemistry ; Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; }, abstract = {Till present, natural wetlands have been continuously subjected to intensive pollution stress in recent years, mainly because of the rapidly growing industrialization and urbanization that are associated with a myriad of anthropogenic activities and land use practices. These man-made sources of pollution change the chemical properties of the natural wetlands, which in turn alter their microbial ecological biodiversity and functions. For the first time, the impact of the current anthropogenic activities and land use practices on the Blesbokspruit wetland chemical status and their consequential effect on the microbial structure and functions were investigated. Sites of high pollution intensity were identified using geographic information systems mapping (GISMapping) and the wetland microbiome and functional profile were studied through the use of high throughput shotgun metagenomics sequencing analysis. The predominant phyla that stemmed along the Blesbokspruit wetland were found to be Proteobacteria which was more dominant in water (93 %) than in the sediments (89 %), followed by firmicutes which was more abundant in sediments (9 %) than in water (6 %), and Bacteroidetes were relatively low in abundance within both the sediments (2 %) and the overlying water (1 %). The genera Klebsiella (70.4 %-28.2 %), Citrobacter (52.0 %-30.6 %), Escherichia (51.0 %-8.4 %), and Lynsinibacillus (9.3 %-1.5 %) were observed in most water and sediment samples. Within the six polluted sites, Site 2 was found to be the most highly polluted site in the Blesbokspruit wetland with very high COD (900 mg/L), TOC (11.60 mg/L), NO3[-] (39.74 mg/L), NO2[-] (12.64 mg/L), PO4[3] (4.14 mg/L), Fl[-] (143.88 mg/L), Cl[-] (145.95 mg/L) concentrations recorded in the water and high levels of TOC (0.37 mg/L), TC (6.92 %), TN (1.82 %), TS (0.53 %) in sediments. The microbial community structure and functions were found to be strongly influenced by the high organic content from the intense agricultural activities and sewage spillages and heavy metals from the mining activities nearby.}, } @article {pmid38218318, year = {2024}, author = {Shen, X and Tilves, C and Kim, H and Tanaka, T and Spira, AP and Chia, CW and Talegawkar, SA and Ferrucci, L and Mueller, NT}, title = {Plant-based diets and the gut microbiome: findings from the Baltimore Longitudinal Study of Aging.}, journal = {The American journal of clinical nutrition}, volume = {119}, number = {3}, pages = {628-638}, pmid = {38218318}, issn = {1938-3207}, support = {K01 HL168232/HL/NHLBI NIH HHS/United States ; K12 HL143957/HL/NHLBI NIH HHS/United States ; P30 AG066507/AG/NIA NIH HHS/United States ; R21 DK132310/DK/NIDDK NIH HHS/United States ; K01 HL141589/HL/NHLBI NIH HHS/United States ; R01 HL166473/HL/NHLBI NIH HHS/United States ; R01 AG051752/AG/NIA NIH HHS/United States ; }, mesh = {Adult ; Aged ; Humans ; Aging ; Baltimore ; Cross-Sectional Studies ; Diet ; Diet, Plant-Based ; Diet, Vegetarian ; *Gastrointestinal Microbiome ; Longitudinal Studies ; *Methylamines ; Male ; Female ; Middle Aged ; }, abstract = {BACKGROUND: Mounting evidence indicates that although some plant-based diets are healthful, others are not. Changes in the gut microbiome and microbiome-dependent metabolites, such as trimethylamine N-oxide (TMAO), may explain differential health effects of plant-based diets. However, human data are sparse on whether qualitatively distinct types of plant-based diets differentially affect gut microbiome diversity, composition, particularly at the species level, and/or metabolites.

OBJECTIVES: We aimed to examine cross-sectional associations of different plant-based indices with adult gut microbiome diversity, composition, and the metabolite TMAO.

METHODS: We studied 705 adults in the Baltimore Longitudinal Study of Aging with data for diet, fecal microbiome (shotgun metagenomic sequencing), and key covariates. We derived healthful plant-based diet index (hPDI) and unhealthful plant-based diet index (uPDI) using data from food frequency questionnaires. We examined plant-based diet indices with microbiome α-diversity (richness and evenness measures), β-diversity (Bray-Curtis and UniFrac measures), composition (species level), and plasma TMAO. We used regression models to determine associations before and after adjustment for age, sex, education, physical activity, smoking status, body mass index, and total energy intake.

RESULTS: The analytic sample (mean age, 71.0 years, SD = 12.8 years) comprised 55.6% female and 67.5% non-Hispanic White participants. hPDI was positively and uPDI negatively associated with microbiome α-diversity, driven by microbial evenness (Pielou P < 0.05). hPDI was also positively associated with relative abundance of 3 polysaccharide-degrading bacterial species (Faecalibacterium prausnitzii, Eubacterium eligens, and Bacteroides thetaiotaomicron) and inversely associated with 6 species (Blautia hydrogenotrophica, Doreasp CAG 317, Eisenbergiella massiliensis, Sellimonas intestinalis, Blautia wexlerae, and Alistipes shahii). Furthermore, hPDI was inversely associated with TMAO. Associations did not differ by age, sex, or race.

CONCLUSIONS: Greater adherence to a healthful plant-based diet is associated with microbiome features that have been linked to positive health; adherence to an unhealthful plant-based diet has opposing or null associations with these features.}, } @article {pmid38217470, year = {2024}, author = {Patangia, DV and Grimaud, G and Wang, S and Ross, RP and Stanton, C}, title = {Influence of age, socioeconomic status, and location on the infant gut resistome across populations.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2297837}, pmid = {38217470}, issn = {1949-0984}, support = {101054719/ERC_/European Research Council/International ; }, mesh = {Infant ; Humans ; Aged ; *Genes, Bacterial ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Escherichia/genetics ; Social Class ; }, abstract = {Antibiotic resistance is a growing global concern, with many ecological niches showing a high abundance of antibiotic resistance genes (ARGs), including the human gut. With increasing indications of ARGs in infants, this study aims to investigate the gut resistome profile during early life at a wider geographic level. To achieve this objective, we utilized stool samples data from 26 studies involving subjects aged up to 3 years from different geographical locations. The 32,277 Metagenome Assembled Genomes (MAGs) previously generated from shotgun sequencing reads from these studies were used for resistome analysis using RGI with the CARD database. This analysis showed that the distribution of ARGs across the countries in our study differed in alpha diversity and compositionally. In particular, the abundance of ARGs was found to vary by socioeconomic status and healthcare access and quality (HAQ) index. Surprisingly, countries having lower socioeconomic status and HAQ indices showed lower ARG abundance, which was contradictory to previous reports. Gram-negative genera, including Escherichia, Enterobacter, Citrobacter, and Klebsiella harbored a particularly rich set of ARGs, which included antibiotics that belong to the Reserve, Access or Watch category, such as glycopeptides, fluoroquinolones, sulfonamides, macrolides, and tetracyclines. We showed that ARG abundance exponentially decreased with time during the first 3 years of life. Many highly ARG-abundant species including Escherichia, Klebsiella, Citrobacter species that we observed are well-known pathobionts found in the infant gut in early life. High abundance of these species and a diverse range of ARGs in their genomes point toward the infant gut, acting as an ARG reservoir. This is a concern and further studies are needed to examine the causal effect and its consequences on long-term health.}, } @article {pmid38217406, year = {2024}, author = {Shen, Y and Li, Y and Wu, T and Dong, Q and Deng, Q and Liu, L and Guo, Y and Cao, Y and Li, Q and Shi, J and Zou, H and Jiao, Y and Ding, L and Li, J and Gao, Y and Hu, S and Wang, Y and Chen, L}, title = {Early microbial intervention reshapes phenotypes of newborn Bos taurus through metabolic regulations.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {38217406}, issn = {2047-217X}, support = {//High-Performance Computing Centre of Nanjing Medical University/ ; 32302756//National Natural Science Foundation of China/ ; CARS36//The Earmarked Fund/ ; HBCT2023180207//Hebei Dairy Cattle Innovation Team of Modern Agro-industry Technology Research System/ ; 6012018//The Top Talent Project of Hebei Province/ ; 1090064//Precision Animal Husbandry Discipline Group Construction Project of Hebei Agricultural University/ ; C2022204248//Natural Science Foundation of Hebei Province/ ; BK20220709//Natural Science Foundation of Jiangsu/ ; CMCM202204//Nanjing Medical University, Changzhou Medical Centre Grant/ ; 303073572NC21//Nanjing Medical University/ ; }, mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome ; Metagenome ; Metabolomics ; Phenotype ; }, abstract = {BACKGROUND: The rumen of neonatal calves has limited functionality, and establishing intestinal microbiota may play a crucial role in their health and performance. Thus, we aim to explore the temporal colonization of the gut microbiome and the benefits of early microbial transplantation (MT) in newborn calves.

RESULTS: We followed 36 newborn calves for 2 months and found that the composition and ecological interactions of their gut microbiomes likely reached maturity 1 month after birth. Temporal changes in the gut microbiome of newborn calves are widely associated with changes in their physiological statuses, such as growth and fiber digestion. Importantly, we observed that MT reshapes the gut microbiome of newborns by altering the abundance and interaction of Bacteroides species, as well as amino acid pathways, such as arginine biosynthesis. Two-year follow-up of those calves further showed that MT improves their later milk production. Notably, MT improves fiber digestion and antioxidant capacity of newborns while reducing diarrhea. MT also contributes to significant changes in the metabolomic landscape, and with putative causal mediation analysis, we suggest that altered gut microbial composition in newborns may influence physiological status through microbial-derived metabolites.

CONCLUSIONS: Our study provides a metagenomic and metabolomic atlas of the temporal development of the gut microbiome in newborn calves. MT can alter the gut microbiome of newborns, leading to improved physiological status and later milk production. The data may help develop strategies to manipulate the gut microbiota during early life, which may be relevant to the health and production of newborn calves.}, } @article {pmid38216924, year = {2024}, author = {Steinke, K and Pamp, SJ and Munk, P}, title = {MAGICIAN: MAG simulation for investigating criteria for bioinformatic analysis.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {55}, pmid = {38216924}, issn = {1471-2164}, mesh = {*Metagenome ; Computer Simulation ; *Microbiota/genetics ; Metagenomics/methods ; Computational Biology ; }, abstract = {BACKGROUND: The possibility of recovering metagenome-assembled genomes (MAGs) from sequence reads allows for further insights into microbial communities and their members, possibly even analyzing such sequences with tools designed for single-isolate genomes. As result quality depends on sequence quality, performance of tools for single-isolate genomes on MAGs should be tested beforehand. Bioinformatics can be leveraged to quickly create varied synthetic test sets with known composition for this purpose.

RESULTS: We present MAGICIAN, a flexible, user-friendly pipeline for the simulation of MAGs. MAGICIAN combines a synthetic metagenome simulator with a metagenomic assembly and binning pipeline to simulate MAGs based on user-supplied input genomes, allowing users to test performance of tools on MAGs while having a ground truth to compare results to. Using MAGICIAN, we found that even very slight (1%) changes in depth of coverage can drastically affect whether a genome can be recovered. We also demonstrate the use of simulated MAGs by evaluating the suitability of such genomes obtained with MAGICIAN's current default pipeline for analysis with the antimicrobial resistance gene identification tool ResFinder.

CONCLUSIONS: Using MAGICIAN, it is possible to simulate MAGs which, while generally high in quality, reflect issues encountered with real-world data, thus providing realistic best-case data. Evaluating the results of ResFinder analysis of these genomes revealed a risk for plausible-looking false positives, which underlines the need for pipeline validation so that researchers are aware of the potential issues when interpreting real-world data. Furthermore, the effects of fluctuations in depth of coverage on genome recovery in our simulated "random sequencing" warrant further investigation and indicate random subsampling of reads may affect discovery of more genomes.}, } @article {pmid38215846, year = {2024}, author = {Zheng, Y and Su, Z and Liu, D and Huang, B and Mu, Q and Li, Y and Wen, D}, title = {Metagenomics reveals the influence of small microplastics on microbial communities in coastal sediments.}, journal = {The Science of the total environment}, volume = {914}, number = {}, pages = {169982}, doi = {10.1016/j.scitotenv.2024.169982}, pmid = {38215846}, issn = {1879-1026}, mesh = {Microplastics/toxicity/analysis ; Plastics/analysis ; Geologic Sediments/chemistry ; *Water Pollutants, Chemical/toxicity/analysis ; Environmental Monitoring ; *Microbiota ; }, abstract = {The ecological impact of microplastics (MPs) in coastal environments has been widely studied. However, the influence of small microplastics in the actual environment is often overlooked due to measurement challenges. In this study, Hangzhou Bay (HZB), China, was selected as our study area. High-throughput metagenomic sequencing and micro-Raman spectrometry were employed to analyze the microbial communities and microplastics of coastal sediment samples, respectively. We aimed to explore the ecological impact of MPs with small sizes (≤ 100 μm) in real coastal sediment environments. Our results revealed that as microplastic size decreased, the environmental behavior of MPs underwent alterations. In the coastal sediments, no significant correlations were observed between the detected MPs and the whole microbial communities, but small MPs posed potential hazards to eukaryotic communities. Moreover, these small MPs were more prone to microbial degradation and significantly affected carbon metabolism in the habitat. This study is the first to reveal the comprehensive impact of small MPs on microbial communities in a real coastal sediment environment.}, } @article {pmid38215740, year = {2024}, author = {Schirmer, M and Stražar, M and Avila-Pacheco, J and Rojas-Tapias, DF and Brown, EM and Temple, E and Deik, A and Bullock, K and Jeanfavre, S and Pierce, K and Jin, S and Invernizzi, R and Pust, MM and Costliow, Z and Mack, DR and Griffiths, AM and Walters, T and Boyle, BM and Kugathasan, S and Vlamakis, H and Hyams, J and Denson, L and Clish, CB and Xavier, RJ}, title = {Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course.}, journal = {Cell host & microbe}, volume = {32}, number = {2}, pages = {209-226.e7}, pmid = {38215740}, issn = {1934-6069}, support = {R01 AT009708/AT/NCCIH NIH HHS/United States ; P30 DK040561/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; U01 DK095745/DK/NIDDK NIH HHS/United States ; R01 AI172147/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Child ; *Colitis, Ulcerative/drug therapy ; Host Microbial Interactions ; *Gastrointestinal Microbiome/genetics ; Disease Progression ; Genes, Microbial ; }, abstract = {Understanding the role of the microbiome in inflammatory diseases requires the identification of microbial effector molecules. We established an approach to link disease-associated microbes to microbial metabolites by integrating paired metagenomics, stool and plasma metabolomics, and culturomics. We identified host-microbial interactions correlated with disease activity, inflammation, and the clinical course of ulcerative colitis (UC) in the Predicting Response to Standardized Colitis Therapy (PROTECT) pediatric inception cohort. In severe disease, metabolite changes included increased dipeptides and tauro-conjugated bile acids (BAs) and decreased amino-acid-conjugated BAs in stool, whereas in plasma polyamines (N-acetylputrescine and N1-acetylspermidine) increased. Using patient samples and Veillonella parvula as a model, we uncovered nitrate- and lactate-dependent metabolic pathways, experimentally linking V. parvula expansion to immunomodulatory tryptophan metabolite production. Additionally, V. parvula metabolizes immunosuppressive thiopurine drugs through xdhA xanthine dehydrogenase, potentially impairing the therapeutic response. Our findings demonstrate that the microbiome contributes to disease-associated metabolite changes, underscoring the importance of these interactions in disease pathology and treatment.}, } @article {pmid38215548, year = {2024}, author = {Ottinger, S and Robertson, CM and Branthoover, H and Patras, KA}, title = {The human vaginal microbiota: from clinical medicine to models to mechanisms.}, journal = {Current opinion in microbiology}, volume = {77}, number = {}, pages = {102422}, pmid = {38215548}, issn = {1879-0364}, support = {F31 HD111236/HD/NICHD NIH HHS/United States ; R01 AI157981/AI/NIAID NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; R01 DK128053/DK/NIDDK NIH HHS/United States ; R01 HD111236/HD/NICHD NIH HHS/United States ; }, mesh = {Pregnancy ; Female ; Humans ; Animals ; Mice ; *Microbiota ; Metagenome ; Host Microbial Interactions ; Vagina ; *Clinical Medicine ; }, abstract = {The composition of the vaginal microbiota is linked to numerous reproductive health problems, including increased susceptibility to infection, pregnancy complications, and impaired vaginal tissue repair; however, the mechanisms contributing to these adverse outcomes are not yet fully defined. In this review, we highlight recent clinical advancements associating vaginal microbiome composition and function with health outcomes. Subsequently, we provide a summary of emerging models employed to identify microbe-microbe interactions contributing to vaginal health, including metagenomic sequencing, multi-omics approaches, and advances in vaginal microbiota cultivation. Last, we review new in vitro, ex vivo, and in vivo models, such as organoids and humanized microbiota murine models, used to define and mechanistically explore host-microbe interactions at the vaginal mucosa.}, } @article {pmid38214523, year = {2024}, author = {Wang, H and Zheng, K and Wang, M and Ma, K and Ren, L and Guo, R and Ma, L and Zhang, H and Liu, Y and Xiong, Y and Wu, M and Shao, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Liang, Y}, title = {Shewanella phage encoding a putative anti-CRISPR-like gene represents a novel potential viral family.}, journal = {Microbiology spectrum}, volume = {12}, number = {2}, pages = {e0336723}, pmid = {38214523}, issn = {2165-0497}, mesh = {*Bacteriophages/genetics ; *Shewanella/genetics ; Phylogeny ; Sequence Analysis, DNA ; Genome, Viral ; Open Reading Frames ; DNA, Viral/genetics ; }, abstract = {Shewanella is a prevalent bacterial genus in deep-sea environments including marine sediments, exhibiting diverse metabolic capabilities that indicate its significant contributions to the marine biogeochemical cycles. However, only a few Shewanella phages were isolated and deposited in the NCBI database. In this study, we report the isolation and characterization of a novel Shewanella phage, vB_SbaS_Y11, that infects Shewanella KR11 and was isolated from the sewage in Qingdao, China. Transmission electron microscopy revealed that vB_SbaS_Y11 has an icosahedral head and a long tail. The genome of vB_SbaS_Y11 is a linear, double-stranded DNA with a length of 62,799 bp and a G+C content of 46.9%, encoding 71 putative open reading frames. No tRNA genes or integrase-related feature genes were identified. An uncharacterized anti-CRISPR AcrVA2 gene was detected in its genome. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analyses indicate that vB_SbaS_Y11 has a novel genomic architecture and shares low similarity to Pseudomonas virus H66 and Pseudomonas phage F116. vB_SbaS_Y11 represents a potential new family-level virus cluster with eight metagenomic assembled viral genomes named Ranviridae.IMPORTANCEThe Gram-negative Shewanella bacterial genus currently includes about 80 species of mostly aquatic Gammaproteobacteria, which were isolated around the globe in a multitude of environments, such as freshwater, seawater, coastal sediments, and the deepest trenches. Here, we present a Shewanella phage vB_SbaS_Y11 that contains an uncharacterized anti-CRISPR AcrVA2 gene and belongs to a potential virus family, Ranviridae. This study will enhance the knowledge about the genome, diversity, taxonomic classification, and global distribution of Shewanella phage populations.}, } @article {pmid38212658, year = {2024}, author = {Ning, D and Wang, Y and Fan, Y and Wang, J and Van Nostrand, JD and Wu, L and Zhang, P and Curtis, DJ and Tian, R and Lui, L and Hazen, TC and Alm, EJ and Fields, MW and Poole, F and Adams, MWW and Chakraborty, R and Stahl, DA and Adams, PD and Arkin, AP and He, Z and Zhou, J}, title = {Environmental stress mediates groundwater microbial community assembly.}, journal = {Nature microbiology}, volume = {9}, number = {2}, pages = {490-501}, pmid = {38212658}, issn = {2058-5276}, support = {DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; EF-2025558//National Science Foundation (NSF)/ ; DEB-2129235//National Science Foundation (NSF)/ ; }, mesh = {Phylogeny ; *Microbiota ; *Groundwater ; Stochastic Processes ; }, abstract = {Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.}, } @article {pmid38212383, year = {2024}, author = {Haytham, H and Kamel, C and Wafa, D and Salma, F and Naima, BM and George, T and Ameur, C and Msaad Guerfali, M}, title = {Probiotic consortium modulating the gut microbiota composition and function of sterile Mediterranean fruit flies.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {1058}, pmid = {38212383}, issn = {2045-2322}, support = {PRFD6P2/2019//Ministère de l'Enseignement Supérieur et de la Recherche Scientifique, Tunisie/ ; }, mesh = {Male ; Animals ; *Ceratitis capitata/physiology ; *Gastrointestinal Microbiome ; Enterobacter/physiology ; Reproduction ; Larva/physiology ; *Probiotics ; Pest Control, Biological/methods ; }, abstract = {The sterile insect technique (SIT) remains a successful approach in managing pest insects. However, the long-term mass rearing and sterilizing radiation associated with SIT have been observed to induce physiological and ecological fitness decline in target insects. This decline may be attributed to various factors, including commensal microbiota dysbiosis, selection procedures, loss of heterozygosity, and other complex interactions.. There is evidence that the bacterial symbiont of insects may play critical roles in digestion, development, reproduction, and behavior. Probiotics are an increasingly common approach for restoring the intestinal microbiota structure and fitness parameters of sterile insects, particularly in the Vienna 8 genetic sexing strain (V8-GSS) of the Mediterranean fruit fly (medfly), Ceratitis capitata. Here, we explore the influence of the previously isolated bacterial strain, Lactococcus lactis, Enterobacter sp., and Klebsiella oxytoca, administration as probiotic consortia (LEK-PC) to the larvae and/or adult diet over the course of 20 rearing generations on fitness parameters. The experiment was carried out in four colonies: a control colony (C), one to which probiotics were not added, one to which probiotics were added to the larval medium (L+), one to which probiotics were added to the adult medium (A+), and one to which probiotics were added to both the larval and adult mediums (AL+). Emergence, flight ability, survival under stress conditions, and mating competitiveness, were all significantly improved by the LEK-PC treatment independently of the administration stage. The intestinal microbiota structure of various medfly V8-GSS colonies also underwent a significant shift, despite the fact that the core microbial community was unaffected by the LEK-PC administration stage, according to 16S metagenomics sequencing. Comparison of the metabolic function prediction and associated carbohydrate enzymes among colonies treated with "LEK-PC" showed an enrichment of metabolic functions related to carbohydrates, amino acids, cofactors, and vitamins metabolism, as well as, glycoside hydrolase enzymes in the AL+ colony compared to the control. This study enriches the knowledge regarding the benefits of probiotic treatment to modulate and restore the intestinal microbiota of C. capitata sterile males for a better effectiveness of the SIT.}, } @article {pmid38211474, year = {2024}, author = {Xie, Y and Su, J and Shao, K and Hu, T and Ming, H and Shi, T and Wang, W and Fan, J}, title = {Long-term response of the microbial community to the degradation of DOC released from Undaria pinnatifida.}, journal = {Marine environmental research}, volume = {194}, number = {}, pages = {106313}, doi = {10.1016/j.marenvres.2023.106313}, pmid = {38211474}, issn = {1879-0291}, mesh = {Dissolved Organic Matter ; *Microbiota ; *Undaria ; Carbon Sequestration ; Carbon/metabolism ; *Edible Seaweeds ; }, abstract = {With the aim to study the mechanism underlying the macroalgal carbon sequestration driven by microbes, we investigated the microbial community using metagenomics methods and its long-term degradation of dissolved organic carbon (DOC) derived from Undaria pinnatifida. It was observed that after removing U. pinnatifida, the concentration of the DOC decreased significantly (p < 0.05) within 4 days. Over a period of 120 days of degradation, the concentration of remaining DOC (26%) remained stable. The succession of microbial community corresponded to the three stages of DOC concentration variation. Moreover, the structure of microbes community and its metabolic function exhibited evident patterns of succession. The concentration of DOC was correlated negatively with the abundances of Planctomycetaceae (p < 0.01), and was correlated positively with the abundances of Roseobacteraceae and Rhodobacteraceae (p < 0.01). In addition, the metabolic pathways related to "Glycolysis/Gluconeogenesis", "Alanine, aspartate, and glutamate metabolism", "Citrate cycle (TCA cycle)" and "Tryptophan metabolism" was significantly correlated with the variations in DOC concentration (p < 0.05). These findings indicate that the variation in the DOC concentration was closely linked to the succession of Planctomycetaceae, Roseobacteraceae, Rhodobacteraceae, and the degradation of DOC derived from U. pinnatifida appeared to be influenced by metabolic functions.}, } @article {pmid38204360, year = {2024}, author = {Kiran, A and Hanachi, M and Alsayed, N and Fassatoui, M and Oduaran, OH and Allali, I and Maslamoney, S and Meintjes, A and Zass, L and Rocha, JD and Kefi, R and Benkahla, A and Ghedira, K and Panji, S and Mulder, N and Fadlelmola, FM and Souiai, O}, title = {The African Human Microbiome Portal: a public web portal of curated metagenomic metadata.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {38204360}, issn = {1758-0463}, support = {U24 HG006941/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *Metadata ; Metagenome ; Databases, Factual ; Metagenomics ; *Microbiota/genetics ; }, abstract = {There is growing evidence that comprehensive and harmonized metadata are fundamental for effective public data reusability. However, it is often challenging to extract accurate metadata from public repositories. Of particular concern is the metagenomic data related to African individuals, which often omit important information about the particular features of these populations. As part of a collaborative consortium, H3ABioNet, we created a web portal, namely the African Human Microbiome Portal (AHMP), exclusively dedicated to metadata related to African human microbiome samples. Metadata were collected from various public repositories prior to cleaning, curation and harmonization according to a pre-established guideline and using ontology terms. These metadata sets can be accessed at https://microbiome.h3abionet.org/. This web portal is open access and offers an interactive visualization of 14 889 records from 70 bioprojects associated with 72 peer reviewed research articles. It also offers the ability to download harmonized metadata according to the user's applied filters. The AHMP thereby supports metadata search and retrieve operations, facilitating, thus, access to relevant studies linked to the African Human microbiome. Database URL: https://microbiome.h3abionet.org/.}, } @article {pmid38203738, year = {2024}, author = {Brīvība, M and Silamiķele, L and Birzniece, L and Ansone, L and Megnis, K and Silamiķelis, I and Pelcmane, L and Borisova, D and Rozenberga, M and Jagare, L and Elbere, I and Kloviņš, J}, title = {Gut Microbiome Composition and Dynamics in Hospitalized COVID-19 Patients and Patients with Post-Acute COVID-19 Syndrome.}, journal = {International journal of molecular sciences}, volume = {25}, number = {1}, pages = {}, pmid = {38203738}, issn = {1422-0067}, support = {1.1.1.1/21/A/029//European Regional Development Fund/ ; }, mesh = {Humans ; *COVID-19 ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Post-Acute COVID-19 Syndrome ; Patients ; Clostridiales ; }, abstract = {The gut microbiome plays a pivotal role in the modulation of host responses during viral infections, and recent studies have underscored its significance in the context of coronavirus disease 2019 (COVID-19). We aimed to investigate the dynamics and compositional changes in the gut microbiome of COVID-19 patients, addressing both the acute phase and the recovery process, with a particular focus on the emergence of post-COVID-19 conditions. Involving 146 COVID-19 patients and 110 healthy controls, this study employed a shotgun metagenomics approach for cross-sectional and longitudinal analyses with one- and three-month follow-ups. We observed a decline in taxonomic diversity among hospitalized COVID-19 patients compared to healthy controls, while a subsequent increase in alpha diversity was shown during the recovery process. A notable contribution of Enterococcus faecium was identified in the acute phase of the infection, accompanied by an increasing abundance of butyrate-producing bacteria (e.g., Roseburia, Lachnospiraceae_unclassified) during the recovery period. We highlighted a protective role of the Prevotella genus in the long-term recovery process and suggested a potential significance of population-specificity in the early gut microbiome markers of post-acute COVID-19 syndrome. Our study represents distinctive gut microbiome signatures in COVID-19, with potential diagnostic and prognostic implications, pinpointing potential modulators of the disease progression.}, } @article {pmid38203712, year = {2023}, author = {Jean Wilson, E and Sirpu Natesh, N and Ghadermazi, P and Pothuraju, R and Prajapati, DR and Pandey, S and Kaifi, JT and Dodam, JR and Bryan, JN and Lorson, CL and Watrelot, AA and Foster, JM and Mansell, TJ and Joshua Chan, SH and Batra, SK and Subbiah, J and Rachagani, S}, title = {Red Cabbage Juice-Mediated Gut Microbiota Modulation Improves Intestinal Epithelial Homeostasis and Ameliorates Colitis.}, journal = {International journal of molecular sciences}, volume = {25}, number = {1}, pages = {}, pmid = {38203712}, issn = {1422-0067}, support = {R01 CA247763/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Mice ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; *Colitis/chemically induced ; *Inflammatory Bowel Diseases ; Homeostasis ; }, abstract = {Gut microbiota plays a crucial role in inflammatory bowel diseases (IBD) and can potentially prevent IBD through microbial-derived metabolites, making it a promising therapeutic avenue. Recent evidence suggests that despite an unclear underlying mechanism, red cabbage juice (RCJ) alleviates Dextran Sodium Sulfate (DSS)-induced colitis in mice. Thus, the study aims to unravel the molecular mechanism by which RCJ modulates the gut microbiota to alleviate DSS-induced colitis in mice. Using C57BL/6J mice, we evaluated RCJ's protective role in DSS-induced colitis through two cycles of 3% DSS. Mice were daily gavaged with PBS or RCJ until the endpoint, and gut microbiota composition was analyzed via shotgun metagenomics. RCJ treatment significantly improved body weight (p ≤ 0.001), survival in mice (p < 0.001) and reduced disease activity index (DAI) scores. Further, RCJ improved colonic barrier integrity by enhancing the expression of protective colonic mucins (p < 0.001) and tight junction proteins (p ≤ 0.01) in RCJ + DSS-treated mice compared to the DSS group. Shotgun metagenomic analysis revealed an enrichment of short-chain fatty acids (SCFAs)-producing bacteria (p < 0.05), leading to increased Peroxisome Proliferator-Activated Receptor Gamma (PPAR-γ) activation (p ≤ 0.001). This, in turn, resulted in repression of the nuclear factor κB (NFκB) signaling pathway, causing decreased production of inflammatory cytokines and chemokines. Our study demonstrates colitis remission in a DSS-induced mouse model, showcasing RCJ as a potential modulator for gut microbiota and metabolites, with promising implications for IBD prevention and treatment.}, } @article {pmid38200287, year = {2024}, author = {Malacrinò, A and Böttner, L and Nouere, S and Huber, M and Schäfer, M and Xu, S}, title = {Induced responses contribute to rapid adaptation of Spirodela polyrhiza to herbivory by Lymnaea stagnalis.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {81}, pmid = {38200287}, issn = {2399-3642}, support = {422213951//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 438887884//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 435681637//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; P400PB_186770//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {Animals ; *Lymnaea ; Herbivory ; *Araceae ; Adaptation, Physiological ; Biological Assay ; }, abstract = {Herbivory-induced responses in plants are typical examples of phenotypic plasticity, and their evolution is thought to be driven by herbivory. However, direct evidence of the role of induced responses in plant adaptive evolution to herbivores is scarce. Here, we experimentally evolve populations of an aquatic plant (Spirodela polyrhiza, giant duckweed) and its native herbivore (Lymnaea stagnalis, freshwater snail), testing whether herbivory drives rapid adaptive evolution in plant populations using a combination of bioassays, pool-sequencing, metabolite analyses, and amplicon metagenomics. We show that snail herbivory drove rapid phenotypic changes, increased herbivory resistance, and altered genotype frequencies in the plant populations. Additional bioassays suggest that evolutionary changes of induced responses contributed to the rapid increase of plant resistance to herbivory. This study provides direct evidence that herbivory-induced responses in plants can be subjected to selection and have an adaptive role by increasing resistance to herbivores.}, } @article {pmid38199973, year = {2024}, author = {Tong, CH and Huo, ZP and Diao, L and Xiao, DY and Zhao, RN and Zeng, ZL and Xiong, WG}, title = {Core and variable antimicrobial resistance genes in the gut microbiomes of Chinese and European pigs.}, journal = {Zoological research}, volume = {45}, number = {1}, pages = {189-200}, pmid = {38199973}, issn = {2095-8137}, mesh = {Humans ; Animals ; Swine ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents/pharmacology ; Manure ; Drug Resistance, Bacterial/genetics ; *Anti-Infective Agents ; }, abstract = {Monitoring the prevalence of antimicrobial resistance genes (ARGs) is vital for addressing the global crisis of antibiotic-resistant bacterial infections. Despite its importance, the characterization of ARGs and microbiome structures, as well as the identification of indicators for routine ARG monitoring in pig farms, are still lacking, particularly concerning variations in antimicrobial exposure in different countries or regions. Here, metagenomics and random forest machine learning were used to elucidate the ARG profiles, microbiome structures, and ARG contamination indicators in pig manure under different antimicrobial pressures between China and Europe. Results showed that Chinese pigs exposed to high-level antimicrobials exhibited higher total and plasmid-mediated ARG abundances compared to those in European pigs (P<0.05). ANT(6)-Ib, APH(3')-IIIa, and tet(40) were identified as shared core ARGs between the two pig populations. Furthermore, the core ARGs identified in pig populations were correlated with those found in human populations within the same geographical regions. Lactobacillus and Prevotella were identified as the dominant genera in the core microbiomes of Chinese and European pigs, respectively. Forty ARG markers and 43 biomarkers were able to differentiate between the Chinese and European pig manure samples with accuracies of 100% and 98.7%, respectively. Indicators for assessing ARG contamination in Chinese and European pigs also achieved high accuracy (r=0.72-0.88). Escherichia flexneri in both Chinese and European pig populations carried between 21 and 37 ARGs. The results of this study emphasize the importance of global collaboration in reducing antimicrobial resistance risk and provide validated indicators for evaluating the risk of ARG contamination in pig farms.}, } @article {pmid38198973, year = {2024}, author = {Xia, Z and Ng, HY and Xu, D and Bae, S}, title = {Lumen air pressure regulated multifunctional microbiotas in membrane-aerated biofilm reactors for simultaneous nitrogen removal and antibiotic elimination from aquaculture wastewater.}, journal = {Water research}, volume = {251}, number = {}, pages = {121102}, doi = {10.1016/j.watres.2024.121102}, pmid = {38198973}, issn = {1879-2448}, mesh = {*Wastewater ; Denitrification ; Nitrogen/metabolism ; Extracellular Polymeric Substance Matrix/metabolism ; Anti-Bacterial Agents/pharmacology ; Air Pressure ; Bioreactors ; Nitrification ; *Microbiota ; Biofilms ; }, abstract = {In this study, two membrane-aerated biofilm reactors (MABRs) were constructed: one solely utilizing biofilm and another hybrid MABR (HMABR) incorporating both suspended-sludge and biofilm to treat low C/N aquaculture wastewater under varying lumen air pressure (LAP). Both HMABR and MABR demonstrated superior nitrogen removal than conventional aeration reactors. Reducing LAP from 10 kPa to 2 kPa could enhance denitrification processes without severely compromising nitrification, resulting in an increase in total inorganic nitrogen (TIN) removal from 50.2±3.1 % to 71.6±1.0 %. The HMABR exhibited better denitrification efficacy than MABR, underscoring its potential for advanced nitrogen removal applications. A decline in LAP led to decreased extracellular polymeric substance (EPS) production, which could potentially augment reactor performance by minimizing mass transfer resistance while maintaining microbial matrix stability and function. Gene-centric metagenomics analysis revealed decreasing LAP impacted nitrogen metabolic potentials and electron flow pathways. The enrichment of napAB at higher LAP and the presence of complete ammonia oxidation (Comammox) Nitrospira at lower LAP indicated aerobic denitrification and Comammox processes in nitrogen removal. Multifunctional microbial communities developed under LAP regulation, diversifying the mechanisms for simultaneous nitrification-denitrification. Increased denitrifying gene pool (narGHI, nirK, norB) and enzymatic activity at a low LAP can amplify denitrification by promoting denitrifying genes and electron flow towards denitrifying enzymes. Sulfamethoxazole (SMX) was simultaneously removed with efficiency up to 80.2 ± 3.7 %, mainly via biodegradation, while antibiotic resistome and mobilome were propagated. Collectively, these findings could improve our understanding of nitrogen and antibiotic removal mechanisms under LAP regulation, offering valuable insights for the effective design and operation of MABR systems in aquaculture wastewater treatment.}, } @article {pmid38197778, year = {2024}, author = {He, J and Zhang, B and Yan, W and Lai, Y and Tang, Y and Han, Y and Liu, J}, title = {Deciphering Vanadium Speciation in Smelting Ash and Adaptive Responses of Soil Microorganisms.}, journal = {ACS nano}, volume = {18}, number = {3}, pages = {2464-2474}, doi = {10.1021/acsnano.3c11204}, pmid = {38197778}, issn = {1936-086X}, mesh = {Vanadium ; Soil/chemistry ; *Soil Pollutants/analysis ; *Microbiota ; }, abstract = {Abundant smelting ash is discharged during pyrometallurgical vanadium (V) production. However, its associated V speciation and resultant ecological impact have remained elusive. In this study, V speciation in smelting ash and its influence on the metabolism of soil microorganisms were investigated. Smelting ashes from V smelters contained abundant V (19.6-115.9 mg/g). V(V) was the dominant species for soluble V, while solid V primarily existed in bioavailable forms. Previously unrevealed V nanoparticles (V-NPs) were prevalently detected, with a peak concentration of 1.3 × 10[13] particles/g, a minimal size of 136.0 ± 0.6 nm, and primary constituents comprising FeVO4, VO2, and V2O5. Incubation experiments implied that smelting ash reshaped the soil microbial community. Metagenomic binning, gene transcription, and component quantification revealed that Microbacterium sp. and Tabrizicola sp. secreted extracellular polymeric substances through epsB and yhxB gene regulation for V-NPs aggregation to alleviate toxicity under aerobic operations. The V K-edge X-ray absorption near-edge structure (XANES) spectra suggested that VO2 NPs were oxidized to V2O5 NPs. In the anaerobic case, Comamonas sp. and Achromobacter sp. reduced V(V) to V(IV) for detoxification regulated by the napA gene. This study provides a deep understanding of the V speciation in smelting ash and microbial responses, inspiring promising bioremediation strategies to reduce its negative environmental impacts.}, } @article {pmid38197657, year = {2024}, author = {You, Y and Wang, L and Liu, X and Wang, X and Jiang, L and Ding, C and Wang, W and Zhang, D and Zhao, X}, title = {Interspecific plant interaction structures the microbiomes of poplar-soil interface to alter nutrient cycling and utilization.}, journal = {Microbiology spectrum}, volume = {12}, number = {2}, pages = {e0336823}, pmid = {38197657}, issn = {2165-0497}, support = {2021YFD2201204//MOST | National Key Research and Development Program of China (NKPs)/ ; }, mesh = {*Soil/chemistry ; Agriculture ; Glycine max ; Bacteria/genetics ; Soil Microbiology ; *Microbiota ; }, abstract = {Terrestrial plants can influence the growth and health of adjacent plants through interspecific interaction. Here, the mechanisms of interspecific plant interaction on microbial function and nutrient utilization in the plant-soil interface (non-rhizosphere soil, rhizosphere soil, and root) were studied by soybean- and potato-poplar intercropping. First, metagenomics showed that soybean- and potato-poplar intercropping influenced the composition and co-occurrence networks of microbial communities in different ecological niches, with higher stability of the microbial community in soybean intercropping. Second, the gene abundance related to carbon metabolism, nitrogen cycling, phosphorus cycling, and sulfur cycling was increased at the poplar-soil interface in soybean intercropping. Moreover, soybean intercropping increased soil nutrient content and enzymatic activity. It showed higher metabolic potential in nutrient metabolism and transportation. Third, functional microorganisms that influenced nutrient cycling and transportation in different intercropping have been identified, namely Acidobacteria, Sphingomonas, Gemmatimonadaceae, Alphaproteobacteria, and Bradyrhizobium. Therefore, intercropping can construct microbial communities to alter metabolic functions and improve nutrient cycling and absorption. Interspecific plant interactions to influence the microbiome were revealed, opening up a new way for the precise regulation of plant microbiome.IMPORTANCEPoplar has the characteristics of wide distribution, strong adaptability, and fast growth, which is an ideal tree species for timber forest. In this study, metagenomics and elemental analysis were used to comprehensively reveal the effects of interspecific plant interactions on microbial communities and functions in different ecological niches. It can provide a theoretical basis for the development and application of the precise management model in poplar.}, } @article {pmid38196273, year = {2024}, author = {Xu, J and Xia, Q and Wu, T and Shao, Y and Wang, Y and Jin, N and Tian, P and Wu, L and Lu, X}, title = {Prophylactic treatment with Bacteroides uniformis and Bifidobacterium bifidum counteracts hepatic NK cell immune tolerance in nonalcoholic steatohepatitis induced by high fat diet.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2302065}, pmid = {38196273}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; Killer Cells, Natural ; Mice ; Animals ; Immune Tolerance ; Proteomics ; Bacteroides ; *Non-alcoholic Fatty Liver Disease/etiology/prevention & control ; *Bifidobacterium bifidum ; Diet, High-Fat/adverse effects ; Humans ; }, abstract = {Hepatic immunity is one of the driving forces for the development of nonalcoholic steatohepatitis (NASH), and targeting gut microbiota is believed to affect the hepatic immune constitution. Here, we aimed to investigate the hepatic immunological state in NASH, with a specific emphasis on natural killer (NK) cells. In addition, we aimed to identify the contributing species that target hepatic immunity to provide new directions and support the feasibility of immunotherapy for NASH. A possible NASH population was determined by combination of long-term severe fatty liver, metabolic disorders and increased serum CK18 to detect serum immune factors and gut microbiota. NASH was induced in mice fed a high-fat diet to verify the prophylactic effect of the functional species on the immunopathology and development of NASH. Hepatic immunologic state was examined, and the effector functions of NK cells were detected. Hepatic transcriptome, proteomic, and fecal metagenome were performed. We observed a statistical increase in serum IL-10 (p < 0.001) and non-statistical decrease in interferon-γ and IL-6 in NASH population, hinting at the possibility of immune tolerance. Fecal Bacteroides uniformis and Bifidobacterium bifidum were abundant in healthy population but depleted in NASH patients. In NASH mice, hepatic CD8+T cells, macrophages, and dendritic cells were increased (p < 0.01), and NK cells were inhibited, which were identified with decreased granzyme B (p < 0.05). Bacteroides uniformis and Bifidobacterium bifidum improved hepatic pathological and metabolic cues, increased hepatic NK cells and reduced macrophages (p < 0.05). Bacteroides uniformis also restored hepatic NK cell function, which was identified as increased CD107a (p < 0.05). Transcriptional and translational profiling revealed that the functional species might restore the function of hepatic NK cells through multiple pathways, such as reduction of inhibitory molecules in NK cells. Bacteroides uniformis and Bifidobacterium bifidum are novel prophylactics for NASH that restore the impaired function of hepatic NK cells.}, } @article {pmid38196163, year = {2024}, author = {Hu, P and Henry, J and Tiesman, JP and Parlov, M and Bacon, R and Charbonneau, D and Venkataraman, A and Locker, KCS and Krigbaum, H and Schwartz, J}, title = {Scalp microbiome composition changes and pathway evaluations due to effective treatment with Piroctone Olamine shampoo.}, journal = {International journal of cosmetic science}, volume = {46}, number = {3}, pages = {333-347}, doi = {10.1111/ics.12933}, pmid = {38196163}, issn = {1468-2494}, support = {//Procter & Gamble Company/ ; }, mesh = {Humans ; *Microbiota/drug effects ; *Scalp/microbiology ; *Hair Preparations ; *Dandruff/microbiology/drug therapy ; Female ; Male ; Middle Aged ; Adult ; Drug Combinations ; Ethanolamines ; Pyridones ; }, abstract = {OBJECTIVE: To characterize the scalp microbial composition, function, and connection to dandruff severity using a metagenomics approach and to understand the impact of a Piroctone Olamine containing anti-dandruff shampoo on the scalp microbiome.

METHODS: Shotgun metagenomics was used to characterize the composition of the scalp microbiomes from 94 subjects with and without clinically defined dandruff. Furthermore, the microbiome of the scalps of 100 dandruff sufferers before and after 3 weeks of treatment with either control or anti-dandruff shampoo containing 0.5% Piroctone Olamine (PO) was characterized and compared to identify microorganisms associated with the dandruff condition and the associated pathways and processes that may contribute to PO's effect on scalp microbiome.

RESULTS: A higher relative abundance of Malassezia restricta and Staphylococcus capitis and a lower abundance of Cutibacterium acnes were associated with the dandruff scalps relative to the no-dandruff scalps. A 3-week PO shampoo treatment reduced the relative abundance of Malassezia species and Staphylococcus capitis and increased the relative abundance of Cutibacterium acnes. This change to the scalp microbiome composition is consistent with a return to a healthy no-dandruff microbiome and improved clinical signs and symptoms as measured by adherent scalp flaking score (ASFS) compared with the control shampoo. Functional genomics analysis showed that the PO shampoo treatment reduced oxidative stress-associated genes and decreased the abundance of protease, urease, and lipase genes. These changes correlated positively to improvements in dandruff severity. PO treatment favourably shifted scalp microbiomes in dandruff subjects toward the no-dandruff state.

CONCLUSION: Our results suggest that part of the aetiology of dandruff can be attributed to dysbiosis of the scalp microbiome. PO treatment can restore a healthier microbiome, reducing oxidative stress and promoting better scalp health.}, } @article {pmid38196020, year = {2024}, author = {Yu, M and Liu, J and Chen, J and Lin, C and Deng, S and Wu, M}, title = {Metagenomic and metabolomic profiling of dried shrimp (Litopenaeus vannamei) prepared by a procedure traditional to the south China coastal area.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {27}, number = {4}, pages = {1307-1319}, pmid = {38196020}, issn = {1618-1905}, support = {2021KCXTD081//Guangdong University Innovation Team Project/ ; 2019GKTSCX120//the Innovation Projects of Colleges and Universities in Guangdong Province/ ; KY201902, KY201903//Foundation of Foshan Polytechnic/ ; 2020A1515110332//Basic and Applied Basic Research Foundation of Guangdong Province/ ; }, mesh = {*Penaeidae/microbiology ; Animals ; China ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Metabolomics/methods ; *Microbiota ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Metabolome ; Food Handling/methods ; Shellfish/microbiology ; }, abstract = {Sun-drying is a traditional process for preparing dried shrimp in coastal area of South China, but its impacts on nutrition and the formation of flavor-contributory substances in dried shrimp remain largely unknown. This study aimed to examine the effects of the production process on the microbiota and metabolites in dried shrimp. 16S rDNA amplicon sequencing was employed to identify 170 operational taxonomic units (OTUs), with Vibrio, Photobacterium, and Shewanella emerging as the primary pathogenic bacteria in shrimp samples. Lactococcus lactis was identified as the principal potential beneficial microorganism to accrue during the dried shrimp production process and found to contribute significantly to the development of desirable shrimp flavors. LC-MS-based analyses of dried shrimp sample metabolomes revealed a notable increase in compounds associated with unsaturated fatty acid biosynthesis, arachidonic acid metabolism, amino acid biosynthesis, and flavonoid and flavanol biosynthesis throughout the drying process. Subsequent exploration of the relationship between metabolites and bacterial communities highlighted the predominant coexistence of Bifidobacterium, Clostridium, and Photobacterium contributing heterocyclic compounds and metabolites of organic acids and their derivatives. Conversely, Arthrobacter and Staphylococcus were found to inhibit each other, primarily in the presence of heterocyclic compounds. This comprehensive investigation provides valuable insights into the dynamic changes in the microbiota and metabolites of dried shrimps spanning different drying periods, which we expect to contribute to enhancing production techniques and safety measures for dried shrimp processing.}, } @article {pmid38195681, year = {2024}, author = {Tapilatu, Y and Fauzan, I and Pradipta, A and Kusuma, AB}, title = {A first report on prokaryotic diversity in northwestern Arafura deep-sea sediments, Indonesia.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {895}, pmid = {38195681}, issn = {2045-2322}, mesh = {Indonesia ; RNA, Ribosomal, 16S/genetics ; *Prokaryotic Cells ; Archaea/genetics ; *Microbiota ; }, abstract = {Indonesia's deep-sea microbial communities remain poorly understood, prompting the need for comprehensive investigations. This study aimed to assess the bacterial and archaeal diversities in northwestern Arafura deep-sea sediments, spanning depths of 100 to 1,457 m using a 16S rRNA based-metagenomic sequencing approach, without technical and biological replicates. Principal component analyses based on the Bray-Curtis dissimilarity index indicated that most of the bacterial and archaeal communities were habitat-specific and influenced by depth. The most prevalent known bacterial phylotypes were detected from all samples belonging to the phylum of Desulfobacteriota, Pseudomonadota, and Firmicutes. In addition, the samples also harbored diverse members of the Archaea domain, including Crenarchaeota, Nanoarchaeota and Haloarchaeota. Notably, the sequencing data revealed the significant presence of rare prokaryotic taxa, including uncultured counterparts with less than 1% abundance. The findings suggest that novel and rare prokaryotic taxa are abundant in northwestern Arafura deep-sea ecosystem, offering unique opportunities for further bioprospecting and functional ecology studies.}, } @article {pmid38194811, year = {2024}, author = {Tang, J and Zhao, H and Li, K and Zhou, H and Chen, Q and Wang, H and Li, S and Xu, J and Sun, Y and Chang, X}, title = {Intestinal microbiota promoted NiONPs-induced liver fibrosis via effecting serum metabolism.}, journal = {Ecotoxicology and environmental safety}, volume = {270}, number = {}, pages = {115943}, doi = {10.1016/j.ecoenv.2024.115943}, pmid = {38194811}, issn = {1090-2414}, mesh = {Rats ; Animals ; *Gastrointestinal Microbiome/genetics ; Linoleic Acid ; Liver Cirrhosis/chemically induced ; Acetyl-CoA Carboxylase ; *Metabolic Diseases ; }, abstract = {Nickel oxide nanoparticles (NiONPs) are toxic heavy metal compounds that induce liver fibrosis and metabolic disorders. Current research shows that the intestinal microbiota regulates liver metabolism through the gut-liver axis. However, it is unclear whether NiONPs affect the intestinal microbiota and the relationship between microbiota and liver metabolic disorders. Therefore, in this study, we established liver fibrosis model by administering 0.015, 0.06 and 0.24 mg/mL NiONPs through tracheal instillation twice a week for 9 weeks in rats, then we collected serum and fecal sample for whole metabolomics and metagenomic sequencing. As the result of sequencing, we screened out seven metabolites (beta-D-glucuronide, methylmalonic acid, linoleic acid, phosphotidylcholine, lysophosphatidylinositol, docosapentaenoic acid and progesterone) that related to functional alterations (p < 0.05), and obtained a decrease of probiotics abundances (p < 0.05) as well as a variation of the microbiota enzyme activity (p < 0.05), indicating that NiONPs inhibited the proliferation of probiotics. As the result of correlation analysis, we found a positive correlation between differential metabolites and probiotics, such as lysophosphatidylinositol was positively correlated with Desulfuribacillus, Jeotgallibacillus and Rummeliibacillus (p < 0.05). We also found that differential metabolites had correlations with differential proteins and enzymes of intestinal microbiota, such as glucarate dehydratase, dihydroorotate dehydrogenase and acetyl-CoA carboxylase (p < 0.05). Finally, we screened six metabolic pathways with both differential intestinal microbiota enzymes and metabolites were involved, such as pentose and glucuronate interconversions, and linoleic acid metabolism. In vitro experiments showed that NiONPs increased the transcriptional expression of Col1A1 in LX-2 cells, while reducing the mRNA expression of serine/threonine activators, acetyl coenzyme carboxylase, and lysophosphatidylinositol synthase, and short chain fatty acid sodium butyrate can alleviate these variation trends. The results proved that the intestinal microbiota enzyme systems were associated with serum metabolites, suggesting that the disturbance of intestinal microbiota and reduction of probiotics promoted the occurrence and development of NiONPs-induced liver fibrosis by affecting metabolic pathways.}, } @article {pmid38193687, year = {2024}, author = {Zhao, L and Yang, X and Liang, Y and Zhang, Z and Ding, Y and Wang, Y and Chen, B and Wu, J and Jin, C and Zhao, G and Li, Z and Zhang, L}, title = {Temporal development and potential interactions between the gut microbiome and resistome in early childhood.}, journal = {Microbiology spectrum}, volume = {12}, number = {2}, pages = {e0317723}, pmid = {38193687}, issn = {2165-0497}, support = {82172320//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022M711915//China Postdoctoral Science Foundation (China Postdoctoral Foundation Project)/ ; ZR2022QC169//Shandong Provincial Natural Science Foundation/ ; tscy20190612//Taishan Industrial Experts Program/ ; //Shandong University Outstanding Young Scholars Program/ ; 82370785//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Infant ; Child ; Humans ; Child, Preschool ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Multiple, Bacterial ; *Microbiota ; }, abstract = {Antimicrobial resistance-associated infections have become a major threat to global health. The gut microbiome serves as a major reservoir of bacteria with antibiotic resistance genes; whereas, the temporal development of gut resistome during early childhood and the factors influencing it remain unclear. Moreover, the potential interactions between gut microbiome and resistome still need to be further explored. In this study, we found that antibiotic treatment led to destabilization of the gut microbiome and resistome structural communities, exhibiting a greater impact on the resistome than on the microbiome. The composition of the gut resistome at various developmental stages was influenced by the abundance and richness of different core microbes. First exposure to antibiotics led to a dramatic increase in the number of opportunistic pathogens carrying multidrug efflux pump encoding genes. Multiple factors could influence the gut microbiome and resistome formation. The data may provide new insights into early-life research.IMPORTANCEIn recent years, the irrational or inappropriate use of antibiotics, an important life-saving medical intervention, has led to the emergence and increase of drug-resistant and even multidrug-resistant bacteria. It remains unclear how antibiotic exposure affects various developmental stages of early childhood and how gut core microbes under antibiotic exposure affect the structural composition of the gut resistome. In this study, we focused on early antibiotic exposure and analyzed these questions in detail using samples from infants at various developmental stages. The significance of our research is to elucidate the impact of early antibiotic exposure on the dynamic patterns of the gut resistome in children and to provide new insights for early-life studies.}, } @article {pmid38193672, year = {2024}, author = {Yu, Y and Zhang, Q and Kang, J and Xu, N and Zhang, Z and Deng, Y and Gillings, M and Lu, T and Qian, H}, title = {Effects of organic fertilizers on plant growth and the rhizosphere microbiome.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {2}, pages = {e0171923}, pmid = {38193672}, issn = {1098-5336}, support = {2022C02029//Key Research and Development Program of Zhejiang Province (Key R&D plan of Zhejiang Province)/ ; 21976161//MOST | National Natural Science Foundation of China (NSFC)/ ; 41907210//MOST | National Natural Science Foundation of China (NSFC)/ ; 42307158//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Rhizosphere ; Fertilizers ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Soil ; Plants/genetics ; Soil Microbiology ; Plant Roots ; }, abstract = {Application of organic fertilizers is an important strategy for sustainable agriculture. The biological source of organic fertilizers determines their specific functional characteristics, but few studies have systematically examined these functions or assessed their health risk to soil ecology. To fill this gap, we analyzed 16S rRNA gene amplicon sequencing data from 637 soil samples amended with plant- and animal-derived organic fertilizers (hereafter plant fertilizers and animal fertilizers). Results showed that animal fertilizers increased the diversity of soil microbiome, while plant fertilizers maintained the stability of soil microbial community. Microcosm experiments verified that plant fertilizers were beneficial to plant root development and increased carbon cycle pathways, while animal fertilizers enriched nitrogen cycle pathways. Compared with animal fertilizers, plant fertilizers harbored a lower abundance of risk factors such as antibiotic resistance genes and viruses. Consequently, plant fertilizers might be more suitable for long-term application in agriculture. This work provides a guide for organic fertilizer selection from the perspective of soil microecology and promotes sustainable development of organic agriculture.IMPORTANCEThis study provides valuable guidance for use of organic fertilizers in agricultural production from the perspective of the microbiome and ecological risk.}, } @article {pmid38193195, year = {2024}, author = {Abdulnour-Nakhoul, SM and Kolls, JK and Flemington, EK and Ungerleider, NA and Nakhoul, HN and Song, K and Nakhoul, NL}, title = {Alterations in gene expression and microbiome composition upon calcium-sensing receptor deletion in the mouse esophagus.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {326}, number = {4}, pages = {G438-G459}, pmid = {38193195}, issn = {1522-1547}, support = {R35 HL139930/HL/NHLBI NIH HHS/United States ; I01 BX001513/BX/BLRD VA/United States ; U54 GM104940/GM/NIGMS NIH HHS/United States ; R01 CA272142/CA/NCI NIH HHS/United States ; R01 CA243793/CA/NCI NIH HHS/United States ; R01 CA262090/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Calcium/metabolism ; Receptors, Calcium-Sensing/genetics/metabolism ; Esophagus/metabolism ; *Microbiota ; Inflammation ; Gene Expression ; }, abstract = {The calcium-sensing receptor (CaSR), a G protein-coupled receptor, regulates Ca[2+] concentration in plasma by regulating parathyroid hormone secretion. In other tissues, it is reported to play roles in cellular differentiation and migration and in secretion and absorption. We reported previously that CaSR can be conditionally deleted in the mouse esophagus. This conditional knockout (KO) ([Eso]CaSR[-/-]) model showed a significant reduction in the levels of adherens and tight junction proteins and had a marked buildup of bacteria on the luminal esophageal surface. To further examine the role of CaSR, we used RNA sequencing to determine gene expression profiles in esophageal epithelia of control and [Eso]CaSR[-/-]mice RNA Seq data indicated upregulation of gene sets involved in DNA replication and cell cycle in [Eso]CaSR[-/-]. This is accompanied by the downregulation of gene sets involved in the innate immune response and protein homeostasis including peptide elongation and protein trafficking. Ingenuity pathway analysis (IPA) demonstrated that these genes are mapped to important biological networks including calcium and Ras homologus A (RhoA) signaling pathways. To further explore the bacterial buildup in [Eso]CaSR[-/-] esophageal tissue, 16S sequencing of the mucosal-associated bacterial microbiome was performed. Three bacterial species, g_Rodentibacter, s_Rodentibacter_unclassified, and s_Lactobacillus_hilgardi were significantly increased in [Eso]CaSR[-/-]. Furthermore, metagenomic analysis of 16S sequences indicated that pathways related to oxidative phosphorylation and metabolism were downregulated in [Eso]CaSR[-/-] tissues. These data demonstrate that CaSR impacts major pathways of cell proliferation, differentiation, cell cycle, and innate immune response in esophageal epithelium. The disruption of these pathways causes inflammation and significant modifications of the microbiome.NEW & NOTEWORTHY Calcium-sensing receptor (CaSR) plays a significant role in maintaining the barrier function of esophageal epithelium. Using RNA sequencing, we show that conditional deletion of CaSR from mouse esophagus causes upregulation of genes involved in DNA replication and cell cycle and downregulation of genes involved in the innate immune response, protein translation, and cellular protein synthesis. Pathway analysis shows disruption of signaling pathways of calcium and actin cytoskeleton. These changes caused inflammation and esophageal dysbiosis.}, } @article {pmid38192240, year = {2024}, author = {Skoog, EJ and Bosak, T}, title = {Predicted metabolic roles and stress responses provide insights into candidate phyla Hydrogenedentota and Sumerlaeota as members of the rare biosphere in biofilms from various environments.}, journal = {Environmental microbiology reports}, volume = {16}, number = {1}, pages = {e13228}, pmid = {38192240}, issn = {1758-2229}, support = {327126//Simons Foundation/ ; 344707//Simons Foundation/ ; }, mesh = {*Bacteria/genetics/metabolism ; *Microbiota ; Metagenome ; Biofilms ; Cellulose/metabolism ; Phylogeny ; }, abstract = {Pustular mats from Shark Bay, Western Australia, host complex microbial communities bound within an organic matrix. These mats harbour many poorly characterized organisms with low relative abundances (<1%), such as candidate phyla Hydrogenedentota and Sumerlaeota. Here, we aim to constrain the metabolism and physiology of these candidate phyla by analyzing two representative metagenome-assembled genomes (MAGs) from a pustular mat. Metabolic reconstructions of these MAGs suggest facultatively anaerobic, chemoorganotrophic lifestyles of both organisms and predict that both MAGs can metabolize a diversity of carbohydrate substrates. Ca. Sumerlaeota possesses genes involved in degrading chitin, cellulose and other polysaccharides, while Ca. Hydrogenedentota can metabolize cellulose derivatives in addition to glycerol, fatty acids and phosphonates. Both Ca. phyla can respond to nitrosative stress and participate in nitrogen metabolism. Metabolic comparisons of MAGs from Shark Bay and those from various polyextreme environments (i.e., hot springs, hydrothermal vents, subsurface waters, anaerobic digesters, etc.) reveal similar metabolic capabilities and adaptations to hypersalinity, oxidative stress, antibiotics, UV radiation, nitrosative stress, heavy metal toxicity and life in surface-attached communities. These adaptations and capabilities may account for the widespread nature of these organisms and their contributions to biofilm communities in a range of extreme surface and subsurface environments.}, } @article {pmid38191834, year = {2024}, author = {Ashiqueali, SA and Chaudhari, D and Zhu, X and Noureddine, S and Siddiqi, S and Garcia, DN and Gostynska, A and Stawny, M and Rubis, B and Zanini, BM and Mansoor, MAM and Schneider, A and Naser, SA and Yadav, H and Masternak, MM}, title = {Fisetin modulates the gut microbiota alongside biomarkers of senescence and inflammation in a DSS-induced murine model of colitis.}, journal = {GeroScience}, volume = {46}, number = {3}, pages = {3085-3103}, pmid = {38191834}, issn = {2509-2723}, support = {R56 AG074499/AG/NIA NIH HHS/United States ; R56 AG074499/GF/NIH HHS/United States ; R56 AG069676/AG/NIA NIH HHS/United States ; R56 AG064075/AG/NIA NIH HHS/United States ; RF1 AG071762/AG/NIA NIH HHS/United States ; R21 AG072379/AG/NIA NIH HHS/United States ; U01 AG076928/AG/NIA NIH HHS/United States ; R21 DE032197/DE/NIDCR NIH HHS/United States ; }, mesh = {Female ; Animals ; Mice ; *Gastrointestinal Microbiome ; Disease Models, Animal ; *Colitis/chemically induced/drug therapy/metabolism ; Inflammation ; *Inflammatory Bowel Diseases/microbiology ; Biomarkers ; *MicroRNAs ; *Flavonols ; }, abstract = {Colitis, a subtype of inflammatory bowel disease (IBD), is a multifactorial disorder characterized by chronic inflammation of the colon. Among various experimental models used in the study of IBD, the chemical colitogenic dextran sulfate sodium (DSS) is most commonly employed to induce colitis in vivo. In the search for new therapeutic strategies, Fisetin, a flavonoid found in many fruits and vegetables, has recently garnered attention for its senolytic properties. Female mice were administered 2.5% DSS in sterile drinking water and were subsequently treated with Fisetin or vehicle by oral gavage. DSS significantly upregulated beta-galactosidase activity in colonic proteins, while Fisetin remarkably inhibited its activity to baseline levels. Particularly, qPCR revealed that the senescence and inflammation markers Vimentin and Ptgs2 were elevated by DSS exposure with Fisetin treatment inhibiting the expression of p53, Bcl2, Cxcl1, and Mcp1, indicating that the treatment reduced senescent cell burden in the DSS targeted intestine. Alongside, senescence and inflammation associated miRNAs miR-149-5p, miR-96-5p, miR-34a-5p, and miR-30e-5p were significantly inhibited by DSS exposure and restored by Fisetin treatment, revealing novel targets for the treatment of IBDs. Metagenomics was implemented to assess impacts on the microbiota, with DSS increasing the prevalence of bacteria in the phyla Bacteroidetes. Meanwhile, Fisetin restored gut health through increased abundance of Akkermansia muciniphila, which is negatively correlated with senescence and inflammation. Our study suggests that Fisetin mitigates DSS-induced colitis by targeting senescence and inflammation and restoring beneficial bacteria in the gut indicating its potential as a therapeutic intervention for IBDs.}, } @article {pmid38191433, year = {2024}, author = {Zhang, RY and Wang, YR and Liu, RL and Rhee, SK and Zhao, GP and Quan, ZX}, title = {Metagenomic characterization of a novel non-ammonia-oxidizing Thaumarchaeota from hadal sediment.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {7}, pmid = {38191433}, issn = {2049-2618}, support = {2021R1A2C3004015//National Research Foundation of Korea/ ; 2018YFC0310600//the National Key R&D Program of China/ ; 31870109, 31811540398//the National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Metagenome/genetics ; *Ammonia ; Ecosystem ; Metagenomics ; Archaea/genetics ; }, abstract = {BACKGROUND: The hadal sediment, found at an ocean depth of more than 6000 m, is geographically isolated and under extremely high hydrostatic pressure, resulting in a unique ecosystem. Thaumarchaeota are ubiquitous marine microorganisms predominantly present in hadal environments. While there have been several studies on Thaumarchaeota there, most of them have primarily focused on ammonia-oxidizing archaea (AOA). However, systematic metagenomic research specifically targeting heterotrophic non-AOA Thaumarchaeota is lacking.

RESULTS: In this study, we explored the metagenomes of Challenger Deep hadal sediment, focusing on the Thaumarchaeota. Functional analysis of sequence reads revealed the potential contribution of Thaumarchaeota to recalcitrant dissolved organic matter degradation. Metagenome assembly binned one new group of hadal sediment-specific and ubiquitously distributed non-AOA Thaumarchaeota, named Group-3.unk. Pathway reconstruction of this new type of Thaumarchaeota also supports heterotrophic characteristics of Group-3.unk, along with ABC transporters for the uptake of amino acids and carbohydrates and catabolic utilization of these substrates. This new clade of Thaumarchaeota also contains aerobic oxidation of carbon monoxide-related genes. Complete glyoxylate cycle is a distinctive feature of this clade in supplying intermediates of anabolic pathways. The pan-genomic and metabolic analyses of metagenome-assembled genomes belonging to Group-3.unk Thaumarchaeota have highlighted distinctions, including the dihydroxy phthalate decarboxylase gene associated with the degradation of aromatic compounds and the absence of genes related to the synthesis of some types of vitamins compared to AOA. Notably, Group-3.unk shares a common feature with deep ocean AOA, characterized by their high hydrostatic pressure resistance, potentially associated with the presence of V-type ATP and di-myo-inositol phosphate syntheses-related genes. The enrichment of organic matter in hadal sediments might be attributed to the high recruitment of sequence reads of the Group-3.unk clade of heterotrophic Thaumarchaeota in the trench sediment. Evolutionary and genetic dynamic analyses suggest that Group-3 non-AOA consists of mesophilic Thaumarchaeota organisms. These results indicate a potential role in the transition from non-AOA to AOA Thaumarchaeota and from thermophilic to mesophilic Thaumarchaeota, shedding light on recent evolutionary pathways.

CONCLUSIONS: One novel clade of heterotrophic non-AOA Thaumarchaeota was identified through metagenome analysis of sediments from Challenger Deep. Our study provides insight into the ecology and genomic characteristics of the new sub-group of heterotrophic non-AOA Thaumarchaeota, thereby extending the knowledge of the evolution of Thaumarchaeota. Video Abstract.}, } @article {pmid38189294, year = {2024}, author = {Zhang, J and Shi, M and Zhao, C and Liang, G and Li, C and Ge, X and Pei, C and Kong, Y and Li, D and Yang, W and Cao, B and Fu, L and Yan, Y and Wu, J and Zhou, J and Fang, Y and Meng, X and Li, Y and Wang, L}, title = {Role of intestinal flora in the development of nonalcoholic fatty liver disease in children.}, journal = {Microbiology spectrum}, volume = {12}, number = {2}, pages = {e0100623}, pmid = {38189294}, issn = {2165-0497}, support = {XXT22//Digestive Medical Coordinated Development Center of Beijing Hospitals Authority/ ; 7222060//Beijing Natural Science Foundation/ ; 2020JH2/10300041//Liaoning Natural Science Foundation/ ; DFL20221003//Beijing Hospitals Authority's Ascent Plan/ ; LC2021A06//Beijing Hope Run Special Fund of Cancer Foundation of China/ ; 7222153//Beijing Natural Science Foundation/ ; Shoufa 2020-1-2024//Capital Health Development Research Project/ ; }, mesh = {Adult ; Adolescent ; Humans ; Child ; *Non-alcoholic Fatty Liver Disease ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; Follow-Up Studies ; Biomarkers/metabolism ; Liver/metabolism ; }, abstract = {In China, 45% of adolescents with obesity develop fatty liver disease, a condition that increases the long-term risk of developing cirrhosis and liver cancer. Although the factors triggering nonalcoholic fatty liver disease (NAFLD) vary in children, the composition of intestinal microflora has been found to play an increasingly important role. However, evidence is limited on the prevalence of nonalcoholic fatty liver (NAFL) and nonalcoholic steatohepatitis (NASH) in Chinese children. Therefore, this study aimed to evaluate the fecal microbiome of Chinese children with NAFLD and further analyze the potential of flora in regulating NAFLD-related symptoms and metabolic functions. Specifically, the study applied a 16S rRNA and metagenomic sequencing to the fecal samples of pediatric patients with NAFLD, NASH, and NAFL, as well as healthy controls, to explore the correlation among NAFLD-related indexes, metabolic pathways, and gut flora. The findings showed that some fecal microbiota had a negative correlation with body mass index, and various NAFLD-related bacteria, including Lachnoclostridium, Escherichia-Shigella, and Faecalibacterium prausnitzii, were detected. Consequently, the study concluded that the variation in gut microbiota might be more important in improving NAFLD/NASH compared with single species, providing a microbiota diagnostic profile of NAFLD/NASH.IMPORTANCEThis study aims to characterize the gut microbiota in Chinese children with nonalcoholic fatty liver disease (NAFLD) through 16S rRNA and metagenomic sequencing. The results highlight the association between fecal microbiota and NAFLD in Chinese children, demonstrating distinct characteristics compared to adults and children from other countries. Based on the sequencing data from our cohort's fecal samples, we propose a microbiota model with a high area under the curve for distinguishing between NAFLD and healthy individuals. Furthermore, our follow-up study reveals that changes in the relative abundance of microbial biomarkers in this model are consistent with variations in patients' body mass index. These findings suggest the potential utility of the microbiota model and microbial biomarkers for diagnosing and treating NAFLD in children.}, } @article {pmid38188628, year = {2023}, author = {Liu, Y and Wen, Z and Fang, Y and Wang, T and Wu, F and Zhang, H and Chen, D and Liu, J}, title = {Herpesvirus reactivation in respiratory tract is associated with increased mortality of severe pneumonia patients and their respiratory microbiome dysbiosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1294142}, pmid = {38188628}, issn = {2235-2988}, mesh = {Humans ; Dysbiosis ; Retrospective Studies ; Respiratory System ; *Pneumonia ; *Herpesviridae/genetics ; *Herpesvirus 1, Human ; Herpesvirus 2, Human ; Herpesvirus 4, Human ; *Microbiota ; }, abstract = {Severe pneumonia (SP) is a respiratory tract disease that seriously threatens human health. The herpesvirus detected in patients, especially with severe and immunodeficient diseases, is gradually attracting the attention of clinical doctors. However, little is known about the effect of herpesvirus on the prognosis of SP patients and the pulmonary microbial community. Here, we retrospectively analyzed respiratory samples from 45 SP patients detected by metagenomic next-generation sequencing (mNGS). A total of five types of herpesviruses were detected, with Human alphaherpesvirus 1 (HHV-1) in 19 patients, Human betaherpesvirus 5 (CMV) in 7 patients, Human betaherpesvirus 7 (HHV-7) in 6 patients, Human alphaherpesvirus 2 (HHV-2) in 5 patients, and Human gammaherpesvirus 4 (EBV) in 4 patients. Further analysis showed that the mortality of the herpesvirus-positive group was significantly higher than that of the negative group. The results also showed that HHV-1 was significantly associated with the prognosis of SP patients, while the other herpesviruses did not have a significant difference in patient mortality. A comparison of the microbial community characteristics of SP patients showed a significant difference in beta-diversity between herpesvirus-positive and negative groups. Species difference analysis showed that the herpesvirus-positive group was related to more conditional pathogens, such as Pneumocystis jirovecii and Burkholderia cepacia. In summary, our results suggest that the presence of herpesvirus is associated with the mortality of SP patients. Furthermore, enrichment of conditional pathogens in the respiratory tract of herpesvirus-positive SP patients may be a potential reason for the increased mortality.}, } @article {pmid38188580, year = {2023}, author = {Wu, D and Yin, C and Fan, Y and Chi, H and Liu, Z and Jin, G}, title = {Effect of forest planting patterns on the formation of soil organic carbon during litter lignocellulose degradation from a microbial perspective.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1327481}, pmid = {38188580}, issn = {1664-302X}, abstract = {Litter decomposition is an important source of soil organic carbon, and it plays a key role in maintaining the stability of forest ecosystems. The microbial mechanism of soil organic carbon (SOC) formation in different urban forest planting patterns during litter lignocellulose degradation is still unclear. The key genes, microbes, and metabolites in the process of lignocellulose degradation and SOC formation were determined by metagenomics and metabolomics in different litter decomposition layers and soil layers in different urban forest planting patterns, including three types of broadleaf forests (BP forests), three types of coniferous forests (CP forests), and two types of mixed coniferous and broadleaf forests (MCBP forests). The results indicated that the cellulose, hemicellulose, and lignin concentrations from the undecomposed layer to the totally decomposed layer decreased by 70.07, 86.83, and 73.04% for CP litter; 74.30, 93.80, and 77.55% for BP litter; and 62.51, 48.58, and 90.61% for MCBP litter, respectively. The soil organic carbon of the BP forests and MCBP forests was higher than that of the CP forests by 38.06 and 94.43% for the 0-10 cm soil layer and by 38.55 and 20.87% for the 10-20 cm soil layer, respectively. Additionally, the gene abundances of glycoside hydrolases (GHs) and polysaccharide lyases (PLs) in the BP forests were higher than those in the MCBP forests and CP forests. Amino acid metabolism, sugar metabolism, TCA metabolism, and cAMP signaling metabolism were mainly between the CP forests and BP forests, while the TCA cycle, pyruvate metabolism, phenylalanine metabolism, and tyrosine metabolism were mainly between the BP forests and MCBP forests during litter decomposition. Additionally, ammonia nitrogen and hemicellulose were key factors driving SOC formation in the CP forests, while ammonia nitrogen, hemicellulose, and lignocellulose-degrading genes were key factors driving SOC formation in the BP forests. For the MCBP forests, cellulose, pH, ammonia nitrogen, and lignin were key factors driving SOC formation. Our findings revealed that the BP forests and MCBP forests had stronger lignocellulose degradation performance in the formation of SOC. This study provided a theoretical basis for the flow and transformation of nutrients in different urban forest management patterns.}, } @article {pmid38185596, year = {2024}, author = {De Coninck, L and Matthijnssens, J}, title = {The mosquito core virome: beyond the buzz.}, journal = {Trends in parasitology}, volume = {40}, number = {3}, pages = {201-202}, doi = {10.1016/j.pt.2023.12.012}, pmid = {38185596}, issn = {1471-5007}, mesh = {Animals ; *Culicidae ; Virome ; Phylogeny ; Mosquito Vectors ; }, } @article {pmid38185288, year = {2024}, author = {Luan, Z and Fu, S and Qi, S and Li, C and Chen, J and Zhao, Y and Zhang, H and Wu, J and Zhao, Z and Zhang, J and Chen, Y and Zhang, W and Jing, Y and Wang, S and Sun, G}, title = {A metagenomics study reveals the gut microbiome as a sex-specific modulator of healthy aging in Hainan centenarians.}, journal = {Experimental gerontology}, volume = {186}, number = {}, pages = {112356}, doi = {10.1016/j.exger.2023.112356}, pmid = {38185288}, issn = {1873-6815}, mesh = {Humans ; Aged, 80 and over ; Male ; Female ; *Gastrointestinal Microbiome ; Centenarians ; Activities of Daily Living ; *Healthy Aging/genetics ; Aging ; }, abstract = {BACKGROUND: Sex differences in health status and life expectancy are widely accepted to exist. The mechanisms underlying it are still poorly understood. In this study, we aimed to clarify the influences and contributions of sex on the gut microbiome in healthy centenarians and to explore the different roles played by the gut microbiome in healthy aging between the sexes.

RESULTS: Taking covariates of different dimensions into account (social demographics, anthropometry, the activities of daily living, dietary structure, mental state, blood tests, lifestyle and disease history), our data showed that sex was one of the most significant covariates affecting the gut microbiome of healthy centenarians at both the species and Kyoto Encyclopedia of Genes and Genomes Orthology (KO) levels. The beta diversity between the sexes were significantly different (Adonis test: p = 0.011, R[2] = 0.031), and the male centenarians had a greater alpha diversity than the females (Simpson and Shannon test: P<0.05). At the species level, we identified 31 species enriched in males and 7 species enriched in females. The composition and function patterns of the microbiome varied between the sexes. Further functional analysis showed that males' gut microbiome exhibited greater resistance to oxidative stress compared to females. In contrast to men, the species associated with healthy aging dominated among healthy female centenarians, while the species associated with unhealthy aging were relatively rare.

CONCLUSIONS: The present study reveals that the gut microbiome structure and resistance to oxidative stress in healthy centenarians differ between the sexes and provides new insights into the possible sex-specific role of the gut microbiome in healthy aging.}, } @article {pmid38184913, year = {2024}, author = {Chen, X and Sheng, Y and Wang, G and Zhou, P and Liao, F and Mao, H and Zhang, H and Qiao, Z and Wei, Y}, title = {Spatiotemporal successions of N, S, C, Fe, and As cycling genes in groundwater of a wetland ecosystem: Enhanced heterogeneity in wet season.}, journal = {Water research}, volume = {251}, number = {}, pages = {121105}, doi = {10.1016/j.watres.2024.121105}, pmid = {38184913}, issn = {1879-2448}, mesh = {Wetlands ; Seasons ; *Microbiota ; *Groundwater/chemistry ; Carbon/metabolism ; *Water Pollutants, Chemical/analysis ; }, abstract = {Microorganisms in wetland groundwater play an essential role in driving global biogeochemical cycles. However, largely due to the dynamics of spatiotemporal surface water-groundwater interaction, the spatiotemporal successions of biogeochemical cycling in wetland groundwater remain poorly delineated. Herein, we investigated the seasonal coevolution of hydrogeochemical variables and microbial functional genes involved in nitrogen, carbon, sulfur, iron, and arsenic cycling in groundwater within a typical wetland, located in Poyang Lake Plain, China. During the dry season, the microbial potentials for dissimilatory nitrate reduction to ammonium and ammonification were dominant, whereas the higher potentials for nitrogen fixation, denitrification, methane metabolism, and carbon fixation were identified in the wet season. A likely biogeochemical hotspot was identified in the area located in the low permeable aquifer near the lake, characterized by reducing conditions and elevated levels of Fe[2+] (6.65-17.1 mg/L), NH4[+] (0.57-3.98 mg/L), total organic carbon (1.02-1.99 mg/L), and functional genes. In contrast to dry season, higher dissimilarities of functional gene distribution were observed in the wet season. Multivariable statistics further indicated that the connection between the functional gene compositions and hydrogeochemical variables becomes less pronounced as the seasons transition from dry to wet. Despite this transition, Fe[2+] remained the dominant driving force on gene distribution during both seasons. Gene-based co-occurrence network displayed reduced interconnectivity among coupled C-N-Fe-S cycles from the dry to the wet season, underpinning a less complex and more destabilizing occurrence pattern. The rising groundwater level may have contributed to a reduction in the stability of functional microbial communities, consequently impacting ecological functions. Our findings shed light on microbial-driven seasonal biogeochemical cycling in wetland groundwater.}, } @article {pmid38183799, year = {2024}, author = {Liu, H and Jiao, P and Guan, L and Wang, C and Zhang, XX and Ma, L}, title = {Functional traits and health implications of the global household drinking-water microbiome retrieved using an integrative genome-centric approach.}, journal = {Water research}, volume = {250}, number = {}, pages = {121094}, doi = {10.1016/j.watres.2023.121094}, pmid = {38183799}, issn = {1879-2448}, mesh = {Humans ; *Drinking Water/metabolism ; Bacteria/metabolism ; *Microbiota ; Archaea/genetics ; Metagenome ; }, abstract = {The biological safety of drinking water plays a crucial role in public health protection. However, research on the drinking water microbiome remains in its infancy, especially little is known about the potentially pathogenic bacteria in and functional characteristics of the microbiome in household tap water that people are directly exposed to. In this study, we used a genomic-centric approach to construct a genetic catalogue of the drinking water microbiome by analysing 116 metagenomic datasets of household tap water worldwide, spanning nine countries/regions on five continents. We reconstructed 859 high-quality metagenome-assembled genomes (MAGs) spanning 27 bacterial and 2 archaeal phyla, and found that the core MAGs belonging to the phylum Proteobacteria encoded the highest metabolic functional diversity of the 33 key complete metabolic modules. In particular, we found that two core MAGs of Brevibacillus and Methylomona encoded genes for methane metabolism, which may support the growth of heterotrophic organisms observed in the oligotrophic ecosystem. Four MAGs of complete ammonia oxidation (comammox) Nitrospira were identified and functional metabolic analysis suggested these may enable mixotrophic growth and encode genes for reactive oxygen stress defence and arsenite reduction that could aid survival in the environment of oligotrophic drinking water systems. Four MAGs were annotated as potentially pathogenic bacteria (PPB) and thus represented a possible public health concern. They belonged to the genera Acinetobacter (n = 3) and Mycobacterium (n = 1), with a total relative abundance of 1.06 % in all samples. The genomes of PPB A. junii and A. ursingii were discovered to contain antibiotic resistance genes and mobile genetic elements that could contribute to antimicrobial dissemination in drinking water. Further network analysis suggested that symbiotic microbes which support the growth of pathogenic bacteria can be targets for future surveillance and removal.}, } @article {pmid38182885, year = {2024}, author = {Zhu, X and Xu, P and Zhu, R and Gao, W and Yin, W and Lan, P and Zhu, L and Jiao, N}, title = {Multi-kingdom microbial signatures in excess body weight colorectal cancer based on global metagenomic analysis.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {24}, pmid = {38182885}, issn = {2399-3642}, support = {82000536//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; Metagenome ; Arginine ; *Gastrointestinal Microbiome/genetics ; Weight Gain ; *Colorectal Neoplasms/diagnosis/genetics ; }, abstract = {Excess body weight (EBW) increases the risk of colorectal cancer (CRC) and is linked to lower colonoscopy compliance. Here, we extensively analyzed 981 metagenome samples from multiple cohorts to pinpoint the specific microbial signatures and their potential capability distinguishing EBW patients with CRC. The gut microbiome displayed considerable variations between EBW and lean CRC. We identify 44 and 37 distinct multi-kingdom microbial species differentiating CRC and controls in EBW and lean populations, respectively. Unique bacterial-fungal associations are also observed between EBW-CRC and lean-CRC. Our analysis revealed specific microbial functions in EBW-CRC, including D-Arginine and D-ornithine metabolism, and lipopolysaccharide biosynthesis. The best-performing classifier for EBW-CRC, comprising 12 bacterial and three fungal species, achieved an AUROC of 0.90, which was robustly validated across three independent cohorts (AUROC = 0.96, 0.94, and 0.80). Pathogenic microbial species, Anaerobutyricum hallii, Clostridioides difficile and Fusobacterium nucleatum, are EBW-CRC specific signatures. This work unearths the specific multi-kingdom microbial signatures for EBW-CRC and lean CRC, which may contribute to precision diagnosis and treatment of CRC.}, } @article {pmid38182877, year = {2024}, author = {Jin, Z and Cao, Y and Wen, Q and Zhang, H and Fang, Z and Zhao, Q and Xi, Y and Luo, Z and Jiang, H and Zhang, Z and Hang, J}, title = {Dapagliflozin ameliorates diabetes-induced spermatogenic dysfunction by modulating the adenosine metabolism along the gut microbiota-testis axis.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {641}, pmid = {38182877}, issn = {2045-2322}, support = {82101676//National Natural Science Foundation of China/ ; 82271630//National Natural Science Foundation of China/ ; 82071698//National Natural Science Foundation of China/ ; 82071658//National Natural Science Foundation of China/ ; 2022M710259//China Postdoctoral Science Foundation/ ; 2021YFC2700203//National Key Research and Development Program of China/ ; 2022YFC2702904//National Key Research and Development Program of China/ ; 7222208//Natural Science Foundation of Beijing Municipality/ ; 20220484160//Beijing Nova Program/ ; BYSYZD2023033//Key Clinical Projects of Peking University Third Hospital/ ; }, mesh = {Male ; Animals ; Mice ; Humans ; Testis ; *Gastrointestinal Microbiome ; Semen ; Sperm Motility ; Spermatogenesis ; Adenosine ; *Infertility, Male/drug therapy/etiology ; *Diabetes Mellitus ; }, abstract = {Male infertility is one of the most common complications of diabetes mellitus (DM). Dapagliflozin is widely used to manage the type II DM. This study aimed to assess the dapagliflozin's effects on the spermatogenesis by administering either dapagliflozin (Dapa) or vehicle (db) to male db/db mice, and using littermate male db/m mice as the control (Con). We further performed the integrative analyses of the cecal shotgun metagenomics, cecal/plasmatic/testicular metabolomics, and testicular proteomics. We found that dapagliflozin treatment significantly alleviated the diabetes-induced spermatogenic dysfunction by improving sperm quality, including the sperm concentration and sperm motility. The overall microbial composition was reshaped in Dapa mice and 13 species (such as Lachnospiraceae bacterium 3-1) were regarded as potential beneficial bacteria. Metabolites exhibited modified profiles, in which adenosine, cAMP, and 2'-deoxyinosine being notably altered in the cecum, plasma, and testis, respectively. Testicular protein expression patterns were similar between the Dapa and Con mice. In vivo results indicated that when compared with db group, dapagliflozin treatment alleviated apoptosis and oxidative stress in testis tissues by down-regulating 2'-deoxyinosine. This was further validated by in vitro experiments using GC-2 cells. Our findings support the potential use of dapagliflozin to prevent the diabetes-induced impaired sperm quality and to treat diabetic male infertility.}, } @article {pmid38182754, year = {2024}, author = {Rhoades, NS and Cinco, IR and Hendrickson, SM and Prongay, K and Haertel, AJ and Flores, GE and Slifka, MK and Messaoudi, I}, title = {Infant diarrheal disease in rhesus macaques impedes microbiome maturation and is linked to uncultured Campylobacter species.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {37}, pmid = {38182754}, issn = {2399-3642}, support = {P51 OD011092/OD/NIH HHS/United States ; }, mesh = {Child ; Infant ; Animals ; Humans ; Macaca mulatta ; *Campylobacter/genetics ; *Microbiota ; Metagenome ; Diarrhea ; }, abstract = {Diarrheal diseases remain one of the leading causes of death for children under 5 globally, disproportionately impacting those living in low- and middle-income countries (LMIC). Campylobacter spp., a zoonotic pathogen, is one of the leading causes of food-borne infection in humans. Yet to be cultured Campylobacter spp. contribute to the total burden in diarrheal disease in children living in LMIC thus hampering interventions. We performed microbiome profiling and metagenomic genome assembly on samples collected from over 100 infant rhesus macaques longitudinally and during cases of clinical diarrhea within the first year of life. Acute diarrhea was associated with long-lasting taxonomic and functional shifts of the infant gut microbiome indicative of microbiome immaturity. We constructed 36 Campylobacter metagenomic assembled genomes (MAGs), many of which fell within 4 yet to be cultured species. Finally, we compared the uncultured Campylobacter MAGs assembled from infant macaques with publicly available human metagenomes to show that these uncultured species are also found in human fecal samples from LMIC. These data highlight the importance of unculturable Campylobacter spp. as an important target for reducing disease burden in LMIC children.}, } @article {pmid38182626, year = {2024}, author = {Rühlemann, MC and Bang, C and Gogarten, JF and Hermes, BM and Groussin, M and Waschina, S and Poyet, M and Ulrich, M and Akoua-Koffi, C and Deschner, T and Muyembe-Tamfum, JJ and Robbins, MM and Surbeck, M and Wittig, RM and Zuberbühler, K and Baines, JF and Leendertz, FH and Franke, A}, title = {Functional host-specific adaptation of the intestinal microbiome in hominids.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {326}, pmid = {38182626}, issn = {2041-1723}, support = {261376515//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 244372499//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 261376515//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 390884018//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Animals ; *Hominidae ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Pan troglodytes ; Pan paniscus ; }, abstract = {Fine-scale knowledge of the changes in composition and function of the human gut microbiome compared that of our closest relatives is critical for understanding the evolutionary processes underlying its developmental trajectory. To infer taxonomic and functional changes in the gut microbiome across hominids at different timescales, we perform high-resolution metagenomic-based analyzes of the fecal microbiome from over two hundred samples including diverse human populations, as well as wild-living chimpanzees, bonobos, and gorillas. We find human-associated taxa depleted within non-human apes and patterns of host-specific gut microbiota, suggesting the widespread acquisition of novel microbial clades along the evolutionary divergence of hosts. In contrast, we reveal multiple lines of evidence for a pervasive loss of diversity in human populations in correlation with a high Human Development Index, including evolutionarily conserved clades. Similarly, patterns of co-phylogeny between microbes and hosts are found to be disrupted in humans. Together with identifying individual microbial taxa and functional adaptations that correlate to host phylogeny, these findings offer insights into specific candidates playing a role in the diverging trajectories of the gut microbiome of hominids. We find that repeated horizontal gene transfer and gene loss, as well as the adaptation to transient microaerobic conditions appear to have played a role in the evolution of the human gut microbiome.}, } @article {pmid38181963, year = {2024}, author = {Li, X and Tang, X and Chen, M and Wang, S and Tong, C and Xu, J and Xie, G and Ma, B and Zou, Y and Wang, Y and Wen, X and Wu, Y}, title = {Intramuscular therapeutic doses of enrofloxacin affect microbial community structure but not the relative abundance of fluoroquinolones resistance genes in swine manure.}, journal = {The Science of the total environment}, volume = {913}, number = {}, pages = {169794}, doi = {10.1016/j.scitotenv.2023.169794}, pmid = {38181963}, issn = {1879-1026}, mesh = {Animals ; Swine ; Enrofloxacin ; Fluoroquinolones ; Manure/microbiology ; Genes, Bacterial ; *Composting ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; Livestock ; }, abstract = {Livestock manure is a major source of veterinary antibiotics and antibiotic resistance genes (ARGs). Elucidation of the residual characteristics of ARGs in livestock manure following the administration of veterinary antibiotics is critical to assess their ecotoxicological effects and environmental contamination risks. Here, we investigated the effects of enrofloxacin (ENR), a fluoroquinolone antibiotic commonly used as a therapeutic drug in animal husbandry, on the characteristics of ARGs, mobile genetic elements, and microbial community structure in swine manure following its intramuscular administration for 3 days and a withdrawal period of 10 days. The results revealed the highest concentrations of ENR and ciprofloxacin (CIP) in swine manure at the end of the administration period, ENR concentrations in swine manure in groups L and H were 88.67 ± 45.46 and 219.75 ± 88.05 mg/kg DM, respectively. Approximately 15 fluoroquinolone resistance genes (FRGs) and 48 fluoroquinolone-related multidrug resistance genes (F-MRGs) were detected in swine manure; the relative abundance of the F-MRGs was considerably higher than that of the FRGs. On day 3, the relative abundance of qacA was significantly higher in group H than in group CK, and no significant differences in the relative abundance of other FRGs, F-MRGs, or MGEs were observed between the three groups on day 3 and day 13. The microbial community structure in swine manure was significantly altered on day 3, and the altered community structure was restored on day 13. The FRGs and F-MRGs with the highest relative abundance were qacA and adeF, respectively, and Clostridium and Lactobacillus were the dominant bacterial genera carrying these genes in swine manure. In summary, a single treatment of intramuscular ENR transiently increased antibiotic concentrations and altered the microbial community structure in swine manure; however, this treatment did not significantly affect the abundance of FRGs and F-MRGs.}, } @article {pmid38180652, year = {2024}, author = {Ben Abdallah, M and Chamkha, M and Karray, F and Sayadi, S}, title = {Microbial diversity in polyextreme salt flats and their potential applications.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {8}, pages = {11371-11405}, pmid = {38180652}, issn = {1614-7499}, mesh = {*Ecosystem ; *Sodium Chloride/metabolism ; Ecology ; Sodium Chloride, Dietary ; Biotechnology ; }, abstract = {Recent geological, hydrochemical, and mineralogical studies performed on hypersaline salt flats have given insights into similar geo-morphologic features on Mars. These salt-encrusted depressions are widely spread across the Earth, where they are characterized by high salt concentrations, intense UV radiation, high evaporation, and low precipitation. Their surfaces are completely dry in summer; intermittent flooding occurs in winter turning them into transitory hypersaline lakes. Thanks to new approaches such as culture-dependent, culture-independent, and metagenomic-based methods, it is important to study microbial life under polyextreme conditions and understand what lives in these dynamic ecosystems and how they function. Regarding these particular features, new halophilic microorganisms have been isolated from some salt flats and identified as excellent producers of primary and secondary metabolites and granules such as halocins, enzymes, carotenoids, polyhydroxyalkanoates, and exopolysaccharides. Additionally, halophilic microorganisms are implemented in heavy metal bioremediation and hypersaline wastewater treatment. As a result, there is a growing interest in the distribution of halophilic microorganisms around the world that can be looked upon as good models to develop sustainable biotechnological processes for all fields. This review provides insights into diversity, ecology, metabolism, and genomics of halophiles in hypersaline salt flats worldwide as well as their potential uses in biotechnology.}, } @article {pmid38180447, year = {2024}, author = {Wu, E and Yang, Y and Zhao, J and Zheng, J and Wang, X and Shen, C and Qiao, L}, title = {High-Abundance Protein-Guided Hybrid Spectral Library for Data-Independent Acquisition Metaproteomics.}, journal = {Analytical chemistry}, volume = {96}, number = {3}, pages = {1029-1037}, doi = {10.1021/acs.analchem.3c03255}, pmid = {38180447}, issn = {1520-6882}, mesh = {Humans ; Proteomics/methods ; Proteins/analysis ; *Microbiota ; Peptides ; *Gastrointestinal Microbiome ; }, abstract = {Metaproteomics offers a direct avenue to identify microbial proteins in microbiota, enabling the compositional and functional characterization of microbiota. Due to the complexity and heterogeneity of microbial communities, in-depth and accurate metaproteomics faces tremendous limitations. One challenge in metaproteomics is the construction of a suitable protein sequence database to interpret the highly complex metaproteomic data, especially in the absence of metagenomic sequencing data. Herein, we present a high-abundance protein-guided hybrid spectral library strategy for in-depth data independent acquisition (DIA) metaproteomic analysis (HAPs-hyblibDIA). A dedicated high-abundance protein database of gut microbial species is constructed and used to mine the taxonomic information on microbiota samples. Then, a sample-specific protein sequence database is built based on the taxonomic information using Uniprot protein sequence for subsequent analysis of the DIA data using hybrid spectral library-based DIA analysis. We evaluated the accuracy and sensitivity of the method using synthetic microbial community samples and human gut microbiome samples. It was demonstrated that the strategy can successfully identify taxonomic compositions of microbiota samples and that the peptides identified by HAPs-hyblibDIA overlapped greatly with the peptides identified using a metagenomic sequencing-derived database. At the peptide and species level, our results can serve as a complement to the results obtained using a metagenomic sequencing-derived database. Furthermore, we validated the applicability of the HAPs-hyblibDIA strategy in a cohort of human gut microbiota samples of colorectal cancer patients and controls, highlighting its usability in biomedical research.}, } @article {pmid38179946, year = {2024}, author = {Bian, G and Yu, S and Cheng, C and Huang, H and Liu, J}, title = {Ruminal microbiota-host crosstalks promote ruminal epithelial development in neonatal lambs with alfalfa hay introduction.}, journal = {mSystems}, volume = {9}, number = {2}, pages = {e0103423}, pmid = {38179946}, issn = {2379-5077}, support = {2021YFF1000703//MOST | National Key Research and Development Program of China (NKPs)/ ; 040521200117//Resrarch Fund of Jinling Inetitute of Techology/ ; }, mesh = {Sheep/genetics ; Animals ; *Medicago sativa/genetics ; RNA, Ribosomal, 16S/genetics ; Rumen/metabolism ; Animal Feed/analysis ; Fatty Acids, Volatile/metabolism ; Sheep, Domestic/genetics ; Ruminants/genetics ; *Microbiota ; Weight Gain ; }, abstract = {Ruminal microbiota is gradually established after birth, while microbiota maturation could be highly diverse because of varied solid dietary accessibility. However, how the ruminal microbiota accreted from postnatal hay diets alters rumen epithelial development, and how this affects animal health remains largely unknown. Here, neonatal lambs were introduced to starchy corn-soybean starter or corn-soybean starter + alfalfa hay (AH) to investigate the influences of early life ruminal microbiome on rumen epithelial development using integrated 16s rRNA sequencing-metagenome-transcriptome approaches. The results showed that AH introduction elevated average daily weight gain, rumen weight and volume, rumen epithelial papillae length, and rumen muscle layer thickness. Meanwhile, the relative abundance of fibrolytic bacteria (Christensenellaceae R-7 group, Prevotellaceae UCG-001, and Succinivibrio), acetate producer (Acetitomaculum and Mitsuokella), and propionate producer Succiniclasticum was increased in the rumen content by AH supplementation (P < 0.05). Moreover, AH introduction decreased the relative abundance of total CAZymes, CBM, and GH and increased the abundance of KO genes related to volatile fatty acid (VFA) generation in the rumen content. AH lambs had a higher relative abundance of Succiniclasticum, Megasphaera, Succinivibrio, and Suttonella (P < 0.05), while a lower relative abundance of Cloacibacillus, Desulfovibrio, Dialister, Intestinimonas, Parabacteroides, and Pseudoscardovia (P < 0.05) in the rumen epithelial samples. Furthermore, these alterations in ruminal microbial structure and function resulted in ruminal epithelial cell proliferation and development pathways activation. In summary, AH introduction benefited ruminal fiber degradation and VFA generation bacteria colonization and promoted ruminal epithelial development. These findings provide new insights into ruminal microbial-host interactions in the early life.IMPORTANCEWhile it is established that a fiber-rich diet promotes rumen development in lambs, further research is needed to investigate the precise response of rumen microbiota and epithelium to high-quality alfalfa hay. Here, we observed that the inclusion of alfalfa hay led to a discernible alteration in the developmental trajectory of the rumen. Notably, there was a favorable shift in the rumen's volume, morphology, and the development of rumen papillae. Furthermore, ruminal microbial structure and function resulted in ruminal epithelial cell proliferation and development pathways activation, collectively provide compelling evidence supporting the capacity of alfalfa hay to enhance rumen development and health through ruminal micrbiota-host crosstalks. Our findings elucidate the functional response of the rumen to alfalfa hay introduction, providing new insights into strategies for promoting healthy development of the rumen in young ruminants.}, } @article {pmid38179421, year = {2023}, author = {Magnan, C and Lancry, T and Salipante, F and Trusson, R and Dunyach-Remy, C and Roger, C and Lefrant, JY and Massanet, P and Lavigne, JP}, title = {Role of gut microbiota and bacterial translocation in acute intestinal injury and mortality in patients admitted in ICU for septic shock.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1330900}, pmid = {38179421}, issn = {2235-2988}, mesh = {Adult ; Female ; Humans ; *Shock, Septic ; *Gastrointestinal Microbiome ; Bacterial Translocation ; Lactation ; Intensive Care Units ; Hospitalization ; Bacteria/genetics ; }, abstract = {INTRODUCTION: Sepsis is a life-threatening organ dysfunction with high mortality rate. The gut origin hypothesis of multiple organ dysfunction syndrome relates to loss of gut barrier function and the ensuing bacterial translocation. The aim of this study was to describe the evolution of gut microbiota in a cohort of septic shock patients over seven days and the potential link between gut microbiota and bacterial translocation.

METHODS: Sixty consecutive adult patients hospitalized for septic shock in intensive care units (ICU) were prospectively enrolled. Non-inclusion criteria included patients with recent or scheduled digestive surgery, having taken laxatives, pre- or probiotic in the previous seven days, a progressive digestive neoplasia, digestive lymphoma, chronic inflammatory bowel disease, moribund patient, and pregnant and lactating patients. The primary objective was to evaluate the evolution of bacterial diversity and richness of gut microbiota during seven days in septic shock. Epidemiological, clinical and biological data were gathered over seven days. Gut microbiota was analyzed through a metagenomic approach. 100 healthy controls were selected among healthy blood donors for reference basal 16S rDNA values.

RESULTS: Significantly lower bacterial diversity and richness was observed in gut microbiota of patients at Day 7 compared with Day 0 (p<0.01). SOFA score at Day 0, Acute Gastrointestinal Injury (AGI) local grade, septic shock origin and bacterial translocation had an impact on alpha diversity. A large increase in Enterococcus genus was observed at Day 7 with a decrease in Enterobacterales, Clostridiales, Bifidobacterium and other butyrate-producing bacteria.

DISCUSSION: This study shows the importance of bacterial translocation during AGI in septic shock patients. This bacterial translocation decreases during hospitalization in ICUs in parallel to the decrease of microbiota diversity. This work highlights the role of gut microbiota and bacterial translocation during septic shock.}, } @article {pmid38178148, year = {2024}, author = {Koller, EJ and Wood, CA and Lai, Z and Borgenheimer, E and Hoffman, KL and Jankowsky, JL}, title = {Doxycycline for transgene control disrupts gut microbiome diversity without compromising acute neuroinflammatory response.}, journal = {Journal of neuroinflammation}, volume = {21}, number = {1}, pages = {11}, pmid = {38178148}, issn = {1742-2094}, support = {F31 AG067676/AG/NIA NIH HHS/United States ; P30 ES030285/NH/NIH HHS/United States ; F31 AG067676-01A1/NH/NIH HHS/United States ; RF1 AG069721/AG/NIA NIH HHS/United States ; RF1 AG058188/AG/NIA NIH HHS/United States ; RF1 AG058188/NH/NIH HHS/United States ; }, mesh = {Mice ; Animals ; *Doxycycline/pharmacology ; Mice, Transgenic ; *Gastrointestinal Microbiome ; Lipopolysaccharides ; Tetracycline/pharmacology ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Trans-Activators/genetics ; Inflammation ; Transgenes ; }, abstract = {The tetracycline transactivator (tTA) system provides controllable transgene expression through oral administration of the broad-spectrum antibiotic doxycycline. Antibiotic treatment for transgene control in mouse models of disease might have undesirable systemic effects resulting from changes in the gut microbiome. Here we assessed the impact of doxycycline on gut microbiome diversity in a tTA-controlled model of Alzheimer's disease and then examined neuroimmune effects of these microbiome alterations following acute LPS challenge. We show that doxycycline decreased microbiome diversity in both transgenic and wild-type mice and that these changes persisted long after drug withdrawal. Despite the change in microbiome composition, doxycycline treatment had minimal effect on basal transcriptional signatures of inflammation the brain or on the neuroimmune response to LPS challenge. Our findings suggest that central neuroimmune responses may be less affected by doxycycline at doses needed for transgene control than by antibiotic cocktails at doses used for experimental microbiome disruption.}, } @article {pmid38177994, year = {2024}, author = {Albuquerque, NK and Silva, SP and Aragão, CF and Cunha, TCAS and Paiva, FAS and Coelho, TFSB and Cruz, ACR}, title = {Virome analysis of Desmodus rotundus tissue samples from the Amazon region.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {34}, pmid = {38177994}, issn = {1471-2164}, support = {314522/2021-02//Coordination for the Improvement of Higher Education Personnel (CAPES)/ ; 314522/2021-02//Coordination for the Improvement of Higher Education Personnel (CAPES)/ ; }, mesh = {Animals ; *Bacteriophages ; *Chiroptera/virology ; Ecology ; Phylogeny ; Virome/genetics ; *Viruses/genetics ; }, abstract = {BACKGROUND: Bats are renowned for harboring a high viral diversity, their characteristics contribute to emerging infectious diseases. However, environmental and anthropic factors also play a significant role in the emergence of zoonotic viruses. Metagenomic is an important tool for investigating the virome of bats and discovering new viruses.

RESULTS: Twenty-four families of virus were detected in lung samples by sequencing and bioinfomatic analysis, the largest amount of reads was focused on the Retroviridae and contigs assembled to Desmodus rotundus endogenous retrovirus, which was feasible to acquire complete sequences. The reads were also abundant for phages.

CONCLUSION: This lung virome of D. rotundus contributes valuable information regarding the viral diversity found in bats, which is useful for understanding the drivers of viral cycles and their ecology in this species. The identification and taxonomic categorization of viruses hosted by bats carry epidemiological significance due to the potential for viral adaptation to other animals and humans, which can have severe repercussions for public health. Furthermore, the characterization of endogenized viruses helps to understanding the host genome and the evolution of the species.}, } @article {pmid38177508, year = {2024}, author = {Cao, L and Kong, Y and Fan, Y and Ni, M and Tourancheau, A and Ksiezarek, M and Mead, EA and Koo, T and Gitman, M and Zhang, XS and Fang, G}, title = {mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome.}, journal = {Nature methods}, volume = {21}, number = {2}, pages = {236-246}, pmid = {38177508}, issn = {1548-7105}, support = {R35 GM139655/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Sequence Analysis, DNA/methods ; *Microbiota/genetics ; Bacteria/genetics ; Metagenome ; DNA Methylation ; Metagenomics/methods ; DNA, Bacterial/genetics ; }, abstract = {Metagenomics has enabled the comprehensive study of microbiomes. However, many applications would benefit from a method that sequences specific bacterial taxa of interest, but not most background taxa. We developed mEnrich-seq (in which 'm' stands for methylation and seq for sequencing) for enriching taxa of interest from metagenomic DNA before sequencing. The core idea is to exploit the self versus nonself differentiation by natural bacterial DNA methylation and rationally choose methylation-sensitive restriction enzymes, individually or in combination, to deplete host and background taxa while enriching targeted taxa. This idea is integrated with library preparation procedures and applied in several applications to enrich (up to 117-fold) pathogenic or beneficial bacteria from human urine and fecal samples, including species that are hard to culture or of low abundance. We assessed 4,601 bacterial strains with mapped methylomes so far and showed broad applicability of mEnrich-seq. mEnrich-seq provides microbiome researchers with a versatile and cost-effective approach for selective sequencing of diverse taxa of interest.}, } @article {pmid38177233, year = {2024}, author = {Kwak, H and Lee, D and Kim, Y and Park, J and Yeum, H and Kim, D and Dong, YW and Nakano, T and Jeong, C and Park, JK}, title = {Genome assembly and population genomic data of a pulmonate snail Ellobium chinense.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {31}, pmid = {38177233}, issn = {2052-4463}, support = {2015R1A4A1041997, 2020R1A2C2005393//National Research Foundation of Korea (NRF)/ ; the management of Marine Fishery Bio-resources Center (2023)//National Marine Biodiversity Institute of Korea (Marine Biodiversity institute of Korea)/ ; }, mesh = {Animals ; Ecosystem ; *Genome ; Genomics ; *Metagenomics ; *Snails/genetics ; }, abstract = {Ellobium chinense is an airbreathing, pulmonate gastropod species that inhabits saltmarshes in estuaries of the northwestern Pacific. Due to a rapid population decline and their unique ecological niche in estuarine ecosystems, this species has attracted special attention regarding their conservation and the genomic basis of adaptation to frequently changing environments. Here we report a draft genome assembly of E. chinense with a total size of 949.470 Mb and a scaffold N50 of 1.465 Mb. Comparative genomic analysis revealed that the GO terms enriched among four gastropod species are related to signal transduction involved in maintaining electrochemical gradients across the cell membrane. Population genomic analysis using the MSMC model for 14 re-sequenced individuals revealed a drastic decline in Korean and Japanese populations during the last glacial period, while the southern Chinese population retained a much larger effective population size (Ne). These contrasting demographic changes might be attributed to multiple environmental factors during the glacial-interglacial cycles. This study provides valuable genomic resources for understanding adaptation and historical demographic responses to climate change.}, } @article {pmid38173792, year = {2023}, author = {Zhou, J and Wu, X and Xiang, T and Liu, F and Gao, H and Tong, L and Yan, B and Li, Z and Zhang, C and Wang, L and Ou, L and Li, Z and Wang, W and Yang, T and Li, F and Ma, H and Zhao, X and Mi, N and Yu, Z and Lan, C and Wang, Q and Li, H and Wang, L and Wang, X and Li, Y and Zeng, Q}, title = {Dynamical alterations of brain function and gut microbiome in weight loss.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1269548}, pmid = {38173792}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; Caloric Restriction/methods ; Escherichia coli ; Obesity ; Weight Loss ; }, abstract = {OBJECTIVE: Intermittent energy restriction (IER) is an effective weight loss strategy. However, little is known about the dynamic effects of IER on the brain-gut-microbiome axis.

METHODS: In this study, a total of 25 obese individuals successfully lost weight after a 2-month IER intervention. FMRI was used to determine the activity of brain regions. Metagenomic sequencing was performed to identify differentially abundant gut microbes and pathways in from fecal samples.

RESULTS: Our results showed that IER longitudinally reduced the activity of obese-related brain regions at different timepoints, including the inferior frontal orbital gyrus in the cognitive control circuit, the putamen in the emotion and learning circuit, and the anterior cingulate cortex in the sensory circuit. IER longitudinally reduced E. coli abundance across multiple timepoints while elevating the abundance of obesity-related Faecalibacterium prausnitzii, Parabacteroides distasonis, and Bacterokles uniformis. Correlation analysis revealed longitudinally correlations between gut bacteria abundance alterations and brain activity changes.

CONCLUSIONS: There was dynamical alteration of BGM axis (the communication of E. coli with specific brain regions) during the weight loss under the IER.}, } @article {pmid38172637, year = {2024}, author = {Zhernakova, DV and Wang, D and Liu, L and Andreu-Sánchez, S and Zhang, Y and Ruiz-Moreno, AJ and Peng, H and Plomp, N and Del Castillo-Izquierdo, Á and Gacesa, R and Lopera-Maya, EA and Temba, GS and Kullaya, VI and van Leeuwen, SS and , and Xavier, RJ and de Mast, Q and Joosten, LAB and Riksen, NP and Rutten, JHW and Netea, MG and Sanna, S and Wijmenga, C and Weersma, RK and Zhernakova, A and Harmsen, HJM and Fu, J}, title = {Host genetic regulation of human gut microbial structural variation.}, journal = {Nature}, volume = {625}, number = {7996}, pages = {813-821}, pmid = {38172637}, issn = {1476-4687}, mesh = {In Vitro Techniques ; Computer Simulation ; Genome, Human/genetics ; *Host Microbial Interactions/genetics ; Humans ; Netherlands ; Genotype ; Faecalibacterium prausnitzii/genetics ; *Bacteria/classification/genetics/isolation & purification ; Multigene Family ; Cohort Studies ; *Metagenome/genetics ; Tanzania ; Acetylgalactosamine/metabolism ; *Gastrointestinal Microbiome/genetics ; Actinobacteria ; }, abstract = {Although the impact of host genetics on gut microbial diversity and the abundance of specific taxa is well established[1-6], little is known about how host genetics regulates the genetic diversity of gut microorganisms. Here we conducted a meta-analysis of associations between human genetic variation and gut microbial structural variation in 9,015 individuals from four Dutch cohorts. Strikingly, the presence rate of a structural variation segment in Faecalibacterium prausnitzii that harbours an N-acetylgalactosamine (GalNAc) utilization gene cluster is higher in individuals who secrete the type A oligosaccharide antigen terminating in GalNAc, a feature that is jointly determined by human ABO and FUT2 genotypes, and we could replicate this association in a Tanzanian cohort. In vitro experiments demonstrated that GalNAc can be used as the sole carbohydrate source for F. prausnitzii strains that carry the GalNAc-metabolizing pathway. Further in silico and in vitro studies demonstrated that other ABO-associated species can also utilize GalNAc, particularly Collinsella aerofaciens. The GalNAc utilization genes are also associated with the host's cardiometabolic health, particularly in individuals with mucosal A-antigen. Together, the findings of our study demonstrate that genetic associations across the human genome and bacterial metagenome can provide functional insights into the reciprocal host-microbiome relationship.}, } @article {pmid38172624, year = {2024}, author = {Hall, B and Levy, S and Dufault-Thompson, K and Arp, G and Zhong, A and Ndjite, GM and Weiss, A and Braccia, D and Jenkins, C and Grant, MR and Abeysinghe, S and Yang, Y and Jermain, MD and Wu, CH and Ma, B and Jiang, X}, title = {BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen.}, journal = {Nature microbiology}, volume = {9}, number = {1}, pages = {173-184}, pmid = {38172624}, issn = {2058-5276}, support = {T32 AI089621/AI/NIAID NIH HHS/United States ; U54 DK110858/DK/NIDDK NIH HHS/United States ; }, mesh = {Infant, Newborn ; Adult ; Humans ; *Bilirubin/metabolism ; Urobilinogen/metabolism ; *Gastrointestinal Microbiome ; Liver/metabolism ; Bacteria/genetics/metabolism ; }, abstract = {Metabolism of haem by-products such as bilirubin by humans and their gut microbiota is essential to human health, as excess serum bilirubin can cause jaundice and even neurological damage. The bacterial enzymes that reduce bilirubin to urobilinogen, a key step in this pathway, have remained unidentified. Here we used biochemical analyses and comparative genomics to identify BilR as a gut-microbiota-derived bilirubin reductase that reduces bilirubin to urobilinogen. We delineated the BilR sequences from similar reductases through the identification of key residues critical for bilirubin reduction and found that BilR is predominantly encoded by Firmicutes species. Analysis of human gut metagenomes revealed that BilR is nearly ubiquitous in healthy adults, but prevalence is decreased in neonates and individuals with inflammatory bowel disease. This discovery sheds light on the role of the gut microbiome in bilirubin metabolism and highlights the significance of the gut-liver axis in maintaining bilirubin homeostasis.}, } @article {pmid38172612, year = {2024}, author = {Rubas, NC and Peres, R and Kunihiro, BP and Allan, NP and Phankitnirundorn, K and Wells, RK and McCracken, T and Lee, RH and Umeda, L and Conching, A and Juarez, R and Maunakea, AK}, title = {HMGB1 mediates microbiome-immune axis dysregulation underlying reduced neutralization capacity in obesity-related post-acute sequelae of SARS-CoV-2.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {355}, pmid = {38172612}, issn = {2045-2322}, support = {R01 MD016593/MD/NIMHD NIH HHS/United States ; }, mesh = {Humans ; *COVID-19/complications ; Disease Progression ; *HMGB1 Protein/genetics ; Longitudinal Studies ; *Microbiota ; Obesity/complications ; Post-Acute COVID-19 Syndrome ; SARS-CoV-2 ; }, abstract = {While obesity is a risk factor for post-acute sequelae of SARS-CoV-2 infection (PASC, "long-COVID"), the mechanism(s) underlying this phenomenon remains poorly understood. To address this gap in knowledge, we performed a 6-week longitudinal study to examine immune activity and gut microbiome dysbiosis in post-acute stage patients recovering from SARS-CoV-2 infection. Self-reported symptom frequencies and blood samples were collected weekly, with plasma assessed by ELISA and Luminex for multiple biomarkers and immune cell profiling. DNA from stool samples were collected at the early stage of recovery for baseline assessments of gut microbial composition and diversity using 16S-based metagenomic sequencing. Multiple regression analyses revealed obesity-related PASC linked to a sustained proinflammatory immune profile and reduced adaptive immunity, corresponding with reduced gut microbial diversity. In particular, enhanced signaling of the high mobility group box 1 (HMGB1) protein was found to associate with this dysregulation, with its upregulated levels in plasma associated with significantly impaired viral neutralization that was exacerbated with obesity. These findings implicate HMGB1 as a candidate biomarker of PASC, with potential applications for risk assessment and targeted therapies.}, } @article {pmid38171069, year = {2024}, author = {Liu, Y and Gao, J and Nie, Z and Wang, J and Sun, Y and Xu, G}, title = {Integration of metagenome and metabolome analysis reveals the correlation of gut microbiota, oxidative stress, and inflammation in Coilia nasus under air exposure stress and salinity mitigation.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {49}, number = {}, pages = {101175}, doi = {10.1016/j.cbd.2023.101175}, pmid = {38171069}, issn = {1878-0407}, mesh = {Animals ; *Gastrointestinal Microbiome ; Metagenome ; Sodium Chloride/metabolism ; Salinity ; Escherichia coli ; Fishes/genetics ; Oxidative Stress ; Inflammation ; Metabolome ; }, abstract = {Due to the strong response to air exposure, high mortality was occurred in Coilia nasus. Previous studies reported that 10 ‰ NaCl could significantly reduce mortality in C. nasus under air exposure. To investigate the mechanisms that 10 ‰ NaCl can alleviate stress, community structure and metabolism of the intestinal flora of C. nasus were detected via metagenome and metabolome. In this study, C. nasus were divided into control group (C), air exposure group without 10 ‰ NaCl (AE), and air exposure group with 10 ‰ NaCl (AES). After air exposure stress and salinity mitigation, the mortality, intestinal microorganisms, metabolites, and physiological biomarkers were analyzed. The results showed that the mortality rate of C. nasus was reduced after salinity reduction; the antioxidant capacity was elevated compared to the AE group; and anti-inflammatory capacity was increased in the AES group compared to the AE group. Metagenomic sequencing results showed that the levels of harmful bacteria (E. coli, Aeromonas) in the Candida nasus gut increased after air exposure; beneficial bacteria (Actinobacteria, Corynebacteria) in the C. nasus gut increased after salinity reduction. Metabolomics analyses showed that AE decreased the expression of beneficial metabolites and increased the expression of harmful metabolites; AES increased beneficial metabolites and decreased harmful metabolites. Correlation analysis showed that in the AE group, beneficial metabolites were negatively correlated with oxidative stress and inflammatory response, while harmful metabolites were positively correlated with oxidative stress and inflammatory response, and were associated with bacterial communities such as Gillisia, Alkalitalia, Avipoxvirus, etc.; the correlation of metabolites with oxidative stress and inflammatory response was opposite to that of AE in the case of AES, and was associated with Lentilactobacillus, Cyanobacterium, and other bacterial communities. Air exposure caused damage to Candida rhinoceros and 10 ‰ salinity was beneficial in alleviating C. nasus stress. These results will provide new insights into methods and mechanisms to mitigate stress in fish.}, } @article {pmid38170981, year = {2024}, author = {Real, MVF and Colvin, MS and Sheehan, MJ and Moeller, AH}, title = {Major urinary protein (Mup) gene family deletion drives sex-specific alterations in the house-mouse gut microbiota.}, journal = {Microbiology spectrum}, volume = {12}, number = {2}, pages = {e0356623}, pmid = {38170981}, issn = {2165-0497}, support = {R24 AG065172/AG/NIA NIH HHS/United States ; R35 GM138284/GM/NIGMS NIH HHS/United States ; }, mesh = {Female ; Mice ; Male ; Animals ; *Gastrointestinal Microbiome ; Phenotype ; Multigene Family ; Bacteria ; }, abstract = {The gut microbiota is shaped by host metabolism. In house mice (Mus musculus), major urinary protein (MUP) pheromone production represents a considerable energy investment, particularly in sexually mature males. Deletion of the Mup gene family shifts mouse metabolism toward an anabolic state, marked by lipogenesis, lipid accumulation, and body mass increases. Given the metabolic implications of MUPs, they may also influence the gut microbiota. Here, we investigated the effect of a deletion of the Mup gene family on the gut microbiota of sexually mature mice. Shotgun metagenomics revealed distinct taxonomic and functional profiles between wild-type and knockout males but not females. Deletion of the Mup gene cluster significantly reduced diversity in microbial families and functions in male mice. Additionally, a species of Ruminococcaceae and several microbial functions, such as transporters involved in vitamin B5 acquisition, were significantly depleted in the microbiota of Mup knockout males. Altogether, these results show that MUPs significantly affect the gut microbiota of house mouse in a sex-specific manner.IMPORTANCEThe community of microorganisms that inhabits the gastrointestinal tract can have profound effects on host phenotypes. The gut microbiota is in turn shaped by host genes, including those involved with host metabolism. In adult male house mice, expression of the major urinary protein (Mup) gene cluster represents a substantial energy investment, and deletion of the Mup gene family leads to fat accumulation and weight gain in males. We show that deleting Mup genes also alters the gut microbiota of male, but not female, mice in terms of both taxonomic and functional compositions. Male mice without Mup genes harbored fewer gut bacterial families and reduced abundance of a species of Ruminococcaceae, a family that has been previously shown to reduce obesity risk. Studying the impact of the Mup gene family on the gut microbiota has the potential to reveal the ways in which these genes affect host phenotypes.}, } @article {pmid38170974, year = {2024}, author = {Jitsuno, K and Hoshino, T and Nishikawa, Y and Kogawa, M and Mineta, K and Strasser, M and Ikehara, K and Everest, J and Maeda, L and Inagaki, F and Takeyama, H and , }, title = {Comparative single-cell genomics of Atribacterota JS1 in the Japan Trench hadal sedimentary biosphere.}, journal = {mSphere}, volume = {9}, number = {1}, pages = {e0033723}, pmid = {38170974}, issn = {2379-5042}, support = {17H06158//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22H00429//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22H01347, 21K19876//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JPMJSP2128//MEXT | Japan Science and Technology Agency (JST)/ ; }, mesh = {Japan ; Phylogeny ; *Bacteria/genetics ; *Microbiota/genetics ; Genomics ; Water ; Carbon ; Methane ; }, abstract = {Deep-sea and subseafloor sedimentary environments host heterotrophic microbial communities that contribute to Earth's carbon cycling. However, the potential metabolic functions of individual microorganisms and their biogeographical distributions in hadal ocean sediments remain largely unexplored. In this study, we conducted single-cell genome sequencing on sediment samples collected from six sites (7,445-8,023 m water depth) along an approximately 500 km transect of the Japan Trench during the International Ocean Discovery Program Expedition 386. A total of 1,886 single-cell amplified genomes (SAGs) were obtained, offering comprehensive genetic insights into sedimentary microbial communities in surface sediments (<1 m depth) above the sulfate-methane transition zone along the Japan Trench. Our genome data set included 269 SAGs from Atribacterota JS1, the predominant bacterial clade in these hadal environments. Phylogenetic analysis classified SAGs into nine distinct phylotypes, whereas metagenome-assembled genomes were categorized into only two phylotypes, advancing JS1 diversity coverage through a single cell-based approach. Comparative genomic analysis of JS1 lineages from different habitats revealed frequent detection of genes related to organic carbon utilization, such as extracellular enzymes like clostripain and α-amylase, and ABC transporters of oligopeptide from Japan Trench members. Furthermore, specific JS1 phylotypes exhibited a strong correlation with in situ methane concentrations and contained genes involved in glycine betaine metabolism. These findings suggest that the phylogenomically diverse and novel Atribacterota JS1 is widely distributed in Japan Trench sediment, playing crucial roles in carbon cycling within the hadal sedimentary biosphere.IMPORTANCEThe Japan Trench represents tectonically active hadal environments associated with Pacific plate subduction beneath the northeastern Japan arc. This study, for the first time, documented a large-scale single-cell and metagenomic survey along an approximately 500 km transect of the Japan Trench, obtaining high-quality genomic information on hadal sedimentary microbial communities. Single-cell genomics revealed the predominance of diverse JS1 lineages not recoverable through conventional metagenomic binning. Their metabolic potential includes genes related to the degradation of organic matter, which contributes to methanogenesis in the deeper layers. Our findings enhance understanding of sedimentary microbial communities at water depths exceeding 7,000 m and provide new insights into the ecological role of biogeochemical carbon cycling in the hadal sedimentary biosphere.}, } @article {pmid38169331, year = {2024}, author = {Campbell, E and Hesser, LA and Berni Canani, R and Carucci, L and Paparo, L and Patry, RT and Nagler, CR}, title = {A Lipopolysaccharide-Enriched Cow's Milk Allergy Microbiome Promotes a TLR4-Dependent Proinflammatory Intestinal Immune Response.}, journal = {Journal of immunology (Baltimore, Md. : 1950)}, volume = {212}, number = {4}, pages = {702-714}, pmid = {38169331}, issn = {1550-6606}, support = {R01 AI146099/AI/NIAID NIH HHS/United States ; R25 GM109439/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Infant ; Female ; Cattle ; Animals ; Mice ; *Milk Hypersensitivity/complications ; Lipopolysaccharides ; Toll-Like Receptor 4/genetics ; *Gastrointestinal Microbiome ; Immunity ; Immunoglobulin A ; }, abstract = {We have previously reported that the gut microbiota of healthy infants harbors allergy-protective bacteria taxa that are depleted in infants with cow's milk allergy (CMA). Few reports have investigated the role of the gut microbiota in promoting allergic responses. In this study we selected a CMA-associated microbiota with increased abundance of Gram-negative bacteria for analysis of its proinflammatory potential. LPS is the major component of the outer membrane of Gram-negative bacteria. Colonization of mice with a global or conditional mutation of the LPS receptor TLR4 with this CMA microbiota induced expression of serum amyloid A1 (Saa1) and other Th17-, B cell-, and Th2-associated genes in the ileal epithelium in a TLR4-dependent manner. In agreement with the gene expression data, mice colonized with the CMA microbiota have expanded populations of Th17 and regulatory T cells and elevated concentrations of fecal IgA. Importantly, we used both antibiotic-treated specific pathogen-free and germ-free rederived mice with a conditional mutation of TLR4 in the CD11c+ compartment to demonstrate that the induction of proinflammatory genes, fecal IgA, and Th17 cells is dependent on TLR4 signaling. Furthermore, metagenomic sequencing revealed that the CMA microbiota has an increased abundance of LPS biosynthesis genes. Taken together, our results show that a microbiota displaying a higher abundance of LPS genes is associated with TLR4-dependent proinflammatory gene expression and a mixed type 2/type 3 response in mice, which may be characteristic of a subset of infants with CMA.}, } @article {pmid38169199, year = {2024}, author = {Liao, Y and Li, S and Ji, G}, title = {Graphene oxide stimulated low-temperature denitrification activity of microbial communities in lake sediments by enhancing anabolism and inhibiting cellular respiration.}, journal = {Chemosphere}, volume = {350}, number = {}, pages = {141090}, doi = {10.1016/j.chemosphere.2023.141090}, pmid = {38169199}, issn = {1879-1298}, mesh = {Temperature ; *Denitrification ; Lakes ; Nitrates/pharmacology ; *Microbiota ; Cell Respiration ; Nitrogen/pharmacology ; *Graphite ; }, abstract = {Nitrate pollution in fresh water is becoming increasingly serious. In this study, the effects of temperature and graphene oxide materials on the potential functions of denitrification communities in lake sediments were investigated by metagenome. The addition of graphene oxide significantly affected the abundance of denitrification genes such as Nap, Nos, and enhanced the contribution of Pseudomonas, making low temperature and material addition conducive to the denitrification process. Module network implied that low temperature increased the centrality of denitrification in community functions. At low temperatures, graphene oxide enhanced community anabolism by stimulation organic carbon consumption and regulating the gene abundance in the citric acid cycle and the semi-phosphorylation Entner-Doudoroff, thus possibly stimulating extracellular polymeric substances (EPS) synthesis and secretion. In addition, graphene oxide may also regulate the transfer of reducing electrons from NADH to denitrifying enzymes by affecting the gene abundances of complex I and complex IV.}, } @article {pmid38168274, year = {2023}, author = {Liu, R and Wang, Y and Cheng, D}, title = {Micro-DeMix: A mixture beta-multinomial model for investigating the fecal microbiome compositions.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38168274}, issn = {2692-8205}, support = {R01 GM145772/GM/NIGMS NIH HHS/United States ; }, abstract = {Extensive research has uncovered the involvement of the human gut microbiome in various facets of human health, including metabolism, nutrition, physiology, and immune function. Researchers often study fecal microbiota as a proxy for understanding the gut microbiome. However, it has been demonstrated that this approach may not suffice to yield a comprehensive understanding of the entire gut microbial community. Emerging research is revealing the heterogeneity of the gut microbiome across different gastrointestinal (GI) locations in both composition and functions. While spatial metagenomics approach has been developed to address these variations in mice, limitations arise when applying it to human-subject research, primarily due to its invasive nature. With these restrictions, we introduce Micro-DeMix, a mixture beta-multinomial model that decomposes the fecal microbiome at compositional level to understand the heterogeneity of the gut microbiome across various GI locations and extract meaningful insights about the biodiversity of the gut microbiome. Moreover, Micro-DeMix facilitates the discovery of differentially abundant microbes between GI regions through a hypothesis testing framework. We utilize the Inflammatory Bowel Disease (IBD) data from the NIH Integrative Human Microbiome Project to demonstrate the effectiveness and efficiency of the proposed Micro-DeMix.}, } @article {pmid38168034, year = {2024}, author = {Zhu, L and Jian, X and Zhou, B and Liu, R and Muñoz, M and Sun, W and Xie, L and Chen, X and Peng, C and Maurer, M and Li, J}, title = {Gut microbiota facilitate chronic spontaneous urticaria.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {112}, pmid = {38168034}, issn = {2041-1723}, support = {81974476//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82173424//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82073458//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81830096//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Dysbiosis/microbiology ; *Dermatitis ; *Chronic Urticaria ; Inflammation ; *Gastrointestinal Microbiome ; Fatty Acids, Volatile/metabolism ; Humans ; Clostridiales ; Mice ; Lipopolysaccharides/pharmacology ; Animals ; }, abstract = {Chronic spontaneous urticaria (CSU) comes with gut dysbiosis, but its relevance remains elusive. Here we use metagenomics sequencing and short-chain fatty acids metabolomics and assess the effects of human CSU fecal microbial transplantation, Klebsiella pneumoniae, Roseburia hominis, and metabolites in vivo. CSU gut microbiota displays low diversity and short-chain fatty acids production, but high gut Klebsiella pneumoniae levels, negatively correlates with blood short-chain fatty acids levels and links to high disease activity. Blood lipopolysaccharide levels are elevated, link to rapid disease relapse, and high gut levels of conditional pathogenic bacteria. CSU microbiome transfer and Klebsiella pneumoniae transplantation facilitate IgE-mediated mast cell(MC)-driven skin inflammatory responses and increase intestinal permeability and blood lipopolysaccharide accumulation in recipient mice. Transplantation of Roseburia hominis and caproate administration protect recipient mice from MC-driven skin inflammation. Here, we show gut microbiome alterations, in CSU, may reduce short-chain fatty acids and increase lipopolysaccharide levels, respectively, and facilitate MC-driven skin inflammation.}, } @article {pmid38167814, year = {2024}, author = {Power, JF and Carere, CR and Welford, HE and Hudson, DT and Lee, KC and Moreau, JW and Ettema, TJG and Reysenbach, AL and Lee, CK and Colman, DR and Boyd, ES and Morgan, XC and McDonald, IR and Craig Cary, S and Stott, MB}, title = {A genus in the bacterial phylum Aquificota appears to be endemic to Aotearoa-New Zealand.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {179}, pmid = {38167814}, issn = {2041-1723}, support = {C05X1203//Ministry of Business, Innovation and Employment (MBIE)/ ; 80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; }, mesh = {New Zealand ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Microbiota ; Metagenome ; }, abstract = {Allopatric speciation has been difficult to examine among microorganisms, with prior reports of endemism restricted to sub-genus level taxa. Previous microbial community analysis via 16S rRNA gene sequencing of 925 geothermal springs from the Taupō Volcanic Zone (TVZ), Aotearoa-New Zealand, revealed widespread distribution and abundance of a single bacterial genus across 686 of these ecosystems (pH 1.2-9.6 and 17.4-99.8 °C). Here, we present evidence to suggest that this genus, Venenivibrio (phylum Aquificota), is endemic to Aotearoa-New Zealand. A specific environmental niche that increases habitat isolation was identified, with maximal read abundance of Venenivibrio occurring at pH 4-6, 50-70 °C, and low oxidation-reduction potentials. This was further highlighted by genomic and culture-based analyses of the only characterised species for the genus, Venenivibrio stagnispumantis CP.B2[T], which confirmed a chemolithoautotrophic metabolism dependent on hydrogen oxidation. While similarity between Venenivibrio populations illustrated that dispersal is not limited across the TVZ, extensive amplicon, metagenomic, and phylogenomic analyses of global microbial communities from DNA sequence databases indicates Venenivibrio is geographically restricted to the Aotearoa-New Zealand archipelago. We conclude that geographic isolation, complemented by physicochemical constraints, has resulted in the establishment of an endemic bacterial genus.}, } @article {pmid38167330, year = {2024}, author = {Li, M and Liang, H and Yang, H and Ding, Q and Xia, R and Chen, J and Zhou, W and Yang, Y and Zhang, Z and Yao, Y and Ran, C and Zhou, Z}, title = {Deciphering the gut microbiome of grass carp through multi-omics approach.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {2}, pmid = {38167330}, issn = {2049-2618}, support = {31925038//National Natural Science Foundation of China/ ; 31925038//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Carps ; Multiomics ; *Microbiota ; Proteobacteria/genetics ; Fusobacteria/genetics ; Bacteroidetes/genetics ; Firmicutes/genetics ; Fusobacterium/genetics ; RNA, Ribosomal, 16S/genetics ; Mammals/genetics ; }, abstract = {BACKGROUND: Aquaculture plays an important role in global protein supplies and food security. The ban on antibiotics as feed additive proposes urgent need to develop alternatives. Gut microbiota plays important roles in the metabolism and immunity of fish and has the potential to give rise to novel solutions for challenges confronted by fish culture. However, our understanding of fish gut microbiome is still lacking.

RESULTS: We identified 575,856 non-redundant genes by metagenomic sequencing of the intestinal content samples of grass carp. Taxonomic and functional annotation of the gene catalogue revealed specificity of the gut microbiome of grass carp compared with mammals. Co-occurrence analysis indicated exclusive relations between the genera belonging to Proteobacteria and Fusobacteria/Firmicutes/Bacteroidetes, suggesting two independent ecological groups of the microbiota. The association pattern of Proteobacteria with the gene expression modules of fish gut and the liver was consistently opposite to that of Fusobacteria, Firmicutes, and Bacteroidetes, implying differential functionality of Proteobacteria and Fusobacteria/Firmicutes/Bacteroidetes. Therefore, the two ecological groups were considered as two functional groups, i.e., Functional Group 1: Proteobacteria and Functional Group 2: Fusobacteria/Firmicutes/Bacteroidetes. Further analysis revealed that the two functional groups differ in genetic capacity for carbohydrate utilization, virulence factors, and antibiotic resistance. Finally, we proposed that the ratio of "Functional Group 2/Functional Group 1" can be used as a biomarker that efficiently reflects the structural and functional characteristics of the microbiota of grass carp.

CONCLUSIONS: The gene catalogue is an important resource for investigating the gut microbiome of grass carp. Multi-omics analysis provides insights into functional implications of the main phyla that comprise the fish microbiota and shed lights on targets for microbiota regulation. Video Abstract.}, } @article {pmid38165420, year = {2024}, author = {Erhardt, R and Steels, E and Harnett, JE and Taing, MW and Steadman, KJ}, title = {Effects of a prebiotic formulation on the composition of the faecal microbiota of people with functional constipation.}, journal = {European journal of nutrition}, volume = {63}, number = {3}, pages = {777-784}, pmid = {38165420}, issn = {1436-6215}, mesh = {Adult ; Humans ; *Prebiotics ; Constipation/drug therapy ; *Microbiota ; }, abstract = {PURPOSE: Prebiotics are defined as substances which selectively promote beneficial gut microbes leading to a health benefit for the host. Limited trials have been carried out investigating their effect on the microbiota composition of individuals afflicted by functional constipation with equivocal outcomes. In a 21-day randomised, controlled clinical trial involving 61 adults with functional constipation, a prebiotic formulation with partially hydrolysed guar gum and acacia gum as its main ingredients, significantly increased complete spontaneous bowel motions in the treatment group. This follow-up exploratory analysis investigated whether the prebiotic was associated with changes to the composition, richness, and diversity of the faecal microbiota.

METHODS: Participants provided a faecal specimen at baseline and on day 21 of the intervention period. Whole genome metagenomic shotgun sequencing comprehensively assessed taxonomic and functional composition of the microbiota.

RESULTS: Linear mixed effects regression models adjusted for potential confounders showed a significant reduction in species richness of 28.15 species (95% CI - 49.86, - 6.43) and Shannon diversity of 0.29 units (95% CI - 0.56, - 0.02) over the trial period in the prebiotic group. These changes were not observed in the control group, and functional composition was unchanged in both groups.

CONCLUSION: In adults with functional constipation, the intake of a prebiotic formulation was associated with a decline of species richness and Shannon diversity. Further research regarding the associations between prebiotics and the composition and function of the gut microbiota is warranted.}, } @article {pmid38163545, year = {2024}, author = {Yang, S and Deng, W and Li, G and Jin, L and Huang, Y and He, Y and Wu, D and Li, D and Zhang, A and Liu, C and Li, C and Zhang, H and Xu, H and Penttinen, P and Zhao, K and Zou, L}, title = {Reference gene catalog and metagenome-assembled genomes from the gut microbiome reveal the microbial composition, antibiotic resistome, and adaptability of a lignocellulose diet in the giant panda.}, journal = {Environmental research}, volume = {245}, number = {}, pages = {118090}, doi = {10.1016/j.envres.2023.118090}, pmid = {38163545}, issn = {1096-0953}, mesh = {Humans ; Animals ; *Ursidae ; Metagenome ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/pharmacology ; Diet/veterinary ; *Lignin ; }, abstract = {The giant panda, a strict herbivore that feeds on bamboo, still retains a typical carnivorous digestive system. Reference catalogs of microbial genes and genomes are lacking, largely limiting the antibiotic resistome and functional exploration of the giant panda gut microbiome. Here, we integrated 177 fecal metagenomes of captive and wild giant pandas to construct a giant panda integrated gene catalog (GPIGC) comprised of approximately 4.5 million non-redundant genes and reconstruct 393 metagenome-assembled genomes (MAGs). Taxonomic and functional characterization of genes revealed that the captivity of the giant panda significantly changed the core microbial composition and the distribution of microbial genes. Higher abundance and prevalence of antibiotic resistance genes (ARGs) were detected in the guts of captive giant pandas, and ARG distribution was influenced by geography, for both captive and wild individuals. Escherichia, as the prevalent genus in the guts of captive giant pandas, was the main carrier of ARGs, meaning there is a high risk of ARG transmission by Escherichia. We also found that multiple mcr gene variants, conferring plasmid-mediated mobile colistin resistance, were widespread in the guts of captive and wild giant pandas. There were low proportions of carbohydrate-active enzyme (CAZyme) genes in GPIGC and MAGs compared with several omnivorous and herbivorous mammals. Many members of Clostridium MAGs were significantly enriched in the guts of adult, old and wild giant pandas. The genomes of isolates and MAGs of Clostridiaceae harbored key genes or enzymes in complete pathways for degrading lignocellulose and producing short-chain fatty acids (SCFAs), indicating the potential of these bacteria to utilize the low-nutrient bamboo diet. Overall, our data presented an exhaustive reference gene catalog and MAGs in giant panda gut and provided a comprehensive understanding of the antibiotic resistome and microbial adaptability for a high-lignocellulose diet.}, } @article {pmid38160549, year = {2024}, author = {Wang, Y and Wang, B and Chen, J and Sun, L and Hou, Y and Wang, Y and Wang, J and Gan, J and Barmukh, R and Li, S and Fan, Z and Bao, P and Cao, B and Cai, C and Jing, X and Singh, BK and Varshney, RK and Zhao, H}, title = {Dynamics of rhizosphere microbial structure and function associated with the biennial bearing of moso bamboo.}, journal = {Journal of environmental management}, volume = {351}, number = {}, pages = {119977}, doi = {10.1016/j.jenvman.2023.119977}, pmid = {38160549}, issn = {1095-8630}, mesh = {*Rhizosphere ; RNA, Ribosomal, 16S/genetics ; *Poaceae ; Forests ; Soil/chemistry ; }, abstract = {Moso bamboo (Phyllostachys edulis) is a valuable nontimber forestry product with a biennial cycle, producing abundant bamboo shoots within one year (on-year) and few shoots within the following year (off-year). Moso bamboo plants undergo clonal reproduction, resulting in similar genetic backgrounds. However, the number of moso bamboo shoots produced each year varies. Despite this variation, the impact of soil nutrients and the root microbiome on the biennial bearing of moso bamboo is poorly understood. We collected 139 soil samples and determined 14 major physicochemical properties of the rhizosphere, rhizoplane, and bulk soil in different seasons (i.e., the growing and deciduous seasons) and different years (i.e., on- and off-years). Based on 16S rRNA and metagenomic sequencing, major variations were found in the rhizospheric microbial composition during different seasons and years in the moso bamboo forest. Environmental driver analysis revealed that essential nutrients (i.e., SOC, TOC, TN, P, and NH4[+]) were the main drivers of the soil microbial community composition and were correlated with the on- and off-year cycles. Moreover, 19 MAGs were identified as important biomarkers that could distinguish on- and off-years. We found that both season and year influenced both the microbial community structure and functional pathways through the biosynthesis of nutrients that potentially interact with the moso bamboo growth rhythm, especially the on-year root-associated microbiome, which had a greater abundance of specific nutrients such as gibberellins and vitamin B6. This work provides a dynamic perspective of the differential responses of various on- and off-year microbial communities and enhances our understanding of bamboo soil microbiome biodiversity and stability.}, } @article {pmid38160303, year = {2024}, author = {Sapoval, N and Tanevski, M and Treangen, TJ}, title = {KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {29}, number = {}, pages = {506-520}, pmid = {38160303}, issn = {2335-6936}, support = {P01 AI152999/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; DNA Copy Number Variations ; Computational Biology ; *Microbiota/genetics ; Metagenome ; Metagenomics/methods ; }, abstract = {The microbes present in the human gastrointestinal tract are regularly linked to human health and disease outcomes. Thanks to technological and methodological advances in recent years, metagenomic sequencing data, and computational methods designed to analyze metagenomic data, have contributed to improved understanding of the link between the human gut microbiome and disease. However, while numerous methods have been recently developed to extract quantitative and qualitative results from host-associated microbiome data, improved computational tools are still needed to track microbiome dynamics with short-read sequencing data. Previously we have proposed KOMB as a de novo tool for identifying copy number variations in metagenomes for characterizing microbial genome dynamics in response to perturbations. In this work, we present KombOver (KO), which includes four key contributions with respect to our previous work: (i) it scales to large microbiome study cohorts, (ii) it includes both k-core and K-truss based analysis, (iii) we provide the foundation of a theoretical understanding of the relation between various graph-based metagenome representations, and (iv) we provide an improved user experience with easier-to-run code and more descriptive outputs/results. To highlight the aforementioned benefits, we applied KO to nearly 1000 human microbiome samples, requiring less than 10 minutes and 10 GB RAM per sample to process these data. Furthermore, we highlight how graph-based approaches such as k-core and K-truss can be informative for pinpointing microbial community dynamics within a myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) cohort. KO is open source and available for download/use at: https://github.com/treangenlab/komb.}, } @article {pmid38159125, year = {2023}, author = {Hao, Z and Wang, Q and Wang, J and Deng, Y and Yan, Z and Tian, L and Jiang, H}, title = {Water Level Fluctuations Modulate the Microbiomes Involved in Biogeochemical Cycling in Floodplains.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {24}, pmid = {38159125}, issn = {1432-184X}, support = {51839011//National Natural Science Foundation of China/ ; }, mesh = {*Water ; Nitrates ; *Microbiota/genetics ; Metagenome ; Nitrogen/metabolism ; }, abstract = {Drastic changes in hydrological conditions within floodplain ecosystems create distinct microbial habitats. However, there remains a lack of exploration regarding the variations in microbial function potentials across the flooding and drought seasons. In this study, metagenomics and environmental analyses were employed in floodplains that experience hydrological variations across four seasons. Analysis of functional gene composition, encompassing nitrogen, carbon, and sulfur metabolisms, revealed apparent differences between the flooding and drought seasons. The primary environmental drivers identified were water level, overlying water depth, submergence time, and temperature. Specific modules, e.g., the hydrolysis of β-1,4-glucosidic bond, denitrification, and dissimilatory/assimilatory nitrate reduction to ammonium, exhibited higher relative abundance in summer compared to winter. It is suggested that cellulose degradation was potentially coupled with nitrate reduction during the flooding season. Phylogenomic analysis of metagenome-assembled genomes (MAGs) unveiled that the Desulfobacterota lineage possessed abundant nitrogen metabolism genes supported by pathway reconstruction. Variation of relative abundance implied its environmental adaptability to both the wet and dry seasons. Furthermore, a novel order was found within Methylomirabilota, containing nitrogen reduction genes in the MAG. Overall, this study highlights the crucial role of hydrological factors in modulating microbial functional diversity and generating genomes with abundant nitrogen metabolism potentials.}, } @article {pmid38158480, year = {2023}, author = {Biswas, S and Foysal, MJ and Mannan, A and Sharifuzzaman, SM and Tanzina, AY and Tanni, AA and Sharmen, F and Hossain, MM and Chowdhury, MSN and Tay, AC and Islam, SMR}, title = {Microbiome pattern and diversity of an anadromous fish, hilsa shad (Tenualosa ilisha).}, journal = {Molecular biology reports}, volume = {51}, number = {1}, pages = {38}, pmid = {38158480}, issn = {1573-4978}, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Fishes/genetics ; Fresh Water ; Bacteria/genetics ; *Microbiota/genetics ; Water ; }, abstract = {BACKGROUND: The host-microbe interactions are complex, dynamic and context-dependent. In this regard, migratory fish species like hilsa shad (Tenualosa ilisha), which migrates from seawater to freshwater for spawning, provides a unique system for investigating the microbiome under an additional change in fish's habitat. This work was undertaken to detect taxonomic variation of microbiome and their function in the migration of hilsa.

METHODS AND RESULTS: The study employed 16S rRNA amplicon-based metagenomic analysis to scrutinize bacterial diversity in hilsa gut, skin mucus and water. Thus, a total of 284 operational taxonomic units (OTUs), 9 phyla, 35 orders and 121 genera were identified in all samples. More than 60% of the identified bacteria were Proteobacteria with modest abundance (> 5%) of Firmicutes, Bacteroidetes and Actinobacteria. Leucobacter in gut and Serratia in skin mucus were the core bacterial genera, while Acinetobacter, Pseudomonas and Psychrobacter exhibited differential compositions in gut, skin mucus and water.

CONCLUSIONS: Representative fresh-, brackish- and seawater samples of hilsa habitats were primarily composed of Vibrio, Serratia and Psychrobacter, and their diversity in seawater was significantly higher (P < 0.05) than freshwater. Overall, salinity and water microbiota had an influence on the microbial composition of hilsa shad, contributing to host metabolism and adaptation processes. This pioneer exploration of hilsa gut and skin mucus bacteria across habitats will advance our insights into microbiome assembly in migratory fish populations.}, } @article {pmid38158469, year = {2024}, author = {Uwaremwe, C and Bao, W and Daoura, BG and Mishra, S and Zhang, X and Shen, L and Xia, S and Yang, X}, title = {Shift in the rhizosphere soil fungal community associated with root rot infection of Plukenetia volubilis Linneo caused by Fusarium and Rhizopus species.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {27}, number = {4}, pages = {1231-1247}, pmid = {38158469}, issn = {1618-1905}, mesh = {*Fusarium/genetics/classification/isolation & purification/pathogenicity ; *Rhizosphere ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Plant Roots/microbiology ; *Rhizopus/genetics/classification/isolation & purification/growth & development ; *Euphorbiaceae/microbiology ; Mycobiome ; Seedlings/microbiology ; Metagenomics ; }, abstract = {BACKGROUND: Plukenetia volubilis Linneo is an oleaginous plant belonging to the family Euphorbiaceae. Due to its seeds containing a high content of edible oil and rich in vitamins, P. volubilis is cultivated as an economical plant worldwide. However, the cultivation and growth of P. volubilis is challenged by phytopathogen invasion leading to production loss.

METHODS: In the current study, we tested the pathogenicity of fungal pathogens isolated from root rot infected P. volubilis plant tissues by inoculating them into healthy P. volubilis seedlings. Metagenomic sequencing was used to assess the shift in the fungal community of P. volubilis rhizosphere soil after root rot infection.

RESULTS: Four Fusarium isolates and two Rhizopus isolates were found to be root rot causative agents of P. volubilis as they induced typical root rot symptoms in healthy seedlings. The metagenomic sequencing data showed that root rot infection altered the rhizosphere fungal community. In root rot infected soil, the richness and diversity indices increased or decreased depending on pathogens. The four most abundant phyla across all samples were Ascomycota, Glomeromycota, Basidiomycota, and Mortierellomycota. In infected soil, the relative abundance of each phylum increased or decreased depending on the pathogen and functional taxonomic classification.

CONCLUSIONS: Based on our results, we concluded that Fusarium and Rhizopus species cause root rot infection of P. volubilis. In root rot infected P. volubilis, the shift in the rhizosphere fungal community was pathogen-dependent. These findings may serve as a key point for a future study on the biocontrol of root rot of P. volubilis.}, } @article {pmid38158092, year = {2024}, author = {DeCola, AC and Toppen, LC and Brown, KP and Dadkhah, A and Rizzo, DM and Ziels, RM and Scarborough, MJ}, title = {Microbiome assembly and stability during start-up of a full-scale, two-phase anaerobic digester fed cow manure and mixed organic feedstocks.}, journal = {Bioresource technology}, volume = {394}, number = {}, pages = {130247}, doi = {10.1016/j.biortech.2023.130247}, pmid = {38158092}, issn = {1873-2976}, mesh = {Animals ; Female ; Cattle ; *Manure/microbiology ; Anaerobiosis ; Bioreactors/microbiology ; Bacteria/genetics ; *Microbiota/genetics ; Methane ; }, abstract = {Carbon transformations during anaerobic digestion are mediated by complex microbiomes, but their assembly is poorly understood, especially in full-scale digesters. Gene-centric metagenomics combining functional and taxonomic classification was performed for an on-farm digester during start-up. Cow manure and organic waste pre-treated in a hydrolysis tank were fed to the methane-producing digester and the volatile solids loading rate was slowly increased from 0 to 3.5 kg volatile solids m[-3] d[-1] over one year. The microbial community in the anaerobic digester exhibited a high ratio of archaea, which were dominated by hydrogenotrophic methanogens. Bacteria in the anaerobic digester had a high abundance of genes for ferredoxin cycling, H2 generation, and more metabolically complex fermentations than in the hydrolysis tank. In total, the results show that a functionally stable microbiome was achieved quickly during start-up and that the microbiome created in the low-pH hydrolysis tank did not persist in the downstream anaerobic digester.}, } @article {pmid38157274, year = {2024}, author = {Zhang, M and Shi, Z and Wu, C and Yang, F and Su, T and Jing, X and Shi, J and Ren, H and Jiang, L and Jiang, Y and Zhang, C and Zhou, W and Zhou, Y and Wu, K and Zheng, S and Zhong, X and Wu, L and Gu, W and Hong, J and Wang, J and Ning, G and Liu, R and Zhong, H and Zhou, W and Wang, W}, title = {Cushing Syndrome Is Associated With Gut Microbial Dysbiosis and Cortisol-Degrading Bacteria.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {109}, number = {6}, pages = {1474-1484}, doi = {10.1210/clinem/dgad766}, pmid = {38157274}, issn = {1945-7197}, support = {//National Key Research and Development Program of China/ ; //Science and Technology Commission of Shanghai Municipality/ ; //Shanghai Municipal Education Commission/ ; }, mesh = {Humans ; *Dysbiosis/microbiology/metabolism ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; *Cushing Syndrome/microbiology/metabolism ; *Hydrocortisone/metabolism ; Middle Aged ; Adult ; *Feces/microbiology ; Case-Control Studies ; Clostridiales/isolation & purification/metabolism ; }, abstract = {CONTEXT: Cushing syndrome (CS) is a severe endocrine disease characterized by excessive secretion of cortisol with multiple metabolic disorders. While gut microbial dysbiosis plays a vital role in metabolic disorders, the role of gut microbiota in CS remains unclear.

OBJECTIVE: The objective of this work is to examine the alteration of gut microbiota in patients with CS.

METHODS: We performed shotgun metagenomic sequencing of fecal samples from 78 patients with CS and 78 healthy controls matched for age and body mass index. Furthermore, we verify the cortisol degradation capacity of Ruminococcus gnavus in vitro and identify the potential metabolite by LC-MC/MS.

RESULTS: We observed significant differences in microbial composition between CS and controls in both sexes, with CS showing reduced Bacteroidetes (Bacteroides vulgatus) and elevated Firmicutes (Erysipelotrichaceae_bacterium_6_1_45) and Proteobacteria (Enterobacter cloacae). Despite distinct causes of hypercortisolism in ACTH-dependent and ACTH-independent CS, we found no significant differences in metabolic profiles or gut microbiota between the 2 subgroups. Furthermore, we identified a group of gut species, including R. gnavus, that were positively correlated with cortisol levels in CS. These bacteria were found to harbor cortisol-degrading desAB genes and were consistently enriched in CS. Moreover, we demonstrated the efficient capacity of R. gnavus to degrade cortisol to 11-oxygenated androgens in vitro.

CONCLUSION: This study provides evidence of gut microbial dysbiosis in patients with CS and identifies a group of CS-enriched bacteria capable of degrading cortisol. These findings highlight the potential role of gut microbiota in regulating host steroid hormone levels, and consequently host health.}, } @article {pmid38156313, year = {2023}, author = {Han, J and Zhang, B and Zhang, Y and Yin, T and Cui, Y and Liu, J and Yang, Y and Song, H and Shang, D}, title = {Gut microbiome: decision-makers in the microenvironment of colorectal cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1299977}, pmid = {38156313}, issn = {2235-2988}, mesh = {Humans ; *Colorectal Neoplasms/etiology ; *Gastrointestinal Microbiome ; Bacteria/genetics ; Carcinogenesis ; Decision Making ; Tumor Microenvironment ; }, abstract = {Colorectal cancer (CRC) is a common malignancy of the gastrointestinal tract, accounting for the second most common cause of gastrointestinal tumors. As one of the intestinal barriers, gut bacteria form biofilm, participate in intestinal work, and form the living environment of intestinal cells. Metagenomic next-generation sequencing (mNGS) of the gut bacteria in a large number of CRC patients has been established, enabling specific microbial signatures to be associated with colorectal adenomato-carcinoma. Gut bacteria are involved in both benign precursor lesions (polyps), in situ growth and metastasis of CRC. Therefore, the term tumorigenic bacteria was proposed in 2018, such as Escherichia coli, Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, etc. Meanwhile, bacteria toxins (such as cytolethal distending toxin (CDT), Colibactin (Clb), B. fragilis toxin) affect the tumor microenvironment and promote cancer occurrence and tumor immune escape. It is important to note that there are differences in the bacteria of different types of CRC. In this paper, the role of tumorigenic bacteria in the polyp-cancer transformation and the effects of their secreted toxins on the tumor microenvironment will be discussed, thereby further exploring new ideas for the prevention and treatment of CRC.}, } @article {pmid38153158, year = {2024}, author = {Littleford-Colquhoun, B and Kartzinel, TR}, title = {A CRISPR-based strategy for targeted sequencing in biodiversity science.}, journal = {Molecular ecology resources}, volume = {24}, number = {3}, pages = {e13920}, doi = {10.1111/1755-0998.13920}, pmid = {38153158}, issn = {1755-0998}, support = {//Institute at Brown for Environment and Society seed award/ ; NSF DEB-2046797//National Science Foundation/ ; }, mesh = {*RNA, Guide, CRISPR-Cas Systems ; *Biodiversity ; Sequence Analysis, DNA/methods ; DNA Barcoding, Taxonomic/methods ; DNA, Plant ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Many applications in molecular ecology require the ability to match specific DNA sequences from single- or mixed-species samples with a diagnostic reference library. Widely used methods for DNA barcoding and metabarcoding employ PCR and amplicon sequencing to identify taxa based on target sequences, but the target-specific enrichment capabilities of CRISPR-Cas systems may offer advantages in some applications. We identified 54,837 CRISPR-Cas guide RNAs that may be useful for enriching chloroplast DNA across phylogenetically diverse plant species. We tested a subset of 17 guide RNAs in vitro to enrich plant DNA strands ranging in size from diagnostic DNA barcodes of 1,428 bp to entire chloroplast genomes of 121,284 bp. We used an Oxford Nanopore sequencer to evaluate sequencing success based on both single- and mixed-species samples, which yielded mean chloroplast sequence lengths of 2,530-11,367 bp, depending on the experiment. In comparison to mixed-species experiments, single-species experiments yielded more on-target sequence reads and greater mean pairwise identity between contigs and the plant species' reference genomes. But nevertheless, these mixed-species experiments yielded sufficient data to provide ≥48-fold increase in sequence length and better estimates of relative abundance for a commercially prepared mixture of plant species compared to DNA metabarcoding based on the chloroplast trnL-P6 marker. Prior work developed CRISPR-based enrichment protocols for long-read sequencing and our experiments pioneered its use for plant DNA barcoding and chloroplast assemblies that may have advantages over workflows that require PCR and short-read sequencing. Future work would benefit from continuing to develop in vitro and in silico methods for CRISPR-based analyses of mixed-species samples, especially when the appropriate reference genomes for contig assembly cannot be known a priori.}, } @article {pmid38153067, year = {2023}, author = {Long, W and Li, M and Gao, Y and Zhang, Y and Yuan, X and Ye, H and Huang, H and Liang, W and Zhang, R and Du, G}, title = {Microbial community, pathogenic bacteria and high-risk anti-biotic resistance genes at two tropical coastal beaches adjacent to villages in Hainan, China.}, journal = {Annals of agricultural and environmental medicine : AAEM}, volume = {30}, number = {4}, pages = {645-653}, doi = {10.26444/aaem/176090}, pmid = {38153067}, issn = {1898-2263}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; Bacteria/genetics ; Anti-Bacterial Agents ; *Microbiota ; }, abstract = {OBJECTIVE: The aim of the study was to explore the correlation between characteristics of microbial community, pathogenic bacteria and high-risk antibiotic-resistant genes, between coastal beaches and a multi-warm-blooded host, as well as to determine potential species biomarkers for faecal source contamination on tropical coastal beaches in China.

MATERIAL AND METHODS: The 'One-Health' approach was used in a microbiological study of beaches and warm-blooded hosts. The microbial.community was analyzed using 16S rRNA gene amplicons and shotgun metagenomics on Illumina NovaSeq.

RESULTS: The Chao, Simpson, Shannon, and ACE indices of non-salt beach were greater than those of salt beaches at the genus and OTU levels (P < 0.001). Bacteroidota, Halanaerobiaeota, Cyanobacteria, and Firmicutes were abundant on salt beaches (P<0.01). Human-sourced microorganisms were more abundant on salt beaches, which accounted for 0.57%. Faecalibacterium prausnitzii and Eubacterium hallii were considered as reliable indicators for the contamination of human faeces. High-risk carbapenem-resistant Klebsiella pneumoniae and the genotypes KPC-14 and KPC-24 were observed on salt beaches. Tet(X3)/tet(X4) genes and four types of MCR genes co-occurred on beaches and humans; MCR9.1 accounted for the majority. Tet(X4) found among Cyanobacteria. Although rarely reported at Chinese beaches, pathogens, such as Vibrio vulnificus, Legionella pneumophila, and Helicobacter pylori, were observed.

CONCLUSIONS: The low microbial community diversity, however, did not indicate a reduced risk. The transfer of high-risk ARGs to extreme coastal environments should be given sufficient attention.}, } @article {pmid38151716, year = {2024}, author = {Fritz, P and Fritz, R and Bóday, P and Bóday, Á and Bató, E and Kesserű, P and Oláh, C}, title = {Gut microbiome composition: link between sports performance and protein absorption?.}, journal = {Journal of the International Society of Sports Nutrition}, volume = {21}, number = {1}, pages = {2297992}, pmid = {38151716}, issn = {1550-2783}, mesh = {Humans ; *Gastrointestinal Microbiome ; Dietary Supplements ; *Athletic Performance ; *Probiotics ; Anthropometry ; Body Composition ; }, abstract = {BACKGROUND: Sufficient protein intake is essential for adequate physical condition and athletic performance. However, numerous factors can influence the absorption of consumed protein, including timing, type of protein intake, and gut microbiota. In the present study, elite male water polo players consumed a plant-based, vegan protein supplement with (n = 10) or without (n = 10) pre- and probiotics daily during the 31-day study period.

METHODS: We determined the anthropometric characteristics and body composition, dietary habits, gut microbiota composition, and blood parameters of the players at the beginning and at the end of the study. Body composition parameters were analyzed using the InBody 970 bioimpedance analyzer. Gut microbiome composition was determined from stool samples by metagenome sequencing. Paired and unpaired t-tests were used to determine differences between body composition and blood parameters within the groups and between the two groups at the two different sampling times. The Wilcoxon test was used to determine the change in bacterial composition during the study. Correlations between changes in body composition, blood parameters, and taxonomic groups were analyzed using a linear correlation calculation.

RESULTS: Skeletal muscle mass (p < 0.001), body cell mass (p = 0.002), arm circumference (p = 0.003), and protein mass (p < 0.001) increased, while body fat mass (p = 0.004) decreased significantly in the intervention group which consumed pre- and probiotics in addition to protein supplement. Activated acetate (reductive TCA cycle I) and propionate (pyruvate fermentation to propanoate I) pathways correlated positively with increased skeletal muscle mass (p < 0.01 and p < 0.05), and the relative abundance of butyrate-producing species showed a significant positive correlation with changes in body fat mass in the intervention group (p < 0.05). These correlations were not observed in the control group without the intake of pre- and probiotics.

CONCLUSIONS: The composition of the gut microbiota may influence protein absorption and therefore body composition and consequently physical condition and sports performance.}, } @article {pmid38150226, year = {2024}, author = {Li, S and Fan, Y and Han, J and Liu, F and Ding, Y and Li, X and Yu, E and Wang, S and Wang, F and Wang, C}, title = {Foodborne Pathogen and Microbial Community Differences in Fresh Processing Tomatoes in Xinjiang, China.}, journal = {Foodborne pathogens and disease}, volume = {21}, number = {4}, pages = {236-247}, doi = {10.1089/fpd.2023.0014}, pmid = {38150226}, issn = {1556-7125}, mesh = {*Solanum lycopersicum ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Fungi/genetics ; Bacteria/genetics ; }, abstract = {The microbes on fresh processing tomatoes correlate closely with diseases, preservation, and quality control. Investigation of the microbial communities on processing tomatoes from different production regions may help define microbial specificity, inform disease prevention methods, and improve quality. In this study, surface microbes on processing tomatoes from 10 samples in two primary production areas of southern and northern Xinjiang were investigated by sequencing fungal internal transcribed spacer and bacterial 16S rRNA hypervariable sequences. A total of 133 different fungal and bacterial taxonomies were obtained from processing tomatoes in the two regions, of which 63 genera were predominant. Bacterial and fungal communities differed significantly between southern and northern Xinjiang, and fungal diversity was higher in southern Xinjiang. Alternaria and Cladosporium on processing tomatoes in southern Xinjiang were associated with plant pathogenic risk. The plant pathogenic fungi of processing tomatoes in northern Xinjiang were more abundant in Alternaria and Fusarium. The abundance of Alternaria on processing tomatoes was higher in four regions of northern Xinjiang, indicating that there is a greater risk of plant pathogenicity in these areas. Processing tomatoes in northern and southern Xinjiang contained bacterial genera identified as gut microbes, such as Pantoea, Erwinia, Enterobacter, Enterococcus, and Serratia, indicating the potential risk of contamination of processing tomatoes with foodborne pathogens. This study highlighted the microbial specificity of processing tomatoes in two tomato production regions, providing a basis for further investigation and screening for foodborne pathogenic microorganisms.}, } @article {pmid38149413, year = {2023}, author = {Lawrence, K and Fibert, P and Hobbs, J and Myrissa, K and Toribio-Mateas, MA and Quadt, F and Cotter, PD and Gregory, AM}, title = {Randomised controlled trial of the effects of kefir on behaviour, sleep and the microbiome in children with ADHD: a study protocol.}, journal = {BMJ open}, volume = {13}, number = {12}, pages = {e071063}, pmid = {38149413}, issn = {2044-6055}, mesh = {Child ; Humans ; *Attention Deficit Disorder with Hyperactivity/therapy/complications ; *Gastrointestinal Microbiome ; *Kefir ; Randomized Controlled Trials as Topic ; Sleep ; Adolescent ; }, abstract = {INTRODUCTION: Current interventions for children with attention-deficit/hyperactivity disorder (ADHD) are primarily medication, behavioural therapy and parent training. However, research suggests dietary manipulations may provide therapeutic benefit for some. There is accumulating evidence that the gut microbiome may be atypical in ADHD, and therefore, manipulating gut bacteria in such individuals may help alleviate some of the symptoms of this condition. The aim of this study is to explore the effects of supplementation with kefir (a fermented dairy drink) on ADHD symptomatology, sleep, attention and the gut microbiome in children diagnosed with ADHD.

METHODS AND ANALYSIS: A 6-week randomised, double-blind, placebo-controlled trial in 70 children aged 8-13 years diagnosed with ADHD. Participants will be recruited throughout the UK, through support groups, community groups, schools, social media and word of mouth. Children will be randomised to consume daily either dairy kefir or a placebo dairy drink for 6 weeks. The primary outcome, ADHD symptomatology, will be measured by The Strengths and Weakness of ADHD-symptoms and Normal-behaviour scale. Secondary outcomes will include gut microbiota composition (using shotgun metagenomic microbiome sequencing), gut symptomatology (The Gastrointestinal Severity Index questionnaire), sleep (using 7-day actigraphy recordings, The Child's Sleep Habits Questionnaire and Sleep Self Report questionnaire), inattention and impulsivity (with a computerised Go/NoGo test). Assessments will be conducted prior to the intervention and at the end of the intervention. Interaction between time (preintervention/postintervention) and group (probiotic/placebo) is to be analysed using a Mixed Model Analysis of Variances.

ETHICS AND DISSEMINATION: Ethical approval for the study was granted by St Mary's University Ethics Committee. Results will be disseminated through peer-reviewed publications, presentations to the scientific community and support groups.

TRIAL REGISTRATION NUMBER: NCT05155696.}, } @article {pmid38147943, year = {2024}, author = {Ma, X and Qiu, Y and Mao, M and Lu, B and Zhao, H and Pang, Z and Li, S}, title = {PuRenDan alleviates type 2 diabetes mellitus symptoms by modulating the gut microbiota and its metabolites.}, journal = {Journal of ethnopharmacology}, volume = {322}, number = {}, pages = {117627}, doi = {10.1016/j.jep.2023.117627}, pmid = {38147943}, issn = {1872-7573}, mesh = {Rats ; Animals ; *Diabetes Mellitus, Type 2/metabolism ; Rats, Sprague-Dawley ; *Gastrointestinal Microbiome ; Blood Glucose ; Bacteria ; *Insulin Resistance ; Biomarkers ; }, abstract = {PuRenDan (PRD) is a traditional Chinese medicine formula comprising five herbs that have been traditionally used to treat type 2 diabetes mellitus (T2DM). While PRD has been shown to be effective in treating T2DM in clinical and animal studies, the mechanisms by which it works on the gut microbiome and metabolites related to T2DM are not well understood.

AIM OF THE STUDY: The objective of this study was to partially elucidate the mechanism of PRD in treating T2DM through analyses of the gut microbiota metagenome and metabolome.

MATERIALS AND METHODS: Sprague-Dawley rats were fed high-fat diets (HFDs) and injected with low-dose streptozotocin (STZ) to replicate T2DM models. Then the therapeutic effects of PRD were evaluated by measuring clinical markers such as blood glucose, insulin resistance (IR), lipid metabolism biomarkers (total cholesterol, low-density lipoprotein, non-esterified fatty acids, and triglycerides), and inflammatory factors (tumor necrosis factor alpha, interleukin-6 [IL-6], interferon gamma, and IL-1β). Colon contents were collected, and metagenomics, combined with ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry metabolic profiling, was performed to evaluate the effects of T2DM and PRD on gut microbiota and its metabolites in rats. Spearman analysis was used to calculate the correlation coefficient among different microbiota, clinical indices, and metabolites.

RESULTS: PRD exhibited significant improvement in blood glucose and IR, and reduced serum levels of lipid metabolism biomarkers and inflammatory factors. Moreover, the diversity and abundance of gut microbiota undergo significant changes in rats with T2DM that PRD was able to reverse. The gut microbiota associated with T2DM including Rickettsiaceae bacterium 4572_127, Psychrobacter pasteurii, Parabacteroides sp. CAG409, and Paludibacter propionicigenes were identified. The gut microbiota most closely related to PRD were Prevotella sp. 10(H), Parabacteroides sp. SN4, Flavobacteriales bacterium, Bacteroides massiliensis, Alistipes indistinctus, and Ruminococcus flavefaciens. Additionally, PRD regulated the levels of gut microbiota metabolites including pantothenic acid, 1-Methylhistamine, and 1-Methylhistidine; these affected metabolites were involved in pantothenate and coenzyme A biosynthesis, histidine metabolism, and secondary bile acid biosynthesis. Correlation analysis illustrated a close relationship among gut microbiota, its metabolites, and T2DM-related indexes.

CONCLUSION: Our study provides insights into the gut microbiota and its metabolites of PRD therapy for T2DM. It clarifies the role of gut microbiota and the metabolites in the pathogenesis of T2DM, highlighting the potential of PRD for the treatment of this disease.}, } @article {pmid38147149, year = {2024}, author = {Zou, Y and Ro, KS and Jiang, C and Yin, D and Zhao, L and Zhang, D and Du, L and Xie, J}, title = {The anti-hyperuricemic and gut microbiota regulatory effects of a novel purine assimilatory strain, Lactiplantibacillus plantarum X7022.}, journal = {European journal of nutrition}, volume = {63}, number = {3}, pages = {697-711}, pmid = {38147149}, issn = {1436-6215}, support = {No. 2021YFC2100300//National Key Research and Development Program of China/ ; No. 2020YFA0907800//National Key Research and Development Program of China/ ; No. 21ZR1416200//Natural Science Foundation of Shanghai Municipality/ ; }, mesh = {Mice ; Animals ; *Hyperuricemia/drug therapy/chemically induced/metabolism ; *Gastrointestinal Microbiome ; Kidney/metabolism ; Uric Acid ; Inflammation/metabolism ; }, abstract = {PURPOSE: Probiotics have been reported to effectively alleviate hyperuricemia and regulate the gut microbiota. The aim of this work was to study the in vivo anti-hyperuricemic properties and the mechanism of a novel strain, Lactiplantibacillus plantarum X7022.

METHODS: Purine content and mRNA expression of purine assimilation related enzymes were determined by HPLC and qPCR, respectively. Hyperuricemic mice were induced by potassium oxonate and hypoxanthine. Uric acid (UA), blood urea nitrogen, creatinine and renal inflammation were examined by kits. The expression of renal UA transporters was subjected to western blotting. Kidney tissues were sectioned for histological analysis. The fecal short-chain fatty acids (SCFAs) were determined by HPLC, and gut microbiota was investigated using the 16S rDNA metagenomic sequencing.

RESULTS: L. plantarum X7022 possesses a complete purine assimilation pathway and can exhaust xanthine, guanine, and adenine by 82.1%, 33.1%, and 12.6%, respectively. The strain exhibited gastrointestinal viability as 44% at the dose of 10[9] CFU/mL in mice. After four-week administration of the strain, a significant decrease of 35.5% in the serum UA level in hyperuricemic mice was achieved. The diminished contents of fecal propionate and butyrate were dramatically boosted. The treatment also alleviated renal inflammation and restored renal damage. The above physiological changes may due to the inhibited xanthine oxidase (XO) activity, as well as the expressional regulation of UA transporters (GLUT9, URAT1 and OAT1) to the normal level. Notably, gut microbiota dysbiosis in hyperuricemic mice was improved with the inflammation and hyperuricemia related flora depressed, and SCFAs production related flora promoted.

CONCLUSION: The strain is a promising probiotic strain for ameliorating hyperuricemia.}, } @article {pmid38146029, year = {2023}, author = {Johnson, J and Jain, KR and Patel, A and Parmar, N and Joshi, C and Madamwar, D}, title = {Chronic industrial perturbation and seasonal change induces shift in the bacterial community from gammaproteobacteria to betaproteobacteria having catabolic potential for aromatic compounds at Amlakhadi canal.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {2}, pages = {52}, pmid = {38146029}, issn = {1573-0972}, support = {BT/1/CEIB/09/V/05//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {Humans ; *Gammaproteobacteria/genetics ; *Betaproteobacteria/genetics/metabolism ; Seasons ; Bacteria/metabolism ; *Microbiota/genetics ; Organic Chemicals/metabolism ; }, abstract = {Escalating proportions of industrially contaminated sites are one of the major catastrophes faced at the present time due to the industrial revolution. The difficulties associated with culturing the microbes, has been circumvent by the direct use of metagenomic analysis of various complex niches. In this study, a metagenomic approach using next generation sequencing technologies was applied to exemplify the taxonomic abundance and metabolic potential of the microbial community residing in Amlakhadi canal, Ankleshwar at two different seasons. All the metagenomes revealed a predominance of Proteobacteria phylum. However, difference was observed within class level where Gammaproteobacteria was relatively high in polluted metagenome in Summer while in Monsoon the abundance shifted to Betaproteobacteria. Similarly, significant statistical differences were obtained while comparing the genera amongst contaminated sites where Serratia, Achromobacter, Stenotrophomonas and Pseudomonas were abundant in summer season and the dominance changed to Thiobacillus, Thauera, Acidovorax, Nitrosomonas, Sulfuricurvum, Novosphingobium, Hyphomonas and Geobacter in monsoon. Further upon functional characterization, the microbiomes revealed the diverse survival mechanisms, in response to the prevailing ecological conditions (such as degradation of aromatic compounds, heavy metal resistance, oxidative stress responses and multidrug resistance efflux pumps, etc.). The results have important implications in understanding and predicting the impacts of human-induced activities on microbial communities inhabiting natural niche and their responses in coping with the fluctuating pollution load.}, } @article {pmid38145758, year = {2024}, author = {Wu, J and Hu, Q and Rao, X and Zhao, H and Tang, H and Wang, Y}, title = {Gut microbiome and metabolic profiles of mouse model for MeCP2 duplication syndrome.}, journal = {Brain research bulletin}, volume = {206}, number = {}, pages = {110862}, doi = {10.1016/j.brainresbull.2023.110862}, pmid = {38145758}, issn = {1873-2747}, mesh = {Animals ; Mice ; Disease Models, Animal ; *Gastrointestinal Microbiome ; *Mental Retardation, X-Linked ; Metabolome ; Mice, Transgenic ; Neurotransmitter Agents ; }, abstract = {The extra copy of the methyl-CpG-binding protein 2 (MeCp2) gene causes MeCP2 duplication syndrome (MDS), a neurodevelopmental disorder characterized by intellectual disability and autistic phenotypes. However, the disturbed microbiome and metabolic profiling underlying the autistic-like behavioral deficits of MDS are rarely investigated. Here we aimed to understand the contributions of microbiome disruption and associated metabolic alterations, especially the disturbed neurotransmitters in MDS employing a transgenic mouse model with MeCP2 overexpression. We analyzed metabolic profiles of plasma, urine, and cecum content and microbiome profiles by both 16 s RNA and shotgun metagenomics sequence technology. We found the decreased levels of Firmicutes and increased levels of Bacteroides in the single MeCP2 gene mutation autism-like mouse model, demonstrating the importance of the host genome in a selection of microbiome, leading to the heterogeneity characteristics of microbiome in MDS. Furthermore, the changed levels of several neurotransmitters (such as dopamine, taurine, and glutamate) implied the excitatory-inhibitory imbalance caused by the single gene mutation. Concurrently, a range of microbial metabolisms of aromatic amino acids (such as tryptophan and phenylalanine) were identified in different biological matrices obtained from MeCP2 transgenic mice. Our investigation revealed the importance of genetic variation in accounting for the differences in microbiomes and confirmed the bidirectional regulatory axis of microbiota-gut-brain in studying the role of microbiome on MDS, which could be useful in deeply understanding the microbiome-based treatment in this autistic-like disease.}, } @article {pmid38145402, year = {2024}, author = {Zimmermann, P and Pittet, LF and Jakob, W and Messina, NL and Falquet, L and Curtis, N}, title = {The Effect of Bacille Calmette-Guérin Vaccination on the Composition of the Intestinal Microbiome in Neonates From the MIS BAIR Trial.}, journal = {The Pediatric infectious disease journal}, volume = {43}, number = {4}, pages = {378-389}, pmid = {38145402}, issn = {1532-0987}, support = {grants GNT1051228 and GNT1099680//Institut National de la Santé et de la Recherche Médicale/ ; }, mesh = {Female ; Humans ; Infant, Newborn ; Pregnancy ; *BCG Vaccine ; Cesarean Section ; *Gastrointestinal Microbiome ; Vaccination ; Randomized Controlled Trials as Topic ; }, abstract = {INTRODUCTION: The early-life intestinal microbiome plays an important role in the development and regulation of the immune system. It is unknown whether the administration of vaccines influences the composition of the intestinal microbiome.

OBJECTIVE: To investigate whether Bacille Calmette-Guérin (BCG) vaccine given in the first few days of life influences the abundance of bacterial taxa and metabolic pathways in the intestinal microbiome at 1 week of age.

METHODS: Healthy, term-born neonates were randomized at birth to receive BCG or no vaccine within the first few days of life. Stool samples were collected at 1 week of age from 335 neonates and analyzed using shotgun metagenomic sequencing and functional analyses.

RESULTS: The composition of the intestinal microbiome was different between neonates born by cesarean section (CS) and those born vaginally. Differences in the composition between BCG-vaccinated and BCG-naïve neonates were only minimal. CS-born BCG-vaccinated neonates had a higher abundance of Staphylococcus lugdunensis compared with CS-born BCG-naïve neonates. The latter had a higher abundance of Streptococcus infantis and Trabulsiella guamensis . Vaginally-born BCG-vaccinated neonates had a higher abundance of Clostridiaceae and Streptococcus parasanguinis compared with vaginally-born BCG-naïve neonates, and a lower abundance of Veillonella atypica and Butyricimonas faecalis. Metabolic pathways that were differently abundant between BCG-vaccinated and BCG-naïve neonates were mainly those involved in sugar degradation and nucleotide/nucleoside biosynthesis.

CONCLUSION: BCG given in the first few days of life has little effect on the composition of the intestinal microbiome at 1 week of age but does influence the abundance of certain metabolic pathways.}, } @article {pmid38145049, year = {2023}, author = {Lemons, JMS and Narrowe, AB and Liu, L and Firrman, J and Mahalak, KK and Van den Abbeele, P and Baudot, A and Deyaert, S and Li, Y and Yu, LL}, title = {Impact of Baizhu, Daqingye, and Hehuanhua extracts on the human gut microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1298392}, pmid = {38145049}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Drugs, Chinese Herbal/pharmacology/chemistry ; Medicine, Chinese Traditional ; }, abstract = {INTRODUCTION: In traditional Chinese medicine, the rhizome of Atractylodes macrocephala (Baizhu), the leaves of Isatis indigotica (Daqingye), and the flowers of Albizia julibrissin (Hehuanhua) have been used to treat gastrointestinal illnesses, epidemics, and mental health issues. Modern researchers are now exploring the underlying mechanisms responsible for their efficacy. Previous studies often focused on the impact of purified chemicals or mixed extracts from these plants on cells in tissue culture or in rodent models.

METHODS: As modulation of the human gut microbiome has been linked to host health status both within the gastrointestinal tract and in distant tissues, the effects of lipid-free ethanol extracts of Baizhu, Daqingye, and Hehuanhua on the human adult gut microbiome were assessed using Systemic Intestinal Fermentation Research (SIFR[®]) technology (n=6).

RESULTS AND DISCUSSION: Baizhu and Daqingye extracts similarly impacted microbial community structure and function, with the extent of effects being more pronounced for Baizhu. These effects included decreases in the Bacteroidetes phylum and increases in health-related Bifidobacterium spp. and short chain fatty acids which may contribute to Baizhu's efficacy against gastrointestinal ailments. The changes upon Hehuanhua treatment were larger and included increases in multiple bacterial species, including Agathobaculum butyriciproducens, Adlercreutzia equolifaciens, and Gordonibacter pamelaeae, known to produce secondary metabolites beneficial to mental health. In addition, many of the changes induced by Hehuanhua correlated with a rise in Enterobacteriaceae spp., which may make the tested dose of this herb contraindicated for some individuals. Overall, there is some evidence to suggest that the palliative effect of these herbs may be mediated, in part, by their impact on the gut microbiome, but more research is needed to elucidate the exact mechanisms.}, } @article {pmid38141256, year = {2024}, author = {Hassan-Zahraee, M and Ye, Z and Xi, L and Dushin, E and Lee, J and Romatowski, J and Leszczyszyn, J and Danese, S and Sandborn, WJ and Banfield, C and Gale, JD and Peeva, E and Longman, RS and Hyde, CL and Hung, KE}, title = {Baseline Serum and Stool Microbiome Biomarkers Predict Clinical Efficacy and Tissue Molecular Response After Ritlecitinib Induction Therapy in Ulcerative Colitis.}, journal = {Journal of Crohn's & colitis}, volume = {18}, number = {9}, pages = {1361-1370}, pmid = {38141256}, issn = {1876-4479}, support = {//Pfizer/ ; }, mesh = {Humans ; *Colitis, Ulcerative/drug therapy/blood/microbiology ; *Feces/microbiology/chemistry ; *Biomarkers/blood/analysis ; Male ; Female ; Adult ; Middle Aged ; Gastrointestinal Microbiome/drug effects ; Proteomics/methods ; Treatment Outcome ; Remission Induction ; Induction Chemotherapy/methods ; Metagenomics/methods ; }, abstract = {BACKGROUND AND AIMS: Ritlecitinib, an oral JAK3/TEC family kinase inhibitor, was well-tolerated and efficacious in the phase 2b VIBRATO study in participants with moderate-to-severe ulcerative colitis [UC]. The aim of this study was to identify baseline serum and microbiome markers that predict subsequent clinical efficacy and to develop noninvasive serum signatures as potential real-time noninvasive surrogates of clinical efficacy after ritlecitinib.

METHODS: Tissue and peripheral blood proteomics, transcriptomics, and faecal metagenomics were performed on samples before and after 8 weeks of oral ritlecitinib induction therapy [20 mg, 70 mg, 200 mg, or placebo once daily, N = 39, 41, 33, and 18, respectively]. Linear mixed models were used to identify baseline and longitudinal protein markers associated with efficacy. The combined predictivity of these proteins was evaluated using a logistic model with permuted efficacy data. Differential expression of faecal metagenomics was used to differentiate responders and nonresponders.

RESULTS: Peripheral blood serum proteomics identified four baseline serum markers [LTA, CCL21, HLA-E, MEGF10] predictive of modified clinical remission [MR], endoscopic improvement [EI], histological remission [HR], and integrative score of tissue molecular improvement. In responders, 37 serum proteins significantly changed at Week 8 compared with baseline [false discovery rate of <0.05]; of these, changes in four [IL4R, TNFRSF4, SPINK4, and LAIR-1] predicted concurrent EI and HR responses. Faecal metagenomics analysis revealed baseline and treatment response signatures that correlated with EI, MR, and tissue molecular improvement.

CONCLUSIONS: Blood and microbiome biomarkers stratify endoscopic, histological, and tissue molecular responses to ritlecitinib, which may help guide future precision medicine approaches to UC treatment. ClinicalTrials.gov NCT02958865.}, } @article {pmid38139456, year = {2023}, author = {Mathieu, E and Léjard, V and Ezzine, C and Govindin, P and Morat, A and Giat, M and Lapaque, N and Doré, J and Blottière, HM}, title = {An Insight into Functional Metagenomics: A High-Throughput Approach to Decipher Food-Microbiota-Host Interactions in the Human Gut.}, journal = {International journal of molecular sciences}, volume = {24}, number = {24}, pages = {}, pmid = {38139456}, issn = {1422-0067}, support = {ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; }, mesh = {Humans ; Host Microbial Interactions ; *Microbiota ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Metagenome ; }, abstract = {Our understanding of the symbiotic relationship between the microbiota and its host has constantly evolved since our understanding that the "self" was not only defined by our genetic patrimony but also by the genomes of bugs living in us. The first culture-based methods highlighted the important functions of the microbiota. However, these methods had strong limitations and did not allow for a full understanding of the complex relationships that occur at the interface between the microbiota and the host. The recent development of metagenomic approaches has been a groundbreaking step towards this understanding. Its use has provided new insights and perspectives. In the present chapter, we will describe the advances of functional metagenomics to decipher food-microbiota and host-microbiota interactions. This powerful high-throughput approach allows for the assessment of the microbiota as a whole (including non-cultured bacteria) and enabled the discovery of new signaling pathways and functions involved in the crosstalk between food, the gut microbiota and its host. We will present the pipeline and highlight the most important studies that helped to develop the field. To conclude, we will emphasize the most recent developments and hot topics in functional metagenomics.}, } @article {pmid38139130, year = {2023}, author = {Popov, IV and Popov, IV and Krikunova, AA and Lipilkina, TA and Derezina, TN and Chikindas, ML and Venema, K and Ermakov, AM}, title = {Gut Microbiota Composition of Insectivorous Synanthropic and Fructivorous Zoo Bats: A Direct Metagenomic Comparison.}, journal = {International journal of molecular sciences}, volume = {24}, number = {24}, pages = {}, pmid = {38139130}, issn = {1422-0067}, support = {23-14-00316//Russian Science Foundation/ ; Agreement 075-10-2021-093, Project [IMB-2102]//Ministry of Science and Higher Education of the Russian Federation/ ; //K.V. was supported by the Dutch Province of Limburg with a grant to the Centre for Healthy Eating & Food Innovation (HEFI) of Maastricht University-campus Venlo/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Chiroptera ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Bacteria/genetics ; }, abstract = {Bats are natural reservoirs for many emerging viral diseases. That is why their virome is widely studied. But at the same time, studies of their bacterial gut microbiota are limited, creating a degree of uncertainty about the role of bats in global microbial ecology. In this study, we analyzed gut microbiota of insectivorous Nyctalus noctula and Vespertilio murinus from rehabilitation centers from Rostov-on-Don and Moscow, respectively, and fructivorous Carollia perspicillata from the Moscow Zoo based on V3-V4 16S rRNA metagenomic sequencing. We revealed that microbial diversity significantly differs between the insectivorous and fructivorous species studied, while the differences between N. noctula and V. murinus are less pronounced, which shows that bats' gut microbiota is not strictly species-specific and depends more on diet type. In the gut microbiota of synanthropic bats, we observed bacteria that are important for public health and animal welfare such as Bacteroides, Enterobacter, Clostridiaceae, Enterococcus, Ureaplasma, Faecalibacterium, and Helicobacter, as well as some lactic acid bacteria such as Pediococcus, Lactobacillus, Lactococcus, and Weisella. All these bacteria, except for Bacteroides and Weisella, were significantly less abundant in C. perspicillata. This study provides a direct metagenomic comparison of synanthropic insectivorous and zoo fructivorous bats, suggesting future directions for studying these animals' role in microbial ecology.}, } @article {pmid38139096, year = {2023}, author = {Hsieh, SY and Savva, GM and Telatin, A and Tiwari, SK and Tariq, MA and Newberry, F and Seton, KA and Booth, C and Bansal, AS and Wileman, T and Adriaenssens, EM and Carding, SR}, title = {Investigating the Human Intestinal DNA Virome and Predicting Disease-Associated Virus-Host Interactions in Severe Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS).}, journal = {International journal of molecular sciences}, volume = {24}, number = {24}, pages = {}, pmid = {38139096}, issn = {1422-0067}, support = {BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *Fatigue Syndrome, Chronic ; Virome ; Host Microbial Interactions ; DNA ; }, abstract = {Understanding how the human virome, and which of its constituents, contributes to health or disease states is reliant on obtaining comprehensive virome profiles. By combining DNA viromes from isolated virus-like particles (VLPs) and whole metagenomes from the same faecal sample of a small cohort of healthy individuals and patients with severe myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), we have obtained a more inclusive profile of the human intestinal DNA virome. Key features are the identification of a core virome comprising tailed phages of the class Caudoviricetes, and a greater diversity of DNA viruses including extracellular phages and integrated prophages. Using an in silico approach, we predicted interactions between members of the Anaerotruncus genus and unique viruses present in ME/CFS microbiomes. This study therefore provides a framework and rationale for studies of larger cohorts of patients to further investigate disease-associated interactions between the intestinal virome and the bacteriome.}, } @article {pmid38136990, year = {2023}, author = {Skoog, EJ and Fournier, GP and Bosak, T}, title = {Assessing the Influence of HGT on the Evolution of Stress Responses in Microbial Communities from Shark Bay, Western Australia.}, journal = {Genes}, volume = {14}, number = {12}, pages = {}, pmid = {38136990}, issn = {2073-4425}, support = {327126//Simons Foundation/ ; 344707//Simons Foundation/ ; }, mesh = {Western Australia ; *Bays ; Gene Transfer, Horizontal ; *Microbiota ; Metagenome ; }, abstract = {Pustular microbial mats in Shark Bay, Western Australia, are modern analogs of microbial systems that colonized peritidal environments before the evolution of complex life. To understand how these microbial communities evolved to grow and metabolize in the presence of various environmental stresses, the horizontal gene transfer (HGT) detection tool, MetaCHIP, was used to identify the horizontal transfer of genes related to stress response in 83 metagenome-assembled genomes from a Shark Bay pustular mat. Subsequently, maximum-likelihood phylogenies were constructed using these genes and their most closely related homologs from other environments in order to determine the likelihood of these HGT events occurring within the pustular mat. Phylogenies of several stress-related genes-including those involved in response to osmotic stress, oxidative stress and arsenic toxicity-indicate a potentially long history of HGT events and are consistent with these transfers occurring outside of modern pustular mats. The phylogeny of a particular osmoprotectant transport gene reveals relatively recent adaptations and suggests interactions between Planctomycetota and Myxococcota within these pustular mats. Overall, HGT phylogenies support a potentially broad distribution in the relative timing of the HGT events of stress-related genes and demonstrate ongoing microbial adaptations and evolution in these pustular mat communities.}, } @article {pmid38135681, year = {2023}, author = {Li, X and Brejnrod, A and Thorsen, J and Zachariasen, T and Trivedi, U and Russel, J and Vestergaard, GA and Stokholm, J and Rasmussen, MA and Sørensen, SJ}, title = {Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {8526}, pmid = {38135681}, issn = {2041-1723}, support = {NNF19OC0057934598//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17OC0025014//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 300489//Norges Forskningsråd (Research Council of Norway)/ ; }, mesh = {Infant ; Young Adult ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/genetics ; Escherichia coli/genetics ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; }, abstract = {Despite their crucial importance for human health, there is still relatively limited knowledge on how the gut resistome changes or responds to antibiotic treatment across ages, especially in the latter case. Here, we use fecal metagenomic data from 662 Danish infants and 217 young adults to fill this gap. The gut resistomes are characterized by a bimodal distribution driven by E. coli composition. The typical profile of the gut resistome differs significantly between adults and infants, with the latter distinguished by higher gene and plasmid abundances. However, the predominant antibiotic resistance genes (ARGs) are the same. Antibiotic treatment reduces bacterial diversity and increased ARG and plasmid abundances in both cohorts, especially core ARGs. The effects of antibiotic treatments on the gut microbiome last longer in adults than in infants, and different antibiotics are associated with distinct impacts. Overall, this study broadens our current understanding of gut resistome dynamics and the impact of antibiotic treatment across age groups.}, } @article {pmid38135052, year = {2024}, author = {Vermeersch, AS and Ali, M and Gansemans, Y and Van Nieuwerburgh, F and Ducatelle, R and Geldhof, P and Deforce, D and Callens, J and Opsomer, G}, title = {An in-depth investigation of the microbiota and its virulence factors associated with severe udder cleft dermatitis lesions.}, journal = {Journal of dairy science}, volume = {107}, number = {5}, pages = {3219-3234}, doi = {10.3168/jds.2023-24180}, pmid = {38135052}, issn = {1525-3198}, mesh = {Animals ; Cattle ; Mammary Glands, Animal/microbiology ; Virulence Factors ; *Skin Diseases/veterinary ; *Microbiota ; Treponema ; Bacteria ; Bacteroidetes ; *Dermatitis/veterinary ; }, abstract = {Udder cleft dermatitis (UCD) is a skin condition affecting the anterior parts of the udder in dairy cattle. In the present study, we aimed to shed light on the microbiota in severe UCD lesions versus healthy udder skin by putting forward a taxonomic and functional profile based on a virulence factor analysis. Through shotgun metagenomic sequencing, we found a high proportion of bacteria in addition to a low abundance of archaea. A distinct clustering of healthy udder skin versus UCD lesion samples was shown by applying principal component analysis and (sparse) partial least squares analysis on the metagenomic data. Proteobacteria, Bacillota, and Actinomycetota were among the most abundant phyla in healthy udder skin samples. In UCD samples, Bacteroidota was the most abundant phylum. At genus level, Bifidobacterium spp. had the highest relative abundance in healthy skin samples, whereas Porphyromonas spp. and Corynebacterium spp. had the highest relative abundance in UCD samples. In the differential abundance analysis, Porphyromonas spp. and Bacteroides spp. were significantly differentially abundant in UCD samples, whereas Bifidobacterium spp., Staphylococcus sp. AntiMn-1, and Staphylococcus equorum were more commonly found in healthy samples. Moreover, the abundance of several treponeme phylotypes was significantly higher in lesion samples. The streptococcal cysteine protease speB was among the most abundant virulence factors present in severe UCD lesions, while a plethora of virulence factors such as the antitoxin relB were downregulated, possibly contributing to creating the ideal wound climate for the dysbiotic community. Network analysis showed healthy lesion samples had a large network ofpositive, correlations between the abundances of beneficial species such as Aerococcus urinaeequi and Bifidobacterium angulatum, indicating that the healthy skin microbiome forms an active protective bacterial network, which is disrupted in case of UCD. In UCD samples, a smaller microbial network mainly consisting of positive correlations between the abundances of Bacteroides fragilis and anaerobic Bacteroidota was exposed. Moreover, a high correlation between the taxonomic data and virulence factors was revealed, concurrently with 2 separate networks of microbes and virulence factors. One network, matching with the taxonomic findings in the healthy udder skin samples, showcased a community of harmless or beneficial bacteria, such as Bifidobacterium spp. and Butyrivibrio proteoclasticus, associated with hcnB, hcnC, relB, glyoxalase, and cupin 2. The other network, corresponding to UCD samples, consisted of pathogenic or facultative pathogenic and mainly anaerobic bacteria such as Treponema spp., Mycoplasmopsis spp., and bovine gammaherpesvirus 4, that correlated with virulence factors SpvB, fhaB, and haemagglutination activity domain-associated factor. Our results point toward a dysbiotic community with a notable decrease in diversity and evenness, with a loss of normal skin inhabitants and innocuous or useful species making way for predominantly anaerobic, facultative pathogens. The shift in the abundance of virulence factors such as fhaB and SpvB could play a role in the manifestation of a local micro-environment favorable to the microbiome associated with udder skin lesions. Lastly, the presence of specific networks between microbial species, and between microbes and virulence factors was shown.}, } @article {pmid38134685, year = {2024}, author = {Huang, JN and Xu, L and Wen, B and Gao, JZ and Chen, ZZ}, title = {Reshaping the plastisphere upon deposition: Promote N2O production through affecting sediment microbial communities in aquaculture pond.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133290}, doi = {10.1016/j.jhazmat.2023.133290}, pmid = {38134685}, issn = {1873-3336}, mesh = {*Ponds ; Plastics/metabolism ; Nitrous Oxide/metabolism ; Bacteria/metabolism ; Microplastics/metabolism ; *Microbiota ; Aquaculture ; Water ; }, abstract = {Microplastics (MPs) could provide vector for microorganisms to form biofilm (plastisphere), but the shaping process of MPs biofilm and its effects on the structure and function of sedimentary microbial communities especially in aquaculture environments are not reported. For this, we incubated MPs biofilm in situ in an aquaculture pond and established a sediment microcosm with plastisphere. We found that the formation of MPs biofilm in surface water was basically stable after 30 d incubation, but the biofilm communities were reshaped after deposition for another 30 d, because they were more similar to plastisphere communities incubated directly within sediment but not surface water. Moreover, microbial communities of MPs-contaminated sediment were altered, which was mainly driven by the biofilm communities present on MPs, because they but not sediment communities in proximity to MPs had a more pronounced separation from the control sediment communities. In the presence of MPs, increased sediment nitrification, denitrification and N2O production rates were observed. The K00371 (NO2[-]⇋NO3[-]) pathway and elevated abundance of nxrB and narH genes were screened by metagenomic analysis. Based on structural equation model, two key bacteria (Alphaproteobacteria bacterium and Rhodobacteraceae bacterium) associated with N2O production were further identified. Overall, the settling of MPs could reshape the original biofilm and promote N2O production by selectively elevating sedimental microorganisms and functional genes in aquaculture pond.}, } @article {pmid38134579, year = {2024}, author = {Cardin, M and Cardazzo, B and Coton, M and Carraro, L and Lucchini, R and Novelli, E and Coton, E and Mounier, J}, title = {Ecological diversity and associated volatilome of typical mountain Caciotta cheese from Italy.}, journal = {International journal of food microbiology}, volume = {411}, number = {}, pages = {110523}, doi = {10.1016/j.ijfoodmicro.2023.110523}, pmid = {38134579}, issn = {1879-3460}, mesh = {Animals ; *Cheese/microbiology ; Bacteria ; *Lactobacillus delbrueckii ; Temperature ; Italy ; Milk/microbiology ; }, abstract = {Traditional products are particularly appreciated by consumers and among these products, cheese is a major contributor to the Italian mountainous area economics. In this study, shotgun metagenomics and volatilomics were used to understand the biotic and abiotic factors contributing to mountain Caciotta cheese typicity and diversity. Results showed that the origin of cheese played a significant role; however, curd cooking temperature, pH, salt concentration and water activity also had an impact. Viral communities exhibited higher biodiversity and discriminated cheese origins in terms of production farms. Among the most dominant bacteria, Streptococcus thermophilus showed higher intraspecific diversity and closer relationship to production farm when compared to Lactobacillus delbrueckii. However, despite a few cases in which the starter culture was phylogenetically separated from the most dominant strains sequenced in the cheese, starter cultures and dominant cheese strains clustered together suggesting substantial starter colonization in mountain Caciotta cheese. The Caciotta cheese volatilome contained prominent levels of alcohols and ketones, accompanied by lower proportions of terpenes. Volatile profile not only demonstrated a noticeable association with production farm but also significant differences in the relative abundances of enzymes connected to flavor development. Moreover, correlations of different non-homologous isofunctional enzymes highlighted specific contributions to the typical flavor of mountain Caciotta cheese. Overall, this study provides a deeper understanding of the factors shaping typical mountain Caciotta cheese, and the potential of metagenomics for characterizing and potentially authenticating food products.}, } @article {pmid38133826, year = {2023}, author = {Odisi, EJ and de Freitas, RC and do Amaral, DS and da Silva, SB and da Silva, MAC and de Oliveira Sant Ana, W and de Souza Lima, AO and Rörig, LR}, title = {Metataxonomy of acid mine drainage microbiomes from the Santa Catarina Carboniferous Basin (Southern Brazil).}, journal = {Extremophiles : life under extreme conditions}, volume = {28}, number = {1}, pages = {8}, pmid = {38133826}, issn = {1433-4909}, support = {FAPESC-2021TR000671//Fundação de Amparo à Pesquisa e Inovação do Estado de Santa Catarina/ ; DS 88882.438331/2019-01//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, mesh = {Brazil ; *Bacteria/genetics ; *Microbiota ; Rivers/microbiology ; Fungi ; Water ; }, abstract = {Mining activities generate large quantities of wastes that significantly alter the biogeochemistry and ecological structure of entire river basins. Microbial communities that develop in these areas present a variety of survival and adaptation mechanisms. Knowing this diversity at the molecular level is strategic both for understanding adaptive processes and for identifying genomes with potential use in bioremediation and bioprospecting. In this work, prokaryotic and eukaryotic communities were evaluated by meta-taxonomics (16S and 18S amplicons) in sediments and water bodies impacted by acid mine drainage in an important coal mining area in southern Brazil. Five sampling stations were defined on a gradient of impacts (pH 2.7-4.25). Taxon diversity was directly proportional to pH, being greater in sediments than in water. The dominant prokaryotic phyla in the samples were Proteobacteria, Actinobacteria, Acidobacteria, OD1, Nitrospirae, and Euryarchaeota, and among the eukaryotes, algae (Ochrophyta, Chlorophyta, Cryptophyceae), fungi (Basidiomycota, Ascomycota, and Cryptomycota), and protists (Ciliophora, Heterolobosea, Cercozoa). The prokaryotic genera Leptospirillum, Acidithiobacillus, Acidiphilium, Thiomonas, Thermogymnomonas, and Acidobacterium, and the eukaryotic genera Pterocystis and Poteriospumella were associated with more acidic conditions and higher metal concentrations, while the prokaryotic genera Sediminibacterium, Gallionella Geothrix, and Geobacter were more abundant in transitional environments.}, } @article {pmid38132570, year = {2024}, author = {Ma, Y and Wu, N and Zhang, T and Li, Y and Cao, L and Zhang, P and Zhang, Z and Zhu, T and Zhang, C}, title = {The microbiome, resistome, and their co-evolution in sewage at a hospital for infectious diseases in Shanghai, China.}, journal = {Microbiology spectrum}, volume = {12}, number = {2}, pages = {e0390023}, pmid = {38132570}, issn = {2165-0497}, support = {No. 20Y11900300//Shanghai Commission of Science and Technology/ ; }, mesh = {Animals ; Humans ; Sewage/microbiology ; Wastewater ; Genes, Bacterial ; Anti-Bacterial Agents ; Angiotensin Receptor Antagonists ; China ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria/genetics ; *Microbiota ; *Communicable Diseases/genetics ; Hospitals ; }, abstract = {The emergence of antibiotic-resistant bacteria (ARB) caused by the overuse of antibiotics severely threatens human health. Hospital sewage may be a key transmission hub for ARB. However, the complex link between the microbiome and resistomeresistance in hospital sewage remains unclear. In this study, metagenomic assembly and binning methods were used to investigate the microbial community, resistome, and association of antibiotic resistance genes (ARGs) with ARB in sewage from 10 representative sites (outpatient building, surgery building, internal medicine buildings [IMB1-4], staff dormitory, laboratory animal building, tuberculosis building [TBB], and hospital wastewater treatment plant) of a hospital in Shanghai from June 2021 to February 2022. A total of 252 ARG subtypes, belonging to 17 antibiotic classes, were identified. The relative abundance of KPC-2 was higher at IMBs and TBB than at other sites. Of the ARG-carrying contigs, 47.3%-62.6% were associated with mobile genetic elements, and the proportion of plasmid-associated ARGs was significantly higher than that of chromosome-associated ARGs. Although a similar microbiome composition was shared, certain bacteria were enriched at different sites. Potential pathogens Enterococcus B faecium and Klebsiella pneumoniae were primarily enriched in IMB2 and IMB4, respectively. The same ARGs were identified in diverse bacterial hosts (especially pathogenic bacteria), and accordingly, the latter possessed multiple ARGs. Furthermore, gene flow was frequently observed in the sewage of different buildings. The results provide crucial information on the characterization profiles of resistomes in hospital sewage in Shanghai.IMPORTANCEEnvironmental antibiotic resistance genes (ARGs) play a critical role in the emergence and spread of antimicrobial resistance, which poses a global health threat. Wastewater from healthcare facilities serves as a significant reservoir for ARGs. Here, we characterized the microbial community along with the resistome (comprising all antibiotic resistance genes) in wastewater from a specialized hospital for infectious diseases in Shanghai. Potential pathogenic bacteria (e.g., Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Enterococcus B faecium) were frequently detected in hospital wastewater and carried multiple ARGs. A complex link between microbiome and resistome was observed in the wastewater of this hospital. The monitoring of ARGs and antibiotic-resistant bacteria (ARB) in hospital wastewater might be of great significance for preventing the spread of ARB.}, } @article {pmid38129922, year = {2023}, author = {Monira, S and Barman, I and Jubyda, FT and Ali, SI and Islam, A and Rahman, KMZ and Rashid, MU and Johura, FT and Sultana, M and Zohura, F and Bhuyian, SI and Parvin, T and Sack, D and Ahmed, T and Saif-Ur-Rahman, KM and Hossain, M and Watanabe, H and George, CM and Alam, M}, title = {Gut microbiota shifts favorably with delivery of handwashing with soap and water treatment intervention in a prospective cohort (CHoBI7 trial).}, journal = {Journal of health, population, and nutrition}, volume = {42}, number = {1}, pages = {146}, pmid = {38129922}, issn = {2072-1315}, mesh = {Humans ; Bangladesh ; *Cholera/prevention & control ; *Gastrointestinal Microbiome ; Hand Disinfection/methods ; Prospective Studies ; Soaps ; *Water Purification/methods ; }, abstract = {BACKGROUND: Cholera can result in the expulsion of important microbiota from the gut and result in death if left untreated. The disease transmits mainly via drinking water carrying Vibrio cholerae; and household contacts (HHC) of cholera patients are at elevated risk during the first week of infection. The gut microbiota profiles of HHC-children of cholera patients at Dhaka city slums were investigated before (day 0) and after (day 8) delivery of chlorinated water as part of the major study 'CHoBI7 trial (cholera-hospital-based intervention for 7 days)'.

RESULT: Results of sequencing and analysis of bacterial community DNA revealed the predominance of two bacterial phyla: Bacteroidetes and Firmicutes at day 0 with a relative abundance of 62 ± 6 (mean ± SEM%) and 32 ± 7, respectively. The pattern reversed at day 8 with a decreased relative abundance of Bacteroidetes (39 ± 12; p = 0.034) and an increased abundance of Firmicutes (49 ± 12; p = 0.057). Of 65 bacterial families confirmed at day 0, six belonging to Proteobacteria including Vibrionaceae disappeared at day 8. Interestingly, the relative abundance of four Firmicutes families-Lachnospiraceae, Bifidobacteriaceae, Clostridiaceae, and Ruminococcaceae was increased in all five study children at day 8.

CONCLUSION: The observed exclusion of pathogenic Proteobacteria and enhancement of beneficial Firmicutes in the gut of children delivered with chlorinated water as part of WASH intervention reflect a great promise of the CHoBI7 program in preventing cholera and improving child health.}, } @article {pmid38129103, year = {2024}, author = {Ammer-Herrmenau, C and Antweiler, KL and Asendorf, T and Beyer, G and Buchholz, SM and Cameron, S and Capurso, G and Damm, M and Dang, L and Frost, F and Gomes, A and Hamm, J and Henker, R and Hoffmeister, A and Meinhardt, C and Nawacki, L and Nunes, V and Panyko, A and Pardo, C and Phillip, V and Pukitis, A and Rasch, S and Riekstina, D and Rinja, E and Ruiz-Rebollo, ML and Sirtl, S and Weingarten, M and Sandru, V and Woitalla, J and Ellenrieder, V and Neesse, A}, title = {Gut microbiota predicts severity and reveals novel metabolic signatures in acute pancreatitis.}, journal = {Gut}, volume = {73}, number = {3}, pages = {485-495}, pmid = {38129103}, issn = {1468-3288}, mesh = {Humans ; *Pancreatitis/therapy ; *Gastrointestinal Microbiome ; Acute Disease ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; }, abstract = {OBJECTIVE: Early disease prediction is challenging in acute pancreatitis (AP). Here, we prospectively investigate whether the microbiome predicts severity of AP (Pancreatitis-Microbiome As Predictor of Severity; P-MAPS) early at hospital admission.

DESIGN: Buccal and rectal microbial swabs were collected from 424 patients with AP within 72 hours of hospital admission in 15 European centres. All samples were sequenced by full-length 16S rRNA and metagenomic sequencing using Oxford Nanopore Technologies. Primary endpoint was the association of the orointestinal microbiome with the revised Atlanta classification (RAC). Secondary endpoints were mortality, length of hospital stay and severity (organ failure >48 hours and/or occurrence of pancreatic collections requiring intervention) as post hoc analysis. Multivariate analysis was conducted from normalised microbial and corresponding clinical data to build classifiers for predicting severity. For functional profiling, gene set enrichment analysis (GSEA) was performed and normalised enrichment scores calculated.

RESULTS: After data processing, 411 buccal and 391 rectal samples were analysed. The intestinal microbiome significantly differed for the RAC (Bray-Curtis, p value=0.009), mortality (Bray-Curtis, p value 0.006), length of hospital stay (Bray-Curtis, p=0.009) and severity (Bray-Curtis, p value=0.008). A classifier for severity with 16 different species and systemic inflammatory response syndrome achieved an area under the receiving operating characteristic (AUROC) of 85%, a positive predictive value of 67% and a negative predictive value of 94% outperforming established severity scores. GSEA revealed functional pathway units suggesting elevated short-chain fatty acid (SCFA) production in severe AP.

CONCLUSIONS: The orointestinal microbiome predicts clinical hallmark features of AP, and SCFAs may be used for future diagnostic and therapeutic concepts.

TRIAL REGISTRATION NUMBER: NCT04777812.}, } @article {pmid38129066, year = {2024}, author = {Sequino, G and Valentino, V and Esposito, A and Volpe, S and Torrieri, E and De Filippis, F and Ercolini, D}, title = {Microbiome dynamics, antibiotic resistance gene patterns and spoilage-associated genomic potential in fresh anchovies stored in different conditions.}, journal = {Food research international (Ottawa, Ont.)}, volume = {175}, number = {}, pages = {113788}, doi = {10.1016/j.foodres.2023.113788}, pmid = {38129066}, issn = {1873-7145}, mesh = {Animals ; *Food Packaging ; Anti-Bacterial Agents/pharmacology ; Food Microbiology ; Food Preservation ; Genomics ; *Microbiota/genetics ; }, abstract = {Fresh fish is a highly perishable product and is easily spoiled by microbiological activity and chemical oxidation of lipids. However, microbial spoilage is the main factor linked with the rapid fish sensorial degradation due to the action of specific spoilage organisms (SSOs) that have the ability to dominate over other microorganisms and produce metabolites responsible for off-flavours. We explored the microbial dynamics in fresh anchovies stored in different packaging (air, modified atmosphere, under vacuum) and temperatures (0, 4 and 10 °C) using shotgun metagenomics, highlighting the selection of different microbial species according to the packaging type. Indeed, Pseudoalteromonas nigrifaciens, Psychrobacter cryohalolentis and Ps. immobilis, Pseudomonas deceptionensis and Vibrio splendidus have been identified as the main SSOs in aerobically stored anchovies, while Shewanella baltica, Photobacterium iliopiscarium, Ps. cryohalolentis and Ps. immobilis prevailed in VP and MAP. In addition, we identified the presence of spoilage-associated genes, leading to the potential production of biogenic amines and different off-flavors (H2S, TMA). In particular, the abundance of microbial genes leading to BA biosynthesis increased at higher storage temperature, while those related to H2S and TMA production were enriched in aerobically and VP packed anchovies, suggesting that MAP could be an effective strategy in delaying the production of these compounds. Finally, we provided evidence of the presence of a wide range of antibiotic resistance genes conferring resistance to different classes of antibiotic (β-lactams, tetracyclines, polymyxins, trimethoprims and phenicols) and highlighted that storage at higher temperature (4 and 10 °C) boosted the abundance of ARG-carrying taxa, especially in aerobically and MAP packed fish.}, } @article {pmid38129049, year = {2024}, author = {Li, L and Li, N and Fu, J and Liu, J and Ping Wen, X and Cao, H and Xu, H and Zhang, Y and Cao, R}, title = {Synthesis of an autochthonous microbial community by analyzing the core microorganisms responsible for the critical flavor of bran vinegar.}, journal = {Food research international (Ottawa, Ont.)}, volume = {175}, number = {}, pages = {113742}, doi = {10.1016/j.foodres.2023.113742}, pmid = {38129049}, issn = {1873-7145}, mesh = {*Acetic Acid/metabolism ; *Microbiota ; Fermentation ; Amino Acids/metabolism ; Metagenomics ; }, abstract = {Traditional bran vinegar brewing unfolds through natural fermentation, a process driven by spontaneous microbial activity. The unique metabolic activities of various microorganisms lead to distinct flavors and qualities in each batch of vinegar, making it challenging to consistently achieve the desired characteristic flavor compounds. Therefore, identifying the critical microbial species responsible for flavor production and designing starter cultures with improved fermentation efficiency and characteristic flavors are effective methods to address this discrepancy. In this study, 11 core functional microbial species affecting the fermentation flavor of Sichuan shai vinegar (Cupei were placed outside solarization and night-dew for more than one year, and vinegar was the liquid leached from Cupei) (SSV), were revealed by combining PacBio full-length diversity sequencing based on previous metagenomics. The effects of environmental factors and microbial interactions on the growth of 11 microorganisms during fermentation were verified using fermentation experiments. Ultimately, the microbial community was strategically synthesized using a 'top-down' approach, successfully replicating the distinctive flavor profile of Sichuan shai vinegar (SSV). The results showed that the interaction between microorganisms and environmental factors affected microorganism growth. Compared with traditional fermentation, the synthetic microbial community's vinegar-fermented grains (Cupei) can reproduce the key flavor of SSV and is conducive to the production of amino acids. In this study, the key flavor of SSV was reproduced through rational design of the synthetic microbial community. This achievement holds profound significance for the broader application of microbiome assembly strategies in the realm of fermented foods.}, } @article {pmid38127978, year = {2023}, author = {Liuu, S and Nepelska, M and Pfister, H and Gamelas Magalhaes, J and Chevalier, G and Strozzi, F and Billerey, C and Maresca, M and Nicoletti, C and Di Pasquale, E and Pechard, C and Bardouillet, L and Girardin, SE and Boneca, IG and Doré, J and Blottière, HM and Bonny, C and Chene, L and Cultrone, A}, title = {Identification of a muropeptide precursor transporter from gut microbiota and its role in preventing intestinal inflammation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {52}, pages = {e2306863120}, pmid = {38127978}, issn = {1091-6490}, support = {FP7/2007-2013//European community's Seventh Framework Programme/ ; FP7/2007-2013//European community's Seventh framework Programme/ ; }, mesh = {Humans ; Mice ; Animals ; *Gastrointestinal Microbiome ; Peptidoglycan/metabolism ; Intestines/pathology ; Inflammation/metabolism ; Membrane Transport Proteins/metabolism ; Anti-Inflammatory Agents/metabolism ; Dextran Sulfate ; *Colitis/metabolism ; Disease Models, Animal ; Colon/metabolism ; Mice, Inbred C57BL ; }, abstract = {The gut microbiota is a considerable source of biologically active compounds that can promote intestinal homeostasis and improve immune responses. Here, we used large expression libraries of cloned metagenomic DNA to identify compounds able to sustain an anti-inflammatory reaction on host cells. Starting with a screen for NF-κB activation, we have identified overlapping clones harbouring a heterodimeric ATP-binding cassette (ABC)-transporter from a Firmicutes. Extensive purification of the clone's supernatant demonstrates that the ABC-transporter allows for the efficient extracellular accumulation of three muropeptide precursor, with anti-inflammatory properties. They induce IL-10 secretion from human monocyte-derived dendritic cells and proved effective in reducing AIEC LF82 epithelial damage and IL-8 secretion in human intestinal resections. In addition, treatment with supernatants containing the muropeptide precursor reduces body weight loss and improves histological parameters in Dextran Sulfate Sodium (DSS)-treated mice. Until now, the source of peptidoglycan fragments was shown to come from the natural turnover of the peptidoglycan layer by endogenous peptidoglycan hydrolases. This is a report showing an ABC-transporter as a natural source of secreted muropeptide precursor and as an indirect player in epithelial barrier strengthening. The mechanism described here might represent an important component of the host immune homeostasis.}, } @article {pmid38127093, year = {2023}, author = {Brown, EL and Essigmann, HT and Hoffman, KL and Petrosino, J and Jun, G and Brown, SA and Aguilar, D and Hanis, CL}, title = {C-Reactive Protein Levels Correlate with Measures of Dysglycemia and Gut Microbiome Profiles.}, journal = {Current microbiology}, volume = {81}, number = {1}, pages = {45}, pmid = {38127093}, issn = {1432-0991}, support = {R01 DK109920/DK/NIDDK NIH HHS/United States ; R01 DK116378/DK/NIDDK NIH HHS/United States ; R01DK109920/NH/NIH HHS/United States ; R01DK116378/NH/NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; C-Reactive Protein ; *Diabetes Mellitus, Type 2 ; *Microbiota ; Inflammation ; }, abstract = {C-reactive protein (CRP) is a commonly used marker of low-grade inflammation as well as a marker of acute infection. CRP levels are elevated in those with diabetes and increased CRP concentrations are a risk factor for developing type 2 diabetes. Gut microbiome effects on metabolism and immune responses can impact chronic inflammation, including affecting CRP levels, that in turn can lead to the development and maintenance of dysglycemia. Using a high-sensitivity C-reactive protein (hsCRP) assay capable of detecting subtle changes in C-reactive protein, we show that higher hsCRP levels specifically correlate with worsening glycemia, reduced microbial richness and evenness, and with a reduction in the Firmicutes/Bacteroidota ratio. These data demonstrate a pivotal role for CRP not only in the context of worsening glycemia and changes to the gut microbiota, but also highlight CRP as a potential target for mitigating type 2 diabetes progression or as a therapeutic target that could be manipulated through the microbiome. Understanding these processes will provide insights into the etiology of type 2 diabetes in addition to opening doors leading to possible novel diagnostic strategies and therapeutics.}, } @article {pmid38126779, year = {2023}, author = {Ahmed, N and Joglekar, P and Deming, C and , and Lemon, KP and Kong, HH and Segre, JA and Conlan, S}, title = {Genomic characterization of the C. tuberculostearicum species complex, a prominent member of the human skin microbiome.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0063223}, pmid = {38126779}, issn = {2379-5077}, support = {R35 GM141806/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Corynebacterium Infections/microbiology ; Genomics ; Whole Genome Sequencing ; *Microbiota/genetics ; }, abstract = {Amplicon sequencing data combined with isolate whole genome sequencing have expanded our understanding of Corynebacterium on the skin. Healthy human skin is colonized by a diverse collection of Corynebacterium species, but Corynebacterium tuberculostearicum predominates on many skin sites. Our work supports the emerging idea that C. tuberculostearicum is a species complex encompassing several distinct species. We produced a collection of genomes that help define this complex, including a potentially new species we term Corynebacterium hallux based on a preference for sites on the feet, whole-genome average nucleotide identity, pangenomic analysis, and growth in skin-like media. This isolate collection and high-quality genome resource set the stage for developing engineered strains for both basic and translational clinical studies.}, } @article {pmid38126754, year = {2024}, author = {Tannock, GW}, title = {Understanding the gut microbiota by considering human evolution: a story of fire, cereals, cooking, molecular ingenuity, and functional cooperation.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {88}, number = {1}, pages = {e0012722}, pmid = {38126754}, issn = {1098-5557}, mesh = {Humans ; *Gastrointestinal Microbiome ; Edible Grain ; Bacteria/metabolism ; *Microbiota ; Cooking ; }, abstract = {SUMMARYThe microbial community inhabiting the human colon, referred to as the gut microbiota, is mostly composed of bacterial species that, through extensive metabolic networking, degrade and ferment components of food and human secretions. The taxonomic composition of the microbiota has been extensively investigated in metagenomic studies that have also revealed details of molecular processes by which common components of the human diet are metabolized by specific members of the microbiota. Most studies of the gut microbiota aim to detect deviations in microbiota composition in patients relative to controls in the hope of showing that some diseases and conditions are due to or exacerbated by alterations to the gut microbiota. The aim of this review is to consider the gut microbiota in relation to the evolution of Homo sapiens which was heavily influenced by the consumption of a nutrient-dense non-arboreal diet, limited gut storage capacity, and acquisition of skills relating to mastering fire, cooking, and cultivation of cereal crops. The review delves into the past to gain an appreciation of what is important in the present. A holistic view of "healthy" microbiota function is proposed based on the evolutionary pathway shared by humans and gut microbes.}, } @article {pmid38126212, year = {2024}, author = {Li, Y and Yu, H and Xiong, L and Zeng, K and Wei, Y and Li, H and Ji, X}, title = {Diversity and function of viral AMGs associated with DNA biosynthesis in the Napahai plateau wetland.}, journal = {Environmental technology}, volume = {45}, number = {26}, pages = {5521-5535}, doi = {10.1080/09593330.2023.2296531}, pmid = {38126212}, issn = {1479-487X}, mesh = {*Wetlands ; China ; Phylogeny ; Genetic Variation ; Metagenomics ; Bacteriophages/genetics/metabolism ; Pseudomonas/genetics/metabolism ; DNA/genetics ; Genes, Viral ; }, abstract = {Viruses play an important role in microbial community structure and biodiversity by lysing host cells, and can also affect host metabolic pathways by expressing auxiliary metabolic genes (AMGs). As a unique low-latitude, high-altitude seasonal plateau wetland in China, Napahai has high research value. However, studies on the genetic diversity of AMGs and viruses associated with DNA biosynthesis have not been reported. Based on metagenomics, with the phylogenetic tree, PCoA, and α diversity analysis, we found that three DNA biosynthesis-related viral AMGs (cobS, mazG, and purM) in the Napahai plateau wetland were rich in genetic diversity, uniqueness, and differences compared with other habitats and host sources. Through the KEGG metabolic pathway and metabolic flow analysis of Pseudomonas mandelii (SW-3) and phage (VSW-3), the AMGs (cobS, mazG, and purM) genes of the three related viruses involved in DNA biosynthesis were upregulated and their expression increased significantly. In general, we systematically described the genetic diversity of AMGs associated with DNA biosynthesis in plateau wetland ecosystems and clarified the contribution of viral AMGs in the Napahai plateau wetland to DNA biosynthesis, as well as the changes of metabolites and genes. It further expands the understanding of phage-host interactions, which is of great significance for further revealing the role of viral AMGs in the biological evolution and biogeochemical cycle of wetland ecosystems.}, } @article {pmid38124452, year = {2024}, author = {Velarde-Garcéz, DA and Mata, VA and Beja, P and da Silva, LP}, title = {DNA metabarcoding, diversity partitioning and null models reveal mechanisms of seasonal trophic specialization in a Mediterranean warbler.}, journal = {Molecular ecology}, volume = {33}, number = {4}, pages = {e17245}, doi = {10.1111/mec.17245}, pmid = {38124452}, issn = {1365-294X}, support = {//EDP Biodiversity Chair/ ; //ERA Chair in Environmental Metagenomics/ ; POCI-01-0145-FEDER-022127//Portuguese E-Infrastructure for Information and Research on Biodiversity/ ; 857251//Teaming Project Biopolis/ ; 668981//Teaming Project Biopolis/ ; 2020.02547.CEECIND//Fundação para a Ciência e Tecnologia/ ; CEECIND/02064/2017//Fundação para a Ciência e Tecnologia/ ; }, mesh = {Humans ; Animals ; Seasons ; *Songbirds ; DNA Barcoding, Taxonomic ; Diet ; Food ; Ecosystem ; }, abstract = {Optimal Foraging Theory (OFT) predicts that a population's trophic niche expansion should occur in periods of food scarcity as individuals begin to opportunistically exploit sub-optimal food items. However, the Niche Variation Hypothesis (NVH) posits that niche widening may result from increased among-individual differentiation due to food partitioning to avoid competition. We tested these hypotheses through a DNA metabarcoding study of the Sardinian Warbler (Curruca melanocephala) diet over a year. We used null models and the decomposition of beta diversity on among-individual dietary differentiation to infer the mechanisms driving the population's niche variation. Warblers fed frequently on berries, with a peak in late summer and, to a lesser extent, in autumn. Their diet also included a wide range of arthropods, with their prevalence varying among seasons. Consistent with OFT, the population's niche width was narrower in spring/summer when the population was strongly specialized in berries. In winter, the population's niche expanded, possibly reflecting seasonal declines in food abundance. As predicted by NVH, among-individual differentiation tended to be higher in winter, but this was mainly due to increased differences in dietary richness rather than to the partitioning of resources. Overall, our results suggest that within-individual niche does not increase in lean periods, and instead, individuals adopt either a more opportunistic or more specialized foraging strategy. Increased competition in periods of scarcity may help explain such patterns, but instead of showing increased food partitioning as expected from NVH, it may reflect OFT mechanisms on individuals with differential competitive ability to access better food resources.}, } @article {pmid38123635, year = {2023}, author = {Park, J and Lee, KE and Choi, DH and Kim, YK and Lee, WH and Kim, MS and Sung, HWJ and Chang, JW and Park, YS}, title = {The association of tonsillar microbiota with biochemical indices based on obesity and tonsillar hypertrophy in children.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22716}, pmid = {38123635}, issn = {2045-2322}, support = {2021R1C1C1014142//National Research Foundation of Korea/ ; 2020R1A2C1101340//National Research Foundation of Korea/ ; 1711138229//Korea Medical Device Development Fund/ ; }, mesh = {Humans ; Child ; Palatine Tonsil ; *Pediatric Obesity/complications ; RNA, Ribosomal, 16S/genetics ; Hypertrophy/complications ; *Microbiota ; }, abstract = {The correlation between tonsil microbiome and tonsillar hypertrophy has not been well established. Given that oral dysbiosis is related to several metabolic diseases and that tonsillar hypertrophy leads to disordered breathing during sleep and obesity in children, it is necessary to investigate the relationship between the oral microbiome and tonsillar hypertrophy. After 16S rRNA amplicon sequencing of tonsillectomy samples, we evaluated the correlation between the tonsil microbiome and biochemical blood indices in pediatric patients who underwent tonsillectomy. Groups are classified into two categories: based on BMI, and grades 2, 3, and 4 based on tonsil size. Children with obesity and tonsillar hypertrophy have similar microbiome compositions and induce comparable changes in microbiome abundance and composition, confirming the association from a metagenomic perspective. In addition, obesity and tonsillar hypertrophy demonstrated a strong correlation with the Proteobacteria to Firmicutes (P/F) ratio, and among various biochemical indicators, alanine aminotransferase (ALT) levels increase with obesity and tonsillar hypertrophy, indicating a possible association of tonsil microbiome and liver metabolism. These novel findings demonstrate the significance of the tonsil microbiome and suggest the need for tonsil regulation, particularly during childhood.}, } @article {pmid38123079, year = {2024}, author = {Fu, Q and Qiu, Y and Zhao, J and Li, J and Xie, S and Liao, Q and Fu, X and Huang, Y and Yao, Z and Dai, Z and Qiu, Y and Yang, Y and Li, F and Chen, H}, title = {Monotonic trends of soil microbiomes, metagenomic and metabolomic functioning across ecosystems along water gradients in the Altai region, northwestern China.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169351}, doi = {10.1016/j.scitotenv.2023.169351}, pmid = {38123079}, issn = {1879-1026}, mesh = {*Ecosystem ; Soil/chemistry ; Water/analysis ; *Microbiota ; China ; Carbon ; Nitrogen/metabolism ; Soil Microbiology ; }, abstract = {To investigate microbial communities and their contributions to carbon and nutrient cycling along water gradients can enhance our comprehension of climate change impacts on ecosystem services. Thus, we conducted an assessment of microbial communities, metagenomic functions, and metabolomic profiles within four ecosystems, i.e., desert grassland (DG), shrub-steppe (SS), forest (FO), and marsh (MA) in the Altai region of Xinjiang, China. Our results showed that soil total carbon (TC), total nitrogen, NH4[+], and NO3[-] increased, but pH decreased with soil water gradients. Microbial abundances and richness also increased with soil moisture except the abundances of fungi and protists being lowest in MA. A shift in microbial community composition is evident along the soil moisture gradient, with Proteobacteria, Basidiomycota, and Evosea proliferating but a decline in Actinobacteria and Cercozoa. The β-diversity of microbiomes, metagenomic, and metabolomic functioning were correlated with soil moisture gradients and have significant associations with specific soil factors of TC, NH4[+], and pH. Metagenomic functions associated with carbohydrate and DNA metabolisms, as well as phages, prophages, TE, plasmids functions diminished with moisture, whereas the genes involved in nitrogen and potassium metabolism, along with certain biological interactions and environmental information processing functions, demonstrated an augmentation. Additionally, MA harbored the most abundant metabolomics dominated by lipids and lipid-like molecules and organic oxygen compounds, except certain metabolites showing decline trends along water gradients, such as N'-Hydroxymethylnorcotinine and 5-Hydroxyenterolactone. Thus, our study suggests that future ecosystem succession facilitated by changes in rainfall patterns will significantly alter soil microbial taxa, functional potential, and metabolite fractions.}, } @article {pmid38118419, year = {2023}, author = {Quesada-Vázquez, S and Castells-Nobau, A and Latorre, J and Oliveras-Cañellas, N and Puig-Parnau, I and Tejera, N and Tobajas, Y and Baudin, J and Hildebrand, F and Beraza, N and Burcelin, R and Martinez-Gili, L and Chilloux, J and Dumas, ME and Federici, M and Hoyles, L and Caimari, A and Del Bas, JM and Escoté, X and Fernández-Real, JM and Mayneris-Perxachs, J}, title = {Potential therapeutic implications of histidine catabolism by the gut microbiota in NAFLD patients with morbid obesity.}, journal = {Cell reports. Medicine}, volume = {4}, number = {12}, pages = {101341}, pmid = {38118419}, issn = {2666-3791}, mesh = {Humans ; Mice ; Rats ; Animals ; *Non-alcoholic Fatty Liver Disease/drug therapy ; Histidine/therapeutic use ; *Obesity, Morbid ; *Gastrointestinal Microbiome/physiology ; Diet, High-Fat ; }, abstract = {The gut microbiota contributes to the pathophysiology of non-alcoholic fatty liver disease (NAFLD). Histidine is a key energy source for the microbiota, scavenging it from the host. Its role in NAFLD is poorly known. Plasma metabolomics, liver transcriptomics, and fecal metagenomics were performed in three human cohorts coupled with hepatocyte, rodent, and Drosophila models. Machine learning analyses identified plasma histidine as being strongly inversely associated with steatosis and linked to a hepatic transcriptomic signature involved in insulin signaling, inflammation, and trace amine-associated receptor 1. Circulating histidine was inversely associated with Proteobacteria and positively with bacteria lacking the histidine utilization (Hut) system. Histidine supplementation improved NAFLD in different animal models (diet-induced NAFLD in mouse and flies, ob/ob mouse, and ovariectomized rats) and reduced de novo lipogenesis. Fecal microbiota transplantation (FMT) from low-histidine donors and mono-colonization of germ-free flies with Enterobacter cloacae increased triglyceride accumulation and reduced histidine content. The interplay among microbiota, histidine catabolism, and NAFLD opens therapeutic opportunities.}, } @article {pmid38118139, year = {2024}, author = {Obayori, OS and Adesina, OD and Salam, LB and Ashade, AO and Nwaokorie, FO}, title = {Depletion of hydrocarbons and concomitant shift in bacterial community structure of a diesel-spiked tropical agricultural soil.}, journal = {Environmental technology}, volume = {45}, number = {25}, pages = {5368-5383}, doi = {10.1080/09593330.2023.2291421}, pmid = {38118139}, issn = {1479-487X}, mesh = {*Soil Microbiology ; *Soil Pollutants/analysis ; *Gasoline ; *Bacteria/classification/genetics ; Hydrocarbons/analysis ; Soil/chemistry ; Biodegradation, Environmental ; Agriculture ; Microbiota ; }, abstract = {Bacterial community of a diesel-spiked agricultural soil was monitored over a 42-day period using the metagenomic approach in order to gain insight into key phylotypes impacted by diesel contamination and be able to predict end point of bioattenuation. Soil physico-chemical parameters showed significant differences (P < 0.05) between the Polluted Soil (PS) and the Unpolluted control (US)across time points. After 21 days, the diesel content decreased by 27.39%, and at the end of 42 days, by 57.11%. Aromatics such as benzene, anthanthrene, propylbenzene, phenanthrenequinone, anthraquinone, and phenanthridine were degraded to non-detected levels within 42 days, while some medium range alkanes and polyaromatics such as acenaphthylene, naphthalene, and anthracene showed significant levels of degradation. After 21 days (LASTD21), there was a massive enrichment of the phylum Proteobacteria (72.94%), a slight decrease in the abundance of phylum Actinobacteriota (12.74%), and > 500% decrease in the abundance of the phylum Acidobacteriodota (5.26%). Day 42 (LASTD42) saw establishment of the dominance of the Proteobacteria (34.95%), Actinobacteriota, (21.71%), and Firmicutes (32.14%), and decimation of phyla such as Gemmatimonadota, Planctomycetota, and Verrucromicrobiota which play important roles in the cycling of elements and soil health. Principal component analysis showed that in PS moisture contents, phosphorus, nitrogen, organic carbon, had greater impacts on the community structure in LASTD21, while acidity, potassium, sodium, calcium and magnesium impacted the control sample. Recovery time of the soil based on the residual hydrocarbons at Day 42 was estimated to be 229.112 d. Thus, additional biostimulation may be required to achieve cleanup within one growing season.}, } @article {pmid38118133, year = {2024}, author = {Bao, Y and Ruan, Y and Wu, J and Wang, WX and Leung, KMY and Lee, PKH}, title = {Metagenomics-Based Microbial Ecological Community Threshold and Indicators of Anthropogenic Disturbances in Estuarine Sediments.}, journal = {Environmental science & technology}, volume = {58}, number = {1}, pages = {780-794}, doi = {10.1021/acs.est.3c08076}, pmid = {38118133}, issn = {1520-5851}, mesh = {Humans ; *Ecosystem ; Anthropogenic Effects ; Geologic Sediments/analysis ; Biota ; Rivers ; *Microbiota ; Estuaries ; Environmental Monitoring ; }, abstract = {Assessing the impacts of cumulative anthropogenic disturbances on estuarine ecosystem health is challenging. Using spatially distributed sediments from the Pearl River Estuary (PRE) in southern China, which are significantly influenced by anthropogenic activities, we demonstrated that metagenomics-based surveillance of benthic microbial communities is a robust approach to assess anthropogenic impacts on estuarine benthic ecosystems. Correlational and threshold analyses between microbial compositions and environmental conditions indicated that anthropogenic disturbances in the PRE sediments drove the taxonomic and functional variations in the benthic microbial communities. An ecological community threshold of anthropogenic disturbances was identified, which delineated the PRE sediments into two groups (H and L) with distinct taxa and functional traits. Group H, located nearshore and subjected to a higher level of anthropogenic disturbances, was enriched with pollutant degraders, putative human pathogens, fecal pollution indicators, and functional traits related to stress tolerance. In contrast, Group L, located offshore and subjected to a lower level of anthropogenic disturbances, was enriched with halotolerant and oligotrophic taxa and functional traits related to growth and resource acquisition. The machine learning random forest model identified a number of taxonomic and functional indicators that could differentiate PRE sediments between Groups H and L. The identified ecological community threshold and microbial indicators highlight the utility of metagenomics-based microbial surveillance in assessing the adverse impacts of anthropogenic disturbances in estuarine sediments, which can assist environmental management to better protect ecosystem health.}, } @article {pmid38117560, year = {2024}, author = {Wu, X and Zhang, T and Zhang, T and Park, S}, title = {The impact of gut microbiome enterotypes on ulcerative colitis: identifying key bacterial species and revealing species co-occurrence networks using machine learning.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2292254}, pmid = {38117560}, issn = {1949-0984}, mesh = {Humans ; *Colitis, Ulcerative ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Clostridioides difficile ; Bacteria/genetics ; Bacteroidaceae ; Machine Learning ; }, abstract = {Ulcerative colitis (UC) is a chronic inflammatory intestinal disease affecting the colon and rectum, with its pathogenesis attributed to genetic background, environmental factors, and gut microbes. This study aimed to investigate the role of enterotypes in UC by conducting a hierarchical analysis, determining differential bacteria using machine learning, and performing Species Co-occurrence Network (SCN) analysis. Fecal bacterial data were collected from UC patients, and a 16S rRNA metagenomic analysis was performed using the QIIME2 bioinformatics pipeline. Enterotype clustering was conducted at the family level, and deep neural network (DNN) classification models were trained for UC and healthy controls (HC) in each enterotype. Results from eleven 16S rRNA gut microbiome datasets revealed three enterotypes: Bacteroidaceae (ET-B), Lachnospiraceae (ET-L), and Clostridiaceae (ET-C). Ruminococcus (R. gnavus) abundance was significantly higher in UC subjects with ET-B and ET-C than in those with ET-L. R. gnavus also showed a positive correlation with Clostridia in UC SCN for ET-B and ET-C subjects, with a higher correlation in ET-C subjects. Conversely, Odoribacter (O.) splanchnicus and Bacteroides (B.) uniformis exhibited a positive correlation with tryptophan metabolism and AMP-activated protein kinase (AMPK) signaling pathways, while R. gnavus showed a negative correlation. In vitro co-culture experiments with Clostridium (C.) difficile demonstrated that fecal microbiota from ET-B subjects had a higher abundance of C. difficile than ET-L subjects. In conclusion, the ET-B enterotype predisposes individuals to UC, with R. gnavus as a potential risk factor and O. splanchnicus and B. uniformis as protective bacteria, and those with UC may have ultimately become ET-C.}, } @article {pmid38117091, year = {2024}, author = {Bommana, S and Hu, Y-J and Kama, M and Wang, R and Kodimerla, R and Jijakli, K and Read, TD and Dean, D}, title = {Unique microbial diversity, community composition, and networks among Pacific Islander endocervical and vaginal microbiomes with and without Chlamydia trachomatis infection in Fiji.}, journal = {mBio}, volume = {15}, number = {1}, pages = {e0306323}, pmid = {38117091}, issn = {2150-7511}, support = {R01 AI151075/AI/NIAID NIH HHS/United States ; R01 GM141074/GM/NIGMS NIH HHS/United States ; }, mesh = {Female ; Humans ; Cervix Uteri/microbiology ; Chlamydia trachomatis/genetics ; Fiji ; *Papillomavirus Infections ; Vagina/microbiology ; *Chlamydia Infections/microbiology ; Pacific Island People ; *Microbiota ; }, abstract = {Chlamydia trachomatis (Ct) is the most common sexually transmitted bacterium globally. Endocervical and vaginal microbiome interactions are rarely examined within the context of Ct or among vulnerable populations. We evaluated 258 vaginal and 92 paired endocervical samples from Fijian women using metagenomic shotgun sequencing. Over 37% of the microbiomes could not be classified into sub-community state types (subCSTs). We, therefore, developed subCSTs IV-D0, IV-D1, IV-D2, and IV-E-dominated primarily by Gardnerella vaginalis-to improve classification. Among paired microbiomes, the endocervix had a significantly higher alpha diversity and, independently, higher diversity for high-risk human papilloma virus (HPV) genotypes compared to low-risk and no HPV. Ct-infected endocervical networks had smaller clusters without interactions with potentially beneficial Lactobacillus spp. Overall, these data suggest that G. vaginalis may generate polymicrobial biofilms that predispose to and/or promote Ct and possibly HPV persistence and pathogenicity. Our findings expand on the existing repertoire of endocervical and vaginal microbiomes and fill in knowledge gaps regarding Pacific Islanders.}, } @article {pmid38115299, year = {2023}, author = {Lu, D and Li, C and Zhong, Z and Abudouaini, M and Amar, A and Wu, H and Wei, X}, title = {Changes in the airway microbiome in patients with bronchiectasis.}, journal = {Medicine}, volume = {102}, number = {50}, pages = {e36519}, pmid = {38115299}, issn = {1536-5964}, mesh = {Humans ; Adult ; Middle Aged ; Aged ; Prospective Studies ; Quality of Life ; *Bronchiectasis ; *Microbiota/genetics ; Respiratory System ; Anti-Bacterial Agents ; High-Throughput Nucleotide Sequencing ; Sensitivity and Specificity ; }, abstract = {This study used metagenomic next-generation sequencing (mNGS) technology to explore the changes of the microbial characteristics in the lower respiratory tract in patients with acute exacerbations of bronchiectasis (noncystic fibrosis) to guide clinical treatment and improve patients' quality of life and prognosis. This prospective study included 54 patients with acute exacerbation and 46 clinically stable patients admitted to the Respiratory and Critical Care Medicine Center of the People's Hospital of Xinjiang Uygur Autonomous Region from January 2020 to July 2022. Sputum was subjected to routine microbiological tests, and bronchoalveolar lavage fluid (BALF) samples were subjected to microbiological tests and mNGS of BALF before empirical antibiotic therapy. Serum inflammatory markers (white blood cell count, interleukin-6, procalcitonin, and C-reactive protein) were measured. In addition, we evaluated the pathogen of mNGS and compared the airway microbiome composition of patients with acute exacerbation and control patients. The mean age of our cohort was 56 ± 15.2 years. Eighty-nine patients had positive results by mNGS. There was a significant difference in the detection of viruses between the groups (χ2 = 6.954, P < .01). The fungal species Candida albicans, Pneumocystis jirovecii, and Aspergillus fumigatus were significantly more common in patients with acute exacerbations (χ2 = 5.98, P = .014). The bacterial species Acinetobacter baumannii, Mycobacterium tuberculosis, Haemophilus influenzae, Haemophilus parahaemolyticus, Abiotrophia defectiva, and Micromonas micros were significantly more prevalent in patients with acute exacerbations (χ2 = 4.065, P = .044). The most common bacterial species isolated from the sputum and BALF samples of patients with acute exacerbation was A. baumannii. Chlamydia psittaci was found in 4 patients. In addition, of 77 patients with negative sputum culture, 66 had positive results by mNGS, demonstrating the increased sensitivity and accuracy of mNGS. Patients with acute exacerbation of bronchiectasis tend to have mixed infections in the lower respiratory tract. The frequency of viruses, fungi, and Mycoplasma was higher in these patients. Our findings suggest that mNGS could be used to identify pathogenic microorganisms in these patients, increasing the effectiveness of antibiotic therapy.}, } @article {pmid38115019, year = {2023}, author = {Liu, X and Liu, D and Tan, C and Feng, W}, title = {Gut microbiome-based machine learning for diagnostic prediction of liver fibrosis and cirrhosis: a systematic review and meta-analysis.}, journal = {BMC medical informatics and decision making}, volume = {23}, number = {1}, pages = {294}, pmid = {38115019}, issn = {1472-6947}, mesh = {Humans ; *Gastrointestinal Microbiome ; Liver Cirrhosis/diagnosis/pathology ; Fibrosis ; Machine Learning ; }, abstract = {BACKGROUND: Invasive detection methods such as liver biopsy are currently the gold standard for diagnosing liver cirrhosis and can be used to determine the degree of liver fibrosis and cirrhosis. In contrast, non-invasive diagnostic methods, such as ultrasonography, elastography, and clinical prediction scores, can prevent patients from invasiveness-related discomfort and risks and are often chosen as alternative or supplementary diagnostic methods for liver fibrosis or cirrhosis. However, these non-invasive methods cannot specify the pathological grading and early diagnosis of the lesions. Recent studies have revealed that gut microbiome-based machine learning can be utilized as a non-invasive diagnostic technique for liver cirrhosis or fibrosis, but there is no evidence-based support. Therefore, this study conducted a systematic review and meta-analysis for the first time to investigate the accuracy of machine learning based on the gut microbiota in the prediction of liver fibrosis and cirrhosis.

METHODS: A comprehensive and systematic search of publications published before April 2th, 2023 in PubMed, Cochrane Library, Embase, and Web of Science was conducted for relevant studies on the application of gut microbiome-based metagenomic sequencing modeling technology to the diagnostic prediction of liver cirrhosis or fibrosis. A bivariate mixed-effects model and Stata software 15.0 were adopted for the meta-analysis.

RESULTS: Ten studies were included in the present study, involving 11 prediction trials and 838 participants, 403 of whom were fibrotic and cirrhotic patients. Meta-analysis showed the pooled sensitivity (SEN) = 0.81 [0.75, 0.85], specificity (SEP) = 0.85 [0.77, 0.91], positive likelihood ratio (PLR) = 5.5 [3.6, 8.7], negative likelihood ratio (NLR) = 0.23 [0.18, 0.29], diagnostic odds ratio (DOR) = 24 [14, 41], and area under curve (AUC) = 0.86 [0.83-0.89]. The results demonstrated that machine learning methods had excellent potential to analyze gut microbiome data and could effectively predict liver cirrhosis or fibrosis. Machine learning provides a powerful tool for non-invasive prediction and diagnosis of liver cirrhosis or liver fibrosis, with broad clinical application prospects. However, these results need to be interpreted with caution due to limited clinical data.

CONCLUSION: Gut microbiome-based machine learning can be utilized as a practical, non-invasive technique for the diagnostic prediction of liver cirrhosis or fibrosis. However, most of the included studies applied the random forest algorithm in modeling, so a diversified prediction system based on microorganisms is needed to improve the non-invasive detection of liver cirrhosis or fibrosis.}, } @article {pmid38115005, year = {2023}, author = {Lan, Q and Zhang, C and Hua, H and Hu, X}, title = {Compositional and functional changes in the salivary microbiota related to oral leukoplakia and oral squamous cell carcinoma: a case control study.}, journal = {BMC oral health}, volume = {23}, number = {1}, pages = {1021}, pmid = {38115005}, issn = {1472-6831}, support = {PKUSSNMP-201907//the 2021 National Program for Multidisciplinary Cooperative Treatment on Major Diseases/ ; PKUSSNMP-202109//the 2022 National Program for Multidisciplinary Cooperative Treatment on Major Diseases/ ; PKUSS20170104//Young People Fund of Peking University School and Hospital of Stomatology/ ; PKUSSNCT-23B11//Program for New Clinical Techniques and Therapies of Peking University School and Hospital of Stomatology/ ; }, mesh = {Humans ; *Mouth Neoplasms/pathology ; Squamous Cell Carcinoma of Head and Neck ; *Carcinoma, Squamous Cell/pathology ; Case-Control Studies ; Cysteine ; Leukoplakia, Oral ; Carcinogenesis ; *Microbiota ; *Head and Neck Neoplasms ; Methionine ; }, abstract = {BACKGROUND: Oral squamous cell carcinoma (OSCC) is one of the most common malignant tumours with increasing incidence, and oral leukoplakia (OLK) has a strong tendency to undergo malignant transformation. The oral microbiota may influence oral cancer progression, but the salivary bacterial composition and functional changes in OSCC and OLK have not been comprehensively elucidated. Therefore, we compared salivary bacteria in OLK and OSCC patients with healthy controls (HC).

METHODS: Metagenomic sequencing was used to compare the bacterial composition and functional changes of 18 OSCC patients, 21 OLK patients and 21 HC. Spearman correlation was used to identify possible associations between functions and bacteria.

RESULTS: Gemella was the most differentially enriched genus in OSCC. At the species level, Streptococcus sp. NPS 308, Streptococcus agalactiae, Gemella haemolysans and Gemella morbillorum were slightly increased in OLK and OSCC. Kyoto Encyclopedia of Genes and Genomes (KEGG) results showed that OSCC was mainly associated with metabolism functions, including lipid metabolism, carbohydrate metabolism and glycan biosynthesis and metabolism. The synthesis and degradation of ketone bodies, cysteine and methionine metabolism and glycerolipid metabolism differed significantly among the three groups, and were highest in OSCC and lowest in HC. And G. haemolysans was significantly associated with these selected metabolic pathways.

CONCLUSIONS: Metagenomic analysis revealed significant differences in the salivary microbiota among OSCC, OLK and HC. Thus, salivary microbiota composition and functional changes may be associated with OSCC progression. Metabolism of nonessential amino acids such as cysteine and methionine in bacteria may play an important role in oral oncogenesis, and more studies of the mechanism between metabolisms of bacteria and oral oncogenesis are needed in the future.}, } @article {pmid38114947, year = {2023}, author = {Trapella, G and Cinti, N and Parma, L and De Marco, A and Dell'Acqua, AN and Turroni, S and Rampelli, S and Scicchitano, D and Iuffrida, L and Bonaldo, A and Franzellitti, S and Candela, M and Palladino, G}, title = {Microbiome variation at the clam-sediment interface may explain changes in local productivity of Chamelea gallina in the North Adriatic sea.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {402}, pmid = {38114947}, issn = {1471-2180}, support = {818290//"Controlling Microbiomes Circulations for Better Food Systems", European Union's Horizon 2020/ ; }, mesh = {Animals ; *Bivalvia ; Seafood ; }, abstract = {BACKGROUND: The clam Chamelea gallina is an ecologically and economically important marine species in the Northwestern Adriatic Sea, which currently suffers from occasional, and still unexplained, widespread mortality events. In order to provide some glimpses in this direction, this study explores the connections between microbiome variations at the clam-sediment interface and the nutritional status of clams collected at four Italian production sites along the Emilia Romagna coast, with different mortality incidence, higher in the Northern sites and lower in the Southern sites.

RESULTS: According to our findings, each production site showed a peculiar microbiome arrangement at the clam-sediment interface, with features that clearly differentiate the Northern and Southern sites, with the latter also being associated with a better nutritional status of the animal. Interestingly, the C. gallina digestive gland microbiome from the Southern sites was enriched in some health-promoting microbiome components, capable of supplying the host with essential nutrients and defensive molecules. Furthermore, in experiments conducted under controlled conditions in aquaria, we provided preliminary evidence of the prebiotic action of sediments from the Southern sites, allowing to boost the acquisition of previously identified health-promoting components of the digestive gland microbiome by clams from the Northern sites.

CONCLUSIONS: Taken together, our findings may help define innovative microbiome-based management strategies for the preservation of the productivity of C. gallina clams in the Adriatic Sea, through the identification and maintenance of a probiotic niche at the animal-sediment interface.}, } @article {pmid38114587, year = {2023}, author = {Roume, H and Mondot, S and Saliou, A and Le Fresne-Languille, S and Doré, J}, title = {Multicenter evaluation of gut microbiome profiling by next-generation sequencing reveals major biases in partial-length metabarcoding approach.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22593}, pmid = {38114587}, issn = {2045-2322}, support = {2017-AdG No. 788191/ERC_/European Research Council/International ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Reproducibility of Results ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; DNA, Bacterial/genetics/analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Next-generation sequencing workflows, using either metabarcoding or metagenomic approaches, have massively contributed to expanding knowledge of the human gut microbiota, but methodological bias compromises reproducibility across studies. Where these biases have been quantified within several comparative analyses on their own, none have measured inter-laboratory reproducibility using similar DNA material. Here, we designed a multicenter study involving seven participating laboratories dedicated to partial- (P1 to P5), full-length (P6) metabarcoding, or metagenomic profiling (MGP) using DNA from a mock microbial community or extracted from 10 fecal samples collected at two time points from five donors. Fecal material was collected, and the DNA was extracted according to the IHMS protocols. The mock and isolated DNA were then provided to the participating laboratories for sequencing. Following sequencing analysis according to the laboratories' routine pipelines, relative taxonomic-count tables defined at the genus level were provided and analyzed. Large variations in alpha-diversity between laboratories, uncorrelated with sequencing depth, were detected among the profiles. Half of the genera identified by P1 were unique to this partner and two-thirds of the genera identified by MGP were not detected by P3. Analysis of beta-diversity revealed lower inter-individual variance than inter-laboratory variances. The taxonomic profiles of P5 and P6 were more similar to those of MGP than those obtained by P1, P2, P3, and P4. Reanalysis of the raw sequences obtained by partial-length metabarcoding profiling, using a single bioinformatic pipeline, harmonized the description of the bacterial profiles, which were more similar to each other, except for P3, and closer to the profiles obtained by MGP. This study highlights the major impact of the bioinformatics pipeline, and primarily the database used for taxonomic annotation. Laboratories need to benchmark and optimize their bioinformatic pipelines using standards to monitor their effectiveness in accurately detecting taxa present in gut microbiota.}, } @article {pmid38114447, year = {2024}, author = {Bucci, L and Ghiotto, G and Zampieri, G and Raga, R and Favaro, L and Treu, L and Campanaro, S}, title = {Adaptation of Anaerobic Digestion Microbial Communities to High Ammonium Levels: Insights from Strain-Resolved Metagenomics.}, journal = {Environmental science & technology}, volume = {58}, number = {1}, pages = {580-590}, pmid = {38114447}, issn = {1520-5851}, mesh = {Anaerobiosis ; Bioreactors/microbiology ; Bacteria/genetics/metabolism ; *Microbiota ; Metagenomics ; Ammonia/metabolism ; *Ammonium Compounds/metabolism ; Methane ; }, abstract = {Ammonia release from proteinaceous feedstocks represents the main inhibitor of the anaerobic digestion (AD) process, which can result in a decreased biomethane yield or even complete failure of the process. The present study focused on the adaptation of mesophilic AD communities to a stepwise increase in the concentration of ammonium chloride in synthetic medium with casein used as the carbon source. An adaptation process occurring over more than 20 months allowed batch reactors to reach up to 20 g of NH4[+] N/L without collapsing in acidification nor ceasing methane production. To decipher the microbial dynamics occurring during the adaptation and determine the genes mostly exposed to selective pressure, a combination of biochemical and metagenomics analyses was performed, reconstructing the strains of key species and tracking them over time. Subsequently, the adaptive metabolic mechanisms were delineated by following the single nucleotide variants (SNVs) characterizing the strains and prioritizing the associated genes according to their function. An in-depth exploration of the archaeon Methanoculleus bourgensis vb3066 and the putative syntrophic acetate-oxidizing bacteria Acetomicrobium sp. ma133 identified positively selected SNVs on genes involved in stress adaptation. The intraspecies diversity with multiple coexisting strains in a temporal succession pattern allows us to detect the presence of an additional level of diversity within the microbial community beyond the species level.}, } @article {pmid38114436, year = {2024}, author = {Wang, HY and Liu, LX and Chen, XY and Zhang, YD and Li, WX and Li, WW and Wang, L and Mo, XL and Wei, H and Ji, P and Xie, P}, title = {Comprehensive analysis of the gut microbiome and post-translational modifications elucidates the route involved in microbiota-host interactions.}, journal = {Zoological research}, volume = {45}, number = {1}, pages = {95-107}, pmid = {38114436}, issn = {2095-8137}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Lysine/metabolism ; Host Microbial Interactions ; Proteomics/methods ; Protein Processing, Post-Translational ; }, abstract = {The gut microbiome interacts with the host to maintain body homeostasis, with gut microbial dysbiosis implicated in many diseases. However, the underlying mechanisms of gut microbe regulation of host behavior and brain functions remain unclear. This study aimed to elucidate the influence of gut microbiota on brain functions via post-translational modification mechanisms in the presence or absence of bacteria without any stimulation. We conducted succinylome analysis of hippocampal proteins in germ-free (GF) and specific pathogen-free (SPF) mice and metagenomic analysis of feces from SPF mice. These results were integrated with previously reported hippocampal acetylome and phosphorylome data from the same batch of mice. Subsequent bioinformatics analyses revealed 584 succinylation sites on 455 proteins, including 54 up-regulated succinylation sites on 91 proteins and 99 down-regulated sites on 51 proteins in the GF mice compared to the SPF mice. We constructed a panoramic map of gut microbiota-regulated succinylation, acetylation, and phosphorylation, and identified cross-talk and relative independence between the different types of post-translational modifications in modulating complicated intracellular pathways. Pearson correlation analysis indicated that 13 taxa, predominantly belonging to the Bacteroidetes phylum, were correlated with the biological functions of post-translational modifications. Positive correlations between these taxa and succinylation and negative correlations between these taxa and acetylation were identified in the modulation of intracellular pathways. This study highlights the hippocampal physiological changes induced by the absence of gut microbiota, and proteomic quantification of succinylation, phosphorylation, and acetylation, contributing to our understanding of the role of the gut microbiome in brain function and behavioral phenotypes.}, } @article {pmid38113887, year = {2024}, author = {Zhu, Y and Jian, X and Chen, S and An, G and Jiang, D and Yang, Q and Zhang, J and Hu, J and Qiu, Y and Feng, X and Guo, J and Chen, X and Li, Z and Zhou, R and Hu, C and He, N and Shi, F and Huang, S and Liu, H and Li, X and Xie, L and Zhu, Y and Zhao, L and Jiang, Y and Li, J and Wang, J and Qiu, L and Chen, X and Jia, W and He, Y and Zhou, W}, title = {Targeting gut microbial nitrogen recycling and cellular uptake of ammonium to improve bortezomib resistance in multiple myeloma.}, journal = {Cell metabolism}, volume = {36}, number = {1}, pages = {159-175.e8}, doi = {10.1016/j.cmet.2023.11.019}, pmid = {38113887}, issn = {1932-7420}, mesh = {Humans ; Bortezomib/pharmacology/therapeutic use/metabolism ; *Multiple Myeloma/drug therapy/metabolism ; *Gastrointestinal Microbiome ; Cell Line, Tumor ; Membrane Proteins/metabolism ; NIMA-Related Kinases/metabolism/therapeutic use ; Solute Carrier Family 12, Member 2/pharmacology ; }, abstract = {The gut microbiome has been found to play a crucial role in the treatment of multiple myeloma (MM), which is still considered incurable due to drug resistance. In previous studies, we demonstrated that intestinal nitrogen-recycling bacteria are enriched in patients with MM. However, their role in MM relapse remains unclear. This study highlights the specific enrichment of Citrobacter freundii (C. freundii) in patients with relapsed MM. Through fecal microbial transplantation experiments, we demonstrate that C. freundii plays a critical role in inducing drug resistance in MM by increasing levels of circulating ammonium. The ammonium enters MM cells through the transmembrane channel protein SLC12A2, promoting chromosomal instability and drug resistance by stabilizing the NEK2 protein. We show that furosemide sodium, a loop diuretic, downregulates SLC12A2, thereby inhibiting ammonium uptake by MM cells and improving progression-free survival and curative effect scores. These findings provide new therapeutic targets and strategies for the intervention of MM progression and drug resistance.}, } @article {pmid38113233, year = {2023}, author = {Troth, TD and McInnes, RS and Dunn, SJ and Mirza, J and Whittaker, AH and Goodchild, SA and Loman, NJ and Harding, SV and van Schaik, W}, title = {Differences in the gut microbiota between Gurkhas and soldiers of British origin.}, journal = {PloS one}, volume = {18}, number = {12}, pages = {e0292645}, pmid = {38113233}, issn = {1932-6203}, mesh = {Humans ; *Gastrointestinal Microbiome ; White People ; Asian People ; *Military Personnel ; Metagenome ; }, abstract = {Previous work indicated that the incidence of travellers' diarrhoea (TD) is higher in soldiers of British origin, when compared to soldiers of Nepalese descent (Gurkhas). We hypothesise that the composition of the gut microbiota may be a contributing factor in the risk of developing TD in soldiers of British origin. This study aimed to characterise the gut microbial composition of Gurkha and non-Gurkha soldiers of the British Army. Recruitment of 38 soldiers (n = 22 Gurkhas, n = 16 non-Gurkhas) and subsequent stool collection, enabled shotgun metagenomic sequencing-based analysis of the gut microbiota. The microbiota of Gurkhas had significantly (P < 0.05) lower diversity, for both Shannon and Simpson diversity indices, using species level markers than the gut microbiota of non-Gurkha soldiers. Non-metric Multidimensional Scaling (NMDS) of the Bray-Curtis distance matrix revealed a significant difference in the composition of the gut microbiota between Gurkhas and non-Gurkha soldiers, at both the species level (P = 0.0178) and the genus level (P = 0.0483). We found three genera and eight species that were significantly enriched in the non-Gurkha group and one genus (Haemophilus) and one species (Haemophilus parainfluenzae) which were enriched in the Gurkha group. The difference in the microbiota composition between Gurkha soldiers and soldiers of British origin may contribute to higher colonization resistance against diarrhoeal pathogens in the former group. Our findings may enable further studies into interventions that modulate the gut microbiota of soldiers to prevent TD during deployment.}, } @article {pmid38112856, year = {2023}, author = {Kannan, P and Verma, I and Banerjee, B and Saleena, LM}, title = {Unveiling bacterial consortium for xenobiotic biodegradation from Pichavaram mangrove forest soil: a metagenomic approach.}, journal = {Archives of microbiology}, volume = {206}, number = {1}, pages = {27}, pmid = {38112856}, issn = {1432-072X}, mesh = {*Wetlands ; *Xenobiotics/metabolism ; Soil/chemistry ; Furaldehyde ; Bacteria/genetics/metabolism ; Microbial Consortia/genetics ; Soil Microbiology ; Biodegradation, Environmental ; Steroids/metabolism ; }, abstract = {Pichavaram mangrove forest was established as a wetland of International Importance by Article 2.1 in April 2022 by the Ministry of Environment, Forest and Climate Change, India. Even though it is a conserved site, xenobiotic agrochemical leaching on the forest land during monsoon is inevitable. These threaten the microbial diversity in the environment. Xenobiotic degradation is achieved using bacterial consortia already acclimatised to this environment. This study aims to identify the indigenous microbial consortia able to degrade xenobiotic compounds such as fluorobenzoate, furfural, and steroids. Pichavaram mangrove metagenomic dataset was obtained by shotgun sequencing of soil DNA and processed using the automated tool SqueezeMeta. Further, the DIAMOND database provided the taxonomical classification of the microbes in each contig. With reference to the KEGG database, the selected xenobiotic degradation pathways were confirmed in the dataset. Of 1,253,029 total contigs, 1332, 72 and 1262 were involved in fluorobenzoate, furfural and steroid degradation, respectively. This study identified that microbial consortia comprising Marinobacter, Methyloceanibacter and Vibrio natriegens/Gramella sp. can degrade fluorobenzoate. While Afipia, Nitrosopumilus sp., and Phototrophicus methaneseepsis favour the degradation of furfural compound. The steroid degradation pathway possessed a plethora of bacteria belonging to the phylum Proteobacteria.}, } @article {pmid38112274, year = {2024}, author = {Gaspari, M and Ghiotto, G and Centurion, VB and Kotsopoulos, T and Santinello, D and Campanaro, S and Treu, L and Kougias, PG}, title = {Decoding Microbial Responses to Ammonia Shock Loads in Biogas Reactors through Metagenomics and Metatranscriptomics.}, journal = {Environmental science & technology}, volume = {58}, number = {1}, pages = {591-602}, pmid = {38112274}, issn = {1520-5851}, mesh = {*Ammonia/metabolism/pharmacology ; Biofuels ; Bioreactors ; *Microbiota ; Metagenome ; Anaerobiosis ; Methane ; Metagenomics ; }, abstract = {The presence of elevated ammonia levels is widely recognized as a significant contributor to process inhibition in biogas production, posing a common challenge for biogas plant operators. The present study employed a combination of biochemical, genome-centric metagenomic and metatranscriptomic data to investigate the response of the biogas microbiome to two shock loads induced by single pulses of elevated ammonia concentrations (i.e., 1.5 g NH4[+]/LR and 5 g NH4[+]/LR). The analysis revealed a microbial community of high complexity consisting of 364 Metagenome Assembled Genomes (MAGs). The hydrogenotrophic pathway was the primary route for methane production during the entire experiment, confirming its efficiency even at high ammonia concentrations. Additionally, metatranscriptomic analysis uncovered a metabolic shift in the methanogens Methanothrix sp. MA6 and Methanosarcina flavescens MX5, which switched their metabolism from the acetoclastic to the CO2 reduction route during the second shock. Furthermore, multiple genes associated with mechanisms for maintaining osmotic balance in the cell were upregulated, emphasizing the critical role of osmoprotection in the rapid response to the presence of ammonia. Finally, this study offers insights into the transcriptional response of an anaerobic digestion community, specifically focusing on the mechanisms involved in recovering from ammonia-induced stress.}, } @article {pmid38109978, year = {2024}, author = {Xiang, P and Ma, P and He, Q and Song, Z and Miao, Z}, title = {Enhanced removal of phenol and chemical oxygen demand from coking wastewater using micro and nano bubbles: Microbial community and metabolic pathways.}, journal = {Bioresource technology}, volume = {394}, number = {}, pages = {130207}, doi = {10.1016/j.biortech.2023.130207}, pmid = {38109978}, issn = {1873-2976}, mesh = {Wastewater ; Phenol/chemistry ; *Coke ; Biological Oxygen Demand Analysis ; Phenols ; *Microbiota ; Metabolic Networks and Pathways ; Bioreactors/microbiology ; *Benzenesulfonates ; }, abstract = {The treatment of coking wastewater with high phenol concentrations has been a challenge for conventional biological treatment technology. In this short communication, phenol-degrading bacteria domesticated by micro and nano bubbles (MNBs) water are used to treat the high- concentration phenol in an MNBs aeration reactor (MNB-AR). The results show that the MNB-AR can greatly improve the removal of phenol and chemical oxygen demand (COD). At a phenol concentration of 1000 mg L[-1], the phenol and COD removal rates in the MNB-AR are 55 % and 39 % higher than in the conventional bubble aeration reactor respectively. MNB-AR performs more stably and reaches a higher phenol tolerance under fluctuating high-phenol-concentration loadings. Metagenomic analysis shows that MNBs promote the growth and metabolism of aerobic microorganisms related to phenol degradation, and enhance gene abundance related to carbon metabolism. MNBs aeration combined with microorganisms is an efficient solution for treating coking wastewater.}, } @article {pmid38108668, year = {2024}, author = {Ye, H-L and Zhi, M-F and Chen, B-Y and Lin, W-Z and Li, Y-L and Huang, S-J and Zhou, L-J and Xu, S and Zhang, J and Zhang, W-C and Feng, Q and Duan, S-Z}, title = {Alterations of oral and gut viromes in hypertension and/or periodontitis.}, journal = {mSystems}, volume = {9}, number = {1}, pages = {e0116923}, pmid = {38108668}, issn = {2379-5077}, support = {81991503 81725003 81921002//MOST | National Natural Science Foundation of China (NSFC)/ ; SHSMU-ZDCX20212500//Innovative Research Team of High-level Local University in Shanghai (Innovative Research Team of High-level Local Universities in Shanghai)/ ; }, mesh = {Humans ; Virome ; *Viruses/genetics ; *Microbiota/genetics ; *Periodontitis ; *Hypertension ; }, abstract = {The microbiota plays an important role in both hypertension (HTN) and periodontitis (PD), and PD exacerbates the development of HTN by oral and gut microbiota. Previous studies have focused on exploring the importance of the bacteriome in HTN and PD but overlooked the impact of the virome, which is also a member of the microbiota. We collected 180 samples of subgingival plaques, saliva, and feces from a cohort of healthy subjects (nHTNnPD), subjects with HTN (HTNnPD) or PD (PDnHTN), and subjects with both HTN and PD (HTNPD). We performed metagenomic sequencing to assess the roles of the oral and gut viromes in HTN and PD. The HTNnPD, PDnHTN, and HTNPD groups all showed significantly distinct beta diversity from the nHTNnPD group in saliva. We analyzed alterations in oral and gut viral composition in HTN and/or PD and identified significantly changed viruses in each group. Many viruses across three sites were significantly associated with blood pressure and other clinical parameters. Combined with these clinical associations, we found that Gillianvirus in subgingival plaques was negatively associated with HTN and that Torbevirus in saliva was positively associated with HTN. We found that Pepyhexavirus from subgingival plaques was indicated to be transferred to the gut. We finally evaluated viral-bacterial transkingdom interactions and found that viruses and bacteria may cooperate to affect HTN and PD. Correspondingly, HTN and PD may synergize to improve communications between viruses and bacteria.IMPORTANCEPeriodontitis (PD) and hypertension (HTN) are both highly prevalent worldwide and cause serious adverse outcomes. Increasing studies have shown that PD exacerbates HTN by oral and gut microbiota. Previous studies have focused on exploring the importance of the bacteriome in HTN and PD but overlooked the impact of the virome, even though viruses are common inhabitants in humans. Alterations in oral and gut viral diversity and composition contribute to diseases. The present study, for the first time, profiled the oral and gut viromes in HTN and/or PD. We identified key indicator viruses and their clinical implications in HTN and/or PD. We also investigated interactions between viruses and bacteria. This work improved the overall understanding of the viromes in HTN and PD, providing vital insights into the role of the virome in the development of HTN and PD.}, } @article {pmid38108654, year = {2024}, author = {Miao, Z and Chen, L and Zhang, Y and Zhang, J and Zhang, H}, title = {Bifidobacterium animalis subsp. lactis Probio-M8 alleviates abnormal behavior and regulates gut microbiota in a mouse model suffering from autism.}, journal = {mSystems}, volume = {9}, number = {1}, pages = {e0101323}, pmid = {38108654}, issn = {2379-5077}, support = {2022YFD2100702//Research Fund for the National Key R&D Program of China/ ; U22A20540//MOST | National Natural Science Foundation of China (NSFC)/ ; 2021ZD0014//Inner Mongolia Science and Technology Major Projects/ ; //CARS36/ ; }, mesh = {Mice ; Animals ; *Bifidobacterium animalis/metabolism ; *Autistic Disorder/therapy ; *Gastrointestinal Microbiome ; Weight Gain ; Neurotransmitter Agents/metabolism ; }, abstract = {Probiotics can effectively improve a variety of neurological diseases, but there is little research on autism, and the specific mechanism is unclear. In this study, shotgun metagenomics analysis was used to investigate the preventive and therapeutic effects of Bifidobacterium animalis subsp. lactis Probio-M8 on autism. The results showed that Probio-M8 treatment significantly alleviated valproate (VPA)-induced autism in mice, with autistic symptoms characterized by increased stereotyped behaviors such as grooming, reduced learning ability, and decreased desire to socialize. Further studies have found that Probio-M8 can alleviate autism by optimizing gut microbiota diversity and regulating metabolic levels. Probio-M8 regulates gut microbiota structure by increasing the abundance of beneficial bacteria such as Bifidobacterium globosum and Akkermansia muciniphila. In addition, Probio-M8 regulates metabolic activity by increasing levels of choline, which corrects CAZy disorders. In conclusion, Probio-M8 is therapeutic in the VPA-induced autism mouse model by regulating the gut microbiome and metabolic levels.IMPORTANCEIndividuals with autism often exhibit symptoms of social invariance, obsessive-compulsive tendencies, and repetitive behaviors. However, early intervention and treatment can be effective in improving social skills and mitigating autism symptoms, including behaviors related to irritability. Although taking medication for autism may lead to side effects such as weight gain, probiotics can be an ideal intervention for alleviating these symptoms. In this study, we investigated the effects of Probio-M8 intervention on the behavior of autistic mice using an open-field test, a three-chamber sociability test, and a novel object recognition test. Metagenomic analysis revealed differences in gut microbiota diversity among groups, predicted changes in metabolite levels, and functionally annotated CAZy. Additionally, we analyzed serum neurotransmitter levels and found that probiotics were beneficial in mitigating neurotransmitter imbalances in mice with autism.}, } @article {pmid38108273, year = {2023}, author = {Zhang, S-h and Jia, X-y and Wu, Q and Jin, J and Xu, L-s and Yang, L and Han, J-g and Zhou, Q-h}, title = {The involvement of the gut microbiota in postoperative cognitive dysfunction based on integrated metagenomic and metabolomics analysis.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0310423}, pmid = {38108273}, issn = {2165-0497}, mesh = {Aged ; Humans ; Animals ; Mice ; *Postoperative Cognitive Complications ; *Gastrointestinal Microbiome ; Metabolomics ; *Cognitive Dysfunction ; Bacteroides ; }, abstract = {As the population ages and medical technology advances, anesthesia procedures for elderly patients are becoming more common, leading to an increased prevalence of postoperative cognitive dysfunction. However, the etiology and correlation between the gut microbiota and cognitive dysfunction are poorly understood, and research in this area is limited. In this study, mice with postoperative cognitive dysfunction were found to have reduced levels of fatty acid production and anti-inflammatory flora in the gut, and Bacteroides was associated with increased depression, leading to cognitive dysfunction and depression. Furthermore, more specific microbial species were identified in the disease model, suggesting that modulation of host metabolism through gut microbes may be a potential avenue for preventing postoperative cognitive dysfunction.}, } @article {pmid38104736, year = {2024}, author = {Bakhti, A and Moghimi, H and Bozorg, A and Stankovic, S and Manafi, Z and Schippers, A}, title = {Comparison of bioleaching of a sulfidic copper ore (chalcopyrite) in column percolators and in stirred-tank bioreactors including microbial community analysis.}, journal = {Chemosphere}, volume = {349}, number = {}, pages = {140945}, doi = {10.1016/j.chemosphere.2023.140945}, pmid = {38104736}, issn = {1879-1298}, mesh = {*Copper ; RNA, Ribosomal, 16S/genetics ; Sodium Chloride ; Bioreactors/microbiology ; Iron ; Sulfur ; Sulfides ; *Microbiota ; }, abstract = {Chalcopyrite is the most abundant Cu-sulfide and economically the most important copper mineral in the world. It is known to be recalcitrant in hydrometallurgical processing and therefore chalcopyrite bioleaching has been thoroughly studied for improvement of processing. In this study, the microbial diversity in 22 samples from the Sarcheshmeh copper mine in Iran was investigated via 16S rRNA gene sequencing. In total, 1063 species were recognized after metagenomic analysis including the ferrous iron- and sulfur-oxidizing acidophilic genera Acidithiobacillus, Leptospirillum, Sulfobacillus and Ferroplasma. Mesophilic as well as moderately thermophilic acidophilic ferrous iron- and sulfur-oxidizing microorganisms were enriched from these samples and bioleaching was studied in shake flask experiments using a chalcopyrite-containing ore sample from the same mine. These enrichment cultures were further used as inoculum for bioleaching experiments in percolation columns for simulating heap bioleaching. Addition of 100 mM NaCl to the bioleaching medium was assessed to improve the dissolution rate of chalcopyrite. For comparison, bioleaching in stirred tank reactors with a defined microbial consortium was carried out as well. While just maximal 32% copper could be extracted in the flask bioleaching experiments, 73% and 76% of copper recovery was recorded after 30 and 10 days bioleaching in columns and bioreactors, respectively. Based on the results, both, the application of moderately thermophilic acidophilic bacteria in stirred tank bioreactors, and natural enrichment cultures of mesoacidophiles, with addition of 100 mM NaCl in column percolators with agglomerated ore allowed for a robust chalcopyrite dissolution and copper recovery from Sarcheshmeh copper ore via bioleaching.}, } @article {pmid38104504, year = {2024}, author = {Valles-Colomer, M and Manghi, P and Cumbo, F and Masetti, G and Armanini, F and Asnicar, F and Blanco-Miguez, A and Pinto, F and Punčochář, M and Garaventa, A and Amoroso, L and Ponzoni, M and Corrias, MV and Segata, N}, title = {Neuroblastoma is associated with alterations in gut microbiome composition subsequent to maternal microbial seeding.}, journal = {EBioMedicine}, volume = {99}, number = {}, pages = {104917}, pmid = {38104504}, issn = {2352-3964}, support = {R01 CA230551/CA/NCI NIH HHS/United States ; U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {Infant ; Child ; Female ; Humans ; Animals ; Mice ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; *Microbiota ; Metagenome ; *Neuroblastoma/etiology ; }, abstract = {BACKGROUND: Neuroblastoma is the most frequent extracranial solid tumour in children, accounting for ∼15% of deaths due to cancer in childhood. The most common clinical presentation are abdominal tumours. An altered gut microbiome composition has been linked to multiple cancer types, and reported in murine models of neuroblastoma. Whether children with neuroblastoma display alterations in gut microbiome composition remains unexplored.

METHODS: We assessed gut microbiome composition by shotgun metagenomic profiling in an observational cross-sectional study on 288 individuals, consisting of patients with a diagnosis of neuroblastoma at disease onset (N = 63), healthy controls matching the patients on the main covariates of microbiome composition (N = 94), healthy siblings of the patients (N = 13), mothers of patients (N = 59), and mothers of the controls (N = 59). We examined taxonomic and functional microbiome composition and mother-infant strain transmission patterns.

FINDINGS: Patients with neuroblastoma displayed alterations in gut microbiome composition characterised by reduced microbiome richness, decreased relative abundances of 18 species (including Phocaeicola dorei and Bifidobacterium bifidum), enriched protein fermentation and reduced carbohydrate fermentation potential. Using machine learning, we could successfully discriminate patients from controls (AUC = 82%). Healthy siblings did not display such alterations but resembled the healthy control group. No significant differences in maternal microbiome composition nor mother-to-offspring transmission were detected.

INTERPRETATION: Patients with neuroblastoma display alterations in taxonomic and functional gut microbiome composition, which cannot be traced to differential maternal seeding. Follow-up research should include investigating potential causal links.

FUNDING: Italian Ministry of Health Ricerca Corrente and Ricerca Finalizzata 5 per mille (to MPonzoni); Fondazione Italiana Neuroblastoma (to MPonzoni); European Research Council (ERC-StG project MetaPG-716575 and ERC-CoG microTOUCH-101045015 to NS); the European H2020 program ONCOBIOME-825410 project (to NS); the National Cancer Institute of the National Institutes of Health 1U01CA230551 (to NS); the Premio Internazionale Lombardia e Ricerca 2019 (to NS); the MIUR Progetti di Ricerca di Rilevante Interesse Nazionale (PRIN) Bando 2017 Grant 2017J3E2W2 (to NS); EMBO ALTF 593-2020 and Knowledge Generation Project from the Spanish Ministry of Science and Innovation (PID2022-139328OA-I00) (to MV-C).}, } @article {pmid38104411, year = {2024}, author = {Jan, TR and Lin, CS and Yang, WY}, title = {Differential cytokine profiling and microbial species involved in cecal microbiota modulations in SPF chicks immunized with a dual vaccine against Salmonella Typhimurium infection.}, journal = {Poultry science}, volume = {103}, number = {2}, pages = {103334}, pmid = {38104411}, issn = {1525-3171}, mesh = {Animals ; Female ; Salmonella typhimurium ; Chickens ; *Salmonella Infections, Animal/microbiology ; *Salmonella Vaccines ; *Microbiota ; Cytokines ; Biomarkers ; *Poultry Diseases/microbiology ; }, abstract = {Salmonella Typhimurium (ST) infection in laying hens is a significant threat to public health and food safety. Host resistance against enteric pathogen invasion primarily relies on immunity and gut barrier integrity. This study applied the ST infection model and a dual live vaccine containing Salmonella Enteritidis (SE) strain Sm24/Rif12/Ssq and ST strain Nal2/Rif9/Rtt to investigate the cellular cytokine expression profiles and the differential community structure in the cecal microbiota of specific-pathogen-free (SPF) chicks and field-raised layers. The results showed that ST challenge significantly upregulated expressions of IL-1β in SPF chicks. Vaccination, on the other hand, led to an elevation in IFNγ expression and restrained IL-1β levels. In the group where vaccination preceded the ST challenge (S.STvc), heightened expressions of IL-1β, IL-6, IL-10, and IL-12β were observed, indicating active involvement of both humoral and cell-mediated immunity in the defense against ST. Regarding the cecal microbiota, the vaccine did not affect alpha diversity nor induce a significant shift in the microbial community. Conversely, ST infection significantly affected the alpha and beta diversity in the cecal microbiota, reducing beneficial commensal genera, such as Blautia and Subdoligranulum. MetagenomeSeq analysis reveals a significant increase in the relative abundance of Faecalibacterium prausnitzii in the groups (S.STvc and STvc) exhibiting protection against ST infection. LEfSe further demonstrated Faecalibacterium prausnitzii as the prominent biomarker within the cecal microbiota of SPF chicks and field layers demonstrating protection. Another biomarker identified in the S.STvc group, Eubacterium coprostanoligenes, displayed an antagonistic relationship with Faecalibacterium prausnitzii, suggesting the limited biological significance of the former in reducing cloacal shedding and tissue invasion. In conclusion, the application of AviPro Salmonella DUO vaccine stimulates host immunity and modulates cecal microbiota to defend against ST infection. Among the microbial modulations observed in SPF chicks and field layers with protection, Faecalibacterium prausnitzii emerges as a significant species in the ceca. Further research is warranted to elucidate its role in protecting layers against ST infection.}, } @article {pmid38104165, year = {2023}, author = {Dash, NR and Al Bataineh, MT and Alili, R and Al Safar, H and Alkhayyal, N and Prifti, E and Zucker, JD and Belda, E and Clément, K}, title = {Functional alterations and predictive capacity of gut microbiome in type 2 diabetes.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22386}, pmid = {38104165}, issn = {2045-2322}, support = {17CVD01//Sorbonne Université/ ; }, mesh = {Humans ; *Diabetes Mellitus, Type 2/metabolism ; *Gastrointestinal Microbiome/genetics ; Firmicutes ; Metagenome ; *Diabetic Cardiomyopathies ; }, abstract = {The gut microbiome plays a significant role in the development of Type 2 Diabetes Mellitus (T2DM), but the functional mechanisms behind this association merit deeper investigation. Here, we used the nanopore sequencing technology for metagenomic analyses to compare the gut microbiome of individuals with T2DM from the United Arab Emirates (n = 40) with that of control (n = 44). DMM enterotyping of the cohort resulted concordantly with previous results, in three dominant groups Bacteroides (K1), Firmicutes (K2), and Prevotella (K3) lineages. The diversity analysis revealed a high level of diversity in the Firmicutes group (K2) both in terms of species richness and evenness (Wilcoxon rank-sum test, p value < 0.05 vs. K1 and K3 groups), consistent with the Ruminococcus enterotype described in Western populations. Additionally, functional enrichment analyses of KEGG modules showed significant differences in abundance between individuals with T2DM and controls (FDR < 0.05). These differences include modules associated with the degradation of amino acids, such as arginine, the degradation of urea as well as those associated with homoacetogenesis. Prediction analysis with the Predomics approach suggested potential biomarkers for T2DM, including a balance between a depletion of Enterococcus faecium and Blautia lineages with an enrichment of Absiella spp or Eubacterium limosum in T2DM individuals, highlighting the potential of metagenomic analysis in predicting predisposition to diabetic cardiomyopathy in T2DM patients.}, } @article {pmid38103344, year = {2024}, author = {Saibu, S and Uhanie Perera, I and Suzuki, S and Rodó, X and Fujiyoshi, S and Maruyama, F}, title = {Resistomes in freshwater bioaerosols and their impact on drinking and recreational water safety: A perspective.}, journal = {Environment international}, volume = {183}, number = {}, pages = {108377}, doi = {10.1016/j.envint.2023.108377}, pmid = {38103344}, issn = {1873-6750}, mesh = {Animals ; Humans ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Microbiota ; Lakes ; *Drinking Water ; }, abstract = {Antibiotic resistance genes (ARGs) are widespread environmental pollutants of biological origin that pose a significant threat to human, animal, and plant health, as well as to ecosystems. ARGs are found in soil, water, air, and waste, and several pathways for global dissemination in the environment have been described. However, studies on airborne ARG transport through atmospheric particles are limited. The ARGs in microorganisms inhabiting an environment are referred to as the "resistome". A global search was conducted of air-resistome studies by retrieving bioaerosol ARG-related papers published in the last 30 years from PubMed. We found that there is no dedicated methodology for isolating ARGs in bioaerosols; instead, conventional methods for microbial culture and metagenomic analysis are used in combination with standard aerosol sampling techniques. There is a dearth of information on the bioaerosol resistomes of freshwater environments and their impact on freshwater sources used for drinking and recreational activities. More studies of aerobiome freshwater environments are needed to ensure the safe use of water and sanitation. In this review we outline and synthesize the few studies that address the freshwater air microbiome (from tap water, bathroom showers, rivers, lakes, and swimming pools) and their resistomes, as well as the likely impacts on drinking and recreational waters. We also discuss current knowledge gaps for the freshwater airborne resistome. This review will stimulate new investigations of the atmospheric microbiome, particularly in areas where both air and water quality are of public health concern.}, } @article {pmid38102689, year = {2023}, author = {Wang, D and Li, J and Su, L and Shen, W and Feng, K and Peng, X and Wang, Z and Zhao, B and Zhang, Z and Zhang, Z and Yergeau, É and Deng, Y}, title = {Phylogenetic diversity of functional genes in deep-sea cold seeps: a novel perspective on metagenomics.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {276}, pmid = {38102689}, issn = {2049-2618}, support = {No. 2019YFC1905001//National Key Research and Development Program of China/ ; 42277104//National Natural Science Foundation of China/ ; Grant No. kf2021003//Open Project of Key Laboratory of Environmental Biotechnology, CAS/ ; }, mesh = {*Geologic Sediments ; Methane/metabolism ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Cold Temperature ; *Oceans and Seas ; }, abstract = {BACKGROUND: Leakages of cold, methane-rich fluids from subsurface reservoirs to the sea floor are termed cold seeps. Recent exploration of the deep sea has shed new light on the microbial communities in cold seeps. However, conventional metagenomic methods largely rely on reference databases and neglect the phylogeny of functional genes.

RESULTS: In this study, we developed the REMIRGE program to retrieve the full-length functional genes from shotgun metagenomic reads and fully explored the phylogenetic diversity in cold seep sediments. The abundance and diversity of functional genes involved in the methane, sulfur, and nitrogen cycles differed in the non-seep site and five cold seep sites. In one Haima cold seep site, the divergence of functional groups was observed at the centimeter scale of sediment depths, with the surface layer potentially acting as a reservoir of microbial species and functions. Additionally, positive correlations were found between specific gene sequence clusters of relevant genes, indicating coupling occurred within specific functional groups.

CONCLUSION: REMIRGE revealed divergent phylogenetic diversity of functional groups and functional pathway preferences in a deep-sea cold seep at finer scales, which could not be detected by conventional methods. Our work highlights that phylogenetic information is conducive to more comprehensive functional profiles, and REMIRGE has the potential to uncover more new insights from shotgun metagenomic data. Video Abstract.}, } @article {pmid38101649, year = {2024}, author = {Hu, J and Wan, K and Deng, X and Liu, X and Fang, Y and Zhou, F and Yu, J and Chi, R and Xiao, C}, title = {Metagenomic analysis revealed the evolution of microbial communities, metabolic pathways, and functional genes in the heterotrophic nitrification-aerobic denitrification process under La[3+] stress.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169243}, doi = {10.1016/j.scitotenv.2023.169243}, pmid = {38101649}, issn = {1879-1026}, mesh = {*Nitrification ; Denitrification ; Ammonia/metabolism ; Bioreactors ; Heterotrophic Processes ; *Microbiota ; Nitrogen/analysis ; Metabolic Networks and Pathways ; Water ; }, abstract = {Trivalent lanthanum (La[3+]) exists widely in ammonia nitrogen (NH4[+]-N) tailing water from ionic rare earth mines; however, its effect on heterotrophic nitrification-aerobic denitrification (HN-AD) is unknown, thereby limiting the application of the HN-AD process in this field. In this study, we conducted an HN-AD process using a sequencing batch reactor (5 L) that was continuously operated to directly treat acidic (NH4)2SO4 wastewater (influent NH4[+]-N concentration of approximately 110 mg/L and influent pH of 5) containing different La[3+] concentrations (0-100 mg/L). The NH4[+]-N removal efficiency of the reactor reached 98.25 % at a La[3+] concentration of 100 mg/L. The reactor was in a neutral-to-alkaline environment, which favored La[3+] precipitation and complexation. Metagenomic analysis revealed that the relative abundance of Thauera in the reactor remained high (88.62-92.27 %) under La[3+] stress. The relative abundances of Pannonobacter and Hyphomonas significantly increased, whereas that of Azoarcus significantly decreased. Metabolic functions in the reactor were mainly contributed by Thauera, and the abundance of metabolic functions under low La[3+] stress (≤5 mg/L) significantly differed from that under high La[3+] stress (≥10 mg/L). The relative abundance of ammonia assimilation-related genes in the reactor was high and significantly correlated with ammonia removal. However, traditional ammonia oxidation genes were not annotated, and unknown ammonia oxidation pathways may have been present in the reactor. Moreover, La[3+] stimulated amino acid biosynthesis and translocation, the citrate cycle, sulfur metabolism, and oxidative phosphorylation and promoted the overproduction of extracellular polymeric substances, which underwent complexation and adsorbed La[3+] to reduce its toxicity. Our results showed that the HN-AD process had a strong tolerance to La[3+], stable NH4[+]-N removal efficiency, the potential to recover La[3+], and considerable application prospects in treating NH4[+]-N tailing water from ionic rare earth mines.}, } @article {pmid38101011, year = {2024}, author = {Rincón-Tomás, B and Lanzén, A and Sánchez, P and Estupiñán, M and Sanz-Sáez, I and Bilbao, ME and Rojo, D and Mendibil, I and Pérez-Cruz, C and Ferri, M and Capo, E and Abad-Recio, IL and Amouroux, D and Bertilsson, S and Sánchez, O and Acinas, SG and Alonso-Sáez, L}, title = {Revisiting the mercury cycle in marine sediments: A potential multifaceted role for Desulfobacterota.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133120}, doi = {10.1016/j.jhazmat.2023.133120}, pmid = {38101011}, issn = {1873-3336}, mesh = {*Mercury/analysis ; Geologic Sediments/microbiology ; Bacteria/genetics ; *Microbiota ; Sulfur ; }, abstract = {Marine sediments impacted by urban and industrial pollutants are typically exposed to reducing conditions and represent major reservoirs of toxic mercury species. Mercury methylation mediated by anaerobic microorganisms is favored under such conditions, yet little is known about potential microbial mechanisms for mercury detoxification. We used culture-independent (metagenomics, metabarcoding) and culture-dependent approaches in anoxic marine sediments to identify microbial indicators of mercury pollution and analyze the distribution of genes involved in mercury reduction (merA) and demethylation (merB). While none of the isolates featured merB genes, 52 isolates, predominantly affiliated with Gammaproteobacteria, were merA positive. In contrast, merA genes detected in metagenomes were assigned to different phyla, including Desulfobacterota, Actinomycetota, Gemmatimonadota, Nitrospirota, and Pseudomonadota. This indicates a widespread capacity for mercury reduction in anoxic sediment microbiomes. Notably, merA genes were predominately identified in Desulfobacterota, a phylum previously associated only with mercury methylation. Marker genes involved in the latter process (hgcAB) were also mainly assigned to Desulfobacterota, implying a potential central and multifaceted role of this phylum in the mercury cycle. Network analysis revealed that Desulfobacterota were associated with anaerobic fermenters, methanogens and sulfur-oxidizers, indicating potential interactions between key players of the carbon, sulfur and mercury cycling in anoxic marine sediments.}, } @article {pmid38100390, year = {2024}, author = {Du, SB and Zhou, HH and Xue, ZP and Gao, S and Li, J and Meng, Y and Zhao, YJ and Wang, PF and Li, N and Bai, JX and Bai, JQ and Wang, XP}, title = {Metagenomic sequencing revealed the regulative effect of Danshen and Honghua herb pair on the gut microbiota in rats with myocardial ischemia injury.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, doi = {10.1093/femsle/fnad133}, pmid = {38100390}, issn = {1574-6968}, support = {81974544//National Natural Science Foundation of China/ ; }, mesh = {Rats ; Animals ; *Salvia miltiorrhiza/chemistry ; *Gastrointestinal Microbiome ; *Myocardial Ischemia/drug therapy/metabolism/pathology ; *Carthamus tinctorius ; Isoproterenol/therapeutic use ; }, abstract = {In recent years, more and more evidence has shown that the disorder of gut microbiota (GM) is closely correlated with myocardial ischemia (MI). Even though the Danshen and Honghua herb pair (DHHP) is widely used in treating cardiovascular disease in China and exhibits obvious clinical efficacy on MI, the anti-MI mechanism of DHHP remains and needs to be explored in depth. Thus, in this study, we investigated whether the amelioration effect and molecular mechanism of DHHP on MI were related to regulating GM through pharmacodynamics evaluation and metagenomic sequencing. Histopathological testing results showed that DHHP treatment could alleviate the pathological changes of myocardial tissue in the acute MI (AMI) rats induced by isoproterenol (ISO), especially structural disorder, irregular distribution, and enlargement of the myocardial space. These pathological changes were all alleviated to some extent by DHHP treatment. Biochemical analysis results suggested that compared with the control group, the serum levels of AST, CTn-I, CK-MB, and TNF-α in model group rats were notably decreased, and the CAT and SOD levels in serum were markedly increased. These abnormal trends were significantly reversed by DHHP treatment. Furthermore, metagenomic sequencing analysis results indicated that DHHP could improve disorders in the composition and function of GM in AMI rats, mainly reflected in increasing diversity and richness, and obviously enhancing the abundance of Bacteroides fluxus, B. uniformis, B. stercoris, Roseburia hominis, Schaedlerella arabinosiphila, and R. intestinalis, and reducing the abundance of Enterococcus avium and E. canintestini, which were associated with purine metabolism, tyrosine metabolism, cyanoamino acid metabolism, and glutathione metabolism. In conclusion, DHHP may attenuate ISO-induced MI by regulating the structure, composition, and function of GM, thus contributing to further our understanding of the anti-MI mechanisms of DHHP and providing new therapeutic ideas and diagnostic targets for the clinical studies of MI.}, } @article {pmid38099689, year = {2024}, author = {Han, N and Peng, X and Zhang, T and Qiang, Y and Li, X and Zhang, W}, title = {Rapid turnover and short-term blooms of Escherichia coli in the human gut.}, journal = {Journal of bacteriology}, volume = {206}, number = {1}, pages = {e0023923}, pmid = {38099689}, issn = {1098-5530}, support = {2018YFC1200100//MOST | National Key Research and Development Program of China (NKPs)/ ; }, mesh = {Humans ; Escherichia coli/genetics ; *Escherichia coli Infections/microbiology ; *Gastrointestinal Microbiome ; Feces/microbiology ; Whole Genome Sequencing ; }, abstract = {Escherichia coli (E. coli) is a common microorganism that is widely present in the environment and closely related to human health. The extent of E. coli presence in the human gut has been a subject of ongoing debate. Through whole-genome shotgun metagenomic sequencing, our study revealed that E. coli exists in the human body at a low abundance (average abundance 1.21%), with occasional short-term bursts leading to temporary increases in abundance, with the highest recorded at 50.91%. Further investigations into the factors contributing to these short-term blooms of E. coli showed significant variations in strain types and genomes within fecal samples collected from the same individuals at different time points. Evolutionary tree analysis indicated that samples from different individuals crossed, suggesting a change in the dominant E. coli strains within the human gut. Therefore, it can be inferred that E. coli in the human body are more likely to be transient bacteria rather than permanent residents in the gut. The rapid rate of turnover among months (87.5% within a month) and short-term blooms of E. coli in the human body can establish "latent infections" of nonpathogenic strains in healthy individuals while also posing a potential risk of introducing pathogenic strains, thereby impacting human health. In summary, our study revealed the variation in E. coli abundance and strains within the human gut, influenced by geographic area and temporal factors. These findings contribute to a better understanding of the relationship between E. coli, the gut microbiota, and human health. IMPORTANCE Escherichia coli (E. coli) is a microorganism closely linked to human health, and its presence in the human gut has been a topic of debate. Our study, using whole-genome shotgun metagenomic sequencing, revealed that E. coli exists at a low abundance in the human body, with occasional short-term bursts leading to temporary increases. Strain and genome variations were observed within fecal samples from the same individuals at different time points, suggesting transient rather than permanent residence of E. coli in the gut. The rapid turnover rate and short-term blooms of E. coli can establish latent infections while also posing a risk of introducing pathogenic strains. These findings enhance our understanding of the relationship between E. coli, the gut microbiota, and human health.}, } @article {pmid38098420, year = {2023}, author = {Duan, LY and Zhang, Y and Ren, XM and Li, YY and Zhang, YJ and Zhang, H and Han, H and Chen, ZJ}, title = {[Effects of Combined Pollution of Microplastics and Cadmium on Microbial Community Structure and Function of Pennisetum hydridum Rhizosphere Soil].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {44}, number = {12}, pages = {6973-6981}, doi = {10.13227/j.hjkx.202212135}, pmid = {38098420}, issn = {0250-3301}, mesh = {Cadmium/analysis ; Microplastics/analysis ; Soil/chemistry ; *Pennisetum/metabolism ; Plastics ; Rhizosphere ; *Metals, Heavy/analysis ; *Microbiota ; Bacteria/metabolism ; Amino Acids ; *Soil Pollutants/analysis ; }, abstract = {The combined pollution of microplastics and heavy metals can potentially interact. This may have an important impact on the growth and development of plants and the rhizosphere microbial community and function. In this study, the effects of heavy metal cadmium combined with different types of microplastics(PE and PS), different particle sizes(13 μm and 550 μm), and different concentrations(0.1% and 1%) on Pennisetum hydridum growth were studied under pot conditions. The results showed that the effects of the combined pollution of MPs and Cd on plant dry weight and Cd accumulation varied with different types, concentrations, and particle sizes of MPs, and the combined pollution stress increased, whereas the Cd content and Cd accumulation decreased. Metagenomic analysis showed that the combined contamination of MPs and Cd could change the composition of the bacterial community and reduce bacterial diversity, among which the ACE index and Chao1 index in the 550 μm 0.1% PE+Cd treatment group were the most significant. Metagenomic analysis of microbial species function showed that the main functional groups were metabolism, amino acid transport and metabolism, energy generation and conversion, and signal transduction mechanisms. Compared with that under single Cd pollution, the addition of MPs could change the gene abundance of functional groups such as metabolism, amino acid transport and metabolism, and energy generation and conversion, and the effects of different MPs types, concentrations, and particle sizes varied. In this study, metagenomics and amplification sequencing were used to analyze the effects of the combined pollution of MPs and Cd on the bacterial community and function in P. hydridum in order to provide basic data and scientific basis for the ecotoxicological effects of the combined heavy metal pollution of MPs and its biological remediation.}, } @article {pmid38098063, year = {2023}, author = {Xie, Z and Canalda-Baltrons, A and d'Enfert, C and Manichanh, C}, title = {Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {275}, pmid = {38098063}, issn = {2049-2618}, support = {812969//Marie Sklodowska-Curie Action/ ; 812969//Marie Sklodowska-Curie Action/ ; 812969//Marie Sklodowska-Curie Action/ ; }, mesh = {Humans ; Fungi/genetics ; *Microbiota ; *Mycobiome/genetics ; Bacteria/genetics ; Metagenomics/methods ; Nutrients ; }, abstract = {BACKGROUND: The accuracy of internal-transcribed-spacer (ITS) and shotgun metagenomics has not been robustly evaluated, and the effect of diet on the composition and function of the bacterial and fungal gut microbiome in a longitudinal setting has been poorly investigated. Here we compared two approaches to study the fungal community (ITS and shotgun metagenomics), proposed an enrichment protocol to perform a reliable mycobiome analysis using a comprehensive in-house fungal database, and correlated dietary data with both bacterial and fungal communities.

RESULTS: We found that shotgun DNA sequencing after a new enrichment protocol combined with the most comprehensive and novel fungal databases provided a cost-effective approach to perform gut mycobiome profiling at the species level and to integrate bacterial and fungal community analyses in fecal samples. The mycobiome was significantly more variable than the bacterial community at the compositional and functional levels. Notably, we showed that microbial diversity, composition, and functions were associated with habitual diet composition instead of driven by global dietary changes. Our study indicates a potential competitive inter-kingdom interaction between bacteria and fungi for food foraging.

CONCLUSION: Together, our present work proposes an efficient workflow to study the human gut microbiome integrating robustly fungal, bacterial, and dietary data. These findings will further advance our knowledge of the interaction between gut bacteria and fungi and pave the way for future investigations in human mycobiome. Video Abstract.}, } @article {pmid38096814, year = {2024}, author = {Lou, YC and Chen, L and Borges, AL and West-Roberts, J and Firek, BA and Morowitz, MJ and Banfield, JF}, title = {Infant gut DNA bacteriophage strain persistence during the first 3 years of life.}, journal = {Cell host & microbe}, volume = {32}, number = {1}, pages = {35-47.e6}, pmid = {38096814}, issn = {1934-6069}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; }, mesh = {Infant ; Female ; Adult ; Humans ; Infant, Newborn ; Child, Preschool ; *Bacteriophages/genetics ; Codon, Terminator ; Infant, Premature ; *Gastrointestinal Microbiome/genetics ; DNA ; }, abstract = {Bacteriophages are key components of gut microbiomes, yet the phage colonization process in the infant gut remains uncertain. Here, we establish a large phage sequence database and use strain-resolved analyses to investigate DNA phage succession in infants throughout the first 3 years of life. Analysis of 819 fecal metagenomes collected from 28 full-term and 24 preterm infants and their mothers revealed that early-life phageome richness increases over time and reaches adult-like complexity by age 3. Approximately 9% of early phage colonizers, which are mostly maternally transmitted and infect Bacteroides, persist for 3 years and are more prevalent in full-term than in preterm infants. Although rare, phages with stop codon reassignment are more likely to persist than non-recoded phages and generally display an increase in in-frame reassigned stop codons over 3 years. Overall, maternal seeding, stop codon reassignment, host CRISPR-Cas locus prevalence, and diverse phage populations contribute to stable viral colonization.}, } @article {pmid38095826, year = {2024}, author = {Kondo, M and Torisu, T and Nagasue, T and Shibata, H and Umeno, J and Kawasaki, K and Fujioka, S and Matsuno, Y and Moriyama, T and Kitazono, T}, title = {Duodenal microbiome in chronic kidney disease.}, journal = {Clinical and experimental nephrology}, volume = {28}, number = {4}, pages = {263-272}, pmid = {38095826}, issn = {1437-7799}, support = {JP21K06783//Japan Society for the Promotion of Science/ ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; Duodenum ; Intestine, Small ; *Renal Insufficiency, Chronic ; *Gastrointestinal Microbiome ; Feces ; }, abstract = {BACKGROUND: The intestinal microbiome is involved in the pathogenesis of chronic kidney disease (CKD). Despite its importance, the microbiome of the small intestinal mucosa has been little studied due to sampling difficulties, and previous studies have mainly focused on fecal sources for microbiome studies. We aimed to characterize the small intestinal microbiome of CKD patients by studying the microbiome collected from duodenal and fecal samples of CKD patients and healthy controls.

METHODS: Overall, 28 stage 5 CKD patients and 21 healthy participants were enrolled. Mucosal samples were collected from the deep duodenum during esophagogastroduodenoscopy and fecal samples were also collected. The 16S ribosomal RNA gene sequencing using Qiime2 was used to investigate and compare the microbial structure and metagenomic function of the duodenal and fecal microbiomes.

RESULTS: The duodenal flora of CKD patients had decreased alpha diversity compared with the control group. On the basis of taxonomic composition, Veillonella and Prevotella were significantly reduced in the duodenal flora of CKD patients. The tyrosine and tryptophan metabolic pathways were enhanced in the urea toxin-related metabolic pathways based on the Kyoto Encyclopedia of Genes and Genomes database.

CONCLUSION: The small intestinal microbiome in CKD patients is significantly altered, indicating that increased intestinal permeability and production of uremic toxin may occur in the upper small intestine of CKD patients.}, } @article {pmid38095693, year = {2023}, author = {Abou Chacra, L and Benatmane, A and Iwaza, R and Ly, C and Alibar, S and Armstrong, N and Mediannikov, O and Bretelle, F and Fenollar, F}, title = {Culturomics reveals a hidden world of vaginal microbiota with the isolation of 206 bacteria from a single vaginal sample.}, journal = {Archives of microbiology}, volume = {206}, number = {1}, pages = {20}, pmid = {38095693}, issn = {1432-072X}, support = {ANR-10-IAHU-03//Agence Nationale de la Recherche/ ; ANR-10-IAHU-03//Agence Nationale de la Recherche/ ; ANR-10-IAHU-03//Agence Nationale de la Recherche/ ; ANR-10-IAHU-03//Agence Nationale de la Recherche/ ; ANR-10-IAHU-03//Agence Nationale de la Recherche/ ; ANR-10-IAHU-03//Agence Nationale de la Recherche/ ; ANR-10-IAHU-03//Agence Nationale de la Recherche/ ; ANR-10-IAHU-03//Agence Nationale de la Recherche/ ; ANR-10-IAHU-03//Agence Nationale de la Recherche/ ; }, mesh = {Humans ; Female ; *Bacteria/genetics ; *Microbiota/genetics ; Firmicutes/genetics ; Vagina/microbiology ; Bacteroidetes ; }, abstract = {The composition of the vaginal microbiota is known to be influenced by various factors and to be associated with several disorders affecting women's health. Although metagenomics is currently a widely used method for studying the human microbiota, it has certain limitations, such as a lack of information on bacterial viability. It is therefore important to use culture-based methods such as culturomics. Here, we used 35 different culture conditions to comprehensively characterize the vaginal bacterial diversity of a single woman's flora. A total of 206 bacterial species, belonging to six phyla (for a little more than half to Firmicutes, followed mainly by Actinobacteria, Bacteroidetes, and Proteobacteria) and 45 families, and 2 fungal species were cultivated. While several species of lactobacilli have been isolated, a wide variety of other bacteria were also separated, including 65 never reported before in vaginal flora, including a new bacterial species, Porphyromonas vaginalis sp. nov. Extensive culture-based methods are essential to establish a comprehensive, evidence-based repertoire of bacterial viability. If combined with molecular methods, they can provide a much more thorough understanding of the vaginal microbiota and fulfil the unknown part of metagenomic studies.}, } @article {pmid38095449, year = {2024}, author = {Arehart, CH and Sterrett, JD and Garris, RL and Quispe-Pilco, RE and Gignoux, CR and Evans, LM and Stanislawski, MA}, title = {Poly-omic risk scores predict inflammatory bowel disease diagnosis.}, journal = {mSystems}, volume = {9}, number = {1}, pages = {e0067723}, pmid = {38095449}, issn = {2379-5077}, support = {K01 HL157658/HL/NHLBI NIH HHS/United States ; P30 DK048520/DK/NIDDK NIH HHS/United States ; T32 MH016880/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Inflammatory Bowel Diseases/diagnosis ; Metagenomics/methods ; Phenotype ; *Microbiota ; Risk Factors ; }, abstract = {Inflammatory bowel disease (IBD) is characterized by complex etiology and a disrupted colonic ecosystem. We provide a framework for the analysis of multi-omic data, which we apply to study the gut ecosystem in IBD. Specifically, we train and validate models using data on the metagenome, metatranscriptome, virome, and metabolome from the Human Microbiome Project 2 IBD multi-omic database, with 1,785 repeated samples from 130 individuals (103 cases and 27 controls). After splitting the participants into training and testing groups, we used mixed-effects least absolute shrinkage and selection operator regression to select features for each omic. These features, with demographic covariates, were used to generate separate single-omic prediction scores. All four single-omic scores were then combined into a final regression to assess the relative importance of the individual omics and the predictive benefits when considered together. We identified several species, pathways, and metabolites known to be associated with IBD risk, and we explored the connections between data sets. Individually, metabolomic and viromic scores were more predictive than metagenomics or metatranscriptomics, and when all four scores were combined, we predicted disease diagnosis with a Nagelkerke's R[2] of 0.46 and an area under the curve of 0.80 (95% confidence interval: 0.63, 0.98). Our work supports that some single-omic models for complex traits are more predictive than others, that incorporating multiple omic data sets may improve prediction, and that each omic data type provides a combination of unique and redundant information. This modeling framework can be extended to other complex traits and multi-omic data sets.IMPORTANCEComplex traits are characterized by many biological and environmental factors, such that multi-omic data sets are well-positioned to help us understand their underlying etiologies. We applied a prediction framework across multiple omics (metagenomics, metatranscriptomics, metabolomics, and viromics) from the gut ecosystem to predict inflammatory bowel disease (IBD) diagnosis. The predicted scores from our models highlighted key features and allowed us to compare the relative utility of each omic data set in single-omic versus multi-omic models. Our results emphasized the importance of metabolomics and viromics over metagenomics and metatranscriptomics for predicting IBD status. The greater predictive capability of metabolomics and viromics is likely because these omics serve as markers of lifestyle factors such as diet. This study provides a modeling framework for multi-omic data, and our results show the utility of combining multiple omic data types to disentangle complex disease etiologies and biological signatures.}, } @article {pmid38095429, year = {2024}, author = {Bogri, A and Jensen, EEB and Borchert, AV and Brinch, C and Otani, S and Aarestrup, FM}, title = {Transmission of antimicrobial resistance in the gut microbiome of gregarious cockroaches: the importance of interaction between antibiotic exposed and non-exposed populations.}, journal = {mSystems}, volume = {9}, number = {1}, pages = {e0101823}, pmid = {38095429}, issn = {2379-5077}, support = {NNF16OC0021856//Novo Nordisk Fonden (NNF)/ ; No. 874735//Horizon 2020 (EU): VEO/ ; }, mesh = {Animals ; Humans ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/genetics ; *Cockroaches ; Drug Resistance, Bacterial ; Bacteria/genetics ; Soil ; }, abstract = {Antimicrobial resistance (AMR) is a major global health concern, further complicated by its spread via the microbiome bacterial members. While mathematical models discuss AMR transmission through the symbiotic microbiome, experimental studies are scarce. Herein, we used a gregarious cockroach, Pycnoscelus surinamensis, as an in vivo animal model for AMR transmission investigations. We explored whether the effect of antimicrobial treatment is detectable with metagenomic sequencing, and whether AMR genes can be spread and established in unchallenged (not treated with antibiotics) individuals following contact with treated donors, and under various frequencies of interaction. Gut and soil substrate microbiomes were investigated by metagenomic sequencing for bacterial community composition and resistome profiling. We found that tetracycline treatment altered the treated gut microbiome by decreasing bacterial diversity and increasing the abundance of tetracycline resistance genes. Untreated cockroaches that interacted with treated donors also had elevated tetracycline resistance. The levels of resistance differed depending on the magnitude and frequency of donor transfer. Additionally, treated donors showed signs of microbiome recovery due to their interaction with the untreated ones. Similar patterns were also recorded in the soil substrate microbiomes. Our results shed light on how interacting microbiomes facilitate AMR gene transmission to previously unchallenged hosts, a dynamic influenced by the interaction frequencies, using an in vivo model to validate theoretical AMR transmission models.IMPORTANCEAntimicrobial resistance is a rising threat to human and animal health. The spread of resistance through the transmission of the symbiotic gut microbiome is of concern and has been explored in theoretical modeling studies. In this study, we employ gregarious insect populations to examine the emergence and transmission of antimicrobial resistance in vivo and validate modeling hypotheses. We find that antimicrobial treatment increases the levels of resistance in treated populations. Most importantly, we show that resistance increased in untreated populations after interacting with the treated ones. The level of resistance transmission was affected by the magnitude and frequency of population mixing. Our results highlight the importance of microbial transmission in the spread of antimicrobial resistance.}, } @article {pmid38093016, year = {2024}, author = {Hibberd, MC and Webber, DM and Rodionov, DA and Henrissat, S and Chen, RY and Zhou, C and Lynn, HM and Wang, Y and Chang, HW and Lee, EM and Lelwala-Guruge, J and Kazanov, MD and Arzamasov, AA and Leyn, SA and Lombard, V and Terrapon, N and Henrissat, B and Castillo, JJ and Couture, G and Bacalzo, NP and Chen, Y and Lebrilla, CB and Mostafa, I and Das, S and Mahfuz, M and Barratt, MJ and Osterman, AL and Ahmed, T and Gordon, JI}, title = {Bioactive glycans in a microbiome-directed food for children with malnutrition.}, journal = {Nature}, volume = {625}, number = {7993}, pages = {157-165}, pmid = {38093016}, issn = {1476-4687}, support = {F30 DK131866/DK/NIDDK NIH HHS/United States ; R01 DK030292/DK/NIDDK NIH HHS/United States ; K01 DK134840/DK/NIDDK NIH HHS/United States ; T32 GM007200/GM/NIGMS NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Infant ; Bacteria/genetics ; Bangladesh ; Body Weight/genetics ; Feces/microbiology ; *Food ; *Gastrointestinal Microbiome/physiology ; Genome, Bacterial/genetics ; *Malnutrition/microbiology ; Metagenome/genetics ; *Polysaccharides/metabolism ; Weight Gain ; }, abstract = {Evidence is accumulating that perturbed postnatal development of the gut microbiome contributes to childhood malnutrition[1-4]. Here we analyse biospecimens from a randomized, controlled trial of a microbiome-directed complementary food (MDCF-2) that produced superior rates of weight gain compared with a calorically more dense conventional ready-to-use supplementary food in 12-18-month-old Bangladeshi children with moderate acute malnutrition[4]. We reconstructed 1,000 bacterial genomes (metagenome-assembled genomes (MAGs)) from the faecal microbiomes of trial participants, identified 75 MAGs of which the abundances were positively associated with ponderal growth (change in weight-for-length Z score (WLZ)), characterized changes in MAG gene expression as a function of treatment type and WLZ response, and quantified carbohydrate structures in MDCF-2 and faeces. The results reveal that two Prevotella copri MAGs that are positively associated with WLZ are the principal contributors to MDCF-2-induced expression of metabolic pathways involved in utilizing the component glycans of MDCF-2. The predicted specificities of carbohydrate-active enzymes expressed by their polysaccharide-utilization loci are correlated with (1) the in vitro growth of Bangladeshi P. copri strains, possessing varying degrees of polysaccharide-utilization loci and genomic conservation with these MAGs, in defined medium containing different purified glycans representative of those in MDCF-2, and (2) the levels of faecal carbohydrate structures in the trial participants. These associations suggest that identifying bioactive glycan structures in MDCFs metabolized by growth-associated bacterial taxa will help to guide recommendations about their use in children with acute malnutrition and enable the development of additional formulations.}, } @article {pmid38092236, year = {2024}, author = {Guo, C and Lin, S and Lyu, T and Ma, Y and Dong, R and Liu, S}, title = {Effect of reactor operation modes on mitigating antibiotic resistance genes (ARGs) and methane production from hydrothermally-pretreated pig manure.}, journal = {Environmental research}, volume = {244}, number = {}, pages = {117894}, doi = {10.1016/j.envres.2023.117894}, pmid = {38092236}, issn = {1096-0953}, mesh = {Humans ; Animals ; Swine ; *Anti-Bacterial Agents/pharmacology ; Manure ; Drug Resistance, Microbial/genetics ; *Microbiota ; Methane ; Anaerobiosis ; Genes, Bacterial ; }, abstract = {Numerous efforts have been made to enhance the performance of anaerobic digestion (AD) for accelerating renewable energy generation, however, it remains unclear whether the intensified measures could enhance the proliferation and transmissions of antibiotic resistance genes (ARGs) in the system. This study assessed the impact of an innovative pig manure AD process, which includes hydrothermal pretreatment (HTP) and a two-stage configuration with separated acidogenic and methanogenic phases, on biomethane (CH4) production and ARGs dynamics. Results showed that HTP significantly increase CH4 production from 0.65 to 0.75 L/L/d in conventional single-stage AD to 0.82 and 0.91 L/L/d in two-stage AD. This improvement correlated with a rise in the relative abundance of Methanosarcina, a key methanogenesis microorganism. In the two-stage AD, the methanogenic stage offered an ideal environment for methanogens growth, resulting in substantially faster and higher CH4 production by about 10% compared to single-stage AD. Overall, the combined use of HTP and the two-stage AD configuration enhanced CH4 production by 40% compared to traditional single-stage AD. The abundance and diversity of ARGs were significantly reduced in the acidogenic reactors after HTP. However, the ARGs levels increased by about two times in the following methanogenesis stage and reached similar or higher levels than in single stage AD. The erm(F), erm(G), ant(6)-Ia, tet(W), mef(A) and erm(B) were the six main ARGs with significant differences in relative abundances in various treatments. The two-stage AD mode could better remove sul2, but it also had a rebound which elevated the risk of ARGs to the environment and human health. Network analysis identified pH and TVFAs as critical factors driving microbial communities and ARG proliferation in the new AD process. With the results, this study offers valuable insights into the trade-offs between AD performance enhancement and ARG-related risks, pinpointing essential areas for future research and practical improvements.}, } @article {pmid38087304, year = {2023}, author = {Kaur, S and Sharma, P and Mayer, MJ and Neuert, S and Narbad, A and Kaur, S}, title = {Beneficial effects of GABA-producing potential probiotic Limosilactobacillus fermentum L18 of human origin on intestinal permeability and human gut microbiota.}, journal = {Microbial cell factories}, volume = {22}, number = {1}, pages = {256}, pmid = {38087304}, issn = {1475-2859}, support = {BBS/E/F/00044453/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 42-478/2013 SR//University Grants Commission (UGC), New Delhi, India/ ; Institute Strategic Programmes Gut Microbes and Health (BB/R012490/1 Theme 3 BBS/E/F/000PR10356)//UK Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BBS/E/F/00042220/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/00042241/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L026953/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *Limosilactobacillus fermentum ; Caco-2 Cells ; Lipopolysaccharides ; *Gastrointestinal Microbiome ; Intestinal Barrier Function ; Bacteria/metabolism ; *Probiotics/therapeutic use ; }, abstract = {BACKGROUND: Gamma-aminobutyric acid (GABA) is a non-protein amino acid with neuroinhibitory, antidiabetic, and antihypertensive properties and is used as a drug for treating anxiety and depression. Some strains of lactobacilli are known to produce GABA and strengthen the gut barrier function which play an important role in ameliorating the effects caused by the pathogen on the gut barrier. The probiotic bacteria are also known to modulate the human fecal microbiota, however, the role of GABA-producing strains on the gut epithelium permeability and gut microbiota is not known.

RESULTS: In this study, we report the production of high levels of GABA by potential probiotic bacterium Limosilactobacillus fermentum L18 for the first time. The kinetics of the production of GABA by L18 showed that the maximum production of GABA in the culture supernatant (CS) occurred at 24 h, whereas in fermented milk it took 48 h of fermentation. The effect of L18 on the restoration of lipopolysaccharide (LPS)-disrupted intestinal cell membrane permeability in Caco-2 monolayers showed that it significantly restored the transepithelial electrical resistance (TEER) values, by significantly increasing the levels of junction proteins, occludin and E-cadherin in L18 and LPS-treated Caco-2 cells as compared to only LPS-treated cells. The effect of GABA-secreting L18 on the metataxonome of human stool samples from healthy individuals was investigated by a batch fermentor that mimics the conditions of the human colon. Although, no differences were observed in the α and β diversities of the L18-treated and untreated samples at 24 h, the relative abundances of bacterial families Lactobacillaceae and Bifidobacteriaceae increased in the L18-treated group, but both decreased in the untreated groups. On the other hand, the relative abundance of Enterobacteriaceae decreased in the L18 samples but it increased in the untreated samples.

CONCLUSION: These results indicate that Li. fermentum L18 is a promising GABA-secreting strain that strengthens the gut epithelial barrier by increasing junction protein concentrations and positively modulating the gut microbiota. It has the potential to be used as a psychobiotic or for the production of functional foods for the management of anxiety-related illnesses.}, } @article {pmid38086977, year = {2023}, author = {Ryu, SW and Moon, JC and Oh, BS and Yu, SY and Bak, JE and Heo, ES and Jeong, JH and Lee, JH}, title = {Anti-obesity activity of human gut microbiota Bacteroides stercoris KGMB02265.}, journal = {Archives of microbiology}, volume = {206}, number = {1}, pages = {19}, pmid = {38086977}, issn = {1432-072X}, support = {NRF-2016M3A9F3947962 and NRF-2019M3A9F3065226//Bio & Medical Technology Development program of the National Research Foundation of Korea/ ; KGM5232322//Korea Research Institute of Bioscience & Biotechnology (KRIBB) Research initiative program/ ; }, mesh = {Humans ; Mice ; Animals ; *Diabetes Mellitus, Type 2/complications ; *Gastrointestinal Microbiome ; Obesity ; Bacteroides/genetics ; Mice, Inbred C57BL ; }, abstract = {Obesity is a global health threat that causes various complications such as type 2 diabetes and nonalcoholic fatty liver disease. Gut microbiota is closely related to obesity. In particular, a higher Firmicutes to Bacteroidetes ratio has been reported as a biomarker of obesity, suggesting that the phylum Bacteroidetes may play a role in inhibiting obesity. Indeed, the genus Bacteroides was enriched in the healthy subjects based on metagenome analysis. In this study, we determined the effects of Bacteroides stercoris KGMB02265, a species belonging to the phylum Bacteroidetes, on obesity both in vitro and in vivo. The cell-free supernatant of B. stercoris KGMB02265 inhibited lipid accumulation in 3T3-L1 preadipocytes, in which the expression of adipogenic marker genes was repressed. In vivo study showed that the oral administration of B. stercoris KGMB02265 substantially reduced body weight and fat weight in high-fat diet induced obesity in mice. Furthermore, obese mice orally administered with B. stercoris KGMB02265 restored glucose sensitivity and reduced leptin and triglyceride levels. Taken together, our study reveals that B. stercoris KGMB02265 has anti-obesity activity and suggests that it may be a promising candidate for treating obesity.}, } @article {pmid38086476, year = {2024}, author = {Zhang, M and Zhao, B and Yan, Y and Cheng, Z and Li, Z and Han, L and Sun, Y and Zheng, Y and Xia, Y}, title = {Comamonas-dominant microbial community in carbon poor aquitard sediments revealed by metagenomic-based growth rate investigation.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169203}, doi = {10.1016/j.scitotenv.2023.169203}, pmid = {38086476}, issn = {1879-1026}, mesh = {Metagenome ; *Arsenic/analysis ; Carbon/metabolism ; *Microbiota ; Bacteria/metabolism ; Geologic Sediments/chemistry ; }, abstract = {The microbiological ecology of a low-nutrient shallow aquifer with high arsenic content in the Yinchuan Plain was investigated in this study. Amplicon sequencing data from five samples (depths: 1.5 m, 3.5 m, 11.2 m, 19.3 m, and 25.5 m) revealed diverse and adaptable microbial community. Among the microbial community, Comamonas was the most prominent, accounting for 10.52 % of the total. This genus displayed high growth rates, with a maximum growth rate of 12.06 d[-1] and a corresponding doubling time of 1.38 days, as determined through an analysis of codon usage bias. Functional annotation of Metagenome-Assembled Genomes (MAGs) for samples at 1.5 m and 11.2 m depths revealed Comamonas' metabolic versatility, including various carbon pathways, assimilative sulfate reduction (ASR), and dissimilatory reduction to ammonium (DNRA). The TPM (Transcripts Per Kilobase of exon model per Million mapped reads) of MAGs at 11.2 m sample was 15.7 and 12.3. The presence of arsenic resistance genes in Comamonas aligns with sediment arsenic levels (65.8 mg/kg for 1.5 m depth, 32.8 mg/kg for 11.2 m depth). This study highlights the role of Comamonas as a 'generalist' bacteria in challenging oligotrophic sediments, emphasizing the significance of such organisms in community stability and ecological functions. ENVIRONMENTAL IMPLICATION: Low-biomass limits the microbial activity and biogeochemical study in oligotrophic environments, which is the typical condition for underground aquatic ecosystems. Facilitated by growth rate estimation, our research focuses on active functional microorganisms and their biogeochemical metabolic in oligotrophic aquifer sediments, revealing their impact on the environment and response to arsenic threats. Findings illuminate the metabolic advantage of a 'generalist life-style' in carbon-scarce environments and contribute to a broader understanding of bacterial ecosystems and environmental impacts in oligotrophic aquifer sediments worldwide.}, } @article {pmid38086007, year = {2024}, author = {Wang, Y and Sharma, A and Weber, KM and Topper, E and Appleton, AA and Gustafson, D and Clish, CB and Kaplan, RC and Burk, RD and Qi, Q and Peters, BA}, title = {The menopause-related gut microbiome: associations with metabolomics, inflammatory protein markers, and cardiometabolic health in women with HIV.}, journal = {Menopause (New York, N.Y.)}, volume = {31}, number = {1}, pages = {52-64}, pmid = {38086007}, issn = {1530-0374}, support = {P30 DK040561/DK/NIDDK NIH HHS/United States ; U01 HL146245/HL/NHLBI NIH HHS/United States ; U01 HL146208/HL/NHLBI NIH HHS/United States ; K01 HL160146/HL/NHLBI NIH HHS/United States ; U01 HL146192/HL/NHLBI NIH HHS/United States ; U01 HL146242/HL/NHLBI NIH HHS/United States ; R01 DK134672/DK/NIDDK NIH HHS/United States ; R01 HL148094/HL/NHLBI NIH HHS/United States ; U01 HL146194/HL/NHLBI NIH HHS/United States ; U01 HL146241/HL/NHLBI NIH HHS/United States ; P30 AI027767/AI/NIAID NIH HHS/United States ; P30 AI050409/AI/NIAID NIH HHS/United States ; U01 HL146333/HL/NHLBI NIH HHS/United States ; U01 HL146205/HL/NHLBI NIH HHS/United States ; P30 MH116867/MH/NIMH NIH HHS/United States ; P30 AI073961/AI/NIAID NIH HHS/United States ; U01 HL146201/HL/NHLBI NIH HHS/United States ; U01 HL146193/HL/NHLBI NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; U01 HL146204/HL/NHLBI NIH HHS/United States ; U01 HL146202/HL/NHLBI NIH HHS/United States ; UL1 TR001881/TR/NCATS NIH HHS/United States ; U01 HL146240/HL/NHLBI NIH HHS/United States ; U01 HL146203/HL/NHLBI NIH HHS/United States ; UL1 TR003098/TR/NCATS NIH HHS/United States ; P30 AI050410/AI/NIAID NIH HHS/United States ; }, mesh = {Female ; Humans ; *Cardiovascular Diseases ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/genetics ; *HIV Infections/complications ; *Menopause ; }, abstract = {OBJECTIVE: This study aimed to identify menopause-related gut microbial features, as well as their related metabolites and inflammatory protein markers, and link with cardiometabolic risk factors in women with and without HIV.

METHODS: In the Women's Interagency HIV Study, we performed shotgun metagenomic sequencing on 696 stool samples from 446 participants (67% women with HIV), and quantified plasma metabolomics and serum proteomics in a subset (~86%). We examined the associations of menopause (postmenopausal vs premenopausal) with gut microbial features in a cross-sectional repeated-measures design and further evaluated those features in relation to metabolites, proteins, and cardiometabolic risk factors.

RESULTS: Different overall gut microbial composition was observed by menopausal status in women with HIV only. We identified a range of gut microbial features that differed between postmenopausal and premenopausal women with HIV (but none in women without HIV), including abundance of 32 species and functional potentials involving 24 enzymatic reactions and lower β-glucuronidase bacterial gene ortholog. Specifically, highly abundant species Faecalibacterium prausnitzii , Bacteroides species CAG:98 , and Bifidobacterium adolescentis were depleted in postmenopausal versus premenopausal women with HIV. Menopause-depleted species (mainly Clostridia) in women with HIV were positively associated with several glycerophospholipids, while negatively associated with imidazolepropionic acid and fibroblast growth factor 21. Mediation analysis suggested that menopause may decrease plasma phosphatidylcholine plasmalogen C36:1 and C36:2 levels via reducing abundance of species F. prausnitzii and Acetanaerobacterium elongatum in women with HIV. Furthermore, waist-to-hip ratio was associated with menopause-related microbes, metabolites, and fibroblast growth factor 21 in women with HIV.

CONCLUSIONS: Menopause was associated with a differential gut microbiome in women with HIV, related to metabolite and protein profiles that potentially contribute to elevated cardiometabolic risk.}, } @article {pmid38085234, year = {2023}, author = {Liao, H and Shang, J and Sun, Y}, title = {GDmicro: classifying host disease status with GCN and deep adaptation network based on the human gut microbiome data.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {12}, pages = {}, pmid = {38085234}, issn = {1367-4811}, support = {9678241//City University of Hong Kong/ ; //Hong Kong Innovation and Technology Commission/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Metagenome ; *Inflammatory Bowel Diseases ; Biomarkers ; }, abstract = {MOTIVATION: With advances in metagenomic sequencing technologies, there are accumulating studies revealing the associations between the human gut microbiome and some human diseases. These associations shed light on using gut microbiome data to distinguish case and control samples of a specific disease, which is also called host disease status classification. Importantly, using learning-based models to distinguish the disease and control samples is expected to identify important biomarkers more accurately than abundance-based statistical analysis. However, available tools have not fully addressed two challenges associated with this task: limited labeled microbiome data and decreased accuracy in cross-studies. The confounding factors, such as the diet, technical biases in sample collection/sequencing across different studies/cohorts often jeopardize the generalization of the learning model.

RESULTS: To address these challenges, we develop a new tool GDmicro, which combines semi-supervised learning and domain adaptation to achieve a more generalized model using limited labeled samples. We evaluated GDmicro on human gut microbiome data from 11 cohorts covering 5 different diseases. The results show that GDmicro has better performance and robustness than state-of-the-art tools. In particular, it improves the AUC from 0.783 to 0.949 in identifying inflammatory bowel disease. Furthermore, GDmicro can identify potential biomarkers with greater accuracy than abundance-based statistical analysis methods. It also reveals the contribution of these biomarkers to the host's disease status.

https://github.com/liaoherui/GDmicro.}, } @article {pmid38085017, year = {2024}, author = {Yang, L and Guo, Y and Yang, H and Li, S and Zhang, Y and Hao, L}, title = {Taxonomic and functional assembly cues enrich the endophytic tobacco microbiota across epiphytic compartments.}, journal = {mSphere}, volume = {9}, number = {1}, pages = {e0060723}, pmid = {38085017}, issn = {2379-5042}, support = {E2DF028//Guizhou Provincial Department of Science and Technology/ ; 2017-020//Startup Funding of the Chinese Academy of Sciences/ ; 41877400//MOST | National Natural Science Foundation of China (NSFC)/ ; 2018YFC1802601//MOST | National Key Research and Development Program of China (NKPs)/ ; XDB40020300//Strategic Priority Research Program of Chinese Academy Sciences/ ; SKLEG2018911//CAS | State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences (SKLEG)/ ; }, mesh = {*Cues ; *Microbiota ; Bacteria/genetics ; Metagenome ; Endophytes/genetics ; Plants ; Nicotiana ; }, abstract = {The plant microbiome plays a critical role in plant growth, development, and health, with endophytes being recognized as essential members due to their close interactions with host plants. However, knowledge gaps remain in understanding the mechanisms driving the colonization and establishment of endophytic communities. To address this issue, we investigated the microbiota of tobacco roots and leaves, including both epiphytic and endophytic microorganisms. We found that Actinobacteria and Alphaproteobacteria were significantly enriched in the root endosphere. Additionally, we identified higher abundances of functional traits involved in antibiotic synthesis, plant cell wall degradation, iron metabolism, secretion systems, and nicotine degradation enzymes in the endosphere. We further studied metagenome-assembled genomes from the rhizosphere and root endosphere, revealing a greater diversity of secondary metabolites in bacteria within the root endosphere. Together, this study provides insights into the taxonomic and functional assembly cues that may contribute to shaping the endophytic plant microbiota.IMPORTANCEThe presence of diverse microorganisms within plant tissues under natural conditions is a well-established fact. However, due to the plant immune system's barrier and the unique microhabitat of the plant interior, it remains unclear what specific characteristics bacteria require to successfully colonize and thrive in the plant endosphere. Recognizing the significance of unraveling these functional features, our study focused on investigating the enriched traits in the endophytic microbiota compared to the epiphytes. Through our research, we have successfully identified the taxonomic and functional assembly cues that drive the enrichment of the endophytic microbiota across the epiphytic compartments. These findings shed new light on the intricate mechanisms of endophyte colonization, thereby deepening our understanding of plant-microbe interactions and paving the way for further advancements in microbiome manipulation.}, } @article {pmid38082149, year = {2024}, author = {Jiang, K and Li, W and Tong, M and Xu, J and Chen, Z and Yang, Y and Zang, Y and Jiao, X and Liu, C and Lim, B and Jiang, X and Wang, J and Wu, D and Wang, M and Liu, SJ and Shao, F and Gao, X}, title = {Bacteroides fragilis ubiquitin homologue drives intraspecies bacterial competition in the gut microbiome.}, journal = {Nature microbiology}, volume = {9}, number = {1}, pages = {70-84}, pmid = {38082149}, issn = {2058-5276}, support = {32122007//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; Animals ; Mice ; Bacteroides fragilis/genetics ; *Gastrointestinal Microbiome ; Ubiquitin/metabolism ; Bacteria/metabolism ; *Bacterial Infections ; Peptidylprolyl Isomerase/metabolism ; }, abstract = {Interbacterial antagonism and associated defensive strategies are both essential during bacterial competition. The human gut symbiont Bacteroides fragilis secretes a ubiquitin homologue (BfUbb) that is toxic to a subset of B. fragilis strains in vitro. In the present study, we demonstrate that BfUbb lyses certain B. fragilis strains by non-covalently binding and inactivating an essential peptidyl-prolyl isomerase (PPIase). BfUbb-sensitivity profiling of B. fragilis strains revealed a key tyrosine residue (Tyr119) in the PPIase and strains that encode a glutamic acid residue at Tyr119 are resistant to BfUbb. Crystal structural analysis and functional studies of BfUbb and the BfUbb-PPIase complex uncover a unique disulfide bond at the carboxy terminus of BfUbb to mediate the interaction with Tyr119 of the PPIase. In vitro coculture assays and mouse studies show that BfUbb confers a competitive advantage for encoding strains and this is further supported by human gut metagenome analyses. Our findings reveal a previously undescribed mechanism of bacterial intraspecies competition.}, } @article {pmid38078817, year = {2023}, author = {Xu, C and Huang, J and Gao, Y and Zhao, W and Shen, Y and Luo, F and Yu, G and Zhu, F and Ni, Y}, title = {OBMeta: a comprehensive web server to analyze and validate gut microbial features and biomarkers for obesity-associated metabolic diseases.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {12}, pages = {}, pmid = {38078817}, issn = {1367-4811}, support = {2021YFC2701904//National Key Research and Development Program of China/ ; 82170583//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/complications ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2/diagnosis ; Obesity/diagnosis/complications/metabolism ; *Metabolic Diseases/diagnosis/complications ; Biomarkers ; }, abstract = {MOTIVATION: Gut dysbiosis is closely associated with obesity and related metabolic diseases including type 2 diabetes (T2D) and nonalcoholic fatty liver disease (NAFLD). The gut microbial features and biomarkers have been increasingly investigated in many studies, which require further validation due to the limited sample size and various confounding factors that may affect microbial compositions in a single study. So far, it lacks a comprehensive bioinformatics pipeline providing automated statistical analysis and integrating multiple independent studies for cross-validation simultaneously.

RESULTS: OBMeta aims to streamline the standard metagenomics data analysis from diversity analysis, comparative analysis, and functional analysis to co-abundance network analysis. In addition, a curated database has been established with a total of 90 public research projects, covering three different phenotypes (Obesity, T2D, and NAFLD) and more than five different intervention strategies (exercise, diet, probiotics, medication, and surgery). With OBMeta, users can not only analyze their research projects but also search and match public datasets for cross-validation. Moreover, OBMeta provides cross-phenotype and cross-intervention-based advanced validation that maximally supports preliminary findings from an individual study. To summarize, OBMeta is a comprehensive web server to analyze and validate gut microbial features and biomarkers for obesity-associated metabolic diseases.

OBMeta is freely available at: http://obmeta.met-bioinformatics.cn/.}, } @article {pmid38078749, year = {2024}, author = {Park, H and Joachimiak, MP and Jungbluth, SP and Yang, Z and Riehl, WJ and Canon, RS and Arkin, AP and Dehal, PS}, title = {A bacterial sensor taxonomy across earth ecosystems for machine learning applications.}, journal = {mSystems}, volume = {9}, number = {1}, pages = {e0002623}, pmid = {38078749}, issn = {2379-5077}, support = {//DOE | NNSA | LDRD | Lawrence Berkeley National Laboratory (LBNL)/ ; }, mesh = {Humans ; *Metagenomics ; *Microbiota ; Metagenome ; Machine Learning ; Earth, Planet ; }, abstract = {Microbial communities have evolved to colonize all ecosystems of the planet, from the deep sea to the human gut. Microbes survive by sensing, responding, and adapting to immediate environmental cues. This process is driven by signal transduction proteins such as histidine kinases, which use their sensing domains to bind or otherwise detect environmental cues and "transduce" signals to adjust internal processes. We hypothesized that an ecosystem's unique stimuli leave a sensor "fingerprint," able to identify and shed insight on ecosystem conditions. To test this, we collected 20,712 publicly available metagenomes from Host-associated, Environmental, and Engineered ecosystems across the globe. We extracted and clustered the collection's nearly 18M unique sensory domains into 113,712 similar groupings with MMseqs2. We built gradient-boosted decision tree machine learning models and found we could classify the ecosystem type (accuracy: 87%) and predict the levels of different physical parameters (R2 score: 83%) using the sensor cluster abundance as features. Feature importance enables identification of the most predictive sensors to differentiate between ecosystems which can lead to mechanistic interpretations if the sensor domains are well annotated. To demonstrate this, a machine learning model was trained to predict patient's disease state and used to identify domains related to oxygen sensing present in a healthy gut but missing in patients with abnormal conditions. Moreover, since 98.7% of identified sensor domains are uncharacterized, importance ranking can be used to prioritize sensors to determine what ecosystem function they may be sensing. Furthermore, these new predictive sensors can function as targets for novel sensor engineering with applications in biotechnology, ecosystem maintenance, and medicine.IMPORTANCEMicrobes infect, colonize, and proliferate due to their ability to sense and respond quickly to their surroundings. In this research, we extract the sensory proteins from a diverse range of environmental, engineered, and host-associated metagenomes. We trained machine learning classifiers using sensors as features such that it is possible to predict the ecosystem for a metagenome from its sensor profile. We use the optimized model's feature importance to identify the most impactful and predictive sensors in different environments. We next use the sensor profile from human gut metagenomes to classify their disease states and explore which sensors can explain differences between diseases. The sensors most predictive of environmental labels here, most of which correspond to uncharacterized proteins, are a useful starting point for the discovery of important environment signals and the development of possible diagnostic interventions.}, } @article {pmid38075934, year = {2023}, author = {Hempel, CA and Buchner, D and Mack, L and Brasseur, MV and Tulpan, D and Leese, F and Steinke, D}, title = {Predicting environmental stressor levels with machine learning: a comparison between amplicon sequencing, metagenomics, and total RNA sequencing based on taxonomically assigned data.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1217750}, pmid = {38075934}, issn = {1664-302X}, abstract = {INTRODUCTION: Microbes are increasingly (re)considered for environmental assessments because they are powerful indicators for the health of ecosystems. The complexity of microbial communities necessitates powerful novel tools to derive conclusions for environmental decision-makers, and machine learning is a promising option in that context. While amplicon sequencing is typically applied to assess microbial communities, metagenomics and total RNA sequencing (herein summarized as omics-based methods) can provide a more holistic picture of microbial biodiversity at sufficient sequencing depths. Despite this advantage, amplicon sequencing and omics-based methods have not yet been compared for taxonomy-based environmental assessments with machine learning.

METHODS: In this study, we applied 16S and ITS-2 sequencing, metagenomics, and total RNA sequencing to samples from a stream mesocosm experiment that investigated the impacts of two aquatic stressors, insecticide and increased fine sediment deposition, on stream biodiversity. We processed the data using similarity clustering and denoising (only applicable to amplicon sequencing) as well as multiple taxonomic levels, data types, feature selection, and machine learning algorithms and evaluated the stressor prediction performance of each generated model for a total of 1,536 evaluated combinations of taxonomic datasets and data-processing methods.

RESULTS: Sequencing and data-processing methods had a substantial impact on stressor prediction. While omics-based methods detected a higher diversity of taxa than amplicon sequencing, 16S sequencing outperformed all other sequencing methods in terms of stressor prediction based on the Matthews Correlation Coefficient. However, even the highest observed performance for 16S sequencing was still only moderate. Omics-based methods performed poorly overall, but this was likely due to insufficient sequencing depth. Data types had no impact on performance while feature selection significantly improved performance for omics-based methods but not for amplicon sequencing.

DISCUSSION: We conclude that amplicon sequencing might be a better candidate for machine-learning-based environmental stressor prediction than omics-based methods, but the latter require further research at higher sequencing depths to confirm this conclusion. More sampling could improve stressor prediction performance, and while this was not possible in the context of our study, thousands of sampling sites are monitored for routine environmental assessments, providing an ideal framework to further refine the approach for possible implementation in environmental diagnostics.}, } @article {pmid38073164, year = {2024}, author = {Sankar, J and Thakral, V and Bharadwaj, K and Agarwal, S and Kabra, SK and Lodha, R and Rathore, S}, title = {The Microbiome and Metabolome of the Gut of Children with Sepsis and Septic Shock.}, journal = {Journal of intensive care medicine}, volume = {39}, number = {6}, pages = {514-524}, doi = {10.1177/08850666231216361}, pmid = {38073164}, issn = {1525-1489}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; *Shock, Septic/microbiology/metabolism ; Child ; Child, Preschool ; Prospective Studies ; *Metabolome/physiology ; *Sepsis/microbiology/metabolism ; Infant ; Feces/microbiology ; Intensive Care Units, Pediatric ; Case-Control Studies ; }, abstract = {BACKGROUND: There is limited understanding of alteration of gut microbiota and metabolome in children with sepsis/septic shock.

METHODS: In this prospective observational study carried out in a pediatric intensive care unit of a tertiary care center from 2020 to 2022, patients aged <17 years with sepsis/septic shock and healthy children (HC) were enrolled. We characterized the gut bacterial compositions by metagenome sequencing and metabolomes by untargeted gas chromatography-mass spectrometry. The primary outcome was to compare the gut microbiota and metabolome of children with sepsis/septic shock with that of HC. The Firmicutes/Bacteroidetes (F/B) ratio was compared between children with sepsis/septic shock and HC. Key secondary outcomes were to evaluate association of factors associated with a low F/B ratio in children with sepsis/septic shock.

RESULTS: A total of 40 children (63% boys) (15 children with sepsis and septic shock and 10 healthy children) with a median (IQR) age of 5.5 (1.5, 10) years were enrolled. In the fecal microbiota, the α-diversity index including Shannon and Simpson indices of the sepsis/septic shock groups was significantly lower than that of the HC. The samples lacked beneficial Bifidobacterium spp. and were dominated by Bacteroides, Enterobacteriaceae, and Enterococcaceae. There was reduction in short-chain fatty acids (SCFAs) in patients with sepsis/septic shock as compared to healthy children. A lower F/B ratio (≤1.57) of the gut microbiota discriminated well between children with sepsis/septic shock and HC. Factors associated with lower F/B ratio were male gender, clinical GI dysfunction, elevated inflammatory markers, and higher organ failure scores.

CONCLUSION: There were significant alterations in the gut microbiota and metabolome in children with sepsis/septic shock as compared to healthy children. Larger study is needed to confirm these exploratory findings and develop potential therapeutic targets that will improve outcomes in children with sepsis/septic shock.}, } @article {pmid38072228, year = {2024}, author = {Zhang, J and Shi, B and Lu, S and Wang, S and Ren, X and Liu, R and Dong, H and Li, K and Fouad, D and Ataya, FS and Mansoor, MK and Qamar, H and Wu, Q}, title = {Metagenomic analysis for exploring the potential of Lactobacillus yoelii FYL1 to mitigate bacterial diarrhea and changes in the gut microbiota of juvenile yaks.}, journal = {Microbial pathogenesis}, volume = {186}, number = {}, pages = {106496}, doi = {10.1016/j.micpath.2023.106496}, pmid = {38072228}, issn = {1096-1208}, mesh = {Cattle ; Animals ; Lactobacillus ; *Gastrointestinal Microbiome ; Escherichia coli ; Diarrhea/veterinary/microbiology ; Bacteria ; *Dysentery ; *Bacterial Infections ; }, abstract = {Diarrhea in calves is a common disease that results in poor nutrient absorption, poor growth and early death which leads to productivity and economic losses. Therefore, it is important to explore the methods to reduce diarrhea in yak's calves. Efficacy of lactic acid bacteria (LAB) for improvement of bacterial diarrhea is well recognized. For this purpose, two different doses (10[7] CFU, 10[11] CFU) of Lactobacillus yoelii FYL1 isolated from yaks were fed to juvenile yaks exposed to E. coli O78. After a trial period of ten days fresh feces and intestinal contents of the experimental yaks were collected and metagenomics sequencing was performed. It was found that feeding a high dose of Lactobacillus yoelii FYL1 decreased abundance of phylum Firmicutes in the E. coli O78 infected group whereas, it was high in animals fed low dose of Lactobacillu yoelii FYL1. Results also revealed that counts of bacteria from the family Oscillospiraceae, genus Synergistes and Megasphaera were higher in control group whereas, order Bifidobacteriales and family Bifidobacteriaceae were higher in infected group. It was observed that bacterial counts for Pseudoruminococcus were significantly (P < 0.05) higher in animals of group that were given high dose of Lactobacillus yoelii FYL1 (HLAB). Compared to infected group multiple beneficial bacterial genera such as Deinococus and Clostridium were found higher in the animals that were given a low dose of Lactobacillus yoelii FYL1 (LLAB). The abundance of pathogenic bacterial genera that included Parascardovia, Bacteroides and Methanobrevibacter was decreased (P < 0.05) in the lower dose treated group. The results of functional analysis revealed that animals of LLAB had a higher metabolism of terpenoids and polyketides compared to animals of infected group. Virus annotation also presented a significant inhibitory effect of LLAB on some viruses (P < 0.05). It was concluded that L. yoelii FYL1 had an improved effect on gut microbiota of young yaks infected with E. coli O78. This experiment contributes to establish the positive effects of LAB supplementation while treating diarrhea.}, } @article {pmid38072100, year = {2024}, author = {Chakraborty, S and Ghosh, S and Banerjee, S and Kumar, S and Bhattacharyya, P}, title = {Elucidating the synergistic effect of acidity and metalloid poisoning on the microbiome through metagenomics and machine learning approaches.}, journal = {Environmental research}, volume = {243}, number = {}, pages = {117885}, doi = {10.1016/j.envres.2023.117885}, pmid = {38072100}, issn = {1096-0953}, mesh = {*Arsenic/toxicity ; *Metalloids/analysis ; Agriculture ; Soil/chemistry ; *Microbiota ; Soil Microbiology ; *Soil Pollutants/toxicity/analysis ; }, abstract = {The abundance and diversity of the microflora in a complex environment such as soil is everchanging. Mica mining has led to metalloid poisoning and changes in soil biogeochemistry affecting the overall produce and leading to toxic dietary exposure. The study focuses on two prominent stressors acidity and arsenic, in mining-contaminated agricultural locations. Soil samples were collected from agricultural fields at a distance of 50 m (zone 1) and 500 m (zone 2) from active mines. Mean arsenic concentration was higher in zone 1 and pH was lower. Geostatistical and self-organizing maps were employed to report that the pattern of localization of soil acidity and arsenic content is similar indicating a causal relationship. Cluster and principal component analysis were further used to materialize a negative effect of soil acidity fractions and arsenic labile pool on soil enzymatic activity (fluorescein diacetate, dehydrogenase, β-1,4-glucosidase, phosphatase, and urease), respiration and Microbial biomass carbon. Soil metagenomic analysis revealed significant differences in the abundance of microbial populations with zone 1 (contaminated zone) having lower alpha and beta diversity. Finally, the efficacy of several machine-learning tools was tested using Taylor diagrams and an effort was made to select a potent algorithm to predict the causal stressors responsible for depreciating soil microbial health. Random Forrest had superior predictive power based on numerical evidence and was therefore chosen as the best-fitted model. The aforementioned insights into soil microbial health and sustenance in stressed conditions can be beneficial for predicting remedial strategies and practicing sustainable agriculture.}, } @article {pmid38071833, year = {2024}, author = {Afridi, MS and Kumar, A and Javed, MA and Dubey, A and de Medeiros, FHV and Santoyo, G}, title = {Harnessing root exudates for plant microbiome engineering and stress resistance in plants.}, journal = {Microbiological research}, volume = {279}, number = {}, pages = {127564}, doi = {10.1016/j.micres.2023.127564}, pmid = {38071833}, issn = {1618-0623}, mesh = {*Plant Roots/microbiology ; *Microbiota/physiology ; Exudates and Transudates/metabolism ; Plant Exudates/metabolism ; Quorum Sensing ; Plants/microbiology ; Rhizosphere ; Soil Microbiology ; }, abstract = {A wide range of abiotic and biotic stresses adversely affect plant's growth and production. Under stress, one of the main responses of plants is the modulation of exudates excreted in the rhizosphere, which consequently leads to alterations in the resident microbiota. Thus, the exudates discharged into the rhizospheric environment play a preponderant role in the association and formation of plant-microbe interactions. In this review, we aimed to provide a synthesis of the latest and most pertinent literature on the diverse biochemical and structural compositions of plant root exudates. Also, this work investigates into their multifaceted role in microbial nutrition and intricate signaling processes within the rhizosphere, which includes quorum-sensing molecules. Specifically, it explores the contributions of low molecular weight compounds, such as carbohydrates, phenolics, organic acids, amino acids, and secondary metabolites, as well as the significance of high molecular weight compounds, including proteins and polysaccharides. It also discusses the state-of-the-art omics strategies that unveil the vital role of root exudates in plant-microbiome interactions, including defense against pathogens like nematodes and fungi. We propose multiple challenges and perspectives, including exploiting plant root exudates for host-mediated microbiome engineering. In this discourse, root exudates and their derived interactions with the rhizospheric microbiota should receive greater attention due to their positive influence on plant health and stress mitigation.}, } @article {pmid38071207, year = {2023}, author = {Ristinmaa, AS and Tafur Rangel, A and Idström, A and Valenzuela, S and Kerkhoven, EJ and Pope, PB and Hasani, M and Larsbrink, J}, title = {Resin acids play key roles in shaping microbial communities during degradation of spruce bark.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {8171}, pmid = {38071207}, issn = {2041-1723}, support = {46559-1//Energimyndigheten (Swedish Energy Agency)/ ; 46559-1//Vetenskapsrådet (Swedish Research Council)/ ; CTS 21:1424//Carl Tryggers Stiftelse för Vetenskaplig Forskning (Carl Trygger Foundation)/ ; NNF20CC0035580//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; }, mesh = {Plant Bark ; *Picea ; *Microbiota ; Metagenome ; Bacteria/genetics ; }, abstract = {The bark is the outermost defense of trees against microbial attack, largely thanks to toxicity and prevalence of extractive compounds. Nevertheless, bark decomposes in nature, though by which species and mechanisms remains unknown. Here, we have followed the development of microbial enrichments growing on spruce bark over six months, by monitoring both chemical changes in the material and performing community and metagenomic analyses. Carbohydrate metabolism was unexpectedly limited, and instead a key activity was metabolism of extractives. Resin acid degradation was principally linked to community diversification with specific bacteria revealed to dominate the process. Metagenome-guided isolation facilitated the recovery of the dominant enrichment strain in pure culture, which represents a new species (Pseudomonas abieticivorans sp. nov.), that can grow on resin acids as a sole carbon source. Our results illuminate key stages in degradation of an abundant renewable resource, and how defensive extractive compounds have major roles in shaping microbiomes.}, } @article {pmid38070726, year = {2024}, author = {Lousada, MB and Edelkamp, J and Lachnit, T and Fehrholz, M and Pastar, I and Jimenez, F and Erdmann, H and Bosch, TCG and Paus, R}, title = {Spatial Distribution and Functional Impact of Human Scalp Hair Follicle Microbiota.}, journal = {The Journal of investigative dermatology}, volume = {144}, number = {6}, pages = {1353-1367.e15}, doi = {10.1016/j.jid.2023.11.006}, pmid = {38070726}, issn = {1523-1747}, mesh = {Humans ; *Scalp ; *Microbiota/physiology ; *Hair Follicle/microbiology ; Adult ; *Staphylococcus epidermidis/physiology ; Malassezia ; Female ; Middle Aged ; Male ; Aged ; Propionibacteriaceae/isolation & purification/physiology ; Young Adult ; }, abstract = {Human hair follicles (HFs) constitute a unique microbiota habitat that differs substantially from the skin surface. Traditional HF sampling methods fail to eliminate skin microbiota contaminants or assess the HF microbiota incompletely, and microbiota functions in human HF physiology remain ill explored. Therefore, we used laser-capture microdissection, metagenomic shotgun sequencing, and FISH to characterize the human scalp HF microbiota in defined anatomical compartments. This revealed significant compartment-, tissue lineage-, and donor age-dependent variations in microbiota composition. Greatest abundance variations between HF compartments were observed for viruses, archaea, Staphylococcus epidermidis, Cutibacterium acnes, and Malassezia restricta, with the latter 2 being the most abundant viable HF colonizers (as tested by propidium monoazide assay) and, surprisingly, most abundant in the HF mesenchyme. Transfection of organ-cultured human scalp HFs with S. epidermidis-specific lytic bacteriophages ex vivo downregulated transcription of genes known to regulate HF growth and development, metabolism, and melanogenesis, suggesting that selected microbial products may modulate HF functions. Indeed, HF treatment with butyrate, a metabolite of S. epidermidis and other HF microbiota, delayed catagen and promoted autophagy, mitochondrial activity, and gp100 and dermcidin expression ex vivo. Thus, human HF microbiota show spatial variations in abundance and modulate the physiology of their host, which invites therapeutic targeting.}, } @article {pmid38070671, year = {2024}, author = {Majumder, S and Kiritkumar Makwana, R and Shetty, V and Mukherjee, S and Narayan, P}, title = {Cardiovascular diseases and the heart-gut cross talk.}, journal = {Indian heart journal}, volume = {76}, number = {2}, pages = {94-100}, pmid = {38070671}, issn = {2213-3763}, mesh = {Humans ; *Cardiovascular Diseases/prevention & control/physiopathology/therapy ; *Gastrointestinal Microbiome/physiology ; Gastrointestinal Tract/physiopathology/physiology ; }, abstract = {The purpose of this narrative review is to provide a comprehensive overview of current research on heart-gut cross talk and its implications for cardiovascular disease. To uncover relevant preclinical and clinical research examining heart-gut cross talk, a thorough literature search was undertaken utilising electronic databases. The chosen publications were critically examined, and major findings were synthesised to offer a thorough perspective on the subject. We want to synthesise the most recent study findings, explain the underlying mechanisms, and provide potential treatment techniques. By exploring bidirectional connection between the heart and the gut, we shed light on novel future options for the prevention and treatment of cardiovascular diseases. The heart-gut cross talk is an exciting field of study with implications for cardiovascular disease. Understanding the complex connection between the heart and the gastrointestinal tract may lead to the development of novel therapeutic targets and therapies for the prevention and management of cardiovascular diseases. Future research should concentrate on identifying the specific processes driving this crosstalk as well as assessing the efficacy of therapies targeting the gut microbiota and the gut-brain axis in improving cardiovascular outcomes.}, } @article {pmid38070437, year = {2024}, author = {Wang, JF and Huang, JW and Cai, ZX and Li, QS and Sun, YY and Zhou, HZ and Zhu, H and Song, XS and Wu, HM}, title = {Differential Nitrous oxide emission and microbiota succession in constructed wetlands induced by nitrogen forms.}, journal = {Environment international}, volume = {183}, number = {}, pages = {108369}, doi = {10.1016/j.envint.2023.108369}, pmid = {38070437}, issn = {1873-6750}, mesh = {*Nitrous Oxide/metabolism ; Denitrification ; Wetlands ; Nitrogen ; Nitrates ; *Microbiota ; }, abstract = {Nitrous oxide (N2O) emission during the sewage treatment process is a serious environmental issue that requires attention. However, the N2O emission in constructed wetlands (CWs) as affected by different nitrogen forms in influents remain largely unknown. This study investigated the N2O emission profiles driven by microorganisms in CWs when exposed to two typical nitrogen sources (NH4[+]-N or NO3[-]-N) along with different carbon source supply (COD/N ratios: 3, 6, and 9). The results showed that CWs receiving NO3[-]-N caused a slight increase in total nitrogen removal (by up to 11.8 %). This increase was accomplished by an enrichment of key bacteria groups, including denitrifiers, dissimilatory nitrate reducers, and assimilatory nitrate reducers, which enhanced the stability of microbial interaction. Additionally, it led to a greater abundance of denitrification genes (e.g., nirK, norB, norC, and nosZ) as inferred from the database. Consequently, this led to a gradual increase in N2O emission from 66.51 to 486.77 ug-N/(m[2]·h) as the COD/N ratio increased in CWs. Conversely, in CWs receiving NH4[+]-N, an increasing influent COD/N ratio had a negative impact on nitrogen biotransformation. This resulted in fluctuating trend of N2O emissions, which decreased initially, followed by an increase at later stage (with values of 122.87, 44.00, and 148.59 ug-N/(m[2]·h)). Furthermore, NH4[+]-N in the aquatic improved the nitrogen uptake by plants and promoted the production of more root exudates. As a result, it adjusted the nitrogen-transforming function, ultimately reducing N2O emissions in CWs. This study highlights the divergence in microbiota succession and nitrogen transformation in CWs induced by nitrogen form and COD/N ratio, contributing to a better understanding of the microbial mechanisms of N2O emission in CWs with NH4[+]-N or NO3[-]-N at different COD/N ratios.}, } @article {pmid38070426, year = {2024}, author = {Mukherjee, P and Sharma, RS and Rawat, D and Sharma, U and Karmakar, S and Yadav, A and Mishra, V}, title = {Microbial communities drive flux of acid orange 7 and crystal violet dyes in water-sediment system.}, journal = {Journal of environmental management}, volume = {351}, number = {}, pages = {119699}, doi = {10.1016/j.jenvman.2023.119699}, pmid = {38070426}, issn = {1095-8630}, mesh = {*Gentian Violet ; Coloring Agents/chemistry ; Azo Compounds/chemistry ; *Microbiota ; *Benzenesulfonates ; }, abstract = {Unchecked dye effluent discharge poses escalating environmental and economic concerns, especially in developing nations. While dyes are well-recognized water pollutants, the mechanisms of their environmental spread are least understood. Therefore, the present study examines the partitioning of Acid Orange 7 (AO7) and Crystal Violet (CV) dyes using water-sediment microcosms and reports that native microbes significantly affect AO7 decolorization and transfer. Both dyes transition from infused to pristine matrices, reaching equilibrium in a fortnight. While microbes influence CV partitioning, their role in decolorization is minimal, emphasizing their varied impact on the environmental fate of dyes. Metagenomic analyses reveal contrasting microbial composition between control and AO7-infused samples. Control water samples displayed a dominance of Proteobacteria (62%), Firmicutes (24%), and Bacteroidetes (9%). However, AO7 exposure led to Proteobacteria reducing to 57% and Bacteroidetes to 3%, with Firmicutes increasing to 34%. Sediment samples, primarily comprising Firmicutes (47%) and Proteobacteria (39%), shifted post-AO7 exposure: Proteobacteria increased to 53%, and Firmicutes dropped to 38%. At the genus level, water samples dominated by Niveispirillum (34%) declined after AO7 exposure, while Bacillus and Pseudomonas increased. Notably, Serratia and Sphingomonas, known for azo dye degradation, rose post-exposure, hinting at their role in AO7 decolorization. Conversely, sediment samples showed a decrease in the growth of Bacillus and an increase in that of Pseudomonas and Serratia. These findings emphasize the significant role of microbial communities in determining the environmental fate of dyes, providing insights on its environmental implications and management.}, } @article {pmid38070135, year = {2023}, author = {Lum, GR and Ha, SM and Olson, CA and Blencowe, M and Paramo, J and Reyes, B and Matsumoto, JH and Yang, X and Hsiao, EY}, title = {Ketogenic diet therapy for pediatric epilepsy is associated with alterations in the human gut microbiome that confer seizure resistance in mice.}, journal = {Cell reports}, volume = {42}, number = {12}, pages = {113521}, pmid = {38070135}, issn = {2211-1247}, support = {R01 NS115537/NS/NINDS NIH HHS/United States ; }, mesh = {Child ; Humans ; Animals ; Mice ; *Diet, Ketogenic ; *Gastrointestinal Microbiome ; *Epilepsy ; *Microbiota ; Ketone Bodies ; Disease Models, Animal ; Seizures ; }, abstract = {The gut microbiome modulates seizure susceptibility and the anti-seizure effects of the ketogenic diet (KD) in animal models, but whether these relationships translate to KD therapies for human epilepsy is unclear. We find that the clinical KD alters gut microbial function in children with refractory epilepsy. Colonizing mice with KD-associated microbes promotes seizure resistance relative to matched pre-treatment controls. Select metagenomic and metabolomic features, including those related to anaplerosis, fatty acid β-oxidation, and amino acid metabolism, are seen with human KD therapy and preserved upon microbiome transfer to mice. Mice colonized with KD-associated gut microbes exhibit altered hippocampal transcriptomes, including pathways related to ATP synthesis, glutathione metabolism, and oxidative phosphorylation, and are linked to susceptibility genes identified in human epilepsy. Our findings reveal key microbial functions that are altered by KD therapies for pediatric epilepsy and linked to microbiome-induced alterations in brain gene expression and seizure protection in mice.}, } @article {pmid38068802, year = {2023}, author = {Cordero-Varela, JA and Reyes-Corral, M and Lao-Pérez, M and Fernández-Santos, B and Montenegro-Elvira, F and Sempere, L and Ybot-González, P}, title = {Analysis of Gut Characteristics and Microbiota Changes with Maternal Supplementation in a Neural Tube Defect Mouse Model.}, journal = {Nutrients}, volume = {15}, number = {23}, pages = {}, pmid = {38068802}, issn = {2072-6643}, support = {DOC_01701//Consejería de Transformación Económica, Industria, Conocimiento y Universidades; Junta de Andalucía/ ; P20_01267//Consejería de Transformación Económica, Industria, Conocimiento y Universidades; Junta de Andalucía/ ; RH-0033-2020//Consejería de Salud y Bienestar Social; Junta de Andalucía/ ; C-0025-2018//Consejería de Salud y Bienestar Social; Junta de Andalucía/ ; EF- 0084-2016//Consejería de Salud y Bienestar Social; Junta de Andalucía/ ; 050561//Consejo Superior de Investigaciones Científicas; Ministerio de Ciencia e Innovación/ ; PI17/00693//Instituto de Salud Carlos III (ISCIII) and co-funded by the European Union/ ; PI20/00769//Instituto de Salud Carlos III (ISCIII) and co-funded by the European Union/ ; 202220/095//Consejo Superior de Investigaciones Científicas; Ministerio de Ciencia e Innovación/ ; }, mesh = {Female ; Pregnancy ; Mice ; Animals ; RNA, Ribosomal, 16S/genetics ; *Neural Tube Defects/prevention & control ; Folic Acid/pharmacology ; Dietary Supplements ; Inositol ; *Microbiota ; Disease Models, Animal ; }, abstract = {Adequate nutrient supply is crucial for the proper development of the embryo. Although nutrient supply is determined by maternal diet, the gut microbiota also influences nutrient availability. While currently there is no cure for neural tube defects (NTDs), their prevention is largely amenable to maternal folic acid and inositol supplementation. The gut microbiota also contributes to the production of these nutrients, which are absorbed by the host, but its role in this context remains largely unexplored. In this study, we performed a functional and morphological analysis of the intestinal tract of loop-tail mice (Vangl2 mutants), a mouse model of folate/inositol-resistant NTDs. In addition, we investigated the changes in gut microbiota using 16S rRNA gene sequencing regarding (1) the host genotype; (2) the sample source for metagenomics analysis; (3) the pregnancy status in the gestational window of neural tube closure; (4) folic acid and (5) D-chiro-inositol supplementation. We observed that Vangl2[+/Lp] mice showed no apparent changes in gastrointestinal transit time or fecal output, yet exhibited increased intestinal length and cecal weight and gut dysbiosis. Moreover, our results showed that the mice supplemented with folic acid and D-chiro-inositol had significant changes in their microbiota composition, which are changes that could have implications for nutrient absorption.}, } @article {pmid38066630, year = {2023}, author = {Baud, GLC and Prasad, A and Ellegaard, KM and Engel, P}, title = {Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {283}, pmid = {38066630}, issn = {1474-760X}, support = {714804//H2020 European Research Council/ ; 180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 179487//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; IZSTZ0_189496//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, mesh = {Humans ; Bees/genetics ; Animals ; *Gastrointestinal Microbiome/genetics ; Symbiosis/physiology ; *Microbiota ; Bacteria/genetics ; Metagenomics ; }, abstract = {BACKGROUND: Strain-level diversity is widespread among bacterial species and can expand the functional potential of natural microbial communities. However, to what extent communities undergo consistent shifts in strain composition in response to environmental/host changes is less well understood.

RESULTS: Here, we used shotgun metagenomics to compare the gut microbiota of two behavioral states of the Western honeybee (Apis mellifera), namely nurse and forager bees. While their gut microbiota is composed of the same bacterial species, we detect consistent changes in strain-level composition between nurses and foragers. Single nucleotide variant profiles of predominant bacterial species cluster by behavioral state. Moreover, we identify strain-specific gene content related to nutrient utilization, vitamin biosynthesis, and cell-cell interactions specifically associated with the two behavioral states.

CONCLUSIONS: Our findings show that strain-level diversity in host-associated communities can undergo consistent changes in response to host behavioral changes modulating the functional potential of the community.}, } @article {pmid38066544, year = {2023}, author = {Liang, Y and Dou, S and Zhao, G and Shen, J and Fu, G and Fu, L and Li, S and Cong, B and Dong, C}, title = {Prediction of BMI traits in the Chinese population based on the gut metagenome.}, journal = {Microbial cell factories}, volume = {22}, number = {1}, pages = {250}, pmid = {38066544}, issn = {1475-2859}, mesh = {Humans ; Metagenome ; Body Mass Index ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; Feces/microbiology ; China ; }, abstract = {BACKGROUND: Identifying individual characteristics based on trace evidence left at a crime scene is crucial in forensic identification. Microbial communities found in fecal traces have high individual specificity and could serve as potential markers for forensic characterization. Previous research has established that predicting body type based on the relative abundance of the gut microbiome is relatively accurate. However, the long-term stability and high individual specificity of the gut microbiome are closely linked to changes at the genome level of the microbiome. No studies have been conducted to deduce body shape from genetic traits. Therefore, in this study, the vital role of gut bacterial community characteristics and genetic traits in predicting body mass index (BMI) was investigated using gut metagenomic data from a healthy Chinese population.

RESULTS: Regarding the gut microbial community, the underweight group displayed increased α-diversity in comparison to the other BMI groups. There were significant differences in the relative abundances of 19 species among these three BMI groups. The BMI prediction model, based on the 31 most significant species, showed a goodness of fit (R[2]) of 0.56 and a mean absolute error (MAE) of 2.09 kg/m[2]. The overweight group exhibited significantly higher α-diversity than the other BMI groups at the level of gut microbial genes. Furthermore, there were significant variations observed in the single-nucleotide polymorphism (SNP) density of 732 contigs between these three BMI groups. The BMI prediction model, reliant on the 62 most contributing contigs, exhibited a model R[2] of 0.72 and an MAE of 1.56 kg/m[2]. The model predicting body type from 44 contigs correctly identified the body type of 93.55% of the study participants.

CONCLUSION: Based on metagenomic data from a healthy Chinese population, we demonstrated the potential of genetic traits of gut bacteria to predict an individual's BMI. The findings of this study suggest the effectiveness of a novel method for determining the body type of suspects in forensic applications using the genetic traits of the gut microbiome and holds great promise for forensic individual identification.}, } @article {pmid38066117, year = {2023}, author = {Likar, M and Grašič, M and Stres, B and Regvar, M and Gaberščik, A}, title = {Metagenomics reveals effects of fluctuating water conditions on functional pathways in plant litter microbial community.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {21741}, pmid = {38066117}, issn = {2045-2322}, support = {P1-0212//Javna Agencija za Raziskovalno Dejavnost RS/ ; P1-0212//Javna Agencija za Raziskovalno Dejavnost RS/ ; P1-0212//Javna Agencija za Raziskovalno Dejavnost RS/ ; P1-0212//Javna Agencija za Raziskovalno Dejavnost RS/ ; }, mesh = {*Soil Microbiology ; Plant Leaves/metabolism ; Ecosystem ; *Microbiota/physiology ; Plants ; Poaceae ; Soil ; }, abstract = {Climate change modifies environmental conditions, resulting in altered precipitation patterns, moisture availability and nutrient distribution for microbial communities. Changes in water availability are projected to affect a range of ecological processes, including the decomposition of plant litter and carbon cycling. However, a detailed understanding of microbial stress response to drought/flooding is missing. In this study, an intermittent lake is taken up as a model for changes in water availability and how they affect the functional pathways in microbial communities of the decomposing Phragmites australis litter. The results show that most enriched functions in both habitats belonged to the classes of Carbohydrates and Clustering-based subsystems (terms with unknown function) from SEED subsystems classification. We confirmed that changes in water availability resulted in altered functional makeup of microbial communities. Our results indicate that microbial communities under more frequent water stress (due to fluctuating conditions) could sustain an additional metabolic cost due to the production or uptake of compatible solutes to maintain cellular osmotic balance. Nevertheless, although prolonged submergence seemed to have a negative impact on several functional traits in the fungal community, the decomposition rate was not affected.}, } @article {pmid38065789, year = {2024}, author = {Koh, C and Saleh, MC}, title = {Translating mosquito viromes into vector management strategies.}, journal = {Trends in parasitology}, volume = {40}, number = {1}, pages = {10-20}, doi = {10.1016/j.pt.2023.11.002}, pmid = {38065789}, issn = {1471-5007}, support = {ANR-10-LABX-62-IBEID//Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases/ ; ANR-22-CE35-0001,//Agence Nationale de la Recherche/ ; HR001118S0017//Defense Advanced Research Projects Agency (DARPA)/ ; }, mesh = {Animals ; Humans ; *Culicidae/genetics ; Virome ; Genome, Viral ; Mosquito Vectors ; *Viruses/genetics ; }, abstract = {Mosquitoes are best known for transmitting human and animal viruses. However, they also harbour mosquito-specific viruses (MSVs) as part of their microbiota. These are a group of viruses whose diversity and prevalence overshadow their medically relevant counterparts. Although metagenomics sequencing has remarkably accelerated the discovery of these viruses, what we know about them is often limited to sequence information, leaving much of their fundamental biology to be explored. Understanding the biology and ecology of MSVs can enlighten our knowledge of virus-virus interactions and lead to new innovations in the management of mosquito-borne viral diseases. We retrace the history of their discovery and discuss research milestones that would line the path from mosquito virome knowledge to vector management strategies.}, } @article {pmid38064782, year = {2024}, author = {Ke, Y and Sun, W and Chen, Z and Zhu, Y and Chen, X and Yan, S and Li, Y and Xie, S}, title = {Effects of disinfectant type and dosage on biofilm's activity, viability, microbiome and antibiotic resistome in bench-scale drinking water distribution systems.}, journal = {Water research}, volume = {249}, number = {}, pages = {120958}, doi = {10.1016/j.watres.2023.120958}, pmid = {38064782}, issn = {1879-2448}, mesh = {*Disinfectants/pharmacology ; *Drinking Water/chemistry ; Chloramines/pharmacology ; Chlorine/pharmacology ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; Bacteria/genetics ; Biofilms ; Adenosine Triphosphate ; *Water Purification ; }, abstract = {Drinking water distribution systems (DWDSs) are important for supplying high-quality water to consumers and disinfectant is widely used to control microbial regrowth in DWDSs. However, the disinfectant's influences on microbial community and antibiotic resistome in DWDS biofilms and the underlying mechanisms driving their dynamics remain elusive. The study investigated the effects of chlorine and chloramine disinfection on the microbiome and antibiotic resistome of biofilms in bench-scale DWDSs using metagenomics assembly. Additionally, the biofilm activity and viability were monitored based on adenosine triphosphate (ATP) and flow cytometer (FCM) staining. The results showed that both chlorine and chloramine disinfectants decreased biofilm ATP, although chloramine at a lower dosage (1 mg/L) could increase it. Chloramine caused a greater decrease in living cells than chlorine. Furthermore, the disinfectants significantly lowered the microbial community diversity and altered microbial community structure. Certain bacterial taxa were enriched, such as Mycobacterium, Sphingomonas, Sphingopyxis, Azospira, and Dechloromonas. Pseudomonas aeruginosa exhibited high resistance towards disinfectants. The disinfectants also decreased the complexity of microbial community networks. Some functional taxa (e.g., Nitrospira, Nitrobacter, Nitrosomonas) were identified as keystones in chloramine-treated DWDS microbial ecological networks. Stochasticity drove biofilm microbial community assembly, and disinfectants increased the contributions of stochastic processes. Chlorine had greater promotion effects on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and ARG hosts than chloramine. The disinfectants also selected pathogens, such as Acinetobacter baumannii and Klebsiella pneumonia, and these pathogens also harbored ARGs and MGEs. Overall, this study provides new insights into the effects of disinfectants on biofilm microbiome and antibiotic resistome, highlighting the importance of monitoring and managing disinfection practices in DWDSs.}, } @article {pmid38063370, year = {2024}, author = {Tamames, J and Jiménez-Lalana, D and Redondo, Á and Martínez-García, S and de Los Rios, A}, title = {In situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day.}, journal = {Molecular ecology resources}, volume = {24}, number = {2}, pages = {e13909}, doi = {10.1111/1755-0998.13909}, pmid = {38063370}, issn = {1755-0998}, mesh = {*Metagenome ; *Microbiota/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Spain ; }, abstract = {We present here a complete system for metagenomic analysis that allows performing the sequencing and analysis of a medium-size metagenome in less than one day. This unprecedented development was possible due to the conjunction of state-of-the-art experimental and computational advances: a portable laboratory suitable for DNA extraction and sequencing with nanopore technology; the powerful metagenomic analysis pipeline SqueezeMeta, capable to provide a complete analysis in a few hours and using scarce computational resources; and tools for the automatic inspection of the results via a graphical user interface, that can be coupled to a web server to allow remote visualization of data (SQMtools and SQMxplore). We have tested the feasibility of our approach in the sequencing of the microbiota associated to volcanic rocks in La Palma, Canary Islands. Also, we did a two-day sampling campaign of marine waters in which the results obtained on the first day guided the experimental design of the second day. We demonstrate that it is possible to generate metagenomic information in less than one day, making it feasible to obtain taxonomic and functional profiles fast and efficiently, even in field conditions. This capacity can be used in the further to perform real-time functional and taxonomic monitoring of microbial communities in remote areas.}, } @article {pmid38062990, year = {2024}, author = {Dunbar, A and Drigo, B and Djordjevic, SP and Donner, E and Hoye, BJ}, title = {Impacts of coprophagic foraging behaviour on the avian gut microbiome.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {99}, number = {2}, pages = {582-597}, doi = {10.1111/brv.13036}, pmid = {38062990}, issn = {1469-185X}, support = {//University of South Australia's Science, Technology, Engineering, and Mathematics/ ; DE200100884//Australian Research Council/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Coprophagia ; Birds ; Diet/veterinary ; Feces ; }, abstract = {Avian gut microbial communities are complex and play a fundamental role in regulating biological functions within an individual. Although it is well established that diet can influence the structure and composition of the gut microbiota, foraging behaviour may also play a critical, yet unexplored role in shaping the composition, dynamics, and adaptive potential of avian gut microbiota. In this review, we examine the potential influence of coprophagic foraging behaviour on the establishment and adaptability of wild avian gut microbiomes. Coprophagy involves the ingestion of faeces, sourced from either self (autocoprophagy), conspecific animals (allocoprophagy), or heterospecific animals. Much like faecal transplant therapy, coprophagy may (i) support the establishment of the gut microbiota of young precocial species, (ii) directly and indirectly provide nutritional and energetic requirements, and (iii) represent a mechanism by which birds can rapidly adapt the microbiota to changing environments and diets. However, in certain contexts, coprophagy may also pose risks to wild birds, and their microbiomes, through increased exposure to chemical pollutants, pathogenic microbes, and antibiotic-resistant microbes, with deleterious effects on host health and performance. Given the potentially far-reaching consequences of coprophagy for avian microbiomes, and the dearth of literature directly investigating these links, we have developed a predictive framework for directing future research to understand better when and why wild birds engage in distinct types of coprophagy, and the consequences of this foraging behaviour. There is a need for comprehensive investigation into the influence of coprophagy on avian gut microbiotas and its effects on host health and performance throughout ontogeny and across a range of environmental perturbations. Future behavioural studies combined with metagenomic approaches are needed to provide insights into the function of this poorly understood behaviour.}, } @article {pmid38061430, year = {2024}, author = {Liu, X and Fu, Z and Liu, TX and Liang, P}, title = {Effects of repeated afidopyropen treatment on the structure and function of the soil microbial community.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {342}, number = {}, pages = {123083}, doi = {10.1016/j.envpol.2023.123083}, pmid = {38061430}, issn = {1873-6424}, mesh = {*Insecticides/toxicity ; Soil/chemistry ; Soil Microbiology ; *Microbiota ; *Heterocyclic Compounds, 4 or More Rings ; *Lactones ; }, abstract = {Chemical insecticides are the most effective pest control agents. Afidopyropen is a novel insecticide used against sap-sucking insects, such as aphids. However, the effects of repeated afidopyropen application on the structure and function of soil microorganisms remain unknown. In this study, the changes in the enzyme activities, community structure and function, and relative abundance of antibiotic resistance ontology (ARO) of soil microorganisms were investigated during three repeated afidopyropen applications under laboratory conditions at the maximum recommended dosage (M1) and 10 times the M1 (M10). The neutral phosphatase (NPA) and catalase (CAT) activities in the soil were significantly suppressed after afidopyropen treatment. The Simpson diversity index (1/D) and Shannon-Wiener diversity index (H) also decreased in both the M1 and M10 afidopyropen-treated soils, indicating a remarkable decrease in soil microorganism diversity. The average well color development (AWCD) first increased and subsequently recovered to normal levels after the third application of the insecticide, suggesting that afidopyropen application could increase the metabolic activity of soil microorganisms. Metagenomic analysis showed that repeated afidopyropen application in both the M1 and M10 treatment groups altered the community structure of soil microorganisms, albeit in different ways. Furthermore, repeated afidopyropen application significantly increased the relative ARO abundance, especially in the M10 treatment, with the most dominant AROs being adeF, baeS, and IND-6. These findings reveal the effects of excessive afidopyropen application on soil microorganisms and lay an important foundation for the comprehensive evaluation of the impact of this insecticide on the environment.}, } @article {pmid38060843, year = {2024}, author = {Prins, FM and Collij, V and Groot, HE and Björk, JR and Swarte, JC and Andreu-Sánchez, S and Jansen, BH and Fu, J and Harmsen, HJM and Zhernakova, A and Lipsic, E and van der Harst, P and Weersma, RK and Gacesa, R}, title = {The gut microbiome across the cardiovascular risk spectrum.}, journal = {European journal of preventive cardiology}, volume = {31}, number = {8}, pages = {935-944}, doi = {10.1093/eurjpc/zwad377}, pmid = {38060843}, issn = {2047-4881}, support = {//University Medical Center Groningen/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Male ; Female ; Middle Aged ; *Feces/microbiology ; *Heart Disease Risk Factors ; Risk Assessment ; Aged ; Bacteria/isolation & purification/classification/genetics ; ST Elevation Myocardial Infarction/microbiology ; Metagenomics ; Cardiovascular Diseases/microbiology/epidemiology ; Dysbiosis ; Adult ; }, abstract = {AIMS: Despite treatment advancements, cardiovascular disease remains a leading cause of death worldwide. Identifying new targets is crucial for enhancing preventive and therapeutic strategies. The gut microbiome has been associated with coronary artery disease (CAD), however our understanding of specific changes during CAD development remains limited. We aimed to investigate microbiome changes in participants without clinically manifest CAD with different cardiovascular risk levels and in patients with ST-elevation myocardial infarction (STEMI).

METHODS AND RESULTS: In this cross-sectional study, we characterized the gut microbiome using metagenomics of 411 faecal samples from individuals with low (n = 130), intermediate (n = 130), and high (n = 125) cardiovascular risk based on the Framingham score, and STEMI patients (n = 26). We analysed diversity, and differential abundance of species and functional pathways while accounting for confounders including medication and technical covariates. Collinsella stercoris, Flavonifractor plautii, and Ruthenibacterium lactatiformans showed increased abundances with cardiovascular risk, while Streptococcus thermophilus was negatively associated. Differential abundance analysis revealed eight species and 49 predicted metabolic pathways that were differently abundant among the groups. In the gut microbiome of STEMI patients, there was a depletion of pathways linked to vitamin, lipid, and amino acid biosynthesis.

CONCLUSION: We identified four microbial species showing a gradual trend in abundance from low-risk individuals to those with STEMI, and observed differential abundant species and pathways in STEMI patients compared to those without clinically manifest CAD. Further investigation is warranted to gain deeper understanding of their precise role in CAD progression and potential implications, with the ultimate goal of identifying novel therapeutic targets.}, } @article {pmid38060520, year = {2023}, author = {Paul, LJ and Ericsson, AC and Andrews, FM and McAdams, Z and Keowen, ML and St Blanc, MP and Banse, HE}, title = {Field study examining the mucosal microbiome in equine glandular gastric disease.}, journal = {PloS one}, volume = {18}, number = {12}, pages = {e0295697}, pmid = {38060520}, issn = {1932-6203}, mesh = {Horses ; Animals ; *Stomach Diseases/pathology ; Gastric Mucosa/pathology ; Risk Factors ; *Horse Diseases/pathology ; *Microbiota ; *Stomach Ulcer/pathology ; }, abstract = {Equine glandular gastric disease (EGGD) is a common disease among athletic horses that can negatively impact health and performance. The pathophysiology of this EGGD remains poorly understood. Previous studies using controlled populations of horses identified differences in the gastric glandular mucosal microbiome associated with disease. The objective of this study was to compare the gastric microbiome in horses with EGGD and those without across multiple barns and differing management practices. We hypothesized that alterations in the microbiome of the gastric glandular mucosa are associated with EGGD. A secondary objective was to perform a risk factor analysis for EGGD using the diet and management data collected. Microbial populations of biopsies from normal pyloric mucosa of horses without EGGD (control biopsies), normal pyloric mucosa of horses with EGGD (normal biopsies) and areas of glandular mucosal disruption in horses with EGGD (lesion biopsies) were compared. Lesion biopsies had a different microbial community structure than control biopsies. Control biopsies had a higher read count for the phylum Actinomycetota compared to lesion biopsies. Control biopsies also had an enrichment of the genera Staphylococcus and Lawsonella and the species Streptococcus salivarius. Lesion biopsies had an enrichment of the genera Lactobacillus and Actinobacillus and the species Lactobacillus equigenerosi. These results demonstrate differences in the gastric glandular microbiome between sites of disrupted mucosa in horses with EGGD compared to pyloric mucosa of horses without EGGD. Risk factor analysis indicated that exercise duration per week was a risk factor for EGGD.}, } @article {pmid38060126, year = {2024}, author = {Jaksa-Czotter, N and Nagyné Galbács, Z and Jahan, A and Demián, E and Várallyay, É}, title = {Viromes of Plants Determined by High-Throughput Sequencing of Virus-Derived siRNAs.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2732}, number = {}, pages = {179-198}, pmid = {38060126}, issn = {1940-6029}, mesh = {RNA, Small Interfering/genetics ; Virome ; RNA, Viral/analysis ; *Viruses/genetics ; RNA, Double-Stranded ; Plants/genetics ; *Virus Diseases ; High-Throughput Nucleotide Sequencing/methods ; Plant Diseases/genetics ; }, abstract = {Plants growing in open airfields can be infected by several viruses even as a multiple infection. Virus infection in crops can lead to a serious damage to the harvest. In addition, virus presence in grapevine, fruit trees, and tuberous vegetables, propagated vegetatively affects the phytosanitary status of the propagation material (both the rootstock and the variety) having profound effect on the lifetime and health of the new plantations. The fast evolution of sequencing techniques provides a new opportunity for metagenomics-based viral diagnostics. Small interfering (si) RNAs produced by the RNA silencing-based host immune system during viral infection can be sequenced by high-throughput techniques and analyzed for the presence of viruses, revealing the presence of all known viral pathogens in the sample and therefore opening new avenues in virus diagnostics. This method is based on Illumina sequencing and bioinformatics analysis of virus-derived siRNAs in the host. Here we describe a protocol for this challenging technique step by step with notes, to ensure success for every user.}, } @article {pmid38059755, year = {2023}, author = {Rosell-Díaz, M and Santos-González, E and Motger-Albertí, A and Ramió-Torrentà, L and Garre-Olmo, J and Pérez-Brocal, V and Moya, A and Jové, M and Pamplona, R and Puig, J and Ramos, R and Fernández-Real, JM and Mayneris-Perxachs, J}, title = {Gut microbiota links to serum ferritin and cognition.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2290318}, pmid = {38059755}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Tandem Mass Spectrometry ; Cognition ; Bacteria/genetics ; Metabolome ; Phenylalanine ; Iron ; Ferritins ; }, abstract = {Iron is required for the replication and growth of almost all bacterial species and in the production of myelin and neurotransmitters. Increasing clinical studies evidence that the gut microbiota plays a critical role in iron metabolism and cognition. However, the understanding of the complex iron-microbiome-cognition crosstalk remains elusive. In a recent study in the Aging Imageomics cohort (n = 1,030), we identified a positive association of serum ferritin (SF) with executive function (EF) as inferred from the semantic verbal fluency (SVF,) the total digit span (TDS) and the phonemic verbal fluency tests (PVF). Here, we explored the potential mechanisms by analyzing the gut microbiome and plasma metabolome using shotgun metagenomics and HPLC-ESI-MS/MS, respectively. Different bacterial species belonging to the Proteobacteria phylum (Klebsiella pneumoniae, Klebsiella michiganensis, Unclassified Escherichia) were negatively associated both with SF and executive function. At the functional level, an enrichment of microbial pathways involved in phenylalanine, arginine, and proline metabolism was identified. Consistently, phenylacetylglutamine, a metabolite derived from microbial catabolism of phenylalanine, was negatively associated with SF, EF, and semantic memory. Other metabolites such as ureidobutyric acid and 19,20-DiHDPA, a DHA-derived oxylipin, were also consistently and negatively associated with SF, EF, and semantic memory, while plasma eicosapentaenoic acid was positively associated. The associations of SF with cognition could be mediated by the gut microbiome through microbial-derived metabolites.}, } @article {pmid38059752, year = {2023}, author = {Dong, C and Guan, Q and Xu, W and Zhang, X and Jin, B and Yu, S and Xu, X and Xia, Y}, title = {Disentangling the age-related manner in the associations between gut microbiome and women's health: a multi-cohort microbiome study.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2290320}, pmid = {38059752}, issn = {1949-0984}, mesh = {Adolescent ; Humans ; Female ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2 ; *Inflammatory Bowel Diseases ; *Microbiota ; Women's Health ; *Atherosclerosis ; }, abstract = {Women's health encompasses life-course healthcare, and mounting evidence emphasizes the pivotal contribution of gut microbiota. Therefore, understanding the temporal dynamics of gut microbiota and how age influences disease-gut microbiota associations is essential for improving women's health. By analyzing metagenomic data from 3625 healthy women, we revealed significant effects of age on gut microbiota and age-dependent patterns in microbial features, such as relative abundance, Shannon index, and microbial network properties. Additionally, declining trends in the predictive accuracy of gut microbiota for age groups were shown using iterative sub-sampling based random forest (ISSRF) model. Age-specific species markers were also identified, many of which were shared across age groups. To investigate the influence of age on disease-gut microbiota associations, metagenomic data from 681 women with various disease conditions and 491 matched healthy controls were collected. A substantial proportion of species markers for inflammatory bowel disease (IBD), type 2 diabetes (T2D), atherosclerotic cardiovascular disease (ACVD), and impaired glucose tolerance (IGT) differed in relative abundance across age groups, and were also age-specific species markers. Besides, the microbiota-based probabilities of IBD and ACVD were positively correlated with age. Furthermore, the age specificity of disease-gut microbiota associations was explored using the ISSRF model. Associations between IBD and gut microbiota were age-specific, with reduced stability of disease species markers in childhood and adolescence, possibly due to decrease in the effect size between patients and controls. Our findings provided valuable insights into promoting healthy aging and developing personalized healthcare strategies for women.}, } @article {pmid38059467, year = {2023}, author = {Ren, CY and Zhao, HP}, title = {Synthetic Nuclease-Producing Microbiome Achieves Efficient Removal of Extracellular Antibiotic Resistance Genes from Wastewater Effluent.}, journal = {Environmental science & technology}, volume = {57}, number = {50}, pages = {21224-21234}, doi = {10.1021/acs.est.3c07974}, pmid = {38059467}, issn = {1520-5851}, mesh = {Humans ; *Anti-Bacterial Agents ; Wastewater ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; *Microbiota ; }, abstract = {Antibiotic resistance gene (ARG) transmission poses significant threats to human health. The effluent of wastewater treatment plants is demonstrated as a hotspot source of ARGs released into the environment. In this study, a synthetic microbiome containing nuclease-producing Deinococcus radiodurans was constructed to remove extracellular ARGs. Results of quantitative polymerase chain reaction (qPCR) showed significant reduction in plasmid RP4-associated ARGs (by more than 3 orders of magnitude) and reduction of indigenous ARG sul1 and mobile genetic element (MGE) intl1 (by more than 1 order of magnitude) in the synthetic microbiome compared to the control without D. radiodurans. Metagenomic analysis revealed a decrease in ARG and MGE diversity in extracellular DNA (eDNA) of the treated group. Notably, whereas eight antibiotic-resistant plasmids with mobility risk were detected in the control, only one was detected in the synthetic microbiome. The abundance of the nuclease encoding gene exeM, quantified by qPCR, indicated its enrichment in the synthetic microbiome, which ensures stable eDNA degradation even when D. radiodurans decreased. Moreover, intracellular ARGs and MGEs and pathogenic ARG hosts in the river receiving treated effluent were lower than those in the river receiving untreated effluent. Overall, this study presents a new approach for removing extracellular ARGs and further reducing the risk of ARG transmission in receiving rivers.}, } @article {pmid38056715, year = {2024}, author = {Maisto, M and Ranauda, MA and Zuzolo, D and Tartaglia, M and Postiglione, A and Prigioniero, A and Falzarano, A and Scarano, P and Castelvetro, V and Corti, A and Modugno, F and La Nasa, J and Biale, G and Sciarrillo, R and Guarino, C}, title = {Effects of microplastics on microbial community dynamics in sediments from the Volturno River ecosystem, Italy.}, journal = {Chemosphere}, volume = {349}, number = {}, pages = {140872}, doi = {10.1016/j.chemosphere.2023.140872}, pmid = {38056715}, issn = {1879-1298}, mesh = {Microplastics ; Plastics ; Ecosystem ; RNA, Ribosomal, 16S ; *Microbiota ; Polymers ; Italy ; Environmental Monitoring ; *Water Pollutants, Chemical ; Geologic Sediments ; }, abstract = {In this study, the sources, abundance, and ecological implications of microplastic (MP) pollution in Volturno, one of the main rivers in southern Italy, were explored by investigating the MP concentration levels in sediments collected along the watercourse. The samples were sieved through 5- and 2-mm sieves and treated with selective organic solvents. The polymer classes polystyrene (PS), polyethylene (PE), polypropylene (PP), polyethylene terephthalate (PET), polycarbonate (PC), nylon 6 (PA6), and nylon 6,6 (PA66) were quantified using pyrolysis-gas chromatography-mass spectrometry (Py-GC/MS) and high-performance liquid chromatography (HPLC). Furthermore, a 16S rRNA metagenomic analysis was performed using next-generation sequencing in Ion Torrent™ to explore the bacterial taxonomy and ecological dynamics of sediment samples. The MPs were detected in all samples collected from the study area. PP and PET were the most abundant and frequently detected polymer types in the analysed samples. The total MP concentration ranged from 1.05 to 14.55 ppm (parts per million), identifying two distinct data populations: high- and low-MP-contaminated sediments. According to the Polymer Hazard Index (PHI), MP pollution was categorised as hazard levels III and IV (corresponding to the danger category). Metagenomic data revealed that the presence of MPs significantly affected the abundance of bacterial taxa; Flavobacteraceae and Nocardiaceae, which are known to degrade polymeric substances, were present in high-MP-contaminated sediments. This study provides new insights into the ecological relevance of MP pollution and suggests that microorganisms may serve as biomarkers of MP pollution.}, } @article {pmid38056648, year = {2024}, author = {Scicchitano, D and Babbi, G and Palladino, G and Turroni, S and Mekonnen, YT and Laczny, C and Wilmes, P and Leekitcharoenphon, P and Castagnetti, A and D'Amico, F and Brigidi, P and Savojardo, C and Manfreda, G and Martelli, P and De Cesare, A and Aarestrup, FM and Candela, M and Rampelli, S}, title = {Routes of dispersion of antibiotic resistance genes from the poultry farm system.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169086}, doi = {10.1016/j.scitotenv.2023.169086}, pmid = {38056648}, issn = {1879-1026}, mesh = {Animals ; Humans ; *Poultry ; Farms ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Microbiota ; Genes, Bacterial ; }, abstract = {Poultry farms are hotspots for the development and spread of antibiotic resistance genes (ARGs), due to high stocking densities and extensive use of antibiotics, posing a threat of spread and contagion to workers and the external environment. Here, we applied shotgun metagenome sequencing to characterize the gut microbiome and resistome of poultry, workers and their households - also including microbiomes from the internal and external farm environment - in three different farms in Italy during a complete rearing cycle. Our results highlighted a relevant overlap among the microbiomes of poultry, workers, and their families (gut and skin), with clinically relevant ARGs and associated mobile elements shared in both poultry and human samples. On a finer scale, the reconstruction of species-level genome bins (SGBs) allowed us to delineate the dynamics of microorganism and ARGs dispersion from farm systems. We found the associations with worker microbiomes representing the main route of ARGs dispersion from poultry to human populations. Collectively, our findings clearly demonstrate the urgent need to implement more effective procedures to counteract ARGs dispersion from poultry food systems and the relevance of metagenomics-based metacommunity approaches to monitor the ARGs dispersion process for the safety of the working environment on farms.}, } @article {pmid38056640, year = {2024}, author = {Zhu La, AT and Li, D and Cheng, Z and Wen, Q and Hu, D and Jin, X and Liu, D and Feng, Y and Guo, Y and Cheng, G and Hu, Y}, title = {Enzymatically prepared neoagarooligosaccharides improve gut health and function through promoting the production of spermidine by Faecalibacterium in chickens.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169057}, doi = {10.1016/j.scitotenv.2023.169057}, pmid = {38056640}, issn = {1879-1026}, mesh = {Chick Embryo ; Animals ; *Chickens/microbiology ; Spermidine/pharmacology ; Faecalibacterium ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Maintaining animal gut health through modulating the gut microbiota is a constant need when antibiotics are not used in animal feed during the food animal production process. Prebiotics is regarded as one of the most promising antibiotic alternatives for such purpose. As an attractive prebiotic, the role and mechanisms of neoagarooligosaccharides (NAOS) in promoting animal growth and gut health have not been elucidated. In this study, we first cloned and expressed marine bacterial β-agarase in yeast to optimize the NAOS preparation and then investigated the role and the underlying mechanisms of the prepared NAOS in improving chicken gut health and function. The marine bacterial β-agarase PDE13B was expressed in Pichia pastoris GS115 and generated even-numbered NAOS. Dietary the prepared NAOS promoted chicken growth and improved intestinal morphology, its barrier, and digestion capabilities, and absorption function. Metagenomic analysis indicated that NAOS modulated the chicken gut microbiota structure and function, and microbial interactions, and promoted the growth of spermidine-producing bacteria especially Faecalibacterium. Through integration of gut metagenome, gut content metabolome, and gut tissue transcriptome, we established connections among NAOS, gut microbes, spermidine, and chicken gut gene expression. The spermidine regulation of genes related to autophagy, immunity, and inflammation was further confirmed in chicken embryo intestinal epithelium cells. We also verified that NAOS can be utilized by Faecalibacterium prausnitzii to grow and produce spermidine in in vitro experiments. Collectively, we provide a systematic investigation of the role of NAOS in regulating gut health and demonstrate the microbial spermidine-mediated mechanism involved in prebiotic effects of NAOS, which lays foundation for future use of NAOS as a new antibiotic alternative in animal production.}, } @article {pmid38054728, year = {2024}, author = {Duarte, VdS and Porcellato, D}, title = {Host DNA depletion methods and genome-centric metagenomics of bovine hindmilk microbiome.}, journal = {mSphere}, volume = {9}, number = {1}, pages = {e0047023}, pmid = {38054728}, issn = {2379-5042}, mesh = {Female ; Cattle ; Animals ; Humans ; *Mastitis, Bovine/microbiology ; *Microbiota/genetics ; Milk/microbiology ; DNA ; }, abstract = {Bovine mastitis is a multi-etiological and complex disease, resulting in serious economic consequences for dairy farmers and industry. In recent years, the microbiological evaluation of raw milk has been investigated in-depth using next-generation sequencing approaches such as metataxonomic analysis. Despite this, host DNA is a major concern in the shotgun metagenomic sequencing of microbial communities in milk samples, and it represents a big challenge. In this study, we aimed to evaluate different methods for host DNA depletion and/or microbial DNA enrichment and assess the use of PCR-based whole genome amplification in milk samples with high somatic cell count (SCC) by using short- and long-read sequencing technologies. Our results evidenced that DNA extraction performed differently in terms of host DNA removal, impacting metagenome composition and functional profiles.. Moreover, the ratio of SCC/bacteria ultimately impacts microbial DNA yield, and samples with low SCC (SCC below 100,000 cells/mL) are the most problematic. When milk samples with high SCC (SCC above 200,000 cells/mL) underwent multiple-displacement amplification (MDA), we successfully recovered high-quality metagenome-assembled genomes (MAGs), and long-read sequencing was feasible even for samples with low DNA concentration. By associating MDA and short-read sequencing, we recovered two times more MAGs than in untreated samples, and an ongoing co-infection not reported by traditional methods was detected for mastitis pathogen. Overall, this new approach will improve the detection of mastitis-associated microorganisms and make it possible to examine host-microbiome interactions in bovine mastitis.IMPORTANCENext-generation sequencing technologies have been widely used to gain new insights into the diversity of the microbial community of milk samples and dairy products for different purposes such as microbial safety, profiling of starter cultures, and host-microbiome interactions. Milk is a complex food matrix, and additionally, the presence of host nucleic acid sequences is considered a contaminant in untargeted high-throughput sequencing studies. Therefore, genomic-centric metagenomic studies of milk samples focusing on the health-disease status in dairy cattle are still scarce, which makes it difficult to evaluate the microbial ecophysiology of bovine hindmilk. This study provides an alternative method for genome-centric metagenome studies applied to hindmilk samples with high somatic cell content, which is indispensable to examining host-microbiome interactions in bovine mastitis.}, } @article {pmid38054020, year = {2023}, author = {Du, L and Dong, X and Song, J and Lei, T and Liu, X and Lan, Y and Liu, X and Wang, J and Yue, B and He, M and Fan, Z and Guo, T}, title = {Temporal and spatial differences in the vaginal microbiome of Chinese healthy women.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16438}, pmid = {38054020}, issn = {2167-8359}, mesh = {Female ; Humans ; *East Asian People ; Vagina/microbiology ; Lactobacillus ; Cervix Uteri/microbiology ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Up the reproductive tract, there are large differences in the composition of vaginal microbes. Throughout the menstrual cycle, the structure of the vaginal microbiome shifts. Few studies have examined both in combination. Our study was designed to explore trends in the microbiome of different parts of the vagina in healthy women over the menstrual cycle.

METHODS: We performed metagenomic sequencing to characterize the microbiome differences between the cervical orifice and mid-vagina throughout the menstrual cycle.

RESULTS: Our results showed the vaginal microbiome of healthy women in the cervical orifice and the mid-vagina was similar during the periovulatory and luteal phases, with Lactobacillus being the dominant bacteria. In the follicular phase, Acinetobacter was detected in the cervical orifice. From the follicular phase to the luteal phase, the community state types (all five community status types were defined as CSTs) in samples No. 10 and No. 11 changed from CST III to CST I. In addition, the composition of the vaginal microbiome in healthy women from different regions of China was significantly different. We also detected viruses including Human alphaherpesvirus 1 (HSV-1) during periovulatory phase.

CONCLUSION: This study is valuable for understanding whether the microbial composition of the vagina is consistent in different parts of the menstrual cycle.}, } @article {pmid38051927, year = {2024}, author = {O'Dwyer, DN and Kim, JS and Ma, SF and Ranjan, P and Das, P and Lipinski, JH and Metcalf, JD and Falkowski, NR and Yow, E and Anstrom, K and Dickson, RP and Huang, Y and Gilbert, JA and Martinez, FJ and Noth, I}, title = {Commensal Oral Microbiota, Disease Severity, and Mortality in Fibrotic Lung Disease.}, journal = {American journal of respiratory and critical care medicine}, volume = {209}, number = {9}, pages = {1101-1110}, pmid = {38051927}, issn = {1535-4970}, support = {K23HL150301/HL/NHLBI NIH HHS/United States ; R01 HL130796/HL/NHLBI NIH HHS/United States ; S10 OD026929/OD/NIH HHS/United States ; R01 HL162659/HL/NHLBI NIH HHS/United States ; K23 HL150301/HL/NHLBI NIH HHS/United States ; U01 HL128964/HL/NHLBI NIH HHS/United States ; UH3 HL145266/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; Male ; Female ; *Microbiota ; Aged ; Middle Aged ; *Idiopathic Pulmonary Fibrosis/mortality/microbiology ; *Severity of Illness Index ; Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Proportional Hazards Models ; }, abstract = {Rationale: Oral microbiota associate with diseases of the mouth and serve as a source of lung microbiota. However, the role of oral microbiota in lung disease is unknown. Objectives: To determine associations between oral microbiota and disease severity and death in idiopathic pulmonary fibrosis (IPF). Methods: We analyzed 16S rRNA gene and shotgun metagenomic sequencing data of buccal swabs from 511 patients with IPF in the multicenter CleanUP-IPF (Study of Clinical Efficacy of Antimicrobial Therapy Strategy Using Pragmatic Design in IPF) trial. Buccal swabs were collected from usual care and antimicrobial cohorts. Microbiome data were correlated with measures of disease severity using principal component analysis and linear regression models. Associations between the buccal microbiome and mortality were determined using Cox additive models, Kaplan-Meier analysis, and Cox proportional hazards models. Measurements and Main Results: Greater buccal microbial diversity associated with lower FVC at baseline (mean difference, -3.60; 95% confidence interval [CI], -5.92 to -1.29% predicted FVC per 1-unit increment). The buccal proportion of Streptococcus correlated positively with FVC (mean difference, 0.80; 95% CI, 0.16 to 1.43% predicted per 10% increase) (n = 490). Greater microbial diversity was associated with an increased risk of death (hazard ratio, 1.73; 95% CI, 1.03-2.90), whereas a greater proportion of Streptococcus was associated with a reduced risk of death (HR, 0.85; 95% CI, 0.73 to 0.99). The Streptococcus genus was mainly composed of Streptococcus mitis species. Conclusions: Increasing buccal microbial diversity predicts disease severity and death in IPF. The oral commensal S. mitis spp associates with preserved lung function and improved survival.}, } @article {pmid38051631, year = {2024}, author = {Jo, J and Hu, C and Begum, K and Wang, W and Le, TM and Agyapong, S and Hanson, BM and Ayele, H and Lancaster, C and Jahangir Alam, M and Gonzales-Luna, AJ and Garey, KW}, title = {Fecal Pharmacokinetics and Gut Microbiome Effects of Oral Omadacycline Versus Vancomycin in Healthy Volunteers.}, journal = {The Journal of infectious diseases}, volume = {229}, number = {1}, pages = {273-281}, pmid = {38051631}, issn = {1537-6613}, support = {G0505124//Paratek Pharmaceuticals, Inc/ ; }, mesh = {Adult ; Humans ; Male ; Female ; Vancomycin/therapeutic use ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Anti-Bacterial Agents/therapeutic use ; Tetracyclines/pharmacology/therapeutic use ; *Clostridium Infections/microbiology ; }, abstract = {BACKGROUND: Clostridioides difficile infection (CDI) is a common healthcare-associated infection with limited treatment options. Omadacycline, an aminomethylcycline tetracycline, has potent in vitro activity against C difficile and a low propensity to cause CDI in clinical trials. We aimed to assess fecal pharmacokinetics and gut microbiome effects of oral omadacycline compared to oral vancomycin in healthy adults.

METHODS: This was a phase 1, nonblinded, randomized clinical trial conducted in healthy volunteers aged 18-40 years. Subjects received a 10-day course of omadacycline or vancomycin. Stool samples were collected at baseline, daily during therapy, and at follow-up visits. Omadacycline and vancomycin stool concentrations were assessed, and microbiome changes were compared.

RESULTS: Sixteen healthy volunteers with a mean age of 26 (standard deviation [SD], 5) years were enrolled; 62.5% were male, and participants' mean body mass index was 23.5 (SD, 4.0) kg/m2. Omadacycline was well tolerated with no safety signal differences between the 2 antibiotics. A rapid initial increase in fecal concentrations of omadacycline was observed compared to vancomycin, with maximum concentrations achieved within 48 hours. A significant difference in alpha diversity was observed following therapy in both the omadacycline and vancomycin groups (P < .05). Bacterial abundance and beta diversity analysis showed differing microbiome changes in subjects who received omadacycline versus vancomycin.

CONCLUSIONS: Subjects given omadacycline had high fecal concentrations with a distinct microbiome profile compared to vancomycin.

CLINICAL TRIALS REGISTRATION: NCT06030219.}, } @article {pmid38051048, year = {2024}, author = {Li, Y and Ma, J and Meng, J and Li, S and Zhang, Y and You, W and Sai, X and Yang, J and Zhang, S and Sun, W}, title = {Structural changes in the gut virome of patients with atherosclerotic cardiovascular disease.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0105023}, pmid = {38051048}, issn = {2165-0497}, support = {2180072120049//Beijing University of Chinese Medicine (BUCM)/ ; 81973849//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Humans ; Virome ; *Cardiovascular Diseases ; *Bacteriophages ; }, abstract = {Existing studies have found that there is a close relationship between human virome and numerous diseases, and diseases may affect the diversity and composition of the virome; at the same time, changes in the virome will in turn affect the onset and progression of the disease. However, the composition and functional capabilities of the gut virome associated with atherosclerotic cardiovascular disease (ACVD) have not been systematically investigated. To our knowledge, this is the first study investigating the gut virome in patients with ACVD. We characterized the structural changes in the gut virome of ACVD patients, which may facilitate additional mechanistic, diagnostic, and interventional studies of ACVD and related diseases.}, } @article {pmid38050061, year = {2024}, author = {Zhu, J and Sun, C and Li, M and Hu, G and Zhao, XM and Chen, WH}, title = {Compared to histamine-2 receptor antagonist, proton pump inhibitor induces stronger oral-to-gut microbial transmission and gut microbiome alterations: a randomised controlled trial.}, journal = {Gut}, volume = {73}, number = {7}, pages = {1087-1097}, pmid = {38050061}, issn = {1468-3288}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Histamine H2 Antagonists/pharmacology ; *Proton Pump Inhibitors/adverse effects/pharmacology ; Male ; Female ; Adult ; *Feces/microbiology ; Saliva/microbiology ; Healthy Volunteers ; Middle Aged ; Young Adult ; }, abstract = {OBJECTIVE: We aim to compare the effects of proton pump inhibitors (PPIs) and histamine-2 receptor antagonists (H2RAs) on the gut microbiota through longitudinal analysis.

DESIGN: Healthy volunteers were randomly assigned to receive either PPI (n=23) or H2RA (n=26) daily for seven consecutive days. We collected oral (saliva) and faecal samples before and after the intervention for metagenomic next-generation sequencing. We analysed intervention-induced alterations in the oral and gut microbiome including microbial abundance and growth rates, oral-to-gut transmissions, and compared differences between the PPI and H2RA groups.

RESULTS: Both interventions disrupted the gut microbiota, with PPIs demonstrating more pronounced effects. PPI usage led to a significantly higher extent of oral-to-gut transmission and promoted the growth of specific oral microbes in the gut. This led to a significant increase in both the number and total abundance of oral species present in the gut, including the identification of known disease-associated species like Fusobacterium nucleatum and Streptococcus anginosus. Overall, gut microbiome-based machine learning classifiers could accurately distinguish PPI from non-PPI users, achieving an area under the receiver operating characteristic curve (AUROC) of 0.924, in contrast to an AUROC of 0.509 for H2RA versus non-H2RA users.

CONCLUSION: Our study provides evidence that PPIs have a greater impact on the gut microbiome and oral-to-gut transmission than H2RAs, shedding light on the mechanism underlying the higher risk of certain diseases associated with prolonged PPI use.

TRIAL REGISTRATION NUMBER: ChiCTR2300072310.}, } @article {pmid38049420, year = {2023}, author = {Yersin, S and Garneau, JR and Schneeberger, PHH and Osman, KA and Cercamondi, CI and Muhummed, AM and Tschopp, R and Zinsstag, J and Vonaesch, P}, title = {Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {21342}, pmid = {38049420}, issn = {2045-2322}, support = {180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; P3P3PA_177877//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 7F-0057.01.02//Direktion für Entwicklung und Zusammenarbeit/ ; 7F-0057.01.02//Direktion für Entwicklung und Zusammenarbeit/ ; 7F-0057.01.02//Direktion für Entwicklung und Zusammenarbeit/ ; 7F-0057.01.02//Direktion für Entwicklung und Zusammenarbeit/ ; 7F-0057.01.02//Direktion für Entwicklung und Zusammenarbeit/ ; 2019-20//Nutricia Research Foundation/ ; 2019-20//Nutricia Research Foundation/ ; 2019-20//Nutricia Research Foundation/ ; 2020//Forschungsfonds der Universität Basel/ ; 2020//Forschungsfonds der Universität Basel/ ; 2020//Forschungsfonds der Universität Basel/ ; }, mesh = {Humans ; Child ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Ethiopia ; Bacteria/genetics ; Feces/microbiology ; Feeding Behavior ; }, abstract = {The composition and function of the intestinal microbiota are major determinants of human health and are strongly influenced by diet, antibiotic treatment, lifestyle and geography. Nevertheless, we currently have only little data on microbiomes of non-westernized communities. We assess the stool microbiota composition in 59 children aged 2-5 years from the Adadle district of Ethiopia, Somali Regional State. Here, milk and starch-rich food are predominant components of the local diet, where the inhabitants live a remote, traditional agropastoral lifestyle. Microbiota composition, function and the resistome were characterized by both 16S rRNA gene amplicon and shotgun metagenomic sequencing and compared to 1471 publicly available datasets from children living in traditional, transitional, and industrial communities with different subsistence strategies. Samples from the Adadle district are low in Bacteroidaceae, and Prevotellaceae, the main bacterial representatives in the feces of children living in industrialized and non-industrialized communities, respectively. In contrast, they had a higher relative abundance in Streptococcaceae, Bifidobacteriaceae and Erysipelatoclostridiaceae. Further, genes involved in degradation pathways of lactose, D-galactose and simple carbohydrates were enriched. Overall, our study revealed a unique composition of the fecal microbiota of these agropastoral children, highlighting the need to further characterize the fecal bacterial composition of human populations living different lifestyles.}, } @article {pmid38048871, year = {2024}, author = {Lan, W and Liu, H and Weng, R and Zeng, Y and Lou, J and Xu, H and Yu, Y and Jiang, Y}, title = {Microbial community of municipal drinking water in Hangzhou using metagenomic sequencing.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {342}, number = {}, pages = {123066}, doi = {10.1016/j.envpol.2023.123066}, pmid = {38048871}, issn = {1873-6424}, mesh = {Humans ; *Drinking Water/microbiology ; Pandemics ; Bacteria/genetics ; Archaea ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {While traditional culture-dependent methods can effectively detect certain microorganisms, the comprehensive composition of the municipal drinking water (DW) microbiome, including bacteria, archaea, and viruses, remains unknown. Metagenomic sequencing has opened the door to accurately determine and analyze the entire microbial community of DW, providing a comprehensive understanding of DW species diversity, especially in the context of public health concerns during the COVID-19 era. In this study, we found that most of the culturable bacteria and some fecal indicator bacteria, such as Escherichia coli and Pseudomonas aeruginosa, were non-culturable using culture-dependent methods in all samples. However, metagenomic analysis showed that the predominant bacterial species in the DW samples belonged to the phyla Proteobacteria and Planctomycetes. Notably, the genus Methylobacterium was the most abundant in all water samples, followed by Sphingomonas, Gemmata, and Azospirilum. While low levels of virulence-associated factors, such as the Esx-5 type VII secretion system (T7SS) and DevR/S, were detected, only the erythromycin resistance gene erm(X), an rRNA methyltransferase, was identified at low abundance in one sample. Hosts corresponding to virulence and resistance genes were identified in some samples, including Mycobacterium spp. Archaeal DNA (Euryarchaeota, Crenarchaeota) was found in trace amounts in some DW samples. Viruses such as rotavirus, coxsackievirus, human enterovirus, and SARS-CoV-2 were negative in all DW samples using colloidal gold and real-time reverse transcription polymerase chain reaction (RT‒PCR) methods. However, DNA encoding a new order of reverse-transcribing viruses (Ortervirales) and Herpesvirales was found in some DW samples. The metabolic pathways of the entire microbial community involve cell‒cell communication and signal secretion, contributing to cooperation between different microbial populations in the water. This study provides insight into the microbial community and metabolic process of DW in Hangzhou, China, utilizing both culture-dependent methods and metagenomic sequencing combined with bioinformatics tools during the COVID-19 pandemic era.}, } @article {pmid38047696, year = {2024}, author = {Klukowski, N and Eden, P and Uddin, MJ and Sarker, S}, title = {Virome of Australia's most endangered parrot in captivity evidenced of harboring hitherto unknown viruses.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0305223}, pmid = {38047696}, issn = {2165-0497}, mesh = {Animals ; *Parrots ; Virome ; *Viruses ; *Virus Diseases/epidemiology/veterinary ; Australia/epidemiology ; }, abstract = {The impact of circulating viruses on the critically endangered, orange-bellied parrot (OBP) population can be devastating. The OBP already faces numerous threats to its survival in the wild, including habitat loss, predation, and small population impacts. Conservation of the wild OBP population is heavily reliant on supplementation using OBPs from a managed captive breeding program. These birds may act as a source for introduction of a novel disease agent to the wild population that may affect survival and reproduction. It is, therefore, essential to monitor and assess the health of OBPs and take appropriate measures to prevent and control the spread of viral infections. This requires knowledge of the existing virome to identify novel and emerging viruses and support development of appropriate measures to manage associated risk. By monitoring and protecting these animals from emerging viral diseases, we can help ensure their ongoing survival and preserve the biodiversity of our planet.}, } @article {pmid38047031, year = {2023}, author = {Zhang, NN and Chen, XX and Liang, J and Zhao, C and Xiang, J and Luo, L and Wang, ET and Shi, F}, title = {Rhizocompartmental microbiomes of arrow bamboo (Fargesia nitida) and their relation to soil properties in Subalpine Coniferous Forests.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16488}, pmid = {38047031}, issn = {2167-8359}, mesh = {*Tracheophyta ; Soil ; beta-Fructofuranosidase ; Soil Microbiology ; *Microbiota/genetics ; Forests ; Bacteria/genetics ; Poaceae ; Plants ; Carbon ; Cellulose ; }, abstract = {Arrow bamboo (Fargesia nitida) is a pioneer plant in secondary forest succession in the Sichuan Province mountains. To comprehensively investigate the microbial communities and their functional variations in different rhizocompartments (root endosphere, rhizosphere, and root zone) of arrow bamboo (Fargesia nitida), a high-throughput metagenomic study was conducted in the present study. The results showed that the abundances of the dominant bacterial phyla Proteobacteria and Actinobacteria in the bamboo root endosphere were significantly lower than those in the rhizosphere and root zones. In contrast, the dominant fungal phyla, Ascomycota and Basidiomycota, showed the opposite tendency. Lower microbial diversity, different taxonomic composition and functional profiles, and a greater abundance of genes involved in nitrogen fixation (nifB), cellulose degradation (beta-glucosidase), and cellobiose transport (cellulose 1, 4-beta-cellobiosidase) were found in the bamboo root endosphere than in the other rhizocompartments. Greater soil total carbon, total nitrogen, NH4[+]-N, microbial biomass carbon, and greater activities of invertase and urease were found in the bamboo root zone than in the adjacent soil (spruce root zone). In contrast, the soil microbial community and functional profiles were similar. At the phylum level, invertase was significantly related to 31 microbial taxa, and the effect of NH4[+]-N on the microbial community composition was greater than that of NO3[-]-N. The soil physicochemical properties and enzyme activities were significantly correlated with microbial function. These results indicate that the root endosphere microbiomes of arrow bamboo were strongly selected by the host plant, which caused changes in the soil nutrient properties in the subalpine coniferous forest.}, } @article {pmid38043895, year = {2024}, author = {Li, Y and Li, R and Hou, J and Sun, X and Wang, Y and Li, L and Yang, F and Yao, Y and An, Y}, title = {Mobile genetic elements affect the dissemination of antibiotic resistance genes (ARGs) of clinical importance in the environment.}, journal = {Environmental research}, volume = {243}, number = {}, pages = {117801}, doi = {10.1016/j.envres.2023.117801}, pmid = {38043895}, issn = {1096-0953}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Clinical Relevance ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; *Microbiota/genetics ; Interspersed Repetitive Sequences ; }, abstract = {The prevalence of antibiotic resistance genes (ARGs) in the environment is a quintessential One Health issue that threats both human and ecosystem health; however, the source and transmission of ARGs, especially clinically important ARGs (CLIARGs), in the environment have not yet been well studied. In the present study, shotgun metagenomic approaches were used to characterize the microbiome, resistome, and mobilome composition in human feces and six different environment sample types in South China. Overall, the resistome harbored 157 CLIARGs, with specific ARG hotspots (e.g., human feces, wastewater treatment plants, livestock manure and wastewater) excreting significantly higher abundance of CLIARGs compared with the natural environment. A redundancy analysis (RDA) was performed and revealed that the bacterial community compositions and mobile genetic elements (MGEs) explained 55.08% and 34.68% of the variations in ARG abundance, respectively, indicating that both bacterial community and MGEs are key contributors to the maintenance and dissemination of CLIARGs in the environment. The network analysis revealed non-random co-occurrence patterns between 200 bacterial genera and 147 CLIARGs, as well as between 135 MGEs and 123 CLIARGs. In addition to numerous co-shared CLIARGs among different sample types, the source tracking program based on the FEAST probabilistic model was used to estimate the relative contributions of the CLIARGs from potential sources to the natural environment. The source tracking analysis results delineated that mobilome, more than microbiome, contributed CLIARG transmission from those ARG hotspots into natural environment, and the MGEs in WWTPs seem to play the most significant role in the spread of CLIARGs to the natural environment (average contribution 32.9%-46.4%). Overall, this study demonstrated the distribution and dissemination of CLIARGs in the environment, and aimed to better inform strategies to control the spread of CLIARGs into the natural environment.}, } @article {pmid38043772, year = {2024}, author = {Shahar, S and Sant, KE and Allsing, N and Kelley, ST}, title = {Metagenomic analysis of microbial communities and antibiotic resistant genes in the Tijuana river, and potential sources.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {342}, number = {}, pages = {123067}, pmid = {38043772}, issn = {1873-6424}, support = {K01 ES031640/ES/NIEHS NIH HHS/United States ; U54 MD012397/MD/NIMHD NIH HHS/United States ; }, mesh = {Humans ; *Rivers/microbiology ; Metagenome ; Sewage/microbiology ; Anti-Bacterial Agents ; Mexico ; *Microbiota ; Bacteria/genetics ; Genes, Bacterial ; Metagenomics ; }, abstract = {The Tijuana River is a transborder river that flows northwest across the border from Baja California in Mexico into Southern California before discharging into the Pacific Ocean. The river is frequently contaminated with raw sewage due to inadequate sanitary infrastructure in Tijuana. To assess the type and degree of microbial contamination, water samples were collected monthly from a near-border and an estuarine site from August 2020 until May 2021. A portion of each sample was used for epifluorescent microscopy and DNA was extracted directly from the rest for shotgun metagenomic sequencing. After sequence quality checking and processing, we used the rapid taxonomic identifier tool Kaiju to characterize the microbial diversity of the metagenomes and matched the sequences against the Comprehensive Antibiotic Resistance Database (CARD) to examine antimicrobial resistance genes (ARGs). Bacterial and viral-like particle (VLP) abundance was consistently higher in the near-border samples than in the estuarine samples, while alpha diversity (within sample biodiversity) was higher in estuarine samples. Beta-diversity analysis found clear compositional separation between samples from the two sites, and the near-border samples were more dissimilar to one another than were the estuarine sites. Near-border samples were dominated by fecal-associated bacteria and bacteria associated with sewage sludge, while estuarine sites were dominated by marine bacteria. ARGs were more abundant at the near-border site, but were also readily detectable in the estuarine samples, and the most abundant ARGs had multi-resistance to beta-lactam antibiotics. SourceTracker analysis identified human feces and sewage sludge to be the largest contributors to the near-border samples, while marine waters dominated estuarine samples except for two sewage overflow dates with high fecal contamination. Overall, our research determined human sewage microbes to be common in the Tijuana River, and the prevalence of ARGs confirms the importance of planned infrastructure treatment upgrades for environmental health.}, } @article {pmid38043766, year = {2024}, author = {Sabatino, R and Sbaffi, T and Corno, G and Cabello-Yeves, PJ and Di Cesare, A}, title = {The diversity of the antimicrobial resistome of lake Tanganyika increases with the water depth.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {342}, number = {}, pages = {123065}, doi = {10.1016/j.envpol.2023.123065}, pmid = {38043766}, issn = {1873-6424}, mesh = {Humans ; Lakes ; Water ; Tanzania ; *Anti-Infective Agents ; Genes, Bacterial ; Anti-Bacterial Agents ; *Microbiota ; }, abstract = {The presence of antimicrobial resistance genes (ARGs) in the microbiome of freshwater communities is a consequence of thousands of years of evolution but also of the pressure exerted by anthropogenic activities, with potential negative impact on environmental and human health. In this study, we investigated the distribution of ARGs in Lake Tanganyika (LT)'s water column to define the resistome of this ancient lake. Additionally, we compared the resistome of LT with that of Lake Baikal (LB), the oldest known lake with different environmental characteristics and a lower anthropogenic pollution than LT. We found that richness and abundance of several antimicrobial resistance classes were higher in the deep water layers in both lakes. LT Kigoma region, known for its higher anthropogenic pollution, showed a greater richness and number of ARG positive MAGs compared to Mahale. Our results provide a comprehensive understanding of the antimicrobial resistome of LT and underscore its importance as reservoir of antimicrobial resistance. In particular, the deepest water layers of LT are the main repository of diverse ARGs, mirroring what was observed in LB and in other aquatic ecosystems. These findings suggest that the deep waters might play a crucial role in the preservation of ARGs in aquatic ecosystems.}, } @article {pmid38042820, year = {2023}, author = {Swarte, JC and Knobbe, TJ and Björk, JR and Gacesa, R and Nieuwenhuis, LM and Zhang, S and Vila, AV and Kremer, D and Douwes, RM and Post, A and Quint, EE and Pol, RA and Jansen, BH and , and de Borst, MH and de Meijer, VE and Blokzijl, H and Berger, SP and Festen, EAM and Zhernakova, A and Fu, J and Harmsen, HJM and Bakker, SJL and Weersma, RK}, title = {Health-related quality of life is linked to the gut microbiome in kidney transplant recipients.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7968}, pmid = {38042820}, issn = {2041-1723}, mesh = {Humans ; Quality of Life ; *Gastrointestinal Microbiome/genetics ; *Kidney Transplantation/adverse effects ; Feces/microbiology ; Dysbiosis/microbiology ; }, abstract = {Kidney transplant recipients (KTR) have impaired health-related quality of life (HRQoL) and suffer from intestinal dysbiosis. Increasing evidence shows that gut health and HRQoL are tightly related in the general population. Here, we investigate the association between the gut microbiome and HRQoL in KTR, using metagenomic sequencing data from fecal samples collected from 507 KTR. Multiple bacterial species are associated with lower HRQoL, many of which have previously been associated with adverse health conditions. Gut microbiome distance to the general population is highest among KTR with an impaired physical HRQoL (R = -0.20, P = 2.3 × 10[-65]) and mental HRQoL (R = -0.14, P = 1.3 × 10[-3]). Physical and mental HRQoL explain a significant part of variance in the gut microbiome (R[2] = 0.58%, FDR = 5.43 × 10[-4] and R[2] = 0.37%, FDR = 1.38 × 10[-3], respectively). Additionally, multiple metabolic and neuroactive pathways (gut brain modules) are associated with lower HRQoL. While the observational design of our study does not allow us to analyze causality, we provide a comprehensive overview of the associations between the gut microbiome and HRQoL while controlling for confounders.}, } @article {pmid38042069, year = {2024}, author = {Zhao, Y and Yu, S and Tan, J and Wang, Y and Li, L and Zhao, H and Liu, M and Jiang, L}, title = {Bioconversion of citrus waste by long-term DMSO-cryopreserved rumen fluid to volatile fatty acids and biogas is feasible: A microbiome perspective.}, journal = {Journal of environmental management}, volume = {351}, number = {}, pages = {119693}, doi = {10.1016/j.jenvman.2023.119693}, pmid = {38042069}, issn = {1095-8630}, mesh = {Animals ; Dimethyl Sulfoxide/metabolism ; Biofuels ; Food ; Rumen/metabolism ; *Refuse Disposal ; Fatty Acids, Volatile/metabolism ; Fermentation ; *Microbiota ; Methane ; Diet ; Fatty Acids/metabolism ; Animal Feed/analysis ; }, abstract = {Preserving rumen fluid as the inoculum for anaerobic digestion of food waste is necessary when access to animal donors or slaughterhouses is limited. This study aims to compare two preservation methods relative to fresh ruminal inoculum: (1) cryoprotected with 5% dimethyl sulfoxide (DMSO) and stored at -20 °C and (2) frozen at -20 °C, both for 6 months. The fermentation activity of different inoculum was evaluated by rumen-based in vitro anaerobic fermentation tests (volatile fatty acids, biomass digestibility, and gas production). Citrus pomace was used as the substrate during a 96-h fermentation. The maximum volatile fatty acids, methane production, and citrus pomace digestibility from fresh rumen fluid were not significantly different from rumen fluid preserved with DMSO. Metagenome analysis revealed a significant difference in the rumen microbial composition and functions between fresh rumen fluid and frozen inoculum without DMSO. Storage of rumen fluid using -20 °C with DMSO demonstrated the less difference compared with fresh rumen fluid in microbial alpha diversity and taxa composition. The hierarchical clustering tree of CAZymes showed that DMSO cryoprotected fluid was clustered much closer to the fresh rumen fluid, showing more similarity in CAZyme profiles than frozen rumen fluid. The abundance of functional genes associated with carbohydrate metabolism and methane metabolism did not differ between fresh rumen fluid and the DMSO-20 °C, whereas the abundance of key functional genes significantly decreased in frozen rumen fluid. These findings suggest that using rumen liquid preserved using DMSO at -20 °C for 180 days is a feasible alternative to fresh rumen fluid. This would reduce the need for laboratories to maintain animal donors and/or reduce the frequency of collecting rumen fluid from slaughterhouses.}, } @article {pmid38041547, year = {2024}, author = {Li, Y and Rao, G and Zhu, G and Cheng, C and Yuan, L and Li, C and Gao, J and Tang, J and Wang, Z and Li, W}, title = {Dysbiosis of lower respiratory tract microbiome are associated with proinflammatory states in non-small cell lung cancer patients.}, journal = {Thoracic cancer}, volume = {15}, number = {2}, pages = {111-121}, pmid = {38041547}, issn = {1759-7714}, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung ; *Lung Neoplasms/microbiology ; Dysbiosis/microbiology ; *Microbiota ; Lung ; Cytokines ; Tumor Microenvironment ; }, abstract = {BACKGROUND: The lung has a sophisticated microbiome, and respiratory illnesses are greatly influenced by the lung microbiota. Despite the fact that numerous studies have shown that lung cancer patients have a dysbiosis as compared to healthy people, more research is needed to explore the association between the microbiota dysbiosis and immune profile within the tumor microenvironment (TME).

METHODS: In this study, we performed metagenomic sequencing of tumor and normal tissues from 61 non-small cell lung cancer (NSCLC) patients and six patients with other lung diseases. In order to characterize the impact of the microbes in TME, the cytokine concentrations of 24 lung tumor and normal tissues were detected using a multiple cytokine panel.

RESULTS: Our results showed that tumors had lower microbiota diversity than the paired normal tissues, and the microbiota of NSCLC was enriched in Proteobacteria, Firmicutes, and Actinobacteria. In addition, proinflammatory cytokines such as IL-8, MIF, TNF- α, and so on, were significantly upregulated in tumor tissues.

CONCLUSION: We discovered a subset of bacteria linked to host inflammatory signaling pathways and, more precisely, to particular immune cells. We determined that lower airway microbiome dysbiosis may be linked to the disruption of the equilibrium of the immune system causing lung inflammation. The spread of lung cancer may be linked to specific bacteria.}, } @article {pmid38040541, year = {2023}, author = {Zhang, X and Irajizad, E and Hoffman, KL and Fahrmann, JF and Li, F and Seo, YD and Browman, GJ and Dennison, JB and Vykoukal, J and Luna, PN and Siu, W and Wu, R and Murage, E and Ajami, NJ and McQuade, JL and Wargo, JA and Long, JP and Do, KA and Lampe, JW and Basen-Engquist, KM and Okhuysen, PC and Kopetz, S and Hanash, SM and Petrosino, JF and Scheet, P and Daniel, CR}, title = {Modulating a prebiotic food source influences inflammation and immune-regulating gut microbes and metabolites: insights from the BE GONE trial.}, journal = {EBioMedicine}, volume = {98}, number = {}, pages = {104873}, pmid = {38040541}, issn = {2352-3964}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Prebiotics ; *Gastrointestinal Microbiome ; Proteomics ; Obesity/microbiology ; Inflammation ; }, abstract = {BACKGROUND: Accessible prebiotic foods hold strong potential to jointly target gut health and metabolic health in high-risk patients. The BE GONE trial targeted the gut microbiota of obese surveillance patients with a history of colorectal neoplasia through a straightforward bean intervention.

METHODS: This low-risk, non-invasive dietary intervention trial was conducted at MD Anderson Cancer Center (Houston, TX, USA). Following a 4-week equilibration, patients were randomized to continue their usual diet without beans (control) or to add a daily cup of study beans to their usual diet (intervention) with immediate crossover at 8-weeks. Stool and fasting blood were collected every 4 weeks to assess the primary outcome of intra and inter-individual changes in the gut microbiome and in circulating markers and metabolites within 8 weeks. This study was registered on ClinicalTrials.gov as NCT02843425, recruitment is complete and long-term follow-up continues.

FINDINGS: Of the 55 patients randomized by intervention sequence, 87% completed the 16-week trial, demonstrating an increase on-intervention in diversity [n = 48; linear mixed effect and 95% CI for inverse Simpson index: 0.16 (0.02, 0.30); p = 0.02] and shifts in multiple bacteria indicative of prebiotic efficacy, including increased Faecalibacterium, Eubacterium and Bifidobacterium (all p < 0.05). The circulating metabolome showed parallel shifts in nutrient and microbiome-derived metabolites, including increased pipecolic acid and decreased indole (all p < 0.002) that regressed upon returning to the usual diet. No significant changes were observed in circulating lipoproteins within 8 weeks; however, proteomic biomarkers of intestinal and systemic inflammatory response, fibroblast-growth factor-19 increased, and interleukin-10 receptor-α decreased (p = 0.01).

INTERPRETATION: These findings underscore the prebiotic and potential therapeutic role of beans to enhance the gut microbiome and to regulate host markers associated with metabolic obesity and colorectal cancer, while further emphasizing the need for consistent and sustainable dietary adjustments in high-risk patients.

FUNDING: This study was funded by the American Cancer Society.}, } @article {pmid38040289, year = {2024}, author = {Mbow, FT and Akbari, A and Dopffel, N and Schneider, K and Mukherjee, S and Meckenstock, RU}, title = {Insights into the effects of anthropogenic activities on oil reservoir microbiome and metabolic potential.}, journal = {New biotechnology}, volume = {79}, number = {}, pages = {30-38}, doi = {10.1016/j.nbt.2023.11.004}, pmid = {38040289}, issn = {1876-4347}, mesh = {Humans ; Oil and Gas Fields ; Anthropogenic Effects ; Bacteria/metabolism ; *Microbiota ; Water ; *Disinfectants/metabolism ; }, abstract = {Microbial communities have long been observed in oil reservoirs, where the subsurface conditions are major drivers shaping their structure and functions. Furthermore, anthropogenic activities such as water flooding during oil production can affect microbial activities and community compositions in oil reservoirs through the injection of recycled produced water, often associated with biocides. However, it is still unclear to what extent the introduced chemicals and microbes influence the metabolic potential of the subsurface microbiome. Here we investigated an onshore oilfield in Germany (Field A) that undergoes secondary oil production along with biocide treatment to prevent souring and microbially induced corrosion (MIC). With the integrated approach of 16 S rRNA gene amplicon and shotgun metagenomic sequencing of water-oil samples from 4 production wells and 1 injection well, we found differences in microbial community structure and metabolic functions. In the injection water samples, amplicon sequence variants (ASVs) belonging to families such as Halanaerobiaceae, Ectothiorhodospiraceae, Hydrogenophilaceae, Halobacteroidaceae, Desulfohalobiaceae, and Methanosarcinaceae were dominant, while in the production water samples, ASVs of families such as Thermotogaceae, Nitrospiraceae, Petrotogaceae, Syntrophaceae, Methanobacteriaceae, and Thermoprotei were also dominant. The metagenomic analysis of the injection water sample revealed the presence of C1-metabolism, namely, genes involved in formaldehyde oxidation. Our analysis revealed that the microbial community structure of the production water samples diverged slightly from that of injection water samples. Additionally, a metabolic potential for oxidizing the applied biocide clearly occurred in the injection water samples indicating an adaptation and buildup of degradation capacity or resistance against the added biocide.}, } @article {pmid38039804, year = {2024}, author = {Duan, B and Gan, M and Xu, Z and Chen, WX}, title = {Tonsil microbiome in pediatric patients with post tonsillectomy hemorrhage for tonsillar hypertrophy.}, journal = {International journal of pediatric otorhinolaryngology}, volume = {176}, number = {}, pages = {111788}, doi = {10.1016/j.ijporl.2023.111788}, pmid = {38039804}, issn = {1872-8464}, mesh = {Child ; Humans ; Palatine Tonsil/surgery/microbiology ; *Tonsillectomy/adverse effects ; Hemorrhage ; *Microbiota ; Hypertrophy ; Neisseria ; }, abstract = {OBJECTIVE: This study aimed to compare the tonsillar microbiota between post tonsillectomy patients with bleeding and without bleeding, and to investigate the potential role of tonsillar microbiota in the development of post-tonsillectomy hemorrhage (PTH).

METHODS: Nineteen tonsillar tissues from PTH patients and 21 tissues from control patients were collected. Metagenomic sequencing was used to compare the microbiota in PTH and control groups. Alpha diversity indices were used to compare the richness and evenness of the microbiota between the two groups. PCoA and NMDS analyses were used to evaluate beta diversity. LDA analysis was conducted to identify significantly abundant genera.

RESULTS: No significant difference in alpha diversity indices was found between PTH and control patients. The dominant bacteria in the tonsillar microbiota were Haemophilus, Streptococcus, and Fusobacterium. PCoA and NMDS analyses showed significant differences in beta diversity between PTH and control patients. PTH patients had a significantly higher relative abundance of Neisseria, Capnocytophaga, and Veillonella. Capnocytophaga was also identified as a significantly abundant genus by LDA analysis.

CONCLUSION: This study demonstrates that there is a difference in the tonsillar microbiota between PTH and control patients. The results suggest that Neisseria, Capnocytophaga, and Veillonella may be associated with the development of PTH. These findings provide new insights into the potential role of the tonsillar microbiota in the development of PTH, and may help to develop new strategies for preventing and treating this potentially life-threatening complication.}, } @article {pmid38038385, year = {2023}, author = {Li, CC and Hsu, WF and Chiang, PC and Kuo, MC and Wo, AM and Tseng, YJ}, title = {Characterization of markers, functional properties, and microbiome composition in human gut-derived bacterial extracellular vesicles.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2288200}, pmid = {38038385}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; Feces/microbiology ; Bacteria/genetics ; *Extracellular Vesicles ; RNA, Ribosomal, 16S/genetics ; DNA ; }, abstract = {Past studies have confirmed the etiologies of bacterial extracellular vesicles (BEVs) in various diseases, including inflammatory bowel disease (IBD) and colorectal cancer (CRC). This study aimed to investigate the characteristics of stool-derived bacterial extracellular vesicles (stBEVs) and discuss their association with stool bacteria. First, three culture models - gram-positive (G+)BcBEVs (from B.coagulans), gram-negative (G-)EcBEVs (from E.coli), and eukaryotic cell-derived EVs (EEV, from Colo205 cell line) - were used to benchmark various fractions of stEVs separated from optimized density gradient approach (DG). As such, WB, TEM, NTA, and functional assays, were utilized to analyze properties and distribution of EVs in cultured and stool samples. Stool samples from healthy individuals were interrogated using the approaches developed. Results demonstrated successful separation of most stBEVs (within DG fractions 8&9) from stEEVs (within DG fractions 5&6). Data also suggest the presence of stBEV DNA within vesicles after extraction of BEV DNA and DNase treatment. Metagenomic analysis from full-length (FL) region sequencing results confirmed significant differences between stool bacteria and stBEVs. Significantly, F8&9 and the pooled sample (F5-F9) exhibited a similar microbial composition, indicating that F8&9 were enriched in most stBEV species, primarily dominated by Firmicutes (89.6%). However, F5&6 and F7 still held low-density BEVs with a significantly higher proportion of Proteobacteria (20.5% and 40.7%, respectively) and Bacteroidetes (24% and 13.7%, respectively), considerably exceeding the proportions in stool and F8&9. Importantly, among five healthy individuals, significant variations were observed in the gut microbiota composition of their respective stBEVs, indicating the potential of stBEVs as a target for personalized medicine and research.}, } @article {pmid38037712, year = {2024}, author = {Gao, M and Xiong, C and Tsui, CKM and Cai, L}, title = {Pathogen invasion increases the abundance of predatory protists and their prey associations in the plant microbiome.}, journal = {Molecular ecology}, volume = {33}, number = {3}, pages = {e17228}, doi = {10.1111/mec.17228}, pmid = {38037712}, issn = {1365-294X}, support = {32330002//National Natural Science Foundation of China/ ; }, mesh = {Plants ; *Microbiota ; *Mycobiome ; Bacteria/genetics ; Soil ; Soil Microbiology ; *Ciliophora ; }, abstract = {Soil and plant-associated protistan communities play a key role in shaping bacterial and fungal communities, primarily through their function as top-down predators. However, our understanding of how pathogen invasion influences these protistan communities and their relationships with bacterial and fungal communities remains limited. Here, we studied the protistan communities along the soil-plant continuum of healthy chilli peppers and those affected by Fusarium wilt disease (FWD), and integrated bacterial and fungal community data from our previous research. Our research showed that FWD was associated with a significant enrichment of phagotrophic protists in roots, and also increased the proportion and connectivity of these protists (especially Cercozoa and Ciliophora) in both intra- and inter-kingdom networks. Furthermore, the microbiome of diseased plants not only showed a higher relative abundance of functional genes related to bacterial anti-predator responses than healthy plants, but also contained a greater abundance of metagenome-assembled genomes with functional traits involved in this response. The increased microbial inter-kingdom associations between bacteria and protists, coupled with the notable bacterial anti-predator feedback in the microbiome of diseased plants, suggest that FWD may catalyse the associations between protists and their microbial prey. These findings highlight the potential role of predatory protists in influencing microbial assembly and functionality through top-down forces under pathogenic stress.}, } @article {pmid38036921, year = {2023}, author = {Gallardo-Becerra, L and Cervantes-Echeverría, M and Cornejo-Granados, F and Vazquez-Morado, LE and Ochoa-Leyva, A}, title = {Perspectives in Searching Antimicrobial Peptides (AMPs) Produced by the Microbiota.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {8}, pmid = {38036921}, issn = {1432-184X}, support = {Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnología/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnología/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnología/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnología/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnología/ ; PAPIIT UNAM (IN219723)//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; PAPIIT UNAM (IN219723)//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; PAPIIT UNAM (IN219723)//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; PAPIIT UNAM (IN219723)//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; PAPIIT UNAM (IN219723)//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; }, mesh = {Humans ; *Antimicrobial Cationic Peptides/genetics/pharmacology ; Antimicrobial Peptides ; Bacteria/genetics ; *Microbiota/genetics ; Anti-Bacterial Agents ; }, abstract = {Changes in the structure and function of the microbiota are associated with various human diseases. These microbial changes can be mediated by antimicrobial peptides (AMPs), small peptides produced by the host and their microbiota, which play a crucial role in host-bacteria co-evolution. Thus, by studying AMPs produced by the microbiota (microbial AMPs), we can better understand the interactions between host and bacteria in microbiome homeostasis. Additionally, microbial AMPs are a new source of compounds against pathogenic and multi-resistant bacteria. Further, the growing accessibility to metagenomic and metatranscriptomic datasets presents an opportunity to discover new microbial AMPs. This review examines the structural properties of microbiota-derived AMPs, their molecular action mechanisms, genomic organization, and strategies for their identification in any microbiome data as well as experimental testing. Overall, we provided a comprehensive overview of this important topic from the microbial perspective.}, } @article {pmid38036425, year = {2024}, author = {Doolin, ML and Dearing, MD}, title = {Differential Effects of Two Common Antiparasitics on Microbiota Resilience.}, journal = {The Journal of infectious diseases}, volume = {229}, number = {3}, pages = {908-917}, doi = {10.1093/infdis/jiad547}, pmid = {38036425}, issn = {1537-6613}, support = {//University of Utah/ ; }, mesh = {Animals ; Mice ; Antiparasitic Agents/pharmacology ; *Resilience, Psychological ; *Microbiota ; *Gastrointestinal Microbiome ; Metronidazole ; Albendazole ; }, abstract = {BACKGROUND: Parasitic infections challenge vertebrate health worldwide, and off-target effects of antiparasitic treatments may be an additional obstacle to recovery. However, there have been few investigations of the effects of antiparasitics on the gut microbiome in the absence of parasites.

METHODS: We investigated whether two common antiparasitics-albendazole (ALB) and metronidazole (MTZ)-significantly alter the gut microbiome of parasite-free mice. We treated mice with ALB or MTZ daily for 7 days and sampled the fecal microbiota immediately before and after treatment and again after a two-week recovery period.

RESULTS: ALB did not immediately change the gut microbiota, while MTZ decreased microbial richness by 8.5% and significantly changed community structure during treatment. The structural changes caused by MTZ included depletion of the beneficial family Lachnospiraceae, and predictive metagenomic analysis revealed that these losses likely depressed microbiome metabolic function. Separately, we compared the fecal microbiotas of treatment groups after recovery, and there were minor differences in community structure between the ALB, MTZ, and sham-treated control groups.

CONCLUSIONS: These results suggest that a healthy microbiome is resilient after MTZ-induced depletions of beneficial gut microbes, and ALB may cause slight, latent shifts in the microbiota but does not deplete healthy gut microbiota diversity.}, } @article {pmid38035404, year = {2024}, author = {Lindner, BG and Gerhardt, K and Feistel, DJ and Rodriguez-R, LM and Hatt, JK and Konstantinidis, KT}, title = {A user's guide to the bioinformatic analysis of shotgun metagenomic sequence data for bacterial pathogen detection.}, journal = {International journal of food microbiology}, volume = {410}, number = {}, pages = {110488}, doi = {10.1016/j.ijfoodmicro.2023.110488}, pmid = {38035404}, issn = {1879-3460}, mesh = {*Metagenome ; *Microbiota/genetics ; Metagenomics/methods ; Computational Biology ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; }, abstract = {Metagenomics, i.e., shotgun sequencing of the total microbial community DNA from a sample, has become a mature technique but its application to pathogen detection in clinical, environmental, and food samples is far from common or standardized. In this review, we summarize ongoing developments in metagenomic sequence analysis that facilitate its wider application to pathogen detection. We examine theoretical frameworks for estimating the limit of detection for a particular level of sequencing effort, current approaches for achieving species and strain analytical resolution, and discuss some relevant modern tools for these tasks. While these recent advances are significant and establish metagenomics as a powerful tool to provide insights not easily attained by culture-based approaches, metagenomics is unlikely to emerge as a widespread, routine monitoring tool in the near future due to its inherently high detection limits, cost, and inability to easily distinguish between viable and non-viable cells. Instead, metagenomics seems best poised for applications involving special circumstances otherwise challenging for culture-based and molecular (e.g., PCR-based) approaches such as the de novo detection of novel pathogens, cases of co-infection by more than one pathogen, and situations where it is important to assess the genomic composition of the pathogenic population(s) and/or its impact on the indigenous microbiome.}, } @article {pmid38034829, year = {2023}, author = {Monleón-Getino, A and Pujol-Muncunill, G and Méndez Viera, J and Álvarez Carnero, L and Sanseverino, W and Paytuví-Gallart, A and Martín de Carpí, J}, title = {A pilot study of the use of the oral and faecal microbiota for the diagnosis of ulcerative colitis and Crohn's disease in a paediatric population.}, journal = {Frontiers in pediatrics}, volume = {11}, number = {}, pages = {1220976}, pmid = {38034829}, issn = {2296-2360}, abstract = {Crohn's disease (CD) and ulcerative colitis (UC) are chronic inflammatory bowel diseases (IBD) that affect the gastrointestinal tract. Changes in the microbiome and its interaction with the immune system are thought to play a key role in their development. The aim of this study was to determine whether metagenomic analysis is a feasible non-invasive diagnostic tool for IBD in paediatric patients. A pilot study of oral and faecal microbiota was proposed with 36 paediatric patients divided in three cohorts [12 with CD, 12 with UC and 12 healthy controls (HC)] with 6 months of follow-up. Finally, 30 participants were included: 13 with CD, 11 with UC and 8 HC (6 dropped out during follow-up). Despite the small size of the study population, a differential pattern of microbial biodiversity was observed between IBD patients and the control group. Twenty-one bacterial species were selected in function of their discriminant accuracy, forming three sets of potential markers of IBD. Although IBD diagnosis requires comprehensive medical evaluation, the findings of this study show that faecal metagenomics or a reduced set of bacterial markers could be useful as a non-invasive tool for an easier and earlier diagnosis.}, } @article {pmid38031968, year = {2023}, author = {Beauvais, M and Schatt, P and Montiel, L and Logares, R and Galand, PE and Bouget, FY}, title = {Functional redundancy of seasonal vitamin B12 biosynthesis pathways in coastal marine microbial communities.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {3753-3770}, doi = {10.1111/1462-2920.16545}, pmid = {38031968}, issn = {1462-2920}, support = {//Agence Nationale de la Recherche (ANR)/ ; }, mesh = {*Vitamin B 12/metabolism ; Seasons ; Archaea/genetics/metabolism ; *Microbiota ; Vitamins/metabolism ; }, abstract = {Vitamin B12 (cobalamin) is a major cofactor required by most marine microbes, but only produced by a few prokaryotes in the ocean, which is globally B12 -depleted. Despite the ecological importance of B12 , the seasonality of B12 metabolisms and the organisms involved in its synthesis in the ocean remain poorly known. Here we use metagenomics to assess the monthly dynamics of B12 -related pathways and the functional diversity of associated microbial communities in the coastal NW Mediterranean Sea over 7 years. We show that genes related to potential B12 metabolisms were characterized by an annual succession of different organisms carrying distinct production pathways. During the most productive winter months, archaea (Nitrosopumilus and Nitrosopelagicus) were the main contributors to B12 synthesis potential through the anaerobic pathway (cbi genes). In turn, Alphaproteobacteria (HIMB11, UBA8309, Puniceispirillum) contributed to B12 synthesis potential in spring and summer through the aerobic pathway (cob genes). Cyanobacteria could produce pseudo-cobalamin from spring to autumn. Finally, we show that during years with environmental perturbations, the organisms usually carrying B12 synthesis genes were replaced by others having the same gene, thus maintaining the potential for B12 production. Such ecological insurance could contribute to the long-term functional resilience of marine microbial communities exposed to contrasting inter-annual environmental conditions.}, } @article {pmid38031339, year = {2023}, author = {Kamenova, S and de Muinck, EJ and Veiberg, V and Utsi, TA and Steyaert, SMJG and Albon, SD and Loe, LE and Trosvik, P}, title = {Gut microbiome biogeography in reindeer supersedes millennia of ecological and evolutionary separation.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {12}, pages = {}, pmid = {38031339}, issn = {1574-6941}, support = {//Horizon 2020/ ; }, mesh = {Animals ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract ; Metagenome ; *Reindeer/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Ruminants are dependent on their gut microbiomes for nutrient extraction from plant diets. However, knowledge about the composition, diversity, function, and spatial structure of gut microbiomes, especially in wild ruminants, is limited, largely because analysis has been restricted to faeces or the rumen. In two geographically separated reindeer subspecies, 16S rRNA gene amplicon sequencing revealed strong spatial structuring, and pronounced differences in microbial diversity of at least 33 phyla across the stomach, small intestine, and large intestine (including faeces). The main structural feature was the Bacteroidota to Firmicutes ratio, which declined from the stomach to the large intestine, likely reflecting functional adaptation. Metagenome shotgun sequencing also revealed highly significant structuring in the relative occurrence of carbohydrate-active enzymes (CAZymes). CAZymes were enriched in the rumen relative to the small and large intestines. Interestingly, taxonomic diversity was highest in the large intestine, suggesting an important and understudied role for this organ. Despite the two study populations being separated by an ocean and six millennia of evolutionary history, gut microbiome structuring was remarkably consistent. Our study suggests a strong selection for gut microbiome biogeography along the gastrointestinal tract in reindeer subspecies.}, } @article {pmid38031142, year = {2023}, author = {Holm, JB and France, MT and Gajer, P and Ma, B and Brotman, RM and Shardell, M and Forney, L and Ravel, J}, title = {Integrating compositional and functional content to describe vaginal microbiomes in health and disease.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {259}, pmid = {38031142}, issn = {2049-2618}, support = {R01 NR015495/NR/NINR NIH HHS/United States ; R01-NR015495/NR/NINR NIH HHS/United States ; R01 AG069915/AG/NIA NIH HHS/United States ; R01 AI116799/AI/NIAID NIH HHS/United States ; F32 AI136400/AI/NIAID NIH HHS/United States ; K01 AI163413/AI/NIAID NIH HHS/United States ; UH2 AI083264/AI/NIAID NIH HHS/United States ; U19 AI158930/AI/NIAID NIH HHS/United States ; U19 AI084044/AI/NIAID NIH HHS/United States ; }, mesh = {Female ; Humans ; Vagina/microbiology ; *Vaginosis, Bacterial/microbiology ; Bacteria/genetics ; Gardnerella vaginalis/genetics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: A Lactobacillus-dominated vaginal microbiome provides the first line of defense against adverse genital tract health outcomes. However, there is limited understanding of the mechanisms by which the vaginal microbiome modulates protection, as prior work mostly described its composition through morphologic assessment and marker gene sequencing methods that do not capture functional information. To address this gap, we developed metagenomic community state types (mgCSTs) which use metagenomic sequences to describe and define vaginal microbiomes based on both composition and functional potential.

RESULTS: MgCSTs are categories of microbiomes classified using taxonomy and the functional potential encoded in their metagenomes. MgCSTs reflect unique combinations of metagenomic subspecies (mgSs), which are assemblages of bacterial strains of the same species, within a microbiome. We demonstrate that mgCSTs are associated with demographics such as age and race, as well as vaginal pH and Gram stain assessment of vaginal smears. Importantly, these associations varied between mgCSTs predominated by the same bacterial species. A subset of mgCSTs, including three of the six predominated by Gardnerella vaginalis mgSs, as well as mgSs of L. iners, were associated with a greater likelihood of bacterial vaginosis diagnosed by Amsel clinical criteria. This L. iners mgSs, among other functional features, encoded enhanced genetic capabilities for epithelial cell attachment that could facilitate cytotoxin-mediated cell lysis. Finally, we report a mgSs and mgCST classifier for which source code is provided and may be adapted for use by the microbiome research community.

CONCLUSIONS: MgCSTs are a novel and easily implemented approach to reduce the dimension of complex metagenomic datasets while maintaining their functional uniqueness. MgCSTs enable the investigation of multiple strains of the same species and the functional diversity in that species. Future investigations of functional diversity may be key to unraveling the pathways by which the vaginal microbiome modulates the protection of the genital tract. Importantly, our findings support the hypothesis that functional differences between vaginal microbiomes, including those that may look compositionally similar, are critical considerations in vaginal health. Ultimately, mgCSTs may lead to novel hypotheses concerning the role of the vaginal microbiome in promoting health and disease, and identify targets for novel prognostic, diagnostic, and therapeutic strategies to improve women's genital health. Video Abstract.}, } @article {pmid38031016, year = {2023}, author = {Li, P and Jiang, J and Li, Y and Lan, Y and Yang, F and Wang, J and Xie, Y and Xiong, F and Wu, J and Liu, H and Fan, Z}, title = {Metagenomic analysis reveals distinct changes in the gut microbiome of obese Chinese children.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {721}, pmid = {38031016}, issn = {1471-2164}, support = {No. 2023YFS0034 and 2020YFS0109//the Science and Technology Bureau of Sichuan Province/ ; No. KL119//the Clinical Discipline Development Fund of West China Second Hospital, Sichuan University/ ; SCU2022D022//the Fundamental Research Funds for the Central Universities/ ; }, mesh = {Humans ; Child ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Pediatric Obesity/genetics ; East Asian People ; Overweight ; Feces/microbiology ; }, abstract = {BACKGROUND: The prevalence of obese children in China is increasing, which poses a great challenge to public health. Gut microbes play an important role in human gut health, and changes in gut status are closely related to obesity. However, how gut microbes contribute to obesity in children remains unclear. In our study, we performed shotgun metagenomic sequencing of feces from 23 obese children, 8 overweight children and 22 control children in Chengdu, Sichuan, China.

RESULTS: We observed a distinct difference in the gut microbiome of obese children and that of controls. Compared with the controls, bacterial pathogen Campylobacter rectus was significantly more abundant in obese children. In addition, functional annotation of microbial genes revealed that there might be gut inflammation in obese children. The guts of overweight children might belong to the transition state between obese and control children due to a gradient in relative abundance of differentially abundant species. Finally, we compared the gut metagenomes of obese Chinese children and obese Mexican children and found that Trichuris trichiura was significantly more abundant in the guts of obese Mexican children.

CONCLUSIONS: Our results contribute to understanding the changes in the species and function of intestinal microbes in obese Chinese children.}, } @article {pmid38030652, year = {2023}, author = {Bacci, G and Meriggi, N and Cheng, CLY and Ng, KH and Iannucci, A and Mengoni, A and Cavalieri, D and Cannicci, S and Fratini, S}, title = {Species-specific gill's microbiome of eight crab species with different breathing adaptations.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {21033}, pmid = {38030652}, issn = {2045-2322}, support = {207080320.088562.26020.430.01//Hong Kong Government/ ; 260008686.088562.26000.400.01//TUYF Charitable Trust funds, Hong Kong/ ; CN00000033//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; }, mesh = {Humans ; Animals ; *Brachyura/physiology ; Gills/metabolism ; Respiration ; Respiratory Rate ; *Microbiota ; }, abstract = {Transitions to physically different environments, such as the water-to-land transition, proved to be the main drivers of relevant evolutionary events. Brachyuran crabs evolved remarkable morphological, behavioral, and physiological adaptations to terrestrial life. Terrestrial species evolved new respiratory structures devoted to replace or support the gills, a multifunctional organ devoted to gas exchanges, ion-regulation and nitrogen excretion. It was hypothesized that microorganisms associated with respiratory apparatus could have facilitated the processes of osmoregulation, respiration, and elimination of metabolites along this evolutionary transition. To test if crab species with different breathing adaptations may host similar microbial communities on their gills, we performed a comparative targeted-metagenomic analysis, selecting two marine and six terrestrial crabs belonging to different families and characterised by different breathing adaptations. We analysed anterior and posterior gills separately according to their different and specific roles. Regardless of their terrestrial or marine adaptations, microbial assemblages were strongly species-specific indicating a non-random association between the host and its microbiome. Significant differences were found in only two terrestrial species when considering posterior vs. anterior gills, without any association with species-specific respiratory adaptations. Our results suggest that all the selected species are strongly adapted to the ecological niche and specific micro-habitat they colonise.}, } @article {pmid38026022, year = {2023}, author = {Tarnowski, MJ and Varliero, G and Scown, J and Phelps, E and Gorochowski, TE}, title = {Soil as a transdisciplinary research catalyst: from bioprospecting to biorespecting.}, journal = {Royal Society open science}, volume = {10}, number = {11}, pages = {230963}, pmid = {38026022}, issn = {2054-5703}, abstract = {The vast microbial biodiversity of soils is beginning to be observed and understood by applying modern DNA sequencing techniques. However, ensuring this potentially valuable information is used in a fair and equitable way remains a challenge. Here, we present a public engagement project that explores this topic through collaborative research of soil microbiomes at six urban locations using nanopore-based DNA sequencing. The project brought together researchers from the disciplines of synthetic biology, environmental humanities and microbial ecology, as well as school students aged 14-16 years old, to gain a broader understanding of views on the use of data from the environment. Discussions led to the transformation of 'bioprospecting', a metaphor with extractive connotations which is often used to frame environmental DNA sequencing studies, towards a more collaborative approach-'biorespecting'. This shift in terminology acknowledges that genetic information contained in soil arises as a result of entire ecosystems, including the people involved in its creation. Therefore, any use of sequence information should be accountable to the ecosystems from which it arose. As knowledge can arise from ecosystems and communities, science and technology should acknowledge this link and reciprocate with care and benefit-sharing to help improve the wellbeing of future generations.}, } @article {pmid38022583, year = {2023}, author = {Liu, X and van Beek, N and Cepic, A and Andreani, NA and Chung, CJ and Hermes, BM and Yilmaz, K and Benoit, S and Drenovska, K and Gerdes, S and Gläser, R and Goebeler, M and Günther, C and von Georg, A and Hammers, CM and Holtsche, MM and Hübner, F and Kiritsi, D and Schauer, F and Linnenmann, B and Huilaja, L and Tasanen-Määttä, K and Vassileva, S and Zillikens, D and Sadik, CD and Schmidt, E and Ibrahim, S and Baines, JF}, title = {The gut microbiome in bullous pemphigoid: implications of the gut-skin axis for disease susceptibility.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1212551}, pmid = {38022583}, issn = {1664-3224}, mesh = {Humans ; Aged ; *Gastrointestinal Microbiome/physiology ; *Pemphigoid, Bullous ; RNA, Ribosomal, 16S/genetics ; Disease Susceptibility ; Pilot Projects ; gamma-Aminobutyric Acid ; }, abstract = {Bullous pemphigoid (BP) is an autoimmune blistering disease that primarily affects the elderly. An altered skin microbiota in BP was recently revealed. Accumulating evidence points toward a link between the gut microbiota and skin diseases; however, the gut microbiota composition of BP patients remains largely underexplored, with only one pilot study to date, with a very limited sample size and no functional profiling of gut microbiota. To thoroughly investigate the composition and function of the gut microbiota in BP patients, and explore possible links between skin conditions and gut microbiota, we here investigated the gut microbiota of 66 patients (81.8% firstly diagnosed) suffering from BP and 66 age-, sex-, and study center-matched controls (CL) with non-inflammatory skin diseases (132 total participants), using 16S rRNA gene and shotgun sequencing data. Decreased alpha-diversity and an overall altered gut microbial community is observed in BP patients. Similar trends are observed in subclassifications of BP patients, including first diagnoses and relapsed cases. Furthermore, we observe a set of BP disease-associated gut microbial features, including reduced Faecalibacterium prausnitzii and greater abundance of pathways related to gamma-aminobutyric acid (GABA) metabolism in BP patients. Interestingly, F. prausnitzii is a well-known microbiomarker of inflammatory diseases, which has been reported to be reduced in the gut microbiome of atopic dermatitis and psoriasis patients. Moreover, GABA plays multiple roles in maintaining skin health, including the inhibition of itching by acting as a neurotransmitter, attenuating skin lesions by balancing Th1 and Th2 levels, and maintaining skin elasticity by increasing the expression of type I collagen. These findings thus suggest that gut microbiota alterations present in BP may play a role in the disease, and certain key microbes and functions may contribute to the link between gut dysbiosis and BP disease activity. Further studies to investigate the underlying mechanisms of the gut-skin interaction are thus clearly warranted, which could aid in the development of potential therapeutic interventions.}, } @article {pmid38020223, year = {2023}, author = {Elshafey, N and Mansour, MAI and Hamedo, HA and Elnosary, ME and Hagagy, N and Ahmed Al-Ghamdi, A and María Martínez-Espinosa, R}, title = {Phylogeny and functional diversity of halophilic microbial communities from a thalasso environment.}, journal = {Saudi journal of biological sciences}, volume = {30}, number = {12}, pages = {103841}, pmid = {38020223}, issn = {1319-562X}, abstract = {The El-Rawda solar saltern, located in North Sinai, Egypt, is formed through the process of water evaporation from the Bradawil lagoon. This evaporation leads to the precipitation of gypsum, halite minerals, and salt flats, which subsequently cover the southern and eastern areas of the lagoon. This study employed the shotgun metagenomic approach, the illumine platform, and bioinformatic tools to investigate the taxonomic composition and functional diversity of halophilic microbial communities in solar saltern. The metagenomic reads obtained from the brine sample exhibited a greater count compared to those from the sediment sample. Notably, the brine sample was primarily characterized by an abundance of archaea, while the sediment sample displayed a dominant abundance of bacteria. Both samples exhibited a relatively low abundance of eukaryotes, while viruses were only found in the brine sample. Furthermore, the comparative analysis of functional pathways showed many important processes related to central metabolism and protein processing in brine and sediment samples. In brief, this research makes a valuable contribution to the understanding of very halophilic ecosystems in Egypt, providing insights into their microbial biodiversity and functional processes.}, } @article {pmid38019198, year = {2023}, author = {Cavalcante, JVF and de Souza, ID and Morais, DAA and Dalmolin, RJS}, title = {Bridging the Gaps in Meta-Omic Analysis: Workflows and Reproducibility.}, journal = {Omics : a journal of integrative biology}, volume = {27}, number = {12}, pages = {547-549}, doi = {10.1089/omi.2023.0232}, pmid = {38019198}, issn = {1557-8100}, mesh = {Humans ; Workflow ; Reproducibility of Results ; *Software ; *Microbiota/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {The past few years have seen significant advances in the study of complex microbial communities associated with the evolution of sequencing technologies and increasing adoption of whole genome shotgun sequencing methods over the once more traditional Amplicon-based methods. Although these advances have broadened the horizon of meta-omic analyses in planetary health, human health, and ecology from simple sample composition studies to comprehensive taxonomic and metabolic profiles, there are still significant challenges in processing these data. First, there is a widespread lack of standardization in data processing, including software choices and the ease of installing and running attendant software. This can lead to several inconsistencies, making comparing results across studies and reproducing original results difficult. We argue that these drawbacks are especially evident in metatranscriptomic analysis, with most analyses relying on ad hoc scripts instead of pipelines implemented in workflow managers. Additional challenges rely on integrating meta-omic data, since methods have to consider the biases in the library preparation and sequencing methods and the technical noise that can arise from it. Here, we critically discuss the current limitations in metagenomics and metatranscriptomics methods with a view to catalyze future innovations in the field of Planetary Health, ecology, and allied fields of life sciences. We highlight possible solutions for these constraints to bring about more standardization, with ease of installation, high performance, and reproducibility as guiding principles.}, } @article {pmid38018980, year = {2024}, author = {Freeman, CN and Russell, JN and Yost, CK}, title = {Temporal metagenomic characterization of microbial community structure and nitrogen modification genes within an activated sludge bioreactor system.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0283223}, pmid = {38018980}, issn = {2165-0497}, mesh = {*Sewage ; Nitrogen ; *Microbiota/genetics ; Wastewater ; Bioreactors ; }, abstract = {Wastewater treatment plays an essential role in minimizing negative impacts on downstream aquatic environments. Microbial communities are known to play a vital role in the wastewater treatment process, particularly in the removal of nitrogen and phosphorus, which can be especially damaging to aquatic ecosystems. There is limited understanding of how these microbial communities may change in response to fluctuating temperatures or how seasonality may impact their ability to participate in the treatment process. The findings of this study indicate that the microbial communities of wastewater are relatively stable both compositionally and functionally across fluctuating temperatures.}, } @article {pmid38017705, year = {2023}, author = {Delavy, M and Sertour, N and Patin, E and Le Chatelier, E and Cole, N and Dubois, F and Xie, Z and Saint-André, V and Manichanh, C and Walker, AW and Quintana-Murci, L and Duffy, D and d'Enfert, C and Bougnoux, ME and Consortium, MI}, title = {Unveiling Candida albicans intestinal carriage in healthy volunteers: the role of micro- and mycobiota, diet, host genetics and immune response.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2287618}, pmid = {38017705}, issn = {1949-0984}, mesh = {Humans ; *Candida albicans/physiology ; Genome-Wide Association Study ; *Gastrointestinal Microbiome/physiology ; Diet ; Immunity ; }, abstract = {Candida albicans is a commensal yeast present in the gut of most healthy individuals but with highly variable concentrations. However, little is known about the host factors that influence colonization densities. We investigated how microbiota, host lifestyle factors, and genetics could shape C. albicans intestinal carriage in 695 healthy individuals from the Milieu Intérieur cohort. C. albicans intestinal carriage was detected in 82.9% of the subjects using quantitative PCR. Using linear mixed models and multiway-ANOVA, we explored C. albicans intestinal levels with regard to gut microbiota composition and lifestyle factors including diet. By analyzing shotgun metagenomics data and C. albicans qPCR data, we showed that Intestinimonas butyriciproducens was the only gut microbiota species whose relative abundance was negatively correlated with C. albicans concentration. Diet is also linked to C. albicans growth, with eating between meals and a low-sodium diet being associated with higher C. albicans levels. Furthermore, by Genome-Wide Association Study, we identified 26 single nucleotide polymorphisms suggestively associated with C. albicans colonization. In addition, we found that the intestinal levels of C. albicans might influence the host immune response, specifically in response to fungal challenge. We analyzed the transcriptional levels of 546 immune genes and the concentration of 13 cytokines after whole blood stimulation with C. albicans cells and showed positive associations between the extent of C. albicans intestinal levels and NLRP3 expression, as well as secreted IL-2 and CXCL5 concentrations. Taken together, these findings open the way for potential new interventional strategies to curb C. albicans intestinal overgrowth.}, } @article {pmid38017389, year = {2023}, author = {Tsakmaklis, A and Farowski, F and Zenner, R and Lesker, TR and Strowig, T and Schlößer, H and Lehmann, J and von Bergwelt-Baildon, M and Mauch, C and Schlaak, M and Knuever, J and Schweinsberg, V and Heinzerling, LM and Vehreschild, MJGT}, title = {TIGIT[+] NK cells in combination with specific gut microbiota features predict response to checkpoint inhibitor therapy in melanoma patients.}, journal = {BMC cancer}, volume = {23}, number = {1}, pages = {1160}, pmid = {38017389}, issn = {1471-2407}, support = {70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; }, mesh = {Receptors, Immunologic ; *Gastrointestinal Microbiome ; Immune Checkpoint Inhibitors/pharmacology/therapeutic use ; *Skin Neoplasms/drug therapy ; Prospective Studies ; Killer Cells, Natural ; *Melanoma/drug therapy ; Humans ; Bacteroidetes ; }, abstract = {BACKGROUND: Composition of the intestinal microbiota has been correlated to therapeutic efficacy of immune checkpoint inhibitors (ICI) in various cancer entities including melanoma. Prediction of the outcome of such therapy, however, is still unavailable. This prospective, non-interventional study was conducted in order to achieve an integrated assessment of the connection between a specific intestinal microbiota profile and antitumor immune response to immune checkpoint inhibitor therapy (anti-PD-1 and/or anti-CTLA-4) in melanoma patients.

METHODS: We assessed blood and stool samples of 29 cutaneous melanoma patients who received immune checkpoint inhibitor therapy. For functional and phenotypical immune analysis, 12-color flow cytometry and FluoroSpot assays were conducted. Gut microbiome was analyzed with shotgun metagenomics sequencing. To combine clinical, microbiome and immune variables, we applied the Random Forest algorithm.

RESULTS: A total of 29 patients was analyzed in this study, among whom 51.7% (n = 15) reached a durable clinical benefit. The Immune receptor TIGIT is significantly upregulated in T cells (p = 0.0139) and CD56[high] NK cells (p = 0.0037) of responders. Several bacterial taxa were associated with response (e.g. Ruminococcus torques) or failure (e.g. Barnesiella intestinihominis) to immune therapy. A combination of two microbiome features (Barnesiella intestinihominis and the Enterobacteriaceae family) and one immune feature (TIGIT[+] CD56[high] NK cells) was able to predict response to ICI already at baseline (AUC = 0.85; 95% CI: 0.841-0.853).

CONCLUSIONS: Our results reconfirm a link between intestinal microbiota and response to ICI therapy in melanoma patients and furthermore point to TIGIT as a promising target for future immunotherapies.}, } @article {pmid38017305, year = {2023}, author = {Singha, NA and Neihsial, R and Kipgen, L and Lyngdoh, WJ and Nongdhar, J and Chettri, B and Singh, P and Singh, AK}, title = {Taxonomic and Predictive Functional Profile of Hydrocarbonoclastic Bacterial Consortia Developed at Three Different Temperatures.}, journal = {Current microbiology}, volume = {81}, number = {1}, pages = {22}, pmid = {38017305}, issn = {1432-0991}, mesh = {Temperature ; RNA, Ribosomal, 16S/genetics/metabolism ; *Microbial Consortia/genetics ; Hydrocarbons/metabolism ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; *Petroleum/metabolism ; Bacteroidetes/genetics ; }, abstract = {Microbial community exhibit shift in composition in response to temperature variation. We report crude oil-degrading activity and high-throughput 16S rRNA gene sequencing (metagenome) profiles of four bacterial consortia enriched at three different temperatures in crude oil-amended Bushnell-Hass Medium from an oily sludge sediment. The consortia were referred to as O (4 ± 2 ℃ in 3% w/v crude oil), A (25 ± 2 ℃ in 1% w/v crude oil), H (25 ± 2 ℃ in 3% w/v crude oil), and X (45 ± 2 ℃ in 3% w/v crude oil). The hydrocarbon-degrading activity was highest for consortium A and H and lowest for consortium O. The metagenome profile revealed the predominance of Proteobacteria (62.12-1.25%) in each consortium, followed by Bacteroidota (18.94-37.77%) in the consortium O, A, and H. Contrarily, consortium X comprised 7.38% Actinomycetota, which was essentially low (< 0.09%) in other consortia, and only 0.41% Bacteroidota. The PICRUSt-based functional analysis predicted major functions associated with the metabolism and 5060 common KEGG Orthology (KOs). A total of 296 KOs were predicted exclusively in consortium X. Additionally, 247 KOs were predicted from xenobiotic biodegradation pathways. This study found that temperature had a stronger influence on the composition and function of the bacterial community than crude oil concentration.}, } @article {pmid38016379, year = {2024}, author = {Kavita, and Om, H and Chand, U and Kushawaha, PK}, title = {Postbiotics: An alternative and innovative intervention for the therapy of inflammatory bowel disease.}, journal = {Microbiological research}, volume = {279}, number = {}, pages = {127550}, doi = {10.1016/j.micres.2023.127550}, pmid = {38016379}, issn = {1618-0623}, mesh = {Female ; Male ; Humans ; *Inflammatory Bowel Diseases/therapy/microbiology ; Intestines/microbiology ; *Microbiota ; Bacteria ; *Gastrointestinal Microbiome ; *Gastrointestinal Diseases ; *Probiotics/therapeutic use ; }, abstract = {Inflammatory Bowel Disease (IBD) is a persistent gastrointestinal (GI) tract inflammatory disease characterized by downregulated mucosal immune activities and a disrupted microbiota environment in the intestinal lumen. The involvement of bacterium postbiotics as mediators between the immune system and gut microbiome could be critical in determining why host-microbial relationships are disrupted in IBD. Postbiotics including Short-chain fatty acids (SCFAs), Organic acids, Proteins, Vitamins, Bacteriocins, and Tryptophan (Trp) are beneficial bioactive compounds formed via commensal microbiota in the gut environment during the fermentation process that can be used to improve consumer health. The use of metabolites or fragments from microorganisms can be a very attractive treatment and prevention technique in modern medicine. Postbiotics are essential in the immune system's development since they alter the barrier tightness, and the gut ecology and indirectly shape the microbiota's structure. As a result, postbiotics may be beneficial in treating or preventing various diseases, even some for which there is no effective causative medication. Postbiotics may be a promising tool for the treatment of IBD in individuals of all ages, genders, and even geographical locations. Direct distribution of postbiotics may provide a new frontier in microbiome-based therapy for IBD since it allows both the management of host homeostasis and the correction of the negative implications of dysbiosis. Further studies of the biological effects of these metabolites are expected to reveal innovative applications in medicine and beyond. This review attempts to explore the possible postbiotic-based interventions for the treatment of IBD.}, } @article {pmid38016224, year = {2024}, author = {Ke, Y and Sun, W and Xue, Y and Zhu, Y and Yan, S and Xie, S}, title = {Effects of treatments and distribution on microbiome and antibiotic resistome from source to tap water in three Chinese geographical regions based on metagenome assembly.}, journal = {Water research}, volume = {249}, number = {}, pages = {120894}, doi = {10.1016/j.watres.2023.120894}, pmid = {38016224}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents/pharmacology ; Metagenome ; *Drinking Water/analysis ; Genes, Bacterial ; *Microbiota ; China ; }, abstract = {Antibiotic resistance genes (ARGs) represent emerging environmental pollutants that present health risks. Drinking water supply systems (DWSSs), including sources to tap water, play crucial roles in the dissemination and propagation of ARGs. However, there was a paucity of knowledge on the relative abundance, diversity, mobility, and pathogenic hosts of ARGs in DWSSs from source to tap. Therefore, the effects of treatments and distributions on the microbial community and ARGs from three geographical regions (downstream areas of the Yellow, Yangtze, and Pearl Rivers) were elucidated in the present study. Treatment processes lowered the complexity of the microbial community network, whereas transportation increased it. The assembly mechanisms of the microbial community and antibiotic resistome were primarily driven by stochastic processes. Distribution greatly increased the contribution of stochastic processes. Multidrug ARGs (for example, multidrug transporter and adeJ) and bacitracin ARG (bacA) were the primary mobile ARGs in drinking water, as identified by the metagenomic assembly. Achromobacter xylosoxidans, Acinetobacter calcoaceticus, and Acinetobacter junii harbored diverse multidrug ARGs and mobile genetic elements (MGEs) (recombinases, integrases, and transposases) as potential pathogens and were abundant in the disinfected water. Environmental factors, including pH, chlorine, latitude, longitude, and temperature, influenced the ARG abundance by directly regulating the MGEs and microbial community diversity. This study provides critical information on the fate, mobility, host pathogenicity, and driving factors of ARGs in drinking water, which is conducive to ARG risk assessment and management to provide high-quality drinking water to consumers.}, } @article {pmid38016054, year = {2023}, author = {Ilinskaya, ON and Gafarova, LF and Kurdy, W and Kolpakov, AI and Yakovleva, GY}, title = {[Microbiome of therapeutic muds used in Tatarstan].}, journal = {Voprosy kurortologii, fizioterapii, i lechebnoi fizicheskoi kultury}, volume = {100}, number = {5}, pages = {27-35}, doi = {10.17116/kurort202310005127}, pmid = {38016054}, issn = {0042-8787}, mesh = {Tatarstan ; *Microbiota ; Bacteria/genetics ; Sulfides ; Anti-Bacterial Agents ; }, abstract = {UNLABELLED: Therapeutic muds (peloids), which are widely used for body healing, improve metabolism and have antibacterial, anti-inflammatory and analgesic effects due to enrichment with necessary microelements and biological active substances. However, the microbiological component of these effects is not well studied.

OBJECTIVE: To characterize the microbiome of therapeutic muds, used in the Tatarstan Republic, by identifying spectrum of cultivated microorganisms, using molecular analysis of bacterial communities, and by determining their biodiversity and functional potential based on revealed genetic determinants.

MATERIAL AND METHODS: The study design of 5 peloids samples (local sapropels and peat deposits of swamp; 3 samples of Crimean sulfide muds) included three main techniques: isolation and taxonomic determination of cultivated microorganisms by time-of-flight mass-spectrometry; molecular analysis of peloids bacterial communities by 16S RNA high-throughput sequencing; identification of functional profiles of communities by their genetic determinant using Global Mapper tool on iVikodak platform.

RESULTS: Experimental studies have confirmed the safety of examined peloids, where non-pathogenic cultivated bacteria belonging mainly to Bacillus and Rhodococcus genera were dominant. Metagenomic analysis showed that Firmicutes, Proteobacteria and Actinobacteria were predominant in all samples in different ratios. It has been established, that there is both the internal biodiversity of each sample and difference between them. The functional profile of microbial communities was determined based on the identification of bacterial genes. It has been revealed that all communities have an ability to synthesize antibiotics, as well as to decompose dangerous xenobiotics - polyaromatic hydrocarbons, cyclic compounds, and dioxins.

CONCLUSION: Various microbial communities, which were identified in the therapeutic muds, contribute both to the clearance of toxicants in the peloids and to the antibacterial properties of the latter. The obtained priority results create a fundamental basis for the subsequent study of the role of peloids' microbiome of different origin in their healing action.}, } @article {pmid38015634, year = {2023}, author = {Gurczynski, SJ and Lipinski, JH and Strauss, J and Alam, S and Huffnagle, GB and Ranjan, P and Kennedy, LH and Moore, BB and O'Dwyer, DN}, title = {Horizontal transmission of gut microbiota attenuates mortality in lung fibrosis.}, journal = {JCI insight}, volume = {9}, number = {1}, pages = {}, pmid = {38015634}, issn = {2379-3708}, support = {R00 HL139996/HL/NHLBI NIH HHS/United States ; R01 HL162659/HL/NHLBI NIH HHS/United States ; R56 HL155055/HL/NHLBI NIH HHS/United States ; }, mesh = {Mice ; Animals ; Humans ; *Gastrointestinal Microbiome/physiology ; *Pulmonary Fibrosis ; Mice, Inbred C57BL ; Lung ; *Microbiota/physiology ; }, abstract = {Pulmonary fibrosis is a chronic and often fatal disease. The pathogenesis is characterized by aberrant repair of lung parenchyma, resulting in loss of physiological homeostasis, respiratory failure, and death. The immune response in pulmonary fibrosis is dysregulated. The gut microbiome is a key regulator of immunity. The role of the gut microbiome in regulating the pulmonary immunity in lung fibrosis is poorly understood. Here, we determine the impact of gut microbiota on pulmonary fibrosis in substrains of C57BL/6 mice derived from different vendors (C57BL/6J and C57BL/6NCrl). We used germ-free models, fecal microbiota transplantation, and cohousing to transmit gut microbiota. Metagenomic studies of feces established keystone species between substrains. Pulmonary fibrosis was microbiota dependent in C57BL/6 mice. Gut microbiota were distinct by β diversity and α diversity. Mortality and lung fibrosis were attenuated in C57BL/6NCrl mice. Elevated CD4+IL-10+ T cells and lower IL-6 occurred in C57BL/6NCrl mice. Horizontal transmission of microbiota by cohousing attenuated mortality in C57BL/6J mice and promoted a transcriptionally altered pulmonary immunity. Temporal changes in lung and gut microbiota demonstrated that gut microbiota contributed largely to immunological phenotype. Key regulatory gut microbiota contributed to lung fibrosis, generating rationale for human studies.}, } @article {pmid38014976, year = {2024}, author = {Zhuang, Y and Guo, W and Cui, K and Tu, Y and Diao, Q and Zhang, N and Bi, Y and Ma, T}, title = {Altered microbiota, antimicrobial resistance genes, and functional enzyme profiles in the rumen of yak calves fed with milk replacer.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0131423}, pmid = {38014976}, issn = {2165-0497}, support = {2022YFA1304201//MOST | National Key Research and Development Program of China (NKPs)/ ; 32222081//MOST | National Natural Science Foundation of China (NSFC)/ ; Y2022QC10//Youth Innovation Program of CAAS/ ; CAAS-ASTIP-2017-FRI-04//CAAS | Agricultural Science and Technology Innovation Program (ASTIP)/ ; }, mesh = {Animals ; Cattle ; Anti-Bacterial Agents/pharmacology/metabolism ; Butyrates ; Drug Resistance, Bacterial/genetics ; *Microbiota/genetics ; *Milk ; Rumen/microbiology ; }, abstract = {Yaks, as ruminants inhabiting high-altitude environments, possess a distinct rumen microbiome and are resistant to extreme living conditions. This study investigated the microbiota, resistome, and functional gene profiles in the rumen of yaks fed milk or milk replacer (MR), providing insights into the regulation of the rumen microbiome and the intervention of antimicrobial resistance in yaks through dietary methods. The abundance of Prevotella members increased significantly in response to MR. Tetracycline resistance was the most predominant. The rumen of yaks contained multiple antimicrobial resistance genes (ARGs) originating from different bacteria, which could be driven by MR, and these ARGs displayed intricate and complex interactions. MR also induced changes in functional genes. The enzymes associated with fiber degradation and butyrate metabolism were activated and showed close correlations with Prevotella members and butyrate concentration. This study allows us to deeply understand the ruminal microbiome and ARGs of yaks and their relationship with rumen bacteria in response to different milk sources.}, } @article {pmid38014952, year = {2023}, author = {Meyer Cifuentes, IE and Degenhardt, J and Neumann-Schaal, M and Jehmlich, N and Ngugi, DK and Öztürk, B}, title = {Comparative biodegradation analysis of three compostable polyesters by a marine microbial community.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {12}, pages = {e0106023}, pmid = {38014952}, issn = {1098-5336}, support = {//BASF/ ; }, mesh = {Polyesters/metabolism ; Plastics/metabolism ; Polymers ; *Biodegradable Plastics/metabolism ; Biodegradation, Environmental ; *Microbiota ; }, abstract = {Biodegradable plastics can be used in applications where the end product cannot be efficiently recycled due to high levels of contaminations, e.g., food or soil. Some of these plastics have a dedicated end of life, such as composting, but their degradation in the marine environment is poorly understood. In this study we showed that marine microbial communities can degrade a range of biodegradable polymers with different physical and chemical properties and use these as a sole carbon source for growth. We have also provided insights into the degradation mechanisms using a combined metagenomic and metaproteomic approach. In addition, we have identified three new enzymes that are capable of degrading both aliphatic polymers and aliphatic-aromatic copolymers, which can be used for biotechnological applications.}, } @article {pmid38013035, year = {2024}, author = {Dong, W and Zhou, R and Li, X and Yan, H and Zheng, J and Peng, N and Zhao, S}, title = {Effect of simplified inoculum agent on performance and microbiome during cow manure-composting at industrial-scale.}, journal = {Bioresource technology}, volume = {393}, number = {}, pages = {130097}, doi = {10.1016/j.biortech.2023.130097}, pmid = {38013035}, issn = {1873-2976}, mesh = {Animals ; Female ; Cattle ; *Composting ; Manure ; Soil ; *Microbiota/genetics ; *Bacillus ; }, abstract = {A simplified inoculum agent, only comprising Bacillus subtilis and Aspergillus niger, was utilized for industrial-scale cow-manure composting to investigate its impact on composting performance and microbiome. Inoculants elevated the average and peak temperatures by up to 7 and 10 °C, respectively, during the thermophilic stage, reduced organic matter content, and raised germination index. Inoculation also extended the period of composting above 50 °C from 12 to 26 days. Sequencing unveiled significant shifts in microbial diversity, composition, and function. Aspergillus thrived during the mesophilic phase, potentially initiating composting, whereas Bacillus, Lysinibacillus, and Clostridium were enriched during the thermophilic stage. Metagenomic sequencing revealed an increased abundance of carbohydrate-active enzymes and glycometabolism-related genes responsible for lignocellulose degradation and heat generation after inoculation. These enriched microbes and functional genes contributed to organic matter degradation and temperature maintenance during thermophilic stage, expediting composting. This suggests the effectiveness of this simplified inoculum in industrial-level cow-manure composting.}, } @article {pmid38010871, year = {2023}, author = {Jinato, T and Sikaroodi, M and Fagan, A and Sterling, RK and Lee, H and Puri, P and Davis, BC and Fuchs, M and Gavis, E and Gillevet, PM and Bajaj, JS}, title = {Alterations in gut virome are associated with cognitive function and minimal hepatic encephalopathy cross-sectionally and longitudinally in cirrhosis.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2288168}, pmid = {38010871}, issn = {1949-0984}, support = {I01 CX001076/CX/CSRD VA/United States ; I01 CX002472/CX/CSRD VA/United States ; R01 AA029398/AA/NIAAA NIH HHS/United States ; }, mesh = {Humans ; *Hepatic Encephalopathy ; Virome ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Liver Cirrhosis/complications ; Fibrosis ; Cognition ; }, abstract = {Cognitive dysfunction due to minimal hepatic encephalopathy (MHE) adversely impacts patients with cirrhosis and more precise therapies are needed. Gut-brain axis changes are therapeutic targets, but prior studies have largely focused on bacterial changes. Our aim was to determine linkages between individual cognitive testing results and bacteria with the virome using a cross-sectional and longitudinal approach. We included cross-sectional (n = 138) and longitudinal analyses (n = 36) of patients with cirrhosis tested using three cognitive modalities, which were psychometric hepatic encephalopathy score (PHES), inhibitory control test (ICT), Stroop, and all three. Stool metagenomics with virome and bacteriome were analyzed studied cross-sectionally and in a subset followed for development/reversal of MHE repeated at 6 months (longitudinally only using PHES). Cross-sectional: We found no significant changes in α/β diversity in viruses or bacteria regardless of cognitive testing. Cognitively impaired patients were more likely to have higher relative abundance of bacteriophages linked with Streptococcus, Faecalibacterium, and Lactobacillus, which were distinct based on modality. These were also linked with cognition on correlation networks. Longitudinally, 27 patients remained stable while 9 changed their MHE status. Similar changes in phages that are linked with Streptococcus, Faecalibacterium, and Lactobacillus were seen. These phages can influence ammonia, lactate, and short-chain fatty acid generation, which are neuro-active. In conclusion, we found linkages between bacteriophages and cognitive function likely due to impact on bacteria that produce neuroactive metabolites cross-sectionally and longitudinally. These findings could help explore bacteriophages as options to influence treatment for MHE in cirrhosis.}, } @article {pmid38010636, year = {2023}, author = {Gladyshev, NS and Baram, DV and Gorbunova, AV and Krivolapov, YA}, title = {[Transcriptome analysis of tissue microbiota diversity in tumor and non-tumor lymph nodes].}, journal = {Arkhiv patologii}, volume = {85}, number = {6}, pages = {26-30}, doi = {10.17116/patol20238506126}, pmid = {38010636}, issn = {0004-1955}, mesh = {Humans ; *Lymphoma, Follicular/diagnosis/pathology ; Hyperplasia/pathology ; Lymph Nodes/pathology ; Gene Expression Profiling ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Metagenomic studies in recent years have demonstrated that all tissues of the human body studied by genomic and transcriptomic sequencing methods, both in pathological processes and in normality, contain fragments of DNA and RNA from a variety of microorganisms. The composition of tissue microbiota and its relationship with development of pathological changes are still poorly understood, despite increasing number of studies in this area every year. In this study, gene expression of the lymph node microbiome in reactive follicular hyperplasia and follicular lymphoma was investigated.

OBJECTIVE: To study expression of lymph node microbiome genes in reactive follicular hyperplasia and follicular lymphoma.

MATERIAL AND METHODS: The work included 38 biopsy samples of lymph nodes with follicular lymphoma of different cytological subtypes and 10 biopsy samples of lymph nodes with reactive follicular hyperplasia. Verification of diagnosis was carried out using standard histological, histochemical and immunohistochemical methods. Using sequencing method, the transcriptome was examined. Statistical analysis and data visualization were performed using the R programming language (version 4.2.1).

RESULTS: Tumor lymph nodes are characterized by large Simpson and Shannon alpha diversity values (p-value = 0.026465 and p-value = 0.007122, respectively). Two clusters were discovered, characterized by different levels of relative abundance of microorganisms.

CONCLUSION: It has been proven that diversity of microorganisms present in tumor tissue and their number are statistically significantly higher than corresponding indicators in the lymph nodes with follicular hyperplasia.}, } @article {pmid38010080, year = {2023}, author = {Luoto, R and Pärtty, A and Vogt, JK and Rautava, S and Isolauri, E}, title = {Reversible aberrancies in gut microbiome of moderate and late preterm infants: results from a randomized, controlled trial.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2283913}, pmid = {38010080}, issn = {1949-0984}, mesh = {Infant ; Child ; Female ; Humans ; Infant, Newborn ; Infant, Premature ; *Gastrointestinal Microbiome/physiology ; *Probiotics ; Prebiotics ; Breast Feeding ; *Lacticaseibacillus rhamnosus ; }, abstract = {The aim of this study was to obtain insight into the composition and function of the deviant gut microbiome throughout infancy in children born moderately and late preterm and their response to microbiome modulation. We characterized the longitudinal development of the gut microbiome from birth to the age of 12 months by metagenomic sequencing in 43 moderate and late preterm children participating in a randomized, controlled trial (ClinicalTrials.gov/no.NCT00167700) assessing the impact of a probiotic (Lactobacillus rhamnosus GG, ATCC 53,103, currently Lacticaseibacillus rhamnosus GG) and a prebiotic (galacto-oligosaccharide and polydextrose mixture, 1:1) intervention as compared to a placebo administered from 3 to 60 days of life. In addition, 9 full-term, vaginally delivered, breast-fed infants, who remained healthy long-term were included as references. Significant differences in taxonomy, but not in functional potential, were found when comparing the gut microbiome composition of preterm and full-term infants during the first month of life. However, the gut microbiome of preterm infants resembled that of full-term infants by 6 months age. Probiotic and prebiotic treatments were found to mitigate the shift in the microbiome of preterm infants by accelerating Bifidobacteria-dominated gut microbiome in beta diversity analysis. This study provides intriguing information regarding the establishment of the gut microbiome in children born moderately and late preterm, representing the majority of children born preterm. Specific pro- and prebiotics may reverse the proinflammatory gut microbiome composition during the vulnerable period, when the microbiome is low in resilience and susceptible to environmental exposure and simultaneously promotes immunological and metabolic maturation.}, } @article {pmid38008755, year = {2023}, author = {Teng, M and Li, Y and Zhao, X and White, JC and Zhao, L and Sun, J and Zhu, W and Wu, F}, title = {Vitamin D modulation of brain-gut-virome disorder caused by polystyrene nanoplastics exposure in zebrafish (Danio rerio).}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {266}, pmid = {38008755}, issn = {2049-2618}, support = {42207335//National Natural Science Foundation of China/ ; 2022QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; 41925031//National Science Fund for Distinguished Young Scholars/ ; 2021YFC3201000//National Key Research and Development Program of China/ ; }, mesh = {Animals ; Polystyrenes/metabolism/toxicity ; Zebrafish ; Vitamin D/metabolism ; *Nanoparticles/metabolism/toxicity ; Microplastics/toxicity/metabolism ; Serotonin/metabolism ; Virome ; *Water Pollutants, Chemical/metabolism/toxicity ; Brain ; Cytochromes/metabolism ; }, abstract = {BACKGROUND: Many studies have investigated how nanoplastics (NPs) exposure mediates nerve and intestinal toxicity through a dysregulated brain-gut axis interaction, but there are few studies aimed at alleviating those effects. To determine whether and how vitamin D can impact that toxicity, fish were supplemented with a vitamin D-low diet and vitamin D-high diet.

RESULTS: Transmission electron microscopy (TEM) showed that polystyrene nanoplastics (PS-NPs) accumulated in zebrafish brain and intestine, resulting in brain blood-brain barrier basement membrane damage and the vacuolization of intestinal goblet cells and mitochondria. A high concentration of vitamin D reduced the accumulation of PS-NPs in zebrafish brain tissues by 20% and intestinal tissues by 58.8% and 52.2%, respectively, and alleviated the pathological damage induced by PS-NPs. Adequate vitamin D significantly increased the content of serotonin (5-HT) and reduced the anxiety-like behavior of zebrafish caused by PS-NPs exposure. Virus metagenome showed that PS-NPs exposure affected the composition and abundance of zebrafish intestinal viruses. Differentially expressed viruses in the vitamin D-low and vitamin D-high group affected the secretion of brain neurotransmitters in zebrafish. Virus AF191073 was negatively correlated with neurotransmitter 5-HT, whereas KT319643 was positively correlated with malondialdehyde (MDA) content and the expression of cytochrome 1a1 (cyp1a1) and cytochrome 1b1 (cyp1b1) in the intestine. This suggests that AF191073 and KT319643 may be key viruses that mediate the vitamin D reduction in neurotoxicity and immunotoxicity induced by PS-NPs.

CONCLUSION: Vitamin D can alleviate neurotoxicity and immunotoxicity induced by PS-NPs exposure by directionally altering the gut virome. These findings highlight the potential of vitamin D to alleviate the brain-gut-virome disorder caused by PS-NPs exposure and suggest potential therapeutic strategies to reduce the risk of NPs toxicity in aquaculture, that is, adding adequate vitamin D to diet. Video Abstract.}, } @article {pmid38008735, year = {2023}, author = {Xiao, X and Cui, Y and Lu, H and Wang, J and Yang, J and Liu, L and Liu, Z and Peng, X and Cao, H and Liu, X and Wei, X}, title = {Strontium ranelate enriched Ruminococcus albus in the gut microbiome of Sprague-Dawley rats with postmenopausal osteoporosis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {365}, pmid = {38008735}, issn = {1471-2180}, support = {2018QDJZR12//Cultivating Project for Young Scholar at Hubei University of Medicine/ ; 2015QDJZR06//Cultivating Project for Young Scholar at Hubei University of Medicine/ ; JC2022002//Innovation Research Program for Graduates of Basic Medical College, Hubei University of Medicine/ ; AD18281029//Guangxi Natural Science Foundation/ ; WJ2021M052//Hubei Provincial Health and Health Commission Funded Projects/ ; WJ2019Q025//Hubei Provincial Health and Health Commission Funded Projects/ ; }, mesh = {Humans ; Female ; Rats ; Animals ; Rats, Sprague-Dawley ; *Osteoporosis, Postmenopausal/drug therapy/metabolism ; *Gastrointestinal Microbiome ; Ruminococcus ; Lycopene/therapeutic use ; RNA, Ribosomal, 16S/genetics ; *Osteoporosis/drug therapy/metabolism ; }, abstract = {BACKGROUND: Gut microbiome is critical to our human health and is related to postmenopausal osteoporosis (PMO). Strontium ranelate (SrR) is an anti-osteoporosis oral drug that can promote osteoblast formation and inhibit osteoclast formation. However, the effect of SrR on gut microbiome has been rarely studied. Therefore, we investigated the effect of oral SrR on gut microbiome and metabolic profiles.

RESULTS: In this study, we used ovariectomized (OVX) Sprague-Dawley rats to construct a PMO model and applied oral SrR for 6 weeks. The relative abundance of intestinal microbiome was investigated by 16S rRNA metagenomic sequencing. Ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) was used to analyze changes in metabolites of intestinal contents. Results demonstrated that 6-week oral SrR alleviated osteoporosis and significantly changed the composition of the gut microbiome and metabolic profiles of OVX rats. Ruminococcus, Akkermansia and Oscillospira were significantly enriched in the gut of OVX rats after 6-week oral SrR. Especially, the species R. albus showed the greatest importance by a random forest classifier between OVX and OVX_Sr group. The enrichment of R. albus in the gut was positively correlated with bone mineral density and the accumulation of lycopene and glutaric acid, which also significantly elevated after oral SrR.

CONCLUSIONS: We discovered that oral SrR can improve bone health while stimulate the accumulation of gut microbe R. albus and metabolites (lycopene and glutaric acid). The results suggested possible connections between oral SrR and the gut-bone axis, which may provide new insight into the treatment/prevention of osteoporosis.}, } @article {pmid38008322, year = {2024}, author = {Hu, S and Xu, C and Xie, Y and Ma, L and Niu, Q and Han, G and Huang, J}, title = {Metagenomic insights into the diversity of 2,4-dichlorophenol degraders and the cooperation patterns in a bacterial consortium.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {168723}, doi = {10.1016/j.scitotenv.2023.168723}, pmid = {38008322}, issn = {1879-1026}, mesh = {Humans ; Bacteria/metabolism ; *Chlorophenols/metabolism ; Biodegradation, Environmental ; *Microbiota ; Microbial Consortia ; }, abstract = {2,4-Dichlorophenol, which is largely employed in herbicides and industrial production, is frequently detected in ecosystems and poses risks to human health and environmental safety. Microbial communities are thought to perform better than individual strains in the complete degradation of organic contaminants. However, the synergistic degradation mechanisms of the microbial consortia involved in 2,4-dichlorophenol degradation are still not widely understood. In this study, a bacterial consortium named DCP-2 that is capable of degrading 2,4-dichlorophenol was obtained. Metagenomic analysis, cultivation-dependent functional verification, and co-occurrence network analysis were combined to reveal the primary 2,4-dichlorophenol degraders and the cooperation patterns in the consortium DCP-2. Metagenomic analysis showed that Pseudomonas, Achromobacter, and Pigmentiphaga were the primary degraders for the complete degradation of 2,4-dichlorophenol. Thirty-nine phylogenetically diverse bacterial genera, such as Brucella, Acinetobacter, Aeromonas, Allochromatium and Bosea, were identified as keystone taxa for 2,4-dichlorophenol degradation by keystone taxa analysis of the co-occurrence networks. In addition, a stable synthetic consortium of isolates from DCP-2 was constructed, consisting of Pseudomonas sp. DD-13 and Brucella sp. FZ-1; this synthetic consortium showed superior degradation capability for 2,4-dichlorophenol in both mineral salt medium and wastewater compared with monoculture. The findings provide valuable insights into the practical bioremediation of 2,4-dichlorophenol-contaminated sites.}, } @article {pmid38007474, year = {2023}, author = {Liu, Y and Brinkhoff, T and Berger, M and Poehlein, A and Voget, S and Paoli, L and Sunagawa, S and Amann, R and Simon, M}, title = {Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {265}, pmid = {38007474}, issn = {2049-2618}, support = {TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; 205321_184955//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 205321_184955//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 51NF40_180575//National Center of Competence in Research Quantum Science and Technology/ ; }, mesh = {*Roseobacter/genetics ; Seawater/microbiology ; Metagenome ; Phylogeny ; Oceans and Seas ; Metagenomics ; }, abstract = {BACKGROUND: The RCA (Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in temperate to polar oceans. Despite its prevalence and abundance, only a few genomes and one described species, Planktomarina temperata, exist. To gain more insights into our limited understanding of this cluster and its taxonomic and functional diversity and biogeography, we screened metagenomic datasets from the global oceans and reconstructed metagenome-assembled genomes (MAG) affiliated to this cluster.

RESULTS: The total of 82 MAGs, plus five genomes of isolates, reveal an unexpected diversity and novel insights into the genomic features, the functional diversity, and greatly refined biogeographic patterns of the RCA cluster. This cluster is subdivided into three genera: Planktomarina, Pseudoplanktomarina, and the most deeply branching Candidatus Paraplanktomarina. Six of the eight Planktomarina species have larger genome sizes (2.44-3.12 Mbp) and higher G + C contents (46.36-53.70%) than the four Pseudoplanktomarina species (2.26-2.72 Mbp, 42.22-43.72 G + C%). Cand. Paraplanktomarina is represented only by one species with a genome size of 2.40 Mbp and a G + C content of 45.85%. Three novel species of the genera Planktomarina and Pseudoplanktomarina are validly described according to the SeqCode nomenclature for prokaryotic genomes. Aerobic anoxygenic photosynthesis (AAP) is encoded in three Planktomarina species. Unexpectedly, proteorhodopsin (PR) is encoded in the other Planktomarina and all Pseudoplanktomarina species, suggesting that this light-driven proton pump is the most important mode of acquiring complementary energy of the RCA cluster. The Pseudoplanktomarina species exhibit differences in functional traits compared to Planktomarina species and adaptations to more resource-limited conditions. An assessment of the global biogeography of the different species greatly expands the range of occurrence and shows that the different species exhibit distinct biogeographic patterns. They partially reflect the genomic features of the species.

CONCLUSIONS: Our detailed MAG-based analyses shed new light on the diversification, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. The taxonomic delineation and validation by the SeqCode nomenclature of prominent genera and species of the RCA cluster may be a promising way for a refined taxonomic identification of major prokaryotic lineages and sublineages in marine and other prokaryotic communities assessed by metagenomics approaches. Video Abstract.}, } @article {pmid38007438, year = {2023}, author = {Al, KF and Joris, BR and Daisley, BA and Chmiel, JA and Bjazevic, J and Reid, G and Gloor, GB and Denstedt, JD and Razvi, H and Burton, JP}, title = {Multi-site microbiota alteration is a hallmark of kidney stone formation.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {263}, pmid = {38007438}, issn = {2049-2618}, mesh = {Humans ; *Kidney Calculi ; *Microbiota/genetics ; Oxalates/metabolism ; Metagenome ; Bacteria ; }, abstract = {BACKGROUND: Inquiry of microbiota involvement in kidney stone disease (KSD) has largely focussed on potential oxalate handling abilities by gut bacteria and the increased association with antibiotic exposure. By systematically comparing the gut, urinary, and oral microbiota of 83 stone formers (SF) and 30 healthy controls (HC), we provide a unified assessment of the bacterial contribution to KSD.

RESULTS: Amplicon and shotgun metagenomic sequencing approaches were consistent in identifying multi-site microbiota disturbances in SF relative to HC. Biomarker taxa, reduced taxonomic and functional diversity, functional replacement of core bioenergetic pathways with virulence-associated gene markers, and community network collapse defined SF, but differences between cohorts did not extend to oxalate metabolism.

CONCLUSIONS: We conclude that multi-site microbiota alteration is a hallmark of SF, and KSD treatment should consider microbial functional restoration and the avoidance of aberrant modulators such as poor diet and antibiotics where applicable to prevent stone recurrence. Video Abstract.}, } @article {pmid38006691, year = {2024}, author = {Hes, C and Desilets, A and Tonneau, M and El Ouarzadi, O and De Figueiredo Sousa, M and Bahig, H and Filion, É and Nguyen-Tan, PF and Christopoulos, A and Benlaïfaoui, M and Derosa, L and Alves Costa Silva, C and Ponce, M and Malo, J and Belkad, W and Charpentier, D and Aubin, F and Hamilou, Z and Jamal, R and Messaoudene, M and Soulières, D and Routy, B}, title = {Gut microbiome predicts gastrointestinal toxicity outcomes from chemoradiation therapy in patients with head and neck squamous cell carcinoma.}, journal = {Oral oncology}, volume = {148}, number = {}, pages = {106623}, doi = {10.1016/j.oraloncology.2023.106623}, pmid = {38006691}, issn = {1879-0593}, mesh = {Male ; Humans ; Female ; Squamous Cell Carcinoma of Head and Neck/complications ; *Head and Neck Neoplasms/complications ; *Mucositis/etiology ; Prospective Studies ; *Gastrointestinal Microbiome ; Chemoradiotherapy/adverse effects ; }, abstract = {OBJECTIVES: Chemoradiation (CRT) in patients with locally advanced head and neck squamous cell cancer (HNSCC) is associated with significant toxicities, including mucositis. The gut microbiome represents an emerging hallmark of cancer and a potentially important biomarker for CRT-related adverse events. This prospective study investigated the association between the gut microbiome composition and CRT-related toxicities in patients with HNSCC, including mucositis.

MATERIALS AND METHODS: Stool samples from patients diagnosed with locally advanced HNSCC were prospectively collected prior to CRT initiation and analyzed using shotgun metagenomic sequencing to evaluate gut microbiome composition at baseline. Concurrently, clinicopathologic data, survival outcomes and the incidence and grading of CRT-emergent adverse events were documented in all patients.

RESULTS: A total of 52 patients were included, of whom 47 had baseline stool samples available for metagenomic analysis. Median age was 62, 83 % patients were men and 54 % had stage III-IV disease. All patients developed CRT-induced mucositis, including 42 % with severe events (i.e. CTCAE v5.0 grade ≥ 3) and 25 % who required enteral feeding. With a median follow-up of 26.5 months, patients with severe mucositis had shorter overall survival (HR = 3.3, 95 %CI 1.0-10.6; p = 0.02) and numerically shorter progression-free survival (HR = 2.8, 95 %CI, 0.8-9.6; p = 0.09). The gut microbiome beta-diversity of patients with severe mucositis differed from patients with grades 1-2 mucositis (p = 0.04), with enrichment in Mediterraneibacter (Ruminococcus gnavus) and Clostridiaceae family members, including Hungatella hathewayi. Grade 1-2 mucositis was associated with enrichment in Eubacterium rectale, Alistipes putredinis and Ruminococcaceae family members. Similar bacterial profiles were observed in patients who required enteral feeding.

CONCLUSION: Patients who developed severe mucositis had decreased survival and enrichment in specific bacteria associated with mucosal inflammation. Interestingly, these same bacteria have been linked to immune checkpoint inhibitor resistance.}, } @article {pmid38006569, year = {2024}, author = {Aminu, S and Ascandari, A and Laamarti, M and Safdi, NEH and El Allali, A and Daoud, R}, title = {Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities.}, journal = {Critical reviews in microbiology}, volume = {50}, number = {5}, pages = {805-829}, doi = {10.1080/1040841X.2023.2282447}, pmid = {38006569}, issn = {1549-7828}, mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Animals ; *Whole Genome Sequencing ; Genome, Bacterial ; }, abstract = {The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables researchers to uncover the metabolic capabilities of the microbial community, providing valuable insights into the microbiome. Herein, we present an overview of the rapid advancements achieved thus far in the use of WGS in microbiome research. There was an upsurge in publications, particularly in 2021 and 2022 with the United States, China, and India leading the metagenomics research landscape. The Illumina platform has emerged as the widely adopted sequencing technology, whereas a significant focus of metagenomics has been on understanding the relationship between the gut microbiome and human health where distinct bacterial species have been linked to various diseases. Additionally, studies have explored the impact of human activities on microbial communities, including the potential spread of pathogenic bacteria and antimicrobial resistance genes in different ecosystems. Furthermore, WGS is used in investigating the microbiome of various animal species and plant tissues such as the rhizosphere microbiome. Overall, this review reflects the importance of WGS in metagenomics studies and underscores its remarkable power in illuminating the variety and intricacy of the microbiome in different environments.}, } @article {pmid38006423, year = {2023}, author = {Bhagchandani, T and Nikita, and Verma, A and Tandon, R}, title = {Exploring the Human Virome: Composition, Dynamics, and Implications for Health and Disease.}, journal = {Current microbiology}, volume = {81}, number = {1}, pages = {16}, pmid = {38006423}, issn = {1432-0991}, support = {(No. 61/06/2020/IMM/BMS)//Indian Council of Medical Research/ ; }, mesh = {Infant ; Humans ; Virome ; *Microbiota ; *Viruses/genetics ; *Bacteriophages/genetics ; Metagenome ; }, abstract = {Humans are colonized by large number of microorganisms-bacteria, fungi, and viruses. The overall genome of entire viruses that either lives on or inside the human body makes up the human virome and is indeed an essential fraction of the human metagenome. Humans are constantly exposed to viruses as they are ubiquitously present on earth. The human virobiota encompasses eukaryotic viruses, bacteriophages, retroviruses, and even giant viruses. With the advent of Next-generation sequencing (NGS) and ongoing development of numerous bioinformatic softwares, identification and taxonomic characterization of viruses have become easier. The viruses are abundantly present in humans; these can be pathogenic or commensal. The viral communities occupy various niches in the human body. The viruses start colonizing the infant gut soon after birth in a stepwise fashion and the viral composition diversify according to their feeding habits. Various factors such as diet, age, medications, etc. influence and shape the human virome. The viruses interact with the host immune system and these interactions have beneficial or detrimental effects on their host. The virome composition and abundance change during the course of disease and these alterations impact the immune system. Hence, the virome population in healthy and disease conditions influences the human host in numerous ways. This review presents an overview of assembly and composition of the human virome in healthy asymptomatic individuals, changes in the virome profiles, and host-virome interactions in various disease states.}, } @article {pmid38006234, year = {2023}, author = {Yadav, A and Ahlawat, S and Sharma, KK}, title = {Culturing the unculturables: strategies, challenges, and opportunities for gut microbiome study.}, journal = {Journal of applied microbiology}, volume = {134}, number = {12}, pages = {}, doi = {10.1093/jambio/lxad280}, pmid = {38006234}, issn = {1365-2672}, support = {5/4/8-1/2019-NCD-II//Indian Council of Medical Research/ ; }, mesh = {*Gastrointestinal Microbiome ; *Microbiota ; Metagenome ; Intestines ; Metagenomics/methods ; }, abstract = {Metagenome sequencing techniques revolutionized the field of gut microbiome study. However, it is equipped with experimental and computational biases, which affect the downstream analysis results. Also, live microbial strains are needed for a better understanding of host-microbial crosstalks and for designing next-generation treatment therapies based on probiotic strains and postbiotic molecules. Conventional culturing methodologies are insufficient to get the dark gut matter on the plate; therefore, there is an urgent need to propose novel culturing methods that can fill the limitations of metagenomics. The current work aims to provide a consolidated evaluation of the available methods for host-microbe interaction with an emphasis on in vitro culturing of gut microbes using organoids, gut on a chip, and gut bioreactor. Further, the knowledge of microbial crosstalk in the gut helps us to identify core microbiota, and key metabolites that will aid in designing culturing media and co-culturing systems for gut microbiome study. After the deeper mining of the current culturing methods, we recommend that 3D-printed intestinal cells in a multistage continuous flow reactor equipped with an extended organoid system might be a good practical choice for gut microbiota-based studies.}, } @article {pmid38003647, year = {2023}, author = {Angelova, IY and Kovtun, AS and Averina, OV and Koshenko, TA and Danilenko, VN}, title = {Unveiling the Connection between Microbiota and Depressive Disorder through Machine Learning.}, journal = {International journal of molecular sciences}, volume = {24}, number = {22}, pages = {}, pmid = {38003647}, issn = {1422-0067}, support = {20-14-00132//Russian Science Foundation/ ; }, mesh = {Humans ; *Depressive Disorder, Major ; *Microbiota ; *Gastrointestinal Microbiome ; Metagenome ; }, abstract = {In the last few years, investigation of the gut-brain axis and the connection between the gut microbiota and the human nervous system and mental health has become one of the most popular topics. Correlations between the taxonomic and functional changes in gut microbiota and major depressive disorder have been shown in several studies. Machine learning provides a promising approach to analyze large-scale metagenomic data and identify biomarkers associated with depression. In this work, machine learning algorithms, such as random forest, elastic net, and You Only Look Once (YOLO), were utilized to detect significant features in microbiome samples and classify individuals based on their disorder status. The analysis was conducted on metagenomic data obtained during the study of gut microbiota of healthy people and patients with major depressive disorder. The YOLO method showed the greatest effectiveness in the analysis of the metagenomic samples and confirmed the experimental results on the critical importance of a reduction in the amount of Faecalibacterium prausnitzii for the manifestation of depression. These findings could contribute to a better understanding of the role of the gut microbiota in major depressive disorder and potentially lead the way for novel diagnostic and therapeutic strategies.}, } @article {pmid38001502, year = {2023}, author = {Li, P and Hong, J and Yuan, Z and Huang, Y and Wu, M and Ding, T and Wu, Z and Sun, X and Lin, D}, title = {Gut microbiota in parasite-transmitting gastropods.}, journal = {Infectious diseases of poverty}, volume = {12}, number = {1}, pages = {105}, pmid = {38001502}, issn = {2049-9957}, support = {2020YFC1200100//the National Key R&D Program of China/ ; 2020YFC1200103//the National Key R&D Program of China/ ; 2021YFC2300800//the National Key R&D Program of China/ ; 2016YFC1200500//the National Key R&D Program of China/ ; 82202560//the National Natural Science Foundation of China/ ; 82161160343//the National Natural Science Foundation of China/ ; 82272361//the National Natural Science Foundation of China/ ; 2021B1212040017//the Science and Technology Planning Project of Guangdong Province/ ; 2022B1111030002//the R&D Program in Key Areas of Guangdong Province/ ; 22qntd4813//the Fundamental Research Funds for the Central University/ ; B12003//the 111 Project/ ; 20201192//the 6th Nuclear Energy R&D Project/ ; NPRC-2019-194-30//the National Parasitic Resource Center and Ministry of Science and Technology/ ; }, mesh = {Animals ; *Parasites ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; Snails/parasitology ; Host-Parasite Interactions ; }, abstract = {BACKGROUND: Gastropoda, the largest class within the phylum Mollusca, houses diverse gut microbiota, and some gastropods serve as intermediate hosts for parasites. Studies have revealed that gut bacteria in gastropods are associated with various biological aspects, such as growth, immunity and host-parasite interactions. Here, we summarize our current knowledge of gastropod gut microbiomes and highlight future research priorities and perspectives.

METHODS: A literature search was undertaken using PubMed, Web of Science and CNKI for the articles on the gut microbiota of gastropods until December 31, 2022. We retrieved a total of 166 articles and identified 73 eligible articles for inclusion in this review based on the inclusion and exclusion criteria.

RESULTS: Our analysis encompassed freshwater, seawater and land snails, with a specific focus on parasite-transmitting gastropods. We found that most studies on gastropod gut microbiota have primarily utilized 16S rRNA gene sequencing to analyze microbial composition, rather than employing metagenomic, metatranscriptomic, or metabolomic approaches. This comprehensive review provided an overview of the parasites carried by snail species in the context of gut microbiota studies. We presented the gut microbial trends, a comprehensive summary of the diversity and composition, influencing factors, and potential functions of gastropod gut microbiota. Additionally, we discussed the potential applications, research gaps and future perspectives of gut microbiomes in parasite-transmitting gastropods. Furthermore, several strategies for enhancing our comprehension of gut microbiomes in snails were also discussed.

CONCLUSIONS: This review comprehensively summarizes the current knowledge on the composition, potential function, influencing factors, potential applications, limitations, and challenges of gut microbiomes in gastropods, with a specific emphasis on parasite-transmitting gastropods. These findings provide important insights for future studies aiming to understand the potential role of gastropod gut microbiota in controlling snail populations and snail-borne diseases.}, } @article {pmid38001408, year = {2023}, author = {Chen, C and Zhang, Y and Yao, X and Yan, Q and Li, S and Zhong, Q and Liu, Z and Tang, F and Liu, C and Li, H and Zhu, D and Lan, W and Ling, Y and Lu, D and Xu, H and Ning, Q and Wang, Y and Jiang, Z and Zhang, Q and Gu, G and Sun, L and Wang, N and Wang, G and Zhang, A and Ullah, H and Sun, W and Ma, W}, title = {Characterizations of the multi-kingdom gut microbiota in Chinese patients with gouty arthritis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {363}, pmid = {38001408}, issn = {1471-2180}, support = {Support [2020]4Y155//Science and Technology Program of Guizhou Province/ ; Platform and talent [2020]2202//Science and Technology Program of Guizhou Province/ ; 82260894//National Natural Science Foundation of China/ ; 81902037//National Natural Science Foundation of China/ ; GZEYK-B[2021]2//Scientific Research Project of the Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Arthritis, Gouty ; East Asian People ; *Microbiota ; *Mycobiome ; Bacteria/genetics ; }, abstract = {OBJECTIVE: The gut microbial composition has been linked to metabolic and autoimmune diseases, including arthritis. However, there is a dearth of knowledge on the gut bacteriome, mycobiome, and virome in patients with gouty arthritis (GA).

METHODS: We conducted a comprehensive analysis of the multi-kingdom gut microbiome of 26 GA patients and 28 healthy controls, using whole-metagenome shotgun sequencing of their stool samples.

RESULTS: Profound alterations were observed in the gut bacteriome, mycobiome, and virome of GA patients. We identified 1,117 differentially abundant bacterial species, 23 fungal species, and 4,115 viral operational taxonomic units (vOTUs). GA-enriched bacteria included Escherichia coli_D GENOME144544, Bifidobacterium infantis GENOME095938, Blautia_A wexlerae GENOME096067, and Klebsiella pneumoniae GENOME147598, while control-enriched bacteria comprised Faecalibacterium prausnitzii_G GENOME147678, Agathobacter rectalis GENOME143712, and Bacteroides_A plebeius_A GENOME239725. GA-enriched fungi included opportunistic pathogens like Cryptococcus neoformans GCA_011057565, Candida parapsilosis GCA_000182765, and Malassezia spp., while control-enriched fungi featured several Hortaea werneckii subclades and Aspergillus fumigatus GCA_000002655. GA-enriched vOTUs mainly attributed to Siphoviridae, Myoviridae, Podoviridae, and Microviridae, whereas control-enriched vOTUs spanned 13 families, including Siphoviridae, Myoviridae, Podoviridae, Quimbyviridae, Phycodnaviridae, and crAss-like. A co-abundance network revealed intricate interactions among these multi-kingdom signatures, signifying their collective influence on the disease. Furthermore, these microbial signatures demonstrated the potential to effectively discriminate between patients and controls, highlighting their diagnostic utility.

CONCLUSIONS: This study yields crucial insights into the characteristics of the GA microbiota that may inform future mechanistic and therapeutic investigations.}, } @article {pmid38000749, year = {2024}, author = {Lewin, S and Wende, S and Wehrhan, M and Verch, G and Ganugi, P and Sommer, M and Kolb, S}, title = {Cereals rhizosphere microbiome undergoes host selection of nitrogen cycle guilds correlated to crop productivity.}, journal = {The Science of the total environment}, volume = {911}, number = {}, pages = {168794}, doi = {10.1016/j.scitotenv.2023.168794}, pmid = {38000749}, issn = {1879-1026}, mesh = {*Rhizosphere ; Edible Grain/chemistry ; Nitrates ; Fertilizers/analysis ; Nitrogen Cycle ; *Microbiota/physiology ; Soil/chemistry ; Crops, Agricultural ; Nitrogen/analysis ; Soil Microbiology ; }, abstract = {Sustainable transformation of agricultural plant production requires the reduction of nitrogen (N) fertilizer application. Such a reduced N fertilizer application may impede crop production due to an altered symbiosis of crops and their rhizosphere microbiome, since reduced N input may affect the competition and synergisms with the plant. The assessment of such changes in the crop microbiome functionalities at spatial scales relevant for agricultural management remains challenging. We investigated in a field plot experiment how and if the N cycling guilds of the rhizosphere of globally relevant cereal crops - winter barley, wheat and rye - are influenced by reduced N fertilization. Crop productivity was assessed by remote sensing of the shoot biomass. Microbial N cycling guilds were investigated by metagenomics targeting diazotrophs, nitrifiers, denitrifiers and the dissimilatory nitrate to ammonium reducing guild (DNRA). The functional composition of microbial N cycling guilds was explained by crop productivity parameters and soil pH, and diverged substantially between the crop species. The responses of individual microbial N cycling guild abundances to shoot dry weight and rhizosphere nitrate content was modulated by the N fertilization treatments and the crop species, which was identified based on regression analyses. Thus, characteristic shifts in the microbial N cycling guild acquisition associated with the crop host species were resolved. Particularly, the rhizosphere of rye was enriched with potentially N-preserving microbial guilds - diazotrophs and the DNRA guild - when no fertilizer was applied. We speculate that the acquisition of microbial N cycling guilds was the result of plant species-specific acquisition strategies. Thus, the investigated cereal crop holobionts have likely different symbiotic strategies that make them differently resilient against reduced N fertilizer inputs. Furthermore, we demonstrated that these belowground patterns of N cycling guilds from the rhizosphere microbiome are linked to remotely sensed aboveground plant productivity.}, } @article {pmid37999453, year = {2023}, author = {Yan, Z and He, X and Ayala, J and Xu, Q and Yu, X and Hou, R and Yao, Y and Huang, H and Wang, H}, title = {The Impact of Bamboo Consumption on the Spread of Antibiotic Resistance Genes in Giant Pandas.}, journal = {Veterinary sciences}, volume = {10}, number = {11}, pages = {}, pmid = {37999453}, issn = {2306-7381}, support = {2022NSFSC0131//Sichuan Science and Technology Provincial Department/ ; 2020CPB-C10//the independent project of Chengdu Research Base of Giant Panda Breeding/ ; 2021CPB-C14//the independent project of Chengdu Research Base of Giant Panda Breeding/ ; }, abstract = {The spread of antibiotic resistance genes (ARGs) in the environment exacerbates the contamination of these genes; therefore, the role plants play in the transmission of resistance genes in the food chain requires further research. Giant pandas consume different bamboo parts at different times, which provides the possibility of investigating how a single food source can affect the variation in the spread of ARGs. In this study, metagenomic analysis and the Comprehensive Antibiotic Resistance Database (CARD) database were used to annotate ARGs and the differences in gut microbiota ARGs during the consumption of bamboo shoots, leaves, and culms by captive giant pandas. These ARGs were then compared to investigate the impact of bamboo part consumption on the spread of ARGs. The results showed that the number of ARGs in the gut microbiota of the subjects was highest during the consumption of bamboo leaves, while the variety of ARGs was highest during the consumption of shoots. Escherichia coli, which poses a higher risk of ARG dissemination, was significantly higher in the leaf group, while Klebsiella, Enterobacter, and Raoultella were significantly higher in the shoot group. The ARG risk brought by bamboo shoots and leaves may originate from soil and environmental pollution. It is recommended to handle the feces of giant pandas properly and regularly monitor the antimicrobial and virulence genes in their gut microbiota to mitigate the threat of antibiotic resistance.}, } @article {pmid37999398, year = {2023}, author = {Jahajeeah, D and Ranghoo-Sanmukhiya, M and Schäfer, G}, title = {Metabolic Profiling, Antiviral Activity and the Microbiome of Some Mauritian Soft Corals.}, journal = {Marine drugs}, volume = {21}, number = {11}, pages = {}, pmid = {37999398}, issn = {1660-3397}, support = {WS/MUS22-01//International Centre for Genetic Engineering and Biotechnology/ ; }, mesh = {Animals ; *Papillomavirus Infections ; Aquatic Organisms ; *Anthozoa/chemistry ; *Microbiota ; Antiviral Agents/pharmacology/metabolism ; }, abstract = {Soft corals, recognized as sessile marine invertebrates, rely mainly on chemical, rather than physical defense, by secreting intricate secondary metabolites with plausible pharmaceutical implication. Their ecological niche encompasses a diverse community of symbiotic microorganisms which potentially contribute to the biosynthesis of these bioactive metabolites. The emergence of new viruses and heightened viral resistance underscores the urgency to explore novel pharmacological reservoirs. Thus, marine organisms, notably soft corals and their symbionts, have drawn substantial attention. In this study, the chemical composition of four Mauritian soft corals: Sinularia polydactya, Cespitularia simplex, Lobophytum patulum, and Lobophytum crassum was investigated using LC-MS techniques. Concurrently, Illumina 16S metagenomic sequencing was used to identify the associated bacterial communities in the named soft corals. The presence of unique biologically important compounds and vast microbial communities found therein was further followed up to assess their antiviral effects against SARS-CoV-2 and HPV pseudovirus infection. Strikingly, among the studied soft corals, L. patulum displayed an expansive repertoire of unique metabolites alongside a heightened bacterial consort. Moreover, L. patulum extracts exerted some promising antiviral activity against SARS-CoV-2 and HPV pseudovirus infection, and our findings suggest that L. patulum may have the potential to serve as a therapeutic agent in the prevention of infectious diseases, thereby warranting further investigation.}, } @article {pmid37996679, year = {2024}, author = {Tilahun, L and Asrat, A and Wessel, GM and Simachew, A}, title = {Ancestors in the Extreme: A Genomics View of Microbial Diversity in Hypersaline Aquatic Environments.}, journal = {Results and problems in cell differentiation}, volume = {71}, number = {}, pages = {185-212}, pmid = {37996679}, issn = {0080-1844}, mesh = {Humans ; Phylogeny ; *Bacteria/genetics/metabolism ; Archaea/genetics/metabolism ; Sodium Chloride/metabolism ; *Microbiota/genetics ; Metagenomics ; }, abstract = {The origin of eukaryotic cells, and especially naturally occurring syncytial cells, remains debatable. While a majority of our biomedical research focuses on the eukaryotic result of evolution, our data remain limiting on the prokaryotic precursors of these cells. This is particularly evident when considering extremophile biology, especially in how the genomes of organisms in extreme environments must have evolved and adapted to unique habitats. Might these rapidly diversifying organisms have created new genetic tools eventually used to enhance the evolution of the eukaryotic single nuclear or syncytial cells? Many organisms are capable of surviving, or even thriving, in conditions of extreme temperature, acidity, organic composition, and then rapidly adapt to yet new conditions. This study identified organisms found in extremes of salinity. A lake and a nearby pond in the Ethiopian Rift Valley were interrogated for life by sequencing the DNA of populations of organism collected from the water in these sites. Remarkably, a vast diversity of microbes were identified, and even though the two sites were nearby each other, the populations of organisms were distinctly different. Since these microbes are capable of living in what for humans would be inhospitable conditions, the DNA sequences identified should inform the next step in these investigations; what new gene families, or modifications to common genes, do these organisms employ to survive in these extreme conditions. The relationship between organisms and their environment can be revealed by decoding genomes of organisms living in extreme environments. These genomes disclose new biological mechanisms that enable life outside moderate environmental conditions, new gene functions for application in biotechnology, and may even result in identification of new species. In this study, we have collected samples from two hypersaline sites in the Danakil depression, the shorelines of Lake As'ale and an actively mixing salt pond called Muda'ara (MUP), to identify the microbial community by metagenomics. Shotgun sequencing was applied to high density sampling, and the relative abundance of Operational Taxonomic Units (OTUs) was calculated. Despite the broad taxonomic similarities among the salt-saturated metagenomes analyzed, MUP stood out from Lake As'ale samples. In each sample site, Archaea accounted for 95% of the total OTUs, largely to the class Halobacteria. The remaining 5% of organisms were eubacteria, with an unclassified strain of Salinibacter ruber as the dominant OTU in both the Lake and the Pond. More than 40 different genes coding for stress proteins were identified in the three sample sites of Lake As'ale, and more than 50% of the predicted stress-related genes were associated with oxidative stress response proteins. Chaperone proteins (DnaK, DnaJ, GrpE, and ClpB) were predicted, with percentage of query coverage and similarities ranging between 9.5% and 99.2%. Long reads for ClpB homologous protein from Lake As'ale metagenome datasets were modeled, and compact 3D structures were generated. Considering the extreme environmental conditions of the Danakil depression, this metagenomics dataset can add and complement other studies on unique gene functions on stress response mechanisms of thriving bio-communities that could have contributed to cellular changes leading to single and/or multinucleated eukaryotic cells.}, } @article {pmid37995844, year = {2023}, author = {Bonnici, V and Mengoni, C and Mangoni, M and Franco, G and Giugno, R}, title = {PanDelos-frags: A methodology for discovering pangenomic content of incomplete microbial assemblies.}, journal = {Journal of biomedical informatics}, volume = {148}, number = {}, pages = {104552}, doi = {10.1016/j.jbi.2023.104552}, pmid = {37995844}, issn = {1532-0480}, mesh = {Humans ; Ecosystem ; Genome ; *Genomics/methods ; Metagenomics/methods ; Software ; *Microbiota/genetics ; }, abstract = {Pangenomics was originally defined as the problem of comparing the composition of genes into gene families within a set of bacterial isolates belonging to the same species. The problem requires the calculation of sequence homology among such genes. When combined with metagenomics, namely for human microbiome composition analysis, gene-oriented pangenome detection becomes a promising method to decipher ecosystem functions and population-level evolution. Established computational tools are able to investigate the genetic content of isolates for which a complete genomic sequence is available. However, there is a plethora of incomplete genomes that are available on public resources, which only a few tools may analyze. Incomplete means that the process for reconstructing their genomic sequence is not complete, and only fragments of their sequence are currently available. However, the information contained in these fragments may play an essential role in the analyses. Here, we present PanDelos-frags, a computational tool which exploits and extends previous results in analyzing complete genomes. It provides a new methodology for inferring missing genetic information and thus for managing incomplete genomes. PanDelos-frags outperforms state-of-the-art approaches in reconstructing gene families in synthetic benchmarks and in a real use case of metagenomics. PanDelos-frags is publicly available at https://github.com/InfOmics/PanDelos-frags.}, } @article {pmid37995075, year = {2024}, author = {Yu, L and Chen, X and Bai, X and Fang, J and Sui, M}, title = {Microbiota Alters and Its Correlation with Molecular Regulation Underlying Depression in PCOS Patients.}, journal = {Molecular neurobiology}, volume = {61}, number = {12}, pages = {9977-9992}, pmid = {37995075}, issn = {1559-1182}, support = {2022J01279//Natural Science Foundation of Fujian Province/ ; BS202203//doctoral research project of the Second Affiliated Hospital of Fujian Medical University/ ; 2019-1-48//Fujian Provincial Health Research Talents Training Project/ ; }, mesh = {Humans ; *Polycystic Ovary Syndrome/microbiology/genetics ; Female ; *Gastrointestinal Microbiome/genetics ; Adult ; *Depression/microbiology/genetics ; Gene Expression Regulation ; Depressive Disorder, Major/microbiology/genetics ; Feces/microbiology ; Microbiota ; }, abstract = {Depression is one of the complications in patients with polycystic ovary syndrome (PCOS) that leads to considerable mental health. Accumulating evidence suggests that human gut microbiomes are associated with the progression of PCOS and depression. However, whether microbiota influences depression development in PCOS patients is still uncharacterized. In this study, we employed metagenomic sequencing and transcriptome sequencing (RNA-seq) to profile the composition of the fecal microbiota and gene expression of peripheral blood mononuclear cells in depressed women with PCOS (PCOS-DP, n = 27) in comparison to mentally healthy women with PCOS (PCOS, n = 18) and compared with healthy control (HC, n = 27) and patients with major depressive disorder (MDD, n = 29). Gut microbiota assessment revealed distinct patterns in the relative abundance in the PCOS-DP compared to HC, MDD, and PCOS groups. Several gut microbes exhibited uniquely and significantly higher abundance in the PCOS-DP compared to PCOS patients, inducing EC Ruminococcus torques, Coprococcus comes, Megasphaera elsdenii, Acidaminococcus intestini, and Barnesiella viscericola. Bacteroides eggerthii was a potential gut microbial biomarker for the PCOS-DP. RNA-seq profiling identified that 35 and 37 genes were significantly elevated and downregulated in the PCOS-DP, respectively. The enhanced differential expressed genes (DEGs) in the PCOS-DP were enriched in pathways involved in signal transduction and endocrine and metabolic diseases, whereas several lipid metabolism pathways were downregulated. Intriguingly, genes correlated with the gut microbiota were found to be significantly enriched in pathways of neurodegenerative diseases and the immune system, suggesting that changes in the microbiota may have a systemic impact on the expression of neurodegenerative diseases and immune genes. Gut microbe-related DEGs of CREB3L3 and CCDC173 were possible molecular biomarkers and therapeutic targets of women with PCOS-DP. Our multi-omics data indicate shifts in the gut microbiome and host gene regulation in PCOS patients with depression, which is of possible etiological and diagnostic importance.}, } @article {pmid37994699, year = {2024}, author = {Hirsch, P and Tagirdzhanov, A and Kushnareva, A and Olkhovskii, I and Graf, S and Schmartz, GP and Hegemann, JD and Bozhüyük, KAJ and Müller, R and Keller, A and Gurevich, A}, title = {ABC-HuMi: the Atlas of Biosynthetic Gene Clusters in the Human Microbiome.}, journal = {Nucleic acids research}, volume = {52}, number = {D1}, pages = {D579-D585}, pmid = {37994699}, issn = {1362-4962}, support = {//Saarland University/ ; 466168626//DFG/ ; }, mesh = {Humans ; *Biosynthetic Pathways/genetics ; Computational Biology/instrumentation ; *Databases, Genetic ; Internet ; *Microbiota/genetics ; *Multigene Family/genetics ; Metagenome/genetics ; }, abstract = {The human microbiome has emerged as a rich source of diverse and bioactive natural products, harboring immense potential for therapeutic applications. To facilitate systematic exploration and analysis of its biosynthetic landscape, we present ABC-HuMi: the Atlas of Biosynthetic Gene Clusters (BGCs) in the Human Microbiome. ABC-HuMi integrates data from major human microbiome sequence databases and provides an expansive repository of BGCs compared to the limited coverage offered by existing resources. Employing state-of-the-art BGC prediction and analysis tools, our database ensures accurate annotation and enhanced prediction capabilities. ABC-HuMi empowers researchers with advanced browsing, filtering, and search functionality, enabling efficient exploration of the resource. At present, ABC-HuMi boasts a catalog of 19 218 representative BGCs derived from the human gut, oral, skin, respiratory and urogenital systems. By capturing the intricate biosynthetic potential across diverse human body sites, our database fosters profound insights into the molecular repertoire encoded within the human microbiome and offers a comprehensive resource for the discovery and characterization of novel bioactive compounds. The database is freely accessible at https://www.ccb.uni-saarland.de/abc_humi/.}, } @article {pmid37993724, year = {2023}, author = {Gutiérrez-García, K and Whitaker, MRL and Bustos-Díaz, ED and Salzman, S and Ramos-Aboites, HE and Reitz, ZL and Pierce, NE and Cibrián-Jaramillo, A and Barona-Gómez, F}, title = {Gut microbiomes of cycad-feeding insects tolerant to β-methylamino-L-alanine (BMAA) are rich in siderophore biosynthesis.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {122}, pmid = {37993724}, issn = {2730-6151}, support = {1541560, 1309425, 1906333//National Science Foundation (NSF)/ ; NAF/R2/180631//Newton Fund/ ; 169701, 179290, 177568, FON.INST./265/2016 285746,//Consejo Nacional de Ciencia y Tecnología (National Council of Science and Technology, Mexico)/ ; }, abstract = {Ingestion of the cycad toxins β-methylamino-L-alanine (BMAA) and azoxyglycosides is harmful to diverse organisms. However, some insects are specialized to feed on toxin-rich cycads with apparent immunity. Some cycad-feeding insects possess a common set of gut bacteria, which might play a role in detoxifying cycad toxins. Here, we investigated the composition of gut microbiota from a worldwide sample of cycadivorous insects and characterized the biosynthetic potential of selected bacteria. Cycadivorous insects shared a core gut microbiome consisting of six bacterial taxa, mainly belonging to the Proteobacteria, which we were able to isolate. To further investigate selected taxa from diverging lineages, we performed shotgun metagenomic sequencing of co-cultured bacterial sub-communities. We characterized the biosynthetic potential of four bacteria from Serratia, Pantoea, and two different Stenotrophomonas lineages, and discovered a suite of biosynthetic gene clusters notably rich in siderophores. Siderophore semi-untargeted metabolomics revealed a broad range of chemically related yet diverse iron-chelating metabolites, including desferrioxamine B, suggesting the occurrence of an unprecedented desferrioxamine-like biosynthetic pathway that remains to be identified. These results provide a foundation for future investigations into how cycadivorous insects tolerate diets rich in azoxyglycosides, BMAA, and other cycad toxins, including a possible role for bacterial siderophores.}, } @article {pmid37993375, year = {2024}, author = {Mouzan, ME and Hussaini, AA and Sarkhy, AA and Assiri, A}, title = {Intestinal fungal profile in healthy Saudi children.}, journal = {Arab journal of gastroenterology : the official publication of the Pan-Arab Association of Gastroenterology}, volume = {25}, number = {1}, pages = {18-21}, doi = {10.1016/j.ajg.2023.11.001}, pmid = {37993375}, issn = {2090-2387}, mesh = {Child ; Humans ; Male ; Adolescent ; Female ; *Fungi ; Saudi Arabia ; *Mycobiome ; Candida ; Research Design ; }, abstract = {BACKGROUND AND STUDY AIM: Fungi have a well-established role in medicine. Herein, we describe the fungal profile and abundance in the gut of healthy Saudi children.

PATIENTS AND METHODS: Fecal samples from a random sample of 20 school-age Saudi children were collected, stored at -80 °C, and dispatched to the laboratory in the USA where fungal DNAs were isolated and shotgun metagenomic sequencing was performed. Abundance was presented as average percentage of fungal taxa.

RESULTS: The median age of the participants was 12.5 years (range: 7-16 years), and 35 % were male. Ascomycota were the most abundant phyla and Eurotiomycetes, Saccharomycetes, were the most abundant class. The average abundance of fungal genera were Histoplasma (36 %) and Saccharomyces (31 %). The most abundant species were Histoplasma capsulatum (36 %) and Saccharomyces pastorianus (23 %). Other less abundant but may be functionally important genera and species included Candida (2.6 %) and Saccharomycescerevisiae (8 %).

CONCLUSION: The profile and abundance of the gut fungi in healthy Saudi children reveals important differences compared to Western literature. Accordingly, this report represents a more appropriate reference than Western data to use as controls for regional studies aiming to identify fungi associated with disease.}, } @article {pmid37992406, year = {2023}, author = {Jesser, KJ and Trueba, G and Konstantinidis, KT and Levy, K}, title = {Why are so many enteric pathogen infections asymptomatic? Pathogen and gut microbiome characteristics associated with diarrhea symptoms and carriage of diarrheagenic E. coli in northern Ecuador.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2281010}, pmid = {37992406}, issn = {1949-0984}, support = {K01 AI103544/AI/NIAID NIH HHS/United States ; T32 ES007032/ES/NIEHS NIH HHS/United States ; T32 ES012870/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; Escherichia coli ; *Escherichia coli Infections/microbiology ; *Gastrointestinal Microbiome/genetics ; Ecuador ; Case-Control Studies ; Diarrhea/microbiology ; }, abstract = {A high proportion of enteric infections, including those caused by diarrheagenic Escherichia coli (DEC), are asymptomatic for diarrhea. The factors responsible for the development of diarrhea symptoms, or lack thereof, remain unclear. Here, we used DEC isolate genome and whole stool microbiome data from a case-control study of diarrhea in Ecuador to examine factors associated with diarrhea symptoms accompanying DEC carriage. We investigated i) pathogen abundance, ii) gut microbiome characteristics, and iii) strain-level pathogen characteristics from DEC infections with diarrhea symptoms (symptomatic infections) and without diarrhea symptoms (asymptomatic infections). We also included data from individuals with and without diarrhea who were not infected with DEC (uninfected cases and controls). i) E. coli relative abundance in the gut microbiome was highly variable, but higher on-average in individuals with symptomatic compared to asymptomatic DEC infections. Similarly, the number and relative abundances of virulence genes in the gut were higher in symptomatic than asymptomatic DEC infections. ii) Measures of microbiome diversity were similar regardless of diarrhea symptoms or DEC carriage. Proteobacterial families that have been described as pathobionts were enriched in symptomatic infections and uninfected cases, whereas potentially beneficial taxa, including the Bacteroidaceae and Bifidobacteriaceae, were more abundant in individuals without diarrhea. An analysis of high-level gene functions recovered in metagenomes revealed that genes that were differentially abundant by diarrhea and DEC infection status were more abundant in symptomatic than asymptomatic DEC infections. iii) DEC isolates from symptomatic versus asymptomatic individuals showed no significant differences in virulence or accessory gene content, and there was no phylogenetic signal associated with diarrhea symptoms. Together, these data suggest signals that distinguish symptomatic from asymptomatic DEC infections. In particular, the abundance of E. coli, the virulence gene content of the gut microbiome, and the taxa present in the gut microbiome have an apparent role.}, } @article {pmid37991826, year = {2023}, author = {Song, H and Xue, H and Zhang, Z and Wang, J and Li, A and Zhang, J and Luo, P and Zhan, M and Zhou, X and Chen, L and Fang, Y}, title = {Amelioration of Type 2 Diabetes Using Four Strains of Lactobacillus Probiotics: Effects on Gut Microbiota Reconstitution-Mediated Regulation of Glucose Homeostasis, Inflammation, and Oxidative Stress in Mice.}, journal = {Journal of agricultural and food chemistry}, volume = {71}, number = {51}, pages = {20801-20814}, doi = {10.1021/acs.jafc.3c04665}, pmid = {37991826}, issn = {1520-5118}, mesh = {Mice ; Animals ; Lactobacillus ; *Diabetes Mellitus, Type 2 ; *Gastrointestinal Microbiome/physiology ; Inflammation ; *Probiotics ; Glucose ; Diet, High-Fat ; Oxidative Stress ; Homeostasis ; }, abstract = {This study aims to explore the preventive effects and underlying mechanisms of Lactobacillus fermentum CKCC1858 (CKCC1), L. fermentum CKCC1369 (CKCC2), Lactobacillus plantarum CKCC1312 (CKCC3), and Lactobacillus gasseri CKCC1913 (CKCC4) on high-fat diet combined with streptozotocin (HFD/STZ)-stimulated type 2 diabetes (T2D) in mice. Generally, the results indicated that most of the four probiotics reduced weight loss and liver and pancreas damage, significantly (p < 0.05) improved glucose metabolism by regulating glucagon-like peptide-1 (GLP-1), fasting glucose and insulin levels, and increasing expression of glucose transporters. Probiotics improved hyperlipemia, inflammation, and oxidative stress by reducing the secretion of blood lipids and proinflammatory cytokines, increasing antioxidant enzymes. Metagenomic results revealed that probiotics restored gut microbiota via enhancing (reducing) the relative abundance of beneficial bacteria (harmful bacteria) and altered specific metabolic pathways in T2D mice. CKCC1, CKCC3, and CKCC4 showed excellent effects compared to CKCC2. These results indicated that probiotics potentially prevented T2D, which is strain-specific.}, } @article {pmid37989857, year = {2023}, author = {Licandro, H and Truntzer, C and Fromentin, S and Morabito, C and Quinquis, B and Pons, N and Martin, C and Blottière, HM and Neyraud, E}, title = {The bacterial species profiles of the lingual and salivary microbiota differ with basic tastes sensitivity in human.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {20339}, pmid = {37989857}, issn = {2045-2322}, support = {ANR-15-IDEX-0003//"Investissements d'Avenir" program, project ISITE-BFC/ ; ANR-15-IDEX-0003//"Investissements d'Avenir" program, project ISITE-BFC/ ; ANR-15-IDEX-0003//"Investissements d'Avenir" program, project ISITE-BFC/ ; ANR-15-IDEX-0003//"Investissements d'Avenir" program, project ISITE-BFC/ ; }, mesh = {Humans ; *Taste Perception ; Taste ; Saliva ; Tongue ; *Microbiota ; }, abstract = {Taste perception is crucial and impairments, which can be linked to pathologies, can lead to eating disorders. It is triggered by taste compounds stimulating receptors located on the tongue. However, the tongue is covered by a film containing saliva and microorganisms suspected to modulate the taste receptor environment. The present study aimed to elucidate the links between taste sensitivity (sweetness, sourness, bitterness, saltiness, umami) and the salivary as well as the tongue microbiota using shotgun metagenomics. 109 bacterial species were correlated with at least one taste. Interestingly, when a species was correlated with at least two tastes, the correlations were unidirectional, indicating a putative global implication. Some Streptococcus, SR1 and Rickenellaceae species correlated with five tastes. When comparing both ecosystems, saliva appears to be a better taste predictor than tongue. This work shows the implication of the oral microbiota in taste and exhibits specificities depending on the ecosystem considered.}, } @article {pmid37987083, year = {2023}, author = {Yavorov-Dayliev, D and Milagro, FI and López-Yoldi, M and Clemente, I and Riezu-Boj, JI and Ayo, J and Oneca, M and Aranaz, P}, title = {Pediococcus acidilactici (pA1c®) alleviates obesity-related dyslipidemia and inflammation in Wistar rats by activating beta-oxidation and modulating the gut microbiota.}, journal = {Food & function}, volume = {14}, number = {24}, pages = {10855-10867}, doi = {10.1039/d3fo01651j}, pmid = {37987083}, issn = {2042-650X}, mesh = {Rats ; Male ; Animals ; Mice ; Rats, Wistar ; *Pediococcus acidilactici ; *Gastrointestinal Microbiome ; Obesity/metabolism ; Inflammation/drug therapy/prevention & control ; Diet, High-Fat/adverse effects ; *Hypercholesterolemia ; Cholesterol ; Mice, Inbred C57BL ; }, abstract = {Due to the importance of the gut microbiota in the regulation of energy homeostasis, probiotics have emerged as an alternative therapy to ameliorate obesity-related disturbances, including cholesterol metabolism dysregulation, dyslipidemia and inflammation. Therefore, the objectives of this study were to evaluate the effect of the probiotic strain Pediococcus acidilactici (pA1c®) on the regulation of adiposity, cholesterol and lipid metabolism, inflammatory markers and gut microbiota composition in diet-induced obese rats. Twenty-nine four-week-old male Wistar rats were divided into three groups: rats fed a control diet (CNT group, n = 8), rats fed a high fat/high sucrose diet (HFS group, n = 11), and rats fed a HFS diet supplemented with pA1c® (pA1c®group, n = 10). Organs and fat depots were weighed, and different biochemical parameters were analysed in serum. Gene expression analyses in the adipose tissue were conducted using real-time quantitative-PCR. Faecal microbiota composition was evaluated using 16S metagenomics. Animals supplemented with pA1c® exhibited a lower proportion of visceral adiposity, a higher proportion of muscle, an improvement in the total-cholesterol/HDL-cholesterol ratio and a decrease in the total cholesterol, triglyceride and aspartate aminotransaminase (AST) serum levels, together with a decrease in several inflammation-related molecules. The expression of key genes related to adipose (Adipoq, Cebpa and Pparg) and glucose (Slc2a1 and Slc2a4) metabolism in the adipose tissue was normalized by pA1c®. Moreover, it was demonstrated that pA1c® supplementation activated fatty acid β-oxidation in the adipose tissue and the liver. Metagenomics demonstrated the presence of pA1c® in the faecal samples, an increase in alpha diversity, an increase in the abundance of beneficial bacteria, and a decrease in the abundance of harmful micro-organisms, including the Streptococcus genus. Thus, our data suggest the potential of pA1c® in the prevention of obesity-related disturbances including hypercholesterolemia, hypertriglyceridemia, inflammation and gut microbiota dysbiosis.}, } @article {pmid37985845, year = {2023}, author = {Ye, Q and Sun, S and Deng, J and Chen, X and Zhang, J and Lin, S and Du, H and Gao, J and Zou, X and Lin, X and Cai, Y and Lu, Z}, title = {Using 16S rDNA and metagenomic sequencing technology to analyze the fecal microbiome of children with avoidant/restrictive food intake disorder.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {20253}, pmid = {37985845}, issn = {2045-2322}, mesh = {Humans ; Child ; Anti-Bacterial Agents ; *Avoidant Restrictive Food Intake Disorder ; Drug Resistance, Bacterial ; Macrolides ; *Microbiota ; Bacteria/genetics ; *Actinobacteria/genetics ; Eating ; RNA, Ribosomal, 16S/genetics ; }, abstract = {To investigate the gut microbiota distribution and its functions in children with avoidant/restrictive food intake disorder (ARFID). A total of 135 children were enrolled in the study, including 102 children with ARFID and 33 healthy children. Fecal samples were analyzed to explore differences in gut microbiota composition and diversity and functional differences between the ARFID and healthy control (HC) groups via 16S rDNA and metagenomic sequencing. The gut microbiota composition and diversity in children with ARFID were different from those in heathy children, but there is no difference in the composition and diversity of gut microbiota between children at the age of 3-6 and 7-12 with ARFID. At the phylum level, the most abundant microbes in the two groups identified by 16S rDNA and metagenomic sequencing were the same. At the genus level, the abundance of Bacteroides was higher in the ARFID group (P > 0.05); however, different from the result of 16SrDNA sequencing, metagenomic sequencing showed that the abundance of Bacteroides in the ARFID group was significantly higher than that in the HC group (P = 0.041). At the species level, Escherichia coli, Streptococcus thermophilus and Lachnospira eligens were the most abundant taxa in the ARFID group, and Prevotella copri, Bifidobacterium pseudocatenulatum, and Ruminococcus gnavus were the top three microbial taxa in the HC group; there were no statistically significant differences between the abundance of these microbial taxa in the two groups. LefSe analysis indicated a greater abundance of the order Enterobacterales and its corresponding family Enterobacteriaceae, the family Bacteroidaceae and corresponding genus Bacteroides, the species Bacteroides vulgatus in ARFID group, while the abundance of the phylum Actinobacteriota and its corresponding class Actinobacteria , the order Bifidobacteriales and corresponding family Bifidobacteriaceae, the genus Bifidobacterium were enriched in the HC group. There were no statistically significant differences in the Chao1, Shannon and Simpson indices between the Y1 and Y2 groups (P = 0.1, P = 0.06, P = 0.06). At the phylum level, Bacillota, Bacteroidota, Proteobacteria and Actinobacteriota were the most abundant taxa in both groups, but there were no statistically significant differences among the abundance of these bacteria (P = 0.958, P = 0.456, P = 0.473, P = 0.065). At the genus level, Faecalibacterium was more abundant in the Y2 group than in the Y1 group, and the difference was statistically significant (P = 0.037). The KEGG annotation results showed no significant difference in gut microbiota function between children with ARFID and healthy children; however, GT26 was significantly enriched in children with ARFID based on the CAZy database. The most abundant antibiotic resistance genes in the ARFID group were the vanT, tetQ, adeF, ermF genes, and the abundance of macrolide resistance genes in the ARFID group was significantly higher than that in the HC group (P = 0.041). Compared with healthy children, children with ARFID have a different distribution of the gut microbiota and functional genes. This indicates that the gut microbiome might play an important role in the pathogenesis of ARFID.Clinical trial registration: ChiCTR2300074759.}, } @article {pmid37985738, year = {2024}, author = {Batalha-Filho, H and Barreto, SB and Silveira, MHB and Miyaki, CY and Afonso, S and Ferrand, N and Carneiro, M and Sequeira, F}, title = {Disentangling the contemporary and historical effects of landscape on the population genomic variation of two bird species restricted to the highland forest enclaves of northeastern Brazil.}, journal = {Heredity}, volume = {132}, number = {2}, pages = {77-88}, pmid = {37985738}, issn = {1365-2540}, mesh = {Animals ; *Genetic Variation ; Brazil ; *Metagenomics ; Forests ; Birds/genetics ; Genetics, Population ; Phylogeny ; Ecosystem ; }, abstract = {Investigating the impact of landscape features on patterns of genetic variation is crucial to understand spatially dependent evolutionary processes. Here, we assess the population genomic variation of two bird species (Conopophaga cearae and Sclerurus cearensis) through the Caatinga moist forest enclaves in northeastern Brazil. To infer the evolutionary dynamics of bird populations through the Late Quaternary, we used genome-wide polymorphism data obtained from double-digestion restriction-site-associated DNA sequencing (ddRADseq), and integrated population structure analyses, historical demography models, paleodistribution modeling, and landscape genetics analyses. We found the population differentiation among enclaves to be significantly related to the geographic distance and historical resistance across the rugged landscape. The climate changes at the end of the Pleistocene to the Holocene likely triggered synchronic population decline in all enclaves for both species. Our findings revealed that both geographic distance and historical connectivity through highlands are important factors that can explain the current patterns of genetic variation. Our results further suggest that levels of population differentiation and connectivity cannot be explained purely on the basis of contemporary environmental conditions. By combining historical demographic analyses and niche modeling predictions in a historical framework, we provide strong evidence that climate fluctuations of the Quaternary promoted population differentiation and a high degree of temporal synchrony among population size changes in both species.}, } @article {pmid37985659, year = {2023}, author = {Mejia, ME and Mercado-Evans, V and Zulk, JJ and Ottinger, S and Ruiz, K and Ballard, MB and Fowler, SW and Britton, RA and Patras, KA}, title = {Vaginal microbial dynamics and pathogen colonization in a humanized microbiota mouse model.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {87}, pmid = {37985659}, issn = {2055-5008}, support = {T32 GM152777/GM/NIGMS NIH HHS/United States ; R25 GM056929/GM/NIGMS NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; T32 GM136554/GM/NIGMS NIH HHS/United States ; R01 DK128053/DK/NIDDK NIH HHS/United States ; F31 AI167547/AI/NIAID NIH HHS/United States ; F31 HD111236/HD/NICHD NIH HHS/United States ; F31 AI167538/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Female ; Animals ; Mice ; RNA, Ribosomal, 16S/genetics ; *Escherichia coli/genetics ; Mice, Inbred C57BL ; Vagina ; *Microbiota ; Disease Models, Animal ; Streptococcus agalactiae/genetics ; }, abstract = {Vaginal microbial composition is associated with differential risk of urogenital infection. Although Lactobacillus spp. are thought to confer protection against infection, the lack of in vivo models resembling the human vaginal microbiota remains a prominent barrier to mechanistic discovery. Using 16S rRNA amplicon sequencing of C57BL/6J female mice, we found that vaginal microbial composition varies within and between colonies across three vivaria. Noting vaginal microbial plasticity in conventional mice, we assessed the vaginal microbiome of humanized microbiota mice ([HMb]mice). Like the community structure in conventional mice, [HMb]mice vaginal microbiota clustered into community state types but, uniquely, [HMb]mice communities were frequently dominated by Lactobacillus or Enterobacteriaceae. Compared to conventional mice, [HMb]mice were less susceptible to uterine ascension by urogenital pathobionts group B Streptococcus (GBS) and Prevotella bivia. Although Escherichia and Lactobacillus both correlated with the absence of uterine GBS, vaginal pre-inoculation with exogenous [HMb]mouse-derived E. coli, but not Ligilactobacillus murinus, reduced vaginal GBS burden. Overall, [HMb]mice serve as a useful model to elucidate the role of endogenous microbes in conferring protection against urogenital pathogens.}, } @article {pmid37984782, year = {2024}, author = {Venkatachalam, S and Vipindas, PV and Jabir, T and Jain, A and Krishnan, KP}, title = {Metagenomic insights into novel microbial lineages with distinct ecological functions in the Arctic glacier foreland ecosystems.}, journal = {Environmental research}, volume = {241}, number = {}, pages = {117726}, doi = {10.1016/j.envres.2023.117726}, pmid = {37984782}, issn = {1096-0953}, mesh = {*Metagenome ; Ice Cover/microbiology ; Phylogeny ; *Microbiota/genetics ; Carbon/metabolism ; Sulfur ; Nitrogen ; }, abstract = {Land-terminating glaciers are retreating globally, resulting in the expansion of the ice-free glacier forelands (GFs). These GFs act as a natural laboratory to study microbial community succession, soil formation, and ecosystem development. Here, we have employed gene-centric and genome-resolved metagenomic approaches to disseminate microbial diversity, community structure, and their associated biogeochemical processes involved in the carbon, nitrogen, and sulfur cycling across three GF ecosystems. Here, we present a compendium of draft Metagenome Assembled Genomes (MAGs) belonging to bacterial (n = 899) and archaeal (n = 4) domains. These MAGs were reconstructed using a total of 27 shotgun metagenomic datasets obtained from three different GFs, including Midtre Lovénbreen glacier (Svalbard), Russell glacier (Greenland), and Storglaciaren (Sweden). The taxonomic classification revealed that 98% of MAGs remained unclassified at species levels, suggesting the presence of novel microbial lineages. The abundance of metabolic genes associated with carbon, nitrogen, and sulfur cycling pathways varied between and within the samples collected across the three GF ecosystems. Our findings indicate that MAGs from different GFs share close phylogenetic relationships but exhibit significant differences in abundance, distribution patterns, and metabolic functions. This compendium of novel MAGs, encompassing autotrophic, phototrophic, and chemolithoautotrophic microbial groups reconstructed from GF ecosystems, represents a valuable resource for further studies.}, } @article {pmid37984136, year = {2024}, author = {Zhang, M and Xiong, Y and Sun, H and Xiao, T and Xiao, E and Sun, X and Li, B and Sun, W}, title = {Selective pressure of arsenic and antimony co-contamination on microbial community in alkaline sediments.}, journal = {Journal of hazardous materials}, volume = {464}, number = {}, pages = {132948}, doi = {10.1016/j.jhazmat.2023.132948}, pmid = {37984136}, issn = {1873-3336}, mesh = {Antimony ; *Arsenic/analysis ; Environmental Monitoring ; *Microbiota ; Biodegradation, Environmental ; }, abstract = {Although response of microbial community to arsenic (As) and antimony (Sb) co-contamination has been investigated in neutral and acidic environments, little is known in alkaline environment. Herein, the microbial response and survival strategies under the stress of As and Sb co-contamination were determined in the alkaline sediments. Elevated concentrations of As (13700 ± 5012 mg/kg) and Sb (10222 ± 1619 mg/kg) were introduced into the alkaline sediments by the mine drainage, which was partially adopted in the aquatic environment and resulted in a relatively lower contamination (As, 6633 ± 1707 mg/kg; Sb, 6108 ± 1095 mg/kg) in the downstream sediments. The microbial richness was significantly damaged and the microbial compositions were dramatically shifted by the As and Sb co-contamination. Metagenomic analysis shed light on the survival strategies of the microbes under the pressure of As and Sb co-contamination including metal oxidation coupled with denitrification, metal reduction, and metal resistance. The representative microbes were revealed in the sediments with higher (Halomonas) and lower (Thiobacillus, Hydrogenophaga and Flavihumibacter) As and Sb concentration, respectively. In addition, antibiotic resistance genes were found to co-occur with metal resistance genes in the assembled bins. These findings might provide theoretical guidance for bioremediation of As and Sb co-contamination in alkaline environment.}, } @article {pmid37982653, year = {2023}, author = {Jang, Y and Kang, J-S and Bae, EH and Lee, J}, title = {Metagenome-assembled genomes of the GU0601 sample (the Han River, South Korea).}, journal = {Microbiology resource announcements}, volume = {12}, number = {12}, pages = {e0068823}, pmid = {37982653}, issn = {2576-098X}, support = {NIBR202314101//Ministry of Environment (MOE)/ ; RS-2023-00209930//National Research Foundation of Korea (NRF)/ ; }, abstract = {We generated metagenome sequences of the GU0601 sample collected from the Han River and constructed metagenome-assembled genomes (MAGs) to identify their bacterial composition. We identified six MAGs belonging to Alphaproteobacteria, Cyanobacteria, and Flavobacteria.}, } @article {pmid37982636, year = {2023}, author = {Gaudino, M and Salem, E and Ducatez, MF and Meyer, G}, title = {Identification of Astrovirus in the virome of the upper and lower respiratory tracts of calves with acute signs of bronchopneumonia.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0302623}, pmid = {37982636}, issn = {2165-0497}, support = {FluD//Agence Nationale de la Recherche (ANR)/ ; RespiCare//Institut Carnot Santé Animale (ICSA)/ ; }, mesh = {Animals ; Cattle ; Humans ; Swine ; *Astroviridae Infections/veterinary ; *Bronchopneumonia/veterinary ; Virome ; Phylogeny ; *Astroviridae/genetics ; *Cattle Diseases/diagnosis ; *Encephalitis ; Respiratory System ; Feces ; }, abstract = {Astroviruses (AstV) are known suspects of enteric disease in humans and livestock. Recently, AstV have been linked to encephalitis in immunocompromised patients and other animals, such as cattle, minks, and swine. In our study, we also identified AstV in the respiratory samples of calves with signs of bronchopneumonia, suggesting that their tropism could be even broader. We obtained one bovine AstV (BAstV) complete genome sequence by next-generation sequencing and showed that respiratory and enteric AstV from different species formed a divergent genetic cluster with AstV isolated from encephalitis cases, indicating that tropism might be strain-specific. These data provide further insight into understanding the biology of these understudied pathogens and suggest BAstV as a potential new candidate for bovine respiratory disease.}, } @article {pmid37980332, year = {2023}, author = {Zeamer, AL and Salive, MC and An, X and Beaudoin, FL and House, SL and Stevens, JS and Zeng, D and Neylan, TC and Clifford, GD and Linnstaedt, SD and Rauch, SL and Storrow, AB and Lewandowski, C and Musey, PI and Hendry, PL and Sheikh, S and Jones, CW and Punches, BE and Swor, RA and Hudak, LA and Pascual, JL and Seamon, MJ and Harris, E and Pearson, C and Peak, DA and Merchant, RC and Domeier, RM and Rathlev, NK and O'Neil, BJ and Sergot, P and Sanchez, LD and Bruce, SE and Kessler, RC and Koenen, KC and McLean, SA and Bucci, V and Haran, JP}, title = {Association between microbiome and the development of adverse posttraumatic neuropsychiatric sequelae after traumatic stress exposure.}, journal = {Translational psychiatry}, volume = {13}, number = {1}, pages = {354}, pmid = {37980332}, issn = {2158-3188}, support = {R01 AG067483/AG/NIA NIH HHS/United States ; RF1 AG067483/AG/NIA NIH HHS/United States ; U01 MH110925/MH/NIMH NIH HHS/United States ; }, mesh = {Adult ; Humans ; *Microbiota ; *Stress Disorders, Post-Traumatic/metabolism ; *Gastrointestinal Microbiome ; Feces/microbiology ; Biological Availability ; }, abstract = {Patients exposed to trauma often experience high rates of adverse post-traumatic neuropsychiatric sequelae (APNS). The biological mechanisms promoting APNS are currently unknown, but the microbiota-gut-brain axis offers an avenue to understanding mechanisms as well as possibilities for intervention. Microbiome composition after trauma exposure has been poorly examined regarding neuropsychiatric outcomes. We aimed to determine whether the gut microbiomes of trauma-exposed emergency department patients who develop APNS have dysfunctional gut microbiome profiles and discover potential associated mechanisms. We performed metagenomic analysis on stool samples (n = 51) from a subset of adults enrolled in the Advancing Understanding of RecOvery afteR traumA (AURORA) study. Two-, eight- and twelve-week post-trauma outcomes for post-traumatic stress disorder (PTSD) (PTSD checklist for DSM-5), normalized depression scores (PROMIS Depression Short Form 8b) and somatic symptom counts were collected. Generalized linear models were created for each outcome using microbial abundances and relevant demographics. Mixed-effect random forest machine learning models were used to identify associations between APNS outcomes and microbial features and encoded metabolic pathways from stool metagenomics. Microbial species, including Flavonifractor plautii, Ruminococcus gnavus and, Bifidobacterium species, which are prevalent commensal gut microbes, were found to be important in predicting worse APNS outcomes from microbial abundance data. Notably, through APNS outcome modeling using microbial metabolic pathways, worse APNS outcomes were highly predicted by decreased L-arginine related pathway genes and increased citrulline and ornithine pathways. Common commensal microbial species are enriched in individuals who develop APNS. More notably, we identified a biological mechanism through which the gut microbiome reduces global arginine bioavailability, a metabolic change that has also been demonstrated in the plasma of patients with PTSD.}, } @article {pmid37979958, year = {2024}, author = {Prinz, E and Schlupp, L and Dyson, G and Barrett, M and Szymczak, A and Velasco, C and Izda, V and Dunn, CM and Jeffries, MA}, title = {OA susceptibility in mice is partially mediated by the gut microbiome, is transferrable via microbiome transplantation and is associated with immunophenotype changes.}, journal = {Annals of the rheumatic diseases}, volume = {83}, number = {3}, pages = {382-393}, pmid = {37979958}, issn = {1468-2060}, support = {K08 AR070891/AR/NIAMS NIH HHS/United States ; R33 AR078075/AR/NIAMS NIH HHS/United States ; I01 CX002494/CX/CSRD VA/United States ; P20 GM125528/GM/NIGMS NIH HHS/United States ; R61 AR078075/AR/NIAMS NIH HHS/United States ; R01 AR076440/AR/NIAMS NIH HHS/United States ; }, mesh = {Mice ; Female ; Animals ; *Gastrointestinal Microbiome ; *Osteophyte/pathology ; Immunophenotyping ; *Microbiota ; *Synovitis/pathology ; Disease Models, Animal ; Mice, Inbred C57BL ; *Cartilage, Articular/pathology ; }, abstract = {OBJECTIVES: The Murphy Roths Large (MRL)/MpJ 'superhealer' mouse strain is protected from post-traumatic osteoarthritis (OA), although no studies have evaluated the microbiome in the context of this protection. This study characterised microbiome differences between MRL and wild-type mice, evaluated microbiome transplantation and OA and investigated microbiome-associated immunophenotypes.

METHODS: Cecal material from mixed sex C57BL6/J (B6) or female MRL/MpJ (MRL) was transplanted into B6 and MRL mice, then OA was induced by disruption of the medial meniscus surgery (DMM). In other experiments, transplantation was performed after DMM and transplantation was performed into germ-free mice. Transplanted mice were bred through F2. OARSI, synovitis and osteophyte scores were determined blindly 8 weeks after DMM. 16S microbiome sequencing was performed and metagenomic function was imputed. Immunophenotypes were determined using mass cytometry.

RESULTS: MRL-into-B6 transplant prior to DMM showed reduced OA histopathology (OARSI score 70% lower transplant vs B6 control), synovitis (60% reduction) and osteophyte scores (30% reduction) 8 weeks after DMM. When performed 48 hours after DMM, MRL-into-B6 transplant improved OA outcomes but not when performed 1-2 weeks after DMM. Protection was seen in F1 (60% reduction) and F2 progeny (30% reduction). Several cecal microbiome clades were correlated with either better (eg, Lactobacillus, R=-0.32, p=0.02) or worse (eg, Rikenellaceae, R=0.43, p=0.001) OA outcomes. Baseline immunophenotypes associated with MRL-into-B6 transplants and MRL included reduced double-negative T cells and increased CD25+CD4+ T cells.

CONCLUSION: The gut microbiome is responsible in part for OA protection in MRL mice and is transferrable by microbiome transplantation. Transplantation induces resting systemic immunophenotyping changes that correlate with OA protection.}, } @article {pmid37979711, year = {2024}, author = {Chen, Q and Luo, Y and Shen, Y and Li, X and Yang, H and Li, J and Wang, J and Xiao, Y}, title = {Fructose corn syrup induces inflammatory injury and obesity by altering gut microbiota and gut microbiota-related arachidonic acid metabolism.}, journal = {The Journal of nutritional biochemistry}, volume = {124}, number = {}, pages = {109527}, doi = {10.1016/j.jnutbio.2023.109527}, pmid = {37979711}, issn = {1873-4847}, mesh = {Mice ; Animals ; *Gastrointestinal Microbiome ; Arachidonic Acid/adverse effects ; Zea mays ; Fructose/adverse effects ; Obesity/metabolism ; Dietary Fats/pharmacology ; *Metabolic Diseases ; Prostaglandins ; Mice, Inbred C57BL ; Diet, High-Fat ; }, abstract = {Excessive fructose corn syrup (FCS) intake brings a series of health problems. The aim of the present study was to explore the mechanism of FCS-induced metabolic disorders from the perspective of gut microbiota. Mice were fed for 16 weeks with normal or 30% FCS drinking water. Compared to the control group, FCS caused significantly higher fat deposition, hepatic steatosis, liver and intestinal inflammatory damages (P<.05). FCS increased the abundance of Muribaculaceae in vivo and in vitro, which was positively correlated with the indices of metabolic disorders (P<.05). In vivo and in vitro data indicated that FCS enhanced the microbial function involved in pentose phosphate pathway and arachidonic acid metabolism, metabolomics further demonstrated that FCS led to an increase in prostaglandins (the catabolites of arachidonic acid) (P<.05). Our study confirmed that FCS can directly promote gut microbiota to synthesize inflammatory factor prostaglandins, which provides new insights and directions for the treatment of FCS-induced metabolic disorders and inflammation.}, } @article {pmid37979568, year = {2024}, author = {Peng, Y and Gu, X and Zhang, M and Yan, P and Sun, S and He, S}, title = {Simultaneously enhanced autotrophic-heterotrophic denitrification in iron-based ecological floating bed by plant biomass: Metagenomics insights into microbial communities, functional genes and nitrogen metabolic pathways.}, journal = {Water research}, volume = {248}, number = {}, pages = {120868}, doi = {10.1016/j.watres.2023.120868}, pmid = {37979568}, issn = {1879-2448}, mesh = {*Denitrification ; Nitrogen ; Iron ; Biomass ; Bioreactors ; Autotrophic Processes ; *Microbiota ; Bacteria/genetics ; Metabolic Networks and Pathways ; Water ; Nitrates ; }, abstract = {In this study, the ecological floating bed supporting with zero-valent iron (ZVI) and plant biomass (EFB-IB) was constructed to improve nitrogen removal from low-polluted water. The effects of ZVI coupling with plant biomass on microbial community structure, metabolic pathways and functional genes were analyzed by metagenomic sequencing, and the mechanism for nitrogen removal was revealed. Results showed that compared with mono-ZVI system (EFB-C), the denitrification efficiencies of EFB-IB were effectively enhanced, with the higher average NO3[-]-N removal efficiencies of 22.60-59.19%. Simultaneously, the average NH4[+]-N removal efficiencies were 73.08-91.10%. Metagenomic analyses showed that EFB-IB enriched microbes that involved in iron cycle, lignocellulosic degradation and nitrogen metabolism. Plant biomass addition simultaneously increased the relative abundances of autotrophic and heterotrophic denitrifying bacteria. Network analysis showed the cooperation between autotrophic and heterotrophic denitrifying bacteria in EFB-IB. Moreover, compared with EFB-C, plant biomass addition increased the relative abundances of genes related to iron cycle, lignocellulose degradation and glycolysis processes, ensuring the production of autotrophic and heterotrophic electron donors. Therefore, the relative abundances of key enzymes and functional genes related to denitrification were higher in EFB-IB, being beneficial to the NO3[-]-N removal. Additionally, the correlation analysis of nitrogen removal and functional genes verified the synergistic mechanism of iron-based autotrophic denitrification and plant biomass-mediated heterotrophic denitrification in EFB-IB. In summary, plant biomass has excellent potential to improve the nitrogen removal of iron-based EFB from low-polluted water.}, } @article {pmid37978289, year = {2023}, author = {Wang, C and Yu, QY and Ji, NN and Zheng, Y and Taylor, JW and Guo, LD and Gao, C}, title = {Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7437}, pmid = {37978289}, issn = {2041-1723}, mesh = {*Ecosystem ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; Genome Size ; Proton-Motive Force ; Bacteria/genetics ; Soil/chemistry ; Genome, Bacterial/genetics ; Soil Microbiology ; }, abstract = {Bacterial gene repertoires reflect adaptive strategies, contribute to ecosystem functioning and are limited by genome size. However, gene functional diversity does not necessarily correlate with taxonomic diversity because average genome size may vary by community. Here, we analyse gene functional diversity (by shotgun metagenomics) and taxonomic diversity (by 16S rRNA gene amplicon sequencing) to investigate soil bacterial communities along a natural pH gradient in 12 tropical, subtropical, and temperate forests. We find that bacterial average genome size and gene functional diversity decrease, whereas taxonomic diversity increases, as soil pH rises from acid to neutral; as a result, bacterial taxonomic and functional diversity are negatively correlated. The gene repertoire of acid-adapted oligotrophs is enriched in functions of signal transduction, cell motility, secretion system, and degradation of complex compounds, while that of neutral pH-adapted copiotrophs is enriched in functions of energy metabolism and membrane transport. Our results indicate that a mismatch between taxonomic and functional diversity can arise when environmental factors (such as pH) select for adaptive strategies that affect genome size distributions.}, } @article {pmid37975314, year = {2023}, author = {Liu, H and Ji, S and Fang, Y and Yi, X and Wu, F and Xing, F and Wang, C and Zhou, H and Xu, J and Sun, W}, title = {Microbiome Alteration in Lung Tissues of Tuberculosis Patients Revealed by Metagenomic Next-Generation Sequencing and Immune-Related Transcriptional Profile Identified by Transcriptome Sequencing.}, journal = {ACS infectious diseases}, volume = {9}, number = {12}, pages = {2572-2582}, pmid = {37975314}, issn = {2373-8227}, mesh = {Humans ; Transcriptome ; *Tuberculosis/microbiology ; Lung/microbiology ; *Microbiota ; High-Throughput Nucleotide Sequencing ; }, abstract = {This study explored alterations in the respiratory microbiome and transcriptome after Mycobacterium tuberculosis infection in tuberculosis (TB) patients. Metagenomic next-generation sequencing (mNGS) was adopted to reveal the microbiome in lung tissues from 110 TB and 25 nontuberculous (NonTB) patients. Transcriptome sequencing was performed in TB tissues (n = 3), tissues adjacent to TB (ParaTB, n = 3), and NonTB tissues (n = 3) to analyze differentially expressed genes (DEGs) and functional pathways. The microbial β diversity (p = 0.01325) in TB patients differed from that in the NonTB group, with 17 microbial species distinctively distributed. Eighty-three co-up-regulated DEGs were identified in the TB versus NonTB and the TB versus ParaTB comparison groups, and six were associated with immune response to Mtb. These DEGs were significantly enriched in the signaling pathways such as immune response, NF-κB, and B cell receptor. Data in the lung tissue microbiome and transcriptome in TB patients offer a sufficient understanding of the pathogenesis of TB.}, } @article {pmid37974518, year = {2023}, author = {Leontidou, K and Abad-Recio, IL and Rubel, V and Filker, S and Däumer, M and Thielen, A and Lanzén, A and Stoeck, T}, title = {Simultaneous analysis of seven 16S rRNA hypervariable gene regions increases efficiency in marine bacterial diversity detection.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {3484-3501}, doi = {10.1111/1462-2920.16530}, pmid = {37974518}, issn = {1462-2920}, support = {STO 414/19-1//Deutsche Forschungsgemeinschaft/ ; Fi 2089/3-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *High-Throughput Nucleotide Sequencing ; Bacteria/genetics ; Sequence Analysis, DNA ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Environmental DNA sequencing is the gold standard to reveal microbial community structures. In most applications, a one-fragment PCR approach is applied to amplify a taxonomic marker gene, usually a hypervariable region of the 16S rRNA gene. We used a new reverse complement (RC)-PCR-based assay that amplifies seven out of the nine hypervariable regions of the 16S rRNA gene, to interrogate bacterial communities in sediment samples collected from different coastal marine sites with an impact gradient. In parallel, we employed a traditional one-fragment analysis of the hypervariable V3-V4 region to investigate whether the RC-PCR reveals more of the 'unseen' diversity obtained by the one-fragment approach. As a benchmark for the full deck of diversity, we subjected the samples to PCR-free metagenomic sequencing. None of the two PCR-based approaches recorded the full taxonomic repertoire obtained from the metagenomics datasets. However, the RC-PCR approach detected 2.8 times more bacterial genera compared to the near-saturation sequenced V3-V4 samples. RC-PCR is an ideal compromise between the standard one-fragment approach and metagenomics sequencing and may guide future environmental sequencing studies, in which bacterial diversity is a central subject.}, } @article {pmid37974103, year = {2023}, author = {Khan, FA and Pandupuspitasari, NS and Huang, C and Negara, W and Ahmed, B and Putri, EM and Lestari, P and Priyatno, TP and Prima, A and Restitrisnani, V and Surachman, M and Akhadiarto, S and Darmawan, IWA and Wahyuni, DS and Herdis, H}, title = {Unlocking gut microbiota potential of dairy cows in varied environmental conditions using shotgun metagenomic approach.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {344}, pmid = {37974103}, issn = {1471-2180}, mesh = {Female ; Cattle ; Animals ; *Lactation ; Diet/veterinary ; *Gastrointestinal Microbiome ; Milk Proteins ; Gases ; Methane/metabolism ; }, abstract = {Food security and environmental pollution are major concerns for the expanding world population, where farm animals are the largest source of dietary proteins and are responsible for producing anthropogenic gases, including methane, especially by cows. We sampled the fecal microbiomes of cows from varying environmental regions of Pakistan to determine the better-performing microbiomes for higher yields and lower methane emissions by applying the shotgun metagenomic approach. We selected managed dairy farms in the Chakwal, Salt Range, and Patoki regions of Pakistan, and also incorporated animals from local farmers. Milk yield and milk fat, and protein contents were measured and correlated with microbiome diversity and function. The average milk protein content from the Salt Range farms was 2.68%, with an average peak milk yield of 45 litters/head/day, compared to 3.68% in Patoki farms with an average peak milk yield of 18 litters/head/day. Salt-range dairy cows prefer S-adenosyl-L-methionine (SAMe) to S-adenosyl-L-homocysteine (SAH) conversion reactions and are responsible for low milk protein content. It is linked to Bacteroides fragilles which account for 10% of the total Bacteroides, compared to 3% in the Patoki region. The solid Non-Fat in the salt range was 8.29%, whereas that in patoki was 6.34%. Moreover, Lactobacillus plantarum high abundance in Salt Range provided propionate as alternate sink to [H], and overcoming a Methanobrevibacter ruminantium high methane emissions in the Salt Range. Furthermore, our results identified ruminant fecal microbiomes that can be used as fecal microbiota transplants (FMT) to high-methane emitters and low-performing herds to increase farm output and reduce the environmental damage caused by anthropogenic gases emitted by dairy cows.}, } @article {pmid37973916, year = {2023}, author = {Liu, R and Zou, Y and Wang, WQ and Chen, JH and Zhang, L and Feng, J and Yin, JY and Mao, XY and Li, Q and Luo, ZY and Zhang, W and Wang, DM}, title = {Gut microbial structural variation associates with immune checkpoint inhibitor response.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7421}, pmid = {37973916}, issn = {2041-1723}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Immune Checkpoint Inhibitors/pharmacology/therapeutic use ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics ; *Neoplasms/genetics ; }, abstract = {The gut microbiota may have an effect on the therapeutic resistance and toxicity of immune checkpoint inhibitors (ICIs). However, the associations between the highly variable genomes of gut bacteria and the effectiveness of ICIs remain unclear, despite the fact that merely a few gene mutations between similar bacterial strains may cause significant phenotypic variations. Here, using datasets from the gut microbiome of 996 patients from seven clinical trials, we systematically identify microbial genomic structural variants (SVs) using SGV-Finder. The associations between SVs and response, progression-free survival, overall survival, and immune-related adverse events are systematically explored by metagenome-wide association analysis and replicated in different cohorts. Associated SVs are located in multiple species, including Akkermansia muciniphila, Dorea formicigenerans, and Bacteroides caccae. We find genes that encode enzymes that participate in glucose metabolism be harbored in these associated regions. This work uncovers a nascent layer of gut microbiome heterogeneity that is correlated with hosts' prognosis following ICI treatment and represents an advance in our knowledge of the intricate relationships between microbiota and tumor immunotherapy.}, } @article {pmid37973867, year = {2023}, author = {Goossens, P and Spooren, J and Baremans, KCM and Andel, A and Lapin, D and Echobardo, N and Pieterse, CMJ and Van den Ackerveken, G and Berendsen, RL}, title = {Obligate biotroph downy mildew consistently induces near-identical protective microbiomes in Arabidopsis thaliana.}, journal = {Nature microbiology}, volume = {8}, number = {12}, pages = {2349-2364}, pmid = {37973867}, issn = {2058-5276}, support = {grant no. 024.004.014//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; grant no. OCENW.GROOT.2019.063//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; t no. OCENW.GROOT.2019.063//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; }, mesh = {*Arabidopsis/genetics/microbiology ; Plant Diseases/microbiology ; *Oomycetes/genetics ; *Arabidopsis Proteins ; *Microbiota ; }, abstract = {Hyaloperonospora arabidopsidis (Hpa) is an obligately biotrophic downy mildew that is routinely cultured on Arabidopsis thaliana hosts that harbour complex microbiomes. We hypothesized that the culturing procedure proliferates Hpa-associated microbiota (HAM) in addition to the pathogen and exploited this model system to investigate which microorganisms consistently associate with Hpa. Using amplicon sequencing, we found nine bacterial sequence variants that are shared between at least three out of four Hpa cultures in the Netherlands and Germany and comprise 34% of the phyllosphere community of the infected plants. Whole-genome sequencing showed that representative HAM bacterial isolates from these distinct Hpa cultures are isogenic and that an additional seven published Hpa metagenomes contain numerous sequences of the HAM. Although we showed that HAM benefit from Hpa infection, HAM negatively affect Hpa spore formation. Moreover, we show that pathogen-infected plants can selectively recruit HAM to both their roots and shoots and form a soil-borne infection-associated microbiome that helps resist the pathogen. Understanding the mechanisms by which infection-associated microbiomes are formed might enable breeding of crop varieties that select for protective microbiomes.}, } @article {pmid37973864, year = {2023}, author = {Littlejohn, PT and Metcalfe-Roach, A and Cardenas Poire, E and Holani, R and Bar-Yoseph, H and Fan, YM and Woodward, SE and Finlay, BB}, title = {Multiple micronutrient deficiencies in early life cause multi-kingdom alterations in the gut microbiome and intrinsic antibiotic resistance genes in mice.}, journal = {Nature microbiology}, volume = {8}, number = {12}, pages = {2392-2405}, pmid = {37973864}, issn = {2058-5276}, mesh = {Humans ; Child ; Animals ; Mice ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/genetics ; *Malnutrition ; Drug Resistance, Microbial ; Bacteria/genetics ; Micronutrients ; }, abstract = {Globally, ~340 million children suffer from multiple micronutrient deficiencies, accompanied by high pathogenic burden and death due to multidrug-resistant bacteria. The microbiome is a reservoir of antimicrobial resistance (AMR), but the implications of undernutrition on the resistome is unclear. Here we used a postnatal mouse model that is deficient in multiple micronutrients (that is, zinc, folate, iron, vitamin A and vitamin B12 deficient) and shotgun metagenomic sequencing of faecal samples to characterize gut microbiome structure and functional potential, and the resistome. Enterobacteriaceae were enriched in micronutrient-deficient mice compared with mice fed an isocaloric experimental control diet. The mycobiome and virome were also altered with multiple micronutrient deficiencies including increased fungal pathogens such as Candida dubliniensis and bacteriophages. Despite being antibiotic naïve, micronutrient deficiency was associated with increased enrichment of genes and gene networks encoded by pathogenic bacteria that are directly or indirectly associated with intrinsic antibiotic resistance. Bacterial oxidative stress was associated with intrinsic antibiotic resistance in these mice. This analysis reveals multi-kingdom alterations in the gut microbiome as a result of co-occurring multiple micronutrient deficiencies and the implications for antibiotic resistance.}, } @article {pmid37973815, year = {2023}, author = {Lou, YC and Rubin, BE and Schoelmerich, MC and DiMarco, KS and Borges, AL and Rovinsky, R and Song, L and Doudna, JA and Banfield, JF}, title = {Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2'-fucosyllactose utilization can be facilitated by coexisting species.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7417}, pmid = {37973815}, issn = {2041-1723}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; }, mesh = {Female ; Child ; Humans ; Infant ; *Bifidobacterium/genetics/metabolism ; Trisaccharides/metabolism ; Milk, Human/chemistry ; Oligosaccharides/metabolism ; *Microbiota ; }, abstract = {The early-life gut microbiome development has long-term health impacts and can be influenced by factors such as infant diet. Human milk oligosaccharides (HMOs), an essential component of breast milk that can only be metabolized by some beneficial gut microorganisms, ensure proper gut microbiome establishment and infant development. However, how HMOs are metabolized by gut microbiomes is not fully elucidated. Isolate studies have revealed the genetic basis for HMO metabolism, but they exclude the possibility of HMO assimilation via synergistic interactions involving multiple organisms. Here, we investigate microbiome responses to 2'-fucosyllactose (2'FL), a prevalent HMO and a common infant formula additive, by establishing individualized microbiomes using fecal samples from three infants as the inocula. Bifidobacterium breve, a prominent member of infant microbiomes, typically cannot metabolize 2'FL. Using metagenomic data, we predict that extracellular fucosidases encoded by co-existing members such as Ruminococcus gnavus initiate 2'FL breakdown, thus critical for B. breve's growth. Using both targeted co-cultures and by supplementation of R. gnavus into one microbiome, we show that R. gnavus can promote extensive growth of B. breve through the release of lactose from 2'FL. Overall, microbiome cultivation combined with genome-resolved metagenomics demonstrates that HMO utilization can vary with an individual's microbiome.}, } @article {pmid37972203, year = {2023}, author = {Zheng, L and Wang, H and Lin, J and Zhou, Y and Xiao, J and Li, K}, title = {Population genomics provides insights into the genetic diversity and adaptation of the Pieris rapae in China.}, journal = {PloS one}, volume = {18}, number = {11}, pages = {e0294521}, pmid = {37972203}, issn = {1932-6203}, mesh = {Humans ; Animals ; *Butterflies/genetics ; Metagenomics ; Biodiversity ; Temperature ; *Brassica ; Genetic Variation ; }, abstract = {The cabbage white butterfly (Pieris rapae), a major agricultural pest, has become one of the most abundant and destructive butterflies in the world. It is widely distributed in a large variety of climates and terrains of China due to its strong adaptability. To gain insight into the population genetic characteristics of P. rapae in China, we resequenced the genome of 51 individuals from 19 areas throughout China. Using population genomics approaches, a dense variant map of P. rapae was observed, indicating a high level of polymorphism that could result in adaptation to a changing environment. The feature of the genetic structure suggested considerable genetic admixture in different geographical groups. Additionally, our analyses suggest that physical barriers may have played a more important role than geographic distance in driving genetic differentiation. Population history showed the effective population size of P. rapae was greatly affected by global temperature changes, with mild periods (i.e., temperatures warmer than those during glaciation but not excessively hot) leading to an increase in population size. Furthermore, by comparing populations from south and north China, we have identified selected genes related to sensing temperature, growth, neuromodulation and immune response, which may reveal the genetic basis of adaptation to different environments. Our study is the first to illustrate the genetic signatures of P. rapae in China at the population genomic level, providing fundamental knowledge of the genetic diversity and adaptation of P. rapae.}, } @article {pmid37971255, year = {2023}, author = {Martínez-Alvarez, L and Ramond, J-B and Vikram, S and León-Sobrino, C and Maggs-Kölling, G and Cowan, DA}, title = {With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {12}, pages = {e0062923}, pmid = {37971255}, issn = {1098-5336}, support = {113308//National Research Foundation (NRF)/ ; }, mesh = {*Bacteria/genetics ; Desert Climate ; Soil Microbiology ; Sodium Chloride ; *Microbiota ; }, abstract = {The hyperarid Namib Desert is one of the oldest deserts on Earth. It contains multiple clusters of playas which are saline-rich springs surrounded by halite evaporites. Playas are of great ecological importance, and their indigenous (poly)extremophilic microorganisms are potentially involved in the precipitation of minerals such as carbonates and sulfates and have been of great biotechnological importance. While there has been a considerable amount of microbial ecology research performed on various Namib Desert edaphic microbiomes, little is known about the microbial communities inhabiting its multiple playas. In this work, we provide a comprehensive taxonomic and functional potential characterization of the microbial, including viral, communities of sediment mats and halites from two distant salt pans of the Namib Desert, contributing toward a better understanding of the ecology of this biome.}, } @article {pmid37971141, year = {2024}, author = {Pečnerová, P and Lord, E and Garcia-Erill, G and Hanghøj, K and Rasmussen, MS and Meisner, J and Liu, X and van der Valk, T and Santander, CG and Quinn, L and Lin, L and Liu, S and Carøe, C and Dalerum, F and Götherström, A and Måsviken, J and Vartanyan, S and Raundrup, K and Al-Chaer, A and Rasmussen, L and Hvilsom, C and Heide-Jørgensen, MP and Sinding, MS and Aastrup, P and Van Coeverden de Groot, PJ and Schmidt, NM and Albrechtsen, A and Dalén, L and Heller, R and Moltke, I and Siegismund, HR}, title = {Population genomics of the muskox' resilience in the near absence of genetic variation.}, journal = {Molecular ecology}, volume = {33}, number = {2}, pages = {e17205}, doi = {10.1111/mec.17205}, pmid = {37971141}, issn = {1365-294X}, support = {CF20-0539//Carlsbergfondet/ ; 8021-00344B//Danmarks Frie Forskningsfond/ ; }, mesh = {Humans ; Animals ; Infant, Newborn ; *Metagenomics ; *Resilience, Psychological ; Biological Evolution ; Genomics ; Ruminants/genetics ; Genetic Variation/genetics ; }, abstract = {Genomic studies of species threatened by extinction are providing crucial information about evolutionary mechanisms and genetic consequences of population declines and bottlenecks. However, to understand how species avoid the extinction vortex, insights can be drawn by studying species that thrive despite past declines. Here, we studied the population genomics of the muskox (Ovibos moschatus), an Ice Age relict that was at the brink of extinction for thousands of years at the end of the Pleistocene yet appears to be thriving today. We analysed 108 whole genomes, including present-day individuals representing the current native range of both muskox subspecies, the white-faced and the barren-ground muskox (O. moschatus wardi and O. moschatus moschatus) and a ~21,000-year-old ancient individual from Siberia. We found that the muskox' demographic history was profoundly shaped by past climate changes and post-glacial re-colonizations. In particular, the white-faced muskox has the lowest genome-wide heterozygosity recorded in an ungulate. Yet, there is no evidence of inbreeding depression in native muskox populations. We hypothesize that this can be explained by the effect of long-term gradual population declines that allowed for purging of strongly deleterious mutations. This study provides insights into how species with a history of population bottlenecks, small population sizes and low genetic diversity survive against all odds.}, } @article {pmid37971084, year = {2023}, author = {Conteville, LC and Oliveira-Ferreira, J and Vicente, ACP}, title = {Heavy metal resistance in the Yanomami and Tunapuco microbiome.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {118}, number = {}, pages = {e230086}, pmid = {37971084}, issn = {1678-8060}, mesh = {Humans ; Copper ; Nickel ; Silver ; *Metals, Heavy ; *Mercury ; Gold ; *Microbiota/genetics ; }, abstract = {BACKGROUND: The Amazon Region hosts invaluable and unique biodiversity as well as mineral resources. Consequently, large illegal and artisanal gold mining areas exist in indigenous territories. Mercury has been used in gold mining, and some has been released into the environment and atmosphere, primarily affecting indigenous people such as the Yanomami. In addition, other heavy metals have been associated with gold mining and other metal-dispersing activities in the region.

OBJECTIVE: Investigate the gut microbiome of two semi-isolated groups from the Amazon, focusing on metal resistance.

METHODS: Metagenomic data from the Yanomami and Tunapuco gut microbiome were assembled into contigs, and their putative proteins were searched against a database of metal resistance proteins.

FINDINGS: Proteins associated with mercury resistance were exclusive in the Yanomami, while proteins associated with silver resistance were exclusive in the Tunapuco. Both groups share 77 non-redundant metal resistance (MR) proteins, mostly associated with multi-MR and operons with potential resistance to arsenic, nickel, zinc, copper, copper/silver, and cobalt/nickel. Although both groups harbour operons related to copper resistance, only the Tunapuco group had the pco operon.

CONCLUSION: The Yanomami and Tunapuco gut microbiome shows that these people have been exposed directly or indirectly to distinct scenarios concerning heavy metals.}, } @article {pmid37970720, year = {2024}, author = {Koponen, K and Kambur, O and Joseph, B and Ruuskanen, MO and Jousilahti, P and Salido, R and Brennan, C and Jain, M and Meric, G and Inouye, M and Lahti, L and Niiranen, T and Havulinna, AS and Knight, R and Salomaa, V}, title = {Role of Gut Microbiota in Statin-Associated New-Onset Diabetes-A Cross-Sectional and Prospective Analysis of the FINRISK 2002 Cohort.}, journal = {Arteriosclerosis, thrombosis, and vascular biology}, volume = {44}, number = {2}, pages = {477-487}, pmid = {37970720}, issn = {1524-4636}, mesh = {Humans ; *Hydroxymethylglutaryl-CoA Reductase Inhibitors/adverse effects ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; *Diabetes Mellitus, Type 2/diagnosis/epidemiology ; *Dyslipidemias/diagnosis/drug therapy/epidemiology ; }, abstract = {BACKGROUND: Dyslipidemia is treated effectively with statins, but treatment has the potential to induce new-onset type-2 diabetes. Gut microbiota may contribute to this outcome variability. We assessed the associations of gut microbiota diversity and composition with statins. Bacterial associations with statin-associated new-onset type-2 diabetes (T2D) risk were also prospectively evaluated.

METHODS: We examined shallow-shotgun-sequenced fecal samples from 5755 individuals in the FINRISK-2002 population cohort with a 17+-year-long register-based follow-up. Alpha-diversity was quantified using Shannon index and beta-diversity with Aitchison distance. Species-specific differential abundances were analyzed using general multivariate regression. Prospective associations were assessed with Cox regression. Applicable results were validated using gradient boosting.

RESULTS: Statin use associated with differing taxonomic composition (R[2], 0.02%; q=0.02) and 13 differentially abundant species in fully adjusted models (MaAsLin; q<0.05). The strongest positive association was with Clostridium sartagoforme (β=0.37; SE=0.13; q=0.02) and the strongest negative association with Bacteroides cellulosilyticus (β=-0.31; SE=0.11; q=0.02). Twenty-five microbial features had significant associations with incident T2D in statin users, of which only Bacteroides vulgatus (HR, 1.286 [1.136-1.457]; q=0.03) was consistent regardless of model adjustment. Finally, higher statin-associated T2D risk was seen with [Ruminococcus] torques (ΔHRstatins, +0.11; q=0.03), Blautia obeum (ΔHRstatins, +0.06; q=0.01), Blautia sp. KLE 1732 (ΔHRstatins, +0.05; q=0.01), and beta-diversity principal component 1 (ΔHRstatin, +0.07; q=0.03) but only when adjusting for demographic covariates.

CONCLUSIONS: Statin users have compositionally differing microbiotas from nonusers. The human gut microbiota is associated with incident T2D risk in statin users and possibly has additive effects on statin-associated new-onset T2D risk.}, } @article {pmid37969059, year = {2024}, author = {Staudacher, HM and Mahoney, S and Canale, K and Opie, RS and Loughman, A and So, D and Beswick, L and Hair, C and Jacka, FN}, title = {Clinical trial: A Mediterranean diet is feasible and improves gastrointestinal and psychological symptoms in irritable bowel syndrome.}, journal = {Alimentary pharmacology & therapeutics}, volume = {59}, number = {4}, pages = {492-503}, doi = {10.1111/apt.17791}, pmid = {37969059}, issn = {1365-2036}, support = {n/a//Alfred Deakin Postdoctoral Research Fellowship/ ; }, mesh = {Adult ; Humans ; *Irritable Bowel Syndrome/diagnosis ; Disaccharides/adverse effects ; *Diet, Mediterranean ; Monosaccharides ; Diet ; *Microbiota ; Fermentation ; }, abstract = {BACKGROUND: Diet is fundamental to the care of irritable bowel syndrome (IBS). However, some approaches are not appropriate for individuals experiencing psychological symptoms.

AIMS: To assess feasibility of a Mediterranean diet in IBS and its impact on gastrointestinal and psychological symptoms.

METHODS: We recruited adults with Rome IV IBS and mild or moderate anxiety and/or depressive symptoms to an unblinded 6-week randomised controlled trial. Patients were randomised to Mediterranean diet counselling or habitual diet. We collected gastrointestinal and psychological symptom data, dietary data and stool samples for metagenomic sequencing.

RESULTS: We randomised 59 individuals (29 Mediterranean diet, 30 control); 48 completed the study. The Mediterranean Diet Adherence Screener score was higher in the Mediterranean diet group than controls at week 6 (7.5 [95% CI: 6.9-8.0] vs. 5.7 [5.2-6.3], p < 0.001), and there was a greater score increase than controls (2.1 [95% CI: 1.3-2.9] vs. 0.5 [95% CI: 0.1-1.0], p = 0.004), demonstrating Mediterranean diet feasibility. There was a greater proportion of gastrointestinal symptom responders in the Mediterranean diet group than controls (24/29, 83% vs. 11/30, 37%, p < 0.001) and depression responders (15/29, 52% vs. 6/30 20%, p = 0.015). There was no difference in FODMAP intake at week 6 (p = 0.51). Gastrointestinal adverse events were similar (p = 0.588). There were no differences in change in microbiome parameters between groups.

CONCLUSIONS: A Mediterranean diet is feasible in IBS and leads to improvement in gastrointestinal and psychological symptoms. Although this study was unblinded, these findings together with the broader benefits of the Mediterranean diet, provide strong impetus for future research in IBS. Australia New Zealand Clinical Trials Registry: ACTRN12620001362987.}, } @article {pmid37968659, year = {2023}, author = {Abouelkhair, MA and Roozitalab, A and Elsakhawy, OK}, title = {Molecular characterization of a reptarenavirus detected in a Colombian Red-Tailed Boa (Boa constrictor imperator).}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {265}, pmid = {37968659}, issn = {1743-422X}, mesh = {Humans ; Animals ; *Arenaviridae/genetics ; *Boidae ; Colombia ; Biological Evolution ; Genotype ; }, abstract = {The global decline in biodiversity is a matter of great concern for members of the class Reptilia. Reptarenaviruses infect snakes, and have been linked to various clinical conditions, such as Boid Inclusion Body Disease (BIBD) in snakes belonging to the families Boidae and Pythonidae. However, there is a scarcity of information regarding reptarenaviruses found in snakes in both the United States and globally. This study aimed to contribute to the understanding of reptarenavirus diversity by molecularly characterizing a reptarenavirus detected in a Colombian Red-Tailed Boa (Boa constrictor imperator). Using a metagenomics approach, we successfully identified, and de novo assembled the whole genomic sequences of a reptarenavirus in a Colombian Red-Tailed Boa manifesting clinically relevant symptoms consistent with BIBD. The analysis showed that the Colombian Red-Tailed Boa in this study carried the University of Giessen virus (UGV-1) S or S6 (UGV/S6) segment and L genotype 7. The prevalence of the UGV/S6 genotype, in line with prior research findings, implies that this genotype may possess specific advantageous characteristics or adaptations that give it a competitive edge over other genotypes in the host population. This research underscores the importance of monitoring and characterizing viral pathogens in captive and wild snake populations. Knowledge of such viruses is crucial for the development of effective diagnostic methods, potential intervention strategies, and the conservation of vulnerable reptilian species. Additionally, our study provides valuable insights for future studies focusing on the evolutionary history, molecular epidemiology, and biological properties of reptarenaviruses in boas and other snake species.}, } @article {pmid37967575, year = {2024}, author = {Adnan, D and Trinh, JQ and Sharma, D and Alsayid, M and Bishehsari, F}, title = {Early-onset Colon Cancer Shows a Distinct Intestinal Microbiome and a Host-Microbe Interaction.}, journal = {Cancer prevention research (Philadelphia, Pa.)}, volume = {17}, number = {1}, pages = {29-38}, pmid = {37967575}, issn = {1940-6215}, support = {K23 AA025387/AA/NIAAA NIH HHS/United States ; R01 CA279487/CA/NCI NIH HHS/United States ; R21 CA277110/CA/NCI NIH HHS/United States ; TL1 TR002388/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Middle Aged ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; *Colonic Neoplasms ; *Microbiota ; Feces ; *Colorectal Neoplasms/genetics ; }, abstract = {UNLABELLED: The incidence rate of colorectal cancer in younger adults has been rising in developed countries. This trend may be attributed to environmental exposures as a result of lifestyle changes. Many of the lifestyle factors that promote colorectal cancer can also affect the gut microbiome, which may be associated with colorectal cancer risks. The role of the microbiome in the ongoing rise of early-onset colorectal cancer is unknown. Here, we aimed to investigate age-related differences in the gut microbiome of patients with colorectal cancer and healthy individuals by examining both the fecal and tumor microbiomes. We utilized the publicly accessible data on fecal shotgun metagenomics from CuratedMetagenomeData and TCGA via the GDC Data Portal. Comparison of 701 colorectal cancer and 693 controls revealed that microbial features were age dependent, with a significant difference in species enrichment between early-onset (<50 years) and late-onset (>65 years) patients with colorectal cancer. Analysis of the tumor-associated microbiome in a separate dataset of 85 patients with colorectal cancer verified age-specific differences in taxon abundance between early- and late-onset patients with colorectal cancer. Finally, using host gene expression data, we found a stronger microbe-host interaction in early- vs. late-onset colorectal cancers. Altogether, these findings indicate that microbial features were age-dependent with stronger microbial-host interactions at the tumor site in early-onset colorectal cancers, suggesting a direct role of microbes in tumorigenesis via interaction with cancer-related pathways in this age group.

PREVENTION RELEVANCE: Early-onset colorectal cancer is on the rise, presumably because of changes in environmental exposures. Lifestyle changes may contribute to colorectal cancer via alterations in gut microbes. Here, we show that microbial association with colorectal cancer is age-dependent, and microbe interactions with tumor pathways are stronger in young versus older colorectal cancers.}, } @article {pmid37967008, year = {2023}, author = {Yew, WC and Young, GR and Nelson, A and Cheung, W and Stewart, CJ and Bridge, SH and Granger, C and Berrington, JE and Embleton, ND and Smith, DL}, title = {The core phageome and its interrelationship with preterm human milk lipids.}, journal = {Cell reports}, volume = {42}, number = {11}, pages = {113373}, doi = {10.1016/j.celrep.2023.113373}, pmid = {37967008}, issn = {2211-1247}, mesh = {Infant ; Female ; Humans ; Infant, Newborn ; *Milk, Human ; Infant, Premature ; Virome ; Lactation ; *Bacteriophages ; Fatty Acids ; }, abstract = {Phages and lipids in human milk (HM) may benefit preterm infant health by preventing gastrointestinal pathobiont overgrowth and microbiome modulation. Lipid association may promote vertical transmission of phages to the infant. Despite this, interrelationships between lipids and phages are poorly characterized in preterm HM. Shotgun metagenomics and untargeted lipidomics of phage and lipid profiles from 99 preterm HM samples reveals that phages are abundant and prevalent from the first week and throughout the first 100 days of lactation. Phage-host richness of preterm HM increases longitudinally. Core phage communities characterized by Staphylococcus- and Propionibacterium-infecting phages are significantly correlated with long-chain fatty acid abundances over lactational age. We report here a phage-lipid interaction in preterm HM, highlighting the potential importance of phage carriage in preterm HM. These results reveal possible strategies for phage carriage in HM and their importance in early-life microbiota development.}, } @article {pmid37966591, year = {2024}, author = {Heinrichs, ME and Piedade, GJ and Popa, O and Sommers, P and Trubl, G and Weissenbach, J and Rahlff, J}, title = {Breaking the Ice: A Review of Phages in Polar Ecosystems.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2738}, number = {}, pages = {31-71}, pmid = {37966591}, issn = {1940-6029}, mesh = {*Bacteriophages ; Ecosystem ; Biomass ; Biological Evolution ; Cell Death ; *Viroids ; }, abstract = {Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges such as restricted ecosystem access and low biomass. Understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage-host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.}, } @article {pmid37966405, year = {2024}, author = {Liu, J and Jiang, J and Lan, Y and Li, C and Han, R and Wang, J and Wang, T and Zhao, Z and Fan, Z and He, L and Fang, J}, title = {Metagenomic analysis of oral and intestinal microbiome of patients during the initial stage of orthodontic treatment.}, journal = {American journal of orthodontics and dentofacial orthopedics : official publication of the American Association of Orthodontists, its constituent societies, and the American Board of Orthodontics}, volume = {165}, number = {2}, pages = {161-172.e3}, doi = {10.1016/j.ajodo.2023.07.019}, pmid = {37966405}, issn = {1097-6752}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Dental Plaque ; Prospective Studies ; Metagenome ; Bacteria/genetics ; *Periodontal Diseases ; Dental Plaque Index ; }, abstract = {INTRODUCTION: This prospective study analyzed changes in the oral and intestinal microbiomes in patients before and after fixed orthodontic treatment, elucidating the impacts of fixed orthodontic treatment on patient health and metabolism.

METHODS: Metagenomic analysis was conducted on stool, dental plaque, and saliva samples from 10 fixed orthodontic patients. All the samples were sequenced with Illumina NovaSeq 6000 with a paired-end sequencing length of 150 bp. Identification of taxa in metagenomes and functional annotation of genes of the microbiota were performed using the data after quality control. Clinical periodontal parameters, including the gingiva index, plaque index, and pocket probing depth, were examined at each time point in triplicates. Patients also received a table to record their oral hygiene habits of brushing, flossing, and dessert consumption frequency over 1 month.

RESULTS: The brushing and flossing times per day of patients were significantly increased after treatment compared with baseline. The number of times a patient ate dessert daily was also fewer after treatment than at baseline. In addition, the plaque index decreased significantly, whereas the pH value of saliva, gingiva index, and pocket probing depth did not change. No significant differences were observed between the participants before and after orthodontic treatment regarding alpha-diversity analysis of the gut, dental plaque, or saliva microbiota. However, on closer analysis, periodontal disease-associated bacteria levels in the oral cavity remain elevated. Alterations in gut microbiota were also observed after orthodontic treatment.

CONCLUSIONS: The richness and diversity of the microbiome did not change significantly during the initial stage of fixed orthodontic treatment. However, the levels of periodontal disease-associated bacteria increased.}, } @article {pmid37965618, year = {2023}, author = {Ogola, HJO and Ijoma, GN and Edokpayi, JN}, title = {Sediment microbiome diversity and functional profiles of unprotected arid-tropical natural wetlands in South Africa revealed by shotgun metagenomics data.}, journal = {Data in brief}, volume = {51}, number = {}, pages = {109726}, pmid = {37965618}, issn = {2352-3409}, abstract = {The Limpopo province, located in the arid-tropical region in northeastern South Africa, is renowned for its diverse natural wetlands, some of which are currently unprotected. These wetlands play a crucial role in preserving biodiversity, purifying water, controlling floods, and supporting agricultural production for rural communities. Unfortunately, human activities such as agricultural effluents, run-offs, domestic wastewater, and plastics pollution, along with the impacts of climate change, are mounting pressures on these ecosystems. However, there is limited information on the microbial ecology of natural wetlands in this region, considering the changing anthropogenic activities. The data presented represents the first report on the microbial and functional diversity of sediment microbiomes associated with unprotected arid-tropical natural wetlands in South Africa. Metagenomic shotgun sequencing was performed on sediment samples from ten different wetlands using the Illumina NextSeq 2000 platform. Taxonomic profiling of 328,625,930 high-quality sequencing reads using the MetaPhlAn v3.0 pipeline revealed that Bacteria were the most abundant kingdom (54.5 %), followed by Viruses (0.40 %), Archaea (0.01 %), and Eukaryota (0.36 %). Among bacteria, the most prevalent taxa belonged to the phylum Proteobacteria, particularly the classes Gammaproteobacteria and Betaproteobacteria, which accounted for 83 % of bacterial sequences. The Terrabacteria group, consisting of the phyla Firmicutes and Actinobacteria, made up 3 % of the bacterial population. The abundance of these top bacterial taxa varied across different wetland samples, both at the genus and species levels. In addition, hierarchical clustering based on Bray-Curtis dissimilarity distances of fungal, protist, archaea, and virus species showed distinct clustering of sediment samples from different wetlands. Functional annotation of the metagenomes identified 1224-1702 enzyme classes, 84,833-198,397 gene families, and 280-400 pathways across the various wetland sediments. The data provide crucial baseline information on the microbial and functional diversity of sediment communities in arid tropical wetlands. This knowledge will contribute to a better understanding of these unique environments and can aid in their management and conservation efforts in rural South Africa.}, } @article {pmid37965266, year = {2023}, author = {Piazzesi, A and Pane, S and Russo, A and Del Chierico, F and Francalanci, P and Cotugno, N and Rossi, P and Locatelli, F and Palma, P and Putignani, L}, title = {Case Report: The impact of severe cryptosporidiosis on the gut microbiota of a pediatric patient with CD40L immunodeficiency.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1281440}, pmid = {37965266}, issn = {2235-2988}, mesh = {Animals ; Humans ; Child ; Child, Preschool ; *Cryptosporidiosis/complications/parasitology ; CD40 Ligand ; *Gastrointestinal Microbiome ; *Cryptosporidium/genetics ; Intestines/microbiology ; *Immunologic Deficiency Syndromes/complications ; *Parasites ; *Cryptosporidium parvum ; Bacteria/genetics ; Propionibacterium acnes ; }, abstract = {Cryptosporidium parvum is a protozoan parasite and one of the leading causes of gastroenteritis in the world, primarily affecting very young children and immunocompromised patients. While infection is usually self-limiting, it can become chronic and even lethal in these vulnerable populations, in whom Cryptosporidium treatments are generally ineffective, due to their acting in concert with a functioning immune system. Here, we describe a case of chronic cryptosporidiosis in a European child with severe CD40L immunodeficiency infected with Cryptosporidium parvum of the IIa20G1 subgenotype, a lineage which has thus far only ever been described in the Middle East. After years of on-off treatment with conventional and non-conventional anti-parasitic drugs failed to clear parasitosis, we performed targeted metagenomics to observe the bacterial composition of the patient's gut microbiota (GM), and to evaluate fecal microbiota transplantation (FMT) as a potential treatment option. We found that C. parvum infection led to significant shifts in GM bacterial composition in our patient, with consequent shifts in predicted intestinal functional signatures consistent with a state of persistent inflammation. This, combined with the patient's poor prognosis and increasing parasitic burden despite many rounds of anti-parasitic drug treatments, made the patient a potential candidate for an experimental FMT procedure. Unfortunately, given the many comorbidities that were precipitated by the patient's immunodeficiency and chronic C. parvum infection, FMT was postponed in favor of more urgently necessary liver and bone marrow transplants. Tragically, after the first liver transplant failed, the patient lost his life before undergoing FMT and a second liver transplant. With this case report, we present the first description of how cryptosporidiosis can shape the gut microbiota of a pediatric patient with severe immunodeficiency. Finally, we discuss how both our results and the current scientific literature suggest that GM modulations, either by probiotics or FMT, can become novel treatment options for chronic Cryptosporidium infection and its consequent complications, especially in those patients who do not respond to the currently available anti-parasitic therapies.}, } @article {pmid37964633, year = {2023}, author = {Bassani, I and Bellini, R and Vizzarro, A and Coti, C and Pozzovivo, V and Barbieri, D and Pirri, CF and Verga, F and Menin, B}, title = {Biogeochemical characterization of four depleted gas reservoirs for conversion into underground hydrogen storage.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {3683-3702}, doi = {10.1111/1462-2920.16538}, pmid = {37964633}, issn = {1462-2920}, mesh = {*Oil and Gas Fields ; RNA, Ribosomal, 16S/genetics/metabolism ; Bacteria/genetics ; Archaea/genetics ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Depleted gas reservoirs are a valuable option for underground hydrogen storage (UHS). However, different classes of microorganisms, which are capable of using free H2 as a reducing agent for their metabolism, inhabit deep underground formations and can potentially affect the storage. This study integrates metagenomics based on Illumina-NGS sequencing of bacterial and archaeal 16S rRNA and dsrB and mcrA functional genes to unveil the composition and the variability of indigenous microbial populations of four Italian depleted reservoirs. The obtained mcrA sequences allow us to implement the existing taxonomic database for mcrA gene sequences with newly classified sequences obtained from the Italian gas reservoirs. Moreover, the KEGG and COG predictive functional annotation was used to highlight the metabolic pathways potentially associated with hydrogenotrophic metabolisms. The analyses revealed the specificity of each reservoir microbial community, and taxonomic and functional data highlighted the presence of an enriched number of taxa, whose activity depends on both reservoir hydrochemical composition and nutrient availability, of potential relevance in the context of UHS. This study is the very first to address the profiling of the microbial population and allowed us to perform a preliminary assessment of UHS feasibility in Italy.}, } @article {pmid37964026, year = {2023}, author = {Chen, X and Liu, J and Zhu, XY and Xue, CX and Yao, P and Fu, L and Yang, Z and Sun, K and Yu, M and Wang, X and Zhang, XH}, title = {Phylogenetically and metabolically diverse autotrophs in the world's deepest blue hole.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {117}, pmid = {37964026}, issn = {2730-6151}, abstract = {The world's deepest yongle blue hole (YBH) is characterized by sharp dissolved oxygen (DO) gradients, and considerably low-organic-carbon and high-inorganic-carbon concentrations that may support active autotrophic communities. To understand metabolic strategies of autotrophic communities for obtaining carbon and energy spanning redox gradients, we presented finer characterizations of microbial community, metagenome and metagenome-assembled genomes (MAGs) in the YBH possessing oxic, hypoxic, essentially anoxic and completely anoxic zones vertically. Firstly, the YBH microbial composition and function shifted across the four zones, linking to different biogeochemical processes. The recovery of high-quality MAGs belonging to various uncultivated lineages reflected high novelty of the YBH microbiome. Secondly, carbon fixation processes and associated energy metabolisms varied with the vertical zones. The Calvin-Benson-Bassham (CBB) cycle was ubiquitous but differed in affiliated taxa at different zones. Various carbon fixation pathways were found in the hypoxic and essentially anoxic zones, including the 3-hyroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle affiliated to Nitrososphaeria, and Wood-Ljungdahl (WL) pathway affiliated to Planctomycetes, with sulfur oxidation and dissimilatory nitrate reduction as primary energy-conserving pathways. The completely anoxic zone harbored diverse taxa (Dehalococcoidales, Desulfobacterales and Desulfatiglandales) utilizing the WL pathway coupled with versatile energy-conserving pathways via sulfate reduction, fermentation, CO oxidation and hydrogen metabolism. Finally, most of the WL-pathway containing taxa displayed a mixotrophic lifestyle corresponding to flexible carbon acquisition strategies. Our result showed a vertical transition of microbial lifestyle from photo-autotrophy, chemoautotrophy to mixotrophy in the YBH, enabling a better understanding of carbon fixation processes and associated biogeochemical impacts with different oxygen availability.}, } @article {pmid37963868, year = {2023}, author = {Diebold, PJ and Rhee, MW and Shi, Q and Trung, NV and Umrani, F and Ahmed, S and Kulkarni, V and Deshpande, P and Alexander, M and Thi Hoa, N and Christakis, NA and Iqbal, NT and Ali, SA and Mathad, JS and Brito, IL}, title = {Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7366}, pmid = {37963868}, issn = {2041-1723}, support = {DP2 HL141007/HL/NHLBI NIH HHS/United States ; MR/R002762/1/MRC_/Medical Research Council/United Kingdom ; R01 AI151059/AI/NIAID NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/genetics ; Drug Resistance, Microbial/genetics ; *Microbiota/genetics ; Genes, Bacterial/genetics ; }, abstract = {The acquisition of antimicrobial resistance (AR) genes has rendered important pathogens nearly or fully unresponsive to antibiotics. It has been suggested that pathogens acquire AR traits from the gut microbiota, which collectively serve as a global reservoir for AR genes conferring resistance to all classes of antibiotics. However, only a subset of AR genes confers resistance to clinically relevant antibiotics, and, although these AR gene profiles are well-characterized for common pathogens, less is known about their taxonomic associations and transfer potential within diverse members of the gut microbiota. We examined a collection of 14,850 human metagenomes and 1666 environmental metagenomes from 33 countries, in addition to nearly 600,000 isolate genomes, to gain insight into the global prevalence and taxonomic range of clinically relevant AR genes. We find that several of the most concerning AR genes, such as those encoding the cephalosporinase CTX-M and carbapenemases KPC, IMP, NDM, and VIM, remain taxonomically restricted to Proteobacteria. Even cfiA, the most common carbapenemase gene within the human gut microbiome, remains tightly restricted to Bacteroides, despite being found on a mobilizable plasmid. We confirmed these findings in gut microbiome samples from India, Honduras, Pakistan, and Vietnam, using a high-sensitivity single-cell fusion PCR approach. Focusing on a set of genes encoding carbapenemases and cephalosporinases, thus far restricted to Bacteroides species, we find that few mutations are required for efficacy in a different phylum, raising the question of why these genes have not spread more widely. Overall, these data suggest that globally prevalent, clinically relevant AR genes have not yet established themselves across diverse commensal gut microbiota.}, } @article {pmid37962956, year = {2024}, author = {Wu, Q and Badu, S and So, SY and Treangen, TJ and Savidge, TC}, title = {The pan-microbiome profiling system Taxa4Meta identifies clinical dysbiotic features and classifies diarrheal disease.}, journal = {The Journal of clinical investigation}, volume = {134}, number = {2}, pages = {}, pmid = {37962956}, issn = {1558-8238}, support = {P01 AI152999/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 DK130517/DK/NIDDK NIH HHS/United States ; R01 NR013497/NR/NINR NIH HHS/United States ; }, mesh = {Humans ; Dysbiosis ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Diarrhea/genetics ; }, abstract = {Targeted metagenomic sequencing is an emerging strategy to survey disease-specific microbiome biomarkers for clinical diagnosis and prognosis. However, this approach often yields inconsistent or conflicting results owing to inadequate study power and sequencing bias. We introduce Taxa4Meta, a bioinformatics pipeline explicitly designed to compensate for technical and demographic bias. We designed and validated Taxa4Meta for accurate taxonomic profiling of 16S rRNA amplicon data acquired from different sequencing strategies. Taxa4Meta offers significant potential in identifying clinical dysbiotic features that can reliably predict human disease, validated comprehensively via reanalysis of individual patient 16S data sets. We leveraged the power of Taxa4Meta's pan-microbiome profiling to generate 16S-based classifiers that exhibited excellent utility for stratification of diarrheal patients with Clostridioides difficile infection, irritable bowel syndrome, or inflammatory bowel diseases, which represent common misdiagnoses and pose significant challenges for clinical management. We believe that Taxa4Meta represents a new "best practices" approach to individual microbiome surveys that can be used to define gut dysbiosis at a population-scale level.}, } @article {pmid37962419, year = {2023}, author = {Tang, J and Li, W and Zhou, Q and Fang, Z and Lin, Y and Xu, S and Feng, B and Zhuo, Y and Jiang, X and Zhao, H and Wu, D and Trabalza-Marinucci, M and Che, L}, title = {Effect of heating, microbial fermentation, and enzymatic hydrolysis of soybean meal on growth performance, nutrient digestibility, and intestinal microbiota of weaned piglets.}, journal = {Journal of animal science}, volume = {101}, number = {}, pages = {}, pmid = {37962419}, issn = {1525-3163}, support = {2021ZDZX0011//Sichuan Science and Technology Program/ ; ARS-35//China Agriculture Research System/ ; 2022ZYDF036//Central Government Funds of Guiding Local Scientific and Technological Development/ ; }, mesh = {Animals ; Swine ; Fermentation ; *Gastrointestinal Microbiome ; Heating ; Flour ; Hydrolysis ; Digestion ; Animal Feed/analysis ; Glycine max ; Diet/veterinary ; Nutrients ; Diarrhea/veterinary ; }, abstract = {The macromolecular proteins, anti-nutritional factors, and allergens contained in soybean meal (SBM) have a negative impact on the growth of weaned piglets. The objective of this study was to investigate the effects of heating, microbial fermentation, and enzymatically hydrolyzed SBM on the growth performance, nutrient digestibility, serum biochemistry, intestinal morphology, volatile fatty acids, and microbiota of weaned piglets. After the preparation of soaked SBM (SSBM), enzymatically hydrolyzed SBM (ESBM), and microbial fermented and enzymatically hydrolyzed SBM (MESBM), 72 weaned piglets were randomly allocated to three groups for a 21-d trial. In the three groups, 17% of conventional SBM in basal corn-soybean meal diet was replaced by an equivalent amount of SSBM (control group), ESBM, or MESBM. The results showed that the contents of glycinin, β-conglycinin, trypsin inhibitor, and proteins above 20 kDa were significantly decreased in ESBM and MESBM, compared with SSBM, and the surface of ESBM and MESBM had more pores and fragmented structure. In the second week and throughout the entire experimental period, the diarrhea index was reduced (P < 0.01) in ESBM and MESBM in contrast with SSBM. Furthermore, the inclusion of ESBM and MESBM in the diet improved the apparent total tract digestibility of dry matter and crude protein (P < 0.05), and increased the abundances of the genera Lactobacillus and Clostridium_sensu_stricto_1, respectively. Metagenomic sequencing further identified that members of six species of Proteobacteria, four species of Clostridiales, and three species of Negativiautes were enriched in the colon of piglets fed MESBM, while two bacterial species, Lachnoclostridium and Lactobacillus_points, were enriched in the colon of piglets fed ESBM. In conclusion, replacing SSBM with ESBM or MESBM in the diet decreased the diarrhea index, which could be associated with improved nutrient digestibility and microbial composition.}, } @article {pmid37960282, year = {2023}, author = {Rohwer, N and El Hage, R and Smyl, C and Ocvirk, S and Goris, T and Grune, T and Swidsinski, A and Weylandt, KH}, title = {Ketogenic Diet Has Moderate Effects on the Fecal Microbiota of Wild-Type Mice.}, journal = {Nutrients}, volume = {15}, number = {21}, pages = {}, pmid = {37960282}, issn = {2072-6643}, support = {WE2908/13-1//Deutsche Forschungsgemeinschaft/ ; GR1240/20-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Female ; Mice ; Animals ; *Diet, Ketogenic ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; *Neuroprotective Agents ; *Microbiota ; Diet, High-Fat ; Bacteria/genetics ; *Actinobacteria/genetics ; Mice, Inbred C57BL ; }, abstract = {The ketogenic diet (KD) is a high-fat, low-carbohydrate diet that has been reported to have neuroprotective effects. The health effects of KD might be linked to an altered gut microbiome, which plays a major role in host health, leading to neuroprotective effects via the gut-brain axis. However, results from different studies, most often based on the 16S rRNA gene and metagenome sequencing, have been inconsistent. In this study, we assessed the effect of a 4-week KD compared to a western diet (WD) on the colonic microbiome of female C57Bl/6J mice by analyzing fecal samples using fluorescence in situ hybridization. Our results showed distinct changes in the total number of gut bacteria following the 4-week KD, in addition to changes in the composition of the microbiome. KD-fed mice showed higher absolute numbers of Actinobacteria (especially Bifidobacteria spp.) and lower absolute levels of Proteobacteria, often linked to gut inflammation, in comparison with WD-fed mice. Furthermore, an increased abundance of the typically rare genus Atopobium was observed. These changes may indicate the possible anti-inflammatory effects of the KD. However, since the overall changes in the microbiota seem low, the KD effects might be linked to the differential abundance of only a few key genera in mice.}, } @article {pmid37956203, year = {2023}, author = {Brunner, JD and Gallegos-Graves, LA and Kroeger, ME}, title = {Inferring microbial interactions with their environment from genomic and metagenomic data.}, journal = {PLoS computational biology}, volume = {19}, number = {11}, pages = {e1011661}, pmid = {37956203}, issn = {1553-7358}, mesh = {Humans ; *Genomics ; Metagenomics/methods ; Metagenome/genetics ; *Microbiota/genetics ; Microbial Interactions/genetics ; }, abstract = {Microbial communities assemble through a complex set of interactions between microbes and their environment, and the resulting metabolic impact on the host ecosystem can be profound. Microbial activity is known to impact human health, plant growth, water quality, and soil carbon storage which has lead to the development of many approaches and products meant to manipulate the microbiome. In order to understand, predict, and improve microbial community engineering, genome-scale modeling techniques have been developed to translate genomic data into inferred microbial dynamics. However, these techniques rely heavily on simulation to draw conclusions which may vary with unknown parameters or initial conditions, rather than more robust qualitative analysis. To better understand microbial community dynamics using genome-scale modeling, we provide a tool to investigate the network of interactions between microbes and environmental metabolites over time. Using our previously developed algorithm for simulating microbial communities from genome-scale metabolic models (GSMs), we infer the set of microbe-metabolite interactions within a microbial community in a particular environment. Because these interactions depend on the available environmental metabolites, we refer to the networks that we infer as metabolically contextualized, and so name our tool MetConSIN: Metabolically Contextualized Species Interaction Networks.}, } @article {pmid37956168, year = {2023}, author = {Stegmüller, S and Qi, W and Torgerson, PR and Fraefel, C and Kubacki, J}, title = {Hazard potential of Swiss Ixodes ricinus ticks: Virome composition and presence of selected bacterial and protozoan pathogens.}, journal = {PloS one}, volume = {18}, number = {11}, pages = {e0290942}, pmid = {37956168}, issn = {1932-6203}, mesh = {Humans ; Animals ; *Ixodes/microbiology ; Switzerland/epidemiology ; Virome/genetics ; Nymph ; *Encephalitis, Tick-Borne/epidemiology ; *Tick-Borne Diseases ; *Encephalitis Viruses, Tick-Borne/genetics ; }, abstract = {Ticks play an important role in transmitting many different emerging zoonotic pathogens that pose a significant threat to human and animal health. In Switzerland and abroad, the number of tick-borne diseases, in particular tick-borne encephalitis (TBE), has been increasing over the last few years. Thus, it remains essential to investigate the pathogen spectrum of ticks to rapidly detect emerging pathogens and initiate the necessary measures. To assess the risk of tick-borne diseases in different regions of Switzerland, we collected a total of 10'286 ticks from rural and urban areas in ten cantons in 2021 and 2022. Ticks were pooled according to species, developmental stage, gender, and collection site, and analyzed using next generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR). The metagenomic analysis revealed for the first time the presence of Alongshan virus (ALSV) in Swiss ticks. Interestingly, the pool-prevalence of ALSV was higher than that of tick-borne encephalitis virus (TBEV). Furthermore, several TBEV foci have been identified and pool prevalence of selected non-viral pathogens determined.}, } @article {pmid37952001, year = {2023}, author = {Boulanger, N and Insonere, JL and Van Blerk, S and Barthel, C and Serres, C and Rais, O and Roulet, A and Servant, F and Duron, O and Lelouvier, B}, title = {Cross-alteration of murine skin and tick microbiome concomitant with pathogen transmission after Ixodes ricinus bite.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {250}, pmid = {37952001}, issn = {2049-2618}, mesh = {Humans ; Animals ; Female ; Mice ; *Ixodes/genetics/microbiology ; *Tick Bites ; RNA, Ribosomal, 16S/genetics ; *Borrelia/genetics ; *Microbiota ; Nymph/microbiology ; }, abstract = {BACKGROUND: Ticks are major vectors of diseases affecting humans such as Lyme disease or domestic animals such as anaplasmosis. Cross-alteration of the vertebrate host skin microbiome and the tick microbiome may be essential during the process of tick feeding and for the mechanism of pathogen transmission. However, it has been poorly investigated.

METHODS: We used mice bitten by field-collected ticks (nymphs and adult ticks) in different experimental conditions to investigate, by 16S rRNA gene metabarcoding, the impact of blood feeding on both the mouse skin microbiome and the tick microbiome. We also investigated by PCR and 16S rRNA gene metabarcoding, the diversity of microorganisms transmitted to the host during the process of tick bite at the skin interface and the dissemination of the pathogen in host tissues (blood, heart, and spleen).

RESULTS: Most of the commensal bacteria present in the skin of control mice were replaced during the blood-feeding process by bacteria originating from the ticks. The microbiome of the ticks was also impacted by the blood feeding. Several pathogens including tick-borne pathogens (Borrelia/Borreliella, Anaplasma, Neoehrlichia, Rickettsia) and opportunistic bacteria (Williamsia) were transmitted to the skin microbiome and some of them disseminated to the blood or spleen of the mice. In the different experiments of this study, skin microbiome alteration and Borrelia/Borreliella transmission were different depending on the tick stages (nymphs or adult female ticks).

CONCLUSIONS: Host skin microbiome at the bite site was deeply impacted by the tick bite, to an extent which suggests a role in the tick feeding, in the pathogen transmission, and a potentially important impact on the skin physiopathology. The diversified taxonomic profiles of the tick microbiome were also modified by the blood feeding. Video Abstract.}, } @article {pmid37951952, year = {2023}, author = {Ma, B and Lu, C and Wang, Y and Yu, J and Zhao, K and Xue, R and Ren, H and Lv, X and Pan, R and Zhang, J and Zhu, Y and Xu, J}, title = {A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7318}, pmid = {37951952}, issn = {2041-1723}, mesh = {*Soil ; *Microbiota/genetics ; Metagenome/genetics ; Biodiversity ; Genomics ; Soil Microbiology ; }, abstract = {Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservo)ir of microbial biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct a large-scale excavation of soil microbial dark matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalogue) from 3304 soil metagenomes. We identify 16,530 of 21,077 species-level genome bins (SGBs) as unknown SGBs (uSGBs), which expand archaeal and bacterial diversity across the tree of life. We also illustrate the pivotal role of uSGBs in augmenting soil microbiome's functional landscape and intra-species genome diversity, providing large proportions of the 43,169 biosynthetic gene clusters and 8545 CRISPR-Cas genes. Additionally, we determine that uSGBs contributed 84.6% of previously unexplored viral-host associations from the SMAG catalogue. The SMAG catalogue provides an useful genomic resource for further studies investigating soil microbial biodiversity and genetic resources.}, } @article {pmid37951857, year = {2023}, author = {Kang, DY and Park, JL and Yeo, MK and Kang, SB and Kim, JM and Kim, JS and Kim, SY}, title = {Diagnosis of Crohn's disease and ulcerative colitis using the microbiome.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {336}, pmid = {37951857}, issn = {1471-2180}, mesh = {Humans ; *Colitis, Ulcerative/therapy ; *Crohn Disease/diagnosis/microbiology ; *Inflammatory Bowel Diseases/microbiology ; *Gastrointestinal Microbiome ; Bacteria/genetics ; Biomarkers ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a multifactorial chronic inflammatory disease resulting from dysregulation of the mucosal immune response and gut microbiota. Crohn's disease (CD) and ulcerative colitis (UC) are difficult to distinguish, and differential diagnosis is essential for establishing a long-term treatment plan for patients. Furthermore, the abundance of mucosal bacteria is associated with the severity of the disease. This study aimed to differentiate and diagnose these two diseases using the microbiome and identify specific biomarkers associated with disease activity.

RESULTS: Differences in the abundance and composition of the microbiome between IBD patients and healthy controls (HC) were observed. Compared to HC, the diversity of the gut microbiome in patients with IBD decreased; the diversity of the gut microbiome in patients with CD was significantly lower. Sixty-eight microbiota members (28 for CD and 40 for UC) associated with these diseases were identified. Additionally, as the disease progressed through different stages, the diversity of the bacteria decreased. The abundances of Alistipes shahii and Pseudodesulfovibrio aespoeensis were negatively correlated with the severity of CD, whereas the abundance of Polynucleobacter wianus was positively correlated. The severity of UC was negatively correlated with the abundance of A. shahii, Porphyromonas asaccharolytica and Akkermansia muciniphilla, while it was positively correlated with the abundance of Pantoea candidatus pantoea carbekii. A regularized logistic regression model was used for the differential diagnosis of the two diseases. The area under the curve (AUC) was used to examine the performance of the model. The model discriminated UC and CD at an AUC of 0.873 (train set), 0.778 (test set), and 0.633 (validation set) and an area under the precision-recall curve (PRAUC) of 0.888 (train set), 0.806 (test set), and 0.474 (validation set).

CONCLUSIONS: Based on fecal whole-metagenome shotgun (WMS) sequencing, CD and UC were diagnosed using a machine-learning predictive model. Microbiome biomarkers associated with disease activity (UC and CD) are also proposed.}, } @article {pmid37949415, year = {2023}, author = {Kahleova, H and Holtz, DN and Strom, N and La Reau, A and Kolipaka, S and Schmidt, N and Hata, E and Znayenko-Miller, T and Holubkov, R and Barnard, ND}, title = {A dietary intervention for postmenopausal hot flashes: A potential role of gut microbiome. An exploratory analysis.}, journal = {Complementary therapies in medicine}, volume = {79}, number = {}, pages = {103002}, doi = {10.1016/j.ctim.2023.103002}, pmid = {37949415}, issn = {1873-6963}, mesh = {*Gastrointestinal Microbiome ; Postmenopause/physiology ; Female ; Humans ; Menopause ; Prevotella ; Clostridiales ; *Hot Flashes/drug therapy ; }, abstract = {OBJECTIVE: This study examined the role of gut microbiome changes in mediating the effects of a dietary intervention on the frequency and severity of postmenopausal vasomotor symptoms METHODS: Postmenopausal women (n = 84) reporting ≥2 moderate-to-severe hot flashes daily were randomly assigned, in 2 successive cohorts, to an intervention including a low-fat, vegan diet and cooked soybeans (½ cup [86 g] daily) or to stay on their usual diet. Over a 12-week period, frequency and severity of hot flashes were recorded with a mobile application. In a subset of 11 women, gut microbiome was analyzed at baseline and after 12 weeks of the dietary intervention (low-fat vegan diet with soybeans), using deep shotgun metagenomic sequencing. Differences in the microbiome between baseline and 12 weeks were assessed by comparing alpha diversity with Wilcoxon signed rank tests, beta diversity with permanovaFL, and taxon abundance with Wilcoxon signed rank tests. Pearson correlations were used to assess the association between changes in hot flashes and gut bacteria.

RESULTS: In the subset for which microbiome testing was done, total hot flashes decreased by 95 % during the dietary intervention (p = 0.007); severe hot flashes disappeared (from 0.6 to 0.0/day; p = 0.06); and moderate-to-severe hot flashes decreased by 96 % (p = 0.01). Daytime and nighttime hot flashes were reduced by 96 % (p = 0.01) and 94 % (p = 0.004), respectively. Alpha and beta diversity did not significantly differ in the intervention group between baseline and 12 weeks. Two families (Enterobacteriaceae and Veillonellaceae), 5 genera (Erysipelatoclostridium, Fusicatenibacter, Holdemanella, Intestinimonas, and Porphyromonas), and 6 species (Clostridium asparagiforme, Clostridium innocuum, Bacteroides thetaiotaomicron, Fusicatenibacter saccharivorans, Intestinimonas butyriciproducens, Prevotella corporis, and Streptococcus sp.) were differentially abundant, but after correction for multiple comparisons, these differences were no longer significant. Changes in the relative abundance of Porphyromonas and Prevotella corporis were associated with the reduction in severe day hot flashes both unadjusted (r = 0.61; p = 0.047; and r = 0.69; p = 0.02), respectively), and after adjustment for changes in body mass index (r = 0.63; p = 0.049; and r = 0.73; p = 0.02), respectively). Changes in relative abundance of Clostridium asparagiforme were associated with the reduction in total severe hot flashes (r = 0.69; p = 0.019) and severe night hot flashes (r = 0.82; p = 0.002) and the latter association remained significant after adjustment for changes in body mass index (r = 0.75; p = 0.01).

CONCLUSIONS: This exploratory analysis revealed potential associations between changes in vasomotor symptoms in response to a diet change and changes in the gut microbiome. Larger randomized clinical trials are needed to investigate these findings.}, } @article {pmid37949212, year = {2023}, author = {Xu, HS and Chen, Y and Patel, A and Wang, Z and McDonough, C and Guo, TL}, title = {Chronic exposure to nanocellulose altered depression-related behaviors in mice on a western diet: The role of immune modulation and the gut microbiome.}, journal = {Life sciences}, volume = {335}, number = {}, pages = {122259}, doi = {10.1016/j.lfs.2023.122259}, pmid = {37949212}, issn = {1879-0631}, mesh = {Male ; Animals ; Mice ; Mice, Inbred NOD ; *Gastrointestinal Microbiome ; Diet, Western/adverse effects ; RNA, Ribosomal, 16S/genetics ; Depression ; Mice, Inbred C57BL ; }, abstract = {AIMS: To determine if cellulose nanofibrils (CNF) have potential applications as food additives.

MATERIALS AND METHODS: Male C57BL/6 mice on a Western diet were exposed to CNF for one month at a dose of 30 mg/kg by gavage. Male NOD mice, a model for type 1 diabetes (T1D), were used in a six-month study.

KEY FINDINGS: Sequencing analysis of 16S rRNA genes suggested significant changes in gut microbiome of male C57BL/6 mice exposed to CNF. Analysis of functional metagenomics indicated that many of the functional contents that might be altered following CNF ingestion were associated with lipid and carbohydrate processing. Further studies in NOD mice suggested that there were some decreases in the blood glucose levels during the insulin tolerance test and glucose tolerance test following CNF treatment. However, these small decreases were not considered biologically meaningful as there were no significant changes in either the area under the curve or the first-order rate constant for glucose disappearance. Moreover, serum concentrations of cytokines/chemokines including IL-3, IL-12(p70) and the keratinocyte chemoattractant were increased following chronic exposure to CNF. In addition, behavioral studies suggested that the percentage of immobility time during the tail-suspension test was significantly increased following six months of exposure to CNF in NOD mice, signifying an increase in depression-related behavior.

SIGNIFICANCE: Collectively, long-term CNF consumption was associated with changes in the ecology of the gut microbiome, immune homeostasis, and possibly energy metabolism and mental health in male NOD mice on a Western diet.}, } @article {pmid37949114, year = {2024}, author = {Shinn, LM and Mansharamani, A and Baer, DJ and Novotny, JA and Charron, CS and Khan, NA and Zhu, R and Holscher, HD}, title = {Fecal Metagenomics to Identify Biomarkers of Food Intake in Healthy Adults: Findings from Randomized, Controlled, Nutrition Trials.}, journal = {The Journal of nutrition}, volume = {154}, number = {1}, pages = {271-283}, doi = {10.1016/j.tjnut.2023.11.001}, pmid = {37949114}, issn = {1541-6100}, mesh = {Adult ; Humans ; *Gastrointestinal Microbiome ; Metagenome ; Diet ; *Juglans ; Feces ; Biomarkers ; Eating ; Metagenomics/methods ; }, abstract = {BACKGROUND: Undigested components of the human diet affect the composition and function of the microorganisms present in the gastrointestinal tract. Techniques like metagenomic analyses allow researchers to study functional capacity, thus revealing the potential of using metagenomic data for developing objective biomarkers of food intake.

OBJECTIVES: As a continuation of our previous work using 16S and metabolomic datasets, we aimed to utilize a computationally intensive, multivariate, machine-learning approach to identify fecal KEGG (Kyoto encyclopedia of genes and genomes) Orthology (KO) categories as biomarkers that accurately classify food intake.

METHODS: Data were aggregated from 5 controlled feeding studies that studied the individual impact of almonds, avocados, broccoli, walnuts, barley, and oats on the adult gastrointestinal microbiota. Deoxyribonucleic acid from preintervention and postintervention fecal samples underwent shotgun genomic sequencing. After preprocessing, sequences were aligned and functionally annotated with Double Index AlignMent Of Next-generation sequencing Data v2.0.11.149 and MEtaGenome ANalyzer v6.12.2, respectively. After the count normalization, the log of the fold change ratio for resulting KOs between pre- and postintervention of the treatment group against its corresponding control was utilized to conduct differential abundance analysis. Differentially abundant KOs were used to train machine-learning models examining potential biomarkers in both single-food and multi-food models.

RESULTS: We identified differentially abundant KOs in the almond (n = 54), broccoli (n = 2474), and walnut (n = 732) groups (q < 0.20), which demonstrated classification accuracies of 80%, 87%, and 86% for the almond, broccoli, and walnut groups using a random forest model to classify food intake into each food group's respective treatment and control arms, respectively. The mixed-food random forest achieved 81% accuracy.

CONCLUSIONS: Our findings reveal promise in utilizing fecal metagenomics to objectively complement self-reported measures of food intake. Future research on various foods and dietary patterns will expand these exploratory analyses for eventual use in feeding study compliance and clinical settings.}, } @article {pmid37947402, year = {2023}, author = {Alexander, H and Hu, SK and Krinos, AI and Pachiadaki, M and Tully, BJ and Neely, CJ and Reiter, T}, title = {Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton.}, journal = {mBio}, volume = {14}, number = {6}, pages = {e0167623}, pmid = {37947402}, issn = {2150-7511}, support = {OCE-1948025//National Science Foundation (NSF)/ ; OCE-0939564, OCE-194777, OCE-2327203//National Science Foundation (NSF)/ ; 931886//Simons Foundation (SF)/ ; DE-SC0020347//U.S. Department of Energy (DOE)/ ; OCE-1924492//National Science Foundation (NSF)/ ; OCE-0939654//National Science Foundation (NSF)/ ; }, mesh = {*Metagenomics/methods ; *Plankton/genetics/classification ; *Eukaryota/genetics/classification ; *Oceans and Seas ; *Metagenome ; Biodiversity ; Computational Biology/methods ; Phylogeny ; Seawater/microbiology ; Phylogeography ; }, abstract = {Single-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers' efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.}, } @article {pmid37946302, year = {2023}, author = {Shen, Z and Robert, L and Stolpman, M and Che, Y and Allen, KJ and Saffery, R and Walsh, A and Young, A and Eckert, J and Deming, C and Chen, Q and Conlan, S and Laky, K and Li, JM and Chatman, L and Kashaf, SS and , and , and Kong, HH and Frischmeyer-Guerrerio, PA and Perrett, KP and Segre, JA}, title = {A genome catalog of the early-life human skin microbiome.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {252}, pmid = {37946302}, issn = {1474-760X}, support = {T32 HD007009/HD/NICHD NIH HHS/United States ; UM1 AI109565/AI/NIAID NIH HHS/United States ; UM1AI109565/NH/NIH HHS/United States ; }, mesh = {Humans ; Infant ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics ; Australia ; North America ; Metagenomics ; }, abstract = {BACKGROUND: Metagenome-assembled genomes have greatly expanded the reference genomes for skin microbiome. However, the current reference genomes are largely based on samples from adults in North America and lack representation from infants and individuals from other continents.

RESULTS: Here we use deep shotgun metagenomic sequencing to profile the skin microbiota of 215 infants at age 2-3 months and 12 months who are part of the VITALITY trial in Australia as well as 67 maternally matched samples. Based on the infant samples, we present the Early-Life Skin Genomes (ELSG) catalog, comprising 9483 prokaryotic genomes from 1056 species, 206 fungal genomes from 13 species, and 39 eukaryotic viral sequences. This genome catalog substantially expands the diversity of species previously known to comprise human skin microbiome and improves the classification rate of sequenced data by 21%. The protein catalog derived from these genomes provides insights into the functional elements such as defense mechanisms that distinguish early-life skin microbiome. We also find evidence for microbial sharing at the community, bacterial species, and strain levels between mothers and infants.

CONCLUSIONS: Overall, the ELSG catalog uncovers the skin microbiome of a previously underrepresented age group and population and provides a comprehensive view of human skin microbiome diversity, function, and development in early life.}, } @article {pmid37946167, year = {2023}, author = {Cecchini, L and Barmaz, C and Cea, MJC and Baeschlin, H and Etter, J and Netzer, S and Bregy, L and Marchukov, D and Trigo, NF and Meier, R and Hirschi, J and Wyss, J and Wick, A and Zingg, J and Christensen, S and Radan, AP and Etter, A and Müller, M and Kaess, M and Surbek, D and Yilmaz, B and Macpherson, AJ and Sokollik, C and Misselwitz, B and Ganal-Vonarburg, SC}, title = {The Bern Birth Cohort (BeBiCo) to study the development of the infant intestinal microbiota in a high-resource setting in Switzerland: rationale, design, and methods.}, journal = {BMC pediatrics}, volume = {23}, number = {1}, pages = {560}, pmid = {37946167}, issn = {1471-2431}, mesh = {Child ; Infant ; Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; Cohort Studies ; Birth Cohort ; Prospective Studies ; Switzerland/epidemiology ; }, abstract = {BACKGROUND: Microbiota composition is fundamental to human health with the intestinal microbiota undergoing critical changes within the first two years of life. The developing intestinal microbiota is shaped by maternal seeding, breast milk and its complex constituents, other nutrients, and the environment. Understanding microbiota-dependent pathologies requires a profound understanding of the early development of the healthy infant microbiota.

METHODS: Two hundred and fifty healthy pregnant women (≥20 weeks of gestation) from the greater Bern area will be enrolled at Bern University hospital's maternity department. Participants will be followed as mother-baby pairs at delivery, week(s) 1, 2, 6, 10, 14, 24, 36, 48, 96, and at years 5 and 10 after birth. Clinical parameters describing infant growth and development, morbidity, and allergic conditions as well as socio-economic, nutritional, and epidemiological data will be documented. Neuro-developmental outcomes and behavior will be assessed by child behavior checklists at and beyond 2 years of age. Maternal stool, milk, skin and vaginal swabs, infant stool, and skin swabs will be collected at enrolment and at follow-up visits. For the primary outcome, the trajectory of the infant intestinal microbiota will be characterized by 16S and metagenomic sequencing regarding composition, metabolic potential, and stability during the first 2 years of life. Secondary outcomes will assess the cellular and chemical composition of maternal milk, the impact of nutrition and environment on microbiota development, the maternal microbiome transfer at vaginal or caesarean birth and thereafter on the infant, and correlate parameters of microbiota and maternal milk on infant growth, development, health, and mental well-being.

DISCUSSION: The Bern birth cohort study will provide a detailed description and normal ranges of the trajectory of microbiota maturation in a high-resource setting. These data will be compared to data from low-resource settings such as from the Zimbabwe-College of Health-Sciences-Birth-Cohort study. Prospective bio-sampling and data collection will allow studying the association of the microbiota with common childhood conditions concerning allergies, obesity, neuro-developmental outcomes , and behaviour. Trial registration The trial has been registered at www.

CLINICALTRIALS: gov , Identifier: NCT04447742.}, } @article {pmid37946009, year = {2024}, author = {Izda, V and Schlupp, L and Prinz, E and Dyson, G and Barrett, M and Dunn, CM and Nguyen, E and Sturdy, C and Jeffries, MA}, title = {Murine cartilage microbial DNA deposition occurs rapidly following the introduction of a gut microbiome and changes with obesity, aging, and knee osteoarthritis.}, journal = {GeroScience}, volume = {46}, number = {2}, pages = {2317-2341}, pmid = {37946009}, issn = {2509-2723}, support = {K08AR070891/AR/NIAMS NIH HHS/United States ; R01AR076440/AR/NIAMS NIH HHS/United States ; K08 AR070891/AR/NIAMS NIH HHS/United States ; R01 AR076440/AR/NIAMS NIH HHS/United States ; P20GM125528/GM/NIGMS NIH HHS/United States ; R61AR078075/AR/NIAMS NIH HHS/United States ; I01 CX002494/CX/CSRD VA/United States ; P20 GM125528/GM/NIGMS NIH HHS/United States ; R61 AR078075/AR/NIAMS NIH HHS/United States ; R33 AR078075/AR/NIAMS NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; *Osteoarthritis, Knee ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Obesity ; *Cartilage, Articular ; DNA ; Aging ; }, abstract = {Cartilage microbial DNA patterns have been recently characterized in osteoarthritis (OA). The objectives of this study were to evaluate the gut origins of cartilage microbial DNA, to characterize cartilage microbial changes with age, obesity, and OA in mice, and correlate these to gut microbiome changes. We used 16S rRNA sequencing performed longitudinally on articular knee cartilage from germ-free (GF) mice following oral microbiome inoculation and cartilage and cecal samples from young and old wild-type mice with/without high-fat diet-induced obesity (HFD) and with/without OA induced by destabilization of the medial meniscus (DMM) to evaluate gut and cartilage microbiota. Microbial diversity was assessed, groups compared, and functional metagenomic profiles reconstructed. Findings were confirmed in an independent cohort by clade-specific qPCR. We found that cartilage microbial patterns developed at 48 h and later timepoints following oral microbiome inoculation of GF mice. Alpha diversity was increased in SPF mouse cartilage samples with age (P = 0.013), HFD (P = 5.6E-4), and OA (P = 0.029) but decreased in cecal samples with age (P = 0.014) and HFD (P = 1.5E-9). Numerous clades were altered with aging, HFD, and OA, including increases in Verrucomicrobia in both cartilage and cecal samples. Functional analysis suggested changes in dihydroorotase, glutamate-5-semialdehyde dehydrogenase, glutamate-5-kinase, and phosphoribosylamine-glycine ligase, in both cecum and cartilage, with aging, HFD, and OA. In conclusion, cartilage microbial DNA patterns develop rapidly after the introduction of a gut microbiome and change in concert with the gut microbiome during aging, HFD, and OA in mice. DMM-induced OA causes shifts in both cartilage and cecal microbiome patterns independent of other factors.}, } @article {pmid37944495, year = {2023}, author = {Huang, X and Hu, M and Sun, T and Li, J and Zhou, Y and Yan, Y and Xuan, B and Wang, J and Xiong, H and Ji, L and Zhu, X and Tong, T and Ning, L and Ma, Y and Zhao, Y and Ding, J and Guo, Z and Zhang, Y and Fang, JY and Hong, J and Chen, H}, title = {Multi-kingdom gut microbiota analyses define bacterial-fungal interplay and microbial markers of pan-cancer immunotherapy across cohorts.}, journal = {Cell host & microbe}, volume = {31}, number = {11}, pages = {1930-1943.e4}, doi = {10.1016/j.chom.2023.10.005}, pmid = {37944495}, issn = {1934-6069}, mesh = {Humans ; *Gastrointestinal Microbiome ; Metagenome ; Immunotherapy ; Bacteria/genetics ; *Neoplasms/therapy ; }, abstract = {The effect of gut bacteria on the response to immune checkpoint inhibitors (ICIs) has been studied, but the relationship between fungi and ICI responses is not fully understood. Herein, 862 fecal metagenomes from 9 different cohorts were integrated for the identification of differentially abundant fungi and subsequent construction of random forest (RF) models to predict ICI responses. Fungal markers demonstrate excellent performance, with an average area under the curve (AUC) of 0.87. Their performance improves even further, reaching an average AUC of 0.89 when combined with bacterial markers. Higher enrichment of exhausted T cells is detected in responders, as predicted by fungal markers. Multi-kingdom network and functional analysis reveal that the fungus Schizosaccharomyces octosporus may ferment starch into short-chain fatty acids in responders. This study provides a fungal profile of the ICI response and the identification of multi-kingdom microbial markers with good performance that may improve the overall applicability of ICI therapy.}, } @article {pmid37941937, year = {2023}, author = {Zhang, H and Wei, T and Li, Q and Fu, L and He, L and Wang, Y}, title = {Metagenomic 16S rDNA reads of in situ preserved samples revealed microbial communities in the Yongle blue hole.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16257}, pmid = {37941937}, issn = {2167-8359}, mesh = {DNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Water ; *Microbiota/genetics ; Sulfates ; }, abstract = {Our knowledge on biogeochemistry and microbial ecology of marine blue holes is limited due to challenges in collecting multilayered water column and oxycline zones. In this study, we collected samples from 16 water layers in Yongle blue hole (YBH) located in the South China Sea using the in situ microbial filtration and fixation (ISMIFF) apparatus. The microbial communities based on 16S rRNA metagenomic reads for the ISMIFF samples showed high microbial diversity and consistency among samples with similar dissolved oxygen levels. At the same depth of the anoxic layer, the ISMIFF samples were dominated by sulfate-reducing bacteria from Desulfatiglandales (17.96%). The sulfide concentration is the most significant factor that drives the division of microbial communities in YBH, which might support the prevalence of sulfate-reducing microorganisms in the anoxic layers. Our results are different from the microbial community structures of a Niskin sample of this study and the reported samples collected in 2017, in which a high relative abundance of Alteromonadales (26.59%) and Thiomicrospirales (38.13%), and Arcobacteraceae (11.74%) was identified. We therefore demonstrate a new profile of microbial communities in YBH probably due to the effect of sampling and molecular biological methods, which provides new possibilities for further understanding of the material circulation mechanism of blue holes and expanding anoxic marine water zones under global warming.}, } @article {pmid37941936, year = {2023}, author = {Liao, F and Xia, Y and Gu, W and Fu, X and Yuan, B}, title = {Comparative analysis of shotgun metagenomics and 16S rDNA sequencing of gut microbiota in migratory seagulls.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16394}, pmid = {37941936}, issn = {2167-8359}, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/genetics ; DNA, Ribosomal/genetics ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; *Salmonella enterica/genetics ; }, abstract = {BACKGROUND: Shotgun metagenomic and 16S rDNA sequencing are commonly used methods to identify the taxonomic composition of microbial communities. Previously, we analysed the gut microbiota and intestinal pathogenic bacteria configuration of migratory seagulls by using 16S rDNA sequencing and culture methods.

METHODS: To continue in-depth research on the gut microbiome and reveal the applicability of the two methods, we compared the metagenome and 16S rDNA amplicon results to further demonstrate the features of this animal.

RESULTS: The number of bacterial species detected by metagenomics gradually increased from the phylum to species level, consistent with 16S rDNA sequencing. Several taxa were commonly shared by both sequencing methods. However, Escherichia, Shigella, Erwinia, Klebsiella, Salmonella, Escherichia albertii, Shigella sonnei, Salmonella enterica, and Shigella flexneri were unique taxa for the metagenome compared with Escherichia-Shigella, Hafnia-Obesumbacterium, Catellicoccus marimammalium, Lactococcus garvieae, and Streptococcus gallolyticus for 16S rDNA sequencing. The largest differences in relative abundance between the two methods were identified at the species level, which identified many pathogenic bacteria to humans using metagenomic sequencing. Pearson correlation analysis indicated that the correlation coefficient for the two methods gradually decreased with the refinement of the taxonomic levels. The high consistency of the correlation coefficient was identified at the genus level for the beta diversity of the two methods.

CONCLUSIONS: In general, relatively consistent patterns and reliability could be identified by both sequencing methods, but the results varied following the refinement of taxonomic levels. Metagenomic sequencing was more suitable for the discovery and detection of pathogenic bacteria of gut microbiota in seagulls. Although there were large differences in the numbers and abundance of bacterial species of the two methods in terms of taxonomic levels, the patterns and reliability results of the samples were consistent.}, } @article {pmid37941395, year = {2022}, author = {Blumberg, K and Miller, M and Ponsero, A and Hurwitz, B}, title = {Ontology-driven analysis of marine metagenomics: what more can we learn from our data?.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {37941395}, issn = {2047-217X}, mesh = {*Ecology ; *Microbiota/genetics ; Metagenome ; Metagenomics ; }, abstract = {BACKGROUND: The proliferation of metagenomic sequencing technologies has enabled novel insights into the functional genomic potentials and taxonomic structure of microbial communities. However, cyberinfrastructure efforts to manage and enable the reproducible analysis of sequence data have not kept pace. Thus, there is increasing recognition of the need to make metagenomic data discoverable within machine-searchable frameworks compliant with the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles for data stewardship. Although a variety of metagenomic web services exist, none currently leverage the hierarchically structured terminology encoded within common life science ontologies to programmatically discover data.

RESULTS: Here, we integrate large-scale marine metagenomic datasets with community-driven life science ontologies into a novel FAIR web service. This approach enables the retrieval of data discovered by intersecting the knowledge represented within ontologies against the functional genomic potential and taxonomic structure computed from marine sequencing data. Our findings highlight various microbial functional and taxonomic patterns relevant to the ecology of prokaryotes in various aquatic environments.

CONCLUSIONS: In this work, we present and evaluate a novel Semantic Web architecture that can be used to ask novel biological questions of existing marine metagenomic datasets. Finally, the FAIR ontology searchable data products provided by our API can be leveraged by future research efforts.}, } @article {pmid37940667, year = {2023}, author = {Hu, M and Caldarelli, G and Gili, T}, title = {Inflammatory bowel disease biomarkers revealed by the human gut microbiome network.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {19428}, pmid = {37940667}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; *Crohn Disease/genetics/microbiology ; *Microbiota ; *Colitis, Ulcerative/genetics ; Biomarkers ; Escherichia coli ; }, abstract = {Inflammatory bowel diseases (IBDs) are complex medical conditions in which the gut microbiota is attacked by the immune system of genetically predisposed subjects when exposed to yet unclear environmental factors. The complexity of this class of diseases makes them suitable to be represented and studied with network science. In this paper, the metagenomic data of control, Crohn's disease, and ulcerative colitis subjects' gut microbiota were investigated by representing this data as correlation networks and co-expression networks. We obtained correlation networks by calculating Pearson's correlation between gene expression across subjects. A percolation-based procedure was used to threshold and binarize the adjacency matrices. In contrast, co-expression networks involved the construction of the bipartite subjects-genes networks and the monopartite genes-genes projection after binarization of the biadjacency matrix. Centrality measures and community detection were used on the so-built networks to mine data complexity and highlight possible biomarkers of the diseases. The main results were about the modules of Bacteroides, which were connected in the control subjects' correlation network, Faecalibacterium prausnitzii, where co-enzyme A became central in IBD correlation networks and Escherichia coli, whose module has different patterns of integration within the whole network in the different diagnoses.}, } @article {pmid37940330, year = {2023}, author = {Ismaeel, A and Valentino, TR and Burke, B and Goh, J and Saliu, TP and Albathi, F and Owen, A and McCarthy, JJ and Wen, Y}, title = {Acetate and succinate benefit host muscle energetics as exercise-associated post-biotics.}, journal = {Physiological reports}, volume = {11}, number = {21}, pages = {e15848}, pmid = {37940330}, issn = {2051-817X}, support = {K99 AR081367/AR/NIAMS NIH HHS/United States ; R21 AG071888/AG/NIA NIH HHS/United States ; }, mesh = {Mice ; Animals ; *Succinic Acid ; Muscle, Skeletal/metabolism ; *Microbiota ; Bacteria ; Bacteroidetes ; Acetates/pharmacology ; Hypertrophy/metabolism ; }, abstract = {Recently, the gut microbiome has emerged as a potent modulator of exercise-induced systemic adaptation and appears to be crucial for mediating some of the benefits of exercise. This study builds upon previous evidence establishing a gut microbiome-skeletal muscle axis, identifying exercise-induced changes in microbiome composition. Metagenomics sequencing of fecal samples from non-exercise-trained controls or exercise-trained mice was conducted. Biodiversity indices indicated exercise training did not change alpha diversity. However, there were notable differences in beta-diversity between trained and untrained microbiomes. Exercise significantly increased the level of the bacterial species Muribaculaceae bacterium DSM 103720. Computation simulation of bacterial growth was used to predict metabolites that accumulate under in silico culture of exercise-responsive bacteria. We identified acetate and succinate as potential gut microbial metabolites that are produced by Muribaculaceae bacterium, which were then administered to mice during a period of mechanical overload-induced muscle hypertrophy. Although no differences were observed for the overall muscle growth response to succinate or acetate administration during the first 5 days of mechanical overload-induced hypertrophy, acetate and succinate increased skeletal muscle mitochondrial respiration. When given as post-biotics, succinate or acetate treatment may improve oxidative metabolism during muscle hypertrophy.}, } @article {pmid37938762, year = {2022}, author = {Lesser, MP and Sabrina Pankey, M and Slattery, M and Macartney, KJ and Gochfeld, DJ}, title = {Microbiome diversity and metabolic capacity determines the trophic ecology of the holobiont in Caribbean sponges.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {112}, pmid = {37938762}, issn = {2730-6151}, support = {OCE 1638296//National Science Foundation (NSF)/ ; OCE 1638296//National Science Foundation (NSF)/ ; OCE 1638289//National Science Foundation (NSF)/ ; OCE 1638296//National Science Foundation (NSF)/ ; OCE 1638289//National Science Foundation (NSF)/ ; }, abstract = {Sponges are increasingly recognized as an ecologically important taxon on coral reefs, representing significant biomass and biodiversity where sponges have replaced scleractinian corals. Most sponge species can be divided into two symbiotic states based on symbiont community structure and abundance (i.e., the microbiome), and are characterized as high microbial abundance (HMA) or low microbial abundance (LMA) sponges. Across the Caribbean, sponge species of the HMA or LMA symbiotic states differ in metabolic capacity, as well as their trophic ecology. A metagenetic analysis of symbiont 16 S rRNA and metagenomes showed that HMA sponge microbiomes are more functionally diverse than LMA microbiomes, offer greater metabolic functional capacity and redundancy, and encode for the biosynthesis of secondary metabolites. Stable isotope analyses showed that HMA and LMA sponges primarily consume dissolved organic matter (DOM) derived from external autotrophic sources, or live particulate organic matter (POM) in the form of bacterioplankton, respectively, resulting in a low degree of resource competition between these symbiont states. As many coral reefs have undergone phase shifts from coral- to macroalgal-dominated reefs, the role of DOM, and the potential for future declines in POM due to decreased picoplankton productivity, may result in an increased abundance of chemically defended HMA sponges on tropical coral reefs.}, } @article {pmid37938241, year = {2023}, author = {Rojas, CA and Marks, SL and Borras, E and Lesea, H and McCartney, MM and Coil, DA and Davis, CE and Eisen, JA}, title = {Characterization of the microbiome and volatile compounds in anal gland secretions from domestic cats (Felis catus) using metagenomics and metabolomics.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {19382}, pmid = {37938241}, issn = {2045-2322}, support = {I01 BX004965/BX/BLRD VA/United States ; U01 TR004083/TR/NCATS NIH HHS/United States ; U18 TR003795/TR/NCATS NIH HHS/United States ; S10 OD010786/OD/NIH HHS/United States ; UG3 OD023365/OD/NIH HHS/United States ; UL1 TR001860/TR/NCATS NIH HHS/United States ; P30 ES023513/ES/NIEHS NIH HHS/United States ; }, mesh = {Cats ; Animals ; *Anal Canal ; Metabolomics ; *Microbiota/genetics ; Metagenome ; Metabolome ; Mammals ; }, abstract = {Many mammals rely on volatile organic chemical compounds (VOCs) produced by bacteria for their communication and behavior, though little is known about the exact molecular mechanisms or bacterial species that are responsible. We used metagenomic sequencing, mass-spectrometry based metabolomics, and culturing to profile the microbial and volatile chemical constituents of anal gland secretions in twenty-three domestic cats (Felis catus), in attempts to identify organisms potentially involved in host odor production. We found that the anal gland microbiome was dominated by bacteria in the genera Corynebacterium, Bacteroides, Proteus, Lactobacillus, and Streptococcus, and showed striking variation among individual cats. Microbiome profiles also varied with host age and obesity. Metabolites such as fatty-acids, ketones, aldehydes and alcohols were detected in glandular secretions. Overall, microbiome and metabolome profiles were modestly correlated (r = 0.17), indicating that a relationship exists between the bacteria in the gland and the metabolites produced in the gland. Functional analyses revealed the presence of genes predicted to code for enzymes involved in VOC metabolism such as dehydrogenases, reductases, and decarboxylases. From metagenomic data, we generated 85 high-quality metagenome assembled genomes (MAGs). Of importance were four MAGs classified as Corynebacterium frankenforstense, Proteus mirabilis, Lactobacillus johnsonii, and Bacteroides fragilis. They represent strong candidates for further investigation of the mechanisms of volatile synthesis and scent production in the mammalian anal gland.}, } @article {pmid37937832, year = {2023}, author = {Hay, MC and Mitchell, AC and Soares, AR and Debbonaire, AR and Mogrovejo, DC and Els, N and Edwards, A}, title = {Metagenome-assembled genomes from High Arctic glaciers highlight the vulnerability of glacier-associated microbiota and their activities to habitat loss.}, journal = {Microbial genomics}, volume = {9}, number = {11}, pages = {}, pmid = {37937832}, issn = {2057-5858}, mesh = {Humans ; *Ice Cover/chemistry/microbiology ; Metagenome ; *Microbiota/genetics ; Biodiversity ; Sulfur ; }, abstract = {The rapid warming of the Arctic is threatening the demise of its glaciers and their associated ecosystems. Therefore, there is an urgent need to explore and understand the diversity of genomes resident within glacial ecosystems endangered by human-induced climate change. In this study we use genome-resolved metagenomics to explore the taxonomic and functional diversity of different habitats within glacier-occupied catchments. Comparing different habitats within such catchments offers a natural experiment for understanding the effects of changing habitat extent or even loss upon Arctic microbiota. Through binning and annotation of metagenome-assembled genomes (MAGs) we describe the spatial differences in taxon distribution and their implications for glacier-associated biogeochemical cycling. Multiple taxa associated with carbon cycling included organisms with the potential for carbon monoxide oxidation. Meanwhile, nitrogen fixation was mediated by a single taxon, although diverse taxa contribute to other nitrogen conversions. Genes for sulphur oxidation were prevalent within MAGs implying the potential capacity for sulphur cycling. Finally, we focused on cyanobacterial MAGs, and those within cryoconite, a biodiverse microbe-mineral granular aggregate responsible for darkening glacier surfaces. Although the metagenome-assembled genome of Phormidesmis priestleyi, the cyanobacterium responsible for forming Arctic cryoconite was represented with high coverage, evidence for the biosynthesis of multiple vitamins and co-factors was absent from its MAG. Our results indicate the potential for cross-feeding to sustain P. priestleyi within granular cryoconite. Taken together, genome-resolved metagenomics reveals the vulnerability of glacier-associated microbiota to the deletion of glacial habitats through the rapid warming of the Arctic.}, } @article {pmid37937647, year = {2023}, author = {Ermakov, VS and Granados, JC and Nigam, SK}, title = {Remote effects of kidney drug transporter OAT1 on gut microbiome composition and urate homeostasis.}, journal = {JCI insight}, volume = {8}, number = {21}, pages = {}, pmid = {37937647}, issn = {2379-3708}, support = {R01 DK109392/DK/NIDDK NIH HHS/United States ; R01 GM132938/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Homeostasis ; Kidney/metabolism ; Membrane Transport Proteins ; *Renal Insufficiency, Chronic/metabolism ; Tryptophan/metabolism ; Uric Acid/metabolism ; }, abstract = {The organic anion transporter OAT1 (SLC22A6, originally identified as NKT) is a multispecific transporter responsible for the elimination by the kidney of small organic anions that derive from the gut microbiome. Many are uremic toxins associated with chronic kidney disease (CKD). OAT1 is among a group of "drug" transporters that act as hubs in a large homeostatic network regulating interorgan and interorganismal communication via small molecules. The Remote Sensing and Signaling Theory predicts that genetic deletion of such a key hub in the network results in compensatory interorganismal communication (e.g., host-gut microbe dynamics). Recent metabolomics data from Oat1-KO mice indicate that some of the most highly affected metabolites derive from bacterial tyrosine, tryptophan, purine, and fatty acid metabolism. Functional metagenomic analysis of fecal 16S amplicon and whole-genome sequencing revealed that loss of OAT1 was impressively associated with microbial pathways regulating production of urate, gut-derived p-cresol, tryptophan derivatives, and fatty acids. Certain changes, such as alterations in gut microbiome urate metabolism, appear compensatory. Thus, Oat1 in the kidney appears to mediate remote interorganismal communication by regulating the gut microbiome composition and metabolic capability. Since OAT1 function in the proximal tubule is substantially affected in CKD, our results may shed light on the associated alterations in gut-microbiome dynamics.}, } @article {pmid37936065, year = {2023}, author = {Li, Z and Cui, R and Wang, YB and Luo, YB and Xue, PX and Tang, QG and Fang, MY}, title = {Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {331}, pmid = {37936065}, issn = {1471-2180}, mesh = {Sheep ; Animals ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Bacteria ; Muscles ; Fatty Acids/metabolism ; Bacteroidetes ; Lauric Acids/metabolism ; }, abstract = {The biological mechanisms underlying meat quality remain unclear. Currently, many studies report that the gastrointestinal microbiota is essential for animal growth and performance. However, it is uncertain which bacterial species are specifically associated with the meat quality traits. In this study, 16S rDNA and metagenomic sequencing were performed to explore the composition and function of microbes in various gastrointestinal segments of Tan sheep and Dorper sheep, as well as the relationship between microbiota and meat quality (specifically, the fatty acid content of the muscle). In the ruminal, duodenal, and colonic microbiome, several bacteria were uniquely identified in respective breeds, including Agrobacterium tumefaciens, Bacteroidales bacterium CF, and several members of the family Oscillospiraceae. The annotation of GO, KEGG, and CAZYme revealed that these different bacterial species were linked to the metabolism of glucose, lipids, and amino acids. Additionally, our findings suggested that 16 microbial species may be essential to the content of fatty acids in the muscle, especially C12:0 (lauric acid). 4 bacterial species, including Achromobacter xylosoxidans, Mageeibacillus indolicus, and Mycobacterium dioxanotrophicus, were positively correlated with C12:0, while 13 bacteria, including Methanobrevibacter millerae, Bacteroidales bacterium CF, and Bacteroides coprosuis were negatively correlated with C12:0. In a word, this study provides a basic data for better understanding the interaction between ruminant gastrointestinal microorganisms and the meat quality traits of hosts.}, } @article {pmid37935462, year = {2023}, author = {Gaike, AH and Kalamkar, SD and Gajjar, V and Divate, U and Karandikar-Iyer, S and Goel, P and Shouche, YS and Ghaskadbi, SS}, title = {Effect of long-term oral glutathione supplementation on gut microbiome of type 2 diabetic individuals.}, journal = {FEMS microbiology letters}, volume = {370}, number = {}, pages = {}, doi = {10.1093/femsle/fnad116}, pmid = {37935462}, issn = {1574-6968}, support = {//UGC/ ; //CAS/ ; //DST/ ; //Savitribai Phule Pune University/ ; //National Centre for Cell Science/ ; //IISER Pune/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Glutathione ; *Diabetes Mellitus, Type 2/drug therapy ; Dietary Supplements ; }, abstract = {The aim of this study was to check the effect of long-term oral glutathione (GSH) supplementation on alteration in gut microbiome of Indian diabetic individuals. Early morning fresh stool sample of diabetic individuals recruited in a randomized clinical trial wherein they were given 500 mg GSH supplementation orally once a day for a period of 6 months was collected and gut microbiome was analysed using high throughput 16S rRNA metagenomic sequencing. Long-term GSH supplementation as reported in our earlier work showed significant increase in body stores of GSH and stabilized decreased glycated haemoglobin (HbA1c). Analysis of gut microbiome revealed that abundance of phylum Proteobacteria significantly decreased (P < 0.05) in individuals with GSH supplementation after 6 months compared to those without it. Beneficial dominant genera such as Megasphaera, Bacteroides, and Megamonas were found to be significantly enriched (P < 0.05), while pathogenic Escherichia/Shigella was found to be depleted (P < 0.05) after supplementation. Data clearly demonstrate that GSH supplementation along with antidiabetic treatment helps restore the gut microbiome by enriching beneficial bacteria of healthy gut and reducing significantly the load of pathogenic bacteria of diabetic gut.}, } @article {pmid37935197, year = {2023}, author = {Tomofuji, Y and Kishikawa, T and Sonehara, K and Maeda, Y and Ogawa, K and Kawabata, S and Oguro-Igashira, E and Okuno, T and Nii, T and Kinoshita, M and Takagaki, M and Yamamoto, K and Arase, N and Yagita-Sakamaki, M and Hosokawa, A and Motooka, D and Matsumoto, Y and Matsuoka, H and Yoshimura, M and Ohshima, S and Nakamura, S and Fujimoto, M and Inohara, H and Kishima, H and Mochizuki, H and Takeda, K and Kumanogoh, A and Okada, Y}, title = {Analysis of gut microbiome, host genetics, and plasma metabolites reveals gut microbiome-host interactions in the Japanese population.}, journal = {Cell reports}, volume = {42}, number = {11}, pages = {113324}, doi = {10.1016/j.celrep.2023.113324}, pmid = {37935197}, issn = {2211-1247}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Genome-Wide Association Study ; East Asian People ; Metabolome ; *Blood Group Antigens ; Repressor Proteins/genetics ; Homeodomain Proteins/genetics ; }, abstract = {Interaction between the gut microbiome and host plays a key role in human health. Here, we perform a metagenome shotgun-sequencing-based analysis of Japanese participants to reveal associations between the gut microbiome, host genetics, and plasma metabolome. A genome-wide association study (GWAS) for microbial species (n = 524) identifies associations between the PDE1C gene locus and Bacteroides intestinalis and between TGIF2 and TGIF2-RAB5IF gene loci and Bacteroides acidifiaciens. In a microbial gene ortholog GWAS, agaE and agaS, which are related to the metabolism of carbohydrates forming the blood group A antigen, are associated with blood group A in a manner depending on the secretor status determined by the East Asian-specific FUT2 variant. A microbiome-metabolome association analysis (n = 261) identifies associations between bile acids and microbial features such as bile acid metabolism gene orthologs including bai and 7β-hydroxysteroid dehydrogenase. Our publicly available data will be a useful resource for understanding gut microbiome-host interactions in an underrepresented population.}, } @article {pmid37932275, year = {2023}, author = {Good, BH and Rosenfeld, LB}, title = {Eco-evolutionary feedbacks in the human gut microbiome.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7146}, pmid = {37932275}, issn = {2041-1723}, support = {R35 GM146949/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Feedback ; *Microbiota ; Metagenome ; }, abstract = {Gut microbiota can evolve within their hosts on human-relevant timescales, but little is known about how these changes influence (or are influenced by) the composition of their local community. Here, by combining ecological and evolutionary analyses of a large cohort of human gut metagenomes, we show that the short-term evolution of the microbiota is linked with shifts in its ecological structure. These correlations are not simply explained by expansions of the evolving species, and often involve additional fluctuations in distantly related taxa. We show that similar feedbacks naturally emerge in simple resource competition models, even in the absence of cross-feeding or predation. These results suggest that the structure and function of host microbiota may be shaped by their local evolutionary history, which could have important implications for personalized medicine and microbiome engineering.}, } @article {pmid37932270, year = {2023}, author = {Ning, L and Zhou, YL and Sun, H and Zhang, Y and Shen, C and Wang, Z and Xuan, B and Zhao, Y and Ma, Y and Yan, Y and Tong, T and Huang, X and Hu, M and Zhu, X and Ding, J and Zhang, Y and Cui, Z and Fang, JY and Chen, H and Hong, J}, title = {Microbiome and metabolome features in inflammatory bowel disease via multi-omics integration analyses across cohorts.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7135}, pmid = {37932270}, issn = {2041-1723}, mesh = {Humans ; Multiomics ; *Inflammatory Bowel Diseases/metabolism ; Metabolome ; *Microbiota ; Biomarkers/metabolism ; }, abstract = {The perturbations of the gut microbiota and metabolites are closely associated with the progression of inflammatory bowel disease (IBD). However, inconsistent findings across studies impede a comprehensive understanding of their roles in IBD and their potential as reliable diagnostic biomarkers. To address this challenge, here we comprehensively analyze 9 metagenomic and 4 metabolomics cohorts of IBD from different populations. Through cross-cohort integrative analysis (CCIA), we identify a consistent characteristic of commensal gut microbiota. Especially, three bacteria, namely Asaccharobacter celatus, Gemmiger formicilis, and Erysipelatoclostridium ramosum, which are rarely reported in IBD. Metagenomic functional analysis reveals that essential gene of Two-component system pathway, linked to fecal calprotectin, are implicated in IBD. Metabolomics analysis shows 36 identified metabolites with significant differences, while the roles of these metabolites in IBD are still unknown. To further elucidate the relationship between gut microbiota and metabolites, we construct multi-omics biological correlation (MOBC) maps, which highlights gut microbial biotransformation deficiencies and significant alterations in aminoacyl-tRNA synthetases. Finally, we identify multi-omics biomarkers for IBD diagnosis, validated across multiple global cohorts (AUROC values ranging from 0.92 to 0.98). Our results offer valuable insights and a significant resource for developing mechanistic hypotheses on host-microbiome interactions in IBD.}, } @article {pmid37932168, year = {2024}, author = {Dike, CR and Ollberding, NJ and Thompson, T and Kotha, N and Minar, P and Vitale, DS and Lin, TK and Nasr, A and Denson, LA and Haslam, DB and Abu-El-Haija, M}, title = {Acute pancreatitis is associated with gut dysbiosis in children.}, journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver}, volume = {56}, number = {3}, pages = {444-450}, pmid = {37932168}, issn = {1878-3562}, support = {K23 DK118190/DK/NIDDK NIH HHS/United States ; R03 DK131156/DK/NIDDK NIH HHS/United States ; T32 DK007727/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Child ; Humans ; Acute Disease ; Dysbiosis/complications/metabolism ; Feces/chemistry ; *Gastrointestinal Microbiome ; *Pancreatitis/complications ; }, abstract = {BACKGROUND: Pediatric acute pancreatitis (AP) is associated with significant morbidity. Therefore, improved understanding of children who will develop severe AP is critical. Adult studies have reported AP associated gut dysbiosis, but pediatric studies are lacking.

AIMS: Assess stool microbial taxonomic and functional profiles of children with first attack of AP compared to those of healthy controls (HC), and between mild and severe AP METHODS: Children under 21 years hospitalized at a tertiary center (n = 30) with first AP attack were recruited including HC (n = 34) from same region. Shotgun metagenomic sequencing was performed on extracted DNA.

RESULTS: Demographics were similar between AP and HC. Alpha diversity (-0.68 ± 0.13, p-value < 0.001), and beta-diversity (R[2]=0.13, p-value < 0.001) differed, in children with AP compared to HC. Species including R.gnavus, V.parvula, E.faecalis, C.innocuum were enriched in AP. MetaCyc pathways involved in amino acid metabolism and fatty acid beta-oxidation were enriched in AP. Beta-diversity (R[2]=0.06, p-value = 0.02) differed for severe AP compared to mild AP with enrichment in E.faecalis and C.citroniae.

CONCLUSIONS: Gut dysbiosis occurs in pediatric AP and is associated with AP severity. A multicenter study confirming these findings could pave way for interventional trials manipulating the gut microbiome to mitigate AP severity.}, } @article {pmid37930866, year = {2024}, author = {Camargo, AP and Call, L and Roux, S and Nayfach, S and Huntemann, M and Palaniappan, K and Ratner, A and Chu, K and Mukherjeep, S and Reddy, TBK and Chen, IA and Ivanova, NN and Eloe-Fadrosh, EA and Woyke, T and Baltrus, DA and Castañeda-Barba, S and de la Cruz, F and Funnell, BE and Hall, JPJ and Mukhopadhyay, A and Rocha, EPC and Stalder, T and Top, E and Kyrpides, NC}, title = {IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata.}, journal = {Nucleic acids research}, volume = {52}, number = {D1}, pages = {D164-D173}, pmid = {37930866}, issn = {1362-4962}, support = {MR/W02666X/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Metagenome ; Metadata ; Software ; Databases, Genetic ; Plasmids/genetics ; *Microbiota ; }, abstract = {Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.}, } @article {pmid37930569, year = {2023}, author = {Wang, F and Zhao, Q and Zhang, L and Chen, J and Wang, T and Qiao, L and Zhang, L and Ding, C and Yuan, Y and Qi, Z and Chen, T}, title = {Co-digestion of chicken manure and sewage sludge in black soldier fly larvae bioconversion system: bacterial biodiversity and nutrients quality of residues for biofertilizer application.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {57}, pages = {119804-119813}, pmid = {37930569}, issn = {1614-7499}, support = {Grant Nos. 42272211//National Natural Science Foundation of China/ ; BK20210946//Natural Science Foundation of Jiangsu Province/ ; No. xjr2021051//School-level research projects of Yancheng Institute of Technology/ ; }, mesh = {Animals ; Larva ; *Sewage ; Manure ; Chickens ; *Diptera ; Nutrients ; Bacteria ; Digestion ; }, abstract = {Black soldier fly larvae (BSFL) bioconversion system is emerging as an effective approach for organic waste pollution treatment. Co-digestion of different organic matters with BSFL can be an effective way to realize the innovative biowaste circular economy. In this study, organic waste mixture of chicken manure and sewage sludge was chosen as substrate for BSFL growth. The bacterial biodiversity and nutrients quality of BSFL residue were evaluated through gene sequencing and other characterizations to confirm their application potential as biofertilizers. The dominant bacteria in BSFL residue were Firmicutes (75.39%) at phylum level, Bacilli (71.61%) at class level and Pseudogracilibacillus (11.08%) at genus level. Antibiotic resistance genes (ARGs) were used to assess the harmlessness of BSFL residue. After BSFL treatment, 36.2% decrease in ARGs was observed. Taking nutrients quality into consideration, dissolved organic carbon, dissolved nitrogen, available phosphorous, and available potassium significantly increased in the co-digestion system. These results demonstrated that co-digestion of chicken manure and excess sludge in BSFL bioconversion system could improve the nutrients quality of residues. However, removal of ARGs in the bioconversion process should be further explored to eliminate environmental concerns associated with application of BSFL residue as biofertilizers.}, } @article {pmid37930060, year = {2023}, author = {Tan, Y and Yu, P and Huang, D and Yuan, MM and Yu, Z and Lu, H and Alvarez, PJJ and Zhu, L}, title = {Enhanced Bacterium-Phage Symbiosis in Attached Microbial Aggregates on a Membrane Surface Facing Elevated Hydraulic Stress.}, journal = {Environmental science & technology}, volume = {57}, number = {45}, pages = {17324-17337}, doi = {10.1021/acs.est.3c05452}, pmid = {37930060}, issn = {1520-5851}, mesh = {*Bacteriophages/genetics ; Symbiosis ; Bacteria/genetics ; *Microbiota ; Metagenome ; }, abstract = {Phages are increasingly recognized for their importance in microbial aggregates, including their influence on microbial ecosystem services and biotechnology applications. However, the adaptive strategies and ecological functions of phages in different aggregates remain largely unexplored. Herein, we used membrane bioreactors to investigate bacterium-phage interactions and related microbial functions within suspended and attached microbial aggregates (SMA vs AMA). SMA and AMA represent distinct microbial habitats where bacterial communities display distinct patterns in terms of dominant species, keystone species, and bacterial networks. However, bacteria and phages in both aggregates exhibited high lysogenicity, with 60% lysogenic phages in the virome and 70% lysogenic metagenome-assembled genomes of bacteria. Moreover, substantial phages exhibited broad host ranges (34% in SMA and 42% in AMA) and closely interacted with habitat generalist species (43% in SMA and 49% in AMA) as adaptive strategies in stressful operation environments. Following a mutualistic pattern, phage-carried auxiliary metabolic genes (pAMGs; 238 types in total) presumably contributed to the bacterial survival and aggregate stability. The SMA-pAMGs were mainly associated with energy metabolism, while the AMA-pAMGs were mainly associated with antioxidant biosynthesis and the synthesis of extracellular polymeric substances, representing habitat-dependent patterns. Overall, this study advanced our understanding of phage adaptive strategies in microbial aggregate habitats and emphasized the importance of bacterium-phage symbiosis in the stability of microbial aggregates.}, } @article {pmid37929823, year = {2024}, author = {Yi, X and Lu, H and Liu, X and He, J and Li, B and Wang, Z and Zhao, Y and Zhang, X and Yu, X}, title = {Unravelling the enigma of the human microbiome: Evolution and selection of sequencing technologies.}, journal = {Microbial biotechnology}, volume = {17}, number = {1}, pages = {e14364}, pmid = {37929823}, issn = {1751-7915}, support = {82202569//National Natural Science Foundation of China/ ; 20210302124635//Shanxi Province Basic Research Program Project/ ; }, mesh = {Humans ; *Microbiota ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics ; Technology ; }, abstract = {The human microbiome plays a crucial role in maintaining health, with advances in high-throughput sequencing technology and reduced sequencing costs triggering a surge in microbiome research. Microbiome studies generally incorporate five key phases: design, sampling, sequencing, analysis, and reporting, with sequencing strategy being a crucial step offering numerous options. Present mainstream sequencing strategies include Amplicon sequencing, Metagenomic Next-Generation Sequencing (mNGS), and Targeted Next-Generation Sequencing (tNGS). Two innovative technologies recently emerged, namely MobiMicrobe high-throughput microbial single-cell genome sequencing technology and 2bRAD-M simplified metagenomic sequencing technology, compensate for the limitations of mainstream technologies, each boasting unique core strengths. This paper reviews the basic principles and processes of these three mainstream and two novel microbiological technologies, aiding readers in understanding the benefits and drawbacks of different technologies, thereby guiding the selection of the most suitable method for their research endeavours.}, } @article {pmid37926838, year = {2023}, author = {Su, Y and Xu, MY and Cui, Y and Chen, RZ and Xie, LX and Zhang, JX and Chen, YQ and Ding, T}, title = {Bacterial quorum sensing orchestrates longitudinal interactions to shape microbiota assembly.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {241}, pmid = {37926838}, issn = {2049-2618}, mesh = {Humans ; *Quorum Sensing ; Bacterial Proteins/metabolism ; Bacteria/genetics/metabolism ; Biofilms ; Streptococcus/genetics/metabolism ; *Microbiota ; }, abstract = {BACKGROUND: The mechanism of microbiota assembly is one of the main problems in microbiome research, which is also the primary theoretical basis for precise manipulation of microbial communities. Bacterial quorum sensing (QS), as the most common means for bacteria to exchange information and interactions, is characterized by universality, specificity, and regulatory power, which therefore may influence the assembly processes of human microbiota. However, the regulating role of QS in microbiota assembly is rarely reported. In this study, we developed an optimized in vitro oral biofilm microbiota assembling (OBMA) model to simulate the time-series assembly of oral biofilm microbiota (OBM), by which to excavate the QS network and its regulating power in the process.

RESULTS: By using the optimized OBMA model, we were able to restore the assembly process of OBM and generate time-series OBM metagenomes of each day. We discovered a total of 2291 QS protein homologues related to 21 QS pathways. Most of these pathways were newly reported and sequentially enriched during OBM assembling. These QS pathways formed a comprehensive longitudinal QS network that included successively enriched QS hubs, such as Streptococcus, Veillonella-Megasphaera group, and Prevotella-Fusobacteria group, for information delivery. Bidirectional cross-talk among the QS hubs was found to play critical role in the directional turnover of microbiota structure, which in turn, influenced the assembly process. Subsequent QS-interfering experiments accurately predicted and experimentally verified the directional shaping power of the longitudinal QS network in the assembly process. As a result, the QS-interfered OBM exhibited delayed and fragile maturity with prolonged membership of Streptococcus and impeded membership of Prevotella and Fusobacterium.

CONCLUSION: Our results revealed an unprecedented longitudinal QS network during OBM assembly and experimentally verified its power in predicting and manipulating the assembling process. Our work provides a new perspective to uncover underlying mechanism in natural complex microbiota assembling and a theoretical basis for ultimately precisely manipulating human microbiota through intervention in the QS network. Video Abstract.}, } @article {pmid37924150, year = {2023}, author = {Li, Y and Mao, K and Zang, Y and Lu, G and Qiu, Q and Ouyang, K and Zhao, X and Song, X and Xu, L and Liang, H and Qu, M}, title = {Revealing the developmental characterization of rumen microbiome and its host in newly received cattle during receiving period contributes to formulating precise nutritional strategies.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {238}, pmid = {37924150}, issn = {2049-2618}, mesh = {Cattle ; Animals ; *Diet/veterinary ; Rumen/microbiology ; *Microbiota ; Bacteria/genetics/metabolism ; Archaea/metabolism ; Inflammation/metabolism ; Methane/metabolism ; Ornithine/metabolism ; Polyamines/metabolism ; Animal Feed/analysis ; Fermentation ; }, abstract = {BACKGROUND: Minimizing mortality losses due to multiple stress and obtaining maximum performance are the production goals for newly received cattle. In recent years, vaccination and metaphylaxis treatment significantly decreased the mortality rate of newly received cattle, while the growth block induced by treatment is still obvious. Assessment of blood metabolites and behavior monitoring offer potential for early identification of morbid animals. Moreover, the ruminal microorganisms' homeostasis is a guarantee of beef steers' growth and health. The most critical period for newly received cattle is the first-month post-transport. Therefore, analyzing rumen metagenomics, rumen metabolomics, host metabolomics, and their interaction during receiving period (1 day before transport and at days 1/4, 16, and 30 after transport) is key to revealing the mechanism of growth retardation, and then to formulating management and nutritional practices for newly received cattle.

RESULTS: The levels of serum hormones (COR and ACTH), and pro-inflammatory factors (IL-1β, TNF-α, and IL-6) were highest at day 16, and lowest at day 30 after arrival. Meanwhile, the antioxidant capacity (SOD, GSH-Px, and T-AOC) was significantly decreased at day 16 and increased at day 30 after arrival. Metagenomics analysis revealed that rumen microbes, bacteria, archaea, and eukaryota had different trends among the four different time points. At day 16 post-transport, cattle had a higher abundance of ruminal bacteria and archaea than those before transport, but the eukaryote abundance was highest at day 30 post-transport. Before transport, most bacteria were mainly involved in polysaccharides digestion. At day 4 post-transport, the most significantly enriched KEGG pathways were nucleotide metabolism (pyrimidine metabolism and purine metabolism). At day 16 post-transport, the energy metabolism (glycolysis/gluconeogenesis, pyruvate metabolism) and ruminal contents of MCP and VFAs were significantly increased, but at the same time, energy loss induced by methane yields (Methanobrevibacter) together with pathogenic bacteria (Saccharopolyspora rectivirgula) were also significantly increased. At this time, the most upregulated ruminal L-ornithine produces more catabolite polyamines, which cause oxidative stress to rumen microbes and their host; the most downregulated ruminal 2',3'-cAMP provided favorable growth conditions for pathogenic bacteria, and the downregulated ruminal vitamin B6 metabolism and serum PC/LysoPC disrupt immune function and inflammation reaction. At day 30 post-transport, the ruminal L-ornithine and its catabolites (mainly spermidine and 1,3-propanediamine) were decreased, and the serum PC/LysoPC and 2',3'-cNMPs pools were increased. This is also consistent with the changes in redox, inflammation, and immune status of the host.

CONCLUSIONS: This study provides new ideas for regulating the health and performance of newly received cattle during the receiving period. The key point is to manage the newly received cattle about day 16 post-transport, specifically to inhibit the production of methane and polyamines, and the reproduction of harmful bacteria in the rumen, therefore improving the immunity and performance of newly received cattle. Video Abstract.}, } @article {pmid37923779, year = {2023}, author = {Flores, GAM and Lopez, RP and Cerrudo, CS and Perotti, MA and Consolo, VF and Berón, CM}, title = {Wolbachia dominance influences the Culex quinquefasciatus microbiota.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {18980}, pmid = {37923779}, issn = {2045-2322}, mesh = {Animals ; *Aedes/genetics ; Bacteria/genetics ; *Culex/genetics ; *Microbiota ; Mosquito Vectors/microbiology ; RNA, Ribosomal, 16S/genetics ; *Wolbachia/genetics ; }, abstract = {Microorganisms present in mosquitoes and their interactions are key factors affecting insect development. Among them, Wolbachia is closely associated with the host and affects several fitness parameters. In this study, the bacterial and fungal microbiota from two laboratory Culex quinquefasciatus isolines (wild type and tetracycline-cured) were characterized by metagenome amplicon sequencing of the ITS2 and 16S rRNA genes at different developmental stages and feeding conditions. We identified 572 bacterial and 61 fungal OTUs. Both isolines presented variable bacterial communities and different trends in the distribution of diversity among the groups. The lowest bacterial richness was detected in sugar-fed adults of the cured isoline, whereas fungal richness was highly reduced in blood-fed mosquitoes. Beta diversity analysis indicated that isolines are an important factor in the differentiation of mosquito bacterial communities. Considering composition, Penicillium was the dominant fungal genus, whereas Wolbachia dominance was inversely related to that of Enterobacteria (mainly Thorsellia and Serratia). This study provides a more complete overview of the mosquito microbiome, emphasizing specific highly abundant components that should be considered in microorganism manipulation approaches to control vector-borne diseases.}, } @article {pmid37921501, year = {2023}, author = {Wang, H and Bi, H and Yang, M and Wang, X and Song, C and Yang, W and Wang, Y and Xie, D and Li, H and Zhou, Z}, title = {Intestinal flora altered and correlated with interleukin-2/4 in patients with primary immune thrombocytopenia.}, journal = {Hematology (Amsterdam, Netherlands)}, volume = {28}, number = {1}, pages = {2277501}, doi = {10.1080/16078454.2023.2277501}, pmid = {37921501}, issn = {1607-8454}, mesh = {Humans ; *Gastrointestinal Microbiome ; Interleukin-2 ; Interleukin-4 ; *Purpura, Thrombocytopenic, Idiopathic ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Little is known about the changes and mechanisms of intestinal flora in primary immune thrombocytopenia (ITP) patients.

AIM: To explore the structural and functional differences of intestinal flora between ITP patients and healthy controls, and clarify the correlation between intestinal flora and Th1/Th2 imbalance.

METHODS: Feces from ITP patients and healthy controls were studied by 16S rRNA and metagenomic techniques at phylum, genus, species or functional levels. Blood samples were collected for the detection of interleukin -2 (IL-2) and IL-4 concentrations.

RESULTS: The following changes in ITP patients were found: a decrease of Bacteroidetes phylum, an increase of Proteobacteria phylum and alterations of ten genera and 1045 species. IL-2 and IL-4 were significantly correlated with six and five genera, respectively. Species of C. freundii, C. rodentium, and C. youngae were negatively correlated with bleeding scores, and S. infantis was positively related to platelet counts. Functionally, the intestinal flora of ITP patients changed mainly in terms of motility, chemotaxis, membrane transport, and metabolism.

CONCLUSION: The mechanism underlying functional and structural changes of intestinal flora in ITP patients may be related to inflammation and immunity, providing possibilities of probiotics or fecal transplants for ITP.}, } @article {pmid37919437, year = {2023}, author = {Zahavi, L and Lavon, A and Reicher, L and Shoer, S and Godneva, A and Leviatan, S and Rein, M and Weissbrod, O and Weinberger, A and Segal, E}, title = {Bacterial SNPs in the human gut microbiome associate with host BMI.}, journal = {Nature medicine}, volume = {29}, number = {11}, pages = {2785-2792}, pmid = {37919437}, issn = {1546-170X}, support = {R01 HL160862/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Body Mass Index ; Polymorphism, Single Nucleotide/genetics ; Genome-Wide Association Study ; *Microbiota ; Bacteria/genetics ; }, abstract = {Genome-wide association studies (GWASs) have provided numerous associations between human single-nucleotide polymorphisms (SNPs) and health traits. Likewise, metagenome-wide association studies (MWASs) between bacterial SNPs and human traits can suggest mechanistic links, but very few such studies have been done thus far. In this study, we devised an MWAS framework to detect SNPs and associate them with host phenotypes systematically. We recruited and obtained gut metagenomic samples from a cohort of 7,190 healthy individuals and discovered 1,358 statistically significant associations between a bacterial SNP and host body mass index (BMI), from which we distilled 40 independent associations. Most of these associations were unexplained by diet, medications or physical exercise, and 17 replicated in a geographically independent cohort. We uncovered BMI-associated SNPs in 27 bacterial species, and 12 of them showed no association by standard relative abundance analysis. We revealed a BMI association of an SNP in a potentially inflammatory pathway of Bilophila wadsworthia as well as of a group of SNPs in a region coding for energy metabolism functions in a Faecalibacterium prausnitzii genome. Our results demonstrate the importance of considering nucleotide-level diversity in microbiome studies and pave the way toward improved understanding of interpersonal microbiome differences and their potential health implications.}, } @article {pmid37916972, year = {2023}, author = {Mostacci, N and Wüthrich, TM and Siegwald, L and Kieser, S and Steinberg, R and Sakwinska, O and Latzin, P and Korten, I and Hilty, M}, title = {Informed interpretation of metagenomic data by StrainPhlAn enables strain retention analyses of the upper airway microbiome.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0072423}, pmid = {37916972}, issn = {2379-5077}, support = {159791//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Haemophilus influenzae/genetics ; Nose ; Trachea ; *Microbiota/genetics ; }, abstract = {The usage of 16S rRNA gene sequencing has become the state-of-the-art method for the characterization of the microbiota in health and respiratory disease. The method is reliable for low biomass samples due to prior amplification of the 16S rRNA gene but has limitations as species and certainly strain identification is not possible. However, the usage of metagenomic tools for the analyses of microbiome data from low biomass samples is not straight forward, and careful optimization is needed. In this work, we show that by validating StrainPhlAn 3 results with the data from bacterial cultures, the strain-level tracking of the respiratory microbiome is feasible despite the high content of host DNA being present when parameters are carefully optimized to fit low biomass microbiomes. This work further proposes that strain retention analyses are feasible, at least for more abundant species. This will help to better understand the longitudinal dynamics of the upper respiratory microbiome during health and disease.}, } @article {pmid37916828, year = {2023}, author = {Cocconcelli, PS and Gatti, M and Giraffa, G and Gobbetti, M and Lanciotti, R and Morelli, L and Neviani, E and Parente, E}, title = {Should the microbiota of raw milk cheeses play a role in the definition of geographical indications and quality schemes within the European Union?.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0052023}, pmid = {37916828}, issn = {2379-5077}, mesh = {Animals ; *Cheese/analysis ; Milk ; European Union ; *Microbiota ; }, } @article {pmid37915846, year = {2023}, author = {Zhang, Y and Chen, X and Wang, Y and Li, L and Ju, Q and Zhang, Y and Xi, H and Wang, F and Qiu, D and Liu, X and Chang, N and Zhang, W and Zhang, C and Wang, K and Li, L and Zhang, J}, title = {Alterations of lower respiratory tract microbiome and short-chain fatty acids in different segments in lung cancer: a multiomics analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1261284}, pmid = {37915846}, issn = {2235-2988}, mesh = {Humans ; *Lung Neoplasms ; Multiomics ; *Microbiota/genetics ; Fatty Acids, Volatile/metabolism ; Carcinogenesis ; }, abstract = {INTRODUCTION: The lower respiratory tract microbiome is widely studied to pinpoint microbial dysbiosis of diversity or abundance that is linked to a number of chronic respiratory illnesses. However, it is vital to clarify how the microbiome, through the release of microbial metabolites, impacts lung health and oncogenesis.

METHODS: In order to discover the powerful correlations between microbial metabolites and disease, we collected, under electronic bronchoscopy examinations, samples of paired bronchoalveolar lavage fluids (BALFs) from tumor-burden lung segments and ipsilateral non-tumor sites from 28 lung cancer participants, further performing metagenomic sequencing, short-chain fatty acid (SCFA) metabolomics, and multiomics analysis to uncover the potential correlations of the microbiome and SCFAs in lung cancer.

RESULTS: In comparison to BALFs from normal lung segments of the same participant, those from lung cancer burden lung segments had slightly decreased microbial diversity in the lower respiratory tract. With 18 differentially prevalent microbial species, including the well-known carcinogens Campylobacter jejuni and Nesseria polysaccharea, the relative species abundance in the lower respiratory tract microbiome did not significantly differ between the two groups. Additionally, a collection of commonly recognized probiotic metabolites called short-chain fatty acids showed little significance in either group independently but revealed a strong predictive value when using an integrated model by machine learning. Multiomics also discovered particular species related to SCFAs, showing a positive correlation with Brachyspira hydrosenteriae and a negative one with Pseudomonas at the genus level, despite limited detection in lower airways. Of note, these distinct microbiota and metabolites corresponded with clinical traits that still required confirmation.

CONCLUSIONS: Further analysis of metagenome functional capacity revealed that genes encoding environmental information processing and metabolism pathways were enriched in the lower respiratory tract metagenomes of lung cancer patients, further supporting the oncogenesis function of various microbial species by different metabolites. These findings point to a potent relationship between particular components of the integrated microbiota-metabolites network and lung cancer, with implications for screening and diagnosis in clinical settings.}, } @article {pmid37913618, year = {2024}, author = {Lu, Z and Cheng, X and Xie, J and Li, Z and Li, X and Jiang, X and Zhu, D}, title = {Iron-based multi-carbon composite and Pseudomonas furukawaii ZS1 co-affect nitrogen removal, microbial community dynamics and metabolism pathways in low-temperature aquaculture wastewater.}, journal = {Journal of environmental management}, volume = {349}, number = {}, pages = {119471}, doi = {10.1016/j.jenvman.2023.119471}, pmid = {37913618}, issn = {1095-8630}, mesh = {*Wastewater ; Denitrification ; Temperature ; Nitrogen/metabolism ; Carbon ; Pseudomonas/metabolism ; *Microbiota ; Bioreactors/microbiology ; Nitrification ; }, abstract = {Aerobic denitrification is the key process in the elimination of nitrogen from aquaculture wastewater, especially for wastewater with high dissolved oxygen and low carbon/nitrogen (C/N) ratio. However, a low C/N ratio, especially in low-temperature environments, restricts the activity of aerobic denitrifiers and decreases the nitrogen elimination efficiency. In this study, an iron-based multi-solid carbon source composite that immobilized aerobic denitrifying bacteria ZS1 (IMCSCP) was synthesized to treat aerobic (DO > 5 mg/L), low temperature (<15 °C) and low C/N ratio (C/N = 4) aquaculture wastewater. The results showed that the sequencing batch biofilm reactor (SBBR) packed with IMCSCP exhibited the highest nitrogen removal performance, with removal rates of 95.63% and 85.44% for nitrate nitrogen and total nitrogen, respectively, which were 33.03% and 30.75% higher than those in the reactor filled with multi-solid carbon source composite (MCSC). Microbial community and network analysis showed that Pseudomonas furukawaii ZS1 successfully colonized the SBBR filled with IMCSCP, and Exiguobacterium, Cellulomonas and Pseudomonas were essential for the nitrogen elimination. Metagenomic analysis showed that an increase in gene abundance related to carbon metabolism, nitrogen metabolism, extracellular polymer substance synthesis and electron transfer in the IMCSCP, enabling denitrification in the SBBR to be achieved via multiple pathways. The results of this study provided new insights into the microbial removal mechanism of nitrogen in SBBR packed with IMCSCP at low temperatures.}, } @article {pmid37910603, year = {2023}, author = {Woodworth, MH and Conrad, RE and Haldopoulos, M and Pouch, SM and Babiker, A and Mehta, AK and Sitchenko, KL and Wang, CH and Strudwick, A and Ingersoll, JM and Philippe, C and Lohsen, S and Kocaman, K and Lindner, BG and Hatt, JK and Jones, RM and Miller, C and Neish, AS and Friedman-Moraco, R and Karadkhele, G and Liu, KH and Jones, DP and Mehta, CC and Ziegler, TR and Weiss, DS and Larsen, CP and Konstantinidis, KT and Kraft, CS}, title = {Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement.}, journal = {Science translational medicine}, volume = {15}, number = {720}, pages = {eabo2750}, pmid = {37910603}, issn = {1946-6242}, support = {P51 OD011132/OD/NIH HHS/United States ; UM1 AI104681/AI/NIAID NIH HHS/United States ; S10 OD026799/OD/NIH HHS/United States ; UL1 TR002378/TR/NCATS NIH HHS/United States ; P30 AI050409/AI/NIAID NIH HHS/United States ; K23 AI144036/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Fecal Microbiota Transplantation/adverse effects ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome ; Drug Resistance, Bacterial ; Feces/microbiology ; Treatment Outcome ; }, abstract = {Multidrug-resistant organism (MDRO) colonization is a fundamental challenge in antimicrobial resistance. Limited studies have shown that fecal microbiota transplantation (FMT) can reduce MDRO colonization, but its mechanisms are poorly understood. We conducted a randomized, controlled trial of FMT for MDRO decolonization in renal transplant recipients called PREMIX (NCT02922816). Eleven participants were enrolled and randomized 1:1 to FMT or an observation period followed by delayed FMT if stool cultures were MDRO positive at day 36. Participants who were MDRO positive after one FMT were treated with a second FMT. At last visit, eight of nine patients who completed all treatments were MDRO culture negative. FMT-treated participants had longer time to recurrent MDRO infection versus PREMIX-eligible controls who were not treated with FMT. Key taxa (Akkermansia muciniphila, Alistipes putredinis, Phocaeicola dorei, Phascolarctobacterium faecium, Alistipes species, Mesosutterella massiliensis, Barnesiella intestinihominis, and Faecalibacterium prausnitzii) from the single feces donor used in the study that engrafted in recipients and metabolites such as short-chain fatty acids and bile acids in FMT-responding participants uncovered leads for rational microbiome therapeutic and diagnostic development. Metagenomic analyses revealed a previously unobserved mechanism of MDRO eradication by conspecific strain competition in an FMT-treated subset. Susceptible Enterobacterales strains that replaced baseline extended-spectrum β-lactamase-producing strains were not detectable in donor microbiota manufactured as FMT doses but in one case were detectable in the recipient before FMT. These data suggest that FMT may provide a path to exploit strain competition to reduce MDRO colonization.}, } @article {pmid37910478, year = {2023}, author = {Lee, J and Peesh, P and Quaicoe, V and Tan, C and Banerjee, A and Mooz, P and Ganesh, BP and Petrosino, J and Bryan, RM and McCullough, LD and Venna, VR}, title = {Estradiol mediates colonic epithelial protection in aged mice after stroke and is associated with shifts in the gut microbiome.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2271629}, pmid = {37910478}, issn = {1949-0984}, support = {R01 NS094543/NS/NINDS NIH HHS/United States ; R21 AG072380/AG/NIA NIH HHS/United States ; R01 NS103592/NS/NINDS NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R35 NS132265/NS/NINDS NIH HHS/United States ; }, mesh = {Mice ; Female ; Male ; Animals ; *Gastrointestinal Microbiome ; Intestinal Mucosa/microbiology ; Estradiol ; RNA, Ribosomal, 16S/genetics ; Mucins/metabolism ; *Brain Injuries/metabolism ; }, abstract = {The gut is a major source of bacteria and antigens that contribute to neuroinflammation after brain injury. Colonic epithelial cells (ECs) are responsible for secreting major cellular components of the innate defense system, including antimicrobial proteins (AMP) and mucins. These cells serve as a critical regulator of gut barrier function and maintain host-microbe homeostasis. In this study, we determined post-stroke host defense responses at the colonic epithelial surface in mice. We then tested if the enhancement of these epithelial protective mechanisms is beneficial in young and aged mice after stroke. AMPs were significantly increased in the colonic ECs of young males, but not in young females after experimental stroke. In contrast, mucin-related genes were enhanced in young females and contributed to mucus formation that maintains the distance between the host and gut bacteria. Bacterial community profiling was done using universal amplification of 16S rRNA gene sequences. The sex-specific colonic epithelial defense responses after stroke in young females were reversed with ovariectomy and led to a shift from a predominately mucin response to the enhanced AMP expression seen in males after stroke. Estradiol (E2) replacement prior to stroke in aged females increased mucin gene expression in the colonic ECs. Interestingly, we found that E2 treatment reduced stroke-associated neuronal hyperactivity in the insular cortex, a brain region that interacts with visceral organs such as the gut, in parallel to an increase in the composition of Lactobacillus and Bifidobacterium in the gut microbiota. This is the first study demonstrating sex differences in host defense mechanisms in the gut after brain injury.}, } @article {pmid37909786, year = {2023}, author = {Richie, TG and Heeren, L and Kamke, A and Monk, K and Pogranichniy, S and Summers, T and Wiechman, H and Ran, Q and Sarkar, S and Plattner, BL and Lee, STM}, title = {Limitation of amino acid availability by bacterial populations during enhanced colitis in IBD mouse model.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0070323}, pmid = {37909786}, issn = {2379-5077}, support = {P30 GM122731/GM/NIGMS NIH HHS/United States ; P20 GM103418/GM/NIGMS NIH HHS/United States ; U54 HD090216/HD/NICHD NIH HHS/United States ; S10 OD021743/OD/NIH HHS/United States ; UL1 TR002366/TR/NCATS NIH HHS/United States ; }, mesh = {Mice ; Animals ; Amino Acids ; *Gastrointestinal Microbiome ; *Colitis/microbiology ; Inflammation ; *Inflammatory Bowel Diseases/drug therapy ; Bacteria ; }, abstract = {Inflammatory bowel disease is associated with an increase in Enterobacteriaceae and Enterococcus species; however, the specific mechanisms are unclear. Previous research has reported the associations between microbiota and inflammation, here we investigate potential pathways that specific bacteria populations use to drive gut inflammation. Richie et al. show that these bacterial populations utilize an alternate sulfur metabolism and are tolerant of host-derived immune-response products. These metabolic pathways drive host gut inflammation and fuel over colonization of these pathobionts in the dysbiotic colon. Cultured isolates from dysbiotic mice indicated faster growth supplemented with L-cysteine, showing these microbes can utilize essential host nutrients.}, } @article {pmid37908118, year = {2023}, author = {Igo, M and Xu, L and Krishna, A and Stewart, S and Xu, L and Li, Z and Weaver, JL and Stone, H and Sacks, L and Bensman, T and Florian, J and Rouse, R and Han, X}, title = {A metagenomic analysis for combination therapy of multiple classes of antibiotics on the prevention of the spread of antibiotic-resistant genes.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2271150}, pmid = {37908118}, issn = {1949-0984}, mesh = {Animals ; Mice ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome ; Ampicillin/pharmacology ; *Microbiota ; Ciprofloxacin/pharmacology ; Bacteria/genetics ; Genes, Bacterial ; }, abstract = {Antibiotics used systemically to treat infections may have off-target effects on the gut microbiome, potentially resulting in the emergence of drug-resistant bacteria or selection of pathogenic species. These organisms may present a risk to the host and spread to the environment with a risk of transmission in the community. To investigate the risk of emergent antibiotic resistance in the gut microbiome following systemic treatment with antibiotics, this metagenomic analysis project used next-generation sequencing, a custom-built metagenomics pipeline, and differential abundance analysis to study the effect of antibiotics (ampicillin, ciprofloxacin, and fosfomycin) in monotherapy and different combinations at high and low doses, to determine the effect on resistome and taxonomic composition in the gut of Balb/c mice. The results showed that low-dose monotherapy treatments showed little change in microbiome composition but did show an increase in expression of many antibiotic-resistant genes (ARGs) posttreatment. Dual combination treatments allowed the emergence of some conditionally pathogenic bacteria and some increase in the abundance of ARGs despite a general decrease in microbiota diversity. Triple combination treatment was the most successful in inhibiting emergence of relevant opportunistic pathogens and completely suppressed all ARGs after 72 h of treatment. The relative abundances of mobile genetic elements that can enhance transmission of antibiotic resistance either decreased or remained the same for combination therapy while increasing for low-dose monotherapy. Combination therapy prevented the emergence of ARGs and decreased bacterial diversity, while low-dose monotherapy treatment increased ARGs and did not greatly change bacterial diversity.}, } @article {pmid37908022, year = {2023}, author = {Zadjelovic, V and Wright, RJ and Borsetto, C and Quartey, J and Cairns, TN and Langille, MGI and Wellington, EMH and Christie-Oleza, JA}, title = {Microbial hitchhikers harbouring antimicrobial-resistance genes in the riverine plastisphere.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {225}, pmid = {37908022}, issn = {2049-2618}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Lincosamides ; Genes, Bacterial/genetics ; *Microbiota/genetics ; Water ; }, abstract = {BACKGROUND: The widespread nature of plastic pollution has given rise to wide scientific and social concern regarding the capacity of these materials to serve as vectors for pathogenic bacteria and reservoirs for Antimicrobial Resistance Genes (ARG). In- and ex-situ incubations were used to characterise the riverine plastisphere taxonomically and functionally in order to determine whether antibiotics within the water influenced the ARG profiles in these microbiomes and how these compared to those on natural surfaces such as wood and their planktonic counterparts.

RESULTS: We show that plastics support a taxonomically distinct microbiome containing potential pathogens and ARGs. While the plastisphere was similar to those biofilms that grew on wood, they were distinct from the surrounding water microbiome. Hence, whilst potential opportunistic pathogens (i.e. Pseudomonas aeruginosa, Acinetobacter and Aeromonas) and ARG subtypes (i.e. those that confer resistance to macrolides/lincosamides, rifamycin, sulfonamides, disinfecting agents and glycopeptides) were predominant in all surface-related microbiomes, especially on weathered plastics, a completely different set of potential pathogens (i.e. Escherichia, Salmonella, Klebsiella and Streptococcus) and ARGs (i.e. aminoglycosides, tetracycline, aminocoumarin, fluoroquinolones, nitroimidazole, oxazolidinone and fosfomycin) dominated in the planktonic compartment. Our genome-centric analysis allowed the assembly of 215 Metagenome Assembled Genomes (MAGs), linking ARGs and other virulence-related genes to their host. Interestingly, a MAG belonging to Escherichia -that clearly predominated in water- harboured more ARGs and virulence factors than any other MAG, emphasising the potential virulent nature of these pathogenic-related groups. Finally, ex-situ incubations using environmentally-relevant concentrations of antibiotics increased the prevalence of their corresponding ARGs, but different riverine compartments -including plastispheres- were affected differently by each antibiotic.

CONCLUSIONS: Our results provide insights into the capacity of the riverine plastisphere to harbour a distinct set of potentially pathogenic bacteria and function as a reservoir of ARGs. The environmental impact that plastics pose if they act as a reservoir for either pathogenic bacteria or ARGs is aggravated by the persistence of plastics in the environment due to their recalcitrance and buoyancy. Nevertheless, the high similarities with microbiomes growing on natural co-occurring materials and even more worrisome microbiome observed in the surrounding water highlights the urgent need to integrate the analysis of all environmental compartments when assessing risks and exposure to pathogens and ARGs in anthropogenically-impacted ecosystems. Video Abstract.}, } @article {pmid37907561, year = {2023}, author = {Li, H and Ma, X and Li, Y and Liu, Q and Tian, Q and Yang, X and Zhou, Z and Ren, J and Sun, B and Feng, X and Zhang, H and Yin, X and Li, H and Ding, X}, title = {The metagenomic and metabolomic profile of the gut microbes in Chinese full-term and late preterm infants treated with Clostridium butyricum.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {18775}, pmid = {37907561}, issn = {2045-2322}, mesh = {Humans ; Infant, Newborn ; Infant ; Infant, Premature ; *Clostridium butyricum/genetics ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Biotin/pharmacology ; East Asian People ; *Probiotics ; }, abstract = {The present study investigated the composition, abundance, and diversity of gut microbes in full-term and late-preterm infants from a medical center in eastern China. A total of 144 genomes of stool samples were captured for 16S rRNA metagenomic analyses. A high abundance of commensal intestinal bacteria was detected in these samples such as Phocaeicola vulgatus, Escherichia coli, and Faecalibacterium prausnitzii, indicating a relatively consistent diversity of gut microbes in the present full-term infants aged 38-40 weeks. However, late preterm infants (n = 50) with mandatory antimicrobials feeding exhibited lower diversity but a higher composition of opportunistic pathogens such as Enterococcus species. Centralized on the situation, we explored the regulatory effect of Clostridium butyricum as probiotics on these late preterm infants. The consumption of C. butyricum did not restore the composition of gut microbes altered by antimicrobials to normal levels, although several opportunistic pathogens decreased significantly after probiotic therapy including Staphylococcus aureus, Sphingomonas echinoides, and Pseudomonas putida. We also compared the effects of day-fed versus night-fed probiotics. Intriguingly, the nighttime feeding showed a higher proportion of C. butyricum compared with probiotic day-feeding. Finally, fecal metabolome and metabolites were analyzed in late preterm infants with (n = 20) or without probiotic therapy (n = 20). The KEGG enrichment analysis demonstrated that vitamin digestion and absorption, synaptic vesicle cycle, and biotin metabolism were significantly increased in the probiotic-treated group, while MSEA indicated that a series of metabolism were significantly enriched in probiotic-treated infants including glycerolipid, biotin, and lysine, indicating the complex effects of probiotic therapy on glutathione metabolism and nutrients digestion and absorption in late preterm infants. Overall, this study provided metagenomic and metabolomic profile of the gut microbes in full-term newborns and late preterm infants in eastern China. Further studies are needed to support and elucidate the role of probiotic feeding in late preterm infants with mandatory antimicrobial treatment.}, } @article {pmid37907101, year = {2024}, author = {Mugnai, G and Borruso, L and Wu, YL and Gallinaro, M and Cappitelli, F and Zerboni, A and Villa, F}, title = {Ecological strategies of bacterial communities in prehistoric stone wall paintings across weathering gradients: A case study from the Borana zone in southern Ethiopia.}, journal = {The Science of the total environment}, volume = {907}, number = {}, pages = {168026}, doi = {10.1016/j.scitotenv.2023.168026}, pmid = {37907101}, issn = {1879-1026}, mesh = {RNA, Ribosomal, 16S/genetics ; Ethiopia ; *Bacteria/metabolism ; *Microbiota/genetics ; Biodiversity ; Phylogeny ; Soil Microbiology ; }, abstract = {Rock art paintings represent fragile ecosystems supporting complex microbial communities tuned to the lithic substrate and climatic conditions. The composition and activity of these microbial communities associated with different weathering patterns affecting rock art sites remain unexplored. This study aimed to explore how bacterial communities adapt their ecological strategies based on substrate weathering, while also examining the role of their metabolic pathways in either biodeterioration or bioprotection of the underlying stone. SEM-EDS investigations coupled with 16S rRNA gene sequencing and PICRUSt2 analysis were applied on different weathered surfaces that affect southern Ethiopian rock paintings to investigate the relationships between the current stone microbiome and weathering patterns. The findings revealed that samples experiencing low and high weathering reached a climax stage characterized by stable microenvironments and limited resources. This condition favored K-strategist microorganisms, leading to reduced α-biodiversity and a community with a positive or neutral impact on the substrate. In contrast, moderately-weathered samples displayed diverse microhabitats, resulting in the prevalence of r-strategist bacteria, increased α-biodiversity, and the presence of specialist microorganisms. Moreover, the bacterial communities in moderately-weathered samples demonstrated the highest potential for carbon fixation, stress responses, and complete nitrogen and sulfur cycles. This bacterial community also showed the potential to negatively impact the underlying substrate. This research provided valuable insights into the little-understood ecology of bacterial communities inhabiting deteriorated surfaces, shedding light on the potential role of these microorganisms in the sustainable conservation of rock art.}, } @article {pmid37906569, year = {2023}, author = {Deng, Y and Yang, X and Chen, J and Yang, S and Chi, H and Chen, C and Yang, X and Hou, C}, title = {Jute (Corchorus olitorius L.) Nanocrystalline Cellulose Inhibits Insect Virus via Gut Microbiota and Metabolism.}, journal = {ACS nano}, volume = {17}, number = {21}, pages = {21662-21677}, doi = {10.1021/acsnano.3c06824}, pmid = {37906569}, issn = {1936-086X}, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome ; Cellulose/pharmacology ; *Corchorus/genetics ; *Dicistroviridae ; Antiviral Agents/pharmacology ; }, abstract = {Natural plant nanocrystalline cellulose (NCC), exhibiting a number of exceptional performance characteristics, is widely used in food fields. However, little is known about the relationship between NCC and the antiviral effect in animals. Here, we tested the function of NCC in antiviral methods utilizing honey bees as the model organism employing Israeli acute paralysis virus (IAPV), a typical RNA virus of honey bees. In both the lab and the field, we fed the IAPV-infected bees various doses of jute NCC (JNCC) under carefully controlled conditions. We found that JNCC can reduce IAPV proliferation and improve gut health. The metagenome profiling suggested that IAPV infection significantly decreased the abundance of gut core bacteria, while JNCC therapy considerably increased the abundance of the gut core bacteria Snodgrassella alvi and Lactobacillus Firm-4. Subsequent metabolome analysis further revealed that JNCC promoted the biosynthesis of fatty acids and unsaturated fatty acids, accelerated the purine metabolism, and then increased the expression of antimicrobial peptides (AMPs) and the genes involved in the Wnt and apoptosis signaling pathways against IAPV infection. Our results highlighted that JNCC could be considered as a prospective candidate agent against a viral infection.}, } @article {pmid37905808, year = {2023}, author = {Ma, C and Zhang, Y and Jiang, S and Teng, F and Huang, S and Zhang, J}, title = {Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0082823}, pmid = {37905808}, issn = {2379-5077}, support = {32160545//National Natural Science Foundation of China/ ; 22-3-7-lczx-7-nsh//Qingdao University (QDU)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Metagenome/genetics ; Metagenomics ; Nucleotides ; }, abstract = {Most studies focused much on the change in abundance and often failed to explain the microbiome variation related to disease conditions, Herein, we argue that microbial genetic changes can precede the ecological changes associated with the host physiological changes and, thus, would offer a new information layer from metagenomic data for predictive modeling of diseases. Interestingly, we preliminarily found a few genetic biomarkers on SCFA production can cover most chronic diseases involved in the meta-analysis. In the future, it is of both scientific and clinical significance to further explore the dynamic interactions between adaptive evolution and ecology of gut microbiota associated with host health status.}, } @article {pmid37902391, year = {2023}, author = {Liu, L and Chen, Y and Shen, J and Pan, Y and Lin, W}, title = {Metabolic versatility of soil microbial communities below the rocks of the hyperarid Dalangtan Playa.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {11}, pages = {e0107223}, pmid = {37902391}, issn = {1098-5336}, support = {T2225011//National Natural Science Foundation of China (NSFC)/ ; ZDBS-SSW-TLC001//Key Research Program of the Chinese Academy of Sciences/ ; IGGCAS-201904, IGGCAS-202102//Key Research Programs of the Institute of Geology and Geophysics, Chinese Academy of Sciences/ ; }, mesh = {*Soil ; China ; Soil Microbiology ; *Microbiota ; Desert Climate ; }, abstract = {The hyperarid Dalangtan Playa in the western Qaidam Basin, northwestern China, is a unique terrestrial analog of Mars. Despite the polyextreme environments of this area, habitats below translucent rocks capable of environmental buffering could serve as refuges for microbial life. In this study, the hybrid assembly of Illumina short reads and Nanopore long reads recovered high-quality and high-continuity genomes, allowing for high-accuracy analysis and a deeper understanding of extremophiles in the sheltered soils of the Dalangtan Playa. Our findings reveal self-supporting and metabolically versatile sheltered soil communities adapted to a hyperarid and hypersaline playa, which provides implications for the search for life signals on Mars.}, } @article {pmid37900322, year = {2023}, author = {Zhan, D and Li, D and Yuan, K and Sun, Y and He, L and Zhong, J and Wang, L}, title = {Characteristics of the pulmonary microbiota in patients with mild and severe pulmonary infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1227581}, pmid = {37900322}, issn = {2235-2988}, mesh = {Humans ; *Pneumonia ; *Microbiota/genetics ; Bronchoalveolar Lavage Fluid ; Metagenome ; *Micrococcaceae ; *Acinetobacter ; *Bacillus ; *Coinfection ; *Fabaceae ; High-Throughput Nucleotide Sequencing ; Klebsiella ; Lung ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Lung infection is a global health problem associated with high morbidity and mortality and increasing rates of hospitalization. The correlation between pulmonary microecology and infection severity remains unclear. Therefore, the purpose of this study was to investigate the differences in lung microecology and potential biomarkers in patients with mild and severe pulmonary infection.

METHOD: Patients with pulmonary infection or suspected infection were divided into the mild group (140 cases) and the severe group (80 cases) according to pneomonia severity index (PSI) scores. Here, we used metagenomic next-generation sequencing (mNGS) to detect DNA mainly from bronchoalveolar lavage fluid (BALF) collected from patients to analyze changes in the lung microbiome of patients with different disease severity.

RESULT: We used the mNGS to analyze the pulmonary microecological composition in patients with pulmonary infection. The results of alpha diversity and beta diversity analysis showed that the microbial composition between mild and severe groups was similar on the whole. The dominant bacteria were Acinetobacter, Bacillus, Mycobacterium, Staphylococcus, and Prevotella, among others. Linear discriminant analysis effect size (LEfSe) results showed that there were significant differences in virus composition between the mild and severe patients, especially Simplexvirus and Cytomegalovirus, which were prominent in the severe group. The random forest model screened 14 kinds of pulmonary infection-related pathogens including Corynebacterium, Mycobacterium, Streptococcus, Klebsiella, and Acinetobacter. In addition, it was found that Rothia was negatively correlated with Acinetobacter, Mycobacterium, Bacillus, Enterococcus, and Klebsiella in the mild group through co-occurrence network, while no significant correlation was found in the severe group.

CONCLUSION: Here, we describe the composition and diversity of the pulmonary microbiome in patients with pulmonary infection. A significant increase in viral replication was found in the severe group, as well as a significant difference in microbial interactions between patients with mild and severe lung infections, particularly the association between the common pathogenic bacteria and Rothia. This suggests that both pathogen co-viral infection and microbial interactions may influence the course of disease. Of course, more research is needed to further explore the specific mechanisms by which microbial interactions influence disease severity.}, } @article {pmid37900308, year = {2023}, author = {Ye, X and Yu, F and Zhou, J and Zhao, C and Wu, J and Ni, X}, title = {Analysis of the gut microbiota in children with gastroesophageal reflux disease using metagenomics and metabolomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1267192}, pmid = {37900308}, issn = {2235-2988}, mesh = {Humans ; Child ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Metabolomics/methods ; Bacteria/genetics ; Metagenomics ; *Gastroesophageal Reflux ; }, abstract = {BACKGROUND: There is no direct evidence of gut microbiota disturbance in children with gastroesophageal reflux disease (GERD). This study aimed to provide direct evidence and a comprehensive understanding of gut microbiota disturbance in children with GERD through combined metagenomic and metabolomic analysis.

METHODS: 30 children with GERD and 30 healthy controls (HCs) were continuously enrolled, and the demographic and clinical characteristics of the subjects were collected. First, 16S rRNA sequencing was used to evaluate differences in the gut microbiota between children with GERD and HC group, and 10 children with GERD and 10 children in the HC group were selected for metagenomic analysis. Nontargeted metabolomic analysis was performed using liquid chromatography/mass spectrometry (LC/MS), and metagenomic and metabolomic data were analyzed together.

RESULTS: There were significant differences in the gut microbiota diversity and composition between children with GERD and HCs. The dominant bacteria in children with GERD were Proteobacteria and Bacteroidota. At the species level, the top three core bacterial groups were Bacteroides stercoris, Bacteroides vulgatus and Alistipes putredinis. The main differential pathways were identified to be related to energy, amino acid, vitamin, carbohydrate and lipid metabolism. LC/MS detected 288 different metabolites in the positive and negative ion modes between children with GERD and HCs, which were mainly involved in arachidonic acid (AA), tyrosine, glutathione and caffeine metabolism.

CONCLUSION: This study provides new evidence of the pathogenesis of GERD. There are significant differences in the gut microbiota, metabolites and metabolic pathways between HCs and children with GERD, and the differences in metabolites are related to specific changes in bacterial abundance. In the future, GERD may be treated by targeting specific bacteria related to AA metabolism.}, } @article {pmid37898635, year = {2023}, author = {de Oliveira Vieira, KC and da Silva, ABB and Felício, SA and Lira, FS and de Figueiredo, C and Bezirtzoglou, E and Pereira, VC and Nakagaki, WR and Nai, GA and Winkelströter, LK}, title = {Orange juice containing Pediococcus acidilactici CE51 modulates the intestinal microbiota and reduces induced inflammation in a murine model of colitis.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {18513}, pmid = {37898635}, issn = {2045-2322}, mesh = {Male ; Mice ; Animals ; *Gastrointestinal Microbiome ; *Pediococcus acidilactici/metabolism ; *Citrus sinensis/metabolism ; Tumor Necrosis Factor-alpha/metabolism ; C-Reactive Protein/metabolism ; Disease Models, Animal ; *Colitis/chemically induced/drug therapy ; Inflammation/pathology ; Dextran Sulfate/toxicity ; *Probiotics/pharmacology/therapeutic use ; Mice, Inbred C57BL ; Colon/pathology ; }, abstract = {The management of inflammatory bowel diseases has been widely investigated, especially ulcerative colitis. Thus, studies with the application of new probiotic products are needed in the prevention/treatment of these clinical conditions. The objective of this work was to evaluate the effects of probiotic orange juice containing Pediococcus acidilactici CE51 in a murine model of colitis. 45 male Swiss lineage mice were used, divided into five groups (n = 9): control, colitis, colitis + probiotic (probiotic orange juice containing CE51), colitis + placebo (orange juice) and colitis + sulfasalazine (10 mg/kg/Weight). The induction of colitis was performed with dextran sodium sulfate (3%). The treatment time was 5 and 15 days after induction. Histopathological analysis, serum measurements of TNF-α and C-reactive protein and metagenomic analysis of feces were performed after euthanasia. Probiotic treatment reduced inflammation in the small intestine, large intestine and spleen. The probiotic did not alter the serum dosages of TNF-α and C-reactive protein. Their use maintained the quantitative ratio of the phylum Firmicutes/Bacteroidetes and increased Lactobacillus helveticus with 15 days of treatment (p < 0.05). The probiotic orange juice containing P. acidilactici CE51 positively modulated the gut microbiota composition and attenuated the inflammation induced in colitis.}, } @article {pmid37898601, year = {2023}, author = {Tisza, M and Javornik Cregeen, S and Avadhanula, V and Zhang, P and Ayvaz, T and Feliz, K and Hoffman, KL and Clark, JR and Terwilliger, A and Ross, MC and Cormier, J and Moreno, H and Wang, L and Payne, K and Henke, D and Troisi, C and Wu, F and Rios, J and Deegan, J and Hansen, B and Balliew, J and Gitter, A and Zhang, K and Li, R and Bauer, CX and Mena, KD and Piedra, PA and Petrosino, JF and Boerwinkle, E and Maresso, AW}, title = {Wastewater sequencing reveals community and variant dynamics of the collective human virome.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {6878}, pmid = {37898601}, issn = {2041-1723}, support = {T42 OH008421/OH/NIOSH CDC HHS/United States ; U19 AI144297/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Virome/genetics ; Wastewater ; Cities ; Disease Outbreaks ; *Poliovirus ; SARS-CoV-2/genetics ; }, abstract = {Wastewater is a discarded human by-product, but its analysis may help us understand the health of populations. Epidemiologists first analyzed wastewater to track outbreaks of poliovirus decades ago, but so-called wastewater-based epidemiology was reinvigorated to monitor SARS-CoV-2 levels while bypassing the difficulties and pit falls of individual testing. Current approaches overlook the activity of most human viruses and preclude a deeper understanding of human virome community dynamics. Here, we conduct a comprehensive sequencing-based analysis of 363 longitudinal wastewater samples from ten distinct sites in two major cities. Critical to detection is the use of a viral probe capture set targeting thousands of viral species or variants. Over 450 distinct pathogenic viruses from 28 viral families are observed, most of which have never been detected in such samples. Sequencing reads of established pathogens and emerging viruses correlate to clinical data sets of SARS-CoV-2, influenza virus, and monkeypox viruses, outlining the public health utility of this approach. Viral communities are tightly organized by space and time. Finally, the most abundant human viruses yield sequence variant information consistent with regional spread and evolution. We reveal the viral landscape of human wastewater and its potential to improve our understanding of outbreaks, transmission, and its effects on overall population health.}, } @article {pmid37897361, year = {2024}, author = {Hu, R and Li, F and Chen, Y and Liu, C and Li, J and Ma, Z and Wang, Y and Cui, C and Luo, C and Zhou, P and Ni, W and Yang, QY and Hu, S}, title = {AnimalMetaOmics: a multi-omics data resources for exploring animal microbial genomes and microbiomes.}, journal = {Nucleic acids research}, volume = {52}, number = {D1}, pages = {D690-D700}, pmid = {37897361}, issn = {1362-4962}, support = {2021ZD01//Foundation of state key laboratory of sheep genetic improvement and healthy production/ ; //Tianshan Talent Project/ ; 2022xjkk1202//The Tird Xinjiang Scientifc Expedition Program/ ; }, mesh = {Animals ; Bacteria/genetics ; Genome, Microbial ; Metagenome/genetics ; *Microbiota/genetics ; *Multiomics ; *Databases, Genetic ; }, abstract = {The Animal Meta-omics landscape database (AnimalMetaOmics, https://yanglab.hzau.edu.cn/animalmetaomics#/) is a comprehensive and freely available resource that includes metagenomic, metatranscriptomic, and metaproteomic data from various non-human animal species and provides abundant information on animal microbiomes, including cluster analysis of microbial cognate genes, functional gene annotations, active microbiota composition, gene expression abundance, and microbial protein identification. In this work, 55 898 microbial genomes were annotated from 581 animal species, including 42 924 bacterial genomes, 12 336 virus genomes, 496 archaea genomes and 142 fungi genomes. Moreover, 321 metatranscriptomic datasets were analyzed from 31 animal species and 326 metaproteomic datasets from four animal species, as well as the pan-genomic dynamics and compositional characteristics of 679 bacterial species and 13 archaea species from animal hosts. Researchers can efficiently access and acquire the information of cross-host microbiota through a user-friendly interface, such as species, genomes, activity levels, expressed protein sequences and functions, and pan-genome composition. These valuable resources provide an important reference for better exploring the classification, functional diversity, biological process diversity and functional genes of animal microbiota.}, } @article {pmid37897342, year = {2024}, author = {Schmidt, TSB and Fullam, A and Ferretti, P and Orakov, A and Maistrenko, OM and Ruscheweyh, HJ and Letunic, I and Duan, Y and Van Rossum, T and Sunagawa, S and Mende, DR and Finn, RD and Kuhn, M and Pedro Coelho, L and Bork, P}, title = {SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.}, journal = {Nucleic acids research}, volume = {52}, number = {D1}, pages = {D777-D783}, pmid = {37897342}, issn = {1362-4962}, support = {NFDI4Microbiota//European Molecular Biology Laboratory/ ; NFDI4Microbiota//German Research Foundation/ ; LAMarCK//German Federal Ministry of Education and Research/ ; 22JC1410900//The Science and Technology Commission of Shanghai Municipality/ ; 51NF40_180575//NCCR Microbiomes/ ; }, mesh = {*Databases, Factual ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; }, abstract = {Meta'omic data on microbial diversity and function accrue exponentially in public repositories, but derived information is often siloed according to data type, study or sampled microbial environment. Here we present SPIRE, a Searchable Planetary-scale mIcrobiome REsource that integrates various consistently processed metagenome-derived microbial data modalities across habitats, geography and phylogeny. SPIRE encompasses 99 146 metagenomic samples from 739 studies covering a wide array of microbial environments and augmented with manually-curated contextual data. Across a total metagenomic assembly of 16 Tbp, SPIRE comprises 35 billion predicted protein sequences and 1.16 million newly constructed metagenome-assembled genomes (MAGs) of medium or high quality. Beyond mapping to the high-quality genome reference provided by proGenomes3 (http://progenomes.embl.de), these novel MAGs form 92 134 novel species-level clusters, the majority of which are unclassified at species level using current tools. SPIRE enables taxonomic profiling of these species clusters via an updated, custom mOTUs database (https://motu-tool.org/) and includes several layers of functional annotation, as well as crosslinks to several (micro-)biological databases. The resource is accessible, searchable and browsable via http://spire.embl.de.}, } @article {pmid37896809, year = {2023}, author = {Hufsky, F and Abecasis, AB and Babaian, A and Beck, S and Brierley, L and Dellicour, S and Eggeling, C and Elena, SF and Gieraths, U and Ha, AD and Harvey, W and Jones, TC and Lamkiewicz, K and Lovate, GL and Lücking, D and Machyna, M and Nishimura, L and Nocke, MK and Renard, BY and Sakaguchi, S and Sakellaridi, L and Spangenberg, J and Tarradas-Alemany, M and Triebel, S and Vakulenko, Y and Wijesekara, RY and González-Candelas, F and Krautwurst, S and Pérez-Cataluña, A and Randazzo, W and Sánchez, G and Marz, M}, title = {The International Virus Bioinformatics Meeting 2023.}, journal = {Viruses}, volume = {15}, number = {10}, pages = {}, pmid = {37896809}, issn = {1999-4915}, support = {MC_UU_00008/9/MRC_/Medical Research Council/United Kingdom ; MC_UU_12010/9/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; Computational Biology ; *Viruses/genetics ; *RNA Viruses ; *Virus Diseases ; *Bacteriophages ; }, abstract = {The 2023 International Virus Bioinformatics Meeting was held in Valencia, Spain, from 24-26 May 2023, attracting approximately 180 participants worldwide. The primary objective of the conference was to establish a dynamic scientific environment conducive to discussion, collaboration, and the generation of novel research ideas. As the first in-person event following the SARS-CoV-2 pandemic, the meeting facilitated highly interactive exchanges among attendees. It served as a pivotal gathering for gaining insights into the current status of virus bioinformatics research and engaging with leading researchers and emerging scientists. The event comprised eight invited talks, 19 contributed talks, and 74 poster presentations across eleven sessions spanning three days. Topics covered included machine learning, bacteriophages, virus discovery, virus classification, virus visualization, viral infection, viromics, molecular epidemiology, phylodynamic analysis, RNA viruses, viral sequence analysis, viral surveillance, and metagenomics. This report provides rewritten abstracts of the presentations, a summary of the key research findings, and highlights shared during the meeting.}, } @article {pmid37895005, year = {2023}, author = {Seton, KA and Defernez, M and Telatin, A and Tiwari, SK and Savva, GM and Hayhoe, A and Noble, A and de Carvalho-KoK, ALS and James, SA and Bansal, A and Wileman, T and Carding, SR}, title = {Investigating Antibody Reactivity to the Intestinal Microbiome in Severe Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS): A Feasibility Study.}, journal = {International journal of molecular sciences}, volume = {24}, number = {20}, pages = {}, pmid = {37895005}, issn = {1422-0067}, support = {BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG1860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *Fatigue Syndrome, Chronic ; *Gastrointestinal Microbiome ; Feasibility Studies ; Bacteria ; Immunoglobulin G ; }, abstract = {Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a multisystemic disease of unknown aetiology that is characterised by disabling chronic fatigue and involves both the immune and gastrointestinal (GI) systems. Patients display alterations in GI microbiome with a significant proportion experiencing GI discomfort and pain and elevated blood biomarkers for altered intestinal permeability compared with healthy individuals. To investigate a possible GI origin of ME/CFS we designed a feasibility study to test the hypothesis that ME/CFS pathogenesis is a consequence of increased intestinal permeability that results in microbial translocation and a breakdown in immune tolerance leading to generation of antibodies reactive to indigenous intestinal microbes. Secretory immunoglobulin (Ig) A and serum IgG levels and reactivity to intestinal microbes were assessed in five pairs of severe ME/CFS patients and matched same-household healthy controls. For profiling serum IgG, we developed IgG-Seq which combines flow-cytometry based bacterial cell sorting and metagenomics to detect mucosal IgG reactivity to the microbiome. We uncovered evidence for immune dysfunction in severe ME/CFS patients that was characterised by reduced capacity and reactivity of serum IgG to stool microbes, irrespective of their source. This study provides the rationale for additional studies in larger cohorts of ME/CFS patients to further explore immune-microbiome interactions.}, } @article {pmid37894982, year = {2023}, author = {Babkin, I and Tikunov, A and Morozova, V and Matveev, A and Morozov, VV and Tikunova, N}, title = {Genomes of a Novel Group of Phages That Use Alternative Genetic Code Found in Human Gut Viromes.}, journal = {International journal of molecular sciences}, volume = {24}, number = {20}, pages = {}, pmid = {37894982}, issn = {1422-0067}, support = {21-14-00360//Russian Science Foundation/ ; 121031300043-8//Ministry of Education and Science/ ; }, mesh = {Humans ; *Bacteriophages/genetics ; Virome ; Codon, Terminator/genetics ; Genome, Viral ; Genetic Code ; RNA, Transfer/genetics ; Phylogeny ; }, abstract = {Metagenomics provides detection of phage genome sequences in various microbial communities. However, the use of alternative genetic codes by some phages precludes the correct analysis of their genomes. In this study, the unusual phage genome (phAss-1, 135,976 bp) was found after the de novo assembly of the human gut virome. Genome analysis revealed the presence of the TAG stop codons in 41 ORFs, including characteristic phage ORFs, and three genes of suppressor tRNA. Comparative analysis indicated that no phages with similar genomes were described. However, two phage genomes (BK046881_ctckW2 and BK025033_ct6IQ4) with substantial similarity to phAss-1 were extracted from the human gut metagenome data. These two complete genomes demonstrated 82.7% and 86.4% of nucleotide identity, respectively, similar genome synteny to phAss-1, the presence of suppressor tRNA genes and suppressor TAG stop codons in many characteristic phage ORFs. These data indicated that phAss-1, BK046881_ctckW2, and BK025033_ct6IQ4 are distinct species within the proposed Phassvirus genus. Moreover, a monophyletic group of divergent phage genomes containing the proposed Phassvirus genus was found among metagenome data. Several phage genomes from the group also contain ORFs with suppressor TAG stop codons, indicating the need to use various translation tables when depositing phage genomes in GenBank.}, } @article {pmid37894951, year = {2023}, author = {Korobeinikova, AV and Zlobovskaya, OA and Sheptulina, AF and Ashniev, GA and Bobrova, MM and Yafarova, AA and Akasheva, DU and Kabieva, SS and Bakoev, SY and Zagaynova, AV and Lukashina, MV and Abramov, IA and Pokrovskaya, MS and Doludin, YV and Tolkacheva, LR and Kurnosov, AS and Zyatenkova, EV and Lavrenova, EA and Efimova, IA and Glazunova, EV and Kiselev, AR and Shipulin, GA and Kontsevaya, AV and Keskinov, AA and Yudin, VS and Makarov, VV and Drapkina, OM and Yudin, SM}, title = {Gut Microbiota Patterns in Patients with Non-Alcoholic Fatty Liver Disease: A Comprehensive Assessment Using Three Analysis Methods.}, journal = {International journal of molecular sciences}, volume = {24}, number = {20}, pages = {}, pmid = {37894951}, issn = {1422-0067}, support = {Contract n. 388-00154-22-00//Federal Medical Biological Agency/ ; }, mesh = {Adult ; Humans ; *Non-alcoholic Fatty Liver Disease/pathology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Fibrosis ; *Microbiota ; Bacteroidetes ; Liver/pathology ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD) is considered the most common chronic liver disease worldwide, affecting nearly 25% of the global adult population. Increasing evidence suggests that functional and compositional changes in the gut microbiota may contribute to the development and promote the progression of NAFLD. 16S rRNA gene next-generation sequencing is widely used to determine specific features of the NAFLD microbiome, but a complex system such as the gut microbiota requires a comprehensive approach. We used three different approaches: MALDI-TOF-MS of bacterial cultures, qPCR, and 16S NGS sequencing, as well as a wide variety of statistical methods to assess the differences in gut microbiota composition between NAFLD patients without significant fibrosis and the control group. The listed methods showed enrichment in Collinsella sp. and Oscillospiraceae for the control samples and enrichment in Lachnospiraceae (and in particular Dorea sp.) and Veillonellaceae in NAFLD. The families, Bifidobacteriaceae, Lactobacillaceae, and Enterococcaceae (particularly Enterococcus faecium and Enterococcus faecalis), were also found to be important taxa for NAFLD microbiome evaluation. Considering individual method observations, an increase in Candida krusei and a decrease in Bacteroides uniformis for NAFLD patients were detected using MALDI-TOF-MS. An increase in Gracilibacteraceae, Chitinophagaceae, Pirellulaceae, Erysipelatoclostridiaceae, Muribaculaceae, and Comamonadaceae, and a decrease in Acidaminococcaceae in NAFLD were observed with 16S NGS, and enrichment in Fusobacterium nucleatum was shown using qPCR analysis. These findings confirm that NAFLD is associated with changes in gut microbiota composition. Further investigations are required to determine the cause-and-effect relationships and the impact of microbiota-derived compounds on the development and progression of NAFLD.}, } @article {pmid37894156, year = {2023}, author = {Gu, S and Zhang, P and Luo, S and Chen, K and Jiang, C and Xiong, J and Miao, W}, title = {Microbial Community Colonization Process Unveiled through eDNA-PFU Technology in Mesocosm Ecosystems.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, pmid = {37894156}, issn = {2076-2607}, support = {2022FY100400//the Science & Technology Fundamental Resources Investigation Program/ ; 2021xjkk0604//the Third Xinjiang Scientific Expedition Program/ ; U22A20454//the National Natural Science Foundation of China/ ; }, abstract = {Microbial communities are essential components of aquatic ecosystems and are widely employed for the detection, protection, and restoration of water ecosystems. The polyurethane foam unit (PFU) method, an effective and widely used environmental monitoring technique, has been improved with the eDNA-PFU method, offering efficiency, rapidity, and standardization advantages. This research aimed to explore the colonization process of microbial communities within PFUs using eDNA-PFU technology. To achieve this, we conducted ten-day monitoring and sequencing of microbial communities within PFUs in a stable and controlled artificial aquatic ecosystem, comparing them with water environmental samples (eDNA samples). Results showed 1065 genera in eDNA-PFU and 1059 in eDNA, with eDNA-PFU detecting 99.95% of eDNA-identified species. Additionally, the diversity indices of bacteria and eukaryotes in both methods showed similar trends over time in the colonization process; however, relative abundance differed. We further analyzed the colonization dynamics of microbes in eDNA-PFU and identified four clusters with varying colonization speeds. Notably, we found differences in colonization rates between bacteria and eukaryotes. Furthermore, the Molecular Ecological Networks (MEN) showed that the network in eDNA-PFU was more modular, forming a unique microbial community differentiated from the aquatic environment. In conclusion, this study, using eDNA-PFU, comprehensively explored microbial colonization and interrelationships in a controlled mesocosm system, providing foundational data and reference standards for its application in aquatic ecosystem monitoring and beyond.}, } @article {pmid37892391, year = {2023}, author = {Xiang, X and Chen, J and Zhu, M and Gao, H and Liu, X and Wang, Q}, title = {Multiomics Revealed the Multi-Dimensional Effects of Late Sleep on Gut Microbiota and Metabolites in Children in Northwest China.}, journal = {Nutrients}, volume = {15}, number = {20}, pages = {}, pmid = {37892391}, issn = {2072-6643}, mesh = {Adult ; Animals ; Humans ; Child ; *Gastrointestinal Microbiome ; Multiomics ; Amino Acids ; Sleep ; China ; Amines ; Bile Acids and Salts ; }, abstract = {Background Sleep plays a pivotal role in children's mental and physical development and has been linked to the gut microbiota in animals and adults. However, the characteristics of the gut microbiota and metabolites and the relationship to late bedtimes in children remain unclear. Methods In total, 88 eligible children, aged from 3 to 8 years, were recruited and divided into two groups according to the bedtime collected by designed questionnaires (early, before 22:00: n = 48; late, after 22:00, n = 40). Stools and plasma samples were collected to examine the characteristics of the gut microbiota and metabolites by shotgun metagenomics and metabolomics. Results The richness and diversity of the gut microbiota in children with early bedtime were significantly increased compared with the late ones. Coprococcus, Collinsella, Akkermansia muciniphila, and Bifidobacterium adolescentis were significantly more abundant in children with early bedtime, while Bacteroides and Clostridium sp. CAG-253 were obviously enriched in the late ones. A total of 106 metabolic pathways, including biosynthesis of ribonucleotide, peptidoglycan, and amino acids, and starch degradation were enriched in children with early bedtime, while 42 pathways were abundant in those with late bedtime. Notably, more gut microbial metabolites were observed in children with late bedtime, which included aldehyde, ketones, esters, amino acids and their metabolites, benzene and substituted derivatives, bile acids, heterocyclic compounds, nucleotide and metabolites, organic acid and derivatives, sugars and acyl carnitine. In plasma, fatty amides, lipids, amino acids, metabolites, hormones, and related compounds were enriched in children with early bedtime, while bile acids were higher in children with late bedtime. Association studies revealed that the different microbial species were correlated with metabolites from gut microbiota and plasma. Conclusions The results of our study revealed that the gut microbiota diversity and richness, and metabolic pathways were significantly extensive in children with early bedtime, whereas the gut microbial metabolites were significantly decreased, which might be related to gut microbial differences.}, } @article {pmid37892187, year = {2023}, author = {Meslier, V and Menozzi, E and David, A and Morabito, C and Lucas Del Pozo, S and Famechon, A and North, J and Quinquis, B and Koletsi, S and Macnaughtan, J and Mezabrovschi, R and Ehrlich, SD and Schapira, AHV and Almeida, M}, title = {Evaluation of an Adapted Semi-Automated DNA Extraction for Human Salivary Shotgun Metagenomics.}, journal = {Biomolecules}, volume = {13}, number = {10}, pages = {}, pmid = {37892187}, issn = {2218-273X}, mesh = {Humans ; Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; *DNA/genetics/chemistry ; *Microbiota/genetics ; Metagenome ; }, abstract = {Recent attention has highlighted the importance of oral microbiota in human health and disease, e.g., in Parkinson's disease, notably using shotgun metagenomics. One key aspect for efficient shotgun metagenomic analysis relies on optimal microbial sampling and DNA extraction, generally implementing commercial solutions developed to improve sample collection and preservation, and provide high DNA quality and quantity for downstream analysis. As metagenomic studies are today performed on a large number of samples, the next evolution to increase study throughput is with DNA extraction automation. In this study, we proposed a semi-automated DNA extraction protocol for human salivary samples collected with a commercial kit, and compared the outcomes with the DNA extraction recommended by the manufacturer. While similar DNA yields were observed between the protocols, our semi-automated DNA protocol generated significantly higher DNA fragment sizes. Moreover, we showed that the oral microbiome composition was equivalent between DNA extraction methods, even at the species level. This study demonstrates that our semi-automated protocol is suitable for shotgun metagenomic analysis, while allowing for improved sample treatment logistics with reduced technical variability and without compromising the structure of the oral microbiome.}, } @article {pmid37892148, year = {2023}, author = {Janusz, G and Mazur, A and Pawlik, A and Kołodyńska, D and Jaroszewicz, B and Marzec-Grządziel, A and Koper, P}, title = {Metagenomic Analysis of the Composition of Microbial Consortia Involved in Spruce Degradation over Time in Białowieża Natural Forest.}, journal = {Biomolecules}, volume = {13}, number = {10}, pages = {}, pmid = {37892148}, issn = {2218-273X}, mesh = {*Microbial Consortia/genetics ; Forests ; Wood/microbiology ; *Microbiota/genetics ; Soil ; Fungi/genetics ; }, abstract = {Deadwood plays an important role in forest ecology; its degradation and, therefore, carbon assimilation is carried out by fungi and bacteria. To quantify the abundance and distribution of microbial taxa inhabiting dead spruce logs fallen over a span of 50 years and the soil beneath, we used taxonomic profiling with NGS sequencing of hypervariable DNA fragments of ITS1 and 16S V3-V4, respectively. The analysis of sequencing data revealed a high level of diversity in microbial communities participating in the degradation of spruce logs. Differences in the relative abundance of microbial taxa between the samples of the wood that died in 1974 and 2014, and of the soil in its immediate vicinity, were visible, especially at the genus level. Based on the Lefse analysis significantly higher numbers of classified bacterial taxa were observed in the wood and soil samples from 2014 (wood: 1974-18 and 2014-28 taxa; soil: 1974-8 and 2014-41 taxa) while the number of classified fungal taxa was significantly higher in the wood and soil samples from 1974 (wood: 1974-17 and 2014-9 taxa; soil: 1974-57 and 2014-28 taxa). Most of the bacterial and fungal amplicon sequence variants (ASVs) unique to wood were found in the samples from 1974, while those unique to soil were detected in the samples from 2014. The ATR-FTIR method supported by CHN analysis revealed physicochemical changes in deadwood induced by the activity of fungal and bacterial organisms.}, } @article {pmid37891627, year = {2023}, author = {Coclet, C and Sorensen, PO and Karaoz, U and Wang, S and Brodie, EL and Eloe-Fadrosh, EA and Roux, S}, title = {Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {237}, pmid = {37891627}, issn = {2049-2618}, mesh = {Humans ; Ecosystem ; Soil ; Altitude ; *Viruses/genetics ; *Bacteriophages/genetics ; Soil Microbiology ; *Microbiota/genetics ; DNA ; }, abstract = {BACKGROUND: Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics' seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes.

RESULTS: We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages (Leviviricetes), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a "seed-bank" viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: "Kill-The-Winner" which proposes that lytic phages are actively infecting abundant bacteria, and "Piggyback-The-Persistent" which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth.

CONCLUSION: Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry. Video Abstract.}, } @article {pmid37891621, year = {2023}, author = {Erculiani, M and Poluzzi, F and Mottadelli, G and Felici, E and Ml, N and Caraccia, M and Grandi, A and Casella, S and Giacometti, L and Montobbio, G and Ceccherini, I and Di Marco, E and Bonaretti, C and Biassoni, R and Squillario, M and Pietrantoni, A and Villanacci, V and Pini Prato, A}, title = {A unicentric cross-sectional observational study on chronic intestinal inflammation in total colonic aganglionosis: beware of an underestimated condition.}, journal = {Orphanet journal of rare diseases}, volume = {18}, number = {1}, pages = {339}, pmid = {37891621}, issn = {1750-1172}, support = {Ricerca Corrente//Ministero della Salute/ ; 2019.0880 - ID ROL 32612//Compagnia di San Paolo/ ; }, mesh = {Humans ; *Hirschsprung Disease/genetics/pathology ; Cross-Sectional Studies ; *Inflammatory Bowel Diseases/complications/pathology ; Inflammation ; }, abstract = {BACKGROUND: Inflammatory Bowel Diseases (IBD) are known to occur in association with Hirschsprung disease (HSCR). Most of cases are represented by Crohn Disease (CD) occurring in patients with Total Colonic Aganglionosis (TCSA) with an estimated prevalence of around 2%. Based on these considerations and on a number of provisional data belonging to our Center for Digestive Diseases, we developed a unicentric cross-sectional observational study aimed at describing phenotype, genotype, pathology and metagenomics of all patients with TCSA and Crohn-like lesions.

RESULTS: Out of a series of 62 eligible TCSA patients, 48 fulfilled inclusion criteria and were enrolled in the study. Ten patients did not complete the study due to non-compliance or withdrawal of consent and were subsequently dropped out. A total of 38 patients completed the study. All patients were tested for chronic intestinal inflammation by a combination of fecal calprotectine (FC) or occult fecal blood (OFB) and underwent fecal metagenomics. Nineteen (50%) tested positive for FC, OFB, or both and subsequently underwent retrograde ileoscopy. Fourteen patients (36.8%) presented Crohn-like lesions, occurring after a median of 11.5 years after surgery (range 8 months - 21.5 years). No statistically significant differences regarding demographic, phenotype and genotype were observed comparing patients with and without lesions, except for need for blood transfusion that was more frequent in those with lesions. Faecal microbiome of patients with lesions (not that of caregivers) was less biodiverse and characterized by a reduction of Bacteroidetes, and an overabundance of Proteobacteria. FC tested negative in 3/14 patients with lesions (21%).

CONCLUSIONS: Our study demonstrated an impressive 10-folds higher incidence of chronic inflammation in TCSA. Up to 50% of patients may develop IBD-like lesions postoperatively. Nonetheless, we failed in identifying specific risk factors to be used to implement prevention strategies. Based on the results of our study, we suggest screening all TCSA patients with retrograde ileoscopy regardless of FC/OFB values. The frequency of endoscopic assessments and the role of FC/OFB screening in prompting endoscopy is yet to be determined.}, } @article {pmid37891427, year = {2023}, author = {Starke, S and Harris, DMM and Zimmermann, J and Schuchardt, S and Oumari, M and Frank, D and Bang, C and Rosenstiel, P and Schreiber, S and Frey, N and Franke, A and Aden, K and Waschina, S}, title = {Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability.}, journal = {The ISME journal}, volume = {17}, number = {12}, pages = {2370-2380}, pmid = {37891427}, issn = {1751-7370}, support = {EXC2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; RU5042//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 1289/17-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Humans ; *Amino Acids/metabolism ; Bacteria/genetics/metabolism ; Metabolomics ; Metabolome ; *Gastrointestinal Microbiome/genetics ; }, abstract = {Amino acid auxotrophies are prevalent among bacteria. They can govern ecological dynamics in microbial communities and indicate metabolic cross-feeding interactions among coexisting genotypes. Despite the ecological importance of auxotrophies, their distribution and impact on the diversity and function of the human gut microbiome remain poorly understood. This study performed the first systematic analysis of the distribution of amino acid auxotrophies in the human gut microbiome using a combined metabolomic, metagenomic, and metabolic modeling approach. Results showed that amino acid auxotrophies are ubiquitous in the colon microbiome, with tryptophan auxotrophy being the most common. Auxotrophy frequencies were higher for those amino acids that are also essential to the human host. Moreover, a higher overall abundance of auxotrophies was associated with greater microbiome diversity and stability, and the distribution of auxotrophs was found to be related to the human host's metabolome, including trimethylamine oxide, small aromatic acids, and secondary bile acids. Thus, our results suggest that amino acid auxotrophies are important factors contributing to microbiome ecology and host-microbiome metabolic interactions.}, } @article {pmid37891335, year = {2023}, author = {Arana, A and Esteves, J and Ramírez, R and Galetti, PM and Pérez Z, J and Ramirez, JL}, title = {Population genomics reveals how 5 ka of human occupancy led the Lima leaf-toed gecko (Phyllodactylus sentosus) to the brink of extinction.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {18465}, pmid = {37891335}, issn = {2045-2322}, mesh = {Male ; Humans ; Animals ; *Metagenomics ; Ecosystem ; Heterozygote ; *Lizards/genetics ; Peru ; Genetic Variation ; Endangered Species ; }, abstract = {Small species with high home fidelity, high ecological specialization or low vagility are particularly prone to suffer from habitat modification and fragmentation. The Lima leaf-toed gecko (Phyllodactylus sentosus) is a critically endangered Peruvian species that shelters mostly in pre-Incan archeological areas called huacas, where the original environmental conditions are maintained. We used genotyping by sequencing to understand the population genomic history of P. sentosus. We found low genetic diversity (He 0.0406-0.134 and nucleotide diversity 0.0812-0.145) and deviations of the observed heterozygosity relative to the expected heterozygosity in some populations (Fis - 0.0202 to 0.0187). In all analyses, a clear population structuring was observed that cannot be explained by isolation by distance alone. Also, low levels of historical gene flow were observed between most populations, which decreased as shown in contemporary migration rate analysis. Demographic inference suggests these populations experienced bottleneck events during the last 5 ka. These results indicate that habitat modification since pre-Incan civilizations severely affected these populations, which currently face even more drastic urbanization threats. Finally, our predictions show that this species could become extinct in a decade without further intervention, which calls for urgent conservation actions being undertaken.}, } @article {pmid37891329, year = {2023}, author = {Lin, X and Xiao, HM and Liu, HM and Lv, WQ and Greenbaum, J and Gong, R and Zhang, Q and Chen, YC and Peng, C and Xu, XJ and Pan, DY and Chen, Z and Li, ZF and Zhou, R and Wang, XF and Lu, JM and Ao, ZX and Song, YQ and Zhang, YH and Su, KJ and Meng, XH and Ge, CL and Lv, FY and Luo, Z and Shi, XM and Zhao, Q and Guo, BY and Yi, NJ and Shen, H and Papasian, CJ and Shen, J and Deng, HW}, title = {Gut microbiota impacts bone via Bacteroides vulgatus-valeric acid-related pathways.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {6853}, pmid = {37891329}, issn = {2041-1723}, support = {R01 AG061917/AG/NIA NIH HHS/United States ; R01 AG068232/AG/NIA NIH HHS/United States ; R01 AR069055/AR/NIAMS NIH HHS/United States ; U19 AG055373/AG/NIA NIH HHS/United States ; P20 GM109036/GM/NIGMS NIH HHS/United States ; R01 MH104680/MH/NIMH NIH HHS/United States ; }, mesh = {Bacteroides ; *Osteoporosis ; *Gastrointestinal Microbiome ; Female ; Humans ; *Bone Resorption ; Mice ; Animals ; }, abstract = {Although the gut microbiota has been reported to influence osteoporosis risk, the individual species involved, and underlying mechanisms, remain largely unknown. We performed integrative analyses in a Chinese cohort of peri-/post-menopausal women with metagenomics/targeted metabolomics/whole-genome sequencing to identify novel microbiome-related biomarkers for bone health. Bacteroides vulgatus was found to be negatively associated with bone mineral density (BMD), which was validated in US white people. Serum valeric acid (VA), a microbiota derived metabolite, was positively associated with BMD and causally downregulated by B. vulgatus. Ovariectomized mice fed B. vulgatus demonstrated increased bone resorption and poorer bone micro-structure, while those fed VA demonstrated reduced bone resorption and better bone micro-structure. VA suppressed RELA protein production (pro-inflammatory), and enhanced IL10 mRNA expression (anti-inflammatory), leading to suppressed maturation of osteoclast-like cells and enhanced maturation of osteoblasts in vitro. The findings suggest that B. vulgatus and VA may represent promising targets for osteoporosis prevention/treatment.}, } @article {pmid37889119, year = {2023}, author = {Seong, HJ and Kim, JJ and Sul, WJ}, title = {ACR: metagenome-assembled prokaryotic and eukaryotic genome refinement tool.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {6}, pages = {}, doi = {10.1093/bib/bbad381}, pmid = {37889119}, issn = {1477-4054}, mesh = {*Metagenome ; Eukaryota/genetics ; *Microbiota/genetics ; Algorithms ; Metagenomics/methods ; Cluster Analysis ; }, abstract = {Microbial genome recovery from metagenomes can further explain microbial ecosystem structures, functions and dynamics. Thus, this study developed the Additional Clustering Refiner (ACR) to enhance high-purity prokaryotic and eukaryotic metagenome-assembled genome (MAGs) recovery. ACR refines low-quality MAGs by subjecting them to iterative k-means clustering predicated on contig abundance and increasing bin purity through validated universal marker genes. Synthetic and real-world metagenomic datasets, including short- and long-read sequences, evaluated ACR's effectiveness. The results demonstrated improved MAG purity and a significant increase in high- and medium-quality MAG recovery rates. In addition, ACR seamlessly integrates with various binning algorithms, augmenting their strengths without modifying core features. Furthermore, its multiple sequencing technology compatibilities expand its applicability. By efficiently recovering high-quality prokaryotic and eukaryotic genomes, ACR is a promising tool for deepening our understanding of microbial communities through genome-centric metagenomics.}, } @article {pmid37888981, year = {2023}, author = {Schönegger, D and Moubset, O and Margaria, P and Menzel, W and Winter, S and Roumagnac, P and Marais, A and Candresse, T}, title = {Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community.}, journal = {Journal of virology}, volume = {97}, number = {11}, pages = {e0130023}, pmid = {37888981}, issn = {1098-5514}, support = {GA 813542//EC | Horizon 2020 Framework Programme (H2020)/ ; 871029//EC | Horizon 2020 Framework Programme (H2020)/ ; ANR-19-CE35-0008-02//Agence Nationale de la Recherche (ANR)/ ; }, mesh = {DNA Viruses/classification/genetics ; *Metagenomics/methods/standards ; Virion/genetics ; *Virome/genetics ; *Synthetic Biology/methods ; RNA, Double-Stranded/genetics ; *Viruses/classification/genetics ; Plant Viruses/classification/genetics ; }, abstract = {We report here efforts to benchmark performance of two widespread approaches for virome analysis, which target either virion-associated nucleic acids (VANA) or highly purified double-stranded RNAs (dsRNAs). This was achieved using synthetic communities of varying complexity levels, up to a highly complex community of 72 viral agents (115 viral molecules) comprising isolates from 21 families and 61 genera of plant viruses. The results obtained confirm that the dsRNA-based approach provides a more complete representation of the RNA virome, in particular, for high complexity ones. However, for viromes of low to medium complexity, VANA appears a reasonable alternative and would be the preferred choice if analysis of DNA viruses is of importance. Several parameters impacting performance were identified as well as a direct relationship between the completeness of virome description and sample sequencing depth. The strategy, results, and tools used here should prove useful in a range of virome analysis efforts.}, } @article {pmid37887008, year = {2023}, author = {Cembrowska-Lech, D and Krzemińska, A and Miller, T and Nowakowska, A and Adamski, C and Radaczyńska, M and Mikiciuk, G and Mikiciuk, M}, title = {An Integrated Multi-Omics and Artificial Intelligence Framework for Advance Plant Phenotyping in Horticulture.}, journal = {Biology}, volume = {12}, number = {10}, pages = {}, pmid = {37887008}, issn = {2079-7737}, abstract = {This review discusses the transformative potential of integrating multi-omics data and artificial intelligence (AI) in advancing horticultural research, specifically plant phenotyping. The traditional methods of plant phenotyping, while valuable, are limited in their ability to capture the complexity of plant biology. The advent of (meta-)genomics, (meta-)transcriptomics, proteomics, and metabolomics has provided an opportunity for a more comprehensive analysis. AI and machine learning (ML) techniques can effectively handle the complexity and volume of multi-omics data, providing meaningful interpretations and predictions. Reflecting the multidisciplinary nature of this area of research, in this review, readers will find a collection of state-of-the-art solutions that are key to the integration of multi-omics data and AI for phenotyping experiments in horticulture, including experimental design considerations with several technical and non-technical challenges, which are discussed along with potential solutions. The future prospects of this integration include precision horticulture, predictive breeding, improved disease and stress response management, sustainable crop management, and exploration of plant biodiversity. The integration of multi-omics and AI holds immense promise for revolutionizing horticultural research and applications, heralding a new era in plant phenotyping.}, } @article {pmid37884755, year = {2023}, author = {Saleem, M and Yahya, S and Razzak, SA and Khawaja, S and Ali, A}, title = {Shotgun metagenomics and computational profiling of the plastisphere microbiome: unveiling the potential of enzymatic production and plastic degradation.}, journal = {Archives of microbiology}, volume = {205}, number = {11}, pages = {359}, pmid = {37884755}, issn = {1432-072X}, mesh = {*Bacteria/genetics ; *Microbiota/genetics ; Proteobacteria/genetics ; Archaea/genetics ; Metagenome ; Metagenomics ; }, abstract = {Plastic pollution is one of the most resilient types of pollution and is considered a global environmental threat, particularly in the marine environment. This study aimed to identify plastic-degrading bacteria from the plastisphere and their pharmaceutical and therapeutic potential. We collected samples from soil and aquatic plastisphere to identify the bacterial communities using shotgun metagenomic sequencing and bioinformatic tools. Results showed that the microbiome comprised 93% bacteria, 0.29% archaea, and 3.87% unidentified microbes. Of these 93% of bacteria, 54% were Proteobacteria, 23.9% were Firmicutes, 13% were Actinobacteria, and 2.1% were other phyla. We found that the plastisphere microbiome was involved in degrading synthetic and polyhydroxy alkanoate (PHA) plastic, biosurfactant production, and can thrive under high temperatures. However, no association existed between thermophiles, synthetic plastic or PHA degraders, and biosurfactant-producing bacterial species except for Pseudomonas. Other plastisphere inhabiting plastic degrading microbes include Streptomyces, Bacillus, Achromobacter, Azospirillum, Bacillus, Brevundimonas, Clostridium, Paenibacillus, Rhodococcus, Serratia, Staphylococcus, Thermobifida, and Thermomonospora. However, the plastisphere microbiome showed potential for producing secondary metabolites that were found to act as anticancer, antitumor, anti-inflammatory, antimicrobial, and enzyme stabilizers. These results revealed that the plastisphere microbiome upholds clinical and environmental significance as it can open future portals in a multi-directional way.}, } @article {pmid37884410, year = {2024}, author = {Karadayı, B and Karaismailoğlu, B and Karadayı, S and Arslan, A and Gözen, ED and Özbek, T}, title = {The uselessness of using salivary microbiota in forensic identification purposes of a person with recent antibiotic use.}, journal = {Legal medicine (Tokyo, Japan)}, volume = {69}, number = {}, pages = {102338}, doi = {10.1016/j.legalmed.2023.102338}, pmid = {37884410}, issn = {1873-4162}, mesh = {Humans ; *Saliva/microbiology ; *Microbiota/genetics ; *Anti-Bacterial Agents ; *RNA, Ribosomal, 16S/genetics ; Male ; Female ; Adult ; Middle Aged ; Polymerase Chain Reaction ; }, abstract = {The detection of microbial flora changes in saliva samples because of antibiotic use through advanced molecular genetic analysis is important for forensic and clinical applications. This study aims to reveal the variability in the microbial structure of human saliva after antibiotic use with metagenomic analysis techniques from a forensic point of view. Within the scope of the study, saliva samples were collected from patients who were under the effect of regional anesthesia to be administered a standardized course of antibiotic therapy that lasted for a week. The analysis was conducted on 56 saliva samples from 14 individuals over four different time intervals. Isolation of the 16S rRNA region and PCR analysis were performed prior to sequence analysis to determine the microbiome structure of the samples at phylum, genus, and species levels. As expected, changes were observed in bacterial species found in saliva samples after administration of antibiotics and this was linked to the specific type of antibiotics that were administered. This change was statistically significant for Firmicutes, Spirochetes, and Verrucomicrobiota. Furthermore, although the oral microbiome tends to return to its former state at the phylum and genus level within a 4-week period after the start of antibiotic use, it is observed that the change, especially in some bacterial species, still continues. The findings of this study show that because of the inability of stabilization at species-level in a period of 4 weeks from the start of antibiotic use, it is not suitable to assess saliva samples at species-level for forensic identification.}, } @article {pmid37884341, year = {2023}, author = {Deng, J and Liu, YJ and Wei, WT and Huang, QX and Zhao, LP and Luo, LY and Zhu, Q and Zhang, L and Chen, Y and Ren, YL and Jia, SG and Lin, YL and Yang, J and Lv, FH and Zhang, HP and Li, FE and Li, L and Li, MH}, title = {Single-cell transcriptome and metagenome profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants.}, journal = {Genome research}, volume = {33}, number = {10}, pages = {1690-1707}, pmid = {37884341}, issn = {1549-5469}, mesh = {Sheep/genetics ; Animals ; *Metagenome ; Transcriptome ; Rumen ; Ruminants/genetics ; *Microbiota ; }, abstract = {The rumen undergoes developmental changes during maturation. To characterize this understudied dynamic process, we profiled single-cell transcriptomes of about 308,000 cells from the rumen tissues of sheep and goats at 17 time points. We built comprehensive transcriptome and metagenome atlases from early embryonic to rumination stages, and recapitulated histomorphometric and transcriptional features of the rumen, revealing key transitional signatures associated with the development of ruminal cells, microbiota, and core transcriptional regulatory networks. In addition, we identified and validated potential cross-talk between host cells and microbiomes and revealed their roles in modulating the spatiotemporal expression of key genes in ruminal cells. Cross-species analyses revealed convergent developmental patterns of cellular heterogeneity, gene expression, and cell-cell and microbiome-cell interactions. Finally, we uncovered how the interactions can act upon the symbiotic rumen system to modify the processes of fermentation, fiber digestion, and immune defense. These results significantly enhance understanding of the genetic basis of the unique roles of rumen.}, } @article {pmid37883976, year = {2023}, author = {Blanco-Míguez, A and Gálvez, EJC and Pasolli, E and De Filippis, F and Amend, L and Huang, KD and Manghi, P and Lesker, TR and Riedel, T and Cova, L and Punčochář, M and Thomas, AM and Valles-Colomer, M and Schober, I and Hitch, TCA and Clavel, T and Berry, SE and Davies, R and Wolf, J and Spector, TD and Overmann, J and Tett, A and Ercolini, D and Segata, N and Strowig, T}, title = {Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions.}, journal = {Cell host & microbe}, volume = {31}, number = {11}, pages = {1804-1819.e9}, pmid = {37883976}, issn = {1934-6069}, support = {R01 CA230551/CA/NCI NIH HHS/United States ; U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Male ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Microbiota ; Phylogeny ; Prevotella ; Female ; }, abstract = {The Segatella copri (formerly Prevotella copri) complex (ScC) comprises taxa that are key members of the human gut microbiome. It was previously described to contain four distinct phylogenetic clades. Combining targeted isolation with large-scale metagenomic analysis, we defined 13 distinct Segatella copri-related species, expanding the ScC complex beyond four clades. Complete genome reconstruction of thirteen strains from seven species unveiled the presence of genetically diverse large circular extrachromosomal elements. These elements are consistently present in most ScC species, contributing to intra- and inter-species diversities. The nine species-level clades present in humans display striking differences in prevalence and intra-species genetic makeup across human populations. Based on a meta-analysis, we found reproducible associations between members of ScC and the male sex and positive correlations with lower visceral fat and favorable markers of cardiometabolic health. Our work uncovers genomic diversity within ScC, facilitating a better characterization of the human microbiome.}, } @article {pmid37881335, year = {2023}, author = {García-López, JD and Barbieri, F and Baños, A and Madero, JMG and Gardini, F and Montanari, C and Tabanelli, G}, title = {Use of two autochthonous bacteriocinogenic strains as starter cultures in the production of salchichónes, a type of Spanish fermented sausages.}, journal = {Current research in food science}, volume = {7}, number = {}, pages = {100615}, pmid = {37881335}, issn = {2665-9271}, abstract = {In this work, two autochthonous LAB strains (Lactiplantibacillus paraplantarum BPF2 and Pediococcus acidilactici ST6), isolated from spontaneously fermented sausages produced in Spain, were tested to produce Spanish fermented sausages (salchichón) in pilot plants, due to their promising technological and anti-listerial activity. These products were compared with a sample obtained with a commercial starter (RAP) and a spontaneously fermented control sample. Physico-chemical parameters, microbial counts, metagenomic analysis, biogenic amines content and organoleptic profile of the obtained samples were studied to assess the performances of the native starters. In fact, traditional and artisanal products obtained through spontaneous fermentations can represent an important biodiversity reservoir of strains to be exploited as new potential starter cultures, to improve the safety, quality and local differentiation of traditional products. The data underlined that ST6 strain resulted in a final lower percentage if compared with the other LAB used as starter cultures. The use of starters reduced the BA concentration observed in the sausages obtained with spontaneous fermentation and the BPF2 and ST6 strains were able to decrease the level of products rancidity. Moreover, a challenge test against L. monocytogenes were performed. The data confirmed the effectiveness in the inhibition of L. monocytogenes by the two bacteriocinogenic strains tested, with respect to RAP and control samples, highlighting their ability to produce bacteriocins in real food systems. This work demonstrated the promising application in meat industry of these autochthonous strains as starter cultures to improve sensory differentiation and recognizability of typical fermented sausages.}, } @article {pmid37880979, year = {2023}, author = {Alessandri, G and Sangalli, E and Facchi, M and Fontana, F and Mancabelli, L and Donofrio, G and Ventura, M}, title = {Metataxonomic analysis of milk microbiota in the bovine subclinical mastitis.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {12}, pages = {}, doi = {10.1093/femsec/fiad136}, pmid = {37880979}, issn = {1574-6941}, mesh = {Cattle ; Animals ; Female ; Humans ; Milk/microbiology ; RNA, Ribosomal, 16S/genetics ; Pilot Projects ; *Mastitis, Bovine/microbiology/pathology ; *Microbiota/genetics ; }, abstract = {Subclinical mastitis is one of the most widespread diseases affecting dairy herds with detrimental effects on animal health, milk productivity, and quality. Despite its multifactorial nature, the presence of pathogenic bacteria is regarded one of the main drivers of subclinical mastitis, causing a disruption of the homeostasis of the bovine milk microbial community. However, bovine milk microbiota alterations associated with subclinical mastitis still represents a largely unexplored research area. Therefore, the species-level milk microbiota of a total of 75 milk samples, collected from both healthy and subclinical mastitis-affected cows from two different stables, was deeply profiled through an ITS, rather than a traditional, and less informative, 16S rRNA gene microbial profiling. Surprisingly, the present pilot study not only revealed that subclinical mastitis is characterized by a reduced biodiversity of the bovine milk microbiota, but also that this disease does not induce standard alterations of the milk microbial community across stables. In addition, a flow cytometry-based total bacterial cell enumeration highlighted that subclinical mastitis is accompanied by a significant increment in the number of milk microbial cells. Furthermore, the combination of the metagenomic and flow cytometry approaches allowed to identify different potential microbial marker strictly correlated with subclinical mastitis across stables.}, } @article {pmid37878664, year = {2023}, author = {Midya, V and Lane, JM and Gennings, C and Torres-Olascoaga, LA and Gregory, JK and Wright, RO and Arora, M and Téllez-Rojo, MM and Eggers, S}, title = {Prenatal Lead Exposure Is Associated with Reduced Abundance of Beneficial Gut Microbial Cliques in Late Childhood: An Investigation Using Microbial Co-Occurrence Analysis (MiCA).}, journal = {Environmental science & technology}, volume = {57}, number = {44}, pages = {16800-16810}, pmid = {37878664}, issn = {1520-5851}, support = {R00 ES032884/ES/NIEHS NIH HHS/United States ; K99 ES032884/ES/NIEHS NIH HHS/United States ; R01 ES013744/ES/NIEHS NIH HHS/United States ; R24 ES028522/ES/NIEHS NIH HHS/United States ; P30 ES023515/ES/NIEHS NIH HHS/United States ; T32 HD049311/HD/NICHD NIH HHS/United States ; UL1 TR004419/TR/NCATS NIH HHS/United States ; R35 ES030435/ES/NIEHS NIH HHS/United States ; }, mesh = {Pregnancy ; Female ; Humans ; Child ; Lead ; *Gastrointestinal Microbiome ; *Microbiota ; Bacteria ; }, abstract = {Many analytical methods used in gut microbiome research focus on either single bacterial taxa or the whole microbiome, ignoring multibacteria relationships (microbial cliques). We present a novel analytical approach to identify microbial cliques within the gut microbiome of children at 9-11 years associated with prenatal lead (Pb) exposure. Data came from a subset of participants (n = 123) in the Programming Research in Obesity, Growth, Environment and Social Stressors cohort. Pb concentrations were measured in maternal whole blood from the second and third trimesters of pregnancy. Stool samples collected at 9-11 years old underwent metagenomic sequencing to assess the gut microbiome. Using a novel analytical approach, Microbial Co-occurrence Analysis (MiCA), we paired a machine learning algorithm with randomization-based inference to first identify microbial cliques that were predictive of prenatal Pb exposure and then estimate the association between prenatal Pb exposure and microbial clique abundance. With second-trimester Pb exposure, we identified a two-taxa microbial clique that included Bifidobacterium adolescentis and Ruminococcus callidus and a three-taxa clique that also included Prevotella clara. Increasing second-trimester Pb exposure was associated with significantly increased odds of having the two-taxa microbial clique below the median relative abundance (odds ratio (OR) = 1.03, 95% confidence interval (CI) [1.01-1.05]). Using a novel combination of machine learning and causal inference, MiCA identified a significant association between second-trimester Pb exposure and the reduced abundance of a probiotic microbial clique within the gut microbiome in late childhood.}, } @article {pmid37877794, year = {2023}, author = {Morissette, A and André, DM and Agrinier, AL and Varin, TV and Pilon, G and Flamand, N and Houde, VP and Marette, A}, title = {The metabolic benefits of substituting sucrose for maple syrup are associated with a shift in carbohydrate digestion and gut microbiota composition in high-fat high-sucrose diet-fed mice.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {325}, number = {6}, pages = {E661-E671}, doi = {10.1152/ajpendo.00065.2023}, pmid = {37877794}, issn = {1522-1555}, support = {//Producteurs et productrices acericoles du Quebec/ ; }, mesh = {Male ; Animals ; Mice ; Sucrose ; *Gastrointestinal Microbiome ; *Acer ; Mice, Obese ; Liver/metabolism ; Diet, High-Fat ; Sweetening Agents ; Digestion ; Mice, Inbred C57BL ; }, abstract = {Overconsumption of added sugars is now largely recognized as a major culprit in the global situation of obesity and metabolic disorders. Previous animal studies reported that maple syrup (MS) is less deleterious than refined sugars on glucose metabolism and hepatic health, but the mechanisms remain poorly studied. Beyond its content in sucrose, MS is a natural sweetener containing several bioactive compounds, such as polyphenols and inulin, which are potential gut microbiota modifiers. We aimed to investigate the impact of MS on metabolic health and gut microbiota in male C57Bl/6J mice fed a high-fat high-sucrose (HFHS + S) diet or an isocaloric HFHS diet in which a fraction (10% of the total caloric intake) of the sucrose was substituted by MS (HFHS + MS). Insulin and glucose tolerance tests were performed at 5 and 7 wk into the diet, respectively. The fecal microbiota was analyzed by whole-genome shotgun sequencing. Liver lipids and inflammation were determined, and hepatic gene expression was assessed by transcriptomic analysis. Maple syrup was less deleterious on insulin resistance and decreased liver steatosis compared with mice consuming sucrose. This could be explained by the decreased intestinal α-glucosidase activity, which is involved in carbohydrate digestion and absorption. Metagenomic shotgun sequencing analysis revealed that MS intake increased the abundance of Faecalibaculum rodentium, Romboutsia ilealis, and Lactobacillus johnsonii, which all possess gene clusters involved in carbohydrate metabolism, such as sucrose utilization and butyric acid production. Liver transcriptomic analyses revealed that the cytochrome P450 (Cyp450) epoxygenase pathway was differently modulated between HFHS + S- and HFHS + MS-fed mice. These results show that substituting sucrose for MS alleviated dysmetabolism in diet-induced obese mice, which were associated with decreased carbohydrate digestion and shifting gut microbiota.NEW & NOTEWORTHY The natural sweetener maple syrup has sparked much interest as an alternative to refined sugars. This study aimed to investigate whether the metabolic benefits of substituting sucrose with an equivalent dose of maple syrup could be linked to changes in gut microbiota composition and digestion of carbohydrates in obese mice. We demonstrated that maple syrup is less detrimental than sucrose on metabolic health and possesses a prebiotic-like activity through novel gut microbiota and liver mechanisms.}, } @article {pmid37877655, year = {2023}, author = {Ahmad, N and Ritz, M and Calchera, A and Otte, J and Schmitt, I and Brueck, T and Mehlmer, N}, title = {Biosynthetic gene cluster synteny: Orthologous polyketide synthases in Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata.}, journal = {MicrobiologyOpen}, volume = {12}, number = {5}, pages = {e1386}, pmid = {37877655}, issn = {2045-8827}, mesh = {Phylogeny ; *Lichens/genetics/microbiology ; Fungi/genetics ; Parmeliaceae ; *Polyketide Synthases/genetics/metabolism ; Multigene Family ; Synteny ; Depsides/metabolism ; }, abstract = {Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus), which together generate a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here, we provide a comparative view of the biosynthetic gene clusters of three lichen mycobionts derived from Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata. In addition, we present a high-quality PacBio metagenome of Parmelia sulcata, from which we extracted the mycobiont bin containing 214 biosynthetic gene clusters. Most biosynthetic gene clusters in these genomes were associated with T1PKSs, followed by NRPSs and terpenes. This study focused on biosynthetic gene clusters related to polyketide synthesis. Based on ketosynthase homology, we identified nine highly syntenic clusters present in all three species. Among the four clusters belonging to nonreducing PKSs, two are putatively linked to lichen substances derived from orsellinic acid (orcinol depsides and depsidones, e.g., lecanoric acid, physodic acid, lobaric acid), one to compounds derived from methylated forms of orsellinic acid (beta orcinol depsides, e.g., atranorin), and one to melanins. Five clusters with orthologs in all three species are linked to reducing PKSs. Our study contributes to sorting and dereplicating the vast PKS diversity found in lichenized fungi. High-quality sequences of biosynthetic gene clusters of these three common species provide a foundation for further exploration into biotechnological applications and the molecular evolution of lichen substances.}, } @article {pmid37875803, year = {2023}, author = {Salman, MM and Nawaz, M and Yaqub, T and Mushtaq, MH}, title = {Investigation of milk microbiota of healthy and mastitic Sahiwal cattle.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {304}, pmid = {37875803}, issn = {1471-2180}, mesh = {RNA, Ribosomal, 16S/genetics ; Female ; Cattle ; Humans ; *Microbiota ; Animals ; *Mastitis, Bovine/microbiology ; Milk/microbiology ; Akkermansia ; }, abstract = {BACKGROUND: Sahiwal cattle is an indigenous cattle breed of Pakistan and mastitis is one of the major problems faced by Sahiwal cattle which hinders its production potential. The study was designed to investigate the milk microbiota of healthy and mastitic Sahiwal cattle as part of a multistep project to develop probiotics for the mitigation and control of mastitis. Milk samples of Sahiwal cattle (healthy clinical mastitis and subclinical mastitis) reared under similar husbandry and management practices were processed for 16S rRNA gene base metagenomics analysis.

RESULTS: Results revealed that Proteobacteria were dominant in the healthy group and subclinical mastitis group (56.48% and 48.77%, respectively) as compared to the clinical mastitis group (2.68%). In contrast, Firmicutes were abundant in the clinical mastitis group (64%) as compared to the healthy and subclinical mastitis groups (15.87% and 38.98%, respectively). Dominant species assigned in the healthy group were Ignavibacterium album, Novosphingobium capsulatum, Akkermansia muciniphila and Lactobacillus fermentum.The clinical mastitis group was dominated by Streptococcus dysgalactiae and Corynebacterium bovis, while subclinical mastitis group included Lactobacillus fermentum and uncultured acidobacteriales and Akkermansia muciniphila as dominant species. Alpha diversity indices showed higher microbial diversity in the healthy group compared to the clinical and sub-clinical mastitis groups.

CONCLUSION: It is concluded that the milk microbiota of healthy sahiwal cattle has higher diversity and dominant taxa in the different groups may be used as signature microbes for mastitis susceptibility. Akkermansia muciniphila is one of candidate specie that was identified and may be used for development of probiotics.}, } @article {pmid37875797, year = {2023}, author = {Fu, Y and Zhang, K and Shan, F and Li, J and Wang, Y and Li, X and Xu, H and Qin, Z and Zhang, L}, title = {Metagenomic analysis of gut microbiome and resistome of Whooper and Black Swans: a one health perspective.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {635}, pmid = {37875797}, issn = {1471-2164}, support = {U1904203//Key program of National Natural Science Foundation of China - Henan Province Joint Fund/ ; 2019YFC1605700//National Key Research and Development Program of China/ ; 19CZ0122//Leading Talents of Thousand Talents Program of Central China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *One Health ; *Anseriformes ; China ; *Microbiota ; Ducks ; Anti-Bacterial Agents/pharmacology ; }, abstract = {BACKGROUND: With the promotion of "One Health," the health of animals and their impact on the environment have become major concerns recently. Widely distributed in China, the whooper swans (Cygnus cygnus) and black swans (Cygnus atratus) are not only important to the ecological environment, but they may also potentially influence public health security. The metagenomic approach was adopted to uncover the impacts of the gut microbiota of swans on host and public health.

RESULTS: In this study, the intestinal microbiome and resistome of migratory whooper swans and captive-bred black swans were identified. The results revealed similar gut microbes and functional compositions in whooper and black swans. Interestingly, different bacteria and probiotics were enriched by overwintering whooper swans. We also found that Acinetobacter and Escherichia were significantly enriched in early wintering period swans and that clinically important pathogens were more abundant in black swans. Whooper swans and black swans are potential reservoirs of antibiotic resistance genes (ARGs) and novel ARGs, and the abundance of novel ARGs in whooper swans was significantly higher than that in black swans. Metagenomic assembly-based host tracking revealed that most ARG-carrying contigs originated from Proteobacteria (mainly Gammaproteobacteria).

CONCLUSIONS: The results revealed spatiotemporal changes in microbiome and resistome in swans, providing a reference for safeguarding public health security and preventing animal epidemics.}, } @article {pmid37875417, year = {2024}, author = {Li, J and Yang, Z and Yuan, W and Bao, Z and Li, MD}, title = {Heme Metabolism Mediates the Effects of Smoking on Gut Microbiome.}, journal = {Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco}, volume = {26}, number = {6}, pages = {742-751}, doi = {10.1093/ntr/ntad209}, pmid = {37875417}, issn = {1469-994X}, support = {2016YFC0906300//China Precision Medicine Initiative/ ; 2021539200340045//Joint Research Institute of Tobacco and Health of China/ ; //Research Center for Air Pollution and Health of Zhejiang University/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Heme/metabolism ; Transcriptome ; Male ; Female ; Metagenome ; Adult ; Smoking/adverse effects ; Bacteroides/genetics ; }, abstract = {INTRODUCTION: The number of smokers worldwide increased greatly during the past decades and reached 1.14 billion in 2019, becoming a leading risk factor for human health. Tobacco smoking has wide effects on human genetics, epigenetics, transcriptome, and gut microbiome. Although many studies have revealed effects of smoking on host transcriptome, research on the relationship between smoking, host gene expression, and the gut microbiome is limited.

AIMS AND METHODS: We first explored transcriptome and metagenome profile differences between smokers and nonsmokers. To evaluate the relationship between host gene expression and gut microbiome, we then applied bidirectional mediation analysis to infer causal relationships between smoking, gene expression, and gut microbes.

RESULTS: Metagenome and transcriptome analyses revealed 71 differential species and 324 differential expressed genes between smokers and nonsmokers. With smoking as an exposure variable, we identified 272 significant causal relationships between gene expression and gut microbes, among which there were 247 genes that mediate the effect of smoking on gut microbes. Pathway-based enrichment analysis showed that these genes were significantly enriched in heme metabolic pathway, which mainly mediated the changes of Bacteroides finegoldii and Lachnospiraceae bacterium 9_1_43BFAA. Additionally, by performing metabolome data analysis in the Integrated Human Microbiome Project (iHMP) database, we verified the correlation between the intermediate products of the heme metabolism pathway (porphobilinogen, bilirubin, and biliverdin) and gut microbiome.

CONCLUSIONS: By investigating the bidirectional interaction between smoking-related host gene expression and gut microbes, this study provided evidence for the mediation of smoking on gut microbes through co-involvement or interaction of heme metabolism.

IMPLICATIONS: By comparing the metagenome and transcriptome sequencing profiles between 34 smokers and 33 age- and gender-matched nonsmokers, we are the first to reveal causal relationships among tobacco smoking, host gene expression, and gut microbes. These findings offer insight into how smoking affects gut microbes through host gene expression and metabolism, which highlights the importance of heme metabolism in modulating the effects of smoking on gut microbiome.}, } @article {pmid37875356, year = {2023}, author = {Cheng, X and Zhang, Z and Dong, W and Lun, Y and Liu, B}, title = {Characteristics of intestinal flora in patients with cerebral infarction complicated with Type 2 diabetes mellitus.}, journal = {Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences}, volume = {48}, number = {8}, pages = {1163-1175}, pmid = {37875356}, issn = {1672-7347}, support = {2020J01903//the grants from the Natural Science Foundations of Fujian Province/ ; 2019013//the Talents Research Project of Putian University/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/complications ; Retrospective Studies ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {OBJECTIVES: The intestinal microbial characteristics of patients with simple cerebral infarction (CI) and CI complicated with Type 2 diabetes mellitus (CI-T2DM) are still not clear. This study aims to analyze the differences in the variable characteristics of intestinal flora between patients simply with CI and CI-T2DM.

METHODS: This study retrospectively collected the patients who were admitted to the Affiliated Hospital of Putian University from September 2021 to September 2022. The patients were divided into a CI group (n=12) and a CI-T2DM group (n=12). Simultaneously, 12 healthy people were selected as a control group. Total DNA was extracted from feces specimens. Illumina Novaseq sequencing platform was used for metagenomic sequencing. The Knead Data software, Kraken2 software, and Bracken software were applied for sequencing analysis.

RESULTS: At phylum level, the average ratio of Firmicutes, Bacteroidetes, and Proteobacteria in the CI-T2DM group were 33.07%, 54.80%, and 7.00%, respectively. In the CI group, the ratios of each were 14.03%, 69.62%, and 11.13%, respectively, while in the control group, the ratios were 50.99%, 37.67%, and 5.24%, respectively. There was significant differences in the distribution of Firmicutes (F=6.130, P=0.011) among the 3 groups. At the family level, compared with the CI group, the relative abundance of Eubacteriaceae (t=8.062, P<0.001) in the CI-T2DM group was significantly increased, while Corynebacteriaceae (t=4.471, P<0.001), Methanobacteriaceae (t=3.406, P=0.003), and Pseudomonadaceae (t=2.352, P=0.028) were decreased significantly. At the genus level, compared with the CI group, there was a relative abundance of Cutibacterium (t=6.242, P<0.001), Eubacterium (t=8.448, P<0.001), and Blautia (t=3.442, P=0.002) in the CI-T2DM group which was significantly increased. In terms of Methanobrevibacter (t=3.466, P=0.002), Pyramidobacter (t=2.846, P=0.009) and Pseudomonas (t=2.352, P=0.028), their distributions were decreased significantly in the CI-T2DM group. At the species level, compared with the CI group, the relative abundance of Cutibacterium acnes (t=6.242, P<0.001) in the CI-T2DM group was significantly increased, while Pseudomonas aeruginosa (t=2.352, P=0.028) was decreased significantly. Still at the genus level, linear discriminant analysis effect size (LEfSe) analysis showed that the distributions of Pseudomonas and Blautia were determined to be the most significantly different between the CI-T2DM and the CI group. At the species level, the total number of operational taxonomic units (OTUs) in the 3 groups was 1 491. There were 169, 221, and 192 kinds of OTUs unique to the CI-T2DM, CI, and control group, respectively.

CONCLUSIONS: From phylum level to species level, the composition of intestinal flora in the patients with CI-T2DM is different from those in the patients simply with CI. The change in the proportion of Firmicutes, Bacteroidetes and Proteus compared with the healthy population is an important feature of intestinal flora imbalance in the patients with CI and with CI-T2DM. Attention should be paid to the differential distribution of Bacteroides monocytogenes and butyrate producing bacteria.}, } @article {pmid37875211, year = {2024}, author = {Go, K and Horiba, K and Yamamoto, H and Morimoto, Y and Fukasawa, Y and Ohashi, N and Yasuda, K and Ishikawa, Y and Kuraishi, K and Suzuki, K and Ito, Y and Takahashi, Y and Kato, T}, title = {Dysbiosis of gut microbiota in patients with protein-losing enteropathy after the Fontan procedure.}, journal = {International journal of cardiology}, volume = {396}, number = {}, pages = {131554}, doi = {10.1016/j.ijcard.2023.131554}, pmid = {37875211}, issn = {1874-1754}, mesh = {Humans ; *Fontan Procedure/adverse effects ; *Protein-Losing Enteropathies/diagnosis/etiology ; *Gastrointestinal Microbiome ; Case-Control Studies ; Dysbiosis/diagnosis/complications ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: There is a lack of predictive biomarkers for the onset or activity of protein-losing enteropathy (PLE), a Fontan procedure-associated complication. Here, we aimed to identify the gut microbiota composition of patients with active PLE and investigate its relationship with PLE activity.

METHODS: This multicenter case-control study involved patients who developed PLE (n = 16) after the Fontan procedure and those who did not (non-PLE; n = 20). Patients with PLE who maintained a serum albumin level of ≥3 g/dL for >1 year were included in the remissive-stage-PLE group (n = 9) and those who did not maintain this level were included in the active-PLE group (n = 7). 16S rRNA gene sequencing analysis of fecal samples was performed using QIIME2 pipeline. Alpha (Shannon and Faith's phylogenetic diversity indices) and beta diversity was assessed using principal coordinate analysis based on unweighted UniFrac distances.

RESULTS: Shannon and Faith's phylogenetic diversity indices were lower in the active-PLE group than in the remissive-stage- (q = 0.028 and 0.025, respectively) and non-PLE (q = 0.028 and 0.017, respectively) groups. Analysis of beta diversity revealed a difference in the microbiota composition between the active-PLE and the other two groups. Linear discriminant effect size analysis demonstrated differences in the relative abundance of Bifidobacterium and Granulicatella spp., and Ruminococcus torques between patients with active- and those with remissive-stage-PLE.

CONCLUSIONS: Gut microbiota dysbiosis was observed in patients with active PLE. Changes in the bacterial composition of the gut microbiota and decreased diversity may be associated with the severity of PLE.}, } @article {pmid37874137, year = {2023}, author = {Taraboletti, A and King, A and Dixon, Y and Orr, O and Parnell, C and Watson, Y and Nash, B and Esimai, C and Ude, G}, title = {Assessing microbial diversity in soil samples along the Potomac River: implications for environmental health.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0254023}, pmid = {37874137}, issn = {2165-0497}, support = {1438902//National Science Foundation (NSF)/ ; 1622811, 183365//National Science Foundation (NSF)/ ; }, mesh = {Humans ; *Rivers ; Environmental Pollution ; *Microbiota ; Environmental Health ; Soil ; Soil Microbiology ; }, abstract = {This study integrates microbial analysis into an undergraduate chemistry class, offering students a hands-on approach to environmental research. We examined the soil along the urbanized Potomac River, discovering a mix of common marine microbes and others that are indicators of urban waste and pollution. Our findings provide valuable insights into the environmental impacts of urbanization on soil health and reveal the effectiveness of using modern genetic tools to teach students about real-world issues. This innovative educational approach not only deepens students' understanding of chemistry and ecology but also prepares them to be thoughtful, informed participants in addressing contemporary environmental challenges while shedding light on the state of the soil microbiome near and around the DC metro area.}, } @article {pmid37872759, year = {2023}, author = {Hurle, GR and Brainard, J and Tyler, KM}, title = {Microbiome diversity is a modifiable virulence factor for cryptosporidiosis.}, journal = {Virulence}, volume = {14}, number = {1}, pages = {2273004}, pmid = {37872759}, issn = {2150-5608}, mesh = {Animals ; Child ; Humans ; Child, Preschool ; *Cryptosporidiosis/parasitology ; *Cryptosporidium ; *Cryptosporidium parvum ; Bacteria/genetics ; *Gastrointestinal Microbiome ; Feces/parasitology ; }, abstract = {Cryptosporidium spp. infection causes significant disease in immunosuppressed individuals and children under the age of 5 years. The severity of the pathological presentation of cryptosporidiosis is a function of the host and parasite genotypes, host immune status, and the enteric environment or microbiome of the host. Cryptosporidiosis often presents with abdominal pain and severe diarrhoea and is associated with intestinal dysbiosis and inflammation. Our systematic analysis of the available literature revealed that bacterial diversity is reduced during infection in larger animal models, lending support to recent studies which indicate that the use of probiotics or the presence of a naturally diverse gut microbiome can prevent or minimise pathology caused by gastrointestinal pathogens. In summary, we present evidence that the presence of a diverse gut microbiome, natural or induced, reduces both symptomatic pathology and oocyst output.}, } @article {pmid37872393, year = {2023}, author = {Li, Y and Xiong, L and Yu, H and Zeng, K and Wei, Y and Li, H and Zeng, W and Ji, X}, title = {Function and distribution of nitrogen-cycling microbial communities in the Napahai plateau wetland.}, journal = {Archives of microbiology}, volume = {205}, number = {11}, pages = {357}, pmid = {37872393}, issn = {1432-072X}, support = {(32160294, 31960033)//the National Natural Science Foundation of China/ ; }, mesh = {*Wetlands ; Phylogeny ; Nitrogen/metabolism ; Nitrates ; *Microbiota/genetics ; }, abstract = {Nitrogen is an essential component of living organisms and a major nutrient that limits life on Earth. Until now, freely available nitrogen mainly comes from atmospheric nitrogen, but most organisms rely on bioavailable forms of nitrogen, which depends on the complex network of microorganisms with a wide variety of metabolic functions. Microbial-mediated nitrogen cycling contributes to the biogeochemical cycling of wetlands, but its specific microbial abundance, composition, and distribution need to be studied. Based on the metagenomic data, we described the composition and functional characteristics of microbial nitrogen cycle-related genes in the Napahai plateau wetland. Six nitrogen cycling pathways existed, such as dissimilatory nitrate reduction, denitrification, nitrogen fixation, nitrification, anammox, and nitrate assimilation. Most genes related to the nitrogen cycling in this region come from bacteria, mainly from Proteobacteria and Acidobacteria. Habitat types and nitrogen cycle-related genes largely explained the relative abundance of total nitrogen pathways. Phylogenetic trees were constructed based on nitrogen cycle-related genes from different habitats and sources, combined with PCoA analysis, most of them clustered separately, indicating richness and uniqueness. Some microbial groups seemed to be special or general in the nitrogen cycling. In conclusion, it suggested that microorganisms regulated the N cycling process, and may lead to N loss throughout the wetland, thus providing a basis for further elucidation of the microbial regulation of N cycling processes and the Earth's elemental cycles.}, } @article {pmid37872094, year = {2023}, author = {Luan, YT and Liu, CH and Jiang, SL and Gu, HT and Lyu, J and Xing, F and Zhao, CQ and Yuan, JL and Liu, P and Mu, YP}, title = {[Comparative analysis of intestinal microbiota distribution characteristics based on metagenomics in patients with hepatitis B cirrhosis with or without ascites].}, journal = {Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology}, volume = {31}, number = {9}, pages = {974-985}, doi = {10.3760/cma.j.cn501113-20220830-00440}, pmid = {37872094}, issn = {1007-3418}, support = {81874390//National Natural Science Foundation of China/ ; shslczdzk01201//Shanghai Key Specialty of Traditional Chinese Clinical Medicine/ ; 21ZR1464100//Shanghai Natural Science Foundation/ ; 22S11901700//Special Project for Biomedical Science and Technology Support of the "Science and Technology Innovation Action Plan" of Shanghai Science and Technology Commission in 2022/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Ascites/complications ; RNA, Ribosomal, 16S/genetics ; Liver Cirrhosis/complications ; *Hepatitis B/complications ; Amino Acids ; }, abstract = {Objective: To use metagenomic sequencing to compare the differences in intestinal microbiota species and metabolic pathways in patients with hepatitis B cirrhosis with or without ascites and further explore the correlation between the differential microbiota and clinical indicators and metabolic pathways. Methods: 20 hepatitis B cirrhosis cases [10 without ascites (HBLC-WOA), 10 with ascites (HBLC-WA), and 5 healthy controls (HC)] were selected from the previously studied 16S rRNA samples. Metagenome sequencing was performed on the intestinal microbiota samples. The Kruskal-Wallis rank sum test and Spearman test were used to identify and analyse differential intestinal microbiota populations, metabolic pathways, and their correlations. Results: (1) The overall structure of the intestinal microbiota differed significantly among the three groups (R = 0.19, P = 0.018). The HC group had the largest abundance of Firmicutes and the lowest abundance of Proteobacteria at the genus level. Firmicutes abundance was significantly decreased (P(fdr) < 0.01), while Proteobacteria abundance was significantly increased (P(fdr) < 0.01) in patients with cirrhosis accompanied by ascites; (2) LEfSe analysis revealed that 29 intestinal microbiota (18 in the HBLC-WA group and 11 in the HBLC-WOA group) played a significant role in the disease group. The unclassified Enterobacteriaceae and Klebsiella species in the HBLC-WA group and Enterobacteriaceae in the HBLC-WOA group were positively correlated with the Child-Turcotte-Pugh (CTP) score, prothrombin time, and international normalized ratio score and negatively correlated with albumin and hemoglobin levels (P < 0.05). Escherichia and Shigella in the HBLC-WA group were positively correlated with CTP scores (P < 0.05); (3) The correlation analysis results between the KEGG pathway and 29 specific intestinal microbiota revealed that Enterobacteriaceae and arachidonic acid, α-linolenic acid, glycerolipid metabolism, and fatty acid degradation were positively correlated in the lipid metabolism pathway, while most Enterobacteriaceae were positively correlated with branched-chain amino acid degradation and negatively correlated with aromatic amino acid biosynthesis in the amino acid metabolic pathway. Conclusion: A significant increment of Enterobacteriaceae in the intestines of HBLC-WA patients influenced hepatic reserve function and was associated with amino acid and lipid metabolic pathways. Therefore, attention should be paid to controlling the intestinal microbiota to prevent complications and improve the prognosis in patients with hepatitis B cirrhosis, especially in those with ascites.}, } @article {pmid37871736, year = {2024}, author = {Chai, L and Song, Y and Chen, A and Jiang, L and Deng, H}, title = {Gut microbiota perturbations during larval stages in Bufo gargarizans tadpoles after Cu exposure with or without the presence of Pb.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {340}, number = {Pt 2}, pages = {122774}, doi = {10.1016/j.envpol.2023.122774}, pmid = {37871736}, issn = {1873-6424}, mesh = {Animals ; Larva ; *Gastrointestinal Microbiome ; Lead/toxicity ; Bufonidae ; Bacteria ; }, abstract = {Cu and Pb are ubiquitous environmental contaminants, but there is limited information on their potential impacts on gut microbiota profile in anuran amphibians at different developmental stages during metamorphosis. In this study, Bufo gargarizans tadpoles were chronically exposed to Cu alone or Cu combined with Pb from Gs26 throughout metamorphosis. Morphology of tadpoles, histological characteristic and bacterial community of intestines were evaluated at three developmental stages: Gs33, Gs36, and Gs42. Results showed that Cu and Cu + Pb exposure caused various degrees of morphological and histological changes in guts at tested three stages. In addition, bacterial richness and diversity in tadpoles especially at Gs33 and Gs42 were disturbed by Cu and Cu + Pb. Beta diversity demonstrated that the bacterial community structures were influenced by both heavy metals exposure and developmental stages. Alterations in taxonomic composition were characterized by increased abundance of Proteobacteria and Firmicutes, reduction of Fusobacteriota, as well as decreased Cetobacterium and increased C39 at all three stages. Overall, response of gut bacterial diversity and composition to Cu stress depends on the developmental stage, while the altered patterns of bacterial community at Cu stress could be modified further by the presence of Pb. Moreover, predicted metabolic disorders were associated with shifts in bacterial community, but needs integrated information from metagenomic and metatranscriptomic analyses. These results contribute to the growing body of research about potential ecotoxicological effects of heavy metals on amphibian gut microbiota during metamorphosis.}, } @article {pmid37871442, year = {2024}, author = {Tiwari, N and Santhiya, D and Sharma, JG}, title = {Significance of landfill microbial communities in biodegradation of polyethylene and nylon 6,6 microplastics.}, journal = {Journal of hazardous materials}, volume = {462}, number = {}, pages = {132786}, doi = {10.1016/j.jhazmat.2023.132786}, pmid = {37871442}, issn = {1873-3336}, mesh = {*Microplastics/metabolism ; Polyethylene/chemistry ; Plastics/chemistry ; *Microbiota ; Waste Disposal Facilities ; Biodegradation, Environmental ; }, abstract = {Plastic pollution, particularly microplastics, poses a significant environmental challenge. This study aimed to address the urgent need for sustainable solutions to manage plastic waste. The degradation of polyethylene microplastics (PEMPs) and nylon 6,6 microplastics (NMPs) were investigated using bacterial culture isolates, isolated from a municipal landfill site and identified through 16 S rDNA as well as metagenomics techniques.The study demonstrated for the first time along with degradation mechanism. The isolates identified as Achromobacter xylosoxidans and mixed culture species in dominance of Pulmonis sp. were used to degrade PEMPs and NMPs. Achromobacter xylosoxidans reduced microplastic's dry weight by 26.7% (PEMPs) and 21.3% (NMPs) in 40 days, while the mixed culture achieved weight reductions of 19.3% (PEMPs) and 20% (NMPs). The release of enzymes, laccase and peroxidases revealed C-C bond cleavage and reduced polymer chain length. The thermal studies (TGA and DSC) revealed changes in the thermal stability and transition characteristics of microplastics. The structural alterations on PEMPs and NMPs were recorded by FTIR analysis. Byproducts such as alkanes, esters, aromatic compounds and carboxylic acids released were identified by GC-MS. These results suggest the effectiveness of bacterial isolates in degrading PEMPs and NMPs, with potential for sustainable plastic waste management solutions.}, } @article {pmid37871298, year = {2023}, author = {Kolodnitsky, AS and Ionov, NS and Rudik, AV and Filimonov, DA and Poroikov, VV}, title = {HGMMX: Host Gut Microbiota Metabolism Xenobiotics Database.}, journal = {Journal of chemical information and modeling}, volume = {63}, number = {21}, pages = {6463-6468}, doi = {10.1021/acs.jcim.3c00837}, pmid = {37871298}, issn = {1549-960X}, mesh = {Humans ; *Gastrointestinal Microbiome ; Xenobiotics/chemistry/metabolism/pharmacology ; *Microbiota ; Biotransformation ; Databases, Factual ; }, abstract = {The metagenome of bacteria colonizing the human intestine is a set of genes that is almost 150 times greater than the set of host genes. Some of these genes encode enzymes whose functioning significantly expands the number of potential pathways for xenobiotic metabolism. The resulting metabolites can exhibit activity different from that of the parent compound. This can decrease the efficacy of pharmacotherapy as well as induce undesirable and potentially life-threatening side effects. Thus, analysis of the biotransformation of small drug-like compounds mediated by the gut microbiota is an important step in the development of new pharmaceutical agents and repurposing of the approved drugs. In vitro research, the interaction of drug-like compounds with the gut microbiota is a multistep and time-consuming process. Systematic testing of large sets of chemical structures is associated with a number of challenges, including the lack of standardized techniques and significant financial costs to identify the structure of the final metabolites. Estimation of the compounds' ability to be biotransformed by the gut microbiota and prediction of the structures of their metabolites are possible in silico. However, the development of computational approaches is limited by the lack of information about chemical structures metabolized by microbiota enzymes. The aim of this study is to create a database containing information on the metabolism of drug-like compounds by the gut microbiota. We created the data set containing information about 368 structures metabolized and 310 structures not metabolized by the human gut microbiota. The HGMMX database is freely available at https://www.way2drug.com/hgmmx. The information presented will be useful in the development of computational approaches for analyzing the impact of the human microbiota on metabolism of drug-like molecules.}, } @article {pmid37867065, year = {2023}, author = {Brookes, Z and Teoh, L and Cieplik, F and Kumar, P}, title = {Mouthwash Effects on the Oral Microbiome: Are They Good, Bad, or Balanced?.}, journal = {International dental journal}, volume = {73 Suppl 2}, number = {Suppl 2}, pages = {S74-S81}, pmid = {37867065}, issn = {1875-595X}, mesh = {Humans ; Mouthwashes/pharmacology ; Chlorhexidine/pharmacology ; Mouth ; *Anti-Infective Agents ; Bacteria ; *Microbiota ; }, abstract = {This narrative review describes the oral microbiome, and its role in oral health and disease, before considering the impact of commonly used over-the-counter (OTC) mouthwashes on oral bacteria, viruses, bacteriophages, and fungi that make up these microbial communities in different niches of the mouth. Whilst certain mouthwashes have proven antimicrobial actions and clinical effectiveness supported by robust evidence, this review reports more recent metagenomics evidence, suggesting that mouthwashes such as chlorhexidine may cause "dysbiosis," whereby certain species of bacteria are killed, leaving others, sometimes unwanted, to predominate. There is little known about the effects of mouthwashes on fungi and viruses in the context of the oral microbiome (virome) in vivo, despite evidence that they "kill" certain viral pathogens ex vivo. Evidence for mouthwashes, much like antibiotics, is also emerging with regards to antimicrobial resistance, and this should further be considered in the context of their widespread use by clinicians and patients. Therefore, considering the potential of currently available OTC mouthwashes to alter the oral microbiome, this article finally proposes that the ideal mouthwash, whilst combatting oral disease, should "balance" antimicrobial communities, especially those associated with health. Which antimicrobial mouthwash best fits this ideal remains uncertain.}, } @article {pmid37866373, year = {2023}, author = {Schwartz, DJ and Langdon, A and Sun, X and Langendorf, C and Berthé, F and Grais, RF and Trehan, I and Isanaka, S and Dantas, G}, title = {Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial.}, journal = {The Lancet. Microbe}, volume = {4}, number = {11}, pages = {e931-e942}, pmid = {37866373}, issn = {2666-5247}, support = {R01 GM099538/GM/NIGMS NIH HHS/United States ; 2021081/DDCF/Doris Duke Charitable Foundation/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; TL1 TR000449/TR/NCATS NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; U01 AI123394/AI/NIAID NIH HHS/United States ; K08 AI159384/AI/NIAID NIH HHS/United States ; }, mesh = {Child, Preschool ; Humans ; Infant ; Amoxicillin/pharmacology ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/genetics ; Niger ; Randomized Controlled Trials as Topic ; Retrospective Studies ; *Severe Acute Malnutrition/drug therapy ; }, abstract = {BACKGROUND: Children with severe acute malnutrition are treated with antibiotics as outpatients. We aimed to determine the effect of 7 days of amoxicillin on acute and long-term changes to the gut microbiome and antibiotic resistome in children treated for severe acute malnutrition.

METHODS: We conducted a secondary analysis of a randomised, double-blinded, placebo-controlled trial (NCT01613547) of amoxicillin in children (aged 6-59 months) with severe acute malnutrition treated as outpatients in Madarounfa, Niger. We randomly selected 161 children from the overall cohort (n=2399) for initial 12-week follow-up from Sept 23, 2013 to Feb 3, 2014. We selected a convenience sample of those 161 children, on the basis of anthropometric measures, for follow-up 2 years later (Sept 28 to Oct 27, 2015). Children provided faecal samples at baseline, week 1, week 4, week 8, week 12, and, for those in the 2-year follow-up cohort, week 104. We conducted metagenomic sequencing followed by microbiome and resistome profiling of faecal samples. 38 children without severe acute malnutrition and six children with severe acute malnutrition matching the baseline ages of the original cohort were used as reference controls.

FINDINGS: In the 12-week follow-up group, amoxicillin led to an immediate decrease in gut microbiome richness from 37·6 species (95% CI 32·6-42·7) and Shannon diversity index (SDI) 2·18 (95% CI 1·97-2·39) at baseline to 27·7 species (95% CI 22·9-32·6) species and SDI 1·55 (95% CI 1·35-1·75) at week 1. Amoxicillin increased gut antibiotic resistance gene abundance to 6044 reads per kilobase million (95% CI 4704-7384) at week 1, up from 4800 (3391-6208) at baseline, which returned to baseline 3 weeks later. 35 children were included in the 2-year follow-up; the amoxicillin-treated children (n=22) had increased number of species in the gut microbiome compared with placebo-treated children (n=13; 60·7 [95% CI 54·7-66·6] vs 36·9 [29·4-44·3]). Amoxicillin-treated children had increased Prevotella spp and decreased Bifidobacterium spp relative to age-matched placebo-treated children, indicating a more mature, adult-like microbiome.

INTERPRETATION: Amoxicillin treatment led to acute but not sustained increases in antimicrobial resistance genes and improved gut microbiome maturation 2 years after severe acute malnutrition treatment.

FUNDING: Bill & Melinda Gates Foundation; Médecins sans Frontières Operational Center Paris; National Institute of Allergy and Infectious Diseases; National Institute of General Medical Sciences; Eunice Kennedy Shriver National Institute of Child Health and Human Development; Edward Mallinckrodt Jr Foundation; Doris Duke Foundation.}, } @article {pmid37866247, year = {2023}, author = {Kleikamp, HBC and Grouzdev, D and Schaasberg, P and van Valderen, R and van der Zwaan, R and Wijgaart, RV and Lin, Y and Abbas, B and Pronk, M and van Loosdrecht, MCM and Pabst, M}, title = {Metaproteomics, metagenomics and 16S rRNA sequencing provide different perspectives on the aerobic granular sludge microbiome.}, journal = {Water research}, volume = {246}, number = {}, pages = {120700}, doi = {10.1016/j.watres.2023.120700}, pmid = {37866247}, issn = {1879-2448}, mesh = {*Sewage/chemistry ; RNA, Ribosomal, 16S/genetics ; Bioreactors ; *Microbiota ; Metagenome ; Metagenomics/methods ; }, abstract = {The tremendous progress in sequencing technologies has made DNA sequencing routine for microbiome studies. Additionally, advances in mass spectrometric techniques have extended conventional proteomics into the field of microbial ecology. However, systematic studies that provide a better understanding of the complementary nature of these 'omics' approaches, particularly for complex environments such as wastewater treatment sludge, are urgently needed. Here, we describe a comparative metaomics study on aerobic granular sludge from three different wastewater treatment plants. For this, we employed metaproteomics, whole metagenome, and 16S rRNA amplicon sequencing to study the same granule material with uniform size. We furthermore compare the taxonomic profiles using the Genome Taxonomy Database (GTDB) to enhance the comparability between the different approaches. Though the major taxonomies were consistently identified in the different aerobic granular sludge samples, the taxonomic composition obtained by the different omics techniques varied significantly at the lower taxonomic levels, which impacts the interpretation of the nutrient removal processes. Nevertheless, as demonstrated by metaproteomics, the genera that were consistently identified in all techniques cover the majority of the protein biomass. The established metaomics data and the contig classification pipeline are publicly available, which provides a valuable resource for further studies on metabolic processes in aerobic granular sludge.}, } @article {pmid37866244, year = {2023}, author = {Hu, X and Yue, J and Yao, D and Zhang, X and Li, Y and Hu, Z and Liang, S and Wu, H and Xie, H and Zhang, J}, title = {Plant development alters the nitrogen cycle in subsurface flow constructed wetlands: Implications to the strategies for intensified treatment performance.}, journal = {Water research}, volume = {246}, number = {}, pages = {120750}, doi = {10.1016/j.watres.2023.120750}, pmid = {37866244}, issn = {1879-2448}, mesh = {*Wetlands ; Denitrification ; Nitrogen Cycle ; *Microbiota ; Nitrogen ; Plant Development ; Waste Disposal, Fluid/methods ; }, abstract = {Plant development greatly influences the composition structure and functions of microbial community in constructed wetlands (CWs) via plant root activities. However, our knowledge of the effect of plant development on microbial nitrogen (N) cycle is poorly understood. Here, we investigated the N removal performance and microbial structure in subsurface flow CWs at three time points corresponding to distinct stages of plant development: seedling, mature and wilting. Overall, the water parameters were profoundly affected by plant development with the increased root activities including radial oxygen loss (ROL) and root exudates (REs). The removal efficiency of NH4[+]-N was significantly highest at the mature stage (p < 0.01), while the removal performance of NO3[-]-N at the seedling stage. The highest relative abundances of nitrification- and anammox-related microbes (Nitrospira, Nitrosomonas, and Candidatus Brocadia, etc.) and functional genes (Amo, Hdh, and Hzs) were observed in CWs at the mature stage, which can be attributed to the enhanced intensity of ROL, creating micro-habitat with high DO concentration. On the other hand, the highest relative abundances of denitrification- and DNRA-related microbes (Petrimonas, Geobacter, and Pseudomonas, etc.) and functional genes (Nxr, Nir, and Nar, etc.) were observed in CWs at the seedling and wilting stages, which can be explained by the absence of ROL and biological denitrification inhibitor derived from REs. Results give insights into microbial N cycle in CWs with different stages of plant development. More importantly, a potential solution for intensified N removal via the combination of practical operation and natural regulation is proposed.}, } @article {pmid37866200, year = {2023}, author = {Wang, X and Sun, T and Yan, S and Chen, S and Zhang, Y}, title = {Sediment microbial community characteristics in sea cucumber restocking area.}, journal = {Marine environmental research}, volume = {192}, number = {}, pages = {106233}, doi = {10.1016/j.marenvres.2023.106233}, pmid = {37866200}, issn = {1879-0291}, mesh = {Animals ; Humans ; Geologic Sediments/chemistry ; *Sea Cucumbers/microbiology ; *Microbiota ; Bacteria ; Water ; Nitrogen ; }, abstract = {Variations of microbial species and functional composition in coastal sediment are usually taken as the results of the provision of supplementary nutrients affected by human activities. However, responses of microbiome stability to restocking biological resources remain less understood in coastal benthic systems without nutrient supplements. Here, combined with metagenomics and microbiome co-occurrence networks, the composition, function, and community stability of microbes were evaluated in a coastal area where sea cucumbers (Apostichopus japonicus) restocked after six months. Also, the physicochemical characteristics of sediments and bottom water were analyzed. We found the total organic carbon, total nitrogen, and total phosphorus of sediment did not change significantly in the restocking area after six months, whereas the concentration of dissolved inorganic nitrogen in bottom water increased significantly. Moreover, the relative abundance of Nitrospina at the class level was increased significantly in the restocking area. Also, enzymes related to nitrate reduction and nitrous oxide reductase were increased in the restocking area. Of note, stock enhancement of sea cucumbers altered associations between bacteria rather than their composition. The elimination of negative associations and reduction of the potential keystone taxa in the restocking area indicated destabilized bacterial communities. Our work may contribute to elucidating the response of microbial stability to stock enhancement. This finding also suggests that microbial community stability can be considered as an indicator of ecological risk under the influence of stock enhancement.}, } @article {pmid37863966, year = {2023}, author = {Marcelino, VR and Welsh, C and Diener, C and Gulliver, EL and Rutten, EL and Young, RB and Giles, EM and Gibbons, SM and Greening, C and Forster, SC}, title = {Disease-specific loss of microbial cross-feeding interactions in the human gut.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {6546}, pmid = {37863966}, issn = {2041-1723}, support = {R01 DK133468/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Case-Control Studies ; *Microbiota ; Metagenome ; *Crohn Disease ; }, abstract = {Many gut microorganisms critical to human health rely on nutrients produced by each other for survival; however, these cross-feeding interactions are still challenging to quantify and remain poorly characterized. Here, we introduce a Metabolite Exchange Score (MES) to quantify those interactions. Using metabolic models of prokaryotic metagenome-assembled genomes from over 1600 individuals, MES allows us to identify and rank metabolic interactions that are significantly affected by a loss of cross-feeding partners in 10 out of 11 diseases. When applied to a Crohn's disease case-control study, our approach identifies a lack of species with the ability to consume hydrogen sulfide as the main distinguishing microbiome feature of disease. We propose that our conceptual framework will help prioritize in-depth analyses, experiments and clinical targets, and that targeting the restoration of microbial cross-feeding interactions is a promising mechanism-informed strategy to reconstruct a healthy gut ecosystem.}, } @article {pmid37863223, year = {2024}, author = {Jiménez-Volkerink, SN and Jordán, M and Smidt, H and Minguillón, C and Vila, J and Grifoll, M}, title = {Metagenomic insights into the microbial cooperative networks of a benz(a)anthracene-7,12-dione degrading community from a creosote-contaminated soil.}, journal = {The Science of the total environment}, volume = {907}, number = {}, pages = {167832}, doi = {10.1016/j.scitotenv.2023.167832}, pmid = {37863223}, issn = {1879-1026}, mesh = {Microbial Consortia ; Creosote ; Sand ; *Polycyclic Aromatic Hydrocarbons/metabolism ; Biodegradation, Environmental ; Carbon ; *Soil Pollutants/metabolism ; Soil Microbiology ; Soil ; }, abstract = {Genotoxicity of PAH-contaminated soils can eventually increase after bioremediation due to the formation and accumulation of polar transformation products, mainly oxygenated PAHs (oxy-PAHs). Biodegradation of oxy-PAHs has been described in soils, but information on the microorganisms and mechanisms involved is still scarce. Benz(a)anthracene-7,12-dione (BaAQ), a transformation product from benz(a)anthracene frequently detected in soils, presents higher genotoxic potential than its parent PAH. Here, using sand-in-liquid microcosms we identified a specialized BaAQ-degrading subpopulation in a PAH-contaminated soil. A BaAQ-degrading microbial consortium was obtained by enrichment in sand-in-liquid cultures with BaAQ as sole carbon source, and its metagenomic analysis identified members of Sphingobium, Stenotrophomonas, Pusillimonas, Olivibacter, Pseudomonas, Achromobacter, and Hyphomicrobiales as major components. The integration of data from metabolomic and metagenomic functional gene analyses of the consortium revealed that the BaAQ metabolic pathway was initiated by Baeyer-Villiger monooxygenases (BVMOs). The presence of plasmid pANTQ-1 in the metagenomic sequences, identified in a previous multi-omic characterization of a 9,10-anthraquinone-degrading isolate recovered from the same soil, suggested the occurrence of a horizontal gene transfer event. Further metagenomic analysis of the BaAQ-degrading consortium also provided insights into the potential roles and interactions within the consortium members. Several potential auxotrophies were detected, indicating that relevant nutritional interdependencies and syntrophic associations were taking place within the community members, not only to provide suitable carbon and energy sources, but also to supply essential nutrients and cofactors. Our work confirms the essential role that BVMO may play as a detoxification mechanism to mitigate the risk posed by oxy-PAH formation during bioremediation of contaminated soils.}, } @article {pmid37863066, year = {2023}, author = {Colbert, LE and El Alam, MB and Wang, R and Karpinets, T and Lo, D and Lynn, EJ and Harris, TA and Elnaggar, JH and Yoshida-Court, K and Tomasic, K and Bronk, JK and Sammouri, J and Yanamandra, AV and Olvera, AV and Carlin, LG and Sims, T and Delgado Medrano, AY and Napravnik, TC and O'Hara, M and Lin, D and Abana, CO and Li, HX and Eifel, PJ and Jhingran, A and Joyner, M and Lin, L and Ramondetta, LM and Futreal, AM and Schmeler, KM and Mathew, G and Dorta-Estremera, S and Zhang, J and Wu, X and Ajami, NJ and Wong, M and Taniguchi, C and Petrosino, JF and Sastry, KJ and Okhuysen, PC and Martinez, SA and Tan, L and Mahmud, I and Lorenzi, PL and Wargo, JA and Klopp, AH}, title = {Tumor-resident Lactobacillus iners confer chemoradiation resistance through lactate-induced metabolic rewiring.}, journal = {Cancer cell}, volume = {41}, number = {11}, pages = {1945-1962.e11}, pmid = {37863066}, issn = {1878-3686}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; R25 MD007607/MD/NIMHD NIH HHS/United States ; U54 CA096300/CA/NCI NIH HHS/United States ; }, mesh = {Female ; Humans ; Lactic Acid/metabolism ; *Uterine Cervical Neoplasms/radiotherapy ; Lactobacillus/genetics/metabolism ; *Microbiota ; Tumor Microenvironment ; }, abstract = {Tumor microbiota can produce active metabolites that affect cancer and immune cell signaling, metabolism, and proliferation. Here, we explore tumor and gut microbiome features that affect chemoradiation response in patients with cervical cancer using a combined approach of deep microbiome sequencing, targeted bacterial culture, and in vitro assays. We identify that an obligate L-lactate-producing lactic acid bacterium found in tumors, Lactobacillus iners, is associated with decreased survival in patients, induces chemotherapy and radiation resistance in cervical cancer cells, and leads to metabolic rewiring, or alterations in multiple metabolic pathways, in tumors. Genomically similar L-lactate-producing lactic acid bacteria commensal to other body sites are also significantly associated with survival in colorectal, lung, head and neck, and skin cancers. Our findings demonstrate that lactic acid bacteria in the tumor microenvironment can alter tumor metabolism and lactate signaling pathways, causing therapeutic resistance. Lactic acid bacteria could be promising therapeutic targets across cancer types.}, } @article {pmid37858797, year = {2024}, author = {Yang, J and Wei, H and Lin, Y and Chu, ESH and Zhou, Y and Gou, H and Guo, S and Lau, HCH and Cheung, AHK and Chen, H and To, KF and Sung, JJY and Wang, Y and Yu, J}, title = {High Soluble Fiber Promotes Colorectal Tumorigenesis Through Modulating Gut Microbiota and Metabolites in Mice.}, journal = {Gastroenterology}, volume = {166}, number = {2}, pages = {323-337.e7}, doi = {10.1053/j.gastro.2023.10.012}, pmid = {37858797}, issn = {1528-0012}, mesh = {Mice ; Animals ; *Gastrointestinal Microbiome ; Inulin/pharmacology ; Mice, Inbred C57BL ; Carcinogenesis ; Dietary Fiber/metabolism ; Cellulose/pharmacology ; Azoxymethane ; *Colorectal Neoplasms/pathology ; }, abstract = {BACKGROUND & AIMS: Dietary fibers are mainly fermented by the gut microbiota, but their roles in colorectal cancer (CRC) are largely unclear. Here, we investigated the associations of different fibers with colorectal tumorigenesis in mice.

METHODS: Apc[min/+] mice and C57BL/6 mice with azoxymethane (AOM) injection were used as CRC mouse models. Mice were fed with mixed high-fiber diet (20% soluble fiber and 20% insoluble fiber), high-inulin diet, high-guar gum diet, high-cellulose diet, or diets with different inulin dose. Germ-free mice were used for validation. Fecal microbiota and metabolites were profiled by shotgun metagenomic sequencing and liquid chromatography-mass spectrometry, respectively.

RESULTS: Mixed high-fiber diet promoted colorectal tumorigenesis with increased tumor number and tumor load in AOM-treated and Apc[min/+] mice. Antibiotics use abolished the pro-tumorigenic effect of mixed high-fiber diet, while transplanting stools from mice fed with mixed high-fiber diet accelerated tumor growth in AOM-treated germ-free mice. We therefore characterized the contribution of soluble and insoluble fiber in CRC separately. Our results revealed that soluble fiber inulin or guar gum, but not insoluble fiber cellulose, promoted colorectal tumorigenesis in AOM-treated and Apc[min/+] mice. Soluble fiber induced gut dysbiosis with Bacteroides uniformis enrichment and Bifidobacterium pseudolongum depletion, accompanied by increased fecal butyrate and serum bile acids and decreased inosine. We also identified a positive correlation between inulin dosage and colorectal tumorigenesis. Moreover, transplanting stools from mice fed with high-inulin diet increased colonic cell proliferation and oncogene expressions in germ-free mice.

CONCLUSION: High-dose soluble but not insoluble fiber potentiates colorectal tumorigenesis in a dose-dependent manner by dysregulating gut microbiota and metabolites in mice.}, } @article {pmid37858269, year = {2023}, author = {Labarthe, S and Plancade, S and Raguideau, S and Plaza Oñate, F and Le Chatelier, E and Leclerc, M and Laroche, B}, title = {Four functional profiles for fibre and mucin metabolism in the human gut microbiome.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {231}, pmid = {37858269}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Mucins ; Dysbiosis ; *Microbiota/genetics ; Metagenome ; Dietary Fiber ; Inflammation ; Metagenomics/methods ; }, abstract = {BACKGROUND: With the emergence of metagenomic data, multiple links between the gut microbiome and the host health have been shown. Deciphering these complex interactions require evolved analysis methods focusing on the microbial ecosystem functions. Despite the fact that host or diet-derived fibres are the most abundant nutrients available in the gut, the presence of distinct functional traits regarding fibre and mucin hydrolysis, fermentation and hydrogenotrophic processes has never been investigated.

RESULTS: After manually selecting 91 KEGG orthologies and 33 glycoside hydrolases further aggregated in 101 functional descriptors representative of fibre and mucin degradation pathways in the gut microbiome, we used nonnegative matrix factorization to mine metagenomic datasets. Four distinct metabolic profiles were further identified on a training set of 1153 samples, thoroughly validated on a large database of 2571 unseen samples from 5 external metagenomic cohorts and confirmed with metatranscriptomic data. Profiles 1 and 2 are the main contributors to the fibre-degradation-related metagenome: they present contrasted involvement in fibre degradation and sugar metabolism and are differentially linked to dysbiosis, metabolic disease and inflammation. Profile 1 takes over Profile 2 in healthy samples, and unbalance of these profiles characterize dysbiotic samples. Furthermore, high fibre diet favours a healthy balance between profiles 1 and profile 2. Profile 3 takes over profile 2 during Crohn's disease, inducing functional reorientations towards unusual metabolism such as fucose and H2S degradation or propionate, acetone and butanediol production. Profile 4 gathers under-represented functions, like methanogenesis. Two taxonomic makes up of the profiles were investigated, using either the covariation of 203 prevalent genomes or metagenomic species, both providing consistent results in line with their functional characteristics. This taxonomic characterization showed that profiles 1 and 2 were respectively mainly composed of bacteria from the phyla Bacteroidetes and Firmicutes while profile 3 is representative of Proteobacteria and profile 4 of methanogens.

CONCLUSIONS: Integrating anaerobic microbiology knowledge with statistical learning can narrow down the metagenomic analysis to investigate functional profiles. Applying this approach to fibre degradation in the gut ended with 4 distinct functional profiles that can be easily monitored as markers of diet, dysbiosis, inflammation and disease. Video Abstract.}, } @article {pmid37858227, year = {2023}, author = {Jia, P and Dong, LF and Tu, Y and Diao, QY}, title = {Bacillus subtilis and Macleaya cordata extract regulate the rumen microbiota associated with enteric methane emission in dairy cows.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {229}, pmid = {37858227}, issn = {2049-2618}, mesh = {Female ; Cattle ; Animals ; *Lactation ; Bacillus subtilis ; Rumen/microbiology ; Propionates/metabolism ; Methane/metabolism ; Diet/veterinary ; *Microbiota ; Acetates/metabolism ; Butyrates/metabolism ; Plant Extracts ; Fermentation ; }, abstract = {BACKGROUND: Ruminant livestock production is a considerable source of enteric methane (CH4) emissions. In a previous study, we found that dietary inclusions of Bacillus subtilis (BS) and Macleaya cordata extract (MCE) increased dry matter intake and milk production, while reduced enteric CH4 emission in dairy cows. The objective of this study was to further elucidate the impact of feeding BS and MCE on rumen methanogenesis in dairy cows using rumen metagenomics techniques.

RESULTS: Sixty dairy cows were blocked in 20 groups of 3 cows accordingly to their live weight, milk yield, and days in milk, and within each group, the 3 cows were randomly allocated to 1 of 3 treatments: control diet (CON), control diet plus BS (BS), and control diet plus MCE (MCE). After 75 days of feeding experimental diets, 12 cows were selected from each treatment for collection of rumen samples for the metagenomic sequencing. Results showed that BS decreased ruminal acetate and butyrate, while increased propionate concentrations, resulting in decreased acetate:propionate ratio. The metagenomics analysis revealed that MCE reduced relative abundances of Methanobrevibacter wolinii, Methanobrevibacter sp. AbM4, Candidatus Methanomassiliicoccus intestinalis, Methanobrevibacter cuticularis, Methanomicrobium mobile, Methanobacterium formicicum, and Methanobacterium congolense. Both BS and MCE reduced relative abundances of Methanosphaera sp. WGK6 and Methanosphaera stadtmanae. The co-occurrence network analysis of rumen bacteria and archaea revealed that dietary treatments influenced microbial interaction patterns, with BS and MCE cows having more and stronger associations than CON cows. The random forest and heatmaps analysis demonstrated that the Halopenitus persicus was positively correlated with fat- and protein-corrected milk yield; Clostridium sp. CAG 269, Clostridium sp. 27 14, Haloarcula rubripromontorii, and Methanobrevibacter curvatus were negatively correlated with rumen acetate and butyrate concentrations, and acetate:propionate ratio, whereas Selenomonas rumiantium was positively correlated with those variables.

CONCLUSIONS: The present results provided new information for mitigation of enteric methane emissions of dairy cows by feeding BS and MCE to influence rumen microbial activities. This fundamental knowledge is essential for developing enteric CH4 reduction strategies to mitigate climate change and reduce dietary energy waste. Video Abstract.}, } @article {pmid37856784, year = {2023}, author = {Dang, H and Ewald, JM and Mattes, TE}, title = {Genome-Resolved Metagenomics and Metatranscriptomics Reveal Insights into the Ecology and Metabolism of Anaerobic Microbial Communities in PCB-Contaminated Sediments.}, journal = {Environmental science & technology}, volume = {57}, number = {43}, pages = {16386-16398}, pmid = {37856784}, issn = {1520-5851}, support = {P30 ES005605/ES/NIEHS NIH HHS/United States ; P42 ES013661/ES/NIEHS NIH HHS/United States ; R01 ES032671/ES/NIEHS NIH HHS/United States ; }, mesh = {*Polychlorinated Biphenyls/analysis/chemistry/metabolism ; *Chloroflexi/genetics/chemistry/metabolism ; Anaerobiosis ; Biodegradation, Environmental ; *Microbiota ; Acetates/metabolism ; Geologic Sediments/analysis ; }, abstract = {Growth of organohalide-respiring bacteria such as Dehalococcoides mccartyi on halogenated organics (e.g., polychlorinated biphenyls (PCBs)) at contaminated sites or in enrichment culture requires interaction and support from other microbial community members. To evaluate naturally occurring interactions between Dehalococcoides and key supporting microorganisms (e.g., production of H2, acetate, and corrinoids) in PCB-contaminated sediments, metagenomic and metatranscriptomic sequencing was conducted on DNA and RNA extracted from sediment microcosms, showing evidence of both Dehalococcoides growth and PCB dechlorination. Using a genome-resolved approach, 160 metagenome-assembled genomes (MAGs), including three Dehalococcoides MAGs, were recovered. A novel reductive dehalogenase gene, distantly related to the chlorophenol dehalogenase gene cprA (pairwise amino acid identity: 23.75%), was significantly expressed. Using MAG gene expression data, 112 MAGs were assigned functional roles (e.g., corrinoid producers, acetate/H2 producers, etc.). A network coexpression analysis of all 160 MAGs revealed correlations between 39 MAGs and the Dehalococcoides MAGs. The network analysis also showed that MAGs assigned with functional roles that support Dehalococcoides growth (e.g., corrinoid assembly, and production of intermediates required for corrinoid synthesis) displayed significant coexpression correlations with Dehalococcoides MAGs. This work demonstrates the power of genome-resolved metagenomic and metatranscriptomic analyses, which unify taxonomy and function, in investigating the ecology of dehalogenating microbial communities.}, } @article {pmid37855624, year = {2023}, author = {Salmaso, N and Boscaini, A and Cerasino, L and Pindo, M and Pinto, F and Segata, N and Donati, C}, title = {Draft genome sequence of the anatoxin-a producing cyanobacterium Tychonema bourrellyi B0820 isolated from the epilimnion of the deep Alpine Lake Garda.}, journal = {Microbiology resource announcements}, volume = {12}, number = {11}, pages = {e0084423}, pmid = {37855624}, issn = {2576-098X}, support = {PNRR Missione 4 Componente 2 Dalla ricerca all'impresa Investimento 1.4 Project CN00000033//Italian Ministry of University and Research - NBFC/ ; HORIZON MSCA 2021 SE 01 AlgaeNet4AV Project ID 101086437//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, abstract = {We report the draft genome sequence of strain B0820 of the cyanobacterium Tychonema bourrellyi isolated from the epilimnion of Lake Garda and assembled from a metagenome of a non-axenic culture. The strain analyzed was shown to produce anatoxin-a, a potent neurotoxin that can cause fatal intoxication in exposed organisms.}, } @article {pmid37855616, year = {2023}, author = {Zhang, Y and Zheng, T and Ma, D and Shi, P and Zhang, H and Li, J and Sun, Z}, title = {Probiotics Bifidobacterium lactis M8 and Lactobacillus rhamnosus M9 prevent high blood pressure via modulating the gut microbiota composition and host metabolic products.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0033123}, pmid = {37855616}, issn = {2379-5077}, mesh = {Adult ; Mice ; Animals ; Female ; Humans ; *Gastrointestinal Microbiome ; *Bifidobacterium animalis ; *Lacticaseibacillus rhamnosus ; *Probiotics/therapeutic use ; *Hypertension/prevention & control ; }, abstract = {Elevated blood pressure affects 40% of the adult population, which accounts for high cardiovascular disease risk and further high mortality yearly. The global understanding of the gut microbiome for hypertension may provide important insights into the prevention. Bifidobacterium lactis M8 and Lactobacillus rhamnosus M9 originated from human breast milk, were able to decrease blood pressure, and modified metabolites in a high fructose-induced elevated blood pressure mouse model. Moreover, we found there was a close relationship between unexplored gut microbes and elevated blood pressure. Also, subsequently, the cross-link was explored among gut microbes, metabolites, and some metabolic pathways in gut microbial environment through introducing novel prediction methodology and bioinformatic analysis. It allowed us to hypothesize that probiotics can prevent elevated blood pressure via gut microbiota and related metabolism.Thus, utilization of dietary strategies (such as probiotics) to maintain the blood pressure level is of crucial importance.}, } @article {pmid37855614, year = {2023}, author = {Lopes, AM and Abrantes, J}, title = {On the virome's hidden diversity: lessons from RHDV.}, journal = {mBio}, volume = {14}, number = {6}, pages = {e0197123}, pmid = {37855614}, issn = {2150-7511}, support = {PTDC/CVT-CVT/0143/2021//Fundação para a Ciência e a Tecnologia (FCT)/ ; CEECIND/01388/2017//Fundação para a Ciência e a Tecnologia (FCT)/ ; CEECIND/00078/2017//Fundação para a Ciência e a Tecnologia (FCT)/ ; }, mesh = {*Virome/genetics ; Humans ; *High-Throughput Nucleotide Sequencing ; Animals ; Metagenomics ; Reoviridae/genetics/classification/isolation & purification ; Genetic Variation ; }, abstract = {Emerging infectious diseases are a major challenge to human and animal health. While predicting the emergence of pathogens is complex, the advent of high-throughput sequencing technologies has allowed the rapid identification of unknown microbiology diversity within organisms. Here, we discuss an example of a metatranscriptomics output to decipher viral evolution.}, } @article {pmid37853813, year = {2023}, author = {Yu, S and Wang, H and Cui, L and Wang, J and Zhang, Z and Wu, Z and Lin, X and He, N and Zou, Y and Li, S}, title = {Pectic oligosaccharides ameliorate high-fat diet-induced obesity and hepatic steatosis in association with modulating gut microbiota in mice.}, journal = {Food & function}, volume = {14}, number = {21}, pages = {9892-9906}, doi = {10.1039/d3fo02168h}, pmid = {37853813}, issn = {2042-650X}, mesh = {Animals ; Mice ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Pectins/pharmacology ; Obesity/prevention & control ; *Fatty Liver/drug therapy/etiology/prevention & control ; Oligosaccharides/pharmacology ; Mice, Inbred C57BL ; }, abstract = {Accumulating evidence has shown that gut microbiota and its metabolites have important significance in the etiology of obesity and related disorders. Prebiotics prevent and alleviate obesity by modulating the gut microbiota. However, how pectin oligosaccharides (POS) derived from pectin degradation affect gut microbiota and obesity remains unclear. To investigate the potential anti-obesity effects of POS, mice were fed a high-fat diet (HFD) for 12 weeks and a POS supplement with drinking water during the last 8 weeks. The outcomes demonstrated that POS supplementation in HFD-fed mice decreased body weight (P < 0.01), improved glucose tolerance (P < 0.001), reduced fat accumulation (P < 0.0001) and hepatic steatosis, protected intestinal barrier, and reduced pro-inflammatory cytokine levels. After fecal metagenomic sequencing, the POS corrected the gut microbiota dysbiosis caused by the HFD, as shown by the increased populations of Bifidobacterium, Lactobacillus taiwanensis, and Bifidobacterium animalis, and decreased populations of Alistipes and Erysipelatoclostridium, which were previously considered harmful bacteria. Notably, the changed gut microbiota was associated with the obesity prevention of POS. These findings demonstrate that POS regulates particular gut microbiota, which is essential owing to its ability to prevent disorders associated with obesity.}, } @article {pmid37853062, year = {2023}, author = {Marimón, JM and Sorarrain, A and Ercibengoa, M and Azcue, N and Alonso, M and Vidaur, L}, title = {Lung microbiome on admission in critically ill patients with acute bacterial and viral pneumonia.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {17724}, pmid = {37853062}, issn = {2045-2322}, mesh = {Humans ; *Pneumonia, Pneumococcal ; *Influenza, Human ; Critical Illness ; *COVID-19 ; SARS-CoV-2 ; Lung/microbiology ; Bacteria/genetics ; *Microbiota ; *Pneumonia, Viral ; Firmicutes ; Proteobacteria ; *Community-Acquired Infections/microbiology ; }, abstract = {Composition of pulmonary microbiome of patients with severe pneumonia is poorly known. The aim of this work was to analyse the lung microbiome of patients admitted to the intensive care unit (ICU) with severe community acquired pneumonia (CAP) between 2019 and 2021 in comparison with a control group of 6 patients undergoing digestive surgery. As a second objective, the diagnostic capabilities of metagenomics was also studied in a small group of selected patients. The lung microbiome of patients with viral (5 with Influenza A and 8 with SARS-CoV-2) pneumonia at admission showed a similar diversity as the control group (p = 0.140 and p = 0.213 respectively). Contrarily, the group of 12 patients with pneumococcal pneumonia showed a significant lower Simpson´s index (p = 0.002). In the control group (n = 6) Proteobacteria (36.6%), Firmicutes (24.2%) and Actinobacteria (23.0%) were the predominant phyla. In SARS-CoV-2 patients (n = 8), there was a predominance of Proteobacteria (mean 41.6%) (Moraxella and Pelomonas at the genus level), Actinobacteria (24.6%) (Microbacterium) and Firmicutes (22.8%) mainly Streptococcus, Staphylococcus and Veillonella. In patients with Influenza A pneumonia (n = 5) there was a predominance of Firmicutes (35.1%) mainly Streptococcus followed by Proteobacteria (29.2%) (Moraxella, Acinetobacter and Pelomonas). In the group of pneumococcal pneumonia (n = 12) two phyla predominated: Firmicutes (53.1%) (Streptococcus) and Proteobacteria (36.5%) (Haemophilus). In the 7 patients with non-pneumococcal bacterial pneumonia Haemophilus influenzae (n = 2), Legionella pneumophila (n = 2), Klebsiella pneumoniae, Streptococcus pyogenes and Leptospira were detected by metagenomics, confirming the diagnosis done using conventional microbiological techniques. The diversity of the respiratory microbiome in patients with severe viral pneumonia at ICU admission was similar to that of the control group. Contrarily, patients with pneumococcal pneumonia showed a lower grade of diversity. At initial stages of SARS-CoV-2 infection, no important alterations in the pulmonary microbiome were observed. The analysis of bacterial microbiome showed promising results as a diagnostic tool.}, } @article {pmid37850871, year = {2022}, author = {Zafeiropoulos, H and Beracochea, M and Ninidakis, S and Exter, K and Potirakis, A and De Moro, G and Richardson, L and Corre, E and Machado, J and Pafilis, E and Kotoulas, G and Santi, I and Finn, RD and Cox, CJ and Pavloudi, C}, title = {metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {37850871}, issn = {2047-217X}, mesh = {Workflow ; *Software ; *Genomics ; Metagenomics ; Computational Biology ; Metagenome ; }, abstract = {BACKGROUND: Genomic Observatories (GOs) are sites of long-term scientific study that undertake regular assessments of the genomic biodiversity. The European Marine Omics Biodiversity Observation Network (EMO BON) is a network of GOs that conduct regular biological community samplings to generate environmental and metagenomic data of microbial communities from designated marine stations around Europe. The development of an effective workflow is essential for the analysis of the EMO BON metagenomic data in a timely and reproducible manner.

FINDINGS: Based on the established MGnify resource, we developed metaGOflow. metaGOflow supports the fast inference of taxonomic profiles from GO-derived data based on ribosomal RNA genes and their functional annotation using the raw reads. Thanks to the Research Object Crate packaging, relevant metadata about the sample under study, and the details of the bioinformatics analysis it has been subjected to, are inherited to the data product while its modular implementation allows running the workflow partially. The analysis of 2 EMO BON samples and 1 Tara Oceans sample was performed as a use case.

CONCLUSIONS: metaGOflow is an efficient and robust workflow that scales to the needs of projects producing big metagenomic data such as EMO BON. It highlights how containerization technologies along with modern workflow languages and metadata package approaches can support the needs of researchers when dealing with ever-increasing volumes of biological data. Despite being initially oriented to address the needs of EMO BON, metaGOflow is a flexible and easy-to-use workflow that can be broadly used for one-sample-at-a-time analysis of shotgun metagenomics data.}, } @article {pmid37849822, year = {2023}, author = {Arrieta-Echeverri, MC and Fernandez, GJ and Duarte-Riveros, A and Correa-Álvarez, J and Bardales, JA and Villanueva-Mejía, DF and Sierra-Zapata, L}, title = {Multi-omics characterization of the microbial populations and chemical space composition of a water kefir fermentation.}, journal = {Frontiers in molecular biosciences}, volume = {10}, number = {}, pages = {1223863}, pmid = {37849822}, issn = {2296-889X}, abstract = {In recent years, the popularity of fermented foods has strongly increased based on their proven health benefits and the adoption of new trends among consumers. One of these health-promoting products is water kefir, which is a fermented sugary beverage based on kefir grains (symbiotic colonies of yeast, lactic acid and acetic acid bacteria). According to previous knowledge and the uniqueness of each water kefir fermentation, the following project aimed to explore the microbial and chemical composition of a water kefir fermentation and its microbial consortium, through the integration of culture-dependent methods, compositional metagenomics, and untargeted metabolomics. These methods were applied in two types of samples: fermentation grains (inoculum) and fermentation samples collected at different time points. A strains culture collection of ∼90 strains was established by means of culture-dependent methods, mainly consisting of individuals of Pichia membranifaciens, Acetobacter orientalis, Lentilactobacillus hilgardii, Lacticaseibacillus paracasei, Acetobacter pomorum, Lentilactobacillus buchneri, Pichia kudriavzevii, Acetobacter pasteurianus, Schleiferilactobacillus harbinensis, and Kazachstania exigua, which can be further studied for their use in synthetic consortia formulation. In addition, metabarcoding of each fermentation time was done by 16S and ITS sequencing for bacteria and yeast, respectively. The results show strong population shifts of the microbial community during the fermentation time course, with an enrichment of microbial groups after 72 h of fermentation. Metataxonomics results revealed Lactobacillus and Acetobacter as the dominant genera for lactic acid and acetic acid bacteria, whereas, for yeast, P. membranifaciens was the dominant species. In addition, correlation and systematic analyses of microbial growth patterns and metabolite richness allowed the recognition of metabolic enrichment points between 72 and 96 h and correlation between microbial groups and metabolite abundance (e.g., Bile acid conjugates and Acetobacter tropicalis). Metabolomic analysis also evidenced the production of bioactive compounds in this fermented matrix, which have been associated with biological activities, including antimicrobial and antioxidant. Interestingly, the chemical family of Isoschaftosides (C-glycosyl flavonoids) was also found, representing an important finding since this compound, with hepatoprotective and anti-inflammatory activity, had not been previously reported in this matrix. We conclude that the integration of microbial biodiversity, cultured species, and chemical data enables the identification of relevant microbial population patterns and the detection of specific points of enrichment during the fermentation process of a food matrix, which enables the future design of synthetic microbial consortia, which can be used as targeted probiotics for digestive and metabolic health.}, } @article {pmid37848997, year = {2023}, author = {Zhang, Z and Liu, Y and Zhao, W and Ji, M}, title = {Radiation impacts gene redundancy and biofilm regulation of cryoconite microbiomes in Northern Hemisphere glaciers.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {228}, pmid = {37848997}, issn = {2049-2618}, mesh = {*Ecosystem ; Ice Cover ; *Microbiota/genetics ; Multigene Family ; Climate Change ; }, abstract = {BACKGROUND: Glaciers harbor diverse microorganisms adapted to extreme conditions with high radiation, fluctuating temperature, and low nutrient availability. In glacial ecosystems, cryoconite granules are hotspots of microbial metabolic activity and could influences the biogeochemical cycle on glacier surface. Climate change could influence glacier dynamics by changing regional meteorological factors (e.g., radiation, precipitation, temperature, wind, and evaporation). Moreover, meteorological factors not only influence glacier dynamics but also directly or indirectly influence cryoconite microbiomes. However, the relationship of the meteorological factors and cryoconite microbiome are poorly understood.

RESULTS: Here, we collected 88 metagenomes from 26 glaciers distributed in the Northern Hemisphere with corresponding public meteorological data to reveal the relationship between meteorological factors and variation of cryoconite microbiome. Our results showed significant differences in taxonomic and genomic characteristics between cryoconite generalists and specialists. Additionally, we found that the biogeography of both generalists and specialists was influenced by solar radiation. Specialists with smaller genome size and lower gene redundancy were more abundant under high radiation stress, implying that streamlined genomes are more adapted to high radiation conditions. Network analysis revealed that biofilm regulation is a ubiquitous function in response to radiation stress, and hub genes were associated with the formation and dispersion of biofilms.

CONCLUSION: These findings enhance our understanding of glacier cryoconite microbiome variation on a hemispheric scale and indicate the response mechanisms to radiation stress, which will support forecasts of the ecological consequences of future climate change. Video Abstract.}, } @article {pmid37848477, year = {2023}, author = {Rajeev, M and Jung, I and Lim, Y and Kim, S and Kang, I and Cho, JC}, title = {Metagenome sequencing and recovery of 444 metagenome-assembled genomes from the biofloc aquaculture system.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {707}, pmid = {37848477}, issn = {2052-4463}, support = {KIMST-20210646//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; NRF-2022R1A2C3008502//National Research Foundation of Korea (NRF)/ ; }, mesh = {Animals ; Aquaculture ; Bacteria ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Biofloc technology is increasingly recognised as a sustainable aquaculture method. In this technique, bioflocs are generated as microbial aggregates that play pivotal roles in assimilating toxic nitrogenous substances, thereby ensuring high water quality. Despite the crucial roles of the floc-associated bacterial (FAB) community in pathogen control and animal health, earlier microbiota studies have primarily relied on the metataxonomic approaches. Here, we employed shotgun sequencing on eight biofloc metagenomes from a commercial aquaculture system. This resulted in the generation of 106.6 Gbp, and the reconstruction of 444 metagenome-assembled genomes (MAGs). Among the recovered MAGs, 230 were high-quality (≥90% completeness, ≤5% contamination), and 214 were medium-quality (≥50% completeness, ≤10% contamination). Phylogenetic analysis unveiled Rhodobacteraceae as dominant members of the FAB community. The reported metagenomes and MAGs are crucial for elucidating the roles of diverse microorganisms and their functional genes in key processes such as nitrification, denitrification, and remineralization. This study will contribute to scientific understanding of phylogenetic diversity and metabolic capabilities of microbial taxa in aquaculture environments.}, } @article {pmid37848186, year = {2023}, author = {Cai, Y and Gu, H and Kenney, T}, title = {Rank selection for non-negative matrix factorization.}, journal = {Statistics in medicine}, volume = {42}, number = {30}, pages = {5676-5693}, doi = {10.1002/sim.9934}, pmid = {37848186}, issn = {1097-0258}, support = {RGPIN-2017-05108//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN/4945-2014//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Humans ; *Algorithms ; *Microbiota ; Research Design ; }, abstract = {Non-Negative Matrix Factorization (NMF) is a widely used dimension reduction method that factorizes a non-negative data matrix into two lower dimensional non-negative matrices: one is the basis or feature matrix which consists of the variables and the other is the coefficients matrix which is the projections of data points to the new basis. The features can be interpreted as sub-structures of the data. The number of sub-structures in the feature matrix is also called the rank. This parameter controls the model complexity and is the only tuning parameter for the NMF model. An appropriate rank will extract the key latent features while minimizing the noise from the original data. However due to the large amount of optimization error always present in the NMF computation, the rank selection has been a difficult problem. We develop a novel rank selection method based on hypothesis testing, using a deconvolved bootstrap distribution to assess the significance level accurately. Through simulations, we compare our method with a rank selection method based on hypothesis testing using bootstrap distribution without deconvolution and a method based on cross-validation; we demonstrate that our method is not only accurate at estimating the true ranks for NMF, especially when the features are hard to distinguish, but also efficient at computation. When applied to real microbiome data (eg, OTU data and functional metagenomic data), our method also shows the ability to extract interpretable subcommunities in the data.}, } @article {pmid37846986, year = {2023}, author = {Jiang, H and Luo, J and Liu, Q and Ogunyemi, SO and Ahmed, T and Li, B and Yu, S and Wang, X and Yan, C and Chen, J and Li, B}, title = {Rice bacterial leaf blight drives rhizosphere microbial assembly and function adaptation.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0105923}, pmid = {37846986}, issn = {2165-0497}, support = {27306C2006/ES/NIEHS NIH HHS/United States ; }, mesh = {*Oryza ; Rhizosphere ; Soil Microbiology ; Bacteria ; *Microbiota ; }, abstract = {Our results suggest that rhizosphere bacteria are more sensitive to bacterial leaf blight (BLB) than fungi. BLB infection decreased the diversity of the rhizosphere bacterial community but increased the complexity and size of the rhizosphere microbial community co-occurrence networks. In addition, the relative abundance of the genera Streptomyces, Chitinophaga, Sphingomonas, and Bacillus increased significantly. Finally, these findings contribute to the understanding of plant-microbiome interactions by providing critical insight into the ecological mechanisms by which rhizosphere microbes respond to phyllosphere diseases. In addition, it also lays the foundation and provides data to support the use of plant microbes to promote plant health in sustainable agriculture, providing critical insight into ecological mechanisms.}, } @article {pmid37846600, year = {2024}, author = {Li, Y and Liu, Q and Zhang, L and Zou, J and He, R and Zhou, Y and Qian, C and Zhu, Y and Chen, R and Zhang, Y and Cai, P and Wang, M and Shao, W and Ji, M and Wu, H and Zhang, F and Liu, Z and Liu, Y}, title = {Washed microbiota transplantation reduces glycemic variability in unstable diabetes.}, journal = {Journal of diabetes}, volume = {16}, number = {2}, pages = {e13485}, pmid = {37846600}, issn = {1753-0407}, support = {2022YFA0806103//National Key R&D Program of China/ ; 81770778//National Natural Science Foundation of China/ ; 81800724//National Natural Science Foundation of China/ ; 81800735//National Natural Science Foundation of China/ ; 82070849//National Natural Science Foundation of China/ ; 82270871//National Natural Science Foundation of China/ ; BK20180672//Natural Science Foundation of Jiangsu Province/ ; 18KJB310005//Natural Science Foundation of the Jiangsu Higher Education Institutions/ ; BE2022794//the Jiangsu Provincial Key Research Development Program/ ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Diabetes Mellitus/therapy ; Insulin ; *Gastrointestinal Microbiome/genetics ; Glucose ; }, abstract = {BACKGROUND: Dysbiosis of gut microbiota is causally linked to impaired host glucose metabolism. We aimed to study effects of the new method of fecal microbiota transplantation, washed microbiota transplantation (WMT), on reducing glycemic variability (GV) in unstable diabetes.

METHODS: Fourteen eligible patients received three allogenic WMTs and were followed up at 1 week, 1 month, and 3 months. Primary outcomes were daily insulin dose, glucose excursions during meal tests, and GV indices calculated from continuous monitoring or self-monitoring glucose values. Secondary outcomes were multiomics data, including 16S rRNA gene sequencing, metagenomics, and metabolomics to explore underlying mechanisms.

RESULTS: Daily insulin dose and glucose excursions markedly dropped, whereas GV indices significantly improved up to 1 month. WMT increased gut microbial alpha diversity, beta diversity, and network complexity. Taxonomic changes featured lower abundance of genera Bacteroides and Escherichia-Shigella, and higher abundance of genus Prevotella. Metagenomics functional annotations revealed enrichment of distinct microbial metabolic pathways, including methane biosynthesis, citrate cycle, amino acid degradation, and butyrate production. Derived metabolites correlated significantly with improved GV indices. WMT did not change circulating inflammatory cytokines, enteroendocrine hormones, or C-peptide.

CONCLUSIONS: WMT showed strong ameliorating effect on GV, raising the possibility of targeting gut microbiota as an effective regimen to reduce GV in diabetes.}, } @article {pmid37843556, year = {2023}, author = {Zheng, X and Hu, N and Liu, J and Zhao, K and Li, H and Wang, J and Zhang, M and Zhang, L and Song, L and Lyu, Y and Cui, M and Ding, L and Wang, J}, title = {Cervicovaginal microbiota disorder combined with the change of cytosine phosphate guanine motif- toll like receptor 9 axis was associated with cervical cancerization.}, journal = {Journal of cancer research and clinical oncology}, volume = {149}, number = {19}, pages = {17371-17381}, pmid = {37843556}, issn = {1432-1335}, mesh = {Female ; Humans ; Bacteria ; *Carcinogenesis ; *Microbiota ; Phosphates ; *Toll-Like Receptor 9/genetics/metabolism ; *Uterine Cervical Dysplasia/genetics/microbiology/pathology ; *Uterine Cervical Neoplasms/genetics/microbiology/pathology ; *Vagina/microbiology ; *Cervix Uteri/microbiology ; }, abstract = {BACKGROUND: Convincing studies demonstrated that cervicovaginal microbiota disorder and toll-like receptor 9 (TLR9) high expression were related to cervical carcinogenesis. However, the effects of cervicovaginal microbiota integration TLR9 in cervical cancerization are unclear. Based on the biological basis that unmethylated cytosine-phosphate-guanine (CpG) motifs of bacteria could activate TLR9, we explored the effects of cervicovaginal microbiota disorder and CpG motif-TLR9 axis change in cervical carcinogenesis.

METHODS: A total of 341 participants, including 124 normal cervical (NC), 90 low-grade cervical intraepithelial neoplasia (CIN1), 78 high-grade cervical intraepithelial neoplasia (CIN2/3) and 49 squamous cervical cancer (SCC), diagnosed by pathology were enrolled in the study. Here, metagenomic shotgun sequencing was used to reveal cervicovaginal microbiota characteristics, and TLR9 protein was detected by western blotting.

RESULTS: Our results showed that the diversity of cervicovaginal microbiota gradually increased along with the poor development of cervical lesions, showing the abundance of Lactobacillus crispatus and Lactobacillus iners decreased, while the abundance of pathogenic bacteria gradually increased. The level of TLR9 expression was gradually increased with cervicovaginal microbiota diversity increasing, the abundance of Lactobacillus decreasing, and we found a positive correlation dependency relationship (r = 0.384, P = 0.002) between TLR9 and GTCGTT motif content. Stratified analysis based on HPV16 infection, we found that the characteristics of cervicovaginal microbiota and increased TLR9 expression were also closely related to HPV16 infection.

CONCLUSIONS: Cervicovaginal microbiota dysbiosis might lead to the CpG motif increased, which was closely associated with TLR9 high expression, and ultimately might promote the progression of cervical lesions.}, } @article {pmid37843286, year = {2023}, author = {Claesen, J and Brown, JM}, title = {Predicting cardiovascular disease risk from gut microbial genes.}, journal = {mBio}, volume = {14}, number = {6}, pages = {e0197023}, pmid = {37843286}, issn = {2150-7511}, support = {R01 DK120679/DK/NIDDK NIH HHS/United States ; R01 AI153173/AI/NIAID NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; R01 DK130227/DK/NIDDK NIH HHS/United States ; P50 AA024333/AA/NIAAA NIH HHS/United States ; R01 AI153173/AI/NIAID NIH HHS/United States ; R01 DK130227, R01 DK120679//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; P50 AA024333/AA/NIAAA NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/genetics ; *Cardiovascular Diseases/genetics/microbiology/metabolism ; *Methylamines/metabolism ; Humans ; *Bacteria/genetics/metabolism/classification ; Feces/microbiology ; Metagenomics ; Risk Factors ; }, abstract = {Gut bacteria-driven production of trimethylamine (TMA) is strongly associated with cardiovascular disease. Borton et al. (mBio 14:e01511-23, 2023, https://doi.org/10.1128/mbio.01511-23) introduce the Methylated Amine Gene Inventory of Catabolism database (MAGICdb), comprehensively cataloging pathways involved in TMA metabolism. By integrating transcriptomics, proteomics, and metagenomic data, this work identifies key bacterial players in the process and can link gut microbial gene content to fecal TMA concentrations. This work shows that methylated amine metabolism is a keystone microbiome process carried out by a small proportion of the community. Proatherogenic pathways are more widely distributed among the gut microbiota, and new TMA-reducing genera were identified that might offer new potential for probiotic strategies or targeted microbiome interventions. Remarkably, MAGICdb's power to predict cardiovascular disease risk matches an approach using more traditional lipid risk factors. This open source will be a valuable tool for the community to link methylated amine metabolism to gut microbiome-related human health conditions.}, } @article {pmid37841999, year = {2023}, author = {Rodenes-Gavidia, A and Lamelas, A and Bloor, S and Hobson, A and Treadway, S and Haworth, J and Vijayakumar, V and Naghibi, M and Day, R and Chenoll, E}, title = {An insight into the functional alterations in the gut microbiome of healthy adults in response to a multi-strain probiotic intake: a single arm open label trial.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1240267}, pmid = {37841999}, issn = {2235-2988}, mesh = {Humans ; Young Adult ; Dietary Supplements ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; *Lacticaseibacillus rhamnosus ; *Probiotics ; }, abstract = {BACKGROUND: Probiotic supplements, by definition, provide a benefit to the host, but few studies have investigated the effect of probiotic supplements in healthy adult populations.

PURPOSE: The present, single arm, open label clinical trial, evaluated compositional and functional changes in the fecal microbiome of healthy adults after supplementation with a 14-strain probiotic.

METHODS: We analysed the effect of a 14-strain probiotic blend (Bacillus subtilis NCIMB 30223, Bifidobacterium bifidum NCIMB 30179, B. breve NCIMB 30180, B. infantis NCIMB 30181, B. longum NCIMB 30182, Lactobacillus helveticus NCIMB 30184, L. delbrueckii subsp. bulgaricus NCIMB 30186, Lacticaseibacillus paracasei NCIMB 30185, Lactiplantibacillus plantarum NCIMB 30187, Lacticaseibacillus rhamnosus NCIMB 30188, L. helveticus NCIMB 30224, Lactobacillus salivarius NCIMB 30225, Lactococcus lactis subsp. lactis NCIMB 30222, and Streptococcus thermophilus NCIMB 30189), on the faecal microbiota of healthy young adults (n=41) in a single arm study. The adults consumed 4 capsules daily of the 14 strain blend(8 billion colony forming units/day) for 8 weeks. Compositional and functional changes in faecal microbiota before and after supplementation were assessed using shotgun metagenomic sequencing. Fasting breath analysis, faecal biochemistry and bowel habits were also assessed.

RESULTS: In healthy adult participants, no significant changes to the overall alpha- or beta-diversity was observed after 8 weeks of multi-strain probiotic supplementation. However, in a simplified model that considered only time and individual differences, significant decreases (p < 0.05) in family Odoribacteraceae and Bacteroidaceae abundance and a significant increase (p < 0.05) in genus Megamonas abundance were observed. At a functional level, there were significant changes in functional gene abundance related to several functional pathways, including phenylalanine metabolism, O-antigen nucleotide sugar biosynthesis, bacterial chemotaxis, and flagellar assembly. No significant changes in stool form or frequency, fecal biochemistry, or methane and hydrogen breath tests were observed.

CONCLUSION: In healthy young adults, overall alpha- and beta-diversity did not change in response to probiotic intake even though modest compositional changes at the family and genus level were observed. However, at functional level, results identified changes in gene abundance for several functional pathways.}, } @article {pmid37839685, year = {2024}, author = {Xiang, F and Zhang, Q and Xu, X and Zhang, Z}, title = {Black soldier fly larvae recruit functional microbiota into the intestines and residues to promote lignocellulosic degradation in domestic biodegradable waste.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {340}, number = {Pt 1}, pages = {122676}, doi = {10.1016/j.envpol.2023.122676}, pmid = {37839685}, issn = {1873-6424}, mesh = {Animals ; Larva ; *Microbiota ; Intestines ; *Diptera ; }, abstract = {Lignocellulose is an important component of domestic biodegradable waste (DBW), and its complex structure makes it an obstacle in the biological treatment of DBW. Here, we identify black soldier fly larvae (Hermetia illucens L., BSFL) as a bioreactor for lignocellulose degradation in DBW based on their ability to effectively recruit lignocellulose-degrading bacteria. This study mainly examined the lignocellulose degradation, dynamic succession of the microbial community, gene expression of carbohydrate-active enzymes (CAZymes), and co-occurrence network analysis. Investigation of lignocellulose degradation by BSFL within 14 days indicated that the lignocellulose biodegradation rate in the larvae treatment (LT, 26.5%) group was higher than in natural composting (NC, 4.06%). In order to gain a more comprehensive understanding of microbiota, we conducted metagenomic sequencing of larvae intestines (LI), along with the LT and NC. The relative abundance of lignocellulose-degrading bacteria and CAZymes genes in LT and LI were higher than those in NC based on metagenomics sequencing. Importantly, genes coding cellulase and hemicellulase in LI were 3.36- and 2.79-fold higher, respectively, than that in LT, while the ligninase genes in LT were 1.82-fold higher than in LI. A co-occurrence network analysis identified Enterocluster and Luteimonas as keystone taxa in larvae intestines and residues, respectively, with a synergistic relationship to lignocellulose-degrading bacteria. The mechanism of recruiting functional bacteria through the larvae intestines promoted lignocellulose degradation in DBW, improving the efficiency of BSFL biotechnology and resource regeneration.}, } @article {pmid37838714, year = {2023}, author = {Schaerer, L and Putman, L and Bigcraft, I and Byrne, E and Kulas, D and Zolghadr, A and Aloba, S and Ong, R and Shonnard, D and Techtmann, S}, title = {Coexistence of specialist and generalist species within mixed plastic derivative-utilizing microbial communities.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {224}, pmid = {37838714}, issn = {2049-2618}, mesh = {Polyethylene/chemistry/metabolism ; *Microbiota ; Metagenome ; *Phthalic Acids ; }, abstract = {BACKGROUND: Plastic-degrading microbial isolates offer great potential to degrade, transform, and upcycle plastic waste. Tandem chemical and biological processing of plastic wastes has been shown to substantially increase the rates of plastic degradation; however, the focus of this work has been almost entirely on microbial isolates (either bioengineered or naturally occurring). We propose that a microbial community has even greater potential for plastic upcycling. A microbial community has greater metabolic diversity to process mixed plastic waste streams and has built-in functional redundancy for optimal resilience.

RESULTS: Here, we used two plastic-derivative degrading communities as a model system to investigate the roles of specialist and generalist species within the microbial communities. These communities were grown on five plastic-derived substrates: pyrolysis treated high-density polyethylene, chemically deconstructed polyethylene terephthalate, disodium terephthalate, terephthalamide, and ethylene glycol. Short-read metagenomic and metatranscriptomic sequencing were performed to evaluate activity of microorganisms in each treatment. Long-read metagenomic sequencing was performed to obtain high-quality metagenome assembled genomes and evaluate division of labor.

CONCLUSIONS: Data presented here show that the communities are primarily dominated by Rhodococcus generalists and lower abundance specialists for each of the plastic-derived substrates investigated here, supporting previous research that generalist species dominate batch culture. Additionally, division of labor may be present between Hydrogenophaga terephthalate degrading specialists and lower abundance protocatechuate degrading specialists. Video Abstract.}, } @article {pmid37837778, year = {2024}, author = {Wu, Z and Yu, X and Ji, Y and Liu, G and Gao, P and Xia, L and Li, P and Liang, B and Freilich, S and Gu, L and Qiao, W and Jiang, J}, title = {Flexible catabolism of monoaromatic hydrocarbons by anaerobic microbiota adapting to oxygen exposure.}, journal = {Journal of hazardous materials}, volume = {462}, number = {}, pages = {132762}, doi = {10.1016/j.jhazmat.2023.132762}, pmid = {37837778}, issn = {1873-3336}, mesh = {Benzene/metabolism ; Anaerobiosis ; Nitrates ; Hydrocarbons/metabolism ; Benzene Derivatives/metabolism ; Toluene/metabolism ; Xylenes/metabolism ; Biodegradation, Environmental ; *Microbiota ; Oxygen ; *Ammonium Compounds ; Carbon ; }, abstract = {Microbe-mediated anaerobic degradation is a practical method for remediation of the hazardous monoaromatic hydrocarbons (BTEX, including benzene, toluene, ethylbenzene and xylenes) under electron-deficient contaminated sites. However, how do the anaerobic functional microbes adapt to oxygen exposure and flexibly catabolize BTEX remain poorly understood. We investigated the switches of substrate spectrum and bacterial community upon oxygen perturbation in a nitrate-amended anaerobic toluene-degrading microbiota which was dominated by Aromatoleum species. DNA-stable isotope probing demonstrated that Aromatoleum species was involved in anaerobic mineralization of toluene. Metagenome-assembled genome of Aromatoleum species harbored both the nirBD-type genes for nitrate reduction to ammonium coupled with toluene oxidation and the additional meta-cleavage pathway for aerobic benzene catabolism. Once the anaerobic microbiota was fully exposed to oxygen and benzene, 1.05 ± 0.06% of Diaphorobacter species rapidly replaced Aromatoleum species and flourished to 96.72 ± 0.01%. Diaphorobacter sp. ZM was isolated, which was not only able to utilize benzene as the sole carbon source for aerobic growth and but also innovatively reduce nitrate to ammonium with citrate/lactate/glucose as the carbon source under anaerobic conditions. This study expands our understanding of the adaptive mechanism of microbiota for environmental redox disturbance and provides theoretical guidance for the bioremediation of BTEX-contaminated sites.}, } @article {pmid37837767, year = {2023}, author = {Lyu, Y and Zhang, J and Chen, Y and Li, Q and Ke, Z and Zhang, S and Li, J}, title = {Distinct diversity patterns and assembly mechanisms of prokaryotic microbial sub-community in the water column of deep-sea cold seeps.}, journal = {Journal of environmental management}, volume = {348}, number = {}, pages = {119240}, doi = {10.1016/j.jenvman.2023.119240}, pmid = {37837767}, issn = {1095-8630}, mesh = {*Ecosystem ; Water ; Geologic Sediments ; Archaea/genetics ; Bacteria/genetics ; *Microbiota ; Methane ; Sulfur ; Phylogeny ; }, abstract = {Methane leakage from deep-sea cold seeps has a major impact on marine ecosystems. Microbes sequester methane in the water column of cold seeps and can be divided into abundant and rare groups. Both abundant and rare groups play an important role in cold seep ecosystems, and the environmental heterogeneity in cold seeps may enhance conversion between taxa with different abundances. Yet, the environmental stratification and assembly mechanisms of these microbial sub-communities remain unclear. We investigated the diversities and assembly mechanisms in microbial sub-communities with distinct abundance in the deep-sea cold seep water column, from 400 m to 1400 m. We found that bacterial β-diversity, as measured by Sørensen dissimilarities, exhibited a significant species turnover pattern that was influenced by several environmental factors including depth, temperature, SiO3[2-], and salinity. In contrast, archaeal β-diversity showed a relatively high percentage of nestedness pattern, which was driven by the levels of soluble reactive phosphate and SiO3[2-]. During the abundance dependency test, abundant taxa of both bacteria and archaea showed a significant species turnover, while the rare taxa possessed a higher percentage of nestedness. Stochastic processes were prominent in shaping the prokaryotic community, but deterministic processes were more pronounced for the abundant taxa than rare ones. Furthermore, the metagenomics results revealed that the abundances of methane oxidation, sulfur oxidation, and nitrogen fixation-related genes and related microbial groups were significantly higher in the bottom water. Our results implied that the carbon, sulfur, and nitrogen cycles were potentially strongly coupled in the bottom water. Overall, the results obtained in this study highlight taxonomic and abundance-dependent microbial community diversity patterns and assembly mechanisms in the water column of cold seeps, which will help understand the impacts of fluid seepage from the sea floor on the microbial community in the water column and further provide guidance for the management of cold seep ecosystem under future environmental pressures.}, } @article {pmid37836447, year = {2023}, author = {Wang, H and Lv, X and Zhao, S and Yuan, W and Zhou, Q and Sadiq, FA and Zhao, J and Lu, W and Wu, W}, title = {Weight Loss Promotion in Individuals with Obesity through Gut Microbiota Alterations with a Multiphase Modified Ketogenic Diet.}, journal = {Nutrients}, volume = {15}, number = {19}, pages = {}, pmid = {37836447}, issn = {2072-6643}, support = {2022YFF1100403//National Key Research and Development Program of China/ ; }, mesh = {Diet, Reducing ; *Gastrointestinal Microbiome ; Weight Loss ; Humans ; Ketone Bodies ; Bacteroidetes ; Clostridiales ; *Diet, Ketogenic ; Obesity ; }, abstract = {The occurrence of obesity and related metabolic disorders is rising, necessitating effective long-term weight management strategies. With growing interest in the potential role of gut microbes due to their association with responses to different weight loss diets, understanding the mechanisms underlying the interactions between diet, gut microbiota, and weight loss remains a challenge. This study aimed to investigate the potential impact of a multiphase dietary protocol, incorporating an improved ketogenic diet (MDP-i-KD), on weight loss and the gut microbiota. Using metagenomic sequencing, we comprehensively analyzed the taxonomic and functional composition of the gut microbiota in 13 participants before and after a 12-week MDP-i-KD intervention. The results revealed a significant reduction in BMI (9.2% weight loss) among obese participants following the MDP-i-KD intervention. Machine learning analysis identified seven key microbial species highly correlated with MDP-i-KD, with Parabacteroides distasonis exhibiting the highest response. Additionally, the co-occurrence network of the gut microbiota in post-weight-loss participants demonstrated a healthier state. Notably, metabolic pathways related to nucleotide biosynthesis, aromatic amino acid synthesis, and starch degradation were enriched in pre-intervention participants and positively correlated with BMI. Furthermore, species associated with obesity, such as Blautia obeum and Ruminococcus torques, played pivotal roles in regulating these metabolic activities. In conclusion, the MDP-i-KD intervention may assist in weight management by modulating the composition and metabolic functions of the gut microbiota. Parabacteroides distasonis, Blautia obeum, and Ruminococcus torques could be key targets for gut microbiota-based obesity interventions.}, } @article {pmid37833670, year = {2023}, author = {Pu, S and Wang, M and Wang, J and Zhang, Q and Ma, X and Wang, R and Yu, S and Wang, L and Pan, Y}, title = {Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions that respond to ovulation regulation in the mouse endometrium.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {615}, pmid = {37833670}, issn = {1471-2164}, support = {Grant No. 20JR10RA561//National Science Foundation for Distinguished Young Scholars of Gansu province/ ; No. 20200624RCC0022//Innovative Talent Project of Gansu Province/ ; Grant No. 32160859//National Natural Science Foundation of China/ ; No. Gaufx-02Y10//Fuxi Foundation for Youth Talent at Gansu Agricultural University/ ; Grant No. GSAU-RCZX201701//Scientific Research Foundation for the New Scholars, Gansu Agricultural University/ ; }, mesh = {Female ; Animals ; Mice ; *Endometrium/metabolism ; Reproduction ; Ovulation/genetics ; *Microbiota/genetics ; Steroids ; }, abstract = {Understanding the microflora inhabiting the reproductive tract is important for a better understanding of female physiology and reproductive health. The endometrial fluid from mice in three reproductive stages (A: Unproductive mice; B: Postovulatory mice; C: Postpartum mice) was extracted for microbial DNA extraction and sequencing. Phenotypic and functional analyses of endometrial microbial enrichment was undertaken using LefSe. The results showed 95 genera and 134 species of microorganisms in the uteri of mice. There were differentially distributed genera, among which Lactobacillus, Enterococcus, and Streptococcus were more abundant in the endometrial fluid of mice in the unproductive group. That of mice in the postovulatory group was colonized with Salmonella enterica and Campylobacter and was mainly enriched in metabolic pathways and steroid biosynthesis. The presence of Chlamydia, Enterococcus, Pseudomonadales, Acinetobacter, and Clostridium in the endometrial fluid of postpartum mice, in addition to the enrichment of the endocrine system and the Apelin and FoxO signaling pathways, resulted in a higher number of pathogenic pathways than in the other two groups. The results showed that the microbial diversity characteristics in the endometrium of mice in different reproductive states differed and that they could be involved in the regulation of animal reproduction through metabolic pathways and steroid biosynthesis, suggesting that reproductive diseases induced by microbial diversity alterations in the regulation of animal reproduction cannot be ignored.}, } @article {pmid37832571, year = {2023}, author = {Musisi, E and Wyness, A and Eldirdiri, S and Dombay, E and Mtafya, B and Ntinginya, NE and Heinrich, N and Kibiki, GS and Hoelscher, M and Boeree, M and Aarnoutse, R and Gillespie, SH and Sabiiti, W and , }, title = {Effect of seven anti-tuberculosis treatment regimens on sputum microbiome: a retrospective analysis of the HIGHRIF study 2 and PanACEA MAMS-TB clinical trials.}, journal = {The Lancet. Microbe}, volume = {4}, number = {11}, pages = {e913-e922}, doi = {10.1016/S2666-5247(23)00191-X}, pmid = {37832571}, issn = {2666-5247}, support = {MC_UU_00004/04/MRC_/Medical Research Council/United Kingdom ; MC_UU_12023/27/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; Antitubercular Agents/pharmacology ; Drug Therapy, Combination ; *Microbiota ; Moxifloxacin/pharmacology ; Retrospective Studies ; RNA, Ribosomal, 16S ; Sputum/microbiology ; Tanzania ; *Tuberculosis/drug therapy ; *Tuberculosis, Pulmonary/drug therapy ; Clinical Trials as Topic ; }, abstract = {BACKGROUND: Respiratory tract microbiota has been described as the gatekeeper for respiratory health. We aimed to assess the impact of standard-of-care and experimental anti-tuberculosis treatment regimens on the respiratory microbiome and implications for treatment outcomes.

METHODS: In this retrospective study, we analysed the sputum microbiome of participants with tuberculosis treated with six experimental regimens versus standard-of-care who were part of the HIGHRIF study 2 (NCT00760149) and PanACEA MAMS-TB (NCT01785186) clinical trials across a 3-month treatment follow-up period. Samples were from participants in Mbeya, Kilimanjaro, Bagamoyo, and Dar es Salaam, Tanzania. Experimental regimens were composed of different combinations of rifampicin (R), isoniazid (H), pyrazinamide (Z), ethambutol (E), moxifloxacin (M), and a new drug, SQ109 (Q). Reverse transcription was used to create complementary DNA for each participant's total sputum RNA and the V3-V4 region of the 16S rRNA gene was sequenced using the Illumina metagenomic technique. Qiime was used to analyse the amplicon sequence variants and estimate alpha diversity. Descriptive statistics were applied to assess differences in alpha diversity pre-treatment and post-treatment initiation and the effect of each treatment regimen.

FINDINGS: Sequence data were obtained from 397 pre-treatment and post-treatment samples taken between Sept 26, 2008, and June 30, 2015, across seven treatment regimens. Pre-treatment microbiome (206 genera) was dominated by Firmicutes (2860 [44%] of 6500 amplicon sequence variants [ASVs]) at the phylum level and Streptococcus (2340 [36%] ASVs) at the genus level. Two regimens had a significant depressing effect on the microbiome after 2 weeks of treatment, HR20mg/kgZM (Shannon diversity index p=0·0041) and HR35mg/kgZE (p=0·027). Gram-negative bacteria were the most sensitive to bactericidal activity of treatment with the highest number of species suppressed being under the moxifloxacin regimen. By week 12 after treatment initiation, microbiomes had recovered to pre-treatment level except for the HR35mg/kgZE regimen and for genus Mycobacterium, which did not show recovery across all regimens. Tuberculosis culture conversion to negative by week 8 of treatment was associated with clearance of genus Neisseria, with a 98% reduction of the pre-treatment level.

INTERPRETATION: HR20mg/kgZM was effective against tuberculosis without limiting microbiome recovery, which implies a shorter efficacious anti-tuberculosis regimen with improved treatment outcomes might be achieved without harming the commensal microbiota.

FUNDING: European and Developing Countries Clinical Trials Partnership and German Ministry of Education and Research.}, } @article {pmid37832205, year = {2024}, author = {Zhang, J and Du, R and Niu, J and Ban, S and Zhang, Y and Xu, L and Nie, H and Wu, Q and Xu, Y}, title = {Daqu and environmental microbiota regulate fatty acid biosynthesis via driving the core microbiota in soy sauce aroma type liquor fermentation.}, journal = {International journal of food microbiology}, volume = {408}, number = {}, pages = {110423}, doi = {10.1016/j.ijfoodmicro.2023.110423}, pmid = {37832205}, issn = {1879-3460}, mesh = {Fermentation ; Odorants/analysis ; *Soy Foods/analysis ; Pichia/genetics ; *Microbiota/genetics ; Alcoholic Beverages/analysis ; Fatty Acids/analysis ; }, abstract = {Fatty acids are considered as important compounds for the aroma and taste of Chinese liquor. Revealing the core microbiota related with fatty acid biosynthesis and how they are influenced are essential to control fatty acids in spontaneous Chinese liquor fermentation. Herein, we identified the core microbiota related with fatty acid biosynthesis based on their microbial abundance, abundance and expression level of genes related with fatty acid biosynthesis, using high-throughput amplicon sequencing, metagenomic and metatranscriptomic analysis, respectively. Acetilactobacillus, Kroppenstedtia, Saccharomyces, Paecilomyces and Pichia were identified as the core microbiota (the criteria for identifying core microbiota: average relative abundance ≥1 %, average abundance of related genes >400 fragments per kilobase of transcript per million fragments mapped [FPKM], and expression level of related genes >1000 FPKM) related with fatty acid biosynthesis. SourceTracker analysis showed that Daqu mainly provided Kroppenstedtia (34.01 %) and Acetilactobacillus (3.31 %). Ground mainly provided Pichia (47.47 %), Saccharomyces (16.17 %) and Paecilomyces (8.55 %). Structural equation model revealed that Daqu and environmental microbiota drove the core microbiota (P < 0.05), and the core microbiota drove the biosynthesis of fatty acids (P < 0.05). This work revealed the important role of Daqu and environmental microbiota in fatty acid biosynthesis in liquor fermentation. It would benefit controlling fatty acids in liquor fermentation, and improving the liquor quality.}, } @article {pmid37830742, year = {2024}, author = {Wigren, MA and Johnson, TA and Griffitt, RJ and Hay, AG and Knott, JA and Sepúlveda, MS}, title = {Limited impact of weathered residues from the Deepwater Horizon oil spill on the gut-microbiome and foraging behavior of sheepshead minnows (Cyprinodon variegatus).}, journal = {Journal of toxicology and environmental health. Part A}, volume = {87}, number = {1}, pages = {1-21}, doi = {10.1080/15287394.2023.2265413}, pmid = {37830742}, issn = {1528-7394}, mesh = {Animals ; *Killifishes/genetics ; *Petroleum/toxicity ; *Gastrointestinal Microbiome ; *Petroleum Pollution/adverse effects ; RNA, Ribosomal, 16S ; *Microbiota ; *Cyprinidae ; Hydrocarbons ; Gulf of Mexico ; *Water Pollutants, Chemical/toxicity ; *Polycyclic Aromatic Hydrocarbons ; }, abstract = {The Deepwater Horizon disaster of April 2010 was the largest oil spill in U.S. history and exerted catastrophic effects on several ecologically important fish species in the Gulf of Mexico (GoM). Within fish, the microbiome plays a key symbiotic role in maintaining host health and aids in acquiring nutrients, supporting immune function, and modulating behavior. The aim of this study was to examine if exposure to weathered oil might produce significant shifts in fish gut-associated microbial communities as determined from taxa and genes known for hydrocarbon degradation, and whether foraging behavior was affected. The gut microbiome (16S rRNA and shotgun metagenomics) of sheepshead minnow (Cyprinodon variegatus) was characterized after fish were exposed to oil in High Energy Water Accommodated Fractions (HEWAF; tPAH = 81.1 ± 12.4 µg/L) for 7 days. A foraging behavioral assay was used to determine feeding efficiency before and after oil exposure. The fish gut microbiome was not significantly altered in alpha or beta diversity. None of the most abundant taxa produced any significant shifts as a result of oil exposure, with only rare taxa showing significant shifts in abundance between treatments. However, several bioindicator taxa known for hydrocarbon degradation were detected in the oil treatment, primarily Sphingomonas and Acinetobacter. Notably, the genus Stenotrophomonas was detected in high abundance in 16S data, which previously was not described as a core member of fish gut microbiomes. Data also demonstrated that behavior was not significantly affected by oil exposure. Potential low bioavailability of the oil may have been a factor in our observation of minor shifts in taxa and no behavioral effects. This study lays a foundation for understanding the microbiome of captive sheepshead minnows and indicates the need for further research to elucidate the responses of the fish gut-microbiome under oil spill conditions.}, } @article {pmid37830211, year = {2024}, author = {Hoang, J and Gilbertson-White, S and Cady, N and Yadav, M and Shahi, S and Aguilar, L and Mangalam, AK and Cherwin, C}, title = {Preliminary Analysis of Gut Microbiome and Gastrointestinal Symptom Burden in Breast Cancer Patients Receiving Chemotherapy Compared to Healthy Controls.}, journal = {Biological research for nursing}, volume = {26}, number = {2}, pages = {219-230}, pmid = {37830211}, issn = {1552-4175}, support = {P20 NR018081/NR/NINR NIH HHS/United States ; P30 ES005605/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; *Breast Neoplasms/drug therapy ; Symptom Burden ; Gastrointestinal Tract/microbiology ; Feces/microbiology ; Bacteria/genetics ; }, abstract = {BACKGROUND: Alterations in the naturally occurring bacteria of the gut, known as the gastrointestinal (GI) microbiome, may influence GI symptoms in women with breast cancer.

OBJECTIVE: This work aims to describe GI symptom occurrence, duration, severity, and distress and measures of the GI microbiome among women with breast cancer receiving chemotherapy compared to age- and sex-matched healthy controls.

INTERVENTIONS/METHODS: 22 women with breast cancer receiving chemotherapy and 17 healthy control women provided stool specimens and GI symptom data using the modified Memorial Symptom Assessment Scale (MSAS). The fecal microbiome was profiled by metagenomic sequencing of 16S Ribosomal RNA (rRNA). GI microbiome was compared between groups using alpha-diversity (Observed OTU number and Shannon index), beta-diversity (UniFrac distances), and relative abundance of select genera.

RESULTS: GI symptoms with high symptom reports among breast cancer patients included nausea, diarrhea, flatulence, dry mouth, taste change, and poor appetite. Indices of differential abundance (beta diversity) significantly distinguished between breast cancer patients and healthy controls. Unique bacterial features differentiating the 2 groups were Prevotella_9, Akkermansia, Lachnospira, Lachnospiraceae_NK4A136, Lachnoclostridium, and Oscillibacter.

CONCLUSIONS: Gut bacteria are associated with GI inflammation and mucus degradation, suggesting the potential role of the GI microbiome in GI symptom burden. Understanding the influence of GI bacteria on gut health and symptoms will help harness the enormous potential of the GI microbiome as a future diagnostic and therapeutic agent to reduce the symptom burden associated with chemotherapy.}, } @article {pmid37828802, year = {2024}, author = {Zhao, J and Feng, T and An, X and Chen, X and Han, N and Wang, J and Chang, G and Hou, X}, title = {Livestock grazing is associated with the gut microbiota and antibiotic resistance genes in sympatric plateau pika (Ochotona curzoniae).}, journal = {Integrative zoology}, volume = {19}, number = {4}, pages = {646-661}, doi = {10.1111/1749-4877.12778}, pmid = {37828802}, issn = {1749-4877}, support = {2019QZKK0501//Second Tibetan Plateau Scientific Expedition and Research Program (STEP)/ ; 32172436//National Natural Science Foundation of China/ ; 2022K-16//Science and Technology Program of Shaanxi Academy of Science/ ; 2019QZKK0501//Scond Tibetan Plateau Scientific Expedition and Research/ ; 32172436//National Natural Science Foundation of China/ ; 2022K-16//Science and Technology Program of Shaanxi Academy of Science/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Lagomorpha/genetics ; *Drug Resistance, Microbial/genetics ; Herbivory ; Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Livestock/microbiology ; Genes, Bacterial ; }, abstract = {With the overuse of antibiotics in health care and animal husbandry, antibiotic resistance becomes a serious threat to public health. Antibiotic residues from veterinary medicine have increased the dissemination of antibiotic resistance genes (ARGs) by horizontal gene transfer globally, leading to the enrichment of ARGs in wildlife. Plateau pika (Ochotona curzoniae) is a small herbivore endemic to the Qinghai-Tibetan Plateau. Previous studies reveal that pika evolves a coprophagy behavior toward cohabitated yak, which makes the pika population a potential reservoir of ARGs. Yet, little is known about the resistome of pika under different grazing intensities. Here, we sampled the cecum content of pika from three different grazing intensity areas in the Qinghai-Tibetan Plateau to evaluate the effect of grazing on its gut microbiota and resistome. By using the 16S full-length amplicon and metagenomic sequencing, our study revealed that livestock grazing significantly altered the gut microbial community of plateau pika as compared to prohibited grazing areas. We found bacterial lineage Prevotellaceae, Lachnospirales, and RF39 increased in grazing areas. Analysis of the resistome revealed that pika from continuous grazing areas enriched a higher abundance of colistin (MCR) and streptogramin (vat) resistance genes. Moreover, we observed significant correlations between the gut microbial community, ARGs, and mobile genetic element profiles, hinting that pika gut microbiota was an important shaping force of the resistome. In future studies, the continuous monitoring of wildlife gut resistome and environmental antibiotic residues is imperative for a better understanding and for tackling the horizontal gene transfer of ARGs across the wildlife-livestock interface.}, } @article {pmid37828586, year = {2023}, author = {Zhang, P and Wang, X and Li, S and Cao, X and Zou, J and Fang, Y and Shi, Y and Xiang, F and Shen, B and Li, Y and Fang, B and Zhang, Y and Guo, R and Lv, Q and Zhang, L and Lu, Y and Wang, Y and Yu, J and Xie, Y and Wang, R and Chen, X and Yu, J and Zhang, Z and He, J and Zhan, J and Lv, W and Nie, Y and Cai, J and Xu, X and Hu, J and Zhang, Q and Gao, T and Jiang, X and Tan, X and Xue, N and Wang, Y and Ren, Y and Wang, L and Zhang, H and Ning, Y and Chen, J and Zhang, L and Jin, S and Ren, F and Ehrlich, SD and Zhao, L and Ding, X}, title = {Metagenome-wide analysis uncovers gut microbial signatures and implicates taxon-specific functions in end-stage renal disease.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {226}, pmid = {37828586}, issn = {1474-760X}, mesh = {Humans ; Metagenome ; *Gastrointestinal Microbiome ; *Kidney Failure, Chronic ; *Microbiota ; *Renal Insufficiency, Chronic/genetics/metabolism ; Feces ; Clostridiales ; }, abstract = {BACKGROUND: The gut microbiota plays a crucial role in regulating host metabolism and producing uremic toxins in patients with end-stage renal disease (ESRD). Our objective is to advance toward a holistic understanding of the gut ecosystem and its functional capacity in such patients, which is still lacking.

RESULTS: Herein, we explore the gut microbiome of 378 hemodialytic ESRD patients and 290 healthy volunteers from two independent cohorts via deep metagenomic sequencing and metagenome-assembled-genome-based characterization of their feces. Our findings reveal fundamental alterations in the ESRD microbiome, characterized by a panel of 348 differentially abundant species, including ESRD-elevated representatives of Blautia spp., Dorea spp., and Eggerthellaceae, and ESRD-depleted Prevotella and Roseburia species. Through functional annotation of the ESRD-associated species, we uncover various taxon-specific functions linked to the disease, such as antimicrobial resistance, aromatic compound degradation, and biosynthesis of small bioactive molecules. Additionally, we show that the gut microbial composition can be utilized to predict serum uremic toxin concentrations, and based on this, we identify the key toxin-contributing species. Furthermore, our investigation extended to 47 additional non-dialyzed chronic kidney disease (CKD) patients, revealing a significant correlation between the abundance of ESRD-associated microbial signatures and CKD progression.

CONCLUSION: This study delineates the taxonomic and functional landscapes and biomarkers of the ESRD microbiome. Understanding the role of gut microbiota in ESRD could open new avenues for therapeutic interventions and personalized treatment approaches in patients with this condition.}, } @article {pmid37828152, year = {2023}, author = {Wu-Woods, NJ and Barlow, JT and Trigodet, F and Shaw, DG and Romano, AE and Jabri, B and Eren, AM and Ismagilov, RF}, title = {Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples.}, journal = {Nature methods}, volume = {20}, number = {11}, pages = {1672-1682}, pmid = {37828152}, issn = {1548-7105}, support = {RC2 DK133947/DK/NIDDK NIH HHS/United States ; T32 GM150375/GM/NIGMS NIH HHS/United States ; RC2 DK122394/DK/NIDDK NIH HHS/United States ; T32 GM112592/GM/NIGMS NIH HHS/United States ; F30 DK121470/DK/NIDDK NIH HHS/United States ; R01 DK067180/DK/NIDDK NIH HHS/United States ; P30 DK042086/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Metagenome ; *Microbiota/genetics ; Bacteria/genetics ; DNA ; Gastrointestinal Tract ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Mammals/genetics ; }, abstract = {Host-microbe interactions have been linked to health and disease states through the use of microbial taxonomic profiling, mostly via 16S ribosomal RNA gene sequencing. However, many mechanistic insights remain elusive, in part because studying the genomes of microbes associated with mammalian tissue is difficult due to the high ratio of host to microbial DNA in such samples. Here we describe a microbial-enrichment method (MEM), which we demonstrate on a wide range of sample types, including saliva, stool, intestinal scrapings, and intestinal mucosal biopsies. MEM enabled high-throughput characterization of microbial metagenomes from human intestinal biopsies by reducing host DNA more than 1,000-fold with minimal microbial community changes (roughly 90% of taxa had no significant differences between MEM-treated and untreated control groups). Shotgun sequencing of MEM-treated human intestinal biopsies enabled characterization of both high- and low-abundance microbial taxa, pathways and genes longitudinally along the gastrointestinal tract. We report the construction of metagenome-assembled genomes directly from human intestinal biopsies for bacteria and archaea at relative abundances as low as 1%. Analysis of metagenome-assembled genomes reveals distinct subpopulation structures between the small and large intestine for some taxa. MEM opens a path for the microbiome field to acquire deeper insights into host-microbe interactions by enabling in-depth characterization of host-tissue-associated microbial communities.}, } @article {pmid37823484, year = {2024}, author = {Straub, TJ and Lombardo, MJ and Bryant, JA and Diao, L and Lodise, TP and Freedberg, DE and Wortman, JR and Litcofsky, KD and Hasson, BR and McGovern, BH and Ford, CB and Henn, MR}, title = {Impact of a Purified Microbiome Therapeutic on Abundance of Antimicrobial Resistance Genes in Patients With Recurrent Clostridioides difficile Infection.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {78}, number = {4}, pages = {833-841}, pmid = {37823484}, issn = {1537-6591}, support = {//Seres Therapeutics/ ; }, mesh = {Adult ; Humans ; Female ; Aged ; Male ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Fecal Microbiota Transplantation ; *Clostridioides difficile/genetics ; Drug Resistance, Bacterial ; *Microbiota ; *Clostridium Infections/microbiology ; Bacteria ; Firmicutes ; }, abstract = {BACKGROUND: The gastrointestinal microbiota is an important line of defense against colonization with antimicrobial resistant (AR) bacteria. In this post hoc analysis of the phase 3 ECOSPOR III trial, we assessed impact of a microbiota-based oral therapeutic (fecal microbiota spores, live; VOWST Oral Spores [VOS], formerly SER-109]; Seres Therapeutics) compared with placebo, on AR gene (ARG) abundance in patients with recurrent Clostridioides difficile infection (rCDI).

METHODS: Adults with rCDI were randomized to receive VOS or placebo orally for 3 days following standard-of-care antibiotics. ARG and taxonomic profiles were generated using whole metagenomic sequencing of stool at baseline and weeks 1, 2, 8, and 24 posttreatment.

RESULTS: Baseline (n = 151) and serial posttreatment stool samples collected through 24 weeks (total N = 472) from 182 patients (59.9% female; mean age: 65.5 years) in ECOSPOR III as well as 68 stool samples obtained at a single time point from a healthy cohort were analyzed. Baseline ARG abundance was similar between arms and significantly elevated versus the healthy cohort. By week 1, there was a greater decline in ARG abundance in VOS versus placebo (P = .003) in association with marked decline of Proteobacteria and repletion of spore-forming Firmicutes, as compared with baseline. We observed abundance of Proteobacteria and non-spore-forming Firmicutes were associated with ARG abundance, while spore-forming Firmicutes abundance was negatively associated.

CONCLUSIONS: This proof-of-concept analysis suggests that microbiome remodeling with Firmicutes spores may be a potential novel approach to reduce ARG colonization in the gastrointestinal tract.}, } @article {pmid37821326, year = {2023}, author = {Muñoz-Tamayo, R and Davoudkhani, M and Fakih, I and Robles-Rodriguez, CE and Rubino, F and Creevey, CJ and Forano, E}, title = {Review: Towards the next-generation models of the rumen microbiome for enhancing predictive power and guiding sustainable production strategies.}, journal = {Animal : an international journal of animal bioscience}, volume = {17 Suppl 5}, number = {}, pages = {100984}, doi = {10.1016/j.animal.2023.100984}, pmid = {37821326}, issn = {1751-732X}, mesh = {Animals ; *Rumen/metabolism ; *Microbiota ; Ruminants/metabolism ; Metagenome ; Fermentation ; Methane/metabolism ; }, abstract = {The rumen ecosystem harbours a galaxy of microbes working in syntrophy to carry out a metabolic cascade of hydrolytic and fermentative reactions. This fermentation process allows ruminants to harvest nutrients from a wide range of feedstuff otherwise inaccessible to the host. The interconnection between the ruminant and its rumen microbiota shapes key animal phenotypes such as feed efficiency and methane emissions and suggests the potential of reducing methane emissions and enhancing feed conversion into animal products by manipulating the rumen microbiota. Whilst significant technological progress in omics techniques has increased our knowledge of the rumen microbiota and its genome (microbiome), translating omics knowledge into effective microbial manipulation strategies remains a great challenge. This challenge can be addressed by modelling approaches integrating causality principles and thus going beyond current correlation-based approaches applied to analyse rumen microbial genomic data. However, existing rumen models are not yet adapted to capitalise on microbial genomic information. This gap between the rumen microbiota available omics data and the way microbial metabolism is represented in the existing rumen models needs to be filled to enhance rumen understanding and produce better predictive models with capabilities for guiding nutritional strategies. To fill this gap, the integration of computational biology tools and mathematical modelling frameworks is needed to translate the information of the metabolic potential of the rumen microbes (inferred from their genomes) into a mathematical object. In this paper, we aim to discuss the potential use of two modelling approaches for the integration of microbial genomic information into dynamic models. The first modelling approach explores the theory of state observers to integrate microbial time series data into rumen fermentation models. The second approach is based on the genome-scale network reconstructions of rumen microbes. For a given microorganism, the network reconstruction produces a stoichiometry matrix of the metabolism. This matrix is the core of the so-called genome-scale metabolic models which can be exploited by a plethora of methods comprised within the constraint-based reconstruction and analysis approaches. We will discuss how these methods can be used to produce the next-generation models of the rumen microbiome.}, } @article {pmid37816267, year = {2023}, author = {Berglund, F and Rodríguez-Molina, D and Gradisteanu Pircalabioru, G and Blaak, H and Chifiriuc, MC and Czobor Barbu, I and Flach, CF and Gheorghe-Barbu, I and Măruțescu, L and Popa, M and de Roda Husman, AM and Wengenroth, L and Schmitt, H and Larsson, DGJ}, title = {The resistome and microbiome of wastewater treatment plant workers - The AWARE study.}, journal = {Environment international}, volume = {180}, number = {}, pages = {108242}, doi = {10.1016/j.envint.2023.108242}, pmid = {37816267}, issn = {1873-6750}, mesh = {Humans ; Female ; Wastewater ; Genes, Bacterial ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology/analysis ; *Microbiota/genetics ; *Water Purification ; *Disinfectants ; }, abstract = {Urban wastewater treatment plants harbor a large collection of antibiotic resistant enteric bacteria. It is therefore reasonable to hypothesize that workers at such plants would possess a more diverse set of resistant enteric bacteria, compared to the general population. To address this hypothesis, we have compared the fecal microbiome and resistome of 87 workers at wastewater treatment plants (WWTPs) from Romania and the Netherlands to those of 87 control individuals, using shotgun metagenomics. Controlling for potential confounders, neither the total antibiotic resistance gene (ARG) abundance, nor the overall bacterial composition were significantly different between the two groups. If anything, the ARG richness was slightly lower in WWTP workers, and in a stratified analysis the total ARG abundance was significantly lower in Dutch workers compared to Dutch control participants. We identified country of residence, together with recent antibiotic intake in the Dutch population, as the largest contributing factors to the total abundance of ARGs. A striking side-finding was that sex was associated with carriage of disinfectant resistance genes, with women in both Romania and the Netherlands having significantly higher abundance compared to men. A follow up investigation including an additional 313 publicly available samples from healthy individuals from three additional countries showed that the difference was significant for three genes conferring resistance to chemicals commonly used in cosmetics and cleaning products. We therefore hypothesize that the use of cosmetics and, possibly, cleaning products leads to higher abundance of disinfectant resistance genes in the microbiome of the users. Altogether, this study shows that working at a WWTP does not lead to a higher abundance or diversity of ARGs and no large shifts in the overall gut microbial composition in comparison to participants not working at a WWTP. Instead, other factors such as country of residence, recent antibiotic intake and sex seem to play a larger role.}, } @article {pmid37816004, year = {2023}, author = {Gu, CH and Khatib, LA and Fitzgerald, AS and Graham-Wooten, J and Ittner, CA and Sherrill-Mix, S and Chuang, Y and Glaser, LJ and Meyer, NJ and Bushman, FD and Collman, RG}, title = {Tracking gut microbiome and bloodstream infection in critically ill adults.}, journal = {PloS one}, volume = {18}, number = {10}, pages = {e0289923}, pmid = {37816004}, issn = {1932-6203}, support = {R01 HL137006/HL/NHLBI NIH HHS/United States ; R01 HL137915/HL/NHLBI NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; R33 HL137063/HL/NHLBI NIH HHS/United States ; R35 HL161196/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; Adult ; *Gastrointestinal Microbiome/genetics ; *Bacteremia/microbiology ; Critical Illness ; *Sepsis ; Bacteria/genetics ; }, abstract = {BACKGROUND: The gut microbiome is believed to contribute to bloodstream infection (BSI) via translocation of dominant gut bacteria in vulnerable patient populations. However, conclusively linking gut and blood organisms requires stringent approaches to establish strain-level identity.

METHODS: We enrolled a convenience cohort of critically ill patients and investigated 86 bloodstream infection episodes that occurred in 57 patients. Shotgun metagenomic sequencing was used to define constituents of their gut microbiomes, and whole genome sequencing and assembly was done on 23 unique bloodstream isolates that were available from 21 patients. Whole genome sequences were downloaded from public databases and used to establish sequence-identity distribution and define thresholds for unrelated genomes of BSI species. Gut microbiome reads were then aligned to whole genome sequences of the cognate bloodstream isolate and unrelated database isolates to assess identity.

RESULTS: Gut microbiome constituents matching the bloodstream infection species were present in half of BSI episodes, and represented >30% relative abundance of gut sequences in 10% of episodes. Among the 23 unique bloodstream organisms that were available for whole genome sequencing, 14 were present in gut at the species level. Sequence alignment applying defined thresholds for identity revealed that 6 met criteria for identical strains in blood and gut, but 8 did not. Sequence identity between BSI isolates and gut microbiome reads was more likely when the species was present at higher relative abundance in gut.

CONCLUSION: In assessing potential gut source for BSI, stringent sequence-based approaches are essential to determine if organisms responsible for BSI are identical to those in gut: of 14 evaluable patients in which the same species was present in both sites, they were identical in 6/14, but were non-identical in 8/14 and thus inconsistent with gut source. This report demonstrates application of sequencing as a key tool to investigate infection tracking within patients.}, } @article {pmid37815749, year = {2024}, author = {Adıgüzel, AO and Şen, F and Könen-Adıgüzel, S and Kıdeyş, AE and Karahan, A and Doruk, T and Tunçer, M}, title = {Identification of Cutinolytic Esterase from Microplastic-Associated Microbiota Using Functional Metagenomics and Its Plastic Degrading Potential.}, journal = {Molecular biotechnology}, volume = {66}, number = {10}, pages = {2995-3012}, pmid = {37815749}, issn = {1559-0305}, support = {120Z329//Türkiye Bilimsel ve Teknolojik Araştırma Kurumu/ ; }, mesh = {*Metagenomics/methods ; *Esterases/metabolism/genetics/chemistry ; *Microbiota ; Escherichia coli/genetics/metabolism ; Microplastics/metabolism ; Biodegradation, Environmental ; Hydrogen-Ion Concentration ; Temperature ; Triglycerides/metabolism ; Plastics/metabolism/chemistry ; Substrate Specificity ; }, abstract = {Plastic pollution has threatened biodiversity and human health by shrinking habitats, reducing food quality, and limiting the activities of organisms. Therefore, global interest in discovering novel enzymes capable of degrading plastics has increased considerably. Within this context, the functional metagenomic approach, which allows for unlocking the functional potential of uncultivable microbial biodiversity, was used to discover a plastic-degrading enzyme. First, metagenomic libraries derived from microplastic-associated microbiota were screened for esterases capable of degrading both tributyrin and polycaprolactone. Clone KAD01 produced esterase highly active against p-nitrophenyl esters (C2-C16). The gene corresponding to the enzyme activity showed moderate identity (≤ 55.94%) to any known esterases/cutinases. The gene was extracellularly expressed with a 6× histidine tag in E. coli BL21(DE3), extracellularly. Titer of the enzyme (CEstKAD01) was raised from 21.32 to 35.17 U/mL by the statistical optimization of expression conditions and media components. CEstKAD01 was most active at pH 7.0 and 30 °C. It was noteworthy stable over a wide pH (6.0-10.0) and temperature (20-50 °C). The enzyme was active and stable in elevated NaCl concentrations up to 12% (w/v). Pre-incubation of CEstKAD01 with Mg[2+], Mn[2+], and Ca[2+] increased the enzyme activity. CEstKAD01 displayed an excellent tolerance against various chemicals and solvents. It was determined that 1 mg of the enzyme caused the release of 5.39 ± 0.18 mM fatty acids from 1 g apple cutin in 120 min. Km and Vmax values of CEstKAD01 against p-nitrophenyl butyrate were calculated to be 1.48 mM and 20.37 µmol/min, respectively. The enzyme caused 6.94 ± 0.55, 8.71 ± 0.56, 7.47 ± 0.47, and 9.22 ± 0.18% of weight loss in polystyrene, high-density polyethylene, low-density polyethylene, and polyvinyl chloride after 30-day incubation. The scanning electron microscopy (SEM) analysis indicated the formation of holes and pits on the plastic surfaces supporting the degradation. In addition, the change in chemical structure in plastics treated with the enzyme was determined by Fourier Transform Infrared Spectroscopy (FTIR) analysis. Finally, the degradation products were found to have no genotoxic potential. To our knowledge, no cutinolytic esterase with the potential to degrade polystyrene (PS), high-density polyethylene (HDPE), low-density polyethylene (LDPE), and polyvinyl chloride (PVC) has been identified from metagenomes derived from microplastic-associated microbiota.}, } @article {pmid37814055, year = {2023}, author = {Wang, Y and Gai, J and Hou, Q and Zhao, H and Shan, C and Guo, Z}, title = {Ultra-high-depth macrogenomic sequencing revealed differences in microbial composition and function between high temperature and medium-high temperature Daqu.}, journal = {World journal of microbiology & biotechnology}, volume = {39}, number = {12}, pages = {337}, pmid = {37814055}, issn = {1573-0972}, support = {2023//Science and technology plan project of Xinjiang Production and Construction Corps/ ; 2023//Science and technology plan project of Xinjiang Production and Construction Corps/ ; 2020kypytd009//Hubei university of arts and science cultivation fund for teachers' scientific research ability: technological innovation team/ ; }, mesh = {*Alcoholic Beverages/microbiology ; Temperature ; Bacteria/genetics ; *Microbiota ; Fermentation ; }, abstract = {Complex microorganisms in Daqu of different temperatures play a vital role in the taste, flavor and quality of Baijiu during fermentation. However, understanding the functional diversity of the whole microbial community between the Daqus of two different temperatures (high temperature Daqu, HD and medium-high temperature Daqu, MD) remains a major challenge. Here, a systematic study of the microbial diversity, functions as well as physiological and biochemical indexes of Daqu are described. The results revealed that the Daqu exhibited unique characteristics. In particular, the diversity of microorganisms in HD and MD was high, with 44 species including 14 novel species (Sphingomonas sp. is the main novel species) detected in all samples. Their profiles of carbohydrate-active enzymes and specific functional components supported the fact that these species were involved in flavor formation. The Daqu microbiome consisted of a high proportion of phage, providing evidence of phage infection/genome integration and horizontal gene transfer from phage to bacteria. Such processes would also regulate Daqu microbiomes and thus flavor quality. These results enrich current knowledge of Daqu and can be used to promote the development of Baijiu fermentation technology.}, } @article {pmid37813622, year = {2024}, author = {Ling, CW and Zhong, H and Zeng, FF and Chen, G and Fu, Y and Wang, C and Zhang, ZQ and Cao, WT and Sun, TY and Ding, D and Liu, YH and Dong, HL and Jing, LP and Ling, W and Zheng, JS and Chen, YM}, title = {Cohort Profile: Guangzhou Nutrition and Health Study (GNHS): A Population-based Multi-omics Study.}, journal = {Journal of epidemiology}, volume = {34}, number = {6}, pages = {301-306}, pmid = {37813622}, issn = {1349-9092}, mesh = {Humans ; Middle Aged ; Aged ; Female ; China/epidemiology ; Male ; Adult ; Aged, 80 and over ; Cohort Studies ; *Nutritional Status ; Metabolic Diseases/epidemiology ; Gastrointestinal Microbiome ; Biomarkers/blood ; Multiomics ; }, abstract = {BACKGROUND: The Guangzhou Nutrition and Health Study (GNHS) aims to assess the determinants of metabolic disease in nutritional aspects, as well as other environmental and genetic factors, and explore possible biomarkers and mechanisms with multi-omics integration.

METHODS: The population-based sample of adults in Guangzhou, China (baseline: 40-83 years old; n = 5,118) was followed up about every 3 years. All are tracked via on-site follow-up and health information systems. We assessed detailed information on lifestyle factors, physical activities, dietary assessments, psychological health, cognitive function, body measurements, and muscle function. Instrument tests included dual-energy X-ray absorptiometry scanning, carotid artery and liver ultrasonography evaluations, vascular endothelial function evaluation, upper-abdomen and brain magnetic resonance imaging, and 14-day real-time continuous glucose monitoring tests. We also measured multi-omics, including host genome-wide genotyping, serum metabolome and proteome, gut microbiome (16S rRNA sequencing, metagenome, and internal transcribed spacer 2 sequencing), and fecal metabolome and proteome.

RESULTS: The baseline surveys were conducted from 2008 to 2015. Now, we have completed 3 waves. The 3rd and 4th follow-ups have started but have yet to end. A total of 5,118 participants aged 40-83 took part in the study. The median age at baseline was approximately 59.0 years and the proportion of female participants was about 69.4%. Among all the participants, 3,628 (71%) completed at least one on-site follow-up, with a median duration of 9.48 years.

CONCLUSION: The cohort will provide data that will be influential in establishing the role of nutrition in metabolic diseases with multi-omics.}, } @article {pmid37812548, year = {2023}, author = {Ma, L and Deng, W and Bai, Y and Du, Z and Xiao, M and Wang, L and Li, J and Nandi, AK}, title = {Identifying Phage Sequences From Metagenomic Data Using Deep Neural Network With Word Embedding and Attention Mechanism.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {20}, number = {6}, pages = {3772-3785}, doi = {10.1109/TCBB.2023.3322870}, pmid = {37812548}, issn = {1557-9964}, mesh = {*Bacteriophages/genetics ; Neural Networks, Computer ; Algorithms ; Metagenome/genetics ; *Microbiota ; }, abstract = {Phages are the functional viruses that infect bacteria and they play important roles in microbial communities and ecosystems. Phage research has attracted great attention due to the wide applications of phage therapy in treating bacterial infection in recent years. Metagenomics sequencing technique can sequence microbial communities directly from an environmental sample. Identifying phage sequences from metagenomic data is a vital step in the downstream of phage analysis. However, the existing methods for phage identification suffer from some limitations in the utilization of the phage feature for prediction, and therefore their prediction performance still need to be improved further. In this article, we propose a novel deep neural network (called MetaPhaPred) for identifying phages from metagenomic data. In MetaPhaPred, we first use a word embedding technique to encode the metagenomic sequences into word vectors, extracting the latent feature vectors of DNA words. Then, we design a deep neural network with a convolutional neural network (CNN) to capture the feature maps in sequences, and with a bi-directional long short-term memory network (Bi-LSTM) to capture the long-term dependencies between features from both forward and backward directions. The feature map consists of a set of feature patterns, each of which is the weighted feature extracted by a convolution filter with convolution kernels in the CNN slide along the input feature vectors. Next, an attention mechanism is used to enhance contributions of important features. Experimental results on both simulated and real metagenomic data with different lengths demonstrate the superiority of the proposed MetaPhaPred over the state-of-the-art methods in identifying phage sequences.}, } @article {pmid37811944, year = {2023}, author = {Gihawi, A and Ge, Y and Lu, J and Puiu, D and Xu, A and Cooper, CS and Brewer, DS and Pertea, M and Salzberg, SL}, title = {Major data analysis errors invalidate cancer microbiome findings.}, journal = {mBio}, volume = {14}, number = {5}, pages = {e0160723}, pmid = {37811944}, issn = {2150-7511}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Computational Biology ; Metagenomics ; *Microbiota ; *Neoplasms ; Data Analysis ; }, abstract = {Recent reports showing that human cancers have a distinctive microbiome have led to a flurry of papers describing microbial signatures of different cancer types. Many of these reports are based on flawed data that, upon re-analysis, completely overturns the original findings. The re-analysis conducted here shows that most of the microbes originally reported as associated with cancer were not present at all in the samples. The original report of a cancer microbiome and more than a dozen follow-up studies are, therefore, likely to be invalid.}, } @article {pmid37810788, year = {2023}, author = {Ochoa-Sánchez, M and Acuña Gomez, EP and Ramírez-Fenández, L and Eguiarte, LE and Souza, V}, title = {Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15978}, pmid = {37810788}, issn = {2167-8359}, mesh = {Animals ; *Eukaryota/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenome ; Fishes/genetics ; Aquatic Organisms/genetics ; Mammals/genetics ; }, abstract = {Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as "microbial gardening". In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.}, } @article {pmid37810459, year = {2023}, author = {Frolov, AV and Akhmetova, LA and Vishnevskaya, MS and Kiriukhin, BA and Montreuil, O and Lopes, F and Tarasov, SI}, title = {Amplicon metagenomics of dung beetles (Coleoptera, Scarabaeidae, Scarabaeinae) as a proxy for lemur (Primates, Lemuroidea) studies in Madagascar.}, journal = {ZooKeys}, volume = {1181}, number = {}, pages = {29-39}, pmid = {37810459}, issn = {1313-2989}, abstract = {Dung beetles (Scarabaeidae, Scarabaeinae) are among the most cost-effective and informative biodiversity indicator groups, conveying rich information about the status of habitats and faunas of an area. Yet their use for monitoring the mammal species, that are the main providers of the food for the dung beetles, has only recently been recognized. In the present work, we studied the diet of four endemic Madagascan dung beetles (Helictopleurusfissicollis (Fairmaire), H.giganteus (Harold), Nanosagaboides (Boucomont), and Epilissussplendidus Fairmaire) using high-throughput sequencing and amplicon metagenomics. For all beetle species, the ⅔-¾ of reads belonged to humans, suggesting that human feces are the main source of food for the beetles in the examined areas. The second most abundant were the reads of the cattle (Bostaurus Linnaeus). We also found lower but significant number of reads of six lemur species belonging to three genera. Our sampling localities agree well with the known ranges of these lemur species. The amplicon metagenomics method proved a promising tool for the lemur inventories in Madagascar.}, } @article {pmid37808297, year = {2023}, author = {Zhang, Y and Ruff, SE and Oskolkov, N and Tierney, BT and Ryon, K and Danko, D and Mason, CE and Elhaik, E}, title = {The microbial biodiversity at the archeological site of Tel Megiddo (Israel).}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1253371}, pmid = {37808297}, issn = {1664-302X}, abstract = {INTRODUCTION: The ancient city of Tel Megiddo in the Jezreel Valley (Israel), which lasted from the Neolithic to the Iron Age, has been continuously excavated since 1903 and is now recognized as a World Heritage Site. The site features multiple ruins in various areas, including temples and stables, alongside modern constructions, and public access is allowed in designated areas. The site has been studied extensively since the last century; however, its microbiome has never been studied. We carried out the first survey of the microbiomes in Tel Megiddo. Our objectives were to study (i) the unique microbial community structure of the site, (ii) the variation in the microbial communities across areas, (iii) the similarity of the microbiomes to urban and archeological microbes, (iv) the presence and abundance of potential bio-corroding microbes, and (v) the presence and abundance of potentially pathogenic microbes.

METHODS: We collected 40 swab samples from ten major areas and identified microbial taxa using next-generation sequencing of microbial genomes. These genomes were annotated and classified taxonomically and pathogenetically.

RESULTS: We found that eight phyla, six of which exist in all ten areas, dominated the site (>99%). The relative sequence abundance of taxa varied between the ruins and the sampled materials and was assessed using all metagenomic reads mapping to a respective taxon. The site hosted unique taxa characteristic of the built environment and exhibited high similarity to the microbiome of other monuments. We identified acid-producing bacteria that may pose a risk to the site through biocorrosion and staining and thus pose a danger to the site's preservation. Differences in the microbiomes of the publicly accessible or inaccessible areas were insignificant; however, pathogens were more abundant in the former.

DISCUSSION: We found that Tel Megiddo combines microbiomes of arid regions and monuments with human pathogens. The findings shed light on the microbial community structures and have relevance for bio-conservation efforts and visitor health.}, } @article {pmid37807043, year = {2023}, author = {Hayes, MG and Langille, MGI and Gu, H}, title = {Cross-study analyses of microbial abundance using generalized common factor methods.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {380}, pmid = {37807043}, issn = {1471-2105}, support = {CGS-M Alexander Graham Bell Scholarship//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN/05108-2017//Natural Sciences and Engineering Research Council of Canada/ ; Scotia Scholars Award//Nova Scotia Health Research Foundation/ ; }, mesh = {*Metagenome ; *Microbiota/genetics ; Metagenomics/methods ; Genomics ; Computational Biology/methods ; }, abstract = {BACKGROUND: By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to a new frontier in microbial ecology, promising the ability to leverage the microbiome to make crucial advancements in the environmental and biomedical sciences. However, this is challenging, as genomic data are high-dimensional, sparse, and noisy. Much of this noise reflects the exact conditions under which sequencing took place, and is so significant that it limits consensus-based validation of study results.

RESULTS: We propose an ensemble approach for cross-study exploratory analyses of microbial abundance data in which we first estimate the variance-covariance matrix of the underlying abundances from each dataset on the log scale assuming Poisson sampling, and subsequently model these covariances jointly so as to find a shared low-dimensional subspace of the feature space.

CONCLUSIONS: By viewing the projection of the latent true abundances onto this common structure, the variation is pared down to that which is shared among all datasets, and is likely to reflect more generalizable biological signal than can be inferred from individual datasets. We investigate several ways of achieving this, demonstrate that they work well on simulated and real metagenomic data in terms of signal retention and interpretability, and recommend a particular implementation.}, } @article {pmid37806995, year = {2023}, author = {Rick, K and Byrne, M and Cameron, S and Cooper, SJB and Dunlop, J and Hill, B and Lohr, C and Mitchell, NJ and Moritz, C and Travouillon, KJ and von Takach, B and Ottewell, K}, title = {Population genomic diversity and structure in the golden bandicoot: a history of isolation, extirpation, and conservation.}, journal = {Heredity}, volume = {131}, number = {5-6}, pages = {374-386}, pmid = {37806995}, issn = {1365-2540}, mesh = {*Genetics, Population ; *Genetic Variation ; Ecosystem ; Metagenomics ; Genetic Drift ; Conservation of Natural Resources ; }, abstract = {Using genetic information to develop and implement conservation programs is vital for maintaining biodiversity and ecosystem resilience. Evaluation of the genetic variability within and among remnant populations can inform management of both natural and translocated populations to maximise species' adaptive potential, mitigate negative impacts of inbreeding, and subsequently minimise risk of extinction. Here we use reduced representation sequencing to undertake a genetic assessment of the golden bandicoot (Isoodon auratus), a threatened marsupial endemic to Australia. The currently recognised taxon consists of three subspecies distributed among multiple natural and translocated populations. After confirming the genetic distinctiveness of I. auratus from two closely related taxa, I. fusciventer and I. macrourus, we identified four genetic clusters within I. auratus. These clusters exhibited substantial genetic differentiation (pairwise FST values ranging from 0.18 to 0.65, pairwise DXY ranging from 0.1 to 0.168), reflecting long-term isolation of some populations on offshore islands and the influence of genetic drift. Mainland natural populations in the Kimberley region had the highest genetic diversity and the largest contribution to overall allelic and gene diversity compared to both natural and translocated island populations. A population translocated to Guluwuru Island in the Northern Territory had the lowest genetic diversity. Our data suggest that island populations can appear genetically unique due to genetic drift and this needs to be taken into account when considering genetic diversity in conservation efforts to maintain overall genetic diversity of the species. We effectively demonstrate how genomic information can guide practical conservation planning, especially when declining species are represented by multiple isolated populations.}, } @article {pmid37806587, year = {2024}, author = {Lin, X and Liu, Z and Wang, W and Duan, G and Zhu, Y}, title = {Effects of artificial sweetener acesulfame on soil-dwelling earthworms (Eisenia fetida) and its gut microbiota.}, journal = {The Science of the total environment}, volume = {907}, number = {}, pages = {167641}, doi = {10.1016/j.scitotenv.2023.167641}, pmid = {37806587}, issn = {1879-1026}, mesh = {Animals ; Soil ; *Oligochaeta/physiology ; *Gastrointestinal Microbiome ; Sweetening Agents/analysis ; *Soil Pollutants/analysis ; }, abstract = {Artificial sweeteners (AS) are the emerging contaminants with potential toxicity to living organisms. The effects of AS to soil typical invertebrates have not been revealed. In this study, the responses of earthworms (Eisenia fetida) and gut microbial communities to acesulfame-contaminated soils (0.1, 1 and 10 mg kg[-1]) were studied using transcriptomics, metabolomics and metagenomics analyses. The fresh weight of earthworms was significantly stimulated by acesulfame at concentrations of 1 mg kg[-1]. Sphingolipid metabolism, purine metabolism, cutin, suberine and wax biosynthesis pathways were significantly affected. At 10 mg kg[-1] treatment, the amount and weight of cocoons were significantly increased and decreased, respectively, accompanied by the significant disorder of ECM-receptor interaction, and carbon fixation in photosynthetic organisms pathways. Lysosome pathway was significantly affected in all the treatments. Moreover, the acesulfame significantly increased the relative abundance of Bacteroidetes and Mucoromycota, and decreased Proteobacteria in the gut of earthworms. Our multi-level investigation indicated that AS at a relatively low concentration induced toxicity to earthworms and AS pollution has significant environmental risks for soil fauna.}, } @article {pmid37805557, year = {2023}, author = {Huang, G and Shi, W and Wang, L and Qu, Q and Zuo, Z and Wang, J and Zhao, F and Wei, F}, title = {PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {221}, pmid = {37805557}, issn = {2049-2618}, mesh = {Animals ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Animals, Wild/microbiology ; Metagenome/genetics ; Bacteria/genetics ; Mammals/genetics ; }, abstract = {BACKGROUND: The gut microbiota play important roles in host adaptation and evolution, but are understudied in natural population of wild mammals. To address host adaptive evolution and improve conservation efforts of threatened mammals from a metagenomic perspective, we established a high-quality gut microbiome catalog of the giant panda (pandaGUT) to resolve the microbiome diversity, functional, and resistome landscapes using approximately 7 Tbp of long- and short-read sequencing data from 439 stool samples.

RESULTS: The pandaGUT catalog comprises 820 metagenome-assembled genomes, including 40 complete closed genomes, and 64.5% of which belong to species that have not been previously reported, greatly expanding the coverage of most prokaryotic lineages. The catalog contains 2.37 million unique genes, with 74.8% possessing complete open read frames, facilitating future mining of microbial functional potential. We identified three microbial enterotypes across wild and captive panda populations characterized by Clostridium, Pseudomonas, and Escherichia, respectively. We found that wild pandas exhibited host genetic-specific microbial structures and functions, suggesting host-gut microbiota phylosymbiosis, while the captive cohorts encoded more multi-drug resistance genes.

CONCLUSIONS: Our study provides largely untapped resources for biochemical and biotechnological applications as well as potential intervention avenues via the rational manipulation of microbial diversity and reducing antibiotic usage for future conservation management of wildlife. Video Abstract.}, } @article {pmid37804763, year = {2024}, author = {Xu, C and Hu, C and Lu, J and Yang, T and Shen, C and Li, F and Wang, J}, title = {Lake plastisphere as a new biotope in the Anthropocene: Potential pathogen colonization and distinct microbial functionality.}, journal = {Journal of hazardous materials}, volume = {461}, number = {}, pages = {132693}, doi = {10.1016/j.jhazmat.2023.132693}, pmid = {37804763}, issn = {1873-3336}, mesh = {*Lakes/microbiology ; Plastics ; Nitrification ; *Microbiota ; Sulfur/metabolism ; }, abstract = {The not-homogenous microplastics (MPs) distribution in freshwaters results in distinct microbial communities. Yet knowledge regarding plastisphere in metabolic pathways and element cycling behaviors remains limited. In this study, we collected MPs from 15 sampling sites in the Taihu Lake in China, and found that MPs were widely distributed in this freshwater lake, and dominantly composed of fibrous polyethylene terephthalate. Based on the metagenomic analysis, we found that MPs were colonized by Bacteroidia, Alpha-Proteobacteria, and Bacilli as a filter, but depleted in Verrucomicrobiae. Potential pathogens of plant eudicots and monocots were significantly enriched in plastisphere. Predicted functional profiles involved in the metabolism of other amino acids, biosynthesis of other secondary metabolites, and glycan biosynthesis and metabolism were overrepresented in plastisphere. Regarding elemental cycling, functional genes related to nitrogen fixation and nitrification showed 39.6% and 67.5% decline in plastisphere, whereas the genes involved in denitrification and nitrate reduction were significantly enriched. For sulfur cycles, the plastisphere exhibited higher sulfate reduction and sulfur oxidation system activities. Additionally, the taxonomic compositions and predicted functions in the plastispheres were mainly driven by the stochastic processes, while the deterministic processes were more important for the planktonic communities. The distinctions in the microbial composition, the predicted functionality, and the underly mechanisms between plastisphere and planktonic communities illustrated the unique ecology of the new anthropogenic-related plastisphere ecosystems.}, } @article {pmid37804481, year = {2023}, author = {Regueira-Iglesias, A and Balsa-Castro, C and Blanco-Pintos, T and Tomás, I}, title = {Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis.}, journal = {Molecular oral microbiology}, volume = {38}, number = {5}, pages = {347-399}, doi = {10.1111/omi.12434}, pmid = {37804481}, issn = {2041-1014}, support = {PI21/00588//Instituto de Salud Carlos III (ISCIII) and co-funded by the European Union/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; Phylogeny ; Workflow ; *High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; }, abstract = {The multi-batch reanalysis approach of jointly reevaluating gene/genome sequences from different works has gained particular relevance in the literature in recent years. The large amount of 16S ribosomal ribonucleic acid (rRNA) gene sequence data stored in public repositories and information in taxonomic databases of the same gene far exceeds that related to complete genomes. This review is intended to guide researchers new to studying microbiota, particularly the oral microbiota, using 16S rRNA gene sequencing and those who want to expand and update their knowledge to optimise their decision-making and improve their research results. First, we describe the advantages and disadvantages of using the 16S rRNA gene as a phylogenetic marker and the latest findings on the impact of primer pair selection on diversity and taxonomic assignment outcomes in oral microbiome studies. Strategies for primer selection based on these results are introduced. Second, we identified the key factors to consider in selecting the sequencing technology and platform. The process and particularities of the main steps for processing 16S rRNA gene-derived data are described in detail to enable researchers to choose the most appropriate bioinformatics pipeline and analysis methods based on the available evidence. We then produce an overview of the different types of advanced analyses, both the most widely used in the literature and the most recent approaches. Several indices, metrics and software for studying microbial communities are included, highlighting their advantages and disadvantages. Considering the principles of clinical metagenomics, we conclude that future research should focus on rigorous analytical approaches, such as developing predictive models to identify microbiome-based biomarkers to classify health and disease states. Finally, we address the batch effect concept and the microbiome-specific methods for accounting for or correcting them.}, } @article {pmid37803768, year = {2023}, author = {Alvarez-Molina, A and Cobo-Díaz, JF and Alexa, EA and Crispie, F and Prieto, M and López, M and Cotter, PD and Alvarez-Ordóñez, A}, title = {Sequencing-based analysis of the microbiomes of Spanish food processing facilities reveals environment-specific variation in the dominant taxa and antibiotic resistance genes.}, journal = {Food research international (Ottawa, Ont.)}, volume = {173}, number = {Pt 2}, pages = {113442}, doi = {10.1016/j.foodres.2023.113442}, pmid = {37803768}, issn = {1873-7145}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Microbiota/genetics ; Drug Resistance, Microbial/genetics ; Bacteria ; Aminoglycosides ; Food Handling ; Tetracyclines ; }, abstract = {In the last years, advances in high throughput sequencing technologies have opened the possibility to broaden environmental monitoring activities in facilities processing food, offering expanded opportunities for characterizing in an untargeted manner the microbiome and resistome of foods and food processing environments (FPE) with huge potential benefits in food safety management systems. Here the microbiome and resistome of FPE from slaughterhouses (n = 3), dairy (n = 12) and meat (n = 10) processing plants were assessed through whole metagenome sequencing of 2 composite samples for each facility, comprising 10 FPE swabs taken from food contact surfaces and 10 FPE samples from non-food contact surfaces, respectively. FPE from slaughterhouses had more diverse microbiomes and resistomes, while FPE from dairy processing plants showed the highest β-dispersion, consistent with a more heterogeneous microbiome and resistome composition. The predominant bacterial genera depended on the industry type, with Pseudomonas and Psychrobacter being highly dominant in surfaces from slaughterhouses and meat industries, while different lactic acid bacteria predominated in dairy industries. The most abundant antimicrobial resistance genes (ARG) found were associated with resistance to aminoglycosides, tetracyclines and quaternary ammonium compounds (QAC). ARGs relating to resistance to aminoglycosides and tetracyclines were significantly more prevalent in slaughterhouses than in food processing plants, while QAC resistance genes were particularly abundant in some food contact surfaces from dairy and meat processing plants, suggesting that daily sanitation under suboptimal conditions may be selecting for persistent microbiota tolerant to these biocides in some facilities. The taxonomic mapping of ARG pointed to specific bacterial genera, such as Escherichia, Bacillus, or Staphylococcus, as carriers of the most relevant resistance determinants. About 63% of all ARG reads were assigned to contigs classified as plasmid-associated, indicating that the resistome of FPE may be strongly shaped through the spread of mobile genetic elements. Overall, the relevance of FPE as reservoirs of ARG was confirmed and it was demonstrated that next generation sequencing technologies allowing a deep characterisation of sources and routes of spread of microorganisms and antimicrobial resistance determinants in food industry settings hold promise to be integrated in monitoring and food safety management programmes.}, } @article {pmid37803564, year = {2023}, author = {Liu, Y and Yu, L and Tian, F and Chen, W and Zhai, Q}, title = {Meta-analysis of microbiomes reveals metagenomic features of fermented vegetables.}, journal = {Food research international (Ottawa, Ont.)}, volume = {173}, number = {Pt 1}, pages = {113248}, doi = {10.1016/j.foodres.2023.113248}, pmid = {37803564}, issn = {1873-7145}, mesh = {Metagenome ; Vegetables/genetics ; *Microbiota/genetics ; *Lactobacillales/genetics ; Drug Resistance, Microbial ; }, abstract = {An insightful exploration of the fermented vegetable microbiome is the key to improving food quality and sustainability. Based on 57 fermented vegetable samples from China, Ireland, the UK, and Germany retrieved from public genome databases, we conducted a high-resolution meta-analysis of the fermented vegetable microbiomes. There were significant differences in the microbiota composition and functional pathway diversity of the tested samples, as reflected by the differences in their geographical origins. Metagenomic analysis also revealed the metagenomic features of carbohydrate-active enzymes and antibiotic resistance genes in the fermented vegetable metagenomes. Five putative new species were detected by recovering 221 metagenome-assembled genomes belonging to the genera Rubrobacteraceae, Bifidobacteriaceae, and Ruminococcaceae. Our results provide new ecological insights into the implications of fermented vegetable microbiota composition and functional potential and highlight the importance of high-resolution metagenomic analysis to further investigate the fermented food microbiome.}, } @article {pmid37803284, year = {2023}, author = {Chen, Z and Xiao, Y and Jia, Y and Lin, Q and Qian, Y and Cui, L and Xiang, Z and Li, M and Yang, C and Zou, H}, title = {Metagenomic analysis of microbiological changes on the ocular surface of diabetic children and adolescents with a dry eye.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {286}, pmid = {37803284}, issn = {1471-2180}, mesh = {Humans ; Adolescent ; Child ; Metagenome ; China ; *Dry Eye Syndromes ; *Diabetes Mellitus/genetics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Microbiome changes on the ocular surface may cause dry eyes. A metagenome assay was used to compare the microbiome composition and function of the ocular surface between diabetic children and adolescents with dry eye, diabetic children and adolescents without dry eye, and normal children.

MATERIALS AND METHODS: Twenty children and adolescents aged 8 to 16 with diabetes were selected from the Shanghai Children and Adolescent Diabetes Eye Study. Ten healthy children and adolescents belonging to the same age group were selected from the outpatient clinic during the same period. The participants were classified into the dry eye group (DM-DE group, n = 10), the non-dry eye group (DM-NDE group, n = 10) and the normal group (NDM group, n = 10). A conjunctival sac swab was collected for metagenomic sequencing, and the relationship between the microbiome composition and functional gene differences on the ocular surface with dry eye was studied.

RESULTS: The classification composition and metabolic function of the microorganisms on the ocular surface of children in the 3 groups were analyzed. It was found that children's ocular microbiota was composed of bacteria, viruses and fungi. There were significant differences in α diversity and β diversity of microbial composition of ocular surface between DM-DE group and NDM group(P<0.05). There were significant differences in α and β diversity of metabolic pathways between the two groups(P<0.05). The functional pathways of ocular surface microorganisms in diabetic children with dry eyes were mainly derived from human disease, antibiotic resistance genes, carbohydrate, coenzyme and lipid transport and metabolism-related functional genes; In normal children, the functional pathways were mainly derived from replication, recombination, repair, signal transduction and defense-related functional genes.

CONCLUSION: The DM-DE group have unique microbial composition and functional metabolic pathways. The dominant species and unique metabolic pathways of the ocular surface in the DM-DE group may be involved in the pathogenesis of dry eye in diabetic children.}, } @article {pmid37802717, year = {2024}, author = {Ellison, JS and Atkinson, SN and Hayward, M and Hokanson, E and Sheridan, KR and Salzman, N}, title = {The intestinal microbiome of children with initial and recurrent nephrolithiasis: A pilot study and exploratory analysis.}, journal = {Journal of pediatric urology}, volume = {20}, number = {1}, pages = {18-25}, pmid = {37802717}, issn = {1873-4898}, support = {UL1 TR001436/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Male ; Female ; Humans ; Child ; Pilot Projects ; *Gastrointestinal Microbiome ; *Nephrolithiasis/epidemiology ; *Kidney Calculi ; *Urolithiasis/epidemiology ; *Hyperoxaluria ; Recurrence ; Risk Factors ; }, abstract = {INTRODUCTION: Kidney stone disease in children is rising disproportionate to the general population, representing a disease population with a distinct biological mechanism as compared to adults. Factors influencing recurrent kidney stone disease in children are poorly characterized and the associations of the intestinal microbiome within sub-populations of kidney stone formers, however, are not well described. We evaluated a pilot cohort of children with nephrolithiasis comparing patients based on recurrent kidney stone episodes and abnormal 24-h urinary parameters, with dual aims to compare the microbiome signal in children with initial and recurrent nephrolithiasis and to explore additional associations in microbiome composition and diversity within this population.

METHODS: Children aged 6-18 with a history of nephrolithiasis, without an active ureteral calculus or antibiotic exposure within 30 days of study entry were eligible to participate. All participants had a 24-h urine study within 6 months of study entry and provided a fecal sample. Microbiome samples were analyzed using 16S ribosomal DNA sequencing techniques for alpha and beta diversity comparing initial and recurrent stone formers as well as microbiome multivariate association (MaAsLin2) to determine differentially abundant taxa. Shotgun sequencing reads were aligned to custom oxidase degradation and butyrate production gene databases (5 databases total). Comparisons for MaAsLin2 and shotgun metagenomics, normalized to sequencing depth, were based on stone recurrence, sex, hypercalcuria (≤4 mg/kg/day), hyperoxaluria (≥45 mg/1.73 m[2]), and hypocitraturia (<310 mg/1.73 m[2] [females] or < 365 mg/1.73 m[2] [males]).

RESULTS: A total of 16 enrolled children provided samples sufficient for analyses, including 9 girls and 7 boys, of whom 5 had experienced recurrent kidney stone events. Three participants had hypercalcuria, 2 had hyperoxaluria, and 4 had hypocitraturia. Comparisons of Formyl-CoA transferase between index and recurrent urinary stone disease revealed a trend towards higher mean abundance of the gene in initial stone formers (0.166% vs 0.0343%, p = 0.2847) (Summary Figure), while trends toward lower biodiversity were also noted in the recurrent stone cohort on both Faith (p = 0.06) and Shannon (p = 0.05) indices. Exploratory analyses found Eubacterium siraeum to be significantly greater in relative abundance in children with documented hypercalciuria (p = 0.001).

DISCUSSION: Our pilot study demonstrates possible signals in both microbial diversity and oxalate gene expression, both of which are lower in recurrent pediatric kidney stone patients. These findings warrant further investigation as a potential diagnostic marker for future kidney stone events.}, } @article {pmid37802272, year = {2024}, author = {Jangi, S and Hsia, K and Zhao, N and Kumamoto, CA and Friedman, S and Singh, S and Michaud, DS}, title = {Dynamics of the Gut Mycobiome in Patients With Ulcerative Colitis.}, journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association}, volume = {22}, number = {4}, pages = {821-830.e7}, pmid = {37802272}, issn = {1542-7714}, support = {KL2 TR002545/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Humans ; *Colitis, Ulcerative/pathology ; *Mycobiome ; Prospective Studies ; *Crohn Disease/complications ; *Inflammatory Bowel Diseases/complications ; Feces/microbiology ; }, abstract = {BACKGROUND & AIMS: Intestinal fungi have been implicated in the pathogenesis of ulcerative colitis (UC). However, it remains unclear if fungal composition is altered during active versus quiescent disease.

METHODS: We analyzed clinical and metagenomic data from the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease (SPARC IBD), available via the IBD Plexus Program of the Crohn's & Colitis Foundation. We evaluated the fungal composition of fecal samples from 421 patients with UC during clinical activity and remission. Within a longitudinal subcohort (n = 52), we assessed for dynamic taxonomic changes across alterations in clinical activity over time. We examined if fungal amplicon sequence variants and fungal-bacterial relationships were altered during activity versus remission. Finally, we classified activity in UC using a supervised machine learning random forest model trained on fungal abundance data.

RESULTS: During clinical activity, the relative abundance of genus Candida was increased 3.5-fold (P-adj < 1 × 10[-4]) compared with during remission. Patients with longitudinal reductions in clinical activity demonstrated parallel reductions in Candida relative abundance (P < .05). Candida relative abundance correlated with Parabacteroides diastonis, Faecalibacterium prausnitzii, and Bacteroides dorei relative abundance (P < .05) during remission; however, these correlations were disrupted during activity. Fungal abundance data successfully classified patients with active or quiescent UC (area under the curve ∼0.80), with Candida relative abundance critical to the success of the model.

CONCLUSIONS: Clinical activity in UC is associated with an increased relative abundance of Candida, cross-sectionally and dynamically over time. The role of fecal Candida as a target for therapeutics in UC should be evaluated.}, } @article {pmid37801779, year = {2023}, author = {Floridia, V and Russo, N and D'Alessandro, E and Lopreiato, V and Pino, A and Amato, A and Liotta, L and Caggia, C and Randazzo, CL}, title = {Effect of olive cake supplementation on faecal microbiota profile of Holstein and Modicana dairy cattle.}, journal = {Microbiological research}, volume = {277}, number = {}, pages = {127510}, doi = {10.1016/j.micres.2023.127510}, pmid = {37801779}, issn = {1618-0623}, mesh = {Female ; Cattle ; Animals ; *Olea ; Milk ; Diet/veterinary ; Dietary Supplements ; *Microbiota ; Animal Feed ; }, abstract = {The present study aimed to investigate the effect of olive cake supplementation on faecal microbiota of Holstein (n = 16) and Modicana (n = 16) dairy cows. Although no difference in richness was detected, within breeds and between the two dietary treatment, the PERMANOVA analysis applied to the beta diversity allowed to discriminate samples according to breeds (p < 0.001) and treatment (p < 0.001). In Holstein cows, the olive cake supplementation led to the increase of Pseudobutyrivibrio and Christensenellaceae_R7-group genera (p < 0.05) recognized as health-promoting or associated with feed efficiency. Differently, no difference was detected between control and treated groups for Modicana suggesting a high adaptive capacity to diet changes. In addition, the higher prevalence of Firmicutes phyla in the Modicana microbiota reflected its better capacity to digest the fibrous sources. Our study supports the suitability of olive cake as a feed supplement for cows and could help validating a sustainable livestock system in the Mediterranean area, characterized by a relevant oil production and by a native breeds reared with extensive systems.}, } @article {pmid37798675, year = {2023}, author = {Avila Santos, AP and Kabiru Nata'ala, M and Kasmanas, JC and Bartholomäus, A and Keller-Costa, T and Jurburg, SD and Tal, T and Camarinha-Silva, A and Saraiva, JP and Ponce de Leon Ferreira de Carvalho, AC and Stadler, PF and Sipoli Sanches, D and Rocha, U}, title = {The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {48}, pmid = {37798675}, issn = {2524-4671}, abstract = {BACKGROUND: Metagenomic data can shed light on animal-microbiome relationships and the functional potential of these communities. Over the past years, the generation of metagenomics data has increased exponentially, and so has the availability and reusability of data present in public repositories. However, identifying which datasets and associated metadata are available is not straightforward. We created the Animal-Associated Metagenome Metadata Database (AnimalAssociatedMetagenomeDB - AAMDB) to facilitate the identification and reuse of publicly available non-human, animal-associated metagenomic data, and metadata. Further, we used the AAMDB to (i) annotate common and scientific names of the species; (ii) determine the fraction of vertebrates and invertebrates; (iii) study their biogeography; and (iv) specify whether the animals were wild, pets, livestock or used for medical research.

RESULTS: We manually selected metagenomes associated with non-human animals from SRA and MG-RAST.  Next, we standardized and curated 51 metadata attributes (e.g., host, compartment, geographic coordinates, and country). The AAMDB version 1.0 contains 10,885 metagenomes associated with 165 different species from 65 different countries. From the collected metagenomes, 51.1% were recovered from animals associated with medical research or grown for human consumption (i.e., mice, rats, cattle, pigs, and poultry). Further, we observed an over-representation of animals collected in temperate regions (89.2%) and a lower representation of samples from the polar zones, with only 11 samples in total. The most common genus among invertebrate animals was Trichocerca (rotifers).

CONCLUSION: Our work may guide host species selection in novel animal-associated metagenome research, especially in biodiversity and conservation studies. The data available in our database will allow scientists to perform meta-analyses and test new hypotheses (e.g., host-specificity, strain heterogeneity, and biogeography of animal-associated metagenomes), leveraging existing data. The AAMDB WebApp is a user-friendly interface that is publicly available at https://webapp.ufz.de/aamdb/ .}, } @article {pmid37797086, year = {2024}, author = {Feng, Y and Comes, HP and Chen, J and Zhu, S and Lu, R and Zhang, X and Li, P and Qiu, J and Olsen, KM and Qiu, Y}, title = {Genome sequences and population genomics provide insights into the demographic history, inbreeding, and mutation load of two 'living fossil' tree species of Dipteronia.}, journal = {The Plant journal : for cell and molecular biology}, volume = {117}, number = {1}, pages = {177-192}, doi = {10.1111/tpj.16486}, pmid = {37797086}, issn = {1365-313X}, support = {2017YFA0605100//National Key R&D Program of China/ ; 2022YFF1301703//National Key R&D Program of China/ ; 31872652//National Natural Science Foundation of China/ ; 32161143003//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Fossils ; Genetic Variation ; *Inbreeding ; Metagenomics ; Mutation ; *Trees/genetics ; }, abstract = {'Living fossils', that is, ancient lineages of low taxonomic diversity, represent an exceptional evolutionary heritage, yet we know little about how demographic history and deleterious mutation load have affected their long-term survival and extinction risk. We performed whole-genome sequencing and population genomic analyses on Dipteronia sinensis and D. dyeriana, two East Asian Tertiary relict trees. We found large-scale genome reorganizations and identified species-specific genes under positive selection that are likely involved in adaptation. Our demographic analyses suggest that the wider-ranged D. sinensis repeatedly recovered from population bottlenecks over late Tertiary/Quaternary periods of adverse climate conditions, while the population size of the narrow-ranged D. dyeriana steadily decreased since the late Miocene, especially after the Last Glacial Maximum (LGM). We conclude that the efficient purging of deleterious mutations in D. sinensis facilitated its survival and repeated demographic recovery. By contrast, in D. dyeriana, increased genetic drift and reduced selection efficacy, due to recent severe population bottlenecks and a likely preponderance of vegetative propagation, resulted in fixation of strongly deleterious mutations, reduced fitness, and continuous population decline, with likely detrimental consequences for the species' future viability and adaptive potential. Overall, our findings highlight the significant impact of demographic history on levels of accumulation and purging of putatively deleterious mutations that likely determine the long-term survival and extinction risk of Tertiary relict trees.}, } @article {pmid37796924, year = {2023}, author = {Tesolato, S and Ortega-Hernández, A and Gómez-Garre, D and Claver, P and De Juan, C and De la Serna, S and Paz, M and Domínguez-Serrano, I and Dziakova, J and Rivera, D and Torres, A and Iniesta, P}, title = {Gut microbiota profiles in feces and paired tumor and non-tumor tissues from Colorectal Cancer patients. Relationship to the Body Mass Index.}, journal = {PloS one}, volume = {18}, number = {10}, pages = {e0292551}, pmid = {37796924}, issn = {1932-6203}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Body Mass Index ; Bacteria/genetics ; *Colonic Neoplasms ; Feces/microbiology ; Obesity ; RNA, Ribosomal, 16S/genetics ; *Colorectal Neoplasms/pathology ; }, abstract = {Colorectal Cancer (CRC) and Obesity constitute two of the most common malignancies in the western world, and previously have been associated with intestinal microbial composition alterations. Our main aim in this study is to provide molecular data on intestinal microbiota patterns in subjects with CRC, as well as to establish possible associations with their Body Mass Index (BMI). A total of 113 samples from 45 subjects were collected and submitted to metagenomics analysis for gut microbiota. This study was performed by 16S ribosomal RNA bacterial gene amplification and sequencing using the Ion Torrent™ technology. The same dominant phyla were observed in feces and colorectal tissues, although a greater proportion of Fusobacteriota was found in tumor samples. Moreover, at the genus level, LEfSe analysis allowed us to detect a significant increase in Fusobacterium and Streptococcus in colorectal tissues with respect to fecal samples, with a significant preponderance of Fusobacterium in tumor tissues. Also, our data revealed relevant associations between gut microbiota composition and tumor location. When comparing bacterial profiles between right and left colon cancers, those from the left-sided colon showed a significant preponderance, among others, of the order Staphylococcales. Moreover, phyla Firmicutes and Spirochaetota were more abundant in the group of right-sided CRCs and phylum Proteobacteria was increased in rectal cancers. In relation to BMI of patients, we detected significant differences in beta diversity between the normal weight and the obese groups of cases. Microbiota from obese patients was significantly enriched, among others, in Bacteroidales. Therefore, our results are useful in the molecular characterization of CRC in obese and non-obese patients, with a clear impact on the establishment of diagnostic and prognosis of CRC.}, } @article {pmid37796016, year = {2023}, author = {Kamer, O and Rinott, E and Tsaban, G and Kaplan, A and Yaskolka Meir, A and Zelicha, H and Knights, D and Tuohy, K and Fava, F and Uwe Scholz, M and Ziv, O and Rubin, E and Blüher, M and Stumvoll, M and Ceglarek, U and Clément, K and Koren, O and Hu, FB and Stampfer, MJ and Wang, DD and Youngster, I and Shai, I}, title = {Successful weight regain attenuation by autologous fecal microbiota transplantation is associated with non-core gut microbiota changes during weight loss; randomized controlled trial.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2264457}, pmid = {37796016}, issn = {1949-0984}, support = {R00 DK119412/DK/NIDDK NIH HHS/United States ; R01 AG077489/AG/NIA NIH HHS/United States ; R01 NR019992/NR/NINR NIH HHS/United States ; }, mesh = {Humans ; Middle Aged ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Feces ; Weight Loss ; Weight Gain ; }, abstract = {We previously reported that autologous-fecal-microbiota-transplantation (aFMT), following 6 m of lifestyle intervention, attenuated subsequent weight regain and insulin rebound for participants consuming a high-polyphenol green-Mediterranean diet. Here, we explored whether specific changes in the core (abundant) vs. non-core (low-abundance) gut microbiome taxa fractions during the weight-loss phase (0-6 m) were differentially associated with weight maintenance following aFMT. Eighty-two abdominally obese/dyslipidemic participants (age = 52 years; 6 m weightloss = -8.3 kg) who provided fecal samples (0 m, 6 m) were included. Frozen 6 m's fecal samples were processed into 1 g, opaque and odorless aFMT capsules. Participants were randomly assigned to receive 100 capsules containing their own fecal microbiota or placebo over 8 m-14 m in ten administrations (adherence rate > 90%). Gut microbiome composition was evaluated using shotgun metagenomic sequencing. Non-core taxa were defined as ≤ 66% prevalence across participants. Overall, 450 species were analyzed. At baseline, 13.3% were classified as core, and Firmicutes presented the highest core proportion by phylum. During 6 m weight-loss phase, abundance of non-core species changed more than core species (P < .0001). Subject-specific changes in core and non-core taxa fractions were strongly correlated (Jaccard Index; r = 0.54; P < .001). Following aFMT treatment, only participants with a low 6 m change in core taxa, and a high change in non-core taxa, avoided 8-14 m weight regain (aFMT = -0.58 ± 2.4 kg, corresponding placebo group = 3.18 ± 3.5 kg; P = .02). In a linear regression model, low core/high non-core 6 m change was the only combination that was significantly associated with attenuated 8-14 m weight regain (P = .038; P = .002 for taxa patterns/treatment intervention interaction). High change in non-core, low-abundance taxa during weight-loss might mediate aFMT treatment success for weight loss maintenance.ClinicalTrials.gov: NCT03020186.}, } @article {pmid37795995, year = {2023}, author = {Cao, Y and Wang, J and Hou, W and Ding, Y and Zhu, Y and Zheng, J and Huang, Q and Cao, Z and Xie, R and Wei, Q and Qin, H}, title = {Colorectal cancer-associated T cell receptor repertoire abnormalities are linked to gut microbiome shifts and somatic cell mutations.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2263934}, pmid = {37795995}, issn = {1949-0984}, mesh = {Humans ; *Colorectal Neoplasms ; *Gastrointestinal Microbiome ; Fusobacterium nucleatum ; Biomarkers ; Mutation ; Receptors, Antigen, T-Cell/genetics ; }, abstract = {As with many diseases, tumor formation in colorectal cancer (CRC) is multifactorial and involves immune, environmental factors and various genetics that contribute to disease development. Accumulating evidence suggests that the gut microbiome is linked to the occurrence and development of CRC, and these microorganisms are important for immune maturation. However, a systematic perspective integrating microbial profiling, T cell receptor (TCR) and somatic mutations in humans with CRC is lacking. Here, we report distinct features of the expressed TCRβ repertoires in the peripheral blood of and CRC patients (n = 107) and healthy donors (n = 30). CRC patients have elevated numbers of large TCRβ clones and they have very low TCR diversity. The metagenomic sequencing data showed that the relative abundance of Fusobacterium nucleatum (F. nucleatum), Escherichia coli and Dasheen mosaic virus were elevated consistently in CRC patients (n = 97) compared to HC individuals (n = 30). The abundance of Faecalibacterium prausnitzii and Roseburia intestinalis was reduced in CRC (n = 97) compared to HC (n = 30). The correlation between somatic mutations of target genes (16 genes, n = 79) and TCR clonality and microbial biomarkers in CRC had been investigated. Importantly, we constructed a random forest classifier (contains 15 features) based on microbiome and TCR repertoires, which can be used as a clinical detection method to screen patients for CRC. We also analysis of F. nucleatum-specific TCR repertoire characteristics. Collectively, our large-cohort multi-omics data aimed to identify novel biomarkers to inform clinical decision-making in the detection and diagnosis of CRC, which is of possible etiological and diagnostic significance.}, } @article {pmid37791411, year = {2023}, author = {Jaarsma, AH and Sipes, K and Zervas, A and Jiménez, FC and Ellegaard-Jensen, L and Thøgersen, MS and Stougaard, P and Benning, LG and Tranter, M and Anesio, AM}, title = {Exploring microbial diversity in Greenland Ice Sheet supraglacial habitats through culturing-dependent and -independent approaches.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {11}, pages = {}, pmid = {37791411}, issn = {1574-6941}, mesh = {*Ice Cover/microbiology ; Greenland ; Biodiversity ; *Microbiota/genetics ; Metagenome ; }, abstract = {The microbiome of Greenland Ice Sheet supraglacial habitats is still underinvestigated, and as a result there is a lack of representative genomes from these environments. In this study, we investigated the supraglacial microbiome through a combination of culturing-dependent and -independent approaches. We explored ice, cryoconite, biofilm, and snow biodiversity to answer: (1) how microbial diversity differs between supraglacial habitats, (2) if obtained bacterial genomes reflect dominant community members, and (3) how culturing versus high throughput sequencing changes our observations of microbial diversity in supraglacial habitats. Genomes acquired through metagenomic sequencing (133 high-quality MAGs) and whole genome sequencing (73 bacterial isolates) were compared to the metagenome assemblies to investigate abundance within the total environmental DNA. Isolates obtained in this study were not dominant taxa in the habitat they were sampled from, in contrast to the obtained MAGs. We demonstrate here the advantages of using metagenome SSU rRNA genes to reflect whole-community diversity. Additionally, we demonstrate a proof-of-concept of the application of in situ culturing in a supraglacial setting.}, } @article {pmid37791391, year = {2023}, author = {Mason, CN and Shahar, S and Beals, KK and Kelley, ST and Lipson, DA and Swingley, WD and Barber, NA}, title = {Taxonomic and functional restoration of tallgrass prairie soil microbial communities in comparison to remnant and agricultural soils.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {11}, pages = {}, doi = {10.1093/femsec/fiad120}, pmid = {37791391}, issn = {1574-6941}, mesh = {*Soil ; Ecosystem ; Grassland ; Soil Microbiology ; Agriculture ; *Microbiota/genetics ; }, abstract = {Restoring ecosystems requires the re-establishment of diverse soil microbial communities that drive critical ecosystem functions. In grasslands, restoration and management require the application of disturbances like fire and grazing. Disturbances can shape microbial taxonomic composition and potentially functional composition as well. We characterized taxonomic and functional gene composition of soil communities using whole genome shotgun metagenomic sequencing to determine how restored soil communities differed from pre-restoration agricultural soils and original remnant soils, how management affects soil microbes, and whether restoration and management affect the number of microbial genes associated with carbohydrate degradation. We found distinct differences in both taxonomic and functional diversity and composition among restored, remnant, and agricultural soils. Remnant soils had low taxonomic and functional richness and diversity, as well as distinct composition, indicating that restoration of agricultural soils does not re-create soil microbial communities that match remnants. Prescribed fire management increased functional diversity, which also was higher in more recently planted restorations. Finally, restored and post-fire soils included high abundances of genes encoding cellulose-degrading enzymes, so restorations and their ongoing management can potentially support functions important in carbon cycling.}, } @article {pmid37789449, year = {2023}, author = {Yang, J and Woo, JJ and Oh, SY and Kim, W and Hur, JS}, title = {Fungal community inside lichen: a curious case of sparse diversity and high modularity.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {73}, pmid = {37789449}, issn = {2524-6372}, support = {NRF-2020R1I1A2073283//National Research Foundation of Korea/ ; NRF-2020R1I1A2073283//National Research Foundation of Korea/ ; NRF-2020R1I1A2073283//National Research Foundation of Korea/ ; NRF-2020R1I1A2073283//National Research Foundation of Korea/ ; NRF-2020R1I1A2073283//National Research Foundation of Korea/ ; }, abstract = {BACKGROUND: Lichens represent not only the mutualism of fungal and photosynthetic partners but also are composed of microbial consortium harboring diverse fungi known as endolichenic fungi. While endolichenic fungi are known to exert a remarkable influence on lichen ecology through their crucial roles in nutrient cycling, bioprospecting and biodiversity, the enigmatic community structures of these fungal inhabitants remain shrouded in mystery, awaiting further exploration and discovery. To address knowledge gap, we conducted metabarcoding on two lichens using 18S gene amplification, Dirinara applanta and Parmotrema tinctorum, and compared their microbial communities to those found in the pine bark to which the lichens were attached. Our hypothesis was that the endolichenic communities would exhibit distinct diversity patterns, community structures, network structures, and specialist composition compared to the surrounding epiphytic community.

RESULTS: Our investigation has shed light on the clear demarcation between the endolichenic and epiphytic fungal communities, as they exhibit markedly different characteristics that set them apart from each other. This research demonstrated that the endolichenic communities are less diverse as compared to the epiphytic communities. Through community similarity analysis, we observed that two endolichenic communities are more similar to each other in terms of community composition than with the adjacent epiphytic communities. Moreover, we unveiled a striking contrast in the network structures between the endolichenic and epiphytic communities, as the former displayed a more modular and less nested features that is evocative of a potent host-filtration mechanism.

CONCLUSIONS: Through our investigation, we have discovered that lichens harbor less intricate and interconnected fungal communities compared to the neighboring epiphytic environment. These observations provide valuable insights into the metagenomic architecture of lichens and offer a tantalizing glimpse into the unique mycobiome.}, } @article {pmid37789055, year = {2023}, author = {Flahaut, M and Leprohon, P and Pham, NP and Gingras, H and Bourbeau, J and Papadopoulou, B and Maltais, F and Ouellette, M}, title = {Distinctive features of the oropharyngeal microbiome in Inuit of Nunavik and correlations of mild to moderate bronchial obstruction with dysbiosis.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {16622}, pmid = {37789055}, issn = {2045-2322}, mesh = {Humans ; *Bronchial Diseases/epidemiology ; *Dysbiosis/epidemiology ; Inuit ; Lung ; *Microbiota ; *Oropharynx/microbiology ; }, abstract = {Inuit of Nunavik are coping with living conditions that can influence respiratory health. Our objective was to investigate associations between respiratory health in Inuit communities and their airway microbiome. Oropharyngeal samples were collected during the Qanuilirpitaa? 2017 Inuit Health Survey and subjected to metagenomic analyses. Participants were assigned to a bronchial obstruction group or a control group based on their clinical history and their pulmonary function, as monitored by spirometry. The Inuit microbiota composition was found to be distinct from other studied populations. Within the Inuit microbiota, differences in diversity measures tend to distinguish the two groups. Bacterial taxa found to be more abundant in the control group included candidate probiotic strains, while those enriched in the bronchial obstruction group included opportunistic pathogens. Crossing taxa affiliation method and machine learning consolidated our finding of distinct core microbiomes between the two groups. More microbial metabolic pathways were enriched in the control participants and these were often involved in vitamin and anti-inflammatory metabolism, while a link could be established between the enriched pathways in the disease group and inflammation. Overall, our results suggest a link between microbial abundance, interactions and metabolic activities and respiratory health in the Inuit population.}, } @article {pmid37788456, year = {2023}, author = {Toyoshima, K and Ohsugi, Y and Lin, P and Komatsu, K and Shiba, T and Takeuchi, Y and Hirota, T and Shimohira, T and Tsuchiya, Y and Katagiri, S and Iwata, T and Aoki, A}, title = {Blue Light-Emitting Diode Irradiation Without a Photosensitizer Alters Oral Microbiome Composition of Ligature-Induced Periodontitis in Mice.}, journal = {Photobiomodulation, photomedicine, and laser surgery}, volume = {41}, number = {10}, pages = {549-559}, doi = {10.1089/photob.2023.0061}, pmid = {37788456}, issn = {2578-5478}, mesh = {Mice ; Male ; Animals ; Photosensitizing Agents/pharmacology ; X-Ray Microtomography/adverse effects ; RNA, Ribosomal, 16S ; *Alveolar Bone Loss/etiology/metabolism ; *Periodontitis/therapy/complications/metabolism ; *Microbiota ; }, abstract = {Objective: This study investigated the suppressive effects of blue light-emitting diode (LED) irradiation on bone resorption and changes in the oral microbiome of mice with ligature-induced periodontitis. Background: Wavelength of blue light has antimicrobial effects; however, whether blue LED irradiation alone inhibits the progression of periodontitis remains unclear. Methods: Nine-week-old male mice ligated ligature around the right maxillary second molar was divided into ligation alone (Li) and ligation with blue LED irradiation (LiBL) groups. The LiBL group underwent blue LED (wavelength, 455 nm) irradiation four times in a week at 150 mW/cm[2] without a photosensitizer on the gingival tissue around the ligated tooth at a distance of 5 mm for 5 min. The total energy density per day was 45 J/cm[2]. Bone resorption was evaluated using micro-computed tomography at 8 days. Differences in the oral microbiome composition of the collected ligatures between the Li and LiBL groups were analyzed using next-generation sequencing based on the 16S rRNA gene from the ligatures. Results: Blue LED irradiation did not suppress bone resorption caused by ligature-induced periodontitis. However, in the LiBL group, the α-diversity, number of observed features, and Chao1 were significantly decreased. The relative abundances in phylum Myxococcota and Bacteroidota were underrepresented, and the genera Staphylococcus, Lactococcus, and Lactobacillus were significantly overrepresented by blue LED exposure. Metagenomic function prediction indicated an increase in the downregulated pathways related to microbial energy metabolism after irradiation. The co-occurrence network was altered to a simpler structure in the LiBL group, and the number of core genera decreased. Conclusions: Blue LED irradiation altered the composition and network of the oral microbiome of ligature-induced periodontitis in mice.}, } @article {pmid37787419, year = {2023}, author = {Zhang, Y and Zhou, Y and Humbert, P and Yuan, D and Yuan, C}, title = {Effect on the Skin Microbiota of Oral Minocycline for Rosacea.}, journal = {Acta dermato-venereologica}, volume = {103}, number = {}, pages = {adv10331}, pmid = {37787419}, issn = {1651-2057}, mesh = {Humans ; Anti-Bacterial Agents/therapeutic use ; *Microbiota ; Minocycline ; RNA, Ribosomal, 16S/genetics ; *Rosacea/diagnosis/drug therapy ; Skin/microbiology ; }, abstract = {In the rosacea an unstable skin microbiota is significant for disease progression. However, data on the influence on the skin microbiota of treatment with systemic antibiotics are limited. This single-arm trial recruited patients with rosacea. Oral minocycline 50 mg was administered twice daily for 6 weeks. The lesions on the cheek and nose were sampled for 16S rRNA amplicon sequencing and metagenomic sequencing at baseline, 3 weeks and 6 weeks of treatment. Physiological parameters were detected using non-invasive instruments. After treatment, distribution of the Investigator Global Assessment scores changed significantly. For the skin microbiota, a notable increase in α-diversity and a shift of structure were observed after treatment. Treatment was accompanied by a reduction in the relative abundance of Cutibacterium and Staphylococcus, indicating negative correlations with increased bacterial metabolic pathways, such as butyrate synthesis and L-tryptophan degradation. The increased butyrate and tryptophan metabolites would be conducive to inhibiting skin inflammation and promoting skin barrier repair. In addition, the abundance of skin bacterial genes related to tetracycline resistance and multidrug resistance increased notably after antibiotic treatment.}, } @article {pmid37786251, year = {2023}, author = {Wang, Y and Ma, W and Mehta, R and Nguyen, LH and Song, M and Drew, DA and Asnicar, F and Huttenhower, C and Segata, N and Wolf, J and Spector, T and Berry, S and Staller, K and Chan, AT}, title = {Diet and gut microbial associations in irritable bowel syndrome according to disease subtype.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2262130}, pmid = {37786251}, issn = {1949-0984}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; K23 DK120945/DK/NIDDK NIH HHS/United States ; K23 DK125838/DK/NIDDK NIH HHS/United States ; /MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; R35 CA253185/CA/NCI NIH HHS/United States ; U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Irritable Bowel Syndrome/microbiology ; *Gastrointestinal Microbiome ; Diarrhea/microbiology ; Constipation/complications ; Diet ; }, abstract = {The role of diet and the gut microbiome in the etiopathogenesis of irritable bowel syndrome (IBS) is not fully understood. Therefore, we investigated the interplay between dietary risk factors and gut microbiota in IBS subtypes using a food frequency questionnaire and stool metagenome data from 969 participants aged 18-65 years in the ZOE PREDICT 1 study, an intervention study designed to predict postprandial metabolic responses. We identified individuals with IBS subtype according to the Rome III criteria based on predominant bowel habits during symptom onset: diarrhea (i.e. looser), constipation (i.e. harder), and mixed. Participants with IBS-D (n = 59) consumed more healthy plant-based foods (e.g. whole grains, leafy vegetables) and fiber, while those with IBS-C (n = 49) tended to consume more unhealthy plant-based foods (e.g. refined grains, fruit juice) than participants without IBS (n = 797). Microbial diversity was nominally lower in patients with IBS-D than in participants without IBS or with IBS-C. Using multivariable-adjusted linear regression, we identified specific microbiota variations in IBS subtypes, including slight increases in pro-inflammatory taxa in IBS-C (e.g. Escherichia coli) and loss of strict anaerobes in IBS-D (e.g. Faecalibacterium prausnitzii). Our analysis also revealed intriguing evidence of interactions between diet and Faecalibacterium prausnitzii. The positive associations between fiber and iron intake and IBS-diarrhea were stronger among individuals with a higher relative abundance of Faecalibacterium prausnitzii, potentially driven by carbohydrate metabolic pathways, including the superpathway of β-D-glucuronide and D-glucuronate degradation. In conclusion, our findings suggest subtype-specific variations in dietary habits, gut microbial composition and function, and diet-microbiota interactions in IBS, providing insights into potential microbiome-informed dietary interventions.}, } @article {pmid37784018, year = {2023}, author = {Tang, X and Yang, L and Miao, Y and Ha, W and Li, Z and Mi, D}, title = {Angelica polysaccharides relieve blood glucose levels in diabetic KKAy mice possibly by modulating gut microbiota: an integrated gut microbiota and metabolism analysis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {281}, pmid = {37784018}, issn = {1471-2180}, mesh = {Mice ; Male ; Animals ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/drug therapy/microbiology ; Blood Glucose/metabolism ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred C57BL ; Polysaccharides/pharmacology ; }, abstract = {BACKGROUND: Angelica polysaccharides (AP) have numerous benefits in relieving type 2 diabetes (T2D). However, the underlying mechanisms have yet to be fully understood. Recent many reports have suggested that altering gut microbiota can have adverse effects on the host metabolism and contribute to the development of T2D. Here, we successfully established the T2D model using the male KKAy mice with high-fat and high-sugar feed. Meanwhile, the male C57BL/6 mice were fed with a normal feed. T2D KKAy mice were fed either with or without AP supplementation. In each group, we measured the mice's fasting blood glucose, weight, and fasting serum insulin levels. We collected the cecum content of mice, the gut microbiota was analyzed by targeted full-length 16S rRNA metagenomic sequencing and metabolites were analyzed by untargeted-metabolomics.

RESULTS: We found AP effectively alleviated glycemic disorders of T2D KKAy mice, with the changes in gut microbiota composition and function. Many bacteria species and metabolites were markedly changed in T2D KKAy mice and reversed by AP. Additionally, 16 altered metabolic pathways affected by AP were figured out by combining metagenomic pathway enrichment analysis and metabolic pathway enrichment analysis. The key metabolites in 16 metabolic pathways were significantly associated with the gut microbial alteration. Together, our findings showed that AP supplementation could attenuate the diabetic phenotype. Significant gut microbiota and gut metabolite changes were observed in the T2D KKAy mice and AP intervention.

CONCLUSIONS: Administration of AP has been shown to improve the composition of intestinal microbiota in T2D KKAy mice, thus providing further evidence for the potential therapeutic application of AP in the treatment of T2D.}, } @article {pmid37784008, year = {2023}, author = {Rumbavicius, I and Rounge, TB and Rognes, T}, title = {HoCoRT: host contamination removal tool.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {371}, pmid = {37784008}, issn = {1471-2105}, support = {190179 and 198048//Kreftforeningen/ ; }, mesh = {Humans ; *Software ; Metagenome ; Sequence Analysis, DNA/methods ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {BACKGROUND: Shotgun metagenome sequencing data obtained from a host environment will usually be contaminated with sequences from the host organism. Host sequences should be removed before further analysis to avoid biases, reduce downstream computational load, or ensure privacy in the case of a human host. The tools that we identified, as designed specifically to perform host contamination sequence removal, were either outdated, not maintained, or complicated to use. Consequently, we have developed HoCoRT, a fast and user-friendly tool that implements several methods for optimised host sequence removal. We have evaluated the speed and accuracy of these methods.

RESULTS: HoCoRT is an open-source command-line tool for host contamination removal. It is designed to be easy to install and use, offering a one-step option for genome indexing. HoCoRT employs a variety of well-known mapping, classification, and alignment methods to classify reads. The user can select the underlying classification method and its parameters, allowing adaptation to different scenarios. Based on our investigation of various methods and parameters using synthetic human gut and oral microbiomes, and on assessment of publicly available data, we provide recommendations for typical datasets with short and long reads.

CONCLUSIONS: To decontaminate a human gut microbiome with short reads using HoCoRT, we found the optimal combination of speed and accuracy with BioBloom, Bowtie2 in end-to-end mode, and HISAT2. Kraken2 consistently demonstrated the highest speed, albeit with a trade-off in accuracy. The same applies to an oral microbiome, but here Bowtie2 was notably slower than the other tools. For long reads, the detection of human host reads is more difficult. In this case, a combination of Kraken2 and Minimap2 achieved the highest accuracy and detected 59% of human reads. In comparison to the dedicated DeconSeq tool, HoCoRT using Bowtie2 in end-to-end mode proved considerably faster and slightly more accurate. HoCoRT is available as a Bioconda package, and the source code can be accessed at https://github.com/ignasrum/hocort along with the documentation. It is released under the MIT licence and is compatible with Linux and macOS (except for the BioBloom module).}, } @article {pmid37781761, year = {2024}, author = {Chandel, N and Somvanshi, PR and Thakur, V}, title = {Characterisation of Indian gut microbiome for B-vitamin production and its comparison with Chinese cohort.}, journal = {The British journal of nutrition}, volume = {131}, number = {4}, pages = {686-697}, pmid = {37781761}, issn = {1475-2662}, mesh = {Humans ; *Vitamin B Complex ; *Gastrointestinal Microbiome/genetics ; Thiamine ; Riboflavin/analysis ; China ; }, abstract = {The human gut microbiota can biosynthesize essential micronutrients such as B-vitamins and is also known for its metabolic cooperative behaviour. The present study characterises such B-vitamin biosynthesizers, their biosynthetic pathways, explores their prevalence and abundance, examines how lifestyle or diet affects them in multiple Indian cohorts and compares it with the Chinese cohort. To achieve this, publicly available faecal metagenome data of healthy individuals from multiple Indian (two urban and three tribal populations) and a Chinese cohort were analysed. The distribution of prevalence and abundance of B-vitamin biosynthesizers showed similar profiles to that of the entire gut community of the Indian cohort, and there were 28 B-vitamin biosynthesizers that had modest or higher prevalence and abundance. The omnivorous diet affected only the prevalence of a few B-vitamin biosynthesizers; however, lifestyle and/or location affected both prevalence and abundance. A comparison with the Chinese cohort showed that fourteen B-vitamin biosynthesizers were significantly more prevalent and abundant in Chinese as compared with Indian samples (False Discovery Rate (FDR) <= 0·05). The metabolic potential of the entire gut community for B-vitamin production showed that within India, the tribal cohort has a higher abundance of B-vitamin biosynthesis pathways as compared with two urban cohorts namely, Bhopal and Kasargod, and comparison with the Chinese cohort revealed a higher abundance in the latter group. Potential metabolic cooperative behaviour of the Indian gut microbiome for biosynthesis of the B-vitamins showed multiple pairs of species showed theoretical complementarity for complete biosynthetic pathways genes of thiamine, riboflavin, niacin and pantothenate.}, } @article {pmid37780855, year = {2023}, author = {Oh, S and Lee, HJ and Park, KU}, title = {Metagenomic characterization of the microbiomes in five different body habitats of otherwise healthy individuals with periodontal disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1257816}, pmid = {37780855}, issn = {2235-2988}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Dental Plaque ; *Microbiota/genetics ; *Periodontal Diseases ; Metagenome ; }, abstract = {INTRODUCTION: Recent studies have proposed several plausible mechanisms supporting the association between periodontal disease and systemic disease. However, characterizing the microbial communities in individuals with periodontal disease before onset of other diseases is an important first step in determining how the altered microbial state contributes to disease progression. This study established microbiome profiles for five body habitats of carefully selected, otherwise healthy individuals with periodontal disease.

METHODS: Blood, oral (buccal mucosa, dental plaque, and saliva), and stool samples were collected from ten healthy subjects with periodontal disease. Using 16S rRNA metagenomics, the taxonomic and functional compositions of microbiomes were investigated.

RESULTS: The most predominant phylum in blood and stool was Bacillota. Pseudomonadota accounted for the largest proportion of microbes in the buccal mucosa and saliva, whereas Bacteroidota were the most prevalent in dental plaque. Differential abundance analysis revealed that 12 phyla and 139 genera were differentially abundant between body habitats. Comparison of alpha diversity showed that the blood microbiome has the most diverse community close to neither oral nor stool microbiomes. We also predicted the functional configurations of the microbiome in otherwise healthy subjects with periodontal disease. Principal coordinate analysis based on functional abundance revealed distinct clustering of the microbial communities between different body habitats, as also observed for taxonomic abundance. In addition, 13 functional pathways, including lipopolysaccharide biosynthesis, glutathione metabolism, and proteasome, showed differential expression between habitats.

DISCUSSION: Our results offer insight into the effects of the microbiome on systemic health and disease in people with periodontal disease.}, } @article {pmid37779211, year = {2023}, author = {Cao, Y and Feng, T and Wu, Y and Xu, Y and Du, L and Wang, T and Luo, Y and Wang, Y and Li, Z and Xuan, Z and Chen, S and Yao, N and Gao, NL and Xiao, Q and Huang, K and Wang, X and Cui, K and Rehman, SU and Tang, X and Liu, D and Han, H and Li, Y and Chen, WH and Liu, Q}, title = {The multi-kingdom microbiome of the goat gastrointestinal tract.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {219}, pmid = {37779211}, issn = {2049-2618}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; Gastrointestinal Tract/microbiology ; *Goats ; Methane ; *Microbiota ; }, abstract = {BACKGROUND: Goat is an important livestock worldwide, which plays an indispensable role in human life by providing meat, milk, fiber, and pelts. Despite recent significant advances in microbiome studies, a comprehensive survey on the goat microbiomes covering gastrointestinal tract (GIT) sites, developmental stages, feeding styles, and geographical factors is still unavailable. Here, we surveyed its multi-kingdom microbial communities using 497 samples from ten sites along the goat GIT.

RESULTS: We reconstructed a goat multi-kingdom microbiome catalog (GMMC) including 4004 bacterial, 71 archaeal, and 7204 viral genomes and annotated over 4,817,256 non-redundant protein-coding genes. We revealed patterns of feeding-driven microbial community dynamics along the goat GIT sites which were likely associated with gastrointestinal food digestion and absorption capabilities and disease risks, and identified an abundance of large intestine-enriched genera involved in plant fiber digestion. We quantified the effects of various factors affecting the distribution and abundance of methane-producing microbes including the GIT site, age, feeding style, and geography, and identified 68 virulent viruses targeting the methane producers via a comprehensive virus-bacterium/archaea interaction network.

CONCLUSIONS: Together, our GMMC catalog provides functional insights of the goat GIT microbiota through microbiome-host interactions and paves the way to microbial interventions for better goat and eco-environmental qualities. Video Abstract.}, } @article {pmid37778796, year = {2024}, author = {Wang, H and Gong, H and Dai, X and Yang, M}, title = {Metagenomics reveals the microbial community and functional metabolism variation in the partial nitritation-anammox process: From collapse to recovery.}, journal = {Journal of environmental sciences (China)}, volume = {135}, number = {}, pages = {210-221}, doi = {10.1016/j.jes.2023.01.002}, pmid = {37778796}, issn = {1001-0742}, mesh = {Anaerobic Ammonia Oxidation ; Oxidation-Reduction ; Bioreactors ; Nitrification ; *Microbiota ; Nitrogen ; *Ammonium Compounds ; Denitrification ; Sewage ; }, abstract = {Mainstream partial nitritation-anammox (PNA) process easily suffers from performance instability and even reactor collapse in application. Thus, it is of great significance to unveil the characteristic of performance recovery, understand the intrinsic mechanism and then propose operational strategy. In this study, we combined long-term reactor operation, batch tests, and metagenomics to reveal the succession of microbial community and functional metabolism variation from system collapse to recovery. Proper aeration control (0.10-0.25 mg O2/L) was critical for performance recovery. It was also found that Candidatus Brocadia became the dominant flora and its abundance increased from 3.5% to 11.0%. Significant enhancements in carbon metabolism and phospholipid biosynthesis were observed during system recovery, and the genes abundance related to signal transduction was dramatically increased. The up-regulation of sdh and suc genes showed the processes of succinate dehydrogenation and succinyl-CoA synthesis might stimulate the production of amino acids and the synthesis of proteins, thereby possibly improving the activity and abundance of AnAOB, which was conducive to the performance recovery. Moreover, the increase in abundance of hzs and hdh genes suggested the enhancement of the anammox process. Changes in the abundance of key genes involved in nitrogen metabolism indicated that nitrogen removal pathway was more diverse after system recovery. The achievement of performance recovery was driven by anammox, nitrification and denitrification coupled with dissimilatory nitrate reduction to ammonium. These results provide deeper insights into the recovery mechanism of PNA system and also provide a potential regulation strategy for the stable operation of the mainstream PNA process.}, } @article {pmid37778601, year = {2023}, author = {Yu, Q and Han, Q and Li, T and Kou, Y and Zhang, X and Wang, Y and Li, G and Zhou, H and Qu, J and Li, H}, title = {Metagenomics reveals the self-recovery and risk of antibiotic resistomes during carcass decomposition of wild mammals.}, journal = {Environmental research}, volume = {238}, number = {Pt 2}, pages = {117222}, doi = {10.1016/j.envres.2023.117222}, pmid = {37778601}, issn = {1096-0953}, mesh = {Animals ; *Genes, Bacterial ; *Anti-Bacterial Agents ; RNA, Ribosomal, 16S ; Mammals/genetics ; Cadaver ; }, abstract = {Animal carcass decomposition may bring serious harm to the environment, including pathogenic viruses, toxic gases and metabolites, and antibiotic resistance genes (ARGs). However, how wild mammal corpses decomposition influence and change ARGs in the environment has less explored. Through metagenomics, 16S rRNA gene sequencing, and physicochemical analysis, this study explored the succession patterns, influencing factors, and assembly process of ARGs and mobile genetic elements (MGEs) in gravesoil during long-term corpse decomposition of wild mammals. Our results indicate that the ARG and MGE communities related to wildlife corpses exhibited a pattern of differentiation first and then convergence. Different from the farmed animals, the decomposition of wild animals first reduced the diversity of ARGs and MGEs, and then recovered to a level similar to that of the control group (untreated soil). ARGs and MGEs of the gravesoil are mainly affected by deterministic processes in different stages. MGEs and bacterial community are the two most important factors affecting ARGs in gravesoil. It is worth noting that the decomposition of wild animal carcasses enriched different high-risk ARGs at different stages (bacA, mecA and floR), which have co-occurrence patterns with opportunistic pathogens (Comamonas and Acinetobacter), thereby posing a great threat to public health. These results are of great significance for wildlife corpse management and environmental and ecological safety.}, } @article {pmid37778473, year = {2023}, author = {Mageiros, L and Megremis, S and Papadopoulos, NG}, title = {The virome in allergy and asthma: A nascent, ineffable player.}, journal = {The Journal of allergy and clinical immunology}, volume = {152}, number = {6}, pages = {1347-1351}, doi = {10.1016/j.jaci.2023.09.022}, pmid = {37778473}, issn = {1097-6825}, mesh = {Humans ; Virome ; Prospective Studies ; *Viruses ; *Bacteriophages/genetics ; *Asthma ; }, abstract = {Allergic diseases can be affected by virus-host interactions and are increasingly linked with the tissue-specific microbiome. High-throughput metagenomic sequencing has offered the opportunity to study the presence of viruses as an ecologic system, namely, the virome. Even though virome studies are technically challenging conceptually and analytically, they are already producing novel data expanding our understanding of the pathophysiologic mechanisms related to chronic inflammation and allergy. The importance of interspecies and intraspecies interactions is becoming apparent, as they can significantly, directly or indirectly, affect the host's response and antigenic state. Here, we emphasize the challenges and potential insights related to study of the virome in the context of allergy and asthma. We review the limited number of studies that have investigated the virome in these conditions, underlining the need for prospective, repeated sampling designs to unravel the virome's impact on disease development and its interplay with microbiota and immunity. The potential therapeutic use of bacteriophages, which are highly complex components of the virome, is discussed. There is clearly a need for further in-depth investigation of the virome as a system in allergic diseases.}, } @article {pmid37777765, year = {2023}, author = {Wen, Y and Yang, L and Wang, Z and Liu, X and Gao, M and Zhang, Y and Wang, J and He, P}, title = {Blocked conversion of Lactobacillus johnsonii derived acetate to butyrate mediates copper-induced epithelial barrier damage in a pig model.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {218}, pmid = {37777765}, issn = {2049-2618}, mesh = {Mice ; Animals ; Swine ; Butyrates/metabolism ; *Lactobacillus johnsonii/metabolism ; Copper ; Acetates ; *Microbiota ; }, abstract = {BACKGROUND: High-copper diets have been widely used to promote growth performance of pigs, but excess copper supplementation can also produce negative effects on ecosystem stability and organism health. High-copper supplementation can damage the intestinal barrier and disturb the gut microbiome community. However, the specific relationship between high-copper-induced intestinal damage and gut microbiota or its metabolites is unclear.

OBJECTIVE: Using fecal microbiota transplantation and metagenomic sequencing, responses of colonic microbiota to a high-copper diet was profiled. In addition, via comparison of specific bacteria and its metabolites rescue, we investigated a network of bacteria-metabolite interactions involving conversion of specific metabolites as a key mechanism linked to copper-induced damage of the colon.

RESULTS: High copper induced colonic damage, Lactobacillus extinction, and reduction of SCFA (acetate and butyrate) concentrations in pigs. LefSe analysis and q-PCR results confirmed the extinction of L. johnsonii. In addition, transplanting copper-rich fecal microbiota to ABX mice reproduced the gut characteristics of the pig donors. Then, L. johnsonii rescue could restore decreased SCFAs (mainly acetate and butyrate) and colonic barrier damage including thinner mucus layer, reduced colon length, and tight junction protein dysfunction. Given that acetate and butyrate concentrations exhibited a positive correlation with L. johnsonii abundance, we investigated how L. johnsonii exerted its effects by supplementing acetate and butyrate. L. johnsonii and butyrate administration but not acetate could correct the damaged colonic barrier. Acetate administration had no effects on butyrate concentration, indicating blocked conversion from acetate to butyrate. Furthermore, L. johnsonii rescue enriched a series of genera with butyrate-producing ability, mainly Lachnospiraceae NK4A136 group.

CONCLUSIONS: For the first time, we reveal the microbiota-mediated mechanism of high-copper-induced colonic damage in piglets. A high-copper diet can induce extinction of L. johnsonii which leads to colonic barrier damage and loss of SCFA production. Re-establishment of L. johnsonii normalizes the SCFA-producing pathway and restores colonic barrier function. Mechanistically, Lachnospiraceae NK4A136 group mediated conversion of acetate produced by L. johnsonii to butyrate is indispensable in the protection of colonic barrier function. Collectively, these findings provide a feasible mitigation strategy for gut damage caused by high-copper diets. Video Abstract.}, } @article {pmid37777125, year = {2023}, author = {Sieber, G and Drees, F and Shah, M and Stach, TL and Hohrenk-Danzouma, L and Bock, C and Vosough, M and Schumann, M and Sures, B and Probst, AJ and Schmidt, TC and Beisser, D and Boenigk, J}, title = {Exploring the efficacy of metabarcoding and non-target screening for detecting treated wastewater.}, journal = {The Science of the total environment}, volume = {903}, number = {}, pages = {167457}, doi = {10.1016/j.scitotenv.2023.167457}, pmid = {37777125}, issn = {1879-1026}, abstract = {Wastewater treatment processes can eliminate many pollutants, yet remainder pollutants contain organic compounds and microorganisms released into ecosystems. These remainder pollutants have the potential to adversely impact downstream ecosystem processes, but their presence is currently not being monitored. This study was set out with the aim of investigating the effectiveness and sensitivity of non-target screening of chemical compounds, 18S V9 rRNA gene, and full-length 16S rRNA gene metabarcoding techniques for detecting treated wastewater in receiving waters. We aimed at assessing the impact of introducing 33 % treated wastewater into a triplicated large-scale mesocosm setup during a 10-day exposure period. Discharge of treated wastewater significantly altered the chemical signature as well as the microeukaryotic and prokaryotic diversity of the mesocosms. Non-target screening, 18S V9 rRNA gene, and full-length 16S rRNA gene metabarcoding detected these changes with significant covariation of the detected pattern between methods. The 18S V9 rRNA gene metabarcoding exhibited superior sensitivity immediately following the introduction of treated wastewater and remained one of the top-performing methods throughout the study. Full-length 16S rRNA gene metabarcoding demonstrated sensitivity only in the initial hour, but became insignificant thereafter. The non-target screening approach was effective throughout the experiment and in contrast to the metabarcoding methods the signal to noise ratio remained similar during the experiment resulting in an increasing relative strength of this method. Based on our findings, we conclude that all methods employed for monitoring environmental disturbances from various sources are suitable. The distinguishing factor of these methods is their ability to detect unknown pollutants and organisms, which sets them apart from previously utilized approaches and allows for a more comprehensive perspective. Given their diverse strengths, particularly in terms of temporal resolution, these methods are best suited as complementary approaches.}, } @article {pmid37776739, year = {2023}, author = {Ji, M and Smith, AF and Rattray, JE and England, WE and Hubert, CRJ}, title = {Potential for natural attenuation of crude oil hydrocarbons in benthic microbiomes near coastal communities in Kivalliq, Nunavut, Canada.}, journal = {Marine pollution bulletin}, volume = {196}, number = {}, pages = {115557}, doi = {10.1016/j.marpolbul.2023.115557}, pmid = {37776739}, issn = {1879-3363}, mesh = {*Petroleum/metabolism ; Nunavut ; RNA, Ribosomal, 16S/genetics ; Hydrocarbons/metabolism ; Canada ; *Microbiota ; Biodegradation, Environmental ; *Petroleum Pollution ; }, abstract = {Oil spilled in marine environments can settle to the seafloor through aggregation and sedimentation processes. This has been predicted to be especially relevant in the Arctic due to plankton blooms initiated by melting sea ice. These conditions exist in the Kivalliq region in Nunavut, Canada, where elevated shipping traffic has increased the risk of accidental spills. Experimental microcosms combining surface sediment and crude oil were incubated at 4 °C over 21 weeks to evaluate the biodegradation potential of seabed microbiomes. Sediments sampled near the communities of Arviat and Chesterfield Inlet were assessed for biodegradation capabilities by combining hydrocarbon geochemistry with 16S rRNA gene and metagenomic sequencing, revealing decreased microbial diversity but enrichment of oil-degrading taxa. Alkane and aromatic hydrocarbon losses corresponded to detection of genes and genomes that encode enzymes for aerobic biodegradation of these compounds, pointing to the utility of marine microbiome surveys for predicting the fate of oil released into Arctic marine environments.}, } @article {pmid37775319, year = {2023}, author = {Ma, C and Li, Y and Mei, Z and Yuan, C and Kang, JH and Grodstein, F and Ascherio, A and Willett, WC and Chan, AT and Huttenhower, C and Stampfer, MJ and Wang, DD}, title = {Association Between Bowel Movement Pattern and Cognitive Function: Prospective Cohort Study and a Metagenomic Analysis of the Gut Microbiome.}, journal = {Neurology}, volume = {101}, number = {20}, pages = {e2014-e2025}, pmid = {37775319}, issn = {1526-632X}, support = {R00 DK119412/DK/NIDDK NIH HHS/United States ; R01 AG077489/AG/NIA NIH HHS/United States ; R01 NR019992/NR/NINR NIH HHS/United States ; K99 DK119412/DK/NIDDK NIH HHS/United States ; UM1 CA186107/CA/NCI NIH HHS/United States ; U01 CA176726/CA/NCI NIH HHS/United States ; U01 CA167552/CA/NCI NIH HHS/United States ; }, mesh = {Male ; Humans ; Female ; Aged ; Prospective Studies ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Defecation ; Cohort Studies ; Cognition/physiology ; }, abstract = {BACKGROUND AND OBJECTIVES: Little is known regarding the association between intestinal motility patterns and cognitive function in individuals who are baseline cognitively healthy. The gut microbiome may contribute to the association. We examined the association between bowel movement (BM) pattern and cognitive function and explored the role of the gut microbiome in explaining this association.

METHODS: In this prospective study, we leveraged 3 cohort studies, Nurses' Health Study (NHS), NHSII, and Health Professionals Follow-Up Study (HPFS). Participants reported BM frequency and subjective cognitive function. In a subset of NHSII participants, we assessed cognitive function using an objective neuropsychological battery. We profiled the gut microbiome in a subset of participants using whole-genome shotgun metagenomics. General linear models, Poisson regression, and logistic regression were used to quantify the association of BM frequency with different cognitive measurements.

RESULTS: We followed 112,753 men and women (women: 87.6%) with a mean age of 67.2 years at baseline (NHS: 76 years, NHSII: 59 years, HPFS: 75 years) for a median follow-up of 4 years (NHSII and HPFS: 4 years, NHS: 2 years). Compared with those with BM once daily, participants with BM frequency every 3+ days had significantly worse objective cognitive function, equivalent to 3.0 (95% confidence interval [CI],1.2-4.7) years of chronological cognitive aging. We observed similar J-shape dose-response relationships of BM frequency with the odds of subjective cognitive decline and the likelihood of having more subsequent subjective cognitive complaints (both p nonlinearity < 0.001). BM frequencies of every 3+ days and ≥twice/day, compared with once daily, were associated with the odds ratios of subjective cognitive decline of 1.73 (95% CI 1.60-1.86) and 1.37 (95% CI 1.33-1.44), respectively. BM frequency and subjective cognitive decline were significantly associated with the overall gut microbiome configuration (both p < 0.005) and specific microbial species in the 515 participants with microbiome data. Butyrate-producing microbial species were depleted in those with less frequent BM and worse cognition, whereas a higher abundance of proinflammatory species was associated with BM frequency of ≥twice/day and worse cognition.

DISCUSSION: Lower BM frequency was associated with worse cognitive function. The gut microbial dysbiosis may be a mechanistic link underlying the association.}, } @article {pmid37774634, year = {2023}, author = {Kharnaior, P and Tamang, JP}, title = {Microbiome and metabolome in home-made fermented soybean foods of India revealed by metagenome-assembled genomes and metabolomics.}, journal = {International journal of food microbiology}, volume = {407}, number = {}, pages = {110417}, doi = {10.1016/j.ijfoodmicro.2023.110417}, pmid = {37774634}, issn = {1879-3460}, mesh = {Humans ; Metagenome ; Glycine max/microbiology ; *Microbiota/genetics ; *Fermented Foods/microbiology ; Metabolome ; Metagenomics ; }, abstract = {Grep-chhurpi, peha, peron namsing and peruñyaan are lesser-known home-made fermented soybean foods prepared by the native people of Arunachal Pradesh in India. Present work aims to study the microbiome, their functional annotations, metabolites and recovery of metagenome-assembled genomes (MAGs) in these four fermented soybean foods. Metagenomes revealed the dominance of bacteria (97.80 %) with minor traces of viruses, eukaryotes and archaea. Bacillota is the most abundant phylum with Bacillus subtilis as the abundant species. Metagenome also revealed the abundance of lactic acid bacteria such as Enterococcus casseliflavus, Enterococcus faecium, Mammaliicoccus sciuri and Staphylococcus saprophyticus in all samples. B. subtilis was the major species found in all products. Predictive metabolic pathways showed the abundance of genes associated with metabolisms. Metabolomics analysis revealed both targeted and untargeted metabolites, which suggested their role in flavour development and therapeutic properties. High-quality MAGs, identified as B. subtilis, Enterococcus faecalis, Pediococcus acidilactici and B. velezensis, showed the presence of several biomarkers corresponding to various bio-functional properties. Gene clusters of secondary metabolites (antimicrobial peptides) and CRISPR-Cas systems were detected in all MAGs. This present work also provides key elements related to the cultivability of identified species of MAGs for future use as starter cultures in fermented soybean food product development. Additionally, comparison of microbiome and metabolites of grep-chhurpi, peron namsing and peruñyaan with that of other fermented soybean foods of Asia revealed a distinct difference.}, } @article {pmid37774039, year = {2023}, author = {Ma, L and Hou, C and Yang, H and Chen, Q and Lyu, W and Wang, Z and Wang, J and Xiao, Y}, title = {Multi-omics analysis reveals the interaction of gut microbiome and host microRNAs in ulcerative colitis.}, journal = {Annals of medicine}, volume = {55}, number = {2}, pages = {2261477}, pmid = {37774039}, issn = {1365-2060}, mesh = {Humans ; Animals ; Mice ; *Colitis, Ulcerative/genetics ; *MicroRNAs/genetics/metabolism ; *Gastrointestinal Microbiome ; Multiomics ; *Colitis/chemically induced/genetics ; Inflammation ; *Inflammatory Bowel Diseases ; Mice, Inbred C57BL ; Disease Models, Animal ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic inflammation of the gastrointestinal tract that co-occurs with gut microbiota dysbiosis; however, its etiology remains unclear. MicroRNA (miRNA)-microbiome interactions play an essential role in host health and disease.

METHODS: To investigate the gut microbiome and host miRNA profiles in colitis, we used a Dextran Sulfate Sodium (DSS)-induced ulcerative colitis (UC) model. Metagenomic sequencing and metabolome profiling were performed to explore typical microbiota and metabolite signatures in colitis, whereas mRNA and miRNA sequencing were used to determine differentially expressed miRNAs and their target genes in the inflamed colon.

RESULTS: A total of 986 miRNAs were identified between the two groups, with 41 upregulated and 21 downregulated miRNAs in colitis mice compared to the control group. Notably, the target genes of these significantly altered miRNAs were primarily enriched in the immune and inflammation-related pathways. Second, LEfSe analysis revealed bacterial biomarkers distinguishing the two groups, with significantly higher levels of commonly encountered pathogens such as Escherichia coli and Shigella flexneri in the UC group, whereas beneficial species such as Bifidobacterium pseudolongum were more abundant in the control group. Microbiota metabolites histamine, N-acetylhistamine, and glycocholic acid were found to be downregulated in colitis mice. Spearman correlation further revealed the potential crosstalk between the microbiota profile and colonic miRNA, revealing the possibility of microbiome-miRNA interactions involved in IBD development.

CONCLUSIONS: Our data reveal the relationships between multi-omic features during UC and suggest that targeting specific miRNAs may provide new avenues for the development of effective miRNA-based therapeutics.}, } @article {pmid37774017, year = {2023}, author = {Wielscher, M and Pfisterer, K and Samardzic, D and Balsini, P and Bangert, C and Jäger, K and Buchberger, M and Selitsch, B and Pjevac, P and Willinger, B and Weninger, W}, title = {The phageome in normal and inflamed human skin.}, journal = {Science advances}, volume = {9}, number = {39}, pages = {eadg4015}, pmid = {37774017}, issn = {2375-2548}, mesh = {Humans ; *Virome ; Skin/microbiology ; *Microbiota ; Metagenome ; Bacteria/genetics ; DNA, Viral/genetics ; }, abstract = {Dysbiosis of skin microbiota drives the progression of atopic dermatitis (AD). The contribution of bacteriophages to bacterial community compositions in normal and inflamed skin is unknown. Using shotgun metagenomics from skin swabs of healthy individuals and patients with AD, we found 13,586 potential viral contiguous DNA sequences, which could be combined into 164 putative viral genomes including 133 putative phages. The Shannon diversity index for the viral metagenome-assembled genomes (vMAGs) did not correlate with AD. In total, we identified 28 vMAGs that differed significantly between normal and AD skin. Quantitative polymerase chain reaction validation of three complete vMAGs revealed their independence from host bacterium abundance. Our data indicate that normal and inflamed skin harbor distinct phageomes and suggest a causative relationship between changing viral and bacterial communities as a driver of skin pathology.}, } @article {pmid37773075, year = {2023}, author = {Trinh, P and Clausen, DS and Willis, AD}, title = {happi: a hierarchical approach to pangenomics inference.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {214}, pmid = {37773075}, issn = {1474-760X}, support = {R21 AI168679/AI/NIAID NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; T32 ES015459/ES/NIEHS NIH HHS/United States ; }, mesh = {*Metagenomics ; *Microbiota/genetics ; Metagenome ; Computer Simulation ; Sequence Analysis, DNA ; }, abstract = {Recovering metagenome-assembled genomes (MAGs) from shotgun sequencing data is an increasingly common task in microbiome studies, as MAGs provide deeper insight into the functional potential of both culturable and non-culturable microorganisms. However, metagenome-assembled genomes vary in quality and may contain omissions and contamination. These errors present challenges for detecting genes and comparing gene enrichment across sample types. To address this, we propose happi, an approach to testing hypotheses about gene enrichment that accounts for genome quality. We illustrate the advantages of happi over existing approaches using published Saccharibacteria MAGs, Streptococcus thermophilus MAGs, and via simulation.}, } @article {pmid37771005, year = {2023}, author = {Park, S and Kang, S}, title = {Association of Pooled Fecal Microbiota on Height Growth in Children According to Enterotypes.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {77}, number = {6}, pages = {801-810}, doi = {10.1097/MPG.0000000000003949}, pmid = {37771005}, issn = {1536-4801}, mesh = {Child ; Humans ; *Phosphatidylinositol 3-Kinases ; Bacteria ; *Gastrointestinal Microbiome/physiology ; Feces/microbiology ; }, abstract = {OBJECTIVES: The association between fecal microbiota and height in children has yielded conflicting findings, warranting further investigation into potential differences in fecal bacterial composition between children with short stature and those of standard height based on enterotypes (ETs).

METHODS: According to the height z score for age and gender, the children were categorized into normal-stature (NS; n = 335) and short-stature (SS; n = 152) groups using a z score of -1.15 as a separator value. The human fecal bacterial FASTA/Q files (n = 487) were pooled and analyzed with the QIIME 2 platform with the National Center for Biotechnology Information alignment search tool. According to ETs, the prediction models by the machine learning algorithms were used for explaining SS, and their quality was validated.

RESULTS: The proportion of SS was 16.4% in ET Enterobacteriaceae (ET-E) and 68.1% in Prevotellaceae (ET-P). The Chao1 and Shannon indexes were significantly lower in the SS than in the NS groups only in ET-P. The fecal bacteria related to SS from the prediction models were similar regardless of ETs. However, in network analysis, the negative correlations between fecal bacteria in the NS and SS groups were much higher in the ET-P than in the ET-E. In the metagenome function, fecal bacteria showed an inverse association of biotin and secondary bile acid synthesis and downregulation of insulin/insulin-like growth factor-1-driven phosphoinositide 3-kinase Akt signaling and AMP-kinase signaling in the SS group compared with the NS group in both ETs.

CONCLUSION: The gut microbial compositions in children were associated with height. Strategies to modify and optimize the gut microbiota composition should be investigated for any potential in promoting height in children.}, } @article {pmid37771003, year = {2023}, author = {Gautam, A and Bhowmik, D and Basu, S and Zeng, W and Lahiri, A and Huson, DH and Paul, S}, title = {Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {6}, pages = {}, doi = {10.1093/bib/bbad325}, pmid = {37771003}, issn = {1477-4054}, mesh = {*Metabolome ; *Microbiota ; Metabolomics/methods ; Internet ; }, abstract = {A microbial community maintains its ecological dynamics via metabolite crosstalk. Hence, knowledge of the metabolome, alongside its populace, would help us understand the functionality of a community and also predict how it will change in atypical conditions. Methods that employ low-cost metagenomic sequencing data can predict the metabolic potential of a community, that is, its ability to produce or utilize specific metabolites. These, in turn, can potentially serve as markers of biochemical pathways that are associated with different communities. We developed MMIP (Microbiome Metabolome Integration Platform), a web-based analytical and predictive tool that can be used to compare the taxonomic content, diversity variation and the metabolic potential between two sets of microbial communities from targeted amplicon sequencing data. MMIP is capable of highlighting statistically significant taxonomic, enzymatic and metabolic attributes as well as learning-based features associated with one group in comparison with another. Furthermore, MMIP can predict linkages among species or groups of microbes in the community, specific enzyme profiles, compounds or metabolites associated with such a group of organisms. With MMIP, we aim to provide a user-friendly, online web server for performing key microbiome-associated analyses of targeted amplicon sequencing data, predicting metabolite signature, and using learning-based linkage analysis, without the need for initial metabolomic analysis, and thereby helping in hypothesis generation.}, } @article {pmid37768087, year = {2023}, author = {Wang, M and Lu, J and Qin, P and Wang, S and Ding, W and Fu, H-H and Zhang, Y-Z and Zhang, W}, title = {Biofilm formation stabilizes metabolism in a Roseobacteraceae bacterium under temperature increase.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {10}, pages = {e0060123}, pmid = {37768087}, issn = {1098-5336}, mesh = {Temperature ; *Bacteria/genetics ; *Carbohydrate Metabolism ; Glycolysis ; Biofilms ; }, abstract = {Ocean warming profoundly impacts microbes in marine environments; yet, how lifestyle (e.g., free living versus biofilm associated) affects the bacterial response to rising temperature is not clear. Here, we compared transcriptional, enzymatic, and physiological responses of free-living and biofilm-associated Leisingera aquaemixtae M597, a member of the Roseobacteraceae family isolated from marine biofilms, to the increase in temperature from 25℃ to 31℃. Complete genome sequencing and metagenomics revealed the prevalence of M597 in global ocean biofilms. Transcriptomics suggested a significant effect on the expression of genes related to carbohydrate metabolism, nitrogen and sulfur metabolism, and phosphorus utilization of free-living M597 cells due to temperature increase, but such drastic alterations were not observed in its biofilms. In the free-living state, the transcription of the key enzyme participating in the Embden-Meyerhof-Parnas pathway was significantly increased due to the increase in temperature, accompanied by a substantial decrease in the Entner-Doudoroff pathway, but transcripts of these glycolytic enzymes in biofilm-forming strains were independent of the temperature variation. The correlation between the growth condition and the shift in glycolytic pathways under temperature change was confirmed by enzymatic activity assays. Furthermore, the rising temperature affected the growth rate and the production of intracellular reactive oxygen species when M597 cells were free living rather than in biofilms. Thus, biofilm formation stabilizes metabolism in M597 when grown under high temperature and this homeostasis is probably related to the glycolytic pathways.IMPORTANCEBiofilm formation is one of the most successful strategies employed by microbes against environmental fluctuations. In this study, using a marine Roseobacteraceae bacterium, we studied how biofilm formation affects the response of marine bacteria to the increase in temperature. This study enhances our understanding of the function of bacterial biofilms and the microbe-environment interactions in the framework of global climate change.}, } @article {pmid37766302, year = {2023}, author = {Ternovoi, VA and Shvalov, AN and Kartashov, MY and Ponomareva, EP and Tupota, NL and Khoroshavin, YA and Bayandin, RB and Gladysheva, AV and Mikryukova, TP and Tregubchak, TV and Loktev, VB}, title = {The Viromes of Mosquitoes from the Natural Landscapes of Western Siberia.}, journal = {Viruses}, volume = {15}, number = {9}, pages = {}, pmid = {37766302}, issn = {1999-4915}, mesh = {Humans ; Animals ; Virome ; Siberia ; *Nodaviridae ; Capsid Proteins/genetics ; *Culicidae ; }, abstract = {The metagenomic analysis of mosquitoes allows for the genetic characterization of mosquito-associated viruses in different regions of the world. This study applied a metagenomic approach to identify novel viral sequences in seven species of mosquitoes collected from the Novosibirsk region of western Siberia. Using NGS sequencing, we identified 15 coding-complete viral polyproteins (genomes) and 15 viral-like partial sequences in mosquitoes. The complete sequences for novel viruses or the partial sequences of capsid proteins, hypothetical viral proteins, and RdRps were used to identify their taxonomy. The novel viral sequences were classified within the orders Tymovirales and Picornavirales and the families Partitiviridae, Totiviridae, Tombusviridae, Iflaviridae, Nodaviridae, Permutotetraviridae, and Solemoviridae, with several attributed to four unclassified RNA viruses. Interestingly, the novel putative viruses and viral sequences were mainly associated with the mosquito Coquillettidia richardii. This study aimed to increase our understanding of the viral diversity in mosquitoes found in the natural habitats of Siberia, which is characterized by very long, snowy, and cold winters.}, } @article {pmid37766257, year = {2023}, author = {de Santana, SF and Santos, VC and Lopes, ÍS and Porto, JAM and Mora-Ocampo, IY and Sodré, GA and Pirovani, CP and Góes-Neto, A and Pacheco, LGC and Fonseca, PLC and Costa, MA and Aguiar, ERGR}, title = {Mining Public Data to Investigate the Virome of Neglected Pollinators and Other Floral Visitors.}, journal = {Viruses}, volume = {15}, number = {9}, pages = {}, pmid = {37766257}, issn = {1999-4915}, mesh = {Humans ; Bees ; Animals ; *Virome ; Phylogeny ; Insecta ; *Viruses/genetics ; Crops, Agricultural ; }, abstract = {This study reports the virome investigation of pollinator species and other floral visitors associated with plants from the south of Bahia: Aphis aurantii, Atrichopogon sp., Dasyhelea sp., Forcipomyia taiwana, and Trigona ventralis hoozana. Studying viruses in insects associated with economically important crops is vital to understand transmission dynamics and manage viral diseases that pose as threats for global food security. Using literature mining and public RNA next-generation sequencing data deposited in the NCBI SRA database, we identified potential vectors associated with Malvaceae plant species and characterized the microbial communities resident in these insects. Bacteria and Eukarya dominated the metagenomic analyses of all taxon groups. We also found sequences showing similarity to elements from several viral families, including Bunyavirales, Chuviridae, Iflaviridae, Narnaviridae, Orthomyxoviridae, Rhabdoviridae, Totiviridae, and Xinmoviridae. Phylogenetic analyses indicated the existence of at least 16 new viruses distributed among A. aurantii (3), Atrichopogon sp. (4), Dasyhelea sp. (3), and F. taiwana (6). No novel viruses were found for T. ventralis hoozana. For F. taiwana, the available libraries also allowed us to suggest possible vertical transmission, while for A. aurantii we followed the infection profile along the insect development. Our results highlight the importance of studying the virome of insect species associated with crop pollination, as they may play a crucial role in the transmission of viruses to economically important plants, such as those of the genus Theobroma, or they will reduce the pollination process. This information may be valuable in developing strategies to mitigate the spread of viruses and protect the global industry.}, } @article {pmid37766228, year = {2023}, author = {Paietta, EN and Kraberger, S and Custer, JM and Vargas, KL and Espy, C and Ehmke, E and Yoder, AD and Varsani, A}, title = {Characterization of Diverse Anelloviruses, Cressdnaviruses, and Bacteriophages in the Human Oral DNA Virome from North Carolina (USA).}, journal = {Viruses}, volume = {15}, number = {9}, pages = {}, pmid = {37766228}, issn = {1999-4915}, mesh = {Humans ; Animals ; *Bacteriophages ; *Anelloviridae ; North Carolina ; Pilot Projects ; Virome ; DNA ; *Lemur ; }, abstract = {The diversity of viruses identified from the various niches of the human oral cavity-from saliva to dental plaques to the surface of the tongue-has accelerated in the age of metagenomics. This rapid expansion demonstrates that our understanding of oral viral diversity is incomplete, with only a few studies utilizing passive drool collection in conjunction with metagenomic sequencing methods. For this pilot study, we obtained 14 samples from healthy staff members working at the Duke Lemur Center (Durham, NC, USA) to determine the viral diversity that can be identified in passive drool samples from humans. The complete genomes of 3 anelloviruses, 9 cressdnaviruses, 4 Caudoviricetes large bacteriophages, 29 microviruses, and 19 inoviruses were identified in this study using high-throughput sequencing and viral metagenomic workflows. The results presented here expand our understanding of the vertebrate-infecting and microbe-infecting viral diversity of the human oral virome in North Carolina (USA).}, } @article {pmid37764199, year = {2023}, author = {Williams, RAJ and Sánchez-Llatas, CJ and Doménech, A and Madrid, R and Fandiño, S and Cea-Callejo, P and Gomez-Lucia, E and Benítez, L}, title = {Emerging and Novel Viruses in Passerine Birds.}, journal = {Microorganisms}, volume = {11}, number = {9}, pages = {}, pmid = {37764199}, issn = {2076-2607}, abstract = {There is growing interest in emerging viruses that can cause serious or lethal disease in humans and animals. The proliferation of cloacal virome studies, mainly focused on poultry and other domestic birds, reveals a wide variety of viruses, although their pathogenic significance is currently uncertain. Analysis of viruses detected in wild birds is complex and often biased towards waterfowl because of the obvious interest in avian influenza or other zoonotic viruses. Less is known about the viruses present in the order Passeriformes, which comprises approximately 60% of extant bird species. This review aims to compile the most significant contributions on the DNA/RNA viruses affecting passerines, from traditional and metagenomic studies. It highlights that most passerine species have never been sampled. Especially the RNA viruses from Flaviviridae, Orthomyxoviridae and Togaviridae are considered emerging because of increased incidence or avian mortality/morbidity, spread to new geographical areas or hosts and their zoonotic risk. Arguably poxvirus, and perhaps other virus groups, could also be considered "emerging viruses". However, many of these viruses have only recently been described in passerines using metagenomics and their role in the ecosystem is unknown. Finally, it is noteworthy that only one third of the viruses affecting passerines have been officially recognized.}, } @article {pmid37763247, year = {2023}, author = {Gong, X and Li, S and Wu, Z and Alhaj Hamoud, Y and Shaghaleh, H and Kalkhajeh, YK and Si, C and Zhu, L and Ma, C}, title = {Biochar Enhances Soil Resource Availability and Suppresses Microbial Metabolism Genes in the Rhizosphere of Wheat.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, pmid = {37763247}, issn = {2075-1729}, abstract = {Despite the well-documented role of biochar in promoting soil quality and crop productivity, the underlying biological mechanisms remain poorly understood. Here, we explored the effects of straw biochar on soil microbiome in the rhizosphere from wheat using metagenomic sequencing. Our results showed that straw return decreased the yields of wheat, while the straw biochar return increased the wheat yields. Further, both the richness and community composition confirmed different effects of the straw return and straw biochar return. The straw biochar return also resulted in greater rhizosphere effects from wheat, represented by resource availability, including soil organic carbon, soil total nitrogen, available phosphorus, and available potassium. The rhizosphere effects from wheat, represented by microbial metabolism genes involved in carbon, nitrogen, phosphorus, and potassium cycling, however, were decreased by straw biochar returning. In addition, the rhizosphere effects from nitrogen content and the nitrogen cycling genes showed negative relationships with wheat yields. Together, these results revealed that straw biochar enhanced soil resource availability but suppressed microbial metabolism genes in the rhizosphere from wheat, supporting the idea that straw biochar serves as a nutrient pool for crops.}, } @article {pmid37762390, year = {2023}, author = {Schlegel, I and De Goüyon Matignon de Pontourade, CMF and Lincke, JB and Keller, I and Zinkernagel, MS and Zysset-Burri, DC}, title = {The Human Ocular Surface Microbiome and Its Associations with the Tear Proteome in Dry Eye Disease.}, journal = {International journal of molecular sciences}, volume = {24}, number = {18}, pages = {}, pmid = {37762390}, issn = {1422-0067}, support = {CF10000044-EPFL SCR0237812//Fondation Bertarelli/ ; n.a.//OPOS foundation/ ; }, mesh = {Humans ; Proteome ; Eye ; *Dry Eye Syndromes ; Face ; *Microbiota ; }, abstract = {Although dry eye disease (DED) is one of the most common ocular surface diseases worldwide, its pathogenesis is incompletely understood, and treatment options are limited. There is growing evidence that complex interactions between the ocular surface microbiome (OSM) and tear fluid constituents, potentially leading to inflammatory processes, are associated with ocular surface diseases such as DED. In this study, we aimed to find unique compositional and functional features of the OSM associated with human and microbial tear proteins in patients with DED. Applying whole-metagenome shotgun sequencing of forty lid and conjunctival swabs, we identified 229 taxa, with Actinobacteria and Proteobacteria being the most abundant phyla and Propionibacterium acnes the dominating species in the cohort. When DED patients were compared to controls, the species Corynebacterium tuberculostearicum was more abundant in conjunctival samples, whereas the family Propionibacteriaceae was more abundant in lid samples. Functional analysis showed that genes of L-lysine biosynthesis, tetrapyrrole biosynthesis, 5-aminoimidazole ribonucleotide biosynthesis, and the super pathway of L-threonine biosynthesis were enriched in conjunctival samples of controls. The relative abundances of Acinetobacter johnsonii correlated with seven human tear proteins, including mucin-16. The three most abundant microbial tear proteins were the chaperone protein DnaK, the arsenical resistance protein ArsH, and helicase. Compositional and functional features of the OSM and the tear proteome are altered in patients with DED. Ultimately, this may help to design novel interventional therapeutics to target DED.}, } @article {pmid37762139, year = {2023}, author = {Gryaznova, M and Kozarenko, O and Smirnova, Y and Burakova, I and Syromyatnikov, M and Maslov, A and Lebedeva, O}, title = {Cervical and Vaginal Microbiomes in Early Miscarriages and Ongoing Pregnancy with and without Dydrogesterone Usage.}, journal = {International journal of molecular sciences}, volume = {24}, number = {18}, pages = {}, pmid = {37762139}, issn = {1422-0067}, support = {22-24-00802//Russian Science Foundation/ ; }, mesh = {Pregnancy ; Female ; Humans ; *Abortion, Spontaneous ; Dydrogesterone/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Vagina ; *Microbiota/genetics ; }, abstract = {Emerging evidence suggests that the reproductive tract microbiota is a key modulator of local inflammatory and immune pathways throughout pregnancy and may subsequently impact pregnancy outcomes. In this study, our objective was to analyze the cervical and vaginal microbiomes during early pregnancy among three groups: women with healthy ongoing pregnancies, women undergoing dydrogesterone treatment, and those who experienced miscarriages. The experiment involved 51 women at 8-11 weeks of gestation. The microbiome was examined using 16S rRNA sequencing on the Ion Torrent PGM platform. Across all groups, Lactobacillus iners was predominant, suggesting that the vaginal community type CST III is common among the majority of participants. Notably, our data highlighted the significant roles of Gardnerella vaginalis and Mycoplasma girerdii in the pathogenesis of early miscarriage. Conversely, L. iners and Bifidobacterium longum have a protective effect in early pregnancy. Moreover, dydrogesterone intake appeared to influence notable differences between the cervical and vaginal microbiomes. Overall, our study enhanced our understanding of the cervical and vaginal microbiome composition in the eastern European population during early pregnancy.}, } @article {pmid37762088, year = {2023}, author = {Aitmanaitė, L and Širmonaitis, K and Russo, G}, title = {Microbiomes, Their Function, and Cancer: How Metatranscriptomics Can Close the Knowledge Gap.}, journal = {International journal of molecular sciences}, volume = {24}, number = {18}, pages = {}, pmid = {37762088}, issn = {1422-0067}, mesh = {Humans ; *Neoplasms/genetics ; Metagenomics ; *Microbiota/genetics ; Transcriptome ; }, abstract = {The interaction between the microbial communities in the human body and the onset and progression of cancer has not been investigated until recently. The vast majority of the metagenomics research in this area has concentrated on the composition of microbiomes, attempting to link the overabundance or depletion of certain microorganisms to cancer proliferation, metastatic behaviour, and its resistance to therapies. However, studies elucidating the functional implications of the microbiome activity in cancer patients are still scarce; in particular, there is an overwhelming lack of studies assessing such implications directly, through analysis of the transcriptome of the bacterial community. This review summarises the contributions of metagenomics and metatranscriptomics to the knowledge of the microbial environment associated with several cancers; most importantly, it highlights all the advantages that metatranscriptomics has over metagenomics and suggests how such an approach can be leveraged to advance the knowledge of the cancer bacterial environment.}, } @article {pmid37757827, year = {2023}, author = {Blaustein, RA and Shen, Z and Kashaf, SS and Lee-Lin, S and Conlan, S and , and Bosticardo, M and Delmonte, OM and Holmes, CJ and Taylor, ME and Banania, G and Nagao, K and Dimitrova, D and Kanakry, JA and Su, H and Holland, SM and Bergerson, JRE and Freeman, AF and Notarangelo, LD and Kong, HH and Segre, JA}, title = {Expanded microbiome niches of RAG-deficient patients.}, journal = {Cell reports. Medicine}, volume = {4}, number = {10}, pages = {101205}, pmid = {37757827}, issn = {2666-3791}, support = {T32 HD007009/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Skin ; Metagenome ; }, abstract = {The complex interplay between microbiota and immunity is important to human health. To explore how altered adaptive immunity influences the microbiome, we characterize skin, nares, and gut microbiota of patients with recombination-activating gene (RAG) deficiency-a rare genetically defined inborn error of immunity (IEI) that results in a broad spectrum of clinical phenotypes. Integrating de novo assembly of metagenomes from RAG-deficient patients with reference genome catalogs provides an expansive multi-kingdom view of microbial diversity. RAG-deficient patient microbiomes exhibit inter-individual variation, including expansion of opportunistic pathogens (e.g., Corynebacterium bovis, Haemophilus influenzae), and a relative loss of body site specificity. We identify 35 and 27 bacterial species derived from skin/nares and gut microbiomes, respectively, which are distinct to RAG-deficient patients compared to healthy individuals. Underscoring IEI patients as potential reservoirs for viral persistence and evolution, we further characterize the colonization of eukaryotic RNA viruses (e.g., Coronavirus 229E, Norovirus GII) in this patient population.}, } @article {pmid37754998, year = {2023}, author = {Pagani, DM and Ventura, SPR and Vu, D and Mendes-Pereira, T and Ribeiro Tomé, LM and Carvalho, DS and Costa-Rezende, DH and Kato, RB and García, GJY and Geml, J and Robert, V and They, NH and Brenig, B and Azevedo, V and Scroferneker, ML and Valente, P and Góes-Neto, A}, title = {Unveiling Fungal Community Structure along Different Levels of Anthropic Disturbance in a South American Subtropical Lagoon.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {9}, pages = {}, pmid = {37754998}, issn = {2309-608X}, support = {NA//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; NA//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; APQ-01411-22//Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG)/ ; 308880/2022-6//CNPq/ ; }, abstract = {Studies of fungal communities through amplicon metagenomics in aquatic environments, particularly in freshwater ecosystems, are still relatively recent. Unfortunately, many of these water bodies are facing growing threats from human expansion, such as effluent discharge from various human activities. As a result, these effluents have the potential to significantly alter the characteristics of water bodies and, subsequently, impact the diversity of their resident microorganisms. In this context, our objective was to investigate whether the fungal community structure varies according to the presence of different anthropic disturbances. We expect (i) the diversity of fungi will be greater and (ii) more specific unique operational taxonomic units (OTUs) related to each ecotonal system will be found compared to other sites of a lagoon. The study was conducted in the Tramandaí Lagoon (subtropical southern Brazil) at four distinct sampling points (estuary, middle of the lagoon, crop field area, and near a residential area where the Tramandaí River flows into the lagoon). As expected, the estuary and residential zones, which are ecotones, exhibited greater fungal diversity and more specific OTUs compared to the middle of the lagoon and crop field area. Moreover, a substantial proportion of fungal taxa could not be identified at the genus level, with many only classified at the phylum level, indicating potential new lineages. These findings underscore our limited understanding of the subtropical freshwater mycobiota.}, } @article {pmid37754684, year = {2023}, author = {Zhang, Y and Kitazumi, A and Liao, Y-T and de Los Reyes, BG and Wu, VCH}, title = {Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0022623}, pmid = {37754684}, issn = {2165-0497}, support = {2030-42000-0055-000-D//USDA | Agricultural Research Service (ARS)/ ; }, mesh = {*Bacteriophages/genetics ; *Gene Transfer, Horizontal ; *Metagenomics ; *Agriculture ; *Bacteria/genetics/virology/drug effects ; *Microbiota/genetics ; Metagenome ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; Drug Resistance, Bacterial/genetics ; Soil Microbiology ; }, abstract = {Antibiotic resistance has become a serious health concern worldwide. The potential impact of viruses, bacteriophages in particular, on spreading antibiotic resistance genes is still controversial due to the complexity of bacteriophage-bacterial interactions within diverse environments. In this study, we determined the microbiome profiles and the potential antibiotic resistance gene (ARG) transfer between bacterial and viral populations in different agricultural samples using a high-resolution analysis of the metagenomes. The results of this study provide compelling genetic evidence for ARG transfer through bacteriophage-bacteria interactions, revealing the inherent risks associated with bacteriophage-mediated ARG transfer across the agricultural microbiome.}, } @article {pmid37754563, year = {2023}, author = {Zhang, A and de Ángel Solá, D and Acevedo Flores, M and Cao, L and Wang, L and Kim, JG and Tarr, PI and Warner, BB and Rosario Matos, N and Wang, L}, title = {Infants exposed in utero to Hurricane Maria have gut microbiomes with reduced diversity and altered metabolic capacity.}, journal = {mSphere}, volume = {8}, number = {5}, pages = {e0013423}, pmid = {37754563}, issn = {2379-5042}, support = {R21 AI139649/AI/NIAID NIH HHS/United States ; UL1 TR002345/TR/NCATS NIH HHS/United States ; UL1TR002345/TR/NCATS NIH HHS/United States ; 1R21AI139649-01A1/AI/NIAID NIH HHS/United States ; }, mesh = {Pregnancy ; Female ; Humans ; Infant ; *Gastrointestinal Microbiome ; *Cyclonic Storms ; Cohort Studies ; Feces/microbiology ; Breast Feeding ; }, abstract = {The gut microbiome is a potentially important mechanism that links prenatal disaster exposures with increased disease risks. However, whether prenatal disaster exposures are associated with alterations in the infant's gut microbiome remains unknown. We established a birth cohort study named Hurricane as the Origin of Later Alterations in Microbiome (HOLA) after Hurricane Maria struck Puerto Rico in 2017. We enrolled vaginally born Latino term infants aged 2 to 6 months, including n = 29 infants who were exposed in utero to Hurricane Maria in Puerto Rico and n = 34 infants who were conceived at least 5 months after the hurricane as controls. Shotgun metagenomic sequencing was performed on infant stool swabs. Infants exposed in utero to Hurricane Maria had a reduced diversity in their gut microbiome compared to the control infants, which was mainly seen in the exclusively formula-fed group (P = 0.02). Four bacterial species, including Bacteroides vulgatus, Clostridium innocuum, Bifidobacterium pseudocatenulatum, and Clostridium neonatale, were depleted in the exposure group compared to the control group. Compositional differences in the microbial community and metabolic genes between the exposure and control groups were significant, which were driven by the formula feeding group (P = 0.02 for the microbial community and P = 0.008 for the metabolic genes). Metabolic modules involved in carbohydrate metabolism were reduced in the exposure group. Prenatal maternal exposure to Hurricane Maria was associated with a reduced gut commensal and an altered microbial composition and metabolic potential in the offspring's gut. Breastfeeding can adjust the composition of the gut microbiomes of exposed infants. IMPORTANCE Climate change is a serious issue that is affecting human health. With more frequent and intense weather disasters due to climate change, there is an urgent need to evaluate and understand the impacts of prenatal disaster exposures on the offspring. The prenatal stage is a particularly vulnerable stage for disease origination. However, the impact of prenatal weather disaster exposures on the offspring's gut microbiome has not been evaluated. Our HOLA study starts to fill this knowledge gap and provides novel insights into the microbiome as a mechanism that links prenatal disaster exposures with elevated disease risks. Our major finding that reduced microbial diversity and altered metabolic capacity are associated with prenatal hurricane exposures warrants further studies to evaluate the impact of weather disasters on the unborn.}, } @article {pmid37752615, year = {2023}, author = {Jin, Z and Yang, Y and Cao, Y and Wen, Q and Xi, Y and Cheng, J and Zhao, Q and Weng, J and Hong, K and Jiang, H and Hang, J and Zhang, Z}, title = {The gut metabolite 3-hydroxyphenylacetic acid rejuvenates spermatogenic dysfunction in aged mice through GPX4-mediated ferroptosis.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {212}, pmid = {37752615}, issn = {2049-2618}, mesh = {Mice ; Male ; Animals ; *Ferroptosis ; Semen ; *Gastrointestinal Microbiome/physiology ; Fecal Microbiota Transplantation ; Spermatogenesis ; }, abstract = {BACKGROUND: Aging-related fertility decline is a prevalent concern globally. Male reproductive system aging is mainly characterized by a decrease in sperm quality and fertility. While it is known that intestinal physiology changes with age and that microbiota is shaped by physiology, the underlying mechanism of how the microbiota affects male reproductive aging is still largely unexplored.

RESULTS: Here, we utilized fecal microbiota transplantation (FMT) to exchange the fecal microbiota between young and old mice. Cecal shotgun metagenomics and metabolomics were used to identify differences in gut microbiota composition and metabolic regulation during aging. Our results demonstrated that FMT from young to old mice alleviated aging-associated spermatogenic dysfunction through an unexpected mechanism mediated by a gut bacteria-derived metabolite, 3-hydroxyphenylacetic acid (3-HPAA). 3-HPAA treatment resulted in an improvement of spermatogenesis in old mice. RNA sequencing analysis, qRT-PCR and Western blot revealed that 3-HPAA induced an upregulation of GPX4, thereby restraining ferroptosis and restoring spermatogenesis. These findings were further confirmed by in vitro induction of ferroptosis and inhibition of GPX4 expression.

CONCLUSIONS: Our results demonstrate that the microbiome-derived metabolite, 3-HPAA, facilitates spermatogenesis of old mice through a ferroptosis-mediated mechanism. Overall, these findings provide a novel mechanism of dysregulated spermatogenesis of old mice, and suggest that 3-HPAA could be a potential therapy for fertility decline of aging males in clinical practice. Video Abstract.}, } @article {pmid37752498, year = {2023}, author = {Fan, Z and Zhang, L and Wei, L and Huang, X and Yang, M and Xing, X}, title = {Tracheal microbiome and metabolome profiling in iatrogenic subglottic tracheal stenosis.}, journal = {BMC pulmonary medicine}, volume = {23}, number = {1}, pages = {361}, pmid = {37752498}, issn = {1471-2466}, support = {202201AY070001-277//the Special and Joint Program of the Yunnan Provincial Science and Technology Department and Kunming Medical University/ ; 202201AY070001-265//the Special and Joint Program of the Yunnan Provincial Science and Technology Department and Kunming Medical University/ ; 2022J0019//Science Research Foundation of Yunnan Provincial Education Department/ ; No. 82160016//the National Natural Science Foundation of China/ ; No. YNWR-MY-2020-013//Famous Doctors of High-level Talent Training Support Program of Yunnan Province/ ; }, mesh = {Humans ; *Tracheal Stenosis ; *Laryngostenosis ; Cicatrix ; Iatrogenic Disease ; *Microbiota ; Metabolome ; Carnitine ; }, abstract = {BACKGROUND: To study the role of microecology and metabolism in iatrogenic tracheal injury and cicatricial stenosis, we investigated the tracheal microbiome and metabolome in patients with tracheal stenosis after endotracheal intubation.

METHODS: We collected 16 protected specimen brush (PSB) and 8 broncho-alveolar lavage (BAL) samples from 8 iatrogenic subglottic tracheal stenosis patients, including 8 PSB samples from tracheal scar sites, 8 PSB samples from scar-free sites and 8 BAL samples, by lavaging the subsegmental bronchi of the right-middle lobe. Metagenomic sequencing was performed to characterize the microbiome profiling of 16 PSB and 8 BAL samples. Untargeted metabolomics was performed in 6 PSB samples (3 from tracheal scar PSB and 3 from tracheal scar-free PSB) using high-performance liquid chromatography‒mass spectrometry (LC‒MS).

RESULTS: At the species level, the top four bacterial species were Neisseria subflava, Streptococcus oralis, Capnocytophaga gingivals, and Haemophilus aegyptius. The alpha and beta diversity among tracheal scar PSB, scar-free PSB and BAL samples were compared, and no significant differences were found. Untargeted metabolomics was performed in 6 PSB samples using LC‒MS, and only one statistically significant metabolite, carnitine, was identified. Pathway enrichment analysis of carnitine revealed significant enrichment in fatty acid oxidation.

CONCLUSION: Our study found that carnitine levels in tracheal scar tissue were significantly lower than those in scar-free tissue, which might be a new target for the prevention and treatment of iatrogenic tracheal stenosis in the future.}, } @article {pmid37750599, year = {2023}, author = {Moeller, AH and Sanders, JG and Sprockett, DD and Landers, A}, title = {Assessing co-diversification in host-associated microbiomes.}, journal = {Journal of evolutionary biology}, volume = {36}, number = {12}, pages = {1659-1668}, pmid = {37750599}, issn = {1420-9101}, support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; R35GM138284/GM/NIGMS NIH HHS/United States ; }, mesh = {Phylogeny ; *Biological Evolution ; *Microbiota ; Evolution, Molecular ; Genome ; Symbiosis ; }, abstract = {When lineages of hosts and microbial symbionts engage in intimate interactions over evolutionary timescales, they can diversify in parallel (i.e., co-diversify), producing associations between the lineages' phylogenetic histories. Tests for co-diversification of individual microbial lineages and their hosts have been developed previously, and these have been applied to discover ancient symbioses in diverse branches of the tree of life. However, most host-microbe relationships are not binary but multipartite, in that a single host-associated microbiota can contain many microbial lineages, generating challenges for assessing co-diversification. Here, we review recent evidence for co-diversification in complex microbiota, highlight the limitations of prior studies, and outline a hypothesis testing approach designed to overcome some of these limitations. We advocate for the use of microbiota-wide scans for co-diversifying symbiont lineages and discuss tools developed for this purpose. Tests for co-diversification for simple host symbiont systems can be extended to entire phylogenies of microbial lineages (e.g., metagenome-assembled or isolate genomes, amplicon sequence variants) sampled from host clades, thereby providing a means for identifying co-diversifying symbionts present within complex microbiota. The relative ages of symbiont clades can corroborate co-diversification, and multi-level permutation tests can account for multiple comparisons and phylogenetic non-independence introduced by repeated sampling of host species. Discovering co-diversifying lineages will generate powerful opportunities for interrogating the molecular evolution and lineage turnover of ancestral, host-species specific symbionts within host-associated microbiota.}, } @article {pmid37749663, year = {2023}, author = {Shen, S and Wang, J and Ma, C and Chen, Y and Ding, H and Zhang, J}, title = {Understanding the "individual drug reaction" from the perspective of the interaction between probiotics and lovastatin in vitro and in vivo.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {209}, pmid = {37749663}, issn = {2049-2618}, mesh = {Animals ; Cricetinae ; Humans ; Lovastatin/pharmacology ; Liver ; Chromatography, High Pressure Liquid ; *Drug-Related Side Effects and Adverse Reactions ; *Gastrointestinal Microbiome ; *Probiotics ; }, abstract = {BACKGROUND: The existence of the gut microbiota produces an "individual drug reaction." As members of the intestinal microbiota, probiotics, although they have prebiotic functions, may accelerate the degradation of drugs, thereby affecting drug efficacy. Lovastatin is one of the well-recognized lipid-lowering drugs. Its main action site is the liver. Therefore, if it is degraded in advance by gastrointestinal probiotics, its efficacy may be reduced.

RESULTS: Here, we designed a two-stage experiment in vitro and in vivo to explore the degradation of lovastatin by probiotics. In vitro, the degradation of lovastatin by 83 strains of Lactiplantibacillus plantarum and the "star strain" Lacticaseibacillus paracasei strain Shirota was investigated by high-performance liquid chromatography (HPLC). The results showed that probiotics could degrade lovastatin to varying degrees. Subsequently, we selected Lactiplantibacillus plantarum A5 (16.87%) with the strongest ability to degrade lovastatin, Lactiplantibacillus plantarum C3 (4.61%) with the weakest ability to degrade lovastatin and Lacticaseibacillus paracasei strain Shirota (17.6%) as representative probiotics for in vivo experiments. In vivo, the therapeutic effect of lovastatin combined with probiotics on golden hamsters with mixed hyperlipidemia was evaluated by measuring blood indicators, intestinal microbiota metagenomic sequencing, and the liver transcriptome. The results showed that the intake of probiotics did not affect the efficacy of lovastatin and could slow the inflammatory reaction of the liver.

CONCLUSIONS: The supplementation of probiotics produced beneficial metabolites in the intestine by promoting beneficial microbes. Intestinal metabolites affected the expression of the liver genes through the gut-liver axis, increased the relative content of the essential amino acids, and finally improved the liver inflammatory response of the host. This study aims to reveal the impact of probiotics on the human body from a unique perspective, suggesting the impact of taking probiotics while taking drugs. Video Abstract.}, } @article {pmid37749660, year = {2023}, author = {Wegner, CE and Stahl, R and Velsko, I and Hübner, A and Fagernäs, Z and Warinner, C and Lehmann, R and Ritschel, T and Totsche, KU and Küsel, K}, title = {A glimpse of the paleome in endolithic microbial communities.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {210}, pmid = {37749660}, issn = {2049-2618}, mesh = {*Genomics ; Paleontology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenome ; }, abstract = {BACKGROUND: The terrestrial subsurface is home to a significant proportion of the Earth's microbial biomass. Our understanding about terrestrial subsurface microbiomes is almost exclusively derived from groundwater and porous sediments mainly by using 16S rRNA gene surveys. To obtain more insights about biomass of consolidated rocks and the metabolic status of endolithic microbiomes, we investigated interbedded limestone and mudstone from the vadose zone, fractured aquifers, and deep aquitards.

RESULTS: By adapting methods from microbial archaeology and paleogenomics, we could recover sufficient DNA for downstream metagenomic analysis from seven rock specimens independent of porosity, lithology, and depth. Based on the extracted DNA, we estimated between 2.81 and 4.25 × 10[5] cells × g[-1] rock. Analyzing DNA damage patterns revealed paleome signatures (genetic records of past microbial communities) for three rock specimens, all obtained from the vadose zone. DNA obtained from deep aquitards isolated from surface input was not affected by DNA decay indicating that water saturation and not flow is controlling subsurface microbial survival. Decoding the taxonomy and functional potential of paleome communities revealed increased abundances for sequences affiliated with chemolithoautotrophs and taxa such as Cand. Rokubacteria. We also found a broader metabolic potential in terms of aromatic hydrocarbon breakdown, suggesting a preferred utilization of sedimentary organic matter in the past.

CONCLUSIONS: Our study suggests that limestones function as archives for genetic records of past microbial communities including those sensitive to environmental stress at modern times, due to their specific conditions facilitating long-term DNA preservation. Video Abstract.}, } @article {pmid37749192, year = {2023}, author = {Akter, S and Rahman, MS and Ali, H and Minch, B and Mehzabin, K and Siddique, MM and Galib, SM and Yesmin, F and Azmuda, N and Adnan, N and Hasan, NA and Rahman, SR and Moniruzzaman, M and Ahmed, MF}, title = {Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15976}, pmid = {37749192}, issn = {2045-2322}, mesh = {Bays ; Phylogeny ; *Microbiota ; *Alteromonas ; *Dinoflagellida ; }, abstract = {The Bay of Bengal, the world's largest bay, is bordered by populous countries and rich in resources like fisheries, oil, gas, and minerals, while also hosting diverse marine ecosystems such as coral reefs, mangroves, and seagrass beds; regrettably, its microbial diversity and ecological significance have received limited research attention. Here, we present amplicon (16S and 18S) profiling and shotgun metagenomics data regarding microbial communities from BoB's eastern coast, viz., Saint Martin and Cox's Bazar, Bangladesh. From the 16S barcoding data, Proteobacteria appeared to be the dominant phylum in both locations, with Alteromonas, Methylophaga, Anaerospora, Marivita, and Vibrio dominating in Cox's Bazar and Pseudoalteromonas, Nautella, Marinomonas, Vibrio, and Alteromonas dominating the Saint Martin site. From the 18S barcoding data, Ochrophyta, Chlorophyta, and Protalveolata appeared among the most abundant eukaryotic divisions in both locations, with significantly higher abundance of Choanoflagellida, Florideophycidae, and Dinoflagellata in Cox's Bazar. The shotgun sequencing data reveals that in both locations, Alteromonas is the most prevalent bacterial genus, closely paralleling the dominance observed in the metabarcoding data, with Methylophaga in Cox's Bazar and Vibrio in Saint Martin. Functional annotations revealed that the microbial communities in these samples harbor genes for biofilm formation, quorum sensing, xenobiotics degradation, antimicrobial resistance, and a variety of other processes. Together, these results provide the first molecular insight into the functional and phylogenetic diversity of microbes along the BoB coast of Bangladesh. This baseline understanding of microbial community structure and functional potential will be critical for assessing impacts of climate change, pollution, and other anthropogenic disturbances on this ecologically and economically vital bay.}, } @article {pmid37748599, year = {2024}, author = {Teng, M and Zhao, X and Zhou, L and Yan, H and Zhao, L and Sun, J and Li, Y and Zhu, W and Wu, F}, title = {An integrated analysis of the fecal metabolome and metagenome reveals the distinct effects of differentially charged nanoplastics on the gut microbiota-associated metabolites in mice.}, journal = {The Science of the total environment}, volume = {906}, number = {}, pages = {167287}, doi = {10.1016/j.scitotenv.2023.167287}, pmid = {37748599}, issn = {1879-1026}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Metagenome ; Microplastics ; Metabolome ; Polystyrenes ; Biomarkers ; RNA, Ribosomal, 16S ; }, abstract = {Whether nanoplastics with differential charges cause intestinal impairment via distinct mechanisms remains unclear. We investigated the relationship between fecal metabolites and the gut microbiome, and potential biomarkers thereof, in mice following exposure to differentially charged polystyrene nanoplastics (PS-NPs). Metagenomic analysis revealed that exposure to differentially charged PS-NPs resulted in alterations in the abundances of Bilophila_wadsworthia, Helicobacter apodemus, and Helicobacter typhlonius. A total of 237 fecal metabolites were significantly altered in mice that exhibited intestinal impairment, and these included 10 gut microbiota-related fecal metabolites that accurately discriminated impaired intestinal samples from the control. Additionally, the specific gut microbiome-related fecal metabolite-based model approach for the prediction of intestinal impairment in mice had an area under the curve (AUC) of 1.0 in the PS (without charge) group, an AUC of 0.94 in the PS-NH2 (positive charge) group, and an AUC of 0.86 in the PS-COOH (negative charge) group. Thus, the model showed promising evaluable accuracy for the prediction of intestinal impairment induced by nanoplastics in a charge-specific manner. Our study demonstrates that the fecal metabolome of mice with intestinal impairment following exposure to differentially charged nanoplastics is associated with changes in the gut microbiome. The identified biomarkers have potential application for the detection of intestinal impairment after exposure to negative, positive, or noncharged nanomaterials.}, } @article {pmid37747149, year = {2023}, author = {Luo, S and Ru, J and Mirzaei, MK and Xue, J and Peng, X and Ralser, A and Mejías-Luque, R and Gerhard, M and Deng, L}, title = {Gut virome profiling identifies an association between temperate phages and colorectal cancer promoted by Helicobacter pylori infection.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2257291}, pmid = {37747149}, issn = {1949-0984}, mesh = {Animals ; Mice ; *Bacteriophages/genetics ; *Helicobacter pylori ; Virome ; *Helicobacter Infections/microbiology ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; *Colorectal Neoplasms/microbiology ; Carcinogenesis ; }, abstract = {Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide. While a close correlation between chronic Helicobacter pylori infection and CRC has been reported, the role of the virome has been overlooked. Here, we infected Apc-mutant mouse models and C57BL/6 mice with H. pylori and conducted a comprehensive metagenomics analysis of H. pylori-induced changes in lower gastrointestinal tract bacterial and viral communities. We observed an expansion of temperate phages in H. pylori infected Apc[+/1638N] mice at the early stage of carcinogenesis. Some of the temperate phages were predicted to infect bacteria associated with CRC, including Enterococcus faecalis. We also observed a high prevalence of virulent genes, such as flgJ, cwlJ, and sleB, encoded by temperate phages. In addition, we identified phages associated with pre-onset and onset of H. pylori-promoted carcinogenesis. Through co-occurrence network analysis, we found strong associations between the viral and bacterial communities in infected mice before the onset of carcinogenesis. These findings suggest that the expansion of temperate phages, possibly caused by prophage induction triggered by H. pylori infection, may have contributed to the development of CRC in mice by interacting with the bacterial community.}, } @article {pmid37743871, year = {2023}, author = {Liu, Y and Chan, MTV and Chan, FKL and Wu, WKK and Ng, SC and Zhang, L}, title = {Lower gut abundance of Eubacterium rectale is linked to COVID-19 mortality.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1249069}, pmid = {37743871}, issn = {2235-2988}, mesh = {Adult ; Humans ; Eubacterium ; *COVID-19 ; Butyrates ; *Gastrointestinal Microbiome ; Metagenome ; }, abstract = {INTRODUCTION: Emerging preclinical and clinical studies suggest that altered gut microbiome composition and functions are associated with coronavirus 2019 (COVID- 19) severity and its long-term complications. We hypothesize that COVID-19 outcome is associated with gut microbiome status in population-based settings.

METHODS: Gut metagenomic data of the adult population consisting of 2871 subjects from 16 countries were obtained from ExperimentHub through R, while the dynamic death data of COVID-19 patients between January 22, 2020 and December 8, 2020 in each country was acquired from Johns Hopkins Coronavirus Resource Center. An adjusted stable mortality rate (SMR) was used to represent these countries' mortality and correlated with the mean relative abundance (mRA) of healthy adult gut microbiome species.

RESULTS: After excluding bacterial species with low prevalence (prevalence <0.2 in the included countries), the β-diversity was significantly higher in the countries with high SMR when compared with those with median or low SMR (p <0.001). We then identified the mRA of two butyrate producers, Eubacterium rectale and Roseburia intestinalis, that were negatively correlated with SMR during the study period. And the reduction of these species was associated with severer COVID-19 manifestation.

CONCLUSION: Population-based microbiome signatures with the stable mortality rate of COVID-19 in different countries suggest that altered gut microbiome composition and functions are associated with mortality of COVID-19.}, } @article {pmid37743870, year = {2023}, author = {Palanisamy, V and Bosilevac, JM and Barkhouse, DA and Velez, SE and Chitlapilly Dass, S}, title = {Shotgun-metagenomics reveals a highly diverse and communal microbial network present in the drains of three beef-processing plants.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1240138}, pmid = {37743870}, issn = {2235-2988}, mesh = {*Metagenomics ; *Microbiota/genetics ; *Biofilms/growth & development ; Cattle ; Animals ; Red Meat/microbiology ; Bacteria/genetics/classification/isolation & purification ; Food Handling/methods ; Food Microbiology ; Food-Processing Industry ; }, abstract = {BACKGROUND: Multi-species biofilms pose a problem in various environments, especially food-processing environments. The diversity of microorganisms in these biofilms plays a critical role in their integrity and protection against external biotic and abiotic factors. Compared to single-species biofilms, mixed-species biofilms are more resistant to various stresses, including antimicrobials like sanitizers. Therefore, understanding the microbiome composition and diversity in biofilms and their metabolic potential is a priority when developing intervention techniques to combat foodborne pathogens in food processing environments.

METHODS: This study aimed to describe and compare the microbiome profile of 75 drain biofilm samples obtained from five different locations (Hotscale, Hotbox, Cooler, Processing, & Grind room) of three beef-processing plants (Plant A, B & C) taken over two timepoints 2017-18 (T1) and 2021 (T2) by shotgun sequencing.

RESULTS: Core microbiome analysis found Pseudomonas, Psychrobacter, and Acinetobacter to be the top three prevalent genera among the plants and locations. Alpha diversity analysis demonstrated a high diversity of microbiome present in all the plants and locations across the time points. Functional analysis showed the high metabolic potential of the microbial community with abundance of genes in metabolism, cell-adhesion, motility, and quorum sensing. Moreover, Quaternary Ammonium Compound (QAC) resistance genes were also observed, this is significant as QAC sanitizers are commonly used in many food processing facilities. Multi-functional genes such as transposases, polymerases, permeases, flagellar proteins, and Mobile Genetic Elements (MGEs) were found suggesting these are dynamic microbial communities that work together to protect themselves against environmental stresses through multiple defense mechanisms.

CONCLUSION: This study provides a framework for understanding the collective microbial network spanning a beef processing system. The results can be used to develop intervention strategies to best control these highly communicative microbial networks.}, } @article {pmid37741805, year = {2023}, author = {Wicaksono, WA and Cernava, T and Wassermann, B and Abdelfattah, A and Soto-Giron, MJ and Toledo, GV and Virtanen, SM and Knip, M and Hyöty, H and Berg, G}, title = {The edible plant microbiome: evidence for the occurrence of fruit and vegetable bacteria in the human gut.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2258565}, pmid = {37741805}, issn = {1949-0984}, mesh = {Humans ; Vegetables ; Plants, Edible ; Fruit ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Bacteria/genetics ; }, abstract = {Diversity of the gut microbiota is crucial for human health. However, whether fruit and vegetable associated bacteria contribute to overall gut bacterial diversity is still unknown. We reconstructed metagenome-assembled genomes from 156 fruit and vegetable metagenomes to investigate the prevalence of associated bacteria in 2,426 publicly available gut metagenomes. The microbiomes of fresh fruits and vegetables and the human gut are represented by members in common such as Enterobacterales, Burkholderiales, and Lactobacillales. Exposure to bacteria via fruit and vegetable consumption potentially has a beneficial impact on the functional diversity of gut microbiota particularly due to the presence of putative health-promoting genes for the production of vitamin and short-chain fatty acids. In the human gut, they were consistently present, although at a low abundance, approx. 2.2%. Host age, vegetable consumption frequency, and the diversity of plants consumed were drivers favoring a higher proportion. Overall, these results provide one of the primary links between the human microbiome and the environmental microbiome. This study revealed evidence that fruit and vegetable-derived microbes could be found in the human gut and contribute to gut microbiome diversity.}, } @article {pmid37741388, year = {2023}, author = {Zhou, T and Xiang, Y and Liu, S and Ma, H and Shao, Z and He, Q and Chai, H}, title = {Microbial community dynamics and metagenomics reveal the potential role of unconventional functional microorganisms in nitrogen and phosphorus removal biofilm system.}, journal = {The Science of the total environment}, volume = {905}, number = {}, pages = {167194}, doi = {10.1016/j.scitotenv.2023.167194}, pmid = {37741388}, issn = {1879-1026}, mesh = {*Ammonia/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; Bacteria/genetics/metabolism ; Archaea/metabolism ; Nitrification ; *Microbiota ; }, abstract = {The conventional functional microorganisms for nitrogen and phosphorus removal, such as Nitrosomonas, Nitrobacter, Nitrospira and Candidatus Accumulibacter, were hotspots in past research. However, the role of diverse unconventional functional microorganisms was neglected. In this study, a biofilm system was developed to explore the potential role of unconventional functional microorganisms in nutrients removal. According to the results of microbial community dynamics and metagenomics, complete ammonia oxidizing (comammox) bacteria was 20 times more abundant than ammonia-oxidizing bacteria (AOB) at day 121 and its abundance of amoA gene was almost the same as AOB. Although Nitrospira dominated the nitrite-oxidizing bacteria (NOB), diverse unconventional nxrB-containing microorganisms, particularly Chloroflexi, also significantly contributed to the nitrite oxidation. Binning analysis showed that Myxococcota-affiliated Haliangium had the necessary genes owns by phosphorus-accumulating organisms (PAO) and was likely to be the primary PAO since its abundance (6.38 %) was much higher than other conventional PAO (0.70 %). Comparing metagenome-assembled genomes of comammox bacteria with AOB and ammonia-oxidizing archaea (AOA), it possessed potential metabolic versatility in hydrogen and phosphorus, which may be the primary reason for the positive effect of the alternating anaerobic and aerobic conditions on the enrichment of comammox bacteria. Collectively, our findings broaden the understanding on the microbial mechanism of nitrogen and phosphorus removal in biofilm system.}, } @article {pmid37741262, year = {2023}, author = {Robinson, SL}, title = {Structure-guided metagenome mining to tap microbial functional diversity.}, journal = {Current opinion in microbiology}, volume = {76}, number = {}, pages = {102382}, doi = {10.1016/j.mib.2023.102382}, pmid = {37741262}, issn = {1879-0364}, mesh = {Humans ; *Metagenome ; *Microbiota/genetics ; Soil Microbiology ; Phenotype ; Drug Resistance, Microbial/genetics ; }, abstract = {Scientists now have access to millions of accurate three-dimensional (3D) models of protein structures. How do we leverage 3D structural models to learn about microbial functions encoded in metagenomes? Here, we review recent developments using protein structural features to mine metagenomes from diverse environments ranging from the human gut to soil and ocean viromes. We compare 3D protein structural methods to characterize antibiotic resistance phenotypes, nutrient cycling, and host-drug-microbe interactions. Broadly, we encourage the scientific community to look beyond global sequence and structure alignments by considering fine-grained descriptors such as distance to ligand, active site, and tertiary interactions between amino acid residues scaling to microbiomes. Finally, we highlight structure-inspired approaches to chart new areas of microbial protein-coding sequence space.}, } @article {pmid37740058, year = {2023}, author = {Komori, E and Kato-Kogoe, N and Imai, Y and Sakaguchi, S and Taniguchi, K and Omori, M and Ohmichi, M and Nakamura, S and Nakano, T and Lee, SW and Ueno, T}, title = {Changes in salivary microbiota due to gastric cancer resection and its relation to gastric fluid microbiota.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15863}, pmid = {37740058}, issn = {2045-2322}, mesh = {Humans ; *Stomach Neoplasms/surgery ; RNA, Ribosomal, 16S/genetics ; Gastrectomy ; *Microbiota/genetics ; }, abstract = {Gastric cancer is one of the leading causes of death worldwide, and resections are performed to cure the disease. We have previously reported the changes in the gastric microbiota after gastric cancer resection, which may be associated with the oral microbiota; however, the changes in the oral microbiota remain uncharacterized. This study aimed to characterize the changes in the salivary microbiota caused by gastric cancer resection and to evaluate their association with the gastric fluid microbiota. Saliva and gastric fluid samples were collected from 63 patients who underwent gastrectomy before and after surgery, and a 16S rRNA metagenomic analysis was performed to compare the microbiota composition. The number of bacterial species in the salivary microbiota decreased, and the bacterial composition changed after the resection of gastric cancer. In addition, we identified several bacterial genera that varied significantly in the salivary microbiota, some of which also showed similar changes in the gastric fluid microbiota. These findings indicate that changes in the gastric environment affect the oral microbiota, emphasizing the close association between the oral and gastric fluid microbiota. Our study signifies the importance of focusing on the oral microbiota in the perioperative period of gastrectomy in patients with gastric cancer.}, } @article {pmid37739268, year = {2023}, author = {Ge, F and Guo, R and Liang, Y and Chen, Y and Shao, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M}, title = {Characterization and genomic analysis of Stutzerimonas stutzeri phage vB_PstS_ZQG1, representing a novel viral genus.}, journal = {Virus research}, volume = {336}, number = {}, pages = {199226}, pmid = {37739268}, issn = {1872-7492}, mesh = {*Bacteriophages ; Phylogeny ; Sequence Analysis, DNA ; Genome, Viral ; Myoviridae ; Genomics ; Nucleotides ; }, abstract = {Stutzerimonas stutzeri is an opportunistic pathogenic bacterium belonging to the Gammaproteobacteria, exhibiting wide distribution in the environment and playing significant ecological roles such as nitrogen fixation or pollutant degradation. Despite its ecological importance, only two S. stutzeri phages have been isolated to date. Here, a novel S. stutzeri phage, vB_PstS_ZQG1, was isolated from the surface seawater of Qingdao, China. Transmission electron microscopy analysis indicates that vB_PstS_ZQG1 has a morphology characterized by a long non-contractile tail. The genomic sequence of vB_PstS_ZQG1 contains a linear, double-strand 61,790-bp with the G+C content of 53.24% and encodes 90 putative open reading frames. Two auxiliary metabolic genes encoding TolA protein and nucleotide pyrophosphohydrolase were identified, which are likely involved in host adaptation and phage reproduction. Phylogenetic and comparative genomic analyses demonstrated that vB_PstS_ZQG1 exhibits low similarity with previously isolated phages or uncultured viruses (average nucleotide identity values range from 21.7 to 29.4), suggesting that it represents a novel viral genus by itself, here named as Fuevirus. Biogeographic analysis showed that vB_PstS_ZQG1 was only detected in epipelagic and mesopelagic zone with low abundance. In summary, our findings of the phage vB_PstS_ZQG1 will provide helpful insights for further research on the interactions between S. stutzeri phages and their hosts, and contribute to discovering unknown viral sequences in the metagenomic database.}, } @article {pmid37738973, year = {2023}, author = {Liu, NN and Yi, CX and Wei, LQ and Zhou, JA and Jiang, T and Hu, CC and Wang, L and Wang, YY and Zou, Y and Zhao, YK and Zhang, LL and Nie, YT and Zhu, YJ and Yi, XY and Zeng, LB and Li, JQ and Huang, XT and Ji, HB and Kozlakidis, Z and Zhong, L and Heeschen, C and Zheng, XQ and Chen, C and Zhang, P and Wang, H}, title = {The intratumor mycobiome promotes lung cancer progression via myeloid-derived suppressor cells.}, journal = {Cancer cell}, volume = {41}, number = {11}, pages = {1927-1944.e9}, doi = {10.1016/j.ccell.2023.08.012}, pmid = {37738973}, issn = {1878-3686}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Humans ; Animals ; Mice ; *Lung Neoplasms/genetics ; *Myeloid-Derived Suppressor Cells ; *Mycobiome ; CD8-Positive T-Lymphocytes ; Lung ; }, abstract = {Although polymorphic microbiomes have emerged as hallmarks of cancer, far less is known about the role of the intratumor mycobiome as living microorganisms in cancer progression. Here, using fungi-enriched DNA extraction and deep shotgun metagenomic sequencing, we have identified enriched tumor-resident Aspergillus sydowii in patients with lung adenocarcinoma (LUAD). By three different syngeneic lung cancer mice models, we find that A. sydowii promotes lung tumor progression via IL-1β-mediated expansion and activation of MDSCs, resulting in suppressed activity of cytotoxic T lymphocyte cells and accumulation of PD-1[+] CD8[+] T cells. This is mediated by IL-1β secretion via β-glucan/Dectin-1/CARD9 pathway. Analysis of human samples confirms that enriched A. sydowii is associated with immunosuppression and poor patient outcome. Our findings suggest that intratumor mycobiome, albeit at low biomass, promotes lung cancer progression and could be targeted at the strain level to improve patients with LUAD outcome.}, } @article {pmid37737585, year = {2023}, author = {Jensen, EEB and Sedor, V and Eshun, E and Njage, P and Otani, S and Aarestrup, FM}, title = {The resistomes of rural and urban pigs and poultry in Ghana.}, journal = {mSystems}, volume = {8}, number = {5}, pages = {e0062923}, pmid = {37737585}, issn = {2379-5077}, support = {NNF16OC0021856: Global Surveillance of Antimicrobial Resistance//Novo Nordisk Foundation/ ; Fellowships//The Fleming Fund/ ; }, mesh = {Animals ; Swine ; Poultry ; Anti-Bacterial Agents ; Ghana ; Bacteria ; *Microbiota/genetics ; *Anti-Infective Agents ; }, abstract = {To the best of our knowledge, this is the first report on the resistomes that are measured using metagenomics in livestock from Sub-Saharan Africa. We find notable differences in the microbiomes between both pigs and poultry, and those also varied markedly compared to similar samples from Europe. However, for both animal species, the same bacterial taxa drove such differences. In pigs and urban free-range poultry, we find a very low abundance of antimicrobial resistance genes (ARGs), whereas rural free-range poultry displayed similarity to the European average, and industrialized poultry exhibited higher levels. These findings show how different African livestock bacterial communities and resistomes are from their European counterparts. They also underscore the importance of continued surveillance and investigation into antimicrobial resistance across diverse ecosystems, contributing significantly to global efforts toward combating the threat of antibiotic resistance.}, } @article {pmid37737154, year = {2023}, author = {Luan, M and Niu, M and Yang, P and Han, D and Zhang, Y and Li, W and He, Q and Zhao, Y and Mao, B and Chen, J and Mou, K and Li, P}, title = {Metagenomic sequencing reveals altered gut microbial compositions and gene functions in patients with non-segmental vitiligo.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {265}, pmid = {37737154}, issn = {1471-2180}, mesh = {Humans ; *Vitiligo/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Bacteroides fragilis ; Clostridiales ; }, abstract = {BACKGROUND: Vitiligo has been correlated with an abnormal gut microbiota. We aimed to systematically identify characteristics of the gut microbial compositions, genetic functions, and potential metabolic features in patients with non-segmental vitiligo.

METHODS: Twenty-five patients with non-segmental vitiligo and 25 matched healthy controls (HCs) were enrolled. Metagenomic sequencing and bioinformatic analysis were performed to determine the gut microbiota profiles. Differences in gut microbiota diversity and composition between patients with vitiligo and HCs were analyzed. Gene functions and gut metabolic modules were predicted with the Kyoto Encyclopedia of Gene and Genomes (KEGG) and MetaCyc databases.

RESULTS: Compared with HCs, alpha diversity of intestinal microbiome in vitiligo patients was significantly reduced. At the species level, the relative abundance of Staphylococcus thermophiles was decreased, and that of Bacteroides fragilis was increased in patients with vitiligo compared with those of the HCs. Linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed representative microbial markers of Lachnospiraceae_bacterium_BX3, Massilioclostridium_coli, TM7_phylum_sp_oral_taxon_348 and Bacteroides_fragilis for patients with vitiligo. KEGG gene function analysis showed that the NOD-like receptor signaling pathway was significantly enriched in patients with vitiligo. Gut metabolic modules (GMMs) analysis showed that cysteine degradation was significantly down-regulated, and galactose degradation was up-regulated in patients with vitiligo. A panel of 28 microbial features was constructed to distinguish patients with vitiligo from HCs.

CONCLUSIONS: The gut microbial profiles and genetic functions of patients with vitiligo were distinct from those of the HCs. The identified gut microbial markers may potentially be used for earlier diagnosis and treatment targets.}, } @article {pmid37737001, year = {2023}, author = {Bernadus, JBB and Pelealu, J and Kandou, GD and Pinaria, AG and Mamahit, JME and Tallei, TE}, title = {Metagenomic Insight into the Microbiome and Virome Associated with Aedes aegypti Mosquitoes in Manado (North Sulawesi, Indonesia).}, journal = {Infectious disease reports}, volume = {15}, number = {5}, pages = {549-563}, pmid = {37737001}, issn = {2036-7430}, abstract = {The aim of this study was to investigate the microbial diversity encompassing bacteria, fungi, and viruses within the composite microbial community associated with Aedes aegypti mosquitoes in Manado, Indonesia, using a whole-genome shotgun metagenomics approach. Female mosquitoes were collected and grouped into pools of 50 individuals, from which genomic DNA (gDNA) and RNA were extracted separately. Whole-genome shotgun metagenomics were performed on gDNA samples. The bioinformatics analysis encompassed quality assessment, taxonomic classification, and visualization. The evaluation of the microbial community entailed an assessment of taxa abundance and diversity using Kraken version 2.1.2. The study delineated the prevalence of dominant bacterial phyla, including Proteobacteria, with varying abundance of Firmicutes, Bacteroidota, and Actinobacteria, and notable occurrence of Tenericutes. Furthermore, the presence of the fungal phylum Ascomycota was also detected. Among the identified barcodes, Barcode04 emerged as the most abundant and diverse, while Barcode06 exhibited greater evenness. Barcode03, 05, and 07 displayed moderate richness and diversity. Through an analysis of the relative abundance, a spectrum of viruses within Ae. aegypti populations was unveiled, with Negarnaviricota constituting the most prevalent phylum, followed by Nucleocytoviricota, Uroviricota, Artverviricota, Kitrinoviricota, Peploviricota, Phixviricota, and Cossaviricota. The presence of Negarnaviricota viruses raises pertinent public health concerns. The presence of other viral phyla underscores the intricate nature of virus-mosquito interactions. The analysis of viral diversity provides valuable insights into the range of viruses carried by Ae. aegypti. The community exhibits low biodiversity, with a few dominant species significantly influencing its composition. This has implications for healthcare and ecological management, potentially simplifying control measures but also posing risks if the dominant species are harmful. This study enriches our comprehension of the microbiome and virome associated with Ae. aegypti mosquitoes, emphasizing the importance of further research to fully comprehend their ecological significance and impact on public health. The findings shed light on the microbial ecology of Ae. aegypti, offering potential insights into mosquito biology, disease transmission, and strategies for vector control. Future studies should endeavor to establish specific associations with Ae. aegypti, elucidate the functional roles of the identified microbial and viral species, and investigate their ecological implications.}, } @article {pmid37736746, year = {2023}, author = {Li, S and Lian, WH and Han, JR and Ali, M and Lin, ZL and Liu, YH and Li, L and Zhang, DY and Jiang, XZ and Li, WJ and Dong, L}, title = {Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {67}, pmid = {37736746}, issn = {2055-5008}, mesh = {*Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Biodiversity ; Metagenome ; Soil ; }, abstract = {Deserts occupy one-third of the Earth's terrestrial surface and represent a potentially significant reservoir of microbial biodiversity, yet the majority of desert microorganisms remain uncharacterized and are seen as "microbial dark matter". Here, we introduce a multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, and shotgun metagenomic sequencing. The results showed that CBM captured a significant amount of taxonomic and functional diversity missed in direct sequencing by increasing the recovery of amplicon sequence variants (ASVs) and high/medium-quality metagenome-assembled genomes (MAGs). Importantly, CBM allowed the post hoc recovery of microbes of interest (e.g., novel or specific taxa), even those with extremely low abundance in the culture. Furthermore, strain-level analyses based on CBM and direct sequencing revealed that the desert soils harbored a considerable number of novel bacterial candidates (1941, 51.4%), of which 1095 (from CBM) were culturable. However, CBM would not exactly reflect the relative abundance of true microbial composition and functional pathways in the in situ environment, and its use coupled with direct metagenomic sequencing could provide greater insight into desert microbiomes. Overall, this study exemplifies the CBM strategy with high-resolution is an ideal way to deeply explore the untapped novel bacterial resources in desert soils, and substantially expands our knowledge on the microbial dark matter hidden in the vast expanse of deserts.}, } @article {pmid37735195, year = {2023}, author = {Malukiewicz, J and D'arc, M and Dias, CA and Cartwright, RA and Grativol, AD and Moreira, SB and Souza, AR and Tavares, MCH and Pissinatti, A and Ruiz-Miranda, CR and Santos, AFA}, title = {Bifidobacteria define gut microbiome profiles of golden lion tamarin (Leontopithecus rosalia) and marmoset (Callithrix sp.) metagenomic shotgun pools.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15679}, pmid = {37735195}, issn = {2045-2322}, mesh = {Leontopithecus ; Callitrichinae ; Bifidobacterium ; Humans ; Animals ; *Callithrix ; *Gastrointestinal Microbiome ; }, abstract = {Gut microbiome disruptions may lead to adverse effects on wildlife fitness and viability, thus maintaining host microbiota biodiversity needs to become an integral part of wildlife conservation. The highly-endangered callitrichid golden lion tamarin (GLT-Leontopithecus rosalia) is a rare conservation success, but allochthonous callitrichid marmosets (Callithrix) serve as principle ecological GLT threats. However, incorporation of microbiome approaches to GLT conservation is impeded by limited gut microbiome studies of Brazilian primates. Here, we carried out analysis of gut metagenomic pools from 114 individuals of wild and captive GLTs and marmosets. More specifically, we analyzed the bacterial component of ultra filtered samples originally collected as part of a virome profiling study. The major findings of this study are consistent with previous studies in showing that Bifidobacterium, a bacterial species important for the metabolism of tree gums consumed by callitrichids, is an important component of the callitrichid gut microbiome - although GTLs and marmosets were enriched for different species of Bifidobacterium. Additionally, the composition of GLT and marmoset gut microbiota is sensitive to host environmental factors. Overall, our data expand baseline gut microbiome data for callitrichids to allow for the development of new tools to improve their management and conservation.}, } @article {pmid37734616, year = {2023}, author = {Sang, Y and Mo, S and Zeng, S and Wu, X and Kashif, M and Song, J and Yu, D and Bai, L and Jiang, C}, title = {Model of shrimp pond-mediated spatiotemporal dynamic distribution of antibiotic resistance genes in the mangrove habitat of a subtropical gulf.}, journal = {The Science of the total environment}, volume = {905}, number = {}, pages = {167199}, doi = {10.1016/j.scitotenv.2023.167199}, pmid = {37734616}, issn = {1879-1026}, mesh = {Animals ; Humans ; *Genes, Bacterial ; Ponds/analysis ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Microbiota ; Crustacea ; China ; }, abstract = {Aquacultures are the main reason for the environmental selection of antibiotic resistance genes (ARGs), resulting in the enrichment of ARGs. As a filter, a marine mangrove ecosystem can reduce antimicrobial resistance (AMR) or eliminate ARGs; however, its elimination mechanism remains unclear. This study investigated the spatiotemporal dynamic distribution of ARGs in two different types of mangrove habitats (shrimp ponds and virgin forests), within a subtropical gulf located in the Beibu Gulf, China, during dry and wet seasons by using metagenomics and real time quantitative polymerase chain reaction (RT-qPCR) analysis. As the key environmental factors, sulfide, salinity, and mobile genetic elements significantly were found to contribute to ARGs distribution, respectively. Wet and dry seasons influenced the dispersal of ARGs but did not affect the microbial community structure. Three potential biomarkers, TEM-116, smeD, and smeE, played key roles in seasonal differences. The key different genes in the biological relevance of absolute abundance were demonstrated by RT-qPCR. Co-occurrence network analysis indicated that high-abundance ARGs were distributed in a modular manner. For the first time, a risk index weighted by risk rank (RIR) was proposed and used to quantify the human risk of ARGs in the mangrove metagenome. The shrimp ponds during the wet season showed the highest RIR detected. In addition to offering a perspective on reducing AMR in mangrove wetlands, this study constructed the first spatiotemporal dynamic model of ARGs in the Beibu Gulf, China and contributed to revealing the global spread of ARGs. Meanwhile, this study proposes a new pipeline for assessing the risk of ARGs, while also exploring the concept of "One Health."}, } @article {pmid37734503, year = {2023}, author = {Yuan, X and Cui, K and Chen, Y and Zhang, Y and Wu, S and Xie, X and Liu, T and Yao, H}, title = {Microbial community and gene dynamics response to high concentrations of gadolinium and sulfamethoxazole in biological nitrogen removal system.}, journal = {Chemosphere}, volume = {342}, number = {}, pages = {140218}, doi = {10.1016/j.chemosphere.2023.140218}, pmid = {37734503}, issn = {1879-1298}, mesh = {Sulfamethoxazole/pharmacology ; Gadolinium ; Denitrification ; Nitrogen ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; *Metals, Heavy ; *Microbiota ; }, abstract = {The impact of high antibiotic and heavy metal pollution levels on biological nitrogen removal in wastewater treatment plants (WWTPs) remains poorly understood, posing a global concern regarding the issue spread of antibiotic resistance induced by these contaminants. Herein, we investigated the effects of gadolinium (Gd) and sulfamethoxazole (SMX), commonly found in medical wastewater, on biological nitrogen removal systems and microbial characteristics, and the fate of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs). Our findings indicated that high SMX and Gd(III) concentrations adversely affected nitrification and denitrification, with Gd(III) exerting a strong inhibitory effect on microbial activity. Metagenomic analysis revealed that high SMX and Gd(III) concentrations could reduce microbial diversity, with Thauera and Pseudomonas emerging as dominant genera across all samples. While the relative abundance of most ARGs decreased under single Gd(III) stress, MRGs increased, and nitrification functional genes were inhibited. Conversely, combined SMX and Gd(III) pollution increased the relative abundance of intl1. Correlation analysis revealed that most genera could host ARGs and MRGs, indicating co-selection and competition between these resistance genes. However, most denitrifying functional genes exhibited a positive correlation with MRGs. Overall, our study provides novel insights into the impact of high concentrations of antibiotics and heavy metal pollution in WWTPs, and laying the groundwork for the spread and proliferation of resistance genes under combined SMX and Gd pollution.}, } @article {pmid37732776, year = {2023}, author = {Mujakić, I and Cabello-Yeves, PJ and Villena-Alemany, C and Piwosz, K and Rodriguez-Valera, F and Picazo, A and Camacho, A and Koblížek, M}, title = {Multi-environment ecogenomics analysis of the cosmopolitan phylum Gemmatimonadota.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0111223}, pmid = {37732776}, issn = {2165-0497}, abstract = {Gemmatimonadota is a diverse bacterial phylum commonly found in environments such as soils, rhizospheres, fresh waters, and sediments. So far, the phylum contains just six cultured species (five of them sequenced), which limits our understanding of their diversity and metabolism. Therefore, we analyzed over 400 metagenome-assembled genomes (MAGs) and 5 culture-derived genomes representing Gemmatimonadota from various aquatic environments, hydrothermal vents, sediments, soils, and host-associated (with marine sponges and coral) species. The principal coordinate analysis based on the presence/absence of genes in Gemmatimonadota genomes and phylogenomic analysis documented that marine and host-associated Gemmatimonadota were the most distant from freshwater and wastewater species. A smaller genome size and coding sequences (CDS) number reduction were observed in marine MAGs, pointing to an oligotrophic environmental adaptation. Several metabolic pathways are restricted to specific environments. For example, genes for anoxygenic phototrophy were found only in freshwater, wastewater, and soda lake sediment genomes. There were several genomes from soda lake sediments and wastewater containing type IC/ID ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Various genomes from wastewater harbored bacterial type II RuBisCO, whereas RuBisCO-like protein was found in genomes from fresh waters, soil, host-associated, and marine sediments. Gemmatimonadota does not contain nitrogen fixation genes; however, the nosZ gene, involved in the reduction of N2O, was present in genomes from most environments, missing only in marine water and host-associated Gemmatimonadota. The presented data suggest that Gemmatimonadota evolved as an organotrophic species relying on aerobic respiration and then remodeled its genome inventory when adapting to particular environments. IMPORTANCE Gemmatimonadota is a rarely studied bacterial phylum consisting of a handful of cultured species. Recent culture-independent studies documented that these organisms are distributed in many environments, including soil, marine, fresh, and waste waters. However, due to the lack of cultured species, information about their metabolic potential and environmental role is scarce. Therefore, we collected Gemmatimonadota metagenome-assembled genomes (MAGs) from different habitats and performed a systematic analysis of their genomic characteristics and metabolic potential. Our results show how Gemmatimonadota have adapted their genomes to different environments.}, } @article {pmid37732569, year = {2023}, author = {O'Brien, PA and Tan, S and Frade, PR and Robbins, SJ and Engelberts, JP and Bell, SC and Vanwonterghem, I and Miller, DJ and Webster, NS and Zhang, G and Bourne, DG}, title = {Validation of key sponge symbiont pathways using genome-centric metatranscriptomics.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {3207-3224}, doi = {10.1111/1462-2920.16509}, pmid = {37732569}, issn = {1462-2920}, support = {//Beijing Genomics Institute/ ; //Earthwatch Institute/ ; //Mitsubishi International Corporation/ ; //AIMS@JCU/ ; }, mesh = {Animals ; Phylogeny ; *Cyanobacteria/genetics ; *Microbiota/genetics ; Vitamins/metabolism ; Carbohydrates ; *Porifera ; Symbiosis ; }, abstract = {The sponge microbiome underpins host function through provision and recycling of essential nutrients in a nutrient poor environment. Genomic data suggest that carbohydrate degradation, carbon fixation, nitrogen metabolism, sulphur metabolism and supplementation of B-vitamins are central microbial functions. However, validation beyond the genomic potential of sponge symbiont pathways is rarely explored. To evaluate metagenomic predictions, we sequenced the metagenomes and metatranscriptomes of three common coral reef sponges: Ircinia ramosa, Ircinia microconulosa and Phyllospongia foliascens. Multiple carbohydrate active enzymes were expressed by Poribacteria, Bacteroidota and Cyanobacteria symbionts, suggesting these lineages have a central role in assimilating dissolved organic matter. Expression of entire pathways for carbon fixation and multiple sulphur compound transformations were observed in all sponges. Gene expression for anaerobic nitrogen metabolism (denitrification and nitrate reduction) were more common than aerobic metabolism (nitrification), where only the I. ramosa microbiome expressed the nitrification pathway. Finally, while expression of the biosynthetic pathways for B-vitamins was common, the expression of additional transporter genes was far more limited. Overall, we highlight consistencies and disparities between metagenomic and metatranscriptomic results when inferring microbial activity, while uncovering new microbial taxa that contribute to the health of their sponge host via nutrient exchange.}, } @article {pmid37732272, year = {2023}, author = {Pan, YF and Zhao, H and Gou, QY and Shi, PB and Tian, JH and Feng, Y and Li, K and Yang, WH and Wu, D and Tang, G and Zhang, B and Ren, Z and Peng, S and Luo, GY and Le, SJ and Xin, GY and Wang, J and Hou, X and Peng, MW and Kong, JB and Chen, XX and Yang, CH and Mei, SQ and Liao, YQ and Cheng, JX and Wang, J and Chaolemen, and Wu, YH and Wang, JB and An, T and Huang, X and Eden, JS and Li, J and Guo, D and Liang, G and Jin, X and Holmes, EC and Li, B and Wang, D and Li, J and Wu, WC and Shi, M}, title = {Metagenomic analysis of individual mosquitos reveals the ecology of insect viruses.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37732272}, issn = {2692-8205}, support = {U01 AI151810/AI/NIAID NIH HHS/United States ; }, abstract = {Mosquito transmitted viruses are responsible for an increasing burden of human disease. Despite this, little is known about the diversity and ecology of viruses within individual mosquito hosts. Using a meta-transcriptomic approach, we analysed the virome of 2,438 individual mosquitos (79 species), spanning ~4000 km along latitudes and longitudes in China. From these data we identified 393 core viral species associated with mosquitos, including seven (putative) arbovirus species. We identified potential species and geographic hotspots of viral richness and arbovirus occurrence, and demonstrated that host phylogeny had a strong impact on the composition of individual mosquito viromes. Our data revealed a large number of viruses shared among mosquito species or genera, expanding our knowledge of host specificity of insect-associated viruses. We also detected multiple virus species that were widespread throughout the country, possibly facilitated by long-distance mosquito migrations. Together, our results greatly expand the known mosquito virome, linked the viral diversity at the scale of individual insects to that at a country-wide scale, and offered unique insights into the ecology of viruses of insect vectors.}, } @article {pmid37731336, year = {2024}, author = {Aizpurua, O and Dunn, RR and Hansen, LH and Gilbert, MTP and Alberdi, A}, title = {Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data.}, journal = {Critical reviews in biotechnology}, volume = {44}, number = {6}, pages = {1164-1182}, doi = {10.1080/07388551.2023.2254933}, pmid = {37731336}, issn = {1549-7801}, mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Bacteria/genetics/classification ; Guidelines as Topic ; Microbiota/genetics ; Humans ; Data Interpretation, Statistical ; Reproducibility of Results ; }, abstract = {Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.}, } @article {pmid37728722, year = {2024}, author = {Zhong, ML and Cai, YQ and Tang, YF and Dai, YL and Jiang, YH and Ni, Y and Zou, CC}, title = {Gut microbiota, a potential cause of higher insulin sensitivity in children with Prader-Willi syndrome.}, journal = {Journal of endocrinological investigation}, volume = {47}, number = {4}, pages = {1029-1036}, pmid = {37728722}, issn = {1720-8386}, support = {81371215//National Natural Science Foundation of China/ ; 81670786//National Natural Science Foundation of China/ ; }, mesh = {Child ; Humans ; *Prader-Willi Syndrome ; *Insulin Resistance ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Obesity ; }, abstract = {PURPOSE: Obesity is the main driving factor for comorbidities in Prader-Willi syndrome (PWS) patients due to overeating behaviors. The gut microbiota has been implicated in the etiology of obesity and associated comorbidities. The purpose of the present study was to characterize the fecal microbiota in Chinese patients with PWS and compare it to that of patients with obesity as well as healthy controls.

METHODS: We conducted a cross-sectional study with 35 PWS patients (PWS), 35 patients with obesity (OB), and 35 healthy controls (HC). Metagenomic sequencing was performed in stool samples.

RESULTS: The composition of the fecal microbiota in PWS patients differed from that of participants in the OB and HC groups. It was characterized by increased Akkermansia Eubacterium, Eubacterium rectale, and Roseburia intestinalis and decreased Parabacteroides and Phascolarctobacterium. Additionally, the homeostatic model assessment of insulin resistance (HOMA-IR) was lower in PWS patients than in patients with obesity. Spearman rank correlation analysis showed that Achromobacter, Acidiphilium, Xylophilus, and Frisingicoccus were significantly negatively correlated with HOMA-IR.

CONCLUSION: The composition of the gut microbiota in Chinese PWS patients differed from that in patients with obesity, which might contribute to higher insulin sensitivity in PWS patients.}, } @article {pmid37727808, year = {2023}, author = {Herzog, EL and Kreuzer, M and Zinkernagel, MS and Zysset-Burri, DC}, title = {Challenges and insights in the exploration of the low abundance human ocular surface microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1232147}, pmid = {37727808}, issn = {2235-2988}, mesh = {Humans ; *Nylons ; Reproducibility of Results ; Face ; Conjunctiva ; *Microbiota ; }, abstract = {PURPOSE: The low microbial abundance on the ocular surface results in challenges in the characterization of its microbiome. The purpose of this study was to reveal factors introducing bias in the pipeline from sample collection to data analysis of low-abundant microbiomes.

METHODS: Lower conjunctiva and lower lid swabs were collected from six participants using either standard cotton or flocked nylon swabs. Microbial DNA was isolated with two different kits (with or without prior host DNA depletion and mechanical lysis), followed by whole-metagenome shotgun sequencing with a high sequencing depth set at 60 million reads per sample. The relative microbial compositions were generated using the two different tools MetaPhlan3 and Kraken2.

RESULTS: The total amount of extracted DNA was increased by using nylon flocked swabs on the lower conjunctiva. In total, 269 microbial species were detected. The most abundant bacterial phyla were Actinobacteria, Firmicutes and Proteobacteria. Depending on the DNA extraction kit and tool used for profiling, the microbial composition and the relative abundance of viruses varied.

CONCLUSION: The microbial composition on the ocular surface is not dependent on the swab type, but on the DNA extraction method and profiling tool. These factors have to be considered in further studies about the ocular surface microbiome and other sparsely colonized microbiomes in order to improve data reproducibility. Understanding challenges and biases in the characterization of the ocular surface microbiome may set the basis for microbiome-altering interventions for treatment of ocular surface associated diseases.}, } @article {pmid37726374, year = {2023}, author = {Hansen, ZA and Vasco, K and Rudrik, JT and Scribner, KT and Zhang, L and Manning, SD}, title = {Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15524}, pmid = {37726374}, issn = {2045-2322}, support = {U01 CK000510/CK/NCEZID CDC HHS/United States ; U01CK000510/ACL/ACL HHS/United States ; U19 AI090872/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/genetics ; Drug Resistance, Bacterial/genetics ; *Anti-Infective Agents ; Aminoglycosides ; }, abstract = {Enteric pathogens cause widespread foodborne illness and are increasingly resistant to important antibiotics yet their ecological impact on the gut microbiome and resistome is not fully understood. Herein, shotgun metagenome sequencing was applied to stool DNA from 60 patients (cases) during an enteric bacterial infection and after recovery (follow-ups). Overall, the case samples harbored more antimicrobial resistance genes (ARGs) with greater resistome diversity than the follow-up samples (p < 0.001), while follow-ups had more diverse gut microbiota (p < 0.001). Although cases were primarily defined by genera Escherichia, Salmonella, and Shigella along with ARGs for multi-compound and multidrug resistance, follow-ups had a greater abundance of Bacteroidetes and Firmicutes phyla and resistance genes for tetracyclines, macrolides, lincosamides, and streptogramins, and aminoglycosides. A host-tracking analysis revealed that Escherichia was the primary bacterial host of ARGs in both cases and follow-ups, with a greater abundance occurring during infection. Eleven distinct extended spectrum beta-lactamase (ESBL) genes were identified during infection, with some detectable upon recovery, highlighting the potential for gene transfer within the community. Because of the increasing incidence of disease caused by foodborne pathogens and their role in harboring and transferring resistance determinants, this study enhances our understanding of how enteric infections impact human gut ecology.}, } @article {pmid37726348, year = {2023}, author = {Warner, BB and Rosa, BA and Ndao, IM and Tarr, PI and Miller, JP and England, SK and Luby, JL and Rogers, CE and Hall-Moore, C and Bryant, RE and Wang, JD and Linneman, LA and Smyser, TA and Smyser, CD and Barch, DM and Miller, GE and Chen, E and Martin, J and Mitreva, M}, title = {Social and psychological adversity are associated with distinct mother and infant gut microbiome variations.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5824}, pmid = {37726348}, issn = {2041-1723}, support = {P30 CA091842/CA/NCI NIH HHS/United States ; UL1 TR000448/TR/NCATS NIH HHS/United States ; R01 MH113883/MH/NIMH NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; UL1 TR002345/TR/NCATS NIH HHS/United States ; }, mesh = {Female ; Pregnancy ; Humans ; Infant ; *Gastrointestinal Microbiome/genetics ; Mothers ; Case-Control Studies ; Bifidobacterium/genetics ; Cytokines ; Vitamins ; }, abstract = {Health disparities are driven by underlying social disadvantage and psychosocial stressors. However, how social disadvantage and psychosocial stressors lead to adverse health outcomes is unclear, particularly when exposure begins prenatally. Variations in the gut microbiome and circulating proinflammatory cytokines offer potential mechanistic pathways. Here, we interrogate the gut microbiome of mother-child dyads to compare high-versus-low prenatal social disadvantage, psychosocial stressors and maternal circulating cytokine cohorts (prospective case-control study design using gut microbiomes from 121 dyads profiled with 16 S rRNA sequencing and 89 dyads with shotgun metagenomic sequencing). Gut microbiome characteristics significantly predictive of social disadvantage and psychosocial stressors in the mothers and children indicate that different discriminatory taxa and related pathways are involved, including many species of Bifidobacterium and related pathways across several comparisons. The lowest inter-individual gut microbiome similarity was observed among high-social disadvantage/high-psychosocial stressors mothers, suggesting distinct environmental exposures driving a diverging gut microbiome assembly compared to low-social disadvantage/low-psychosocial stressors controls (P = 3.5 × 10[-5] for social disadvantage, P = 2.7 × 10[-15] for psychosocial stressors). Children's gut metagenome profiles at 4 months also significantly predicted high/low maternal prenatal IL-6 (P = 0.029), with many bacterial species overlapping those identified by social disadvantage and psychosocial stressors. These differences, based on maternal social and psychological status during a critical developmental window early in life, offer potentially modifiable targets to mitigate health inequities.}, } @article {pmid37724888, year = {2023}, author = {Jiang, X and Liu, J and Xi, Y and Zhang, Q and Wang, Y and Zhao, M and Lu, X and Wu, H and Shan, T and Ni, B and Zhang, W and Ma, X}, title = {Virome of high-altitude canine digestive tract and genetic characterization of novel viruses potentially threatening human health.}, journal = {mSphere}, volume = {8}, number = {5}, pages = {e0034523}, pmid = {37724888}, issn = {2379-5042}, mesh = {Animals ; Humans ; Dogs ; *Virome ; Phylogeny ; Altitude ; *Viruses/genetics ; Zoonoses ; Gastrointestinal Tract ; }, abstract = {The majority of currently emerging infectious illnesses are zoonotic infections, which have caused serious public health and economic implications. The development of viral metagenomics has helped us to explore unknown viruses. We collected 1,970 canine feces from Yushu and Guoluo in the plateau region of China for this study to do a metagenomics analysis of the viral community of the canine digestive tract. Our analysis identified 203 novel viruses, classified into 11 known families and 2 unclassified groups. These viruses include the hepatitis E virus, first identified in dogs, and the astrovirus, coronavirus, polyomavirus, and others. The relationship between the newly identified canine viruses and known viruses was investigated through the use of phylogenetic analysis. Furthermore, we demonstrated the cross-species transmission of viruses and predicted new viruses that may cause diseases in both humans and animals, providing technical support for the prevention and control of diseases caused by environmental pollution viruses. IMPORTANCE Most emerging infectious diseases are due to zoonotic disease agents. Because of their effects on the security of human or animal life, agriculture production, and food safety, zoonotic illnesses and livestock diseases are of worldwide significance. Because dogs are closely related to humans and domestic animals, they serve as one of the important links in the transmission of zoonotic and livestock diseases. Canines can contaminate the environment in which humans live such as water and soil through secretions, potentially altering the human gut microbiota or causing diseases. Our study enriched the viral community in the digestive tract microbiome of dogs and found types of viruses that threaten human health, providing technical support for the prevention and control of early warning of diseases caused by environmental contaminant viruses.}, } @article {pmid37724520, year = {2023}, author = {Yan, Z and Wang, Y and Zeng, W and Xia, R and Liu, Y and Wu, Z and Deng, W and Zhu, M and Xu, J and Deng, H and Miao, Y}, title = {Microbiota of long-term indwelling hemodialysis catheters during renal transplantation perioperative period: a cross-sectional metagenomic microbial community analysis.}, journal = {Renal failure}, volume = {45}, number = {2}, pages = {2256421}, pmid = {37724520}, issn = {1525-6049}, mesh = {Humans ; *Kidney Transplantation/adverse effects ; Cross-Sectional Studies ; Catheters, Indwelling/adverse effects ; *Microbiota ; *Catheter-Related Infections/diagnosis ; Renal Dialysis/adverse effects ; }, abstract = {Background: Catheter-related infection (CRI) is a major complication in patients undergoing hemodialysis. The lack of high-throughput research on catheter-related microbiota makes it difficult to predict the occurrence of CRI. Thus, this study aimed to delineate the microbial structure and diversity landscape of hemodialysis catheter tips among patients during the perioperative period of kidney transplantation (KTx) and provide insights into predicting the occurrence of CRI.Methods: Forty patients at the Department of Transplantation undergoing hemodialysis catheter removal were prospectively included. Samples, including catheter tip, catheter outlet skin swab, catheter blood, peripheral blood, oropharynx swab, and midstream urine, from the separate pre- and post-KTx groups were collected and analyzed using metagenomic next-generation sequencing (mNGS). All the catheter tips and blood samples were cultured conventionally.Results: The positive detection rates for bacteria using mNGS and traditional culture were 97.09% (200/206) and 2.65% (3/113), respectively. Low antibiotic-sensitivity biofilms with colonized bacteria were detected at the catheter tip. In asymptomatic patients, no statistically significant difference was observed in the catheter tip microbial composition and diversity between the pre- and post-KTx group. The catheter tip microbial composition and diversity were associated with fasting blood glucose levels. Microorganisms at the catheter tip most likely originated from catheter outlet skin and peripheral blood.Conclusions: The long-term colonization microbiota at the catheter tip is in a relatively stable state and is not readily influenced by KTx. It does not act as the source of infection in all CRIs, but could reflect hematogenous infection to some extent.}, } @article {pmid37723422, year = {2023}, author = {Hess, MK and Hodgkinson, HE and Hess, AS and Zetouni, L and Budel, JCC and Henry, H and Donaldson, A and Bilton, TP and van Stijn, TC and Kirk, MR and Dodds, KG and Brauning, R and McCulloch, AF and Hickey, SM and Johnson, PL and Jonker, A and Morton, N and Hendy, S and Oddy, VH and Janssen, PH and McEwan, JC and Rowe, SJ}, title = {Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {551}, pmid = {37723422}, issn = {1471-2164}, support = {SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; Curiosity Fund//AgResearch/ ; Curiosity Fund//AgResearch/ ; 119400343//Meat and Livestock Australia and the Australian Commonwealth Government/ ; 119400343//Meat and Livestock Australia and the Australian Commonwealth Government/ ; Breeding low emitting ruminants MET5.1//New Zealand Agricultural Greenhouse Gas Research Centre/ ; Breeding low emitting ruminants MET5.1//New Zealand Agricultural Greenhouse Gas Research Centre/ ; Breeding low emitting ruminants MET5.1//New Zealand Agricultural Greenhouse Gas Research Centre/ ; Breeding low emitting ruminants MET5.1//New Zealand Agricultural Greenhouse Gas Research Centre/ ; C10X1306//Ministry of Business, Innovation and Employment/ ; }, mesh = {Animals ; Sheep/genetics ; *Metagenome ; Rumen ; *Microbiota ; Livestock ; Methane ; }, abstract = {BACKGROUND: Producing animal protein while reducing the animal's impact on the environment, e.g., through improved feed efficiency and lowered methane emissions, has gained interest in recent years. Genetic selection is one possible path to reduce the environmental impact of livestock production, but these traits are difficult and expensive to measure on many animals. The rumen microbiome may serve as a proxy for these traits due to its role in feed digestion. Restriction enzyme-reduced representation sequencing (RE-RRS) is a high-throughput and cost-effective approach to rumen metagenome profiling, but the systematic (e.g., sequencing) and biological factors influencing the resulting reference based (RB) and reference free (RF) profiles need to be explored before widespread industry adoption is possible.

RESULTS: Metagenome profiles were generated by RE-RRS of 4,479 rumen samples collected from 1,708 sheep, and assigned to eight groups based on diet, age, time off feed, and country (New Zealand or Australia) at the time of sample collection. Systematic effects were found to have minimal influence on metagenome profiles. Diet was a major driver of differences between samples, followed by time off feed, then age of the sheep. The RF approach resulted in more reads being assigned per sample and afforded greater resolution when distinguishing between groups than the RB approach. Normalizing relative abundances within the sampling Cohort abolished structures related to age, diet, and time off feed, allowing a clear signal based on methane emissions to be elucidated. Genus-level abundances of rumen microbes showed low-to-moderate heritability and repeatability and were consistent between diets.

CONCLUSIONS: Variation in rumen metagenomic profiles was influenced by diet, age, time off feed and genetics. Not accounting for environmental factors may limit the ability to associate the profile with traits of interest. However, these differences can be accounted for by adjusting for Cohort effects, revealing robust biological signals. The abundances of some genera were consistently heritable and repeatable across different environments, suggesting that metagenomic profiles could be used to predict an individual's future performance, or performance of its offspring, in a range of environments. These results highlight the potential of using rumen metagenomic profiles for selection purposes in a practical, agricultural setting.}, } @article {pmid37723360, year = {2023}, author = {Xu, S and Zhang, X and Yang, Q and Li, J and Yu, Z}, title = {Identification of Microbial Community in Otomycosis by Metagenomic Next Generation Sequencing (mNGS): Potential Implication of Treatment with Terbinafine.}, journal = {Mycopathologia}, volume = {188}, number = {6}, pages = {995-1005}, pmid = {37723360}, issn = {1573-0832}, support = {82071039//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 82101215//Innovative Research Group Project of the National Natural Science Foundation of China/ ; }, mesh = {Humans ; Terbinafine/therapeutic use ; *Otomycosis/drug therapy/microbiology ; Antifungal Agents/pharmacology/therapeutic use ; High-Throughput Nucleotide Sequencing ; Aspergillus/genetics ; Fungi/genetics ; *Microbiota ; }, abstract = {The present study was designed to identify the microbial community as well as to analyze its diversity by means of metagenomic Next Generation Sequencing (mNGS) in 17 patients with otomycosis treated with terbinafine in the Department of Otolaryngology of Shandong Provincial Hospital from June 2021 to June 2022, so as to evaluate the relationship between microbial community and terbinafine resistance. Those 17 patients were divided into two groups, i.e., Terbinafine Effective Group (TEG, n = 14 cases) and Terbinafine Resistance Group (TRG, n = 3 cases) according to the therapy effect, whose microbial community of secretion of external auditory canal was identified using mNGS. We found that the sequence of bacteria was significantly more than that of fungi and, whereas, the difference between the two groups of bacteria was not significant. There were significant differences in fungal community between the two groups. Aspergillus was the main pathogenic fungus of TEG patients while Malassezia was a dominant fungus in TRG patients. In conclusion, the results from this work indicate that Aspergillus terreusis is the main pathogenic fungus in this cohort of otomycosis patients and MNGS sequencing can offer comprehensive information about the microbial community of otomycosis. The fungus community dominated by Malassezia is more likely to be resistant to terbinafine, which provides certain guidance for clinical treatment of otomycosis with terbinafine.}, } @article {pmid37723339, year = {2023}, author = {Li, S and Mosier, D and Dong, X and Kouris, A and Ji, G and Strous, M and Diao, M}, title = {Frequency of change determines effectiveness of microbial response strategies.}, journal = {The ISME journal}, volume = {17}, number = {11}, pages = {2047-2057}, pmid = {37723339}, issn = {1751-7370}, mesh = {RNA, Ribosomal, 16S/genetics/metabolism ; *Microbiota ; Bacteria ; Metagenome ; Bacteroidetes/genetics ; Metagenomics/methods ; }, abstract = {Nature challenges microbes with change at different frequencies and demands an effective response for survival. Here, we used controlled laboratory experiments to investigate the effectiveness of different response strategies, such as post-translational modification, transcriptional regulation, and specialized versus adaptable metabolisms. For this, we inoculated replicated chemostats with an enrichment culture obtained from sulfidic stream microbiomes 16 weeks prior. The chemostats were submitted to alternatingly oxic and anoxic conditions at three frequencies, with periods of 1, 4 and 16 days. The microbial response was recorded with 16S rRNA gene amplicon sequencing, shotgun metagenomics, transcriptomics and proteomics. Metagenomics resolved provisional genomes of all abundant bacterial populations, mainly affiliated with Proteobacteria and Bacteroidetes. Almost all these populations maintained a steady growth rate under both redox conditions at all three frequencies of change. Our results supported three conclusions: (1) Oscillating oxic/anoxic conditions selected for generalistic species, rather than species specializing in only a single condition. (2) A high frequency of change selected for strong codon usage bias. (3) Alignment of transcriptomes and proteomes required multiple generations and was dependent on a low frequency of change.}, } @article {pmid37722584, year = {2023}, author = {Wang, S and Han, Y and Wu, X and Sun, H}, title = {Metagenomics reveals the effects of glyphosate on soil microbial communities and functional profiles of C and P cycling in the competitive vegetation control process of Chinese fir plantation.}, journal = {Environmental research}, volume = {238}, number = {Pt 1}, pages = {117162}, doi = {10.1016/j.envres.2023.117162}, pmid = {37722584}, issn = {1096-0953}, mesh = {Soil ; *Cunninghamia ; RNA, Ribosomal, 16S ; Soil Microbiology ; *Microbiota ; Bacteria ; Glyphosate ; }, abstract = {Although considerable efforts have been devoted to investigate the behavior of glyphosate on microbiome in various environment, knowledge about the soil microbial community and functional profile in weeds control process of the Chinese fir plantation are limited. In this study, shotgun metagenomic sequencing was used to determine the abundance and diversity of microbial communities and functional genes after foliar application of glyphosate for 1, 2, 3 and 4 months in a Chinese fir plantation. The results showed that glyphosate increased the copy numbers (qPCR) of 16S rRNA gene for 16.9%, improved the bacterial diversity (Shannon index) and complexity of bacterial co-occurrence network, and changed the abundances of some bacterial and fungal taxa, but had no effects on ITS gene copy numbers, fungal Shannon index, and bacterial and fungal communities (PCoA). Glyphosate application significantly decreased the amount of microbial function potentials involved in organic P mineralization for 10.7%, chitin degradation for 13.1%, and CAZy gene families with an exception of PL for 11.5% at the first month, while did not affect the profile of microbial genes response to P and C cycling in longer term. In addition, glyphosate reduced the contents of soil TOC, DOC and NH4[+]-H for 17.6%, 52.3% and 44.6% respectively, and decreased the starch, soluble sugar, Zn and Fe of Chinese fir leaves for 20.6%, 19.8%, 32.8% and 48.4% respectively. Mantle test, Spearman's correlation, and PLS-PM model revealed the connections among soil properties, tree nutrients, bacterial and fungal communities, and microbial function potentials were influenced by glyphosate. While our findings need to be validated in other filed and mechanistic studies, they may indicate that the foliar application of glyphosate has a potential effect on Chinese fir seedlings, and this effect may contribute to the changes of the bacterial community and soil properties including AN, DON and NH4[+]-H.}, } @article {pmid37717754, year = {2023}, author = {Jain, R and Gaur, A and Suravajhala, R and Chauhan, U and Pant, M and Tripathi, V and Pant, G}, title = {Microplastic pollution: Understanding microbial degradation and strategies for pollutant reduction.}, journal = {The Science of the total environment}, volume = {905}, number = {}, pages = {167098}, doi = {10.1016/j.scitotenv.2023.167098}, pmid = {37717754}, issn = {1879-1026}, mesh = {Humans ; Microplastics ; Plastics/chemistry ; *Environmental Pollutants ; Ecosystem ; *Water Pollutants, Chemical/analysis ; Environmental Pollution ; *Microbiota ; Environmental Monitoring ; }, abstract = {Microplastics are ubiquitous environmental pollutants with the potential for adverse impacts on ecosystems and human health. These particles originate from the fragmentation of larger plastic items, shedding from synthetic fibers, tire abrasions, and direct release from personal care products and industrial processes. Once released into the environment, microplastics can disrupt ecosystems, accumulate in organisms, cause physical harm, and carry chemical pollutants that pose risks to both wildlife and human health. There is an urgent need to comprehensively explore the multifaceted issue of microplastic pollution and understand microbial degradation to reduce environmental pollution caused by microplastics. This paper presents a comprehensive exploration of microplastics, including their types, composition, advantages, and disadvantages, as well as the journey and evolution of microplastic pollution. The impact of microplastics on the microbiome and microbial communities is elucidated, highlighting the intricate interactions between microplastics and microbial ecosystems. Furthermore, the microbial degradation of microplastics is discussed, including the identification, characterization, and culturing methods of microplastic-degrading microorganisms. Mechanisms of microplastic degradation and the involvement of microbial enzymes are elucidated to shed light on potential biotechnological applications. Strategies for reducing microplastic pollution are presented, encompassing policy recommendations and the importance of enhanced waste management practices. Finally, the paper addresses future challenges and prospects in the field, emphasizing the need for international collaboration, research advancements, and public engagement. Overall, this study underscores the urgent need for concerted efforts to mitigate microplastic pollution and offers valuable insights for researchers, policymakers, and stakeholders involved in environmental preservation.}, } @article {pmid37716364, year = {2023}, author = {Worby, CJ and Sridhar, S and Turbett, SE and Becker, MV and Kogut, L and Sanchez, V and Bronson, RA and Rao, SR and Oliver, E and Walker, AT and Walters, MS and Kelly, P and Leung, DT and Knouse, MC and Hagmann, SHF and Harris, JB and Ryan, ET and Earl, AM and LaRocque, RC}, title = {Gut microbiome perturbation, antibiotic resistance, and Escherichia coli strain dynamics associated with international travel: a metagenomic analysis.}, journal = {The Lancet. Microbe}, volume = {4}, number = {10}, pages = {e790-e799}, pmid = {37716364}, issn = {2666-5247}, support = {U01 CK000633/CK/NCEZID CDC HHS/United States ; U01CK000490/ACL/ACL HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; }, mesh = {United States ; Humans ; *Escherichia coli/genetics ; *Gastrointestinal Microbiome/genetics ; Travel ; Metagenome ; Travel-Related Illness ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Microbial ; beta-Lactamases/genetics ; DNA ; }, abstract = {BACKGROUND: Culture-based studies have shown that acquisition of extended-spectrum β-lactamase-producing Enterobacterales is common during international travel; however, little is known about the role of the gut microbiome before and during travel, nor about acquisition of other antimicrobial-resistant organisms. We aimed to identify (1) whether the gut microbiome provided colonisation resistance against antimicrobial-resistant organism acquisition, (2) the effect of travel and travel behaviours on the gut microbiome, and (3) the scale and global heterogeneity of antimicrobial-resistant organism acquisition.

METHODS: In this metagenomic analysis, participants were recruited at three US travel clinics (Boston, MA; New York, NY; and Salt Lake City, UT) before international travel. Participants had to travel internationally between Dec 8, 2017, and April 30, 2019, and have DNA extractions for stool samples both before and after travel for inclusion. Participants were excluded if they had at least one low coverage sample (<1 million read pairs). Stool samples were collected at home before and after travel, sent to a clinical microbiology laboratory to be screened for three target antimicrobial-resistant organisms (extended-spectrum β-lactamase-producing Enterobacterales, carbapenem-resistant Enterobacterales, and mcr-mediated colistin-resistant Enterobacterales), and underwent DNA extraction and shotgun metagenomic sequencing. We profiled metagenomes for taxonomic composition, antibiotic-resistant gene content, and characterised the Escherichia coli population at the strain level. We analysed pre-travel samples to identify the gut microbiome risk factors associated with acquisition of the three targeted antimicrobial resistant organisms. Pre-travel and post-travel samples were compared to identify microbiome and resistome perturbation and E coli strain acquisition associated with travel.

FINDINGS: A total of 368 individuals travelled between the required dates, and 296 had DNA extractions available for both before and after travel. 29 travellers were excluded as they had at least one low coverage sample, leaving a final group of 267 participants. We observed a perturbation of the gut microbiota, characterised by a significant depletion of microbial diversity and enrichment of the Enterobacteriaceae family. Metagenomic strain tracking confirmed that 67% of travellers acquired new strains of E coli during travel that were phylogenetically distinct from their pre-travel strains. We observed widespread enrichment of antibiotic-resistant genes in the gut, with a median 15% (95% CI 10-20, p<1 × 10[-10]) increase in burden (reads per kilobase per million reads). This increase included antibiotic-resistant genes previously classified as threats to public health, which were 56% (95% CI 36-91, p=2 × 10[-11]) higher in abundance after travel than before. Fluoroquinolone antibiotic-resistant genes were aquired by 97 (54%) of 181 travellers with no detected pre-travel carriage. Although we found that visiting friends or relatives, travel to south Asia, and eating uncooked vegetables were risk factors for acquisition of the three targeted antimicrobial resistant organisms, we did not observe an association between the pre-travel microbiome structure and travel-related antimicrobial-resistant organism acquisition.

INTERPRETATION: This work highlights a scale of E coli and antimicrobial-resistant organism acquisition by US travellers not apparent from previous culture-based studies, and suggests that strategies to control antimicrobial-resistant organisms addressing international traveller behaviour, rather than modulating the gut microbiome, could be worthwhile.

FUNDING: US Centers for Disease Control and Prevention and National Institute of Allergy and Infectious Diseases.}, } @article {pmid37714737, year = {2023}, author = {Guo, Z and Yiu, N and Hu, Z and Zhou, W and Long, X and Yang, M and Liao, J and Zhang, G and Lu, Q and Zhao, M}, title = {Alterations of fecal microbiome and metabolome in pemphigus patients.}, journal = {Journal of autoimmunity}, volume = {141}, number = {}, pages = {103108}, doi = {10.1016/j.jaut.2023.103108}, pmid = {37714737}, issn = {1095-9157}, mesh = {Humans ; *Pemphigus/diagnosis ; *Microbiota ; Metabolome ; Feces/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; }, abstract = {The role of gut microbiome and metabolic substances in the development of autoimmune diseases has gradually been revealed. However, the relevant gut features in pemphigus have not been well clarified. We collected stool samples from pemphigus patients and healthy controls (HCs). Metagenomic sequencing and liquid chromatography-mass spectrometry (LC/MS) metabolome sequencing were performed to analyze the compositional and metabolic alternations of the gut microbiome in pemphigus patients and HCs. We observed the reduced richness and diversity and greater heterogeneity in pemphigus patients, which was characterized by a significant decrease in Firmicutes and an increase in Proteobacteria. At the species level, Intestinal pathogenic bacteria such as Escherichia coli and Bacteroides fragilis were significantly enriched, while anti-inflammatory bacteria and butyric acid-producing bacteria were significantly reduced, which were related to clinical indicators (Dsg1/3 and PDAI). 4 species were selected by the machine learning algorithm to better distinguish pemphigus patients from healthy people. Metabolomic analysis showed that the composition of pemphigus patients was different from that of HCs. PE (18:3 (6Z,9Z, 12Z)/14:1 (9Z)) was the main metabolic substance in pemphigus and involved in a variety of metabolic pathways. While Retinol, flavonoid compounds and various amino acids decreased significantly compared with HCs. Furthermore, we found that differences in the levels of these metabolites correlated with changes in the abundance of specific species. Our study provides a comprehensive picture of gut microbiota and metabolites in pemphigus patients and suggests a potential mechanism of the aberrant gut microbiota and metabolites in the pathogenesis of pemphigus.}, } @article {pmid37714349, year = {2023}, author = {Sun, Y and Hao, Y and Zhang, Q and Liu, X and Wang, L and Li, J and Li, M and Li, D}, title = {Coping with extremes: Alternations in diet, gut microbiota, and hepatic metabolic functions in a highland passerine.}, journal = {The Science of the total environment}, volume = {905}, number = {}, pages = {167079}, doi = {10.1016/j.scitotenv.2023.167079}, pmid = {37714349}, issn = {1879-1026}, mesh = {Animals ; Male ; Female ; Humans ; *Gastrointestinal Microbiome/physiology ; RNA, Ribosomal, 16S/genetics ; Diet/veterinary ; *Microbiota ; Adaptation, Psychological ; *Passeriformes ; }, abstract = {In wild animals, diet and gut microbiota interactions are critical moderators of metabolic functions and are highly contingent on habitat conditions. Challenged by the extreme conditions of high-altitude environments, the strategies implemented by highland animals to adjust their diet and gut microbial composition and modulate their metabolic substrates remain largely unexplored. By employing a typical human commensal species, the Eurasian tree sparrow (Passer montanus, ETS), as a model species, we studied the differences in diet, digestive tract morphology and enzyme activity, gut microbiota, and metabolic energy profiling between highland (the Qinghai-Tibet Plateau, QTP; 3230 m) and lowland (Shijiazhuang, Hebei; 80 m) populations. Our results showed that highland ETSs had enlarged digestive organs and longer small intestinal villi, while no differences in key digestive enzyme activities were observed between the two populations. The 18S rRNA sequencing results revealed that the dietary composition of highland ETSs were more animal-based and less plant-based than those of the lowland ones. Furthermore, 16S rRNA sequencing results suggested that the intestinal microbial communities were structurally segregated between populations. PICRUSt metagenome predictions further indicated that the expression patterns of microbial genes involved in material and energy metabolism, immune system and infection, and xenobiotic biodegradation were strikingly different between the two populations. Analysis of liver metabolomics revealed significant metabolic differences between highland and lowland ETSs in terms of substrate utilization, as well as distinct sex-specific alterations in glycerophospholipids. Furthermore, the interplay between diet, liver metabolism, and gut microbiota suggests a dietary shift resulting in corresponding changes in gut microbiota and metabolic functions. Our findings indicate that highland ETSs have evolved to optimize digestion and absorption, rely on more protein-rich foods, and possess gut microbiota tailored to their dietary composition, likely adaptive physiological and ecological strategies adopted to cope with extreme highland environments.}, } @article {pmid37714338, year = {2023}, author = {Liu, D and Gao, X and Huang, X and Fan, Y and Wang, YE and Zhang, Y and Chen, X and Wen, J and He, H and Hong, Y and Liang, Y and Zhang, Y and Liu, Z and Chen, S and Li, X}, title = {Moderate altitude exposure impacts host fasting blood glucose and serum metabolome by regulation of the intestinal flora.}, journal = {The Science of the total environment}, volume = {905}, number = {}, pages = {167016}, doi = {10.1016/j.scitotenv.2023.167016}, pmid = {37714338}, issn = {1879-1026}, mesh = {Humans ; Mice ; Animals ; *Gastrointestinal Microbiome ; Blood Glucose ; Propionates ; Glutamic Acid ; Altitude ; Escherichia coli ; Metabolome ; Glucose ; Fasting ; }, abstract = {Moderate altitude exposure has shown beneficial effects on diabetes incidence but the underlying mechanisms are not understood. Our study aimed to investigate how the human gut microbiome impacted the serum metabolome and associated with glucose homeostasis in healthy Chinese individuals upon moderate-altitude exposure. Faecal microbiome composition was assessed using shotgun metagenomic sequencing. Serum metabolome was acquired by untargeted metabolomics technology, and amino acids (AAs) and propionic acid in serum were quantified by targeted metabolomics technology. The results indicated that the moderate-altitude exposed individuals presented lowered fasting blood glucose (FBG) and propionic acid, increased circulating L-Glutamine but decreased L-Glutamate and L-Valine, which correlated with enriched Bacteroidetes and decreased Proteobacteria. Additionally, the silico causality associations among gut microbiota, serum metabolome and host FBG were analyzed by mediation analysis. It showed that increased Bacteroides ovatus (B. ovatus) and decreased Escherichia coli (E. coli) were identified as the main antagonistic species driving the association between L-Glutamate and FBG in silico causality. Furthermore, the high-fat diet (HFD) fed mice subjected to faecal microbiota transplantation (FMT) were applied to validate the cause-in-fact effects of gut microbiota on the beneficial glucose response. We found that microbiome in the moderate-altitude exposed donor could predict the extent of the FBG response in recipient mice, which showed lowered FBG, L-Glutamate and Firmicutes/Bacteroidetes ratio. Our findings suggest that moderate-altitude exposure targeting gut microbiota and circulating metabolome, may pave novel avenues to counter dysglycemia.}, } @article {pmid37707718, year = {2024}, author = {Rambia, A and Veluchamy, C and Rawat, JM and Jamdhade, MD and Purohit, S and Pawar, KD and Rajasekaran, C and Rawat, B and Sharma, A}, title = {Revealing bacterial and fungal communities of the untapped forest and alpine grassland zones of the Western-Himalayan region.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {27}, number = {3}, pages = {781-795}, pmid = {37707718}, issn = {1618-1905}, mesh = {*Fungi/classification/genetics/isolation & purification ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Forests ; *Grassland ; Microbiota ; Mycobiome ; Phylogeny ; Biodiversity ; Metagenomics ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The Western Himalayas offer diverse environments for investigating the diversity and distribution of microbial communities and their response to both the abiotic and biotic factors across the entire altitudinal gradient. Such investigations contribute significantly to our understanding of the complex ecological processes that shape microbial diversity. The proposed study focuses on the investigation of the bacterial and fungal communities in the forest and alpine grasslands of the Western Himalayan region, as well as their relationship with the physicochemical parameters of soil. A total of 185 isolates were obtained using the culture-based technique belonging to Bacillus (37%), Micrococcus (16%), and Staphylococcus (7%). Targeted metagenomics revealed the abundance of bacterial phyla Pseudomonadota (23%) followed by Acidobacteriota (20.2%), Chloroflexota (15%), and Bacillota (11.3%). At the genera level, CandidatusUdaeobacter (6%), Subgroup_2 (5.5%) of phylum Acidobacteriota, and uncultured Ktedonobacterales HSB_OF53-F07 (5.2%) of Choloroflexota phylum were found to be preponderant. Mycobiome predominantly comprised of phyla Ascomycota (54.1%), Basidiomycota (24%), and Mortierellomycota (19.1%) with Archaeorhizomyces (19.1%), Mortierella (19.1%), and Russula (5.4%) being the most abundant genera. Spearman's correlation revealed that the bacterial community was most influenced by total nitrogen in the soil followed by soil organic carbon as compared to other soil physicochemical factors. The study establishes a fundamental relationship between microbial communities and the physicochemical properties of soil. Furthermore, the study provides valuable insights into the complex interplay between biotic and abiotic factors that influence the microbial community composition of this unique region across various elevations.}, } @article {pmid37705113, year = {2023}, author = {De Filippis, F and Bonelli, M and Bruno, D and Sequino, G and Montali, A and Reguzzoni, M and Pasolli, E and Savy, D and Cangemi, S and Cozzolino, V and Tettamanti, G and Ercolini, D and Casartelli, M and Caccia, S}, title = {Plastics shape the black soldier fly larvae gut microbiome and select for biodegrading functions.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {205}, pmid = {37705113}, issn = {2049-2618}, mesh = {Animals ; Larva ; *Gastrointestinal Microbiome/genetics ; Plastics ; RNA, Ribosomal, 16S/genetics ; *Diptera ; }, abstract = {BACKGROUND: In the last few years, considerable attention has been focused on the plastic-degrading capability of insects and their gut microbiota in order to develop novel, effective, and green strategies for plastic waste management. Although many analyses based on 16S rRNA gene sequencing are available, an in-depth analysis of the insect gut microbiome to identify genes with plastic-degrading potential is still lacking.

RESULTS: In the present work, we aim to fill this gap using Black Soldier Fly (BSF) as insect model. BSF larvae have proven capability to efficiently bioconvert a wide variety of organic wastes but, surprisingly, have never been considered for plastic degradation. BSF larvae were reared on two widely used plastic polymers and shotgun metagenomics was exploited to evaluate if and how plastic-containing diets affect composition and functions of the gut microbial community. The high-definition picture of the BSF gut microbiome gave access for the first time to the genomes of culturable and unculturable microorganisms in the gut of insects reared on plastics and revealed that (i) plastics significantly shaped bacterial composition at species and strain level, and (ii) functions that trigger the degradation of the polymer chains, i.e., DyP-type peroxidases, multicopper oxidases, and alkane monooxygenases, were highly enriched in the metagenomes upon exposure to plastics, consistently with the evidences obtained by scanning electron microscopy and [1]H nuclear magnetic resonance analyses on plastics.

CONCLUSIONS: In addition to highlighting that the astonishing plasticity of the microbiota composition of BSF larvae is associated with functional shifts in the insect microbiome, the present work sets the stage for exploiting BSF larvae as "bioincubators" to isolate microbial strains and enzymes for the development of innovative plastic biodegradation strategies. However, most importantly, the larvae constitute a source of enzymes to be evolved and valorized by pioneering synthetic biology approaches. Video Abstract.}, } @article {pmid37704808, year = {2023}, author = {Pan, Z and Chen, Z and Zhu, L and Avellán-Llaguno, RD and Liu, B and Huang, Q}, title = {Antibiotic resistome and associated bacterial communities in agricultural soil following the amendments of swine manure-derived fermentation bed waste.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {47}, pages = {104520-104531}, pmid = {37704808}, issn = {1614-7499}, support = {(2020R1034002//Fujian Special Fund for Scientific Research Institutes in the Public Interest/ ; 3502Z20227240//Natural Science Foundation of Xiamen City/ ; DWHZ2021-15//External cooperation project of Fujian Academy of Agricultural Sciences/ ; }, mesh = {Swine ; Animals ; *Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; Manure/analysis ; Fermentation ; Genes, Bacterial ; Soil Microbiology ; Agriculture ; Bacteria/genetics ; *Microbiota ; }, abstract = {The practice of utilizing animal manures on land is widespread in agriculture, but it has raised concerns about the possible spread of antibiotic resistance genes (ARGs) and the potential risk it poses to public health through food production. Fermentation bed culture is an effective circular agricultural practice commonly utilized in pig farming that minimizes the environmental impact of livestock farming. However, this method generates a significant amount of fermentation bed waste (FBW), which can be turned into organic fertilizer for land application. The objective of this research was to examine the impacts of amending agricultural soil samples with swine manure-derived FBW on microbial communities, mobile genetic elements (MGEs), and ARG profiles over different periods. The study findings indicated that the amendment of swine manure-derived FBW significantly increased the diversity and abundance of ARGs and MGEs during the early stages of amendment, but this effect diminished over time, and after 12 months of FBW amendments, the levels returned to those comparable to control samples. The shift in the bacterial communities played a significant role in shaping the patterns of ARGs. Actinobacteriota, Proteobacteria, and Bacteroidetes were identified as the primary potential hosts of ARGs through metagenomic binning analysis. Furthermore, the pH of soil samples was identified as the most important property in driving the composition of the bacterial community and soil resistome. These findings provided valuable insights into the temporal patterns and dissemination risks of ARGs in FBW-amended agriculture soil, which could contribute to the development of effective strategies to manage the dissemination risks of FBW-derived ARGs.}, } @article {pmid37704738, year = {2023}, author = {Chang, YH and Yanckello, LM and Chlipala, GE and Green, SJ and Aware, C and Runge, A and Xing, X and Chen, A and Wenger, K and Flemister, A and Wan, C and Lin, AL}, title = {Prebiotic inulin enhances gut microbial metabolism and anti-inflammation in apolipoprotein E4 mice with sex-specific implications.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15116}, pmid = {37704738}, issn = {2045-2322}, support = {P30 AG072946/AG/NIA NIH HHS/United States ; RF1 AG062480/AG/NIA NIH HHS/United States ; UL1 TR002003/TR/NCATS NIH HHS/United States ; }, mesh = {Female ; Male ; Animals ; Mice ; Apolipoprotein E4/genetics ; Apolipoprotein E3 ; Dysbiosis ; *Gastrointestinal Microbiome ; Inulin/pharmacology ; *Alzheimer Disease ; Anti-Inflammatory Agents ; Escherichia coli ; }, abstract = {Gut dysbiosis has been identified as a crucial factor of Alzheimer's disease (AD) development for apolipoprotein E4 (APOE4) carriers. Inulin has shown the potential to mitigate dysbiosis. However, it remains unclear whether the dietary response varies depending on sex. In the study, we fed 4-month-old APOE4 mice with inulin for 16 weeks and performed shotgun metagenomic sequencing to determine changes in microbiome diversity, taxonomy, and functional gene pathways. We also formed the same experiments with APOE3 mice to identify whether there are APOE-genotype dependent responses to inulin. We found that APOE4 female mice fed with inulin had restored alpha diversity, significantly reduced Escherichia coli and inflammation-associated pathway responses. However, compared with APOE4 male mice, they had less metabolic responses, including the levels of short-chain fatty acids-producing bacteria and the associated kinases, especially those related to acetate and Erysipelotrichaceae. These diet- and sex- effects were less pronounced in the APOE3 mice, indicating that different APOE variants also play a significant role. The findings provide insights into the higher susceptibility of APOE4 females to AD, potentially due to inefficient energy production, and imply the importance of considering precision nutrition for mitigating dysbiosis and AD risk in the future.}, } @article {pmid37704113, year = {2023}, author = {Gou, H and Su, H and Liu, D and Wong, CC and Shang, H and Fang, Y and Zeng, X and Chen, H and Li, Y and Huang, Z and Fan, M and Wei, C and Wang, X and Zhang, X and Li, X and Yu, J}, title = {Traditional Medicine Pien Tze Huang Suppresses Colorectal Tumorigenesis Through Restoring Gut Microbiota and Metabolites.}, journal = {Gastroenterology}, volume = {165}, number = {6}, pages = {1404-1419}, doi = {10.1053/j.gastro.2023.08.052}, pmid = {37704113}, issn = {1528-0012}, mesh = {Mice ; Animals ; Signal Transduction ; *Gastrointestinal Microbiome ; Dextran Sulfate/toxicity ; Phosphatidylinositol 3-Kinases/metabolism ; Apoptosis ; Medicine, Traditional ; *Colorectal Neoplasms/chemically induced/prevention & control/metabolism ; Carcinogenesis ; Azoxymethane/toxicity ; }, abstract = {BACKGROUND & AIMS: Pien Tze Huang (PZH) is a well-established traditional medicine with beneficial effects against inflammation and cancer. We aimed to explore the chemopreventive effect of PZH in colorectal cancer (CRC) through modulating gut microbiota.

METHODS: CRC mouse models were established by azoxymethane plus dextran sulfate sodium treatment or in Apc[min/+] mice treated with or without PZH (270 mg/kg and 540 mg/kg). Gut barrier function was determined by means of intestinal permeability assays and transmission electron microscopy. Fecal microbiota and metabolites were analyzed by means of metagenomic sequencing and liquid chromatography mass spectrometry, respectively. Germ-free mice or antibiotic-treated mice were used as models of microbiota depletion.

RESULTS: PZH inhibited colorectal tumorigenesis in azoxymethane plus dextran sulfate sodium-treated mice and in Apc[min/+] mice in a dose-dependent manner. PZH treatment altered the gut microbiota profile, with an increased abundance of probiotics Pseudobutyrivibrio xylanivorans and Eubacterium limosum, while pathogenic bacteria Aeromonas veronii, Campylobacter jejuni, Collinsella aerofaciens, and Peptoniphilus harei were depleted. In addition, PZH increased beneficial metabolites taurine and hypotaurine, bile acids, and unsaturated fatty acids, and significantly restored gut barrier function. Transcriptomic profiling revealed that PZH inhibited PI3K-Akt, interleukin-17, tumor necrosis factor, and cytokine-chemokine signaling. Notably, the chemopreventive effect of PZH involved both microbiota-dependent and -independent mechanisms. Fecal microbiota transplantation from PZH-treated mice to germ-free mice partly recapitulated the chemopreventive effects of PZH. PZH components ginsenoside-F2 and ginsenoside-Re demonstrated inhibitory effects on CRC cells and primary organoids, and PZH also inhibited tumorigenesis in azoxymethane plus dextran sulfate sodium-treated germ-free mice.

CONCLUSIONS: PZH manipulated gut microbiota and metabolites toward a more favorable profile, improved gut barrier function, and suppressed oncogenic and pro-inflammatory pathways, thereby suppressing colorectal carcinogenesis.}, } @article {pmid37702461, year = {2023}, author = {Hussan, H and Clinton, SK and Grainger, EM and Webb, M and Wang, C and Webb, A and Needleman, B and Noria, S and Zhu, J and Choueiry, F and Pietrzak, M and Bailey, MT}, title = {Distinctive patterns of sulfide- and butyrate-metabolizing bacteria after bariatric surgery: potential implications for colorectal cancer risk.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2255345}, pmid = {37702461}, issn = {1949-0984}, support = {P30 CA016058/CA/NCI NIH HHS/United States ; R35 GM133510/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Female ; Middle Aged ; Aged ; Male ; Butyrates ; Cross-Sectional Studies ; Escherichia coli ; *Gastrointestinal Microbiome ; *Bariatric Surgery ; Bacteria/genetics ; *Colorectal Neoplasms/surgery ; }, abstract = {Despite improved cardiometabolic outcomes following bariatric surgery, its long-term impact on colorectal cancer (CRC) risk remains uncertain. In parallel, the influence of bariatric surgery on the host microbiome and relationships with disease outcomes is beginning to be appreciated. Therefore, we investigated the impact of Roux-en-Y gastric bypass (RYGB) and vertical sleeve gastrectomy (VSG) on the patterns of sulfide-reducing and butyrate-producing bacteria, which are hypothesized to modulate CRC risk after bariatric surgery. In this single-center, cross-sectional study, we included 15 pre-surgery subjects with severe obesity and patients who are at a median (range) of 25.6 (9.9-46.5) months after RYGB (n = 16) or VSG (n = 10). The DNA abundance of fecal bacteria and enzymes involved in butyrate and sulfide metabolism were identified using metagenomic sequencing. Differences between pre-surgery and post-RYGB or post-VSG cohorts were quantified using the linear discriminant analysis (LDA) effect size (LEfSe) method. Our sample was predominantly female (87%) with a median (range) age of 46 (23-71) years. Post-RYGB and post-VSG patients had a higher DNA abundance of fecal sulfide-reducing bacteria than pre-surgery controls (LDA = 1.3-4.4, p < .05). The most significant enrichments were for fecal E. coli, Acidaminococcus and A. finegoldii after RYGB, and for A. finegoldii, S. vestibularis, V. parvula after VSG. As for butyrate-producing bacteria, R. faecis was more abundant, whereas B. dentium and A. hardus were lower post-RYGB vs. pre-surgery. B. dentium was also lower in post-VSG vs. pre-surgery. Consistent with these findings, our analysis showed a greater enrichment of sulfide-reducing enzymes after bariatric surgery, especially RYGB, vs. pre-surgery. The DNA abundance of butyrate-producing enzymes was lower post-RYGB. In conclusion, the two most used bariatric surgeries, RYGB and VSG, are associated with microbiome patterns that are potentially implicated in CRC risk. Future studies are needed to validate and understand the impact of these microbiome changes on CRC risk after bariatric surgery.}, } @article {pmid37701837, year = {2023}, author = {Bulygin, I and Shatov, V and Rykachevskiy, A and Raiko, A and Bernstein, A and Burnaev, E and Gelfand, MS}, title = {Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15838}, pmid = {37701837}, issn = {2167-8359}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Metagenome ; Algorithms ; }, abstract = {Enterotypes of the human gut microbiome have been proposed to be a powerful prognostic tool to evaluate the correlation between lifestyle, nutrition, and disease. However, the number of enterotypes suggested in the literature ranged from two to four. The growth of available metagenome data and the use of exact, non-linear methods of data analysis challenges the very concept of clusters in the multidimensional space of bacterial microbiomes. Using several published human gut microbiome datasets of variable 16S rRNA regions, we demonstrate the presence of a lower-dimensional structure in the microbiome space, with high-dimensional data concentrated near a low-dimensional non-linear submanifold, but the absence of distinct and stable clusters that could represent enterotypes. This observation is robust with regard to diverse combinations of dimensionality reduction techniques and clustering algorithms.}, } @article {pmid37700504, year = {2023}, author = {Bender, SF and Schulz, S and Martínez-Cuesta, R and Laughlin, RJ and Kublik, S and Pfeiffer-Zakharova, K and Vestergaard, G and Hartman, K and Parladé, E and Römbke, J and Watson, CJ and Schloter, M and van der Heijden, MGA}, title = {Simplification of soil biota communities impairs nutrient recycling and enhances above- and belowground nitrogen losses.}, journal = {The New phytologist}, volume = {240}, number = {5}, pages = {2020-2034}, doi = {10.1111/nph.19252}, pmid = {37700504}, issn = {1469-8137}, support = {31003A-166079//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Soil ; *Nitrogen/analysis ; Agriculture ; Gases ; Biota ; Nutrients ; Nitrous Oxide ; Fertilizers ; }, abstract = {Agriculture is a major source of nutrient pollution, posing a threat to the earth system functioning. Factors determining the nutrient use efficiency of plant-soil systems need to be identified to develop strategies to reduce nutrient losses while ensuring crop productivity. The potential of soil biota to tighten nutrient cycles by improving plant nutrition and reducing soil nutrient losses is still poorly understood. We manipulated soil biota communities in outdoor lysimeters, planted maize, continuously collected leachates, and measured N2 O- and N2 -gas emissions after a fertilization pulse to test whether differences in soil biota communities affected nutrient recycling and N losses. Lysimeters with strongly simplified soil biota communities showed reduced crop N (-20%) and P (-58%) uptake, strongly increased N leaching losses (+65%), and gaseous emissions (+97%) of N2 O and N2 . Soil metagenomic analyses revealed differences in the abundance of genes responsible for nutrient uptake, nitrate reduction, and denitrification that helped explain the observed nutrient losses. Soil biota are major drivers of nutrient cycling and reductions in the diversity or abundance of certain groups (e.g. through land-use intensification) can disrupt nutrient cycling, reduce agricultural productivity and nutrient use efficiency, and exacerbate environmental pollution and global warming.}, } @article {pmid37699793, year = {2023}, author = {Chakraborty, M and Acharya, D and Dutta, TK}, title = {Diversity analysis of hilsa (Tenualosa ilisha) gut microbiota using culture-dependent and culture-independent approaches.}, journal = {Journal of applied microbiology}, volume = {134}, number = {9}, pages = {}, doi = {10.1093/jambio/lxad208}, pmid = {37699793}, issn = {1365-2672}, support = {760/CSIR-UGC NET/June 2017//University Grants Commission/ ; //Department of Science and Technology, Government of West Bengal/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Fishes ; Firmicutes/genetics ; Bacteroidetes/genetics ; Bangladesh ; Proteobacteria/genetics ; }, abstract = {AIMS: The bacterial communities associated with the gastrointestinal (GI) tract are primarily involved in digestion, physiology, and the immune response against pathogenic bacteria for the overall development and health of the host. Hilsa shad (Tenualosa ilisha), a tropical anadromous fish, found predominantly in Bangladesh and India, has so far been poorly investigated for its gut bacterial communities. In this study, both culture-based and metagenomic approaches were used to detect intestinal isolates of hilsa, captured from both freshwater and seawater to investigate the community structure of intestinal microbiota.

METHODS AND RESULTS: Culture-dependent approach allowed to isolate a total of 23 distinct bacterial species comprising 16 Gram-negative, and 7 Gram-positive isolates, where Proteobacteria and Firmicutes were identified as the two most dominant phyla. While metagenomic approach explored a wide range of important GI bacteria, primarily dominated by Proteobacteria, Firmicutes, and Bacteroidetes, with Proteobacteria and Firmicutes, being the most abundant in freshwater and seawater samples, respectively.

CONCLUSIONS: A combination of these approaches provided the differential GI-associated bacterial diversity in freshwater and seawater hilsa with the prediction of overall functional potential.

IMPACT STATEMENT: The study explored the diversity of gut microbiota in hilsa, one of the most preferred nutritious dietary fish, captured from freshwater and seawater habitats, which may encourage to comprehend the composition of the gut microbiome in relation to the migratory behavior and polyunsaturated fatty acid profile of anadromous fish in general.}, } @article {pmid37698879, year = {2023}, author = {Danhof, HA and Lee, J and Thapa, A and Britton, RA and Di Rienzi, SC}, title = {Microbial stimulation of oxytocin release from the intestinal epithelium via secretin signaling.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2256043}, pmid = {37698879}, issn = {1949-0984}, support = {R01 DK056388/DK/NIDDK NIH HHS/United States ; F32 AI136404/AI/NIAID NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; Secretin ; Oxytocin ; *Gastrointestinal Microbiome ; *Gastrointestinal Hormones ; Intestinal Mucosa ; *Limosilactobacillus reuteri ; }, abstract = {Intestinal microbes impact the health of the intestine and organs distal to the gut. Limosilactobacillus reuteri is a human intestinal microbe that promotes normal gut transit, the anti-inflammatory immune system, wound healing, normal social behavior in mice, and prevents bone reabsorption. Oxytocin impacts these functions and oxytocin signaling is required for L. reuteri-mediated wound healing and social behavior; however, the events in the gut leading to oxytocin stimulation and beneficial effects are unknown. Here we report evolutionarily conserved oxytocin production in the intestinal epithelium through analysis of single-cell RNA-Seq datasets and imaging of human and mouse intestinal tissues. Moreover, human intestinal organoids produce oxytocin, demonstrating that the intestinal epithelium is sufficient to produce oxytocin. We find that L. reuteri facilitates oxytocin secretion from human intestinal tissue and human intestinal organoids. Finally, we demonstrate that stimulation of oxytocin secretion by L. reuteri is dependent on the gut hormone secretin, which is produced in enteroendocrine cells, while oxytocin itself is produced in enterocytes. Altogether, this work demonstrates that oxytocin is produced and secreted from enterocytes in the intestinal epithelium in response to secretin stimulated by L. reuteri. This work thereby identifies oxytocin as an intestinal hormone and provides mechanistic insight into avenues by which gut microbes promote host health.}, } @article {pmid37697496, year = {2023}, author = {Zhang, P and Fang, Z and Zhao, M and Yi, B and Huang, Y and Yang, H and Guo, N and Zhao, C}, title = {Ethanol extract of Pueraria lobata improve acute myocardial infarction in rats via regulating gut microbiota and bile acid metabolism.}, journal = {Phytotherapy research : PTR}, volume = {37}, number = {12}, pages = {5932-5946}, doi = {10.1002/ptr.8005}, pmid = {37697496}, issn = {1099-1573}, support = {2017YFC1702901//the National Key Research and Development Program of China/ ; 2019YFC1708900//the National Key Research and Development Program of China/ ; CI2021A05031//CACMS Innovation Fund/ ; CI2021B017//Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; 2019-0894//Shandong Province Traditional Chinese Medicine Science and Technology Development Plan Project/ ; JBGS2021002//the Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; 81370095//Innovative Research Group Project of the National Natural Science Foundation of China/ ; }, mesh = {Rats ; Animals ; Ethanol ; *Gastrointestinal Microbiome ; *Pueraria ; Chromatography, Liquid ; Tandem Mass Spectrometry ; *Myocardial Infarction/drug therapy ; Plant Extracts/pharmacology ; Bile Acids and Salts ; }, abstract = {BACKGROUND AND AIM: Acute myocardial infarction (AMI) is a multifactorial disease with high mortality rate worldwide. Ethanol extract of Pueraria lobata (EEPL) has been widely used in treating cardiovascular diseases in China. This study aimed to explore the underlying therapeutic mechanism of EEPL in AMI rats.

EXPERIMENTAL PROCEDURE: We first evaluated the anti-AMI efficacy of EEPL through immunohistochemistry staining and biochemical indexes. Then, UPLC-MS/MS, 16S rDNA, and shotgun metagenomic sequencing were used to analyze the alterations in bile acid metabolism and intestinal flora. Finally, the influence of EEPL on ilem bile acid metabolism, related enzymes expression, and transporter proteins expression in rats were verified by mass spectrometry image and ELISA.

KEY RESULTS: The results showed that EEPL can reduce cardiac impairment in AMI rats. Besides, EEPL effectively increased bile acid levels and regulated gut microbiota disturbance in AMI rats via increasing CYP7A1 expression and restoring intestinal microbiota diversity, separately. Moreover, it can increase bile acids reabsorption and fecal excretion through inhibiting FXR-FGF15 signaling pathway and increasing OST-α expression, which associated with Lachnoclostridium.

CONCLUSIONS AND IMPLICATIONS: Our findings demonstrated that EEPL alleviated AMI partially by remediating intestinal dysbiosis and promoting bile acid biosynthesis, which provided new targets for AMI treatment.}, } @article {pmid37697305, year = {2023}, author = {Magnuson, E and Altshuler, I and Freyria, NJ and Leveille, RJ and Whyte, LG}, title = {Sulfur-cycling chemolithoautotrophic microbial community dominates a cold, anoxic, hypersaline Arctic spring.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {203}, pmid = {37697305}, issn = {2049-2618}, mesh = {Calcium Sulfate ; Canada ; *Microbiota/genetics ; Oxygen ; Sulfates ; *Gammaproteobacteria ; }, abstract = {BACKGROUND: Gypsum Hill Spring, located in Nunavut in the Canadian High Arctic, is a rare example of a cold saline spring arising through thick permafrost. It perennially discharges cold (~ 7 °C), hypersaline (7-8% salinity), anoxic (~ 0.04 ppm O2), and highly reducing (~ - 430 mV) brines rich in sulfate (2.2 g.L[-1]) and sulfide (9.5 ppm), making Gypsum Hill an analog to putative sulfate-rich briny habitats on extraterrestrial bodies such as Mars.

RESULTS: Genome-resolved metagenomics and metatranscriptomics were utilized to describe an active microbial community containing novel metagenome-assembled genomes and dominated by sulfur-cycling Desulfobacterota and Gammaproteobacteria. Sulfate reduction was dominated by hydrogen-oxidizing chemolithoautotrophic Desulfovibrionaceae sp. and was identified in phyla not typically associated with sulfate reduction in novel lineages of Spirochaetota and Bacteroidota. Highly abundant and active sulfur-reducing Desulfuromusa sp. highly transcribed non-coding RNAs associated with transcriptional regulation, showing potential evidence of putative metabolic flexibility in response to substrate availability. Despite low oxygen availability, sulfide oxidation was primarily attributed to aerobic chemolithoautotrophic Halothiobacillaceae. Low abundance and transcription of photoautotrophs indicated sulfur-based chemolithoautotrophy drives primary productivity even during periods of constant illumination.

CONCLUSIONS: We identified a rare surficial chemolithoautotrophic, sulfur-cycling microbial community active in a unique anoxic, cold, hypersaline Arctic spring. We detected Mars-relevant metabolisms including hydrogenotrophic sulfate reduction, sulfur reduction, and sulfide oxidation, which indicate the potential for microbial life in analogous S-rich brines on past and present Mars. Video Abstract.}, } @article {pmid37696680, year = {2024}, author = {Del Chierico, F and Cardile, S and Baldelli, V and Alterio, T and Reddel, S and Bramuzzo, M and Knafelz, D and Lega, S and Bracci, F and Torre, G and Maggiore, G and Putignani, L}, title = {Characterization of the Gut Microbiota and Mycobiota in Italian Pediatric Patients With Primary Sclerosing Cholangitis and Ulcerative Colitis.}, journal = {Inflammatory bowel diseases}, volume = {30}, number = {4}, pages = {529-537}, pmid = {37696680}, issn = {1536-4844}, support = {//Italian Ministry of Health/ ; }, mesh = {Humans ; Child ; *Colitis, Ulcerative/complications ; *Gastrointestinal Microbiome ; *Cholangitis, Sclerosing/complications ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Bacteroidetes ; Italy ; }, abstract = {BACKGROUND: Primary sclerosing cholangitis (PSC) is a chronic, fibroinflammatory, cholestatic liver disease of unknown etiopathogenesis, often associated with inflammatory bowel diseases. Recent evidence ascribes, together with immunologic and environmental components, a significant role to the intestinal microbiota or its molecules in the PSC pathogenesis.

METHODS: By metagenomic sequencing of 16S rRNA and ITS2 loci, we describe the fecal microbiota and mycobiota of 26 pediatric patients affected by PSC and concomitant ulcerative colitis (PSC-UC), 27 patients without PSC but with UC (UC), and 26 healthy subjects (CTRLs).

RESULTS: Compared with CTRL, the bacterial and fungal gut dysbiosis was evident for both PSC-UC and UC groups; in particular, Streptococcus, Saccharomyces, Sporobolomyces, Tilletiopsis, and Debaryomyces appeared increased in PSC-UC, whereas Klebsiella, Haemophilus, Enterococcus Collinsella, Piptoporus, Candida, and Hyphodontia in UC. In both patient groups, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma and Malassezia were decreased. Co-occurrence analysis evidenced the lowest number of nodes and edges for fungi networks compared with bacteria. Finally, we identified a specific patient profile, based on liver function tests, bacterial and fungal signatures, that is able to distinguish PSC-UC from UC patients.

CONCLUSIONS: We describe the gut microbiota and mycobiota dysbiosis associated to PSC-UC disease. Our results evidenced a gut imbalance, with the reduction of gut commensal microorganisms with stated anti-inflammatory properties (ie, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma, and Malassezia) and the increase of pathobionts (ie, Streptococcus, Saccharomyces, and Debaryomyces) that could be involved in PSC progression. Altogether, these events may concur in the pathophysiology of PSC in the framework of UC.}, } @article {pmid37696473, year = {2023}, author = {Kelly, SA and O'Connell, NH and Thompson, TP and Dillon, L and Wu, J and Creevey, C and Kiely, P and Slevin, B and Powell, J and Gilmore, BF and Dunne, CP}, title = {Large-scale characterization of hospital wastewater system microbiomes and clinical isolates from infected patients: profiling of multi-drug-resistant microbial species.}, journal = {The Journal of hospital infection}, volume = {141}, number = {}, pages = {152-166}, doi = {10.1016/j.jhin.2023.09.001}, pmid = {37696473}, issn = {1532-2939}, mesh = {Humans ; Wastewater ; *Microbiota/genetics ; Hospitals, Teaching ; Anti-Bacterial Agents ; *Biological Products ; *Cross Infection/epidemiology ; Genes, Bacterial ; }, abstract = {BACKGROUND: Hospital-acquired infections (HAIs) and infectious agents exhibiting antimicrobial resistance (AMR) are challenges globally. Environmental patient-facing wastewater apparatus including handwashing sinks, showers and toilets are increasingly identified as sources of infectious agents and AMR genes.

AIM: To provide large-scale metagenomics analysis of wastewater systems in a large teaching hospital in the Republic of Ireland experiencing multi-drug-resistant HAI outbreaks.

METHODS: Wastewater pipe sections (N=20) were removed immediately prior to refurbishment of a medical ward where HAIs had been endemic. These comprised toilet U-bends, and sink and shower drains. Following DNA extraction, each pipe section underwent metagenomic analysis.

FINDINGS: Diverse taxonomic and resistome profiles were observed, with members of phyla Proteobacteria and Actinobacteria dominating (38.23 ± 5.68% and 15.78 ± 3.53%, respectively). Genomes of five clinical isolates were analysed. These AMR bacterial isolates were from patients >48 h post-admission to the ward. Genomic analysis determined that the isolates bore a high number of antimicrobial resistance genes (ARGs).

CONCLUSION: Comparison of resistome profiles of isolates and wastewater metagenomes revealed high degrees of similarity, with many identical ARGs shared, suggesting probable acquisition post-admission. The highest numbers of ARGs observed were those encoding resistance to clinically significant and commonly used antibiotic classes. Average nucleotide identity analysis confirmed the presence of highly similar or identical genomes in clinical isolates and wastewater pipes. These unique large-scale analyses reinforce the need for regular cleaning and decontamination of patient-facing hospital wastewater pipes and effective infection control policies to prevent transmission of nosocomial infection and emergence of AMR within potential wastewater reservoirs.}, } @article {pmid37695138, year = {2023}, author = {Borton, MA and Shaffer, M and Hoyt, DW and Jiang, R and Ellenbogen, JB and Purvine, S and Nicora, CD and Eder, EK and Wong, AR and Smulian, AG and Lipton, MS and Krzycki, JA and Wrighton, KC}, title = {Targeted curation of the gut microbial gene content modulating human cardiovascular disease.}, journal = {mBio}, volume = {14}, number = {5}, pages = {e0151123}, pmid = {37695138}, issn = {2150-7511}, support = {P30 CA016058/CA/NCI NIH HHS/United States ; P30 CA046934/CA/NCI NIH HHS/United States ; R01 DK109345/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Cardiovascular Diseases/genetics ; *Microbiota ; *Gastrointestinal Microbiome ; Amines ; Genes, Microbial ; Methylamines/metabolism ; }, abstract = {One of the most-cited examples of the gut microbiome modulating human disease is the microbial metabolism of quaternary amines from protein-rich foods. By-products of this microbial processing promote atherosclerotic heart disease, a leading cause of human mortality globally. Our research addresses current knowledge gaps in our understanding of this microbial metabolism by holistically inventorying the microorganisms and expressed genes catalyzing critical atherosclerosis-promoting and -ameliorating reactions in the human gut. This led to the creation of an open-access resource, the Methylated Amine Gene Inventory of Catabolism database, the first systematic inventory of gut methylated amine metabolism. More importantly, using this resource we deliver here, we show for the first time that these gut microbial genes can predict human disease, paving the way for microbiota-inspired diagnostics and interventions.}, } @article {pmid37695074, year = {2023}, author = {Park, H and Lim, SJ and Cosme, J and O'Connell, K and Sandeep, J and Gayanilo, F and Cutter, GR and Montes, E and Nitikitpaiboon, C and Fisher, S and Moustahfid, H and Thompson, LR}, title = {Investigation of machine learning algorithms for taxonomic classification of marine metagenomes.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0523722}, pmid = {37695074}, issn = {2165-0497}, support = {NA21OAR4320190//National Oceanic and Atmospheric Administration/ ; NA20OAR4320472//DOC | National Oceanic and Atmospheric Administration (NOAA)/ ; }, mesh = {*Machine Learning ; *Classification/methods ; *Aquatic Organisms ; *Metagenome/genetics ; *Microbiota/genetics ; Models, Biological ; Neural Networks, Computer ; }, abstract = {Taxonomic profiling of microbial communities is essential to model microbial interactions and inform habitat conservation. This work develops approaches in constructing training/testing data sets from publicly available marine metagenomes and evaluates the performance of machine learning (ML) approaches in read-based taxonomic classification of marine metagenomes. Predictions from two models are used to test accuracy in metagenomic classification and to guide improvements in ML approaches. Our study provides insights on the methods, results, and challenges of deep learning on marine microbial metagenomic data sets. Future machine learning approaches can be improved by rectifying genome coverage and class imbalance in the training data sets, developing alternative models, and increasing the accessibility of computational resources for model training and refinement.}, } @article {pmid37695063, year = {2023}, author = {Cerri, A and Bolatti, EM and Zorec, TM and Montani, ME and Rimondi, A and Hosnjak, L and Casal, PE and Di Domenica, V and Barquez, RM and Poljak, M and Giri, AA}, title = {Identification and characterization of novel alphacoronaviruses in Tadarida brasiliensis (Chiroptera, Molossidae) from Argentina: insights into recombination as a mechanism favoring bat coronavirus cross-species transmission.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0204723}, pmid = {37695063}, issn = {2165-0497}, abstract = {Bats are reservoirs of various coronaviruses that can jump between bat species or other mammalian hosts, including humans. This article explores coronavirus infection in three bat species (Tadarida brasiliensis, Eumops bonariensis, and Molossus molossus) of the family Molossidae from Argentina using whole viral metagenome analysis. Fecal samples of 47 bats from three semiurban or highly urbanized areas of the province of Santa Fe were investigated. After viral particle enrichment, total RNA was sequenced using the Illumina NextSeq 550 instrument; the reads were assembled into contigs and taxonomically and phylogenetically analyzed. Three novel complete Alphacoronavirus (AlphaCoV) genomes (Tb1-3) and two partial sequences were identified in T. brasiliensis (Tb4-5), and an additional four partial sequences were identified in M. molossus (Mm1-4). Phylogenomic analysis showed that the novel AlphaCoV clustered in two different lineages distinct from the 15 officially recognized AlphaCoV subgenera. Tb2 and Tb3 isolates appeared to be variants of the same virus, probably involved in a persistent infectious cycle within the T. brasiliensis colony. Using recombination analysis, we detected a statistically significant event in Spike gene, which was reinforced by phylogenetic tree incongruence analysis, involving novel Tb1 and AlphaCoVs identified in Eptesicus fuscus (family Vespertilionidae) from the U.S. The putative recombinant region is in the S1 subdomain of the Spike gene, encompassing the potential receptor-binding domain of AlphaCoVs. This study reports the first AlphaCoV genomes in molossids from the Americas and provides new insights into recombination as an important mode of evolution of coronaviruses involved in cross-species transmission. IMPORTANCE This study generated three novel complete AlphaCoV genomes (Tb1, Tb2, and Tb3 isolates) identified in individuals of Tadarida brasiliensis from Argentina, which showed two different evolutionary patterns and are the first to be reported in the family Molossidae in the Americas. The novel Tb1 isolate was found to be involved in a putative recombination event with alphacoronaviruses identified in bats of the genus Eptesicus from the U.S., whereas isolates Tb2 and Tb3 were found in different collection seasons and might be involved in persistent viral infections in the bat colony. These findings contribute to our knowledge of the global diversity of bat coronaviruses in poorly studied species and highlight the different evolutionary aspects of AlphaCoVs circulating in bat populations in Argentina.}, } @article {pmid37692394, year = {2023}, author = {Nemchinov, LG and Irish, BM and Uschapovsky, IV and Grinstead, S and Shao, J and Postnikova, OA}, title = {Composition of the alfalfa pathobiome in commercial fields.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1225781}, pmid = {37692394}, issn = {1664-302X}, abstract = {Through the recent advances of modern high-throughput sequencing technologies, the "one microbe, one disease" dogma is being gradually replaced with the principle of the "pathobiome". Pathobiome is a comprehensive biotic environment that not only includes a diverse community of all disease-causing organisms within the plant but also defines their mutual interactions and resultant effect on plant health. To date, the concept of pathobiome as a major component in plant health and sustainable production of alfalfa (Medicago sativa L.), the most extensively cultivated forage legume in the world, is non-existent. Here, we approached this subject by characterizing the biodiversity of the alfalfa pathobiome using high-throughput sequencing technology. Our metagenomic study revealed a remarkable abundance of different pathogenic communities associated with alfalfa in the natural ecosystem. Profiling the alfalfa pathobiome is a starting point to assess known and identify new and emerging stress challenges in the context of plant disease management. In addition, it allows us to address the complexity of microbial interactions within the plant host and their impact on the development and evolution of pathogenesis.}, } @article {pmid37690468, year = {2023}, author = {Liu, L and Hu, J and Teng, Y and Wang, J and Chen, H and Guo, X and Zhai, Y}, title = {Response of microbial community to different media in start-up period of Annan constructed wetland in Beijing of China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {337}, number = {}, pages = {122529}, doi = {10.1016/j.envpol.2023.122529}, pmid = {37690468}, issn = {1873-6424}, mesh = {Humans ; *Wetlands ; Beijing ; Bacteria/genetics ; *Microbiota ; China ; }, abstract = {Microbial community, as the decomposers of constructed wetland (CW), plays crucial role in biodegradation and biotransformation of pollutants, nutrient cycling and the maintenance of ecosystem balance. In this study, 9 water samples, 6 sediment samples, and 8 plant samples were collected in Annan CW, which has the functions of water treatment and wetland culture park. The characteristics of microbial community structure in different media were illustrated by using of high-throughput sequencing-based metagenomics approach and statistical analysis. Meanwhile, this study identified and classified human pathogens in CW to avoid potential risks to human health. The results showed that dominant bacteria phyla in CW include Proteobacteria, Bacteroides, Actinobacteria, Firmicutes and Verrucomicrobia. The distribution of microorganisms in three media is different, but not significant. And the pH and DO profoundly affected microbe abundance, followed by water temperature. The microbial diversity in sediments is the highest, which is similar with the detection of human pathogens in sediments. Moreover, compared with Calamus, Lythrum salicaria and Reed, Scirpus tabernaemontani has fewer pathogenic microorganisms. The distribution of microorganisms in the CW is complex, and a variety of human pathogens are detected, which is more prone to create potential risks to human health and should receive additional attention.}, } @article {pmid37689857, year = {2023}, author = {Zhu, C and Cheng, Y and Shi, Q and Ge, X and Yang, Y and Huang, Y}, title = {Metagenomic analyses reveal microbial communities and functional differences between Daqu from seven provinces.}, journal = {Food research international (Ottawa, Ont.)}, volume = {172}, number = {}, pages = {113076}, doi = {10.1016/j.foodres.2023.113076}, pmid = {37689857}, issn = {1873-7145}, mesh = {Metagenome ; *Microbiota ; *Bacillus ; Amino Acids ; Lactic Acid ; *Lactobacillales/genetics ; }, abstract = {Microbial communities perform the brewing function in Daqu. Macrogenomics and PICRUST II analyses revealed the differences in microbes and metabolic functions among Daqu from the seven Baijiu-producing provinces. Jiang-flavored Daqu (Guizhou, Shandong, and Hubei provinces) generally forms an aroma-producing functional microbiota with Kroppenstedtia, Bacillus, Thermoascus, Virgibacillus, and Thermomyces as the core, which promotes the metabolism of various amino acids and aroma compounds. Light-flavored Daqu (Shanxi Province) enriched the Saccharomycopsis, Saccharomyces, and lactic acid bacteria (LAB) microbiota through low-temperature fermentation. These microbes can synthesize alcohol and lactic acid but inhibit amino acid metabolism within the Light-flavored Daqu. Bifidobacterium and Saccharomycopsis were dominant in the Tao-flavored Daqu (Henan province). This unique microbial structure is beneficial for pyruvate fermentation to lactate. Research also found that Strong-flavored Daqu from Jiangsu and Sichuan provinces differed significantly. The microbial communities and metabolic pathways within Jiangsu Daqu were similar to those within Jiang-flavored Daqu, but Sichuan Daqu was dominated by Thermoascus, LAB, and Thermoactinomyces. In addition, Spearman correlation analysis indicated that Kroppenstedtia, Bacillus, and Thermomyces were not only positively related to flavor metabolism but also negatively correlated with Saccharomycopsis. This research will help establish a systematic understanding of the microbial community and functional characteristics in Daqu.}, } @article {pmid37688597, year = {2023}, author = {Wang, L and Lian, C and Wan, W and Qiu, Z and Luo, X and Huang, Q and Deng, Y and Zhang, T and Yu, K}, title = {Salinity-triggered homogeneous selection constrains the microbial function and stability in lakes.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {21}, pages = {6591-6605}, pmid = {37688597}, issn = {1432-0614}, abstract = {Climate change and anthropogenic exploitation have led to the gradual salinization of inland waters worldwide. However, the impacts of this process on the prokaryotic plankton communities and their role in biogeochemical cycles in the inland lake are poorly known. Here, we take a space-for-time substitution approach, using 16S rRNA gene amplicon sequencing and metagenomic sequencing. We analyzed the prokaryotic plankton communities of 11 lakes in northwest China, with average water salinities ranging from 0.002 to 14.370%. The results demonstrated that, among the various environmental parameters, salinity was the most important driver of prokaryotic plankton β-diversity (Mantel test, r = 0.53, P < 0.001). (1) Under low salinity, prokaryotic planktons were assembled by stochastic processes and employed diverse halotolerant strategies, including the synthesis and uptake of compatible solutes and extrusion of Na[+] or Li[+] in exchange for H[+]. Under elevated salinity pressure, strong homogeneous selection meant that only planktonic prokaryotes showing an energetically favorable halotolerant strategy employing an Mnh-type Na[+]/H[+] antiporter remained. (2) The decreasing taxonomic diversity caused by intense environmental filtering in high-salinity lakes impaired functional diversity related to substance metabolism. The prokaryotes enhanced the TCA cycle, carbon fixation, and low-energy-consumption amino acid biosynthesis in high-salinity lakes. (3) Elevated salinity pressure decreased the negative:positive cohesion and the modularity of the molecular ecology networks for the planktonic prokaryotes, indicating a precarious microbial network. Our findings provide new insights into plankton ecology and are helpful for the protecting of the biodiversity and function of inland lakes against the background of salinization. KEY POINTS: • Increased salinity enhances homogeneous selection in the microbial assembly. • Elevated salinity decreases the microbial co-occurrence networks stability. • High salinity damages the microbial function diversity.}, } @article {pmid37684694, year = {2023}, author = {Liu, S and Men, X and Guo, Y and Cai, W and Wu, R and Gao, R and Zhong, W and Guo, H and Ruan, H and Chou, S and Mai, J and Ping, S and Jiang, C and Zhou, H and Mou, X and Zhao, W and Lu, Z}, title = {Gut microbes exacerbate systemic inflammation and behavior disorders in neurologic disease CADASIL.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {202}, pmid = {37684694}, issn = {2049-2618}, mesh = {Animals ; Mice ; *CADASIL ; *Gastrointestinal Microbiome ; *Mental Disorders ; Cytokines ; gamma-Aminobutyric Acid ; }, abstract = {BACKGROUND: Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a cerebral small vessel disease that carries mutations in NOTCH3. The clinical manifestations are influenced by genetic and environmental factors that may include gut microbiome.

RESULTS: We investigated the fecal metagenome, fecal metabolome, serum metabolome, neurotransmitters, and cytokines in a cohort of 24 CADASIL patients with 28 healthy household controls. The integrated-omics study showed CADASIL patients harbored an altered microbiota composition and functions. The abundance of bacterial coenzyme A, thiamin, and flavin-synthesizing pathways was depleted in patients. Neurotransmitter balance, represented by the glutamate/GABA (4-aminobutanoate) ratio, was disrupted in patients, which was consistent with the increased abundance of two major GABA-consuming bacteria, Megasphaera elsdenii and Eubacterium siraeum. Essential inflammatory cytokines were significantly elevated in patients, accompanied by an increased abundance of bacterial virulence gene homologs. The abundance of patient-enriched Fusobacterium varium positively correlated with the levels of IL-1β and IL-6. Random forest classification based on gut microbial species, serum cytokines, and neurotransmitters showed high predictivity for CADASIL with AUC = 0.89. Targeted culturomics and mechanisms study further showed that patient-derived F. varium infection caused systemic inflammation and behavior disorder in Notch3[R170C/+] mice potentially via induction of caspase-8-dependent noncanonical inflammasome activation in macrophages.

CONCLUSION: These findings suggested the potential linkage among the brain-gut-microbe axis in CADASIL. Video Abstract.}, } @article {pmid37684524, year = {2023}, author = {Lee, J and Ju, F and Beck, K and Bürgmann, H}, title = {Differential effects of wastewater treatment plant effluents on the antibiotic resistomes of diverse river habitats.}, journal = {The ISME journal}, volume = {17}, number = {11}, pages = {1993-2002}, pmid = {37684524}, issn = {1751-7370}, mesh = {*Anti-Bacterial Agents/pharmacology ; Wastewater ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; *Microbiota ; Water ; beta-Lactamases/genetics ; }, abstract = {Wastewater treatment plants (WWTPs) are key sources of antimicrobial resistance genes (ARGs) that could influence the resistomes of microbial communities in various habitats of the receiving river ecosystem. However, it is currently unknown which habitats are most impacted and whether ARGs, like certain chemical contaminants, could be accumulated or enriched in the river ecosystem. We conducted a systematic metagenomic survey on the antibiotic resistomes of WWTP effluent, four riverine habitats (water, suspended particles, sediment, epilithic biofilm), and freshwater amphipod gut microbiomes. The impact of WWTP effluent on the downstream habitats was assessed in nine Swiss rivers. While there were significant differences in resistomes across habitats, the wastewater resistome was more similar to the resistome of receiving river water than to the resistomes of other habitats, and river water was the habitat most strongly impacted by the WWTPs effluent. The sulfonamide, beta-lactam, and aminoglycoside resistance genes were among the most abundant ARGs in the WWTP effluents, and especially aadA, sul1, and class A beta-lactamase genes showed significantly increased abundance in the river water of downstream compared to upstream locations (p < 0.05). However, this was not the case for the sediment, biofilm, and amphipod gut habitats. Accordingly, evidence for accumulation or enrichment of ARGs through the riverine food web was not identified. Our study suggests that monitoring riverine antimicrobial resistance determinants could be conducted using "co-occurrence" of aadA, sul1, and class A beta-lactamase genes as an indicator of wastewater-related pollution and should focus on the water as the most affected habitat.}, } @article {pmid37683845, year = {2023}, author = {Kang, J and Qiu, W and Zhang, W and Liu, J and Yang, Z and Wu, Z and Ge, J}, title = {Understanding how various forms of phosphorus stress affect microbiome functions and boost plant disease resistance: Insights from metagenomic analysis.}, journal = {The Science of the total environment}, volume = {904}, number = {}, pages = {166899}, doi = {10.1016/j.scitotenv.2023.166899}, pmid = {37683845}, issn = {1879-1026}, mesh = {*Disease Resistance ; Soil Microbiology ; *Microbiota ; Metagenome ; Plant Diseases/microbiology ; Rhizosphere ; Soil ; Plant Roots/microbiology ; }, abstract = {The plant's response to phosphorus (P) starvation suppresses its immunity and regulates rhizosphere microbial colonization. However, the impact of various P forms on plant disease resistance and microbial composition remains underreported. This paper examines the soybean rhizosphere microbiome facing co-stress from Fusarium oxysporum and diverse P forms. Macrogenomic analysis evaluates whether P addition enhances plant disease resistance and rhizosphere microbial function, and if such effects relate to P forms. Results show that different P forms mitigate F. oxysporum-induced plant inhibition by promoting P turnover. P forms predominantly affect microbial composition, followed by soil and plant properties. In soybean, the phosphate transport strategy (ugpA/Q) was selected to maintain high P to enhance immunity in the KH2PO4 treatment, while organo-P mineralization (phnH/F/W/G) was selected for superphosphate treatment. The Frankiales, a P-turnover microorganism, copiotrophic microorganisms, and indicator bacteria of plant properties, initially increase after F. oxysporum inoculation and then decrease post P addition, regardless of P forms. Additionally, the rhizosphere microbial community's metabolic activities and compounds significantly aid soybean defense against F. oxysporum, with functional types depending on P forms. Therefore, these findings establish a novel approach to enhance host defense against soil-borne diseases through P nutrition regulation to mediate host-driven metabolic activities of microbial communities.}, } @article {pmid37680093, year = {2023}, author = {de la Cuesta-Zuluaga, J and Huus, KE and Youngblut, ND and Escobar, JS and Ley, RE}, title = {Obesity is the main driver of altered gut microbiome functions in the metabolically unhealthy.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2246634}, pmid = {37680093}, issn = {1949-0984}, mesh = {Adult ; Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Obesity ; Adipose Tissue ; Anthropometry ; }, abstract = {Obesity (OB) and cardiometabolic disease are major public health issues linked to changes in the gut microbiome. OB and poor cardiometabolic health status (CHS) are often comorbid, which hinders efforts to identify components of the microbiome uniquely linked to either one. Here, we used a deeply phenotyped cohort of 408 adults from Colombia, including subjects with OB, unhealthy CHS, or both, to validate previously reported features of gut microbiome function and diversity independently correlated with OB or CHS using fecal metagenomes. OB was defined by body mass index, waist circumference, and body fat; CHS as healthy or unhealthy according to blood biochemistry and anthropometric data. We found that OB, more so than metabolic status, drove associations with gut microbiome structure and functions. The microbiome of obese individuals with and without co-existing unhealthy CHS was characterized by reduced metagenomic diversity, reduced fermentative potential and elevated capacity to respond to oxidative stress and produce bacterial antigens. Disease-linked features were correlated with increased host blood pressure and inflammatory markers, and were mainly contributed by members of the family Enterobacteriaceae. Our results link OB with a microbiome able to tolerate an inflammatory and oxygenated gut state, and suggest that OB is the main driver of microbiome functional differences when poor CHS is a comorbidity.}, } @article {pmid37679294, year = {2023}, author = {Umar, M and Bowman, JP and Asis, C and McConchie, C and Eyles, A and Stanley, R and Gracie, A}, title = {Microbial communities associated with resin canal discoloration in mango fruit.}, journal = {Letters in applied microbiology}, volume = {76}, number = {9}, pages = {}, doi = {10.1093/lambio/ovad104}, pmid = {37679294}, issn = {1472-765X}, support = {IC140100024//Australian Research Council/ ; }, mesh = {*Mangifera ; Fruit ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Enterobacteriaceae ; }, abstract = {Resin canal discoloration (RCD) severely impacts the fruit quality of mango, diminishes consumer confidence, and reduces sales, but the biological cause is still unclear. Using next-generation sequencing, the overall microbial community composition of RCD+ and visually healthy mango fruits was determined for the first time to examine the possible role of bacterial and fungal pathogens in RCD. The diversity profile of bacterial and fungal communities was determined using primers targeting the 16S rRNA gene and Internal Transcribed Spacer (ITS) regions. Results showed that bacterial communities in healthy fruits are clustered together and significantly different from those in RCD+ fruits. Tatumella and Pantoea species were the most abundant bacterial taxa on RCD+ fruit, and both have been linked to disease outbreaks in a variety of fruit crops. Fungal communities were generally similar between RCD+ and normal samples, though non-pathogenic yeasts Meyerozyma and Naganishia tended to dominate the fungal communities on RCD+ fruit. The study indicates that bacteria rather than fungal organisms are more likely to be associated with RCD in mango. This finding will facilitate the isolation and confirmation of RCD-causing organisms and the development of control strategies to manage RCD problem in mango.}, } @article {pmid37673036, year = {2023}, author = {Ni, Y and Qian, L and Siliceo, SL and Long, X and Nychas, E and Liu, Y and Ismaiah, MJ and Leung, H and Zhang, L and Gao, Q and Wu, Q and Zhang, Y and Jia, X and Liu, S and Yuan, R and Zhou, L and Wang, X and Li, Q and Zhao, Y and El-Nezami, H and Xu, A and Xu, G and Li, H and Panagiotou, G and Jia, W}, title = {Resistant starch decreases intrahepatic triglycerides in patients with NAFLD via gut microbiome alterations.}, journal = {Cell metabolism}, volume = {35}, number = {9}, pages = {1530-1547.e8}, doi = {10.1016/j.cmet.2023.08.002}, pmid = {37673036}, issn = {1932-7420}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Microbiota ; *Non-alcoholic Fatty Liver Disease ; Resistant Starch ; Triglycerides ; Humans ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD) is a hepatic manifestation of metabolic dysfunction for which effective interventions are lacking. To investigate the effects of resistant starch (RS) as a microbiota-directed dietary supplement for NAFLD treatment, we coupled a 4-month randomized placebo-controlled clinical trial in individuals with NAFLD (ChiCTR-IOR-15007519) with metagenomics and metabolomics analysis. Relative to the control (n = 97), the RS intervention (n = 99) resulted in a 9.08% absolute reduction of intrahepatic triglyceride content (IHTC), which was 5.89% after adjusting for weight loss. Serum branched-chain amino acids (BCAAs) and gut microbial species, in particular Bacteroides stercoris, significantly correlated with IHTC and liver enzymes and were reduced by RS. Multi-omics integrative analyses revealed the interplay among gut microbiota changes, BCAA availability, and hepatic steatosis, with causality supported by fecal microbiota transplantation and monocolonization in mice. Thus, RS dietary supplementation might be a strategy for managing NAFLD by altering gut microbiota composition and functionality.}, } @article {pmid37672426, year = {2023}, author = {Prado, T and Magalhães, MGP and Moreira, DA and Brandão, ML and Fumian, TM and Ferreira, FC and Chame, M and Leomil, L and Degrave, WMS and Leite, JPG and Miagostovich, MP}, title = {Microbiome and virome on indoor surfaces of an Antarctic research ship.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {118}, number = {}, pages = {e230084}, pmid = {37672426}, issn = {1678-8060}, mesh = {Humans ; *Virome ; Ships ; Antarctic Regions ; *Microbiota ; Archaea/genetics ; }, abstract = {BACKGROUND: Few studies have focused on microbial diversity in indoor environments of ships, as well as the role of the microbiome and its ecological interconnections. In this study, we investigated the microbiome and virome present on the internal surfaces of a polar ship in different stages (beginning, during, and at the end) of the Brazilian Antarctic expedition in order to evaluate abundance of microorganisms in different periods.

OBJECTIVES AND METHODS: We used shotgun metagenomic analysis on pooled samples from sampling surfaces in the ship's interior to track the microbial diversity.

FINDINGS: Considering the total fraction of the microbiome, the relative abundance of bacteria, eukaryotes, viruses, and archaea was 83.7%, 16.2%, 0.04%, and 0.002%, respectively. Proteobacteria was the most abundant bacterial phyla, followed by Firmicutes, Actinobacteria, and Bacteroidetes. Concerning the virome, the greatest richness of viral species was identified during the middle of the trip, including ten viral families after de novo assembly: Autographiviridae, Chrysoviridae, Genomoviridae, Herelleviridae, Myoviridae, Partitiviridae, Podoviridae, Potyviridae, Siphoviridae, and Virgaviridae.

MAIN CONCLUSIONS: This study contributed to the knowledge of microbial diversity in naval transportation facilities, and variations in the abundance of microorganisms probably occurred due to factors such as the number of passengers and activities on the ship.}, } @article {pmid37672116, year = {2024}, author = {Camacho-Sanchez, M}, title = {A new spike-in-based method for quantitative metabarcoding of soil fungi and bacteria.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {27}, number = {3}, pages = {719-730}, pmid = {37672116}, issn = {1618-1905}, mesh = {*Soil Microbiology ; *Fungi/genetics/classification/isolation & purification ; *DNA Barcoding, Taxonomic/methods ; *Bacteria/genetics/classification/isolation & purification ; Biodiversity ; Reproducibility of Results ; Real-Time Polymerase Chain Reaction/methods ; Microbiota/genetics ; Metagenomics/methods ; DNA, Fungal/genetics ; DNA, Bacterial/genetics ; }, abstract = {Metabarcoding is a powerful tool to characterize biodiversity in biological samples. The interpretation of taxonomic profiles from metabarcoding data has been hindered by their compositional nature. Several strategies have been proposed to transform compositional data into quantitative data, but they have intrinsic limitations. Here, I propose a workflow based on bacterial and fungal cellular internal standards (spike-ins) for absolute quantification of the microbiota in soil samples. These standards were added to the samples before DNA extraction in amounts estimated after qPCRs, to target around 1-2% coverage in the sequencing run. In bacteria, proportions of spike-in reads in the sequencing run were very similar (< 2-fold change) to those predicted by the qPCR assessment, and for fungi they differed up to 40-fold. The low variation among replicates highlights the reproducibility of the method. Estimates based on multiple bacterial spike-ins were highly correlated (r = 0.99). Procrustes analysis evidenced significant biological effects on the community composition when normalizing compositional data. A protocol based on qPCR estimation of input amounts of cellular spikes is proposed as a cheap and reliable strategy for quantitative metabarcoding of biological samples.}, } @article {pmid37670231, year = {2023}, author = {Guo, R and Zhang, W and Shen, W and Zhang, G and Xie, T and Li, L and Jinmei, J and Liu, Y and Kong, F and Guo, B and Li, B and Sun, Y and Liu, S}, title = {Analysis of gut microbiota in chinese donkey in different regions using metagenomic sequencing.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {524}, pmid = {37670231}, issn = {1471-2164}, support = {SDAIT-27//Donkey Innovation Team of Shandong Modern Agricultural Industry Technology System/ ; SD2019 XM 008//Major Agricultural Application Technology Innovation Projects of Shandong Province/ ; 225A6601D//Hebei Provincial science and Technology Planning Project/ ; 2022DZ01//Systematic Evaluation and Screening of donkey germplasm Resources in the Yellow River Basin/ ; 2021E02035//Autonomous region science and technology branch Xinjiang project/ ; ZR2022QC091//Shandong Province Natural Science Foundation/ ; 20210021//Experimental Technology Research Pro-gramme of Qingdao Agriculture University/ ; }, mesh = {Bacteroidetes ; China ; Clostridiales ; Firmicutes ; *Gastrointestinal Microbiome ; *Equidae/microbiology ; }, abstract = {BACKGROUND: Gut microbiota plays a significant role in host survival, health, and diseases; however, compared to other livestock, research on the gut microbiome of donkeys is limited.

RESULTS: In this study, a total of 30 donkey samples of rectal contents from six regions, including Shigatse, Changdu, Yunnan, Xinjiang, Qinghai, and Dezhou, were collected for metagenomic sequencing. The results of the species annotation revealed that the dominant phyla were Firmicutes and Bacteroidetes, and the dominant genera were Bacteroides, unclassified_o_Clostridiales (short for Clostridiales) and unclassified_f_Lachnospiraceae (short for Lachnospiraceae). The dominant phyla, genera and key discriminators were Bacteroidetes, Clostridiales and Bacteroidetes in Tibet donkeys (Shigatse); Firmicutes, Clostridiales and Clostridiales in Tibet donkeys (Changdu); Firmicutes, Fibrobacter and Tenericutes in Qinghai donkeys; Firmicutes, Clostridiales and Negativicutes in Yunnan donkeys; Firmicutes, Fibrobacter and Fibrobacteres in Xinjiang donkeys; Firmicutes, Clostridiales and Firmicutes in Dezhou donkeys. In the functional annotation, it was mainly enriched in the glycolysis and gluconeogenesis of carbohydrate metabolism, and the abundance was the highest in Dezhou donkeys. These results combined with altitude correlation analysis demonstrated that donkeys in the Dezhou region exhibited strong glucose-conversion ability, those in the Shigatse region exhibited strong glucose metabolism and utilization ability, those in the Changdu region exhibited a strong microbial metabolic function, and those in the Xinjiang region exhibited the strongest ability to decompose cellulose and hemicellulose.

CONCLUSION: According to published literature, this is the first study to construct a dataset with multi-regional donkey breeds. Our study revealed the differences in the composition and function of gut microbes in donkeys from different geographic regions and environmental settings and is valuable for donkey gut microbiome research.}, } @article {pmid37669363, year = {2023}, author = {Sireci, M and Muñoz, MA and Grilli, J}, title = {Environmental fluctuations explain the universal decay of species-abundance correlations with phylogenetic distance.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {37}, pages = {e2217144120}, pmid = {37669363}, issn = {1091-6490}, mesh = {Phylogeny ; Cross-Sectional Studies ; *Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Multiple ecological forces act together to shape the composition of microbial communities. Phyloecology approaches-which combine phylogenetic relationships between species with community ecology-have the potential to disentangle such forces but are often hard to connect with quantitative predictions from theoretical models. On the other hand, macroecology, which focuses on statistical patterns of abundance and diversity, provides natural connections with theoretical models but often neglects interspecific correlations and interactions. Here, we propose a unified framework combining both such approaches to analyze microbial communities. In particular, by using both cross-sectional and longitudinal metagenomic data for species abundances, we reveal the existence of an empirical macroecological law establishing that correlations in species-abundance fluctuations across communities decay from positive to null values as a function of phylogenetic dissimilarity in a consistent manner across ecologically distinct microbiomes. We formulate three variants of a mechanistic model-each relying on alternative ecological forces-that lead to radically different predictions. From these analyses, we conclude that the empirically observed macroecological pattern can be quantitatively explained as a result of shared population-independent fluctuating resources, i.e., environmental filtering and not as a consequence of, e.g., species competition. Finally, we show that the macroecological law is also valid for temporal data of a single community and that the properties of delayed temporal correlations can be reproduced as well by the model with environmental filtering.}, } @article {pmid37667515, year = {2023}, author = {Baker, JL}, title = {Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research.}, journal = {FEMS microbiology reviews}, volume = {47}, number = {5}, pages = {}, pmid = {37667515}, issn = {1574-6976}, support = {K99 DE029228/DE/NIDCR NIH HHS/United States ; R00 DE029228/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Quality of Life ; Computational Biology ; Genomics ; Metabolomics ; *Microbiota/genetics ; }, abstract = {The oral microbiota has an enormous impact on human health, with oral dysbiosis now linked to many oral and systemic diseases. Recent advancements in sequencing, mass spectrometry, bioinformatics, computational biology, and machine learning are revolutionizing oral microbiome research, enabling analysis at an unprecedented scale and level of resolution using omics approaches. This review contains a comprehensive perspective of the current state-of-the-art tools available to perform genomics, metagenomics, phylogenomics, pangenomics, transcriptomics, proteomics, metabolomics, lipidomics, and multi-omics analysis on (all) microbiomes, and then provides examples of how the techniques have been applied to research of the oral microbiome, specifically. Key findings of these studies and remaining challenges for the field are highlighted. Although the methods discussed here are placed in the context of their contributions to oral microbiome research specifically, they are pertinent to the study of any microbiome, and the intended audience of this includes researchers would simply like to get an introduction to microbial omics and/or an update on the latest omics methods. Continued research of the oral microbiota using omics approaches is crucial and will lead to dramatic improvements in human health, longevity, and quality of life.}, } @article {pmid37666802, year = {2023}, author = {Kieft, B and Finke, N and McLaughlin, RJ and Nallan, AN and Krzywinski, M and Crowe, SA and Hallam, SJ}, title = {Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5380}, pmid = {37666802}, issn = {2041-1723}, mesh = {*Wastewater ; *Metagenome ; Microbial Consortia/genetics ; Sewage ; Methane ; }, abstract = {Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus, as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood-Ljungdahl pathway.}, } @article {pmid37666133, year = {2023}, author = {Ahmed, B and Gahlot, P and Balasundaram, G and Tyagi, VK and Banu J, R and Vivekanand, V and Kazmi, AA}, title = {Semi-continuous anaerobic co-digestion of thermal and thermal-alkali processed organic fraction of municipal solid waste: Methane yield, energy analysis, anaerobic microbiome.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118907}, doi = {10.1016/j.jenvman.2023.118907}, pmid = {37666133}, issn = {1095-8630}, mesh = {Anaerobiosis ; *Solid Waste ; *Microbiota ; Alkalies ; Methane ; Digestion ; }, abstract = {The semi-continuous anaerobic co-digestion (AcoD) of thermal and thermal-alkali pretreated organic fraction of municipal solid waste (OFMSW) and sewage sludge (SS) was studied under varying hydraulic retention times (HRT) and organic loading rates (OLR Three semi-continuous digesters were operated under control (non-pre-treated), thermally pretreated (125 °C), and thermal-alkali pretreated (125°C-3g/L NaOH) conditions at variable OLRs at 2.5, 4.0, 5.1, and 7.6 kgVS/m[3].d and corresponding HRTs of 30, 20, 15, and 10 days. The 10 and 43% higher methane yield (0.445 m[3]/kgVS) and 11 and 57% higher VS removal (52%) was achieved for thermal-alkali pretreated digester at 5.1 kgVS/m[3].d OLR over thermally pretreated (0.408 m[3]/kgVS, 45% VS removal) and control digesters (0.310 m[3]/kgVS, 33% VS removal), respectively. Thermal and thermal-alkali digesters failed on increasing the OLR to 7.6 kgVS/m[3].d, whereas the control digester becomes upset at 5.1 kgVS/m[3].d OLR. The metagenomic study revealed that Firmicutes, Bacteroidetes, Chloroflexi, Euryarchaeota, Proteobacteria, and Actinobacteria were the predominant bacterial population, whereas Methanosarcina and Methanothrix dominated the archaeal community. Energy balance analysis revealed that thermal alkali pretreatment showed the highest positive energy balance of 114.6 MJ/ton with an energy ratio of 1.25 compared with thermally pretreated (81.5 MJ/ton) and control samples (-46.9 MJ/ton). This work pave the way for scaleup of both thermal and thermal-alkali pre-treatment at 125 °C to realize the techno-economic and energy potential of the process.}, } @article {pmid37666128, year = {2023}, author = {Wang, S and Chen, D and Liu, Q and Zang, L and Zhang, G and Sui, M and Dai, Y and Zhou, C and Li, Y and Yang, Y and Ding, F}, title = {Dominant influence of plants on soil microbial carbon cycling functions during natural restoration of degraded karst vegetation.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118889}, doi = {10.1016/j.jenvman.2023.118889}, pmid = {37666128}, issn = {1095-8630}, mesh = {*Ecosystem ; Soil ; Soil Microbiology ; Plants ; China ; *Microbiota ; Carbon ; }, abstract = {The impacts of natural restoration projects on soil microbial carbon (C) cycling functions have not been well recognized despite their wide implementation in the degraded karst areas of southwest China. In this study, metagenomic sequencing assays were conducted on functional genes and microorganisms related to soil C-cycling at three natural restoration stages (shrubbery, TG; secondary forest, SG; old-growth forest, OG) in the southeast of Guizhou Province, China. The aims were to investigate the changes in microbial potentials responsible for soil C cycling and the underlying driving forces. The natural restoration resulted in vegetation establishment at all three restoration stages, rendering alterations of soil microbial C cycle functions as indicated by metagenomic gene assays. When TG was restored into OG, the number and diversity of genes and microorganisms involved in soil C cycling remained unchanged, but their composition underwent significant shifts. Specifically, microbial potentials for soil C decomposition exhibited an increase driven by the collaborative efforts of plants and soils, while microbial potentials for soil C biosynthesis displayed an initial upswing followed by a subsequent decline which was primarily influenced by plants alone. In comparison to soil nutrients, it was determined that plant diversities served as the primary driving factor for the alterations in microbial carbon cycle potentials. Soil microbial communities involved in C cycling were predominantly attributed to Proteobacteria (31.87%-40.25%) and Actinobacteria (11.29%-26.07%), although their contributions varied across the three restoration stages. The natural restoration of degraded karst vegetation thus influences soil microbial C cycle functions by enhancing C decomposition potentials and displaying a nuanced pattern of biosynthesis potentials, primarily influenced by above-ground plants. These results provide valuable new insights into the regulation of soil C cycling during the restoration of degraded karst vegetation from genetic and microbial perspectives.}, } @article {pmid37665015, year = {2024}, author = {Sinjab, K and Sawant, S and Ou, A and Fenno, JC and Wang, HL and Kumar, P}, title = {Impact of surface characteristics on the peri-implant microbiome in health and disease.}, journal = {Journal of periodontology}, volume = {95}, number = {3}, pages = {244-255}, pmid = {37665015}, issn = {1943-3670}, support = {R01 DE022579/DE/NIDCR NIH HHS/United States ; R01 DE027857/DE/NIDCR NIH HHS/United States ; R01DE027857/NH/NIH HHS/United States ; }, mesh = {Humans ; *Peri-Implantitis/microbiology ; *Dental Implants/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Because little is known about the impact of implant surface modifications on the peri-implant microbiome, we aimed to examine peri-implant communities in various surface types in order to better understand the impact of these surfaces on the development of peri-implantitis (PI).

METHODS: One hundred and six systemically healthy individuals with anodized (AN), hydroxyapatite-coated (HA), or sandblasted acid-etched (SLA) implants that were >6 months in function were recruited and categorized into health (H) or PI. Peri-implant biofilm was analyzed using 16S rRNA gene sequencing and compared between health/disease and HA/SLA/AN using community-level and taxa-level metrics.

RESULTS: Healthy implants did not demonstrate significant differences in clustering, alpha- or beta-diversity based on surface modification. AN and HA surfaces displayed significant differences between health and PI (p < 0.05); however, such a clustering was not evident with SLA (p > 0.05). AN and HA surfaces also differed in the magnitude and diversity of differences between health and PI. Six species belonging to the genera Shuttleworthia, Scardovia, and Prevotella demonstrated lower abundances in AN implants with PI, and 18 species belonging to the genera Fretibacterium, Tannerella, Treponema, and Fusobacterium were elevated, while in HA implants with PI, 20 species belonging to the genera Streptococcus, Lactobacillus, Veillonella, Rothia, and family Ruminococcaceae were depleted and Peptostreptococcaceae, Atopobiaceae, Veillonellaceae, Porphyromonadaceae, Desulfobulbaceae, and order Synergistales were enriched.

CONCLUSIONS: Within the limitations of this study, we demonstrate that implant surface can differentially modify the disease-associated microbiome, suggesting that surface topography must be considered in the multi-factorial etiology of peri-implant diseases.}, } @article {pmid37664974, year = {2024}, author = {Schuetz, R and Claypool, J and Sfriso, R and Vollhardt, JH}, title = {Sunscreens can preserve human skin microbiome upon erythemal UV exposure.}, journal = {International journal of cosmetic science}, volume = {46}, number = {1}, pages = {71-84}, doi = {10.1111/ics.12910}, pmid = {37664974}, issn = {1468-2494}, mesh = {Humans ; Female ; Ultraviolet Rays ; Sunscreening Agents/pharmacology ; Pilot Projects ; RNA, Ribosomal, 16S ; Skin ; Erythema ; *Acne Vulgaris/drug therapy ; *Microbiota ; }, abstract = {OBJECTIVE: Ultraviolet radiation (UVR) is a known environmental key factor for premature skin ageing. Only few scientific evidence is available to support the effects of UVR on the skin microbiome. This in vivo pilot study aimed to evaluate the impact on the skin microbiome upon erythemal UV exposure and the protection of UV-exposed skin microbiome by UV filters.

METHODS: Ten female volunteers were treated with an sun protection factor (SPF) 20 sunscreen and placebo formulation (without UV filters) on their upper middle backs and irradiated with an erythemal dose (2 MED) by a solar simulator. Skin swabbing samples from four zones (i.e., unexposed, exposed, sunscreen- and placebo-treated on exposed skin) were collected for the microbiome analysis before and 2 h after UV exposure, respectively, and processed via shallow 16S rRNA Amplicon and Shotgun metagenomic sequencing. An in vitro UV method was developed to confirm the protection of isolated bacterial strains by single UV filters and combinations.

RESULTS: Alpha diversity was impacted by significant inter-individual differences and by treatment rather than by irradiation. Cutibacterium acnes was found to be the most abundant and a confounding factor for diversity. On a species level, Lactobacillus crispatus was negatively associated with UVR and placebo treatment, whereas there was a positive association with sunscreen treatment. The sunscreen treatment also favoured an interaction network with central Micrococcus genus. The in vitro results showed that both single UV filters and combinations had specific effects on the survival rates of L. crispatus, C. acnes, and Staphylococcus epidermidis.

CONCLUSION: We identified potential microorganisms and bacterial interactions that were associated with an SPF 20 sunscreen treatment. The specific protection of L. crispatus as a key player in the UV-exposed skin microbiome and reduction of C. acnes population by UV filters might lead to new cosmetic concepts for photoprotection.}, } @article {pmid37664620, year = {2023}, author = {Mao, C and Li, Q and Komijani, M and Huang, J and Li, T}, title = {Metagenomic analysis reveals the dissemination mechanisms and risks of resistance genes in plateau lakes.}, journal = {iScience}, volume = {26}, number = {9}, pages = {107508}, pmid = {37664620}, issn = {2589-0042}, abstract = {Antibiotic resistance genes (ARGs) are emerging as environmental pollutants that can persist and disseminate in aquatic environments. Lakes, as important sources of freshwater, also serve as potential natural reservoirs of ARGs. In this study, we analyzed the distribution and potential risks of resistance genes in five typical freshwater lakes on the Yunnan-Guizhou Plateau. Our findings revealed that multidrug and MLS ARGs dominated in the studied lakes. Notably, while Lugu Lake exhibited higher abundance of ARGs, mobile genetic elements (MGEs), and metal resistance genes (MRGs), a greater resistome risk was observed in the eutrophic Xingyun Lake. The dissemination processes of ARGs and MRGs are primarily driven by microbial communities and the horizontal gene transfer via MGEs. Limnohabitans, Flavobacterium, and Acinetobacter were identified as key players in the dissemination of ARGs. Our study highlights the persistence of ARGs and provides valuable baseline data and risk assessment of ARGs in plateau freshwater lakes.}, } @article {pmid37660237, year = {2023}, author = {Li, R and Hu, M and Jiang, X and Xu, C}, title = {Metagenomic insights into the microbiota involved in lactate and butyrate production and manipulating their synthesis in alfalfa silage.}, journal = {Journal of applied microbiology}, volume = {134}, number = {9}, pages = {}, doi = {10.1093/jambio/lxad197}, pmid = {37660237}, issn = {1365-2672}, support = {31872420//National Natural Science Foundation of China/ ; }, mesh = {*Lactic Acid ; Medicago sativa/genetics ; Butyrates ; L-Lactate Dehydrogenase/genetics ; Silage ; *Microbiota/genetics ; Escherichia coli ; }, abstract = {AIMS: Lactate and butyrate are important indicators of silage quality. However, the microorganisms and mechanisms responsible for lactate and butyrate production in silage are not well documented.

METHODS AND RESULTS: whole-metagenomic sequencing was used to analyse metabolic pathways, microbiota composition, functional genes, and their contributions to lactate and butyrate production in alfalfa silage with (SA) and without (CK) sucrose addition. Carbon metabolism was the most abundant metabolic pathway. We identified 11 and 2 functional genes associated with lactate and butyrate metabolism, respectively. Among them, D-lactate dehydrogenase (ldhA) and L-lactate dehydrogenase (ldhB) were most important for the transition between D/L-lactate and pyruvate and were primarily related to Lactobacillus in the SA group. The genes encoding L-lactate dehydrogenase (lldD), which decomposes lactate, were the most abundant and primarily associated with Enterobacter cloacae. Butyrate-related genes, mainly encoding butyryl-CoA: acetate CoA-transferase (but), were predominantly associated with Klebsiella oxytoca and Escherichia coli in the CK group.

CONCLUSIONS: Enterobacteriaceae and Lactobacillaceae were mainly responsible for butyrate and lactate formation, respectively.}, } @article {pmid37659809, year = {2023}, author = {Li, Z and Wen, Q and Pi, J and Zhang, D and Nie, J and Wei, W and Li, W and Guo, DA}, title = {An inulin-type fructan isolated from Serratula chinensis alleviated the dextran sulfate sodium-induced colitis in mice through regulation of intestinal barrier and gut microbiota.}, journal = {Carbohydrate polymers}, volume = {320}, number = {}, pages = {121206}, doi = {10.1016/j.carbpol.2023.121206}, pmid = {37659809}, issn = {1879-1344}, mesh = {Animals ; Mice ; Inulin/pharmacology/therapeutic use ; Fructans/pharmacology/therapeutic use ; *Gastrointestinal Microbiome ; Dextran Sulfate/toxicity ; Spectroscopy, Fourier Transform Infrared ; *Colitis/chemically induced/drug therapy ; }, abstract = {Herein, we aimed to explore the polysaccharide material basis of Serratula chinensis and establish its beneficial effects against colitis. A neutral polysaccharide (SCP) was extracted from S. chinensis in high yield using hot water. The molecular weights were calculated by HPSEC as Mw = 2928 Da, Mn = 2634 Da, and Mw/Mn = 1.11. FT-IR and 1D/2D-NMR spectroscopic analyses confirmed that SCP was an inulin-type fructan with α-D-Glcp-(1 → [1)-β-D-Fruf-(2]17) linkages. Treatment with SCP (200 or 400 mg/kg) alleviated dextran sulfate sodium (DSS)-induced mouse colitis symptoms, including the loss of body weight, increase of disease activity index score, and shortening of colon length. Histopathological and immunofluorescence assessments revealed that SCP could reduce pathological damage to the colon, restore the number of goblet cells, increase the content of glycoproteins in goblet cells and mucins in crypts, and enhance the expression of tight junction proteins ZO-1 and occludin. In addition, metagenomic sequencing revealed that SCP could improve the dysbiosis of gut microbiomes and act on multiple microbial functions. Moreover, SCP treatment increased the content of colonic acetic acid and butanoic acid. Collectively, these results indicated that SCP could alleviate the DSS-induced colitis in mice through regulation of intestinal barrier and gut microbiota.}, } @article {pmid37658654, year = {2023}, author = {Couso, LL and Soler-Bistué, A and Aptekmann, AA and Sánchez, IE}, title = {Ecology theory disentangles microbial dichotomies.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {3052-3063}, doi = {10.1111/1462-2920.16495}, pmid = {37658654}, issn = {1462-2920}, mesh = {*Bacteria/genetics ; *Microbiota ; Heterotrophic Processes ; Metagenomics ; Carbon ; }, abstract = {Microbes are often discussed in terms of dichotomies such as copiotrophic/oligotrophic and fast/slow-growing microbes, defined using the characterisation of microbial growth in isolated cultures. The dichotomies are usually qualitative and/or study-specific, sometimes precluding clear-cut results interpretation. We can unravel microbial dichotomies as life history strategies by combining ecology theory with Monod curves, a laboratory mathematical tool of bacterial physiology that relates the specific growth rate of a microbe with the concentration of a limiting nutrient. Fitting of Monod curves provides quantities that directly correspond to key parameters in ecological theories addressing species coexistence and diversity, such as r/K selection theory, resource competition and community structure theory and the CSR triangle of life strategies. The resulting model allows us to reconcile the copiotrophic/oligotrophic and fast/slow-growing dichotomies as different subsamples of a life history strategy triangle that also includes r/K strategists. We also used the number of known carbon sources together with community structure theory to partially explain the diversity of heterotrophic microbes observed in metagenomics experiments. In sum, we propose a theoretical framework for the study of natural microbial communities that unifies several existing proposals. Its application would require the integration of metagenomics, metametabolomics, Monod curves and carbon source data.}, } @article {pmid37658443, year = {2023}, author = {Paulo, AC and Lança, J and Almeida, ST and Hilty, M and Sá-Leão, R}, title = {The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {199}, pmid = {37658443}, issn = {2049-2618}, mesh = {Adult ; Child ; Humans ; Streptococcus pneumoniae/genetics ; Smoking ; Nose ; *Microbiota ; Metagenome ; *Bacillus ; Firmicutes ; }, abstract = {BACKGROUND: The microbiota of the upper respiratory tract is increasingly recognized as a gatekeeper of respiratory health. Despite this, the microbiota of healthy adults remains understudied. To address this gap, we investigated the composition of the nasopharyngeal and oropharyngeal microbiota of healthy adults, focusing on the effect of Streptococcus pneumoniae carriage, smoking habits, and contact with children.

RESULTS: Differential abundance analysis indicated that the microbiota of the oropharynx was significantly different from that of the nasopharynx (P < 0.001) and highly discriminated by a balance between the classes Negativicutes and Bacilli (AUC of 0.979). Moreover, the oropharynx was associated with a more homogeneous microbiota across individuals, with just two vs. five clusters identified in the nasopharynx. We observed a shift in the nasopharyngeal microbiota of carriers vs. noncarriers with an increased relative abundance of Streptococcus, which summed up to 30% vs. 10% in noncarriers and was not mirrored in the oropharynx. The oropharyngeal microbiota of smokers had a lower diversity than the microbiota of nonsmokers, while no differences were observed in the nasopharyngeal microbiota. In particular, the microbiota of smokers, compared with nonsmokers, was enriched (on average 16-fold) in potential pathogenic taxa involved in periodontal diseases of the genera Bacillus and Burkholderia previously identified in metagenomic studies of cigarettes. The microbiota of adults with contact with children resembled the microbiota of children. Specifically, the nasopharyngeal microbiota of these adults had, on average, an eightfold increase in relative abundance in Streptococcus sp., Moraxella catarrhalis, and Haemophilus influenzae, pathobionts known to colonize the children's upper respiratory tract, and a fourfold decrease in Staphylococcus aureus and Staphylococcus lugdunensis.

CONCLUSIONS: Our study showed that, in adults, the presence of S. pneumoniae in the nasopharynx is associated with a shift in the microbiota and dominance of the Streptococcus genus. Furthermore, we observed that smoking habits are associated with an increase in bacterial genera commonly linked to periodontal diseases. Interestingly, our research also revealed that adults who have regular contact with children have a microbiota enriched in pathobionts frequently carried by children. These findings collectively contribute to a deeper understanding of how various factors influence the upper respiratory tract microbiota in adults. Video Abstract.}, } @article {pmid37658428, year = {2023}, author = {Mao, Q and Liu, Y and Zhang, J and Li, W and Zhang, W and Zhou, C}, title = {Blood virome of patients with traumatic sepsis.}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {198}, pmid = {37658428}, issn = {1743-422X}, mesh = {Humans ; Virome ; *Sepsis/diagnosis ; *Anelloviridae/genetics ; Immunocompromised Host ; Metagenome ; }, abstract = {Sepsis is one of the possible outcomes of severe trauma, and it poses a dire threat to human life, particularly in immunocompromised people. The most prevalent pathogens are bacteria and fungi, but viruses should not be overlooked. For viral metagenomic analysis, we collected blood samples from eight patients with post-traumatic sepsis before and seven days after treatment. The results demonstrated that Anellovirus predominated the viral community, followed by Siphoviridae and Myoviridae, and that the variations in viral community and viral load before and after treatment were not statistically significant. This study allows us to investigate methods for establishing NGS-based viral diagnostic instruments for detecting viral infections in the blood of sepsis patients so that antiviral therapy can be administered quickly.}, } @article {pmid37657622, year = {2023}, author = {Dong, Z and Xie, Q and Yuan, Y and Shen, X and Hao, Y and Li, J and Xu, H and Kuang, W}, title = {Strain-level structure of gut microbiome showed potential association with cognitive function in major depressive disorder: A pilot study.}, journal = {Journal of affective disorders}, volume = {341}, number = {}, pages = {236-247}, doi = {10.1016/j.jad.2023.08.129}, pmid = {37657622}, issn = {1573-2517}, mesh = {Animals ; Humans ; *Depressive Disorder, Major ; *Gastrointestinal Microbiome/genetics ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Cognition ; }, abstract = {BACKGROUND: Although the association between gut microbiota and the pathogenesis of major depressive disorder (MDD) has been well studied, it is unclear whether gut microbiota affects cognitive function in patients with MDD. In this study, we explored the association between gut microbiota and cognitive function in MDD and its possible mechanisms.

METHODS: We enrolled 57 patients with MDD and 30 healthy controls (HCs) and used 16S rRNA gene sequencing analysis and shotgun metagenomic sequencing analysis to determine gut microbial composition.

RESULTS: The richness and diversity of gut microbiota in patients with MDD were the same as those in HCs, but there were differences in the abundance of Bifidobacterium and Blautia. Compared with HCs, two strains (bin_32 and bin_55) were significantly increased, and one strain (bin_31) was significantly decreased in patients with MDD based on the strain-level meta-analysis. Time to complete the Stroop-C had significant negative correlations with bin_31 and bin_32. Bin_55 had significant negative correlations with time to complete the Stroop-C, time to complete the Stroop-CW, and repeated animal words in 60 s but significant positive correlations with correct answers in 120 s on the Stroop-CW.

LIMITATIONS: This study only tested the cognitive function of MDD in a small sample, which may have caused some bias.

CONCLUSIONS: Based on our strain-level analysis, we found that gut microbiota may be associated with the pathogenesis of MDD and may have potential effects on cognitive function.}, } @article {pmid37655299, year = {2023}, author = {Shen, H and Liu, T and Shen, M and Zhang, Y and Chen, W and Chen, H and Wang, Y and Liu, J and Tao, J and He, L and Lu, G and Yan, G}, title = {Utilizing metagenomic next-generation sequencing for diagnosis and lung microbiome probing of pediatric pneumonia through bronchoalveolar lavage fluid in pediatric intensive care unit: results from a large real-world cohort.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1200806}, pmid = {37655299}, issn = {2235-2988}, mesh = {Humans ; Child ; Bronchoalveolar Lavage Fluid ; Retrospective Studies ; *Pneumonia/diagnosis ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; Intensive Care Units, Pediatric ; Lung ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection in various infections. In this study, we assessed the value of mNGS in the pathogen diagnosis and microbiome analysis of pneumonia in pediatric intensive care units (PICU) using bronchoalveolar lavage fluid (BALF) samples.

METHODS: A total of 104 pediatric patients with pneumonia who were admitted into PICU between June 2018 and February 2020 were retrospectively enrolled. Among them, 101 subjects who had intact clinical information were subject to parallel comparison of mNGS and conventional microbiological tests (CMTs) for pathogen detection. The performance was also evaluated and compared between BALF-mNGS and BALF-culture methods. Moreover, the diversity and structure of all 104 patients' lung BALF microbiomes were explored using the mNGS data.

RESULTS: Combining the findings of mNGS and CMTs, 94.06% (95/101) pneumonia cases showed evidence of causative pathogenic infections, including 79.21% (80/101) mixed and 14.85% (15/101) single infections. Regarding the pathogenesis of pneumonia in the PICU, the fungal detection rates were significantly higher in patients with immunodeficiency (55.56% vs. 25.30%, P =0.025) and comorbidities (40.30% vs. 11.76%, P=0.007). There were no significant differences in the α-diversity either between patients with CAP and HAP or between patients with and without immunodeficiency. Regarding the diagnostic performance, the detection rate of DNA-based BALF-mNGS was slightly higher than that of the BALF-culture although statistically insignificant (81.82% vs.77.92%, P=0.677) and was comparable to CMTs (81.82% vs. 89.61%, P=0.211). The overall sensitivity of DNA-based mNGS was 85.14% (95% confidence interval [CI]: 74.96%-92.34%). The detection rate of RNA-based BALF-mNGS was the same with CMTs (80.00% vs 80.00%, P>0.999) and higher than BALF-culture (80.00% vs 52.00%, P=0.045), with a sensitivity of 90.91% (95%CI: 70.84%-98.88%).

CONCLUSIONS: mNGS is valuable in the etiological diagnosis of pneumonia, especially in fungal infections, and can reveal pulmonary microecological characteristics. For pneumonia patients in PICU, the mNGS should be implemented early and complementary to CMTs.}, } @article {pmid37652953, year = {2023}, author = {Wu, J and Li, C and Gao, P and Zhang, C and Zhang, P and Zhang, L and Dai, C and Zhang, K and Shi, B and Liu, M and Zheng, J and Pan, B and Chen, Z and Zhang, C and Liao, W and Pan, W and Fang, W and Chen, C}, title = {Intestinal microbiota links to allograft stability after lung transplantation: a prospective cohort study.}, journal = {Signal transduction and targeted therapy}, volume = {8}, number = {1}, pages = {326}, pmid = {37652953}, issn = {2059-3635}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Prospective Studies ; *Lung Transplantation ; Cytokines ; Allografts ; }, abstract = {Whether the alternated microbiota in the gut contribute to the risk of allograft rejection (AR) and pulmonary infection (PI) in the setting of lung transplant recipients (LTRs) remains unexplored. A prospective multicenter cohort of LTRs was identified in the four lung transplant centers. Paired fecal and serum specimens were collected and divided into AR, PI, and event-free (EF) groups according to the diagnosis at sampling. Fecal samples were determined by metagenomic sequencing. And metabolites and cytokines were detected in the paired serum to analyze the potential effect of the altered microbiota community. In total, we analyzed 146 paired samples (AR = 25, PI = 43, and EF = 78). Notably, we found that the gut microbiome of AR followed a major depletion pattern with decreased 487 species and compositional diversity. Further multi-omics analysis showed depleted serum metabolites and increased inflammatory cytokines in AR and PI. Bacteroides uniformis, which declined in AR (2.4% vs 0.6%) and was negatively associated with serum IL-1β and IL-12, was identified as a driven specie in the network of gut microbiome of EF. Functionally, the EF specimens were abundant in probiotics related to mannose and cationic antimicrobial peptide metabolism. Furthermore, a support-vector machine classifier based on microbiome, metabolome, and clinical parameters highly predicted AR (AUPRC = 0.801) and PI (AUPRC = 0.855), whereby the microbiome dataset showed a particularly high diagnostic power. In conclusion, a disruptive gut microbiota showed a significant association with allograft rejection and infection and with systemic cytokines and metabolites in LTRs.}, } @article {pmid37652940, year = {2023}, author = {Jacobs, JP and Lee, ML and Rechtman, DJ and Sun, AK and Autran, C and Niklas, V}, title = {Human milk oligosaccharides modulate the intestinal microbiome of healthy adults.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {14308}, pmid = {37652940}, issn = {2045-2322}, mesh = {Adult ; Female ; Humans ; Infant, Newborn ; *Gastrointestinal Microbiome ; *Milk, Human/chemistry ; *Oligosaccharides/pharmacology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Human milk contains over 200 distinct oligosaccharides, which are critical to shaping the developing neonatal gut microbiome. To investigate whether a complex mixture of human milk oligosaccharides (HMOs) would similarly modulate the adult gut microbiome, HMO-Concentrate derived from pooled donor breast milk was administered orally to 32 healthy adults for 7 days followed by 21 days of monitoring. Fecal samples were collected for 16S rRNA gene sequencing, shotgun metagenomics, and metabolomics analyses. HMO-Concentrate induced dose-dependent Bifidobacterium expansion, reduced microbial diversity, and altered microbial gene content. Following HMO cessation, a microbial succession occurred with diverse taxonomic changes-including Bacteroides expansion-that persisted through day 28. This was associated with altered microbial gene content, shifts in serum metabolite levels, and increased circulating TGFβ and IL-10. Incubation of cultured adult microbiota with HMO-Concentrate induced dose-dependent compositional shifts that were not recapitulated by individual HMOs or defined mixtures of the 10 most abundant HMOs in HMO-Concentrate at their measured concentrations. These findings support that pooled donor HMOs can exert direct effects on adult gut microbiota and that complex mixtures including low abundance HMOs present in donor milk may be required for maximum effect.Registration: ClinicalTrials.gov NCT05516225.}, } @article {pmid37652786, year = {2023}, author = {Delavy, M and Sertour, N and d'Enfert, C and Bougnoux, ME}, title = {Metagenomics and metabolomics approaches in the study of Candida albicans colonization of host niches: a framework for finding microbiome-based antifungal strategies.}, journal = {Trends in microbiology}, volume = {31}, number = {12}, pages = {1276-1286}, doi = {10.1016/j.tim.2023.08.002}, pmid = {37652786}, issn = {1878-4380}, mesh = {Female ; Humans ; Candida albicans/genetics ; Antifungal Agents/pharmacology ; *Gastrointestinal Microbiome ; *Microbiota ; Metabolomics ; Bacteria ; }, abstract = {In silico and experimental approaches have allowed an ever-growing understanding of the interactions within the microbiota. For instance, recently acquired data have increased knowledge of the mechanisms that support, in the gut and vaginal microbiota, the resistance to colonization by Candida albicans, an opportunistic fungal pathogen whose overgrowth can initiate severe infections in immunocompromised patients. Here, we review how bacteria from the microbiota interact with C. albicans. We show how recent OMICs-based pipelines, using metagenomics and/or metabolomics, have identified bacterial species and metabolites modulating C. albicans growth. We finally discuss how the combined use of cutting-edge OMICs-based and experimental approaches could provide new means to control C. albicans overgrowth within the microbiota and prevent its consequences.}, } @article {pmid37652264, year = {2024}, author = {Zhang, B and Zhang, X and Luo, Z and Ren, J and Yu, X and Zhao, H and Wang, Y and Zhang, W and Tian, W and Wei, X and Ding, Q and Yang, H and Jin, Z and Tong, X and Wang, J and Zhao, L}, title = {Microbiome and metabolome dysbiosis analysis in impaired glucose tolerance for the prediction of progression to diabetes mellitus.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {51}, number = {1}, pages = {75-86}, doi = {10.1016/j.jgg.2023.08.005}, pmid = {37652264}, issn = {1673-8527}, mesh = {Humans ; *Glucose Intolerance/metabolism ; Glucose Tolerance Test ; Dysbiosis/microbiology ; *Diabetes Mellitus ; Metabolome ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2/metabolism ; Blood Glucose/metabolism ; }, abstract = {Gut microbiota and circulating metabolite dysbiosis predate important pathological changes in glucose metabolic disorders; however, comprehensive studies on impaired glucose tolerance (IGT), a diabetes mellitus (DM) precursor, are lacking. Here, we perform metagenomic sequencing and metabolomics on 47 pairs of individuals with IGT and newly diagnosed DM and 46 controls with normal glucose tolerance (NGT); patients with IGT are followed up after 4 years for progression to DM. Analysis of baseline data reveals significant differences in gut microbiota and serum metabolites among the IGT, DM, and NGT groups. In addition, 13 types of gut microbiota and 17 types of circulating metabolites showed significant differences at baseline before IGT progressed to DM, including higher levels of Eggerthella unclassified, Coprobacillus unclassified, Clostridium ramosum, L-valine, L-norleucine, and L-isoleucine, and lower levels of Eubacterium eligens, Bacteroides faecis, Lachnospiraceae bacterium 3_1_46FAA, Alistipes senegalensis, Megaspaera elsdenii, Clostridium perfringens, α-linolenic acid, 10E,12Z-octadecadienoic acid, and dodecanoic acid. A random forest model based on differential intestinal microbiota and circulating metabolites can predict the progression from IGT to DM (AUC = 0.87). These results suggest that microbiome and metabolome dysbiosis occur in individuals with IGT and have important predictive values and potential for intervention in preventing IGT from progressing to DM.}, } @article {pmid37650630, year = {2023}, author = {Koziol, A and Odriozola, I and Leonard, A and Eisenhofer, R and San José, C and Aizpurua, O and Alberdi, A}, title = {Mammals show distinct functional gut microbiome dynamics to identical series of environmental stressors.}, journal = {mBio}, volume = {14}, number = {5}, pages = {e0160623}, pmid = {37650630}, issn = {2150-7511}, support = {R250-2017-1351//Lundbeck Foundation (Lundbeckfonden)/ ; DNRF143//Danmarks Grundforskningsfond (DNRF)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Phylogeny ; Mammals ; *Microbiota ; Metagenomics ; RNA, Ribosomal, 16S ; }, abstract = {In our manuscript, we report the first interspecific comparative study about the plasticity of the gut microbiota. We conducted a captivity experiment that exposed wild-captured mammals to a series of environmental challenges over 45 days. We characterized their gut microbial communities using genome-resolved metagenomics and modeled how the taxonomic, phylogenetic, and functional microbial dynamics varied across a series of disturbances in both species. Our results indicate that the intrinsic properties (e.g., diversity and functional redundancy) of microbial communities coupled with physiological attributes (e.g., thermal plasticity) of hosts shape the taxonomic, phylogenetic, and functional response of gut microbiomes to environmental stressors, which might influence their contribution to the acclimation and adaptation capacity of animal hosts.}, } @article {pmid37650612, year = {2023}, author = {Teullet, S and Tilak, M-K and Magdeleine, A and Schaub, R and Weyer, NM and Panaino, W and Fuller, A and Loughry, WJ and Avenant, NL and de Thoisy, B and Borrel, G and Delsuc, F}, title = {Metagenomics uncovers dietary adaptations for chitin digestion in the gut microbiota of convergent myrmecophagous mammals.}, journal = {mSystems}, volume = {8}, number = {5}, pages = {e0038823}, pmid = {37650612}, issn = {2379-5077}, support = {683257//EC | European Research Council (ERC)/ ; ANR-10-LABX-0025//Agence Nationale de la Recherche (ANR)/ ; ANR-10-LABX-0004//Agence Nationale de la Recherche (ANR)/ ; }, mesh = {Pregnancy ; Animals ; Female ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; Chitin ; Placenta ; Mammals/microbiology ; Digestion ; }, abstract = {Myrmecophagous mammals are specialized in the consumption of ants and/or termites. They do not share a direct common ancestor and evolved convergently in five distinct placental orders raising questions about the underlying adaptive mechanisms involved and the relative contribution of natural selection and phylogenetic constraints. Understanding how these species digest their prey can help answer these questions. More specifically, the role of their gut microbial symbionts in the digestion of the insect chitinous exoskeleton has not been investigated in all myrmecophagous orders. We generated 29 new gut metagenomes from nine myrmecophagous species to reconstruct more than 300 bacterial genomes in which we identified chitin-degrading enzymes. Studying the distribution of these chitinolytic bacteria among hosts revealed both shared and specific bacteria between ant-eating species. Overall, our results highlight the potential role of gut symbionts in the convergent dietary adaptation of myrmecophagous mammals and the evolutionary mechanisms shaping their gut microbiota.}, } @article {pmid37650395, year = {2024}, author = {Huang, G and Qi, D and Yang, Z and Hou, R and Shi, W and Zhao, F and Li, Z and Yan, L and Wei, F}, title = {Gut microbiome as a key monitoring indicator for reintroductions of captive animals.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {38}, number = {1}, pages = {e14173}, doi = {10.1111/cobi.14173}, pmid = {37650395}, issn = {1523-1739}, support = {31821001//National Natural Science Foundation of China/ ; 31970386//National Natural Science Foundation of China/ ; 2023090//Chinese Academy of Sciences/ ; XDB31000000//Chinese Academy of Sciences/ ; }, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome ; Conservation of Natural Resources ; Biodiversity ; Feces ; Diet ; *Ursidae ; }, abstract = {Reintroduction programs seek to restore degraded populations and reverse biodiversity loss. To examine the hypothesis that gut symbionts could be used as an indicator of reintroduction success, we performed intensive metagenomic monitoring over 10 years to characterize the ecological succession and adaptive evolution of the gut symbionts of captive giant pandas reintroduced to the wild. We collected 63 fecal samples from 3 reintroduced individuals and 22 from 9 wild individuals and used 96 publicly available samples from another 3 captive individuals. By microbial composition analysis, we identified 3 community clusters of the gut microbiome (here termed enterotypes) with interenterotype succession that was closely related to the reintroduction process. Each of the 3 enterotypes was identified based on significant variation in the levels of 1 of 3 genera: Clostridium, Pseudomonas, and Escherichia. The enterotype of captive pandas was Escherichia. This enterotype was gradually replaced by the Clostridium enterotype during the wild-training process, which in turn was replaced by the Pseudomonas enterotype that resembled the enterotype of wild pandas, an indicator of conversion to wildness and a successful reintroduction. We also isolated 1 strain of Pseudomonas protegens from the wild enterotype, a previously reported free-living microbe, and found that its within-host evolution contributed to host dietary adaptation in the wild. Monitoring gut microbial structure provides a novel, noninvasive tool that can be used as an indicator of successful reintroduction of a captive individual to the wild.}, } @article {pmid37648982, year = {2023}, author = {Diba, F and Hoque, MN and Rahman, MS and Haque, F and Rahman, KMJ and Moniruzzaman, M and Khan, M and Hossain, MA and Sultana, M}, title = {Metagenomic and culture-dependent approaches unveil active microbial community and novel functional genes involved in arsenic mobilization and detoxification in groundwater.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {241}, pmid = {37648982}, issn = {1471-2180}, mesh = {*Arsenic ; *Arsenites ; Phylogeny ; *Microbiota ; }, abstract = {BACKGROUND: Arsenic (As) and its species are major pollutants in ecological bodied including groundwater in Bangladesh rendering serious public health concern. Bacteria with arsenotrophic genes have been found in the aquifer, converting toxic arsenite [As (III)] to less toxic arsenate [As (V)] that is easily removed using chemical and biological trappers. In this study, genomic and metagenomic approaches parallel to culture-based assay (Graphical abstract) have made it possible to decipher phylogenetic diversity of groundwater arsenotrophic microbiomes along with elucidation of their genetic determinants.

RESULTS: Seventy-two isolates were retrieved from six As-contaminated (average As concentration of 0.23 mg/L) groundwater samples from Munshiganj and Chandpur districts of Bangladesh. Twenty-three isolates harbored arsenite efflux pump (arsB) gene with high abundance, and ten isolates possessing arsenite oxidase (aioA) gene, with a wide range of minimum inhibitory concentration, MICAs (2 to 32 mM), confirming their role in arsenite metabolism. There was considerable heterogeneity in species richness and microbial community structure. Microbial taxa from Proteobacteria, Firmicutes and Acidobacteria dominated these diversities. Through these combinatorial approaches, we have identified potential candidates such as, Pseudomonas, Acinetobacter, Stenotrophomonas, Achromobacter, Paraburkholderia, Comamonas and Klebsiella and associated functional genes (arsB, acr3, arsD, arsH, arsR) that could significantly contribute to arsenite detoxification, accumulation, and immobilization.

CONCLUSIONS: Culture-dependent and -independent shotgun metagenomic investigation elucidated arsenotrophic microbiomes and their functions in As biogeochemical transformation. These findings laid a foundation for further large-scale researches on the arsenotrophic microbiomes and their concurrent functions in As biogeochemical transformation in As-contaminated areas of Bangladesh and beyond.}, } @article {pmid37648852, year = {2023}, author = {Takeuchi, T and Kubota, T and Nakanishi, Y and Tsugawa, H and Suda, W and Kwon, AT and Yazaki, J and Ikeda, K and Nemoto, S and Mochizuki, Y and Kitami, T and Yugi, K and Mizuno, Y and Yamamichi, N and Yamazaki, T and Takamoto, I and Kubota, N and Kadowaki, T and Arner, E and Carninci, P and Ohara, O and Arita, M and Hattori, M and Koyasu, S and Ohno, H}, title = {Gut microbial carbohydrate metabolism contributes to insulin resistance.}, journal = {Nature}, volume = {621}, number = {7978}, pages = {389-395}, pmid = {37648852}, issn = {1476-4687}, mesh = {Animals ; Humans ; Mice ; *Carbohydrate Metabolism ; Diabetes Mellitus, Type 2/metabolism ; *Gastrointestinal Microbiome/physiology ; *Insulin Resistance/physiology ; Monosaccharides/metabolism ; Insulin/metabolism ; Metabolic Syndrome/metabolism ; Feces/chemistry/microbiology ; Metabolomics ; }, abstract = {Insulin resistance is the primary pathophysiology underlying metabolic syndrome and type 2 diabetes[1,2]. Previous metagenomic studies have described the characteristics of gut microbiota and their roles in metabolizing major nutrients in insulin resistance[3-9]. In particular, carbohydrate metabolism of commensals has been proposed to contribute up to 10% of the host's overall energy extraction[10], thereby playing a role in the pathogenesis of obesity and prediabetes[3,4,6]. Nevertheless, the underlying mechanism remains unclear. Here we investigate this relationship using a comprehensive multi-omics strategy in humans. We combine unbiased faecal metabolomics with metagenomics, host metabolomics and transcriptomics data to profile the involvement of the microbiome in insulin resistance. These data reveal that faecal carbohydrates, particularly host-accessible monosaccharides, are increased in individuals with insulin resistance and are associated with microbial carbohydrate metabolisms and host inflammatory cytokines. We identify gut bacteria associated with insulin resistance and insulin sensitivity that show a distinct pattern of carbohydrate metabolism, and demonstrate that insulin-sensitivity-associated bacteria ameliorate host phenotypes of insulin resistance in a mouse model. Our study, which provides a comprehensive view of the host-microorganism relationships in insulin resistance, reveals the impact of carbohydrate metabolism by microbiota, suggesting a potential therapeutic target for ameliorating insulin resistance.}, } @article {pmid37648570, year = {2023}, author = {Robinson, JM and Hodgson, R and Krauss, SL and Liddicoat, C and Malik, AA and Martin, BC and Mohr, JJ and Moreno-Mateos, D and Muñoz-Rojas, M and Peddle, SD and Breed, MF}, title = {Opportunities and challenges for microbiomics in ecosystem restoration.}, journal = {Trends in ecology & evolution}, volume = {38}, number = {12}, pages = {1189-1202}, doi = {10.1016/j.tree.2023.07.009}, pmid = {37648570}, issn = {1872-8383}, mesh = {*Ecosystem ; Soil Microbiology ; Ecology ; Soil/chemistry ; *Microbiota ; Plants ; }, abstract = {Microbiomics is the science of characterizing microbial community structure, function, and dynamics. It has great potential to advance our understanding of plant-soil-microbe processes and interaction networks which can be applied to improve ecosystem restoration. However, microbiomics may be perceived as complex and the technology is not accessible to all. The opportunities of microbiomics in restoration ecology are considerable, but so are the practical challenges. Applying microbiomics in restoration must move beyond compositional assessments to incorporate tools to study the complexity of ecosystem recovery. Advances in metaomic tools provide unprecedented possibilities to aid restoration interventions. Moreover, complementary non-omic applications, such as microbial inoculants and biopriming, have the potential to improve restoration objectives by enhancing the establishment and health of vegetation communities.}, } @article {pmid37648499, year = {2023}, author = {Hagihara, M and Kato, H and Shibata, Y and Umemura, T and Ariyoshi, T and Hirai, J and Asai, N and Mori, N and Mikamo, H}, title = {Mycobiome and Mycobiome-Associated Diseases.}, journal = {Medical mycology journal}, volume = {64}, number = {3}, pages = {55-62}, doi = {10.3314/mmj.23-002}, pmid = {37648499}, issn = {2186-165X}, mesh = {Humans ; *Mycobiome ; Carcinogenesis ; Knowledge ; Metagenome ; Metagenomics ; }, abstract = {The human body is host to a large number of commensal microbial species such as bacteria, fungi, and viruses. Among these, the human mycobiome is often neglected as a potential cause of disease, as it is thought to be comparatively much less abundant and less diverse than the human bacteriome. Additionally, most fungi are not easily cultured, even in specific media. Hence, their study has been limited to date, mainly because of the unavailability of methods used for their detection. However, the utilization of a novel metagenomic methodology will enable the identification of well-characterized mycobiomes in several parts of the human body and broaden our knowledge of their contribution to human health and disease. In this article, we review the role of the human mycobiome in the gut, respiratory organs, skin, genital tract, and carcinogenesis, highlighting the correlations between the human mycobiome and mycobiome-associated diseases.}, } @article {pmid37648438, year = {2023}, author = {Lajoie, G and Kembel, SW}, title = {Data-driven identification of major axes of functional variation in bacteria.}, journal = {Environmental microbiology}, volume = {25}, number = {11}, pages = {2580-2591}, doi = {10.1111/1462-2920.16487}, pmid = {37648438}, issn = {1462-2920}, mesh = {*Ecosystem ; Phylogeny ; *Biodiversity ; Plants ; Bacteria/genetics ; }, abstract = {The discovery of major axes of correlated functional variation among species and habitats has revealed the fundamental trade-offs structuring both functional and taxonomic diversity in eukaryotes such as plants. Whether such functional axes exist in the bacterial realm and whether they could explain bacterial taxonomic turnover among ecosystems remains unknown. Here, we use a data-driven approach to leverage global genomic and metagenomic datasets to reveal the existence of major axes of functional variation explaining both evolutionary differentiation within Bacteria and their ecological sorting across diverse habitats. We show that metagenomic variation among bacterial communities from various ecosystems is structured along a few axes of correlated functional pathways. Similar clusters of traits explained phylogenetic trait variation among >16,000 bacterial genomes, suggesting that functional turnover among bacterial communities from distinct habitats does not only result from the differential filtering of similar functions among communities, but also from phylogenetic correlations among these functions. Concordantly, functional pathways associated with trait clusters that were most important for defining functional turnover among bacterial communities were also those that had the highest phylogenetic signal in the bacterial genomic phylogeny. This study overall underlines the important role of evolutionary history in shaping contemporary distributions of bacteria across ecosystems.}, } @article {pmid37647765, year = {2023}, author = {Young, GR and Nelson, A and Stewart, CJ and Smith, DL}, title = {Bacteriophage communities are a reservoir of unexplored microbial diversity in neonatal health and disease.}, journal = {Current opinion in microbiology}, volume = {75}, number = {}, pages = {102379}, doi = {10.1016/j.mib.2023.102379}, pmid = {37647765}, issn = {1879-0364}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Infant, Newborn ; Infant ; Humans ; Infant Health ; Infant, Premature ; *Microbiota ; *Bacteriophages/genetics ; *Gastrointestinal Microbiome ; }, abstract = {Acquisition and development of the gut microbiome are vital for immune education in neonates, especially those born preterm. As such, microbial communities have been extensively studied in the context of postnatal health and disease. Bacterial communities have been the focus of research in this area due to the relative ease of targeted bacterial sequencing and the availability of databases to align and validate sequencing data. Recent increases in high-throughput metagenomic sequencing accessibility have facilitated research to investigate bacteriophages within the context of neonatal gut microbial communities. Focusing on unexplored viral diversity, has identified novel bacteriophage species and previously uncharacterised viral diversity. In doing so, studies have highlighted links between bacteriophages and bacterial community structure in the context of health and disease. However, much remains unknown about the complex relationships between bacteriophages, the bacteria they infect and their human host. With a particular focus on preterm infants, this review highlights opportunities to explore the influence of bacteriophages on developing microbial communities and the tripartite relationships between bacteriophages, bacteria and the neonatal human host. We suggest a focus on expanding collections of isolated bacteriophages that will further our understanding of the growing numbers of bacteriophages identified in metagenomes.}, } @article {pmid37647089, year = {2024}, author = {Zhu, Z and Yu, C and Dong, Z and Mo, R and Zhang, C and Liu, X and Zuo, Y and Li, Y and Deng, W and Hu, X}, title = {Phylogeny and Fungal Community Structures of Helotiales Associated with Sclerotial Disease of Mulberry Fruits in China.}, journal = {Plant disease}, volume = {108}, number = {2}, pages = {502-512}, doi = {10.1094/PDIS-02-23-0223-RE}, pmid = {37647089}, issn = {0191-2917}, mesh = {Fruit ; *Mycobiome ; Phylogeny ; Bayes Theorem ; *Morus ; China ; *Coinfection ; }, abstract = {Mulberry fruit sclerotiniose is a prevalent disease caused by the fungal species Ciboria shiraiana, C. carunculoides, and Scleromitrula shiraiana of the order Helotiales, and severely affects the production of mulberry. However, these species have only been identified using morphological and rDNA-ITS sequence analyses, and their genetic variation is unclear. To address this, morphological and two-locus (ITS and RPB2) phylogenetic analyses were conducted using culture-dependent and independent methods for 49 samples from 31 orchards across four provinces in China. Illumina MiSeq sequencing was used to assess the fungal communities obtained from fruits varying in disease severity and color from an orchard in Wuhan. Conidial suspensions of C. shiraiana and C. carunculoides isolated from diseased fruits, diseased fruits affected with hypertrophy and pellet sorosis sclerotiniose, and mycelia of Sclerotinia sclerotiorum were determined to be pathogenic to the mulberry cultivar YSD10. However, fruits inoculated with S. sclerotiorum mycelia exhibited nontypical disease symptoms, and mycelia and conidia obtained from C. carunculoides and S. shiraiana strains were not pathogenic. Maximum parsimony and Bayesian analyses using the sequences of the assessed loci indicated species variability with no evidence of geographic specialization. Metagenomic analysis revealed that the diversity of fungal communities was reduced with disease progression. Furthermore, within a single fruit, the presence of two Ciboria spp. was detected. These results provide novel insights into Ciboria spp., revealing the secondary infections caused by conidia in diseased fruits, genetic variations of the pathogens, and the occurrence of coinfection. This improved understanding of fungal pathogens will aid in developing effective disease control strategies.}, } @article {pmid37644066, year = {2023}, author = {Yan, M and Pratama, AA and Somasundaram, S and Li, Z and Jiang, Y and Sullivan, MB and Yu, Z}, title = {Interrogating the viral dark matter of the rumen ecosystem with a global virome database.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5254}, pmid = {37644066}, issn = {2041-1723}, mesh = {Humans ; Animals ; Virome ; Rumen ; *Microbiota ; *Caudovirales ; Databases, Factual ; }, abstract = {The diverse rumen virome can modulate the rumen microbiome, but it remains largely unexplored. Here, we mine 975 published rumen metagenomes for viral sequences, create a global rumen virome database (RVD), and analyze the rumen virome for diversity, virus-host linkages, and potential roles in affecting rumen functions. Containing 397,180 species-level viral operational taxonomic units (vOTUs), RVD substantially increases the detection rate of rumen viruses from metagenomes compared with IMG/VR V3. Most of the classified vOTUs belong to Caudovirales, differing from those found in the human gut. The rumen virome is predicted to infect the core rumen microbiome, including fiber degraders and methanogens, carries diverse auxiliary metabolic genes, and thus likely impacts the rumen ecosystem in both a top-down and a bottom-up manner. RVD and the findings provide useful resources and a baseline framework for future research to investigate how viruses may impact the rumen ecosystem and digestive physiology.}, } @article {pmid37644001, year = {2023}, author = {Hoskinson, C and Dai, DLY and Del Bel, KL and Becker, AB and Moraes, TJ and Mandhane, PJ and Finlay, BB and Simons, E and Kozyrskyj, AL and Azad, MB and Subbarao, P and Petersen, C and Turvey, SE}, title = {Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4785}, pmid = {37644001}, issn = {2041-1723}, mesh = {Infant ; Humans ; Child ; *Gastrointestinal Microbiome/genetics ; *Hypersensitivity ; *Microbiota ; *Asthma ; *Dermatitis, Atopic ; }, abstract = {Allergic diseases affect millions of people worldwide. An increase in their prevalence has been associated with alterations in the gut microbiome, i.e., the microorganisms and their genes within the gastrointestinal tract. Maturation of the infant immune system and gut microbiota occur in parallel; thus, the conformation of the microbiome may determine if tolerant immune programming arises within the infant. Here we show, using deeply phenotyped participants in the CHILD birth cohort (n = 1115), that there are early-life influences and microbiome features which are uniformly associated with four distinct allergic diagnoses at 5 years: atopic dermatitis (AD, n = 367), asthma (As, n = 165), food allergy (FA, n = 136), and allergic rhinitis (AR, n = 187). In a subset with shotgun metagenomic and metabolomic profiling (n = 589), we discover that impaired 1-year microbiota maturation may be universal to pediatric allergies (AD p = 0.000014; As p = 0.0073; FA p = 0.00083; and AR p = 0.0021). Extending this, we find a core set of functional and metabolic imbalances characterized by compromised mucous integrity, elevated oxidative activity, decreased secondary fermentation, and elevated trace amines, to be a significant mediator between microbiota maturation at age 1 year and allergic diagnoses at age 5 years (βindirect = -2.28; p = 0.0020). Microbiota maturation thus provides a focal point to identify deviations from normative development to predict and prevent allergic disease.}, } @article {pmid37643149, year = {2023}, author = {Song, Y and Finkelstein, R and Rhoads, W and Edwards, MA and Pruden, A}, title = {Shotgun Metagenomics Reveals Impacts of Copper and Water Heater Anodes on Pathogens and Microbiomes in Hot Water Plumbing Systems.}, journal = {Environmental science & technology}, volume = {57}, number = {36}, pages = {13612-13624}, pmid = {37643149}, issn = {1520-5851}, mesh = {*Water ; Copper ; Metagenomics ; Sanitary Engineering ; *Microbiota ; Electrodes ; Phosphates ; }, abstract = {Hot water building plumbing systems are vulnerable to the proliferation of opportunistic pathogens (OPs), including Legionella pneumophila and Mycobacterium avium. Implementation of copper as a disinfectant could help reduce OPs, but a mechanistic understanding of the effects on the microbial community under real-world plumbing conditions is lacking. Here, we carried out a controlled pilot-scale study of hot water systems and applied shotgun metagenomic sequencing to examine the effects of copper dose (0-2 mg/L), orthophosphate corrosion control agent, and water heater anode materials (aluminum vs magnesium vs powered anode) on the bulk water and biofilm microbiome composition. Metagenomic analysis revealed that, even though a copper dose of 1.2 mg/L was required to reduce Legionella and Mycobacterium numbers, lower doses (e.g., ≤0.6 mg/L) measurably impacted the broader microbial community, indicating that the OP strains colonizing these systems were highly copper tolerant. Orthophosphate addition reduced bioavailability of copper, both to OPs and to the broader microbiome. Functional gene analysis indicated that both membrane damage and interruption of nucleic acid replication are likely at play in copper inactivation mechanisms. This study identifies key factors (e.g., orthophosphate, copper resistance, and anode materials) that can confound the efficacy of copper for controlling OPs in hot water plumbing.}, } @article {pmid37640834, year = {2023}, author = {van Dijk, B and Buffard, P and Farr, AD and Giersdorf, F and Meijer, J and Dutilh, BE and Rainey, PB}, title = {Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {90}, pmid = {37640834}, issn = {2730-6151}, abstract = {Microbial evolution is driven by rapid changes in gene content mediated by horizontal gene transfer (HGT). While mobile genetic elements (MGEs) are important drivers of gene flux, the nanobiome-the zoo of Darwinian replicators that depend on microbial hosts-remains poorly characterised. New approaches are necessary to increase our understanding beyond MGEs shaping individual populations, towards their impacts on complex microbial communities. A bioinformatic pipeline (xenoseq) was developed to cross-compare metagenomic samples from microbial consortia evolving in parallel, aimed at identifying MGE dissemination, which was applied to compost communities which underwent periodic mixing of MGEs. We show that xenoseq can distinguish movement of MGEs from demographic changes in community composition that otherwise confounds identification, and furthermore demonstrate the discovery of various unexpected entities. Of particular interest was a nanobacterium of the candidate phylum radiation (CPR) which is closely related to a species identified in groundwater ecosystems (Candidatus Saccharibacterium), and appears to have a parasitic lifestyle. We also highlight another prolific mobile element, a 313 kb plasmid hosted by a Cellvibrio lineage. The host was predicted to be capable of nitrogen fixation, and acquisition of the plasmid coincides with increased ammonia production. Taken together, our data show that new experimental strategies combined with bioinformatic analyses of metagenomic data stand to provide insight into the nanobiome as a driver of microbial community evolution.}, } @article {pmid37639475, year = {2023}, author = {Rangel-Pineros, G and Almeida, A and Beracochea, M and Sakharova, E and Marz, M and Reyes Muñoz, A and Hölzer, M and Finn, RD}, title = {VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models.}, journal = {PLoS computational biology}, volume = {19}, number = {8}, pages = {e1011422}, pmid = {37639475}, issn = {1553-7358}, support = {MR/W016184/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Eukaryota ; Eukaryotic Cells ; Genome, Viral/genetics ; Metagenome/genetics ; *Microbiota ; }, abstract = {The study of viral communities has revealed the enormous diversity and impact these biological entities have on various ecosystems. These observations have sparked widespread interest in developing computational strategies that support the comprehensive characterisation of viral communities based on sequencing data. Here we introduce VIRify, a new computational pipeline designed to provide a user-friendly and accurate functional and taxonomic characterisation of viral communities. VIRify identifies viral contigs and prophages from metagenomic assemblies and annotates them using a collection of viral profile hidden Markov models (HMMs). These include our manually-curated profile HMMs, which serve as specific taxonomic markers for a wide range of prokaryotic and eukaryotic viral taxa and are thus used to reliably classify viral contigs. We tested VIRify on assemblies from two microbial mock communities, a large metagenomics study, and a collection of publicly available viral genomic sequences from the human gut. The results showed that VIRify could identify sequences from both prokaryotic and eukaryotic viruses, and provided taxonomic classifications from the genus to the family rank with an average accuracy of 86.6%. In addition, VIRify allowed the detection and taxonomic classification of a range of prokaryotic and eukaryotic viruses present in 243 marine metagenomic assemblies. Finally, the use of VIRify led to a large expansion in the number of taxonomically classified human gut viral sequences and the improvement of outdated and shallow taxonomic classifications. Overall, we demonstrate that VIRify is a novel and powerful resource that offers an enhanced capability to detect a broad range of viral contigs and taxonomically classify them.}, } @article {pmid37635357, year = {2023}, author = {Gao, W and Gao, X and Zhu, L and Gao, S and Sun, R and Feng, Z and Wu, D and Liu, Z and Zhu, R and Jiao, N}, title = {Multimodal metagenomic analysis reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2245562}, pmid = {37635357}, issn = {1949-0984}, mesh = {*Colorectal Neoplasms/diagnosis/microbiology ; *Polymorphism, Single Nucleotide ; *Early Detection of Cancer/methods ; Metagenomics ; *Precancerous Conditions/diagnosis/microbiology ; *Adenoma/diagnosis/microbiology ; Metagenome ; *Gastrointestinal Microbiome/genetics ; Genetic Markers ; Feces/microbiology ; Humans ; Fungi/genetics/isolation & purification ; Bacteria/genetics/isolation & purification ; Archaea/genetics/isolation & purification ; Viruses/genetics/isolation & purification ; Cohort Studies ; }, abstract = {Microbial signatures show remarkable potentials in predicting colorectal cancer (CRC). This study aimed to evaluate the diagnostic powers of multimodal microbial signatures, multi-kingdom species, genes, and single-nucleotide variants (SNVs) for detecting precancerous adenomas. We performed cross-cohort analyses on whole metagenome sequencing data of 750 samples via xMarkerFinder to identify adenoma-associated microbial multimodal signatures. Our data revealed that fungal species outperformed species from other kingdoms with an area under the ROC curve (AUC) of 0.71 in distinguishing adenomas from controls. The microbial SNVs, including dark SNVs with synonymous mutations, displayed the strongest diagnostic capability with an AUC value of 0.89, sensitivity of 0.79, specificity of 0.85, and Matthews correlation coefficient (MCC) of 0.74. SNV biomarkers also exhibited outstanding performances in three independent validation cohorts (AUCs = 0.83, 0.82, 0.76; sensitivity = 1.0, 0.72, 0.93; specificity = 0.67, 0.81, 0.67, MCCs = 0.69, 0.83, 0.72) with high disease specificity for adenoma. In further support of the above results, functional analyses revealed more frequent inter-kingdom associations between bacteria and fungi, and abnormalities in quorum sensing, purine and butanoate metabolism in adenoma, which were validated in a newly recruited cohort via qRT-PCR. Therefore, these data extend our understanding of adenoma-associated multimodal alterations in the gut microbiome and provide a rationale of microbial SNVs for the early detection of CRC.}, } @article {pmid37633998, year = {2023}, author = {Odom, AR and Faits, T and Castro-Nallar, E and Crandall, KA and Johnson, WE}, title = {Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13957}, pmid = {37633998}, issn = {2045-2322}, support = {R21 AI154387/AI/NIAID NIH HHS/United States ; R01 GM127430/GM/NIGMS NIH HHS/United States ; }, mesh = {Metagenomics ; *Polyarteritis Nodosa ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Severe Combined Immunodeficiency ; Bone Plates ; *Cercozoa ; Humans ; *Microbiota ; Agammaglobulinemia ; }, abstract = {Most experiments studying bacterial microbiomes rely on the PCR amplification of all or part of the gene for the 16S rRNA subunit, which serves as a biomarker for identifying and quantifying the various taxa present in a microbiome sample. Several computational methods exist for analyzing 16S amplicon sequencing. However, the most-used bioinformatics tools cannot produce high quality genus-level or species-level taxonomic calls and may underestimate the potential accuracy of these calls. We used 16S sequencing data from mock bacterial communities to evaluate the sensitivity and specificity of several bioinformatics pipelines and genomic reference libraries used for microbiome analyses, concentrating on measuring the accuracy of species-level taxonomic assignments of 16S amplicon reads. We evaluated the tools DADA2, QIIME 2, Mothur, PathoScope 2, and Kraken 2 in conjunction with reference libraries from Greengenes, SILVA, Kraken 2, and RefSeq. Profiling tools were compared using publicly available mock community data from several sources, comprising 136 samples with varied species richness and evenness, several different amplified regions within the 16S rRNA gene, and both DNA spike-ins and cDNA from collections of plated cells. PathoScope 2 and Kraken 2, both tools designed for whole-genome metagenomics, outperformed DADA2, QIIME 2 using the DADA2 plugin, and Mothur, which are theoretically specialized for 16S analyses. Evaluations of reference libraries identified the SILVA and RefSeq/Kraken 2 Standard libraries as superior in accuracy compared to Greengenes. These findings support PathoScope and Kraken 2 as fully capable, competitive options for genus- and species-level 16S amplicon sequencing data analysis, whole genome sequencing, and metagenomics data tools.}, } @article {pmid37633814, year = {2023}, author = {Liu, X and Xu, J and Wang, Z and Xu, X and Wen, H and Su, H and Han, Y and Luo, Y and Zhang, Y and Li, W and Yao, X}, title = {Differential changes in the gut microbiota between extrinsic and intrinsic atopic dermatitis.}, journal = {Journal of autoimmunity}, volume = {141}, number = {}, pages = {103096}, doi = {10.1016/j.jaut.2023.103096}, pmid = {37633814}, issn = {1095-9157}, mesh = {Humans ; *Dermatitis, Atopic ; *Gastrointestinal Microbiome ; Histidine ; Metagenome ; Immunoglobulin E ; }, abstract = {Elevated serum level of total and (or) allergen-specific IgE is one of the key features of atopic dermatitis (AD). Previous studies have shown that the gut microbiome mediates interactions between external exposures and the immune system in AD; however, the relationship between the gut microbiota and IgE remains unclear. In the present study, analyses of environmental exposures for 250 AD patients and 138 healthy volunteers revealed an association between hygiene levels in the residential environment and the occurrence of AD and the IgE level. Metagenomic sequencing of the gut microbiota from 68 AD patients and 77 healthy controls showed that AD patients had a distinct gut microbiota composition; moreover, while L-histidine degradation was enriched in healthy controls, L-histidine biosynthesis was enriched in AD patients. Extrinsic and intrinsic AD showed different enrichment patterns of specific microbes and differential associations of functional pathways. Our study indicated that elevated levels of IgE in AD were related to specific microbes in the gut microbiota, which showed extensive interactions with environmental factors.}, } @article {pmid37632061, year = {2023}, author = {Richard, JC and Blevins, E and Dunn, CD and Leis, EM and Goldberg, TL}, title = {Viruses of Freshwater Mussels during Mass Mortality Events in Oregon and Washington, USA.}, journal = {Viruses}, volume = {15}, number = {8}, pages = {}, pmid = {37632061}, issn = {1999-4915}, mesh = {Animals ; Oregon ; Washington/epidemiology ; *Fresh Water ; *Bivalvia ; Rivers ; }, abstract = {Freshwater mussels (Unionida) are globally imperiled, in part due to largely unexplained mass mortality events (MMEs). While recent studies have begun to investigate the possibility that mussel MMEs in the Eastern USA may be caused by infectious diseases, mussels in the Western USA have received relatively little attention in this regard. We conducted a two-year epidemiologic investigation of the role of viruses in ongoing MMEs of the Western pearlshell (Margaritifera falcata) and the Western ridged mussel (Gonidea angulata) in the Chehalis River and Columbia River watersheds in the Western USA. We characterized viromes of mussel hemolymph from 5 locations in 2018 and 2020 using metagenomic methods and identified 557 viruses based on assembled contiguous sequences, most of which are novel. We also characterized the distribution and diversity of a previously identified mussel Gammarhabdovirus related to pathogenic finfish viruses. Overall, we found few consistent associations between viruses and mussel health status. Variation in mussel viromes was most strongly driven by location, with little influence from date, species, or health status, though these variables together only explained ~1/3 of variation in virome composition. Our results demonstrate that Western freshwater mussels host remarkably diverse viromes, but no single virus or combination of viruses appears to be associated with morbidity or mortality during MMEs. Our findings have implications for the conservation of imperiled freshwater mussels, including efforts to enhance natural populations through captive propagation.}, } @article {pmid37631163, year = {2023}, author = {Aleynova, OA and Nityagovsky, NN and Ananev, AA and Suprun, AR and Ogneva, ZV and Dneprovskaya, AA and Beresh, AA and Tyunin, AP and Dubrovina, AS and Kiselev, KV}, title = {The Endophytic Microbiome of Wild Grapevines Vitis amurensis Rupr. and Vitis coignetiae Pulliat Growing in the Russian Far East.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {16}, pages = {}, pmid = {37631163}, issn = {2223-7747}, support = {22-74-10001//Russian Science Foundation/ ; 121031000144-5//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Many grape endophytic microorganisms exhibit high potential for suppressing the development of grape diseases and stimulating grapevine growth and fitness, as well as beneficial properties of the crop. The microbiome of wild grapevines is a promising source of biocontrol agents, which can be beneficial for domesticated grapevines. Using next-generation sequencing (NGS) and classical microbiology techniques, we performed an analysis of bacterial and fungal endophytic communities of wild grapevines Vitis amurensis Rupr. and Vitis coignetiae Pulliat growing in the Russian Far East. According to the NGS analysis, 24 and 18 bacterial taxa from the class level were present in V. amurensis and V. coignetiae grapevines, respectively. Gammaproteobacteria (35%) was the predominant class of endophytic bacteria in V. amurensis and Alphaproteobacteria (46%) in V. coignetiae. Three taxa, namely Sphingomonas, Methylobacterium, and Hymenobacter, were the most common bacterial genera for V. amurensis and V. coignetiae. Metagenomic analysis showed the presence of 23 and 22 fungi and fungus-like taxa of class level in V. amurensis and V. coignetiae, respectively. The predominant fungal classes were Dothideomycetes (61-65%) and Tremellomycetes (10-11%), while Cladosporium and Aureobasidium were the most common fungal genera in V. amurensis and V. coignetiae, respectively. A comparative analysis of the endophytic communities of V. amurensis and V. coignetiae with the previously reported endophytic communities of V. vinifera revealed that the bacterial biodiversity of V. amurensis and V. coignetiae was similar in alpha diversity to V. vinifera's bacterial biodiversity. The fungal alpha diversity of V. amurensis and V. coignetiae was statistically different from that of V. vinifera. The beta diversity analysis of bacterial and fungal endophytes showed that samples of V. vinifera formed separate clusters, while V. amurensis samples formed a separate cluster including V. coignetiae samples. The data revealed that the endophytic community of bacteria and fungi from wild V. amurensis was richer than that from V. coignetiae grapes and cultivated V. vinifera grapes. Therefore, the data obtained in this work could be of high value in the search for potentially useful microorganisms for viticulture.}, } @article {pmid37628701, year = {2023}, author = {Soriano, B and Hafez, AI and Naya-Català, F and Moroni, F and Moldovan, RA and Toxqui-Rodríguez, S and Piazzon, MC and Arnau, V and Llorens, C and Pérez-Sánchez, J}, title = {SAMBA: Structure-Learning of Aquaculture Microbiomes Using a Bayesian Approach.}, journal = {Genes}, volume = {14}, number = {8}, pages = {}, pmid = {37628701}, issn = {2073-4425}, mesh = {Animals ; Humans ; Bayes Theorem ; RNA, Ribosomal, 16S/genetics ; Learning ; *Microbiota/genetics ; Aquaculture ; *Sea Bream ; }, abstract = {Gut microbiomes of fish species consist of thousands of bacterial taxa that interact among each other, their environment, and the host. These complex networks of interactions are regulated by a diverse range of factors, yet little is known about the hierarchy of these interactions. Here, we introduce SAMBA (Structure-Learning of Aquaculture Microbiomes using a Bayesian Approach), a computational tool that uses a unified Bayesian network approach to model the network structure of fish gut microbiomes and their interactions with biotic and abiotic variables associated with typical aquaculture systems. SAMBA accepts input data on microbial abundance from 16S rRNA amplicons as well as continuous and categorical information from distinct farming conditions. From this, SAMBA can create and train a network model scenario that can be used to (i) infer information of how specific farming conditions influence the diversity of the gut microbiome or pan-microbiome, and (ii) predict how the diversity and functional profile of that microbiome would change under other variable conditions. SAMBA also allows the user to visualize, manage, edit, and export the acyclic graph of the modelled network. Our study presents examples and test results of Bayesian network scenarios created by SAMBA using data from a microbial synthetic community, and the pan-microbiome of gilthead sea bream (Sparus aurata) in different feeding trials. It is worth noting that the usage of SAMBA is not limited to aquaculture systems as it can be used for modelling microbiome-host network relationships of any vertebrate organism, including humans, in any system and/or ecosystem.}, } @article {pmid37628698, year = {2023}, author = {Pandey, S and Avuthu, N and Guda, C}, title = {StrainIQ: A Novel n-Gram-Based Method for Taxonomic Profiling of Human Microbiota at the Strain Level.}, journal = {Genes}, volume = {14}, number = {8}, pages = {}, pmid = {37628698}, issn = {2073-4425}, support = {P20 GM103427/GM/NIGMS NIH HHS/United States ; P30 CA036727/CA/NCI NIH HHS/United States ; U54 GM115458/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; Metagenome/genetics ; Algorithms ; Computational Biology ; High-Throughput Nucleotide Sequencing ; }, abstract = {The emergence of next-generation sequencing (NGS) technology has greatly influenced microbiome research and led to the development of novel bioinformatics tools to deeply analyze metagenomics datasets. Identifying strain-level variations in microbial communities is important to understanding the onset and progression of diseases, host-pathogen interrelationships, and drug resistance, in addition to designing new therapeutic regimens. In this study, we developed a novel tool called StrainIQ (strain identification and quantification) based on a new n-gram-based (series of n number of adjacent nucleotides in the DNA sequence) algorithm for predicting and quantifying strain-level taxa from whole-genome metagenomic sequencing data. We thoroughly evaluated our method using simulated and mock metagenomic datasets and compared its performance with existing methods. On average, it showed 85.8% sensitivity and 78.2% specificity on simulated datasets. It also showed higher specificity and sensitivity using n-gram models built from reduced reference genomes and on models with lower coverage sequencing data. It outperforms alternative approaches in genus- and strain-level prediction and strain abundance estimation. Overall, the results show that StrainIQ achieves high accuracy by implementing customized model-building and is an efficient tool for site-specific microbial community profiling.}, } @article {pmid37628619, year = {2023}, author = {Notario, E and Visci, G and Fosso, B and Gissi, C and Tanaskovic, N and Rescigno, M and Marzano, M and Pesole, G}, title = {Amplicon-Based Microbiome Profiling: From Second- to Third-Generation Sequencing for Higher Taxonomic Resolution.}, journal = {Genes}, volume = {14}, number = {8}, pages = {}, pmid = {37628619}, issn = {2073-4425}, mesh = {RNA, Ribosomal, 16S/genetics ; Computational Biology ; *Microbiota/genetics ; Technology ; }, abstract = {The 16S rRNA amplicon-based sequencing approach represents the most common and cost-effective strategy with great potential for microbiome profiling. The use of second-generation sequencing (NGS) technologies has led to protocols based on the amplification of one or a few hypervariable regions, impacting the outcome of the analysis. Nowadays, comparative studies are necessary to assess different amplicon-based approaches, including the full-locus sequencing currently feasible thanks to third-generation sequencing (TGS) technologies. This study compared three different methods to achieve the deepest microbiome taxonomic characterization: (a) the single-region approach, (b) the multiplex approach, covering several regions of the target gene/region, both based on NGS short reads, and (c) the full-length approach, which analyzes the whole length of the target gene thanks to TGS long reads. Analyses carried out on benchmark microbiome samples, with a known taxonomic composition, highlighted a different classification performance, strongly associated with the type of hypervariable regions and the coverage of the target gene. Indeed, the full-length approach showed the greatest discriminating power, up to species level, also on complex real samples. This study supports the transition from NGS to TGS for the study of the microbiome, even if experimental and bioinformatic improvements are still necessary.}, } @article {pmid37628582, year = {2023}, author = {Gagnon, JC and Beauregard-Tousignant, S and Marcil, JS and Lazar, CS}, title = {Deep Isolated Aquifer Brines Harbor Atypical Halophilic Microbial Communities in Quebec, Canada.}, journal = {Genes}, volume = {14}, number = {8}, pages = {}, pmid = {37628582}, issn = {2073-4425}, mesh = {Humans ; Quebec ; Canada ; *Groundwater ; *Microbiota/genetics ; }, abstract = {The deep terrestrial subsurface, hundreds of meters to kilometers below the surface, is characterized by oligotrophic conditions, dark and often anoxic settings, with fluctuating pH, salinity, and water availability. Despite this, microbial populations are detected and active, contributing to biogeochemical cycles over geological time. Because it is extremely difficult to access the deep biosphere, little is known about the identity and metabolisms of these communities, although they likely possess unknown pathways and might interfere with deep waste deposits. Therefore, we analyzed rock and groundwater microbial communities from deep, isolated brine aquifers in two regions dating back to the Ordovician and Devonian, using amplicon and whole genome sequencing. We observed significant differences in diversity and community structure between both regions, suggesting an impact of site age and composition. The deep hypersaline groundwater did not contain typical halophilic bacteria, and genomes suggested pathways involved in protein and hydrocarbon degradation, and carbon fixation. We identified mainly one strategy to cope with osmotic stress: compatible solute uptake and biosynthesis. Finally, we detected many bacteriophage families, potentially indicating that bacteria are infected. However, we also found auxiliary metabolic genes in the viral genomes, probably conferring an advantage to the infected hosts.}, } @article {pmid37626351, year = {2023}, author = {Ghaly, TM and Focardi, A and Elbourne, LDH and Sutcliffe, B and Humphreys, W and Paulsen, IT and Tetu, SG}, title = {Stratified microbial communities in Australia's only anchialine cave are taxonomically novel and drive chemotrophic energy production via coupled nitrogen-sulphur cycling.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {190}, pmid = {37626351}, issn = {2049-2618}, mesh = {Humans ; *Nitrogen Cycle ; *Microbiota/genetics ; Sulfur ; Nitrification ; Australia ; }, abstract = {BACKGROUND: Anchialine environments, in which oceanic water mixes with freshwater in coastal aquifers, are characterised by stratified water columns with complex physicochemical profiles. These environments, also known as subterranean estuaries, support an abundance of endemic macro and microorganisms. There is now growing interest in characterising the metabolisms of anchialine microbial communities, which is essential for understanding how complex ecosystems are supported in extreme environments, and assessing their vulnerability to environmental change. However, the diversity of metabolic strategies that are utilised in anchialine ecosystems remains poorly understood.

RESULTS: Here, we employ shotgun metagenomics to elucidate the key microorganisms and their dominant metabolisms along a physicochemical profile in Bundera Sinkhole, the only known continental subterranean estuary in the Southern Hemisphere. Genome-resolved metagenomics suggests that the communities are largely represented by novel taxonomic lineages, with 75% of metagenome-assembled genomes assigned to entirely new or uncharacterised families. These diverse and novel taxa displayed depth-dependent metabolisms, reflecting distinct phases along dissolved oxygen and salinity gradients. In particular, the communities appear to drive nutrient feedback loops involving nitrification, nitrate ammonification, and sulphate cycling. Genomic analysis of the most highly abundant members in this system suggests that an important source of chemotrophic energy is generated via the metabolic coupling of nitrogen and sulphur cycling.

CONCLUSION: These findings substantially contribute to our understanding of the novel and specialised microbial communities in anchialine ecosystems, and highlight key chemosynthetic pathways that appear to be important in these energy-limited environments. Such knowledge is essential for the conservation of anchialine ecosystems, and sheds light on adaptive processes in extreme environments. Video Abstract.}, } @article {pmid37624549, year = {2023}, author = {Pal, P and Shastry, RP}, title = {Exploring the complex role of gut microbiome in the development of precision medicine strategies for targeting microbial imbalance-induced colon cancer.}, journal = {Folia microbiologica}, volume = {68}, number = {5}, pages = {691-701}, pmid = {37624549}, issn = {1874-9356}, support = {ICMR/5/13/84/2020/NCD-III dated 16/03/2021//ICMR-DHR, Government of India, New Delhi/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Precision Medicine/methods ; Dysbiosis/therapy ; *Probiotics/therapeutic use ; *Colonic Neoplasms/therapy ; }, abstract = {The gut microbiome has been increasingly recognized as a key player in the development and progression of colon cancer. Alterations in the gut microbiota, known as dysbiosis, can lead to a variety of medical issues. Microbial adaptation through signals and small molecules can enhance pathogen colonization and modulate host immunity, significantly impacting disease progression. Quorum sensing peptides and molecules have been linked to the progression of colon cancer. Various interventions, such as fecal microbiota transplantation, probiotics, prebiotics, synbiotics, and antibiotics, have been used to reverse dysbiosis with mixed results and potential side effects. Thus, a personalized approach to treatment selection based on patient characteristics, such as individual gut microbiota manipulation, is necessary to prevent and treat diseases like colon cancer. With advances in metagenomic sequencing and other omics technologies, there has been a growing interest in developing precision medicine strategies for microbial imbalance-induced colon cancer. This review serves as a comprehensive synthesis of current knowledge on the gut microbiome involvement in colon cancer. By exploring the potential of utilizing the gut microbiome as a target for precision medicine, this review underscores the exciting opportunities that lie ahead. Although challenges exist, the integration of microbiome data into precision medicine approaches has the potential to revolutionize the management of colon cancer, providing patients with more personalized and effective treatment options.}, } @article {pmid37623326, year = {2023}, author = {Sun, K and Yu, M and Zhu, XY and Xue, CX and Zhang, Y and Chen, X and Yao, P and Chen, L and Fu, L and Yang, Z and Zhang, XH}, title = {Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0114923}, pmid = {37623326}, issn = {2165-0497}, abstract = {The Sansha Yongle Blue Hole (SYBH), the deepest blue hole in the world, is an excellent habitat for revealing biogeochemical cycles in the anaerobic environment. However, how sulfur cycling is mediated by microorganisms in the SYBH hasn't been fully understood. In this study, the water layers of the SYBH were divided into oxic zone, hypoxic zone, anoxic zone I and II, and microbial-mediated sulfur cycling in the SYBH was comprehensively interpreted. The 16S rRNA genes/transcripts analyses showed that the microbial community structures associated with the sulfur cycling in each zone had distinctive features. Sulfur-oxidizing bacteria were mostly constituted by Gammaproteobacteria, Alphaproteobacteria, Campylobacterota, and Chlorobia above the anoxic zone I and sulfate-reducing bacteria were dominated by Desulfobacterota in anoxic zones. Metagenomic analyses showed that the sulfide-oxidation-related gene sqr and genes encoding the Sox system were mainly distributed in the anoxic zone I, while genes related to dissimilatory sulfate reduction and sulfur intermediate metabolite reduction were mainly distributed in the anoxic zone II, indicating different sulfur metabolic processes between these two zones. Moreover, sulfur-metabolism-related genes were identified in 81 metagenome-assembled genomes (MAGs), indicating a high diversity of microbial communities involved in sulfur cycling. Among them, three MAGs from the candidate phyla JdFR-76 and AABM5-125-24 with genes related to dissimilatory sulfate reduction exhibited distinctive metabolic features. Our results showed unique and novel microbial populations in the SYBH sulfur cycle correlated to the sharp redox gradients, revealing complex biogeochemical processes in this extreme environment. IMPORTANCE Oxygen-deficient regions in the global ocean are expanding rapidly and affect the growth, reproduction and ecological processes of marine organisms. The anaerobic water body of about 150 m in the Sansha Yongle Blue Hole (SYBH) provided a suitable environment to study the specific microbial metabolism in anaerobic seawater. Here, we found that the vertical distributions of the total and active communities of sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) were different in each water layer of the SYBH according to the dissolved oxygen content. Genes related to sulfur metabolism also showed distinct stratification characteristics. Furthermore, we have obtained diverse metagenome-assembled genomes, some of which exhibit special sulfur metabolic characteristics, especially candidate phyla JdFR-76 and AABM5-125-24 were identified as potential novel SRB. The results of this study will promote further understanding of the sulfur cycle in extreme environments, as well as the environmental adaptability of microorganisms in blue holes.}, } @article {pmid37622724, year = {2023}, author = {Xia, Y}, title = {Statistical normalization methods in microbiome data with application to microbiome cancer research.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2244139}, pmid = {37622724}, issn = {1949-0984}, mesh = {RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; *Microbiota ; Metagenome ; Research Design ; *Neoplasms ; }, abstract = {Mounting evidence has shown that gut microbiome is associated with various cancers, including gastrointestinal (GI) tract and non-GI tract cancers. But microbiome data have unique characteristics and pose major challenges when using standard statistical methods causing results to be invalid or misleading. Thus, to analyze microbiome data, it not only needs appropriate statistical methods, but also requires microbiome data to be normalized prior to statistical analysis. Here, we first describe the unique characteristics of microbiome data and the challenges in analyzing them (Section 2). Then, we provide an overall review on the available normalization methods of 16S rRNA and shotgun metagenomic data along with examples of their applications in microbiome cancer research (Section 3). In Section 4, we comprehensively investigate how the normalization methods of 16S rRNA and shotgun metagenomic data are evaluated. Finally, we summarize and conclude with remarks on statistical normalization methods (Section 5). Altogether, this review aims to provide a broad and comprehensive view and remarks on the promises and challenges of the statistical normalization methods in microbiome data with microbiome cancer research examples.}, } @article {pmid37622435, year = {2023}, author = {Juge, N}, title = {Microbe Profile: Ruminococcus gnavus: the yin and yang of human gut symbionts.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {8}, pages = {}, pmid = {37622435}, issn = {1465-2080}, support = {BB/P008895/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13630/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13633/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13631/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Gastrointestinal Microbiome ; Humans ; Clostridiales ; *Ruminococcus/genetics ; Symbiosis ; }, abstract = {Ruminococcus gnavus is a human gut symbiont, part of the infant and adult gut microbiota and associated with intestinal and extra-intestinal disorders. R. gnavus mechanisms of adaptation to the gut are strain-specific and underpinned by the capacity of R. gnavus strains to utilize mucin and dietary glycans and produce bacteriocins and adhesins. Several potential mediators underpinning the association between R. gnavus strains and diseases have been identified, including the capacity to elicit a pro- or anti-inflammatory host response and modulate host metabolism, secondary bile acids and tryptophan metabolic pathways. Based on increasing evidence from metagenomics studies in humans and functional investigations in vitro and in mouse models, R. gnavus is emerging as a main player in influencing health and disease outcomes from infants to the elderly.}, } @article {pmid37621874, year = {2023}, author = {Zhou, Q and Tao, X and Guo, F and Zhu, Y and Wu, Y and Xiang, H and Shang, D}, title = {The crosstalk between microbiota and metabolites in AP mice: an analysis based on metagenomics and untargeted metabolomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1134321}, pmid = {37621874}, issn = {2235-2988}, mesh = {Animals ; Mice ; Metagenomics ; Acute Disease ; *Pancreatitis ; *Microbiota ; Signal Transduction ; Bacteroidetes ; Lactobacillus ; }, abstract = {BACKGROUND AND PURPOSE: Microbiome dysfunction is known to aggravate acute pancreatitis (AP); however, the relationship between this dysfunction and metabolite alterations is not fully understood. This study explored the crosstalk between the microbiome and metabolites in AP mice.

METHODS: Experimental AP models were established by injecting C57/BL mice with seven doses of cerulein and one dose of lipopolysaccharide (LPS). Metagenomics and untargeted metabolomics were used to identify systemic disturbances in the microbiome and metabolites, respectively, during the progression of AP.

RESULTS: The gut microbiome of AP mice primarily included Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria, and "core microbiota" characterized by an increase in Proteobacteria and a decrease in Actinobacteria. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that significantly different microbes were involved in several signaling networks. Untargeted metabolomics identified 872 metabolites, of which lipids and lipid-like molecules were the most impacted. An integrated analysis of metagenomics and metabolomics indicated that acetate kinase (ackA) gene expression was associated with various gut microbiota, including Alistipes, Butyricimonas, and Lactobacillus, and was strongly correlated with the metabolite daphnoretin. The functional gene, O-acetyl-L-serine sulfhydrylase (cysK), was associated with Alistipes, Jeotgalicoccus, and Lactobacillus, and linked to bufalin and phlorobenzophenone metabolite production.

CONCLUSION: This study identified the relationship between the gut microbiome and metabolite levels during AP, especially the Lactobacillus-, Alistipes-, and Butyricimonas-associated functional genes, ackA and cysK. Expression of these genes was significantly correlated to the production of the anti-inflammatory and antitumor metabolites daphnoretin and bufalin.}, } @article {pmid37621652, year = {2023}, author = {Liang, J and Ali, S and Lv, C and Yang, H and Zhao, X and Ni, X and Li, C and Danzeng, B and Wang, Y and Quan, G}, title = {Dietary protein levels modulate the gut microbiome composition through fecal samples derived from lactating ewes.}, journal = {Frontiers in endocrinology}, volume = {14}, number = {}, pages = {1194425}, pmid = {37621652}, issn = {1664-2392}, mesh = {Sheep ; Animals ; Female ; *Gastrointestinal Microbiome ; Lactation ; Feces ; Dietary Proteins ; Sheep, Domestic ; Clostridiales ; }, abstract = {In ruminants, the digestion and utilization of dietary proteins are closely linked to the bacterial populations that are present in the gastrointestinal tract. In the present study, 16S rDNA sequencing, together with a metagenomic strategy was used to characterize the fecal bacteria of ewes in the early lactation stage after feeding with three levels of dietary proteins 8.58%, 10.34%, and 13.93%, in three different groups (H_1), (H_m) and (H_h), respectively. A total of 376,278,516 clean data-points were obtained by metagenomic sequencing. Firmicutes and Bacteroidetes were the dominant phyla, regardless of the dietary protein levels. In the H_h group, the phyla Proteobacteria, Caldiserica, and Candidatus_Cryosericota were less abundant than those in the H_I group. In contrast, Lentisphaerae, Chlamydiae, and Planctomycetes were significantly more abundant in the H_h group. Some genera, such as Prevotella, Roseburia, and Firmicutes_unclassified, were less abundant in the H_h group than those in the H_I group. In contrast, Ruminococcus, Ruminococcaceae_noname, Anaerotruncus, Thermotalae, Lentisphaerae_noname, and Paraprevotella were enriched in the H_h group. The acquired microbial genes were mainly clustered into biological processes; molecular functions; cytosol; cellular components; cytoplasm; structural constituents of ribosomes; plasma membranes; translation; and catalytic activities. 205987 genes were significantly enriched in the H_h group. In contrast, 108129 genes were more abundant in the H_I group. Our findings reveal that dynamic changes in fecal bacteria and their genes are strongly influenced by the levels of dietary proteins. We discovered that differentially expressed genes mainly regulate metabolic activity and KEGG demonstrated the primary involvement of these genes in the metabolism of carbohydrates, amino acids, nucleotides, and vitamins. Additionally, genes responsible for metabolism were more abundant in the H_h group. Investigating fecal bacterial characteristics may help researchers develop a dietary formula for lactating ewes to optimize the growth and health of ewes and lambs.}, } @article {pmid37620878, year = {2023}, author = {Abrantes, J and Varsani, A and Pereira, P and Maia, C and Farias, I and Veríssimo, A and Neves, F}, title = {Identification and characterization of a polyomavirus in the thornback skate (Raja clavata).}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {190}, pmid = {37620878}, issn = {1743-422X}, mesh = {Animals ; *Polyomavirus/genetics ; *Skates, Fish ; Ecosystem ; Phylogeny ; Polyomaviridae ; Mammals ; }, abstract = {Members of the family Polyomaviridae have a circular double-stranded DNA genome that have been identified in various hosts ranging from mammals to arachnids. Here we report the identification and analysis of a complete genome sequence of a novel polyomavirus, Raja clavata polyomavirus (RcPyV1), from a cartilaginous fish, the thornback skate (Raja clavata). The genome sequence was determined using a metagenomics approach with an aim to provide baseline viral data in cartilaginous fish in different ecosystems. The RcPyV1 genome (4,195 nucleotides) had typical organization of polyomavirus, including early antigens (small T; Large T) encoded on one strand and late viral proteins (VP1; VP2) on the complementary strand. Maximum-likelihood phylogenetic analysis of the large T-antigen revealed that RcPyV1 clusters with a polyomavirus obtained from another cartilaginous fish, the guitarfish polyomavirus 1 (GfPyV1). These two share ~ 56% pairwise identity in LT and VP1 protein sequences. These analyses support the hypothesis that cartilaginous fishes have a specific lineage of polyomaviruses.}, } @article {pmid37620368, year = {2023}, author = {Mutti, G and Oteo-Garcia, G and Caldon, M and da Silva, MJF and Minhós, T and Cowlishaw, G and Gottelli, D and Huchard, E and Carter, A and Martinez, FI and Raveane, A and Capelli, C}, title = {Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13839}, pmid = {37620368}, issn = {2045-2322}, mesh = {Humans ; Male ; Animals ; *Metagenomics ; *Theropithecus ; Papio ; Macaca mulatta ; Microsatellite Repeats/genetics ; }, abstract = {Y chromosome markers can shed light on male-specific population dynamics but for many species no such markers have been discovered and are available yet, despite the potential for recovering Y-linked loci from available genome sequences. Here, we investigated how effective available bioinformatic tools are in recovering informative Y chromosome microsatellites from whole genome sequence data. In order to do so, we initially explored a large dataset of whole genome sequences comprising individuals at various coverages belonging to different species of baboons (genus: Papio) using Y chromosome references belonging to the same genus and more distantly related species (Macaca mulatta). We then further tested this approach by recovering Y-STRs from available Theropithecus gelada genomes using Papio and Macaca Y chromosome as reference sequences. Identified loci were validated in silico by a) comparing within-species relationships of Y chromosome lineages and b) genotyping male individuals in available pedigrees. Each STR was selected not to extend in its variable region beyond 100 base pairs, so that loci can be developed for PCR-based genotyping of non-invasive DNA samples. In addition to assembling a first set of Papio and Theropithecus Y-specific microsatellite markers, we released TYpeSTeR, an easy-to-use script to identify and genotype Y chromosome STRs using population genomic data which can be modulated according to available male reference genomes and genomic data, making it widely applicable across taxa.}, } @article {pmid37615434, year = {2023}, author = {Shi, Z and Wang, Y and Yan, X and Ma, X and Duan, A and Hassan, F-u and Wang, W and Deng, T}, title = {Metagenomic and metabolomic analyses reveal the role of gut microbiome-associated metabolites in diarrhea calves.}, journal = {mSystems}, volume = {8}, number = {5}, pages = {e0058223}, pmid = {37615434}, issn = {2379-5077}, support = {HARS-22-13-S//Henan Beef Cattle Industrial Technology System/ ; 2020GXNSFDA297032//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; 2023ZC057//Independent Innovation Project of Henan Academy of Agricultural Sciences/ ; }, mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome/genetics ; Diarrhea/veterinary ; Feces ; Metagenome ; Metabolomics ; }, abstract = {Calf diarrhea is of great concern to the global dairy industry as it results in significant economic losses due to lower conception rates, reduced milk production, and early culling. Although there is evidence of an association between altered gut microbiota and diarrhea, remarkably little is known about the microbial and metabolic mechanisms underlying the link between gut microbiota dysbiosis and the occurrence of calf diarrhea. Here, we used fecal metagenomic and metabolomic analyses to demonstrate that gut microbiota-driven metabolic disorders of purine or arachidonic acid were associated with calf diarrhea. These altered gut microbiotas play vital roles in diarrhea pathogenesis and indicate that gut microbiota-targeted therapies could be useful for both prevention and treatment of diarrhea.}, } @article {pmid37615431, year = {2023}, author = {Armour, CR and Sovacool, KL and Close, WL and Topçuoğlu, BD and Wiens, J and Schloss, PD}, title = {Machine learning classification by fitting amplicon sequences to existing OTUs.}, journal = {mSphere}, volume = {8}, number = {5}, pages = {e0033623}, pmid = {37615431}, issn = {2379-5042}, support = {R01 CA215574/CA/NCI NIH HHS/United States ; R01CA215574/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Algorithms ; *Microbiota/genetics ; }, abstract = {The ability to use 16S rRNA gene sequence data to train machine learning classification models offers the opportunity to diagnose patients based on the composition of their microbiome. In some applications, the taxonomic resolution that provides the best models may require the use of de novo operational taxonomic units (OTUs) whose composition changes when new data are added. We previously developed a new reference-based approach, OptiFit, that fits new sequence data to existing de novo OTUs without changing the composition of the original OTUs. While OptiFit produces OTUs that are as high quality as de novo OTUs, it is unclear whether this method for fitting new sequence data into existing OTUs will impact the performance of classification models relative to models trained and tested only using de novo OTUs. We used OptiFit to cluster sequences into existing OTUs and evaluated model performance in classifying a dataset containing samples from patients with and without colonic screen relevant neoplasia (SRN). We compared the performance of this model to standard methods including de novo and database-reference-based clustering. We found that using OptiFit performed as well or better in classifying SRNs. OptiFit can streamline the process of classifying new samples by avoiding the need to retrain models using reclustered sequences. IMPORTANCE There is great potential for using microbiome data to aid in diagnosis. A challenge with de novo operational taxonomic unit (OTU)-based classification models is that 16S rRNA gene sequences are often assigned to OTUs based on similarity to other sequences in the dataset. If data are generated from new patients, the old and new sequences must be reclustered to OTUs and the classification model retrained. Yet there is a desire to have a single, validated model that can be widely deployed. To overcome this obstacle, we applied the OptiFit clustering algorithm to fit new sequence data to existing OTUs allowing for reuse of the model. A random forest model implemented using OptiFit performed as well as the traditional reassign and retrain approach. This result shows that it is possible to train and apply machine learning models based on OTU relative abundance data that do not require retraining or the use of a reference database.}, } @article {pmid37612768, year = {2023}, author = {Zhang, ZF and Liu, LR and Pan, YP and Pan, J and Li, M}, title = {Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {188}, pmid = {37612768}, issn = {2049-2618}, mesh = {*Metagenome/genetics ; *Microbiota/genetics ; Metagenomics ; Fermentation ; Carbon ; }, abstract = {BACKGROUND: Mangrove wetlands are coastal ecosystems with important ecological features and provide habitats for diverse microorganisms with key roles in nutrient and biogeochemical cycling. However, the overall metabolic potentials and ecological roles of microbial community in mangrove sediment are remained unanswered. In current study, the microbial and metabolic profiles of prokaryotic and fungal communities in mangrove sediments were investigated using metagenomic analysis based on PacBio single-molecule real time (SMRT) and Illumina sequencing techniques.

RESULTS: Comparing to Illumina short reads, the incorporation of PacBio long reads significantly contributed to more contiguous assemblies, yielded more than doubled high-quality metagenome-assembled genomes (MAGs), and improved the novelty of the MAGs. Further metabolic reconstruction for recovered MAGs showed that prokaryotes potentially played an essential role in carbon cycling in mangrove sediment, displaying versatile metabolic potential for degrading organic carbons, fermentation, autotrophy, and carbon fixation. Mangrove fungi also functioned as a player in carbon cycling, potentially involved in the degradation of various carbohydrate and peptide substrates. Notably, a new candidate bacterial phylum named as Candidatus Cosmopoliota with a ubiquitous distribution is proposed. Genomic analysis revealed that this new phylum is capable of utilizing various types of organic substrates, anaerobic fermentation, and carbon fixation with the Wood-Ljungdahl (WL) pathway and the reverse tricarboxylic acid (rTCA) cycle.

CONCLUSIONS: The study not only highlights the advantages of HiSeq-PacBio Hybrid assembly for a more complete profiling of environmental microbiomes but also expands our understanding of the microbial diversity and potential roles of distinct microbial groups in biogeochemical cycling in mangrove sediment. Video Abstract.}, } @article {pmid37608207, year = {2023}, author = {Russell, AL and McAdams, ZL and Donovan, E and Seilhamer, N and Siegrist, M and Franklin, CL and Ericsson, AC}, title = {The contribution of maternal oral, vaginal, and gut microbiota to the developing offspring gut.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13660}, pmid = {37608207}, issn = {2045-2322}, support = {R03 OD028259/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Female ; Animals ; Mice ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Disease Models, Animal ; Feces ; }, abstract = {There is limited understanding of how the microbiota colonizing various maternal tissues contribute to the development of the neonatal gut microbiota (GM). To determine the contribution of various maternal microbiotic sites to the offspring microbiota in the upper and lower gastrointestinal tract (GIT) during early life, litters of mice were sacrificed at 7, 9, 10, 11, 12, 14, and 21 days of age, and fecal and ileal samples were collected. Dams were euthanized alongside their pups, and oral, vaginal, ileal, and fecal samples were collected. This was done in parallel using mice with either a low-richness or high-richness microbiota to assess the consistency of findings across multiple microbial compositions. Samples were analyzed using 16S rRNA amplicon sequencing. The compositional similarity between pup and dam samples were used to determine the contribution of each maternal source to the composition of the neonate fecal and ileal samples at each timepoint. As expected, similarity between neonate and maternal feces increased significantly over time. During earlier time-points however, the offspring fecal and ileal microbiotas were closer in composition to the maternal oral microbiota than other maternal sites. Prominent taxa contributed by the maternal oral microbiota to the neonate GM were supplier-dependent and included Lactobacillus spp., Streptococcus spp., and a member of the Pasteurellaceae family. These findings align with the microbial taxa reported in infant microbiotas, highlighting the translatability of mouse models in this regard, as well as the dynamic nature of the GM during early life.}, } @article {pmid37607924, year = {2023}, author = {Li, X and Chen, D and Carrión, VJ and Revillini, D and Yin, S and Dong, Y and Zhang, T and Wang, X and Delgado-Baquerizo, M}, title = {Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5090}, pmid = {37607924}, issn = {2041-1723}, mesh = {*Fusariosis ; *Microbiota ; *Fusarium ; Metagenome ; Hydrogen-Ion Concentration ; }, abstract = {Soil-borne pathogens pose a major threat to food production worldwide, particularly under global change and with growing populations. Yet, we still know very little about how the soil microbiome regulates the abundance of soil pathogens and their impact on plant health. Here we combined field surveys with experiments to investigate the relationships of soil properties and the structure and function of the soil microbiome with contrasting plant health outcomes. We find that soil acidification largely impacts bacterial communities and reduces the capacity of soils to combat fungal pathogens. In vitro assays with microbiomes from acidified soils further highlight a declined ability to suppress Fusarium, a globally important plant pathogen. Similarly, when we inoculate healthy plants with an acidified soil microbiome, we show a greatly reduced capacity to prevent pathogen invasion. Finally, metagenome sequencing of the soil microbiome and untargeted metabolomics reveals a down regulation of genes associated with the synthesis of sulfur compounds and reduction of key traits related to sulfur metabolism in acidic soils. Our findings suggest that changes in the soil microbiome and disruption of specific microbial processes induced by soil acidification can play a critical role for plant health.}, } @article {pmid37606634, year = {2023}, author = {Liu, D and Wang, S and Liu, Y and Luo, Y and Wen, B and Wu, W and Zeng, H and Huang, J and Liu, Z}, title = {Fuzhuan brick tea ameliorates hepatic steatosis and steatohepatitis through gut microbiota-derived aryl hydrocarbon receptor ligands in high-fat diet-induced obese mice.}, journal = {Food & function}, volume = {14}, number = {18}, pages = {8351-8368}, doi = {10.1039/d3fo01782f}, pmid = {37606634}, issn = {2042-650X}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Diet, High-Fat/adverse effects ; Ligands ; Mice, Obese ; Receptors, Aryl Hydrocarbon/genetics ; *Fatty Liver/drug therapy ; Escherichia coli ; Tea ; }, abstract = {High-fat diet (HFD) induced obesity and its associated conditions, such as hepatic steatosis and steatohepatitis, are major health concerns worldwide. Previous studies have reported the excellent efficiency of Fuzhuan brick tea (FBT) in attenuating HFD-induced obesity and metabolic disorders. In this study, we investigated the effects of FBT on hepatic steatosis and simple steatohepatitis in HFD-induced obese mice, as well as the metabolic function of the gut microbiome using metagenomics and metabolomics. The results showed that FBT ameliorated dyslipidemia, hepatic steatosis and steatohepatitis in HFD-induced obese mice by normalizing the gut microbiota structure and tryptophan metabolism. FBT increased the cecal abundance of aryl hydrocarbon receptor (AhR)-ligand producing bacteria such as Lactobacillus_reuteri and Lactobacillus_johnsonii, at the expense of AhR-ligand consuming bacteria, such as Faecalibaculum_rodentium and Escherichia_coli, and elevated the cecal contents of AhR-ligands such as IAA, IPA, and KYNA. Furthermore, FBT regulated the expressions of AhR and its targeted lipometabolic genes such as Pemt, Fasn, and SREBP-1c, as well as other inflammatory genes including TNF-α, IL-6, and IL-1β in the liver of mice. Overall, these findings highlight the beneficial effects of FBT on obesity-related hepatic steatosis and steatohepatitis via microbiota-derived AhR signaling.}, } @article {pmid37604017, year = {2023}, author = {Xu, N and Qiu, D and Zhang, Z and Wang, Y and Chen, B and Zhang, Q and Wang, T and Hong, W and Zhou, NY and Penuelas, J and Gillings, M and Zhu, YG and Qian, H}, title = {A global atlas of marine antibiotic resistance genes and their expression.}, journal = {Water research}, volume = {244}, number = {}, pages = {120488}, doi = {10.1016/j.watres.2023.120488}, pmid = {37604017}, issn = {1879-2448}, mesh = {Humans ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Phylogeny ; Drug Resistance, Microbial/genetics ; *Microbiota ; }, abstract = {Oceans serve as global reservoirs of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). However, little is known about the traits and expression of ARGs in response to environmental factors. We analyzed 347 metagenomes and 182 metatranscriptomes to determine the distribution, hosts, and expression of ARGs in oceans. Our study found that the diversity and abundance of ARGs varied with latitude and depth. The core marine resistome mainly conferred glycopeptide and multidrug resistance. The hosts of this resistome were mainly limited to the core marine microbiome, with phylogenetic barriers to the horizontal transfer of ARGs, transfers being more frequent within species than between species. Sixty-five percent of the marine ARGs identified were expressed. More than 90% of high-risk ARGs were more likely to be expressed. Anthropogenic activity might affect the expression of ARGs by altering nitrate and phosphate concentrations and ocean temperature. Machine-learning models predict >97% of marine ARGs will change expression by 2100. High-risk ARGs will shift to low latitudes and regions with high anthropogenic activity, such as the Pacific and Atlantic Oceans. Certain ARGs serve a dual role in antibiotic resistance and potentially participate in element cycling, along with other unknown functions. Determining whether changes in ARG expression are beneficial to ecosystems and human health is challenging without comprehensive understanding of their functions. Our study identified a core resistome in the oceans and quantified the expression of ARGs for the development of future control strategies under global change.}, } @article {pmid37603566, year = {2023}, author = {Velasco-Álvarez, JR and Torres Y Torres, N and Chairez, I and Castrejón-Flores, JL}, title = {Microbiome distribution modeling using gradient descent strategies for mock, in vitro and clinical community distributions.}, journal = {PloS one}, volume = {18}, number = {8}, pages = {e0290082}, pmid = {37603566}, issn = {1932-6203}, mesh = {Humans ; *Microbiota ; Metagenome ; Algorithms ; Computer Simulation ; Data Analysis ; }, abstract = {The human gut is home to a complex array of microorganisms interacting with the host and each other, forming a community known as the microbiome. This community has been linked to human health and disease, but understanding the underlying interactions is still challenging for researchers. Standard studies typically use high-throughput sequencing to analyze microbiome distribution in patient samples. Recent advancements in meta-omic data analysis have enabled computational modeling strategies to integrate this information into an in silico model. However, there is a need for improved parameter fitting and data integration features in microbial community modeling. This study proposes a novel alternative strategy utilizing state-of-the-art dynamic flux balance analysis (dFBA) to provide a simple protocol enabling accurate replication of abundance data composition through dynamic parameter estimation and integration of metagenomic data. We used a recurrent optimization algorithm to replicate community distributions from three different sources: mock, in vitro, and clinical microbiome. Our results show an accuracy of 98% and 96% when using in vitro and clinical bacterial abundance distributions, respectively. The proposed modeling scheme allowed us to observe the evolution of metabolites. It could provide a deeper understanding of metabolic interactions while taking advantage of the high contextualization features of GEM schemes to fit the study case. The proposed modeling scheme could improve the approach in cases where external factors determine specific bacterial distributions, such as drug intake.}, } @article {pmid37599091, year = {2023}, author = {Arrington, EC and Tarn, J and Kittner, HE and Kivenson, V and Liu, RM and Valentine, DL}, title = {Methylated cycloalkanes fuel a novel genus in the Porticoccaceae family (Ca. Reddybacter gen. nov).}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {2958-2971}, doi = {10.1111/1462-2920.16474}, pmid = {37599091}, issn = {1462-2920}, support = {OAC-1928147//National Science Foundation/ ; OCE-1634478//National Science Foundation/ ; OCE-1756947//National Science Foundation/ ; OCE-2126625//National Science Foundation/ ; }, mesh = {Geologic Sediments/microbiology ; *Cycloparaffins ; Hydrocarbons/metabolism ; Seawater/microbiology ; *Microbiota ; *Gammaproteobacteria/genetics ; *Petroleum/metabolism ; Gulf of Mexico ; *Petroleum Pollution ; Biodegradation, Environmental ; }, abstract = {Cycloalkanes are abundant and toxic compounds in subsurface petroleum reservoirs and their fate is important to ecosystems impacted by natural oil seeps and spills. This study focuses on the microbial metabolism of methylcyclohexane (MCH) and methylcyclopentane (MCP) in the deep Gulf of Mexico. MCH and MCP are often abundant cycloalkanes observed in petroleum and will dissolve into the water column when introduced at the seafloor via a spill or natural seep. We conducted incubations with deep Gulf of Mexico (GOM) seawater amended with MCH and MCP at four stations. Within incubations with active respiration of MCH and MCP, we found that a novel genus of bacteria belonging to the Porticoccaceae family (Candidatus Reddybacter) dominated the microbial community. Using metagenome-assembled genomes, we reconstructed the central metabolism of Candidatus Reddybacter, identifying a novel clade of the particulate hydrocarbon monooxygenase (pmo) that may play a central role in MCH and MCP metabolism. Through comparative analysis of 174 genomes, we parsed the taxonomy of the Porticoccaceae family and found evidence suggesting the acquisition of pmo and other genes related to the degradation of cyclic and branched hydrophobic compounds were likely key events in the ecology and evolution of this group of organisms.}, } @article {pmid37598984, year = {2023}, author = {Jian, J and Yuan, Y and Vilatersana, R and Li, L and Wang, Y and Zhang, W and Song, Z and Kong, H and Peter Comes, H and Yang, J}, title = {Phylogenomic and population genomic analyses reveal the spatial-temporal dynamics of diversification of the Nigella arvensis complex (Ranunculaceae) in the Aegean archipelago.}, journal = {Molecular phylogenetics and evolution}, volume = {188}, number = {}, pages = {107908}, doi = {10.1016/j.ympev.2023.107908}, pmid = {37598984}, issn = {1095-9513}, mesh = {*Ranunculaceae ; *Nigella ; Phylogeny ; Metagenomics ; Genomics ; }, abstract = {The continental-shelf islands of the Aegean Sea provide an ideal geographical setting for evolutionary-biogeographical studies but disentangling the relationships between palaeogeographical history and the times, orders of modes of taxon divergence is not straightforward. Here, we used phylogenomic and population genomic approaches, based on orthologous gene sequences and transcriptome-derived SNP data, to reconstruct the spatial-temporal evolution of the Aegean Nigella arvensis complex (Ranunculaceae; 11 out of 12 taxa). The group's early diversification in the Early/Mid-Pliocene (c. 3.77 Mya) resulted in three main lineages (Greek mainland vs. central Aegean + Turkish mainland/eastern Aegean islands), while all extant taxa are of Late Plio-/Early Pleistocene origin (c. 3.30-1.59 Mya). Demographic modelling of the outcrossing taxa uncovered disparate modes of (sub)speciation, including divergence with gene flow on the Greek mainland, para- or peripatric diversification across eastern Aegean islands, and a 'mixing-isolation-mixing (MIM)' mode of subspeciation in the Cyclades. The two selfing species (N. stricta, N. doerfleri) evolved independently from the outcrossers. Present-day island configurations are clearly insufficient to explain the spatial-temporal history of lineage diversification and modes of (sub)speciation in Aegean Nigella. Moreover, our identification of positively selected genes in almost all taxa calls into question that this plant group represents a case of 'non-adaptive' radiation. Our study revealed an episodic diversification history of the N. arvensis complex, giving new insight into the modes and drivers of island speciation and adaption across multiple spatiotemporal scales.}, } @article {pmid37597851, year = {2023}, author = {Li, J and Guo, Y and Liu, J and Guo, F and Du, L and Yang, Y and Li, X and Ma, Y}, title = {Depicting the landscape of gut microbial-metabolic interaction and microbial-host immune heterogeneity in deficient and proficient DNA mismatch repair colorectal cancers.}, journal = {Journal for immunotherapy of cancer}, volume = {11}, number = {8}, pages = {}, pmid = {37597851}, issn = {2051-1426}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; CD8-Positive T-Lymphocytes ; DNA Mismatch Repair/genetics ; Succinic Acid ; Lactic Acid ; *Colorectal Neoplasms/genetics ; }, abstract = {BACKGROUND: Accumulating evidence has indicated the role of gut microbiota in remodeling host immune signatures, but various interplays underlying colorectal cancers (CRC) with deficient DNA mismatch repair (dMMR) and proficient DNA mismatch repair (pMMR) remain poorly understood. This study aims to decipher the gut microbiome-host immune interactions between dMMR and pMMR CRC.

METHOD: We performed metagenomic sequencing and metabolomic analysis of fecal samples from a cohort encompassing 455 participants, including 21 dMMR CRC, 207 pMMR CRC, and 227 healthy controls. Among them, 50 tumor samples collected from 5 dMMR CRC and 45 pMMR CRC were conducted bulk RNA sequencing.

RESULTS: Pronounced microbiota and metabolic heterogeneity were identified with 211 dMMR-enriched species, such as Fusobacterium nucleatum and Akkermansia muciniphila, 2 dMMR-depleted species, such as Flavonifractor plautii, 13 dMMR-enriched metabolites, such as retinoic acid, and 77 dMMR-depleted metabolites, such as lactic acid, succinic acid, and 2,3-dihydroxyvaleric acid. F. plautii was enriched in pMMR CRC and it was positively associated with fatty acid degradation, which might account for the accumulation of dMMR-depleted metabolites classified as short chain organic acid (lactic acid, succinic acid, and 2,3-dihydroxyvaleric acid) in pMMR CRC. The microbial-metabolic association analysis revealed the characterization of pMMR CRC as the accumulation of lactate induced by the depletion of specific gut microbiota which was negatively associated with antitumor immune, whereas the nucleotide metabolism and peptide degradation mediated by dMMR-enriched species characterized dMMR CRC. MMR-specific metabolic landscapes were related to distinctive immune features, such as CD8[+] T cells, dendritic cells and M2-like macrophages.

CONCLUSIONS: Our mutiomics results delineate a heterogeneous landscape of microbiome-host immune interactions within dMMR and pMMR CRC from aspects of bacterial communities, metabolic features, and correlation with immunocyte compartment, which infers the underlying mechanism of heterogeneous immune responses.}, } @article {pmid37597746, year = {2024}, author = {Gu, W and Wu, S and Liu, X and Wang, L and Wang, X and Qiu, Q and Wang, G}, title = {Algal-bacterial consortium promotes carbon sink formation in saline environment.}, journal = {Journal of advanced research}, volume = {60}, number = {}, pages = {111-125}, pmid = {37597746}, issn = {2090-1224}, mesh = {*Microalgae/metabolism ; *Carbon Dioxide/metabolism ; Carbon Sequestration ; Salinity ; Photosynthesis ; Lakes/microbiology ; Bacteria/metabolism ; Carbon/metabolism ; Ecosystem ; Geologic Sediments/microbiology ; Calcium Carbonate/metabolism ; Microbial Consortia ; Carbon Cycle ; Carbonates/metabolism ; }, abstract = {INTRODUCTION: The level of atmospheric CO2 has continuously been increasing and the resulting greenhouse effects are receiving attention globally. Carbon removal from the atmosphere occurs naturally in various ecosystems. Among them, saline environments contribute significantly to the global carbon cycle. Carbonate deposits in the sediments of salt lakes are omnipresent, and the biological effects, especially driven by halophilic microalgae and bacteria, on carbonate formation remain to be elucidated.

OBJECTIVES: The present study aims to characterize the carbonates formed in saline environments and demonstrate the mechanisms underlying biological-driven CO2 removal via microalgal-bacterial consortium.

METHODS: The carbonates naturally formed in saline environments were collected and analyzed. Two saline representative organisms, the photosynthetic microalga Dunaliella salina and its mutualistic halophilic bacteria Nesterenkonia sp. were isolated from the inhabiting saline environment and co-cultivated to study their biological effects on carbonates precipitation and isotopic composition. During this process, electrochemical parameters and Ca[2+] flux, and expression of genes related to CaCO3 formation were analyzed. Genome sequencing and metagenomic analysis were conducted to provide molecular evidence.

RESULTS: The results showed that natural saline sediments are enriched with CaCO3 and enrichment of genes related to photosynthesis and ureolysis. The co-cultivation stimulated 54.54% increase in CaCO3 precipitation and significantly promoted the absorption of external CO2 by 49.63%. A pH gradient was formed between the bacteria and algae culture, creating 150.22 mV of electronic potential, which might promote Ca[2+] movement toward D. salina cells. Based on the results of lab-scale induction and [13]C analysis, a theoretical calculation indicates a non-negligible amount of 0.16 and 2.3 Tg C/year carbon sequestration in China and global saline lakes, respectively.

CONCLUSION: The combined effects of these two typical representative species have contributed to the carbon sequestration in saline environments, by promoting Ca[2+] influx and increase of pH via microalgal and bacterial metabolic processes.}, } @article {pmid37597572, year = {2023}, author = {Joslin, GR and Barber, DG and Aston, L and Liu, P and Kuloyo, O and Oentoro, K and Liu, J and Baugh, AV and Fedenko, JR and Melas, I and Hamilton, PG and Allen, DJ and Tennant, RK}, title = {Metagenomic analysis of ethylene glycol contamination in anaerobic digestion.}, journal = {Bioresource technology}, volume = {387}, number = {}, pages = {129683}, doi = {10.1016/j.biortech.2023.129683}, pmid = {37597572}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Metagenome ; *Microbiota ; Biofuels ; Ethylene Glycols ; }, abstract = {Anaerobic digestion is an established method for the biological conversion of waste feedstocks to biogas and biomethane. While anaerobic digestion is an excellent waste management technique, it can be susceptible to toxins and pollutants from contaminated feedstocks, which may have a detrimental impact on a digester's efficiency and productivity. Ethylene glycol (EG) is readily used in the heat-transfer loops of anaerobic digestion facilities to maintain reactor temperature. Failure of the structural integrity of these heat transfer loops can cause EG to leak into the digester, potentially causing a decrease in the resultant gas yields. Batch fermentations were incubated with 0, 10, 100 and 500 ppm (parts per million) of EG, and analysis showed that the EG was completely metabolised by the digester microbiome. The concentrations of EG tested showed significant increases in gas yields, however there were no significant changes to the digester microbiome.}, } @article {pmid37597444, year = {2023}, author = {Heinze, BM and Küsel, K and Jehmlich, N and von Bergen, M and Taubert, M}, title = {Metabolic versatility enables sulfur-oxidizers to dominate primary production in groundwater.}, journal = {Water research}, volume = {244}, number = {}, pages = {120426}, doi = {10.1016/j.watres.2023.120426}, pmid = {37597444}, issn = {1879-2448}, mesh = {Carbon Dioxide/metabolism ; Bacteria/metabolism ; *Microbiota ; Sulfur/metabolism ; *Groundwater/chemistry ; }, abstract = {High rates of CO2 fixation and the genetic potential of various groundwater microbes for autotrophic activity have shown that primary production is an important source of organic C in groundwater ecosystems. However, the contribution of specific chemolithoautotrophic groups such as S-oxidizing bacteria (SOB) to groundwater primary production and their adaptation strategies remain largely unknown. Here, we stimulated anoxic groundwater microcosms with reduced S and sampled the microbial community after 1, 3 and 6 weeks. Genome-resolved metaproteomics was combined with 50at-% [13]CO2 stable isotope probing to follow the C flux through the microbial food web and infer traits expressed by active SOB in the groundwater microcosms. Already after 7 days, 90% of the total microbial biomass C in the microcosms was replaced by CO2-derived C, increasing to 97% at the end of incubation. Stable Isotope Cluster Analysis revealed active autotrophs, characterized by a uniform [13]C-incorporation of 45% in their peptides, to dominate the microbial community throughout incubation. Mixo- and heterotrophs, characterized by 10 to 40% [13]C-incorporation, utilized the primarily produced organic C. Interestingly, obligate autotrophs affiliated with Sulfuricella and Sulfuritalea contained traits enabling the storage of elemental S in globules to maintain primary production under energy limitation. Others related to Sulfurimonas seemed to rapidly utilize substrates for fast proliferation, and most autotrophs further maximized their energy yield via efficient denitrification and the potential for H2 oxidation. Mixotrophic SOB, belonging to Curvibacter or Polaromonas, enhanced metabolic flexibility by using organic compounds to satisfy their C requirements. Time series data spanning eight years further revealed that key taxa of our microcosms composed up to 15% of the microbial groundwater community, demonstrating their in-situ importance. This showed that SOB, by using different metabolic strategies, are able to account for high rates of primary production in groundwater, especially at sites limited to geogenic nutrient sources. The widespread presence of SOB with traits such as S storage, H2 oxidation, and organic C utilization in many aquatic habitats further suggested that metabolic versatility governs S-fueled primary production in the environment.}, } @article {pmid37596696, year = {2023}, author = {Pavia, MJ and Chede, A and Wu, Z and Cadillo-Quiroz, H and Zhu, Q}, title = {BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {186}, pmid = {37596696}, issn = {2049-2618}, mesh = {Humans ; *Metagenome/genetics ; *Microbiota/genetics ; Algorithms ; Biological Evolution ; Diarrhea ; }, abstract = {BACKGROUND: Exploring metagenomic contigs and "binning" them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure.

RESULTS: We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time. In demonstration of BinaRena's usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset.

CONCLUSIONS: BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted at https://github.com/qiyunlab/binarena , together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data. Video Abstract.}, } @article {pmid37596536, year = {2023}, author = {Araújo, V and Fehn, AM and Phiri, A and Wills, J and Rocha, J and Gayà-Vidal, M}, title = {Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {226}, pmid = {37596536}, issn = {1471-2180}, mesh = {Humans ; Zimbabwe ; Angola ; Africa, Southern ; *Citrobacter ; *Microbiota/genetics ; }, abstract = {BACKGROUND: While the human oral microbiome is known to play an important role in systemic health, its average composition and diversity patterns are still poorly understood. To gain better insights into the general composition of the microbiome on a global scale, the characterization of microbiomes from a broad range of populations, including non-industrialized societies, is needed. Here, we used the portion of non-human reads obtained through an expanded exome capture sequencing approach to characterize the saliva microbiomes of 52 individuals from eight ethnolinguistically diverse southern African populations from Angola (Kuvale, Kwepe, Himba, Tjimba, Kwisi, Twa, !Xun) and Zimbabwe (Tshwa), including foragers, food-producers, and peripatetic groups (low-status communities who provide services to their dominant neighbors).

RESULTS: Our results indicate that neither host genetics nor livelihood seem to influence the oral microbiome profile, with Neisseria, Streptococcus, Prevotella, Rothia, and Porphyromonas being the five most frequent genera in southern African groups, in line with what has been shown for other human populations. However, we found that some Tshwa and Twa individuals display an enrichment of pathogenic genera from the Enterobacteriaceae family (i.e. Enterobacter, Citrobacter, Salmonella) of the Proteobacteria phylum, probably reflecting deficient sanitation and poor health conditions associated with social marginalization.

CONCLUSIONS: Taken together, our results suggest that socio-economic status, rather than ethnolinguistic affiliation or subsistence mode, is a key factor in shaping the salivary microbial profiles of human populations in southern Africa.}, } @article {pmid37596518, year = {2023}, author = {Galperine, T and Choi, Y and Pagani, JL and Kritikos, A and Papadimitriou-Olivgeris, M and Méan, M and Scherz, V and Opota, O and Greub, G and Guery, B and Bertelli, C and , }, title = {Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {537}, pmid = {37596518}, issn = {1471-2334}, mesh = {Humans ; *COVID-19 ; SARS-CoV-2 ; *Microbiota ; *Gastrointestinal Microbiome ; Bacteroides ; Butyrates ; }, abstract = {BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a multifaceted disease potentially responsible for various clinical manifestations including gastro-intestinal symptoms. Several evidences suggest that the intestine is a critical site of immune cell development, gut microbiota could therefore play a key role in lung immune response. We designed a monocentric longitudinal observational study to describe the gut microbiota profile in COVID-19 patients and compare it to a pre-existing cohort of ventilated non-COVID-19 patients.

METHODS: From March to December 2020, we included patients admitted for COVID-19 in medicine (43 not ventilated) or intensive care unit (ICU) (14 ventilated) with a positive SARS-CoV-2 RT-PCR assay in a respiratory tract sample. 16S metagenomics was performed on rectal swabs from these 57 COVID-19 patients, 35 with one and 22 with multiple stool collections. Nineteen non-COVID-19 ICU controls were also enrolled, among which 14 developed ventilator-associated pneumonia (pneumonia group) and five remained without infection (control group). SARS-CoV-2 viral loads in fecal samples were measured by qPCR.

RESULTS: Although similar at inclusion, Shannon alpha diversity appeared significantly lower in COVID-19 and pneumonia groups than in the control group at day 7. Furthermore, the microbiota composition became distinct between COVID-19 and non-COVID-19 groups. The fecal microbiota of COVID-19 patients was characterized by increased Bacteroides and the pneumonia group by Prevotella. In a distance-based redundancy analysis, only COVID-19 presented significant effects on the microbiota composition. Moreover, patients in ICU harbored increased Campylobacter and decreased butyrate-producing bacteria, such as Lachnospiraceae, Roseburia and Faecalibacterium as compared to patients in medicine. Both the stay in ICU and patient were significant factors affecting the microbiota composition. SARS-CoV-2 viral loads were higher in ICU than in non-ICU patients.

CONCLUSIONS: Overall, we identified distinct characteristics of the gut microbiota in COVID-19 patients compared to control groups. COVID-19 patients were primarily characterized by increased Bacteroides and decreased Prevotella. Moreover, disease severity showed a negative correlation with butyrate-producing bacteria. These features could offer valuable insights into potential targets for modulating the host response through the microbiota and contribute to a better understanding of the disease's pathophysiology.

TRIAL REGISTRATION: CER-VD 2020-00755 (05.05.2020) & 2017-01820 (08.06.2018).}, } @article {pmid37596370, year = {2023}, author = {Vigneron, A and Vincent, WF and Lovejoy, C}, title = {Discovery of a novel bacterial class with the capacity to drive sulfur cycling and microbiome structure in a paleo-ocean analog.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {82}, pmid = {37596370}, issn = {2730-6151}, support = {Sentinel North//Canada First Research Excellence Fund (Fonds d'excellence en recherche Apogée Canada)/ ; Sentinel North//Canada First Research Excellence Fund (Fonds d'excellence en recherche Apogée Canada)/ ; Sentinel North//Canada First Research Excellence Fund (Fonds d'excellence en recherche Apogée Canada)/ ; ArcticNet//Gouvernement du Canada | Réseaux de centres d'excellence | AUTO21 Network of Centres of Excellence (Réseau de Centres d'Excellence AUTO21)/ ; Arctic Net//Gouvernement du Canada | Réseaux de centres d'excellence | AUTO21 Network of Centres of Excellence (Réseau de Centres d'Excellence AUTO21)/ ; }, abstract = {Uncultivated microbial taxa represent a large fraction of global microbial diversity and likely drive numerous biogeochemical transformations in natural ecosystems. Geographically isolated, polar ecosystems are complex microbial biomes and refuges of underexplored taxonomic and functional biodiversity. Combining amplicon sequencing with genome-centric metagenomic analysis of samples from one of the world's northernmost lakes (Lake A, Ellesmere Island, Canadian High Arctic), we identified a novel bacterial taxon that dominates in the bottom layer of anoxic, sulfidic, relict sea water that was isolated from the Arctic Ocean some 3000 years ago. Based on phylogenomic comparative analyses, we propose that these bacteria represent a new Class within the poorly described Electryoneota/AABM5-125-24 candidate phylum. This novel class, for which we propose the name Tariuqbacteria, may be either a relict of ancient ocean conditions or endemic to this High Arctic system, provisionally providing a rare example of high-taxonomy level endemism. Consistent with the geochemistry of the bottom water, the genetic composition of the Candidatus Tariuqbacter genome revealed a strictly anaerobic lifestyle with the potential for sulfate and sulfur reduction, a versatile carbon metabolism and the capability to eliminate competing bacteria through methylarsenite production, suggesting an allelochemical influence on microbiome structure by this planktonic microbe.}, } @article {pmid37595937, year = {2023}, author = {Li, Y and Xu, J and Hong, Y and Li, Z and Xing, X and Zhufeng, Y and Lu, D and Liu, X and He, J and Li, Y and Sun, X}, title = {Metagenome-wide association study of gut microbiome features for myositis.}, journal = {Clinical immunology (Orlando, Fla.)}, volume = {255}, number = {}, pages = {109738}, doi = {10.1016/j.clim.2023.109738}, pmid = {37595937}, issn = {1521-7035}, mesh = {Retrospective Studies ; Bacteria ; *Myositis/complications ; Bacteroidetes ; *Gastrointestinal Microbiome/genetics ; *Lung Diseases, Interstitial ; Escherichia coli/genetics ; Metagenome ; Humans ; Autoantibodies ; }, abstract = {PURPOSE: The clinical relevance and pathogenic role of gut microbiome in both myositis and its associated interstitial lung disease (ILD) are still unclear. The purpose of this study was to investigate the role of gut microbiome in myositis through comprehensive metagenomic-wide association studies (MWAS).

METHODS: We conducted MWAS of the myositis gut microbiome in a Chinese cohort by using whole-genome shotgun sequencing of high depth, including 30 myositis patients and 31 healthy controls (HC). Among the myositis patients, 11 developed rapidly progressive interstitial lung disease (RP-ILD) and 10 had chronic ILD (C-ILD).

RESULTS: Analysis for overall distribution level of the bacteria showed Alistipes onderdonkii, Parabacteroides distasonis and Escherichia coli were upregulated, Lachnospiraceae bacterium GAM79, Roseburia intestinalis, and Akkermansia muciniphila were downregulated in patients with myositis compared to HC. Bacteroides thetaiotaomicron, Parabacteroides distasonis and Escherichia coli were upregulated, Bacteroides A1C1 and Bacteroides xylanisolvens were downregulated in RP-ILD cases compared with C-ILD cases. A variety of biological pathways related to metabolism were enriched in the myositis and HC, RP-ILD and C-ILD comparison. And in the analyses for microbial contribution in metagenomic biological pathways, we have found that E. coli played an important role in the pathway expression in both myositis group and myositis-associated RP-ILD group. Anti-PL-12 antibody, anti-Ro-52 antibody, and anti-EJ antibody were found to have positive correlation with bacterial diversity (Shannon-wiener diversity index and Chao1, richness estimator) between myositis group and control groups. The combination of E. coli and R. intestinalis could distinguish myositis group from HC effectively. R. intestinalis can also be applied in the distinguishment of RP-ILD group vs. C-ILD group in myositis patients.

CONCLUSION: Our MWAS study first revealed the link between gut microbiome and pathgenesis of myositis, which may help us understand the role of gut microbiome in the etiology of myositis and myositis-associated RP-ILD.}, } @article {pmid37595469, year = {2023}, author = {Rolbiecki, D and Paukszto, Ł and Krawczyk, K and Korzeniewska, E and Sawicki, J and Harnisz, M}, title = {Chlorine disinfection modifies the microbiome, resistome and mobilome of hospital wastewater - A nanopore long-read metagenomic approach.}, journal = {Journal of hazardous materials}, volume = {459}, number = {}, pages = {132298}, doi = {10.1016/j.jhazmat.2023.132298}, pmid = {37595469}, issn = {1873-3336}, mesh = {Humans ; Chlorine/pharmacology ; Wastewater ; Angiotensin Receptor Antagonists ; Disinfection ; *Nanopores ; Angiotensin-Converting Enzyme Inhibitors ; Halogens ; *Microbiota/genetics ; Chlorides ; Anti-Bacterial Agents ; Hospitals ; }, abstract = {The aim of the present study was to analyze changes in the microbiome, resistome, and mobilome of hospital wastewater (HWW) induced by disinfection with chlorine compounds. Changes in bacterial communities and specific antibiotic resistance genes (ARGs) in HWW were determined with the use of a nanopore long-read metagenomic approach. The main hosts of ARGs in HWW were identified, and the mobility of resistance mechanisms was analyzed. Special attention was paid to the prevalence of critical-priority pathogens in the HWW microbiome, which pose the greatest threat to human health. The results of this study indicate that chlorine disinfection of HWW can induce significant changes in the structure of the total bacterial population and antibiotic resistant bacteria (ARB) communities, and that it can modify the resistome and mobilome of HWW. Disinfection favored the selection of ARGs, decreased their prevalence in HWW, while increasing their diversity. The mobility of the HWW resistome increased after disinfection. Disinfection led to the emergence of new drug resistance mechanisms in previously sensitive bacterial taxa. In conclusion, this study demonstrated that HWW disinfected with low (sublethal) concentrations of free chlorine significantly contributes to the mobility and transfer of drug resistance mechanisms (including critical mechanisms) between bacteria (including pathogens).}, } @article {pmid37594964, year = {2023}, author = {Li, W and Kari, L and Yu, Y and Hug, LA}, title = {MT-MAG: Accurate and interpretable machine learning for complete or partial taxonomic assignments of metagenomeassembled genomes.}, journal = {PloS one}, volume = {18}, number = {8}, pages = {e0283536}, pmid = {37594964}, issn = {1932-6203}, mesh = {Animals ; Cattle ; Female ; Humans ; *Metagenome/genetics ; Benchmarking ; Computational Biology ; *Gastrointestinal Microbiome ; Machine Learning ; }, abstract = {We propose MT-MAG, a novel machine learning-based software tool for the complete or partial hierarchically-structured taxonomic classification of metagenome-assembled genomes (MAGs). MT-MAG is alignment-free, with k-mer frequencies being the only feature used to distinguish a DNA sequence from another (herein k = 7). MT-MAG is capable of classifying large and diverse metagenomic datasets: a total of 245.68 Gbp in the training sets, and 9.6 Gbp in the test sets analyzed in this study. In addition to complete classifications, MT-MAG offers a "partial classification" option, whereby a classification at a higher taxonomic level is provided for MAGs that cannot be classified to the Species level. MT-MAG outputs complete or partial classification paths, and interpretable numerical classification confidences of its classifications, at all taxonomic ranks. To assess the performance of MT-MAG, we define a "weighted classification accuracy," with a weighting scheme reflecting the fact that partial classifications at different ranks are not equally informative. For the two benchmarking datasets analyzed (genomes from human gut microbiome species, and bacterial and archaeal genomes assembled from cow rumen metagenomic sequences), MT-MAG achieves an average of 87.32% in weighted classification accuracy. At the Species level, MT-MAG outperforms DeepMicrobes, the only other comparable software tool, by an average of 34.79% in weighted classification accuracy. In addition, MT-MAG is able to completely classify an average of 67.70% of the sequences at the Species level, compared with DeepMicrobes which only classifies 47.45%. Moreover, MT-MAG provides additional information for sequences that it could not classify at the Species level, resulting in the partial or complete classification of 95.13%, of the genomes in the datasets analyzed. Lastly, unlike other taxonomic assignment tools (e.g., GDTB-Tk), MT-MAG is an alignment-free and genetic marker-free tool, able to provide additional bioinformatics analysis to confirm existing or tentative taxonomic assignments.}, } @article {pmid37593763, year = {2023}, author = {Cui, S and Pan, M and Tang, X and Liu, G and Mao, B and Zhao, J and Yang, K}, title = {Metagenomic insights into the effects of cosmetics containing complex polysaccharides on the composition of skin microbiota in females.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1210724}, pmid = {37593763}, issn = {2235-2988}, mesh = {Female ; Humans ; Metagenome ; *Microbiota ; *Cosmetics ; Skin ; *Actinobacteria ; Bifidobacterium ; }, abstract = {INTRODUCTION: The use of cosmetics has become a habit for women. However, their influence on the microbial diversity of the skin has rarely been studied.

METHODS: Herein, the effect of cosmetics containing complex polysaccharides on the skin bacterial microbiota of female forehead and cheek areas was analyzed. Eighty volunteers were recruited and split into two groups (40 people each); one group was treated with cosmetics containing complex polysaccharides and the other with basic cream for 28 days. Skin samples were collected using sterilized cotton swabs, and 16S rDNA high-throughput sequencing was used to analyze the changes in skin bacterial microbiota composition before and after the intervention.

RESULTS AND DISCUSSION: A total of twenty-four phyla were detected in the forehead and cheek skin samples of 80 volunteers, the top three of which were Proteobacteria, Firmicutes, and Actinobacteria. The main genera of the forehead skin bacterial microbiota were Cutibacterium (11.1%), Acinetobacter (10.4%), Enterococcus (8.9%), Ralstonia (8.8%), and Staphylococcus (8.7%), while those of the cheek skin bacterial microbiota were Staphylococcus (20.0%), Ralstonia (8.7%), Propionibacterium (7.9%), Acinetobacter (7.2%), and Bifidobacterium (6.0%). Compared with basic cream, the use of cosmetics containing complex polysaccharides significantly increased the relative abundance of Staphylococcus and Bacillus in the forehead and cheek and reduced the relative abundance of Propionibacterium and Bifidobacterium. Thus, cosmetics containing complex polysaccharides could modify the composition of skin bacterial microbiota, which may help to maintain stable conditions of the skin.}, } @article {pmid37593761, year = {2023}, author = {Fukuoka, H and Tourlousse, DM and Ohashi, A and Suzuki, S and Nakagawa, K and Ozawa, M and Ishibe, A and Endo, I and Sekiguchi, Y}, title = {Elucidating colorectal cancer-associated bacteria through profiling of minimally perturbed tissue-associated microbiota.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1216024}, pmid = {37593761}, issn = {2235-2988}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Gastrointestinal Microbiome ; Bacteria/genetics ; *Colorectal Neoplasms ; }, abstract = {Sequencing-based interrogation of gut microbiota is a valuable approach for detecting microbes associated with colorectal cancer (CRC); however, such studies are often confounded by the effect of bowel preparation. In this study, we evaluated the viability of identifying CRC-associated mucosal bacteria through centimeter-scale profiling of the microbiota in tumors and adjacent noncancerous tissue from eleven patients who underwent colonic resection without preoperative bowel preparation. High-throughput 16S rRNA gene sequencing revealed that differences between on- and off-tumor microbiota varied considerably among patients. For some patients, phylotypes affiliated with genera previously implicated in colorectal carcinogenesis, as well as genera with less well-understood roles in CRC, were enriched in tumor tissue, whereas for other patients, on- and off-tumor microbiota were very similar. Notably, the enrichment of phylotypes in tumor-associated mucosa was highly localized and no longer apparent even a few centimeters away from the tumor. Through short-term liquid culturing and metagenomics, we further generated more than one-hundred metagenome-assembled genomes, several representing bacteria that were enriched in on-tumor samples. This is one of the first studies to analyze largely unperturbed mucosal microbiota in tissue samples from the resected colons of unprepped CRC patients. Future studies with larger cohorts are expected to clarify the causes and consequences of the observed variability in the emergence of tumor-localized microbiota among patients.}, } @article {pmid37591872, year = {2023}, author = {Liao, J and Shenhav, L and Urban, JA and Serrano, M and Zhu, B and Buck, GA and Korem, T}, title = {Microdiversity of the vaginal microbiome is associated with preterm birth.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4997}, pmid = {37591872}, issn = {2041-1723}, support = {R01 HD106017/HD/NICHD NIH HHS/United States ; U54 HD080784/HD/NICHD NIH HHS/United States ; }, mesh = {Infant, Newborn ; Pregnancy ; Humans ; Female ; *Premature Birth/genetics ; *Microbiota/genetics ; Metagenome/genetics ; Acclimatization ; Biological Evolution ; }, abstract = {Preterm birth (PTB) is the leading cause of neonatal morbidity and mortality. The vaginal microbiome has been associated with PTB, yet the mechanisms underlying this association are not fully understood. Understanding microbial genetic adaptations to selective pressures, especially those related to the host, may yield insights into these associations. Here, we analyze metagenomic data from 705 vaginal samples collected during pregnancy from 40 women who delivered preterm spontaneously and 135 term controls from the Multi-Omic Microbiome Study-Pregnancy Initiative. We find that the vaginal microbiome of pregnancies that ended preterm exhibited unique genetic profiles. It was more genetically diverse at the species level, a result which we validate in an additional cohort, and harbored a higher richness and diversity of antimicrobial resistance genes, likely promoted by transduction. Interestingly, we find that Gardnerella species drove this higher genetic diversity, particularly during the first half of the pregnancy. We further present evidence that Gardnerella spp. underwent more frequent recombination and stronger purifying selection in genes involved in lipid metabolism. Overall, our population genetics analyses reveal associations between the vaginal microbiome and PTB and suggest that evolutionary processes acting on vaginal microbes may play a role in adverse pregnancy outcomes such as PTB.}, } @article {pmid37591518, year = {2023}, author = {Liu, X and Wu, J and Tang, J and Xu, Z and Zhou, B and Liu, Y and Hu, F and Zhang, G and Cheng, R and Xia, X and Chen, Y and Wu, H and Wang, D and Yue, J and Dong, B and Fu, J and Yu, H and Dong, B}, title = {Prevotella copri alleviates sarcopenia via attenuating muscle mass loss and function decline.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {14}, number = {5}, pages = {2275-2288}, pmid = {37591518}, issn = {2190-6009}, support = {32100927//National Natural Science Foundation of China/ ; 82101653//National Natural Science Foundation of China/ ; 2021YFS0158//Project of the Sichuan Province Science and Technology/ ; Z2018B09//National Clinical Research Center for Geriatric, West China Hospital, Sichuan University/ ; 2020HXBH011//West China Hospital Postdoctoral Fund/ ; HXYS19005//1.3.5 Project for Disciplines of Excellence, West China Hospital, Sichuan University, Project of Max Cynader Academy of Brain Workstation, WCHSCU/ ; 2019YF0900083SN//Chengdu Science and Technology Bureau Major Science and Technology Application Demonstration Project/ ; CSC 202108510037//China Scholarship Council/ ; CVON2018-27//Dutch Heart Foundation IN-CONTROL/ ; 101001678//ERC Consolidator Grant/ ; VI.C.202.022//NWO-VICI Grant/ ; 024.003.001//The Netherlands Organ-on-Chip Initiative, an NWO Gravitation Project/ ; }, mesh = {*Sarcopenia/metabolism ; Humans ; Male ; Female ; Aged ; Animals ; Mice ; *Gastrointestinal Microbiome ; *Prevotella ; Middle Aged ; Muscle, Skeletal/metabolism ; Feces/microbiology ; China ; }, abstract = {BACKGROUND: The gut microbiome and fecal metabolites have been found to influence sarcopenia, but whether there are potential bacteria that can alleviate sarcopenia has been under-investigated, and the molecular mechanism remains unclear.

METHODS: To investigate the relationships between the gut microbiome, fecal metabolites and sarcopenia, subjects were selected from observational multi-ethnic study conducted in Western China. Sarcopenia was diagnosed according to the criteria of the Asian Working Group for Sarcopenia 2014. The gut microbiome was profiled by shotgun metagenomic sequencing. Untargeted metabolomic analysis was performed to analyse the differences in fecal metabolites. We investigated bacterium with the greatest relative abundance difference between healthy individuals and sarcopenia patients, and the differences in metabolites associated with the bacteria, to verify its effects on muscle mass and function in a mouse model.

RESULTS: The study included 283 participants (68.90% females, mean age: 66.66 years old) with and without sarcopenia (141 and 142 participants, respectively) and from the Han (98 participants), Zang (88 participants) and Qiang (97 participants) ethnic groups. This showed an overall reduction (15.03% vs. 20.77%, P = 0.01) of Prevotella copri between the sarcopenia and non-sarcopenia subjects across the three ethnic groups. Functional characterization of the differential bacteria showed enrichment (odds ratio = 15.97, P = 0.0068) in branched chain amino acid (BCAA) metabolism in non-sarcopenia group. A total of 13 BCAA and their derivatives have relatively low levels in sarcopenia. In the in vivo experiment, we found that the blood BCAA level was higher in the mice gavaged with live P. copri (LPC) (P < 0.001). The LPC mice had significantly longer wire and grid hanging time (P < 0.02), longer time on rotor (P = 0.0001) and larger grip strength (P < 0.0001), indicating better muscle function. The weight of gastrocnemius mass and rectus femoris mass (P < 0.05) was higher in LPC mice. The micro-computed tomography showed a larger leg area (P = 0.0031), and a small animal analyser showed a higher lean mass ratio in LPC mice (P = 0.0157), indicating higher muscle mass.

CONCLUSIONS: The results indicated that there were lower levels of both P. copri and BCAA in sarcopenia individuals. In vivo experiments, gavage with LPC could attenuate muscle mass and function decline, indicating alleviating sarcopenia. This suggested that P. copri may play a therapeutic potential role in the management of sarcopenia.}, } @article {pmid37587527, year = {2023}, author = {Liao, H and Ji, Y and Sun, Y}, title = {High-resolution strain-level microbiome composition analysis from short reads.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {183}, pmid = {37587527}, issn = {2049-2618}, mesh = {*Microbiota/genetics ; Metagenome/genetics ; Metagenomics ; Software ; }, abstract = {BACKGROUND: Bacterial strains under the same species can exhibit different biological properties, making strain-level composition analysis an important step in understanding the dynamics of microbial communities. Metagenomic sequencing has become the major means for probing the microbial composition in host-associated or environmental samples. Although there are a plethora of composition analysis tools, they are not optimized to address the challenges in strain-level analysis: highly similar strain genomes and the presence of multiple strains under one species in a sample. Thus, this work aims to provide a high-resolution and more accurate strain-level analysis tool for short reads.

RESULTS: In this work, we present a new strain-level composition analysis tool named StrainScan that employs a novel tree-based k-mers indexing structure to strike a balance between the strain identification accuracy and the computational complexity. We tested StrainScan extensively on a large number of simulated and real sequencing data and benchmarked StrainScan with popular strain-level analysis tools including Krakenuniq, StrainSeeker, Pathoscope2, Sigma, StrainGE, and StrainEst. The results show that StrainScan has higher accuracy and resolution than the state-of-the-art tools on strain-level composition analysis. It improves the F1 score by 20% in identifying multiple strains at the strain level.

CONCLUSIONS: By using a novel k-mer indexing structure, StrainScan is able to provide strain-level analysis with higher resolution than existing tools, enabling it to return more informative strain composition analysis in one sample or across multiple samples. StrainScan takes short reads and a set of reference strains as input and its source codes are freely available at https://github.com/liaoherui/StrainScan . Video Abstract.}, } @article {pmid37580828, year = {2023}, author = {Deng, F and Wang, C and Li, D and Peng, Y and Deng, L and Zhao, Y and Zhang, Z and Wei, M and Wu, K and Zhao, J and Li, Y}, title = {The unique gut microbiome of giant pandas involved in protein metabolism contributes to the host's dietary adaption to bamboo.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {180}, pmid = {37580828}, issn = {2049-2618}, mesh = {Animals ; Mice ; *Ursidae ; *Gastrointestinal Microbiome/genetics ; Feces/chemistry ; Metagenome ; Diet ; }, abstract = {BACKGROUND: The gut microbiota of the giant panda (Ailuropoda melanoleuca), a global symbol of conservation, are believed to be involved in the host's dietary switch to a fibrous bamboo diet. However, their exact roles are still largely unknown.

RESULTS: In this study, we first comprehensively analyzed a large number of gut metagenomes giant pandas (n = 322), including 98 pandas sequenced in this study with deep sequencing (Illumina) and third-generation sequencing (nanopore). We reconstructed 408 metagenome-assembled genomes (MAGs), and 148 of which (36.27%) were near complete. The most abundant MAG was classified as Streptococcus alactolyticus. A pairwise comparison of the metagenomes and meta-transcriptomes in 14 feces revealed genes involved in carbohydrate metabolism were lower, but those involved in protein metabolism were greater in abundance and expression in giant pandas compared to those in herbivores and omnivores. Of note, S. alactolyticus was positively correlated to the KEGG modules of essential amino-acid biosynthesis. After being isolated from pandas and gavaged to mice, S. alactolyticus significantly increased the relative abundance of essential amino acids in mice jejunum.

CONCLUSIONS: The study highlights the unique protein metabolic profiles in the giant panda's gut microbiome. The findings suggest that S. alactolyticus is an important player in the gut microbiota that contributes to the giant panda's dietary adaptation by more involvement in protein rather than carbohydrate metabolism. Video Abstract.}, } @article {pmid37580683, year = {2023}, author = {Józefiak, A and Rawski, M and Kierończyk, B and Józefiak, D and Mazurkiewicz, J}, title = {Effect of two insect meals on the gut commensal microbiome of healthy sea trout (Salmo trutta vr. trutta).}, journal = {BMC veterinary research}, volume = {19}, number = {1}, pages = {124}, pmid = {37580683}, issn = {1746-6148}, support = {POIR 4.4//Narodowe Centrum Nauki/ ; TEAM TECH no. POIR.04.04.00-00-204E/16-00//Narodowe Centrum Badań i Rozwoju/ ; }, mesh = {Animals ; *Trout/microbiology ; Diet/veterinary ; Insecta ; Bacteria ; *Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: The balance of the intestinal commensal microbiome of fish and other animals plays an important role in the physiological processes of healthy animals, contributes to the defense against pathogens, stimulates the immune system and facilitates nutrient metabolism. In the last decade, the interest in the application of the insects in fish nutrition increased, although little is known regarding the effects of insect meals on the gastrointenstinal tract microbiome of the sea trout fingerlings. The aim of this study was to evaluate the effect of two diets containing mealworm (MW) and superworm (SW) on the microbiome of the digesta of sea trout fingerlings and the relative abundances of different taxa among communities under controlled conditions.

RESULTS: The insect meals produced a similar weight gain and survival rate to sea trout fed fishmeal. The most abundant bacterial phylum in all the treatment groups was Firmicutes followed by Proteobacteria and Actinobacteria, and significant differences in the amount of Cyanobacteria were observed in the SW group.

CONCLUSIONS: The insect meals did not produce differences in the three most abundant phyla in the sea trout digesta. However, the effect of each type of meal on the lower taxonomic levels was evident, particularly in the case of the superworm meal. These microbiome differences indicated that mealworm meal was more related to fishmeal than superworm meal. Our results highlight the potential effects of insect meals, such as mealworm and superworm meals, on the microbiota of sea trout.}, } @article {pmid37579703, year = {2023}, author = {Li, Z and Wang, J and Fan, J and Yue, H and Zhang, X}, title = {Marine toxin domoic acid alters protistan community structure and assembly process in sediments.}, journal = {Marine environmental research}, volume = {191}, number = {}, pages = {106131}, doi = {10.1016/j.marenvres.2023.106131}, pmid = {37579703}, issn = {1879-0291}, mesh = {*Marine Toxins ; Kainic Acid/toxicity ; Eukaryota ; *Microbiota ; }, abstract = {Domoic acid (DA)-producing algal blooms have been the issue of worldwide concerns in recent decades, but there has never been any attempt to investigate the effects of DA on microbial ecology in marine environments. Protists are considered to be key regulators of microbial activity, community structure and evolution, we therefore explore the effect of DA on the ecology of protists via metagenome in this work. The results indicate that trace amounts of DA can act as a stressor to alter alpha and beta diversity of protistan community. Among trophic functional groups, consumers and phototrophs are negative responders of DA, implying DA is potentially capable of functional-level effects in the ocean. Moreover, microecological theory reveals that induction of DA increases the role of deterministic processes in microbial community assembly, thus altering the biotic relationships and successional processes in symbiotic patterns. Finally, we demonstrate that the mechanism by which DA shapes protistan ecological network is by acting on phototrophs, which triggers cascading effects in networks and eventually leading to shifts in ecological succession of protists. Overall, our results present the first perspective regarding the effects of DA on marine microbial ecology, which will supplement timely information on the ecological impacts of DA in the ocean.}, } @article {pmid37578240, year = {2023}, author = {Cabrol, L and Capo, E and van Vliet, DM and von Meijenfeldt, FAB and Bertilsson, S and Villanueva, L and Sánchez-Andrea, I and Björn, E and G Bravo, A and Heimburger Boavida, LE}, title = {Redox gradient shapes the abundance and diversity of mercury-methylating microorganisms along the water column of the Black Sea.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0053723}, pmid = {37578240}, issn = {2379-5077}, mesh = {Humans ; *Mercury/analysis ; *Methylmercury Compounds/analysis ; Ecosystem ; Water/analysis ; Black Sea ; Bacteria/genetics ; *Chloroflexi/metabolism ; Oxidation-Reduction ; Planctomycetes ; Oxygen/analysis ; }, abstract = {In the global context of seawater deoxygenation triggered by climate change and anthropogenic activities, changes in redox gradients impacting biogeochemical transformations of pollutants, such as mercury, become more likely. Being the largest anoxic basin worldwide, with high concentrations of the potent neurotoxic methylmercury (MeHg), the Black Sea is an ideal natural laboratory to provide new insights about the link between dissolved oxygen concentration and hgcAB gene-carrying (hgc[+]) microorganisms involved in the formation of MeHg. We combined geochemical and microbial approaches to assess the effect of vertical redox gradients on abundance, diversity, and metabolic potential of hgc[+] microorganisms in the Black Sea water column. The abundance of hgcA genes [congruently estimated by quantitative PCR (qPCR) and metagenomics] correlated with MeHg concentration, both maximal in the upper part of the anoxic water. Besides the predominant Desulfobacterales, hgc[+] microorganisms belonged to a unique assemblage of diverse-previously underappreciated-anaerobic fermenters from Anaerolineales, Phycisphaerae (characteristic of the anoxic and sulfidic zone), Kiritimatiellales, and Bacteroidales (characteristic of the suboxic zone). The metabolic versatility of Desulfobacterota differed from strict sulfate reduction in the anoxic water to reduction of various electron acceptors in the suboxic water. Linking microbial activity and contaminant concentration in environmental studies is rare due to the complexity of biological pathways. In this study, we disentangle the role of oxygen in shaping the distribution of Hg-methylating microorganisms consistently with MeHg concentration, and we highlight their taxonomic and metabolic niche partitioning across redox gradients, improving the prediction of the response of marine communities to the expansion of oxygen-deficient zones. IMPORTANCE Methylmercury (MeHg) is a neurotoxin detected at high concentrations in certain marine ecosystems, posing a threat to human health. MeHg production is mainly mediated by hgcAB gene-carrying (hgc[+]) microorganisms. Oxygen is one of the main factors controlling Hg methylation; however, its effect on the diversity and ecology of hgc[+] microorganisms remains unknown. Under the current context of seawater deoxygenation, mercury cycling is expected to be disturbed. Here, we show the strong effect of oxygen gradients on the distribution of potential Hg methylators. In addition, we show for the first time the significant contribution of a unique assemblage of potential fermenters from Anaerolineales, Phycisphaerae, and Kiritimatiellales to Hg methylation, stratified in different redox niches along the Black Sea gradient. Our results considerably expand the known taxonomic diversity and ecological niches prone to the formation of MeHg and contribute to better apprehend the consequences of oxygen depletion in seawater.}, } @article {pmid37578199, year = {2024}, author = {Gwak, HJ and Lee, HA and Jeong, JY and Lee, Y and Rho, M and Cho, SH}, title = {Antibiotic Sensitivity and Nasal Microbiome in Patients with Acute Bacterial Rhinosinusitis.}, journal = {The Laryngoscope}, volume = {134}, number = {3}, pages = {1081-1088}, doi = {10.1002/lary.30950}, pmid = {37578199}, issn = {1531-4995}, support = {RS-2023-00217123//National Research Foundation of Korea (NRF) grant and Basic Science Research Program funded by the Korean government (MSIT), South Korea/ ; 2021M3H4A4079522//National Research Foundation of Korea (NRF) grant and Basic Science Research Program funded by the Korean government (MSIT), South Korea/ ; 2021R1F1A1049413//National Research Foundation of Korea (NRF) grant and Basic Science Research Program funded by the Korean government (MSIT), South Korea/ ; }, mesh = {Humans ; Anti-Bacterial Agents/pharmacology/therapeutic use ; RNA, Ribosomal, 16S ; Prospective Studies ; *Rhinosinusitis ; *Rhinitis/diagnosis ; *Sinusitis/diagnosis ; Amoxicillin ; Acute Disease ; *Microbiota ; }, abstract = {OBJECTIVES: Acute rhinosinusitis (ARS) is a common upper respiratory tract infection that is mostly of viral origin. However, little is known about the nasal microbiome profile at presentation and the changes caused by antibiotics in acute bacterial rhinosinusitis (ABRS).

METHODS: This was a prospective single-center study. Overall, 43 ARS patients were screened and were assessed with the symptom questionnaires, nasal endoscopy, and Water's view. Five healthy subjects were recruited as controls. Middle meatal mucus samples were obtained using a cotton swab (for bacterial culture and antimicrobial susceptibility testing) and the suction technique (for 16S rRNA sequencing). After 1 week of antibiotic use (amoxicillin with clavulanic acid), we enrolled 13 patients with ABRS with positive isolates and middle meatal samples for 16S rRNA sequencing were obtained again.

RESULTS: Overall, we demonstrated a significantly lower abundance of the Lactobacillaceae family in ABRS patients than in healthy controls. Resistant ABRS had different characteristics of middle meatal microbiomes when compared to sensitive ABRS as follows: (1) lower proportion of lactic acid bacteria, (2) increased pathogens such as Rhodococcus sp., Massila sp., Acinetobacter sp., and H. influenza, and (3) increased beta diversity. However, no remarkable changes were observed in the middle meatal microbiome after antibiotic use.

CONCLUSION: We showed the roles of Lactobacillaceae in ABRS, and Acinetobacter and Massilia in case of amoxicillin resistance.

LEVEL OF EVIDENCE: 3 Laryngoscope, 134:1081-1088, 2024.}, } @article {pmid37577374, year = {2023}, author = {Avellaneda-Franco, L and Dahlman, S and Barr, JJ}, title = {The gut virome and the relevance of temperate phages in human health.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1241058}, pmid = {37577374}, issn = {2235-2988}, mesh = {Humans ; *Bacteriophages/genetics ; Virome ; Bacteria/genetics ; }, abstract = {Alterations in the gut virome impact human health. Bacteriophages, viruses that infect bacteria, dominate the gut virome and are mainly composed by virulent and temperate phages. While virulent phages exclusively replicate within and lyse their bacterial host's cell, temperate phages switch from an integrated state residing within their bacterial host's chromosome to an induced free virion state via an induction event. How often do these induction events occur and what are their implications on gut homeostasis? Here, we summarize the current knowledge of the gut virome based on metagenomics and present how the proportion of induced temperate phages varies amongst individuals, age, and disease states. Finally, we highlight the importance of building upon classical culture-dependent techniques and sequencing approaches to improve our understanding of temperate phages to enable their potential therapeutic use.}, } @article {pmid37577371, year = {2023}, author = {Naud, S and Valles, C and Abdillah, A and Abou Chacra, L and Mekhalif, FZ and Ibrahim, A and Caputo, A and Baudoin, JP and Gouriet, F and Bittar, F and Lagier, JC and Ranque, S and Fenollar, F and Tidjani Alou, M and Raoult, D}, title = {Preliminary landscape of Candidatus Saccharibacteria in the human microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1195679}, pmid = {37577371}, issn = {2235-2988}, mesh = {Female ; Humans ; Prospective Studies ; Retrospective Studies ; *Bacteria/genetics ; *Microbiota ; Real-Time Polymerase Chain Reaction ; }, abstract = {INTRODUCTION: Candidate Phyla Radiation (CPR) and more specifically Candidatus Saccharibacteria (TM7) have now been established as ubiquitous members of the human oral microbiota. Additionally, CPR have been reported in the gastrointestinal and urogenital tracts. However, the exploration of new human niches has been limited to date.

METHODS: In this study, we performed a prospective and retrospective screening of TM7 in human samples using standard PCR, real-time PCR, scanning electron microscopy (SEM) and shotgun metagenomics.

RESULTS: Using Real-time PCR and standard PCR, oral samples presented the highest TM7 prevalence followed by fecal samples, breast milk samples, vaginal samples and urine samples. Surprisingly, TM7 were also detected in infectious samples, namely cardiac valves and blood cultures at a low prevalence (under 3%). Moreover, we observed CPR-like structures using SEM in all sample types except cardiac valves. The reconstruction of TM7 genomes in oral and fecal samples from shotgun metagenomics reads further confirmed their high prevalence in some samples.

CONCLUSION: This study confirmed, through their detection in multiple human samples, that TM7 are human commensals that can also be found in clinical settings. Their detection in clinical samples warrants further studies to explore their role in a pathological setting.}, } @article {pmid37575934, year = {2023}, author = {Kakkar, RA and Haneen, MA and Parida, AC and Sharma, G}, title = {The known, unknown, and the intriguing about members of a critically endangered traditional medicinal plant genus Aconitum.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1139215}, pmid = {37575934}, issn = {1664-462X}, abstract = {Humanity will always be indebted to plants. In the ongoing scientific era, the 'Herbal Revolution' has helped discover several valuable medicinal plants and associated novel secondary metabolites from the diverse unexplored ecosystems, treating several diseases via phytotherapy. The Aconitum genus comprises several economically-important poisonous mountainous medicinal plant species whose unique biodiversity is on the verge of extinction due to illegal human intervention triggered habitat loss, over-harvesting, and unrestricted trading. Owing to its vast diversity of diterpene alkaloids, most species are extensively used to treat several ailments in rural parts of the world. Irrespective of this, many unexplored and intriguing prospects exist to understand and utilize this critical plant for human benefit. This systematic review tries to fill this gap by compiling information from the sporadically available literature known for ~300 Aconitum spp. regarding its nomenclature and classification, endangerment, plant morphology, ploidy, secondary metabolites, drug pharmacokinetics, conservation, and omics-based computational studies. We also depicted the disparity in the studied model organisms for this diverse genus. The absence of genomic/metagenomic data is becoming a limiting factor in understanding its plant physiology, metabolic pathways, and plant-microbes interactions, and therefore must be promoted. Additionally, government support and public participation are crucial in establishing conservation protocols to save this plant from endangerment.}, } @article {pmid37573460, year = {2023}, author = {Dwiyanto, J and Huët, MAL and Hussain, MH and Su, TT and Tan, JBL and Toh, KY and Lee, JWJ and Rahman, S and Chong, CW}, title = {Social demographics determinants for resistome and microbiome variation of a multiethnic community in Southern Malaysia.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {55}, pmid = {37573460}, issn = {2055-5008}, mesh = {Humans ; Malaysia ; Escherichia coli/genetics ; Saccharomyces cerevisiae ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; Demography ; }, abstract = {The prevalence of antibiotic-resistant bacteria in Southeast Asia is a significant concern, yet there is limited research on the gut resistome and its correlation with lifestyle and environmental factors in the region. This study aimed to profile the gut resistome of 200 individuals in Malaysia using shotgun metagenomic sequencing and investigate its association with questionnaire data comprising demographic and lifestyle variables. A total of 1038 antibiotic resistance genes from 26 classes were detected with a mean carriage rate of 1.74 ± 1.18 gene copies per cell per person. Correlation analysis identified 14 environmental factors, including hygiene habits, health parameters, and intestinal colonization, that were significantly associated with the resistome (adjusted multivariate PERMANOVA, p < 0.05). Notably, individuals with positive yeast cultures exhibited a reduced copy number of 15 antibiotic resistance genes. Network analysis highlighted Escherichia coli as a major resistome network hub, with a positive correlation to 36 antibiotic-resistance genes. Our findings suggest that E. coli may play a pivotal role in shaping the resistome dynamics in Segamat, Malaysia, and its abundance is strongly associated with the community's health and lifestyle habits. Furthermore, the presence of yeast appears to be associated with the suppression of antibiotic-resistance genes.}, } @article {pmid37573429, year = {2023}, author = {Zhou, Y and Li, J and Huang, F and Ai, H and Gao, J and Chen, C and Huang, L}, title = {Characterization of the pig lower respiratory tract antibiotic resistome.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4868}, pmid = {37573429}, issn = {2041-1723}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microbiota/genetics ; Respiratory System ; Swine ; }, abstract = {Respiratory diseases and its treatments are highly concerned in both the pig industry and human health. However, the composition and distribution of antibiotic resistance genes (ARGs) in swine lower respiratory tract microbiome remain unknown. The relationships of ARGs with mobile genetic elements (MGEs) and lung health are unclear. Here, we characterize antibiotic resistomes of the swine lower respiratory tract microbiome containing 1228 open reading frames belonging to 372 ARGs using 745 metagenomes from 675 experimental pigs. Twelve ARGs conferring resistance to tetracycline are related to an MGE Tn916 family, and multiple types of ARGs are related to a transposase gene tnpA. Most of the linkage complexes between ARGs and MGEs (the Tn916 family and tnpA) are also observed in pig gut microbiomes and human lung microbiomes, suggesting the high risk of these MGEs mediating ARG transfer to both human and pig health. Gammaproteobacteria are the major ARG carriers, within which Escherichia coli harbored >50 ARGs and >10 MGEs. Although the microbial compositions structure the compositions of ARGs, we identify 73 ARGs whose relative abundances are significantly associated with the severity of lung lesions. Our results provide the first overview of ARG profiles in the swine lower respiratory tract microbiome.}, } @article {pmid37572887, year = {2023}, author = {Li, L and Guan, W and Fan, Y and He, Q and Guo, D and Yuan, A and Xing, Q and Wang, Y and Ma, Z and Ni, J and Chen, J and Zhou, Q and Zhong, Y and Li, J and Zhang, H}, title = {Zinc/carbon nanomaterials inhibit antibiotic resistance genes by affecting quorum sensing and microbial community in cattle manure production.}, journal = {Bioresource technology}, volume = {387}, number = {}, pages = {129648}, doi = {10.1016/j.biortech.2023.129648}, pmid = {37572887}, issn = {1873-2976}, mesh = {Cattle ; Animals ; Manure ; Genes, Bacterial ; Zinc ; Carbon ; Anti-Bacterial Agents/pharmacology ; *Zinc Oxide ; Quorum Sensing/genetics ; Drug Resistance, Microbial/genetics ; *Microbiota ; *Nanostructures ; }, abstract = {This study used metagenomic sequencing to examine the effects of carbon-based zinc oxide nanoparticles (CZnONPs) and graphene-based zinc oxide nanoparticles (GZnONPs) on quorum sensing (QS), antibiotic resistance genes (ARGs) and microbial community changes during cattle manure production. The manure zinc content was significantly reduced in GZnONPs group. In the QS pathway, the autoinducer gene increases significantly in Control group, while the transporter and repressor genes experience a substantial increase in CZnONPs group. These results contributed to the significantly decreased the abundance of ARGs in GZnONPs group. The co-occurrence network analysis revealed a correlation between core ARGs and QS-related KEGG Orthology or ARGs' hosts, indicating that the selective pressure of zinc influences microbial QS, forming a unique ARG pattern in in vivo anaerobic fermentation. These findings suggest that implementing nutritional regulation in farming practices can serve as a preventive measure to mitigate the potential transmission of ARGs resulting from livestock waste.}, } @article {pmid37570344, year = {2023}, author = {Yue, L and Wang, C and Meng, B and Xie, B and Cao, H and Su, H and Zhang, M}, title = {The Food Niche Overlap and Interspecific Relationship between the Sympatric Tibetan Macaque and Grey Snub-Nosed Monkey.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {15}, pages = {}, pmid = {37570344}, issn = {2076-2615}, support = {Grant No. 32260331//National Natural Science Foundation of China/ ; }, abstract = {Assessing the trophic niche and interspecific relationships between related species and determining how the species maintain differences in nutritional niches while coexisting in the same area are important topics in ecological research. Therefore, exploring the mechanism of food resource utilization, competition and coexistence among species distributed in the same region is important. In this study, we used fecal samples and metagenome sequencing technology to study the plant feeding habits and coexistence mechanisms of Tibetan macaques (Macaca thibetana) and grey snub-nosed monkeys (Rhinopithecus brelichi) within the same area. In the winter of 2020, we collected a total of 40 fecal samples from Tibetan macaques and grey snub-nosed monkeys; of those, 29 samples were considered valid and were analyzed using DNA metabarcoding. The results showed that in winter, Tibetan macaques consumed plants from 117 families and 184 genera, whereas grey snub-nosed monkeys consumed plants from 109 families and 165 genera. Diversity analysis revealed that there was a significant difference in the food composition of Tibetan macaques and grey snub-nosed monkeys. Tibetan macaques had a broader food niche width than grey snub-nosed monkeys at the family and genus levels. In winter, the food niches of Tibetan macaques and grey snub-nosed monkeys almost entirely overlapped (0.99). Our research provides detailed dietary data for Tibetan macaques and grey snub-nosed monkeys and valuable information that can aid in conservation efforts targeting these species.}, } @article {pmid37569608, year = {2023}, author = {Oñate, FP and Chamignon, C and Burz, SD and Lapaque, N and Monnoye, M and Philippe, C and Bredel, M and Chêne, L and Farin, W and Paillarse, JM and Boursier, J and Ratziu, V and Mousset, PY and Doré, J and Gérard, P and Blottière, HM}, title = {Adlercreutzia equolifaciens Is an Anti-Inflammatory Commensal Bacterium with Decreased Abundance in Gut Microbiota of Patients with Metabolic Liver Disease.}, journal = {International journal of molecular sciences}, volume = {24}, number = {15}, pages = {}, pmid = {37569608}, issn = {1422-0067}, support = {MetaGenoPolis ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; FunAMetaGen ANR-15-CE14-0021//Agence Nationale de la Recherche/ ; }, mesh = {*Non-alcoholic Fatty Liver Disease/metabolism ; *Gastrointestinal Microbiome ; Mice ; Anti-Inflammatory Agents/pharmacology/therapeutic use/metabolism ; *Liver Neoplasms/metabolism ; Dysbiosis/microbiology ; Liver/metabolism ; Actinobacteria ; Animals ; *Metabolic Diseases/metabolism ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD) affects about 20-40% of the adult population in high-income countries and is now a leading indication for liver transplantation and can lead to hepatocellular carcinoma. The link between gut microbiota dysbiosis and NAFLD is now clearly established. Through analyses of the gut microbiota with shotgun metagenomics, we observe that compared to healthy controls, Adlercreutzia equolifaciens is depleted in patients with liver diseases such as NAFLD. Its abundance also decreases as the disease progresses and eventually disappears in the last stages indicating a strong association with disease severity. Moreover, we show that A. equolifaciens possesses anti-inflammatory properties, both in vitro and in vivo in a humanized mouse model of NAFLD. Therefore, our results demonstrate a link between NAFLD and the severity of liver disease and the presence of A. equolifaciens and its anti-inflammatory actions. Counterbalancing dysbiosis with this bacterium may be a promising live biotherapeutic strategy for liver diseases.}, } @article {pmid37563687, year = {2023}, author = {Lai, S and Yan, Y and Pu, Y and Lin, S and Qiu, JG and Jiang, BH and Keller, MI and Wang, M and Bork, P and Chen, WH and Zheng, Y and Zhao, XM}, title = {Enterotypes of the human gut mycobiome.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {179}, pmid = {37563687}, issn = {2049-2618}, mesh = {Humans ; Aged ; *Mycobiome/genetics ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Candida ; Aging ; }, abstract = {BACKGROUND: The fungal component of the human gut microbiome, also known as the mycobiome, plays a vital role in intestinal ecology and human health. However, the overall structure of the gut mycobiome as well as the inter-individual variations in fungal composition remains largely unknown. In this study, we collected a total of 3363 fungal sequencing samples from 16 cohorts across three continents, including 572 newly profiled samples from China.

RESULTS: We identify and characterize four mycobiome enterotypes using ITS profiling of 3363 samples from 16 cohorts. These enterotypes exhibit stability across populations and geographical locations and significant correlation with bacterial enterotypes. Particularly, we notice that fungal enterotypes have a strong age preference, where the enterotype dominated by Candida (i.e., Can_type enterotype) is enriched in the elderly population and confers an increased risk of multiple diseases associated with a compromised intestinal barrier. In addition, bidirectional mediation analysis reveals that the fungi-contributed aerobic respiration pathway associated with the Can_type enterotype might mediate the association between the compromised intestinal barrier and aging.

CONCLUSIONS: We show that the human gut mycobiome has stable compositional patterns across individuals and significantly correlates with multiple host factors, such as diseases and host age. Video Abstract.}, } @article {pmid37563185, year = {2023}, author = {Xue, Z and Han, Y and Tian, W and Zhang, W}, title = {Metagenome sequencing and 103 microbial genomes from ballast water and sediments.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {536}, pmid = {37563185}, issn = {2052-4463}, mesh = {Archaea/genetics ; Bacteria/genetics ; Genome, Microbial ; *Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {The great threat of microbes carried by ballast water calls for figuring out the species composition of the ballast-tank microbial community, where the dark, cold, and anoxic tank environment might select special taxa. In this study, we reconstructed 103 metagenome-assembled genomes (MAGs), including 102 bacteria and one archaea, from four vessels on international voyages. Of these MAGs, 60 were 'near complete' (completeness >90%), 34 were >80% complete, and nine were >75% complete. Phylogenomic analysis revealed that over 70% (n = 74) of these MAGs represented new taxa at different taxonomical levels, including one order, three families, 12 genera, and 58 species. The species composition of these MAGs was most consistent with the previous reports, with the most abundant phyla being Proteobacteria (n = 69), Bacteroidota (n = 17), and Actinobacteriota (n = 7). These draft genomes provided novel data on species diversity and function in the ballast-tank microbial community, which will facilitate ballast water and sediments management.}, } @article {pmid37561193, year = {2023}, author = {Samanta, B and Sharma, S and Budhwar, R}, title = {Metagenome Analysis of Speleothem Microbiome from Subterranean Cave Reveals Insight into Community Structure, Metabolic Potential, and BGCs Diversity.}, journal = {Current microbiology}, volume = {80}, number = {10}, pages = {317}, pmid = {37561193}, issn = {1432-0991}, support = {F. No: 2021/0003//Gandhi Institute of Technology and Management/ ; }, mesh = {Caves/microbiology ; *Metagenome ; *Microbiota/genetics ; Phylogeny ; Sulfur ; *Bacteria/chemistry/classification/isolation & purification ; }, abstract = {The Borra caves, the second largest subterranean karst cave ecosystem in the Indian sub-continent, are located at the Ananthagiri hills of Araku Valley in the Alluri district of Andhra Pradesh, India. The present investigation applied a shotgun metagenomic approach to gain insights into the microbial community structure, metabolic potential, and biosynthetic gene cluster (BGC) diversity of the microbes colonizing the surface of the speleothems from the aphotic zone of Borra caves. The taxonomic analysis of the metagenome data illustrated that the speleothem-colonizing core microbial community was dominated mainly by Alpha-, Beta-, and Gamma-Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The key energy metabolic pathways analysis provides strong evidence of chemolithoautotrophic and chemoheterotrophic modes of nutrition in the speleothem-colonizing microbial community. Metagenome data suggests that sulfur reducers and sulfur-disproportionating microbes might play a vital role in energy generation in this ecosystem. Our metagenome data also suggest that the dissimilatory nitrifiers and nitrifying denitrifiers might play an essential role in conserving nitrogen pools in the ecosystem. Furthermore, metagenome-wide BGCs mining retrieved 451 putative BGCs; NRPS was the most abundant (24%). Phylogenetic analysis of the C domain of NRPS showed that sequences were distributed across all six function categories of the known C domain, including several novel subclades. For example, a novel subclade had been recovered within the LCL domain clade as a sister subclade of immunosuppressant cyclosporin encoding C domain sequences. Our result suggested that subterranean cave microbiomes might be a potential reservoir of novel microbial metabolites.}, } @article {pmid37556397, year = {2023}, author = {Hunter, S and Flaten, E and Petersen, C and Gervain, J and Werker, JF and Trainor, LJ and Finlay, BB}, title = {Babies, bugs and brains: How the early microbiome associates with infant brain and behavior development.}, journal = {PloS one}, volume = {18}, number = {8}, pages = {e0288689}, pmid = {37556397}, issn = {1932-6203}, support = {//CIHR/Canada ; }, mesh = {Humans ; Infant ; Pilot Projects ; *Gastrointestinal Microbiome ; *Microbiota ; Bacteria ; Feces/microbiology ; Brain ; }, abstract = {Growing evidence is demonstrating the connection between the microbiota gut-brain axis and neurodevelopment. Microbiota colonization occurs before the maturation of many neural systems and is linked to brain health. Because of this it has been hypothesized that the early microbiome interactions along the gut-brain axis evolved to promote advanced cognitive functions and behaviors. Here, we performed a pilot study with a multidisciplinary approach to test if the microbiota composition of infants is associated with measures of early cognitive development, in particular neural rhythm tracking; language (forward speech) versus non-language (backwards speech) discrimination; and social joint attention. Fecal samples were collected from 56 infants between four and six months of age and sequenced by shotgun metagenomic sequencing. Of these, 44 performed the behavioral Point and Gaze test to measure joint attention. Infants were tested on either language discrimination using functional near-infrared spectroscopy (fNIRS; 25 infants had usable data) or neural rhythm tracking using electroencephalogram (EEG; 15 had usable data). Infants who succeeded at the Point and Gaze test tended to have increased Actinobacteria and reduced Firmicutes at the phylum level; and an increase in Bifidobacterium and Eggerthella along with a reduction in Hungatella and Streptococcus at the genus level. Measurements of neural rhythm tracking associated negatively to the abundance of Bifidobacterium and positively to the abundance of Clostridium and Enterococcus for the bacterial abundances, and associated positively to metabolic pathways that can influence neurodevelopment, including branched chain amino acid biosynthesis and pentose phosphate pathways. No associations were found for the fNIRS language discrimination measurements. Although the tests were underpowered due to the small pilot sample sizes, potential associations were identified between the microbiome and measurements of early cognitive development that are worth exploring further.}, } @article {pmid37554329, year = {2023}, author = {Jeong, S and Cho, WK and Jo, Y and Choi, SR and Lee, N and Jeon, K and Park, MJ and Song, W and Lee, KY}, title = {Immune-checkpoint proteins, cytokines, and microbiome impact on patients with cervical insufficiency and preterm birth.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1228647}, pmid = {37554329}, issn = {1664-3224}, mesh = {*Immune Checkpoint Proteins/metabolism ; Humans ; Female ; Pregnancy ; *Microbiota ; *Cytokines/metabolism ; *Premature Birth/diagnosis ; Cerclage, Cervical ; *Cervix Uteri/microbiology ; Prospective Studies ; *Uterine Cervical Incompetence ; }, abstract = {BACKGROUND: Microenvironmental factors, including microbe-induced inflammation and immune-checkpoint proteins that modulate immune cells have been associated with both cervical insufficiency and preterm delivery. These factors are incompletely understood. This study aimed to explore and compare interactions among microbiome and inflammatory factors, such as cytokines and immune-checkpoint proteins, in patients with cervical insufficiency and preterm birth. In particular, factors related to predicting preterm birth were identified and the performance of the combination of these factors was evaluated.

METHODS: A total of 220 swab samples from 110 pregnant women, prospectively recruited at the High-Risk Maternal Neonatal Intensive Care Center, were collected between February 2020 and March 2021. This study included 63 patients with cervical insufficiency receiving cerclage and 47 control participants. Endo- and exocervical swabs and fluids were collected simultaneously. Shotgun metagenomic sequencing for the microbiome and the measurement of 34 immune-checkpoint proteins and inflammatory cytokines were performed.

RESULTS: First, we demonstrated that immune-checkpoint proteins, the key immune-regulatory molecules, could be measured in endocervical and exocervical samples. Secondly, we identified significantly different microenvironments in cervical insufficiency and preterm birth, with precise cervical locations, to provide information about practically useful cervical locations in clinical settings. Finally, the presence of Moraxella osloensis (odds ratio = 14.785; P = 0.037) and chemokine CC motif ligand 2 levels higher than 73 pg/mL (odds ratio = 40.049; P = 0.005) in endocervical samples were associated with preterm birth. Combining M. osloensis and chemokine CC motif ligand 2 yielded excellent performance for predicting preterm birth (area under the receiver operating characteristic curve = 0.846, 95% confidence interval = 0.733-0.925).

CONCLUSION: Multiple relationships between microbiomes, immune-checkpoint proteins, and inflammatory cytokines in the cervical microenvironment were identified. We focus on these factors to aid in the comprehensive understanding and therapeutic modulation of local microbial and immunologic compositions for the management of cervical insufficiency and preterm birth.}, } @article {pmid37553697, year = {2023}, author = {Chen, J and Siliceo, SL and Ni, Y and Nielsen, HB and Xu, A and Panagiotou, G}, title = {Identification of robust and generalizable biomarkers for microbiome-based stratification in lifestyle interventions.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {178}, pmid = {37553697}, issn = {2049-2618}, support = {H2020-MSCA-ITN-2018/MCCC_/Marie Curie/United Kingdom ; }, mesh = {Humans ; *Microbiota ; *Gastrointestinal Microbiome ; Biomarkers ; Diet ; Life Style ; }, abstract = {BACKGROUND: A growing body of evidence suggests that the gut microbiota is strongly linked to general human health. Microbiome-directed interventions, such as diet and exercise, are acknowledged as a viable and achievable strategy for preventing disorders and improving human health. However, due to the significant inter-individual diversity of the gut microbiota between subjects, lifestyle recommendations are expected to have distinct and highly variable impacts to the microbiome structure.

RESULTS: Here, through a large-scale meta-analysis including 1448 shotgun metagenomics samples obtained longitudinally from 396 individuals during lifestyle studies, we revealed Bacteroides stercoris, Prevotella copri, and Bacteroides vulgatus as biomarkers of microbiota's resistance to structural changes, and aromatic and non-aromatic amino acid biosynthesis as important regulator of microbiome dynamics. We established criteria for distinguishing between significant compositional changes from normal microbiota fluctuation and classified individuals based on their level of response. We further developed a machine learning model for predicting "responders" and "non-responders" independently of the type of intervention with an area under the curve of up to 0.86 in external validation cohorts of different ethnicities.

CONCLUSIONS: We propose here that microbiome-based stratification is possible for identifying individuals with highly plastic or highly resistant microbial structures. Identifying subjects that will not respond to generalized lifestyle therapeutic interventions targeting the restructuring of gut microbiota is important to ensure that primary end-points of clinical studies are reached. Video Abstract.}, } @article {pmid37553373, year = {2023}, author = {Muzeniek, T and Perera, T and Siriwardana, S and Bas, D and Bayram, F and Öruc, M and Becker-Ziaja, B and Perera, I and Weerasena, J and Handunnetti, S and Schwarz, F and Premawansa, G and Premawansa, S and Yapa, W and Nitsche, A and Kohl, C}, title = {Comparative virome analysis of individual shedding routes of Miniopterus phillipsi bats inhabiting the Wavul Galge cave, Sri Lanka.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12859}, pmid = {37553373}, issn = {2045-2322}, mesh = {Animals ; Humans ; *Chiroptera ; Phylogeny ; Virome ; Sri Lanka ; *Coronavirus/genetics ; }, abstract = {Bats are described as the natural reservoir host for a wide range of viruses. Although an increasing number of bat-associated, potentially human pathogenic viruses were discovered in the past, the full picture of the bat viromes is not explored yet. In this study, the virome composition of Miniopterus phillipsi bats (formerly known as Miniopterus fuliginosus bats in Sri Lanka) inhabiting the Wavul Galge cave, Sri Lanka, was analyzed. To assess different possible excretion routes, oral swabs, feces and urine were collected and analyzed individually by using metagenomic NGS. The data obtained was further evaluated by using phylogenetic reconstructions, whereby a special focus was set on RNA viruses that are typically associated with bats. Two different alphacoronavirus strains were detected in feces and urine samples. Furthermore, a paramyxovirus was detected in urine samples. Sequences related to Picornaviridae, Iflaviridae, unclassified Riboviria and Astroviridae were identified in feces samples and further sequences related to Astroviridae in urine samples. No viruses were detected in oral swab samples. The comparative virome analysis in this study revealed a diversity in the virome composition between the collected sample types which also represent different potential shedding routes for the detected viruses. At the same time, several novel viruses represent first reports of these pathogens from bats in Sri Lanka. The detection of two different coronaviruses in the samples indicates the potential general persistence of this virus species in M. phillipsi bats. Based on phylogenetics, the identified viruses are closely related to bat-associated viruses with comparably low estimation of human pathogenic potential. In further studies, the seasonal variation of the virome will be analyzed to identify possible shedding patterns for particular viruses.}, } @article {pmid37553333, year = {2023}, author = {Hessler, T and Huddy, RJ and Sachdeva, R and Lei, S and Harrison, STL and Diamond, S and Banfield, JF}, title = {Vitamin interdependencies predicted by metagenomics-informed network analyses and validated in microbial community microcosms.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4768}, pmid = {37553333}, issn = {2041-1723}, mesh = {Metagenomics ; Vitamins ; *Microbiota/genetics ; Metagenome/genetics ; *Comamonadaceae ; Thiamine ; }, abstract = {Metagenomic or metabarcoding data are often used to predict microbial interactions in complex communities, but these predictions are rarely explored experimentally. Here, we use an organism abundance correlation network to investigate factors that control community organization in mine tailings-derived laboratory microbial consortia grown under dozens of conditions. The network is overlaid with metagenomic information about functional capacities to generate testable hypotheses. We develop a metric to predict the importance of each node within its local network environments relative to correlated vitamin auxotrophs, and predict that a Variovorax species is a hub as an important source of thiamine. Quantification of thiamine during the growth of Variovorax in minimal media show high levels of thiamine production, up to 100 mg/L. A few of the correlated thiamine auxotrophs are predicted to produce pantothenate, which we show is required for growth of Variovorax, supporting that a subset of vitamin-dependent interactions are mutualistic. A Cryptococcus yeast produces the B-vitamin pantothenate, and co-culturing with Variovorax leads to a 90-130-fold fitness increase for both organisms. Our study demonstrates the predictive power of metagenome-informed, microbial consortia-based network analyses for identifying microbial interactions that underpin the structure and functioning of microbial communities.}, } @article {pmid37551852, year = {2023}, author = {Vientós-Plotts, AI and Ericsson, AC and Reinero, CR}, title = {The respiratory microbiota and its impact on health and disease in dogs and cats: A One Health perspective.}, journal = {Journal of veterinary internal medicine}, volume = {37}, number = {5}, pages = {1641-1655}, pmid = {37551852}, issn = {1939-1676}, mesh = {Cats ; Dogs ; Humans ; Animals ; Dysbiosis/veterinary/microbiology ; *Cat Diseases ; *One Health ; *Dog Diseases ; Lung/microbiology ; *Microbiota ; *Respiratory Tract Diseases/veterinary ; }, abstract = {Healthy lungs were long thought of as sterile, with presence of bacteria identified by culture representing contamination. Recent advances in metagenomics have refuted this belief by detecting rich, diverse, and complex microbial communities in the healthy lower airways of many species, albeit at low concentrations. Although research has only begun to investigate causality and potential mechanisms, alterations in these microbial communities (known as dysbiosis) have been described in association with inflammatory, infectious, and neoplastic respiratory diseases in humans. Similar studies in dogs and cats are scarce. The microbial communities in the respiratory tract are linked to distant microbial communities such as in the gut (ie, the gut-lung axis), allowing interplay of microbes and microbial products in health and disease. This review summarizes considerations for studying local microbial communities, key features of the respiratory microbiota and its role in the gut-lung axis, current understanding of the healthy respiratory microbiota, and examples of dysbiosis in selected respiratory diseases of dogs and cats.}, } @article {pmid37550964, year = {2023}, author = {Li, J and Ghosh, TS and McCann, R and Mallon, P and Hill, C and Draper, L and Schult, D and Fanning, LJ and Shannon, R and Sadlier, C and Horgan, M and O'Mahony, L and O'Toole, PW}, title = {Robust cross-cohort gut microbiome associations with COVID-19 severity.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2242615}, pmid = {37550964}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; *COVID-19 ; RNA, Ribosomal, 16S/genetics ; SARS-CoV-2 ; Biomarkers ; }, abstract = {Although many recent studies have examined associations between the gut microbiome and COVID-19 disease severity in individual patient cohorts, questions remain on the robustness across international cohorts of the biomarkers they reported. Here, we performed a meta-analysis of eight shotgun metagenomic studies of COVID-19 patients (comprising 1,023 stool samples) and 23 > 16S rRNA gene amplicon sequencing (16S) cohorts (2,415 total stool samples). We found that disease severity (as defined by the WHO clinical progression scale) was associated with taxonomic and functional microbiome differences. This alteration in gut microbiome configuration peaks at days 7-30 post diagnosis, after which the gut microbiome returns to a configuration that becomes more similar to that of healthy controls over time. Furthermore, we identified a core set of species that were consistently associated with disease severity across shotgun metagenomic and 16S cohorts, and whose abundance can accurately predict disease severity category of SARS-CoV-2 infected subjects, with Actinomyces oris abundance predicting population-level mortality rate of COVID-19. Additionally, we used relational diet-microbiome databases constructed from cohort studies to predict microbiota-targeted diet patterns that would modulate gut microbiota composition toward that of healthy controls. Finally, we demonstrated the association of disease severity with the composition of intestinal archaeal, fungal, viral, and parasitic communities. Collectively, this study has identified robust COVID-19 microbiome biomarkers, established accurate predictive models as a basis for clinical prognostic tests for disease severity, and proposed biomarker-targeted diets for managing COVID-19 infection.}, } @article {pmid37550758, year = {2023}, author = {Hao, C and Elias, JE and Lee, PKH and Lam, H}, title = {metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {176}, pmid = {37550758}, issn = {2049-2618}, mesh = {Animals ; Mice ; *Tandem Mass Spectrometry ; Workflow ; Proteomics ; *Microbiota/genetics ; Peptides ; }, abstract = {BACKGROUND: The high diversity and complexity of the microbial community make it a formidable challenge to identify and quantify the large number of proteins expressed in the community. Conventional metaproteomics approaches largely rely on accurate identification of the MS/MS spectra to their corresponding short peptides in the digested samples, followed by protein inference and subsequent taxonomic and functional analysis of the detected proteins. These approaches are dependent on the availability of protein sequence databases derived either from sample-specific metagenomic data or from public repositories. Due to the incompleteness and imperfections of these protein sequence databases, and the preponderance of homologous proteins expressed by different bacterial species in the community, this computational process of peptide identification and protein inference is challenging and error-prone, which hinders the comparison of metaproteomes across multiple samples.

RESULTS: We developed metaSpectraST, an unsupervised and database-independent metaproteomics workflow, which quantitatively profiles and compares metaproteomics samples by clustering experimentally observed MS/MS spectra based on their spectral similarity. We applied metaSpectraST to fecal samples collected from littermates of two different mother mice right after weaning. Quantitative proteome profiles of the microbial communities of different mice were obtained without any peptide-spectrum identification and used to evaluate the overall similarity between samples and highlight any differentiating markers. Compared to the conventional database-dependent metaproteomics analysis, metaSpectraST is more successful in classifying the samples and detecting the subtle microbiome changes of mouse gut microbiomes post-weaning. metaSpectraST could also be used as a tool to select the suitable biological replicates from samples with wide inter-individual variation.

CONCLUSIONS: metaSpectraST enables rapid profiling of metaproteomic samples quantitatively, without the need for constructing the protein sequence database or identification of the MS/MS spectra. It maximally preserves information contained in the experimental MS/MS spectra by clustering all of them first and thus is able to better profile the complex microbial communities and highlight their functional changes, as compared with conventional approaches. tag the videobyte in this section as ESM4 Video Abstract.}, } @article {pmid37550707, year = {2023}, author = {Zhu, XY and Li, Y and Xue, CX and Lidbury, IDEA and Todd, JD and Lea-Smith, DJ and Tian, J and Zhang, XH and Liu, J}, title = {Deep-sea Bacteroidetes from the Mariana Trench specialize in hemicellulose and pectin degradation typically associated with terrestrial systems.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {175}, pmid = {37550707}, issn = {2049-2618}, support = {BB/X005968/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Bacteroidetes/genetics/metabolism ; *Ecosystem ; Polysaccharides/metabolism ; Pectins/metabolism ; }, abstract = {BACKGROUND: Hadal trenches (>6000 m) are the deepest oceanic regions on Earth and depocenters for organic materials. However, how these enigmatic microbial ecosystems are fueled is largely unknown, particularly the proportional importance of complex polysaccharides introduced through deposition from the photic surface waters above. In surface waters, Bacteroidetes are keystone taxa for the cycling of various algal-derived polysaccharides and the flux of carbon through the photic zone. However, their role in the hadal microbial loop is almost unknown.

RESULTS: Here, culture-dependent and culture-independent methods were used to study the potential of Bacteroidetes to catabolize diverse polysaccharides in Mariana Trench waters. Compared to surface waters, the bathypelagic (1000-4000 m) and hadal (6000-10,500 m) waters harbored distinct Bacteroidetes communities, with Mesoflavibacter being enriched at ≥ 4000 m and Bacteroides and Provotella being enriched at 10,400-10,500 m. Moreover, these deep-sea communities possessed distinct gene pools encoding for carbohydrate active enzymes (CAZymes), suggesting different polysaccharide sources are utilised in these two zones. Compared to surface counterparts, deep-sea Bacteroidetes showed significant enrichment of CAZyme genes frequently organized into polysaccharide utilization loci (PULs) targeting algal/plant cell wall polysaccharides (i.e., hemicellulose and pectin), that were previously considered an ecological trait associated with terrestrial Bacteroidetes only. Using a hadal Mesoflavibacter isolate (MTRN7), functional validation of this unique genetic potential was demonstrated. MTRN7 could utilize pectic arabinans, typically associated with land plants and phototrophic algae, as the carbon source under simulated deep-sea conditions. Interestingly, a PUL we demonstrate is likely horizontally acquired from coastal/land Bacteroidetes was activated during growth on arabinan and experimentally shown to encode enzymes that hydrolyze arabinan at depth.

CONCLUSIONS: Our study implies that hadal Bacteroidetes exploit polysaccharides poorly utilized by surface populations via an expanded CAZyme gene pool. We propose that sinking cell wall debris produced in the photic zone can serve as an important carbon source for hadal heterotrophs and play a role in shaping their communities and metabolism. Video Abstract.}, } @article {pmid37550406, year = {2023}, author = {Doane, MP and Reed, MB and McKerral, J and Farias Oliveira Lima, L and Morris, M and Goodman, AZ and Johri, S and Papudeshi, B and Dillon, T and Turnlund, AC and Peterson, M and Mora, M and de la Parra Venegas, R and Pillans, R and Rohner, CA and Pierce, SJ and Legaspi, CG and Araujo, G and Ramirez-Macias, D and Edwards, RA and Dinsdale, EA}, title = {Emergent community architecture despite distinct diversity in the global whale shark (Rhincodon typus) epidermal microbiome.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12747}, pmid = {37550406}, issn = {2045-2322}, mesh = {Animals ; *Sharks/physiology ; Epidermis ; Epidermal Cells ; *Microbiota/genetics ; Metagenome ; }, abstract = {Microbiomes confer beneficial physiological traits to their host, but microbial diversity is inherently variable, challenging the relationship between microbes and their contribution to host health. Here, we compare the diversity and architectural complexity of the epidermal microbiome from 74 individual whale sharks (Rhincodon typus) across five aggregations globally to determine if network properties may be more indicative of the microbiome-host relationship. On the premise that microbes are expected to exhibit biogeographic patterns globally and that distantly related microbial groups can perform similar functions, we hypothesized that microbiome co-occurrence patterns would occur independently of diversity trends and that keystone microbes would vary across locations. We found that whale shark aggregation was the most important factor in discriminating taxonomic diversity patterns. Further, microbiome network architecture was similar across all aggregations, with degree distributions matching Erdos-Renyi-type networks. The microbiome-derived networks, however, display modularity indicating a definitive microbiome structure on the epidermis of whale sharks. In addition, whale sharks hosted 35 high-quality metagenome assembled genomes (MAGs) of which 25 were present from all sample locations, termed the abundant 'core'. Two main MAG groups formed, defined here as Ecogroup 1 and 2, based on the number of genes present in metabolic pathways, suggesting there are at least two important metabolic niches within the whale shark microbiome. Therefore, while variability in microbiome diversity is high, network structure and core taxa are inherent characteristics of the epidermal microbiome in whale sharks. We suggest the host-microbiome and microbe-microbe interactions that drive the self-assembly of the microbiome help support a functionally redundant abundant core and that network characteristics should be considered when linking microbiomes with host health.}, } @article {pmid37548643, year = {2023}, author = {Li, Z and Ju, Y and Xia, J and Zhang, Z and Zhen, H and Tong, X and Sun, Y and Lu, H and Zong, Y and Chen, P and Cai, K and Wang, Z and Yang, H and Wang, J and Wang, J and Hou, Y and Jin, X and Zhang, T and Zhang, W and Xu, X and Xiao, L and Guo, R and Nie, C}, title = {Integrated Human Skin Bacteria Genome Catalog Reveals Extensive Unexplored Habitat-Specific Microbiome Diversity and Function.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {10}, number = {28}, pages = {e2300050}, pmid = {37548643}, issn = {2198-3844}, support = {2022ZD0211600//STI2030-Major Projects/ ; 2019-I2M-5-066//CAMS Innovation Fund for Medical Sciences/ ; }, mesh = {Humans ; *Skin/microbiology/metabolism ; *Microbiota/genetics ; *Genome, Bacterial/genetics ; *Bacteria/genetics/classification ; Metagenome/genetics ; Ecosystem ; Metagenomics/methods ; }, abstract = {The skin is the largest organ in the human body. Various skin environments on its surface constitutes a complex ecosystem. One of the characteristics of the skin micro-ecosystem is low biomass, which greatly limits a comprehensive identification of the microbial species through sequencing. In this study, deep-shotgun sequencing (average 21.5 Gigabyte (Gb)) from 450 facial samples and publicly available skin metagenomic datasets of 2069 samples to assemble a Unified Human Skin Genome (UHSG) catalog is integrated. The UHSG encompasses 813 prokaryotic species derived from 5779 metagenome-assembled genomes, among which 470 are novel species covering 20 phyla with 1385 novel assembled genomes. Based on the UHSG, the core functions of the skin microbiome are described and the differences in amino acid metabolism, carbohydrate metabolism, and drug resistance functions among different phyla are identified. Furthermore, analysis of secondary metabolites of the near-complete genomes further find 1220 putative novel secondary metabolites, several of which are found in previously unknown genomes. Single nucleotide variant (SNV) reveals a possible skin protection mechanism: the negative selection process of the skin environment to conditional pathogens. UHSG offers a convenient reference database that will facilitate a more in-depth understanding of the role of skin microorganisms in the skin.}, } @article {pmid37548515, year = {2024}, author = {Hakimzadeh, A and Abdala Asbun, A and Albanese, D and Bernard, M and Buchner, D and Callahan, B and Caporaso, JG and Curd, E and Djemiel, C and Brandström Durling, M and Elbrecht, V and Gold, Z and Gweon, HS and Hajibabaei, M and Hildebrand, F and Mikryukov, V and Normandeau, E and Özkurt, E and M Palmer, J and Pascal, G and Porter, TM and Straub, D and Vasar, M and Větrovský, T and Zafeiropoulos, H and Anslan, S}, title = {A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses.}, journal = {Molecular ecology resources}, volume = {24}, number = {5}, pages = {e13847}, pmid = {37548515}, issn = {1755-0998}, support = {P20 GM103449/GM/NIGMS NIH HHS/United States ; EXC2124//Deutsche Forschungsgemeinschaft (DFG)/ ; MOBTP198//European Regional Development Fund and the programme Mobilitas Pluss/ ; //Genome Canada and Ontario Genomics/ ; U24 CA248454/CA/NCI NIH HHS/United States ; P20GM103449/GM/NIGMS NIH HHS/United States ; 21-17749S//Grantová Agentura České Republiky/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Computational Biology/methods ; *Software ; High-Throughput Nucleotide Sequencing/methods ; Archaea/genetics/classification ; DNA, Environmental/genetics ; Metagenomics/methods ; Data Analysis ; Bacteria/genetics/classification ; Eukaryota/genetics/classification ; }, abstract = {Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high-throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon-specific primers have been developed, extending the usability of metabarcoding across archaea, bacteria and eukaryotes. Accordingly, a multitude of metabarcoding data analysis tools and pipelines have also been developed. Often, several developed workflows are designed to process the same amplicon sequencing data, making it somewhat puzzling to choose one among the plethora of existing pipelines. However, each pipeline has its own specific philosophy, strengths and limitations, which should be considered depending on the aims of any specific study, as well as the bioinformatics expertise of the user. In this review, we outline the input data requirements, supported operating systems and particular attributes of thirty-two amplicon processing pipelines with the goal of helping users to select a pipeline for their metabarcoding projects.}, } @article {pmid37548332, year = {2023}, author = {Wu, Y and Zhuang, J and Zhang, Q and Zhao, X and Chen, G and Han, S and Hu, B and Wu, W and Han, S}, title = {Aging characteristics of colorectal cancer based on gut microbiota.}, journal = {Cancer medicine}, volume = {12}, number = {17}, pages = {17822-17834}, pmid = {37548332}, issn = {2045-7634}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/pathology ; Bacteria/genetics ; *Microbiota ; Aging ; }, abstract = {BACKGROUND: Aging is one of the factors leading to cancer. Gut microbiota is related to aging and colorectal cancer (CRC).

METHODS: A total of 11 metagenomic data sets related to CRC were collected from the R package curated Metagenomic Data. After batch effect correction, healthy individuals and CRC samples were divided into three age groups. Ggplot2 and Microbiota Process packages were used for visual description of species composition and PCA in healthy individuals and CRC samples. LEfSe analysis was performed for species relative abundance data in healthy/CRC groups according to age. Spearman correlation coefficient of age-differentiated bacteria in healthy individuals and CRC samples was calculated separately. Finally, the age prediction model and CRC risk prediction model were constructed based on the age-differentiated bacteria.

RESULTS: The structure and composition of the gut microbiota were significantly different among the three groups. For example, the abundance of Bacteroides vulgatus in the old group was lower than that in the other two groups, the abundance of Bacteroides fragilis increased with aging. In addition, seven species of bacteria whose abundance increases with aging were screened out. Furthermore, the abundance of pathogenic bacteria (Escherichia_coli, Butyricimonas_virosa, Ruminococcus_bicirculans, Bacteroides_fragilis and Streptococcus_vestibularis) increased with aging in CRCs. The abundance of probiotics (Eubacterium_eligens) decreased with aging in CRCs. The age prediction model for healthy individuals based on the 80 age-related differential bacteria and model of CRC patients based on the 58 age-related differential bacteria performed well, with AUC of 0.79 and 0.71, respectively. The AUC of CRC risk prediction model based on 45 disease differential bacteria was 0.83. After removing the intersection between the disease-differentiated bacteria and the age-differentiated bacteria from the healthy samples, the AUC of CRC risk prediction model based on remaining 31 bacteria was 0.8. CRC risk prediction models for each of the three age groups showed no significant difference in accuracy (young: AUC=0.82, middle: AUC=0.83, old: AUC=0.85).

CONCLUSION: Age as a factor affecting microbial composition should be considered in the application of gut microbiota to predict the risk of CRC.}, } @article {pmid37545858, year = {2023}, author = {Yuan, X and Xie, L and Shi, Z and Zhou, M}, title = {Application of mNGS in the study of pulmonary microbiome in pneumoconiosis complicated with pulmonary infection patients and exploration of potential biomarkers.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1200157}, pmid = {37545858}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *Pneumonia ; *Microbiota ; High-Throughput Nucleotide Sequencing ; Biomarkers ; Lung ; Sensitivity and Specificity ; Metagenomics ; }, abstract = {BACKGROUND: Pneumoconiosis patients have a high prevalence of pulmonary infections, which can complicate diagnosis and treatment. And there is no comprehensive study of the microbiome of patients with pneumoconiosis. The application of metagenomic next-generation sequencing (mNGS) fills the gap to some extent by analyzing the lung microbiota of pneumoconiosis population while achieving accurate diagnosis.

METHODS: We retrospectively analyzed 44 patients with suspected pneumoconiosis complicated with pulmonary infection between Jan 2020 and Nov 2022. Bronchoalveolar lavage fluid (BALF) specimens from 44 patients were collected and tested using the mNGS technology.

RESULTS: Among the lung microbiome of pneumoconiosis patients with complicated pulmonary infection (P group), the most frequently detected bacteria and fungi at the genus level were Streptococcus and Aspergillus, at the species level were Streptococcus pneumoniae and Aspergillus flavus, respectively, and the most frequently detected DNA virus was Human gammaherpesvirus 4. There was no significant difference in α diversity between the P group and the non-pneumoconiosis patients complicated with pulmonary infection group (Non-P group) in pulmonary flora, while P< 0.01 for β diversity analysis, and the differential species between the two groups were Mycobacterium colombiense and Fusobacterium nucleatum. In addition, we monitored a high distribution of Malassezia and Pneumocystis in the P group, while herpes virus was detected in the majority of samples.

CONCLUSIONS: Overall, we not only revealed a comprehensive lung microbiome profile of pneumoconiosis patients, but also compared the differences between their microbiome and that of non-pneumoconiosis complicated with pulmonary infection patients. This provides a good basis for a better understanding of the relationship between pneumoconiosis and microorganisms, and for the search of potential biomarkers.}, } @article {pmid37541802, year = {2023}, author = {Pfisterer, N and Ammer-Herrmenau, C and Antweiler, K and Küffer, S and Ellenrieder, V and Neesse, A}, title = {Dynamics of intestinal and intratumoral microbiome signatures in genetically engineered mice and human pancreatic ductal adenocarcinoma.}, journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]}, volume = {23}, number = {6}, pages = {663-673}, doi = {10.1016/j.pan.2023.07.008}, pmid = {37541802}, issn = {1424-3911}, mesh = {Humans ; Mice ; Animals ; In Situ Hybridization, Fluorescence ; RNA, Ribosomal, 16S ; *Pancreatic Neoplasms/genetics/pathology ; *Carcinoma, Pancreatic Ductal/genetics/pathology ; Disease Models, Animal ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Emerging evidence has recently revealed a prominent role of the microbiome in pancreatic ductal adenocarcinoma (PDAC). However, while most observations were made in patients, mouse models still require a precise characterization of their disease-related microbiome to employ them for mechanistic and interventional preclinical studies.

METHODS: To investigate the fecal and tumoral microbiome of LSL-Kras[G12D/+];LSL-Trp53[R172H/+];Pdx-1-Cre (KPC) and control (CTRL) mice, Oxford Nanopore sequencing was applied. Feces were collected from 10 KPC mice and 10 CTRLs at 3 timepoints (6 weeks, 12 weeks, and when tumor-bearing (KPC) or 6 months (CTRL), respectively). Metagenomic sequencing was performed on feces DNA. KPC tumor and healthy pancreas DNA samples were subjected to 16S rRNA gene sequencing. Bacterial marker components were detected in KPC tumor tissue over time by fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC).

RESULTS: Murine fecal samples showed a significantly different microbiome compared to age-matched healthy CTRLs regarding beta diversity (p = 0.001, R2 = 0.2-0.25 for Bray-Curtis). Adjusted human PDAC classifiers predicted disease status from feces of KPC mice achieving area under the receiver operating characteristic (AUROC) values of 80%. Furthermore, KPC tumors harbored significantly more bacterial components than healthy pancreas. Also the microbial composition differs significantly between KPC tumors and healthy pancreas tissue (p = 0.042 for Bray-Curtis). Microbiota found highly abundant in human PDAC samples were considerably more abundant in KPC tumors as compared to healthy pancreas samples (p-value <0.001).

CONCLUSION: KPC fecal samples show similarities with the microbial composition of stool samples from human PDAC patients.}, } @article {pmid37541570, year = {2023}, author = {Liu, YC and Chen, TH and Huang, YF and Chen, CL and Nai, YS}, title = {Investigation of the fall armyworm (Spodoptera frugiperda) gut microbiome and entomopathogenic fungus-induced pathobiome.}, journal = {Journal of invertebrate pathology}, volume = {200}, number = {}, pages = {107976}, doi = {10.1016/j.jip.2023.107976}, pmid = {37541570}, issn = {1096-0805}, mesh = {Animals ; Spodoptera ; *Gastrointestinal Microbiome ; Zea mays ; *Beauveria ; Larva ; }, abstract = {The gut microflora plays an important role in insect development and physiology. The gut bacterial microbiome of the fall armyworm (FAW), Spodoptera frugiperda, in both cornfield and laboratory-reared populations was investigated using a 16S metagenomic approach. The alpha- and beta-diversity of the cornfield FAW populations varied among sampling sites and were higher than those of the laboratory-reared FAW population, indicating that different diets and environments influence the gut bacterial composition. To better understand the interaction between the microbiome and entomopathogenic fungi (EPF), FAWs from organic and conventionally managed corn fields and from the laboratory-reared colony were inoculated with Beauveria bassiana NCHU-153 (Bb-NCHU-153). A longer median lethal time (LT50) was observed in the Bb-NCHU-153-infected cornfield FAW population than in the laboratory-reared FAWs. In terms of the microbiome, three Bb-NCHU-153-infected FAW groups showed different gut bacterial compositions compared to noninfected FAW. Further investigation of the cooccurrence network and linear discriminant analysis (LDA) of effect size (LEfSe) revealed that the enriched bacterial genera, such as Enterococcus, Serratia, Achromobacter, and Tsukamurella, in the gut might play the role of opportunistic pathogens after fungal infection; in contrast, some gut bacteria of Methylobacterium, Marinomonas, Paenochrobactrum, Pseudomonas, Acinetobacter, Delftia, Dietzia, Gordonia, Leucobacter, Paracoccus, and Stenotrophomonas might be probiotics against EPF infection. These results indicated that EPF infection can change the gut bacterial composition and lead to a pathobiome in the FAW and that some bacterial species might protect the FAW from EPF infection. These findings could be applied to the design of pathobiome-inducing biocontrol strategies.}, } @article {pmid37533931, year = {2023}, author = {Zou, Y and Zeng, S and Chen, M and Li, S and Fu, Q and Zhou, S and Zhou, J}, title = {Gut microbiota in children with split-dose bowel preparations revealed by metagenomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1202007}, pmid = {37533931}, issn = {2235-2988}, mesh = {Humans ; Child ; *Cathartics/adverse effects ; *Gastrointestinal Microbiome ; Metagenomics ; Polyethylene Glycols ; Colonoscopy/adverse effects ; }, abstract = {OBJECTIVE: Split-dose polyethylene glycol (PEG) is routinely used for bowel preparation before colonoscopy. This study aimed to investigate the composition of gut microbiota and its functions in pediatric patients undergoing split-dose PEG bowel preparation for colonoscopy to understand the stability and resilience of gut microbiota.

MATERIAL AND METHODS: From September to December 2021, 19 pediatric patients were enrolled at Shenzhen Children's Hospital and 76 samples (4 time points) were analyzed using metagenomics. Time points included Time_1 (one day before bowel preparation), Time_2 (one day after colonoscopy), Time_3 (two weeks after bowel preparation), and Time_4 (four weeks after bowel preparation).

RESULT: Alpha diversity comparison at both the species and gene levels showed a decrease in community richness after colonoscopy, with little statistical significance. However, the Shannon diversity index significantly decreased (P<0.05) and gradually returned to pre-preparation levels at two weeks after bowel preparation. The genus level analysis showed six genera (Eubacterium, Escherichia, Intertinibacter, Veillonella, Ruminococcaceae unclassified, and Coprobacillus) significantly different across the four time periods. Additionally, at the species level, the abundance of Escherichia coli, Bacteroides fragilis, and Veillonella parvula significantly increased at one day after colonoscopy before gradually decreasing at two weeks after bowel preparation. In contrast, the abundance of Intertinibacter bartlettii decreased at one day after colonoscopy but then recovered at two weeks after bowel preparation, reaching the preoperative level at four weeks after bowel preparation. Furthermore, five functional pathways (base excision repair, biosynthesis of ansamycins, biosynthesis of siderophore group nonribosomal peptide, flavonoid biosynthesis, and biosynthesis of type II polyketide products) were significantly different across the four time periods, with recovery at two weeks after bowel preparation and reaching preoperative levels at four weeks after bowel preparation.

CONCLUSIONS: Gut microbiota at the genus level, species level, and functional pathways are impacted in pediatric patients undergoing split-dose PEG bowel preparation and colonoscopy, with recovery two weeks following bowel preparation. However, the phylum level was not impacted. Modifications in gut microbiota composition and function may be investigated in future studies of bowel preparation. This study highlights the stability and resilience of gut microbiota among pediatric patients during bowel preparation.}, } @article {pmid37532062, year = {2023}, author = {Liu, J and Yu, J and Tan, Y and Dang, R and Zhou, M and Hernández, M and Lichtfouse, E and Xiao, L}, title = {Biomethane is produced by acetate cleavage, not direct interspecies electron transfer: genome-centric view and carbon isotope.}, journal = {Bioresource technology}, volume = {387}, number = {}, pages = {129589}, doi = {10.1016/j.biortech.2023.129589}, pmid = {37532062}, issn = {1873-2976}, mesh = {Electrons ; Carbon Isotopes ; Carbon Dioxide/metabolism ; Bacteria/metabolism ; Acetates ; Anaerobiosis ; *Microbiota ; *Euryarchaeota/metabolism ; Methane/metabolism ; }, abstract = {Understanding the source of methane (CH4) is of great significance for improving the anaerobic fermentation efficiency in bioengineering, and for mitigating the emission potential of natural ecosystems. Microbes involved in the process named direct interspecies electron transfer coupling with CO2 reduction, i.e., electrons released from electroactive bacteria to reduce CO2 into CH4, have attracted considerable attention for wastewater treatment in the past decade. However, how the synergistic effect of microbiota contributes to this anaerobic carbon metabolism accompanied by CH4 production still remains poorly understood, especial for wastewater with antibiotic exposure. Results show that enhancing lower-abundant acetoclastic methanogens and acetogenic bacteria, rather than electroactive bacteria, contributed to CH4 production, based on a metagenome-assembled genomes network analysis. Natural and artificial isotope tracing of CH4 further confirmed that CH4 mainly originated from acetoclastic methanogenesis. These findings reveal the contribution of direct acetate cleavage (acetoclastic methanogenesis) and provide insightsfor further regulation of methanogenic strategies.}, } @article {pmid37528534, year = {2024}, author = {Hu, X and Yu, L and Li, Y and Li, X and Zhao, Y and Xiong, L and Ai, J and Chen, Q and Wang, X and Chen, X and Ba, Y and Wang, Y and Wu, X}, title = {Piperine improves levodopa availability in the 6-OHDA-lesioned rat model of Parkinson's disease by suppressing gut bacterial tyrosine decarboxylase.}, journal = {CNS neuroscience & therapeutics}, volume = {30}, number = {2}, pages = {e14383}, pmid = {37528534}, issn = {1755-5949}, support = {82173943//National Natural Science Foundation of China/ ; 81473333//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Rats ; Animals ; Levodopa/pharmacology ; *Parkinson Disease/drug therapy ; Oxidopamine/toxicity ; Tyrosine Decarboxylase ; *Gastrointestinal Microbiome ; Dopamine/metabolism ; Bacteria/metabolism ; Antiparkinson Agents/pharmacology/therapeutic use ; Disease Models, Animal ; *Alkaloids ; *Piperidines ; *Benzodioxoles ; *Polyunsaturated Alkamides ; }, abstract = {AIM: Tyrosine decarboxylase (TDC) presented in the gut-associated strain Enterococcus faecalis can convert levodopa (L-dopa) into dopamine (DA), and its increased abundance would potentially minimize the availability and efficacy of L-dopa. However, the known human decarboxylase inhibitors are ineffective in this bacteria-mediated conversion. This study aims to investigate the inhibition of piperine (PIP) on L-dopa bacterial metabolism and evaluates the synergistic effect of PIP combined with L-dopa on Parkinson's disease (PD).

METHODS: Metagenomics sequencing was adopted to determine the regulation of PIP on rat intestinal microbiota structure, especially on the relative abundance of E. faecalis. Then, the inhibitory effects of PIP on L-dopa conversion and TDC expression of E. faecalis were tested in vitro. We examined the synergetic effect of the combination of L-dopa and PIP on 6-hydroxydopamine (6-OHDA)-lesioned rats and tested the regulations of L-dopa bioavailability and brain DA level by pharmacokinetics study and MALDI-MS imaging. Finally, we evaluated the microbiota-dependent improvement effect of PIP on L-dopa availability using pseudo-germ-free and E. faecalis-transplanted rats.

RESULTS: We found that PIP combined with L-dopa could better ameliorate the move disorders of 6-OHDA-lesioned rats by remarkably improving L-dopa availability and brain DA level than L-dopa alone, which was associated with the effect of PIP on suppressing the bacterial decarboxylation of L-dopa via effectively downregulating the abnormal high abundances of E. faecalis and TDC in 6-OHDA-lesioned rats.

CONCLUSION: Oral administration of L-dopa combined with PIP can improve L-dopa availability and brain DA level in 6-OHDA-lesioned rats by suppressing intestinal bacterial TDC.}, } @article {pmid37528457, year = {2023}, author = {Hoedt, EC and Hueston, CM and Cash, N and Bongers, RS and Keane, JM and van Limpt, K and Ben Amor, K and Knol, J and MacSharry, J and van Sinderen, D}, title = {A synbiotic mixture of selected oligosaccharides and bifidobacteria assists murine gut microbiota restoration following antibiotic challenge.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {168}, pmid = {37528457}, issn = {2049-2618}, support = {SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Humans ; Infant ; Animals ; Pregnancy ; Mice ; Female ; *Synbiotics ; *Gastrointestinal Microbiome ; Bifidobacterium ; Anti-Bacterial Agents/pharmacology ; Cesarean Section ; Clindamycin ; Oligosaccharides ; }, abstract = {BACKGROUND: Typically, animal models studying gastrointestinal microbiotas compromised in early life have employed either germ-free animals or mice treated with a cocktail of antibiotics. Such studies intend to mimic scenarios of infants born by caesarean section and/or subjected to antibiotic treatment. However, the antibiotics used in these studies are rarely prescribed to infants. Therefore, an early life model was developed in which the murine gastrointestinal microbiota was severely disrupted by clindamycin treatment.

RESULTS: In this mouse model, we investigated the extent supplementation with a synbiotic mixture of prebiotics, being scGOS/lcFOS with the human milk oligosaccharide 2'-Fucosyllactose (2'-FL), in combination with or without single strain or mix of "infant type" bifidobacteria, can rescue an antibiotic-compromised microbiota. Shotgun metagenomic sequencing showed that the microbiota was severely disrupted by the clindamycin challenge. No recovery was observed 3 weeks post-challenge in the scGOS/lcFOS/2'FL group, while the group that received the synbiotic treatment of scGOS/lcFOS/2'-FL with Bifidobacterium breve NRBB01 showed partial recovery. Strikingly in the scGOS/lcFOS/2'-FL group receiving the mixture of bifidobacteria resulted in a recovery of the microbiota disruption. Histological analyses showed that the clindamycin-treated animals at the end of the experiment still suffered from mild oedema and villi/colonic crypt irregularities which was ameliorated by the synbiotic intervention.

CONCLUSION: Our study demonstrates that supplementation of synbiotic mixture of scGOS/lcFOS/2'-FL in combination with a specific mix of infant-type bifidobacterial strains is able to partially revive an antibiotic-perturbed gastrointestinal microbiota. Video Abstract.}, } @article {pmid37528259, year = {2023}, author = {Bermingham, KM and Stensrud, S and Asnicar, F and Valdes, AM and Franks, PW and Wolf, J and Hadjigeorgiou, G and Davies, R and Spector, TD and Segata, N and Berry, SE and Hall, WL}, title = {Exploring the relationship between social jetlag with gut microbial composition, diet and cardiometabolic health, in the ZOE PREDICT 1 cohort.}, journal = {European journal of nutrition}, volume = {62}, number = {8}, pages = {3135-3147}, pmid = {37528259}, issn = {1436-6215}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/W026813/1/MRC_/Medical Research Council/United Kingdom ; 212904/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Male ; *Cardiovascular Diseases/complications ; Circadian Rhythm ; Diet ; *Gastrointestinal Microbiome ; Jet Lag Syndrome/complications ; Sleep ; }, abstract = {PURPOSE: In this study, we explore the relationship between social jetlag (SJL), a parameter of circadian misalignment, and gut microbial composition, diet and cardiometabolic health in the ZOE PREDICT 1 cohort (NCT03479866).

METHODS: We assessed demographic, diet, cardiometabolic, stool metagenomics and postprandial metabolic measures (n = 1002). We used self-reported habitual sleep (n = 934) to calculate SJL (difference in mid-sleep time point of ≥ 1.5 h on week versus weekend days). We tested group differences (SJL vs no-SJL) in cardiometabolic markers and diet (ANCOVA) adjusting for sex, age, BMI, ethnicity, and socio-economic status. We performed comparisons of gut microbial composition using machine learning and association analyses on the species level genome bins present in at least 20% of the samples.

RESULTS: The SJL group (16%, n = 145) had a greater proportion of males (39% vs 25%), shorter sleepers (average sleep < 7 h; 5% vs 3%), and were younger (38.4 ± 11.3y vs 46.8 ± 11.7y) compared to the no-SJL group. SJL was associated with a higher relative abundance of 9 gut bacteria and lower abundance of 8 gut bacteria (q < 0.2 and absolute Cohen's effect size > 0.2), in part mediated by diet. SJL was associated with unfavourable diet quality (less healthful Plant-based Diet Index), higher intakes of potatoes and sugar-sweetened beverages, and lower intakes of fruits, and nuts, and slightly higher markers of inflammation (GlycA and IL-6) compared with no-SJL (P < 0.05 adjusted for covariates); rendered non-significant after multiple testing adjustments.

CONCLUSIONS: Novel associations between SJL and a more disadvantageous gut microbiome in a cohort of predominantly adequate sleepers highlight the potential implications of SJL for health.}, } @article {pmid37526383, year = {2023}, author = {Esteban-Torres, M and Ruiz, L and Rossini, V and Nally, K and van Sinderen, D}, title = {Intracellular glycogen accumulation by human gut commensals as a niche adaptation trait.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2235067}, pmid = {37526383}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Gastrointestinal Tract/microbiology ; Bacteria/genetics ; *Microbiota ; Glycogen/metabolism ; }, abstract = {The human gut microbiota is a key contributor to host metabolism and physiology, thereby impacting in various ways on host health. This complex microbial community has developed many metabolic strategies to colonize, persist and survive in the gastrointestinal environment. In this regard, intracellular glycogen accumulation has been associated with important physiological functions in several bacterial species, including gut commensals. However, the role of glycogen storage in shaping the composition and functionality of the gut microbiota offers a novel perspective in gut microbiome research. Here, we review what is known about the enzymatic machinery and regulation of glycogen metabolism in selected enteric bacteria, while we also discuss its potential impact on colonization and adaptation to the gastrointestinal tract. Furthermore, we survey the presence of such glycogen biosynthesis pathways in gut metagenomic data to highlight the relevance of this metabolic trait in enhancing survival in the highly competitive and dynamic gut ecosystem.}, } @article {pmid37525141, year = {2023}, author = {Oliveros, A and Terraube, J and Levengood, AL and Powell, D and Frère, CH}, title = {Influence of scat ageing on the gut microbiome: how old is too old?.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {427}, pmid = {37525141}, issn = {1471-2164}, mesh = {Animals ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Microbiota ; Animals, Wild ; *Phascolarctidae ; }, abstract = {BACKGROUND: The study of the host-microbiome by the collection of non-invasive samples has the potential to become a powerful tool for conservation monitoring and surveillance of wildlife. However, multiple factors can bias the quality of data recovered from scats, particularly when field-collected samples are used given that the time of defecation is unknown. Previous studies using scats have shown that the impact of aerobic exposure on the microbial composition is species-specific, leading to different rates of change in microbial communities. However, the impact that this aging process has on the relationship between the bacterial and fungal composition has yet to be explored. In this study, we measured the effects of time post-defecation on bacterial and fungal compositions in a controlled experiment using scat samples from the endangered koala (Phascolarctos cinereus).

RESULTS: We found that the bacterial composition remained stable through the scat aging process, while the fungal composition did not. The absence of an increase in facultative anaerobes and the stable population of obligate anaerobic bacteria were likely due to our sampling from the inner portion of the scat. We report a cluster of fungal taxa that colonises scats after defecation which can dilute the genetic material from the autochthonous mycoflora and inhibit recovery.

CONCLUSION: We emphasize the need to preserve the integrity of scat samples collected in the wild and combat the effects of time and provide strategies for doing so.}, } @article {pmid37524802, year = {2023}, author = {Garner, RE and Kraemer, SA and Onana, VE and Fradette, M and Varin, MP and Huot, Y and Walsh, DA}, title = {A genome catalogue of lake bacterial diversity and its drivers at continental scale.}, journal = {Nature microbiology}, volume = {8}, number = {10}, pages = {1920-1934}, pmid = {37524802}, issn = {2058-5276}, mesh = {Humans ; *Lakes/microbiology ; RNA, Ribosomal, 16S/genetics ; Canada ; Bacteria/genetics ; *Microbiota/genetics ; }, abstract = {Lakes are heterogeneous ecosystems inhabited by a rich microbiome whose genomic diversity is poorly defined. We present a continental-scale study of metagenomes representing 6.5 million km[2] of the most lake-rich landscape on Earth. Analysis of 308 Canadian lakes resulted in a metagenome-assembled genome (MAG) catalogue of 1,008 mostly novel bacterial genomospecies. Lake trophic state was a leading driver of taxonomic and functional diversity among MAG assemblages, reflecting the responses of communities profiled by 16S rRNA amplicons and gene-centric metagenomics. Coupling the MAG catalogue with watershed geomatics revealed terrestrial influences of soils and land use on assemblages. Agriculture and human population density were drivers of turnover, indicating detectable anthropogenic imprints on lake bacteria at the continental scale. The sensitivity of bacterial assemblages to human impact reinforces lakes as sentinels of environmental change. Overall, the LakePulse MAG catalogue greatly expands the freshwater genomic landscape, advancing an integrative view of diversity across Earth's microbiomes.}, } @article {pmid37524154, year = {2023}, author = {Yan, J and Duan, W and Gao, Q and Mao, T and Wang, M and Duan, J and Li, J}, title = {ENPP2 inhibitor improves proliferation in AOM/DSS-induced colorectal cancer mice via remodeling the gut barrier function and gut microbiota composition.}, journal = {Pharmacological research}, volume = {195}, number = {}, pages = {106877}, doi = {10.1016/j.phrs.2023.106877}, pmid = {37524154}, issn = {1096-1186}, mesh = {Animals ; Mice ; Azoxymethane/adverse effects ; Cell Proliferation ; Colitis/chemically induced ; *Colorectal Neoplasms/drug therapy/metabolism ; Dextran Sulfate/pharmacology ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; *Phosphoric Diester Hydrolases/metabolism ; }, abstract = {In our previous multicenter study, we delineated the inherent metabolic features of colorectal cancer (CRC). Therein, we identified a member of the ectonucleotide pyrophosphatase/ phosphodiesterase family (ENPP2) as a significant differential metabolite of CRC. In this study, the role of ENPP2 in CRC has been demonstrated using established in vitro and in vivo models including ENPP2 gene knockdown, and use of the ENPP2 inhibitor, GLPG1690. We found that CRC proliferation was decreased after either ENPP2 gene knockdown or use of ENPP2 inhibitors. We further evaluated the role of GLPG1690 in AOM/DSS-induced CRC mice via intestinal barrier function, macrophage polarization, inflammatory response and microbial homeostasis. Results of immunofluorescence staining and Western blotting showed that GLPG1690 can restore gut-barrier function by increasing the expression of tight junction proteins, claudin-1, occludin and ZO-1. M2 tumor-associated macrophage polarization and colonic inflammation were attenuated after treatment with GLPG1690 using the Azoxymethane/Dextran Sodium Sulfate (AOM/DSS) model. Moreover, 16 S rDNA pyrosequencing and metagenomic analysis showed that GLPG1690 could alleviate gut dysbiosis in mice. Furthermore, administration of GLPG1690 with antibiotics as well as fecal microbiota transplantation assays demonstrated a close link between the efficacy of GLPG1690 and the gut microbiota composition. Finally, results of metabolomic analysis implicated mainly the gut microbiota-derived metabolites of aromatic amino acids in CRC progression. These findings may provide novel insights into the development of small-molecule ENPP2 inhibitors for the treatment of CRC.}, } @article {pmid37521121, year = {2023}, author = {Khatiebi, S and Kiprotich, K and Onyando, Z and Wekesa, C and Chi, CN and Mulambalah, C and Okoth, P}, title = {Shotgun Metagenomic Analyses of Microbial Assemblages in the Aquatic Ecosystem of Winam Gulf of Lake Victoria, Kenya Reveals Multiclass Pollution.}, journal = {BioMed research international}, volume = {2023}, number = {}, pages = {3724531}, pmid = {37521121}, issn = {2314-6141}, mesh = {Animals ; Humans ; Lakes ; Ecosystem ; Kenya ; Plastics ; *Water Pollutants, Chemical/analysis ; Environmental Monitoring ; *Microbiota/genetics ; Water ; Pharmaceutical Preparations ; }, abstract = {Lake Victoria, the second-largest freshwater lake in the world, provides an important source of food and income, particularly fish for both domestic consumption and for export market. In recent years, Lake Victoria has suffered massive pollution from both industrial and wastewater discharge. Microplastic biomes, pharmaceutical residues, drugs of abuse, heavy metals, agrochemicals, and personal care products are ubiquitous in the aquatic ecosystem of Winam Gulf. These pollutants are known to alter microbial assemblages in aquatic ecosystems with far-reaching ramification including a calamitous consequence to human health. Indeed, some of these pollutants have been associated with human cancers and antimicrobial resistance. There is a paucity of data on the microbial profiles of this important but heavily polluted aquatic ecosystem. The current study sought to investigate the metagenomic profiles of microbial assemblages in the Winam Gulf ecosystem. Water and sediment samples were collected from several locations within the study sites. Total genomic DNA pooled from all sampling sites was extracted and analyzed by whole-genome shotgun sequencing. Analyses revealed three major kingdoms: bacteria, archaea and eukaryotes belonging to 3 phyla, 13 classes, 14 families, 9 orders, 14 genera, and 10 species. Proteobacteria, Betaproteobacteria, Comamonadaceae, Burkholdariales, and Arcobacter were the dominated phyla, class, family, order, genera, and species, respectively. The Kyoto Encyclopedia of Genes and Genomes indicated the highest number of genes involved in metabolism. The presence of carbohydrate metabolism genes and enzymes was used to infer organic pollutions from sewage and agricultural runoffs. Similarly, the presence of xylene and nutrotoluene degradation genes and enzyme was used to infer industrial pollution into the lake. Drug metabolism genes lend credence to the possibility of pharmaceutical pollutants in water. Taken together, there is a clear indication of massive pollution. In addition, carbohydrate-active enzymes were the most abundant and included genes in glycoside hydrolases. Shotgun metagenomic analyses conveyed an understanding of the microbial communities of the massively polluted aquatic ecosystem of Winam Gulf, Lake Vicoria, Kenya. The current study documents the presence of multiclass pollutants in Lake Victoria and reveals information that might be useful for a potential bioremediation strategy using the native microbial communities.}, } @article {pmid37517669, year = {2023}, author = {Ozsefil, IC and Miraloglu, IH and Ozbayram, EG and Uzun, O and Ince, B and Ince, O}, title = {Is a floodplain forest a valuable source for lignin-degrading anaerobic microbial communities: A metagenomic approach.}, journal = {Chemosphere}, volume = {339}, number = {}, pages = {139675}, doi = {10.1016/j.chemosphere.2023.139675}, pmid = {37517669}, issn = {1879-1298}, mesh = {*Lignin/metabolism ; Anaerobiosis ; *Microbiota ; Metagenome ; Microbial Consortia ; Forests ; }, abstract = {Lignin is one of the most substantial obstacles in the evaluation of lignocellulosic compounds. Although there are numerous approaches for the enhancement of lignin digestion in the literature, there has yet to be an optimized system to date. In this study, samples taken from Igneada floodplain forests were enriched anaerobically at 25 °C and 37 °C, with alkali lignin as the sole carbon source. The activity of the anaerobic lignin-degrading microbial consortium was detected more efficiently at 37 °C, where biogas production exceeded 3.5 mLgas/mLmedium. It was observed that the microbial community initially dominated by Proteobacteria (around 60%) changed completely after enrichment and was led by members of the Firmicutes phylum (up to 90%). The dominant species (Sporomusa termitida, Desulfitobacterium hafniense, Citrobacter freundii, Citrobacter portucalensis, Alkalibacter rhizosphaerae, and Gudongella oleilytica) occupying more than 50% in the final enrichment culture were only around 2% in the raw samples. Therefore, this study, one of the few in which enriched environmental samples were sequenced using MinION, demonstrated that longoses are exceptional reservoirs for lignin-digesting anaerobic microorganisms.}, } @article {pmid37517495, year = {2023}, author = {Veerasamy, V and Jagannathan, UM and Arakkala, SD and Shafee, WA and Kaliannan, T}, title = {Exploring the bacterial genetic diversity and community structure of crude oil contaminated soils using microbiomics.}, journal = {Environmental research}, volume = {236}, number = {Pt 2}, pages = {116779}, doi = {10.1016/j.envres.2023.116779}, pmid = {37517495}, issn = {1096-0953}, mesh = {*Petroleum ; Ecosystem ; Sewage ; *Soil Pollutants/analysis ; Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Biodegradation, Environmental ; Soil/chemistry ; Genetic Variation ; }, abstract = {The impact of environmental pollution in air and water is reflected mainly in the soil ecosystem as it impairs soil functions. Also, since the soil is the habitat for billions of organisms, the biodiversity is in turn altered. Microbes are precise sensors of ecological contamination, and bacteria have a key and important function in terms of bioremediation of the contaminated soil. Hence in the current work, we aimed at assessing the unidentified bacterial population through Illumina MiSeq sequencing technology and their community structural changes in different levels of petroleum-contaminated soil and sludge samples (aged, sludge, and leakage soil) to identify unique bacteria for their potential application in remediation. The studies showed that major bacterial consortiums namely, Proteobacteria (57%), Alphaproteobacteria (31%), and Moraxellaceae (23%) were present in aged soil, whereas Proteobacteria (52%), Alphaproteobacteria (33%), and Rhodobacteraceae (28%) were dominantly found in sludge soil. In leakage soil, Proteobacteria (59%), Alphaproteobacteria (33%), and Rhodobacteraceae (29%) were abundantly present. The Venn diagrams are used to analyze the distribution of abundances in individual operational taxonomic units (OTUs) within three soil samples. After data filtering, they were grouped into OTU clusters and 329 OTUs were identified from the three soil samples. Among the 329, 160 OTUs were common in the three soil samples. The bacterial diversity is estimated using alpha diversity indices and Shanon index and was found to be 4.490, 4.073 and 4.631 in aged soil, sludge soil and leakage soil, respectively and similarly richness was found to be 618, 417 and 418. The heat map was generated by QIIME software and from the top 50 enriched genera few microbes such as Pseudomonas, Bacillus, Mycobacterium, Sphingomonas and Paracoccus, were shown across all the samples. In addition, we also analyzed various physicochemical properties of soil including pH, temperature, salinity, electrical conductivity, alkalinity, total carbon, total organic matter, nitrogen, phosphorus and potassium to calculate the soil quality index (SQI). The SQI of aged, sludge and leakage soil samples were 0.73, 0.64, and 0.89, respectively. These findings show the presence of unexplored bacterial species which could be applied for hydrocarbon remediation and further they can be exploited for the same.}, } @article {pmid37516054, year = {2023}, author = {He, S and Deng, X and Han, Y and Gong, Z and Wang, J and Tao, X and Tong, H and Chen, Y}, title = {Metabolites and metagenomic analysis reveals the quality of Pu-erh "tea head".}, journal = {Food chemistry}, volume = {429}, number = {}, pages = {136992}, doi = {10.1016/j.foodchem.2023.136992}, pmid = {37516054}, issn = {1873-7072}, mesh = {Tea/chemistry ; *Microbiota ; Bacteria/genetics ; *Catechin ; Fermentation ; }, abstract = {Tea head, a derivative product of Pu-erh tea, are tight tea lumps formed during pile-fermentation. The aim of this study was to reveal the differences of quality-related metabolites and microbial communities between ripened Pu-erh tea (PE-21) and tea heads (CT-21). Compared with PE-21, CT-21 showed a more mellow and smooth taste with slight bitterness and astringency, and can withstand multiple infusions. Metabolites analysis indicated CT-21 had more abundant water-soluble substances (47.39%) and showed significant differences with PE-21 in the main compositions of amino acids, catechins and saccharides which contributed to the viscosity of tea liquor, mellow taste and the tight tea lumps formation. Microbial communities and COG annotation analysis revealed CT-21 had lower abundance of Bacteria (84.05%), and higher abundance of Eukaryota (15.10%), carbohydrate transport and metabolism (8.28%) and glycoside hydrolases (37.36%) compared with PE-21. The different microbial communities may cause metabolites changes, forming distinct flavor of Pu-erh.}, } @article {pmid37515113, year = {2023}, author = {Thijssen, M and Khamisipour, G and Maleki, M and Devos, T and Li, G and Van Ranst, M and Matthijnssens, J and Pourkarim, MR}, title = {Characterization of the Human Blood Virome in Iranian Multiple Transfused Patients.}, journal = {Viruses}, volume = {15}, number = {7}, pages = {}, pmid = {37515113}, issn = {1999-4915}, mesh = {Humans ; Iran/epidemiology ; Virome ; *Viruses/genetics ; *Anelloviridae/genetics ; Metagenome ; Metagenomics/methods ; }, abstract = {Blood transfusion safety is an essential element of public health. Current blood screening strategies rely on targeted techniques that could miss unknown or unexpected pathogens. Recent studies have demonstrated the presence of a viral community (virobiota/virome) in the blood of healthy individuals. Here, we characterized the blood virome in patients frequently exposed to blood transfusion by using Illumina metagenomic sequencing. The virome of these patients was compared to viruses present in healthy blood donors. A total number of 155 beta-thalassemia, 149 hemodialysis, and 100 healthy blood donors were pooled with five samples per pool. Members of the Anelloviridae and Flaviviridae family were most frequently observed. Interestingly, samples of healthy blood donors harbored traces of potentially pathogenic viruses, including adeno-, rota-, and Merkel cell polyomavirus. Viruses of the Anelloviridae family were most abundant in the blood of hemodialysis patients and displayed a higher anellovirus richness. Pegiviruses (Flaviviridae) were only observed in patient populations. An overall trend of higher eukaryotic read abundance in both patient groups was observed. This might be associated with increased exposure through blood transfusion. Overall, the findings in this study demonstrated the presence of various viruses in the blood of Iranian multiple-transfused patients and healthy blood donors.}, } @article {pmid37512841, year = {2023}, author = {Santiago, BCF and de Souza, ID and Cavalcante, JVF and Morais, DAA and da Silva, MB and Pasquali, MAB and Dalmolin, RJS}, title = {Metagenomic Analyses Reveal the Influence of Depth Layers on Marine Biodiversity on Tropical and Subtropical Regions.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, pmid = {37512841}, issn = {2076-2607}, support = {312305/2021-4//National Council for Scientific and Technological Development/ ; 302949/2020-8//National Council for Scientific and Technological Development/ ; xxx//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; xxxx//Propesq UFRN/ ; xxx//APC - UFCG/ ; }, abstract = {The emergence of open ocean global-scale studies provided important information about the genomics of oceanic microbial communities. Metagenomic analyses shed light on the structure of marine habitats, unraveling the biodiversity of different water masses. Many biological and environmental factors can contribute to marine organism composition, such as depth. However, much remains unknown about microbial communities' taxonomic and functional features in different water layer depths. Here, we performed a metagenomic analysis of 76 publicly available samples from the Tara Ocean Project, distributed in 8 collection stations located in tropical or subtropical regions, and sampled from three layers of depth (surface water layer-SRF, deep chlorophyll maximum layer-DCM, and mesopelagic zone-MES). The SRF and DCM depth layers are similar in abundance and diversity, while the MES layer presents greater diversity than the other layers. Diversity clustering analysis shows differences regarding the taxonomic content of samples. At the domain level, bacteria prevail in most samples, and the MES layer presents the highest proportion of archaea among all samples. Taken together, our results indicate that the depth layer influences microbial sample composition and diversity.}, } @article {pmid37511184, year = {2023}, author = {Boulangé, CL and Pedersen, HK and Martin, FP and Siegwald, L and Pallejà Caro, A and Eklund, AC and Jia, W and Zhang, H and Berger, B and Sprenger, N and Heine, RG and Cinnamon Study Investigator Group, }, title = {An Extensively Hydrolyzed Formula Supplemented with Two Human Milk Oligosaccharides Modifies the Fecal Microbiome and Metabolome in Infants with Cow's Milk Protein Allergy.}, journal = {International journal of molecular sciences}, volume = {24}, number = {14}, pages = {}, pmid = {37511184}, issn = {1422-0067}, mesh = {Child ; Female ; Animals ; Cattle ; Humans ; Infant ; Child, Preschool ; *Milk Hypersensitivity ; Milk, Human ; Oligosaccharides ; Dietary Supplements ; *Gastrointestinal Microbiome ; Metabolome ; Infant Formula/chemistry ; }, abstract = {Cow's milk protein allergy (CMPA) is a prevalent food allergy among infants and young children. We conducted a randomized, multicenter intervention study involving 194 non-breastfed infants with CMPA until 12 months of age (clinical trial registration: NCT03085134). One exploratory objective was to assess the effects of a whey-based extensively hydrolyzed formula (EHF) supplemented with 2'-fucosyllactose (2'-FL) and lacto-N-neotetraose (LNnT) on the fecal microbiome and metabolome in this population. Thus, fecal samples were collected at baseline, 1 and 3 months from enrollment, as well as at 12 months of age. Human milk oligosaccharides (HMO) supplementation led to the enrichment of bifidobacteria in the gut microbiome and delayed the shift of the microbiome composition toward an adult-like pattern. We identified specific HMO-mediated changes in fecal amino acid degradation and bile acid conjugation, particularly in infants commencing the HMO-supplemented formula before the age of three months. Thus, HMO supplementation partially corrected the dysbiosis commonly observed in infants with CMPA. Further investigation is necessary to determine the clinical significance of these findings in terms of a reduced incidence of respiratory infections and other potential health benefits.}, } @article {pmid37510347, year = {2023}, author = {Aragão, CF and da Silva, SP and do Nascimento, BLS and da Silva, FS and Nunes Neto, JP and Pinheiro, VCS and Cruz, ACR}, title = {Shotgun Metagenomic Sequencing Reveals Virome Composition of Mosquitoes from a Transition Ecosystem of North-Northeast Brazil.}, journal = {Genes}, volume = {14}, number = {7}, pages = {}, pmid = {37510347}, issn = {2073-4425}, mesh = {Animals ; Humans ; Brazil ; Ecosystem ; Virome ; *Culex ; *Aedes ; *Viruses ; *RNA Viruses ; }, abstract = {A wide diversity of pathogenic mosquito-borne viruses circulate in the Brazilian Amazon, and the intense deforestation can contribute to the spread of these viruses. In this context, this study aimed to investigate the viral diversity in mosquitoes of the genera Aedes, Culex, Haemagogus, and Sabethes from a transition area between the Amazon, Cerrado, and Caatinga biomes in Brazil. Metagenomic high-throughput sequencing was used to characterize the virome of 20 mosquito pools. A total of 15 virus-like genomes were identified, comprising species genomically close to insect-specific viruses of the families Iflaviridae, Metaviridae, Lispiviridae, Rhabdoviridae, Xinmoviridae, and Parvoviridae and species of plant viruses of the families Solemoviridae, Virgaviridae, and Partitiviridae. However, sequences of viruses associated with human and animal diseases were not detected. Most of the recovered genomes were divergent from those previously described. These findings reveal that there are a large number of unknown viruses to be explored in the middle-north of Brazil.}, } @article {pmid37508354, year = {2023}, author = {Machuca-Sepúlveda, J and Miranda, J and Lefin, N and Pedroso, A and Beltrán, JF and Farias, JG}, title = {Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring.}, journal = {Biology}, volume = {12}, number = {7}, pages = {}, pmid = {37508354}, issn = {2079-7737}, support = {2020/06982-3//Universidad de La Frontera/ ; }, abstract = {Freshwater ecosystems have been experiencing various forms of threats, mainly since the last century. The severity of this adverse scenario presents unprecedented challenges to human health, water supply, agriculture, forestry, ecological systems, and biodiversity, among other areas. Despite the progress made in various biomonitoring techniques tailored to specific countries and biotic communities, significant constraints exist, particularly in assessing and quantifying biodiversity and its interplay with detrimental factors. Incorporating modern techniques into biomonitoring methodologies presents a challenging topic with multiple perspectives and assertions. This review aims to present a comprehensive overview of the contemporary advancements in freshwater biomonitoring, specifically by utilizing omics methodologies such as genomics, metagenomics, transcriptomics, proteomics, metabolomics, and multi-omics. The present study aims to elucidate the rationale behind the imperative need for modernization in this field. This will be achieved by presenting case studies, examining the diverse range of organisms that have been studied, and evaluating the potential benefits and drawbacks associated with the utilization of these methodologies. The utilization of advanced high-throughput bioinformatics techniques represents a sophisticated approach that necessitates a significant departure from the conventional practices of contemporary freshwater biomonitoring. The significant contributions of omics techniques in the context of biological quality elements (BQEs) and their interpretations in ecological problems are crucial for biomonitoring programs. Such contributions are primarily attributed to the previously overlooked identification of interactions between different levels of biological organization and their responses, isolated and combined, to specific critical conditions.}, } @article {pmid37507809, year = {2023}, author = {Fredriksen, S and de Warle, S and van Baarlen, P and Boekhorst, J and Wells, JM}, title = {Resistome expansion in disease-associated human gut microbiomes.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {166}, pmid = {37507809}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; }, abstract = {BACKGROUND: The resistome, the collection of antibiotic resistance genes (ARGs) in a microbiome, is increasingly recognised as relevant to the development of clinically relevant antibiotic resistance. Many metagenomic studies have reported resistome differences between groups, often in connection with disease and/or antibiotic treatment. However, the consistency of resistome associations with antibiotic- and non-antibiotic-treated diseases has not been established. In this study, we re-analysed human gut microbiome data from 26 case-control studies to assess the link between disease and the resistome.

RESULTS: The human gut resistome is highly variable between individuals both within and between studies, but may also vary significantly between case and control groups even in the absence of large taxonomic differences. We found that for diseases commonly treated with antibiotics, namely cystic fibrosis and diarrhoea, patient microbiomes had significantly elevated ARG abundances compared to controls. Disease-associated resistome expansion was found even when ARG abundance was high in controls, suggesting ongoing and additive ARG acquisition in disease-associated strains. We also found a trend for increased ARG abundance in cases from some studies on diseases that are not treated with antibiotics, such as colorectal cancer.

CONCLUSIONS: Diseases commonly treated with antibiotics are associated with expanded gut resistomes, suggesting that historical exposure to antibiotics has exerted considerable selective pressure for ARG acquisition in disease-associated strains. Video Abstract.}, } @article {pmid37506647, year = {2023}, author = {Zhou, Y and Zhou, S}, title = {Role of microplastics in microbial community structure and functions in urban soils.}, journal = {Journal of hazardous materials}, volume = {459}, number = {}, pages = {132141}, doi = {10.1016/j.jhazmat.2023.132141}, pmid = {37506647}, issn = {1873-3336}, mesh = {Humans ; *Microplastics/pharmacology ; Plastics ; Soil Microbiology ; Soil/chemistry ; *Microbiota ; }, abstract = {Evidence from the laboratory suggests that microplastics (MPs) can harm soil microorganisms, affecting the structures and functions of microbial communities. The impact of soil MPs on microbes in actual urban environments with high human activity levels, however, has not been well reported. To investigate the MP effect on urban soil microorganisms under complex scenarios, we analyzed 42 soil samples from standardized plots of 7 urban functional zones. We report that urban green spaces are important for studying microbial diversity in the study area, and they also contribute to the global homogenization of soil microbes and genes. Bacterial communities in soils enriched with various MPs showed greater differences in OTUs than fungi. Compared to low-MP soils, most ARGs and nutrient cycling genes had similar or slightly lower abundances in soils with high levels of MPs. The coupling of pollutant factors with MPs as independent variables had significant explanatory power for both positive and negative correlations in PLS-PM analysis. Specifically, PET and PP MPs explained 3.54% and 6.03%, respectively, of the microbial community and functional genes. This study fills knowledge gaps on the effects of MPs on urban soil microbial communities in real environments, facilitating better management of urban green spaces.}, } @article {pmid37505986, year = {2023}, author = {Shetty, P and Shetty, S and Rai, P and Kumar, BK and Bhat, R}, title = {Role of oral microbiota in irreversible pulpitis - Current strategies and future perspectives.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {70}, number = {3}, pages = {177-186}, doi = {10.1556/030.2023.02082}, pmid = {37505986}, issn = {1588-2640}, mesh = {Humans ; *Pulpitis/microbiology ; Bacteria/genetics ; *Microbiota ; Inflammation ; }, abstract = {Irreversible pulpitis is an inflammation of the tooth pulp caused by an opportunity-driven invasion of the pulp space by oral microbiota typically prevalent in the oral cavity. Microbial organisms are extensively recognised to be the fundamental cause of endodontic infections and treatment failures. Previously, bacterial species responsible for these infections were largely recognised using conventional microbial culture techniques, lending credence to the widely held belief that anaerobic Gram-negative bacteria frequently enter the pulp space and trigger endodontic infections. The advent of novel technologies grants the advantage of detecting and studying microbial populations via an amalgamation of the modern "Omics" techniques and meticulous bioinformatics analysis, additionally detecting the metatranscriptome, metaproteome and metabolome along with the metagenome. Amongst these analytical strategies, metagenomic analyses are essentially pragmatic for investigating the oral microbiome. Metagenomics favor not only assessment of microbial composition in diseased conditions, but also contributes to detection of novel, potentially pathogenic species inclusive of non-viable bacteria. The present review describes current knowledge of root canal microbiome, including its composition and functional attributes, the novel strategies available for detection of microbiome as well as challenges associated and provides some crucial pointers for areas of future research.}, } @article {pmid37504575, year = {2023}, author = {Li, J and Sauers, L and Zhuang, D and Ren, H and Guo, J and Wang, L and Zhuang, M and Guo, Y and Zhang, Z and Wu, J and Yao, J and Yang, H and Huang, J and Wang, C and Lin, Q and Zhang, Z and Sadd, BM}, title = {Divergence and convergence of gut microbiomes of wild insect pollinators.}, journal = {mBio}, volume = {14}, number = {4}, pages = {e0127023}, pmid = {37504575}, issn = {2150-7511}, support = {R15 GM129681/GM/NIGMS NIH HHS/United States ; }, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome/physiology ; Phylogeny ; Insecta/physiology ; *Microbiota ; *Wasps ; Pollination ; }, abstract = {Pollination services provided by wild insect pollinators are critical to natural ecosystems and crops around the world. There is an increasing appreciation that the gut microbiota of these insects influences their health and consequently their services. However, pollinator gut microbiota studies have focused on well-described social bees, but rarely include other, more phylogenetically divergent insect pollinators. To expand our understanding, we explored the insect pollinator microbiomes across three insect orders through two DNA sequencing approaches. First, in an exploratory 16S amplicon sequencing analysis of taxonomic community assemblages, we found lineage-specific divergences of dominant microbial genera and microbiota community composition across divergent insect pollinator genera. However, we found no evidence for a strong broad-scale phylogenetic signal, which we see for community relatedness at finer scales. Subsequently, we utilized metagenomic shotgun sequencing to obtain metagenome-assembled genomes and assess the functionality of the microbiota from pollinating flies and social wasps. We uncover a novel gut microbe from pollinating flies in the family Orbaceae that is closely related to Gilliamella spp. from social bees but with divergent functions. We propose this novel species be named Candidatus Gilliamella eristali. Further metagenomes of dominant fly and wasp microbiome members suggest that they are largely not host-insect adapted and instead may be environmentally derived. Overall, this study suggests selective processes involving ecology or physiology, or neutral processes determining microbe colonization may predominate in the turnover of lineages in insect pollinators broadly, while evolution with hosts may occur only under certain circumstances and on smaller phylogenetic scales. IMPORTANCE Wild insect pollinators provide many key ecosystem services, and the microbes associated with these insect pollinators may influence their health. Therefore, understanding the diversity in microbiota structure and function, along with the potential mechanisms shaping the microbiota across diverse insect pollinators, is critical. Our study expands beyond existing knowledge of well-studied social bees, like honey bees, including members from other bee, wasp, butterfly, and fly pollinators. We infer ecological and evolutionary factors that may influence microbiome structure across diverse insect pollinator hosts and the functions that microbiota members may play. We highlight significant differentiation of microbiomes among diverse pollinators. Closer analysis suggests that dominant members may show varying levels of host association and functions, even in a comparison of closely related microbes found in bees and flies. This work suggests varied importance of ecological, physiological, and non-evolutionary filters in determining structure and function across largely divergent wild insect pollinator microbiomes.}, } @article {pmid37501535, year = {2023}, author = {Pavia, MJ and Finn, D and Macedo-Tafur, F and Tello-Espinoza, R and Penaccio, C and Bouskill, N and Cadillo-Quiroz, H}, title = {Genes and genome-resolved metagenomics reveal the microbial functional make up of Amazon peatlands under geochemical gradients.}, journal = {Environmental microbiology}, volume = {25}, number = {11}, pages = {2388-2403}, doi = {10.1111/1462-2920.16469}, pmid = {37501535}, issn = {1462-2920}, mesh = {*Bacteria/genetics/metabolism ; *Microbiota/genetics ; Metagenome ; Metagenomics ; Soil ; }, abstract = {The Pastaza-Marañón Foreland Basin (PMFB) holds the most extensive tropical peatland area in South America. PMFB peatlands store ~7.07 Gt of organic carbon interacting with multiple microbial heterotrophic, methanogenic, and other aerobic/anaerobic respirations. Little is understood about the contribution of distinct microbial community members inhabiting tropical peatlands. Here, we studied the metagenomes of three geochemically distinct peatlands spanning minerotrophic, mixed, and ombrotrophic conditions. Using gene- and genome-centric approaches, we evaluate the functional potential of the underlying microbial communities. Abundance analyses show significant differences in C, N, P, and S acquisition genes. Furthermore, community interactions mediated by toxin-antitoxin and CRISPR-Cas systems were enriched in oligotrophic soils, suggesting that non-metabolic interactions may exert additional controls in low-nutrient environments. Additionally, we reconstructed 519 metagenome-assembled genomes spanning 28 phyla. Our analyses detail key differences across the geochemical gradient in the predicted microbial populations involved in degradation of organic matter, and the cycling of N and S. Notably, we observed differences in the nitric oxide (NO) reduction strategies between sites with high and low N2 O fluxes and found phyla putatively capable of both NO and sulfate reduction. Our findings detail how gene abundances and microbial populations are influenced by geochemical differences in tropical peatlands.}, } @article {pmid37501202, year = {2023}, author = {Anzà, S and Schneider, D and Daniel, R and Heistermann, M and Sangmaneedet, S and Ostner, J and Schülke, O}, title = {The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {165}, pmid = {37501202}, issn = {2049-2618}, mesh = {Female ; Animals ; Pregnancy ; Humans ; Glucocorticoids ; *Gastrointestinal Microbiome/physiology ; Cross-Sectional Studies ; Primates ; Bacteria/genetics ; *Prenatal Exposure Delayed Effects/microbiology ; }, abstract = {BACKGROUND: During development, elevated levels of maternal glucocorticoids (GCs) can have detrimental effects on offspring morphology, cognition, and behavior as well as physiology and metabolism. Depending on the timing of exposure, such effects may vary in strength or even reverse in direction, may alleviate with age, or may concern more stable and long-term programming of phenotypic traits. Maternal effects on gut bacterial diversity, composition, and function, and the persistence of such effects into adulthood of long-lived model species in the natural habitats remain underexplored.

RESULTS: In a cross-sectional sample of infant, juvenile, and adult Assamese macaques, the timing of exposure to elevated maternal GCs during ontogeny was associated with the gut bacterial community of the offspring. Specifically, naturally varying maternal GC levels during early but not late gestation or lactation were associated with reduced bacterial richness. The overall effect of maternal GCs during early gestation on the gut bacterial composition and function exacerbated with offspring age and was 10 times stronger than the effect associated with exposure during late prenatal or postnatal periods. Instead, variation in maternal GCs during the late prenatal or postnatal period had less pronounced or less stable statistical effects and therefore a weaker effect on the entire bacterial community composition, particularly in adult individuals. Finally, higher early prenatal GCs were associated with an increase in the relative abundance of several potential pro-inflammatory bacteria and a decrease in the abundance of Bifidobacterium and other anti-inflammatory taxa, an effect that exacerbated with age.

CONCLUSIONS: In primates, the gut microbiota can be shaped by developmental effects with strong timing effects on plasticity and potentially detrimental consequences for adult health. Together with results on other macaque species, this study suggests potential detrimental developmental effects similar to rapid inflammaging, suggesting that prenatal exposure to high maternal GC concentrations is a common cause underlying both phenomena. Our findings await confirmation by metagenomic functional and causal analyses and by longitudinal studies of long-lived, ecologically flexible primates in their natural habitat, including developmental effects that originate before birth. Video Abstract.}, } @article {pmid37499616, year = {2023}, author = {Xiong, X and Rao, Y and Ma, J and Wang, Z and He, Q and Gong, J and Sheng, W and Xu, J and Zhu, X and Tan, Y and Yang, Y}, title = {A catalog of microbial genes and metagenome-assembled genomes from the quail gut microbiome.}, journal = {Poultry science}, volume = {102}, number = {10}, pages = {102931}, pmid = {37499616}, issn = {1525-3171}, mesh = {Animals ; *Metagenome ; *Gastrointestinal Microbiome ; Quail/genetics ; Chickens/genetics ; Genes, Microbial ; }, abstract = {The gut microbiome plays an important role in quail feed efficiency, immunity, production, and even behavior. Gut microbial gene catalogs and reference genomes are important for understanding the quail gut microbiome. However, quail gut microbes are lacked sequenced genomes and functional information to date. In this study, we report the first catalog of the microbial genes and metagenome-assembled genomes (MAGs) in fecal and cecum luminal content samples from 3 quail breeds using deep metagenomic sequencing. We identified a total of 2,419,425 nonredundant genes in the quail genome catalog, and a total of 473 MAGs were reconstructed through binning analysis. At 95% average nucleotide identity, the 473 MAGs were clustered into 283 species-level genome bins (SGBs), of which 225 SGBs belonged to species without any available genomes in the current database. Based on the quail gene catalog and MAGs, we identified 142 discriminative bacterial species and 244 discriminative MAGs between Chinese yellow quails and Japanese quails. The discriminative MAGs suggested a strain-level difference in the gut microbial composition. Additionally, a total of 25 Kyoto Encyclopedia of Genes and Genomes functional terms and 88 carbohydrate-active enzymes were distinctly enriched between Chinese yellow quails and Japanese quails. Most of the different species and MAGs were significantly interrelated with the shifts in the functional capacities of the quail gut microbiome. Taken together, we constructed a quail gut microbial gene catalog and enlarged the reference of quail gut microbial genomes. The results of this study provide a powerful and invaluable resource for quail gut microbiome-related research.}, } @article {pmid37496083, year = {2023}, author = {Liang, X and Zhang, Z and Wang, H and Lu, X and Li, W and Lu, H and Roy, A and Shen, X and Irwin, DM and Shen, Y}, title = {Early-life prophylactic antibiotic treatment disturbs the stability of the gut microbiota and increases susceptibility to H9N2 AIV in chicks.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {163}, pmid = {37496083}, issn = {2049-2618}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/genetics ; *Influenza A Virus, H9N2 Subtype/genetics ; Chickens/microbiology ; *Microbiota ; }, abstract = {BACKGROUND: Antibiotics are widely used for prophylactic therapy and for improving the growth performance of chicken. The problem of bacterial drug resistance caused by antibiotic abuse has previously attracted extensive attention; however, the influence of early-day use of prophylactic antibiotics on the gut microflora and on the disease resistance ability in chicks has not been explored. Here, we comprehensively evaluate the growth performance, gut microbial dynamics, level of antibiotic resistance genes (ARGs) in the gut microbial community, and resistance to H9N2 avian influenza virus (AIV) in chickens following long-term and short-term early-day prophylactic antibiotic treatment.

RESULTS: Unexpectedly, long-term prophylactic enrofloxacin treatment slowed the growth rate of chickens, whereas short-term antibiotics treatments were found to increase the growth rate, but these changes were not statistically significant. Strikingly, expansions of Escherichia-Shigella populations were observed in early-life prophylactic antibiotics-treated groups of chickens, which is in contrast to the general perception that antibiotics should control their pathogenicity in chicks. The gut microbiota composition of chickens treated long term with antibiotics or received early-day antibiotics treatment tend to be more dramatically disturbed compared to the gut microbiome of chickens treated with antibiotics for a short term at a later date, especially after H9N2 AIV infection.

CONCLUSIONS: Our data provide evidence that early-day and long-term antibiotic treatments have a more adverse effect on the intestinal microbiome of chickens, compared to short-term late age antibiotic treatment. Furthermore, our metagenomic data reveal that both long-term and short-term antibiotic treatment increase the relative abundance of ARGs. Our findings highlight the adverse effects of prophylactic antibiotic treatment and provide a theoretical basis for the cautious administration of antibiotics in food-producing animal management. Video Abstract.}, } @article {pmid37495367, year = {2023}, author = {Lee, SH and Kim, J and Kim, NH and Kim, OH and Shon, CH and Kim, SJ and Jang, Y and Yun, S and Lim, SE and Jung, SY and Yoo, HJ and Heo, SH and Lee, SW}, title = {Gut microbiota composition and metabolite profiling in smokers: a comparative study between emphysema and asymptomatic individuals with therapeutic implications.}, journal = {Thorax}, volume = {78}, number = {11}, pages = {1080-1089}, doi = {10.1136/thorax-2021-217923}, pmid = {37495367}, issn = {1468-3296}, mesh = {Humans ; Animals ; Mice ; Smokers ; *Gastrointestinal Microbiome ; Propionates ; Disease Models, Animal ; *Pulmonary Emphysema ; *Pulmonary Disease, Chronic Obstructive ; Forced Expiratory Volume ; *Emphysema/complications ; Acetates ; }, abstract = {BACKGROUND: Diet has a crucial role in the gut microbiota, and dysbiosis in the gut and lungs has been suggested to be associated with chronic obstructive pulmonary disease. We compared the diet, microbiome and metabolome between asymptomatic smokers and those with emphysema.

METHODS: We enrolled 10 asymptomatic smokers with preserved lung function and 16 smokers with emphysema with severe airflow limitation. Dietary intake information was gathered by a self-reported questionnaire. Sputum and faecal samples were collected for microbial and metabolomics analysis. A murine model of emphysema was used to determine the effect of metabolite supplementation.

RESULTS: Despite having a similar smoking history with emphysema patients, asymptomatic smokers had higher values of body mass index, fibre intake and faecal acetate level. Linear discriminant analysis identified 17 microbial taxonomic members that were relatively enriched in the faeces of asymptomatic smokers. Analysis of similarity results showed dissimilarity between the two groups (r=0.287, p=0.003). Higher acetate level was positively associated with forced expiratory volume in one second in the emphysema group (r=0.628, p=0.012). Asymptomatic smokers had a greater number of species associated with acetate and propionate (r>0.6) than did those with emphysema (30 vs 19). In an emphysema mouse model, supplementation of acetate and propionate reduced alveolar destruction and the production of proinflammatory cytokines, and propionate decreased the CD3[+]CD4[+]IL-17[+] T-cell population in the lung and spleen.

CONCLUSION: Smokers with emphysema showed differences in diet, microbiome and short-chain fatty acids compared with asymptomatic smokers. Acetate and propionate showed therapeutic effects in a smoking-induced murine model of emphysema.}, } @article {pmid37494472, year = {2023}, author = {Thompson, KN and Bonham, KS and Ilott, NE and Britton, GJ and Colmenero, P and Bullers, SJ and McIver, LJ and Ma, S and Nguyen, LH and Filer, A and Brough, I and Pearson, C and Moussa, C and Kumar, V and Lam, LH and Jackson, MA and Pawluk, A and , and Kiriakidis, S and Taylor, PC and Wedderburn, LR and Marsden, B and Young, SP and Littman, DR and Faith, JJ and Pratt, AG and Bowness, P and Raza, K and Powrie, F and Huttenhower, C and , }, title = {Alterations in the gut microbiome implicate key taxa and metabolic pathways across inflammatory arthritis phenotypes.}, journal = {Science translational medicine}, volume = {15}, number = {706}, pages = {eabn4722}, doi = {10.1126/scitranslmed.abn4722}, pmid = {37494472}, issn = {1946-6242}, support = {21593/VAC_/Versus Arthritis/United Kingdom ; 22203/VAC_/Versus Arthritis/United Kingdom ; MR/R013926/1/MRC_/Medical Research Council/United Kingdom ; 22072/VAC_/Versus Arthritis/United Kingdom ; 21226/VAC_/Versus Arthritis/United Kingdom ; 203141/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; /DH_/Department of Health/United Kingdom ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Arthritis, Rheumatoid ; Inflammation ; *Microbiota ; Phenotype ; Metabolic Networks and Pathways ; }, abstract = {Musculoskeletal diseases affect up to 20% of adults worldwide. The gut microbiome has been implicated in inflammatory conditions, but large-scale metagenomic evaluations have not yet traced the routes by which immunity in the gut affects inflammatory arthritis. To characterize the community structure and associated functional processes driving gut microbial involvement in arthritis, the Inflammatory Arthritis Microbiome Consortium investigated 440 stool shotgun metagenomes comprising 221 adults diagnosed with rheumatoid arthritis, ankylosing spondylitis, or psoriatic arthritis and 219 healthy controls and individuals with joint pain without an underlying inflammatory cause. Diagnosis explained about 2% of gut taxonomic variability, which is comparable in magnitude to inflammatory bowel disease. We identified several candidate microbes with differential carriage patterns in patients with elevated blood markers for inflammation. Our results confirm and extend previous findings of increased carriage of typically oral and inflammatory taxa and decreased abundance and prevalence of typical gut clades, indicating that distal inflammatory conditions, as well as local conditions, correspond to alterations to the gut microbial composition. We identified several differentially encoded pathways in the gut microbiome of patients with inflammatory arthritis, including changes in vitamin B salvage and biosynthesis and enrichment of iron sequestration. Although several of these changes characteristic of inflammation could have causal roles, we hypothesize that they are mainly positive feedback responses to changes in host physiology and immune homeostasis. By connecting taxonomic alternations to functional alterations, this work expands our understanding of the shifts in the gut ecosystem that occur in response to systemic inflammation during arthritis.}, } @article {pmid37494371, year = {2023}, author = {Xie, M and Tsai, CY and McAdams, ZL and Oo, M and Hansen, M and Dougher, M and Sansano, A and Watson, A and LoMauro, K and Antilus-Sainte, R and Ericsson, A and Dartois, V and Gengenbacher, M}, title = {Wild mouse gut microbiota limits initial tuberculosis infection in BALB/c mice.}, journal = {PloS one}, volume = {18}, number = {7}, pages = {e0288290}, pmid = {37494371}, issn = {1932-6203}, support = {T32 GM008396/GM/NIGMS NIH HHS/United States ; U19 AI111143/AI/NIAID NIH HHS/United States ; U19 AI162568/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Mice, Inbred BALB C ; *Tuberculosis ; *Latent Tuberculosis/pathology ; Lung/pathology ; Dysbiosis/pathology ; }, abstract = {Mouse models are critical tools in tuberculosis (TB) research. Recent studies have demonstrated that the wild mouse gut microbiota promotes host fitness and improves disease resistance. Here we examine whether the wild mouse gut microbiota alters the immunopathology of TB in BALB/c mice. Conventional BALB/c mice (LabC) and mice born to germ-free BALB/c mothers reconstituted with the wild mouse gut microbiota (WildR) were used in our studies. WildR mice controlled initial TB infection better than LabC mice. The microbial gut communities of LabC mice and WildR mice had similar richness but significantly different composition prior to infection. TB reduced the gut community richness in both cohorts while differences in community composition remained indicating a general TB-induced dysbiosis. The wild mouse gut microbiota did not alter the typical lung histopathology of TB in the BALB/c model that includes unstructured immune cell infiltrates with infected foamy macrophages invading alveolar spaces. Animals of both cohorts mounted robust T cell responses in lungs and spleen with lower absolute counts of CD4 and CD8 T cells in lungs of WildR mice during acute infection, corresponding with observed differences in pathogen load. In summary, LabC mice and WildR mice showed largely overlapping TB immunopathology and pathogen kinetics, with WildR mice controlling early acute infection better than LabC mice.}, } @article {pmid37493648, year = {2023}, author = {Breusing, C and Xiao, Y and Russell, SL and Corbett-Detig, RB and Li, S and Sun, J and Chen, C and Lan, Y and Qian, PY and Beinart, RA}, title = {Ecological differences among hydrothermal vent symbioses may drive contrasting patterns of symbiont population differentiation.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0028423}, pmid = {37493648}, issn = {2379-5077}, support = {R35 GM128932/GM/NIGMS NIH HHS/United States ; K99 GM135583/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Hydrothermal Vents/microbiology ; *Mytilidae/genetics ; Bacteria/genetics ; Ecosystem ; Geography ; *Gastropoda/microbiology ; }, abstract = {The intra-host composition of horizontally transmitted microbial symbionts can vary across host populations due to interactive effects of host genetics, environmental, and geographic factors. While adaptation to local habitat conditions can drive geographic subdivision of symbiont strains, it is unknown how differences in ecological characteristics among host-symbiont associations influence the genomic structure of symbiont populations. To address this question, we sequenced metagenomes of different populations of the deep-sea mussel Bathymodiolus septemdierum, which are common at Western Pacific deep-sea hydrothermal vents and show characteristic patterns of niche partitioning with sympatric gastropod symbioses. Bathymodiolus septemdierum lives in close symbiotic relationship with sulfur-oxidizing chemosynthetic bacteria but supplements its symbiotrophic diet through filter-feeding, enabling it to occupy ecological niches with little exposure to geochemical reductants. Our analyses indicate that symbiont populations associated with B. septemdierum show structuring by geographic location, but that the dominant symbiont strain is uncorrelated with vent site. These patterns are in contrast to co-occurring Alviniconcha and Ifremeria gastropod symbioses that exhibit greater symbiont nutritional dependence and occupy habitats with higher spatial variability in environmental conditions. Our results suggest that relative habitat homogeneity combined with sufficient symbiont dispersal and genomic mixing might promote persistence of similar symbiont strains across geographic locations, while mixotrophy might decrease selective pressures on the host to affiliate with locally adapted symbiont strains. Overall, these data contribute to our understanding of the potential mechanisms influencing symbiont population structure across a spectrum of marine microbial symbioses that occupy contrasting ecological niches. IMPORTANCE Beneficial relationships between animals and microbial organisms (symbionts) are ubiquitous in nature. In the ocean, microbial symbionts are typically acquired from the environment and their composition across geographic locations is often shaped by adaptation to local habitat conditions. However, it is currently unknown how generalizable these patterns are across symbiotic systems that have contrasting ecological characteristics. To address this question, we compared symbiont population structure between deep-sea hydrothermal vent mussels and co-occurring but ecologically distinct snail species. Our analyses show that mussel symbiont populations are less partitioned by geography and do not demonstrate evidence for environmental adaptation. We posit that the mussel's mixotrophic feeding mode may lower its need to affiliate with locally adapted symbiont strains, while microhabitat stability and symbiont genomic mixing likely favors persistence of symbiont strains across geographic locations. Altogether, these findings further our understanding of the mechanisms shaping symbiont population structure in marine environmentally transmitted symbioses.}, } @article {pmid37493577, year = {2023}, author = {Zhu, J and Song, Y and Xiao, Y and Ma, L and Hu, C and Yang, H and Wang, X and Lyu, W}, title = {Metagenomic reconstructions of caecal microbiome in Landes, Roman and Zhedong White geese.}, journal = {British poultry science}, volume = {64}, number = {5}, pages = {565-576}, doi = {10.1080/00071668.2023.2239172}, pmid = {37493577}, issn = {1466-1799}, mesh = {Animals ; *Geese ; Chickens ; *Microbiota ; Bacteria/genetics ; Cecum ; Carbohydrates ; }, abstract = {1. The caecal microbiota in geese play a crucial role in determining the host's health, disease status and behaviour, as evidenced by extensive epidemiological data. The present investigation conducted 10× metagenomic sequencing of caecal content samples obtained from three distinct goose species, namely Landes geese, Roman geese and Zhedong White geese (n = 5), to explore the contribution of the gut microbiome to carbohydrate metabolism.2. In total, 337GB of Illumina data were generated, which identified 1,048,575 complete genes and construction of 331 metagenomic bins, encompassing 78 species from nine phyla. Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Bacteria were identified as the dominant phyla while Prevotella, Bacteroides, Streptococcus, and Subdoligranulum were the most abundant genera in the caecum of geese.3. The genes were allocated to 375 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) analysis. The most abundant classes in the caecum of geese were confirmed to be glycoside hydrolases (GHs), glycosyl transferases (GTs), as identified through the carbohydrate-active enzyme (CAZyme) database mapping. Subdoligranulum variabile and Mediterraneibacter glycyrrhizinilyticus were discovered to potentially facilitate carbohydrate digestion in geese.4. Notwithstanding, further investigation and validation are required to establish a connection between these species and CAZymes. Based on binning analysis, Mediterraneibacter glycyrrhizinilyticus and Ruminococcus sp. CAG:177 are potential species in LD geese that contribute to the production of fatty liver.}, } @article {pmid37491386, year = {2023}, author = {Zhang, D and Li, X and Wu, Y and Xu, X and Liu, Y and Shi, B and Peng, Y and Dai, D and Sha, Z and Zheng, J}, title = {Microbe-driven elemental cycling enables microbial adaptation to deep-sea ferromanganese nodule sediment fields.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {160}, pmid = {37491386}, issn = {2049-2618}, mesh = {*Manganese/metabolism ; *Ferric Compounds/metabolism ; Geologic Sediments/microbiology ; Bacteria ; Iron/metabolism ; Archaea ; }, abstract = {BACKGROUND: Ferromanganese nodule-bearing deep-sea sediments cover vast areas of the ocean floor, representing a distinctive habitat in the abyss. These sediments harbor unique conditions characterized by high iron concentration and low degradable nutrient levels, which pose challenges to the survival and growth of most microorganisms. While the microbial diversity in ferromanganese nodule-associated sediments has been surveyed several times, little is known about the functional capacities of the communities adapted to these unique habitats.

RESULTS: Seven sediment samples collected adjacent to ferromanganese nodules from the Clarion-Clipperton Fracture Zone (CCFZ) in the eastern Pacific Ocean were subjected to metagenomic analysis. As a result, 179 high-quality metagenome-assembled genomes (MAGs) were reconstructed and assigned to 21 bacterial phyla and 1 archaeal phylum, with 88.8% of the MAGs remaining unclassified at the species level. The main mechanisms of resistance to heavy metals for microorganisms in sediments included oxidation (Mn), reduction (Cr and Hg), efflux (Pb), synergy of reduction and efflux (As), and synergy of oxidation and efflux (Cu). Iron, which had the highest content among all metallic elements, may occur mainly as Fe(III) that potentially functioned as an electron acceptor. We found that microorganisms with a diverse array of CAZymes did not exhibit higher community abundance. Instead, microorganisms mainly obtained energy from oxidation of metal (e.g., Mn(II)) and sulfur compounds using oxygen or nitrate as an electron acceptor. Chemolithoautotrophic organisms (Thaumarchaeota and Nitrospirota phyla) were found to be potential manganese oxidizers. The functional profile analysis of the dominant microorganisms further indicated that utilization of inorganic nutrients by redox reactions (rather than organic nutrient metabolism) is a major adaptive strategy used by microorganisms to support their survival in the ferromanganese nodule sediments.

CONCLUSIONS: This study provides a comprehensive metagenomic analysis of microbes inhabiting metal-rich ferromanganese nodule sediments. Our results reveal extensive redundancy across taxa for pathways of metal resistance and transformation, the highly diverse mechanisms used by microbes to obtain nutrition, and their participation in various element cycles in these unique environments. Video Abstract.}, } @article {pmid37490989, year = {2024}, author = {Deng, Z and Ouyang, Z and Mei, S and Zhang, X and Li, Q and Meng, F and Hu, Y and Dai, X and Zhou, S and Mao, K and Huang, C and Dai, J and Yi, C and Tan, N and Feng, T and Long, H and Tian, X}, title = {Enhancing NKT cell-mediated immunity against hepatocellular carcinoma: Role of XYXD in promoting primary bile acid synthesis and improving gut microbiota.}, journal = {Journal of ethnopharmacology}, volume = {318}, number = {Pt B}, pages = {116945}, doi = {10.1016/j.jep.2023.116945}, pmid = {37490989}, issn = {1872-7573}, mesh = {Animals ; *Carcinoma, Hepatocellular/drug therapy ; *Drugs, Chinese Herbal/pharmacology ; *Gastrointestinal Microbiome ; *Liver Neoplasms/drug therapy ; Bile Acids and Salts ; Immunity, Cellular ; }, abstract = {'Xiayuxue decoction' (XYXD) is a traditional Chinese medicine compound, composing of three natural medicines: Rheum officinale Baill., Prunus persica (L.) Batsch and Eupolyphaga sinensis Walker. It is derived from the famous traditional Chinese medical classics 'Jingui Yaolue' and has been used for thousands of years. In the Guidelines for the Diagnosis and Treatment of Primary liver Cancer issued by China's Health Commission, XYXD was applied in the treatment of primary liver cancer.

AIM OF THE STUDY: To clarify the pharmacodynamic material basis and mechanism of XYXD in the treatment of hepatocellular carcinoma (HCC).

MATERIALS AND METHODS: Firstly, the active components of XYXD and its distribution in vivo were identified by Ultraperformance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). Then, the effective components and mechanism of XYXD against HCC were explored by network pharmacology combined with cell experiments in vitro. Furthermore, the anti-HCC effect of XYXD was determined by animal experiments in vivo. Metagenomic sequencing was used to detect its effect in gut microbiota, and targeted metabolism was used to detect the changes of bile acids in the liver. Finally, the related targets of NKT cell immune function activation were detected by RT-qPCR and Elisa.

RESULTS: A total of 113 active ingredients in XYXD were identified, and the distribution of active ingredients in blood, liver, tumor, cecum, intestinal contents and feces was clarified. The circulation process and active ingredient group of XYXD were preliminarily clarified. In addition, we found five anti-HCC active ingredients in XYXD through network pharmacology combined with cell experiments in vitro, among which aloe emodin had the most significant effect, and predicted the potential mechanism of XYXD against HCC through NKT cell pathway. Moreover, the inhibitory effect of XYXD on liver tumor growth was clarified by animal experiments in vivo. The mechanism was mainly to promote the production of bile salt hydrolase (BSH) by increasing the abundance of Bacteroides and Lactobacillus, BSH converts conjugated bile acids into primary bile acids, and reduces the conversion of primary bile acids to secondary bile acids by reducing the abundance of Eubacterium, thereby increasing the content of primary bile acids. Primary bile acids trigger NKT cells in the liver to produce interferon-γ to exert anti-HCC immune effects.

CONCLUSION: This study found that the traditional Chinese herbal formula XYXD can trigger the immune effect of NKT cells against HCC by regulating the interaction between gut microbiota and bile acids.}, } @article {pmid37489282, year = {2023}, author = {Thorburn, DJ and Sagonas, K and Binzer-Panchal, M and Chain, FJJ and Feulner, PGD and Bornberg-Bauer, E and Reusch, TBH and Samonte-Padilla, IE and Milinski, M and Lenz, TL and Eizaguirre, C}, title = {Origin matters: Using a local reference genome improves measures in population genomics.}, journal = {Molecular ecology resources}, volume = {23}, number = {7}, pages = {1706-1723}, doi = {10.1111/1755-0998.13838}, pmid = {37489282}, issn = {1755-0998}, support = {EI 841/4-1//Deutsche Forschungsgemeinschaft/ ; EI 841/6-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Metagenomics ; Genome/genetics ; Chromosome Mapping ; Genomics/methods ; Sequence Analysis, DNA/methods ; *Smegmamorpha/genetics ; }, abstract = {Genome sequencing enables answering fundamental questions about the genetic basis of adaptation, population structure and epigenetic mechanisms. Yet, we usually need a suitable reference genome for mapping population-level resequencing data. In some model systems, multiple reference genomes are available, giving the challenging task of determining which reference genome best suits the data. Here, we compared the use of two different reference genomes for the three-spined stickleback (Gasterosteus aculeatus), one novel genome derived from a European gynogenetic individual and the published reference genome of a North American individual. Specifically, we investigated the impact of using a local reference versus one generated from a distinct lineage on several common population genomics analyses. Through mapping genome resequencing data of 60 sticklebacks from across Europe and North America, we demonstrate that genetic distance among samples and the reference genomes impacts downstream analyses. Using a local reference genome increased mapping efficiency and genotyping accuracy, effectively retaining more and better data. Despite comparable distributions of the metrics generated across the genome using SNP data (i.e. π, Tajima's D and FST), window-based statistics using different references resulted in different outlier genes and enriched gene functions. A marker-based analysis of DNA methylation distributions had a comparably high overlap in outlier genes and functions, yet with distinct differences depending on the reference genome. Overall, our results highlight how using a local reference genome decreases reference bias to increase confidence in downstream analyses of the data. Such results have significant implications in all reference-genome-based population genomic analyses.}, } @article {pmid37488221, year = {2023}, author = {Sun, J and Germain, A and Kaglan, G and Servant, F and Lelouvier, B and Federici, M and Fernandez-Real, JM and Sala, DT and Neagoe, RM and Bouloumié, A and Burcelin, R}, title = {The visceral adipose tissue bacterial microbiota provides a signature of obesity based on inferred metagenomic functions.}, journal = {International journal of obesity (2005)}, volume = {47}, number = {10}, pages = {1008-1022}, pmid = {37488221}, issn = {1476-5497}, mesh = {Animals ; Humans ; *Intra-Abdominal Fat/metabolism ; Obesity/metabolism ; *Microbiota ; Obesity, Abdominal/metabolism ; Inflammation/metabolism ; Adipose Tissue/metabolism ; }, abstract = {BACKGROUND: Metabolic inflammation mediated obesity requires bacterial molecules to trigger immune and adipose cells leading to inflammation and adipose depot development. In addition to the well-established gut microbiota dysbiosis, a leaky gut has been identified in patients with obesity and animal models, characterized by the presence of a tissue microbiota in the adipose fat pads.

METHODS: To determine its potential role, we sequenced the bacterial 16 S rRNA genes in the visceral adipose depot of patients with obesity. Taking great care (surgical, biochemical, and bioinformatic) to avoid environmental contaminants. We performed statistical discriminant analyses to identify specific signatures and constructed network of interactions between variables.

RESULTS: The data showed that a specific 16SrRNA gene signature was composed of numerous bacterial families discriminating between lean versus patients with obesity and people with severe obesity. The main discriminant families were Burkholderiaceae, Yearsiniaceae, and Xanthomonadaceae, all of which were gram-negative. Interestingly, the Morganellaceae were totally absent from people without obesity while preponderant in all in patients with obesity. To generate hypotheses regarding their potential role, we inferred metabolic pathways from the 16SrRNA gene signatures. We identified several pathways associated with adenosyl-cobalamine previously described to be linked with adipose tissue development. We further identified chorismate biosynthesis, which is involved in aromatic amino-acid metabolism and could play a role in fat pad development. This innovative approach generates novel hypotheses regarding the gut to adipose tissue axis.

CONCLUSIONS: This innovative approach generates novel hypotheses regarding the gut to adipose tissue axis in obesity and notably the potential role of tissue microbiota.}, } @article {pmid37487417, year = {2023}, author = {Armstrong, AJS and Horton, DB and Andrews, T and Greenberg, P and Roy, J and Gennaro, ML and Carson, JL and Panettieri, RA and Barrett, ES and Blaser, MJ}, title = {Saliva microbiome in relation to SARS-CoV-2 infection in a prospective cohort of healthy US adults.}, journal = {EBioMedicine}, volume = {94}, number = {}, pages = {104731}, pmid = {37487417}, issn = {2352-3964}, support = {R01 AI158911/AI/NIAID NIH HHS/United States ; R33 HD105619/HD/NICHD NIH HHS/United States ; R61 HD105619/HD/NICHD NIH HHS/United States ; UL1 TR003017/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Adult ; *COVID-19 ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; SARS-CoV-2 ; Saliva ; *Microbiota ; }, abstract = {BACKGROUND: The clinical outcomes of SARS-CoV-2 infection vary in severity, potentially influenced by the resident human microbiota. There is limited consensus on conserved microbiome changes in response to SARS-CoV-2 infection, with many studies focusing on severely ill individuals. This study aimed to assess the variation in the upper respiratory tract microbiome using saliva specimens in a cohort of individuals with primarily mild to moderate disease.

METHODS: In early 2020, a cohort of 831 adults without known SARS-CoV-2 infection was followed over a six-month period to assess the occurrence and natural history of SARS-CoV-2 infection. From this cohort, 81 participants with a SARS-CoV-2 infection, along with 57 unexposed counterparts were selected with a total of 748 serial saliva samples were collected for analysis. Total bacterial abundance, composition, population structure, and gene function of the salivary microbiome were measured using 16S rRNA gene and shotgun metagenomic sequencing.

FINDINGS: The salivary microbiome remained stable in unexposed individuals over the six-month study period, as evidenced by all measured metrics. Similarly, participants with mild to moderate SARS-CoV-2 infection showed microbiome stability throughout and after their infection. However, there were significant reductions in microbiome diversity among SARS-CoV-2-positive participants with severe symptoms early after infection. Over time, the microbiome diversity in these participants showed signs of recovery.

INTERPRETATION: These findings demonstrate the resilience of the salivary microbiome in relation to SARS-CoV-2 infection. Mild to moderate infections did not significantly disrupt the stability of the salivary microbiome, suggesting its ability to maintain its composition and function. However, severe SARS-CoV-2 infection was associated with temporary reductions in microbiome diversity, indicating the limits of microbiome resilience in the face of severe infection.

FUNDING: This project was supported in part by Danone North America and grants from the National Institutes of Health, United States.}, } @article {pmid37485826, year = {2023}, author = {Jaramillo-Jaramillo, AS and Coulson, TJD and Hofacre, C and Jones, M and O'Neill, L and Nguyen, N and Labbe, A}, title = {Effect of in-water administration of quorum system inhibitors in broilers' productive performance and intestinal microbiome in a mild necrotic enteritis challenge.}, journal = {Avian pathology : journal of the W.V.P.A}, volume = {52}, number = {5}, pages = {309-322}, doi = {10.1080/03079457.2023.2224260}, pmid = {37485826}, issn = {1465-3338}, mesh = {Animals ; *Bacterial Toxins/metabolism ; Enterotoxins/metabolism ; *Clostridium Infections/veterinary/microbiology ; Chickens/microbiology ; *Enteritis/veterinary/microbiology ; *Gastrointestinal Microbiome ; Clostridium perfringens/genetics ; Water/metabolism ; *Poultry Diseases/microbiology ; }, abstract = {The poultry industry has been facing the impact of necrotic enteritis (NE), a disease caused by the bacterium Clostridium perfringens producing the haemolytic toxin NetB. NE severity may vary from mild clinical to prominent enteric signs causing reduced growth rates and affecting feed conversion ratio. NetB production is controlled by the Agr-like quorum-sensing (QS) system, which coordinates virulence gene expression in response to bacterial cell density. In this study, the peptide-containing cell-free spent media (CFSM) from Enterococcus faecium was tested in NE challenged broilers in two battery cage and one floor pen studies. Results showed a significant reduction of NE mortality. Metagenomic sequencing of the jejunum microbiome revealed no impact of the CFSM on the microbial community, and growth of C. perfringens was unaffected by CFSM in vitro. The expression of QS-controlled virulence genes netB, plc and pfoA was found to be significantly repressed by CFSM during the mid-logarithmic stage of C. perfringens growth and this corresponded with a significant decrease in haemolytic activity. Purified fractions of CFSM containing bioactive peptides were found to cause reduced haemolysis. These results showed that bioactive peptides reduce NE mortality in broilers by interfering with the QS system of C. perfringens and reducing bacterial virulence. Furthermore, the microbiome of C. perfringens-challenged broilers is not affected by quorum sensing inhibitor containing CFSM.}, } @article {pmid37485738, year = {2023}, author = {Wuyts, S and Alves, R and Zimmermann-Kogadeeva, M and Nishijima, S and Blasche, S and Driessen, M and Geyer, PE and Hercog, R and Kartal, E and Maier, L and Müller, JB and Garcia Santamarina, S and Schmidt, TSB and Sevin, DC and Telzerow, A and Treit, PV and Wenzel, T and Typas, A and Patil, KR and Mann, M and Kuhn, M and Bork, P}, title = {Consistency across multi-omics layers in a drug-perturbed gut microbial community.}, journal = {Molecular systems biology}, volume = {19}, number = {9}, pages = {e11525}, pmid = {37485738}, issn = {1744-4292}, support = {MC_UU_00025/11/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Multiomics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metabolomics/methods ; Bacteria/genetics ; Metagenomics/methods ; }, abstract = {Multi-omics analyses are used in microbiome studies to understand molecular changes in microbial communities exposed to different conditions. However, it is not always clear how much each omics data type contributes to our understanding and whether they are concordant with each other. Here, we map the molecular response of a synthetic community of 32 human gut bacteria to three non-antibiotic drugs by using five omics layers (16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics and metabolomics). We find that all the omics methods with species resolution are highly consistent in estimating relative species abundances. Furthermore, different omics methods complement each other for capturing functional changes. For example, while nearly all the omics data types captured that the antipsychotic drug chlorpromazine selectively inhibits Bacteroidota representatives in the community, the metatranscriptome and metaproteome suggested that the drug induces stress responses related to protein quality control. Metabolomics revealed a decrease in oligosaccharide uptake, likely caused by Bacteroidota depletion. Our study highlights how multi-omics datasets can be utilized to reveal complex molecular responses to external perturbations in microbial communities.}, } @article {pmid37482646, year = {2024}, author = {Liu, K and Guo, Q and Ding, Y and Luo, L and Huang, J and Zhang, Q}, title = {Alterations in nasal microbiota of patients with amyotrophic lateral sclerosis.}, journal = {Chinese medical journal}, volume = {137}, number = {2}, pages = {162-171}, pmid = {37482646}, issn = {2542-5641}, mesh = {Humans ; *Amyotrophic Lateral Sclerosis/microbiology ; Feces/microbiology ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Links between alterations in gut microbiota composition and amyotrophic lateral sclerosis (ALS) have previously been reported. This study aimed to examine the microbiota in the nasal cavity of ALS.

METHODS: Sixty-six ALS patients and 40 healthy caregivers who live in close proximity with patients were enrolled. High throughput metagenomic sequencing of the 16S ribosomal deoxyribonucleic acid (rDNA) gene V3-V4 region of nasal microbiota was used to characterize the alpha and beta diversity and relative abundance of bacterial taxa, predict function, and conduct correlation analysis between specific taxa and clinical features.

RESULTS: The nasal microbiome of ALS patients showed lower alpha diversity than that of corresponding healthy family members. Genera Gaiella , Sphingomonas , Polaribacter _1, Lachnospiraceae _NK4A136_group, Klebsiella , and Alistipes were differentially enriched in ALS patients compared to controls. Nasal microbiota composition in ALS patients significantly differed from that in healthy subjects (unweighted UniFrac P = 0.001), while Linear discriminant analysis Effect Size (LEfSe) analysis indicated that Bacteroidetes and Firmicutes dominated healthy nasal communities at the phylum level, whereas Actinobacteria was the predominant phylum and Thermoleophilia was the predominant class in ALS patients. Genus Faecalibacterium and Alistipes were positively correlated with ALS functional rating scale revised (ALSFRS-R; rs = 0.349, P = 0.020 and rs = 0.393, P = 0.008), while Prevotella -9 and Bacteroides operational taxonomic units (OTUs) were positively associated with lung function (FVC) in ALS patients (rs = 0.304, P = 0.045, and rs = 0.300, P = 0.048, respectively). Prevotella -1 was positively correlated with white blood cell counts (WBC, rs = 0.347, P = 0.021), neutrophil percentage (Neu%, rs = 0.428, P = 0.004), and neutrophil-to-lymphocyte ratio (NLR, rs = 0.411, P = 0.006), but negatively correlated with lymphocyte percentage (Lym%, rs = -0.408, P = 0.006). In contrast, Streptococcus was negatively associated with Neu% (rs = -0.445, P = 0.003) and NLR (rs = -0.436, P = 0.003), while positively associated with Lym% (rs = 0.437, P = 0.003). No significant differences in nasal microbiota richness and evenness were detected among the severe and mild ALS patients.

CONCLUSIONS: ALS is accompanied by altered nasal microbial community composition and diversity. The findings presented here highlight the need to understand how dysbiosis of nasal microbiota may contribute to the development of ALS.}, } @article {pmid37482039, year = {2023}, author = {Yue, Z and Zhang, J and Zhang, J and Wang, X and Li, L and Yu, H and Liu, B and Li, Q and Zhu, D and Zou, Y}, title = {Combined virome analysis and metagenomic sequencing to reveal the viral communities and risk of virus-associated antibiotic resistance genes during composting.}, journal = {Journal of hazardous materials}, volume = {459}, number = {}, pages = {132088}, doi = {10.1016/j.jhazmat.2023.132088}, pmid = {37482039}, issn = {1873-3336}, mesh = {Humans ; Animals ; Swine ; *Metagenome ; Genes, Bacterial ; Virome ; *Composting/methods ; Anti-Bacterial Agents/pharmacology ; Biofuels ; Drug Resistance, Microbial/genetics ; Manure/microbiology ; }, abstract = {The issue of antibiotic resistance genes (ARGs) pollution in manure has garnered significant attention, with viruses now being recognized as crucial carriers and disseminators of ARGs. However, the virus-associated ARG profiles and potential health risks in composts are still unclear. In this study, the viral communities and associated ARGs in biogas residue and pig faeces composts were profiled by virome analysis. The viral communities were dominated by Caudovirales, and non-thermophilic viruses were inactivated during composting. The diversity and abundance of ARGs were lower in virome than in metagenome, while ARGs' risk was greater in virome than in metagenome. There were six bacterial genera identified as viral hosts at the genomic level, Pseudomonas and Clostridium carried high-risk ARGs. Virus-associated ARGs in viral hosts had a higher risk rank than non-virus-associated ARGs. Composting reduced the diversity, abundance and risk of viral ARGs. The risk of ARGs in biogas residues was significantly lower than that of pig faeces in the initial period of composting, and the two different substracts equally less harmful after composting. These results revealed that viruses play a non-negligible role in spreading ARGs, posing high risk to environmental and human health.}, } @article {pmid37480075, year = {2023}, author = {Tinta, T and Zhao, Z and Bayer, B and Herndl, GJ}, title = {Jellyfish detritus supports niche partitioning and metabolic interactions among pelagic marine bacteria.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {156}, pmid = {37480075}, issn = {2049-2618}, support = {J 4426/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Aquatic Organisms ; Bacteria/genetics/metabolism ; Carbohydrates ; Ecosystem ; *Gammaproteobacteria ; *Microbiota ; *Scyphozoa/chemistry/microbiology ; }, abstract = {BACKGROUND: Jellyfish blooms represent a significant but largely overlooked source of labile organic matter (jelly-OM) in the ocean, characterized by a high protein content. Decaying jellyfish are important carriers for carbon export to the ocean's interior. To accurately incorporate them into biogeochemical models, the interactions between microbes and jelly-OM have yet to be fully characterized. We conducted jelly-OM enrichment experiments in microcosms to simulate the scenario experienced by the coastal pelagic microbiome after the decay of a jellyfish bloom. We combined metagenomics, endo- and exo-metaproteomic approaches to obtain a mechanistic understanding on the metabolic network operated by the jelly-OM degrading bacterial consortium.

RESULTS: Our analysis revealed that OM released during the decay of jellyfish blooms triggers a rapid shuffling of the taxonomic and functional profile of the pelagic bacterial community, resulting in a significant enrichment of protein/amino acid catabolism-related enzymes in the jelly-OM degrading community dominated by Pseudoalteromonadaceae, Alteromonadaceae and Vibrionaceae, compared to unamended control treatments. In accordance with the proteinaceous character of jelly-OM, Pseudoalteromonadaceae synthesized and excreted enzymes associated with proteolysis, while Alteromonadaceae contributed to extracellular hydrolysis of complex carbohydrates and organophosphorus compounds. In contrast, Vibrionaceae synthesized transporter proteins for peptides, amino acids and carbohydrates, exhibiting a cheater-type lifestyle, i.e. benefiting from public goods released by others. In the late stage of jelly-OM degradation, Rhodobacteraceae and Alteromonadaceae became dominant, growing on jelly-OM left-overs or bacterial debris, potentially contributing to the accumulation of dissolved organic nitrogen compounds and inorganic nutrients, following the decay of jellyfish blooms.

CONCLUSIONS: Our findings indicate that specific chemical and metabolic fingerprints associated with decaying jellyfish blooms are substantially different to those previously associated with decaying phytoplankton blooms, potentially altering the functioning and biogeochemistry of marine systems. We show that decaying jellyfish blooms are associated with the enrichment in extracellular collagenolytic bacterial proteases, which could act as virulence factors in human and marine organisms' disease, with possible implications for marine ecosystem services. Our study also provides novel insights into niche partitioning and metabolic interactions among key jelly-OM degraders operating a complex metabolic network in a temporal cascade of biochemical reactions to degrade pulses of jellyfish-bloom-specific compounds in the water column. Video Abstract.}, } @article {pmid37479827, year = {2023}, author = {Hirata, K and Asahi, T and Kataoka, K}, title = {Spatial and Sexual Divergence of Gut Bacterial Communities in Field Cricket Teleogryllus occipitalis (Orthoptera: Gryllidae).}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2627-2641}, pmid = {37479827}, issn = {1432-184X}, mesh = {Animals ; Female ; Male ; *Gastrointestinal Microbiome ; *Gryllidae ; RNA, Ribosomal, 16S/genetics ; *Cricket Sport ; Bacteria/genetics ; }, abstract = {The insect gut is colonized by microbes that confer a myriad of beneficial services to the host, including nutritional support, immune enhancement, and even influence behavior. Insect gut microbes show dynamic changes due to the gut compartments, sex, and seasonal and geographic influences. Crickets are omnivorous hemimetabolous insects that have sex-specific roles, such as males producing chirping sounds for communication and exhibiting fighting behavior. However, limited information is available on their gut bacterial communities, hampering studies on functional compartmentalization of the gut and sex-specific roles of the gut microbiota in omnivorous insects. Here, we report a metagenomic analysis of the gut bacteriome of the field cricket Teleogryllus occipitalis using 16S rRNA V3-V4 amplicon sequencing to identify sex- and compartment-dependent influences on its diversity and function. The structure of the gut microbiota is strongly influenced by their gut compartments rather than sex. The species richness and diversity analyses revealed large difference in the bacterial communities between the gut compartments while minor differences were observed between the sexes. Analysis of relative abundance and predicted functions revealed that nitrogen- and oxygen-dependent metabolism and amino acid turnover were subjected to functional compartmentalization in the gut. Comparisons between the sexes revealed differences in the gut microbiota, reflecting efficiency in energy use, including glycolytic and carbohydrate metabolism, suggesting a possible involvement in egg production in females. This study provides insights into the gut compartment dependent and sex-specific roles of host-gut symbiont interactions in crickets and the industrial production of crickets.}, } @article {pmid37478939, year = {2023}, author = {Jin, L and Wu, H and Li, G and Yang, S and Wei, R and Huang, Y and Penttinen, P and Deng, W and Chen, J and Han, X and Li, C and Hu, L and Li, T and Zhang, H and Zhao, K and Zou, L}, title = {Gastrointestinal microbiome, resistance genes, and risk assessment of heavy metals in wild giant pandas.}, journal = {The Science of the total environment}, volume = {899}, number = {}, pages = {165671}, doi = {10.1016/j.scitotenv.2023.165671}, pmid = {37478939}, issn = {1879-1026}, mesh = {Animals ; *Ursidae ; *Gastrointestinal Microbiome ; *Metals, Heavy/analysis ; Anti-Bacterial Agents ; Risk Assessment ; Soil ; Genes, Bacterial ; }, abstract = {The gastrointestinal microbiome (GM) of giant panda (GP) plays an important role in food utilization and health and is also an essential reservoir of resistance genes. Currently, little knowledge is available on the GM, acid resistance genes (AcRGs), antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs) in wild GPs. We sampled the gastrointestinal tract of a dead GP and explored the composition and function of GM and resistance genes through cryo-scanning electron microscopy, metagenomic sequencing, and genome-resolved metagenomics. The concentration of metals in the gastrointestinal lumen, feces, bamboo, and soil was measured by inductively coupled plasma mass spectrometry. Results showed that the composition of the microbiota varied in different gastrointestinal regions. Fecal microbiota was highly associated with small intestinal and colonic microbes. The lignocellulosic cross-linked structure of bamboo was destroyed in the stomach initially and destroying degree increased from stomach to anus. Reconstruction of metagenome-assembled-genomes confirmed that core GM, e.g., Streptococcus, Clostridium, Lactococcus, Leuconostoc, and Enterococcus, carried genes encoding the lignocellulose degradation enzyme. There were no significant differences of resistance genes between gastrointestinal and fecal samples, except MGEs. Multidrug and multi-metal resistance genes were predominant in all samples, while the transposase gene tnpA was the major type of MGE. Significant correlations were observed among the abundance of GM, resistance genes, and MGEs. Gastrointestinal and fecal mercury and chromium were the main metals influencing GM and resistance genes. The content of gastrointestinal and fecal metals was significantly associated with the presence of the same metals in bamboo, which could pose a threat to the health of wild GPs. This study characterized the gastrointestinal microbiome of wild GPs, providing new evidence for the role of the gastrointestinal microbiome in degrading lignocellulose from bamboo and highlighting the urgent need to monitor metal levels in soil and bamboo.}, } @article {pmid37478933, year = {2023}, author = {Yan, Q and Xu, Y and Zhong, Z and Xu, Y and Lin, X and Cao, Z and Feng, G}, title = {Insights into antibiotic resistance-related changes in microbial communities, resistome and mobilome in paddy irrigated with reclaimed wastewater.}, journal = {The Science of the total environment}, volume = {900}, number = {}, pages = {165672}, doi = {10.1016/j.scitotenv.2023.165672}, pmid = {37478933}, issn = {1879-1026}, mesh = {*Wastewater ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology/analysis ; Soil ; *Microbiota ; Drug Resistance, Microbial/genetics ; }, abstract = {Reclaimed wastewater (reclaimed wastewater, RWW) from municipal wastewater treatment plants for paddy irrigation is a well-established practice to alleviate water scarcity. However, the reuse may result in the persistent exposure of the paddy to residual antibiotics in RWW. Continuous presence of even low-level antibiotics can exert selective pressure on microbiota, resulting in the proliferation and dissemination of antibiotic resistance genes (ARGs) in paddy. In this study, metagenomic analysis was applied to firstly deciphered the effects of residual antibiotics on microbiome and resistome in constructed mesocosm-scale paddy soils. The diversity and abundance of ARG have remarkably risen with the increasing antibiotic concentration in RWW. Network analysis revealed that 28 genera belonging to six phyla were considered as the potential ARG hosts, and their abundances were enhanced with increasing antibiotic concentrations. A partial least-squares path model indicated that the microbial community was the principal direct driver of the ARG abundance and the resistome alteration in paddy soil under long-term RWW irrigation. Microbes may acquire ARGs via horizontal gene transfer. IntI1 could play an essential role in the propagation and spread of ARGs. Functional analysis suggested that enhanced SOS response and T4SSs (Type IV secretion systems) modules could stimulate horizontal transfer potential and promote the ARG abundance. The obtained results provide a scientific decision for assessing the ecological risk of RWW application.}, } @article {pmid37478472, year = {2023}, author = {Ke, Y and Sun, W and Chen, X and Zhu, Y and Guo, X and Yan, W and Xie, S}, title = {Seasonality Determines the Variations of Biofilm Microbiome and Antibiotic Resistome in a Pilot-Scale Chlorinated Drinking Water Distribution System Deciphered by Metagenome Assembly.}, journal = {Environmental science & technology}, volume = {57}, number = {31}, pages = {11430-11441}, doi = {10.1021/acs.est.3c01980}, pmid = {37478472}, issn = {1520-5851}, mesh = {Anti-Bacterial Agents/pharmacology ; Metagenome ; *Drinking Water ; Genes, Bacterial ; *Microbiota ; Biofilms ; }, abstract = {Understanding the biofilm microbiome and antibiotic resistome evolution in drinking water distribution systems (DWDSs) is crucial to ensure the safety of drinking water. We explored the 10 month evolution of the microbial community, antibiotic resistance genes (ARGs), mobile gene elements (MGEs) co-existing with ARGs and pathogenic ARG hosts, and the ARG driving factors in DWDS biofilms using metagenomics assembly. Sampling season was critical in determining the microbial community and antibiotic resistome shift. Pseudomonas was the primary biofilm colonizer, and biofilms diversified more as the formation time increased. Most genera tended to cooperate to adapt to an oligotrophic environment with disinfectant stress. Biofilm microbial community and antibiotic resistome assembly were mainly determined by stochastic processes and changed with season. Metagenome assembly provided the occurrence and fates of MGEs co-existing with ARGs and ARG hosts in DWDS biofilms. The abundance of ARG- and MGE-carrying pathogen Stenotrophomonas maltophilia was high in summer. It primarily harbored the aph(3)-IIb, multidrug transporter, smeD, and metallo-beta-lactamase ARGs, which were transferred via recombination. The microbial community was the most crucial factor driving the antibiotic resistance shift. We provide novel insights about the evolution of pathogens and ARGs and their correlations in DWDS biofilms to ensure the safety of drinking water.}, } @article {pmid37475130, year = {2023}, author = {Yang, G and Cao, JM and Cui, HL and Zhan, XM and Duan, G and Zhu, YG}, title = {Artificial Sweetener Enhances the Spread of Antibiotic Resistance Genes During Anaerobic Digestion.}, journal = {Environmental science & technology}, volume = {57}, number = {30}, pages = {10919-10928}, doi = {10.1021/acs.est.2c08673}, pmid = {37475130}, issn = {1520-5851}, mesh = {*Sweetening Agents/pharmacology ; Drug Resistance, Microbial/drug effects/genetics ; Anaerobiosis/drug effects ; Genes, Bacterial ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; }, abstract = {Artificial sweeteners have been frequently detected in the feedstocks of anaerobic digestion. As these sweeteners can lead to the shift of anaerobic microbiota in the gut similar to that caused by antibiotics, we hypothesize that they may have an antibiotic-like impact on antibiotic resistance genes (ARGs) in anaerobic digestion. However, current understanding on this topic is scarce. This investigation aimed to examine the potential impact of acesulfame, a typical artificial sweetener, on ARGs in anaerobic digestion by using metagenomics sequencing and qPCR. It was found that acesulfame increased the number of detected ARG classes and the abundance of ARGs during anaerobic digestion. The abundance of typical mobile genetic elements (MGEs) and the number of potential hosts of ARGs also increased under acesulfame exposure, suggesting the enhanced potential of horizontal gene transfer of ARGs, which was further confirmed by the correlation analysis between absolute abundances of the targeted ARGs and MGEs. The increased horizontal dissemination of ARGs may be associated with the SOS response induced by the increased ROS production, and the increased cellular membrane permeability. These findings indicate that artificial sweeteners may accelerate ARG spread through digestate disposal, thus corresponding strategies should be considered to prevent potential risks in practice.}, } @article {pmid37474497, year = {2023}, author = {Mirhakkak, MH and Chen, X and Ni, Y and Heinekamp, T and Sae-Ong, T and Xu, LL and Kurzai, O and Barber, AE and Brakhage, AA and Boutin, S and Schäuble, S and Panagiotou, G}, title = {Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4369}, pmid = {37474497}, issn = {2041-1723}, mesh = {Male ; Female ; Humans ; Aspergillus fumigatus/genetics ; *Cystic Fibrosis/microbiology ; Lung ; *Microbiota/genetics ; }, abstract = {Aspergillus fumigatus, an opportunistic human pathogen, frequently infects the lungs of people with cystic fibrosis and is one of the most common causes of infectious-disease death in immunocompromised patients. Here, we construct 252 strain-specific, genome-scale metabolic models of this important fungal pathogen to study and better understand the metabolic component of its pathogenic versatility. The models show that 23.1% of A. fumigatus metabolic reactions are not conserved across strains and are mainly associated with amino acid, nucleotide, and nitrogen metabolism. Profiles of non-conserved reactions and growth-supporting reaction fluxes are sufficient to differentiate strains, for example by environmental or clinical origin. In addition, shotgun metagenomics analysis of sputum from 40 cystic fibrosis patients (15 females, 25 males) before and after diagnosis with an A. fumigatus colonization suggests that the fungus shapes the lung microbiome towards a more beneficial fungal growth environment associated with aromatic amino acid availability and the shikimate pathway. Our findings are starting points for the development of drugs or microbiome intervention strategies targeting fungal metabolic needs for survival and colonization in the non-native environment of the human lung.}, } @article {pmid37474105, year = {2023}, author = {Kyaw, TS and Upadhyay, V and Tolstykh, I and Van Loon, K and Laffan, A and Stanfield, D and Gempis, D and Kenfield, SA and Chan, JM and Piawah, S and Atreya, CE and Ng, K and Venook, A and Kidder, W and Turnbaugh, PJ and Van Blarigan, EL}, title = {Variety of Fruit and Vegetables and Alcohol Intake are Associated with Gut Microbial Species and Gene Abundance in Colorectal Cancer Survivors.}, journal = {The American journal of clinical nutrition}, volume = {118}, number = {3}, pages = {518-529}, pmid = {37474105}, issn = {1938-3207}, support = {K08 HL165106/HL/NHLBI NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; F30 CA257378/CA/NCI NIH HHS/United States ; R01 AT011117/AT/NCCIH NIH HHS/United States ; R37 CA248774/CA/NCI NIH HHS/United States ; R01 DK114034/DK/NIDDK NIH HHS/United States ; R21 CA227232/CA/NCI NIH HHS/United States ; R01 CA205406/CA/NCI NIH HHS/United States ; R01 AR074500/AR/NIAMS NIH HHS/United States ; P30 DK098722/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Vegetables ; Fruit ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Diet/methods ; Alcohol Drinking ; *Cancer Survivors ; *Colorectal Neoplasms ; }, abstract = {BACKGROUND: Adherence to the American Cancer Society (ACS) guidelines of avoiding obesity, maintaining physical activity, and consuming a diet rich in fruits, vegetables, and whole grains is associated with longer survival in colorectal cancer (CRC) survivors. Dietary components of the ACS guidelines may act in part by changing the microbiome, which is implicated in CRC outcomes.

OBJECTIVES: We conducted a pilot cross-sectional study to explore associations between ACS guidelines and the gut microbiome.

METHODS: Stool samples and questionnaires were collected from 28 CRC survivors at the University of California, San Francisco from 2019 to 2020. ACS scores were calculated based on validated questionnaires. Gut microbial community structure from 16S amplicons and gene/pathway abundances from metagenomics were tested for associations with the ACS score and its components using ANOVA and general linear models.

RESULTS: The overall ACS score was not significantly associated with variations in the fecal microbiota. However, fruit and vegetable intake and alcohol intake accounted for 19% (P = 0.005) and 13% (P = 0.01) of variation in the microbiota, respectively. Fruit/vegetable consumption was associated with increased microbial diversity, increased Firmicutes, decreased Bacteroidota, and changes to multiple genes and metabolic pathways, including enriched pathways for amino acid and short-chain fatty acid biosynthesis and plant-associated sugar degradation. In contrast, alcohol consumption was positively associated with overall microbial diversity, negatively associated with Bacteroidota abundance, and associated with changes to multiple genes and metabolic pathways. The other components of the ACS score were not statistically significantly associated with the fecal microbiota in our sample.

CONCLUSIONS: These results guide future studies examining the impact of changes in the intake of fruits, vegetables, and alcoholic drinks on the gut microbiome of CRC survivors.}, } @article {pmid37471465, year = {2024}, author = {Essex, M and Rios Rodriguez, V and Rademacher, J and Proft, F and Löber, U and Markó, L and Pleyer, U and Strowig, T and Marchand, J and Kirwan, JA and Siegmund, B and Forslund, SK and Poddubnyy, D}, title = {Shared and Distinct Gut Microbiota in Spondyloarthritis, Acute Anterior Uveitis, and Crohn's Disease.}, journal = {Arthritis & rheumatology (Hoboken, N.J.)}, volume = {76}, number = {1}, pages = {48-58}, doi = {10.1002/art.42658}, pmid = {37471465}, issn = {2326-5205}, support = {Food allergy and tolerance (FOOD@-Project ID 428046232)//Deutsche Forschungsgemeinschaft/ ; CRC1449//Deutsche Forschungsgemeinschaft/ ; CRC-TRR241//Deutsche Forschungsgemeinschaft/ ; EXC 2155 "RESIST" (Project ID 390874280//Deutsche Forschungsgemeinschaft/ ; //German Research Foundation/ ; //German Federal Ministry for Health and Research (BMBF)/ ; //Novartis/ ; //BIH-Charité Clinician Scientist Program/ ; //Charité-Universitätsmedizin Berlin/ ; }, mesh = {Humans ; *Crohn Disease/drug therapy/complications ; *Gastrointestinal Microbiome/genetics ; *Spondylarthritis/drug therapy/complications ; *Uveitis, Anterior/drug therapy ; *Antirheumatic Agents ; Clostridiales/metabolism ; HLA-B27 Antigen/genetics ; Acute Disease ; }, abstract = {OBJECTIVE: Spondyloarthritis (SpA) is a group of immune-mediated diseases highly concomitant with nonmusculoskeletal inflammatory disorders, such as acute anterior uveitis (AAU) and Crohn's disease (CD). The gut microbiome represents a promising avenue to elucidate shared and distinct underlying pathophysiology.

METHODS: We performed 16S ribosomal RNA sequencing on stool samples of 277 patients (72 CD, 103 AAU, and 102 SpA) included in the German Spondyloarthritis Inception Cohort and 62 back pain controls without any inflammatory disorder. Discriminatory statistical methods were used to disentangle microbial disease signals from one another and a wide range of potential confounders. Patients were naive to or had not received treatment with biological disease-modifying antirheumatic drugs (DMARDs) for >3 months before enrollment, providing a better approximation of a true baseline disease signal.

RESULTS: We identified a shared, immune-mediated disease signal represented by low abundances of Lachnospiraceae taxa relative to controls, most notably Fusicatenibacter, which was most abundant in controls receiving nonsteroidal antiinflammatory drug monotherapy and implied to partially mediate higher serum C-reactive protein. Patients with SpA showed an enrichment of Collinsella, whereas human leukocyte antigen (HLA)-B27+ individuals displayed enriched Faecalibacterium. CD patients had higher abundances of a Ruminococcus taxon, and previous conventional/synthetic DMARD therapy was associated with increased Akkermansia.

CONCLUSION: Our work supports the existence of a common gut dysbiosis in SpA and related inflammatory pathologies. We reveal shared and disease-specific microbial associations and suggest potential mediators of disease activity. Validation studies are needed to clarify the role of Fusicatenibacter in gut-joint inflammation, and metagenomic resolution is needed to understand the relationship between Faecalibacterium commensals and HLA-B27.}, } @article {pmid37467988, year = {2023}, author = {Wu, ZH and Yang, XD and Huang, LY and Li, SL and Xia, FY and Qiu, YZ and Yi, XZ and Jia, P and Liao, B and Liang, JL and Shu, WS and Li, JT}, title = {In situ enrichment of sulphate-reducing microbial communities with different carbon sources stimulating the acid mine drainage sediments.}, journal = {The Science of the total environment}, volume = {898}, number = {}, pages = {165584}, doi = {10.1016/j.scitotenv.2023.165584}, pmid = {37467988}, issn = {1879-1026}, mesh = {*Sulfates ; Phylogeny ; Bacteria/genetics ; Archaea ; *Microbiota ; Acids ; }, abstract = {The applications of sulphate-reducing microorganisms (SRMs) in acid mine drainage (AMD) treatment systems have received extensive attention due to their ability to reduce sulphate and stabilize metal(loid)s. Despite great phylogenetic diversity of SRMs, only a few have been used in AMD treatment bioreactors. In situ enrichment could be an efficient approach to select new effective SRMs for AMD treatment. Here, we performed in situ enrichment of SRMs in highly stratified AMD sediment cores using different kinds of carbon source mixture. The dsrAB (dissimilatory sulfite reductase) genes affiliated with nine phyla (two archaeal and seven bacterial phyla) and 26 genera were enriched. Remarkably, those genes affiliated with Aciduliprofundum and Vulcanisaeta were enriched in situ in AMD-related environments for the first time, and their relative abundances were negatively correlated with pH. Furthermore, 107 dsrAB-containing metagenome-assembled genomes (MAGs) were recovered from metagenomic datasets, with 14 phyla (two archaeal and 12 bacterial phyla) and 15 genera. The relative abundances of MAGs were positively correlated with total carbon and sulphate contents. Our findings expanded the diversity of SRMs that can be enriched in AMD sediment, and revealed the physiochemical properties that might affect the growth of SRMs, which provided guidance for AMD treatment bioreators.}, } @article {pmid37465976, year = {2023}, author = {White, MG and Damania, A and Alshenaifi, J and Sahasrabhojane, P and Peacock, O and Losh, J and Wong, MC and Lutter-Berkova, Z and Chang, GJ and Futreal, A and Wargo, JA and Ajami, NJ and Kopetz, S and You, YN}, title = {Young-onset Rectal Cancer: Unique Tumoral Microbiome and Correlation With Response to Neoadjuvant Therapy.}, journal = {Annals of surgery}, volume = {278}, number = {4}, pages = {538-548}, pmid = {37465976}, issn = {1528-1140}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Middle Aged ; Neoadjuvant Therapy ; *Rectal Neoplasms/therapy/pathology ; Biopsy ; *Microbiota ; }, abstract = {OBJECTIVE: External exposures, the host, and the microbiome interact in oncology. We aimed to investigate tumoral microbiomes in young-onset rectal cancers (YORCs) for profiles potentially correlative with disease etiology and biology.

BACKGROUND: YORC is rapidly increasing, with 1 in 4 new rectal cancer cases occurring under the age of 50 years. Its etiology is unknown.

METHODS: YORC (<50 y old) or later-onset rectal cancer (LORC, ≥50 y old) patients underwent pretreatment biopsied of tumor and tumor-adjacent normal (TAN) tissue. After whole genome sequencing, metagenomic analysis quantified microbial communities comparing tumors versus TANs and YORCs versus LORCs, controlling for multiple testing. Response to neoadjuvant therapy (NT) was categorized as major pathological response (MPR, ≤10% residual viable tumor) versus non-MPR.

RESULTS: Our 107 tumors, 75 TANs from 37 (35%) YORCs, and 70 (65%) LORCs recapitulated bacterial species were previously associated with colorectal cancers (all P <0.0001). YORC and LORC tumoral microbiome signatures were distinct. After NT, 13 patients (12.4%) achieved complete pathologic response, whereas MPR occurred in 47 patients (44%). Among YORCs, MPR was associated with Fusobacterium nucleaum , Bacteroides dorei, and Ruminococcus bromii (all P <0.001), but MPR in LORC was associated with R. bromii (P <0.001). Network analysis of non-MPR tumors demonstrated a preponderance of oral bacteria not observed in MPR tumors.

CONCLUSIONS: Microbial signatures were distinct between YORC and LORC. Failure to achieve an MPR was associated with oral bacteria in tumors. These findings urge further studies to decipher correlative versus mechanistic associations but suggest a potential for microbial modulation to augment current treatments.}, } @article {pmid37464937, year = {2023}, author = {Chen, HY and Li, CQ and Chen, SY and Xiao, H}, title = {Metagenomic analysis reveals hidden links between gut microbes and habitat adaptation among cave and surface dwelling Sinocyclocheilus species.}, journal = {Zoological research}, volume = {44}, number = {4}, pages = {793-807}, pmid = {37464937}, issn = {2095-8137}, mesh = {Animals ; Phylogeny ; Caves ; *Gastrointestinal Microbiome ; *Cyprinidae/genetics ; Ecosystem ; }, abstract = {Intestinal microbes are closely related to vital host functions such as digestion and nutrient absorption, which play important roles in enhancing host adaptability. As a natural "laboratory", caves provide an outstanding model for understanding the significance of gut microbes and feeding habits in the habitat adaptability of hosts. However, research on the relationship between gut microbes, feeding habits, and the adaptability of troglobites remains insufficient. In this study, we compared the characteristics of the intestinal microbes of Sinocyclocheilus cavefish and surface fish and further established the relationship between intestinal and habitat microbes. Furthermore, we conducted environmental DNA (eDNA) (metabarcoding) analysis of environmental samples to clarify the composition of potential food resources in the habitats of the Sinocyclocheilus cavefish and surface fish. Results showed that the structure of the Sinocyclocheilus gut microbes was more related to ecological type (habitat type) than phylogenetic relationships. While horizontal transfer of habitat microbes was a source of gut microbes, hosts also showed strong selection for inherent microbes as dominant microorganisms. Differences in the composition and structure of gut microbes, especially dominant microbes, may enhance the adaptability of the two Sinocyclocheilus fish types from the perspectives of food intake, nutrient utilization, and harmful substance metabolism, suggesting that food resources, predation patterns, intestinal flora, digestive and absorptive capacity, and feeding habits and preferences are linked to habitat adaptability. These results should facilitate our understanding of the significance of fish gut microbes to habitat adaptation and provide a new perspective for studying the adaptive mechanisms of cavefish.}, } @article {pmid37464386, year = {2023}, author = {McGregor, BA and Razmjou, E and Hooshyar, H and Seeger, DR and Golovko, SA and Golovko, MY and Singer, SM and Hur, J and Solaymani-Mohammadi, S}, title = {A shotgun metagenomic analysis of the fecal microbiome in humans infected with Giardia duodenalis.}, journal = {Parasites & vectors}, volume = {16}, number = {1}, pages = {239}, pmid = {37464386}, issn = {1756-3305}, support = {P20 GM113123/GM/NIGMS NIH HHS/United States ; R15 AI109591/AI/NIAID NIH HHS/United States ; R21 AI166467/AI/NIAID NIH HHS/United States ; NIH/NIGMSP20GM113123/NH/NIH HHS/United States ; }, mesh = {Humans ; *Giardia lamblia ; *Giardiasis/parasitology ; Phylogeny ; Genotype ; *Microbiota ; Feces/parasitology ; Multilocus Sequence Typing ; }, abstract = {BACKGROUND: The mechanisms underlying the clinical outcome disparity during human infection with Giardia duodenalis are still unclear. In recent years, evidence has pointed to the roles of host factors as well as parasite's genetic heterogeneity as major contributing factors in the development of symptomatic human giardiasis. However, it remains contested as to how only a small fraction of individuals infected with G. duodenalis develop clinical gastrointestinal manifestations, whereas the majority of infected individuals remain asymptomatic. Here, we demonstrate that diversity in the fecal microbiome correlates with the clinical outcome of human giardiasis.

METHODS: The genetic heterogeneity of G. duodenalis clinical isolates from human subjects with asymptomatic and symptomatic giardiasis was determined using a multilocus analysis approach. We also assessed the genetic proximity of G. duodenalis isolates by constructing phylogenetic trees using the maximum likelihood. Total genomic DNA (gDNA) from fecal specimens was utilized to construct DNA libraries, followed by performing paired-end sequencing using the HiSeq X platform. The Kraken2-generated, filtered FASTQ files were assigned to microbial metabolic pathways and functions using HUMAnN 3.04 and the UniRef90 diamond annotated full reference database (version 201901b). Results from HUMAnN for each sample were evaluated for differences among the biological groups using the Kruskal-Wallis non-parametric test with a post hoc Dunn test.

RESULTS: We found that a total of 8/11 (72.73%) human subjects were infected with assemblage A (sub-assemblage AII) of G. duodenalis, whereas 3/11 (27.27%) human subjects in the current study were infected with assemblage B of the parasite. We also found that the parasite's genetic diversity was not associated with the clinical outcome of the infection. Further phylogenetic analysis based on the tpi and gdh loci indicated that those clinical isolates belonging to assemblage A of G. duodenalis subjects clustered compactly together in a monophyletic clade despite being isolated from human subjects with asymptomatic and symptomatic human giardiasis. Using a metagenomic shotgun sequencing approach, we observed that infected individuals with asymptomatic and symptomatic giardiasis represented distinctive microbial diversity profiles, and that both were distinguishable from the profiles of healthy volunteers.

CONCLUSIONS: These findings identify a potential association between host microbiome disparity with the development of clinical disease during human giardiasis, and may provide insights into the mechanisms by which the parasite induces pathological changes in the gut. These observations may also lead to the development of novel selective therapeutic targets for preventing human enteric microbial infections.}, } @article {pmid37462611, year = {2023}, author = {Hou, R and Zhang, S and Huang, Q and Lin, L and Li, H and Li, J and Liu, S and Sun, C and Xu, X}, title = {Role of Gastrointestinal Microbiota from Crucian Carp in Microbial Transformation and Estrogenicity Modification of Novel Plastic Additives.}, journal = {Environmental science & technology}, volume = {57}, number = {31}, pages = {11476-11488}, doi = {10.1021/acs.est.3c03595}, pmid = {37462611}, issn = {1520-5851}, mesh = {Animals ; *Carps ; *Gastrointestinal Microbiome ; Plastics ; Estrone ; *Environmental Pollutants ; }, abstract = {Ingestion is a major exposure route for hydrophobic organic pollutants in fish, but the microbial transformation and estrogenic modification of the novel plastic additives by the gut microbiota of fish remain obscure. Using an in vitro approach, we provide evidence that structure-related transformation of various plastic additives by the gastric and intestinal (GI) microbiota from crucian carp, with the degradation ratio of bisphenols and triphenyl phosphate faster than those of brominated compounds. The degradation kinetics for these pollutants could be limited by oxygen and cometabolic substrates (i.e., glucose). The fish GI microbiota could utilize the vast majority of carbon sources in a Biolog EcoPlate, suggesting their high metabolic potential and ability to transform various organic compounds. Unique microorganisms associated with transformation of the plastic additives including genera of Citrobacter, Klebsiella, and some unclassified genera in Enterobacteriaceae were identified by combining high-throughput genetic analyses and metagenomic analyses. Through identification of anaerobic transformation products by high-resolution mass spectrometry, alkyl-cleavage was found the common transformation mechanism, and hydrolysis was the major pathway for ester-containing pollutants. After anaerobic incubation, the estrogenic activities of triphenyl phosphate and bisphenols A, F, and AF declined, whereas that of bisphenol AP increased.}, } @article {pmid37459997, year = {2023}, author = {Liu, M and Wei, Y and Lian, L and Wei, B and Bi, Y and Liu, N and Yang, G and Zhang, Y}, title = {Macrofungi promote SOC decomposition and weaken sequestration by modulating soil microbial function in temperate steppe.}, journal = {The Science of the total environment}, volume = {899}, number = {}, pages = {165556}, doi = {10.1016/j.scitotenv.2023.165556}, pmid = {37459997}, issn = {1879-1026}, mesh = {*Soil/chemistry ; Carbon/metabolism ; Soil Microbiology ; Biomass ; *Microbiota ; Carbon Sequestration ; }, abstract = {Soil organic carbon (SOC) sequestration is a key grassland ecosystem function, and the magnitude of SOC reservoirs depends on microbial involvement, especially that of fungi. Mycelia developed by macrofungi potentially influence carbon (C) fixation and decomposition; however, the mechanisms underlying their effects on SOC storage in grassland ecosystems remain poorly understood. The fairy rings formed by macrofungi in grasslands are natural platform for exploring macrofungal effects on SOC. In this study, we collected topsoil (0-10 cm) from four different fairy ring zones in a temperate steppe to reveal the macrofungal effects on SOC fractions, including particulate organic carbon (POC) and mineral-associated organic carbon (MAOC), and the SOC storage microbial mechanism using metagenomic sequencing technology. Both POC and MAOC decreased after macrofungal passage, resulting in a 7.37 % reduction in SOC. Macrofungal presence reduced microbial biomass carbon (MBC), but significantly enhanced the β-1,4-glucosidase (BG) activity, which increased dissolved organic carbon (DOC). In addition, the abundance of copiotrophs (Proteobacteria and Bacteroidetes) with lower C metabolic rates increased, and that of oligotrophs (Actinobacteria, Acidobacteria, Chloroflexi, and Verrucomicrobia) with higher substrate utilization efficiency decreased in the presence of macrofungi. This may further promote SOC decomposition. Correspondingly, there was a lower abundance of C-fixation genes but more C-degradation genes (especially hemicellulosic degradation genes) during macrofungal passage. Our results indicate that the presence of macrofungi can modulate the soil microbial community and functional genes to reduce SOC storage by inhibiting microbial C sequestration while promoting C decomposition in grassland ecosystems. These findings refine our mechanistic understanding of SOC persistence through the interactions between macrofungi and other microbes.}, } @article {pmid37459963, year = {2023}, author = {Wang, Y and Guo, Z and Li, J and Sui, F and Dai, W and Zhang, W and Du, H}, title = {Unraveling the differential perturbations of species-level functional profiling of gut microbiota among phases of methamphetamine-induced conditioned place preference.}, journal = {Progress in neuro-psychopharmacology & biological psychiatry}, volume = {127}, number = {}, pages = {110828}, doi = {10.1016/j.pnpbp.2023.110828}, pmid = {37459963}, issn = {1878-4216}, mesh = {*Methamphetamine/pharmacology ; *Central Nervous System Stimulants/pharmacology ; *Gastrointestinal Microbiome ; Conditioning, Classical ; Reward ; }, abstract = {The gut microbiome plays a significant role in methamphetamine addiction. Previous studies using short-read amplicon sequencing have described alterations in microbiota at the genus level and predicted function, in which taxonomic resolution is insufficient for accurate functional measurements. To address this limitation, we employed metagenome sequencing to intuitively associate species to functions of gut microbiota in methamphetamine-induced conditioned place preference. We observed differential perturbations of species-level functional profiling of the gut microbiota across phases of METH-induced CPP, with alterations in SCFA metabolism and bacterial motility at the acquisition phase and substance dependence-alcoholism pathway and amino acid metabolism at the extinction phase. Our findings suggest that reduced beneficial bacteria, i.e., Lactobacillus reuteri, contributed to the alteration of SCFA metabolism, while the increased abundance of Akkermansia muciniphila during the extinction phase may be associated with altered phenylalanine, tyrosine, and tryptophan metabolism and substance dependence pathway. Our study further supports the association between specific microbial taxa and METH-induced rewarding.}, } @article {pmid37459167, year = {2023}, author = {Cisneros-Martínez, AM and Eguiarte, LE and Souza, V}, title = {Metagenomic comparisons reveal a highly diverse and unique viral community in a seasonally fluctuating hypersaline microbial mat.}, journal = {Microbial genomics}, volume = {9}, number = {7}, pages = {}, pmid = {37459167}, issn = {2057-5858}, support = {BB/P024378/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P024270/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 223743/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Metagenomics ; Seasons ; *Microbiota ; *Virome ; }, abstract = {In spring 2016, a shallow hypersaline pond (50×25 m) was found in the Cuatro Cienegas Basin (CCB). This pond, known as Archaean Domes (AD) because of its elastic microbial mats that form dome-shaped structures due to the production of reducing gases reminiscent of the Archaean eon, such as methane and hydrogen sulfide, harbour a highly diverse microbial community, rich in halophilic and methanogenic archaea. AD is a seasonally fluctuating hypersaline site, with salinity ranging from low hypersaline (5.3%) during the wet season to high hypersaline (saturation) during the dry season. To characterize the viral community and to test whether it resembles those of other hypersaline sites (whose diversity is conditioned by salinity), or if it is similar to other CCB sites (with which it shares a common geological history), we generated 12 metagenomes from different seasons and depths over a 4 year period and compared them to 35 metagenomes from varied environments. Haloarchaeaviruses were detected, but were never dominant (average of 15.37 % of the total viral species), and the viral community structure and diversity were not affected by environmental fluctuations. In fact, unlike other viral communities at hypersaline sites, AD remained more diverse than other environments regardless of season. β-Diversity analyses show that AD is closely related to other CCB sites, although it has a unique viral community that forms a cluster of its own. The similarity of two surface samples to the 30 and 50 cm depth samples, as well as the observed increase in diversity at greater depths, supports the hypothesis that the diversity of CCB has evolved as a result of a long time environmental stability of a deep aquifer that functions as a 'seed bank' of great microbial diversity that is transported to the surface by sporadic groundwater upwelling events.}, } @article {pmid37455607, year = {2025}, author = {Hutchins, L and Mc Cartney, A and Graham, N and Gillespie, R and Guzman, A}, title = {Arthropods are kin: Operationalizing Indigenous data sovereignty to respectfully utilize genomic data from Indigenous lands.}, journal = {Molecular ecology resources}, volume = {25}, number = {2}, pages = {e13822}, pmid = {37455607}, issn = {1755-0998}, support = {//Berkeley Food Institute Faculty Seed Grant/ ; //National Science Foundation Innovations at the Nexus of Food, Energy, and Water Systems/ ; }, mesh = {*Arthropods/genetics/classification ; Animals ; Hawaii ; Genomics/methods ; Indigenous Peoples/genetics ; Biodiversity ; Metagenomics/methods ; Humans ; Ecosystem ; }, abstract = {Indigenous peoples have cultivated biodiverse agroecosystems since time immemorial. The rise of metagenomics and high-throughput sequencing technologies in biodiversity studies has rapidly expanded the scale of data collection from these lands. A respectful approach to the data life cycle grounded in the sovereignty of indigenous communities is imperative to not perpetuate harm. In this paper, we operationalize an indigenous data sovereignty (IDS) framework to outline realistic considerations for genomic data that span data collection, governance, and communication. As a case study for this framework, we use arthropod genomic data collected from diversified and simplified farm sites close to and far from natural habitats within a historic Kānaka 'Ōiwi (Indigenous Hawaiian) agroecosystem. Diversified sites had the highest Operational Taxonomic Unit (OTU) richness for native and introduced arthropods. There may be a significant spillover effect between forest and farm sites, as farm sites near a natural habitat had higher OTU richness than those farther away. We also provide evidence that management factors such as the number of Polynesian crops cultivated may drive arthropod community composition. Through this case study, we emphasize the context-dependent opportunities and challenges for operationalizing IDS by utilizing participatory research methods, expanding novel data management tools through the Local Contexts Hub, and developing and nurturing community partnerships-all while highlighting the potential of agroecosystems for arthropod conservation. Overall, the workflow and the example presented here can help researchers take tangible steps to achieve IDS, which often seems elusive with the expanding use of genomic data.}, } @article {pmid37455332, year = {2023}, author = {Chang, WS and Wille, M}, title = {Winter is coming-The role of seasonality through the lens of the rodent virome.}, journal = {Molecular ecology}, volume = {32}, number = {17}, pages = {4709-4712}, doi = {10.1111/mec.17078}, pmid = {37455332}, issn = {1365-294X}, mesh = {Animals ; *Virome ; Rodentia ; *Viruses/genetics ; Seasons ; Phylogeny ; Metagenomics ; }, abstract = {Rodent virus communities (viromes) are overrepresented with zoonotic viruses, and as such are a key host system for the study of zoonotic viruses. However, the extent of viral diversity beyond characterized zoonotic viruses, and the factors that modulate the viromes of rodents remain opaque. In this issue of Molecular Ecology, Raghwani et al. (2023) use rodents as a model to understand the role of seasonality in dictating virome abundance and composition-a factor known to play an important role in most animal one-host, one-pathogen systems. These data are not only highly relevant to rodents, but have broad applications across understanding and disentangling animal virome ecology.}, } @article {pmid37454444, year = {2023}, author = {Schettini, F and Fontana, A and Gattazzo, F and Strina, C and Milani, M and Cappelletti, MR and Cervoni, V and Morelli, L and Curigliano, G and Iebba, V and Generali, D}, title = {Faecal microbiota composition is related to response to CDK4/6-inhibitors in metastatic breast cancer: A prospective cross-sectional exploratory study.}, journal = {European journal of cancer (Oxford, England : 1990)}, volume = {191}, number = {}, pages = {112948}, doi = {10.1016/j.ejca.2023.112948}, pmid = {37454444}, issn = {1879-0852}, mesh = {Humans ; Female ; *Breast Neoplasms/pathology ; Cross-Sectional Studies ; Prospective Studies ; Progression-Free Survival ; Receptor, ErbB-2/metabolism ; *Microbiota ; Protein Kinase Inhibitors/adverse effects ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Cyclin-Dependent Kinase 4 ; }, abstract = {BACKGROUND: Cyclin-dependent kinase (CDK)4/6-inhibitors with endocrine therapy represent the standard of treatment of hormone receptor-positive(HR+)/human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer (MBC). Gut microbiota seems to predict treatment response in several tumour types, being directly implied in chemotherapy resistance and development of adverse effects. No evidence is available on gut microbiota impact on efficacy of HR+ breast cancer treatment.

PATIENTS AND METHODS: We assessed the potential association among faecal microbiota and therapeutic efficacy of CDK4/6-inhibitors on 14 MBC patients classified as responders (R) and non-responders (NR) according to progression-free survival. A stool sample was collected at baseline and V3-V4 16S targeted sequencing was employed to assess its bacterial composition. Statistical associations with R and NR were studied.

RESULTS: No significant differences were observed between R and NR in terms of α-/β-diversity at the phylum and species level. Machine-learning (ML) algorithms evidenced four bacterial species as a discriminant for R (Bifidobacterium longum, Ruminococcus callidus) and NR (Clostridium innocuum, Schaalia odontolytica), and an area under curve (AUC) of 0.946 after Random Forest modelling. Network analysis evidenced two major clusters of bacterial species, named Species Interacting Groups (SIG)1-2, with SIG1 harbouring 75% of NR-related bacterial species, and SIG2 regrouping 76% of R-related species (p < 0.001). Cross-correlations among several patients' circulating immune cells or biomarkers and bacterial species' relative abundances showed associations with potential prognostic implications.

CONCLUSIONS: Our results provide initial insights into the gut microbiota involvement in sensitivity and/or resistance to CDK4/6-inhibitors + endocrine therapy in MBC. If confirmed in larger trials, several microbiota manipulation strategies might be hypothesised to improve response to CDK4/6-inhibitors.}, } @article {pmid37454234, year = {2023}, author = {Ustick, LJ and Larkin, AA and Martiny, AC}, title = {Global scale phylogeography of functional traits and microdiversity in Prochlorococcus.}, journal = {The ISME journal}, volume = {17}, number = {10}, pages = {1671-1679}, pmid = {37454234}, issn = {1751-7370}, support = {T32 AI141346/AI/NIAID NIH HHS/United States ; }, mesh = {Phylogeography ; Phylogeny ; *Prochlorococcus/genetics ; Seawater ; Ecotype ; }, abstract = {Prochlorococcus is the most numerically abundant photosynthetic organism in the surface ocean. The Prochlorococcus high-light and warm-water adapted ecotype (HLII) is comprised of extensive microdiversity, but specific functional differences between microdiverse sub-clades remain elusive. Here we characterized both functional and phylogenetic diversity within the HLII ecotype using Bio-GO-SHIP metagenomes. We found widespread variation in gene frequency connected to local environmental conditions. Metagenome-assembled marker genes and genomes revealed a globally distributed novel HLII haplotype defined by adaptation to chronically low P conditions (HLII-P). Environmental correlation analysis revealed different factors were driving gene abundances verses phylogenetic differences. An analysis of cultured HLII genomes and metagenome-assembled genomes revealed a subclade within HLII, which corresponded to the novel HLII-P haplotype. This work represents the first global assessment of the HLII ecotype's phylogeography and corresponding functional differences. These findings together expand our understanding of how microdiversity structures functional differences and reveals the importance of nutrients as drivers of microdiversity in Prochlorococcus.}, } @article {pmid37452210, year = {2023}, author = {Najah, H and Edelmuth, RCL and Riascos, MC and Grier, A and Al Asadi, H and Greenberg, JA and Miranda, I and Crawford, CV and Finnerty, BM and Fahey, TJ and Zarnegar, R}, title = {Long-term potassium-competitive acid blockers administration causes microbiota changes in rats.}, journal = {Surgical endoscopy}, volume = {37}, number = {10}, pages = {7980-7990}, pmid = {37452210}, issn = {1432-2218}, mesh = {Animals ; Rats ; Anti-Bacterial Agents/therapeutic use ; Drug Therapy, Combination ; *Gastrointestinal Microbiome ; *Helicobacter Infections ; *Helicobacter pylori/physiology ; Potassium/pharmacology/therapeutic use ; Prospective Studies ; Proton Pump Inhibitors/therapeutic use ; Pyrroles/pharmacology/therapeutic use ; Rats, Wistar ; }, abstract = {BACKGROUND: Vonoprazan is a new potassium-competitive acid blocker (P-CAB) that was recently approved by the FDA. It is associated with a fast onset of action and a longer acid inhibition time. Vonoprazan-containing therapy for helicobacter pylori eradication is highly effective and several studies have demonstrated that a vonoprazan-antibiotic regimen affects gut microbiota. However, the impact of vonoprazan alone on gut microbiota is still unclear.Please check and confirm the authors (Maria Cristina Riascos, Hala Al Asadi) given name and family name are correct. Also, kindly confirm the details in the metadata are correct.Yes they are correct. METHODS: We conducted a prospective randomized 12-week experimental trial with 18 Wistar rats. Rats were randomly assigned to one of 3 groups: (1) drinking water as negative control group, (2) oral vonoprazan (4 mg/kg) for 12 weeks, and (3) oral vonoprazan (4 mg/kg) for 4 weeks, followed by 8 weeks off vonoprazan. To investigate gut microbiota, we carried out a metagenomic shotgun sequencing of fecal samples at week 0 and week 12.Please confirm the inserted city and country name is correct for affiliation 2.Yes it's correct.

RESULTS: For alpha diversity metrics at week 12, both long and short vonoprazan groups had lower Pielou's evenness index than the control group (p = 0.019); however, observed operational taxonomic units (p = 0.332) and Shannon's diversity index (p = 0.070) were not statistically different between groups. Beta diversity was significantly different in the three groups, using Bray-Curtis (p = 0.003) and Jaccard distances (p = 0.002). At week 12, differences in relative abundance were observed at all levels. At phylum level, short vonoprazan group had less of Actinobacteria (log fold change = - 1.88, adjusted p-value = 0.048) and Verrucomicrobia (lfc = - 1.76, p = 0.009).Please check and confirm that the author (Ileana Miranda) and their respective affiliation 3 details have been correctly identified and amend if necessary.Yes it's correct. At the genus level, long vonoprazan group had more Bacteroidales (lfc = 5.01, p = 0.021) and Prevotella (lfc = 7.79, p = 0.001). At family level, long vonoprazan group had more Lactobacillaceae (lfc = 0.97, p = 0.001), Prevotellaceae (lfc = 8.01, p < 0.001), and less Erysipelotrichaceae (lfc = - 2.9, p = 0.029).

CONCLUSION: This study provides evidence that vonoprazan impacts the gut microbiota and permits a precise delineation of the composition and relative abundance of the bacteria at all different taxonomic levels.}, } @article {pmid37452041, year = {2023}, author = {Tarracchini, C and Alessandri, G and Fontana, F and Rizzo, SM and Lugli, GA and Bianchi, MG and Mancabelli, L and Longhi, G and Argentini, C and Vergna, LM and Anzalone, R and Viappiani, A and Turroni, F and Taurino, G and Chiu, M and Arboleya, S and Gueimonde, M and Bussolati, O and van Sinderen, D and Milani, C and Ventura, M}, title = {Genetic strategies for sex-biased persistence of gut microbes across human life.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4220}, pmid = {37452041}, issn = {2041-1723}, mesh = {Male ; Humans ; Female ; *Gastrointestinal Microbiome/genetics ; Bifidobacterium/genetics/metabolism ; *Microbiota ; Bacteria/genetics ; }, abstract = {Although compositional variation in the gut microbiome during human development has been extensively investigated, strain-resolved dynamic changes remain to be fully uncovered. In the current study, shotgun metagenomic sequencing data of 12,415 fecal microbiomes from healthy individuals are employed for strain-level tracking of gut microbiota members to elucidate its evolving biodiversity across the human life span. This detailed longitudinal meta-analysis reveals host sex-related persistence of strains belonging to common, maternally-inherited species, such as Bifidobacterium bifidum and Bifidobacterium longum subsp. longum. Comparative genome analyses, coupled with experiments including intimate interaction between microbes and human intestinal cells, show that specific bacterial glycosyl hydrolases related to host-glycan metabolism may contribute to more efficient colonization in females compared to males. These findings point to an intriguing ancient sex-specific host-microbe coevolution driving the selective persistence in women of key microbial taxa that may be vertically passed on to the next generation.}, } @article {pmid37450589, year = {2023}, author = {Shi, B and Zhang, X and Song, Z and Dai, Z and Luo, K and Chen, B and Zhou, Z and Cui, Y and Feng, B and Zhu, Z and Zheng, J and Zhang, H and He, X}, title = {Targeting gut microbiota-derived kynurenine to predict and protect the remodeling of the pressure-overloaded young heart.}, journal = {Science advances}, volume = {9}, number = {28}, pages = {eadg7417}, pmid = {37450589}, issn = {2375-2548}, mesh = {Animals ; Mice ; *Kynurenine/metabolism ; *Gastrointestinal Microbiome ; Heart ; Fibroblasts/metabolism ; Metabolomics ; }, abstract = {Pressure-overloaded left ventricular remodeling in young population is progressive and readily degenerate into heart failure. The aims of this study were to identify a plasma metabolite that predicts and is mechanistically linked to the disease. Untargeted metabolomics determined elevated plasma kynurenine (Kyn) in both the patient cohorts and the mice model, which was correlated with remodeling parameters. In vitro and in vivo evidence, combined with single-nucleus RNA sequencing (snRNA-seq), demonstrated that Kyn affected both cardiomyocytes and cardiac fibroblasts by activating aryl hydrocarbon receptors (AHR) to up-regulate hypertrophy- and fibrosis-related genes. Shotgun metagenomics and fecal microbiota transplantation revealed the existence of the altered gut microbiota-Kyn relationship. Supplementation of selected microbes reconstructed the gut microbiota, reduced plasma Kyn, and alleviated ventricular remodeling. Our data collectively discovered a gut microbiota-derived metabolite to activate AHR and its gene targets in remodeling young heart, a process that could be prevented by specific gut microbiota modulation.}, } @article {pmid37450270, year = {2024}, author = {Salam, LB}, title = {Diverse hydrocarbon degradation genes, heavy metal resistome, and microbiome of a fluorene-enriched animal-charcoal polluted soil.}, journal = {Folia microbiologica}, volume = {69}, number = {1}, pages = {59-80}, pmid = {37450270}, issn = {1874-9356}, mesh = {Humans ; Animals ; Charcoal ; Soil ; Biodegradation, Environmental ; *Microbiota/genetics ; *Metals, Heavy ; *Polycyclic Aromatic Hydrocarbons/metabolism ; Fluorenes ; Hydrocarbons ; *Gammaproteobacteria ; *Soil Pollutants/analysis ; Soil Microbiology ; }, abstract = {Environmental compartments polluted with animal charcoal from the skin and hide cottage industries are rich in toxic heavy metals and diverse hydrocarbon classes, some of which are carcinogenic, mutagenic, and genotoxic, and thus require a bio-based eco-benign decommission strategies. A shotgun metagenomic approach was used to decipher the microbiome, hydrocarbon degradation genes, and heavy metal resistome of a microbial consortium (FN8) from an animal-charcoal polluted site enriched with fluorene. Structurally, the FN8 microbial consortium consists of 26 phyla, 53 classes, 119 orders, 245 families, 620 genera, and 1021 species. The dominant phylum, class, order, family, genus, and species in the consortium are Proteobacteria (51.37%), Gammaproteobacteria (39.01%), Bacillales (18.09%), Microbulbiferaceae (11.65%), Microbulbifer (12.21%), and Microbulbifer sp. A4B17 (19.65%), respectively. The microbial consortium degraded 57.56% (28.78 mg/L) and 87.14% (43.57 mg/L) of the initial fluorene concentration in 14 and 21 days. Functional annotation of the protein sequences (ORFs) of the FN8 metagenome using the KEGG GhostKOALA, KofamKOALA, NCBI's conserved domain database, and BacMet revealed the detection of hydrocarbon degradation genes for benzoate, aminobenzoate, polycyclic aromatic hydrocarbons (PAHs), chlorocyclohexane/chlorobenzene, chloroalkane/chloroalkene, toluene, xylene, styrene, naphthalene, nitrotoluene, and several others. The annotation also revealed putative genes for the transport, uptake, efflux, and regulation of heavy metals such as arsenic, cadmium, chromium, mercury, nickel, copper, zinc, and several others. Findings from this study have established that members of the FN8 consortium are well-adapted and imbued with requisite gene sets and could be a potential bioresource for on-site depuration of animal charcoal polluted sites.}, } @article {pmid37450112, year = {2023}, author = {Ji, X and Ni, S and Tian, G and Zhang, L and Wang, W}, title = {Detection of Microorganisms in Body Fluid Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2695}, number = {}, pages = {73-88}, pmid = {37450112}, issn = {1940-6029}, mesh = {RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; *Body Fluids ; }, abstract = {Next-generation sequencing (NGS) has been widely applied to the identification of microbiome in body fluids. The methodology of 16S rRNA amplicon sequencing is simple, fast, and cost-effective. It overcomes the problem that some microorganisms cannot be isolated or cultured. Low abundant bacteria can also be amplified and sequenced, but the resolution of classification can hardly reach species or sub-species level; moreover, this methodology is mainly used to identify bacterial populations, and other microorganisms like viruses or fungi cannot be sequenced. On the other hand, the microbiome profiling obtained by shotgun metagenomic sequencing is more comprehensive with better resolution, and more accurate classification can be expected due to higher coverage of genomic sequences from microorganisms. By combining the capture-based method with metagenomic sequencing, we can further enrich and detect low abundant microorganisms and identify the viral integration sites in host gDNA at once.}, } @article {pmid37448812, year = {2023}, author = {Chafra, F and Borim Correa, F and Oni, F and Konu Karakayalı, Ö and Stadler, PF and Nunes da Rocha, U}, title = {StandEnA: a customizable workflow for standardized annotation and generating a presence-absence matrix of proteins.}, journal = {Bioinformatics advances}, volume = {3}, number = {1}, pages = {vbad069}, pmid = {37448812}, issn = {2635-0041}, abstract = {MOTIVATION: Several genome annotation tools standardize annotation outputs for comparability. During standardization, these tools do not allow user-friendly customization of annotation databases; limiting their flexibility and applicability in downstream analysis.

RESULTS: StandEnA is a user-friendly command-line tool for Linux that facilitates the generation of custom databases by retrieving protein sequences from multiple databases. Directed by a user-defined list of standard names, StandEnA retrieves synonyms to search for corresponding sequences in a set of public databases. Custom databases are used in prokaryotic genome annotation to generate standardized presence-absence matrices and reference files containing standard database identifiers. To showcase StandEnA, we applied it to six metagenome-assembled genomes to analyze three different pathways.

StandEnA is an open-source software available at https://github.com/mdsufz/StandEnA.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.}, } @article {pmid37448101, year = {2023}, author = {Bao, S and Wang, H and Li, W and Wu, H and Lu, C and Yong, L and Zhang, Q and Lu, X and Zhao, M and Lu, J and Liu, J and Ikechukwu, CK and Xu, J and Ni, P and Xiong, Y and Zhang, W and Zhou, C}, title = {Viral metagenomics of the gut virome of diarrheal children with Rotavirus A infection.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2234653}, pmid = {37448101}, issn = {1949-0984}, mesh = {Humans ; Child ; *Rotavirus/genetics ; Metagenomics ; *Gastrointestinal Microbiome ; China/epidemiology ; Diarrhea/epidemiology ; *Rotavirus Infections ; Feces ; }, abstract = {Diarrhea is a leading cause of morbidity and mortality in children worldwide and represents a major dysbiosis event. Rotavirus has been recognized as a global leading pathogen of diarrhea. This study is aimed at investigating differences in the gut virome between diarrheal children and healthy controls. In 2018, 76 diarrheal fecal samples and 27 healthy fecal samples in Shanghai and 40 diarrheal fecal samples and 19 healthy fecal samples in Taizhou were collected to investigate the composition of the gut virome. Viral metagenomic analyses revealed that the alpha diversity of the diarrheal virome was not significantly different from that of the healthy virome, and the beta diversity had a significant difference between diarrheal and healthy children. The diarrheal virome was mainly dominated by the families Adenoviridae, Astroviridae, Caliciviridae, and Picornaviridae. Meanwhile, the healthy virome also contains phages, including Microviridae and Caudovirales. The high prevalence of diverse enteric viruses in all samples and the little abundance of Microviridae and Caudovirales in diarrheal groups were identified. The study introduced a general overview of the gut virome in diarrheal children, revealed the compositional differences in the gut viral community compared to healthy controls, and provided a reference for efficient treatments and prevention of virus-infectious diarrhea in children.}, } @article {pmid37446198, year = {2023}, author = {Gu, X and Cao, Z and Zhao, L and Seswita-Zilda, D and Zhang, Q and Fu, L and Li, J}, title = {Metagenomic Insights Reveal the Microbial Diversity and Associated Algal-Polysaccharide-Degrading Enzymes on the Surface of Red Algae among Remote Regions.}, journal = {International journal of molecular sciences}, volume = {24}, number = {13}, pages = {}, pmid = {37446198}, issn = {1422-0067}, support = {RFSOCC2023-2025//Impact and Response of Antarctic Seas to Climate Change/ ; RFSOCC2023-2025//Jiang Li/ ; }, mesh = {Metagenomics ; Bacteria/genetics/metabolism ; *Rhodophyta/genetics ; Metagenome ; *Seaweed ; Polysaccharides/metabolism ; }, abstract = {Macroalgae and macroalgae-associated bacteria together constitute the most efficient metabolic cycling system in the ocean. Their interactions, especially the responses of macroalgae-associated bacteria communities to algae in different geographical locations, are mostly unknown. In this study, metagenomics was used to analyze the microbial diversity and associated algal-polysaccharide-degrading enzymes on the surface of red algae among three remote regions. There were significant differences in the macroalgae-associated bacteria community composition and diversity among the different regions. At the phylum level, Proteobacteria, Bacteroidetes, and Actinobacteria had a significantly high relative abundance among the regions. From the perspective of species diversity, samples from China had the highest macroalgae-associated bacteria diversity, followed by those from Antarctica and Indonesia. In addition, in the functional prediction of the bacterial community, genes associated with amino acid metabolism, carbohydrate metabolism, energy metabolism, metabolism of cofactors and vitamins, and membrane transport had a high relative abundance. Canonical correspondence analysis and redundancy analysis of environmental factors showed that, without considering algae species and composition, pH and temperature were the main environmental factors affecting bacterial community structure. Furthermore, there were significant differences in algal-polysaccharide-degrading enzymes among the regions. Samples from China and Antarctica had high abundances of algal-polysaccharide-degrading enzymes, while those from Indonesia had extremely low abundances. The environmental differences between these three regions may impose a strong geographic differentiation regarding the biodiversity of algal microbiomes and their expressed enzyme genes. This work expands our knowledge of algal microbial ecology, and contributes to an in-depth study of their metabolic characteristics, ecological functions, and applications.}, } @article {pmid37446076, year = {2023}, author = {Xu, J and Molin, G and Davidson, S and Roth, B and Sjöberg, K and Håkansson, Å}, title = {CRP in Outpatients with Inflammatory Bowel Disease Is Linked to the Blood Microbiota.}, journal = {International journal of molecular sciences}, volume = {24}, number = {13}, pages = {}, pmid = {37446076}, issn = {1422-0067}, support = {Dnr 143587//Direktör Albert Påhlssons Stiftelse för Välgörenhet/ ; }, mesh = {Humans ; C-Reactive Protein ; Outpatients ; *Inflammatory Bowel Diseases/microbiology ; *Colitis, Ulcerative/microbiology ; *Crohn Disease/microbiology ; *Microbiota ; }, abstract = {The circulation is a closed system that has been assumed to be free from bacteria, but evidence for the existence of a low-density blood microbiota is accumulating. The present study aimed to map the blood microbiota of outpatients with Crohn's disease (CD) or with ulcerative colitis (UC) by 16S metagenomics. A diverse microbiota was observed in the blood samples. Regardless of the type of disease, the alpha diversity of the microbiota was positively associated with C-reactive protein (CRP). The blood microbiota had a surprisingly high proportion of Proteobacteria in comparison with human oral and colonic microbiotas. There was no clear difference in the overall pattern of the microbiota between CD and UC. A non-template control (NTC) was included in the whole process to control for the potential contamination from the environment and reagents. Certain bacterial taxa were concomitantly detected in both blood samples and NTC. However, Acinetobacter, Lactobacillus, Thermicanus and Paracoccus were found in blood from both CD and UC patients but not in NTC, indicating the existence of a specific blood-borne microbiota in the patients. Achromobacter dominated in all blood samples, but a minor amount was also found in NTC. Micrococcaceae was significantly enriched in CD, but it was also detected in high abundance in NTC. Whether the composition of the blood microbiota could be a marker of a particular phenotype in inflammatory bowel disease (IBD) or whether the blood microbiota could be used for diagnostic or therapeutic purposes deserves further attention.}, } @article {pmid37445967, year = {2023}, author = {He, K and Xiong, J and Yang, W and Zhao, L and Wang, T and Qian, W and Hu, S and Wang, Q and Aleem, MT and Miao, W and Yan, W}, title = {Metagenome of Gut Microbiota Provides a Novel Insight into the Pathogenicity of Balantioides coli in Weaned Piglets.}, journal = {International journal of molecular sciences}, volume = {24}, number = {13}, pages = {}, pmid = {37445967}, issn = {1422-0067}, support = {31772733//National Natural Science Foundation of China/ ; }, mesh = {Swine ; Animals ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Balantidiasis ; Virulence ; Diarrhea/microbiology ; }, abstract = {Balantioides coli plays an important role in the diarrhea of weaned piglets, but its pathogenic potential and interaction with gut microbes remain unclear. To investigate the impact of B. coli colonization on the gut bacterial structure and function of weaned piglets, a metagenomic analysis based on shotgun sequencing was performed on fresh fecal samples collected from ten B. coli-colonized piglets and eight B. coli-free ones in this study. The results showed that decreasing diversity and shifted composition and function of the bacterial community were detected in the weaned piglets infected by B. coli. In contrast to the B. coli-negative group, the relative abundances of some members of the Firmicutes phylum including Clostridium, Ruminococcus species, and Intestinimonas butyriciproducens, which produce short-chain fatty acids, were significantly reduced in the B. coli-positive group. Notably, some species of the Prevotella genus (such as Prevotella sp. CAG:604 and Prevotella stercorea) were significantly increased in abundance in the B. coli-positive piglets. A functional analysis of the gut microbiota demonstrated that the differential gene sets for the metabolism of carbohydrates and amino acids were abundant in both groups, and the more enriched pathways in B. coli-infected piglets were associated with the sugar-specific phosphotransferase system (PTS) and the two-component regulatory system, as well as lipopolysaccharide (LPS) biosynthesis. Furthermore, several species of Prevotella were significantly positively correlated to the synthesis of lipid A, leading to the exporting of endotoxins and, thereby, inducing inflammation in the intestines of weaned piglets. Taken together, these findings revealed that colonization by B. coli was distinctly associated with the dysbiosis of gut bacterial structure and function in weaned piglets. Lower relative abundances of Clostridiaceae and Ruminococcaceae and higher abundances of Prevotella species were biomarkers of B. coli infection in weaned piglets.}, } @article {pmid37443184, year = {2023}, author = {Tataru, C and Peras, M and Rutherford, E and Dunlap, K and Yin, X and Chrisman, BS and DeSantis, TZ and Wall, DP and Iwai, S and David, MM}, title = {Topic modeling for multi-omic integration in the human gut microbiome and implications for Autism.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {11353}, pmid = {37443184}, issn = {2045-2322}, support = {R44 DA043954/DA/NIDA NIH HHS/United States ; }, mesh = {Child ; Humans ; *Gastrointestinal Microbiome/genetics ; Multiomics ; RNA, Ribosomal, 16S/genetics ; *Autistic Disorder ; *Microbiota/genetics ; }, abstract = {While healthy gut microbiomes are critical to human health, pertinent microbial processes remain largely undefined, partially due to differential bias among profiling techniques. By simultaneously integrating multiple profiling methods, multi-omic analysis can define generalizable microbial processes, and is especially useful in understanding complex conditions such as Autism. Challenges with integrating heterogeneous data produced by multiple profiling methods can be overcome using Latent Dirichlet Allocation (LDA), a promising natural language processing technique that identifies topics in heterogeneous documents. In this study, we apply LDA to multi-omic microbial data (16S rRNA amplicon, shotgun metagenomic, shotgun metatranscriptomic, and untargeted metabolomic profiling) from the stool of 81 children with and without Autism. We identify topics, or microbial processes, that summarize complex phenomena occurring within gut microbial communities. We then subset stool samples by topic distribution, and identify metabolites, specifically neurotransmitter precursors and fatty acid derivatives, that differ significantly between children with and without Autism. We identify clusters of topics, deemed "cross-omic topics", which we hypothesize are representative of generalizable microbial processes observable regardless of profiling method. Interpreting topics, we find each represents a particular diet, and we heuristically label each cross-omic topic as: healthy/general function, age-associated function, transcriptional regulation, and opportunistic pathogenesis.}, } @article {pmid37442576, year = {2023}, author = {Grandchamp, A and Kühl, L and Lebherz, M and Brüggemann, K and Parsch, J and Bornberg-Bauer, E}, title = {Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster.}, journal = {Genome research}, volume = {33}, number = {6}, pages = {872-890}, pmid = {37442576}, issn = {1549-5469}, mesh = {Animals ; *Drosophila melanogaster/genetics ; Open Reading Frames ; *Metagenomics ; DNA Transposable Elements/genetics ; Biological Evolution ; Evolution, Molecular ; }, abstract = {Novel genes are essential for evolutionary innovations and differ substantially even between closely related species. Recently, multiple studies across many taxa showed that some novel genes arise de novo, that is, from previously noncoding DNA. To characterize the underlying mutations that allowed de novo gene emergence and their order of occurrence, homologous regions must be detected within noncoding sequences in closely related sister genomes. So far, most studies do not detect noncoding homologs of de novo genes because of incomplete assemblies and annotations, and long evolutionary distances separating genomes. Here, we overcome these issues by searching for de novo expressed open reading frames (neORFs), the not-yet fixed precursors of de novo genes that emerged within a single species. We sequenced and assembled genomes with long-read technology and the corresponding transcriptomes from inbred lines of Drosophila melanogaster, derived from seven geographically diverse populations. We found line-specific neORFs in abundance but few neORFs shared by lines, suggesting a rapid turnover. Gain and loss of transcription is more frequent than the creation of ORFs, for example, by forming new start and stop codons. Consequently, the gain of ORFs becomes rate limiting and is frequently the initial step in neORFs emergence. Furthermore, transposable elements (TEs) are major drivers for intragenomic duplications of neORFs, yet TE insertions are less important for the emergence of neORFs. However, highly mutable genomic regions around TEs provide new features that enable gene birth. In conclusion, neORFs have a high birth-death rate, are rapidly purged, but surviving neORFs spread neutrally through populations and within genomes.}, } @article {pmid37442461, year = {2023}, author = {Yang, J and He, J and Jia, L and Gu, H}, title = {Integrating metagenomics and metabolomics to study the response of microbiota in black soil degradation.}, journal = {The Science of the total environment}, volume = {899}, number = {}, pages = {165486}, doi = {10.1016/j.scitotenv.2023.165486}, pmid = {37442461}, issn = {1879-1026}, mesh = {*Soil/chemistry ; Metagenomics ; Soil Microbiology ; Bacteria/metabolism ; *Microbiota ; Metabolomics ; }, abstract = {As the largest commercial food production base and ecological security barrier, land degradation in black soil areas seriously threatens the global food supply and natural ecosystems. Therefore, determining the response of soil microbiota is crucial to restoring degraded soils. This study combined metagenomics and metabolomics to investigate the effect of different degrees of soil degradation on microbial community composition and metabolic function in black soils. It was found that alpha diversity in degraded soils (Shannon: 22.3) was higher than in nondegraded soil (ND) (Shannon: 21.8), and the degree of degradation significantly altered the structure and composition of soil microbial communities. The results of LEfSe analysis obtained 9 (ND), 7 (lightly degraded, LD), 10 (moderately degraded, MD), and 1 (severely degraded, SD) biomarkers in four samples. Bradyrhizobium, Sphingomonas, and Ramlibacter were significantly affected by soil degradation and can be considered biomarkers of ND, MD, and SD, respectively. Soil nutrient and enzyme activities decreased significantly with increasing black soil degradation, soil organic matter (SOM) content decreased from 11.12 % to 1.97 %, and Sucrase decreased from 23.53 to 6.59 mg/g/d. In addition, C was the critical driver affecting microbial community structure, contributing 61.2 % to differences in microbial community distribution, and microbial altering relative abundance which participle in the carbon cycle to respond to soil degradation. Metabolomic analyses indicated that soil degradation significantly modified the soil metabolite spectrum, and the metabolic functions of most microorganisms responding to soil degradation were adversely affected. The combined multi-omics analysis further indicated that biomarkers dominate in accumulating metabolites. These findings confirmed that due to their role in the composition and functioning of these degraded soils, these biomarkers could be employed in strategies for managing and restoring degraded black soils.}, } @article {pmid37442053, year = {2023}, author = {Durand, M and Touchette, D and Chen, YJ and Magnuson, E and Wasserscheid, J and Greer, CW and Whyte, LG and Altshuler, I}, title = {Effects of marine diesel on microbial diversity and activity in high Arctic beach sediments.}, journal = {Marine pollution bulletin}, volume = {194}, number = {Pt A}, pages = {115226}, doi = {10.1016/j.marpolbul.2023.115226}, pmid = {37442053}, issn = {1879-3363}, mesh = {RNA, Ribosomal, 16S/genetics ; *Bacteria/metabolism ; Arctic Regions ; *Microbiota ; Hydrocarbons/metabolism ; }, abstract = {Global warming induced sea ice loss increases Arctic maritime traffic, enhancing the risk of ecosystem contamination from fuel spills and nutrient loading. The impact of marine diesel on bacterial metabolic activity and diversity, assessed by colorimetric assay, 16S rRNA and metagenomic sequencing, of Northwest Passage (Arctic Ocean) beach sediments was assessed with nutrient amendment at environmentally relevant temperatures (5 and 15 °C). Higher temperature and nutrients stimulated microbial activity, while diesel reduced it, with metabolism inhibited at and above 0.01 % (without nutrients) and at 1 % (with nutrients) diesel inclusions. Diesel exposure significantly decreased microbial diversity and selected for Psychrobacter genus. Microbial hydrocarbon degradation, organic compound metabolism, and exopolysaccharide production gene abundances increased under higher diesel concentrations. Metagenomic binning recovered nine MAGs/bins with hydrocarbon degradation genes. We demonstrate a nutrients' rescue-type effect in diesel contaminated microbial communities via enrichment of microorganisms with stress response, aromatic compound, and ammonia assimilation metabolisms.}, } @article {pmid37441819, year = {2023}, author = {Ren, Z and Jiang, W and Sun, N and Shi, J and Zhang, D and Zhang, J and Wang, Z and Yang, J and Yu, J and Lv, Z}, title = {Responses of the structure and function of microbes in Yellow River Estuary sediments to different levels of mercury.}, journal = {Marine environmental research}, volume = {190}, number = {}, pages = {106097}, doi = {10.1016/j.marenvres.2023.106097}, pmid = {37441819}, issn = {1879-0291}, mesh = {*Mercury/analysis ; Estuaries ; Rivers/chemistry ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/chemistry ; *Water Pollutants, Chemical/toxicity/analysis ; *Methylmercury Compounds ; *Metals, Heavy/analysis ; *Microbiota ; Environmental Monitoring ; }, abstract = {The health and stability of the estuary of the Yellow River ecosystem have come under increasing pressure from land-based inputs of heavy metals. While it is known that heavy metals affect the function and health of the microbial community, there remains little knowledge on the responses of the microbial community to heavy metals, particularly highly toxic mercury. The research aimed to characterize the responses of the sediment microbial community of the estuary of the Yellow River to different levels of mercury stress. Estuary sediment samples were collected for microbial community analysis, measurement of mercury [including total mercury (THg) and methylmercury (MeHg)], and measurement of other physicochemical factors, including pH, total organic carbon (TOC), sulfide, iron ratio (Fe[3+]/Fe[2+]), ammonium salt (NH4[+]), and biochemical oxygen demand (BOD). The application of 16S rRNA sequencing identified 60 phyla of bacteria, dominated by Proteobacteria, Firmicutes, and Bacteroidetes. Stations with higher THg or MeHg and lower microbial abundance and diversity were generally distributed further outside of the estuary. Besides mercury, the measured physicochemical factors had impacts on microbial diversities and distribution. Metagenomics assessment of three stations, representative of low, moderate, and high mercury concentrations and measured physicochemical factors, revealed the abundances and functions of predicted genes. The most abundant genes regulating the metabolic pathways were categorized as metabolic, environmental information processing, and genetic information processing, genes. At stations with high levels of mercury, the dominant genes were related to energy metabolism, signal transport, and membrane transport. Functional genes with a mercury-resistance function were generally in the mer system (merA, merC, merT, merR), alkylmercury lyase, and metal-transporting ATPase. These results offer insight into the microbial community structure of the sediments in the Yellow River Estuary and the microbial function of mercury resistance under mercury stress.}, } @article {pmid37440367, year = {2023}, author = {Muralitharan, RR and Snelson, M and Meric, G and Coughlan, MT and Marques, FZ}, title = {Guidelines for microbiome studies in renal physiology.}, journal = {American journal of physiology. Renal physiology}, volume = {325}, number = {3}, pages = {F345-F362}, doi = {10.1152/ajprenal.00072.2023}, pmid = {37440367}, issn = {1522-1466}, mesh = {Animals ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; Anti-Bacterial Agents ; }, abstract = {Gut microbiome research has increased dramatically in the last decade, including in renal health and disease. The field is moving from experiments showing mere association to causation using both forward and reverse microbiome approaches, leveraging tools such as germ-free animals, treatment with antibiotics, and fecal microbiota transplantations. However, we are still seeing a gap between discovery and translation that needs to be addressed, so that patients can benefit from microbiome-based therapies. In this guideline paper, we discuss the key considerations that affect the gut microbiome of animals and clinical studies assessing renal function, many of which are often overlooked, resulting in false-positive results. For animal studies, these include suppliers, acclimatization, baseline microbiota and its normalization, littermates and cohort/cage effects, diet, sex differences, age, circadian differences, antibiotics and sweeteners, and models used. Clinical studies have some unique considerations, which include sampling, gut transit time, dietary records, medication, and renal phenotypes. We provide best-practice guidance on sampling, storage, DNA extraction, and methods for microbial DNA sequencing (both 16S rRNA and shotgun metagenome). Finally, we discuss follow-up analyses, including tools available, metrics, and their interpretation, and the key challenges ahead in the microbiome field. By standardizing study designs, methods, and reporting, we will accelerate the findings from discovery to translation and result in new microbiome-based therapies that may improve renal health.}, } @article {pmid37439894, year = {2023}, author = {Torres Manno, MA and Gizzi, FO and Martín, M and Espariz, M and Magni, C and Blancato, VS}, title = {Metagenomic approach to infer rumen microbiome derived traits of cattle.}, journal = {World journal of microbiology & biotechnology}, volume = {39}, number = {9}, pages = {250}, pmid = {37439894}, issn = {1573-0972}, support = {PICT2019-1771//Agencia Nacional de Promoción Científica y Tecnológica/ ; PICT2015-2361//Agencia Nacional de Promoción Científica y Tecnológica/ ; PICT2014-3482//Agencia Nacional de Promoción Científica y Tecnológica/ ; PIP 11220150100855//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; }, mesh = {Female ; Cattle ; Animals ; *Rumen ; *Microbiota/genetics ; Metagenome ; Bacteria ; Glycoside Hydrolases/genetics/metabolism ; Methane/metabolism ; Animal Feed ; Diet ; }, abstract = {Ruminants enable the conversion of indigestible plant material into animal consumables, including dairy products, meat, and valuable fibers. Microbiome research is gaining popularity in livestock species because it aids in the knowledge of illnesses and efficiency processes in animals. In this study, we use WGS metagenomic data to thoroughly characterize the ruminal ecosystem of cows to infer positive and negative livestock traits determined by the microbiome. The rumen of cows from Argentina were described by combining different gene biomarkers, pathways composition and taxonomic information. Taxonomic characterization indicated that the two major phyla were Bacteroidetes and Firmicutes; in third place, Proteobacteria was highly represented followed by Actinobacteria; Prevotella, and Bacteroides were the most abundant genera. Functional profiling of carbohydrate-active enzymes indicated that members of the Glycoside Hydrolase (GH) class accounted for 52.2 to 55.6% of the total CAZymes detected, among them the most abundant were the oligosaccharide degrading enzymes. The diversity of GH families found suggested efficient hydrolysis of complex biomass. Genes of multidrug, macrolides, polymyxins, beta-lactams, rifamycins, tetracyclines, and bacitracin resistance were found below 0.12% of relative abundance. Furthermore, the clustering analysis of genera and genes that correlated to methane emissions or feed efficiency, suggested that the cows analysed could be regarded as low methane emitters and clustered with high feed efficiency reference animals. Finally, the combination of bioinformatic analyses used in this study can be applied to assess cattle traits difficult to measure and guide enhanced nutrition and breeding methods.}, } @article {pmid37439777, year = {2023}, author = {Holman, DB and Gzyl, KE and Kommadath, A}, title = {The gut microbiome and resistome of conventionally vs. pasture-raised pigs.}, journal = {Microbial genomics}, volume = {9}, number = {7}, pages = {}, pmid = {37439777}, issn = {2057-5858}, mesh = {Animals ; Swine ; *Gastrointestinal Microbiome/genetics ; Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents ; }, abstract = {Conventional swine production typically houses pigs indoors and in large groups, whereas pasture-raised pigs are reared outdoors at lower stocking densities. Antimicrobial use also differs, with conventionally raised pigs often being exposed to antimicrobials directly or indirectly to control and prevent infectious disease. However, antimicrobial use can be associated with the development and persistence of antimicrobial resistance. In this study, we used shotgun metagenomic sequencing to compare the gut microbiomes and resistomes of pigs raised indoors on a conventional farm with those raised outdoors on pasture. The microbial compositions as well as the resistomes of both groups of pigs were significantly different from each other. Bacterial species such as Intestinibaculum porci, Pseudoscardovia radai and Sharpea azabuensis were relatively more abundant in the gut microbiomes of pasture-raised pigs and Hallella faecis and Limosilactobacillus reuteri in the conventionally raised swine. The abundance of antimicrobial resistance genes (ARGs) was significantly higher in the conventionally raised pigs for nearly all antimicrobial classes, including aminoglycosides, beta-lactams, macrolides-lincosamides-streptogramin B, and tetracyclines. Functionally, the gut microbiomes of the two group of pigs also differed significantly based on their carbohydrate-active enzyme (CAZyme) profiles, with certain CAZyme families associated with host mucin degradation enriched in the conventional pig microbiomes. We also recovered 1043 dereplicated strain-level metagenome-assembled genomes (≥90 % completeness and <5 % contamination) to provide taxonomic context for specific ARGs and metabolic functions. Overall, the study provides insights into the differences between the gut microbiomes and resistomes of pigs raised under two very different production systems.}, } @article {pmid37438876, year = {2023}, author = {Basile, A and Heinken, A and Hertel, J and Smarr, L and Li, W and Treu, L and Valle, G and Campanaro, S and Thiele, I}, title = {Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2226921}, pmid = {37438876}, issn = {1949-0984}, support = {757922/ERC_/European Research Council/International ; RF1 AG058942/AG/NIA NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Microbiota ; Inflammation ; Liver ; Anti-Bacterial Agents ; Escherichia coli ; }, abstract = {We report the first use of constraint-based microbial community modeling on a single individual with episodic inflammation of the gastrointestinal tract, who has a well documented set of colonic inflammatory biomarkers, as well as metagenomically-sequenced fecal time series covering seven dates over 16 months. Between the first two time steps the individual was treated with both steroids and antibiotics. Our methodology enabled us to identify numerous time-correlated microbial species and metabolites. We found that the individual's dynamical microbial ecology in the disease state led to time-varying in silico overproduction, compared to healthy controls, of more than 24 biologically important metabolites, including methane, thiamine, formaldehyde, trimethylamine N-oxide, folic acid, serotonin, histamine, and tryptamine. The microbe-metabolite contribution analysis revealed that some Dialister species changed metabolic pathways according to the inflammation phases. At the first time point, characterized by the highest levels of serum (complex reactive protein) and fecal (calprotectin) inflammation biomarkers, they produced L-serine or formate. The production of the compounds, through a cascade effect, was mediated by the interaction with pathogenic Escherichia coli strains and Desulfovibrio piger. We integrated the microbial community metabolic models of each time point with a male whole-body, organ-resolved model of human metabolism to track the metabolic consequences of dysbiosis at different body sites. The presence of D. piger in the gut microbiome influenced the sulfur metabolism with a domino effect affecting the liver. These results revealed large longitudinal variations in an individual's gut microbiome ecology and metabolite production, potentially impacting other organs in the body. Future simulations with more time points from an individual could permit us to assess how external drivers, such as diet change or medical interventions, drive microbial community dynamics.}, } @article {pmid37438797, year = {2023}, author = {Nguyen, LH and Okin, D and Drew, DA and Battista, VM and Jesudasen, SJ and Kuntz, TM and Bhosle, A and Thompson, KN and Reinicke, T and Lo, CH and Woo, JE and Caraballo, A and Berra, L and Vieira, J and Huang, CY and Das Adhikari, U and Kim, M and Sui, HY and Magicheva-Gupta, M and McIver, L and Goldberg, MB and Kwon, DS and Huttenhower, C and Chan, AT and Lai, PS}, title = {Metagenomic assessment of gut microbial communities and risk of severe COVID-19.}, journal = {Genome medicine}, volume = {15}, number = {1}, pages = {49}, pmid = {37438797}, issn = {1756-994X}, support = {K01 DK120742/DK/NIDDK NIH HHS/United States ; K23 DK125838/DK/NIDDK NIH HHS/United States ; UL1 TR002541/TR/NCATS NIH HHS/United States ; T32 HL116275/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; Post-Acute COVID-19 Syndrome ; *COVID-19 ; *Microbiota ; Metagenome ; *Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure.

METHODS: We profiled 127 hospitalized patients with COVID-19 (n = 79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites.

RESULTS: Forty-eight species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or "long COVID," suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with classifying whether stool was obtained from patients with severe vs. moderate COVID-19, a finding that was externally validated in an independent cohort. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease.

CONCLUSIONS: Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to expand upon these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention.}, } @article {pmid37438354, year = {2023}, author = {Lacunza, E and Fink, V and Salas, ME and Canzoneri, R and Naipauer, J and Williams, S and Coso, O and Sued, O and Cahn, P and Mesri, EA and Abba, MC}, title = {Oral and anal microbiome from HIV-exposed individuals: role of host-associated factors in taxa composition and metabolic pathways.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {48}, pmid = {37438354}, issn = {2055-5008}, support = {U54 CA221208/CA/NCI NIH HHS/United States ; }, mesh = {Male ; Humans ; Female ; *HIV Infections/complications ; Homosexuality, Male ; *Sexual and Gender Minorities ; *Microbiota ; Metabolic Networks and Pathways ; }, abstract = {Evidence indicates that the microbiome plays a significant role in HIV immunopathogenesis and associated complications. This study aimed to characterize the oral and anal microbiome of Men who have Sex with Men (MSM) and Transgender Women (TGW), with and without HIV. One hundred and thirty oral and anal DNA-derived samples were obtained from 78 participants and subjected to shotgun metagenomics sequencing for further microbiome analysis. Significant differences in the microbiome composition were found among subjects associated with HIV infection, gender, sex behavior, CD4+ T-cell counts, antiretroviral therapy (ART), and the presence of HPV-associated precancerous anal lesions. Results confirm the occurrence of oncogenic viromes in this high HIV-risk population. The oral microbiome in HIV-associated cases exhibited an enrichment of bacteria associated with periodontal disease pathogenesis. Conversely, anal bacteria showed a significant decrease in HIV-infected subjects (Coprococcus comes, Finegoldia magna, Blautia obeum, Catenibacterium mitsuokai). TGW showed enrichment in species related to sexual transmission, which concurs that most recruited TGW are or have been sex workers. Prevotella bivia and Fusobacterium gonidiaformans were positively associated with anal precancerous lesions among HIV-infected subjects. The enrichment of Holdemanella biformis and C. comes was associated with detectable viral load and ART-untreated patients. Metabolic pathways were distinctly affected by predominant factors linked to sexual behavior or HIV pathogenesis. Gene family analysis identified bacterial gene signatures as potential prognostic and predictive biomarkers for HIV/AIDS-associated malignancies. Conclusions: Identified microbial features at accessible sites are potential biomarkers for predicting precancerous anal lesions and therapeutic targets for HIV immunopathogenesis.}, } @article {pmid37437419, year = {2023}, author = {Gundogdu, A and Nalbantoglu, OU}, title = {The role of the Mediterranean diet in modulating the gut microbiome: A review of current evidence.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {114}, number = {}, pages = {112118}, doi = {10.1016/j.nut.2023.112118}, pmid = {37437419}, issn = {1873-1244}, mesh = {Humans ; *Diet, Mediterranean ; *Gastrointestinal Microbiome ; Nutrients ; Nutritional Status ; Micronutrients ; }, abstract = {The Mediterranean diet (MedDiet) is recognized as one of the United Nations Educational, Scientific and Cultural Organization Intangible Cultural Heritage assets associated with lower rates of cardiometabolic diseases; lower prevalence of cancer, Alzheimer's disease, depression, and onset of inflammatory bowel disease; and more generally low-grade inflammation and mortality risks. Beyond being an input source of beneficial micronutrients, it recently has been discovered that the MedDiet plays a role in a more complex human microbiome-mediated mechanism. An interesting hypothesis suggests a bidirectional relationship between the MedDiet and the gut microbiome, where gut microbiota assembly and biosynthetic capacity are responsive to the diet; in return, the microbiome-reachable nutrients shape and modulate the microbiome toward a characteristic probiotic state. It can be speculated that that primary health benefits of the MedDiet exerted via the gut microbiome are mediated by the bioactive compounds transformed by the microbiome. Furthermore, it is possible that additional probiotic properties of the organisms promoted by diet adherence have secondary benefits. As more detailed omic-based studies take place, more evidence on the MedDiet as a core generic probiotic microbiome modulation strategy surface. However, individual-specific microbiome compositions might impose personal variations on the diet outcome. Therefore, a prospective strategy of a fine-tuned precision nutrition approach might deliver optimized benefits of the MedDiet.}, } @article {pmid37436481, year = {2023}, author = {Xing, Y and Bian, C and Xue, H and Song, Y and Men, W and Hou, W and Yang, Y and Cai, Q and Xu, L}, title = {The effect of plant compartment and geographical location on shaping microbiome of Pulsatilla chinensis.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {17}, pages = {5555-5567}, pmid = {37436481}, issn = {1432-0614}, support = {L201942//019 Liaoning Provincial Department of Education Scientific Research Project/ ; XLYC2002004//Liaoning Revitalization Talents Program/ ; 2020-MS-224//Natural Science Foundation of Liaoning Province/ ; }, mesh = {*Pulsatilla ; Rhizosphere ; Soil Microbiology ; Plant Roots/microbiology ; *Microbiota ; Bacteria/genetics ; Soil/chemistry ; *Plants, Medicinal ; }, abstract = {The plant-associated microbiome has an effect on plant growth. Pulsatilla chinensis (Bge.) Regel is an important Chinese medicinal plant. Currently, there is little understanding of the P. chinensis-associated microbiome and its diversity and composition. Here, the core microbiome associated with the root, leaf, and rhizospheric soil compartments of P. chinensis from five geographical locations was analyzed by the metagenomics approach. The alpha and beta diversity analysis showed that the microbiome associated with P. chinensis was shaped by the compartment, especially in the bacterial community. The geographical location had little influence on microbial community diversity associated with root and leaf. Hierarchical clustering distinguished the microbial communities of rhizospheric soil based on their geographical location and among the soil properties, pH was showed the more stronger effect on the diversity of rhizospheric soil microbial communities. Proteobacteria was the most dominant bacterial phylum in the root, leaf, and rhizospheric soil. Ascomycota and Basidiomycota were the most dominant fungal phyla in different compartments. Rhizobacter, Anoxybacillus, and IMCC26256 were the most important marker bacterial species for root, leaf, and rhizospheric soil screened by random forest, respectively. The fungal marker species for root, leaf, and rhizospheric soil were not only different across the compartments but also the geographical locations. Functional analysis showed that P. chinensis-associated microbiome had the similar function which had no obvious relationship with geographical location and compartment. The associated microbiome indicated in this study can be used for identifying microorganisms related to the quality and growth of P. chinensis. KEY POINTS: • Microbiome associated with P. chinensis was shaped by the compartment • Microbiome composition and abundance associated with rhizospheric soil were affected by the geographical location • Compared with fungi, bacterial associated with P. chinensis composition and diversity were more stable in different geographical locations and compartments.}, } @article {pmid37436163, year = {2023}, author = {Tan, Y and Chen, Z and Zeng, Z and Wu, S and Liu, J and Zou, S and Wang, M and Liang, K}, title = {Microbiomes Detected by Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing among HIV-Infected and Uninfected Patients with Pulmonary Infection.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0000523}, pmid = {37436163}, issn = {2165-0497}, mesh = {Humans ; Bronchoalveolar Lavage Fluid ; *Pneumonia ; *HIV Infections ; *Microbiota ; High-Throughput Nucleotide Sequencing ; Metagenomics ; }, abstract = {Comparison of lung microbiomes between HIV-infected and uninfected patients with pulmonary infection by metagenomic next-generation sequencing (mNGS) has not been described in China. The lung microbiomes detected in bronchoalveolar fluid (BALF) by mNGS among HIV-infected and uninfected patients with pulmonary infection were reviewed in the First Hospital of Changsha between January 2019 and June 2022. In total, 476 HIV-infected and 280 uninfected patients with pulmonary infection were enrolled. Compared with HIV-uninfected patients, the proportions of Mycobacterium (P = 0.011), fungi (P < 0.001), and viruses (P < 0.001) were significantly higher in HIV-infected patients. The higher positive rate of Mycobacterium tuberculosis (MTB; P = 0.018), higher positive rates of Pneumocystis jirovecii and Talaromyces marneffei (all P < 0.001), and higher positive rate of cytomegalovirus (P < 0.001) contributed to the increased proportions of Mycobacterium, fungi, and viruses among HIV-infected patients, respectively. The constituent ratios of Streptococcus pneumoniae (P = 0.007) and Tropheryma whipplei (P = 0.002) in the bacteria spectrum were significantly higher, while the constituent ratio of Klebsiella pneumoniae (P = 0.005) was significantly lower in HIV-infected patients than in HIV-uninfected patients. Compared with HIV-uninfected patients, the constituent ratios of P. jirovecii and T. marneffei (all P < 0.001) in the fungal spectrum were significantly higher, while the constituent ratios of Candida and Aspergillus (all P < 0.001) were significantly lower in HIV-infected patients. In comparison to HIV-infected patients without antiretroviral therapy (ART), the proportions of T. whipplei (P = 0.001), MTB (P = 0.024), P. jirovecii (P < 0.001), T. marneffei (P < 0.001), and cytomegalovirus (P = 0.008) were significantly lower in HIV-infected patients on ART. Significant differences in lung microbiomes exist between HIV-infected and uninfected patients with pulmonary infection, and ART influences the lung microbiomes among HIV-infected patients with pulmonary infection. IMPORTANCE A better understanding of lung microorganisms is conducive to early diagnosis and treatment and will improve the prognosis of HIV-infected patients with pulmonary infection. Currently, few studies have systematically described the spectrum of pulmonary infection among HIV-infected patients. This study is the first to provide comprehensive information on the lung microbiomes of HIV-infected patients with pulmonary infection (as assessed by more sensitive metagenomic next-generation sequencing of bronchoalveolar fluid) compared with those from HIV-uninfected patients, which could provide a reference for the etiology of pulmonary infection among HIV-infected patients.}, } @article {pmid37434868, year = {2023}, author = {Martinez-Hernandez, JE and Berrios, P and Santibáñez, R and Cuesta Astroz, Y and Sanchez, C and Martin, AJM and Trombert, AN}, title = {First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15235}, pmid = {37434868}, issn = {2167-8359}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; *Falconiformes ; Acclimatization ; Chile ; Clostridium perfringens ; }, abstract = {BACKGROUND: The Andean condor (Vultur gryphus) is the largest scavenger in South America. This predatory bird plays a crucial role in their ecological niche by removing carcasses. We report the first metagenomic analysis of the Andean condor gut microbiome.

METHODS: This work analyzed shotgun metagenomics data from a mixture of fifteen captive Chilean Andean condors. To filter eukaryote contamination, we employed BWA-MEM v0.7. Taxonomy assignment was performed using Kraken2 and MetaPhlAn v2.0 and all filtered reads were assembled using IDBA-UD v1.1.3. The two most abundant species were used to perform a genome reference-guided assembly using MetaCompass. Finally, we performed a gene prediction using Prodigal and each gene predicted was functionally annotated. InterproScan v5.31-70.0 was additionally used to detect homology based on protein domains and KEGG mapper software for reconstructing metabolic pathways.

RESULTS: Our results demonstrate concordance with the other gut microbiome data from New World vultures. In the Andean condor, Firmicutes was the most abundant phylum present, with Clostridium perfringens, a potentially pathogenic bacterium for other animals, as dominating species in the gut microbiome. We assembled all reads corresponding to the top two species found in the condor gut microbiome, finding between 94% to 98% of completeness for Clostridium perfringens and Plesiomonas shigelloides, respectively. Our work highlights the ability of the Andean condor to act as an environmental reservoir and potential vector for critical priority pathogens which contain relevant genetic elements. Among these genetic elements, we found 71 antimicrobial resistance genes and 1,786 virulence factors that we associated with several adaptation processes.}, } @article {pmid37434780, year = {2023}, author = {Xie, G and Hu, Q and Cao, X and Wu, W and Dai, P and Guo, W and Wang, O and Wei, L and Ren, R and Li, Y}, title = {Clinical identification and microbiota analysis of Chlamydia psittaci- and Chlamydia abortus- pneumonia by metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1157540}, pmid = {37434780}, issn = {2235-2988}, mesh = {Humans ; *Chlamydophila psittaci/genetics ; *Chlamydial Pneumonia/diagnosis ; *Coinfection ; *Chlamydia/genetics ; *Microbiota ; *Pneumonia/diagnosis ; *Chlamydia Infections/diagnosis ; High-Throughput Nucleotide Sequencing ; }, abstract = {INTRODUCTION: Recently, the incidence of chlamydial pneumonia caused by rare pathogens such as C. psittaci or C. abortus has shown a significant upward trend. The non-specific clinical manifestations and the limitations of traditional pathogen identification methods determine that chlamydial pneumonia is likely to be poorly diagnosed or even misdiagnosed, and may further result in delayed treatment or unnecessary antibiotic use. mNGS's non-preference and high sensitivity give us the opportunity to obtain more sensitive detection results than traditional methods for rare pathogens such as C. psittaci or C. abortus.

METHODS: In the present study, we investigated both the pathogenic profile characteristics and the lower respiratory tract microbiota of pneumonia patients with different chlamydial infection patterns using mNGS.

RESULTS: More co-infecting pathogens were found to be detectable in clinical samples from patients infected with C. psittaci compared to C. abortus, suggesting that patients infected with C. psittaci may have a higher risk of mixed infection, which in turn leads to more severe clinical symptoms and a longer disease course cycle. Further, we also used mNGS data to analyze for the first time the characteristic differences in the lower respiratory tract microbiota of patients with and without chlamydial pneumonia, the impact of the pattern of Chlamydia infection on the lower respiratory tract microbiota, and the clinical relevance of these characteristics. Significantly different profiles of lower respiratory tract microbiota and microecological diversity were found among different clinical subgroups, and in particular, mixed infections with C. psittaci and C. abortus resulted in lower lung microbiota diversity, suggesting that chlamydial infections shape the unique lung microbiota pathology, while mixed infections with different Chlamydia may have important effects on the composition and diversity of the lung microbiota.

DISCUSSION: The present study provides possible evidences supporting the close correlation between chlamydial infection, altered microbial diversity in patients' lungs and clinical parameters associated with infection or inflammation in patients, which also provides a new research direction to better understand the pathogenic mechanisms of pulmonary infections caused by Chlamydia.}, } @article {pmid37433843, year = {2023}, author = {Hintikka, JE and Ahtiainen, JP and Permi, P and Jalkanen, S and Lehtonen, M and Pekkala, S}, title = {Aerobic exercise training and gut microbiome-associated metabolic shifts in women with overweight: a multi-omic study.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {11228}, pmid = {37433843}, issn = {2045-2322}, mesh = {Adult ; Humans ; Female ; *Overweight/therapy ; *Gastrointestinal Microbiome ; Multiomics ; Exercise ; Obesity/therapy ; Lecithins ; }, abstract = {Physical activity is essential in weight management, improves overall health, and mitigates obesity-related risk markers. Besides inducing changes in systemic metabolism, habitual exercise may improve gut's microbial diversity and increase the abundance of beneficial taxa in a correlated fashion. Since there is a lack of integrative omics studies on exercise and overweight populations, we studied the metabolomes and gut microbiota associated with programmed exercise in obese individuals. We measured the serum and fecal metabolites of 17 adult women with overweight during a 6-week endurance exercise program. Further, we integrated the exercise-responsive metabolites with variations in the gut microbiome and cardiorespiratory parameters. We found clear correlation with several serum and fecal metabolites, and metabolic pathways, during the exercise period in comparison to the control period, indicating increased lipid oxidation and oxidative stress. Especially, exercise caused co-occurring increase in levels of serum lyso-phosphatidylcholine moieties and fecal glycerophosphocholine. This signature was associated with several microbial metagenome pathways and the abundance of Akkermansia. The study demonstrates that, in the absence of body composition changes, aerobic exercise can induce metabolic shifts that provide substrates for beneficial gut microbiota in overweight individuals.}, } @article {pmid37433373, year = {2023}, author = {Huang, X and Chen, C and Xie, W and Zhou, C and Tian, X and Zhang, Z and Wang, Q and Chang, H and Xiao, W and Zhang, R and Gao, Y}, title = {Metagenomic Analysis of Intratumoral Microbiome Linking to Response to Neoadjuvant Chemoradiotherapy in Rectal Cancer.}, journal = {International journal of radiation oncology, biology, physics}, volume = {117}, number = {5}, pages = {1255-1269}, doi = {10.1016/j.ijrobp.2023.06.2515}, pmid = {37433373}, issn = {1879-355X}, mesh = {Humans ; Neoadjuvant Therapy ; Metagenome ; Chemoradiotherapy/methods ; *Rectal Neoplasms/pathology ; Biomarkers ; *Microbiota ; Butyrates ; Treatment Outcome ; }, abstract = {PURPOSE: To assess taxonomic and functional characteristics of tumor-bearing microbiota and its association with response to neoadjuvant chemoradiation therapy (nCRT) in patients with locally advanced rectal cancer.

METHODS AND MATERIALS: We performed metagenomic sequencing of biopsy tumoral tissues from 73 patients with locally advanced rectal cancer before nCRT. Patients were classified into poor responders (PR) and good responders (GR) according to response to nCRT. Subsequent investigation of network alteration, key community, microbial biomarkers, and function related to nCRT responses were carried out.

RESULTS: The network-driven analysis systematically revealed 2 co-occurring bacteria modules that exhibited opposite relationship with rectal cancer radiosensitivity. In the 2 modules, prominent alteration of global graph properties and community structure was observed between networks of PR and GR group. By quantifying changes in between-group association patterns and abundances, a total of 115 discriminative biomarker species linked to nCRT response were found, and 35 microbial variables were selected to establish the optimal randomForest classifier for nCRT response prediction. It yielded an area under the curve value of 85.5% (95% CI, 73.3%-97.8%) in the training cohort and 88.4% (95% CI, 77.5%-99.4%) in the validation cohort. In a comprehensive consideration, 5 key bacteria showed high relevance with inducing resistance to nCRT, including Streptococcus equinus, Schaalia odontolytica, Clostridium hylemonae, Blautia producta, and Pseudomonas azotoformans. One key hub including several butyrate-formation bacteria involving with driving network alteration from GR to PR indicate that microbiota-derived butyrate may also be involved in reducing the antitumor effects of nCRT, especially Coprococcus. The functional analysis of metagenome linked the nitrate and sulfate-sulfur assimilation, histidine catabolic process, and resistance to cephamycin to the reduced therapeutic response. It also linked to leucine degradation, isoleucine biosynthesis, taurine, and hypotaurine metabolism to the improved response to nCRT.

CONCLUSIONS: Our data offer novel potential microbial factors and shared metagenome function linked to resistance to nCRT.}, } @article {pmid37432727, year = {2023}, author = {Wang, J and Shi, K and Jing, Z and Ge, Y}, title = {Metagenomic Evidence for Cobamide Producers Driving Prokaryotic Co-occurrence Associations and Potential Function in Wastewater Treatment Plants.}, journal = {Environmental science & technology}, volume = {57}, number = {29}, pages = {10640-10651}, doi = {10.1021/acs.est.3c02181}, pmid = {37432727}, issn = {1520-5851}, mesh = {*Cobamides ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Cobamides are required by most organisms but are only produced by specific prokaryotic taxa. These commonly shared cofactors play significant roles in shaping the microbial community and ecosystem function. Wastewater treatment plants (WWTPs) are the world's most common biotechnological systems; knowledge about sharing of cobamides among microorganisms is predicted to be important to decipher the complex microbial relationships in these systems. Herein, we explored prokaryotic potential cobamide producers in global WWTP systems based on metagenomic analyses. A set of 8253 metagenome-assembled genomes (MAGs) were recovered and 1276 (15.5%) of them were identified as cobamide producers, which could potentially be used for the practical biological manipulation of WWTP systems. Moreover, 8090 of the total recovered MAGs (98.0%) contained at least one enzyme family dependent on cobamides, indicating the sharing of cobamides among microbial members in WWTP systems. Importantly, our results showed that the relative abundance and number of cobamide producers improved the complexity of microbial co-occurrence networks and most nitrogen, sulfur, and phosphorus cycling gene abundances, indicating the significance of cobamides in microbial ecology and their potential function in WWTP systems. These findings enhance the knowledge of cobamide producers and their functions in WWTP systems, which has important implications for improving the efficiency of microbial wastewater treatment processes.}, } @article {pmid37432374, year = {2023}, author = {Silvano, A and Meriggi, N and Renzi, S and Seravalli, V and Torcia, MG and Cavalieri, D and Di Tommaso, M}, title = {Vaginal Microbiome in Pregnant Women with and without Short Cervix.}, journal = {Nutrients}, volume = {15}, number = {9}, pages = {}, pmid = {37432374}, issn = {2072-6643}, support = {B15F21003630007//Ente Cassa di Risparmio di Firenze/ ; }, mesh = {Pregnancy ; Humans ; Female ; *Cervix Uteri ; Pregnant Women ; Vagina ; *Microbiota ; Metagenome ; }, abstract = {Cervical shortening is a recognised risk factor for pre-term birth. The vaginal microbiome plays an essential role in pregnancy and in maternal and foetal outcomes. We studied the vaginal microbiome in 68 women with singleton gestation and a cervical length ≤25 mm and in 29 pregnant women with a cervix >25 mm in the second or early third trimester. Illumina protocol 16S Metagenomic Sequencing Library Preparation was used to detail amplified 16SrRNA gene. Statistical analyses were performed in R environment. Firmicutes was the phylum most represented in all pregnant women. The mean relative abundance of Proteobacteria and Actinobacteriota was higher in women with a short cervix. Bacterial abundance was higher in women with a normal length cervix compared to the group of women with a short cervix. Nonetheless, a significant enrichment in bacterial taxa poorly represented in vaginal microbiome was observed in the group of women with a short cervix. Staphylococcus and Pseudomonas, taxa usually found in aerobic vaginitis, were more common in women with a short cervix compared with the control group, while Lactobacillus iners and Bifidobacterium were associated with a normal cervical length. Lactobacillus jensenii and Gardenerella vaginalis were associated with a short cervix.}, } @article {pmid37432207, year = {2023}, author = {Chen, BY and Li, YL and Lin, WZ and Bi, C and Du, LJ and Liu, Y and Zhou, LJ and Liu, T and Xu, S and Zhang, J and Liu, Y and Zhu, H and Zhang, WC and Zhang, ZY and Duan, SZ}, title = {Integrated Omic Analysis of Human Plasma Metabolites and Microbiota in a Hypertension Cohort.}, journal = {Nutrients}, volume = {15}, number = {9}, pages = {}, pmid = {37432207}, issn = {2072-6643}, support = {81725003, 81991503, 81991500, 81921002//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Gastrointestinal Microbiome ; *Hypertension ; }, abstract = {Hypertension is closely related to metabolic dysregulation, which is associated with microbial dysbiosis and altered host-microbiota interactions. However, plasma metabolite profiles and their relationships to oral/gut microbiota in hypertension have not been evaluated in depth. Plasma, saliva, subgingival plaques, and feces were collected from 52 hypertensive participants and 24 healthy controls in a cross-sectional cohort. Untargeted metabolomic profiling of plasma was performed using high-performance liquid chromatography-mass spectrometry. Microbial profiling of oral and gut samples was determined via 16S rRNA and metagenomic sequencing. Correlations between metabolites and clinic parameters/microbiota were identified using Spearman's correlation analysis. Metabolomic evaluation showed distinct clusters of metabolites in plasma between hypertensive participants and control participants. Hypertensive participants had six significantly increased and thirty-seven significantly decreased plasma metabolites compared to controls. The plasma metabolic similarity significantly correlated with the community similarity of microbiota. Both oral and gut microbial community composition had significant correlations with metabolites such as Sphingosine 1-phosphate, a molecule involved in the regulation of blood pressure. Plasma metabolites had a larger number of significant correlations with bacterial genera than fungal genera. The shared oral/gut bacterial genera had more correlations with metabolites than unique genera but shared fungal genera and metabolites did not show clear clusters. The hypertension group had fewer correlations between plasma metabolites and bacteria/fungi than controls at species level. The integrative analysis of plasma metabolome and oral/gut microbiome identified unreported alterations of plasma metabolites in hypertension and revealed correlations between altered metabolites and oral/gut microbiota. These observations suggested metabolites and microbiota may become valuable targets for therapeutic and preventive interventions of hypertension.}, } @article {pmid37431863, year = {2023}, author = {Han, B and Lv, X and Liu, G and Li, S and Fan, J and Chen, L and Huang, Z and Lin, G and Xu, X and Huang, Z and Zhan, L and Lv, X}, title = {Gut microbiota-related bile acid metabolism-FXR/TGR5 axis impacts the response to anti-α4β7-integrin therapy in humanized mice with colitis.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2232143}, pmid = {37431863}, issn = {1949-0984}, mesh = {Animals ; Mice ; Humans ; *Gastrointestinal Microbiome ; Caco-2 Cells ; *Colitis/chemically induced/drug therapy ; *Inflammatory Bowel Diseases ; Bile Acids and Salts ; Integrins ; }, abstract = {The gut microbiota and bile acid metabolism are key determinants of the response of inflammatory bowel disease to biologic therapy. However, the molecular mechanisms underlying the interactions between the response to anti-α4β7-integrin therapy and the gut microbiota and bile acid metabolism remain unknown. In this research, we investigated the role of gut microbiota-related bile acid metabolism on the response to anti-α4β7-integrin therapy in a humanized immune system mouse model with colitis induced by 2,4,6-trinitrobenzene sulfonic acid. We found that anti-α4β7-integrin significantly mitigated intestinal inflammation, pathological symptoms, and gut barrier disruption in remission-achieving colitis mice. Whole-genome shotgun metagenomic sequencing demonstrated that employing baseline microbiome profiles to predict remission and the treatment response was a promising strategy. Antibiotic-mediated gut microbiota depletion and fecal microbiome transplantation revealed that the baseline gut microbiota contained common microbes with anti-inflammatory effects and reduced mucosal barrier damage, improving the treatment response. Targeted metabolomics analysis illustrated that bile acids associated with microbial diversity were involved in colitis remission. Furthermore, the activation effects of the microbiome and bile acids on FXR and TGR5 were evaluated in colitis mice and Caco-2 cells. The findings revealed that the production of gastrointestinal bile acids, particularly CDCA and LCA, further directly promoted the stimulation of FXR and TGR5, significantly improving gut barrier function and suppressing the inflammatory process. Taken together, gut microbiota-related bile acid metabolism-FXR/TGR5 axis may be a potential mechanism for impacting the response to anti-α4β7-integrin in experimental colitis. Thus, our research provides novel insights into the treatment response in inflammatory bowel disease.}, } @article {pmid37429473, year = {2023}, author = {Yue, Y and Zhang, H and Deng, P and Tan, M and Chen, C and Tang, B and Li, J and Chen, F and Zhao, Q and Li, L and Hao, R and Wang, H and Luo, Y and Tian, L and Xie, J and Chen, M and Yu, Z and Zhou, Z and Pi, H}, title = {Environmental cadmium exposure facilitates mammary tumorigenesis via reprogramming gut microbiota-mediated glutamine metabolism in MMTV-Erbb2 mice.}, journal = {The Science of the total environment}, volume = {897}, number = {}, pages = {165348}, doi = {10.1016/j.scitotenv.2023.165348}, pmid = {37429473}, issn = {1879-1026}, mesh = {Mice ; Animals ; Cadmium/toxicity ; Glutamine ; *Gastrointestinal Microbiome ; Ki-67 Antigen ; *Mammary Neoplasms, Experimental/chemically induced/metabolism/pathology ; Cell Transformation, Neoplastic/metabolism ; Mice, Transgenic ; Carcinogenesis/chemically induced ; Necrosis ; }, abstract = {Cadmium (Cd) is a heavy metal that has been widely reported to be linked to the onset and progression of breast cancer (BC). However, the mechanism of Cd-induced mammary tumorigenesis remains elusive. In our study, a transgenic mouse model that spontaneously develops tumors through overexpression of wild-type Erbb2 (MMTV-Erbb2) was constructed to investigate the effects of Cd exposure on BC tumorigenesis. The results showed that oral exposure to 3.6 mg/L Cd for 23 weeks dramatically accelerated tumor appearance and growth, increased Ki67 density and enhanced focal necrosis and neovascularization in the tumor tissue of MMTV-Erbb2 mice. Notably, Cd exposure enhanced glutamine (Gln) metabolism in tumor tissue, and 6-diazo-5-oxo-l-norleucine (DON), a Gln metabolism antagonist, inhibited Cd-induced breast carcinogenesis. Then our metagenomic sequencing and mass spectrometry-based metabolomics confirmed that Cd exposure disturbed gut microbiota homeostasis, especially Helicobacter and Campylobacter abundance remodeling, which altered the gut metabolic homeostasis of Gln. Moreover, intratumoral Gln metabolism profoundly increased under Cd-elevated gut permeability. Importantly, depletion of microbiota with an antibiotic cocktail (AbX) treatment led to a significant delay in the appearance of palpable tumors, inhibition of tumor growth, decrease in tumor weight, reduction in Ki67 expression and low-grade pathology in Cd-exposed MMTV-Erbb2 mice. Also, transplantation of Cd-modulated microbiota decreased tumor latency, accelerated tumor growth, increased tumor weight, upregulated Ki67 expression and exacerbated neovascularization as well as focal necrosis in MMTV-Erbb2 mice. In summary, Cd exposure induced gut microbiota dysbiosis, elevated gut permeability and increased intratumoral Gln metabolism, leading to the promotion of mammary tumorigenesis. This study provides novel insights into environmental Cd exposure-mediated carcinogenesis.}, } @article {pmid37428148, year = {2023}, author = {Serghiou, IR and Baker, D and Evans, R and Dalby, MJ and Kiu, R and Trampari, E and Phillips, S and Watt, R and Atkinson, T and Murphy, B and Hall, LJ and Webber, MA}, title = {An efficient method for high molecular weight bacterial DNA extraction suitable for shotgun metagenomics from skin swabs.}, journal = {Microbial genomics}, volume = {9}, number = {7}, pages = {}, pmid = {37428148}, issn = {2057-5858}, support = {BBS/E/F/00044409/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10349/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 100974/C/13/Z/WT_/Wellcome Trust/United Kingdom ; 220876/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T508974/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T014644/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adult ; Humans ; DNA, Bacterial/genetics ; *Metagenomics/methods ; Molecular Weight ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota/genetics ; DNA ; }, abstract = {The human skin microbiome represents a variety of complex microbial ecosystems that play a key role in host health. Molecular methods to study these communities have been developed but have been largely limited to low-throughput quantification and short amplicon-based sequencing, providing limited functional information about the communities present. Shotgun metagenomic sequencing has emerged as a preferred method for microbiome studies as it provides more comprehensive information about the species/strains present in a niche and the genes they encode. However, the relatively low bacterial biomass of skin, in comparison to other areas such as the gut microbiome, makes obtaining sufficient DNA for shotgun metagenomic sequencing challenging. Here we describe an optimised high-throughput method for extraction of high molecular weight DNA suitable for shotgun metagenomic sequencing. We validated the performance of the extraction method, and analysis pipeline on skin swabs collected from both adults and babies. The pipeline effectively characterised the bacterial skin microbiota with a cost and throughput suitable for larger longitudinal sets of samples. Application of this method will allow greater insights into community compositions and functional capabilities of the skin microbiome.}, } @article {pmid37428087, year = {2023}, author = {Bai, H and Liu, T and Wang, S and Gong, W and Shen, L and Zhang, S and Wang, Z}, title = {Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0059023}, pmid = {37428087}, issn = {2165-0497}, mesh = {Cats ; Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Feces/microbiology ; Diarrhea/veterinary/microbiology ; Firmicutes/genetics ; }, abstract = {Changes in diet and environment can lead to acute diarrhea in companion animals, but the composition and interactions of the gut microbiome during acute diarrhea remain unclear. In this multicenter case-control study, we investigated the relationship between intestinal flora and acute diarrhea in two breeds of cats. Acutely diarrheic American Shorthair (MD, n = 12) and British Shorthair (BD, n = 12) and healthy American Shorthair (MH, n = 12) and British Shorthair (BH, n = 12) cats were recruited. Gut microbial 16S rRNA sequencing, metagenomic sequencing, and untargeted metabolomic analysis were performed. We observed significant differences in beta-diversity (Adonis, P < 0.05) across breeds and disease state cohorts. Profound differences in gut microbial structure and function were found between the two cat breeds. In comparison to healthy British Shorthair cats, Prevotella, Providencia, and Sutterella were enriched while Blautia, Peptoclostridium, and Tyzzerella were reduced in American Shorthair cats. In the case-control cohort, cats with acute diarrhea exhibited an increased abundance of Bacteroidota, Prevotella, and Prevotella copri and a decreased abundance of Bacilli, Erysipelotrichales, and Erysipelatoclostridiaceae (both MD and BD cats, P < 0.05). Metabolomic analysis identified significant changes in the BD intestine, affecting 45 metabolic pathways. Moreover, using a random forest classifier, we successfully predicted the occurrence of acute diarrhea with an area under the curve of 0.95. Our findings indicate a distinct gut microbiome profile that is associated with the presence of acute diarrhea in cats. However, further investigations using larger cohorts of cats with diverse conditions are required to validate and extend these findings. IMPORTANCE Acute diarrhea is common in cats, and our understanding of the gut microbiome variations across breeds and disease states remains unclear. We investigated the gut microbiome of two cat breeds (British Shorthair and American Shorthair) with acute diarrhea. Our study revealed significant effects of breeds and disease states on the structure and function of the gut microbiota in cats. These findings emphasize the need to consider breed-related factors in animal nutrition and research models. Additionally, we observed an altered gut metabolome in cats with acute diarrhea, closely linked to changes in bacterial genera. We identified a panel of microbial biomarkers with high diagnostic accuracy for feline acute diarrhea. These findings provide novel insights into the diagnosis, classification, and treatment of feline gastrointestinal diseases.}, } @article {pmid37422700, year = {2023}, author = {Chaudhary, PP and Myles, IA and Zeldin, J and Dabdoub, S and Deopujari, V and Baveja, R and Baker, R and Bengtson, S and Sutton, A and Levy, S and Hourigan, SK}, title = {Shotgun metagenomic sequencing on skin microbiome indicates dysbiosis exists prior to the onset of atopic dermatitis.}, journal = {Allergy}, volume = {78}, number = {10}, pages = {2724-2731}, pmid = {37422700}, issn = {1398-9995}, support = {ZIA AI001043/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Child ; Infant, Newborn ; Humans ; *Dermatitis, Atopic/diagnosis/microbiology ; Dysbiosis ; Reproducibility of Results ; Skin/microbiology ; *Microbiota ; }, abstract = {BACKGROUND: While the microbiome is increasingly seen as a targetable contributor to atopic dermatitis (AD), questions remain as to whether the dysbiosis is secondary to diseased skin or if it predates symptom onset. Previous work has evaluated how the skin microbiome changes with age and established the influence of factors like delivery mode and breastfeeding on global microbiome diversity. However, these studies were unable to identify taxa which predict subsequent AD.

METHODS: Skin swab samples were collected from the first week of life for 72 children in the neonatal intensive care unit (NICU) at a single site hospital. Participants were followed for 3 years to determine their health status. We applied shotgun metagenomic sequencing to assess the microbiome differences between 31 children who went on to develop AD and 41 controls.

RESULTS: We identified that subsequent development of AD was associated with differential abundance of several bacterial and fungal taxa as well as several metabolic pathways, each of which have been previously associated with active AD.

CONCLUSIONS: Our work provides evidence of reproducibility for the previously reported dysbiotic signatures predating AD onset while also expanding prior findings through the first use of metagenomic assessment prior to AD onset. While extrapolation of our findings beyond the pre-term, NICU cohort is limited, our findings add to the evidence that the dysbiosis associated with AD pre-dates disease onset rather than reflect a secondary consequence of skin inflammation.}, } @article {pmid37422083, year = {2023}, author = {Lee, H and Yoon, S and Park, YH and Lee, JS and Rhyu, DY and Kim, KT}, title = {Microbiota dysbiosis associated with type 2 diabetes-like effects caused by chronic exposure to a mixture of chlorinated persistent organic pollutants in zebrafish.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {334}, number = {}, pages = {122108}, doi = {10.1016/j.envpol.2023.122108}, pmid = {37422083}, issn = {1873-6424}, mesh = {Animals ; Male ; Female ; *Diabetes Mellitus, Type 2/metabolism ; Zebrafish/metabolism ; Persistent Organic Pollutants/metabolism/pharmacology ; Dysbiosis/chemically induced/microbiology ; *Gastrointestinal Microbiome ; *Microbiota ; *Environmental Pollutants/metabolism ; }, abstract = {Mixtures of chlorinated persistent organic pollutants (C-POPs-Mix) are chemically related risk factors for type 2 diabetes mellitus (T2DM); however, the effects of chronic exposure to C-POPs-Mix on microbial dysbiosis remain poorly understood. Herein, male and female zebrafish were exposed to C-POPs-Mix at a 1:1 ratio of five organochlorine pesticides and Aroclor 1254 at concentrations of 0.02, 0.1, and 0.5 μg/L for 12 weeks. We measured T2DM indicators in blood and profiled microbial abundance and richness in the gut as well as transcriptomic and metabolomic alterations in the liver. Exposure to C-POPs-Mix significantly increased blood glucose levels while decreasing the abundance and alpha diversity of microbial communities only in females at concentrations of 0.02 and 0.1 μg/L. The majorly identified microbial contributors to microbial dysbiosis were Bosea minatitlanensis, Rhizobium tibeticum, Bifidobacterium catenulatum, Bifidobacterium adolescentis, and Collinsella aerofaciens. PICRUSt results suggested that altered pathways were associated with glucose and lipid production and inflammation, which are linked to changes in the transcriptome and metabolome of the zebrafish liver. Metagenomics outcomes revealed close relationships between intestinal and liver disruptions to T2DM-related molecular pathways. Thus, microbial dysbiosis in T2DM-triggered zebrafish occurred as a result of chronic exposure to C-POPs-Mix, indicating strong host-microbiome interactions.}, } @article {pmid37419993, year = {2023}, author = {Bei, Q and Reitz, T and Schnabel, B and Eisenhauer, N and Schädler, M and Buscot, F and Heintz-Buschart, A}, title = {Extreme summers impact cropland and grassland soil microbiomes.}, journal = {The ISME journal}, volume = {17}, number = {10}, pages = {1589-1600}, pmid = {37419993}, issn = {1751-7370}, mesh = {*Grassland ; Soil/chemistry ; *Microbiota ; Bacteria ; Droughts ; Crops, Agricultural ; Soil Microbiology ; }, abstract = {The increasing frequency of extreme weather events highlights the need to understand how soil microbiomes respond to such disturbances. Here, metagenomics was used to investigate the effects of future climate scenarios (+0.6 °C warming and altered precipitation) on soil microbiomes during the summers of 2014-2019. Unexpectedly, Central Europe experienced extreme heatwaves and droughts during 2018-2019, causing significant impacts on the structure, assembly, and function of soil microbiomes. Specifically, the relative abundance of Actinobacteria (bacteria), Eurotiales (fungi), and Vilmaviridae (viruses) was significantly increased in both cropland and grassland. The contribution of homogeneous selection to bacterial community assembly increased significantly from 40.0% in normal summers to 51.9% in extreme summers. Moreover, genes associated with microbial antioxidant (Ni-SOD), cell wall biosynthesis (glmSMU, murABCDEF), heat shock proteins (GroES/GroEL, Hsp40), and sporulation (spoIID, spoVK) were identified as potential contributors to drought-enriched taxa, and their expressions were confirmed by metatranscriptomics in 2022. The impact of extreme summers was further evident in the taxonomic profiles of 721 recovered metagenome-assembled genomes (MAGs). Annotation of contigs and MAGs suggested that Actinobacteria may have a competitive advantage in extreme summers due to the biosynthesis of geosmin and 2-methylisoborneol. Future climate scenarios caused a similar pattern of changes in microbial communities as extreme summers, but to a much lesser extent. Soil microbiomes in grassland showed greater resilience to climate change than those in cropland. Overall, this study provides a comprehensive framework for understanding the response of soil microbiomes to extreme summers.}, } @article {pmid37418475, year = {2023}, author = {Badr, AA and Fouad, WM}, title = {Comparative study of multiple approaches for identifying cultivable microalgae population diversity from freshwater samples.}, journal = {PloS one}, volume = {18}, number = {7}, pages = {e0285913}, pmid = {37418475}, issn = {1932-6203}, mesh = {*Microalgae/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; *Rivers/microbiology ; Egypt ; Microbiota ; }, abstract = {The vast diversity of microalgae imposes the challenge of identifying them through the most common and economical identification method, morphological identification, or through using the more recent molecular-level identification tools. Here we report an approach combining enrichment and metagenomic molecular techniques to enhance microalgae identification and identify microalgae diversity from environmental water samples. From this perspective, we aimed to identify the most suitable culturing media and molecular approach (using different primer sets and reference databases) for detecting microalgae diversity. Using this approach, we have analyzed three water samples collected from the River Nile on several enrichment media. A total of 37 microalgae were identified morphologically to the genus level. While sequencing the three-primer sets (16S rRNA V1-V3 and V4-V5 and 18S rRNA V4 region) and aligning them to three reference databases (GG, SILVA, and PR2), a total of 87 microalgae were identified to the genus level. The highest eukaryotic microalgae diversity was identified using the 18S rRNA V4 region and alignment to the SILVA database (43 genera). The two 16S rRNA regions sequenced added to the eukaryotic microalgae identification, 26 eukaryotic microalgae. Cyanobacteria were identified through the two sequenced 16S rRNA regions. Alignment to the SILVA database served to identify 14 cyanobacteria to the genera level, followed by Greengenes, 11 cyanobacteria genera. Our multiple-media, primer, and reference database approach revealed a high microalgae diversity that would have been overlooked if a single approach had been used over the other.}, } @article {pmid37417976, year = {2023}, author = {Santos-Pereira, C and Sousa, J and Costa, ÂMA and Santos, AO and Rito, T and Soares, P and Franco-Duarte, R and Silvério, SC and Rodrigues, LR}, title = {Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {17}, pages = {5379-5401}, pmid = {37417976}, issn = {1432-0614}, support = {UIDB/04469/2020//Fundação para a Ciência e a Tecnologia/ ; POCI-01-0145-FEDER-029773//Fundação para a Ciência e a Tecnologia/ ; PTDC/BII-BIO/5554/2020//Fundação para a Ciência e a Tecnologia/ ; CPCA/A0/408464/2021//Fundação para a Ciência e a Tecnologia/ ; UMINHO/BID/2021/12//Fundação para a Ciência e a Tecnologia/ ; 2022.11695.BD//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {*Composting ; Metagenomics ; Lignin/metabolism ; Carbohydrates ; *Microbiota ; Bacteria/metabolism ; *Cellulases/metabolism ; }, abstract = {The renewable, abundant , and low-cost nature of lignocellulosic biomass can play an important role in the sustainable production of bioenergy and several added-value bioproducts, thus providing alternative solutions to counteract the global energetic and industrial demands. The efficient conversion of lignocellulosic biomass greatly relies on the catalytic activity of carbohydrate-active enzymes (CAZymes). Finding novel and robust biocatalysts, capable of being active under harsh industrial conditions, is thus imperative to achieve an economically feasible process. In this study, thermophilic compost samples from three Portuguese companies were collected, and their metagenomic DNA was extracted and sequenced through shotgun sequencing. A novel multi-step bioinformatic pipeline was developed to find CAZymes and characterize the taxonomic and functional profiles of the microbial communities, using both reads and metagenome-assembled genomes (MAGs) as input. The samples' microbiome was dominated by bacteria, where the classes Gammaproteobacteria, Alphaproteobacteria, and Balneolia stood out for their higher abundance, indicating that the degradation of compost biomass is mainly driven by bacterial enzymatic activity. Furthermore, the functional studies revealed that our samples are a rich reservoir of glycoside hydrolases (GH), particularly of GH5 and GH9 cellulases, and GH3 oligosaccharide-degrading enzymes. We further constructed metagenomic fosmid libraries with the compost DNA and demonstrated that a great number of clones exhibited β-glucosidase activity. The comparison of our samples with others from the literature showed that, independently of the composition and process conditions, composting is an excellent source of lignocellulose-degrading enzymes. To the best of our knowledge, this is the first comparative study on the CAZyme abundance and taxonomic/functional profiles of Portuguese compost samples. KEY POINTS: • Sequence- and function-based metagenomics were used to find CAZymes in compost samples. • Thermophilic composts proved to be rich in bacterial GH3, GH5, and GH9 enzymes. • Compost-derived fosmid libraries are enriched in clones with β-glucosidase activity.}, } @article {pmid37413798, year = {2023}, author = {Wu, T and Zhong, L and Ding, J and Pang, JW and Sun, HJ and Ding, MQ and Ren, NQ and Yang, SS}, title = {Microplastics perturb nitrogen removal, microbial community and metabolism mechanism in biofilm system.}, journal = {Journal of hazardous materials}, volume = {458}, number = {}, pages = {131971}, doi = {10.1016/j.jhazmat.2023.131971}, pmid = {37413798}, issn = {1873-3336}, mesh = {*Denitrification ; Wastewater ; Microplastics ; Plastics ; Nitrogen/metabolism ; Bioreactors ; *Microbiota ; Biofilms ; Polystyrenes ; }, abstract = {Microplastics (MPs) are a significant component of global pollution and cause widespread concern, particularly in wastewater treatment plants. While understanding the impact of MPs on nutrient removal and potential metabolism in biofilm systems is limited. This work investigated the impact of polystyrene (PS) and polyethylene terephthalate (PET) on the performance of biofilm systems. The results revealed that at concentrations of 100 and 1000 μg/L, both PS and PET had almost no effect on the removal of ammonia nitrogen, phosphorus, and chemical oxygen demand, but reduced the removal of total nitrogen by 7.40-16.6%. PS and PET caused cell and membrane damage, as evidenced by increases in reactive oxygen species and lactate dehydrogenase to 136-355% and 144-207% of the control group. Besides, metagenomic analysis demonstrated both PS and PET changed the microbial structure and caused functional differences. Some important genes in nitrite oxidation (e.g. nxrA), denitrification (e.g. narB, nirABD, norB, and nosZ), and electron production process (e.g. mqo, sdh, and mdh) were restrained, meanwhile, species contribution to nitrogen-conversion genes was altered, therefore disturbing nitrogen-conversion metabolism. This work contributes to evaluating the potential risks of biofilm systems exposed to PS and PET, maintaining high nitrogen removal and system stability.}, } @article {pmid37406526, year = {2023}, author = {Meng, J and Li, W and Diao, C and Li, Z and Zhao, J and Haider, G and Zhang, H and Xu, J and Hu, M and Shan, S and Chen, H}, title = {Microplastics drive microbial assembly, their interactions, and metagenomic functions in two soils with distinct pH and heavy metal availability.}, journal = {Journal of hazardous materials}, volume = {458}, number = {}, pages = {131973}, doi = {10.1016/j.jhazmat.2023.131973}, pmid = {37406526}, issn = {1873-3336}, mesh = {Microplastics ; Soil ; Plastics ; *Metals, Heavy/analysis ; Bacteria ; *Microbiota ; Hydrogen-Ion Concentration ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Microplastics (MPs) have emerged as widely existing global environmental concerns in terrestrial ecosystems. However, the mechanisms that how MPs are affecting soil microbes and their metagenomic functioning is currently uncertain. Herein, we investigated the response mechanisms of bacterial and fungal communities as well as the metagenomic functions to the addition of MPs in two soils with distinct pH and heavy metals. In this study, the acidic soil (Xintong) and the neutral soil (Huanshan) contaminated by heavy metals were incubated with Polyvinyl Chloride (PVC) MPs at ratios of 2.5% and 5% on 60 and 120 days. We aimed to evaluate the responding, assembly, and interactions of the metagenomic taxonomy and function. Results showed that only in the acidic soil, PVC MPs significantly increased soil pH and decreased CaCl2-extractable heavy metals, and also reduced bacterial alpha diversity and interaction networks. The relative proportions of Proteobacteria and Bacteroidota in bacteria, and Mortierellomycota in fungi, were increased, but Chloroflexi and Acidobacteriota in bacteria, Ascomycota and Basidiomycota in fungi, were significantly decreased by PVC MPs. Metagenomic functions related to C cycling were repressed but the nutrient cycles were enriched with PVC MPs. In conclusion, our study suggests that the addition of PVC MPs could shift soil microbial community and metagenomic functioning, as well as increasing soil pH and reduced heavy metal availability.}, } @article {pmid37406521, year = {2023}, author = {Zeng, J and Pan, Y and Hu, R and Liu, F and Gu, H and Ding, J and Liu, S and Liu, S and Yang, X and Peng, Y and Tian, Y and He, Q and Wu, Y and Yan, Q and Shu, L and He, Z and Wang, C}, title = {The vertically-stratified resistomes in mangrove sediments was driven by the bacterial diversity.}, journal = {Journal of hazardous materials}, volume = {458}, number = {}, pages = {131974}, doi = {10.1016/j.jhazmat.2023.131974}, pmid = {37406521}, issn = {1873-3336}, mesh = {Humans ; *Genes, Bacterial ; Bacteria/genetics ; Anti-Bacterial Agents ; *Microbiota ; }, abstract = {Early evidence has elucidated that the spread of antibiotic (ARGs) and metal resistance genes (MRGs) are mainly attributed to the selection pressure in human-influenced environments. However, whether and how biotic and abiotic factors mediate the distribution of ARGs and MRGs in mangrove sediments under natural sedimentation is largely unclear. Here, we profiled the abundance and diversity of ARGs and MRGs and their relationships with sedimental microbiomes in 0-100 cm mangrove sediments. Our results identified multidrug-resistance and multimetal-resistance as the most abundant ARG and MRG classes, and their abundances generally decreased with the sediment depth. Instead of abiotic factors such as nutrients and antibiotics, the bacterial diversity was significantly negatively correlated with the abundance and diversity of resistomes. Also, the majority of resistance classes (e.g., multidrug and arsenic) were carried by more diverse bacterial hosts in deep layers with low abundances of resistance genes. Together, our results indicated that bacterial diversity was the most important biotic factor driving the vertical profile of ARGs and MRGs in the mangrove sediment. Given that there is a foreseeable increasing human impact on natural environments, this study emphasizes the important role of biodiversity in driving the abundance and diversity of ARGs and MRGs.}, } @article {pmid37404173, year = {2023}, author = {Kiledal, EA and Shaw, M and Polson, SW and Maresca, JA}, title = {Metagenomic Analysis of a Concrete Bridge Reveals a Microbial Community Dominated by Halophilic Bacteria and Archaea.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0511222}, pmid = {37404173}, issn = {2165-0497}, support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; }, mesh = {*Archaea/genetics ; *Microbiota/genetics ; Metagenome ; Sewage ; Sequence Analysis, DNA ; Metagenomics/methods ; Bacteria/genetics ; }, abstract = {Concrete hosts a small but diverse microbiome that changes over time. Shotgun metagenomic sequencing would enable assessment of both the diversity and function of the microbial community in concrete, but a number of unique challenges make this difficult for concrete samples. The high concentration of divalent cations in concrete interferes with nucleic acid extraction, and the extremely low biomass in concrete means that DNA from laboratory contamination may be a large fraction of the sequence data. Here, we develop an improved method for DNA extraction from concrete, with higher yield and lower laboratory contamination. To show that this method provides DNA of sufficient quality and quantity to do shotgun metagenomic sequencing, DNA was extracted from a sample of concrete obtained from a road bridge and sequenced with an Illumina MiSeq system. This microbial community was dominated by halophilic Bacteria and Archaea, with enriched functional pathways related to osmotic stress responses. Although this was a pilot-scale effort, we demonstrate that metagenomic sequencing can be used to characterize microbial communities in concrete and that older concrete structures may host different microbes than recently poured concrete. IMPORTANCE Prior work on the microbial communities of concrete focused on the surfaces of concrete structures such as sewage pipes or bridge pilings, where thick biofilms were easy to observe and sample. Because the biomass inside concrete is so low, more recent analyses of the microbial communities inside concrete used amplicon sequencing methods to describe those communities. However, to understand the activity and physiology of microbes in concrete, or to develop living infrastructure, we must develop more direct methods of community analysis. The method developed here for DNA extraction and metagenomic sequencing can be used for analysis of microbial communities inside concrete and can likely be adapted for other cementitious materials.}, } @article {pmid37404032, year = {2023}, author = {Deschênes, T and Tohoundjona, FWE and Plante, PL and Di Marzo, V and Raymond, F}, title = {Gene-based microbiome representation enhances host phenotype classification.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0053123}, pmid = {37404032}, issn = {2379-5077}, mesh = {Humans ; *Diabetes Mellitus, Type 2/genetics ; *Microbiota/genetics ; Metagenome ; *Gastrointestinal Microbiome/genetics ; Phenotype ; }, abstract = {With the concomitant advances in both the microbiome and machine learning fields, the gut microbiome has become of great interest for the potential discovery of biomarkers to be used in the classification of the host health status. Shotgun metagenomics data derived from the human microbiome is composed of a high-dimensional set of microbial features. The use of such complex data for the modeling of host-microbiome interactions remains a challenge as retaining de novo content yields a highly granular set of microbial features. In this study, we compared the prediction performances of machine learning approaches according to different types of data representations derived from shotgun metagenomics. These representations include commonly used taxonomic and functional profiles and the more granular gene cluster approach. For the five case-control datasets used in this study (Type 2 diabetes, obesity, liver cirrhosis, colorectal cancer, and inflammatory bowel disease), gene-based approaches, whether used alone or in combination with reference-based data types, allowed improved or similar classification performances as the taxonomic and functional profiles. In addition, we show that using subsets of gene families from specific functional categories of genes highlight the importance of these functions on the host phenotype. This study demonstrates that both reference-free microbiome representations and curated metagenomic annotations can provide relevant representations for machine learning based on metagenomic data. IMPORTANCE Data representation is an essential part of machine learning performance when using metagenomic data. In this work, we show that different microbiome representations provide varied host phenotype classification performance depending on the dataset. In classification tasks, untargeted microbiome gene content can provide similar or improved classification compared to taxonomical profiling. Feature selection based on biological function also improves classification performance for some pathologies. Function-based feature selection combined with interpretable machine learning algorithms can generate new hypotheses that can potentially be assayed mechanistically. This work thus proposes new approaches to represent microbiome data for machine learning that can potentiate the findings associated with metagenomic data.}, } @article {pmid37404011, year = {2023}, author = {Rooney, AM and Cochrane, K and Fedsin, S and Yao, S and Anwer, S and Dehmiwal, S and Hota, S and Poutanen, S and Allen-Vercoe, E and Coburn, B and , }, title = {A microbial consortium alters intestinal Pseudomonadota and antimicrobial resistance genes in individuals with recurrent Clostridioides difficile infection.}, journal = {mBio}, volume = {14}, number = {4}, pages = {e0348222}, pmid = {37404011}, issn = {2150-7511}, mesh = {Humans ; Microbial Consortia ; Anti-Bacterial Agents/pharmacology ; *Clostridioides difficile ; *Gastrointestinal Microbiome ; Drug Resistance, Bacterial ; Fecal Microbiota Transplantation ; *Clostridium Infections/therapy/microbiology ; Feces/microbiology ; *Microbiota ; Treatment Outcome ; }, abstract = {Intestinal colonization with pathogens and antimicrobial-resistant organisms (AROs) is associated with increased risk of infection. Fecal microbiota transplant (FMT) has successfully been used to cure recurrent Clostridioides difficile infection (rCDI) and to decolonize intestinal AROs. However, FMT has significant practical barriers to safe and broad implementation. Microbial consortia represent a novel strategy for ARO and pathogen decolonization, with practical and safety advantages over FMT. We undertook an investigator-initiated analysis of stool samples collected from previous interventional studies of a microbial consortium, microbial ecosystem therapeutic (MET-2), and FMT for rCDI before and after treatment. Our aim was to assess whether MET-2 was associated with decreased Pseudomonadota (Proteobacteria) and antimicrobial resistance gene (ARG) burden with similar effects to FMT. Participants were selected for inclusion if baseline stool had Pseudomonadota relative abundance ≥10%. Pre- and post-treatment Pseudomonadota relative abundance, total ARGs, and obligate anaerobe and butyrate-producer relative abundances were determined by shotgun metagenomic sequencing. MET-2 administration had similar effects to FMT on microbiome outcomes. The median Pseudomonadota relative abundance decreased by four logs after MET-2 treatment, a greater decrease than that observed after FMT. Total ARGs decreased, while beneficial obligate anaerobe and butyrate-producer relative abundances increased. The observed microbiome response remained stable over 4 months post-administration for all outcomes. IMPORTANCE Overgrowth of intestinal pathogens and AROs is associated with increased risk of infection. With the rise in antimicrobial resistance, new therapeutic strategies that decrease pathogen and ARO colonization in the gut are needed. We evaluated whether a microbial consortium had similar effects to FMT on Pseudomonadota abundances and ARGs as well as obligate anaerobes and beneficial butyrate producers in individuals with high Pseudomonadota relative abundance at baseline. This study provides support for a randomized, controlled clinical trial of microbial consortia (such as MET-2) for ARO decolonization and anaerobe repletion.}, } @article {pmid37403552, year = {2023}, author = {Pioli, S and Clagnan, E and Chowdhury, AA and Bani, A and Borruso, L and Ventura, M and Tonon, G and Brusetti, L}, title = {Structural and functional microbial diversity in deadwood respond to decomposition dynamics.}, journal = {Environmental microbiology}, volume = {25}, number = {11}, pages = {2351-2367}, doi = {10.1111/1462-2920.16459}, pmid = {37403552}, issn = {1462-2920}, mesh = {*Fungi/genetics ; Forests ; Wood/microbiology ; *Microbiota/genetics ; Bacteria/genetics ; Cellulose ; }, abstract = {We investigated the changes in microbial community diversities and functions in natural downed wood at different decay stages in a natural oak forest in the Italian Alps, through metagenomics analysis and in vitro analysis. Alfa diversity of bacterial communities was affected by the decay stage and log characteristics, while beta diversity was mainly driven by log diameter. Fungal and archaeal beta diversities were affected by the size of the sampled wood (log diameter), although, fungi were prominently driven by wood decay stage. The analysis of genes targeting cell wall degradation revealed higher abundances of cellulose and pectin-degrading enzymes in bacteria, while in fungi the enzymes targeting cellulose and hemicellulose were more abundant. The decay class affected the abundance of single enzymes, revealing a shift in complex hydrocarbons degradation pathways along the decay process. Moreover, we found that the genes related to Coenzyme M biosynthesis to be the most abundant especially at early stages of wood decomposition while the overall methanogenesis did not seem to be influenced by the decay stage. Intra- and inter-kingdom interactions between bacteria and fungi revealed complex pattern of community structure in response to decay stage possibly reflecting both direct and indirect interactions.}, } @article {pmid37402745, year = {2023}, author = {Amit, G and Bashan, A}, title = {Top-down identification of keystone taxa in the microbiome.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3951}, pmid = {37402745}, issn = {2041-1723}, mesh = {Humans ; Cross-Sectional Studies ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Microbial Interactions ; }, abstract = {Keystone taxa in ecological communities are native taxa that play an especially important role in the stability of their ecosystem. However, we still lack an effective framework for identifying these taxa from the available high-throughput sequencing without the notoriously difficult step of reconstructing the detailed network of inter-specific interactions. In addition, while most microbial interaction models assume pair-wise relationships, it is yet unclear whether pair-wise interactions dominate the system, or whether higher-order interactions are relevant. Here we propose a top-down identification framework, which detects keystones by their total influence on the rest of the taxa. Our method does not assume a priori knowledge of pairwise interactions or any specific underlying dynamics and is appropriate to both perturbation experiments and metagenomic cross-sectional surveys. When applied to real high-throughput sequencing of the human gastrointestinal microbiome, we detect a set of candidate keystones and find that they are often part of a keystone module - multiple candidate keystone species with correlated occurrence. The keystone analysis of single-time-point cross-sectional data is also later verified by the evaluation of two-time-points longitudinal sampling. Our framework represents a necessary advancement towards the reliable identification of these key players of complex, real-world microbial communities.}, } @article {pmid37401755, year = {2023}, author = {Ronkainen, A and Khan, I and Krzyżewska-Dudek, E and Hiippala, K and Freitag, TL and Satokari, R}, title = {In vitro adhesion, pilus expression, and in vivo amelioration of antibiotic-induced microbiota disturbance by Bifidobacterium spp. strains from fecal donors.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2229944}, pmid = {37401755}, issn = {1949-0984}, mesh = {Animals ; Mice ; Anti-Bacterial Agents/pharmacology ; Bifidobacterium ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; *Clostridioides difficile ; Mice, Inbred C57BL ; Feces/microbiology ; Fecal Microbiota Transplantation ; *Microbiota ; *Clostridium Infections/microbiology ; }, abstract = {Fecal microbiota transplantation (FMT) is used routinely to treat recurrent Clostridioides difficile infection (rCDI) and investigated as a treatment for numerous conditions associated with gut microbiota alterations. Metagenomic analyses have indicated that recipient colonization by donor bacteria may be associated with favorable clinical outcomes. Bifidobacteria are abundant gut commensals associated with health. We have previously demonstrated that Bifidobacterium strains transferred in FMT can colonize recipients in long term, at least for a year, and recovered such strains by cultivation. This study addressed in vitro adhesion and pilus gene expression of long-term colonizing Bifidobacterium strains from FMT donors as well as in vivo colonization and capability to ameliorate antibiotic-induced microbiota disturbance. RNA-Seq differential gene expression analysis showed that the strongly adherent B. longum strains DY_pv11 and DX_pv23 expressed tight adherence and sortase-dependent pilus genes, respectively. Two B. longum strains, adherent DX_pv23 and poorly adhering DX_pv18, were selected to address in vivo colonization and efficacy to restore antibiotic-disturbed microbiota in C57BL/6 murine model. DX_pv23 colonized mice transiently with a rate comparable to that of the B. animalis BB-12 used as a reference. Although long-term colonization was not observed with any of the three strains, 16S rRNA gene profiling revealed that oral administration of DX_pv23 enhanced the recovery of antibiotic-disturbed microbiota to the original configuration significantly better than the other strains. The findings suggest that selected strains from FMT donors, such as DX_pv23 in this study, may have therapeutic potential by in vitro expression of colonization factors and boosting endogenous gut microbiota.}, } @article {pmid37401151, year = {2023}, author = {Daga-Quisbert, J and Rajarao, GK and Ugarte, F and van Maris, AJA and Quillaguamán, J}, title = {Analysis of the microbiome of the Bolivian high-altitude Lake Pastos Grandes.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {8}, pages = {}, doi = {10.1093/femsec/fiad073}, pmid = {37401151}, issn = {1574-6941}, mesh = {Humans ; *Lakes/microbiology ; Bolivia ; Altitude ; *Microbiota/genetics ; Sodium Chloride ; Water ; }, abstract = {Lake Pastos Grandes in Bolivia is mainly composed of salt flats, which are sporadically and only partially submerged during the wet season. In the present study, the chemical composition of water samples of the lake and some influent rivers was determined. We found that it is likely that the lake was influenced by the dilution of metals from ancient evaporites. We performed the first metagenomic studies of this lake. Analyses of shotgun metagenomics revealed that the relative abundances of Burkholderiales and Pseudomonadales were noteworthy in the water samples, whereas the archaea belonging to the Halobacteriales and Cyanobacteria from subsection III had high abundances in the salt flat. The eukaryotes Crustacea and Diatomea exhibited the highest abundances in the water samples. We investigated further the potential effect of human activities on the nitrogen cycle mobilization in the lake and the propagation of antimicrobial resistance genes. This is the first report about the cycle in the lake. Additionally, rifamycin resistance genes and genes related to efflux pumps, which are not considered a hazard when identified in metagenomes, had the uppermost relative abundances in all sampling points. We found that Lake Pastos Grandes hitherto does not show an appreciable influence by anthropogenic actions.}, } @article {pmid37400907, year = {2023}, author = {Casto-Rebollo, C and Argente, MJ and García, ML and Pena, RN and Blasco, A and Ibáñez-Escriche, N}, title = {Selection for environmental variance shifted the gut microbiome composition driving animal resilience.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {147}, pmid = {37400907}, issn = {2049-2618}, mesh = {Animals ; Rabbits ; *Gastrointestinal Microbiome/genetics ; Feces ; *Microbiota ; Phenotype ; Metagenome ; }, abstract = {BACKGROUND: Understanding how the host's microbiome shapes phenotypes and participates in the host response to selection is fundamental for evolutionists and animal and plant breeders. Currently, selection for resilience is considered a critical step in improving the sustainability of livestock systems. Environmental variance (V E), the within-individual variance of a trait, has been successfully used as a proxy for animal resilience. Selection for reduced V E could effectively shift gut microbiome composition; reshape the inflammatory response, triglyceride, and cholesterol levels; and drive animal resilience. This study aimed to determine the gut microbiome composition underlying the V E of litter size (LS), for which we performed a metagenomic analysis in two rabbit populations divergently selected for low (n = 36) and high (n = 34) V E of LS. Partial least square-discriminant analysis and alpha- and beta-diversity were computed to determine the differences in gut microbiome composition among the rabbit populations.

RESULTS: We identified 116 KEGG IDs, 164 COG IDs, and 32 species with differences in abundance between the two rabbit populations studied. These variables achieved a classification performance of the V E rabbit populations of over than 80%. Compared to the high V E population, the low V E (resilient) population was characterized by an underrepresentation of Megasphaera sp., Acetatifactor muris, Bacteroidetes rodentium, Ruminococcus bromii, Bacteroidetes togonis, and Eggerthella sp. and greater abundances of Alistipes shahii, Alistipes putredinis, Odoribacter splanchnicus, Limosilactobacillus fermentum, and Sutterella, among others. Differences in abundance were also found in pathways related to biofilm formation, quorum sensing, glutamate, and amino acid aromatic metabolism. All these results suggest differences in gut immunity modulation, closely related to resilience.

CONCLUSIONS: This is the first study to show that selection for V E of LS can shift the gut microbiome composition. The results revealed differences in microbiome composition related to gut immunity modulation, which could contribute to the differences in resilience among rabbit populations. The selection-driven shifts in gut microbiome composition should make a substantial contribution to the remarkable genetic response observed in the V E rabbit populations. Video Abstract.}, } @article {pmid37399986, year = {2023}, author = {Magnuson, JT and Monticelli, G and Schlenk, D and Bisesi, JH and Pampanin, DM}, title = {Connecting gut microbiome changes with fish health conditions in juvenile Atlantic cod (Gadus morhua) exposed to dispersed crude oil.}, journal = {Environmental research}, volume = {234}, number = {}, pages = {116516}, doi = {10.1016/j.envres.2023.116516}, pmid = {37399986}, issn = {1096-0953}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Gadus morhua/metabolism ; *Petroleum/analysis/metabolism/toxicity ; Fishes ; *Microbiota/genetics ; *Water Pollutants, Chemical/analysis ; }, abstract = {Polycyclic aromatic hydrocarbons found in crude oil can impair fish health following sublethal exposure. However, the dysbiosis of microbial communities within the fish host and influence it has on the toxic response of fish following exposure has been less characterized, particularly in marine species. To better understand the effect of dispersed crude oil (DCO) on juvenile Atlantic cod (Gadus morhua) microbiota composition and potential targets of exposure within the gut, fish were exposed to 0.05 ppm DCO for 1, 3, 7, or 28 days and 16 S metagenomic and metatranscriptomic sequencing on the gut and RNA sequencing on intestinal content were conducted. In addition to assessing species composition, richness, and diversity from microbial gut community analysis and transcriptomic profiling, the functional capacity of the microbiome was determined. Mycoplasma and Aliivibrio were the two most abundant genera after DCO exposure and Photobacterium the most abundant genus in controls, after 28 days. Metagenomic profiles were only significantly different between treatments after a 28-day exposure. The top identified pathways were involved in energy and the biosynthesis of carbohydrates, fatty acids, amino acids, and cellular structure. Biological processes following fish transcriptomic profiling shared common pathways with microbial functional annotations such as energy, translation, amide biosynthetic process, and proteolysis. There were 58 differently expressed genes determined from metatranscriptomic profiling after 7 days of exposure. Predicted pathways that were altered included those involved in translation, signal transduction, and Wnt signaling. EIF2 signaling was consistently dysregulated following exposure to DCO, regardless of exposure duration, with impairments in IL-22 signaling and spermine and spermidine biosynthesis in fish after 28 days. Data were consistent with predictions of a potentially reduced immune response related to gastrointestinal disease. Herein, transcriptomic-level responses helped explain the relevance of differences in gut microbial communities in fish following DCO exposure.}, } @article {pmid37398670, year = {2023}, author = {Park, EJ and Yadav, H and Singh, TP}, title = {Editorial: Microbiota in skin inflammatory diseases.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1235314}, pmid = {37398670}, issn = {1664-3224}, mesh = {Humans ; Skin ; *Skin Diseases ; *Microbiota ; }, } @article {pmid37393724, year = {2023}, author = {He, Y and Pan, J and Huang, D and Sanford, RA and Peng, S and Wei, N and Sun, W and Shi, L and Jiang, Z and Jiang, Y and Hu, Y and Li, S and Li, Y and Li, M and Dong, Y}, title = {Distinct microbial structure and metabolic potential shaped by significant environmental gradient impacted by ferrous slag weathering.}, journal = {Environment international}, volume = {178}, number = {}, pages = {108067}, doi = {10.1016/j.envint.2023.108067}, pmid = {37393724}, issn = {1873-6750}, mesh = {Humans ; *Bacteria/genetics ; Metagenome ; *Microbiota ; Weather ; Carbon/metabolism ; }, abstract = {Alkaline ferrous slags pose global environmental issues and long-term risks to ambient environments. To explore the under-investigated microbial structure and biogeochemistry in such unique ecosystems, combined geochemical, microbial, ecological and metagenomic analyses were performed in the areas adjacent to a ferrous slag disposal plant in Sichuan, China. Different levels of exposure to ultrabasic slag leachate had resulted in a significant geochemical gradient of pH (8.0-12.4), electric potential (-126.9 to 437.9 mV), total organic carbon (TOC, 1.5-17.3 mg/L), and total nitrogen (TN, 0.17-1.01 mg/L). Distinct microbial communities were observed depending on their exposure to the strongly alkaline leachate. High pH and Ca[2+] concentrations were associated with low microbial diversity and enrichment of bacterial classes Gamma-proteobacteria and Deinococci in the microbial communities exposed to the leachate. Combined metagenomic analyses of 4 leachate-unimpacted and 2-impacted microbial communities led to the assembly of one Serpentinomonas pangenome and 81 phylogenetically diversified metagenome assembled genomes (MAGs). The prevailing taxa in the leachate-impacted habitats (e.g., Serpentinomonas and Meiothermus spp.) were phylogenetically related to those in active serpentinizing ecosystems, suggesting the analogous processes between the man-made and natural systems. More importantly, they accounted for significant abundance of most functional genes associated with environmental adaptation and major element cycling. Their metabolic potential (e.g., cation/H[+] antiporters, carbon fixation on lithospheric carbon source, and respiration coupling sulfur oxidization and oxygen or nitrate reduction) may support these taxa to survive and prosper in these unique geochemical niches. This study provides fundamental understandings of the adaptive strategies of microorganisms in response to the strong environmental perturbation by alkali tailings. It also contributes to a better comprehension of how to remediate environments affected by alkaline industrial material.}, } @article {pmid37393557, year = {2023}, author = {Madrigal-Trejo, D and Sánchez-Pérez, J and Espinosa-Asuar, L and Valdivia-Anistro, JA and Eguiarte, LE and Souza, V}, title = {A Metagenomic Time-Series Approach to Assess the Ecological Stability of Microbial Mats in a Seasonally Fluctuating Environment.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2252-2270}, pmid = {37393557}, issn = {1432-184X}, support = {IG200319//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; 970341//Consejo Nacional de Ciencia y Tecnología (CONACYT)/ ; R20F009//http://dx.doi.org/10.13039/501100020884/ ; }, mesh = {Metagenome ; *Cyanobacteria/genetics ; Archaea/genetics ; *Microbiota ; Bacteroidetes/genetics ; }, abstract = {Microbial mats are complex ecological assemblages that have been present in the rock record since the Precambrian and can still be found in extant marginalized environments. These structures are considered highly stable ecosystems. In this study, we evaluate the ecological stability of dome-forming microbial mats in a modern, water-level fluctuating, hypersaline pond located in the Cuatro Ciénegas Basin, Mexico. We conducted metagenomic sampling of the site from 2016 to 2019 and detected 2250 genera of Bacteria and Archaea, with only <20 belonging to the abundant taxa (>1%). The microbial community was dominated by Proteobacteria, Euryarchaeota, Bacteroidetes, Firmicutes, and Cyanobacteria, and was compositionally sensitive to disturbances, leading to high taxonomic replacement even at the phylum level, with a significant increase in Archaea from [Formula: see text]1-4% to [Formula: see text]33% throughout the 2016-2019 study period. Although a core community represented most of the microbial community (>75%), relative abundances shifted significantly between samples, as demonstrated by changes in the abundance of Coleofasciculus from 10.2% in 2017 to 0.05% in 2019. Although functional differences between seasons were subtle, co-occurrence networks suggest differential ecological interactions between the seasons, with the addition of a new module during the rainy season and the potential shift in hub taxa. Functional composition was slightly more similar between samples, but basic processes such as carbohydrate, amino acid, and nucleic acid metabolisms were widely distributed among samples. Major carbon fixation processes included sulfur oxidation, nitrogen fixation, and photosynthesis (both oxygenic and anoxygenic), as well as the Wood-Ljundgahl and Calvin cycles.}, } @article {pmid37392922, year = {2023}, author = {Tian, F and Zhou, B and Li, X and Zhang, Y and Qi, D and Qi, H and Jiang, H and Zhao, K and Liu, S}, title = {Population genomics analysis to identify ion and water transporter genes involved in the adaptation of Tibetan naked carps to brackish water.}, journal = {International journal of biological macromolecules}, volume = {247}, number = {}, pages = {125605}, doi = {10.1016/j.ijbiomac.2023.125605}, pmid = {37392922}, issn = {1879-0003}, mesh = {*Carps/genetics/physiology ; Animals ; Polymorphism, Single Nucleotide ; *Aquaporin 3/genetics ; *Fish Proteins/genetics ; Adaptation, Physiological ; Salinity ; Metagenomics ; }, abstract = {Understanding how evolutionary processes shape the genetic variations and influence the response of species to environmental alterations is critical for biodiversity conservation and molecular breeding. Gymnocypris przewalskii przewalskii is the only known cyprinid fish that dwells in the brackish water of Lake Qinghai on the Qinghai-Tibetan Plateau. To reveal the genetic basis of its adaptation to high salinity and alkalinity, whole-genome sequencing was performed in G. p. przewalskii and its freshwater relatives Gymnocypris eckloni and Gymnocypris przewalskii ganzihonensis. Compared with freshwater species, lower genetic diversity and higher linkage disequilibrium were observed in G. p. przewalskii. Selective sweep analysis identified 424 core-selective genes enriched in transport activities. Transfection analysis showed that genetic changes in the positively selected gene aquaporin 3 (AQP3) improved cell viability after salt treatment, suggesting its involvement in brackish water adaptation. Our analysis indicates that ion and water transporter genes experienced intensive selection, which might have contributed to the maintenance of high osmolality and ion content in G. p. przewalskii. The current study identified key molecules involved in the adaptation of fish to brackish water, providing valuable genomic resources for the molecular breeding of salt-tolerant fish.}, } @article {pmid37392873, year = {2023}, author = {Li, ZT and Yang, SY and Zhao, HP}, title = {The effects of arsenic on dechlorination of trichloroethene by consortium DH: Microbial response and resistance.}, journal = {The Science of the total environment}, volume = {896}, number = {}, pages = {165219}, doi = {10.1016/j.scitotenv.2023.165219}, pmid = {37392873}, issn = {1879-1026}, mesh = {*Chloroflexi/metabolism ; *Trichloroethylene/metabolism ; *Arsenic/metabolism ; Bacteria/metabolism ; *Microbiota ; Biodegradation, Environmental ; *Vinyl Chloride ; }, abstract = {Inorganic arsenic and organochlorines are frequently co-occurring contaminants in anoxic groundwater environments, and the bioremediation of their composite pollution has long been a rigorous predicament. Currently, the dechlorination behaviors and stress responses of microbial dechlorination consortia to arsenic are not yet fully understood. This study assessed the reductive dechlorination performance of a Dehalococcoides-bearing microcosm DH under gradient concentrations of arsenate [As(V)] or arsenite [As(III)] and investigated the response patterns of different functional microorganisms. Our results demonstrated that although the dechlorination rates declined with increasing arsenic concentrations in both As(III/V) scenarios, the inhibitory impact was more pronounced in As(III)-amended groups compared to As(V)-amended groups. Moreover, the vinyl chloride (VC)-to-ethene step was more susceptible to arsenic exposure compared to the trichloroethene (TCE)-to-dichloroethane (DCE) step, while high levels of arsenic exposure [e.g. As(III) > 75 μM] can induce significant accumulation of VC. Functional gene variations and microbial community analyses revealed that As(III/V) affected reductive dechlorination by directly inhibiting organohalide-respiring bacteria (OHRB) and indirectly inhibiting synergistic populations such as acetogens. Metagenomic results indicated that arsenic metabolic and efflux mechanisms were identical among different Dhc strains, and variations in arsenic uptake pathways were possibly responsible for their differential responses to arsenic exposures. By comparison, fermentative bacteria showed high potential for arsenic resistance due to their inherent advantages in arsenic detoxification and efflux mechanisms. Collectively, our findings expanded the understanding of the response patterns of different functional populations to arsenic stress in the dechlorinating consortium and provided insights into modifying bioremediation strategies at co-contaminated sites for furtherance.}, } @article {pmid37392645, year = {2023}, author = {Sułowicz, S and Borymski, S and Dulski, M and Nowak, A and Bondarczuk, K and Markowicz, A}, title = {Nanopesticide risk assessment based on microbiome profiling - Community structure and functional potential as biomarkers in captan@ZnO35-45 nm and captan@SiO220-30 nm treated orchard soil.}, journal = {Journal of hazardous materials}, volume = {458}, number = {}, pages = {131948}, doi = {10.1016/j.jhazmat.2023.131948}, pmid = {37392645}, issn = {1873-3336}, mesh = {Microbiota/drug effects ; Nanostructures ; *Pesticides/toxicity ; Risk Assessment ; *Captan/toxicity ; Biomarkers ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Nanoformulation should minimise the usage of pesticides and limit their environmental footprint. The risk assessment of two nanopesticides with fungicide captan as an active organic substance and ZnO35-45 nm or SiO220-30 nm as nanocarriers was evaluated using the non-target soil microorganisms as biomarkers. The first time for that kind of nanopesticides next-generation sequencing (NGS) of bacterial 16 S rRNA and fungal ITS region and metagenomics functional predictions (PICRUST2) was made to study structural and functional biodiversity. During a 100-day microcosm study in soil with pesticide application history, the effect of nanopesticides was compared to pure captan and both nanocarriers. Nanoagrochemicals affected microbial composition, especially Acidobacteria-6 class, and alpha diversity, but the observed effect was generally more substantial for pure captan. As for beta diversity, the negative impact was detected only in response to captan and still observed on day 100. Fungal community in the orchard soil showed only a decrease in phylogenetic diversity in captan set-up since day 30. PICRUST2 analysis confirmed several times lower impact of nanopesticides considering the abundance of functional pathways and genes encoding enzymes. Furthermore, the overall data indicated that using SiO220-30 nm as a nanocarrier speeds up a recovery process compared to ZnO35-45 nm.}, } @article {pmid37392210, year = {2023}, author = {Coe, GL and Krout, IN and Munro-Ehrlich, M and Beamish, CR and Vorojeikina, D and Colman, DR and Boyd, EJ and Walk, ST and Rand, MD}, title = {Assessing the role of the gut microbiome in methylmercury demethylation and elimination in humans and gnotobiotic mice.}, journal = {Archives of toxicology}, volume = {97}, number = {9}, pages = {2399-2418}, pmid = {37392210}, issn = {1432-0738}, support = {T32 207026/ES/NIEHS NIH HHS/United States ; P30 ES001247/ES/NIEHS NIH HHS/United States ; ES001247/ES/NIEHS NIH HHS/United States ; R01 ES030940/ES/NIEHS NIH HHS/United States ; ES030940/ES/NIEHS NIH HHS/United States ; T32 ES007026/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; *Methylmercury Compounds/toxicity/metabolism ; *Gastrointestinal Microbiome ; *Microbiota ; Kinetics ; Demethylation ; }, abstract = {The risk of methylmercury (MeHg) toxicity following ingestion of contaminated foodstuffs (e.g., fish) is directly related to the kinetics of MeHg elimination among individuals. Yet, the factors driving the wide range of inter-individual variability in MeHg elimination within a population are poorly understood. Here, we investigated the relationship between MeHg elimination, gut microbiome demethylation activity, and gut microbiome composition using a coordinated human clinical trial and gnotobiotic mouse modeling approach together with metagenomic sequence analysis. We first observed MeHg elimination half-lives (t1/2) ranging from 28 to 90 days across 27 volunteers. Subsequently, we found that ingestion of a prebiotic induced changes in the gut microbiome and mixed effects (increased, decrease, and no effect) on elimination in these same individuals. Nonetheless, elimination rates were found to correlate with MeHg demethylation activity in cultured stool samples. In mice, attempts to remove the microbiome via generation of germ-free (GF) animals or through antibiotic (Abx) treatment both diminished MeHg demethylation to a similar extent. While both conditions substantially slowed elimination, Abx treatment resulted in significantly slower elimination than the GF condition, indicating an additional role for host-derived factors in supporting elimination. Human fecal microbiomes transplanted to GF mice restored elimination rates to that seen in control mice. Metagenomic sequence analysis of human fecal DNA did not identify genes encoding proteins typically involved in demethylation (e.g., merB, organomercury lyase). However, the abundance of several anaerobic taxa, notably Alistipes onderdonkii, were positively correlated with MeHg elimination. Surprisingly, mono-colonization of GF free mice with A. onderdonkii did not restore MeHg elimination to control levels. Collectively, our findings indicate the human gut microbiome uses a non-conventional pathway of demethylation to increase MeHg elimination that relies on yet to be resolved functions encoded by the gut microbes and the hostClinical Trial NCT04060212, prospectively registered 10/1/2019.}, } @article {pmid37391847, year = {2023}, author = {Lv, J and Wang, J and Yu, Y and Zhao, M and Yang, W and Liu, J and Zhao, Y and Yang, Y and Wang, G and Guo, L and Zhao, H}, title = {Alterations of gut microbiota are associated with blood pressure: a cross-sectional clinical trial in Northwestern China.}, journal = {Journal of translational medicine}, volume = {21}, number = {1}, pages = {429}, pmid = {37391847}, issn = {1479-5876}, mesh = {Female ; Humans ; Male ; Blood Pressure ; China ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; *Hypertension ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The human gut microbiota (GM) is involved in the pathogenesis of hypertension (HTN), and could be affected by various factors, including sex and geography. However, available data directly linking GM to HTN based on sex differences are limited.

METHODS: This study investigated the GM characteristics in HTN subjects in Northwestern China, and evaluate the associations of GM with blood pressure levels based on sex differences. A total of 87 HTN subjects and 45 controls were recruited with demographic and clinical characteristics documented. Fecal samples were collected for 16S rRNA gene sequencing and metagenomic sequencing.

RESULTS: GM diversity was observed higher in females compared to males, and principal coordinate analysis showed an obvious segregation of females and males. Four predominant phyla of fecal GM included Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria. LEfSe analysis indicated that phylum unidentified_Bacteria was enriched in HTN females, while Leuconostocaceae, Weissella and Weissella_cibaria were enriched in control females (P < 0.05). Functionally, ROC analysis revealed that Cellular Processes (0.796, 95% CI 0.620 ~ 0.916), Human Diseases (0.773, 95% CI 0.595 ~ 0.900), Signal transduction (0.806, 95% CI 0.631 ~ 0.922) and Two-component system (0.806, 95% CI 0.631 ~ 0.922) could differentiate HTN females as effective functional classifiers, which were also positively correlated with systolic blood pressure levels.

CONCLUSIONS: This work provides evidence of fecal GM characteristics in HTN females and males in a northwestern Chinese population, further supporting the notion that GM dysbiosis may participate in the pathogenesis of HTN, and the role of sex differences should be considered. Trial registration Chinese Clinical Trial Registry, ChiCTR1800019191. Registered 30 October 2018 - Retrospectively registered, http://www.chictr.org.cn/ .}, } @article {pmid37391160, year = {2023}, author = {Hsiao, TH and Chen, PH and Wang, PH and Brandon-Mong, GJ and Li, CW and Horinouchi, M and Hayashi, T and Ismail, W and Meng, M and Chen, YL and Chiang, YR}, title = {Harnessing microbial phylum-specific molecular markers for assessment of environmental estrogen degradation.}, journal = {The Science of the total environment}, volume = {896}, number = {}, pages = {165152}, doi = {10.1016/j.scitotenv.2023.165152}, pmid = {37391160}, issn = {1879-1026}, mesh = {*Ecosystem ; *Estrogens/metabolism ; Estrone/metabolism ; Biodegradation, Environmental ; Bacteria/metabolism ; Proteobacteria/genetics ; }, abstract = {Steroidal estrogens are ubiquitous contaminants that have garnered attention worldwide due to their endocrine-disrupting and carcinogenic activities at sub-nanomolar concentrations. Microbial degradation is one of the main mechanisms through which estrogens can be removed from the environment. Numerous bacteria have been isolated and identified as estrogen degraders; however, little is known about their contribution to environmental estrogen removal. Here, our global metagenomic analysis indicated that estrogen degradation genes are widely distributed among bacteria, especially among aquatic actinobacterial and proteobacterial species. Thus, by using the Rhodococcus sp. strain B50 as the model organism, we identified three actinobacteria-specific estrogen degradation genes, namely aedGHJ, by performing gene disruption experiments and metabolite profile analysis. Among these genes, the product of aedJ was discovered to mediate the conjugation of coenzyme A with a unique actinobacterial C17 estrogenic metabolite, 5-oxo-4-norestrogenic acid. However, proteobacteria were found to exclusively adopt an α-oxoacid ferredoxin oxidoreductase (i.e., the product of edcC) to degrade a proteobacterial C18 estrogenic metabolite, namely 3-oxo-4,5-seco-estrogenic acid. We employed actinobacterial aedJ and proteobacterial edcC as specific biomarkers for quantitative polymerase chain reaction (qPCR) to elucidate the potential of microbes for estrogen biodegradation in contaminated ecosystems. The results indicated that aedJ was more abundant than edcC in most environmental samples. Our results greatly expand the understanding of environmental estrogen degradation. Moreover, our study suggests that qPCR-based functional assays are a simple, cost-effective, and rapid approach for holistically evaluating estrogen biodegradation in the environment.}, } @article {pmid37387148, year = {2023}, author = {Wang, Q and Nute, M and Treangen, TJ}, title = {Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {39 Suppl 1}, pages = {i47-i56}, pmid = {37387148}, issn = {1367-4811}, support = {P01 AI152999/AI/NIAID NIH HHS/United States ; R21 NS106640/NS/NINDS NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; *Gastrointestinal Microbiome ; Metagenome ; Bacteria/genetics ; *Crohn Disease ; }, abstract = {MOTIVATION: Interactions among microbes within microbial communities have been shown to play crucial roles in human health. In spite of recent progress, low-level knowledge of bacteria driving microbial interactions within microbiomes remains unknown, limiting our ability to fully decipher and control microbial communities.

RESULTS: We present a novel approach for identifying species driving interactions within microbiomes. Bakdrive infers ecological networks of given metagenomic sequencing samples and identifies minimum sets of driver species (MDS) using control theory. Bakdrive has three key innovations in this space: (i) it leverages inherent information from metagenomic sequencing samples to identify driver species, (ii) it explicitly takes host-specific variation into consideration, and (iii) it does not require a known ecological network. In extensive simulated data, we demonstrate identifying driver species identified from healthy donor samples and introducing them to the disease samples, we can restore the gut microbiome in recurrent Clostridioides difficile (rCDI) infection patients to a healthy state. We also applied Bakdrive to two real datasets, rCDI and Crohn's disease patients, uncovering driver species consistent with previous work. Bakdrive represents a novel approach for capturing microbial interactions.

Bakdrive is open-source and available at: https://gitlab.com/treangenlab/bakdrive.}, } @article {pmid37385198, year = {2023}, author = {Tian, Z and Li, G and Xiong, Y and Cao, X and Pang, H and Tang, W and Liu, Y and Bai, M and Zhu, Q and Du, C and Li, M and Zhang, L}, title = {Step-feeding food waste fermentation liquid as supplementary carbon source for low C/N municipal wastewater treatment: Bench scale performance and response of microbial community.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118434}, doi = {10.1016/j.jenvman.2023.118434}, pmid = {37385198}, issn = {1095-8630}, mesh = {Humans ; Wastewater ; Fermentation ; Food ; Waste Disposal, Fluid/methods ; Carbon ; Sewage ; *Severe Fever with Thrombocytopenia Syndrome ; Bioreactors ; *Refuse Disposal ; *Microbiota ; Nitrogen ; Denitrification ; }, abstract = {Municipal wastewater treatment often lacks carbon source, while carbon-rich organics in food waste are deficiently utilized. In this study, the food waste fermentation liquid (FWFL) was step-fed into a bench-scale step-feed three-stage anoxic/aerobic system (SFTS-A/O), to investigate its performance in nutrients removal and the response of microbial community as a supplementary carbon source. The results showed that the total nitrogen (TN) removal rate increased by 21.8-109.3% after step-feeding FWFL. However, the biomass of the SFTS-A/O system was increased by 14.6% and 11.9% in the two phases of the experiment, respectively. Proteobacteria was found to be the dominant functional phyla induced by FWFL, and the increase of its abundance attributed to the enrichment of denitrifying bacteria and carbohydrate-metabolizing bacteria was responsible for the biomass increase. Azospira belonged to Proteobacteria phylum was the dominant denitrifying genera when step-fed with FWFL, its abundance was increased from 2.7% in series 1 (S1) to 18.6% in series 2 (S2) and became the keystone species in the microbial networks. Metagenomics analysis revealed that step-feeding FWFL enhanced the abundance of denitrification and carbohydrates-metabolism genes, which were encode mainly by Proteobacteria. This study constitutes a key step towards the application of FWFL as a supplementary carbon source for low C/N municipal wastewater treatment.}, } @article {pmid37385196, year = {2023}, author = {Hao, DC and Su, XY and Xie, HT and Bao, XL and Zhang, XD and Wang, LF}, title = {Effects of tillage patterns and stover mulching on N2O production, nitrogen cycling genes and microbial dynamics in black soil.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118458}, doi = {10.1016/j.jenvman.2023.118458}, pmid = {37385196}, issn = {1095-8630}, mesh = {*Soil/chemistry ; Ammonia/analysis ; Carbon/analysis ; Agriculture ; China ; *Microbiota ; Nitrogen/analysis ; Alkynes/analysis ; Soil Microbiology ; Nitrous Oxide/analysis ; }, abstract = {Stover-covered no-tillage (NT) is of great significance to the rational utilization of stover resources and improvement of cultivated land quality, and also has a profound impact on ensuring groundwater, food and ecosystem security. However, the effects of tillage patterns and stover mulching on soil nitrogen turnover remain elusive. Based on the long-term conservation tillage field experiment in the mollisol area of Northeast China since 2007, the shotgun metagenomic sequencing of soils and microcosm incubation were combined with physical and chemical analyses, alkyne inhibition analysis to elucidate the regulatory mechanisms of NT and stover mulching on the farmland soil nitrogen emissions and microbial nitrogen cycling genes. Compared with conventional tillage (CT), NT stover mulching significantly reduced the emission of N2O instead of CO2, especially when 33% mulching was adopted, and correspondingly the nitrate nitrogen of NT33 was higher than that of other mulching amounts. The stover mulching was associated with higher total nitrogen, soil organic carbon and pH. The abundance of AOB (ammonia-oxidizing bacteria)-amoA (ammonia monooxygenase subunit A) was substantially increased by stover mulching, while the abundance of denitrification genes was reduced in most cases. Under alkyne inhibition, the tillage mode, treatment time, gas condition and interactions between them noticeably influenced the N2O emission and nitrogen transformation. In CT, NT0 (no mulching) and NT100 (full mulching), the relative contribution of AOB to N2O production was markedly higher than that of ammonia oxidizing archaea. Different tillage modes were associated with distinct microbial community composition, albeit NT100 was closer to CT than to NT0. Compared with CT, the co-occurrence network of microbial communities was more complex in NT0 and NT100. Our findings suggest that maintaining a low-quantity stover mulching could regulate soil nitrogen turnover toward proficiently enhancing soil health and regenerative agriculture, and coping with global climate change.}, } @article {pmid37384733, year = {2023}, author = {Pinsky, ML and Clark, RD and Bos, JT}, title = {Coral Reef Population Genomics in an Age of Global Change.}, journal = {Annual review of genetics}, volume = {57}, number = {}, pages = {87-115}, doi = {10.1146/annurev-genet-022123-102748}, pmid = {37384733}, issn = {1545-2948}, mesh = {Animals ; Humans ; *Coral Reefs ; *Anthozoa/genetics ; Metagenomics ; Genome/genetics ; Biological Evolution ; Climate Change ; Ecosystem ; }, abstract = {Coral reefs are both exceptionally biodiverse and threatened by climate change and other human activities. Here, we review population genomic processes in coral reef taxa and their importance for understanding responses to global change. Many taxa on coral reefs are characterized by weak genetic drift, extensive gene flow, and strong selection from complex biotic and abiotic environments, which together present a fascinating test of microevolutionary theory. Selection, gene flow, and hybridization have played and will continue to play an important role in the adaptation or extinction of coral reef taxa in the face of rapid environmental change, but research remains exceptionally limited compared to the urgent needs. Critical areas for future investigation include understanding evolutionary potential and the mechanisms of local adaptation, developing historical baselines, and building greater research capacity in the countries where most reef diversity is concentrated.}, } @article {pmid37382555, year = {2023}, author = {Yi, S and Zhang, C and Yin, P and Yu, L and Tian, F and Chen, W and Zhai, Q}, title = {Compositional and functional features of the intestinal lactobacilli associated with different long-term diet types.}, journal = {Food & function}, volume = {14}, number = {14}, pages = {6570-6581}, doi = {10.1039/d3fo02182c}, pmid = {37382555}, issn = {2042-650X}, mesh = {Humans ; Lactobacillus/genetics/metabolism ; Diet ; *Gastrointestinal Microbiome ; *Probiotics ; }, abstract = {It is well known that diet is one of the most important factors in shaping the host's intestinal microbiota. Lactobacillus, a common group of probiotic bacteria, is widely distributed in the host gut, and studies have linked changes in lactobacilli in the gut to differences in dietary habits. Different dietary habits may affect not only the structural composition but also the function of lactobacilli in the intestine. Therefore, we dissected 283 metagenomes from samples collected from individuals with different dietary habits, investigating the presence of different species of lactobacilli. We demonstrated that the highest abundance of lactobacilli was found in stool samples from omnivorous populations and that Ligilactobacillus ruminis (L. ruminis) and Lactiplantibacillus plantarum (L. plantarum) were more prevalent in these samples than in vegetarian and vegan samples. In addition, we determined that different dietary structures affected the functional potential of lactobacilli by reconstructing the metagenome-assembled genomes (MAGs) of L. ruminis (highest abundance) in the samples. L. ruminis strains associated with a vegetarian diet had a higher "replication, recombination and repair" functional potential and may also have a greater capacity for glutathione (GSH) synthesis and metabolism. The results of our analysis provide evidence for the possibility of a specific selection of lactobacillus strains for people with different dietary habits.}, } @article {pmid37382302, year = {2023}, author = {Puente-Sánchez, F and Hoetzinger, M and Buck, M and Bertilsson, S}, title = {Exploring environmental intra-species diversity through non-redundant pangenome assemblies.}, journal = {Molecular ecology resources}, volume = {23}, number = {7}, pages = {1724-1736}, doi = {10.1111/1755-0998.13826}, pmid = {37382302}, issn = {1755-0998}, support = {892961//H2020 Marie Skłodowska-Curie Actions/ ; 2019-02336//Svenska Forskningsrådet Formas/ ; 2017-04422//Vetenskapsrådet/ ; 2018-05973//Vetenskapsrådet/ ; }, mesh = {Phylogeny ; *Bacteria/genetics ; Metagenome ; Algorithms ; *Microbiota ; Metagenomics/methods ; }, abstract = {At the genome level, microorganisms are highly adaptable both in terms of allele and gene composition. Such heritable traits emerge in response to different environmental niches and can have a profound influence on microbial community dynamics. As a consequence, any individual genome or population will contain merely a fraction of the total genetic diversity of any operationally defined "species", whose ecological potential can thus be only fully understood by studying all of their genomes and the genes therein. This concept, known as the pangenome, is valuable for studying microbial ecology and evolution, as it partitions genomes into core (present in all the genomes from a species, and responsible for housekeeping and species-level niche adaptation among others) and accessory regions (present only in some, and responsible for intra-species differentiation). Here we present SuperPang, an algorithm producing pangenome assemblies from a set of input genomes of varying quality, including metagenome-assembled genomes (MAGs). SuperPang runs in linear time and its results are complete, non-redundant, preserve gene ordering and contain both coding and non-coding regions. Our approach provides a modular view of the pangenome, identifying operons and genomic islands, and allowing to track their prevalence in different populations. We illustrate this by analysing intra-species diversity in Polynucleobacter, a bacterial genus ubiquitous in freshwater ecosystems, characterized by their streamlined genomes and their ecological versatility. We show how SuperPang facilitates the simultaneous analysis of allelic and gene content variation under different environmental pressures, allowing us to study the drivers of microbial diversification at unprecedented resolution.}, } @article {pmid37381590, year = {2023}, author = {Han, Z and Cheng, S and Dai, D and Kou, Y and Zhang, X and Li, F and Yin, X and Ji, J and Zhang, Z and Wang, X and Zhu, N and Zhang, Q and Tan, Y and Guo, X and Shen, L and Peng, Z}, title = {The gut microbiome affects response of treatments in HER2-negative advanced gastric cancer.}, journal = {Clinical and translational medicine}, volume = {13}, number = {7}, pages = {e1312}, pmid = {37381590}, issn = {2001-1326}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; B7-H1 Antigen/genetics ; *Stomach Neoplasms/drug therapy/genetics ; Immune Checkpoint Inhibitors ; Reproducibility of Results ; *Adenocarcinoma ; Lactobacillus ; }, abstract = {BACKGROUND: Common treatments for metastatic/unresectable HER2-negative gastric cancer include chemotherapy, immune checkpoint inhibitor monotherapy and chemotherapy plus immune checkpoint inhibitor. However, significant drug resistance exists regardless of the treatment regimen.

METHODS: Patients with metastatic/unresectable HER2-negative gastric/gastroesophageal junction adenocarcinoma were enrolled. All patients were divided into three groups according to the treatment regimen and were further divided into responders and non-responders according to efficacy evaluation. Metagenomics sequencing were performed to analyze gut microbiome signature of patients receiving different treatments at baseline and throughout treatment.

RESULTS: One hundred seventeen patients with HER2-negative advanced gastric or gastroesophageal junction adenocarcinoma receiving chemotherapy alone, anti PD-1/PD-L1 immunotherapy alone or combined regimen were included in this study. Microbiome signatures related to clinical response are distinct among the three treatment groups. Among which, 14, 8 and 13 species were significantly different between responders and non-responders in immunotherapy, immunotherapy plus chemotherapy and chemotherapy group, respectively. Patients with higher relative abundance of Lactobacillus possessed higher microbiome diversity and significantly better response to anti-PD-1/PD-L1 immunotherapy and had a trend to achieve better progression-free survival. Another cohort of 101 patients has been used as an external validation set to confirm the stability and reliability of these findings.

CONCLUSIONS: Gut microbiome affects response of treatments in HER2-negative advanced gastric cancer in a treatment-specific way, immunotherapy plus chemotherapy did not equal to a simple superposition of immunotherapy and chemotherapy. Lactobacillus is expected to become a novel choice as an adjuvant agent in promoting the efficacy of immunotherapy in gastric cancer.}, } @article {pmid37380422, year = {2023}, author = {Fan, YF and Li, ZP and Yu, XJ and Li, Z and Zhou, HJ and Zhang, YL and Gan, XT and Hua, D and Lu, X and Kan, B}, title = {[Study of the urban-impact on microbial communities and their virulence factors and antibiotic resistance genomes in the Nandu River, Haikou].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {44}, number = {6}, pages = {974-981}, doi = {10.3760/cma.j.cn112338-20221229-01090}, pmid = {37380422}, issn = {0254-6450}, support = {2020YFE0205700, 2022YFC2303900//National Key Research and Development Program of China/ ; 22193064//National Natural Science Foundation of China/ ; 2018ZX10714002//National Science and Technology Major Project of China/ ; }, mesh = {Humans ; *Rivers ; Virulence Factors/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Anti-Bacterial Agents ; Drug Resistance, Microbial/genetics ; }, abstract = {Objective: To explore the changes in bacterial community structure, antibiotic resistance genome, and pathogen virulence genome in river water before and after the river flowing through Haikou City and their transmission and dispersal patterns and to reveal anthropogenic disturbance's effects on microorganisms and resistance genes in the aquatic environment. Methods: The Nandu River was divided into three study areas: the front, middle and rear sections from the upstream before it flowed through Haikou City to the estuary. Three sampling sites were selected in each area, and six copies of the sample were collected in parallel at each site and mixed for 3 L per sample. Microbial community structure, antibiotic resistance, virulence factors, and mobile genetic elements were analyzed through bioinformatic data obtained by metagenomic sequencing and full-length sequencing of 16S rRNA genes. Variations in the distribution of bacterial communities between samples and correlation of transmission patterns were analyzed by principal co-ordinates analysis, procrustes analysis, and Mantel test. Results: As the river flowed through Haikou City, microbes' alpha diversity gradually decreased. Among them, Proteobacteria dominates in the bacterial community in the front, middle, and rear sections, and the relative abundance of Proteobacteria in the middle and rear sections was higher than that in the front segment. The diversity and abundance of antibiotic resistance genes, virulence factors, and mobile genetic elements were all at low levels in the front section and all increased significantly after flow through Haikou City. At the same time, horizontal transmission mediated by mobile genetic elements played a more significant role in the spread of antibiotic-resistance genes and virulence factors. Conclusions: Urbanization significantly impacts river bacteria and the resistance genes, virulence factors, and mobile genetic elements they carry. The Nandu River in Haikou flows through the city, receiving antibiotic-resistant and pathogen-associated bacteria excreted by the population. In contrast, antibiotic-resistant genes and virulence factors are enriched in bacteria, which indicates a threat to environmental health and public health. Comparison of river microbiomes and antibiotic resistance genomes before and after flow through cities is a valuable early warning indicator for monitoring the spread of antibiotic resistance.}, } @article {pmid37379385, year = {2023}, author = {Wang, J and Qu, YN and Evans, PN and Guo, Q and Zhou, F and Nie, M and Jin, Q and Zhang, Y and Zhai, X and Zhou, M and Yu, Z and Fu, QL and Xie, YG and Hedlund, BP and Li, WJ and Hua, ZS and Wang, Z and Wang, Y}, title = {Evidence for nontraditional mcr-containing archaea contributing to biological methanogenesis in geothermal springs.}, journal = {Science advances}, volume = {9}, number = {26}, pages = {eadg6004}, pmid = {37379385}, issn = {2375-2548}, mesh = {*Archaea/genetics/metabolism ; Ecosystem ; *Hot Springs ; Methane/metabolism ; Temperature ; Phylogeny ; }, abstract = {Recent discoveries of methyl-coenzyme M reductase-encoding genes (mcr) in uncultured archaea beyond traditional euryarchaeotal methanogens have reshaped our view of methanogenesis. However, whether any of these nontraditional archaea perform methanogenesis remains elusive. Here, we report field and microcosm experiments based on [13]C-tracer labeling and genome-resolved metagenomics and metatranscriptomics, revealing that nontraditional archaea are predominant active methane producers in two geothermal springs. Archaeoglobales performed methanogenesis from methanol and may exhibit adaptability in using methylotrophic and hydrogenotrophic pathways based on temperature/substrate availability. A five-year field survey found Candidatus Nezhaarchaeota to be the predominant mcr-containing archaea inhabiting the springs; genomic inference and mcr expression under methanogenic conditions strongly suggested that this lineage mediated hydrogenotrophic methanogenesis in situ. Methanogenesis was temperature-sensitive , with a preference for methylotrophic over hydrogenotrophic pathways when incubation temperatures increased from 65° to 75°C. This study demonstrates an anoxic ecosystem wherein methanogenesis is primarily driven by archaea beyond known methanogens, highlighting diverse nontraditional mcr-containing archaea as previously unrecognized methane sources.}, } @article {pmid37379127, year = {2023}, author = {Deek, RA and Li, H}, title = {Inference of microbial covariation networks using copula models with mixture margins.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {7}, pages = {}, pmid = {37379127}, issn = {1367-4811}, support = {R01 GM129781/GM/NIGMS NIH HHS/United States ; GM123056/NH/NIH HHS/United States ; }, mesh = {Likelihood Functions ; RNA, Ribosomal, 16S/genetics ; *Microbial Consortia ; Computer Simulation ; *Metagenome ; }, abstract = {MOTIVATION: Quantification of microbial covariations from 16S rRNA and metagenomic sequencing data is difficult due to their sparse nature. In this article, we propose using copula models with mixed zero-beta margins for the estimation of taxon-taxon covariations using data of normalized microbial relative abundances. Copulas allow for separate modeling of the dependence structure from the margins, marginal covariate adjustment, and uncertainty measurement.

RESULTS: Our method shows that a two-stage maximum-likelihood approach provides accurate estimation of model parameters. A corresponding two-stage likelihood ratio test for the dependence parameter is derived and is used for constructing covariation networks. Simulation studies show that the test is valid, robust, and more powerful than tests based upon Pearson's and rank correlations. Furthermore, we demonstrate that our method can be used to build biologically meaningful microbial networks based on a dataset from the American Gut Project.

R package for implementation is available at https://github.com/rebeccadeek/CoMiCoN.}, } @article {pmid37377419, year = {2023}, author = {Vyshenska, D and Sampara, P and Singh, K and Tomatsu, A and Kauffman, WB and Nuccio, EE and Blazewicz, SJ and Pett-Ridge, J and Louie, KB and Varghese, N and Kellom, M and Clum, A and Riley, R and Roux, S and Eloe-Fadrosh, EA and Ziels, RM and Malmstrom, RR}, title = {A standardized quantitative analysis strategy for stable isotope probing metagenomics.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0128022}, pmid = {37377419}, issn = {2379-5077}, mesh = {Humans ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; DNA/genetics ; Isotopes ; *Microbiota/genetics ; }, abstract = {Stable isotope probing (SIP) facilitates culture-independent identification of active microbial populations within complex ecosystems through isotopic enrichment of nucleic acids. Many DNA-SIP studies rely on 16S rRNA gene sequences to identify active taxa, but connecting these sequences to specific bacterial genomes is often challenging. Here, we describe a standardized laboratory and analysis framework to quantify isotopic enrichment on a per-genome basis using shotgun metagenomics instead of 16S rRNA gene sequencing. To develop this framework, we explored various sample processing and analysis approaches using a designed microbiome where the identity of labeled genomes and their level of isotopic enrichment were experimentally controlled. With this ground truth dataset, we empirically assessed the accuracy of different analytical models for identifying active taxa and examined how sequencing depth impacts the detection of isotopically labeled genomes. We also demonstrate that using synthetic DNA internal standards to measure absolute genome abundances in SIP density fractions improves estimates of isotopic enrichment. In addition, our study illustrates the utility of internal standards to reveal anomalies in sample handling that could negatively impact SIP metagenomic analyses if left undetected. Finally, we present SIPmg, an R package to facilitate the estimation of absolute abundances and perform statistical analyses for identifying labeled genomes within SIP metagenomic data. This experimentally validated analysis framework strengthens the foundation of DNA-SIP metagenomics as a tool for accurately measuring the in situ activity of environmental microbial populations and assessing their genomic potential. IMPORTANCE Answering the questions, "who is eating what?" and "who is active?" within complex microbial communities is paramount for our ability to model, predict, and modulate microbiomes for improved human and planetary health. These questions can be pursued using stable isotope probing to track the incorporation of labeled compounds into cellular DNA during microbial growth. However, with traditional stable isotope methods, it is challenging to establish links between an active microorganism's taxonomic identity and genome composition while providing quantitative estimates of the microorganism's isotope incorporation rate. Here, we report an experimental and analytical workflow that lays the foundation for improved detection of metabolically active microorganisms and better quantitative estimates of genome-resolved isotope incorporation, which can be used to further refine ecosystem-scale models for carbon and nutrient fluxes within microbiomes.}, } @article {pmid37375584, year = {2023}, author = {Fernandes, A and Oliveira, A and Carvalho, AL and Soares, R and Barata, P}, title = {Faecalibacterium prausnitzii in Differentiated Thyroid Cancer Patients Treated with Radioiodine.}, journal = {Nutrients}, volume = {15}, number = {12}, pages = {}, pmid = {37375584}, issn = {2072-6643}, support = {UID/BIM/04293/2019//Fundação para a Ciência e Tecnologia/ ; }, mesh = {Humans ; Faecalibacterium prausnitzii ; Iodine Radioisotopes/therapeutic use ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; Fatty Acids, Volatile ; *Thyroid Neoplasms/radiotherapy ; }, abstract = {BACKGROUND: Faecalibacterium prausnitzii, one of the most important bacteria of the human gut microbiota, produces butyrate (a short-chain fatty acid). Short-chain fatty acids are known to influence thyroid physiology and thyroid cancer's response to treatment. We aimed to analyze the relative abundance of Faecalibacterium prausnitzii on the gut microbiota of differentiated thyroid cancer patients compared to controls and its variation after radioiodine therapy (RAIT).

METHODS: Fecal samples were collected from 37 patients diagnosed with differentiated thyroid cancer before and after radioiodine therapy and from 10 volunteers. The abundance of F. prausnitzii was determined using shotgun metagenomics.

RESULTS: Our study found that the relative abundance of F. prausnitzii is significantly reduced in thyroid cancer patients compared to volunteers. We also found that there was a mixed response to RAIT, with an increase in the relative and absolute abundances of this bacterium in most patients.

CONCLUSIONS: Our study confirms that thyroid cancer patients present a dysbiotic gut microbiota, with a reduction in F. prausnitzii's relative abundance. In our study, radioiodine did not negatively affect F. prausnitzii, quite the opposite, suggesting that this bacterium might play a role in resolving radiation aggression issues.}, } @article {pmid37371491, year = {2023}, author = {Stupak, A and Kwaśniewski, W}, title = {Evaluating Current Molecular Techniques and Evidence in Assessing Microbiome in Placenta-Related Health and Disorders in Pregnancy.}, journal = {Biomolecules}, volume = {13}, number = {6}, pages = {}, pmid = {37371491}, issn = {2218-273X}, mesh = {Infant, Newborn ; Pregnancy ; Female ; Humans ; Placenta ; *Microbiota ; *Gastrointestinal Microbiome ; Pregnancy Trimester, First ; *Pre-Eclampsia ; }, abstract = {The microbiome is of great interest due to its potential influence on the occurrence and treatment of some human illnesses. It may be regarded as disruptions to the delicate equilibrium that humans ordinarily maintain with their microorganisms or the microbiota in their environment. The focus of this review is on the methodologies and current understanding of the functional microbiome in pregnancy outcomes. We present how novel techniques bring new insights to the contemporary field of maternal-fetal medicine with a critical analysis. The maternal microbiome in late pregnancy has been extensively studied, although data on maternal microbial changes during the first trimester are rare. Research has demonstrated that, in healthy pregnancies, the origin of the placental microbiota is oral (gut) rather than vaginal. Implantation, placental development, and maternal adaptation to pregnancy are complex processes in which fetal and maternal cells interact. Microbiome dysbiosis or microbial metabolites are rising as potential moderators of antenatal illnesses related to the placenta, such as fetal growth restriction, preeclampsia, and others, including gestational diabetes and preterm deliveries. However, because of the presence of antimicrobial components, it is likely that the bacteria identified in placental tissue are (fragments of) bacteria that have been destroyed by the placenta's immune cells. Using genomic techniques (metagenomics, metatranscriptomics, and metaproteomics), it may be possible to predict some properties of a microorganism's genome and the biochemical (epigenetic DNA modification) and physical components of the placenta as its environment. Despite the results described in this review, this subject needs further research on some major and crucial aspects. The phases of an in utero translocation of the maternal gut microbiota to the fetus should be explored. With a predictive knowledge of the impacts of the disturbance on microbial communities that influence human health and the environment, genomics may hold the answer to the development of novel therapies for the health of pregnant women.}, } @article {pmid37369825, year = {2023}, author = {Österdahl, MF and Whiston, R and Sudre, CH and Asnicar, F and Cheetham, NJ and Blanco Miguez, A and Bowyer, V and Antonelli, M and Snell, O and Dos Santos Canas, L and Hu, C and Wolf, J and Menni, C and Malim, M and Hart, D and Spector, T and Berry, S and Segata, N and Doores, K and Ourselin, S and Duncan, EL and Steves, CJ}, title = {Metabolomic and gut microbiome profiles across the spectrum of community-based COVID and non-COVID disease.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {10407}, pmid = {37369825}, issn = {2045-2322}, support = {215010/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; /BHF_/British Heart Foundation/United Kingdom ; MR/W005611/1/MRC_/Medical Research Council/United Kingdom ; /DH_/Department of Health/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 203148/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_20059/MRC_/Medical Research Council/United Kingdom ; MR/S023747/1/MRC_/Medical Research Council/United Kingdom ; MR/T005351/1/MRC_/Medical Research Council/United Kingdom ; MR/M004422/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *COVID-19 ; SARS-CoV-2 ; *Gastrointestinal Microbiome ; *Pneumonia ; Hospitalization ; }, abstract = {Whilst most individuals with SARS-CoV-2 infection have relatively mild disease, managed in the community, it was noted early in the pandemic that individuals with cardiovascular risk factors were more likely to experience severe acute disease, requiring hospitalisation. As the pandemic has progressed, increasing concern has also developed over long symptom duration in many individuals after SARS-CoV-2 infection, including among the majority who are managed acutely in the community. Risk factors for long symptom duration, including biological variables, are still poorly defined. Here, we examine post-illness metabolomic profiles, using nuclear magnetic resonance (Nightingale Health Oyj), and gut-microbiome profiles, using shotgun metagenomic sequencing (Illumina Inc), in 2561 community-dwelling participants with SARS-CoV-2. Illness duration ranged from asymptomatic (n = 307) to Post-COVID Syndrome (n = 180), and included participants with prolonged non-COVID-19 illnesses (n = 287). We also assess a pre-established metabolomic biomarker score, previously associated with hospitalisation for both acute pneumonia and severe acute COVID-19 illness, for its association with illness duration. We found an atherogenic-dyslipidaemic metabolic profile, including biomarkers such as fatty acids and cholesterol, was associated with longer duration of illness, both in individuals with and without SARS-CoV-2 infection. Greater values of a pre-existing metabolomic biomarker score also associated with longer duration of illness, regardless of SARS-CoV-2 infection. We found no association between illness duration and gut microbiome profiles in convalescence. This highlights the potential role of cardiometabolic dysfunction in relation to the experience of long duration symptoms after symptoms of acute infection, both COVID-19 as well as other illnesses.}, } @article {pmid37369278, year = {2023}, author = {Hazime, H and Ducasa, GM and Santander, AM and Brito, N and González, EE and Ban, Y and Kaunitz, J and Akiba, Y and Fernández, I and Burgueño, JF and Abreu, MT}, title = {Intestinal Epithelial Inactivity of Dual Oxidase 2 Results in Microbiome-Mediated Metabolic Syndrome.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {16}, number = {4}, pages = {557-572}, pmid = {37369278}, issn = {2352-345X}, support = {I01 BX001245/BX/BLRD VA/United States ; R01 DK099076/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Female ; Male ; Mice ; Anti-Bacterial Agents ; Dual Oxidases ; *Gastrointestinal Microbiome ; *Glucose Intolerance ; Hydrogen Peroxide ; Lipopolysaccharides ; *Metabolic Syndrome ; Obesity/metabolism ; }, abstract = {BACKGROUND & AIMS: Metabolic syndrome (MetS) is characterized by obesity, glucose intolerance, and hepatic steatosis. Alterations in the gut microbiome play important roles in the development of MetS. However, the mechanisms by which this occurs are poorly understood. Dual oxidase 2 (DUOX2) is an antimicrobial reduced nicotinamide adenine dinucleotide phosphate oxidase expressed in the gut epithelium. Here, we posit that epithelial DUOX2 activity provides a mechanistic link between the gut microbiome and the development of MetS.

METHODS: Mice carrying an intestinal epithelial-specific deletion of dual oxidase maturation factor 1/2 (DA IEC-KO), and wild-type littermates were fed a standard diet and killed at 24 weeks. Metabolic alterations were determined by glucose tolerance, lipid tests, and body and organ weight measurements. DUOX2 activity was determined by Amplex Red. Intestinal permeability was determined by fluorescein isothiocyanate-dextran, microbial translocation assessments, and portal vein lipopolysaccharide measurements. Metagenomic analysis of the stool microbiome was performed. The role of the microbiome was assessed in antibiotic-treated mice.

RESULTS: DA IEC-KO males showed increased body and organ weights accompanied by glucose intolerance and increased plasma lipid and liver enzyme levels, and increased adiposity in the liver and adipose tissue. Expression of F4/80, CD68, uncoupling protein 1, carbohydrate response element binding protein, leptin, and adiponectin was altered in the liver and adipose tissue of DA IEC-KO males. DA IEC-KO males produced less epithelial H2O2, had altered relative abundance of Akkermansiaceae and Lachnospiraceae in stool, and showed increased portal vein lipopolysaccharides and intestinal permeability. Females were protected from barrier defects and MetS, despite producing less H2O2. Antibiotic depletion abrogated all MetS phenotypes observed.

CONCLUSIONS: Intestinal epithelial inactivity of DUOX2 promotes MetS in a microbiome-dependent manner.}, } @article {pmid37365713, year = {2023}, author = {Zhu, J and Liu, S and Zhang, H and Zhao, W and Ding, J and Dai, R and Xu, K and He, C and Liu, J and Yang, L and Meng, H}, title = {Dynamic distribution of gut microbiota during Alzheimer's disease progression in a mice model.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {131}, number = {9}, pages = {480-490}, doi = {10.1111/apm.13339}, pmid = {37365713}, issn = {1600-0463}, mesh = {Humans ; Mice ; Animals ; *Alzheimer Disease/pathology ; *Gastrointestinal Microbiome ; *Neurodegenerative Diseases ; Mice, Transgenic ; *Microbiota ; Disease Models, Animal ; }, abstract = {Alzheimer's disease (AD) is an irreversible neurodegenerative disease that affects more than 44 million people worldwide. The pathogenic mechanisms of AD still remain unclear. Currently, there are numerous studies investigating the microbiota-gut-brain axis in humans and rodents indicated that gut microbiota played a role in neurodegenerative diseases, including AD. However, the underlying relationship between the progress of AD disease and the dynamic distribution of gut microbiota is not well understood. In the present study, APP[swe] /PS1[ΔE9] transgenic mice of different ages and sex were employed. After the evaluation of the AD mice model, gut metagenomic sequencing was conducted to reveal gut microbiota, moreover, probiotics intervention was treated in the AD mice. The results showed that (1) AD mice had reduced microbiota richness and a changed gut microbiota composition, and AD mice gut microbiota richness was correlated with cognitive performance. We have also found some potential AD-related microbes, for example, in AD-prone mice, the genus Mucispirillum was strongly associated with immune inflammation. (2) Probiotics intervention improved cognitive performance and changed gut microbiota richness and composition of AD mice. We revealed the dynamics distribution of gut microbiota and the effect of probiotics on AD in a mice model, which provides an important reference for the pathogenesis of AD, intestinal microbial markers associated with AD, and AD probiotic intervention.}, } @article {pmid37365664, year = {2023}, author = {Zhao, L and Lin, LZ and Zeng, Y and Teng, WK and Chen, MY and Brand, JJ and Zheng, LL and Gan, NQ and Gong, YH and Li, XY and Lv, J and Chen, T and Han, BP and Song, LR and Shu, WS}, title = {The facilitating role of phycospheric heterotrophic bacteria in cyanobacterial phosphonate availability and Microcystis bloom maintenance.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {142}, pmid = {37365664}, issn = {2049-2618}, mesh = {*Microcystis/genetics/metabolism ; Ecosystem ; *Organophosphonates/metabolism ; *Cyanobacteria/genetics ; Phytoplankton ; Lakes/microbiology ; Phosphorus/metabolism ; }, abstract = {BACKGROUND: Phosphonates are the main components in the global phosphorus redox cycle. Little is known about phosphonate metabolism in freshwater ecosystems, although rapid consumption of phosphonates has been observed frequently. Cyanobacteria are often the dominant primary producers in freshwaters; yet, only a few strains of cyanobacteria encode phosphonate-degrading (C-P lyase) gene clusters. The phycosphere is defined as the microenvironment in which extensive phytoplankton and heterotrophic bacteria interactions occur. It has been demonstrated that phytoplankton may recruit phycospheric bacteria based on their own needs. Therefore, the establishment of a phycospheric community rich in phosphonate-degrading-bacteria likely facilitates cyanobacterial proliferation, especially in waters with scarce phosphorus. We characterized the distribution of heterotrophic phosphonate-degrading bacteria in field Microcystis bloom samples and in laboratory cyanobacteria "phycospheres" by qPCR and metagenomic analyses. The role of phosphonate-degrading phycospheric bacteria in cyanobacterial proliferation was determined through coculturing of heterotrophic bacteria with an axenic Microcystis aeruginosa strain and by metatranscriptomic analysis using field Microcystis aggregate samples.

RESULTS: Abundant bacteria that carry C-P lyase clusters were identified in plankton samples from freshwater Lakes Dianchi and Taihu during Microcystis bloom periods. Metagenomic analysis of 162 non-axenic laboratory strains of cyanobacteria (consortia cultures containing heterotrophic bacteria) showed that 20% (128/647) of high-quality bins from eighty of these consortia encode intact C-P lyase clusters, with an abundance ranging up to nearly 13%. Phycospheric bacterial phosphonate catabolism genes were expressed continually across bloom seasons, as demonstrated through metatranscriptomic analysis using sixteen field Microcystis aggregate samples. Coculturing experiments revealed that although Microcystis cultures did not catabolize methylphosphonate when axenic, they demonstrated sustained growth when cocultured with phosphonate-utilizing phycospheric bacteria in medium containing methylphosphonate as the sole source of phosphorus.

CONCLUSIONS: The recruitment of heterotrophic phosphonate-degrading phycospheric bacteria by cyanobacteria is a hedge against phosphorus scarcity by facilitating phosphonate availability. Cyanobacterial consortia are likely primary contributors to aquatic phosphonate mineralization, thereby facilitating sustained cyanobacterial growth, and even bloom maintenance, in phosphate-deficient waters. Video Abstract.}, } @article {pmid37365419, year = {2024}, author = {Gryaznova, M and Smirnova, Y and Burakova, I and Syromyatnikov, M and Chizhkov, P and Popov, E and Popov, V}, title = {Changes in the Human Gut Microbiome Caused by the Short-Term Impact of Lactic Acid Bacteria Consumption in Healthy People.}, journal = {Probiotics and antimicrobial proteins}, volume = {16}, number = {4}, pages = {1240-1250}, pmid = {37365419}, issn = {1867-1314}, support = {FZGW-2020-0001//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Probiotics/administration & dosage ; *Lactobacillales/physiology/classification ; Adult ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification/metabolism ; Young Adult ; }, abstract = {The gut microbiome is one of the main factors affecting human health. It has been proven that probiotics can regulate the metabolism in the host body. A large number of people use probiotics not as medicines, but as a prophylactic supplement. The aim of our study was to evaluate the effect of lactic acid bacteria on the gut microbiome of healthy people using the V3 region of the 16S rRNA gene. Our study showed changes in the generic composition in the gut of healthy people when taking the supplement. There was an increase in the members responsible for the production of short-chain fatty acids in the gut of the host (Blautia, Fusicatenibacter, Eubacterium hallii group, Ruminococcus), as well as bacteria that improve intestinal homeostasis (Dorea and Barnesiella). There was also a decrease in the abundance of bacteria in the genera Catenibacterium, Hungatella, Escherichia-Shigella, and Pseudomonas, associated with an unhealthy profile of the human gut microbiome. An increase in members of the phylum Actinobacteriota was also observed, which has a positive effect on the host organism. Our results indicate that short-term prophylactic use of lactic acid bacteria-based supplements can be effective, as it contributes to a beneficial effect on the gut microbiome of healthy people.}, } @article {pmid37365103, year = {2023}, author = {Ojala, T and Häkkinen, AE and Kankuri, E and Kankainen, M}, title = {Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics.}, journal = {Trends in genetics : TIG}, volume = {39}, number = {9}, pages = {686-702}, doi = {10.1016/j.tig.2023.05.004}, pmid = {37365103}, issn = {0168-9525}, mesh = {Humans ; *Metagenomics ; *Microbiota/genetics ; Transcriptome/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {Metatranscriptomics refers to the analysis of the collective microbial transcriptome of a sample. Its increased utilization for the characterization of human-associated microbial communities has enabled the discovery of many disease-state related microbial activities. Here, we review the principles of metatranscriptomics-based analysis of human-associated microbial samples. We describe strengths and weaknesses of popular sample preparation, sequencing, and bioinformatics approaches and summarize strategies for their use. We then discuss how human-associated microbial communities have recently been examined and how their characterization may change. We conclude that metatranscriptomics insights into human microbiotas under health and disease have not only expanded our knowledge on human health, but also opened avenues for rational antimicrobial drug use and disease management.}, } @article {pmid37364294, year = {2023}, author = {Sipriyadi, S and Khairina, Y and Masrukhin, M and Yulandi, A and Wibowo, R and Nisa, D}, title = {Bacterial community structure in the rhizosphere of fungi-infected Amorphophallus titanum.}, journal = {Canadian journal of microbiology}, volume = {69}, number = {11}, pages = {439-448}, doi = {10.1139/cjm-2022-0256}, pmid = {37364294}, issn = {1480-3275}, mesh = {Fungi ; *Microbiota ; *Amorphophallus ; Rhizosphere ; Plant Roots/microbiology ; Soil Microbiology ; Bacteria ; Soil/chemistry ; *Trichoderma ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The rhizosphere is a narrow soil area directly affected by plant root exudates. Microbes inhabiting the rhizosphere have been widely studied for their beneficial effects on plant nutrition, growth, and disease prevention. Many factors affect the rhizosphere microbial composition, including plant pathogen infection. Here, we analyzed the bacterial community structure in the rhizosphere of fungi-infected Amorphophallus titanum. Soil samples were collected from rhizosphere and non-rhizosphere areas of fungi-infected A. titanum. The 16S metagenomic analysis was conducted to investigate the bacterial community of the samples by amplifying the V3-V4 region. The results showed that the phylum Firmicutes was prevalent in the rhizosphere, whereas the phyla Proteobacteria, Acidobacteria, and Actinobacteria were limited. Some major fungal genera were isolated from infected tubers and rhizosphere soil of A. titanum, including Trichoderma sp., Aspergillus sp., Perenniporia sp., and Cerrena sp. The fungal-isolate Aspergillus spp. is a well-known agricultural pest in several reports. While Cerrena sp. was reported to be pathogenic in plants, including the family of Arecaceae. Overall, the data revealed a potential relationship between fungal infections and the dominant bacterial community in the rhizosphere of A. titanum. Additionally, this research may contribute to the development of microbe-based technology to mitigate diseases in A. titanum.}, } @article {pmid37361045, year = {2023}, author = {Wang, D and Ren, H}, title = {Microbial community in buckwheat rhizosphere with different nitrogen application rates.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15514}, pmid = {37361045}, issn = {2167-8359}, mesh = {Rhizosphere ; *Fagopyrum/metabolism ; Nitrogen/analysis ; Fertilizers/analysis ; *Neurodegenerative Diseases ; Soil Microbiology ; *Microbiota/genetics ; }, abstract = {Microorganism plays a pivotal role in regulating sustainable development of agriculture. The excessive application of nitrogen fertilizer is considered to affect the microbial structure in many agricultural systems. The present study aimed to assess the impacts of nitrogen application rate on microbial diversity, community and functionality in rhizosphere of Tartary buckwheat in short-time. The nitrogen fertilizer was applied at rates of 90 kg (N90), 120 kg (N120) and 150 kg (N150) urea per hectare, respectively. The soil properties were measured chemical analysis and displayed no difference among treatments. Metagenome analysis results showed that the microbial diversity was not affected, but the microbial community and functionality were affected by the nitrogen application rate. According to the Linear discriminant analysis effect size (LEfSe) analysis, 15 taxa were significantly enriched in the N120 and N150 groups, no taxon was enriched in the N90 group. Kyoto Encyclopaedia of Genes and Genomes (KEGG) annotation results revealed that the genes related to butanoate and beta alanine metabolism were significantly enriched in the N90 group, the genes related to thiamine metabolism, lipopolysaccharide biosynthesis and biofilm formation were significantly enriched in the N120 group, and the genes related to neurodegenerative disease was significantly enriched in the N150 group. In conclusion, short-time nitrogen fertilizer application shifted the microbial community structure and functionality.}, } @article {pmid37358243, year = {2023}, author = {He, Y and Liang, J and Liu, Y and Zhou, X and Peng, C and Long, C and Huang, P and Feng, J and Zhang, Z}, title = {Combined supplementation with Lactobacillus sp. and Bifidobacterium thermacidophilum isolated from Tibetan pigs improves growth performance, immunity, and microbiota composition in weaned piglets.}, journal = {Journal of animal science}, volume = {101}, number = {}, pages = {}, pmid = {37358243}, issn = {1525-3163}, support = {U2002206//National Natural Science Foundation of China/ ; CARS-35//Youth Innovation Promotion Association/ ; KFZDSW-219//Key Research Program of the Chinese Academy of Sciences/ ; 2019QZKK0503//Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; 202001BB050001//Major Science and Technology Project in Yunnan Province of China/ ; }, mesh = {Animals ; Swine ; *Lactobacillus ; Prospective Studies ; Tibet ; Dietary Supplements ; *Microbiota ; Bifidobacterium ; Weaning ; }, abstract = {Probiotics, such as Lactobacillus and Bifidobacterium, promote growth in piglets by modulating gut microbiota composition and improving the host immune system. A strain of Lactobacillus sp. and Bifidobacterium thermacidophilum were previously isolated from fresh feces of Tibetan pigs. The effects of these isolated strains on growth performance, intestinal morphology, immunity, microbiota composition, and their metabolites were evaluated in weaned piglets. Thirty crossbred piglets were selected and fed either a basal diet (CON), a basal diet supplemented with aureomycin (ANT), or a basal diet supplemented with Lactobacillus sp. and B. thermacidophilum (LB) for 28 d. The piglets in the ANT and LB groups had significantly higher body weight gain than those in the CON group (P < 0.05). Piglets in the ANT and LB groups had regularly arranged villi and microvilli in the small intestine. Furthermore, they had improved immune function, as indicated by decreased serum concentrations of inflammatory cytokines (P < 0.05), improved components of immune cells in the blood, mesenteric lymph nodes, and spleen. Additionally, metagenomic sequencing indicated a significant shift in cecal bacterial composition and alterations in microbiota functional profiles following Lactobacillus sp. and B. thermacidophilum supplementation. Metabolomic results revealed that the metabolites were also altered, and Kyoto Encyclopedia of Genes and Genomes analysis revealed that several significantly altered metabolites were enriched in glycerophospholipid and cholesterol metabolism (P < 0.05). Furthermore, correlation analysis showed that several bacterial members were closely related to the alterations in metabolites, including Bacteroides sp., which were negatively correlated with triglyceride (16:0/18:0/20:4[5Z,8Z,11Z,14Z]), the metabolite that owned the highest variable importance of projection scores. Collectively, our findings suggest that combined supplementation with Lactobacillus sp. and B. thermacidophilum significantly improved the growth performance, immunity, and microbiota composition in weaned piglets, making them prospective alternatives to antibiotics in swine production.}, } @article {pmid37357866, year = {2023}, author = {Wang, YH and Luan, YX and Luo, JY and Men, Y and Engel, MS and Damgaard, J and Khila, A and Chen, PP and Figueiredo Moreira, FF and Rafael, JA and Xie, Q}, title = {300 Million years of coral treaders (Insecta: Heteroptera: Hermatobatidae) back to the ocean in the phylogenetic context of Arthropoda.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {2001}, pages = {20230855}, pmid = {37357866}, issn = {1471-2954}, mesh = {Animals ; Phylogeny ; *Anthozoa/genetics ; Ecosystem ; *Arthropods ; *Heteroptera ; Coral Reefs ; Insecta ; }, abstract = {Among hundreds of insect families, Hermatobatidae (commonly known as coral treaders) is one of the most unique. They are small, wingless predaceous bugs in the suborder Heteroptera. Adults are almost black in colour, measuring about 5 mm in body length and 3 mm in width. Thirteen species are known from tropical coral reefs or rocky shores, but their origin and evolutionary adaptation to their unusual marine habitat were unexplored. We report here the genome and metagenome of Hermatobates lingyangjiaoensis, hitherto known only from its type locality in the South China Sea. We further reconstructed the evolutionary history and origin of these marine bugs in the broader context of Arthropoda. The dated phylogeny indicates that Hexapoda diverged from their marine sister groups approximately 498 Ma and that Hermatobatidae originated 192 Ma, indicating that they returned to an oceanic life some 300 Myr after their ancestors became terrestrial. Their origin is consistent with the recovery of tropical reef ecosystems after the end-Triassic mass extinction, which might have provided new and open niches for them to occupy and thrive. Our analyses also revealed that both the genome changes and the symbiotic bacteria might have contributed to adaptations necessary for life in the sea.}, } @article {pmid37355726, year = {2023}, author = {Elie, C and Perret, M and Hage, H and Sentausa, E and Hesketh, A and Louis, K and Fritah-Lafont, A and Leissner, P and Vachon, C and Rostaing, H and Reynier, F and Gervasi, G and Saliou, A}, title = {Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {10279}, pmid = {37355726}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; DNA ; *Microbiota/genetics ; }, abstract = {The gut microbiome is widely analyzed using high-throughput sequencing, such as 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing (SMS). DNA extraction is known to have a large impact on the metagenomic analyses. The aim of this study was to compare DNA extraction protocols for 16S sequencing. In that context, four commonly used DNA extraction methods were compared for the analysis of the gut microbiota. Commercial versions were evaluated against modified protocols using a stool preprocessing device (SPD, bioMérieux) upstream DNA extraction. Stool samples from nine healthy volunteers and nine patients with a Clostridium difficile infection were extracted with all protocols and 16S sequenced. Protocols were ranked using wet- and dry-lab criteria, including quality controls of the extracted genomic DNA, alpha-diversity, accuracy using a mock community of known composition and repeatability across technical replicates. SPD improved overall efficiency of three of the four tested protocols compared with their commercial version, in terms of DNA extraction yield, sample alpha-diversity, and recovery of Gram-positive bacteria. The best overall performance was obtained for the S-DQ protocol, SPD combined with the DNeasy PowerLyser PowerSoil protocol from QIAGEN. Based on this evaluation, we strongly believe that the use of such stool preprocessing device improves both the standardization and the quality of the DNA extraction in the human gut microbiome studies.}, } @article {pmid37355675, year = {2023}, author = {Wang, Y and Guo, A and Zou, Y and Mu, W and Zhang, S and Shi, Z and Liu, Z and Cai, X and Zhu, XQ and Wang, S}, title = {Interaction between tissue-dwelling helminth and the gut microbiota drives mucosal immunoregulation.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {43}, pmid = {37355675}, issn = {2055-5008}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Microbiota ; *Colitis/metabolism ; *Helminths ; }, abstract = {Tissue-dwelling helminths affect billions of people around the world. They are potent manipulators of the host immune system, prominently by promoting regulatory T cells (Tregs) and are generally associated with a modified host gut microbiome. However, the role of the gut microbiota in the immunomodulatory processes for these non-intestinal parasites is still unclear. In the present study, we used an extra-intestinal cestode helminth model-larval Echinococcus multilocularis to explore the tripartite partnership (host-helminth-bacteria) in the context of regulating colonic Tregs in Balb/c mice. We showed that larval E. multilocularis infection in the peritoneal cavity attenuated colitis in Balb/c mice and induced a significant expansion of colonic Foxp3[+] Treg populations. Fecal microbiota depletion and transplantation experiments showed that the gut microbiota contributed to increasing Tregs after the helminth infection. Shotgun metagenomic and metabolic analyses revealed that the gut microbiome structure after infection was significantly shifted with a remarkable increase of Lactobacillus reuteri and that the microbial metabolic capability was reprogrammed to produce more Treg cell regulator-short-chain fatty acids in feces. Furthermore, we also prove that the L. reuteri strain elevated in infected mice was sufficient to promote the colonic Treg frequency and its growth was potentially associated with T cell-dependent immunity in larval E. multilocularis infection. Collectively, these findings indicate that the extraintestinal helminth drives expansions of host colonic Tregs through the gut microbes. This study suggests that the gut microbiome serves as a critical component of anti-inflammation effects even for a therapy based on an extraintestinal helminth.}, } @article {pmid37355612, year = {2023}, author = {Lin, X and Qiao, B and Chang, R and Li, Y and Zheng, W and He, Z and Tian, Y}, title = {Characterization of two keystone taxa, sulfur-oxidizing, and nitrate-reducing bacteria, by tracking their role transitions in the benzo[a]pyrene degradative microbiome.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {139}, pmid = {37355612}, issn = {2049-2618}, mesh = {*Nitrates/metabolism ; Benzo(a)pyrene/metabolism ; Bacteria ; *Microbiota/genetics ; Sulfur/metabolism ; Oxidation-Reduction ; }, abstract = {BACKGROUND: Keystone taxa are drivers of microbiome structure and functioning, which may play critical roles in microbiome-level responses to recalcitrant pollution and are a key to bioremediation. However, the characterization and manipulation of such taxa is a major challenge due to the complexity of microbial communities and rapid turnover in both time and space. Here, microcosms were set up with benzo[a]-pyrene (BaP) and/or nitrate based on C-rich, S-rich, and N-limited mangrove sediments as reductive experimental models to trigger and track the turnover of keystone taxa to address this challenge.

RESULTS: Based on microbial co-occurrence network analysis, two keystone taxa, Sulfurovum and Sulfurimonas, were found to exhibit significant role transitions in different microcosms, where these two taxa played nonkeystone roles with neutral relationships in in situ mangrove sediments. However, Sulfurimonas transitioned to be keystone taxa in nitrate-replenished microcosms and formed a keystone guild with Thioalkalispira. Sulfurovum stood out in BaP-added microcosms and mutualized in a densely polycyclic aromatic hydrocarbon (PAH)-degrader-centric keystone guild with Novosphingobium and Robiginitalea, where 63.25% of added BaP was removed. Under the occurrence of nitrate and BaP, they simultaneously played roles as keystone taxa in their respective guilds but exhibited significant competition. Comparative genomics and metagenome-assembled genome (MAG) analysis was then performed to reveal the metabolic potential of those keystone taxa and to empirically deduce their functional role in keystone guilds. Sulfurimonas possesses a better sense system and motility, indicative of its aggressive role in nitrate acquisition and conversion; Sulfurovum exhibited a better ability for oxidation resistance and transporting nutrients and electrons. High-efficiency thermal asymmetric interlaced polymerase reaction (hiTAIL-PCR) and enhanced green fluorescent protein (eGFP)-labeling approaches were employed to capture and label the BaP key degrader to further experimentally verify the roles of keystone taxa Sulfurovum in the keystone guilds. Observations of the enhancement in reactive oxygen species (ROS) removal, cell growth, and degradation efficiency by co-culture of isolated keystone taxa strains experimentally demonstrated that Sulfurovum contributes to the BaP degradative microbiome against BaP toxicity.

CONCLUSIONS: Our findings suggest that the combined use of co-occurrence network analysis, comparative genomics, and co-culture of captured keystone taxa (3C-strategy) in microbial communities whose structure is strongly shaped by changing environmental factors can characterize keystone taxa roles in keystone guilds and may provide targets for manipulation to improve the function of the microbiome. Video Abstract.}, } @article {pmid37355217, year = {2023}, author = {Wanvimonsuk, S and Somboonwiwat, K}, title = {Peroxiredoxin-4 supplementation modulates the immune response, shapes the intestinal microbiome, and enhances AHPND resistance in Penaeus vannamei.}, journal = {Fish & shellfish immunology}, volume = {139}, number = {}, pages = {108915}, doi = {10.1016/j.fsi.2023.108915}, pmid = {37355217}, issn = {1095-9947}, mesh = {Animals ; Immunity, Innate/genetics ; *Penaeidae ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; Dietary Supplements ; Peroxiredoxins ; *Vibrio parahaemolyticus/physiology ; }, abstract = {Peroxiredoxin-4 from Penaeus vannamei (LvPrx4) is considered a damage-associated molecular pattern (DAMP) that can activate the expression of immune-related genes through the Toll pathway. We previously demonstrated that the recombinant LvPrx4 (rLvPrx4) can enhance shrimp resistance against Vibrio parahaemolyticus, causing acute hepatopancreatic necrosis disease (VPAHPND), which causes great production losses in shrimp farming. Herein, we showed that the rLvPrx4 had a thermal tolerance of around 60 °C and that the ionic strength had no noticeable effect on its activity. We discovered that feeding a diet containing rLvPrx4 to shrimp for three weeks increased the expression of the immune-related genes LvPEN4 and LvVago5. Furthermore, pre-treatment with rLvPrx4 feeding could significantly prolong shrimp survival following the VPAHPND challenge. The shrimp intestinal microbiome was then characterized using PCR amplification of the 16S rRNA gene and Illumina sequencing. Three weeks of rLvPrx4 supplementation altered the bacterial community structure (beta diversity) and revealed the induction of differentially abundant families, including Cryomorphaceae, Flavobacteriaceae, Pirellulaceae, Rhodobacteraceae, and Verrucomicrobiaceae, in the rLvPrx4 group. Metagenomic predictions indicated that some amino acid metabolism pathways, such as arginine and proline metabolism, and genetic information processing were significantly elevated in the rLvPrx4 group compared to the control group. This study is the first to describe the potential use of rLvPrx4 supplementation to enhance shrimp resistance to VPAHPND and alter the composition of a beneficial bacterial community in shrimp, making rLvPrx4 a promising feed supplement as an alternative to antibiotics for controlling VPAHPND infection in shrimp aquaculture.}, } @article {pmid37350694, year = {2023}, author = {Li, JM and Ou, JH and Verpoort, F and Surmpalli, RY and Huang, WY and Kao, CM}, title = {Toxicity evaluation of a heavy-metal-polluted river: Pollution identification and bacterial community assessment.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {95}, number = {7}, pages = {e10904}, doi = {10.1002/wer.10904}, pmid = {37350694}, issn = {1554-7531}, support = {//Taiwan National Science and Technology Council/ ; }, mesh = {Humans ; Wastewater ; Geologic Sediments ; *Water Pollutants, Chemical/toxicity/analysis ; Environmental Monitoring/methods ; *Metals, Heavy/toxicity/analysis ; Proteobacteria ; Risk Assessment ; *Microbiota ; China ; }, abstract = {The Salt River is an important urban river in Kaohsiung, Taiwan. In this study, the source identification and risk and toxicity assessment of the heavy-metal-contaminated sediments in the Salt River were investigated. The geo-accumulation index (Igeo), enrichment factor (EF), sediment quality guidelines (SQGs), potential ecological risk index (RI), pollution load index (PLI), and toxic units (TU) were applied to determine effects of heavy metals on microbial diversities and ecosystems. Results from the ecological and environmental risk assessment show that high concentrations of Zn, Cr, and Ni were detected in the midstream area and the sum of toxic units (ΣTUs) in the midstream (7.2-32.0) is higher than in the downstream (14.0-19.7) and upstream (9.2-17.1). It could be because of the continuous inputs of heavy-metal-contained wastewaters from adjacent industrial parks. Results also inferred that the detected heavy metals in the upstream residential and commercial areas were possibly caused by nearby vehicle emissions, non-point source pollution, and domestic wastewater discharges. Results of metagenomic assays show that the sediments contained significant microbial diversities. Metal-tolerant bacterial phyla (Proteobacteria: 24.4%-46.4%, Bacteroidetes: 1.3%-14.8%, and Actinobacteria: 2.3%-11.1%) and pathogenic bacterial phyla (Chlamydiae: 0.5%-37.6% and Chloroflexi: 5.8%-7.2%) with relatively high abundance were detected. Metal-tolerant bacteria would adsorb metals and cause the increased metal concentrations in sediments. Results indicate that the bacterial composition in sediment environments was affected by anthropogenic pollution and human activities and the heavy-metal-polluted ecosystem caused the variations in bacterial communities. PRACTITIONER POINTS: Microbial community in sediments is highly affected by heavy metal pollution. Wastewaters and vehicle traffic contribute to river sediments pollution by heavy metals. Proteobacteria, Bacteroidota, and Actinobacteria are dominant heavy-metal-tolerant bacterial phyla in sediments. Toxicity assessment is required to study risk levels of heavy-metal contained sediments.}, } @article {pmid37350639, year = {2023}, author = {Lee, EM and Srinivasan, S and Purvine, SO and Fiedler, TL and Leiser, OP and Proll, SC and Minot, SS and Deatherage Kaiser, BL and Fredricks, DN}, title = {Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0067822}, pmid = {37350639}, issn = {2379-5077}, support = {P41 GM103493/GM/NIGMS NIH HHS/United States ; R01 AI061628/AI/NIAID NIH HHS/United States ; }, mesh = {Female ; Humans ; RNA, Ribosomal, 16S/genetics ; *Proteomics/methods ; *Microbiota/genetics ; Bacterial Proteins/genetics ; Peptides/metabolism ; Bacteria ; }, abstract = {Metaproteomics, a method for untargeted, high-throughput identification of proteins in complex samples, provides functional information about microbial communities and can tie functions to specific taxa. Metaproteomics often generates less data than other omics techniques, but analytical workflows can be improved to increase usable data in metaproteomic outputs. Identification of peptides in the metaproteomic analysis is performed by comparing mass spectra of sample peptides to a reference database of protein sequences. Although these protein databases are an integral part of the metaproteomic analysis, few studies have explored how database composition impacts peptide identification. Here, we used cervicovaginal lavage (CVL) samples from a study of bacterial vaginosis (BV) to compare the performance of databases built using six different strategies. We evaluated broad versus sample-matched databases, as well as databases populated with proteins translated from metagenomic sequencing of the same samples versus sequences from public repositories. Smaller sample-matched databases performed significantly better, driven by the statistical constraints on large databases. Additionally, large databases attributed up to 34% of significant bacterial hits to taxa absent from the sample, as determined orthogonally by 16S rRNA gene sequencing. We also tested a set of hybrid databases which included bacterial proteins from NCBI RefSeq and translated bacterial genes from the samples. These hybrid databases had the best overall performance, identifying 1,068 unique human and 1,418 unique bacterial proteins, ~30% more than a database populated with proteins from typical vaginal bacteria and fungi. Our findings can help guide the optimal identification of proteins while maintaining statistical power for reaching biological conclusions. IMPORTANCE Metaproteomic analysis can provide valuable insights into the functions of microbial and cellular communities by identifying a broad, untargeted set of proteins. The databases used in the analysis of metaproteomic data influence results by defining what proteins can be identified. Moreover, the size of the database impacts the number of identifications after accounting for false discovery rates (FDRs). Few studies have tested the performance of different strategies for building a protein database to identify proteins from metaproteomic data and those that have largely focused on highly diverse microbial communities. We tested a range of databases on CVL samples and found that a hybrid sample-matched approach, using publicly available proteins from organisms present in the samples, as well as proteins translated from metagenomic sequencing of the samples, had the best performance. However, our results also suggest that public sequence databases will continue to improve as more bacterial genomes are published.}, } @article {pmid37350224, year = {2023}, author = {Zhou, W and Fleming, E and Legendre, G and Roux, L and Latreille, J and Gendronneau, G and Forestier, S and Oh, J}, title = {Skin microbiome attributes associate with biophysical skin ageing.}, journal = {Experimental dermatology}, volume = {32}, number = {9}, pages = {1546-1556}, pmid = {37350224}, issn = {1600-0625}, support = {R01 AR078634/AR/NIAMS NIH HHS/United States ; P30 CA034196/CA/NCI NIH HHS/United States ; R56 AG060746/AG/NIA NIH HHS/United States ; R21 AR075174/AR/NIAMS NIH HHS/United States ; DP2 GM126893/GM/NIGMS NIH HHS/United States ; }, mesh = {*Skin Aging ; *Microbiota/genetics ; Bacteria ; Anti-Bacterial Agents ; Skin/microbiology ; }, abstract = {Two major arms of skin ageing are changes in the skin's biophysical conditions and alterations in the skin microbiome. This work partitioned both arms to study their interaction in detail. Leveraging the resolution provided by shotgun metagenomics, we explored how skin microbial species, strains and gene content interact with the biophysical traits of the skin during ageing. With a dataset well-controlled for confounding factors, we found that skin biophysical traits, especially the collagen diffusion coefficient, are associated with the composition and the functional potential of the skin microbiome, including the abundance of bacterial strains found in nosocomial infections and the abundance of antibiotic resistance genes. Our findings reveal important associations between skin biophysical features and ageing-related changes in the skin microbiome and generate testable hypotheses for the mechanisms of such associations.}, } @article {pmid37349979, year = {2023}, author = {Fan, G and Cao, F and Kuang, T and Yi, H and Zhao, C and Wang, L and Peng, J and Zhuang, Z and Xu, T and Luo, Y and Xie, Y and Li, H and Zhang, K and Zeng, Y and Zhang, X and Peng, S and Qiu, X and Zhou, D and Liang, H and Yang, B and Kang, J and Liu, Y and Zhang, Y}, title = {Alterations in the gut virome are associated with type 2 diabetes and diabetic nephropathy.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2226925}, pmid = {37349979}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Diabetic Nephropathies ; Virome ; *Diabetes Mellitus, Type 2/complications/microbiology ; *Bacteriophages/genetics ; Bacteria/genetics ; }, abstract = {Although changes in gut microbiome have been associated with the development of T2D and its complications, the role of the gut virome remains largely unknown. Here, we characterized the gut virome alterations in T2D and its complications diabetic nephropathy (DN) by metagenomic sequencing of fecal viral-like particles. Compared with controls, T2D subjects, especially those with DN, had significantly lower viral richness and diversity. 81 viral species were identified to be significantly altered in T2D subjects, including a decrease in some phages (e.g. Flavobacterium phage and Cellulophaga phaga). DN subjects were depleted of 12 viral species, including Bacteroides phage, Anoxybacillus virus and Brevibacillus phage, and enriched in 2 phages (Shigella phage and Xylella phage). Multiple viral functions, particularly those of phage lysing host bacteria, were markedly reduced in T2D and DN. Strong viral-bacterial interactions in healthy controls were disrupted in both T2D and DN. Moreover, the combined use of gut viral and bacterial markers achieved a powerful diagnostic performance for T2D and DN, with AUC of 99.03% and 98.19%, respectively. Our results suggest that T2D and its complication DN are characterized by a significant decrease in gut viral diversity, changes in specific virus species, loss of multiple viral functions, and disruption of viral-bacterial correlations. The combined gut viral and bacterial markers have diagnostic potential for T2D and DN.}, } @article {pmid37349686, year = {2023}, author = {Li, H and Fu, J and Erlong, N and Li, R and Xu, C and Hao, L and Chen, J and Chai, W}, title = {Characterization of periprosthetic environment microbiome in patients after total joint arthroplasty and its potential correlation with inflammation.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {423}, pmid = {37349686}, issn = {1471-2334}, support = {No.82102585//Youth Project of National Natural Science Foundation of China/ ; No.2020YFC2004900//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Prosthesis-Related Infections/microbiology ; Prospective Studies ; Arthroplasty/adverse effects ; Inflammation/complications ; *Arthritis, Infectious/etiology ; *Microbiota ; Staphylococcus ; Retrospective Studies ; *Arthroplasty, Replacement, Hip/adverse effects ; Sensitivity and Specificity ; }, abstract = {AIMS: Periprosthetic joint infection (PJI) is one of the most serious complications after total joint arthroplasty (TJA) but the characterization of the periprosthetic environment microbiome after TJA remains unknown. Here, we performed a prospective study based on metagenomic next-generation sequencing to explore the periprosthetic microbiota in patients with suspected PJI.

METHODS: We recruited 28 patients with culture-positive PJI, 14 patients with culture-negative PJI, and 35 patients without PJI, which was followed by joint aspiration, untargeted metagenomic next-generation sequencing (mNGS), and bioinformatics analysis. Our results showed that the periprosthetic environment microbiome was significantly different between the PJI group and the non-PJI group. Then, we built a "typing system" for the periprosthetic microbiota based on the RandomForest Model. After that, the 'typing system' was verified externally.

RESULTS: We found the periprosthetic microbiota can be classified into four types generally: "Staphylococcus type," "Pseudomonas type," "Escherichia type," and "Cutibacterium type." Importantly, these four types of microbiotas had different clinical signatures, and the patients with the former two microbiota types showed obvious inflammatory responses compared to the latter ones. Based on the 2014 Musculoskeletal Infection Society (MSIS) criteria, clinical PJI was more likely to be confirmed when the former two types were encountered. In addition, the Staphylococcus spp. with compositional changes were correlated with C-reactive protein levels, the erythrocyte sedimentation rate, and the synovial fluid white blood cell count and granulocyte percentage.

CONCLUSIONS: Our study shed light on the characterization of the periprosthetic environment microbiome in patients after TJA. Based on the RandomForest model, we established a basic "typing system" for the microbiota in the periprosthetic environment. This work can provide a reference for future studies about the characterization of periprosthetic microbiota in periprosthetic joint infection patients.}, } @article {pmid37349537, year = {2023}, author = {Lin, L and Yi, X and Liu, H and Meng, R and Li, S and Liu, X and Yang, J and Xu, Y and Li, C and Wang, Y and Xiao, N and Li, H and Liu, Z and Xiang, Z and Shu, W and Guan, WJ and Zheng, XY and Sun, J and Wang, Z}, title = {The airway microbiome mediates the interaction between environmental exposure and respiratory health in humans.}, journal = {Nature medicine}, volume = {29}, number = {7}, pages = {1750-1759}, pmid = {37349537}, issn = {1546-170X}, mesh = {Humans ; Respiratory System ; *Pulmonary Disease, Chronic Obstructive/etiology/microbiology ; Environmental Exposure/adverse effects ; *Microbiota ; Sputum/microbiology ; }, abstract = {Exposure to environmental pollution influences respiratory health. The role of the airway microbial ecosystem underlying the interaction of exposure and respiratory health remains unclear. Here, through a province-wide chronic obstructive pulmonary disease surveillance program, we conducted a population-based survey of bacterial (n = 1,651) and fungal (n = 719) taxa and metagenomes (n = 1,128) from induced sputum of 1,651 household members in Guangdong, China. We found that cigarette smoking and higher PM2.5 concentration were associated with lung function impairment through the mediation of bacterial and fungal communities, respectively, and that exposure was associated with an enhanced inter-kingdom microbial interaction resembling the pattern seen in chronic obstructive pulmonary disease. Enrichment of Neisseria was associated with a 2.25-fold increased risk of high respiratory symptom burden, coupled with an elevation in Aspergillus, in association with occupational pollution. We developed an individualized microbiome-based health index, which covaried with exposure, respiratory symptoms and diseases, with potential generalizability to global datasets. Our results may inform environmental risk prevention and guide interventions that harness airway microbiome.}, } @article {pmid37348505, year = {2023}, author = {Carter, MM and Olm, MR and Merrill, BD and Dahan, D and Tripathi, S and Spencer, SP and Yu, FB and Jain, S and Neff, N and Jha, AR and Sonnenburg, ED and Sonnenburg, JL}, title = {Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes.}, journal = {Cell}, volume = {186}, number = {14}, pages = {3111-3124.e13}, pmid = {37348505}, issn = {1097-4172}, support = {DP1 AT009892/AT/NCCIH NIH HHS/United States ; F32 DK128865/DK/NIDDK NIH HHS/United States ; R01 DK085025/DK/NIDDK NIH HHS/United States ; T32 AI007328/AI/NIAID NIH HHS/United States ; T32 DK007056/DK/NIDDK NIH HHS/United States ; K08 DK134856/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Metagenome ; Eukaryota ; High-Throughput Nucleotide Sequencing ; Metagenomics ; }, abstract = {The gut microbiome modulates immune and metabolic health. Human microbiome data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers of Tanzania and comparative populations in Nepal and California. We recovered 91,662 genomes of bacteria, archaea, bacteriophages, and eukaryotes, 44% of which are absent from existing unified datasets. We identified 124 gut-resident species vanishing in industrialized populations and highlighted distinct aspects of the Hadza gut microbiome related to in situ replication rates, signatures of selection, and strain sharing. Industrialized gut microbes were found to be enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource, expands our understanding of microbes capable of colonizing the human gut, and clarifies the extensive perturbation induced by the industrialized lifestyle.}, } @article {pmid37348417, year = {2023}, author = {Peng, Y and Li, L and Yang, P and Liu, H and Ye, W and Xue, Z and Peng, X and Wang, X}, title = {Integrated genome-centric metagenomic and metaproteomic analyses unravel the responses of the microbial community to ammonia stress.}, journal = {Water research}, volume = {242}, number = {}, pages = {120239}, doi = {10.1016/j.watres.2023.120239}, pmid = {37348417}, issn = {1879-2448}, mesh = {*Propionates ; Ammonia/metabolism ; Anaerobiosis ; Metagenome ; Fatty Acids, Volatile/metabolism ; *Microbiota ; Acetates ; Butyrates ; Valerates ; Firmicutes/metabolism ; Methane/metabolism ; Bioreactors/microbiology ; }, abstract = {Ammonia is a major inhibitor in anaerobic digestion of nitrogen-rich organic wastes. In this study, integrated genome-centric metagenomic and metaproteomic analyses were used to identify the key microorganisms and metabolic links causing instability by characterizing the process performance, microbial community, and metabolic responses of key microorganisms during endogenous ammonia accumulation. The identification of 89 metagenome-assembled genomes and analysis of their abundance profile in different operational phases permitted the identification of key taxa (Firmicutes and Proteobacteria) causing poor performance. Metabolic reconstruction indicated that the key taxa had the genetic potential to participate in the metabolism of C2C5 volatile fatty acids (VFAs). Further investigation suggested that during Phase I, the total ammonia nitrogen (TAN) level was maintained below 2000 mg N/L, and the reactor showed a high methane yield (478.30 ± 33.35 mL/g VS) and low VFAs concentration. When the TAN accumulated to > 2000 mg N/L, acid accumulation, mainly of acetate, began to occur, and the methane yield gradually decreased to 330.44 mL/g VS (Phase II). During this phase, the VFA degradation functions of the community were mainly mediated by Firmicutes. Approximately 61.54% of significant differentially expressed proteins (DEPs) related to acetate metabolism in Firmicutes were down-regulated, which led to an increase in acetate concentration to 4897.91 ± 1558.96 mg/L. However, the reactor performance showed spontaneous recovery without any interference (Phase III), during which Firmicutes gradually adapted to the high ammonia conditions. Approximately 75% of the significant DEPs related to acetate metabolism of Proteobacteria were also up-regulated in Phase III compared with Phase II; thus, VFA-related metabolic functions of the community were enhanced, which resulted in a decrease in the total VFA concentration to 195.39 mg/L. When the TAN increased above 4000 mg N/L, the system gradually showed acid accumulation dominated by propionate, accompanied by a second decrease in methane yield (Phase IV). During this phase, the number of up-regulated and down-regulated proteins related to acetate metabolism of Firmicutes and butyrate/valerate metabolism of Proteobacteria was comparable with that of Phase III, indicating that the metabolic functions related to acetate, butyrate, and valerate of the microbial community were not significantly affected. However, for propionate metabolism, the expression activity of fumarate hydratase from Firmicutes and Proteobacteria was severely inhibited by ammonia, as shown by down-regulation ratios of 63.64% and 85.71%, respectively. No protein with the same function that was not inhibited by ammonia could be detected, and the fumarate degradation function of the microbial community was severely damaged, leading to blocked propionate metabolism and irreversible deterioration of reactor performance. This study has provided a new perspective on the microecological mechanisms of ammonia inhibition.}, } @article {pmid37346030, year = {2023}, author = {Yu, H and Wang, Q and Tang, J and Dong, L and Dai, G and Zhang, T and Zhang, G and Xie, K and Wang, H and Zhao, Z}, title = {Comprehensive analysis of gut microbiome and host transcriptome in chickens after Eimeria tenella infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1191939}, pmid = {37346030}, issn = {2235-2988}, mesh = {Animals ; *Eimeria tenella/genetics ; Chickens/genetics ; *Gastrointestinal Microbiome/genetics ; Transcriptome ; *Poultry Diseases/genetics ; }, abstract = {BACKGROUND: Coccidiosis is an intestinal parasitic disease caused by Eimeria protozoa, which endangers the health and growth of animals, and causes huge economic losses to the poultry industry worldwide every year. Studies have shown that poultry gut microbiota plays an important role in preventing the colonization of pathogens and maintaining the health of the host. Coccidia infection also affects host gene expression. However, the underlying potential relationship between gut microbiome and host transcriptome during E. tenella infection in chickens remain unclear.

METHODS: In this study, metagenomic and transcriptome sequencing were applied to identify microbiota and genes in cecal contents and cecal tissues of infected (JS) and control (JC) chickens on day 4.5 postinfection (pi), respectively.

RESULTS: First, microbial sequencing results of cecal contents showed that the abundance of Lactobacillus, Roseburia sp. and Faecalibacterium sp decreased significantly after E. tenella infection (P < 0.05), while the abundance of Alistipes and Prevotella pectinovora increased significantly (P < 0.05). Second, transcriptome sequencing results showed that a total of 434 differentially expressed mRNAs were identified, including 196 up-regulated and 238 down-regulated genes. These differentially expressed genes related to inflammation and immunity, such as GAMA, FABP1, F2RL1 and RSAD2, may play an important role in the process of host resistance to coccidia infection. Functional studies showed that the enriched pathways of differentially expressed genes included the TGF-beta signaling pathway and the ErbB signaling pathways. Finally, the integrated analysis of gut microbiome and host transcriptome suggested that Prevotella pectinovora associated with FABP1, Butyricicoccus porcorum and Colidextribacter sp. associated with RSAD2 were involved in the immune response upon E. tenella infection.

CONCLUSION: In conclusion, this study provides valuable information on the microbiota and key immune genes after chicken E. tenella infection, with the aim of providing reference for the impact of coccidia infection on cecal microbiome and host.}, } @article {pmid37345674, year = {2023}, author = {Feng, K and Zhang, H and Chen, C and Ho, CT and Kang, M and Zhu, S and Xu, J and Deng, X and Huang, Q and Cao, Y}, title = {Heptamethoxyflavone Alleviates Metabolic Syndrome in High-Fat Diet-Fed Mice by Regulating the Composition, Function, and Metabolism of Gut Microbiota.}, journal = {Journal of agricultural and food chemistry}, volume = {71}, number = {26}, pages = {10050-10064}, doi = {10.1021/acs.jafc.3c01881}, pmid = {37345674}, issn = {1520-5118}, mesh = {Mice ; Animals ; *Metabolic Syndrome/drug therapy/genetics ; *Gastrointestinal Microbiome ; Diet, High-Fat/adverse effects ; Lipid Metabolism ; Fatty Acids, Volatile/pharmacology ; Bile Acids and Salts/pharmacology ; Mice, Inbred C57BL ; }, abstract = {3,5,6,7,8,3',4'-Heptamethoxyflavone (HMF) could prevent obesity and hyperlipidemia, but its effects on gut microbiota and fecal metabolites remain unclear. Here, the effect of HMF on metabolic syndrome (MS) was evaluated in high-fat diet (HFD)-fed mice, and its underlying mechanisms were revealed by integrative metagenomic and metabolomic analyses. We demonstrated that HMF could effectively ameliorate HFD-induced MS by alleviating body-weight gain, fat accumulation, hepatic steatosis, and lipid and glucose abnormalities. HMF significantly altered the gut microbiota composition in HFD-fed mice with enrichment of short-chain fatty acid (SCFA)- and bile acid-producing beneficial bacteria and inhibition of harmful bacteria. Also, HMF improved microbial functions by up-regulating bile acid metabolism and down-regulating fatty acid metabolism and inflammatory response-related pathways. Consistent with the gut microbial changes, HMF altered the fecal metabolite profile of HFD-fed mice, mainly characterized by increasing SCFA and several bile acid levels as well as lowering several lysophospholipids and fatty acid levels. Correlation analysis indicated that three key species Faecalibaculum rodentium, Collinsella aerofaciens, and Lactobacillus fermentum and the increase in microbial metabolites, i.e., SCFAs and secondary bile acids, might play a positive role in alleviating MS. Our results suggested that HMF alleviated HFD-induced MS possibly by modulating the composition, function, and metabolism of gut microbiota.}, } @article {pmid37345233, year = {2023}, author = {Shtossel, O and Isakov, H and Turjeman, S and Koren, O and Louzoun, Y}, title = {Ordering taxa in image convolution networks improves microbiome-based machine learning accuracy.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2224474}, pmid = {37345233}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Artificial Intelligence ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Machine Learning ; }, abstract = {The human gut microbiome is associated with a large number of disease etiologies. As such, it is a natural candidate for machine-learning-based biomarker development for multiple diseases and conditions. The microbiome is often analyzed using 16S rRNA gene sequencing or shotgun metagenomics. However, several properties of microbial sequence-based studies hinder machine learning (ML), including non-uniform representation, a small number of samples compared with the dimension of each sample, and sparsity of the data, with the majority of taxa present in a small subset of samples. We show here using a graph representation that the cladogram structure is as informative as the taxa frequency. We then suggest a novel method to combine information from different taxa and improve data representation for ML using microbial taxonomy. iMic (image microbiome) translates the microbiome to images through an iterative ordering scheme, and applies convolutional neural networks to the resulting image. We show that iMic has a higher precision in static microbiome gene sequence-based ML than state-of-the-art methods. iMic also facilitates the interpretation of the classifiers through an explainable artificial intelligence (AI) algorithm to iMic to detect taxa relevant to each condition. iMic is then extended to dynamic microbiome samples by translating them to movies.}, } @article {pmid37344611, year = {2024}, author = {Acar, C and Celik, SK and Ozdemirel, HO and Tuncdemir, BE and Alan, S and Mergen, H}, title = {Composition of the colon microbiota in the individuals with inflammatory bowel disease and colon cancer.}, journal = {Folia microbiologica}, volume = {69}, number = {2}, pages = {333-345}, pmid = {37344611}, issn = {1874-9356}, support = {FCD-2020-2065//Inönü Üniversitesi/ ; }, mesh = {Humans ; *Crohn Disease/microbiology ; *Inflammatory Bowel Diseases/microbiology ; *Microbiota ; *Colonic Neoplasms ; *Basidiomycota ; Intestinal Mucosa/microbiology ; }, abstract = {The human intestine is a habitat for microorganisms and, recently, the composition of the intestinal microbiota has been correlated with the etiology of diseases such as inflammations, sores, and tumors. Although many studies have been conducted to understand the composition of that microbiota, expanding these studies to more samples and different backgrounds will improve our knowledge. In this work, we showed the colon microbiota composition and diversity of healthy subjects, patients with inflammatory bowel disease (IBD), and colon cancer by metagenomic sequencing. Our results indicated that the relative abundance of prokaryotic and eukaryotic microbes differs between the healthy vs. tumor biopsies, tumor vs. IBD biopsies, and fresh vs. paraffin-embedded tumor biopsies. Fusobacterium, Escherichia-Shigella, and Streptococcus genera were relatively abundant in fresh tumor biopsies, while Pseudomonas was significantly elevated in IBD biopsies. Additionally, another opportunist pathogen Malasseziales was revealed as the most abundant fungal clade in IBD biopsies, especially in ulcerative colitis. We also found that, while the Basidiomycota:Ascomycota ratio was slightly lower in tumor biopsies compared to biopsies from healthy subjects, there was a significant increase in IBD biopsies. Our work will contribute to the known diversity of prokaryotic and eukaryotic microbes in the colon biopsies in patients with IBD and colon cancer.}, } @article {pmid37343864, year = {2023}, author = {Zhao, W and Chen, Z and Yang, X and Sheng, L and Mao, H and Zhu, S}, title = {Metagenomics reveal arbuscular mycorrhizal fungi altering functional gene expression of rhizosphere microbial community to enhance Iris tectorum's resistance to Cr stress.}, journal = {The Science of the total environment}, volume = {895}, number = {}, pages = {164970}, doi = {10.1016/j.scitotenv.2023.164970}, pmid = {37343864}, issn = {1879-1026}, mesh = {*Mycorrhizae/physiology ; *Iris Plant ; Chromium/analysis ; Plant Roots/microbiology ; Rhizosphere ; Metagenomics ; *Metals, Heavy/analysis ; Soil/chemistry ; *Microbiota ; Gene Expression ; Soil Microbiology ; Fungi ; }, abstract = {Chromium (Cr) can disrupt a plant's normal physiological and metabolic functions and severely impact the microenvironment. However, limited studies have investigated the impact of arbuscular mycorrhizal fungi (AMF) inoculation on the rhizosphere microorganisms of Iris tectorum under Cr stress, and the mechanisms of how rhizosphere microorganisms interact with hosts and contaminants. In this study, we investigated the effects of AMF inoculation on the growth, absorption of nutrients and heavy metals, and functional genes of the rhizosphere microbial community of I. tectorum under Cr stress in a greenhouse pot experiment. The results showed that AMF significantly increased the biomass and nutrient levels of I. tectorum, while decreasing the content of Cr in soil. Furthermore, metagenome analysis demonstrated significant changes in the structure and composition of the rhizosphere microbial community after AMF formed a mycorrhizal symbiosis system with the I. tectorum. Specifically, the abundance of functional genes related to nutrient cycling (N, P) and heavy metal resistance (chrA and arsB), as well as the abundance of heavy metal transporter family (P-atPase, MIT, CDF, and ABC) in the rhizosphere microbial community were up-regulated and their expression. Additionally, the synergies between rhizosphere microbial communities were regulated, and the complexity and stability of the rhizosphere microbial ecological network were enhanced. This study provides evidence that AMF can regulate rhizosphere microbial communities to improve plant growth and heavy metal stress tolerance, and helps us to understand the potential mechanism of wetland plant remediation of Cr-contaminated soil under AMF symbiosis.}, } @article {pmid37343848, year = {2023}, author = {Xin, Y and Wu, Y and Zhang, H and Li, X and Qu, X}, title = {Soil depth exerts a stronger impact on microbial communities and the sulfur biological cycle than salinity in salinized soils.}, journal = {The Science of the total environment}, volume = {894}, number = {}, pages = {164898}, doi = {10.1016/j.scitotenv.2023.164898}, pmid = {37343848}, issn = {1879-1026}, mesh = {*Soil/chemistry ; Salinity ; Soil Microbiology ; Bacteria/genetics ; *Microbiota ; Sulfur ; Sulfur Compounds ; }, abstract = {The distribution of microbial communities along salinity gradients in the surface layer of salinized soils has been widely studied. However, it is unknown whether microbial communities exhibit similar distribution patterns in surface and deep soils. Additionally, the relationship between soil depth, salinity, and sulfur metabolism remains unclear. Herein, bulk soils in the surface (S, 5-10 cm) and deep (D, 20-25 cm) layers from high- and low-salinity soils were analyzed using metagenomic and physicochemical analyses. Soil depth was significantly correlated to the concentration of sulfur compounds in the soil and exerted a stronger effect than salinity. Non-metric multidimensional scaling analysis revealed significant differences in microbial community structure with varying soil depths and salinities. However, soil depth clearly influenced microbial community abundance, homogeneity, and diversity, while salinity had a limited effect on microbial abundance. Archaea and bacteria were enriched in the surface and deep soils, respectively. Gene abundance analysis revealed significant differences in the abundance of sulfur-related genes at different soil depths. The abundance of sulfur oxidation genes was lower in deep soil than in surface soil, whereas the abundance of other sulfur-related genes showed the opposite trend. Redundancy analysis (RDA) showed that environmental factors and sulfur compounds have a significant impact on sulfur metabolism genes, with sulfide significantly affecting low-salinity soils in the surface and deep layers, whereas salinity and sulfane sulfur had a greater correlation with high-salinity soils. Correlation analysis further showed that Euryarchaeota clustered with Bacteroidetes and Balneolaeota, while Proteobacteria clustered with many phyla, such as Acidobacteria. Various sulfur metabolism genes were widely distributed in both clusters. Our results indicate that microorganisms actively participate in the sulfur cycle in saline soils and that soil depth can affect these processes and the structure of microbial communities to a greater extent than soil salinity.}, } @article {pmid37343363, year = {2023}, author = {Kang, X and Ng, SK and Liu, C and Lin, Y and Zhou, Y and Kwong, TNY and Ni, Y and Lam, TYT and Wu, WKK and Wei, H and Sung, JJY and Yu, J and Wong, SH}, title = {Altered gut microbiota of obesity subjects promotes colorectal carcinogenesis in mice.}, journal = {EBioMedicine}, volume = {93}, number = {}, pages = {104670}, pmid = {37343363}, issn = {2352-3964}, mesh = {Humans ; Mice ; Animals ; *Gastrointestinal Microbiome ; *Colonic Neoplasms ; Carcinogenesis ; Obesity/complications ; Azoxymethane/toxicity ; *Colorectal Neoplasms/genetics ; Mice, Inbred C57BL ; Disease Models, Animal ; }, abstract = {BACKGROUND: Obesity is a risk factor for colorectal cancer (CRC). The role of gut microbiota in mediating the cancer-promoting effect of obesity is unknown.

METHODS: Azoxymethane (AOM)-treated, Apc[Min/+] and germ-free mice were gavaged with feces from obese individuals and control subjects respectively. The colonic tumor load and number were recorded at the endpoint in two carcinogenic models. The gut microbiota composition and colonic transcriptome were assessed by metagenomic sequencing and RNA sequencing, respectively. The anticancer effects of bacteria depleted in fecal samples of obese individuals were validated.

FINDINGS: Conventional AOM-treated and Apc[Min/+] mice receiving feces from obese individuals showed significantly increased colon tumor formation compared with those receiving feces from control subjects. AOM-treated mice receiving feces from obese individuals showed impaired intestinal barrier function and significant upregulation of pro-inflammatory cytokines and activation of oncogenic Wnt signaling pathway. Consistently, transferring feces from obese individuals to germ-free mice led to increased colonic cell proliferation, intestinal barrier function impairment, and induction of oncogenic and proinflammatory gene expression. Moreover, germ-free mice transplanted with feces from obese human donors had increased abundance of potential pathobiont Alistipes finegoldii, and reduced abundance of commensals Bacteroides vulgatus and Akkermansia muciniphila compared with those receiving feces from human donors with normal body mass index (BMI). Validation experiments showed that B. vulgatus and A. muciniphila demonstrated anti-proliferative effects in CRC, while A. finegoldii promoted CRC tumor growth.

INTERPRETATION: Our results supported the role of obesity-associated microbiota in colorectal carcinogenesis and identified putative bacterial candidates that may mediate its mechanisms. Microbiota modulation in obese individuals may provide new approaches to prevent or treat obesity-related cancers including CRC.

FUNDING: This work was funded by National Key Research and Development Program of China (2020YFA0509200/2020YFA0509203), National Natural Science Foundation of China (81922082), RGC Theme-based Research Scheme Hong Kong (T21-705/20-N), RGC Research Impact Fund Hong Kong (R4632-21F), RGC-CRF Hong Kong (C4039-19GF and C7065-18GF), RGC-GRF Hong Kong (14110819, 14111621), and NTU Start-Up Grant (021337-00001).}, } @article {pmid37342148, year = {2023}, author = {Gugliucci, W and Cirillo, V and Maggio, A and Romano, I and Ventorino, V and Pepe, O}, title = {Valorisation of hydrothermal liquefaction wastewater in agriculture: effects on tobacco plants and rhizosphere microbiota.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1180061}, pmid = {37342148}, issn = {1664-462X}, abstract = {Industrial wastewater obtained from hydrothermal liquefaction (HTL-WW) of food wastes for biofuels production could represent a source of crop nutrients since it is characterized by a high amount of organic and inorganic compounds. In the present work, the potential use of HTL-WW as irrigation water for industrial crops was investigated. The composition of the HTL-WW was rich in nitrogen, phosphorus, and potassium with high level of organic carbon. A pot experiment with Nicotiana tabacum L. plants was conducted using diluted wastewater to reduce the concentration of some chemical elements below the official accepted threshold values. Plants were grown in the greenhouse under controlled conditions for 21 days and irrigated with diluted HTL-WW every 24 hours. Soils and plants were sampled every seven days to evaluate, over time, the effect of wastewater irrigation both on soil microbial populations, through high-throughput sequencing, and plant growth parameters, through the measurement of different biometric indices. Metagenomic results highlighted that, in the HTL-WW treated rhizosphere, the microbial populations shifted via their mechanisms of adaptation to the new environmental conditions, establishing a new balance among bacterial and fungal communities. Identification of microbial taxa occurring in the rhizosphere of tobacco plants during the experiment highlighted that the HTL-WW application improved the growth of Micrococcaceae, Nocardiaceae and Nectriaceae, which included key species for denitrification, organic compounds degradation and plant growth promotion. As a result, irrigation with HTL-WW improved the overall performance of tobacco plants which showed higher leaf greenness and increased number of flowers compared to irrigated control plants. Overall, these results demonstrate the potential feasibility of using of HTL-WW in irrigated agriculture.}, } @article {pmid37341942, year = {2023}, author = {Li, X and Zhang, M and Dang, C and Wu, Z and Xia, Y}, title = {In situ Nanopore sequencing reveals metabolic characteristics of the Qilian glacier meltwater microbiome.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {35}, pages = {84805-84813}, pmid = {37341942}, issn = {1614-7499}, support = {42277103//National Natural Science Foundation of China/ ; 42177357//National Natural Science Foundation of China/ ; }, mesh = {Ice Cover ; *Nanopore Sequencing ; China ; Lakes ; *Microbiota ; }, abstract = {Nanopore metagenomic sequencing enables rapid annotating microbiological ecosystems, and the previous glacier-related sequencing applications (e.g., targeted ice sheets, ice lake, and cryoconite holes) inspire us to explore high-altitude glacier meltwater at Qilian Mountain, China (3000 to 4000 m above sea level, MASL). Our findings suggest that (1) despite only several hundred meters apart, the microbial communities and functionalities are quite different among vertical alpine distributions; (2) the high-altitude Qilian meltwater microbiome serve several main metabolic functions, including sulfur oxidation, selenite decomposing, photosynthesis, energy production, enzymic, and UV tolerant activities. Meanwhile, our Nanopore metagenomic results indicate that the microbial classifications and functionalities (e.g., chaperones, cold-shock, specific tRNA species, oxidative stress, and resistance to toxic compounds) of Qilian meltwater are highly consistent with the other glacial microbiome, emphasizing that only certain microbial species can survive in the cold environment and the molecular adaptions and lifestyles remain stable all over the world. Besides, we have shown Nanopore metagenomic sequencing can provide reliable prokaryotic classifications within or among studies, which therefore can encourage more applications in the field given faster turnaround time. However, we recommend accumulating at least 400 ng nucleic acids (after extraction) and maximizing Nanopore library preparation efficiency before on-site sequencing to obtain better resolutions.}, } @article {pmid37340081, year = {2023}, author = {Yang, C and Xu, J and Xu, X and Xu, W and Tong, B and Wang, S and Ji, R and Tan, Y and Zhu, Y}, title = {Characteristics of gut microbiota in patients with metabolic associated fatty liver disease.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {9988}, pmid = {37340081}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Carcinoma, Hepatocellular ; RNA, Ribosomal, 16S/genetics ; *Liver Neoplasms ; *Microbiota ; *Non-alcoholic Fatty Liver Disease ; Bacteroidetes ; Clostridiaceae ; }, abstract = {Metabolic associated fatty liver disease (MAFLD) is rising in incidence and is an increasingly common cause of cirrhosis and hepatocellular carcinoma (HCC). Alterations in the gut microbiota have been shown to correlate with the development and progression of MAFLD. However, little is known regarding differences in the gut microbiomes of MAFLD patients and healthy cohorts, and subgroups at the abnormal activity of hepatic enzymes in China. In this study, we enrolled 81 MAFLD patients and 25 healthy volunteers. The fecal microbiota was assessed using 16S rRNA gene sequencing and metagenomic sequencing. The results suggested that Ruminococcus obeum and Alistipes were most enriched in healthy individuals when compared with MAFLD patients. Microbe-set Enrichment Analysis (MSEA) results showed Dorea, Lactobacillus and Megasphaera are enriched in MAFLD group. We also found that Alistipes has negatively related to serum glucose (GLU), gamma-glutamyl transferase (GGT), and alanine aminotransferase (ALT). Moreover, the abundance of Dorea was found to be significantly overrepresented in the MAFLD patients and the degree of enrichment increased with the increasing abnormal liver enzyme. An increase in Dorea, combined with decreases in Alistipes appears to be characteristic of MAFLD patients. Further study of microbiota may provide a novel insight into the pathogenesis of MAFLD as well as a novel treatment strategy.}, } @article {pmid37339968, year = {2023}, author = {Narat, V and Salmona, M and Kampo, M and Heyer, T and Rachik, AS and Mercier-Delarue, S and Ranger, N and Rupp, S and Ambata, P and Njouom, R and Simon, F and Le Goff, J and Giles-Vernick, T}, title = {Higher convergence of human-great ape enteric eukaryotic viromes in central African forest than in a European zoo: a One Health analysis.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3674}, pmid = {37339968}, issn = {2041-1723}, mesh = {Animals ; Humans ; Eukaryota ; *One Health ; Virome ; *Hominidae ; Gorilla gorilla ; }, abstract = {Human-animal pathogenic transmissions threaten both human and animal health, and the processes catalyzing zoonotic spillover and spillback are complex. Prior field studies offer partial insight into these processes but overlook animal ecologies and human perceptions and practices facilitating human-animal contact. Conducted in Cameroon and a European zoo, this integrative study elucidates these processes, incorporating metagenomic, historical, anthropological and great ape ecological analyses, and real-time evaluation of human-great ape contact types and frequencies. We find more enteric eukaryotic virome sharing between Cameroonian humans and great apes than in the zoo, virome convergence between Cameroonian humans and gorillas, and adenovirus and enterovirus taxa as most frequently shared between Cameroonian humans and great apes. Together with physical contact from hunting, meat handling and fecal exposure, overlapping human cultivation and gorilla pillaging in forest gardens help explain these findings. Our multidisciplinary study identifies environmental co-use as a complementary mechanism for viral sharing.}, } @article {pmid37339742, year = {2023}, author = {Arora, J and Buček, A and Hellemans, S and Beránková, T and Arias, JR and Fisher, BL and Clitheroe, C and Brune, A and Kinjo, Y and Šobotník, J and Bourguignon, T}, title = {Evidence of cospeciation between termites and their gut bacteria on a geological time scale.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {2001}, pages = {20230619}, pmid = {37339742}, issn = {1471-2954}, mesh = {Animals ; *Isoptera ; Phylogeny ; Symbiosis ; Bacteria/genetics ; *Gastrointestinal Microbiome ; Mammals ; }, abstract = {Termites host diverse communities of gut microbes, including many bacterial lineages only found in this habitat. The bacteria endemic to termite guts are transmitted via two routes: a vertical route from parent colonies to daughter colonies and a horizontal route between colonies sometimes belonging to different termite species. The relative importance of both transmission routes in shaping the gut microbiota of termites remains unknown. Using bacterial marker genes derived from the gut metagenomes of 197 termites and one Cryptocercus cockroach, we show that bacteria endemic to termite guts are mostly transferred vertically. We identified 18 lineages of gut bacteria showing cophylogenetic patterns with termites over tens of millions of years. Horizontal transfer rates estimated for 16 bacterial lineages were within the range of those estimated for 15 mitochondrial genes, suggesting that horizontal transfers are uncommon and vertical transfers are the dominant transmission route in these lineages. Some of these associations probably date back more than 150 million years and are an order of magnitude older than the cophylogenetic patterns between mammalian hosts and their gut bacteria. Our results suggest that termites have cospeciated with their gut bacteria since first appearing in the geological record.}, } @article {pmid37339626, year = {2023}, author = {Frioux, C and Ansorge, R and Özkurt, E and Ghassemi Nedjad, C and Fritscher, J and Quince, C and Waszak, SM and Hildebrand, F}, title = {Enterosignatures define common bacterial guilds in the human gut microbiome.}, journal = {Cell host & microbe}, volume = {31}, number = {7}, pages = {1111-1125.e6}, doi = {10.1016/j.chom.2023.05.024}, pmid = {37339626}, issn = {1934-6069}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Bacteria/genetics ; Metagenome ; Firmicutes ; Bacteroides/genetics ; Feces/microbiology ; }, abstract = {The human gut microbiome composition is generally in a stable dynamic equilibrium, but it can deteriorate into dysbiotic states detrimental to host health. To disentangle the inherent complexity and capture the ecological spectrum of microbiome variability, we used 5,230 gut metagenomes to characterize signatures of bacteria commonly co-occurring, termed enterosignatures (ESs). We find five generalizable ESs dominated by either Bacteroides, Firmicutes, Prevotella, Bifidobacterium, or Escherichia. This model confirms key ecological characteristics known from previous enterotype concepts, while enabling the detection of gradual shifts in community structures. Temporal analysis implies that the Bacteroides-associated ES is "core" in the resilience of westernized gut microbiomes, while combinations with other ESs often complement the functional spectrum. The model reliably detects atypical gut microbiomes correlated with adverse host health conditions and/or the presence of pathobionts. ESs provide an interpretable and generic model that enables an intuitive characterization of gut microbiome composition in health and disease.}, } @article {pmid37338686, year = {2023}, author = {Zhang, Y and Li, J and Wu, T and Ma, K and Cheng, Z and Yi, Q and Dai, Y and Wang, B and Chen, Y and Wang, B and Hu, X and Yang, A and Yang, Q and Zhong, X}, title = {Characteristics of antibiotic resistance genes and microbial community distribution in Wanfeng Lake, upper Pearl River, China.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {35}, pages = {83214-83230}, pmid = {37338686}, issn = {1614-7499}, support = {[2020]1Z051//Science and Technology Program of Guizhou Province/ ; QKZYD [2022]4022//Science and Technology Program of Guizhou Province/ ; QKHJC-ZK[2022]YB102//Science and Technology Program of Guizhou Province/ ; }, mesh = {Animals ; Humans ; Anti-Bacterial Agents/pharmacology/analysis ; Lakes/analysis ; Rivers/chemistry ; Drug Resistance, Bacterial/genetics ; Macrolides ; Ofloxacin ; Sulfonamides ; *Quinolones ; China ; Water/analysis ; *Microbiota ; Genes, Bacterial ; }, abstract = {Wanfeng Lake, a highland lake in the upper part of the Pearl River Basin, China, has long been disturbed by aquaculture and human activities, resulting in the accumulation of antibiotics and antibiotic resistance genes (ARGs), which pose a major threat to humans and animals. In this study, 20 antibiotics, 9 ARGs, 2 mobile genetic elements (intl1 and intl2), and microbial community structure were investigated in Wanfeng Lake. The results of the study showed that the total concentration of antibiotics in surface water was 372.72 ng/L, with ofloxacin (OFX) having the highest concentration (169.48 ng/L), posing a high ecological risk to aquatic organisms. The total concentration of antibiotics in sediments was 235.86 ng/g, with flumequine (FLU) having the highest concentration (122.54 ng/g). This indicates that the main type of antibiotics in Wanfeng Lake are quinolones. QPCR analysis results of the relative abundance of ARGs in both surface water and sediments showed that sulfonamide resistance genes > macrolide resistance genes > tetracycline resistance genes > quinolone resistance genes, indicating that sulfonamide resistance genes were the dominant type. The metagenomic results showed that the predominant microorganisms in the sediment under the phylum level were Planctomycetes, Proteobacteria, Euryarchaeota, and Chloroflexi. Pearson's correlation analysis showed a significantly positive correlation between antibiotics and environmental factors with ARGs in Wanfeng Lake and a significant positive correlation between antibiotics and ARGs with microorganisms in sediments. This suggests that there is a potential pressure of antibiotics on ARGs, while microorganisms provide the driving force for the evolution and spread of ARGs. This study provides a basis for further research on the occurrence and spread of antibiotics and ARGs in Wanfeng Lake. A total of 14 antibiotics were detected in surface water and sediments. OFX poses a high ecological risk in all points of surface water. Antibiotics and ARGs were significantly positively correlated in Wanfeng Lake. Antibiotics and ARGs in sediments were positively correlated with microorganisms.}, } @article {pmid37338635, year = {2023}, author = {Salam, LB and Obayori, OS and Ilori, MO and Amund, OO}, title = {Chromium contamination accentuates changes in the microbiome and heavy metal resistome of a tropical agricultural soil.}, journal = {World journal of microbiology & biotechnology}, volume = {39}, number = {9}, pages = {228}, pmid = {37338635}, issn = {1573-0972}, mesh = {Soil/chemistry ; *Soil Pollutants/analysis ; *Metals, Heavy/toxicity/analysis ; Chromium/toxicity/analysis ; Cadmium/analysis ; *Microbiota ; Environmental Monitoring ; China ; }, abstract = {The impacts of hexavalent chromium (Cr) contamination on the microbiome, soil physicochemistry, and heavy metal resistome of a tropical agricultural soil were evaluated for 6 weeks in field-moist microcosms consisting of a Cr-inundated agricultural soil (SL9) and an untreated control (SL7). The physicochemistry of the two microcosms revealed a diminution in the total organic matter content and a significant dip in macronutrients phosphorus, potassium, and nitrogen concentration in the SL9 microcosm. Heavy metals analysis revealed the detection of seven heavy metals (Zn, Cu, Fe, Cd, Se, Pb, Cr) in the agricultural soil (SL7), whose concentrations drastically reduced in the SL9 microcosm. Illumina shotgun sequencing of the DNA extracted from the two microcosms showed the preponderance of the phyla, classes, genera, and species of Actinobacteria (33.11%), Actinobacteria_class (38.20%), Candidatus Saccharimonas (11.67%), and Candidatus Saccharimonas aalborgensis (19.70%) in SL7, and Proteobacteria (47.52%), Betaproteobacteria (22.88%), Staphylococcus (16.18%), Staphylococcus aureus (9.76%) in SL9, respectively. Functional annotation of the two metagenomes for heavy metal resistance genes revealed diverse heavy metal resistomes involved in the uptake, transport, efflux, and detoxification of various heavy metals. It also revealed the exclusive detection in SL9 metagenome of resistance genes for chromium (chrB, chrF, chrR, nfsA, yieF), cadmium (czcB/czrB, czcD), and iron (fbpB, yqjH, rcnA, fetB, bfrA, fecE) not annotated in SL7 metagenome. The findings from this study revealed that Cr contamination induces significant shifts in the soil microbiome and heavy metal resistome, alters the soil physicochemistry, and facilitates the loss of prominent members of the microbiome not adapted to Cr stress.}, } @article {pmid37337895, year = {2023}, author = {Banzragch, M and Sanli, K and Stensvold, CR and Kurt, O and Ari, S}, title = {Metabarcoding of colonic cleansing fluid reveals unique bacterial members of mucosal microbiota associated with Inflammatory Bowel Disease.}, journal = {Scandinavian journal of gastroenterology}, volume = {58}, number = {11}, pages = {1253-1263}, doi = {10.1080/00365521.2023.2223708}, pmid = {37337895}, issn = {1502-7708}, mesh = {Humans ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; *Inflammatory Bowel Diseases/complications ; *Microbiota/genetics ; *Colitis, Ulcerative/complications ; Intestinal Mucosa/microbiology ; Bacteria/genetics ; }, abstract = {BACKGROUND: Inflammatory Bowel Disease (IBD) is a group of chronic idiopathic inflammatory diseases of the gastrointestinal (GI) tract associated with the dysbiosis of gut microbiota. Metabarcoding-based profiling of the gut microbiota of IBD patients is generally based on the stool samples collected from individual patients which rarely represent the mucosa-associated microbiota. The ideal sampling strategy for routine monitoring of the mucosal component of IBD has yet to be determined.

METHODS: We hereby compare the microbiota composition of the colonic cleansing fluid (CCF) collected during colonoscopy with stool samples from IBD patients. The relationship between IBD and gut microbiota was revealed through the application of the 16S rRNA amplicon sequencing-based metabarcoding approach. CCF and stool samples were collected from IBD patients with Crohn's disease and ulcerative colitis.

RESULTS: The present study shows significant differences in the microbial composition of CCF samples, presumably indicating changes in the mucosal microbiota of IBD patients as compared to the control group. Short-chain fatty acid-producing bacteria under the family Lachnospiraceae, the actinobacterial genus Bifidobacterium, the proteobacterial Sutterella and Raoultella are found to contribute to the microbial dysbiosis of the mucosal flora in IBD patients.

CONCLUSIONS: CCF microbiota has the capacity to distinguish IBD patients from healthy controls and, thus, may constitute an alternative analysis strategy for the early diagnosis and disease progression in IBD biomarker research.}, } @article {pmid37336582, year = {2024}, author = {Colston, SM and Barbato, RA and Goodson, MS and Karl, JP and Kokoska, RJ and Leary, DD and Racicot, K and Varaljay, V and Soares, JW}, title = {Current advances in microbiome sciences within the US Department of Defense: part 2 - enabling technologies and environmental microbiomes.}, journal = {BMJ military health}, volume = {170}, number = {5}, pages = {435-439}, doi = {10.1136/military-2022-002308}, pmid = {37336582}, issn = {2633-3775}, mesh = {Humans ; *Microbiota/physiology ; United States ; *United States Department of Defense/organization & administration ; Metagenomics/methods/trends ; }, abstract = {Microbiomes involve complex microbial communities wherein the micro-organisms interact with one another as well as their associated hosts or environmental niches. Much of the characterisation of these communities and the associations have been achieved through 'omics' technologies, such as metagenomics, metaproteomics and metametabolomics, and model systems. Recent research in host-associated microbiomes has been aimed at understanding the role microbes may play in host fitness or conversely how host activities/conditions may perturb the microbial community, which can further affect host health. These studies have led to the investigation of detection, intervention or modulation methods, which may serve to provide benefits to the host and advance our understanding of microbiome associations. With the clear implications on human health and disease, the US Department of Defense (DoD) has made microbiome research a priority, with the founding of the Tri-Service Microbiome Consortium (TSMC) to enhance collaboration, coordination,and communication of microbiome research among DoD organisations and partners in academia and industry. DoD microbiome research focuses mainly on the following themes: (1) human health and performance, (2) environmental microbiomes and (3) enabling technologies. This review provides an update of current DoD microbiome research efforts centred on enabling technologies and environmental microbiomes and highlights innovative research being done in academia and industry that can be leveraged by the DoD. These topics were also communicated and further discussed in the Fifth Annual TSMC Symposium. This paper forms part of the special issue of BMJ Military Health dedicated to personalised digital technology for mental health in the Armed Forces.}, } @article {pmid37336455, year = {2023}, author = {Xiao, C and Wan, K and Hu, J and Deng, X and Liu, X and Zhou, F and Yu, J and Chi, R}, title = {Performance changes in the anammox process under the stress of rare-earth element Ce(III) and the evolution of microbial community and functional genes.}, journal = {Bioresource technology}, volume = {384}, number = {}, pages = {129349}, doi = {10.1016/j.biortech.2023.129349}, pmid = {37336455}, issn = {1873-2976}, mesh = {*Anaerobic Ammonia Oxidation ; Oxidation-Reduction ; *Microbiota ; Wastewater ; Bacteria/genetics/metabolism ; Anaerobiosis ; Nitrogen/metabolism ; Bioreactors/microbiology ; Sewage/microbiology ; Denitrification ; }, abstract = {The high Ce(III) content in ionic rare-earth tailings wastewater has hindered the application of anammox process in this field. Here, the effect of Ce(III) on the performance of anammox processes was investigated, and the evolution of microbial communities and functional genes was explored using metagenomic sequencing. The results showed that the reactor nitrogen removal rate decreased when the Ce(III) concentration reached 25 mg/L, although ammonia nitrogen removal (92.31%) and nitrogen removal efficiency (81.33%) remained at a high level; however, both showed a significant decreasing trend. The relative abundance of anammox bacteria increased continuously from P1-P5, reaching 48.81%, whereas the relative abundance of Candidatus jettenia reached 33.71% at P5, which surpassed that of Candidatus brocadia as the most abundant anammox bacteria, and further analysis of functional genes and metabolic pathways revealed that Candidatus brocadia was richer in biochemical metabolic genes, whereas Candidatus jettenia had richer efflux genes.}, } @article {pmid37333852, year = {2023}, author = {Xu, Y and Xu, J and Liu, T and Liu, P and Chen, XG}, title = {Metagenomic analysis reveals the virome profiles of Aedes albopictus in Guangzhou, China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1133120}, pmid = {37333852}, issn = {2235-2988}, support = {R01 AI136850/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Aedes ; Metagenomics ; Phylogeny ; Virome/genetics ; Mosquito Vectors ; *Viruses/genetics ; }, abstract = {INTRODUCTION: Aedes albopictus is an aggressive invasive mosquito species widely distributed around the world, and it is also a known vector of arboviruses. Virus metagenomics and RNA interference (RNAi) are important in studying the biology and antiviral defense of Ae. albopictus. However, the virome and potential transmission of plant viruses by Ae. albopictus remain understudied.

METHODS: Mosquito samples of Ae. albopictus were collected from Guangzhou, China, and small RNA sequencing was performed. Raw data were filtered, and virus-associated contigs were generated using VirusDetect. The small RNA profiles were analyzed, and maximum-likelihood phylogenetic trees were constructed.

RESULTS: The small RNA sequencing of pooled Ae. albopictus revealed the presence of five known viruses, including Wenzhou sobemo-like virus 4, mosquito nodavirus, Aedes flavivirus, Hubei chryso-like virus 1, and Tobacco rattle virus RNA1. Additionally, 21 new viruses that had not been previously reported were identified. The mapping of reads and contig assembly provided insights into the viral diversity and genomic characteristics of these viruses. Field survey confirmed the detection of the identified viruses in Ae. albopictus collected from Guangzhou.

DISCUSSION: The comprehensive analysis of the virus metagenomics of Ae. albopictus in this study sheds light on the diversity and prevalence of viruses in mosquito populations. The presence of known and novel viruses highlights the need for continued surveillance and investigation into their potential impact on public health. The findings also emphasize the importance of understanding the virome and potential transmission of plant viruses by Ae. albopictus.

CONCLUSION: This study provides valuable insights into the virome of Ae. albopictus and its potential role as a vector for both known and novel viruses. Further research is needed to expand the sample size, explore additional viruses, and investigate the implications for public health.}, } @article {pmid37331553, year = {2023}, author = {Zhang, T and Ji, Z and Chen, X and Yu, L}, title = {Shotgun metagenomics reveals a diverse mycobiome in the seawater from a High Arctic fjord (Kongsfjorden, Svalbard).}, journal = {Environmental research}, volume = {233}, number = {}, pages = {116437}, doi = {10.1016/j.envres.2023.116437}, pmid = {37331553}, issn = {1096-0953}, mesh = {Humans ; *Mycobiome ; Estuaries ; Ecosystem ; Svalbard ; Metagenomics ; Seawater ; Arctic Regions ; }, abstract = {In the Arctic fjords, the marine mycobiome experiences significant changes under environmental conditions driven by climate change. However, research on the ecological roles and the adaptive mechanisms of marine mycobiome in the Arctic fjord remains insufficiently explored. The present study employed shotgun metagenomics to comprehensively characterize the mycobiome in 24 seawater samples from Kongsfjorden, a High Arctic fjord situated in Svalbard. It revealed the presence of a diverse mycobiome with eight phyla, 34 classes, 71 orders, 152 families, 214 genera, and 293 species. The taxonomic and functional composition of the mycobiome differed significantly among the three layers, i.e., upper layer (depth of 0 m), middle layer (depths of 30-100 m), and lower layer (depths of 150-200 m). Several taxonomic groups (e.g., phylum Ascomycota, class Eurotiomycetes, order Eurotiales, family Aspergillaceae, and genus Aspergillus) and KOs (e.g., K03236/EIF1A, K03306/TC.PIT, K08852/ERN1, and K03119/tauD) were significantly distinct among the three layers. Among the measured environmental parameters, depth, NO2[-], and PO4[3-] were identified as the key factors influencing the mycobiome composition. Conclusively, our findings revealed that the mycobiome was diverse in the Arctic seawater and significantly impacted by the variability of environmental conditions in the High Arctic fjord. These results will assist future studies in exploring the ecological and adaptive responses towards the changes within the Arctic ecosystems.}, } @article {pmid37331548, year = {2024}, author = {Michaelis, L and Berg, L and Maier, L}, title = {Confounder or Confederate? The Interactions Between Drugs and the Gut Microbiome in Psychiatric and Neurological Diseases.}, journal = {Biological psychiatry}, volume = {95}, number = {4}, pages = {361-369}, doi = {10.1016/j.biopsych.2023.06.004}, pmid = {37331548}, issn = {1873-2402}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Nervous System Diseases/drug therapy ; Brain ; Psychotropic Drugs/pharmacology ; }, abstract = {The gut microbiome is emerging as an important factor in signaling along the gut-brain axis. The intimate physiological connection between the gut and the brain allows perturbations in the microbiome to be directly transmitted to the central nervous system and thereby contribute to psychiatric and neurological diseases. Common microbiome perturbations result from the ingestion of xenobiotic compounds including pharmaceuticals such as psychotropic drugs. In recent years, a variety of interactions between these drug classes and the gut microbiome have been reported, ranging from direct inhibitory effects on gut bacteria to microbiome-mediated drug degradation or sequestration. Consequently, the microbiome may play a critical role in influencing the intensity, duration, and onset of therapeutic effects, as well as in influencing the side effects that patients may experience. Furthermore, because the composition of the microbiome varies from person to person, the microbiome may contribute to the frequently observed interpersonal differences in the response to these drugs. In this review, we first summarize the known interactions between xenobiotics and the gut microbiome. Then, for psychopharmaceuticals, we address the question of whether these interactions with gut bacteria are irrelevant for the host (i.e., merely confounding factors in metagenomic analyses) or whether they may even have therapeutic or adverse effects.}, } @article {pmid37330554, year = {2023}, author = {Zhang, L and Rahman, J and Chung, M and Lashua, L and Gordon, A and Balmaseda, A and Kuan, G and Bonneau, R and Ghedin, E}, title = {CRISPR arrays as high-resolution markers to track microbial transmission during influenza infection.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {136}, pmid = {37330554}, issn = {2049-2618}, support = {HHSN272201400031C/AI/NIAID NIH HHS/United States ; U01 AI111598/AI/NIAID NIH HHS/United States ; U01 AI088654/AI/NIAID NIH HHS/United States ; HHSN272201400006C/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Clustered Regularly Interspaced Short Palindromic Repeats ; *Influenza, Human/prevention & control ; Bacteria ; Metagenome/genetics ; *Microbiota/genetics ; *Micrococcaceae/genetics ; }, abstract = {BACKGROUND: Disruption of the microbial community in the respiratory tract due to infections, like influenza, could impact transmission of bacterial pathogens. Using samples from a household study, we determined whether metagenomic-type analyses of the microbiome provide the resolution necessary to track transmission of airway bacteria. Microbiome studies have shown that the microbial community across various body sites tends to be more similar between individuals who cohabit in the same household than between individuals from different households. We tested whether there was increased sharing of bacteria from the airways within households with influenza infections as compared to control households with no influenza.

RESULTS: We obtained 221 respiratory samples that were collected from 54 individuals at 4 to 5 time points across 10 households, with and without influenza infection, in Managua, Nicaragua. From these samples, we generated metagenomic (whole genome shotgun sequencing) datasets to profile microbial taxonomy. Overall, specific bacteria and phages were differentially abundant between influenza positive households and control (no influenza infection) households, with bacteria like Rothia, and phages like Staphylococcus P68virus that were significantly enriched in the influenza-positive households. We identified CRISPR spacers detected in the metagenomic sequence reads and used these to track bacteria transmission within and across households. We observed a clear sharing of bacterial commensals and pathobionts, such as Rothia, Neisseria, and Prevotella, within and between households. However, due to the relatively small number of households in our study, we could not determine if there was a correlation between increased bacterial transmission and influenza infection.

CONCLUSION: We observed that airway microbial composition differences across households were associated with what appeared to be different susceptibility to influenza infection. We also demonstrate that CRISPR spacers from the whole microbial community can be used as markers to study bacterial transmission between individuals. Although additional evidence is needed to study transmission of specific bacterial strains, we observed sharing of respiratory commensals and pathobionts within and across households. Video Abstract.}, } @article {pmid37330070, year = {2023}, author = {Liang, J and Chang, J and Zhang, R and Fang, W and Chen, L and Ma, W and Zhang, Y and Yang, W and Li, Y and Zhang, P and Zhang, G}, title = {Metagenomic analysis reveals the efficient digestion mechanism of corn stover in Angus bull rumen: Microbial community succession, CAZyme composition and functional gene expression.}, journal = {Chemosphere}, volume = {336}, number = {}, pages = {139242}, doi = {10.1016/j.chemosphere.2023.139242}, pmid = {37330070}, issn = {1879-1298}, mesh = {Cattle ; Animals ; Male ; *Zea mays ; Rumen/microbiology ; Fermentation ; *Microbiota/genetics ; Bacteria/genetics ; Gene Expression ; Digestion ; }, abstract = {Ruminant rumen is a biological fermentation system that can efficiently degrade lignocellulosic biomass. The knowledge about mechanisms of efficient lignocellulose degradation with rumen microorganisms is still limited. In this study, composition and succession of bacteria and fungi, carbohydrate-active enzymes (CAZymes), and functional genes involved in hydrolysis and acidogenesis were revealed during fermentation in Angus bull rumen via metagenomic sequencing. Results showed that degradation efficiency of hemicellulose and cellulose reached 61.2% and 50.4% at 72 h fermentation, respectively. Main bacterial genera were composed of Prevotella, Butyrivibrio, Ruminococcus, Eubacterium, and Fibrobacter, and main fungal genera were composed of Piromyces, Neocallimastix, Anaeromyces, Aspergillus, and Orpinomyces. Principal coordinates analysis indicated that community structure of bacteria and fungi dynamically changed during 72 h fermentation. Bacterial networks with higher complexity had stronger stability than fungal networks. Most CAZyme families showed a significant decrease trend after 48 h fermentation. Functional genes related to hydrolysis decreased at 72 h, while functional genes involved in acidogenesis did not change significantly. These findings provide a in-depth understanding of mechanisms of lignocellulose degradation in Angus bull rumen, and may guide the construction and enrichment of rumen microorganisms in anaerobic fermentation of waste biomass.}, } @article {pmid37328529, year = {2023}, author = {Guan, Y and Zhang, Y and Zhu, Y and Wang, Y}, title = {CXCL10 as a shared specific marker in rheumatoid arthritis and inflammatory bowel disease and a clue involved in the mechanism of intestinal flora in rheumatoid arthritis.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {9754}, pmid = {37328529}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Arthritis, Rheumatoid/genetics/metabolism ; Computational Biology ; *Microbiota ; *Inflammatory Bowel Diseases/genetics ; Chemokine CXCL10/genetics ; }, abstract = {This study aimed to identify shared specific genes associated with rheumatoid arthritis (RA) and inflammatory bowel disease (IBD) through bioinformatic analysis and to examine the role of the gut microbiome in RA. The data were extracted from the 3 RA and 1 IBD gene expression datasets and 1 RA gut microbiome metagenomic dataset. Weighted correlation network analysis (WGCNA) and machine learnings was performed to identify candidate genes associated with RA and IBD. Differential analysis and two different machine learning algorithms were used to investigate RA's gut microbiome characteristics. Subsequently, the shared specific genes related to the gut microbiome in RA were identified, and an interaction network was constructed utilizing the gutMGene, STITCH, and STRING databases. We identified 15 candidates shared genes through a joint analysis of the WGCNA for RA and IBD. The candidate gene CXCL10 was identified as the shared hub gene by the interaction network analysis of the corresponding WGCNA module gene to each disease, and CXCL10 was further identified as the shared specific gene by two machine learning algorithms. Additionally, we identified 3 RA-associated characteristic intestinal flora (Prevotella, Ruminococcus, and Ruminococcus bromii) and built a network of interactions between the microbiomes, genes, and pathways. Finally, it was discovered that the gene CXCL10 shared between IBD and RA was associated with the three gut microbiomes mentioned above. This study demonstrates the relationship between RA and IBD and provides a reference for research into the role of the gut microbiome in RA.}, } @article {pmid37327948, year = {2023}, author = {Naz, S and Ali, Z and Minhas, A and Fatima, A and Waseem, S}, title = {Generation of dysbiotic microbiota in cutaneous leishmaniasis and enhancement of skin inflammation.}, journal = {Microbial pathogenesis}, volume = {181}, number = {}, pages = {106202}, doi = {10.1016/j.micpath.2023.106202}, pmid = {37327948}, issn = {1096-1208}, mesh = {Humans ; *Leishmaniasis, Cutaneous ; *Microbiota/genetics ; Bacteria/genetics ; Metagenome ; Proteobacteria/genetics ; Inflammation/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cutaneous Leishmaniasis (CL) affects millions of people globally and has a significant impact on morbidity and mortality. Innate immune mediators are likely to influence the clinical phenotype of CL through primary responses that restrict or facilitate parasite spread. The aim of this preliminary study was to bring to attention the significance of microbiota in the development of CL and emphasized the necessity of including the role of microbiota in CL while promoting a One Health approach for managing diseases. To achieve this, we used 16S amplicon metagenome sequencing and QIIME2 pipeline to analyze the microbiome composition of CL-infected patients compared to non-infected, healthy subjects. 16S sequencing analysis showed serum microbiome was dominated by Firmicutes, Proteobacteria, Bacteroidota, and Actinobacteria. CL-infected individuals, Proteobacteria were the most prevalent (27.63 ± 9.79), with the relative abundance (10.73 ± 5.33) of Proteobacteria in control. Bacilli class was found to be the most prevalent in healthy controls (30.71 ± 8.44) while (20.57 ± 9.51) in CL-infected individuals. The class Alphaproteobacteria was found to be more in CL-infected individuals (5.47 ± 2.07) as compared to healthy controls (1.85 ± 0.39). The CL-infected individuals had a significantly lower relative abundance of the Clostridia class (p < 0.0001). An altered serum microbiome of CL infection and higher microbial abundance in the serum of healthy individuals was observed.}, } @article {pmid37327214, year = {2023}, author = {Potgieter, MG and Nel, AJM and Fortuin, S and Garnett, S and Wendoh, JM and Tabb, DL and Mulder, NJ and Blackburn, JM}, title = {MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.}, journal = {PLoS computational biology}, volume = {19}, number = {6}, pages = {e1011163}, pmid = {37327214}, issn = {1553-7358}, mesh = {Humans ; *Tandem Mass Spectrometry ; RNA, Ribosomal, 16S/genetics ; Databases, Protein ; Peptides/genetics/analysis ; *Microbiota/genetics ; Bacteria/genetics ; Proteome/genetics ; }, abstract = {BACKGROUND: Microbiome research is providing important new insights into the metabolic interactions of complex microbial ecosystems involved in fields as diverse as the pathogenesis of human diseases, agriculture and climate change. Poor correlations typically observed between RNA and protein expression datasets make it hard to accurately infer microbial protein synthesis from metagenomic data. Additionally, mass spectrometry-based metaproteomic analyses typically rely on focused search sequence databases based on prior knowledge for protein identification that may not represent all the proteins present in a set of samples. Metagenomic 16S rRNA sequencing only targets the bacterial component, while whole genome sequencing is at best an indirect measure of expressed proteomes. Here we describe a novel approach, MetaNovo, that combines existing open-source software tools to perform scalable de novo sequence tag matching with a novel algorithm for probabilistic optimization of the entire UniProt knowledgebase to create tailored sequence databases for target-decoy searches directly at the proteome level, enabling metaproteomic analyses without prior expectation of sample composition or metagenomic data generation and compatible with standard downstream analysis pipelines.

RESULTS: We compared MetaNovo to published results from the MetaPro-IQ pipeline on 8 human mucosal-luminal interface samples, with comparable numbers of peptide and protein identifications, many shared peptide sequences and a similar bacterial taxonomic distribution compared to that found using a matched metagenome sequence database-but simultaneously identified many more non-bacterial peptides than the previous approaches. MetaNovo was also benchmarked on samples of known microbial composition against matched metagenomic and whole genomic sequence database workflows, yielding many more MS/MS identifications for the expected taxa, with improved taxonomic representation, while also highlighting previously described genome sequencing quality concerns for one of the organisms, and identifying an experimental sample contaminant without prior expectation.

CONCLUSIONS: By estimating taxonomic and peptide level information directly on microbiome samples from tandem mass spectrometry data, MetaNovo enables the simultaneous identification of peptides from all domains of life in metaproteome samples, bypassing the need for curated sequence databases to search. We show that the MetaNovo approach to mass spectrometry metaproteomics is more accurate than current gold standard approaches of tailored or matched genomic sequence database searches, can identify sample contaminants without prior expectation and yields insights into previously unidentified metaproteomic signals, building on the potential for complex mass spectrometry metaproteomic data to speak for itself.}, } @article {pmid37325707, year = {2023}, author = {Wang, Y and Zhang, R and Pu, Y and Wang, D and Wang, Y and Wu, X and Pan, Y and Luo, C and Zhao, G and Quan, Z and Zheng, Y}, title = {Sample Collection, DNA Extraction, and Library Construction Protocols of the Human Microbiome Studies in the International Human Phenome Project.}, journal = {Phenomics (Cham, Switzerland)}, volume = {3}, number = {3}, pages = {300-308}, pmid = {37325707}, issn = {2730-5848}, abstract = {UNLABELLED: The human microbiome plays a crucial role in human health. In the past decade, advances in high-throughput sequencing technologies and analytical software have significantly improved our knowledge of the human microbiome. However, most studies concerning the human microbiome did not provide repeatable protocols to guide the sample collection, handling, and processing procedures, which impedes obtaining valid and timely microbial taxonomic and functional results. This protocol provides detailed operation methods of human microbial sample collection, DNA extraction, and library construction for both the amplicon sequencing-based measurements of the microbial samples from the human nasal cavity, oral cavity, and skin, as well as the shotgun metagenomic sequencing-based measurements of the human stool samples among adult participants. This study intends to develop practical procedure standards to improve the reproducibility of microbiota profiling of human samples.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-023-00097-y.}, } @article {pmid37323848, year = {2023}, author = {Soundararajan, S and Selvakumar, J and Maria Joseph, ZM and Gopinath, Y and Saravanan, V and Santhanam, R}, title = {Investigating the modulatory effects of Moringa oleifera on the gut microbiota of chicken model through metagenomic approach.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1153769}, pmid = {37323848}, issn = {2297-1769}, abstract = {INTRODUCTION: This study aimed to assess the effects of supplementing chicken feed with Moringa oleifera leaf powder, a phytobiotic, on the gastrointestinal microbiota. The objective was to examine the microbial changes induced by the supplementation.

METHODS: A total of 40, one-day-old chickens were fed their basal diet for 42 days and then divided into two groups: SG1 (basal diet) and SG2 (basal diet + 10 g/kg Moringa oleifera leaf powder). Metagenomics analysis was conducted to analyze operational taxonomic units (OTUs), species annotation, and biodiversity. Additionally, 16S rRNA sequencing was performed for molecular characterization of isolated gut bacteria, identified as Enterococcus faecium. The isolated bacteria were tested for essential metabolites, demonstrating antibacterial, antioxidant, and anticancer activities.

RESULTS AND DISCUSSION: The analysis revealed variations in the microbial composition between the control group (SG1) and the M. oleifera-treated group (SG2). SG2 showed a 47% increase in Bacteroides and a 30% decrease in Firmicutes, Proteobacteria, Actinobacteria, and Tenericutes compared to SG1. TM7 bacteria were observed exclusively in the M. oleifera-treated group. These findings suggest that Moringa oleifera leaf powder acts as a modulator that enhances chicken gut microbiota, promoting the colonization of beneficial bacteria. PICRUSt analysis supported these findings, showing increased carbohydrate and lipid metabolism in the M.oleifera-treated gut microbiota.

CONCLUSION: This study indicates that supplementing chicken feed with Moringa oleifera leaf powder as a phytobiotic enhances the gut microbiota in chicken models, potentially improving overall health. The observed changes in bacterial composition, increased presence of Bacteroides, and exclusive presence of TM7 bacteria suggest a positive modulation of microbial balance. The essential metabolites from isolated Enterococcus faecium bacteria further support the potential benefits of Moringa oleifera supplementation.}, } @article {pmid37322412, year = {2023}, author = {Yang, R and Li, X and Ying, Z and Zhao, Z and Wang, Y and Wang, Q and Shen, B and Peng, W}, title = {Prematurely delivering mothers show reductions of lachnospiraceae in their gut microbiomes.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {169}, pmid = {37322412}, issn = {1471-2180}, mesh = {Infant, Newborn ; Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; Mothers ; *Premature Birth ; *Microbiota ; Bacteria/genetics ; Clostridiales ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Preterm birth is the leading cause of perinatal morbidity and mortality. Despite evidence shows that imbalances in the maternal microbiome associates to the risk of preterm birth, the mechanisms underlying the association between a perturbed microbiota and preterm birth remain poorly understood.

METHOD: Applying shotgun metagenomic analysis on 80 gut microbiotas of 43 mothers, we analyzed the taxonomic composition and metabolic function in gut microbial communities between preterm and term mothers.

RESULTS: Gut microbiome of mothers delivering prematurely showed decreased alpha diversity and underwent significant reorganization, especially during pregnancy. SFCA-producing microbiomes, particularly species of Lachnospiraceae, Ruminococcaceae, and Eubacteriaceae, were significantly depleted in preterm mothers. Lachnospiraceae and its species were the main bacteria contributing to species' differences and metabolic pathways.

CONCLUSION: Gut microbiome of mothers delivering prematurely has altered and demonstrates the reduction of Lachnospiraceae.}, } @article {pmid37322285, year = {2023}, author = {López, JL and Fourie, A and Poppeliers, SWM and Pappas, N and Sánchez-Gil, JJ and de Jonge, R and Dutilh, BE}, title = {Growth rate is a dominant factor predicting the rhizosphere effect.}, journal = {The ISME journal}, volume = {17}, number = {9}, pages = {1396-1405}, pmid = {37322285}, issn = {1751-7370}, mesh = {*Rhizosphere ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Plant Roots/microbiology ; Bacteria ; Soil/chemistry ; Plants/genetics ; }, abstract = {The root microbiome is shaped by plant root activity, which selects specific microbial taxa from the surrounding soil. This influence on the microorganisms and soil chemistry in the immediate vicinity of the roots has been referred to as the rhizosphere effect. Understanding the traits that make bacteria successful in the rhizosphere is critical for developing sustainable agriculture solutions. In this study, we compared the growth rate potential, a complex trait that can be predicted from bacterial genome sequences, to functional traits encoded by proteins. We analyzed 84 paired rhizosphere- and soil-derived 16S rRNA gene amplicon datasets from 18 different plants and soil types, performed differential abundance analysis, and estimated growth rates for each bacterial genus. We found that bacteria with higher growth rate potential consistently dominated the rhizosphere, and this trend was confirmed in different bacterial phyla using genome sequences of 3270 bacterial isolates and 6707 metagenome-assembled genomes (MAGs) from 1121 plant- and soil-associated metagenomes. We then identified which functional traits were enriched in MAGs according to their niche or growth rate status. We found that predicted growth rate potential was the main feature for differentiating rhizosphere and soil bacteria in machine learning models, and we then analyzed the features that were important for achieving faster growth rates, which makes bacteria more competitive in the rhizosphere. As growth rate potential can be predicted from genomic data, this work has implications for understanding bacterial community assembly in the rhizosphere, where many uncultivated bacteria reside.}, } @article {pmid37321733, year = {2023}, author = {Yao, T and Deemer, DG and Chen, MH and Reuhs, BL and Hamaker, BR and Lindemann, SR}, title = {Differences in fine arabinoxylan structures govern microbial selection and competition among human gut microbiota.}, journal = {Carbohydrate polymers}, volume = {316}, number = {}, pages = {121039}, doi = {10.1016/j.carbpol.2023.121039}, pmid = {37321733}, issn = {1879-1344}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Scattering, Small Angle ; X-Ray Diffraction ; *Microbiota ; Feces/microbiology ; Dietary Fiber ; Fermentation ; }, abstract = {Dietary fibers are known to modulate microbiome composition, but it is unclear to what extent minor fiber structural differences impact community assembly, microbial division of labor, and organismal metabolic responses. To test the hypothesis that fine linkage variations afford different ecological niches for distinct communities and metabolism, we employed a 7-day in vitro sequential batch fecal fermentation with four fecal inocula and measured responses using an integrated multi-omics approach. Two sorghum arabinoxylans (SAXs) were fermented, with one (RSAX) having slightly more complex branch linkages than the other (WSAX). Although there were minor glycoysl linkage differences, consortia on RSAX retained much higher species diversity (42 members) than on WSAX (18-23 members) with distinct species-level genomes and metabolic outcomes (e.g., higher short chain fatty acid production from RSAX and more lactic acid produced from WSAX). The major SAX-selected members were from genera of Bacteroides and Bifidobacterium and family Lachnospiraceae. Carbohydrate active enzyme (CAZyme) genes in metagenomes revealed broad AX-related hydrolytic potentials among key members; however, CAZyme genes enriched in different consortia displayed various catabolic domain fusions with diverse accessory motifs that differ among the two SAX types. These results suggest that fine polysaccharide structure exerts deterministic selection effect for distinct fermenting consortia.}, } @article {pmid37321678, year = {2024}, author = {Colston, SM and Barbato, RA and Goodson, MS and Karl, JP and Kokoska, RJ and Leary, DD and Racicot, K and Varaljay, V and Soares, JW}, title = {Current advances in microbiome sciences within the US Department of Defense-part 1: microbiomes for human health and performance.}, journal = {BMJ military health}, volume = {170}, number = {5}, pages = {430-434}, doi = {10.1136/military-2022-002307}, pmid = {37321678}, issn = {2633-3775}, mesh = {Humans ; *Microbiota/physiology ; United States ; *United States Department of Defense/organization & administration ; Military Personnel ; }, abstract = {Microbiomes involve complex microbial communities where the microorganisms interact with one another as well as their associated hosts or environmental niches. The characterisation of these communities and associations have largely been achieved through 'omics' technologies, such as metagenomics, metaproteomics and metametabolomics, and model systems. Recent research in host-associated microbiomes have been aimed at understanding the roles microbes may play in host fitness or conversely how host activities/conditions may perturb the microbial community, which can further affect host health. These studies have led to the investigation of detection, intervention or modulation methods, which may serve to provide benefits to the host and advance our understanding of microbiome associations. With the clear implications on human health and disease, the US Department of Defense (DoD) has made microbiome research a priority, with the founding of the Tri-Service Microbiome Consortium (TSMC) to enhance collaboration, coordination and communication of microbiome research among DoD organisations and partners in academia and industry. DoD microbiome research focuses mainly on the following themes: (1) Human health and performance; (2) Environmental microbiomes; and (3) Enabling technologies. This review provides an update of current DoD microbiome research efforts centred on human health and performance and highlights innovative research being done in academia and industry that can be leveraged by the DoD. These topics were also communicated and further discussed during the fifth Annual TSMC Symposium. This paper forms part of the special issue of BMJ Military Health dedicated to Personalised Digital Technology for Mental Health in the Armed Forces.}, } @article {pmid37316519, year = {2023}, author = {Jin, X and Yu, FB and Yan, J and Weakley, AM and Dubinkina, V and Meng, X and Pollard, KS}, title = {Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3510}, pmid = {37316519}, issn = {2041-1723}, support = {R01 HL160862/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Hydrogels ; Metagenome ; *Microbiota/genetics ; Mucins ; }, abstract = {Microbial community function depends on both taxonomic composition and spatial organization. While composition of the human gut microbiome has been deeply characterized, less is known about the organization of microbes between regions such as lumen and mucosa and the microbial genes regulating this organization. Using a defined 117 strain community for which we generate high-quality genome assemblies, we model mucosa/lumen organization with in vitro cultures incorporating mucin hydrogel carriers as surfaces for bacterial attachment. Metagenomic tracking of carrier cultures reveals increased diversity and strain-specific spatial organization, with distinct strains enriched on carriers versus liquid supernatant, mirroring mucosa/lumen enrichment in vivo. A comprehensive search for microbial genes associated with this spatial organization identifies candidates with known adhesion-related functions, as well as novel links. These findings demonstrate that carrier cultures of defined communities effectively recapitulate fundamental aspects of gut spatial organization, enabling identification of key microbial strains and genes.}, } @article {pmid37315663, year = {2023}, author = {Xiao, J and Tsim, KWK and Hajisamae, S and Wang, WX}, title = {Chromosome-level genome and population genomics provide novel insights into adaptive divergence in allopatric Eleutheronema tetradactylum.}, journal = {International journal of biological macromolecules}, volume = {244}, number = {}, pages = {125299}, doi = {10.1016/j.ijbiomac.2023.125299}, pmid = {37315663}, issn = {1879-0003}, mesh = {Animals ; *Metagenomics ; *Genome/genetics ; Fishes ; Base Sequence ; Chromosomes ; }, abstract = {Understanding the adaptive ecological divergence provides important information for revealing biodiversity generation and maintenance. Adaptive ecology divergence in populations occurs in various environments and locations, but its genetic underpinnings remain elusive. We generated a chromosome-level genome of Eleutheronema tetradactylum (~582 Mb) and re-sequenced 50 allopatric E. tetradactylum in two independent environmental axes in China and Thailand Coastal waters as well as 11 cultured relatives. A low level of whole genome-wide diversity explained their decreased adaptive potential in the wild environment. Demographic analysis showed evidence of historically high abundance followed by a continuous distinct decline, plus signs of recent inbreeding and accumulation of deleterious mutations. Extensive signals of selective sweeps with signs of local adaptation to environmental differentiation between China and Thailand at genes related to thermal and salinity adaptation were discovered, which might be the driving factors of the geographical divergence of E. tetradactylum. Many genes and pathways subjected to strong selection under artificial breeding were associated with fatty acids and immunity (ELOVL6L, MAPK, p53/NF-kB), likely contributing to the eventual adaptation of artificial selective breeding. Our comprehensive study provided crucial genetic information for E. tetradactylum, with implications for the further conservation efforts of this threatened and ecologically valuable fish.}, } @article {pmid37314861, year = {2023}, author = {Palacios, N and Wilkinson, J and Bjornevik, K and Schwarzschild, MA and McIver, L and Ascherio, A and Huttenhower, C}, title = {Metagenomics of the Gut Microbiome in Parkinson's Disease: Prodromal Changes.}, journal = {Annals of neurology}, volume = {94}, number = {3}, pages = {486-501}, pmid = {37314861}, issn = {1531-8249}, support = {UM1 CA186107/NH/NIH HHS/United States ; U01 CA167552/CA/NCI NIH HHS/United States ; R01NS097723/NS/NINDS NIH HHS/United States ; U01 CA167552/NH/NIH HHS/United States ; UM1 CA186107/CA/NCI NIH HHS/United States ; R01 NS097723/NS/NINDS NIH HHS/United States ; }, mesh = {Humans ; *Parkinson Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Case-Control Studies ; Metagenomics ; Follow-Up Studies ; Prodromal Symptoms ; }, abstract = {OBJECTIVE: Prior studies on the gut microbiome in Parkinson's disease (PD) have yielded conflicting results, and few studies have focused on prodromal (premotor) PD or used shotgun metagenomic profiling to assess microbial functional potential. We conducted a nested case-control study within 2 large epidemiological cohorts to examine the role of the gut microbiome in PD.

METHODS: We profiled the fecal metagenomes of 420 participants in the Nurses' Health Study and the Health Professionals Follow-up Study with recent onset PD (N = 75), with features of prodromal PD (N = 101), controls with constipation (N = 113), and healthy controls (N = 131) to identify microbial taxonomic and functional features associated with PD and features suggestive of prodromal PD. Omnibus and feature-wise analyses identified bacterial species and pathways associated with prodromal and recently onset PD.

RESULTS: We observed depletion of several strict anaerobes associated with reduced inflammation among participants with PD or features of prodromal PD. A microbiome-based classifier had moderate accuracy (area under the curve [AUC] = 0.76 for species and 0.74 for pathways) to discriminate between recently onset PD cases and controls. These taxonomic shifts corresponded with functional shifts indicative of carbohydrate source preference. Similar, but less marked, changes were observed in participants with features of prodromal PD, in both microbial features and functions.

INTERPRETATION: PD and features of prodromal PD were associated with similar changes in the gut microbiome. These findings suggest that changes in the microbiome could represent novel biomarkers for the earliest phases of PD. ANN NEUROL 2023;94:486-501.}, } @article {pmid37314057, year = {2023}, author = {Van Etten, J and Stephens, TG and Bhattacharya, D}, title = {A k-mer-Based Approach for Phylogenetic Classification of Taxa in Environmental Genomic Data.}, journal = {Systematic biology}, volume = {72}, number = {5}, pages = {1101-1118}, doi = {10.1093/sysbio/syad037}, pmid = {37314057}, issn = {1076-836X}, support = {80NSSC19K1542/NASA/NASA/United States ; 80NSSC19K0462/NASA/NASA/United States ; }, mesh = {*Metagenomics/methods ; Phylogeny ; *Genome ; Base Sequence ; }, abstract = {In the age of genome sequencing, whole-genome data is readily and frequently generated, leading to a wealth of new information that can be used to advance various fields of research. New approaches, such as alignment-free phylogenetic methods that utilize k-mer-based distance scoring, are becoming increasingly popular given their ability to rapidly generate phylogenetic information from whole-genome data. However, these methods have not yet been tested using environmental data, which often tends to be highly fragmented and incomplete. Here, we compare the results of one alignment-free approach (which utilizes the D2 statistic) to traditional multi-gene maximum likelihood trees in 3 algal groups that have high-quality genome data available. In addition, we simulate lower-quality, fragmented genome data using these algae to test method robustness to genome quality and completeness. Finally, we apply the alignment-free approach to environmental metagenome assembled genome data of unclassified Saccharibacteria and Trebouxiophyte algae, and single-cell amplified data from uncultured marine stramenopiles to demonstrate its utility with real datasets. We find that in all instances, the alignment-free method produces phylogenies that are comparable, and often more informative, than those created using the traditional multi-gene approach. The k-mer-based method performs well even when there are significant missing data that include marker genes traditionally used for tree reconstruction. Our results demonstrate the value of alignment-free approaches for classifying novel, often cryptic or rare, species, that may not be culturable or are difficult to access using single-cell methods, but fill important gaps in the tree of life.}, } @article {pmid37313947, year = {2023}, author = {El Mouzan, MI and Assiri, AA and Al Sarkhy, AA and Alasmi, MM}, title = {Gut virome profile in healthy Saudi children.}, journal = {Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association}, volume = {29}, number = {3}, pages = {171-176}, pmid = {37313947}, issn = {1998-4049}, mesh = {Male ; Humans ; Child ; Adolescent ; Female ; *Virome ; Phylogeny ; Saudi Arabia/epidemiology ; *DNA, Viral ; Feces ; }, abstract = {BACKGROUND: The role of viruses is well known in health and disease. The aim of this report was to describe the profile of viruses in the gut of healthy Saudi children.

METHODS: In 20 randomly selected school age children from Riyadh, stool samples were collected in cryovials and stored at -80° C. At the time of analysis, the samples were sent by express mail in a temperature-controlled container to the laboratory in the USA, Viral DNA was isolated and shotgun metagenomic sequencing was performed. The abundance of each organism was expressed as an average relative percentage across the viral phylogenetic tree from phyla to species.

RESULTS: The median age of the children was 11.3 (range 6.8-15.4) years, and 35% were males. Caudovirales were the most abundant bacteriophage order (77%) and Siphoviridae, Myoviridae, and Podoviridae families predominated, accounting for 41%, 25%, and 11%, respectively. Among the viral bacteriophage species, the most abundant were the Enterobacteria phages.

CONCLUSION: The profile and abundance of the gut virome in healthy Saudi children reveal important differences from the literature. Further studies from different populations with larger sample sizes are needed to understand the role of gut viruses in the pathogenesis of disease in general and in the response to fecal microbiota therapy in particular.}, } @article {pmid37311764, year = {2023}, author = {Ruff, SE and Humez, P and de Angelis, IH and Diao, M and Nightingale, M and Cho, S and Connors, L and Kuloyo, OO and Seltzer, A and Bowman, S and Wankel, SD and McClain, CN and Mayer, B and Strous, M}, title = {Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3194}, pmid = {37311764}, issn = {2041-1723}, mesh = {Oxygen ; Oxygen Isotopes ; *Groundwater ; Hydrogen ; *Microbiota ; }, abstract = {Around 50% of humankind relies on groundwater as a source of drinking water. Here we investigate the age, geochemistry, and microbiology of 138 groundwater samples from 95 monitoring wells (<250 m depth) located in 14 aquifers in Canada. The geochemistry and microbiology show consistent trends suggesting large-scale aerobic and anaerobic hydrogen, methane, nitrogen, and sulfur cycling carried out by diverse microbial communities. Older groundwaters, especially in aquifers with organic carbon-rich strata, contain on average more cells (up to 1.4 × 10[7] mL[-1]) than younger groundwaters, challenging current estimates of subsurface cell abundances. We observe substantial concentrations of dissolved oxygen (0.52 ± 0.12 mg L[-1] [mean ± SE]; n = 57) in older groundwaters that seem to support aerobic metabolisms in subsurface ecosystems at an unprecedented scale. Metagenomics, oxygen isotope analyses and mixing models indicate that dark oxygen is produced in situ via microbial dismutation. We show that ancient groundwaters sustain productive communities and highlight an overlooked oxygen source in present and past subsurface ecosystems of Earth.}, } @article {pmid37310219, year = {2023}, author = {Riley, R and Bowers, RM and Camargo, AP and Campbell, A and Egan, R and Eloe-Fadrosh, EA and Foster, B and Hofmeyr, S and Huntemann, M and Kellom, M and Kimbrel, JA and Oliker, L and Yelick, K and Pett-Ridge, J and Salamov, A and Varghese, NJ and Clum, A}, title = {Terabase-Scale Coassembly of a Tropical Soil Microbiome.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0020023}, pmid = {37310219}, issn = {2165-0497}, mesh = {*Soil ; *Microbiota/genetics ; Bacteria/genetics ; Metagenome ; Genome, Viral ; Metagenomics/methods ; }, abstract = {Petabases of environmental metagenomic data are publicly available, presenting an opportunity to characterize complex environments and discover novel lineages of life. Metagenome coassembly, in which many metagenomic samples from an environment are simultaneously analyzed to infer the underlying genomes' sequences, is an essential tool for achieving this goal. We applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 terabases (Tbp) of metagenome data from a tropical soil in the Luquillo Experimental Forest (LEF), Puerto Rico. The resulting coassembly yielded 39 high-quality (>90% complete, <5% contaminated, with predicted 23S, 16S, and 5S rRNA genes and ≥18 tRNAs) metagenome-assembled genomes (MAGs), including two from the candidate phylum Eremiobacterota. Another 268 medium-quality (≥50% complete, <10% contaminated) MAGs were extracted, including the candidate phyla Dependentiae, Dormibacterota, and Methylomirabilota. In total, 307 medium- or higher-quality MAGs were assigned to 23 phyla, compared to 294 MAGs assigned to nine phyla in the same samples individually assembled. The low-quality (<50% complete, <10% contaminated) MAGs from the coassembly revealed a 49% complete rare biosphere microbe from the candidate phylum FCPU426 among other low-abundance microbes, an 81% complete fungal genome from the phylum Ascomycota, and 30 partial eukaryotic MAGs with ≥10% completeness, possibly representing protist lineages. A total of 22,254 viruses, many of them low abundance, were identified. Estimation of metagenome coverage and diversity indicates that we may have characterized ≥87.5% of the sequence diversity in this humid tropical soil and indicates the value of future terabase-scale sequencing and coassembly of complex environments. IMPORTANCE Petabases of reads are being produced by environmental metagenome sequencing. An essential step in analyzing these data is metagenome assembly, the computational reconstruction of genome sequences from microbial communities. "Coassembly" of metagenomic sequence data, in which multiple samples are assembled together, enables more complete detection of microbial genomes in an environment than "multiassembly," in which samples are assembled individually. To demonstrate the potential for coassembling terabases of metagenome data to drive biological discovery, we applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 Tbp of reads from a humid tropical soil environment. The resulting coassembly, its functional annotation, and analysis are presented here. The coassembly yielded more, and phylogenetically more diverse, microbial, eukaryotic, and viral genomes than the multiassembly of the same data. Our resource may facilitate the discovery of novel microbial biology in tropical soils and demonstrates the value of terabase-scale metagenome sequencing.}, } @article {pmid37308527, year = {2023}, author = {Kozhakhmetov, S and Meiirmanova, Z and Mukhanbetzhanov, N and Jarmukhanov, Z and Vinogradova, E and Mureyev, S and Kozhakhmetova, S and Morenko, M and Shnaider, K and Duisbayeva, A and Kushugulova, A}, title = {Compositional and functional variability of the gut microbiome in children with infantile colic.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {9530}, pmid = {37308527}, issn = {2045-2322}, mesh = {Infant, Newborn ; Infant ; Humans ; Child ; *Gastrointestinal Microbiome ; *Colic ; *Microbiota ; Amino Acids ; Anxiety ; Bacteroides ; }, abstract = {The inconsolable crying of a child for no apparent reason at an early age is a source of excitement and anxiety for parents. Previous studies have reported that crying may be caused by discomfort associated with the occupation of the intestines of the newborn by microbiota and its vital activity. We conducted a prospective observational study in which 62 newborns and their mothers were recruited. The study comprised two groups, each consisting of 15 infants with colic and 21 controls. Colic and control groups were vaginally born and exclusively breastfed. Fecal samples from children were collected over time from day 1 to 12 months. Full metagenomic sequencing of fecal samples from children and their mothers was carried out. It was determined that the trajectory of the development of the intestinal microbiome of children with colic was different from the group without colic. In the colic group, a depleted relative abundance of Bifidobacterium and enrichment of Bacteroides Clostridiales was found, while the microbial biodiversity in this group was enriched. Metabolic pathway profiling showed that the non-colic group was enriched by amino acid biosynthetic pathways, while the feces microbiome of the colic group was enriched by glycolysis metabolic pathways that correlated with the Bacteroides taxon. This study shows that infantile colic has a definite relationship with the microbiome structure of infants.}, } @article {pmid37306708, year = {2023}, author = {Amin, AB and Zhang, L and Zhang, J and Mao, S}, title = {Metagenomics analysis reveals differences in rumen microbiota in cows with low and high milk protein percentage.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {15}, pages = {4887-4902}, pmid = {37306708}, issn = {1432-0614}, support = {2021YFF1000703-01//National key Research and Development program of China/ ; }, mesh = {Female ; Cattle ; Animals ; *Milk Proteins/metabolism ; Lactation ; Rumen/microbiology ; Metagenomics ; Lysine/metabolism ; Diet/veterinary ; *Microbiota ; Carbohydrates ; Nitrogen/metabolism ; Fermentation ; Animal Feed/analysis ; }, abstract = {Variation exists in milk protein concentration of dairy cows of the same breed that are fed and managed in the same environment, and little information was available on this variation which might be attributed to differences in rumen microbial composition as well as their fermentation metabolites. This study is aimed at investigating the difference in the composition and functions of rumen microbiota as well as fermentation metabolites in Holstein cows with high and low milk protein concentrations. In this study, 20 lactating Holstein cows on the same diet were divided into two groups (10 cows each), high degree of milk protein group (HD), and low degree of milk protein (LD) concentrations based on previous milk composition history. Rumen content samples were obtained to explore the rumen fermentation parameters and rumen microbial composition. Shotgun metagenomics sequencing was employed to investigate the rumen microbial composition and sequences were assembled via the metagenomics binning technique. Metagenomics revealed that 6 Archaea genera, 5 Bacteria genera, 7 Eukaryota genera, and 7 virus genera differed significantly between the HD and LD group. The analysis of metagenome-assembled genomes (MAGs) showed that 2 genera (g__Eubacterium_H and g__Dialister) were significantly enriched (P < 0.05, linear discriminant analysis (LDA) > 2) in the HD group. However, the LD group recorded an increased abundance (P < 0.05, LDA > 2) of 8 genera (g__CAG-603, g__UBA2922, g__Ga6A1, g__RUG13091, g__Bradyrhizobium, g__Sediminibacterium, g__UBA6382, and g__Succinivibrio) when compared to the HD group. Furthermore, investigation of the KEGG genes revealed an upregulation in a higher number of genes associated with nitrogen metabolism and lysine biosynthesis pathways in the HD group as compared to the LD group. Therefore, the high milk protein concentration in the HD group could be explained by an increased ammonia synthesis by ruminal microbes which were converted to microbial amino acids and microbial protein (MCP) in presence of an increased energy source made possible by higher activities of carbohydrate-active enzymes (CAZymes). This MCP gets absorbed in the small intestine as amino acids and might be utilized for the synthesis of milk protein. KEY POINTS: • Rumen microbiota and their functions differed between cows with high milk protein % and those with low milk protein %. • The rumen microbiome of cows with high milk protein recorded a higher number of enriched genes linked to the nitrogen metabolism pathway and lysine biosynthesis pathway. • The activities of carbohydrate-active enzymes were found to be higher in the rumen of cows with high milk protein %.}, } @article {pmid37306587, year = {2023}, author = {Cheng, H and Zhang, Y and Guo, Z and He, X and Liu, R and Zhu, XY and Li, J and Liu, J and Zhang, XH}, title = {Microbial Dimethylsulfoniopropionate Cycling in Deep Sediment of the Mariana Trench.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {7}, pages = {e0025123}, pmid = {37306587}, issn = {1098-5336}, mesh = {*Seawater/microbiology ; Bacteria ; Sulfides/metabolism ; *Sulfonium Compounds/metabolism ; }, abstract = {Dimethylsulfoniopropionate (DMSP) and related organic sulfur compounds play key roles in global sulfur cycling. Bacteria have been found to be important DMSP producers in seawater and surface sediments of the aphotic Mariana Trench (MT). However, detailed bacterial DMSP cycling in the Mariana Trench subseafloor remains largely unknown. Here, the bacterial DMSP-cycling potential in a Mariana Trench sediment core (7.5 m in length) obtained at a 10,816-m water depth was investigated using culture-dependent and -independent methods. The DMSP content fluctuated along the sediment depth and reached the highest concentration at 15 to 18 cm below the seafloor (cmbsf). dsyB was the dominant known DMSP synthetic gene, existing in 0.36 to 1.19% of the bacteria, and was identified in the metagenome-assembled genomes (MAGs) of previously unknown bacterial DMSP synthetic groups such as Acidimicrobiia, Phycisphaerae, and Hydrogenedentia. dddP, dmdA, and dddX were the major DMSP catabolic genes. The DMSP catabolic activities of DddP and DddX retrieved from Anaerolineales MAGs were confirmed by heterologous expression, indicating that such anaerobic bacteria might participate in DMSP catabolism. Moreover, genes involved in methanethiol (MeSH) production from methylmercaptopropionate (MMPA) and dimethyl sulfide (DMS), MeSH oxidation, and DMS production were highly abundant, suggesting active conversions between different organic sulfur compounds. Finally, most culturable DMSP synthetic and catabolic isolates possessed no known DMSP synthetic and catabolic genes, and actinomycetes could be important groups involved in both DMSP synthesis and catabolism in Mariana Trench sediment. This study extends the current understanding of DMSP cycling in Mariana Trench sediment and highlights the need to uncover novel DMSP metabolic genes/pathways in extreme environments. IMPORTANCE Dimethylsulfoniopropionate (DMSP) is an abundant organosulfur molecule in the ocean and is the precursor for the climate-active volatile gas dimethyl sulfide. Previous studies focused mainly on bacterial DMSP cycling in seawater, coastal sediment, and surface trench sediment samples, but DMSP metabolism in the Mariana Trench (MT) subseafloor sediments remains unknown. Here, we describe the DMSP content and metabolic bacterial groups in the subseafloor of the MT sediment. We found that the tendency for vertical variation of the DMSP content in the MT was distinct from that of the continent shelf sediment. Although dsyB and dddP were the dominant DMSP synthetic and catabolic genes in the MT sediment, respectively, both metagenomic and culture methods revealed multiple previously unknown DMSP metabolic bacterial groups, especially anaerobic bacteria and actinomycetes. The active conversion of DMSP, DMS, and methanethiol may also occur in the MT sediments. These results provide novel insights for understanding DMSP cycling in the MT.}, } @article {pmid37306468, year = {2023}, author = {Shen, Y and Qu, W and Yu, F and Zhang, D and Zou, Q and Han, D and Xie, M and Chen, X and Yuan, L and Lou, B and Xie, G and Wang, R and Yang, X and Chen, W and Wang, Q and Teng, Y and Dong, Y and Huang, L and Bao, J and Liu, C and Wu, W and Shen, E and Fan, L and Timko, MP and Zheng, S and Chen, Y}, title = {Dynamic associations between the respiratory tract and gut antibiotic resistome of patients with COVID-19 and its prediction power for disease severity.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2223340}, pmid = {37306468}, issn = {1949-0984}, mesh = {Humans ; Anti-Bacterial Agents ; Vancomycin ; Leukocytes, Mononuclear ; *COVID-19 ; *Gastrointestinal Microbiome ; Respiratory System ; Patient Acuity ; }, abstract = {The antibiotic resistome is the collection of all antibiotic resistance genes (ARGs) present in an individual. Whether an individual's susceptibility to infection and the eventual severity of coronavirus disease 2019 (COVID-19) is influenced by their respiratory tract antibiotic resistome is unknown. Additionally, whether a relationship exists between the respiratory tract and gut ARGs composition has not been fully explored. We recruited 66 patients with COVID-19 at three disease stages (admission, progression, and recovery) and conducted a metagenome sequencing analysis of 143 sputum and 97 fecal samples obtained from them. Respiratory tract, gut metagenomes, and peripheral blood mononuclear cell (PBMC) transcriptomes are analyzed to compare the gut and respiratory tract ARGs of intensive care unit (ICU) and non-ICU (nICU) patients and determine relationships between ARGs and immune response. Among the respiratory tract ARGs, we found that Aminoglycoside, Multidrug, and Vancomycin are increased in ICU patients compared with nICU patients. In the gut, we found that Multidrug, Vancomycin, and Fosmidomycin were increased in ICU patients. We discovered that the relative abundances of Multidrug were significantly correlated with clinical indices, and there was a significantly positive correlation between ARGs and microbiota in the respiratory tract and gut. We found that immune-related pathways in PBMC were enhanced, and they were correlated with Multidrug, Vancomycin, and Tetracycline ARGs. Based on the ARG types, we built a respiratory tract-gut ARG combined random-forest classifier to distinguish ICU COVID-19 patients from nICU patients with an AUC of 0.969. Cumulatively, our findings provide some of the first insights into the dynamic alterations of respiratory tract and gut antibiotic resistome in the progression of COVID-19 and disease severity. They also provide a better understanding of how this disease affects different cohorts of patients. As such, these findings should contribute to better diagnosis and treatment scenarios.}, } @article {pmid37306408, year = {2023}, author = {Tang, W and Zheng, H and Xu, S and Li, P and Zhan, L and Luo, X and Dai, Z and Wang, Q and Yu, G}, title = {MMINP: A computational framework of microbe-metabolite interactions-based metabolic profiles predictor based on the O2-PLS algorithm.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2223349}, pmid = {37306408}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; Least-Squares Analysis ; Algorithms ; Computational Biology ; Metabolome ; }, abstract = {The gut metabolome acts as an intermediary between the gut microbiota and host, and has tremendous diagnostic and therapeutic potential. Several studies have utilized bioinformatic tools to predict metabolites based on the different aspects of the gut microbiome. Although these tools have contributed to a better understanding of the relationship between the gut microbiota and various diseases, most of them have focused on the impact of microbial genes on the metabolites and the relationship between microbial genes. In contrast, relatively little is known regarding the effect of metabolites on the microbial genes or the relationship between these metabolites. In this study, we constructed a computational framework of Microbe-Metabolite INteractions-based metabolic profiles Predictor (MMINP), based on the Two-Way Orthogonal Partial Least Squares (O2-PLS) algorithm to predict the metabolic profiles associated with gut microbiota. We demonstrated the predictive value of MMINP relative to that of similar methods. Additionally, we identified the features that would profoundly impact the prediction performance of data-driven methods (O2-PLS, MMINP, MelonnPan, and ENVIM), including the training sample size, host disease state, and the upstream data processing methods of the different technical platforms. We suggest that when using data-driven methods, similar host disease states and preprocessing methods, and a sufficient number of training samples are necessary to achieve accurate prediction.}, } @article {pmid37305949, year = {2023}, author = {Nandi, D and Parida, S and Sharma, D}, title = {The gut microbiota in breast cancer development and treatment: The good, the bad, and the useful!.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2221452}, pmid = {37305949}, issn = {1949-0984}, support = {R01 CA204555/CA/NCI NIH HHS/United States ; }, mesh = {Female ; Humans ; *Breast Neoplasms/therapy ; *Gastrointestinal Microbiome ; *Microbiota ; Metagenome ; Cognition ; }, abstract = {Regardless of the global progress in early diagnosis and novel therapeutic regimens, breast carcinoma poses a devastating threat, and the advances are somewhat marred by high mortality rates. Breast cancer risk prediction models based on the known risk factors are extremely useful, but a large number of breast cancers develop in women with no/low known risk. The gut microbiome exerts a profound impact on the host health and physiology and has emerged as a pivotal frontier in breast cancer pathogenesis. Progress in metagenomic analysis has enabled the identification of specific changes in the host microbial signature. In this review, we discuss the microbial and metabolomic changes associated with breast cancer initiation and metastatic progression. We summarize the bidirectional impact of various breast cancer-related therapies on gut microbiota and vice-versa. Finally, we discuss the strategies to modulate the gut microbiota toward a more favorable state that confers anticancer effects.}, } @article {pmid37303219, year = {2023}, author = {Diao, Z and Zhang, Y and Chen, Y and Han, Y and Chang, L and Ma, Y and Feng, L and Huang, T and Zhang, R and Li, J}, title = {Assessing the Quality of Metagenomic Next-Generation Sequencing for Pathogen Detection in Lower Respiratory Infections.}, journal = {Clinical chemistry}, volume = {69}, number = {9}, pages = {1038-1049}, doi = {10.1093/clinchem/hvad072}, pmid = {37303219}, issn = {1530-8561}, mesh = {Humans ; Reproducibility of Results ; *Respiratory Tract Infections/diagnosis ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Biological Assay ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Laboratory-developed metagenomic next-generation sequencing (mNGS) assays are increasingly being used for the diagnosis of infectious disease. To ensure comparable results and advance the quality control for the mNGS assay, we initiated a large-scale multicenter quality assessment to scrutinize the ability of mNGS to detect pathogens in lower respiratory infections.

METHODS: A reference panel containing artificial microbial communities and real clinical samples was used to assess the performance of 122 laboratories. We comprehensively evaluated the reliability, the source of false-positive and false-negative microbes, as well as the ability to interpret the results.

RESULTS: A wide variety of weighted F1-scores was observed across 122 participants, with a range from 0.20 to 0.97. The majority of false positive microbes (68.56%, 399/582) were introduced from "wet lab." The loss of microbial sequence during wet labs was the chief cause (76.18%, 275/361) of false-negative errors. When the human context is 2 × 105 copies/mL, most DNA and RNA viruses at titers above 104 copies/mL could be detected by >80% of the participants, while >90% of the laboratories could detect bacteria and fungi at titers lower than 103 copies/mL. A total of 10.66% (13/122) to 38.52% (47/122) of the participants could detect the target pathogens but failed to reach a correct etiological diagnosis.

CONCLUSIONS: This study clarified the sources of false-positive and false-negative results and evaluated the performance of interpreting the results. This study was valuable for clinical mNGS laboratories to improve method development, avoid erroneous results being reported, and implement regulatory quality controls in the clinic.}, } @article {pmid37301875, year = {2023}, author = {Li, L and Wang, T and Ning, Z and Zhang, X and Butcher, J and Serrana, JM and Simopoulos, CMA and Mayne, J and Stintzi, A and Mack, DR and Liu, YY and Figeys, D}, title = {Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3428}, pmid = {37301875}, issn = {2041-1723}, support = {U19 AI095219/AI/NIAID NIH HHS/United States ; U01 HL089856/HL/NHLBI NIH HHS/United States ; RF1 AG067744/AG/NIA NIH HHS/United States ; R01 AI141529/AI/NIAID NIH HHS/United States ; R01 HD093761/HD/NICHD NIH HHS/United States ; UH3 OD023268/OD/NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Proteome ; Proteomics ; Xenobiotics ; Feces ; *Microbiota ; }, abstract = {Functional redundancy is a key ecosystem property representing the fact that different taxa contribute to an ecosystem in similar ways through the expression of redundant functions. The redundancy of potential functions (or genome-level functional redundancy [Formula: see text]) of human microbiomes has been recently quantified using metagenomics data. Yet, the redundancy of expressed functions in the human microbiome has never been quantitatively explored. Here, we present an approach to quantify the proteome-level functional redundancy [Formula: see text] in the human gut microbiome using metaproteomics. Ultra-deep metaproteomics reveals high proteome-level functional redundancy and high nestedness in the human gut proteomic content networks (i.e., the bipartite graphs connecting taxa to functions). We find that the nested topology of proteomic content networks and relatively small functional distances between proteomes of certain pairs of taxa together contribute to high [Formula: see text] in the human gut microbiome. As a metric comprehensively incorporating the factors of presence/absence of each function, protein abundances of each function and biomass of each taxon, [Formula: see text] outcompetes diversity indices in detecting significant microbiome responses to environmental factors, including individuality, biogeography, xenobiotics, and disease. We show that gut inflammation and exposure to specific xenobiotics can significantly diminish the [Formula: see text] with no significant change in taxonomic diversity.}, } @article {pmid37301103, year = {2023}, author = {Dou, L and Liu, C and Chen, X and Yang, Z and Hu, G and Zhang, M and Sun, L and Su, L and Zhao, L and Jin, Y}, title = {Supplemental Clostridium butyricum modulates skeletal muscle development and meat quality by shaping the gut microbiota of lambs.}, journal = {Meat science}, volume = {204}, number = {}, pages = {109235}, doi = {10.1016/j.meatsci.2023.109235}, pmid = {37301103}, issn = {1873-4138}, mesh = {Female ; Sheep ; Animals ; *Clostridium butyricum/physiology ; *Gastrointestinal Microbiome ; Dietary Supplements/analysis ; Meat/analysis ; Muscle Development ; Animal Feed/analysis ; Muscle, Skeletal/metabolism ; }, abstract = {This study evaluated the contributions of Clostridium butyricum on skeletal muscle development, gastrointestinal flora and meat quality of lambs. Eighteen Dorper (♂) × Small Tailed Han sheep (♀) crossed ewe lambs of similar weight (27.43 ± 1.94 kg; age, 88 ± 5 days) were divided into two dietary treatments. The control group was fed the basal diet (C group), and the probiotic group was supplemented with C. butyricum on the basis of the C group (2.5 × 10[8] cfu/g, 5 g/day/lamb; P group) for 90 d. The results showed that dietary C. butyricum elevated growth performance, muscle mass, muscle fiber diameter and cross-sectional area, and decreased the shear force value of meat (P < 0.05). Moreover, C. butyricum supplementation accelerated protein synthesis by regulating the gene expression of IGF-1/Akt/mTOR pathway. We identified 54 differentially expressed proteins that regulated skeletal muscle development through different mechanisms by quantitative proteomics. These proteins were associated with ubiquitin-protease, apoptosis, muscle structure, energy metabolism, heat shock, and oxidative stress. The metagenomics sequencing results showed that Petrimonas at the genus level and Prevotella brevis at the species level in the rumen, while Lachnoclostridium, Alloprevotella and Prevotella at the genus level in the feces, were significantly enriched in the P group. Also, butyric acid and valeric acid levels were elevated in both rumen and feces of the P group. Overall, our results support the idea that C. butyricum could change gastrointestinal flora, and affect skeletal muscle development and meat quality of lambs by modulating gut-muscle axis.}, } @article {pmid37298483, year = {2023}, author = {Park, S and Zhang, T and Kang, S}, title = {Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes.}, journal = {International journal of molecular sciences}, volume = {24}, number = {11}, pages = {}, pmid = {37298483}, issn = {1422-0067}, support = {RS-2023-00208567//National Research Foundation of Korea/ ; }, mesh = {Adult ; Humans ; Metagenome ; *Diabetes Mellitus, Type 2/genetics ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Bacteria/genetics ; }, abstract = {T2DM etiology differs among Asians and Caucasians and may be associated with gut microbiota influenced by different diet patterns. However, the association between fecal bacterial composition, enterotypes, and T2DM susceptibility remained controversial. We investigated the fecal bacterial composition, co-abundance network, and metagenome function in US adults with T2DM compared to healthy adults based on enterotypes. We analyzed 1911 fecal bacterial files of 1039 T2DM and 872 healthy US adults from the Human Microbiome Projects. Operational taxonomic units were obtained after filtering and cleaning the files using Qiime2 tools. Machine learning and network analysis identified primary bacteria and their interactions influencing T2DM incidence, clustered into enterotypes, Bacteroidaceae (ET-B), Lachnospiraceae (ET-L), and Prevotellaceae (ET-P). ET-B showed higher T2DM incidence. Alpha-diversity was significantly lower in T2DM in ET-L and ET-P (p < 0.0001), but not in ET-B. Beta-diversity revealed a distinct separation between T2DM and healthy groups across all enterotypes (p < 0.0001). The XGBoost model exhibited high accuracy and sensitivity. Enterocloster bolteae, Facalicatena fissicatena, Clostridium symbiosum, and Facalibacterium prausnitizii were more abundant in the T2DM group than in the healthy group. Bacteroides koreensis, Oscillibacter ruminantium, Bacteroides uniformis, and Blautia wexlerae were lower in the T2DM than in the healthy group regardless of the enterotypes in the XGBoost model (p < 0.0001). However, the patterns of microbial interactions varied among different enterotypes affecting T2DM risk. The interaction between fecal bacteria was more tightly regulated in the ET-L than in the ET-B and ET-P groups (p < 0.001). Metagenomic analysis revealed an inverse association between bacteria abundance in T2DM, energy utility, butanoate and propanoate metabolism, and the insulin signaling pathway (p < 0.0001). In conclusion, fecal bacteria play a role in T2DM pathogenesis, particularly within different enterotypes, providing valuable insights into the link between gut microbiota and T2DM in the US population.}, } @article {pmid37298198, year = {2023}, author = {Zubeldia-Varela, E and Barker-Tejeda, TC and Mera-Berriatua, L and Bazire, R and Cabrera-Freitag, P and Ubeda, C and Barber, D and Francino, MP and Rojo, D and Ibáñez-Sandín, MD and Pérez-Gordo, M}, title = {Further Insights into the Gut Microbiota of Cow's Milk Allergic Infants: Analysis of Microbial Functionality and Its Correlation with Three Fecal Biomarkers.}, journal = {International journal of molecular sciences}, volume = {24}, number = {11}, pages = {}, pmid = {37298198}, issn = {1422-0067}, support = {PI17/01087//Instituto de Salud Carlos III/ ; FSEAIC_2016//Sociedad Española de Alergia e Inmunología Clínica/ ; ARADyAL RD16/00060015 and RD16/0006/0026//European Regional Development Fund/ ; PI19/00044//Instituto de Salud Carlos III/ ; PI20/01366//Instituto de Salud Carlos III/ ; }, mesh = {Female ; Animals ; Cattle ; Milk/chemistry ; *Gastrointestinal Microbiome ; Lactoferrin/metabolism ; *Milk Hypersensitivity/diagnosis ; Feces/chemistry ; Biomarkers/analysis ; }, abstract = {Cow's milk allergy (CMA) is one of the most prevalent food allergies in children. Several studies have demonstrated that gut microbiota influences the acquisition of oral tolerance to food antigens at initial stages of life. Changes in the gut microbiota composition and/or functionality (i.e., dysbiosis) have been linked to inadequate immune system regulation and the emergence of pathologies. Moreover, omic sciences have become an essential tool for the analysis of the gut microbiota. On the other hand, the use of fecal biomarkers for the diagnosis of CMA has recently been reviewed, with fecal calprotectin, α-1 antitrypsin, and lactoferrin being the most relevant. This study aimed at evaluating functional changes in the gut microbiota in the feces of cow's milk allergic infants (AI) compared to control infants (CI) by metagenomic shotgun sequencing and at correlating these findings with the levels of fecal biomarkers (α-1 antitrypsin, lactoferrin, and calprotectin) by an integrative approach. We have observed differences between AI and CI groups in terms of fecal protein levels and metagenomic analysis. Our findings suggest that AI have altered glycerophospholipid metabolism as well as higher levels of lactoferrin and calprotectin that could be explained by their allergic status.}, } @article {pmid37295406, year = {2023}, author = {Nguyen, CL and Markey, KA and Miltiadous, O and Dai, A and Waters, N and Sadeghi, K and Fei, T and Shouval, R and Taylor, BP and Liao, C and Slingerland, JB and Slingerland, AE and Clurman, AG and Maloy, MA and Bohannon, L and Giardina, PA and Brereton, DG and Armijo, GK and Fontana, E and Gradissimo, A and Gyurkocza, B and Sung, AD and Chao, NJ and Devlin, SM and Taur, Y and Giralt, SA and Perales, MA and Xavier, JB and Pamer, EG and Peled, JU and Gomes, ALC and van den Brink, MRM}, title = {High-resolution analyses of associations between medications, microbiome, and mortality in cancer patients.}, journal = {Cell}, volume = {186}, number = {12}, pages = {2705-2718.e17}, pmid = {37295406}, issn = {1097-4172}, support = {P01 CA023766/CA/NCI NIH HHS/United States ; R01 CA228308/CA/NCI NIH HHS/United States ; U01 AI124275/AI/NIAID NIH HHS/United States ; R56 AI137269/AI/NIAID NIH HHS/United States ; R01 HL125571/HL/NHLBI NIH HHS/United States ; R01 CA228358/CA/NCI NIH HHS/United States ; R01 HL123340/HL/NHLBI NIH HHS/United States ; R21 AG066388/AG/NIA NIH HHS/United States ; R01 HL151365/HL/NHLBI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; P01 AG052359/AG/NIA NIH HHS/United States ; K08 HL143189/HL/NHLBI NIH HHS/United States ; R01 CA203950/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Metagenome ; *Hematopoietic Stem Cell Transplantation ; Anti-Bacterial Agents ; *Neoplasms/drug therapy ; }, abstract = {Discerning the effect of pharmacological exposures on intestinal bacterial communities in cancer patients is challenging. Here, we deconvoluted the relationship between drug exposures and changes in microbial composition by developing and applying a new computational method, PARADIGM (parameters associated with dynamics of gut microbiota), to a large set of longitudinal fecal microbiome profiles with detailed medication-administration records from patients undergoing allogeneic hematopoietic cell transplantation. We observed that several non-antibiotic drugs, including laxatives, antiemetics, and opioids, are associated with increased Enterococcus relative abundance and decreased alpha diversity. Shotgun metagenomic sequencing further demonstrated subspecies competition, leading to increased dominant-strain genetic convergence during allo-HCT that is significantly associated with antibiotic exposures. We integrated drug-microbiome associations to predict clinical outcomes in two validation cohorts on the basis of drug exposures alone, suggesting that this approach can generate biologically and clinically relevant insights into how pharmacological exposures can perturb or preserve microbiota composition. The application of a computational method called PARADIGM to a large dataset of cancer patients' longitudinal fecal specimens and detailed daily medication records reveals associations between drug exposures and the intestinal microbiota that recapitulate in vitro findings and are also predictive of clinical outcomes.}, } @article {pmid37292198, year = {2023}, author = {Han, X and He, X and Zhan, X and Yao, L and Sun, Z and Gao, X and Wang, S and Wang, Z}, title = {Disturbed microbiota-metabolites-immune interaction network is associated with olfactory dysfunction in patients with chronic rhinosinusitis.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1159112}, pmid = {37292198}, issn = {1664-3224}, mesh = {Humans ; *Rhinitis/diagnosis ; *Olfaction Disorders/diagnosis/etiology ; Smell ; *Sinusitis/diagnosis ; Chronic Disease ; Inflammation/complications ; *Microbiota ; }, abstract = {PURPOSE: Olfactory dysfunction (OD) is a debilitating symptom frequently reported by patients with chronic rhinosinusitis (CRS) and it is associated with a dysregulated sinonasal inflammation. However, little information is available about the effect of the inflammation-related nasal microbiota and related metabolites on the olfactory function in these patients. Therefore, the current study aimed to investigate the nasal microbiota-metabolites-immune interactions and their role in the pathogenesis of OD in CRS patients.

METHODS: 23 and 19 CRS patients with and without OD, respectively, were enrolled in the present study. The "Sniffin' Sticks" was used to measure the olfactory function, while the metagenomic shotgun sequencing and the untargeted metabolite profiling were performed to assess the differences in terms of the nasal microbiome and metabolome between the two groups. The levels of nasal mucus inflammatory mediators were investigated by a multiplex flow Cytometric Bead Array (CBA).

RESULTS: A decreased diversity in the nasal microbiome from the OD group compared to the NOD group was evidenced. The metagenomic analysis revealed a significant enrichment of Acinetobacter johnsonii in the OD group, while Mycoplasma arginini, Aeromonas dhakensis, and Salmonella enterica were significantly less represented (LDA value > 3, p < 0.05). The nasal metabolome profiles were significantly different between the OD and NOD groups (P < 0.05). The purine metabolism was the most significantly enriched metabolic subpathway in OD patients compared with NOD patients (P < 0.001). The expressions of IL-5, IL-8, MIP-1α, MCP-1, and TNF were statistically and significantly increased in the OD group (P < 0.05). All these data, including the dysregulation of the nasal microbiota, differential metabolites, and elevated inflammatory mediators in OD patients demonstrated a clear interaction relationship.

CONCLUSION: The disturbed nasal microbiota-metabolite-immune interaction networks may be implicated in the pathogenesis of OD in CRS patients and the underlying pathophysiological mechanisms need to be further investigated in future studies.}, } @article {pmid37290887, year = {2023}, author = {Yancey, CE and Kiledal, EA and Chaganti, SR and Denef, VJ and Errera, RM and Evans, JT and Hart, LN and Isailovic, D and James, WS and Kharbush, JJ and Kimbrel, JA and Li, W and Mayali, X and Nitschky, H and Polik, CA and Powers, MA and Premathilaka, SH and Rappuhn, NA and Reitz, LA and Rivera, SR and Zwiers, CC and Dick, GJ}, title = {The Western Lake Erie culture collection: A promising resource for evaluating the physiological and genetic diversity of Microcystis and its associated microbiome.}, journal = {Harmful algae}, volume = {126}, number = {}, pages = {102440}, doi = {10.1016/j.hal.2023.102440}, pmid = {37290887}, issn = {1878-1470}, mesh = {Humans ; *Microcystis/genetics ; Lakes/microbiology ; *Cyanobacteria/genetics ; *Microbiota ; Genetic Variation ; }, abstract = {Cyanobacterial harmful algal blooms (cyanoHABs) dominated by Microcystis spp. have significant public health and economic implications in freshwater bodies around the world. These blooms are capable of producing a variety of cyanotoxins, including microcystins, that affect fishing and tourism industries, human and environmental health, and access to drinking water. In this study, we isolated and sequenced the genomes of 21 primarily unialgal Microcystis cultures collected from western Lake Erie between 2017 and 2019. While some cultures isolated in different years have a high degree of genetic similarity (genomic Average Nucleotide Identity >99%), genomic data show that these cultures also represent much of the breadth of known Microcystis diversity in natural populations. Only five isolates contained all the genes required for microcystin biosynthesis while two isolates contained a previously described partial mcy operon. Microcystin production within cultures was also assessed using Enzyme-Linked Immunosorbent Assay (ELISA) and supported genomic results with high concentrations (up to 900 μg L[-1]) in cultures with complete mcy operons and no or low toxin detected otherwise. These xenic cultures also contained a substantial diversity of bacteria associated with Microcystis, which has become increasingly recognized as an essential component of cyanoHAB community dynamics. These results highlight the genomic diversity among Microcystis strains and associated bacteria in Lake Erie, and their potential impacts on bloom development, toxin production, and toxin degradation. This culture collection significantly increases the availability of environmentally relevant Microcystis strains from temperate North America.}, } @article {pmid37290480, year = {2023}, author = {Gan, J and Chen, J and Ma, RL and Deng, Y and Ding, XS and Zhu, SY and Sun, AJ}, title = {Metagenomics study on taxonomic and functional change of gut microbiota in patients with obesity with PCOS treated with exenatide combination with metformin or metformin alone.}, journal = {Gynecological endocrinology : the official journal of the International Society of Gynecological Endocrinology}, volume = {39}, number = {1}, pages = {2219342}, doi = {10.1080/09513590.2023.2219342}, pmid = {37290480}, issn = {1473-0766}, mesh = {Female ; Humans ; *Metformin ; *Polycystic Ovary Syndrome/complications/drug therapy/metabolism ; Exenatide/therapeutic use ; *Gastrointestinal Microbiome ; Metagenomics ; Obesity/complications/drug therapy/chemically induced ; }, abstract = {OBJECTIVE: To investigate the effect of exenatide treatment on the composition of intestinal flora and metabolic pathways in patients with obesity with polycystic ovary syndrome.

METHODS: Patients with obesity with polycystic ovary syndrome (PCOS) were distributed to two groups: one received exenatide combined with metformin (COM group, n = 14) and the other used metformin alone (MF group, n = 15). Fresh fecal specimens from the participants, including 29 patients with obesity with PCOS and 6 healthy controls, were collected for metagenomic sequencing. The effect of exenatide combination with metformin or metformin alone on the composition and function of intestinal flora in patients with obesity with PCOS were compared by bioinformatics analysis.

RESULTS: The level of BMI, TT, HbA1c, and HDL-c was significantly improved in both groups. The MF and COM groups were abundant in Firmicutes, Bacteroidetes, Uroviricota, Actinobacteria, and Proteobacteria. Abundance of Bacteroidetes, Proteobacteria, Hungatella, and certain probiotics like Phocaeicola and Anaerobutyricum significantly increased in both groups after treatment. Enriched microbial species in the MF and COM group were different. Clostridium, Fusobacterium, and Oxalobacter were the main bacteria in the post-MF group, while Lactococcus_garvieae, Clostridium_perfringens, and Coprococcus_sp_AF16_5 were the main bacteria in the post-COM group. The post-COM group had more probiotic species including Bifidobacterium, Prevotella, and Anaerobutyricum after treatment.

CONCLUSION: Both exenatide combined with metformin and metformin monotherapy can improve metabolic and endocrine markers, and the diversity and abundance of gut microbiota in patients with obesity with PCOS. The effects of the combination and monotherapy agents on intestinal flora were consistent to some extent but also unique respectively.}, } @article {pmid37290262, year = {2023}, author = {Mokhtari, P and Jambal, P and Metos, JM and Shankar, K and Anandh Babu, PV}, title = {Microbial taxonomic and functional shifts in adolescents with type 1 diabetes are associated with clinical and dietary factors.}, journal = {EBioMedicine}, volume = {93}, number = {}, pages = {104641}, pmid = {37290262}, issn = {2352-3964}, support = {P30 DK048520/DK/NIDDK NIH HHS/United States ; R01 AT010247/AT/NCCIH NIH HHS/United States ; }, mesh = {Humans ; Adolescent ; *Diabetes Mellitus, Type 1 ; Feces/microbiology ; *Microbiota ; Bacteria ; Vitamins/metabolism ; Amino Acids/metabolism ; }, abstract = {BACKGROUND: Evidence indicates a link between the pathogenesis of type 1 diabetes (T1D) and the gut microbiome. However, the regulation of microbial metabolic pathways and the associations of bacterial species with dietary factors in T1D are largely unknown. We investigated whether microbial metagenomic signatures in adolescents with T1D are associated with clinical/dietary factors.

METHODS: Adolescents with T1D (case) and healthy adolescents (control) were recruited, and microbiome profiling in participants' stool samples was performed using shotgun metagenomic sequencing. The bioBakery3 pipeline (Kneaddata, Metaphlan 4 and HUMAnN) was used to assign taxonomy and functional annotations. Clinical (HbA1c) and dietary information (3-day food record) were collected for conducting association analysis using Spearman's correlation.

FINDINGS: Adolescents with T1D exhibited modest changes in taxonomic composition of gut microbiome. Nineteen microbial metabolic pathways were altered in T1D, including downregulation of biosynthesis of vitamins (B2/flavin, B7/biotin and B9/folate), enzyme cofactors (NAD[+] and s-adenosyl methionine) and amino acids (aspartate, asparagine and lysine) with an upregulation in the fermentation pathways. Furthermore, bacterial species associated with dietary and clinical factors differed between healthy adolescents and adolescents with T1D. Supervised models modeling identified taxa predictive of T1D status, and the top features included Coprococcus and Streptococcus.

INTERPRETATION: Our study provides new insight into the alteration of microbial and metabolic signatures in adolescents with T1D, suggesting that microbial biosynthesis of vitamins, enzyme cofactors and amino acids may be potentially altered in T1D.

FUNDING: Research grants from NIH/NCCIH: R01AT010247 and USDA/NIFA: 2019-67017-29253; and Larry & Gail Miller Family Foundation Assistantship.}, } @article {pmid37288587, year = {2023}, author = {Noh, CK and Jung, W and Yang, MJ and Kim, WH and Hwang, JC}, title = {Alteration of the fecal microbiome in patients with cholecystectomy: potential relationship with postcholecystectomy diarrhea - before and after study.}, journal = {International journal of surgery (London, England)}, volume = {109}, number = {9}, pages = {2585-2597}, pmid = {37288587}, issn = {1743-9159}, mesh = {Humans ; *Gallstones ; *Microbiota ; Feces ; Diarrhea/etiology ; Cholecystectomy/adverse effects ; }, abstract = {BACKGROUND: Bile acid (BA) is a crucial determinant of the gut microbiome, and cholecystectomy can alter the physiology of BA. Physiological changes in BA resulting from cholecystectomy can also influence the gut microbiome. We aimed to identify the specific taxa associated with perioperative symptoms, including postcholecystectomy diarrhea (PCD), and to evaluate the effect of cholecystectomy on the microbiome by investigating the fecal microbiome of patients with gallstones.

METHODS: We analyzed the fecal samples of 39 patients with gallstones (GS group) and 26 healthy controls (HC group) to evaluate their gut microbiome. We also collected fecal samples from GS group 3 months postcholecystectomy. Symptoms of patients were evaluated before and after cholecystectomy. Further, 16S ribosomal RNA amplification and sequencing were performed to determine the metagenomic profile of fecal samples.

RESULTS: The microbiome composition of GS differed from that of HC; however, the alpha diversity was not different. No significant microbiome alterations were observed before and after cholecystectomy. Moreover, GS group showed a significantly lower Firmicutes to Bacteroidetes ratio before and after cholecystectomy than the HC group (6.2, P< 0.05). The inter-microbiome relationship was lower in GS than in HC and tended to recover 3 months after surgery. Furthermore, ~28.1% (n =9) of patients developed PCD after surgery. The most prominent species among PCD (+) patients was Phocaeicola vulgatus. Compared with the preoperative state, Sutterellaceae , Phocaeicola , and Bacteroidals were the most dominant taxa among PCD (+) patients.

CONCLUSION: GS group showed a different microbiome from that of HC; however, their microbiomes were not different 3 months after cholecystectomy. Our data revealed taxa-associated PCD, highlighting the possibility of symptom relief by restoring the gut microbiome.}, } @article {pmid37288545, year = {2023}, author = {Lu, F and Lei, T and Zhou, J and Liang, H and Cui, P and Zuo, T and Ye, L and Chen, H and Huang, J}, title = {Using gut microbiota as a diagnostic tool for colorectal cancer: machine learning techniques reveal promising results.}, journal = {Journal of medical microbiology}, volume = {72}, number = {6}, pages = {}, doi = {10.1099/jmm.0.001699}, pmid = {37288545}, issn = {1473-5644}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/diagnosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Bayes Theorem ; Feces/microbiology ; Escherichia coli/genetics ; Machine Learning ; Prevotella/genetics ; }, abstract = {Introduction. Increasing evidence suggests a correlation between gut microbiota and colorectal cancer (CRC).Hypothesis/Gap Statement. However, few studies have used gut microbiota as a diagnostic biomarker for CRC.Aim. The objective of this study was to explore whether a machine learning (ML) model based on gut microbiota could be used to diagnose CRC and identify key biomarkers in the model.Methodology. We sequenced the 16S rRNA gene from faecal samples of 38 participants, including 17 healthy subjects and 21 CRC patients. Eight supervised ML algorithms were used to diagnose CRC based on faecal microbiota operational taxonomic units (OTUs), and the models were evaluated in terms of identification, calibration and clinical practicality for optimal modelling parameters. Finally, the key gut microbiota was identified using the random forest (RF) algorithm.Results. We found that CRC was associated with the dysregulation of gut microbiota. Through a comprehensive evaluation of supervised ML algorithms, we found that different algorithms had significantly different prediction performance using faecal microbiomes. Different data screening methods played an important role in optimization of the prediction models. We found that naïve Bayes algorithms [NB, accuracy=0.917, area under the curve (AUC)=0.926], RF (accuracy=0.750, AUC=0.926) and logistic regression (LR, accuracy=0.750, AUC=0.889) had high predictive potential for CRC. Furthermore, important features in the model, namely s__metagenome_g__Lachnospiraceae_ND3007_group (AUC=0.814), s__Escherichia_coli_g__Escherichia-Shigella (AUC=0.784) and s__unclassified_g__Prevotella (AUC=0.750), could each be used as diagnostic biomarkers of CRC.Conclusions. Our results suggested an association between gut microbiota dysregulation and CRC, and demonstrated the feasibility of the gut microbiota to diagnose cancer. The bacteria s__metagenome_g__Lachnospiraceae_ND3007_group, s__Escherichia_coli_g__Escherichia-Shigella and s__unclassified_g__Prevotella were key biomarkers for CRC.}, } @article {pmid37286586, year = {2023}, author = {Leung, H and Xiong, L and Ni, Y and Busch, A and Bauer, M and Press, AT and Panagiotou, G}, title = {Impaired flux of bile acids from the liver to the gut reveals microbiome-immune interactions associated with liver damage.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {35}, pmid = {37286586}, issn = {2055-5008}, mesh = {Mice ; Animals ; Bile Acids and Salts ; Ecosystem ; *Cholestasis/complications/pathology ; *Liver Diseases/complications ; Cytokines ; *Gastrointestinal Microbiome ; }, abstract = {Currently, there is evidence that alteration in the gut ecosystem contributes to the development of liver diseases, however, the complex mechanisms involved are still unclear. We induced cholestasis in mice by bile duct ligation (BDL), mirroring the phenotype of a bile duct obstruction, to understand how gut microbiota alterations caused by an impaired flow of bile acid to the gut contribute to the pathogenesis and progression of liver disease. We performed longitudinal stool, heart, and liver sampling using mice receiving BDL and controls receiving sham operation (ShamOP). Shotgun metagenomics profiling using fecal samples taken before and on day 1, day 3, and day 7 after surgery was performed, and the cytokines and clinical chemistry profiles from heart blood, as well as the liver bile acids profile, were measured. The BDL surgery reshaped the microbiome of mice, resulting in highly distinct characteristics compared to the ShamOP. Our analysis of the microbiome pathways and ECs revealed that BDL reduces the production of hepatoprotective compounds in the gut, such as biotin, spermidine, arginine, and ornithine, which were negatively associated with inflammatory cytokines (IL-6, IL-23, MCP-1). The reduction of the functional potential of the gut microbiota in producing those hepatoprotective compounds is associated with the decrease of beneficial bacteria species from Anaerotruncus, Blautia, Eubacterium, and Lachnoclostridium genera, as well as the increase of disease-associated bacteria e.g., Escherichia coli and Entercoccus faecalis. Our findings advances our knowledge of the gut microbiome-bile acids-liver triangle, which may serve as a potential therapeutic strategy for liver diseases.}, } @article {pmid37285993, year = {2023}, author = {Wu, F and Ding, X and Zhang, Y and Gu, JD and Liu, X and Guo, Q and Li, J and Feng, H}, title = {Metagenomic and metaproteomic insights into the microbiome and the key geobiochemical potentials on the sandstone of rock-hewn Beishiku Temple in Northwest China.}, journal = {The Science of the total environment}, volume = {893}, number = {}, pages = {164616}, doi = {10.1016/j.scitotenv.2023.164616}, pmid = {37285993}, issn = {1879-1026}, mesh = {*Metagenome ; Metagenomics/methods ; *Microbiota/physiology ; Bacteria/metabolism ; Sulfur/metabolism ; }, abstract = {Metagenomics and metaproteomics analyses were used to determine the microbial diversity and taxon composition, as well as the biochemical potentials of the microbiome on the sandstone of Beishiku Temple located in Northwest China. Taxonomic annotation of the metagenomic dataset revealed the predominant taxa of the stone microbiome on this cave temple with characteristics of resistance to harsh environmental conditions. Meanwhile, there were also taxa in the microbiome that showed sensitivity to environmental factors. The taxa distribution and the metabolic functional distribution patterns by the metagenome and metaproteome, respectively, showed clear differences. The high abundance of energy metabolism represented in the metaproteome suggested that there were active geomicrobiological cycles of elements within the microbiome. The taxa responsible for reactions in the nitrogen cycle from both metagenome and metaproteome supported a metabolically active nitrogen cycle, and the high activity of Comammox bacteria indicated the strong metabolic activity of ammonia oxidation to nitrate in the outdoor site. The SOX-related taxa involved in the sulfur cycle showed higher activity outdoors than indoors, and on the outdoor ground than at the outdoor cliff, as detected through metaproteomic analysis. The development of petrochemical industry in the vicinity resulting in the deposition of sulfur/oxidized sulfur via atmosphere may stimulate the physiological activity of SOX. Our findings provide metagenomic and metaproteomic evidence for microbially driven geobiochemical cycles that result in the biodeterioration of stone monuments.}, } @article {pmid37285974, year = {2023}, author = {Ya, H and Zhang, T and Xing, Y and Lv, M and Wang, X and Jiang, B}, title = {Co-existence of polyethylene microplastics and tetracycline on soil microbial community and ARGs.}, journal = {Chemosphere}, volume = {335}, number = {}, pages = {139082}, doi = {10.1016/j.chemosphere.2023.139082}, pmid = {37285974}, issn = {1879-1298}, mesh = {Humans ; *Microplastics ; Plastics ; Polyethylene ; Soil/chemistry ; Genes, Bacterial ; Soil Microbiology ; Anti-Bacterial Agents ; Tetracycline/pharmacology ; *Microbiota ; Aminoglycosides ; }, abstract = {Microplastics are plastic particles with particle size less than 5 mm in the environment. As an emerging organic pollutant, the presence of microplastics in the soil environment has been widely noticed. Also, due to the overuse of antibiotics, a large amount of antibiotics that cannot be fully absorbed by humans and livestock enter the soil environment in the form of urine or manure, making the soils suffer from serious antibiotic contamination problems. To address the environmental problems of microplastics and antibiotic contamination in soils, this study was conducted to investigate the effects of PE microplastics on antibiotic degradation, microbial community characteristics and ARGs in tetracycline-contaminated soils. The results showed that the addition of PE microplastics inhibited the degradation of tetracycline, and significantly increased the organic carbon content and decreased the neutral phosphatase activity. The addition of PE microplastics significantly reduced the alpha diversity of soil microbial community. Compared to the single tetracycline contamination. In addition, combined contamination with PE microplastics and tetracycline significantly affected bacterial genera such as Aeromicrobium, Rhodococcus, Mycobacterium and Intrasporangium. Metagenome sequencing studies revealed that the addition of PE microplastics inhibited the dissipation of ARGs in tetracycline-contaminated soils. There were strong positive correlations between Multidrug, Aminoglycoside and Clycopeptide resistance genes and Chloroflexi and Proteobacteria in tetracycline contaminated soils, and there was a strong positive correlation between Aminoglycoside resistance genes and Actinobacteria in combined contamination of PE microplastics and tetracycline. This study will provide some data support for the current environmental risk assessment of the coexistence of multiple contaminants in soil.}, } @article {pmid37283894, year = {2023}, author = {Adedayo, AA and Fadiji, AE and Babalola, OO}, title = {Unraveling the functional genes present in rhizosphere microbiomes of Solanum lycopersicum.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15432}, pmid = {37283894}, issn = {2167-8359}, mesh = {*Solanum lycopersicum/genetics ; Rhizosphere ; Soil Microbiology ; *Microbiota/genetics ; Soil/chemistry ; Plants ; }, abstract = {The microbiomes living in the rhizosphere soil of the tomato plant contribute immensely to the state of health of the tomato plant alongside improving sustainable agriculture. With the aid of shotgun metagenomics sequencing, we characterized the putative functional genes (plant-growth-promoting and disease-resistant genes) produced by the microbial communities dwelling in the rhizosphere soil of healthy and powdery mildew-diseased tomato plants. The results identified twenty-one (21) plant growth promotion (PGP) genes in the microbiomes inhabiting the healthy rhizosphere (HR) which are more predomiant as compared to diseased rhizosphere (DR) that has nine (9) genes and four (4) genes in bulk soil (BR). Likewise, we identified some disease-resistant genes which include nucleotide binding genes and antimicrobial genes. Our study revealed fifteen (15) genes in HR which made it greater in comparison to DR that has three (3) genes and three (3) genes in bulk soil. Further studies should be conducted by isolating these microorganisms and introduce them to field experiments for cultivation of tomatoes.}, } @article {pmid37280708, year = {2023}, author = {Rutjens, S and Vereecke, N and Sauer, J and Croubels, S and Devreese, M}, title = {Cefquinome shows a higher impact on the pig gut microbiome and resistome compared to ceftiofur.}, journal = {Veterinary research}, volume = {54}, number = {1}, pages = {45}, pmid = {37280708}, issn = {1297-9716}, mesh = {Swine ; Animals ; Anti-Bacterial Agents/therapeutic use ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Cephalosporins/pharmacology ; Feces/microbiology ; *Anti-Infective Agents/pharmacology ; Escherichia coli/genetics ; }, abstract = {Cephalosporins are licensed for treatment of severe bacterial infections in different species. However, the effect of these antimicrobials on the fecal microbiome and potential spread of resistance-associated genes causes great concern. This highlights the need to understand the impact of cephalosporins on the porcine fecal microbiome and resistome. A combination of long-read 16S rRNA gene and shotgun metagenomic sequencing was applied to investigate the effect of conventional treatment with either ceftiofur (3 mg.kg[-1] intramuscular, 3 consecutive days) or cefquinome (2 mg.kg[-1] intramuscular, 5 consecutive days) on the porcine microbiome and resistome. Fecal samples were collected from 17 pigs (6 ceftiofur treated, 6 cefquinome treated, 5 control pigs) at four different timepoints. Treatment with ceftiofur resulted in an increase in Proteobacteria members on microbiome level, while on resistome level selection in TetQ containing Bacteroides, CfxA6 containing Prevotella and blaTEM-1 containing Escherichia coli was observed. Cefquinome treatment resulted in a decline in overall species richness (α-diversity) and increase in Proteobacteria members. On genus level, administration of cefquinome significantly affected more genera than ceftiofur (18 vs 8). On resistome level, cefquinome resulted in a significant increase of six antimicrobial resistance genes, with no clear correlation with certain genera. For both antimicrobials, the resistome levels returned back to the control levels 21 days post-treatment. Overall, our study provides novel insights on the effect of specific cephalosporins on the porcine gut microbiome and resistome after conventional intramuscular treatment. These results might contribute to better tailoring of the most ideal treatment strategy for some bacterial infections.}, } @article {pmid37279755, year = {2023}, author = {Münch, PC and Eberl, C and Woelfel, S and Ring, D and Fritz, A and Herp, S and Lade, I and Geffers, R and Franzosa, EA and Huttenhower, C and McHardy, AC and Stecher, B}, title = {Pulsed antibiotic treatments of gnotobiotic mice manifest in complex bacterial community dynamics and resistance effects.}, journal = {Cell host & microbe}, volume = {31}, number = {6}, pages = {1007-1020.e4}, doi = {10.1016/j.chom.2023.05.013}, pmid = {37279755}, issn = {1934-6069}, mesh = {Animals ; Mice ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; Bacteria/genetics ; *Gastrointestinal Microbiome ; Germ-Free Life ; }, abstract = {Bacteria can evolve to withstand a wide range of antibiotics (ABs) by using various resistance mechanisms. How ABs affect the ecology of the gut microbiome is still poorly understood. We investigated strain-specific responses and evolution during repeated AB perturbations by three clinically relevant ABs, using gnotobiotic mice colonized with a synthetic bacterial community (oligo-mouse-microbiota). Over 80 days, we observed resilience effects at the strain and community levels, and we found that they were correlated with modulations of the estimated growth rate and levels of prophage induction as determined from metagenomics data. Moreover, we tracked mutational changes in the bacterial populations, and this uncovered clonal expansion and contraction of haplotypes and selection of putative AB resistance-conferring SNPs. We functionally verified these mutations via reisolation of clones with increased minimum inhibitory concentration (MIC) of ciprofloxacin and tetracycline from evolved communities. This demonstrates that host-associated microbial communities employ various mechanisms to respond to selective pressures that maintain community stability.}, } @article {pmid37279136, year = {2023}, author = {Wassan, JT and Wang, H and Zheng, H}, title = {Developing a New Phylogeny-Driven Random Forest Model for Functional Metagenomics.}, journal = {IEEE transactions on nanobioscience}, volume = {22}, number = {4}, pages = {763-770}, doi = {10.1109/TNB.2023.3283462}, pmid = {37279136}, issn = {1558-2639}, mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Random Forest ; Metagenome/genetics ; *Microbiota/genetics ; Metagenomics/methods ; }, abstract = {Metagenomics is an unobtrusive science linking microbial genes to biological functions or environmental states. Classifying microbial genes into their functional repertoire is an important task in the downstream analysis of Metagenomic studies. The task involves Machine Learning (ML) based supervised methods to achieve good classification performance. Random Forest (RF) has been applied rigorously to microbial gene abundance profiles, mapping them to functional phenotypes. The current research targets tuning RF by the evolutionary ancestry of microbial phylogeny, developing a Phylogeny-RF model for functional classification of metagenomes. This method facilitates capturing the effects of phylogenetic relatedness in an ML classifier itself rather than just applying a supervised classifier over the raw abundances of microbial genes. The idea is rooted in the fact that closely related microbes by phylogeny are highly correlated and tend to have similar genetic and phenotypic traits. Such microbes behave similarly; and hence tend to be selected together, or one of these could be dropped from the analysis, to improve the ML process. The proposed Phylogeny-RF algorithm has been compared with state-of-the-art classification methods including RF and the phylogeny-aware methods of MetaPhyl and PhILR, using three real-world 16S rRNA metagenomic datasets. It has been observed that the proposed method not only achieved significantly better performance than the traditional RF model but also performed better than the other phylogeny-driven benchmarks (p < 0.05). For example, Phylogeny-RF attained a highest AUC of 0.949 and Kappa of 0.891 over soil microbiomes in comparison to other benchmarks.}, } @article {pmid37279013, year = {2023}, author = {Medina-Chávez, NO and Viladomat-Jasso, M and Zarza, E and Islas-Robles, A and Valdivia-Anistro, J and Thalasso-Siret, F and Eguiarte, LE and Olmedo-Álvarez, G and Souza, V and De la Torre-Zavala, S}, title = {A Transiently Hypersaline Microbial Mat Harbors a Diverse and Stable Archaeal Community in the Cuatro Cienegas Basin, Mexico.}, journal = {Astrobiology}, volume = {23}, number = {7}, pages = {796-811}, doi = {10.1089/ast.2021.0047}, pmid = {37279013}, issn = {1557-8070}, mesh = {*Archaea/genetics ; Mexico ; Phylogeny ; Bacteria/genetics ; *Microbiota ; Water ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; }, abstract = {Microbial mats are biologically diverse communities that are analogs to some of the earliest ecosystems on Earth. In this study, we describe a unique transiently hypersaline microbial mat uncovered in a shallow pond within the Cuatro Cienegas Basin (CCB) in northern México. The CCB is an endemism-rich site that harbors living stromatolites that have been studied to understand the conditions of the Precambrian Earth. These microbial mats form elastic domes filled with biogenic gas, and the mats have a relatively large and stable subpopulation of archaea. For this reason, this site has been termed archaean domes (AD). The AD microbial community was analyzed by metagenomics over three seasons. The mat exhibited a highly diverse prokaryotic community dominated by bacteria. Bacterial sequences are represented in 37 phyla, mainly Proteobacteria, Firmicutes, and Actinobacteria, that together comprised >50% of the sequences from the mat. Archaea represented up to 5% of the retrieved sequences, with up to 230 different archaeal species that belong to 5 phyla (Euryarchaeota, Crenarchaeota, Thaumarchaeota, Korarchaeota, and Nanoarchaeota). The archaeal taxa showed low variation despite fluctuations in water and nutrient availability. In addition, predicted functions highlight stress responses to extreme conditions present in the AD, including salinity, pH, and water/drought fluctuation. The observed complexity of the AD mat thriving in high pH and fluctuating water and salt conditions within the CCB provides an extant model of great value for evolutionary studies, as well as a suitable analog to the early Earth and Mars.}, } @article {pmid37278524, year = {2023}, author = {Dedrick, S and Warrier, V and Lemon, KP and Momeni, B}, title = {When does a Lotka-Volterra model represent microbial interactions? Insights from in vitro nasal bacterial communities.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0075722}, pmid = {37278524}, issn = {2379-5077}, support = {R35 GM141806/GM/NIGMS NIH HHS/United States ; R01 GM117174/GM/NIGMS NIH HHS/United States ; T32 HL007427/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; Microbial Interactions ; Models, Theoretical ; Models, Biological ; Bacteria ; }, abstract = {To alter microbial community composition for therapeutic purposes, an accurate and reliable modeling framework capable of predicting microbial community outcomes is required. Lotka-Volterra (LV) equations have been utilized to describe a breadth of microbial communities, yet, the conditions in which this modeling framework is successful remain unclear. Here, we propose that a set of simple in vitro experiments-growing each member in cell-free spent medium obtained from other members-can be used as a test to decide whether an LV model is appropriate for describing microbial interactions of interest. We show that for LV to be a good candidate, the ratio of growth rate to carrying capacity of each isolate when grown in the cell-free spent media of other isolates should remain constant. Using an in vitro community of human nasal bacteria as a tractable system, we find that LV can be a good approximation when the environment is low-nutrient (i.e., when growth is limited by the availability of nutrients) and complex (i.e., when multiple resources, rather than a few, determine growth). These findings can help clarify the range of applicability of LV models and reveal when a more complex model may be necessary for predictive modeling of microbial communities. IMPORTANCE Although mathematical modeling can be a powerful tool to draw useful insights in microbial ecology, it is crucial to know when a simplified model adequately represents the interactions of interest. Here, we take advantage of bacterial isolates from the human nasal passages as a tractable model system and conclude that the commonly used Lotka-Volterra model can represent interactions among microbes well when the environment is complex (with many interaction mediators) and low-nutrient. Our work highlights the importance of considering both realism and simplicity when choosing a model to represent microbial interactions.}, } @article {pmid37278203, year = {2023}, author = {Gao, S and Gao, X and Zhu, R and Wu, D and Feng, Z and Jiao, N and Sun, R and Gao, W and He, Q and Liu, Z and Zhu, L}, title = {Microbial genes outperform species and SNVs as diagnostic markers for Crohn's disease on multicohort fecal metagenomes empowered by artificial intelligence.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2221428}, pmid = {37278203}, issn = {1949-0984}, mesh = {Humans ; *Crohn Disease/diagnosis/genetics ; Metagenome ; Artificial Intelligence ; *Gastrointestinal Microbiome/genetics ; Feces ; Genes, Microbial ; Dysbiosis/diagnosis/genetics ; }, abstract = {Dysbiosis of gut microbial community is associated with the pathogenesis of CD and may serve as a promising noninvasive diagnostic tool. We aimed to compare the performances of the microbial markers of different biological levels by conducting a multidimensional analysis on the microbial metagenomes of CD. We collected fecal metagenomic datasets generated from eight cohorts that altogether include 870 CD patients and 548 healthy controls. Microbial alterations in CD patients were assessed at multidimensional levels including species, gene, and SNV level, and then diagnostic models were constructed using artificial intelligence algorithm. A total of 227 species, 1047 microbial genes, and 21,877 microbial SNVs were identified that differed between CD and controls. The species, gene, and SNV models achieved an average AUC of 0.97, 0.95, and 0.77, respectively. Notably, the gene model exhibited superior diagnostic capability, achieving an average AUC of 0.89 and 0.91 for internal and external validations, respectively. Moreover, the gene model was specific for CD against other microbiome-related diseases. Furthermore, we found that phosphotransferase system (PTS) contributed substantially to the diagnostic capability of the gene model. The outstanding performance of PTS was mainly explained by genes celB and manY, which demonstrated high predictabilities for CD with metagenomic datasets and was validated in an independent cohort by qRT-PCR analysis. Our global metagenomic analysis unravels the multidimensional alterations of the microbial communities in CD and identifies microbial genes as robust diagnostic biomarkers across geographically and culturally distinct cohorts.}, } @article {pmid37277984, year = {2023}, author = {Chen, LL and Abbaspour, A and Aspvall, K and Rück, C and Bulik, CM and Pascal, D}, title = {Longitudinal study of gut microbiome in obsessive-compulsive disorder.}, journal = {Brain and behavior}, volume = {13}, number = {8}, pages = {e3115}, pmid = {37277984}, issn = {2162-3279}, mesh = {Humans ; Longitudinal Studies ; *Gastrointestinal Microbiome ; *Obsessive-Compulsive Disorder/diagnosis ; *Cognitive Behavioral Therapy ; Psychiatric Status Rating Scales ; }, abstract = {INTRODUCTION: Patients with obsessive-compulsive disorder (OCD) often have limited exposure to a diverse environment and perform repetitive compulsions such as excessive cleaning and washing, which could lead to altered gut microbiome. Therefore, longitudinal studies that investigate changes in gut microbiome before and after cognitive behavioral therapy based on exposure and response prevention (ERP) are warranted.

METHODS: All study participants (N = 64) underwent a structured psychiatric diagnostic interview prior to inclusion. Nutritional intake was assessed with a comprehensive food frequency questionnaire. Stool samples were collected from OCD patients before ERP (n = 32) and 1 month after completion of ERP (n = 15), as well as from healthy controls (HCs; n = 32). Taxonomic and functional analyses were performed using data from microbiome whole genome sequencing.

RESULTS: Patients with OCD at baseline reported consuming significantly less fiber than HCs (R[2]  = .12, F(2, 59) = 5.2, p ≤ .01). There were no significant differences in α- and β-diversity indices, or taxonomic dissimilarities at the species level between patients with OCD and HCs, or within patients before and after ERP. Functional profiling based on gut microbial gene expression was grouped into 56 gut-brain modules with neuroactive potential. None of the gut-brain modules differed significantly in expression between patients with OCD at baseline and HCs or within patients before and after ERP.

CONCLUSIONS: The diversity, composition, and functional profile of the gut microbiome in patients with OCD did not differ significantly from HCs and remained stable over time, despite behavioral changes.}, } @article {pmid37276653, year = {2023}, author = {Huang, S and Zhang, B and Zhao, Z and Yang, C and Zhang, B and Cui, F and Lens, PNL and Shi, W}, title = {Metagenomic analysis reveals the responses of microbial communities and nitrogen metabolic pathways to polystyrene micro(nano)plastics in activated sludge systems.}, journal = {Water research}, volume = {241}, number = {}, pages = {120161}, doi = {10.1016/j.watres.2023.120161}, pmid = {37276653}, issn = {1879-2448}, mesh = {*Sewage/chemistry ; Plastics ; Polystyrenes ; Waste Disposal, Fluid/methods ; Nitrogen/metabolism ; *Microbiota ; Microplastics ; Metabolic Networks and Pathways ; }, abstract = {Microplastics (MPs) and nanoplastics (NPs) are prevalent in sewage and pose a potential threat to nitrogen biotransformation in wastewater treatment systems. However, investigations on how MPs and NPs affect the microbial nitrogen conversion and metabolism of the activated sludge are still scanty. Herein, the responses of microbiomes and functional genes to polystyrene MPs and NPs in activated sludge systems were investigated by metagenomic analysis. Results indicated that 1 mg/L MPs and NPs had marginal impacts on the nitrogen removal performance of the activated sludge systems, whereas high concentrations of MPs and NPs (20 and 100 mg/L) decreased the total nitrogen removal efficiency (13.4%-30.6%) by suppressing the nitrogen transformation processes. Excessive reactive oxygen species induced by MPs and NPs caused cytotoxicity, as evidenced by impaired cytomembranes and decreased bioactivity. Metagenomic analysis revealed that MPs and NPs diminished the abundance of denitrifiers (e.g. Mesorhizobium, Rhodobacter and Thauera), and concurrently reduced the abundance of functional genes (e.g. napA, napB and nirS) encoding for key enzymes involved in the nitrogen transformations, as well as the genes (e.g. mdh) related to the electron donor production, thereby declining the nitrogen removal efficiency. Network analysis further clarified the attenuate association between denitrifiers and denitrification-related genes in the plastic-exposed systems, elucidating that MPs and NPs restrained the nitrogen removal by inhibiting the contributions of microorganisms to nitrogen transformation processes. This study provides vital insights into the responses of the microbial community structure and nitrogen conversion processes to micro(nano)plastics disturbance in activated sludge systems.}, } @article {pmid37275543, year = {2023}, author = {Zheng, K and Dong, Y and Liang, Y and Liu, Y and Zhang, X and Zhang, W and Wang, Z and Shao, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M}, title = {Genomic diversity and ecological distribution of marine Pseudoalteromonas phages.}, journal = {Marine life science & technology}, volume = {5}, number = {2}, pages = {271-285}, pmid = {37275543}, issn = {2662-1746}, abstract = {UNLABELLED: Pseudoalteromonas, with a ubiquitous distribution, is one of the most abundant marine bacterial genera. It is especially abundant in the deep sea and polar seas, where it has been found to have a broad metabolic capacity and unique co-existence strategies with other organisms. However, only a few Pseudoalteromonas phages have so far been isolated and investigated and their genomic diversity and distribution patterns are still unclear. Here, the genomes, taxonomic features and distribution patterns of Pseudoalteromonas phages are systematically analyzed, based on the microbial and viral genomes and metagenome datasets. A total of 143 complete or nearly complete Pseudoalteromonas-associated phage genomes (PSAPGs) were identified, including 34 Pseudoalteromonas phage isolates, 24 proviruses, and 85 Pseudoalteromonas-associated uncultured viral genomes (UViGs); these were assigned to 47 viral clusters at the genus level. Many integrated proviruses (n = 24) and filamentous phages were detected (n = 32), suggesting the prevalence of viral lysogenic life cycle in Pseudoalteromonas. PSAPGs encoded 66 types of 249 potential auxiliary metabolic genes (AMGs) relating to peptidases and nucleotide metabolism. They may also participate in marine biogeochemical cycles through the manipulation of the metabolism of their hosts, especially in the phosphorus and sulfur cycles. Siphoviral and filamentous PSAPGs were the predominant viral lineages found in polar areas, while some myoviral and siphoviral PSAPGs encoding transposase were more abundant in the deep sea. This study has expanded our understanding of the taxonomy, phylogenetic and ecological scope of marine Pseudoalteromonas phages and deepens our knowledge of viral impacts on Pseudoalteromonas. It will provide a baseline for the study of interactions between phages and Pseudoalteromonas in the ocean.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-022-00160-z.}, } @article {pmid37938746, year = {2022}, author = {Palladino, G and Caroselli, E and Tavella, T and D'Amico, F and Prada, F and Mancuso, A and Franzellitti, S and Rampelli, S and Candela, M and Goffredo, S and Biagi, E}, title = {Correction to: Metagenomic shifts in mucus, tissue and skeleton of the coral Balanophyllia europaea living along a natural CO2 gradient.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {79}, doi = {10.1038/s43705-022-00165-w}, pmid = {37938746}, issn = {2730-6151}, } @article {pmid37938252, year = {2022}, author = {Palladino, G and Caroselli, E and Tavella, T and D'Amico, F and Prada, F and Mancuso, A and Franzellitti, S and Rampelli, S and Candela, M and Goffredo, S and Biagi, E}, title = {Metagenomic shifts in mucus, tissue and skeleton of the coral Balanophyllia europaea living along a natural CO2 gradient.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {65}, pmid = {37938252}, issn = {2730-6151}, abstract = {Using the Mediterranean coral Balanophyllia europaea naturally growing along a pH gradient close to Panarea island (Italy) as a model, we explored the role of host-associated microbiomes in coral acclimatization to ocean acidification (OA). Coral samples were collected at three sites along the gradient, mimicking seawater conditions projected for 2100 under different IPCC (The Intergovernmental Panel on Climate Change) scenarios, and mucus, soft tissue and skeleton associated microbiomes were characterized by shotgun metagenomics. According to our findings, OA induced functional changes in the microbiomes genetic potential that could mitigate the sub-optimal environmental conditions at three levels: i. selection of bacteria genetically equipped with functions related to stress resistance; ii. shifts in microbial carbohydrate metabolism from energy production to maintenance of cell membranes and walls integrity; iii. gain of functions able to respond to variations in nitrogen needs at the holobiont level, such as genes devoted to organic nitrogen mobilization. We hence provided hypotheses about the functional role of the coral associated microbiome in favoring host acclimatation to OA, remarking on the importance of considering the crosstalk among all the components of the holobiont to unveil how and to what extent corals will maintain their functionality under forthcoming ocean conditions.}, } @article {pmid37938275, year = {2021}, author = {Ponsero, AJ and Hurwitz, BL and Magain, N and Miadlikowska, J and Lutzoni, F and U'Ren, JM}, title = {Cyanolichen microbiome contains novel viruses that encode genes to promote microbial metabolism.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {56}, pmid = {37938275}, issn = {2730-6151}, abstract = {Lichen thalli are formed through the symbiotic association of a filamentous fungus and photosynthetic green alga and/or cyanobacterium. Recent studies have revealed lichens also host highly diverse communities of secondary fungal and bacterial symbionts, yet few studies have examined the viral component within these complex symbioses. Here, we describe viral biodiversity and functions in cyanolichens collected from across North America and Europe. As current machine-learning viral-detection tools are not trained on complex eukaryotic metagenomes, we first developed efficient methods to remove eukaryotic reads prior to viral detection and a custom pipeline to validate viral contigs predicted with three machine-learning methods. Our resulting high-quality viral data illustrate that every cyanolichen thallus contains diverse viruses that are distinct from viruses in other terrestrial ecosystems. In addition to cyanobacteria, predicted viral hosts include other lichen-associated bacterial lineages and algae, although a large fraction of viral contigs had no host prediction. Functional annotation of cyanolichen viral sequences predicts numerous viral-encoded auxiliary metabolic genes (AMGs) involved in amino acid, nucleotide, and carbohydrate metabolism, including AMGs for secondary metabolism (antibiotics and antimicrobials) and fatty acid biosynthesis. Overall, the diversity of cyanolichen AMGs suggests that viruses may alter microbial interactions within these complex symbiotic assemblages.}, } @article {pmid37273228, year = {2023}, author = {Liu, F and Li, R and Zhong, Y and Liu, X and Deng, W and Huang, X and Price, M and Li, J}, title = {Age-related alterations in metabolome and microbiome provide insights in dietary transition in giant pandas.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0025223}, pmid = {37273228}, issn = {2379-5077}, support = {KLSFGAGP2020.006//National Forestry and Grassland Administration (NFGA)/ ; }, mesh = {Animals ; *Ursidae/genetics ; RNA, Ribosomal, 16S/genetics ; Chromatography, Liquid ; Tandem Mass Spectrometry ; *Microbiota ; *Carnivora/genetics ; Metabolome ; Diet ; Bacteria/genetics ; Cellulose/metabolism ; }, abstract = {We conducted UPLC-MS-based metabolomics, 16S rRNA, and metagenome sequencing on the fecal samples of 44 captive giant pandas (Ailuropoda melanoleuca) from four age groups (i.e., Cub, Young, Adult, and Old) to comprehensively understand age-related changes in the metabolism and gut microbiota of giant pandas. We characterized the metabolite profiles of giant pandas based on 1,376 identified metabolites, with 152 significantly differential metabolites (SDMs) found across the age groups. We found that the metabolites and the composition/function of the gut microbiota changed in response to the transition from a milk-dominant diet in panda cubs to a bamboo-specific diet in young and adult pandas. Lipid metabolites such as choline and hippuric acid were enriched in the Cub group, and many plant secondary metabolites were significantly higher in the Young and Adult groups, while oxidative stress and inflammatory related metabolites were only found in the Old group. However, there was a decrease in the α-diversity of gut microbiota in adult and old pandas, who exclusively consume bamboo. The abundance of bacteria related to the digestion of cellulose-rich food, such as Firmicutes, Streptococcus, and Clostridium, significantly increased from the Cub to the Adult group, while the abundance of beneficial bacteria such as Faecalibacterium, Sarcina, and Blautia significantly decreased. Notably, several potential pathogenic bacteria had relatively high abundances, especially in the Young group. Metagenomic analysis identified 277 CAZyme genes including cellulose degrading genes, and seven of the CAZymes had abundances that significantly differed between age groups. We also identified 237 antibiotic resistance genes (ARGs) whose number and diversity increased with age. We also found a significant positive correlation between the abundance of bile acids and gut bacteria, especially Lactobacillus and Bifidobacterium. Our results from metabolome, 16S rRNA, and metagenome data highlight the important role of the gut microbiota-bile acid axis in the regulation of age-related metabolism and provide new insights into the lipid metabolism of giant pandas. IMPORTANCE The giant panda is a member of the order Carnivora but is entirely herbivorous. The giant panda's specialized diet and related metabolic mechanisms have not been fully understood. It is therefore crucial to investigate the dynamic changes in metabolites as giant pandas grow and physiologically adapt to their herbivorous diet. This study conducted UPLC-MS-based metabolomics 16S rRNA, and metagenome sequencing on the fecal samples of captive giant pandas from four age groups. We found that metabolites and the composition/function of gut microbiota changed in response to the transition from a milk-dominant diet in cubs to a bamboo-specific diet in young and adult pandas. The metabolome, 16S rRNA, and metagenome results highlight that the gut microbiota-bile acid axis has an important role in the regulation of age-related metabolism, and our study provides new insights into the lipid metabolism of giant pandas.}, } @article {pmid37272818, year = {2023}, author = {Wang, H and Ren, L and Liang, Y and Zheng, K and Guo, R and Liu, Y and Wang, Z and Han, Y and Zhang, X and Shao, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M}, title = {Psychrobacter Phage Encoding an Antibiotics Resistance Gene Represents a Novel Caudoviral Family.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0533522}, pmid = {37272818}, issn = {2165-0497}, mesh = {*Bacteriophages/genetics ; *Psychrobacter/genetics ; Phylogeny ; Phosphoadenosine Phosphosulfate ; DNA, Viral/genetics ; Genome, Viral ; Escherichia coli/genetics ; Open Reading Frames ; }, abstract = {Psychrobacter is an important bacterial genus that is widespread in Antarctic and marine environments. However, to date, only two complete Psychrobacter phage sequences have been deposited in the NCBI database. Here, the novel Psychrobacter phage vB_PmaS_Y8A, infecting Psychrobacter HM08A, was isolated from sewage in the Qingdao area, China. The morphology of vB_PmaS_Y8A was characterized by transmission electron microscopy, revealing an icosahedral head and long tail. The genomic sequence of vB_PmaS_Y8A is linear, double-stranded DNA with a length of 40,226 bp and 44.1% G+C content, and encodes 69 putative open reading frames. Two auxiliary metabolic genes (AMGs) were identified, encoding phosphoadenosine phosphosulfate reductase and MarR protein. The first AMG uses thioredoxin as an electron donor for the reduction of phosphoadenosine phosphosulfate to phosphoadenosine phosphate. MarR regulates multiple antibiotic resistance mechanisms in Escherichia coli and is rarely found in viruses. No tRNA genes were identified and no lysogeny-related feature genes were detected. However, many similar open reading frames (ORFs) were found in the host genome, which may indicate that Y8A also has a lysogenic stage. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analysis indicate that vB_PmaS_Y8A contains a novel genomic architecture similar only to that of Psychrobacter phage pOW20-A, although at a low similarity. vB_PmaS_Y8A represents a new family-level virus cluster with 22 metagenomic assembled viral genomes, here named Minviridae. IMPORTANCE Although Psychrobacter is a well-known and important bacterial genus that is widespread in Antarctic and marine environments, genetic characterization of its phages is still rare. This study describes a novel Psychrobacter phage containing an uncharacterized antibiotic resistance gene and representing a new virus family, Minviridae. The characterization provided here will bolster current understanding of genomes, diversity, evolution, and phage-host interactions in Psychrobacter populations.}, } @article {pmid37272792, year = {2023}, author = {Wu, X and Gushgari-Doyle, S and Lui, LM and Hendrickson, AJ and Liu, Y and Jagadamma, S and Nielsen, TN and Justice, NB and Simmons, T and Hess, NJ and Joyner, DC and Hazen, TC and Arkin, AP and Chakraborty, R}, title = {Distinct Depth-Discrete Profiles of Microbial Communities and Geochemical Insights in the Subsurface Critical Zone.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {6}, pages = {e0050023}, pmid = {37272792}, issn = {1098-5336}, mesh = {*Bacteria/metabolism ; *Microbiota ; Carbon/metabolism ; Tennessee ; }, abstract = {Microbial assembly and metabolic potential in the subsurface critical zone (SCZ) are substantially impacted by subsurface geochemistry and hydrogeology, selecting for microbes distinct from those in surficial soils. In this study, we integrated metagenomics and geochemistry to elucidate how microbial composition and metabolic potential are shaped and impacted by vertical variations in geochemistry and hydrogeology in terrestrial subsurface sediment. A sediment core from an uncontaminated, pristine well at Oak Ridge Field Research Center in Oak Ridge, Tennessee, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone, was used in this study. Our results showed that subsurface microbes were highly localized and that communities were rarely interconnected. Microbial community composition as well as metabolic potential in carbon and nitrogen cycling varied even over short vertical distances. Further analyses indicated a strong depth-related covariation of community composition with a subset of 12 environmental variables. An analysis of dissolved organic carbon (DOC) quality via ultrahigh resolution mass spectrometry suggested that the SCZ was generally a low-carbon environment, with the relative portion of labile DOC decreasing and that of recalcitrant DOC increasing along the depth, selecting microbes from copiotrophs to oligotrophs and also impacting the microbial metabolic potential in the carbon cycle. Our study demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolism in the SCZ. IMPORTANCE In this study, we explored the links between geochemical parameters, microbial community structure and metabolic potential across the depth of sediment, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone. Our results revealed that microbes in the terrestrial subsurface can be highly localized, with communities rarely being interconnected along the depth. Overall, our research demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolic potential in different depths of subsurface terrestrial sediment. Such studies correlating microbial community analyses and geochemistry analyses, including high resolution mass spectrometry analyses of natural organic carbon, will further the fundamental understanding of microbial ecology and biogeochemistry in subsurface terrestrial ecosystems and will benefit the future development of predictive models on nutrient turnover in these environments.}, } @article {pmid37272702, year = {2023}, author = {Lu, J and Wang, H and Wang, C and Zhao, M and Hou, R and Shen, Q and Yang, S and Ji, L and Liu, Y and Wang, X and Liu, S and Shan, T and Zhang, W}, title = {Gut phageome of the giant panda (Ailuropoda melanoleuca) reveals greater diversity than relative species.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0016123}, pmid = {37272702}, issn = {2379-5077}, support = {2022YFC2603801//MOST | National Key Research and Development Program of China (NKPs)/ ; 2020CPB-C11 and 2021CPB-B11//Chendu Research Base of Giant Panda Breeding/ ; no. 20210467//Donghai People's Hospital-School of Medicine UJS Joint Laboratory Foundation/ ; BE2017693//Jiangsu Provincial Key Research and Development Program (Key Technologies R&D Program of Jiangsu Province)/ ; HUDF2020105//The Youth Doctoral Scientific Research Foundation of Harbin University/ ; }, mesh = {Animals ; *Ursidae/microbiology ; Virome ; Phylogeny ; Metagenome ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages ; }, abstract = {The gut flora is a treasure house of diverse bacteriophages maintaining a harmonious and coexistent relationship with their hosts. The giant panda (Ailuropoda melanoleuca), as a vulnerable endemic species in China, has existed for millions of years and is regarded as a flagship species for biodiversity conservation. And yet, limited studies have analyzed the phage communities in the gut of giant pandas. Using viral metagenomic analysis, the phageomes of giant pandas and other relative species were investigated. Our study explored and compared the composition of phage communities from different animal sources. Giant pandas possessed more diverse and abundant phage communities in the gut compared with other relevant animals. Phylogenetic analyses based on the phage terminase large subunit (TerL) showed that the Caudovirales phages in giant pandas also presented highly genetic diversity. Our study revealed the diversity of phage communities in giant pandas and other relative species, contributing to the health maintenance of giant pandas and laying the groundwork for molecular evolution research of bacteriophages in mammals. IMPORTANCE Gut phageome plays an important role in shaping gut microbiomes by direct interactions with bacteria or indirect influences on the host immune system, potentially regulating host health and disease status. The giant panda (Ailuropoda melanoleuca) is a vulnerable and umbrella species for biodiversity conservation. Our work explored and compared the gut phageome of giant pandas and relative species, contributing to the health maintenance of giant pandas.}, } @article {pmid37271802, year = {2023}, author = {Rolon, ML and Tan, X and Chung, T and Gonzalez-Escalona, N and Chen, Y and Macarisin, D and LaBorde, LF and Kovac, J}, title = {The composition of environmental microbiota in three tree fruit packing facilities changed over seasons and contained taxa indicative of L. monocytogenes contamination.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {128}, pmid = {37271802}, issn = {2049-2618}, mesh = {Food Microbiology ; Fruit ; Seasons ; Longitudinal Studies ; Cross-Sectional Studies ; *Listeria monocytogenes/genetics ; *Microbiota/genetics ; Food Contamination/analysis ; }, abstract = {BACKGROUND: Listeria monocytogenes can survive in cold and wet environments, such as tree fruit packing facilities and it has been implicated in outbreaks and recalls of tree fruit products. However, little is known about microbiota that co-occurs with L. monocytogenes and its stability over seasons in tree fruit packing environments. In this 2-year longitudinal study, we aimed to characterize spatial and seasonal changes in microbiota composition and identify taxa indicative of L. monocytogenes contamination in wet processing areas of three tree fruit packing facilities (F1, F2, F3).

METHODS: A total of 189 samples were collected during two apple packing seasons from floors under the washing, drying, and waxing areas. The presence of L. monocytogenes was determined using a standard culturing method, and environmental microbiota was characterized using amplicon sequencing. PERMANOVA was used to compare microbiota composition among facilities over two seasons, and abundance-occupancy analysis was used to identify shared and temporal core microbiota. Differential abundance analysis and random forest were applied to detect taxa indicative of L. monocytogenes contamination. Lastly, three L. monocytogenes-positive samples were sequenced using shotgun metagenomics with Nanopore MinION, as a proof-of-concept for direct detection of L. monocytogenes' DNA in environmental samples.

RESULTS: The occurrence of L. monocytogenes significantly increased from 28% in year 1 to 46% in year 2 in F1, and from 41% in year 1 to 92% in year 2 in F3, while all samples collected from F2 were L. monocytogenes-positive in both years. Samples collected from three facilities had a significantly different microbiota composition in both years, but the composition of each facility changed over years. A subset of bacterial taxa including Pseudomonas, Stenotrophomonas, and Microbacterium, and fungal taxa, including Yarrowia, Kurtzmaniella, Cystobasidium, Paraphoma, and Cutaneotrichosporon, were identified as potential indicators of L. monocytogenes within the monitored environments. Lastly, the DNA of L. monocytogenes was detected through direct Nanopore sequencing of metagenomic DNA extracted from environmental samples.

CONCLUSIONS: This study demonstrated that a cross-sectional sampling strategy may not accurately reflect the representative microbiota of food processing facilities. Our findings also suggest that specific microorganisms are indicative of L. monocytogenes, warranting further investigation of their role in the survival and persistence of L. monocytogenes. Video Abstract.}, } @article {pmid37270585, year = {2023}, author = {Liu, S and Zeng, J and Yu, H and Wang, C and Yang, Y and Wang, J and He, Z and Yan, Q}, title = {Antimony efflux underpins phosphorus cycling and resistance of phosphate-solubilizing bacteria in mining soils.}, journal = {The ISME journal}, volume = {17}, number = {8}, pages = {1278-1289}, pmid = {37270585}, issn = {1751-7370}, mesh = {Antimony/analysis/chemistry ; Soil/chemistry ; Phosphates/analysis ; Phosphorus/analysis ; Phylogeny ; Environmental Monitoring ; *Soil Pollutants/analysis ; *Metals, Heavy/analysis ; Bacteria/genetics ; *Microbiota ; China ; Soil Microbiology ; }, abstract = {Microorganisms play crucial roles in phosphorus (P) turnover and P bioavailability increases in heavy metal-contaminated soils. However, microbially driven P-cycling processes and mechanisms of their resistance to heavy metal contaminants remain poorly understood. Here, we examined the possible survival strategies of P-cycling microorganisms in horizontal and vertical soil samples from the world's largest antimony (Sb) mining site, which is located in Xikuangshan, China. We found that total soil Sb and pH were the primary factors affecting bacterial community diversity, structure and P-cycling traits. Bacteria with the gcd gene, encoding an enzyme responsible for gluconic acid production, largely correlated with inorganic phosphate (Pi) solubilization and significantly enhanced soil P bioavailability. Among the 106 nearly complete bacterial metagenome-assembled genomes (MAGs) recovered, 60.4% carried the gcd gene. Pi transportation systems encoded by pit or pstSCAB were widely present in gcd-harboring bacteria, and 43.8% of the gcd-harboring bacteria also carried the acr3 gene encoding an Sb efflux pump. Phylogenetic and potential horizontal gene transfer (HGT) analyses of acr3 indicated that Sb efflux could be a dominant resistance mechanism, and two gcd-harboring MAGs appeared to acquire acr3 through HGT. The results indicated that Sb efflux could enhance P cycling and heavy metal resistance in Pi-solubilizing bacteria in mining soils. This study provides novel strategies for managing and remediating heavy metal-contaminated ecosystems.}, } @article {pmid37269991, year = {2023}, author = {Peng, K and Liu, YX and Sun, X and Wang, Q and Du, P and Zhang, Y and Wang, M and Wang, Z and Li, R}, title = {Long-read metagenomic sequencing reveals that high-copy small plasmids shape the highly prevalent antibiotic resistance genes in animal fecal microbiome.}, journal = {The Science of the total environment}, volume = {893}, number = {}, pages = {164585}, doi = {10.1016/j.scitotenv.2023.164585}, pmid = {37269991}, issn = {1879-1026}, mesh = {Animals ; Female ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Genes, Bacterial ; Chickens/genetics ; *Microbiota ; Drug Resistance, Multiple, Bacterial ; Plasmids ; }, abstract = {The emergence and prevalence of animal-derived antibiotic resistance genes (ARGs) pose a great threat to public health globally. Long-read metagenomic sequencing is increasingly being used to decipher the fate of environmental ARGs. However, the investigations of the distribution, co-occurrence patterns, and host information of animal-derived environmental ARGs with long-read metagenomic sequencing have received little attention. To cover the gap, we employed a novel QitanTech nanopore long-read metagenomic sequencing method to perform a comprehensive and systematic investigation of the microbial communities and antibiotic resistance profiles, as well as to analyze the host information and genetic structures of ARGs in the feces of laying hens. Our results showed that highly abundant and diverse ARGs were detected in the feces of different ages of laying hens, indicating that feeding animal feces was an important reservoir for the enrichment and maintenance of ARGs. The distribution pattern of chromosomal ARGs was more strongly associated with fecal microbial communities than plasmid-mediated ARGs. Further long-read host tracking analysis revealed that ARGs from Proteobacteria are commonly located on plasmids, whereas in Firmicutes, they are usually carried by chromosomes. Co-occurrence analysis displayed that co-selection phenomena of different ARGs were common occurrences and highly active insertion sequences (ISs) could result in the serious prevalence of many ARGs. Notably, small high-copy plasmids played a significant role in the dissemination of several ARGs, such as floR and tet(L), which could disturb the compositions of fecal ARGs. Overall, our findings significantly expand our knowledge of the comprehensive landscape of feeding animal feces resistome, which is important for the prevention and management of multi-drug resistant bacteria in laying hens.}, } @article {pmid37269417, year = {2023}, author = {Jiao, G and Huang, Y and Dai, H and Gou, H and Li, Z and Shi, H and Yang, J and Ni, S}, title = {Responses of rhizosphere microbial community structure and metabolic function to heavy metal coinhibition.}, journal = {Environmental geochemistry and health}, volume = {45}, number = {8}, pages = {6177-6198}, pmid = {37269417}, issn = {1573-2983}, support = {41977289//National Natural Science Foundation of China/ ; 2021YFQ0066//Sichuan Province Science and Technology Support Program/ ; 2020ZF11405//Everest Scientific Research Program/ ; SKLGP2021Z002//State Key Laboratory of Geological Disaster Prevention and Geological Environmental Protection Independent Project/ ; SKLGP2021Z002//State Key Laboratory of Geohazard Prevention and Geoenvironment Protection Independent Research Project/ ; }, mesh = {Humans ; Cadmium/analysis ; Rhizosphere ; *Metals, Heavy/analysis ; *Microbiota ; Soil/chemistry ; Zea mays/metabolism ; *Soil Pollutants/analysis ; Soil Microbiology ; }, abstract = {Metal mineral mining results in releases of large amounts of heavy metals into the environment, and it is necessary to better understand the response of rhizosphere microbial communities to simultaneous stress from multiple heavy metals (HMs), which directly impacts plant growth and human health. In this study, by adding different concentrations of cadmium (Cd) to a soil with high background concentrations of vanadium (V) and chromium (Cr), the growth of maize during the jointing stage was explored under limiting conditions. High-throughput sequencing was used to explore the response and survival strategies of rhizosphere soil microbial communities to complex HM stress. The results showed that complex HMs inhibited the growth of maize at the jointing stage, and the diversity and abundance of maize rhizosphere soil microorganisms were significantly different at different metal enrichment levels. In addition, according to the different stress levels, the maize rhizosphere attracted many tolerant colonizing bacteria, and cooccurrence network analysis showed that these bacteria interacted very closely. The effects of residual heavy metals on beneficial microorganisms (such as Xanthomonas, Sphingomonas, and lysozyme) were significantly stronger than those of bioavailable metals and soil physical and chemical properties. PICRUSt analysis revealed that the different forms of V and Cd had significantly greater effects on microbial metabolic pathways than all forms of Cr. Cr mainly affected the two major metabolic pathways: microbial cell growth and division and environmental information transmission. In addition, significant differences in rhizosphere microbial metabolism under different concentrations were found, and this can serve as a reference for subsequent metagenomic analysis. This study is helpful for exploring the threshold for the growth of crops in toxic HM soils in mining areas and achieving further biological remediation.}, } @article {pmid37267060, year = {2023}, author = {Du, B and Xiao, X and Wang, H and Li, W and Xia, Z and Yang, P and Huang, SK and Yuan, R and Liu, J and Han, M and Zou, Y and Zhu, J and He, D and Lyu, J and Jin, X and Xu, X and Wang, J and Yang, H and Xiao, L and Liu, X and Kristiansen, K}, title = {Evaluation of the Impact of BaP Exposure on the Gut Microbiota and Allergic Responses in an OVA-Sensitized Mouse Model.}, journal = {Environmental health perspectives}, volume = {131}, number = {6}, pages = {67004}, pmid = {37267060}, issn = {1552-9924}, mesh = {Humans ; Female ; Animals ; Mice ; *Gastrointestinal Microbiome ; Ovalbumin/pharmacology ; Caco-2 Cells ; *Hypersensitivity ; Inflammation ; Bacteria ; }, abstract = {BACKGROUND: Exposure to environmental pollutants, including benzo[a]pyrene (BaP), has been implicated in allergic diseases and intestinal microbiota homeostasis, but the environment-microbiota-immunity triangular relationship and to what extent BaP-induced remodeling of the gut microbiota contributes to intestinal allergic inflammation remain to be established.

OBJECTIVES: We investigated the impact of BaP on intestinal allergic inflammation and examined the relationship between this effect and gut microbiota dysbiosis. We explored the potential ability of intestinal bacteria to degrade BaP and alleviate cytotoxicity as a detoxification strategy to counteract the effects of BaP exposure.

METHODS: We combined microbiome shotgun metagenomics with animal histological and intestinal allergic inflammatory responses to assess the effects of BaP (50μg/mouse per day) in a 23-d toxicity test in antigen-induced allergic female mice. In addition, genome annotation, quantitative analysis of BaP, and in vitro cytotoxicity-tests using CaCo-2 cells were conducted to infer the role of intestinal bacteria in BaP detoxification.

RESULTS: BaP exposure impacted the taxonomic composition and the functional potential of the gut microbiota and aggravated antigen-induced intestinal allergic inflammatory responses. The level of inflammatory cytokines correlated with the abundance of specific bacterial taxa, including Lachnospiraceae bacterium 28-4 and Alistipes inops. We identified 614 bacteria harboring genes implicated in the degradation of BaP, and 4 of these bacterial strains were shown to significantly reduce the cytotoxicity of BaP to CaCo-2 cells in vitro.

DISCUSSION: Using allergic female mice as a model, we investigated the relationship between BaP, microbiota, and host immune reactions, highlighting the role of gut bacteria in BaP-aggravated allergic reactions. Our findings offer novel insight toward establishing the causal relationship between BaP exposure and the occurrence of allergic disorders. Identifying gut bacteria that degrade BaP may provide new strategies for ameliorating BaP cytotoxicity. https://doi.org/10.1289/EHP11874.}, } @article {pmid37264698, year = {2024}, author = {Bull, K and Davies, G and Jenkins, TP and Peachey, L}, title = {The faecal microbiome of Exmoor ponies shows step-wise compositional changes with increasing levels of management by humans.}, journal = {Equine veterinary journal}, volume = {56}, number = {1}, pages = {159-170}, doi = {10.1111/evj.13961}, pmid = {37264698}, issn = {2042-3306}, support = {//University of Bristol/ ; }, mesh = {Humans ; Horses/genetics ; Animals ; Female ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; *Microbiota ; Feces/chemistry ; Diet/veterinary ; }, abstract = {BACKGROUND: Horses can suffer from gastrointestinal (GI) disease in domestic environments, often precipitated by human-led changes in management. Understanding the consequences of these changes on equine gut microbiota is key to the prevention of such disease episodes.

OBJECTIVE: Profile the faecal microbiota of adult female Exmoor ponies under three management conditions, representing increasing levels of management by humans, encompassing different diets; whilst controlling for age, breed and sex.

STUDY DESIGN: Cross-sectional descriptive.

METHODS: Faecal samples were collected from three populations of Exmoor ponies kept under contrasting management conditions: 29 adult female ponies in groups with low management (LM) (n = 10), medium management (MM) (n = 10) and high management (HM) (n = 9) levels, based on diet, drug use, handling and exercise. Faecal microbial composition was profiled via high-throughput sequencing of the bacterial 16S rRNA gene, and functional metagenome predictions.

RESULTS: We observed profound step-wise changes in microbiome structure in the transition from LM to MM to HM. A relatively high abundance of Proteobacteria and Tenericutes was associated with the HM group; higher abundance of Methanobacteria was observed in the LM group. The MM group had intermediate levels of these taxa and exhibited high 'within group' variation in alpha diversity. Functional predictions revealed increased amino acid and lipid metabolism in HM; energy metabolism in LM and carbohydrate metabolism and immune/metabolic disease pathways in MM.

MAIN LIMITATIONS: Low group sizes, incomplete knowledge of bacterial genomes in equine gut microbiota and it was not possible to assess the relative impact of diet, drug use, handling and exercise on the microbiome as variables were confounded.

CONCLUSIONS: Human-led management factors had profound step-wise effects on faecal microbial composition. Based on functional metagenome predictions, we hypothesise that dietary differences between groups were the major driver of observed differences.}, } @article {pmid37264481, year = {2023}, author = {Liu, Y and Daniel, SG and Kim, HE and Koo, H and Korostoff, J and Teles, F and Bittinger, K and Hwang, G}, title = {Addition of cariogenic pathogens to complex oral microflora drives significant changes in biofilm compositions and functionalities.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {123}, pmid = {37264481}, issn = {2049-2618}, support = {R01 DE027970/DE/NIDCR NIH HHS/United States ; }, mesh = {Child, Preschool ; Humans ; Biofilms ; Candida albicans/genetics ; Cross-Sectional Studies ; *Dental Caries ; *Microbiota ; Streptococcus mutans/genetics ; Sugars/metabolism ; }, abstract = {BACKGROUND: Dental caries is a microbe and sugar-mediated biofilm-dependent oral disease. Of particular significance, a virulent type of dental caries, known as severe early childhood caries (S-ECC), is characterized by the synergistic polymicrobial interaction between the cariogenic bacterium, Streptococcus mutans, and an opportunistic fungal pathogen, Candida albicans. Although cross-sectional studies reveal their important roles in caries development, these exhibit limitations in determining the significance of these microbial interactions in the pathogenesis of the disease. Thus, it remains unclear the mechanism(s) through which the cross-kingdom interaction modulates the composition of the plaque microbiome. Here, we employed a novel ex vivo saliva-derived microcosm biofilm model to assess how exogenous pathogens could impact the structural and functional characteristics of the indigenous native oral microbiota.

RESULTS: Through shotgun whole metagenome sequencing, we observed that saliva-derived biofilm has decreased richness and diversity but increased sugar-related metabolism relative to the planktonic phase. Addition of S. mutans and/or C. albicans to the native microbiome drove significant changes in its bacterial composition. In addition, the effect of the exogenous pathogens on microbiome diversity and taxonomic abundances varied depending on the sugar type. While the addition of S. mutans induced a broader effect on Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog abundances with glucose/fructose, S. mutans-C. albicans combination under sucrose conditions triggered unique and specific changes in microbiota composition/diversity as well as specific effects on KEGG pathways. Finally, we observed the presence of human epithelial cells within the biofilms via confocal microscopy imaging.

CONCLUSIONS: Our data revealed that the presence of S. mutans and C. albicans, alone or in combination, as well as the addition of different sugars, induced unique alterations in both the composition and functional attributes of the biofilms. In particular, the combination of S. mutans and C. albicans seemed to drive the development (and perhaps the severity) of a dysbiotic/cariogenic oral microbiome. Our work provides a unique and pragmatic biofilm model for investigating the functional microbiome in health and disease as well as developing strategies to modulate the microbiome. Video Abstract.}, } @article {pmid37264459, year = {2023}, author = {Leung, MHY and Tong, X and Shen, Z and Du, S and Bastien, P and Appenzeller, BMR and Betts, RJ and Mezzache, S and Bourokba, N and Cavusoglu, N and Aguilar, L and Misra, N and Clavaud, C and Lee, PKH}, title = {Skin microbiome differentiates into distinct cutotypes with unique metabolic functions upon exposure to polycyclic aromatic hydrocarbons.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {124}, pmid = {37264459}, issn = {2049-2618}, mesh = {*Polycyclic Aromatic Hydrocarbons ; Skin/chemistry ; *Air Pollutants/analysis ; Biodegradation, Environmental ; *Microbiota/genetics ; Environmental Monitoring ; }, abstract = {BACKGROUND: The effects of air pollutants, particularly polycyclic aromatic hydrocarbons (PAHs), on the skin microbiome remain poorly understood. Thus, to better understand the interplay between air pollutants, microbiomes, and skin conditions, we applied metagenomics and metabolomics to analyze the effects of PAHs in air pollution on the skin microbiomes of over 120 subjects residing in two cities in China with different levels of air pollution.

RESULTS: The skin microbiomes differentiated into two cutotypes (termed 1 and 2) with distinct taxonomic, functional, resistome, and metabolite compositions as well as skin phenotypes that transcended geography and host factors. High PAH exposure was linked to dry skin and cutotype 2, which was enriched with species with potential biodegradation functions and had reduced correlation network structure integrity. The positive correlations identified between dominant taxa, key functional genes, and metabolites in the arginine biosynthesis pathway in cutotype 1 suggest that arginine from bacteria contributes to the synthesis of filaggrin-derived natural moisturizing factors (NMFs), which provide hydration for the skin, and could explain the normal skin phenotype observed. In contrast, no correlation with the arginine biosynthesis pathway was observed in cutotype 2, which indicates the limited hydration functions of NMFs and explains the observed dry skin phenotype. In addition to dryness, skin associated with cutotype 2 appeared prone to other adverse conditions such as inflammation.

CONCLUSIONS: This study revealed the roles of PAHs in driving skin microbiome differentiation into cutotypes that vary extensively in taxonomy and metabolic functions and may subsequently lead to variations in skin-microbe interactions that affect host skin health. An improved understanding of the roles of microbiomes on skin exposed to air pollutants can aid the development of strategies that harness microbes to prevent undesirable skin conditions. Video Abstract.}, } @article {pmid37264413, year = {2023}, author = {Lu, DC and Wang, FQ and Amann, RI and Teeling, H and Du, ZJ}, title = {Epiphytic common core bacteria in the microbiomes of co-located green (Ulva), brown (Saccharina) and red (Grateloupia, Gelidium) macroalgae.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {126}, pmid = {37264413}, issn = {2049-2618}, mesh = {*Seaweed/microbiology ; *Ulva/genetics/microbiology ; *Laminaria/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria ; *Rhodophyta/genetics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Macroalgal epiphytic microbial communities constitute a rich resource for novel enzymes and compounds, but studies so far largely focused on tag-based microbial diversity analyses or limited metagenome sequencing of single macroalgal species.

RESULTS: We sampled epiphytic bacteria from specimens of Ulva sp. (green algae), Saccharina sp. (brown algae), Grateloupia sp. and Gelidium sp. (both red algae) together with seawater and sediment controls from a coastal reef in Weihai, China, during all seasons. Using 16S rRNA amplicon sequencing, we identified 14 core genera (consistently present on all macroalgae), and 14 dominant genera (consistently present on three of the macroalgae). Core genera represented ~ 0.7% of all genera, yet accounted for on average 51.1% of the bacterial abundances. Plate cultivation from all samples yielded 5,527 strains (macroalgae: 4,426) representing 1,235 species (685 potentially novel). Sequencing of selected strains yielded 820 non-redundant draft genomes (506 potentially novel), and sequencing of 23 sampled metagenomes yielded 1,619 metagenome-assembled genomes (MAGs), representing further 1,183 non-redundant genomes. 230 isolates and 153 genomes were obtained from the 28 core/dominant genera. We analyzed the genomic potential of phycosphere bacteria to degrade algal polysaccharides and to produce bioactive secondary metabolites. We predicted 4,451 polysaccharide utilization loci (PULs) and 8,810 biosynthetic gene clusters (BGCs). These were particularly prevalent in core/dominant genera.

CONCLUSIONS: Our metabolic annotations and analyses of MAGs and genomes provide new insights into novel species of phycosphere bacteria and their ecological niches for an improved understanding of the macroalgal phycosphere microbiome. Video Abstract.}, } @article {pmid37263438, year = {2023}, author = {Phulpoto, AH and Pirzada, T and Kanhar, NA}, title = {Exploring community dynamics: Cultivable and uncultivable for the microbial-mediated bioremediation of oil-based paints polluted soil from aqueous media by Plackett-Burman statistically designed conditions.}, journal = {The Science of the total environment}, volume = {891}, number = {}, pages = {164505}, doi = {10.1016/j.scitotenv.2023.164505}, pmid = {37263438}, issn = {1879-1026}, mesh = {Biodegradation, Environmental ; RNA, Ribosomal, 16S/genetics ; *Soil ; Soil Microbiology ; Bacteria/metabolism ; *Soil Pollutants/metabolism ; }, abstract = {Oil-based paint seriously threatens biodiversity due to its complex composition and biocide toxicity. Therefore, it alters the microbial diversity abundance and in modern approaches like metagenomic, a powerful tool to get insight into pollutants effect on soil microbial community abundance. Thus, present study aimed at "exploring community dynamics: cultivable and uncultivable for the microbial-mediated bioremediation of oil-based paints polluted soil from aqueous media by Plackett-Burman statistical designed conditions". The total DNA from oil-based paints polluted soil was extracted by PowerSoil DNA Isolation Kit. The 16S rDNA genes were amplified using universal primers and PCR amplicons were sequenced for analysis of metagenomes to determine the bacterial microbiome abundance. A total 133,140 sequence reads, 2857 Operational Taxonomic Units (OTUs) of 16S rRNA genes, and 30 bacterial phyla were retrieved from all the oil-based paints polluted samples (C, R498, B698 and G492) with the significant increase in Firmicutes (18.90 %, 52.39 %, 49.75 %, 44.36 %) and Actinobacteria (26.66 %, 28.93 %, 28.17 %, 14.68 %) whereas a decrease in Proteobacteria (19.53 %, 6.32 %, 9.37 %, 16.21 %), Chloroflexi (16.93 %, 8.71 %, 9.78 %, 18.17 %), and Bacteroidetes (8.96 %, 0.36 %, 0.41 %, 0.11 %) was recorded respectively. Additionally, the 100 % removal of oil-based paints (R498, B698 and G492) was achieved by the cultivable microbial consortia in laboratory settings. On the other hand for the R498 single cultivable pure isolates exhibited biodegradation potential as "PDB20, 91 %", "PDB14, 81 %", and "PDB16, 87 %" while for the blue B698, "PDB4, 86 %", "PDB20, 89 %", "PDB5, and PDB2, 80%". Moreover, in case of G492, maximum % removal was achieved with "PDB20, 93 %", "PDB5, 90 %", "PDB6, 90 %", "PDB16, 88 %", "PDB2, and PDB4, 89%". Conclusively, in comparison to R498 and B698, maximum percent removal was displayed by G492 and this might be attributed due to difference in pigment. Cultivable consortia and individual pure isolates demonstrated >80 % contribution in the % removal of oil-based paints.}, } @article {pmid37261715, year = {2023}, author = {Andrianjakarivony, FH and Bettarel, Y and Desnues, C}, title = {Searching for a Reliable Viral Indicator of Faecal Pollution in Aquatic Environments.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {61}, number = {6}, pages = {589-602}, pmid = {37261715}, issn = {1976-3794}, mesh = {Humans ; Ecosystem ; Reproducibility of Results ; Water Microbiology ; *Bacteriophages/genetics ; *Viruses/genetics ; Bacteria ; Feces/microbiology ; Environmental Monitoring/methods ; }, abstract = {The disposal of sewage in significant quantities poses a health hazard to aquatic ecosystems. These effluents can contain a wide range of pathogens, making faecal contamination a leading source of waterborne diseases around the world. Yet monitoring bacteria or viruses in aquatic environments is time consuming and expensive. The standard indicators of faecal pollution all have limitations, including difficulty in determining the source due to lack of host specificity, poor connection with the presence of non-bacterial pathogens, or low environmental persistence. Innovative monitoring techniques are sorely needed to provide more accurate and targeted solutions. Viruses are a promising alternative to faecal indicator bacteria for monitoring, as they are more persistent in ambient water, more abundant in faeces, and are extremely host-specific. Given the range of viruses found in diverse contexts, it is not easy to find one "ideal" viral indicator of faecal pollution; however, several are of interest. In parallel, the ongoing development of molecular techniques coupled with metagenomics and bioinformatics should enable improved ways to detect faecal contamination using viruses. This review examines the evolution of faecal contamination monitoring with the following aims (i) to identify the characteristics of the main viral indicators of faecal contamination, including human enteric viruses, bacteriophages, CRESS and plant viruses, (ii) to assess how these have been used to monitor water pollution in recent years, (iii) to evaluate the reliability of recent detection methods of such viruses, and (iv) to tentatively determine which viruses may be most effective as markers of faecal pollution.}, } @article {pmid37261381, year = {2023}, author = {Shao, Z and Shan, X and Jing, L and Wang, W and Li, W and Ren, Z and Zhang, BN and Huang, Y}, title = {Metagenome Investigation of Ocular Microbiota of Cataract Patients With and Without Type 2 Diabetes.}, journal = {Translational vision science & technology}, volume = {12}, number = {6}, pages = {1}, pmid = {37261381}, issn = {2164-2591}, mesh = {Humans ; Bacteria/genetics ; *Cataract/complications/genetics ; Conjunctiva ; *Diabetes Mellitus, Type 2/complications/epidemiology/genetics ; Metagenome/genetics ; *Microbiota/genetics ; Male ; Female ; }, abstract = {PURPOSE: Our objective was to investigate differences in the ocular surface bacterial composition in cataract patients with and without type 2 diabetes (T2D).

METHODS: Twenty-four diabetic patients with cataracts (group D) and 14 sex- and age-matched patients with age-related cataracts (group N) were recruited for this study. All samples underwent DNA extraction, fragmentation, purification, library construction, and metagenomic sequencing.

RESULTS: The overall conjunctival sac bacterial composition was similar between group D and group N, as determined by alpha diversity and beta diversity. Nevertheless, significant differences were observed in the relative abundance of specific bacteria. At the phylum level, group D had a significantly lower abundance of Chlamydiae, Tenericutes, Chloroflexi, Cyanobacteria, Cossaviricota, Chytridiomycota, Artverviricota, Zoopagomycota, Peploviricota, Deinococcus-Thermus, Preplasmiviricota, and Nucleocytoviricota. At the genus level, group D had a significantly lower abundance of Chlamydia, Mycoplasma, Salmonella, Chryseobacterium, Roseovarius, Desulfococcus, Kangiella, Anaerococcus, and Idiomarina but a significantly higher abundance of Parabacteroides, Phocaeicola, and Sphingomonas. Bacteria such as Aquificae, Parabacteroides, Flavobacterium, Austwickia, Aquifex, Tenacibaculum, and Chryseobacterium in group D and Tenericutes, Chlamydiae, Porphyromonas, Mycoplasma, Chlamydia, Kangiella, Idiomarina, Roseovarius, Aliiroseovarius, and Desulfococcus in group N could be used as conjunctival sac biomarkers, according to the linear discriminant analysis effect size. Gene Ontology functional annotation indicated that bacterial catalytic activity, metabolic processes, locomotion, virion, and reproduction were enriched in group D, while immune system processes were enriched in group N. In addition, the top 30 differentially expressed virulence factors (VFs) were all more enriched in group D.

CONCLUSIONS: The bacterial composition was similar between the two groups. Several bacterial strains that were reported beneficial in gut were decreased, and pathogenic bacteria were increased in T2D. Furthermore, group D had more active bacterial terms and increased VF expression, suggesting that the susceptibility of diabetic patients to infection is closely related to functional changes in the ocular surface flora. Our conjunctival microbiota atlas provides a reference for investigating ocular complications related to diabetes.

TRANSLATIONAL RELEVANCE: The altered composition and functional profile of the ocular microbial community in diabetic patients offer evidence for the need to prevent infection during cataract surgery.}, } @article {pmid37260707, year = {2023}, author = {Li, X and Yi, Y and Wu, T and Chen, N and Gu, X and Xiang, L and Jiang, Z and Li, J and Jin, H}, title = {Integrated microbiome and metabolome analysis reveals the interaction between intestinal flora and serum metabolites as potential biomarkers in hepatocellular carcinoma patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1170748}, pmid = {37260707}, issn = {2235-2988}, mesh = {Humans ; *Carcinoma, Hepatocellular/diagnosis ; *Liver Neoplasms/diagnosis ; *Gastrointestinal Microbiome ; Quality of Life ; Metabolome ; Biomarkers ; Liver Cirrhosis/diagnosis ; Biomarkers, Tumor ; }, abstract = {Globally, liver cancer poses a serious threat to human health and quality of life. Despite numerous studies on the microbial composition of the gut in hepatocellular carcinoma (HCC), little is known about the interactions of the gut microbiota and metabolites and their role in HCC. This study examined the composition of the gut microbiota and serum metabolic profiles in 68 patients with HCC, 33 patients with liver cirrhosis (LC), and 34 healthy individuals (NC) using a combination of metagenome sequencing and liquid chromatography-mass spectrometry (LC-MS). The composition of the serum metabolites and the structure of the intestinal microbiota were found to be significantly altered in HCC patients compared to non-HCC patients. LEfSe and metabolic pathway enrichment analysis were used to identify two key species (Odoribacter splanchnicus and Ruminococcus bicirculans) and five key metabolites (ouabain, taurochenodeoxycholic acid, glycochenodeoxycholate, theophylline, and xanthine) associated with HCC, which then were combined to create panels for HCC diagnosis. The study discovered that the diagnostic performance of the metabolome was superior to that of the microbiome, and a panel comprised of key species and key metabolites outperformed alpha-fetoprotein (AFP) in terms of diagnostic value. Spearman's rank correlation test was used to determine the relationship between the intestinal flora and serum metabolites and their impact on hepatocarcinogenesis and progression. A random forest model was used to assess the diagnostic performance of the different histologies alone and in combination. In summary, this study describes the characteristics of HCC patients' intestinal flora and serum metabolism, demonstrates that HCC is caused by the interaction of intestinal flora and serum metabolites, and suggests that two key species and five key metabolites may be potential markers for the diagnosis of HCC.}, } @article {pmid37260265, year = {2023}, author = {Hosszu-Fellous, K and Zanella, MC and Kaiser, L and Neofytos, D}, title = {The present and future of blood virome in allogeneic hematopoietic cell transplant recipients.}, journal = {Current opinion in infectious diseases}, volume = {36}, number = {4}, pages = {243-249}, doi = {10.1097/QCO.0000000000000928}, pmid = {37260265}, issn = {1473-6527}, mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Transplant Recipients ; Virome ; Immunosuppression Therapy ; }, abstract = {PURPOSE OF REVIEW: Allogeneic hematopoietic cell transplantation (allogeneic HCT) is a highly effective therapy for a broad range of hematological diseases and its use is increasing worldwide. Despite advances in antiviral prophylaxis and treatment, viral infections are still one of the leading causes of post-HCT morbidity and mortality. In this patient population, metagenomic next-generation sequencing (mNGS) revealed a much larger diversity of viruses than previously suspected via the targeted screening approach. In the context of profound immunosuppression, these viral infections may cause transient viremia or protracted replication and potentially be associated with yet unrecognized or unspecific clinical manifestations. On the contrary, by constantly interacting with the immune system, viral infections may have a significant impact on posttransplant outcomes. Here, we review the latest advances in research assessing the role of the blood virome in the development of post-HCT complications.

RECENT FINDINGS: Research efforts are under way to uncover the potential role of several previously undetected viruses in the development of allogeneic HCT complications and their impact on transplant outcomes.

SUMMARY: The identification of viral actors impacting post-HCT morbidity and survival is key to optimize monitoring and infection prevention/treatment strategies.}, } @article {pmid37260140, year = {2023}, author = {Zhang, H and Jin, K and Xiong, K and Jing, W and Pang, Z and Feng, M and Cheng, X}, title = {Disease-associated gut microbiome and critical metabolomic alterations in patients with colorectal cancer.}, journal = {Cancer medicine}, volume = {12}, number = {14}, pages = {15720-15735}, pmid = {37260140}, issn = {2045-7634}, mesh = {*Microbiota/genetics ; *Gastrointestinal Microbiome ; Carcinogenesis ; Bacteria/genetics ; Fusobacterium ; Humans ; *Colorectal Neoplasms/pathology ; }, abstract = {BACKGROUND: Gut microbiota plays a significant role in the colorectal cancer (CRC) process. Ectopic colonization of multiple oral bacteria is reportedly associated with CRC pathogenesis and progression, but the details remain unclear.

METHODS: We enrolled a cohort of 50 CRC patients and 52 healthy controls from an East China population. Taxonomic and functional analysis of the fecal microbiota were performed using 16S rDNA (50 + 52 samples) and shotgun metagenomic sequencing (8 + 6 samples), respectively, with particular attention paid to gut-colonized oral bacteria.

RESULTS AND CONCLUSIONS: The results showed more detected bacterial species but lower species evenness within the samples from CRC patients. To determine the specific bacteria enriched in each group, we analyzed their possible protective, carcinogenic, or opportunistic roles in the CRC process. Among the ectopic oral bacteria, we observed a significant increase in the abundance of Fusobacterium and decreased abundance of Prevotella and Ruminococcus in the CRC group. Main differences in the functional composition of these two groups were related to energy metabolism and biosynthesis, especially the glycolytic pathway. Furthermore, we validated the colonization of Fusobacterium nucleatum subsp. animalis within CRC tissues and studied its impact on the host intestinal epithelium and tumor cells. With high selectivity for cancerous tissues, this subspecies promoted CRC cell proliferation and induced potential DNA damage.}, } @article {pmid37259063, year = {2023}, author = {Ormaasen, I and Rudi, K and Diep, DB and Snipen, L}, title = {Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {295}, pmid = {37259063}, issn = {1471-2164}, mesh = {*Metagenome ; Humans ; Child, Preschool ; Child ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Aged ; Aged, 80 and over ; Data Mining ; *Gastrointestinal Microbiome/drug effects ; Bacteriocins/pharmacology ; Genome ; }, abstract = {BACKGROUND: Our knowledge about the ecological role of bacterial antimicrobial peptides (bacteriocins) in the human gut is limited, particularly in relation to their role in the diversification of the gut microbiota during early life. The aim of this paper was therefore to address associations between bacteriocins and bacterial diversity in the human gut microbiota. To investigate this, we did an extensive screening of 2564 healthy human gut metagenomes for the presence of predicted bacteriocin-encoding genes, comparing bacteriocin gene presence to strain diversity and age.

RESULTS: We found that the abundance of bacteriocin genes was significantly higher in infant-like metagenomes (< 2 years) compared to adult-like metagenomes (2-107 years). By comparing infant-like metagenomes with and without a given bacteriocin, we found that bacteriocin presence was associated with increased strain diversities.

CONCLUSIONS: Our findings indicate that bacteriocins may play a role in the strain diversification during the infant gut microbiota establishment.}, } @article {pmid37258870, year = {2023}, author = {Yung, PYM and Tan, SM}, title = {Targeted Enrichment of Low-Abundance and Uncharacterized Taxon Members in Complex Microbial Community with Primer-Free FISH Probes Designed from Next Generation Sequencing Dataset.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {303-315}, pmid = {37258870}, issn = {1940-6029}, mesh = {*High-Throughput Nucleotide Sequencing ; In Situ Hybridization, Fluorescence/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Methods to obtain high-quality assembled genomic information of rare and unclassified member species in complex microbial communities remain a high priority in microbial ecology. Additionally, the supplementation of three-dimensional spatial information that highlights the morphology and spatial interaction would provide additional insights to its ecological role in the community. Fluorescent in-situ hybridization (FISH) coupling with fluorescence-activated cell sorting (FACS) is a powerful tool that enables the detection, visualization, and separation of low-abundance microbial members in samples containing complex microbial compositions. Here, we have described the workflow from designing the appropriate FISH probes from metagenomics or metatranscriptomics datasets to the preparation and treatment of samples to be used in FISH-FACS procedures.}, } @article {pmid37258866, year = {2023}, author = {Arumugam, K and Bessarab, I and Haryono, MAS and Williams, RBH}, title = {Recovery and Analysis of Long-Read Metagenome-Assembled Genomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {235-259}, pmid = {37258866}, issn = {1940-6029}, mesh = {*Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Sequence Analysis, DNA/methods ; Base Sequence ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {The development of long-read nucleic acid sequencing is beginning to make very substantive impact on the conduct of metagenome analysis, particularly in relation to the problem of recovering the genomes of member species of complex microbial communities. Here we outline bioinformatics workflows for the recovery and characterization of complete genomes from long-read metagenome data and some complementary procedures for comparison of cognate draft genomes and gene quality obtained from short-read sequencing and long-read sequencing.}, } @article {pmid37258863, year = {2023}, author = {Jadeja, NB and Kapley, A}, title = {Designing Knowledge-Based Bioremediation Strategies Using Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {195-208}, pmid = {37258863}, issn = {1940-6029}, mesh = {Biodegradation, Environmental ; *Metagenomics/methods ; Wastewater ; *Microbiota ; Metagenome ; }, abstract = {Functional capacities for bioremediation are governed by metabolic mechanisms of inhabiting microbial communities at polluted niches. Process fluctuations lead to stress scenarios where microbes evolve continuously to adapt to sustain the harsh conditions. The biological wastewater treatment (WWT) process harbors the potential of these catabolic microbes for the degradation of organic molecules. In a typical biological WWT or soil bioremediation process, several microbial species coexist which code for enzymes that degrade complex compounds.High throughput DNA sequencing techniques for microbiome analysis in bioremediation processes have led to a powerful paradigm revealing the significance of metabolic functions and microbial diversity. The present chapter describes techniques in taxonomy and functional gene analysis for understanding bioremediation potential and novel strategies built on in silico analysis for the improvisation of existing aerobic wastewater treatment methods. Methods explaining comparative metagenomics by Metagenome Analysis server (MG-RAST) are described with successful case studies by focusing on industrial wastewaters and soil bioremediation studies.}, } @article {pmid37258862, year = {2023}, author = {Arumugam, R and Ravichandran, P and Yeap, SK and Sharma, RSK and Zulkifly, SB and Yawah, D and Annavi, G}, title = {Application of High-Throughput Sequencing (HTS) to Enhance the Well-Being of an Endangered Species (Malayan Tapir): Characterization of Gut Microbiome Using MG-RAST.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {175-194}, pmid = {37258862}, issn = {1940-6029}, mesh = {Animals ; *Endangered Species ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Animals, Wild ; High-Throughput Nucleotide Sequencing ; }, abstract = {The Tapirus indicus, also known as Malayan tapir, has been listed as a rapidly declining animal species in the past decades, along with being declared and categorized as an endangered species by the International Union for Conservation of Nature (IUCN) 2016. This tapir species is geographically distributed across several countries in Southeast Asia such as Peninsular Malaysia, Indonesia (Sumatra), South Thailand, and Myanmar. Amongst these countries, the Peninsula Malaysia forest is recorded to contain the highest number of Malayan tapir population. Unfortunately, in the past decades, the population of Malayan tapirs has declined swiftly due to serious deforestation, habitat fragmentation, and heavy vehicle accidents during road crossings at forest routes. Concerned by this predicament, the Department of Wildlife and National Parks (DWNP) Peninsular Malaysia collaborated with a few local universities to conduct various studies aimed at increasing the population number of tapirs in Malaysia. Several studies were conducted with the aim of enhancing the well-being of tapirs in captivity. Veterinarians face problems when it comes to selecting healthy and suitable tapirs for breeding programs at conservation centers. Conventional molecular methods using high-throughput sequencing provides a solution in determining the health condition of Malayan tapirs using the Next-Generation Sequencing (NGS) technology. Unaware by most, gut microbiome plays an important role in determining the health condition of an organism by various aspects: (1) digestion control; (2) benefiting the immune system; and (3) playing a role as a "second brain." Commensal gut bacterial communities (microbiomes) are predicted to influence organism health and disease. Imbalance of unhealthy and healthy microbes in the gut may contribute to weight gain, high blood sugar, high cholesterol, and other disorders. In infancy, neonatal gut microbiomes are colonized with maternal and environmental flora, and mature toward a stable composition in two to three years. Interactions between the microorganism communities and the host allow for the establishment of microbiological roles. Identifying the core microbiome(s) are essential in the prediction of diseases and changes in environmental behavior of microorganisms. The dataset of 16S rRNA amplicon sequencing of Malayan tapir was deposited in the MG-RAST portal. Parameters such as quality control, taxonomic prediction (unknown and predicted), diversity (rarefaction), and diversity (alpha) were analyzed using sequencing approaches (Amplicon sequencing). Comparisons of parameters, according to the type of sequencing, showed significant differences, except for the prediction variable. In the Amplicon sequencing datasets, the parameters Rarefaction and Unknown had the highest correlation, while Alpha and Predicted had the lowest. Firmicutes, Bacteroidetes, Proteobacteria, Bacilli, and Bacteroidia were the most representative genera in Malayan tapir amplicon sequences, which indicated that most of the tapirs were healthy. However, continuous assessment to maintain the well-being of tapir for long term is still required. This chapter focuses on the introduction of 16S rRNA amplicon metagenomics in analyzing Malayan tapir gut microbiome dataset.}, } @article {pmid37258861, year = {2023}, author = {Abdelsalam, NA and Elshora, H and El-Hadidi, M}, title = {Interactive Web-Based Services for Metagenomic Data Analysis and Comparisons.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {133-174}, pmid = {37258861}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; Metagenome ; *Microbiota/genetics ; Ecology ; Computational Biology/methods ; Data Analysis ; }, abstract = {Recently, sequencing technologies have become readily available, and scientists are more motivated to conduct metagenomic research to unveil the potential of a myriad of ecosystems and biomes. Metagenomics studies the composition and functions of microbial communities and paves the way to multiple applications in medicine, industry, and ecology. Nonetheless, the immense amount of sequencing data of metagenomics research and the few user-friendly analysis tools and pipelines carry a new challenge to the data analysis.Web-based bioinformatics tools are now being developed to facilitate the analysis of complex metagenomic data without prior knowledge of any programming languages or special installation. Specialized web tools help answer researchers' main questions on the taxonomic classification, functional capabilities, discrepancies between two ecosystems, and the probable functional correlations between the members of a specific microbial community. With an Internet connection and a few clicks, researchers can conveniently and efficiently analyze the metagenomic datasets, summarize results, and visualize key information on the composition and the functional potential of metagenomic samples under study. This chapter provides a simple guide to a few of the fundamental web-based services used for metagenomic data analyses, such as BV-BRC, RDP, MG-RAST, MicrobiomeAnalyst, METAGENassist, and MGnify.}, } @article {pmid37258860, year = {2023}, author = {Gautam, A and Zeng, W and Huson, DH}, title = {DIAMOND + MEGAN Microbiome Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {107-131}, pmid = {37258860}, issn = {1940-6029}, mesh = {*Software ; *Microbiota/genetics ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; Databases, Factual ; Metagenome ; Algorithms ; }, abstract = {Metagenomics is the study of microbiomes using DNA sequencing technologies. Basic computational tasks are to determine the taxonomic composition (who is out there?), the functional composition (what can they do?), and also to correlate changes of composition to changes in external parameters (how do they compare?). One approach to address these issues is to first align all sequences against a protein reference database such as NCBI-nr and to then perform taxonomic and functional binning of all sequences based on their alignments. The resulting classifications can then be interactively analyzed and compared. Here we illustrate how to pursue this approach using the DIAMOND+MEGAN pipeline, on two different publicly available datasets, one containing short-read samples and other containing long-read samples.}, } @article {pmid37258857, year = {2023}, author = {Wang, D}, title = {Metagenomics Databases for Bacteria.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {55-67}, pmid = {37258857}, issn = {1940-6029}, mesh = {Phylogeny ; *Metagenomics ; Bacteria/genetics ; Databases, Genetic ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The booming sequencing technologies have turned metagenomics into a widely used tool for microbe-related studies, especially in the areas of clinical medicine and ecology. Accordingly, the toolkit of metagenomics data analysis is growing stronger to provide multiple approaches for solving various biological questions and understanding the component and function of microbiome. As part of the toolkit, metagenomics databases play a central role in the creation and maintenance of processed data such as definition of taxonomic classifications, annotation of gene functions, sequence alignment, and phylogenetic tree inference. The availability of a large quantity of high-quality bacterial genomic sequences contributes significantly to the construction and update of metagenomics databases, which constitute the core resource for metagenomics data analysis at various scales. This chapter presents the key concepts, technical options, and challenges for metagenomics projects as well as the curation processes and versatile functions for the four representative bacterial metagenomics databases, including Greengenes, SILVA, Ribosomal Database Project (RDP), and Genome Taxonomy Database (GTDB).}, } @article {pmid37258856, year = {2023}, author = {Gihawi, A and Cardenas, R and Hurst, R and Brewer, DS}, title = {Quality Control in Metagenomics Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {21-54}, pmid = {37258856}, issn = {1940-6029}, mesh = {Reproducibility of Results ; *Metagenomics/methods ; Computational Biology/methods ; *Microbiota ; Research Design ; }, abstract = {Experiments involving metagenomics data are become increasingly commonplace. Processing such data requires a unique set of considerations. Quality control of metagenomics data is critical to extracting pertinent insights. In this chapter, we outline some considerations in terms of study design and other confounding factors that can often only be realized at the point of data analysis.In this chapter, we outline some basic principles of quality control in metagenomics, including overall reproducibility and some good practices to follow. The general quality control of sequencing data is then outlined, and we introduce ways to process this data by using bash scripts and developing pipelines in Snakemake (Python).A significant part of quality control in metagenomics is in analyzing the data to ensure you can spot relationships between variables and to identify when they might be confounded. This chapter provides a walkthrough of analyzing some microbiome data (in the R statistical language) and demonstrates a few days to identify overall differences and similarities in microbiome data. The chapter is concluded by discussing remarks about considering taxonomic results in the context of the study and interrogating sequence alignments using the command line.}, } @article {pmid37258855, year = {2023}, author = {Benz, S and Mitra, S}, title = {From Genomics to Metagenomics in the Era of Recent Sequencing Technologies.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {1-20}, pmid = {37258855}, issn = {1940-6029}, mesh = {Humans ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Genomics ; *Microbiota/genetics ; Metagenome ; }, abstract = {Metagenomics, also known as environmental genomics, is the study of the genomic content of a sample of organisms obtained from a common habitat. Metagenomics and other "omics" disciplines have captured the attention of researchers for several decades. The effect of microbes in our body is a relevant concern for health studies. Through sampling the sequences of microbial genomes within a certain environment, metagenomics allows study of the functional metabolic capacity of a community as well as its structure based upon distribution and richness of species. Exponentially increasing number of microbiome literatures illustrate the importance of sequencing techniques which have allowed the expansion of microbial research into areas, including the human gut, antibiotics, enzymes, and more. This chapter illustrates how metagenomics field has evolved with the progress of sequencing technologies.Further, from this chapter, researchers will be able to learn about all current options for sequencing techniques and comparison of their cost and read statistics, which will be helpful for planning their own studies.}, } @article {pmid37258543, year = {2023}, author = {Liu, J and Sun, J and Yu, J and Chen, H and Zhang, D and Zhang, T and Ma, Y and Zou, C and Zhang, Z and Ma, L and Yu, X}, title = {Gut microbiome determines therapeutic effects of OCA on NAFLD by modulating bile acid metabolism.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {29}, pmid = {37258543}, issn = {2055-5008}, mesh = {Mice ; Animals ; *Non-alcoholic Fatty Liver Disease/drug therapy/metabolism ; *Gastrointestinal Microbiome ; Chenodeoxycholic Acid/pharmacology/therapeutic use ; Bile Acids and Salts ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD), the most common chronic liver disease, had no approved pharmacological agents yet. Obeticholic acid (OCA), a novel bile acid derivative, was demonstrated to ameliorate NAFLD-related manifestations. Regarding the role of gut-liver axis in liver disease development, this study aimed to explore the potential role of gut microbiota in the treatment of OCA in NAFLD mice induced by the high-fat diet (HFD). Antibiotic-induced microbiome depletion (AIMD) and fecal microbiota transplantation (FMT) confirmed the critical role of gut microbiota in OCA treatment for NAFLD by effectively alleviating histopathological lesions and restoring liver function impaired by HFD. Metagenomic analysis indicated that OCA intervention in HFD mice remarkably increased the abundance of Akkermansia muciniphila, Bifidobacterium spp., Bacteroides spp., Alistipes spp., Lactobacillus spp., Streptococcus thermophilus, and Parasutterella excrementihominis. Targeted metabolomics analysis indicated that OCA could modulate host bile acids pool by reducing levels of serum hydrophobic cholic acid (CA) and chenodeoxycholic acid (CDCA), and increasing levels of serum-conjugated bile acids, such as taurodeoxycholic acid (TDCA) and tauroursodesoxycholic acid (TUDCA) in the HFD-fed mice. Strong correlations were observed between differentially abundant microbes and the shifted bile acids. Furthermore, bacteria enriched by OCA intervention exhibited much greater potential in encoding 7alpha-hydroxysteroid dehydrogenase (7α-HSDs) producing secondary bile acids rather than bile salt hydrolases (BSHs) mainly responsible for primary bile acid deconjugation. In conclusion, this study demonstrated that OCA intervention altered gut microbiota composition with specially enriched gut microbes modulating host bile acids, thus effectively alleviating NAFLD in the mice.}, } @article {pmid37257865, year = {2024}, author = {Favale, N and Farina, R and Carrieri, A and Simonelli, A and Severi, M and Sabbioni, S and Trombelli, L and Scapoli, C}, title = {Functional profile of oral plaque microbiome: Further insight into the bidirectional relationship between type 2 diabetes and periodontitis.}, journal = {Molecular oral microbiology}, volume = {39}, number = {2}, pages = {62-79}, doi = {10.1111/omi.12418}, pmid = {37257865}, issn = {2041-1014}, support = {//Research Centre for the Study of Periodontal and Peri-implant Diseases, University of Ferrara, Italy/ ; FIR2017//University of Ferrara, Italy/ ; FAR2018-2019//University of Ferrara, Italy/ ; }, mesh = {Humans ; *Diabetes Mellitus, Type 2/complications ; *Periodontitis ; *Microbiota/genetics ; *Periodontal Diseases ; *Dental Plaque ; Inflammation ; }, abstract = {Increasing evidence support the association between the oral microbiome and human systemic diseases. This association may be attributed to the ability of many oral microbes to influence the inflammatory microenvironment. Herein, we focused our attention on the bidirectional relationship between periodontitis and type 2 diabetes using high-resolution whole metagenomic shotgun analysis to explore the composition and functional profile of the subgingival microbiome in diabetics and non-diabetics subjects with different periodontal conditions. In the present study, the abundance of metabolic pathways encoded by oral microbes was reconstructed from the metagenome, and we identified a set of dysregulated metabolic pathways significantly enriched in the periodontitis and/or diabetic patients. These pathways were mainly involved in branched and aromatic amino acids metabolism, fatty acid biosynthesis and adipocytokine signaling pathways, ferroptosis and iron homeostasis, nucleotide metabolism, and finally in the peptidoglycan and lipopolysaccharides synthesis. Overall, the results of the present study provide evidence in favor of the hypothesis that during the primary inflammatory challenge, regardless of whether it is induced by periodontitis or diabetes, endotoxemia and/or the release of inflammatory cytokines cause a change in precursor and/or in circulating innate immune cells. Dysbiosis and inflammation, also via oral-gut microbiome axis or adipose tissue, reduce the efficacy of the host immune response, while fueling inflammation and can induce that metabolic/epigenetic reprogramming of chromatin accessibility of genes related to the immune response. Moreover, the presence of an enhanced ferroptosis and an imbalance in purine/pyrimidine metabolism provides new insights into the role of ferroptotic death in this comorbidity.}, } @article {pmid37257591, year = {2023}, author = {Guo, Y and Li, D and Gao, Y and Gao, J and Zhang, S and Bao, F}, title = {The knock-on effects of different wastewater feeding modes: Change in microbial communities versus resistance genes in pilot-scale aerobic sludge granulation reactors.}, journal = {The Science of the total environment}, volume = {892}, number = {}, pages = {164500}, doi = {10.1016/j.scitotenv.2023.164500}, pmid = {37257591}, issn = {1879-1026}, mesh = {*Wastewater ; Sewage/microbiology ; Waste Disposal, Fluid ; Bioreactors/microbiology ; Bacteria/genetics ; *Microbiota ; Anti-Bacterial Agents ; }, abstract = {To explore the effects of wastewater feeding modes on the formation of aerobic granular sludge (AGS) and the complex relationships between resistance genes and bacteria, two pilot-scale sequencing batch reactors (SBRs) were established. The SBR with influent wastewater introduced uniformly through pipes at bottom was designated as BSBR, and the SBR with inlet wastewater flowing directly from top was TSBR. BSBR formed dense AGS due to uniform wastewater feeding at bottom, while TSBR failed to cultivate AGS. Metagenomic sequencing illustrated that rapid growth of AGS in BSBR was accompanied with increase of antibiotic resistance genes (ARGs) abundance, but ARGs diminished when the size of AGS was stable. The ARGs continued to elevate in TSBR, and abundance of metal resistance genes (MRGs) was always higher than that in BSBR. Two reactors had markedly different bacterial community, microbes in BSBR owned stronger activity, conferred greater potential to proliferate. AdeF in two systems had the most complex gene-bacteria relationships which would undergo HGT within bacterial genus. The different feeding modes of wastewater directly led to the changing size of sludge, which caused knock-on effects of variations in the abundance of microbial communities and resistance genes. This study provided promising suggestions for the rapid cultivation of AGS and control of resistance genes at pilot-scale.}, } @article {pmid37257294, year = {2023}, author = {Chen, J and Ke, Y and Zhu, Y and Chen, X and Xie, S}, title = {Deciphering of sulfonamide biodegradation mechanism in wetland sediments: from microbial community and individual populations to pathway and functional genes.}, journal = {Water research}, volume = {240}, number = {}, pages = {120132}, doi = {10.1016/j.watres.2023.120132}, pmid = {37257294}, issn = {1879-2448}, mesh = {Humans ; Biodegradation, Environmental ; *Wetlands ; Anti-Bacterial Agents/metabolism ; Sulfonamides ; Sulfanilamide ; Sulfadiazine ; *Microbiota ; }, abstract = {Figuring out the comprehensive metabolic mechanism of sulfonamide antibiotics (SA) is critical to improve and optimize SA removal in the bioremediation process, but relevant studies are still lacking. Here, an approach integrating metagenomic analysis, degraders' isolation, reverse transcriptional quantification and targeted metabolite determination was used to decipher microbial interactions and functional genes' characteristics in SA-degrading microbial consortia enriched from wetland sediments. The SA-degrading consortia could rapidly catalyze ipso-hydroxylation and subsequent reactions of SA to achieve the complete mineralization of sulfadiazine and partial mineralization of the other two typical SA (sulfamethoxazole and sulfamethazine). Paenarthrobacter, Achromobacter, Pseudomonas and Methylobacterium were identified as the primary participants for the initial transformation of SA. Among them, Methylobacterium could metabolize the heterocyclic intermediate of sulfadiazine (2-aminopyrimidine), and the owning of sadABC genes (SA degradation genes) made Paenarthrobacter have relatively higher SA-degrading activity. Besides, the coexistence of sadABC genes and sul1 gene (SA resistance gene) gave Paenarthrobacter a dual resistance mechanism to SA. The results of reverse transcription quantification further demonstrated that the activity of sadA gene was related to the biodegradation of SA. Additionally, sadABC genes were relatively conserved in a few Microbacteriaceae and Micrococcaceae SA-degraders, but the multiple recombination events caused by densely nested transposase encoding genes resulted in the differential sequence of sadAB genes in Paenarthrobacter genome. These new findings provide valuable information for the selection and construction of engineered microbiomes.}, } @article {pmid37254939, year = {2023}, author = {Gager, Y and Koppe, J and Vogl, I and Gabert, J and Jentsch, H}, title = {Antibiotic resistance genes in the subgingival microbiome and implications for periodontitis therapy.}, journal = {Journal of periodontology}, volume = {94}, number = {11}, pages = {1295-1301}, doi = {10.1002/JPER.22-0696}, pmid = {37254939}, issn = {1943-3670}, support = {//European Regional Development Fund/ ; }, mesh = {Humans ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Periodontal Pocket/drug therapy ; *Periodontitis/drug therapy/genetics ; Drug Resistance, Microbial ; Macrolides ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Antibiotic resistance is emerging as a global public threat. However, it remains poorly investigated in the context of periodontal therapy. The aim of the study was to investigate the complete diversity of antibiotic resistance genes in a German population.

METHODS: Thirty-nine volunteers with periodontitis contributed to the present study with one to four periodontal pockets for a total of 124 subgingival samples. Samples were analyzed using shotgun metagenomics.

RESULTS: A total of 19 antibiotic resistance genes from six antibiotic classes were detected in subgingival biofilm. Two thirds of the volunteers (n = 26/39) showed antibiotic resistance genes for at least one of the antibiotic classes used for periodontal treatment in dental practice or research: beta-lactam, lincosamide, macrolide, nitroimidazole, and tetracycline. Macrolide was the most abundant class detected (21/39 patients).

CONCLUSIONS: Findings from our study suggest a high prevalence of antibiotic resistance genes in periodontal pockets from German volunteers. We recommend the development and broader use of molecular diagnostic tests for antibiotic resistance in dental practice to ensure treatment success and to minimize antibiotic resistance.}, } @article {pmid37254732, year = {2023}, author = {Chittimalli, K and Jahan, J and Sakamuri, A and McAdams, ZL and Ericsson, AC and Jarajapu, YPR}, title = {Restoration of the gut barrier integrity and restructuring of the gut microbiome in aging by angiotensin-(1-7).}, journal = {Clinical science (London, England : 1979)}, volume = {137}, number = {11}, pages = {913-930}, pmid = {37254732}, issn = {1470-8736}, support = {R01 AG056881/AG/NIA NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Mice ; Male ; Animals ; *Gastrointestinal Microbiome ; Angiotensin-Converting Enzyme 2 ; Dysbiosis ; Claudin-1 ; Occludin ; Angiotensin I/pharmacology/metabolism ; Peptidyl-Dipeptidase A/metabolism ; Peptide Fragments/pharmacology/metabolism ; Aging ; Angiotensin II/metabolism ; }, abstract = {Compromised barrier function of colon epithelium with aging is largely due to gut microbial dysbiosis. Recent studies implicate an important role for angiotensin converting enzymes, ACE and ACE2, angiotensins, and the receptors, AT1 receptor (AT1R) and Mas receptor (MasR), in the regulation of colon functions. The present study tested the hypothesis that leaky gut in aging is associated with an imbalance in ACE2/ACE and that the treatment with angiotenisn-(1-7) (Ang-(1-7)) will restore gut barrier integrity and microbiome. Studies were carried out in Young (3-4 months) and old (20-24 months) male mice. Ang-(1-7) was administered by using osmotic pumps. Outcome measures included expressions of ACE, ACE2, AT1R, and MasR, intestinal permeability by using FITC-dextran, and immunohistochemistry of claudin 1 and occludin, and intestinal stem cells (ISCs). ACE2 protein and activity were decreased in Old group while that of ACE were unchanged. Increased intestinal permeability and plasma levels of zonulin-1 in the Old group were normalized by Ang-(1-7). Epithelial disintegrity, reduced number of goblet cells and ISCs in the old group were restored by Ang-(1-7). Expression of claudin 1 and occludin in the aging colon was increased by Ang-(1-7). Infiltration of CD11b+ or F4/80+ inflammatory cells in the old colons were decreased by Ang-(1-7). Gut microbial dysbiosis in aging was evident by decreased richness and altered beta diversity that were reversed by Ang-(1-7) with increased abundance of Lactobacillus or Lachnospiraceae. The present study shows that Ang-(1-7) restores gut barrier integrity and reduces inflammation in the aging colon by restoring the layer of ISCs and by restructuring the gut microbiome.}, } @article {pmid37254344, year = {2023}, author = {Yao, L and Zhang, J and Lu, J and Chen, D and Song, S and Wang, H and Sun, M and Feng, T}, title = {Revealing the influence of microbiota on the flavor of kombucha during natural fermentation process by metagenomic and GC-MS analysis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {169}, number = {}, pages = {112909}, doi = {10.1016/j.foodres.2023.112909}, pmid = {37254344}, issn = {1873-7145}, mesh = {Fermentation ; Gas Chromatography-Mass Spectrometry ; *Microbiota/genetics ; Metagenome ; Saccharomyces cerevisiae ; Tea/chemistry ; }, abstract = {In this work, raw Pu-erh tea (RAPT) was employed for kombucha preparation, and the microbial composition and volatile flavor compounds of the fermented tea had been investigated during natural fermentation process. The head space-solid phase microextraction-gas chromatograph mass spectrometry (HS-SPME-GC-MS) was performed for volatiles analysis of unfermented tea and kombucha fermented for 3 days (KF-3) and 6 days (KF-6). Meanwhile, the microbial community of KF-3 and KF-6 were evaluated by metagenomic analysis. A total of 72 volatile compounds were identified and obvious changes in volatiles were observed during the fermentation process based on the results of GC-MS and principal component analysis (PCA). Metagenomic sequencing analysis demonstrated that bacterium Komagataeibacter saccharivorans and unclassified-g-komagataeibacter and yeast Saccharomyces cerevisiae and Brettanomyces bruxellensis were the most common microbes contained in the sampled kombucha communities. Furthermore, the relevance among microbial community and volatile compounds was evaluated through correlation heatmap analysis. The results suggested that the main flavor volatiles of kombucha (i.e., acids, esters and terpenes) were closely related to species of genus Komagataeibacter, Gluconacetobacter, Saccharomyces, Brettanomyces, Acetobacter, Novacetimonas and Pichia microorganisms. The obtained results would help to better understand microbial communities and volatile compounds of kombucha, which could provide useful information for enhancing the flavor quality of kombucha products.}, } @article {pmid37254152, year = {2023}, author = {Wang, K and Mehta, RS and Ma, W and Nguyen, LH and Wang, DD and Ghazi, AR and Yan, Y and Al-Shaar, L and Wang, Y and Hang, D and Fu, BC and Ogino, S and Rimm, EB and Hu, FB and Carmody, RN and Garrett, WS and Sun, Q and Chan, AT and Huttenhower, C and Song, M}, title = {The gut microbiome modifies the associations of short- and long-term physical activity with body weight changes.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {121}, pmid = {37254152}, issn = {2049-2618}, support = {K24 DK098311/NH/NIH HHS/United States ; R01 CA137178/CA/NCI NIH HHS/United States ; R35 CA197735/NH/NIH HHS/United States ; UM1 CA167552/CA/NCI NIH HHS/United States ; R01 AG077489/AG/NIA NIH HHS/United States ; R00 CA215314/NH/NIH HHS/United States ; P01 CA087969/CA/NCI NIH HHS/United States ; R00 CA215314/CA/NCI NIH HHS/United States ; UM1 CA186107/CA/NCI NIH HHS/United States ; P01 CA055075/CA/NCI NIH HHS/United States ; R00 DK119412/DK/NIDDK NIH HHS/United States ; R01 CA202704/CA/NCI NIH HHS/United States ; U01 CA176726/CA/NCI NIH HHS/United States ; U01 CA167552/CA/NCI NIH HHS/United States ; R01 CA151993/CA/NCI NIH HHS/United States ; U01 CA261961/CA/NCI NIH HHS/United States ; R01 CA263776/CA/NCI NIH HHS/United States ; K99 CA283146/CA/NCI NIH HHS/United States ; R01 NR019992/NR/NINR NIH HHS/United States ; }, mesh = {Female ; Humans ; Male ; Young Adult ; Body Weight ; Exercise/physiology ; Follow-Up Studies ; *Gastrointestinal Microbiome/genetics ; Obesity/metabolism ; Weight Gain ; Aged ; }, abstract = {BACKGROUND: The gut microbiome regulates host energy balance and adiposity-related metabolic consequences, but it remains unknown how the gut microbiome modulates body weight response to physical activity (PA).

METHODS: Nested in the Health Professionals Follow-up Study, a subcohort of 307 healthy men (mean[SD] age, 70[4] years) provided stool and blood samples in 2012-2013. Data from cohort long-term follow-ups and from the accelerometer, doubly labeled water, and plasma biomarker measurements during the time of stool collection were used to assess long-term and short-term associations of PA with adiposity. The gut microbiome was profiled by shotgun metagenomics and metatranscriptomics. A subcohort of 209 healthy women from the Nurses' Health Study II was used for validation.

RESULTS: The microbial species Alistipes putredinis was found to modify the association between PA and body weight. Specifically, in individuals with higher abundance of A. putredinis, each 15-MET-hour/week increment in long-term PA was associated with 2.26 kg (95% CI, 1.53-2.98 kg) less weight gain from age 21 to the time of stool collection, whereas those with lower abundance of A. putredinis only had 1.01 kg (95% CI, 0.41-1.61 kg) less weight gain (pinteraction = 0.019). Consistent modification associated with A. putredinis was observed for short-term PA in relation to BMI, fat mass%, plasma HbA1c, and 6-month weight change. This modification effect might be partly attributable to four metabolic pathways encoded by A. putredinis, including folate transformation, fatty acid β-oxidation, gluconeogenesis, and stearate biosynthesis.

CONCLUSIONS: A greater abundance of A. putredinis may strengthen the beneficial association of PA with body weight change, suggesting the potential of gut microbial intervention to improve the efficacy of PA in body weight management. Video Abstract.}, } @article {pmid37253538, year = {2023}, author = {Mori, H and Kato, T and Ozawa, H and Sakamoto, M and Murakami, T and Taylor, TD and Toyoda, A and Ohkuma, M and Kurokawa, K and Ohno, H}, title = {Assessment of metagenomic workflows using a newly constructed human gut microbiome mock community.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {30}, number = {3}, pages = {}, pmid = {37253538}, issn = {1756-1663}, support = {JP19gm6010007//Japan Agency for Medical Research and Development/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Workflow ; *Microbiota/genetics ; Metagenome ; Metagenomics/methods ; }, abstract = {To quantify the biases introduced during human gut microbiome studies, analyzing an artificial mock community as the reference microbiome is indispensable. However, there are still limited resources for a mock community which well represents the human gut microbiome. Here, we constructed a novel mock community comprising the type strains of 18 major bacterial species in the human gut and assessed the influence of experimental and bioinformatics procedures on the 16S rRNA gene and shotgun metagenomic sequencing. We found that DNA extraction methods greatly affected the DNA yields and taxonomic composition of sequenced reads, and that some of the commonly used primers for 16S rRNA genes were prone to underestimate the abundance of some gut commensal taxa such as Erysipelotrichia, Verrucomicrobiota and Methanobacteriota. Binning of the assembled contigs of shotgun metagenomic sequences by MetaBAT2 produced phylogenetically consistent, less-contaminated bins with varied completeness. The ensemble approach of multiple binning tools by MetaWRAP can improve completeness but sometimes increases the contamination rate. Our benchmark study provides an important foundation for the interpretation of human gut microbiome data by providing means for standardization among gut microbiome data obtained with different methodologies and will facilitate further development of analytical methods.}, } @article {pmid37249588, year = {2023}, author = {Li, W and Zhao, J and Tian, H and Shen, Y and Wang, Y and Shao, M and Xiong, T and Yao, Y and Zhang, L and Chen, X and Xiao, H and Xiong, Y and Yang, S and Tan, C and Xu, H}, title = {Gut microbiota enhance energy accumulation of black-necked crane to cope with impending migration.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {14}, pages = {4635-4646}, pmid = {37249588}, issn = {1432-0614}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Proteobacteria ; Birds/genetics/microbiology ; Cellulose ; }, abstract = {Less is known about the role of gut microbiota in overwintering environmental adaptation in migratory birds. Here, we performed metagenomic sequencing on fresh fecal samples (n = 24) collected during 4 periods of overwintering (Dec: early; Jan: middle I; Feb: middle II; Mar: late) to characterize gut microbial taxonomic and functional characteristics of black-necked crane (Grus nigricollis). The results demonstrated no significant change in microbial diversity among overwintering periods. Analysis of compositions of microbiomes with bias correction (ANCOM-BC) determined 15 Proteobacteria species enriched in late overwintering period. Based on previous reports, these species are associated with degradation of chitin, cellulose, and lipids. Meanwhile, fatty acid degradation and betalain biosynthesis pathways are enriched in late overwintering period. Furthermore, metagenomic binning obtained 91 high-quality bins (completeness >70% and contamination <10%), 5 of which enriched in late overwintering period. Carnobacterium maltaromaticum, unknown Enterobacteriaceae, and Yersinia frederiksenii have genes for chitin and cellulose degradation, acetate, and glutamate production. Unknown Enterobacteriaceae and Y. frederiksenii hold genes for synthesis of 10 essential amino acids required by birds, and the latter has genes for γ-aminobutyrate production. C. maltaromaticum has genes for pyridoxal synthesis. These results implied the gut microbiota is adapted to the host diet and may help black-necked cranes in pre-migratory energy accumulation by degrading the complex polysaccharide in their diet, supplying essential amino acids and vitamin pyridoxal, and producing acetate, glutamate, and γ-aminobutyrate that could stimulate host feeding. Additionally, enriched Proteobacteria also encoded more carbohydrate-active enzymes (CAZymes) and antibiotic resistance genes (ARGs) in late overwintering period. KEY POINTS: • Differences in gut microbiota function during overwintering period of black-necked cranes depend mainly on changes in core microbiota abundance • Gut microbiota of black-necked crane adapted to the diet during overwintering period • Gut microbiota could help black-necked cranes to accumulate more energy in the late overwintering period.}, } @article {pmid37249085, year = {2023}, author = {Ting, HSL and Chen, Z and Chan, JYK}, title = {Systematic review on oral microbial dysbiosis and its clinical associations with head and neck squamous cell carcinoma.}, journal = {Head & neck}, volume = {45}, number = {8}, pages = {2120-2135}, doi = {10.1002/hed.27422}, pmid = {37249085}, issn = {1097-0347}, mesh = {Humans ; Bacteria ; Dysbiosis/diagnosis/microbiology ; *Head and Neck Neoplasms/diagnosis ; *Microbiota/genetics ; Squamous Cell Carcinoma of Head and Neck ; }, abstract = {OBJECTIVES: The relationship between head and neck squamous cell carcinoma (HNSCC) and the oral microbiome has been drawn in various studies. Microbial diversities, microbiome profiles, metagenomic analysis, and host-pathogen interactions were collected from these studies to highlight similarities and account for inconsistencies. We also evaluate the possible clinical applications of the microbiome regarding screening and diagnosis of HNSCC.

METHODS: Systematic analysis of studies regarding HNSCC and the microbiome was done according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement guidelines. Articles were retrieved from four databases (PubMed, ScienceDirect, CUHK Full-Text Journals, and Cochrane database) and were screened using predefined criteria.

RESULTS: Twenty studies were chosen after screening for full-text review. α-diversity comparison was inconsistent whereas β-diversity between HNSCC and normal samples showed distinct clustering. Microbial dysbiosis characterized by change in the relative abundances of several bacterial species were also seen in HNSCC patients. At a phylum level, inconsistencies were seen between studies using HNSCC tumor tissue samples and saliva samples. At a genus level, Fusobacterium, Peptostreptococcus, Alloprevotella, Capnocytophaga, Catonella, and Prevotella were differentially enriched in HNSCC while Streptococcus, Actinomyces Veillonella, and Rothia were differentially depleted. Co-occurrence network analysis revealed a positive correlation of HNSCC with periodontal pathogens and a negative correlation with commensal bacteria. Metagenomic analysis of microbiota revealed a differential enrichment of pro-inflammatory genomic pathways which was consistent across various studies. Microbial dysbiosis was applied in clinical use as a tool for HNSCC screening. Random-forest analysis was adopted to differentiate between tumor and normal tissue, at 95.7% and 70.0% accuracies respectively in two studies. Microbial dysbiosis index was also used to predict prognosis.

CONCLUSIONS: Oral microbial dysbiosis could be a promising tool for HNSCC screening and diagnosis. However, more research should be conducted pertaining to clinical applications to improve diagnostic accuracy and explore other clinical uses.}, } @article {pmid37249060, year = {2023}, author = {Wolf, M and Schallert, K and Knipper, L and Sickmann, A and Sczyrba, A and Benndorf, D and Heyer, R}, title = {Advances in the clinical use of metaproteomics.}, journal = {Expert review of proteomics}, volume = {20}, number = {4-6}, pages = {71-86}, doi = {10.1080/14789450.2023.2215440}, pmid = {37249060}, issn = {1744-8387}, mesh = {Humans ; *Proteomics/methods ; *Microbiota/genetics ; Bacterial Proteins/metabolism ; Computational Biology/methods ; Obesity ; }, abstract = {INTRODUCTION: Investigating the taxonomic and functional composition of human microbiomes can aid in the understanding of disease etiologies, diagnosis, and therapy monitoring for several diseases, including inflammatory bowel disease or obesity. One method for microbiome monitoring is metaproteomics, which assesses human and microbial proteins and thus enables the study of host-microbiome interactions. This advantage led to increased interest in metaproteome analyses and significant developments to introduce this method into a clinical context.

AREAS COVERED: This review summarizes the recent progress from a technical side and an application-related point of view.

EXPERT OPINION: Numerous publications imply the massive potential of metaproteomics to impact human health care. However, the key challenges of standardization and validation of experimental and bioinformatic workflows and accurate quantification methods must be overcome.}, } @article {pmid37248474, year = {2023}, author = {Stiller, J and Wilson, NG and Rouse, GW}, title = {Range-wide population genomics of common seadragons shows secondary contact over a former barrier and insights on illegal capture.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {129}, pmid = {37248474}, issn = {1741-7007}, mesh = {Humans ; Animals ; Phylogeny ; *Metagenomics ; Biodiversity ; *Smegmamorpha ; Australia ; Genetic Variation ; }, abstract = {BACKGROUND: Common seadragons (Phyllopteryx taeniolatus, Syngnathidae) are an emblem of the diverse endemic fauna of Australia's southern rocky reefs, the newly recognized "Great Southern Reef." A lack of assessments spanning this global biodiversity hotspot in its entirety is currently hampering an understanding of the factors that have contributed to its diversity. The common seadragon has a wide range across Australia's entire temperate south and includes a geogenetic break over a former land bridge, which has called its status as a single species into question. As a popular aquarium display that sells for high prices, common seadragons are also vulnerable to illegal capture.

RESULTS: Here, we provide range-wide nuclear sequences (986 variable Ultraconserved Elements) for 198 individuals and mitochondrial genomes for 140 individuals to assess species status, identify genetic units and their diversity, and trace the source of two poached individuals. Using published data of the other two seadragon species, we found that lineages of common seadragons have diverged relatively recently (< 0.63 Ma). Within common seadragons, we found pronounced genetic structure, falling into three major groups in the western, central, and eastern parts of the range. While populations across the Bassian Isthmus were divergent, there is also evidence for secondary contact since the passage opened. We found a strong cline of genetic diversity from the range center tapering symmetrically towards the range peripheries. Based on their genetic similarities, the poached individuals were inferred to have originated from around Albany in southwestern Australia.

CONCLUSIONS: We conclude that common seadragons constitute a single species with strong geographic structure but coherence through gene flow. The low genetic diversity on the east and west coasts is concerning given that these areas are projected to face fast climate change. Our results suggest that in addition to their life history, geological events and demographic expansions have all played a role in shaping populations in the temperate south. These insights are an important step towards understanding the historical determinants of the diversity of species endemic to the Great Southern Reef.}, } @article {pmid37247730, year = {2023}, author = {Liu, Y and Yan, Y and Fu, L and Li, X}, title = {Metagenomic insights into the response of rhizosphere microbial to precipitation changes in the alpine grasslands of northern Tibet.}, journal = {The Science of the total environment}, volume = {892}, number = {}, pages = {164212}, doi = {10.1016/j.scitotenv.2023.164212}, pmid = {37247730}, issn = {1879-1026}, mesh = {Tibet ; *Ecosystem ; Grassland ; Rhizosphere ; *Microbiota ; Soil Microbiology ; Soil/chemistry ; Water ; }, abstract = {Water changes caused by precipitation may affect the elemental cycle of ecosystems by influencing soil microorganisms. In this study, precipitation control experiment was conducted in semi-arid alpine grasslands in northern Tibet, and plots were set up and divided into increased water (IW) and decreased water (DW) plots. Moreover, the link between functional genes and soil environmental factors, and the responses of the microbial community functions to precipitation-induced water variations were studied using metagenomic sequencing. To clarify the roles of various proteins and metabolites in the semi-arid alpine grasslands of northern Tibet, functional annotations of clusters of orthologous groups of proteins, Kyoto Encyclopedia of Genes and Genomes, and carbohydrate-active enzyme of the sequencing data were conducted. The results showed that the absolute abundance of microbial functional genes in IW was significantly higher than that in the control check (CK, natural precipitation) and DW. However, the absolute abundance did not significantly differ between CK and DW. There was no significant difference among the four plant species (Stipa purpurea, Carex moocroftii, Othropis microphylla, and Artemisia capillaris) considered in this study. These results indicated that microbial functions were mainly affected by water and do not depend on the species, and that the effect of IW was greater than that of DW. Further, we found that soil C, N, K, and other nutrients play vital roles in microbial growth, microbial functional genes were not affected by pH; however, soil C, N, and K nutrients and functional genes were negative correlated. Overall, this study enhances our understanding of the responses of microorganisms to precipitation and can be used as a valuable reference for understanding the drought resistance of soil microorganisms in semi-arid and alpine regions.}, } @article {pmid37246304, year = {2023}, author = {Arredondo, A and Àlvarez, G and Isabal, S and Teughels, W and Laleman, I and Contreras, MJ and Isbej, L and Huapaya, E and Mendoza, G and Mor, C and Nart, J and Blanc, V and León, R}, title = {Comparative 16S rRNA gene sequencing study of subgingival microbiota of healthy subjects and patients with periodontitis from four different countries.}, journal = {Journal of clinical periodontology}, volume = {50}, number = {9}, pages = {1176-1187}, doi = {10.1111/jcpe.13827}, pmid = {37246304}, issn = {1600-051X}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; Healthy Volunteers ; *Dental Plaque/microbiology ; *Periodontitis/microbiology ; Bacteria/genetics ; *Microbiota/genetics ; }, abstract = {AIM: To investigate the differences between the subgingival microbiota of healthy subjects (HS) and periodontitis patients (PP) from four different countries through a metagenomic approach.

MATERIALS AND METHODS: Subgingival samples were obtained from subjects from four different countries. Microbial composition was analysed through high-throughput sequencing of the V3-V4 region of the 16S rRNA gene. The country of origin, diagnosis and clinical and demographic variables of the subjects were used to analyse the microbial profiles.

RESULTS: In total, 506 subgingival samples were analysed: 196 from HS and 310 from patients with periodontitis. Differences in richness, diversity and microbial composition were observed when comparing samples pertaining to different countries of origin and different subject diagnoses. Clinical variables, such as bleeding on probing, did not significantly affect the bacterial composition of the samples. A highly conserved core of microbiota associated with periodontitis was detected, while the microbiota associated with periodontally HS was much more diverse.

CONCLUSIONS: Periodontal diagnosis of the subjects was the main variable explaining the composition of the microbiota in the subgingival niche. Nevertheless, the country of origin also had a significant impact on the microbiota and is therefore an important factor to consider when describing subgingival bacterial communities.}, } @article {pmid37245312, year = {2023}, author = {Gong, X and Ge, Z and Ma, Z and Li, Y and Huang, D and Zhang, J}, title = {Effect of different size microplastic particles on the construction of algal-bacterial biofilms and microbial communities.}, journal = {Journal of environmental management}, volume = {343}, number = {}, pages = {118246}, doi = {10.1016/j.jenvman.2023.118246}, pmid = {37245312}, issn = {1095-8630}, mesh = {Bacteria/metabolism ; Biofilms ; *Microbiota ; *Microplastics/metabolism/pharmacology ; Plastics ; Sewage ; }, abstract = {Algal-bacterial symbiotic system is a biological purification system that combines sewage treatment with resource utilization and has the dual effects of carbon sequestration and pollution reduction. In this study, an immobilized algal-bacterial biofilm system was constructed for the treatment of natural sewage. Effects of exposure to microplastics (MPs) with different particle diameters (0.065 μm, 0.5 μm and 5 μm) were determined in terms of algal biomass recovery efficiency, the composition of extracellular polymeric substances (EPS) and morphologic characteristics. The impacts of MPs on the bacterial diversity and community structure of biofilms were also examined. The metagenomic analysis of key microorganisms and related metabolism pathways involved in system was further investigated. Results showed that following exposure to 5 μm MP, a maximum algal recovery efficiency of 80% was achieved, with a minimum PSII primary light energy conversion efficiency (Fv/Fm ratio) of 0.513. Furthermore, 5 μm MP caused the highest level of damage to the algal-bacterial biofilm, enhancing the secretion of protein-rich EPS. The biofilm morphology became rough and loose following exposure to 0.5 μm and 5 μm MP. Community diversity and richness were significantly high in biofilms exposed to 5 μm MP. Proteobacteria (15.3-24.1%), Firmicutes (5.0-7.8%) and Actinobacteria (4.2-4.9%) were dominant in all groups, with exposure to 5 μm MP resulting in the highest relative abundance for these species. The addition of MPs promoted the related metabolic functions while inhibited the degradation of harmful substances by algal-bacterial biofilms. The findings have environmental significance for the practical application of algal-bacterial biofilms for sewage treatment, providing novel insights into the potential effects of MPs on immobilized algal-bacterial biofilm systems.}, } @article {pmid37245209, year = {2023}, author = {Zhao, B and Osbelt, L and Lesker, TR and Wende, M and Galvez, EJC and Hönicke, L and Bublitz, A and Greweling-Pils, MC and Grassl, GA and Neumann-Schaal, M and Strowig, T}, title = {Helicobacter spp. are prevalent in wild mice and protect from lethal Citrobacter rodentium infection in the absence of adaptive immunity.}, journal = {Cell reports}, volume = {42}, number = {6}, pages = {112549}, doi = {10.1016/j.celrep.2023.112549}, pmid = {37245209}, issn = {2211-1247}, mesh = {Animals ; Mice ; Citrobacter rodentium ; *Enterobacteriaceae Infections ; Adaptive Immunity ; *Microbiota ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; }, abstract = {Transfer of the gut microbiota from wild to laboratory mice alters the host's immune status and enhances resistance to infectious and metabolic diseases, but understanding of which microbes and how they promote host fitness is only emerging. Our analysis of metagenomic sequencing data reveals that Helicobacter spp. are enriched in wild compared with specific-pathogen-free (SPF) and conventionally housed mice, with multiple species commonly co-colonizing their hosts. We create laboratory mice harboring three non-SPF Helicobacter spp. to evaluate their effect on mucosal immunity and colonization resistance to the enteropathogen Citrobacter rodentium. Our experiments reveal that Helicobacter spp. interfere with C. rodentium colonization and attenuate C. rodentium-induced gut inflammation in wild-type (WT) mice, even preventing lethal infection in Rag2[-/-] SPF mice. Further analyses suggest that Helicobacter spp. interfere with tissue attachment of C. rodentium, putatively by reducing the availability of mucus-derived sugars. These results unveil pivotal protective functions of wild mouse microbiota constituents against intestinal infection.}, } @article {pmid37244770, year = {2023}, author = {Mincer, TJ and Bos, RP and Zettler, ER and Zhao, S and Asbun, AA and Orsi, WD and Guzzetta, VS and Amaral-Zettler, LA}, title = {Sargasso Sea Vibrio bacteria: Underexplored potential pathovars in a perturbed habitat.}, journal = {Water research}, volume = {242}, number = {}, pages = {120033}, doi = {10.1016/j.watres.2023.120033}, pmid = {37244770}, issn = {1879-2448}, mesh = {Oceans and Seas ; *Seawater/microbiology ; *Vibrio/genetics ; Ecosystem ; Atlantic Ocean ; }, abstract = {We fully sequenced the genomes of 16 Vibrio cultivars isolated from eel larvae, plastic marine debris (PMD), the pelagic brown macroalga Sargassum, and seawater samples collected from the Caribbean and Sargasso Seas of the North Atlantic Ocean. Annotation and mapping of these 16 bacterial genome sequences to a PMD-derived Vibrio metagenome-assembled genome created for this study showcased vertebrate pathogen genes closely-related to cholera and non-cholera pathovars. Phenotype testing of cultivars confirmed rapid biofilm formation, hemolytic, and lipophospholytic activities, consistent with pathogenic potential. Our study illustrates that open ocean vibrios represent a heretofore undescribed group of microbes, some representing potential new species, possessing an amalgam of pathogenic and low nutrient acquisition genes, reflecting their pelagic habitat and the substrates and hosts they colonize.}, } @article {pmid37243505, year = {2023}, author = {Bruggeling, CE and Te Groen, M and Garza, DR and van Heeckeren Tot Overlaer, F and Krekels, JPM and Sulaiman, BC and Karel, D and Rulof, A and Schaaphok, AR and Hornikx, DLAH and Nagtegaal, ID and Dutilh, BE and Hoentjen, F and Boleij, A}, title = {Bacterial Oncotraits Rather than Spatial Organization Are Associated with Dysplasia in Ulcerative Colitis.}, journal = {Journal of Crohn's & colitis}, volume = {17}, number = {11}, pages = {1870-1881}, pmid = {37243505}, issn = {1876-4479}, support = {//Scientific Research 'Veni/ ; //Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; *Colitis, Ulcerative/pathology ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Hyperplasia ; Biomarkers ; }, abstract = {BACKGROUND AND AIMS: Colonic bacterial biofilms are frequently present in ulcerative colitis [UC] and may increase dysplasia risk through pathogens expressing oncotraits. This prospective cohort study aimed to determine [1] the association of oncotraits and longitudinal biofilm presence with dysplasia risk in UC, and [2] the relation of bacterial composition with biofilms and dysplasia risk.

METHODS: Faeces and left- and right-sided colonic biopsies were collected from 80 UC patients and 35 controls. Oncotraits [FadA of Fusobacterium, BFT of Bacteroides fragilis, colibactin [ClbB] and Intimin [Eae] of Escherichia coli] were assessed in faecal DNA with multiplex quantitative polymerase chain reaction [qPCR]. Biopsies were screened for biofilms [n = 873] with 16S rRNA fluorescent in situ hybridiation. Shotgun metagenomic sequencing [n = 265], and ki67-immunohistochemistry were performed. Associations were determined with a mixed-effects regression model.

RESULTS: Biofilms were highly prevalent in UC patients [90.8%] with a median persistence of 3 years (interquartile range [IQR] 2-5 years). Biofilm-positive biopsies showed increased epithelial hypertrophy [p = 0.025] and a reduced Shannon diversity independent of disease status [p = 0.015], but were not significantly associated with dysplasia in UC: adjusted odds ratio [aOR] 1.45, 95% confidence interval [CI] 0.63-3.40. In contrast, ClbB independently associated with dysplasia [aOR 7.16, 95% CI 1.75-29.28], and FadA and Fusobacteriales were associated with a decreased dysplasia risk in UC [aOR 0.23, 95% CI 0.06-0.83, p <0.01].

CONCLUSIONS: Biofilms are a hallmark of UC; however, because of their high prevalence are a poor biomarker for dysplasia. In contrast, colibactin presence and FadA absence independently associate with dysplasia in UC and might therefore be valuable biomarkers for future risk stratification and intervention strategies.}, } @article {pmid37240180, year = {2023}, author = {Lafleur, S and Bodein, A and Mbuya Malaïka Mutombo, J and Mathieu, A and Joly Beauparlant, C and Minne, X and Chandad, F and Droit, A and Houde, VP}, title = {Multi-Omics Data Integration Reveals Key Variables Contributing to Subgingival Microbiome Dysbiosis-Induced Inflammatory Response in a Hyperglycemic Microenvironment.}, journal = {International journal of molecular sciences}, volume = {24}, number = {10}, pages = {}, pmid = {37240180}, issn = {1422-0067}, support = {Biocodex Microbiota Foundation//Biocodex (France)/ ; }, mesh = {Humans ; Multiomics ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; U937 Cells ; *Periodontitis/microbiology ; *Microbiota/genetics ; Bacteria/metabolism ; Cytokines/metabolism ; RNA-Binding Proteins ; }, abstract = {Subgingival microbiome dysbiosis promotes the development of periodontitis, an irreversible chronic inflammatory disease associated with metabolic diseases. However, studies regarding the effects of a hyperglycemic microenvironment on host-microbiome interactions and host inflammatory response during periodontitis are still scarce. Here, we investigated the impacts of a hyperglycemic microenvironment on the inflammatory response and transcriptome of a gingival coculture model stimulated with dysbiotic subgingival microbiomes. HGF-1 cells overlaid with U937 macrophage-like cells were stimulated with subgingival microbiomes collected from four healthy donors and four patients with periodontitis. Pro-inflammatory cytokines and matrix metalloproteinases were measured while the coculture RNA was submitted to a microarray analysis. Subgingival microbiomes were submitted to 16s rRNA gene sequencing. Data were analyzed using an advanced multi-omics bioinformatic data integration model. Our results show that the genes krt76, krt27, pnma5, mansc4, rab41, thoc6, tm6sf2, and znf506 as well as the pro-inflammatory cytokines IL-1β, GM-CSF, FGF2, IL-10, the metalloproteinases MMP3 and MMP8, and bacteria from the ASV 105, ASV 211, ASV 299, Prevotella, Campylobacter and Fretibacterium genera are key intercorrelated variables contributing to periodontitis-induced inflammatory response in a hyperglycemic microenvironment. In conclusion, our multi-omics integration analysis unveiled the complex interrelationships involved in the regulation of periodontal inflammation in response to a hyperglycemic microenvironment.}, } @article {pmid37239442, year = {2023}, author = {Choudhury, N and Sahu, TK and Rao, AR and Rout, AK and Behera, BK}, title = {An Improved Machine Learning-Based Approach to Assess the Microbial Diversity in Major North Indian River Ecosystems.}, journal = {Genes}, volume = {14}, number = {5}, pages = {}, pmid = {37239442}, issn = {2073-4425}, mesh = {*Rivers ; Software ; Machine Learning ; Metagenome/genetics ; *Microbiota/genetics ; }, abstract = {The rapidly evolving high-throughput sequencing (HTS) technologies generate voluminous genomic and metagenomic sequences, which can help classify the microbial communities with high accuracy in many ecosystems. Conventionally, the rule-based binning techniques are used to classify the contigs or scaffolds based on either sequence composition or sequence similarity. However, the accurate classification of the microbial communities remains a major challenge due to massive data volumes at hand as well as a requirement of efficient binning methods and classification algorithms. Therefore, we attempted here to implement iterative K-Means clustering for the initial binning of metagenomics sequences and applied various machine learning algorithms (MLAs) to classify the newly identified unknown microbes. The cluster annotation was achieved through the BLAST program of NCBI, which resulted in the grouping of assembled scaffolds into five classes, i.e., bacteria, archaea, eukaryota, viruses and others. The annotated cluster sequences were used to train machine learning algorithms (MLAs) to develop prediction models to classify unknown metagenomic sequences. In this study, we used metagenomic datasets of samples collected from the Ganga (Kanpur and Farakka) and the Yamuna (Delhi) rivers in India for clustering and training the MLA models. Further, the performance of MLAs was evaluated by 10-fold cross validation. The results revealed that the developed model based on the Random Forest had a superior performance compared to the other considered learning algorithms. The proposed method can be used for annotating the metagenomic scaffolds/contigs being complementary to existing methods of metagenomic data analysis. An offline predictor source code with the best prediction model is available at (https://github.com/Nalinikanta7/metagenomics).}, } @article {pmid37237391, year = {2023}, author = {Wang, Z and Peters, BA and Bryant, M and Hanna, DB and Schwartz, T and Wang, T and Sollecito, CC and Usyk, M and Grassi, E and Wiek, F and Peter, LS and Post, WS and Landay, AL and Hodis, HN and Weber, KM and French, A and Golub, ET and Lazar, J and Gustafson, D and Sharma, A and Anastos, K and Clish, CB and Burk, RD and Kaplan, RC and Knight, R and Qi, Q}, title = {Gut microbiota, circulating inflammatory markers and metabolites, and carotid artery atherosclerosis in HIV infection.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {119}, pmid = {37237391}, issn = {2049-2618}, support = {P30 MH116867/MH/NIMH NIH HHS/United States ; P30 DK040561/DK/NIDDK NIH HHS/United States ; U01 HL146245/HL/NHLBI NIH HHS/United States ; U01 HL146205/HL/NHLBI NIH HHS/United States ; R01 HL126543/HL/NHLBI NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; P30 AI124414/AI/NIAID NIH HHS/United States ; U01 HL146241/HL/NHLBI NIH HHS/United States ; U01 HL146208/HL/NHLBI NIH HHS/United States ; R01HL140976/HL/NHLBI NIH HHS/United States ; R01 HL132794/HL/NHLBI NIH HHS/United States ; P30 AI050410/AI/NIAID NIH HHS/United States ; U01 HL146194/HL/NHLBI NIH HHS/United States ; UL1 TR001881/TR/NCATS NIH HHS/United States ; K01 HL137557/HL/NHLBI NIH HHS/United States ; UL1 TR003098/TR/NCATS NIH HHS/United States ; P30 AI073961/AI/NIAID NIH HHS/United States ; P30 AI027767/AI/NIAID NIH HHS/United States ; U01 HL146333/HL/NHLBI NIH HHS/United States ; R01 HL095140/HL/NHLBI NIH HHS/United States ; U01 HL146240/HL/NHLBI NIH HHS/United States ; R01 HL083760/HL/NHLBI NIH HHS/United States ; U01 HL146242/HL/NHLBI NIH HHS/United States ; U01 HL146192/HL/NHLBI NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; U01 HL146204/HL/NHLBI NIH HHS/United States ; U01 HL146193/HL/NHLBI NIH HHS/United States ; U01 HL146202/HL/NHLBI NIH HHS/United States ; K01 HL160146/HL/NHLBI NIH HHS/United States ; P30 AI050409/AI/NIAID NIH HHS/United States ; U01 HL146201/HL/NHLBI NIH HHS/United States ; U01 HL146203/HL/NHLBI NIH HHS/United States ; P30 CA013330/CA/NCI NIH HHS/United States ; UL1 TR000004/TR/NCATS NIH HHS/United States ; K01 HL129892/HL/NHLBI NIH HHS/United States ; U01 AI035004/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; *HIV Infections/complications/pathology ; *Carotid Stenosis/complications/pathology ; Proteomics ; *Carotid Artery Diseases/complications/pathology ; *Atherosclerosis/complications/pathology ; Carotid Arteries/metabolism/pathology ; Biomarkers/metabolism ; Inflammation/pathology ; }, abstract = {BACKGROUND: Alterations in gut microbiota have been implicated in HIV infection and cardiovascular disease. However, how gut microbial alterations relate to host inflammation and metabolite profiles, and their relationships with atherosclerosis, have not been well-studied, especially in the context of HIV infection. Here, we examined associations of gut microbial species and functional components measured by shotgun metagenomics with carotid artery plaque assessed by B-mode carotid artery ultrasound in 320 women with or at high risk of HIV (65% HIV +) from the Women's Interagency HIV Study. We further integrated plaque-associated microbial features with serum proteomics (74 inflammatory markers measured by the proximity extension assay) and plasma metabolomics (378 metabolites measured by liquid chromatography tandem mass spectrometry) in relation to carotid artery plaque in up to 433 women.

RESULTS: Fusobacterium nucleatum, a potentially pathogenic bacteria, was positively associated with carotid artery plaque, while five microbial species (Roseburia hominis, Roseburia inulinivorans, Johnsonella ignava, Odoribacter splanchnicus, Clostridium saccharolyticum) were inversely associated with plaque. Results were consistent between women with and without HIV. Fusobacterium nucleatum was positively associated with several serum proteomic inflammatory markers (e.g., CXCL9), and the other plaque-related species were inversely associated with proteomic inflammatory markers (e.g., CX3CL1). These microbial-associated proteomic inflammatory markers were also positively associated with plaque. Associations between bacterial species (especially Fusobacterium nucleatum) and plaque were attenuated after further adjustment for proteomic inflammatory markers. Plaque-associated species were correlated with several plasma metabolites, including the microbial metabolite imidazole-propionate (ImP), which was positively associated with plaque and several pro-inflammatory markers. Further analysis identified additional bacterial species and bacterial hutH gene (encoding enzyme histidine ammonia-lyase in ImP production) associated with plasma ImP levels. A gut microbiota score based on these ImP-associated species was positively associated with plaque and several pro-inflammatory markers.

CONCLUSION: Among women living with or at risk of HIV, we identified several gut bacterial species and a microbial metabolite ImP associated with carotid artery atherosclerosis, which might be related to host immune activation and inflammation. Video Abstract.}, } @article {pmid37237317, year = {2023}, author = {Coutinho, FH and Silveira, CB and Sebastián, M and Sánchez, P and Duarte, CM and Vaqué, D and Gasol, JM and Acinas, SG}, title = {Water mass age structures the auxiliary metabolic gene content of free-living and particle-attached deep ocean viral communities.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {118}, pmid = {37237317}, issn = {2049-2618}, mesh = {Seawater/microbiology ; Water ; Genes, Viral ; *Viruses/genetics ; *Microbiota/genetics ; Oceans and Seas ; }, abstract = {BACKGROUND: Viruses play important roles in the ocean's biogeochemical cycles. Yet, deep ocean viruses are one of the most under-explored fractions of the global biosphere. Little is known about the environmental factors that control the composition and functioning of their communities or how they interact with their free-living or particle-attached microbial hosts.

RESULTS: We analysed 58 viral communities associated with size-fractionated free-living (0.2-0.8 μm) and particle-attached (0.8-20 μm) cellular metagenomes from bathypelagic (2150-4018 m deep) microbiomes obtained during the Malaspina expedition. These metagenomes yielded 6631 viral sequences, 91% of which were novel, and 67 represented high-quality genomes. Taxonomic classification assigned 53% of the viral sequences to families of tailed viruses from the order Caudovirales. Computational host prediction associated 886 viral sequences to dominant members of the deep ocean microbiome, such as Alphaproteobacteria (284), Gammaproteobacteria (241), SAR324 (23), Marinisomatota (39), and Chloroflexota (61). Free-living and particle-attached viral communities had markedly distinct taxonomic composition, host prevalence, and auxiliary metabolic gene content, which led to the discovery of novel viral-encoded metabolic genes involved in the folate and nucleotide metabolisms. Water mass age emerged as an important factor driving viral community composition. We postulated this was due to changes in quality and concentration of dissolved organic matter acting on the host communities, leading to an increase of viral auxiliary metabolic genes associated with energy metabolism among older water masses.

CONCLUSIONS: These results shed light on the mechanisms by which environmental gradients of deep ocean ecosystems structure the composition and functioning of free-living and particle-attached viral communities. Video Abstract.}, } @article {pmid37236370, year = {2023}, author = {Řezanka, T and Kyselová, L and Murphy, DJ}, title = {Archaeal lipids.}, journal = {Progress in lipid research}, volume = {91}, number = {}, pages = {101237}, doi = {10.1016/j.plipres.2023.101237}, pmid = {37236370}, issn = {1873-2194}, mesh = {*Archaea/chemistry/metabolism ; *Membrane Lipids/metabolism ; Bacteria/metabolism ; Terpenes/metabolism ; Ethers/chemistry/metabolism ; }, abstract = {The major archaeal membrane glycerolipids are distinguished from those of bacteria and eukaryotes by the contrasting stereochemistry of their glycerol backbones, and by the use of ether-linked isoprenoid-based alkyl chains rather than ester-linked fatty acyl chains for their hydrophobic moieties. These fascinating compounds play important roles in the extremophile lifestyles of many species, but are also present in the growing numbers of recently discovered mesophilic archaea. The past decade has witnessed significant advances in our understanding of archaea in general and their lipids in particular. Much of the new information has come from the ability to screen large microbial populations via environmental metagenomics, which has revolutionised our understanding of the extent of archaeal biodiversity that is coupled with a strict conservation of their membrane lipid compositions. Significant additional progress has come from new culturing and analytical techniques that are gradually enabling archaeal physiology and biochemistry to be studied in real time. These studies are beginning to shed light on the much-discussed and still-controversial process of eukaryogenesis, which probably involved both bacterial and archaeal progenitors. Puzzlingly, although eukaryotes retain many attributes of their putative archaeal ancestors, their lipid compositions only reflect their bacterial progenitors. Finally, elucidation of archaeal lipids and their metabolic pathways have revealed potentially interesting applications that have opened up new frontiers for biotechnological exploitation of these organisms. This review is concerned with the analysis, structure, function, evolution and biotechnology of archaeal lipids and their associated metabolic pathways.}, } @article {pmid37234538, year = {2023}, author = {Sarrocco, S and Herrera-Estrella, A and Collinge, DB}, title = {Editorial: Plant disease management in the post-genomic era: from functional genomics to genome editing, Volume II.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1203870}, pmid = {37234538}, issn = {1664-302X}, } @article {pmid37233257, year = {2023}, author = {Ahmad, N and Ritz, M and Calchera, A and Otte, J and Schmitt, I and Brueck, T and Mehlmer, N}, title = {Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {5}, pages = {}, pmid = {37233257}, issn = {2309-608X}, support = {031B0824A//Federal Ministry of Education and Research/ ; }, abstract = {Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus). They are known to produce a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here we provide a comprehensive view of the biosynthetic gene clusters of all organisms comprising a lichen thallus: fungi, green algae, and bacteria. We present two high-quality PacBio metagenomes, in which we identified a total of 460 biosynthetic gene clusters. Lichen mycobionts yielded 73-114 clusters, other lichen associated ascomycetes 8-40, green algae of the genus Trebouxia 14-19, and lichen-associated bacteria 101-105 clusters. The mycobionts contained mainly T1PKSs, followed by NRPSs, and terpenes; Trebouxia reads harbored mainly clusters linked to terpenes, followed by NRPSs and T3PKSs. Other lichen-associated ascomycetes and bacteria contained a mix of diverse biosynthetic gene clusters. In this study, we identified for the first time the biosynthetic gene clusters of entire lichen holobionts. The yet untapped biosynthetic potential of two species of the genus Hypogymnia is made accessible for further research.}, } @article {pmid37231976, year = {2023}, author = {Gao, H and Jiang, F and Zhang, J and Chi, X and Song, P and Li, B and Cai, Z and Zhang, T}, title = {Effects of ex situ conservation on diversity and function of the gut microbiota of the Tibetan wild ass (Equus kiang).}, journal = {Integrative zoology}, volume = {18}, number = {6}, pages = {1089-1104}, doi = {10.1111/1749-4877.12726}, pmid = {37231976}, issn = {1749-4877}, support = {XDA23060602//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDA2002030302//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2021-ZJ-951Q//Qinghai Province Science and Technology Plan/ ; 2019QZKK0501//Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019-SF-150//Qinghai Key R&D and Transformation Program/ ; LHZX-2020-01//Joint Grant from Chinese Academy of Sciences-People's Government of Qinghai Province on Sanjiangyuan National Park/ ; //Science and Technology Department of Qinghai Province Major Project "Sanjiangyaun National Park Animal Genome Program"/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Tibet ; Bacteria/genetics ; Animals, Wild/microbiology ; Equidae/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Ex situ conservation is the main method for the protection of endangered wildlife. To explore the effect of ex situ conservation on the gut microbiota of the kiang (Equus kiang), metagenomic sequencing combined with bioinformatics analysis was used to investigate the composition and function of the gut microbiota of the kiang. The results showed that ex situ conservation not only protected wildlife, but also affected the composition and function of gut microbiota, as well as the health of animals. In the zoo, the ratio of the relative abundance of Firmicutes to that of Bacteroidetes (F/B) is higher, clusters of potentially pathogenic bacteria (such as Catonella, Catonella, and Mycoplasma) are more numerous, the abundance of resistance genes is higher, and the abundance of metabolic functions is increased. The dynamic changes of the gut microbiota also played an important role in the nutritional absorption, energy metabolism, and environmental adaptation of the kiang. Improving the rearing environment and increasing food diversity play important roles for increasing the diversity of gut microbiota, reducing the spread of potentially pathogenic bacteria, and reducing diseases. In the wild, especially in winter and in food-deficient areas, food supplementation can enhance the gut microbial homeostasis of wild animals and reduce the impact of crises. In depth studies of the gut microbial function of wildlife have important implications for improving ex situ conservation.}, } @article {pmid37231829, year = {2023}, author = {Kawasaki, Y and Kakimoto, K and Tanaka, Y and Shimizu, H and Nishida, K and Numa, K and Kinoshita, N and Tatsumi, Y and Nakazawa, K and Koshiba, R and Hirata, Y and Ota, K and Sakiyama, N and Terazawa, T and Takeuchi, T and Miyazaki, T and Goto, M and Yokota, H and Makizaki, Y and Tanaka, Y and Nakajima, S and Ohno, H and Higuchi, K and Nakamura, S and Nishikawa, H}, title = {Relationship between Chemotherapy-Induced Diarrhea and Intestinal Microbiome Composition.}, journal = {Digestion}, volume = {104}, number = {5}, pages = {357-369}, pmid = {37231829}, issn = {1421-9867}, mesh = {Humans ; *Gastrointestinal Microbiome ; Dysbiosis/chemically induced ; Diarrhea/drug therapy ; Bacteria ; *Antineoplastic Agents/therapeutic use ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND AND AIM: Fluoropyrimidines (FPs) are key drugs in many chemotherapy regimens; however, recipients are often prone to diarrhea due to gastrointestinal toxicity. Disruption of the intestinal epithelial barrier function by FPs leads to dysbiosis, which may exacerbate intestinal epithelial cell damage as a secondary effect and trigger diarrhea. However, despite studies on chemotherapy-induced changes in the intestinal microbiome of humans, the relationship between dysbiosis and diarrhea is unclear. In this study, we aimed to investigate the relationship between chemotherapy-induced diarrhea and the intestinal microbiome.

METHODS: We conducted a single-center prospective observational study. Twenty-three patients who received chemotherapy, including FPs as first-line chemotherapy for colorectal cancer, were included. Stool samples were collected before the start of chemotherapy and after one cycle of treatment to analyze intestinal microbiome composition and perform PICRUSt predictive metagenomic analysis.

RESULTS: Gastrointestinal toxicity was observed in 7 of 23 patients (30.4%), diarrhea was observed in 4 (17.4%), and nausea and anorexia were observed in 3 (13.0%). In 19 patients treated with oral FPs, the α diversity of the microbial community decreased significantly following chemotherapy only in the diarrheal group. At the phylum level, the diarrheal group showed a significant decrease in the abundance of Firmicutes and a significant increase in the abundance of Bacteroidetes with chemotherapy (p = 0.013 and 0.011, respectively). In the same groups, at the genus level, Bifidobacterium abundance was significantly decreased (p = 0.019). In contrast, in the non-diarrheal group, Actinobacteria abundance increased significantly with chemotherapy at the phylum level (p = 0.011). Further, Bifidobacterium, Fusicatenibacter, and Dorea abundance significantly increased at the genus level (p = 0.006, 0.019, and 0.011, respectively). The PICRUSt predictive metagenomic analysis revealed that chemotherapy caused significant differences in membrane transport in KEGG pathway level 2 and in 8 KEGG pathway level 3, including transporters and oxidative phosphorylation in the diarrhea group.

CONCLUSION: Organic-acid-producing bacteria seem to be involved in diarrhea associated with chemotherapy, including FPs.}, } @article {pmid37231259, year = {2024}, author = {Pinto, Y and Chakraborty, M and Jain, N and Bhatt, AS}, title = {Phage-inclusive profiling of human gut microbiomes with Phanta.}, journal = {Nature biotechnology}, volume = {42}, number = {4}, pages = {651-662}, pmid = {37231259}, issn = {1546-1696}, support = {R01AI14862302//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01AI14375702//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1S10OD02014101//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 5T32HG000044-25//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; n/a//EIF | Stand Up To Cancer (SU2C)/ ; n/a//Alfred P. Sloan Foundation/ ; Dean's Fellowship//SU | School of Medicine, Stanford University (Stanford School of Medicine, Stanford University)/ ; NDSEG fellowship//U.S. Department of Defense (United States Department of Defense)/ ; }, mesh = {Adult ; Humans ; *Bacteriophages/genetics ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; *Viruses/genetics ; DNA Viruses/genetics ; }, abstract = {Due to technical limitations, most gut microbiome studies have focused on prokaryotes, overlooking viruses. Phanta, a virome-inclusive gut microbiome profiling tool, overcomes the limitations of assembly-based viral profiling methods by using customized k-mer-based classification tools and incorporating recently published catalogs of gut viral genomes. Phanta's optimizations consider the small genome size of viruses, sequence homology with prokaryotes and interactions with other gut microbes. Extensive testing of Phanta on simulated data demonstrates that it quickly and accurately quantifies prokaryotes and viruses. When applied to 245 fecal metagenomes from healthy adults, Phanta identifies ~200 viral species per sample, ~5× more than standard assembly-based methods. We observe a ~2:1 ratio between DNA viruses and bacteria, with higher interindividual variability of the gut virome compared to the gut bacteriome. In another cohort, we observe that Phanta performs equally well on bulk versus virus-enriched metagenomes, making it possible to study prokaryotes and viruses in a single experiment, with a single analysis.}, } @article {pmid37230981, year = {2023}, author = {Feehily, C and O'Neill, IJ and Walsh, CJ and Moore, RL and Killeen, SL and Geraghty, AA and Lawton, EM and Byrne, D and Sanchez-Gallardo, R and Nori, SRC and Nielsen, IB and Wortmann, E and Matthews, E and O'Flaherty, R and Rudd, PM and Groeger, D and Shanahan, F and Saldova, R and McAuliffe, FM and Van Sinderen, D and Cotter, PD}, title = {Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3015}, pmid = {37230981}, issn = {2041-1723}, mesh = {Humans ; Infant ; Female ; Pregnancy ; *Bifidobacterium ; Mothers ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; Parturition ; Feces/microbiology ; }, abstract = {A significant proportion of the infant gut microbiome is considered to be acquired from the mother during and after birth. Thus begins a lifelong and dynamic relationship with microbes that has an enduring impact on host health. Based on a cohort of 135 mother-infant (F = 72, M = 63) dyads (MicrobeMom: ISRCTN53023014), we investigated the phenomenon of microbial strain transfer, with a particular emphasis on the use of a combined metagenomic-culture-based approach to determine the frequency of strain transfer involving members of the genus Bifidobacterium, including species/strains present at low relative abundance. From the isolation and genome sequencing of over 449 bifidobacterial strains, we validate and augment metagenomics-based evidence to reveal strain transfer in almost 50% of dyads. Factors important in strain transfer include vaginal birth, spontaneous rupture of amniotic membranes, and avoidance of intrapartum antibiotics. Importantly, we reveal that several transfer events are uniquely detected employing either cultivation or metagenomic sequencing, highlighting the requirement for a dual approach to obtain an in-depth insight into this transfer process.}, } @article {pmid37228141, year = {2023}, author = {Young, BD and Rosales, SM and Enochs, IC and Kolodziej, G and Formel, N and Moura, A and D'Alonso, GL and Traylor-Knowles, N}, title = {Different disease inoculations cause common responses of the host immune system and prokaryotic component of the microbiome in Acropora palmata.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0286293}, pmid = {37228141}, issn = {1932-6203}, mesh = {Animals ; Viverridae/genetics ; *Anthozoa/genetics/microbiology ; *Microbiota/genetics ; Gene Expression Profiling ; Serratia marcescens/genetics ; Coral Reefs ; }, abstract = {Reef-building corals contain a complex consortium of organisms, a holobiont, which responds dynamically to disease, making pathogen identification difficult. While coral transcriptomics and microbiome communities have previously been characterized, similarities and differences in their responses to different pathogenic sources has not yet been assessed. In this study, we inoculated four genets of the Caribbean branching coral Acropora palmata with a known coral pathogen (Serratia marcescens) and white band disease. We then characterized the coral's transcriptomic and prokaryotic microbiomes' (prokaryiome) responses to the disease inoculations, as well as how these responses were affected by a short-term heat stress prior to disease inoculation. We found strong commonality in both the transcriptomic and prokaryiomes responses, regardless of disease inoculation. Differences, however, were observed between inoculated corals that either remained healthy or developed active disease signs. Transcriptomic co-expression analysis identified that corals inoculated with disease increased gene expression of immune, wound healing, and fatty acid metabolic processes. Co-abundance analysis of the prokaryiome identified sets of both healthy-and-disease-state bacteria, while co-expression analysis of the prokaryiomes' inferred metagenomic function revealed infected corals' prokaryiomes shifted from free-living to biofilm states, as well as increasing metabolic processes. The short-term heat stress did not increase disease susceptibility for any of the four genets with any of the disease inoculations, and there was only a weak effect captured in the coral hosts' transcriptomic and prokaryiomes response. Genet identity, however, was a major driver of the transcriptomic variance, primarily due to differences in baseline immune gene expression. Despite genotypic differences in baseline gene expression, we have identified a common response for components of the coral holobiont to different disease inoculations. This work has identified genes and prokaryiome members that can be focused on for future coral disease work, specifically, putative disease diagnostic tools.}, } @article {pmid37227475, year = {2023}, author = {Bou Orm, E and Sauvagère, S and Rocher, J and Benezet, JC and Bayle, S and Siatka, C and Bergeret, A and Malhautier, L}, title = {Estimating the bias related to DNA recovery from hemp stems for retting microbial community investigation.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {14}, pages = {4665-4681}, pmid = {37227475}, issn = {1432-0614}, mesh = {*Cannabis/genetics/metabolism ; DNA/metabolism ; Bacteria/genetics ; *Microbiota ; Soil ; }, abstract = {The industrial hemp plant Cannabis sativa is a source of vegetable fiber for both textiles and biocomposite applications. After harvesting, the plant stems are laid out on the ground and colonized by microorganisms (bacteria and fungi) naturally present in the soil and on the stems. By producing hydrolytic enzymes that degrade the plant wall polymers, the natural cement that binds the fiber bundles together is removed, thus facilitating their dissociation (retting process) which is required for producing high-performant fibers. To investigate temporal dynamics of retting microbial communities (density levels, diversity, and structure), a reliable protocol for extracting genomic DNA from stems is mandatory. However, very little attention has been paid to the methodological aspects of nucleic acid extraction, although they are crucial for the significance of the final result. Three protocols were selected and tested: a commercial kit (FastDNA™ Spin Kit for soil), the Gns-GII procedure, and a custom procedure from the Genosol platform. A comparative analysis was carried out on soil and two different varieties of hemp stem. The efficiency of each method was measured by evaluating both the quantity and quality of the extracted DNA and the abundance and taxonomy of bacterial and fungal populations. The Genosol protocol provides interesting yields in terms of quantity and quality of genomic DNA compared to the other two protocols. However, no major difference was observed in microbial diversity between the two extraction procedures (FastDNA™ SPIN Kit and Genosol protocol). Based on these results, the FastDNA™ SPIN kit or the Genosol procedure seems to be suitable for studying bacterial and fungal communities of the retting process. It should be noted that this work has demonstrated the importance of evaluating biases associated with DNA recovery from hemp stems. KEY POINTS: • Metagenomic DNA was successfully extracted from hemp stem samples using three different protocols. • Further evaluation was performed in terms of DNA yield and purity, abundance level, and microbial community structure. • This work exhibited the crucial importance of DNA recovery bias evaluation.}, } @article {pmid37225687, year = {2023}, author = {Zhao, F and Yang, L and Zhang, T and Zhuang, D and Wu, Q and Yu, J and Tian, C and Zhang, Z}, title = {Gut microbiome signatures of extreme environment adaption in Tibetan pig.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {27}, pmid = {37225687}, issn = {2055-5008}, mesh = {Swine ; Animals ; *Gastrointestinal Microbiome ; Tibet ; Ultraviolet Rays ; Acclimatization ; Acetic Acid ; Extreme Environments ; Mammals ; }, abstract = {Tibetan pigs (TPs) can adapt to the extreme environments in the Tibetan plateau implicated by their self-genome signals, but little is known about roles of the gut microbiota in the host adaption. Here, we reconstructed 8210 metagenome-assembled genomes from TPs (n = 65) living in high-altitude and low-altitude captive pigs (87 from China-CPs and 200 from Europe-EPs) that were clustered into 1050 species-level genome bins (SGBs) at the threshold of 95% average nucleotide identity. 73.47% of SGBs represented new species. The gut microbial community structure analysis based on 1,048 SGBs showed that TPs was significantly different from low-altitude captive pigs. TP-associated SGBs enabled to digest multiple complex polysaccharides, including cellulose, hemicellulose, chitin and pectin. Especially, we found TPs showed the most common enrichment of phyla Fibrobacterota and Elusimicrobia, which were involved in the productions of short- and medium-chain fatty acids (acetic acid, butanoate and propanoate; octanomic, decanoic and dodecanoic acids), as well as in the biosynthesis of lactate, 20 essential amino acids, multiple B vitamins (B1, B2, B3, B5, B7 and B9) and cofactors. Unexpectedly, Fibrobacterota solely showed powerful metabolic capacity, including the synthesis of acetic acid, alanine, histidine, arginine, tryptophan, serine, threonine, valine, B2, B5, B9, heme and tetrahydrofolate. These metabolites might contribute to host adaptation to high-altitude, such as energy harvesting and resistance against hypoxia and ultraviolet radiation. This study provides insights into understanding the role of gut microbiome played in mammalian high-altitude adaptation and discovers some potential microbes as probiotics for improving animal health.}, } @article {pmid37224782, year = {2023}, author = {Xu, M and Su, S and Jiang, S and Li, W and Zhang, Z and Zhang, J and Hu, X}, title = {Short-term arecoline exposure affected the systemic health state of mice, in which gut microbes played an important role.}, journal = {Ecotoxicology and environmental safety}, volume = {259}, number = {}, pages = {115055}, doi = {10.1016/j.ecoenv.2023.115055}, pmid = {37224782}, issn = {1090-2414}, mesh = {Animals ; Mice ; *Arecoline/pharmacology/toxicity ; Interleukin-6/metabolism ; *Gastrointestinal Microbiome ; Lipid Metabolism ; Liver ; }, abstract = {Arecoline is a critical bioactive component in areca nuts with toxicity and pharmacological activities. However, its effects on body health remain unclear. Here, we investigated the effects of arecoline on physiologic and biochemical parameters in mouse serum, liver, brain, and intestine. The effect of arecoline on gut microbiota was investigated based on shotgun metagenomic sequencing. The results showed that arecoline promoted lipid metabolism in mice, manifested as significantly reduced serum TC and TG and liver TC levels and a reduction in abdominal fat accumulation. Arecoline intake significantly modulated the neurotransmitters 5-HT and NE levels in the brain. Notably, arecoline intervention significantly increased serum IL-6 and LPS levels, leading to inflammation in the body. High-dose arecoline significantly reduced liver GSH levels and increased MDA levels, which led to oxidative stress in the liver. Arecoline intake promoted the release of intestinal IL-6 and IL-1β, causing intestinal injury. In addition, we observed a significant response of gut microbiota to arecoline intake, reflecting significant changes in diversity and function of the gut microbes. Further mechanistic exploration suggested that arecoline intake can regulate gut microbes and ultimately affect the host's health. This study provided technical help for the pharmacochemical application and toxicity control of arecoline.}, } @article {pmid37223792, year = {2023}, author = {Bertola, M and Righetti, L and Gazza, L and Ferrarini, A and Fornasier, F and Cirlini, M and Lolli, V and Galaverna, G and Visioli, G}, title = {Perenniality, more than genotypes, shapes biological and chemical rhizosphere composition of perennial wheat lines.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1172857}, pmid = {37223792}, issn = {1664-462X}, abstract = {Perennial grains provide various ecosystem services compared to the annual counterparts thanks to their extensive root system and permanent soil cover. However, little is known about the evolution and diversification of perennial grains rhizosphere and its ecological functions over time. In this study, a suite of -OMICSs - metagenomics, enzymomics, metabolomics and lipidomics - was used to compare the rhizosphere environment of four perennial wheat lines at the first and fourth year of growth in comparison with an annual durum wheat cultivar and the parental species Thinopyrum intermedium. We hypothesized that wheat perenniality has a greater role in shaping the rhizobiome composition, biomass, diversity, and activity than plant genotypes because perenniality affects the quality and quantity of C input - mainly root exudates - hence modulating the plant-microbes crosstalk. In support of this hypothesis, the continuous supply of sugars in the rhizosphere along the years created a favorable environment for microbial growth which is reflected in a higher microbial biomass and enzymatic activity. Moreover, modification in the rhizosphere metabolome and lipidome over the years led to changes in the microbial community composition favoring the coexistence of more diverse microbial taxa, increasing plant tolerance to biotic and abiotic stresses. Despite the dominance of the perenniality effect, our data underlined that the OK72 line rhizobiome distinguished from the others by the increase in abundance of Pseudomonas spp., most of which are known as potential beneficial microorganisms, identifying this line as a suitable candidate for the study and selection of new perennial wheat lines.}, } @article {pmid37222807, year = {2023}, author = {Broman, E and Abdelgadir, M and Bonaglia, S and Forsberg, SC and Wikström, J and Gunnarsson, JS and Nascimento, FJA and Sjöling, S}, title = {Long-Term Pollution Does Not Inhibit Denitrification and DNRA by Adapted Benthic Microbial Communities.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2357-2372}, pmid = {37222807}, issn = {1432-184X}, support = {3150-3.1.1-2017//Östersjöstiftelsen/ ; 2020-0002//Naturvårdsverket/ ; 1.1-1602-0106//Statens geotekniska institut/ ; }, mesh = {Nitrates ; *Ammonium Compounds ; Denitrification ; Nitrogen ; *Microbiota ; Oxidation-Reduction ; }, abstract = {Denitrification in sediments is a key microbial process that removes excess fixed nitrogen, while dissimilatory nitrate reduction to ammonium (DNRA) converts nitrate to ammonium. Although microorganisms are responsible for essential nitrogen (N) cycling, it is not yet fully understood how these microbially mediated processes respond to toxic hydrophobic organic compounds (HOCs) and metals. In this study, we sampled long-term polluted sediment from the outer harbor of Oskarshamn (Baltic Sea), measured denitrification and DNRA rates, and analyzed taxonomic structure and N-cycling genes of microbial communities using metagenomics. Results showed that denitrification and DNRA rates were within the range of a national reference site and other unpolluted sites in the Baltic Sea, indicating that long-term pollution did not significantly affect these processes. Furthermore, our results indicate an adaptation to metal pollution by the N-cycling microbial community. These findings suggest that denitrification and DNRA rates are affected more by eutrophication and organic enrichment than by historic pollution of metals and organic contaminants.}, } @article {pmid37222264, year = {2023}, author = {Carr, RM and Li, Y and Chau, L and Friedman, ES and Lee, JJ and Adorini, L and Erickson, M and Zaru, L and Shringarpure, R and MacConell, L and Bittinger, K and Li, H and Wu, GD}, title = {An integrated analysis of fecal microbiome and metabolomic features distinguish non-cirrhotic NASH from healthy control populations.}, journal = {Hepatology (Baltimore, Md.)}, volume = {78}, number = {6}, pages = {1843-1857}, pmid = {37222264}, issn = {1527-3350}, support = {P30 DK050306/DK/NIDDK NIH HHS/United States ; R01 AA026302/AA/NIAAA NIH HHS/United States ; R01 GM123056/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/complications ; Cross-Sectional Studies ; Liver Cirrhosis/complications ; Fibrosis ; *Gastrointestinal Microbiome ; Bile Acids and Salts ; Feces/microbiology ; Biomarkers ; }, abstract = {BACKGROUND AND AIMS: There is great interest in identifying microbiome features as reliable noninvasive diagnostic and/or prognostic biomarkers for non-cirrhotic NASH fibrosis. Several cross-sectional studies have reported gut microbiome features associated with advanced NASH fibrosis and cirrhosis, where the most prominent features are associated with cirrhosis. However, no large, prospectively collected data exist establishing microbiome features that discern non-cirrhotic NASH fibrosis, integrate the fecal metabolome as disease biomarkers, and are unconfounded by BMI and age.

APPROACH AND RESULTS: Results from shotgun metagenomic sequencing performed on fecal samples prospectively collected from 279 US patients with biopsy-proven NASH (F1-F3 fibrosis) enrolled in the REGENERATE I303 study were compared to those from 3 healthy control cohorts and integrated with the absolute quantification of fecal bile acids. Microbiota beta-diversity was different, and BMI- and age-adjusted logistic regression identified 12 NASH-associated species. Random forest prediction models resulted in an AUC of 0.75-0.81 in a receiver operator characteristic analysis. In addition, specific fecal bile acids were significantly lower in NASH and correlated with plasma C4 levels. Microbial gene abundance analysis revealed 127 genes increased in controls, many involving protein synthesis, whereas 362 genes were increased in NASH many involving bacterial environmental responses (false discovery rate < 0.01). Finally, we provide evidence that fecal bile acid levels may be a better discriminator of non-cirrhotic NASH versus health than either plasma bile acids or gut microbiome features.

CONCLUSIONS: These results may have value as a set of baseline characteristics of non-cirrhotic NASH against which therapeutic interventions to prevent cirrhosis can be compared and microbiome-based diagnostic biomarkers identified.}, } @article {pmid37221274, year = {2023}, author = {Megremis, S and Constantinides, B and Xepapadaki, P and Yap, CF and Sotiropoulos, AG and Bachert, C and Finotto, S and Jartti, T and Tapinos, A and Vuorinen, T and Andreakos, E and Robertson, DL and Papadopoulos, NG}, title = {Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8319}, pmid = {37221274}, issn = {2045-2322}, support = {MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Child ; Humans ; Child, Preschool ; Eukaryota ; *Bacteriophages ; Virome ; Eukaryotic Cells ; *Asthma ; *Anelloviridae ; Asymptomatic Diseases ; }, abstract = {Asthma development and exacerbation is linked to respiratory virus infections. There is limited information regarding the presence of viruses during non-exacerbation/infection periods. We investigated the nasopharyngeal/nasal virome during a period of asymptomatic state, in a subset of 21 healthy and 35 asthmatic preschool children from the Predicta cohort. Using metagenomics, we described the virome ecology and the cross-species interactions within the microbiome. The virome was dominated by eukaryotic viruses, while prokaryotic viruses (bacteriophages) were independently observed with low abundance. Rhinovirus B species consistently dominated the virome in asthma. Anelloviridae were the most abundant and rich family in both health and asthma. However, their richness and alpha diversity were increased in asthma, along with the co-occurrence of different Anellovirus genera. Bacteriophages were richer and more diverse in healthy individuals. Unsupervised clustering identified three virome profiles that were correlated to asthma severity and control and were independent of treatment, suggesting a link between the respiratory virome and asthma. Finally, we observed different cross-species ecological associations in the healthy versus the asthmatic virus-bacterial interactome, and an expanded interactome of eukaryotic viruses in asthma. Upper respiratory virome "dysbiosis" appears to be a novel feature of pre-school asthma during asymptomatic/non-infectious states and merits further investigation.}, } @article {pmid37221272, year = {2023}, author = {Hsia, K and Zhao, N and Chung, M and Algarrahi, K and Montaser Kouhsari, L and Fu, M and Chen, H and Singh, S and Michaud, DS and Jangi, S}, title = {Alterations in the Fungal Microbiome in Ulcerative Colitis.}, journal = {Inflammatory bowel diseases}, volume = {29}, number = {10}, pages = {1613-1621}, pmid = {37221272}, issn = {1536-4844}, support = {KL2 TR002545/TR/NCATS NIH HHS/United States ; R01 DK135937/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Humans ; *Colitis, Ulcerative/therapy ; *Mycobiome ; Prospective Studies ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; Candida ; *Biological Products ; }, abstract = {BACKGROUND: Although gut fungi have been implicated in the immunopathogenesis of inflammatory bowel disease, the fungal microbiome has not been deeply explored across endohistologic activity and treatment exposure in ulcerative colitis.

METHODS: We analyzed data from the SPARC IBD (Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease) registry. We evaluated the fungal composition of fecal samples from 98 patients with ulcerative colitis across endoscopic activity (n = 43), endohistologic activity (n = 41), and biologic exposure (n = 82). Across all subgroups, we assessed fungal diversity and differential abundance of taxonomic groups.

RESULTS: We identified 500 unique fungal amplicon sequence variants across the cohort of 82 patients, dominated by phylum Ascomycota. Compared with endoscopic remission, patients with endoscopic activity had increased Saccharomyces (log2 fold change = 4.54; adjusted P < 5 × 10-5) and increased Candida (log2 fold change = 2.56; adjusted P < .03). After adjusting for age, sex, and biologic exposure among patients with endoscopic activity, Saccharomyces (log2 fold change = 7.76; adjusted P < 1 × 10-15) and Candida (log2 fold change = 7.28; adjusted P< 1 × 10-8) remained enriched during endoscopic activity compared with quiescence.

CONCLUSIONS: Endoscopic inflammation in ulcerative colitis is associated with an expansion of Saccharomyces and Candida compared with remission. The role of these fungal taxa as potential biomarkers and targets for personalized approaches to therapeutics in ulcerative colitis should be evaluated.}, } @article {pmid37217592, year = {2023}, author = {Waldrop, MP and Chabot, CL and Liebner, S and Holm, S and Snyder, MW and Dillon, M and Dudgeon, SR and Douglas, TA and Leewis, MC and Walter Anthony, KM and McFarland, JW and Arp, CD and Bondurant, AC and Taş, N and Mackelprang, R}, title = {Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients.}, journal = {The ISME journal}, volume = {17}, number = {8}, pages = {1224-1235}, pmid = {37217592}, issn = {1751-7370}, support = {RL5 GM118975/GM/NIGMS NIH HHS/United States ; }, mesh = {*Permafrost/chemistry ; Soil/chemistry ; Soil Microbiology ; *Microbiota/genetics ; Metagenome ; Carbon/metabolism ; }, abstract = {Permafrost underlies approximately one quarter of Northern Hemisphere terrestrial surfaces and contains 25-50% of the global soil carbon (C) pool. Permafrost soils and the C stocks within are vulnerable to ongoing and future projected climate warming. The biogeography of microbial communities inhabiting permafrost has not been examined beyond a small number of sites focused on local-scale variation. Permafrost is different from other soils. Perennially frozen conditions in permafrost dictate that microbial communities do not turn over quickly, thus possibly providing strong linkages to past environments. Thus, the factors structuring the composition and function of microbial communities may differ from patterns observed in other terrestrial environments. Here, we analyzed 133 permafrost metagenomes from North America, Europe, and Asia. Permafrost biodiversity and taxonomic distribution varied in relation to pH, latitude and soil depth. The distribution of genes differed by latitude, soil depth, age, and pH. Genes that were the most highly variable across all sites were associated with energy metabolism and C-assimilation. Specifically, methanogenesis, fermentation, nitrate reduction, and replenishment of citric acid cycle intermediates. This suggests that adaptations to energy acquisition and substrate availability are among some of the strongest selective pressures shaping permafrost microbial communities. The spatial variation in metabolic potential has primed communities for specific biogeochemical processes as soils thaw due to climate change, which could cause regional- to global- scale variation in C and nitrogen processing and greenhouse gas emissions.}, } @article {pmid37215132, year = {2023}, author = {Zhang, L and Wang, F and Jia, L and Yan, H and Gao, L and Tian, Y and Su, X and Zhang, X and Lv, C and Ma, Z and Xue, Y and Lin, Q and Wang, K}, title = {Edwardsiella piscicida infection reshapes the intestinal microbiome and metabolome of big-belly seahorses: mechanistic insights of synergistic actions of virulence factors.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1135588}, pmid = {37215132}, issn = {1664-3224}, mesh = {*Enteritis ; Metabolome ; *Gastrointestinal Microbiome ; *Smegmamorpha/metabolism ; Virulence ; Edwardsiella ; Virulence Factors/metabolism ; Fishes/metabolism ; Animals ; }, abstract = {Uncovering the mechanism underlying the pathogenesis of Edwardsiella piscicida-induced enteritis is essential for global aquaculture. In the present study, we identified E. piscicida as a lethal pathogen of the big-belly seahorse (Hippocampus abdominalis) and revealed its pathogenic pattern and characteristics by updating our established bacterial enteritis model and evaluation system. Conjoint analysis of metagenomic and metabolomic data showed that 15 core virulence factors could mutually coordinate the remodeling of intestinal microorganisms and host metabolism and induce enteritis in the big-belly seahorse. Specifically, the Flagella, Type IV pili, and Lap could significantly increase the activities of the representative functional pathways of both flagella assembly and bacterial chemotaxis in the intestinal microbiota (P < 0.01) to promote pathogen motility, adherence, and invasion. Legiobactin, IraAB, and Hpt could increase ABC transporter activity (P < 0.01) to compete for host nutrition and promote self-replication. Capsule1, HP-NAP, and FarAB could help the pathogen to avoid phagocytosis. Upon entering epithelial cells and phagocytes, Bsa T3SS and Dot/Icm could significantly increase bacterial secretion system activity (P < 0.01) to promote the intracellular survival and replication of the pathogen and the subsequent invasion of the neighboring tissues. Finally, LPS3 could significantly increase lipopolysaccharide biosynthesis (P < 0.01) to release toxins and kill the host. Throughout the pathogenic process, BopD, PhoP, and BfmRS significantly activated the two-component system (P < 0.01) to coordinate with other VFs to promote deep invasion. In addition, the levels of seven key metabolic biomarkers, Taurine, L-Proline, Uridine, L-Glutamate, Glutathione, Xanthosine, and L-Malic acid, significantly decreased (P < 0.01), and they can be used for characterizing E. piscicida infection. Overall, the present study systematically revealed how a combination of virulence factors mediate E. piscicida-induced enteritis in fish for the first time, providing a theoretical reference for preventing and controlling this disease in the aquaculture of seahorses and other fishes.}, } @article {pmid37213492, year = {2023}, author = {Zhang, X and Liang, Y and Zheng, K and Wang, Z and Dong, Y and Liu, Y and Ren, L and Wang, H and Han, Y and McMinn, A and Sung, YY and Mok, WJ and Wong, LL and He, J and Wang, M}, title = {Characterization and genomic analysis of phage vB_ValR_NF, representing a new viral family prevalent in the Ulva prolifera blooms.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1161265}, pmid = {37213492}, issn = {1664-302X}, abstract = {INTRODUCTION: Vibrio is an important bacterial genus containing many pathogenic species. Although more and more Vibrio phages were isolated, the genome, ecology and evolution of Vibrio phages and their roles in bacteriophage therapy, have not been fully revealed.

METHODS: Novel Vibrio phage vB_ValR_NF infecting Vibrio alginolyticus was isolated from the coastal waters of Qingdao during the Ulva prolifera blooms, Characterization and genomic feature of phage vB_ValR_NF has been analysed using phage isolation, sequencing and metagenome method.

RESULTS AND DISCUSSION: Phage vB_ValR_NF has a siphoviral morphology (icosahedral head 114±1 nm in diameter; a tail length of 231±1 nm), a short latent period (30 minutes) and a large burst size (113 virions per cell), and the thermal/pH stability study showed that phage vB_ValR_NF was highly tolerant to a range of pHs (4-12) and temperatures (-20 - 45 °C), respectively. Host range analysis suggests that phage vB_ValR_NF not only has a high inhibitory ability against the host strain V. alginolyticus, but also can infect 7 other Vibrio strains. In addition, the phage vB_ValR_NF has a double-stranded 44, 507 bp DNA genome, with 43.10 % GC content and 75 open reading frames. Three auxiliary metabolic genes associated with aldehyde dehydrogenase, serine/threonine protein phosphatase and calcineurin-like phosphoesterase were predicted, might help the host V. alginolyticus occupy the survival advantage, thus improving the survival chance of phage vB_ValR_NF under harsh conditions. This point can be supported by the higher abundance of phage vB_ValR_NF during the U. prolifera blooms than in other marine environments. Further phylogenetic and genomic analysis shows that the viral group represented by Vibrio phage vB_ValR_NF is different from other well-defined reference viruses, and can be classified into a new family, named Ruirongviridae. In general, as a new marine phage infecting V. alginolyticus, phage vB_ValR_NF provides basic information for further molecular research on phage-host interactions and evolution, and may unravel a novel insight into changes in the community structure of organisms during the U. prolifera blooms. At the same time, its high tolerance to extreme conditions and excellent bactericidal ability will become important reference factors when evaluating the potential of phage vB_ValR_NF in bacteriophage therapy in the future.}, } @article {pmid37213047, year = {2023}, author = {Chaudhari, DS and Jain, S and Yata, VK and Mishra, SP and Kumar, A and Fraser, A and Kociolek, J and Dangiolo, M and Smith, A and Golden, A and Masternak, MM and Holland, P and Agronin, M and White-Williams, C and Arikawa, AY and Labyak, CA and Yadav, H}, title = {Unique trans-kingdom microbiome structural and functional signatures predict cognitive decline in older adults.}, journal = {GeroScience}, volume = {45}, number = {5}, pages = {2819-2834}, pmid = {37213047}, issn = {2509-2723}, support = {RF1AG071762/AG/NIA NIH HHS/United States ; R56AG069676/AG/NIA NIH HHS/United States ; R21AG072379/AG/NIA NIH HHS/United States ; R56AG064075/AG/NIA NIH HHS/United States ; U01 AG076928/AG/NIA NIH HHS/United States ; U01AG076928/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Aged ; RNA, Ribosomal, 16S/genetics ; Pilot Projects ; *Microbiota/genetics ; *Cognitive Dysfunction ; Bacteria/genetics ; *Dementia ; }, abstract = {The prevalence of age-related cognitive disorders/dementia is increasing, and effective prevention and treatment interventions are lacking due to an incomplete understanding of aging neuropathophysiology. Emerging evidence suggests that abnormalities in gut microbiome are linked with age-related cognitive decline and getting acceptance as one of the pillars of the Geroscience hypothesis. However, the potential clinical importance of gut microbiome abnormalities in predicting the risk of cognitive decline in older adults is unclear. Till now the majority of clinical studies were done using 16S rRNA sequencing which only accounts for analyzing bacterial abundance, while lacking an understanding of other crucial microbial kingdoms, such as viruses, fungi, archaea, and the functional profiling of the microbiome community. Utilizing data and samples of older adults with mild cognitive impairment (MCI; n = 23) and cognitively healthy controls (n = 25). Our whole-genome metagenomic sequencing revealed that the gut of older adults with MCI harbors a less diverse microbiome with a specific increase in total viruses and a decrease in bacterial abundance compared with controls. The virome, bacteriome, and microbial metabolic signatures were significantly distinct in subjects with MCI versus controls. Selected bacteriome signatures show high predictive potential of cognitive dysfunction than virome signatures while combining virome and metabolic signatures with bacteriome boosts the prediction power. Altogether, the results from our pilot study indicate that trans-kingdom microbiome signatures are significantly distinct in MCI gut compared with controls and may have utility for predicting the risk of developing cognitive decline and dementia- debilitating public health problems in older adults.}, } @article {pmid37212075, year = {2023}, author = {Brown, EL and Essigmann, HT and Hoffman, KL and Alexander, AS and Newmark, M and Jiang, ZD and Suescun, J and Schiess, MC and Hanis, CL and DuPont, HL}, title = {IgA-Biome Profiles Correlate with Clinical Parkinson's Disease Subtypes.}, journal = {Journal of Parkinson's disease}, volume = {13}, number = {4}, pages = {501-513}, pmid = {37212075}, issn = {1877-718X}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Parkinson Disease/complications ; Tremor/etiology ; *Gastrointestinal Microbiome/physiology ; Disease Progression ; Immunoglobulin A ; }, abstract = {BACKGROUND: Parkinson's disease is a heterogeneous neurodegenerative disorder with distinctive gut microbiome patterns suggesting that interventions targeting the gut microbiota may prevent, slow, or reverse disease progression and severity.

OBJECTIVE: Because secretory IgA (SIgA) plays a key role in shaping the gut microbiota, characterization of the IgA-Biome of individuals classified into either the akinetic rigid (AR) or tremor dominant (TD) Parkinson's disease clinical subtypes was used to further define taxa unique to these distinct clinical phenotypes.

METHODS: Flow cytometry was used to separate IgA-coated and -uncoated bacteria from stool samples obtained from AR and TD patients followed by amplification and sequencing of the V4 region of the 16 S rDNA gene on the MiSeq platform (Illumina).

RESULTS: IgA-Biome analyses identified significant alpha and beta diversity differences between the Parkinson's disease phenotypes and the Firmicutes/Bacteroides ratio was significantly higher in those with TD compared to those with AR. In addition, discriminant taxa analyses identified a more pro-inflammatory bacterial profile in the IgA+ fraction of those with the AR clinical subclass compared to IgA-Biome analyses of those with the TD subclass and with the taxa identified in the unsorted control samples.

CONCLUSION: IgA-Biome analyses underscores the importance of the host immune response in shaping the gut microbiome potentially affecting disease progression and presentation. In the present study, IgA-Biome analyses identified a unique proinflammatory microbial signature in the IgA+ fraction of those with AR that would have otherwise been undetected using conventional microbiome analysis approaches.}, } @article {pmid37211644, year = {2023}, author = {Urvois, T and Perrier, C and Roques, A and Sauné, L and Courtin, C and Kajimura, H and Hulcr, J and Cognato, AI and Auger-Rozenberg, MA and Kerdelhué, C}, title = {The worldwide invasion history of a pest ambrosia beetle inferred using population genomics.}, journal = {Molecular ecology}, volume = {32}, number = {15}, pages = {4381-4400}, doi = {10.1111/mec.16993}, pmid = {37211644}, issn = {1365-294X}, mesh = {Animals ; *Coleoptera/genetics ; *Weevils ; Ambrosia/genetics ; Metagenomics ; Europe ; Introduced Species ; }, abstract = {Xylosandrus crassiusculus, a fungus-farming wood borer native to Southeastern Asia, is the most rapidly spreading invasive ambrosia species worldwide. Previous studies focusing on its genetic structure suggested the existence of cryptic genetic variation in this species. Yet, these studies used different genetic markers, focused on different geographical areas and did not include Europe. Our first goal was to determine the worldwide genetic structure of this species based on both mitochondrial and genomic markers. Our second goal was to study X. crassiusculus' invasion history on a global level and identify the origins of the invasion in Europe. We used a COI and RAD sequencing design to characterize 188 and 206 specimens worldwide, building the most comprehensive genetic data set for any ambrosia beetle to date. The results were largely consistent between markers. Two differentiated genetic clusters were invasive, albeit in different regions of the world. The markers were inconsistent only for a few specimens found exclusively in Japan. Mainland USA could have acted as a source for further expansion to Canada and Argentina through stepping stone expansion and bridgehead events. We showed that Europe was only colonized by Cluster II through a complex invasion history including several arrivals from multiple origins in the native area, and possibly including bridgehead from the United States. Our results also suggested that Spain was colonized directly from Italy through intracontinental dispersion. It is unclear whether the mutually exclusive allopatric distribution of the two clusters is due to neutral effects or due to different ecological requirements.}, } @article {pmid37210808, year = {2023}, author = {Lamichhane, S and Härkönen, T and Vatanen, T and Hyötyläinen, T and Knip, M and Orešič, M}, title = {Impact of exposure to per- and polyfluoroalkyl substances on fecal microbiota composition in mother-infant dyads.}, journal = {Environment international}, volume = {176}, number = {}, pages = {107965}, doi = {10.1016/j.envint.2023.107965}, pmid = {37210808}, issn = {1873-6750}, support = {DP3 DK094338/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Female ; Humans ; Infant ; Mothers ; *Microbiota ; Maternal Exposure ; Bacteria/genetics ; *Fluorocarbons/toxicity ; *Environmental Pollutants ; *Alkanesulfonic Acids ; }, abstract = {There is growing evidence suggesting that chemical exposure alters gut microbiota composition. However, not much is known about the impact of per- and polyfluoroalkyl substances (PFAS) on the gut microbial community. Here, in a mother-infant study, we set out to identify the gut bacterial species that associate with chemical exposure before (maternal) and after (maternal, infant) birth. Paired serum and stool samples were collected from mother-infant dyads (n = 30) in a longitudinal setting. PFAS were quantified in maternal serum to examine their associations with the microbial compositions (determined by shotgun metagenomic sequencing) in mothers and infants. High maternal exposure to PFAS was consistently associated with increased abundance of Methanobrevibacter smithii in maternal stool. Among individual PFAS compounds, PFOS and PFHpS showed the strongest association with M. smithii. However, maternal total PFAS exposure associated only weakly with the infant microbiome. Our findings suggest that PFAS exposure affects the composition of the adult gut microbiome.}, } @article {pmid37210515, year = {2023}, author = {Leleiwi, I and Rodriguez-Ramos, J and Shaffer, M and Sabag-Daigle, A and Kokkinias, K and Flynn, RM and Daly, RA and Kop, LFM and Solden, LM and Ahmer, BMM and Borton, MA and Wrighton, KC}, title = {Exposing new taxonomic variation with inflammation - a murine model-specific genome database for gut microbiome researchers.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {114}, pmid = {37210515}, issn = {2049-2618}, support = {R01 AI143288/AI/NIAID NIH HHS/United States ; T32 GM132057/GM/NIGMS NIH HHS/United States ; R01AI143288/NH/NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; Disease Models, Animal ; Mice, Inbred CBA ; *Microbiota ; Inflammation ; Bacteroidetes ; }, abstract = {BACKGROUND: The murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs.

RESULTS: Here we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated and Salmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~ 42.4 Gbps/sample), we reconstructed 2281 bacterial and 4516 viral draft genomes. Salmonella challenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of the Alistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation-resistant strains.

CONCLUSIONS: This CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on how Salmonella remodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches. Salmonella-induced inflammation suppressed Alistipes and other dominant members, while rarer commensals like Lactobacillus and Enterococcus endure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally. Video Abstract.}, } @article {pmid37209986, year = {2023}, author = {Zhang, M and Tang, H and Chen, Y and Chen, Z and Xu, Y and Fu, X and Sun, Y and Zhao, Z}, title = {Impact of environmental characteristics on children's gut microbiota - A pilot study in assessing the role of indoor microbiome and metabolites.}, journal = {Environmental research}, volume = {234}, number = {}, pages = {116114}, doi = {10.1016/j.envres.2023.116114}, pmid = {37209986}, issn = {1096-0953}, mesh = {Humans ; Child ; *Gastrointestinal Microbiome/physiology ; Pilot Projects ; Tryptophan/metabolism ; China ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Indoles ; }, abstract = {BACKGROUND: A diverse and balanced human gut microbiota is crucial for maintaining normal human physiological functions. However, the impact of indoor microbiome and metabolites on gut microbiota is not well understood.

METHODS: A self-administered questionnaire was used to collect information on more than 40 personal and environmental characteristics and dietary habits from 56 children in Shanghai, China. Shotgun metagenomics and untargeted liquid chromatography-mass spectrometry (LC-MS) were used to characterize the indoor microbiome and metabolomic/chemical exposure in children's living rooms. PacBio full-length 16 S rRNA sequencing was used to characterize children's gut microbiota. Associations between environmental characteristics and gut microbiota diversity/composition were assessed using PERMANOVA and regression.

RESULTS: In total, 6247 and 318 indoor and gut microbial species and 1442 indoor metabolites were characterized. Age of children (R[2] = 0.033, p = 0.008), age start kindergarten (R[2] = 0.029, p = 0.03), living adjacent to heavy traffic (R[2] = 0.031, p = 0.01) and drinking soft drinks (R[2] = 0.028, p = 0.04) significantly impacted overall gut microbial composition, consistent with previous studies. Having pets/plants and frequent vegetable intake were positively associated with gut microbiota diversity and the Gut Microbiome Health Index (GMHI), while frequent juice and fries intake decreased gut microbiota diversity (p < 0.05). The abundance of indoor Clostridia and Bacilli was positively associated with gut microbial diversity and GMHI (p < 0.01). Total indoor indole derivatives and 6 indole metabolites (L-tryptophan, indole, 3-methylindole, indole-3-acetate, 5-hydroxy-L-tryptophan and indolelactic acid, p < 0.05) were positively associated with the abundance of total protective gut bacteria, suggesting a potential role in promoting gut health. Neural network analysis revealed that these indole derivatives were derived from indoor microorganisms.

CONCLUSIONS: The study is the first to report associations between indoor microbiome/metabolites and gut microbiota, highlighting the potential role of indoor microbiome in shaping human gut microbiota.}, } @article {pmid37209654, year = {2023}, author = {Xiong, X and Xu, J and Yan, X and Wu, S and Ma, J and Wang, Z and He, Q and Gong, J and Rao, Y}, title = {Gut microbiome and serum metabolome analyses identify biomarkers associated with sexual maturity in quails.}, journal = {Poultry science}, volume = {102}, number = {7}, pages = {102762}, pmid = {37209654}, issn = {1525-3171}, mesh = {Animals ; *Gastrointestinal Microbiome ; Chickens ; Metabolome ; Metagenome ; Bacteria ; Biomarkers ; }, abstract = {Increasing evidence indicates that the gut microbiome plays an important role in host aging and sexual maturity. However, the gut microbial taxa associated with sexual maturity in quails are unknown. This study used shotgun metagenomic sequencing to identify bacterial taxa associated with sexual maturity in d 20 and d 70 quails. We found that 17 bacterial species and 67 metagenome-assembled genomes (e.g., Bacteroides spp. and Enterococcus spp.) significantly differed between the d 20 and d 70 groups, including 5 bacterial species (e.g., Enterococcus faecalis) enriched in the d 20 group and 12 bacterial species (e.g., Christensenella massiliensis, Clostridium sp. CAG:217, and Bacteroides neonati) which had high abundances in the d 70 group. The bacterial species enriched in d 20 or d 70 were key biomarkers distinguishing sexual maturity and significantly correlated with the shifts in the functional capacities of the gut microbiome. Untargeted serum metabolome analysis revealed that 5 metabolites (e.g., nicotinamide riboside) were enriched in the d 20 group, and 6 metabolites (e.g., D-ribose, stevioside, and barbituric acid) were enriched in the d 70 group. Furthermore, metabolites with high abundances in the d 20 group were significantly enriched for the KEGG pathways of arginine biosynthesis, nicotinate and nicotinamide metabolism, and lysine degradation. However, glutathione metabolism and valine, leucine and isoleucine biosynthesis were enriched in high-abundance metabolites from the d 70 group. These results provide important insights into the effects of gut microbiome and host metabolism on quail sexual maturity.}, } @article {pmid37208728, year = {2023}, author = {Yu, J and Meng, J and Qin, Z and Yu, Y and Liang, Y and Wang, Y and Min, D}, title = {Dysbiosis of gut microbiota inhibits NMNAT2 to promote neurobehavioral deficits and oxidative stress response in the 6-OHDA-lesioned rat model of Parkinson's disease.}, journal = {Journal of neuroinflammation}, volume = {20}, number = {1}, pages = {117}, pmid = {37208728}, issn = {1742-2094}, support = {NO. 2020-274//Scientific Research Project of Heilongjiang Provincial Health Commission/ ; GXZYB20220437//Project of Guangxi Zhuang Autonomous Region Administration of Traditional Chinese Medicine/ ; }, mesh = {Animals ; Rats ; Dysbiosis/metabolism ; *Gastrointestinal Microbiome/physiology ; NAD ; Oxidative Stress ; Oxidopamine/toxicity ; *Parkinson Disease/metabolism ; *Nicotinamide-Nucleotide Adenylyltransferase/metabolism ; }, abstract = {BACKGROUND: New data are accumulating on gut microbial dysbiosis in Parkinson's disease (PD), while the specific mechanism remains uncharacterized. This study aims to investigate the potential role and pathophysiological mechanism of dysbiosis of gut microbiota in 6-hydroxydopamine (6-OHDA)-induced PD rat models.

METHODS: The shotgun metagenome sequencing data of fecal samples from PD patients and healthy individuals were obtained from the Sequence Read Archive (SRA) database. The diversity, abundance, and functional composition of gut microbiota were further analyzed in these data. After the exploration of the functional pathway-related genes, KEGG and GEO databases were used to obtain PD-related microarray datasets for differential expression analysis. Finally, in vivo experiments were performed to confirm the roles of fecal microbiota transplantation (FMT) and upregulated NMNAT2 in neurobehavioral symptoms and oxidative stress response in 6-OHDA-lesioned rats.

RESULTS: Significant differences were found in the diversity, abundance, and functional composition of gut microbiota between PD patients and healthy individuals. Dysbiosis of gut microbiota could regulate NAD[+] anabolic pathway to affect the occurrence and development of PD. As a NAD[+] anabolic pathway-related gene, NMNAT2 was poorly expressed in the brain tissues of PD patients. More importantly, FMT or overexpression of NMNAT2 alleviated neurobehavioral deficits and reduced oxidative stress in 6-OHDA-lesioned rats.

CONCLUSIONS: Taken together, we demonstrated that dysbiosis of gut microbiota suppressed NMNAT2 expression, thus exacerbating neurobehavioral deficits and oxidative stress response in 6-OHDA-lesioned rats, which could be rescued by FMT or NMNAT2 restoration.}, } @article {pmid37208617, year = {2023}, author = {Liao, F and Qian, J and Yang, R and Gu, W and Li, R and Yang, T and Fu, X and Yuan, B and Zhang, Y}, title = {Metagenomics of gut microbiome for migratory seagulls in Kunming city revealed the potential public risk to human health.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {269}, pmid = {37208617}, issn = {1471-2164}, mesh = {Animals ; Humans ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Viruses/genetics ; Bacteria/genetics ; DNA ; }, abstract = {BACKGROUND: Seagull as a migratory wild bird has become most popular species in southwest China since 1980s. Previously, we analyzed the gut microbiota and intestinal pathogenic bacteria configuration for this species by using 16S rRNA sequencing and culture methods. To continue in-depth research on the gut microbiome of migratory seagulls, the metagenomics, DNA virome and RNA virome were both investigated for their gut microbial communities of abundance and diversity in this study.

RESULTS: The metagenomics results showed 99.72% of total species was bacteria, followed by viruses, fungi, archaea and eukaryota. In particular, Shigella sonnei, Escherichia albertii, Klebsiella pneumonia, Salmonella enterica and Shigella flexneri were the top distributed taxa at species level. PCoA, NMDS, and statistics indicated some drug resistant genes, such as adeL, evgS, tetA, PmrF, and evgA accumulated as time went by from November to January of the next year, and most of these genes were antibiotic efflux. DNA virome composition demonstrated that Caudovirales was the most abundance virus, followed by Cirlivirales, Geplafuvirales, Petitvirales and Piccovirales. Most of these phages corresponded to Enterobacteriaceae and Campylobacteriaceae bacterial hosts respectively. Caliciviridae, Coronaviridae and Picornaviridae were the top distributed RNA virome at family level of this migratory animal. Phylogenetic analysis indicated the sequences of contigs of Gammacoronavirus and Deltacoronavirus had highly similarity with some coronavirus references.

CONCLUSIONS: In general, the characteristics of gut microbiome of migratory seagulls were closely related to human activities, and multiomics still revealed the potential public risk to human health.}, } @article {pmid37208450, year = {2023}, author = {Mo, S and Yan, B and Gao, T and Li, J and Kashif, M and Song, J and Bai, L and Yu, D and Liao, J and Jiang, C}, title = {Sulfur metabolism in subtropical marine mangrove sediments fundamentally differs from other habitats as revealed by SMDB.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8126}, pmid = {37208450}, issn = {2045-2322}, mesh = {*Microbiota ; Geologic Sediments ; Bacteria ; Archaea/genetics ; Sulfur/metabolism ; Phylogeny ; }, abstract = {Shotgun metagenome sequencing provides the opportunity to recover underexplored rare populations and identify difficult-to-elucidate biochemical pathways. However, information on sulfur genes, including their sequences, is scattered in public databases. Here, we introduce SMDB (https://smdb.gxu.edu.cn/)-a manually curated database of sulfur genes based on an in-depth review of the scientific literature and orthology database. The SMDB contained a total of 175 genes and covered 11 sulfur metabolism processes with 395,737 representative sequences affiliated with 110 phyla and 2340 genera of bacteria/archaea. The SMDB was applied to characterize the sulfur cycle from five habitats and compared the microbial diversity of mangrove sediments with that of other habitats. The structure and composition of microorganism communities and sulfur genes were significantly different among the five habitats. Our results show that microorganism alpha diversity in mangrove sediments was significantly higher than in other habitats. Genes involved in dissimilatory sulfate reduction were abundant in subtropical marine mangroves and deep-sea sediments. The neutral community model results showed that microbial dispersal was higher in the marine mangrove ecosystem than in others habitats. The Flavilitoribacter of sulfur-metabolizing microorganism becomes a reliable biomarker in the five habitats. SMDB will assist researchers to analyze genes of sulfur cycle from the metagenomic efficiently.}, } @article {pmid37208257, year = {2023}, author = {Wang, Q and Wu, S and Ye, X and Tan, S and Huang, F and Su, G and Kijlstra, A and Yang, P}, title = {Gut microbial signatures and their functions in Behcet's uveitis and Vogt-Koyanagi-Harada disease.}, journal = {Journal of autoimmunity}, volume = {137}, number = {}, pages = {103055}, doi = {10.1016/j.jaut.2023.103055}, pmid = {37208257}, issn = {1095-9157}, mesh = {Humans ; *Uveomeningoencephalitic Syndrome ; Leukocytes, Mononuclear ; *Gastrointestinal Microbiome ; *Uveitis/etiology ; *Behcet Syndrome ; }, abstract = {BACKGROUND: A number of public metagenomic studies reveal an association between the gut microbiome and various immune-mediated diseases including Behcet's uveitis (BU) and Vogt-Koyanagi-Harada disease (VKH). Integrated-analysis and subsequent validation of these results could be a potentially powerful way to understand the microbial signatures and their functions in these two uveitis entities.

METHODS: We integrated the sequencing data of our previous metagenomic studies on two major uveitis entities, BU and VKH as well as four other publicly available immune-mediated diseases datasets, including Ankylosing Spondylitis (AS), Rheumatoid Arthritis (RA), Crohn's disease (CD) and Ulcerative Colitis (UC). Alpha-diversity and beta-diversity analysis were used to compare the gut microbiome signatures between both uveitis entities and other immune-mediated diseases and healthy controls. Amino acid homology between microbial proteins and a uveitogenic peptide of the interphotoreceptor retinoid-binding protein (IRBP)161-180 was investigated using a similarity search in the NCBI protein BLAST program (BLASTP). Enzyme-linked Immunosorbent Assay (ELISA) was performed to evaluate the cross-reactive responses of experimental autoimmune uveitis (EAU)-derived lymphocytes and BU patients-derived peripheral blood mononuclear cells (PBMCs) against homologous peptides. The area under the curve (AUC) analysis was used to test the sensitivity and specificity of gut microbial biomarkers.

RESULTS: Depleted Dorea, Blautia, Coprococcus, Erysipelotrichaceae and Lachnospiraceae as well as enriched Bilophila and Stenotrophomonas were identified in BU patients. An enriched Alistipes along with a lower level of Dorea were observed in VKH patients. A peptide antigen (SteTDR) encoded by BU specifically enriched Stenotrophomonas was identified to share homology with IRBP161-180. In vitro experiments showed that lymphocytes from EAU or PBMCs from BU patients reacted to this peptide antigen as shown by the production of IFN-γ and IL-17. Addition of the SteTDR peptide to the classical IRBP immunization protocol exacerbated EAU severity. Gut microbial marker profiles consisted of 24 species and 32 species respectively differentiated BU and VKH from each other as well as from the other four immune-mediated diseases and healthy controls. Protein annotation identified 148 and 119 specific microbial proteins associated with BU and VKH, respectively. For metabolic function analysis, 108 and 178 metabolic pathways were shown to be associated with BU and VKH, respectively.

CONCLUSIONS: Our study revealed specific gut microbial signatures and their potentially functional roles in BU and VKH pathogenesis that differ significantly from other immune-mediated diseases as well as healthy controls.}, } @article {pmid37207186, year = {2023}, author = {Hao, SR and Zhou, YY and Zhang, X and Jiang, HY}, title = {Gut microbiome profiles may be related to atypical antipsychotic associated overweight in Asian children with psychiatric disorder: a preliminary study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1124846}, pmid = {37207186}, issn = {2235-2988}, mesh = {Humans ; Child ; Overweight/chemically induced/drug therapy/microbiology ; *Gastrointestinal Microbiome/physiology ; *Antipsychotic Agents/adverse effects ; Cross-Sectional Studies ; *Mental Disorders ; Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; }, abstract = {OBJECTIVE: Atypical antipsychotics (APs) modify the gut microbiome, and weight gain in response to AP could be mediated by the gut microbiome. Thus, the present study aimed to explore the changes in the gut bacterial microbiome in AP-exposed children with obesity.

METHODS: To rule out the confounder of AP indication, the gut bacterial microbiome was compared between healthy controls (Con) and AP-exposed individuals with overweight (APO) or normal weight (APN). Fifty-seven AP-treated outpatients (21 APO and 36 APN) and 25 Con were included in this cross-sectional microbiota study.

RESULTS: AP users, regardless of body mass index, exhibited decreased microbial richness and diversity and a distinct metagenomic composition compared to the Con. Although no differences in the microbiota structure were observed between APO and APN groups, the APO group was characterised by a higher abundance of Megamonas and Lachnospira. Additionally, the differences in the microbial functions were observed between APO and APN groups.

CONCLUSIONS: The gut bacterial microbiota of APO children revealed taxonomic and functional differences compared to Con and APN. Further studies are needed to verify these findings and to explore the temporal and causal relationships between these variables.}, } @article {pmid37204286, year = {2023}, author = {Shankar, A and Das, DJ and Nayar, S and Thomas, S}, title = {Deciphering the effect of maternal postpartum antibiotic prophylaxis on the infant gut microbiome: a whole metagenomic analysis.}, journal = {Future microbiology}, volume = {18}, number = {}, pages = {427-441}, doi = {10.2217/fmb-2022-0200}, pmid = {37204286}, issn = {1746-0921}, support = {AC1-250/2018/SPHCL//Department of Health and Family Welfare, Government of Kerala, India/ ; }, mesh = {Female ; Humans ; Infant ; *Gastrointestinal Microbiome ; Antibiotic Prophylaxis ; Mothers ; Milk, Human ; Postpartum Period ; Feces ; }, abstract = {Aim: To analyze the impact of postpartum antibiotic (Ab) prophylaxis on the infant gut microbiome. Materials & methods: Whole metagenomic analysis was performed on breast milk and infant fecal samples collected from mother-infant pairs who belonged to two groups: an Ab group comprising mothers who had received a single course of Abs in the immediate postpartum period and a non-Ab group comprising mothers who had not received Abs. Results: The characteristic presence of Citrobacter werkmanii, an emerging multidrug-resistant uropathogen, and a higher relative abundance of genes encoding resistance to specific Abs were noted in samples from the Ab group compared with those from the non-Ab group. Conclusion: Policies regarding prophylactic Ab prescription across government and private health sectors in the postpartum period need to be strengthened.}, } @article {pmid37204034, year = {2023}, author = {Liu, M and Liu, H and Li, F and Shen, Y and Zhang, L and Wang, G and Wang, H and Qu, C and Chen, G and Zhao, X and Liu, L and Zhou, J}, title = {Metagenomic surveillance in Jinan, China, reveals serum microbiome and biochemistry features in fever of unknown origin (FUO) patients.}, journal = {Letters in applied microbiology}, volume = {76}, number = {6}, pages = {}, doi = {10.1093/lambio/ovad060}, pmid = {37204034}, issn = {1472-765X}, support = {2020-4-113//National Health Commission/ ; 21320061330000//College of Public Health/ ; }, mesh = {Humans ; *Fever of Unknown Origin/diagnosis ; Metagenomics/methods ; *Microbiota/genetics ; Bacteria/genetics ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; }, abstract = {Here we aim to build up a metagenomics-centered surveillance on the infectious microbiome showing in the fever of unknown origin (FUO) patients. We collected venous blood, bronchoalveolar lavage fluid, cerebrospinal fluid, tissue block, sputum, bone marrow biopsy, and purulent liquid samples from 123 patients. Metagenomic sequencing (mNGS) for both DNA and RNA sequences was performed to profile the total pathogenic microbiome in the samples. A large pool of infectious or conditional infectious bacteria was found, belonging to Enterobacteriaceae, Staphylococcaceae (10.55%), Burkholderiaceae (10.05%), and Comamonadaceae (4.25%). The major virus families detected from mNGS analysis include Adenoviridae, Anelloviridae, Peribunyaviridae, Flaviviridae, and Herpesviridae, showing up in 34.96%, 47.37%, 30.89%, 5.69%, 3.25%, and 1.63% of patients, respectively. Using the Ward clustering method, two clusters of patients were organized: high-variety group and low-variety group. The patients in the high-variety group demonstrated higher levels of immune cells and inflammatory indicators such as lactate dehydrogenase, aspartate aminotransferase, and alanine aminotransferase. The patients in the low-variety group showed higher levels of inflammatory lipids such as 13,14-dihy-15-keto PGE2 (fold > 10, P = 0.021); tetra-PGDM (fold = 5.29, P = 0.037); and 20-HETE (fold > 10, P = 0.02). The mNGS surveillance system demonstrated remarkable potential in preventing infectious diseases using mNGS data.}, } @article {pmid37203688, year = {2023}, author = {Bucholz, JR and Hopper, GW and González, IS and Kelley, TE and Jackson, CR and Garrick, RC and Atkinson, CL and Lozier, JD}, title = {Community-wide correlations between species richness, abundance and population genomic diversity in a freshwater biodiversity hotspot.}, journal = {Molecular ecology}, volume = {32}, number = {22}, pages = {5894-5912}, doi = {10.1111/mec.16991}, pmid = {37203688}, issn = {1365-294X}, support = {1831512//National Science Foundation/ ; 1831531//National Science Foundation/ ; }, mesh = {Humans ; Animals ; Metagenomics ; Biodiversity ; Fresh Water ; Rivers ; *Unionidae ; *Bivalvia/genetics ; Ecosystem ; }, abstract = {Understanding patterns of diversity across macro (e.g. species-level) and micro (e.g. molecular-level) scales can shed light on community function and stability by elucidating the abiotic and biotic drivers of diversity within ecological communities. We examined the relationships among taxonomic and genetic metrics of diversity in freshwater mussels (Bivalvia: Unionidae), an ecologically important and species-rich group in the southeastern United States. Using quantitative community surveys and reduced-representation genome sequencing across 22 sites in seven rivers and two river basins, we surveyed 68 mussel species and sequenced 23 of these species to characterize intrapopulation genetic variation. We tested for the presence of species diversity-abundance correlations (i.e. the more-individuals hypothesis, MIH), species-genetic diversity correlations (SGDCs) and abundance-genetic diversity correlations (AGDCs) across all sites to evaluate relationships between different metrics of diversity. Sites with greater cumulative multispecies density (a standardized metric of abundance) had a greater number of species, consistent with the MIH hypothesis. Intrapopulation genetic diversity was strongly associated with the density of most species, indicating the presence of AGDCs. However, there was no consistent evidence for SGDCs. Although sites with greater overall densities of mussels had greater species richness, sites with higher genetic diversity did not always exhibit positive correlations with species richness, suggesting that there are spatial and evolutionary scales at which the processes influencing community-level diversity and intraspecific diversity differ. Our work reveals the importance of local abundance as indicator (and possibly a driver) of intrapopulation genetic diversity.}, } @article {pmid37202853, year = {2023}, author = {Velsko, IM and Gallois, S and Stahl, R and Henry, AG and Warinner, C}, title = {High conservation of the dental plaque microbiome across populations with differing subsistence strategies and levels of market integration.}, journal = {Molecular ecology}, volume = {32}, number = {14}, pages = {3872-3891}, doi = {10.1111/mec.16988}, pmid = {37202853}, issn = {1365-294X}, mesh = {Humans ; *Dental Plaque ; *Microbiota/genetics ; Mouth ; Diet ; North America ; }, abstract = {Industrialization-including urbanization, participation in the global food chain and consumption of heavily processed foods-is thought to drive substantial shifts in the human microbiome. While diet strongly influences stool microbiome composition, the influence of diet on the oral microbiome is largely speculative. Multiple ecologically distinct surfaces in the mouth, each harbouring a unique microbial community, pose a challenge to assessing changes in the oral microbiome in the context of industrialization, as the results depend on the oral site under study. Here, we investigated whether microbial communities of dental plaque, the dense biofilm on non-shedding tooth surfaces, are distinctly different across populations with dissimilar subsistence strategies and degree of industrialized market integration. Using a metagenomic approach, we compared the dental plaque microbiomes of Baka foragers and Nzime subsistence agriculturalists in Cameroon (n = 46) with the dental plaque and calculus microbiomes of highly industrialized populations in North America and Europe (n = 38). We found that differences in microbial taxonomic composition between populations were minimal, with high conservation of abundant microbial taxa and no significant differences in microbial diversity related to dietary practices. Instead, we find that the major source of variation in dental plaque microbial species composition is related to tooth location and oxygen availability, which may be influenced by toothbrushing or other dental hygiene measures. Our results support that dental plaque, in contrast to the stool microbiome, maintains an inherent stability against ecological perturbations in the oral environment.}, } @article {pmid37202728, year = {2023}, author = {Xing, W and Qi, B and Chen, R and Ding, W and Zhang, F}, title = {Metagenomic analysis reveals taxonomic and functional diversity of microbial communities on the deteriorated wall paintings of Qinling Tomb in the Southern Tang Dynasty, China.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {140}, pmid = {37202728}, issn = {1471-2180}, mesh = {*Microbiota ; Metagenome ; *Cyanobacteria ; Proteobacteria ; China ; }, abstract = {The microbial colonization on ancient murals attracts more and more attention since the threaten by microorganisms was first reported in Lascaux, Spain. However, the biodeterioration or biodegradation of mural paintings resulted by microorganisms is not clear yet. Especially the biological function of microbial communities in different conditions remained largely unaddressed. The two mausoleums of the Southern Tang Dynasty are the largest group of emperor mausoleums during the Five Dynasties and Ten Kingdoms period in China, which are of great significance to the study of the architecture, imperial mausoleum systems and art in the Tang and Song Dynasties. To make clear the species composition and metabolic functions of different microbial communities (MID and BK), we analyzed the samples from the wall paintings in one of the two mausoleums of the Southern Tang Dynasty with metagenomics method. The result showed totally 55 phyla and 1729 genera were detected in the mural paintings. The two microbial community structure were similar with the dominance of Proteobacteria, Actinobacteria and Cyanobacteria. However, the species abundance presented a significant difference between two communities at genus level --- MID is Lysobacter, Luteimonas are predominant in MID while Sphingomonas and Streptomyces are popular in BK, which is partially attributed to the different substrate materials of murals. As a result, the two communities presented the different metabolic patterns that MID community was mainly participated in the formation of biofilm as well as the degradation of exogenous pollutants while the BK was predominantly related to the photosynthesis process and biosynthesis of secondary metabolites. Taken together, these findings indicated the effect of environmental factor on the taxonomic composition and functional diversity of the microbial populations. The installation of artificial lighting needs to be considered carefully in the future protection of cultural relics.}, } @article {pmid37202719, year = {2023}, author = {Wang, XY and Meng, JX and Ren, WX and Ma, H and Liu, G and Liu, R and Geng, HL and Zhao, Q and Zhang, XX and Ni, HB}, title = {Amplicon-based metagenomic association analysis of gut microbiota in relation to egg-laying period and breeds of hens.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {138}, pmid = {37202719}, issn = {1471-2180}, mesh = {Animals ; Female ; *Gastrointestinal Microbiome/genetics ; Chickens/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Cyanobacteria/genetics ; }, abstract = {BACKGROUND: The gut microbiota plays an essential role in maintaining gut homeostasis and improving performance, with the composition of microbial communities visibly differing across different laying stages in hens and significantly correlating with egg production. To gain further insights into the association between microbial community characteristics and laying periods in Hy-Line variety brown and Isa brown laying hens, we conducted a 16S rRNA amplicon sequencing survey.

RESULTS: Our result revealed the diversity of bacteria in the early laying period was commonly higher than peak, and in Hy-Line variety brown laying hens were generally higher than Isa brown. Principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) revealed that the structure and composition of the gut microbiota of laying hens exhibited significant differences among different groups. Phylum Firmicutes, Bacteroidota, Proteobacteria, and Fusobacteriota were found that dominant in the host's feces. Therein, the abundance of Fusobacteriota was higher in the peak period than in the early period, while the abundance of Cyanobacteria in the early period was higher in two breeds of hens. Furthermore, random forest based on machine learning showed that there were several distinctly abundant genera, which can be used as potential biomarkers to differentiate the different groups of laying periods and breeds. In addition, the prediction of biological function indicated the existing discrepancy in microbial function among the microbiota of four groups.

CONCLUSIONS: Our findings offer new insights into the bacterial diversity and intestinal flora composition of different strains of laying hens during various laying periods, contributing significantly to the improvement of production performance and the prevention of chicken diseases.}, } @article {pmid37202543, year = {2024}, author = {Zeng, N and Wu, F and Lu, J and Li, X and Lin, S and Zhou, L and Wang, Z and Wu, G and Huang, Q and Zheng, D and Gao, J and Wu, S and Chen, X and Chen, M and Meng, F and Shang, H and He, Y and Chen, P and Wei, H and Li, Z and Zhou, H}, title = {High-fat diet impairs gut barrier through intestinal microbiota-derived reactive oxygen species.}, journal = {Science China. Life sciences}, volume = {67}, number = {5}, pages = {879-891}, pmid = {37202543}, issn = {1869-1889}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Diet, High-Fat/adverse effects ; *Reactive Oxygen Species/metabolism ; Mice ; *Fecal Microbiota Transplantation ; *Mice, Inbred C57BL ; Male ; Intestinal Mucosa/metabolism/microbiology ; Dysbiosis/microbiology ; Superoxide Dismutase/metabolism ; Feces/microbiology ; Tight Junctions/metabolism ; }, abstract = {Gut barrier disruption is a key event in bridging gut microbiota dysbiosis and high-fat diet (HFD)-associated metabolic disorders. However, the underlying mechanism remains elusive. In the present study, by comparing HFD- and normal diet (ND)-treated mice, we found that the HFD instantly altered the composition of the gut microbiota and subsequently damaged the integrity of the gut barrier. Metagenomic sequencing revealed that the HFD upregulates gut microbial functions related to redox reactions, as confirmed by the increased reactive oxygen species (ROS) levels in fecal microbiota incubation in vitro and in the lumen, which were detected using in vivo fluorescence imaging. This microbial ROS-producing capability induced by HFD can be transferred through fecal microbiota transplantation (FMT) into germ-free (GF) mice, downregulating the gut barrier tight junctions. Similarly, mono-colonizing GF mice with an Enterococcus strain excelled in ROS production, damaged the gut barrier, induced mitochondrial malfunction and apoptosis of the intestinal epithelial cells, and exacerbated fatty liver, compared with other low-ROS-producing Enterococcus strains. Oral administration of recombinant high-stability-superoxide dismutase (SOD) significantly reduced intestinal ROS, protected the gut barrier, and improved fatty liver against the HFD. In conclusion, our study suggests that extracellular ROS derived from gut microbiota play a pivotal role in HFD-induced gut barrier disruption and is a potential therapeutic target for HFD-associated metabolic diseases.}, } @article {pmid37201335, year = {2023}, author = {Laragione, T and Harris, C and Azizgolshani, N and Beeton, C and Bongers, G and Gulko, PS}, title = {Magnesium increases numbers of Foxp3+ Treg cells and reduces arthritis severity and joint damage in an IL-10-dependent manner mediated by the intestinal microbiome.}, journal = {EBioMedicine}, volume = {92}, number = {}, pages = {104603}, pmid = {37201335}, issn = {2352-3964}, support = {R01 AR073165/AR/NIAMS NIH HHS/United States ; }, mesh = {Mice ; Animals ; T-Lymphocytes, Regulatory ; Magnesium/metabolism/pharmacology ; Interleukin-10/genetics/metabolism ; *Gastrointestinal Microbiome ; Cytokines/metabolism ; *Arthritis, Rheumatoid/metabolism ; Mice, Knockout ; Th17 Cells ; Forkhead Transcription Factors/genetics/metabolism ; }, abstract = {BACKGROUND: Rheumatoid arthritis (RA) is a common autoimmune disease with emerging environmental and microbiome risk factors. The western diet is typically deficient in magnesium (Mg), and there is some evidence suggesting that Mg may have anti-inflammatory properties. But the actual role of Mg supplementation in arthritis or in T cell subsets has not been explored.

METHODS: We investigated the role of a high Mg diet in two different mouse models of RA induced with the KRN serum, and collagen-induced arthritis. We also characterized the phenotypes of splenocytes, gene expression, and an extensive intestinal microbiome analyses including fecal material transplantation (FMT).

FINDINGS: The high Mg diet group was significantly protected with reduced arthritis severity and joint damage, and reduced expression of IL-1β, IL-6, and TNFα. The high Mg group also had increased numbers of Foxp3+ Treg cells and IL-10-producing T cells. The high Mg protective effect disappeared in IL-10 knockout mice. FMT from the high Mg diet mice recreated the phenotypes seen in the diet-treated mice, with reduced arthritis severity, increased Foxp3+ Treg, and increased IL-10-producing T cells. Intestinal microbiome analyses using 16S rDNA sequencing revealed diet-specific changes, including reduced levels of RA-associated Prevotella in the high Mg group, while increasing levels of Bacteroides and other bacteria associated with increased production of short-chain fatty acids. Metagenomic analyses implicated additional pathways including L-tryptophan biosynthesis and arginine deiminase.

INTERPRETATION: We describe a new role for Mg in suppressing arthritis, in expanding Foxp3+ T reg cells and in the production of IL-10, and show that these effects are mediated by the intestinal microbiome. Our discoveries suggest a novel strategy for modifying the intestinal microbiome to treat RA and other autoimmune and inflammatory diseases.

FUNDING: None.}, } @article {pmid37199622, year = {2023}, author = {Kristensen, M and de Koff, EM and Chu, ML and Groendijk, S and Tramper-Stranders, GA and de Winter-de Groot, KM and Janssens, HM and Tiddens, HA and van Westreenen, M and Sanders, EAM and Arets, BHGM and van der Ent, CK and Prevaes, SMPJ and Bogaert, D}, title = {16S rRNA-Based Microbiota Profiling Assists Conventional Culture Analysis of Airway Samples from Pediatric Cystic Fibrosis Patients.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0405722}, pmid = {37199622}, issn = {2165-0497}, mesh = {Infant ; Humans ; Child ; Infant, Newborn ; *Cystic Fibrosis/diagnosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Respiratory System/microbiology ; Bacteria/genetics ; *Microbiota/genetics ; }, abstract = {16S-based sequencing provides broader information on the respiratory microbial community than conventional culturing. However, it (often) lacks species- and strain-level information. To overcome this issue, we used 16S rRNA-based sequencing results from 246 nasopharyngeal samples obtained from 20 infants with cystic fibrosis (CF) and 43 healthy infants, which were all 0 to 6 months old, and compared them to both standard (blind) diagnostic culturing and a 16S-sequencing-informed "targeted" reculturing approach. Using routine culturing, we almost uniquely detected Moraxella catarrhalis, Staphylococcus aureus, and Haemophilus influenzae (42%, 38%, and 33% of samples, respectively). Using the targeted reculturing approach, we were able to reculture 47% of the top-5 operational taxonomical units (OTUs) in the sequencing profiles. In total, we identified 60 species from 30 genera with a median of 3 species per sample (range, 1 to 8). We also identified up to 10 species per identified genus. The success of reculturing the top-5 genera present from the sequencing profile depended on the genus. In the case of Corynebacterium being in the top 5, we recultured them in 79% of samples, whereas for Staphylococcus, this value was only 25%. The success of reculturing was also correlated with the relative abundance of those genera in the corresponding sequencing profile. In conclusion, revisiting samples using 16S-based sequencing profiles to guide a targeted culturing approach led to the detection of more potential pathogens per sample than conventional culturing and may therefore be useful in the identification and, consequently, treatment of bacteria considered relevant for the deterioration or exacerbation of disease in patients like those with CF. IMPORTANCE Early and effective treatment of pulmonary infections in cystic fibrosis is vital to prevent chronic lung damage. Although microbial diagnostics and treatment decisions are still based on conventional culture methods, research is gradually focusing more on microbiome and metagenomic-based approaches. This study compared the results of both methods and proposed a way to combine the best of both worlds. Many species can relatively easily be recultured based on the 16S-based sequencing profile, and it provides more in-depth information about the microbial composition of a sample than that obtained through routine (blind) diagnostic culturing. Still, well-known pathogens can be missed by both routine diagnostic culture methods as well as by targeted reculture methods, sometimes even when they are highly abundant, which may be a consequence of either sample storage conditions or antibiotic treatment at the time of sampling.}, } @article {pmid37196884, year = {2023}, author = {Lehman, PC and Cady, N and Ghimire, S and Shahi, SK and Shrode, RL and Lehmler, HJ and Mangalam, AK}, title = {Low-dose glyphosate exposure alters gut microbiota composition and modulates gut homeostasis.}, journal = {Environmental toxicology and pharmacology}, volume = {100}, number = {}, pages = {104149}, pmid = {37196884}, issn = {1872-7077}, support = {T32 AI007485/AI/NIAID NIH HHS/United States ; I01 CX002212/CX/CSRD VA/United States ; R01 AI137075/AI/NIAID NIH HHS/United States ; T90 DE023520/DE/NIDCR NIH HHS/United States ; P30 ES005605/ES/NIEHS NIH HHS/United States ; }, mesh = {Mice ; Humans ; Animals ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; *Herbicides/toxicity ; Homeostasis ; Glyphosate ; }, abstract = {The widespread use of glyphosate, a broad-spectrum herbicide, has resulted in significant human exposure, and recent studies have challenged the notion that glyphosate is safe for humans. Although the link between disease states and glyphosate exposure is increasingly appreciated, the mechanistic links between glyphosate and its toxic effects on human health are poorly understood. Recent studies have suggested that glyphosate may cause toxicity through modulation of the gut microbiome, but evidence for glyphosate-induced gut dysbiosis and its effect on host physiology at doses approximating the U.S. Acceptable Daily Intake (ADI = 1.75 mg/kg body weight) is limited. Here, utilizing shotgun metagenomic sequencing of fecal samples from C57BL/6 J mice, we show that glyphosate exposure at doses approximating the U.S. ADI significantly impacts gut microbiota composition. These gut microbial alterations were associated with effects on gut homeostasis characterized by increased proinflammatory CD4[+]IL17A[+] T cells and Lipocalin-2, a known marker of intestinal inflammation.}, } @article {pmid37196747, year = {2023}, author = {Zhang, Z and Yang, H and Wang, B and Chen, C and Zou, X and Cheng, T and Li, J}, title = {Aerobic co-composting of mature compost with cattle manure: Organic matter conversion and microbial community characterization.}, journal = {Bioresource technology}, volume = {382}, number = {}, pages = {129187}, doi = {10.1016/j.biortech.2023.129187}, pmid = {37196747}, issn = {1873-2976}, mesh = {Cattle ; Animals ; Soil ; Manure ; *Composting ; *Microbiota ; Carbohydrates ; }, abstract = {The production of organic fertilizer by aerobic composting of cattle manure is an important way of its resource utilization. This study evaluated the effects of adding mature compost on the decomposition and microbial communities in the aerobic composting of cattle manure. The addition of mature compost shortens the composting cycle and results in a final lignocellulosic degradation rate of 35%. Metagenomic analysis showed that this was due to the proliferation of thermophilic and organic matter-degrading functional microorganisms, which enhanced the activity of carbohydrate-active enzymes. With the addition of mature compost, the microbial community exhibited stronger metabolic functions, especially carbohydrate and amino acid metabolism, which are the driving forces of organic matter degradation. This study deepens the understanding of organic matter conversion and microbial community metabolic functions when mature compost is used for livestock manure composting and provides a promising technology for livestock manure composting.}, } @article {pmid37195657, year = {2023}, author = {Xue, W and Peng, P and Wen, X and Meng, H and Qin, Y and Deng, T and Guo, S and Chen, T and Li, X and Liang, J and Zhang, F and Xie, Z and Jin, M and Liang, Q and Wei, L}, title = {Metagenomic Sequencing Analysis Identifies Cross-Cohort Gut Microbial Signatures Associated With Age-Related Macular Degeneration.}, journal = {Investigative ophthalmology & visual science}, volume = {64}, number = {5}, pages = {11}, pmid = {37195657}, issn = {1552-5783}, mesh = {Humans ; Metagenome ; *Gastrointestinal Microbiome/genetics ; Dysbiosis/microbiology ; Bacteria/genetics/metabolism ; Bacteroidetes ; *Macular Degeneration/genetics ; }, abstract = {PURPOSE: Alterations in the gut microbiota have been associated with age-related macular degeneration (AMD). However, the dysbiosis shared by different ethnicity and geographic groups, which may associate with the disease pathogenesis, remain underexplored. Here, we characterized dysbiosis of the gut microbiota in patients with AMD from Chinese and Swiss cohorts and identified cross-cohort signatures associated with AMD.

METHODS: Shotgun metagenomic sequencing was performed on fecal samples from 30 patients with AMD and 30 healthy subjects. Published datasets with 138 samples from Swiss patients with AMD and healthy subjects were re-analyzed. Comprehensive taxonomic profiling was conducted by matching to the RefSeq genome database, metagenome-assembled genome (MAG) database, and Gut Virome Database (GVD). Functional profiling was performed by reconstruction of the MetaCyc pathways.

RESULTS: The α-diversity of the gut microbiota was decreased in patients with AMD according to taxonomic profiles generated using MAG but not RefSeq database as reference. The Firmicutes/Bacteroidetes ratio was also decreased in patients with AMD. Among AMD-associated bacteria shared between Chinese and Swiss cohorts, Ruminococcus callidus, Lactobacillus gasseri, and Prevotellaceae (f) uSGB 2135 were enriched in patients with AMD, whereas Bacteroidaceae (f) uSGB 1825 was depleted in patients with AMD and was negatively associated with hemorrhage size. Bacteroidaceae was one of the major hosts of phages associated with AMD. Three degradation pathways were reduced in AMD.

CONCLUSIONS: These results demonstrated that dysbiosis of the gut microbiota was associated with AMD. We identified cross-cohort gut microbial signatures involving bacteria, viruses, and metabolic pathways, which potentially serve as promising targets for the prevention or treatment of AMD.}, } @article {pmid37195254, year = {2023}, author = {Free, T}, title = {Long-read sequencing for the metagenomic analysis of microbiomes.}, journal = {BioTechniques}, volume = {74}, number = {4}, pages = {153-155}, doi = {10.2144/btn-2023-0028}, pmid = {37195254}, issn = {1940-9818}, mesh = {*High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; Metagenome/genetics ; Sequence Analysis, DNA ; Metagenomics ; }, abstract = {One technology, long-read sequencing, and one research field, microbiome studies, have risen to prominence over the last decade. But how can one be used in the other? What changes are being wrought? And what limitations remain? [Formula: see text].}, } @article {pmid37194081, year = {2023}, author = {Gallet, A and Halary, S and Duval, C and Huet, H and Duperron, S and Marie, B}, title = {Disruption of fish gut microbiota composition and holobiont's metabolome during a simulated Microcystis aeruginosa (Cyanobacteria) bloom.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {108}, pmid = {37194081}, issn = {2049-2618}, mesh = {Animals ; *Microcystis/physiology ; *Gastrointestinal Microbiome ; *Cyanobacteria/genetics ; Lakes/microbiology ; Metabolome ; *Oryzias/physiology ; }, abstract = {BACKGROUND: Cyanobacterial blooms are one of the most common stressors encountered by metazoans living in freshwater lentic systems such as lakes and ponds. Blooms reportedly impair fish health, notably through oxygen depletion and production of bioactive compounds including cyanotoxins. However, in the times of the "microbiome revolution", it is surprising that so little is still known regarding the influence of blooms on fish microbiota. In this study, an experimental approach is used to demonstrate that blooms affect fish microbiome composition and functions, as well as the metabolome of holobionts. To this end, the model teleost Oryzias latipes is exposed to simulated Microcystis aeruginosa blooms of various intensities in a microcosm setting, and the response of bacterial gut communities is evaluated in terms of composition and metabolome profiling. Metagenome-encoded functions are compared after 28 days between control individuals and those exposed to highest bloom level.

RESULTS: The gut bacterial community of O. latipes exhibits marked responses to the presence of M. aeruginosa blooms in a dose-dependent manner. Notably, abundant gut-associated Firmicutes almost disappear, while potential opportunists increase. The holobiont's gut metabolome displays major changes, while functions encoded in the metagenome of bacterial partners are more marginally affected. Bacterial communities tend to return to original composition after the end of the bloom and remain sensitive in case of a second bloom, reflecting a highly reactive gut community.

CONCLUSION: Gut-associated bacterial communities and holobiont functioning are affected by both short and long exposure to M. aeruginosa, and show evidence of post-bloom resilience. These findings point to the significance of bloom events to fish health and fitness, including survival and reproduction, through microbiome-related effects. In the context of increasingly frequent and intense blooms worldwide, potential outcomes relevant to conservation biology as well as aquaculture warrant further investigation. Video Abstract.}, } @article {pmid37194043, year = {2023}, author = {Yao, S and Jin, T and Zhang, L and Zhang, Y and Chen, R and Wang, Q and Lv, M and Hu, C and Ma, T and Xia, W}, title = {N/S element transformation modulating lithospheric microbial communities by single-species manipulation.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {107}, pmid = {37194043}, issn = {2049-2618}, mesh = {Nitrates/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Petroleum/metabolism/microbiology ; Sulfur/metabolism ; Nitrogen/metabolism ; Sulfates ; }, abstract = {BACKGROUND: The lithospheric microbiome plays a vital role in global biogeochemical cycling, yet their mutual modulation mechanisms remain largely uncharted. Petroleum reservoirs are important lithosphere ecosystems that provide desirable resources for understanding microbial roles in element cycling. However, the strategy and mechanism of modulating indigenous microbial communities for the optimization of community structures and functions are underexplored, despite its significance in energy recovery and environmental remediation.

RESULTS: Here we proposed a novel selective stimulation of indigenous functional microbes by driving nitrogen and sulfur cycling in petroleum reservoirs using injections of an exogenous heterocycle-degrading strain of Pseudomonas. We defined such bacteria capable of removing and releasing organically bound sulfur and nitrogen from heterocycles as "bioredox triggers". High-throughput 16S rRNA amplicon sequencing, metagenomic, and gene transcription-level analyses of extensive production water and sandstone core samples spanning the whole oil production process clarified the microbiome dynamics following the intervention. These efforts demonstrated the feasibility of in situ N/S element release and electron acceptor generation during heterocycle degradation, shifting microbiome structures and functions and increasing phylogenetic diversity and genera engaged in sulfur and nitrogen cycling, such as Desulfovibrio, Shewanella, and Sulfurospirillum. The metabolic potentials of sulfur- and nitrogen-cycling processes, particularly dissimilatory sulfate reduction and dissimilatory nitrate reduction, were elevated in reservoir microbiomes. The relative expression of genes involved in sulfate reduction (dsrA, dsrB) and nitrate reduction (napA) was upregulated by 85, 28, and 22 folds, respectively. Field trials showed significant improvements in oil properties, with a decline in asphaltenes and aromatics, hetero-element contents, and viscosity, hence facilitating the effective exploitation of heavy oil.

CONCLUSIONS: The interactions between microbiomes and element cycling elucidated in this study will contribute to a better understanding of microbial metabolic involvement in, and response to, biogeochemical processes in the lithosphere. The presented findings demonstrated the immense potential of our microbial modulation strategy for green and enhanced heavy oil recovery. Video Abstract.}, } @article {pmid37193854, year = {2023}, author = {Atsawawaranunt, K and Ewart, KM and Major, RE and Johnson, RN and Santure, AW and Whibley, A}, title = {Tracing the introduction of the invasive common myna using population genomics.}, journal = {Heredity}, volume = {131}, number = {1}, pages = {56-67}, pmid = {37193854}, issn = {1365-2540}, mesh = {Metagenomics ; Animals ; *Introduced Species ; *Starlings/genetics ; Genetic Variation ; }, abstract = {The common myna (Acridotheres tristis) is one of the most invasive bird species in the world, yet its colonisation history is only partly understood. We identified the introduction history and population structure, and quantified the genetic diversity of myna populations from the native range in India and introduced populations in New Zealand, Australia, Fiji, Hawaii, and South Africa, based on thousands of single nucleotide polymorphism markers in 814 individuals. We were able to identify the source population of mynas in several invasive locations: mynas from Fiji and Melbourne, Australia, were likely founded by individuals from a subpopulation in Maharashtra, India, while mynas in Hawaii and South Africa were likely independently founded by individuals from other localities in India. Our findings suggest that New Zealand mynas were founded by individuals from Melbourne, which, in turn, were founded by individuals from Maharashtra. We identified two genetic clusters among New Zealand mynas, divided by New Zealand's North Island's axial mountain ranges, confirming previous observations that mountains and thick forests may form barriers to myna dispersal. Our study provides a foundation for other population and invasion genomic studies and provides useful information for the management of this invasive species.}, } @article {pmid37191684, year = {2023}, author = {Lu, J and Sha, H and Chen, J and Yi, X and Xiong, J}, title = {Characterizing sediment functional traits and ecological consequences respond to increasing antibiotic pollution.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {12}, pages = {4093-4107}, pmid = {37191684}, issn = {1432-0614}, support = {32071549//National Natural Science Foundation of China/ ; HZ202201//One health Interdisciplinary Research Project, Ningbo University/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; *Microbiota ; Environmental Pollution ; Nitrification ; Sulfates ; }, abstract = {Current studies have shown that the taxonomic structures of ecologically important microbial communities are altered by antibiotic exposure, but the resulting effects on functional potentials and subsequent biogeochemical processes are poorly understood. However, this knowledge is indispensable for developing an accurate projection of nutrient dynamics in the future. Using metagenomic analyses, here we explored the responses of taxonomical and functional structures of a sediment microbial community, and their links with key biogeochemical processes to increasing antibiotic pollution from the pristine inlet to the outfall sites along an aquaculture discharge channel. We identified sharply contrasting sedimentary microbial communities and functional traits along increasing antibiotic pollution. Functional structures exhibited steeper distance-decay relationships than taxonomical structures along both the antibiotic distance and physicochemical distance, revealing higher functional sensitivity. Sediment enzyme activities were significantly and positively coupled with the relative abundances of their coding genes, thus the abundances of genes were indicative of functional potentials. The nitrogen cycling pathways were commonly inhibited by antibiotics, but not for the first step of nitrification, which could synergistically mitigate nitrous oxide emission. However, antibiotic pollution stimulated methanogens and inhibited methanotrophs, thereby promoting methane efflux. Furthermore, microbes could adapt to antibiotic pollution through enriched potential of sulfate uptake. Antibiotics indirectly affected taxonomic structures through alterations in network topological features, which in turn affected sediment functional structures and biogeochemical processes. Notably, only 13 antibiotics concentration-discriminatory genes contributed an overall 95.9% accuracy in diagnosing in situ antibiotic concentrations, in which just two indicators were antibiotic resistance genes. Our study comprehensively integrates sediment compositional and functional traits, biotic interactions, and enzymatic activities, thus generating a better understanding about ecological consequences of increasing antibiotics pollution. KEY POINTS: • Contrasting functional traits respond to increasing antibiotic pollution. • Antibiotics pollution stimulates CH4 efflux, while mitigating N2O emission and may drive an adaptive response of enriched sulfate uptake. • Indicator genes contribute 95.9% accuracy in diagnosing antibiotic concentrations.}, } @article {pmid37191543, year = {2023}, author = {Rizzo, SM and Alessandri, G and Lugli, GA and Fontana, F and Tarracchini, C and Mancabelli, L and Viappiani, A and Bianchi, MG and Bussolati, O and van Sinderen, D and Ventura, M and Turroni, F}, title = {Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0066523}, pmid = {37191543}, issn = {2165-0497}, mesh = {Infant ; Humans ; Infant, Newborn ; Female ; Pregnancy ; Milk, Human/metabolism/microbiology ; Bifidobacterium/genetics/metabolism ; Insulin/metabolism ; *Microbiota ; *Gastrointestinal Microbiome ; Feces/microbiology ; }, abstract = {Multiple millennia of human evolution have shaped the chemical composition of breast milk toward an optimal human body fluid for nutrition and protection and for shaping the early gut microbiota of newborns. This biological fluid is composed of water, lipids, simple and complex carbohydrates, proteins, immunoglobulins, and hormones. Potential interactions between hormones present in mother's milk and the microbial community of the newborn are a very fascinating yet unexplored topic. In this context, insulin, in addition to being one of the most prevalent hormones in breast milk, is also involved in a metabolic disease that affects many pregnant women, i.e., gestational diabetes mellitus (GDM). Analysis of 3,620 publicly available metagenomic data sets revealed that the bifidobacterial community varies in relation to the different concentrations of this hormone in breast milk of healthy and diabetic mothers. Starting from this assumption, in this study, we explored possible molecular interactions between this hormone and bifidobacterial strains that represent bifidobacterial species commonly occurring in the infant gut using 'omics' approaches. Our findings revealed that insulin modulates the bifidobacterial community by apparently improving the persistence of the Bifidobacterium bifidum taxon in the infant gut environment compared to other typical infant-associated bifidobacterial species. IMPORTANCE Breast milk is a key factor in modulating the infant's intestinal microbiota composition. Even though the interaction between human milk sugars and bifidobacteria has been extensively studied, there are other bioactive compounds in human milk that may influence the gut microbiota, such as hormones. In this article, the molecular interaction of the human milk hormone insulin and the bifidobacterial communities colonizing the human gut in the early stages of life has been explored. This molecular cross talk was assessed using an in vitro gut microbiota model and then analyzed by various omics approaches, allowing the identification of genes associated with bacterial cell adaptation/colonization in the human intestine. Our findings provide insights into the manner by which assembly of the early gut microbiota may be regulated by host factors such as hormones carried by human milk.}, } @article {pmid37191511, year = {2023}, author = {Zhang, JW and Wang, R and Liang, X and Han, P and Zheng, YL and Li, XF and Gao, DZ and Liu, M and Hou, LJ and Dong, HP}, title = {Novel Gene Clusters for Natural Product Synthesis Are Abundant in the Mangrove Swamp Microbiome.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {6}, pages = {e0010223}, pmid = {37191511}, issn = {1098-5336}, mesh = {*Wetlands ; Multigene Family ; Biosynthetic Pathways ; *Metagenome ; *Bacteria/genetics/isolation & purification/metabolism ; Metabolomics ; China ; Biodiversity ; }, abstract = {Natural microbial communities produce a diverse array of secondary metabolites with ecologically and biotechnologically relevant activities. Some of them have been used clinically as drugs, and their production pathways have been identified in a few culturable microorganisms. However, since the vast majority of microorganisms in nature have not been cultured, identifying the synthetic pathways of these metabolites and tracking their hosts remain a challenge. The microbial biosynthetic potential of mangrove swamps remains largely unknown. Here, we examined the diversity and novelty of biosynthetic gene clusters in dominant microbial populations in mangrove wetlands by mining 809 newly reconstructed draft genomes and probing the activities and products of these clusters by using metatranscriptomic and metabolomic techniques. A total of 3,740 biosynthetic gene clusters were identified from these genomes, including 1,065 polyketide and nonribosomal peptide gene clusters, 86% of which showed no similarity to known clusters in the Minimum Information about a Biosynthetic Gene Cluster (MIBiG) repository. Of these gene clusters, 59% were harbored by new species or lineages of Desulfobacterota-related phyla and Chloroflexota, whose members are highly abundant in mangrove wetlands and for which few synthetic natural products have been reported. Metatranscriptomics revealed that most of the identified gene clusters were active in field and microcosm samples. Untargeted metabolomics was also used to identify metabolites from the sediment enrichments, and 98% of the mass spectra generated were unrecognizable, further supporting the novelty of these biosynthetic gene clusters. Our study taps into a corner of the microbial metabolite reservoir in mangrove swamps, providing clues for the discovery of new compounds with valuable activities. IMPORTANCE At present, the majority of known clinical drugs originated from cultivated species of a few bacterial lineages. It is vital for the development of new pharmaceuticals to explore the biosynthetic potential of naturally uncultivable microorganisms using new techniques. Based on the large numbers of genomes reconstructed from mangrove wetlands, we identified abundant and diverse biosynthetic gene clusters in previously unsuspected phylogenetic groups. These gene clusters exhibited a variety of organizational architectures, especially for nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS), implying the presence of new compounds with valuable activities in the mangrove swamp microbiome.}, } @article {pmid37189387, year = {2023}, author = {Aljuraiban, GS and Alfhili, MA and Aldhwayan, MM and Aljazairy, EA and Al-Musharaf, S}, title = {Metagenomic Shotgun Sequencing Reveals Specific Human Gut Microbiota Associated with Insulin Resistance and Body Fat Distribution in Saudi Women.}, journal = {Biomolecules}, volume = {13}, number = {4}, pages = {}, pmid = {37189387}, issn = {2218-273X}, mesh = {Humans ; Female ; *Insulin Resistance ; Saudi Arabia ; *Gastrointestinal Microbiome/genetics ; Body Fat Distribution ; Obesity ; Insulin ; }, abstract = {(1) Background: Gut microbiota dysbiosis may lead to diseases such as insulin resistance and obesity. We aimed to investigate the relationship between insulin resistance, body fat distribution, and gut microbiota composition. (2) Methods: The present study included 92 Saudi women (18-25 years) with obesity (body mass index (BMI) ≥ 30 kg/m[2], n = 44) and with normal weight (BMI 18.50-24.99 kg/m[2], n = 48). Body composition indices, biochemical data, and stool samples were collected. The whole-genome shotgun sequencing technique was used to analyze the gut microbiota. Participants were divided into subgroups stratified by the homeostatic model assessment for insulin resistance (HOMA-IR) and other adiposity indices. (3) Results: HOMA-IR was inversely correlated with Actinobacteria (r = -0.31, p = 0.003), fasting blood glucose was inversely correlated with Bifidobacterium kashiwanohense (r = -0.22, p = 0.03), and insulin was inversely correlated with Bifidobacterium adolescentis (r = -0.22, p = 0.04). There were significant differences in α- and β-diversities in those with high HOMA-IR and waist-hip ratio (WHR) compared to low HOMA-IR and WHR (p = 0.02, 0.03, respectively). (4) Conclusions: Our findings highlight the relationship between specific gut microbiota at different taxonomic levels and measures of glycemic control in Saudi Arabian women. Future studies are required to determine the role of the identified strains in the development of insulin resistance.}, } @article {pmid37189337, year = {2023}, author = {Dossey, AT and Oppert, B and Chu, FC and Lorenzen, MD and Scheffler, B and Simpson, S and Koren, S and Johnston, JS and Kataoka, K and Ide, K}, title = {Genome and Genetic Engineering of the House Cricket (Acheta domesticus): A Resource for Sustainable Agriculture.}, journal = {Biomolecules}, volume = {13}, number = {4}, pages = {}, pmid = {37189337}, issn = {2218-273X}, mesh = {Animals ; *Gryllidae/genetics/metabolism ; Agriculture ; Crops, Agricultural ; Allergens/metabolism ; Genetic Engineering ; }, abstract = {Background: The house cricket, Acheta domesticus, is one of the most farmed insects worldwide and the foundation of an emerging industry using insects as a sustainable food source. Edible insects present a promising alternative for protein production amid a plethora of reports on climate change and biodiversity loss largely driven by agriculture. As with other crops, genetic resources are needed to improve crickets for food and other applications. Methods: We present the first high quality annotated genome assembly of A. domesticus from long read data and scaffolded to chromosome level, providing information needed for genetic manipulation. Results: Gene groups related to immunity were annotated and will be useful for improving value to insect farmers. Metagenome scaffolds in the A. domesticus assembly, including Invertebrate Iridescent Virus 6 (IIV6), were submitted as host-associated sequences. We demonstrate both CRISPR/Cas9-mediated knock-in and knock-out of A. domesticus and discuss implications for the food, pharmaceutical, and other industries. RNAi was demonstrated to disrupt the function of the vermilion eye-color gene producing a useful white-eye biomarker phenotype. Conclusions: We are utilizing these data to develop technologies for downstream commercial applications, including more nutritious and disease-resistant crickets, as well as lines producing valuable bioproducts, such as vaccines and antibiotics.}, } @article {pmid37189333, year = {2023}, author = {Cres, CM and Tritt, A and Bouchard, KE and Zhang, Y}, title = {DL-TODA: A Deep Learning Tool for Omics Data Analysis.}, journal = {Biomolecules}, volume = {13}, number = {4}, pages = {}, pmid = {37189333}, issn = {2218-273X}, mesh = {Humans ; *Deep Learning ; Neural Networks, Computer ; Bacteria/genetics ; Metagenome ; *Microbiota/genetics ; Algorithms ; }, abstract = {Metagenomics is a technique for genome-wide profiling of microbiomes; this technique generates billions of DNA sequences called reads. Given the multiplication of metagenomic projects, computational tools are necessary to enable the efficient and accurate classification of metagenomic reads without needing to construct a reference database. The program DL-TODA presented here aims to classify metagenomic reads using a deep learning model trained on over 3000 bacterial species. A convolutional neural network architecture originally designed for computer vision was applied for the modeling of species-specific features. Using synthetic testing data simulated with 2454 genomes from 639 species, DL-TODA was shown to classify nearly 75% of the reads with high confidence. The classification accuracy of DL-TODA was over 0.98 at taxonomic ranks above the genus level, making it comparable with Kraken2 and Centrifuge, two state-of-the-art taxonomic classification tools. DL-TODA also achieved an accuracy of 0.97 at the species level, which is higher than 0.93 by Kraken2 and 0.85 by Centrifuge on the same test set. Application of DL-TODA to the human oral and cropland soil metagenomes further demonstrated its use in analyzing microbiomes from diverse environments. Compared to Centrifuge and Kraken2, DL-TODA predicted distinct relative abundance rankings and is less biased toward a single taxon.}, } @article {pmid37189332, year = {2023}, author = {Smith, L and Goldobina, E and Govi, B and Shkoporov, AN}, title = {Bacteriophages of the Order Crassvirales: What Do We Currently Know about This Keystone Component of the Human Gut Virome?.}, journal = {Biomolecules}, volume = {13}, number = {4}, pages = {}, pmid = {37189332}, issn = {2218-273X}, support = {/WT_/Wellcome Trust/United Kingdom ; 220646/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Humans ; *Bacteriophages/genetics ; Virome ; Metagenomics ; Genomics ; DNA ; Mammals/genetics ; }, abstract = {The order Crassvirales comprises dsDNA bacteriophages infecting bacteria in the phylum Bacteroidetes that are found in a variety of environments but are especially prevalent in the mammalian gut. This review summarises available information on the genomics, diversity, taxonomy, and ecology of this largely uncultured viral taxon. With experimental data available from a handful of cultured representatives, the review highlights key properties of virion morphology, infection, gene expression and replication processes, and phage-host dynamics.}, } @article {pmid37188814, year = {2023}, author = {Johansen, J and Atarashi, K and Arai, Y and Hirose, N and Sørensen, SJ and Vatanen, T and Knip, M and Honda, K and Xavier, RJ and Rasmussen, S and Plichta, DR}, title = {Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan.}, journal = {Nature microbiology}, volume = {8}, number = {6}, pages = {1064-1078}, pmid = {37188814}, issn = {2058-5276}, support = {DP3 DK094338/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Aged, 80 and over ; Humans ; Longevity ; Virome ; Centenarians ; *Viruses/genetics ; *Microbiota ; *Bacteriophages/genetics ; }, abstract = {Distinct gut microbiome ecology may be implicated in the prevention of aging-related diseases as it influences systemic immune function and resistance to infections. Yet, the viral component of the microbiome throughout different stages in life remains unexplored. Here we present a characterization of the centenarian gut virome using previously published metagenomes from 195 individuals from Japan and Sardinia. Compared with gut viromes of younger adults (>18 yr) and older individuals (>60 yr), centenarians had a more diverse virome including previously undescribed viral genera, such as viruses associated with Clostridia. A population shift towards higher lytic activity was also observed. Finally, we investigated phage-encoded auxiliary functions that influence bacterial physiology, which revealed an enrichment of genes supporting key steps in sulfate metabolic pathways. Phage and bacterial members of the centenarian microbiome displayed an increased potential for converting methionine to homocysteine, sulfate to sulfide and taurine to sulfide. A greater metabolic output of microbial hydrogen sulfide in centenarians may in turn support mucosal integrity and resistance to pathobionts.}, } @article {pmid37188713, year = {2023}, author = {Orihara, K and Yahagi, K and Saito, Y and Watanabe, Y and Sasai, T and Hara, T and Tsukuda, N and Oki, K and Fujimoto, J and Matsuki, T}, title = {Characterization of Bifidobacterium kashiwanohense that utilizes both milk- and plant-derived oligosaccharides.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2207455}, pmid = {37188713}, issn = {1949-0984}, mesh = {Phylogeny ; *Gastrointestinal Microbiome ; Oligosaccharides/metabolism ; Bifidobacterium ; Humans ; alpha-L-Fucosidase/metabolism ; Milk, Human/metabolism ; Infant ; Child ; }, abstract = {Bifidobacteria are prominent members of the human gut microbiota throughout life. The ability to utilize milk- and plant-derived carbohydrates is important for bifidobacterial colonization of the infant and adult gut. The Bifidobacterium catenulatum subspecies kashiwanohense (B. kashiwanohense) was originally isolated from infant feces. However, only a few strains have been described, and the characteristics of this subspecies have been poorly investigated. Here, we characterized genotypes and phenotypes of 23 B. kashiwanohense-associated strains, including 12 newly sequenced isolates. Genome-based analysis clarified the phylogenetic relationship between these strains, revealing that only 13 strains are genuine B. kashiwanohense. We defined specific marker sequences and investigated the worldwide prevalence of B. kashiwanohense based on metagenome data. This revealed that not only infants but also adults and weaning children harbor this subspecies in the gut. Most B. kashiwanohense strains utilize long-chain xylans and possess genes for extracellular xylanase (GH10), arabinofuranosidase and xylosidase (GH43), and ABC transporters that contribute to the utilization of xylan-derived oligosaccharides. We also confirmed that B. kashiwanohense strains utilize short- and long-chain human milk oligosaccharides and possess genes for fucosidase (GH95 and GH29) and specific ABC transporter substrate-binding proteins that contribute to the utilization of a wide range of human milk oligosaccharides. Collectively, we found that B. kashiwanohense strains utilize both plant- and milk-derived carbohydrates and identified key genetic factors that allow them to assimilate various carbohydrates.}, } @article {pmid37187470, year = {2023}, author = {Wu, C and Yi, H and Hu, Y and Luo, D and Tang, Z and Wen, X and Zhang, Y and Tang, M and Zhang, L and Wu, S and Chen, M}, title = {Effects of second-line anti-tuberculosis drugs on the intestinal microbiota of patients with rifampicin-resistant tuberculosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1127916}, pmid = {37187470}, issn = {2235-2988}, mesh = {Humans ; Antitubercular Agents/pharmacology/therapeutic use ; Rifampin/pharmacology/therapeutic use ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Tryptophan ; *Tuberculosis, Multidrug-Resistant/drug therapy ; *Tuberculosis/drug therapy ; *Mycobacterium tuberculosis ; }, abstract = {OBJECTIVE: To determine the effects of second-line anti-tuberculosis (TB) drugs on the composition and functions of intestinal microbiota in patients with rifampicin-resistant TB (RR-TB).

METHODS: In this cross-sectional study, stool samples and relevant clinical information were collected from patients with RR-TB admitted to the Drug-resistant Specialty Department at Hunan Chest Hospital (Hunan Institute For Tuberculosis Control). The composition and functions of intestinal microbiota were analyzed using metagenomic sequencing and bioinformatics methods.

RESULTS: Altered structural composition of the intestinal microbiota was found when patients from the control, intensive phase treatment, and continuation phase treatment groups were compared (P<0.05). Second-line anti-TB treatment resulted in a decrease in the relative abundance of species, such as Prevotella copri, compared with control treatment. However, the relative abundance of Escherichia coli, Salmonella enterica, and 11 other conditionally pathogenic species increased significantly in the intensive phase treatment group. Based on differential functional analysis, some metabolism-related functions, such as the biosynthesises of phenylalanine, tyrosine, and tryptophan, were significantly inhibited during second-line anti-TB drug treatment, while other functions, such as phenylalanine metabolism, were significantly promoted during the intensive phase of treatment.

CONCLUSION: Second-line anti-TB drug treatment caused changes in the structural composition of the intestinal microbiota in patients with RR-TB. In particular, this treatment induced a significant increase in the relative abundance of 11 conditionally pathogenic species, including Escherichia coli. Functional analysis revealed significantly decreased biosynthesises of phenylalanine, tyrosine, and tryptophan and significantly increased phenylalanine metabolism.}, } @article {pmid37187112, year = {2023}, author = {Bargheet, A and Klingenberg, C and Esaiassen, E and Hjerde, E and Cavanagh, JP and Bengtsson-Palme, J and Pettersen, VK}, title = {Development of early life gut resistome and mobilome across gestational ages and microbiota-modifying treatments.}, journal = {EBioMedicine}, volume = {92}, number = {}, pages = {104613}, pmid = {37187112}, issn = {2352-3964}, mesh = {Infant ; Infant, Newborn ; Humans ; Gestational Age ; *Microbiota ; Gastrointestinal Tract/microbiology ; Infant, Extremely Premature ; Anti-Bacterial Agents/adverse effects ; Feces/microbiology ; *Probiotics/therapeutic use ; }, abstract = {BACKGROUND: Gestational age (GA) and associated level of gastrointestinal tract maturation are major factors driving the initial gut microbiota composition in preterm infants. Besides, compared to term infants, premature infants often receive antibiotics to treat infections and probiotics to restore optimal gut microbiota. How GA, antibiotics, and probiotics modulate the microbiota's core characteristics, gut resistome and mobilome, remains nascent.

METHODS: We analysed metagenomic data from a longitudinal observational study in six Norwegian neonatal intensive care units to describe the bacterial microbiota of infants of varying GA and receiving different treatments. The cohort consisted of probiotic-supplemented and antibiotic-exposed extremely preterm infants (n = 29), antibiotic-exposed very preterm (n = 25), antibiotic-unexposed very preterm (n = 8), and antibiotic-unexposed full-term (n = 10) infants. The stool samples were collected on days of life 7, 28, 120, and 365, and DNA extraction was followed by shotgun metagenome sequencing and bioinformatical analysis.

FINDINGS: The top predictors of microbiota maturation were hospitalisation length and GA. Probiotic administration rendered the gut microbiota and resistome of extremely preterm infants more alike to term infants on day 7 and ameliorated GA-driven loss of microbiota interconnectivity and stability. GA, hospitalisation, and both microbiota-modifying treatments (antibiotics and probiotics) contributed to an elevated carriage of mobile genetic elements in preterm infants compared to term controls. Finally, Escherichia coli was associated with the highest number of antibiotic-resistance genes, followed by Klebsiella pneumoniae and Klebsiella aerogenes.

INTERPRETATION: Prolonged hospitalisation, antibiotics, and probiotic intervention contribute to dynamic alterations in resistome and mobilome, gut microbiota characteristics relevant to infection risk.

FUNDING: Odd-Berg Group, Northern Norway Regional Health Authority.}, } @article {pmid37186335, year = {2023}, author = {Zuo, K and Fang, C and Gao, Y and Fu, Y and Wang, H and Li, J and Zhong, J and Yang, X and Xu, L}, title = {Suppression of the gut microbiota-bile acid-FGF19 axis in patients with atrial fibrillation.}, journal = {Cell proliferation}, volume = {56}, number = {11}, pages = {e13488}, pmid = {37186335}, issn = {1365-2184}, support = {7222068//Beijing Natural Science Foundation/ ; 31771021//National Natural Science Foundation of China/ ; 81670214//National Natural Science Foundation of China/ ; 81770253//National Natural Science Foundation of China/ ; 81970271//National Natural Science Foundation of China/ ; 82100334//National Natural Science Foundation of China/ ; 91849111//National Natural Science Foundation of China/ ; 92168117//National Natural Science Foundation of China/ ; CYJZ202107//the Golden-seed training plan/ ; QML20230316//Beijing Hospitals Authority Youth Programme/ ; }, mesh = {Humans ; Bile Acids and Salts ; *Gastrointestinal Microbiome ; *Atrial Fibrillation ; Cross-Sectional Studies ; Palmitic Acid ; Fibroblast Growth Factors/metabolism ; }, abstract = {This study aimed to investigate the role of the gut microbiota (GM)-bile acid (BA)-fibroblast growth factor (FGF) 19 axis in patients with atrial fibrillation (AF). Gut bacterial metabolisms of BAs were determined in an AF metagenomic dataset. The composition of faecal BAs pools was characterized by targeted metabolomics in an independent AF cross-sectional cohort. Circulating levels of FGF19 were measured by ELISA. In vitro cell experiments were conducted to validate the regulatory role of FGF19 in atrial cardiomyocytes stimulated with palmitic acid. First, metagenomic profiling revealed that gut microbial biotransformation from primary to secondary BAs was dysregulated in AF patients. Second, the proportion of secondary BAs decreased in the faeces of patients with AF. Also, eight BAs were identified as AF-associated BAs, including seven AF-enriched BAs (ursodeoxycholic acid, chenodeoxycholic acid, etc.), and AF-decreased dehydrolithocholic acid. Third, reduced levels of circulating FGF19 were observed in patients with AF. Subsequently, FGF19 was found to protect against palmitic acid-induced lipid accumulation and dysregulated signalling in atrial cardiomyocytes, including attenuated phosphorylation of YAP and Ca[2+] /calmodulin-dependent protein kinases II and secretion of interleukin-1β, mediated via peroxisome proliferator-activated receptor α. Our data found decreased levels of secondary BAs and circulating FGF19, resulting in the impaired protective function of FGF19 against lipid accumulation in atrial cardiomyocytes.}, } @article {pmid37186231, year = {2023}, author = {Stach, TL and Sieber, G and Shah, M and Simon, SA and Soares, A and Bornemann, TLV and Plewka, J and Künkel, J and Becker, C and Meyer, F and Boenigk, J and Probst, AJ}, title = {Temporal disturbance of a model stream ecosystem by high microbial diversity from treated wastewater.}, journal = {MicrobiologyOpen}, volume = {12}, number = {2}, pages = {e1347}, pmid = {37186231}, issn = {2045-8827}, mesh = {*Ecosystem ; Rivers/microbiology ; Wastewater ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota/genetics ; }, abstract = {Microbial communities in freshwater streams play an essential role in ecosystem functioning via biogeochemical cycling. Yet, the impacts of treated wastewater influx into stream ecosystems on microbial strain diversity remain mostly unexplored. Here, we coupled full-length 16S ribosomal RNA gene Nanopore sequencing and strain-resolved metagenomics to investigate the impact of treated wastewater on a mesocosm system (AquaFlow) run with restored river water. Over 10 days, community Bray-Curtis dissimilarities between treated and control mesocosm decreased (0.57 ± 0.058 to 0.26 ± 0.046) based on ribosomal protein S3 gene clustering, finally converging to nearly identical communities. Similarly, strain-resolved metagenomics revealed a high diversity of bacteria and viruses after the introduction of treated wastewater; these microbes also decreased over time resulting in the same strain clusters in control and treatment at the end of the experiment. Specifically, 39.2% of viral strains detected in all samples were present after the introduction of treated wastewater only. Although bacteria present at low abundance in the treated wastewater introduced additional antibiotic resistance genes, signals of naturally occurring ARG-encoding organisms resembled the resistome at the endpoint. Our results suggest that the previously stressed freshwater stream and its microbial community are resilient to a substantial introduction of treated wastewater.}, } @article {pmid37183784, year = {2023}, author = {Ma, L and Lyu, W and Song, Y and Chen, K and Lv, L and Yang, H and Wang, W and Xiao, Y}, title = {Anti-Inflammatory Effect of Clostridium butyricum-Derived Extracellular Vesicles in Ulcerative Colitis: Impact on Host microRNAs Expressions and Gut Microbiome Profiles.}, journal = {Molecular nutrition & food research}, volume = {67}, number = {13}, pages = {e2200884}, doi = {10.1002/mnfr.202200884}, pmid = {37183784}, issn = {1613-4133}, mesh = {Mice ; Animals ; *Colitis, Ulcerative/chemically induced/drug therapy ; *Clostridium butyricum/genetics ; *Gastrointestinal Microbiome ; *Colitis/drug therapy ; *Inflammatory Bowel Diseases ; Inflammation/drug therapy ; Colon ; *MicroRNAs/genetics ; Anti-Inflammatory Agents ; Dextran Sulfate/toxicity ; Disease Models, Animal ; *Extracellular Vesicles ; }, abstract = {SCORE: Probiotics extracellular vesicles (EVs) have shown potential as EV-based nanomaterials therapy for the treatment of inflammatory bowel disease (IBD). Although probiotic Clostridium butyricum has been reported to be protective in various models of intestinal inflammation, the therapeutic effects of C. butyricum-derived extracellular vesicles (CbEVs) in IBD remain to be demonstrated.

METHODS AND RESULTS: In this study, multi-omics sequencing is combined with an in vitro model of lipopolysaccharide-induced RAW264.7 cells and an in vivo mouse model of dextran sodium sulfate-induced colitis to explore the regulatory impact and mechanism of CbEVs in ulcerative colitis. Through small RNA sequencing, the study finds that microRNA is involved in the alleviation of colonic inflammation under CbEVs treatment. Mechanistically, CbEVs restore miR-199a-3p expression, interacting with map3k4, and thereby suppress proinflammatory MAPK and NF-κB signaling. Additionally, metagenomic sequencing demonstrate that CbEVs alleviate bacterial dysbiosis in colitis mice and significantly reduces the abundance of the bacterial pathogens Escherichia coli and Shigella flexneri. Furthermore, CbEVs regulate the microbial tryptophan metabolites, which further improve intestinal barrier integrity and inhibit the inflammatory response in colitis mice.

CONCLUSION: C. butyricum-derived extracellular vesicles can be a novel agent for the treatment of colitis and miR-199a-3p can be a potential target for IBD treatment.}, } @article {pmid37180439, year = {2023}, author = {Niu, C and Tu, Y and Jin, Q and Chen, Z and Yuan, K and Wang, M and Zhang, P and Luo, J and Li, H and Yang, Y and Liu, X and Mao, M and Dong, T and Tan, W and Hu, X and Pan, Y and Hou, L and Ma, R and Huang, Z}, title = {Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1157368}, pmid = {37180439}, issn = {2235-2988}, mesh = {Humans ; *Mycobiome ; Fungi/genetics ; *Gastrointestinal Microbiome ; Feces/microbiology ; Saliva ; *Non-alcoholic Fatty Liver Disease ; }, abstract = {Metabolic dysfunction-associated fatty liver disease (MAFLD) is a phenotype of liver diseases associated with metabolic syndrome. The pathogenesis MAFLD remains unclear. The liver maintains is located near the intestine and is physiologically interdependent with the intestine via metabolic exchange and microbial transmission, underpinning the recently proposed "oral-gut-liver axis" concept. However, little is known about the roles of commensal fungi in the disease development. This study aimed to characterize the alterations of oral and gut mycobiota and their roles in MAFLD. Twenty-one MAFLD participants and 20 healthy controls were enrolled. Metagenomics analyses of saliva, supragingival plaques, and feces revealed significant alterations in the gut fungal composition of MAFLD patients. Although no statistical difference was evident in the oral mycobiome diversity within MAFLD and healthy group, significantly decreased diversities were observed in fecal samples of MAFLD patients. The relative abundance of one salivary species, five supragingival species, and seven fecal species was significantly altered in MAFLD patients. Twenty-two salivary, 23 supragingival, and 22 fecal species were associated with clinical parameters. Concerning the different functions of fungal species, pathways involved in metabolic pathways, biosynthesis of secondary metabolites, microbial metabolism in diverse environments, and carbon metabolism were abundant both in the oral and gut mycobiomes. Moreover, different fungal contributions in core functions were observed between MAFLD patients and the healthy controls, especially in the supragingival plaque and fecal samples. Finally, correlation analysis between oral/gut mycobiome and clinical parameters identified correlations of certain fungal species in both oral and gut niches. Particularly, Mucor ambiguus, which was abundant both in saliva and feces, was positively correlated with body mass index, total cholesterol, low-density lipoprotein, alanine aminotransferase, and aspartate aminotransferase, providing evidence of a possible "oral-gut-liver" axis. The findings illustrate the potential correlation between core mycobiome and the development of MAFLD and could propose potential therapeutic strategies.}, } @article {pmid37180436, year = {2023}, author = {Che, Y and Wang, N and Ma, Q and Liu, J and Xu, Z and Li, Q and Wang, J and Sun, Y}, title = {Microbial characterization of the nasal cavity in patients with allergic rhinitis and non-allergic rhinitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1166389}, pmid = {37180436}, issn = {2235-2988}, mesh = {Humans ; Male ; Female ; Young Adult ; Adult ; *Rhinitis, Allergic/microbiology ; *Rhinitis/microbiology ; *Nasal Cavity/microbiology ; Metagenome ; Biodiversity ; *Microbiota ; RNA, Ribosomal, 16S/analysis ; *Bacteria/classification/genetics/isolation & purification ; }, abstract = {INTRODUCTION: Although recent studies have shown that the human microbiome is involved in the pathogenesis of allergic diseases, the impact of microbiota on allergic rhinitis (AR) and non-allergic rhinitis (nAR) has not been elucidated. The aim of this study was to investigate the differences in the composition of the nasal flora in patients with AR and nAR and their role in the pathogenesis.

METHOD: From February to September 2022, 35 AR patients and 35 nAR patients admitted to Harbin Medical University's Second Affiliated Hospital, as well as 20 healthy subjects who underwent physical examination during the same period, were subjected to 16SrDNA and metagenomic sequencing of nasal flora.

RESULTS: The microbiota composition of the three groups of study subjects differs significantly. The relative abundance of Vibrio vulnificus and Acinetobacter baumanni in the nasal cavity of AR patients was significantly higher when compared to nAR patients, while the relative abundance of Lactobacillus murinus, Lactobacillus iners, Proteobacteria, Pseudomonadales, and Escherichia coli was lower. In addition, Lactobacillus murinus and Lacttobacillus kunkeei were also negatively correlated with IgE, while Lacttobacillus kunkeei was positively correlated with age. The relative distribution of Faecalibacterium was higher in moderate than in severe AR patients. According to KEGG functional enrichment annotation, ICMT(protein-S-isoprenylcysteine O-methyltransferase,ICMT) is an AR microbiota-specific enzyme that plays a role, while glycan biosynthesis and metabolism are more active in AR microbiota. For AR, the model containing Parabacteroides goldstemii, Sutterella-SP-6FBBBBH3, Pseudoalteromonas luteoviolacea, Lachnospiraceae bacterium-615, and Bacteroides coprocola had the highest the area under the curve (AUC), which was 0.9733(95%CI:0.926-1.000) in the constructed random forest prediction model. The largest AUC for nAR is 0.984(95%CI:0.949-1.000) for the model containing Pseudomonas-SP-LTJR-52, Lachnospiraceae bacterium-615, Prevotella corporis, Anaerococcus vaginalis, and Roseburia inulinivorans.

CONCLUSION: In conclusion, patients with AR and nAR had significantly different microbiota profiles compared to healthy controls. The results suggest that the nasal microbiota may play a key role in the pathogenesis and symptoms of AR and nAR, providing us with new ideas for the treatment of AR and nAR.}, } @article {pmid37180114, year = {2023}, author = {Britto, AMA and Siqueira, JD and Curty, G and Goes, LR and Policarpo, C and Meyrelles, AR and Furtado, Y and Almeida, G and Giannini, ALM and Machado, ES and Soares, MA}, title = {Microbiome analysis of Brazilian women cervix reveals specific bacterial abundance correlation to RIG-like receptor gene expression.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1147950}, pmid = {37180114}, issn = {1664-3224}, mesh = {Female ; Humans ; Cervix Uteri ; *Uterine Cervical Neoplasms/genetics/metabolism ; *Papillomavirus Infections ; Brazil ; Toll-Like Receptor 3/genetics ; Bacteria/genetics ; *Microbiota ; Gene Expression ; }, abstract = {The relationship among microbiome, immunity and cervical cancer has been targeted by several studies, yet many questions remain unanswered. We characterized herein the virome and bacteriome from cervical samples and correlated these findings with innate immunity gene expression in a Brazilian convenience sample of HPV-infected (HPV+) and uninfected (HPV-) women. For this purpose, innate immune gene expression data were correlated to metagenomic information. Correlation analysis showed that interferon (IFN) is able to differentially modulate pattern recognition receptors (PRRs) expression based on HPV status. Virome analysis indicated that HPV infection correlates to the presence of Anellovirus (AV) and seven complete HPV genomes were assembled. Bacteriome results unveiled that vaginal community state types (CST) distribution was independent of HPV or AV status, although bacterial phyla distribution differed between groups. Furthermore, TLR3 and IFNαR2 levels were higher in the Lactobacillus no iners-dominated mucosa and we detected correlations among RIG-like receptors (RLR) associated genes and abundance of specific anaerobic bacteria. Collectively, our data show an intriguing connection between HPV and AV infections that could foster cervical cancer development. Besides that, TLR3 and IFNαR2 seem to create a protective milieu in healthy cervical mucosa (L. no iners-dominated), and RLRs, known to recognize viral RNA, were correlated to anaerobic bacteria suggesting that they might be related to dysbiosis.}, } @article {pmid37179329, year = {2023}, author = {Anderson, AC and von Ohle, C and Frese, C and Boutin, S and Bridson, C and Schoilew, K and Peikert, SA and Hellwig, E and Pelz, K and Wittmer, A and Wolff, D and Al-Ahmad, A}, title = {The oral microbiota is a reservoir for antimicrobial resistance: resistome and phenotypic resistance characteristics of oral biofilm in health, caries, and periodontitis.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {22}, number = {1}, pages = {37}, pmid = {37179329}, issn = {1476-0711}, mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Dental Caries Susceptibility ; *Microbiota/genetics ; *Periodontitis/genetics ; Bacteria ; Genes, Bacterial ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is an ever-growing threat to modern medicine and, according to the latest reports, it causes nearly twice as many deaths globally as AIDS or malaria. Elucidating reservoirs and dissemination routes of antimicrobial resistance genes (ARGs) are essential in fighting AMR. Human commensals represent an important reservoir, which is underexplored for the oral microbiota. Here, we set out to investigate the resistome and phenotypic resistance of oral biofilm microbiota from 179 orally healthy (H), caries active (C), and periodontally diseased (P) individuals (TRN: DRKS00013119, Registration date: 22.10.2022). The samples were analysed using shotgun metagenomic sequencing combined, for the first time, with culture technique. A selection of 997 isolates was tested for resistance to relevant antibiotics.

RESULTS: The shotgun metagenomics sequencing resulted in 2,069,295,923 reads classified into 4856 species-level OTUs. PERMANOVA analysis of beta-diversity revealed significant differences between the groups regarding their microbiota composition and their ARG profile. The samples were clustered into three ecotypes based on their microbial composition. The bacterial composition of H and C samples greatly overlapped and was based on ecotypes 1 and 2 whereas ecotype 3 was only detected in periodontitis. We found 64 ARGs conveying resistance to 36 antibiotics, particularly to tetracycline, macrolide-lincosamide-streptogramin, and beta-lactam antibiotics, and a correspondingly high prevalence of phenotypic resistance. Based on the microbiota composition, these ARGs cluster in different resistotypes, and a higher prevalence is found in healthy and caries active than in periodontally diseased individuals. There was a significant association between the resistotypes and the ecotypes. Although numerous associations were found between specific antibiotic resistance and bacterial taxa, only a few taxa showed matching associations with both genotypic and phenotypic analyses.

CONCLUSIONS: Our findings show the importance of the oral microbiota from different niches within the oral cavity as a reservoir for antibiotic resistance. Additionally, the present study showed the need for using more than one method to reveal antibiotic resistance within the total oral biofilm, as a clear mismatch between the shotgun metagenomics method and the phenotypic resistance characterization was shown.}, } @article {pmid37178843, year = {2023}, author = {Liu, B and Yu, D and Ge, C and Luo, X and Du, L and Zhang, X and Hui, C}, title = {Combined effects of microplastics and chlortetracycline on the intestinal barrier, gut microbiota, and antibiotic resistome of Muscovy ducks (Cairina moschata).}, journal = {The Science of the total environment}, volume = {887}, number = {}, pages = {164050}, doi = {10.1016/j.scitotenv.2023.164050}, pmid = {37178843}, issn = {1879-1026}, mesh = {Animals ; Microplastics ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome ; Plastics ; Ducks ; Polystyrenes ; *Chlortetracycline/pharmacology ; Intestines ; *Microbiota ; }, abstract = {Antibiotics and microplastics (MPs) have become critical concerns worldwide because of their increasing amount and ecological risks to ecosystems. However, how MPs exposure affects the bioaccumulation and risks of antibiotics in waterfowls remains poorly understood. In this study, Muscovy ducks were exposed to single and combined contamination with polystyrene MPs and chlortetracycline (CTC) for 56 days, and the effects of MPs on CTC bioaccumulation and their risks in duck intestines were investigated. MPs exposure reduced the bioaccumulation of CTC in the intestine and liver of ducks and increased their fecal CTC excretion. MPs exposure caused severe oxidative stress, inflammatory response, and intestinal barrier damages. Microbiome analysis showed that MPs exposure induced microbiota dysbiosis by increasing the abundance of Streptococcus and Helicobacter, the increase of which may exacerbate intestinal damages. Co-exposure to MPs and CTC alleviated the intestinal damage by regulating the gut microbiome. Metagenomic sequencing revealed that the combined exposure to MPs and CTC increased the abundance of Prevotella, Faecalibacterium, and Megamonas and incidence of total antibiotic resistance genes (ARGs), especially tetracycline ARGs subtypes in the gut microbiota. The results obtained herein provide new insights into the potential risks of polystyrene MPs and antibiotics in waterfowls living in aquatic environments.}, } @article {pmid37178644, year = {2023}, author = {Wang, M and Qin, Y and Liu, Y and Yang, H and Wang, J and Ru, S and Cui, P}, title = {Short-term exposure to enrofloxacin causes hepatic metabolism disorder associated with intestinal flora dysbiosis in adult marine medaka (Oryzias melastigma).}, journal = {Marine pollution bulletin}, volume = {192}, number = {}, pages = {114966}, doi = {10.1016/j.marpolbul.2023.114966}, pmid = {37178644}, issn = {1879-3363}, mesh = {Animals ; *Oryzias/physiology ; Enrofloxacin ; *Gastrointestinal Microbiome ; Dysbiosis/chemically induced/veterinary ; Metabolomics ; *Water Pollutants, Chemical/toxicity ; }, abstract = {Enrofloxacin (ENR) is a widely used fluoroquinolone antibiotic that is frequently detected in the environment. Our study assessed the impact of short-term ENR exposure on the intestinal and liver health of marine medaka (Oryzias melastigma) using gut metagenomic shotgun sequencing and liver metabolomics. We found that ENR exposure resulted in imbalances of Vibrio and Flavobacteria and enrichments of multiple antibiotic resistance genes. Additionally, we found a potential link between the host's response to ENR exposure and the intestinal microbiota disorder. Liver metabolites, including phosphatidylcholine, lysophosphatidylcholine, taurocholic acid, and cholic acid, in addition to several metabolic pathways in the liver that are closely linked to the imbalance of intestinal flora were severely maladjusted. These findings suggest that ENR exposure has the potential to negatively affect the gut-liver axis as the primary toxicological mechanism. Our findings provide evidence regarding the negative physiological impacts of antibiotics on marine fish.}, } @article {pmid37178322, year = {2023}, author = {Pandey, U and Tambat, S and Aich, P}, title = {Postnatal 14D is the Key Window for Mice Intestinal Development- An Insight from Age-Dependent Antibiotic-Mediated Gut Microbial Dysbiosis Study.}, journal = {Advanced biology}, volume = {7}, number = {7}, pages = {e2300089}, doi = {10.1002/adbi.202300089}, pmid = {37178322}, issn = {2701-0198}, mesh = {Mice ; Animals ; *Intestines/microbiology ; Intestinal Mucosa/metabolism ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome ; Dysbiosis/metabolism/microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {The postnatal period is one of the critical windows for the structure-function development of the gastrointestinal tract and associated mucosal immunity. Along with other constituent members, recent studies suggest the contribution of gut microbiota in maintaining host health, immunity, and development. Although the gut microbiota's role in maintaining barrier integrity is known, its function in early life development still needs to be better understood. To understand the details of gut microbiota's effects on intestinal integrity, epithelium development, and immune profile, the route of antibiotic-mediated perturbation is taken. Mice on days 7(P7D), 14(P14D), 21(P21D) and 28(P28D) are sacrificed and 16S rRNA metagenomic analysis is performed. The barrier integrity, tight junction proteins (TJPs) expression, intestinal epithelial cell (IEC) markers, and inflammatory cytokines are analyzed. Results reveal a postnatal age-related impact of gut microbiota perturbation, with a gradual increase in the relative abundance of Proteobacteria and a reduction in Bacteroidetes and Firmicutes. Significant barrier integrity disruption, reduced TJPs and IECs marker expression, and increased systemic inflammation at P14D of AVNM-treated mice are found. Moreover, the microbiota transplantation shows recolonization of Verrucomicrobia, proving a causal role in barrier functions. The investigation reveals P14D as a critical period for neonatal intestinal development, regulated by specific microbiota composition.}, } @article {pmid37177963, year = {2023}, author = {Luo, ZM and Liu, JX and Hu, YQ and He, L and Zhou, YY and Zheng, QR and Chai, BF}, title = {[Taxonomic and Functional Diversity of Soil Microbial Communities in Subalpine Meadow with Different Degradation Degrees in Mount Wutai].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {44}, number = {5}, pages = {2918-2927}, doi = {10.13227/j.hjkx.202204330}, pmid = {37177963}, issn = {0250-3301}, mesh = {*Ecosystem ; Grassland ; Carbon ; Soil ; Soil Microbiology ; *Microbiota ; Bacteria/genetics ; }, abstract = {Although soil microbes play a key role in grassland ecosystem functioning, the response of their diversity to grassland degradation has not been fully investigated. Here, we used shotgun metagenomic sequencing to analyze the characteristics and influencing factors of soil microbial taxonomic and functional diversity at four different degradation stages[i.e., non-degraded (ND), lightly degraded (LD), moderately degraded (MD), and heavily degraded (HD)]of subalpine meadow in the Mount Wutai. The results showed that there were significant differences in the relative abundances of Actinobacteria, Bacteroidetes, Nitrospirae, and Parcubacteria among the four subalpine grasslands with different degradation degrees (P<0.05).Compared with that in ND, the degraded meadows increased the proportion of genes related to carbon metabolism, biosynthesis of amino acids, pyruvate metabolism, citric acid cycle, propanoate metabolism, butanoate metabolism, and fatty acid metabolism (P<0.05), indicating that the degradation of subalpine grassland changed the metabolic potential of energy metabolism and the nutrient cycle of the soil microbial community. Grassland degradation changed soil microbial taxonomic and functional α diversity, especially in MD and HD.Grassland degradation resulted in significant changes in the taxonomic and functional compositions of the microbial communities. The total nitrogen, pH, and soil organic carbon significantly affected the taxonomic and functional compositions of the microbial communities.The β diversity of the plant community was significantly correlated with the taxonomic and functional β diversity of the microbial community (P<0.05), indicating strong coupling. The results of this study revealed the changes and driving mechanisms of subsurface microbial taxonomic and functional diversity during grassland degradation, which can provide a theoretical basis for subalpine meadow protection and ecological restoration.}, } @article {pmid37175775, year = {2023}, author = {Kazakova, P and Abasolo, N and de Cripan, SM and Marquès, E and Cereto-Massagué, A and Garcia, L and Canela, N and Tormo, R and Torrell, H}, title = {Gut Microbiome and Small RNA Integrative-Omic Perspective of Meconium and Milk-FED Infant Stool Samples.}, journal = {International journal of molecular sciences}, volume = {24}, number = {9}, pages = {}, pmid = {37175775}, issn = {1422-0067}, mesh = {Infant, Newborn ; Humans ; Infant ; *Meconium ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Milk, Human ; Bacteria/genetics ; DNA, Viral ; }, abstract = {The human gut microbiome plays an important role in health, and its initial development is conditioned by many factors, such as feeding. It has also been claimed that this colonization is guided by bacterial populations, the dynamic virome, and transkingdom interactions between host and microbial cells, partially mediated by epigenetic signaling. In this article, we characterized the bacteriome, virome, and smallRNome and their interaction in the meconium and stool samples from infants. Bacterial and viral DNA and RNA were extracted from the meconium and stool samples of 2- to 4-month-old milk-fed infants. The bacteriome, DNA and RNA virome, and smallRNome were assessed using 16S rRNA V4 sequencing, viral enrichment sequencing, and small RNA sequencing protocols, respectively. Data pathway analysis and integration were performed using the R package mixOmics. Our findings showed that the bacteriome differed among the three groups, while the virome and smallRNome presented significant differences, mainly between the meconium and stool of milk-fed infants. The gut environment is rapidly acquired after birth, and it is highly adaptable due to the interaction of environmental factors. Additionally, transkingdom interactions between viruses and bacteria can influence host and smallRNome profiles. However, virome characterization has several protocol limitations that must be considered.}, } @article {pmid37175619, year = {2023}, author = {Even, G and Mouray, A and Vandenabeele, N and Martel, S and Merlin, S and Lebrun-Ruer, S and Chabé, M and Audebert, C}, title = {Bact-to-Batch: A Microbiota-Based Tool to Determine Optimal Animal Allocation in Experimental Designs.}, journal = {International journal of molecular sciences}, volume = {24}, number = {9}, pages = {}, pmid = {37175619}, issn = {1422-0067}, mesh = {Mice ; Animals ; *Research Design ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Pilot Projects ; *Microbiota/genetics ; Feces ; }, abstract = {The basis of any animal experimentation begins with the housing of animals that should take into account the need for splitting animals into similar groups. Even if it is generally recommended to use the minimum number of animals necessary to obtain reliable and statistically significant results (3Rs rule), the allocation of animals is currently mostly based on randomness. Since variability in gut microbiota is an important confounding factor in animal experiments, the main objective of this study was to develop a new approach based on 16S rRNA gene sequencing analysis of the gut microbiota of animals participating in an experiment, in order to correctly assign the animals across batches. For this purpose, a pilot study was performed on 20 mouse faecal samples with the aim of establishing two groups of 10 mice as similar as possible in terms of their faecal microbiota fingerprinting assuming that this approach limits future analytical bias and ensures reproducibility. The suggested approach was challenged with previously published data from a third-party study. This new method allows to embrace the unavoidable microbiota variability between animals in order to limit artefacts and to provide an additional assurance for the reproducibility of animal experiments.}, } @article {pmid37173775, year = {2023}, author = {Vigneron, A and Cruaud, P and Lovejoy, C and Vincent, WF}, title = {Genomic insights into cryptic cycles of microbial hydrocarbon production and degradation in contiguous freshwater and marine microbiomes.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {104}, pmid = {37173775}, issn = {2049-2618}, mesh = {Canada ; *Hydrocarbons/metabolism ; *Microbiota/genetics ; Alkanes/metabolism ; Bacteria/genetics ; Genomics ; Water ; Lakes/microbiology ; Oxygen/metabolism ; Sulfur/metabolism ; }, abstract = {BACKGROUND: Cyanobacteria and eukaryotic phytoplankton produce long-chain alkanes and generate around 100 times greater quantities of hydrocarbons in the ocean compared to natural seeps and anthropogenic sources. Yet, these compounds do not accumulate in the water column, suggesting rapid biodegradation by co-localized microbial populations. Despite their ecological importance, the identities of microbes involved in this cryptic hydrocarbon cycle are mostly unknown. Here, we identified genes encoding enzymes involved in the hydrocarbon cycle across the salinity gradient of a remote, vertically stratified, seawater-containing High Arctic lake that is isolated from anthropogenic petroleum sources and natural seeps. Metagenomic analysis revealed diverse hydrocarbon cycling genes and populations, with patterns of variation along gradients of light, salinity, oxygen, and sulfur that are relevant to freshwater, oceanic, hadal, and anoxic deep sea ecosystems.

RESULTS: Analyzing genes and metagenome-assembled genomes down the water column of Lake A in the Canadian High Arctic, we detected microbial hydrocarbon production and degradation pathways at all depths, from surface freshwaters to dark, saline, anoxic waters. In addition to Cyanobacteria, members of the phyla Flavobacteria, Nitrospina, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia had pathways for alkane and alkene production, providing additional sources of biogenic hydrocarbons. Known oil-degrading microorganisms were poorly represented in the system, while long-chain hydrocarbon degradation genes were identified in various freshwater and marine lineages such as Actinobacteria, Schleiferiaceae, and Marinimicrobia. Genes involved in sulfur and nitrogen compound transformations were abundant in hydrocarbon producing and degrading lineages, suggesting strong interconnections with nitrogen and sulfur cycles and a potential for widespread distribution in the ocean.

CONCLUSIONS: Our detailed metagenomic analyses across water column gradients in a remote petroleum-free lake derived from the Arctic Ocean suggest that the current estimation of bacterial hydrocarbon production in the ocean could be substantially underestimated by neglecting non-phototrophic production and by not taking low oxygen zones into account. Our findings also suggest that biogenic hydrocarbons may sustain a large fraction of freshwater and oceanic microbiomes, with global biogeochemical implications for carbon, sulfur, and nitrogen cycles. Video Abstract.}, } @article {pmid37169918, year = {2023}, author = {Sanders, JG and Sprockett, DD and Li, Y and Mjungu, D and Lonsdorf, EV and Ndjango, JN and Georgiev, AV and Hart, JA and Sanz, CM and Morgan, DB and Peeters, M and Hahn, BH and Moeller, AH}, title = {Widespread extinctions of co-diversified primate gut bacterial symbionts from humans.}, journal = {Nature microbiology}, volume = {8}, number = {6}, pages = {1039-1050}, pmid = {37169918}, issn = {2058-5276}, support = {R01 AI050529/AI/NIAID NIH HHS/United States ; R35 GM138284/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Humans ; Phylogeny ; Pan troglodytes ; *Gastrointestinal Microbiome ; Primates ; *Hominidae/microbiology ; Bacteria/genetics ; }, abstract = {Humans and other primates harbour complex gut bacterial communities that influence health and disease, but the evolutionary histories of these symbioses remain unclear. This is partly due to limited information about the microbiota of ancestral primates. Here, using phylogenetic analyses of metagenome-assembled genomes (MAGs), we show that hundreds of gut bacterial clades diversified in parallel (that is, co-diversified) with primate species over millions of years, but that humans have experienced widespread losses of these ancestral symbionts. Analyses of 9,460 human and non-human primate MAGs, including newly generated MAGs from chimpanzees and bonobos, revealed significant co-diversification within ten gut bacterial phyla, including Firmicutes, Actinobacteriota and Bacteroidota. Strikingly, ~44% of the co-diversifying clades detected in African apes were absent from available metagenomic data from humans and ~54% were absent from industrialized human populations. In contrast, only ~3% of non-co-diversifying clades detected in African apes were absent from humans. Co-diversifying clades present in both humans and chimpanzees displayed consistent genomic signatures of natural selection between the two host species but differed in functional content from co-diversifying clades lost from humans, consistent with selection against certain functions. This study discovers host-species-specific bacterial symbionts that predate hominid diversification, many of which have undergone accelerated extinctions from human populations.}, } @article {pmid37169816, year = {2023}, author = {La Reau, AJ and Strom, NB and Filvaroff, E and Mavrommatis, K and Ward, TL and Knights, D}, title = {Shallow shotgun sequencing reduces technical variation in microbiome analysis.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {7668}, pmid = {37169816}, issn = {2045-2322}, mesh = {Humans ; Reproducibility of Results ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; Metagenomics ; }, abstract = {The microbiome is known to play a role in many human diseases, but identifying key microbes and their functions generally requires large studies due to the vast number of species and genes, and the high levels of intra-individual and inter-individual variation. 16S amplicon sequencing of the rRNA gene is commonly used for large studies due to its comparatively low sequencing cost, but it has poor taxonomic and functional resolution. Deep shotgun sequencing is a more accurate and comprehensive alternative for small studies, but can be cost-prohibitive for biomarker discovery in large populations. Shallow or moderate-depth shotgun metagenomics may serve as a viable alternative to 16S sequencing for large-scale and/or dense longitudinal studies, but only if resolution and reproducibility are comparable. Here we applied both 16S and shallow shotgun stool microbiome sequencing to a cohort of 5 subjects sampled twice daily and weekly, with technical replication at the DNA extraction and the library preparation/sequencing steps, for a total of 80 16S samples and 80 shallow shotgun sequencing samples. We found that shallow shotgun sequencing produced lower technical variation and higher taxonomic resolution than 16S sequencing, at a much lower cost than deep shotgun sequencing. These findings suggest that shallow shotgun sequencing provides a more specific and more reproducible alternative to 16S sequencing for large-scale microbiome studies where costs prohibit deep shotgun sequencing and where bacterial species are expected to have good coverage in whole-genome reference databases.}, } @article {pmid37169786, year = {2023}, author = {Lugli, GA and Mancabelli, L and Milani, C and Fontana, F and Tarracchini, C and Alessandri, G and van Sinderen, D and Turroni, F and Ventura, M}, title = {Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {25}, pmid = {37169786}, issn = {2055-5008}, mesh = {Humans ; Infant ; Infant, Newborn ; Adult ; *Gastrointestinal Microbiome ; *Microbiota ; Bacteria/genetics ; Metagenome ; Biodiversity ; }, abstract = {During infancy, gut microbiota development is a crucial process involved in the establishment of microbe-host interactions which may persist throughout adulthood, and which are believed to influence host health. To fully understand the complexities of such interactions, it is essential to assess gut microbiota diversity of newborns and its associated microbial dynamics and relationships pertaining to health and disease. To explore microbial biodiversity during the first 3 years of human life, 10,935 shotgun metagenomic datasets were taxonomically and functionally classified. Microbial species distribution between infants revealed the presence of eight major Infant Community State Types (ICSTs), being dominated by 17 bacterial taxa, whose distribution was shown to correspond to the geographical origin and infant health status. In total, 2390 chromosomal sequences of the predominant taxa were reconstructed from metagenomic data and used in combination with 44,987 publicly available genomes to trace the distribution of microbial Population Subspecies (PS) within the different infant groups, revealing patterns of multistrain coexistence among ICSTs. Finally, implementation of a metagenomic- and metatranscriptomic-based metabolic profiling highlighted different enzymatic expression patterns of the gut microbiota that allowed us to acquire insights into mechanistic aspects of health-gut microbiota interplay in newborns. Comparison between metagenomic and metatranscriptomic data highlights how a complex environment like the human gut must be investigated by employing both sequencing methodologies and possibly supplemented with metabolomics approaches. While metagenomic analyses are very useful for microbial classification aimed at unveiling key players driving microbiota balances, using these data to explain functionalities of the microbiota is not always warranted.}, } @article {pmid37169197, year = {2023}, author = {Wang, Y and Li, Q}, title = {Competition and interaction between DNRA and denitrification in composting ecosystems: Insights from metagenomic analysis.}, journal = {Bioresource technology}, volume = {381}, number = {}, pages = {129140}, doi = {10.1016/j.biortech.2023.129140}, pmid = {37169197}, issn = {1873-2976}, mesh = {Nitrates ; *Ammonium Compounds ; Denitrification ; *Composting ; *Microbiota ; Nitrogen ; Bacteria/genetics ; Oxidation-Reduction ; }, abstract = {This study investigated denitrification and dissimilatory nitrate reduction to ammonium (DNRA) competition for nitrite in composting of sugarcane pith and cow manure. Metagenomic analysis showed that Actinobacteria was the main DNRA microorganism. During heating phase and thermophilic phase, the abundances of denitrification functional genes (nirK and nirS decreased by 40.22% and 98.60%, respectively) and DNRA functional genes (nirB, nirD increased by 195.24% and 176.61%, and nrfA decreased by 45%, respectively) showed different trends. Interestingly, the abundance of nrfA increased by 250% during cooling and maturity phases. Mantel test revealed that competition between denitrification and DNRA microorganisms for NO2[-]-N limited the succession of their respective communities (P < 0.01). Network analysis showed that unclassified Solirubrobacterales, Altererythrobacter and Microbacterium were the key microorganisms in DNRA microbial communities. The results provided new insights into the key microorganisms and their driving factors affecting DNRA and nitrogen management in the composting ecosystems.}, } @article {pmid37169166, year = {2023}, author = {Chen, MM and Wang, P and Xie, XH and Nie, Z and Xu, SX and Zhang, N and Wang, W and Yao, L and Liu, Z}, title = {Young Adults with Major Depression Show Altered Microbiome.}, journal = {Neuroscience}, volume = {522}, number = {}, pages = {23-32}, doi = {10.1016/j.neuroscience.2023.05.002}, pmid = {37169166}, issn = {1873-7544}, mesh = {Humans ; Young Adult ; *Depressive Disorder, Major ; Depression ; Pilot Projects ; *Microbiota ; *Gastrointestinal Microbiome ; }, abstract = {There is growing basic and clinical evidence that major depressive disorder (MDD) is associated with gut microbiome alterations, but clinical studies have tended not to adjust for confounding factors. And few studies on the gut microbiome focused on young adults with MDD. Here we performed a pilot study to compare the gut microbiome of young adults with MDD with healthy controls. Shotgun metagenomic sequencing was performed on stool samples obtained from 40 young adults with MDD and 42 healthy controls. After controlling for confounding factors including sex, age, BMI, alcohol or cigarette consumption, bowel movement quality, exercise or defecation frequency, we compared microbiome diversity between groups, identified differentially abundant taxa, and further compared functional differences through gut-brain and gut-metabolic module analysis. There were no significant differences in overall gut microbiome structure and function in young adults with MDD compared with controls. Abundance of Sutterellaceae and species belonging to Clostridium, Eubacterium, and Ruminococcus were significantly different between groups. The cysteine degradation I pathway was increased in MDD. After controlling for most confounding factors, this pilot study provides new evidence on the specific, often subtle gut dysbiosis affecting young adults with depression.}, } @article {pmid37166318, year = {2023}, author = {Chen, Q and Zhang, X and Shi, W and Du, X and Ma, L and Wang, W and Tao, S and Xiao, Y}, title = {Longitudinal Investigation of Enteric Virome Signatures from Parental-Generation to Offspring Pigs.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0002323}, pmid = {37166318}, issn = {2165-0497}, mesh = {Pregnancy ; Swine ; Animals ; Male ; Female ; Longitudinal Studies ; *Virome ; Lactation ; Feces/microbiology ; Bacteria/genetics ; *Enterovirus Infections ; }, abstract = {To date, studies on the swine gut microbiome have focused almost exclusively on bacteria. Despite recent advances in the understanding of the swine gut bacteriome at different growth stages, a comprehensive longitudinal study of the lifetime dynamics of the swine gut virome is lacking. Here, we used metagenomic sequencing combined with bioinformatic analysis techniques to characterize the gut viromes of parental-generation and offspring pigs at different biological classification levels. We collected 54 fecal samples from 36 parental-generation pigs (18 breeding boars [Duroc] and 18 pregnant/lactating sows [Landrace]) and 108 fecal samples from 18 offspring pigs during the lactation (day 3), nursery (days 26, 35, and 49), growing (day 120), and finishing (day 180) stages. Alpha diversity, including community richness (richness index) and diversity (Shannon index), showed an overall increasing trend in offspring pigs. Distinct shifts (beta diversity) in the microbiome structure along different growth stages were observed. The linear discriminant analysis effect size (LEfSe) algorithm revealed 53 viral genus that are stage specific. Host prediction results showed that enteric viruses are probably correlated with carbohydrate decomposition. We identified abundant auxiliary carbohydrate-active enzyme (CAZyme) genes from enteric viruses, most of which are glycoside hydrolase genes and participate in the biolysis of complex polysaccharides. IMPORTANCE This study shows that distinct stage-associated swine gut viromes may be determined by age and/or gut physiology at different growth stages, and enteric viruses probably manipulate carbohydrate decomposition by abundant glycoside hydrolases. These findings fill a gap in the longitudinal pattern of the swine gut virome and lay the foundation for research on the function of swine enteric viruses.}, } @article {pmid37166164, year = {2023}, author = {Sun, H and Lv, B and Zhu, H and Zeng, Z and El-Ashram, S and Li, J and Chao, Y and Wang, J and Wang, Z}, title = {Selenized glucose improves rat semen quality by improving the gut microbiota and serum metabolome.}, journal = {Food & function}, volume = {14}, number = {11}, pages = {5105-5119}, doi = {10.1039/d3fo00692a}, pmid = {37166164}, issn = {2042-650X}, mesh = {Male ; Rats ; Animals ; Semen Analysis ; Semen/metabolism ; *Gastrointestinal Microbiome ; *Selenium/metabolism ; Glucose/metabolism ; Rats, Sprague-Dawley ; Metabolome ; Testosterone ; }, abstract = {Selenium (Se), a well-known antioxidant, is important for male fertility and sperm quality. The gut microbiota is involved in vital activities and cross-talk between reproduction and the gut axis. It is still unclear whether the gut microbiota mediates the impact of selenium on semen quality, and what the underlying mechanisms may be. A selenized glucose (SeGlu) derivative is a novel organic Se compound. After 7 days of acclimation, the Sprague-Dawley (SD) male rats (230 g, 6 weeks) were divided into three drinking groups: deionized water group (CK), SeGlu 0.15 group (0.15 mg Se per L), and SeGlu 0.4 group (0.4 mg Se per L). All animals were euthanized 30 days post-treatment. Serum and intratesticular testosterone and semen parameters were measured. Metagenomic and non-targeted metabolomic approaches were used to study the effects of SeGlu on the gut microbiota and serum metabolites of rats. In both the SeGlu 0.15 Group and the SeGlu 0.4 Group, we found a significant increase in seminiferous epithelium thickness. While the SeGlu 0.4 Group had a tendency to increase with insignificant difference, the SeGlu 0.15 Group significantly improved the sperm viability, survival rate, and seminal plasma fructose. SeGlu had no effect on intratesticular testosterone levels, or abnormal sperm counts. Measured serum testosterone levels using ELISA and LC-MS, which showed a decreasing trend. ELISA did not reveal significant differences, but LC-MS indicated a significant decrease in SeGlu 0.4 group. Meanwhile, the SeGlu 0.15 Group reduced the abundance of harmful bacteria such as Rikenella, Barnesiella, Tenacibaculum, and Aeromonas while increasing the abundance of beneficial microbiota such as Intestinimonas, Christensenella, Coprococcus, and Butyrivibrio. Linear discriminant analysis Effect Size (LEfSe) identified the SeGlu 0.15 group's feature genera as Roseburia, Clostridium, Ruminococcus, and Eubacterium. Serum metabolites showed that the SeGlu 0.15 Group increased 5 beta-androstane-3,17-dione while decreasing estrone and 2-methoxyestradiol (2-MeOE2). In conclusion, the SeGlu 0.15 Group can significantly alter the levels of several sex hormones in serum, improve the quality of rats' sperm, and reduce harmful bacterial colonization. SeGlu 0.15 may be used as an effective dietary supplement.}, } @article {pmid37161271, year = {2023}, author = {Chen, B and Zhang, Z and Zhang, Q and Xu, N and Lu, T and Wang, T and Hong, W and Fu, Z and Penuelas, J and Gillings, M and Qian, H}, title = {Antimicrobial Peptides in the Global Microbiome: Biosynthetic Genes and Resistance Determinants.}, journal = {Environmental science & technology}, volume = {57}, number = {20}, pages = {7698-7708}, doi = {10.1021/acs.est.3c01664}, pmid = {37161271}, issn = {1520-5851}, mesh = {Humans ; Antimicrobial Cationic Peptides/genetics/pharmacology/chemistry ; Antimicrobial Peptides ; *Anti-Infective Agents ; *Microbiota ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antimicrobial peptides are a promising new class of antimicrobials that could address the antibiotic resistance crisis, which poses a major threat to human health. These peptides are present in all kingdoms of life, but especially in microorganisms, having multiple origins in diverse taxa. To date, there has been no global study on the diversity of antimicrobial peptides, the hosts in which these occur, and the potential for resistance to these agents. Here, we investigated the diversity and number of antimicrobial peptides in four main habitats (aquatic, terrestrial, human, and engineered) by analyzing 52,515 metagenome-assembled genomes. The number of antimicrobial peptides was higher in the human gut microbiome than in other habitats, and most hosts of antimicrobial peptides were habitat-specific. The relative abundance of genes that confer resistance to antimicrobial peptides varied between habitats and was generally low, except for the built environment and on human skin. The horizontal transfer of potential resistance genes among these habitats was probably constrained by ecological barriers. We systematically quantified the risk of each resistance determinant to human health and found that nearly half of them pose a threat, especially those that confer resistance to multiple AMPs and polymyxin B. Our results help identify the biosynthetic potential of antimicrobial peptides in the global microbiome, further identifying peptides with a low risk of developing resistance.}, } @article {pmid37160588, year = {2024}, author = {Hou, X and Dai, P and Song, X and Long, X and Gao, J and Chai, T}, title = {Understanding the Effect of Compound Probiotics on the Health of Rabbits and Its Mechanisms Through Metagenomics.}, journal = {Probiotics and antimicrobial proteins}, volume = {16}, number = {3}, pages = {815-828}, pmid = {37160588}, issn = {1867-1314}, support = {2016GNC110014//Key Technology Research and Development Program of Shandong/ ; }, mesh = {Animals ; Rabbits ; *Probiotics/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Metagenomics ; Cecum/microbiology/metabolism ; Bacteria/classification/genetics/drug effects/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Male ; Lactobacillus ; Superoxide Dismutase/metabolism/genetics ; }, abstract = {In this study, we investigated the effects of probiotics on growth performance, immunity, intestinal flora, and antioxidant capacity of rabbits. Three hundred New Zealand white rabbits were randomly divided into four groups. Groups A, B, C, and D were the lactobacillus group, compound probiotic group, control group, and antibiotic group, respectively. The results showed compared with the control group, the average weight of groups A, B, and D increased by 14.88%, 12.33%, and 11.97%, respectively. Moreover, the index of immune organs and the IgG and IgM in serum of group B were significantly increased (P < 0.05). Meanwhile, the activities of superoxide dismutase (SOD) in group B and catalase (CAT) in group A were significantly increased (P < 0.05). At week 5, the contents of rabbit cecum were taken for metagenome sequencing, and the results showed probiotics increased the relative abundance of Akkermansia, and decreased the relative abundance of Bacteroides. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we found probiotics could enrich metabolic pathways such as carbohydrates, amino acids, and lipids. According to the Comprehensive Antibiotic Resistance Database (CARD), we found antibiotic resistance ontology (ARO) in cecum mainly included β-lactamases, macrolide 2'-phosphotransferase II, and plasmid-mediated quinolone resistance protein. Among them, there were 1964, 2105, and 1982 types of ARO in group B, group D, and groups A and C, respectively. These results showed probiotics played a beneficial role in maintaining or enhancing the health and growth of rabbits and could replace antibiotics under certain feeding conditions.}, } @article {pmid37159524, year = {2023}, author = {Arnoriaga-Rodríguez, M and Leal, Y and Mayneris-Perxachs, J and Pérez-Brocal, V and Moya, A and Ricart, W and Fernández-Balsells, M and Fernández-Real, JM}, title = {Gut Microbiota Composition and Functionality Are Associated With REM Sleep Duration and Continuous Glucose Levels.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {108}, number = {11}, pages = {2931-2939}, doi = {10.1210/clinem/dgad258}, pmid = {37159524}, issn = {1945-7197}, mesh = {Humans ; Middle Aged ; Blood Glucose/metabolism ; Blood Glucose Self-Monitoring ; Case-Control Studies ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Glucose ; Obesity ; Prospective Studies ; Sleep Duration ; *Sleep, REM ; Adult ; }, abstract = {CONTEXT: Sleep disruption is associated with worse glucose metabolic control and altered gut microbiota in animal models.

OBJECTIVE: We aimed to evaluate the possible links among rapid eye movement (REM) sleep duration, continuous glucose levels, and gut microbiota composition.

METHODS: This observational, prospective, real-life, cross-sectional case-control study included 118 (60 with obesity), middle-aged (39.1-54.8 years) healthy volunteers recruited at a tertiary hospital. Glucose variability and REM sleep duration were assessed by 10-day continuous glucose monitoring (CGM) (Dexcom G6) and wrist actigraphy (Fitbit Charge 3), respectively. The coefficient of variation (CV), interquartile range (IQR), and SD of glucose variability was assessed and the percentage of time in range (% TIR), at 126-139 mg/dL (TIR2), and 140-199 mg/dL (TIR3) were calculated. Shotgun metagenomics sequencing was applied to study gut microbiota taxonomy and functionality.

RESULTS: Increased glycemic variability (SD, CV, and IQR) was observed among subjects with obesity in parallel to increased % TIR2 and % TIR3. REM sleep duration was independently associated with % TIR3 (β = -.339; P < .001) and glucose variability (SD, β = -.350; P < .001). Microbial taxa from the Christensenellaceae family (Firmicutes phylum) were positively associated with REM sleep and negatively with CGM levels, while bacteria from Enterobacteriacea family and bacterial functions involved in iron metabolism showed opposite associations.

CONCLUSION: Decreased REM sleep duration was independently associated with a worse glucose profile. The associations of species from Christensenellaceae and Enterobacteriaceae families with REM sleep duration and continuous glucose values suggest an integrated picture of metabolic health.}, } @article {pmid37158970, year = {2023}, author = {Hu, J and Chen, J and Xu, X and Hou, Q and Ren, J and Yan, X}, title = {Gut microbiota-derived 3-phenylpropionic acid promotes intestinal epithelial barrier function via AhR signaling.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {102}, pmid = {37158970}, issn = {2049-2618}, mesh = {Animals ; Mice ; Swine ; *Gastrointestinal Microbiome ; Receptors, Aryl Hydrocarbon/genetics ; DNA, Ribosomal ; Fecal Microbiota Transplantation ; }, abstract = {BACKGROUND: The intestinal epithelial barrier confers protection against the intestinal invasion by pathogens and exposure to food antigens and toxins. Growing studies have linked the gut microbiota to the intestinal epithelial barrier function. The mining of the gut microbes that facilitate the function of intestinal epithelial barrier is urgently needed.

RESULTS: Here, we studied a landscape of the gut microbiome of seven pig breeds using metagenomics and 16S rDNA gene amplicon sequencing. The results indicated an obvious difference in the gut microbiome between Congjiang miniature (CM) pigs (a native Chinese breed) and commercial Duroc × [Landrace × Yorkshire] (DLY) pigs. CM finishing pigs had stronger intestinal epithelial barrier function than the DLY finishing pigs. Fecal microbiota transplantation from CM and DLY finishing pigs to germ-free (GF) mice transferred the intestinal epithelial barrier characteristics. By comparing the gut microbiome of the recipient GF mice, we identified and validated Bacteroides fragilis as a microbial species that contributes to the intestinal epithelial barrier. B. fragilis-derived 3-phenylpropionic acid metabolite had an important function on the enhancement of intestinal epithelial barrier. Furthermore, 3-phenylpropionic acid facilitated the intestinal epithelial barrier by activating aryl hydrocarbon receptor (AhR) signaling.

CONCLUSIONS: These findings suggest that manipulation of B. fragilis and 3-phenylpropionic acid is a promising strategy for improving intestinal epithelial barrier. Video Abstract.}, } @article {pmid37158954, year = {2023}, author = {Ettinger, CL and Saunders, M and Selbmann, L and Delgado-Baquerizo, M and Donati, C and Albanese, D and Roux, S and Tringe, S and Pennacchio, C and Del Rio, TG and Stajich, JE and Coleine, C}, title = {Highly diverse and unknown viruses may enhance Antarctic endoliths' adaptability.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {103}, pmid = {37158954}, issn = {2049-2618}, mesh = {Antarctic Regions ; *Acclimatization ; Bicycling ; Climate ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology, and further still, viruses in these communities have been largely unexplored despite important roles related to host metabolism and nutrient cycling. To begin to address this, we present a large-scale viral catalog from Antarctic rock microbial communities.

RESULTS: We performed metagenomic analyses on rocks from across Antarctica representing a broad range of environmental and spatial conditions, and which resulted in a predicted viral catalog comprising > 75,000 viral operational taxonomic units (vOTUS). We found largely undescribed, highly diverse and spatially structured virus communities which had predicted auxiliary metabolic genes (AMGs) with functions indicating that they may be potentially influencing bacterial adaptation and biogeochemistry.

CONCLUSION: This catalog lays the foundation for expanding knowledge of virosphere diversity, function, spatial ecology, and dynamics in extreme environments. This work serves as a step towards exploring adaptability of microbial communities in the face of a changing climate. Video Abstract.}, } @article {pmid37157891, year = {2023}, author = {Zhang, R and Debeljak, P and Blain, S and Obernosterer, I}, title = {Seasonal shifts in Fe-acquisition strategies in Southern Ocean microbial communities revealed by metagenomics and autonomous sampling.}, journal = {Environmental microbiology}, volume = {25}, number = {10}, pages = {1816-1829}, doi = {10.1111/1462-2920.16397}, pmid = {37157891}, issn = {1462-2920}, mesh = {Seasons ; *Phytoplankton/genetics ; Carbon/analysis ; *Microbiota ; Oceans and Seas ; Seawater/chemistry ; }, abstract = {Iron (Fe) governs the cycling of organic carbon in large parts of the Southern Ocean. The strategies of diverse microbes to acquire the different chemical forms of Fe under seasonally changing organic carbon regimes remain, however, poorly understood. Here, we report high-resolution seasonal metagenomic observations from the region off Kerguelen Island (Indian Sector of the Southern Ocean) where natural Fe-fertilization induces consecutive spring and summer phytoplankton blooms. Our data illustrate pronounced, but distinct seasonal patterns in the abundance of genes implicated in the transport of different forms of Fe and organic substrates, of siderophore biosynthesis and carbohydrate-active enzymes. The seasonal dynamics suggest a temporal decoupling in the prokaryotic requirements of Fe and organic carbon during the spring phytoplankton bloom and a concerted access to these resources after the summer bloom. Taxonomic assignments revealed differences in the prokaryotic groups harbouring genes of a given Fe-related category and pronounced seasonal successions were observed. Using MAGs we could decipher the respective Fe- and organic substrate-related genes of individual taxa assigned to abundant groups. The ecological strategies related to Fe-acquisition provide insights on how this element could shape microbial community composition with potential implications on organic matter transformations in the Southern Ocean.}, } @article {pmid37157031, year = {2023}, author = {Tian, J and Li, C and Dong, Z and Yang, Y and Xing, J and Yu, P and Xin, Y and Xu, F and Wang, L and Mu, Y and Guo, X and Sun, Q and Zhao, G and Gu, Y and Qin, G and Jiang, W}, title = {Inactivation of the antidiabetic drug acarbose by human intestinal microbial-mediated degradation.}, journal = {Nature metabolism}, volume = {5}, number = {5}, pages = {896-909}, pmid = {37157031}, issn = {2522-5812}, mesh = {*Hypoglycemic Agents/metabolism ; Humans ; *Gastrointestinal Microbiome ; *Acarbose/metabolism ; Klebsiella/genetics/metabolism ; Glycoside Hydrolase Inhibitors/metabolism ; Drug Resistance ; Diabetes Mellitus, Type 2/drug therapy ; Male ; Female ; Middle Aged ; Animals ; Mice ; Mice, Inbred C57BL ; RNA-Seq ; Adolescent ; Young Adult ; Adult ; Aged ; Aged, 80 and over ; }, abstract = {Drugs can be modified or degraded by the gut microbiota, which needs to be considered in personalized therapy. The clinical efficacy of the antidiabetic drug acarbose, an inhibitor of α-glucosidase, varies greatly among individuals for reasons that are largely unknown. Here we identify in the human gut acarbose-degrading bacteria, termed Klebsiella grimontii TD1, whose presence is associated with acarbose resistance in patients. Metagenomic analyses reveal that the abundance of K. grimontii TD1 is higher in patients with a weak response to acarbose and increases over time with acarbose treatment. In male diabetic mice, co-administration of K. grimontii TD1 reduces the hypoglycaemic effect of acarbose. Using induced transcriptome and protein profiling, we further identify an acarbose preferred glucosidase, Apg, in K. grimontii TD1, which can degrade acarbose into small molecules with loss of inhibitor function and is widely distributed in human intestinal microorganisms, especially in Klebsiella. Our results suggest that a comparatively large group of individuals could be at risk of acarbose resistance due to its degradation by intestinal bacteria, which may represent a clinically relevant example of non-antibiotic drug resistance.}, } @article {pmid37157029, year = {2023}, author = {Yoshiba, S and Nakagawa, H and Kuwata, H and Nabuchi, A and Yaso, A and Shirota, T}, title = {Metagenomic analysis of oral plaques and aortic valve tissues reveals oral bacteria associated with aortic stenosis.}, journal = {Clinical oral investigations}, volume = {27}, number = {8}, pages = {4335-4344}, pmid = {37157029}, issn = {1436-3771}, mesh = {Humans ; Aortic Valve/microbiology ; Bacteria/genetics ; Mouth/microbiology ; *Aortic Valve Stenosis/microbiology ; *Microbiota ; }, abstract = {OBJECTIVES: Bacteria derived from the oral cavity enter the bloodstream and cause the onset of various systemic diseases, including heart valve disease. However, information on the oral bacteria involved in aortic stenosis is limited.

MATERIALS AND METHODS: We comprehensively analyzed the microbiota in aortic valve tissues collected from aortic stenosis patients using metagenomic sequencing and investigated the relationships between the valve microbiota, the oral microbiota, and oral cavity conditions.

RESULTS: Metagenomic analysis revealed the presence of 629 bacterial species in five oral plaques and 15 aortic valve clinical specimens. Patients were classified into two groups (A and B) according to their aortic valve microbiota composition using principal coordinate analysis. Examination of the oral conditions of the patients showed no difference in the decayed/missing/filled teeth index. Bacteria in group B tend to be associated with severe disease, and the number of bacteria on the dorsum of the tongue and the positive rate of bleeding during probing were significantly higher in this group than in group A. The pathophysiology of aortic stenosis may be related to the presence of oral bacteria such as Streptococcus oralis and Streptococcus sanguinis following bacteremia.

CONCLUSIONS: Systemic inflammation in severe periodontitis may be driven by the oral microbiota, supporting the indirect (inflammatory) association between oral bacteria and aortic stenosis.

CLINICAL RELEVANCE: Appropriate oral hygiene management may contribute to the prevention and treatment of aortic stenosis.}, } @article {pmid37156688, year = {2023}, author = {Polo, TCF and Lai, MRR and Miot, LDB and Bento, GFC and Silva, MGD and Marques, SA and Miot, HA}, title = {Intestinal microbiome characterization of adult Brazilian men with psoriasis compared to omnivore and vegetarian controls.}, journal = {Anais brasileiros de dermatologia}, volume = {98}, number = {5}, pages = {635-643}, pmid = {37156688}, issn = {1806-4841}, mesh = {Male ; Humans ; Adult ; Diet ; Diet, Vegetarian ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Brazil ; Vegetarians ; Dietary Fiber ; *Psoriasis ; }, abstract = {BACKGROUND: Psoriasis is a chronic inflammatory disease associated with systemic inflammation and comorbidities. Changes in the composition of the intestinal microbiome are involved in the pathogenesis of inflammatory diseases and metabolic syndrome. Characterizing the intestinal microbiome of patients with psoriasis may be relevant for the understanding of its clinical course and comorbidity prevention.

OBJECTIVE: To characterize the intestinal microbiome of men with psoriasis compared to omnivore and vegetarian controls (without psoriasis).

METHOD: Cross-sectional study of 42 adult males: 21 omnivores with psoriasis; and controls: 14 omnivores and 7 vegetarian individuals. The characterization of the intestinal microbiome was performed by metagenomic analysis. Serum levels of lipopolysaccharide-binding protein (LPB) and C-reactive protein (CRP) were evaluated.

RESULTS: The groups differed from each other regarding nutritional aspects and microbiome; individuals with psoriasis had a higher consumption of protein and lower consumption of fibers. Levels of LPB, CRP, and the Firmicutes/Bacteroidetes ratio were higher in the group with psoriasis than in the vegetarian group (p<0.05). The genera Prevotella, Mogibacterium, Dorea, Bifidobacterium and Coprococcus, differed in the group with psoriasis compared to vegetarians; the genera Mogibacterium, Collinsella and Desulfovibrio differed from omnivores. A microbiome pattern linked to psoriasis (plsPSO) was identified, which was associated with higher LPB levels (rho=0.39; p=0.02), and lower dietary fiber intake (rho=-0.71; p<0.01).

STUDY LIMITATIONS: Only adult men were evaluated.

CONCLUSION: A difference was identified in the intestinal microbiome of adult men with psoriasis when compared to healthy omnivores and vegetarian controls. The identified microbiome pattern was correlated with dietary fiber intake and serum levels of LPB.}, } @article {pmid37155936, year = {2023}, author = {Peng, Y and Jin, M and Li, Z and Li, H and Zhang, L and Yu, S and Zhang, Z and Fan, R and Liu, J and Xu, Q and Wilson, K and Xiao, Y}, title = {Population Genomics Provide Insights into the Evolution and Adaptation of the Asia Corn Borer.}, journal = {Molecular biology and evolution}, volume = {40}, number = {5}, pages = {}, pmid = {37155936}, issn = {1537-1719}, mesh = {Animals ; *Zea mays/genetics ; Metagenomics ; Biodiversity ; Temperature ; *Moths/genetics ; Asia ; }, abstract = {Understanding the genetic basis of pest adaptive evolution and the risk of adaptation in response to climate change is essential for the development of sustainable agricultural practices. However, the genetic basis of climatic adaptation for the Asian corn borer (ACB), Ostrinia furnacalis, the main pest of corn in Asia and Oceania, is poorly understood. Here, we revealed the genomic loci underlying the climatic adaptation and evolution in ACB by integrating population genomic and environmental factors. We assembled a 471-Mb chromosome-scale reference genome of ACB and resequenced 423 individuals covering 27 representative geographic areas. We inferred that the ACB effective population size changes tracked with the global temperature and followed by a recent decline. Based on an integrated analysis of whole-genome selection scans and genome-wide genotype-environment association studies, we revealed the genetic basis of ACB adaption to diverse climates. For diapause traits, we identified a major effect association locus containing a circadian clock gene (period) by analyzing a diapause-segregating population. Moreover, our predictions indicated that the northern populations were more ecologically resilient to climate change than the southern populations. Together, our results revealed the genomic basis for ACB environmental adaptation and provided potential candidate genes for future evolutionary studies and genetic adaptation to climate change, intending to maintain the efficacy and sustainability of novel control techniques.}, } @article {pmid37155494, year = {2023}, author = {Gomez-Alvarez, V and Siponen, S and Kauppinen, A and Hokajärvi, AM and Tiwari, A and Sarekoski, A and Miettinen, IT and Torvinen, E and Pitkänen, T}, title = {A comparative analysis employing a gene- and genome-centric metagenomic approach reveals changes in composition, function, and activity in waterworks with different treatment processes and source water in Finland.}, journal = {Water research}, volume = {229}, number = {}, pages = {119495}, pmid = {37155494}, issn = {1879-2448}, support = {EPA999999/ImEPA/Intramural EPA/United States ; }, mesh = {Metagenome ; *Drinking Water/microbiology ; Finland ; Bacteria/metabolism ; *Microbiota/genetics ; Archaea/genetics ; *Disinfectants ; Metagenomics ; }, abstract = {The emergence and development of next-generation sequencing technologies (NGS) has made the analysis of the water microbiome in drinking water distribution systems (DWDSs) more accessible and opened new perspectives in microbial ecology studies. The current study focused on the characterization of the water microbiome employing a gene- and genome-centric metagenomic approach to five waterworks in Finland with different raw water sources, treatment methods, and disinfectant. The microbial communities exhibit a distribution pattern of a few dominant taxa and a large representation of low-abundance bacterial species. Changes in the community structure may correspond to the presence or absence and type of disinfectant residual which indicates that these conditions exert selective pressure on the microbial community. The Archaea domain represented a small fraction (up to 2.5%) and seemed to be effectively controlled by the disinfection of water. Their role particularly in non-disinfected DWDS may be more important than previously considered. In general, non-disinfected DWDSs harbor higher microbial richness and maintaining disinfectant residual is significantly important for ensuring low microbial numbers and diversity. Metagenomic binning recovered 139 (138 bacterial and 1 archaeal) metagenome-assembled genomes (MAGs) that had a >50% completeness and <10% contamination consisting of 20 class representatives in 12 phyla. The presence and occurrence of nitrite-oxidizing bacteria (NOB)-like microorganisms have significant implications for nitrogen biotransformation in drinking water systems. The metabolic and functional complexity of the microbiome is evident in DWDSs ecosystems. A comparative analysis found a set of differentially abundant taxonomic groups and functional traits in the active community. The broader set of transcribed genes may indicate an active and diverse community regardless of the treatment methods applied to water. The results indicate a highly dynamic and diverse microbial community and confirm that every DWDS is unique, and the community reflects the selection pressures exerted at the community structure, but also at the levels of functional properties and metabolic potential.}, } @article {pmid37149537, year = {2023}, author = {Ferrillo, A and Kobel, CM and Vera-Ponce de León, A and La Rosa, SL and Kunath, BJ and Pope, PB and Hagen, LH}, title = {Long-Read Metagenomics and CAZyme Discovery.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2657}, number = {}, pages = {253-284}, pmid = {37149537}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Microbiota ; Metagenome ; Carbohydrates ; High-Throughput Nucleotide Sequencing ; }, abstract = {Microorganisms play a primary role in regulating biogeochemical cycles and are a valuable source of enzymes that have biotechnological applications, such as carbohydrate-active enzymes (CAZymes). However, the inability to culture the majority of microorganisms that exist in natural ecosystems restricts access to potentially novel bacteria and beneficial CAZymes. While commonplace molecular-based culture-independent methods such as metagenomics enable researchers to study microbial communities directly from environmental samples, recent progress in long-read sequencing technologies are advancing the field. We outline key methodological stages that are required as well as describe specific protocols that are currently used for long-read metagenomic projects dedicated to CAZyme discovery.}, } @article {pmid37149185, year = {2023}, author = {Palladino, G and Rampelli, S and Scicchitano, D and Nanetti, E and Iuffrida, L and Wathsala, RHGR and Interino, N and Marini, M and Porru, E and Turroni, S and Fiori, J and Franzellitti, S and Candela, M}, title = {Seasonal dynamics of the microbiome-host response to pharmaceuticals and pesticides in Mytilus galloprovincialis farmed in the Northwestern Adriatic Sea.}, journal = {The Science of the total environment}, volume = {887}, number = {}, pages = {163948}, doi = {10.1016/j.scitotenv.2023.163948}, pmid = {37149185}, issn = {1879-1026}, mesh = {Animals ; *Mytilus/metabolism ; Seasons ; *Pesticides/analysis ; Xenobiotics/metabolism ; *Microbiota ; *Water Pollutants, Chemical/analysis ; }, abstract = {Marine mussels, especially Mytilus galloprovincialis, are well-established sentinel species, being naturally resistant to the exposure to multiple xenobiotics of natural and anthropogenic origin. Even if the response to multiple xenobiotic exposure is well known at the host level, the role of the mussel-associated microbiome in the animal response to environmental pollution is poorly explored, despite its potential in xenobiotic detoxification and its important role in host development, protection, and adaptation. Here, we characterized the microbiome-host integrative response of M. galloprovincialis in a real-world setting, involving exposure to a complex pattern of emerging pollutants, as occurs in the Northwestern Adriatic Sea. A total of 387 mussel individuals from 3 commercial farms, spanning about 200 km along the Northwestern Adriatic coast, and in 3 different seasons, were collected. Multiresidue analysis (for quantitative xenobiotic determination), transcriptomics (for host physiological response), and metagenomics (for host-associated microbial taxonomical and functional features) analyses were performed on the digestive glands. According to our findings, M. galloprovincialis responds to the presence of the complex pattern of multiple emerging pollutants - including the antibiotics sulfamethoxazole, erythromycin, and tetracycline, the herbicides atrazine and metolachlor, and the insecticide N,N-diethyl-m-toluamide - integrating host defense mechanisms, e.g., through upregulation of transcripts involved in animal metabolic activity, and microbiome-mediated detoxification functions, including microbial functionalities involved in multidrug or tetracycline resistance. Overall, our data highlight the importance of the mussel-associated microbiome as a strategic player for the orchestration of resistance to the multixenobiotic exposure at the holobiont level, providing strategic functionalities for the detoxification of multiple xenobiotic substances, as occurring in real world exposure settings. Complementing the host with microbiome-dependent xenobiotic degradative and resistance genes, the M. galloprovincialis digestive gland associated microbiome can have an important role in the detoxification of emerging pollutants in a context of high anthropogenic pressure, supporting the relevance of mussel systems as potential animal-based bioremediation tool.}, } @article {pmid37148792, year = {2023}, author = {Wang, Y and Tian, X and Song, T and Jiang, Z and Zhang, G and He, C and Li, P}, title = {Linking DOM characteristics to microbial community: The potential role of DOM mineralization for arsenic release in shallow groundwater.}, journal = {Journal of hazardous materials}, volume = {454}, number = {}, pages = {131566}, doi = {10.1016/j.jhazmat.2023.131566}, pmid = {37148792}, issn = {1873-3336}, mesh = {Dissolved Organic Matter ; *Arsenic/analysis ; *Groundwater/chemistry ; Carbon ; *Microbiota ; Nitrogen/analysis ; }, abstract = {Dissolved organic matter (DOM) play critical roles in arsenic (As) biotransformation in groundwater, but its compositional characteristics and interactions with indigenous microbial communities remain unclear. In this study, DOM signatures coupled with taxonomy and functions of microbial community were characterized in As-enriched groundwater by excitation-emission matrix, Fourier transform ion cyclotron resonance mass spectrometry and metagenomic sequencing. Results showed that As concentrations were significantly positively correlated with DOM humification (r = 0.707, p < 0.01) and the most dominant humic acid-like DOM components (r = 0.789, p < 0.01). Molecular characterization further demonstrated high DOM oxidation degree, with the prevalence of unsaturated oxygen-low aromatics, nitrogen (N1/N2)-containing compounds and unique CHO molecules in high As groundwater. These DOM properties were consistent with microbial composition and functional potentials. Both taxonomy and binning analyses demonstrated the dominance of Pseudomonas stutzeri, Microbacterium and Sphingobium xenophagum in As-enriched groundwater which possessed abundant As-reducing gene, with organic carbon degrading genes capable of labile to recalcitrant compounds degradation and high potentials of organic nitrogen mineralization to generate ammonium. Besides, most assembled bins in high As groundwater presented strong fermentation potentials which could facilitate carbon utilization by heterotrophic microbes. This study provides better insight into the potential role of DOM mineralization for As release in groundwater system.}, } @article {pmid37145100, year = {2023}, author = {Zhang, Y and Gan, Y and Bao, H and Wang, R}, title = {Perturbations of gut microbiome and metabolome of pigs infected with Mycoplasma hyorhinis.}, journal = {Journal of the science of food and agriculture}, volume = {103}, number = {13}, pages = {6219-6232}, doi = {10.1002/jsfa.12690}, pmid = {37145100}, issn = {1097-0010}, support = {//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; //Jiangsu Province Belt and Road International Cooperation Project/ ; }, mesh = {Swine ; Animals ; *Mycoplasma hyorhinis ; *Mycoplasma Infections ; *Gastrointestinal Microbiome ; *Swine Diseases ; Chromatography, Liquid ; Tandem Mass Spectrometry ; Metabolome ; Amino Acids ; Lipids ; }, abstract = {BACKGROUND: Mycoplasma hyorhinis is a prevalent respiratory pathogen in swine, causing significant economic loss to pig producers. There is growing evidence that respiratory pathogen infections have a large impact on intestinal microecology. To study the effect of M. hyorhinis infection on gut microbial composition and metabolome profile, pigs were infected with M. hyorhinis. Metagenomic sequencing analysis was performed of fecal samples and a liquid chromatography/tandem mass spectrometry (LC-MS/MS) analysis of gut digesta was made.

RESULTS: Pigs infected with M. hyorhinis had enriched Sutterella and Mailhella, and depleted Dechloromonas, Succinatimonas, Campylobacter, Blastocystis, Treponema, and Megasphaera. The pigs infected with M. hyorhinis also had greater abundances of bacterium_0_1xD8_71, Ruminococcus_sp__CAG_353, Firmicutes_bacterium_CAG_194, Firmicutes_bacterium_CAG_534, bacterium_1xD42_87, and lower abundances of Chlamydia_suis, Megasphaera_elsdenii, Treponema_porcinum, Bacteroides_sp__CAG_1060, Faecalibacterium_prausnitzii. Metabolomic analysis revealed that some lipids and lipid-like molecules increased in the small intestine, whereas most lipids and lipid-like molecule metabolites decreased in the large intestine. These altered metabolites induce changes in intestinal sphingolipid metabolism, amino acid metabolism, and thiamine metabolism.

CONCLUSION: These findings demonstrate that infection with M. hyorhinis can alter the gut microbial composition and metabolite structure in pigs, which may further affect amino acid metabolism and lipid metabolism in the intestine. © 2023 Society of Chemical Industry.}, } @article {pmid37142190, year = {2023}, author = {Moore, RL and Feehily, C and Killeen, SL and Yelverton, CA and Geraghty, AA and Walsh, CJ and O'Neill, IJ and Nielsan, IB and Lawton, EM and Sanchez-Gallardo, R and Nori, SRC and Shanahan, F and Murphy, EF and Van Sinderen, D and Cotter, PD and McAuliffe, FM}, title = {Ability of Bifidobacterium breve 702258 to transfer from mother to infant: the MicrobeMom randomized controlled trial.}, journal = {American journal of obstetrics & gynecology MFM}, volume = {5}, number = {7}, pages = {100994}, doi = {10.1016/j.ajogmf.2023.100994}, pmid = {37142190}, issn = {2589-9333}, mesh = {Infant, Newborn ; Humans ; Infant ; Female ; Pregnancy ; Adult ; *Bifidobacterium breve ; Mothers ; *Probiotics ; Gestational Age ; *Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: The composition of the infant microbiome can have a variety of short- and long-term implications for health. It is unclear if maternal probiotic supplementation in pregnancy can affect the infant gut microbiome.

OBJECTIVE: This study aimed to investigate if maternal supplementation of a formulation of Bifidobacterium breve 702258 from early pregnancy until 3 months postpartum could transfer to the infant gut.

STUDY DESIGN: This was a double-blinded, placebo-controlled, randomized controlled trial of B breve 702258 (minimum 1 × 10[9] colony-forming units) or placebo taken orally from 16 weeks' gestation until 3 months postpartum in healthy pregnant women. The primary outcome was presence of the supplemented strain in infant stool up to 3 months of life, detected by at least 2 of 3 methods: strain-specific polymerase chain reaction, shotgun metagenomic sequencing, or genome sequencing of cultured B breve. A total of 120 individual infants' stool samples were required for 80% power to detect a difference in strain transfer between groups. Rates of detection were compared using the Fisher exact test.

RESULTS: A total of 160 pregnant women with average age of 33.6 (3.9) years and mean body mass index of 24.3 (22.5-26.5) kg/m[2], of whom 43% were nulliparous (n=58), were recruited from September 2016 to July 2019. Neonatal stool samples were obtained from 135 infants (65 in intervention and 70 in control group). The presence of the supplemented strain was detected through at least 2 methods (polymerase chain reaction and culture) in 2 infants in the intervention group (n=2/65; 3.1%) and none in the control group (n=0; 0%; P=.230).

CONCLUSION: Direct mother-to-infant strain transfer of B breve 702258 occurred, albeit infrequently. This study highlights the potential for maternal supplementation to introduce microbial strains into the infant microbiome.}, } @article {pmid37141097, year = {2023}, author = {Manghi, P and Blanco-Míguez, A and Manara, S and NabiNejad, A and Cumbo, F and Beghini, F and Armanini, F and Golzato, D and Huang, KD and Thomas, AM and Piccinno, G and Punčochář, M and Zolfo, M and Lesker, TR and Bredon, M and Planchais, J and Glodt, J and Valles-Colomer, M and Koren, O and Pasolli, E and Asnicar, F and Strowig, T and Sokol, H and Segata, N}, title = {MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice.}, journal = {Cell reports}, volume = {42}, number = {5}, pages = {112464}, pmid = {37141097}, issn = {2211-1247}, support = {R01 CA230551/CA/NCI NIH HHS/United States ; U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Microbiota/genetics ; Metagenome ; *Gastrointestinal Microbiome ; Diet ; Metagenomics/methods ; }, abstract = {Mouse models are key tools for investigating host-microbiome interactions. However, shotgun metagenomics can only profile a limited fraction of the mouse gut microbiome. Here, we employ a metagenomic profiling method, MetaPhlAn 4, which exploits a large catalog of metagenome-assembled genomes (including 22,718 metagenome-assembled genomes from mice) to improve the profiling of the mouse gut microbiome. We combine 622 samples from eight public datasets and an additional cohort of 97 mouse microbiomes, and we assess the potential of MetaPhlAn 4 to better identify diet-related changes in the host microbiome using a meta-analysis approach. We find multiple, strong, and reproducible diet-related microbial biomarkers, largely increasing those identifiable by other available methods relying only on reference information. The strongest drivers of the diet-induced changes are uncharacterized and previously undetected taxa, confirming the importance of adopting metagenomic methods integrating metagenomic assemblies for comprehensive profiling.}, } @article {pmid37140369, year = {2023}, author = {Castañeda, S and Muñoz, M and Hotez, PJ and Bottazzi, ME and Paniz-Mondolfi, AE and Jones, KM and Mejia, R and Poveda, C and Ramírez, JD}, title = {Microbiome Alterations Driven by Trypanosoma cruzi Infection in Two Disjunctive Murine Models.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0019923}, pmid = {37140369}, issn = {2165-0497}, mesh = {Mice ; Animals ; Disease Models, Animal ; Mice, Inbred C57BL ; *Chagas Disease/parasitology ; *Trypanosoma cruzi ; *Microbiota ; }, abstract = {Alterations caused by Trypanosoma cruzi in the composition of gut microbiome may play a vital role in the host-parasite interactions that shapes physiology and immune responses against infection. Thus, a better understanding of this parasite-host-microbiome interaction may yield relevant information in the comprehension of the pathophysiology of the disease and the development of new prophylactic and therapeutic alternatives. Therefore, we implemented a murine model with two mice strains (BALB/c and C57BL/6) to evaluate the impact of Trypanosoma cruzi (Tulahuen strain) infection on the gut microbiome utilizing cytokine profiling and shotgun metagenomics. Higher parasite burdens were observed in cardiac and intestinal tissues, including changes in anti-inflammatory (interleukin-4 [IL-4] and IL-10) and proinflammatory (gamma interferon, tumor necrosis factor alpha, and IL-6) cytokines. Bacterial species such as Bacteroides thetaiotaomicron, Faecalibaculum rodentium, and Lactobacillus johnsonii showed a decrease in relative abundance, while Akkermansia muciniphila and Staphylococcus xylosus increased. Likewise, as infection progressed, there was a decrease in gene abundances related to metabolic processes such as lipid synthesis (including short-chain fatty acids) and amino acid synthesis (including branched-chain amino acids). High-quality metagenomic assembled genomes of L. johnsonii and A. muciniphila among other species were reconstructed, confirming, functional changes associated with metabolic pathways that are directly affected by the loss of abundance of specific bacterial taxa. IMPORTANCE Chagas disease (CD) is caused by the protozoan Trypanosoma cruzi, presenting acute and chronic phases where cardiomyopathy, megaesophagus, and/or megacolon stand out. During the course of its life cycle, the parasite has an important gastrointestinal tract transit that leads to severe forms of CD. The intestinal microbiome plays an essential role in the immunological, physiological, and metabolic homeostasis of the host. Therefore, parasite-host-intestinal microbiome interactions may provide information on certain biological and pathophysiological aspects related to CD. The present study proposes a comprehensive evaluation of the potential effects of this interaction based on metagenomic and immunological data from two mice models with different genetic, immunological, and microbiome backgrounds. Our findings suggest that there are alterations in the immune and microbiome profiles that affect several metabolic pathways that can potentially promote the infection's establishment, progression, and persistence. In addition, this information may prove essential in the research of new prophylactic and therapeutic alternatives for CD.}, } @article {pmid37140125, year = {2023}, author = {Li, M and Liu, J and Zhu, J and Wang, H and Sun, C and Gao, NL and Zhao, XM and Chen, WH}, title = {Performance of Gut Microbiome as an Independent Diagnostic Tool for 20 Diseases: Cross-Cohort Validation of Machine-Learning Classifiers.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2205386}, pmid = {37140125}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Machine Learning ; Research Design ; Metagenome ; Metagenomics/methods ; }, abstract = {Cross-cohort validation is essential for gut-microbiome-based disease stratification but was only performed for limited diseases. Here, we systematically evaluated the cross-cohort performance of gut microbiome-based machine-learning classifiers for 20 diseases. Using single-cohort classifiers, we obtained high predictive accuracies in intra-cohort validation (~0.77 AUC), but low accuracies in cross-cohort validation, except the intestinal diseases (~0.73 AUC). We then built combined-cohort classifiers trained on samples combined from multiple cohorts to improve the validation of non-intestinal diseases, and estimated the required sample size to achieve validation accuracies of >0.7. In addition, we observed higher validation performance for classifiers using metagenomic data than 16S amplicon data in intestinal diseases. We further quantified the cross-cohort marker consistency using a Marker Similarity Index and observed similar trends. Together, our results supported the gut microbiome as an independent diagnostic tool for intestinal diseases and revealed strategies to improve cross-cohort performance based on identified determinants of consistent cross-cohort gut microbiome alterations.}, } @article {pmid37137684, year = {2023}, author = {Ben-Yacov, O and Godneva, A and Rein, M and Shilo, S and Lotan-Pompan, M and Weinberger, A and Segal, E}, title = {Gut microbiome modulates the effects of a personalised postprandial-targeting (PPT) diet on cardiometabolic markers: a diet intervention in pre-diabetes.}, journal = {Gut}, volume = {72}, number = {8}, pages = {1486-1496}, pmid = {37137684}, issn = {1468-3288}, mesh = {Adult ; Humans ; *Prediabetic State ; *Gastrointestinal Microbiome ; Blood Glucose Self-Monitoring ; Blood Glucose/metabolism ; Diet ; *Diet, Mediterranean ; *Cardiovascular Diseases ; }, abstract = {OBJECTIVE: To explore the interplay between dietary modifications, microbiome composition and host metabolic responses in a dietary intervention setting of a personalised postprandial-targeting (PPT) diet versus a Mediterranean (MED) diet in pre-diabetes.

DESIGN: In a 6-month dietary intervention, adults with pre-diabetes were randomly assigned to follow an MED or PPT diet (based on a machine-learning algorithm for predicting postprandial glucose responses). Data collected at baseline and 6 months from 200 participants who completed the intervention included: dietary data from self-recorded logging using a smartphone application, gut microbiome data from shotgun metagenomics sequencing of faecal samples, and clinical data from continuous glucose monitoring, blood biomarkers and anthropometrics.

RESULTS: PPT diet induced more prominent changes to the gut microbiome composition, compared with MED diet, consistent with overall greater dietary modifications observed. Particularly, microbiome alpha-diversity increased significantly in PPT (p=0.007) but not in MED arm (p=0.18). Post hoc analysis of changes in multiple dietary features, including food-categories, nutrients and PPT-adherence score across the cohort, demonstrated significant associations between specific dietary changes and species-level changes in microbiome composition. Furthermore, using causal mediation analysis we detect nine microbial species that partially mediate the association between specific dietary changes and clinical outcomes, including three species (from Bacteroidales, Lachnospiraceae, Oscillospirales orders) that mediate the association between PPT-adherence score and clinical outcomes of hemoglobin A1c (HbA1c), high-density lipoprotein cholesterol (HDL-C) and triglycerides. Finally, using machine-learning models trained on dietary changes and baseline clinical data, we predict personalised metabolic responses to dietary modifications and assess features importance for clinical improvement in cardiometabolic markers of blood lipids, glycaemic control and body weight.

CONCLUSIONS: Our findings support the role of gut microbiome in modulating the effects of dietary modifications on cardiometabolic outcomes, and advance the concept of precision nutrition strategies for reducing comorbidities in pre-diabetes.

TRIAL REGISTRATION NUMBER: NCT03222791.}, } @article {pmid37137392, year = {2023}, author = {Jin, Y and Xiong, W and Liu, D and Wu, Z and Xiao, G and Wang, S and Su, H}, title = {Responses of straw foam-based aerobic granular sludge to atrazine: Insights from metagenomics and microbial community variations.}, journal = {Chemosphere}, volume = {331}, number = {}, pages = {138828}, doi = {10.1016/j.chemosphere.2023.138828}, pmid = {37137392}, issn = {1879-1298}, mesh = {Sewage/chemistry ; Waste Disposal, Fluid/methods ; *Atrazine ; Metagenomics ; Bioreactors/microbiology ; Aerobiosis ; *Microbiota ; Bacteria/genetics ; Nitrogen ; }, abstract = {Atrazine (ATZ) has caused serious environmental pollution, but the biodegradation of ATZ is relatively slow and inefficient. Herein, a straw foam-based aerobic granular sludge (SF-AGS) was developed, the spatially ordered architectures of which could greatly improve the drug tolerance and biodegradation efficiency of ATZ. The results showed that, in the presence of ATZ, chemical oxygen demand (COD), ammonium nitrogen (NH4[+]-N), total phosphorus (TP), and total nitrogen (TN) were effectively removed within 6 h, and the removal efficiencies were as high as 93.37%, 85.33%, 84.7%, and 70%, respectively. Furthermore, ATZ stimulated microbial consortia to secrete three times more extracellular polymers compared to without ATZ. Illumina MiSeq sequencing results showed that bacterial diversity and richness decreased, leading to significant changes in microbial population structure and composition. ATZ-resistant bacteria including Proteobacteria, Actinobacteria, and Burkholderia laid the biological basis for the stability of aerobic particles, efficient removal of pollutants, and degradation of ATZ. The study demonstrated that SF-AGS is feasible for ATZ-laden low-strength wastewater treatment.}, } @article {pmid37134153, year = {2023}, author = {Schwartz, DJ and Shalon, N and Wardenburg, K and DeVeaux, A and Wallace, MA and Hall-Moore, C and Ndao, IM and Sullivan, JE and Radmacher, P and Escobedo, M and Burnham, CD and Warner, BB and Tarr, PI and Dantas, G}, title = {Gut pathogen colonization precedes bloodstream infection in the neonatal intensive care unit.}, journal = {Science translational medicine}, volume = {15}, number = {694}, pages = {eadg5562}, pmid = {37134153}, issn = {1946-6242}, support = {R01 AI155893/AI/NIAID NIH HHS/United States ; UH3 AI083265/AI/NIAID NIH HHS/United States ; 2021081/DDCF/Doris Duke Charitable Foundation/United States ; T32 GM139774/GM/NIGMS NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; K08 AI159384/AI/NIAID NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; }, mesh = {Infant ; Infant, Newborn ; Humans ; Infant, Premature ; *Gastrointestinal Microbiome/genetics ; Intensive Care Units, Neonatal ; Vancomycin/pharmacology/therapeutic use ; *Sepsis/microbiology ; *Bacterial Infections ; Bacteria/genetics ; Gentamicins ; Ampicillin ; }, abstract = {Bacterial bloodstream infections (BSIs) resulting in late-onset sepsis affect up to half of extremely preterm infants and have substantial morbidity and mortality. Bacterial species associated with BSIs in neonatal intensive care units (NICUs) commonly colonize the preterm infant gut microbiome. Accordingly, we hypothesized that the gut microbiome is a reservoir of BSI-causing pathogenic strains that increase in abundance before BSI onset. We analyzed 550 previously published fecal metagenomes from 115 hospitalized neonates and found that recent ampicillin, gentamicin, or vancomycin exposure was associated with increased abundance of Enterobacteriaceae and Enterococcaceae in infant guts. We then performed shotgun metagenomic sequencing on 462 longitudinal fecal samples from 19 preterm infants (cases) with BSI and 37 non-BSI controls, along with whole-genome sequencing of the BSI isolates. Infants with BSI caused by Enterobacteriaceae were more likely than infants with BSI caused by other organisms to have had ampicillin, gentamicin, or vancomycin exposure in the 10 days before BSI. Relative to controls, gut microbiomes of cases had increased relative abundance of the BSI-causing species and clustered by Bray-Curtis dissimilarity according to BSI pathogen. We demonstrated that 11 of 19 (58%) of gut microbiomes before BSI, and 15 of 19 (79%) of gut microbiomes at any time, harbored the BSI isolate with fewer than 20 genomic substitutions. Last, BSI strains from the Enterobacteriaceae and Enterococcaceae families were detected in multiple infants, indicating BSI-strain transmission. Our findings support future studies to evaluate BSI risk prediction strategies based on gut microbiome abundance in hospitalized preterm infants.}, } @article {pmid37133495, year = {2023}, author = {Saikrishna, K and Talukdar, D and Das, S and Bakshi, S and Chakravarti, P and Jana, P and Karmakar, S and Wig, N and Das, B and Ray, A}, title = {Study on Effects of Probiotics on Gut Microbiome and Clinical Course in Patients with Critical Care Illnesses.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1814-1828}, pmid = {37133495}, issn = {1432-184X}, support = {5/9/1208/2019-Nut, Dt. 16.09.2019//Indian Council of Medical Research/ ; No. BT/PR30159/MED/15/188/2018//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Probiotics/therapeutic use ; Critical Care ; Disease Progression ; }, abstract = {Ventilator-associated pneumonia (VAP) is a nosocomial infection contracted by ventilator patients in which bacteria colonize the upper digestive tract and contaminated secretions are released into the lower airway. This nosocomial infection increases the morbidity and mortality of the patients as well as the cost of treatment. Probiotic formulations have recently been proposed to prevent the colonization of these pathogenic bacteria. In this prospective observational study, we aimed to investigate the effects of probiotics on gut microbiota and their relation to clinical outcomes in mechanically ventilated patients. For this study, 35 patients were recruited (22 probiotic-treated and 13 without probiotic treatment) from a cohort of 169 patients. Patients in the probiotic group were given a dose of 6 capsules of a commercially available probiotic (VSL#3®:112.5 billion CFU/cap) in three divided doses for 10 days. Sampling was carried out after each dose to monitor the temporal change in the gut microbiota composition. To profile the microbiota, we used a 16S rRNA metagenomic approach, and differences among the groups were computed using multivariate statistical analyses. Differences in gut microbial diversity (Bray Curtis and Jaccard distance, p-value > 0.05) between the probiotic-treated group and the control group were not observed. Furthermore, treatment with probiotics resulted in the enrichment of Lactobacillus and Streptococcus in the gut microbiota of the probiotic-treated groups. Our results demonstrated that probiotics might lead to favorable alterations in gut microbiome characteristics. Future studies should focus on the appropriate dosages and frequency of probiotics, which can lead to improved clinical outcomes.}, } @article {pmid37133385, year = {2023}, author = {Podell, S and Oliver, A and Kelly, LW and Sparagon, WJ and Plominsky, AM and Nelson, RS and Laurens, LML and Augyte, S and Sims, NA and Nelson, CE and Allen, EE}, title = {Herbivorous Fish Microbiome Adaptations to Sulfated Dietary Polysaccharides.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {5}, pages = {e0215422}, pmid = {37133385}, issn = {1098-5336}, support = {R01 ES030316/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Polysaccharides ; Sulfates ; Coral Reefs ; Fishes ; *Microbiota ; *Seaweed ; Bacteria/genetics ; }, abstract = {Marine herbivorous fish that feed primarily on macroalgae, such as those from the genus Kyphosus, are essential for maintaining coral health and abundance on tropical reefs. Here, deep metagenomic sequencing and assembly of gut compartment-specific samples from three sympatric, macroalgivorous Hawaiian kyphosid species have been used to connect host gut microbial taxa with predicted protein functional capacities likely to contribute to efficient macroalgal digestion. Bacterial community compositions, algal dietary sources, and predicted enzyme functionalities were analyzed in parallel for 16 metagenomes spanning the mid- and hindgut digestive regions of wild-caught fishes. Gene colocalization patterns of expanded carbohydrate (CAZy) and sulfatase (SulfAtlas) digestive enzyme families on assembled contigs were used to identify likely polysaccharide utilization locus associations and to visualize potential cooperative networks of extracellularly exported proteins targeting complex sulfated polysaccharides. These insights into the gut microbiota of herbivorous marine fish and their functional capabilities improve our understanding of the enzymes and microorganisms involved in digesting complex macroalgal sulfated polysaccharides. IMPORTANCE This work connects specific uncultured bacterial taxa with distinct polysaccharide digestion capabilities lacking in their marine vertebrate hosts, providing fresh insights into poorly understood processes for deconstructing complex sulfated polysaccharides and potential evolutionary mechanisms for microbial acquisition of expanded macroalgal utilization gene functions. Several thousand new marine-specific candidate enzyme sequences for polysaccharide utilization have been identified. These data provide foundational resources for future investigations into suppression of coral reef macroalgal overgrowth, fish host physiology, the use of macroalgal feedstocks in terrestrial and aquaculture animal feeds, and the bioconversion of macroalgae biomass into value-added commercial fuel and chemical products.}, } @article {pmid37132662, year = {2023}, author = {Bos, RP and Kaul, D and Zettler, ER and Hoffman, JM and Dupont, CL and Amaral-Zettler, LA and Mincer, TJ}, title = {Plastics select for distinct early colonizing microbial populations with reproducible traits across environmental gradients.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {2761-2775}, doi = {10.1111/1462-2920.16391}, pmid = {37132662}, issn = {1462-2920}, support = {OCE-1155379//NSF/ ; OCE-1155571//NSF/ ; OCE-1155671//NSF/ ; 432343//NSF-EFRI/ ; }, mesh = {*Plastics/chemistry ; Oceans and Seas ; Biofilms ; Metagenome ; *Microbiota ; }, abstract = {Little is known about early plastic biofilm assemblage dynamics and successional changes over time. By incubating virgin microplastics along oceanic transects and comparing adhered microbial communities with those of naturally occurring plastic litter at the same locations, we constructed gene catalogues to contrast the metabolic differences between early and mature biofilm communities. Early colonization incubations were reproducibly dominated by Alteromonadaceae and harboured significantly higher proportions of genes associated with adhesion, biofilm formation, chemotaxis, hydrocarbon degradation and motility. Comparative genomic analyses among the Alteromonadaceae metagenome assembled genomes (MAGs) highlighted the importance of the mannose-sensitive hemagglutinin (MSHA) operon, recognized as a key factor for intestinal colonization, for early colonization of hydrophobic plastic surfaces. Synteny alignments of MSHA also demonstrated positive selection for mshA alleles across all MAGs, suggesting that mshA provides a competitive advantage for surface colonization and nutrient acquisition. Large-scale genomic characteristics of early colonizers varied little, despite environmental variability. Mature plastic biofilms were composed of predominantly Rhodobacteraceae and displayed significantly higher proportions of carbohydrate hydrolysis enzymes and genes for photosynthesis and secondary metabolism. Our metagenomic analyses provide insight into early biofilm formation on plastics in the ocean and how early colonizers self-assemble, compared to mature, phylogenetically and metabolically diverse biofilms.}, } @article {pmid37128855, year = {2023}, author = {Wen, T and Niu, G and Chen, T and Shen, Q and Yuan, J and Liu, YX}, title = {The best practice for microbiome analysis using R.}, journal = {Protein & cell}, volume = {14}, number = {10}, pages = {713-725}, pmid = {37128855}, issn = {1674-8018}, support = {CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; 42277297//Natural Science Foundation of China/ ; 2022ZB325//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; //Scientific and Technology Innovation Project/ ; C12021A04115//China Academy of Chinese Medical Sciences/ ; //Fundamental Research Funds/ ; ZZ13-YQ-095//Central Public Welfare Research Institutes/ ; }, mesh = {*Software ; *Microbiota ; Sequence Analysis, DNA ; Language ; }, abstract = {With the gradual maturity of sequencing technology, many microbiome studies have published, driving the emergence and advance of related analysis tools. R language is the widely used platform for microbiome data analysis for powerful functions. However, tens of thousands of R packages and numerous similar analysis tools have brought major challenges for many researchers to explore microbiome data. How to choose suitable, efficient, convenient, and easy-to-learn tools from the numerous R packages has become a problem for many microbiome researchers. We have organized 324 common R packages for microbiome analysis and classified them according to application categories (diversity, difference, biomarker, correlation and network, functional prediction, and others), which could help researchers quickly find relevant R packages for microbiome analysis. Furthermore, we systematically sorted the integrated R packages (phyloseq, microbiome, MicrobiomeAnalystR, Animalcules, microeco, and amplicon) for microbiome analysis, and summarized the advantages and limitations, which will help researchers choose the appropriate tools. Finally, we thoroughly reviewed the R packages for microbiome analysis, summarized most of the common analysis content in the microbiome, and formed the most suitable pipeline for microbiome analysis. This paper is accompanied by hundreds of examples with 10,000 lines codes in GitHub, which can help beginners to learn, also help analysts compare and test different tools. This paper systematically sorts the application of R in microbiome, providing an important theoretical basis and practical reference for the development of better microbiome tools in the future. All the code is available at GitHub github.com/taowenmicro/EasyMicrobiomeR.}, } @article {pmid37125649, year = {2023}, author = {Zheng, J and Ge, Q and Yan, Y and Zhang, X and Huang, L and Yin, Y}, title = {dbCAN3: automated carbohydrate-active enzyme and substrate annotation.}, journal = {Nucleic acids research}, volume = {51}, number = {W1}, pages = {W115-W121}, pmid = {37125649}, issn = {1362-4962}, support = {R01 GM140370/GM/NIGMS NIH HHS/United States ; R21 AI171952/AI/NIAID NIH HHS/United States ; }, mesh = {*Carbohydrates ; Carbohydrate Metabolism/genetics ; Polysaccharides ; Databases, Factual ; *Microbiota ; }, abstract = {Carbohydrate active enzymes (CAZymes) are made by various organisms for complex carbohydrate metabolism. Genome mining of CAZymes has become a routine data analysis in (meta-)genome projects, owing to the importance of CAZymes in bioenergy, microbiome, nutrition, agriculture, and global carbon recycling. In 2012, dbCAN was provided as an online web server for automated CAZyme annotation. dbCAN2 (https://bcb.unl.edu/dbCAN2) was further developed in 2018 as a meta server to combine multiple tools for improved CAZyme annotation. dbCAN2 also included CGC-Finder, a tool for identifying CAZyme gene clusters (CGCs) in (meta-)genomes. We have updated the meta server to dbCAN3 with the following new functions and components: (i) dbCAN-sub as a profile Hidden Markov Model database (HMMdb) for substrate prediction at the CAZyme subfamily level; (ii) searching against experimentally characterized polysaccharide utilization loci (PULs) with known glycan substates of the dbCAN-PUL database for substrate prediction at the CGC level; (iii) a majority voting method to consider all CAZymes with substrate predicted from dbCAN-sub for substrate prediction at the CGC level; (iv) improved data browsing and visualization of substrate prediction results on the website. In summary, dbCAN3 not only inherits all the functions of dbCAN2, but also integrates three new methods for glycan substrate prediction.}, } @article {pmid37125210, year = {2023}, author = {Rzoska-Smith, E and Stelzer, R and Monterio, M and Cary, SC and Williamson, A}, title = {DNA repair enzymes of the Antarctic Dry Valley metagenome.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1156817}, pmid = {37125210}, issn = {1664-302X}, abstract = {Microbiota inhabiting the Dry Valleys of Antarctica are subjected to multiple stressors that can damage deoxyribonucleic acid (DNA) such as desiccation, high ultraviolet light (UV) and multiple freeze-thaw cycles. To identify novel or highly-divergent DNA-processing enzymes that may enable effective DNA repair, we have sequenced metagenomes from 30 sample-sites which are part of the most extensive Antarctic biodiversity survey undertaken to date. We then used these to construct wide-ranging sequence similarity networks from protein-coding sequences and identified candidate genes involved in specialized repair processes including unique nucleases as well as a diverse range of adenosine triphosphate (ATP) -dependent DNA ligases implicated in stationary-phase DNA repair processes. In one of the first direct investigations of enzyme function from these unique samples, we have heterologously expressed and assayed a number of these enzymes, providing insight into the mechanisms that may enable resident microbes to survive these threats to their genomic integrity.}, } @article {pmid37124044, year = {2023}, author = {Hotta, F and Eguchi, H and Kuwahara, T and Nakayama-Imaohji, H and Shimomura, Y and Kusaka, S}, title = {Disturbances in the ocular surface microbiome by perioperative antimicrobial eye drops.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1172345}, pmid = {37124044}, issn = {2235-2988}, mesh = {Humans ; Aged ; Ophthalmic Solutions/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Eye/microbiology ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Microbiota/genetics ; }, abstract = {We aimed to elucidate the effects of antimicrobial eye drops used in the perioperative period of ophthalmic surgery on the ocular surface microbiome by metagenomic analysis. Twenty-eight eyes from 15 patients (mean age 74.1 years) with no history of eye drop use within 3 months before cataract surgery were included in this study. Gatifloxacin eye drops were used in all patients in the perioperative period. The antimicrobial eye drops were started 3 days before surgery. They were discontinued after conjunctival sac specimen collection for 2 weeks after the surgery. Conjunctival sac specimens were collected to investigate the alterations in the ocular surface microbiome by meta-16S analysis targeting the V3-V4 region of the bacterial 16S rRNA gene. Principal coordinate analysis showed that the bacterial composition tended to be different before and 2 and 4 weeks after surgery. Individual observations on six eyes showed that the bacterial composition at 12 weeks after surgery was closer to that before surgery than to that at 4 weeks after surgery in two eyes, while the bacterial composition in the remaining four eyes was different at various time points. Before surgery, Firmicutes, Proteobacteria, and Bacteroidetes were predominant; however, 2 weeks after surgery, the proportion of Proteobacteria increased and that of Firmicutes decreased. A similar trend was noticed 4 weeks after surgery, although antibacterial eye drops had been discontinued 2 weeks after surgery. The Shannon-Weaver coefficient showed a decreasing trend at 2-, 4-, and 12-weeks post operation compared to that before operation. The diversity of the microbiome decreased significantly at 2- and 4-weeks after surgery when compared to that before surgery (p < 0.05). The ocular surface microbiome is easily disrupted by antimicrobial eye drops, and it needs recovery time. In such cases, the ocular surface microbiome is presumed to contain many antimicrobial-resistant bacteria. In some cases, it may not recover, and a new microbiome is formed.}, } @article {pmid37122759, year = {2023}, author = {Wang, Y and Xia, X and Zhou, X and Zhan, T and Dai, Q and Zhang, Y and Zhang, W and Shu, Y and Li, W and Xu, H}, title = {Association of gut microbiome and metabolites with onset and treatment response of patients with pemphigus vulgaris.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1114586}, pmid = {37122759}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Pemphigus/therapy ; Glucocorticoids ; Eubacterium/metabolism ; Fatty Acids, Volatile/metabolism ; Bacteria/metabolism ; }, abstract = {BACKGROUND: Gut dysbiosis and gut microbiome-derived metabolites have been implicated in both disease onset and treatment response, but this has been rarely demonstrated in pemphigus vulgaris (PV). Here, we aim to systematically characterize the gut microbiome to assess the specific microbial species and metabolites associated with PV.

METHODS: We enrolled 60 PV patients and 19 matched healthy family members, and collected 100 fecal samples (60 treatment-naïve, 21 matched post-treatment, and 19 controls). Metagenomic shotgun sequencing and subsequent quality control/alignment/annotation were performed to assess the composition and microbial species, in order to establish the association between gut microbiome with PV onset and treatment response. In addition, we evaluated short-chain fatty acids (SCFAs) in PV patients through targeted metabolomics analysis.

RESULTS: The diversity of the gut microbiome in PV patients deviates from the healthy family members but not between responder and non-responder, or before and after glucocorticoid treatment. However, the relative abundance of several microbial species, including the pathogenic bacteria (e.g., Escherichia coli) and some SCFA-producing probiotics (e.g., Eubacterium ventriosum), consistently differed between the two groups in each comparison. Escherichia coli was enriched in PV patients and significantly decreased after treatment in responders. In contrast, Eubacterium ventriosum was enriched in healthy family members and significantly increased particularly in responders after treatment. Consistently, several gut microbiome-derived SCFAs were enriched in healthy family members and significantly increased after treatment (e.g., butyric acid and valeric acid).

CONCLUSIONS: This study supports the association between the gut microbiome and PV onset, possibly through disrupting the balance of gut pathogenic bacteria and probiotics and influencing the level of gut microbiome-derived SCFAs. Furthermore, we revealed the potential relationship between specific microbial species and glucocorticoid treatment.}, } @article {pmid37122075, year = {2023}, author = {Simpson, JB and Sekela, JJ and Carry, BS and Beaty, V and Patel, S and Redinbo, MR}, title = {Diverse but desolate landscape of gut microbial azoreductases: A rationale for idiopathic IBD drug response.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2203963}, pmid = {37122075}, issn = {1949-0984}, support = {P30 CA016086/CA/NCI NIH HHS/United States ; R01 GM135218/GM/NIGMS NIH HHS/United States ; R01 GM137286/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Prodrugs ; *Amlodipine Besylate, Olmesartan Medoxomil Drug Combination ; *Crohn Disease ; *Colitis, Ulcerative ; Mesalamine/therapeutic use ; *Inflammatory Bowel Diseases/drug therapy ; }, abstract = {Prodrugs reliant on microbial activation are widely used but exhibit a range of efficacies that remain poorly understood. The anti-inflammatory compound 5-aminosalicylic acid (5-ASA), which is packaged in a variety of azo-linked prodrugs provided to most Ulcerative Colitis (UC) patients, shows confounding inter-individual variabilities in response. Such prodrugs must be activated by azo-bond reduction to form 5-ASA, a process that has been attributed to both enzymatic and non-enzymatic catalysis. Gut microbial azoreductases (AzoRs) are the first catalysts shown to activate azo-linked drugs and to metabolize toxic azo-chemicals. Here, we chart the scope of the structural and functional diversity of AzoRs in health and in patients with the inflammatory bowel diseases (IBDs) UC and Crohn's Disease (CD). Using structural metagenomics, we define the landscape of gut microbial AzoRs in 413 healthy donor and 1059 IBD patient fecal samples. Firmicutes encode a significantly higher number of unique AzoRs compared to other phyla. However, structural and biochemical analyses of distinct AzoRs from the human microbiome reveal significant differences between prevalent orthologs in the processing of toxic azo-dyes, and their generally poor activation of IBD prodrugs. Furthermore, while individuals with IBD show higher abundances of AzoR-encoding gut microbial taxa than healthy controls, the overall abundance of AzoR-encoding microbes is markedly low in both disease and health. Together, these results establish that gut microbial AzoRs are functionally diverse but sparse in both health and disease, factors that may contribute to non-optimal processing of azo-linked prodrugs and idiopathic IBD drug responses.}, } @article {pmid37121198, year = {2023}, author = {Li, L and Yan, W and Zhang, B and Zhang, H and Geng, R and Sun, S and Guan, X}, title = {Coupling of selenate reduction and pyrrhotite oxidation by indigenous microbial consortium in natural aquifer.}, journal = {Water research}, volume = {238}, number = {}, pages = {119987}, doi = {10.1016/j.watres.2023.119987}, pmid = {37121198}, issn = {1879-2448}, mesh = {Selenic Acid ; *Microbial Consortia ; Ferric Compounds ; Oxidation-Reduction ; Ferrous Compounds ; *Groundwater ; }, abstract = {Pyrrhotite is ubiquitously found in natural environment and involved in diverse (bio)processes. However, the pyrrhotite-driven bioreduction of toxic selenate [Se(VI)] remains largely unknown. This study demonstrates that Se(VI) is successfully bioreduced under anaerobic condition with the participation of pyrrhotite for the first time. Completely removal of Se(VI) was achieved at initial concentration of 10 mg/L Se(VI) and 0.56 mL/min flow rate in continuous column experiment with indigenous microbial consortium and pyrrhotite. Variation in hydrochemistry and hydrodynamics affected Se(VI) removal performance. Se(VI) was reduced to insoluble Se(0) while elements in pyrrhotite were oxidized to Fe(III) and SO4[2-]. Breakthrough study indicated that biotic activity contributed 81.4 ± 1.07% to Se(VI) transformation. Microbial community analysis suggested that chemoautotrophic genera (e.g., Thiobacillus) could realize pyrrhotite oxidation and Se(VI) reduction independently, while heterotrophic genera (e.g., Bacillus, Pseudomonas) contributed to Se(VI) detoxification by utilizing metabolic intermediates generated through Fe(II) and S(-II) oxidation, which were further verified by pure culture tests. Metagenomic and qPCR analyses indicated genes encoding enzymes for Se(VI) reduction (e.g., serA, napA and srdBAC), S oxidation (e.g., soxB) and Fe oxidation (e.g., mtrA) were upregulated. The elevated electron transporters (e.g., nicotinamide adenine dinucleotide, cytochrome c) promoted electron transfer from pyrrhotite to Se(VI). This study gains insights into Se biogeochemistry under the effect of Fe(II)-bearing minerals and provides a sustainable strategy for Se(VI) bioremediation in natural aquifer.}, } @article {pmid37120327, year = {2023}, author = {Jia, XM and Wu, BX and Chen, BD and Li, KT and Liu, YD and Xu, Y and Wang, J and Zhang, X}, title = {Compositional and functional aberrance of the gut microbiota in treatment-naïve patients with primary Sjögren's syndrome.}, journal = {Journal of autoimmunity}, volume = {141}, number = {}, pages = {103050}, doi = {10.1016/j.jaut.2023.103050}, pmid = {37120327}, issn = {1095-9157}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Sjogren's Syndrome/genetics ; *Lupus Erythematosus, Systemic/complications ; Metagenome ; *Lung Diseases, Interstitial ; }, abstract = {OBJECTIVES: To investigate the compositional and functional characteristics of the gut microbiota in primary Sjögren's syndrome (pSS) and compare them with those in systemic lupus erythematosus (SLE).

METHODS: Stool samples from 78 treatment-naïve pSS patients and 78 matched healthy controls were detected by shotgun metagenomic sequencing and compared with those from 49 treatment-naïve SLE patients. The virulence loads and mimotopes of the gut microbiota were also assessed by sequence alignment.

RESULTS: The gut microbiota of treatment-naïve pSS patients had lower richness and evenness and showed a different community distribution than that of healthy controls. The microbial species enriched in the pSS-associated gut microbiota included Lactobacillus salivarius, Bacteroides fragilis, Ruminococcus gnavus, Clostridium bartlettii, Clostridium bolteae, Veillonella parvula, and Streptococcus parasanguinis. Lactobacillus salivarius was the most discriminating species in the pSS patients, especially in those with interstitial lung disease (ILD). Among the differentiating microbial pathways, the superpathway of l-phenylalanine biosynthesis was also further enriched in pSS complicated with ILD. There were more virulence genes carried by the gut microbiota in pSS patients, most of which encoded peritrichous flagella, fimbriae, or curli fimbriae, three types of bacterial surface organelles involved in bacterial colonization and invasion. Five microbial peptides with the potential to mimic pSS-related autoepitopes were also enriched in the pSS gut. SLE and pSS shared significant gut microbial traits, including community distribution, altered microbial taxonomy and pathways, and enriched virulence genes. However, Ruminococcus torques was depleted in pSS patients but enriched in SLE patients compared to healthy controls.

CONCLUSIONS: The gut microbiota in treatment-naïve pSS patients was disturbed and shared significant similarity with that in SLE patients.}, } @article {pmid37119735, year = {2023}, author = {Palmu, J and Börschel, CS and Ortega-Alonso, A and Markó, L and Inouye, M and Jousilahti, P and Salido, RA and Sanders, K and Brennan, C and Humphrey, GC and Sanders, JG and Gutmann, F and Linz, D and Salomaa, V and Havulinna, AS and Forslund, SK and Knight, R and Lahti, L and Niiranen, T and Schnabel, RB}, title = {Gut microbiome and atrial fibrillation-results from a large population-based study.}, journal = {EBioMedicine}, volume = {91}, number = {}, pages = {104583}, pmid = {37119735}, issn = {2352-3964}, mesh = {Humans ; *Atrial Fibrillation/etiology/complications ; *Gastrointestinal Microbiome ; Heart ; Bacteria/genetics ; Aging ; Incidence ; }, abstract = {BACKGROUND: Atrial fibrillation (AF) is an important heart rhythm disorder in aging populations. The gut microbiome composition has been previously related to cardiovascular disease risk factors. Whether the gut microbial profile is also associated with the risk of AF remains unknown.

METHODS: We examined the associations of prevalent and incident AF with gut microbiota in the FINRISK 2002 study, a random population sample of 6763 individuals. We replicated our findings in an independent case-control cohort of 138 individuals in Hamburg, Germany.

FINDINGS: Multivariable-adjusted regression models revealed that prevalent AF (N = 116) was associated with nine microbial genera. Incident AF (N = 539) over a median follow-up of 15 years was associated with eight microbial genera with false discovery rate (FDR)-corrected P < 0.05. Both prevalent and incident AF were associated with the genera Enorma and Bifidobacterium (FDR-corrected P < 0.001). AF was not significantly associated with bacterial diversity measures. Seventy-five percent of top genera (Enorma, Paraprevotella, Odoribacter, Collinsella, Barnesiella, Alistipes) in Cox regression analyses showed a consistent direction of shifted abundance in an independent AF case-control cohort that was used for replication.

INTERPRETATION: Our findings establish the basis for the use of microbiome profiles in AF risk prediction. However, extensive research is still warranted before microbiome sequencing can be used for prevention and targeted treatment of AF.

FUNDING: This study was funded by European Research Council, German Ministry of Research and Education, Academy of Finland, Finnish Medical Foundation, and the Finnish Foundation for Cardiovascular Research, the Emil Aaltonen Foundation, and the Paavo Nurmi Foundation.}, } @article {pmid37119525, year = {2024}, author = {Wang, Z and Yuan, X and Zhu, Z and Pang, L and Ding, S and Li, X and Kang, Y and Hei, G and Zhang, L and Zhang, X and Wang, S and Jian, X and Li, Z and Zheng, C and Fan, X and Hu, S and Shi, Y and Song, X}, title = {Multiomics Analyses Reveal Microbiome-Gut-Brain Crosstalk Centered on Aberrant Gamma-Aminobutyric Acid and Tryptophan Metabolism in Drug-Naïve Patients with First-Episode Schizophrenia.}, journal = {Schizophrenia bulletin}, volume = {50}, number = {1}, pages = {187-198}, pmid = {37119525}, issn = {1745-1701}, support = {U21A20367//National Natural Science Foundation of China/ ; 2021YFC2702100//National Key R&D Program of China/ ; 32070679//Natural Science Foundation of China/ ; 21IRTSTHN027//Science and Technology Innovation Teams in Universities of Henan Province/ ; 204200510019//Zhong Yuan Technological Innovation Leading Talents/ ; SBGJ201808//Medical Science and Technology Foundation of Health and Family Planning Commission of Henan Province/ ; 2017-BSTDJJ-04//Zhengzhou University/ ; SBGJ202003029//Henan Provincial Health Commission/ ; 2017SHZDZX01//Shanghai Municipal Science and Technology Major Project/ ; tsqn201812153//Taishan Scholar Program of Shandong Province/ ; ZR2019YQ14//Natural Science Foundation of Shandong Province/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Tryptophan ; *Schizophrenia/genetics ; Multiomics ; Brain ; *Microbiota ; gamma-Aminobutyric Acid/metabolism ; Neurotransmitter Agents/metabolism/pharmacology ; }, abstract = {BACKGROUND AND HYPOTHESIS: Schizophrenia (SCZ) is associated with complex crosstalk between the gut microbiota and host metabolism, but the underlying mechanism remains elusive. Investigating the aberrant neurotransmitter processes reflected by alterations identified using multiomics analysis is valuable to fully explain the pathogenesis of SCZ.

STUDY DESIGN: We conducted an integrative analysis of multiomics data, including the serum metabolome, fecal metagenome, single nucleotide polymorphism data, and neuroimaging data obtained from a cohort of 127 drug-naïve, first-episode SCZ patients and 92 healthy controls to characterize the microbiome-gut-brain axis in SCZ patients. We used pathway-based polygenic risk score (PRS) analyses to determine the biological pathways contributing to genetic risk and mediation effect analyses to determine the important neuroimaging features. Additionally, a random forest model was generated for effective SCZ diagnosis.

STUDY RESULTS: We found that the altered metabolome and dysregulated microbiome were associated with neuroactive metabolites, including gamma-aminobutyric acid (GABA), tryptophan, and short-chain fatty acids. Further structural and functional magnetic resonance imaging analyses highlighted that gray matter volume and functional connectivity disturbances mediate the relationships between Ruminococcus_torgues and Collinsella_aerofaciens and symptom severity and the relationships between species Lactobacillus_ruminis and differential metabolites l-2,4-diaminobutyric acid and N-acetylserotonin and cognitive function. Moreover, analyses of the Polygenic Risk Score (PRS) support that alterations in GABA and tryptophan neurotransmitter pathways are associated with SCZ risk, and GABA might be a more dominant contributor.

CONCLUSIONS: This study provides new insights into systematic relationships among genes, metabolism, and the gut microbiota that affect brain functional connectivity, thereby affecting SCZ pathogenesis.}, } @article {pmid37119391, year = {2023}, author = {Di Ciaula, A and Bonfrate, L and Khalil, M and Garruti, G and Portincasa, P}, title = {Contribution of the microbiome for better phenotyping of people living with obesity.}, journal = {Reviews in endocrine & metabolic disorders}, volume = {24}, number = {5}, pages = {839-870}, pmid = {37119391}, issn = {1573-2606}, mesh = {Animals ; Humans ; Overweight/complications ; Obesity/metabolism ; *Microbiota ; *Gastrointestinal Microbiome/physiology ; Diet ; Inflammation/complications ; }, abstract = {Obesity has reached epidemic proportion worldwide and in all ages. Available evidence points to a multifactorial pathogenesis involving gene predisposition and environmental factors. Gut microbiota plays a critical role as a major interface between external factors, i.e., diet, lifestyle, toxic chemicals, and internal mechanisms regulating energy and metabolic homeostasis, fat production and storage. A shift in microbiota composition is linked with overweight and obesity, with pathogenic mechanisms involving bacterial products and metabolites (mainly endocannabinoid-related mediators, short-chain fatty acids, bile acids, catabolites of tryptophan, lipopolysaccharides) and subsequent alterations in gut barrier, altered metabolic homeostasis, insulin resistance and chronic, low-grade inflammation. Although animal studies point to the links between an "obesogenic" microbiota and the development of different obesity phenotypes, the translational value of these results in humans is still limited by the heterogeneity among studies, the high variation of gut microbiota over time and the lack of robust longitudinal studies adequately considering inter-individual confounders. Nevertheless, available evidence underscores the existence of several genera predisposing to obesity or, conversely, to lean and metabolically health phenotype (e.g., Akkermansia muciniphila, species from genera Faecalibacterium, Alistipes, Roseburia). Further longitudinal studies using metagenomics, transcriptomics, proteomics, and metabolomics with exact characterization of confounders are needed in this field. Results must confirm that distinct genera and specific microbial-derived metabolites represent effective and precision interventions against overweight and obesity in the long-term.}, } @article {pmid37118882, year = {2023}, author = {Ceylani, T}, title = {Effect of SCD probiotics supplemented with tauroursodeoxycholic acid (TUDCA) application on the aged rat gut microbiota composition.}, journal = {Journal of applied microbiology}, volume = {134}, number = {5}, pages = {}, doi = {10.1093/jambio/lxad092}, pmid = {37118882}, issn = {1365-2672}, mesh = {Rats ; Animals ; Rats, Sprague-Dawley ; *Gastrointestinal Microbiome ; Taurochenodeoxycholic Acid/pharmacology ; *Probiotics/pharmacology ; }, abstract = {AIMS: In this study, the effects of SCD Probiotics with tauroursodeoxycholic acid (TUDCA) application on the aged rat gut microbiota (GM) composition were investigated.

METHODS AND RESULTS: Twenty-four-month-old Sprague-Dawley rats were given 300 mg/kg of TUDCA along with 3 mL (1 × 108 CFU) of SCD probiotics for 7 days. The bacterial profile was determined by the metagenome applied to the cecum content. TUDCA, SCD probiotics, and TUDCA with SCD probiotics designed GM differently. TUDCA and SCD probiotics have the most different dominant species profiles.

CONCLUSIONS: SCD probiotics and TUDCA have their own unique effects on the species found in GM, and when they are evaluated together, the species found in GM are restructured differently.}, } @article {pmid37117202, year = {2023}, author = {Hu, X and Li, Y and Wu, J and Zhang, H and Huang, Y and Tan, X and Wen, L and Zhou, X and Xie, P and Olasunkanmi, OI and Zhou, J and Sun, Z and Liu, M and Zhang, G and Yang, J and Zheng, P and Xie, P}, title = {Changes of gut microbiota reflect the severity of major depressive disorder: a cross sectional study.}, journal = {Translational psychiatry}, volume = {13}, number = {1}, pages = {137}, pmid = {37117202}, issn = {2158-3188}, mesh = {Humans ; *Depressive Disorder, Major/microbiology ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; *Microbiota ; Feces/microbiology ; Bacteria ; }, abstract = {Disturbed gut microbiota is a potential factor in the pathogenesis of major depressive disorder (MDD), yet whether gut microbiota dysbiosis is associated with the severity of MDD remains unclear. Here, we performed shotgun metagenomic profiling of cross-sectional stool samples from MDD (n = 138) and healthy controls (n = 155). The patients with MDD were divided into three groups according to Hamilton Depression Rating Scale 17 (HAMD-17), including mild (n = 24), moderate (n = 72) and severe (n = 42) individuals, respectively. We found that microbial diversity was closely related to the severity of MDD. Compared to HCs, the abundance of Bacteroides was significantly increased in both moderate and severe MDD, while Ruminococcus and Eubacterium depleted mainly in severe group. In addition, we identified 99 bacteria species specific to severity of depression. Furthermore, a panel of microbiota marker comprising of 37 bacteria species enabled to effectively distinguish MDD patients with different severity. Together, we identified different perturbation patterns of gut microbiota in mild-to-severe depression, and identified potential diagnostic and therapeutic targets.}, } @article {pmid37116481, year = {2023}, author = {Manara, S and Selma-Royo, M and Huang, KD and Asnicar, F and Armanini, F and Blanco-Miguez, A and Cumbo, F and Golzato, D and Manghi, P and Pinto, F and Valles-Colomer, M and Amoroso, L and Corrias, MV and Ponzoni, M and Raffaetà, R and Cabrera-Rubio, R and Olcina, M and Pasolli, E and Collado, MC and Segata, N}, title = {Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population.}, journal = {Current biology : CB}, volume = {33}, number = {10}, pages = {1939-1950.e4}, pmid = {37116481}, issn = {1879-0445}, support = {R01 CA230551/CA/NCI NIH HHS/United States ; U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {Female ; Humans ; Infant ; Infant, Newborn ; *Microbiota ; Bacteria ; Milk, Human/microbiology ; Mothers ; *Gastrointestinal Microbiome ; Feces/microbiology ; }, abstract = {The human microbiome seeding starts at birth, when pioneer microbes are acquired mainly from the mother. Mode of delivery, antibiotic prophylaxis, and feeding method have been studied as modulators of mother-to-infant microbiome transmission, but other key influencing factors like modern westernized lifestyles with high hygienization, high-calorie diets, and urban settings, compared with non-westernized lifestyles have not been investigated yet. In this study, we explored the mother-infant sharing of characterized and uncharacterized microbiome members via strain-resolved metagenomics in a cohort of Ethiopian mothers and infants, and we compared them with four other cohorts with different lifestyles. The westernized and non-westernized newborns' microbiomes composition overlapped during the first months of life more than later in life, likely reflecting similar initial breast-milk-based diets. Ethiopian and other non-westernized infants shared a smaller fraction of the microbiome with their mothers than did most westernized populations, despite showing a higher microbiome diversity, and uncharacterized species represented a substantial fraction of those shared in the Ethiopian cohort. Moreover, we identified uncharacterized species belonging to the Selenomonadaceae and Prevotellaceae families specifically present and shared only in the Ethiopian cohort, and we showed that a locally produced fermented food, injera, can contribute to the higher diversity observed in the Ethiopian infants' gut with bacteria that are not part of the human microbiome but are acquired through fermented food consumption. Taken together, these findings highlight the fact that lifestyle can impact the gut microbiome composition not only through differences in diet, drug consumption, and environmental factors but also through its effect on mother-infant strain-sharing patterns.}, } @article {pmid37115265, year = {2023}, author = {Houttu, N and Benchraka, C and Lotankar, M and Muhli, E and Niinikoski, H and Lahti, L and Laitinen, K}, title = {Gut microbiota composition and function in pregnancy as determinants of prediabetes at two-year postpartum.}, journal = {Acta diabetologica}, volume = {60}, number = {8}, pages = {1045-1054}, pmid = {37115265}, issn = {1432-5233}, support = {258606//Academy of Finland/ ; 295741//Academy of Finland/ ; }, mesh = {Pregnancy ; Humans ; Female ; *Prediabetic State ; *Gastrointestinal Microbiome ; *Diabetes, Gestational ; Blood Glucose ; Postpartum Period ; }, abstract = {AIMS: Deep metagenomics offers an advanced tool for examining the relationship between gut microbiota composition and function and the onset of disease; in this case, does the composition and function of gut microbiota during pregnancy differ in women who develop prediabetes and those who do not at two-year postpartum, and whether the gut microbiota composition associates with glycemic traits.

METHODS: In total, 439 women were recruited in early pregnancy. Gut microbiota was assessed by metagenomics analysis in early (13.9 ± 2.0 gestational weeks) and late pregnancy (35.1 ± 1.0 gestational weeks). Prediabetes was determined using American Diabetes Association criteria as fasting plasma glucose 5.6-6.9 mmol/l analyzed by an enzymatic hexokinase method. Of the women, 39 (22.1%) developed prediabetes by two-year postpartum.

RESULTS: The relative abundances of Escherichia unclassified (FDR < 0.05), Clostridiales bacterium 1_7_ 47FAA (FDR < 0.25) and Parabacteroides (FDR < 0.25) were higher, and those of Ruminococcaceae bacterium D16 (FDR < 0.25), Anaerotruncus unclassified (FDR < 0.25) and Ruminococcaceae noname (FDR < 0.25) were lower in early pregnancy in those women who later developed prediabetes. In late pregnancy, Porphyromonas was higher and Ruminococcus sp 5_1_39BFAA was lower in prediabetes (FDR < 0.25). Furthermore, fasting glucose concentrations associated inversely with Anaerotruncus unclassified in early pregnancy and directly with Ruminococcus sp 5_1_39BFAA in late pregnancy (FDR < 0.25). α-Diversity or β-diversity did not differ significantly between the groups. Predictions of community function during pregnancy were not associated with prediabetes.

CONCLUSIONS: Our study shows that some bacterial species during pregnancy contributed to the onset of prediabetes within two-year postpartum. These were attributable primarily to a lower abundance of short-chain fatty acids-producing bacteria.}, } @article {pmid37115189, year = {2023}, author = {Salamzade, R and Cheong, JZA and Sandstrom, S and Swaney, MH and Stubbendieck, RM and Starr, NL and Currie, CR and Singh, AM and Kalan, LR}, title = {Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC.}, journal = {Microbial genomics}, volume = {9}, number = {4}, pages = {}, pmid = {37115189}, issn = {2057-5858}, support = {R35 GM137828/GM/NIGMS NIH HHS/United States ; U19 AI142720/AI/NIAID NIH HHS/United States ; }, mesh = {*Microbiota/genetics ; Metagenome ; Biological Evolution ; }, abstract = {Bacterial secondary metabolites, synthesized by enzymes encoded in biosynthetic gene clusters (BGCs), can underlie microbiome homeostasis and serve as commercialized products, which have historically been mined from a select group of taxa. While evolutionary approaches have proven beneficial for prioritizing BGCs for experimental characterization efforts to uncover new natural products, dedicated bioinformatics tools designed for comparative and evolutionary analysis of BGCs within focal taxa are limited. We thus developed lineage specific analysis of BGCs (lsaBGC; https://github.com/Kalan-Lab/lsaBGC) to aid exploration of microdiversity and evolutionary trends across homologous groupings of BGCs, gene cluster families (GCFs), in any bacterial taxa of interest. lsaBGC enables rapid and direct identification of GCFs in genomes, calculates evolutionary statistics and conservation for BGC genes, and builds a framework to allow for base resolution mining of novel variants through metagenomic exploration. Through application of the suite to four genera commonly found in skin microbiomes, we uncover new insights into the evolution and diversity of their BGCs. We show that the BGC of the virulence-associated carotenoid staphyloxanthin in Staphylococcus aureus is ubiquitous across the genus Staphylococcus . While one GCF encoding the biosynthesis of staphyloxanthin showcases evidence for plasmid-mediated horizontal gene transfer (HGT) between species, another GCF appears to be transmitted vertically amongst a sub-clade of skin-associated Staphylococcus . Further, the latter GCF, which is well conserved in S. aureus , has been lost in most Staphylococcus epidermidis , which is the most common Staphylococcus species on human skin and is also regarded as a commensal. We also identify thousands of novel single-nucleotide variants (SNVs) within BGCs from the Corynebacterium tuberculostearicum sp. complex, a narrow, multi-species clade that features the most prevalent Corynebacterium in healthy skin microbiomes. Although novel SNVs were approximately 10 times as likely to correspond to synonymous changes when located in the top five percentile of conserved sites, lsaBGC identified SNVs that defied this trend and are predicted to underlie amino acid changes within functionally key enzymatic domains. Ultimately, beyond supporting evolutionary investigations of BGCs, lsaBGC also provides important functionalities to aid efforts for the discovery or directed modification of natural products.}, } @article {pmid37112831, year = {2023}, author = {Sánchez, C and Doménech, A and Gomez-Lucia, E and Méndez, JL and Ortiz, JC and Benítez, L}, title = {A Novel Dependoparvovirus Identified in Cloacal Swabs of Monk Parakeet (Myiopsitta monachus) from Urban Areas of Spain.}, journal = {Viruses}, volume = {15}, number = {4}, pages = {}, pmid = {37112831}, issn = {1999-4915}, mesh = {Humans ; Animals ; Parakeets/genetics ; Dependovirus ; Spain ; Phylogeny ; Ecosystem ; *Parrots ; *Parvovirus ; }, abstract = {The introduction of invasive birds into new ecosystems frequently has negative consequences for the resident populations. Accordingly, the increasing population of monk parakeets (Myiopsitta monachus) in Europe may pose a threat because we have little knowledge of the viruses they can transmit to native naïve species. In this study, we describe a new dependoparvovirus detected by metagenomic analysis of cloacal samples from 28 apparently healthy individuals captured in urban areas of Madrid, Spain. The genomic characterization revealed that the genome encoded the NS and VP proteins typical of parvoviruses and was flanked by inverted terminal repeats. No recombination signal was detected. The phylogenetic analysis showed that it was closely related to a parvovirus isolated in a wild psittacid in China. Both viruses share 80% Rep protein sequence identity and only 64% with other dependoparvoviruses identified in Passeriformes, Anseriformes, and Piciformes and are included in a highly supported clade, which could be considered a new species. The prevalence was very low, and none of the additional 73 individuals tested positive by PCR. These results highlight the importance of exploring the viral genome in invasive species to prevent the emergence of novel viral pathogenic species.}, } @article {pmid37111144, year = {2023}, author = {Rehner, J and Schmartz, GP and Kramer, T and Keller, V and Keller, A and Becker, SL}, title = {The Effect of a Planetary Health Diet on the Human Gut Microbiome: A Descriptive Analysis.}, journal = {Nutrients}, volume = {15}, number = {8}, pages = {}, pmid = {37111144}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome ; Diet, Healthy ; Feces/microbiology ; Diet ; Bacteria/genetics ; }, abstract = {In 2019, researchers from the EAT-Lancet Commission developed the 'Planetary Health (PH) diet'. Specifically, they provided recommendations pertaining to healthy diets derived from sustainable food systems. Thus far, it has not been analysed how such a diet affects the human intestinal microbiome, which is important for health and disease development. Here, we present longitudinal genome-wide metagenomic sequencing and mass spectrometry data on the gut microbiome of healthy volunteers adhering to the PH diet, as opposed to vegetarian or vegan (VV) and omnivorous (OV) diets. We obtained basic epidemiological information from 41 healthy volunteers and collected stool samples at inclusion and after 2, 4, and 12 weeks. Individuals opting to follow the PH diet received detailed instructions and recipes, whereas individuals in the control groups followed their habitual dietary pattern. Whole-genome DNA was extracted from stool specimens and subjected to shotgun metagenomic sequencing (~3 GB per patient). Conventional bacterial stool cultures were performed in parallel and bacterial species were identified with matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. We analysed samples from 16 PH, 16 OV, and 9 VV diet patterns. The α-diversity remained relatively stable for all dietary groups. In the PH group, we observed a constant increase from 3.79% at inclusion to 4.9% after 12 weeks in relative abundance of Bifidobacterium adolescentis. Differential PH abundance analysis highlighted a non-significant increase in possible probiotics such as Paraprevotella xylaniphila and Bacteroides clarus. The highest abundance of these bacteria was observed in the VV group. Dietary modifications are associated with rapid alterations to the human gut microbiome, and the PH diet led to a slight increase in probiotic-associated bacteria at ≥4 weeks. Additional research is required to confirm these findings.}, } @article {pmid37110724, year = {2023}, author = {Bhandari, MP and Polaka, I and Vangravs, R and Mezmale, L and Veliks, V and Kirshners, A and Mochalski, P and Dias-Neto, E and Leja, M}, title = {Volatile Markers for Cancer in Exhaled Breath-Could They Be the Signature of the Gut Microbiota?.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {8}, pages = {}, pmid = {37110724}, issn = {1420-3049}, support = {Postdoctoral project number: 1.1.1.2/VIAA/3/19/495 (Activity 1.1.1.2 "Post-doctoral Research Aid")//European Regional Development Fund/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Stomach Neoplasms/diagnosis ; Gas Chromatography-Mass Spectrometry ; *Volatile Organic Compounds/analysis ; Feces/chemistry ; }, abstract = {It has been shown that the gut microbiota plays a central role in human health and disease. A wide range of volatile metabolites present in exhaled breath have been linked with gut microbiota and proposed as a non-invasive marker for monitoring pathological conditions. The aim of this study was to examine the possible correlation between volatile organic compounds (VOCs) in exhaled breath and the fecal microbiome by multivariate statistical analysis in gastric cancer patients (n = 16) and healthy controls (n = 33). Shotgun metagenomic sequencing was used to characterize the fecal microbiota. Breath-VOC profiles in the same participants were identified by an untargeted gas chromatography-mass spectrometry (GC-MS) technique. A multivariate statistical approach involving a canonical correlation analysis (CCA) and sparse principal component analysis identified the significant relationship between the breath VOCs and fecal microbiota. This relation was found to differ between gastric cancer patients and healthy controls. In 16 cancer cases, 14 distinct metabolites identified from the breath belonging to hydrocarbons, alcohols, aromatics, ketones, ethers, and organosulfur compounds were highly correlated with 33 fecal bacterial taxa (correlation of 0.891, p-value 0.045), whereas in 33 healthy controls, 7 volatile metabolites belonging to alcohols, aldehydes, esters, phenols, and benzamide derivatives correlated with 17 bacterial taxa (correlation of 0.871, p-value 0.0007). This study suggested that the correlation between fecal microbiota and breath VOCs was effective in identifying exhaled volatile metabolites and the functional effects of microbiome, thus helping to understand cancer-related changes and improving the survival and life expectancy in gastric cancer patients.}, } @article {pmid37107615, year = {2023}, author = {Boccuto, L and Tack, J and Ianiro, G and Abenavoli, L and Scarpellini, E}, title = {Human Genes Involved in the Interaction between Host and Gut Microbiome: Regulation and Pathogenic Mechanisms.}, journal = {Genes}, volume = {14}, number = {4}, pages = {}, pmid = {37107615}, issn = {2073-4425}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Artificial Intelligence ; *Microbiota ; Immune System ; Biological Evolution ; }, abstract = {INTRODUCTION: The umbrella term "human gut microbiota" describes the complex ecosystem harboring our gut. It includes bacteria, viruses, protozoa, archaea, fungi, and yeasts. This taxonomic classification does not describe its functions, which encompass nutrients digestion and absorption, immune system regulation, and host metabolism. "Gut microbiome" indicates instead the genome belonging to these "microbes" actively involved in these functions. However, the interaction between the host genome and the microbial ones determines the fine functioning of our organism.

METHODS: We reviewed the data available in the scientific literature on the definition of gut microbiota, gut microbiome, and the data on human genes involved in the interaction with the latter. We consulted the main medical databases using the following keywords, acronyms, and their associations: gut microbiota, gut microbiome, human genes, immune function, and metabolism.

RESULTS: Candidate human genes encoding enzymes, inflammatory cytokines, and proteins show similarity with those included in the gut microbiome. These findings have become available through newer artificial intelligence (AI) algorithms allowing big data analysis. From an evolutionary point of view, these pieces of evidence explain the strict and sophisticated interaction at the basis of human metabolism and immunity regulation in humans. They unravel more and more physiopathologic pathways included in human health and disease.

DISCUSSION: Several lines of evidence also obtained through big data analysis support the bi-directional role of gut microbiome and human genome in host metabolism and immune system regulation.}, } @article {pmid37106038, year = {2024}, author = {Maghini, DG and Dvorak, M and Dahlen, A and Roos, M and Doyle, B and Kuersten, S and Bhatt, AS}, title = {Quantifying bias introduced by sample collection in relative and absolute microbiome measurements.}, journal = {Nature biotechnology}, volume = {42}, number = {2}, pages = {328-338}, pmid = {37106038}, issn = {1546-1696}, support = {Lieberman Fellowship//Stanford University (SU)/ ; T32GM007276//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P30CA124435//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1S10OD02014101//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01AI14862302//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01AI14375702//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; }, mesh = {Feces ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenome ; DNA ; }, abstract = {To gain insight into the accuracy of microbial measurements, it is important to evaluate sources of bias related to sample condition, preservative method and bioinformatic analyses. There is increasing evidence that measurement of the total count and concentration of microbes in the gut, or 'absolute abundance', provides a richer source of information than relative abundance and can correct some conclusions drawn from relative abundance data. However, little is known about how preservative choice can affect these measurements. In this study, we investigated how two common preservatives and short-term storage conditions impact relative and absolute microbial measurements. OMNIgene GUT OMR-200 yields lower metagenomic taxonomic variation between different storage temperatures, whereas Zymo DNA/RNA Shield yields lower metatranscriptomic taxonomic variation. Absolute abundance quantification reveals two different causes of variable Bacteroidetes:Firmicutes ratios across preservatives. Based on these results, we recommend OMNIgene GUT OMR-200 preservative for field studies and Zymo DNA/RNA Shield for metatranscriptomics studies, and we strongly encourage absolute quantification for microbial measurements.}, } @article {pmid37104181, year = {2023}, author = {Jin, J and Zhang, C and Ren, X and Tai, B and Xing, F}, title = {Metagenome Analysis Identifies Microbial Shifts upon Deoxynivalenol Exposure and Post-Exposure Recovery in the Mouse Gut.}, journal = {Toxins}, volume = {15}, number = {4}, pages = {}, pmid = {37104181}, issn = {2072-6651}, mesh = {Mice ; Humans ; Animals ; Metagenome ; Inulin ; *Trichothecenes/toxicity ; *Microbiota ; Prebiotics ; *Lactobacillales ; }, abstract = {Deoxynivalenol (DON) is one of the most prevalent food-associated mycotoxins, and is known to cause a variety of adverse health effects on human and animals. Upon oral exposure, the intestine is the main target organ of DON. The current study unraveled that DON exposure (2 mg/kg bw/day or 5 mg/kg bw/day) can significantly reshape the gut microbiota in a mouse model. The study characterized the specific gut microbial strains and genes changed after DON exposure and also investigated the recovery of the microbiota upon either 2 weeks daily prebiotic inulin administration or 2 weeks recovery without intervention after termination of DON exposure (spontaneous recovery). The results obtained reveal that DON exposure causes a shift in gut microorganisms, increasing the relative abundance of Akkermansia muciniphila, Bacteroides vulgatus, Hungatella hathewayi, and Lachnospiraceae bacterium 28-4, while the relative abundance of Mucispirillum schaedleri, Pseudoflavonifractor sp. An85, Faecalibacterium prausnitzii, Firmicutes bacterium ASF500, Flavonifractor plautii, Oscillibacter sp. 1-3, and uncultured Flavonifractor sp. decreased. Notably, DON exposure enhanced the prevalence of A. muciniphila, a species considered as a potential prebiotic in previous studies. Most of the gut microbiome altered by DON in the low- and high-dose exposure groups recovered after 2 weeks of spontaneous recovery. Inulin administration appeared to promote the recovery of the gut microbiome and functional genes after low-dose DON exposure, but not after high-dose exposure, at which changes were exacerbated by inulin-supplemented recovery. The results obtained help to better understand the effect of DON on the gut microbiome, and the gut microbiota's recovery upon termination of DON exposure.}, } @article {pmid37103739, year = {2024}, author = {Balakrishnan, K and Krishnaa, D and Balakrishnan, G and Manickam, M and Abdulkader, AM and Dharumadurai, D}, title = {Association of Bacterial Communities with Psychedelic Mushroom and Soil as Revealed in 16S rRNA Gene Sequencing.}, journal = {Applied biochemistry and biotechnology}, volume = {196}, number = {5}, pages = {2566-2590}, pmid = {37103739}, issn = {1559-0291}, mesh = {*Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Microbiota/drug effects ; Agaricales/genetics ; Psilocybe ; Rhizosphere ; }, abstract = {Microbial communities' resident in the mushroom fruiting body and the soil around it play critical roles in the growth and propagation of the mushroom. Among the microbial communities associated with psychedelic mushrooms and the rhizosphere soil, bacterial communities are considered vital since their presence greatly influences the health of the mushrooms. The present study aimed at finding the microbiota present in the psychedelic mushroom Psilocybe cubensis and the soil the mushroom inhabits. The study was conducted at two different locations in Kodaikanal, Tamil Nadu, India. The composition and structure of microbial communities in the mushroom fruiting body and the soil were deciphered. The genomes of the microbial communities were directly assessed. High-throughput amplicon sequencing revealed distinct microbial diversity in the mushroom and the related soil. The interaction of environmental and anthropogenic factors appeared to have a significant impact on the mushroom and soil microbiome. The most abundant bacterial genera were Ochrobactrum, Stenotrophomonas, Achromobacter, and Brevundimonas. Thus, the study advances the knowledge of the composition of the microbiome and microbial ecology of a psychedelic mushroom, and paves the way for in-depth investigation of the influence of microbiota on the mushroom, with special emphasis on the impact of bacterial communities on mushroom growth. Further studies are required for a deeper understanding of the microbial communities that influence the growth of P. cubensis mushroom.}, } @article {pmid37102874, year = {2023}, author = {Colbert, JF and Kirsch, JM and Erzen, CL and Langouët-Astrié, CJ and Thompson, GE and McMurtry, SA and Kofonow, JM and Robertson, CE and Kovacs, EJ and Sullivan, RC and Hippensteel, JA and Sawant, NV and De Nisco, NJ and McCollister, BD and Schwartz, RS and Horswill, AR and Frank, DN and Duerkop, BA and Schmidt, EP}, title = {Aging-Associated Augmentation of Gut Microbiome Virulence Capability Drives Sepsis Severity.}, journal = {mBio}, volume = {14}, number = {3}, pages = {e0005223}, pmid = {37102874}, issn = {2150-7511}, support = {R01 AI141479/AI/NIAID NIH HHS/United States ; K08 AG061144/AG/NIA NIH HHS/United States ; R03 AG056353/AG/NIA NIH HHS/United States ; R01 GM125095/GM/NIGMS NIH HHS/United States ; R01 AI141479/AI/NIAID NIH HHS/United States ; T32 AI052066/AI/NIAID NIH HHS/United States ; R01 AG018859/AG/NIA NIH HHS/United States ; R01 DK131267/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; Aged ; *Gastrointestinal Microbiome/physiology ; Virulence ; Bacteria/genetics ; Aging ; *Sepsis/microbiology ; }, abstract = {Prior research has focused on host factors as mediators of exaggerated sepsis-associated morbidity and mortality in older adults. This focus on the host, however, has failed to identify therapies that improve sepsis outcomes in the elderly. We hypothesized that the increased susceptibility of the aging population to sepsis is not only a function of the host but also reflects longevity-associated changes in the virulence of gut pathobionts. We utilized two complementary models of gut microbiota-induced experimental sepsis to establish the aged gut microbiome as a key pathophysiologic driver of heightened disease severity. Further murine and human investigations into these polymicrobial bacterial communities demonstrated that age was associated with only subtle shifts in ecological composition but also an overabundance of genomic virulence factors that have functional consequence on host immune evasion. IMPORTANCE Older adults suffer more frequent and worse outcomes from sepsis, a critical illness secondary to infection. The reasons underlying this unique susceptibility are incompletely understood. Prior work in this area has focused on how the immune response changes with age. The current study, however, focuses instead on alterations in the community of bacteria that humans live with within their gut (i.e., the gut microbiome). The central concept of this paper is that the bacteria in our gut evolve along with the host and "age," making them more efficient at causing sepsis.}, } @article {pmid37102867, year = {2023}, author = {Zhang, W and Fan, X and Shi, H and Li, J and Zhang, M and Zhao, J and Su, X}, title = {Comprehensive Assessment of 16S rRNA Gene Amplicon Sequencing for Microbiome Profiling across Multiple Habitats.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0056323}, pmid = {37102867}, issn = {2165-0497}, mesh = {RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; Phylogeny ; *Microbiota/genetics ; Metagenome ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {The 16S rRNA gene works as a rapid and effective marker for the identification of microorganisms in complex communities; hence, a huge number of microbiomes have been surveyed by 16S amplicon-based sequencing. The resolution of the 16S rRNA gene is always considered only at the genus level; however, it has not been verified on a wide range of microbes yet. To fully explore the ability and potential of the 16S rRNA gene in microbial profiling, here, we propose Qscore, a comprehensive method to evaluate the performance of amplicons by integrating the amplification rate, multitier taxonomic annotation, sequence type, and length. Our in silico assessment by a "global view" of 35,889 microbe species across multiple reference databases summarizes the optimal sequencing strategy for 16S short reads. On the other hand, since microbes are unevenly distributed according to their habitats, we also provide the recommended configuration for 16 typical ecosystems based on the Qscores of 157,390 microbiomes in the Microbiome Search Engine (MSE). Detailed data simulation further proves that the 16S amplicons produced with Qscore-suggested parameters exhibit high precision in microbiome profiling, which is close to that of shotgun metagenomes under CAMI metrics. Therefore, by reconsidering the precision of 16S-based microbiome profiling, our work not only enables the high-quality reusability of massive sequence legacy that has already been produced but is also significant for guiding microbiome studies in the future. We have implemented the Qscore as an online service at http://qscore.single-cell.cn to parse the recommended sequencing strategy for specific habitats or expected microbial structures. IMPORTANCE 16S rRNA has long been used as a biomarker to identify distinct microbes from complex communities. However, due to the influence of the amplification region, sequencing type, sequence processing, and reference database, the accuracy of 16S rRNA has not been fully verified on a global range. More importantly, the microbial composition of different habitats varies greatly, and it is necessary to adopt different strategies according to the corresponding target microbes to achieve optimal analytical performance. Here, we developed Qscore, which evaluates the comprehensive performance of 16S amplicons from multiple perspectives, thus providing the best sequencing strategies for common ecological environments by using big data.}, } @article {pmid37101458, year = {2022}, author = {Li, Y and Gao, P and Sun, X and Li, B and Guo, L and Yang, R and Su, X and Gao, W and Xu, Z and Yan, G and Wang, Q and Sun, W}, title = {Primary Succession Changes the Composition and Functioning of the Protist Community on Mine Tailings, Especially Phototrophic Protists.}, journal = {ACS environmental Au}, volume = {2}, number = {5}, pages = {396-408}, pmid = {37101458}, issn = {2694-2518}, abstract = {Primary succession in mine tailings is a prerequisite for tailing vegetation. Microorganisms, including bacteria, fungi, and protists, play an important role in this process in the driving force for improving the nutritional status. Compared to bacteria and fungi, protist populations have rarely been investigated regarding their role in mine tailings, especially for those inhabiting tailings associated with primary succession. Protists are the primary consumers of fungi and bacteria, and their predatory actions promote the release of nutrients immobilized in the microbial biomass, as well as the uptake and turnover of nutrients, affecting the functions of the wider ecosystems. In this study, three different types of mine tailings associated with three successional stages (original tailings, biological crusts, and Miscanthus sinensis grasslands) were selected to characterize the protistan community diversity, structure, and function during primary succession. Some members classified as consumers dominated the network of microbial communities in the tailings, especially in the original bare land tailings. The keystone phototrophs of Chlorophyceae and Trebouxiophyceae showed the highest relative abundance in the biological crusts and grassland rhizosphere, respectively. In addition, the co-occurrences between protist and bacterial taxa demonstrated that the proportion of protistan phototrophs gradually increased during primary succession. Further, the metagenomic analysis of protistan metabolic potential showed that abundances of many functional genes associated with photosynthesis increased during the primary succession of tailings. Overall, these results suggest that the primary succession of mine tailings drives the changes observed in the protistan community, and in turn, the protistan phototrophs facilitate the primary succession of tailings. This research offers an initial insight into the changes in biodiversity, structure, and function of the protistan community during ecological succession on tailings.}, } @article {pmid37101246, year = {2023}, author = {Zhang, D and Zhang, J and Kalimuthu, S and Liu, J and Song, ZM and He, BB and Cai, P and Zhong, Z and Feng, C and Neelakantan, P and Li, YX}, title = {A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {91}, pmid = {37101246}, issn = {2049-2618}, mesh = {Female ; Humans ; *Bacteriocins/genetics ; *Lactobacillales/genetics ; *Microbiota/genetics ; Metagenome ; Anti-Bacterial Agents/pharmacology ; }, abstract = {BACKGROUND: Lactic acid bacteria (LAB) produce various bioactive secondary metabolites (SMs), which endow LAB with a protective role for the host. However, the biosynthetic potentials of LAB-derived SMs remain elusive, particularly in their diversity, abundance, and distribution in the human microbiome. Thus, it is still unknown to what extent LAB-derived SMs are involved in microbiome homeostasis.

RESULTS: Here, we systematically investigate the biosynthetic potential of LAB from 31,977 LAB genomes, identifying 130,051 secondary metabolite biosynthetic gene clusters (BGCs) of 2,849 gene cluster families (GCFs). Most of these GCFs are species-specific or even strain-specific and uncharacterized yet. Analyzing 748 human-associated metagenomes, we gain an insight into the profile of LAB BGCs, which are highly diverse and niche-specific in the human microbiome. We discover that most LAB BGCs may encode bacteriocins with pervasive antagonistic activities predicted by machine learning models, potentially playing protective roles in the human microbiome. Class II bacteriocins, one of the most abundant and diverse LAB SMs, are particularly enriched and predominant in the vaginal microbiome. We utilized metagenomic and metatranscriptomic analyses to guide our discovery of functional class II bacteriocins. Our findings suggest that these antibacterial bacteriocins have the potential to regulate microbial communities in the vagina, thereby contributing to the maintenance of microbiome homeostasis.

CONCLUSIONS: Our study systematically investigates LAB biosynthetic potential and their profiles in the human microbiome, linking them to the antagonistic contributions to microbiome homeostasis via omics analysis. These discoveries of the diverse and prevalent antagonistic SMs are expected to stimulate the mechanism study of LAB's protective roles for the microbiome and host, highlighting the potential of LAB and their bacteriocins as therapeutic alternatives. Video Abstract.}, } @article {pmid37100380, year = {2023}, author = {Tang, H and Zhou, T and Jin, W and Zong, S and Mamtimin, T and Salama, ES and Jeon, BH and Liu, P and Han, H and Li, X}, title = {Tumor-targeting engineered probiotic Escherichia coli Nissle 1917 inhibits colorectal tumorigenesis and modulates gut microbiota homeostasis in mice.}, journal = {Life sciences}, volume = {324}, number = {}, pages = {121709}, doi = {10.1016/j.lfs.2023.121709}, pmid = {37100380}, issn = {1879-0631}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Azurin/adverse effects ; Carcinogenesis ; Cell Transformation, Neoplastic ; *Probiotics/therapeutic use ; *Colorectal Neoplasms/metabolism ; Escherichia coli/genetics ; Dextran Sulfate/pharmacology ; Disease Models, Animal ; *Colitis/chemically induced ; }, abstract = {AIMS: Preliminary studies have identified the use of probiotics as a potential treatment strategy against colorectal cancer (CRC). However, natural probiotics lack direct tumor-targeting and tumor-killing activity in the intestine. This study aimed to construct a tumor-targeting engineered probiotic to combat CRC.

MAIN METHODS: Standard adhesion assay was performed to analyze the adherence ability of tumor-binding protein HlpA to CT26 cells. CCK-8 assay, Hoechst 33258 staining and flow cytometry analysis were used for examining cytotoxicity of tumoricidal protein azurin toward CT26 cells. An engineered probiotic Ep-AH harboring azurin and hlpA genes was developed using Escherichia coli Nissle 1917 (EcN) chassis. Antitumor effects of Ep-AH were evaluated in the azoxymethane (AOM) and dextran sodium sulfate salt (DSS)-induced CRC mice. Moreover, analysis of gut microbiota was conducted via fecal 16S rRNA gene sequencing and shotgun metagenomic sequencing.

KEY FINDINGS: Azurin caused a dose-dependent increase of apoptosis in CT26 cells. Ep-AH treatment reversed weight loss (p < 0.001), fecal occult blood (p < 0.01), and shortening of colon length (p < 0.001) than model group, as well as reducing tumorigenesis by 36 % (p < 0.001). Both Ep-H and Ep-A (EcN expressing HlpA or azurin) were less effective than Ep-AH. Furthermore, Ep-AH enriched the members of beneficial bacteria (e.g., Blautia and Bifidobacterium) and reversed abnormal changes of genes associated with several metabolic pathways (e.g., lipopolysaccharide biosynthesis).

SIGNIFICANCE: These results demonstrated that Ep-AH had excellent therapeutic benefits on cancer remission and gut microbiota modulation. Our study provides an effective strategy for anti-CRC treatment.}, } @article {pmid37100126, year = {2023}, author = {Du, X and Li, X and Cheng, K and Zhao, W and Cai, Z and Chen, G and Zhou, J}, title = {Virome reveals effect of Ulva prolifera green tide on the structural and functional profiles of virus communities in coastal environments.}, journal = {The Science of the total environment}, volume = {883}, number = {}, pages = {163609}, doi = {10.1016/j.scitotenv.2023.163609}, pmid = {37100126}, issn = {1879-1026}, mesh = {Ecosystem ; Virome ; *Ulva ; Bacteria ; Eutrophication ; *Viruses ; China ; }, abstract = {Viruses are widely distributed in marine environments, where they influence the transformation of matter and energy by modulating host metabolism. Driven by eutrophication, green tides are a rising concern in Chinese coastal areas, and are a serious ecological disaster that negatively affects coastal ecosystems and disrupts biogeochemical cycles. Although the composition of bacterial communities in green algae has been investigated, the diversity and roles of viruses in green algal blooms are largely unexplored. Therefore, the diversity, abundance, lifestyle, and metabolic potential of viruses in a natural bloom in Qingdao coastal area were investigated at three different stages (pre-bloom, during-bloom, and post-bloom) by metagenomics analysis. The dsDNA viruses, Siphoviridae, Myoviridae, Podoviridae, and Phycodnaviridae, were found to dominate the viral community. The viral dynamics exhibited distinct temporal patterns across different stages. The composition of the viral community varied during the bloom, especially in populations with low abundance. The lytic cycle was most predominant, and the abundance of lytic viruses increased slightly in the post-bloom stage. The diversity and richness of the viral communities varied distinctly during the green tide, and the post-bloom stage favored viral diversity and richness. The total organic carbon, dissolved oxygen, NO[3-], NO[2-], PO4[3-], chlorophyll-a contents, and temperature variably co-influenced the viral communities. The primary hosts included bacteria, algae, and other microplankton. Network analysis revealed the closer links between the viral communities as the bloom progressed. Functional prediction revealed that the viruses possibly influenced the biodegradation of microbial hydrocarbons and carbon by metabolic augmentation via auxiliary metabolic genes. The composition, structure, metabolic potential, and interaction taxonomy of the viromes differed significantly across the different stages of the green tide. The study demonstrated that the ecological event shaped the viral communities during algal bloom, and the viral communities played a significant role in phycospheric microecology.}, } @article {pmid37099155, year = {2023}, author = {Wang, B and Qi, M and Ma, Y and Zhang, B and Hu, Y}, title = {Microbiome Diversity and Cellulose Decomposition Processes by Microorganisms on the Ancient Wooden Seawall of Qiantang River of Hangzhou, China.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2109-2119}, pmid = {37099155}, issn = {1432-184X}, mesh = {Humans ; *Cellulose/metabolism ; Rivers ; *Microbiota/genetics ; Fungi/genetics ; Bacteria/genetics ; Wood/microbiology ; }, abstract = {Archaeological wood, also known as wooden cultural relics, refers to ancient wood that has been worked by humans. Further insights into the decomposition mechanism of archaeological wood are needed for its preventive conservation. In this study, we assessed the microbiome diversity and cellulose decomposition processes on a 200-year-old ancient wooden seawall - the Qiantang River of Hangzhou, China. We used high-throughput sequencing (HTS) to deduce the metagenomic functions, particularly the cellulose-decomposing pathway of the microbial communities, through bioinformatical approaches. The predominant cellulose-decomposing microorganisms were then verified with traditional isolation, culture, and identification method. The results showed that the excavation of archaeological wood significantly altered the environment, accelerating the deterioration process of the archaeological wood through the carbohydrate metabolism and the xenobiotic biodegradation and metabolism pathways, under the comprehensive metabolism of complex ecosystem formed by bacteria, archaea, fungi, microfauna, plants, and algae. Bacteroidetes, Proteobacteria, Firmicutes, and Actinobacteria were found to be the predominant source of bacterial cellulose-decomposing enzymes. Accordingly, we suggest relocating the wooden seawall to an indoor environment with controllable conditions to better preserve it. In addition, these results provide further evidence for our viewpoints that HTS techniques, combined with rational bioinformatical data interpretation approaches, can serve as powerful tools for the preventive protection of cultural heritage.}, } @article {pmid37098427, year = {2023}, author = {Ruiz-Barba, JL and Sánchez, AH and López-López, A and Cortés-Delgado, A and Montaño, A}, title = {Microbial community and volatilome changes in brines along the spontaneous fermentation of Spanish-style and natural-style green table olives (Manzanilla cultivar).}, journal = {Food microbiology}, volume = {113}, number = {}, pages = {104286}, doi = {10.1016/j.fm.2023.104286}, pmid = {37098427}, issn = {1095-9998}, mesh = {Fermentation ; *Olea/microbiology ; Food Microbiology ; Yeasts ; *Microbiota ; }, abstract = {Microbial community and volatilome of brines were monitored during the spontaneous fermentations of Spanish-style and Natural-style green table olives from Manzanilla cultivar. Fermentation of olives in the Spanish style was carried out by lactic acid bacteria (LAB) and yeasts, whereas halophilic Gram-negative bacteria and archaea, along with yeasts, drove the fermentation in the Natural style. Clear differences between the two olive fermentations regarding physicochemical and biochemical features were found. Lactobacillus, Pichia, and Saccharomyces were the dominant microbial communities in the Spanish style, whereas Allidiomarina, Halomonas, Saccharomyces, Pichia, and Nakazawaea predominated in the Natural style. Numerous qualitative and quantitative differences in individual volatiles between both fermentations were found. The final products mainly differed in total amounts of volatile acids and carbonyl compounds. In addition, in each olive style, strong positive correlations were found between the dominant microbial communities and various volatile compounds, some of them previously reported as aroma-active compounds in table olives. The findings from this study provide a better understanding of each fermentation process and may help the development of controlled fermentations using starter cultures of bacteria and/or yeasts for the production of high-quality green table olives from Manzanilla cultivar.}, } @article {pmid37098420, year = {2023}, author = {Brandl, MT and Mammel, MK and Simko, I and Richter, TKS and Gebru, ST and Leonard, SR}, title = {Weather factors, soil microbiome, and bacteria-fungi interactions as drivers of the epiphytic phyllosphere communities of romaine lettuce.}, journal = {Food microbiology}, volume = {113}, number = {}, pages = {104260}, doi = {10.1016/j.fm.2023.104260}, pmid = {37098420}, issn = {1095-9998}, mesh = {Lactuca/microbiology ; Soil ; Weather ; Bacteria/genetics ; *Microbiota ; *Shiga-Toxigenic Escherichia coli ; Fungi/genetics ; Plant Leaves/microbiology ; }, abstract = {Lettuce is associated with seasonal outbreaks of Shiga toxin-producing Escherichia coli (STEC) infections. Little is known about how various biotic and abiotic factors affect the lettuce microbiome, which in turn impacts STEC colonization. We characterized the lettuce phyllosphere and surface soil bacterial, fungal, and oomycete communities at harvest in late-spring and -fall in California using metagenomics. Harvest season and field type, but not cultivar, significantly influenced the microbiome composition of leaves and surface soil near plants. Phyllosphere and soil microbiome compositions were correlated with specific weather factors. The relative abundance of Enterobacteriaceae, but not E. coli, was enriched on leaves (5.2%) compared to soil (0.4%) and correlated positively with minimum air temperature and wind speed. Co-occurrence networks revealed seasonal trends in fungi-bacteria interactions on leaves. These associations represented 39%-44% of the correlations between species. All significant E. coli co-occurrences with fungi were positive, while all negative associations were with bacteria. A large proportion of the leaf bacterial species was shared with those in soil, indicating microbiome transmission from the soil surface to the canopy. Our findings provide new insight into factors that shape lettuce microbial communities and the microbial context of foodborne pathogen immigration events in the lettuce phyllosphere.}, } @article {pmid37095530, year = {2023}, author = {Hao, Z and Meng, C and Li, L and Feng, S and Zhu, Y and Yang, J and Han, L and Sun, L and Lv, W and Figeys, D and Liu, H}, title = {Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the "Lunar Palace 365" experiment.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {88}, pmid = {37095530}, issn = {2049-2618}, mesh = {Animals ; Humans ; *Gastrointestinal Microbiome ; Moon ; Multiomics ; Tryptophan ; Glutamates ; Mammals ; }, abstract = {BACKGROUND: Psychological health risk is one of the most severe and complex risks in manned deep-space exploration and long-term closed environments. Recently, with the in-depth research of the microbiota-gut-brain axis, gut microbiota has been considered a new approach to maintain and improve psychological health. However, the correlation between gut microbiota and psychological changes inside long-term closed environments is still poorly understood. Herein, we used the "Lunar Palace 365" mission, a 1-year-long isolation study in the Lunar Palace 1 (a closed manned Bioregenerative Life Support System facility with excellent performance), to investigate the correlation between gut microbiota and psychological changes, in order to find some new potential psychobiotics to maintain and improve the psychological health of crew members.

RESULTS: We report some altered gut microbiota that were associated with psychological changes in the long-term closed environment. Four potential psychobiotics (Bacteroides uniformis, Roseburia inulinivorans, Eubacterium rectale, and Faecalibacterium prausnitzii) were identified. On the basis of metagenomic, metaproteomic, and metabolomic analyses, the four potential psychobiotics improved mood mainly through three pathways related to nervous system functions: first, by fermenting dietary fibers, they may produce short-chain fatty acids, such as butyric and propionic acids; second, they may regulate amino acid metabolism pathways of aspartic acid, glutamic acid, tryptophan, etc. (e.g., converting glutamic acid to gamma-aminobutyric acid; converting tryptophan to serotonin, kynurenic acid, or tryptamine); and third, they may regulate other pathways, such as taurine and cortisol metabolism. Furthermore, the results of animal experiments confirmed the positive regulatory effect and mechanism of these potential psychobiotics on mood.

CONCLUSIONS: These observations reveal that gut microbiota contributed to a robust effect on the maintenance and improvement of mental health in a long-term closed environment. Our findings represent a key step towards a better understanding the role of the gut microbiome in mammalian mental health during space flight and provide a basis for future efforts to develop microbiota-based countermeasures that mitigate risks to crew mental health during future long-term human space expeditions on the moon or Mars. This study also provides an essential reference for future applications of psychobiotics to neuropsychiatric treatments. Video Abstract.}, } @article {pmid37094914, year = {2023}, author = {Brunetto, MR and Salvati, A and Petralli, G and Bonino, F}, title = {Nutritional intervention in the management of non-alcoholic fatty liver disease.}, journal = {Best practice & research. Clinical gastroenterology}, volume = {62-63}, number = {}, pages = {101830}, doi = {10.1016/j.bpg.2023.101830}, pmid = {37094914}, issn = {1532-1916}, mesh = {Animals ; Humans ; *Non-alcoholic Fatty Liver Disease/pathology ; Diet ; Nutritional Status ; Life Style ; *Microbiota ; Liver/metabolism/pathology ; }, abstract = {Lifestyle modification is the primary intervention to control NAFLD progression, but despite evidence-based effectiveness it is difficult to distinguish the benefits of nutrition from physical activity and the optimal diet composition is not established. Macronutrients as saturated fatty acids, sugars and animal proteins are harmful in NAFLD and the Mediterranean Diet reducing sugar, red meat and refined carbohydrates and increasing unsaturated-fatty-acids was reported to be beneficial. However one size cannot fit all since NAFLD is a multifaceted syndrome encompassing many diseases of unknown etiologies, different clinical severity and outcomes. Studies of the intestinal metagenome, provided new insights into the physio-pathological interplay between intestinal microbiota and NAFLD. How much the microbiota heterogeneity can influence response to diet remains unknown. New knowledge indicates that AI guided personalized nutrition based on clinic-pathologic and genetic data combined with pre/post nutritional intervention gut metagenomics/metabolomics will be part of the future management of NAFLD.}, } @article {pmid37093508, year = {2023}, author = {Wijdeveld, M and van Olst, N and van der Vossen, EWJ and de Brauw, M and Acherman, YIZ and de Goffau, MC and Gerdes, VEA and Nieuwdorp, M}, title = {Identifying Gut Microbiota associated with Gastrointestinal Symptoms upon Roux-en-Y Gastric Bypass.}, journal = {Obesity surgery}, volume = {33}, number = {6}, pages = {1635-1645}, pmid = {37093508}, issn = {1708-0428}, mesh = {Humans ; *Gastric Bypass/adverse effects ; *Gastrointestinal Microbiome ; *Obesity, Morbid/surgery ; Quality of Life ; *Microbiota ; }, abstract = {PURPOSE: Roux-en-Y gastric bypasses (RYGB) are frequently accompanied by long-term gastrointestinal (GI) symptoms. Direct mechanistic insight into the causation of these symptoms is lacking, but changes in the intestinal microbiome have been proposed to play a role. With this study, we aimed to investigate whether a microbial predisposition exists before RYGB which is associated with GI symptoms during follow-up and to evaluate which microbial groups are involved.

MATERIALS AND METHODS: In total, 67 RYGB patients were included. Shotgun metagenomic sequencing was performed on fecal samples obtained just before and 1 year after surgery. To assess GI symptoms, patients filled out Gastrointestinal Quality of Life Index (GIQLI) questionnaires and were divided into groups based on their total GIQLI score and change in score (postsurgery versus baseline). Extremely randomized tree predictor models were used to identify the most distinctive microbial species associated with postoperative GI symptoms.

RESULTS: Beta diversity differed significantly between baseline and 1-year post-surgery samples, with the post-surgery microbiome resembling a more dysbiotic profile. The most predictive species regarding total GIQLI (AUC 0.77) or delta GIQLI score (AUC 0.83) were identified. Many of these species are known butyrate producers or species known to support them and/or species with anti-inflammatory properties, including Coprococcus eutactus, Faecalibacterium prausnitzii, and Ruminococcus callidus.

CONCLUSION: Beneficial commensal gut microbiota related to a high GI score were associated to adequate intestinal fermentative capacity, suggesting these species might have protective properties against postoperative GI malfunctioning.}, } @article {pmid37093231, year = {2023}, author = {Ichige, R and Urabe, J}, title = {Divergence of the Host-Associated Microbiota with the Genetic Distance of Host Individuals Within a Parthenogenetic Daphnia Species.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2097-2108}, pmid = {37093231}, issn = {1432-184X}, support = {JPMJSP2114//Japan Science and Technology Agency/ ; KAKENHI:20H03315//Japan Society for the Promotion of Science Grant-in-Aid for Scientific Research/ ; }, mesh = {Animals ; *Daphnia/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Genotype ; }, abstract = {The taxonomic composition of the microbiota in the gut and epidermis of animals is known to vary among genetically and physiologically different host individuals within the same species. However, it is not clear whether the taxonomic composition diverges with increasing genetic distance of the host individuals. To unveil this uncertainty, we compared the host-associated microbiota among the genotypes within and between genetically distant lineages of parthenogenetic Daphnia cf. pulex across different physiological states, namely, well-fed, starved, and dead. Metagenomic analysis with 16S rRNA showed that, regardless of the host genotypes, diversity of the host-associated microbiota was high when the host individuals were fed food and gradually decreased when they were starved until they died. However, the difference in the host-associated microbiota, that is, β-diversity, was significant among the genotypes within and between the host lineages when they were fed. Although some bacteria in the microbiota, such as Limnohabitans, Rhodococcus, and Aeromicrobium, were found abundantly and commonly in all host genotypes; others, such as those of Holosoporacea, were found only in the genotypes of a specific lineage. Accordingly, the β-diversity tended to increase with increasing genetic distance of the host individuals. These results support an idea that the host-associated microbiota diverged with genetic divergence in the host species and that at least some bacteria are highly dependent on the genetically specific metabolites produced by the host individuals.}, } @article {pmid37092330, year = {2023}, author = {Castillo, DF and Denson, LA and Haslam, DB and Hommel, KA and Ollberding, NJ and Sahay, R and Santucci, NR}, title = {The microbiome in adolescents with irritable bowel syndrome and changes with percutaneous electrical nerve field stimulation.}, journal = {Neurogastroenterology and motility}, volume = {35}, number = {7}, pages = {e14573}, pmid = {37092330}, issn = {1365-2982}, support = {K23 DK135797/DK/NIDDK NIH HHS/United States ; P30 DK078392/DK/NIDDK NIH HHS/United States ; T32 DK007727/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Female ; Adolescent ; Child ; *Irritable Bowel Syndrome/diagnosis ; *Microbiota ; Abdominal Pain/complications ; Catastrophization ; Carbohydrates ; }, abstract = {BACKGROUND: Irritable bowel syndrome (IBS), a disorder of the gut-brain axis, is affected by the microbiome. Microbial studies in pediatric IBS, especially for centrally mediated treatments, are lacking. We compared the microbiome between pediatric IBS patients and healthy controls (HC), in relation to symptom severity, and with percutaneous electrical nerve field stimulation (PENFS), a non-invasive treatment targeting central pain pathways.

METHODS: We collected a stool sample, questionnaires and a 1-2 week stool and pain diary from 11 to 18 years patients with IBS. A patient subset completed 4 weeks of PENFS and repeated data collection immediately after and/or 3 months after treatment. Stool samples were collected from HC. Samples underwent metagenomic sequencing to evaluate diversity, composition, and abundance of species and MetaCyc pathways.

KEY RESULTS: We included 27 cases (15.4 ± 2.5 year) and 34 HC (14.2 ± 2.9 year). Twelve species including Firmicutes spp., and carbohydrate degradation/long-chain fatty acid (LCFA) synthesis pathways, were increased in IBS but not statistically significantly associated with symptom severity. Seventeen participants (female) who completed PENFS showed improvements in pain (p = 0.012), disability (p = 0.007), and catastrophizing (p = 0.003). Carbohydrate degradation and LCFA synthesis pathways decreased post-treatment and at follow-up (FDR p-value <0.1).

CONCLUSIONS AND INFERENCES: Firmicutes, including Clostridiaceae spp., and LCFA synthesis pathways were increased in IBS patients suggesting pain-potentiating effects. PENFS led to marked improvements in abdominal pain, functioning, and catastrophizing, while Clostridial species and LCFA microbial pathways decreased with treatment, suggesting these as potential targets for IBS centrally mediated treatments.}, } @article {pmid37090719, year = {2023}, author = {Meng, JX and Wei, XY and Guo, H and Chen, Y and Wang, W and Geng, HL and Yang, X and Jiang, J and Zhang, XX}, title = {Metagenomic insights into the composition and function of the gut microbiota of mice infected with Toxoplasma gondii.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1156397}, pmid = {37090719}, issn = {1664-3224}, mesh = {Animals ; Mice ; *Toxoplasma ; *Gastrointestinal Microbiome ; Persistent Infection ; Dysbiosis ; *Toxoplasmosis ; Inflammation ; }, abstract = {INTRODUCTION: Despite Toxoplasma gondii infection leading to dysbiosis and enteritis, the function of gut microbiota in toxoplasmosis has not been explored.

METHODS: Here, shotgun metagenomics was employed to characterize the composition and function of mouse microbial community during acute and chronic T. gondii infection, respectively.

RESULTS: The results revealed that the diversity of gut bacteria was decreased immediately after T. gondii infection, and was increased with the duration of infection. In addition, T. gondii infection led to gut microbiota dysbiosis both in acute and chronic infection periods. Therein, several signatures, including depression of Firmicutes to Bacteroidetes ratio and infection-enriched Proteobacteria, were observed in the chronic period, which may contribute to aggravated gut inflammation and disease severity. Functional analysis showed that a large amount of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and carbohydrate-active enzymes (CAZy) family displayed distinct variation in abundance between infected and healthy mice. The lipopolysaccharide biosynthesis related pathways were activated in the chronic infection period, which might lead to immune system imbalance and involve in intestinal inflammation. Moreover, microbial and functional spectrums were more disordered in chronic than acute infection periods, thus implying gut microbiota was more likely to participate in disease process in the chronically infected mice, even exacerbated immunologic derangement and disease progression.

DISCUSSION: Our data indicate that the gut microbiota plays a potentially important role in protecting mice from T. gondii infection, and contributes to better understand the association between gut microbiota and toxoplasmosis.}, } @article {pmid37088586, year = {2023}, author = {Takaori, A and Hashimoto, D and Ikeura, T and Ito, T and Nakamaru, K and Masuda, M and Nakayama, S and Yamaki, S and Yamamoto, T and Fujimoto, K and Matsuo, Y and Akagawa, S and Ishida, M and Yamaguchi, K and Imoto, S and Hirota, K and Uematsu, S and Satoi, S and Sekimoto, M and Naganuma, M}, title = {Impact of neoadjuvant therapy on gut microbiome in patients with resectable/borderline resectable pancreatic ductal adenocarcinoma.}, journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]}, volume = {23}, number = {4}, pages = {367-376}, doi = {10.1016/j.pan.2023.04.001}, pmid = {37088586}, issn = {1424-3911}, mesh = {Humans ; Neoadjuvant Therapy ; *Gastrointestinal Microbiome ; *Carcinoma, Pancreatic Ductal/drug therapy/surgery ; Deoxycytidine/therapeutic use ; RNA, Ribosomal, 16S ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; *Pancreatic Neoplasms/drug therapy/surgery ; Fluorouracil/therapeutic use ; Leucovorin/therapeutic use ; }, abstract = {BACKGROUND: /Objectives: Effects of chemotherapy on gut microbiota have been reported in various carcinomas. The current study aimed to evaluate the changes in the gut microbiota before and after neoadjuvant chemotherapy (NAC) in patients with resectable (R) and borderline resectable (BR) pancreatic ductal adenocarcinoma (PDAC) and understand their clinical implications.

METHODS: Twenty patients diagnosed with R/BR-PDAC were included in this study. Stool samples were collected at two points, before and after NAC, for microbiota analysis using 16S ribosomal RNA (16S rRNA) gene sequences.

RESULTS: Of the 20 patients, 18 (90%) were treated with gemcitabine plus S-1 as NAC, and the remaining patients received gemcitabine plus nab-paclitaxel and a fluorouracil, leucovorin, irinotecan, and oxaliplatin combination. No significant differences were observed in the α- and β-diversity before and after NAC. Bacterial diversity was not associated with Evans classification (histological grade of tumor destruction by NAC) or postoperative complications. The relative abundance of Actinobacteria phylum after NAC was significantly lower than that before NAC (P = 0.02). At the genus level, the relative abundance of Bifidobacterium before NAC in patients with Evans grade 2 disease was significantly higher than that in patients with Evans grade 1 disease (P = 0.03). Patients with Evans grade 2 lost significantly more Bifidobacterium than patients with Evans grade 1 (P = 0.01).

CONCLUSIONS: The diversity of gut microbiota was neither decreased by NAC for R/BR-PDAC nor associated with postoperative complications. Lower incidence of Bifidobacterium genus before NAC may be associated with a lower pathological response to NAC.}, } @article {pmid37087457, year = {2023}, author = {Gu, F and Zhu, S and Hou, J and Tang, Y and Liu, JX and Xu, Q and Sun, HZ}, title = {The hindgut microbiome contributes to host oxidative stress in postpartum dairy cows by affecting glutathione synthesis process.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {87}, pmid = {37087457}, issn = {2049-2618}, mesh = {Animals ; Cattle ; Female ; Mice ; Cysteine ; Glutamates ; *Glutamine ; Glutathione ; *Microbiota ; Oxidative Stress ; Postpartum Period ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Dairy cows are susceptible to postpartum systemic oxidative stress (OS), which leads to significant production loss and metabolic disorders. The gut microbiota has been linked to host health and stress levels. However, to what extent the gut microbiota is associated with postpartum OS remains unknown. In this study, the contribution of the fecal microbiota to postpartum systemic OS and its underlying mechanisms were investigated by integrating 16S rRNA gene sequencing, metagenomics, and metabolomics in postpartum dairy cattle and by transplanting fecal microbiota from cattle to mice.

RESULTS: A strong link was found between fecal microbial composition and postpartum OS, with an explainability of 43.1%. A total of 17 significantly differential bacterial genera and 19 species were identified between cows with high (HOS) and low OS (LOS). Among them, 9 genera and 16 species showed significant negative correlations with OS, and Marasmitruncus and Ruminococcus_sp._CAG:724 had the strongest correlations. The microbial functional analysis showed that the fecal microbial metabolism of glutamine, glutamate, glycine, and cysteine involved in glutathione synthesis was lower in HOS cows. Moreover, 58 significantly different metabolites were identified between HOS and LOS cows, and of these metabolites, 19 were produced from microbiota or cometabolism of microbiota and host. Furthermore, these microbial metabolites were enriched in the metabolism of glutamine, glutamate, glycine, and cysteine. The mice gavaged with HOS fecal microbiota had significantly higher OS and lower plasma glutathione peroxidase and glutathione content than those orally administered saline or LOS fecal microbiota.

CONCLUSIONS: Integrated results suggest that the fecal microbiota is responsible for OS and that lower glutathione production plays a causative role in HOS. These findings provide novel insights into the mechanisms of postpartum OS and potential regulatory strategies to alleviate OS in dairy cows. Video Abstract.}, } @article {pmid37087286, year = {2023}, author = {Li, X and Tan, G and Chen, P and Cai, K and Dong, W and Peng, N and Zhao, S}, title = {Uncovering acid resistance genes in lactic acid bacteria and impact of non-viable bacteria on bacterial community during Chinese strong-flavor baijiu fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {167}, number = {}, pages = {112741}, doi = {10.1016/j.foodres.2023.112741}, pmid = {37087286}, issn = {1873-7145}, mesh = {Fermentation ; *Lactobacillales/genetics ; Alcoholic Beverages/analysis ; Bacteria/genetics/metabolism ; *Microbiota/genetics ; Lactobacillus/genetics ; }, abstract = {Chinese strong-flavor baijiu (CSFB) brewing is a spontaneously solid-state fermentation process for approximately 60 days. Numerous microorganisms grow, die, and spark a series of metabolic reactions during fermentation. In this study, the microbial community and structure between total and viable bacteria in zaopei from the 5- and 20-year pits of CSFB are revealed by amplicon sequencing. Metagenome sequencing was applied to investigate acid resistance genes in Lactobacillus and predict carbohydrate active enzyme in zaopei. Besides, SourceTracker was conducted to expose bacterial sources. Results revealed that there was no significant difference in the bacterial community and structure between the total and viable bacteria; Lactobacillus was the most dominant bacterium in zaopei of two types of pits. Meanwhile, acid resistance genes argR, aspA, ilvE, gshA, DnaK, and cfa were genes that sustained Lactobacillus survival in the late stages of fermentation with high contents of acid and ethanol, and glycosyltransferases were identified as the predominated enzymes during the CSFB fermentation which catalyzed the process of lactic acid generation via Embden-Meyerhof-Parnas pathway and Hexose Monophosphate Pathway. Moreover, the environment contributed most bacteria to zaopei of the 5- and 20-year pits. These findings will provide a deeper understanding of the microbial community structure of viable and total bacteria and the reason for the dominance of Lactobacillus in the later stages of CSFB fermentation.}, } @article {pmid37086993, year = {2023}, author = {Yang, J and Yu, Q and Su, W and Wang, S and Wang, X and Han, Q and Qu, J and Li, H}, title = {Metagenomics reveals elevated temperature causes nitrogen accumulation mainly by inhibiting nitrate reduction process in polluted water.}, journal = {The Science of the total environment}, volume = {882}, number = {}, pages = {163631}, doi = {10.1016/j.scitotenv.2023.163631}, pmid = {37086993}, issn = {1879-1026}, mesh = {Animals ; *Nitrates ; Temperature ; Nitrogen/metabolism ; Metagenomics ; *Microbiota ; Water ; Glutamates ; Denitrification ; }, abstract = {Determining the response of functional genes and microbiota involved in the nitrogen (N) cycle to warming in the face of global climate change is a hotpot topic. However, whether and how elevated temperature affects the N-cycle genes in polluted water remains unclear. Based on metagenomics, we investigated the responses of the whole N-cycling genes and their microbial communities to the temperature gradients (23, 26, 29, 32, and 35 °C) using animal cadavers as an N-pollution model. We found that the abundance of gene families involved in glutamate metabolism, assimilatory nitrate reduction to nitrite (ANRN), and denitrification pathways decreased with temperature. Moreover, warming reduced the diversity of N-cycling microbial communities. Ecological network analysis indicated that elevated temperature intensified the mutual competition of N-cycle genes. The partial least squares path model (PLS-PM) showed that warming directly suppressed most N-cycle pathways, especially glutamate metabolism, denitrification, and ANRN pathways. Corpse decay also indirectly inhibited N-cycling via regulating N content and microbial communities. Our results highlight warming leads to N accumulation by inhibiting the ANRN and denitrification pathways, which may jeopardize ecological environment security. Our study is expected to provide valuable insights into the complex N-cycle process and N-pollution in warmer aquatic ecosystems.}, } @article {pmid37086309, year = {2023}, author = {Sasaki, T and Matsumoto, Y and Murakami, K and Endo, S and Toyozumi, T and Otsuka, R and Kinoshita, K and Hu, J and Iida, S and Morishita, H and Nishioka, Y and Nakano, A and Uesato, M and Matsubara, H}, title = {Gut microbiome can predict chemoradiotherapy efficacy in patients with esophageal squamous cell carcinoma.}, journal = {Esophagus : official journal of the Japan Esophageal Society}, volume = {20}, number = {4}, pages = {691-703}, pmid = {37086309}, issn = {1612-9067}, mesh = {Humans ; *Esophageal Squamous Cell Carcinoma/therapy ; *Esophageal Neoplasms/therapy/pathology ; *Carcinoma, Squamous Cell/therapy/pathology ; *Gastrointestinal Microbiome ; Chemoradiotherapy ; }, abstract = {PURPOSE: The gut microbiome plays an important role in cancer pathogenesis and therapy. Some studies have reported that specific bacteria in tumor tissues may contribute to the prognosis and treatment of esophageal squamous cell carcinoma (ESCC). However, there is limited evidence that the gut microbiome is associated with ESCC. This study assessed the utility of the gut microbiome as a predictive marker of the therapeutic effect in patients with ESCC undergoing chemo-radiotherapy (CRT).

PATIENTS AND METHODS: Fecal samples were collected from 51 patients with ESCC who had never undergone treatment between April 2021 and May 2022 in the Department of Frontier Surgery, Chiba University. The gut microbiome was analyzed using 16S metagenomics sequencing. The association between the gut microbiome composition and stage according to the TNM classification (American Joint Committee on Cancer 7.0) and CRT response according to the RECIST criteria was evaluated.

RESULTS: The relative abundance of Fusobacteriaceae was enriched in cStage III-IVb group. Among the 27 patients who received CRT, the relative abundance of Lactobacillaceae was enriched in those with a partial and complete response. Lactobacillaceae also did not correlate with any clinical data, but the high Lactobacillales group had a higher LMR (P = 0.032) and lower PLR (P = 0.045) than in the low Lactobacillales group.

CONCLUSIONS: In conclusion, we found that the relative abundance of Lactobacillaceae was enriched in patients with a partial or complete response among CRT those with ESCC, thus suggesting that the relative abundance of Lactobacillaceae can predict the effect of CRT.}, } @article {pmid37085924, year = {2023}, author = {Ho, SFS and Wheeler, NE and Millard, AD and van Schaik, W}, title = {Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {84}, pmid = {37085924}, issn = {2049-2618}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; 215154/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; BB/S017941/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Bacteriophages/genetics ; Sequence Analysis, DNA/methods ; Metagenome/genetics ; *Microbiota ; Metagenomics/methods ; }, abstract = {BACKGROUND: The prediction of bacteriophage sequences in metagenomic datasets has become a topic of considerable interest, leading to the development of many novel bioinformatic tools. A comparative analysis of ten state-of-the-art phage identification tools was performed to inform their usage in microbiome research.

METHODS: Artificial contigs generated from complete RefSeq genomes representing phages, plasmids, and chromosomes, and a previously sequenced mock community containing four phage species, were used to evaluate the precision, recall, and F1 scores of the tools. We also generated a dataset of randomly shuffled sequences to quantify false-positive calls. In addition, a set of previously simulated viromes was used to assess diversity bias in each tool's output.

RESULTS: VIBRANT and VirSorter2 achieved the highest F1 scores (0.93) in the RefSeq artificial contigs dataset, with several other tools also performing well. Kraken2 had the highest F1 score (0.86) in the mock community benchmark by a large margin (0.3 higher than DeepVirFinder in second place), mainly due to its high precision (0.96). Generally, k-mer-based tools performed better than reference similarity tools and gene-based methods. Several tools, most notably PPR-Meta, called a high number of false positives in the randomly shuffled sequences. When analysing the diversity of the genomes that each tool predicted from a virome set, most tools produced a viral genome set that had similar alpha- and beta-diversity patterns to the original population, with Seeker being a notable exception.

CONCLUSIONS: This study provides key metrics used to assess performance of phage detection tools, offers a framework for further comparison of additional viral discovery tools, and discusses optimal strategies for using these tools. We highlight that the choice of tool for identification of phages in metagenomic datasets, as well as their parameters, can bias the results and provide pointers for different use case scenarios. We have also made our benchmarking dataset available for download in order to facilitate future comparisons of phage identification tools. Video Abstract.}, } @article {pmid37085819, year = {2023}, author = {Oosterlinck, B and Ceuleers, H and Arras, W and De Man, JG and Geboes, K and De Schepper, H and Peeters, M and Lebeer, S and Skieceviciene, J and Hold, GL and Kupcinskas, J and Link, A and De Winter, BY and Smet, A}, title = {Mucin-microbiome signatures shape the tumor microenvironment in gastric cancer.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {86}, pmid = {37085819}, issn = {2049-2618}, mesh = {Humans ; *Stomach Neoplasms/genetics/metabolism/pathology ; Mucin-2/genetics ; Tumor Microenvironment ; RNA, Ribosomal, 16S/genetics ; Mucin-6/genetics ; *Adenocarcinoma ; *Microbiota ; Phenotype ; }, abstract = {BACKGROUND AND AIMS: We aimed to identify mucin-microbiome signatures shaping the tumor microenvironment in gastric adenocarcinomas and clinical outcomes.

METHODS: We performed high-throughput profiling of the mucin phenotypes present in 108 gastric adenocarcinomas and 20 functional dyspepsia cases using validated mucin-based RT-qPCRs with subsequent immunohistochemistry validation and correlated the data with clinical outcome parameters. The gastric microbiota was assessed by 16S rRNA gene sequencing, taxonomy, and community composition determined, microbial networks analyzed, and the metagenome inferred in association with mucin phenotypes and expression.

RESULTS: Gastric adenocarcinomas with an intestinal mucin environment or high-level MUC13 expression are associated with poor survival. On the contrary, gastric MUC5AC or MUC6 abundance was associated with a more favorable outcome. The oral taxa Neisseria, Prevotella, and Veillonella had centralities in tumors with intestinal and mixed phenotypes and were associated with MUC13 overexpression, highlighting their role as potential drivers in MUC13 signaling in GC. Furthermore, dense bacterial networks were observed in intestinal and mixed mucin phenotype tumors whereas the lowest community complexity was shown in null mucin phenotype tumors due to higher Helicobacter abundance resulting in a more decreased diversity. Enrichment of oral or intestinal microbes was mucin phenotype dependent. More specifically, intestinal mucin phenotype tumors favored the establishment of pro-inflammatory oral taxa forming strong co-occurrence networks.

CONCLUSIONS: Our results emphasize key roles for mucins in gastric cancer prognosis and shaping microbial networks in the tumor microenvironment. Specifically, the enriched oral taxa associated with aberrant MUC13 expression can be potential biomarkers in predicting disease outcomes. Video Abstract.}, } @article {pmid37085482, year = {2023}, author = {Li, Q and Fei, HL and Luo, ZH and Gao, SM and Wang, PD and Lan, LY and Zhao, XF and Huang, LN and Fan, PF}, title = {Gut microbiome responds compositionally and functionally to the seasonal diet variations in wild gibbons.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {21}, pmid = {37085482}, issn = {2055-5008}, mesh = {Diet ; Seasons ; China ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Longitudinal Studies ; Hylobatidae ; Animals ; *Hylobates ; }, abstract = {Wild animals may encounter multiple challenges especially food shortage and altered diet composition in their suboptimal ranges. Yet, how the gut microbiome responds to dietary changes remains poorly understood. Prior studies on wild animal microbiomes have typically leaned upon relatively coarse dietary records and individually unresolved fecal samples. Here, we conducted a longitudinal study integrating 514 time-series individually recognized fecal samples with parallel fine-grained dietary data from two Skywalker hoolock gibbon (Hoolock tianxing) groups populating high-altitude mountainous forests in western Yunnan Province, China. 16S rRNA gene amplicon sequencing showed a remarkable seasonal fluctuation in the gibbons' gut microbial community structure both across individuals and between the social groups, especially driven by the relative abundances of Lanchnospiraceae and Oscillospiraceae associated with fluctuating consumption of leaf. Metagenomic functional profiling revealed that diverse metabolisms associated with cellulose degradation and short-chain fatty acids (SCFAs) production were enriched in the high-leaf periods possibly to compensate for energy intake. Genome-resolved metagenomics further enabled the resolving metabolic capacities associated with carbohydrate breakdown among community members which exhibited a high degree of functional redundancy. Our results highlight a taxonomically and functionally sensitive gut microbiome actively responding to the seasonally shifting diet, facilitating the survival and reproduction of the endangered gibbon species in their suboptimal habitats.}, } @article {pmid37085283, year = {2023}, author = {Rofael, SAD and Brown, J and Lipman, MCI and Lowe, DM and Spratt, D and Quaderi, S and Hurst, JR and McHugh, TD}, title = {Impact of prophylactic and 'rescue pack' antibiotics on the airway microbiome in chronic lung disease.}, journal = {BMJ open respiratory research}, volume = {10}, number = {1}, pages = {}, pmid = {37085283}, issn = {2052-4439}, mesh = {Humans ; Anti-Bacterial Agents/therapeutic use ; Quality of Life ; Phylogeny ; *Pulmonary Disease, Chronic Obstructive/genetics ; *Microbiota ; }, abstract = {UNLABELLED: The management of many chronic lung diseases involves multiple antibiotic prescriptions either to treat acute exacerbations or as prophylactic therapy to reduce the frequency of exacerbations and improve patients' quality of life.

AIM: To investigate the effects of antibiotics on the homeostasis of bacterial communities in the airways, and how this may contribute to antimicrobial resistance (AMR) among respiratory pathogens and microbiota.

METHODS: Within an observational cohort study, sputum was collected from 84 patients with chronic obstructive pulmonary disease and/or bronchiectasis at stable state: 47 were receiving antibiotic prophylaxis therapy. V3-V4 16S-rRNA sequencing on Illumina MiSeq, quantitative PCR for typical respiratory pathogens, bacteriology cultures and antimicrobial susceptibility testing of sputum isolates, resistome analysis on a subset of 17 sputum samples using MinION metagenomics sequencing were performed.

FINDING: The phylogenetic α-diversity and the total bacterial density in sputum were significantly lower in patients receiving prophylactic antibiotics (p=0.014 and 0.029, respectively). Antibiotic prophylaxis was associated with significantly lower relative abundance of respiratory pathogens such as Pseudomonas aeruginosa, Moraxella catarrhalis and members of family Enterobacteriaceae in the airway microbiome, but not Haemophilus influenzae and Streptococcus pneumoniae. No major definite directional shifts in the microbiota composition were identified with prophylactic antibiotic use at the cohort level. Surveillance of AMR and resistome analysis revealed a high frequency of resistance to macrolide and tetracycline in the cohort. AMR expressed by pathogenic bacterial isolates was associated with antibiotics prescribed as 'rescue packs' for prompt initiation of self-treatment of exacerbations (Spearman's rho=0.408, p=0.02).

CONCLUSIONS: Antibiotic prophylactic therapy suppresses recognised pathogenic bacteria in the sputum of patients with chronic lung disease. The use of antibiotic rescue packs may be driving AMR in this cohort rather than prophylactic antibiotics.}, } @article {pmid37084583, year = {2023}, author = {El Samak, M and Zakeer, S and Hanora, A and Solyman, SM}, title = {Metagenomic and metatranscriptomic exploration of the Egyptian Red Sea sponge Theonella sp. associated microbial community.}, journal = {Marine genomics}, volume = {70}, number = {}, pages = {101032}, doi = {10.1016/j.margen.2023.101032}, pmid = {37084583}, issn = {1876-7478}, mesh = {Animals ; *Porifera/genetics ; *Theonella/microbiology ; Metagenomics ; Indian Ocean ; Egypt ; Phylogeny ; Bacteria/genetics ; *Microbiota ; }, abstract = {Marine sponges associated microorganisms are considered to be prolific source of bioactive natural products. Omics-based techniques such as metagenomics and metatranscriptomics have been used as effective tools to discover natural products. In this study, we used integrated metagenomic and metatranscriptomic analysis of three samples of the Egyptian Red Sea sponge Theonella sp. microbiome to obtain a complete picture of its biosynthetic activity to produce bioactive compounds. Our data revealed high biodiversity of the Egyptian sponge microbiota represented by 38 bacterial phyla with Candidate Phylum Poribacteria as the most abundant phyla with an average of 27.5% of the microbial community. The analysis also revealed high biosynthetic activity of the sponge microbiome through detecting different types of biosynthetic gene clusters (BGCs) with predicted antibacterial, cytotoxic and inhibitory bioactivity and the majority of these clusters were found to be actively transcribed. The complete BGCs of the cytotoxic theonellamide and misakinolide were detected and found to be actively transcribed. The majority of the detected BGCs were predicted to be novel as they did not show any similarity with any known cluster in the MIBiG database.}, } @article {pmid37083735, year = {2023}, author = {Roux, S and Camargo, AP and Coutinho, FH and Dabdoub, SM and Dutilh, BE and Nayfach, S and Tritt, A}, title = {iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria.}, journal = {PLoS biology}, volume = {21}, number = {4}, pages = {e3002083}, pmid = {37083735}, issn = {1545-7885}, mesh = {*Archaea/genetics ; Metagenome/genetics ; *Viruses/genetics ; Bacteria/genetics ; Metagenomics/methods ; Machine Learning ; Genome, Viral/genetics ; }, abstract = {The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied through metagenomics. While metagenomes enable high-throughput exploration of the viral sequence space, metagenome-derived sequences lack key information compared to isolated viruses, in particular host association. Different computational approaches are available to predict the host(s) of uncultivated viruses based on their genome sequences, but thus far individual approaches are limited either in precision or in recall, i.e., for a number of viruses they yield erroneous predictions or no prediction at all. Here, we describe iPHoP, a two-step framework that integrates multiple methods to reliably predict host taxonomy at the genus rank for a broad range of viruses infecting bacteria and archaea, while retaining a low false discovery rate. Based on a large dataset of metagenome-derived virus genomes from the IMG/VR database, we illustrate how iPHoP can provide extensive host prediction and guide further characterization of uncultivated viruses.}, } @article {pmid37081873, year = {2023}, author = {Chen, Y and Knight, R and Gallo, RL}, title = {Evolving approaches to profiling the microbiome in skin disease.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1151527}, pmid = {37081873}, issn = {1664-3224}, support = {R37 AI052453/AI/NIAID NIH HHS/United States ; R01 AR076082/AR/NIAMS NIH HHS/United States ; U01 AI152038/AI/NIAID NIH HHS/United States ; R01 DK128787/DK/NIDDK NIH HHS/United States ; R01 AI153185/AI/NIAID NIH HHS/United States ; P50 AR080594/AR/NIAMS NIH HHS/United States ; }, mesh = {Humans ; Dysbiosis ; RNA, Ribosomal, 16S/genetics ; Skin/microbiology ; *Microbiota/genetics ; *Psoriasis ; Bacteria/genetics ; }, abstract = {Despite its harsh and dry environment, human skin is home to diverse microbes, including bacteria, fungi, viruses, and microscopic mites. These microbes form communities that may exist at the skin surface, deeper skin layers, and within microhabitats such as the hair follicle and sweat glands, allowing complex interactions with the host immune system. Imbalances in the skin microbiome, known as dysbiosis, have been linked to various inflammatory skin disorders, including atopic dermatitis, acne, and psoriasis. The roles of abundant commensal bacteria belonging to Staphylococcus and Cutibacterium taxa and the fungi Malassezia, where particular species or strains can benefit the host or cause disease, are increasingly appreciated in skin disorders. Furthermore, recent research suggests that the interactions between microorganisms and the host's immune system on the skin can have distant and systemic effects on the body, such as on the gut and brain, known as the "skin-gut" or "skin-brain" axes. Studies on the microbiome in skin disease have typically relied on 16S rRNA gene sequencing methods, which cannot provide accurate information about species or strains of microorganisms on the skin. However, advancing technologies, including metagenomics and other functional 'omic' approaches, have great potential to provide more comprehensive and detailed information about the skin microbiome in health and disease. Additionally, inter-species and multi-kingdom interactions can cause cascading shifts towards dysbiosis and are crucial but yet-to-be-explored aspects of many skin disorders. Better understanding these complex dynamics will require meta-omic studies complemented with experiments and clinical trials to confirm function. Evolving how we profile the skin microbiome alongside technological advances is essential to exploring such relationships. This review presents the current and emerging methods and their findings for profiling skin microbes to advance our understanding of the microbiome in skin disease.}, } @article {pmid37081531, year = {2023}, author = {Zhang, D and Yu, H and Yang, Y and Liu, F and Li, M and Huang, J and Yu, Y and Wang, C and Jiang, F and He, Z and Yan, Q}, title = {Ecological interactions and the underlying mechanism of anammox and denitrification across the anammox enrichment with eutrophic lake sediments.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {82}, pmid = {37081531}, issn = {2049-2618}, mesh = {*Lakes/microbiology ; *Denitrification ; Anaerobic Ammonia Oxidation ; Oxidation-Reduction ; Bacteria/genetics/metabolism ; Bioreactors/microbiology ; }, abstract = {BACKGROUND: Increasing attention has recently been devoted to the anaerobic ammonium oxidation (anammox) in eutrophic lakes due to its potential key functions in nitrogen (N) removal for eutrophication control. However, successful enrichment of anammox bacteria from lake sediments is still challenging, partly due to the ecological interactions between anammox and denitrifying bacteria across such enrichment with lake sediments remain unclear.

RESULTS: This study thus designed to fill such knowledge gaps using bioreactors to enrich anammox bacteria with eutrophic lake sediments for more than 365 days. We continuously monitored the influent and effluent water, measured the anammox and denitrification efficiencies, quantified the anammox and denitrifying bacteria, as well as the related N cycling genes. We found that the maximum removal efficiencies of NH4[+] and NO2[-] reached up to 85.92% and 95.34%, respectively. Accordingly, the diversity of anammox and denitrifying bacteria decreased significantly across the enrichment, and the relative dominant anammox (e.g., Candidatus Jettenia) and denitrifying bacteria (e.g., Thauera, Afipia) shifted considerably. The ecological cooperation between anammox and denitrifying bacteria tended to increase the microbial community stability, indicating a potential coupling between anammox and denitrifying bacteria. Moreover, the nirS-type denitrifiers showed stronger coupling with anammox bacteria than that of nirK-type denitrifiers during the enrichment. Functional potentials as depicted by metagenome sequencing confirmed the ecological interactions between anammox and denitrification. Metagenome-assembled genomes-based ecological model indicated that the most dominant denitrifiers could provide various materials such as amino acid, cofactors, and vitamin for anammox bacteria. Cross-feeding in anammox and denitrifying bacteria highlights the importance of microbial interactions for increasing the anammox N removal in eutrophic lakes.

CONCLUSIONS: This study greatly expands our understanding of cooperation mechanisms among anammox and denitrifying bacteria during the anammox enrichment with eutrophic lake sediments, which sheds new insights into N removal for controlling lake eutrophication. Video Abstract.}, } @article {pmid37081217, year = {2023}, author = {Gao, FZ and He, LY and Chen, X and Chen, JL and Yi, X and He, LX and Huang, XY and Chen, ZY and Bai, H and Zhang, M and Liu, YS and Ying, GG}, title = {Swine farm groundwater is a hidden hotspot for antibiotic-resistant pathogenic Acinetobacter.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {34}, pmid = {37081217}, issn = {2730-6151}, abstract = {Acinetobacter is present in the livestock environment, but little is known about their antibiotic resistance and pathogenic species in the farm groundwater. Here we investigated antibiotic resistance of Acinetobacter in the swine farm groundwater (JZPG) and residential groundwater (JZG) of a swine farming village, in comparison to a nearby (3.5 km) non-farming village (WTG) using metagenomic and culture-based approaches. Results showed that the abundance of antibiotic resistome in some JZG and all JZPG (~3.4 copies/16S rRNA gene) was higher than that in WTG (~0.7 copies/16S rRNA gene), indicating the influence of farming activities on both groundwater types. Acinetobacter accounted for ~95.7% of the bacteria in JZG and JZPG, but only ~8.0% in WTG. They were potential hosts of ~95.6% of the resistome in farm affected groundwater, which includes 99 ARG subtypes against 23 antibiotic classes. These ARGs were associated with diverse intrinsic and acquired resistance mechanisms, and the predominant ARGs were tetracyclines and fluoroquinolones resistance genes. Metagenomic binning analysis elucidated that non-baumannii Acinetobacter including A. oleivorans, A. beijerinckii, A. seifertii, A. bereziniae and A. modestus might pose environmental risks because of multidrug resistance, pathogenicity and massive existence in the groundwater. Antibiotic susceptibility tests showed that the isolated strains were resistant to multiple antibiotics including sulfamethoxazole (resistance ratio: 96.2%), levofloxacin (42.5%), gatifloxacin (39.0%), ciprofloxacin (32.6%), tetracycline (32.0%), doxycycline (29.0%) and ampicillin (12.0%) as well as last-resort polymyxin B (31.7%), colistin (24.1%) and tigecycline (4.1%). The findings highlight potential prevalence of groundwater-borne antibiotic-resistant pathogenic Acinetobacter in the livestock environment.}, } @article {pmid37081021, year = {2023}, author = {Zhao, J and Yao, Y and Li, D and Zhu, W and Xiao, H and Xie, M and Xiong, Y and Wu, J and Ni, Q and Zhang, M and Xu, H}, title = {Metagenome and metabolome insights into the energy compensation and exogenous toxin degradation of gut microbiota in high-altitude rhesus macaques (Macaca mulatta).}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {20}, pmid = {37081021}, issn = {2055-5008}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Macaca mulatta/genetics/microbiology ; Metagenome ; Altitude ; Acetyl Coenzyme A/genetics ; Metabolome ; }, abstract = {There have been many reports on the genetic mechanism in rhesus macaques (RMs) for environmental adaptation to high altitudes, but the synergistic involvement of gut microbiota in this adaptation remains unclear. Here we performed fecal metagenomic and metabolomic studies on samples from high- and low-altitude populations to assess the synergistic role of gut microbiota in the adaptation of RMs to high-altitude environments. Microbiota taxonomic annotation yielded 7471 microbiota species. There were 37 bacterial species whose abundance was significantly enriched in the high-altitude populations, 16 of which were previously reported to be related to the host's dietary digestion and energy metabolism. Further functional gene enrichment found a stronger potential for gut microbiota to synthesize energy substrate acetyl-CoA using CO2 and energy substrate pyruvate using oxaloacetate, as well as a stronger potential to transform acetyl-CoA to energy substrate acetate in high-altitude populations. Interestingly, there were no apparent differences between low-altitude and high-altitude populations in terms of genes enriched in the main pathways by which the microbiota consumed the three energy substrates, and none of the three energy substrates were detected in the fecal metabolites. These results strongly suggest that gut microbiota plays an important energy compensatory role that helps RMs to adapt to high-altitude environments. Further functional enrichment after metabolite source analysis indicated the abundance of metabolites related to the degradation of exogenous toxins was also significantly higher in high-altitude populations, which suggested a contributory role of gut microbiota to the degradation of exogenous toxins in wild RMs adapted to high-altitude environments.}, } @article {pmid37080313, year = {2023}, author = {Ovis-Sánchez, JO and Perera-Pérez, VD and Buitrón, G and Quintela-Baluja, M and Graham, DW and Morales-Espinosa, R and Carrillo-Reyes, J}, title = {Exploring resistomes and microbiomes in pilot-scale microalgae-bacteria wastewater treatment systems for use in low-resource settings.}, journal = {The Science of the total environment}, volume = {882}, number = {}, pages = {163545}, doi = {10.1016/j.scitotenv.2023.163545}, pmid = {37080313}, issn = {1879-1026}, support = {MR/P028195/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; Waste Disposal, Fluid ; *Microalgae/metabolism ; Wastewater ; Bacteria/genetics ; Anti-Bacterial Agents/metabolism ; *Water Purification ; *Microbiota ; Genes, Bacterial ; }, abstract = {Antibiotic resistance genes (ARGs) released into the environment are an emerging human and environmental health concern, including ARGs spread in wastewater treatment effluents. In low-to-middle income countries (LMICs), an alternate wastewater treatment option instead of conventional systems are low-energy, high-rate algal ponds (HRAP) that use microalgae-bacteria aggregates (MABA) for waste degradation. Here we studied the robustness of ARG removal in MABA-based pilot-scale outdoor systems for 140 days of continuous operation. The HRAP system successfully removed 73 to 88 % chemical oxygen demand and up to 97.4 % ammonia, with aggregate size increasing over operating time. Fourteen ARG classes were identified in the HRAP influent, MABA, and effluent using metagenomics, with the HRAP process reducing total ARG abundances by up to 5-fold from influent to effluent. Parallel qPCR analyses showed the HRAP system significantly reduced exemplar ARGs (p < 0.05), with 1.2 to 4.9, 2.7 to 6.3, 0 to 1.5, and 1.2 to 4.8 log-removals for sul1, tetQ, blaKPC, and intl1 genes, respectively. Sequencing of influent, effluent and MABAs samples showed associated microbial communities differed significantly, with influent communities by Enterobacteriales (clinically relevant ARGs carrying bacteria), which were less evident in MABA and effluent. In this sense, such bacteria might be excluded from MABA due to their good settling properties and the presence of antimicrobial peptides. Microalgae-bacteria treatment systems steadily reduced ARGs from wastewater during operation time, using sunlight as the energetic driver, making them ideal for use in LMIC wastewater treatment applications.}, } @article {pmid37080086, year = {2023}, author = {Usié, A and Leão, C and Gaspar, D and Monteiro, H and Tábuas, L and Bettencourt, E and Caetano, P and Padre, L and Carolino, N and Ramos, AM and de Matos, C and Branco, S}, title = {A metagenomics approach to characterize the footrot microbiome in Merino sheep.}, journal = {Veterinary microbiology}, volume = {281}, number = {}, pages = {109745}, doi = {10.1016/j.vetmic.2023.109745}, pmid = {37080086}, issn = {1873-2542}, mesh = {Animals ; Sheep ; *Sheep Diseases/microbiology ; *Foot Rot/microbiology ; Fusobacterium necrophorum ; *Dichelobacter nodosus/genetics ; Bacteria/genetics ; Sheep, Domestic ; *Microbiota/genetics ; *Gram-Negative Bacterial Infections/microbiology/veterinary ; }, abstract = {In the Portuguese Alentejo region, Merino sheep breed is the most common breed, reared for the production of meat, dairy, and wool. Footrot is responsible for lameness, decreased animal welfare, and higher production losses, generating a negative economic impact. The disease is caused by Dichelobacter nodosus that interacts with the sheep foot microbiome, to date largely uncharacterized. In fact, Dichelobacter nodosus is not able to induce footrot by itself being required the presence of a second pathogen known as Fusobacterium necrophorum. To understand and characterize the footrot microbiome dynamics of different footrot lesion scores, a whole metagenome sequencing (WMGS) approach was used. Foot tissue samples were collected from 212 animals with different degrees of footrot lesion scores, ranging from 0 to 5. Distinct bacterial communities were associated with feet with different footrot scores identifying a total of 63 phyla and 504 families. As the severity of footrot infection increases the microorganisms' diversity decreases triggering a shift in the composition of the microbiome from a dominant gram-positive in mild stages to a dominant gram-negative in the severe stages. Several species previously associated with footrot and other polymicrobial diseases affecting the epidermis and provoking inflammatory responses such as Treponema spp., Staphylococcus spp., Streptococcus spp. and Campylobacter spp. were identified proliferating along with the lesions' severity. Although these bacteria are not able to initiate footrot, several evidences have been described supporting their association with the severity and incidence increase of footrot lesions caused by Dichelobacter nodosus and Fusobacterium necrophorum. Further investigation is required to establish the roles of particular taxa and identify which of them play a role in the disease process and which are opportunistic pathogens.}, } @article {pmid37078491, year = {2024}, author = {Rehman, A and Pham, V and Seifert, N and Richard, N and Sybesma, W and Steinert, RE}, title = {The Polyunsaturated Fatty Acids Eicosapentaenoic Acid and Docosahexaenoic Acid, and Vitamin K1 Modulate the Gut Microbiome: A Study Using an In Vitro Shime Model.}, journal = {Journal of dietary supplements}, volume = {21}, number = {2}, pages = {135-153}, doi = {10.1080/19390211.2023.2198007}, pmid = {37078491}, issn = {1939-022X}, mesh = {Humans ; Vitamin K 1 ; *Gastrointestinal Microbiome ; Docosahexaenoic Acids/pharmacology ; Eicosapentaenoic Acid/pharmacology ; Caco-2 Cells ; Vitamin K ; *Fatty Acids, Omega-3 ; Fatty Acids, Unsaturated ; *Microbiota ; Fatty Acids ; }, abstract = {Omega-3 polyunsaturated fatty acids (PUFAs) and vitamins exert multiple beneficial effects on host health, some of which may be mediated through the gut microbiome. We investigated the prebiotic potential of eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) and lipid-soluble phylloquinone (vitamin K1), each at 0.2x, 1x and 5x using the simulator of the human intestinal microbial ecosystem (SHIME®) to exclude in vivo systemic effects and host-microbe interactions.Microbial community composition and, diversity [shotgun metagenomic sequencing] and microbial activity [pH, gas pressure, and production of short-chain fatty acids (SCFAs)] were measured over a period of 48 h. Fermentations supernatants were used to investigate the effect on gut barrier integrity using a Caco-2/goblet cell co-culture model.We found that EPA, DHA and vitamin K1 increased alpha-diversity at 24 h when compared with control. Moreover, there was an effect on beta-diversity with changes in gut microbial composition, such as an increase in the Firmicutes/Bacteroidetes (F/B) ratio and a consistent increase in Veillonella and Dialister abundances with all treatments. DHA, EPA, and vitamin K1 also modulated metabolic activity of the gut microbiome by increasing total SCFAs which was related mainly to an increase in propionate (highest with EPA and vitamin K1 at 0.2x). Finally, we found that EPA and DHA increased gut barrier integrity with DHA at 1x and EPA at 5x (p < 0.05, respectively). In conclusion, our in vitro data further establish a role of PUFAs and vitamin K to modulate the gut microbiome with effects on the production of SCFAs and barrier integrity.}, } @article {pmid37078124, year = {2023}, author = {Vázquez, L and Cabrera-Rubio, R and Tamames, J and Mayo, B and Flórez, AB}, title = {Assessment of short-read shotgun sequencing and microbiome analysis of faecal samples to discriminate between equol producers and non-producers.}, journal = {Beneficial microbes}, volume = {14}, number = {3}, pages = {255-268}, doi = {10.3920/BM2022.0027}, pmid = {37078124}, issn = {1876-2891}, mesh = {*Equol ; Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Metagenomics/methods ; Metagenome ; Isoflavones/metabolism ; Adult ; Sequence Analysis, DNA/methods ; Phylogeny ; }, abstract = {Among the isoflavones and isoflavone-derived metabolites, equol, which in the human gut is synthesised from daidzein by minority bacterial populations, shows the strongest estrogenic and antioxidant activity. The beneficial effects on human health of isoflavone consumption might be partially or indeed totally attributable to this equol. Although some of the bacterial strains involved in its formation have been identified, the interplay between the composition and functionality of the gut microbiota and equol producer phenotype has hardly been studied. In this study, after shotgun metagenomic sequencing, different pipelines for the taxonomic and functional annotation of sequencing data were used in the search for similarities and differences in the faecal metagenome of equol-producing (n=3) and non-producing (n=2) women, with special focus on equol-producing taxa and their equol-associated genes. The taxonomic profiles of the samples differed significantly depending on the analytical method followed, although the microbial diversity detected by each tool was very similar at the phylum, genus and species levels. Equol-producing taxa were detected in both equol producers and non-producers, but no correlation between the abundance of equol-producing taxa and the equol producing/non-producing phenotype was found. Indeed, functional metagenomic analysis was unable to identify the genes involved in equol production, even in samples from equol producers. By aligning equol operons with the collected metagenomics data, a small number of reads mapping to equol-associated sequences were recognised in samples from both equol producers and equol non-producers, but only two reads mapping onto equol reductase-encoding genes in a sample from an equol producer. In conclusion, the taxonomic analysis of metagenomic data might not be suitable for detecting and quantifying equol-producing microbes in human faeces. Functional analysis of the data might provide an alternative. However, to detect the genetic makeup of the minority gut populations, more extensive sequencing than that achieved in the present study might be required.}, } @article {pmid37075861, year = {2024}, author = {He, T and Jin, M and Cui, P and Sun, X and He, X and Huang, Y and Xiao, X and Zhang, T and Zhang, X}, title = {Environmental viromes reveal the global distribution signatures of deep-sea DNA viruses.}, journal = {Journal of advanced research}, volume = {57}, number = {}, pages = {107-117}, pmid = {37075861}, issn = {2090-1224}, mesh = {Humans ; *Ecosystem ; *Virome ; DNA Viruses/genetics ; DNA, Viral/genetics ; Energy Metabolism ; }, abstract = {INTRODUCTION: Viruses are abundant and ecologically significant in marine ecosystems. However, the virome of deep-sea sediments is not extensively investigated.

OBJECTIVES: To explore the distribution pattern of deep-sea viruses on a global scale, the viromes of DNA viruses isolated from 138 sediments of 5 deep-sea ecosystems were characterized.

METHODS: The viral particles were purified from each sediment sample. Then the viral DNAs were extracted and subjected to viral metagenomic analysis.

RESULTS: Here, we constructed a global deep-sea environmental virome dataset by analyzing the viral DNA of 138 sediment samples. A total of 347,737 viral operational taxonomic units (vOTUs) were identified, of which 84.94% were hitherto unknown, indicating that deep sea was a reservoir of novel DNA viruses. Furthermore, circular viral genome analysis revealed 98,581 complete genomes. The classified vOTUs included eukaryotic (44.55%) and prokaryotic (25.75%) viruses, and were taxonomically assigned to 63 viral families. The composition and abundance of the deep-sea sediment viromes were dependent on the deep-sea ecosystem as opposed to geographical region. Further analysis revealed that the viral community differentiation in different deep-sea ecosystems was driven by the virus-mediated energy metabolism.

CONCLUSION: Our findings showed that deep-sea ecosystems are a reservoir of novel DNA viruses and the viral community is shaped by the environmental characteristics of deep-sea ecosystems, thus presenting critical information for determining the ecological significance of viruses in global deep-sea ecosystems.}, } @article {pmid37075636, year = {2023}, author = {Wang, R and An, Z and Fan, L and Zhou, Y and Su, X and Zhu, J and Zhang, Q and Chen, C and Lin, H and Sun, F}, title = {Effect of quorum quenching on biofouling control and microbial community in membrane bioreactors by Brucella sp. ZJ1.}, journal = {Journal of environmental management}, volume = {339}, number = {}, pages = {117961}, doi = {10.1016/j.jenvman.2023.117961}, pmid = {37075636}, issn = {1095-8630}, mesh = {Quorum Sensing ; *Biofouling/prevention & control ; Extracellular Polymeric Substance Matrix ; *Brucella ; Bioreactors/microbiology ; *Microbiota ; Membranes, Artificial ; }, abstract = {Quorum quenching (QQ) has been demonstrated to be a novel technique for controlling biofouling in membrane bioreactors (MBRs), as it can significantly inhibit biofilm formation by disrupting quorum sensing (QS). The exploration of new QQ bacterial strains and the evaluation of their performance in mitigating membrane fouling in MBR systems is significant. In this study, an efficient QQ strain, Brucella sp. ZJ1 was encapsulated in alginate beads and evaluated for its ability to mitigate biofouling. The findings revealed that MBR with QQ beads extended the operation time by 2-3 times without affecting pollutant degradation. QQ beads maintained approximately 50% QQ activity after more than 50 days operation, indicating a long-lasting and endurable QQ effect. The QQ effect reduced extracellular polymeric substance (EPS) production especially in terms of polysaccharide and protein by more than 40%. QQ beads in the MBR also reduced the cake resistance and the irreversible resistance of membrane biofouling. Metagenomic sequencing suggests that QQ beads suppressed the QS effect and increased the abundance of QQ enzyme genes, ultimately inducing efficient membrane biofouling control.}, } @article {pmid37074327, year = {2023}, author = {Elnaggar, JH and Lammons, JW and Taylor, CM and Toh, E and Ardizzone, CM and Dong, A and Aaron, KJ and Luo, M and Tamhane, A and Lefkowitz, EJ and Quayle, AJ and Nelson, DE and Muzny, CA}, title = {Characterization of Vaginal Microbial Community Dynamics in the Pathogenesis of Incident Bacterial Vaginosis, a Pilot Study.}, journal = {Sexually transmitted diseases}, volume = {50}, number = {8}, pages = {523-530}, pmid = {37074327}, issn = {1537-4521}, support = {UL1 TR003096/TR/NCATS NIH HHS/United States ; K23 AI106957/AI/NIAID NIH HHS/United States ; R01 AI118860/AI/NIAID NIH HHS/United States ; R01 AI146065/AI/NIAID NIH HHS/United States ; P20 GM103424/GM/NIGMS NIH HHS/United States ; }, mesh = {Female ; Humans ; *Vaginosis, Bacterial/diagnosis ; Pilot Projects ; Vagina/microbiology ; Gardnerella vaginalis/genetics ; *Microbiota ; Bacteria/genetics ; Lactobacillus/genetics ; }, abstract = {BACKGROUND: Despite more than 60 years of research, the etiology of bacterial vaginosis (BV) remains controversial. In this pilot study, we used shotgun metagenomic sequencing to characterize vaginal microbial community changes before the development of incident BV (iBV).

METHODS: A cohort of African American women with a baseline healthy vaginal microbiome (no Amsel criteria, Nugent score 0-3 with no Gardnerella vaginalis morphotypes) were followed for 90 days with daily self-collected vaginal specimens for iBV (≥2 consecutive days of a Nugent score of 7-10). Shotgun metagenomic sequencing was performed on select vaginal specimens from 4 women, every other day for 12 days before iBV diagnosis. Sequencing data were analyzed through Kraken2 and bioBakery 3 workflows, and specimens were classified into community state types. Quantitative polymerase chain reaction was performed to compare the correlation of read counts with bacterial abundance.

RESULTS: Common BV-associated bacteria such as G. vaginalis , Prevotella bivia , and Fannyhessea vaginae were increasingly identified in the participants before iBV. Linear modeling indicated significant increases in G. vaginalis and F . vaginae relative abundance before iBV, whereas the relative abundance of Lactobacillus species declined over time. The Lactobacillus species decline correlated with the presence of Lactobacillus phages. We observed enrichment in bacterial adhesion factor genes on days before iBV. There were also significant correlations between bacterial read counts and abundances measured by quantitative polymerase chain reaction.

CONCLUSIONS: This pilot study characterizes vaginal community dynamics before iBV and identifies key bacterial taxa and mechanisms potentially involved in the pathogenesis of iBV.}, } @article {pmid37072468, year = {2023}, author = {Khachatryan, L and Xiang, Y and Ivanov, A and Glaab, E and Graham, G and Granata, I and Giordano, M and Maddalena, L and Piccirillo, M and Manipur, I and Baruzzo, G and Cappellato, M and Avot, B and Stan, A and Battey, J and Lo Sasso, G and Boue, S and Ivanov, NV and Peitsch, MC and Hoeng, J and Falquet, L and Di Camillo, B and Guarracino, MR and Ulyantsev, V and Sierro, N and Poussin, C}, title = {Results and lessons learned from the sbv IMPROVER metagenomics diagnostics for inflammatory bowel disease challenge.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {6303}, pmid = {37072468}, issn = {2045-2322}, mesh = {Humans ; *Inflammatory Bowel Diseases/diagnosis/genetics ; *Colitis, Ulcerative/diagnosis ; *Crohn Disease/diagnosis/genetics ; Metagenomics ; *Gastrointestinal Microbiome/genetics ; }, abstract = {A growing body of evidence links gut microbiota changes with inflammatory bowel disease (IBD), raising the potential benefit of exploiting metagenomics data for non-invasive IBD diagnostics. The sbv IMPROVER metagenomics diagnosis for inflammatory bowel disease challenge investigated computational metagenomics methods for discriminating IBD and nonIBD subjects. Participants in this challenge were given independent training and test metagenomics data from IBD and nonIBD subjects, which could be wither either raw read data (sub-challenge 1, SC1) or processed Taxonomy- and Function-based profiles (sub-challenge 2, SC2). A total of 81 anonymized submissions were received between September 2019 and March 2020. Most participants' predictions performed better than random predictions in classifying IBD versus nonIBD, Ulcerative Colitis (UC) versus nonIBD, and Crohn's Disease (CD) versus nonIBD. However, discrimination between UC and CD remains challenging, with the classification quality similar to the set of random predictions. We analyzed the class prediction accuracy, the metagenomics features by the teams, and computational methods used. These results will be openly shared with the scientific community to help advance IBD research and illustrate the application of a range of computational methodologies for effective metagenomic classification.}, } @article {pmid37071008, year = {2023}, author = {Vassallo, A and Modi, A and Quagliariello, A and Bacci, G and Faddetta, T and Gallo, M and Provenzano, A and La Barbera, A and Lombardo, G and Maggini, V and Firenzuoli, F and Zaccaroni, M and Gallo, G and Caramelli, D and Aleo Nero, C and Baldi, F and Fani, R and Palumbo Piccionello, A and Pucciarelli, S and Puglia, AM and Sineo, L}, title = {Novel Sources of Biodiversity and Biomolecules from Bacteria Isolated from a High Middle Ages Soil Sample in Palermo (Sicily, Italy).}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0437422}, pmid = {37071008}, issn = {2165-0497}, mesh = {Animals ; Humans ; Sicily ; *Bacteria ; *Biodiversity ; Anti-Bacterial Agents ; Soil/chemistry ; }, abstract = {The urban plan of Palermo (Sicily, Italy) has evolved throughout Punic, Roman, Byzantine, Arab, and Norman ages until it stabilized within the borders that correspond to the current historic center. During the 2012 to 2013 excavation campaign, new remains of the Arab settlement, directly implanted above the structures of the Roman age, were found. The materials investigated in this study derived from the so-called Survey No 3, which consists of a rock cavity of subcylindrical shape covered with calcarenite blocks: it was probably used to dispose of garbage during the Arabic age and its content, derived from daily activities, included grape seeds, scales and bones of fish, small animal bones, and charcoals. Radiocarbon dating confirmed the medieval origin of this site. The composition of the bacterial community was characterized through a culture-dependent and a culture-independent approach. Culturable bacteria were isolated under aerobic and anaerobic conditions and the total bacterial community was characterized through metagenomic sequencing. Bacterial isolates were tested for the production of compounds with antibiotic activity: a Streptomyces strain, whose genome was sequenced, was of particular interest because of its inhibitory activity, which was due to the Type I polyketide aureothin. Moreover, all strains were tested for the production of secreted proteases, with those belonging to the genus Nocardioides having the most active enzymes. Finally, protocols commonly used for ancient DNA studies were applied to evaluate the antiquity of isolated bacterial strains. Altogether these results show how paleomicrobiology might represent an innovative and unexplored source of novel biodiversity and new biotechnological tools. IMPORTANCE One of the goals of paleomicrobiology is the characterization of the microbial community present in archaeological sites. These analyses can usually provide valuable information about past events, such as occurrence of human and animal infectious diseases, ancient human activities, and environmental changes. However, in this work, investigations about the composition of the bacterial community of an ancient soil sample (harvested in Palermo, Italy) were carried out aiming to screen ancient culturable strains with biotechnological potential, such as the ability to produce bioactive molecules and secreted hydrolytic enzymes. Besides showing the biotechnological relevance of paleomicrobiology, this work reports a case of germination of putatively ancient bacterial spores recovered from soil rather than extreme environments. Moreover, in the case of spore-forming species, these results raise questions about the accuracy of techniques usually applied to estimate antiquity of DNA, as they could lead to its underestimation.}, } @article {pmid37069665, year = {2023}, author = {Watson, AR and Füssel, J and Veseli, I and DeLongchamp, JZ and Silva, M and Trigodet, F and Lolans, K and Shaiber, A and Fogarty, E and Runde, JM and Quince, C and Yu, MK and Söylev, A and Morrison, HG and Lee, STM and Kao, D and Rubin, DT and Jabri, B and Louie, T and Eren, AM}, title = {Metabolic independence drives gut microbial colonization and resilience in health and disease.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {78}, pmid = {37069665}, issn = {1474-760X}, support = {P30 CA014599/CA/NCI NIH HHS/United States ; P30 DK042086/DK/NIDDK NIH HHS/United States ; RC2 DK122394/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; *Microbiota ; Metagenomics ; Amino Acids ; Feces ; }, abstract = {BACKGROUND: Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge.

RESULTS: Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients.

CONCLUSIONS: These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of "dysbiosis" that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.}, } @article {pmid37069399, year = {2023}, author = {Fan, Y and Støving, RK and Berreira Ibraim, S and Hyötyläinen, T and Thirion, F and Arora, T and Lyu, L and Stankevic, E and Hansen, TH and Déchelotte, P and Sinioja, T and Ragnarsdottir, O and Pons, N and Galleron, N and Quinquis, B and Levenez, F and Roume, H and Falony, G and Vieira-Silva, S and Raes, J and Clausen, L and Telléus, GK and Bäckhed, F and Oresic, M and Ehrlich, SD and Pedersen, O}, title = {The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice.}, journal = {Nature microbiology}, volume = {8}, number = {5}, pages = {787-802}, pmid = {37069399}, issn = {2058-5276}, mesh = {Humans ; Female ; Animals ; Mice ; Male ; *Gastrointestinal Microbiome ; *Anorexia Nervosa/microbiology ; Metabolomics ; Feces/microbiology ; Feeding Behavior ; Bacteria/genetics ; }, abstract = {Anorexia nervosa (AN) is an eating disorder with a high mortality. About 95% of cases are women and it has a population prevalence of about 1%, but evidence-based treatment is lacking. The pathogenesis of AN probably involves genetics and various environmental factors, and an altered gut microbiota has been observed in individuals with AN using amplicon sequencing and relatively small cohorts. Here we investigated whether a disrupted gut microbiota contributes to AN pathogenesis. Shotgun metagenomics and metabolomics were performed on faecal and serum samples, respectively, from a cohort of 77 females with AN and 70 healthy females. Multiple bacterial taxa (for example, Clostridium species) were altered in AN and correlated with estimates of eating behaviour and mental health. The gut virome was also altered in AN including a reduction in viral-bacterial interactions. Bacterial functional modules associated with the degradation of neurotransmitters were enriched in AN and various structural variants in bacteria were linked to metabolic features of AN. Serum metabolomics revealed an increase in metabolites associated with reduced food intake (for example, indole-3-propionic acid). Causal inference analyses implied that serum bacterial metabolites are potentially mediating the impact of an altered gut microbiota on AN behaviour. Further, we performed faecal microbiota transplantation from AN cases to germ-free mice under energy-restricted feeding to mirror AN eating behaviour. We found that the reduced weight gain and induced hypothalamic and adipose tissue gene expression were related to aberrant energy metabolism and eating behaviour. Our 'omics' and mechanistic studies imply that a disruptive gut microbiome may contribute to AN pathogenesis.}, } @article {pmid37069233, year = {2023}, author = {Xia, R and Sun, M and Balcázar, JL and Yu, P and Hu, F and Alvarez, PJJ}, title = {Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes.}, journal = {The ISME journal}, volume = {17}, number = {7}, pages = {1004-1014}, pmid = {37069233}, issn = {1751-7370}, mesh = {Animals ; Benzo(a)pyrene/toxicity ; *Oligochaeta ; Virome ; *Bacteriophages/genetics ; Prophages/genetics ; }, abstract = {The earthworm gut virome influences the structure and function of the gut microbiome, which in turn influences worm health and ecological functions. However, despite its ecological and soil quality implications, it remains elusive how earthworm intestinal phages respond to different environmental stress, such as soil pollution. Here we used metagenomics and metatranscriptomics to investigate interactions between the worm intestinal phages and their bacteria under different benzo[a]pyrene (BaP) concentrations. Low-level BaP (0.1 mg kg[-1]) stress stimulated microbial metabolism (1.74-fold to control), and enhanced the antiphage defense system (n = 75) against infection (8 phage-host pairs). Low-level BaP exposure resulted in the highest proportion of lysogenic phages (88%), and prophages expressed auxiliary metabolic genes (AMGs) associated with nutrient transformation (e.g., amino acid metabolism). In contrast, high-level BaP exposure (200 mg kg[-1]) disrupted microbial metabolism and suppressed the antiphage systems (n = 29), leading to the increase in phage-bacterium association (37 phage-host pairs) and conversion of lysogenic to lytic phages (lysogenic ratio declined to 43%). Despite fluctuating phage-bacterium interactions, phage-encoded AMGs related to microbial antioxidant and pollutant degradation were enriched, apparently to alleviate pollution stress. Overall, these findings expand our knowledge of complex phage-bacterium interactions in pollution-stressed worm guts, and deepen our understanding of the ecological and evolutionary roles of phages.}, } @article {pmid37069161, year = {2023}, author = {Wang, L and Yao, H and Morgan, DC and Lau, KS and Leung, SY and Ho, JWK and Leung, WK}, title = {Altered human gut virome in patients undergoing antibiotics therapy for Helicobacter pylori.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2196}, pmid = {37069161}, issn = {2041-1723}, mesh = {Humans ; *Helicobacter pylori/genetics ; *Helicobacter Infections/microbiology ; Virome ; Anti-Bacterial Agents/adverse effects ; Drug Therapy, Combination ; }, abstract = {Transient gut microbiota alterations have been reported after antibiotic therapy for Helicobacter pylori. However, alteration in the gut virome after H. pylori eradication remains uncertain. Here, we apply metagenomic sequencing to fecal samples of 44 H. pylori-infected patients at baseline, 6-week (N = 44), and 6-month (N = 33) after treatment. Following H. pylori eradication, we discover contraction of the gut virome diversity, separation of virome community with increased community difference, and shifting towards a higher proportion of core virus. While the gut microbiota is altered at 6-week and restored at 6-month, the virome community shows contraction till 6-month after the treatment with enhanced phage-bacteria interactions at 6-week. Multiple courses of antibiotic treatments further lead to lower virus community diversity when compared with treatment naive patients. Our results demonstrate that H. pylori eradication therapies not only result in transient alteration in gut microbiota but also significantly alter the previously less known gut virome community.}, } @article {pmid37067438, year = {2023}, author = {Pu, J and Yang, J and Lu, S and Jin, D and Luo, X and Xiong, Y and Bai, X and Zhu, W and Huang, Y and Wu, S and Niu, L and Liu, L and Xu, J}, title = {Species-Level Taxonomic Characterization of Uncultured Core Gut Microbiota of Plateau Pika.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0349522}, pmid = {37067438}, issn = {2165-0497}, mesh = {Animals ; Humans ; Ecosystem ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Lagomorpha/genetics/microbiology ; }, abstract = {Rarely has the vast diversity of bacteria on Earth been profiled, particularly on inaccessible plateaus. These uncultured microbes, which are also known as "microbial dark matter," may play crucial roles in maintaining the ecosystem and are linked to human health, regarding pathogenicity and prebioticity. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is a keystone species in the maintenance of ecological balance. We used a combination of full-length 16S rRNA amplicon sequencing, shotgun metagenomics, and metabolomics to elucidate the species-level community structure and the metabolic potential of the gut microbiota of the plateau pika. Using a full-length 16S rRNA metataxonomic approach, we clustered 618 (166 ± 35 per sample) operational phylogenetic units (OPUs) from 105 plateau pika samples and assigned them to 215 known species, 226 potentially new species, and 177 higher hierarchical taxa. Notably, 39 abundant OPUs (over 60% total relative abundance) are found in over 90% of the samples, thereby representing a "core microbiota." They are all classified as novel microbial lineages, from the class to the species level. Using metagenomic reads, we independently assembled and binned 109 high-quality, species-level genome bins (SGBs). Then, a precise taxonomic assignment was performed to clarify the phylogenetic consistency of the SGBs and the 16S rRNA amplicons. Thus, the majority of the core microbes possess their genomes. SGBs belonging to the genus Treponema, the families Muribaculaceae, Lachnospiraceae, and Oscillospiraceae, and the order Eubacteriales are abundant in the metagenomic samples. In addition, multiple CAZymes are detected in these SGBs, indicating their efficient utilization of plant biomass. As the most widely connected metabolite with the core microbiota, tryptophan may relate to host environmental adaptation. Our investigation allows for a greater comprehension of the composition and functional capacity of the gut microbiota of the plateau pika. IMPORTANCE The great majority of microbial species remain uncultured, severely limiting their taxonomic characterization and biological understanding. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is considered to be the keystone species in the maintenance of ecological stability. We comprehensively investigated the gut microbiota of the plateau pika via a multiomics endeavor. Combining full-length 16S rRNA metataxonomics, shotgun metagenomics, and metabolomics, we elucidated the species-level taxonomic assignment of the core uncultured intestinal microbiota of the plateau pika and revealed their correlation to host nutritional metabolism and adaptation. Our findings provide insights into the microbial diversity and biological significance of alpine animals.}, } @article {pmid37067419, year = {2023}, author = {Bhattacharyya, C and Barman, D and Tripathi, D and Dutta, S and Bhattacharya, C and Alam, M and Choudhury, P and Devi, U and Mahanta, J and Rasaily, R and Basu, A and Paine, SK}, title = {Influence of Maternal Breast Milk and Vaginal Microbiome on Neonatal Gut Microbiome: a Longitudinal Study during the First Year.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0496722}, pmid = {37067419}, issn = {2165-0497}, mesh = {Infant ; Infant, Newborn ; Adult ; Humans ; Pregnancy ; Female ; Cesarean Section ; *Gastrointestinal Microbiome ; Milk, Human ; Longitudinal Studies ; *Microbiota ; }, abstract = {It is believed that establishment of the gut microbiome starts very early in life and is crucial for growth, immunity, and long-term metabolic health. In this longitudinal study, we recruited 25 mothers in their third trimester, of whom 15 had vaginal delivery while 10 had an unplanned cesarean section (C-section). The mother-neonate pairs were followed for 1 year, and we generated 16S metagenomic data to study the neonatal gut microbiome along with mother's breast milk and vaginal microbiomes through 12 months after delivery, at 1, 3, 6, and 12 months. We inferred (i) mode of delivery is an important factor influencing both composition and entropy of the neonatal gut microbiome, and the genus Streptococcus plays an important role in the temporal differentiation. (ii) Microbial diversity monotonically increases with age, irrespective of the mode of delivery, and it is significantly altered once exclusive breastfeeding is stopped. (iii) We found little evidence in favor of the microflora of mother's breast milk and a vaginal swab being directly reflected in the offspring's gut microbiome; however, some distinction could be made in the gut microbiome of neonates whose mothers were classified as community state type III (CSTIII) and CSTIV, based on their vaginal microbiomes. (iv) A lot of the mature gut microbiome is possibly acquired from the environment, as the genera Prevotella and Faecalibacterium, two of the most abundant flora in the neonatal gut microbiome, are introduced after initiation of solidified food. The distinction between the gut microbiome of babies born by vaginal delivery and babies born by C-section becomes blurred after introduction of solid food, although the diversity in the gut microbiota drastically increases in both cases. IMPORTANCE Gut microbiome architecture seems to have a potential impact on host metabolism, health, and nutrition. Early life gut microbiome development is considered a crucial phenomenon for neonatal health as well as adulthood metabolic complications. In this longitudinal study, we examined the association of neonatal gut microbiome entropy and its temporal variation. The study revealed that adult-like gut microbiome architecture starts taking shape after initiation of solidified food. Further, we also observed that the difference of microbial diversity was reduced between vaginally delivered and C-section babies compared to exclusive breastfeeding tenure. We found evidence in favor of the inheritance of the microflora of mother's posterior vaginal wall to the offspring's gut microbiome.}, } @article {pmid37067276, year = {2023}, author = {Zhang, F and Blackburn, D and Hosea, CN and Assié, A and Samuel, BS}, title = {Application of Flow Vermimetry for Quantification and Analysis of the Caenorhabditis elegans Gut Microbiome.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {193}, pages = {}, doi = {10.3791/64605}, pmid = {37067276}, issn = {1940-087X}, support = {DP2 DK116645/DK/NIDDK NIH HHS/United States ; S10 OD025251/OD/NIH HHS/United States ; P40 OD010440/OD/NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Caenorhabditis elegans ; *Microbiota ; }, abstract = {The composition of the gut microbiome can have a dramatic impact on host physiology throughout the development and the life of the animal. Measuring compositional changes in the microbiome is crucial in identifying the functional relationships between these physiological changes. Caenorhabditis elegans has emerged as a powerful host system to examine the molecular drivers of host-microbiome interactions. With its transparent body plan and fluorescent-tagged natural microbes, the relative levels of microbes within the gut microbiome of an individual C. elegans animal can be easily quantified using a large particle sorter. Here we describe the procedures for the experimental setup of a microbiome, collection, and analysis of C. elegans populations in the desired life stage, operation, and maintenance of the sorter, and statistical analyses of the resulting datasets. We also discuss considerations for optimizing sorter settings based on the microbes of interest, the development of effective gating strategies for C. elegans life stages, and how to utilize sorter capabilities to enrich animal populations based on gut microbiome composition. Examples of potential applications will be presented as part of the protocol, including the potential for scalability to high-throughput applications.}, } @article {pmid37065124, year = {2023}, author = {Yavari-Bafghi, M and Rezaei Somee, M and Amoozegar, MA and Dastgheib, SMM and Shavandi, M}, title = {Genome-resolved analyses of oligotrophic groundwater microbial communities along phenol pollution in a continuous-flow biodegradation model system.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1147162}, pmid = {37065124}, issn = {1664-302X}, abstract = {Groundwater pollution is one of the major environmental concerns. The entrance of pollutants into the oligotrophic groundwater ecosystems alters native microbial community structure and metabolism. This study investigated the application of innovative Small Bioreactor Chambers and CaO2 nanoparticles for phenol removal within continuous-flow sand-packed columns for 6 months. Scanning electron microscopy and confocal laser scanning microscopy analysis were conducted to indicate the impact of attached biofilm on sand surfaces in bioremediation columns. Then, the influence of each method on the microbial biodiversity of the column's groundwater was investigated by next-generation sequencing of the 16S rRNA gene. The results indicated that the simultaneous application of biostimulation and bioaugmentation completely eliminated phenol during the first 42 days. However, 80.2% of phenol remained in the natural bioremediation column at the end of the experiment. Microbial diversity was decreased by CaO2 injection while order-level groups known for phenol degradation such as Rhodobacterales and Xanthomonadales dominated in biostimulation columns. Genome-resolved comparative analyses of oligotrophic groundwater prokaryotic communities revealed that Burkholderiales, Micrococcales, and Cytophagales were the dominant members of the pristine groundwater. Six-month exposure of groundwater to phenol shifted the microbial population towards increasing the heterotrophic members of Desulfobacterales, Pseudomonadales, and Xanthomonadales with the degradation potential of phenol and other hydrocarbons.}, } @article {pmid37063855, year = {2023}, author = {Li, C and Zhang, Y and Yan, Q and Guo, R and Chen, C and Li, S and Zhang, Y and Meng, J and Ma, J and You, W and Wu, Z and Sun, W}, title = {Alterations in the gut virome in patients with ankylosing spondylitis.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1154380}, pmid = {37063855}, issn = {1664-3224}, mesh = {Humans ; *Spondylitis, Ankylosing ; Virome ; *Gastrointestinal Microbiome ; *Viruses ; *Bacteriophages/genetics ; *Autoimmune Diseases ; }, abstract = {INTRODUCTION: Ankylosing spondylitis (AS), a chronic autoimmune disease, has been linked to the gut bacteriome.

METHODS: To investigate the characteristics of the gut virome in AS, we profiled the gut viral community of 193 AS patients and 59 healthy subjects based on a metagenome-wide analysis of fecal metagenomes from two publicly available datasets.

RESULTS: AS patients revealed a significant decrease in gut viral richness and a considerable alteration of the overall viral structure. At the family level, AS patients had an increased abundance of Gratiaviridae and Quimbyviridae and a decreased abundance of Drexlerviridae and Schitoviridae. We identified 1,004 differentially abundant viral operational taxonomic units (vOTUs) between patients and controls, including a higher proportion of AS-enriched Myoviridae viruses and control-enriched Siphoviridae viruses. Moreover, the AS-enriched vOTUs were more likely to infect bacteria such as Flavonifractor, Achromobacter, and Eggerthellaceae, whereas the control-enriched vOTUs were more likely to be Blautia, Ruminococcus, Collinsella, Prevotella, and Faecalibacterium bacteriophages. Additionally, some viral functional orthologs differed significantly in frequency between the AS-enriched and control-enriched vOTUs, suggesting the functional role of these AS-associated viruses. Moreover, we trained classification models based on gut viral signatures to discriminate AS patients from healthy controls, with an optimal area under the receiver operator characteristic curve (AUC) up to 0.936, suggesting the clinical potential of the gut virome for diagnosing AS.

DISCUSSION: This work provides novel insight into the AS gut virome, and the findings may guide future mechanistic and therapeutic studies for other autoimmune diseases.}, } @article {pmid37063829, year = {2023}, author = {Elnaggar, JH and Huynh, VO and Lin, D and Hillman, RT and Abana, CO and El Alam, MB and Tomasic, KC and Karpinets, TV and Kouzy, R and Phan, JL and Wargo, J and Holliday, EB and Das, P and Mezzari, MP and Ajami, NJ and Lynn, EJ and Minsky, BD and Morris, VK and Milbourne, A and Messick, CA and Klopp, AH and Futreal, PA and Taniguchi, CM and Schmeler, KM and Colbert, LE}, title = {HPV-related anal cancer is associated with changes in the anorectal microbiome during cancer development.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1051431}, pmid = {37063829}, issn = {1664-3224}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; T32 CA101642/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Female ; *Papillomavirus Infections ; Prospective Studies ; Cross-Sectional Studies ; *Anus Neoplasms ; *Carcinoma, Squamous Cell/complications ; *Microbiota ; Tumor Microenvironment ; }, abstract = {BACKGROUND: Squamous cell carcinoma of the anus (SCCA) is a rare gastrointestinal cancer. Factors associated with progression of HPV infection to anal dysplasia and cancer are unclear and screening guidelines and approaches for anal dysplasia are less clear than for cervical dysplasia. One potential contributing factor is the anorectal microbiome. In this study, we aimed to identify differences in anal microbiome composition in the settings of HPV infection, anal dysplasia, and anal cancer in this rare disease.

METHODS: Patients were enrolled in two prospective studies. Patients with anal dysplasia were part of a cross-sectional cohort that enrolled women with high-grade lower genital tract dysplasia. Anorectal tumor swabs were prospectively collected from patients with biopsy-confirmed locally advanced SCCA prior to receiving standard-of-care chemoradiotherapy (CRT). Patients with high-grade lower genital tract dysplasia without anal dysplasia were considered high-risk (HR Normal). 16S V4 rRNA Microbiome sequencing was performed for anal swabs. Alpha and Beta Diversity and composition were compared for HR Normal, anal dysplasia, and anal cancer.

RESULTS: 60 patients with high-grade lower genital tract dysplasia were initially enrolled. Seven patients had concurrent anal dysplasia and 44 patients were considered HR Normal. Anorectal swabs from 21 patients with localized SCCA were included, sequenced, and analyzed in the study. Analysis of weighted and unweighted UniFrac distances demonstrated significant differences in microbial community composition between anal cancer and HR normal (p=0.018). LEfSe identified that all three groups exhibited differential enrichment of specific taxa. Peptoniphilus (p=0.028), Fusobacteria (p=0.0295), Porphyromonas (p=0.034), and Prevotella (p=0.029) were enriched in anal cancer specimens when compared to HR normal.

CONCLUSION: Although alpha diversity was similar between HR Normal, dysplasia and cancer patients, composition differed significantly between the three groups. Increased anorectal Peptoniphilus, Fusobacteria, Porphyromonas, and Prevotella abundance were associated with anal cancer. These organisms have been reported in various gastrointestinal cancers with roles in facilitating the proinflammatory microenvironment and neoplasia progression. Future work should investigate a potential role of microbiome analysis in screening for anal dysplasia and investigation into potential mechanisms of how these microbial imbalances influence the immune system and anal carcinogenesis.}, } @article {pmid37060793, year = {2023}, author = {Phua, YH and Tejeda, J and Roy, MC and Husnik, F and Wakeman, KC}, title = {Bacterial communities and toxin profiles of Ostreopsis (Dinophyceae) from the Pacific island of Okinawa, Japan.}, journal = {European journal of protistology}, volume = {89}, number = {}, pages = {125976}, doi = {10.1016/j.ejop.2023.125976}, pmid = {37060793}, issn = {1618-0429}, mesh = {Japan ; Pacific Islands ; Phylogeny ; *Dinoflagellida/genetics/metabolism ; Bacteria ; }, abstract = {Variations in toxicity of the benthic dinoflagellate Ostreopsis Schmidt 1901 have been attributed to specific molecular clades, biogeography of isolated strains, and the associated bacterial community. Here, we attempted to better understand the biodiversity and the basic biology influencing toxin production of Ostreopsis. Nine clonal cultures were established from Okinawa, Japan, and identified using phylogenetic analysis of the ITS-5.8S rRNA and 28S rRNA genes. Morphological analysis suggests that the apical pore complex L/W ratio could be a feature for differentiating Ostreopsis sp. 2 from the O. ovata species complex. We analyzed the toxicity and bacterial communities using liquid chromatography-mass spectrometry, and PCR-free metagenomic sequencing. Ovatoxin was detected in three of the seven strains of O. cf. ovata extracts, highlighting intraspecies variation in toxin production. Additionally, two new potential analogs of ovatoxin-a and ostreocin-A were identified. Commonly associated bacteria clades of Ostreopsis were identified from the established cultures. While some of these bacteria groups may be common to Ostreopsis (Rhodobacterales, Flavobacteria-Sphingobacteria, and Enterobacterales), it was not clear from our analysis if any one or more of these plays a role in toxin biosynthesis. Further examination of biosynthetic pathways in metagenomic data and additional experiments isolating specific bacteria from Ostreopsis would aid these efforts.}, } @article {pmid37060094, year = {2023}, author = {Qu, A and Duan, B and Wang, Y and Cui, Z and Zhang, N and Wu, D}, title = {Children with autism show differences in the gut DNA virome compared to non-autistic children: a case control study.}, journal = {BMC pediatrics}, volume = {23}, number = {1}, pages = {174}, pmid = {37060094}, issn = {1471-2431}, mesh = {Humans ; *Autism Spectrum Disorder/genetics ; *Autistic Disorder ; Case-Control Studies ; Virome ; DNA ; }, abstract = {BACKGROUND: Several previous studies have identified a potential role that the gut microbiome can play in autism spectrum disorder (ASD) in children, but little is known about how variations in the virome may be involved in ASD. We aimed to understand the changes in the gut DNA virome of children with ASD.

METHODS: A case-control study was presented, in which 13 two-children families were observed while considering the age, mode of birth, history of antibiotic use, and vaccination history to minimize the influence of confounding factors. DNA viral metagenomic sequencing was successfully performed on stool samples from 11 children with ASD and 12 healthy non-ASD children. The basic composition and gene function of the participants' fecal DNA virome were detected and analyzed. Finally, the abundance and diversity of the DNA virome of children with ASD and their healthy siblings were compared.

RESULTS: The gut DNA virome in children aged 3-11 years was found to be dominated by the Siphoviridae family of Caudovirales. The proteins encoded by the DNA genes mainly carry out the functions of genetic information transmission and metabolism. Compared the gut DNA virome of ASD and healthy non-ASD children, their abundance of Caudovirales and Petitvirales both showed a significant negative correlation (r = -0.902, P < 0.01), there was no statistically significant difference in the relative abundance of viruses at the order and family levels, and a difference in the relative abundance at the genus level for Skunavirus (Ζ = -2.157, P = 0.031). Viral α diversity was reduced in children with ASD, but α diversity and β diversity did not differ statistically between groups.

CONCLUSIONS: This study indicates that elevated Skunavirus abundance and decreased α diversity in the gut DNA virulence group of children with ASD, but no statistically significant difference in the change in alpha and beta diversity. This provides preliminary cumulative information on virological aspects of the relationship between the microbiome and ASD, and should benefit future multi-omics and large sample studies on the gut microbes in children with ASD.}, } @article {pmid37060052, year = {2023}, author = {Liu, Y and Wang, M and Li, W and Gao, Y and Li, H and Cao, N and Hao, W and Zhao, L}, title = {Differences in gut microbiota and its metabolic function among different fasting plasma glucose groups in Mongolian population of China.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {102}, pmid = {37060052}, issn = {1471-2180}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2 ; Blood Glucose ; Diet ; Bacteria/genetics ; Fasting ; }, abstract = {BACKGROUND: Many studies reported the association between gut microbiota and type 2 diabetes mellitus (T2D), but it is still unclear which bacterial genus plays a key role and how the metabolic function of gut microbiota changes in the occurrence and development of T2D. Besides, there is a high diabetic prevalence in Mongolian population, which may be partly affected by their high calorie diet. This study identified the main bacterial genus influencing T2D in Mongolian population, and analyzed the changes of metabolic function of gut microbiome. The association between dietary factors and the relative abundance of main bacterial genus and its metabolic function was also studied.

METHODS: Dietary surveys and gut microbiota test were performed on 24 Mongolian volunteers that were divided into T2D (6 cases), PRET2D (6 cases) and Control group (12 cases) according to fasting plasma glucose (FPG) values. The relative abundance and metabolic function of gut microbiome from their fecal samples were measured by metagenomic analysis. Statistic method was used to evaluate the association between dietary factors and the relative abundance of the main bacterial genus or its metabolic function.

RESULTS: This study found that the Clostridium genus may be one of the key bacterial genera affecting the process of T2D. First, the relative abundance of Clostridium genus was significantly different among the three groups. Second, there was a higher relative abundance of metabolic enzymes of gut bacteria in PRET2D and T2D group than that in Control group. Third, a strong correlation between Clostridium genus and many metabolic enzymes was uncovered, many of which may be produced by the Clostridium. Last, carotene intake daily was negatively correlated with the Clostridium but positively correlated with tagaturonate reductase catalyzing interconversions of pentose and glucuronate.

CONCLUSIONS: The gut Clostridium genus may play an important role in the development of T2D and it could be a potential biomarker for T2D in Mongolian population. Meanwhile, the metabolic function of gut bacteria has changed during the early stage of T2D and the changes in carbohydrate, amino acid, lipid or energy metabolism of Clostridium genus may play a critical role. In addition, the carotene intake may affect reproduction and metabolic function of Clostridium genus.}, } @article {pmid37058886, year = {2023}, author = {Russo, E and Gloria, LD and Nannini, G and Meoni, G and Niccolai, E and Ringressi, MN and Baldi, S and Fani, R and Tenori, L and Taddei, A and Ramazzotti, M and Amedei, A}, title = {From adenoma to CRC stages: the oral-gut microbiome axis as a source of potential microbial and metabolic biomarkers of malignancy.}, journal = {Neoplasia (New York, N.Y.)}, volume = {40}, number = {}, pages = {100901}, pmid = {37058886}, issn = {1476-5586}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/pathology ; *Adenoma/diagnosis ; *Microbiota ; Bacteria ; *Rectal Neoplasms ; Biomarkers ; }, abstract = {BACKGROUND: Approximately 95% of Colorectal cancers (CRC) consist of adenocarcinomas originating from colonic Adenomatous polyps (AP). Increasing importance in CRC occurrence and progression has been attributed to the gut microbiota; however, a huge proportion of microorganisms inhabit the human digestive system. So, to comprehensively study the microbial spatial variations and their role in CRC progression, from AP to the different CRC phases, a holistic vision is imperative, including the simultaneous evaluation of multiple niches from the gastrointestinal system. Through an integrated approach, we identified potential microbial and metabolic biomarkers, able to discriminate human CRC from AP and/or also the different Tumor node metastasis (TNM) staging. In addition, as the microbiota contributes to the production of essential metabolic products detectable in fecal samples, we analysed and compared metabolites obtained from CRC and AP patients by using a Nuclear magnetic resonance (NMR) approach.

METHODS: In this observational study, saliva, tissue and stool samples from 61 patients, have been collected, including 46 CRC and 15 AP patients, age and sex-matched, undergoing surgery in 2018 at the Careggi University Hospital (Florence, Italy). First, the microbiota in the three-district between CRC and AP patients has been characterized, as well as in different CRC TNM stages. Subsequently, proton NMR spectroscopy has been used in combination with multivariate and univariate statistical approaches, to define the fecal metabolic profile of a restricted group of CRC and AP patients.

RESULTS: CRC patients display a different profile of tissue and fecal microbiota with respect to AP patients. Significant differences have been observed in CRC tissue microbial clades, with a rise of the Fusobacterium genus. In addition, significant taxa increase at the genus level has been observed in stool samples of CRC patients. Furthermore, Fusobacterium found in intestinal tissue has been positively correlated with fecal Parvimonas, for the first time. Moreover, as predicted by metagenomics pathway analysis, a significant increase of lactate (p=0.037) has been observed in the CRC fecal metabolic profiles, and positively correlated with Bifidobacterium (p=0.036). Finally, minor bacterial differences in CRC patients at stage T2 (TNM classification) have been detected, with a raise of the Spirochaetota phylum in CRC samples, with a slight increase of the Alphaproteobacteria class in fecal samples.

CONCLUSION: Our results suggest the importance of microbiota communities and oncometabolites in CRC development. Further studies on CRC/AP management with a focus on CRC assessment are needed to investigate novel microbial-related diagnostic tools aimed to improve therapeutic interventions.}, } @article {pmid37057308, year = {2023}, author = {Ķimsis, J and Pokšāne, A and Kazarina, A and Vilcāne, A and Petersone-Gordina, E and Zayakin, P and Gerhards, G and Ranka, R}, title = {Tracing microbial communities associated with archaeological human samples in Latvia, 7-11th centuries AD.}, journal = {Environmental microbiology reports}, volume = {15}, number = {5}, pages = {383-391}, pmid = {37057308}, issn = {1758-2229}, mesh = {Animals ; Humans ; Latvia ; *Microbiota/genetics ; DNA ; Burial ; }, abstract = {In the grave environment, microorganisms are major ecological participants in the successional decomposition of vertebrates and could infiltrate the skeleton/skeletal material during taphonomic processes. The diversity of archaeological skeleton-associated microbial assemblages and the impact of various factors are poorly understood. This study aimed to evaluate the taxonomic microbial composition of archaeological human bone and teeth samples from the 7th to 11th centuries AD from two burial sites in Latvia. Samples were analysed by a shotgun metagenomics-based approach. The results showed a strong presence of the environmental DNA in the samples, and variability in microbial community structure between individual samples. Differences in microbial composition were observed between bone and tooth samples, as well as between different burial sites. Furthermore, the presence of endogenous ancient DNA (aDNA) in tooth samples was detected. Overall, compositions of microbial communities associated with archaeological human remains in Latvia dated 7-11th century AD were influenced by the sample type and burial location. These findings indicate that, while the content of historical DNA in archaeological samples is low, the comparison of archaeological skeleton-associated microbial assemblages across time and space, along with aDNA damage profile analysis, is important and could help to reveal putative ancient microorganisms.}, } @article {pmid37055869, year = {2023}, author = {Wu, X and Almatari, AL and Cyr, WA and Williams, DE and Pfiffner, SM and Rivkina, EM and Lloyd, KG and Vishnivetskaya, TA}, title = {Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {33}, pmid = {37055869}, issn = {2524-6372}, abstract = {This study describes the composition and potential metabolic adaptation of microbial communities in northeastern Siberia, a repository of the oldest permafrost in the Northern Hemisphere. Samples of contrasting depth (1.75 to 25.1 m below surface), age (from ~ 10 kyr to 1.1 Myr) and salinity (from low 0.1-0.2 ppt and brackish 0.3-1.3 ppt to saline 6.1 ppt) were collected from freshwater permafrost (FP) of borehole AL1_15 on the Alazeya River, and coastal brackish permafrost (BP) overlying marine permafrost (MP) of borehole CH1_17 on the East Siberian Sea coast. To avoid the limited view provided with culturing work, we used 16S rRNA gene sequencing to show that the biodiversity decreased dramatically with permafrost age. Nonmetric multidimensional scaling (NMDS) analysis placed the samples into three groups: FP and BP together (10-100 kyr old), MP (105-120 kyr old), and FP (> 900 kyr old). Younger FP/BP deposits were distinguished by the presence of Acidobacteriota, Bacteroidota, Chloroflexota_A, and Gemmatimonadota, older FP deposits had a higher proportion of Gammaproteobacteria, and older MP deposits had much more uncultured groups within Asgardarchaeota, Crenarchaeota, Chloroflexota, Patescibacteria, and unassigned archaea. The 60 recovered metagenome-assembled genomes and un-binned metagenomic assemblies suggested that despite the large taxonomic differences between samples, they all had a wide range of taxa capable of fermentation coupled to nitrate utilization, with the exception of sulfur reduction present only in old MP deposits.}, } @article {pmid37054879, year = {2024}, author = {Zhang, X and Wan, H and Jin, M and Huang, L and Zhang, X}, title = {Environmental viromes reveal global virosphere of deep-sea sediment RNA viruses.}, journal = {Journal of advanced research}, volume = {56}, number = {}, pages = {87-102}, pmid = {37054879}, issn = {2090-1224}, mesh = {Humans ; *Ecosystem ; Virome ; Oceans and Seas ; *RNA Viruses/genetics ; RNA ; }, abstract = {INTRODUCTION: Viruses are the most abundant and diverse life forms on the earth. Both DNA viruses and RNA viruses play important roles in marine ecosystems via regulating biogeochemical cycles.

OBJECTIVES: However, the virome of marine RNA viruses has been rarely explored so far. In this study, therefore, the environmental viromes of deep-sea sediment RNA viruses were characterized on a global scale to reveal the global virosphere of deep-sea RNA viruses.

METHODS: The viral particles were purified from each of 133 deep-sea sediment samples and then characterized based on metagenomes of RNA viruses.

RESULTS: In this study, we established the global virome dataset of deep-sea RNA viruses purified from 133 sediment samples that were collected from typical deep-sea ecosystems of three oceans. A total of 85,059 viral operational taxonomic units (vOTUs) were identified, of which only 1.72% were hitherto known, indicating that the deep-sea sediment is a repository of novel RNA viruses. These vOTUs were classified into 20 viral families, including prokaryotic (7.09%) and eukaryotic (65.81%) RNA viruses. Furthermore, 1,463 deep-sea RNA viruses with complete genomes were obtained. The differentiation of RNA viral communities was driven by the deep-sea ecosystems as opposed to geographical region. Specifically, the virus-encoded metabolic genes took great effects on the differentiation of RNA viral communities by mediating the energy metabolism in the deep-sea ecosystems.

CONCLUSIONS: Therefore, our findings indicate that the deep sea is a vast reservoir of novel RNA viruses for the first time, and the differentiation of RNA viral communities is driven by the deep-sea ecosystems through energy metabolism.}, } @article {pmid37054839, year = {2023}, author = {Chunxiao, D and Ma, F and Wu, W and Li, S and Yang, J and Chen, Z and Lian, S and Qu, Y}, title = {Metagenomic analysis reveals indole signaling effect on microbial community in sequencing batch reactors: Quorum sensing inhibition and antibiotic resistance enrichment.}, journal = {Environmental research}, volume = {229}, number = {}, pages = {115897}, doi = {10.1016/j.envres.2023.115897}, pmid = {37054839}, issn = {1096-0953}, mesh = {*Quorum Sensing/physiology ; Drug Resistance, Microbial ; Lactones/pharmacology ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; Indoles/pharmacology ; }, abstract = {Indole is an essential signal molecule in microbial studies. However, its ecological role in biological wastewater treatments remains enigmatic. This study explores the links between indole and complex microbial communities using sequencing batch reactors exposed to 0, 15, and 150 mg/L indole concentrations. A concentration of 150 mg/L indole enriched indole degrader Burkholderiales, while pathogens, such as Giardia, Plasmodium, and Besnoitia were inhibited at 15 mg/L indole concentration. At the same time, indole reduced the abundance of predicted genes in the "signaling transduction mechanisms" pathway via the Non-supervised Orthologous Groups distributions analysis. Indole significantly decreased the concentration of homoserine lactones, especially C14-HSL. Furthermore, the quorum-sensing signaling acceptors containing LuxR, the dCACHE domain, and RpfC showed negative distributions with indole and indole oxygenase genes. Signaling acceptors' potential origins were mainly Burkholderiales, Actinobacteria, and Xanthomonadales. Meanwhile, concentrated indole (150 mg/L) increased the total abundance of antibiotic resistance genes by 3.52 folds, especially on aminoglycoside, multidrug, tetracycline, and sulfonamide. Based on Spearman's correlation analysis, the homoserine lactone degradation genes which were significantly impacted by indole negatively correlated with the antibiotic resistance gene abundance. This study brings new insights into the effect of indole signaling on in biological wastewater treatment plants.}, } @article {pmid37052633, year = {2023}, author = {Nagar, S and Bharti, M and Negi, RK}, title = {Genome-resolved metagenomics revealed metal-resistance, geochemical cycles in a Himalayan hot spring.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {10}, pages = {3273-3289}, pmid = {37052633}, issn = {1432-0614}, mesh = {*Hot Springs/microbiology ; Metagenomics ; Bacteria/genetics/metabolism ; Archaea/genetics/metabolism ; Metagenome ; *Microbiota ; Metals/metabolism ; Sulfur/metabolism ; Nitrogen/metabolism ; Phylogeny ; }, abstract = {The hot spring microbiome is a complex assemblage of micro- and macro-organisms; however, the understanding and projection of enzymatic repertoire that access earth's integral ecosystem processes remains ambivalent. Here, the Khirganga hot spring characterized with white microbial mat and ions rich in sulfate, chlorine, sodium, and magnesium ions is investigated and displayed the examination of 41 high and medium qualified metagenome-assembled genomes (MAGs) belonged to at least 12 bacterial and 2 archaeal phyla which aids to drive sulfur, oxygen, iron, and nitrogen cycles with metabolic mechanisms involved in heavy metal tolerance. These MAGs possess over 1749 genes putatively involved in crucial metabolism of elements viz. nitrogen, phosphorus, and sulfur and 598 genes encoding enzymes for czc efflux system, chromium, arsenic, and copper heavy metals resistance. The MAGs also constitute 229 biosynthetic gene clusters classified abundantly as bacteriocins and terpenes. The metabolic roles possibly involved in altering linkages in nitrogen biogeochemical cycles and explored a discerned rate of carbon fixation exclusively in archaeal member Methanospirillum hungatei inhabited in microbial mat. Higher Pfam entropy scores of biogeochemical cycling in Proteobacteria members assuring their major contribution in assimilation of ammonia and sequestration of nitrate and sulfate components as electron acceptors. This study will readily improve the understanding of the composite relationship between bacterial species owning metal resistance genes (MRGs) and underline the exploration of adaptive mechanism of these MAGs in multi-metal contaminated environment. KEY POINTS: • Identification of 41 novel bacterial and archaeal species in habitats of hot spring • Genome-resolved metagenomics revealed MRGs (n = 598) against Cr, Co, Zn, Cd, As, and Cu • Highest entropies of N (0.48) and Fe (0.44) cycles were detected within the MAGs.}, } @article {pmid37052495, year = {2023}, author = {Morgan, SJ and Chaston, JM}, title = {Flagellar Genes Are Associated with the Colonization Persistence Phenotype of the Drosophila melanogaster Microbiota.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0458522}, pmid = {37052495}, issn = {2165-0497}, support = {R15 GM140388/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Drosophila melanogaster/genetics/microbiology ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Bacteria/genetics ; Phenotype ; }, abstract = {In this work, we use Drosophila melanogaster as a model to identify bacterial genes necessary for bacteria to colonize their hosts independent of the bulk flow of diet. Early work on this model system established that dietary replenishment drives the composition of the D. melanogaster gut microbiota, and subsequent research has shown that some bacterial strains can stably colonize, or persist within, the fly independent of dietary replenishment. Here, we reveal transposon insertions in specific bacterial genes that influence the bacterial colonization persistence phenotype by using a gene association approach. We initially established that different bacterial strains persist at various levels, independent of dietary replenishment. We then repeated the analysis with an expanded panel of bacterial strains and performed a metagenome-wide association (MGWA) study to identify distinct bacterial genes that are significantly correlated with the level of colonization by persistent bacterial strains. Based on the MGWA study, we tested if 44 bacterial transposon insertion mutants from 6 gene categories affect bacterial persistence within the flies. We identified that transposon insertions in four flagellar genes, one urea carboxylase gene, one phosphatidylinositol gene, one bacterial secretion gene, and one antimicrobial peptide (AMP) resistance gene each significantly influenced the colonization of D. melanogaster by an Acetobacter fabarum strain. Follow-up experiments revealed that each flagellar mutant was nonmotile, even though the wild-type strain was motile. Taken together, these results reveal that transposon insertions in specific bacterial genes, including motility genes, are necessary for at least one member of the fly microbiota to persistently colonize the fly. IMPORTANCE Despite the growing body of research on the microbiota, the mechanisms by which the microbiota colonizes a host can still be further elucidated. This study identifies bacterial genes that are associated with the colonization persistence phenotype of the microbiota in Drosophila melanogaster, which reveals specific bacterial factors that influence the establishment of the microbiota within its host. The identification of specific genes that affect persistence can help inform how the microbiota colonizes a host. Furthermore, a deeper understanding of the genetic mechanisms of the establishment of the microbiota could aid in the further development of the Drosophila microbiota as a model for microbiome research.}, } @article {pmid37052201, year = {2023}, author = {Jansen, D and Falony, G and Vieira-Silva, S and Simsek, C and Marcelis, T and Caenepeel, C and Machiels, K and Raes, J and Vermeire, S and Matthijnssens, J}, title = {Community Types of the Human Gut Virome are Associated with Endoscopic Outcome in Ulcerative Colitis.}, journal = {Journal of Crohn's & colitis}, volume = {17}, number = {9}, pages = {1504-1513}, pmid = {37052201}, issn = {1876-4479}, support = {1S78021N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {Humans ; *Virome ; *Gastrointestinal Microbiome ; *Colitis, Ulcerative/virology/therapy ; Male ; Female ; *Feces/virology/microbiology ; Adult ; Middle Aged ; Bacteriophages/isolation & purification ; Dysbiosis/virology ; Treatment Outcome ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Inflammatory bowel disease [IBD] is a major debilitating disease. Recently, the gut microbiota has gained attention as an important factor involved in the pathophysiology of IBD. As a complement to the established bacterial 'enterotypes' associated with IBD, we focused here on viruses. We investigated the intestinal virome of IBD patients undergoing biological therapy for the presence of virome configurations associated with IBD, and to uncover how those configurations are associated with therapeutic success.

METHODS: Viral-like particle enrichment followed by deep sequencing was performed on 432 faecal samples from 181 IBD patients starting biological therapy. Redundancy analysis and Dirichlet Multinomial Mixtures were applied to determine covariates of the virome composition and to condense the gut virota into 'viral community types', respectively.

RESULTS: Patients were stratified based on unsupervised clustering into two viral community types. Community type CA showed a low α-diversity and a high relative abundance of Caudoviricetes [non-CrAss] phages and was associated with the dysbiotic Bact2-enterotype. Community type CrM showed a high α-diversity and a high relative abundance of Crassvirales and Malgrandaviricetes phages. During post-interventional analysis, endoscopic outcome was associated with gut virome composition. Remitting UC patients had a high percentage of community type CrM, a high Shannon diversity and a low lysogenic potential. Pre-interventional analyses also identified five novel phages associated with treatment success.

CONCLUSIONS: This study proposed two gut virome configurations that may be involved in the pathophysiology of IBD. Interestingly, those viral configurations are further associated with therapeutic success, suggesting a potential clinical relevance.}, } @article {pmid37051296, year = {2023}, author = {Zhang, Y and Cheng, S and Zou, H and Han, Z and Xie, T and Zhang, B and Dai, D and Yin, X and Liang, Y and Kou, Y and Tan, Y and Shen, L and Peng, Z}, title = {Correlation of the gut microbiome and immune-related adverse events in gastrointestinal cancer patients treated with immune checkpoint inhibitors.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1099063}, pmid = {37051296}, issn = {2235-2988}, mesh = {Humans ; Immune Checkpoint Inhibitors/adverse effects ; *Gastrointestinal Microbiome ; Prospective Studies ; *Neoplasms/drug therapy ; *Gastrointestinal Neoplasms/drug therapy/etiology ; *Colonic Neoplasms ; Immunotherapy/adverse effects/methods ; }, abstract = {INTRODUCTION: The wide application of immune checkpoint inhibitors has significantly improved the survival expectation of cancer patients. While immunotherapy brings benefits to patients, it also results in a series of immune-related adverse events (irAEs). Increasing evidence suggests that the gut microbiome is critical for immunotherapy response and the development of irAEs.

METHODS: In this prospective study, we recruited 95 patients with advanced/unresectable gastrointestinal cancers treated with immunotherapy and report a comprehensive analysis of the association of the gut microbiome with irAEs. Metagenome sequencing was used to analyze the differences in bacterial composition and metabolic pathways of baseline fecal samples.

RESULTS: In summary, we identified bacterial species and metabolic pathways that might be associated with the occurrence of irAEs in gastric, esophageal, and colon cancers. Ruminococcus callidus and Bacteroides xylanisolvens were enriched in patients without severe irAEs. Several microbial metabolic pathways involved in the urea cycle, including citrulline and arginine biosynthesis, were associated with irAEs. We also found that irAEs in different cancer types and toxicity in specific organs and the endocrine system were associated with different gut microbiota profiles. These findings provide the basis for future mechanistic exploration.}, } @article {pmid37049841, year = {2023}, author = {Chudan, S and Ishibashi, R and Nishikawa, M and Tabuchi, Y and Nagai, Y and Ikushiro, S and Furusawa, Y}, title = {Effect of Wheat-Derived Arabinoxylan on the Gut Microbiota Composition and Colonic Regulatory T Cells.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {7}, pages = {}, pmid = {37049841}, issn = {1420-3049}, support = {20K05929//Japan Society for the Promotion of Science/ ; n/a//LOTTE Foundation/ ; n/a//Tamura Science and Technology Foundation/ ; n/a//Takeda Science Foundation/ ; n/a//Kanamori Foundation/ ; n/a//Tojuro Iijima Foundation for Food Science and Technology/ ; }, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; T-Lymphocytes, Regulatory ; Triticum ; *Colitis/chemically induced/drug therapy/metabolism ; Butyrates/pharmacology ; Mice, Inbred C57BL ; }, abstract = {The health benefits of wheat-derived arabinoxylan, a commonly consumed dietary fiber, have been studied for decades. However, its effect on the gut microenvironment and inflammatory bowel disease remains unclear. The objective of this study was to understand the effect of wheat-derived arabinoxylan on gut microbiota, colonic regulatory T cells (Tregs), and experimental colitis. In this study, healthy and chronic colitis model mice were fed chow containing cellulose or wheat-derived arabinoxylan for 2-6 weeks and subjected to subsequent analysis. A 16S-based metagenomic analysis of the fecal DNA revealed that Lachnospiraceae, comprising butyrate-producing and Treg-inducing bacteria, were overrepresented in arabinoxylan-fed mice. In line with the changes in the gut microbiota, both the fecal butyrate concentration and the colonic Treg population were elevated in the arabinoxylan-fed mice. In a T cell transfer model of chronic colitis, wheat-derived arabinoxylan ameliorated body weight loss and colonic tissue inflammation, which may, in part, be mediated by Treg induction. Moreover, wheat-derived arabinoxylan suppressed TNFα production from type 1 helper T cells in this colitis model. In conclusion, wheat-derived arabinoxylans, by altering the gut microenvironment, may be a promising prebiotic for the prevention of colitis.}, } @article {pmid37049587, year = {2023}, author = {Dai, A and Hoffman, K and Xu, AA and Gurwara, S and White, DL and Kanwal, F and Jang, A and El-Serag, HB and Petrosino, JF and Jiao, L}, title = {The Association between Caffeine Intake and the Colonic Mucosa-Associated Gut Microbiota in Humans-A Preliminary Investigation.}, journal = {Nutrients}, volume = {15}, number = {7}, pages = {}, pmid = {37049587}, issn = {2072-6643}, support = {000//Golfers against cancer organization/ ; I01 CX001430/CX/CSRD VA/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; 000//Gillson Longenbaugh Foundation/ ; CX001430/VA/VA/United States ; DK56338/NH/NIH HHS/United States ; RP#140767//Cancer Prevention and Research Institute of Texas/ ; }, mesh = {Adult ; Humans ; *Caffeine ; Coffee ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Intestinal Mucosa/microbiology ; Risk Factors ; }, abstract = {We examined the association between caffeine and coffee intake and the community composition and structure of colonic microbiota. A total of 34 polyp-free adults donated 97 colonic biopsies. Microbial DNA was sequenced for the 16S rRNA gene V4 region. The amplicon sequence variant was assigned using DADA2 and SILVA. Food consumption was ascertained using a food frequency questionnaire. We compared the relative abundance of taxonomies by low (<82.9 mg) vs. high (≥82.9 mg) caffeine intake and by never or <2 cups vs. 2 cups vs. ≥3 cups coffee intake. False discovery rate-adjusted p values (q values) <0.05 indicated statistical significance. Multivariable negative binomial regression models were used to estimate the incidence rate ratio and its 95% confidence interval of having a non-zero count of certain bacteria by intake level. Higher caffeine and coffee intake was related to higher alpha diversity (Shannon index p < 0.001), higher relative abundance of Faecalibacterium and Alistipes, and lower relative abundance of Erysipelatoclostridium (q values < 0.05). After adjustment of vitamin B2 in multivariate analysis, the significant inverse association between Erysipelatoclostridium count and caffeine intake remained statistically significant. Our preliminary study could not evaluate other prebiotics in coffee.}, } @article {pmid37047594, year = {2023}, author = {Laterza, L and Putignani, L and Settanni, CR and Petito, V and Varca, S and De Maio, F and Macari, G and Guarrasi, V and Gremese, E and Tolusso, B and Wlderk, G and Pirro, MA and Fanali, C and Scaldaferri, F and Turchini, L and Amatucci, V and Sanguinetti, M and Gasbarrini, A}, title = {Ecology and Machine Learning-Based Classification Models of Gut Microbiota and Inflammatory Markers May Evaluate the Effects of Probiotic Supplementation in Patients Recently Recovered from COVID-19.}, journal = {International journal of molecular sciences}, volume = {24}, number = {7}, pages = {}, pmid = {37047594}, issn = {1422-0067}, support = {na//Actial Farmaceutica/ ; na//Fondazione Roma/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Citrulline ; *COVID-19 ; *Probiotics/therapeutic use/pharmacology ; Cytokines ; Bifidobacterium ; Machine Learning ; }, abstract = {Gut microbiota (GM) modulation can be investigated as possible solution to enhance recovery after COVID-19. An open-label, single-center, single-arm, pilot, interventional study was performed by enrolling twenty patients recently recovered from COVID-19 to investigate the role of a mixed probiotic, containing Lactobacilli, Bifidobacteria and Streptococcus thermophilus, on gastrointestinal symptoms, local and systemic inflammation, intestinal barrier integrity and GM profile. Gastrointestinal Symptom Rating Scale, cytokines, inflammatory, gut permeability, and integrity markers were evaluated before (T0) and after 8 weeks (T1) of probiotic supplementation. GM profiling was based on 16S-rRNA targeted-metagenomics and QIIME 2.0, LEfSe and PICRUSt computational algorithms. Multiple machine learning (ML) models were trained to classify GM at T0 and T1. A statistically significant reduction of IL-6 (p < 0.001), TNF-α (p < 0.001) and IL-12RA (p < 0.02), citrulline (p value < 0.001) was reported at T1. GM global distribution and microbial biomarkers strictly reflected probiotic composition, with a general increase in Bifidobacteria at T1. Twelve unique KEGG orthologs were associated only to T0, including tetracycline resistance cassettes. ML classified the GM at T1 with 100% score at phylum level. Bifidobacteriaceae and Bifidobacterium spp. inversely correlated to reduction of citrulline and inflammatory cytokines. Probiotic supplementation during post-COVID-19 may trigger anti-inflammatory effects though Bifidobacteria and related-metabolism enhancement.}, } @article {pmid37047542, year = {2023}, author = {Choy, CT and Chan, UK and Siu, PLK and Zhou, J and Wong, CH and Lee, YW and Chan, HW and Tsui, JCC and Loo, SKF and Tsui, SKW}, title = {A Novel E3 Probiotics Formula Restored Gut Dysbiosis and Remodelled Gut Microbial Network and Microbiome Dysbiosis Index (MDI) in Southern Chinese Adult Psoriasis Patients.}, journal = {International journal of molecular sciences}, volume = {24}, number = {7}, pages = {}, pmid = {37047542}, issn = {1422-0067}, support = {Nil//Hong Kong Society of Gut Microbiome/ ; }, mesh = {Adult ; Humans ; *Dysbiosis/complications/drug therapy ; East Asian People ; *Gastrointestinal Microbiome/drug effects/physiology ; *Probiotics/pharmacology/therapeutic use ; *Psoriasis/complications/drug therapy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Psoriasis is a common chronic immune-mediated inflammatory skin disease with the association of various comorbidities. Despite the introduction of highly effective biologic therapies over the past few decades, the exact trigger for an immune reaction in psoriasis is unclear. With the majority of immune cells residing in the gut, the effect of gut microbiome dysbiosis goes beyond the gastrointestinal site and may exacerbate inflammation and regulate the immune system elsewhere, including but not limited to the skin via the gut-skin axis. In order to delineate the role of the gut microbiome in Southern Chinese psoriasis patients, we performed targeted 16S rRNA sequencing and comprehensive bioinformatic analysis to compare the gut microbiome profile of 58 psoriasis patients against 49 healthy local subjects presumably with similar lifestyles. Blautia wexlerae and Parabacteroides distasonis were found to be enriched in psoriasis patients and in some of the healthy subjects, respectively. Metabolic functional pathways were predicted to be differentially abundant, with a clear shift toward SCFA synthesis in healthy subjects. The alteration of the co-occurrence network was also evident in the psoriasis group. In addition, we also profiled the gut microbiome in 52 of the 58 recruited psoriasis patients after taking 8 weeks of an orally administrated novel E3 probiotics formula (with prebiotics, probiotics and postbiotics). The Dermatological Life Quality Index (p = 0.009) and Psoriasis Area and Severity Index (p < 0.001) were significantly improved after taking 8 weeks of probiotics with no adverse effect observed. We showed that probiotics could at least partly restore gut dysbiosis via the modulation of the gut microbiome. Here, we also report the potential application of a machine learning-derived gut dysbiosis index based on a quantitative PCR panel (AUC = 0.88) to monitor gut dysbiosis in psoriasis patients. To sum up, our study suggests the gut microbial landscape differed in psoriasis patients at the genera, species, functional and network levels. Additionally, the dysbiosis index could be a cost-effective and rapid tool to monitor probiotics use in psoriasis patients.}, } @article {pmid37047466, year = {2023}, author = {Lu, J and Shu, Y and Zhang, H and Zhang, S and Zhu, C and Ding, W and Zhang, W}, title = {The Landscape of Global Ocean Microbiome: From Bacterioplankton to Biofilms.}, journal = {International journal of molecular sciences}, volume = {24}, number = {7}, pages = {}, pmid = {37047466}, issn = {1422-0067}, mesh = {*Aquatic Organisms ; Oceans and Seas ; *Microbiota ; Plankton ; Metagenomics ; Biofilms ; }, abstract = {The development of metagenomics has opened up a new era in the study of marine microbiota, which play important roles in biogeochemical cycles. In recent years, the global ocean sampling expeditions have spurred this research field toward a deeper understanding of the microbial diversities and functions spanning various lifestyles, planktonic (free-living) or sessile (biofilm-associated). In this review, we deliver a comprehensive summary of marine microbiome datasets generated in global ocean expeditions conducted over the last 20 years, including the Sorcerer II GOS Expedition, the Tara Oceans project, the bioGEOTRACES project, the Micro B3 project, the Bio-GO-SHIP project, and the Marine Biofilms. These datasets have revealed unprecedented insights into the microscopic life in our oceans and led to the publication of world-leading research. We also note the progress of metatranscriptomics and metaproteomics, which are confined to local marine microbiota. Furthermore, approaches to transforming the global ocean microbiome datasets are highlighted, and the state-of-the-art techniques that can be combined with data analyses, which can present fresh perspectives on marine molecular ecology and microbiology, are proposed.}, } @article {pmid37047311, year = {2023}, author = {Kimeklis, AK and Gladkov, GV and Orlova, OV and Afonin, AM and Gribchenko, ES and Aksenova, TS and Kichko, AA and Pinaev, AG and Andronov, EE}, title = {The Succession of the Cellulolytic Microbial Community from the Soil during Oat Straw Decomposition.}, journal = {International journal of molecular sciences}, volume = {24}, number = {7}, pages = {}, pmid = {37047311}, issn = {1422-0067}, support = {18-16-00073//Russian Science Foundation/ ; }, mesh = {Soil/chemistry ; Avena ; *Microbiota ; Bacteria/genetics/metabolism ; *Ascomycota ; Glycoside Hydrolases/metabolism ; Soil Microbiology ; }, abstract = {The process of straw decomposition is dynamic and is accompanied by the succession of the microbial decomposing community, which is driven by poorly understood interactions between microorganisms. Soil is a complex ecological niche, and the soil microbiome can serve as a source of potentially active cellulolytic microorganisms. Here, we performed an experiment on the de novo colonization of oat straw by the soil microbial community by placing nylon bags with sterilized oat straw in the pots filled with chernozem soil and incubating them for 6 months. The aim was to investigate the changes in decomposer microbiota during this process using conventional sequencing techniques. The bacterial succession during straw decomposition occurred in three phases: the early phase (first month) was characterized by high microbial activity and low diversity, the middle phase (second to third month) was characterized by low activity and low diversity, and the late phase (fourth to sixth months) was characterized by low activity and high diversity. Analysis of amplicon sequencing data revealed three groups of co-changing phylotypes corresponding to these phases. The early active phase was abundant in the cellulolytic members from Pseudomonadota, Bacteroidota, Bacillota, and Actinobacteriota for bacteria and Ascomycota for fungi, and most of the primary phylotypes were gone by the end of the phase. The second intermediate phase was marked by the set of phylotypes from the same phyla persisting in the community. In the mature community of the late phase, apart from the core phylotypes, non-cellulolytic members from Bdellovibrionota, Myxococcota, Chloroflexota, and Thermoproteota appeared. Full metagenome sequencing of the microbial community from the end of the middle phase confirmed that major bacterial and fungal members of this consortium had genes of glycoside hydrolases (GH) connected to cellulose and chitin degradation. The real-time analysis of the selection of these genes showed that their representation varied between phases, and this occurred under the influence of the host, and not the GH family factor. Our findings demonstrate that soil microbial community may act as an efficient source of cellulolytic microorganisms and that colonization of the cellulolytic substrate occurs in several phases, each characterized by its own taxonomic and functional profile.}, } @article {pmid37044345, year = {2023}, author = {Sánchez-Reyes, A and Gaytán, I and Pulido-García, J and Burelo, M and Vargas-Suárez, M and Cruz-Gómez, MJ and Loza-Tavera, H}, title = {Genetic basis for the biodegradation of a polyether-polyurethane-acrylic copolymer by a landfill microbial community inferred by metagenomic deconvolution analysis.}, journal = {The Science of the total environment}, volume = {881}, number = {}, pages = {163367}, doi = {10.1016/j.scitotenv.2023.163367}, pmid = {37044345}, issn = {1879-1026}, mesh = {*Polyurethanes/chemistry ; Metagenome ; Plastics ; *Microbiota ; Biodegradation, Environmental ; Waste Disposal Facilities ; }, abstract = {Plastic accumulation in the world amounts to approximately 8300 million tons. Polyurethanes (PU) account for 7.7 % of total plastics production worldwide, and their diverse chemical composition makes them highly recalcitrant to biodegradation. Several works have reported polyurethane-degrading microbial communities. However, it is still necessary to learn more about the chemical, biochemical, and genetic bases linked to the polyurethanolytic phenotype and the microbial taxonomic determinants responsible for metabolizing the PU polymer and its associated chemical additives. To shed light on this problem, we applied physical, chemical, biochemical, metagenomic, and bioinformatic analyses to explore the biodegradation capability and related biochemical and genetic determinants of the BP6 microbial community that can grow in PolyLack, a commercial coating containing a polyether polyurethane acrylate (PE-PU-A) copolymer and several additives, as sole carbon source. We observed complete additives (isopropanol, N-methyl-2-pyrrolidone, 2-butoxyethanol, alkyl glycol ethers) biodegradation and the appearance of released polymer components (toluene diisocyanate (TDI) and methylene diphenyl diisocyanate (MDI) derivatives), and multiple degradation products since early cultivation times. The Hi-C metagenomic analysis identified a complex microbiome with 35 deconvolved Metagenome-Assembled Genomes (MAGs) - several new species - and biodegradation markers that suggest the coexistence of hydrolytic, oxidative, and reductive metabolic strategies for degrading the additives and the PU copolymer. This work also provides evidence of the metabolic capability the BP6 community has for biodegrading polyether polyurethane foams. Based on these analyses, we propose a novel metabolic pathway for 4,4'-methylenedianiline (MDA), an initial biodegradation intermediate of MDI-based PU, encoded in the complex BP6 community metagenome and suggest that this community is a potential biotechnological tool for PU bio-recycling.}, } @article {pmid37042774, year = {2023}, author = {Ley, Y and Cheng, XY and Ying, ZY and Zhou, NY and Xu, Y}, title = {Characterization of Two Marine Lignin-Degrading Consortia and the Potential Microbial Lignin Degradation Network in Nearshore Regions.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0442422}, pmid = {37042774}, issn = {2165-0497}, mesh = {*Lignin/metabolism ; *Microbial Consortia ; Biodegradation, Environmental ; Bacteria/metabolism ; Alkalies ; Carbon/metabolism ; }, abstract = {Terrestrial organic carbon such as lignin is an important component of the global marine carbon. However, the structural complexity and recalcitrant nature of lignin are deemed challenging for biodegradation. It has been speculated that bacteria play important roles in lignin degradation in the marine system. However, the extent of the involvement of marine microorganisms in lignin degradation and their contribution to the oceanic carbon cycle remains elusive. In this study, two bacterial consortia capable of degrading alkali lignin (a model compound of lignin), designated LIG-B and LIG-S, were enriched from the nearshore sediments of the East and South China Seas. Consortia LIG-B and LIG-S mainly comprised of the Proteobacteria phylum with Nitratireductor sp. (71.6%) and Halomonas sp. (91.6%), respectively. Lignin degradation was found more favorable in consortium LIG-B (max 57%) than in LIG-S (max 18%). Ligninolytic enzymes laccase (Lac), manganese peroxidase (MnP), and lignin peroxidase (LiP) capable of decomposing lignin into smaller fragments were all active in both consortia. The newly emerged low-molecular-weight aromatics, organic acids, and other lignin-derived compounds in biotreated alkali lignin also evidently showed the depolymerization of lignin by both consortia. The lignin degradation pathways reconstructed from consortium LIG-S were found to be more comprehensive compared to consortium LIG-B. It was further revealed that catabolic genes, involved in the degradation of lignin and its derivatives through multiple pathways via protocatechuate and catechol, are present not only in lignin-degrading consortia LIG-B and LIG-S but also in 783 publicly available metagenomic-assembled genomes from nine nearshore regions. IMPORTANCE Numerous terrigenous lignin-containing plant materials are constantly discharged from rivers and estuaries into the marine system. However, only low levels of terrigenous organic carbon, especially lignin, are detected in the global marine system due to the abundance of active heterotrophic microorganisms driving the carbon cycle. Simultaneously, the lack of knowledge on lignin biodegradation has hindered our understanding of the oceanic carbon cycle. Moreover, bacteria have been speculated to play important roles in the marine lignin biodegradation. Here, we enriched two bacterial consortia from nearshore sediments capable of utilizing alkali lignin for cell growth while degrading it into smaller molecules and reconstructed the lignin degradation network. In particular, this study highlights that marine microorganisms in nearshore regions mostly undergo similar pathways using protocatechuate and catechol as ring-cleavage substrates to drive lignin degradation as part of the oceanic carbon cycle, regardless of whether they are in sediments or water column.}, } @article {pmid37042768, year = {2023}, author = {Zhang, P and Zhang, Y and Cao, L and Li, J and Wu, C and Tian, M and Zhang, Z and Zhang, C and Zhang, W and Li, Y}, title = {A Diverse Virome Is Identified in Parasitic Flatworms of Domestic Animals in Xinjiang, China.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0070223}, pmid = {37042768}, issn = {2165-0497}, mesh = {Adult ; Animals ; Dogs ; Humans ; Animals, Domestic ; Phylogeny ; Virome ; *Viruses/genetics ; *RNA Viruses ; Metagenome ; *Platyhelminths ; }, abstract = {Parasitic flatworms infect diverse vertebrates and are major threats to animal and even human health; however, little is known about the virome of these lower life forms. Using viral metagenomic sequencing, we characterized the virome of the parasitic flatworms collected from major domestic animals, including Dicrocoelium lanceatum and Taenia hydatigena, Echinococcus granulosus sensu stricto and Echinococcus multilocularis. Seven and three different viruses were discovered from D. lanceatum and T. hydatigena, respectively, and no viral sequences were found in adult tapeworms and protoscoleces of E. granulosus sensu stricto and E. multilocularis. Two out of the five parasitic flatworm species carry viruses, showing a host specificity of these viruses. These viruses belong to the Parvoviridae, Circoviridae, unclassified circular, Rep-encoding single-stranded (CRESS) DNA virus, Rhabdoviridae, Endornaviridae, and unclassified RNA viruses. The presence of multiple highly divergent RNA viruses, especially those that cluster with viruses found in marine animals, implies a deep evolutionary history of parasite-associated viruses. In addition, we found viruses with high identity to common pathogens in dogs, including canine circovirus and canine parvovirus 2. The presence of these viruses in the parasites implies that they may infect parasitic flatworms but does not completely exclude the possibility of contamination from host intestinal contents. Furthermore, we demonstrated that certain viruses, such as CRESS DNA virus may integrate into the genome of their host. Our results expand the knowledge of viral diversity in parasites of important domestic animals, highlighting the need for further investigations of their prevalence among other parasites of key animals. IMPORTANCE Characterizing the virome of parasites is important for unveiling the viral diversity, evolution, and ecology and will help to understand the "Russian doll" pattern among viruses, parasites, and host animals. Our data indicate that diverse viruses are present in specific parasitic flatworms, including viruses that may have an ancient evolutionary history and viruses currently circulating in parasite-infected host animals. These data also raise the question of whether parasitic flatworms acquire and/or carry some viruses that may have transmission potential to animals. In addition, through the study of virus-parasite-host interactions, including the influence of viral infection on the life cycle of the parasite, as well as its fitness and pathogenicity to the host, we could find new strategies to prevent and control parasitic diseases.}, } @article {pmid37041201, year = {2023}, author = {Ding, W and Wang, S and Qin, P and Fan, S and Su, X and Cai, P and Lu, J and Cui, H and Wang, M and Shu, Y and Wang, Y and Fu, HH and Zhang, YZ and Li, YX and Zhang, W}, title = {Anaerobic thiosulfate oxidation by the Roseobacter group is prevalent in marine biofilms.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2033}, pmid = {37041201}, issn = {2041-1723}, mesh = {*Thiosulfates/metabolism ; *Roseobacter/genetics/metabolism ; Anaerobiosis ; Proteomics ; Biofilms ; }, abstract = {Thiosulfate oxidation by microbes has a major impact on global sulfur cycling. Here, we provide evidence that bacteria within various Roseobacter lineages are important for thiosulfate oxidation in marine biofilms. We isolate and sequence the genomes of 54 biofilm-associated Roseobacter strains, finding conserved sox gene clusters for thiosulfate oxidation and plasmids, pointing to a niche-specific lifestyle. Analysis of global ocean metagenomic data suggests that Roseobacter strains are abundant in biofilms and mats on various substrates, including stones, artificial surfaces, plant roots, and hydrothermal vent chimneys. Metatranscriptomic analysis indicates that the majority of active sox genes in biofilms belong to Roseobacter strains. Furthermore, we show that Roseobacter strains can grow and oxidize thiosulfate to sulfate under both aerobic and anaerobic conditions. Transcriptomic and membrane proteomic analyses of biofilms formed by a representative strain indicate that thiosulfate induces sox gene expression and alterations in cell membrane protein composition, and promotes biofilm formation and anaerobic respiration. We propose that bacteria of the Roseobacter group are major thiosulfate-oxidizers in marine biofilms, where anaerobic thiosulfate metabolism is preferred.}, } @article {pmid37041035, year = {2023}, author = {Sun, Y and Cheng, Z and Li, X and Yang, Q and Zhao, B and Wu, Z and Xia, Y}, title = {Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing.}, journal = {Genome research}, volume = {33}, number = {4}, pages = {612-621}, pmid = {37041035}, issn = {1549-5469}, mesh = {Humans ; *Nanopores ; *Microbiota/genetics ; Metagenome ; Metagenomics ; }, abstract = {Rare species are vital members of a microbial community, but retrieving their genomes is difficult because of their low abundance. The ReadUntil (RU) approach allows nanopore devices to sequence specific DNA molecules selectively in real time, which provides an opportunity for enriching rare species. Despite the robustness of enriching rare species by reducing the sequencing depth of known host sequences, such as the human genome, there is still a gap in RU-based enriching of rare species in environmental samples whose community composition is unclear, and many rare species have poor or incomplete reference genomes in public databases. Therefore, here we present metaRUpore to overcome this challenge. When we applied metaRUpore to a thermophilic anaerobic digester (TAD) community and human gut microbial community, it reduced coverage of the high-abundance populations and modestly increased (∼2×) the genome coverage of the rare taxa, facilitating successful recovery of near-finished metagenome-assembled genomes (nf-MAGs) of rare species. The simplicity and robustness of the approach make it accessible for laboratories with moderate computational resources, and hold the potential to become the standard practice in future metagenomic sequencing of complicated microbiomes.}, } @article {pmid37040073, year = {2023}, author = {Wurm, P and Stampfer, L and Greimel, T and Leitner, E and Zechner, EL and Bauchinger, S and Hauer, AC and Gorkiewicz, G and Högenauer, C and Hoffmann, KM}, title = {Gut Microbiota Dysbiosis in Suspected Food Protein Induced Proctocolitis-A Prospective Comparative Cohort Trial.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {77}, number = {1}, pages = {31-38}, doi = {10.1097/MPG.0000000000003789}, pmid = {37040073}, issn = {1536-4801}, mesh = {Humans ; Infant ; Bifidobacterium ; Dysbiosis ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Proctocolitis ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVES: In infants with suspected food protein induced proctocolitis (sFPIP) only a minority of patients are finally diagnosed with the disease following diagnostic dietary intervention (DDI). There is a need for a pathophysiological explanation for the cause of hematochezia in the majority of sFPIP infants.

METHODS: We prospectively recruited infants with sFPIP and healthy controls. Fecal samples were collected at inclusion, week 4 (end of DDI in sFPIP), and week 8. For 16S rRNA sequencing (515F/806R) we used Illumina MiSeq sequencing system. Amplicon sequence variants were generated using Qiime2 and DADA2. Qiime diversity alpha and beta group comparisons and linear discriminant analysis effect size analysis was performed. For shotgun metagenomic analysis on species level we used KneadData and MetaPhlAn2.

RESULTS: Fourteen sFPIP infants were compared to 55 healthy infants. At inclusion overall microbial composition of sFPIP infants differed significantly from controls (weighted UniFrac; Pairwise PERMANOVA, P = 0.002, pseudo- F = 5.008). On genus level healthy infant microbiota was significantly enriched with Bifidobacterium (B) compared to sFPIP patients (linear discriminant analysis [LDA] = 5.5, P < 0.001, 31.3% vs 12.1%). sFPIP stool was significantly enriched by Clostridium sensu stricto 1 over controls (LDA = 5.3, P = 0.003, 3.5% vs 18.3%). DDI caused a significant and sustained increase of Bifidobacterium (LDA = 5.4, P = 0.048, 27.9%) in sFPIP infants. Species level analysis revealed significant reduction of abundance of B longum in sFPIP patients, which after DDI was reversed by B. species other than B longum .

CONCLUSIONS: We revealed a gut microbiota dysbiosis phenomenon in sFPIP infants. DDI induces a microbiota composition comparable to that of healthy infants. In most sFPIP infants hematochezia might be triggered by a gut microbiota dysbiosis phenomenon.}, } @article {pmid37039875, year = {2023}, author = {Chen, Y and Li, X and Yu, C and Wang, E and Luo, C and Jin, Y and Zhang, L and Ma, Y and Jin, Y and Yang, L and Sun, B and Qiao, J and Zhou, X and Rasche, L and Einsele, H and Song, J and Bai, T and Hou, X}, title = {Gut microbiome alterations in patients with COVID-19-related coagulopathy.}, journal = {Annals of hematology}, volume = {102}, number = {6}, pages = {1589-1598}, pmid = {37039875}, issn = {1432-0584}, support = {XGFY2020000027//Department of Science and Technology, Hubei Provincial People's Government/ ; YFYB2020001694//Department of Science and Technology, Hubei Provincial People's Government/ ; 2020FCA014//Department of Science and Technology, Hubei Provincial People's Government/ ; 2020BHB017//Department of Science and Technology, Hubei Provincial People's Government/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; *COVID-19/complications ; *Blood Coagulation Disorders/etiology ; *Microbiota ; }, abstract = {COVID-19 is characterized by a predominantly prothrombotic state, which underlies severe disease and poor outcomes. Imbalances of the gut microbiome have been linked with abnormal hemostatic processes. Understanding the relationship between the gut microbiome and abnormal coagulation parameters in COVID-19 could provide a novel framework for the diagnosis and management of COVID-related coagulopathies (CRC). This cross-sectional study used shotgun metagenomic sequencing to examine the gut microbiota of patients with CRC (n = 66) and compared it to COVID control (CCs) (n = 27) and non-COVID control (NCs) (n = 22) groups. Three, 1, and 3 taxa were found enriched in CRCs, CCs, and NCs. Next, random forest models using 7 microbial biomarkers and differential clinical characteristics were constructed and achieved strong diagnostic potential in distinguishing CRC. Specifically, the most promising biomarker species for CRC were Streptococcus thermophilus, Enterococcus faecium, and Citrobacter portucalensis. Conversely, Enterobacteriaceae family and Fusicatenibacter genus are potentially protective against CRC in COVID patients. We further identified 4 species contributing to 20 MetaCyc pathways that were differentially abundant among groups, with S. thermophilus as the main coding species in CRCs. Our findings suggest that the alterations of gut microbiota compositional and functional profiles may influence the pathogenesis of CRC and that microbiota-based diagnosis and treatment could potentially benefit COVID patients in preventing and alleviating thrombosis-related clinical outcomes.}, } @article {pmid37039637, year = {2023}, author = {Gemler, BT and Mukherjee, C and Howland, C and Fullerton, PA and Spurbeck, RR and Catlin, LA and Smith, A and Minard-Smith, AT and Bartling, C}, title = {UltraSEQ, a Universal Bioinformatic Platform for Information-Based Clinical Metagenomics and Beyond.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0416022}, pmid = {37039637}, issn = {2165-0497}, support = {75D30121C11398//HHS | Centers for Disease Control and Prevention (CDC)/ ; }, mesh = {Humans ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; Metagenome ; Computational Biology/methods ; }, abstract = {Applied metagenomics is a powerful emerging capability enabling the untargeted detection of pathogens, and its application in clinical diagnostics promises to alleviate the limitations of current targeted assays. While metagenomics offers a hypothesis-free approach to identify any pathogen, including unculturable and potentially novel pathogens, its application in clinical diagnostics has so far been limited by workflow-specific requirements, computational constraints, and lengthy expert review requirements. To address these challenges, we developed UltraSEQ, a first-of-its-kind accurate and scalable metagenomic bioinformatic tool for potential clinical diagnostics and biosurveillance utility. Here, we present the results of the evaluation of our novel UltraSEQ pipeline using an in silico-synthesized metagenome, mock microbial community data sets, and publicly available clinical data sets from samples of different infection types, including both short-read and long-read sequencing data. Our results show that UltraSEQ successfully detected all expected species across the tree of life in the in silico sample and detected all 10 bacterial and fungal species in the mock microbial community data set. For clinical data sets, even without requiring data set-specific configuration setting changes, background sample subtraction, or prior sample information, UltraSEQ achieved an overall accuracy of 91%. Furthermore, as an initial demonstration with a limited patient sample set, we show UltraSEQ's ability to provide antibiotic resistance and virulence factor genotypes that are consistent with phenotypic results. Taken together, the above-described results demonstrate that the UltraSEQ platform offers a transformative approach for microbial and metagenomic sample characterization, employing a biologically informed detection logic, deep metadata, and a flexible system architecture for the classification and characterization of taxonomic origin, gene function, and user-defined functions, including disease-causing infections. IMPORTANCE Traditional clinical microbiology-based diagnostic tests rely on targeted methods that can detect only one to a few preselected organisms or slow, culture-based methods. Although widely used today, these methods have several limitations, resulting in rates of cases of an unknown etiology of infection of >50% for several disease types. Massive developments in sequencing technologies have made it possible to apply metagenomic methods to clinical diagnostics, but current offerings are limited to a specific disease type or sequencer workflow and/or require laboratory-specific controls. The limitations associated with current clinical metagenomic offerings result from the fact that the backend bioinformatic pipelines are optimized for the specific parameters described above, resulting in an excess of unmaintained, redundant, and niche tools that lack standardization and explainable outputs. In this paper, we demonstrate that UltraSEQ uses a novel, information-based approach that enables accurate, evidence-based predictions for diagnosis as well as the functional characterization of a sample.}, } @article {pmid37039269, year = {2023}, author = {Riveros Escalona, MA and Poloni, JF and Krause, MJ and Dorn, M}, title = {Meta-analyses of host metagenomes from colorectal cancer patients reveal strong relationship between colorectal cancer-associated species.}, journal = {Molecular omics}, volume = {19}, number = {5}, pages = {429-444}, doi = {10.1039/d3mo00021d}, pmid = {37039269}, issn = {2515-4184}, mesh = {Humans ; Metagenome ; *Colorectal Neoplasms ; *Gastrointestinal Microbiome ; Cell Transformation, Neoplastic ; Carcinogenesis ; }, abstract = {Colorectal cancer (CRC) is one of the most common types of cancer, with many studies associating its development with changes in the gut microbiota. Recent developments in sequencing technologies and subsequent meta-analyses of gut metagenome provided a better understanding of species related to CRC tumorigenesis. Still, the importance of high-importance taxonomic singletons (i.e. species highly associated with a given condition but observed only in the minority of datasets) and the species interactions and co-occurrence across cohorts need further exploration. It has been shown that the gut metagenome presents a high functional redundancy, meaning that species interactions could mitigate the absence of any given species. In a CRC framework, this implies that species co-occurrence could play a role in tumorigenesis, even if CRC-associated species show low abundance. We propose to evaluate the prevalence of microbial species in tumor by initially analyzing each dataset individually and subsequently intersecting the results for differentially abundant species between CRC and healthy samples. We then identify metabolic pathways from these species based on KEGG orthologs, highlighting metabolic pathways associated with CRC. Our results indicate seven species with high prevalence across all projects and with high association to CRC, including the genus Bacteroides, Enterocloster and Prevotella. Finally, we show that CRC is also characterized by the co-occurrence of species that do not present significant differential abundance, but have been described in the literature as potential CRC biomarkers. These results indicate that between-species interactions could also play a role in CRC tumorigenesis.}, } @article {pmid37037946, year = {2023}, author = {Yang, P and Zhu, X and Ning, K}, title = {Microbiome-based enrichment pattern mining has enabled a deeper understanding of the biome-species-function relationship.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {391}, pmid = {37037946}, issn = {2399-3642}, mesh = {*Copper ; Biological Evolution ; *Microbiota/genetics ; Soil ; Metagenome ; }, abstract = {Microbes live in diverse habitats (i.e. biomes), yet their species and genes were biome-specific, forming enrichment patterns. These enrichment patterns have mirrored the biome-species-function relationship, which is shaped by ecological and evolutionary principles. However, a grand picture of these enrichment patterns, as well as the roles of external and internal factors in driving these enrichment patterns, remain largely unexamined. In this work, we have examined the enrichment patterns based on 1705 microbiome samples from four representative biomes (Engineered, Gut, Freshwater, and Soil). Moreover, an "enrichment sphere" model was constructed to elucidate the regulatory principles behind these patterns. The driving factors for this model were revealed based on two case studies: (1) The copper-resistance genes were enriched in Soil biomes, owing to the copper contamination and horizontal gene transfer. (2) The flagellum-related genes were enriched in the Freshwater biome, due to high fluidity and vertical gene accumulation. Furthermore, this enrichment sphere model has valuable applications, such as in biome identification for metagenome samples, and in guiding 3D structure modeling of proteins. In summary, the enrichment sphere model aims towards creating a bluebook of the biome-species-function relationships and be applied in many fields.}, } @article {pmid37037943, year = {2023}, author = {Shah, SA and Deng, L and Thorsen, J and Pedersen, AG and Dion, MB and Castro-Mejía, JL and Silins, R and Romme, FO and Sausset, R and Jessen, LE and Ndela, EO and Hjelmsø, M and Rasmussen, MA and Redgwell, TA and Leal Rodríguez, C and Vestergaard, G and Zhang, Y and Chawes, B and Bønnelykke, K and Sørensen, SJ and Bisgaard, H and Enault, F and Stokholm, J and Moineau, S and Petit, MA and Nielsen, DS}, title = {Expanding known viral diversity in the healthy infant gut.}, journal = {Nature microbiology}, volume = {8}, number = {5}, pages = {986-998}, pmid = {37037943}, issn = {2058-5276}, support = {143924//CIHR/Canada ; }, mesh = {Infant ; Humans ; Prospective Studies ; *Bacteriophages/genetics ; Lysogeny ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; }, abstract = {The gut microbiome is shaped through infancy and impacts the maturation of the immune system, thus protecting against chronic disease later in life. Phages, or viruses that infect bacteria, modulate bacterial growth by lysis and lysogeny, with the latter being especially prominent in the infant gut. Viral metagenomes (viromes) are difficult to analyse because they span uncharted viral diversity, lacking marker genes and standardized detection methods. Here we systematically resolved the viral diversity in faecal viromes from 647 1-year-olds belonging to Copenhagen Prospective Studies on Asthma in Childhood 2010, an unselected Danish cohort of healthy mother-child pairs. By assembly and curation we uncovered 10,000 viral species from 248 virus family-level clades (VFCs). Most (232 VFCs) were previously unknown, belonging to the Caudoviricetes viral class. Hosts were determined for 79% of phage using clustered regularly interspaced short palindromic repeat spacers within bacterial metagenomes from the same children. Typical Bacteroides-infecting crAssphages were outnumbered by undescribed phage families infecting Clostridiales and Bifidobacterium. Phage lifestyles were conserved at the viral family level, with 33 virulent and 118 temperate phage families. Virulent phages were more abundant, while temperate ones were more prevalent and diverse. Together, the viral families found in this study expand existing phage taxonomy and provide a resource aiding future infant gut virome research.}, } @article {pmid37037312, year = {2023}, author = {Wang, H and Min, C and Xia, F and Xia, Y and Tang, M and Li, J and Hu, Y and Zou, M}, title = {Metagenomic analysis reveals the short-term influences on conjugation of blaNDM-1 and microbiome in hospital wastewater by silver nanoparticles at environmental-related concentration.}, journal = {Environmental research}, volume = {228}, number = {}, pages = {115866}, doi = {10.1016/j.envres.2023.115866}, pmid = {37037312}, issn = {1096-0953}, mesh = {Wastewater ; Silver ; Metagenome ; *Metal Nanoparticles ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Microbiota ; Hospitals ; }, abstract = {Hospital wastewater contains large amounts of antibiotic-resistant bacteria and serves as an important reservoir for horizontal gene transfer (HGT). However, the response of the microbiome in hospital wastewater to silver remains unclear. In this study, the short-term impacts of silver on the microbiome in hospital wastewater were investigated by metagenome next-generation sequencing. The influence of silver on the conjugation of plasmid carrying blaNDM-1 was further examined. Our results showed that in hospital wastewater, high abundances of antibiotic resistance genes (ARGs) were detected. The distribution tendencies of certain ARG types on chromosomes or plasmids were different. Clinically important ARGs were identified in phage-like contigs, indicating potential transmission via transduction. Pseudomonadales, Enterobacterales, and Bacteroidales were the major ARG hosts. Mobile genetic elements were mainly detected in plasmids and associated with various types of ARGs. The binning approach identified 29 bins that were assigned to three phyla. Various ARGs and virulence factors were identified in 14 and 11 bins, respectively. MetaCHIP identified 49 HGT events. The transferred genes were annotated as ARGs, mobile genetic elements, and functional genes, and they mainly originated from donors belonging to Bacteroides and Pseudomonadales. In addition, 20 nm AgNPs reduced microbial diversity and enhanced the relative abundance of Acinetobacter. The changes induced by 20 nm AgNPs included increases in the abundances of ARGs and genes involved lipid metabolism pathway. Conjugation experiments showed that Ag[+] and 20 nm AgNPs caused 2.38-, 3.31-, 4.72-, and 4.57-fold and 1.46-, 1.61-, 3.86-, and 2.16-fold increases in conjugation frequencies of plasmid with blaNDM-1 at 0.1, 1, 10, and 100 μg/L, respectively. Our findings provide insight into the response of the microbiome in hospital wastewater to silver, emphasize the adaptation capability of Acinetobacter inhabiting hospitals against adverse environments, and highlight the promotion of silver for antibiotic resistance.}, } @article {pmid37033728, year = {2023}, author = {Hauck, LL and Atkinson, CL and Homyack, JA and Penaluna, BE and Mangum, C and Coble, AA and Nettles, J and Thornton-Frost, JE and Fix, MJ}, title = {Molecular identity crisis: environmental DNA metabarcoding meets traditional taxonomy-assessing biodiversity and freshwater mussel populations (Unionidae) in Alabama.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15127}, pmid = {37033728}, issn = {2167-8359}, mesh = {Animals ; *DNA, Environmental/genetics ; Ecosystem ; DNA Barcoding, Taxonomic/methods ; Phylogeny ; Alabama ; Identity Crisis ; Fresh Water ; Biodiversity ; *Bivalvia/genetics ; *Unionidae/genetics ; Fishes ; }, abstract = {The use of environmental DNA (eDNA) to assess aquatic biodiversity is a growing field with great potential for monitoring and managing threatened species, like freshwater mussel (Unionidae) populations. Freshwater mussels are globally imperiled and serve essential roles in aquatic systems as a food source and as a natural water filter making their management essential for ecosystem health. Unfortunately, mussel populations are often understudied, and challenges exist to accurately and efficiently describe the full suite of species present. Multispecies eDNA approaches may also be more challenging where freshwater mussel populations are most diverse due to ongoing and significant taxonomic restructuring that has been further complicated by molecular phylogenies using mitochondrial genes. For this study, we developed a microfluidic metabarcoding array that targets a wide range of species, from invertebrates to fishes, with an emphasis on detecting unionid mussels known to be present in the Sipsey River, Alabama. We compared mussel species diversity across six sites with well-studied mussel assemblages using eDNA surveys and traditional quadrat surveys in 2016. We examined how factors such as mussel population density, biomass and location in the river substrate impacted our ability to detect certain species; and investigated unexpected eDNA detections through phylogenetic analysis. Our eDNA results for fish and mussel species were broadly consistent with the data from traditional electrofishing and quadrat-based field surveys, although both community eDNA and conventional sampling detected species unique to that method. Our phylogenetic analysis agreed with other studies that treat Pleurobema decisum and P. chattanoogaense as synonymous species; however, they are still listed as unique species in molecular databases which complicates their identity in a metabarcoding assay. We also found that Fusconaia flava and F. cerina are indistinguishable from one another using a portion of the NADH dehydrogenase Subunit 1 (ND1) marker, which may warrant further investigation into whether or not they are synonymous. Our results show that many factors impacted our ability to detect and correctly identify Unionidae mussel species. Here we describe the obstacles we faced, including the murky phylogeny of Unionidae mussels and turbid river conditions, and our development of a potentially impactful freshwater mussel monitoring eDNA assay.}, } @article {pmid37033478, year = {2023}, author = {Li, W and Li, C and Ren, C and Zhou, S and Cheng, H and Chen, Y and Han, X and Zhong, Y and Zhou, L and Xie, D and Liu, H and Xie, J}, title = {Bidirectional effects of oral anticoagulants on gut microbiota in patients with atrial fibrillation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1038472}, pmid = {37033478}, issn = {2235-2988}, mesh = {Humans ; *Atrial Fibrillation/complications/drug therapy/chemically induced ; *Gastrointestinal Microbiome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Stroke ; Risk Factors ; Anticoagulants/therapeutic use ; Hemorrhage/chemically induced/complications ; Administration, Oral ; Risk Assessment ; }, abstract = {BACKGROUND: The imbalance of gut microbiota (GM) is associated with a higher risk of thrombosis in patients with atrial fibrillation (AF). Oral anticoagulants (OACs) have been found to significantly reduce the risk of thromboembolism and increase the risk of bleeding. However, the OAC-induced alterations in gut microbiota in patients with AF remain elusive.

METHODS: In this study, the microbial composition in 42 AF patients who received long-term OAC treatment (AF-OAC group), 47 AF patients who did not (AF group), and 40 volunteers with the risk of AF (control group) were analyzed by 16S rRNA gene sequencing of fecal bacterial DNA. The metagenomic functional prediction of major bacterial taxa was performed using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) software package.

RESULTS: The gut microbiota differed between the AF-OAC and AF groups. The abundance of Bifidobacterium and Lactobacillus decreased in the two disease groups at the genus level, but OACs treatment mitigated the decreasing tendency and increased beneficial bacterial genera, such as Megamonas. In addition, OACs reduced the abundance of pro-inflammatory taxa on the genus Ruminococcus but increased certain potential pathogenic taxa, such as genera Streptococcus, Escherichia-Shigella, and Klebsiella. The Subgroup Linear discriminant analysis effect size (LEfSe) analyses revealed that Bacteroidetes, Brucella, and Ochrobactrum were more abundant in the anticoagulated bleeding AF patients, Akkermansia and Faecalibacterium were more abundant in the non-anticoagulated-bleeding-AF patients. The neutrophil-to-lymphocyte ratio (NLR) was lower in the AF-OAC group compared with the AF group (P < 0.05). Ruminococcus was positively correlated with the NLR and negatively correlated with the CHA2DS2-VASc score (P < 0.05), and the OACs-enriched species (Megamonas and Actinobacteria) was positively correlated with the prothrombin time (PT) (P < 0.05). Ruminococcus and Roseburia were negatively associated with bleeding events (P < 0.05).

CONCLUSIONS: Our study suggested that OACs might benefit AF patients by reducing the inflammatory response and modulating the composition and abundance of gut microbiota. In particular, OACs increased the abundance of some gut microbiota involved in bleeding and gastrointestinal dysfunction indicating that the exogenous supplementation with Faecalibacterium and Akkermansia might be a prophylactic strategy for AF-OAC patients to lower the risk of bleeding after anticoagulation.}, } @article {pmid37033411, year = {2023}, author = {Maddah, R and Goodarzi, V and Asadi-Yousefabad, SL and Abbasluo, M and Shariati, P and Shafiei Kafraj, A}, title = {Evaluation of the gut microbiome associated with COVID-19.}, journal = {Informatics in medicine unlocked}, volume = {38}, number = {}, pages = {101239}, pmid = {37033411}, issn = {2352-9148}, abstract = {INTRODUCTION: In 2019, a new virus from the coronavirus family called SARS-CoV-2, infected populations throughout the world. Coronavirus disease 2019 (COVID-19), an illness induced by this virus, attacks vital organs in the body, such as the respiratory system and the gastrointestinal tract. Recent studies have confirmed changes in the gut microbiome caused by the COVID-19 disease. We examined the alteration of the gut microbiome in COVID-19 patients compared to healthy individuals.

MATERIALS AND METHODS: in this study, the 16s metagenomics dataset, publicly available in the Sequence Read Archive (SRA) database, was used for analysis (accession number PRJNA636824). The analysis processes were performed using the CLC Microbial Genomics Module 20.1.1 (Qiagen). At first, the sequence reads of samples were trimmed and classified into operational taxonomic units (OTUs) with 97% similarity and then assigned to the Greengenes reference database (v138). Differential abundance analysis was used to determine statistically significant differences in OTUs between COVID-19 and healthy groups. Next, biodiversity analyses including the alpha diversity (intragroup diversity) and beta diversity (intergroup diversity) using defined indexes were estimated. Then, the co-occurrence network at the species level was constructed using the Pearson correlation coefficient calculation between pairs of OTUs in R software and visualized using Cytoscape software. Ultimately, the hub OTUs at the species level were identified using the cytoHubba plugin of Cytoscape based on Maximal Clique Centrality (MCC) algorithm.

RESULTS: The results of the metagenomic analysis revealed that the intestinal microbiome in healthy individuals has a higher biodiversity compared to COVID-19 patients. Indeed, healthy people also have a higher percentage of beneficial bacteria such as bifidobacteria adolescentis compared to COVID-19 patients; in contrast, COVID-19 patients have higher levels of opportunistic and pathogenic bacteria such as Streptococcus anginosus than healthy people. Also, by constructing a co-occurrence network at the species level, Bifidobacterium longum in the healthy group and Veillonella parvulain the COVID-19 group were found as hub species.

CONCLUSION: The results of this study shed light on the relationship between the gut microbiome and COVID-19. These results could be helpful for understanding the pathogenesis, clinical features, and treatment of COVID-9.}, } @article {pmid37032854, year = {2023}, author = {Merges, D and Dal Grande, F and Valim, H and Singh, G and Schmitt, I}, title = {Gene abundance linked to climate zone: Parallel evolution of gene content along elevation gradients in lichenized fungi.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1097787}, pmid = {37032854}, issn = {1664-302X}, abstract = {INTRODUCTION: Intraspecific genomic variability affects a species' adaptive potential toward climatic conditions. Variation in gene content across populations and environments may point at genomic adaptations to specific environments. The lichen symbiosis, a stable association of fungal and photobiont partners, offers an excellent system to study environmentally driven gene content variation. Many of these species have remarkable environmental tolerances, and often form populations across different climate zones. Here, we combine comparative and population genomics to assess the presence and absence of genes in high and low elevation genomes of two lichenized fungi of the genus Umbilicaria.

METHODS: The two species have non-overlapping ranges, but occupy similar climatic niches in North America (U. phaea) and Europe (U. pustulata): high elevation populations are located in the cold temperate zone and low elevation populations in the Mediterranean zone. We assessed gene content variation along replicated elevation gradients in each of the two species, based on a total of 2050 individuals across 26 populations. Specifically, we assessed shared orthologs across species within the same climate zone, and tracked, which genes increase or decrease in abundance within populations along elevation.

RESULTS: In total, we found 16 orthogroups with shared orthologous genes in genomes at low elevation and 13 at high elevation. Coverage analysis revealed one ortholog that is exclusive to genomes at low elevation. Conserved domain search revealed domains common to the protein kinase superfamily. We traced the discovered ortholog in populations along five replicated elevation gradients on both continents and found that the number of this protein kinase gene linearly declined in abundance with increasing elevation, and was absent in the highest populations.

DISCUSSION: We consider the parallel loss of an ortholog in two species and in two geographic settings a rare find, and a step forward in understanding the genomic underpinnings of climatic tolerances in lichenized fungi. In addition, the tracking of gene content variation provides a widely applicable framework for retrieving biogeographical determinants of gene presence/absence patterns. Our work provides insights into gene content variation of lichenized fungi in relation to climatic gradients, suggesting a new research direction with implications for understanding evolutionary trajectories of complex symbioses in relation to climatic change.}, } @article {pmid37032329, year = {2023}, author = {Bazant, W and Blevins, AS and Crouch, K and Beiting, DP}, title = {Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {72}, pmid = {37032329}, issn = {2049-2618}, mesh = {Humans ; *Metagenome/genetics ; Eukaryota/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Archaea/genetics ; Metagenomics/methods ; }, abstract = {BACKGROUND: Eukaryotes such as fungi and protists frequently accompany bacteria and archaea in microbial communities. Unfortunately, their presence is difficult to study with "shotgun" metagenomic sequencing since prokaryotic signals dominate in most environments. Recent methods for eukaryotic detection use eukaryote-specific marker genes, but they do not incorporate strategies to handle the presence of eukaryotes that are not represented in the reference marker gene set, and they are not compatible with web-based tools for downstream analysis.

RESULTS: Here, we present CORRAL (for Clustering Of Related Reference ALignments), a tool for the identification of eukaryotes in shotgun metagenomic data based on alignments to eukaryote-specific marker genes and Markov clustering. Using a combination of simulated datasets, mock community standards, and large publicly available human microbiome studies, we demonstrate that our method is not only sensitive and accurate but is also capable of inferring the presence of eukaryotes not included in the marker gene reference, such as novel strains. Finally, we deploy CORRAL on our MicrobiomeDB.org resource, producing an atlas of eukaryotes present in various environments of the human body and linking their presence to study covariates.

CONCLUSIONS: CORRAL allows eukaryotic detection to be automated and carried out at scale. Implementation of CORRAL in MicrobiomeDB.org creates a running atlas of microbial eukaryotes in metagenomic studies. Since our approach is independent of the reference used, it may be applicable to other contexts where shotgun metagenomic reads are matched against redundant but non-exhaustive databases, such as the identification of bacterial virulence genes or taxonomic classification of viral reads. Video Abstract.}, } @article {pmid37031672, year = {2023}, author = {Senthil Kumar, R and Koner, S and Tsai, HC and Chen, JS and Huang, SW and Hsu, BM}, title = {Deciphering endemic rhizosphere microbiome community's structure towards the host-derived heavy metals tolerance and plant growth promotion functions in serpentine geo-ecosystem.}, journal = {Journal of hazardous materials}, volume = {452}, number = {}, pages = {131359}, doi = {10.1016/j.jhazmat.2023.131359}, pmid = {37031672}, issn = {1873-3336}, mesh = {Nickel/analysis ; Rhizosphere ; RNA, Ribosomal, 16S/genetics/analysis ; *Metals, Heavy/toxicity/analysis ; *Microbiota ; Flavobacterium ; Soil/chemistry ; Plants ; Chromium/toxicity/analysis ; Soil Microbiology ; Plant Roots/microbiology ; }, abstract = {Environmental microbes in rhizosphere soil and surrounding plants have the potential to alter ecosystem functions. We investigated the microbial communities inhabiting the rhizosphere soils of both serpentine and non-serpentine rhizosphere zones to evaluate their heavy metal tolerance and ability to promote plant growth, utilizing 16S rRNA metabarcoding. The Biolog-EcoPlate technique was employed to determine how abiotic stress factors affect carbon utilization capacity by rhizospheric microbial communities in the serpentine geo-ecosystem. The phyla Proteobacteria, Acidobacteria, Bacteroidetes, and Nitrospirae colonized in the roots of Miscanthus sp., Biden sp., and Oryza sp. showed noticeable differences in different rhizosphere zones. The PICRUSt2-based analysis identified chromium/iron resistance genes (ceuE, chrA) and arsenic resistance genes (arsR, acr3, arsC) abundant in all the studied rhizosphere soils. Notably, nickel resistance genes (nikA, nikD, nikE, and nikR) from Arthrobacter, Microbacterium, and Streptomyces strongly correlate with functions related to solubilization of nickel and an increase in siderophore and IAA production. The abundance of Arthrobacter, Clostridium, Geobacter, Dechloromonas, Pseudomonas, and Flavobacterium was positively correlated with chromium and nickel but negatively correlated with the calcium/magnesium ratio. Our results contribute to a better understanding of the functions of plant-tolerant PGPR interaction in the heavy metal-contaminated rhizosphere and eco-physiological responses from long-term biological weathering.}, } @article {pmid37031344, year = {2023}, author = {Liao, H and Liu, C and Ai, C and Gao, T and Yang, QE and Yu, Z and Gao, S and Zhou, S and Friman, VP}, title = {Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting.}, journal = {The ISME journal}, volume = {17}, number = {6}, pages = {916-930}, pmid = {37031344}, issn = {1751-7370}, mesh = {*Composting ; *Viruses/genetics ; Archaea ; Bacteria/genetics ; *Microbiota/genetics ; Nutrients ; }, abstract = {While decomposition of organic matter by bacteria plays a major role in nutrient cycling in terrestrial ecosystems, the significance of viruses remains poorly understood. Here we combined metagenomics and metatranscriptomics with temporal sampling to study the significance of mesophilic and thermophilic bacteria and their viruses on nutrient cycling during industrial-scale hyperthermophilic composting (HTC). Our results show that virus-bacteria density dynamics and activity are tightly coupled, where viruses specific to mesophilic and thermophilic bacteria track their host densities, triggering microbial community succession via top-down control during HTC. Moreover, viruses specific to mesophilic bacteria encoded and expressed several auxiliary metabolic genes (AMGs) linked to carbon cycling, impacting nutrient turnover alongside bacteria. Nutrient turnover correlated positively with virus-host ratio, indicative of a positive relationship between ecosystem functioning, viral abundances, and viral activity. These effects were predominantly driven by DNA viruses as most detected RNA viruses were associated with eukaryotes and not associated with nutrient cycling during the thermophilic phase of composting. Our findings suggest that DNA viruses could drive nutrient cycling during HTC by recycling bacterial biomass through cell lysis and by expressing key AMGs. Viruses could hence potentially be used as indicators of microbial ecosystem functioning to optimize productivity of biotechnological and agricultural systems.}, } @article {pmid37029236, year = {2023}, author = {Dreisbach, C and Prescott, S and Siega-Riz, AM and McCulloch, J and Habermeyer, L and Dudley, D and Trinchieri, G and Kelsey, C and Alhusen, J}, title = {Composition of the maternal gastrointestinal microbiome as a predictor of neonatal birth weight.}, journal = {Pediatric research}, volume = {94}, number = {3}, pages = {1158-1165}, pmid = {37029236}, issn = {1530-0447}, support = {F31 NR017821/NR/NINR NIH HHS/United States ; }, mesh = {Infant, Newborn ; Pregnancy ; Female ; Humans ; Birth Weight ; *Gastrointestinal Microbiome ; Blood Glucose ; Retrospective Studies ; Cross-Sectional Studies ; Body Mass Index ; }, abstract = {BACKGROUND: The biological mechanism by which the maternal gastrointestinal microbiota contributes to fetal growth and neonatal birth weight is currently unknown. The purpose of this study was to explore how the composition of the maternal microbiome in varying pre-gravid body mass index (BMI) groups are associated with neonatal birth weight adjusted for gestational age.

METHODS: Retrospective, cross-sectional metagenomic analysis of bio-banked fecal swab biospecimens (n = 102) self-collected by participants in the late second trimester of pregnancy.

RESULTS: Through high-dimensional regression analysis using principal components (PC) of the microbiome, we found that the best performing multivariate model explained 22.9% of the variation in neonatal weight adjusted for gestational age. Pre-gravid BMI (p = 0.05), PC3 (p = 0.03), and the interaction of the maternal microbiome with maternal blood glucose on the glucose challenge test (p = 0.01) were significant predictors of neonatal birth weight after adjusting for potential confounders including maternal antibiotic use during gestation and total gestational weight gain.

CONCLUSIONS: Our results indicate a significant association between the maternal gastrointestinal microbiome in the late second trimester and neonatal birth weight adjusted for gestational age. Moderated by blood glucose at the time of the universal glucose screening, the gastrointestinal microbiome may have a role in the regulation of fetal growth.

IMPACT: Maternal blood glucose in the late second trimester significantly moderates the relationship between the maternal gastrointestinal microbiome and neonatal size adjusted for gestational age. Our findings provide preliminary evidence for fetal programming of neonatal birth weight through the maternal gastrointestinal microbiome during pregnancy.}, } @article {pmid37029135, year = {2023}, author = {Hu, X and Xia, K and Dai, M and Han, X and Yuan, P and Liu, J and Liu, S and Jia, F and Chen, J and Jiang, F and Yu, J and Yang, H and Wang, J and Xu, X and Jin, X and Kristiansen, K and Xiao, L and Chen, W and Han, M and Duan, S}, title = {Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {19}, pmid = {37029135}, issn = {2055-5008}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Intermittent Fasting ; Obesity ; Metagenome ; }, abstract = {Intermittent fasting (IF) is a promising paradigm for weight loss which has been shown to modulate the gut microbiota based on 16S rRNA gene amplicon sequencing. Here, 72 Chinese volunteers with a wide range of body mass index (BMI) participated in a three-week IF program during which an average loss of 3.67 kg body weight accompanied with improved clinical parameters was observed irrespective of initial anthropometric and gut microbiota status. Fecal samples were collected before and after the intervention and subjected to shotgun metagenomic sequencing. De novo assembly yielded 2934 metagenome-assembled genomes (MAGs). Profiling revealed significant enrichment of Parabacteroides distasonis and Bacteroides thetaiotaomicron after the intervention, with inverse correlations between their relative abundances and parameters related to obesity and atherosclerotic cardiovascular diseases (ASCVD). MAGs enriched after the intervention showed high richness and diversity of carbohydrate-active enzymes, with an increased relative abundances of genes related to succinate production and glutamate fermentation.}, } @article {pmid37027361, year = {2023}, author = {Xu, R and Rajeev, S and Salvador, LCM}, title = {The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection.}, journal = {PloS one}, volume = {18}, number = {4}, pages = {e0284031}, pmid = {37027361}, issn = {1932-6203}, mesh = {Animals ; Mice ; *Metagenomics/methods ; Software ; *Microbiota/genetics ; Algorithms ; Metagenome ; Sequence Analysis, DNA/methods ; }, abstract = {Shotgun metagenomic sequencing analysis is widely used for microbial profiling of biological specimens and pathogen detection. However, very little is known about the technical biases caused by the choice of analysis software and databases on the biological specimen. In this study, we evaluated different direct read shotgun metagenomics taxonomic profiling software to characterize the microbial compositions of simulated mice gut microbiome samples and of biological samples collected from wild rodents across multiple taxonomic levels. Using ten of the most widely used metagenomics software and four different databases, we demonstrated that obtaining an accurate species-level microbial profile using the current direct read metagenomics profiling software is still a challenging task. We also showed that the discrepancies in results when different databases and software were used could lead to significant variations in the distinct microbial taxa classified, in the characterizations of the microbial communities, and in the differentially abundant taxa identified. Differences in database contents and read profiling algorithms are the main contributors for these discrepancies. The inclusion of host genomes and of genomes of the interested taxa in the databases is important for increasing the accuracy of profiling. Our analysis also showed that software included in this study differed in their ability to detect the presence of Leptospira, a major zoonotic pathogen of one health importance, especially at the species level resolution. We concluded that using different databases and software combinations can result in confounding biological conclusions in microbial profiling. Our study warrants that software and database selection must be based on the purpose of the study.}, } @article {pmid37023405, year = {2023}, author = {Cavattoni, M and Comin, M}, title = {ClassGraph: Improving Metagenomic Read Classification with Overlap Graphs.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {30}, number = {6}, pages = {633-647}, doi = {10.1089/cmb.2022.0208}, pmid = {37023405}, issn = {1557-8666}, mesh = {*Algorithms ; Sequence Analysis, DNA ; Metagenome ; *Microbiota ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; }, abstract = {Current technologies allow the sequencing of microbial communities directly from the environment without prior culturing. One of the major problems when analyzing a microbial sample is to taxonomically annotate its reads to identify the species it contains. Most methods that are currently available focus on the classification of reads using a set of reference genomes and their k-mers. While in terms of precision these methods have reached percentages of correctness close to perfection, in terms of sensitivity (the actual number of classified reads), the performance is often poor. One reason is that the reads in a sample can be very different from the corresponding reference genomes; for example, viral genomes are usually highly mutated. To address this issue, in this article, we propose ClassGraph, a new taxonomic classification method that makes use of the read overlap graph and applies a label propagation algorithm to refine the results of existing tools. We evaluated its performance on simulated and real datasets with several taxonomic classification tools, and the results showed an improved sensitivity and F-measure, while maintaining high precision. ClassGraph is capable of improving the classification accuracy, especially in difficult cases such as virus and real datasets, where traditional tools can classify <40% of reads.}, } @article {pmid37022232, year = {2023}, author = {Zimmerman, S and Tierney, BT and Patel, CJ and Kostic, AD}, title = {Quantifying Shared and Unique Gene Content across 17 Microbial Ecosystems.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0011823}, pmid = {37022232}, issn = {2379-5077}, support = {P30 DK036836/DK/NIDDK NIH HHS/United States ; R01 AI127250/AI/NIAID NIH HHS/United States ; R01 ES032470/ES/NIEHS NIH HHS/United States ; T32 DK110919/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; Metagenome/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Genome, Bacterial ; }, abstract = {Measuring microbial diversity is traditionally based on microbe taxonomy. Here, in contrast, we aimed to quantify heterogeneity in microbial gene content across 14,183 metagenomic samples spanning 17 ecologies, including 6 human associated, 7 nonhuman host associated, and 4 in other nonhuman host environments. In total, we identified 117,629,181 nonredundant genes. The vast majority of genes (66%) occurred in only one sample (i.e., "singletons"). In contrast, we found 1,864 sequences present in every metagenome, but not necessarily every bacterial genome. Additionally, we report data sets of other ecology-associated genes (e.g., abundant in only gut ecosystems) and simultaneously demonstrated that prior microbiome gene catalogs are both incomplete and inaccurately cluster microbial genetic life (e.g., at gene sequence identities that are too restrictive). We provide our results and the sets of environmentally differentiating genes described above at http://www.microbial-genes.bio. IMPORTANCE The amount of shared genetic elements has not been quantified between the human microbiome and other host- and non-host-associated microbiomes. Here, we made a gene catalog of 17 different microbial ecosystems and compared them. We show that most species shared between environment and human gut microbiomes are pathogens and that prior gene catalogs described as "nearly complete" are far from it. Additionally, over two-thirds of all genes only appear in a single sample, and only 1,864 genes (0.001%) are found in all types of metagenomes. These results highlight the large diversity between metagenomes and reveal a new, rare class of genes, those found in every type of metagenome, but not every microbial genome.}, } @article {pmid37022183, year = {2023}, author = {Wang, Q and Wang, D and Agathokleous, E and Cheng, C and Shang, B and Feng, Z}, title = {Soil Microbial Community Involved in Nitrogen Cycling in Rice Fields Treated with Antiozonant under Ambient Ozone.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {4}, pages = {e0018023}, pmid = {37022183}, issn = {1098-5336}, mesh = {Soil/chemistry ; *Oryza ; *Ozone/pharmacology ; *Microbiota ; Soil Microbiology ; Nitrogen ; }, abstract = {Ethylenediurea (EDU) can effectively mitigate the crop yield loss caused by ozone (O3), a major, phytotoxic air pollutant. However, the relevant mechanisms are poorly understood, and the effect of EDU on soil ecosystems has not been comprehensively examined. In this study, a hybrid rice variety (Shenyou 63) was cultivated under ambient O3 and sprayed with 450 ppm EDU or water every 10 days. Real time quantitative polymerase chain reaction (RT-qPCR) showed that EDU had no significant effect on the microbial abundance in either rhizospheric or bulk soils. By applying both metagenomic sequencing and the direct assembly of nitrogen (N)-cycling genes, EDU was found to decrease the abundance of functional genes related to nitrification and denitrification processes. Moreover, EDU increased the abundance of genes involved in N-fixing. Although the abundance of some functional genes did not change significantly, nonmetric multidimensional scaling (NMDS) and a principal coordinates analysis (PCoA) suggested that the microbial community structure involved in N cycling was altered by EDU. The relative abundances of nifH-and norB-harboring microbial genera in the rhizosphere responded differently to EDU, suggesting the existence of functional redundancy, which may play a key role in sustaining microbially mediated N-cycling under ambient O3. IMPORTANCE Ethylenediurea (EDU) is hitherto the most efficient phytoprotectant agent against O3 stress. However, the underlying biological mechanisms of its mode of action are not clear, and the effects of EDU on the environment are still unknown, limiting its large-scale application in agriculture. Due to its sensitivity to environmental changes, the microbial community can be used as an indicator to assess the environmental impacts of agricultural practices on soil quality. This study aimed to unravel the effects of EDU spray on the abundance, community structure, and ecological functions of microbial communities in the rhizosphere of rice plants. Our study provides a deep insight into the impact of EDU spray on microbial-mediated N cycling and the structure of N-cycling microbial communities. Our findings help to elucidate the mode of action of EDU in alleviating O3 stress in crops from the perspective of regulating the structure and function of the rhizospheric soil microbial community.}, } @article {pmid37020239, year = {2023}, author = {Qian, L and Yu, X and Gu, H and Liu, F and Fan, Y and Wang, C and He, Q and Tian, Y and Peng, Y and Shu, L and Wang, S and Huang, Z and Yan, Q and He, J and Liu, G and Tu, Q and He, Z}, title = {Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {71}, pmid = {37020239}, issn = {2049-2618}, mesh = {Methane/metabolism ; Nitrogen/metabolism ; *Microbiota ; *Desulfovibrio ; Sulfur/metabolism ; Sulfides ; Geologic Sediments/microbiology ; }, abstract = {BACKGROUND: Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove wetlands remain elusive. Here we investigated the vertical profile of methane (CH4), nitrogen (N) and sulphur (S) cycling genes/pathways and their potential coupling mechanisms using metagenome sequencing approaches.

RESULTS: Our results showed that the metabolic pathways involved in CH4, N and S cycling were mainly shaped by pH and acid volatile sulphide (AVS) along a sediment depth, and AVS was a critical electron donor impacting mangrove sediment S oxidation and denitrification. Gene families involved in S oxidation and denitrification significantly (P < 0.05) decreased along the sediment depth and could be coupled by S-driven denitrifiers, such as Burkholderiaceae and Sulfurifustis in the surface sediment (0-15 cm). Interestingly, all S-driven denitrifier metagenome-assembled genomes (MAGs) appeared to be incomplete denitrifiers with nitrate/nitrite/nitric oxide reductases (Nar/Nir/Nor) but without nitrous oxide reductase (Nos), suggesting such sulphide-utilizing groups might be an important contributor to N2O production in the surface mangrove sediment. Gene families involved in methanogenesis and S reduction significantly (P < 0.05) increased along the sediment depth. Based on both network and MAG analyses, sulphate-reducing bacteria (SRB) might develop syntrophic relationships with anaerobic CH4 oxidizers (ANMEs) by direct electron transfer or zero-valent sulphur, which would pull forward the co-existence of methanogens and SRB in the middle and deep layer sediments.

CONCLUSIONS: In addition to offering a perspective on the vertical distribution of microbially driven CH4, N and S cycling genes/pathways, this study emphasizes the important role of S-driven denitrifiers on N2O emissions and various possible coupling mechanisms of ANMEs and SRB along the mangrove sediment depth. The exploration of potential coupling mechanisms provides novel insights into future synthetic microbial community construction and analysis. This study also has important implications for predicting ecosystem functions within the context of environmental and global change. Video Abstract.}, } @article {pmid37019943, year = {2023}, author = {Akhtar, A and Lata, M and Sunsunwal, S and Yadav, A and Lnu, K and Subramanian, S and Ramya, TNC}, title = {New carbohydrate binding domains identified by phage display based functional metagenomic screens of human gut microbiota.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {371}, pmid = {37019943}, issn = {2399-3642}, support = {P41 GM103694/GM/NIGMS NIH HHS/United States ; R24 GM098791/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Genomics ; Carbohydrates ; *Bacteriophages ; }, abstract = {Uncultured microbes represent a huge untapped biological resource of novel genes and gene products. Although recent genomic and metagenomic sequencing efforts have led to the identification of numerous genes that are homologous to existing annotated genes, there remains, yet, an enormous pool of unannotated genes that do not find significant sequence homology to existing annotated genes. Functional metagenomics offers a way to identify and annotate novel gene products. Here, we use functional metagenomics to mine novel carbohydrate binding domains that might aid human gut commensals in adherence, gut colonization, and metabolism of complex carbohydrates. We report the construction and functional screening of a metagenomic phage display library from healthy human fecal samples against dietary, microbial and host polysaccharides/glycoconjugates. We identify several protein sequences that do not find a hit to any known protein domain but are predicted to contain carbohydrate binding module-like folds. We heterologously express, purify and biochemically characterize some of these protein domains and demonstrate their carbohydrate-binding function. Our study reveals several previously unannotated carbohydrate-binding domains, including a levan binding domain and four complex N-glycan binding domains that might be useful for the labeling, visualization, and isolation of these glycans.}, } @article {pmid37019259, year = {2023}, author = {Sun, J and Yuan, Y and Cai, L and Zeng, M and Li, X and Yao, F and Chen, W and Huang, Y and Shafiq, M and Xie, Q and Zhang, Q and Wong, N and Wang, Z and Jiao, X}, title = {Metagenomic evidence for antibiotics-driven co-evolution of microbial community, resistome and mobilome in hospital sewage.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {327}, number = {}, pages = {121539}, doi = {10.1016/j.envpol.2023.121539}, pmid = {37019259}, issn = {1873-6424}, mesh = {Angiotensin Receptor Antagonists/pharmacology ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Genes, Bacterial ; *Microbiota ; *Sewage/microbiology ; Metagenome ; }, abstract = {Overconsumption of antibiotics is an immediate cause for the emergence of antimicrobial resistance (AMR) and antibiotic resistant bacteria (ARB), though its environmental impact remains inadequately clarified. There is an urgent need to dissect the complex links underpinning the dynamic co-evolution of ARB and their resistome and mobilome in hospital sewage. Metagenomic and bioinformatic methods were employed to analyze the microbial community, resistome and mobilome in hospital sewage, in relation to data on clinical antibiotic use collected from a tertiary-care hospital. In this study, resistome (1,568 antibiotic resistance genes, ARGs, corresponding to 29 antibiotic types/subtypes) and mobilome (247 types of mobile genetic elements, MGEs) were identified. Networks connecting co-occurring ARGs with MGEs encompass 176 nodes and 578 edges, in which over 19 types of ARGs had significant correlations with MGEs. Prescribed dosage and time-dependent antibiotic consumption were associated with the abundance and distributions of ARGs, and conjugative transfer of ARGs via MGEs. Variation partitioning analyses show that effects of conjugative transfer were most likely the main contributors to transient propagation and persistence of AMR. We have presented the first evidence supporting idea that use of clinical antibiotics is a potent driving force for the development of co-evolving resistome and mobilome, which in turn supports the growth and evolution of ARB in hospital sewage. The use of clinical antibiotics calls for greater attention in antibiotic stewardship and management.}, } @article {pmid37019075, year = {2023}, author = {Pietruska, A and Bortoluzzi, C and Hauck, R}, title = {A meta-analysis of the effect of Eimeria spp. and/or Clostridium perfringens infection on the microbiota of broiler chickens.}, journal = {Poultry science}, volume = {102}, number = {6}, pages = {102652}, pmid = {37019075}, issn = {1525-3171}, mesh = {Animals ; *Eimeria ; Chickens/microbiology ; *Enteritis/veterinary ; *Poultry Diseases/microbiology ; *Clostridium Infections/veterinary/microbiology ; *Coccidiosis/veterinary/microbiology ; Clostridium perfringens ; *Microbiota ; }, abstract = {Coccidiosis in chickens is caused by Eimeria spp. The infection provides a growth advantage to Clostridium perfringens (CP), frequently leading to necrotic enteritis. One approach to alleviate the negative impacts of the diseases is to improve the bacterial composition in chickens, and many experiments investigating chicken enteric health in recent years include the characterization of the bacterial microbiota. This meta-analysis synthesized the data of studies investigating the intestinal microbiota after infection with coccidia and/or CP to provide a basis for future research. Inclusion criteria were that experiments contained a group infected with one or both pathogens and an uninfected control group, the use of 16SrRNA Illumina sequencing and the availability of raw data. A total of 17 studies could be included. Meta-analyses of 3 different data sets were performed: 1 on data of 9 experiments on chickens infected with coccidia only; the second on data of 4 studies on chickens infected with CP only; the third on raw data of 8 experiments with chickens infected with coccidia and CP. The meta-analysis of relative abundance and alpha diversity of the data sets was performed in R using the SIAMCAT and metafor packages. The number of families of interest identified by the analyses of experiments with infection with coccidia only, CP only and the combined infection were 23, 2, and 29, respectively. There was an overlap of 13 families identified by analyses of experiments with infection with coccidia only and of experiments with the combined infections. Machine learning was not able to find a model to predict changes of the microbiota in either 1 of the 3 analyses. Meta-analyses of functional profiles showed a more uniform reaction to the infections with the relative abundance of many pathways significantly altered. Alpha diversity was not affected by infection with either pathogen or the combination. In conclusion, the heterogeneity of these microbiota studies makes recognizing common trends difficult, although it seems that coccidia infection affects the microbiota more than an infection with CP. Future studies should focus on the bacterial functions that are changed due to these infections using metagenome techniques.}, } @article {pmid37018898, year = {2023}, author = {Rasmussen, JA and Chua, PYS}, title = {Genome-resolving metagenomics reveals wild western capercaillies (Tetrao urogallus) as avian hosts for antibiotic-resistance bacteria and their interactions with the gut-virome community.}, journal = {Microbiological research}, volume = {271}, number = {}, pages = {127372}, doi = {10.1016/j.micres.2023.127372}, pmid = {37018898}, issn = {1618-0623}, mesh = {Animals ; Humans ; *Virome ; *Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Birds/genetics ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Metagenome ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; }, abstract = {The gut microbiome is a critical component of avian health, influencing nutrient uptake and immune functions. While the gut microbiomes of agriculturally important birds have been studied, the microbiomes of wild birds still need to be explored. Filling this knowledge gap could have implications for the microbial rewilding of captive birds and managing avian hosts for antibiotic-resistant bacteria (ARB). Using genome-resolved metagenomics, we recovered 112 metagenome-assembled genomes (MAGs) from the faeces of wild and captive western capercaillies (Tetrao urogallus) (n = 8). Comparisons of bacterial diversity between the wild and captive capercaillies suggest that the reduced diversity in the captive individual could be due to differences in diet. This was further substantiated through the analyses of 517,657 clusters of orthologous groups (COGs), which revealed that gene functions related to amino acids and carbohydrate metabolisms were more abundant in wild capercaillies. Metagenomics mining of resistome identified 751 antibiotic resistance genes (ARGs), of which 40.7 % were specific to wild capercaillies suggesting that capercaillies could be potential reservoirs for hosting ARG-associated bacteria. Additionally, the core resistome shared between wild and captive capercaillies indicates that birds can acquire these ARG-associated bacteria naturally from the environment (43.1 % of ARGs). The association of 26 MAGs with 120 ARGs and 378 virus operational taxonomic units (vOTUs) also suggests a possible interplay between these elements, where putative phages could have roles in modulating the gut microbiota of avian hosts. These findings can have important implications for conservation and human health, such as avian gut microbiota rewilding, identifying the emerging threats or opportunities due to phage-microbe interactions, and monitoring the potential spread of ARG-associated bacteria from wild avian populations.}, } @article {pmid37017718, year = {2023}, author = {Thompson, CC and Tschoeke, D and Coutinho, FH and Leomil, L and Garcia, GD and Otsuki, K and Turcq, BJ and Moreira, LS and Turcq, PFM and Cordeiro, RC and Asp, NE and Thompson, FL}, title = {Diversity of Microbiomes Across a 13,000-Year-Old Amazon Sediment.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2202-2209}, pmid = {37017718}, issn = {1432-184X}, mesh = {*Microbiota/genetics ; Bacteria ; Metagenome ; Rivers/microbiology ; Lakes/microbiology ; Geologic Sediments/microbiology ; }, abstract = {The microbiome is fundamental for understanding bacterial activities in sediments. However, only a limited number of studies have addressed the microbial diversity of Amazonian sediments. Here, we studied the microbiome of sediments from a 13,000-year BP core retrieved in a floodplain lake in Amazonia using metagenomics and biogeochemistry. Our aim was to evaluate the possible environmental influence over a river to a lake transition using a core sample. To this end, we sampled a core in the Airo Lake, a floodplain lake in the Negro River basin. The Negro River is the largest tributary of the Amazon River. The obtained core was divided into three strata: (i) surface, almost complete separation of the Airo Lake from the Negro River when the environment becomes more lentic with greater deposition of organic matter (black-colored sediment); (ii) transitional environment (reddish brown); and (iii) deep, environment with a tendency for greater past influence of the Negro River (brown color). The deepest sample possibly had the greatest influence of the Negro River as it represented the bottom of this river in the past, while the surface sample is the current Airo Lake bottom. In total, six metagenomes were obtained from the three different depth strata (total number of reads: 10.560.701; sequence length: 538 ± 24, mean ± standard deviation). The older (deeper) sediment strata contained a higher abundance of Burkholderia, Chitinophaga, Mucilaginibacter, and Geobacter, which represented ~ 25% of the metagenomic sequences. On the other hand, the more recent sediment strata had mainly Thermococcus, Termophilum, Sulfolobus, Archaeoglobus, and Methanosarcina (in total 11% of the metagenomic sequences). The sequence data were binned into metagenome-assembled genomes (MAGs). The majority of the obtained MAGs (n = 16) corresponded to unknown taxa, suggesting they may belong to new species. The older strata sediment microbiome was enriched with sulfur cycle genes, TCA cycle, YgfZ, and ATP-dependent proteolysis in bacteria. Meanwhile, serine-glyoxylate cycle, stress response genes, bacterial cell division, cell division-ribosomal stress protein cluster, and oxidative stress increased in the younger strata. Metal resistance and antimicrobial resistance genes were found across the entire core, including genes coding for fluoroquinolones, polymyxin, vancomycin, and multidrug resistance transporters. These findings depict the possible microbial diversity during the depositional past events and provided clues of the past microbial metabolism throughout time.}, } @article {pmid37017243, year = {2023}, author = {Dilmore, AH and Martino, C and Neth, BJ and West, KA and Zemlin, J and Rahman, G and Panitchpakdi, M and Meehan, MJ and Weldon, KC and Blach, C and Schimmel, L and Kaddurah-Daouk, R and Dorrestein, PC and Knight, R and Craft, S and , }, title = {Effects of a ketogenic and low-fat diet on the human metabolome, microbiome, and foodome in adults at risk for Alzheimer's disease.}, journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association}, volume = {19}, number = {11}, pages = {4805-4816}, pmid = {37017243}, issn = {1552-5279}, support = {R01 AG046171/AG/NIA NIH HHS/United States ; U24 AG021886/AG/NIA NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; RF1 AG059093/AG/NIA NIH HHS/United States ; /NH/NIH HHS/United States ; U01 AG061359/AG/NIA NIH HHS/United States ; RF1 AG057452/AG/NIA NIH HHS/United States ; P30 AG072947/AG/NIA NIH HHS/United States ; RF1 AG051550/AG/NIA NIH HHS/United States ; RF1 AG0151550/AG/NIA NIH HHS/United States ; }, mesh = {United States ; Humans ; Adult ; *Alzheimer Disease/metabolism ; Diet, Fat-Restricted ; *Microbiota ; Metabolome/physiology ; Seizures ; Ketone Bodies ; gamma-Aminobutyric Acid/metabolism ; }, abstract = {INTRODUCTION: The ketogenic diet (KD) is an intriguing therapeutic candidate for Alzheimer's disease (AD) given its protective effects against metabolic dysregulation and seizures. Gut microbiota are essential for KD-mediated neuroprotection against seizures as well as modulation of bile acids, which play a major role in cholesterol metabolism. These relationships motivated our analysis of gut microbiota and metabolites related to cognitive status following a controlled KD intervention compared with a low-fat-diet intervention.

METHODS: Prediabetic adults, either with mild cognitive impairment (MCI) or cognitively normal (CN), were placed on either a low-fat American Heart Association diet or high-fat modified Mediterranean KD (MMKD) for 6 weeks; then, after a 6-week washout period, they crossed over to the alternate diet. We collected stool samples for shotgun metagenomics and untargeted metabolomics at five time points to investigate individuals' microbiome and metabolome throughout the dietary interventions.

RESULTS: Participants with MCI on the MMKD had lower levels of GABA-producing microbes Alistipes sp. CAG:514 and GABA, and higher levels of GABA-regulating microbes Akkermansia muciniphila. MCI individuals with curcumin in their diet had lower levels of bile salt hydrolase-containing microbes and an altered bile acid pool, suggesting reduced gut motility.

DISCUSSION: Our results suggest that the MMKD may benefit adults with MCI through modulation of GABA levels and gut-transit time.}, } @article {pmid37017219, year = {2024}, author = {Dindhoria, K and Manyapu, V and Ali, A and Kumar, R}, title = {Unveiling the role of emerging metagenomics for the examination of hypersaline environments.}, journal = {Biotechnology & genetic engineering reviews}, volume = {40}, number = {3}, pages = {2090-2128}, doi = {10.1080/02648725.2023.2197717}, pmid = {37017219}, issn = {2046-5556}, mesh = {*Metagenomics/methods ; *Salinity ; *Microbiota ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Ecosystem ; Phylogeny ; }, abstract = {Hypersaline ecosystems are distributed all over the globe. They are subjected to poly-extreme stresses and are inhabited by halophilic microorganisms possessing multiple adaptations. The halophiles have many biotechnological applications such as nutrient supplements, antioxidant synthesis, salt tolerant enzyme production, osmolyte synthesis, biofuel production, electricity generation etc. However, halophiles are still underexplored in terms of complex ecological interactions and functions as compared to other niches. The advent of metagenomics and the recent advancement of next-generation sequencing tools have made it feasible to investigate the microflora of an ecosystem, its interactions and functions. Both target gene and shotgun metagenomic approaches are commonly employed for the taxonomic, phylogenetic, and functional analyses of the hypersaline microbial communities. This review discusses different types of hypersaline niches, their residential microflora, and an overview of the metagenomic approaches used to investigate them. Various applications, hurdles and the recent advancements in metagenomic approaches have also been focused on here for their better understanding and utilization in the study of hypersaline microbiome.}, } @article {pmid37016727, year = {2023}, author = {Tilves, C and Tanaka, T and Differding, MK and Spira, AP and Chia, CW and Ferrucci, L and Mueller, NT}, title = {The gut microbiome and regional fat distribution: Findings from the Baltimore Longitudinal Study of Aging.}, journal = {Obesity (Silver Spring, Md.)}, volume = {31}, number = {5}, pages = {1425-1435}, pmid = {37016727}, issn = {1930-739X}, support = {K01 HL141589/HL/NHLBI NIH HHS/United States ; R01 AG050507/AG/NIA NIH HHS/United States ; T32 HL007024/HL/NHLBI NIH HHS/United States ; }, mesh = {Male ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Aging ; Female ; Longitudinal Studies ; Humans ; Clostridiales ; Body Mass Index ; Absorptiometry, Photon ; Baltimore ; }, abstract = {OBJECTIVE: The aim of this study was to examine associations of gut microbiome diversity and composition with directly measured regional fat distribution, including central fat, in a large community-based cohort.

METHODS: A cross-sectional investigation was conducted in the Baltimore Longitudinal Study of Aging (N = 815, 55.2% female, 65.9% White). The fecal microbiome was assessed using whole-genome shotgun metagenomic sequencing, and trunk and leg fat was measured using dual x-ray absorptiometry. Multivariable-adjusted associations of regional fat measures, BMI, or waist circumference with microbiome alpha diversity metrics, microbiome beta diversity metrics, and species differential abundance (verified using two compositional statistical approaches) were examined.

RESULTS: Trunk fat, leg fat, BMI, and waist circumference all significantly explained similar amounts of variance in microbiome structure. Differential abundance testing identified 11 bacterial species significantly associated with at least one measure of body composition or anthropometry. Ruminococcus gnavus was strongly and consistently associated with trunk fat mass, which is congruent with prior literature.

CONCLUSIONS: Microbiome diversity and composition, in particular higher abundance of Ruminococcus gnavus, were associated with greater trunk fat, in addition to other measures of obesity. Longitudinal studies are needed to replicate these findings, and if replicated, randomized trials are needed to determine whether interventions targeting microbiome features such as abundance of Ruminococcus gnavus can lead to reductions in trunk fat and its metabolic sequelae.}, } @article {pmid37016075, year = {2023}, author = {Weeraphan, T and Somphong, A and Poengsungnoen, V and Buaruang, K and Harunari, E and Igarashi, Y and Tanasupawat, S and Phongsopitanun, W}, title = {Bacterial microbiome in tropical lichens and the effect of the isolation method on culturable lichen-derived actinobacteria.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {5483}, pmid = {37016075}, issn = {2045-2322}, mesh = {*Actinobacteria ; *Lichens/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota/genetics ; *Actinomycetales ; Phylogeny ; Biodiversity ; }, abstract = {Ten samples of tropical lichens collected from Doi Inthanon, Thailand, were explored for the diversity of their bacterial microbiomes through 16S rRNA-based metagenomics analysis. The five predominant lichen-associated bacteria belonged to the phyla Proteobacteria (31.84%), Planctomycetota (17.08%), Actinobacteriota (15.37%), Verrucomicrobiota (12.17%), and Acidobacteriota (7.87%). The diversity analysis metric showed that Heterodermia contained the highest bacterial species richness. Within the lichens, Ramalina conduplicans and Cladonia rappii showed a distinct bacterial community from the other lichen species. The community of lichen-associated actinobacteria was investigated as a potential source of synthesized biologically active compounds. From the total Operational Taxonomic Units (OTUs) found across the ten different lichen samples, 13.21% were identified as actinobacteria, including the rare actinobacterial genera that are not commonly found, such as Pseudonocardia, Kineosporia, Dactylosporangium, Amycolatopsis, Actinoplanes, and Streptosporangium. Evaluation of the pretreatment method (heat, air-drying, phenol, and flooding) and isolation media used for the culture-dependent actinobacterial isolation revealed that the different pretreatments combined with different isolation media were effective in obtaining several species of actinobacteria. However, metagenomics analyses revealed that there were still several strains, including rare actinobacterial species, that were not isolated. This research strongly suggests that lichens appear to be a promising source for obtaining actinobacteria.}, } @article {pmid37015876, year = {2023}, author = {Crost, EH and Coletto, E and Bell, A and Juge, N}, title = {Ruminococcus gnavus: friend or foe for human health.}, journal = {FEMS microbiology reviews}, volume = {47}, number = {2}, pages = {}, pmid = {37015876}, issn = {1574-6976}, support = {BB/P008895/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adult ; *Ruminococcus/physiology ; *Gastrointestinal Microbiome ; Humans ; Gastrointestinal Tract ; Clostridiales ; }, abstract = {Ruminococcus gnavus was first identified in 1974 as a strict anaerobe in the gut of healthy individuals, and for several decades, its study has been limited to specific enzymes or bacteriocins. With the advent of metagenomics, R. gnavus has been associated both positively and negatively with an increasing number of intestinal and extraintestinal diseases from inflammatory bowel diseases to neurological disorders. This prompted renewed interest in understanding the adaptation mechanisms of R. gnavus to the gut, and the molecular mediators affecting its association with health and disease. From ca. 250 publications citing R. gnavus since 1990, 94% were published in the last 10 years. In this review, we describe the biological characterization of R. gnavus, its occurrence in the infant and adult gut microbiota and the factors influencing its colonization of the gastrointestinal tract; we also discuss the current state of our knowledge on its role in host health and disease. We highlight gaps in knowledge and discuss the hypothesis that differential health outcomes associated with R. gnavus in the gut are strain and niche specific.}, } @article {pmid37013357, year = {2023}, author = {Mills, DA and German, JB and Lebrilla, CB and Underwood, MA}, title = {Translating neonatal microbiome science into commercial innovation: metabolism of human milk oligosaccharides as a basis for probiotic efficacy in breast-fed infants.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2192458}, pmid = {37013357}, issn = {1949-0984}, support = {R01 HD061923/HD/NICHD NIH HHS/United States ; U01 CA179582/CA/NCI NIH HHS/United States ; F32 AT008533/AT/NCCIH NIH HHS/United States ; F32 HD093185/HD/NICHD NIH HHS/United States ; R21 AT006180/AT/NCCIH NIH HHS/United States ; R01 HD059127/HD/NICHD NIH HHS/United States ; R01 AT008759/AT/NCCIH NIH HHS/United States ; R01 AT007079/AT/NCCIH NIH HHS/United States ; F32 AT006642/AT/NCCIH NIH HHS/United States ; R01 HD065122/HD/NICHD NIH HHS/United States ; }, mesh = {Infant, Newborn ; Female ; Infant ; Humans ; Milk, Human/metabolism ; *Gastrointestinal Microbiome ; Bifidobacterium/metabolism ; *Probiotics ; Feces/microbiology ; *Microbiota ; Oligosaccharides/metabolism ; }, abstract = {For over a century, physicians have witnessed a common enrichment of bifidobacteria in the feces of breast-fed infants that was readily associated with infant health status. Recent advances in bacterial genomics, metagenomics, and glycomics have helped explain the nature of this unique enrichment and enabled the tailored use of probiotic supplementation to restore missing bifidobacterial functions in at-risk infants. This review documents a 20-year span of discoveries that set the stage for the current use of human milk oligosaccharide-consuming bifidobacteria to beneficially colonize, modulate, and protect the intestines of at-risk, human milk-fed, neonates. This review also presents a model for probiotic applications wherein bifidobacterial functions, in the form of colonization and HMO-related catabolic activity in situ, represent measurable metabolic outcomes by which probiotic efficacy can be scored toward improving infant health.}, } @article {pmid37012285, year = {2023}, author = {Yang, X and Zhang, M and Zhang, Y and Wei, H and Guan, Q and Dong, C and Deng, S and Tun, HM and Xia, Y}, title = {Ecological change of the gut microbiota during pregnancy and progression to dyslipidemia.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {14}, pmid = {37012285}, issn = {2055-5008}, mesh = {Humans ; Pregnancy ; Female ; *Gastrointestinal Microbiome/physiology ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; *Microbiota ; Bacteroidetes ; Lipids ; }, abstract = {The composition of the gut microbiome was previously found to be associated with clinical responses to dyslipidemia, but there is limited consensus on the dynamic change of the gut microbiota during pregnancy and the specific microbiome characteristics linked to dyslipidemia in pregnant women. We collected fecal samples from 513 pregnant women at multiple time points during pregnancy in a prospective cohort. Taxonomic composition and functional annotations were determined by 16S rRNA amplicon sequencing and shotgun metagenomic sequencing. The predictive potential of gut microbiota on the risk of dyslipidemia was determined. The gut microbiome underwent dynamic changes during pregnancy, with significantly lower alpha diversity observed in dyslipidemic patients compared to their healthy counterparts. Several genera, including Bacteroides, Paraprevotella, Alistipes, Christensenellaceae R7 group, Clostridia UCG-014, and UCG-002 were negatively associated with lipid profiles and dyslipidemia. Further metagenomic analysis recognized a common set of pathways involved in gastrointestinal inflammation, where disease-specific microbes played an important role. Machine learning analysis confirmed the link between the microbiome and its progression to dyslipidemia, with a micro-averaged AUC of 0.824 (95% CI: 0.782-0.855) combined with blood biochemical data. Overall, the human gut microbiome, including Alistipes and Bacteroides, was associated with the lipid profile and maternal dyslipidemia during pregnancy by perturbing inflammatory functional pathways. Gut microbiota combined with blood biochemical data at the mid-pregnancy stage could predict the risk of dyslipidemia in late pregnancy. Therefore, the gut microbiota may represent a potential noninvasive diagnostic and therapeutic strategy for preventing dyslipidemia in pregnancy.}, } @article {pmid37011797, year = {2023}, author = {Wang, L and Zhu, M and Li, Y and Zhao, Z}, title = {Assessing the effects of aquaculture on tidal flat ecological status using multi-metrics interaction-based index of biotic integrity (Mt-IBI).}, journal = {Environmental research}, volume = {228}, number = {}, pages = {115789}, doi = {10.1016/j.envres.2023.115789}, pmid = {37011797}, issn = {1096-0953}, mesh = {Humans ; *Ecosystem ; Benchmarking ; Environmental Monitoring/methods ; *Microbiota ; Nitrogen ; Aquaculture ; Rivers ; China ; }, abstract = {Given tidal flat special environmental conditions and the degree of pollution caused by human activities, there is an urgent need to quantitatively assess their ecological status. Bioindication has become an indispensable part of environmental quality monitoring on account of its sensitivity to environmental disturbance. Thus, this study used bio-indicators to establish a multi-metrics-based index of biotic integrity (Mt-IBI) to evaluate the ecological status of the tidal flats with/without aquaculture through metagenomic sequencing. Four core indexes that were significantly correlated to other indexes with redundancy (p < 0.05), including Escherichia, beta-lactam antibiotic resistance genes, cellulase and xyloglucanases and the keystone species with 21° in the network, were selected after the screening processes. By implementing Mt-IBI in the tidal flats, the ecological health of the sampling sites was categorized into three levels, with Mt-IBI values of 2.01-2.63 (severe level), 2.81-2.93 (moderate level) and 3.23-4.18 (mild level), respectively. Through SEM analysis, water chemical oxygen demand and antibiotics were determined to be the primary controlling factors of the ecological status of tidal flat regions influenced by aquaculture, followed by salinity and total nitrogen. It is worth noting that the alteration of microbial communities impacted ecological status through the mediation of antibiotics. It is hoped that the results of our study will provide a theoretical basis for coastal environment restoration and that the use of Mt-IBI to assess ecosystem status in different aquatic environments will be further popularized in the future.}, } @article {pmid37010966, year = {2023}, author = {Serbanescu, MA and Apple, CG and Fernandez-Moure, JS}, title = {Role of Resident Microbial Communities in Biofilm-Related Implant Infections: Recent Insights and Implications.}, journal = {Surgical infections}, volume = {24}, number = {3}, pages = {258-264}, pmid = {37010966}, issn = {1557-8674}, support = {T32 GM008600/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Staphylococcal Infections ; Biofilms ; Postoperative Complications ; *Microbiota ; Prostheses and Implants/adverse effects ; }, abstract = {The use of medical implants continues to grow as the population ages. Biofilm-related implant infection is the leading cause of medical implant failure and remains difficult to diagnose and treat. Recent technologies have enhanced our understanding of the composition and complex functions of microbiota occupying various body site niches. In this review, we leverage data from molecular sequencing technologies to explore how silent changes in microbial communities from various sites can influence the development of biofilm-related infections. Specifically, we address biofilm formation and recent insights of the organisms involved in biofilm-related implant infections; how composition of microbiomes from skin, nasopharyngeal, and nearby tissue can impact biofilm-formation, and infection; the role of the gut microbiome in implant-related biofilm formation; and therapeutic strategies to mitigate implant colonization.}, } @article {pmid37010293, year = {2023}, author = {Maranga, M and Szczerbiak, P and Bezshapkin, V and Gligorijevic, V and Chandler, C and Bonneau, R and Xavier, RJ and Vatanen, T and Kosciolek, T}, title = {Comprehensive Functional Annotation of Metagenomes and Microbial Genomes Using a Deep Learning-Based Method.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0117822}, pmid = {37010293}, issn = {2379-5077}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Metagenome/genetics ; *Deep Learning ; Molecular Sequence Annotation ; *Microbiota/genetics ; Genome, Microbial ; }, abstract = {Comprehensive protein function annotation is essential for understanding microbiome-related disease mechanisms in the host organisms. However, a large portion of human gut microbial proteins lack functional annotation. Here, we have developed a new metagenome analysis workflow integrating de novo genome reconstruction, taxonomic profiling, and deep learning-based functional annotations from DeepFRI. This is the first approach to apply deep learning-based functional annotations in metagenomics. We validate DeepFRI functional annotations by comparing them to orthology-based annotations from eggNOG on a set of 1,070 infant metagenomes from the DIABIMMUNE cohort. Using this workflow, we generated a sequence catalogue of 1.9 million nonredundant microbial genes. The functional annotations revealed 70% concordance between Gene Ontology annotations predicted by DeepFRI and eggNOG. DeepFRI improved the annotation coverage, with 99% of the gene catalogue obtaining Gene Ontology molecular function annotations, although they are less specific than those from eggNOG. Additionally, we constructed pangenomes in a reference-free manner using high-quality metagenome-assembled genomes (MAGs) and analyzed the associated annotations. eggNOG annotated more genes on well-studied organisms, such as Escherichia coli, while DeepFRI was less sensitive to taxa. Further, we show that DeepFRI provides additional annotations in comparison to the previous DIABIMMUNE studies. This workflow will contribute to novel understanding of the functional signature of the human gut microbiome in health and disease as well as guiding future metagenomics studies. IMPORTANCE The past decade has seen advancement in high-throughput sequencing technologies resulting in rapid accumulation of genomic data from microbial communities. While this growth in sequence data and gene discovery is impressive, the majority of microbial gene functions remain uncharacterized. The coverage of functional information coming from either experimental sources or inferences is low. To solve these challenges, we have developed a new workflow to computationally assemble microbial genomes and annotate the genes using a deep learning-based model DeepFRI. This improved microbial gene annotation coverage to 1.9 million metagenome-assembled genes, representing 99% of the assembled genes, which is a significant improvement compared to 12% Gene Ontology term annotation coverage by commonly used orthology-based approaches. Importantly, the workflow supports pangenome reconstruction in a reference-free manner, allowing us to analyze the functional potential of individual bacterial species. We therefore propose this alternative approach combining deep-learning functional predictions with the commonly used orthology-based annotations as one that could help us uncover novel functions observed in metagenomic microbiome studies.}, } @article {pmid37009964, year = {2023}, author = {Glidden, CK and Karakoç, C and Duan, C and Jiang, Y and Beechler, B and Jabbar, A and Jolles, AE}, title = {Distinct life history strategies underpin clear patterns of succession in microparasite communities infecting a wild mammalian host.}, journal = {Molecular ecology}, volume = {32}, number = {13}, pages = {3733-3746}, pmid = {37009964}, issn = {1365-294X}, support = {R01 GM126549/GM/NIGMS NIH HHS/United States ; R35 GM133439/GM/NIGMS NIH HHS/United States ; BB/L011085/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Biological Evolution ; Biota ; *Host-Parasite Interactions ; *Life History Traits ; Mammals ; *Parasites ; }, abstract = {Individual animals in natural populations tend to host diverse parasite species concurrently over their lifetimes. In free-living ecological communities, organismal life histories shape interactions with their environment, which ultimately forms the basis of ecological succession. However, the structure and dynamics of mammalian parasite communities have not been contextualized in terms of primary ecological succession, in part because few datasets track occupancy and abundance of multiple parasites in wild hosts starting at birth. Here, we studied community dynamics of 12 subtypes of protozoan microparasites (Theileria spp.) in a herd of African buffalo. We show that Theileria communities followed predictable patterns of succession underpinned by four different parasite life history strategies. However, in contrast to many free-living communities, network complexity decreased with host age. Examining parasite communities through the lens of succession may better inform the effect of complex within host eco-evolutionary dynamics on infection outcomes, including parasite co-existence through the lifetime of the host.}, } @article {pmid37009900, year = {2023}, author = {Mick, E and Tsitsiklis, A and Kamm, J and Kalantar, KL and Caldera, S and Lyden, A and Tan, M and Detweiler, AM and Neff, N and Osborne, CM and Williamson, KM and Soesanto, V and Leroue, M and Maddux, AB and Simões, EA and Carpenter, TC and Wagner, BD and DeRisi, JL and Ambroggio, L and Mourani, PM and Langelier, CR}, title = {Integrated host/microbe metagenomics enables accurate lower respiratory tract infection diagnosis in critically ill children.}, journal = {The Journal of clinical investigation}, volume = {133}, number = {7}, pages = {}, pmid = {37009900}, issn = {1558-8238}, support = {UG1 HD049983/HD/NICHD NIH HHS/United States ; UG1 HD050096/HD/NICHD NIH HHS/United States ; UG1 HD063108/HD/NICHD NIH HHS/United States ; R01 HL155418/HL/NHLBI NIH HHS/United States ; K23 HL138461/HL/NHLBI NIH HHS/United States ; U01 HD049934/HD/NICHD NIH HHS/United States ; UG1 HD049981/HD/NICHD NIH HHS/United States ; UG1 HD083170/HD/NICHD NIH HHS/United States ; UG1 HD083166/HD/NICHD NIH HHS/United States ; R01 HL124103/HL/NHLBI NIH HHS/United States ; UG1 HD083171/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; Child ; Metagenomics ; Critical Illness ; *Respiratory Tract Infections/diagnosis/microbiology ; Lung ; *Microbiota ; }, abstract = {BACKGROUNDLower respiratory tract infection (LRTI) is a leading cause of death in children worldwide. LRTI diagnosis is challenging because noninfectious respiratory illnesses appear clinically similar and because existing microbiologic tests are often falsely negative or detect incidentally carried microbes, resulting in antimicrobial overuse and adverse outcomes. Lower airway metagenomics has the potential to detect host and microbial signatures of LRTI. Whether it can be applied at scale and in a pediatric population to enable improved diagnosis and treatment remains unclear.METHODSWe used tracheal aspirate RNA-Seq to profile host gene expression and respiratory microbiota in 261 children with acute respiratory failure. We developed a gene expression classifier for LRTI by training on patients with an established diagnosis of LRTI (n = 117) or of noninfectious respiratory failure (n = 50). We then developed a classifier that integrates the host LRTI probability, abundance of respiratory viruses, and dominance in the lung microbiome of bacteria/fungi considered pathogenic by a rules-based algorithm.RESULTSThe host classifier achieved a median AUC of 0.967 by cross-validation, driven by activation markers of T cells, alveolar macrophages, and the interferon response. The integrated classifier achieved a median AUC of 0.986 and increased the confidence of patient classifications. When applied to patients with an uncertain diagnosis (n = 94), the integrated classifier indicated LRTI in 52% of cases and nominated likely causal pathogens in 98% of those.CONCLUSIONLower airway metagenomics enables accurate LRTI diagnosis and pathogen identification in a heterogeneous cohort of critically ill children through integration of host, pathogen, and microbiome features.FUNDINGSupport for this study was provided by the Eunice Kennedy Shriver National Institute of Child Health and Human Development and the National Heart, Lung, and Blood Institute (UG1HD083171, 1R01HL124103, UG1HD049983, UG01HD049934, UG1HD083170, UG1HD050096, UG1HD63108, UG1HD083116, UG1HD083166, UG1HD049981, K23HL138461, and 5R01HL155418) as well as by the Chan Zuckerberg Biohub.}, } @article {pmid37007517, year = {2023}, author = {Zhang, Y and Pan, D and Xiao, P and Xu, Q and Geng, F and Zhang, X and Zhou, X and Xu, H}, title = {A novel lytic polysaccharide monooxygenase from enrichment microbiota and its application for shrimp shell powder biodegradation.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1097492}, pmid = {37007517}, issn = {1664-302X}, abstract = {Lytic polysaccharide monooxygenases (LPMO) are expected to change the current status of chitin resource utilization. This study reports that targeted enrichment of the microbiota was performed with chitin by the selective gradient culture technique, and a novel LPMO (M2822) was identified from the enrichment microbiota metagenome. First, soil samples were screened based on soil bacterial species and chitinase biodiversity. Then gradient enrichment culture with different chitin concentrations was carried out. The efficiency of chitin powder degradation was increased by 10.67 times through enrichment, and chitin degradation species Chitiniphilus and Chitinolyticbacter were enriched significantly. A novel LPMO (M2822) was found in the metagenome of the enriched microbiota. Phylogenetic analysis showed that M2822 had a unique phylogenetic position in auxiliary activity (AA) 10 family. The analysis of enzymatic hydrolysate showed that M2822 had chitin activity. When M2822 synergized with commercial chitinase to degrade chitin, the yield of N-acetyl glycosamine was 83.6% higher than chitinase alone. The optimum temperature and pH for M2822 activity were 35°C and 6.0. The synergistic action of M2822 and chitin-degrading enzymes secreted by Chitiniphilus sp. LZ32 could efficiently hydrolyze shrimp shell powder. After 12 h of enzymatic hydrolysis, chitin oligosaccharides (COS) yield reached 4,724 μg/mL. To our knowledge, this work is the first study to mine chitin activity LPMO in the metagenome of enriched microbiota. The obtained M2822 showed application prospects in the efficient production of COS.}, } @article {pmid37004601, year = {2023}, author = {do Socorro Fôro Ramos, E and Bahia, SL and de Oliveira Ribeiro, G and Villanova, F and de Pádua Milagres, FA and Brustulin, R and Pandey, RP and Deng, X and Delwart, E and da Costa, AC and Leal, É}, title = {Characterization of Phietavirus Henu 2 in the virome of individuals with acute gastroenteritis.}, journal = {Virus genes}, volume = {59}, number = {3}, pages = {464-472}, pmid = {37004601}, issn = {1572-994X}, support = {302677/2019-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Humans ; *Methicillin-Resistant Staphylococcus aureus ; Virome ; *Bacteriophages ; *Siphoviridae ; *Gastroenteritis ; *Staphylococcal Infections/microbiology ; }, abstract = {There is a growing interest in phages as potential biotechnological tools in human health owing to the antibacterial activity of these viruses. In this study, we characterized a new member (named PhiV_005_BRA/2016) of the recently identified phage species Phietavirus Henu 2. PhiV_005_BRA/2016 was detected through metagenomic analysis of stool samples of individuals with acute gastroenteritis. PhiV_005_BRA/2016 contains double-stranded linear DNA (dsDNA), it has a genome of 43,513 base pairs (bp), with a high identity score (99%) with phage of the genus Phietavirus, species of Phietavirus Henu 2. Life style prediction indicated that PhiV_005_BRA/2016 is a lysogenic phage whose the main host is methicillin-resistant Staphylococcus aureus (MRSA). Indeed, we found PhiV_005_BRA/2016 partially integrated in the genome of distinct MRSA strains. Our findings highlights the importance of large-scale screening of bacteriophages to better understand the emergence of multi-drug resistant bacterial.}, } @article {pmid37004105, year = {2023}, author = {Yue, H and Yue, W and Jiao, S and Kim, H and Lee, YH and Wei, G and Song, W and Shu, D}, title = {Plant domestication shapes rhizosphere microbiome assembly and metabolic functions.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {70}, pmid = {37004105}, issn = {2049-2618}, mesh = {Domestication ; Rhizosphere ; Plant Roots/microbiology ; *Microbiota/genetics ; *Mycobiome ; Plants ; Bacteria/genetics ; Soil Microbiology ; }, abstract = {BACKGROUND: The rhizosphere microbiome, which is shaped by host genotypes, root exudates, and plant domestication, is crucial for sustaining agricultural plant growth. Despite its importance, how plant domestication builds up specific rhizosphere microbiomes and metabolic functions, as well as the importance of these affected rhizobiomes and relevant root exudates in maintaining plant growth, is not well understood. Here, we firstly investigated the rhizosphere bacterial and fungal communities of domestication and wild accessions of tetraploid wheat using amplicon sequencing (16S and ITS) after 9 years of domestication process at the main production sites in China. We then explored the ecological roles of root exudation in shaping rhizosphere microbiome functions by integrating metagenomics and metabolic genomics approaches. Furthermore, we established evident linkages between root morphology traits and keystone taxa based on microbial culture and plant inoculation experiments.

RESULTS: Our results suggested that plant rhizosphere microbiomes were co-shaped by both host genotypes and domestication status. The wheat genomes contributed more variation in the microbial diversity and composition of rhizosphere bacterial communities than fungal communities, whereas plant domestication status exerted much stronger influences on the fungal communities. In terms of microbial interkingdom association networks, domestication destabilized microbial network and depleted the abundance of keystone fungal taxa. Moreover, we found that domestication shifted the rhizosphere microbiome from slow growing and fungi dominated to fast growing and bacteria dominated, thereby resulting in a shift from fungi-dominated membership with enrichment of carbon fixation genes to bacteria-dominated membership with enrichment of carbon degradation genes. Metagenomics analyses further indicated that wild cultivars of wheat possess higher microbial function diversity than domesticated cultivars. Notably, we found that wild cultivar is able to harness rhizosphere microorganism carrying N transformation (i.e., nitrification, denitrification) and P mineralization pathway, whereas rhizobiomes carrying inorganic N fixation, organic N ammonification, and inorganic P solubilization genes are recruited by the releasing of root exudates from domesticated wheat. More importantly, our metabolite-wide association study indicated that the contrasting functional roles of root exudates and the harnessed keystone microbial taxa with different nutrient acquisition strategies jointly determined the aboveground plant phenotypes. Furthermore, we observed that although domesticated and wild wheats recruited distinct microbial taxa and relevant functions, domestication-induced recruitment of keystone taxa led to a consistent growth regulation of root regardless of wheat domestication status.

CONCLUSIONS: Our results indicate that plant domestication profoundly influences rhizosphere microbiome assembly and metabolic functions and provide evidence that host plants are able to harness a differentiated ecological role of root-associated keystone microbiomes through the release of root exudates to sustain belowground multi-nutrient cycles and plant growth. These findings provide valuable insights into the mechanisms underlying plant-microbiome interactions and how to harness the rhizosphere microbiome for crop improvement in sustainable agriculture. Video Abstract.}, } @article {pmid37003965, year = {2023}, author = {Syama, K and Jothi, JAA and Khanna, N}, title = {Automatic disease prediction from human gut metagenomic data using boosting GraphSAGE.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {126}, pmid = {37003965}, issn = {1471-2105}, mesh = {Humans ; Metagenome ; *Microbiota/genetics ; Machine Learning ; Metagenomics/methods ; *Inflammatory Bowel Diseases/genetics ; *Colorectal Neoplasms/genetics ; }, abstract = {BACKGROUND: The human microbiome plays a critical role in maintaining human health. Due to the recent advances in high-throughput sequencing technologies, the microbiome profiles present in the human body have become publicly available. Hence, many works have been done to analyze human microbiome profiles. These works have identified that different microbiome profiles are present in healthy and sick individuals for different diseases. Recently, several computational methods have utilized the microbiome profiles to automatically diagnose and classify the host phenotype.

RESULTS: In this work, a novel deep learning framework based on boosting GraphSAGE is proposed for automatic prediction of diseases from metagenomic data. The proposed framework has two main components, (a). Metagenomic Disease graph (MD-graph) construction module, (b). Disease prediction Network (DP-Net) module. The graph construction module constructs a graph by considering each metagenomic sample as a node in the graph. The graph captures the relationship between the samples using a proximity measure. The DP-Net consists of a boosting GraphSAGE model which predicts the status of a sample as sick or healthy. The effectiveness of the proposed method is verified using real and synthetic datasets corresponding to diseases like inflammatory bowel disease and colorectal cancer. The proposed model achieved a highest AUC of 93%, Accuracy of 95%, F1-score of 95%, AUPRC of 95% for the real inflammatory bowel disease dataset and a best AUC of 90%, Accuracy of 91%, F1-score of 87% and AUPRC of 93% for the real colorectal cancer dataset.

CONCLUSION: The proposed framework outperforms other machine learning and deep learning models in terms of classification accuracy, AUC, F1-score and AUPRC for both synthetic and real metagenomic data.}, } @article {pmid37003055, year = {2023}, author = {Jamal, R and Messaoudene, M and de Figuieredo, M and Routy, B}, title = {Future indications and clinical management for fecal microbiota transplantation (FMT) in immuno-oncology.}, journal = {Seminars in immunology}, volume = {67}, number = {}, pages = {101754}, doi = {10.1016/j.smim.2023.101754}, pmid = {37003055}, issn = {1096-3618}, support = {//CIHR/Canada ; }, mesh = {Humans ; Animals ; Mice ; Fecal Microbiota Transplantation/adverse effects ; Immune Checkpoint Inhibitors ; Treatment Outcome ; *Microbiota ; *Neoplasms/therapy/etiology ; }, abstract = {The gut microbiota has rapidly emerged as one of the "hallmarks of cancers" and a key contributor to cancer immunotherapy. Metagenomics profiling has established the link between microbiota compositions and immune checkpoint inhibitors response and toxicity, while murine experiments demonstrating the synergistic benefits of microbiota modification with immune checkpoint inhibitors (ICIs) pave a clear path for translation. Fecal microbiota transplantation (FMT) is one of the most effective treatments for patients with Clostridioides difficile, but its utility in other disease contexts has been limited. Nonetheless, promising data from the first trials combining FMT with ICIs have provided strong clinical rationale to pursue this strategy as a novel therapeutic avenue. In addition to the safety considerations surrounding new and emerging pathogens potentially transmissible by FMT, several other challenges must be overcome in order to validate the use of FMT as a therapeutic option in oncology. In this review, we will explore how the lessons learned from FMT in other specialties will help shape the design and development of FMT in the immuno-oncology arena.}, } @article {pmid37002975, year = {2023}, author = {Stockdale, SR and Hill, C}, title = {Incorporating plasmid biology and metagenomics into a holistic model of the human gut microbiome.}, journal = {Current opinion in microbiology}, volume = {73}, number = {}, pages = {102307}, doi = {10.1016/j.mib.2023.102307}, pmid = {37002975}, issn = {1879-0364}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Plasmids/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Metagenomics ; }, abstract = {The human gut microbiome is often described as the collection of bacteria, archaea, fungi, protists, and viruses associated with an individual, with no acknowledgement of the plasmid constituents. However, like viruses, plasmids are autonomous intracellular replicating entities that can influence the genotype and phenotype of their host and mediate trans-kingdom interactions. Plasmids are frequently noted as vehicles for horizontal gene transfer and for spreading antibiotic resistance, yet their multifaceted contribution to mutualistic and antagonistic interactions within the human microbiome and impact on human health is overlooked. In this review, we highlight the importance of plasmids and their biological properties as overlooked components of microbiomes. Subsequent human microbiome studies should include dedicated analyses of plasmids, particularly as a holistic understanding of human-microbial interactions is required before effective and safe interventions can be implemented to improve human well-being.}, } @article {pmid37002522, year = {2023}, author = {Wagh, MS and Sivarajan, S and Osborne, WJ}, title = {A new paradigm in the bioremoval of lead, nickel, and cadmium using a cocktail of biosystems: a metagenomic approach.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {20}, pages = {58967-58985}, pmid = {37002522}, issn = {1614-7499}, mesh = {Animals ; Cadmium/analysis ; Nickel/analysis ; Lead/analysis ; RNA, Ribosomal, 16S ; *Metals, Heavy/analysis ; Biodegradation, Environmental ; *Microbiota ; Bacteria ; Soil/chemistry ; *Oligochaeta ; *Soil Pollutants/analysis ; }, abstract = {Lead (Pb), nickel (Ni), and cadmium (Cd) are known for its harmful effects on the environment. Microbial community related to soil plays a pivotal role in configuring several properties of the ecosystem. Thus, remediation of such heavy metals using multiple biosystems had shown excellent bioremoval potential. The current study demonstrates the integrated approach of Chrysopogon zizanioides in combination with earthworm Eisenia fetida augmented with VITMSJ3 potent strain for the uptake of metals like Pb, Ni, and Cd from the contaminated soil. For the uptake of heavy metals, Pb, Ni, and Cd with the concentrations of 50, 100, and 150 mg kg[-1] were supplemented in pots with plants and earthworms. C. zizanioides was used for bioremoval due to their massive fibrous root system which can absorb heavy metals. A substantial increase of 70-80% Pb, Ni, and Cd was found for VITMSJ3 augmented setup. A total of 12 earthworms were introduced in each setup and were tested for the toxicity and damages in the various internal structures. Reduction in malondialdehyde (MDA) content was observed in the earthworms with VITMSJ3 strain proving less toxicity and damages. Metagenomic analysis of the soil associated bacterial diversity was assessed by amplifying the V3V4 region of the 16S rRNA gene and the annotations were studied. Firmicutes were found to be the predominant genus with 56.65% abundance in the bioaugmented soil R (60) proving the detoxification of metals in the bioaugmented soil. Our study proved that a synergistic effect of plant and earthworm in association with potent bacterial strain had higher uptake of Pb, Ni, and Cd. Metagenomic analysis revealed the changes in microbial abundance in the soil before and after treatment.}, } @article {pmid37001916, year = {2023}, author = {Magner, C and Jenkins, D and Koc, F and Tan, MH and O'Toole, M and Boyle, J and Maguire, N and Duignan, S and Murphy, K and Ross, P and Stanton, C and McMahon, CJ}, title = {Protocol for a prospective cohort study exploring the gut microbiota of infants with congenital heart disease undergoing cardiopulmonary bypass (the GuMiBear study).}, journal = {BMJ open}, volume = {13}, number = {3}, pages = {e067016}, pmid = {37001916}, issn = {2044-6055}, mesh = {Infant, Newborn ; Infant ; Humans ; Child ; *Gastrointestinal Microbiome ; Cardiopulmonary Bypass ; Prospective Studies ; *Heart Defects, Congenital/surgery ; *Cardiac Surgical Procedures ; }, abstract = {INTRODUCTION: The gut microbiota develops from birth and matures significantly during the first 24 months of life, playing a major role in infant health and development. The composition of the gut microbiota is influenced by several factors including mode of delivery, gestational age, feed type and treatment with antibiotics. Alterations in the pattern of gut microbiota development and composition can be associated with illness and compromised health outcomes.Infants diagnosed with 'congenital heart disease' (CHD) often require surgery involving cardiopulmonary bypass (CPB) early in life. The impact of this type of surgery on the integrity of the gut microbiome is poorly understood. In addition, these infants are at significant risk of developing the potentially devastating intestinal condition necrotising enterocolitis.

METHODS AND ANALYSIS: This study will employ a prospective cohort study methodology to investigate the gut microbiota and urine metabolome of infants with CHD undergoing surgery involving CPB. Stool and urine samples, demographic and clinical data will be collected from eligible infants based at the National Centre for Paediatric Cardiac Surgery in Ireland. Shotgun metagenome sequencing will be performed on stool samples and urine metabolomic analysis will identify metabolic biomarkers. The impact of the underlying diagnosis, surgery involving CPB, and the influence of environmental factors will be explored. Data from healthy age-matched infants from the INFANTMET study will serve as a control for this study.

ETHICS AND DISSEMINATION: This study has received full ethical approval from the Clinical Research Ethics Committee of Children's Health Ireland, GEN/826/20.}, } @article {pmid37001571, year = {2023}, author = {Song, C and Ma, Y and Wang, Y and Li, P and Chen, Y and Liu, H and Zhang, Z}, title = {Diosgenin reduces bone loss through the regulation of gut microbiota in ovariectomized rats.}, journal = {Gene}, volume = {869}, number = {}, pages = {147383}, doi = {10.1016/j.gene.2023.147383}, pmid = {37001571}, issn = {1879-0038}, mesh = {Female ; Rats ; Animals ; Humans ; Rats, Sprague-Dawley ; Bone Density ; *Gastrointestinal Microbiome ; *Diosgenin/pharmacology/therapeutic use ; *Bone Diseases, Metabolic ; *Osteoporosis/drug therapy/metabolism ; Estradiol/pharmacology ; Ovariectomy ; }, abstract = {Diosgenin (DIO) is an aglycone of steroid saponins acquired from plants, including Dioscorea alata, Smilax China, and Trigonella foenum graecum, acting as an anti-osteoporosis, anti-diabetic, anti-hyperlipidemic, anti-inflammatory. Recent studies have demonstrated that DIO reduces bone loss. This study aimed to investigate the effects of DIO on the gut microbiota (GM) of ovariectomized (OVX) osteoporotic rats. Female Sprague-Dawley rats were randomly divided into sham operation (sham + vehicle group) or ovariectomy. For 12 weeks, OVX rats were treated using a vehicle (OVX + vehicle group) and DIO (OVX + DIO group). Subsequently, ELISA was conducted to determine serum estradiol levels, micro-CT scanning was performed to evaluate bone quality, and feces were collected for metagenomics sequencing to examine the structure and function of GM. Raw reads were filtered to remove chimera sequences. Operational taxonomic units (OTUs) were clustered in the filtered reads. A Venn diagram analysis was conducted to study the common and unique OTUs in the sham + vehicle, OVX + vehicle, and OVX + DIO groups. LEfSe analysis was conducted to evaluate the specific GM of the three groups. The GM functions were analyzed using the KEGG and CAZy databases. After a 12-week treatment, DIO administration prevented OVX-induced weight gain and increased the estradiol levels. DIO treatment improved the bone microstructure and structural parameters of rat tibias. Metagenomics sequencing results identified 1139, 1207, and 1235 operational taxonomic units (OTUs) in the sham + vehicle, OVX + vehicle, and OVX + DIO groups, respectively. The percentage of common OTUs was 41.2%. Treatment with DIO restored the composition of GM in OVX rats by increasing the abundance of Coriobacteriia Adlercreutzia, Romboutsia, and Romboutsia_idealis and reducing the abundance of Betaproteobacteria, Gammaproteobacteria, Methanobacteria, Bacteroides, Phocaeicola, Alistipes, Bacteroids_uniformis, Bacteroids_xylanisolvens. The anti-osteoporosis effect of DIO can be regulated through environmental information processing, organismal Systems, Cellular Processes, human diseases, metabolism, and genetic information processing. Meanwhile, treatment with DIO improved GM homeostasis by increasing the metabolism of carbohydrates, other amino acids, and glycans and reducing translation, energy metabolism, and nucleotide metabolism. DIO can reduce bone loss by regulating the structural composition and function of GM, a novel strategy for preventing osteoporosis.}, } @article {pmid37000389, year = {2024}, author = {Ganesan, R and Gupta, H and Jeong, JJ and Sharma, SP and Won, SM and Oh, KK and Yoon, SJ and Han, SH and Yang, YJ and Baik, GH and Bang, CS and Kim, DJ and Suk, KT}, title = {Characteristics of microbiome-derived metabolomics according to the progression of alcoholic liver disease.}, journal = {Hepatology international}, volume = {18}, number = {2}, pages = {486-499}, pmid = {37000389}, issn = {1936-0541}, support = {NRF-2018M3A9F3020956//Ministry of National Defense/ ; NRF-2019R1I1A3A01060447//Ministry of National Defense/ ; NRF-2020R1A6A1A03043026//Ministry of National Defense/ ; P0020622//Korea Institute for Advancement of Technology/ ; }, mesh = {Humans ; Propionates ; RNA, Ribosomal, 16S/genetics ; *Liver Diseases, Alcoholic ; Liver Cirrhosis, Alcoholic ; *Gastrointestinal Microbiome ; Indoles ; Bile Acids and Salts ; }, abstract = {BACKGROUND AND AIM: The prevalence and severity of alcoholic liver disease (ALD) are increasing. The incidence of alcohol-related cirrhosis has risen up to 2.5%. This study aimed to identify novel metabolite mechanisms involved in the development of ALD in patients. The use of gut microbiome-derived metabolites is increasing in targeted therapies. Identifying metabolic compounds is challenging due to the complex patterns that have long-term effects on ALD. We investigated the specific metabolite signatures in ALD patients.

METHODS: This study included 247 patients (heathy control, HC: n = 62, alcoholic fatty liver, AFL; n = 25, alcoholic hepatitis, AH; n = 80, and alcoholic cirrhosis, AC, n = 80) identified, and stool samples were collected. 16S rRNA sequencing and metabolomics were performed with MiSeq sequencer and liquid chromatography coupled to time-of-flight-mass spectrometry (LC-TOF-MS), respectively. The untargeted metabolites in AFL, AH, and AC samples were evaluated by multivariate statistical analysis and metabolic pathotypic expression. Metabolic network classifiers were used to predict the pathway expression of the AFL, AH, and AC stages.

RESULTS: The relative abundance of Proteobacteria was increased and the abundance of Bacteroides was decreased in ALD samples (p = 0.001) compared with that in HC samples. Fusobacteria levels were higher in AH samples (p = 0.0001) than in HC samples. Untargeted metabolomics was applied to quantitatively screen 103 metabolites from each stool sample. Indole-3-propionic acid levels are significantly lower in AH and AC (vs. HC, p = 0.001). Indole-3-lactic acid (ILA: p = 0.04) levels were increased in AC samples. AC group showed an increase in indole-3-lactic acid (vs. HC, p = 0.040) level. Compared with that in HC samples, the levels of short-chain fatty acids (SCFAs: acetic acid, butyric acid, propionic acid, iso-butyric acid, and iso-valeric acid) and bile acids (lithocholic acids) were significantly decreased in AC. The pathways of linoleic acid metabolism, indole compounds, histidine metabolism, fatty acid degradation, and glutamate metabolism were closely associated with ALD metabolism.

CONCLUSIONS: This study identified that microbial metabolic dysbiosis is associated with ALD-related metabolic dysfunction. The SCFAs, bile acids, and indole compounds were depleted during ALD progression.

CLINICAL TRIAL: Clinicaltrials.gov, number NCT04339725.}, } @article {pmid36998174, year = {2023}, author = {Ru, J and Khan Mirzaei, M and Xue, J and Peng, X and Deng, L}, title = {ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2192522}, pmid = {36998174}, issn = {1949-0984}, mesh = {Software ; *Gastrointestinal Microbiome ; Reproducibility of Results ; Metagenome ; *Microbiota ; Metagenomics/methods ; Computational Biology/methods ; Data Analysis ; }, abstract = {Bacteriophages play central roles in the maintenance and function of most ecosystems by regulating bacterial communities. Yet, our understanding of their diversity remains limited due to the lack of robust bioinformatics standards. Here we present ViroProfiler, an in-silico workflow for analyzing shotgun viral metagenomic data. ViroProfiler can be executed on a local Linux computer or cloud computing environments. It uses the containerization technique to ensure computational reproducibility and facilitate collaborative research. ViroProfiler is freely available at https://github.com/deng-lab/viroprofiler.}, } @article {pmid36997838, year = {2023}, author = {Jacky, D and Bibi, C and Meng, LMC and Jason, F and Gwendoline, T and Jeremy, L and Wie, CC}, title = {Effects of OsomeFood Clean Label plant-based meals on the gut microbiome.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {88}, pmid = {36997838}, issn = {1471-2180}, mesh = {Humans ; *Gastrointestinal Microbiome ; Overweight ; Feces/microbiology ; Diet ; Meals ; }, abstract = {BACKGROUND: Plant-based diets offer more beneficial microbes and can modulate gut microbiomes to improve human health. We evaluated the effects of the plant-based OsomeFood Clean Label meal range ('AWE' diet), on the human gut microbiome.

METHODS: Over 21 days, ten healthy participants consumed OsomeFood meals for five consecutive weekday lunches and dinners and resumed their regular diets for other days/meals. On follow-up days, participants completed questionnaires to record satiety, energy and health, and provided stool samples. To document microbiome variations and identify associations, species and functional pathway annotations were analyzed by shotgun sequencing. Shannon diversity and regular diet calorie intake subsets were also assessed.

RESULTS: Overweight participants gained more species and functional pathway diversity than normal BMI participants. Nineteen disease-associated species were suppressed in moderate-responders without gaining diversity, and in strong-responders with diversity gains along with health-associated species. All participants reported improved short-chain fatty acids production, insulin and γ-aminobutyric acid signaling. Moreover, fullness correlated positively with Bacteroides eggerthii; energetic status with B. uniformis, B. longum, Phascolarctobacterium succinatutens, and Eubacterium eligens; healthy status with Faecalibacterium prausnitzii, Prevotella CAG 5226, Roseburia hominis, and Roseburia sp. CAG 182; and overall response with E. eligens and Corprococcus eutactus. Fiber consumption was negatively associated with pathogenic species.

CONCLUSION: Although the AWE diet was consumed for only five days a week, all participants, especially overweight ones, experienced improved fullness, health status, energy and overall responses. The AWE diet benefits all individuals, especially those of higher BMI or low-fiber consumption.}, } @article {pmid36996985, year = {2023}, author = {Yan, S and Zhang, Z and Wang, J and Xia, Y and Chen, S and Xie, S}, title = {River sediment microbial community composition and function impacted by thallium spill.}, journal = {The Science of the total environment}, volume = {880}, number = {}, pages = {163101}, doi = {10.1016/j.scitotenv.2023.163101}, pmid = {36996985}, issn = {1879-1026}, mesh = {Humans ; *Thallium/analysis ; Rivers ; Metals/analysis ; *Microbiota ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Anti-Bacterial Agents ; }, abstract = {Thallium (Tl) is widely used in various industries, which increases the risk of leakage into the environment. Since Tl is highly toxic, it can do a great harm to human health and ecosystem. In order to explore the response of freshwater sediment microorganisms to sudden Tl spill, metagenomic technique was used to elucidate the changes of microbial community composition and functional genes in river sediments. Tl pollution could have profound impacts on microbial community composition and function. Proteobacteria remained the dominance in contaminated szediments, indicating that it had a strong resistance to Tl contamination, and Cyanobacteria also showed a certain resistance. Tl pollution also had a certain screening effect on resistance genes and affected the abundance of resistance genes. Metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) were enriched at the site near the spill site, where Tl concentration was relatively low among polluted sites. When Tl concentration was higher, the screening effect was not obvious and the resistance genes even became lower. Moreover, there was a significant correlation between MRGs and ARGs. In addition, co-occurrence network analysis showed that Sphingopyxis had the most links with resistance genes, indicating that it was the biggest potential host of resistance genes. This study provided new insight towards the shifts in the composition and function of microbial communities after sudden serious Tl contamination.}, } @article {pmid36996123, year = {2023}, author = {Ostenfeld, LJ and Munk, P and Aarestrup, FM and Otani, S}, title = {Detection of specific uncultured bacteriophages by fluorescence in situ hybridisation in pig microbiome.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0283676}, pmid = {36996123}, issn = {1932-6203}, mesh = {Animals ; Bacteria/genetics ; *Bacteriophages/genetics ; Fluorescence ; Metagenome ; *Microbiota ; Swine ; }, abstract = {Microbial communities have huge impacts on their ecosystems and local environments spanning from marine and soil communities to the mammalian gut. Bacteriophages (phages) are important drivers of population control and diversity in the community, but our understanding of complex microbial communities is halted by biased detection techniques. Metagenomics have provided a method of novel phage discovery independent of in vitro culturing techniques and have revealed a large proportion of understudied phages. Here, five jumbophage genomes, that were previously assembled in silico from pig faecal metagenomes, are detected and observed directly in their natural environment using a modified phageFISH approach, and combined with methods to decrease bias against large-sized phages (e.g., jumbophages). These phages are uncultured with unknown hosts. The specific phages were detected by PCR and fluorescent in situ hybridisation in their original faecal samples as well as across other faecal samples. Co-localisation of bacterial signals and phage signals allowed detection of the different stages of phage life cycle. All phages displayed examples of early infection, advanced infection, burst, and free phages. To our knowledge, this is the first detection of jumbophages in faeces, which were investigated independently of culture, host identification, and size, and based solely on the genome sequence. This approach opens up opportunities for characterisation of novel in silico phages in vivo from a broad range of gut microbiomes.}, } @article {pmid36995244, year = {2023}, author = {Herviou, P and Balvay, A and Bellet, D and Bobet, S and Maudet, C and Staub, J and Alric, M and Leblond-Bourget, N and Delorme, C and Rabot, S and Denis, S and Payot, S}, title = {Transfer of the Integrative and Conjugative Element ICESt3 of Streptococcus thermophilus in Physiological Conditions Mimicking the Human Digestive Ecosystem.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0466722}, pmid = {36995244}, issn = {2165-0497}, mesh = {Animals ; Mice ; Humans ; *Streptococcus thermophilus/genetics ; Conjugation, Genetic ; Gastrointestinal Tract ; Gene Transfer, Horizontal ; *Microbiota ; }, abstract = {Metagenome analyses of the human microbiome suggest that horizontal gene transfer (HGT) is frequent in these rich and complex microbial communities. However, so far, only a few HGT studies have been conducted in vivo. In this work, three different systems mimicking the physiological conditions encountered in the human digestive tract were tested, including (i) the TNO gastro-Intestinal tract Model 1 (TIM-1) system (for the upper part of the intestine), (ii) the ARtificial COLon (ARCOL) system (to mimic the colon), and (iii) a mouse model. To increase the likelihood of transfer by conjugation of the integrative and conjugative element studied in the artificial digestive systems, bacteria were entrapped in alginate, agar, and chitosan beads before being placed in the different gut compartments. The number of transconjugants detected decreased, while the complexity of the ecosystem increased (many clones in TIM-1 but only one clone in ARCOL). No clone was obtained in a natural digestive environment (germfree mouse model). In the human gut, the richness and diversity of the bacterial community would offer more opportunities for HGT events to occur. In addition, several factors (SOS-inducing agents, microbiota-derived factors) that potentially increase in vivo HGT efficiency were not tested here. Even if HGT events are rare, expansion of the transconjugant clones can happen if ecological success is fostered by selecting conditions or by events that destabilize the microbial community. IMPORTANCE The human gut microbiota plays a key role in maintaining normal host physiology and health, but its homeostasis is fragile. During their transit in the gastrointestinal tract, bacteria conveyed by food can exchange genes with resident bacteria. New traits acquired by HGT (e.g., new catabolic properties, bacteriocins, antibiotic resistance) can impact the gut microbial composition and metabolic potential. We showed here that TIM-1, a system mimicking the upper digestive tract, is a useful tool to evaluate HGT events in conditions closer to the physiological ones. Another important fact pointed out in this work is that Enterococcus faecalis is a good candidate for foreign gene acquisition. Due to its high ability to colonize the gut and acquire mobile genetic elements, this commensal bacterium could serve as an intermediate for HGT in the human gut.}, } @article {pmid36995238, year = {2023}, author = {Zhao, X and Sun, C and Jin, M and Chen, J and Xing, L and Yan, J and Wang, H and Liu, Z and Chen, WH}, title = {Enrichment Culture but Not Metagenomic Sequencing Identified a Highly Prevalent Phage Infecting Lactiplantibacillus plantarum in Human Feces.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0434022}, pmid = {36995238}, issn = {2165-0497}, mesh = {Humans ; *Bacteriophages/classification/genetics/isolation & purification ; *Feces/microbiology/virology ; *Lactobacillus plantarum/virology ; Metagenomics ; Culture Techniques ; Genome, Viral/genetics ; Biodiversity ; }, abstract = {Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum) is increasingly used as a probiotic to treat human diseases, but its phages in the human gut remain unexplored. Here, we report its first gut phage, Gut-P1, which we systematically screened using metagenomic sequencing, virus-like particle (VLP) sequencing, and enrichment culture from 35 fecal samples. Gut-P1 is virulent, belongs to the Douglaswolinvirus genus, and is highly prevalent in the gut (~11% prevalence); it has a genome of 79,928 bp consisting of 125 protein coding genes and displaying low sequence similarities to public L. plantarum phages. Physiochemical characterization shows that it has a short latent period and adapts to broad ranges of temperatures and pHs. Furthermore, Gut-P1 strongly inhibits the growth of L. plantarum strains at a multiplicity of infection (MOI) of 1e-6. Together, these results indicate that Gut-P1 can greatly impede the application of L. plantarum in humans. Strikingly, Gut-P1 was identified only in the enrichment culture, not in our metagenomic or VLP sequencing data nor in any public human phage databases, indicating the inefficiency of bulk sequencing in recovering low-abundance but highly prevalent phages and pointing to the unexplored hidden diversity of the human gut virome despite recent large-scale sequencing and bioinformatics efforts. IMPORTANCE As Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum) is increasingly used as a probiotic to treat human gut-related diseases, its bacteriophages may pose a certain threat to their further application and should be identified and characterized more often from the human intestine. Here, we isolated and identified the first gut L. plantarum phage that is prevalent in a Chinese population. This phage, Gut-P1, is virulent and can strongly inhibit the growth of multiple L. plantarum strains at low MOIs. Our results also show that bulk sequencing is inefficient at recovering low-abundance but highly prevalent phages such as Gut-P1, suggesting that the hidden diversity of human enteroviruses has not yet been explored. Our results call for innovative approaches to isolate and identify intestinal phages from the human gut and to rethink our current understanding of the enterovirus, particularly its underestimated diversity and overestimated individual specificity.}, } @article {pmid36993556, year = {2023}, author = {Fogarty, EC and Schechter, MS and Lolans, K and Sheahan, ML and Veseli, I and Moore, R and Kiefl, E and Moody, T and Rice, PA and Yu, MK and Mimee, M and Chang, EB and Mclellan, SL and Willis, AD and Comstock, LE and Eren, AM}, title = {A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36993556}, issn = {2692-8205}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; RC2 DK122394/DK/NIDDK NIH HHS/United States ; }, abstract = {Plasmids are extrachromosomal genetic elements that often encode fitness enhancing features. However, many bacteria carry 'cryptic' plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes, and is 14 times as numerous as crAssphage, currently established as the most abundant genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales and although it does not appear to impact bacterial host fitness in vivo, can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an inexpensive alternative for detecting human colonic inflammatory states.}, } @article {pmid36992458, year = {2023}, author = {Chen, Z and Zhao, H and Li, Z and Huang, M and Si, N and Zhao, H and Wei, X and Sun, B and Gao, GF and Xu, Z and Liu, WJ}, title = {First Discovery of Phenuiviruses within Diverse RNA Viromes of Asiatic Toad (Bufo gargarizans) by Metagenomics Sequencing.}, journal = {Viruses}, volume = {15}, number = {3}, pages = {}, pmid = {36992458}, issn = {1999-4915}, mesh = {Animals ; RNA ; Metagenomics ; Phylogeny ; Virome ; *RNA Viruses/genetics ; Bufonidae/genetics ; *Picornaviridae/genetics ; Mammals ; *Astroviridae/genetics ; Rodentia ; Genome, Viral ; }, abstract = {Most zoonotic pathogens originate from mammals and avians, but viral diversity and related biosafety risk assessment in lower vertebrates also need to be explored. Amphibians are an important group of lower vertebrates that played a momentous role in animal evolution. To elucidate the diversity of RNA viruses in one important species of amphibians, the Asiatic toad (Bufo gargarizans), we obtained 44 samples including lung, gut, liver, and kidney tissues from Asiatic toads in Sichuan and Jilin provinces, China, for viral metagenomics sequencing. More than 20 novel RNA viruses derived from the order Bunyavirales and 7 families of Astroviridae, Dicistroviridae, Leviviridae, Partitiviridae, Picornaviridae, Rhabdoviridae, and Virgaviridae were discovered, which were distinct from previously described viruses and formed new clusters, as revealed by phylogenetic analyses. Notably, a novel bastrovirus, AtBastV/GCCDC11/2022, of the family Astroviridae was identified from the gut library, the genome of which contains three open reading frames, with the RNA-dependent RNA polymerase (RdRp) coded by ORF1 closely related to that of hepeviruses, and ORF2 encoding an astrovirus-related capsid protein. Notably, phenuiviruses were discovered for the first time in amphibians. AtPhenV1/GCCDC12/2022 and AtPhenV2/GCCDC13/2022 clustered together and formed a clade with the group of phenuiviruses identified from rodents. Picornaviruses and several invertebrate RNA viruses were also detected. These findings improve our understanding of the high RNA viral diversity in the Asiatic toad and provide new insights in the evolution of RNA viruses in amphibians.}, } @article {pmid36992315, year = {2023}, author = {Ramos, EDSF and Abreu, WU and Rodrigues, LRR and Marinho, LF and Morais, VDS and Villanova, F and Pandey, RP and Araújo, ELL and Deng, X and Delwart, E and da Costa, AC and Leal, E}, title = {Novel Chaphamaparvovirus in Insectivorous Molossus molossus Bats, from the Brazilian Amazon Region.}, journal = {Viruses}, volume = {15}, number = {3}, pages = {}, pmid = {36992315}, issn = {1999-4915}, mesh = {Animals ; *Chiroptera ; Phylogeny ; Brazil/epidemiology ; Mammals ; *Parvovirus ; }, abstract = {Chaphamaparvovirus (CHPV) is a recently characterized genus of the Parvoviridae family whose members can infect different hosts, including bats, which constitute the second most diverse order of mammals and are described worldwide as important transmitters of zoonotic diseases. In this study, we identified a new CHPV in bat samples from the municipality of Santarém (Pará state, North Brazil). A total of 18 Molossus molossus bats were analyzed using viral metagenomics. In five animals, we identified CHPVs. These CHPV sequences presented the genome with a size ranging from 3797 to 4284 bp. Phylogenetic analysis-based nucleotide and amino acid sequences of the VP1 and NS1 regions showed that all CHPV sequences are monophyletic. They are also closely related to CHPV sequences previously identified in bats in southern and southeast Brazil. According to the International Committee on Taxonomy of Viruses (ICTV) classification criteria for this species (the CHPV NS1 gene region must have 85% identity to be classified in the same species), our sequences are likely a new specie within the genus Chaphamaparvovirus, since they have less than 80% identity with other CHPV described earlier in bats. We also make some phylogenetic considerations about the interaction between CHPV and their host. We suggest a high level of specificity of CPHV and its hosts. Thus, the findings contribute to improving information about the viral diversity of parvoviruses and show the importance of better investigating bats, considering that they harbor a variety of viruses that may favor zoonotic events.}, } @article {pmid36990340, year = {2023}, author = {Qin, G and Zhang, Q and Zhang, Z and Chen, Y and Zhu, J and Yang, Y and Peijnenburg, WJGM and Qian, H}, title = {Understanding the ecological effects of the fungicide difenoconazole on soil and Enchytraeus crypticus gut microbiome.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {326}, number = {}, pages = {121518}, doi = {10.1016/j.envpol.2023.121518}, pmid = {36990340}, issn = {1873-6424}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Fungicides, Industrial/pharmacology ; Soil/chemistry ; *Pesticides/toxicity ; Bacteria ; *Oligochaeta ; *Soil Pollutants/analysis ; }, abstract = {Increasing knowledge of the impacts of pesticides on soil ecological communities is fundamental to a comprehensive understanding of the functional changes in the global agroecosystem industry. In this study, we examined microbial community shifts in the gut of the soil-dwelling organism Enchytraeus crypticus and functional shifts in the soil microbiome (bacteria and viruses) after 21 d of exposure to difenoconazole, one of the main fungicides in intensified agriculture. Our results demonstrated reduced body weight and increased oxidative stress levels of E. crypticus under difenoconazole treatment. Meanwhile, difenoconazole not only altered the composition and structure of the gut microbial community, but also interfered with the soil-soil fauna microecology stability by impairing the abundance of beneficial bacteria. Using soil metagenomics, we revealed that bacterial genes encoding detoxification and viruses encoding carbon cycle genes exhibited a dependent enrichment in the toxicity of pesticides via metabolism. Taken together, these findings advance the understanding of the ecotoxicological impact of residual difenoconazole on the soil-soil fauna micro-ecology, and the ecological importance of virus-encoded auxiliary metabolic genes under pesticide stress.}, } @article {pmid36990166, year = {2023}, author = {Yang, H and Wu, C and Chen, L and Chang, X and Luo, G and Wu, K and Tian, W}, title = {A. macrocephala polysaccharide induces alterations to gut microbiome and serum metabolome in constipated mice.}, journal = {Microbial pathogenesis}, volume = {178}, number = {}, pages = {106084}, doi = {10.1016/j.micpath.2023.106084}, pmid = {36990166}, issn = {1096-1208}, mesh = {Mice ; Animals ; *Gastrointestinal Microbiome ; Tryptophan ; Constipation/metabolism ; Polysaccharides/pharmacology ; Metabolome ; }, abstract = {Atractylodes macrocephala polysaccharide (AC1) is extracted from the root of the Chinese herb Atractylodes Macrocephala and is used in the treatment of constipation due to its effects on strengthening cellular immunity and regulating intestinal function. In this study, Metagenomics and Metabolomic are used to analyze the effects of AC1 on the gut microbiota and host metabolites in mice models of constipation. The results show that the abundance of Lachnospiraceae_bacterium_A4, Bact-oides_vulgatus and Prevotella_sp_CAG:891 increased significantly, indicating that AC1-targeted strain modulation effectively alleviated the dysbiosis of the gut microbiota. Besides, the microbial alterations also influenced the metabolic pathways of the mice, including tryptophan metabolism, unsaturated fatty acid synthesis and bile acid metabolism. The physiological parameters of the mice treated with AC1 are improved, such as tryptophan in the colon, 5-hydroxytryptamine (5-HT) and short-chain fatty acids (SCFAs). In conclusion, AC1 as a probiotic can regulate intestinal flora to normal levels and achieve the effect of treating constipation.}, } @article {pmid36989799, year = {2023}, author = {Calderón-Franco, D and Corbera-Rubio, F and Cuesta-Sanz, M and Pieterse, B and de Ridder, D and van Loosdrecht, MCM and van Halem, D and Laureni, M and Weissbrodt, DG}, title = {Microbiome, resistome and mobilome of chlorine-free drinking water treatment systems.}, journal = {Water research}, volume = {235}, number = {}, pages = {119905}, doi = {10.1016/j.watres.2023.119905}, pmid = {36989799}, issn = {1879-2448}, mesh = {*Drinking Water/analysis ; Angiotensin Receptor Antagonists/analysis ; Angiotensin-Converting Enzyme Inhibitors/analysis ; Bacteria/genetics ; Genes, Bacterial ; Anti-Bacterial Agents/analysis ; *Water Purification ; Chlorine/analysis ; *Microbiota ; }, abstract = {Drinking water treatment plants (DWTPs) are designed to remove physical, chemical, and biological contaminants. However, until recently, the role of DWTPs in minimizing the cycling of antibiotic resistance determinants has got limited attention. In particular, the risk of selecting antibiotic-resistant bacteria (ARB) is largely overlooked in chlorine-free DWTPs where biological processes are applied. Here, we combined high-throughput quantitative PCR and metagenomics to analyze the abundance and dynamics of microbial communities, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) across the treatment trains of two chlorine-free DWTPs involving dune-based and reservoir-based systems. The microbial diversity of the water increased after all biological unit operations, namely rapid and slow sand filtration (SSF), and granular activated carbon filtration. Both DWTPs reduced the concentration of ARGs and MGEs in the water by circa 2.5 log gene copies mL[-1], despite their relative increase in the disinfection sub-units (SSF in dune-based and UV treatment in reservoir-based DWTPs). The total microbial concentration was also reduced (2.5 log units), and none of the DWTPs enriched for bacteria containing genes linked to antibiotic resistance. Our findings highlight the effectiveness of chlorine-free DWTPs in supplying safe drinking water while reducing the concentration of antibiotic resistance determinants. To the best of our knowledge, this is the first study that monitors the presence and dynamics of antibiotic resistance determinants in chlorine-free DWTPs.}, } @article {pmid36985314, year = {2023}, author = {Lozano, FM and Lledó, B and Morales, R and Cascales, A and Hortal, M and Bernabeu, A and Bernabeu, R}, title = {Characterization of the Endometrial Microbiome in Patients with Recurrent Implantation Failure.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985314}, issn = {2076-2607}, abstract = {An abnormal endometrial microbiota has been associated with implantation failure; therefore, it may be important to evaluate it in order to improve reproductive outcomes in infertile patients. The main objective of our study was to compare the endometrial microbiome of patients with recurrent implantation failure (RIF) and control patients undergoing assisted reproduction treatment (ART). A prospective cohort study including forty-five patients with their own or donated gametes. The endometrial microbiome was analysed by massive sequencing of the bacterial 16S rRNA gene. Different bacterial communities were detected in RIF and control patients. Lactobacillus stands out as the most frequent genus, with 92.27% in RIF patients and 97.96% in control patients, and significant differences were reported between the two groups (p = 0.002). No significant differences were found regarding alpha diversity index. In beta diversity analysis, a significant trend was observed in the separation of the bacterial community between established groups (p < 0.07). Relative abundance analysis identified genera Prevotella (p < 0.001), Streptococcus (p < 0.001), Bifidobacterium (p = 0.002), Lactobacillus (p = 0.002) and Dialister (p = 0.003). Our results demonstrated the existence of an endometrial microbiota characteristic of RIF patients and showed that there might be a relationship between population of the endometrial microbiome and embryo implantation failure, providing us the possibility to improve clinical results in this patients.}, } @article {pmid36982303, year = {2023}, author = {Giuffrè, M and Moretti, R and Tiribelli, C}, title = {Gut Microbes Meet Machine Learning: The Next Step towards Advancing Our Understanding of the Gut Microbiome in Health and Disease.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, pmid = {36982303}, issn = {1422-0067}, mesh = {Humans ; *Gastrointestinal Microbiome ; Reproducibility of Results ; *Microbiota ; Metagenomics/methods ; Machine Learning ; }, abstract = {The human gut microbiome plays a crucial role in human health and has been a focus of increasing research in recent years. Omics-based methods, such as metagenomics, metatranscriptomics, and metabolomics, are commonly used to study the gut microbiome because they provide high-throughput and high-resolution data. The vast amount of data generated by these methods has led to the development of computational methods for data processing and analysis, with machine learning becoming a powerful and widely used tool in this field. Despite the promising results of machine learning-based approaches for analyzing the association between microbiota and disease, there are several unmet challenges. Small sample sizes, disproportionate label distribution, inconsistent experimental protocols, or a lack of access to relevant metadata can all contribute to a lack of reproducibility and translational application into everyday clinical practice. These pitfalls can lead to false models, resulting in misinterpretation biases for microbe-disease correlations. Recent efforts to address these challenges include the construction of human gut microbiota data repositories, improved data transparency guidelines, and more accessible machine learning frameworks; implementation of these efforts has facilitated a shift in the field from observational association studies to experimental causal inference and clinical intervention.}, } @article {pmid36980929, year = {2023}, author = {Baeza, JA and Barata, R and Rajapakse, D and Penaloza, J and Harrison, P and Haberski, A}, title = {Mitochondrial Genomes Assembled from Non-Invasive eDNA Metagenomic Scat Samples in Critically Endangered Mammals.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, pmid = {36980929}, issn = {2073-4425}, mesh = {Animals ; *DNA, Environmental ; *Genome, Mitochondrial/genetics ; *Ursidae/genetics ; Endangered Species ; *Metagenome ; Feces ; }, abstract = {The abundance of many large-bodied vertebrates, both in marine and terrestrial environments, has declined substantially due to global and regional climate stressors that define the Anthropocene. The development of genetic tools that can serve to monitor population's health non-intrusively and inform strategies for the recovery of these species is crucial. In this study, we formally evaluate whether whole mitochondrial genomes can be assembled from environmental DNA (eDNA) metagenomics scat samples. Mitogenomes of four different large vertebrates, the panda bear (Ailuropoda melanoleuca), the moon bear (Ursus thibetanus), the Java pangolin (Manis javanica), and the the North Atlantic right whale (Eubalaena glacialis) were assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 12x to 480x in 14 out of 18 different eDNA samples. Partial mitochondrial genomes were retrieved from three other eDNA samples. The complete mitochondrial genomes of the studied species were AT-rich and comprised 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative D-loop/control region. Synteny observed in all assembled mitogenomes was identical to that reported for specimens of the same and other closely related species. This study demonstrates that it is possible to assemble accurate whole mitochondrial chromosomes from eDNA samples (scats) using forthright bench and bioinformatics workflows. The retrieval of mitochondrial genomes from eDNA samples represents a tool to support bioprospecting, bio-monitoring, and other non-intrusive conservation strategies in species considered 'vulnerable', 'endangered', and/or 'critically endangered' by the IUCN Red List of Threatened Species.}, } @article {pmid36977970, year = {2023}, author = {Amin, DH and Nageeb, WM and Elkelish, A and Makharita, RR}, title = {Mining metagenomes reveals diverse antibiotic biosynthetic genes in uncultured microbial communities.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {54}, number = {2}, pages = {983-995}, pmid = {36977970}, issn = {1678-4405}, mesh = {*Metagenome ; Phylogeny ; *Microbiota ; Anti-Bacterial Agents/pharmacology ; Soil ; }, abstract = {Pathogens resistant to antimicrobials form a significant threat to public health worldwide. Tackling multidrug-resistant pathogens via screening metagenomic libraries has become a common approach for the discovery of new antibiotics from uncultured microorganisms. This study focuses on capturing nonribosomal peptide synthase (NRPS) gene clusters implicated in the synthesis of many natural compounds of industrial relevance. A NRPS PCR assay was used to screen 2976 Escherichia coli clones in a soil metagenomic library to target NRPS genes. DNA extracts from 4 clones were sequenced and subjected to bioinformatic analysis to identify NRPS domains, their phylogeny, and substrate specificity.Successfully, 17 NRPS-positive hits with a biosynthetic potential were identified. DNA sequencing and BLAST analysis confirmed that NRPS protein sequences shared similarities with members of the genus Delftia in the Proteobacteria taxonomic position. Multiple alignment and phylogenetic analysis demonstrated that clones no. 15cd35 and 15cd37 shared low bootstrap values (54%) and were distantly far from close phylogenetic neighbors. Additionally, NRPS domain substrate specificity has no hits with the known ones; hence, they are more likely to use different substrates to produce new diverse antimicrobials. Further analysis confirmed that the NRPS hits resemble several transposon elements from other bacterial taxa, confirming its diversity. We confirmed that the analyses of the soil metagenomic library revealed a diverse set of NRPS related to the genus Delftia. An in-depth understanding of those positive NRPS hits is a crucial step for genetic manipulation of NRPS, shedding light on alternative novel antimicrobial compounds that can be used in drug discovery and hence supports the pharmaceutical sector.}, } @article {pmid36977954, year = {2023}, author = {Mahiddine, FY and You, I and Park, H and Kim, MJ}, title = {Management of dog sperm parameters and gut microbiota composition with Lactobacillus rhamnosus supplementation.}, journal = {Veterinary research communications}, volume = {47}, number = {3}, pages = {1629-1640}, pmid = {36977954}, issn = {1573-7446}, mesh = {Animals ; Dogs ; *Spermatozoa/cytology/physiology ; *Probiotics/administration & dosage ; *Gastrointestinal Microbiome ; *Lactobacillus ; *Dietary Supplements ; Semen Analysis/veterinary ; Male ; Feces/microbiology ; }, abstract = {The effects of probiotics supplementation on the reproductive function have been evaluated in many species, but no study has evaluated the changes in the gut microbiome along with the sperm quality changes simultaneously. This study evaluated the effects of dietary supplementation with probiotics on the gut microbiome, sperm quality and gene expression, along with possible correlations between these parameters in dogs. The dogs were supplemented with Lactobacillus rhamnosus for six weeks, and fecal and semen samples were collected at 0, 3, and 6 weeks. Fecal samples were assessed using 16S Metagenomic Sequencing for gut microbiome analysis; and semen samples were analyzed using computer-assisted sperm analysis, DNA and acrosome integrity assessment, viability and morphology assessment, and real-time PCR. The analyses suggested that probiotic supplementation improved kinematic parameters, viability, DNA and acrosome integrity, and morphology of sperms. The mRNA levels of genes associated with fertility, DNA repair and integrity, and antioxidation were also upregulated. The sperm parameters were positively correlated with the relative abundance of Actinobacteria, Allobaculum, Phascolarctobacterium and Catenibacterium, and negatively correlated with Faecalibacterium and Streptococcus. Taken together, the sperm quality enhancement through the gut-testis axis may be due to a change in the gut microorganisms populations.}, } @article {pmid36976214, year = {2023}, author = {Elvheim, AI and Li, C and Landfald, B}, title = {Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates.}, journal = {Marine drugs}, volume = {21}, number = {3}, pages = {}, pmid = {36976214}, issn = {1660-3397}, support = {282567//The Regional Research Fund of Northern Norway/ ; 390017303//UiT The Arctic University of Norway/ ; }, mesh = {*Metagenome/genetics ; Genomics ; Metagenomics/methods ; *Microbiota ; Bacteria/genetics ; Multigene Family ; }, abstract = {Marine invertebrate microbiomes have been a rich source of bioactive compounds and interesting genomic features. In cases where the achievable amounts of metagenomic DNA are too low for direct sequencing, multiple displacement amplification (MDA) can be used for whole genome amplification. However, MDA has known limitations which can affect the quality of the resulting genomes and metagenomes. In this study, we evaluated the conservation of biosynthetic gene clusters (BGCs) and enzymes in MDA products from low numbers of prokaryotic cells (estimated 2-850). Marine invertebrate microbiomes collected from Arctic and sub-Arctic areas served as source material. The cells were separated from the host tissue, lysed, and directly subjected to MDA. The MDA products were sequenced by Illumina sequencing. Corresponding numbers of bacteria from a set of three reference strains were treated the same way. The study demonstrated that useful information on taxonomic, BGC, and enzyme diversities was obtainable from such marginal quantities of metagenomic material. Although high levels of assembly fragmentation resulted in most BGCs being incomplete, we conclude that this genome mining approach has the potential to reveal interesting BGCs and genes from hard-to-reach biological sources.}, } @article {pmid36975940, year = {2023}, author = {Manee, MM and Alqahtani, FH and Al-Shomrani, BM and El-Shafie, HAF and Dias, GB}, title = {Omics in the Red Palm Weevil Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae): A Bridge to the Pest.}, journal = {Insects}, volume = {14}, number = {3}, pages = {}, pmid = {36975940}, issn = {2075-4450}, support = {20-0078//King Abdulaziz City for Science and Technology/ ; }, abstract = {The red palm weevil (RPW), Rhynchophorus ferrugineus (Coleoptera: Curculionidae), is the most devastating pest of palm trees worldwide. Mitigation of the economic and biodiversity impact it causes is an international priority that could be greatly aided by a better understanding of its biology and genetics. Despite its relevance, the biology of the RPW remains poorly understood, and research on management strategies often focuses on outdated empirical methods that produce sub-optimal results. With the development of omics approaches in genetic research, new avenues for pest control are becoming increasingly feasible. For example, genetic engineering approaches become available once a species's target genes are well characterized in terms of their sequence, but also population variability, epistatic interactions, and more. In the last few years alone, there have been major advances in omics studies of the RPW. Multiple draft genomes are currently available, along with short and long-read transcriptomes, and metagenomes, which have facilitated the identification of genes of interest to the RPW scientific community. This review describes omics approaches previously applied to RPW research, highlights findings that could be impactful for pest management, and emphasizes future opportunities and challenges in this area of research.}, } @article {pmid36975809, year = {2023}, author = {Falardeau, J and Yildiz, E and Yan, Y and Castellarin, SD and Wang, S}, title = {Microbiome and Physicochemical Features Associated with Differential Listeria monocytogenes Growth in Soft, Surface-Ripened Cheeses.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {4}, pages = {e0200422}, pmid = {36975809}, issn = {1098-5336}, mesh = {*Listeria monocytogenes ; Food Microbiology ; *Cheese/microbiology ; RNA, Ribosomal, 16S ; *Microbiota ; Colony Count, Microbial ; }, abstract = {Soft-ripened cheeses (SRCs) are at a higher risk for the growth of the foodborne pathogen Listeria monocytogenes due to favorable moisture content and pH compared to other cheeses. L. monocytogenes growth is not consistent across SRCs, however, and may be affected by physicochemical and/or microbiome characteristics of the cheeses. Therefore, the purpose of this study was to investigate how the physicochemical and microbiome profiles of SRCs may affect L. monocytogenes growth. Forty-three SRCs produced from raw (n = 12) or pasteurized (n = 31) milk were inoculated with L. monocytogenes (10[3] CFU/g), and the pathogen growth was monitored over 12 days at 8°C. In parallel, the pH, water activity (aw), microbial plate counts, and organic acid content of cheeses were measured, and the taxonomic profiles of the cheese microbiomes were measured using 16S rRNA gene targeted amplicon sequencing and shotgun metagenomic sequencing. L. monocytogenes growth differed significantly between cheeses (analysis of variance [ANOVA]; P < 0.001), with increases ranging from 0 to 5.4 log CFU (mean of 2.5 ± 1.2 log CFU), and was negatively correlated with aw. Raw milk cheeses showed significantly lower L. monocytogenes growth than pasteurized-milk cheeses (t test; P = 0.008), possibly due to an increase in microbial competition. L. monocytogenes growth in cheeses was positively correlated with the relative abundance of Streptococcus thermophilus (Spearman correlation; P < 0.0001) and negatively correlated with the relative abundances of Brevibacterium aurantiacum (Spearman correlation; P = 0.0002) and two Lactococcus spp. (Spearman correlation; P < 0.01). These results suggest that the cheese microbiome may influence the food safety in SRCs. IMPORTANCE Previous studies have identified differences in L. monocytogenes growth between SRCs, but no clear mechanism has yet been elucidated. To the best of our knowledge, this is the first study to collect a wide range of SRCs from retail sources and attempt to identify key factors associated with pathogen growth. A key finding in this research was the positive correlation between the relative abundance of S. thermophilus and the growth of L. monocytogenes. The inclusion of S. thermophilus as a starter culture is more common in industrialized SRC production, suggesting that industrial production of SRC may increase the risk of L. monocytogenes growth. Overall, the results of this study further our understanding of the impact of aw and the cheese microbiome on the growth of L. monocytogenes in SRCs, hopefully leading toward the development of SRC starter/ripening cultures that can prevent L. monocytogenes growth.}, } @article {pmid36975807, year = {2023}, author = {Zhang, W and Liu, Y and Zheng, K and Xing, J and Li, Q and Gu, C and Wang, Z and Shao, H and Guo, C and He, H and Wang, H and Sung, YY and Mok, WJ and Wong, LL and Liang, Y and McMinn, A and Wang, M}, title = {Discovery of an Abundant Viral Genus in Polar Regions through the Isolation and Genomic Characterization of a New Virus against Oceanospirillaceae.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {4}, pages = {e0189622}, pmid = {36975807}, issn = {1098-5336}, mesh = {*Oceanospirillaceae ; Phylogeny ; Cold Climate ; Genomics ; *Bacteriophages ; Genome, Viral ; }, abstract = {The marine bacterial family Oceanospirillaceae, is well-known for its ability to degrade hydrocarbons and for its close association with algal blooms. However, only a few Oceanospirillaceae-infecting phages have been reported thus far. Here, we report on a novel Oceanospirillum phage, namely, vB_OsaM_PD0307, which has a 44,421 bp linear dsDNA genome and is the first myovirus infecting Oceanospirillaceae. A genomic analysis demonstrated that vB_OsaM_PD0307 is a variant of current phage isolates from the NCBI data set but that it has similar genomic features to two high-quality, uncultured viral genomes identified from marine metagenomes. Hence, we propose that vB_OsaM_PD0307 can be classified as the type phage of a new genus, designated Oceanospimyovirus. Additionally, metagenomic read mapping results have further shown that Oceanospimyovirus species are widespread in the global ocean, display distinct biogeographic distributions, and are abundant in polar regions. In summary, our findings expand the current understanding of the genomic characteristics, phylogenetic diversity, and distribution of Oceanospimyovirus phages. IMPORTANCE Oceanospirillum phage vB_OsaM_PD0307 is the first myovirus found to infect Oceanospirillaceae, and it represents a novel abundant viral genus in polar regions. This study provides insights into the genomic, phylogenetic, and ecological characteristics of the new viral genus, namely Oceanospimyovirus.}, } @article {pmid36975801, year = {2023}, author = {Carter, KA and Fodor, AA and Balkus, JE and Zhang, A and Serrano, MG and Buck, GA and Engel, SM and Wu, MC and Sun, S}, title = {Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0100322}, pmid = {36975801}, issn = {2379-5077}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 MD011504/MD/NIMHD NIH HHS/United States ; T32 AI007140/AI/NIAID NIH HHS/United States ; }, mesh = {Infant, Newborn ; Pregnancy ; Female ; Humans ; Metagenome/genetics ; RNA, Ribosomal, 16S/genetics ; *Premature Birth/genetics ; *Microbiota/genetics ; Vagina/microbiology ; }, abstract = {Several studies have compared metagenome inference performance in different human body sites; however, none specifically reported on the vaginal microbiome. Findings from other body sites cannot easily be generalized to the vaginal microbiome due to unique features of vaginal microbial ecology, and investigators seeking to use metagenome inference in vaginal microbiome research are "flying blind" with respect to potential bias these methods may introduce into analyses. We compared the performance of PICRUSt2 and Tax4Fun2 using paired 16S rRNA gene amplicon sequencing and whole-metagenome sequencing data from vaginal samples from 72 pregnant individuals enrolled in the Pregnancy, Infection, and Nutrition (PIN) cohort. Participants were selected from those with known birth outcomes and adequate 16S rRNA gene amplicon sequencing data in a case-control design. Cases experienced early preterm birth (<32 weeks of gestation), and controls experienced term birth (37 to 41 weeks of gestation). PICRUSt2 and Tax4Fun2 performed modestly overall (median Spearman correlation coefficients between observed and predicted KEGG ortholog [KO] relative abundances of 0.20 and 0.22, respectively). Both methods performed best among Lactobacillus crispatus-dominated vaginal microbiotas (median Spearman correlation coefficients of 0.24 and 0.25, respectively) and worst among Lactobacillus iners-dominated microbiotas (median Spearman correlation coefficients of 0.06 and 0.11, respectively). The same pattern was observed when evaluating correlations between univariable hypothesis test P values generated with observed and predicted metagenome data. Differential metagenome inference performance across vaginal microbiota community types can be considered differential measurement error, which often causes differential misclassification. As such, metagenome inference will introduce hard-to-predict bias (toward or away from the null) in vaginal microbiome research. IMPORTANCE Compared to taxonomic composition, the functional potential within a bacterial community is more relevant to establishing mechanistic understandings and causal relationships between the microbiome and health outcomes. Metagenome inference attempts to bridge the gap between 16S rRNA gene amplicon sequencing and whole-metagenome sequencing by predicting a microbiome's gene content based on its taxonomic composition and annotated genome sequences of its members. Metagenome inference methods have been evaluated primarily among gut samples, where they appear to perform fairly well. Here, we show that metagenome inference performance is markedly worse for the vaginal microbiome and that performance varies across common vaginal microbiome community types. Because these community types are associated with sexual and reproductive outcomes, differential metagenome inference performance will bias vaginal microbiome studies, obscuring relationships of interest. Results from such studies should be interpreted with substantial caution and the understanding that they may over- or underestimate associations with metagenome content.}, } @article {pmid36973750, year = {2023}, author = {Rivarez, MPS and Pecman, A and Bačnik, K and Maksimović, O and Vučurović, A and Seljak, G and Mehle, N and Gutiérrez-Aguirre, I and Ravnikar, M and Kutnjak, D}, title = {In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {60}, pmid = {36973750}, issn = {2049-2618}, mesh = {*Solanum lycopersicum ; Virome ; *Plant Viruses/genetics ; Plants ; }, abstract = {BACKGROUND: In agroecosystems, viruses are well known to influence crop health and some cause phytosanitary and economic problems, but their diversity in non-crop plants and role outside the disease perspective is less known. Extensive virome explorations that include both crop and diverse weed plants are therefore needed to better understand roles of viruses in agroecosystems. Such unbiased exploration is available through viromics, which could generate biological and ecological insights from immense high-throughput sequencing (HTS) data.

RESULTS: Here, we implemented HTS-based viromics to explore viral diversity in tomatoes and weeds in farming areas at a nation-wide scale. We detected 125 viruses, including 79 novel species, wherein 65 were found exclusively in weeds. This spanned 21 higher-level plant virus taxa dominated by Potyviridae, Rhabdoviridae, and Tombusviridae, and four non-plant virus families. We detected viruses of non-plant hosts and viroid-like sequences and demonstrated infectivity of a novel tobamovirus in plants of Solanaceae family. Diversities of predominant tomato viruses were variable, in some cases, comparable to that of global isolates of the same species. We phylogenetically classified novel viruses and showed links between a subgroup of phylogenetically related rhabdoviruses to their taxonomically related host plants. Ten classified viruses detected in tomatoes were also detected in weeds, which might indicate possible role of weeds as their reservoirs and that these viruses could be exchanged between the two compartments.

CONCLUSIONS: We showed that even in relatively well studied agroecosystems, such as tomato farms, a large part of very diverse plant viromes can still be unknown and is mostly present in understudied non-crop plants. The overlapping presence of viruses in tomatoes and weeds implicate possible presence of virus reservoir and possible exchange between the weed and crop compartments, which may influence weed management decisions. The observed variability and widespread presence of predominant tomato viruses and the infectivity of a novel tobamovirus in solanaceous plants, provided foundation for further investigation of virus disease dynamics and their effect on tomato health. The extensive insights we generated from such in-depth agroecosystem virome exploration will be valuable in anticipating possible emergences of plant virus diseases and would serve as baseline for further post-discovery characterization studies. Video Abstract.}, } @article {pmid36973710, year = {2023}, author = {Li, H and Wang, H and Ju, H and Lv, J and Yang, S and Zhang, W and Lu, H}, title = {Comparison of gut viral communities in children under 5 years old and newborns.}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {52}, pmid = {36973710}, issn = {1743-422X}, mesh = {Infant, Newborn ; Humans ; Child ; Child, Preschool ; *Viruses/genetics ; *Bacteriophages/genetics ; Gastrointestinal Tract ; *Gastrointestinal Microbiome ; Feces ; Metagenomics ; }, abstract = {OBJECTIVES: The gut virome of humans is mainly composed of bacteriophages and their role in shaping the gut microbiome and influencing human health is increasingly recognized. However, little is known about the dynamic changes of the gut virome in children and its role in growth and development. In this study, we collected fecal samples from newborns and children under 5 years old from the same area during the same time period to investigate the gut viral community using viral metagenomic technique.

METHODS: We used viral metagenomics to compare the gut bacteriophage composition between newborns and children under 5 years of age. We collected fecal samples from 45 newborns who were born at the Affiliated Hospital of Jiangsu University and 45 healthy children who were examined at the same hospital. The two groups were classified as the newborn group and the children group.

RESULTS: Our sequencing analysis showed that the number of seqeunce reads of the children group were more than that of the newborn group. The results of alpha diversity and beta diversity both indicated that the diversity of the children group was significantly higher than that of the newborn group and the children group is different from the newborn group. The abundance of gut virome in the children group was also higher than that in the newborn group. The analysis of the genetic characteristics of the viruses showed that the phage genome was scattered and clustered with specificity.

CONCLUSION: Our findings indicate that the gut bacteriophage communities undergo changes over time, presenting diversity and dynamic characteristics. We characterized the composition of gut virome in children and newborns in this region. However, further research is needed to investigate the function of bacteriophages in the ecology of the gastrointestinal tract.}, } @article {pmid36972958, year = {2023}, author = {Muzny, CA and Van Gerwen, OT and Schroeder, JA and Kay-Duncan, ES and Siwakoti, K and Aaron, KJ and Eastlund, IC and Graves, KJ and Elnaggar, JH and Tamhane, A and Long, D and Van Wagoner, N and Toh, E and Taylor, CM}, title = {Impact of testosterone use on the vaginal microbiota of transgender men, including susceptibility to bacterial vaginosis: study protocol for a prospective, observational study.}, journal = {BMJ open}, volume = {13}, number = {3}, pages = {e073068}, pmid = {36972958}, issn = {2044-6055}, support = {R21 AI167754/AI/NIAID NIH HHS/United States ; UL1 TR003096/TR/NCATS NIH HHS/United States ; P20 GM103424/GM/NIGMS NIH HHS/United States ; U19 AG055373/AG/NIA NIH HHS/United States ; R01 AI146065/AI/NIAID NIH HHS/United States ; }, mesh = {Male ; Female ; Humans ; *Vaginosis, Bacterial/drug therapy/microbiology ; Prospective Studies ; *Transgender Persons ; Testosterone ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; Vagina/microbiology ; *Microbiota ; Observational Studies as Topic ; }, abstract = {INTRODUCTION: The effect of testosterone (T) therapy on the vaginal microbiota of transgender men (TGM) is not well characterised, although one cross-sectional study comparing the vaginal microbiota of cisgender women to TGM on T≥1 year found that, in 71% of the TGM, the vaginal microbiota was less likely to be Lactobacillus-dominated and more likely to be enriched with >30 other bacterial species, many associated with bacterial vaginosis (BV). This prospective study aims to investigate changes in the composition of the vaginal microbiota over time in TGM who retain their natal genitalia (ie, vagina) and initiate T. In addition, we will identify changes in the vaginal microbiota preceding incident BV (iBV) in this cohort while investigating behavioural factors, along with hormonal shifts, which may be associated with iBV.

METHODS AND ANALYSIS: T-naïve TGM who have not undergone gender-affirming genital surgery with normal baseline vaginal microbiota (ie, no Amsel criteria, normal Nugent Score with no Gardnerella vaginalis morphotypes) will self-collect daily vaginal specimens for 7 days prior to initiating T and for 90 days thereafter. These specimens will be used for vaginal Gram stain, 16S rRNA gene sequencing and shotgun metagenomic sequencing to characterise shifts in the vaginal microbiota over time, including development of iBV. Participants will complete daily diaries on douching, menses and behavioural factors including sexual activity during the study.

ETHICS AND DISSEMINATION: This protocol is approved through the single Institutional Review Board mechanism by the University of Alabama at Birmingham. External relying sites are the Louisiana State University Health Sciences Center, New Orleans Human Research Protection Program and the Indiana University Human Research Protection Program. Study findings will be presented at scientific conferences and peer-reviewed journals as well as shared with community advisory boards at participating gender health clinics and community-based organisations servicing transgender people.

REGISTRATION DETAILS: Protocol # IRB-300008073.}, } @article {pmid36971593, year = {2023}, author = {Liu, F and Lu, H and Dong, B and Huang, X and Cheng, H and Qu, R and Hu, Y and Zhong, L and Guo, Z and You, Y and Xu, ZZ}, title = {Systematic Evaluation of the Viable Microbiome in the Human Oral and Gut Samples with Spike-in Gram+/- Bacteria.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0073822}, pmid = {36971593}, issn = {2379-5077}, mesh = {Humans ; *Microbiota/genetics ; DNA ; Feces/microbiology ; DNA, Bacterial/genetics ; Bacteria/genetics ; Firmicutes/genetics ; }, abstract = {PMA (propidium monoazide) is one of the few methods that are compatible with metagenomic sequencing to characterize the live/intact microbiota. However, its efficiency in complex communities such as saliva and feces is still controversial. An effective method for depleting host and dead bacterial DNA in human microbiome samples is lacking. Here, we systematically evaluate the efficiency of osmotic lysis and PMAxx treatment (lyPMAxx) in characterizing the viable microbiome with four live/dead Gram+/Gram- microbial strains in simple synthetic and spiked-in complex communities. We show that lyPMAxx-quantitative PCR (qPCR)/sequencing eliminated more than 95% of the host and heat-killed microbial DNA and had a much smaller effect on the live microbes in both simple mock and spiked-in complex communities. The overall microbial load and the alpha diversity of the salivary and fecal microbiome were decreased by lyPMAxx, and the relative abundances of the microbes were changed. The relative abundances of Actinobacteria, Fusobacteria, and Firmicutes in saliva were decreased by lyPMAxx, as was that of Firmicutes in feces. We also found that the frequently used sample storage method, freezing with glycerol, killed or injured 65% and 94% of the living microbial cells in saliva and feces, respectively, with the Proteobacteria phylum affected most in saliva and the Bacteroidetes and Firmicutes phyla affected most in feces. By comparing the absolute abundance variation of the shared species among different sample types and individuals, we found that sample habitat and personal differences affected the response of microbial species to lyPMAxx and freezing. IMPORTANCE The functions and phenotypes of microbial communities are largely defined by viable microbes. Through advanced nucleic acid sequencing technologies and downstream bioinformatic analyses, we gained an insight into the high-resolution microbial community composition of human saliva and feces, yet we know very little about whether such community DNA sequences represent viable microbes. PMA-qPCR was used to characterize the viable microbes in previous studies. However, its efficiency in complex communities such as saliva and feces is still controversial. By spiking-in four live/dead Gram+/Gram- bacterial strains, we demonstrate that lyPMAxx can effectively discriminate between live and dead microbes in the simple synthetic community and complex human microbial communities (saliva and feces). In addition, freezing storage was found to kill or injure the microbes in saliva and feces significantly, as measured with lyPMAxx-qPCR/sequencing. This method has a promising prospect in the viable/intact microbiota detection of complex human microbial communities.}, } @article {pmid36970947, year = {2023}, author = {Ermolenko, E and Sitkin, S and Vakhitov, T and Solovyeva, O and Karaseva, A and Morozova, A and Kotyleva, M and Shumikhina, I and Lavrenova, N and Demyanova, E and Dmitriev, A and Suvorov, A}, title = {Evaluation of the effectiveness of personalised therapy for the patients with irritable bowel syndrome.}, journal = {Beneficial microbes}, volume = {14}, number = {2}, pages = {119-130}, doi = {10.3920/BM2022.0053}, pmid = {36970947}, issn = {1876-2891}, mesh = {Humans ; Bacteroidetes/genetics ; Enterococcus/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Gram-Positive Cocci ; *Irritable Bowel Syndrome/microbiology ; *Microbiota ; *Probiotics/therapeutic use ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Intestinal microbiota correction in the therapy of irritable bowel syndrome (IBS) is an important medical problem. We conducted a laboratory and pilot clinical trial to investigate the effect of autoprobiotic bacteria, indigenous bifidobacteria and enterococci isolated from faeces and grown on artificial media to use as personified food additives in IBS treatment. Convincing evidence of the clinical efficacy of autoprobiotic was demonstrated by the disappearance of dyspeptic symptoms. The microbiome of patients with IBS was compared to a group of healthy volunteers and changes in the microbiome after autoprobiotic use were detected by quantitative polymerase chain reaction and 16S rRNA metagenome analysis. The possibility of reducing opportunistic microorganisms in the treatment of IBS with autoprobiotics has been convincingly proven. The quantitative content of enterococci in the intestinal microbiota was higher in IBS patients than in healthy volunteers and increased after therapy. An increase in the relative abundance of genera Coprococcus, Blautia and a decrease in the relative abundance of Paraprevotella spp. were found at the end of therapy. A metabolome study which was performed by gas chromatography and mass spectrometry demonstrated an increase in the content of oxalic acid, a decrease of dodecanoate, lauric acid, and other metabolome components after taking autoprobiotics. Some of these parameters correlated with the relative abundances of Paraprevotella spp., Enterococcus spp., and Coprococcus spp. representative of the microbiome. Apparently, they reflected the peculiarities of metabolic compensation and changes in the microbiota. Therefore, the use of autoprobiotics for treatment of IBS may lead to a stable positive clinical effect, associated with compensatory changes in the intestinal microbiota, and accompanied by corresponding changes in metabolic processes in the organism.}, } @article {pmid36969214, year = {2023}, author = {Feng, R and Zhu, Q and Li, Q and Zhai, Y and Wang, J and Qin, C and Liang, D and Zhang, R and Tian, H and Liu, H and Chen, Y and Fu, Y and Wang, X and Ding, X}, title = {Microbiota-ear-brain interaction is associated with generalized anxiety disorder through activation of inflammatory cytokine responses.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1117726}, pmid = {36969214}, issn = {1664-3224}, mesh = {Humans ; *Cytokines ; RNA, Ribosomal, 16S ; Anxiety Disorders/microbiology ; Brain ; *Microbiota ; Inflammation ; }, abstract = {INTRODUCTION: Generalized anxiety disorder (GAD) is one of the most enduring anxiety disorders, being associated with increased systemic inflammation. However, the trigger and mechanisms underlying the activation of inflammatory cytokine responses in GAD remain poorly understood.

MATERIALS AND METHODS: We characterized the ear canal microbiome in GAD patients through 16S rRNA gene sequencing and metagenomic sequencing and identified the serum inflammatory markers in GAD patients. Spearman correlations were applied to test the relationship between the microbiota changes and systemic inflammation.

RESULTS: Our findings showed the higher microbial diversity, accompanied with the significantly increased abundance of Proteobacteria, and decreased abundance of Firmicutes in the ear canal of GAD participants compared to that of the age- and sex-matched healthy controls (HC). Metagenomic sequencing showed that Pseudomonas aeruginosa were significantly increased at species-level in GAD patients. Furthermore, we observed the relative abundance of Pseudomonas aeruginosa was positively associated with elevated systemic inflammatory markers and the severity of disease, suggesting that these ear canal microbiota alterations might be correlated with GAD by activating the inflammatory response.

CONCLUSIONS: These findings indicate that microbiota-ear-brain interaction via upregulating inflammatory reaction involve in the development of GAD, as well as suggest that ear canal bacterial communities may be a target for therapeutic intervention.}, } @article {pmid36966280, year = {2023}, author = {Zhao, Y and Yi, J and Xiang, J and Jia, W and Chen, A and Chen, L and Zheng, L and Zhou, W and Wu, M and Yu, Z and Tang, J}, title = {Exploration of lung mycobiome in the patients with non-small-cell lung cancer.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {81}, pmid = {36966280}, issn = {1471-2180}, mesh = {Humans ; *Mycobiome ; *Carcinoma, Non-Small-Cell Lung ; Fungi/genetics ; *Lung Neoplasms ; Lung ; }, abstract = {As the Human Microbiome Project (HMP) progresses, the relationship between microbes and human health has been receiving increasing attention. A growing number of reports support the correlation between cancer and microbes. However, most studies have focused on bacteria, rather than fungal communities. In this study, we studied the alteration in lung mycobiome in patients with non-small-cell lung cancer (NSCLC) using metagenomic sequencing and qPCR. The higher fungal diversity and more complex network were observed in the patients with NSCLC. In addition, Alternaria arborescens was found as the most relevant fungus to NSCLC, and the enrichment of it in cancerous tissue was also detected. This study proposes that the changes in fungal communities may be closely related to lung cancer, and provides insights into further exploration the relationship between lung cancer and fungi.}, } @article {pmid36966151, year = {2023}, author = {Lin, X and Hu, T and Chen, J and Liang, H and Zhou, J and Wu, Z and Ye, C and Jin, X and Xu, X and Zhang, W and Jing, X and Yang, T and Wang, J and Yang, H and Kristiansen, K and Xiao, L and Zou, Y}, title = {The genomic landscape of reference genomes of cultivated human gut bacteria.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1663}, pmid = {36966151}, issn = {2041-1723}, mesh = {Humans ; Genome, Bacterial/genetics ; Genomics ; Metagenome/genetics ; *Gastrointestinal Microbiome/genetics ; Bacteria ; Metagenomics ; *Bacteriophages/genetics ; }, abstract = {Culture-independent metagenomic studies have revolutionized our understanding of the gut microbiota. However, the lack of full genomes from cultured species is still a limitation for in-depth studies of the gut microbiota. Here we present a substantially expanded version of our Cultivated Genome Reference (CGR), termed CGR2, providing 3324 high-quality draft genomes from isolates selected from a large-scale cultivation of bacterial isolates from fecal samples of healthy Chinese individuals. The CGR2 classifies 527 species (179 previously unidentified species) from 8 phyla, and uncovers a genomic and functional diversity of Collinsella aerofaciens. The CGR2 genomes match 126 metagenome-assembled genomes without cultured representatives in the Unified Human Gastrointestinal Genome (UHGG) collection and harbor 3767 unidentified secondary metabolite biosynthetic gene clusters, providing a source of natural compounds with pharmaceutical potentials. We uncover accurate phage-bacterium linkages providing information on the evolutionary characteristics of interaction between bacteriophages and bacteria at the strain level.}, } @article {pmid36965360, year = {2023}, author = {Li, Z and Qing, Y and Cui, G and Li, M and Liu, T and Zeng, Y and Zhou, C and Hu, X and Jiang, J and Wang, D and Gao, Y and Zhang, J and Cai, C and Wang, T and Wan, C}, title = {Shotgun metagenomics reveals abnormal short-chain fatty acid-producing bacteria and glucose and lipid metabolism of the gut microbiota in patients with schizophrenia.}, journal = {Schizophrenia research}, volume = {255}, number = {}, pages = {59-66}, doi = {10.1016/j.schres.2023.03.005}, pmid = {36965360}, issn = {1573-2509}, mesh = {Humans ; *Gastrointestinal Microbiome ; Lipid Metabolism ; Metagenomics ; Glucose ; *Schizophrenia ; Bacteria/metabolism ; Fatty Acids, Volatile/metabolism ; }, abstract = {Evidence has shown that the gut microbiota is closely related to the pathogenesis of schizophrenia, but temporal changes in the gut microbiota of patients with schizophrenia (SZ) during treatment remain unclear. Here, to evaluate temporal changes in the gut microbiota in schizophrenia, we performed whole-genome shotgun metagenomics on fecal samples from 36 healthy controls (HCs) and 19 baseline-period patients, and followed up with patients upon treatment. Compared to that in HCs, beta diversity in SZ was significantly distinct. The genera Bacteroides, Prevotella and Clostridium were the top 3 altered genera between SZ and HCs, and the Bacteroides-Prevotella ratio was significantly increased in SZ. Thirty-three percent of differentially abundant species were short-chain fatty acid (SCFA)-producing bacteria. Functional analysis showed that glucose and lipid metabolism of the gut microbiota was decreased in SZ compared with those in HCs. The abundances of two rate-limiting enzymes in glucose and lipid metabolism, phosphofructokinase (PFK) and acetyl-CoA carboxylase (ACC), were significantly decreased in SZ, and differentially abundant metabolism-related enzymes were significantly associated with SCFA-producing bacteria. Next, we found that the abundance of SCFA-producing bacteria also changed after treatment and that Clostridium was significantly negatively correlated with the total positive and negative syndrome scale (PANSS) score in patients. Functional analysis showed that glycoside hydrolase family 30 incrementally increased in abundance during treatment and were significantly associated with SCFA-producing bacteria. Our findings help to provide evidence for the role of gut microbiota in the occurrence and development of schizophrenia.}, } @article {pmid36965279, year = {2023}, author = {Viver, T and Conrad, RE and Lucio, M and Harir, M and Urdiain, M and Gago, JF and Suárez-Suárez, A and Bustos-Caparros, E and Sanchez-Martinez, R and Mayol, E and Fassetta, F and Pang, J and Mădălin Gridan, I and Venter, S and Santos, F and Baxter, B and Llames, ME and Cristea, A and Banciu, HL and Hedlund, BP and Stott, MB and Kämpfer, P and Amann, R and Schmitt-Kopplin, P and Konstantinidis, KT and Rossello-Mora, R}, title = {Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov.}, journal = {Systematic and applied microbiology}, volume = {46}, number = {3}, pages = {126416}, doi = {10.1016/j.syapm.2023.126416}, pmid = {36965279}, issn = {1618-0984}, mesh = {RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Phylogeny ; *Bacteroidetes ; *Fatty Acids/analysis ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; }, abstract = {Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new Salinibacter species. For these species we propose the names Salinibacter pepae sp. nov. and Salinibacter grassmerensis sp. nov. (showing average nucleotide identity (ANI) values < 95.09% and 87.08% with Sal. ruber M31[T], respectively). Metabolomics revealed species-specific discriminative profiles. Sal. ruber strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and Sal. altiplanensis was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus Salinibacter. These species dominated in different sites and always coexisted with Sal. ruber and Sal. pepae. Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund, we describe the species Salinibacter pampae sp. nov. and Salinibacter abyssi sp. nov. respectively (showing ANI values 90.94% and 91.48% with Sal. ruber M31[T], respectively). Sal. grassmerensis sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and Sal. pepae, Sal. pampae sp. nov. and Sal. abyssi sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.}, } @article {pmid36965198, year = {2023}, author = {Ceylani, T and Allahverdi, H and Teker, HT}, title = {Role of age-related plasma in the diversity of gut bacteria.}, journal = {Archives of gerontology and geriatrics}, volume = {111}, number = {}, pages = {105003}, doi = {10.1016/j.archger.2023.105003}, pmid = {36965198}, issn = {1872-6976}, mesh = {Rats ; Humans ; Animals ; Feces/microbiology ; *Bacteria/genetics ; *Gastrointestinal Microbiome ; Bacteroidetes ; Plasma ; }, abstract = {Recent studies have demonstrated the efficacy of young blood plasma factors in reversing aging-related deformities. However, the impact of plasma exchange between young and old individuals on gut microbiota remains understudied. To investigate this, we evaluated the effects of plasma exchange between 5-week-old and 24-month-old rats on gut microbiota composition. In this study, old rats were administered 0.5 ml of young plasma, while young rats were administered 0.25 ml of old plasma daily for 30 days. Metagenome analysis was performed on the contents of the cecum after completing plasma transfer. Results showed that transferring young plasma to old rats significantly increased the alpha diversity indices (Shannon and Simpson values), while the Firmicutes to Bacteroidetes ratio decreased significantly. Conversely, transferring aged plasma to young rats led to a significant decrease in Shannon value and F/B ratio but no change in Simpson value. Plasma exchange also caused substantial changes in the top ten dominant genera and species found in the gut microbiota of young and old rats. After young blood plasma transfer, the dominant bacterial profile in the old gut microbiota shifted toward the bacterial profile found in the young control group. Notably, old plasma also altered the gut microbiota structure of young rats toward that of old rats. Our findings suggest that age-related changes in plasma play a crucial role in gut microbiota species diversity and their presence rates.}, } @article {pmid36963164, year = {2023}, author = {Beliaeva, MA and Wilmanns, M and Zimmermann, M}, title = {Decipher enzymes from human microbiota for drug discovery and development.}, journal = {Current opinion in structural biology}, volume = {80}, number = {}, pages = {102567}, doi = {10.1016/j.sbi.2023.102567}, pmid = {36963164}, issn = {1879-033X}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Bacteria/genetics ; Genomics ; Drug Discovery ; }, abstract = {The human microbiota plays an important role in human health and contributes to the metabolism of therapeutic drugs affecting their potency. However, the current knowledge on human gut bacterial metabolism is limited and lacks an understanding of the underlying mechanisms of observed drug biotransformations. Despite the complexity of the gut microbial community, genomic and metagenomic sequencing provides insights into the diversity of chemical reactions that can be carried out by the microbiota and poses new challenges to functionally annotate thousands of bacterial enzymes. Here, we outline methods to systematically address the structural and functional space of the human microbiome, highlighting a combination of in silico and in vitro approaches. Systematic knowledge about microbial enzymes could eventually be applied for personalized therapy, the development of prodrugs and modulators of unwanted bacterial activity, and the further discovery of new antibiotics.}, } @article {pmid36960043, year = {2023}, author = {Lin, T}, title = {Editorial: New techniques in microbiome research.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1158392}, doi = {10.3389/fcimb.2023.1158392}, pmid = {36960043}, issn = {2235-2988}, mesh = {*Microbiota ; }, } @article {pmid36959975, year = {2023}, author = {Baltoumas, FA and Karatzas, E and Paez-Espino, D and Venetsianou, NK and Aplakidou, E and Oulas, A and Finn, RD and Ovchinnikov, S and Pafilis, E and Kyrpides, NC and Pavlopoulos, GA}, title = {Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters.}, journal = {Frontiers in bioinformatics}, volume = {3}, number = {}, pages = {1157956}, pmid = {36959975}, issn = {2673-7647}, abstract = {Metagenomics has enabled accessing the genetic repertoire of natural microbial communities. Metagenome shotgun sequencing has become the method of choice for studying and classifying microorganisms from various environments. To this end, several methods have been developed to process and analyze the sequence data from raw reads to end-products such as predicted protein sequences or families. In this article, we provide a thorough review to simplify such processes and discuss the alternative methodologies that can be followed in order to explore biodiversity at the protein family level. We provide details for analysis tools and we comment on their scalability as well as their advantages and disadvantages. Finally, we report the available data repositories and recommend various approaches for protein family annotation related to phylogenetic distribution, structure prediction and metadata enrichment.}, } @article {pmid36959686, year = {2023}, author = {Yang, Y and Han, Z and Gao, Z and Chen, J and Song, C and Xu, J and Wang, H and Huang, A and Shi, J and Gu, J}, title = {Metagenomic and targeted metabolomic analyses reveal distinct phenotypes of the gut microbiota in patients with colorectal cancer and type 2 diabetes mellitus.}, journal = {Chinese medical journal}, volume = {136}, number = {23}, pages = {2847-2856}, pmid = {36959686}, issn = {2542-5641}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2 ; *Microbiota ; Bacteria/genetics ; Fatty Acids, Volatile ; *Colorectal Neoplasms/metabolism ; Butyrates ; Feces/microbiology ; }, abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM) is an independent risk factor for colorectal cancer (CRC), and the patients with CRC and T2DM have worse survival. The human gut microbiota (GM) is linked to the development of CRC and T2DM, respectively. However, the GM characteristics in patients with CRC and T2DM remain unclear.

METHODS: We performed fecal metagenomic and targeted metabolomics studies on 36 samples from CRC patients with T2DM (DCRC group, n = 12), CRC patients without diabetes (CRC group, n = 12), and healthy controls (Health group, n = 12). We analyzed the fecal microbiomes, characterized the composition and function based on the metagenomics of DCRC patients, and detected the short-chain fatty acids (SCFAs) and bile acids (BAs) levels in all fecal samples. Finally, we performed a correlation analysis of the differential bacteria and metabolites between different groups.

RESULTS: Compared with the CRC group, LefSe analysis showed that there is a specific GM community in DCRC group, including an increased abundance of Eggerthella , Hungatella , Peptostreptococcus , and Parvimonas , and decreased Butyricicoccus , Lactobacillus , and Paraprevotella . The metabolomics analysis results revealed that the butyric acid level was lower but the deoxycholic acid and 12-keto-lithocholic acid levels were higher in the DCRC group than other groups (P < 0.05). The correlation analysis showed that the dominant bacterial abundance in the DCRC group (Parvimonas , Desulfurispora , Sebaldella , and Veillonellales , among others) was negatively correlated with butyric acid, hyodeoxycholic acid, ursodeoxycholic acid, glycochenodeoxycholic acid, chenodeoxycholic acid, cholic acid and glycocholate. However, the abundance of mostly inferior bacteria was positively correlated with these metabolic acid levels, including Faecalibacterium , Thermococci , and Cellulophaga .

CONCLUSIONS: Unique fecal microbiome signatures exist in CRC patients with T2DM compared to those with non-diabetic CRC. Alterations in GM composition and SCFAs and secondary BAs levels may promote CRC development.}, } @article {pmid36952228, year = {2023}, author = {Lai, JL and Li, ZG and Wang, Y and Xi, HL and Luo, XG}, title = {Tritium and Carbon-14 Contamination Reshaping the Microbial Community Structure, Metabolic Network, and Element Cycle in the Seawater Environment.}, journal = {Environmental science & technology}, volume = {57}, number = {13}, pages = {5305-5316}, doi = {10.1021/acs.est.3c00422}, pmid = {36952228}, issn = {1520-5851}, mesh = {Carbon Radioisotopes/metabolism ; Tritium/metabolism ; *Bacteria/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Seawater ; Metabolic Networks and Pathways ; Carbon/metabolism ; Nitrogen/metabolism ; Phosphorus/metabolism ; Geologic Sediments/chemistry ; }, abstract = {The potential ecological risks caused by entering radioactive wastewater containing tritium and carbon-14 into the sea require careful evaluation. This study simulated seawater's tritium and carbon-14 pollution and analyzed the effects on the seawater and sediment microenvironments. Tritium and carbon-14 pollution primarily altered nitrogen and phosphorus metabolism in the seawater environment. Analysis by 16S rRNA sequencing showed changes in the relative abundance of microorganisms involved in carbon, nitrogen, and phosphorus metabolism and organic matter degradation in response to tritium and carbon-14 exposure. Metabonomics and metagenomic analysis showed that tritium and carbon-14 exposure interfered with gene expression involving nucleotide and amino acid metabolites, in agreement with the results seen for microbial community structure. Tritium and carbon-14 exposure also modulated the abundance of functional genes involved in carbohydrate, phosphorus, sulfur, and nitrogen metabolic pathways in sediments. Tritium and carbon-14 pollution in seawater adversely affected microbial diversity, metabolic processes, and the abundance of nutrient-cycling genes. These results provide valuable information for further evaluating the risks of tritium and carbon-14 in marine environments.}, } @article {pmid36949609, year = {2023}, author = {Hagh-Doust, N and Mikryukov, V and Anslan, S and Bahram, M and Puusepp, R and Dulya, O and Tedersoo, L}, title = {Effects of nitrogen deposition on carbon and nutrient cycling along a natural soil acidity gradient as revealed by metagenomics.}, journal = {The New phytologist}, volume = {238}, number = {6}, pages = {2607-2620}, doi = {10.1111/nph.18897}, pmid = {36949609}, issn = {1469-8137}, mesh = {*Ecosystem ; Soil/chemistry ; Nitrogen/metabolism ; Carbon/metabolism ; Forests ; *Microbiota ; Soil Microbiology ; }, abstract = {Nitrogen (N) deposition and soil acidification are environmental challenges affecting ecosystem functioning, health, and biodiversity, but their effects on functional genes are poorly understood. Here, we utilized metabarcoding and metagenomics to investigate the responses of soil functional genes to N deposition along a natural soil pH gradient. Soil N content was uncorrelated with pH, enabling us to investigate their effects separately. Soil acidity strongly and negatively affected the relative abundances of most cluster of orthologous gene categories of the metabolism supercategory. Similarly, soil acidity negatively affected the diversity of functional genes related to carbon and N but not phosphorus cycling. Multivariate analyses showed that soil pH was the most important factor affecting microbial and functional gene composition, while the effects of N deposition were less important. Relative abundance of KEGG functional modules related to different parts of the studied cycles showed variable responses to soil acidity and N deposition. Furthermore, our results suggested that the diversity-function relationship reported for other organisms also applies to soil microbiomes. Since N deposition and soil pH affected microbial taxonomic and functional composition to a different extent, we conclude that N deposition effects might be primarily mediated through soil acidification in forest ecosystems.}, } @article {pmid36949545, year = {2023}, author = {Graham, EH and Tom, WA and Neujahr, AC and Adamowicz, MS and Clarke, JL and Herr, JR and Fernando, SC}, title = {The persistence and stabilization of auxiliary genes in the human skin virome.}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {49}, pmid = {36949545}, issn = {1743-422X}, mesh = {Humans ; Virome ; *Bacteriophages/genetics ; *Viruses/genetics ; *Microbiota ; Metagenome ; Bacteria/genetics ; }, abstract = {BACKGROUND: The human skin contains a diverse microbiome that provides protective functions against environmental pathogens. Studies have demonstrated that bacteriophages modulate bacterial community composition and facilitate the transfer of host-specific genes, potentially influencing host cellular functions. However, little is known about the human skin virome and its role in human health. Especially, how viral-host relationships influence skin microbiome structure and function is poorly understood.

RESULTS: Population dynamics and genetic diversity of bacteriophage communities in viral metagenomic data collected from three anatomical skin locations from 60 subjects at five different time points revealed that cutaneous bacteriophage populations are mainly composed of tailed Caudovirales phages that carry auxiliary genes to help improve metabolic remodeling to increase bacterial host fitness through antimicrobial resistance. Sequence variation in the MRSA associated antimicrobial resistance gene, erm(C) was evaluated using targeted sequencing to further confirm the presence of antimicrobial resistance genes in the human virome and to demonstrate how functionality of such genes may influence persistence and in turn stabilization of bacterial host and their functions.

CONCLUSIONS: This large temporal study of human skin associated viruses indicates that the human skin virome is associated with auxiliary metabolic genes and antimicrobial resistance genes to help increase bacterial host fitness.}, } @article {pmid36949471, year = {2023}, author = {Volmer, JG and Soo, RM and Evans, PN and Hoedt, EC and Astorga Alsina, AL and Woodcroft, BJ and Tyson, GW and Hugenholtz, P and Morrison, M}, title = {Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {59}, pmid = {36949471}, issn = {1741-7007}, mesh = {Animals ; Australia ; *Methane/metabolism ; Metagenome ; *Microbiota ; }, abstract = {BACKGROUND: With an increasing interest in the manipulation of methane produced from livestock cultivation, the microbiome of Australian marsupials provides a unique ecological and evolutionary comparison with 'low-methane' emitters. Previously, marsupial species were shown to be enriched for novel lineages of Methanocorpusculum, as well as Methanobrevibacter, Methanosphaera, and Methanomassiliicoccales. Despite sporadic reports of Methanocorpusculum from stool samples of various animal species, there remains little information on the impacts of these methanogens on their hosts.

RESULTS: Here, we characterise novel host-associated species of Methanocorpusculum, to explore unique host-specific genetic factors and their associated metabolic potential. We performed comparative analyses on 176 Methanocorpusculum genomes comprising 130 metagenome-assembled genomes (MAGs) recovered from 20 public animal metagenome datasets and 35 other publicly available Methanocorpusculum MAGs and isolate genomes of host-associated and environmental origin. Nine MAGs were also produced from faecal metagenomes of the common wombat (Vombatus ursinus) and mahogany glider (Petaurus gracilis), along with the cultivation of one axenic isolate from each respective animal; M. vombati (sp. nov.) and M. petauri (sp. nov.).

CONCLUSIONS: Through our analyses, we substantially expand the available genetic information for this genus by describing the phenotypic and genetic characteristics of 23 host-associated species of Methanocorpusculum. These lineages display differential enrichment of genes associated with methanogenesis, amino acid biosynthesis, transport system proteins, phosphonate metabolism, and carbohydrate-active enzymes. These results provide insights into the differential genetic and functional adaptations of these novel host-associated species of Methanocorpusculum and suggest that this genus is ancestrally host-associated.}, } @article {pmid36949342, year = {2023}, author = {Nosalova, L and Kiskova, J and Fecskeova, LK and Piknova, M and Pristas, P}, title = {Bacterial Community Structure of Two Cold Sulfur Springs in Slovakia (Central Europe).}, journal = {Current microbiology}, volume = {80}, number = {5}, pages = {145}, pmid = {36949342}, issn = {1432-0991}, support = {VVGS-PF-2021-1745//Pavol Jozef Safarik University/ ; }, mesh = {Slovakia ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Biodiversity ; Bacteria ; *Hot Springs/microbiology ; Sulfur ; }, abstract = {Sulfur-oxidizing bacteria, especially those from hot springs, have attracted the attention of microbiologists for more than 150 years. In contrast, the microbial diversity of cold sulfur springs remains largely unrecognized. Culture-dependent and culture-independent approaches were used to study the diversity of sulfur-oxidizing bacterial communities in two cold sulfur springs in Slovakia. Geological conditions and resulting spring water chemistry appear to be major factors influencing the composition of the sulfur-oxidizing bacterial community. Bacterial communities in both springs were found to be dominated by Proteobacteria with Epsilonproteobacteria being prevalent in the high-salinity Stankovany spring and Alpha- and Gammaproteobacteria in the low-salinity Jovsa spring. Limited overlap was found between culture-dependent and culture-independent approaches with multiple taxa of cultivated sulfur-oxidizing bacteria not being detected by the culture-independent metagenomics approach. Moreover, four cultivated bacterial isolates could represent novel taxa based on the low similarity of their 16S rRNA gene sequence (similarity lower than 98%) to sequences of known bacteria. Our study supports the current view that multiple approaches are required to assess the bacterial diversity in natural habitats and indicates that sulfur springs in Slovakia harbor unique, yet-undescribed microorganisms.}, } @article {pmid36948151, year = {2023}, author = {Toh, E and Xing, Y and Gao, X and Jordan, SJ and Batteiger, TA and Batteiger, BE and Van Der Pol, B and Muzny, CA and Gebregziabher, N and Williams, JA and Fortenberry, LJ and Fortenberry, JD and Dong, Q and Nelson, DE}, title = {Sexual behavior shapes male genitourinary microbiome composition.}, journal = {Cell reports. Medicine}, volume = {4}, number = {3}, pages = {100981}, pmid = {36948151}, issn = {2666-3791}, support = {K23 AI106957/AI/NIAID NIH HHS/United States ; R01 AI116706/AI/NIAID NIH HHS/United States ; }, mesh = {*Sexual Behavior ; *Urethra/microbiology ; *Microbiota ; Humans ; Male ; }, abstract = {The origin, composition, and significance of the distal male urethral microbiome are unclear, but vaginal microbiome dysbiosis is linked to new sex partners and several urogynecological syndromes. We characterized 110 urethral specimens from men without urethral symptoms, infections, or inflammation using shotgun metagenomics. Most urethral specimens contain characteristic lactic acid bacteria and Corynebacterium spp. In contrast, several bacteria associated with vaginal dysbiosis were present only in specimens from men who reported vaginal intercourse. Sexual behavior, but not other evaluated behavioral, demographic, or clinical variables, strongly associated with inter-specimen variance in urethral microbiome composition. Thus, the male urethra supports a simple core microbiome that is established independent of sexual exposures but can be re-shaped by vaginal sex. Overall, the results suggest that urogenital microbiology and sexual behavior are inexorably intertwined, and show that the male urethra harbors female urogenital pathobionts.}, } @article {pmid36946508, year = {2023}, author = {Mannan, A and Hoque, MN and Noyon, SH and Mehedi, HMH and Foysal, MJ and Salauddin, A and Islam, SMR and Sharmen, F and Tanni, AA and Siddiki, AZ and Tay, A and Siddique, MM and Rahman, MS and Galib, SM and Akter, F}, title = {SARS-CoV-2 infection alters the gut microbiome in diabetes patients: A cross-sectional study from Bangladesh.}, journal = {Journal of medical virology}, volume = {95}, number = {4}, pages = {e28691}, doi = {10.1002/jmv.28691}, pmid = {36946508}, issn = {1096-9071}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/complications ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; Bangladesh/epidemiology ; *COVID-19 ; SARS-CoV-2/genetics ; Bacteria/genetics ; }, abstract = {Populations of different South Asian nations including Bangladesh reportedly have a high risk of developing diabetes in recent years. This study aimed to investigate the differences in the gut microbiome of COVID-19-positive participants with or without type 2 diabetes mellitus (T2DM) compared with healthy control subjects. Microbiome data of 30 participants with T2DM were compared with 22 age-, sex-, and body mass index (BMI)-matched individuals. Clinical features were recorded while fecal samples were collected aseptically from the participants. Amplicon-based (16S rRNA) metagenome analyses were employed to explore the dysbiosis of gut microbiota and its correlation with genomic and functional features in COVID-19 patients with or without T2DM. Comparing the detected bacterial genera across the sample groups, 98 unique genera were identified, of which 9 genera had unique association with COVID-19 T2DM patients. Among different bacterial groups, Shigella (25%), Bacteroides (23.45%), and Megamonas (15.90%) had higher mean relative abundances in COVID-19 patients with T2DM. An elevated gut microbiota dysbiosis in T2DM patients with COVID-19 was observed while some metabolic functional changes correlated with bidirectional microbiome dysbiosis between diabetes and non-diabetes humans gut were also found. These results further highlight the possible association of COVID-19 infection that might be linked with alteration of gut microbiome among T2DM patients.}, } @article {pmid36943059, year = {2023}, author = {Durán-Viseras, A and Sánchez-Porro, C and Viver, T and Konstantinidis, KT and Ventosa, A}, title = {Discovery of the Streamlined Haloarchaeon Halorutilus salinus, Comprising a New Order Widespread in Hypersaline Environments across the World.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0119822}, pmid = {36943059}, issn = {2379-5077}, mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Analysis, DNA ; *Euryarchaeota/genetics ; *Halobacteriales/genetics ; }, abstract = {The class Halobacteria is one of the most diverse groups within the Euryarchaeota phylum, whose members are ubiquitously distributed in hypersaline environments, where they often constitute the major population. Here, we report the discovery and isolation of a new halophilic archaeon, strain F3-133[T] exhibiting ≤86.3% 16S rRNA gene identity to any previously cultivated archaeon, and, thus, representing a new order. Analysis of available 16S rRNA gene amplicon and metagenomic data sets showed that the new isolate represents an abundant group in intermediate-to-high salinity ecosystems and is widely distributed across the world. The isolate presents a streamlined genome, which probably accounts for its ecological success in nature and its fastidious growth in culture. The predominant osmoprotection mechanism appears to be the typical salt-in strategy used by other haloarchaea. Furthermore, the genome contains the complete gene set for nucleotide monophosphate degradation pathway through archaeal RuBisCO, being within the first halophilic archaea representatives reported to code this enzyme. Genomic comparisons with previously described representatives of the phylum Euryarchaeota were consistent with the 16S rRNA gene data in supporting that our isolate represents a novel order within the class Halobacteria for which we propose the names Halorutilales ord. nov., Halorutilaceae fam. nov., Halorutilus gen. nov. and Halorutilus salinus sp. nov. IMPORTANCE The discovery of the new halophilic archaeon, Halorutilus salinus, representing a novel order, family, genus, and species within the class Halobacteria and phylum Euryarchaeota clearly enables insights into the microbial dark matter, expanding the current taxonomical knowledge of this group of archaea. The in-depth comparative genomic analysis performed on this new taxon revealed one of the first known examples of an Halobacteria representative coding the archaeal RuBisCO gene and with a streamlined genome, being ecologically successful in nature and explaining its previous non-isolation. Altogether, this research brings light into the understanding of the physiology of the Halobacteria class members, their ecological distribution, and capacity to thrive in hypersaline environments.}, } @article {pmid36940753, year = {2023}, author = {Stiernborg, M and Debelius, JW and Yang, LL and Skott, E and Millischer, V and Giacobini, M and Melas, PA and Boulund, F and Lavebratt, C}, title = {Bacterial gut microbiome differences in adults with ADHD and in children with ADHD on psychostimulant medication.}, journal = {Brain, behavior, and immunity}, volume = {110}, number = {}, pages = {310-321}, doi = {10.1016/j.bbi.2023.03.012}, pmid = {36940753}, issn = {1090-2139}, mesh = {Humans ; Child ; Adult ; *Attention Deficit Disorder with Hyperactivity/drug therapy ; *Gastrointestinal Microbiome ; *Central Nervous System Stimulants/therapeutic use ; Diet ; Feces ; }, abstract = {Recent evidence suggests that there is a link between neurodevelopmental disorders, such as attention-deficit hyperactivity disorder (ADHD), and the gut microbiome. However, most studies to date have had low sample sizes, have not investigated the impact of psychostimulant medication, and have not adjusted for potential confounders, including body mass index, stool consistency and diet. To this end, we conducted the largest, to our knowledge, fecal shotgun metagenomic sequencing study in ADHD, with 147 well-characterized adult and child patients. For a subset of individuals, plasma levels of inflammatory markers and short-chain fatty acids were also measured. In adult ADHD patients (n = 84), compared to controls (n = 52), we found a significant difference in beta diversity both regarding bacterial strains (taxonomic) and bacterial genes (functional). In children with ADHD (n = 63), we found that those on psychostimulant medication (n = 33 on medication vs. n = 30 not on medication) had (i) significantly different taxonomic beta diversity, (ii) lower functional and taxonomic evenness, (iii) lower abundance of the strain Bacteroides stercoris CL09T03C01 and bacterial genes encoding an enzyme in vitamin B12 synthesis, and (iv) higher plasma levels of vascular inflammatory markers sICAM-1 and sVCAM-1. Our study continues to support a role for the gut microbiome in neurodevelopmental disorders and provides additional insights into the effects of psychostimulant medication. However, additional studies are needed to replicate these findings and examine causal relationships with the disorder.}, } @article {pmid36934910, year = {2023}, author = {Greses, S and De Bernardini, N and Treu, L and Campanaro, S and González-Fernández, C}, title = {Genome-centric metagenomics revealed the effect of pH on the microbiome involved in short-chain fatty acids and ethanol production.}, journal = {Bioresource technology}, volume = {377}, number = {}, pages = {128920}, doi = {10.1016/j.biortech.2023.128920}, pmid = {36934910}, issn = {1873-2976}, mesh = {Fatty Acids ; Ethanol ; Food ; Metagenomics ; *Refuse Disposal ; Fermentation ; Bioreactors ; *Microbiota/genetics ; Hydrogen-Ion Concentration ; Anaerobiosis ; }, abstract = {Added-value chemicals production via food waste (FWs) valorization using open-mixed cultures is an emerging approach to replace petrochemical-based compounds. Nevertheless, the effects of operational parameters on the product spectrum remain uncertain given the wide number of co-occurring species and metabolisms. In this study, the identification of 58 metagenome-assembled genomes and their investigation assessed the effect of slight pH variations on microbial dynamics and the corresponding functions when FWs were subjected to anaerobic fermentation (AF) in 1-L continuous stirred tank reactors at 25 °C. The initial pH of 6.5 promoted a microbial community involved in acetate, butyrate and ethanol production, mediated by Bifidobacterium subtile IE007 and Eubacteriaceae IE027 as main species. A slight pH decrease to 6.1 shaped microbial functions that resulted in caproate and H2 production, increasing the relevance of Eubacteriaceae IE037 role. This study elucidated the strong pH effect on product outputs when minimal variations take place in AF.}, } @article {pmid36934439, year = {2023}, author = {Runde, J and Veseli, I and Fogarty, EC and Watson, AR and Clayssen, Q and Yosef, M and Shaiber, A and Verma, R and Quince, C and Gerasimidis, K and Rubin, DT and Eren, AM}, title = {Transient Suppression of Bacterial Populations Associated with Gut Health is Critical in Success of Exclusive Enteral Nutrition for Children with Crohn's Disease.}, journal = {Journal of Crohn's & colitis}, volume = {17}, number = {7}, pages = {1103-1113}, doi = {10.1093/ecco-jcc/jjad031}, pmid = {36934439}, issn = {1876-4479}, mesh = {Humans ; *Crohn Disease ; Enteral Nutrition ; Remission Induction ; Bacteria ; *Microbiota ; }, abstract = {BACKGROUND AND AIMS: Exclusive enteral nutrition [EEN] is a dietary intervention to induce clinical remission in children with active luminal Crohn's disease [CD]. While changes in the gut microbial communities have been implicated in achieving this remission, a precise understanding of the role of microbial ecology in the restoration of gut homeostasis is lacking.

METHODS: Here we reconstructed genomes from the gut metagenomes of 12 paediatric subjects who were sampled before, during and after EEN. We then classified each microbial population into distinct 'phenotypes' or patterns of response based on changes in their relative abundances throughout the therapy on a per-individual basis.

RESULTS: Our data show that children achieving clinical remission during therapy were enriched with microbial populations that were either suppressed or that demonstrated a transient bloom as a function of EEN. In contrast, this ecosystem-level response was not observed in cases of EEN failure. Further analysis revealed that populations that were suppressed during EEN were significantly more prevalent in healthy children and adults across the globe compared with those that bloomed ephemerally during the therapy.

CONCLUSIONS: These observations taken together suggest that successful outcomes of EEN are marked by a temporary emergence of microbial populations that are rare in healthy individuals, and a concomitant reduction in microbes that are commonly associated with gut homeostasis. Our work is a first attempt to highlight individual-specific, complex environmental factors that influence microbial response in EEN. This model offers a novel, alternative viewpoint to traditional taxonomic strategies used to characterize associations with health and disease states.}, } @article {pmid36933668, year = {2023}, author = {Rohr, JC and Bourassa, KA and Thompson, DS and Fowler, JC and Frueh, BC and Weinstein, BL and Petrosino, J and Madan, A}, title = {History of childhood physical abuse is associated with gut microbiota diversity among adult psychiatric inpatients.}, journal = {Journal of affective disorders}, volume = {331}, number = {}, pages = {50-56}, pmid = {36933668}, issn = {1573-2517}, support = {P30 ES030285/ES/NIEHS NIH HHS/United States ; R25 GM056929/GM/NIGMS NIH HHS/United States ; R25 GM069234/GM/NIGMS NIH HHS/United States ; U54 HG004973/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; Adult ; Child, Preschool ; *Gastrointestinal Microbiome/genetics ; Inpatients ; RNA, Ribosomal, 16S/genetics ; Physical Abuse ; *Microbiota ; }, abstract = {BACKGROUND: Traumatic life events are associated with the development of psychiatric and chronic medical illnesses. This exploratory study examined the relationship between traumatic life events and the gut microbiota among adult psychiatric inpatients.

METHODS: 105 adult psychiatric inpatients provided clinical data and a single fecal sample shortly after admission. A modified version of the Stressful Life Events Screening Questionnaire was used to quantify history of traumatic life events. 16S rRNA gene sequencing was used to analyze the gut microbial community.

RESULTS: Gut microbiota diversity was not associated with overall trauma score or any of the three trauma factor scores. Upon item-level analysis, history of childhood physical abuse was uniquely associated with beta diversity. Linear Discriminant Analysis Effect Size (LefSe) analyses revealed that childhood physical abuse was associated with abundance of distinct bacterial taxa associated with inflammation.

LIMITATIONS: This study did not account for dietary differences, though diet was highly restricted as all participants were psychiatric inpatients. Absolute variance accounted for by the taxa was small though practically meaningful. The study was not powered for full subgroup analysis based on race and ethnicity.

CONCLUSIONS: This study is among the first to demonstrate a relationship between childhood physical abuse and gut microbiota composition among adult psychiatric patients. These findings suggest that early childhood adverse events may have long-conferred systemic consequences. Future efforts may target the gut microbiota for the prevention and/or treatment of psychiatric and medical risk associated with traumatic life events.}, } @article {pmid36933182, year = {2023}, author = {Li, J and Huang, T and Zhang, M and Tong, X and Chen, J and Zhang, Z and Huang, F and Ai, H and Huang, L}, title = {Metagenomic sequencing reveals swine lung microbial communities and metagenome-assembled genomes associated with lung lesions-a pilot study.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {26}, number = {4}, pages = {893-906}, pmid = {36933182}, issn = {1618-1905}, support = {2016YT03H062//Guangdong Sail Plan Introduction of Innovative and Entrepreneurship Research Team Program/ ; nycytx-009//National Swine Industry and Technology System of China/ ; }, mesh = {Swine ; *Metagenome ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Lung/microbiology ; Metagenomics ; Animals ; }, abstract = {Low microbial biomass in the lungs, high host-DNA contamination and sampling difficulty limit the study on lung microbiome. Therefore, little is still known about lung microbial communities and their functions. Here, we perform a preliminary exploratory study to investigate the composition of swine lung microbial community using shotgun metagenomic sequencing and compare the microbial communities between healthy and severe-lesion lungs. We collected ten lavage-fluid samples from swine lungs (five from healthy lungs and five from severe-lesion lungs), and obtained their metagenomes by shotgun metagenomic sequencing. After filtering host genomic DNA contamination (93.5% ± 1.2%) in the lung metagenomic data, we annotated swine lung microbial communities ranging from four domains to 645 species. Compared with previous taxonomic annotation of the same samples by the 16S rRNA gene amplicon sequencing, it annotated the same number of family taxa but more genera and species. We next performed an association analysis between lung microbiome and host lung-lesion phenotype. We found three species (Mycoplasma hyopneumoniae, Ureaplasma diversum, and Mycoplasma hyorhinis) were associated with lung lesions, suggesting they might be the key species causing swine lung lesions. Furthermore, we successfully reconstructed the metagenome-assembled genomes (MAGs) of these three species using metagenomic binning. This pilot study showed us the feasibility and relevant limitations of shotgun metagenomic sequencing for the characterization of swine lung microbiome using lung lavage-fluid samples. The findings provided an enhanced understanding of the swine lung microbiome and its role in maintaining lung health and/or causing lung lesions.}, } @article {pmid36933058, year = {2023}, author = {Balachandran, KRS and Sankara Subramanianan, SH and Dhassiah, MP and Rengarajan, A and Chandrasekaran, M and Rangamaran, VR and Gopal, D}, title = {Microbial community structure and exploration of bioremediation enzymes: functional metagenomics insight into Arabian Sea sediments.}, journal = {Molecular genetics and genomics : MGG}, volume = {298}, number = {3}, pages = {627-651}, pmid = {36933058}, issn = {1617-4623}, mesh = {*Metagenomics/methods ; Biodegradation, Environmental ; *Microbiota/genetics ; Bacteria/genetics ; Hydrocarbons/metabolism ; }, abstract = {Deep-sea sediments provide important information on oceanic biogeochemical processes mediated by the microbiome and their functional roles which could be unravelled using genomic tools. The present study aimed to delineate microbial taxonomic and functional profiles from Arabian Sea sediment samples through whole metagenome sequencing using Nanopore technology. Arabian Sea is considered as a major microbial reservoir with significant bio-prospecting potential which needs to be explored extensively using recent advances in genomics. Assembly, co-assembly, and binning methods were used to predict Metagenome Assembled Genomes (MAGs) which were further characterized by their completeness and heterogeneity. Nanopore sequencing of Arabian Sea sediment samples generated around 1.73 tera basepairs of data. Proteobacteria (78.32%) was found to be the most dominant phylum followed by Bacteroidetes (9.55%) and Actinobacteria (2.14%) in the sediment metagenome. Further, 35 MAGs from assembled and 38 MAGs of co-assembled reads were generated from long-read sequence dataset with major representations from the genera Marinobacter, Kangiella, and Porticoccus. RemeDB analysis revealed a high representation of pollutant-degrading enzymes involved in hydrocarbon, plastic and dye degradation. Validation of enzymes with long nanopore reads using BlastX resulted in better characterization of complete gene signatures involved in hydrocarbon (6-monooxygenase and 4-hydroxyacetophenone monooxygenase) and dye degradation (Arylsulfatase). Enhancing the cultivability of deep-sea microbes predicted from the uncultured WGS approaches by I-tip method resulted in isolation of facultative extremophiles. This study presents a comprehensive insight into the taxonomic and functional profiles of Arabian Sea sediments, indicating a potential hotspot for bioprospection.}, } @article {pmid36931094, year = {2023}, author = {Correia, GD and Marchesi, JR and MacIntyre, DA}, title = {Moving beyond DNA: towards functional analysis of the vaginal microbiome by non-sequencing-based methods.}, journal = {Current opinion in microbiology}, volume = {73}, number = {}, pages = {102292}, doi = {10.1016/j.mib.2023.102292}, pmid = {36931094}, issn = {1879-0364}, support = {MR/X004996/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Female ; Humans ; *Microbiota/genetics ; Metagenomics/methods ; Host Microbial Interactions ; DNA ; }, abstract = {Over the last two decades, sequencing-based methods have revolutionised our understanding of niche-specific microbial complexity. In the lower female reproductive tract, these approaches have enabled identification of bacterial compositional structures associated with health and disease. Application of metagenomics and metatranscriptomics strategies have provided insight into the putative function of these communities but it is increasingly clear that direct measures of microbial and host cell function are required to understand the contribution of microbe-host interactions to pathophysiology. Here we explore and discuss current methods and approaches, many of which rely upon mass-spectrometry, being used to capture functional insight into the vaginal mucosal interface. In addition to improving mechanistic understanding, these methods offer innovative solutions for the development of diagnostic and therapeutic strategies designed to improve women's health.}, } @article {pmid36930418, year = {2023}, author = {Thakur, N and Nigam, M and Awasthi, G and Shukla, A and Shah, AA and Negi, N and Khan, SA and Casini, R and Elansary, HO}, title = {Synergistic soil-less medium for enhanced yield of crops: a step towards incorporating genomic tools for attaining net zero hunger.}, journal = {Functional & integrative genomics}, volume = {23}, number = {2}, pages = {86}, pmid = {36930418}, issn = {1438-7948}, support = {RSP2023R118//Researchers Supporting Project (RSP2023R118), King Saud University/ ; }, mesh = {Humans ; *CRISPR-Cas Systems ; *Soil ; Proteomics ; Hunger ; Phylogeny ; Genome, Plant ; Plant Breeding/methods ; Crops, Agricultural/genetics ; Genomics ; }, abstract = {Globally, industrial farming endangers crucial ecological mechanisms upon which food production relies, while 815 million people are undernourished and a significant number are malnourished. Zero Hunger aims to concurrently solve global ecological sustainability and food security concerns. Recent breakthroughs in molecular tools and approaches have allowed scientists to detect and comprehend the nature and structure of agro-biodiversity at the molecular and genetic levels, providing us an advantage over traditional methods of crop breeding. These bioinformatics techniques let us optimize our target plants for our soil-less medium and vice versa. Most of the soil-borne and seed-borne diseases are the outcomes of non-treated seed and growth media, which are important factors in low productivity. The farmers do not consider these issues, thereby facing problems growing healthy crops and suffering economic losses. This study is going to help the farmers increase their eco-friendly, chemical residue-free, quality yield of crops and their economic returns. The present invention discloses a synergistic soil-less medium that consists of only four ingredients mixed in optimal ratios by weight: vermicompost (70-80%), vermiculite (10-15%), coco peat (10-15%), and Rhizobium (0-1%). The medium exhibits better physical and chemical characteristics than existing conventional media. The vermiculite to coco peat ratio is reduced, while the vermicompost ratio is increased, with the goals of lowering toxicity, increasing plant and water holding capacity, avoiding drying of the media, and conserving water. The medium provides balanced nutrition and proper ventilation for seed germination and the growth of seedlings. Rhizobium is also used to treat the plastic bags and seeds. The results clearly show that the current synergistic soil-less environment is best for complete plant growth. Securing genetic advantages via sexual recombination, induced random mutations, and transgenic techniques have been essential for the development of improved agricultural varieties. The recent availability of targeted genome-editing technology provides a new path for integrating beneficial genetic modifications into the most significant agricultural species on the planet. Clustered regularly interspaced short palindromic repeats and associated protein 9 (CRISPR/Cas9) has evolved into a potent genome-editing tool for imparting genetic modifications to crop species. In addition, the integration of analytical methods like population genomics, phylogenomics, and metagenomics addresses conservation problems, while whole genome sequencing has opened up a new dimension for explaining the genome architecture and its interactions with other species. The in silico genomic and proteomic investigation was also conducted to forecast future investigations for the growth of French beans on a synergistic soil-less medium with the purpose of studying how a blend of vermicompost, vermiculite, cocopeat, and Rhizobium secrete metal ions, and other chemical compounds into the soil-less medium and affect the development of our target plant as well as several other plants. This interaction was studied using functional and conserved region analysis, phylogenetic analysis, and docking tools.}, } @article {pmid36929732, year = {2023}, author = {Ma, ZS}, title = {Virome comparison (VC): A novel approach to comparing viromes based on virus species specificity and virome specificity diversity.}, journal = {Journal of medical virology}, volume = {95}, number = {4}, pages = {e28682}, doi = {10.1002/jmv.28682}, pmid = {36929732}, issn = {1096-9071}, mesh = {Humans ; *Virome/genetics ; Species Specificity ; *Viruses/genetics ; Metagenomics ; }, abstract = {The human virome, or the viral communities distributed on or in our body, is estimated to contain about 380 trillion of viruses (individuals), which has far reaching influences on our health and diseases. Obviously, the sheer numbers of viruses alone make the comparisons of two or multiple viromes extremely challenging. In fact, the theory of computation in computer science for so-termed NP-hard problems stipulates that the problem is unsolvable when the size of virome is sufficiently large even with fastest supercomputers. Practically, one has to develop heuristic and approximate algorithms to obtain practically satisfactory solutions for NP-hard problems. Here, we extend the species-specificity and specificity-diversity framework to develop a method for virome comparison (VC). The VC method consists of a pair of metrics: virus species specificity (VS) and virome specificity diversity (VSD) and corresponding pair of random search algorithms. Specifically, the VS and VS permutation (VSP) test can detect unique virus species (US) or enriched virus species (ES) in each virome (treatment), and the VSD and VSD permutation (VSDP) test can further determine holistic differences between two viromes or their subsets (assemblages of viruses). The test with four virome data sets demonstrated that the VC method is effective, efficient, and robust.}, } @article {pmid36929191, year = {2023}, author = {Sharma, P and Singh, S and Das, K and Mahant, S and Das, R}, title = {Dysbiosis of gut microbiota due to diet, alcohol intake, body mass index, and gastrointestinal diseases in India.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {7-8}, pages = {2547-2560}, pmid = {36929191}, issn = {1432-0614}, support = {EMR/2016/003676//Department of Science and Technology, India/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Body Mass Index ; RNA, Ribosomal, 16S/genetics ; Dysbiosis ; Diet ; Bacteria/genetics ; Alcohol Drinking ; *Gastrointestinal Diseases ; }, abstract = {The human gut is composed of diverse microflora which is influenced by dietary intake. Body mass index (BMI) and lifestyle patterns also play a vital role in human health to alter gut microbial composition. Our study aims to determine the impact of alcohol intake, BMI, and diet on gut microbiota and its relationship with gastrointestinal disorders. Thirty-nine gastric biopsies were taken from patients with various gastrointestinal (GI) diseases, and all the patient's lifestyle behavior were recorded in a written proforma. 16S rRNA metagenome analysis for V3-V4 regions was used to examine microbial compositions. The richness and diversity of gut microbiota were analyzed by PERMANOVA using the Bray-Curtis dissimilarity index and principal component analysis. The difference in relative abundance was calculated by ANOVA (p < 0.05). Alpha diversity indexes between vegetarians and non-vegetarians showed no significant difference based on BMI, alcohol status, and GI diseases. We found that in overweight vegetarian individuals Faecalibacterium and Rumicococcus might play a role in the control of Helicobacter pylori. Similarly, the increased abundance of Akkermansia muciniphila in non-vegetarian individuals with normal BMI might play a role to decrease the level of harmful bacteria like H. pylori, and Corynebacterium sp. Also, the relative abundance of Corynebacterium sp. among the vegetarians and Streptococcus sp. in the non-vegetarians was increased in alcoholics while H. pylori was increased in non-alcoholics irrespective of diet. There is an increased abundance of Faecalibacterium prausnitzii in vegetarians among all categories; however, we did not find any correlation between disease outcomes. Our study shows that alcohol intake and dietary habits have independent effects on gut microbial composition. The relative abundance of F. prausnitzii was high among vegetarians in all categories. KEY POINTS: • The presence of H. pylori is less among alcoholics. • Good bacteria help to maintain a normal body mass index. • Gut microbiota richness is high in vegetarians and diversity in non-vegetarians.}, } @article {pmid36929080, year = {2023}, author = {Ma, S and Li, H}, title = {Statistical and Computational Methods for Microbial Strain Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2629}, number = {}, pages = {231-245}, pmid = {36929080}, issn = {1940-6029}, mesh = {*Microbiota/genetics ; Metagenome ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; }, abstract = {Microbial strains are interpreted as a lineage derived from a recent ancestor that have not experienced "too many" recombination events and can be successfully retrieved with culture-independent techniques using metagenomic sequencing. Such a strain variability has been increasingly shown to display additional phenotypic heterogeneities that affect host health, such as virulence, transmissibility, and antibiotics resistance. New statistical and computational methods have recently been developed to track the strains in samples based on shotgun metagenomics data either based on reference genome sequences or Metagenome-assembled genomes (MAGs). In this paper, we review some recent statistical methods for strain identifications based on frequency counts at a set of single nucleotide variants (SNVs) within a set of single-copy marker genes. These methods differ in terms of whether reference genome sequences are needed, how SNVs are called, what methods of deconvolution are used and whether the methods can be applied to multiple samples. We conclude our review with areas that require further research.}, } @article {pmid36929079, year = {2023}, author = {Kim, Y}, title = {Bioinformatic and Statistical Analysis of Microbiome Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2629}, number = {}, pages = {183-229}, pmid = {36929079}, issn = {1940-6029}, mesh = {Humans ; Phylogeny ; *Microbiota/genetics ; Biodiversity ; Computational Biology/methods ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Since advances in next-generation sequencing (NGS) technique enabled to investigate uncultured microbiota and their genomes in unbiased manner, many microbiome researches have been reporting strong evidences for close links of microbiome to human health and disease. Bioinformatic and statistical analysis of NGS-based microbiome data are essential components in those microbiome researches to explore the complex composition of microbial community and understand the functions of community members in relation to host and environment. This chapter introduces bioinformatic analysis methods that generate taxonomy and functional feature count table along with phylogenetic tree from raw NGS microbiome data and then introduce statistical methods and machine learning approaches for analyzing the outputs of the bioinformatic analysis to infer the biodiversity of a microbial community and unravel host-microbiome association. Understanding the advantages and limitations of the analysis methods will help readers use the methods correctly in microbiome data analysis and may give a new opportunity to develop new analytic techniques for microbiome research.}, } @article {pmid36928772, year = {2023}, author = {Zhao, X and Guo, Y and Kang, L and Yin, C and Bi, A and Xu, D and Zhang, Z and Zhang, J and Yang, X and Xu, J and Xu, S and Song, X and Zhang, M and Li, Y and Kear, P and Wang, J and Liu, Z and Fu, X and Lu, F}, title = {Population genomics unravels the Holocene history of bread wheat and its relatives.}, journal = {Nature plants}, volume = {9}, number = {3}, pages = {403-419}, pmid = {36928772}, issn = {2055-0278}, support = {32225038//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31970631//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Humans ; *Genome, Plant ; *Triticum/genetics ; Metagenomics ; Bread ; Europe ; }, abstract = {Deep knowledge of crop biodiversity is essential to improving global food security. Despite bread wheat serving as a keystone crop worldwide, the population history of bread wheat and its relatives, both cultivated and wild, remains elusive. By analysing whole-genome sequences of 795 wheat accessions, we found that bread wheat originated from the southwest coast of the Caspian Sea and underwent a slow speciation process, lasting ~3,300 yr owing to persistent gene flow from its relatives. Soon after, bread wheat spread across Eurasia and reached Europe, South Asia and East Asia ~7,000 to ~5,000 yr ago, shaping a diversified but occasionally convergent adaptive landscape in novel environments. By contrast, the cultivated relatives of bread wheat experienced a population decline by ~82% over the past ~2,000 yr due to the food choice shift of humans. Further biogeographical modelling predicted a continued population shrinking of many bread wheat relatives in the coming decades because of their vulnerability to the changing climate. These findings will guide future efforts in protecting and utilizing wheat biodiversity to enhance global wheat production.}, } @article {pmid36927795, year = {2023}, author = {Yi, X and Huang, C and Huang, C and Zhao, M and Lu, Q}, title = {Fecal microbiota from MRL/lpr mice exacerbates pristane-induced lupus.}, journal = {Arthritis research & therapy}, volume = {25}, number = {1}, pages = {42}, pmid = {36927795}, issn = {1478-6362}, mesh = {Mice ; Animals ; Mice, Inbred MRL lpr ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Feces ; *Lupus Erythematosus, Systemic/chemically induced ; }, abstract = {BACKGROUND: The roles of gut microbiota in the pathogenesis of SLE have been receiving much attention during recent years. However, it remains unknown how fecal microbiota transplantation (FMT) and microbial metabolites affect immune responses and lupus progression.

METHODS: We transferred fecal microbiota from MRL/lpr (Lpr) mice and MRL/Mpj (Mpj) mice or PBS to pristane-induced lupus mice and observed disease development. We also screened gut microbiota and metabolite spectrums of pristane-induced lupus mice with FMT via 16S rRNA sequencing, metagenomic sequencing, and metabolomics, followed by correlation analysis.

RESULTS: FMT from MRL/lpr mice promoted the pathogenesis of pristane-induced lupus and affected immune cell profiles in the intestine, particularly the plasma cells. The structure and composition of microbial communities in the gut of the FMT-Lpr mice were different from those of the FMT-Mpj mice and FMT-PBS mice. The abundances of specific microbes such as prevotella taxa were predominantly elevated in the gut microbiome of the FMT-Lpr mice, which were positively associated with functional pathways such as cyanoamino acid metabolism. Differential metabolites such as valine and L-isoleucine were identified with varied abundances among the three groups. The abundance alterations of the prevotella taxa may affect the phenotypic changes such as proteinuria levels in the pristane-induced lupus mice.

CONCLUSION: These findings further confirm that gut microbiota play an important role in the pathogenesis of lupus. Thus, altering the gut microbiome may provide a novel way to treat lupus.}, } @article {pmid36927601, year = {2023}, author = {Thorn, CS and Maness, RW and Hulke, JM and Delmore, KE and Criscione, CD}, title = {Population genomics of helminth parasites.}, journal = {Journal of helminthology}, volume = {97}, number = {}, pages = {e29}, doi = {10.1017/S0022149X23000123}, pmid = {36927601}, issn = {1475-2697}, support = {DEB-1655147//National Science Foundation/ ; }, mesh = {*Metagenomics ; Host-Parasite Interactions/physiology ; *Helminths/classification/genetics ; Hybridization, Genetic/genetics ; Genetic Variation ; Chromosome Mapping ; Drug Resistance/genetics ; Biological Evolution ; Parasitology/trends ; }, abstract = {Next generation sequencing technologies have facilitated a shift from a few targeted loci in population genetic studies to whole genome approaches. Here, we review the types of questions and inferences regarding the population biology and evolution of parasitic helminths being addressed within the field of population genomics. Topics include parabiome, hybridization, population structure, loci under selection and linkage mapping. We highlight various advances, and note the current trends in the field, particularly a focus on human-related parasites despite the inherent biodiversity of helminth species. We conclude by advocating for a broader application of population genomics to reflect the taxonomic and life history breadth displayed by helminth parasites. As such, our basic knowledge about helminth population biology and evolution would be enhanced while the diversity of helminths in itself would facilitate population genomic comparative studies to address broader ecological and evolutionary concepts.}, } @article {pmid36926893, year = {2023}, author = {Shi, C and Tong, M and Cai, Q and Li, Z and Li, P and Lu, Y and Cao, Z and Liu, H and Zhao, HP and Yuan, S}, title = {Electrokinetic-Enhanced Bioremediation of Trichloroethylene-Contaminated Low-Permeability Soils: Mechanistic Insight from Spatio-Temporal Variations of Indigenous Microbial Community and Biodehalogenation Activity.}, journal = {Environmental science & technology}, volume = {57}, number = {12}, pages = {5046-5055}, doi = {10.1021/acs.est.3c00278}, pmid = {36926893}, issn = {1520-5851}, mesh = {*Trichloroethylene ; Biodegradation, Environmental ; Ferric Compounds ; Bacteria ; *Microbiota ; Soil ; Permeability ; Iron ; }, abstract = {Electrokinetic-enhanced bioremediation (EK-Bio), particularly bioaugmentation with injection of biodehalogenation functional microbes such as Dehalococcoides, has been documented to be effective in treating a low-permeability subsurface matrix contaminated with chlorinated ethenes. However, the spatio-temporal variations of indigenous microbial community and biodehalogenation activity of the background matrix, a fundamental aspect for understanding EK-Bio, remain unclear. To fill this gap, we investigated the variation of trichloroethylene (TCE) biodehalogenation activity in response to indigenous microbial community succession in EK-Bio by both column and batch experiments. For a 195 day EK-Bio column (∼1 V/cm, electrolyte circulation, lactate addition), biodehalogenation activity occurred first near the cathode (<60 days) and then spread to the anode (>90 days), which was controlled by electron acceptor (i.e., Fe(III)) competition and microbe succession. Amplicon sequencing and metagenome analysis revealed that iron-reducing bacteria (Geobacter, Anaeromyxobacter, Geothrix) were enriched within initial 60 d and were gradually replaced by organohalide-respiring bacteria (versatile Geobacter and obligate Dehalobacter) afterward. Iron-reducing bacteria required an initial long time to consume the competitive electron acceptors so that an appropriate reductive condition could be developed for the enrichment of organohalide-respiring bacteria and the enhancement of TCE biodehalogenation activity.}, } @article {pmid36925044, year = {2023}, author = {Baldanzi, G and Sayols-Baixeras, S and Theorell-Haglöw, J and Dekkers, KF and Hammar, U and Nguyen, D and Lin, YT and Ahmad, S and Holm, JB and Nielsen, HB and Brunkwall, L and Benedict, C and Cedernaes, J and Koskiniemi, S and Phillipson, M and Lind, L and Sundström, J and Bergström, G and Engström, G and Smith, JG and Orho-Melander, M and Ärnlöv, J and Kennedy, B and Lindberg, E and Fall, T}, title = {OSA Is Associated With the Human Gut Microbiota Composition and Functional Potential in the Population-Based Swedish CardioPulmonary bioImage Study.}, journal = {Chest}, volume = {164}, number = {2}, pages = {503-516}, pmid = {36925044}, issn = {1931-3543}, mesh = {Adult ; Animals ; Humans ; *Sleep Apnea, Obstructive ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Sweden/epidemiology ; Hypoxia ; }, abstract = {BACKGROUND: OSA is a common sleep-breathing disorder linked to increased risk of cardiovascular disease. Intermittent upper airway obstruction and hypoxia, hallmarks of OSA, have been shown in animal models to induce substantial changes to the gut microbiota composition, and subsequent transplantation of fecal matter to other animals induced changes in BP and glucose metabolism.

RESEARCH QUESTION: Does OSA in adults associate with the composition and functional potential of the human gut microbiota?

STUDY DESIGN AND METHODS: We used respiratory polygraphy data from up to 3,570 individuals 50 to 64 years of age from the population-based Swedish Cardiopulmonary bioimage Study combined with deep shotgun metagenomics of fecal samples to identify cross-sectional associations between three OSA parameters covering apneas and hypopneas, cumulative sleep time in hypoxia, and number of oxygen desaturation events with gut microbiota composition. Data collection about potential confounders was based on questionnaires, onsite anthropometric measurements, plasma metabolomics, and linkage with the Swedish Prescribed Drug Register.

RESULTS: We found that all three OSA parameters were associated with lower diversity of species in the gut. Furthermore, in multivariable-adjusted analysis, the OSA-related hypoxia parameters were associated with the relative abundance of 128 gut bacterial species, including higher abundance of Blautia obeum and Collinsella aerofaciens. The latter species was also independently associated with increased systolic BP. Furthermore, the cumulative time in hypoxia during sleep was associated with the abundance of genes involved in nine gut microbiota metabolic pathways, including propionate production from lactate. Finally, we observed two heterogeneous sets of plasma metabolites with opposite association with species positively and negatively associated with hypoxia parameters, respectively.

INTERPRETATION: OSA-related hypoxia, but not the number of apneas/hypopneas, is associated with specific gut microbiota species and functions. Our findings lay the foundation for future research on the gut microbiota-mediated health effects of OSA.}, } @article {pmid36922730, year = {2023}, author = {Omori, M and Kato-Kogoe, N and Sakaguchi, S and Komori, E and Inoue, K and Yamamoto, K and Hamada, W and Hayase, T and Tano, T and Nakamura, S and Nakano, T and Une, H and Ueno, T}, title = {Characterization of Oral Microbiota Following Chemotherapy in Patients With Hematopoietic Malignancies.}, journal = {Integrative cancer therapies}, volume = {22}, number = {}, pages = {15347354231159309}, pmid = {36922730}, issn = {1552-695X}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Stomatitis/chemically induced ; *Microbiota ; *Hematologic Neoplasms/drug therapy ; Bacteria ; }, abstract = {Oral microbiota may be associated with serious local or systemic medical conditions resulting from chemotherapy. This study was conducted to evaluate the changes in the oral microbiota following the initiation of chemotherapy in patients with hematopoietic malignancies and to identify the characteristics of the oral microbiota associated with oral mucositis. Oral samples were collected from 57 patients with hematopoietic malignancies at 2 time points: before the start of chemotherapy and 8 to 20 days after the start of chemotherapy, when chemotherapy-induced oral mucositis often occurs, and 16S rRNA metagenomic analyses were performed. Comparative and linear discriminant analysis effect size (LEfSe) analyses were used to determine the characteristic bacterial groups before and after the initiation of chemotherapy and in those who developed oral mucositis. The alpha and beta diversities of oral microbiota before and after the initiation of chemotherapy differed significantly (operational taxonomic unit index, P < .001; Shannon's index, P < .001; unweighted UniFrac distances, P = .001; and weighted UniFrac distances, P = .001). The LEfSe analysis revealed a group of bacteria whose abundance differed significantly before and after the initiation of chemotherapy. In the group of patients who developed oral mucositis, a characteristic group of bacteria was identified before the start of chemotherapy. In conclusion, we characterized the oral microbiota associated with the initiation of chemotherapy in patients with hematopoietic malignancies. In addition, our findings suggest that oral microbiota composition before the start of chemotherapy may be associated with oral mucositis. The results of this study emphasize the importance of oral management focusing on the oral microbiota during chemotherapy in patients with hematologic malignancies.}, } @article {pmid36922572, year = {2023}, author = {Michishita, R and Shimoda, M and Furukawa, S and Uehara, T}, title = {Inoculation with black soldier fly larvae alters the microbiome and volatile organic compound profile of decomposing food waste.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {4297}, pmid = {36922572}, issn = {2045-2322}, mesh = {Animals ; Larva/metabolism ; Food ; *Volatile Organic Compounds/metabolism ; *Refuse Disposal ; *Diptera/metabolism ; *Microbiota ; }, abstract = {The black soldier fly (BSF; Hermetia illucens) is used in sustainable processing of many types of organic waste. However, organic waste being decomposed by BSF produces strong odors, hindering more widespread application. The odor components and how they are produced have yet to be characterized. We found that digestion of food waste by BSF significantly alters the microbial flora, based on metagenomic analyses, and the odor components generated, as shown by thermal desorption gas chromatography mass spectrometry analysis. Inoculation with BSF significantly decreased production of volatile organic sulfur compounds (dimethyl disulfide and dimethyl trisulfide), which are known to be released during methionine and cysteine metabolism by Lactobacillus and Enterococcus bacteria. BSF inoculation significantly changed the abundance of Lactobacillus and Enterococcus and decreased microbial diversity overall. These findings may help in optimizing use of BSF for deodorization of composting food waste.}, } @article {pmid36922385, year = {2023}, author = {Yang, S and Fan, Z and Li, J and Wang, X and Lan, Y and Yue, B and He, M and Zhang, A and Li, J}, title = {Assembly of novel microbial genomes from gut metagenomes of rhesus macaque (Macaca mulatta).}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2188848}, pmid = {36922385}, issn = {1949-0984}, mesh = {Animals ; Humans ; *Metagenome ; Macaca mulatta/genetics ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; Genome, Microbial ; Diarrhea/microbiology ; Metagenomics/methods ; }, abstract = {Rhesus macaque (RM, Macaca mulatta), as an important model animal, commonly suffers from chronic diarrheal disease, challenging the breeding of RMs. Gut microbiomes play key roles in maintaining intestinal health of RMs. However, it is still unclear about more features of gut microbiome as responsible for intestinal health of RMs. In this study, we performed de novo assembly of metagenome-assembled genomes (MAGs) based on fecal metagenomes from chronic diarrheal RMs and asymptomatic individuals. In total of 731 non-redundant MAGs with at least 80% completeness were reconstructed in this study. More than 97% MAGs were novel genomes compared with more than 250,000 reference genomes. MAGs of Campylobacter and Helicobacteraceae from RM guts mainly carried flagella-associated virulence genes and chemotaxis-associated virulence genes, which might mediate motility and adhesion of bacteria. Comparing to MAGs of Campylobacter from humans, distributions and functions of these MAGs of Campylobacter from RMs exhibited significant differences. Most members of Bacteroidota, Spirochaetota, Helicobacteraceae, Lactobacillaceae and Anaerovibrio significantly decreased in guts of chronic diarrhea RMs. More than 92% MAGs in this study were not contained in 2,985 MAGs previously reported from other 22 non-human primates (NHPs), expanding the microbial diversity in guts of NHPs. The distributions and functions of gut microbiome were prominently influenced by host phylogeny of NHPs. Our results could help to more clearly understand about the diversity and function of RMs gut microbiome.}, } @article {pmid36921777, year = {2023}, author = {Li, P and Chen, CZ and Zhao, XL and Liu, L and Li, ZH}, title = {Metagenomics analysis reveals the effects of norfloxacin on the gut microbiota of juvenile common carp (Cyprinus carpio).}, journal = {Chemosphere}, volume = {325}, number = {}, pages = {138389}, doi = {10.1016/j.chemosphere.2023.138389}, pmid = {36921777}, issn = {1879-1298}, mesh = {Animals ; *Gastrointestinal Microbiome ; Norfloxacin/toxicity ; *Carps ; Metagenomics ; Bacteria/genetics ; Anti-Bacterial Agents/toxicity ; }, abstract = {Norfloxacin (NOR) is an early third-generation quinolone antibiotic that has been widely used in animal husbandry and aquaculture because of its bactericidal properties. As an emerging contaminant, NOR may have toxic effects on fish. This study assessed the chronic toxicity (6 weeks) of 0 (control group), 100 ng/L (environmental concentration), and 1 mg/L NOR to the gut microbiota of juvenile common carp (Cyprinus carpio) based on metagenomic sequencing. Metagenomic analysis revealed that the Proteobacteria, Bacteroidetes, Fusobacteria, Firmicutes, and Actinobacteria were the dominant bacteria in the gut of common carp. The relative abundance of Actinobacteria was highest in the control group. The alpha diversity of the environmental concentration NOR was significantly lower than the control group. Principal coordinates analysis (PCoA) indicated that the bacterial community between the different groups formed clear separate clusters. NOR exposure adversely could affect immune function and some substance metabolic pathways in the gut microbiota of common carp. Furthermore, environmental concentrations of NOR produce antibiotic resistance genes (ARGs) in the gut microbiota, enhancing resistance to drugs. In conclusion, environmental concentrations of NOR could alter the composition, structure, and abundance of ARGs in the gut microbiota, thereby affecting the intestinal health of fish.}, } @article {pmid36921697, year = {2023}, author = {Wong, D and Norman, H and Creedy, TJ and Jordaens, K and Moran, KM and Young, A and Mengual, X and Skevington, JH and Vogler, AP}, title = {The phylogeny and evolutionary ecology of hoverflies (Diptera: Syrphidae) inferred from mitochondrial genomes.}, journal = {Molecular phylogenetics and evolution}, volume = {184}, number = {}, pages = {107759}, doi = {10.1016/j.ympev.2023.107759}, pmid = {36921697}, issn = {1095-9513}, mesh = {Animals ; Phylogeny ; *Genome, Mitochondrial ; *Diptera/genetics ; Bayes Theorem ; Larva ; }, abstract = {Hoverflies (Diptera: Syrphidae) are a diverse group of pollinators and a major research focus in ecology, but their phylogenetic relationships remain incompletely known. Using a genome skimming approach we generated mitochondrial genomes for 91 species, capturing a wide taxonomic diversity of the family. To reduce the required amount of input DNA and overall cost of the library construction, sequencing and assembly was conducted on mixtures of specimens, which raises the problem of chimera formation of mitogenomes. We present a novel chimera detection test based on gene tree incongruence, but identified only a single mitogenome of chimeric origin. Together with existing data for a final set of 127 taxa, phylogenetic analysis on nucleotide and amino acid sequences using Maximum Likelihood and Bayesian Inference revealed a basal split of Microdontinae from all other syrphids. The remainder consists of several deep clades assigned to the subfamily Eristalinae in the current classification, including a clade comprising the subfamily Syrphinae (plus Pipizinae). These findings call for a re-definition of subfamilies, but basal nodes had insufficient support to fully justify such action. Molecular-clock dating placed the origin of the Syrphidae crown group in the mid-Cretaceous while the Eristalinae-Syrphinae clade likely originated near the K/Pg boundary. Transformation of larval life history characters on the tree suggests that Syrphidae initially had sap feeding larvae, which diversified greatly in diet and habitat association during the Eocene and Oligocene, coinciding with the diversification of angiosperms and the evolution of various insect groups used as larval host, prey, or mimicry models. Mitogenomes proved to be a powerful phylogenetic marker for studies of Syrphidae at subfamily and tribe levels, allowing dense taxon sampling that provided insight into the great ecological diversity and rapid evolution of larval life history traits of the hoverflies.}, } @article {pmid36921549, year = {2023}, author = {Bortoluzzi, C and Tamburini, I and Geremia, J}, title = {Microbiome modulation, microbiome protein metabolism index, and growth performance of broilers supplemented with a precision biotic.}, journal = {Poultry science}, volume = {102}, number = {5}, pages = {102595}, pmid = {36921549}, issn = {1525-3171}, mesh = {Animals ; *Chickens ; Diet/veterinary ; Dietary Supplements/analysis ; *Microbiota ; Body Weight ; Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; }, abstract = {The objectives of the present studies were to evaluate: 1) the in vivo impact of the supplementation with a precision biotic (PB) on the growth performance and microbiome modulation of broiler chickens; 2) the role of PB on the modulation of functional pathways of the microbiome collected from animals with low and high body weight gain, and 3) to develop a Microbiome Protein Metabolism Index (MPMI) derived from gut metagenomic data to link microbial protein metabolism with performance. The in vivo work consisted of 2 experiments with 2 treatments: Control vs. PB at 1.1 kg/MT of PB with 21 or 14 replicates of 40 birds per replicate, in experiments 1 and 2, respectively. Growth performance was evaluated in both experiments, and from experiment 1, cecal samples from one bird/replicate was collected on d 21 and 42 (n = 21/treatment) to evaluate the microbiome through whole genome sequencing. In the ex vivo assay, 6 cecal samples were collected from low body weight (BW) birds (at 10% below average), and 6 samples from high BW birds (at least 10% above average). The samples were incubated in the presence or absence of PB. After incubation, DNA was isolated to develop a functional genomic assay and the supernatant was separated to measure short-chain fatty acid (SCFA) production. The MPMI is the sum of beneficial genes in the pathways related to protein metabolism. In the in vivo grow out experiments, it was observed that the supplementation improved the BW gain by 3% in both studies, and the corrected feed conversion ratio (cFCR) by 3.7 and 3.4% in studies 1 and 2, respectively (P < 0.05). The functional microbiome analysis revealed that the PB shifted the microbiome pathways toward a beneficial increase in protein utilization, as shown by higher MPMI. In the ex vivo experiment, the PB increased the abundance of genes related to the beneficial metabolism of protein (quantitative MPMI), and the concentration of SCFA, regardless of the underline BW of the birds. Taken together, the microbiome metabolic shift observed in the in vivo study and higher MPMI, plus the observations from the ex vivo assay with higher SFCA production, may explain the improvement in growth performance obtained with the supplementation of PB.}, } @article {pmid36920617, year = {2023}, author = {Kumar, R and Yadav, G and Kuddus, M and Ashraf, GM and Singh, R}, title = {Unlocking the microbial studies through computational approaches: how far have we reached?.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {17}, pages = {48929-48947}, pmid = {36920617}, issn = {1614-7499}, mesh = {*Artificial Intelligence ; Metagenomics ; *Microbiota ; Proteomics ; DNA ; }, abstract = {The metagenomics approach accelerated the study of genetic information from uncultured microbes and complex microbial communities. In silico research also facilitated an understanding of protein-DNA interactions, protein-protein interactions, docking between proteins and phyto/biochemicals for drug design, and modeling of the 3D structure of proteins. These in silico approaches provided insight into analyzing pathogenic and nonpathogenic strains that helped in the identification of probable genes for vaccines and antimicrobial agents and comparing whole-genome sequences to microbial evolution. Artificial intelligence, more precisely machine learning (ML) and deep learning (DL), has proven to be a promising approach in the field of microbiology to handle, analyze, and utilize large data that are generated through nucleic acid sequencing and proteomics. This enabled the understanding of the functional and taxonomic diversity of microorganisms. ML and DL have been used in the prediction and forecasting of diseases and applied to trace environmental contaminants and environmental quality. This review presents an in-depth analysis of the recent application of silico approaches in microbial genomics, proteomics, functional diversity, vaccine development, and drug design.}, } @article {pmid36920536, year = {2023}, author = {Kazarina, A and Kuzmicka, J and Bortkevica, S and Zayakin, P and Kimsis, J and Igumnova, V and Sadovska, D and Freimane, L and Kivrane, A and Namina, A and Capligina, V and Poksane, A and Ranka, R}, title = {Oral microbiome variations related to ageing: possible implications beyond oral health.}, journal = {Archives of microbiology}, volume = {205}, number = {4}, pages = {116}, pmid = {36920536}, issn = {1432-072X}, mesh = {Humans ; *Oral Health ; *Microbiota ; Bacteria/genetics ; Aging ; Cluster Analysis ; RNA, Ribosomal, 16S ; }, abstract = {The global population is getting older due to a combination of longer life expectancy and declining birth rates. Growing evidence suggests that the oral microbiota composition and distribution may have a profound effect on how well we age. The purpose of this study was to investigate age-related oral microbiome variations of supragingival plaque and buccal mucosa samples in the general population in Latvia. Our results indicated significant difference between supragingival plaque bacterial profiles of three age groups (20-40; 40-60; 60 + years). Within supragingival plaque samples, age group 20-40 showed the highest bacterial diversity with a decline during the 40-60 age period and uprise again after the age of 60. Among other differences, the important oral commensal Neisseria had declined after the age of 40. Additionally, prevalence of two well-documented opportunistic pathogens Streptococcus anginosus and Gemella sanguinis gradually rose with age within our samples. Furthermore, supragingival plaque and buccal mucosa samples significantly differed in overall bacterial composition.}, } @article {pmid36920238, year = {2023}, author = {Kallner, A and Debelius, J and Schuppe-Koistinen, I and Pereira, M and Engstrand, L}, title = {Effects of Consuming Fermented Fish (Surströmming) on the Fecal Microflora in Healthy Individuals.}, journal = {Journal of medicinal food}, volume = {26}, number = {3}, pages = {185-192}, doi = {10.1089/jmf.2021.0195}, pmid = {36920238}, issn = {1557-7600}, mesh = {Animals ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Bacteria ; *Gastrointestinal Microbiome/genetics ; }, abstract = {Surströmming, a Swedish fermented fish, loved by some and avoided by others, occurs in many reports on improved or cured gastrointestinal problems even by a single meal. We tested the hypothesis that the microbes of the fermented food might have a potency to modify the gut microbiome. Two groups of voluntary participants (11 male, 8 female; aged 20-80 years) were exposed to a single meal containing the fish. A 7-day dietary intervention was carried out comprising the fish as the main source of protein in a single adult. The microbiome was characterized using 16S rRNA and metagenomic sequencing. Individual community-level changes in the microbiome were compared, as well as the presence of bacteria associated with the fermented fish. We focused on Shannon alpha and UniFrac beta diversity. We did not detect any global changes in the gut microbiome in response to Surströmming, nor were we able to recover and identify any members of Halanaerobium, which were associated with and abundant in the ingested fish, in the stool samples of the participants. Our results suggest that Surströmming consumption does not alter the microbiome of healthy individuals. However, beneficial effects on a diseased gut, impaired gut microbiome, or other effects in disease remain to be studied.}, } @article {pmid36917471, year = {2023}, author = {Zhang, Z and Yang, C and Veldsman, WP and Fang, X and Zhang, L}, title = {Benchmarking genome assembly methods on metagenomic sequencing data.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {2}, pages = {}, doi = {10.1093/bib/bbad087}, pmid = {36917471}, issn = {1477-4054}, mesh = {Humans ; *Metagenome ; Benchmarking ; *Microbiota/genetics ; Metagenomics/methods ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenome assembly is an efficient approach to reconstruct microbial genomes from metagenomic sequencing data. Although short-read sequencing has been widely used for metagenome assembly, linked- and long-read sequencing have shown their advancements in assembly by providing long-range DNA connectedness. Many metagenome assembly tools were developed to simplify the assembly graphs and resolve the repeats in microbial genomes. However, there remains no comprehensive evaluation of metagenomic sequencing technologies, and there is a lack of practical guidance on selecting the appropriate metagenome assembly tools. This paper presents a comprehensive benchmark of 19 commonly used assembly tools applied to metagenomic sequencing datasets obtained from simulation, mock communities or human gut microbiomes. These datasets were generated using mainstream sequencing platforms, such as Illumina and BGISEQ short-read sequencing, 10x Genomics linked-read sequencing, and PacBio and Oxford Nanopore long-read sequencing. The assembly tools were extensively evaluated against many criteria, which revealed that long-read assemblers generated high contig contiguity but failed to reveal some medium- and high-quality metagenome-assembled genomes (MAGs). Linked-read assemblers obtained the highest number of overall near-complete MAGs from the human gut microbiomes. Hybrid assemblers using both short- and long-read sequencing were promising methods to improve both total assembly length and the number of near-complete MAGs. This paper also discussed the running time and peak memory consumption of these assembly tools and provided practical guidance on selecting them.}, } @article {pmid36917170, year = {2023}, author = {Wang, X and Wang, T and Xie, Z and Zhang, Y and Xia, S and Sun, R and He, X and Xiang, R and Zheng, Q and Liu, Z and Wang, J and Wu, H and Jin, X and Chen, W and Li, D and He, Z}, title = {GPMeta: a GPU-accelerated method for ultrarapid pathogen identification from metagenomic sequences.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {2}, pages = {}, doi = {10.1093/bib/bbad092}, pmid = {36917170}, issn = {1477-4054}, mesh = {*Metagenome ; *Microbiota ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Sensitivity and Specificity ; }, abstract = {Metagenomic sequencing (mNGS) is a powerful diagnostic tool to detect causative pathogens in clinical microbiological testing owing to its unbiasedness and substantially reduced costs. Rapid and accurate classification of metagenomic sequences is a critical procedure for pathogen identification in dry-lab step of mNGS test. However, clinical practices of the testing technology are hampered by the challenge of classifying sequences within a clinically relevant timeframe. Here, we present GPMeta, a novel GPU-accelerated approach to ultrarapid pathogen identification from complex mNGS data, allowing users to bypass this limitation. Using mock microbial community datasets and public real metagenomic sequencing datasets from clinical samples, we show that GPMeta has not only higher accuracy but also significantly higher speed than existing state-of-the-art tools such as Bowtie2, Bwa, Kraken2 and Centrifuge. Furthermore, GPMeta offers GPMetaC clustering algorithm, a statistical model for clustering and rescoring ambiguous alignments to improve the discrimination of highly homologous sequences from microbial genomes with average nucleotide identity >95%. GPMetaC exhibits higher precision and recall rate than others. GPMeta underlines its key role in the development of the mNGS test in infectious diseases that require rapid turnaround times. Further study will discern how to best and easily integrate GPMeta into routine clinical practices. GPMeta is freely accessible to non-commercial users at https://github.com/Bgi-LUSH/GPMeta.}, } @article {pmid36916422, year = {2023}, author = {Wang, AJ and Song, D and Hong, YM and Liu, NN}, title = {Multi-omics insights into the interplay between gut microbiota and colorectal cancer in the "microworld" age.}, journal = {Molecular omics}, volume = {19}, number = {4}, pages = {283-296}, doi = {10.1039/d2mo00288d}, pmid = {36916422}, issn = {2515-4184}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Multiomics ; *Microbiota ; Metabolomics/methods ; *Colorectal Neoplasms/genetics ; }, abstract = {Colorectal cancer (CRC) is a multifactorial heterogeneous disease largely due to both genetic predisposition and environmental factors including the gut microbiota, a dynamic microbial ecosystem inhabiting the gastrointestinal tract. Elucidation of the molecular mechanisms by which the gut microbiota interacts with the host may contribute to the pathogenesis, diagnosis, and promotion of CRC. However, deciphering the influence of genetic variants and interactions with the gut microbial ecosystem is rather challenging. Despite recent advancements in single omics analysis, the application of multi-omics approaches to integrate multiple layers of information in the microbiome and host to introduce effective prevention, diagnosis, and treatment strategies is still in its infancy. Here, we integrate host- and microbe-based multi-omics studies, respectively, to provide a strategy to explore potential causal relationships between gut microbiota and colorectal cancer. Specifically, we summarize the recent multi-omics studies such as metagenomics combined with metabolomics and metagenomics combined with genomics. Meanwhile, the sample size and sample types commonly used in multi-omics research, as well as the methods of data analysis, were also generalized. We highlight multiple layers of information from multi-omics that need to be verified by different types of models. Together, this review provides new insights into the clinical diagnosis and treatment of colorectal cancer patients.}, } @article {pmid36915639, year = {2023}, author = {Roslund, MI and Parajuli, A and Hui, N and Puhakka, R and Grönroos, M and Soininen, L and Nurminen, N and Oikarinen, S and Cinek, O and Kramná, L and Schroderus, AM and Laitinen, OH and Kinnunen, T and Hyöty, H and Sinkkonen, A}, title = {Skin, gut, and sand metagenomic data on placebo-controlled sandbox biodiversity intervention study.}, journal = {Data in brief}, volume = {47}, number = {}, pages = {109003}, pmid = {36915639}, issn = {2352-3409}, abstract = {The metagenomic data presented in this article are related to the published research of "A Placebo-controlled double-blinded test of the biodiversity hypothesis of immune-mediated diseases: Environmental microbial diversity elicits changes in cytokines and increase in T regulatory cells in young children" This database contains 16S ribosomal RNA (rRNA) metagenomics of sandbox sand and skin and gut microbiota of children in the intervention and placebo daycares. In intervention daycares, children aged 3-5 years were exposed to playground sand enriched with microbially diverse soil. In placebo daycares, children were exposed to visually similar as in intervention daycares, but microbially poor sand colored with peat. Sand, skin and gut metagenomics were analyzed at baseline and after 14 and 28 days of intervention by high throughput sequencing of bacterial 16S rRNA gene on the Illumina MiSeq platform. This dataset shows how skin bacterial community composition, including classes Gammaproteobacteria and Bacilli, changed, and how the relative abundance of over 30 bacterial genera shifted on the skin of children in the intervention treatment, while no shifts occurred in the placebo group.}, } @article {pmid36915411, year = {2023}, author = {Thippabhotla, S and Liu, B and Podgorny, A and Yooseph, S and Yang, Y and Zhang, J and Zhong, C}, title = {Integrated de novo gene prediction and peptide assembly of metagenomic sequencing data.}, journal = {NAR genomics and bioinformatics}, volume = {5}, number = {1}, pages = {lqad023}, pmid = {36915411}, issn = {2631-9268}, abstract = {Metagenomics is the study of all genomic content contained in given microbial communities. Metagenomic functional analysis aims to quantify protein families and reconstruct metabolic pathways from the metagenome. It plays a central role in understanding the interaction between the microbial community and its host or environment. De novo functional analysis, which allows the discovery of novel protein families, remains challenging for high-complexity communities. There are currently three main approaches for recovering novel genes or proteins: de novo nucleotide assembly, gene calling and peptide assembly. Unfortunately, their information dependency has been overlooked, and each has been formulated as an independent problem. In this work, we develop a sophisticated workflow called integrated Metagenomic Protein Predictor (iMPP), which leverages the information dependencies for better de novo functional analysis. iMPP contains three novel modules: a hybrid assembly graph generation module, a graph-based gene calling module, and a peptide assembly-based refinement module. iMPP significantly improved the existing gene calling sensitivity on unassembled metagenomic reads, achieving a 92-97% recall rate at a high precision level (>85%). iMPP further allowed for more sensitive and accurate peptide assembly, recovering more reference proteins and delivering more hypothetical protein sequences. The high performance of iMPP can provide a more comprehensive and unbiased view of the microbial communities under investigation. iMPP is freely available from https://github.com/Sirisha-t/iMPP.}, } @article {pmid36914646, year = {2023}, author = {Ngugi, DK and Acinas, SG and Sánchez, P and Gasol, JM and Agusti, S and Karl, DM and Duarte, CM}, title = {Abiotic selection of microbial genome size in the global ocean.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1384}, pmid = {36914646}, issn = {2041-1723}, mesh = {Genome Size ; Oceans and Seas ; *Genome, Microbial ; Metagenome/genetics ; *Microbiota ; Seawater ; }, abstract = {Strong purifying selection is considered a major evolutionary force behind small microbial genomes in the resource-poor photic ocean. However, very little is currently known about how the size of prokaryotic genomes evolves in the global ocean and whether patterns reflect shifts in resource availability in the epipelagic and relatively stable deep-sea environmental conditions. Using 364 marine microbial metagenomes, we investigate how the average genome size of uncultured planktonic prokaryotes varies across the tropical and polar oceans to the hadal realm. We find that genome size is highest in the perennially cold polar ocean, reflecting elongation of coding genes and gene dosage effects due to duplications in the interior ocean microbiome. Moreover, the rate of change in genome size due to temperature is 16-fold higher than with depth up to 200 m. Our results demonstrate how environmental factors can influence marine microbial genome size selection and ecological strategies of the microbiome.}, } @article {pmid36913841, year = {2023}, author = {Vermote, L and De Roos, J and Cnockaert, M and Vandamme, P and Weckx, S and De Vuyst, L}, title = {New insights into the role of key microorganisms and wooden barrels during lambic beer fermentation and maturation.}, journal = {International journal of food microbiology}, volume = {394}, number = {}, pages = {110163}, doi = {10.1016/j.ijfoodmicro.2023.110163}, pmid = {36913841}, issn = {1879-3460}, mesh = {*Beer/microbiology ; Fermentation ; Bacteria/genetics ; Plasmids ; *Microbiota ; }, abstract = {Belgian lambic beers are still produced through traditional craftsmanship. They rely on a spontaneous fermentation and maturation process that is entirely carried out in wooden barrels. The latter are used repetitively and may introduce some batch-to-batch variability. The present systematic and multiphasic study dealt with two parallel lambic beer productions carried out in nearly identical wooden barrels making use of the same cooled wort. It encompassed a microbiological and metabolomic approach. Further, a taxonomic classification and metagenome-assembled genome (MAG) investigation was based on shotgun metagenomics. These investigations provided new insights into the role of these wooden barrels and key microorganisms for this process. Indeed, besides their role in traditionality, the wooden barrels likely helped in establishing the stable microbial ecosystem of lambic beer fermentation and maturation by acting as an inoculation source of the necessary microorganisms, thereby minimizing batch-to-batch variations. They further provided a microaerobic environment, which aided in achieving the desirable succession of the different microbial communities for a successful lambic beer production process. Moreover, these conditions prevented excessive growth of acetic acid bacteria and, therefore, uncontrolled production of acetic acid and acetoin, which may lead to flavor deviations in lambic beer. Concerning the role of less studied key microorganisms for lambic beer production, it was shown that the Acetobacter lambici MAG contained several acid tolerance mechanisms toward the harsh environment of maturing lambic beer, whereas genes related to sucrose and maltose/maltooligosaccharide consumption and the glyoxylate shunt were absent. Further, a Pediococcus damnosus MAG possessed a gene encoding ferulic acid decarboxylase, possibly contributing to 4-vinyl compound production, as well as several genes, likely plasmid-based, related to hop resistance and biogenic amine production. Finally, contigs related to Dekkera bruxellensis and Brettanomyces custersianus did not possess genes involved in glycerol production, emphasizing the need for alternative external electron acceptors for redox balancing.}, } @article {pmid36913445, year = {2023}, author = {Strobel, KM and Del Vecchio, G and Devaskar, SU and Calkins, KL}, title = {Gut Microbes and Circulating Cytokines in Preterm Infants with Growth Failure.}, journal = {The Journal of nutrition}, volume = {153}, number = {1}, pages = {120-130}, pmid = {36913445}, issn = {1541-6100}, support = {R01 HD081206/HD/NICHD NIH HHS/United States ; T32 DK007180/DK/NIDDK NIH HHS/United States ; KL2 TR000122/TR/NCATS NIH HHS/United States ; }, mesh = {Infant ; Humans ; Infant, Newborn ; *Infant, Premature ; *Gastrointestinal Microbiome/genetics ; Cytokines/genetics ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Birth Weight ; }, abstract = {BACKGROUND: Growth failure (GF) is a multifactorial problem in preterm infants. The intestinal microbiome and inflammation may contribute to GF.

OBJECTIVES: This study's objective was to compare the gut microbiome and plasma cytokines in preterm infants with and without GF.

METHODS: This was a prospective cohort study of infants with birth weights of <1750 g. Infants with a weight or length z-score change from birth to discharge or death that was less than or equal to -0.8 (GF group) were compared with infants without GF [control (CON) group]. The primary outcome was the gut microbiome (at weeks 1-4 of age), assessed by 16S rRNA gene sequencing using Deseq2. Secondary outcomes included inferred metagenomic function and plasma cytokines. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States determined metagenomic function, which was compared using ANOVA. Cytokines were measured by 2-multiplexed immunometric assays and compared using Wilcoxon tests and linear mixed models.

RESULTS: GF (n = 14) and CON group (n = 13) had similar median (IQR) birth weight (1380 [780-1578] g vs. 1275 [1013-1580] g) and gestational age (29 [25-31] weeks vs. 30 [29-32] weeks). Compared with the CON group, the GF group had a greater abundance of Escherichia/Shigella in weeks 2 and 3, Staphylococcus in week 4, and Veillonella in weeks 3 and 4 (P-adjusted < 0.001 for all). Plasma cytokine concentrations did not differ significantly between the cohorts. When all time points are combined, fewer microbes were involved in TCA cycle activity in the GF group compared with the CON group (P = 0.023).

CONCLUSIONS: In this study, when compared with CON infants, GF infants had a distinct microbial signature with increased Escherichia/Shigella and Firmicutes and fewer microbes associated with energy production at later weeks of hospitalization. These findings may suggest a mechanism for aberrant growth.}, } @article {pmid36913444, year = {2023}, author = {Larke, JA and Bacalzo, N and Castillo, JJ and Couture, G and Chen, Y and Xue, Z and Alkan, Z and Kable, ME and Lebrilla, CB and Stephensen, CB and Lemay, DG}, title = {Dietary Intake of Monosaccharides from Foods is Associated with Characteristics of the Gut Microbiota and Gastrointestinal Inflammation in Healthy US Adults.}, journal = {The Journal of nutrition}, volume = {153}, number = {1}, pages = {106-119}, pmid = {36913444}, issn = {1541-6100}, support = {R01 DK124193/DK/NIDDK NIH HHS/United States ; }, mesh = {Male ; Female ; Adult ; Humans ; *Gastrointestinal Microbiome ; Monosaccharides ; Cross-Sectional Studies ; Dietary Fiber ; Eating ; Diet ; Feces/chemistry ; Inflammation ; }, abstract = {BACKGROUND: Current assessment of dietary carbohydrates does not adequately reflect the nutritional properties and effects on gut microbial structure and function. Deeper characterization of food carbohydrate composition can serve to strengthen the link between diet and gastrointestinal health outcomes.

OBJECTIVES: The present study aims to characterize the monosaccharide composition of diets in a healthy US adult cohort and use these features to assess the relationship between monosaccharide intake, diet quality, characteristics of the gut microbiota, and gastrointestinal inflammation.

METHODS: This observational, cross-sectional study enrolled males and females across age (18-33 y, 34-49 y, and 50-65 y) and body mass index (normal, 18.5-24.99 kg/m[2]; overweight, 25-29.99 kg/m[2]; and obese, 30-44 kg/m[2]) categories. Recent dietary intake was assessed by the automated self-administered 24-h dietary recall system, and gut microbiota were assessed with shotgun metagenome sequencing. Dietary recalls were mapped to the Davis Food Glycopedia to estimate monosaccharide intake. Participants with >75% of carbohydrate intake mappable to the glycopedia were included (N = 180).

RESULTS: Diversity of monosaccharide intake was positively associated with the total Healthy Eating Index score (Pearson's r = 0.520, P = 1.2 × 10[-13]) and negatively associated with fecal neopterin (Pearson's r = -0.247, P = 3.0 × 10[-3]). Comparing high with low intake of specific monosaccharides revealed differentially abundant taxa (Wald test, P < 0.05), which was associated with the functional capacity to break down these monomers (Wilcoxon rank-sum test, P < 0.05).

CONCLUSIONS: Monosaccharide intake was associated with diet quality, gut microbial diversity, microbial metabolism, and gastrointestinal inflammation in healthy adults. As specific food sources were rich in particular monosaccharides, it may be possible in the future to tailor diets to fine-tune the gut microbiota and gastrointestinal function. This trial is registered at www.

CLINICALTRIALS: gov as NCT02367287.}, } @article {pmid36912756, year = {2023}, author = {Jiang, C and Wang, G and Zhang, J and Gu, S and Wang, X and Qin, W and Chen, K and Yuan, D and Chai, X and Yang, M and Zhou, F and Xiong, J and Miao, W}, title = {iGDP: An integrated genome decontamination pipeline for wild ciliated microeukaryotes.}, journal = {Molecular ecology resources}, volume = {23}, number = {5}, pages = {1182-1193}, doi = {10.1111/1755-0998.13782}, pmid = {36912756}, issn = {1755-0998}, support = {32122015, 31872221, 31900339 and 31900316//National Natural Science Foundation of China/ ; }, mesh = {*Decontamination ; *Genomics ; Metagenome ; Phylogeny ; Eukaryota ; }, abstract = {Ciliates are a large group of ubiquitous and highly diverse single-celled eukaryotes that play an essential role in the functioning of microbial food webs. However, their genomic diversity is far from clear due to the need to develop cultivation methods for most species, so most research is based on wild organisms that almost invariably contain contaminants. Here we establish an integrated Genome Decontamination Pipeline (iGDP) that combines homology search, telomere reads-assisted and clustering approaches to filter contaminated ciliate genome assemblies from wild specimens. We benchmarked the performance of iGDP using genomic data from a contaminated ciliate culture and the results showed that iGDP could recall 91.9% of the target sequences with 96.9% precision. We also used a synthetic dataset to offer guidelines for the application of iGDP in the removal of various groups of contaminants. Compared with several popular metagenome binning tools, iGDP could show better performance. To further validate the effectiveness of iGDP on real-world data, we applied it to decontaminate genome assemblies of three wild ciliate specimens and obtained their genomes with high quality comparable to that of previously well-studied model ciliate genomes. It is anticipated that the newly generated genomes and the established iGDP method will be valuable community resources for detailed studies on ciliate biodiversity, phylogeny, ecology and evolution. The pipeline (https://github.com/GWang2022/iGDP) can be implemented automatically to reduce manual filtering and classification and may be further developed to apply to other microeukaryotes.}, } @article {pmid36910183, year = {2023}, author = {Xi, M and Deyett, E and Stajich, JE and El-Kereamy, A and Roper, MC and Rolshausen, PE}, title = {Microbiome diversity, composition and assembly in a California citrus orchard.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1100590}, pmid = {36910183}, issn = {1664-302X}, abstract = {The citrus root and rhizosphere microbiomes have been relatively well described in the literature, especially in the context of Huanglonbing disease. Yet questions addressing the assembly of root microbial endophytes have remained unanswered. In the above ground tree tissues, leaves and stems have been the research focus point, while flush and flower microbiomes, two important tissues in the vegetative and reproductive cycles of the tree, are not well described. In this study, the fungal and bacterial taxa in five biocompartments (bulk soil, rhizosphere, root endosphere, flower and flush) of citrus trees grown in a single California orchard were profiled using an amplicon-based metagenomic Illumina sequencing approach. Trees with no observable signs of abiotic or biotic stresses were sampled for two consecutive years during the floral development phase. The rhizosphere was the most biodiverse compartment compared to bulk soil, root endosphere, flower and flush microbiomes. In addition, the belowground bacteriome was more diverse than the mycobiome. Microbial richness decreased significantly from the root exosphere to the endosphere and was overall low in the above ground tissues. Root endophytic microbial community composition shared strong similarities to the rhizosphere but also contained few taxa from above ground tissues. Our data indicated compartmentalization of the microbiome with distinct profiles between above and below ground microbial communities. However, several taxa were present across all compartments suggesting the existence of a core citrus microbiota. These findings highlight key microbial taxa that could be engineered as biopesticides and biofertilizers for citriculture.}, } @article {pmid36909733, year = {2023}, author = {Chang, L and Qiu, L and Lei, N and Zhou, J and Guo, R and Gao, F and Dong, S and Chen, M and Wu, F and Qin, B}, title = {Characterization of fecal microbiota in cervical cancer patients associated with tumor stage and prognosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1145950}, pmid = {36909733}, issn = {2235-2988}, mesh = {Humans ; Female ; *Uterine Cervical Neoplasms ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Feces ; }, abstract = {Cervical cancer (CC) is the fourth most frequent malignancy among women worldwide, and its prevention and treatment are evolving rapidly. The gut microbiota has been reported to play a crucial role both in the preservation of homeostasis and the development of cervical cancer. In this study, we collected fecal samples to investigate the microbial signatures in cervical cancer patients compared with healthy controls using 16S rRNA sequencing analysis and metagenomic next-generation sequencing (mNGS) testing. Our findings demonstrated a substantial difference in the gut microbiota composition of cervical cancer patients and healthy controls. The disease and stage were most significantly negatively correlated with Ruminococcus 2, which might be considered a potential clinically relevant biomarker. Functions of differential microbiomes were also analyzed, indicating significant differences in metabolisms and biosynthesis between the two groups. These findings demonstrate that patients with cervical cancer have certain species of gut microbiota that are exclusive to them and particular species have the potential to be used in the prognosis of cervical cancer.}, } @article {pmid36907988, year = {2023}, author = {Mannion, A and Sheh, A and Shen, Z and Dzink-Fox, J and Piazuelo, MB and Wilson, KT and Peek, R and Fox, JG}, title = {Shotgun Metagenomics of Gastric Biopsies Reveals Compositional and Functional Microbiome Shifts in High- and Low-Gastric-Cancer-Risk Populations from Colombia, South America.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2186677}, pmid = {36907988}, issn = {1949-0984}, support = {P01 CA028842/CA/NCI NIH HHS/United States ; R01 CA077955/CA/NCI NIH HHS/United States ; R01 CA281732/CA/NCI NIH HHS/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; R35 CA210088/CA/NCI NIH HHS/United States ; P30 ES002109/ES/NIEHS NIH HHS/United States ; P01 CA116087/CA/NCI NIH HHS/United States ; I01 CX002171/CX/CSRD VA/United States ; R01 DK058587/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Stomach Neoplasms/microbiology ; Colombia ; RNA, Ribosomal, 16S/genetics ; *Helicobacter Infections/microbiology ; *Gastritis/pathology ; *Gastrointestinal Microbiome ; *Helicobacter pylori/genetics ; Biopsy ; Risk Factors ; *Microbiota ; South America ; }, abstract = {Along with Helicobacter pylori infection, the gastric microbiota is hypothesized to modulate stomach cancer risk in susceptible individuals. Whole metagenomic shotgun sequencing (WMS) is a sequencing approach to characterize the microbiome with advantages over traditional culture and 16S rRNA sequencing including identification of bacterial and non-bacterial taxa, species/strain resolution, and functional characterization of the microbiota. In this study, we used WMS to survey the microbiome in extracted DNA from antral gastric biopsy samples from Colombian patients residing in the high-risk gastric cancer town Túquerres (n = 10, H. pylori-positive = 7) and low-risk town of Tumaco (n = 10, H. pylori-positive = 6). Kraken2/Bracken was used for taxonomic classification and abundance. Functional gene profiles were inferred by InterProScan and KEGG analysis of assembled contigs and gene annotation. The most abundant taxa represented bacteria, non-human eukaryota, and viral genera found in skin, oral, food, and plant/soil environments including Staphylococus, Streptococcus, Bacillus, Aspergillus, and Siphoviridae. H. pylori was the predominant taxa present in H. pylori-positive samples. Beta diversity was significantly different based on H. pylori-status, risk group, and sex. WMS detected more bacterial taxa than 16S rRNA sequencing and aerobic, anaerobic, and microaerobic culture performed on the same gastric biopsy samples. WMS identified significant differences in functional profiles found between H. pylori-status, but not risk or sex groups. H. pylori-positive samples were significantly enriched for H. pylori-specific genes including virulence factors such as vacA, cagA, and urease, while carbohydrate and amino acid metabolism genes were enriched in H. pylori-negative samples. This study shows WMS has the potential to characterize the taxonomy and function of the gastric microbiome as risk factors for H. pylori-associated gastric disease. Future studies will be needed to compare and validate WMS versus traditional culture and 16S rRNA sequencing approaches for characterization of the gastric microbiome.}, } @article {pmid36906612, year = {2023}, author = {Neumann, CJ and Mahnert, A and Kumpitsch, C and Kiu, R and Dalby, MJ and Kujawska, M and Madl, T and Kurath-Koller, S and Urlesberger, B and Resch, B and Hall, LJ and Moissl-Eichinger, C}, title = {Clinical NEC prevention practices drive different microbiome profiles and functional responses in the preterm intestine.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1349}, pmid = {36906612}, issn = {2041-1723}, support = {W 1226/FWF_/Austrian Science Fund FWF/Austria ; 100974/C/13/Z/WT_/Wellcome Trust/United Kingdom ; P 32697/FWF_/Austrian Science Fund FWF/Austria ; 220876/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; BBS/E/F/00044409/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DOC 31/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Infant ; Infant, Newborn ; Humans ; Female ; *Infant, Premature ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Intestines ; Feces/microbiology ; Bifidobacterium longum subspecies infantis/genetics ; *Gastrointestinal Microbiome ; }, abstract = {Preterm infants with very low birthweight are at serious risk for necrotizing enterocolitis. To functionally analyse the principles of three successful preventive NEC regimens, we characterize fecal samples of 55 infants (<1500 g, n = 383, female = 22) longitudinally (two weeks) with respect to gut microbiome profiles (bacteria, archaea, fungi, viruses; targeted 16S rRNA gene sequencing and shotgun metagenomics), microbial function, virulence factors, antibiotic resistances and metabolic profiles, including human milk oligosaccharides (HMOs) and short-chain fatty acids (German Registry of Clinical Trials, No.: DRKS00009290). Regimens including probiotic Bifidobacterium longum subsp. infantis NCDO 2203 supplementation affect microbiome development globally, pointing toward the genomic potential to convert HMOs. Engraftment of NCDO 2203 is associated with a substantial reduction of microbiome-associated antibiotic resistance as compared to regimens using probiotic Lactobacillus rhamnosus LCR 35 or no supplementation. Crucially, the beneficial effects of Bifidobacterium longum subsp. infantis NCDO 2203 supplementation depends on simultaneous feeding with HMOs. We demonstrate that preventive regimens have the highest impact on development and maturation of the gastrointestinal microbiome, enabling the establishment of a resilient microbial ecosystem that reduces pathogenic threats in at-risk preterm infants.}, } @article {pmid36904265, year = {2023}, author = {Wang, Z and Xu, X and Deji, Y and Gao, S and Wu, C and Song, Q and Shi, Z and Xiang, X and Zang, J and Su, J}, title = {Bifidobacterium as a Potential Biomarker of Sarcopenia in Elderly Women.}, journal = {Nutrients}, volume = {15}, number = {5}, pages = {}, pmid = {36904265}, issn = {2072-6643}, support = {20194Y0443//The young fund of Shanghai municipal health commission/ ; DIC2019-03//Dietary Nutrition Research and Education Foundation of Danone Nutrition Center/ ; GWV-10.3-YQ22//Outstanding young Talents in the three-year Plan of Shanghai municipal public health system (2020-2022)/ ; GWV-10.2-XD18//Academic leader in the three-year Plan of Shanghai municipal public health system (2020-2022)/ ; GWV-10.1-XK11//Key disciplines in the three-year Plan of Shanghai municipal public health system(2020-2022)/ ; }, mesh = {Humans ; Female ; Aged ; Bifidobacterium ; *Sarcopenia ; Case-Control Studies ; *Gastrointestinal Microbiome ; *Bifidobacterium longum ; Biomarkers ; }, abstract = {Gut microbial dysbiosis influences the development of sarcopenia. This case-control study explored the gut microbiota composition in elderly Chinese women with sarcopenia. The information from 50 cases and 50 controls was collected. Grip strength, body weight, body mass index, skeletal muscle mass, energy intake, and total and high-quality protein intake were lower in cases than in controls (p < 0.05). Gut microbiota metagenomic sequencing showed that phylum Bacteroides was significantly reduced in the case group, whereas genus Prevotella was more abundant (p < 0.05). Linear discriminant analysis (LDA) effect size showed that 9 and 13 distinct microbial taxa were enriched in the case and control groups, respectively (LDA > 2, p < 0.05), among which Prevotella copri and Bifidobacterium longum were significantly different (LDA > 4, p < 0.05). The AUC of Bifidobacterium longum was 0.674 (95% CI: 0.539-0.756). Elderly women with sarcopenia exhibited significantly different gut microbiota compositions than healthy controls.}, } @article {pmid36902349, year = {2023}, author = {Melo, NCO and Cuevas-Sierra, A and Fernández-Cruz, E and de la O, V and Martínez, JA}, title = {Fecal Microbiota Composition as a Metagenomic Biomarker of Dietary Intake.}, journal = {International journal of molecular sciences}, volume = {24}, number = {5}, pages = {}, pmid = {36902349}, issn = {1422-0067}, support = {AC21/00038//Instituto de Salud Carlos III/ ; FELLOWSHIP//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; Y2020/BIO-6600.//Comunidad de Madrid/ ; FACINGLCOVID-CM//European Union/ ; }, mesh = {Feces/microbiology ; *Gastrointestinal Tract/microbiology ; *Gastrointestinal Microbiome ; Eating ; Biomarkers ; }, abstract = {Gut microbiota encompasses the set of microorganisms that colonize the gastrointestinal tract with mutual relationships that are key for host homeostasis. Increasing evidence supports cross intercommunication between the intestinal microbiome and the eubiosis-dysbiosis binomial, indicating a networking role of gut bacteria as potential metabolic health surrogate markers. The abundance and diversity of the fecal microbial community are already recognized to be associated with several disorders, such as obesity, cardiometabolic events, gastrointestinal alterations, and mental diseases, which suggests that intestinal microbes may be a valuable tool as causal or as consequence biomarkers. In this context, the fecal microbiota could also be used as an adequate and informative proxy of the nutritional composition of the food intake and about the adherence to dietary patterns, such as the Mediterranean or Western diets, by displaying specific fecal microbiome signatures. The aim of this review was to discuss the potential use of gut microbial composition as a putative biomarker of food intake and to screen the sensitivity value of fecal microbiota in the evaluation of dietary interventions as a reliable and precise alternative to subjective questionnaires.}, } @article {pmid36899176, year = {2023}, author = {von Takach, B and Sargent, H and Penton, CE and Rick, K and Murphy, BP and Neave, G and Davies, HF and Hill, BM and Banks, SC}, title = {Population genomics and conservation management of the threatened black-footed tree-rat (Mesembriomys gouldii) in northern Australia.}, journal = {Heredity}, volume = {130}, number = {5}, pages = {278-288}, pmid = {36899176}, issn = {1365-2540}, mesh = {Animals ; Rats ; Australia ; *Conservation of Natural Resources ; *Metagenomics ; Biodiversity ; Ecosystem ; }, abstract = {Genomic diversity is a fundamental component of Earth's total biodiversity, and requires explicit consideration in efforts to conserve biodiversity. To conserve genomic diversity, it is necessary to measure its spatial distribution, and quantify the contribution that any intraspecific evolutionary lineages make to overall genomic diversity. Here, we describe the range-wide population genomic structure of a threatened Australian rodent, the black-footed tree-rat (Mesembriomys gouldii), aiming to provide insight into the timing and extent of population declines across a large region with a dearth of long-term monitoring data. By estimating recent trajectories in effective population sizes at four localities, we confirm widespread population decline across the species' range, but find that the population in the peri-urban area of the Darwin region has been more stable. Based on current sampling, the Melville Island population made the greatest contribution to overall allelic richness of the species, and the prioritisation analysis suggested that conservation of the Darwin and Cobourg Peninsula populations would be the most cost-effective scenario to retain more than 90% of all alleles. Our results broadly confirm current sub-specific taxonomy, and provide crucial data on the spatial distribution of genomic diversity to help prioritise limited conservation resources. Along with additional sampling and genomic analysis from the far eastern and western edges of the black-footed tree-rat distribution, we suggest a range of conservation and research priorities that could help improve black-footed tree-rat population trajectories at large and fine spatial scales, including the retention and expansion of structurally complex habitat patches.}, } @article {pmid36898564, year = {2023}, author = {Xu, Y and Meng, X and Song, Y and Lv, X and Sun, Y}, title = {Effects of different concentrations of butyrate on microbial community construction and metabolic pathways in anaerobic digestion.}, journal = {Bioresource technology}, volume = {377}, number = {}, pages = {128845}, doi = {10.1016/j.biortech.2023.128845}, pmid = {36898564}, issn = {1873-2976}, mesh = {Anaerobiosis ; Butyric Acid ; Biofuels ; Bioreactors/microbiology ; *Microbiota ; *Euryarchaeota/metabolism ; Metabolic Networks and Pathways ; Methane ; }, abstract = {Investigating the effect of butyric acid concentration on anaerobic digestion systems in complex systems is important for the efficient degradation of butyric acid and improving the efficiency of anaerobic digestion. In this study, different loadings of butyric acid with 2.8, 3.2, and 3.6 g/(L·d) were added to the anaerobic reactor. At a high organic loading rate of 3.6 g/(L·d), methane was efficiently produced with VBP (Volumetric Biogas Production) of 1.50 L/(L·d) and biogas content between 65% and 75%. VFAs concentration remained below 2000 mg/L. Metagenome sequencing revealed changes in the functional flora within different stages. Methanosarcina, Syntrophomonas, and Lentimicrobium were the main and functional microorganisms. That the relative abundance of methanogens exceeded 35% and methanogenic metabolic pathways were increased indicated the methanogenic capacity of the system significantly improved. The presence of a large number of hydrolytic acid-producing bacteria also indicated the importance of the hydrolytic acid-producing stage in the system.}, } @article {pmid36896778, year = {2023}, author = {Obregon Alvarez, D and Fonseca de Souza, L and Mendes, LW and de Moraes, MT and Tosi, M and Venturini, AM and Meyer, KM and Barbosa de Camargo, P and Bohannan, BJM and Mazza Rodrigues, JL and Dunfield, KE and Tsai, SM}, title = {Shifts in functional traits and interactions patterns of soil methane-cycling communities following forest-to-pasture conversion in the Amazon Basin.}, journal = {Molecular ecology}, volume = {32}, number = {12}, pages = {3257-3275}, doi = {10.1111/mec.16912}, pmid = {36896778}, issn = {1365-294X}, mesh = {*Soil/chemistry ; Methane/metabolism ; Forests ; Genes, Bacterial ; *Microbiota/genetics ; Soil Microbiology ; }, abstract = {Deforestation threatens the integrity of the Amazon biome and the ecosystem services it provides, including greenhouse gas mitigation. Forest-to-pasture conversion has been shown to alter the flux of methane gas (CH4) in Amazonian soils, driving a switch from acting as a sink to a source of atmospheric CH4 . This study aimed to better understand this phenomenon by investigating soil microbial metagenomes, focusing on the taxonomic and functional structure of methane-cycling communities. Metagenomic data from forest and pasture soils were combined with measurements of in situ CH4 fluxes and soil edaphic factors and analysed using multivariate statistical approaches. We found a significantly higher abundance and diversity of methanogens in pasture soils. As inferred by co-occurrence networks, these microorganisms seem to be less interconnected within the soil microbiota in pasture soils. Metabolic traits were also different between land uses, with increased hydrogenotrophic and methylotrophic pathways of methanogenesis in pasture soils. Land-use change also induced shifts in taxonomic and functional traits of methanotrophs, with bacteria harbouring genes encoding the soluble form of methane monooxygenase enzyme (sMMO) depleted in pasture soils. Redundancy analysis and multimodel inference revealed that the shift in methane-cycling communities was associated with high pH, organic matter, soil porosity and micronutrients in pasture soils. These results comprehensively characterize the effect of forest-to-pasture conversion on the microbial communities driving the methane-cycling microorganisms in the Amazon rainforest, which will contribute to the efforts to preserve this important biome.}, } @article {pmid36894986, year = {2023}, author = {de Nies, L and Galata, V and Martin-Gallausiaux, C and Despotovic, M and Busi, SB and Snoeck, CJ and Delacour, L and Budagavi, DP and Laczny, CC and Habier, J and Lupu, PC and Halder, R and Fritz, JV and Marques, T and Sandt, E and O'Sullivan, MP and Ghosh, S and Satagopam, V and , and Krüger, R and Fagherazzi, G and Ollert, M and Hefeng, FQ and May, P and Wilmes, P}, title = {Altered infective competence of the human gut microbiome in COVID-19.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {46}, pmid = {36894986}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *COVID-19 ; SARS-CoV-2/genetics ; *Microbiota ; Multiomics ; }, abstract = {BACKGROUND: Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group.

RESULTS: We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls.

CONCLUSIONS: Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract.}, } @article {pmid36894760, year = {2023}, author = {Sajid, M and Srivastava, S and Yadav, RK and Joshi, L and Bharadwaj, M}, title = {Fungal Community Composition and Function Associated with Loose Smokeless Tobacco Products.}, journal = {Current microbiology}, volume = {80}, number = {4}, pages = {131}, pmid = {36894760}, issn = {1432-0991}, support = {ISRM/14(04)/TF/2018//Indian Council of Medical Research/ ; }, mesh = {*Tobacco, Smokeless/analysis/microbiology ; *Mycobiome ; Chromatography, Liquid ; Tandem Mass Spectrometry ; *Mycotoxins ; }, abstract = {Smokeless tobacco products (STPs) contain several microbial communities which are responsible for the formation of carcinogens, like tobacco-specific nitrosamine (TSNAs). A majority of STPs are sold in loose/unpackaged form which can be loaded with a diverse microbial population. Here, the fungal population and mycotoxins level of three popular Indian loose STPs, Dohra, Mainpuri Kapoori (MK), and loose leaf-chewing tobacco (LCT) was examined using metagenomic sequencing of ITS1 DNA segment of the fungal genome and LC-MS/MS, respectively. We observed that Ascomycota was the most abundant phylum and Sterigmatomyces and Pichia were the predominant fungal genera in loose STPs. MK displayed the highest α-diversity being enriched with pathogenic fungi Apiotrichum, Aspergillus, Candida, Fusarium, Trichosporon, and Wallemia. Further, FUNGuild analysis revealed an abundance of saprotrophs in MK, while pathogen-saprotroph-symbiotroph were abundant in Dohra and LCT. The level of a fungal toxin (ochratoxins A) was high in the MK product. This study caution that loose STPs harbor various harmful fungi that can infect their users and deliver fungal toxins or disrupt the oral microbiome of SLT users which can contribute to several oral pathologies.}, } @article {pmid36894632, year = {2023}, author = {Molari, M and Hassenrueck, C and Laso-Pérez, R and Wegener, G and Offre, P and Scilipoti, S and Boetius, A}, title = {A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes.}, journal = {Nature microbiology}, volume = {8}, number = {4}, pages = {651-665}, pmid = {36894632}, issn = {2058-5276}, mesh = {*Seawater/microbiology ; Bacteria/genetics ; *Microbiota ; Hydrogen/metabolism ; Oxygen/metabolism ; }, abstract = {Members of the bacterial genus Sulfurimonas (phylum Campylobacterota) dominate microbial communities in marine redoxclines and are important for sulfur and nitrogen cycling. Here we used metagenomics and metabolic analyses to characterize a Sulfurimonas from the Gakkel Ridge in the Central Arctic Ocean and Southwest Indian Ridge, showing that this species is ubiquitous in non-buoyant hydrothermal plumes at Mid Ocean Ridges across the global ocean. One Sulfurimonas species, [U]Sulfurimonas pluma, was found to be globally abundant and active in cold (<0-4 °C), oxygen-saturated and hydrogen-rich hydrothermal plumes. Compared with other Sulfurimonas species, [U]S. pluma has a reduced genome (>17%) and genomic signatures of an aerobic chemolithotrophic metabolism using hydrogen as an energy source, including acquisition of A2-type oxidase and loss of nitrate and nitrite reductases. The dominance and unique niche of [U]S. pluma in hydrothermal plumes suggest an unappreciated biogeochemical role for Sulfurimonas in the deep ocean.}, } @article {pmid36894532, year = {2023}, author = {Sukumar, S and Wang, F and Simpson, CA and Willet, CE and Chew, T and Hughes, TE and Bockmann, MR and Sadsad, R and Martin, FE and Lydecker, HW and Browne, GV and Davis, KM and Bui, M and Martinez, E and Adler, CJ}, title = {Development of the oral resistome during the first decade of life.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1291}, pmid = {36894532}, issn = {2041-1723}, support = {R01 DE019665/DE/NIDCR NIH HHS/United States ; R01 DE029838/DE/NIDCR NIH HHS/United States ; }, mesh = {Male ; Female ; Humans ; Child ; Drug Resistance, Bacterial/genetics ; *Dental Caries/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Microbiota/genetics ; }, abstract = {Antibiotic overuse has promoted the spread of antimicrobial resistance (AMR) with significant health and economic consequences. Genome sequencing reveals the widespread presence of antimicrobial resistance genes (ARGs) in diverse microbial environments. Hence, surveillance of resistance reservoirs, like the rarely explored oral microbiome, is necessary to combat AMR. Here, we characterise the development of the paediatric oral resistome and investigate its role in dental caries in 221 twin children (124 females and 97 males) sampled at three time points over the first decade of life. From 530 oral metagenomes, we identify 309 ARGs, which significantly cluster by age, with host genetic effects detected from infancy onwards. Our results suggest potential mobilisation of ARGs increases with age as the AMR associated mobile genetic element, Tn916 transposase was co-located with more species and ARGs in older children. We find a depletion of ARGs and species in dental caries compared to health. This trend reverses in restored teeth. Here we show the paediatric oral resistome is an inherent and dynamic component of the oral microbiome, with a potential role in transmission of AMR and dysbiosis.}, } @article {pmid36893594, year = {2023}, author = {Saibu, S and Adebusoye, SA and Oyetibo, GO}, title = {Soil microbiome response to 2-chlorodibenzo-p-dioxin during bioremediation of contaminated tropical soil in a microcosm-based study.}, journal = {Journal of hazardous materials}, volume = {451}, number = {}, pages = {131105}, doi = {10.1016/j.jhazmat.2023.131105}, pmid = {36893594}, issn = {1873-3336}, mesh = {*Dioxins ; Biodegradation, Environmental ; Soil ; *Soil Pollutants/metabolism ; Bacteria/metabolism ; *Bacillus/metabolism ; *Microbiota ; Soil Microbiology ; }, abstract = {A pristine soil was artificially contaminated with 2-chlorodibenzo-p-dioxin (2-CDD) and separated into three portions. Microcosms SSOC and SSCC were seeded with Bacillus sp. SS2 and a three-member bacterial consortium respectively; SSC was untreated, while heat-sterilized contaminated soil served as overall control. Significant degradation of 2-CDD occurred in all microcosms except for the control where the concentration remained unchanged. Degradation of 2-CDD was highest in SSCC (94.9%) compared to SSOC (91.66%) and SCC (85.9%). There was also a notable reduction in the microbial composition complexity both in species richness and evenness following dioxin contamination, a trend that nearly lasted the study period; particularly in setups SSC and SSOC. Irrespective of the bioremediation strategies, the soil microflora was practically dominated by the Firmicutes and at the genus level, the phylotype Bacillus was the most dominant. Other dominant taxa though negatively impacted were Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteria. Overall, this study demonstrated the feasibility of microbial seeding as an effective strategy to cleanup tropical soil contaminated with dioxins and the importance of metagenomics in elucidating the microbial diversities of contaminated soils. Meanwhile, the seeded organisms, owed their success not only to metabolic competence, but survivability, adaptability and ability to compete favourably with autochthonous microflora.}, } @article {pmid36889095, year = {2023}, author = {Li, B and Tao, Y and Mao, Z and Gu, Q and Han, Y and Hu, B and Wang, H and Lai, A and Xing, P and Wu, QL}, title = {Iron oxides act as an alternative electron acceptor for aerobic methanotrophs in anoxic lake sediments.}, journal = {Water research}, volume = {234}, number = {}, pages = {119833}, doi = {10.1016/j.watres.2023.119833}, pmid = {36889095}, issn = {1879-2448}, mesh = {Humans ; *Lakes/chemistry ; *Electrons ; Oxidation-Reduction ; Oxidants ; Iron ; Hypoxia ; Oxides ; Methane ; Geologic Sediments/chemistry ; }, abstract = {Conventional aerobic CH4-oxidizing bacteria (MOB) are frequently detected in anoxic environments, but their survival strategy and ecological contribution are still enigmatic. Here we explore the role of MOB in enrichment cultures under O2 gradients and an iron-rich lake sediment in situ by combining microbiological and geochemical techniques. We found that enriched MOB consortium used ferric oxides as alternative electron acceptors for oxidizing CH4 with the help of riboflavin when O2 was unavailable. Within the MOB consortium, MOB transformed CH4 to low molecular weight organic matter such as acetate for consortium bacteria as a carbon source, while the latter secrete riboflavin to facilitate extracellular electron transfer (EET). Iron reduction coupled to CH4 oxidation mediated by the MOB consortium was also demonstrated in situ, reducing 40.3% of the CH4 emission in the studied lake sediment. Our study indicates how MOBs survive under anoxia and expands the knowledge of this previously overlooked CH4 sink in iron-rich sediments.}, } @article {pmid36888627, year = {2023}, author = {Leonard, MM and Kenyon, V and Valitutti, F and Pennacchio-Harrington, R and Piemontese, P and Francavilla, R and Norsa, L and Passaro, T and Crocco, M and Baldassarre, M and Trovato, CM and Fasano, A and , }, title = {Cohort profile: Celiac disease genomic, environmental, microbiome and metabolome study; a prospective longitudinal birth cohort study of children at-risk for celiac disease.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0282739}, pmid = {36888627}, issn = {1932-6203}, support = {K23 DK122127/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Child ; Child, Preschool ; *Celiac Disease ; Prospective Studies ; Cohort Studies ; Birth Cohort ; Metabolome ; Genomics ; *Microbiota/genetics ; }, abstract = {The Celiac Disease Genomic, Environmental, Microbiome and Metabolomic (CDGEMM) study is an international prospective birth cohort in children at-risk of developing celiac disease (CD). The CDGEMM study has been designed to take a multi-omic approach to predicting CD onset in at-risk individuals. Participants are required to have a first-degree family member with biopsy diagnosed CD and must be enrolled prior to the introduction of solid food. Participation involves providing blood and stool samples longitudinally over a period of five years as well as answering questionnaires related to the participant, their family, and environment. Recruitment and data collection have been ongoing since 2014. As of 2022 we have a total of 554 participants and the average age of the cohort is 56.4 months. A total of 54 participants have developed positive antibodies for CD and 31 have confirmed CD. Approximately 80% of the 54 participants with CD have developed it by 3 years of age. To date we have identified several microbial strains, pathways, and metabolites occurring in increased abundance and detected before CD onset, which have previously been linked to autoimmune and inflammatory conditions while others occurred in decreased abundance before CD onset and are known to have anti-inflammatory effects. Our ongoing analysis includes expanding our metagenomic and metabolomic analyses, evaluating environmental risk factors linked to CD onset, and mechanistic studies investigating how alterations in the microbiome and metabolites may protect against or contribute to CD development.}, } @article {pmid36882798, year = {2023}, author = {Inda-Díaz, JS and Lund, D and Parras-Moltó, M and Johnning, A and Bengtsson-Palme, J and Kristiansson, E}, title = {Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {44}, pmid = {36882798}, issn = {2049-2618}, mesh = {Animals ; Humans ; Drug Resistance, Microbial/genetics ; *Microbiota/genetics ; Metagenome ; Anti-Bacterial Agents/pharmacology ; Databases, Factual ; }, abstract = {BACKGROUND: Bacterial communities in humans, animals, and the external environment maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs are well-characterized and thus established in existing resistance gene databases. In contrast, the remaining latent ARGs are typically unknown and overlooked in most sequencing-based studies. Our view of the resistome and its diversity is therefore incomplete, which hampers our ability to assess risk for promotion and spread of yet undiscovered resistance determinants.

RESULTS: A reference database consisting of both established and latent ARGs (ARGs not present in current resistance gene repositories) was created. By analyzing more than 10,000 metagenomic samples, we showed that latent ARGs were more abundant and diverse than established ARGs in all studied environments, including the human- and animal-associated microbiomes. The pan-resistomes, i.e., all ARGs present in an environment, were heavily dominated by latent ARGs. In comparison, the core-resistome, i.e., ARGs that were commonly encountered, comprised both latent and established ARGs. We identified several latent ARGs shared between environments and/or present in human pathogens. Context analysis of these genes showed that they were located on mobile genetic elements, including conjugative elements. We, furthermore, identified that wastewater microbiomes had a surprisingly large pan- and core-resistome, which makes it a potentially high-risk environment for the mobilization and promotion of latent ARGs.

CONCLUSIONS: Our results show that latent ARGs are ubiquitously present in all environments and constitute a diverse reservoir from which new resistance determinants can be recruited to pathogens. Several latent ARGs already had high mobile potential and were present in human pathogens, suggesting that they may constitute emerging threats to human health. We conclude that the full resistome-including both latent and established ARGs-needs to be considered to properly assess the risks associated with antibiotic selection pressures. Video Abstract.}, } @article {pmid36879274, year = {2023}, author = {Lousada, MB and Edelkamp, J and Lachnit, T and Fehrholz, M and Jimenez, F and Paus, R}, title = {Laser capture microdissection as a method for investigating the human hair follicle microbiome reveals region-specific differences in the bacteriome profile.}, journal = {BMC research notes}, volume = {16}, number = {1}, pages = {29}, pmid = {36879274}, issn = {1756-0500}, support = {Monasterium Laboratory//Monasterium Laboratory/ ; CRC 1182//Deutsche Forschungsgemeinschaft/ ; Giuliani S.p.a//Giuliani S.p.a/ ; }, mesh = {Humans ; Laser Capture Microdissection ; *Hair Follicle ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; }, abstract = {OBJECTIVE: Human hair follicles (HFs) are populated by a rich and diverse microbiome, traditionally evaluated by methods that inadvertently sample the skin microbiome and/or miss microbiota located in deeper HF regions. Thereby, these methods capture the human HF microbiome in a skewed and incomplete manner. This pilot study aimed to use laser-capture microdissection of human scalp HFs, coupled with 16S rRNA gene sequencing to sample the HF microbiome and overcome these methodological limitations.

RESULTS: HFs were laser-capture microdissected (LCM) into three anatomically distinct regions. All main known core HF bacterial colonisers, including Cutibacterium, Corynebacterium and Staphylococcus, were identified, in all three HF regions. Interestingly, region-specific variations in α-diversity and microbial abundance of the core microbiome genera and Reyranella were identified, suggestive of variations in microbiologically relevant microenvironment characteristics. This pilot study therefore shows that LCM-coupled with metagenomics is a powerful tool for analysing the microbiome of defined biological niches. Refining and complementing this method with broader metagenomic techniques will facilitate the mapping of dysbiotic events associated with HF diseases and targeted therapeutic interventions.}, } @article {pmid36878288, year = {2023}, author = {Chai, X and Wen, L and Song, Y and He, X and Yue, J and Wu, J and Chen, X and Cai, Z and Qi, Z}, title = {DEHP exposure elevated cardiovascular risk in obese mice by disturbing the arachidonic acid metabolism of gut microbiota.}, journal = {The Science of the total environment}, volume = {875}, number = {}, pages = {162615}, doi = {10.1016/j.scitotenv.2023.162615}, pmid = {36878288}, issn = {1879-1026}, mesh = {*Diethylhexyl Phthalate/toxicity/metabolism ; RNA, Ribosomal, 16S ; Obesity/metabolism ; *Cardiovascular Diseases/chemically induced ; Firmicutes ; Risk Factors ; Humans ; Mice ; Animals ; *Gastrointestinal Microbiome ; Heart Disease Risk Factors ; Arachidonic Acid ; Mice, Obese ; }, abstract = {Phthalate esters (PAEs) are one of the significant classes of emerging contaminants that are increasingly detected in environmental and human samples. Nevertheless, the current toxicity studies rarely report how PAEs affect the cardiovascular system, especially in obese individuals. In this study, diet-induced obese mice and corresponding normal mice were exposed to di(2-ethylhexyl) phthalate (DEHP) by oral gavage at environmentally relevant concentrations and key characteristics of cardiovascular risk were examined. The 16S rRNA and high-resolution mass spectrometry were used to investigate the alterations in the gut microbial profile and metabolic homeostasis. The results indicated that the cardiovascular system of fat individuals was more susceptible to DEHP exposure than mice in the lean group. 16S rRNA-based profiling and correlation analysis collectively suggested DEHP-induced gut microbial remodeling in fed a high-fat diet mice, represented by the abundance of the genus Faecalibaculum. Using metagenomic approaches, Faecalibaculum rodentium was identified as the top-ranked candidate bacterium. Additionally, metabolomics data revealed that DEHP exposure altered the gut metabolic homeostasis of arachidonic acid (AA), which is associated with adverse cardiovascular events. Finally, cultures of Faecalibaculum rodentium were treated with AA in vitro to verify the role of Faecalibaculum rodentium in altering AA metabolism. Our findings provide novel insights into DEHP exposure induced cardiovascular damage in obese individuals and suggest that AA could be used as a potential modulator of gut microbiota to prevent related diseases.}, } @article {pmid36875075, year = {2023}, author = {Xu, XJ and Lang, JD and Yang, J and Long, B and Liu, XD and Zeng, XF and Tian, G and You, X}, title = {Differences of gut microbiota and behavioral symptoms between two subgroups of autistic children based on γδT cells-derived IFN-γ Levels: A preliminary study.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1100816}, pmid = {36875075}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Autistic Disorder ; Behavioral Symptoms ; Amino Acids ; *Autism Spectrum Disorder ; }, abstract = {BACKGROUND: Autism Spectrum Disorders (ASD) are defined as a group of pervasive neurodevelopmental disorders, and the heterogeneity in the symptomology and etiology of ASD has long been recognized. Altered immune function and gut microbiota have been found in ASD populations. Immune dysfunction has been hypothesized to involve in the pathophysiology of a subtype of ASD.

METHODS: A cohort of 105 ASD children were recruited and grouped based on IFN-γ levels derived from ex vivo stimulated γδT cells. Fecal samples were collected and analyzed with a metagenomic approach. Comparison of autistic symptoms and gut microbiota composition was made between subgroups. Enriched KEGG orthologues markers and pathogen-host interactions based on metagenome were also analyzed to reveal the differences in functional features.

RESULTS: The autistic behavioral symptoms were more severe for children in the IFN-γ-high group, especially in the body and object use, social and self-help, and expressive language performance domains. LEfSe analysis of gut microbiota revealed an overrepresentation of Selenomonadales, Negatiyicutes, Veillonellaceae and Verrucomicrobiaceae and underrepresentation of Bacteroides xylanisolvens and Bifidobacterium longum in children with higher IFN-γ level. Decreased metabolism function of carbohydrate, amino acid and lipid in gut microbiota were found in the IFN-γ-high group. Additional functional profiles analyses revealed significant differences in the abundances of genes encoding carbohydrate-active enzymes between the two groups. And enriched phenotypes related to infection and gastroenteritis and underrepresentation of one gut-brain module associated with histamine degradation were also found in the IFN-γ-High group. Results of multivariate analyses revealed relatively good separation between the two groups.

CONCLUSIONS: Levels of IFN-γ derived from γδT cell could serve as one of the potential candidate biomarkers to subtype ASD individuals to reduce the heterogeneity associated with ASD and produce subgroups which are more likely to share a more similar phenotype and etiology. A better understanding of the associations among immune function, gut microbiota composition and metabolism abnormalities in ASD would facilitate the development of individualized biomedical treatment for this complex neurodevelopmental disorder.}, } @article {pmid36874978, year = {2023}, author = {Fuchsman, CA and Garcia Prieto, D and Hays, MD and Cram, JA}, title = {Associations between picocyanobacterial ecotypes and cyanophage host genes across ocean basins and depth.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e14924}, pmid = {36874978}, issn = {2167-8359}, mesh = {*Ecotype ; Phylogeny ; *Genes, Viral ; Genome, Viral ; Cycadopsida ; }, abstract = {BACKGROUND: Cyanophages, viruses that infect cyanobacteria, are globally abundant in the ocean's euphotic zone and are a potentially important cause of mortality for marine picocyanobacteria. Viral host genes are thought to increase viral fitness by either increasing numbers of genes for synthesizing nucleotides for virus replication, or by mitigating direct stresses imposed by the environment. The encoding of host genes in viral genomes through horizontal gene transfer is a form of evolution that links viruses, hosts, and the environment. We previously examined depth profiles of the proportion of cyanophage containing various host genes in the Eastern Tropical North Pacific Oxygen Deficient Zone (ODZ) and at the subtropical North Atlantic (BATS). However, cyanophage host genes have not been previously examined in environmental depth profiles across the oceans.

METHODOLOGY: We examined geographical and depth distributions of picocyanobacterial ecotypes, cyanophage, and their viral-host genes across ocean basins including the North Atlantic, Mediterranean Sea, North Pacific, South Pacific, and Eastern Tropical North and South Pacific ODZs using phylogenetic metagenomic read placement. We determined the proportion of myo and podo-cyanophage containing a range of host genes by comparing to cyanophage single copy core gene terminase (terL). With this large dataset (22 stations), network analysis identified statistical links between 12 of the 14 cyanophage host genes examined here with their picocyanobacteria host ecotypes.

RESULTS: Picyanobacterial ecotypes, and the composition and proportion of cyanophage host genes, shifted dramatically and predictably with depth. For most of the cyanophage host genes examined here, we found that the composition of host ecotypes predicted the proportion of viral host genes harbored by the cyanophage community. Terminase is too conserved to illuminate the myo-cyanophage community structure. Cyanophage cobS was present in almost all myo-cyanophage and did not vary in proportion with depth. We used the composition of cobS phylotypes to track changes in myo-cyanophage composition.

CONCLUSIONS: Picocyanobacteria ecotypes shift with changes in light, temperature, and oxygen and many common cyanophage host genes shift concomitantly. However, cyanophage phosphate transporter gene pstS appeared to instead vary with ocean basin and was most abundant in low phosphate regions. Abundances of cyanophage host genes related to nutrient acquisition may diverge from host ecotype constraints as the same host can live in varying nutrient concentrations. Myo-cyanophage community in the anoxic ODZ had reduced diversity. By comparison to the oxic ocean, we can see which cyanophage host genes are especially abundant (nirA, nirC, and purS) or not abundant (myo psbA) in ODZs, highlighting both the stability of conditions in the ODZ and the importance of nitrite as an N source to ODZ endemic LLV Prochlorococcus.}, } @article {pmid36871189, year = {2023}, author = {Peterson, BD and Krabbenhoft, DP and McMahon, KD and Ogorek, JM and Tate, MT and Orem, WH and Poulin, BA}, title = {Environmental formation of methylmercury is controlled by synergy of inorganic mercury bioavailability and microbial mercury-methylation capacity.}, journal = {Environmental microbiology}, volume = {25}, number = {8}, pages = {1409-1423}, doi = {10.1111/1462-2920.16364}, pmid = {36871189}, issn = {1462-2920}, mesh = {*Methylmercury Compounds ; *Mercury ; Methylation ; Biological Availability ; *Microbiota ; *Water Pollutants, Chemical/analysis ; }, abstract = {Methylmercury (MeHg) production is controlled by the bioavailability of inorganic divalent mercury (Hg(II)i) and Hg-methylation capacity of the microbial community (conferred by the hgcAB gene cluster). However, the relative importance of these factors and their interaction in the environment remain poorly understood. Here, metagenomic sequencing and a full-factorial MeHg formation experiment were conducted across a wetland sulfate gradient with different microbial communities and pore water chemistries. From this experiment, the relative importance of each factor on MeHg formation was isolated. Hg(II)i bioavailability correlated with the dissolved organic matter composition, while the microbial Hg-methylation capacity correlated with the abundance of hgcA genes. MeHg formation responded synergistically to both factors. Notably, hgcA sequences were from diverse taxonomic groups, none of which contained genes for dissimilatory sulfate reduction. This work expands our understanding of the geochemical and microbial constraints on MeHg formation in situ and provides an experimental framework for further mechanistic studies.}, } @article {pmid36871005, year = {2023}, author = {Wu, TT and Sohn, M and Manning, S and Beblavy, R and Gill, S and Quataert, S and Vasani, S and Jang, H and Zeng, Y and Bruno, J and Vazquez, A and Fiscella, K and Xiao, J}, title = {Metagenomic analysis examines oral microbiome changes and interplay with immune response following prenatal total oral rehabilitation.}, journal = {Journal of translational medicine}, volume = {21}, number = {1}, pages = {172}, pmid = {36871005}, issn = {1479-5876}, support = {K23 DE027412/DE/NIDCR NIH HHS/United States ; R01 DE031025/DE/NIDCR NIH HHS/United States ; R01DE031025/DE/NIDCR NIH HHS/United States ; K23DE027412/DE/NIDCR NIH HHS/United States ; }, mesh = {Pregnancy ; Child ; Female ; Humans ; Infant, Newborn ; *Dental Caries ; Prospective Studies ; *Microbiota ; Physical Therapy Modalities ; Family ; }, abstract = {BACKGROUND: Suboptimal maternal oral health during pregnancy is potentially associated with adverse birth outcomes and increased dental caries risks in children. This study aimed to assess the oral microbiome and immune response following an innovative clinical regimen, Prenatal Total Oral Rehabilitation (PTOR), that fully restores women's oral health to a "disease-free status" before delivery.

METHODS: This prospective cohort study assessed 15 pregnant women at baseline and 3 follow-up visits (1 week, 2 weeks, and 2 months) after receiving PTOR. The salivary and supragingival plaque microbiomes were analyzed using metagenomic sequencing. Multiplexed Luminex cytokine assays were performed to examine immune response following PTOR. The association between salivary immune markers and oral microbiome was further examined.

RESULTS: PTOR was associated with a reduction of periodontal pathogens in plaque, for instance, a lower relative abundance of Tannerella forsythia and Treponema denticola at 2 weeks compared to the baseline (p < 0.05). The alpha diversity of plaque microbial community was significantly reduced at the 1-week follow-up (p < 0.05). Furthermore, we observed significant changes in the Actinomyces defective-associated carbohydrate degradation pathway and Streptococcus Gordonii-associated fatty acid biosynthesis pathway. Two immune markers related to adverse birth outcomes significantly differed between baseline and follow-up. ITAC, negatively correlated with preeclampsia severity, significantly increased at 1-week follow-up; MCP-1, positively correlated with gestational age, was elevated at 1-week follow-up. Association modeling between immune markers and microbiome further revealed specific oral microorganisms that are potentially correlated with the host immune response.

CONCLUSIONS: PTOR is associated with alteration of the oral microbiome and immune response among a cohort of underserved US pregnant women. Future randomized clinical trials are warranted to comprehensively assess the impact of PTOR on maternal oral flora, birth outcomes, and their offspring's oral health.}, } @article {pmid36869370, year = {2023}, author = {Gu, F and Zhu, S and Tang, Y and Liu, X and Jia, M and Malmuthuge, N and Valencak, TG and McFadden, JW and Liu, JX and Sun, HZ}, title = {Gut microbiome is linked to functions of peripheral immune cells in transition cows during excessive lipolysis.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {40}, pmid = {36869370}, issn = {2049-2618}, mesh = {Female ; Animals ; Cattle ; *Gastrointestinal Microbiome ; Lipolysis ; Bacteroides ; Down-Regulation ; Metabolome ; }, abstract = {BACKGROUND: Postpartum dairy cows experiencing excessive lipolysis are prone to severe immunosuppression. Despite the extensive understanding of the gut microbial regulation of host immunity and metabolism, its role during excessive lipolysis in cows is largely unknown. Herein, we investigated the potential links between the gut microbiome and postpartum immunosuppression in periparturient dairy cows with excessive lipolysis using single immune cell transcriptome, 16S amplicon sequencing, metagenomics, and targeted metabolomics.

RESULTS: The use of single-cell RNA sequencing identified 26 clusters that were annotated to 10 different immune cell types. Enrichment of functions of these clusters revealed a downregulation of functions in immune cells isolated from a cow with excessive lipolysis compared to a cow with low/normal lipolysis. The results of metagenomic sequencing and targeted metabolome analysis together revealed that secondary bile acid (SBA) biosynthesis was significantly activated in the cows with excessive lipolysis. Moreover, the relative abundance of gut Bacteroides sp. OF04 - 15BH, Paraprevotella clara, Paraprevotella xylaniphila, and Treponema sp. JC4 was mainly associated with SBA synthesis. The use of an integrated analysis showed that the reduction of plasma glycolithocholic acid and taurolithocholic acid could contribute to the immunosuppression of monocytes (CD14[+]MON) during excessive lipolysis by decreasing the expression of GPBAR1.

CONCLUSIONS: Our results suggest that alterations in the gut microbiota and their functions related to SBA synthesis suppressed the functions of monocytes during excessive lipolysis in transition dairy cows. Therefore, we concluded that altered microbial SBA synthesis during excessive lipolysis could lead to postpartum immunosuppression in transition cows. Video Abstract.}, } @article {pmid36867161, year = {2023}, author = {Wright, RJ and Comeau, AM and Langille, MGI}, title = {From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools.}, journal = {Microbial genomics}, volume = {9}, number = {3}, pages = {}, pmid = {36867161}, issn = {2057-5858}, mesh = {Humans ; *Metagenome ; *Microbiota ; Databases, Factual ; Metagenomics ; }, abstract = {In metagenomic analyses of microbiomes, one of the first steps is usually the taxonomic classification of reads by comparison to a database of previously taxonomically classified genomes. While different studies comparing metagenomic taxonomic classification methods have determined that different tools are 'best', there are two tools that have been used the most to-date: Kraken (k-mer-based classification against a user-constructed database) and MetaPhlAn (classification by alignment to clade-specific marker genes), the latest versions of which are Kraken2 and MetaPhlAn 3, respectively. We found large discrepancies in both the proportion of reads that were classified as well as the number of species that were identified when we used both Kraken2 and MetaPhlAn 3 to classify reads within metagenomes from human-associated or environmental datasets. We then investigated which of these tools would give classifications closest to the real composition of metagenomic samples using a range of simulated and mock samples and examined the combined impact of tool-parameter-database choice on the taxonomic classifications given. This revealed that there may not be a one-size-fits-all 'best' choice. While Kraken2 can achieve better overall performance, with higher precision, recall and F1 scores, as well as alpha- and beta-diversity measures closer to the known composition than MetaPhlAn 3, the computational resources required for this may be prohibitive for many researchers, and the default database and parameters should not be used. We therefore conclude that the best tool-parameter-database choice for a particular application depends on the scientific question of interest, which performance metric is most important for this question and the limit of available computational resources.}, } @article {pmid36864882, year = {2023}, author = {Wang, M and Yan, LY and Qiao, CY and Zheng, CC and Niu, CG and Huang, ZW and Pan, YH}, title = {Ecological shifts of salivary microbiota associated with metabolic-associated fatty liver disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1131255}, pmid = {36864882}, issn = {2235-2988}, mesh = {Humans ; Metagenome ; *Microbiota ; *Non-alcoholic Fatty Liver Disease/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; }, abstract = {INTRODUCTION: Metabolic-associated fatty liver disease (MAFLD) is the most common chronic liver disease related to metabolic syndrome. However, ecological shifts in the saliva microbiome in patients with MAFLD remain unknown. This study aimed to investigate the changes to the salivary microbial community in patients with MAFLD and explore the potential function of microbiota.

METHODS: Salivary microbiomes from ten MAFLD patients and ten healthy participants were analyzed by 16S rRNA amplicon sequencing and bioinformatics analysis. Body composition, plasma enzymes, hormones, and blood lipid profiles were assessed with physical examinations and laboratory tests.

RESULTS: The salivary microbiome of MAFLD patients was characterized by increased α-diversity and distinct β-diversity clustering compared with control subjects. Linear discriminant analysis effect size analysis showed a total of 44 taxa significantly differed between the two groups. Genera Neisseria, Filifactor, and Capnocytophaga were identified as differentially enriched genera for comparison of the two groups. Co-occurrence networks suggested that the salivary microbiota from MAFLD patients exhibited more intricate and robust interrelationships. The diagnostic model based on the salivary microbiome achieved a good diagnostic power with an area under the curve of 0.82(95% CI: 0.61-1). Redundancy analysis and spearman correlation analysis revealed that clinical variables related to insulin resistance and obesity were strongly associated with the microbial community. Metagenomic predictions based on Phylogenetic Investigation of Communities by Reconstruction of Unobserved States revealed that pathways related to metabolism were more prevalent in the two groups.

CONCLUSIONS: Patients with MAFLD manifested ecological shifts in the salivary microbiome, and the saliva microbiome-based diagnostic model provides a promising approach for auxiliary MAFLD diagnosis.}, } @article {pmid36864573, year = {2023}, author = {Cheung, MK and Ng, RWY and Lai, CKC and Zhu, C and Au, ETK and Yau, JWK and Li, C and Wong, HC and Wong, BCK and Kwok, KO and Chen, Z and Chan, PKS and Lui, GCY and Ip, M}, title = {Alterations in faecal microbiome and resistome in Chinese international travellers: a metagenomic analysis.}, journal = {Journal of travel medicine}, volume = {30}, number = {6}, pages = {}, pmid = {36864573}, issn = {1708-8305}, support = {//The Chinese University of Hong Kong/ ; //Health and Medical Research Fund/ ; 18170082//Food and Health Bureau of the Hong Kong Special Administrative Region, China/ ; }, mesh = {Adult ; Humans ; Anti-Bacterial Agents/pharmacology ; Antimalarials/pharmacology ; Doxycycline ; East Asian People ; *Microbiota/genetics/physiology ; *Feces/microbiology ; Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: International travel increases the risk of acquisition of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). Previous studies have characterized the changes in the gut microbiome and resistome of Western travellers; however, information on non-Western populations and the effects of travel-related risk factors on the gut microbiome and resistome remains limited.

METHODS: We conducted a prospective observational study on a cohort of 90 healthy Chinese adult residents of Hong Kong. We characterized the microbiome and resistome in stools collected from the subjects before and after travelling to diverse international locations using shotgun metagenomic sequencing and examined their associations with travel-related variables.

RESULTS: Our results showed that travel neither significantly changed the taxonomic composition of the faecal microbiota nor altered the alpha (Shannon) or beta diversity of the faecal microbiome or resistome. However, travel significantly increased the number of ARGs. Ten ARGs, including aadA, TEM, mgrB, mphA, qnrS9 and tetR, were significantly enriched in relative abundance after travel, eight of which were detected in metagenomic bins belonging to Escherichia/Shigella flexneri in the post-trip samples. In sum, 30 ARGs significantly increased in prevalence after travel, with the largest changes observed in tetD and a few qnrS variants (qnrS9, qnrS and qnrS8). We found that travel to low- or middle-income countries, or Africa or Southeast Asia, increased the number of ARG subtypes, whereas travel to low- or middle-income countries and the use of alcohol-based hand sanitizer (ABHS) or doxycycline as antimalarial prophylaxis during travel resulted in increased changes in the beta diversity of the faecal resistome.

CONCLUSIONS: Our study highlights travel to low- or middle-income countries, Africa or Southeast Asia, a long travel duration, or the use of ABHS or doxycycline as antimalarial prophylaxis as important risk factors for the acquisition/enrichment of ARGs during international travel.}, } @article {pmid36864482, year = {2023}, author = {Lou, YC and Hoff, J and Olm, MR and West-Roberts, J and Diamond, S and Firek, BA and Morowitz, MJ and Banfield, JF}, title = {Using strain-resolved analysis to identify contamination in metagenomics data.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {36}, pmid = {36864482}, issn = {2049-2618}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; RAI092531A/NH/NIH HHS/United States ; }, mesh = {*Metagenomics ; Biomass ; DNA Contamination ; *Microbiota/genetics ; DNA ; }, abstract = {BACKGROUND: Metagenomics analyses can be negatively impacted by DNA contamination. While external sources of contamination such as DNA extraction kits have been widely reported and investigated, contamination originating within the study itself remains underreported.

RESULTS: Here, we applied high-resolution strain-resolved analyses to identify contamination in two large-scale clinical metagenomics datasets. By mapping strain sharing to DNA extraction plates, we identified well-to-well contamination in both negative controls and biological samples in one dataset. Such contamination is more likely to occur among samples that are on the same or adjacent columns or rows of the extraction plate than samples that are far apart. Our strain-resolved workflow also reveals the presence of externally derived contamination, primarily in the other dataset. Overall, in both datasets, contamination is more significant in samples with lower biomass.

CONCLUSION: Our work demonstrates that genome-resolved strain tracking, with its essentially genome-wide nucleotide-level resolution, can be used to detect contamination in sequencing-based microbiome studies. Our results underscore the value of strain-specific methods to detect contamination and the critical importance of looking for contamination beyond negative and positive controls. Video Abstract.}, } @article {pmid36864029, year = {2023}, author = {Lee, K and Raguideau, S and Sirén, K and Asnicar, F and Cumbo, F and Hildebrand, F and Segata, N and Cha, CJ and Quince, C}, title = {Population-level impacts of antibiotic usage on the human gut microbiome.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1191}, pmid = {36864029}, issn = {2041-1723}, support = {BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Microbiota ; Metagenome/genetics ; Genome, Human ; }, abstract = {The widespread usage of antimicrobials has driven the evolution of resistance in pathogenic microbes, both increased prevalence of antimicrobial resistance genes (ARGs) and their spread across species by horizontal gene transfer (HGT). However, the impact on the wider community of commensal microbes associated with the human body, the microbiome, is less well understood. Small-scale studies have determined the transient impacts of antibiotic consumption but we conduct an extensive survey of ARGs in 8972 metagenomes to determine the population-level impacts. Focusing on 3096 gut microbiomes from healthy individuals not taking antibiotics we demonstrate highly significant correlations between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Samples from China were notable outliers. We use a collection of 154,723 human-associated metagenome assembled genomes (MAGs) to link these ARGs to taxa and detect HGT. This reveals that the correlations in ARG abundance are driven by multi-species mobile ARGs shared between pathogens and commensals, within a highly connected central component of the network of MAGs and ARGs. We also observe that individual human gut ARG profiles cluster into two types or resistotypes. The less frequent resistotype has higher overall ARG abundance, is associated with certain classes of resistance, and is linked to species-specific genes in the Proteobacteria on the periphery of the ARG network.}, } @article {pmid36862079, year = {2023}, author = {Pino, V and Fajardo, M and McBratney, A and Minasny, B and Wilson, N and Baldock, C}, title = {Australian soil microbiome: A first sightseeing regional prediction driven by cycles of soil temperature and pedogenic variations.}, journal = {Molecular ecology}, volume = {32}, number = {23}, pages = {6243-6259}, doi = {10.1111/mec.16911}, pmid = {36862079}, issn = {1365-294X}, support = {//Comisión Nacional de Investigación Científica y Tecnológica/ ; //University of Sydney/ ; }, mesh = {*Soil ; Australia ; Temperature ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; *Microbiota/genetics ; }, abstract = {Declines in soil multifunctionality (e.gsoil capacity to provide food and energy) are closely related to changes in the soil microbiome (e.g., diversity) Determining ecological drivers promoting such microbiome changes is critical knowledge for protecting soil functions. However, soil-microbe interactions are highly variable within environmental gradients and may not be consistent across studies. Here we propose that analysis of community dissimilarity (β-diversity) is a valuable tool for overviewing soil microbiome spatiotemporal changes. Indeed, β-diversity studies at larger scales (modelling and mapping) simplify complex multivariate interactions and refine our understanding of ecological drivers by also giving the possibility of expanding the environmental scenarios. This study represents the first spatial investigation of β-diversity in the soil microbiome of New South Wales (800,642 km[2]), Australia. We used metabarcoding soil data (16S rRNA and ITS genes) as exact sequence variants (ASVs) and UMAP (Uniform Manifold Approximation and Projection) as the distance metric. β-Diversity maps (1000-m resolution)-concordance correlations of 0.91-0.96 and 0.91-0.95 for bacteria and fungi, respectively-showed soil biome dissimilarities driven primarily by soil chemistry-pH and effective cation exchange capacity (ECEC)-and cycles of soil temperature-land surface temperature (LST-phase and LST-amplitude). Regionally, the spatial patterns of microbes parallel the distribution of soil classes (e.g., Vertosols) beyond spatial distances and rainfall, for example. Soil classes can be valuable discriminants for monitoring approaches, for example pedogenons and pedophenons. Ultimately, cultivated soils exhibited lower richness due to declines in rare microbes which might compromise soil functions over time.}, } @article {pmid36861850, year = {2024}, author = {Ordinola-Zapata, R and Costalonga, M and Dietz, M and Lima, BP and Staley, C}, title = {The root canal microbiome diversity and function. A whole-metagenome shotgun analysis.}, journal = {International endodontic journal}, volume = {57}, number = {7}, pages = {872-884}, doi = {10.1111/iej.13911}, pmid = {36861850}, issn = {1365-2591}, support = {UL1-TR002494/TR/NCATS NIH HHS/United States ; UL1-TR002494/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; *Dental Pulp Cavity/microbiology ; *Periapical Periodontitis/microbiology ; Metagenome ; Adult ; Female ; Male ; Middle Aged ; Bacteria/classification/genetics ; }, abstract = {AIM: To evaluate the root canal microbiome composition and bacterial functional capability in cases of primary and secondary apical periodontitis utilizing whole-metagenome shotgun sequencing.

METHODOLOGY: Twenty-two samples from patients with primary root canal infections, and 18 samples obtained from previously treated teeth currently diagnosed with apical periodontitis were analysed with whole-metagenome shotgun sequencing at a depth of 20 M reads. Taxonomic and functional gene annotations were made using MetaPhlAn3 and HUMAnN3 software. The Shannon and Chao1 indices were utilized to measure alpha diversity. Differences in community composition were evaluated utilizing analysis of similarity (ANOSIM) using Bray-Curtis dissimilarities. The Wilcoxon rank sum test was used to compare differences in taxa and functional genes.

RESULTS: Microbial community variations within a community were significantly lower in secondary relative to primary infections (alpha diversity p = .001). Community composition was significantly different in primary versus secondary infection (R = .11, p = .005). The predominant taxa observed among samples (>2.5%) were Pseudopropionibacterium propionicum, Prevotella oris, Eubacterium infirmum, Tannerella forsythia, Atopobium rimae, Peptostreptococcus stomatis, Bacteroidetes bacterium oral taxon 272, Parvimonas micra, Olsenella profusa, Streptococcus anginosus, Lactobacillus rhamnosus, Porphyromonas endodontalis, Pseudoramibacter alactolyticus, Fusobacterium nucleatum, Eubacterium brachy and Solobacterium moorei. The Wilcoxon rank test revealed no significant differences in relative abundances of functional genes in both groups. Genes with greater relative abundances (top 25) were associated with genetic, signalling and cellular processes including the iron and peptide/nickel transport system. Numerous genes encoding toxins were identified: exfoliative toxin, haemolysins, thiol-activated cytolysin, phospholipase C, cAMP factor, sialidase, and hyaluronic glucosaminidase.

CONCLUSIONS: Despite taxonomic differences between primary and secondary apical periodontitis, the functional capability of the microbiomes was similar.}, } @article {pmid36860056, year = {2023}, author = {Chen, X and Ke, Y and Zhu, Y and Xu, M and Chen, C and Xie, S}, title = {Enrichment of tetracycline-degrading bacterial consortia: Microbial community succession and degradation characteristics and mechanism.}, journal = {Journal of hazardous materials}, volume = {448}, number = {}, pages = {130984}, doi = {10.1016/j.jhazmat.2023.130984}, pmid = {36860056}, issn = {1873-3336}, mesh = {*Tetracycline ; Anti-Bacterial Agents ; *Microbiota ; Microbial Consortia ; Metagenome ; }, abstract = {Tetracycline (TC) is an antibiotic that is recently found as an emerging pollutant with low biodegradability. Biodegradation shows great potential for TC dissipation. In this study, two TC-degrading microbial consortia (named SL and SI) were respectively enriched from activated sludge and soil. Bacterial diversity decreased in these finally enriched consortia compared with the original microbiota. Moreover, most ARGs quantified during the acclimation process became less abundant in the finally enriched microbial consortia. Microbial compositions of the two consortia as revealed by 16 S rRNA sequencing were similar to some extent, and the dominant genera Pseudomonas, Sphingobacterium, and Achromobacter were identified as the potential TC degraders. In addition, consortia SL and SI were capable of biodegrading TC (initial 50 mg/L) by 82.92% and 86.83% within 7 days, respectively. They could retain high degradation capabilities under a wide pH range (4-10) and at moderate/high temperatures (25-40 °C). Peptone with concentrations of 4-10 g/L could serve as a desirable primary growth substrate for consortia to remove TC through co-metabolism. A total of 16 possible intermediates including a novel biodegradation product TP245 were detected during TC degradation. Peroxidase genes, tetX-like genes and the enriched genes related to aromatic compound degradation as revealed by metagenomic sequencing were likely responsible for TC biodegradation.}, } @article {pmid36860032, year = {2023}, author = {Ge, L and Song, L and Wang, L and Li, Y and Sun, Y and Wang, C and Chen, J and Wu, G and Pan, A and Wu, Y and Quan, Z and Li, P}, title = {Evaluating response mechanisms of soil microbiomes and metabolomes to Bt toxin additions.}, journal = {Journal of hazardous materials}, volume = {448}, number = {}, pages = {130904}, doi = {10.1016/j.jhazmat.2023.130904}, pmid = {36860032}, issn = {1873-3336}, mesh = {*Soil ; Bacillus thuringiensis Toxins ; RNA, Ribosomal, 16S ; Metabolome ; *Microbiota ; }, abstract = {The accumulation and persistence of Bt toxins in soils from Bt plants and Bt biopesticides may result in environmental hazards such as adverse impacts on soil microorganisms. However, the dynamic relationships among exogenous Bt toxins, soil characteristics, and soil microorganisms are not well understood. Cry1Ab is one of the most commonly used Bt toxins and was added to soils in this study to evaluate subsequent changes in soil physiochemical properties, microbial taxa, microbial functional genes, and metabolites profiles via 16S rRNA gene pyrosequencing, high-throughput qPCR, metagenomic shotgun sequencing, and untargeted metabolomics. Higher additions of Bt toxins led to higher concentrations of soil organic matter (SOM), ammonium (NH[+]4-N), and nitrite (NO2[-]-N) compared against controls without addition after 100 days of soil incubation. High-throughput qPCR analysis and shotgun metagenomic sequencing analysis revealed that the 500 ng/g Bt toxin addition significantly affected profiles of soil microbial functional genes involved in soil carbon (C), nitrogen (N), and phosphorus (P) cycling after 100 days of incubation. Furthermore, combined metagenomic and metabolomic analyses indicated that the 500 ng/g Bt toxin addition significantly altered low molecular weight metabolite profiles of soils. Importantly, some of these altered metabolites are involved in soil nutrient cycling, and robust associations were identified among differentially abundant metabolites and microorganisms due to Bt toxin addition treatments. Taken together, these results suggest that higher levels of Bt toxin addition can alter soil nutrients, probably by affecting the activities of Bt toxin-degrading microorganisms. These dynamics would then activate other microorganisms involved in nutrient cycling, finally leading to broad changes in metabolite profiles. Notably, the addition of Bt toxins did not cause the accumulation of potential microbial pathogens in soils, nor did it adversely affect the diversity and stability of microbial communities. This study provides new insights into the putative mechanistic associations among Bt toxins, soil characteristics, and microorganisms, providing new understanding into the ecological impacts of Bt toxins on soil ecosystems.}, } @article {pmid36856771, year = {2023}, author = {Shi, ZJ and Nayfach, S and Pollard, KS}, title = {Identifying species-specific k-mers for fast and accurate metagenotyping with Maast and GT-Pro.}, journal = {STAR protocols}, volume = {4}, number = {1}, pages = {101964}, pmid = {36856771}, issn = {2666-1667}, support = {R01 HL160862/HL/NHLBI NIH HHS/United States ; }, mesh = {*Genome ; *Microbiota/genetics ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {Genotyping single-nucleotide polymorphisms (SNPs) in microbiomes enables strain-level quantification. In this protocol, we describe a computational pipeline that performs fast and accurate SNP genotyping using metagenomic data. We first demonstrate how to use Maast to catalog SNPs from microbial genomes. Then we use GT-Pro to extract unique SNP-covering k-mers, optimize a data structure for storing these k-mers, and finally perform metagenotyping. For proof of concept, the protocol leverages public whole-genome sequences to metagenotype a synthetic community. For complete details on the use and execution of this protocol, please refer to Shi et al. (2022a)[1] and Shi et al. (2022b).[2].}, } @article {pmid36853013, year = {2023}, author = {Ren, Y and Hao, L and Liu, J and Wang, P and Ding, Q and Chen, C and Song, Y}, title = {Alterations in the Gut Microbiota in Pregnant Women with Pregestational Type 2 Diabetes Mellitus.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0114622}, pmid = {36853013}, issn = {2379-5077}, mesh = {Infant, Newborn ; Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/microbiology ; Pregnant Women ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Pregnancy Outcome ; *Hyperglycemia ; }, abstract = {Human gut dysbiosis is associated with type 2 diabetes mellitus (T2DM); however, the gut microbiome in pregnant women with pregestational type 2 diabetes mellitus (PGDM) remains unexplored. We investigated the alterations in the gut microbiota composition in pregnant women with or without PGDM. The gut microbiota was examined using 16S rRNA sequencing data of 234 maternal fecal samples that were collected during the first (T1), second (T2), and third (T3) trimesters. The PGDM group presented a reduction in the number of gut bacteria taxonomies as the pregnancies progressed. Linear discriminant analyses revealed that Megamonas, Bacteroides, and Roseburia intestinalis were enriched in the PGDM group, whereas Bacteroides vulgatus, Faecalibacterium prausnitzii, Eubacterium rectale, Bacteroides uniformis, Eubacterium eligens, Subdoligranulum, Bacteroides fragilis, Dialister, Lachnospiraceae, Christensenellaceae R-7, Roseburia inulinivorans, Streptococcus oralis, Prevotella melaninogenica, Neisseria perflava, Bacteroides ovatus, Bacteroides caccae, Veillonella dispar, and Haemophilus parainfluenzae were overrepresented in the control group. Correlation analyses showed that the PGDM-enriched taxa were correlated with higher blood glucose levels during pregnancy, whereas the taxonomic biomarkers of normoglycemic pregnancies exhibited negative correlations with glycemic traits. The microbial networks in the PGDM group comprised weaker microbial interactions than those in the control group. Our study reveals the distinct characteristics of the gut microbiota composition based on gestational ages between normoglycemic and PGDM pregnancies. Further longitudinal research involving women with T2DM at preconception stages and investigations using shotgun metagenomic sequencing should be performed to elucidate the relationships between specific bacterial functions and PGDM metabolic statuses during pregnancy and to identify potential therapeutic targets. IMPORTANCE The incidence of pregestational type 2 diabetes mellitus (PGDM) is increasing, with high rates of serious adverse maternal and neonatal outcomes that are strongly correlated with hyperglycemia. Recent studies have shown that type 2 diabetes mellitus is associated with gut microbial dysbiosis; however, the gut microbiome composition and its associations with the metabolic features of patients with PGDM remain largely unknown. In this study, we investigated the changes in the gut microbiota composition in pregnant women with and without PGDM. We identified differential taxa that may be correlated with maternal metabolic statuses during pregnancy. Additionally, we observed that the number of taxonomic and microbial networks of gut bacteria were distinctly reduced in women with hyperglycemia as their pregnancies progressed. These results extend our understanding of the associations between the gut microbial composition, PGDM-related metabolic changes, and pregnancy outcomes.}, } @article {pmid36851669, year = {2023}, author = {Ambrose, RK and Blakebrough-Hall, C and Gravel, JL and Gonzalez, LA and Mahony, TJ}, title = {Characterisation of the Upper Respiratory Tract Virome of Feedlot Cattle and Its Association with Bovine Respiratory Disease.}, journal = {Viruses}, volume = {15}, number = {2}, pages = {}, pmid = {36851669}, issn = {1999-4915}, mesh = {Animals ; Cattle ; Case-Control Studies ; Virome ; *Respiratory Tract Diseases ; Trachea ; Nose ; *Cattle Diseases ; *Coronavirus, Bovine/genetics ; *Nidovirales ; Mammals ; }, abstract = {Bovine respiratory disease (BRD) is a major health problem within the global cattle industry. This disease has a complex aetiology, with viruses playing an integral role. In this study, metagenomics was used to sequence viral nucleic acids in the nasal swabs of BRD-affected cattle. The viruses detected included those that are well known for their association with BRD in Australia (bovine viral diarrhoea virus 1), as well as viruses known to be present but not fully characterised (bovine coronavirus) and viruses that have not been reported in BRD-affected cattle in Australia (bovine rhinitis, bovine influenza D, and bovine nidovirus). The nasal swabs from a case-control study were subsequently tested for 10 viruses, and the presence of at least one virus was found to be significantly associated with BRD. Some of the more recently detected viruses had inconsistent associations with BRD. Full genome sequences for bovine coronavirus, a virus increasingly associated with BRD, and bovine nidovirus were completed. Both viruses belong to the Coronaviridae family, which are frequently associated with disease in mammals. This study has provided greater insights into the viral pathogens associated with BRD and highlighted the need for further studies to more precisely elucidate the roles viruses play in BRD.}, } @article {pmid36850017, year = {2023}, author = {Theelen, MJP and Luiken, REC and Wagenaar, JA and Sloet van Oldruitenborgh-Oosterbaan, MM and Rossen, JWA and Schaafstra, FJWC and van Doorn, DA and Zomer, AL}, title = {Longitudinal study of the short- and long-term effects of hospitalisation and oral trimethoprim-sulfadiazine administration on the equine faecal microbiome and resistome.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {33}, pmid = {36850017}, issn = {2049-2618}, mesh = {Humans ; Horses ; Animals ; *Trimethoprim/pharmacology ; Longitudinal Studies ; RNA, Ribosomal, 16S/genetics ; Hospitalization ; Feces ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Hospitalisation and antimicrobial treatment are common in horses and significantly impact the intestinal microbiota. Antimicrobial treatment might also increase levels of resistant bacteria in faeces, which could spread to other ecological compartments, such as the environment, other animals and humans. In this study, we aimed to characterise the short- and long-term effects of transportation, hospitalisation and trimethoprim-sulfadiazine (TMS) administration on the faecal microbiota and resistome of healthy equids.

METHODS: In a longitudinal experimental study design, in which the ponies served as their own control, faecal samples were collected from six healthy Welsh ponies at the farm (D0-D13-1), immediately following transportation to the hospital (D13-2), during 7 days of hospitalisation without treatment (D14-D21), during 5 days of oral TMS treatment (D22-D26) and after discharge from the hospital up to 6 months later (D27-D211). After DNA extraction, 16S rRNA gene sequencing was performed on all samples. For resistome analysis, shotgun metagenomic sequencing was performed on selected samples.

RESULTS: Hospitalisation without antimicrobial treatment did not significantly affect microbiota composition. Oral TMS treatment reduced alpha-diversity significantly. Kiritimatiellaeota, Fibrobacteres and Verrucomicrobia significantly decreased in relative abundance, whereas Firmicutes increased. The faecal microbiota composition gradually recovered after discontinuation of TMS treatment and discharge from the hospital and, after 2 weeks, was more similar to pre-treatment composition than to composition during TMS treatment. Six months later, however, microbiota composition still differed significantly from that at the start of the study and Spirochaetes and Verrucomicrobia were less abundant. TMS administration led to a significant (up to 32-fold) and rapid increase in the relative abundance of resistance genes sul2, tetQ, ant6-1a, and aph(3")-lb. lnuC significantly decreased directly after treatment. Resistance genes sul2 (15-fold) and tetQ (six-fold) remained significantly increased 6 months later.

CONCLUSIONS: Oral treatment with TMS has a rapid and long-lasting effect on faecal microbiota composition and resistome, making the equine hindgut a reservoir and potential source of resistant bacteria posing a risk to animal and human health through transmission. These findings support the judicious use of antimicrobials to minimise long-term faecal presence, excretion and the spread of antimicrobial resistance in the environment. Video Abstract.}, } @article {pmid36848210, year = {2023}, author = {Rojas-Gätjens, D and Avey-Arroyo, J and Chaverri, P and Rojas-Jimenez, K and Chavarría, M}, title = {Differences in fungal communities in the fur of two- and three-toed sloths revealed by ITS metabarcoding.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {2}, pages = {}, pmid = {36848210}, issn = {1465-2080}, mesh = {Animals ; *Mycobiome ; *Sloths ; Ecosystem ; Host Specificity ; Metagenomics ; }, abstract = {Sloths have dense fur on which insects, algae, bacteria and fungi coexist. Previous studies using cultivation-dependent methods and 18S rRNA sequencing revealed that the fungal communities in their furs comprise members of the phyla Ascomycota and Basidiomycota. In this note, we increase the resolution and knowledge of the mycobiome inhabiting the fur of the two- (Choloepus hoffmanni) and three-toed (Bradypus variegatus) sloths. Targeted amplicon metagenomic analysis of ITS2 nrDNA sequences obtained from 10 individuals of each species inhabiting the same site revealed significant differences in the structure of their fungal communities and also in the alpha-diversity estimators. The results suggest a specialization by host species and that the host effect is stronger than that of sex, age and animal weight. Capnodiales were the dominant order in sloths' fur and Cladosporium and Neodevriesia were the most abundant genera in Bradypus and Choloepus, respectively. The fungal communities suggest that the green algae that inhabit the fur of sloths possibly live lichenized with Ascomycota fungal species. The data shown in this note offer a more detailed view of the fungal content in the fur of these extraordinary animals and could help explain other mutualistic relationships in this complex ecosystem.}, } @article {pmid36847620, year = {2023}, author = {Gu, BH and Choi, JP and Park, T and Kim, AS and Jung, HY and Choi, DY and Lee, SJ and Chang, YS and Kim, M and Park, HK}, title = {Adult asthma with symptomatic eosinophilic inflammation is accompanied by alteration in gut microbiome.}, journal = {Allergy}, volume = {78}, number = {7}, pages = {1909-1921}, doi = {10.1111/all.15691}, pmid = {36847620}, issn = {1398-9995}, support = {NRF-2022R1C1C1003256//Korea Government/ ; NRF-2020R1C1C1011678//Korea Government/ ; }, mesh = {Humans ; Adult ; *Gastrointestinal Microbiome ; *Asthma/genetics ; *Pulmonary Eosinophilia ; Inflammation/genetics ; Metagenome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Accumulating evidence suggests that the gut microbiome is associated with asthma. However, altered gut microbiome in adult asthma is not yet well established. We aimed to investigate the gut microbiome profiles of adult asthmatic patients with symptomatic eosinophilic inflammation.

METHODS: The 16 s rRNA gene metagenomic analysis of feces in the symptomatic eosinophilic asthma group (EA, n = 28) was compared with the healthy control (HC, n = 18) and the chronic cough control (CC, n = 13). A correlation analysis between individual taxa and clinical markers was performed within the EA group. Changes in the gut microbiome were examined in patients with significant symptom improvement in the EA group.

RESULTS: The relative abundances of Lachnospiraceae and Oscillospiraceae significantly decreased and Bacteroidetes increased in the EA group. Within EA group, Lachnospiraceae was negatively correlated with indicators of type 2 inflammation and lung function decline. Enterobacteriaceae and Prevotella was positively associated with type 2 inflammation and lung function decline, respectively. The abundance of predicted genes associated with amino acid metabolism and secondary bile acid biosynthesis was diminished in the EA group. These functional gene family alterations could be related to gut permeability, and the serum lipopolysaccharide concentration was actually high in the EA group. EA patients with symptom improvement after 1 month did not show a significant change in the gut microbiome.

CONCLUSIONS: Symptomatic eosinophilic adult asthma patients showed altered the gut microbiome composition. Specifically, a decrease in commensal clostridia was observed, and a decrease in Lachnospiraceae was correlated with blood eosinophilia and lung function decline.}, } @article {pmid36844406, year = {2023}, author = {Stout, MJ and Brar, AK and Herter, BN and Rankin, A and Wylie, KM}, title = {The plasma virome in longitudinal samples from pregnant patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1061230}, pmid = {36844406}, issn = {2235-2988}, mesh = {Infant, Newborn ; Pregnancy ; Female ; Humans ; Virome ; *Premature Birth ; *Virus Diseases/diagnosis ; Plasma ; *Anelloviridae/genetics ; *Herpesviridae ; Metagenomics/methods ; }, abstract = {INTRODUCTION: Nucleic acid from viruses is common in peripheral blood, even in asymptomatic individuals. How physiologic changes of pregnancy impact host-virus dynamics for acute, chronic, and latent viral infections is not well described. Previously we found higher viral diversity in the vagina during pregnancy associated with preterm birth (PTB) and Black race. We hypothesized that higher diversity and viral copy numbers in the plasma would show similar trends.

METHODS: To test this hypothesis, we evaluated longitudinally collected plasma samples from 23 pregnant patients (11 term and 12 preterm) using metagenomic sequencing with ViroCap enrichment to enhance virus detection. Sequence data were analyzed with the ViroMatch pipeline.

RESULTS: We detected nucleic acid from at least 1 virus in at least 1 sample from 87% (20/23) of the maternal subjects. The viruses represented 5 families: Herpesviridae, Poxviridae, Papillomaviridae, Anelloviridae, and Flaviviridae. We analyzed cord plasma from 18 of the babies from those patients and found nucleic acid from viruses in 33% of the samples (6/18) from 3 families: Herpesviridae, Papillomaviridae, and Anelloviridae. Some viral genomes were found in both maternal plasma and cord plasma from maternal-fetal pairs (e.g. cytomegalovirus, anellovirus). We found that Black race associated with higher viral richness (number of different viruses detected) in the maternal blood samples (P=0.003), consistent with our previous observations in vaginal samples. We did not detect associations between viral richness and PTB or the trimester of sampling. We then examined anelloviruses, a group of viruses that is ubiquitous and whose viral copy numbers fluctuate with immunological state. We tested anellovirus copy numbers in plasma from 63 pregnant patients sampled longitudinally using qPCR. Black race associated with higher anellovirus positivity (P<0.001) but not copy numbers (P=0.1). Anellovirus positivity and copy numbers were higher in the PTB group compared to the term group (P<0.01, P=0.003, respectively). Interestingly, these features did not occur at the time of delivery but appeared earlier in pregnancy, suggesting that although anelloviruses were biomarkers for PTB they were not triggering parturition.

DISCUSSION: These results emphasize the importance of longitudinal sampling and diverse cohorts in studies of virome dynamics during pregnancy.}, } @article {pmid36843227, year = {2023}, author = {Lynch, LE and Hair, AB and Soni, KG and Yang, H and Gollins, LA and Narvaez-Rivas, M and Setchell, KDR and Preidis, GA}, title = {Cholestasis impairs gut microbiota development and bile salt hydrolase activity in preterm neonates.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2183690}, pmid = {36843227}, issn = {1949-0984}, support = {K08 DK113114/DK/NIDDK NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; T32 GM136554/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Infant, Newborn ; *Gastrointestinal Microbiome ; Case-Control Studies ; Infant, Premature ; *Cholestasis ; Ursodeoxycholic Acid ; Bile Acids and Salts ; }, abstract = {Cholestasis refers to impaired bile flow from the liver to the intestine. In neonates, cholestasis causes poor growth and may progress to liver failure and death. Normal bile flow requires an intact liver-gut-microbiome axis, whereby liver-derived primary bile acids are transformed into secondary bile acids. Microbial bile salt hydrolase (BSH) enzymes are responsible for the first step, deconjugating glycine- and taurine-conjugated primary bile acids. Cholestatic neonates often are treated with the potent choleretic bile acid ursodeoxycholic acid (UDCA), although interactions between UDCA, gut microbes, and other bile acids are poorly understood. To gain insight into how the liver-gut-microbiome axis develops in extreme prematurity and how cholestasis alters this maturation, we conducted a nested case-control study collecting 124 stool samples longitudinally from 24 preterm infants born at mean 27.2 ± 1.8 weeks gestation and 946 ± 249.6 g, half of whom developed physiologic cholestasis. Samples were analyzed by whole metagenomic sequencing, in vitro BSH enzyme activity assays optimized for low biomass fecal samples, and quantitative mass spectrometry to measure the bile acid metabolome. In extremely preterm neonates, acquisition of the secondary bile acid biosynthesis pathway and BSH genes carried by Clostridium perfringens are the most prominent features of early microbiome development. Cholestasis interrupts this developmental pattern. BSH gene abundance and enzyme activity are profoundly reduced in cholestatic neonates, resulting in decreased quantities of unconjugated bile acids. UDCA restores total fecal bile acid levels in cholestatic neonates, but this is due to a 522-fold increase in fecal UDCA. A majority of bile acids in early development are atypical positional and stereo-isomers of bile acids. We report novel associations linking isomeric bile acids and BSH activity to neonatal growth trajectories. These data highlight deconjugation of bile acids as a key microbial function that is acquired in early neonatal development and impaired by cholestasis.}, } @article {pmid36842848, year = {2023}, author = {Ojala, T and Kankuri, E and Kankainen, M}, title = {Understanding human health through metatranscriptomics.}, journal = {Trends in molecular medicine}, volume = {29}, number = {5}, pages = {376-389}, doi = {10.1016/j.molmed.2023.02.002}, pmid = {36842848}, issn = {1471-499X}, mesh = {Humans ; *Metagenomics ; *Microbiota ; }, abstract = {Metatranscriptomics has revolutionized our ability to explore and understand transcriptional programs in microbial communities. Moreover, it has enabled us to gain deeper and more specific insight into the microbial activities in human gut, respiratory, oral, and vaginal communities. Perhaps the most important contribution of metatranscriptomics arises, however, from the analyses of disease-associated communities. We review the advantages and disadvantages of metatranscriptomics analyses in understanding human health and disease. We focus on human tissues low in microbial biomass and conditions associated with dysbiotic microbiota. We conclude that a more widespread use of metatranscriptomics and increased knowledge on microbe activities will uncover critical interactions between microbes and host in human health and provide diagnostic basis for culturing-independent, direct functional pathogen identification.}, } @article {pmid36839335, year = {2023}, author = {Ezzatpour, S and Mondragon Portocarrero, ADC and Cardelle-Cobas, A and Lamas, A and López-Santamarina, A and Miranda, JM and Aguilar, HC}, title = {The Human Gut Virome and Its Relationship with Nontransmissible Chronic Diseases.}, journal = {Nutrients}, volume = {15}, number = {4}, pages = {}, pmid = {36839335}, issn = {2072-6643}, support = {R01 AI109022/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Virome ; *Viruses/metabolism ; *Bacteriophages ; *Microbiota ; *Gastrointestinal Microbiome ; }, abstract = {The human gastrointestinal tract contains large communities of microorganisms that are in constant interaction with the host, playing an essential role in the regulation of several metabolic processes. Among the gut microbial communities, the gut bacteriome has been most widely studied in recent decades. However, in recent years, there has been increasing interest in studying the influences that other microbial groups can exert on the host. Among them, the gut virome is attracting great interest because viruses can interact with the host immune system and metabolic functions; this is also the case for phages, which interact with the bacterial microbiota. The antecedents of virome-rectification-based therapies among various diseases were also investigated. In the near future, stool metagenomic investigation should include the identification of bacteria and phages, as well as their correlation networks, to better understand gut microbiota activity in metabolic disease progression.}, } @article {pmid36839205, year = {2023}, author = {Ye, W and Chen, Z and He, Z and Gong, H and Zhang, J and Sun, J and Yuan, S and Deng, J and Liu, Y and Zeng, A}, title = {Lactobacillus plantarum-Derived Postbiotics Ameliorate Acute Alcohol-Induced Liver Injury by Protecting Cells from Oxidative Damage, Improving Lipid Metabolism, and Regulating Intestinal Microbiota.}, journal = {Nutrients}, volume = {15}, number = {4}, pages = {}, pmid = {36839205}, issn = {2072-6643}, support = {LGF21C010002//Zhejiang Provincial Natural Science Foundation/ ; LQ18H020005//Zhejiang Provincial Natural Science Foundation/ ; Y2020218//Science and Technology Plan Project of Wenzhou/ ; QJD2002011//Qianjiang Talent Project of Zhejiang/ ; Y20210108//Science and Technology Plan Project of Wenzhou/ ; }, mesh = {Male ; Humans ; Animals ; Mice ; *Lactobacillus plantarum/physiology ; Lipid Metabolism ; *Gastrointestinal Microbiome/physiology ; *Chemical and Drug Induced Liver Injury, Chronic ; Mice, Inbred C57BL ; Liver/metabolism ; Ethanol/metabolism ; Oxidative Stress ; Superoxide Dismutase/metabolism ; }, abstract = {Here, the aim was to evaluate the protective effect of Lactobacillus plantarum-derived postbiotics, i.e., LP-cs, on acute alcoholic liver injury (ALI). After preincubation with LP-cs, HL7702 human hepatocytes were treated with alcohol, and then the cell survival rate was measured. C57BL/6 male mice were presupplemented with or without LP-cs and LP-cs-loaded calcium alginate hydrogel (LP-cs-Gel) for 3 weeks and given 50% alcohol gavage to establish the mouse model of ALI, LP-cs presupplementation, and LP-cs-Gel presupplementation. The histomorphology of the liver and intestines; the levels of serum AST, ALT, lipid, and SOD activity; liver transcriptomics; and the metagenome of intestinal microbiota were detected in all mouse models. In vitro, LP-cs significantly increased the survival rate of alcohol-treated cells. In vivo, presupplementation with LP-cs and LP-cs-Gel restored the levels of serum AST, ALT, and SOD activity, as well as TC and TG, after acute alcohol intake. In the LP-cs-presupplemented mice, the genes involved in fatty acid metabolic processes were upregulated and the genes involved in steroid biosynthesis were downregulated significantly as compared with the ALI mice. LP-cs significantly increased the abundance of intestinal microbiota, especially Akkermansia muciniphila. In conclusion, LP-cs ameliorates ALI by protecting hepatocytes against oxidative damage, thereby, improving lipid metabolism and regulating the intestinal microbiota. The effect of LP-cs-Gel is similar to that of LP-cs.}, } @article {pmid36835363, year = {2023}, author = {Smythe, P and Wilkinson, HN}, title = {The Skin Microbiome: Current Landscape and Future Opportunities.}, journal = {International journal of molecular sciences}, volume = {24}, number = {4}, pages = {}, pmid = {36835363}, issn = {1422-0067}, mesh = {Humans ; Dysbiosis ; Skin ; *Microbiota ; *Skin Diseases ; Skin Physiological Phenomena ; }, abstract = {Our skin is the largest organ of the body, serving as an important barrier against the harsh extrinsic environment. Alongside preventing desiccation, chemical damage and hypothermia, this barrier protects the body from invading pathogens through a sophisticated innate immune response and co-adapted consortium of commensal microorganisms, collectively termed the microbiota. These microorganisms inhabit distinct biogeographical regions dictated by skin physiology. Thus, it follows that perturbations to normal skin homeostasis, as occurs with ageing, diabetes and skin disease, can cause microbial dysbiosis and increase infection risk. In this review, we discuss emerging concepts in skin microbiome research, highlighting pertinent links between skin ageing, the microbiome and cutaneous repair. Moreover, we address gaps in current knowledge and highlight key areas requiring further exploration. Future advances in this field could revolutionise the way we treat microbial dysbiosis associated with skin ageing and other pathologies.}, } @article {pmid36834289, year = {2023}, author = {Zhao, F and Wang, B and Huang, K and Yin, J and Ren, X and Wang, Z and Zhang, XX}, title = {Correlations among Antibiotic Resistance Genes, Mobile Genetic Elements and Microbial Communities in Municipal Sewage Treatment Plants Revealed by High-Throughput Sequencing.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {4}, pages = {}, pmid = {36834289}, issn = {1660-4601}, mesh = {*Sewage/microbiology ; Genes, Bacterial ; Angiotensin Receptor Antagonists ; Anti-Bacterial Agents/pharmacology ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Drug Resistance, Microbial/genetics ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Interspersed Repetitive Sequences ; }, abstract = {Municipal sewage treatment plants (MSTPs) are environmental pools for antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), which is cause for growing environmental-health concerns. In this study, the effects of different wastewater treatment processes on microbial antibiotic resistance in four MSTPs were investigated. PCR, q-PCR, and molecular cloning integrally indicated that the tetracycline resistance (tet) genes significantly reduced after activated-sludge treatment. Illumina high-throughput sequencing revealed that the broad-spectrum profile of ARGs and mobile element genes (MGEs) were also greatly decreased by one order of magnitude via activated sludge treatment and were closely associated with each other. Correlations between ARGs and bacterial communities showed that potential ARB, such as Acinetobacter, Bacteroides, and Cloaibacterium, were removed by the activated-sludge process. Sedimentation processes cannot significantly affect the bacterial structure, resulting in the relative abundance of ARGs, MGEs, and ARB in second-clarifier effluent water being similar to activated sludge. A comprehensive study of ARGs associated with MGEs and bacterial structure might be technologically guided for activated sludge design and operation in the MSTPs, to purposefully control ARGs carried by pathogenic hosts and mobility.}, } @article {pmid36833250, year = {2023}, author = {ZeinEldin, RA and Ahmed, MM and Hassanein, WS and Elshafey, N and Sofy, AR and Hamedo, HA and Elnosary, ME}, title = {Diversity and Distribution Characteristics of Viruses from Soda Lakes.}, journal = {Genes}, volume = {14}, number = {2}, pages = {}, pmid = {36833250}, issn = {2073-4425}, mesh = {Humans ; Lakes ; Capsid Proteins/genetics ; *Viruses/genetics ; Myoviridae/genetics ; Biodiversity ; *Siphoviridae ; }, abstract = {Viruses are the most abundant living things and a source of genetic variation. Despite recent research, we know little about their biodiversity and geographic distribution. We used different bioinformatics tools, MG-RAST, genome detective web tools, and GenomeVx, to describe the first metagenomic examination of haloviruses in Wadi Al-Natrun. The discovered viromes had remarkably different taxonomic compositions. Most sequences were derived from double-stranded DNA viruses, especially from Myoviridae, Podoviridae, Siphoviridae, Herpesviridae, Bicaudaviridae, and Phycodnaviridae families; single-stranded DNA viruses, especially from the family Microviridae; and positive-strand RNA viruses, especially from the family Potyviridae. Additionally, our results showed that Myohalovirus chaoS9 has eight Contigs and is annotated to 18 proteins as follows: tail sheath protein, tco, nep, five uncharacterized proteins, HCO, major capsid protein, putative pro head protease protein, putative head assembly protein, CxxC motive protein, terl, HTH domain protein, and terS Exon 2. Additionally, Halorubrum phage CGphi46 has 19 proteins in the brine sample as follows: portal protein, 17 hypothetical proteins, major capsid protein, etc. This study reveals viral lineages, suggesting the Virus's global dispersal more than other microorganisms. Our study clarifies how viral communities are connected and how the global environment changes.}, } @article {pmid36828753, year = {2023}, author = {Mazza Rodrigues, JL and Melotto, M}, title = {Naturally engineered plant microbiomes in resource-limited ecosystems.}, journal = {Trends in microbiology}, volume = {31}, number = {4}, pages = {329-331}, doi = {10.1016/j.tim.2023.02.006}, pmid = {36828753}, issn = {1878-4380}, mesh = {*Ecosystem ; Rhizosphere ; Soil Microbiology ; Plant Roots ; Plants ; *Microbiota/genetics ; }, abstract = {Nature-designed plant microbiomes may offer solutions to improve crop production and ecosystem restoration in less than optimum environments. Through a full exploration of metagenomic data, Camargo et al. showed that a previously unknown microbial diversity enhances nutrient mobilization in stress-adapted plants.}, } @article {pmid36828645, year = {2023}, author = {Ao, Z and Xu, H and Li, M and Liu, H and Deng, M and Liu, Y}, title = {Clinical characteristics, diagnosis, outcomes and lung microbiome analysis of invasive pulmonary aspergillosis in the community-acquired pneumonia patients.}, journal = {BMJ open respiratory research}, volume = {10}, number = {1}, pages = {}, pmid = {36828645}, issn = {2052-4439}, mesh = {Humans ; *Invasive Pulmonary Aspergillosis/complications/diagnosis/microbiology ; Retrospective Studies ; Sensitivity and Specificity ; Bronchoalveolar Lavage Fluid/microbiology ; *Aspergillosis/complications ; Lung ; *Pneumonia/complications ; *Microbiota ; }, abstract = {BACKGROUND: Invasive pulmonary aspergillosis (IPA) remains underestimated in patients with community-acquired pneumonia (CAP). This study aims to describe clinical features and outcomes of IPA in CAP patients, assess diagnostic performance of metagenomic next-generation sequencing (mNGS) for IPA and analyse lung microbiome via mNGS data.

METHODS: This retrospective cohort study included CAP patients from 22 April 2019 to 30 September 2021. Clinical and microbiological data were analysed. Diagnostic performance of mNGS was compared with traditional detection methods. The lung microbiome detected by mNGS was characterised and its association with clinical features was evaluated.

MAIN RESULTS: IPA was diagnosed in 26 (23.4%) of 111 CAP patients. Patients with IPA displayed depressed immunity, higher hospital mortality (30.8% vs 11.8%) and intensive care unit mortality (42.1% vs 17.5%) compared with patients without IPA. The galactomannan (GM) antigen test had the highest sensitivity (57.7%) in detecting the Aspergillus spp, followed by mNGS (42.3%), culture (30.8%) and smear (7.7%). The mNGS, culture and smear had 100% specificity, while GM test had 92.9% specificity. The microbial structure of IPA significantly differed from non-IPA patients (p<0.001; Wilcoxon test). Nineteen different species were significantly correlated with clinical outcomes and laboratory biomarkers, particularly for Streptococcus salivarius, Prevotella timonensis and Human betaherpesvirus 5.

CONCLUSIONS: Our results reveal that patients with Aspergillus infection tend to have a higher early mortality rate. The mNGS may be suggested as a complement to routine microbiological test in diagnosis of patients at risk of Aspergillus infection. The lung microbiota is associated with inflammatory, immune and metabolic conditions of IPA, and thus influences clinical outcomes.}, } @article {pmid36827387, year = {2023}, author = {Zhao, M and Zhao, Q and Guan, Z and Liu, Q and Zhou, H and Huang, Q and Huo, B}, title = {Effect of Panax ginseng and Fructus Mume on Intestinal Barrier and Gut Microbiota in Rats with Diarrhea.}, journal = {Journal of medicinal food}, volume = {26}, number = {3}, pages = {165-175}, doi = {10.1089/jmf.2022.K.0069}, pmid = {36827387}, issn = {1557-7600}, mesh = {Rats ; Animals ; NF-kappa B/genetics/metabolism ; *Gastrointestinal Microbiome ; Phosphatidylinositol 3-Kinases/genetics ; Proto-Oncogene Proteins c-akt ; *Panax/chemistry ; Diarrhea/drug therapy ; Tumor Necrosis Factor-alpha ; Tight Junction Proteins/metabolism ; }, abstract = {Panax ginseng and Fructus mume (Renshen Wumei in Chinese, RW) are natural medicines with high nutritional and pharmacological value. They have been widely used together in China to treat gastrointestinal diseases, especially persistent diarrhea, but the potential mechanisms remain elusive. In this study, a diarrhea model was established in rats using a 30% aqueous extract of senna. The therapeutic effects of RW were evaluated by recording the prevalence of loose stools, the diarrhea index, and histopathological changes in colon tissue. The levels of mucins, tight junction (TJ) proteins, inflammatory cytokines, and phosphoinositide 3-kinase/Akt/nuclear factor-κB (PI3K/Akt/NF-κB) signaling pathway proteins were measured. Metagenomic sequencing was used to analyze the gut microbiota. Treatment with RW alleviated injury to the intestinal barrier in rats with diarrhea and also upregulated levels of Muc2 and TJ proteins, such as occludin, zonula occludens-1, and claudin-1. Administration of RW regulated the structure of the gut microbiota in diarrheal rats. Furthermore, RW suppressed levels of interleukin (IL), tumor necrosis factor (TNF)-α, IL-1, PI3K, Akt, and p-NF-κB p65 and also increased IL-4 levels. Our study indicates that P. ginseng and Fructus mume help improve the symptoms of diarrhea, possibly by alleviating the intestinal barrier injury, regulating intestinal flora composition, and inhibiting the PI3K/Akt/NF-κB signaling pathway.}, } @article {pmid36826808, year = {2023}, author = {Tan, TC and Chandrasekaran, L and Leung, YY and Purbojati, R and Pettersson, S and Low, AHL}, title = {Gut microbiome profiling in systemic sclerosis: a metagenomic approach.}, journal = {Clinical and experimental rheumatology}, volume = {41}, number = {8}, pages = {1578-1588}, doi = {10.55563/clinexprheumatol/jof7nx}, pmid = {36826808}, issn = {0392-856X}, mesh = {Adult ; Humans ; Female ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; Feces ; *Scleroderma, Systemic/diagnosis/microbiology ; Bacteria/genetics ; *Scleroderma, Limited ; }, abstract = {OBJECTIVES: The early gastrointestinal (GI) manifestation of systemic sclerosis (SSc) suggests a possible GI microbiota engagement in the pathophysiology and/or progression of SSc. Previous studies have revealed dysbiosis among Caucasian SSc patients. This study extends these findings to Asian SSc patients.

METHODS: Adult SSc patients, stratified according to 1) on immunosuppressive (On-IS) drugs or 2) no immunosuppressive drugs (No-IS), and age-and-sex-matched healthy controls (HC) were recruited. Metagenomic sequencing of stool DNA was compared between SSc patients and HC, and between SSc (On-IS) and (No-IS) patients. Alpha and beta-diversity, taxonomic and functional profiling were evaluated.

RESULTS: Twenty-three female SSc patients (12 On-IS; 11 No-IS; 5 diffuse and 18 limited SSc subtype) and 19 female HC, with median age of 54 years and 56 years, respectively, were recruited. Median SSc disease duration was 3.3 years. Alpha diversity was significantly higher in SSc versus HC (p=0.014) and in SSc (No-IS) versus HC (p=0.006). There was no significant difference in beta diversity between SSc and HC (p=0.307). At the phyla level, there were significantly increased abundance of Firmicutes and Actinobacteria in SSc versus HC, and reduced abundance of Bacteroidetes (all p<0.001). At the species level, there were significantly increased abundance of several Lactobacillus, Bifidobacterium, and Coprococcus species in SSc, and increased abundance of Odoribacter, Bacteroides and Prevotella species in HC. KEGG pathway analysis demonstrated distinct differences between SSc versus HC, and between SSc (No-IS) and SSc (On-IS).

CONCLUSIONS: Using metagenomic sequencing, our study further underlines distinct alterations in microbiota profiling among Asian SSc patients.}, } @article {pmid36825940, year = {2023}, author = {Almas, S and Carpenter, RE and Singh, A and Rowan, C and Tamrakar, VK and Sharma, R}, title = {Deciphering Microbiota of Acute Upper Respiratory Infections: A Comparative Analysis of PCR and mNGS Methods for Lower Respiratory Trafficking Potential.}, journal = {Advances in respiratory medicine}, volume = {91}, number = {1}, pages = {49-65}, pmid = {36825940}, issn = {2543-6031}, mesh = {Humans ; *Respiratory Tract Infections/diagnosis ; *Microbiota ; Bacteria/genetics ; Polymerase Chain Reaction ; }, abstract = {Although it is clinically important for acute respiratory tract (co)infections to have a rapid and accurate diagnosis, it is critical that respiratory medicine understands the advantages of current laboratory methods. In this study, we tested nasopharyngeal samples (n = 29) with a commercially available PCR assay and compared the results with those of a hybridization-capture-based mNGS workflow. Detection criteria for positive PCR samples was Ct < 35 and for mNGS samples it was >40% target coverage, median depth of 1X and RPKM > 10. A high degree of concordance (98.33% PPA and 100% NPA) was recorded. However, mNGS yielded positively 29 additional microorganisms (23 bacteria, 4 viruses, and 2 fungi) beyond PCR. We then characterized the microorganisms of each method into three phenotypic categories using the IDbyDNA Explify[®] Platform (Illumina[®] Inc, San Diego, CA, USA) for consideration of infectivity and trafficking potential to the lower respiratory region. The findings are significant for providing a comprehensive yet clinically relevant microbiology profile of acute upper respiratory infection, especially important in immunocompromised or immunocompetent with comorbidity respiratory cases or where traditional syndromic approaches fail to identify pathogenicity. Accordingly, this technology can be used to supplement current syndrome-based tests, and data can quickly and effectively be phenotypically characterized for trafficking potential, clinical (co)infection, and comorbid consideration-with promise to reduce morbidity and mortality.}, } @article {pmid36823661, year = {2023}, author = {Haro-Moreno, JM and Cabello-Yeves, PJ and Garcillán-Barcia, MP and Zakharenko, A and Zemskaya, TI and Rodriguez-Valera, F}, title = {A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {12}, pmid = {36823661}, issn = {2524-6372}, abstract = {BACKGROUND: Lake Baikal, the world's deepest freshwater lake, contains important numbers of Candidatus Patescibacteria (formerly CPR) in its deepest reaches. However, previously obtained CPR metagenome-assembled genomes recruited very poorly indicating the potential of other groups being present. Here, we have applied for the first time a long-read (PacBio CCS) metagenomic approach to analyze in depth the Ca. Patescibacteria living in the bathypelagic water column of Lake Baikal at 1600 m.

RESULTS: The retrieval of nearly complete 16S rRNA genes before assembly has allowed us to detect the presence of a novel and a likely endemic group of Ca. Patescibacteria inhabiting bathypelagic Lake Baikal. This novel group seems to possess extremely high intra-clade diversity, precluding complete genomes' assembly. However, read binning and scaffolding indicate that these microbes are similar to other Ca. Patescibacteria (i.e. parasites or symbionts), although they seem to carry more anabolic pathways, likely reflecting the extremely oligotrophic habitat they inhabit. The novel bins have not been found anywhere, but one of the groups appears in small amounts in an oligotrophic and deep alpine Lake Thun. We propose this novel group be named Baikalibacteria.

CONCLUSION: The recovery of 16S rRNA genes via long-read metagenomics plus the use of long-read binning to uncover highly diverse "hidden" groups of prokaryotes are key strategies to move forward in ecogenomic microbiology. The novel group possesses enormous intraclade diversity akin to what happens with Ca. Patescibacteria at the interclade level, which is remarkable in an environment that has changed little in the last 25 million years.}, } @article {pmid36823539, year = {2023}, author = {Ekhlas, D and Argüello, H and Leonard, FC and Manzanilla, EG and Burgess, CM}, title = {Insights on the effects of antimicrobial and heavy metal usage on the antimicrobial resistance profiles of pigs based on culture-independent studies.}, journal = {Veterinary research}, volume = {54}, number = {1}, pages = {14}, pmid = {36823539}, issn = {1297-9716}, support = {2018027//Teagasc/ ; }, mesh = {Humans ; Animals ; Swine ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; *Anti-Infective Agents/pharmacology ; *Metals, Heavy/pharmacology ; *Microbiota ; }, abstract = {Antimicrobial resistance is a global threat to human, animal, and environmental health. In pig production, antimicrobials and heavy metals such as zinc oxide are commonly used for treatment and prevention of disease. Nevertheless, the effects of antimicrobials and heavy metals on the porcine resistome composition and the factors influencing this resistance profile are not fully understood. Advances in technologies to determine the presence of antimicrobial resistance genes in diverse sample types have enabled a more complete understanding of the resistome and the factors which influence its composition. The aim of this review is to provide a greater understanding of the influence of antimicrobial and heavy metal usage on the development and transmission of antimicrobial resistance on pig farms. Furthermore, this review aims to identify additional factors that can affect the porcine resistome. Relevant literature that used high-throughput sequencing or quantitative PCR methods to examine links between antimicrobial resistance and antimicrobial and heavy metal use was identified using a systematic approach with PubMed (NCBI), Scopus (Elsevier), and Web of Science (Clarivate Analytics) databases. In total, 247 unique records were found and 28 publications were identified as eligible for inclusion in this review. Based on these, there is clear evidence that antimicrobial and heavy metal use are positively linked with antimicrobial resistance in pigs. Moreover, associations of genes conferring antimicrobial resistance with mobile genetic elements, the microbiome, and the virome were reported, which were further influenced by the host, the environment, or the treatment itself.}, } @article {pmid36823480, year = {2023}, author = {Bai, H and Liu, T and Wang, S and Shen, L and Wang, Z}, title = {Variations in gut microbiome and metabolites of dogs with acute diarrhea in poodles and Labrador retrievers.}, journal = {Archives of microbiology}, volume = {205}, number = {3}, pages = {97}, pmid = {36823480}, issn = {1432-072X}, mesh = {Dogs ; Animals ; *Gastrointestinal Microbiome ; *Microbiota ; Metabolomics ; Metabolome ; Starch/analysis ; Diarrhea ; Feces ; RNA, Ribosomal, 16S ; }, abstract = {For different breeds of dogs with acute diarrhea, the gut microbiota and metabolome profiles are unclear. This prospective observational study analyzed the gut microbiomes of poodles with acute diarrhea and Labrador retrievers with acute diarrhea based on 16S amplicon sequencing, with respective healthy dogs as controls. Fecal non-target metabolomics and metagenomics were performed on poodles with acute diarrhea. This study found that the diversity and structure of the microbial community differed significantly between the two breeds in cohorts of healthy dogs. Two breeds of dogs with acute diarrhea demonstrated different changes in microbial communities and metabolic functions. The metabolism of starch and sucrose was significantly decreased in dogs with acute diarrhea, which may be attributed to the reduced activity of dextran dextrinase. Non-targeted metabolomics identified 21 abnormal metabolic pathways exhibited by dogs with acute diarrhea, including starch, amino acid, bile acid metabolism, etc., and were closely related to specific intestinal flora. This study provided new insights into breed specificity and the development of dietary treatment strategy in canine gastrointestinal disease.}, } @article {pmid36823356, year = {2023}, author = {Blanco-Míguez, A and Beghini, F and Cumbo, F and McIver, LJ and Thompson, KN and Zolfo, M and Manghi, P and Dubois, L and Huang, KD and Thomas, AM and Nickols, WA and Piccinno, G and Piperni, E and Punčochář, M and Valles-Colomer, M and Tett, A and Giordano, F and Davies, R and Wolf, J and Berry, SE and Spector, TD and Franzosa, EA and Pasolli, E and Asnicar, F and Huttenhower, C and Segata, N}, title = {Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4.}, journal = {Nature biotechnology}, volume = {41}, number = {11}, pages = {1633-1644}, pmid = {36823356}, issn = {1546-1696}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; U01 CA230551/CA/NCI NIH HHS/United States ; U19 AI110820/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; Metagenome/genetics ; *Microbiota/genetics ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Phylogeny ; }, abstract = {Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms from most metagenomes. Here we present MetaPhlAn 4, which integrates information from metagenome assemblies and microbial isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference and metagenome-assembled genomes, we define unique marker genes for 26,970 species-level genome bins, 4,992 of them taxonomically unidentified at the species level. MetaPhlAn 4 explains ~20% more reads in most international human gut microbiomes and >40% in less-characterized environments such as the rumen microbiome and proves more accurate than available alternatives on synthetic evaluations while also reliably quantifying organisms with no cultured isolates. Application of the method to >24,500 metagenomes highlights previously undetected species to be strong biomarkers for host conditions and lifestyles in human and mouse microbiomes and shows that even previously uncharacterized species can be genetically profiled at the resolution of single microbial strains.}, } @article {pmid36823301, year = {2023}, author = {Mehta, RS and Mayers, JR and Zhang, Y and Bhosle, A and Glasser, NR and Nguyen, LH and Ma, W and Bae, S and Branck, T and Song, K and Sebastian, L and Pacheco, JA and Seo, HS and Clish, C and Dhe-Paganon, S and Ananthakrishnan, AN and Franzosa, EA and Balskus, EP and Chan, AT and Huttenhower, C}, title = {Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease.}, journal = {Nature medicine}, volume = {29}, number = {3}, pages = {700-709}, pmid = {36823301}, issn = {1546-170X}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; S10 OD021527/OD/NIH HHS/United States ; K23 DK125838/DK/NIDDK NIH HHS/United States ; P30 GM124165/GM/NIGMS NIH HHS/United States ; R35 CA253185/CA/NCI NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Mesalamine/therapeutic use ; *Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; *Inflammatory Bowel Diseases/drug therapy ; Treatment Outcome ; }, abstract = {For decades, variability in clinical efficacy of the widely used inflammatory bowel disease (IBD) drug 5-aminosalicylic acid (5-ASA) has been attributed, in part, to its acetylation and inactivation by gut microbes. Identification of the responsible microbes and enzyme(s), however, has proved elusive. To uncover the source of this metabolism, we developed a multi-omics workflow combining gut microbiome metagenomics, metatranscriptomics and metabolomics from the longitudinal IBDMDB cohort of 132 controls and patients with IBD. This associated 12 previously uncharacterized microbial acetyltransferases with 5-ASA inactivation, belonging to two protein superfamilies: thiolases and acyl-CoA N-acyltransferases. In vitro characterization of representatives from both families confirmed the ability of these enzymes to acetylate 5-ASA. A cross-sectional analysis within the discovery cohort and subsequent prospective validation within the independent SPARC IBD cohort (n = 208) found three of these microbial thiolases and one acyl-CoA N-acyltransferase to be epidemiologically associated with an increased risk of treatment failure among 5-ASA users. Together, these data address a longstanding challenge in IBD management, outline a method for the discovery of previously uncharacterized gut microbial activities and advance the possibility of microbiome-based personalized medicine.}, } @article {pmid36823282, year = {2023}, author = {Pérez-Cataluña, A and Randazzo, W and Martínez-Blanch, JF and Codoñer, FM and Sánchez, G}, title = {Sample and library preparation approaches for the analysis of the virome of irrigation water.}, journal = {Journal of the science of food and agriculture}, volume = {103}, number = {9}, pages = {4450-4457}, doi = {10.1002/jsfa.12522}, pmid = {36823282}, issn = {1097-0010}, support = {2018CPS10//Center for Produce Safety/ ; APOSTD/2021/292//Generalitat Valenciana/ ; APOTIP/2018/007//Generalitat Valenciana/ ; AGL2017-82909//Ministerio de Ciencia e Innovación/ ; }, mesh = {Humans ; Virome ; *Viruses/genetics ; *Bacteriophages/genetics ; Water ; Metagenomics/methods ; }, abstract = {BACKGROUND: The virome (i.e. community of mainly RNA and DNA eukaryotic viruses and bacteriophages) of waters is yet to be extensively explored. In particular, the virome of waters used for irrigation could therefore potentially carry viral pathogens that can contaminate fresh produce. One problem in obtaining viral sequences from irrigation waters is the relatively low amount of virus particles, as well as the presence of human, bacterial and protozoan cells. The present aimed study was to compare different processing, amplification, and sequencing approaches for virome characterization in irrigation waters.

RESULTS: Our analyses considered percentages of viral reads, values for diversity indices and number of families found in sequencing results. The results obtained suggest that enrichment protocols using two (bezonase and microccocal nuclease) or four enzymes at once (bezonase, microccocal nuclease, DNAse and RNase), regardless of an Amicon filtration step, are more appropriate than separated enzymatic treatments for virome characterization in irrigation water. The NetoVIR protocol combined with the ScriptSeq v2 RNA-Seq Library (P0-L20 protocol) showed the highest percentages of RNA viruses and identified the higher number of families.

CONCLUSION: Although virome characterization applied in irrigation waters is an important tool for protecting public health by informing on circulating human and zoonotic infections, optimized and standardized procedures should be followed to reduce the variability of results related to either the sample itself and the downstream bioinformatics analyses. Our results show that virome characterization can be an important tool in the discovery of pathogenic viruses in the environment and can be used to inform and optimize reference-based detection methods provided that appropriate and rigorous controls are included. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.}, } @article {pmid36823152, year = {2023}, author = {Howe, A and Stopnisek, N and Dooley, SK and Yang, F and Grady, KL and Shade, A}, title = {Seasonal activities of the phyllosphere microbiome of perennial crops.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1039}, pmid = {36823152}, issn = {2041-1723}, mesh = {Seasons ; *Microbiota/genetics ; Bacteria/genetics ; Metagenome ; *Panicum ; }, abstract = {Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on replicated plots of field-grown switchgrass and miscanthus, and to quantify their activities over two growing seasons for switchgrass. We use metagenome and metatranscriptome sequencing and curate 40 medium- and high-quality metagenome-assembled-genomes (MAGs). We find that classes represented by these MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) are active in the late season, and upregulate transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase. Stress-associated pathways are expressed for most MAGs, suggesting engagement with the host environment. We also detect seasonally activated biosynthetic pathways for terpenes and various non-ribosomal peptide pathways that are poorly annotated. Our findings support that leaf-associated bacterial populations are seasonally dynamic and responsive to host cues.}, } @article {pmid36823020, year = {2023}, author = {Yan, A and Butcher, J and Schramm, L and Mack, DR and Stintzi, A}, title = {Multiomic spatial analysis reveals a distinct mucosa-associated virome.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2177488}, pmid = {36823020}, issn = {1949-0984}, support = {ECD-144627//CIHR/Canada ; }, mesh = {Humans ; Virome ; Multiomics ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics ; Metagenomics ; Intestinal Mucosa ; Spatial Analysis ; }, abstract = {The human gut virome has been increasingly explored in recent years. However, nearly all virome-sequencing efforts rely solely on fecal samples and few studies leverage multiomic approaches to investigate phage-host relationships. Here, we combine metagenomics, metaviromics, and metatranscriptomics to study virome-bacteriome interactions at the colonic mucosal-luminal interface in a cohort of three individuals with inflammatory bowel disease; non-IBD controls were not included in this study. We show that the mucosal viral population is distinct from the stool virome and houses abundant crAss-like phages that are undetectable by fecal sampling. Through viral protein prediction and metatranscriptomic analysis, we explore viral gene transcription, prophage activation, and the relationship between the presence of integrase and temperate phages in IBD subjects. We also show the impact of deep sequencing on virus recovery and offer guidelines for selecting optimal sequencing depths in future metaviromic studies. Systems biology approaches such as those presented in this report will enhance our understanding of the human virome and its interactions with our microbiome and our health.}, } @article {pmid36816590, year = {2023}, author = {Liu, T and Chen, YC and Jeng, SL and Chang, JJ and Wang, JY and Lin, CH and Tsai, PF and Ko, NY and Ko, WC and Wang, JL}, title = {Short-term effects of Chlorhexidine mouthwash and Listerine on oral microbiome in hospitalized patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1056534}, pmid = {36816590}, issn = {2235-2988}, mesh = {Humans ; *Chlorhexidine ; Mouthwashes ; Nitrates ; Bacteria ; *Microbiota ; }, abstract = {INTRODUCTION: Chlorhexidine (CHX) and essential oil containing mouthwashes like Listerine[®] can improve oral hygiene via suppressing oral microbes. In hospitalized patients, CHX mouthwash reduces the incidence of ventilator-associated pneumonia. However, CHX use was also associated with increased mortality, which might be related to nitrate-reducing bacteria. Currently, no study determines oral bacteria targeted by essential oils mouthwash in hospitalized patients using a metagenomic approach.

METHODS: We recruited 87 hospitalized patients from a previous randomized control study, and assigned them to three mouthwash groups: CHX, Listerine, and normal saline (control). Before and after gargling the mouthwash twice a day for 5-7 days, oral bacteria were examined using a 16S rDNA approach.

RESULTS: Alpha diversities at the genus level decreased significantly only for the CHX and Listerine groups. Only for the two groups, oral microbiota before and after gargling were significantly different, but not clearly distinct. Paired analysis eliminated the substantial individual differences and revealed eight bacterial genera (including Prevotella, Fusobacterium, and Selenomonas) with a decreased relative abundance, while Rothia increased after gargling the CHX mouthwash. After gargling Listerine, seven genera (including Parvimonas, Eubacterium, and Selenomonas) showed a decreased relative abundance, and the magnitudes were smaller compared to the CHX group. Fewer bacteria targeted by Listerine were reported to be nitrate-reducing compared to the CHX mouthwash.

DISCUSSION: In conclusion, short-term gargling of the CHX mouthwash and Listerine altered oral microbiota in our hospitalized patients. The bacterial genera targeted by the CHX mouthwash and Listerine were largely different and the magnitudes of changes were smaller using Listerine. Functional alterations of gargling CHX and Listerine were also different. These findings can be considered for managing oral hygiene of hospitalized patients.}, } @article {pmid36815859, year = {2023}, author = {Han, M and Sun, J and Yang, Q and Liang, Y and Jiang, Y and Gao, C and Gu, C and Liu, Q and Chen, X and Liu, G and Shao, H and Guo, C and He, H and Wang, H and Sung, YY and Mok, WJ and Wong, LL and Wang, Z and McMinn, A and Wang, M}, title = {Spatiotemporal Dynamics of Coastal Viral Community Structure and Potential Biogeochemical Roles Affected by an Ulva prolifera Green Tide.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0121122}, pmid = {36815859}, issn = {2379-5077}, mesh = {*Ulva/genetics ; Ecosystem ; Eutrophication ; China ; *Synechococcus ; }, abstract = {The world's largest macroalgal green tide, caused by Ulva prolifera, has resulted in serious consequences for coastal waters of the Yellow Sea, China. Although viruses are considered to be one of the key factors in controlling microalgal bloom demise, understanding of the relationship between viral communities and the macroalgal green tide is still poor. Here, a Qingdao coastal virome (QDCV) time-series data set was constructed based on the metagenomic analysis of 17 DNA viromes along three coastal stations of the Yellow Sea, covering different stages of the green tide from Julian days 165 to 271. A total of 40,076 viral contigs were detected and clustered into 28,058 viral operational taxonomic units (vOTUs). About 84% of the vOTUs could not be classified, and 62% separated from vOTUs in other ecosystems. Green tides significantly influenced the spatiotemporal dynamics of the viral community structure, diversity, and potential functions. For the classified vOTUs, the relative abundance of Pelagibacter phages declined with the arrival of the bloom and rebounded after the bloom, while Synechococcus and Roseobacter phages increased, although with a time lag from the peak of their hosts. More than 80% of the vOTUs reached peaks in abundance at different specific stages, and the viral peaks were correlated with specific hosts at different stages of the green tide. Most of the viral auxiliary metabolic genes (AMGs) were associated with carbon and sulfur metabolism and showed spatiotemporal dynamics relating to the degradation of the large amount of organic matter released by the green tide. IMPORTANCE To the best of our knowledge, this study is the first to investigate the responses of viruses to the world's largest macroalgal green tide. It revealed the spatiotemporal dynamics of the unique viral assemblages and auxiliary metabolic genes (AMGs) following the variation and degradation of Ulva prolifera. These findings demonstrate a tight coupling between viral assemblages, and prokaryotic and eukaryotic abundances were influenced by the green tide.}, } @article {pmid36814842, year = {2023}, author = {Zampieri, G and Campanaro, S and Angione, C and Treu, L}, title = {Metatranscriptomics-guided genome-scale metabolic modeling of microbial communities.}, journal = {Cell reports methods}, volume = {3}, number = {1}, pages = {100383}, pmid = {36814842}, issn = {2667-2375}, mesh = {Humans ; *Microbiota/genetics ; Metagenome/genetics ; Archaea/genetics ; *Gastrointestinal Microbiome/genetics ; }, abstract = {Multi-omics data integration via mechanistic models of metabolism is a scalable and flexible framework for exploring biological hypotheses in microbial systems. However, although most microorganisms are unculturable, such multi-omics modeling is limited to isolate microbes or simple synthetic communities. Here, we developed an approach for modeling microbial activity and interactions that leverages the reconstruction of metagenome-assembled genomes and associated genome-centric metatranscriptomes. At its core, we designed a method for condition-specific metabolic modeling of microbial communities through the integration of metatranscriptomic data. Using this approach, we explored the behavior of anaerobic digestion consortia driven by hydrogen availability and human gut microbiota dysbiosis associated with Crohn's disease, identifying condition-dependent amino acid requirements in archaeal species and a reduced short-chain fatty acid exchange network associated with disease, respectively. Our approach can be applied to complex microbial communities, allowing a mechanistic contextualization of multi-omics data on a metagenome scale.}, } @article {pmid36814836, year = {2023}, author = {Usyk, M and Peters, BA and Karthikeyan, S and McDonald, D and Sollecito, CC and Vazquez-Baeza, Y and Shaffer, JP and Gellman, MD and Talavera, GA and Daviglus, ML and Thyagarajan, B and Knight, R and Qi, Q and Kaplan, R and Burk, RD}, title = {Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies.}, journal = {Cell reports methods}, volume = {3}, number = {1}, pages = {100391}, pmid = {36814836}, issn = {2667-2375}, support = {N01HC65236/HL/NHLBI NIH HHS/United States ; R01 DK126698/DK/NIDDK NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; N01HC65235/HL/NHLBI NIH HHS/United States ; U01 HL146204/HL/NHLBI NIH HHS/United States ; HHSN261201300005I/CA/NCI NIH HHS/United States ; P30 CA013330/CA/NCI NIH HHS/United States ; HHSN268201000001I/HL/NHLBI NIH HHS/United States ; N01HC65237/HL/NHLBI NIH HHS/United States ; N01HC65234/HL/NHLBI NIH HHS/United States ; HHSN261201300004I/CA/NCI NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; N01HC65233/HL/NHLBI NIH HHS/United States ; P30 AI124414/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; Bacteria ; Metagenome ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {In a large cohort of 1,772 participants from the Hispanic Community Health Study/Study of Latinos with overlapping 16SV4 rRNA gene (bacterial amplicon), ITS1 (fungal amplicon), and shotgun sequencing data, we demonstrate that 16SV4 amplicon sequencing and shotgun metagenomics offer the same level of taxonomic accuracy for bacteria at the genus level even at shallow sequencing depths. In contrast, for fungal taxa, we did not observe meaningful agreements between shotgun and ITS1 amplicon results. Finally, we show that amplicon and shotgun data can be harmonized and pooled to yield larger microbiome datasets with excellent agreement (<1% effect size variance across three independent outcomes) using pooled amplicon/shotgun data compared to pure shotgun metagenomic analysis. Thus, there are multiple approaches to study the microbiome in epidemiological studies, and we provide a demonstration of a powerful pooling approach that will allow researchers to leverage the massive amount of amplicon sequencing data generated over the last two decades.}, } @article {pmid36814443, year = {2023}, author = {Yu, S and Ge, X and Xu, H and Tan, B and Tian, B and Shi, Y and Dai, Y and Li, Y and Hu, S and Qian, J}, title = {Gut microbiome and mycobiome in inflammatory bowel disease patients with Clostridioides difficile infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1129043}, pmid = {36814443}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Mycobiome ; *Clostridioides difficile ; *Inflammatory Bowel Diseases/microbiology ; Bacteria ; *Clostridium Infections/microbiology ; }, abstract = {BACKGROUND: Clostridium difficile infection (CDI) is common in patients with inflammatory bowel disease (IBD) and has been reported as a risk factor for poor outcome. However, gut microbiome and mycobiome of IBD patients with CDI have been barely investigated. This study aimed to assess the gut microbiome and mycobiome in IBD patients with CDI.

METHODS: We collected fecal samples from patients with active IBD and concomitant CDI (IBD-CDI group, n=25), patients with active IBD and no CDI (IBD-only group, n=51), and healthy subjects (HC, n=40). Patients' characteristics including demographic data, disease severity, and medication history were collected. Metagenomic sequencing, taxonomic and functional analysis were carried out in the samples.

RESULTS: We found that the bacterial alpha diversity of the IBD-CDI group was decreased. The bacterial and fungal beta diversity variations between IBD patients and HC were significant, regardless of CDI status. But the IBD-CDI group did not significantly cluster separately from the IBD-only group. Several bacterial taxa, including Enterococcus faecium, Ruminococcus gnavus, and Clostridium innocuum were overrepresented in the IBD-CDI group. Furthermore, IBD patients with CDI were distinguished by several fungal taxa, including overrepresentation of Saccharomyces cerevisiae. We also identified functional differences in IBD patients with CDI include enrichment of peptidoglycan biosynthesis. The network analysis indicated specific interactions between microbial markers in IBD-CDI patients.

CONCLUSION: IBD patients with CDI had pronounced microbial dysbiosis. Gut micro-ecological changes in IBD patients with CDI might provide insight into the pathological process and potential strategies for diagnosis and treatment in this subset of patients.}, } @article {pmid36813961, year = {2023}, author = {Tintelnot, J and Xu, Y and Lesker, TR and Schönlein, M and Konczalla, L and Giannou, AD and Pelczar, P and Kylies, D and Puelles, VG and Bielecka, AA and Peschka, M and Cortesi, F and Riecken, K and Jung, M and Amend, L and Bröring, TS and Trajkovic-Arsic, M and Siveke, JT and Renné, T and Zhang, D and Boeck, S and Strowig, T and Uzunoglu, FG and Güngör, C and Stein, A and Izbicki, JR and Bokemeyer, C and Sinn, M and Kimmelman, AC and Huber, S and Gagliani, N}, title = {Microbiota-derived 3-IAA influences chemotherapy efficacy in pancreatic cancer.}, journal = {Nature}, volume = {615}, number = {7950}, pages = {168-174}, pmid = {36813961}, issn = {1476-4687}, mesh = {Animals ; Humans ; Mice ; *Carcinoma, Pancreatic Ductal/diet therapy/drug therapy/metabolism/microbiology ; Glutathione Peroxidase/metabolism ; *Microbiota ; *Pancreatic Neoplasms/diet therapy/drug therapy/metabolism/microbiology ; Peroxidase/metabolism ; Reactive Oxygen Species/metabolism ; Tryptophan/metabolism/pharmacology/therapeutic use ; Neutrophils/enzymology ; Autophagy ; Metagenome ; Metabolomics ; Fecal Microbiota Transplantation ; Indoleacetic Acids/pharmacology/therapeutic use ; Disease Models, Animal ; Germ-Free Life ; }, abstract = {Pancreatic ductal adenocarcinoma (PDAC) is expected to be the second most deadly cancer by 2040, owing to the high incidence of metastatic disease and limited responses to treatment[1,2]. Less than half of all patients respond to the primary treatment for PDAC, chemotherapy[3,4], and genetic alterations alone cannot explain this[5]. Diet is an environmental factor that can influence the response to therapies, but its role in PDAC is unclear. Here, using shotgun metagenomic sequencing and metabolomic screening, we show that the microbiota-derived tryptophan metabolite indole-3-acetic acid (3-IAA) is enriched in patients who respond to treatment. Faecal microbiota transplantation, short-term dietary manipulation of tryptophan and oral 3-IAA administration increase the efficacy of chemotherapy in humanized gnotobiotic mouse models of PDAC. Using a combination of loss- and gain-of-function experiments, we show that the efficacy of 3-IAA and chemotherapy is licensed by neutrophil-derived myeloperoxidase. Myeloperoxidase oxidizes 3-IAA, which in combination with chemotherapy induces a downregulation of the reactive oxygen species (ROS)-degrading enzymes glutathione peroxidase 3 and glutathione peroxidase 7. All of this results in the accumulation of ROS and the downregulation of autophagy in cancer cells, which compromises their metabolic fitness and, ultimately, their proliferation. In humans, we observed a significant correlation between the levels of 3-IAA and the efficacy of therapy in two independent PDAC cohorts. In summary, we identify a microbiota-derived metabolite that has clinical implications in the treatment of PDAC, and provide a motivation for considering nutritional interventions during the treatment of patients with cancer.}, } @article {pmid36813387, year = {2023}, author = {Leis, ML}, title = {An Update on the Ocular Surface Bacterial Microbiota in Small Animals.}, journal = {The Veterinary clinics of North America. Small animal practice}, volume = {53}, number = {2}, pages = {299-318}, doi = {10.1016/j.cvsm.2022.10.004}, pmid = {36813387}, issn = {1878-1306}, mesh = {Animals ; *Bacteria/genetics ; *Microbiota ; High-Throughput Nucleotide Sequencing/methods/veterinary ; }, abstract = {High-throughput sequencing (HTS) techniques have revolutionized the way we understand microbial communities in both research and clinical settings and are bringing new insights into what constitutes a healthy ocular surface (and a diseased one). As more diagnostic laboratories incorporate HTS into their technique repertoire, practitioners can expect this technology to become increasingly accessible for clinical practice, potentially becoming the new standard. However, particularly regarding ophthalmic microbiota, considerable research remains to render HTS accessible and applicable.}, } @article {pmid36812328, year = {2023}, author = {Kiefl, E and Esen, OC and Miller, SE and Kroll, KL and Willis, AD and Rappé, MS and Pan, T and Eren, AM}, title = {Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution.}, journal = {Science advances}, volume = {9}, number = {8}, pages = {eabq4632}, doi = {10.1126/sciadv.abq4632}, pmid = {36812328}, issn = {2375-2548}, support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; }, mesh = {*Genetics, Population ; *Ecology ; Oceans and Seas ; Organic Chemicals ; Base Sequence ; Genetic Variation ; Evolution, Molecular ; }, abstract = {Comprehensive sampling of natural genetic diversity with metagenomics enables highly resolved insights into the interplay between ecology and evolution. However, resolving adaptive, neutral, or purifying processes of evolution from intrapopulation genomic variation remains a challenge, partly due to the sole reliance on gene sequences to interpret variants. Here, we describe an approach to analyze genetic variation in the context of predicted protein structures and apply it to a marine microbial population within the SAR11 subclade 1a.3.V, which dominates low-latitude surface oceans. Our analyses reveal a tight association between genetic variation and protein structure. In a central gene in nitrogen metabolism, we observe decreased occurrence of nonsynonymous variants from ligand-binding sites as a function of nitrate concentrations, revealing genetic targets of distinct evolutionary pressures maintained by nutrient availability. Our work yields insights into the governing principles of evolution and enables structure-aware investigations of microbial population genetics.}, } @article {pmid36810808, year = {2023}, author = {Kunasegaran, T and Balasubramaniam, VRMT and Arasoo, VJT and Palanisamy, UD and Ramadas, A}, title = {Diet Gut Microbiota Axis in Pregnancy: A Systematic Review of Recent Evidence.}, journal = {Current nutrition reports}, volume = {12}, number = {1}, pages = {203-214}, pmid = {36810808}, issn = {2161-3311}, mesh = {Pregnancy ; Female ; Humans ; *Gastrointestinal Microbiome ; Prospective Studies ; Diet ; }, abstract = {PURPOSE OF REVIEW: Although gut microbiota have been associated with the etiology of some diseases, the influence of foods on gut microbiota, especially among pregnant women, remains unclear. Hence, a systematic review was performed to investigate the association between diet and gut microbiota and their influence on metabolic health in pregnant women.

RECENT FINDINGS: We performed the systematic review using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 protocol to investigate the association between diet and gut microbiota and their influence on metabolic role in pregnant women. Five databases were searched for relevant peer-reviewed articles published in English since 2011. Two-staged screening of 659 retrieved records resulted in the inclusion of 10 studies. The collated findings suggested associations between nutrient intakes and four key microbes: Collinsella, Lachnospira, Sutterella, Faecalibacterium, and the Firmicutes/Bacteroidetes ratio in pregnant women. Dietary intakes in pregnancy were found to modify the gut microbiota and positively influence the cell metabolism in pregnant women. This review, however, emphasizes the importance of conducting well-designed prospective cohorts to investigate the role of changes in dietary intakes within the pregnancy and the influence of such changes on gut microbiota.}, } @article {pmid36809182, year = {2023}, author = {Olekhnovich, EI and Ivanov, AB and Babkina, AA and Sokolov, AA and Ulyantsev, VI and Fedorov, DE and Ilina, EN}, title = {Consistent Stool Metagenomic Biomarkers Associated with the Response To Melanoma Immunotherapy.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0102322}, pmid = {36809182}, issn = {2379-5077}, mesh = {Humans ; Metagenome ; *Melanoma/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Biomarkers ; Immunotherapy/methods ; }, abstract = {The human gut microbiome plays an important role in both health and disease. Recent studies have demonstrated a strong influence of the gut microbiome composition on the efficacy of cancer immunotherapy. However, available studies have not yet succeeded in finding reliable and consistent metagenomic markers that are associated with the response to immunotherapy. Therefore, the reanalysis of the published data may improve our understanding of the association between the composition of the gut microbiome and the treatment response. In this study, we focused on melanoma-related metagenomic data, which are more abundant than are data from other tumor types. We analyzed the metagenomes of 680 stool samples from 7 studies that were published earlier. The taxonomic and functional biomarkers were selected after comparing the metagenomes of patients showing different treatment responses. The list of selected biomarkers was also validated on additional metagenomic data sets that were dedicated to the influence of fecal microbiota transplantation on the response to melanoma immunotherapy. According to our analysis, the resulting cross-study taxonomic biomarkers included three bacterial species: Faecalibacterium prausnitzii, Bifidobacterium adolescentis, and Eubacterium rectale. 101 groups of genes were identified to be functional biomarkers, including those potentially involved in the production of immune-stimulating molecules and metabolites. Moreover, we ranked the microbial species by the number of genes encoding functionally relevant biomarkers that they contained. Thus, we put together a list of potentially the most beneficial bacteria for immunotherapy success. F. prausnitzii, E. rectale, and three species of bifidobacteria stood out as the most beneficial species, even though some useful functions were also present in other bacterial species. IMPORTANCE In this study, we put together a list of potentially the most beneficial bacteria that were associated with a responsiveness to melanoma immunotherapy. Another important result of this study is the list of functional biomarkers of responsiveness to immunotherapy, which are dispersed among different bacterial species. This result possibly explains the existing irregularities between studies regarding the bacterial species that are beneficial to melanoma immunotherapy. Overall, these findings can be utilized to issue recommendations for gut microbiome correction in cancer immunotherapy, and the resulting list of biomarkers might serve as a good stepping stone for the development of a diagnostic test that is aimed at predicting patients' responses to melanoma immunotherapy.}, } @article {pmid36809109, year = {2023}, author = {Wolff, R and Shoemaker, W and Garud, N}, title = {Ecological Stability Emerges at the Level of Strains in the Human Gut Microbiome.}, journal = {mBio}, volume = {14}, number = {2}, pages = {e0250222}, pmid = {36809109}, issn = {2150-7511}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; *Microbiota ; Models, Theoretical ; }, abstract = {The human gut microbiome harbors substantial ecological diversity at the species level as well as at the strain level within species. In healthy hosts, species abundance fluctuations in the microbiome are thought to be stable, and these fluctuations can be described by macroecological laws. However, it is less clear how strain abundances change over time. An open question is whether individual strains behave like species themselves, exhibiting stability and following the macroecological relationships known to hold at the species level, or whether strains have different dynamics, perhaps due to the relatively close phylogenetic relatedness of cocolonizing lineages. Here, we analyze the daily dynamics of intraspecific genetic variation in the gut microbiomes of four healthy, densely longitudinally sampled hosts. First, we find that the overall genetic diversity of a large majority of species is stationary over time despite short-term fluctuations. Next, we show that fluctuations in abundances in approximately 80% of strains analyzed can be predicted with a stochastic logistic model (SLM), an ecological model of a population experiencing environmental fluctuations around a fixed carrying capacity, which has previously been shown to capture statistical properties of species abundance fluctuations. The success of this model indicates that strain abundances typically fluctuate around a fixed carrying capacity, suggesting that most strains are dynamically stable. Finally, we find that the strain abundances follow several empirical macroecological laws known to hold at the species level. Together, our results suggest that macroecological properties of the human gut microbiome, including its stability, emerge at the level of strains. IMPORTANCE To date, there has been an intense focus on the ecological dynamics of the human gut microbiome at the species level. However, there is considerable genetic diversity within species at the strain level, and these intraspecific differences can have important phenotypic effects on the host, impacting the ability to digest certain foods and metabolize drugs. Thus, to fully understand how the gut microbiome operates in times of health and sickness, its ecological dynamics may need to be quantified at the level of strains. Here, we show that a large majority of strains maintain stable abundances for periods of months to years, exhibiting fluctuations in abundance that can be well described by macroecological laws known to hold at the species level, while a smaller percentage of strains undergo rapid, directional changes in abundance. Overall, our work indicates that strains are an important unit of ecological organization in the human gut microbiome.}, } @article {pmid36809072, year = {2023}, author = {Yuan, S and Friman, VP and Balcazar, JL and Zheng, X and Ye, M and Sun, M and Hu, F}, title = {Viral and Bacterial Communities Collaborate through Complementary Assembly Processes in Soil to Survive Organochlorine Contamination.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {3}, pages = {e0181022}, pmid = {36809072}, issn = {1098-5336}, mesh = {Soil ; Bacteria ; *Microbiota ; Soil Microbiology ; *Viruses ; *Pesticides/metabolism ; *Hydrocarbons, Chlorinated/metabolism ; }, abstract = {The ecological drivers that direct the assembly of viral and host bacterial communities are largely unknown, even though viral-encoded accessory genes help host bacteria survive in polluted environments. To understand the ecological mechanism(s) of viruses and hosts synergistically surviving under organochlorine pesticide (OCP) stress, we investigated the community assembly processes of viruses and bacteria at the taxon and functional gene levels in clean and OCP-contaminated soils in China using a combination of metagenomics/viromics and bioinformatics approaches. We observed a decreased richness of bacterial taxa and functional genes but an increased richness of viral taxa and auxiliary metabolic genes (AMGs) in OCP-contaminated soils (from 0 to 2,617.6 mg · kg[-1]). In OCP-contaminated soils, the assembly of bacterial taxa and genes was dominated by a deterministic process, of which the relative significance was 93.0% and 88.7%, respectively. In contrast, the assembly of viral taxa and AMGs was driven by a stochastic process, which contributed 83.1% and 69.2%, respectively. The virus-host prediction analysis, which indicated Siphoviridae was linked to 75.0% of bacterial phyla, and the higher migration rate of viral taxa and AMGs in OCP-contaminated soil suggested that viruses show promise for the dissemination of functional genes among bacterial communities. Taken together, the results of this study indicated that the stochastic assembly processes of viral taxa and AMGs facilitated bacterial resistance to OCP stress in soils. Moreover, our findings provide a novel avenue for understanding the synergistic interactions between viruses and bacteria from the perspective of microbial ecology, highlighting the significance of viruses in mediating bioremediation of contaminated soils. IMPORTANCE The interaction between viral communities and microbial hosts has been studied extensively, and the viral community affects host community metabolic function through AMGs. Microbial community assembly is the process by which species colonize and interact to establish and maintain communities. This is the first study that aimed to understand the assembly process of bacterial and viral communities under OCP stress. The findings of this study provide information about microbial community responses to OCP stress and reveal the collaborative interactions between viral and bacterial communities to resist pollutant stress. Thereby, we highlight the importance of viruses in soil bioremediation from the perspective of community assembly.}, } @article {pmid36807860, year = {2023}, author = {Kumar, J and Sharma, N and Singh, SP}, title = {Genome-resolved metagenomics inferred novel insights into the microbial community, metabolic pathways, and biomining potential of Malanjkhand acidic copper mine tailings.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {17}, pages = {50864-50882}, pmid = {36807860}, issn = {1614-7499}, mesh = {*Copper/metabolism ; Metagenomics ; Phylogeny ; *Microbiota ; Archaea/metabolism ; Metagenome ; Acidobacteria/genetics ; Metabolic Networks and Pathways ; Soil ; Water/metabolism ; }, abstract = {Mine tailing sites provide profound opportunities to elucidate the microbial mechanisms involved in ecosystem functioning. In the present study, metagenomic analysis of dumping soil and adjacent pond around India's largest copper mine at Malanjkhand has been done. Taxonomic analysis deciphered the abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi. Genomic signatures of viruses were predicted in the soil metagenome, whereas Archaea and Eukaryotes were noticed in water samples. Mesophilic chemolithotrophs, such as Acidobacteria bacterium, Chloroflexi bacterium, and Verrucomicrobia bacterium, were predominant in soil, whereas, in the water sample, the abundance of Methylobacterium mesophilicum, Pedobacter sp., and Thaumarchaeota archaeon was determined. The functional potential analysis highlighted the abundance of genes related to sulfur, nitrogen, methane, ferrous oxidation, carbon fixation, and carbohydrate metabolisms. The genes for copper, iron, arsenic, mercury, chromium, tellurium, hydrogen peroxide, and selenium resistance were found to be predominant in the metagenomes. Metagenome-assembled genomes (MAGs) were constructed from the sequencing data, indicating novel microbial species genetically related to the phylum predicted through whole genome metagenomics. Phylogenetic analysis, genome annotations, functional potential, and resistome analysis showed the resemblance of assembled novel MAGs with traditional organisms used in bioremediation and biomining applications. Microorganisms harboring adaptive mechanisms, such as detoxification, hydroxyl radical scavenging, and heavy metal resistance, could be the potent benefactions for their utility as bioleaching agents. The genetic information produced in the present investigation provides a foundation for pursuing and understanding the molecular aspects of bioleaching and bioremediation applications.}, } @article {pmid36807446, year = {2023}, author = {Bartuv, R and Berihu, M and Medina, S and Salim, S and Feygenberg, O and Faigenboim-Doron, A and Zhimo, VY and Abdelfattah, A and Piombo, E and Wisniewski, M and Freilich, S and Droby, S}, title = {Functional analysis of the apple fruit microbiome based on shotgun metagenomic sequencing of conventional and organic orchard samples.}, journal = {Environmental microbiology}, volume = {25}, number = {9}, pages = {1728-1746}, doi = {10.1111/1462-2920.16353}, pmid = {36807446}, issn = {1462-2920}, mesh = {*Malus ; Fruit ; Phylogeny ; *Ascomycota ; *Microbiota/genetics ; }, abstract = {Fruits harbour abundant and diverse microbial communities that protect them from post-harvest pathogens. Identification of functional traits associated with a given microbiota can provide a better understanding of their potential influence. Here, we focused on the epiphytic microbiome of apple fruit. We suggest that shotgun metagenomic data can indicate specific functions carried out by different groups and provide information on their potential impact. Samples were collected from the surface of 'Golden Delicious' apples from four orchards that differ in their geographic location and management practice. Approximately 1 million metagenes were predicted based on a high-quality assembly. Functional profiling of the microbiome of fruits from orchards differing in their management practice revealed a functional shift in the microbiota. The organic orchard microbiome was enriched in pathways involved in plant defence activities; the conventional orchard microbiome was enriched in pathways related to the synthesis of antibiotics. The functional significance of the variations was explored using microbial network modelling algorithms to reveal the metabolic role of specific phylogenetic groups. The analysis identified several associations supported by other published studies. For example, the analysis revealed the nutritional dependencies of the Capnodiales group, including the Alternaria pathogen, on aromatic compounds.}, } @article {pmid36807409, year = {2023}, author = {Rasmussen, JA and Kiilerich, P and Madhun, AS and Waagbø, R and Lock, ER and Madsen, L and Gilbert, MTP and Kristiansen, K and Limborg, MT}, title = {Co-diversification of an intestinal Mycoplasma and its salmonid host.}, journal = {The ISME journal}, volume = {17}, number = {5}, pages = {682-692}, pmid = {36807409}, issn = {1751-7370}, mesh = {Animals ; *Salmonidae ; Bacteria ; *Gastrointestinal Microbiome ; *Salmo salar ; }, abstract = {Understanding the evolutionary relationships between a host and its intestinal resident bacteria can transform how we understand adaptive phenotypic traits. The interplay between hosts and their resident bacteria inevitably affects the intestinal environment and, thereby, the living conditions of both the host and the microbiota. Thereby this co-existence likely influences the fitness of both bacteria and host. Whether this co-existence leads to evolutionary co-diversification in animals is largely unexplored, mainly due to the complexity of the environment and microbial communities and the often low host selection. We present the gut metagenome from wild Atlantic salmon (Salmo salar), a new wild organism model with an intestinal microbiota of low complexity and a well-described population structure, making it well-suited for investigating co-evolution. Our data reveal a strong host selection of a core gut microbiota dominated by a single Mycoplasma species. We found a clear co-diversification between the population structure of Atlantic salmon and nucleotide variability of the intestinal Mycoplasma populations conforming to expectations from co-evolution between host and resident bacteria. Our results show that the stable microbiota of Atlantic salmon has evolved with its salmonid host populations while potentially providing adaptive traits to the salmon host populations, including defence mechanisms, biosynthesis of essential amino acids, and metabolism of B vitamins. We highlight Atlantic salmon as a novel model for studying co-evolution between vertebrate hosts and their resident bacteria.}, } @article {pmid36807001, year = {2023}, author = {Ghare, U and Narvekar, S and Lodha, T and Mallebhari, R and Dastager, S and Barvkar, VT and Dhotre, D and Karmalkar, NR and Pable, AA}, title = {Bacterial Communities and Diversity of Western Ghats Soil: A Study of a Biodiversity Hotspot.}, journal = {Current microbiology}, volume = {80}, number = {4}, pages = {108}, pmid = {36807001}, issn = {1432-0991}, mesh = {Animals ; *Soil/chemistry ; Soil Microbiology ; India ; Bacteria/genetics ; Biodiversity ; Proteobacteria ; *Actinobacteria/genetics ; RNA, Ribosomal, 16S/metabolism ; }, abstract = {The Western Ghats is one of India's mega-diversity hotspots and an ecologically and geologically important area for the diversity of endemic plants and animals. The present study provides insights into the aerobic bacterial diversity and composition of the soils of North Western Ghats located in Maharashtra state (NWGM), India. The samples for the culture-dependent study were collected from 6 different locations namely Malshej Ghat, Bhimashankar, Lonavala, Mulshi, Tail-Baila, and Mahabaleshwar. A total of 173 isolates were obtained from the different samples, which belonged to Proteobacteria (43%), Firmicutes (36%), and Actinobacteria (19%). Sequences of 15 strains shared ≤ 98.7% similarity (a species cut-off) which represent potential novel species. Metagenomic analysis revealed the presence of Actinobacteria and Proteobacteria as the most dominant phyla at both MB and MG. However, both sites showed variation in the composition of rare phyla and other dominant phyla. This difference in bacterial community composition could be due to differences in altitude or other physicochemical properties. The functional prediction from the amplicon sequencing showed the abundance of carbohydrate, protein, and lipid metabolism which was corroborated by screening the isolated bacterial strains for the same. The present study has a unique take on microbial diversity and defines the importance of community assembly processes such as drift, dispersal, and selection. Such processes are relatively important in controlling community diversity, distribution, as well as succession. This study has shown that the microbial community of NWGM is a rich source of polysaccharide degrading bacteria having biotechnological potential.}, } @article {pmid36806692, year = {2023}, author = {Gurbich, TA and Almeida, A and Beracochea, M and Burdett, T and Burgin, J and Cochrane, G and Raj, S and Richardson, L and Rogers, AB and Sakharova, E and Salazar, GA and Finn, RD}, title = {MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues.}, journal = {Journal of molecular biology}, volume = {435}, number = {14}, pages = {168016}, pmid = {36806692}, issn = {1089-8638}, support = {BB/W002965/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R015228/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/V01868X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/W016184/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Genome, Microbial ; *Metagenome/genetics ; Metagenomics ; }, abstract = {An increasingly common output arising from the analysis of shotgun metagenomic datasets is the generation of metagenome-assembled genomes (MAGs), with tens of thousands of MAGs now described in the literature. However, the discovery and comparison of these MAG collections is hampered by the lack of uniformity in their generation, annotation and storage. To address this, we have developed MGnify Genomes, a growing collection of biome-specific non-redundant microbial genome catalogues generated using MAGs and publicly available isolate genomes. Genomes within a biome-specific catalogue are organised into species clusters. For species that contain multiple conspecific genomes, the highest quality genome is selected as the representative, always prioritising an isolate genome over a MAG. The species representative sequences and annotations can be visualised on the MGnify website and the full catalogue and associated analysis outputs can be downloaded from MGnify servers. A suite of online search tools is provided allowing users to compare their own sequences, ranging from a gene to sets of genomes, against the catalogues. Seven biomes are available currently, comprising over 300,000 genomes that represent 11,048 non-redundant species, and include 36 taxonomic classes not currently represented by cultured genomes. MGnify Genomes is available at https://www.ebi.ac.uk/metagenomics/browse/genomes/.}, } @article {pmid36805473, year = {2023}, author = {Jia, Y and Liu, ML and López-Pujol, J and Jia, RW and Kou, YX and Yue, M and Guan, TX and Li, ZH}, title = {The hybridization origin of the Chinese endemic herb genus Notopterygium (Apiaceae): Evidence from population genomics and ecological niche analysis.}, journal = {Molecular phylogenetics and evolution}, volume = {182}, number = {}, pages = {107736}, doi = {10.1016/j.ympev.2023.107736}, pmid = {36805473}, issn = {1095-9513}, mesh = {*Apiaceae/genetics ; Bayes Theorem ; Ecosystem ; Metagenomics ; Phylogeny ; *Hybridization, Genetic ; }, abstract = {Hybridization is recognized as a major force in species evolution and biodiversity formation, generally leading to the origin and differentiation of new species. Multiple hybridization events cannot easily be reconstructed, yet they offer the potential to study a number of evolutionary processes. Here, we used nuclear expressed sequence tag-simple sequence repeat and large-scale single nucleotide polymorphism variation data, combined with niche analysis, to investigate the putative independent hybridization events in Notopterygium, a group of perennial herb plants endemic to China. Population genomic analysis indicated that the four studied species are genetically well-delimited and that N. forrestii and N. oviforme have originated by hybridization. According to Approximate Bayesian Computation, the best-fit model involved the formation of N. forrestii from the crossing of N. franchetii and N. incisum, with N. forrestii further backcrossing to N. franchetii to form N. oviforme. The niche analyses indicated that niche divergence [likely triggered by the regional climate changes, particularly the intensification of East Asian winter monsoon, and tectonic movements (affecting both Qinghai-Tibetan Plateau and Qinling Mountains)] may have promoted and maintained the reproductive isolation among hybrid species. N. forrestii shows ecological specialization with respect to their parental species, whereas N. oviforme has completely shifted its niche. These results suggested that the climate and environmental factors together triggered the two-step hybridization of the East Asia herb plants. Our study also emphasizes the power of genome-wide SNPs for investigating suspected cases of hybridization, particularly unravelling old hybridization events.}, } @article {pmid36804804, year = {2023}, author = {Yorki, S and Shea, T and Cuomo, CA and Walker, BJ and LaRocque, RC and Manson, AL and Earl, AM and Worby, CJ}, title = {Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {2}, pages = {}, pmid = {36804804}, issn = {1477-4054}, support = {U01 CK000633/CK/NCEZID CDC HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; U01 CK000490/CK/NCEZID CDC HHS/United States ; }, mesh = {*Metagenome ; Sequence Analysis, DNA/methods ; Escherichia coli/genetics ; *Microbiota/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Recent technological and computational advances have made metagenomic assembly a viable approach to achieving high-resolution views of complex microbial communities. In previous benchmarking, short-read (SR) metagenomic assemblers had the highest accuracy, long-read (LR) assemblers generated the most contiguous sequences and hybrid (HY) assemblers balanced length and accuracy. However, no assessments have specifically compared the performance of these assemblers on low-abundance species, which include clinically relevant organisms in the gut. We generated semi-synthetic LR and SR datasets by spiking small and increasing amounts of Escherichia coli isolate reads into fecal metagenomes and, using different assemblers, examined E. coli contigs and the presence of antibiotic resistance genes (ARGs). For ARG assembly, although SR assemblers recovered more ARGs with high accuracy, even at low coverages, LR assemblies allowed for the placement of ARGs within longer, E. coli-specific contigs, thus pinpointing their taxonomic origin. HY assemblies identified resistance genes with high accuracy and had lower contiguity than LR assemblies. Each assembler type's strengths were maintained even when our isolate was spiked in with a competing strain, which fragmented and reduced the accuracy of all assemblies. For strain characterization and determining gene context, LR assembly is optimal, while for base-accurate gene identification, SR assemblers outperform other options. HY assembly offers contiguity and base accuracy, but requires generating data on multiple platforms, and may suffer high misassembly rates when strain diversity exists. Our results highlight the trade-offs associated with each approach for recovering low-abundance taxa, and that the optimal approach is goal-dependent.}, } @article {pmid36804561, year = {2023}, author = {Wang, F and Zhang, Q and Cui, J and Bao, B and Deng, X and Liu, L and Guo, MY}, title = {Polystyrene microplastics induce endoplasmic reticulum stress, apoptosis and inflammation by disrupting the gut microbiota in carp intestines.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {323}, number = {}, pages = {121233}, doi = {10.1016/j.envpol.2023.121233}, pmid = {36804561}, issn = {1873-6424}, mesh = {Animals ; Microplastics/toxicity ; Polystyrenes ; Plastics ; *Gastrointestinal Microbiome ; *Carps ; Intestines ; Inflammation/chemically induced ; Apoptosis ; Endoplasmic Reticulum Stress ; }, abstract = {Microplastics have been recognized as a widespread new pollutant in nature and have induced an increase in the occurrence of a variety of diseases in carp. An animal model of microplastic ingestion was successfully established in an aqueous environment. The gut microbiota was analysed using a metagenomic approach. The results showed a significant reduction in the relative abundances of Lactococcus garvieae, Bacteroides_paurosaccharolyticus, and Romboutsia_ilealis after PS-MPs treatment. The 16S Silva database was used to predict and analyse the known genes. Intestinal flora disorders related to infectious diseases, cancers, neurodegenerative diseases, endocrine and metabolic diseases, cardiovascular diseases, and other diseases were found. The intake of PS-MPs resulted in damage to carp intestinal tissue and apoptosis of intestinal epithelial cells. The levels of the inflammatory cytokines IL-1β, IL-6, and TNF-α were significantly increased with the intake of PS-MPs. The gene and protein levels of GRP78, Caspase-3, Caspase-7, Caspase-9, Caspase-12, PERK, IRE1, and ATF6 were further examined in PS group. The occurrence of ERS and apoptosis in carp intestines was confirmed. These results suggest that the accumulation of PS-MPs in the aquatic environment can disturb the carp gut microbiota and induce ERS, apoptosis, and inflammation in the intestinal tissue.}, } @article {pmid36804142, year = {2023}, author = {Prosenkov, A and Cagnon, C and Gallego, JLR and Pelaez, AI}, title = {The microbiome of a brownfield highly polluted with mercury and arsenic.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {323}, number = {}, pages = {121305}, doi = {10.1016/j.envpol.2023.121305}, pmid = {36804142}, issn = {1873-6424}, mesh = {*Mercury/analysis ; *Arsenic/analysis ; Soot/analysis ; *Microbiota ; Eukaryota ; Soil/chemistry ; Soil Microbiology ; *Soil Pollutants/analysis ; *Ascomycota ; }, abstract = {Abandoned brownfields represent a challenge for their recovery. To apply sustainable remediation technologies, such as bioremediation or phytoremediation, indigenous microorganisms are essential agents since they are adapted to the ecology of the soil. Better understanding of microbial communities inhabiting those soils, identification of microorganisms that drive detoxification process and recognising their needs and interactions will significantly improve the outcome of the remediation. With this in mind we have carried out a detailed metagenomic analysis to explore the taxonomic and functional diversity of the prokaryotic and eukaryotic microbial communities in soils, several mineralogically distinct types of pyrometallurgic waste, and groundwater sediments of a former mercury mining and metallurgy site which harbour very high levels of arsenic and mercury pollution. Prokaryotic and eukaryotic communities were identified, which turned out to be more diverse in the surrounding contaminated soils compared to the pyrometallurgic waste. The highest diversity loss was observed in two environments most contaminated with mercury and arsenic (stupp, a solid mercury condenser residue and arsenic-rich soot from arsenic condensers). Interestingly, microbial communities in the stupp were dominated by an overwhelming majority of archaea of the phylum Crenarchaeota, while Ascomycota and Basidiomycota fungi comprised the fungal communities of both stump and soot, results that show the impressive ability of these previously unreported microorganisms to colonize these extreme brownfield environments. Functional predictions for mercury and arsenic resistance/detoxification genes show their increase in environments with higher levels of pollution. Our work establishes the bases to design sustainable remediation methods and, equally important, to study in depth the genetic and functional mechanisms that enable the subsistence of microbial populations in these extremely selective environments.}, } @article {pmid36802428, year = {2023}, author = {Wilson, K and de Rond, T and Burkhardt, I and Steele, TS and Schäfer, RJB and Podell, S and Allen, EE and Moore, BS}, title = {Terpene biosynthesis in marine sponge animals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {9}, pages = {e2220934120}, pmid = {36802428}, issn = {1091-6490}, support = {F32 GM129960/GM/NIGMS NIH HHS/United States ; R01 ES030316/ES/NIEHS NIH HHS/United States ; R01 GM085770/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Porifera/genetics ; Aquatic Organisms/genetics ; *Microbiota/genetics ; Metagenome ; *Biological Products ; Phylogeny ; }, abstract = {Sea sponges are the largest marine source of small-molecule natural products described to date. Sponge-derived molecules, such as the chemotherapeutic eribulin, the calcium-channel blocker manoalide, and antimalarial compound kalihinol A, are renowned for their impressive medicinal, chemical, and biological properties. Sponges contain microbiomes that control the production of many natural products isolated from these marine invertebrates. In fact, all genomic studies to date investigating the metabolic origins of sponge-derived small molecules concluded that microbes-not the sponge animal host-are the biosynthetic producers. However, early cell-sorting studies suggested the sponge animal host may play a role particularly in the production of terpenoid molecules. To investigate the genetic underpinnings of sponge terpenoid biosynthesis, we sequenced the metagenome and transcriptome of an isonitrile sesquiterpenoid-containing sponge of the order Bubarida. Using bioinformatic searches and biochemical validation, we identified a group of type I terpene synthases (TSs) from this sponge and multiple other species, the first of this enzyme class characterized from the sponge holobiome. The Bubarida TS-associated contigs consist of intron-containing genes homologous to sponge genes and feature GC percentage and coverage consistent with other eukaryotic sequences. We identified and characterized TS homologs from five different sponge species isolated from geographically distant locations, thereby suggesting a broad distribution amongst sponges. This work sheds light on the role of sponges in secondary metabolite production and speaks to the possibility that other sponge-specific molecules originate from the animal host.}, } @article {pmid36801683, year = {2023}, author = {Yan, M and Tian, H and Song, S and Tan, HTW and Lee, JTE and Zhang, J and Sharma, P and Tiong, YW and Tong, YW}, title = {Effects of digestate-encapsulated biochar on plant growth, soil microbiome and nitrogen leaching.}, journal = {Journal of environmental management}, volume = {334}, number = {}, pages = {117481}, doi = {10.1016/j.jenvman.2023.117481}, pmid = {36801683}, issn = {1095-8630}, mesh = {Soil/chemistry ; Fertilizers/analysis ; Food ; Nitrogen/analysis ; *Refuse Disposal ; Charcoal/chemistry ; Minerals ; *Microbiota ; }, abstract = {The increasing amount of food waste and the excessive use of mineral fertilizers have caused detrimental impacts on soil, water, and air quality. Though digestate derived from food waste has been reported to partially replace fertilizer, its efficiency requires further improvement. In this study, the effects of digestate-encapsulated biochar were comprehensively investigated based on growth of an ornamental plant, soil characteristics, nutrient leaching and soil microbiome. Results showed that except for biochar, the tested fertilizers and soil additives, i.e., digestate, compost, commercial fertilizer, digestate-encapsulated biochar had positive effects on plants. Especially, the digestate-encapsulated biochar had the best effectiveness as evidenced by 9-25% increase in chlorophyll content index, fresh weight, leaf area and blossom frequency. For the effects of fertilizers or soil additives on soil characteristics and nutrient retention, the digestate-encapsulated biochar leached least N-nutrients (<8%), while the compost, digestate and mineral fertilizer leached up to 25% N-nutrients. All the treatments had minimal effects on the soil properties of pH and electrical conductivity. According to the microbial analysis, the digestate-encapsulated biochar has the comparable role with compost in improving the soil immune system against pathogen infection. The metagenomics coupling with qPCR analysis suggested that digestate-encapsulated biochar boosted the nitrification process and inhibited the denitrification process. This study provides an extensive understanding into the impacts of the digestate-encapsulated biochar on an ornamental plant and offers practical implications for the choice of sustainable fertilizers or soil additives and food-waste digestate management.}, } @article {pmid36801350, year = {2023}, author = {Sammouri, J and Wong, MC and Lynn, EJ and El Alam, MB and Lo, DK and Lin, D and Harris, TH and Karpinets, TV and Court, K and Napravnik, TC and Wu, X and Zhang, J and Klopp, AH and Ajami, NJ and Colbert, LE}, title = {Serial Genotyping of the Human Papillomavirus in Cervical Cancer: An Insight Into Virome Dynamics During Chemoradiation Therapy.}, journal = {International journal of radiation oncology, biology, physics}, volume = {116}, number = {5}, pages = {1043-1054}, doi = {10.1016/j.ijrobp.2023.02.018}, pmid = {36801350}, issn = {1879-355X}, mesh = {Humans ; Female ; *Uterine Cervical Neoplasms/pathology ; Human Papillomavirus Viruses ; *Papillomavirus Infections/complications ; Prospective Studies ; Genotype ; Virome ; Papillomaviridae/genetics ; DNA, Viral/analysis ; }, abstract = {PURPOSE: Human papillomavirus (HPV) is the primary driver of cervical cancer. Although studies in other malignancies correlated peripheral blood DNA clearance with favorable outcomes, research on the prognostic value of HPV clearance in gynecologic cancers using intratumoral HPV is scarce. We aimed to quantify the intratumoral HPV virome in patients undergoing chemoradiation therapy (CRT) and associate this with clinical characteristics and outcomes.

METHODS AND MATERIALS: This prospective study enrolled 79 patients with stage IB-IVB cervical cancer undergoing definitive CRT. Cervical tumor swabs collected at baseline and week 5 (end of intensity modulated radiation therapy) were sent for shotgun metagenome sequencing and processed via VirMAP, a viral genome sequencing and identification tool for all known HPV types. The data were categorized into HPV groups (16, 18, high risk [HR], and low risk [LR]). We used independent t tests and Wilcoxon signed-rank to compare continuous variables and χ[2] and Fisher exact tests to compare categorical variables. Kaplan-Meier survival modeling was performed with log-rank testing. HPV genotyping was verified using quantitative polymerase chain reaction to validate VirMAP results using receiver operating characteristic curve and Cohen's kappa.

RESULTS: At baseline, 42%, 12%, 25%, and 16% of patients were positive for HPV 16, HPV 18, HPV HR, and HPV LR, respectively, and 8% were HPV negative. HPV type was associated with insurance status and CRT response. Patients with HPV 16+ and other HPV HR+ tumors were significantly more likely to have a complete response to CRT versus patients with HPV 18 and HPV LR/HPV-negative tumors. Overall HPV viral loads predominantly decreased throughout CRT, except for HPV LR viral load.

CONCLUSIONS: Rarer, less well-studied HPV types in cervical tumors are clinically significant. HPV 18 and HPV LR/negative tumors are associated with poor CRT response. This feasibility study provides a framework for a larger study of intratumoral HPV profiling to predict outcomes in patients with cervical cancer.}, } @article {pmid36799472, year = {2023}, author = {Renall, N and Lawley, B and Vatanen, T and Merz, B and Douwes, J and Corbin, M and Te Morenga, L and Kruger, R and Breier, BH and Tannock, GW}, title = {The fecal microbiotas of women of Pacific and New Zealand European ethnicities are characterized by distinctive enterotypes that reflect dietary intakes and fecal water content.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2178801}, pmid = {36799472}, issn = {1949-0984}, mesh = {Humans ; Female ; Ethnicity ; *Diabetes Mellitus, Type 2 ; New Zealand ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Microbiota ; Obesity ; Eating ; }, abstract = {Obesity is a complex, multifactorial condition that is an important risk factor for noncommunicable diseases including cardiovascular disease and type 2 diabetes. While prevention and management require a healthy and energy balanced diet and adequate physical activity, the taxonomic composition and functional attributes of the colonic microbiota may have a supplementary role in the development of obesity. The taxonomic composition and metabolic capacity of the fecal microbiota of 286 women, resident in Auckland New Zealand, was determined by metagenomic analysis. Associations with BMI (obese, nonobese), body fat composition, and ethnicity (Pacific, n = 125; NZ European women [NZE], n = 161) were assessed using regression analyses. The fecal microbiotas were characterized by the presence of three distinctive enterotypes, with enterotype 1 represented in both Pacific and NZE women (39 and 61%, respectively), enterotype 2 mainly in Pacific women (84 and 16%) and enterotype 3 mainly in NZE women (13 and 87%). Enterotype 1 was characterized mainly by the relative abundances of butyrate producing species, Eubacterium rectale and Faecalibacterium prausnitzii, enterotype 2 by the relative abundances of lactic acid producing species, Bifidobacterium adolescentis, Bifidobacterium bifidum, and Lactobacillus ruminis, and enterotype 3 by the relative abundances of Subdoligranulum sp., Akkermansia muciniphila, Ruminococcus bromii, and Methanobrevibacter smithii. Enterotypes were also associated with BMI, visceral fat %, and blood cholesterol. Habitual food group intake was estimated using a 5 day nonconsecutive estimated food record and a 30 day, 220 item semi-quantitative Food Frequency Questionnaire. Higher intake of 'egg' and 'dairy' products was associated with enterotype 3, whereas 'non-starchy vegetables', 'nuts and seeds' and 'plant-based fats' were positively associated with enterotype 1. In contrast, these same food groups were inversely associated with enterotype 2. Fecal water content, as a proxy for stool consistency/colonic transit time, was associated with microbiota taxonomic composition and gene pools reflective of particular bacterial biochemical pathways. The fecal microbiotas of women of Pacific and New Zealand European ethnicities are characterized by distinctive enterotypes, most likely due to differential dietary intake and fecal consistency/colonic transit time. These parameters need to be considered in future analyses of human fecal microbiotas.}, } @article {pmid36797573, year = {2023}, author = {Jiang, MJ and Tang, HN and Tang, LL}, title = {[Research progress of the application of metagenomics technology in female reproductive tract diseases].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {57}, number = {2}, pages = {172-178}, doi = {10.3760/cma.j.cn112150-20220905-00871}, pmid = {36797573}, issn = {0253-9624}, support = {kq2202415//Natural Science Foundation of Changsha City/ ; }, mesh = {Female ; Humans ; *Microbiota/genetics ; Vagina ; Metagenomics/methods ; }, abstract = {In recent years, many studies have found that vaginal microbiota is closely related to female reproductive tract diseases. However, traditional microbial culture technology has the defects of long culture cycle and most microorganisms cannot be cultured. The development of metagenomics technique has broken the limitations of culture technology, and has been gradually applied to the study of vaginal microorganisms with the characteristics of high throughput, short time, identification of microbial population structure and gene function. It also provides technical support for elucidating the relationship between vaginal microbiota and female reproductive tract diseases. This article mainly introduces the metagenomics techniques and their applications in prevention, screening and diagnosis of common female reproductive tract diseases, and discusses their promising development and limitations to be overcome.}, } @article {pmid36797305, year = {2023}, author = {Linz, DM and Sienkiewicz, N and Struewing, I and Stelzer, EA and Graham, JL and Lu, J}, title = {Metagenomic mapping of cyanobacteria and potential cyanotoxin producing taxa in large rivers of the United States.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {2806}, pmid = {36797305}, issn = {2045-2322}, mesh = {United States ; *Cyanobacteria/genetics ; *Microcystis ; Rivers/microbiology ; Lakes/microbiology ; Microcystins/genetics ; *Microbiota ; }, abstract = {Cyanobacteria and cyanotoxin producing cyanobacterial blooms are a trending focus of current research. Many studies focus on bloom events in lentic environments such as lakes or ponds. Comparatively few studies have explored lotic environments and fewer still have examined the cyanobacterial communities and potential cyanotoxin producers during ambient, non-bloom conditions. Here we used a metagenomics-based approach to profile non-bloom microbial communities and cyanobacteria in 12 major U.S. rivers at multiple time points during the summer months of 2019. Our data show that U.S. rivers possess microbial communities that are taxonomically rich, yet largely consistent across geographic location and time. Within these communities, cyanobacteria often comprise significant portions and frequently include multiple species with known cyanotoxin producing strains. We further characterized these potential cyanotoxin producing taxa by deep sequencing amplicons of the microcystin E (mcyE) gene. We found that rivers containing the highest levels of potential cyanotoxin producing cyanobacteria consistently possess taxa with the genetic potential for cyanotoxin production and that, among these taxa, the predominant genus of origin for the mcyE gene is Microcystis. Combined, these data provide a unique perspective on cyanobacteria and potential cyanotoxin producing taxa that exist in large rivers across the U.S. and can be used to better understand the ambient conditions that may precede bloom events in lotic freshwater ecosystems.}, } @article {pmid36796333, year = {2023}, author = {Venturelli, OS and Wang, HH and Estrela, S and Huang, KC and Ledesma-Amaro, R and Fedorec, AJH and Stecher, B and Lawson, CE and Zarrinpar, A and Guo, CJ and Soyer, OS}, title = {What is the key challenge in engineering microbiomes?.}, journal = {Cell systems}, volume = {14}, number = {2}, pages = {85-90}, doi = {10.1016/j.cels.2023.01.002}, pmid = {36796333}, issn = {2405-4720}, mesh = {*Microbiota ; Engineering ; }, } @article {pmid36796164, year = {2023}, author = {Liu, WH and Chai, LJ and Wang, HM and Lu, ZM and Zhang, XJ and Xiao, C and Wang, ST and Shen, CH and Shi, JS and Xu, ZH}, title = {Bacteria and filamentous fungi running a relay race in Daqu fermentation enable macromolecular degradation and flavor substance formation.}, journal = {International journal of food microbiology}, volume = {390}, number = {}, pages = {110118}, doi = {10.1016/j.ijfoodmicro.2023.110118}, pmid = {36796164}, issn = {1879-3460}, mesh = {Fermentation ; *Bacteria/genetics/metabolism ; Fungi/genetics ; *Microbiota ; Pichia ; Biodiversity ; Alcoholic Beverages/microbiology ; }, abstract = {As the saccharifying and fermentative agent, medium-temperature Daqu (MT-Daqu) plays an irreplaceable role in the production of strong-flavor Baijiu. Numerous studies have focused on the microbial community structure and potential functional microorganisms, however, little is known about the succession of active microbial community and the formation mechanism of community function during MT-Daqu fermentation. In this study, we presented an integrated analysis of metagenomics, metatranscriptomics, and metabonomics covering the whole fermentation process of MT-Daqu to reveal the active microorganisms and their participations in metabolic networks. The results showed that dynamic of metabolites were time-specific, and the metabolites and co-expressed active unigenes were further classified into four clusters according to their accumulation patterns, with members within each cluster displaying a uniform and clear pattern of abundance across fermentation. Based on KEGG enrichment analysis in co-expression clusters and succession of active microbial community, we revealed that Limosilactobacillus, Staphylococcus, Pichia, Rhizopus, and Lichtheimia were metabolically active members at the early stage, and their metabolic activities were conducive to releasing abundant energy to drive multiple basal metabolisms such as carbohydrates and amino acids. Thereafter, during the high temperature period and at the end of fermentation, multiple heat-resistant filamentous fungi were transcriptionally active populations, and they acted as both the saccharifying agents and flavor compound producers, especially aromatic compounds, suggesting their crucial contribution to enzymatic activity and aroma of mature MT-Daqu. Our findings revealed the succession and metabolic functions of the active microbial community, providing a deeper understanding of their contribution to MT-Daqu ecosystem.}, } @article {pmid36795181, year = {2024}, author = {Yao, T and Wang, H and Lin, K and Wang, R and Guo, S and Chen, P and Wu, H and Liu, T and Wang, R}, title = {Exercise-induced microbial changes in preventing type 2 diabetes.}, journal = {Science China. Life sciences}, volume = {67}, number = {5}, pages = {892-899}, pmid = {36795181}, issn = {1869-1889}, mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/prevention & control ; *Gastrointestinal Microbiome ; *Exercise ; Male ; Hand Strength ; Female ; Young Adult ; Adult ; Physical Fitness/physiology ; Prediabetic State/microbiology ; China ; }, abstract = {The metabolic benefits associated with long-term physical activity are well appreciated and growing evidence suggests that it involves the gut microbiota. Here we re-evaluated the link between exercise-induced microbial changes and those associated with prediabetes and diabetes. We found that the relative abundances of substantial amounts of diabetes-associated metagenomic species associated negatively with physical fitness in a Chinese athlete students cohort. We additionally showed that those microbial changes correlated more with handgrip strength, a simple but valuable biomarker suggestive of the diabetes states, than maximum oxygen intake, one of the key surrogates for endurance training. Moreover, the causal relationships among exercise, risks for diabetes, and gut microbiota were explored based on mediation analysis. We propose that the protective roles of exercise against type 2 diabetes are mediated, at least partly, by the gut microbiota.}, } @article {pmid36794885, year = {2023}, author = {Adeleke, BS and Muller, D and Babalola, OO}, title = {A metagenomic lens into endosphere microbial communities, promises, and discoveries.}, journal = {Letters in applied microbiology}, volume = {76}, number = {2}, pages = {}, doi = {10.1093/lambio/ovac030}, pmid = {36794885}, issn = {1472-765X}, support = {123634//National Research Foundation/ ; //TWAS/ ; }, mesh = {*Metagenome ; Metagenomics ; *Microbiota/genetics ; Endophytes ; Plants ; }, abstract = {The word endosphere represents the internal tissues of plants harboring diverse microbes capable of producing active biological products for various biotechnological and agricultural applications. The discreet standalone genes and interdependent association of microbial endophytes with plants can be an underlining factor in predicting their ecological functions. Yet-to-be-cultured endophytic microbes have geared the invention of metagenomics in various environmental studies to determine their structural diversity and functional genes with novel attributes. This review presents an overview of the general concept of metagenomics in microbial endophytic studies. First, the endosphere microbial communities were introduced, followed by metagenomic insights in endosphere biology, a promising technology. Also, the major application of metagenomics and a short brief on DNA stable isotope probing in determining functions and metabolic pathways of microbial metagenome were highlighted. Therefore, the use of metagenomics promises to provide answers to yet-to-be-cultured microbes by unraveling their diversity, functional attributes, and metabolic pathways with prospects in integrated and sustainable agriculture.}, } @article {pmid36794865, year = {2023}, author = {Mukherjee, S and Ovchinnikova, G and Stamatis, D and Li, CT and Chen, IA and Kyrpides, NC and Reddy, TBK}, title = {Standardized naming of microbiome samples in Genomes OnLine Database.}, journal = {Database : the journal of biological databases and curation}, volume = {2023}, number = {}, pages = {}, pmid = {36794865}, issn = {1758-0463}, mesh = {*Software ; *Microbiota/genetics ; Metagenome/genetics ; Metagenomics/methods ; Data Management ; }, abstract = {The power of next-generation sequencing has resulted in an explosive growth in the number of projects aiming to understand the metagenomic diversity of complex microbial environments. The interdisciplinary nature of this microbiome research community, along with the absence of reporting standards for microbiome data and samples, poses a significant challenge for follow-up studies. Commonly used names of metagenomes and metatranscriptomes in public databases currently lack the essential information necessary to accurately describe and classify the underlying samples, which makes a comparative analysis difficult to conduct and often results in misclassified sequences in data repositories. The Genomes OnLine Database (GOLD) (https:// gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute has been at the forefront of addressing this challenge by developing a standardized nomenclature system for naming microbiome samples. GOLD, currently in its twenty-fifth anniversary, continues to enrich the research community with hundreds of thousands of metagenomes and metatranscriptomes with well-curated and easy-to-understand names. Through this manuscript, we describe the overall naming process that can be easily adopted by researchers worldwide. Additionally, we propose the use of this naming system as a best practice for the scientific community to facilitate better interoperability and reusability of microbiome data.}, } @article {pmid36794816, year = {2023}, author = {Derrien, M and Mikulic, N and Uyoga, MA and Chenoll, E and Climent, E and Howard-Varona, A and Nyilima, S and Stoffel, NU and Karanja, S and Kottler, R and Stahl, B and Zimmermann, MB and Bourdet-Sicard, R}, title = {Gut microbiome function and composition in infants from rural Kenya and association with human milk oligosaccharides.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2178793}, pmid = {36794816}, issn = {1949-0984}, mesh = {Humans ; Infant ; *Milk, Human/chemistry ; *Gastrointestinal Microbiome/genetics ; Kenya/epidemiology ; Oligosaccharides ; Bifidobacterium/genetics ; }, abstract = {The gut microbiota evolves rapidly after birth, responding dynamically to environmental factors and playing a key role in short- and long-term health. Lifestyle and rurality have been shown to contribute to differences in the gut microbiome, including Bifidobacterium levels, between infants. We studied the composition, function and variability of the gut microbiomes of 6- to 11-month-old Kenyan infants (n = 105). Shotgun metagenomics showed Bifidobacterium longum to be the dominant species. A pangenomic analysis of B. longum in gut metagenomes revealed a high prevalence of B. longum subsp. infantis (B. infantis) in Kenyan infants (80%), and possible co-existence of this subspecies with B. longum subsp. longum. Stratification of the gut microbiome into community (GMC) types revealed differences in composition and functional features. GMC types with a higher prevalence of B. infantis and abundance of B. breve also had a lower pH and a lower abundance of genes encoding pathogenic features. An analysis of human milk oligosaccharides (HMOs) classified the human milk (HM) samples into four groups defined on the basis of secretor and Lewis polymorphisms revealed a higher prevalence of HM group III (Se+, Le-) (22%) than in most previously studied populations, with an enrichment in 2'-fucosyllactose. Our results show that the gut microbiome of partially breastfed Kenyan infants over the age of six months is enriched in bacteria from the Bifidobacterium community, including B. infantis, and that the high prevalence of a specific HM group may indicate a specific HMO-gut microbiome association. This study sheds light on gut microbiome variation in an understudied population with limited exposure to modern microbiome-altering factors.}, } @article {pmid36792209, year = {2023}, author = {Tsuchida, S and Ueda, A and Kakooza, S and Okubo, T and Wampande, EM and Yamada, T and Ushida, K}, title = {The fecal microbiomes analysis of Marabou storks (Leptoptilos crumenifer) reveals their acclimatization to the feeding environment in the Kampala urban areas, Uganda.}, journal = {The Journal of veterinary medical science}, volume = {85}, number = {4}, pages = {450-458}, pmid = {36792209}, issn = {1347-7439}, mesh = {Animals ; Uganda ; RNA, Ribosomal, 16S/genetics ; *Birds ; Acclimatization ; *Microbiota ; Feces ; }, abstract = {The Marabou stork (Leptoptilos crumenifer) is a typical scavenging bird and adapted to the Savannah environment, where they show a carnivorous feeding style. However, Marabou stork recently penetrated into the city areas and acclimatized to the urban environment, where they modified their feeding habits to an omnivorous type toward more carbohydrate. To reveal their adaptation to the variable feeding customs, this study compared the gut microbiomes and chemical compositions of feces of Marabou storks inhabiting two different locations in peri urban Kampala: one is a slaughter house floc that predicted their original carnivorous feeding, and the other is a landfill floc that adapted more to the omnivorous feeding. 16S rRNA gene sequencing analysis revealed more diverse gut microbiome, more enriched Lactobacilli, and less abundant Peptostreptococci in the landfill flock comparing to the slaughter house flock. Isolation work and predicted metagenome analysis confirmed more diverse Lactobacilli and more enriched functions for carbohydrate metabolism in the landfill flock. In addition, chemical composition of feces revealed higher ammonia in the former, which is consisting with higher Peptostreptococci and their practice of carnivorous feeding. These results highlighted their adaptation to the variable feeding environment, which presumably protects their health and ensure survival of species.}, } @article {pmid36791852, year = {2023}, author = {Zhang, L and Guo, H and Gu, J and Hu, T and Wang, X and Sun, Y and Li, H and Sun, W and Qian, X and Song, Z and Xie, J and An, L}, title = {Metagenomic insights into dietary remodeling of gut microbiota and antibiotic resistome in meat rabbits.}, journal = {The Science of the total environment}, volume = {874}, number = {}, pages = {162006}, doi = {10.1016/j.scitotenv.2023.162006}, pmid = {36791852}, issn = {1879-1026}, mesh = {Humans ; Animals ; Rabbits ; Cattle ; Swine ; *Gastrointestinal Microbiome ; Genes, Bacterial ; Manure ; Anti-Bacterial Agents/pharmacology ; Diet/veterinary ; Lactuca ; }, abstract = {The gut microbiota is a repository of antibiotic resistance genes (ARGs), which may affect the health of humans and animals. The intestinal flora is affected by many factors but it is unclear how the intestinal microflora and antibiotic resistome in rabbits might change under dietary intervention. Feeding with lettuce led to the amplification and transfer of exogenous ARGs in the intestinal flora, but there were no significant differences when fed lettuces grown with different manure types. For example, the lsaC of lettuce fed with bovine, chicken and pig manure without adding organic fertilizer increased by 0.143, 0.151, 0.179 and 0.169 logs respectively after 4 weeks, and the efrB also increased by 0.074, 0.068, 0.079 and 0.106 logs respectively. Network analysis showed that Clostridium_ sensu_ stricto_ 18 was a potential host of type 6 virulence factor genes (VFGs). Mantel analysis showed that ARGs were directly influenced by mobile genetic elements (MGEs) and VFGs. Thus, feeding rabbits lettuce grown with different manure types contribute to the transmission of ARGs by remodeling the intestinal microenvironment. In addition, diet may affect exogenous ARGs to change the intestinal antibiotic resistome and possibly threaten health.}, } @article {pmid36790127, year = {2023}, author = {Salloum, PM and Jorge, F and Dheilly, NM and Poulin, R}, title = {Eco-evolutionary implications of helminth microbiomes.}, journal = {Journal of helminthology}, volume = {97}, number = {}, pages = {e22}, doi = {10.1017/S0022149X23000056}, pmid = {36790127}, issn = {1475-2697}, mesh = {Animals ; *Helminths/genetics ; *Microbiota ; *Parasites ; Host-Parasite Interactions ; Symbiosis ; }, abstract = {The evolution of helminth parasites has long been seen as an interplay between host resistance to infection and the parasite's capacity to bypass such resistance. However, there has recently been an increasing appreciation of the role of symbiotic microbes in the interaction of helminth parasites and their hosts. It is now clear that helminths have a different microbiome from the organisms they parasitize, and sometimes amid large variability, components of the microbiome are shared among different life stages or among populations of the parasite. Helminths have been shown to acquire microbes from their parent generations (vertical transmission) and from their surroundings (horizontal transmission). In this latter case, natural selection has been strongly linked to the fact that helminth-associated microbiota is not simply a random assemblage of the pool of microbes available from their organismal hosts or environments. Indeed, some helminth parasites and specific microbial taxa have evolved complex ecological relationships, ranging from obligate mutualism to reproductive manipulation of the helminth by associated microbes. However, our understanding is still very elementary regarding the net effect of all microbiome components in the eco-evolution of helminths and their interaction with hosts. In this non-exhaustible review, we focus on the bacterial microbiome associated with helminths (as opposed to the microbiome of their hosts) and highlight relevant concepts and key findings in bacterial transmission, ecological associations, and taxonomic and functional diversity of the bacteriome. We integrate the microbiome dimension in a discussion of the evolution of helminth parasites and identify fundamental knowledge gaps, finally suggesting research avenues for understanding the eco-evolutionary impacts of the microbiome in host-parasite interactions in light of new technological developments.}, } @article {pmid36788222, year = {2023}, author = {Gupta, Y and Ernst, AL and Vorobyev, A and Beltsiou, F and Zillikens, D and Bieber, K and Sanna-Cherchi, S and Christiano, AM and Sadik, CD and Ludwig, RJ and Sezin, T}, title = {Impact of diet and host genetics on the murine intestinal mycobiome.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {834}, pmid = {36788222}, issn = {2041-1723}, mesh = {Male ; Female ; Animals ; Mice ; *Mycobiome/genetics ; Ecosystem ; Diet ; Quantitative Trait Loci ; Bacteria/genetics ; Fungi/genetics ; Mammals/genetics ; }, abstract = {The mammalian gut is home to a diverse microbial ecosystem, whose composition affects various physiological traits of the host. Next-generation sequencing-based metagenomic approaches demonstrated how the interplay of host genetics, bacteria, and environmental factors shape complex traits and clinical outcomes. However, the role of fungi in these complex interactions remains understudied. Here, using 228 males and 363 females from an advanced-intercross mouse line, we provide evidence that fungi are regulated by host genetics. In addition, we map quantitative trait loci associated with various fungal species to single genes in mice using whole genome sequencing and genotyping. Moreover, we show that diet and its' interaction with host genetics alter the composition of fungi in outbred mice, and identify fungal indicator species associated with different dietary regimes. Collectively, in this work, we uncover an association of the intestinal fungal community with host genetics and a regulatory role of diet in this ecological niche.}, } @article {pmid36788215, year = {2023}, author = {Robertson, RC and Edens, TJ and Carr, L and Mutasa, K and Gough, EK and Evans, C and Geum, HM and Baharmand, I and Gill, SK and Ntozini, R and Smith, LE and Chasekwa, B and Majo, FD and Tavengwa, NV and Mutasa, B and Francis, F and Tome, J and Stoltzfus, RJ and Humphrey, JH and Prendergast, AJ and Manges, AR}, title = {The gut microbiome and early-life growth in a population with high prevalence of stunting.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {654}, pmid = {36788215}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; 206455/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; R01 HD060338/HD/NICHD NIH HHS/United States ; }, mesh = {Infant ; Child ; Humans ; Child, Preschool ; *Gastrointestinal Microbiome/genetics ; Prevalence ; *HIV Infections ; Growth Disorders/epidemiology ; Water Supply ; }, abstract = {Stunting affects one-in-five children globally and is associated with greater infectious morbidity, mortality and neurodevelopmental deficits. Recent evidence suggests that the early-life gut microbiome affects child growth through immune, metabolic and endocrine pathways. Using whole metagenomic sequencing, we map the assembly of the gut microbiome in 335 children from rural Zimbabwe from 1-18 months of age who were enrolled in the Sanitation, Hygiene, Infant Nutrition Efficacy Trial (SHINE; NCT01824940), a randomized trial of improved water, sanitation and hygiene (WASH) and infant and young child feeding (IYCF). Here, we show that the early-life gut microbiome undergoes programmed assembly that is unresponsive to the randomized interventions intended to improve linear growth. However, maternal HIV infection is associated with over-diversification and over-maturity of the early-life gut microbiome in their uninfected children, in addition to reduced abundance of Bifidobacterium species. Using machine learning models (XGBoost), we show that taxonomic microbiome features are poorly predictive of child growth, however functional metagenomic features, particularly B-vitamin and nucleotide biosynthesis pathways, moderately predict both attained linear and ponderal growth and growth velocity. New approaches targeting the gut microbiome in early childhood may complement efforts to combat child undernutrition.}, } @article {pmid36786595, year = {2023}, author = {Szóstak, N and Handschuh, L and Samelak-Czajka, A and Tomela, K and Schmidt, M and Pruss, Ł and Milanowska-Zabel, K and Kozlowski, P and Philips, A}, title = {Host Factors Associated with Gut Mycobiome Structure.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0098622}, pmid = {36786595}, issn = {2379-5077}, mesh = {Humans ; *Mycobiome ; Cohort Studies ; Fungi/genetics ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Candida ; *Saccharomyces ; Saccharomyces cerevisiae ; }, abstract = {Recent studies revealed a significant role of the gut fungal community in human health. Here, we investigated the content and variation of gut mycobiota among subjects from the European population. We explored the interplay between gut fungi and various host-related sociodemographic, lifestyle, health, and dietary factors. The study included 923 participants. Fecal DNA samples were analyzed by whole-metagenome high-throughput sequencing. Subsequently, fungi taxonomic profiles were determined and accompanied by computational and statistical analyses of the association with 53 host-related factors. Fungal communities were characterized by a high prevalence of Saccharomyces, Candida, and Sporisorium. Ten factors were found to correlate significantly with the overall mycobiota variation. Most were diet related, including the consumption of chips, meat, sodas, sweetening, processed food, and alcohol, followed by age and marital status. Differences in α- and/or β-diversity were also reported for other factors such as body mass index (BMI), job type, autoimmunological diseases, and probiotics. Differential abundance analysis revealed fungal species that exhibited different patterns of changes under specific conditions. The human gut mycobiota is dominated by yeast, including Saccharomyces, Malassezia, and Candida. Although intervolunteer variability was high, several fungal species persisted across most samples, which may be evidence that a core gut mycobiota exists. Moreover, we showed that host-related factors such as diet, age, and marital status influence the variability of gut mycobiota. To our knowledge, this is the first large and comprehensive study of the European cohort in terms of gut mycobiota associations with such an extensive and differentiated host-related set of factors. IMPORTANCE The human gut is inhabited by many organisms, including bacteria and fungi, that may affect human health. However, research on human gut mycobiome is still rare. Moreover, the large European-based cohort study is missing. Here, we analyzed the first large European cohort in terms of gut mycobiota associations with a differentiated host-related set of factors. Our results showed that chips, meat, sodas, sweetening, processed food, beer, alcohol consumption, age, and marital status were associated with the variability of gut mycobiota. Moreover, our analysis revealed changes in abundances at the fungal species level for many investigated factors. Our results can suggest potentially valuable paths for further, narrowly focused research on gut mycobiome and its impact on human health. In the coming era of gut microbiome-based precision medicine, further research into the relationship between different mycobial structures and host-related factors may result in new preventive approaches or therapeutic procedures.}, } @article {pmid36786580, year = {2023}, author = {Gittins, DA and Bhatnagar, S and Hubert, CRJ}, title = {Environmental Selection and Biogeography Shape the Microbiome of Subsurface Petroleum Reservoirs.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0088422}, pmid = {36786580}, issn = {2379-5077}, mesh = {*Petroleum/metabolism ; RNA, Ribosomal, 16S/genetics ; Oil and Gas Fields ; *Microbiota/genetics ; Carbon ; }, abstract = {Petroleum reservoirs within the deep biosphere are extreme environments inhabited by diverse microbial communities and represent biogeochemical hot spots in the subsurface. Despite the ecological and industrial importance of oil reservoir microbiomes, systematic study of core microbial taxa and their associated genomic attributes spanning different environmental conditions is limited. Here, we compile and compare 343 16S rRNA gene amplicon libraries and 25 shotgun metagenomic libraries from oil reservoirs in different parts of the world to test for the presence of core taxa and functions. These oil reservoir libraries do not share any core taxa at the species, genus, family, or order levels, and Gammaproteobacteria was the only taxonomic class detected in all samples. Instead, taxonomic composition varies among reservoirs with different physicochemical characteristics and with geographic distance highlighting environmental selection and biogeography in these deep biosphere habitats. Gene-centric metagenomic analysis reveals a functional core of metabolic pathways including carbon acquisition and energy-yielding strategies consistent with biogeochemical cycling in other subsurface environments. Genes for anaerobic hydrocarbon degradation are observed in a subset of the samples and are therefore not considered to represent core functions in oil reservoirs despite hydrocarbons representing an abundant source of carbon in these deep biosphere settings. Overall, this work reveals common and divergent features of oil reservoir microbiomes that are shaped by and responsive to environmental factors, highlighting controls on subsurface microbial community assembly. IMPORTANCE This comprehensive analysis showcases how environmental selection and geographic distance influence the microbiome of subsurface petroleum reservoirs. We reveal substantial differences in the taxonomy of the inhabiting microbes but shared metabolic function between reservoirs with different in situ temperatures and between reservoirs separated by large distances. The study helps understand and advance the field of deep biosphere science by providing an ecological framework and footing for geologists, chemists, and microbiologists studying these habitats to elucidate major controls on deep biosphere microbial ecology.}, } @article {pmid36782241, year = {2023}, author = {Fontana, F and Longhi, G and Tarracchini, C and Mancabelli, L and Lugli, GA and Alessandri, G and Turroni, F and Milani, C and Ventura, M}, title = {The human gut microbiome of athletes: metagenomic and metabolic insights.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {27}, pmid = {36782241}, issn = {2049-2618}, mesh = {Adult ; Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Metagenome ; Bacteria/genetics ; Athletes ; Feces/microbiology ; Metagenomics ; }, abstract = {BACKGROUND: The correlation between the physical performance of athletes and their gut microbiota has become of growing interest in the past years, since new evidences have emerged regarding the importance of the gut microbiota as a main driver of the health status of athletes. In addition, it has been postulated that the metabolic activity of the microbial population harbored by the large intestine of athletes might influence their physical performances. Here, we analyzed 418 publicly available shotgun metagenomics datasets obtained from fecal samples of healthy athletes and healthy sedentary adults.

RESULTS: This study evidenced how agonistic physical activity and related lifestyle can be associated with the modulation of the gut microbiota composition, inducing modifications of the taxonomic profiles with an enhancement of gut microbes able to produce short-fatty acid (SCFAs). In addition, our analyses revealed a correlation between specific bacterial species and high impact biological synthases (HIBSs) responsible for the generation of a range of microbially driven compounds such vitamin B12, amino acidic derivatives, and other molecules linked to cardiovascular and age-related health-risk reduction.

CONCLUSIONS: Notably, our findings show how subsist an association between competitive athletes, and modulation of the gut microbiota, and how this modulation is reflected in the potential production of microbial metabolites that can lead to beneficial effects on human physical performance and health conditions. Video Abstract.}, } @article {pmid36782070, year = {2023}, author = {Pascal Andreu, V and Augustijn, HE and Chen, L and Zhernakova, A and Fu, J and Fischbach, MA and Dodd, D and Medema, MH}, title = {gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota.}, journal = {Nature biotechnology}, volume = {41}, number = {10}, pages = {1416-1423}, pmid = {36782070}, issn = {1546-1696}, support = {R01 DK101674/DK/NIDDK NIH HHS/United States ; K08 DK110335/DK/NIDDK NIH HHS/United States ; R35 GM142873/GM/NIGMS NIH HHS/United States ; R01 AT011396/AT/NCCIH NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; DP1 DK113598/DK/NIDDK NIH HHS/United States ; DP1 DK113598/DK/NIDDK NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; K08 DK110335/DK/NIDDK NIH HHS/United States ; R35 GM142873/GM/NIGMS NIH HHS/United States ; R01 AT011396/AT/NCCIH NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Feces/microbiology ; Bacteria ; Metabolic Networks and Pathways/genetics ; }, abstract = {The gut microbiota produce hundreds of small molecules, many of which modulate host physiology. Although efforts have been made to identify biosynthetic genes for secondary metabolites, the chemical output of the gut microbiome consists predominantly of primary metabolites. Here we introduce the gutSMASH algorithm for identification of primary metabolic gene clusters, and we used it to systematically profile gut microbiome metabolism, identifying 19,890 gene clusters in 4,240 high-quality microbial genomes. We found marked differences in pathway distribution among phyla, reflecting distinct strategies for energy capture. These data explain taxonomic differences in short-chain fatty acid production and suggest a characteristic metabolic niche for each taxon. Analysis of 1,135 individuals from a Dutch population-based cohort shows that the level of microbiome-derived metabolites in plasma and feces is almost completely uncorrelated with the metagenomic abundance of corresponding metabolic genes, indicating a crucial role for pathway-specific gene regulation and metabolite flux. This work is a starting point for understanding differences in how bacterial taxa contribute to the chemistry of the microbiome.}, } @article {pmid36781125, year = {2023}, author = {Yang, Z and Wang, H and Yang, S and Wang, X and Shen, Q and Ji, L and Zeng, J and Zhang, W and Gong, H and Shan, T}, title = {Virome diversity of ticks feeding on domestic mammals in China.}, journal = {Virologica Sinica}, volume = {38}, number = {2}, pages = {208-221}, pmid = {36781125}, issn = {1995-820X}, mesh = {Animals ; Sheep ; Humans ; *Ticks ; Virome ; Phylogeny ; *Viruses/genetics ; *RNA Viruses/genetics ; Mammals ; *Flaviviridae ; China ; }, abstract = {Ticks are considered the second most common pathogen vectors transmitting a broad range of vital human and veterinary viruses. From 2017 to 2018, 640 ticks were collected in eight different provinces in central and western China. Six species were detected, including H.longicornis, De.everestianus, Rh.microplus, Rh.turanicus, Rh.sanguineous, and Hy.asiaticum. Sixty-four viral metagenomic libraries were constructed on the MiSeq Illumina platform, resulting in 13.44 G (5.88 × 10[7]) of 250-bp-end reads, in which 2,437,941 are viral reads. We found 27 nearly complete genome sequences, including 16 genome sequences encoding entire protein-coding regions (lack of 3' or 5' end non-coding regions) and complete viral genomes, distributed in the arboviral family (Chuviridae, Rhabdoviridae, Nairoviridae, Phenuiviridae, Flaviviridae, Iflaviridae) as well as Parvoviridae and Polyomaviridae that cause disease in mammals and even humans. In addition, 13 virus sequences found in Chuviridae, Nairoviridae, Flaviviridae, Iflaviridae, Hepeviridae, Parvoviridae, and Polyomaviridae were identified as belonging to a new virus species in the identified viral genera. Besides, an epidemiological survey shows a high prevalence (9.38% and 15.63%) of two viruses (Ovine Copiparvovirus and Bovine parvovirus 2) in the tick cohort.}, } @article {pmid36780542, year = {2023}, author = {Plantinga, AM and Kamp, KJ and Wu, Q and Chen, L and Yoo, L and Burr, RL and Cain, KC and Raftery, D and Carnevale Neto, F and Badu, S and So, SY and Savidge, T and Shulman, RJ and Heitkemper, MM}, title = {Exploration of associations among dietary tryptophan, microbiome composition and function, and symptom severity in irritable bowel syndrome.}, journal = {Neurogastroenterology and motility}, volume = {35}, number = {5}, pages = {e14545}, pmid = {36780542}, issn = {1365-2982}, support = {T32 NR016913/NR/NINR NIH HHS/United States ; K23 NR020044/NR/NINR NIH HHS/United States ; R01 NS015547/NS/NINDS NIH HHS/United States ; R01 NR013497/NR/NINR NIH HHS/United States ; R01 NR014479/NR/NINR NIH HHS/United States ; U01 AI042590/AI/NIAID NIH HHS/United States ; P30 DK035816/DK/NIDDK NIH HHS/United States ; R01 DK130517/DK/NIDDK NIH HHS/United States ; P01 AI152999/AI/NIAID NIH HHS/United States ; U01 AI124290/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; K24 AI121296/AI/NIAID NIH HHS/United States ; }, mesh = {Female ; Humans ; Adult ; *Irritable Bowel Syndrome ; Tryptophan ; Diet ; *Microbiota ; *Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: Imbalance of the tryptophan (TRP) pathway may influence symptoms among patients with irritable bowel syndrome (IBS). This study explored relationships among different components that contribute to TRP metabolism (dietary intake, stool metabolite levels, predicted microbiome metabolic capability) in females with IBS and healthy controls (HCs). Within the IBS group, we also investigated relationships between TRP metabolic determinants, Bifidobacterium abundance, and symptoms of IBS.

METHODS: Participants with IBS (Rome III) and HCs completed a 28-day diary of gastrointestinal symptoms and a 3-day food record for TRP intake. They provided a stool sample for shotgun metagenomics, 16 S rRNA analyses, and quantitative measurement of TRP by mass spectrometry.

RESULTS: Our cohort included 115 females, 69 with IBS and 46 HCs, with a mean age of 28.5 years (SD 7.4). TRP intake (p = 0.71) and stool TRP level (p = 0.27) did not differ between IBS and HC. Bifidobacterium abundance was lower in the IBS group than in HCs (p = 0.004). Predicted TRP metabolism gene content was higher in IBS than HCs (FDR-corrected q = 0.006), whereas predicted biosynthesis gene content was lower (q = 0.045). Within the IBS group, there was no association between symptom severity and TRP intake or stool TRP, but there was a significant interaction between Bifidobacterium abundance and TRP intake (q = 0.029) in predicting stool character.

CONCLUSIONS: Dietary TRP intake, microbiome composition, and differences in TRP metabolism constitute a complex interplay of factors that could modulate IBS symptom severity.}, } @article {pmid36780432, year = {2023}, author = {Simmonds, P and Adriaenssens, EM and Zerbini, FM and Abrescia, NGA and Aiewsakun, P and Alfenas-Zerbini, P and Bao, Y and Barylski, J and Drosten, C and Duffy, S and Duprex, WP and Dutilh, BE and Elena, SF and García, ML and Junglen, S and Katzourakis, A and Koonin, EV and Krupovic, M and Kuhn, JH and Lambert, AJ and Lefkowitz, EJ and Łobocka, M and Lood, C and Mahony, J and Meier-Kolthoff, JP and Mushegian, AR and Oksanen, HM and Poranen, MM and Reyes-Muñoz, A and Robertson, DL and Roux, S and Rubino, L and Sabanadzovic, S and Siddell, S and Skern, T and Smith, DB and Sullivan, MB and Suzuki, N and Turner, D and Van Doorslaer, K and Vandamme, AM and Varsani, A and Vasilakis, N}, title = {Four principles to establish a universal virus taxonomy.}, journal = {PLoS biology}, volume = {21}, number = {2}, pages = {e3001922}, pmid = {36780432}, issn = {1545-7885}, support = {MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; U24 AI162625/AI/NIAID NIH HHS/United States ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; U01 AI151807/AI/NIAID NIH HHS/United States ; R24 AI120942/AI/NIAID NIH HHS/United States ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; HHSN272201800013C/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Bacteriophages ; Metagenomics ; Phylogeny ; *Viruses/genetics ; }, abstract = {A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., "arboviruses"), infecting a certain type of host (e.g., "mycoviruses," "bacteriophages") or displaying specific pathogenicity (e.g., "human immunodeficiency viruses"), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.}, } @article {pmid36780083, year = {2023}, author = {Lach, J and Królikowska, K and Baranowska, M and Krupińska, M and Strapagiel, D and Matera-Witkiewicz, A and Stączek, P}, title = {A first insight into the Polish Bochnia Salt Mine metagenome.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {17}, pages = {49551-49566}, pmid = {36780083}, issn = {1614-7499}, support = {POWR.03.02.00-00-I033/16-00//Narodowe Centrum Badań i Rozwoju/ ; WBIOŚ B1811000000038.01//Wydział Biologii i Ochrony Środowiska, Uniwersytet Łódzki/ ; SUB.D250.22.018//Uniwersytet Medyczny im. Piastów Slaskich we Wroclawiu/ ; }, mesh = {Humans ; *Metagenome ; Poland ; RNA, Ribosomal, 16S/genetics ; *Sodium Chloride ; Bacteria/genetics ; Sodium Chloride, Dietary ; Pharmaceutical Preparations ; Metagenomics ; }, abstract = {The Bochnia Salt Mine is one of the oldest mines in Europe. It was established in the thirteenth century, and actively operated until 1990. The mine has been placed on the UNESCO World Heritage List. Previous research describing Polish salt mines has been focused on bioaerosol characteristics and the identification of microorganisms potentially important for human health. The use of Polish salt mines as inhalation chambers for patients of health resorts has also been investigated. Nevertheless, the biodiversity of salt mines associated with biotechnological potential has not been well characterized. The present study paper examines the biodiversity of microorganisms in the Bochnia Salt Mine based on 16S rRNA gene and shotgun sequencing. Biodiversity studies revealed a significantly higher relative abundance of Chlamydiae at the first level of the mine (3.5%) compared to the other levels (< 0.1%). Patescibacteria microorganisms constituted a high percentage (21.6%) in the sample from site RA6. Shotgun sequencing identified 16 unique metagenome-assembled genomes (MAGs). Although one was identified as Halobacterium bonnevillei, the others have not yet been assigned to any species; it is possible that these species may be undescribed. Preliminary analyses of the biotechnological and pharmaceutical potential of microorganisms inhabiting the mine were also performed, and the biosynthetic gene cluster (BGC) profiles and antimicrobial peptide (AMP) coding genes in individual samples were characterized. Hundreds of BGCs and dozens of AMP coding genes were identified in metagenomes. Our findings indicate that Polish salt mines are promising sites for further research aimed at identifying microorganisms that are producers of potentially important substances with biotechnological and pharmaceutical applications.}, } @article {pmid36779183, year = {2023}, author = {Xie, XH and Huang, YJ and Han, GS and Yu, ZG and Ma, YL}, title = {Microbial characterization based on multifractal analysis of metagenomes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1117421}, pmid = {36779183}, issn = {2235-2988}, mesh = {Humans ; Infant ; Infant, Newborn ; Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Ecology ; }, abstract = {INTRODUCTION: The species diversity of microbiomes is a cutting-edge concept in metagenomic research. In this study, we propose a multifractal analysis for metagenomic research.

METHOD AND RESULTS: Firstly, we visualized the chaotic game representation (CGR) of simulated metagenomes and real metagenomes. We find that metagenomes are visualized with self-similarity. Then we defined and calculated the multifractal dimension for the visualized plot of simulated and real metagenomes, respectively. By analyzing the Pearson correlation coefficients between the multifractal dimension and the traditional species diversity index, we obtain that the correlation coefficients between the multifractal dimension and the species richness index and Shannon diversity index reached the maximum value when q = 0, 1, and the correlation coefficient between the multifractal dimension and the Simpson diversity index reached the maximum value when q = 5. Finally, we apply our method to real metagenomes of the gut microbiota of 100 infants who are newborn and 4 and 12 months old. The results show that the multifractal dimensions of an infant's gut microbiomes can distinguish age differences.

CONCLUSION AND DISCUSSION: There is self-similarity among the CGRs of WGS of metagenomes, and the multifractal spectrum is an important characteristic for metagenomes. The traditional diversity indicators can be unified under the framework of multifractal analysis. These results coincided with similar results in macrobial ecology. The multifractal spectrum of infants' gut microbiomes are related to the development of the infants.}, } @article {pmid36778897, year = {2022}, author = {Delmont, TO and Gaia, M and Hinsinger, DD and Frémont, P and Vanni, C and Fernandez-Guerra, A and Eren, AM and Kourlaiev, A and d'Agata, L and Clayssen, Q and Villar, E and Labadie, K and Cruaud, C and Poulain, J and Da Silva, C and Wessner, M and Noel, B and Aury, JM and , and de Vargas, C and Bowler, C and Karsenti, E and Pelletier, E and Wincker, P and Jaillon, O}, title = {Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean.}, journal = {Cell genomics}, volume = {2}, number = {5}, pages = {100123}, pmid = {36778897}, issn = {2666-979X}, abstract = {Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years.}, } @article {pmid36774720, year = {2023}, author = {Nguyen, VH and Wemheuer, B and Song, W and Bennett, H and Palladino, G and Burgsdorf, I and Sizikov, S and Steindler, L and Webster, NS and Thomas, T}, title = {Functional characterization and taxonomic classification of novel gammaproteobacterial diversity in sponges.}, journal = {Systematic and applied microbiology}, volume = {46}, number = {2}, pages = {126401}, doi = {10.1016/j.syapm.2023.126401}, pmid = {36774720}, issn = {1618-0984}, mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Bacteria ; Metagenome ; *Microbiota ; Sulfur Compounds/metabolism ; }, abstract = {Sponges harbour exceptionally diverse microbial communities, whose members are largely uncultured. The class Gammaproteobacteria often dominates the microbial communities of various sponge species, but most of its diversity remains functional and taxonomically uncharacterised. Here we reconstructed and characterised 32 metagenome-assembled genomes (MAGs) derived from three sponge species. These MAGs represent ten novel species and belong to seven orders, of which one is new. We propose nomenclature for all these taxa. These new species comprise sponge-specific bacteria with varying levels of host specificity. Functional gene profiling highlights significant differences in metabolic capabilities across the ten species, though each also often exhibited a large degree of metabolic diversity involving various nitrogen- and sulfur-based compounds. The genomic features of the ten species suggest they have evolved to form symbiotic interaction with their hosts or are well-adapted to survive within the sponge environment. These Gammaproteobacteria are proposed to scavenge substrates from the host environment, including metabolites or cellular components of the sponge. Their diverse metabolic capabilities may allow for efficient cycling of organic matter in the sponge environment, potentially to the benefit of the host and other symbionts.}, } @article {pmid36774423, year = {2023}, author = {Aboshady, HM and Choury, A and Montout, L and Félicité, Y and Godard, X and Bambou, JC}, title = {Metagenome reveals caprine abomasal microbiota diversity at early and late stages of Haemonchus contortus infection.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {2450}, pmid = {36774423}, issn = {2045-2322}, mesh = {Animals ; Sheep ; Metagenome ; *Haemonchus/genetics ; Goats ; *Microbiota/genetics ; Abomasum ; *Haemonchiasis/veterinary/parasitology ; *Sheep Diseases/parasitology ; }, abstract = {Haemonchus contortus is one of the most detrimental gastrointestinal nematode parasites for small ruminants, especially in tropics and subtropics. Gastrointestinal nematode and microbiota share the same microhabitat; thus they interact with each other and their host. Metagenomics tools provide a promising way to examine the alterations in the gastric microbial composition induces by gastrointestinal parasites. In this study, we used metagenomics tools to characterize the impact of H. contortus infection on the caprine abomasal microbiota at early and late stage of infection and compared it with non-infected control. Our results showed that H. contortus infection caused a significant increase in abomasal pH at early (7 days post-infection) and late stage of infection (56 days post-infection). The analysis of alpha and beta diversity showed that the microbiota diversity both in number and in proportion was significantly affected at early and late stage of infection. All microbiota classes are impacted by H. contortus infection but Clostridia and Bacteroidia are more concerned. In infected animals, the genera Prevotella decreased at 7 and 56 days post-infection. Here we showed that the abomasal microbiota was significantly affected early after H. contortus infection, and these changes persist at late stage of the infection.}, } @article {pmid36773904, year = {2023}, author = {Samson, R and Rajput, V and Yadav, R and Shah, M and Dastager, S and Khairnar, K and Dharne, M}, title = {Spatio-temporal variation of the microbiome and resistome repertoire along an anthropogenically dynamic segment of the Ganges River, India.}, journal = {The Science of the total environment}, volume = {872}, number = {}, pages = {162125}, doi = {10.1016/j.scitotenv.2023.162125}, pmid = {36773904}, issn = {1879-1026}, mesh = {*Genes, Bacterial ; Rivers/chemistry ; Bacteria/genetics ; *Microbiota ; India ; Metals ; Anti-Bacterial Agents ; }, abstract = {Aquatic ecosystems are regarded as a hub of antibiotic and metal resistance genes. River Ganges is a unique riverine system in India with socio-cultural and economic significance. However, it remains underexplored for its microbiome and associated resistomes along its anthropogenically impacted course. The present study utilized a nanopore sequencing approach to depict the microbial community structure in the sediments of the river Ganges harboring antibiotic and metal resistance genes (A/MRGs) in lower stretches known for anthropogenic impact. Comprehensive microbiome analyses revealed resistance genes against 23 different types of metals and 28 classes of antibiotics. The most dominant ARG category was multidrug resistance, while the most prevalent MRGs conferred resistance against copper and zinc. Seasonal differences dismally affected the microbiota of the Ganges. However, resistance genes for fosmidomycin and tetracycline varied with season ANOVA, p < 0.05. Interestingly, 333 and 334 ARG subtypes were observed at all the locations in pre-monsoon and post-monsoon, respectively. The taxa associated with the dominant ARGs and MRGs were Pseudomonas and Burkholderia, which are important nosocomial pathogens. A substantial phage diversity for pathogenic and putrefying bacteria at all locations attracts attention for its use to tackle the dissemination of antibiotic and metal-resistant bacteria. This study suggests the accumulation of antibiotics and metals as the driving force for the emergence of resistance genes and the affiliated bacteria trafficking them. The present metagenomic assessment highlights the need for comprehensive, long-term biological and physicochemical monitoring and mitigation strategies toward the contaminants associated with ARGs and MRGs in this nationally important river.}, } @article {pmid36772850, year = {2023}, author = {Kong, C and Liu, G and Kalady, MF and Jin, T and Ma, Y}, title = {Dysbiosis of the stool DNA and RNA virome in Crohn's disease.}, journal = {Journal of medical virology}, volume = {95}, number = {2}, pages = {e28573}, doi = {10.1002/jmv.28573}, pmid = {36772850}, issn = {1096-9071}, mesh = {Humans ; *Crohn Disease/microbiology ; Virome ; Dysbiosis ; DNA Replication ; DNA, Viral/genetics ; Virus Replication ; *Viruses/genetics ; *Bacteriophages/genetics ; Bacteria/genetics ; }, abstract = {Pathogenesis of Crohn's disease (CD) relates to gut microbiome dysbiosis. However, less is known about the viral microbiome, consisting of bacteriophages and eukaryotic viruses, in CD. Here, we profiled the stool virome, viral functions, and viral-bacterial correlations that involved in CD pathogenesis. Metagenomics and metaviromics with novel viral identification and data analysis workflow were performed on stool of non-CD household controls, CD flare and remission patients. Both bacteriome and DNA/RNA virome alterations were characterized and correlated with disease status. There was a decreased diversity and extreme heterogeneity in both DNA and RNA virome in CD. We observed CD-specific dysbiosis in virome, particularly the prominent DNA eukaryotic Torque teno virus (TTV), disease-associated Faecalibacterium phage and Escherichia phage, and RNA tomato diet-related virus in CD, while some diverse prokaryotic viruses were more abundant in healthy subjects. Compared with the remission, inflammation-associated eukaryotic TTV and prokaryotic Staphylococcus phages were predominated in the flare, and displayed a link with complications and multiple therapeutic approaches. Multiple viral functions, particularly functions of viral DNA replication, integration and modification as well as the eukaryotic TTV-related capsid protein, were markedly enriched in CD. Furthermore, the virus-bacteria interactions became more specialized in CD, and the combination of bacteriome and virome composition provided better classification between CD and health. Our study presents a global view of the comprehensive viral component change in the CD patients' gut microbiome, and highlights the great potential of virome biomarkers in pathogenesis and accurate diagnostics of CD risk and disease status.}, } @article {pmid36771402, year = {2023}, author = {Leech, SM and Gilbert, MC and Clifton, VL and Kumar, S and Rae, KM and Borg, D and Dekker Nitert, M}, title = {Insufficient Evidence of a Breastmilk Microbiota at Six-Weeks Postpartum: A Pilot Study.}, journal = {Nutrients}, volume = {15}, number = {3}, pages = {}, pmid = {36771402}, issn = {2072-6643}, support = {RTP scholarship//Australian Government Research Training Program/ ; KMR//Mater Foundation and Equity Trustees/ ; RSP fellowship to DJB//University of Queensland/ ; QFC funding//Mater Foundation, The University of Queensland, Giffith University, QUT/ ; 75002_GC_20//The Lott, Golden Casket/ ; 1033//Brisbane Diamantina Health Partners/ ; 2041//Perpetual Impact Funding/ ; 2441//Advance Queensland/ ; equipment support//Qiagen/ ; Equipment support//Microba/ ; }, mesh = {Infant ; Pregnancy ; Humans ; Female ; *Milk, Human/microbiology ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Evidence Gaps ; *Microbiota/genetics ; Postpartum Period ; Mouth ; }, abstract = {Breastmilk is thought to influence the infant gut by supplying prebiotics in the form of human milk oligosaccharides and potentially seeding the gut with breastmilk microbes. However, the presence of a breastmilk microbiota and origins of these microbes are still debated. As a pilot study, we assessed the microbes present in expressed breastmilk at six-weeks postpartum using shotgun metagenomic sequencing in a heterogenous cohort of women who delivered by vaginal (n = 8) and caesarean delivery (n = 8). In addition, we estimated the microbial load of breastmilk at six-weeks post-partum with quantitative PCR targeting the 16S rRNA gene. Breastmilk at six-weeks postpartum had a low microbial mass, comparable with PCR no-template and extraction controls. Microbes identified through metagenomic sequencing were largely consistent with skin and oral microbes, with four samples returning no identifiable bacterial sequences. Our results do not provide convincing evidence for the existence of a breastmilk microbiota at six-weeks postpartum. It is more likely that microbes present in breastmilk are sourced by ejection from the infant's mouth and from surrounding skin, as well as contamination during sampling and processing.}, } @article {pmid36771397, year = {2023}, author = {Seo, H and Yoon, SY and Ul-Haq, A and Jo, S and Kim, S and Rahim, MA and Park, HA and Ghorbanian, F and Kim, MJ and Lee, MY and Kim, KH and Lee, N and Won, JH and Song, HY}, title = {The Effects of Iron Deficiency on the Gut Microbiota in Women of Childbearing Age.}, journal = {Nutrients}, volume = {15}, number = {3}, pages = {}, pmid = {36771397}, issn = {2072-6643}, support = {2021R1G1A1094322//National Research Foundation of Korea/ ; 20018499//Technology Innovation program/ ; Soonchunhyang University Research Fund.//Soonchunhyang University/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; *Iron Deficiencies ; *Anemia, Iron-Deficiency/complications/drug therapy ; Iron/therapeutic use ; *Microbiota ; }, abstract = {Iron deficiency anemia (IDA) is the most prevalent and common nutritional deficiency worldwide and is a global health problem with significant risk, particularly among women of reproductive age. Oral iron supplementation is the most widely used and cost-effective treatment for iron deficiency and IDA. However, there are limitations regarding side effects such as enteritis, treatment compliance, and bioavailability. Intestinal microbiome characteristic research has been recently conducted to overcome these issues, but more is needed. Against this background, a metagenomics study on the 16S gene in the feces of young women vulnerable to IDA was conducted. As a result of analyzing 16 normal subjects and 15 IDA patients, significant differences in bacterial community distribution were identified. In particular, a significant decrease in Faecalibacterium was characteristic in IDA patients compared with normal subjects. Furthermore, in the case of patients who recovered from IDA following iron supplementation treatment, it was confirmed that Faecalibacterium significantly recovered to normal levels. However, no significance in beta diversity was seen compared with before treatment. There were also no differences in the beta diversity results between the recovered and normal subjects. Therefore, intestinal dysbiosis during the disease state was considered to be restored as IDA improved. Although the results were derived from a limited number of subjects and additional research is needed, the results of this study are expected to be the basis for developing treatment and prevention strategies based on host-microbiome crosstalk in IDA.}, } @article {pmid36771396, year = {2023}, author = {Gow, ML and Chua, XY and El-Omar, E and Susic, D and Henry, A}, title = {Relationship between Diet Quality and Maternal Stool Microbiota in the MUMS Australian Pregnancy Cohort.}, journal = {Nutrients}, volume = {15}, number = {3}, pages = {}, pmid = {36771396}, issn = {2072-6643}, support = {UNSW RG188959//St George and Sutherland Medical Research Foundation/ ; N/A//The Royal Australian and New Zealand College of Obstetricians and Gynaecologists/ ; APP1158876//National Health and Medical Research Council/ ; }, mesh = {Humans ; Pregnancy ; Female ; Cohort Studies ; Australia ; *Diet ; Postpartum Period ; *Microbiota ; }, abstract = {Dietary intake during pregnancy may influence the antenatal microbiome, which is proposed to impact maternal and infant health during the pregnancy and beyond. The aim of this sub-study was to examine associations between dietary intake and microbiota diversity during pregnancy using whole metagenomic sequencing and examine associations in low-risk versus high-risk pregnancies, as well as complicated versus uncomplicated pregnancies. Pregnancy data were analysed from women participating in the MUMS cohort study in Sydney, Australia (women followed from trimester 1 of pregnancy to 1-year postpartum), who had dietary intake data at either trimester 1 or 3, assessed using the Australian Eating Survey, and a matched stool sample (n = 86). Correlations of microbial alpha diversity with dietary intake data were determined using the repeated-measures correlation, rmcorr, in R. In the combined cohort, no associations were found between diet quality or diet composition and microbial alpha diversity or beta diversity. However, trends in our analysis suggested that dietary intake of specific macro- and micronutrients may influence microbial diversity differently, depending on particular pregnancy conditions. Our findings suggest that dietary intake during pregnancy may have a variable influence on the maternal microbiota, unique to the individual maternal pregnancy phenotype. More research is needed to disentangle these associations.}, } @article {pmid36771360, year = {2023}, author = {Duysburgh, C and Verstrepen, L and Broeck, MVD and Righetto, Z and Perez, M}, title = {Investigation of Enterogermina's Protective and Restorative Mechanisms on the Gut Microbiota with PPI, Using SHIME Technology.}, journal = {Nutrients}, volume = {15}, number = {3}, pages = {}, pmid = {36771360}, issn = {2072-6643}, support = {N/A//Sanofi/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Dysbiosis/chemically induced ; Proton Pump Inhibitors/adverse effects ; *Microbiota ; Feces ; *Probiotics ; }, abstract = {Proton pump inhibitors (PPIs) are commonly prescribed medications associated with changes in the gut microbiome and dysbiosis when used long-term. Probiotics, such as Enterogermina[®] (containing four strains of Bacillus clausii) reduce side effects from triple therapy with PPI+antibiotics. We aim to assess the ability of this probiotic in preventing and/or treating the dysbiosis induced by PPI use. Faecal samples from six healthy donors were used to colonise a Triple-Mucosal-Simulator of the Human Intestinal Microbial Ecosystem[®] model with added ileal compartment. Changes in the microbial community composition and metabolite production were measured for PPI alone (control), PPI+Enterogermina (preventative), and Enterogermina treatment after PPI (curative). Differences were assessed by one-way ANOVA with Tukey's multiple comparisons test. The model was shown to replicate some of the effects of long-term PPI use. There were significant changes in microbial diversity and an increase in butyrate levels in the preventative and curative arms, indicative of a beneficial effect to gut health. Probiotic use countered some of the effects of PPI use: Streptococcus bovis levels increased in the control arm but reduced following probiotic treatment. These results show that probiotic treatment with B. clausii may have beneficial effects on the gut microbiota following PPI treatment.}, } @article {pmid36769278, year = {2023}, author = {Tiew, PY and Meldrum, OW and Chotirmall, SH}, title = {Applying Next-Generation Sequencing and Multi-Omics in Chronic Obstructive Pulmonary Disease.}, journal = {International journal of molecular sciences}, volume = {24}, number = {3}, pages = {}, pmid = {36769278}, issn = {1422-0067}, support = {Clinician Scientist Award (MOH-000710)//Singapore Ministry of Health's National Medical Research Council/ ; Open Fund-Individual Research Grant (MOH-000955)//Singapore Ministry of Health's National Medical Research Council/ ; }, mesh = {Humans ; Multiomics ; *Pulmonary Disease, Chronic Obstructive/diagnosis/genetics/therapy ; *Microbiota/genetics ; Host Microbial Interactions ; High-Throughput Nucleotide Sequencing ; }, abstract = {Microbiomics have significantly advanced over the last decade, driven by the widespread availability of next-generation sequencing (NGS) and multi-omic technologies. Integration of NGS and multi-omic datasets allow for a holistic assessment of endophenotypes across a range of chronic respiratory disease states, including chronic obstructive pulmonary disease (COPD). Valuable insight has been attained into the nature, function, and significance of microbial communities in disease onset, progression, prognosis, and response to treatment in COPD. Moving beyond single-biome assessment, there now exists a growing literature on functional assessment and host-microbe interaction and, in particular, their contribution to disease progression, severity, and outcome. Identifying specific microbes and/or metabolic signatures associated with COPD can open novel avenues for therapeutic intervention and prognosis-related biomarkers. Despite the promise and potential of these approaches, the large amount of data generated by such technologies can be challenging to analyze and interpret, and currently, there remains a lack of standardized methods to address this. This review outlines the current use and proposes future avenues for the application of NGS and multi-omic technologies in the endophenotyping, prognostication, and treatment of COPD.}, } @article {pmid36769093, year = {2023}, author = {Dora, D and Bokhari, SMZ and Aloss, K and Takacs, P and Desnoix, JZ and Szklenárik, G and Hurley, PD and Lohinai, Z}, title = {Implication of the Gut Microbiome and Microbial-Derived Metabolites in Immune-Related Adverse Events: Emergence of Novel Biomarkers for Cancer Immunotherapy.}, journal = {International journal of molecular sciences}, volume = {24}, number = {3}, pages = {}, pmid = {36769093}, issn = {1422-0067}, support = {OTKA #124652; OTKA #129664; OTKA #142287//Hungarian National Research, Development and Innovation Office/ ; }, mesh = {Humans ; *Antineoplastic Agents, Immunological/therapeutic use ; Immune Checkpoint Inhibitors/adverse effects ; *Gastrointestinal Microbiome ; *Neoplasms/drug therapy ; *Melanoma/drug therapy ; *Drug-Related Side Effects and Adverse Reactions/etiology ; Immunotherapy/adverse effects/methods ; Biomarkers ; }, abstract = {Immune checkpoint inhibitors (ICIs) have changed how we think about tumor management. Combinations of anti-programmed death ligand-1 (PD-L1) immunotherapy have become the standard of care in many advanced-stage cancers, including as a first-line therapy. Aside from improved anti-tumor immunity, the mechanism of action of immune checkpoint inhibitors (ICIs) exposes a new toxicity profile known as immune-related adverse effects (irAEs). This novel toxicity can damage any organ, but the skin, digestive and endocrine systems are the most frequently afflicted. Most ICI-attributed toxicity symptoms are mild, but some are severe and necessitate multidisciplinary side effect management. Obtaining knowledge on the various forms of immune-related toxicities and swiftly changing treatment techniques to lower the probability of experiencing severe irAEs has become a priority in oncological care. In recent years, there has been a growing understanding of an intriguing link between the gut microbiome and ICI outcomes. Multiple studies have demonstrated a connection between microbial metagenomic and metatranscriptomic patterns and ICI efficacy in malignant melanoma, lung and colorectal cancer. The immunomodulatory effect of the gut microbiome can have a real effect on the biological background of irAEs as well. Furthermore, specific microbial signatures and metabolites might be associated with the onset and severity of toxicity symptoms. By identifying these biological factors, novel biomarkers can be used in clinical practice to predict and manage potential irAEs. This comprehensive review aims to summarize the clinical aspects and biological background of ICI-related irAEs and their potential association with the gut microbiome and metabolome. We aim to explore the current state of knowledge on the most important and reliable irAE-related biomarkers of microbial origin and discuss the intriguing connection between ICI efficacy and toxicity.}, } @article {pmid36768851, year = {2023}, author = {Nunzi, E and Mezzasoma, L and Bellezza, I and Zelante, T and Orvietani, P and Coata, G and Giardina, I and Sagini, K and Manni, G and Di Michele, A and Gargaro, M and Talesa, VN and Di Renzo, GC and Fallarino, F and Romani, R}, title = {Microbiota-Associated HAF-EVs Regulate Monocytes by Triggering or Inhibiting Inflammasome Activation.}, journal = {International journal of molecular sciences}, volume = {24}, number = {3}, pages = {}, pmid = {36768851}, issn = {1422-0067}, support = {GGP17094/TI_/Telethon/Italy ; }, mesh = {Humans ; Female ; Pregnancy ; Monocytes/metabolism ; Inflammasomes/metabolism ; Amniotic Fluid ; Proteomics ; *Extracellular Vesicles/metabolism ; *Microbiota ; Endotoxins/metabolism ; }, abstract = {In pregnancy, human amniotic fluid extracellular vesicles (HAF-EVs) exert anti-inflammatory effects on T cells and on monocytes, supporting their immunoregulatory roles. The specific mechanisms are still not completely defined. The aim of this study was to investigate the ability of HAF-EVs, isolated from pregnant women who underwent amniocentesis and purified by gradient ultracentrifugation, to affect inflammasome activation in the human monocytes. Proteomic studies revealed that HAF-EV samples expressed several immunoregulatory molecules as well as small amounts of endotoxin. Surprisingly, metagenomic analysis shows the presence of specific bacterial strain variants associated with HAF-EVs as potential sources of the endotoxin. Remarkably, we showed that a single treatment of THP-1 cells with HAF-EVs triggered inflammasome activation, whereas the same treatment followed by LPS and ATP sensitization prevented inflammasome activation, a pathway resembling monocyte refractories. A bioinformatics analysis of microbiota-HAF-EVs functional pathways confirmed the presence of enzymes for endotoxin biosynthesis as well as others associated with immunoregulatory functions. Overall, these data suggest that HAF-EVs could serve as a source of the isolation of a specific microbiota during early pregnancy. Moreover, HAF-EVs could act as a novel system to balance immune training and tolerance by modulating the inflammasome in monocytes or other cells.}, } @article {pmid36768793, year = {2023}, author = {Kaplina, A and Kononova, S and Zaikova, E and Pervunina, T and Petrova, N and Sitkin, S}, title = {Necrotizing Enterocolitis: The Role of Hypoxia, Gut Microbiome, and Microbial Metabolites.}, journal = {International journal of molecular sciences}, volume = {24}, number = {3}, pages = {}, pmid = {36768793}, issn = {1422-0067}, support = {22-25-00484//Russian Science Foundation/ ; }, mesh = {Infant ; Pregnancy ; Female ; Infant, Newborn ; Humans ; Infant, Premature ; *Gastrointestinal Microbiome ; *Enterocolitis, Necrotizing/etiology ; *Infant, Newborn, Diseases ; Fetal Growth Retardation ; Hypoxia ; }, abstract = {Necrotizing enterocolitis (NEC) is a life-threatening disease that predominantly affects very low birth weight preterm infants. Development of NEC in preterm infants is accompanied by high mortality. Surgical treatment of NEC can be complicated by short bowel syndrome, intestinal failure, parenteral nutrition-associated liver disease, and neurodevelopmental delay. Issues surrounding pathogenesis, prevention, and treatment of NEC remain unclear. This review summarizes data on prenatal risk factors for NEC, the role of pre-eclampsia, and intrauterine growth retardation in the pathogenesis of NEC. The role of hypoxia in NEC is discussed. Recent data on the role of the intestinal microbiome in the development of NEC, and features of the metabolome that can serve as potential biomarkers, are presented. The Pseudomonadota phylum is known to be associated with NEC in preterm neonates, and the role of other bacteria and their metabolites in NEC pathogenesis is also discussed. The most promising approaches for preventing and treating NEC are summarized.}, } @article {pmid36768705, year = {2023}, author = {Timmers, ER and Swarte, JC and Gacesa, R and Björk, JR and Weersma, RK and Tijssen, MAJ and de Koning, TJ and Harmsen, HJM and Niezen-Koning, KE}, title = {Gut Microbiome Composition in Dystonia Patients.}, journal = {International journal of molecular sciences}, volume = {24}, number = {3}, pages = {}, pmid = {36768705}, issn = {1422-0067}, mesh = {Humans ; *Dystonia ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Mental Disorders ; *Dystonic Disorders ; *Dyskinesias ; }, abstract = {Dystonia is a movement disorder in which patients have involuntary abnormal movements or postures. Non-motor symptoms, such as psychiatric symptoms, sleep problems and fatigue, are common. We hypothesise that the gut microbiome might play a role in the pathophysiology of the (non-)motor symptoms in dystonia via the gut-brain axis. This exploratory study investigates the composition of the gut microbiome in dystonia patients compared to healthy controls. Furthermore, the abundance of neuro-active metabolic pathways, which might be implicated in the (non-)motor symptoms, was investigated. We performed both metagenomic and 16S rRNA sequencing on the stool samples of three subtypes of dystonia (27 cervical dystonia, 20 dopa-responsive dystonia and 24 myoclonus-dystonia patients) and 25 controls. While microbiome alpha and beta diversity was not different between dystonia patients and controls, dystonia patients had higher abundances of Ruminococcus torques and Dorea formicigenerans, and a lower abundance of Butyrivibrio crossotus compared to controls. For those with dystonia, non-motor symptoms and the levels of neurotransmitters in plasma explained the variance in the gut microbiome composition. Several neuro-active metabolic pathways, especially tryptophan degradation, were less abundant in the dystonia patients compared to controls. This suggest that the gut-brain axis might be involved in the pathophysiology of dystonia. Further studies are necessary to confirm our preliminary findings.}, } @article {pmid36768286, year = {2023}, author = {Dionisio, F and Domingues, CPF and Rebelo, JS and Monteiro, F and Nogueira, T}, title = {The Impact of Non-Pathogenic Bacteria on the Spread of Virulence and Resistance Genes.}, journal = {International journal of molecular sciences}, volume = {24}, number = {3}, pages = {}, pmid = {36768286}, issn = {1422-0067}, mesh = {Humans ; Virulence/genetics ; *Bacteria/genetics ; Anti-Bacterial Agents ; *Microbiota/genetics ; }, abstract = {This review discusses the fate of antimicrobial resistance and virulence genes frequently present among microbiomes. A central concept in epidemiology is the mean number of hosts colonized by one infected host in a population of susceptible hosts: R0. It characterizes the disease's epidemic potential because the pathogen continues its propagation through susceptible hosts if it is above one. R0 is proportional to the average duration of infections, but non-pathogenic microorganisms do not cause host death, and hosts do not need to be rid of them. Therefore, commensal bacteria may colonize hosts for prolonged periods, including those harboring drug resistance or even a few virulence genes. Thus, their R0 is likely to be (much) greater than one, with peculiar consequences for the spread of virulence and resistance genes. For example, computer models that simulate the spread of these genes have shown that their diversities should correlate positively throughout microbiomes. Bioinformatics analysis with real data corroborates this expectation. Those simulations also anticipate that, contrary to the common wisdom, human's microbiomes with a higher diversity of both gene types are the ones that took antibiotics longer ago rather than recently. Here, we discuss the mechanisms and robustness behind these predictions and other public health consequences.}, } @article {pmid36768285, year = {2023}, author = {Zaragoza-García, O and Castro-Alarcón, N and Pérez-Rubio, G and Falfán-Valencia, R and Briceño, O and Navarro-Zarza, JE and Parra-Rojas, I and Tello, M and Guzmán-Guzmán, IP}, title = {Serum Levels of IFABP2 and Differences in Lactobacillus and Porphyromonas gingivalis Abundance on Gut Microbiota Are Associated with Poor Therapeutic Response in Rheumatoid Arthritis: A Pilot Study.}, journal = {International journal of molecular sciences}, volume = {24}, number = {3}, pages = {}, pmid = {36768285}, issn = {1422-0067}, mesh = {Female ; Humans ; *Antirheumatic Agents/therapeutic use ; *Arthritis, Rheumatoid/drug therapy/genetics/metabolism ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/genetics/physiology ; Interleukin-17 ; Pilot Projects ; Porphyromonas gingivalis ; Tumor Necrosis Factor-alpha/therapeutic use ; *Lactobacillus ; Intestines/microbiology/physiopathology ; Cell Membrane Permeability ; }, abstract = {Intestinal dysbiosis is related to the physiopathology and clinical manifestation of rheumatoid arthritis (RA) and the response to pharmacologic treatment. The objectives of this study were (1) to analyze the effect of conventional synthetic disease modifying anti-rheumatic drugs (csDMARDs) on the abundance of gut microbiota's bacteria; (2) to evaluate the relationship between the differences in microbial abundance with the serum levels of intestinal fatty-acid binding protein 2 (IFABP2), cytokines, and the response phenotype to csDMARDs therapy in RA. A cross-sectional study was conducted on 23 women diagnosed with RA. The abundance of bacteria in gut microbiota was determined with qPCR. The ELISA technique determined serum levels of IFABP2, TNF-α, IL-10, and IL-17A. We found that the accumulated dose of methotrexate or prednisone is negatively associated with the abundance of Lactobacillus but positively associated with the abundance of Bacteroides fragilis. The Lactobacillus/Porphyromonas gingivalis ratio was associated with the Disease Activity Score-28 for RA with Erythrocyte Sedimentation Rate (DAS28-ESR) (r = 0.778, p = 0.030) and with the levels of IL-17A (r = 0.785, p = 0.027) in the group treated with csDMARD. Moreover, a relation between the serum levels of IFABP2 and TNF-α (r = 0.593, p = 0.035) was observed in the group treated with csDMARD. The serum levels of IFABP2 were higher in patients with secondary non-response to csDMARDs therapy. In conclusion, our results suggest that the ratios of gut microbiota's bacteria and intestinal permeability seems to establish the preamble for therapeutic secondary non-response in RA.}, } @article {pmid36764550, year = {2023}, author = {Jiang, W and Hu, C and Chen, Y and Li, Y and Sun, X and Wu, H and Yang, R and Tang, Y and Niu, F and Wei, W and Sun, C and Han, T}, title = {Dysregulation of the microbiota-brain axis during long-term exposure to polystyrene nanoplastics in rats and the protective role of dihydrocaffeic acid.}, journal = {The Science of the total environment}, volume = {874}, number = {}, pages = {162101}, doi = {10.1016/j.scitotenv.2023.162101}, pmid = {36764550}, issn = {1879-1026}, mesh = {Rats ; Animals ; Microplastics/metabolism ; Polystyrenes/metabolism ; *Microbiota ; *Drug-Related Side Effects and Adverse Reactions ; *Water Pollutants, Chemical/metabolism ; Brain/metabolism ; *Nanoparticles/chemistry ; Mammals/metabolism ; }, abstract = {Polystyrene nano-plastics (PS-NPs) can be accumulated in the food chain and can penetrate biological barriers to affect multiple physiological functions. However, the adverse effects of nano-plastics on mammals and the underlying mechanism still remain unknown. To fill the gaps, our study administrated low-dose PS-NPs (50 and 100 μg/L) for 24 consecutive weeks in rats. Behavioral and morphological evaluations were performed to assess the neurobehavoirs. A combined analysis of multiple omics was used to evaluate the dysfunctions of the gut-microbe-brain axis. After dihydrochalcone(NHDC) treatment in the PS-NPs rat model, the inflammation response and apoptosis process were assessed and proteomics was used to explore the underlying mechanism. Our results indicated that long-term exposure to low-dose PS-NPs could induce abnormal neurobehaviors and amygdaloid nucleus impairment, and stimulate inflammatory responses and apoptosis. Metagenomics results revealed that four microbial phyla including Proteobacteria, Firmicutes, Defferibacteres, and Bacteroidetes changed significantly compared to the control. Targeted metabolomics analysis in the feces showed alteration of 122 metabolites induced by the PS-NPs exposure, among which the content of dihydrocaffeic acid was significantly associated with the different microbial genera and pivotal differential metabolites in the amygdaloid nucleus. And NHDC treatment significantly alleviated PS-NP-induced neuroinflammation and apoptosis and the cyclic adenosine monophosphate(cAMP)/protein kinase A(PKA)/phosphorylated cAMP-response element binding protein(p-CREB)/plasma membrane calcium-transporting ATPase 2(Atp2b2) signaling pathway was identified in the proteomics. In conclusion, long-term exposure to low-dose PS-NPs has adverse effects on emotion through the dysregulation of the gut-brain axis, and dihydrocaffeic acid can alleviate these effects via the cAMP/PKA/p-CREB/Atp2b2 signaling pathway.}, } @article {pmid36764487, year = {2023}, author = {Nakamura, A and Komatsu, M}, title = {Performance evaluation of whole genome metagenomics sequencing with the MinION nanopore sequencer: Microbial community analysis and antimicrobial resistance gene detection.}, journal = {Journal of microbiological methods}, volume = {206}, number = {}, pages = {106688}, doi = {10.1016/j.mimet.2023.106688}, pmid = {36764487}, issn = {1872-8359}, mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; *Nanopores ; Drug Resistance, Bacterial/genetics ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; }, abstract = {Recently, the human gut microbiota has been implicated in various diseases such as immunological and neuropsychiatric disorders, and comprehensive gut microbiota analysis by metagenomic analysis using next-generation sequencers has been attracting attention. In this study, we compared microbial communities of 16S rDNA metagenome sequencing (16S-meta) and whole genome metagenome sequencing (WG-meta) using the nanopore sequencer MinION and 16S-meta using the Illumina Miseq sequencer with simulated and fecal samples, and evaluated the ability of WG-meta to detect antimicrobial resistance genes. We used the commercial Microbial Community DNA Standard as the DNA standard and a simulated sample comprising 17 strains of 15 bacterial species. In the detection of antimicrobial resistance genes, we used a simulated sample and spiked fecal samples containing Escherichia coli carrying blaCTX-M-27, Klebsiella pneumoniae carrying blaOXA-48, and Staphylococcus aureus carrying mecA. WG-meta using MinION was superior to 16S-meta and could accurately analyze the microbial communities at the species level, but it underestimated or misidentified the Bacillus subtilis group, Cryptococcus neoformans, Shigella sonnei, and Campylobacter jejuni. WG-meta using MinION could analyze the microbial communities in 5 min, and antimicrobial resistance gene detection using WG-meta could be performed in >30 min in the simulated sample with fewer bacterial counts.}, } @article {pmid36764107, year = {2023}, author = {Liu, R and Li, Z and Han, G and Cun, S and Hou, D and Yu, Z and Xue, K and Liu, X}, title = {Microbial density-dependent viral dynamics and low activity of temperate phages in the activated sludge process.}, journal = {Water research}, volume = {232}, number = {}, pages = {119709}, doi = {10.1016/j.watres.2023.119709}, pmid = {36764107}, issn = {1879-2448}, mesh = {*Bacteriophages ; Sewage ; Lysogeny ; Prophages ; *Microbiota ; }, abstract = {The ecological behavior of bacteriophages (phages), the most abundant biological entity in wastewater treatment systems, is poorly understood, especially that of temperate phages. Here, the temporal dynamics of lytic and temperate phages in a laboratory-scale activated sludge reactor with a sludge bulking issue was investigated using coupled sludge metagenomic and viromic analyses. The lysogenic fragments (prophages) identified were widely distributed in the reconstructed metagenome-assembled genomes (61.7%, n = 227). However, only 12.3% of the identified prophages experienced lysogenic-lytic switching, and the abundance contribution of prophages to free virus communities was only 0.02-0.3%, indicating low activity of temperate phages. Although the sludge community changed dramatically during reactor operation, no massive prophage induction events were detected. Statistical analyses showed strong correlations between sludge concentration and free virus and temperate phage communities, suggesting microbial density-dependent virus dynamics in the sludge microbiota.}, } @article {pmid36762879, year = {2023}, author = {Xu, Y and Chen, Z and Li, X and Tan, J and Liu, F and Wu, J}, title = {The mechanism of promoting rhizosphere nutrient turnover for arbuscular mycorrhizal fungi attributes to recruited functional bacterial assembly.}, journal = {Molecular ecology}, volume = {32}, number = {9}, pages = {2335-2350}, doi = {10.1111/mec.16880}, pmid = {36762879}, issn = {1365-294X}, mesh = {*Mycorrhizae/genetics ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Fungi ; Symbiosis ; Bacteria/genetics ; Soil/chemistry ; Soil Microbiology ; Plant Roots/microbiology ; }, abstract = {Symbiosis with arbuscular mycorrhizal (AM) fungi improves plant nutrient capture from the soil, yet there is limited knowledge about the diversity, structure, functioning, and assembly processes of AM fungi-related microbial communities. Here, 16S rRNA gene sequencing and metagenomic sequencing were used to detect bacteria in the rhizosphere of Lotus japonicus inoculated with and without AM fungi, and the L. japonicus mutant ljcbx (defective in symbiosis) inoculated with AM fungi in southern grassland soil. Our results show that AM symbiosis significantly increased bacterial diversity and promoted deterministic processes of bacterial community construction, suggesting that mycorrhizal symbiosis resulted in the directional enrichment of bacterial communities. AM fungi promoted the enrichment of nine bacteria, including Ohtaekwangia, Niastella, Gemmatimonas, Devosia, Sphingomonas, Novosphingobium, Opitutus, Lysobacter, Brevundimonas, which are positively correlated with NPK-related parameters. Through a functional identification experiment, we found that six of these genera, including Brevundimonas, Lysobacter, Ohtaekwangia, Sphingomonas, Devosia, and Gemmatimonas, demonstrated the ability to mineralize organophosphate and dissolve inorganic phosphorus, nitrogen, and potassium. Our study revealed that AM fungi can regulate rhizosphere bacterial community assembly and attract specific rhizosphere bacteria to promote soil nutrient turnover in southern grasslands.}, } @article {pmid36761901, year = {2023}, author = {Kwon, M and Jung, C and Kil, EJ}, title = {Metagenomic analysis of viromes in honey bee colonies (Apis mellifera; Hymenoptera: Apidae) after mass disappearance in Korea.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1124596}, pmid = {36761901}, issn = {2235-2988}, mesh = {*Hymenoptera ; Bees ; *Viruses/genetics ; Republic of Korea ; RNA Viruses ; Virome ; Animals ; }, abstract = {After the nationwide, massive winter losses of honey bees in Korea during the winter of 2021, samplings were conducted from live honey bees in colonies and dead honey bees nearby colonies in the same bee-farms in six regions in Korea. Each sample was subjected to virome analysis using high-throughput sequencing technology. The number of viral reads was the lowest in the live honey bee group sample with 370,503 reads and the highest in the dead honey bee group sample with 42,659,622 reads. Viral contigs were matched with the viral genomes of the black queen cell virus, deformed wing virus, Israeli acute paralysis virus, and sacbrood virus, all of which have been previously reported in Korea. However, Apis rhabdovirus 5, bee macula-like virus, Varroa orthomyxovirus-1, Hubei partiti-like virus 34, Lake Sinai virus 2, 3, and 4, and the Ditton virus, were also discovered in this study, which are the first records in Korea. Plant viral sequences resembling those of Arabidopsis latent virus 1, and a novel viral sequence was also discovered. In the present study 55 complete viral genome sequences were identified. This study is the first virome analysis of domestic honey bees and provides the latest information on the diversity of honey bee viruses in Korea.}, } @article {pmid36759753, year = {2023}, author = {Zhang, Q and Linke, V and Overmyer, KA and Traeger, LL and Kasahara, K and Miller, IJ and Manson, DE and Polaske, TJ and Kerby, RL and Kemis, JH and Trujillo, EA and Reddy, TR and Russell, JD and Schueler, KL and Stapleton, DS and Rabaglia, ME and Seldin, M and Gatti, DM and Keele, GR and Pham, DT and Gerdt, JP and Vivas, EI and Lusis, AJ and Keller, MP and Churchill, GA and Blackwell, HE and Broman, KW and Attie, AD and Coon, JJ and Rey, FE}, title = {Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut.}, journal = {Nature microbiology}, volume = {8}, number = {3}, pages = {424-440}, pmid = {36759753}, issn = {2058-5276}, support = {R01 HL144651/HL/NHLBI NIH HHS/United States ; R01 HL148577/HL/NHLBI NIH HHS/United States ; T15 LM007359/LM/NLM NIH HHS/United States ; R01 DK108259/DK/NIDDK NIH HHS/United States ; R35 GM131817/GM/NIGMS NIH HHS/United States ; R35 GM138376/GM/NIGMS NIH HHS/United States ; P41 GM108538/GM/NIGMS NIH HHS/United States ; R01 GM070683/GM/NIGMS NIH HHS/United States ; T32 GM008505/GM/NIGMS NIH HHS/United States ; R01 DK101573/DK/NIDDK NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; RC2 DK125961/DK/NIDDK NIH HHS/United States ; T32 DK007665/DK/NIDDK NIH HHS/United States ; T32 AI055397/AI/NIAID NIH HHS/United States ; }, mesh = {Mice ; Animals ; *Verrucomicrobia/genetics ; *Gastrointestinal Microbiome/genetics ; Akkermansia/genetics ; Phenotype ; }, abstract = {The molecular bases of how host genetic variation impacts the gut microbiome remain largely unknown. Here we used a genetically diverse mouse population and applied systems genetics strategies to identify interactions between host and microbe phenotypes including microbial functions, using faecal metagenomics, small intestinal transcripts and caecal lipids that influence microbe-host dynamics. Quantitative trait locus (QTL) mapping identified murine genomic regions associated with variations in bacterial taxa; bacterial functions including motility, sporulation and lipopolysaccharide production and levels of bacterial- and host-derived lipids. We found overlapping QTL for the abundance of Akkermansia muciniphila and caecal levels of ornithine lipids. Follow-up in vitro and in vivo studies revealed that A. muciniphila is a major source of these lipids in the gut, provided evidence that ornithine lipids have immunomodulatory effects and identified intestinal transcripts co-regulated with these traits including Atf3, which encodes for a transcription factor that plays vital roles in modulating metabolism and immunity. Collectively, these results suggest that ornithine lipids are potentially important for A. muciniphila-host interactions and support the role of host genetics as a determinant of responses to gut microbes.}, } @article {pmid36758522, year = {2023}, author = {Guo, C and Che, X and Briese, T and Ranjan, A and Allicock, O and Yates, RA and Cheng, A and March, D and Hornig, M and Komaroff, AL and Levine, S and Bateman, L and Vernon, SD and Klimas, NG and Montoya, JG and Peterson, DL and Lipkin, WI and Williams, BL}, title = {Deficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS.}, journal = {Cell host & microbe}, volume = {31}, number = {2}, pages = {288-304.e8}, pmid = {36758522}, issn = {1934-6069}, support = {R56 AI120724/AI/NIAID NIH HHS/United States ; U54 AI138370/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Fatigue Syndrome, Chronic/metabolism/microbiology ; *Gastrointestinal Microbiome ; Butyrates ; Bacteria/genetics ; Metabolomics ; }, abstract = {Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is characterized by unexplained debilitating fatigue, cognitive dysfunction, gastrointestinal disturbances, and orthostatic intolerance. Here, we report a multi-omic analysis of a geographically diverse cohort of 106 cases and 91 healthy controls that revealed differences in gut microbiome diversity, abundances, functional pathways, and interactions. Faecalibacterium prausnitzii and Eubacterium rectale, which are both recognized as abundant, health-promoting butyrate producers in the human gut, were reduced in ME/CFS. Functional metagenomics, qPCR, and metabolomics of fecal short-chain fatty acids confirmed a deficient microbial capacity for butyrate synthesis. Microbiome-based machine learning classifier models were robust to geographic variation and generalizable in a validation cohort. The abundance of Faecalibacterium prausnitzii was inversely associated with fatigue severity. These findings demonstrate the functional nature of gut dysbiosis and the underlying microbial network disturbance in ME/CFS, providing possible targets for disease classification and therapeutic trials.}, } @article {pmid36758521, year = {2023}, author = {Xiong, R and Gunter, C and Fleming, E and Vernon, SD and Bateman, L and Unutmaz, D and Oh, J}, title = {Multi-'omics of gut microbiome-host interactions in short- and long-term myalgic encephalomyelitis/chronic fatigue syndrome patients.}, journal = {Cell host & microbe}, volume = {31}, number = {2}, pages = {273-287.e5}, pmid = {36758521}, issn = {1934-6069}, support = {R01 AR078634/AR/NIAMS NIH HHS/United States ; U19 AI142733/AI/NIAID NIH HHS/United States ; U54 NS105539/NS/NINDS NIH HHS/United States ; R21 AR075174/AR/NIAMS NIH HHS/United States ; DP2 GM126893/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Fatigue Syndrome, Chronic/metabolism ; *Gastrointestinal Microbiome ; Dysbiosis ; Metabolomics ; Feces ; }, abstract = {Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a complex, debilitating disorder manifesting as severe fatigue and post-exertional malaise. The etiology of ME/CFS remains elusive. Here, we present a deep metagenomic analysis of stool combined with plasma metabolomics and clinical phenotyping of two ME/CFS cohorts with short-term (<4 years, n = 75) or long-term disease (>10 years, n = 79) compared with healthy controls (n = 79). First, we describe microbial and metabolomic dysbiosis in ME/CFS patients. Short-term patients showed significant microbial dysbiosis, while long-term patients had largely resolved microbial dysbiosis but had metabolic and clinical aberrations. Second, we identified phenotypic, microbial, and metabolic biomarkers specific to patient cohorts. These revealed potential functional mechanisms underlying disease onset and duration, including reduced microbial butyrate biosynthesis and a reduction in plasma butyrate, bile acids, and benzoate. In addition to the insights derived, our data represent an important resource to facilitate mechanistic hypotheses of host-microbiome interactions in ME/CFS.}, } @article {pmid36758519, year = {2023}, author = {Walters, WA and Granados, AC and Ley, C and Federman, S and Stryke, D and Santos, Y and Haggerty, T and Sotomayor-Gonzalez, A and Servellita, V and Ley, RE and Parsonnet, J and Chiu, CY}, title = {Longitudinal comparison of the developing gut virome in infants and their mothers.}, journal = {Cell host & microbe}, volume = {31}, number = {2}, pages = {187-198.e3}, pmid = {36758519}, issn = {1934-6069}, support = {R01 HD063142/HD/NICHD NIH HHS/United States ; R01 HD088837/HD/NICHD NIH HHS/United States ; Z01 HD008837/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Female ; Humans ; Virome/genetics ; *Viruses/genetics ; *Bacteriophages/genetics ; Mothers ; Metagenome ; Metagenomics ; }, abstract = {The human gut virome and its early life development are poorly understood. Prior studies have captured single-point assessments with the evolution of the infant virome remaining largely unexplored. We performed viral metagenomic sequencing on stool samples collected longitudinally from a cohort of 53 infants from age 2 weeks to 3 years (80.7 billion reads), and from their mothers (9.8 billion reads) to examine and compare viromes. The asymptomatic infant virome consisted of bacteriophages, nonhuman dietary/environmental viruses, and human-host viruses, predominantly picornaviruses. In contrast, human-host viruses were largely absent from the maternal virome. Previously undescribed, sequence-divergent vertebrate viruses were detected in the maternal but not infant virome. As infants aged, the phage component evolved to resemble the maternal virome, but by age 3, the human-host component remained dissimilar from the maternal virome. Thus, early life virome development is determined predominantly by dietary, infectious, and environmental factors rather than direct maternal acquisition.}, } @article {pmid36758508, year = {2023}, author = {Ariaeenejad, S and Kavousi, K and Zolfaghari, B and Roy, S and Koshiba, T and Hosseini Salekdeh, G}, title = {Efficient bioconversion of lignocellulosic waste by a novel computationally screened hyperthermostable enzyme from a specialized microbiota.}, journal = {Ecotoxicology and environmental safety}, volume = {252}, number = {}, pages = {114587}, doi = {10.1016/j.ecoenv.2023.114587}, pmid = {36758508}, issn = {1090-2414}, mesh = {Animals ; *Endo-1,4-beta Xylanases/chemistry/metabolism ; Lignin/metabolism ; Temperature ; Hydrolysis ; *Microbiota ; }, abstract = {A large amount of lignocellulosic waste is generated every day in the world, and their accumulation in the agroecosystems, integration in soil compositions, or incineration for energy production has severe environmental pollution effects. Using enzymes as biocatalysts for the biodegradation of lignocellulosic materials, especially in harsh processing conditions, is a practical step towards green energy and environmental biosafety. Hence, the current study focuses on enzyme computationally screened from camel rumen metagenomics data as specialized microbiota that have the capacity to degrade lignocellulosic-rich and recalcitrant materials. The novel hyperthermostable xylanase named PersiXyn10 with the performance at extreme conditions was proper activity within a broad temperature (30-100 ℃) and pH range (4.0-11.0) but showed the maximum xylanolytic activity in severe alkaline and temperature conditions, pH 8.0 and temperature 90 ℃. Also, the enzyme had highly resistant to metals, surfactants, and organic solvents in optimal conditions. The introduced xylanase had unique properties in terms of thermal stability by maintaining over 82% of its activity after 15 days of incubation at 90 ℃. Considering the crucial role of hyperthermostable xylanases in the paper industry, the PersiXyn10 was subjected to biodegradation of paper pulp. The proper performance of hyperthermostable PersiXyn10 on the paper pulp was confirmed by structural analysis (SEM and FTIR) and produced 31.64 g/L of reducing sugar after 144 h hydrolysis. These results proved the applicability of the hyperthermostable xylanase in biobleaching and saccharification of lignocellulosic biomass for declining the environmental hazards.}, } @article {pmid36757364, year = {2023}, author = {Madi, N and Chen, D and Wolff, R and Shapiro, BJ and Garud, NR}, title = {Community diversity is associated with intra-species genetic diversity and gene loss in the human gut microbiome.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {36757364}, issn = {2050-084X}, support = {R25 MH109172/MH/NIMH NIH HHS/United States ; R25 MH 109172/NH/NIH HHS/United States ; }, mesh = {Humans ; Biodiversity ; *Gastrointestinal Microbiome/genetics ; Genetic Variation ; RNA, Ribosomal, 16S/genetics ; }, abstract = {How the ecological process of community assembly interacts with intra-species diversity and evolutionary change is a longstanding question. Two contrasting hypotheses have been proposed: Diversity Begets Diversity (DBD), in which taxa tend to become more diverse in already diverse communities, and Ecological Controls (EC), in which higher community diversity impedes diversification. Previously, using 16S rRNA gene amplicon data across a range of microbiomes, we showed a generally positive relationship between taxa diversity and community diversity at higher taxonomic levels, consistent with the predictions of DBD (Madi et al., 2020). However, this positive 'diversity slope' plateaus at high levels of community diversity. Here we show that this general pattern holds at much finer genetic resolution, by analyzing intra-species strain and nucleotide variation in static and temporally sampled metagenomes from the human gut microbiome. Consistent with DBD, both intra-species polymorphism and strain number were positively correlated with community Shannon diversity. Shannon diversity is also predictive of increases in polymorphism over time scales up to ~4-6 months, after which the diversity slope flattens and becomes negative - consistent with DBD eventually giving way to EC. Finally, we show that higher community diversity predicts gene loss at a future time point. This observation is broadly consistent with the Black Queen Hypothesis, which posits that genes with functions provided by the community are less likely to be retained in a focal species' genome. Together, our results show that a mixture of DBD, EC, and Black Queen may operate simultaneously in the human gut microbiome, adding to a growing body of evidence that these eco-evolutionary processes are key drivers of biodiversity and ecosystem function.}, } @article {pmid36751856, year = {2023}, author = {Francavilla, A and Ferrero, G and Pardini, B and Tarallo, S and Zanatto, L and Caviglia, GP and Sieri, S and Grioni, S and Francescato, G and Stalla, F and Guiotto, C and Crocella, L and Astegiano, M and Bruno, M and Calvo, PL and Vineis, P and Ribaldone, DG and Naccarati, A}, title = {Gluten-free diet affects fecal small non-coding RNA profiles and microbiome composition in celiac disease supporting a host-gut microbiota crosstalk.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2172955}, pmid = {36751856}, issn = {1949-0984}, mesh = {Adult ; Humans ; Child ; *Celiac Disease/microbiology ; Diet, Gluten-Free ; Glutens/adverse effects ; *Gastrointestinal Microbiome ; *MicroRNAs ; }, abstract = {Current treatment for celiac disease (CD) is adhering to a gluten-free diet (GFD), although its long-term molecular effects are still undescribed. New molecular features detectable in stool may improve and facilitate noninvasive clinical management of CD. For this purpose, fecal small non-coding RNAs (sncRNAs) and gut microbiome profiles were concomitantly explored in CD subjects in relation to strict (or not) GFD adherence over time. In this observational study, we performed small RNA and shotgun metagenomic sequencing in stool from 63 treated CD (tCD) and 3 untreated subjects as well as 66 sex- and age-matched healthy controls. tCD included 51 individuals on strict GFD and with negative transglutaminase (TG) serology (tCD-TG-) and 12 symptomatic with not strict/short-time of GFD adherence and positive TG serology (tCD-TG+). Samples from additional 40 healthy adult individuals and a cohort of 19 untreated pediatric CD subjects and 19 sex/age matched controls were analyzed to further test the outcomes. Several miRNA and microbial profiles were altered in tCD subjects (adj. p < .05). Findings were validated in the external group of adult controls. In tCD-TG-, GFD duration correlated with five miRNA levels (p < .05): for miR-4533-3p and miR-2681-3p, the longer the diet adherence, the less the expression differed from controls. tCD-TG+ and untreated pediatric CD patients showed a similar miRNA dysregulation. Immune-response, trans-membrane transport and cell death pathways were enriched in targets of identified miRNAs. Bifidobacterium longum, Ruminococcus bicirculans, and Haemophilus parainfluenzae abundances shifted (adj. p < .05) with a progressive reduction of denitrification pathways with GFD length. Integrative analysis highlighted 121 miRNA-bacterial relationships (adj. p < .05). Specific molecular patterns in stool characterize CD subjects, reflecting either the long-term GFD effects or the gut inflammatory status, in case of a not strict/short-time adherence. Our findings suggest novel host-microbial interplays and could help the discovery of biomarkers for GFD monitoring over time.}, } @article {pmid36751730, year = {2023}, author = {Nørgaard, JC and Jørgensen, M and Moestrup, KS and Ilett, EE and Zucco, AG and Marandi, RZ and Julian, MN and Paredes, R and Lundgren, JD and Sengeløv, H and MacPherson, C}, title = {Impact of Antibiotic Treatment on the Gut Microbiome and its Resistome in Hematopoietic Stem Cell Transplant Recipients.}, journal = {The Journal of infectious diseases}, volume = {228}, number = {1}, pages = {28-36}, doi = {10.1093/infdis/jiad033}, pmid = {36751730}, issn = {1537-6613}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/adverse effects ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; *Hematopoietic Stem Cell Transplantation/adverse effects ; }, abstract = {Antibiotic-resistant bacterial infections are increasingly an issue in allogenic hematopoietic stem cell transplant patients. How antibiotic treatment impacts antibiotic resistance in the human gut microbiome remains poorly understood in vivo. Here, a total of 577 fecal samples from 233 heavily antibiotic-treated transplant patients were examined using high-resolution prescription data and shotgun metagenomics. The 13 most frequently used antibiotics were significantly associated with 154 (40% of tested associations) microbiome features. Use of broad-spectrum β-lactam antibiotics was most markedly associated with microbial disruption and increase in resistome features. The enterococcal vanA gene was positively associated with 8 of the 13 antibiotics, and in particular piperacillin/tazobactam and vancomycin. Here, we highlight the need for a high-resolution approach in understanding the development of antibiotic resistance in the gut microbiome. Our findings can be used to inform antibiotic stewardship and combat the increasing threat of antibiotic resistance.}, } @article {pmid36749039, year = {2023}, author = {Zang, X and Wang, W and Gu, S and Gu, T and Yang, H and Zheng, E and Xu, Z and Huang, S and Li, Z and Cai, G and Hong, L and Wu, Z}, title = {Interaction between Microbes and Host in Sow Vaginas in Early Pregnancy.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0119222}, pmid = {36749039}, issn = {2379-5077}, mesh = {Pregnancy ; Animals ; Female ; Swine ; RNA, Ribosomal, 16S/genetics ; *Vagina/chemistry ; Uterus/chemistry ; *Microbiota/genetics ; Metagenome ; }, abstract = {Extensive research has explored the causes of embryo losses during early pregnancy by analyzing interaction mechanisms in sows' uterus, ignoring the importance of the lower reproductive tract in pregnancy development regulation. Despite recent progress in understanding the diversity of vaginal microbes under different physiological states, the dynamic of sows' vaginal microbiotas during pregnancy and the interaction between vaginal microbes and the host are poorly understood. Here, we performed a comprehensive analysis of sows' vaginal microbial communities in early pregnancy coupled with overall patterns of vaginal mucosal epithelium gene expression. The vaginal microbiota was analyzed by 16s rRNA or metagenome sequencing, and the vaginal mucosal epithelium transcriptome was analyzed by RNA sequencing, followed by integration of the data layers. We found that the sows' vaginal microbiotas in early pregnancy develop dynamically, and there is a homeostasis balance of Firmicutes and Proteobacteria. Subsequently, we identified two pregnancy-specific communities, which play diverse roles. The microbes in the vagina stimulate the epithelial cells, while vaginal epithelium changes its structure and functions in response to stimulation. These changes produce specific inflammation responses to promote pregnancy development. Our findings demonstrate the interaction between microbes and host in the sow vagina in early pregnancy to promote pregnancy development, meanwhile providing a reference data set for the study of targeted therapies of microbial homeostasis dysregulation in the female reproductive tract. IMPORTANCE This work sheds light on the dynamics of the sow vaginal microbiotas in early pregnancy and its roles in pregnancy development. Furthermore, this study provides insight into the functional mechanisms of reproductive tract microbes by outlining vaginal microbe-host interactions, which might identify new research and intervention targets for improving pregnancy development by modulating lower reproductive tract microbiota.}, } @article {pmid36748614, year = {2022}, author = {Durán-Manuel, EM and Loyola-Cruz, MÁ and Cruz-Cruz, C and Ibáñez-Cervantes, G and Gaytán-Cervantes, J and González-Torres, C and Quiroga-Vargas, E and Calzada-Mendoza, CC and Cureño-Díaz, MA and Fernández-Sánchez, V and Castro-Escarpulli, G and Bello-López, JM}, title = {Massive sequencing of the V3-V4 hypervariable region of bronchoalveolar lavage from patients with COVID-19 and VAP reveals the collapse of the pulmonary microbiota.}, journal = {Journal of medical microbiology}, volume = {71}, number = {12}, pages = {}, doi = {10.1099/jmm.0.001634}, pmid = {36748614}, issn = {1473-5644}, mesh = {Humans ; *Pneumonia, Ventilator-Associated/diagnosis/epidemiology ; Anti-Bacterial Agents/therapeutic use ; *COVID-19/diagnosis ; SARS-CoV-2/genetics ; Bronchoalveolar Lavage ; Bacteria/genetics ; *Cross Infection/drug therapy ; *Microbiota ; Intensive Care Units ; }, abstract = {Background. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is a predisposing factor for the development of healthcare-associated infections, of which ventilator-associated pneumonia (VAP) is one.Hypothesis. VAP is caused by ESKAPE bacteria and other pathogens not detected by microbiological culture.Aim. To elucidate the bacterial pathogens of severe coronavirus disease 2019 (COVID-19) and VAP patients by massive sequencing and to predict their degree of relationship with the age and sex of the patients.Methods. Analysis of ribosomal libraries of the V3-V4 hypervariable region obtained by Illumina sequencing of bronchoalveolar lavages from COVID-19 and VAP (first wave) patients from Hospital Juárez de México.Results. Acinetobacter and Pseudomonas were the main bacterial genera in the bronchoalveolar lavages (BALs) analysed. Other members of the ESKAPE group, such as Enterococcus and Klebsiella, were also identified. Taxonomic composition per patient showed that non-ESKAPE genera were present with significant relative abundances, such as Prevotella, Stenotrophomas, Enterococcus, Mycoplasma, Serratia and Corynebacterium. Kruskal-Wallis analysis proved that VAP acquisition is an adverse event that is not influenced by the sex and age of COVID-19 patients.Discussion. Metagenomic findings in COVID-19/VAP patients highlight the importance of implementing comprehensive microbiological diagnostics by including alternative tools for the detection of the causal agents of healthcare-associated infections (HAIs).Conclusions. Timely identification of bacteria 'not sought' in diagnostic bacteriology laboratories will allow specific and targeted treatments. Implications for the restricted diagnosis of VAP causative agents in COVID-19 patients and the presence of pathogens not detected by classical microbiology are analysed and discussed.}, } @article {pmid36748565, year = {2022}, author = {Ghosh, A and Saha, S}, title = {Meta-analysis of sputum microbiome studies identifies airway disease-specific taxonomic and functional signatures.}, journal = {Journal of medical microbiology}, volume = {72}, number = {12}, pages = {}, doi = {10.1099/jmm.0.001617}, pmid = {36748565}, issn = {1473-5644}, mesh = {Humans ; *Cystic Fibrosis/microbiology ; Sputum/microbiology ; *Microbiota/genetics ; *Pulmonary Disease, Chronic Obstructive/microbiology ; *Bronchiectasis/microbiology ; *Asthma/microbiology ; }, abstract = {Introduction. Studying taxonomic and functional signatures of respiratory microbiomes provide a better understanding of airway diseases.Gap Statement. Several human airway metagenomics studies have identified taxonomic and functional features restricted to a single disease condition and the findings are not comparable across airway diseases due to use of different samples, NGS platforms, and bioinformatics databases and tools.Aim. To study the microbial taxonomic and functional components of sputum microbiome across airway diseases and healthy smokers.Methodology. Here, 57 whole metagenome shotgun sequencing (WMSS) runs coming from the sputum of five airway diseases: asthma, bronchiectasis, chronic obstructive pulmonary diseases (COPD), cystic fibrosis (CF), tuberculosis (TB), and healthy smokers as the control were reanalysed using a common WMSS analysis pipeline.Results. Shannon's index (alpha diversity) of the healthy smoker group was the highest among all. The beta diversity showed that the sputum microbiome is distinct in major airway diseases such as asthma, COPD and cystic fibrosis. The microbial composition based on differential analysis showed that there are specific markers for each airway disease like Acinetobacter bereziniae as a marker for COPD and Achromobacter xylosoxidans as a marker of cystic fibrosis. Pathways and metabolites identified from the sputum microbiome of these five diseases and healthy smokers also show specific markers. 'ppGpp biosynthesis' and 'purine ribonucleosides degradation' pathways were identified as differential markers for bronchiectasis and COPD. In this meta-analysis, besides bacteria kingdom, Aspergillus fumigatus was detected in asthma and COPD, and Roseolovirus human betaherpesvirus 7 was detected in COPD. Our analysis showed that the majority of the gene families specific to the drug-resistant associated genes were detected from opportunistic pathogens across all the groups.Conclusion. In summary, the specific species in the sputum of airway diseases along with the microbial features like specific gene families, pathways, and metabolites were identified which can be explored for better diagnosis and therapy.}, } @article {pmid36748549, year = {2023}, author = {Soares, A and Edwards, A and An, D and Bagnoud, A and Bradley, J and Barnhart, E and Bomberg, M and Budwill, K and Caffrey, SM and Fields, M and Gralnick, J and Kadnikov, V and Momper, L and Osburn, M and Mu, A and Moreau, JW and Moser, D and Purkamo, L and Rassner, SM and Sheik, CS and Sherwood Lollar, B and Toner, BM and Voordouw, G and Wouters, K and Mitchell, AC}, title = {A global perspective on bacterial diversity in the terrestrial deep subsurface.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {1}, pages = {}, pmid = {36748549}, issn = {1465-2080}, mesh = {Water Microbiology ; Bacteria/genetics ; *Microbiota/genetics ; Biomass ; Metagenomics ; *Gammaproteobacteria ; RNA, Ribosomal, 16S ; }, abstract = {While recent efforts to catalogue Earth's microbial diversity have focused upon surface and marine habitats, 12-20 % of Earth's biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8 % in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.}, } @article {pmid36746960, year = {2023}, author = {Geller-McGrath, D and Mara, P and Taylor, GT and Suter, E and Edgcomb, V and Pachiadaki, M}, title = {Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {656}, pmid = {36746960}, issn = {2041-1723}, mesh = {*Seawater/microbiology ; Bacteria/metabolism ; Metagenome ; *Microbiota/genetics ; Water/metabolism ; }, abstract = {Secondary metabolites play essential roles in ecological interactions and nutrient acquisition, and are of interest for their potential uses in medicine and biotechnology. Genome mining for biosynthetic gene clusters (BGCs) can be used for the discovery of new compounds. Here, we use metagenomics and metatranscriptomics to analyze BGCs in free-living and particle-associated microbial communities through the stratified water column of the Cariaco Basin, Venezuela. We recovered 565 bacterial and archaeal metagenome-assembled genomes (MAGs) and identified 1154 diverse BGCs. We show that differences in water redox potential and microbial lifestyle (particle-associated vs. free-living) are associated with variations in the predicted composition and production of secondary metabolites. Our results indicate that microbes, including understudied clades such as Planctomycetota, potentially produce a wide range of secondary metabolites in these anoxic/euxinic waters.}, } @article {pmid36746446, year = {2023}, author = {Wu, HZ and Zhang, X and Cheng, XG and Yu, Q}, title = {[Saliva microbiota and metabolite in individuals with caries or periodontitis].}, journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology}, volume = {58}, number = {2}, pages = {131-142}, doi = {10.3760/cma.j.cn112144-20220829-00464}, pmid = {36746446}, issn = {1002-0098}, support = {82170937, 81870751//National Natural Science Foundation of China/ ; 2022KJXX‑101//Shaanxi Natural Science Basic Research Plan (Innovative Talent Promotion Plan) Youth Science and Technology Star Program/ ; 2021JQ‑353//Shaanxi Natural Science Basic Research Plan Youth Program/ ; 2020cyjhcxg//Air Force Military Medical University Lingyun Project Young Eagle Plan/ ; 2022KJXX-101//Shaanxi Innovation Capability Support Plan/ ; 2021JQ-353//Shaanxi Natural Science Basic Research Plan/ ; 2020cyjhcxg//Air Force Military Medical University Talent Support "Lingyun Project" Plan/ ; }, mesh = {*Microbiota/genetics ; Porphyromonas gingivalis/genetics ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; Humans ; *Periodontitis/microbiology ; Prevotella ; Dental Caries Susceptibility ; }, abstract = {Objective: To detect and analyze the characteristics of oral microbiota in species composition, function and metabolism among caries, periodontitis and oral healthy individuals, hunting for the microbiome-derived biomarkers with specificity and sensitivity to estimate the occurrence of these two diseases. Methods: Saliva samples were collected from 10 patients with high caries risk [decayed-missing-filled teeth (DMFT)≥6, HC group] in Department of Endodontics, 10 patients with periodontitis of grade Ⅱ A-Ⅲ C (PG group) in Department of Periodontology and 10 oral healthy individuals (HH group) from School of Stomatology, The Fourth Military Medical University during from March 2022 to June 2022. A baseline examination was conducted on all participants, including their oral conditions of caries and periodontal health. Metagenomic sequencing (Illumina PE150 platform) and liquid chromatography-mass spectrometry were used to detect microorganisms and their metabolites in the samples respectively. The sequencing data were analyzed to obtain the information of microbial taxonomic composition, functional genes and metabolites in each group of samples. The basic oral conditions and saliva samples of subjects in each group were evaluated and collected by the same professional endodontist. Results: There were no significant difference in baseline characteristics such as age and sex among the subjects in each group (P>0.05). DMFT in HC group (9.0±1.7) was significantly higher than that in HH group (0) and PG group (0) (F=243.00, P<0.001). Sequencing data analysis showed that the taxonomic compositions of salivary microbiota in each group were mainly Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria at the phylum level, and Streptococcus, Neisseria, Rothia, Prevotella at the genus level. Differential analysis showed that, compared with the HH group, HC group and PG group had significant differences in taxonomic composition (P<0.05), and the most significant among them was Prevotella. At the species level, Prevotella pallens was the most significant change in HC group, and Porphyromonas gingivalis in PG group. Metabolite analysis showed that there were significant differences in metabolites between HC group and PG group. The results showed that, compared with the HH group, the most significant metabolite change was 3-hydroxy-1, 5-diphenylpentan-1-one in HC group (P=0.001) and N1 acetylspermine in PG group (P=0.002) respectively. Compared with the PG group, the metabolite of HC group with the most significant difference is D-glucosamine 6-phosphate (P=0.006). The metabolism gene function analysis showed that, the enrichment of carbohydrate metabolism related genes was highest in HC group, followed with HH group, and it was lowest in PG group. In addition, compared with the HH group, the abundance of functional genes related to glucose metabolism, such as ABC transporter and phosphotransferase system, were significantly decreased in PG group (P<0.05), but significantly increased in HC group (P<0.05). Conclusions: There is a significant correlation between the alternation of carbohydrate metabolism of salivary microbiota with the occurrence of caries and periodontitis. In the future, Prevotella pallens and 3-hydroxy-1, 5-diphenylpentan-1-one may be the potential biomarkers of caries; while Porphyromonas gingivalis and N1 acetylspermine work in the predictions of periodontitis.}, } @article {pmid36746286, year = {2023}, author = {Cui, W and Li, R and Fan, Z and Wu, L and Zhao, X and Wei, G and Shu, D}, title = {Weak environmental adaptation of rare phylotypes sustaining soil multi-element cycles in response to decades-long fertilization.}, journal = {The Science of the total environment}, volume = {871}, number = {}, pages = {162063}, doi = {10.1016/j.scitotenv.2023.162063}, pmid = {36746286}, issn = {1879-1026}, mesh = {*Soil ; Phylogeny ; Soil Microbiology ; *Microbiota ; Bacteria/genetics ; Nitrogen ; }, abstract = {Deciphering the ecological role of soil communities in the maintenance of multiple ecosystem functions is pivotal for the conservation and sustainability of soil biodiversity. However, few studies have investigated niche differentiation of abundant and rare microbiota, as well as their contributions to multiple soil elemental cycles, particularly in agroecosystems that have received decades of intense fertilization. Here, we characterized the environmental thresholds and phylogenetic signals for the environmental adaptation of both abundant and rare microbial subcommunities via amplicon sequencing and metagenomic sequencing and explored their importance in sustaining soil multiple nutrient cycling in agricultural fields that were fertilized for two decades. The results showed that rare taxa exhibited narrower niche breadths and weaker phylogenetic signals than abundant species. The assembly of abundant subcommunity was shaped predominantly by dispersal limitation (explained 71.1 % of the variation in bacteria) and undominated processes (explained 75 % of the variation in fungi), whereas the assembly of rare subcommunity was dominated by homogeneous selection process (explained 100 % of the variation in bacteria and 60 % of the variation in fungi). Soil ammonia nitrogen was the leading factor mediating the balance between stochastic and deterministic processes in both abundant (R[2] = 0.15, P < 0.001) and rare (R[2] = 0.08, P < 0.001) bacterial communities. Notably, the rare biosphere largely contributed to key soil processes such as carbon (R[2]bacteria = 0.03, P < 0.05; R[2]fungi = 0.05, P < 0.05) and nitrogen (R[2]bacteria = 0.03, P < 0.05; R[2]fungi = 0.17, P < 0.001) cycling. Collectively, these findings facilitate our understanding of the maintenance of rhizosphere bacterial and fungal diversity in response to agricultural fertilization and highlight the key role of rare taxa in sustaining agricultural ecosystem functions.}, } @article {pmid36746030, year = {2023}, author = {Liao, Y and Bian, J and Miao, S and Xu, S and Li, R and Liu, R and Liu, H and Qu, J}, title = {Regulation of denitrification performance and microbial topology by lights: Insight into wavelength effects towards microbiota.}, journal = {Water research}, volume = {232}, number = {}, pages = {119434}, doi = {10.1016/j.watres.2022.119434}, pmid = {36746030}, issn = {1879-2448}, mesh = {*Nitrites ; Denitrification ; Oxidation-Reduction ; Bioreactors ; *Microbiota ; Nitrogen ; Sewage ; }, abstract = {The low efficiency of conventional complete denitrification, as well as the unstable nitrite supply for partial-denitrification coupled anammox (PD/A) restrict the efficient removal of nitrogen from industrial wastewaters. Herein, we proposed an optical strategy to bidirectionally regulate denitrification by introducing lights at different wavelengths, and the underlying mechanisms were elucidated accordingly. It turned out that yellow light at wavelength of 590 nm accelerated denitrification by 35.4%, while blue light delayed denitrification with stable nitrite accumulation above 86.9% and high nitrate removal (99.8%). Microbial physiology and viability further supported the positive effects of yellow light on microbial activity. Additionally, despite the sluggish denitrification aroused by blue light, negligible cellular damage was observed. Antioxidant capability divergence, microbial community shifting and metabolic flux redirection contributed to the wavelength-dependent effects. Halomonas and Pseudomonas were identified as high-credit taxonomic biomarkers of yellow and blue light. As revealed by metabolomics, pantothenate and CoA biosynthesis, glutamate metabolism and alkaloid biosynthesis presented high impact values. Co-analysis of metabolomics and metagenomics based on microbial topology further distinguished pivotal metabolic pathways and genes. Oxidative phosphorylation contributed to the divergent denitrification performance through electron transfer chains, whereas glutamate and glutathione metabolism contributed to oxidative stress alleviation and mediated the metabolic flux between peroxisome and nitrogen metabolism. This study shed a light on the application of optical strategy to regulate denitrification performance and achieve either complete denitrification or PD/A.}, } @article {pmid36744984, year = {2023}, author = {Banerjee, P and Sarkar, A and Ghosh, K and Mazumdar, A}, title = {A Metagenomic Based Approach on Abundance and Diversity of Bacterial Communities Across the Life Stages of Culicoides peregrinus (Diptera: Ceratopogonidae) a Vector of Bluetongue Virus.}, journal = {Journal of medical entomology}, volume = {60}, number = {2}, pages = {373-383}, doi = {10.1093/jme/tjad011}, pmid = {36744984}, issn = {1938-2928}, mesh = {Animals ; *Ceratopogonidae ; *Bluetongue virus ; Bacteria/genetics ; Larva ; *Microbiota ; }, abstract = {During larval rearing of Culicoides peregrinus Kieffer (Diptera: Ceratopogonidae) it was obligatory to add a small quantity of mud from larval habitat to nutrient broth in culture plates. This initiated microbial growth in rearing plates which facilitated growth and development of immature. The primary aim was to enumerate gut microbial communities across the different life stages of C. peregrinus. Amplicon sequencing of the V3-V4 hypervariable region (16S rDNA) was done on Illumina Miseq platform to detect gut bacterial communities at different life stages, while ITS regions (18S rRNA) were targeted for fungal communities of the 4th instar larvae. The major findings were: 1) Phylum Proteobacteria and Firmicutes were the most abundant throughout the life stages, along with the highest bacterial alpha diversity in the egg, 2) bacterial compositions were similar to laboratory reared and field collected adults, and 3) abundant fungal phyla associated with the larval gut were Ascomycota and Basidiomycota. Furthermore, analyses of the gut microbiome with METAGENassist might be indicative of their likely function in the natural habitat. Abundant gut-associated bacteria and/or fungal genera detected in the present study could be used as dietary supplements to establish laboratory colonies for further vectorial research. While, individual roles of the bacteria or fungi in paratransgenesis are warned for their possible utilization to frame the management strategy in upcoming works.}, } @article {pmid36744910, year = {2023}, author = {Guo, M and Wu, G and Tan, Y and Li, Y and Jin, X and Qi, W and Guo, X and Zhang, C and Zhu, Z and Zhao, L}, title = {Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis.}, journal = {mBio}, volume = {14}, number = {1}, pages = {e0351922}, pmid = {36744910}, issn = {2150-7511}, mesh = {Humans ; *COVID-19 ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Feces ; Prognosis ; }, abstract = {Coronavirus disease 2019 (COVID-19) severity has been associated with alterations of the gut microbiota. However, the relationship between gut microbiome alterations and COVID-19 prognosis remains elusive. Here, we performed a genome-resolved metagenomic analysis on fecal samples from 300 in-hospital COVID-19 patients, collected at the time of admission. Among the 2,568 high quality metagenome-assembled genomes (HQMAGs), redundancy analysis identified 33 HQMAGs which showed differential distribution among mild, moderate, and severe/critical severity groups. Co-abundance network analysis determined that the 33 HQMAGs were organized as two competing guilds. Guild 1 harbored more genes for short-chain fatty acid biosynthesis, and fewer genes for virulence and antibiotic resistance, compared with Guild 2. Based on average abundance difference between the two guilds, the guild-level microbiome index (GMI) classified patients from different severity groups (average AUROC [area under the receiver operating curve] = 0.83). Moreover, age-adjusted partial Spearman's correlation showed that GMIs at admission were correlated with 8 clinical parameters, which are predictors for COVID-19 prognosis, on day 7 in hospital. In addition, GMI at admission was associated with death/discharge outcome of the critical patients. We further validated that GMI was able to consistently classify patients with different COVID-19 symptom severities in different countries and differentiated COVID-19 patients from healthy subjects and pneumonia controls in four independent data sets. Thus, this genome-based guild-level signature may facilitate early identification of hospitalized COVID-19 patients with high risk of more severe outcomes at time of admission. IMPORTANCE Previous reports on the associations between COVID-19 and gut microbiome have been constrained by taxonomic-level analysis and overlook the interaction between microbes. By applying a genome-resolved, reference-free, guild-based metagenomic analysis, we demonstrated that the relationship between gut microbiota and COVID-19 is genome-specific instead of taxon-specific or even species-specific. Moreover, the COVID-19-associated genomes were not independent but formed two competing guilds, with Guild 1 potentially beneficial and Guild 2 potentially more detrimental to the host based on comparative genomic analysis. The dominance of Guild 2 over Guild 1 at time of admission was associated with hospitalized COVID-19 patients at high risk for more severe outcomes. Moreover, the guild-level microbiome signature is not only correlated with the symptom severity of COVID-19 patients, but also differentiates COVID-19 patients from pneumonia controls and healthy subjects across different studies. Here, we showed the possibility of using genome-resolved and guild-level microbiome signatures to identify hospitalized COVID-19 patients with a high risk of more severe outcomes at the time of admission.}, } @article {pmid36743964, year = {2023}, author = {Li, Y and Jones, FG and Zhang, B and Cui, J and Zhang, W}, title = {The effect of short-term fallowing on the microbial communities in forest soil cultivated with ginseng: Preliminary research.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e14758}, pmid = {36743964}, issn = {2167-8359}, mesh = {Soil/chemistry ; *Panax ; *Microbiota/genetics ; *Ascomycota ; Forests ; }, abstract = {BACKGROUND: Continuous cultivation of ginseng crops in fixed plots can lead to disease outbreaks, yield losses and replanting failures. Fallow periods can help restore soil health and increase the sustainability of agricultural systems; however, taking land out of production for extended periods is often not feasible. Short-term fallow periods could restore soil health, but few studies have examined the effects of short-term fallow treatment on the health of soil in ginseng fields.

METHODS: In this preliminary study, we used metagenomic analysis to assess changes in the abundance of major ginseng pathogens and soil health overall following a short-term fallow period in a region in the Changbai Mountains. A sample from a forest plot (Hx0ks), was compared to a sample from a field where ginseng was previously cultivated and then had been left fallow for two years (Hx2), and a sample from a field that had been fallow for two years and was subsequently replanted with ginseng (Clsd).

RESULTS: Soil that was fallow for two years, and then replanted with ginseng, showed reduced nutrient content and lower diversity of soil bacterial and fungal communities than soil that remained fallow. Candidatus Solibacter (5%) and Rhizomicrobium (3%) were the most abudant bacterial genera in Hx2. Rhizomicrobium (4%) and Gemmatimonas (3%) were the most abundant bacterial genera in Clsd. Mortierella (22%) and Peziza (12%) dominated the fungal community in Hx2. Lecanicillium (38%) and Mortierella (13%) dominated the fungal community in Clsd. Fallow periods also increased the functional diversity of soil as predicted by PICRUSt and decreased the relative abundance of the pathogenic fungi.

CONCLUSIONS: Preliminary findings were consistent with the hypothesis that fallow management in ginseng cultivation can improve soil microbial community structure and function and reduces the number of plant pathogens; however, testing this hypothesis will require replicated plots.}, } @article {pmid36741405, year = {2022}, author = {Chen, Z and Yang, H and Fu, H and Wu, L and Liu, M and Jiang, H and Liu, Q and Wang, Y and Xiong, S and Zhou, M and Sun, X and Chen, C and Huang, L}, title = {Gut bacterial species in late trimester of pregnant sows influence the occurrence of stillborn piglet through pro-inflammation response.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1101130}, pmid = {36741405}, issn = {1664-3224}, mesh = {Humans ; Animals ; Swine ; Pregnancy ; Female ; *Stillbirth ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; Lipopolysaccharides ; Bacteria ; Inflammation ; }, abstract = {Maternal gut microbiota is an important regulator for the metabolism and immunity of the fetus during pregnancy. Recent studies have indicated that maternal intestinal microbiota is closely linked to the development of fetus and infant health. Some bacterial metabolites are considered to be directly involved in immunoregulation of fetus during pregnancy. However, the detailed mechanisms are largely unknown. In this study, we exploited the potential correlation between the gut microbiota of pregnant sows and the occurrence of stillborn piglets by combining the 16S rRNA gene and metagenomic sequencing data, and fecal metabolome in different cohorts. The results showed that several bacterial species from Bacteroides, potential pathogens, and LPS-producing bacteria exhibited significantly higher abundances in the gut of sows giving birth to stillborn piglets. Especially, Bacteroides fragilis stood out as the key driver in both tested cohorts and showed the most significant association with the occurrence of stillborn piglets in the DN1 cohort. However, several species producing short-chain fatty acids (SCFAs), such as Prevotella copri, Clostridium butyricum and Faecalibacterium prausnitzii were enriched in the gut of normal sows. Functional capacity analysis of gut microbiome revealed that the pathways associated with infectious diseases and immune diseases were enriched in sows giving birth to stillborn piglets. However, energy metabolism had higher abundance in normal sows. Fecal metabolome profiling analysis found that Lysophosphatidylethanolamine and phosphatidylethanolamine which are the main components of cell membrane of Gram-negative bacteria showed significantly higher concentration in stillbirth sows, while SCFAs had higher concentration in normal sows. These metabolites were significantly associated with the stillborn-associated bacterial species including Bacteroides fragilis. Lipopolysaccharide (LPS), IL-1β, IL-6, FABP2, and zonulin had higher concentration in the serum of stillbirth sows, indicating increased intestinal permeability and pro-inflammatory response. The results from this study suggested that certain sow gut bacterial species in late trimester of pregnancy, e.g., an excess abundance of Bacteroides fragilis, produced high concentration of LPS which induced sow pro-inflammatory response and might cause the death of the relatively weak piglets in a farrow. This study provided novel evidences about the effect of maternal gut microbiota on the fetus development and health.}, } @article {pmid36740746, year = {2023}, author = {Voidaleski, MF and Costa, FF and de Hoog, GS and Gomes, RR and Vicente, VA}, title = {Metagenomics reveals an abundance of black yeast-like fungi in the skin microbiome.}, journal = {Mycoses}, volume = {66}, number = {6}, pages = {488-496}, doi = {10.1111/myc.13574}, pmid = {36740746}, issn = {1439-0507}, support = {//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, mesh = {Humans ; Saccharomyces cerevisiae ; Metagenomics ; Skin/microbiology ; *Exophiala/genetics ; *Microbiota/genetics ; Fungi/genetics ; }, abstract = {BACKGROUND: The skin is the first line of defence against communities of resident viruses, bacteria and fungi. The composition of the microbiome might change with factors related to the environment and host. The microbiome is dominated by bacteria. Dermatophytes and yeasts are the predominant fungi that are also involved in opportunistic infections of skin, hair and nails. Among environmental fungi, Chaetothyriales (black yeasts and relatives) are enriched by hydrocarbon pollution in domesticated habitats and comprise numerous species that cause mild-to-severe disease.

METHODS: We investigated the presence of black fungi in the skin microbiome by conducting an analysis in the publicly available metagenomic SRA database (NCBI). We focused on the causative agents of chromoblastomycosis and phaeohyphomycosis and used barcodes and padlock probe sequences as diagnostic tools.

RESULTS: A total of 132,159,577 MB was analysed and yielded 18,360 reads that matched with 24 species of black fungi. Exophiala was the most prevalent genus, and Cyphellophora europaea was the most abundant species.

CONCLUSION: This study reveals the abundant presence of Chaetothyriales on the skin without necessarily being associated with infection. Most of the detected causal agents are known from mild skin diseases, while also species were revealed that had been reported from CARD9-deficient patients.}, } @article {pmid36739853, year = {2023}, author = {Yu, Y and Huang, J and Jin, L and Yu, M and Yu, X and Zhu, X and Sun, J and Zhu, L}, title = {Translocation and metabolism of tricresyl phosphate in rice and microbiome system: Isomer-specific processes and overlooked metabolites.}, journal = {Environment international}, volume = {172}, number = {}, pages = {107793}, doi = {10.1016/j.envint.2023.107793}, pmid = {36739853}, issn = {1873-6750}, mesh = {Humans ; *Tritolyl Phosphates ; *Oryza ; Organophosphates ; *Microbiota ; *Flame Retardants/analysis ; Phosphates ; }, abstract = {Tricresyl phosphate (TCP) is extensively used organophosphorus flame retardants and plasticizers that posed risks to organisms and human beings. In this study, the translocation and biotransformation behavior of isomers tri-p-cresyl phosphate (TpCP), tri-m-cresyl phosphate (TmCP), and tri-o-cresyl phosphate (ToCP) in rice and rhizosphere microbiome was explored by hydroponic exposure. TpCP and TmCP were found more liable to be translocated acropetally, compared with ToCP, although they have same molecular weight and similar Kow. Rhizosphere microbiome named microbial consortium GY could reduce the uptake of TpCP, TmCP, and ToCP in rice tissues, and promote rice growth. New metabolites were successfully identified in rice and microbiome, including hydrolysis, hydroxylated, methylated, demethylated, methoxylated, and glucuronide- products. The methylation, demethylation, methoxylation, and glycosylation pathways of TCP isomers were observed for the first time in organisms. What is more important is that the demethylation of TCPs could be an important and overlooked source of triphenyl phosphate (TPHP), which broke the traditional understanding of the only manmade source of toxic TPHP in the environment. Active members of the microbial consortium GY during degradation were revealed and metagenomic analysis indicated that most of active populations contained TCP-degrading genes. It is noteworthy that the strains and function genes in microbial consortium GY that responsible for TCP isomers' transformation were different. These results can improve our understanding of the translocation and transformation of organic pollutant isomers in plants and rhizosphere microbiome.}, } @article {pmid36739716, year = {2023}, author = {Doni, L and Oliveri, C and Lasa, A and Di Cesare, A and Petrin, S and Martinez-Urtaza, J and Coman, F and Richardson, A and Vezzulli, L}, title = {Large-scale impact of the 2016 Marine Heatwave on the plankton-associated microbial communities of the Great Barrier Reef (Australia).}, journal = {Marine pollution bulletin}, volume = {188}, number = {}, pages = {114685}, doi = {10.1016/j.marpolbul.2023.114685}, pmid = {36739716}, issn = {1879-3363}, mesh = {Animals ; Ecosystem ; Coral Reefs ; Plankton ; RNA, Ribosomal, 16S ; *Anthozoa ; Australia ; Bacteria/genetics ; *Microbiota ; }, abstract = {The Great Barrier Reef (GBR) is the world's largest coral ecosystem and is threatened by climate change. This study investigated the impact of the 2016 Marine Heatwave (MHW) on plankton associated microbial communities along a ∼800 km transect in the GBR. 16S rRNA gene metabarcoding of archived plankton samples collected from November 2014 to August 2016 in this region showed a significant increase in Planctomycetes and bacteria belonging to the genus Vibrio and Synechococcus during and after the heatwave. Notably, Droplet Digital PCR and targeted metagenomic analysis applied on samples collected four months after the MHW event revealed the presence of several potential pathogenic Vibrio species previously associated with diseases in aquatic animals. Overall, the 2016 MHW significantly impacted the surface picoplankton community and fostered the spread of potentially pathogenic bacteria across the GBR providing an additional threat for marine biodiversity in this area.}, } @article {pmid36737703, year = {2023}, author = {Zhao, G and Qi, M and Wang, Q and Hu, C and Li, X and Chen, Y and Yang, J and Yu, H and Chen, H and Guo, A}, title = {Gut microbiome variations in Rhinopithecus roxellanae caused by changes in the environment.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {62}, pmid = {36737703}, issn = {1471-2164}, support = {2021CFB118//Nature Science Foundation of Hubei Province/ ; 2013BAD03B01-01//National Science and Technology Infrastructure Program of China/ ; }, mesh = {Animals ; *Presbytini/genetics ; *Gastrointestinal Microbiome/genetics ; *Colobinae/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; Endangered Species ; Bacteria/genetics ; Diarrhea ; }, abstract = {BACKGROUND: The snub-nosed monkey (Rhinopithecus roxellanae) is an endangered animal species mainly distributed in China and needs to be protected. Gut microbiome is an important determinant of animal health and population survival as it affects the adaptation of the animals to different foods and environments under kinetic changes of intrinsic and extrinsic factors. Therefore, this study aimed to elucidate gut fecal microbiome profiles of snub-nosed monkeys affected by several extrinsic and intrinsic factors, including raising patterns (captive vs. wild), age, sex, and diarrheal status to provide a reference for making protection strategies.

RESULTS: The 16S rRNA gene sequencing was firstly used to pre-check clustering of 38 fecal samples from the monkeys including 30 wild and 8 captive (5 healthy and 3 diarrheal) from three Regions of Shennongjia Nature Reserve, Hubei Province, China. Then the 24 samples with high-quality DNA from 18 wild and 6 captive (4 healthy and 2 diarrheal) monkeys were subjected to shotgun metagenomic sequencing to characterize bacterial gut microbial communities. We discovered that the raising pattern (captive and wild) rather than age and sex was the predominant factor attributed to gut microbiome structure and proportionality. Wild monkeys had significantly higher bacterial diversity and lower Bacteroidetes/Firmicutes ratios than captive animals. Moreover, the gut microbiomes in wild healthy monkeys were enriched for the genes involved in fatty acid production, while in captive animals, genes were enriched for vitamin biosynthesis and metabolism and amino acid biosynthesis from carbohydrate intermediates. Additionally, a total of 37 antibiotic resistant genes (ARG) types were detected. Unlike the microbiome diversity, the captive monkeys have a higher diversity of ARG than the wild animals.

CONCLUSION: Taken together, we highlight the importance of self-reprogramed metabolism in the snub-nosed monkey gut microbiome to help captive and wild monkeys adapt to different intrinsic and extrinsic environmental change.}, } @article {pmid36736410, year = {2023}, author = {Wang, J and Lou, Y and Ma, D and Feng, K and Chen, C and Zhao, L and Xing, D}, title = {Co-treatment with free nitrous acid and calcium peroxide regulates microbiome and metabolic functions of acidogenesis and methanogenesis in sludge anaerobic digestion.}, journal = {The Science of the total environment}, volume = {870}, number = {}, pages = {161924}, doi = {10.1016/j.scitotenv.2023.161924}, pmid = {36736410}, issn = {1879-1026}, mesh = {*Sewage/chemistry ; Anaerobiosis ; Fermentation ; Nitrous Acid/analysis ; Fatty Acids, Volatile/analysis ; *Microbiota ; Carbon ; }, abstract = {Wasted activated sludge (WAS) is a promising feedstock for carbon management because of its abundance and carbon-neutral features. Currently, the goal is to maximize the energy in WAS and avoid secondary toxic effects or accumulation of harmful substances in the environment. Chemical pretreatment is an effective strategy for enhancing WAS disintegration and production of short chain fatty acids (SCFAs). However, the role of pretreatment in shaping the core microbiome and functional metabolism of anaerobic microorganisms remains obscure. Here, the mechanisms of SCFA synthesis and microbiome response to free nitrous acid (FNA) and calcium peroxide (CaO2) co-treatment during sludge anaerobic digestion (AD) were investigated. The combination of FNA and CaO2 enriched acidogenic Macellibacteroides, Petrimonas, and Sedimentibacter to a relative abundance of 15.0%, 10.3%, and 7.3%, respectively, resulting in an apparent increase in SCFA production. Metagenome analysis indicated that FNA + CaO2 co-treatment facilitated glycolysis, phosphate acetyltransferase-acetate kinase pathway, amino acid metabolism, and acetate transport, but inhibited CO2 reduction and common pathway of methanogenesis compared with the untreated control. This work provides theoretical insights into the functional activity and interaction of microorganisms with ecological factors.}, } @article {pmid36735064, year = {2023}, author = {Tessler, M and Cunningham, SW and Ingala, MR and Warring, SD and Brugler, MR}, title = {An Environmental DNA Primer for Microbial and Restoration Ecology.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {796-808}, pmid = {36735064}, issn = {1432-184X}, mesh = {*DNA, Environmental/genetics ; DNA Primers ; DNA Barcoding, Taxonomic/methods ; Ecology ; DNA/genetics ; Environmental Monitoring ; Biodiversity ; }, abstract = {Environmental DNA (eDNA) sequencing-DNA collected from the environment from living cells or shed DNA-was first developed for working with microbes and has greatly benefitted microbial ecologists for decades since. These tools have only become increasingly powerful with the advent of metabarcoding and metagenomics. Most new studies that examine diverse assemblages of bacteria, archaea, protists, fungi, and viruses lean heavily into eDNA using these newer technologies, as the necessary sequencing technology and bioinformatic tools have become increasingly affordable and user friendly. However, eDNA methods are rapidly evolving, and sometimes it can feel overwhelming to simply keep up with the basics. In this review, we provide a starting point for microbial ecologists who are new to DNA-based methods by detailing the eDNA methods that are most pertinent, including study design, sample collection and storage, selecting the right sequencing technology, lab protocols, equipment, and a few bioinformatic tools. Furthermore, we focus on how eDNA work can benefit restoration and what modifications are needed when working in this subfield.}, } @article {pmid36732517, year = {2023}, author = {Deng, K and Xu, JJ and Shen, L and Zhao, H and Gou, W and Xu, F and Fu, Y and Jiang, Z and Shuai, M and Li, BY and Hu, W and Zheng, JS and Chen, YM}, title = {Comparison of fecal and blood metabolome reveals inconsistent associations of the gut microbiota with cardiometabolic diseases.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {571}, pmid = {36732517}, issn = {2041-1723}, mesh = {Adult ; Middle Aged ; Aged ; Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2 ; RNA, Ribosomal, 16S ; Metabolome ; Metabolomics/methods ; Feces ; *Cardiovascular Diseases ; }, abstract = {Blood metabolome is commonly used in human studies to explore the associations of gut microbiota-derived metabolites with cardiometabolic diseases. Here, in a cohort of 1007 middle-aged and elderly adults with matched fecal metagenomic (149 species and 214 pathways) and paired fecal and blood targeted metabolomics data (132 metabolites), we find disparate associations with taxonomic composition and microbial pathways when using fecal or blood metabolites. For example, we observe that fecal, but not blood butyric acid significantly associates with both gut microbiota and prevalent type 2 diabetes. These findings are replicated in an independent validation cohort involving 103 adults. Our results suggest that caution should be taken when inferring microbiome-cardiometabolic disease associations from either blood or fecal metabolome data.}, } @article {pmid36731616, year = {2023}, author = {Li, X and Li, K and Wang, Y and Huang, Y and Yang, H and Zhu, P and Li, Q}, title = {Diversity of lignocellulolytic functional genes and heterogeneity of thermophilic microbes during different wastes composting.}, journal = {Bioresource technology}, volume = {372}, number = {}, pages = {128697}, doi = {10.1016/j.biortech.2023.128697}, pmid = {36731616}, issn = {1873-2976}, mesh = {*Composting ; Manure/microbiology ; Lignin/metabolism ; Bacteria/genetics/metabolism ; Fungi/genetics/metabolism ; *Microbiota ; Soil ; }, abstract = {The goal of this study was to investigate the heterogeneity of thermophilic microorganisms and their lignocellulose-degrading gene diversity during composting. In this study, bagasse pith/dairy manure (BAG) and sawdust/dairy manure (SAW) were used as experimental subjects. The pour plate method indicated that thermophilic bacteria and thermophilic actinobacteria were more culturable than thermophilic fungi. Metagenomics analysis showed that the Actinobacteria, Firmicutes and Proteobacteria were the dominant phyla during composting. In addition, auxiliary activity and glycoside hydrolase families were critical for lignocellulosic degradation, which were found to be more abundant in BAG. As a result, the degradation rates of cellulose, hemicellulose and lignin in BAG (7.36%, 13.99% and 5.68%) were observably higher than those in SAW (6.13%, 12.09% and 2.62%). These findings contribute to understanding how thermophilic microbial communities play a role in the deconstruction of different lignocelluloses and provide a potential strategy to comprehensively utilize the resources of lignocellulosic biomass.}, } @article {pmid36731187, year = {2023}, author = {Bai, H and He, LY and Gao, FZ and Wu, DL and Yao, KS and Zhang, M and Jia, WL and He, LX and Zou, HY and Yao, MS and Ying, GG}, title = {Airborne antibiotic resistome and human health risk in railway stations during COVID-19 pandemic.}, journal = {Environment international}, volume = {172}, number = {}, pages = {107784}, pmid = {36731187}, issn = {1873-6750}, mesh = {Humans ; Genes, Bacterial ; Pandemics ; Anti-Bacterial Agents/pharmacology ; Bayes Theorem ; *COVID-19 ; Bacteria/genetics ; *Microbiota ; }, abstract = {Antimicrobial resistance is recognized as one of the greatest public health concerns. It is becoming an increasingly threat during the COVID-19 pandemic due to increasing usage of antimicrobials, such as antibiotics and disinfectants, in healthcare facilities or public spaces. To explore the characteristics of airborne antibiotic resistome in public transport systems, we assessed distribution and health risks of airborne antibiotic resistome and microbiome in railway stations before and after the pandemic outbreak by culture-independent and culture-dependent metagenomic analysis. Results showed that the diversity of airborne antibiotic resistance genes (ARGs) decreased following the pandemic, while the relative abundance of core ARGs increased. A total of 159 horizontally acquired ARGs, predominantly confering resistance to macrolides and aminoglycosides, were identified in the airborne bacteria and dust samples. Meanwhile, the abundance of horizontally acquired ARGs hosted by pathogens increased during the pandemic. A bloom of clinically important antibiotic (tigecycline and meropenem) resistant bacteria was found following the pandemic outbreak. 251 high-quality metagenome-assembled genomes (MAGs) were recovered from 27 metagenomes, and 86 genera and 125 species were classified. Relative abundance of ARG-carrying MAGs, taxonomically assigned to genus of Bacillus, Pseudomonas, Acinetobacter, and Staphylococcus, was found increased during the pandemic. Bayesian source tracking estimated that human skin and anthropogenic activities were presumptive resistome sources for the public transit air. Moreover, risk assessment based on resistome and microbiome data revealed elevated airborne health risks during the pandemic.}, } @article {pmid36730456, year = {2023}, author = {Satoh, S and Tanaka, R and Yokono, M and Endoh, D and Yabuki, T and Tanaka, A}, title = {Phylogeny analysis of whole protein-coding genes in metagenomic data detected an environmental gradient for the microbiota.}, journal = {PloS one}, volume = {18}, number = {2}, pages = {e0281288}, pmid = {36730456}, issn = {1932-6203}, mesh = {Phylogeny ; *Metagenome ; *Microbiota/genetics ; Japan ; Metagenomics/methods ; }, abstract = {Environmental factors affect the growth of microorganisms and therefore alter the composition of microbiota. Correlative analysis of the relationship between metagenomic composition and the environmental gradient can help elucidate key environmental factors and establishment principles for microbial communities. However, a reasonable method to quantitatively compare whole metagenomic data and identify the primary environmental factors for the establishment of microbiota has not been reported so far. In this study, we developed a method to compare whole proteomes deduced from metagenomic shotgun sequencing data, and quantitatively display their phylogenetic relationships as metagenomic trees. We called this method Metagenomic Phylogeny by Average Sequence Similarity (MPASS). We also compared one of the metagenomic trees with dendrograms of environmental factors using a comparison tool for phylogenetic trees. The MPASS method correctly constructed metagenomic trees of simulated metagenomes and soil and water samples. The topology of the metagenomic tree of samples from the Kirishima hot springs area in Japan was highly similarity to that of the dendrograms based on previously reported environmental factors for this area. The topology of the metagenomic tree also reflected the dynamics of microbiota at the taxonomic and functional levels. Our results strongly suggest that MPASS can successfully classify metagenomic shotgun sequencing data based on the similarity of whole protein-coding sequences, and will be useful for the identification of principal environmental factors for the establishment of microbial communities. Custom Perl script for the MPASS pipeline is available at https://github.com/s0sat/MPASS.}, } @article {pmid36727264, year = {2023}, author = {Gendron, EM and Sevigny, JL and Byiringiro, I and Thomas, WK and Powers, TO and Porazinska, DL}, title = {Nematode mitochondrial metagenomics: A new tool for biodiversity analysis.}, journal = {Molecular ecology resources}, volume = {23}, number = {5}, pages = {975-989}, doi = {10.1111/1755-0998.13761}, pmid = {36727264}, issn = {1755-0998}, support = {AWD07689//National Institute of Food and Agriculture/ ; NH00694//National Institute of Food and Agriculture/ ; }, mesh = {Animals ; Phylogeny ; Metagenomics ; *Nematoda/genetics ; Biodiversity ; DNA ; DNA Barcoding, Taxonomic ; *Genome, Mitochondrial/genetics ; }, abstract = {DNA barcoding approaches have greatly increased our understanding of biodiversity on the planet, and metabarcoding is widely used for classifying members of the phylum Nematoda. However, loci typically utilized in metabarcoding studies are often unable to resolve closely related species or are unable to recover all taxa present in a sample due to inadequate PCR primer binding. Mitochondrial metagenomics (mtMG) is an alternative approach utilizing shotgun sequencing of total DNA to recover the mitochondrial genomes of all species present in samples. However, this approach requires a comprehensive reference database for identification and currently available mitochondrial sequences for nematodes are highly dominated by sequences from the order Rhabditida, and excludes many clades entirely. Here, we analysed the efficacy of mtMG for the recovery of nematode taxa and the generation of mitochondrial genomes. We first developed a curated reference database of nematode mitochondrial sequences and expanded it with 40 newly sequenced taxa. We then tested the mito-metagenomics approach using a series of nematode mock communities consisting of morphologically identified nematode species representing various feeding traits, life stages, and phylogenetic relationships. We were able to identify all but two species through the de novo assembly of COX1 genes. We were also able to recover additional mitochondrial protein coding genes (PCGs) for 23 of the 24 detected species including a full array of 12 PCGs from five of the species. We conclude that mtMG offers a potential for the effective recovery of nematode biodiversity but remains limited by the breadth of the reference database.}, } @article {pmid36725284, year = {2023}, author = {Shinde, PB and Mohite, SV and Yadav, A and Singh, MK and Kedia, S and Ahuja, V and Sharma, KK}, title = {Functional analysis of metalloenzymes from human gut microbiota and their role in ulcerative colitis.}, journal = {Journal of applied microbiology}, volume = {134}, number = {3}, pages = {}, doi = {10.1093/jambio/lxad016}, pmid = {36725284}, issn = {1365-2672}, support = {5/4/8-1/2019-NCD-II//Indian Council of Medical Research/ ; 1196SR/FST/LS-I/2017/4//DST-FIST/ ; }, mesh = {Humans ; *Colitis, Ulcerative/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {AIM: Metalloenzymes produced by gut microbiota play an essential role in various physiological processes, and maintains homeostasis of gastrointestinal tract. Our study includes functional analysis of microbial metalloenzymes using metagenomics and metatranscriptomics data from Inflammatory Bowel Disease Multiomics Database.

METHODS AND RESULTS: The distance matrix calculated by using metalloenzymes data produced significant results for bacterial taxonomy, with higher variance compared to HMP analysis in both Western and Indian population. Differential gene expression analysis revealed altered expression of ulcerative colitis (UC)-associated enzymes, increased folds changes in Prevotella and Megamonas transcripts; whereas, low transcripts of Alistipes genera. Further, docking and simulation studies performed on screened UC-associated enzymes revealed changes in catalytic efficiency and ligand interacting residues.

CONCLUSION: The β-diversity using microbes containing metalloenzymes suggests considering small group of specific genes or enzymes for understanding the diversity between UC and healthy individuals. The docking and differential gene expression analysis collectively indicate the probable role of metalloenzymes and few UC-associated enzymes in the severity of UC.}, } @article {pmid36725208, year = {2023}, author = {Walsh, AM and Leech, J and Huttenhower, C and Delhomme-Nguyen, H and Crispie, F and Chervaux, C and Cotter, PD}, title = {Integrated molecular approaches for fermented food microbiome research.}, journal = {FEMS microbiology reviews}, volume = {47}, number = {2}, pages = {}, pmid = {36725208}, issn = {1574-6976}, mesh = {Animals ; Humans ; *Microbiota ; Diet ; *Fermented Foods ; Fermentation ; High-Throughput Nucleotide Sequencing ; }, abstract = {Molecular technologies, including high-throughput sequencing, have expanded our perception of the microbial world. Unprecedented insights into the composition and function of microbial communities have generated large interest, with numerous landmark studies published in recent years relating the important roles of microbiomes and the environment-especially diet and nutrition-in human, animal, and global health. As such, food microbiomes represent an important cross-over between the environment and host. This is especially true of fermented food microbiomes, which actively introduce microbial metabolites and, to a lesser extent, live microbes into the human gut. Here, we discuss the history of fermented foods, and examine how molecular approaches have advanced research of these fermented foods over the past decade. We highlight how various molecular approaches have helped us to understand the ways in which microbes shape the qualities of these products, and we summarize the impacts of consuming fermented foods on the gut. Finally, we explore how advances in bioinformatics could be leveraged to enhance our understanding of fermented foods. This review highlights how integrated molecular approaches are changing our understanding of the microbial communities associated with food fermentation, the creation of unique food products, and their influences on the human microbiome and health.}, } @article {pmid36725090, year = {2023}, author = {Verburgt, CM and Dunn, KA and Otley, A and Heyman, MB and Verstraete, S and Sunseri, W and Sylvester, F and de Meij, T and Comeau, A and Langille, M and de Jonge, WJ and Benninga, MA and Van Limbergen, JE}, title = {Personalised azithromycin+metronidazole (PAZAZ), in combination with standard induction therapy, to achieve a faecal microbiome community structure and metagenome changes associated with sustained remission in paediatric Crohn's disease (CD): protocol of a pilot study.}, journal = {BMJ open}, volume = {13}, number = {2}, pages = {e064944}, pmid = {36725090}, issn = {2044-6055}, mesh = {Humans ; Child ; *Crohn Disease/drug therapy ; Azithromycin/therapeutic use ; Metronidazole/therapeutic use ; Pilot Projects ; Induction Chemotherapy/methods ; Metagenome ; Bayes Theorem ; RNA, Ribosomal, 16S ; Anti-Bacterial Agents/therapeutic use ; Remission Induction ; *Microbiota ; Recurrence ; Randomized Controlled Trials as Topic ; Multicenter Studies as Topic ; }, abstract = {INTRODUCTION: Early relapse in Crohn's disease (CD) is associated with a more severe disease course. The microbiome plays a crucial role, yet strategies targeting the microbiome are underrepresented in current guidelines. We hypothesise that early manipulation of the microbiome will improve clinical response to standard-of-care (SOC) induction therapy in patients with a relapse-associated microbiome profile. We describe the protocol of a pilot study assessing feasibility of treatment allocation based on baseline faecal microbiome profiles.

METHODS AND ANALYSIS: This is a 52-week, multicentre, randomised, controlled, open-label, add-on pilot study to test the feasibility of a larger multicontinent trial evaluating the efficacy of adjuvant antibiotic therapy in 20 paediatric patients with mild-to-moderate-CD (10
ETHICS AND DISSEMINATION: This study was approved by METC-AMC and CCMO (Netherlands) and IWK Health Centre (Canada). The first version of this protocol was approved by North Carolina Children's Hospital (USA), Wolfson Medical Centre (Israel). The FDA (USA), Health Canada and Ministry of Health (Israel) have reviewed and approved the protocol. Results will be published in international peer-reviewed journals and summaries will be provided to the funders and participants.

TRIAL REGISTRATION NUMBER: NCT04186247.}, } @article {pmid36724220, year = {2023}, author = {Ngugi, DK and Salcher, MM and Andrei, AS and Ghai, R and Klotz, F and Chiriac, MC and Ionescu, D and Büsing, P and Grossart, HP and Xing, P and Priscu, JC and Alymkulov, S and Pester, M}, title = {Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes.}, journal = {Science advances}, volume = {9}, number = {5}, pages = {eadc9392}, pmid = {36724220}, issn = {2375-2548}, mesh = {*Archaea/genetics ; *Lakes ; Ammonia ; Ecosystem ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline in lacustrine systems. An unbiased global assessment of lacustrine AOA diversity is critical for understanding their origins, dispersal mechanisms, and ecosystem roles. Here, we leveraged continental-scale metagenomics to document that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We show that the uncultured freshwater AOA, "Candidatus Nitrosopumilus limneticus," is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia.}, } @article {pmid36722794, year = {2023}, author = {Guo, W and Ren, K and Ning, R and Li, C and Zhang, Y and Gan, Y and Fu, X and Xiao, C and Pang, Y and Cheng, L and Zhang, S and Li, D and Zhao, J and Dai, M and Li, Y}, title = {Microbial species from multiple maternal body sites shape the developing giant panda (Ailuropoda melanoleuca) cub gut microbiome.}, journal = {Molecular ecology}, volume = {32}, number = {9}, pages = {2271-2286}, doi = {10.1111/mec.16869}, pmid = {36722794}, issn = {1365-294X}, mesh = {Animals ; Female ; Bacteria/genetics ; Diet/veterinary ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Ursidae/genetics ; }, abstract = {The gut microbiome of the giant panda (Ailuropoda melanoleuca) plays a vital role in nutrient acquisition from its specialized bamboo diet. Giant panda cubs harbour significantly different gut microbiota during their growth and development when feeding on milk before switching to bamboo. The fetal gut is sterile, and following birth, mother-to-infant microbial transmission has been implicated as a seeding source for the infant gut microbiota. Details of this transmission in giant pandas remain unclear. In this study, faecal samples were collected from seven panda mother-cub pairs when the cubs were 4-16 months old. Additional samples from the cubs' diet, soil and drinking water, and multiple body sites of the mothers were collected. Bacterial 16S rRNA gene sequencing and shotgun metagenomic sequencing were performed to determine the source and potential transmission routes of the cub gut microbiome. Source tracking analysis showed that maternal vagina, milk and faeces were the primary contributory sources of microbes, shaping the cub gut microbiome. Bacterial species from maternal faeces persisted the longest in the cub gut. Bacterial species in the diet contributed to the microbial community. Metagenomics analysis indicated that the predicted metabolic pathways of the gut microbiome also varied at different growth stages. Gut colonization with bacteria from various body sites of the mothers provides a foundational microbial community that is beneficial in fulfilling the evolving dietary needs of the cubs. This study suggests that mother-to-cub transmission is indispensable in shaping the gut microbiome of the developing panda cub.}, } @article {pmid36722516, year = {2023}, author = {Kwa, WT and Sundarajoo, S and Toh, KY and Lee, J}, title = {Application of emerging technologies for gut microbiome research.}, journal = {Singapore medical journal}, volume = {64}, number = {1}, pages = {45-52}, pmid = {36722516}, issn = {2737-5935}, mesh = {Humans ; *Gastrointestinal Microbiome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Health Status ; }, abstract = {Microbiome is associated with a wide range of diseases. The gut microbiome is also a dynamic reflection of health status, which can be modified, thus representing great potential to exploit the mechanisms that influence human physiology. Recent years have seen a dramatic rise in gut microbiome studies, which has been enabled by the rapidly evolving high-throughput sequencing methods (i.e. 16S rRNA sequencing and shotgun sequencing). As the emerging technologies for microbiome research continue to evolve (i.e. metatranscriptomics, metabolomics, culturomics, synthetic biology), microbiome research has moved beyond phylogenetic descriptions and towards mechanistic analyses. In this review, we highlight different approaches to study the microbiome, in particular, the current limitations and future promise of these techniques. This review aims to provide clinicians with a framework for studying the microbiome, as well as to accelerate the adoption of these techniques in clinical practice.}, } @article {pmid36721270, year = {2023}, author = {Yang, K and Wang, X and Hou, R and Lu, C and Fan, Z and Li, J and Wang, S and Xu, Y and Shen, Q and Friman, VP and Wei, Z}, title = {Rhizosphere phage communities drive soil suppressiveness to bacterial wilt disease.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {16}, pmid = {36721270}, issn = {2049-2618}, mesh = {Rhizosphere ; Bacteria/genetics ; *Bacteriophages ; *Microbiota ; Soil ; }, abstract = {BACKGROUND: Bacterial viruses, phages, play a key role in nutrient turnover and lysis of bacteria in terrestrial ecosystems. While phages are abundant in soils, their effects on plant pathogens and rhizosphere bacterial communities are poorly understood. Here, we used metagenomics and direct experiments to causally test if differences in rhizosphere phage communities could explain variation in soil suppressiveness and bacterial wilt plant disease outcomes by plant-pathogenic Ralstonia solanacearum bacterium. Specifically, we tested two hypotheses: (1) that healthy plants are associated with stronger top-down pathogen control by R. solanacearum-specific phages (i.e. 'primary phages') and (2) that 'secondary phages' that target pathogen-inhibiting bacteria play a stronger role in diseased plant rhizosphere microbiomes by indirectly 'helping' the pathogen.

RESULTS: Using a repeated sampling of tomato rhizosphere soil in the field, we show that healthy plants are associated with distinct phage communities that contain relatively higher abundances of R. solanacearum-specific phages that exert strong top-down pathogen density control. Moreover, 'secondary phages' that targeted pathogen-inhibiting bacteria were more abundant in the diseased plant microbiomes. The roles of R. solanacearum-specific and 'secondary phages' were directly validated in separate greenhouse experiments where we causally show that phages can reduce soil suppressiveness, both directly and indirectly, via top-down control of pathogen densities and by alleviating interference competition between pathogen-inhibiting bacteria and the pathogen.

CONCLUSIONS: Together, our findings demonstrate that soil suppressiveness, which is most often attributed to bacteria, could be driven by rhizosphere phage communities that regulate R. solanacearum densities and strength of interference competition with pathogen-suppressing bacteria. Rhizosphere phage communities are hence likely to be important in determining bacterial wilt disease outcomes and soil suppressiveness in agricultural fields. Video Abstract.}, } @article {pmid36720887, year = {2023}, author = {Du, Y and Fuhrman, JA and Sun, F}, title = {ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {502}, pmid = {36720887}, issn = {2041-1723}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; R01 GM131407/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cattle ; Female ; Humans ; Metagenome/genetics ; Metagenomics ; Wastewater ; Genome, Viral/genetics ; *Microbiota ; *Bacteriophages/genetics ; }, abstract = {The introduction of high-throughput chromosome conformation capture (Hi-C) into metagenomics enables reconstructing high-quality metagenome-assembled genomes (MAGs) from microbial communities. Despite recent advances in recovering eukaryotic, bacterial, and archaeal genomes using Hi-C contact maps, few of Hi-C-based methods are designed to retrieve viral genomes. Here we introduce ViralCC, a publicly available tool to recover complete viral genomes and detect virus-host pairs using Hi-C data. Compared to other Hi-C-based methods, ViralCC leverages the virus-host proximity structure as a complementary information source for the Hi-C interactions. Using mock and real metagenomic Hi-C datasets from several different microbial ecosystems, including the human gut, cow fecal, and wastewater, we demonstrate that ViralCC outperforms existing Hi-C-based binning methods as well as state-of-the-art tools specifically dedicated to metagenomic viral binning. ViralCC can also reveal the taxonomic structure of viruses and virus-host pairs in microbial communities. When applied to a real wastewater metagenomic Hi-C dataset, ViralCC constructs a phage-host network, which is further validated using CRISPR spacer analyses. ViralCC is an open-source pipeline available at https://github.com/dyxstat/ViralCC .}, } @article {pmid36717776, year = {2023}, author = {Champion, C and Neagoe, RM and Effernberger, M and Sala, DT and Servant, F and Christensen, JE and Arnoriaga-Rodriguez, M and Amar, J and Lelouvier, B and Loubieres, P and Azalbert, V and Minty, M and Thomas, C and Blasco-Baque, V and Gamboa, F and Tilg, H and Cardellini, M and Federici, M and Fernández-Real, JM and Loubes, JM and Burcelin, R}, title = {Human liver microbiota modeling strategy at the early onset of fibrosis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {34}, pmid = {36717776}, issn = {1471-2180}, support = {6869/12.06.2014//VAIOMER SAS/ ; }, mesh = {Humans ; DNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Fibrosis ; *Liver Cirrhosis ; *Microbiota ; }, abstract = {BACKGROUND: Gut microbiota is involved in the development of liver diseases such as fibrosis. We and others identified that selected sets of gut bacterial DNA and bacteria translocate to tissues, notably the liver, to establish a non-infectious tissue microbiota composed of microbial DNA and a low frequency live bacteria. However, the precise set of bacterial DNA, and thereby the corresponding taxa associated with the early stages of fibrosis need to be identified. Furthermore, to overcome the impact of different group size and patient origins we adapted innovative statistical approaches. Liver samples with low liver fibrosis scores (F0, F1, F2), to study the early stages of the disease, were collected from Romania(n = 36), Austria(n = 10), Italy(n = 19), and Spain(n = 17). The 16S rRNA gene was sequenced. We considered the frequency, sparsity, unbalanced sample size between cohorts to identify taxonomic profiles and statistical differences.

RESULTS: Multivariate analyses, including adapted spectral clustering with L1-penalty fair-discriminant strategies, and predicted metagenomics were used to identify that 50% of liver taxa associated with the early stage fibrosis were Enterobacteriaceae, Pseudomonadaceae, Xanthobacteriaceae and Burkholderiaceae. The Flavobacteriaceae and Xanthobacteriaceae discriminated between F0 and F1. Predicted metagenomics analysis identified that the preQ0 biosynthesis and the potential pathways involving glucoryranose and glycogen degradation were negatively associated with liver fibrosis F1-F2 vs F0.

CONCLUSIONS: Without demonstrating causality, our results suggest first a role of bacterial translocation to the liver in the progression of fibrosis, notably at the earliest stages. Second, our statistical approach can identify microbial signatures and overcome issues regarding sample size differences, the impact of environment, and sets of analyses.

TRIAL REGISTRATION: TirguMECCH ROLIVER Prospective Cohort for the Identification of Liver Microbiota, registration 4065/2014. Registered 01 01 2014.}, } @article {pmid36715883, year = {2024}, author = {Song, Y and Sun, M and Ma, F and Xu, D and Mu, G and Jiao, Y and Yu, P and Tuo, Y}, title = {Lactiplantibacillus plantarum DLPT4 Protects Against Cyclophosphamide-Induced Immunosuppression in Mice by Regulating Immune Response and Intestinal Flora.}, journal = {Probiotics and antimicrobial proteins}, volume = {16}, number = {2}, pages = {321-333}, pmid = {36715883}, issn = {1867-1314}, support = {31571813//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Mice ; Cytokines/metabolism ; *Gastrointestinal Microbiome ; Immunosuppression Therapy ; Cyclophosphamide/adverse effects/analysis ; Tumor Necrosis Factor-alpha/genetics ; Immunity ; *Lactobacillus plantarum/metabolism ; *Probiotics ; }, abstract = {In this study, the strain Lactiplantibacillus plantarum DLPT4 was investigated for the immunostimulatory activity in cyclophosphamide (CTX)-induced immunosuppressed BALB/c mice. L. plantarum DLPT4 was administered to BALB/c mice by oral gavage for 30 days, and CTX was injected intraperitoneally from the 25th to the 27th days. Intraperitoneal injection of CTX caused damage to the thymic cortex and intestines, and the immune dysfunction of the BALB/c mice. L. plantarum DLPT4 oral administration exerted immunoregulating effects evidenced by increasing serum immunoglobulin (IgA, IgG, and IgM) levels and reducing the genes expression of pro-inflammatory factors (IL-6, IL-1β, and TNF-α) of the CTX-induced immunosuppressed mice. The results of the metagenome-sequencing analysis showed that oral administration of L. plantarum DLPT4 could regulate the intestinal microbial community of the immunosuppressed mice by changing the ratio of Lactiplantibacillus and Bifidobacterium. Meanwhile, the abundance of carbohydrate enzyme (CAZyme), immune diseases metabolic pathways, and AP-1/MAPK signaling pathways were enriched in the mice administrated with L. plantarum DLPT4. In conclusion, oral administration of L. plantarum DLPT4 ameliorated symptoms of CTX-induced immunosuppressed mice by regulating gut microbiota, influencing the abundance of carbohydrate esterase in the intestinal flora, and enhancing immune metabolic activity. L. plantarum DLPT4 could be a potential probiotic to regulate the immune response.}, } @article {pmid36715435, year = {2023}, author = {Liu, J and Ding, H and Yan, C and He, Z and Zhu, H and Ma, KY}, title = {Effect of tea catechins on gut microbiota in high fat diet-induced obese mice.}, journal = {Journal of the science of food and agriculture}, volume = {103}, number = {5}, pages = {2436-2445}, doi = {10.1002/jsfa.12476}, pmid = {36715435}, issn = {1097-0010}, support = {//Joint Laboratory for International Cooperation in Grain Circulation and Security/ ; //Natural Science Foundation of the Higher Education Institutions of Jiangsu Province/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD)/ ; //Jiangsu Province/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; //International Cooperation/ ; }, mesh = {Mice ; Animals ; Diet, High-Fat ; *Gastrointestinal Microbiome ; Mice, Obese ; *Catechin ; Mice, Inbred C57BL ; Obesity/metabolism ; Tea/chemistry ; }, abstract = {BACKGROUND: Tea catechins have been shown to have beneficial effects on the alleviation of obesity, the prevention of diabetes, and the amelioration of metabolic syndrome. The purpose of the present work is to explore the underlying mechanisms linking the intestinal microbiota and anti-obesity benefits of green tea, oolong tea, and black tea catechins in C57BL/6J mice fed with a high-fat diet (HFD).

RESULTS: The results indicated that, after the dietary intake of three tea catechins, obesity and low-grade inflammation were significantly alleviated. Hepatic steatosis was prevented, and this was accompanied by the upregulation of the mRNA and protein expressions of hepatic peroxisome proliferator-activated receptor α (PPARα). Metagenomic analysis of fecal samples suggested that the three tea catechins similarly changed the microbiota in terms of overall structure, composition, and protein functions by regulating the metabolites, facilitating the generation of short-chain fatty acids (SCFAs), and repressing lipopolysaccharides.

CONCLUSION: The anti-obese properties of three tea catechins were partially mediated by their positive effect on gut microbiota, hepatic steatosis alleviation, and anti-inflammatory activity. © 2023 Society of Chemical Industry.}, } @article {pmid36713446, year = {2022}, author = {Chen, C and Yan, Q and Yao, X and Li, S and Lv, Q and Wang, G and Zhong, Q and Tang, F and Liu, Z and Huang, Y and An, Y and Zhou, J and Zhang, Q and Zhang, A and Ullah, H and Zhang, Y and Liu, C and Zhu, D and Li, H and Sun, W and Ma, W}, title = {Alterations of the gut virome in patients with systemic lupus erythematosus.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1050895}, pmid = {36713446}, issn = {1664-3224}, mesh = {Humans ; Virome ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Lupus Erythematosus, Systemic/microbiology ; Bacteria/genetics ; *Viruses/genetics ; }, abstract = {BACKGROUND: Systemic lupus erythematosus (SLE) is a systemic autoimmune disease that has been linked to the dysbiosis of the gut microbiome and virome. However, the potential characterization of the gut virome in SLE patients needs to be explored more extensively.

METHODS: Herein, we analyzed the gut viral community of 16 SLE patients and 31 healthy controls using both bulk and virus-like particle (VLP)-based metagenomic sequencing of their fecal samples. A total of 15,999 non-redundant viral operational taxonomic units (vOTUs) were identified from the metagenomic assembled contigs and used for gut virome profiling.

RESULTS: SLE patients exhibited a significant decrease in gut viral diversity in the bulk metagenome dataset, but this change was not significant in the VLP metagenome dataset. Also, considerable alterations of the overall gut virome composition and remarkable changes in the viral family compositions were observed in SLE patients compared with healthy controls, as observed in both two technologies. We identified 408 vOTUs (177 SLE-enriched and 231 control-enriched) with significantly different relative abundances between patients and controls in the bulk virome, and 18 vOTUs (17 SLE-enriched in 1 control-enriched) in the VLP virome. The SLE-enriched vOTUs included numerous Siphoviridae, Microviridae, and crAss-like viruses and were frequently predicted to infect Bacteroides, Parabacteroides, and Ruminococcus_E, while the control-enriched contained numerous members of Siphoviridae and Myoviridae and were predicted to infect Prevotella and Lachnospirales_CAG-274. We explored the correlations between gut viruses and bacteria and found that some Lachnospirales_CAG-274 and Hungatella_A phages may play key roles in the virus-bacterium network. Furthermore, we explored the gut viral signatures for disease discrimination and achieved an area under the receiver operator characteristic curve (AUC) of above 0.95, suggesting the potential of the gut virome in the prediction of SLE.

CONCLUSION: Our findings demonstrated the alterations in viral diversity and taxonomic composition of the gut virome of SLE patients. Further research into the etiology of SLE and the gut viral community will open up new avenues for treating and preventing SLE and other autoimmune diseases.}, } @article {pmid36710967, year = {2022}, author = {Xiao, QY and Ye, TY and Wang, XL and Qi, DM and Cheng, XR}, title = {Effects of Qi-Fu-Yin on aging of APP/PS1 transgenic mice by regulating the intestinal microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1048513}, pmid = {36710967}, issn = {2235-2988}, mesh = {Mice ; Animals ; Mice, Transgenic ; *Gastrointestinal Microbiome ; Amyloid beta-Protein Precursor/genetics ; *Alzheimer Disease ; Aging/metabolism ; Carbohydrates ; Disease Models, Animal ; }, abstract = {INTRODUCTION: Alzheimer's disease is the most common form of dementia and closely related to aging. Qi-Fu-Yin is widely used to treat dementia, but its anti-aging effects is unknown.

METHODS: We used 11-month-old APP/PS1 transgenic mice for behavioral tests to observe the changes in cognitive function and age-related symptoms after Qi-Fu-Yin treatment. Fecal samples were collected for 16sRNA sequencing and metagenomic sequencing. Differences among the groups of intestinal microbiota and the associations with aging and intestinal microbiota were analyzed based on the results.

RESULTS: Here we found that Qi-Fu-Yin improved the ability of motor coordination, raised survival rate and prolonged the survival days under cold stress stimulation in aged APP/ PS1 transgenic mice. Our data from 16sRNA and metagenomic sequencing showed that at the Family level, the intestinal microbiota was significantly different among wild-type mice, APP/PS1 transgenic mice and the Qi-Fu-Yin group by PCA analysis. Importantly, Qi-Fu-Yin improved the functional diversity of the major KEGG pathways, carbohydrate-active enzymes, and major virulence factors in the intestinal flora of APP/PS1 transgenic mice. Among them, the functions of eight carbohydrate-active enzymes (GT2_Glycos_transf_2, GT4, GT41, GH2, CE1, CE10, CE3, and GH24) and the functions of top three virulence factors (defensive virulence factors, offensive virulence factors and nonspecific virulence factors) were significantly and positively correlated with the level of grasping ability. We further indicated that the Qi-Fu-Yin significantly reduced the plasma levels of IL-6.

CONCLUSION: Our results indicated that the effects of Qi-Fu-Yin anti-aging of APP/PS1 transgenic mice might be through the regulation of intestinal flora diversity, species richness and the function of major active enzymes.}, } @article {pmid36707995, year = {2023}, author = {Chang, D and Gupta, VK and Hur, B and Cunningham, KY and Sung, J}, title = {GMWI-webtool: a user-friendly browser application for assessing health through metagenomic gut microbiome profiling.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {2}, pages = {}, pmid = {36707995}, issn = {1367-4811}, support = {UL1 TR002377/TR/NCATS NIH HHS/United States ; UL1 TR002494/TR/NCATS NIH HHS/United States ; }, mesh = {*Metagenome ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Feces ; }, abstract = {SUMMARY: We recently introduced the Gut Microbiome Wellness Index (GMWI), a stool metagenome-based indicator for assessing health by determining the likelihood of disease given the state of one's gut microbiome. The calculation of our wellness index depends on the relative abundances of health-prevalent and health-scarce species. Encouragingly, GMWI has already been utilized in various studies focusing on differences in the gut microbiome between cases and controls. Herein, we introduce the GMWI-webtool, a user-friendly browser application that computes GMWI, health-prevalent/-scarce species' relative abundances, and α-diversities from stool shotgun metagenome taxonomic profiles. Users of our interactive online tool can visualize their results and compare them side-by-side with those from our pooled reference dataset of metagenomes, as well as export data in.csv format and high-resolution figures.

GMWI-webtool is freely available here: https://gmwi-webtool.github.io/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36707764, year = {2023}, author = {Pantoja-Feliciano, IG and Karl, JP and Perisin, M and Doherty, LA and McClung, HL and Armstrong, NJ and Renberg, R and Racicot, K and Branck, T and Arcidiacono, S and Soares, JW}, title = {In vitro gut microbiome response to carbohydrate supplementation is acutely affected by a sudden change in diet.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {32}, pmid = {36707764}, issn = {1471-2180}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Diet ; Feces/microbiology ; Carbohydrates ; Starch/metabolism ; Dietary Supplements ; }, abstract = {BACKGROUND: Interactions between diet, stress and the gut microbiome are of interest as a means to modulate health and performance. Here, in vitro fermentation was used to explore the effects of a sudden change in diet, 21 days sole sustenance on the Meal, Ready-to-Eat (MRE) U.S. military combat ration, on inter-species competition and functional potential of the human gut microbiota. Human fecal samples collected before and after MRE intervention or consuming a habitual diet (HAB) were introduced to nutrient-rich media supplemented with starch for in vitro fermentation under ascending colon conditions. 16S rRNA amplicon and Whole-metagenome sequencing (WMS) were used to measure community composition and functional potential. Specific statistical analyses were implemented to detect changes in relative abundance from taxa, genes and pathways.

RESULTS: Differential changes in relative abundance of 11 taxa, Dorea, Lachnospira, Bacteroides fragilis, Akkermansia muciniphila, Bifidobacterium adolescentis, Betaproteobacteria, Enterobacteriaceae, Bacteroides egerthii, Ruminococcus bromii, Prevotella, and Slackia, and nine Carbohydrate-Active Enzymes, specifically GH13_14, over the 24 h fermentation were observed as a function of the diet intervention and correlated to specific taxa of interest.

CONCLUSIONS: These findings suggest that consuming MRE for 21 days acutely effects changes in gut microbiota structure in response to carbohydrate but may induce alterations in metabolic capacity. Additionally, these findings demonstrate the potential of starch as a candidate supplemental strategy to functionally modulate specific gut commensals during stress-induced states.}, } @article {pmid36706527, year = {2023}, author = {Wei, X and Peng, H and Li, Y and Meng, B and Wang, S and Bi, S and Zhao, X}, title = {Pyrethroids exposure alters the community and function of the internal microbiota in Aedes albopictus.}, journal = {Ecotoxicology and environmental safety}, volume = {252}, number = {}, pages = {114579}, doi = {10.1016/j.ecoenv.2023.114579}, pmid = {36706527}, issn = {1090-2414}, mesh = {Animals ; *Insecticides/pharmacology ; Permethrin/toxicity ; *Aedes ; Mosquito Vectors ; *Pyrethrins/pharmacology ; Insecticide Resistance/genetics ; *Microbiota ; }, abstract = {Large amounts of insecticides bring selection pressure and then develop insecticide resistance in Aedes albopictus. This study demonstrated for the first time the effect of pyrethroid exposure on the internal microbiota in Ae. albopictus. 36, 48, 57 strains of virgin adult Ae. albopictus were exposed to the pyrethroids deltamethrin (Dme group), β-cypermethrin (Bcy group), and cis-permethrin (Cper group), respectively, with n-hexane exposure (Hex group) as the controls (n = 36). The internal microbiota community and functions were analyzed based on the metagenomic analysis. The analysis of similarity (ANOSIM) results showed that the Hex/Bcy (p = 0.001), Hex/Cper (p = 0.006), Hex/Dme (p = 0.001) groups were well separated, and the internal microbes of Ae. albopictus vary in the composition and functions depending on the type of pyrethroid insecticide they are applied. Four short chain fatty acid-producing genera, Butyricimonas, Prevotellaceae, Anaerococcus, Pseudorhodobacter were specifically absent in the pyrethroid-exposed mosquitoes. Morganella and Streptomyces were significantly enriched in cis-permethrin-exposed mosquitoes. Wolbachia and Chryseobacterium showed significant enrichment in β-cypermethrin-exposed mosquitoes. Pseudomonas was significantly abundant in deltamethrin-exposed mosquitoes. The significant proliferation of these bacteria may be closely related to insecticide metabolism. Our study recapitulated a specifically enhanced metabolic networks relevant to the exposure to cis-permethrin and β-cypermethrin, respectively. Benzaldehyde dehydrogenase (EC 1.2.1.28), key enzyme in aromatic compounds metabolism, was detected enhanced in cis-permethrin and β-cypermethrin exposed mosquitoes. The internal microbiota metabolism of aromatic compounds may be important influencing factors for pyrethroid resistance. Future work will be needed to elucidate the specific mechanisms by which mosquito microbiota influences host resistance and vector ability.}, } @article {pmid36705037, year = {2023}, author = {Chiu, CY and Chang, KC and Chang, LC and Wang, CJ and Chung, WH and Hsieh, WP and Su, SC}, title = {Phenotype-specific signatures of systems-level gut microbiome associated with childhood airway allergies.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {34}, number = {1}, pages = {e13905}, doi = {10.1111/pai.13905}, pmid = {36705037}, issn = {1399-3038}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Rhinitis ; *Rhinitis, Allergic ; *Asthma ; Immunoglobulin E/metabolism ; Phenotype ; }, abstract = {BACKGROUND: Perturbation of gut symbiosis has been linked to childhood allergic diseases. However, the underlying host-microbe interaction connected with specific phenotypes is poorly understood.

METHODS: To address this, integrative analyses of stool metagenomic and metabolomic profiles associated with IgE reactions in 56 children with mite-sensitized airway allergies (25 with rhinitis and 31 with asthma) and 28 nonallergic healthy controls were conducted.

RESULTS: We noted a decrease in the number and abundance of gut microbiome-encoded carbohydrate-active enzyme (CAZyme) genes, accompanied with a reduction in species richness, in the asthmatic gut microflora but not in that from allergic rhinitis. Such loss of CAZymes was consistent with the observation that a CAZyme-linked decrease in fecal butyrate was found in asthmatics and negatively correlated with mite-specific IgE responses. Different from the CAZymes, we demonstrated an increase in α diversity at the virulome levels in asthmatic gut microbiota and identified phenotype-specific variations of gut virulome. Moreover, use of fecal metagenomic and metabolomic signatures resulted in distinct effects on differentiating rhinitis and asthma from nonallergic healthy controls.

CONCLUSION: Overall, our integrative analyses reveal several signatures of systems-level gut microbiome in robust associations with fecal metabolites and disease phenotypes, which may be of etiological and diagnostic implications in childhood airway allergies.}, } @article {pmid36704910, year = {2023}, author = {Yuan, X and Zhang, Y and Lin, X and Yang, X and Chen, R}, title = {Association of gut microbiota and glucose metabolism in children with disparate degrees of adiposity.}, journal = {Pediatric obesity}, volume = {18}, number = {4}, pages = {e13009}, doi = {10.1111/ijpo.13009}, pmid = {36704910}, issn = {2047-6310}, mesh = {Male ; Female ; Humans ; Child ; *Gastrointestinal Microbiome ; Blood Glucose ; Adiposity ; *Obesity, Morbid ; Phylogeny ; Obesity/metabolism ; Bacteria ; }, abstract = {OBJECTIVE: To investigate the characteristics of gut microbiota in children with disparate degrees of adiposity, and analyze the association between gut microbiota, glucose metabolism indicators, and inflammatory factors.

METHODS: Clinical data were examined in 89 Chinese children. Children with a body fat percentage ≥ 30% were diagnosed as obese, and ≥ 35% in males and ≥ 40% in females were further defined as severe obesity. The composition of gut microbiota was determined by 16S rDNA-based metagenomics.

RESULTS: The study population (9.75 ± 1.92-year-old) was characterized as normal weight (n = 29), mild obesity (n = 27) and severe obesity (n = 33) groups. Linear discriminant analysis Effect Size (LEfSe) analysis found that compared to the severe obesity group, subjects with mild obesity had more prevalent members of the phylum Fusobacteria, the genus Alistipes, and fewer members of genus Granulicatella and Clostridium (p < 0.05). For subjects with mild obesity, Spearman's correlation analysis revealed that fasting plasma glucose positively correlated with species A. indistinctus, A. putredinis, and negatively correlated with species Ruminococcus gnavus; LBP negatively correlated with species Clostridium hathewayi, and Blautia producta. For subjects with severe obesity, oral glucose tolerance test 2 h plasma glucose (OGTT2HPG) negatively correlated with the phylum Synergistetes, genus Pyramidobacter, species Veillonella parvula, P. piscolens, and positively correlated with species B. producta, INS and HOMA-IR negatively correlated with the genus Haemophilus, species H. parainfluenzae, lipopolysaccharide-binding protein (LBP) negatively correlated with the phylum Actinobacteria, genus Bifidobacterium, Lactobacillus, and species B. longum (all p < 0.05). Phylogenetic investigation of communities by reconstruction of unobserved states 2 (PICRUSt2) analysis discerned that the glucose metabolism pathway, gluconeogenesis I was curtailed in the severe obesity group.

CONCLUSION: The gut microbiota could favourably compensate for glucose metabolism in children with obesity. Genus Haemophilus and Bifidobacterium longum may influence glucose tolerance and insulin resistance in children with severe obesity.}, } @article {pmid36701053, year = {2023}, author = {Li, Y and He, C and Dong, F and Yuan, S and Hu, Z and Wang, W}, title = {Performance of anaerobic digestion of phenol using exogenous hydrogen and granular activated carbon and analysis of microbial community.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {15}, pages = {45077-45087}, pmid = {36701053}, issn = {1614-7499}, support = {2019YFC0408502//the Project of National Key Research and development Program of China/ ; 51878232//National Science Foundation of China/ ; PA2021KCPY0029//the Fundamental Research Funds for the Central Universities of China/ ; DHSZ202203//Anhui Province Key Laboratory of Industrial Wastewater and Environmental Treatment/ ; }, mesh = {*Phenol ; Anaerobiosis ; Charcoal ; Hydrogen ; Phenols ; *Microbiota ; Methane/metabolism ; Bioreactors ; }, abstract = {Anaerobic conversion rate of phenol to methane was low due to its biological toxicity. In this study, the coupling of granular activated carbon (GAC) and exogenous hydrogen (EH) could enhance greatly methane production of phenol anaerobic digestion, and the metagenomic was firstly used to analyze its potential mechanism. The results indicated that a mass of syntrophic acetate-oxidizing bacteria and hydrogen-utilizing methanogens were enriched on the GAC surface, and SAO-HM pathway has become the dominant pathway. The energy transfer analysis implied that the abundance of adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide (NADH) oxidase increased. Furthermore, direct interspecies electron transfer (DIET) was formed by promoting type IV e-pili between Methanobacterium and Syntrophus, thereby improving the interspecies electron transfer efficiency. The dominant SAO-HM pathway was induced and DIET was formed, which was the internal mechanism of the coupling of GAC and EH to enhance anaerobic biotransformation of phenol.}, } @article {pmid36695828, year = {2023}, author = {Hilderbrand, RH and Bambakidis, T and Crump, BC}, title = {The Roles of Microbes in Stream Restorations.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {853-861}, pmid = {36695828}, issn = {1432-184X}, mesh = {Animals ; *Ecosystem ; Rivers ; Fishes ; Biomass ; *Microbiota ; Biofilms ; }, abstract = {The goods and services provided by riverine systems are critical to humanity, and our reliance increases with our growing population and demands. As our activities expand, these systems continue to degrade throughout the world even as we try to restore them, and many efforts have not met expectations. One way to increase restoration effectiveness could be to explicitly design restorations to promote microbial communities, which are responsible for much of the organic matter breakdown, nutrient removal or transformation, pollutant removal, and biomass production in river ecosystems. In this paper, we discuss several design concepts that purposefully create conditions for these various microbial goods and services, and allow microbes to act as ecological restoration engineers. Focusing on microbial diversity and function could improve restoration effectiveness and overall ecosystem resilience to the stressors that caused the need for the restoration. Advances in next-generation sequencing now allow the use of microbial 'omics techniques (e.g., metagenomics, metatranscriptomics) to assess stream ecological conditions in similar fashion to fish and benthic macroinvertebrates. Using representative microbial communities from stream sediments, biofilms, and the water column may greatly advance assessment capabilities. Microbes can assess restorations and ecosystem function where animals may not currently be present, and thus may serve as diagnostics for the suitability of animal reintroductions. Emerging applications such as ecological metatranscriptomics may further advance our understanding of the roles of specific restoration designs towards ecological services as well as assess restoration effectiveness.}, } @article {pmid36695592, year = {2023}, author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Site Specialization of Human Oral Veillonella Species.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0404222}, pmid = {36695592}, issn = {2165-0497}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Veillonella/genetics ; Mouth/microbiology ; Tongue/microbiology ; Palatine Tonsil ; *Microbiota ; }, abstract = {Veillonella species are abundant members of the human oral microbiome with multiple interspecies commensal relationships. Examining the distribution patterns of Veillonella species across the oral cavity is fundamental to understanding their oral ecology. In this study, we used a combination of pangenomic analysis and oral metagenomic information to clarify Veillonella taxonomy and to test the site specialist hypothesis for the Veillonella genus, which contends that most oral bacterial species are adapted to live at specific oral sites. Using isolate genome sequences combined with shotgun metagenomic sequence data, we showed that Veillonella species have clear, differential site specificity: Veillonella parvula showed strong preference for supra- and subgingival plaque, while closely related V. dispar, as well as more distantly related V. atypica, preferred the tongue dorsum, tonsils, throat, and hard palate. In addition, the provisionally named Veillonella sp. Human Microbial Taxon 780 showed strong site specificity for keratinized gingiva. Using comparative genomic analysis, we identified genes associated with thiamine biosynthesis and the reductive pentose phosphate cycle that may enable Veillonella species to occupy their respective habitats. IMPORTANCE Understanding the microbial ecology of the mouth is fundamental for understanding human physiology. In this study, metapangenomics demonstrated that different Veillonella species have clear ecological preferences in the oral cavity of healthy humans, validating the site specialist hypothesis. Furthermore, the gene pool of different Veillonella species was found to be reflective of their ecology, illuminating the potential role of vitamins and carbohydrates in determining Veillonella distribution patterns and interspecies interactions.}, } @article {pmid36694900, year = {2022}, author = {Naumova, NB and Kabilov, MR}, title = {About the Biodiversity of the Air Microbiome.}, journal = {Acta naturae}, volume = {14}, number = {4}, pages = {50-56}, pmid = {36694900}, issn = {2075-8251}, abstract = {This brief review focuses on the properties of bioaerosols, presenting some recent results of metagenomic studies of the air microbiome performed using next-generation sequencing. The taxonomic composition and structure of the bioaerosol microbiome may display diurnal and seasonal dynamics and be dependent on meteorological events such as dust storms, showers, fogs, etc., as well as air pollution. The Proteobacteria and Ascomycota members are common dominants in bioaerosols in different troposphere layers. The microbiological composition of the lower troposphere air affects the composition and diversity of the indoor bioaerosol microbiome, and information about the latter is very important, especially during exacerbated epidemiological situations. Few studies focusing on the bioaerosol microbiome of the air above Russia urge intensification of such research.}, } @article {pmid36694293, year = {2023}, author = {Wang, G and Jin, Z and George, TS and Feng, G and Zhang, L}, title = {Arbuscular mycorrhizal fungi enhance plant phosphorus uptake through stimulating hyphosphere soil microbiome functional profiles for phosphorus turnover.}, journal = {The New phytologist}, volume = {238}, number = {6}, pages = {2578-2593}, doi = {10.1111/nph.18772}, pmid = {36694293}, issn = {1469-8137}, mesh = {*Mycorrhizae/metabolism ; Phosphorus/metabolism ; Soil ; Phytic Acid/metabolism ; Fungi/metabolism ; *Microbiota ; Bacteria/metabolism ; Plant Roots/metabolism ; Soil Microbiology ; }, abstract = {The extraradical hyphae of arbuscular mycorrhizal (AM) fungi are colonized by different bacteria in natural and agricultural systems, but the mechanisms by which AM fungi interact with the hyphosphere soil microbiome and influence soil organic phosphorus (P) mobilization remain unclear. We grew Medicago in two-compartment microcosms, inoculated with Rhizophagus irregularis, or not, in the root compartment and set up P treatments (without P, with P addition as KH2 PO4 or nonsoluble phytate) in the hyphal compartment. We studied the processes of soil P turnover and characterized the microbiome functional profiles for P turnover in the hyphosphere soil by metagenomic sequencing. Compared with the bulk soil, the hyphosphere soil of R. irregularis was inhabited by a specific bacterial community and their functional profiles for P turnover was stimulated. At the species level, the shift in hyphosphere soil microbiome was characterized by the recruitment of the genome bin2.39 harbouring both gcd and phoD genes and genome bin2.97 harbouring the phoD gene, which synergistically drove nonsoluble phytate mobilization in the hyphosphere soil. Our results suggest that AM fungi recruits a specific hyphosphere soil microbiome and stimulated their functional profiles for P turnover to enhance utilization of phytate.}, } @article {pmid36694290, year = {2023}, author = {Urana, R and Yadav, J and Panchal, S and Sharma, P and Singh, N}, title = {Phytoremediation of PAH compounds by microbial communities in sodic soil.}, journal = {International journal of phytoremediation}, volume = {25}, number = {11}, pages = {1501-1509}, doi = {10.1080/15226514.2023.2170321}, pmid = {36694290}, issn = {1549-7879}, mesh = {Biodegradation, Environmental ; Soil ; *Polycyclic Aromatic Hydrocarbons ; *Microbiota ; Microbial Consortia ; *Soil Pollutants ; Soil Microbiology ; }, abstract = {The PAH degrading microbial consortium was collected from sodic soil of the nursery of Guru Jambheshwar University of Science and Technology, Hisar, Haryana (India). And the soil was artificially amended with phenanthrene and naphthalene to isolate the PAHs degrading microbial consortium. The diversity of microbial consortium was analyzed using the NGS (Next Generation Sequencing) based metagenomic approach. The result of diversity analysis showed species Tepidanaerobacter syntrophicus, Sphingomonas oliophenolica, Arthrobacter psychrochitinipnius, Bifidobacterium bombi, Nocardiodies islandensis, Rhodovibrio sodomensis, Thiorhodococus pfennigii, Aeromicrobium ponti, Steroidobacter dentrificans, Actinomaduria maheshkhaliensis, Dactylosporangium maewongense, Pelotomaculum isophthalicicum, and Nocardioides islandensis were present in the consortium. Moreover, Sphingomonas, Arthrobacter, Sphingobium, Azospirillium, Thirohodococcus, and Pelotomaculum were the prominent pollutant degrader genera in the microbial consortium. Since the bioremediation of these pollutants occurs with a significant reduction in toxicity, the study's perspective is to use this type of consortium for bioremediation of specifically contaminated soil.}, } @article {pmid36693851, year = {2023}, author = {Panda, A and Tuller, T}, title = {Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {5}, pmid = {36693851}, issn = {2055-5008}, mesh = {Codon ; *Amino Acids ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Codon and amino acid usage were associated with almost every aspect of microbial life. However, how the environment may impact the codon and amino acid choice of microbial communities at the habitat level is not clearly understood. Therefore, in this study, we analyzed codon and amino acid usage patterns of a large number of environmental samples collected from diverse ecological niches. Our results suggested that samples derived from similar environmental niches, in general, show overall similar codon and amino acid distribution as compared to samples from other habitats. To substantiate the relative impact of the environment, we considered several factors, such as their similarity in GC content, or in functional or taxonomic abundance. Our analysis demonstrated that none of these factors can fully explain the trends that we observed at the codon or amino acid level implying a direct environmental influence on them. Further, our analysis demonstrated different levels of selection on codon bias in different microbial communities with the highest bias in host-associated environments such as the digestive system or oral samples and the lowest level of selection in soil and water samples. Considering a large number of metagenomic samples here we showed that microorganisms collected from similar environmental backgrounds exhibit similar patterns of codon and amino acid usage irrespective of the location or time from where the samples were collected. Thus our study suggested a direct impact of the environment on codon and amino usage of microorganisms that cannot be explained considering the influence of other factors.}, } @article {pmid36692711, year = {2023}, author = {Li, Y and Xiong, L and Yu, H and Xiang, Y and Wei, Y and Zhang, Q and Ji, X}, title = {Biogeochemical sulfur cycling of virus auxiliary metabolic genes involved in Napahai plateau wetland.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {15}, pages = {44430-44438}, pmid = {36692711}, issn = {1614-7499}, support = {32160294//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 31860147//Innovative Research Group Project of the National Natural Science Foundation of China/ ; }, mesh = {*Wetlands ; Phylogeny ; Oxidation-Reduction ; *Microbiota ; Sulfur/metabolism ; }, abstract = {Virus plays important roles in regulating microbial community structure, horizontal gene transfer, and promoting biological evolution, also augmenting host metabolism during infection via the expression of auxiliary metabolic genes (AMGs), and thus affect biogeochemical cycling in the oceans. As the "kidney of the earth," wetlands have rich biodiversity and abundant resources. Based on metagenomic data, 10 AMGs associated with sulfur cycling, i.e., tusA, moaD, dsrE, soxA, soxB, soxC, soxD, soxX, soxY, and soxZ, were analyzed in Napahai plateau wetland. The phylogenetic trees of AMGs involved in sulfur metabolism from different habitats and host origins were constructed. Combined with principal coordinate analysis, it revealed that most AMGs associated with sulfur metabolism clustered separately, indicating the abundance and uniqueness in this region. The sulfur metabolism pathways involved by AMGs were mainly SOX systems, among which sulfur oxidation was associated with moaD and dsrE genes, while sulfur transport was related to tusA genes. It provides an insight into the biogeochemical sulfur cycling in plateau wetlands and lays the foundation for further study on the co-evolution of virus and host.}, } @article {pmid36691982, year = {2023}, author = {Boktor, JC and Sharon, G and Verhagen Metman, LA and Hall, DA and Engen, PA and Zreloff, Z and Hakim, DJ and Bostick, JW and Ousey, J and Lange, D and Humphrey, G and Ackermann, G and Carlin, M and Knight, R and Keshavarzian, A and Mazmanian, SK}, title = {Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome.}, journal = {Movement disorders : official journal of the Movement Disorder Society}, volume = {38}, number = {3}, pages = {399-409}, doi = {10.1002/mds.29300}, pmid = {36691982}, issn = {1531-8257}, mesh = {Humans ; *Parkinson Disease/diagnosis ; Metagenome/genetics ; Cohort Studies ; *Gastrointestinal Microbiome/genetics ; Feces ; }, abstract = {BACKGROUND: The gut microbiome is altered in several neurologic disorders, including Parkinson's disease (PD).

OBJECTIVES: The aim is to profile the fecal gut metagenome in PD for alterations in microbial composition, taxon abundance, metabolic pathways, and microbial gene products, and their relationship with disease progression.

METHODS: Shotgun metagenomic sequencing was conducted on 244 stool donors from two independent cohorts in the United States, including individuals with PD (n = 48, n = 47, respectively), environmental household controls (HC, n = 29, n = 30), and community population controls (PC, n = 41, n = 49). Microbial features consistently altered in PD compared to HC and PC subjects were identified. Data were cross-referenced to public metagenomic data sets from two previous studies in Germany and China to determine generalizable microbiome features.

RESULTS: We find several significantly altered taxa between PD and controls within the two cohorts sequenced in this study. Analysis across global cohorts returns consistent changes only in Intestinimonas butyriciproducens. Pathway enrichment analysis reveals disruptions in microbial carbohydrate and lipid metabolism and increased amino acid and nucleotide metabolism in PD. Global gene-level signatures indicate an increased response to oxidative stress, decreased cellular growth and microbial motility, and disrupted intercommunity signaling.

CONCLUSIONS: A metagenomic meta-analysis of PD shows consistent and novel alterations in functional metabolic potential and microbial gene abundance across four independent studies from three continents. These data reveal that stereotypic changes in the functional potential of the gut microbiome are a consistent feature of PD, highlighting potential diagnostic and therapeutic avenues for future research. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.}, } @article {pmid36691230, year = {2023}, author = {Blohs, M and Mahnert, A and Brunnader, K and Flucher, C and Castellani, C and Till, H and Singer, G and Moissl-Eichinger, C}, title = {Acute appendicitis manifests as two microbiome state types with oral pathogens influencing severity.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2145845}, pmid = {36691230}, issn = {1949-0984}, support = {P 32697/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Child ; Adolescent ; Humans ; *Appendicitis/drug therapy/pathology/surgery ; *Gastrointestinal Microbiome ; *Appendix/microbiology/pathology ; *Microbiota ; Bacteria ; Acute Disease ; }, abstract = {Mounting evidence suggests that acute appendicitis (AA) is not one but two diseases: complicated appendicitis, which is associated with necrosis leading to perforation or periappendicular abscess, and uncomplicated appendicitis, which does not necessarily result in perforation. Even though AA is the most frequent cause of surgery from abdominal pain, little is known about the origins and etiopathogenesis of this disease, much less regarding the different disease types. In this study, we investigated the microbiome (inter-domain amplicon and metagenome sequencing) of samples from the appendix, rectum and peritoneum of 60 children and adolescents with AA to assess the composition and potential function of bacteria, archaea and fungi. The analysis of the appendix microbial community revealed a shift depending on the severity of the AA. This shift was reflected by two major community state types that represented the complicated and uncomplicated cases. We could demonstrate that complicated, but not uncomplicated, appendicitis is associated with a significant local expansion of oral, bacterial pathogens in the appendix, most strongly influenced by necrotizing Fusobacterium spp., Porphyromonas and Parvimonas. Uncomplicated appendicitis, however, was characterized by gut-associated microbiomes. Our findings support the hypothesis that two disease types exist in AA, which cannot be distinguished beyond doubt using standard clinical characterization methods or by analysis of the patient's rectal microbiome. An advanced microbiome diagnosis, however, could improve non-surgical treatment of uncomplicated AA.}, } @article {pmid36691096, year = {2023}, author = {King, WL and Richards, SC and Kaminsky, LM and Bradley, BA and Kaye, JP and Bell, TH}, title = {Leveraging microbiome rediversification for the ecological rescue of soil function.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {7}, pmid = {36691096}, issn = {2524-6372}, abstract = {BACKGROUND: Global biodiversity losses threaten ecosystem services and can impact important functional insurance in a changing world. Microbial diversity and function can become depleted in agricultural systems and attempts to rediversify agricultural soils rely on either targeted microbial introductions or retaining natural lands as biodiversity reservoirs. As many soil functions are provided by a combination of microbial taxa, rather than outsized impacts by single taxa, such functions may benefit more from diverse microbiome additions than additions of individual commercial strains. In this study, we measured the impact of soil microbial diversity loss and rediversification (i.e. rescue) on nitrification by quantifying ammonium and nitrate pools. We manipulated microbial assemblages in two distinct soil types, an agricultural and a forest soil, with a dilution-to-extinction approach and performed a microbiome rediversification experiment by re-introducing microorganisms lost from the dilution. A microbiome water control was included to act as a reference point. We assessed disruption and potential restoration of (1) nitrification, (2) bacterial and fungal composition through 16S rRNA gene and fungal ITS amplicon sequencing and (3) functional genes through shotgun metagenomic sequencing on a subset of samples.

RESULTS: Disruption of nitrification corresponded with diversity loss, but nitrification was successfully rescued in the rediversification experiment when high diversity inocula were introduced. Bacterial composition clustered into groups based on high and low diversity inocula. Metagenomic data showed that genes responsible for the conversion of nitrite to nitrate and taxa associated with nitrogen metabolism were absent in the low diversity inocula microcosms but were rescued with high diversity introductions.

CONCLUSIONS: In contrast to some previous work, our data suggest that soil functions can be rescued by diverse microbiome additions, but that the concentration of the microbial inoculum is important. By understanding how microbial rediversification impacts soil microbiome performance, we can further our toolkit for microbial management in human-controlled systems in order to restore depleted microbial functions.}, } @article {pmid36690342, year = {2023}, author = {Barrón-Sandoval, A and Martiny, JBH and Pérez-Carbajal, T and Bullock, SH and Leija, A and Hernández, G and Escalante, AE}, title = {Functional significance of microbial diversity in arid soils: biological soil crusts and nitrogen fixation as a model system.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {2}, pages = {}, pmid = {36690342}, issn = {1574-6941}, mesh = {Ecosystem ; Nitrogen Fixation ; *Cyanobacteria/genetics ; Desert Climate ; Soil ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; *Microbiota/genetics ; Nitrogen ; }, abstract = {Microbial communities respond to changes in environmental conditions; however, how compositional shifts affect ecosystem processes is still not well-understood and it is often assumed that different microbial communities will function equally under similar environmental conditions. We evaluated this assumption of functional redundancy using biological soil crusts (BSCs) from two arid ecosystems in Mexico with contrasting climate conditions (hot and cold deserts) following an experimental approach both in the field (reciprocal transplants) and in laboratory conditions (common garden), focusing on the community's composition and potential for nitrogen fixation. Potential of nitrogen fixation was assessed through the acetylene reduction assay. Community composition and diversity was determined with T-RFLPs of nifH gene, high throughput sequencing of 16S rRNA gene amplicons and metagenomic libraries. BSCs tended to show higher potential nitrogen fixation rates when experiencing temperatures more similar to their native environment. Moreover, changes in potential nitrogen fixation, taxonomic and functional community composition, and diversity often depended on an interactive effect of origin of the communities and the environment they experienced. We interpret our results as legacy effects that result from ecological specialization of the BSC communities to their native environment. Overall, we present evidence of nonfunctional redundancy of BSCs in terms of nitrogen fixation.}, } @article {pmid36689828, year = {2023}, author = {Mi, T and Jin, Y and Che, Y and Huang, J and Zhou, R and Wu, C}, title = {Profiling the composition and metabolic functions of microbial community in pellicle-forming radish paocai.}, journal = {International journal of food microbiology}, volume = {388}, number = {}, pages = {110087}, doi = {10.1016/j.ijfoodmicro.2023.110087}, pmid = {36689828}, issn = {1879-3460}, mesh = {*Raphanus ; Fermentation ; Vegetables/microbiology ; Lactobacillus/metabolism ; Bacteria/genetics ; *Yarrowia ; *Microbiota ; }, abstract = {Pellicle formation is an obvious indicator of spoilage and is followed by a loss of flavor in a variety of fermented vegetables. In this study, the pellicle-forming microorganisms were isolated using culture-dependent approaches, then a comparative analysis between the pellicle-forming (PF) radish paocai and normal fermented paocai in the diversity and function of microbial community was conducted by metagenome sequencing. Based on a pairwise t-test and OPLS-DA analysis, diallyl sulfide, (z)-1-allyl-2-(prop-1-en-1-yl) disulfane, and terpineol were considered to be the main components responsible for the unpleasant flavor of PF paocai. Yarrowia spp., Enterobacter spp., and Pichia spp. were the main pellicle-forming microorganisms. All 17 isolated Enterobacter strains showed pectinase-producing and cellulase-producing abilities, and 3 isolated Pichia strains showed gas-producing capacity. According to LEfSe analysis based on metagenomes, unclassified_g__Citrobacter and Yarrowia lipolytica were the uppermost biomarkers that distinguished the PF paocai from normal paocai. Unclassified_g__Lactobacillus and Lactobacillus plantarum were found to be actively engaged in starch and sucrose metabolism, cysteine and methionine metabolism, galactose metabolism, fructose and mannose metabolism, lysine biosynthesis, fatty acid biosynthesis, and arginine biosynthesis, all of which contributed to the flavor formation of paocai. Combining the results of metagenome sequencing with the data obtained based on the culture-dependent method, we could deduce that the growth of Yarrowia lipolytica first promoted the increase of pH and the formation of pellicle, which provided a suitable niche for the growth of some harmful bacteria such as Enterobacter, Citrobacter, and Serratia. These hazardous bacteria then worked in concert to induce the odorous stench and texture softening of paocai, as well as more pellicle formation.}, } @article {pmid36688869, year = {2023}, author = {Fontana, F and Longhi, G and Alessandri, G and Lugli, GA and Mancabelli, L and Tarracchini, C and Viappiani, A and Anzalone, R and Ventura, M and Turroni, F and Milani, C}, title = {Multifactorial Microvariability of the Italian Raw Milk Cheese Microbiota and Implication for Current Regulatory Scheme.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0106822}, pmid = {36688869}, issn = {2379-5077}, mesh = {Animals ; *Cheese/analysis ; Milk/chemistry ; *Microbiota/genetics ; Food Handling/methods ; Whey Proteins/analysis ; Italy ; }, abstract = {Raw milk cheese manufactory is strictly regulated in Europe by the Protected Designation of Origin (PDO) quality scheme, which protects indigenous food products based on geographical and biotechnological features. This study encompassed the collection of 128 raw milk cheese samples across Italy to investigate the resident microbiome correlated to current PDO specifications. Shotgun metagenomic approaches highlighted how the microbial communities are primarily linked to each cheesemaking site and consequently to the use of site-specific Natural Whey Cultures (NWCs), defined by a multifactorial set of local environmental factors rather than solely by cheese type or geographical origin that guide the current PDO specification. Moreover, in-depth functional characterization of Cheese Community State Types (CCSTs) and comparative genomics efforts, including metagenomically assembled genomes (MAGs) of the dominant microbial taxa, revealed NWCs-related unique enzymatic profiles impacting the organoleptic features of the produced cheeses and availability of bioactive compounds to consumers, with putative health implications. Thus, these results highlighted the need for a profound rethinking of the current PDO designation with a focus on the production site-specific microbial metabolism to understand and guarantee the organoleptic features of the final product recognized as PDO. IMPORTANCE The Protected Designation of Origin (PDO) guarantees the traceability of food production processes, and that the production takes place in a well-defined restricted geographical area. Nevertheless, the organoleptic qualities of the same dairy products, i.e., cheeses under the same PDO denomination, differ between manufacturers. The final product's flavor and qualitative aspects can be related to the resident microbial population, not considered by the PDO denomination. Here, we analyzed a complete set of different Italian cheeses produced from raw milk through shotgun sequencing in order to study the variability of the different microbial profiles resident in Italian PDO cheeses. Furthermore, an in-depth functional analysis, along with a comparative genomic analysis, was performed in order to correlate the taxonomic information with the organoleptic properties of the final product. This analysis made it possible to highlight how the PDO denomination should be revisited to understand the effect that Natural Whey Cultures (NWCs), used in the traditional production of raw milk cheese and unique to each manufacturer, impacts on the organoleptic features of the final product.}, } @article {pmid36688698, year = {2023}, author = {Busi, SB and de Nies, L and Pramateftaki, P and Bourquin, M and Kohler, TJ and Ezzat, L and Fodelianakis, S and Michoud, G and Peter, H and Styllas, M and Tolosano, M and De Staercke, V and Schön, M and Galata, V and Wilmes, P and Battin, T}, title = {Glacier-Fed Stream Biofilms Harbor Diverse Resistomes and Biosynthetic Gene Clusters.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0406922}, pmid = {36688698}, issn = {2165-0497}, mesh = {Humans ; *Rivers/microbiology ; Ice Cover ; Bacteria/genetics ; *Microbiota ; Multigene Family ; Biofilms ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antimicrobial resistance (AMR) is a universal phenomenon the origins of which lay in natural ecological interactions such as competition within niches, within and between micro- to higher-order organisms. To study these phenomena, it is crucial to examine the origins of AMR in pristine environments, i.e., limited anthropogenic influences. In this context, epilithic biofilms residing in glacier-fed streams (GFSs) are an excellent model system to study diverse, intra- and inter-domain, ecological crosstalk. We assessed the resistomes of epilithic biofilms from GFSs across the Southern Alps (New Zealand) and the Caucasus (Russia) and observed that both bacteria and eukaryotes encoded twenty-nine distinct AMR categories. Of these, beta-lactam, aminoglycoside, and multidrug resistance were both abundant and taxonomically distributed in most of the bacterial and eukaryotic phyla. AMR-encoding phyla included Bacteroidota and Proteobacteria among the bacteria, alongside Ochrophyta (algae) among the eukaryotes. Additionally, biosynthetic gene clusters (BGCs) involved in the production of antibacterial compounds were identified across all phyla in the epilithic biofilms. Furthermore, we found that several bacterial genera (Flavobacterium, Polaromonas, Superphylum Patescibacteria) encode both atimicrobial resistance genes (ARGs) and BGCs within close proximity of each other, demonstrating their capacity to simultaneously influence and compete within the microbial community. Our findings help unravel how naturally occurring BGCs and AMR contribute to the epilithic biofilms mode of life in GFSs. Additionally, we report that eukaryotes may serve as AMR reservoirs owing to their potential for encoding ARGs. Importantly, these observations may be generalizable and potentially extended to other environments that may be more or less impacted by human activity. IMPORTANCE Antimicrobial resistance is an omnipresent phenomenon in the anthropogenically influenced ecosystems. However, its role in shaping microbial community dynamics in pristine environments is relatively unknown. Using metagenomics, we report the presence of antimicrobial resistance genes and their associated pathways in epilithic biofilms within glacier-fed streams. Importantly, we observe biosynthetic gene clusters associated with antimicrobial resistance in both pro- and eukaryotes in these biofilms. Understanding the role of resistance in the context of this pristine environment and complex biodiversity may shed light on previously uncharacterized mechanisms of cross-domain interactions.}, } @article {pmid36685560, year = {2022}, author = {Liu, X and He, G and Lan, Y and Guo, W and Liu, X and Li, J and Liu, A and He, M and Liu, X and Fan, Z and Zhang, Y}, title = {Virome and metagenomic analysis reveal the distinct distribution of microbiota in human fetal gut during gestation.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1079294}, pmid = {36685560}, issn = {1664-3224}, mesh = {Adult ; Humans ; Pregnancy ; Female ; Virome ; *Microbiota ; Bacteria/genetics ; Metagenome ; *Viruses/genetics ; Fetus ; }, abstract = {Studies have shown that fetal immune cell activation may result from potential exposure to microbes, although the presence of microbes in fetus has been a controversial topic. Here, we combined metagenomic and virome techniques to investigate the presence of bacteria and viruses in fetal tissues (small intestine, cecum, and rectum). We found that the fetal gut is not a sterile environment and has a low abundance but metabolically rich microbiome. Specifically, Proteobacteria and Actinobacteria were the dominant bacteria phyla of fetal gut. In total, 700 species viruses were detected, and Human betaherpesvirus 5 was the most abundant eukaryotic viruses. Especially, we first identified Methanobrevibacter smithii in fetal gut. Through the comparison with adults' gut microbiota we found that Firmicutes and Bacteroidetes gradually became the main force of gut microbiota during the process of growth and development. Interestingly, 6 antibiotic resistance genes were shared by the fetus and adults. Our results indicate the presence of microbes in the fetal gut and demonstrate the diversity of bacteria, archaea and viruses, which provide support for the studies related to early fetal immunity. This study further explores the specific composition of viruses in the fetal gut and the similarities between fetal and adults' gut microbiota, which is valuable for understanding human fetal immunity development during gestation.}, } @article {pmid36683075, year = {2023}, author = {Turner, D and Shkoporov, AN and Lood, C and Millard, AD and Dutilh, BE and Alfenas-Zerbini, P and van Zyl, LJ and Aziz, RK and Oksanen, HM and Poranen, MM and Kropinski, AM and Barylski, J and Brister, JR and Chanisvili, N and Edwards, RA and Enault, F and Gillis, A and Knezevic, P and Krupovic, M and Kurtböke, I and Kushkina, A and Lavigne, R and Lehman, S and Lobocka, M and Moraru, C and Moreno Switt, A and Morozova, V and Nakavuma, J and Reyes Muñoz, A and Rūmnieks, J and Sarkar, BL and Sullivan, MB and Uchiyama, J and Wittmann, J and Yigang, T and Adriaenssens, EM}, title = {Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee.}, journal = {Archives of virology}, volume = {168}, number = {2}, pages = {74}, pmid = {36683075}, issn = {1432-8798}, support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; RC2 DK116713/DK/NIDDK NIH HHS/United States ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; RC2DK116713/DK/NIDDK NIH HHS/United States ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 220646/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Bacteriophages ; *Viruses/genetics ; *Caudovirales ; Myoviridae ; *Siphoviridae ; }, abstract = {This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021-March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.}, } @article {pmid36681701, year = {2023}, author = {Ezzamouri, B and Rosario, D and Bidkhori, G and Lee, S and Uhlen, M and Shoaie, S}, title = {Metabolic modelling of the human gut microbiome in type 2 diabetes patients in response to metformin treatment.}, journal = {NPJ systems biology and applications}, volume = {9}, number = {1}, pages = {2}, pmid = {36681701}, issn = {2056-7189}, support = {EP/S001301/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; }, mesh = {Humans ; *Metformin/pharmacology/therapeutic use ; *Diabetes Mellitus, Type 2/drug therapy/metabolism/microbiology ; *Gastrointestinal Microbiome/genetics ; Hypoglycemic Agents/pharmacology/therapeutic use ; Diet ; Bacteria ; }, abstract = {The human gut microbiome has been associated with several metabolic disorders including type 2 diabetes mellitus. Understanding metabolic changes in the gut microbiome is important to elucidate the role of gut bacteria in regulating host metabolism. Here, we used available metagenomics data from a metformin study, together with genome-scale metabolic modelling of the key bacteria in individual and community-level to investigate the mechanistic role of the gut microbiome in response to metformin. Individual modelling predicted that species that are increased after metformin treatment have higher growth rates in comparison to species that are decreased after metformin treatment. Gut microbial enrichment analysis showed prior to metformin treatment pathways related to the hypoglycemic effect were enriched. Our observations highlight how the key bacterial species after metformin treatment have commensal and competing behavior, and how their cellular metabolism changes due to different nutritional environment. Integrating different diets showed there were specific microbial alterations between different diets. These results show the importance of the nutritional environment and how dietary guidelines may improve drug efficiency through the gut microbiota.}, } @article {pmid36680214, year = {2023}, author = {Jansen, D and Matthijnssens, J}, title = {The Emerging Role of the Gut Virome in Health and Inflammatory Bowel Disease: Challenges, Covariates and a Viral Imbalance.}, journal = {Viruses}, volume = {15}, number = {1}, pages = {}, pmid = {36680214}, issn = {1999-4915}, mesh = {Humans ; Virome ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases ; *Bacteriophages ; *Microviridae ; Metagenomics ; }, abstract = {Virome research is a rapidly growing area in the microbiome field that is increasingly associated with human diseases, such as inflammatory bowel disease (IBD). Although substantial progress has been made, major methodological challenges limit our understanding of the virota. In this review, we describe challenges that must be considered to accurately report the virome composition and the current knowledge on the virome in health and IBD. First, the description of the virome shows strong methodological biases related to wetlab (e.g., VLP enrichment) and bioinformatics approaches (viral identification and classification). Second, IBD patients show consistent viral imbalances characterized by a high relative abundance of phages belonging to the Caudovirales and a low relative abundance of phages belonging to the Microviridae. Simultaneously, a sporadic contraction of CrAss-like phages and a potential expansion of the lysogenic potential of the intestinal virome are observed. Finally, despite numerous studies that have conducted diversity analysis, it is difficult to draw firm conclusions due to methodological biases. Overall, we present the many methodological and environmental factors that influence the virome, its current consensus in health and IBD, and a contributing hypothesis called the "positive inflammatory feedback loop" that may play a role in the pathophysiology of IBD.}, } @article {pmid36680116, year = {2022}, author = {Andrianjakarivony, HF and Bettarel, Y and Armougom, F and Desnues, C}, title = {Phage-Host Prediction Using a Computational Tool Coupled with 16S rRNA Gene Amplicon Sequencing.}, journal = {Viruses}, volume = {15}, number = {1}, pages = {}, pmid = {36680116}, issn = {1999-4915}, mesh = {*Bacteria/genetics/virology ; *Bacteriophages/genetics ; Cote d'Ivoire ; Genes, rRNA ; Metagenomics/methods ; Reproducibility of Results ; RNA, Ribosomal, 16S/genetics ; Water ; }, abstract = {Metagenomics studies have revealed tremendous viral diversity in aquatic environments. Yet, while the genomic data they have provided is extensive, it is unannotated. For example, most phage sequences lack accurate information about their bacterial host, which prevents reliable phage identification and the investigation of phage-host interactions. This study aimed to take this knowledge further, using a viral metagenomic framework to decipher the composition and diversity of phage communities and to predict their bacterial hosts. To this end, we used water and sediment samples collected from seven sites with varying contamination levels in the Ebrié Lagoon in Abidjan, Ivory Coast. The bacterial communities were characterized using the 16S rRNA metabarcoding approach, and a framework was developed to investigate the virome datasets that: (1) identified phage contigs with VirSorter and VIBRANT; (2) classified these contigs with MetaPhinder using the phage database (taxonomic annotation); and (3) predicted the phages' bacterial hosts with a machine learning-based tool: the Prokaryotic Virus-Host Predictor. The findings showed that the taxonomic profiles of phages and bacteria were specific to sediment or water samples. Phage sequences assigned to the Microviridae family were widespread in sediment samples, whereas phage sequences assigned to the Siphoviridae, Myoviridae and Podoviridae families were predominant in water samples. In terms of bacterial communities, the phyla Latescibacteria, Zixibacteria, Bacteroidetes, Acidobacteria, Calditrichaeota, Gemmatimonadetes, Cyanobacteria and Patescibacteria were most widespread in sediment samples, while the phyla Epsilonbacteraeota, Tenericutes, Margulisbacteria, Proteobacteria, Actinobacteria, Planctomycetes and Marinimicrobia were most prevalent in water samples. Significantly, the relative abundance of bacterial communities (at major phylum level) estimated by 16S rRNA metabarcoding and phage-host prediction were significantly similar. These results demonstrate the reliability of this novel approach for predicting the bacterial hosts of phages from shotgun metagenomic sequencing data.}, } @article {pmid36680094, year = {2022}, author = {Zhang, F and Gia, A and Chen, G and Gong, L and Behary, J and Hold, GL and Zekry, A and Tang, X and Sun, Y and El-Omar, E and Jiang, XT}, title = {Critical Assessment of Whole Genome and Viral Enrichment Shotgun Metagenome on the Characterization of Stool Total Virome in Hepatocellular Carcinoma Patients.}, journal = {Viruses}, volume = {15}, number = {1}, pages = {}, pmid = {36680094}, issn = {1999-4915}, mesh = {Humans ; Metagenome ; *Carcinoma, Hepatocellular/genetics ; Virome ; Ecosystem ; *Liver Neoplasms/genetics ; *Viruses/genetics ; Metagenomics/methods ; Genome, Viral ; }, abstract = {Viruses are the most abundant form of life on earth and play important roles in a broad range of ecosystems. Currently, two methods, whole genome shotgun metagenome (WGSM) and viral-like particle enriched metagenome (VLPM) sequencing, are widely applied to compare viruses in various environments. However, there is no critical assessment of their performance in recovering viruses and biological interpretation in comparative viral metagenomic studies. To fill this gap, we applied the two methods to investigate the stool virome in hepatocellular carcinoma (HCC) patients and healthy controls. Both WGSM and VLPM methods can capture the major diversity patterns of alpha and beta diversities and identify the altered viral profiles in the HCC stool samples compared with healthy controls. Viral signatures identified by both methods showed reductions of Faecalibacterium virus Taranis in HCC patients' stool. Ultra-deep sequencing recovered more viruses in both methods, however, generally, 3 or 5 Gb were sufficient to capture the non-fragmented long viral contigs. More lytic viruses were detected than lysogenetic viruses in both methods, and the VLPM can detect the RNA viruses. Using both methods would identify shared and specific viral signatures and would capture different parts of the total virome.}, } @article {pmid36678360, year = {2022}, author = {Cholleti, H and de Jong, J and Blomström, AL and Berg, M}, title = {Investigation of the Virome and Characterization of Issyk-Kul Virus from Swedish Myotis brandtii Bats.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {36678360}, issn = {2076-0817}, support = {50800//Section of Virology, Dept. of Biomedical Sciences and Veterinary Public Health, Swedish University Of Agricultural Sciences, Uppsala, Sweden/ ; }, abstract = {Bats are reservoirs for many different viruses, including some that can be transmitted to and cause disease in humans and/or animals. However, less is known about the bat-borne viruses circulating in Northern European countries such as in Sweden. In this study, saliva from Myotis brandtii bats, collected from south-central Sweden, was analyzed for viruses. The metagenomic analysis identified viral sequences belonging to different viral families, including, e.g., Nairoviridae, Retroviridae, Poxviridae, Herpesviridae and Siphoviridae. Interestingly, through the data analysis, the near-complete genome of Issyk-Kul virus (ISKV), a zoonotic virus within the Nairoviridae family, was obtained, showing 95-99% protein sequence identity to previously described ISKVs. This virus is believed to infect humans via an intermediate tick host or through contact with bat excrete. ISKV has previously been found in bats in Europe, but not previously in the Nordic region. In addition, near full-length genomes of two novel viruses belonging to Picornavirales order and Tymoviridae family were characterized. Taken together, our study has not only identified novel viruses, but also the presence of a zoonotic virus not previously known to circulate in this region. Thus, the results from these types of studies can help us to better understand the diversity of viruses circulating in bat populations, as well as identify viruses with zoonotic potential that could possibly be transmitted to humans.}, } @article {pmid36675151, year = {2023}, author = {Karpe, AV and Hutton, ML and Mileto, SJ and James, ML and Evans, C and Ghodke, AB and Shah, RM and Metcalfe, SS and Liu, JW and Walsh, T and Lyras, D and Palombo, EA and Beale, DJ}, title = {Gut Microbial Perturbation and Host Response Induce Redox Pathway Upregulation along the Gut-Liver Axis during Giardiasis in C57BL/6J Mouse Model.}, journal = {International journal of molecular sciences}, volume = {24}, number = {2}, pages = {}, pmid = {36675151}, issn = {1422-0067}, support = {Probing Biosystems Future Science Platform (FSP)//Commonwealth Scientific and Industrial Research Organisation/ ; }, mesh = {Mice ; Animals ; Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics/metabolism ; *Giardiasis ; Up-Regulation ; Proteome/metabolism ; *Cryptosporidiosis/metabolism ; Mice, Inbred C57BL ; *Cryptosporidium/metabolism ; Metabolomics ; Metabolome ; *Microbiota ; Liver/metabolism ; Oxidation-Reduction ; }, abstract = {Apicomplexan infections, such as giardiasis and cryptosporidiosis, negatively impact a considerable proportion of human and commercial livestock populations. Despite this, the molecular mechanisms of disease, particularly the effect on the body beyond the gastrointestinal tract, are still poorly understood. To highlight host-parasite-microbiome biochemical interactions, we utilised integrated metabolomics-16S rRNA genomics and metabolomics-proteomics approaches in a C57BL/6J mouse model of giardiasis and compared these to Cryptosporidium and uropathogenic Escherichia coli (UPEC) infections. Comprehensive samples (faeces, blood, liver, and luminal contents from duodenum, jejunum, ileum, caecum and colon) were collected 10 days post infection and subjected to proteome and metabolome analysis by liquid and gas chromatography-mass spectrometry, respectively. Microbial populations in faeces and luminal washes were examined using 16S rRNA metagenomics. Proteome-metabolome analyses indicated that 12 and 16 key pathways were significantly altered in the gut and liver, respectively, during giardiasis with respect to other infections. Energy pathways including glycolysis and supporting pathways of glyoxylate and dicarboxylate metabolism, and the redox pathway of glutathione metabolism, were upregulated in small intestinal luminal contents and the liver during giardiasis. Metabolomics-16S rRNA genetics integration indicated that populations of three bacterial families-Autopobiaceae (Up), Desulfovibrionaceae (Up), and Akkermanasiaceae (Down)-were most significantly affected across the gut during giardiasis, causing upregulated glycolysis and short-chained fatty acid (SCFA) metabolism. In particular, the perturbed Akkermanasiaceae population seemed to cause oxidative stress responses along the gut-liver axis. Overall, the systems biology approach applied in this study highlighted that the effects of host-parasite-microbiome biochemical interactions extended beyond the gut ecosystem to the gut-liver axis. These findings form the first steps in a comprehensive comparison to ascertain the major molecular and biochemical contributors of host-parasite interactions and contribute towards the development of biomarker discovery and precision health solutions for apicomplexan infections.}, } @article {pmid36674562, year = {2023}, author = {Ong, SS and Xu, J and Sim, CK and Khng, AJ and Ho, PJ and Kwan, PKW and Ravikrishnan, A and Tan, KB and Tan, QT and Tan, EY and Tan, SM and Putti, TC and Lim, SH and Tang, ELS and Nagarajan, N and Karnani, N and Li, J and Hartman, M}, title = {Profiling Microbial Communities in Idiopathic Granulomatous Mastitis.}, journal = {International journal of molecular sciences}, volume = {24}, number = {2}, pages = {}, pmid = {36674562}, issn = {1422-0067}, support = {NUHSRO/2020/027/T1/Seed-Aug/11//National University Health System/ ; Not applicable//Agency for Science, Technology and Research/ ; }, mesh = {Humans ; Female ; *Granulomatous Mastitis/complications/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Immunoglobulin M ; Suppuration/complications ; }, abstract = {Idiopathic granulomatous mastitis (IGM) is a rare and benign inflammatory breast disease with ambiguous aetiology. Contrastingly, lactational mastitis (LM) is commonly diagnosed in breastfeeding women. To investigate IGM aetiology, we profiled the microbial flora of pus and skin in patients with IGM and LM. A total of 26 patients with IGM and 6 patients with LM were included in the study. The 16S rRNA sequencing libraries were constructed from 16S rRNA gene amplified from total DNA extracted from pus and skin swabs in patients with IGM and LM controls. Constructed libraries were multiplexed and paired-end sequenced on HiSeq4000. Metagenomic analysis was conducted using modified microbiome abundance analysis suite customised R-resource for paired pus and skin samples. Microbiome multivariable association analyses were performed using linear models. A total of 21 IGM and 3 LM paired pus and skin samples underwent metagenomic analysis. Bray−Curtis ecological dissimilarity distance showed dissimilarity across four sample types (IGM pus, IGM skin, LM pus, and LM skin; PERMANOVA, p < 0.001). No characteristic dominant genus was observed across the IGM samples. The IGM pus samples were more diverse than corresponding IGM skin samples (Shannon and Simpson index; Wilcoxon paired signed-rank tests, p = 0.022 and p = 0.07). Corynebacterium kroppenstedtii, reportedly associated with IGM in the literature, was higher in IGM pus samples than paired skin samples (Wilcoxon, p = 0.022). Three other species and nineteen genera were statistically significant in paired IGM pus−skin comparison after antibiotic treatment adjustment and multiple comparisons correction. Microbial profiles are unique between patients with IGM and LM. Inter-patient variability and polymicrobial IGM pus samples cannot implicate specific genus or species as an infectious cause for IGM.}, } @article {pmid36672969, year = {2023}, author = {Zhang, M and Wang, X and Wang, Z and Mao, S and Zhang, J and Li, M and Pan, H}, title = {Metatranscriptomic Analyses Reveal Important Roles of the Gut Microbiome in Primate Dietary Adaptation.}, journal = {Genes}, volume = {14}, number = {1}, pages = {}, pmid = {36672969}, issn = {2073-4425}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Primates/genetics ; Diet ; Bacteria/metabolism ; Feces/microbiology ; }, abstract = {The gut microbiome plays a vital role in host ecological adaptation, especially dietary adaptations. Primates have evolved a variety of dietary and gut physiological structures that are useful to explore the role of the gut microbiome in host dietary adaptations. Here, we characterize gut microbiome transcriptional activity in ten fecal samples from primates with three different diets and compare the results to their previously reported metagenomic profile. Bacteria related to cellulose degradation, like Bacteroidaceae and Alcaligenaceae, were enriched and actively expressed in the gut microbiome of folivorous primates, and functional analysis revealed that the glycan biosynthesis and metabolic pathways were significantly active. In omnivorous primates, Helicobacteraceae, which promote lipid metabolism, were significantly enriched in expression, and activity and xenobiotic biodegradation and metabolism as well as lipid metabolism pathways were significantly active. In frugivorous primates, the abundance and activity of Elusimicrobiaceae, Neisseriaceae, and Succinivibrionaceae, which are associated with digestion of pectin and fructose, were significantly elevated, and the functional pathways involved in the endocrine system were significantly enriched. In conclusion, the gut microbiome contributes to host dietary adaptation by helping hosts digest the inaccessible nutrients in their specific diets.}, } @article {pmid36671499, year = {2023}, author = {De Lise, F and Iacono, R and Moracci, M and Strazzulli, A and Cobucci-Ponzano, B}, title = {Archaea as a Model System for Molecular Biology and Biotechnology.}, journal = {Biomolecules}, volume = {13}, number = {1}, pages = {}, pmid = {36671499}, issn = {2218-273X}, support = {2019-3-U.O.//Agenzia Spaziale Italiana/ ; }, mesh = {*Archaea/metabolism ; Bacteria/genetics ; *Euryarchaeota/genetics/metabolism ; Biotechnology ; Molecular Biology ; }, abstract = {Archaea represents the third domain of life, displaying a closer relationship with eukaryotes than bacteria. These microorganisms are valuable model systems for molecular biology and biotechnology. In fact, nowadays, methanogens, halophiles, thermophilic euryarchaeota, and crenarchaeota are the four groups of archaea for which genetic systems have been well established, making them suitable as model systems and allowing for the increasing study of archaeal genes' functions. Furthermore, thermophiles are used to explore several aspects of archaeal biology, such as stress responses, DNA replication and repair, transcription, translation and its regulation mechanisms, CRISPR systems, and carbon and energy metabolism. Extremophilic archaea also represent a valuable source of new biomolecules for biological and biotechnological applications, and there is growing interest in the development of engineered strains. In this review, we report on some of the most important aspects of the use of archaea as a model system for genetic evolution, the development of genetic tools, and their application for the elucidation of the basal molecular mechanisms in this domain of life. Furthermore, an overview on the discovery of new enzymes of biotechnological interest from archaea thriving in extreme environments is reported.}, } @article {pmid36670455, year = {2023}, author = {Lin, L and Lai, Z and Zhang, J and Zhu, W and Mao, S}, title = {The gastrointestinal microbiome in dairy cattle is constrained by the deterministic driver of the region and the modified effect of diet.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {10}, pmid = {36670455}, issn = {2049-2618}, mesh = {Female ; Humans ; Cattle ; Animals ; *Gastrointestinal Microbiome/genetics ; Lactation ; Rumen/metabolism ; Plant Breeding ; Diet/veterinary ; Fermentation ; Animal Feed/analysis ; }, abstract = {BACKGROUND: Dairy cattle (Bos taurus), especially Holstein cows, which are the highest-producing dairy animals and are widely bred to provide milk products to humans, rely critically on their associated gastrointestinal tract (GIT) microbiota to digest plant feed. However, the region-specific taxonomic composition and function of the GIT microbiome in dairy cattle and the mechanistic basis for the diet-induced effects remain to be elucidated. RESULTS: We collected 120 digesta samples from 10 GIT regions of 12 Holstein cows fed forage- and grain-based diets and characterized their GIT microbiome via functional shotgun metagenomics and the resolution of metagenome-assembled genomes. Our results demonstrated that the GIT microbiome was mainly partitioned into three distinct clusters, four-chambered stomach, small intestine, and large intestine. Moreover, we found that the four-chambered stomach microbiome with the highest diversity had a strong ability to degrade recalcitrant polysaccharide substrates, underpinned by the prevalence of potential cellulosome--producing and plant-derived polysaccharide utilization loci-encoding consortia. In contrast, the post-gastric intestinal microbiome orchestrated alternative fermentation pathways to adapt to nutrient availability and energy acquisition. Diet shifts selectively modified the metabolic cascades of the microbiome in specific GIT regions, evidenced by the loss of fiber-degrading taxa and increased hydrogen sinks in propionate after grain introduction.

CONCLUSIONS: Our findings provide new insights into GIT microbial organization and function in dairy cattle by GIT regions and diet regimes, which offers clues for improving animal production and health in the future. Video Abstract.}, } @article {pmid36670134, year = {2023}, author = {Zhao, P and Liu, B and Zhao, H and Lei, Z and Zhou, T}, title = {Significant changes in soil microbial community structure and metabolic function after Mikania micrantha invasion.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {1141}, pmid = {36670134}, issn = {2045-2322}, mesh = {*Mikania ; Soil ; Carbon ; China ; Forests ; Soil Microbiology ; *Microbiota ; Nitrogen ; Phosphorus ; }, abstract = {Currently, Mikania micrantha (M. micrantha) has invaded Guangdong, Guangxi and other provinces in China, causing serious harm to the forests of southeastern China. Soil microorganisms play an important role in the establishment of M. micrantha invasion, affecting plant productivity, community dynamics, and ecosystem function. However, at present, how M. micrantha invasion affects soil carbon, nitrogen, and phosphorus phase functional genes and the environmental factors that cause gene expression changes remain unclear, especially in subtropical forest ecosystems. This study was conducted in Xiangtoushan National Forest Park in Guangdong Province to compare the changes in soil nutrients and microorganisms after M. micrantha invasion of a forest. The microbial community composition and metabolic function were explored by metagenome sequencing. Our results showed that after M. micrantha invasion, the soil was more suitable for the growth of gram-positive bacteria (Gemmatimonadetes). In addition, the soil microbial community structure and enzyme activity increased significantly after M. micrantha invasion. Correlation analysis and Mantel test results suggested that total phosphorus (TP), nitrate nitrogen (NO3[-]-N), and soil dissolved organic matter (DOM; DOC and DON), were the strong correlates of soil microbial nitrogen functional genes, while soil organic matter (SOM), soil organic carbon (SOC), total nitrogen (TN), and available phosphorus (Soil-AP) were strongly correlated with the expression of soil microbial phosphorus functional gene. Mikania micrantha invasion alters soil nutrients, microbial community composition and metabolic function in subtropical forests, creates a more favorable growth environment, and may form a positive feedback process conducive to M. micrantha invasion.}, } @article {pmid36669400, year = {2023}, author = {Sun, S and Wang, Y and Xu, C and Qiao, C and Chen, S and Zhao, C and Liu, Q and Zhang, X}, title = {Reconstruction of microbiome and functionality accelerated crude oil biodegradation of 2,4-DCP-oil-contaminated soil systems using composite microbial agent B-Cl.}, journal = {Journal of hazardous materials}, volume = {447}, number = {}, pages = {130808}, doi = {10.1016/j.jhazmat.2023.130808}, pmid = {36669400}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; Bacteria/genetics/metabolism ; *Petroleum/metabolism ; Soil Microbiology ; Alkanes/metabolism ; *Microbiota ; Soil ; *Soil Pollutants/metabolism ; }, abstract = {Biodegradation is one of the safest and most economical methods for the elimination of toxic chlorophenols and crude oil from the environment. In this study, aerobic degradation of the aforementioned compounds by composite microbial agent B-Cl, which consisted of Bacillus B1 and B2 in a 3:2 ratio, was analyzed. The biodegradation mechanism of B-Cl was assessed based on whole genome sequencing, Fourier transform infrared spectroscopy and gas chromatographic analyses. B-Cl was most effective at reducing Cl[-] concentrations (65.17%) and crude oil biodegradation (59.18%) at 7 d, which was when the content of alkanes ≤ C30 showed the greatest decrease. Furthermore, adding B-Cl solution to soil significantly decreased the 2,4-DCP and oil content to below the detection limit and by 80.68%, respectively, and reconstructed of the soil microbial into a system containing more CPs-degrading (exaA, frmA, L-2-HAD, dehH, ALDH, catABE), aromatic compounds-degrading (pcaGH, catAE, benA-xylX, paaHF) and alkane- and fatty acid-degrading (alkB, atoB, fadANJ) microorganisms. Moreover, the presence of 2,4-DCP was the main hinder of the observed effects. This study demonstrates the importance of adding B-Cl solution to determine the interplay of CPs with microbes and accelerating oil degradation, which can be used for in-situ bioremediation of CPs and oil-contaminated soil.}, } @article {pmid36659812, year = {2023}, author = {Shang, J and Tang, X and Sun, Y}, title = {PhaTYP: predicting the lifestyle for bacteriophages using BERT.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {1}, pages = {}, pmid = {36659812}, issn = {1477-4054}, support = {9678241//City University of Hong Kong/ ; //Hong Kong Innovation and Technology Commission/ ; }, mesh = {Infant, Newborn ; Humans ; *Bacteriophages/genetics ; Metagenomics/methods ; Bacteria ; *Microbiota ; Metagenome ; }, abstract = {Bacteriophages (or phages), which infect bacteria, have two distinct lifestyles: virulent and temperate. Predicting the lifestyle of phages helps decipher their interactions with their bacterial hosts, aiding phages' applications in fields such as phage therapy. Because experimental methods for annotating the lifestyle of phages cannot keep pace with the fast accumulation of sequenced phages, computational method for predicting phages' lifestyles has become an attractive alternative. Despite some promising results, computational lifestyle prediction remains difficult because of the limited known annotations and the sheer amount of sequenced phage contigs assembled from metagenomic data. In particular, most of the existing tools cannot precisely predict phages' lifestyles for short contigs. In this work, we develop PhaTYP (Phage TYPe prediction tool) to improve the accuracy of lifestyle prediction on short contigs. We design two different training tasks, self-supervised and fine-tuning tasks, to overcome lifestyle prediction difficulties. We rigorously tested and compared PhaTYP with four state-of-the-art methods: DeePhage, PHACTS, PhagePred and BACPHLIP. The experimental results show that PhaTYP outperforms all these methods and achieves more stable performance on short contigs. In addition, we demonstrated the utility of PhaTYP for analyzing the phage lifestyle on human neonates' gut data. This application shows that PhaTYP is a useful means for studying phages in metagenomic data and helps extend our understanding of microbial communities.}, } @article {pmid36658397, year = {2023}, author = {Laso-Pérez, R and Wu, F and Crémière, A and Speth, DR and Magyar, JS and Zhao, K and Krupovic, M and Orphan, VJ}, title = {Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome.}, journal = {Nature microbiology}, volume = {8}, number = {2}, pages = {231-245}, pmid = {36658397}, issn = {2058-5276}, mesh = {*Archaea ; *Ecosystem ; Phylogeny ; Virome ; Geologic Sediments ; Anaerobiosis ; Methane/metabolism ; Alkanes/metabolism ; }, abstract = {'Candidatus Methanophagales' (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus-host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, 'Candidatus Methanospirareceae', closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems.}, } @article {pmid36657438, year = {2023}, author = {Zhao, C and Shi, ZJ and Pollard, KS}, title = {Pitfalls of genotyping microbial communities with rapidly growing genome collections.}, journal = {Cell systems}, volume = {14}, number = {2}, pages = {160-176.e3}, pmid = {36657438}, issn = {2405-4720}, support = {R01 HL160862/HL/NHLBI NIH HHS/United States ; }, mesh = {Sequence Analysis, DNA ; Genotype ; *Algorithms ; *Microbiota/genetics ; Metagenome ; }, abstract = {Detecting genetic variants in metagenomic data is a priority for understanding the evolution, ecology, and functional characteristics of microbial communities. Many tools that perform this metagenotyping rely on aligning reads of unknown origin to a database of sequences from many species before calling variants. In this synthesis, we investigate how databases of increasingly diverse and closely related species have pushed the limits of current alignment algorithms, thereby degrading the performance of metagenotyping tools. We identify multi-mapping reads as a prevalent source of errors and illustrate a trade-off between retaining correct alignments versus limiting incorrect alignments, many of which map reads to the wrong species. Then we evaluate several actionable mitigation strategies and review emerging methods showing promise to further improve metagenotyping in response to the rapid growth in genome collections. Our results have implications beyond metagenotyping to the many tools in microbial genomics that depend upon accurate read mapping.}, } @article {pmid36656265, year = {2023}, author = {Yu, Y and Yu, X and Zhang, D and Jin, L and Huang, J and Zhu, X and Sun, J and Yu, M and Zhu, L}, title = {Biotransformation of Organophosphate Esters by Rice and Rhizosphere Microbiome: Multiple Metabolic Pathways, Mechanism, and Toxicity Assessment.}, journal = {Environmental science & technology}, volume = {57}, number = {4}, pages = {1776-1787}, doi = {10.1021/acs.est.2c07796}, pmid = {36656265}, issn = {1520-5851}, mesh = {*Oryza ; Rhizosphere ; Esters/metabolism ; *Flame Retardants/analysis ; Organophosphates ; Biotransformation ; Phosphates ; *Microbiota ; Metabolic Networks and Pathways ; Environmental Monitoring ; China ; }, abstract = {The biotransformation behavior and toxicity of organophosphate esters (OPEs) in rice and rhizosphere microbiomes were comprehensively studied by hydroponic experiments. OPEs with lower hydrophobicity were liable to be translocated acropetally, and rhizosphere microbiome could reduce the uptake and translocation of OPEs in rice tissues. New metabolites were successfully identified in rice and rhizosphere microbiome, including hydrolysis, hydroxylated, methylated, and glutathione-, glucuronide-, and sulfate-conjugated products. Rhizobacteria and plants could cooperate to form a complex ecological interaction web for OPE elimination. Furthermore, active members of the rhizosphere microbiome during OPE degradation were revealed and the metagenomic analysis indicated that most of these active populations contained OPE-degrading genes. The results of metabolomics analyses for phytotoxicity assessment implied that several key function metabolic pathways of the rice plant were found perturbed by metabolites, such as diphenyl phosphate and monophenyl phosphate. In addition, the involved metabolism mechanisms, such as the carbohydrate metabolism, amino acid metabolism and synthesis, and nucleotide metabolism in Escherichia coli, were significantly altered after exposure to the products mixture of OPEs generated by rhizosphere microbiome. This work for the first time gives a comprehensive understanding of the entire metabolism of OPEs in plants and associated microbiome, and provides support for the ongoing risk assessment of emerging contaminants and, most critically, their transformation products.}, } @article {pmid36656039, year = {2023}, author = {Liu, Z and Huang, Y and Zhang, T and Meng, D and Jiang, Z and Yang, Z and Yang, Z and Li, L and Gu, Y and Wang, J and Liu, X and Jiang, C and Yin, H}, title = {Viruses Regulate Microbial Community Assembly Together with Environmental Factors in Acid Mine Drainage.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {2}, pages = {e0197322}, pmid = {36656039}, issn = {1098-5336}, mesh = {Humans ; Bacteria/genetics ; Mining ; *Microbiota/genetics ; Microbial Consortia ; *Viruses/genetics ; }, abstract = {Viruses are widespread in various ecosystems, and they play important roles in regulating the microbial community via host-virus interactions. Recently, metagenomic studies showed that there are extremely diverse viruses in different environments from the ocean to the human gut, but the influences of viral communities on microbial communities are poorly understood, especially in extreme environments. Here, we used metagenomics to characterize microbial communities and viral communities in acid mine drainage (AMD) and evaluated how viruses shape microbial community constrained by the harsh environments. Our results showed that AMD viral communities are significantly associated with the microbial communities, and viral diversity has positive correlations with microbial diversity. Viral community explained more variations of microbial community composition than environmental factors in AMD of a polymetallic mine. Moreover, we found that viruses harboring adaptive genes regulate a relative abundance of hosts under the modulation of environmental factors, such as pH. We also observed that viral diversity has significant correlations with the global properties of microbial cooccurrence networks, such as modularity. In addition, the results of null modeling analyses revealed that viruses significantly affect microbial community phylogeny and play important roles in regulating ecological processes of community assembly, such as dispersal limitation and homogenous dispersal. Together, these results revealed that AMD viruses are critical forces driving microbial network and community assembly via host-virus interactions. IMPORTANCE Viruses as mobile genetic elements play critical roles in the adaptive evolution of their hosts in extreme environments. However, how viruses further influence microbial community structure and assembly is still unclear. A recent metagenomic study observed diverse viruses unexplored in acid mine drainage, revealing the associations between the viral community and environmental factors. Here, we showed that viruses together with environmental factors can constrain the relative abundance of host and microbial community assembly in AMD of copper mines and polymetallic mines. Our results highlight the importance of viruses in shaping the microbial community from the individual host level to the community level.}, } @article {pmid36655544, year = {2023}, author = {Sun, H and Wang, P and Li, Y}, title = {An integrated microbiome project for charactering microbial diversity in classroom based on virtual simulation experiments.}, journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology}, volume = {51}, number = {2}, pages = {171-179}, doi = {10.1002/bmb.21706}, pmid = {36655544}, issn = {1539-3429}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Learning ; Students ; Computational Biology/education ; *Microbiota/genetics ; }, abstract = {Microbiome study requires both molecular techniques and bioinformatics skills, which are challenging for biologists to participate in this growing field. To introduce microbiome concepts and skills to students, a 6-week wet-lab and bioinformatics course for undergraduates was implemented through the project-based learning (PBL) approach. In the saliva microbiome project, students collected their saliva samples, performed DNA extraction and PCR amplification, followed by metagenomic analysis to compare the diversity and abundances of microbes among samples. First, students are required to practice molecular techniques and bioinformatics analysis skills in a virtual simulation lab. To our knowledge, our study is the first one to incorporate a virtual lab into microbiome experience. Then, students applied their recently acquired skills to produce and analyze their own 16S amplicon sequencing data and reported their results via a scientific report. The student learning outcomes show that the Virtual lab can improve students' laboratory techniques and research capabilities. Moreover, a simple pipeline to analyze 16S rRNA gene amplicon sequencing data is introduced in a step-by-step manner that helps students to develop analysis skills. This project can be modified as either a virtual course or a module within another course such as microbiology, molecular biology, and bioinformatics. Our study provides evidence on the positive impact of virtual labs on learning outcomes in undergraduate science education.}, } @article {pmid36653448, year = {2023}, author = {Valles-Colomer, M and Blanco-Míguez, A and Manghi, P and Asnicar, F and Dubois, L and Golzato, D and Armanini, F and Cumbo, F and Huang, KD and Manara, S and Masetti, G and Pinto, F and Piperni, E and Punčochář, M and Ricci, L and Zolfo, M and Farrant, O and Goncalves, A and Selma-Royo, M and Binetti, AG and Becerra, JE and Han, B and Lusingu, J and Amuasi, J and Amoroso, L and Visconti, A and Steves, CM and Falchi, M and Filosi, M and Tett, A and Last, A and Xu, Q and Qin, N and Qin, H and May, J and Eibach, D and Corrias, MV and Ponzoni, M and Pasolli, E and Spector, TD and Domenici, E and Collado, MC and Segata, N}, title = {The person-to-person transmission landscape of the gut and oral microbiomes.}, journal = {Nature}, volume = {614}, number = {7946}, pages = {125-135}, pmid = {36653448}, issn = {1476-4687}, support = {MR/N01183X/1/MRC_/Medical Research Council/United Kingdom ; MR/S005013/1/MRC_/Medical Research Council/United Kingdom ; R01 CA230551/CA/NCI NIH HHS/United States ; U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {Female ; Humans ; Infant ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Microbiota/genetics ; Mothers ; *Mouth/microbiology ; Infectious Disease Transmission, Vertical ; Family Characteristics ; Aging ; *Disease Transmission, Infectious ; Time Factors ; Microbial Viability ; *Home Environment ; }, abstract = {The human microbiome is an integral component of the human body and a co-determinant of several health conditions[1,2]. However, the extent to which interpersonal relations shape the individual genetic makeup of the microbiome and its transmission within and across populations remains largely unknown[3,4]. Here, capitalizing on more than 9,700 human metagenomes and computational strain-level profiling, we detected extensive bacterial strain sharing across individuals (more than 10 million instances) with distinct mother-to-infant, intra-household and intra-population transmission patterns. Mother-to-infant gut microbiome transmission was considerable and stable during infancy (around 50% of the same strains among shared species (strain-sharing rate)) and remained detectable at older ages. By contrast, the transmission of the oral microbiome occurred largely horizontally and was enhanced by the duration of cohabitation. There was substantial strain sharing among cohabiting individuals, with 12% and 32% median strain-sharing rates for the gut and oral microbiomes, and time since cohabitation affected strain sharing more than age or genetics did. Bacterial strain sharing additionally recapitulated host population structures better than species-level profiles did. Finally, distinct taxa appeared as efficient spreaders across transmission modes and were associated with different predicted bacterial phenotypes linked with out-of-host survival capabilities. The extent of microorganism transmission that we describe underscores its relevance in human microbiome studies[5], especially those on non-infectious, microbiome-associated diseases.}, } @article {pmid36651919, year = {2023}, author = {Fernandes-Martins, MC and Colman, DR and Boyd, ES}, title = {Relationships between fluid mixing, biodiversity, and chemosynthetic primary productivity in Yellowstone hot springs.}, journal = {Environmental microbiology}, volume = {25}, number = {5}, pages = {1022-1040}, doi = {10.1111/1462-2920.16340}, pmid = {36651919}, issn = {1462-2920}, mesh = {*Bacteria/genetics ; Ecosystem ; *Hot Springs ; Biodiversity ; Metagenome ; }, abstract = {The factors that influence biodiversity and productivity of hydrothermal ecosystems are not well understood. Here we investigate the relationship between fluid mixing, biodiversity, and chemosynthetic primary productivity in three co-localized hot springs (RSW, RSN, and RSE) in Yellowstone National Park that have different geochemistry. All three springs are sourced by reduced hydrothermal fluid, but RSE and RSN receive input of vapour phase gas and oxidized groundwaters, with input of both being substantially higher in RSN. Metagenomic sequencing revealed that communities in RSN were more biodiverse than those of RSE and RSW in all dimensions evaluated. Microcosm activity assays indicate that rates of dissolved inorganic carbon (DIC) uptake were also higher in RSN than in RSE and RSW. Together, these results suggest that increased mixing of reduced volcanic fluid with oxidized fluids generates additional niche space capable of supporting increasingly biodiverse communities that are more productive. These results provide insight into the factors that generate and maintain chemosynthetic biodiversity in hydrothermal systems and that influence the distribution, abundance, and diversity of microbial life in communities supported by chemosynthesis. These factors may also extend to other ecosystems not supported by photosynthesis, including the vast subterranean biosphere and biospheres beneath ice sheets and glaciers.}, } @article {pmid36651762, year = {2023}, author = {Zünd, M and Dunham, SJB and Rothman, JA and Whiteson, KL}, title = {What Lies Beneath? Taking the Plunge into the Murky Waters of Phage Biology.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0080722}, pmid = {36651762}, issn = {2379-5077}, support = {T32 AG000096/AG/NIA NIH HHS/United States ; T32 AG00096-38//HHS | NIH | National Institute on Aging (NIA)/ ; }, mesh = {*Bacteriophages/genetics ; *Microbiota ; Biology ; }, abstract = {The sequence revolution revealed that bacteria-infecting viruses, known as phages, are Earth's most abundant biological entities. Phages have far-reaching impacts on the form and function of microbial communities and play a fundamental role in ecological processes. However, even well into the sequencing revolution, we have only just begun to explore the murky waters around the phage biology iceberg. Many viral reads cannot be assigned to a culturable isolate, and reference databases are biased toward more easily collectible samples, which likely distorts our conclusions. This minireview points out alternatives to mapping reads to reference databases and highlights innovative bioinformatic and experimental approaches that can help us overcome some of the challenges in phage research and better decipher the impact of phages on microbial communities. Moving beyond the identification of novel phages, we highlight phage metabolomics as an important influencer of bacterial host cell physiology and hope to inspire the reader to consider the effects of phages on host metabolism and ecosystems at large. We encourage researchers to report unassigned/unknown sequencing reads and contigs and to continue developing alternative methods to investigate phages within sequence data.}, } @article {pmid36651521, year = {2023}, author = {Petrone, ME and Holmes, EC and Harvey, E}, title = {Through an ecological lens: An ecosystem-based approach to zoonotic risk assessment: An ecosystem-based approach to zoonotic risk assessment.}, journal = {EMBO reports}, volume = {24}, number = {2}, pages = {e56578}, pmid = {36651521}, issn = {1469-3178}, mesh = {*Ecosystem ; Biodiversity ; *Viruses ; Public Health ; Risk Assessment ; }, abstract = {Public health strategies to mitigate the emergence of novel pathogenic viruses should implement longitudinal metagenomic surveillance of ecosystems experiencing biodiversity changes to identify generalist viruses.}, } @article {pmid36650527, year = {2023}, author = {Zhao, N and Zhang, Q and Guo, Y and Cui, S and Tian, Y and Zhang, Y and Zhou, Y and Wang, X}, title = {Oral microbiome contributes to the failure of orthodontic temporary anchorage devices (TADs).}, journal = {BMC oral health}, volume = {23}, number = {1}, pages = {22}, pmid = {36650527}, issn = {1472-6831}, support = {62076011//National Natural Science Foundation of China,China/ ; PKUSSNMP-202013//National Program for Multidisciplinary Cooperative Treatment on Major Diseases/ ; A2021-021//China Oral Health Foundation/ ; 81671015//National Natural Science Foundation of China/ ; Z171100001017128//Beijing Municipal Science and Technology Commission/ ; }, mesh = {Humans ; *Orthodontic Anchorage Procedures ; Orthodontic Appliance Design ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: The stability of temporary anchorage devices (TADs) is critical in orthodontic clinics. The failure of TADs is multifactorial, and the role of the oral microbiome has not been clearly defined. Herein, we attempted to analyze the contribution of the oral microbiome to the failure of TADs.

METHODS: Next-generation sequencing was adopted for analyzing the microbiome on the TADs from orthodontic patients. 29 TADs (15 failed TADs and 14 successful TADs) were used for 16S rRNA gene sequencing. A total of 135 TADs (62 failed TADs and 73 successful TADs) were collected to conduct metagenomic sequencing. Additionally, 34 verified samples (18 failed TADs and 16 successful TADs) were collected for quantitative real-time polymerase chain reaction analysis (qRT-PCR).

RESULTS: Successful and failed TADs demonstrated discrepancies in microbiome structure, composition, and function. Clear separations were found in β-diversity in 16S rRNA gene sequencing as well as metagenomic sequencing (p < 0.05). Metagenomic sequencing showed that Prevotella intermedia, Eikenella corrodens, Parvimonas spp., Neisseria elongata, and Catonella morbi were enriched in the failed groups. qRT-PCR also demonstrated that the absolute bacteria load of Prevotella intermedia was higher in failed TADs (p < 0.05). Considering functional aspects, the failed group showed enriched genes involved in flagellar assembly, bacterial chemotaxis, and oxidative phosphorylation.

CONCLUSIONS: This study illustrated the compositional and functional differences of microorganisms found on successful and failed TADs, indicating that controlling bacterial adhesion on the surface of TADs is essential for their success rate.}, } @article {pmid36650368, year = {2023}, author = {Raiyani, NM and Singh, SP}, title = {Microbial community and predictive functionalities associated with the marine sediment of Coastal Gujarat.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {15}, pages = {43245-43266}, pmid = {36650368}, issn = {1614-7499}, mesh = {Geologic Sediments/chemistry ; *Microbiota ; *Cyanobacteria ; Bacteroidetes ; Proteobacteria ; RNA, Ribosomal, 16S ; }, abstract = {Marine sediments are complex ecosystems where structures and functions constantly change due to natural and anthropogenic influences. In this investigation, a comprehensive and comparative analysis of the bacterial communities and their functional potential of the pristine and polluted marine sediments were carried out using MiSeq. The phylum Proteobacteria was dominant in all study sites. Other phyla were Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Chloroflexi, Nitrospirae, Cyanobacteria, Verrucomicrobia, Tenericutes, and Chlorobi. Interestingly, about 50% of genera belong to the unclassified categories. The key genera were identified as Acinetobacter, Bacillus, Pseudomona, Idiomarina, Thalassospira, and Marinobacter, Halomonas, Planctomyces, Psychrobacter, and Vogesella. PICRUSt analysis revealed that major functions are associated with the metabolism category. Additionally, metabolism related to amino acids, carbohydrates, energy generation, xenobiotics degradation, nitrogen, sulfate, and methane were prominent. Similarly, the predicted metabolisms by COG and KEGG were observed in the microbial communities of the marine sediments. To date, a comprehensive description of the microbial life with metabolic potential in these study sites has not been investigated. This study therefore significantly adds to our understanding of the microbiome and its functional attributes of marine sediments.}, } @article {pmid36650178, year = {2023}, author = {Rivera-Gutiérrez, X and Morán, P and Taboada, B and Serrano-Vázquez, A and Isa, P and Rojas-Velázquez, L and Pérez-Juárez, H and López, S and Torres, J and Ximénez, C and Arias, CF}, title = {The fecal and oropharyngeal eukaryotic viromes of healthy infants during the first year of life are personal.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {938}, pmid = {36650178}, issn = {2045-2322}, mesh = {Child ; Humans ; Infant ; Eukaryota ; Virome ; *Picornaviridae ; Feces ; *Herpesviridae ; Oropharynx ; Metagenomics/methods ; }, abstract = {Using a metagenomic sequencing approach, we described and compared the diversity and dynamics of the oropharyngeal and fecal eukaryotic virome of nine asymptomatic children in a semi-rural community setting located in the State of Morelos, Mexico. Ninety oropharyngeal swabs and 97 fecal samples were collected starting 2 weeks after birth and monthly thereafter until 12 months of age. In both niches, more than 95% of the total sequence reads were represented by viruses that replicate either in humans or in plants. Regarding human viruses, three families were most abundant and frequent in the oropharynx: Herpesviridae, Picornaviridae, and Reoviridae; in fecal samples, four virus families predominated: Caliciviridae, Picornaviridae, Reoviridae, and Anelloviridae. Both niches showed a high abundance of plant viruses of the family Virgaviridae. Differences in the frequency and abundance of sequence reads and diversity of virus species were observed in both niches and throughout the year of study, with some viruses already present in the first months of life. Our results suggest that the children's virome is dynamic and likely shaped by the environment, feeding, and age. Moreover, composition analysis suggests that the virome composition is mostly individual. Whether this constant exposition to different viruses has a long-term impact on children's health or development remains to be studied.}, } @article {pmid36649845, year = {2023}, author = {Xing, L and Zhang, M and Liu, L and Hu, X and Liu, J and Zhou, X and Chai, Z and Yin, H}, title = {Multiomics provides insights into the succession of microbiota and metabolite during plant leaf fermentation.}, journal = {Environmental research}, volume = {221}, number = {}, pages = {115304}, doi = {10.1016/j.envres.2023.115304}, pmid = {36649845}, issn = {1096-0953}, mesh = {Fermentation ; *Multiomics ; *Microbiota ; Bacteria/genetics/metabolism ; Odorants/analysis ; }, abstract = {The quality of fermented plant products is closely related to microbial metabolism. Here, the associations of bacterial communities, metabolites, and functional genes were explored using multi-omics techniques based on plant leaf fermentation systems. The results showed significant changes in the structure of the microbial community, with a significant decrease in Firmicutes and a significant increase in Proteobacteria. In addition, the concentration of metabolites with antibacterial, antioxidant and aroma properties increased significantly, enhancing the quality of the fermented plant leaves. Integrated macrogenomic and metabolomic analyses indicated that amino acid metabolism could be key metabolic pathway affecting fermentation quality. Actinobacteria, Proteobacteria, Firmicutes were actively involved in tyrosine metabolism (ko00350) and phenylalanine metabolism (ko00360), and are presumed to be the major groups responsible for synthesizing growth and flavor compounds. This study emphasized the important role of microorganisms in the changes of metabolites during the fermentation of plant leaves.}, } @article {pmid36646520, year = {2023}, author = {Gao, P and Fan, K and Zhang, G and Yin, X and Jia, C and Tian, H}, title = {Coal-mining subsidence changed distribution of the microbiomes and their functional genes in a farmland.}, journal = {Journal of basic microbiology}, volume = {63}, number = {5}, pages = {542-557}, doi = {10.1002/jobm.202200582}, pmid = {36646520}, issn = {1521-4028}, support = {LNY2020-Z06//Foundation of Shandong Provincial Lunan Geology and Exploration Institute/ ; }, mesh = {Farms ; *Coal Mining ; *Microbiota ; Carbon ; Soil/chemistry ; Coal ; China ; }, abstract = {Land subsidence is a serious geological event, and can trigger severe environmental and ecological issues. In this study, the influences of coal-mining subsidence on distribution of farmland microbiomes and their functional genes were investigated by 16 S ribosomal RNA (rRNA) gene and metagenome sequencing. The results showed the existence of a core microbiome, which determined the community compositions across the subsidence farmland. Subsidence decreased the relative abundances of dominant Streptomyces, Nocardioides, and Rhizophagus, but increased the relative abundances of dominant Bradyrhizobium, Rhizobium, and Trichoderma. Subsidence also decreased the relative abundances of genes related to carbon metabolism, Quorum sensing, aminoacyl-transfer RNA (tRNA) biosynthesis, and oxidative phosphorylation, and increased the relative abundances of genes related to two-component system and bacterial chemotaxis. Furthermore, subsidence weakened the biosynthesis of organic carbons by decreasing the relative abundances of genes encoding glycosyl transferases, and strengthened decomposition of degradable organic carbons of the microbiomes and auxiliary activities by increasing the relative abundances of genes encoding glycoside hydrolases and polysaccharide lyases. The concentrations of total phosphorus, Mg[2+] , and Ca[2+] at the lower areas were significantly higher than those at the upper areas, indicating an associated loss of soil nutrients. Canonical correspondence analysis showed that soil moisture, pH, and the concentrations of NH4 [+] and Ca[2+] were the main factors affecting the distribution of the microbiomes and their functional genes. Collectively, this study shows that coal-mining subsidence alters soil physicochemical properties and distribution of farmland microbiomes and their functional genes.}, } @article {pmid36646037, year = {2023}, author = {Bostancıklıoğlu, M and Kaplan, DS and Temiz, E and Yiğit, E}, title = {Local myelin damage in the hippocampus fluctuates gut microbiome profile and memory.}, journal = {Journal of psychiatric research}, volume = {158}, number = {}, pages = {392-402}, doi = {10.1016/j.jpsychires.2023.01.006}, pmid = {36646037}, issn = {1879-1379}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Myelin Sheath ; Dysbiosis/genetics ; RNA, Ribosomal, 16S/genetics ; Hippocampus ; }, abstract = {The concept of the gut-brain axis has focused research on how gut dysbiosis affects myelin biology in the brain. However, this axis has not been tested to determine whether it conveys the effects of myelin damage on the gut microbiome profile. Therefore, we aimed to investigate how myelin biology is correlated with gut microbiome profile. The impact of local myelin damage in the hippocampus on gut microbiome profile was investigated with 16S rRNA metagenomic sequence and molecular analysis of myelin biology-associated proteins, and its reflections on memory performance were tested with behavioral tests. Local myelin damage in the hippocampus triggered severe gut dysbiosis, p < .05, changed memory performance, p < .05, and deviated emotional responses. Moreover, myelin treatment with clemastine improved gut dysbiosis and behavioral deviations. Our study provides animal-based evidence on the direct interaction between glial biology in the hippocampus and gut microbiome profile. This study proposes a framework for generating new hypotheses bridging different systems to the gut-brain axis.}, } @article {pmid36645293, year = {2023}, author = {Huang, X and Erickson, DL and Meng, J}, title = {PhyloPlus: a Universal Tool for Phylogenetic Interrogation of Metagenomic Communities.}, journal = {mBio}, volume = {14}, number = {1}, pages = {e0345522}, pmid = {36645293}, issn = {2150-7511}, support = {U01 FD001418/FD/FDA HHS/United States ; }, mesh = {Humans ; Phylogeny ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Phylogeny is a powerful tool that can be incorporated into quantitative descriptions of community diversity, yet its use has been limited largely due to the difficulty in constructing phylogenies which incorporate the wide genomic diversity of microbial communities. Here, we describe the development of a web portal, PhyloPlus, which enables users to generate customized phylogenies that may be applied to any bacterial or archaeal communities. We demonstrate the power of phylogeny by comparing metrics that employ phylogeny with those that do not when applied to data sets from two metagenomic studies (fermented food, n = 58; human microbiome, n = 60). This example shows how inclusion of all bacterial species identified by taxonomic classifiers (Kraken2 and Kaiju) made the phylogeny perfectly congruent to the corresponding classification outputs. Our phylogeny-based approach also enabled the construction of more constrained null models which (i) shed light into community structure and (ii) minimize potential inflation of type I errors. Construction of such null models allowed for the observation of under-dispersion in 44 (75.86%) food samples, with the metacommunity defined as bacteria that were found in different food matrices. We also observed that closely related species with high abundance and uneven distribution across different sites could potentially exaggerate the dissimilarity between phylogenetically similar communities if they were measured using traditional species-based metrics (Padj. = 0.003), whereas this effect was mitigated by incorporating phylogeny (Padj. = 1). In summary, our tool can provide additional insights into microbial communities of interest and facilitate the use of phylogeny-based approaches in metagenomic analyses. IMPORTANCE There has been an explosion of interest in how microbial diversity affects human health, food safety, and environmental functions among many other processes. Accurately measuring the diversity and structure of those communities is central to understanding their effects. Here, we describe the development of a freely available online tool, PhyloPlus, which allows users to generate custom phylogenies that may be applied to any data set, thereby removing a major obstacle to the application of phylogeny to metagenomic data analysis. We demonstrate that the genetic relatedness of the organisms within those communities is a critical feature of their overall diversity, and that using a phylogeny which captures and quantifies this diversity allows for much more accurate descriptions while preventing misleading conclusions based on estimates that ignore evolutionary relationships.}, } @article {pmid36641850, year = {2023}, author = {Luo, ZH and Li, Q and Chen, N and Tang, LY and Liao, B and Yang, TT and Huang, LN}, title = {Genome-resolved metagenomics reveals depth-related patterns of microbial community structure and functions in a highly stratified, AMD overlaying mine tailings.}, journal = {Journal of hazardous materials}, volume = {447}, number = {}, pages = {130774}, doi = {10.1016/j.jhazmat.2023.130774}, pmid = {36641850}, issn = {1873-3336}, mesh = {*Metagenomics ; *Microbiota ; Acids ; Iron ; Metagenome ; Nitrogen/metabolism ; Sulfur ; }, abstract = {Acid mine drainage (AMD) is a worldwide environmental problem, yet bioremediation is hampered by a limited knowledge of the reductive microbial processes in the AMD ecosystem. Here, we generate extensive metagenome and geochemical datasets to investigate how microbial populations and metabolic capacities driving major element cycles are structured in a highly stratified, AMD overlaying tailings environment. The results demonstrated an explicit depth-dependent differentiation of microbial community composition and function profiles between the surface and deeper tailings layers, paralleling the dramatic shifts in major physical and geochemical properties. Specifically, key genes involved in sulfur and iron oxidation were significantly enriched in the surface tailings, whereas those associated with reductive nitrogen, sulfur, and iron processes were enriched in the deeper layers. Genome-resolved metagenomics retrieved 406 intermediate or high-quality genomes spanning 26 phyla, including major new groups (e.g., Patescibacteria and DPANN). Metabolic models involving nitrogen, sulfur, iron, and carbon cycles were proposed based on the functional potentials of the abundant microbial genomes, emphasizing syntrophy and the importance of lesser-known taxa in the degradation of complex carbon compounds. These results have implications for in situ AMD bioremediation.}, } @article {pmid36641060, year = {2023}, author = {Papaiakovou, M and Fraija-Fernández, N and James, K and Briscoe, AG and Hall, A and Jenkins, TP and Dunn, J and Levecke, B and Mekonnen, Z and Cools, P and Doyle, SR and Cantacessi, C and Littlewood, DTJ}, title = {Evaluation of genome skimming to detect and characterise human and livestock helminths.}, journal = {International journal for parasitology}, volume = {53}, number = {2}, pages = {69-79}, doi = {10.1016/j.ijpara.2022.12.002}, pmid = {36641060}, issn = {1879-0135}, support = {MR/T020733/1//Medical Research Council/United Kingdom ; 108413/A/15/D//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Humans ; Livestock ; Phylogeny ; *Helminths/genetics ; DNA ; *Parasites ; }, abstract = {The identification of gastrointestinal helminth infections of humans and livestock almost exclusively relies on the detection of eggs or larvae in faeces, followed by manual counting and morphological characterisation to differentiate species using microscopy-based techniques. However, molecular approaches based on the detection and quantification of parasite DNA are becoming more prevalent, increasing the sensitivity, specificity and throughput of diagnostic assays. High-throughput sequencing, from single PCR targets through to the analysis of whole genomes, offers significant promise towards providing information-rich data that may add value beyond traditional and conventional molecular approaches; however, thus far, its utility has not been fully explored to detect helminths in faecal samples. In this study, low-depth whole genome sequencing, i.e. genome skimming, has been applied to detect and characterise helminth diversity in a set of helminth-infected human and livestock faecal material. The strengths and limitations of this approach are evaluated using three methods to characterise and differentiate metagenomic sequencing data based on (i) mapping to whole mitochondrial genomes, (ii) whole genome assemblies, and (iii) a comprehensive internal transcribed spacer 2 (ITS2) database, together with validation using quantitative PCR (qPCR). Our analyses suggest that genome skimming can successfully identify most single and multi-species infections reported by qPCR and can provide sufficient coverage within some samples to resolve consensus mitochondrial genomes, thus facilitating phylogenetic analyses of selected genera, e.g. Ascaris spp. Key to this approach is both the availability and integrity of helminth reference genomes, some of which are currently contaminated with bacterial and host sequences. The success of genome skimming of faecal DNA is dependent on the availability of vouchered sequences of helminths spanning both taxonomic and geographic diversity, together with methods to detect or amplify minute quantities of parasite nucleic acids in mixed samples.}, } @article {pmid36640575, year = {2023}, author = {Zhang, Z and Li, J and Jiang, S and Xu, M and Ma, T and Sun, Z and Zhang, J}, title = {Lactobacillus fermentum HNU312 alleviated oxidative damage and behavioural abnormalities during brain development in early life induced by chronic lead exposure.}, journal = {Ecotoxicology and environmental safety}, volume = {251}, number = {}, pages = {114543}, doi = {10.1016/j.ecoenv.2023.114543}, pmid = {36640575}, issn = {1090-2414}, mesh = {Mice ; Animals ; *Limosilactobacillus fermentum ; Lead/toxicity ; *Microbiota/physiology ; *Probiotics/pharmacology ; Oxidative Stress ; Brain ; }, abstract = {Lead exposure is a global public health safety issue that severely disrupts brain development and causes damage to the nervous system in early life. Probiotics and gut microbes have been highlighted for their critical roles in mitigating lead toxicity. However, the underlying mechanisms by which they work yet to be fully explored. Here, we designed a two-stage experiment using the probiotic Lactobacillus fermentum HNU312 (Lf312) to uncover how probiotics alleviate lead toxicity to the brain during early life. First, we explored the tolerance and adsorption of Lf312 to lead in vitro. Second, the adsorption capacity of the strain was determined and confirmed in vivo. The shotgun metagenome sequencing showed lead exposure-induced imbalance and dysfunction of the gut microbiome. In contrast, Lf312 intake significantly modulated the structure of the microbiome, increased the abundance of beneficial bacteria and short-chain fatty acids (SCFAs)-producing bacteria, and upregulated function-related metabolic pathways such as antioxidants. Notably, Lf312 enhanced the integrity of the blood-brain barrier by increasing the levels of SCFAs in the gut, alleviated inflammation in the brain, and ultimately improved anxiety-like and depression-like behaviours induced by lead exposure in mice. Subsequently, the effective mechanism was confirmed, highlighting that Lf312 worked through integrated strategies, including ionic adsorption and microbiota-gut-brain axis regulation. Collectively, this work elucidated the mechanism by which the gut microbiota mitigates the toxic effects of lead in the brain and provides preventive measures and intervention measures for brain damage due to mass lead poisoning in children.}, } @article {pmid36639537, year = {2023}, author = {Osvatic, JT and Yuen, B and Kunert, M and Wilkins, L and Hausmann, B and Girguis, P and Lundin, K and Taylor, J and Jospin, G and Petersen, JM}, title = {Gene loss and symbiont switching during adaptation to the deep sea in a globally distributed symbiosis.}, journal = {The ISME journal}, volume = {17}, number = {3}, pages = {453-466}, pmid = {36639537}, issn = {1751-7370}, mesh = {Phylogeny ; *Symbiosis/genetics ; Adaptation, Physiological ; Biological Evolution ; Bacteria/genetics ; Water ; *Hydrothermal Vents ; }, abstract = {Chemosynthetic symbioses between bacteria and invertebrates occur worldwide from coastal sediments to the deep sea. Most host groups are restricted to either shallow or deep waters. In contrast, Lucinidae, the most species-rich family of chemosymbiotic invertebrates, has both shallow- and deep-sea representatives. Multiple lucinid species have independently colonized the deep sea, which provides a unique framework for understanding the role microbial symbionts play in evolutionary transitions between shallow and deep waters. Lucinids acquire their symbionts from their surroundings during early development, which may allow them to flexibly acquire symbionts that are adapted to local environments. Via metagenomic analyses of museum and other samples collected over decades, we investigated the biodiversity and metabolic capabilities of the symbionts of 22 mostly deep-water lucinid species. We aimed to test the theory that the symbiont played a role in adaptation to life in deep-sea habitats. We identified 16 symbiont species, mostly within the previously described genus Ca. Thiodiazotropha. Most genomic functions were shared by both shallow-water and deep-sea Ca. Thiodiazotropha, though nitrogen fixation was exclusive to shallow-water species. We discovered multiple cases of symbiont switching near deep-sea hydrothermal vents and cold seeps, where distantly related hosts convergently acquired novel symbionts from a different bacterial order. Finally, analyses of selection revealed consistently stronger purifying selection on symbiont genomes in two extreme habitats - hydrothermal vents and an oxygen-minimum zone. Our findings reveal that shifts in symbiont metabolic capability and, in some cases, acquisition of a novel symbiont accompanied adaptation of lucinids to challenging deep-sea habitats.}, } @article {pmid36639043, year = {2023}, author = {Qian, Y and Hu, L and Wang, Y and Xu, K}, title = {Arsenic methylation behavior and microbial regulation mechanisms in landfill leachate saturated zones.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {320}, number = {}, pages = {121064}, doi = {10.1016/j.envpol.2023.121064}, pmid = {36639043}, issn = {1873-6424}, mesh = {*Arsenic/analysis ; Methylation ; *Water Pollutants, Chemical/analysis ; Bacteria/metabolism ; *Microbiota ; Bacteroidetes/metabolism ; }, abstract = {Arsenic (As) is a potential contaminant in landfill. As methylation has been considered as a detoxification mechanism to address this problem. In this study, microcosm incubation was used to simulate leachate saturation zone (LSZ) and other landfill zones scenarios to explore the As methylation behavior. The As methylation rate of LSZ is 11.75%, which is slightly higher than that of other zone of landfill (10.87%). However, the difference was greatly increased by the addition of moderate content of As(III), with values of 29.25% in LSZ and 4.61% in other zones. The microbial community structure varied greatly between zones and a higher abundance of arsM was observed in the LSZ, which enhanced As methylation. Based on the annotated As functional genes from the KEGG database, the microbial As methylated pathway was summarized. Higher relative abundances of gst and arsC promoted the formation of more trivalent As substrates, stimulating the methylation behavior for As detoxification in the LSZ. According to microbial arsM contribution analysis, unclassified_p__Gemmatimonadetes, unclassified_p__Actinobacteria, unclassified_o_Hydrogenophilales, and Intrasporangium were the primary As methylation bacteria in the LSZ, while unclassified_f__Chitinophagaceae and unclassified_c_Gammaproteobacteria were the primary contributors in other landfill zones. These results highlight the specific As methylation process in the LSZ, and these insights could improve the control of As contamination in landfill sites.}, } @article {pmid36638095, year = {2023}, author = {Maki, KA and Wolff, B and Varuzza, L and Green, SJ and Barb, JJ}, title = {Multi-amplicon microbiome data analysis pipelines for mixed orientation sequences using QIIME2: Assessing reference database, variable region and pre-processing bias in classification of mock bacterial community samples.}, journal = {PloS one}, volume = {18}, number = {1}, pages = {e0280293}, pmid = {36638095}, issn = {1932-6203}, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Databases, Factual ; High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics ; Data Analysis ; }, abstract = {Microbiome research relies on next-generation sequencing and on downstream data analysis workflows. Several manufacturers have introduced multi-amplicon kits for microbiome characterization, improving speciation, but present unique challenges for analysis. The goal of this methodology study was to develop two analysis pipelines specific to mixed-orientation reads from multi-hypervariable (V) region amplicons. A secondary aim was to assess agreement with expected abundance, considering database and variable region. Mock community sequence data (n = 41) generated using the Ion16S™ Metagenomics Kit and Ion Torrent Sequencing Platform were analyzed using two workflows. Amplicons from V2, V3, V4, V6-7, V8 and V9 were deconvoluted using a specialized plugin based on CutPrimers. A separate workflow using Cutadapt is also presented. Three reference databases (Ribosomal Database Project, Greengenes and Silva) were used for taxonomic assignment. Bray-Curtis, Euclidean and Jensen-Shannon distance measures were used to evaluate overall annotation consistency, and specific taxon agreement was determined by calculating the ratio of observed to expected relative abundance. Reads that mapped to regions V2-V9 varied for both CutPrimers and Cutadapt-based methods. Within the CutPrimers-based pipeline, V3 amplicons had the best agreement with the expected distribution, tested using global distance measures, while V9 amplicons had the worst agreement. Accurate taxonomic annotation varied by genus-level taxon and V region analyzed. For the first time, we present a microbiome analysis pipeline that employs a specialized plugin to allow microbiome researchers to separate multi-amplicon data from the Ion16S Metagenomics Kit into V-specific reads. We also present an additional analysis workflow, modified for Ion Torrent mixed orientation reads. Overall, the global agreement of amplicons with the expected mock community abundances differed across V regions and reference databases. Benchmarking data should be referenced when planning a microbiome study to consider these biases related to sequencing and data analysis for multi-amplicon sequencing kits.}, } @article {pmid36638091, year = {2023}, author = {Kibegwa, FM and Bett, RC and Gachuiri, CK and Machuka, E and Stomeo, F and Mujibi, FD}, title = {Diversity and functional analysis of rumen and fecal microbial communities associated with dietary changes in crossbreed dairy cattle.}, journal = {PloS one}, volume = {18}, number = {1}, pages = {e0274371}, pmid = {36638091}, issn = {1932-6203}, mesh = {Animals ; Cattle ; *Rumen/microbiology ; *Microbiota/genetics ; Metagenome ; Proteobacteria/genetics ; Dietary Fiber/metabolism ; Diet/veterinary ; Animal Feed/analysis ; }, abstract = {The objective of this study was to investigate the effect of varying roughage and concentrate proportions, in diet of crossbreed dairy cattle, on the composition and associated functional genes of rumen and fecal microbiota. We also explored fecal samples as a proxy for rumen liquor samples. Six crossbred dairy cattle were reared on three diets with an increasing concentrate and reducing roughage amount in three consecutive 10-day periods. After each period, individual rumen liquor and fecal samples were collected and analyzed through shotgun metagenomic sequencing. Average relative abundance of identified Operational Taxonomic Units (OTU) and microbial functional roles from all animals were compared between diets and sample types (fecal and rumen liquor). Results indicated that dietary modifications significantly affected several rumen and fecal microbial OTUs. In the rumen, an increase in dietary concentrate resulted in an upsurge in the abundance of Proteobacteria, while reducing the proportions of Bacteroidetes and Firmicutes. Conversely, changes in microbial composition in fecal samples were not consistent with dietary modification patterns. Microbial functional pathway classification identified that carbohydrate metabolism and protein metabolism pathways dominated microbial roles. Assessment of dietary effects on the predicted functional roles of these microbiota revealed that a high amount of dietary concentrate resulted in an increase in central carbohydrate metabolism and a corresponding reduction in protein synthesis. Moreover, we identified several microbial stress-related responses linked to dietary changes. Bacteroides and Clostridium genera were the principal hosts of these microbial functions. Therefore, the roughage to concentrate proportion has more influence on the microbial composition and microbial functional genes in rumen samples than fecal samples. As such, we did not establish a significant relationship between the rumen and fecal metagenome profiles, and the rumen and fecal microbiota from one animal did not correlate more than those from different animals.}, } @article {pmid36637649, year = {2023}, author = {Wani, AK and Akhtar, N and Naqash, N and Rahayu, F and Djajadi, D and Chopra, C and Singh, R and Mulla, SI and Sher, F and Américo-Pinheiro, JHP}, title = {Discovering untapped microbial communities through metagenomics for microplastic remediation: recent advances, challenges, and way forward.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {34}, pages = {81450-81473}, pmid = {36637649}, issn = {1614-7499}, mesh = {Humans ; Microplastics ; Plastics/metabolism ; Metagenomics ; Ecosystem ; *Microbiota ; *Environmental Pollutants/analysis ; *Water Pollutants, Chemical/analysis ; }, abstract = {Microplastics (MPs) are ubiquitous pollutants persisting almost everywhere in the environment. With the increase in anthropogenic activities, MP accumulation is increasing enormously in aquatic, marine, and terrestrial ecosystems. Owing to the slow degradation of plastics, MPs show an increased biomagnification probability of persistent, bioaccumulative, and toxic substances thereby creating a threat to environmental biota. Thus, remediation of MP-pollutants requires efficient strategies to circumvent the mobilization of contaminants leaching into the water, soil, and ultimately to human beings. Over the years, several microorganisms have been characterized by the potential to degrade different plastic polymers through enzymatic actions. Metagenomics (MGs) is an effective way to discover novel microbial communities and access their functional genetics for the exploration and characterization of plastic-degrading microbial consortia and enzymes. MGs in combination with metatranscriptomics and metabolomics approaches are a powerful tool to identify and select remediation-efficient microbes in situ. Advancement in bioinformatics and sequencing tools allows rapid screening, mining, and prediction of genes that are capable of polymer degradation. This review comprehensively summarizes the growing threat of microplastics around the world and highlights the role of MGs and computational biology in building effective response strategies for MP remediation.}, } @article {pmid36636774, year = {2023}, author = {Ferrocino, I and Rantsiou, K and McClure, R and Kostic, T and de Souza, RSC and Lange, L and FitzGerald, J and Kriaa, A and Cotter, P and Maguin, E and Schelkle, B and Schloter, M and Berg, G and Sessitsch, A and Cocolin, L and , }, title = {The need for an integrated multi-OMICs approach in microbiome science in the food system.}, journal = {Comprehensive reviews in food science and food safety}, volume = {22}, number = {2}, pages = {1082-1103}, doi = {10.1111/1541-4337.13103}, pmid = {36636774}, issn = {1541-4337}, mesh = {Humans ; *Artificial Intelligence ; Multiomics ; *Microbiota ; Metabolomics/methods ; Metagenomics/methods ; }, abstract = {Microbiome science as an interdisciplinary research field has evolved rapidly over the past two decades, becoming a popular topic not only in the scientific community and among the general public, but also in the food industry due to the growing demand for microbiome-based technologies that provide added-value solutions. Microbiome research has expanded in the context of food systems, strongly driven by methodological advances in different -omics fields that leverage our understanding of microbial diversity and function. However, managing and integrating different complex -omics layers are still challenging. Within the Coordinated Support Action MicrobiomeSupport (https://www.microbiomesupport.eu/), a project supported by the European Commission, the workshop "Metagenomics, Metaproteomics and Metabolomics: the need for data integration in microbiome research" gathered 70 participants from different microbiome research fields relevant to food systems, to discuss challenges in microbiome research and to promote a switch from microbiome-based descriptive studies to functional studies, elucidating the biology and interactive roles of microbiomes in food systems. A combination of technologies is proposed. This will reduce the biases resulting from each individual technology and result in a more comprehensive view of the biological system as a whole. Although combinations of different datasets are still rare, advanced bioinformatics tools and artificial intelligence approaches can contribute to understanding, prediction, and management of the microbiome, thereby providing the basis for the improvement of food quality and safety.}, } @article {pmid36635724, year = {2023}, author = {Berihu, M and Somera, TS and Malik, A and Medina, S and Piombo, E and Tal, O and Cohen, M and Ginatt, A and Ofek-Lalzar, M and Doron-Faigenboim, A and Mazzola, M and Freilich, S}, title = {A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {8}, pmid = {36635724}, issn = {2049-2618}, mesh = {*Soil ; Bacteria/genetics ; *Microbiota/genetics ; Metagenome ; Metagenomics ; Rhizosphere ; Soil Microbiology ; Plant Roots/microbiology ; }, abstract = {BACKGROUND: The design of ecologically sustainable and plant-beneficial soil systems is a key goal in actively manipulating root-associated microbiomes. Community engineering efforts commonly seek to harness the potential of the indigenous microbiome through substrate-mediated recruitment of beneficial members. In most sustainable practices, microbial recruitment mechanisms rely on the application of complex organic mixtures where the resources/metabolites that act as direct stimulants of beneficial groups are not characterized. Outcomes of such indirect amendments are unpredictable regarding engineering the microbiome and achieving a plant-beneficial environment.

RESULTS: This study applied network analysis of metagenomics data to explore amendment-derived transformations in the soil microbiome, which lead to the suppression of pathogens affecting apple root systems. Shotgun metagenomic analysis was conducted with data from 'sick' vs 'healthy/recovered' rhizosphere soil microbiomes. The data was then converted into community-level metabolic networks. Simulations examined the functional contribution of treatment-associated taxonomic groups and linked them with specific amendment-induced metabolites. This analysis enabled the selection of specific metabolites that were predicted to amplify or diminish the abundance of targeted microbes functional in the healthy soil system. Many of these predictions were corroborated by experimental evidence from the literature. The potential of two of these metabolites (dopamine and vitamin B12) to either stimulate or suppress targeted microbial groups was evaluated in a follow-up set of soil microcosm experiments. The results corroborated the stimulant's potential (but not the suppressor) to act as a modulator of plant beneficial bacteria, paving the way for future development of knowledge-based (rather than trial and error) metabolic-defined amendments. Our pipeline for generating predictions for the selective targeting of microbial groups based on processing assembled and annotated metagenomics data is available at https://github.com/ot483/NetCom2 .

CONCLUSIONS: This research demonstrates how genomic-based algorithms can be used to formulate testable hypotheses for strategically engineering the rhizosphere microbiome by identifying specific compounds, which may act as selective modulators of microbial communities. Applying this framework to reduce unpredictable elements in amendment-based solutions promotes the development of ecologically-sound methods for re-establishing a functional microbiome in agro and other ecosystems. Video Abstract.}, } @article {pmid36635540, year = {2023}, author = {Albertsen, M}, title = {Long-read metagenomics paves the way toward a complete microbial tree of life.}, journal = {Nature methods}, volume = {20}, number = {1}, pages = {30-31}, pmid = {36635540}, issn = {1548-7105}, mesh = {*Metagenomics ; *Microbiota ; High-Throughput Nucleotide Sequencing ; Metagenome ; Sequence Analysis, DNA ; }, } @article {pmid36634616, year = {2023}, author = {Song, CH and Kim, N and Nam, RH and Choi, SI and Jang, JY and Choi, J and Lee, HN}, title = {Anti-PD-L1 Antibody and/or 17β-Estradiol Treatment Induces Changes in the Gut Microbiome in MC38 Colon Tumor Model.}, journal = {Cancer research and treatment}, volume = {55}, number = {3}, pages = {894-909}, pmid = {36634616}, issn = {2005-9256}, support = {2019R1A2C2085149//National Research Foundation of Korea/ ; }, mesh = {*Colonic Neoplasms/drug therapy ; Male ; Estradiol/pharmacology ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Female ; Bacteroidetes ; Mice ; Estrogens/pharmacology ; Animals ; Cell Line, Tumor ; }, abstract = {PURPOSE: 17β-Estradiol (E2) supplementation suppresses MC38 tumor growth by downregulating the expression of programmed death-ligand 1 (PD-L1). This study aims to figure out the gut microbiota that respond to anti-PD-L1 and/or estrogen treatment in MC38 colon cancer model.

MATERIALS AND METHODS: A syngeneic colon tumor model was developed by injection of MC38 cells into C57BL/6 background male and female mice. Three days before MC38 cells injection, E2 was supplemented to male mice daily for 1 week. Male and female mice with MC38 tumors (50-100 mm3) were injected with anti-PD-L1 antibody. Fresh feces were collected 26 days after injection of MC38 cells and 16S rRNA metagenomics sequencing of DNA extracted from feces was used to assess gut microbial composition.

RESULTS: At the taxonomic family level, Muribaculaceae was enriched only in the MC38 male control group. In male mice, linear discriminant analysis effect size analysis at the species level revealed that the four microorganisms were commonly regulated in single and combination treatment with anti-PD-L1 and/or E2; a decrease in PAC001068_g_uc and PAC001070_s (family Muribaculaceae) and increase in PAC001716_s and PAC001785_s (family Ruminococcaceae). Interestingly, in the anti-PD-L1 plus E2 group, a decrease in opportunistic pathogens (Enterobacteriaceae group) and an increase in commensal bacteria (Lactobacillus murinus group and Parabacteroides goldsteinii) were observed. Furthermore, the abundance of Parabacteroides goldsteinii was increased in both males and females in the anti-PD-L1 group.

CONCLUSION: Our results suggest that gut microbial changes induced by the pretreatment of estrogen before anti-PD-L1 might contribute to treatment of MC38 colon cancer.}, } @article {pmid36631912, year = {2023}, author = {Li, C and Li, X and Guo, R and Ni, W and Liu, K and Liu, Z and Dai, J and Xu, Y and Abduriyim, S and Wu, Z and Zeng, Y and Lei, B and Zhang, Y and Wang, Y and Zeng, W and Zhang, Q and Chen, C and Qiao, J and Liu, C and Hu, S}, title = {Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {7}, pmid = {36631912}, issn = {2049-2618}, mesh = {Horses/genetics ; Humans ; Animals ; Metagenome ; Genome, Bacterial ; *Gastrointestinal Microbiome/genetics ; Drug Resistance, Microbial ; *Athletic Performance ; Metagenomics ; }, abstract = {BACKGROUND: As a domesticated species vital to humans, horses are raised worldwide as a source of mechanical energy for sports, leisure, food production, and transportation. The gut microbiota plays an important role in the health, diseases, athletic performance, and behaviour of horses.

RESULTS: Here, using approximately 2.2 Tb of metagenomic sequencing data from gut samples from 242 horses, including 110 samples from the caecum and 132 samples from the rectum (faeces), we assembled 4142 microbial metagenome-assembled genomes (MAG), 4015 (96.93%) of which appear to correspond to new species. From long-read data, we successfully assembled 13 circular whole-chromosome bacterial genomes representing novel species. The MAG contained over 313,568 predicted carbohydrate-active enzymes (CAZy), over 59.77% of which had low similarity match in CAZy public databases. High abundance and diversity of antibiotic resistance genes (ARG) were identified in the MAG, likely showing the wide use of antibiotics in the management of horse. The abundances of at least 36 MAG (e.g. MAG belonging to Lachnospiraceae, Oscillospiraceae, and Ruminococcus) were higher in racehorses than in nonracehorses. These MAG enriched in racehorses contained every gene in a major pathway for producing acetate and butyrate by fibre fermentation, presenting potential for greater amount of short-chain fatty acids available to fuel athletic performance.

CONCLUSION: Overall, we assembled 4142 MAG from short- and long-read sequence data in the horse gut. Our dataset represents an exhaustive microbial genome catalogue for the horse gut microbiome and provides a valuable resource for discovery of performance-enhancing microbes and studies of horse gut microbiome. Video Abstract.}, } @article {pmid36631668, year = {2023}, author = {Fan, K and Chu, H and Eldridge, DJ and Gaitan, JJ and Liu, YR and Sokoya, B and Wang, JT and Hu, HW and He, JZ and Sun, W and Cui, H and Alfaro, FD and Abades, S and Bastida, F and Díaz-López, M and Bamigboye, AR and Berdugo, M and Blanco-Pastor, JL and Grebenc, T and Duran, J and Illán, JG and Makhalanyane, TP and Mukherjee, A and Nahberger, TU and Peñaloza-Bojacá, GF and Plaza, C and Verma, JP and Rey, A and Rodríguez, A and Siebe, C and Teixido, AL and Trivedi, P and Wang, L and Wang, J and Yang, T and Zhou, XQ and Zhou, X and Zaady, E and Tedersoo, L and Delgado-Baquerizo, M}, title = {Soil biodiversity supports the delivery of multiple ecosystem functions in urban greenspaces.}, journal = {Nature ecology & evolution}, volume = {7}, number = {1}, pages = {113-126}, pmid = {36631668}, issn = {2397-334X}, mesh = {Humans ; *Ecosystem ; *Soil ; Parks, Recreational ; Biodiversity ; Plants ; }, abstract = {While the contribution of biodiversity to supporting multiple ecosystem functions is well established in natural ecosystems, the relationship of the above- and below-ground diversity with ecosystem multifunctionality remains virtually unknown in urban greenspaces. Here we conducted a standardized survey of urban greenspaces from 56 municipalities across six continents, aiming to investigate the relationships of plant and soil biodiversity (diversity of bacteria, fungi, protists and invertebrates, and metagenomics-based functional diversity) with 18 surrogates of ecosystem functions from nine ecosystem services. We found that soil biodiversity across biomes was significantly and positively correlated with multiple dimensions of ecosystem functions, and contributed to key ecosystem services such as microbially driven carbon pools, organic matter decomposition, plant productivity, nutrient cycling, water regulation, plant-soil mutualism, plant pathogen control and antibiotic resistance regulation. Plant diversity only indirectly influenced multifunctionality in urban greenspaces via changes in soil conditions that were associated with soil biodiversity. These findings were maintained after controlling for climate, spatial context, soil properties, vegetation and management practices. This study provides solid evidence that conserving soil biodiversity in urban greenspaces is key to supporting multiple dimensions of ecosystem functioning, which is critical for the sustainability of urban ecosystems and human wellbeing.}, } @article {pmid36631002, year = {2023}, author = {Hsu, CL and Lang, S and Demir, M and Fouts, DE and Stärkel, P and Schnabl, B}, title = {Any alcohol use in NAFLD patients is associated with significant changes to the intestinal virome.}, journal = {Hepatology (Baltimore, Md.)}, volume = {77}, number = {6}, pages = {2073-2083}, pmid = {36631002}, issn = {1527-3350}, support = {I01 BX004594/BX/BLRD VA/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; R37 AA020703/AA/NIAAA NIH HHS/United States ; T32 DK007202/DK/NIDDK NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 AA026939/AA/NIAAA NIH HHS/United States ; }, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease ; Virome ; Alcohol Drinking/adverse effects ; *Alcoholism ; Ethanol ; *Liver Diseases, Alcoholic ; }, abstract = {BACKGROUND AND AIMS: The prevalence of alcohol use disorder (AUD) and metabolic dysfunction-associated fatty liver disease (MAFLD) are increasing worldwide, leading to the increasing likelihood of both etiologies contributing to a patient's liver disease. However, the effects of modest alcohol use in NAFLD are controversial and more studies are needed. We compared the intestinal viromes of patients with AUD and NAFLD in order to evaluate the effect of alcohol consumption on the intestinal viromes of NAFLD patients by extracting virus-like particles and performing metagenomic sequencing.

APPROACH AND RESULTS: Viral nucleic acids were extracted from fecal samples and subjected to metagenomic sequencing. We demonstrate significant differences in the intestinal viromes of NAFLD and AUD patients, and that alcohol use in NAFLD patients reclassified to MAFLD accounted for significant differences in the intestinal viromes. The relative abundance of several Lactococcus phages was more similar between AUD patients and alcohol-consuming MAFLD patients than non-alcohol-consuming MAFLD patients and control subjects, and multivariate modeling using the most discriminating Lactococcus phages could better predict alcohol use in the MAFLD population than the alcohol-associated liver disease/NAFLD Index. Significant differences in the viral composition and diversity were also seen between MAFLD patients with low and moderate alcohol consumption compared with no alcohol consumption.

CONCLUSIONS: The intestinal virome of MAFLD patients who consume low to moderate amounts of alcohol are significantly different from those who do not, and many features of the intestinal virome of alcohol-consuming MAFLD patients resemble that of AUD patients.}, } @article {pmid36629118, year = {2023}, author = {Chou, PH and Hu, MY and Guh, YJ and Wu, GC and Yang, SH and Tandon, K and Shao, YT and Lin, LY and Chen, C and Tseng, KY and Wang, MC and Zhang, CM and Han, BC and Lin, CC and Tang, SL and Jeng, MS and Chang, CF and Tseng, YC}, title = {Cellular mechanisms underlying extraordinary sulfide tolerance in a crustacean holobiont from hydrothermal vents.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1990}, pages = {20221973}, pmid = {36629118}, issn = {1471-2954}, mesh = {Animals ; *Hydrothermal Vents ; Thiosulfates ; Sulfides/toxicity ; *Brachyura/physiology ; Bacteria ; }, abstract = {The shallow-water hydrothermal vent system of Kueishan Island has been described as one of the world's most acidic and sulfide-rich marine habitats. The only recorded metazoan species living in the direct vicinity of the vents is Xenograpsus testudinatus, a brachyuran crab endemic to marine sulfide-rich vent systems. Despite the toxicity of hydrogen sulfide, X. testudinatus occupies an ecological niche in a sulfide-rich habitat, with the underlying detoxification mechanism remaining unknown. Using laboratory and field-based experiments, we characterized the gills of X. testudinatus that are the major site of sulfide detoxification. Here sulfide is oxidized to thiosulfate or bound to hypotaurine to generate the less toxic thiotaurine. Biochemical and molecular analyses demonstrated that the accumulation of thiosulfate and hypotaurine is mediated by the sodium-independent sulfate anion transporter (SLC26A11) and taurine transporter (Taut), which are expressed in gill epithelia. Histological and metagenomic analyses of gill tissues demonstrated a distinct bacterial signature dominated by Epsilonproteobacteria. Our results suggest that thiotaurine synthesized in gills is used by sulfide-oxidizing endo-symbiotic bacteria, creating an effective sulfide-buffering system. This work identified physiological mechanisms involving host-microbe interactions that support life of a metazoan in one of the most extreme environments on our planet.}, } @article {pmid36628835, year = {2023}, author = {Liang, Y and Zheng, K and McMinn, A and Wang, M}, title = {Expanding diversity and ecological roles of RNA viruses.}, journal = {Trends in microbiology}, volume = {31}, number = {3}, pages = {229-232}, doi = {10.1016/j.tim.2022.12.004}, pmid = {36628835}, issn = {1878-4380}, mesh = {*Ecosystem ; *RNA Viruses/genetics ; Genome, Viral ; Phylogeny ; }, abstract = {While the diversity of global environmental RNA viruses has remained largely unexplored, recent advances have reported on the discovery of over 10[6] RNA viral contigs from both terrestrial and marine ecosystems that will help us to better understand the diversity, evolution, ecological roles, and transmission of RNA viruses.}, } @article {pmid36627827, year = {2023}, author = {Li, ZM and Kong, CY and Mao, YQ and Huang, JT and Chen, HL and Han, B and Wang, LS}, title = {Ampicillin exacerbates acetaminophen-induced acute liver injury by inducing intestinal microbiota imbalance and butyrate reduction.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {43}, number = {4}, pages = {865-877}, doi = {10.1111/liv.15512}, pmid = {36627827}, issn = {1478-3231}, mesh = {Animals ; Mice ; Acetaminophen/toxicity ; *Gastrointestinal Microbiome ; Butyrates/pharmacology ; Liver ; Ampicillin/adverse effects ; *Chemical and Drug Induced Liver Injury/etiology ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND AND AIMS: Antibiotics (ATBx) and acetaminophen (APAP) are widely used worldwide. APAP is the most common cause of acute liver injury (ALI) and might be used in combination with ATBx in clinics. However, the impact of ATBx on APAP-induced ALI has rarely been studied.

METHODS: First, we compared the effects of seven ATBx on APAP-induced ALI. Then, we analysed faecal, serum and liver samples to investigate the impact of the gut microbiota on this process. Finally, we assessed the role of short-chain fatty acids in this process.

RESULTS: In this work, we found that the ALI was significantly aggravated in the mice treated with ampicillin (Amp) instead of other ATBx. Amp exposure reduced the diversity and altered the composition of gut microbiota. The altered gut microbiota aggravated APAP-induced ALF, which was proven by faecal microbiota transplantation from ATBx-treated mice. Metagenomic analysis showed a significantly decreased Lactobacillus abundance in Amp-treated mice. Gavage with Lactobacillus, especially Lactobacillus rhamnosus, significantly reversed the severer ALF induced by APAP and Amp. Moreover, Lactobacillus supplementation increased butyrate-producing clostridia and lowered butyrate levels in Amp-treated mice. In accordance, butyrate supplementation could also alleviate Amp-aggravated ALI. In addition, inhibition of nuclear factor erythroid 2-related factor 2 counteracted the protective effect of butyrate on aggravated ALI induced by Amp and APAP.

CONCLUSION: Together, this study revealed a potential health impact of Amp that may exacerbate liver damage when co-exposed to excess APAP.}, } @article {pmid36627170, year = {2023}, author = {Nii, T and Maeda, Y and Motooka, D and Naito, M and Matsumoto, Y and Ogawa, T and Oguro-Igashira, E and Kishikawa, T and Yamashita, M and Koizumi, S and Kurakawa, T and Okumura, R and Kayama, H and Murakami, M and Sakaguchi, T and Das, B and Nakamura, S and Okada, Y and Kumanogoh, A and Takeda, K}, title = {Genomic repertoires linked with pathogenic potency of arthritogenic Prevotella copri isolated from the gut of patients with rheumatoid arthritis.}, journal = {Annals of the rheumatic diseases}, volume = {82}, number = {5}, pages = {621-629}, pmid = {36627170}, issn = {1468-2060}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Arthritis, Rheumatoid/genetics ; Prevotella/genetics ; Genomics ; Disease Models, Animal ; }, abstract = {OBJECTIVES: Prevotella copri is considered to be a contributing factor in rheumatoid arthritis (RA). However, in some non-Westernised countries, healthy individuals also harbour an abundance of P. copri in the intestine. This study investigated the pathogenicity of RA patient-derived P. copri (P. copri RA) compared with healthy control-derived P. copri (P. copri HC).

METHODS: We obtained 13 P. copri strains from the faeces of patients with RA and healthy controls. Following whole genome sequencing, the sequences of P. copri RA and P. copri HC were compared. To analyse the arthritis-inducing ability of P. copri, we examined two arthritis models (1) a collagen-induced arthritis model harbouring P. copri under specific-pathogen-free conditions and (2) an SKG mouse arthritis model under P. copri-monocolonised conditions. Finally, to evaluate the ability of P. copri to activate innate immune cells, we performed in vitro stimulation of bone marrow-derived dendritic cells (BMDCs) by P. copri RA and P. copri HC.

RESULTS: Comparative genomic analysis revealed no apparent differences in the core gene contents between P. copri RA and P. copri HC, but pangenome analysis revealed the high genome plasticity of P. copri. We identified a P. copri RA-specific genomic region as a conjugative transposon. In both arthritis models, P. copri RA-induced more severe arthritis than P. copri HC. In vitro BMDC stimulation experiments revealed the upregulation of IL-17 and Th17-related cytokines (IL-6, IL-23) by P. copri RA.

CONCLUSION: Our findings reveal the genetic diversity of P. copri, and the genomic signatures associated with strong arthritis-inducing ability of P. copri RA. Our study contributes towards elucidation of the complex pathogenesis of RA.}, } @article {pmid36625891, year = {2023}, author = {Snyder, C and Centlivre, JP and Bhute, S and Shipman, G and Friel, AD and Viver, T and Palmer, M and Konstantinidis, KT and Sun, HJ and Rossello-Mora, R and Nadeau, J and Hedlund, BP}, title = {Microbial Motility at the Bottom of North America: Digital Holographic Microscopy and Genomic Motility Signatures in Badwater Spring, Death Valley National Park.}, journal = {Astrobiology}, volume = {23}, number = {3}, pages = {295-307}, doi = {10.1089/ast.2022.0090}, pmid = {36625891}, issn = {1557-8070}, mesh = {*Microscopy ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Parks, Recreational ; Metagenome ; Metagenomics/methods ; North America ; }, abstract = {Motility is widely distributed across the tree of life and can be recognized by microscopy regardless of phylogenetic affiliation, biochemical composition, or mechanism. Microscopy has thus been proposed as a potential tool for detection of biosignatures for extraterrestrial life; however, traditional light microscopy is poorly suited for this purpose, as it requires sample preparation, involves fragile moving parts, and has a limited volume of view. In this study, we deployed a field-portable digital holographic microscope (DHM) to explore microbial motility in Badwater Spring, a saline spring in Death Valley National Park, and complemented DHM imaging with 16S rRNA gene amplicon sequencing and shotgun metagenomics. The DHM identified diverse morphologies and distinguished run-reverse-flick and run-reverse types of flagellar motility. PICRUSt2- and literature-based predictions based on 16S rRNA gene amplicons were used to predict motility genotypes/phenotypes for 36.0-60.1% of identified taxa, with the predicted motile taxa being dominated by members of Burkholderiaceae and Spirochaetota. A shotgun metagenome confirmed the abundance of genes encoding flagellar motility, and a Ralstonia metagenome-assembled genome encoded a full flagellar gene cluster. This study demonstrates the potential of DHM for planetary life detection, presents the first microbial census of Badwater Spring and brine pool, and confirms the abundance of mobile microbial taxa in an extreme environment.}, } @article {pmid36625596, year = {2023}, author = {Li, Y and Qian, F and Cheng, X and Wang, D and Wang, Y and Pan, Y and Chen, L and Wang, W and Tian, Y}, title = {Dysbiosis of Oral Microbiota and Metabolite Profiles Associated with Type 2 Diabetes Mellitus.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0379622}, pmid = {36625596}, issn = {2165-0497}, mesh = {Humans ; *Diabetes Mellitus, Type 2 ; Dysbiosis ; Cadaverine ; *Dental Caries ; *Microbiota ; }, abstract = {Several previous studies have shown that oral microbial disorders may be closely related to the occurrence and development of type 2 diabetes mellitus (T2DM). However, whether the function of oral microorganisms and their metabolites have changed in patients with T2DM who have not suffered from any oral diseases has not been reported. We performed metagenomic analyses and nontargeted metabolic analysis of saliva and supragingival plaque samples from patients with T2DM who have not suffered any oral diseases and normal controls. We found that periodontal pathogens such as Porphyromonas gingivalis and Prevotella melaninogenica were significantly enriched, while the abundances of dental caries pathogens such as Streptococcus mutans and Streptococcus sobrinus were not significantly different in patients with T2DM compared to those in normal controls. Metabolomic analyses showed that the salivary levels of cadaverine and L-(+)-leucine of patients with T2DM were significantly higher than those of normal controls, while the supragingival plaque levels of N-acetyldopamine and 3,4-dimethylbenzoic acid in patients with T2DM were significantly higher than those in the normal controls. Additionally, we identified the types of oral microorganisms related to the changes in the levels of circulating metabolites, and the oral microorganisms were involved in the dysregulation of harmful metabolites such as cadaverine and n, n-dimethylarginine. Overall, our study first described the changes in the composition of oral microorganisms and their metabolites in patients with T2DM who have not suffered any oral diseases, which will provide a direct basis for finding oral biomarkers for early warning of oral diseases in T2DM. IMPORTANCE The incidence of oral diseases in type 2 diabetic patients might increase, and the severity might also be more serious. At present, the relationship between oral microorganisms and type 2 diabetes mellitus (T2DM) has become a hot topic in systemic health research. However, whether the function of oral microorganisms and their metabolites have changed in patients with T2DM who have not suffered from any oral diseases has not been reported. We found that even if the oral condition of T2DM is healthy, their oral microbes and metabolites have changed, thus increasing the risk of periodontal disease. Our study first described the changes in the composition of oral microorganisms and their metabolites in T2DM who have not suffered any oral diseases and revealed the correlation between oral microorganisms and their metabolites, which will provide a direct basis for finding oral biomarkers for early warning of oral diseases in patients with T2DM.}, } @article {pmid36625585, year = {2023}, author = {Wicaksono, WA and Egamberdieva, D and Cernava, T and Berg, G}, title = {Viral Community Structure and Potential Functions in the Dried-Out Aral Sea Basin Change along a Desiccation Gradient.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0099422}, pmid = {36625585}, issn = {2379-5077}, mesh = {Humans ; Desiccation ; Bacteria/genetics ; *Viruses ; Metagenome ; *Microbiota/genetics ; }, abstract = {The dried-out Aral Sea basin represents an extreme environment due to a man-made ecological disaster. Studies conducted in this unique environment revealed high levels of pollution and a specifically adapted microbiota; however, viral populations remained entirely unexplored. By employing an in-depth analysis based on the sequencing of metagenomic DNA recovered from rhizosphere samples of Suaeda acuminata (C. A. Mey.) Moq. along a desiccation gradient of 5, 10, and 40 years, we detected a diverse viral community comprising 674 viral populations (viral operational taxonomic units [vOTUs]) dominated by Caudovirales. Targeted analyses highlighted that viral populations in this habitat are subjected to certain dynamics that are driven mainly by the gradient of desiccation, the corresponding salinity, and the rhizosphere bacterial populations. In silico predictions linked the viruses to dominant prokaryotic taxa in the Aral Sea basin, such as Gammaproteobacteria, Actinomycetia, and Bacilli. The lysogenic lifestyle was predicted to be predominant in areas that dried out 5 years ago, representing the early revegetation phase. Metabolic prediction of viral auxiliary metabolic genes (AMGs) suggests that viruses may play a role in the biogeochemical cycles, stress resilience, and competitiveness of their hosts due to the presence of genes that are involved in biofilm formation. Overall, our study provides important insights into viral ecology in an extreme environment and expands our knowledge related to virus occurrence in terrestrial systems. IMPORTANCE Environmental viruses have added a wealth of knowledge to ecological studies with the emergence of metagenomic technology and approaches. They are also becoming recognized as important genetic repositories that underpin the functioning of terrestrial ecosystems but have remain moslty unexplored. Using shotgun metagenome sequencing and bioinformatic tools, we found that the viral community structure was affected during natural revegetation in the dried-up Aral Sea area, a model habitat for investigating natural ecological restoration but still understudied. In this study, we highlight the importance of viruses, elements that are overlooked, for their potential contribution to terrestrial ecosystems, i.e., nutrient cycles, stress resilience, and host competitiveness, during natural revegetation.}, } @article {pmid36625575, year = {2023}, author = {Zhang, XL and Zhou, YR and Xu, SS and Xu, S and Xiong, YJ and Xu, K and Xu, CJ and Che, JJ and Huang, L and Liu, ZG and Wang, BY and Mu, YL and Xiao, SB and Li, K}, title = {Characterization of Gut Microbiota Compositions along the Intestinal Tract in CD163/pAPN Double Knockout Piglets and Their Potential Roles in Iron Absorption.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0190622}, pmid = {36625575}, issn = {2165-0497}, mesh = {Animals ; Swine ; *Gastrointestinal Microbiome/physiology ; RNA, Ribosomal, 16S/genetics ; Antigens, CD ; Colon/microbiology ; }, abstract = {The gut microbiota is known to play a role in regulating host metabolism, yet the mechanisms underlying this regulation are not well elucidated. Our study aimed to characterize the differences in gut microbiota compositions and their roles in iron absorption between wild-type (WT) and CD163/pAPN double-gene-knockout (DKO) weaned piglets. A total of 58 samples along the entire digestive tract were analyzed for microbial community using 16S rRNA gene sequencing. The colonic microbiota and their metabolites were determined by metagenomic sequencing and untargeted liquid chromatography-mass spectrometry (LC-MS), respectively. Our results showed that no alterations in microbial community structure and composition were observed between DKO and WT weaned piglets, with the exception of colonic microbiota. Interestingly, the DKO piglets had selectively increased the relative abundance of the Leeia genus belonging to the Neisseriaceae family and decreased the Ruminococcaceae_UCG_014 genus abundance. Functional capacity analysis showed that organic acid metabolism was enriched in the colon in DKO piglets. In addition, the DKO piglets showed increased iron levels in important tissues compared with WT piglets without any pathological changes. Pearson's correlation coefficient indicated that the specific bacteria such as Leeia and Ruminococcaceae_UCG_014 genus played a key role in host iron absorption. Moreover, the iron levels had significantly (P < 0.05) positive correlation with microbial metabolites, particularly carboxylic acids and their derivatives, which might increase iron absorption by preventing iron precipitation. Overall, this study reveals an interaction between colonic microbiota and host metabolism and has potential significance for alleviating piglet iron deficiency. IMPORTANCE Iron deficiency is a major risk factor for iron deficiency anemia, which is among the most common nutritional disorders in piglets. However, it remains unclear how the gut microbiota interacts with host iron absorption. The current report provides the first insight into iron absorption-microbiome connection in CD163/pAPN double knockout piglets. The present results showed that carboxylic acids and their derivatives contributed to the absorption of nonheme iron by preventing ferric iron precipitation.}, } @article {pmid36624530, year = {2023}, author = {Jacobs, JP and Lagishetty, V and Hauer, MC and Labus, JS and Dong, TS and Toma, R and Vuyisich, M and Naliboff, BD and Lackner, JM and Gupta, A and Tillisch, K and Mayer, EA}, title = {Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {5}, pmid = {36624530}, issn = {2049-2618}, support = {U01 DK077738/DK/NIDDK NIH HHS/United States ; P30 DK041301/DK/NIDDK NIH HHS/United States ; U54 DK123755/DK/NIDDK NIH HHS/United States ; R01 DK096606/DK/NIDDK NIH HHS/United States ; IK2 CX001717/CX/CSRD VA/United States ; R03 DK121025/DK/NIDDK NIH HHS/United States ; R01 DK048351/DK/NIDDK NIH HHS/United States ; K23 DK106528/DK/NIDDK NIH HHS/United States ; }, mesh = {Craniosynostoses ; RNA, Ribosomal, 16S/genetics ; Multiomics ; Humans ; Intellectual Disability ; *Gastrointestinal Microbiome/genetics ; Habits ; Feces ; *Irritable Bowel Syndrome ; }, abstract = {BACKGROUND: Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that is thought to involve alterations in the gut microbiome, but robust microbial signatures have been challenging to identify. As prior studies have primarily focused on composition, we hypothesized that multi-omics assessment of microbial function incorporating both metatranscriptomics and metabolomics would further delineate microbial profiles of IBS and its subtypes.

METHODS: Fecal samples were collected from a racially/ethnically diverse cohort of 495 subjects, including 318 IBS patients and 177 healthy controls, for analysis by 16S rRNA gene sequencing (n = 486), metatranscriptomics (n = 327), and untargeted metabolomics (n = 368). Differentially abundant microbes, predicted genes, transcripts, and metabolites in IBS were identified by multivariate models incorporating age, sex, race/ethnicity, BMI, diet, and HAD-Anxiety. Inter-omic functional relationships were assessed by transcript/gene ratios and microbial metabolic modeling. Differential features were used to construct random forests classifiers.

RESULTS: IBS was associated with global alterations in microbiome composition by 16S rRNA sequencing and metatranscriptomics, and in microbiome function by predicted metagenomics, metatranscriptomics, and metabolomics. After adjusting for age, sex, race/ethnicity, BMI, diet, and anxiety, IBS was associated with differential abundance of bacterial taxa such as Bacteroides dorei; metabolites including increased tyramine and decreased gentisate and hydrocinnamate; and transcripts related to fructooligosaccharide and polyol utilization. IBS further showed transcriptional upregulation of enzymes involved in fructose and glucan metabolism as well as the succinate pathway of carbohydrate fermentation. A multi-omics classifier for IBS had significantly higher accuracy (AUC 0.82) than classifiers using individual datasets. Diarrhea-predominant IBS (IBS-D) demonstrated shifts in the metatranscriptome and metabolome including increased bile acids, polyamines, succinate pathway intermediates (malate, fumarate), and transcripts involved in fructose, mannose, and polyol metabolism compared to constipation-predominant IBS (IBS-C). A classifier incorporating metabolites and gene-normalized transcripts differentiated IBS-D from IBS-C with high accuracy (AUC 0.86).

CONCLUSIONS: IBS is characterized by a multi-omics microbial signature indicating increased capacity to utilize fermentable carbohydrates-consistent with the clinical benefit of diets restricting this energy source-that also includes multiple previously unrecognized metabolites and metabolic pathways. These findings support the need for integrative assessment of microbial function to investigate the microbiome in IBS and identify novel microbiome-related therapeutic targets. Video Abstract.}, } @article {pmid36624507, year = {2023}, author = {Bay, V and Gillespie, A and Ganda, E and Evans, NJ and Carter, SD and Lenzi, L and Lucaci, A and Haldenby, S and Barden, M and Griffiths, BE and Sánchez-Molano, E and Bicalho, R and Banos, G and Darby, A and Oikonomou, G}, title = {The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {4}, pmid = {36624507}, issn = {2049-2618}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Female ; Cattle ; Animals ; *Digital Dermatitis/microbiology ; RNA, Ribosomal, 16S/genetics ; Genome-Wide Association Study ; *Cattle Diseases/microbiology ; *Communicable Diseases ; *Microbiota/genetics ; Genotype ; }, abstract = {BACKGROUND: Bovine Digital Dermatitis (BDD) is a prevalent infectious disease, causing painful foot skin lesions and lameness in cattle. We describe herein the bovine foot skin microbiota and its associations with BDD using 16S rRNA gene amplicon and shotgun metagenomic sequencing on samples from 259 dairy cows from three UK dairy farms.

RESULTS: We show evidence of dysbiosis, and differences in taxonomy and functional profiles in the bovine foot skin microbiome of clinically healthy animals that subsequently develop BDD lesions, compared to those that do not. Our results suggest that taxonomical and functional differences together with alterations in ecological interactions between bacteria in the normal foot skin microbiome may predispose an animal to develop BDD lesions. Using genome-wide association and regional heritability mapping approaches, we provide first evidence for interactions between host genotype and certain members of the foot skin microbiota. We show the existence of significant genetic variation in the relative abundance of Treponema spp. and Peptoclostridium spp. and identify regions in the bovine genome that explain a significant proportion of this variation.

CONCLUSIONS: Collectively this work shows early changes in taxonomic and functional profiles of the bovine foot-skin microbiota in clinically healthy animals which are associated with subsequent development of BDD and could be relevant to prevention of disease. The description of host genetic control of members of the foot skin microbiota, combined with the association of the latter with BDD development offer new insights into a complex relationship that can be exploited in selective breeding programmes. Video Abstract.}, } @article {pmid36624472, year = {2023}, author = {Wang, H and Ainiwaer, A and Song, Y and Qin, L and Peng, A and Bao, H and Qin, H}, title = {Perturbed gut microbiome and fecal and serum metabolomes are associated with chronic kidney disease severity.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {3}, pmid = {36624472}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome ; Hydroquinones ; Creatinine ; Reactive Oxygen Species ; Metabolome ; Feces/microbiology ; Metabolomics ; *Renal Insufficiency, Chronic/metabolism/microbiology ; }, abstract = {BACKGROUND: Chronic kidney disease (CKD) is a severe public health problem associated with a disordered gut microbiome. However, the functional alterations of microbiota and their cross talk with metabolism pathways based on disease severity remain unclear.

RESULTS: We performed metagenomics and untargeted metabolomics in a cohort of 68 patients with CKD of differing severities and 20 healthy controls to characterize the complex interplay between the gut microbiome and fecal and serum metabolites during CKD progression. We identified 26 microbial species that significantly changed in patients with CKD; 18 species changed as the disease progressed, and eight species changed only in a specific CKD group. These distinct changes in gut microbiota were accompanied by functional alterations in arginine and proline, arachidonic acid, and glutathione metabolism and ubiquinone and other terpenoid-quinone biosynthesis pathways during CKD progression. Further metabolomic analyses revealed that the distributions of toxic and pro-oxidant metabolites from these four essential metabolic pathways varied in the feces and serum as CKD progressed. Furthermore, we observed a complex co-occurrence between CKD severity-related bacteria and the characterized metabolites from the four essential metabolic pathways. Notably, Ruminococcus bromii, fecal hydroquinone, and serum creatinine were identified as the main contributors to the integrated network, indicating their key roles in CKD progression. Moreover, a noninvasive model including R. bromii and fecal hydroquinone, L-cystine, and 12-keto-tetrahydro-LTB4 levels classified the CKD severity (area under the curve [AUC]: > 0.9) and had better performance than the serum creatinine level for mild CKD (AUC: 0.972 vs. 0.896).

CONCLUSIONS: Perturbed CKD severity-related gut microbiota may contribute to unbalanced toxic and pro-oxidant metabolism in the gut and host, accelerating CKD progression, which may be an early diagnostic and therapeutic target for CKD. Video Abstract.}, } @article {pmid36623385, year = {2023}, author = {Wang, Q and Chen, J and Qi, W and Wang, D and Lin, H and Wu, X and Wang, D and Bai, Y and Qu, J}, title = {Dam construction alters planktonic microbial predator‒prey communities in the urban reaches of the Yangtze River.}, journal = {Water research}, volume = {230}, number = {}, pages = {119575}, doi = {10.1016/j.watres.2023.119575}, pmid = {36623385}, issn = {1879-2448}, mesh = {*Plankton ; Ecosystem ; Rivers/microbiology ; Food Chain ; Bacteroidetes ; *Microbiota ; China ; }, abstract = {While dam construction supports social and economic development, changes in hydraulic conditions can also affect natural aquatic ecosystems, especially microbial ecosystems. The compositional and functional traits of multi-trophic microbiota can be altered by dam construction, which may result in changes in aquatic predator-prey interactions. To understand this process, we performed a large-scale sampling campaign in the urban reaches of the dam-impacted Yangtze River (1 995 km) and obtained 211 metagenomic datasets and water quality data. We first compared the compositional traits of planktonic microbial communities upstream, downstream, and in a dam reservoir. Results showed that Bacteroidetes (R-strategy) bacteria were more likely to survive upstream, whilst the reservoir and downstream regions were more conducive to the survival of K-strategy bacteria such as Actinobacteria. Eukaryotic predators tended to be enriched upstream, whilst phototrophs tended to be enriched in the reservoir and downstream regions. Based on bipartite networks, we inferred that the potential microbial predator-prey interactions gradually and significantly decreased from upstream to the downstream and dam regions, affecting 56% of keystone microbial species. Remarkably, functional analysis showed that the abundance of the photosynthetic gene psbO was higher in the reservoir and downstream regions, whilst the abundance of the KEGG carbohydrate metabolic pathway was higher upstream. These results indicate that dam construction in the Yangtze River induced planktonic microbial ecosystem transformation from detritus-based food webs to autotroph-based food webs.}, } @article {pmid36622853, year = {2023}, author = {Hiltemann, S and Rasche, H and Gladman, S and Hotz, HR and Larivière, D and Blankenberg, D and Jagtap, PD and Wollmann, T and Bretaudeau, A and Goué, N and Griffin, TJ and Royaux, C and Le Bras, Y and Mehta, S and Syme, A and Coppens, F and Droesbeke, B and Soranzo, N and Bacon, W and Psomopoulos, F and Gallardo-Alba, C and Davis, J and Föll, MC and Fahrner, M and Doyle, MA and Serrano-Solano, B and Fouilloux, AC and van Heusden, P and Maier, W and Clements, D and Heyl, F and , and Grüning, B and Batut, B}, title = {Galaxy Training: A powerful framework for teaching!.}, journal = {PLoS computational biology}, volume = {19}, number = {1}, pages = {e1010752}, pmid = {36622853}, issn = {1553-7358}, support = {U24 HG010263/HG/NHGRI NIH HHS/United States ; R01 AI134384/AI/NIAID NIH HHS/United States ; U24 HG006620/HG/NHGRI NIH HHS/United States ; MR/S035931/1/MRC_/Medical Research Council/United Kingdom ; U24 CA231877/CA/NCI NIH HHS/United States ; U24 CA199347/CA/NCI NIH HHS/United States ; BB/CCG1720/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *Software ; *Computational Biology/methods ; Data Analysis ; Research Personnel ; }, abstract = {There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analysis, and stewardship are still rarely taught in life science educational programs, resulting in a skills gap in many of the researchers tasked with analysing these big datasets. In order to address this skills gap and empower researchers to perform their own data analyses, the Galaxy Training Network (GTN) has previously developed the Galaxy Training Platform (https://training.galaxyproject.org), an open access, community-driven framework for the collection of FAIR (Findable, Accessible, Interoperable, Reusable) training materials for data analysis utilizing the user-friendly Galaxy framework as its primary data analysis platform. Since its inception, this training platform has thrived, with the number of tutorials and contributors growing rapidly, and the range of topics extending beyond life sciences to include topics such as climatology, cheminformatics, and machine learning. While initially aimed at supporting researchers directly, the GTN framework has proven to be an invaluable resource for educators as well. We have focused our efforts in recent years on adding increased support for this growing community of instructors. New features have been added to facilitate the use of the materials in a classroom setting, simplifying the contribution flow for new materials, and have added a set of train-the-trainer lessons. Here, we present the latest developments in the GTN project, aimed at facilitating the use of the Galaxy Training materials by educators, and its usage in different learning environments.}, } @article {pmid36622155, year = {2023}, author = {Saak, CC and Pierce, EC and Dinh, CB and Portik, D and Hall, R and Ashby, M and Dutton, RJ}, title = {Longitudinal, Multi-Platform Metagenomics Yields a High-Quality Genomic Catalog and Guides an In Vitro Model for Cheese Communities.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0070122}, pmid = {36622155}, issn = {2379-5077}, support = {DP2 AT010401/AT/NCCIH NIH HHS/United States ; }, mesh = {Humans ; *Cheese/microbiology ; Metagenomics ; Bacteria ; Metagenome/genetics ; *Microbiota/genetics ; }, abstract = {Microbiomes are intricately intertwined with human health, geochemical cycles, and food production. While many microbiomes of interest are highly complex and experimentally intractable, cheese rind microbiomes have proven to be powerful model systems for the study of microbial interactions. To provide a more comprehensive view of the genomic potential and temporal dynamics of cheese rind communities, we combined longitudinal, multi-platform metagenomics of three ripening washed-rind cheeses with whole-genome sequencing of community isolates. Sequencing-based approaches revealed a highly reproducible microbial succession in each cheese and the coexistence of closely related Psychrobacter species and enabled the prediction of plasmid and phage diversity and their host associations. In combination with culture-based approaches, we established a genomic catalog and a paired 16-member in vitro washed-rind cheese system. The combination of multi-platform metagenomic time-series data and an in vitro model provides a rich resource for further investigation of cheese rind microbiomes both computationally and experimentally. IMPORTANCE Metagenome sequencing can provide great insights into microbiome composition and function and help researchers develop testable hypotheses. Model microbiomes, such as those composed of cheese rind bacteria and fungi, allow the testing of these hypotheses in a controlled manner. Here, we first generated an extensive longitudinal metagenomic data set. This data set reveals successional dynamics, yields a phyla-spanning bacterial genomic catalog, associates mobile genetic elements with their hosts, and provides insights into functional enrichment of Psychrobacter in the cheese environment. Next, we show that members of the washed-rind cheese microbiome lend themselves to in vitro community reconstruction. This paired metagenomic data and in vitro system can thus be used as a platform for generating and testing hypotheses related to the dynamics within, and the functions associated with, cheese rind microbiomes.}, } @article {pmid36621696, year = {2023}, author = {Wen, C and Pan, Y and Gao, M and Wang, J and Huang, K and Tu, P}, title = {Altered gut microbiome composition in nontreated plaque psoriasis patients.}, journal = {Microbial pathogenesis}, volume = {175}, number = {}, pages = {105970}, doi = {10.1016/j.micpath.2023.105970}, pmid = {36621696}, issn = {1096-1208}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Psoriasis ; *Microbiota/genetics ; Bacteria/genetics ; Bacteroidetes ; Feces/microbiology ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recent studies have demonstrated that dysbiosis of the gut microbiota is associated with psoriasis, but these studies showed some conflicting results. Our study examined differences in microbiome composition associated in people with psoriasis and those without. Comparing individuals with their healthy partners was a second strategy. We explored the fecal microbiota among 32 nontreated plaque psoriasis patients, 15 healthy controls and 17 healthy couples by metagenomic gene sequencing. The relative levels of intestinal microbiota of the psoriasis cohort differed from those in healthy controls and these patients' partners. However, there was no microbial diversity among these three cohorts. On the level of the phylum, Firmicutes and Bacteroidetes' relative abundances were reversed. Escherichia coli was significantly enriched in the psoriasis group compared with the healthy people and the healthy spouses. Gene functional analysis indicated that Ribosome (ko03010) was upregulated, Flagellar assembly (ko02040) and Bacterial chemotaxis (ko02030) were downregulated in the psoriasis cohort compared with the healthy individuals and the healthy spouses. The microbiota in severe psoriasis patients differed from those with milder conditions. These findings strongly support the association between intestinal flora and psoriasis. It is necessary to perform more meaningful experiments to identify whether the differences of gut microbiota are the cause or consequences of psoriasis in future.}, } @article {pmid36621001, year = {2024}, author = {Ramos, JGVDS and Richter, CP and Silva, MA and Singolano, GL and Hauagge, G and Lorençon, E and Junior, ILC and Edwiges, T and de Arruda, PV and Vidal, CMS}, title = {Effects of ciprofloxacin on biogas production and microbial community composition in anaerobic digestion of swine wastewater in ASBR type reactor.}, journal = {Environmental technology}, volume = {45}, number = {10}, pages = {2076-2088}, doi = {10.1080/09593330.2022.2164744}, pmid = {36621001}, issn = {1479-487X}, mesh = {Animals ; Swine ; *Wastewater ; Anaerobiosis ; Biofuels ; Bioreactors ; Ciprofloxacin/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Methane ; }, abstract = {In swine farming, antibiotics are often used to reduce disease and promote animal growth. Part of these compounds is not absorbed by the swine body, being excreted and later reaching the treatment systems, soil, and nearby waterbodies. This research sought to investigate the influence of adding ciprofloxacin (CIP) on the anaerobic digestion of swine wastewater. For that, a bench-scale anaerobic sequential batch reactor (ASBR) was used, with 5 L of working volume in six different phases, with volumetric organic loading rate (VOLR) and CIP dosage variation. According to the results, the optimal VOLR for the reactor was 0.60 ± 0.11 gSV L[-1] d[-1], resulting in biogas productivity of 0.51 ± 0.03 Lbiogas L[-1] d[-1]. After initial stability, adding substrate with 0.5 mgCIP L[-1] resulted in an abrupt drop of 82% in the productivity from the 7[th] to 11[th] day of addition, coinciding with volatile acids accumulation. Afterward, the reactor recovered and reached apparent stability, with productivity similar to the previous step without the drug. For 2.5 mgCIP L[-1] in the substrate, the biogas productivity at equilibrium was 11.8% lower than in the phases with the same VOLR and 0.0 and 0.5 mgCIP L[-1]. Organic matter removals near 80% were achieved for both dosages. The 16S rRNA metagenomic analyses showed an increase in the relative abundance of most of the phyla found, indicating that the dosages used allowed the acclimatization of microorganisms and possibly the compound biodegradation.}, } @article {pmid36619744, year = {2022}, author = {Wells, RK and Kunihiro, BP and Phankitnirundorn, K and Peres, R and McCracken, TA and Umeda, L and Lee, RH and Kim, DY and Juarez, R and Maunakea, AK}, title = {Gut microbial indicators of metabolic health underlie age-related differences in obesity and diabetes risk among Native Hawaiians and Pacific Islanders.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1035641}, pmid = {36619744}, issn = {2235-2988}, support = {R01 MD016593/MD/NIMHD NIH HHS/United States ; U54 MD007601/MD/NIMHD NIH HHS/United States ; P30 GM131944/GM/NIGMS NIH HHS/United States ; P20 GM103466/GM/NIGMS NIH HHS/United States ; R56 MD014630/MD/NIMHD NIH HHS/United States ; }, mesh = {Humans ; *Diabetes Mellitus, Type 2/epidemiology/microbiology ; *Gastrointestinal Microbiome ; Glycated Hemoglobin ; Hawaii/epidemiology ; Native Hawaiian or Other Pacific Islander ; *Obesity/epidemiology/microbiology ; }, abstract = {Native Hawaiians and Pacific Islanders (NHPIs) suffer from higher prevalence of and mortality to type 2 diabetes mellitus (T2DM) than any other major race/ethnic group in Hawaii. Health inequities in this indigenous population was further exacerbated by the SARS-CoV-2 pandemic. T2DM progression and medical complications exacerbated by COVID-19 are partially regulated by the gut microbiome. However, there is limited understanding of the role of gut bacteria in the context of inflammation-related diseases of health disparities including T2DM and obesity. To address these gaps, we used a community-based research approach from a cohort enriched with NHPI residents on the island of Oahu, Hawaii (N=138). Gut microbiome profiling was achieved via 16s rDNA metagenomic sequencing analysis from stool DNA. Gut bacterial capacity for butyrate-kinase (BUK)-mediated fiber metabolism was assessed using quantitative PCR to measure the abundance of BUK DNA and RNA relative to total bacterial load per stool sample. In our cohort, age positively correlated with hemoglobin A1c (%; R=0.39; P<0.001) and body mass index (BMI; R=0.28; P<0.001). The relative abundance of major gut bacterial phyla significantly varied across age groups, including Bacteroidetes (P<0.001), Actinobacteria (P=0.007), and Proteobacteria (P=0.008). A1c was negatively correlated with the relative levels of BUK DNA copy number (R=-0.17; P=0.071) and gene expression (R=-0.33; P=0.003). Interestingly, we identified specific genera of gut bacteria potentially mediating the effects of diet on metabolic health in this cohort. Additionally, α-diversity among gut bacterial genera significantly varied across T2DM and BMI categories. Together, these results provide insight into age-related differences in gut bacteria that may influence T2DM and obesity in NHPIs. Furthermore, we observed overlapping patterns between gut bacteria and T2DM risk factors, indicating more nuanced, interdependent interactions among these factors as partial determinants of health outcomes. This study adds to the paucity of NHPI-specific data to further elucidate the biological characteristics associated with pre-existing health inequities in this racial/ethnic group that is significantly underrepresented in biomedical research.}, } @article {pmid36619742, year = {2022}, author = {Chen, L and Wang, S and Zhang, Y and Li, Y and Zhang, X and Ma, J and Zou, X and Yao, T and Li, S and Chen, J and Zhou, H and Wu, L and Zhou, Y and Zhang, L}, title = {Multi-omics reveals specific host metabolism-microbiome associations in intracerebral hemorrhage.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {999627}, pmid = {36619742}, issn = {2235-2988}, mesh = {Humans ; Multiomics ; *Microbiota ; Metabolomics ; Metabolome ; Cerebral Hemorrhage ; *Stroke ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Intracerebral hemorrhage (ICH) is the most devastating subtype of stroke, but effective prevention and treatment strategies are lacking. Recently, gut microbiome and its metabolitesis are considered to be an influencing factor of stroke. However, little is known about the effects of the gut microbiome on ICH and host metabolic activity. Therefore, we used 16S sequencing, macrogenomics sequencing and untargeted metabolomics to explore the differences in gut microbial-metabolome interactions between patients with intracerebral hemorrhage and healthy control populations. We found a significant decrease in the phylum of Firmicutes and a significant increase of Bacteroidetes in ICH patients. At the genus level, Streptococcus, Bifidobacterium, Akkermansia, and Lactobacillus were more abundant in ICH patients. Macrogenomic analysis revealed active glycosaminoglycan degradation, heme synthesis, galactose degradation, lipopolysaccharide core region synthesis, and beta-Lactam resistance in ICH patients. Serum untargeted metabolomic analysis combined with ROC curves showed that octanoylcarnitine, decanoylcarnitine, dodecanoylcarnitine, glyceric acid, pyruvic acid, aspartic acid, methylcysteine, pyroglutamic acid, 9E-tetradecenoic acid, N-Acetylneuraminic acid, and aconitic acid were the best markers for the diagnosis of ICH. Correlation analysis showed that microbiome enriched in the gut of ICH patients were significantly correlated with serum metabolites, revealing a close correlation between the gut microbiome of ICH patients and the host metabolome, and significant differences from the healthy population. microbiota-host co-metabolites including pyruvic acid and 9E-tetradecenoic acid is associated with the the National Institutes of Health Stroke Scale (NIHSS) scores. In conclusion, microbiome-related metabolites in ICH patients was associated with the severity of ICH, the microbiota-host co-metabolites may be a potential may be potential therapeutic targets.}, } @article {pmid36617187, year = {2023}, author = {Yang, L and Chen, J}, title = {Benchmarking differential abundance analysis methods for correlated microbiome sequencing data.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {1}, pages = {}, pmid = {36617187}, issn = {1477-4054}, support = {R01 GM144351/GM/NIGMS NIH HHS/United States ; R21 HG011662/HG/NHGRI NIH HHS/United States ; R01 GM144351/NH/NIH HHS/United States ; }, mesh = {*Microbiota/genetics ; Linear Models ; Databases, Factual ; Metagenomics/methods ; }, abstract = {Differential abundance analysis (DAA) is one central statistical task in microbiome data analysis. A robust and powerful DAA tool can help identify highly confident microbial candidates for further biological validation. Current microbiome studies frequently generate correlated samples from different microbiome sampling schemes such as spatial and temporal sampling. In the past decade, a number of DAA tools for correlated microbiome data (DAA-c) have been proposed. Disturbingly, different DAA-c tools could sometimes produce quite discordant results. To recommend the best practice to the field, we performed the first comprehensive evaluation of existing DAA-c tools using real data-based simulations. Overall, the linear model-based methods LinDA, MaAsLin2 and LDM are more robust than methods based on generalized linear models. The LinDA method is the only method that maintains reasonable performance in the presence of strong compositional effects.}, } @article {pmid36614337, year = {2023}, author = {Ahmad, MF and Abdullah, H and Hassan, MN and Jamaludin, MI and Sivam, A and Komatsu, K and Sapian, IS and Alias, H and Mat Isa, MN and Kuwahara, VS and Yaacob, NS}, title = {Topographically Distinguished Microbiome Taxonomy and Stress-Response Genes of Royal Belum Rainforest and Raja Muda Musa Peat Swamp Revealed through Metagenomic Inquisition.}, journal = {International journal of molecular sciences}, volume = {24}, number = {1}, pages = {}, pmid = {36614337}, issn = {1422-0067}, support = {JPMJSA1509//Ministry of Higher Education/ ; }, mesh = {Animals ; Metagenome ; Wetlands ; Rainforest ; *Musa/genetics ; *Skates, Fish/genetics ; Soil/chemistry ; *Microbiota/genetics ; Bacteria/metabolism ; Archaea/genetics ; Forests ; Eukaryota/genetics ; Soil Microbiology ; }, abstract = {Soil ecosystems are home to a diverse range of microorganisms, but they are only partially understood because no single-cell sequencing or whole-community sequencing provides a complete picture of these complex communities. Using one of such metagenomics approaches, we succeeded in monitoring the microbial diversity and stress-response gene in the soil samples. This study aims to test whether known differences in taxonomic diversity and composition are reflected in functional gene profiles by implementing whole gene sequencing (WGS) metagenomic analysis of geographically dispersed soils from two distinct pristine forests. The study was commenced by sequencing three rainforest soil samples and three peat swamp soil samples. Soil richness effects were assessed by exploring the changes in specific functional gene abundances to elucidate physiological constraints acting on different soil systems and identify variance in functional pathways relevant to soil biogeochemical cycling. Proteobacteria shows abundances of microbial diversity for 52.15% in Royal Belum Reserved Forest and 48.28% in Raja Musa; 177 out of 1,391,841 and 449 out of 3,586,577 protein coding represent acidic stress-response genes for Royal Belum and Raja Musa, respectively. Raja Musa indicates pH 2.5, which is extremely acidic. The analysis of the taxonomic community showed that Royal Belum soils are dominated by bacteria (98% in Sungai Kooi (SK), 98% in Sungai Papan (SP), and 98% in Sungai Ruok (SR), Archaea (0.9% in SK, 0.9% in SP, and 1% in SR), and the remaining were classed under Eukaryota and viruses. Likewise, the soils of Raja Muda Musa are also dominated by bacteria (95% in Raja Musa 1 (RM1), 98% in Raja Musa 2 (RM2), and 96% in Raja Musa 3 (RM3)), followed by Archaea (4% in RM1, 1% in RM2, and 3% in RM3), and the remaining were classed under Eukaryota and viruses. This study revealed that RBFR (Royal Belum Foresr Reserve) and RMFR (Raja Musa Forest Reserve) metagenomes contained abundant stress-related genes assigned to various stress-response pathways, many of which did not show any difference among samples from both sites. Our findings indicate that the structure and functional potential of the microbial community will be altered by future environmental potential as the first glimpse of both the taxonomic and functional composition of soil microbial communities.}, } @article {pmid36611217, year = {2023}, author = {Jiang, JZ and Fang, YF and Wei, HY and Zhu, P and Liu, M and Yuan, WG and Yang, LL and Guo, YX and Jin, T and Shi, M and Yao, T and Lu, J and Ye, LT and Shi, SK and Wang, M and Duan, M and Zhang, DC}, title = {A remarkably diverse and well-organized virus community in a filter-feeding oyster.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {2}, pmid = {36611217}, issn = {2049-2618}, mesh = {Animals ; *Crassostrea/genetics ; DNA ; *Microbiota ; Seawater ; *Viruses/genetics ; }, abstract = {BACKGROUND: Viruses play critical roles in the marine environment because of their interactions with an extremely broad range of potential hosts. Many studies of viruses in seawater have been published, but viruses that inhabit marine animals have been largely neglected. Oysters are keystone species in coastal ecosystems, yet as filter-feeding bivalves with very large roosting numbers and species co-habitation, it is not clear what role they play in marine virus transmission and coastal microbiome regulation.

RESULTS: Here, we report a Dataset of Oyster Virome (DOV) that contains 728,784 nonredundant viral operational taxonomic unit contigs (≥ 800 bp) and 3473 high-quality viral genomes, enabling the first comprehensive overview of both DNA and RNA viral communities in the oyster Crassostrea hongkongensis. We discovered tremendous diversity among novel viruses that inhabit this oyster using multiple approaches, including reads recruitment, viral operational taxonomic units, and high-quality virus genomes. Our results show that these viruses are very different from viruses in the oceans or other habitats. In particular, the high diversity of novel circoviruses that we found in the oysters indicates that oysters may be potential hotspots for circoviruses. Notably, the viruses that were enriched in oysters are not random but are well-organized communities that can respond to changes in the health state of the host and the external environment at both compositional and functional levels.

CONCLUSIONS: In this study, we generated a first "knowledge landscape" of the oyster virome, which has increased the number of known oyster-related viruses by tens of thousands. Our results suggest that oysters provide a unique habitat that is different from that of seawater, and highlight the importance of filter-feeding bivalves for marine virus exploration as well as their essential but still invisible roles in regulating marine ecosystems. Video Abstract.}, } @article {pmid36610618, year = {2023}, author = {Meng, LJ and Hu, X and Wen, B and Liu, YH and Luo, GZ and Gao, JZ and Chen, ZZ}, title = {Microplastics inhibit biofloc formation and alter microbial community composition and nitrogen transformation function in aquaculture.}, journal = {The Science of the total environment}, volume = {866}, number = {}, pages = {161362}, doi = {10.1016/j.scitotenv.2022.161362}, pmid = {36610618}, issn = {1879-1026}, mesh = {*Microplastics ; Plastics ; Nitrogen ; Nitrogen Dioxide ; *Microbiota ; Aquaculture/methods ; }, abstract = {Biofloc technology, extensively used in intensive aquaculture systems, can prompt the formation of microbial aggregates. Microplastics (MPs) are detected abundantly in aquaculture waters. This study explored the effects of MPs on biofloc formation, microbial community composition and nitrogen transformation function in simulated biofloc aquaculture production systems. The formation process and settling performance of bioflocs were examined. High-throughput sequencing of 16S and 18S rRNA genes was used to investigate the microbial community compositions of bioflocs. Nitrogen dynamics were monitored and further explained from functional genes and microorganisms related to nitrogen transformation by metagenome sequencing. We found that the aggregates consisting of bioflocs and MPs were formed and the systems with MPs had relatively weak settling performance. No significant differences in bacterial diversity (p > 0.05) but significant differences in eukaryotic diversity (p < 0.05) were found between systems without and with MPs. Significant separations in the microbial communities of prokaryotes (p = 0.01) and eukaryotes (p = 0.01) between systems without and with MPs were observed. The peak concentration of nitrite nitrogen (NO2[-]-N) in systems with MPs was lower than that in systems without MPs (pControl/MPs Low = 0.02 and pControl/MPs High = 0.03), probably due to the low abundance of hao and affiliated Alphaproteobacteria_bacterium_HGW-Alphaproteobacteria-1 and Alphaproteobacteria_bacterium, but the high abundance of nxrA and affiliated Alphaproteobacteria_bacterium_SYSU_XM001 and Hydrogenophaga_pseudoflava that related to nitrification. The low concentration of NO2[-]-N in systems with MPs suggested that the presence of MPs might inhibit ammonia oxidation but promote nitrite oxidation by altering the microbial community structure and function. These results indicated that aggregates consisting of bioflocs and MPs could be formed in aquaculture water, and thus, inhibiting their settlement and altering nitrogen transformation function by affecting the microbial community composition.}, } @article {pmid36610232, year = {2023}, author = {Wu, Z and Han, Y and Wan, Y and Hua, X and Chill, SS and Teshome, K and Zhou, W and Liu, J and Wu, D and Hutchinson, A and Jones, K and Dagnall, CL and Hicks, BD and Liao, L and Hallen-Adams, H and Shi, J and Abnet, CC and Sinha, R and Chaturvedi, A and Vogtmann, E}, title = {Oral microbiome and risk of incident head and neck cancer: A nested case-control study.}, journal = {Oral oncology}, volume = {137}, number = {}, pages = {106305}, pmid = {36610232}, issn = {1879-0593}, support = {ZIA CP010215/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Humans ; Case-Control Studies ; *Head and Neck Neoplasms/epidemiology ; *Microbiota ; Diet ; Porphyromonas gingivalis ; }, abstract = {OBJECTIVES: This nested case-control study in the NIH-AARP Diet and Health Study was carried out to prospectively investigate the relationship of oral microbiome with head and neck cancer (HNC).

MATERIALS AND METHODS: 56 incident HNC cases were identified, and 112 controls were incidence-density matched to cases. DNA extracted from pre-diagnostic oral wash samples was whole-genome shotgun metagenomic sequenced to measure the overall oral microbiome. ITS2 gene qPCR was used to measure the presence of fungi. ITS2 gene sequencing was performed on ITS2 gene qPCR positive samples. We computed taxonomic and functional alpha-diversity and beta-diversity metrics. The presence and relative abundance of groups of red-complex (e.g., Porphyromonas gingivalis) and/or orange-complex (e.g., Fusobacterium nucleatum) periodontal pathogens were compared between cases and controls using conditional logistic regression models and MiRKAT.

RESULTS: Participants with higher taxonomic microbial alpha-diversity had a non-statistically significant decreased risk of HNC. No case-control differences were found for beta diversity by MiRKAT model (all p > 0.05). A greater relative abundance of red-complex periodontal pathogens (OR = 0.51, 95 % CI = 0.26-1.00), orange-complex (OR = 0.38, 95 % CI = 0.18-0.83), and both complexes' pathogens (OR = 0.32, 95 % CI = 0.14-0.75), were associated with reduced risk of HNC. The presence of oral fungi was also strongly associated with reduced risk of HNC compared with controls (OR = 0.39, 95 % CI = 0.17-0.92).

CONCLUSION: Greater taxonomic alpha-diversity, the presence of oral fungi, and the presence or relative abundance of multiple microbial species, including the red- and orange-complex periodontal pathogens, were associated with reduced risk of HNC. Future studies with larger sample sizes are needed to evaluate these associations.}, } @article {pmid36609515, year = {2023}, author = {Wang, Z and Huang, P and You, R and Sun, F and Zhu, S}, title = {MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {1}, pmid = {36609515}, issn = {1474-760X}, mesh = {*Algorithms ; *Microbiota/genetics ; Metagenome ; Genome, Microbial ; Metagenomics/methods ; Sequence Analysis, DNA ; }, abstract = {Binning aims to recover microbial genomes from metagenomic data. For complex metagenomic communities, the available binning methods are far from satisfactory, which usually do not fully use different types of features and important biological knowledge. We developed a novel ensemble binner, MetaBinner, which generates component results with multiple types of features by k-means and uses single-copy gene information for initialization. It then employs a two-stage ensemble strategy based on single-copy genes to integrate the component results efficiently and effectively. Extensive experimental results on three large-scale simulated datasets and one real-world dataset demonstrate that MetaBinner outperforms the state-of-the-art binners significantly.}, } @article {pmid36606725, year = {2023}, author = {Candel, S and Tyrkalska, SD and Álvarez-Santacruz, C and Mulero, V}, title = {The nasopharyngeal microbiome in COVID-19.}, journal = {Emerging microbes & infections}, volume = {12}, number = {1}, pages = {e2165970}, pmid = {36606725}, issn = {2222-1751}, mesh = {Humans ; *COVID-19 ; Pandemics ; Nasopharynx ; *Microbiota ; Nose ; }, abstract = {The development of novel culture-independent techniques of microbial identification has allowed a rapid progress in the knowledge of the nasopharyngeal microbiota and its role in health and disease. Thus, it has been demonstrated that the nasopharyngeal microbiota defends the host from invading pathogens that enter the body through the upper airways by participating in the modulation of innate and adaptive immune responses. The current COVID-19 pandemic has created an urgent need for fast-track research, especially to identify and characterize biomarkers to predict the disease severity and outcome. Since the nasopharyngeal microbiota diversity and composition could potentially be used as a prognosis biomarker for COVID-19 patients, which would pave the way for strategies aiming to reduce the disease severity by modifying such microbiota, dozens of research articles have already explored the possible associations between changes in the nasopharyngeal microbiota and the severity or outcome of COVID-19 patients. Unfortunately, results are controversial, as many studies with apparently similar experimental designs have reported contradictory data. Herein we put together, compare, and discuss all the relevant results on this issue reported to date. Even more interesting, we discuss in detail which are the limitations of these studies, that probably are the main sources of the high variability observed. Therefore, this work is useful not only for people interested in current knowledge about the relationship between the nasopharyngeal microbiota and COVID-19, but also for researchers who want to go further in this field while avoiding the limitations and variability of previous works.}, } @article {pmid36606497, year = {2023}, author = {Tang, L and Yan, L and Jia, H and Xiong, Y and Ma, X and Chu, H and Sun, Z and Wang, L and Shalitanati, M and Li, K and Hu, D and Zhang, D}, title = {Gut microbial community structure and function of Przewalski's horses varied across reintroduced sites in China.}, journal = {Integrative zoology}, volume = {18}, number = {6}, pages = {1027-1040}, doi = {10.1111/1749-4877.12699}, pmid = {36606497}, issn = {1749-4877}, support = {2019JQ0318//the Beijing Forestry University Outstanding Young Talent Cultivation Project/ ; BX20190042//the Postdoctoral Innovative Talents Support Program/ ; 2020M670177//the China Postdoctoral Science Foundation/ ; }, mesh = {Humans ; Animals ; Horses ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; China ; }, abstract = {Host-associated microbiota can significantly impact host fitness. Therefore, naturally occurring variations in microbiota may influence the health and persistence of their hosts. This finding is particularly important in reintroduced animals, as they typically experience habitat changes during translocations. However, little is known about how microbiomes are altered in response to conservation translocation. Here, we accessed the gut microbiome of Przewalski's horse (Equus przewalskii) populations in China from three nature reserves (i.e. Xinjiang Kalamaili Nature Reserve, KNR; Dunhuang Xihu National Nature Reserve, DXNNR; and Anxi Extreme-arid Desert Nature Reserve, AENR) using 16s rRNA gene and metagenome sequencing. The results showed that the microbial composition and function differed significantly across locations, while a subset of core taxa was consistently present in most of the samples. The abundance of genes encoding microbe-produced enzymes involved in the metabolism of carbohydrates, especially for glycoside hydrolases, was significantly higher in open-spaced KNR populations than in more confined AENR individuals. This study offers detailed and significant differential characters related to the microbial community and metabolic pathways in various reintroduced sites of Przewalski's horse, which might provide a basis for future microecological and conservation research on endangered reintroduced animals.}, } @article {pmid36604505, year = {2023}, author = {Jin, H and Quan, K and He, Q and Kwok, LY and Ma, T and Li, Y and Zhao, F and You, L and Zhang, H and Sun, Z}, title = {A high-quality genome compendium of the human gut microbiome of Inner Mongolians.}, journal = {Nature microbiology}, volume = {8}, number = {1}, pages = {150-161}, pmid = {36604505}, issn = {2058-5276}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Metagenome ; RNA, Ribosomal ; }, abstract = {Metagenome-based resources have revealed the diversity and function of the human gut microbiome, but further understanding is limited by insufficient genome quality and a lack of samples from typically understudied populations. Here we used hybrid long-read PromethION and short-read HiSeq sequencing to characterize the faecal microbiota of 60 Inner Mongolian individuals (n = 180 samples over three time points) who were part of a probiotic yogurt intervention trial. We present the Inner Mongolian Gut Genome catalogue, comprising 802 closed and 5,927 high-quality metagenome-assembled genomes. This approach achieved high genome continuity and substantially increased the resolution of genomic elements, including ribosomal RNA operons, metabolic gene clusters, prophages and insertion sequences. Particularly, we report the ribosomal RNA operon copy numbers for uncultured species, over 12,000 previously undescribed gut prophages and the distribution of insertion sequence elements across gut bacteria. Overall, these data provide a high-quality, large-scale resource for studying the human gut microbiota.}, } @article {pmid36603585, year = {2023}, author = {Dai, DLY and Petersen, C and Hoskinson, C and Del Bel, KL and Becker, AB and Moraes, TJ and Mandhane, PJ and Finlay, BB and Simons, E and Kozyrskyj, AL and Patrick, DM and Subbarao, P and Bode, L and Azad, MB and Turvey, SE}, title = {Breastfeeding enrichment of B. longum subsp. infantis mitigates the effect of antibiotics on the microbiota and childhood asthma risk.}, journal = {Med (New York, N.Y.)}, volume = {4}, number = {2}, pages = {92-112.e5}, doi = {10.1016/j.medj.2022.12.002}, pmid = {36603585}, issn = {2666-6340}, support = {//CIHR/Canada ; }, mesh = {Child ; Infant ; Female ; Humans ; Breast Feeding ; Anti-Bacterial Agents/adverse effects ; *Sulfalene ; *Microbiota/genetics ; Bifidobacterium longum subspecies infantis ; Oligosaccharides/therapeutic use ; British Columbia ; *Asthma/epidemiology ; }, abstract = {BACKGROUND: Early antibiotic exposure is linked to persistent disruption of the infant gut microbiome and subsequent elevated pediatric asthma risk. Breastfeeding acts as a primary modulator of the gut microbiome during early life, but its effect on asthma development has remained unclear.

METHODS: We harnessed the CHILD cohort to interrogate the influence of breastfeeding on antibiotic-associated asthma risk in a subset of children (n = 2,521). We then profiled the infant microbiomes in a subset of these children (n = 1,338) using shotgun metagenomic sequencing and compared human milk oligosaccharide and fatty acid composition from paired maternal human milk samples for 561 of these infants.

FINDINGS: Children who took antibiotics without breastfeeding had 3-fold higher asthma odds, whereas there was no such association in children who received antibiotics while breastfeeding. This benefit was associated with widespread "re-balancing" of taxonomic and functional components of the infant microbiome. Functional changes associated with asthma protection were linked to enriched Bifidobacterium longum subsp. infantis colonization. Network analysis identified a selection of fucosylated human milk oligosaccharides in paired maternal samples that were positively associated with B. infantis and these broader functional changes.

CONCLUSIONS: Our data suggest that breastfeeding and antibiotics have opposing effects on the infant microbiome and that breastfeeding enrichment of B. infantis is associated with reduced antibiotic-associated asthma risk.

FUNDING: This work was supported in part by the Canadian Institutes of Health Research; the Allergy, Genes and Environment Network of Centres of Excellence; Genome Canada; and Genome British Columbia.}, } @article {pmid36602384, year = {2023}, author = {Joo, H and Eom, H and Cho, Y and Rho, M and Song, WJ}, title = {Discovery and Characterization of Polymyxin-Resistance Genes pmrE and pmrF from Sediment and Seawater Microbiome.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0273622}, pmid = {36602384}, issn = {2165-0497}, mesh = {*Polymyxins/pharmacology/metabolism ; Lipid A/chemistry ; Escherichia coli/genetics ; Anti-Bacterial Agents/pharmacology/metabolism ; *Microbiota/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Polymyxins are the last-line antibiotics used to treat Gram-negative pathogens. Thus, the discovery and biochemical characterization of the resistance genes against polymyxins are urgently needed for diagnosis, treatment, and novel antibiotic design. Herein, we report novel polymyxin-resistance genes identified from sediment and seawater microbiome. Despite their low sequence identity against the known pmrE and pmrF, they show in vitro activities in UDP-glucose oxidation and l-Ara4N transfer to undecaprenyl phosphate, respectively, which occur as the part of lipid A modification that leads to polymyxin resistance. The expression of pmrE and pmrF also showed substantially high MICs in the presence of vanadate ions, indicating that they constitute polymyxin resistomes. IMPORTANCE Polymyxins are one of the last-resort antibiotics. Polymyxin resistance is a severe threat to combat multidrug-resistant pathogens. Thus, up-to-date identification and understanding of the related genes are crucial. Herein, we performed structure-guided sequence and activity analysis of five putative polymyxin-resistant metagenomes. Despite relatively low sequence identity to the previously reported polymyxin-resistance genes, at least four out of five discovered genes show reactivity essential for lipid A modification and polymyxin resistance, constituting antibiotic resistomes.}, } @article {pmid36602332, year = {2023}, author = {Distaso, M and Cea-Rama, I and Coscolín, C and Chernikova, TN and Tran, H and Ferrer, M and Sanz-Aparicio, J and Golyshin, PN}, title = {The Mobility of the Cap Domain Is Essential for the Substrate Promiscuity of a Family IV Esterase from Sorghum Rhizosphere Microbiome.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {1}, pages = {e0180722}, pmid = {36602332}, issn = {1098-5336}, mesh = {Esterases/metabolism ; *Sorghum/metabolism ; Rhizosphere ; *Microbiota ; Esters/metabolism ; Substrate Specificity ; Hydrogen-Ion Concentration ; }, abstract = {Metagenomics offers the possibility to screen for versatile biocatalysts. In this study, the microbial community of the Sorghum bicolor rhizosphere was spiked with technical cashew nut shell liquid, and after incubation, the environmental DNA (eDNA) was extracted and subsequently used to build a metagenomic library. We report the biochemical features and crystal structure of a novel esterase from the family IV, EH0, retrieved from an uncultured sphingomonad after a functional screen in tributyrin agar plates. EH0 (optimum temperature [Topt], 50°C; melting temperature [Tm], 55.7°C; optimum pH [pHopt], 9.5) was stable in the presence of 10 to 20% (vol/vol) organic solvents and exhibited hydrolytic activity against p-nitrophenyl esters from acetate to palmitate, preferably butyrate (496 U mg[-1]), and a large battery of 69 structurally different esters (up to 30.2 U mg[-1]), including bis(2-hydroxyethyl)-terephthalate (0.16 ± 0.06 U mg[-1]). This broad substrate specificity contrasts with the fact that EH0 showed a long and narrow catalytic tunnel, whose access appears to be hindered by a tight folding of its cap domain. We propose that this cap domain is a highly flexible structure whose opening is mediated by unique structural elements, one of which is the presence of two contiguous proline residues likely acting as possible hinges, which together allow for the entrance of the substrates. Therefore, this work provides a new role for the cap domain, which until now was thought to be an immobile element that contained hydrophobic patches involved in substrate prerecognition and in turn substrate specificity within family IV esterases. IMPORTANCE A better understanding of structure-function relationships of enzymes allows revelation of key structural motifs or elements. Here, we studied the structural basis of the substrate promiscuity of EH0, a family IV esterase, isolated from a sample of the Sorghum bicolor rhizosphere microbiome exposed to technical cashew nut shell liquid. The analysis of EH0 revealed the potential of the sorghum rhizosphere microbiome as a source of enzymes with interesting properties, such as pH and solvent tolerance and remarkably broad substrate promiscuity. Its structure resembled those of homologous proteins from mesophilic Parvibaculum and Erythrobacter spp. and hyperthermophilic Pyrobaculum and Sulfolobus spp. and had a very narrow, single-entry access tunnel to the active site, with access controlled by a capping domain that includes a number of nonconserved proline residues. These structural markers, distinct from those of other substrate-promiscuous esterases, can help in tuning substrate profiles beyond tunnel and active site engineering.}, } @article {pmid36599469, year = {2023}, author = {Perry, LM and Cruz, SM and Kleber, KT and Judge, SJ and Darrow, MA and Jones, LB and Basmaci, UN and Joshi, N and Settles, ML and Durbin-Johnson, BP and Gingrich, AA and Monjazeb, AM and Carr-Ascher, J and Thorpe, SW and Murphy, WJ and Eisen, JA and Canter, RJ}, title = {Human soft tissue sarcomas harbor an intratumoral viral microbiome which is linked with natural killer cell infiltrate and prognosis.}, journal = {Journal for immunotherapy of cancer}, volume = {11}, number = {1}, pages = {}, pmid = {36599469}, issn = {2051-1426}, support = {P30 CA093373/CA/NCI NIH HHS/United States ; S10 OD018223/OD/NIH HHS/United States ; S10 RR026825/RR/NCRR NIH HHS/United States ; T32 CA251007/CA/NCI NIH HHS/United States ; U01 CA224166/CA/NCI NIH HHS/United States ; S10 OD010786/OD/NIH HHS/United States ; }, mesh = {Adult ; Humans ; Virome ; *Sarcoma/genetics ; Prognosis ; Extremities/pathology ; Killer Cells, Natural ; *Soft Tissue Neoplasms ; Tumor Microenvironment ; }, abstract = {BACKGROUND: Groundbreaking studies have linked the gut microbiome with immune homeostasis and antitumor immune responses. Mounting evidence has also demonstrated an intratumoral microbiome, including in soft tissue sarcomas (STS), although detailed characterization of the STS intratumoral microbiome is limited. We sought to characterize the intratumoral microbiome in patients with STS undergoing preoperative radiotherapy and surgery, hypothesizing the presence of a distinct intratumoral microbiome with potentially clinically significant microbial signatures.

METHODS: We prospectively obtained tumor and stool samples from adult patients with non-metastatic STS using a strict sterile collection protocol to minimize contamination. Metagenomic classification was used to estimate abundance using genus and species taxonomic levels across all classified organisms, and data were analyzed with respect to clinicopathologic factors.

RESULTS: Fifteen patients were enrolled. Most tumors were located at an extremity (67%) and were histologic grade 3 (87%). 40% were well-differentiated/dedifferentiated liposarcoma histology. With a median follow-up of 24 months, 4 (27%) patients developed metastases, and 3 (20%) died. Despite overwhelming human DNA (>99%) intratumorally, we detected a small but consistent proportion of bacterial DNA (0.02-0.03%) in all tumors, including Proteobacteria, Bacteroidetes, and Firmicutes, as well as viral species. In the tumor microenvironment, we observed a strong positive correlation between viral relative abundance and natural killer (NK) infiltration, and higher NK infiltration was associated with superior metastasis-free and overall survival by immunohistochemical, flow cytometry, and multiplex immunofluorescence analyses.

CONCLUSIONS: We prospectively demonstrate the presence of a distinct and measurable intratumoral microbiome in patients with STS at multiple time points. Our data suggest that the STS tumor microbiome has prognostic significance with viral relative abundance associated with NK infiltration and oncologic outcome. Additional studies are warranted to further assess the clinical impact of these findings.}, } @article {pmid36597727, year = {2023}, author = {Böttner, L and Malacrinò, A and Schulze Gronover, C and van Deenen, N and Müller, B and Xu, S and Gershenzon, J and Prüfer, D and Huber, M}, title = {Natural rubber reduces herbivory and alters the microbiome below ground.}, journal = {The New phytologist}, volume = {239}, number = {4}, pages = {1475-1489}, doi = {10.1111/nph.18709}, pmid = {36597727}, issn = {1469-8137}, mesh = {Animals ; Rubber/chemistry/metabolism ; Latex/metabolism ; Herbivory ; *Coleoptera ; Larva ; Plants, Genetically Modified/metabolism ; *Taraxacum/genetics ; }, abstract = {Laticifers are hypothesized to mediate both plant-herbivore and plant-microbe interactions. However, there is little evidence for this dual function. We investigated whether the major constituent of natural rubber, cis-1,4-polyisoprene, a phylogenetically widespread and economically important latex polymer, alters plant resistance and the root microbiome of the Russian dandelion (Taraxacum koksaghyz) under attack of a root herbivore, the larva of the May cockchafer (Melolontha melolontha). Rubber-depleted transgenic plants lost more shoot and root biomass upon herbivory than normal rubber content near-isogenic lines. Melolontha melolontha preferred to feed on artificial diet supplemented with rubber-depleted rather than normal rubber content latex. Likewise, adding purified cis-1,4-polyisoprene in ecologically relevant concentrations to diet deterred larval feeding and reduced larval weight gain. Metagenomics and metabarcoding revealed that abolishing biosynthesis of natural rubber alters the structure but not the diversity of the rhizosphere and root microbiota (ecto- and endophytes) and that these changes depended on M. melolontha damage. However, the assumption that rubber reduces microbial colonization or pathogen load is contradicted by four lines of evidence. Taken together, our data demonstrate that natural rubber biosynthesis reduces herbivory and alters the plant microbiota, which highlights the role of plant-specialized metabolites and secretory structures in shaping multitrophic interactions.}, } @article {pmid36596171, year = {2023}, author = {Duarte-Coimbra, S and Forcina, G and Pérez-Pardal, L and Beja-Pereira, A}, title = {Characterization of tongue dorsum microbiome in wine tasters.}, journal = {Food research international (Ottawa, Ont.)}, volume = {163}, number = {}, pages = {112259}, doi = {10.1016/j.foodres.2022.112259}, pmid = {36596171}, issn = {1873-7145}, mesh = {*Wine/analysis ; RNA, Ribosomal, 16S/genetics ; Taste ; Tongue ; *Microbiota/genetics ; }, abstract = {Taste plays a paramount role in food and beverage choice, with recent studies pointing to a potential influence of the microorganisms from the tongue dorsum - particularly bacteria - on flavor perception. Thus, the association between tongue dorsum biofilm and taste is a fundamental prerequisite for a better understanding of the role played by these bacteria in wine tasting. To study this impact, we have analyzed the microbiomes from 58 samples of the tongue dorsum surface from professional wine tasters and 30 samples from non professional wine tasters. The microbiome of each sample was characterized through metagenome sequencing of the 16S rRNA gene for taxonomic discrimination of bacteria. A total of 497 taxa were identified in the tongue dorsum, and significant differences in diversity were observed between the wine taster and the control group. The comparison of bacterial diversity between samples collected before and after wine tasting along with the presence of new bacterial taxa indicates a direct effect of wine on the microbiome of frequent wine tasters, particularly in those tasting sparkling wines.}, } @article {pmid36595290, year = {2023}, author = {Rovira Rubió, J and Megremis, S and Pasioti, M and Lakoumentas, J and Constantinides, B and Xepapadaki, P and Bachert, C and Finotto, S and Jartti, T and Andreakos, E and Stanic, B and Akdis, CA and Akdis, M and Papadopoulos, NG}, title = {Respiratory virome profiles reflect antiviral immune responses.}, journal = {Allergy}, volume = {78}, number = {5}, pages = {1258-1268}, doi = {10.1111/all.15634}, pmid = {36595290}, issn = {1398-9995}, mesh = {Child, Preschool ; Child ; Humans ; *Antiviral Agents ; Virome ; Leukocytes, Mononuclear ; *Asthma ; Interferons ; Immunity ; }, abstract = {BACKGROUND: From early life, respiratory viruses are implicated in the development, exacerbation and persistence of respiratory conditions such as asthma. Complex dynamics between microbial communities and host immune responses shape immune maturation and homeostasis, influencing health outcomes. We evaluated the hypothesis that the respiratory virome is linked to systemic immune responses, using peripheral blood and nasopharyngeal swab samples from preschool-age children in the PreDicta cohort.

METHODS: Peripheral blood mononuclear cells from 51 children (32 asthmatics and 19 healthy controls) participating in the 2-year multinational PreDicta cohort were cultured with bacterial (Bacterial-DNA, LPS) or viral (R848, Poly:IC, RV) stimuli. Supernatants were analysed by Luminex for the presence of 22 relevant cytokines. Virome composition was obtained using untargeted high throughput sequencing of nasopharyngeal samples. The metagenomic data were used for the characterization of virome profiles and the presence of key viral families (Picornaviridae, Anelloviridae, Siphoviridae). These were correlated to cytokine secretion patterns, identified through hierarchical clustering and principal component analysis.

RESULTS: High spontaneous cytokine release was associated with increased presence of Prokaryotic virome profiles and reduced presence of Eukaryotic and Anellovirus profiles. Antibacterial responses did not correlate with specific viral families or virome profile; however, low antiviral responders had more Prokaryotic and less Eukaryotic virome profiles. Anelloviruses and Anellovirus-dominated profiles were equally distributed among immune response clusters. The presence of Picornaviridae and Siphoviridae was associated with low interferon-λ responses. Asthma or allergy did not modify these correlations.

CONCLUSION: Antiviral cytokine responses at a systemic level reflect the upper airway virome composition. Individuals with low innate interferon responses have higher abundance of Picornaviruses (mostly Rhinoviruses) and bacteriophages. Bacteriophages, particularly Siphoviridae, appear to be sensitive sensors of host antimicrobial capacity, while Anelloviruses are not correlated with TLR-induced immune responses.}, } @article {pmid36593662, year = {2022}, author = {Wu, H and Wang, X and Fang, X and Lian, F and Li, M and Liao, J and Dai, D and Tian, J}, title = {Metformin modulates the gut microbiome in a mice model of high-fat diet-induced glycolipid metabolism disorder.}, journal = {BMJ open diabetes research & care}, volume = {10}, number = {6}, pages = {}, pmid = {36593662}, issn = {2052-4897}, mesh = {Male ; Animals ; Mice ; Diet, High-Fat/adverse effects ; *Metformin/pharmacology ; Glycolipids/pharmacology ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Glucose ; Disease Models, Animal ; }, abstract = {INTRODUCTION: Metformin (MET) can regulate glucose and lipid levels, and the gut microbiota may be involved in the control of metabolism. We hypothesized that MET alleviates glucolipid metabolism disorder by modulating gut microbiota and microbial metabolites.

RESEARCH DESIGN AND METHODS: A total of 24 male C57BL/6 J mice were equally divided into three groups (normal control, model control (MC), and MET-treated groups). Model mice were established by feeding a high-fat diet for 6 weeks. The MET-treated group was administered MET solution (2.5 g/100 mL, 250 mg/kg). Fecal samples were collected to characterize the microbiota system using metagenomic shotgun sequencing and gas chromatography-time of flight-mass spectrometry analysis. Phenotypic and biochemical indices were obtained for further correlation analysis.

RESULTS: Compared with the MC group, MET reduced the levels of weight, glucose, areas under the glucose curve in the glucose tolerance test, triglyceride (TG), and total cholesterol (TC). A decreasing abundance of bacteria, including Parabacteroides distasonis, and an increasing abundance of bacteria, including Bacteroides vulgatus, were observed in the MET-treated group. The 2-deoxytetronic acid declined after MET intervention and was positively correlated with species over-represented in the MC group and negatively correlated with species enriched in the MET-treated group. Additionally, species enriched in the MET-treated group negatively correlated with glucose, areas under the glucose curve in the glucose tolerance test, and TGs. Further, the correlation between the differential metabolites, which decreased after MET intervention, and the phenotypic indices was positive.

CONCLUSIONS: MET-induced restoration of intestinal homeostasis correlates with the amelioration of host glucolipid metabolism.}, } @article {pmid36590585, year = {2022}, author = {Wang, Y and Chen, J and Wang, X and Guo, C and Peng, X and Liu, Y and Li, T and Du, J}, title = {Novel investigations in retinoic-acid-induced cleft palate about the gut microbiome of pregnant mice.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1042779}, pmid = {36590585}, issn = {2235-2988}, mesh = {Pregnancy ; Female ; Mice ; Animals ; Tretinoin/adverse effects ; *Cleft Palate/chemically induced ; *Gastrointestinal Microbiome ; *Microbiota ; }, abstract = {INTRODUCTION: Cleft palate (CP) is one of the most common congenital birth defects in the craniofacial region, retinoic acid (RA) gavage is the most common method for inducing cleft palate model. Although several mechanisms have been proposed to illuminate RA-induced cleft palate during embryonic development, these findings are far from enough. Many efforts remain to be devoted to studying the etiology and pathogenesis of cleft palate. Recent research is gradually shifting the focus to the effect of retinoic acid on gut microbiota. However, few reports focus on the relationship between the occurrence of CP in embryos and gut microbiota.

METHODS: In our research, we used RA to induce cleft palate model for E10.5 the feces of 5 RA-treated pregnant mice and 5 control pregnant mice were respectively metagenomics analysis.

RESULTS: Compared with the control group, Lactobacillus in the gut microbiome the RA group was significantly increased. GO, KEGG and CAZy analysis of differentially unigenes demonstrated the most abundant metabolic pathway in different groups, lipopolysaccharide biosynthesis, and histidine metabolism.

DISCUSSION: Our findings indicated that changes in the maternal gut microbiome palatal development, which might be related to changes in Lactobacillus and These results provide a new direction in the pathogenesis of CP induced by RA.}, } @article {pmid36588603, year = {2023}, author = {Silva, JR and Henrique-Bana, FC and Villas-Bôas, JK and Colombo Pimentel, T and Spinosa, WA and Prudencio, SH}, title = {Maturation of honey from Uruçú-Amarela (Melipona mondury): Metagenomics, metabolomics by NMR [1]H, physicochemical and antioxidant properties.}, journal = {Food chemistry. Molecular sciences}, volume = {6}, number = {}, pages = {100157}, pmid = {36588603}, issn = {2666-5662}, abstract = {The objective of this study was to characterize the microbiota biodiversity of Uruçú-Amarela honey through metagenomics. Furthermore, the impact of maturation temperatures (20 and 30 °C) and time (0-180 days) on the physicochemical and antioxidant properties was investigated. [1]H NMR was performed to verify metabolites formed during maturation. Uruçú-Amarela honey was mainly composed by lactic acid bacteria and osmophilic yeasts of genus Zygosaccharomyces. Maturation at 30 °C led to a higher fermentation activity, resulting in greater carbohydrate consumption, ethanol formation (0.0-0.6 %) and increased acidity (34.78-45.74 meq/kg) over the 180 days. It also resulted in honey with higher brown color (a* 0.7 to 3.89, b* 17.50-25.29) and antioxidant capacity, corroborating that the maturation is a suitable preservation technique for stingless bee honey, because it does not cause negative changes as it extends the shelf life of the stingless bee honey.}, } @article {pmid36587850, year = {2023}, author = {Liu, Y and Teo, SM and Méric, G and Tang, HHF and Zhu, Q and Sanders, JG and Vázquez-Baeza, Y and Verspoor, K and Vartiainen, VA and Jousilahti, P and Lahti, L and Niiranen, T and Havulinna, AS and Knight, R and Salomaa, V and Inouye, M}, title = {The gut microbiome is a significant risk factor for future chronic lung disease.}, journal = {The Journal of allergy and clinical immunology}, volume = {151}, number = {4}, pages = {943-952}, pmid = {36587850}, issn = {1097-6825}, support = {/WT_/Wellcome Trust/United Kingdom ; RG/13/13/30194/BHF_/British Heart Foundation/United Kingdom ; RG/18/13/33946/BHF_/British Heart Foundation/United Kingdom ; BRC-1215-20014/DH_/Department of Health/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; /CSO_/Chief Scientist Office/United Kingdom ; }, mesh = {Adult ; Humans ; *Gastrointestinal Microbiome ; Prospective Studies ; *Pulmonary Disease, Chronic Obstructive ; *Asthma ; Risk Factors ; }, abstract = {BACKGROUND: The gut-lung axis is generally recognized, but there are few large studies of the gut microbiome and incident respiratory disease in adults.

OBJECTIVE: We sought to investigate the association and predictive capacity of the gut microbiome for incident asthma and chronic obstructive pulmonary disease (COPD).

METHODS: Shallow metagenomic sequencing was performed for stool samples from a prospective, population-based cohort (FINRISK02; N = 7115 adults) with linked national administrative health register-derived classifications for incident asthma and COPD up to 15 years after baseline. Generalized linear models and Cox regressions were used to assess associations of microbial taxa and diversity with disease occurrence. Predictive models were constructed using machine learning with extreme gradient boosting. Models considered taxa abundances individually and in combination with other risk factors, including sex, age, body mass index, and smoking status.

RESULTS: A total of 695 and 392 statistically significant associations were found between baseline taxonomic groups and incident asthma and COPD, respectively. Gradient boosting decision trees of baseline gut microbiome abundance predicted incident asthma and COPD in the validation data sets with mean area under the curves of 0.608 and 0.780, respectively. Cox analysis showed that the baseline gut microbiome achieved higher predictive performance than individual conventional risk factors, with C-indices of 0.623 for asthma and 0.817 for COPD. The integration of the gut microbiome and conventional risk factors further improved prediction capacities.

CONCLUSIONS: The gut microbiome is a significant risk factor for incident asthma and incident COPD and is largely independent of conventional risk factors.}, } @article {pmid36587599, year = {2023}, author = {Zhu, G and Chao, H and Sun, M and Jiang, Y and Ye, M}, title = {Toxicity sharing model of earthworm intestinal microbiome reveals shared functional genes are more powerful than species in resisting pesticide stress.}, journal = {Journal of hazardous materials}, volume = {446}, number = {}, pages = {130646}, doi = {10.1016/j.jhazmat.2022.130646}, pmid = {36587599}, issn = {1873-3336}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Oligochaeta/genetics/microbiology ; *Pesticides/toxicity ; *Microbiota ; Bacteria/genetics ; Soil/chemistry ; *Soil Pollutants/analysis ; }, abstract = {Earthworm intestinal bacteria and indigenous soil bacteria work closely during various biochemical processes and play a crucial role in maintaining the internal stability of the soil environment. However, the response mechanism of these bacterial communities to external pesticide disturbance is unknown. In this study, soil and earthworm gut contents were metagenomically sequenced after exposure to various concentrations of nitrochlorobenzene (0-1026.7 mg kg[-1]). A high degree of similarity was found between the microbial community composition and abundance in the worm gut and soil, both of which decreased significantly (P < 0.05) under elevated pesticide stress. The toxicity sharing model (TSM) showed that the toxicity sharing capacity was 97.4-125.7 % and 100.4-130.2 % for Egenes (genes in the worm gut) and Emet(degradation genes in the worm gut) in the earthworm intestinal microbiome, respectively. This indicated that the earthworm intestinal microbiome assisted in relieving the pesticide toxicity of the indigenous soil microbiome. This study showed that the TSM could quantitatively describe the toxic effect of pesticides on the earthworm intestinal microbiome. It provides a new analytical model for investigating the ecological alliance between earthworm intestinal microbiome and indigenous soil microbiome under pesticide stress while contributing a more profound understanding of the potential to use earthworms to mitigate pesticide pollution in soils and develop earthworm-based soil remediation techniques.}, } @article {pmid36585105, year = {2023}, author = {Chen, BY and Lin, WZ and Li, YL and Bi, C and Du, LJ and Liu, Y and Zhou, LJ and Liu, T and Xu, S and Shi, CJ and Zhu, H and Wang, YL and Sun, JY and Liu, Y and Zhang, WC and Lu, HX and Wang, YH and Feng, Q and Chen, FX and Wang, CQ and Tonetti, MS and Zhu, YQ and Zhang, H and Duan, SZ}, title = {Roles of oral microbiota and oral-gut microbial transmission in hypertension.}, journal = {Journal of advanced research}, volume = {43}, number = {}, pages = {147-161}, pmid = {36585105}, issn = {2090-1224}, mesh = {Humans ; Animals ; Mice ; *Gastrointestinal Microbiome/physiology ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; Follow-Up Studies ; Mice, Inbred C57BL ; *Microbiota ; *Hypertension ; *Periodontitis ; }, abstract = {INTRODUCTION: Considerable evidence has linked periodontitis (PD) to hypertension (HTN), but the nature behind this connection is unclear. Dysbiosis of oral microbiota leading to PD is known to aggravate different systematic diseases, but the alteration of oral microbiota in HTN and their impacts on blood pressure (BP) remains to be discovered.

OBJECTIVES: To characterize the alterations of oral and gut microbiota and their roles in HTN.

METHODS: We performed a cross-sectional (95 HTN participants and 39 controls) and a 6-month follow-up study (52 HTN participants and 26 controls) to analyze the roles of oral and gut microbiota in HTN. Saliva, subgingival plaques, and feces were collected for 16S rRNA gene sequencing or metagenomic analysis. C57BL/6J mice were pretreated with antibiotics to deplete gut microbiota, and then transplanted with human saliva by gavage to test the impacts of abnormal oral-gut microbial transmission on HTN.

RESULTS: BP in participants with PD was higher than no PD in both cross-sectional and follow-up cohort. Relative abundances of 14 salivary genera, 15 subgingival genera and 10 gut genera significantly altered in HTN and those of 7 salivary genera, 12 subgingival genera and 6 gut genera significantly correlated with BP. Sixteen species under 5 genera were identified as oral-gut transmitters, illustrating the presence of oral-gut microbial transmission in HTN. Veillonella was a frequent oral-gut transmitter stably enriched in HTN participants of both cross-sectional and follow-up cohorts. Saliva from HTN participants increased BP in hypertensive mice. Human saliva-derived Veillonella successfully colonized in mouse gut, more abundantly under HTN condition.

CONCLUSIONS: PD and oral microbiota are strongly associated with HTN, likely through oral-gut transmission of microbes. Ectopic colonization of saliva-derived Veillonella in the gut may aggravate HTN. Therefore, precise manipulations of oral microbiota and/or oral-gut microbial transmission may be useful strategies for better prevention and treatment of HTN.}, } @article {pmid36585101, year = {2023}, author = {Adi Wicaksono, W and Reisenhofer-Graber, T and Erschen, S and Kusstatscher, P and Berg, C and Krause, R and Cernava, T and Berg, G}, title = {Phyllosphere-associated microbiota in built environment: Do they have the potential to antagonize human pathogens?.}, journal = {Journal of advanced research}, volume = {43}, number = {}, pages = {109-121}, pmid = {36585101}, issn = {2090-1224}, mesh = {Humans ; Bacteria ; *Bacillus ; Plants ; *Microbiota ; }, abstract = {INTRODUCTION: The plant microbiota is known to protect its host against invasion by plant pathogens. Recent studies have indicated that the microbiota of indoor plants is transmitted to the local built environment where it might fulfill yet unexplored functions. A better understanding of the interplay of such microbial communities with human pathogens might provide novel cues related to natural inhibition of them.

OBJECTIVE: We studied the plant microbiota of two model indoor plants, Musa acuminata and Chlorophytum comosum, and their effect on human pathogens. The main objective was to identify mechanisms by which the microbiota of indoor plants inhibits human-pathogenic bacteria.

METHODS: Microbial communities and functioning were investigated using a comprehensive set of experiments and methods combining amplicon and shotgun metagenomic analyses with results from interaction assays.

RESULTS: A diverse microbial community was found to be present on Musa and Chlorophytum grown in different indoor environments; the datasets comprised 1066 bacterial, 1261 fungal, and 358 archaeal ASVs. Bacterial communities were specific for each plant species, whereas fungal and archaeal communities were primarily shaped by the built environment. Sphingomonas and Bacillus were found to be prevalent components of a ubiquitous core microbiome in the two model plants; they are well-known for antagonistic activity towards plant pathogens. Interaction assays indicated that they can also antagonize opportunistic human pathogens. Moreover, the native plant microbiomes harbored a broad spectrum of biosynthetic gene clusters, and in parallel, a variety of antimicrobial resistance genes. By conducting comparative metagenomic analyses between plants and abiotic surfaces, we found that the phyllosphere microbiota harbors features that are clearly distinguishable from the surrounding abiotic surfaces.

CONCLUSIONS: Naturally occurring phyllosphere bacteria can potentially act as a protective shield against opportunistic human pathogens. This knowledge and the underlying mechanisms can provide an important basis to establish a healthy microbiome in built environments.}, } @article {pmid36584949, year = {2023}, author = {Fraser, MW and Martin, BC and Wong, HL and Burns, BP and Kendrick, GA}, title = {Sulfide intrusion in a habitat forming seagrass can be predicted from relative abundance of sulfur cycling genes in sediments.}, journal = {The Science of the total environment}, volume = {864}, number = {}, pages = {161144}, doi = {10.1016/j.scitotenv.2022.161144}, pmid = {36584949}, issn = {1879-1026}, mesh = {*Geologic Sediments ; Ecosystem ; Sulfides ; Sulfur ; Australia ; *Microbiota ; }, abstract = {Sulfide intrusion from sediments is an increasingly recognized contributor to seagrass declines globally, yet the relationship between sediment microorganisms and sulfide intrusion has received little attention. Here, we use metagenomic sequencing and stable isotope ([34]S) analysis to examine this relationship in Cockburn Sound, Australia, a seagrass-dominated embayment with a gradient of sulfide stress and seagrass declines. There was a significant positive relationship between sulfide intrusion into seagrasses and sulfate reduction genes in sediment microbial communities, which was greatest at sites with long term seagrass declines. This is the first demonstration of a significant link between sulfur cycling genes present in seagrass sediments and sulfide intrusion in a habitat-forming seagrass that is experiencing long-term shoot density decline. Given that microorganisms respond rapidly to environmental change, the quantitative links established in this study can be used as a potential management tool to enable the prediction of sulfide stress on large habitat forming seagrasses; a global issue expected to worsen with climate change.}, } @article {pmid36584858, year = {2023}, author = {Tang, F and Li, Q and Yue, J and Ge, F and Li, F and Liu, Y and Zhang, D and Tian, J}, title = {Penicillium oxalicum augments soil lead immobilization by affecting indigenous microbial community structure and inorganic phosphate solubilization potential during microbial-induced phosphate precipitation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {319}, number = {}, pages = {120953}, doi = {10.1016/j.envpol.2022.120953}, pmid = {36584858}, issn = {1873-6424}, mesh = {Phosphates/chemistry ; Soil/chemistry ; Lead ; *Penicillium ; Soil Microbiology ; *Soil Pollutants/chemistry ; *Microbiota ; Durapatite ; }, abstract = {Phosphate-solubilizing microorganisms (PSMs) are critically important for increasing soil phosphate (P) and decreasing lead (Pb) bioavailability during microbial-induced phosphate precipitation (MIPP). However, their relative contributions to the indigenous soil microbial communities and P-cycling genes during the MIPP process remain unclear. In this study, inoculation of the PSM P. oxalicum in hydroxyapatite-cultured and Pb-contaminated soil increased soil phosphatase activities, available P (AP) concentrations and reduced available Pb levels. Metagenomics revealed a 3.9-44.0% increase in the abundance of P-cycling genes by P. oxalicum inoculation. No P-cycling genes were assigned to Penicillium. While P. oxalicum increased the complexity of microbial community co-occurrence networks, and improved the directly interrelationships between Penicillium and genera containing P-cycling gene. These results suggesting that P. oxalicum obviously positively affected the regulation of indigenous P-cycling functional communities during the MIPP process. Inorganic P solubilization genes (gcd, ppa, and ppx) have been shown to affect soil AP, suggesting that inorganic P solubilization is the major driver of Pb immobilization improvement following P. oxalicum inoculation. These results enhance our understanding of the significant ecological role of PSMs in governing soil P-cycling and alleviating Pb[2+] biotoxicity during the MIPP process.}, } @article {pmid36584150, year = {2022}, author = {Nakamura, S and Yumioka, J and Kachi, S and Baba, Y and Kawai, S}, title = {Bacterial and fungal gut microbiota of supralittoral talitrid amphipods feeding on brown macroalgae and paper.}, journal = {PloS one}, volume = {17}, number = {12}, pages = {e0279834}, pmid = {36584150}, issn = {1932-6203}, mesh = {Animals ; *Seaweed/metabolism ; *Gastrointestinal Microbiome ; *Amphipoda/metabolism ; Ecosystem ; Bacteria/genetics/metabolism ; Alginates/metabolism ; }, abstract = {Some macroalgae drift on the ocean and are stranded on coasts, and these stranded brown macroalgae are regarded to be degraded by organisms. Alginate is a major component of brown macroalgae. An uncovering of how carbon is cycled through brown macroalgae is needed to deeply understand coastal ecosystems. In this study, to gain insights into metabolism of brown macroalgae and alginate in the organisms, we initially confirmed that supralittoral talitrid amphipods (beach fleas or sandhoppers collected on the Shibagaki coast in Ishikawa Prefecture, Japan) fed on the brown macroalgae. We then isolated bacteria such as Vibrio sp. with alginate-assimilating capability from the gut of the amphipods. Metagenomic analysis of the gut of amphipods housed in several conditions (e.g. macroalgae or paper as feed, non-sterilized or sterilized environment) showed no condition-dependent compositions of bacteria and fungi, but Vibrio sp. were detected at high frequency, in good agreement with the isolation of Vibrio sp. An intervention study using antibiotics showed that amphipods fed on algae or paper at about the same rate in the presence or absence of antibiotics, and that the antibiotics had no effects on the life span. Moreover, intervention with antibiotics completely killed Vibrio sp. and some other bacteria, and had significant effects on the composition of the flora in the gut, with elimination of the variations observed in the guts of amphipods housed without antibiotics. These data suggest that microbes that were killed by antibiotics, including Vibrio sp., in the gut of talitrid amphipods are not essential for assimilation of brown macroalgae.}, } @article {pmid36583859, year = {2022}, author = {Lau, HCH and Yu, J}, title = {Uncovering novel human gut virome using ultra-deep metagenomic sequencing.}, journal = {Chinese medical journal}, volume = {135}, number = {20}, pages = {2395-2397}, pmid = {36583859}, issn = {2542-5641}, mesh = {Humans ; *Virome ; *Bacteriophages ; Feces ; Metagenome ; Metagenomics ; }, } @article {pmid36583109, year = {2022}, author = {Szabó, BG and Kiss, R and Makra, N and Pénzes, K and Vad, E and Kamotsay, K and Szabó, D and Ostorházi, E}, title = {Composition and changes of blood microbiota in adult patients with community-acquired sepsis: A pilot study from bench to bedside.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1067476}, pmid = {36583109}, issn = {2235-2988}, mesh = {Humans ; Adult ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Sepsis/microbiology ; Metagenome ; }, abstract = {BACKGROUND: Characteristics of the blood microbiota among adult patients with community-acquired sepsis are poorly understood. Our aim was to analyze the composition of blood microbiota in adult patients with community-acquired sepsis, and correlate changes with non-septic control patients.

METHODS: A prospective observational study was carried out by including adult patients hospitalized for community-acquired sepsis at our center between January and November 2019, by random selection from a pool of eligible patients. Study inclusion was done on the day of sepsis diagnosis. Community acquisition was ascertained by a priori exclusion criteria; sepsis was defined according to the SEPSIS-3 definitions. Each included patient was matched with non-septic control patients by age and gender in a 1:1 fashion enrolled from the general population. Conventional culturing with BacT/ALERT system and 16S rRNA microbiota analysis were performed from blood samples taken in a same time from a patient. Abundance data was analyzed by the CosmosID HUB Microbiome software.

RESULTS: Altogether, 13 hospitalized patients were included, 6/13 (46.2%) with sepsis and 7/13 (53.8%) with septic shock at diagnosis. The most prevalent etiopathogen isolated from blood cultures was Escherichia coli, patients mostly had intraabdominal septic source. At day 28, all-cause mortality was 15.4% (2/13). Compared to non-septic control patients, a relative scarcity of Faecalibacterium, Blautia, Coprococcus and Roseburia genera, with an abundance of Enhydrobacter, Pseudomonas and Micrococcus genera was observed among septic patients. Relative differences between septic vs. non-septic patients were more obvious at the phylum level, mainly driven by Firmicutes (25.7% vs. 63.1%; p<0.01) and Proteobacteria (36.9% vs. 16.6%; p<0.01). The alpha diversity, quantified by the Chao1 index showed statistically significant difference between septic vs. non-septic patients (126 ± 51 vs. 66 ± 26; p<0.01). The Bray-Curtis beta diversity, reported by principal coordinate analysis of total hit frequencies, revealed 2 potentially separate clusters among septic vs. non-septic patients.

CONCLUSION: In adult patients with community-acquired sepsis, specific changes in the composition and abundance of blood microbiota could be detected by 16S rRNA metagenome sequencing, compared to non-septic control patients. Traditional blood culture results only partially correlate with microbiota test results.}, } @article {pmid36581858, year = {2022}, author = {Huang, Y and Lu, W and Zeng, M and Hu, X and Su, Z and Liu, Y and Liu, Z and Yuan, J and Li, L and Zhang, X and Huang, L and Hu, W and Wang, X and Li, S and Zhang, H}, title = {Mapping the early life gut microbiome in neonates with critical congenital heart disease: multiomics insights and implications for host metabolic and immunological health.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {245}, pmid = {36581858}, issn = {2049-2618}, mesh = {Infant, Newborn ; Humans ; *Gastrointestinal Microbiome/genetics ; Multiomics ; Inflammation ; Bacteria ; *Heart Defects, Congenital ; Dysbiosis/microbiology ; }, abstract = {BACKGROUND: The early life gut microbiome is crucial in maintaining host metabolic and immune homeostasis. Though neonates with critical congenital heart disease (CCHD) are at substantial risks of malnutrition and immune imbalance, the microbial links to CCHD pathophysiology remain poorly understood. In this study, we aimed to investigate the gut microbiome in neonates with CCHD in association with metabolomic traits. Moreover, we explored the clinical implications of the host-microbe interactions in CCHD.

METHODS: Deep metagenomic sequencing and metabolomic profiling of paired fecal samples from 45 neonates with CCHD and 50 healthy controls were performed. The characteristics of gut microbiome were investigated in three dimensions (microbial abundance, functionality, and genetic variation). An in-depth analysis of gut virome was conducted to elucidate the ecological interaction between gut viral and bacterial communities. Correlations between multilevel microbial features and fecal metabolites were determined using integrated association analysis. Finally, we conducted a subgroup analysis to examine whether the interactions between gut microbiota and metabolites could mediate inflammatory responses and poor surgical prognosis.

RESULTS: Gut microbiota dysbiosis was observed in neonates with CCHD, characterized by the depletion of Bifidobacterium and overgrowth of Enterococcus, which was highly correlated with metabolomic perturbations. Genetic variations of Bifidobacterium and Enterococcus orchestrate the metabolomic perturbations in CCHD. A temperate core virome represented by Siphoviridae was identified to be implicated in shaping the gut bacterial composition by modifying microbial adaptation. The overgrowth of Enterococcus was correlated with systemic inflammation and poor surgical prognosis in subgroup analysis. Mediation analysis indicated that the overgrowth of Enterococcus could mediate gut barrier impairment and inflammatory responses in CCHD.

CONCLUSIONS: We demonstrate for the first time that an aberrant gut microbiome associated with metabolomic perturbations is implicated in immune imbalance and adverse clinical outcomes in neonates with CCHD. Our data support the importance of reconstituting optimal gut microbiome in maintaining host metabolic and immunological homeostasis in CCHD. Video Abstract.}, } @article {pmid36581612, year = {2022}, author = {Li, R and Wang, Y and Hu, H and Tan, Y and Ma, Y}, title = {Metagenomic analysis reveals unexplored diversity of archaeal virome in the human gut.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7978}, pmid = {36581612}, issn = {2041-1723}, mesh = {Humans ; Archaea/genetics ; Metagenome/genetics ; Virome ; *Viruses/genetics ; Metagenomics ; *Archaeal Viruses/genetics ; }, abstract = {The human gut microbiome has been extensively explored, while the archaeal viruses remain largely unknown. Here, we present a comprehensive analysis of the archaeal viruses from the human gut metagenomes and the existing virus collections using the CRISPR spacer and viral signature-based approach. This results in 1279 viral species, of which, 95.2% infect Methanobrevibacteria_A, 56.5% shared high identity (>95%) with the archaeal proviruses, 37.2% have a host range across archaeal species, and 55.7% are highly prevalent in the human population (>1%). A methanogenic archaeal virus-specific gene for pseudomurein endoisopeptidase (PeiW) frequently occurs in the viral sequences (n = 150). Analysis of 33 Caudoviricetes viruses with a complete genome often discovers the genes (integrase, n = 29; mazE, n = 10) regulating the viral lysogenic-lytic cycle, implying the dominance of temperate viruses in the archaeal virome. Together, our work uncovers the unexplored diversity of archaeal viruses, revealing the novel facet of the human gut microbiome.}, } @article {pmid36580984, year = {2023}, author = {Xu, L and Yang, Y and Su, J and He, C and Shi, J and Yan, H and Wei, H}, title = {Simultaneous removal of nitrate, lead, and tetracycline by a fixed-biofilm reactor assembled with kapok fiber and sponge iron: Comparative analysis of operating conditions and biotic community.}, journal = {Environmental research}, volume = {219}, number = {}, pages = {115163}, doi = {10.1016/j.envres.2022.115163}, pmid = {36580984}, issn = {1096-0953}, mesh = {*Nitrates ; *Iron ; Lead ; Tetracycline ; Anti-Bacterial Agents ; Biofilms ; Carbon ; Biota ; Bioreactors ; Nitrogen ; }, abstract = {In recent years, under the condition of lack of carbon source, the presence of composite micro-pollutants make the removal of nitrate seriously damaged, and to find a suitable way to solve this problem is imminent. A fixed-biofilm carrier modified by mixing sponge iron (SI) and kapok fiber (KF) combined with strain Zoogloea sp. FY6 was constructed in this study to get a fixed-biofilm reactor with merit denitrification performance. By adjusting the operation parameters, it can be concluded that when the carbon to nitrogen (C/N) ratio was 1.5, the hydraulic retention time (HRT) was 6.0 h, and the pH was 6.0, the nitrate removal efficiency (NRE) of the fixed-biofilm reactor was up to 95.4% (2.95 mg L[-1] h[-1]). In addition, the fixed-biofilm reactor constructed in this study can remove lead (Pb[2+]) and tetracycline (TC) excellently in the presence of SI and Zoogloea sp. FY6, and the denitrification performance can still maintain a high level under the influence of different concentrations of Pb[2+] and TC. Furthermore, the addition of SI not only removes the compound pollutants, but also protects the toxicity of the pollutant inflow in the bioreactor, and the metabolic process of microorganisms in the bioreactor also removes some of the compound pollutants. The high-throughput data showed the abundance of strain Zoogloea sp. FY6 was still the highest value under the influence of various pollutants, and the metagenomic prediction showed that the fixed-biofilm reactor had perfect denitrification process and iron redox cycle benefits. This study provides a valuable reference for sustainable utilization of natural biological resources and reduction of material costs in wastewater treatment plants (WWTPs).}, } @article {pmid36580779, year = {2023}, author = {Tao, Y and Shen, L and Han, S and Li, Z and Cui, Y and Lin, Y and Qu, J and Zhang, Y}, title = {Metagenomic study of carbon metabolism in black soil microbial communities under lead-lanthanum stress.}, journal = {Journal of hazardous materials}, volume = {446}, number = {}, pages = {130666}, doi = {10.1016/j.jhazmat.2022.130666}, pmid = {36580779}, issn = {1873-3336}, mesh = {Soil/chemistry ; Lanthanum ; Lead/toxicity ; *Metals, Heavy/analysis ; *Microbiota ; *Soil Pollutants/metabolism ; Soil Microbiology ; }, abstract = {Pollution of soil environments with heavy metals (HMs) and rare earth elements (REEs) cannot be ignored. We aimed to determine the effects of lead combined with lanthanum (Pb-La) on microbial community structure, carbon metabolism, and differences in carbon source utilization in black soils using EcoPlates™ and a macrogenomic approach. We found that Pb and La contents and the microbial community structure together influence and shape the response of soil carbon metabolism to Pb-La. Compared with controls, microorganisms under pollution stress preferentially use phenolic and carboxylic acids as growth carbon sources. Under Pb-La stress, the relative abundance of Proteobacteria significantly increased, thereby selectively displacing heavy metal-sensitive phyla, such as Chloroflexi, Acidobacteria, and Thaumarchaeota. Altered functional potential of the microbial carbon cycle manifested as differences in carbon metabolism, methane metabolism, and carbon fixation pathways. Furthermore, an appropriate concentration of La can reduce the environmental toxicity of Pb, whereas a high concentration of La has synergistic toxicity with Pb. These findings have important implications for understanding the impact of HM-REE contamination in microbial communities and the functions associated with carbon metabolism in black soils.}, } @article {pmid36578059, year = {2022}, author = {Kunath, BJ and Hickl, O and Queirós, P and Martin-Gallausiaux, C and Lebrun, LA and Halder, R and Laczny, CC and Schmidt, TSB and Hayward, MR and Becher, D and Heintz-Buschart, A and de Beaufort, C and Bork, P and May, P and Wilmes, P}, title = {Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {243}, pmid = {36578059}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 1/microbiology ; Proteomics ; Multiomics ; *Microbiota/genetics ; Mouth/microbiology ; Enterobacteriaceae ; }, abstract = {BACKGROUND: Alterations to the gut microbiome have been linked to multiple chronic diseases. However, the drivers of such changes remain largely unknown. The oral cavity acts as a major route of exposure to exogenous factors including pathogens, and processes therein may affect the communities in the subsequent compartments of the gastrointestinal tract. Here, we perform strain-resolved, integrated meta-genomic, transcriptomic, and proteomic analyses of paired saliva and stool samples collected from 35 individuals from eight families with multiple cases of type 1 diabetes mellitus (T1DM).

RESULTS: We identified distinct oral microbiota mostly reflecting competition between streptococcal species. More specifically, we found a decreased abundance of the commensal Streptococcus salivarius in the oral cavity of T1DM individuals, which is linked to its apparent competition with the pathobiont Streptococcus mutans. The decrease in S. salivarius in the oral cavity was also associated with its decrease in the gut as well as higher abundances in facultative anaerobes including Enterobacteria. In addition, we found evidence of gut inflammation in T1DM as reflected in the expression profiles of the Enterobacteria as well as in the human gut proteome. Finally, we were able to follow transmitted strain-variants from the oral cavity to the gut at the individual omic levels, highlighting not only the transfer, but also the activity of the transmitted taxa along the gastrointestinal tract.

CONCLUSIONS: Alterations of the oral microbiome in the context of T1DM impact the microbial communities in the lower gut, in particular through the reduction of "mouth-to-gut" transfer of Streptococcus salivarius. Our results indicate that the observed oral-cavity-driven gut microbiome changes may contribute towards the inflammatory processes involved in T1DM. Through the integration of multi-omic analyses, we resolve strain-variant "mouth-to-gut" transfer in a disease context. Video Abstract.}, } @article {pmid36576579, year = {2022}, author = {Bora, SS and Hazarika, DJ and Churaman, A and Naorem, RS and Dasgupta, A and Chakrabarty, R and Kalita, H and Barooah, M}, title = {Common scab disease-induced changes in geocaulosphere microbiome assemblages and functional processes in landrace potato (Solanum tuberosum var. Rongpuria) of Assam, India.}, journal = {Archives of microbiology}, volume = {205}, number = {1}, pages = {44}, pmid = {36576579}, issn = {1432-072X}, mesh = {*Solanum tuberosum ; Plant Diseases ; Soil Microbiology ; *Microbiota ; India ; }, abstract = {Common scab (CS) caused by pathogenic Streptomyces spp. plays a decisive role in the qualitative and quantitative production of potatoes worldwide. Although the CS pathogen is present in Assam's soil, disease signs and symptoms are less obvious in the landrace Rongpuria potatoes that indicate an interesting interaction between the plant and the geocaulosphere microbial population. Toward this, a comparative metagenomics study was performed to elucidate the geocaulosphere microbiome assemblages and functions of low CS-severe (LSG) and moderately severe (MSG) potato plants. Alpha diversity indices showed that CS occurrence modulated microbiome composition and decreased overall microbial abundances. Functional analysis involving cluster of orthologous groups (COG) too confirmed reduced microbial metabolism under disease incidence. The top-three most dominant genera were Pseudomonas (relative abundance: 2.79% in LSG; 12.31% in MSG), Streptomyces (2.55% in LSG; 5.28% in MSG), and Pantoea (2.30% in LSG; 3.51% in MSG). As shown by the high Pielou's J evenness index, the potato geocaulosphere core microbiome was adaptive and resilient to CS infection. The plant growth-promoting traits and potential antagonistic activity of major taxa (Pseudomonads, non-pathogenic Streptomyces spp., and others) against the CS pathogen, i.e., Streptomyces scabiei, point toward selective microbial recruitment and colonization strategy by the plants to its own advantage. KEGG Orthology analysis showed that the CS infection resulted in high abundances of ATP-binding cassette transporters and a two-component system, ubiquitous to the transportation and regulation of metabolites. As compared to the LSG metagenome, the MSG counterpart had a higher representation of important PGPTs related to 1-aminocyclopropane-1-carboxylate deaminase, IAA production, betaine utilization, and siderophore production.}, } @article {pmid36576106, year = {2023}, author = {Dhariwal, A and Haugli Bråten, LC and Sturød, K and Salvadori, G and Bargheet, A and Åmdal, H and Junges, R and Berild, D and Zwart, JA and Storheim, K and Petersen, FC}, title = {Differential response to prolonged amoxicillin treatment: long-term resilience of the microbiome versus long-lasting perturbations in the gut resistome.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2157200}, pmid = {36576106}, issn = {1949-0984}, mesh = {Humans ; Amoxicillin/pharmacology/therapeutic use ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Microbiota ; Feces ; }, abstract = {The collateral impact of antibiotics on the microbiome has attained increasing attention. However, the ecological consequences of long-term antibiotic exposure on the gut microbiome, including antibiotic resistance, are still limited. Here, we investigated long-term exposure effects to amoxicillin on the human gut microbiome and resistome. Fecal samples were collected from 20 patients receiving 3-months of amoxicillin or placebo treatment as part of a Norwegian multicenter clinical trial on chronic low back pain (AIM study). Samples were collected at baseline, last day of treatment, and 9 months after antibiotic cessation. The abundance and diversity of microbial and resistome composition were characterized using whole shotgun and functional metagenomic sequencing data. While the microbiome profiles of placebo subjects were stable over time, discernible changes in diversity and overall microbiome composition were observed after amoxicillin treatment. In particular, health-associated short-chain fatty acid producing species significantly decreased in proportion. However, these changes were short-lived as the microbiome showed overall recovery 9 months post-treatment. On the other hand, exposure to long-term amoxicillin was associated with an increase in total antimicrobial resistance gene load and diversity of antimicrobial resistance genes, with persistent changes even at 9 months post-treatment. Additionally, beta-lactam resistance was the most affected antibiotic class, suggesting a targeted response to amoxicillin, although changes at the gene level varied across individuals. Overall, our results suggest that the impact of prolonged amoxicillin exposure was more explicit and long-lasting in the fecal resistome than in microbiome composition. Such information is relevant for designing rational administration guidelines for antibiotic therapies.}, } @article {pmid36575453, year = {2022}, author = {Barone, M and Garelli, S and Rampelli, S and Agostini, A and Matysik, S and D'Amico, F and Krautbauer, S and Mazza, R and Salituro, N and Fanelli, F and Iozzo, P and Sanz, Y and Candela, M and Brigidi, P and Pagotto, U and Turroni, S}, title = {Multi-omics gut microbiome signatures in obese women: role of diet and uncontrolled eating behavior.}, journal = {BMC medicine}, volume = {20}, number = {1}, pages = {500}, pmid = {36575453}, issn = {1741-7015}, support = {613979//Seventh Framework Programme/ ; 245009//Seventh Framework Programme/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Multiomics ; Obesity/genetics ; Diet ; Feeding Behavior/physiology ; Feces/microbiology ; }, abstract = {BACKGROUND: Obesity and related co-morbidities represent a major health challenge nowadays, with a rapidly increasing incidence worldwide. The gut microbiome has recently emerged as a key modifier of human health that can affect the development and progression of obesity, largely due to its involvement in the regulation of food intake and metabolism. However, there are still few studies that have in-depth explored the functionality of the human gut microbiome in obesity and even fewer that have examined its relationship to eating behaviors.

METHODS: In an attempt to advance our knowledge of the gut-microbiome-brain axis in the obese phenotype, we thoroughly characterized the gut microbiome signatures of obesity in a well-phenotyped Italian female cohort from the NeuroFAST and MyNewGut EU FP7 projects. Fecal samples were collected from 63 overweight/obese and 37 normal-weight women and analyzed via a multi-omics approach combining 16S rRNA amplicon sequencing, metagenomics, metatranscriptomics, and lipidomics. Associations with anthropometric, clinical, biochemical, and nutritional data were then sought, with particular attention to cognitive and behavioral domains of eating.

RESULTS: We identified four compositional clusters of the gut microbiome in our cohort that, although not distinctly associated with weight status, correlated differently with eating habits and behaviors. These clusters also differed in functional features, i.e., transcriptional activity and fecal metabolites. In particular, obese women with uncontrolled eating behavior were mostly characterized by low-diversity microbial steady states, with few and poorly interconnected species (e.g., Ruminococcus torques and Bifidobacterium spp.), which exhibited low transcriptional activity, especially of genes involved in secondary bile acid biosynthesis and neuroendocrine signaling (i.e., production of neurotransmitters, indoles and ligands for cannabinoid receptors). Consistently, high amounts of primary bile acids as well as sterols were found in their feces.

CONCLUSIONS: By finding peculiar gut microbiome profiles associated with eating patterns, we laid the foundation for elucidating gut-brain axis communication in the obese phenotype. Subject to confirmation of the hypotheses herein generated, our work could help guide the design of microbiome-based precision interventions, aimed at rewiring microbial networks to support a healthy diet-microbiome-gut-brain axis, thus counteracting obesity and related complications.}, } @article {pmid36575246, year = {2022}, author = {Bornbusch, SL and Clarke, TA and Hobilalaina, S and Reseva, HS and LaFleur, M and Drea, CM}, title = {Microbial rewilding in the gut microbiomes of captive ring-tailed lemurs (Lemur catta) in Madagascar.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {22388}, pmid = {36575246}, issn = {2045-2322}, mesh = {Animals ; Humans ; *Lemur ; *Gastrointestinal Microbiome/genetics ; Madagascar ; Diet ; Ecosystem ; *Strepsirhini ; }, abstract = {Microbial rewilding, whereby exposure to naturalistic environments can modulate or augment gut microbiomes and improve host-microbe symbiosis, is being harnessed as an innovative approach to human health, one that may also have significant value to animal care and conservation. To test for microbial rewilding in animal microbiomes, we used a unique population of wild-born ring-tailed lemurs (Lemur catta) that were initially held as illegal pets in unnatural settings and, subsequently, relocated to a rescue center in Madagascar where they live in naturalistic environments. Using amplicon and shotgun metagenomic sequencing of lemur and environmental microbiomes, we found multiple lines of evidence for microbial rewilding in lemurs that were transitioned from unnatural to naturalistic environments: A lemur's duration of exposure to naturalistic settings significantly correlated with (a) increased compositional similarly to the gut communities of wild lemurs, (b) decreased proportions of antibiotic resistance genes that were likely acquired via human contact during pethood, and (c) greater covariation with soil microbiomes from natural habitats. Beyond the inherent psychosocial value of naturalistic environments, we find that actions, such as providing appropriate diets, minimizing contact with humans, and increasing exposure to natural environmental consortia, may assist in maximizing host-microbe symbiosis in animals under human care.}, } @article {pmid36572924, year = {2022}, author = {Zhou, Z and St John, E and Anantharaman, K and Reysenbach, AL}, title = {Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {241}, pmid = {36572924}, issn = {2049-2618}, mesh = {Humans ; *Hydrothermal Vents/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Bacteria ; Archaea ; *Microbiota/genetics ; Sulfur/metabolism ; Carbon/metabolism ; Nitrogen/metabolism ; Hydrogen/metabolism ; }, abstract = {BACKGROUND: When deep-sea hydrothermal fluids mix with cold oxygenated fluids, minerals precipitate out of solution and form hydrothermal deposits. These actively venting deep-sea hydrothermal deposits support a rich diversity of thermophilic microorganisms which are involved in a range of carbon, sulfur, nitrogen, and hydrogen metabolisms. Global patterns of thermophilic microbial diversity in deep-sea hydrothermal ecosystems have illustrated the strong connectivity between geological processes and microbial colonization, but little is known about the genomic diversity and physiological potential of these novel taxa. Here we explore this genomic diversity in 42 metagenomes from four deep-sea hydrothermal vent fields and a deep-sea volcano collected from 2004 to 2018 and document their potential implications in biogeochemical cycles.

RESULTS: Our dataset represents 3635 metagenome-assembled genomes encompassing 511 novel and recently identified genera from deep-sea hydrothermal settings. Some of the novel bacterial (107) and archaeal genera (30) that were recently reported from the deep-sea Brothers volcano were also detected at the deep-sea hydrothermal vent fields, while 99 bacterial and 54 archaeal genera were endemic to the deep-sea Brothers volcano deposits. We report some of the first examples of medium- (≥ 50% complete, ≤ 10% contaminated) to high-quality (> 90% complete, < 5% contaminated) MAGs from phyla and families never previously identified, or poorly sampled, from deep-sea hydrothermal environments. We greatly expand the novel diversity of Thermoproteia, Patescibacteria (Candidate Phyla Radiation, CPR), and Chloroflexota found at deep-sea hydrothermal vents and identify a small sampling of two potentially novel phyla, designated JALSQH01 and JALWCF01. Metabolic pathway analysis of metagenomes provides insights into the prevalent carbon, nitrogen, sulfur, and hydrogen metabolic processes across all sites and illustrates sulfur and nitrogen metabolic "handoffs" in community interactions. We confirm that Campylobacteria and Gammaproteobacteria occupy similar ecological guilds but their prevalence in a particular site is driven by shifts in the geochemical environment.

CONCLUSION: Our study of globally distributed hydrothermal vent deposits provides a significant expansion of microbial genomic diversity associated with hydrothermal vent deposits and highlights the metabolic adaptation of taxonomic guilds. Collectively, our results illustrate the importance of comparative biodiversity studies in establishing patterns of shared phylogenetic diversity and physiological ecology, while providing many targets for enrichment and cultivation of novel and endemic taxa. Video Abstract.}, } @article {pmid36571495, year = {2023}, author = {Sun, M and Yuan, S and Xia, R and Ye, M and Balcázar, JL}, title = {Underexplored viral auxiliary metabolic genes in soil: Diversity and eco-evolutionary significance.}, journal = {Environmental microbiology}, volume = {25}, number = {4}, pages = {800-810}, doi = {10.1111/1462-2920.16329}, pmid = {36571495}, issn = {1462-2920}, mesh = {Genes, Viral ; *Bacteriophages/genetics ; Biological Evolution ; Bacteria/metabolism ; *Microbiota/genetics ; Soil ; }, abstract = {Bacterial viruses are the most abundant biological entities in soil ecosystems. Owing to the advent of metagenomics and viromics approaches, an ever-increasing diversity of virus-encoded auxiliary metabolic genes (AMGs) have been identified in soils, including those involved in the transformation of carbon, phosphorus, and sulfur, degradation of organic pollutants, and antibiotic resistance, among other processes. These viral AMGs can alter soil biogeochemical processes and metabolic activities by interfering with bacterial host metabolism. It is recognized that viral AMGs compensate for host bacterial metabolism outputs by encoding accessory functional genes and are favourable for the hosts' adaptation to stressed soil environments. The eco-evolutionary mechanisms behind this fascinating diversity of viral AMGs in soil microbiomes have begun to emerge, such as horizontal gene transfer, lytic-lysogenic conversion, and single-nucleotide polymorphisms. In this mini-review, we summarize recent advances in the diversity and function of virus-encoded AMGs in the soil environment, especially focusing on the evolutionary significance of AMGs involved in virus-host interactions. This mini-review also sheds light on the existing gaps and future perspectives that could have major significance for viral AMGs research in soils.}, } @article {pmid36567334, year = {2022}, author = {Blostein, F and Bhaumik, D and Davis, E and Salzman, E and Shedden, K and Duhaime, M and Bakulski, KM and McNeil, DW and Marazita, ML and Foxman, B}, title = {Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {240}, pmid = {36567334}, issn = {2049-2618}, support = {F31 DE029992/DE/NIDCR NIH HHS/United States ; P30 ES017885/ES/NIEHS NIH HHS/United States ; R01 DE014899/DE/NIDCR NIH HHS/United States ; T32 HG000040/HG/NHGRI NIH HHS/United States ; }, mesh = {Child ; Child, Preschool ; Humans ; Infant ; Case-Control Studies ; *Dental Caries/epidemiology/microbiology ; Membrane Transport Proteins ; *Microbiota/genetics ; *Saliva/microbiology ; *Streptococcus mutans/genetics/isolation & purification ; }, abstract = {BACKGROUND: Early childhood caries (ECC)-dental caries (cavities) occurring in primary teeth up to age 6 years-is a prevalent childhood oral disease with a microbial etiology. Streptococcus mutans was previously considered a primary cause, but recent research promotes the ecologic hypothesis, in which a dysbiosis in the oral microbial community leads to caries. In this incident, density sampled case-control study of 189 children followed from 2 months to 5 years, we use the salivary bacteriome to (1) prospectively test the ecological hypothesis of ECC in salivary bacteriome communities and (2) identify co-occurring salivary bacterial communities predicting future ECC.

RESULTS: Supervised classification of future ECC case status using salivary samples from age 12 months using bacteriome-wide data (AUC-ROC 0.78 95% CI (0.71-0.85)) predicts future ECC status before S. mutans can be detected. Dirichlet multinomial community state typing and co-occurrence network analysis identified similar robust and replicable groups of co-occurring taxa. Mean relative abundance of a Haemophilus parainfluenzae/Neisseria/Fusobacterium periodonticum group was lower in future ECC cases (0.14) than controls (0.23, P value < 0.001) in pre-incident visits, positively correlated with saliva pH (Pearson rho = 0.33, P value < 0.001) and reduced in individuals who had acquired S. mutans by the next study visit (0.13) versus those who did not (0.20, P value < 0.01). In a subset of whole genome shotgun sequenced samples (n = 30), case plaque had higher abundances of antibiotic production and resistance gene orthologs, including a major facilitator superfamily multidrug resistance transporter (MFS DHA2 family PBH value = 1.9 × 10[-28]), lantibiotic transport system permease protein (PBH value = 6.0 × 10[-6]) and bacitracin synthase I (PBH value = 5.6 × 10[-6]). The oxidative phosphorylation KEGG pathway was enriched in case plaque (PBH value = 1.2 × 10[-8]), while the ABC transporter pathway was depleted (PBH value = 3.6 × 10[-3]).

CONCLUSIONS: Early-life bacterial interactions predisposed children to ECC, supporting a time-dependent interpretation of the ecological hypothesis. Bacterial communities which assemble before 12 months of age can promote or inhibit an ecological succession to S. mutans dominance and cariogenesis. Intragenera competitions and intergenera cooperation between oral taxa may shape the emergence of these communities, providing points for preventive interventions. Video Abstract.}, } @article {pmid36566300, year = {2022}, author = {Abed, JY and Godon, T and Mehdaoui, F and Plante, PL and Boissinot, M and Bergeron, MG and Bélanger, RE and Muckle, G and Poliakova, N and Ayotte, P and Corbeil, J and Rousseau, E}, title = {Gut metagenome profile of the Nunavik Inuit youth is distinct from industrial and non-industrial counterparts.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1415}, pmid = {36566300}, issn = {2399-3642}, mesh = {Humans ; Adolescent ; Young Adult ; Adult ; *Metagenome ; Inuit/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; }, abstract = {Comparative metagenomics studies have highlighted differences in microbiome community structure among human populations over diverse lifestyles and environments. With their unique environmental and historical backgrounds, Nunavik Inuit have a distinctive gut microbiome with undocumented health-related implications. Using shotgun metagenomics, we explored the taxonomic and functional structure of the gut microbiome from 275 Nunavik Inuit ranging from 16 to 30-year-old. Whole-metagenome analyses revealed that Nunavik Inuit youths have a more diverse microbiome than their non-industrialized and industrialized counterparts. A comparison of k-mer content illustrated the uniqueness of the Nunavik gut microbiome. Short-chain fatty acids producing species, and carbohydrates degradation pathways dominated Inuit metagenomes. We identified a taxonomic and functional signature unique to the Nunavik gut microbiome contrasting with other populations using a random forest classifier. Here, we show that the Nunavik Inuit gut microbiome exhibits high diversity and a distinct community structure.}, } @article {pmid36566218, year = {2022}, author = {Grevesse, T and Guéguen, C and Onana, VE and Walsh, DA}, title = {Degradation pathways for organic matter of terrestrial origin are widespread and expressed in Arctic Ocean microbiomes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {237}, pmid = {36566218}, issn = {2049-2618}, mesh = {*Humic Substances/analysis ; Oceans and Seas ; Bacteria/genetics ; Carbon ; *Microbiota/genetics ; }, abstract = {BACKGROUND: The Arctic Ocean receives massive freshwater input and a correspondingly large amount of humic-rich organic matter of terrestrial origin. Global warming, permafrost melt, and a changing hydrological cycle will contribute to an intensification of terrestrial organic matter release to the Arctic Ocean. Although considered recalcitrant to degradation due to complex aromatic structures, humic substances can serve as substrate for microbial growth in terrestrial environments. However, the capacity of marine microbiomes to process aromatic-rich humic substances, and how this processing may contribute to carbon and nutrient cycling in a changing Arctic Ocean, is relatively unexplored. Here, we used a combination of metagenomics and metatranscriptomics to assess the prevalence and diversity of metabolic pathways and bacterial taxa involved in aromatic compound degradation in the salinity-stratified summer waters of the Canada Basin in the western Arctic Ocean.

RESULTS: Community-scale meta-omics profiling revealed that 22 complete pathways for processing aromatic compounds were present and expressed in the Canada Basin, including those for aromatic ring fission and upstream funneling pathways to access diverse aromatic compounds of terrestrial origin. A phylogenetically diverse set of functional marker genes and transcripts were associated with fluorescent dissolved organic matter, a component of which is of terrestrial origin. Pathways were common throughout global ocean microbiomes but were more abundant in the Canada Basin. Genome-resolved analyses identified 12 clades of Alphaproteobacteria, including Rhodospirillales, as central contributors to aromatic compound processing. These genomes were mostly restricted in their biogeographical distribution to the Arctic Ocean and were enriched in aromatic compound processing genes compared to their closest relatives from other oceans.

CONCLUSION: Overall, the detection of a phylogenetically diverse set of genes and transcripts implicated in aromatic compound processing supports the view that Arctic Ocean microbiomes have the capacity to metabolize humic substances of terrestrial origin. In addition, the demonstration that bacterial genomes replete with aromatic compound degradation genes exhibit a limited distribution outside of the Arctic Ocean suggests that processing humic substances is an adaptive trait of the Arctic Ocean microbiome. Future increases in terrestrial organic matter input to the Arctic Ocean may increase the prominence of aromatic compound processing bacteria and their contribution to Arctic carbon and nutrient cycles. Video Abstract.}, } @article {pmid36566203, year = {2022}, author = {Dang, T and Kumaishi, K and Usui, E and Kobori, S and Sato, T and Toda, Y and Yamasaki, Y and Tsujimoto, H and Ichihashi, Y and Iwata, H}, title = {Stochastic variational variable selection for high-dimensional microbiome data.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {236}, pmid = {36566203}, issn = {2049-2618}, mesh = {Humans ; Bayes Theorem ; Algorithms ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; }, abstract = {BACKGROUND: The rapid and accurate identification of a minimal-size core set of representative microbial species plays an important role in the clustering of microbial community data and interpretation of clustering results. However, the huge dimensionality of microbial metagenomics datasets is a major challenge for the existing methods such as Dirichlet multinomial mixture (DMM) models. In the approach of the existing methods, the computational burden of identifying a small number of representative species from a large number of observed species remains a challenge.

RESULTS: We propose a novel approach to improve the performance of the widely used DMM approach by combining three ideas: (i) we propose an indicator variable to identify representative operational taxonomic units that substantially contribute to the differentiation among clusters; (ii) to address the computational burden of high-dimensional microbiome data, we propose a stochastic variational inference, which approximates the posterior distribution using a controllable distribution called variational distribution, and stochastic optimization algorithms for fast computation; and (iii) we extend the finite DMM model to an infinite case by considering Dirichlet process mixtures and estimating the number of clusters as a variational parameter. Using the proposed method, stochastic variational variable selection (SVVS), we analyzed the root microbiome data collected in our soybean field experiment, the human gut microbiome data from three published datasets of large-scale case-control studies and the healthy human microbiome data from the Human Microbiome Project.

CONCLUSIONS: SVVS demonstrates a better performance and significantly faster computation than those of the existing methods in all cases of testing datasets. In particular, SVVS is the only method that can analyze massive high-dimensional microbial data with more than 50,000 microbial species and 1000 samples. Furthermore, a core set of representative microbial species is identified using SVVS that can improve the interpretability of Bayesian mixture models for a wide range of microbiome studies. Video Abstract.}, } @article {pmid36566015, year = {2023}, author = {Wang, T and Gao, H and He, C and Gao, L and Wang, B and Hua, R and Du, Y and Liang, C and Xin, S and Shang, H and Wang, Y and Wang, W and Xu, J}, title = {Adult hypertensive rats are more prone to gut microflora perturbation and fibrosis in response to moderate restraint stress.}, journal = {Translational research : the journal of laboratory and clinical medicine}, volume = {254}, number = {}, pages = {92-114}, doi = {10.1016/j.trsl.2022.10.006}, pmid = {36566015}, issn = {1878-1810}, mesh = {Rats ; Animals ; *Gastrointestinal Microbiome ; Blood Pressure ; Rats, Inbred SHR ; *Hypertension ; Fibrosis ; }, abstract = {Hypertension (HTN) is a common endpoint for numerous cardiovascular diseases, the prevalence of which has been quickly increasing due to a wide range of reasons. Previous research has found that following stress, ELISA and 16S rDNA sequencing indicated substantial changes in plasma cytokines or hormones, as well as alterations in gut microbiota in juvenile hypertensive rats. However, it remains still unclear how such interaction modifications affect microbial populations and organismal function. Stress-related hormones show a significant drop. Similar to earlier research, the stress group had dramatically increased release of pro-inflammatory cytokines such as IL-17. Importantly, a unified collection of tools that allows for deep and comprehensive colonic structural investigation has been developed. Stress may limit the transition of macrophages (Mφs) to M1Mφs while increasing the transfer to M2Mφs. Evidence highlighted that tight junction proteins were decreased along with enhancement in intestinal permeability. Morphological analysis revealed that the SHR-S group exhibited considerably higher levels of morphological alterations and fibrosis in colon, heart, and thoracic aorta tissues.Significant improvements in bacteria linked with short-chain fatty acid synthesis, such as Prevotella and Ruminococcus, were discovered by metagenomic analysis. Adult hypertensive rats are more susceptible to gut microbiota disruption and fibrosis as a result of mild restraint stress. This might contribute to some innovative ideas for HTN both treatment and prevention.}, } @article {pmid36565853, year = {2023}, author = {Olorocisimo, JP and Diaz, LA and Co, DE and Carag, HM and Ibana, JA and Velarde, MC}, title = {Lactobacillus delbrueckii reduces anxiety-like behavior in zebrafish through a gut microbiome - brain crosstalk.}, journal = {Neuropharmacology}, volume = {225}, number = {}, pages = {109401}, doi = {10.1016/j.neuropharm.2022.109401}, pmid = {36565853}, issn = {1873-7064}, mesh = {Animals ; *Lactobacillus delbrueckii/genetics/metabolism ; Zebrafish/genetics/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics/metabolism ; Brain/metabolism ; Anxiety ; }, abstract = {Certain bacteria possess the ability to reduce anxiety- and stress-related behaviors through the gut microbiome-brain axis. Such bacteria are called psychobiotics, and can be used to improve mood and cognition. However, only a few bacteria have been characterized as psychobiotics, and their exact mechanism of action remains unclear. Hence, in this study we analyzed three different species under the Lactobacillacea family, namely, Lactobacillus delbrueckii, Lacticaseibacillus casei, and Lacticaseibacillus paracasei for their potential psychobiotic activities. L. delbrueckii treatment reduced anxiety-like behavior and increased brain and gut glutamic acid decarboxylase (gad) gene expression in zebrafish. It also altered zebrafish gut microbial community as determined by PCR-DGGE and 16S rRNA-based metagenomics analysis. Overall, this paper showed that L. delbrueckii but not L. paracasei and L. casei, induced a consistent improvement in anxiety-like behavior in zebrafish, implicating its potential role as a psychobiotic to reduce anxiety. This article is part of the Special Issue on 'Microbiome & the Brain: Mechanisms & Maladies'.}, } @article {pmid36565815, year = {2023}, author = {Miranda, TDS and Schiffler, FB and D'arc, M and Moreira, FRR and Cosentino, MAC and Coimbra, A and Mouta, R and Medeiros, G and Girardi, DL and Wanderkoke, V and Soares, CFA and Francisco, TM and Henry, MD and Afonso, BC and Soffiati, FL and Ferreira, SS and Ruiz-Miranda, CR and Soares, MA and Santos, AFA}, title = {Metagenomic analysis reveals novel dietary-related viruses in the gut virome of marmosets hybrids (Callithrix jacchus x Callithrix penicillata), Brazil.}, journal = {Virus research}, volume = {325}, number = {}, pages = {199017}, pmid = {36565815}, issn = {1872-7492}, mesh = {Animals ; *Callithrix/genetics ; Brazil ; Phylogeny ; Virome ; Metagenomics ; *Viruses/genetics ; Diet ; Genome, Viral ; }, abstract = {Viral metagenomics has contributed enormously to the characterization of a wide range of viruses infecting animals of all phyla in the last decades. Among Neotropical primates, especially those introduced, knowledge about viral diversity remains poorly studied. Therefore, using metagenomics based on virus enrichment, we explored the viral microbiota present in the feces of introduced common marmosets (Callithrix sp.) in three locations from the Silva Jardim region in the State of Rio de Janeiro, Brazil. Fecal samples were collected from nine marmosets, pooled into three sample pools, and sequenced on Illumina MiSeq platform. Sequence reads were analyzed using a viral metagenomic analysis pipeline and two novel insect viruses belonging to the Parvoviridae and Baculoviridae families were identified. The complete genome of a densovirus (Parvoviridae family) of 5,309 nucleotides (nt) was obtained. The NS1 and VP1 proteins share lower than 32% sequence identity with the corresponding proteins of known members of the subfamily Densovirinae. Phylogenetic analysis suggests that this virus represents a new genus, provisionally named Afoambidensovirus due to its discovery in the Brazilian Atlantic Forest. The novel species received the name Afoambidensovirus incertum 1. The complete circular genome of a baculovirus of 107,191 nt was also obtained, showing 60.8% sequence identity with the most closely related member of the Baculoviridae family. Phylogenetic analysis suggests that this virus represents a new species in the Betabaculovirus genus, provisionally named Betabaculovirus incertum 1. In addition, sequences from several families of arthropods in the three pools evaluated were characterized (contigs ranging from 244 to 6,750 nt), corroborating the presence of possible insect hosts with which these new viruses may be associated. Our study expands the knowledge about two viral families known to infect insects, an important component of the marmosets' diet. This identification in hosts' feces samples demonstrates one of the many uses of this type of data and could serve as a basis for future research characterizing viruses in wildlife using noninvasive samples.}, } @article {pmid36565811, year = {2023}, author = {Li, Y and Cao, L and Han, X and Ma, Y and Liu, Y and Gao, S and Zhang, C}, title = {Altered vaginal eukaryotic virome is associated with different cervical disease status.}, journal = {Virologica Sinica}, volume = {38}, number = {2}, pages = {184-197}, pmid = {36565811}, issn = {1995-820X}, mesh = {Female ; Humans ; Virome ; *Papillomavirus Infections/microbiology/pathology ; Eukaryota ; *Uterine Cervical Neoplasms/microbiology/pathology ; *Viruses ; Biomarkers ; Papillomaviridae ; }, abstract = {Viruses are important components of the human body. Growing evidence suggests that they are engaged in the physiology and disease status of the host. Even though the vaginal microbiome is involved in human papillomavirus (HPV) infection and cervical cancer (CC) progression, little is known about the role of the vaginal virome. In this pilot exploratory study, using unbiased viral metagenomics, we aim to investigate the vaginal eukaryotic virome in women with different levels of cervical lesions, and examine their associations with different cervical disease status. An altered eukaryotic virome was observed in women with different levels of lesions and Lactobacillus profiles. Anelloviruses and papillomaviruses are the most commonly detected eukaryotic viruses of the vaginal virome. Higher abundance and richness of anelloviruses and papillomaviruses were associated with low-grade squamous intraepithelial lesion (LSIL) and CC. Besides, higher anellovirus abundance was also associated with lactobacillus-depleted microbiome profiles and bacterial community state (CST) type IV. Furthermore, increased correlations between Anelloviridae and Papillomaviridae occurred in the women with increased cervical disease severity level from LSIL to CC. These data suggest underlying interactions between different microbes as well as the host physiology. Higher abundance and diversity of both anelloviruses and papillomaviruses shared by LSIL and CC suggest that anellovirus may be used as a potential adjunct biomarker to predict the risk of HPV persistent infection and/or CC. Future studies need to focus on the clinical relevance of anellovirus abundance with cervical disease status, and the evaluation of their potential as a new adjunct biomarker for the prediction and prognoses of CC.}, } @article {pmid36565637, year = {2023}, author = {Alvarenga, BO and Paiva, JB and Souza, AIS and Rodrigues, DR and Tizioto, PC and Ferreira, AJP}, title = {Metagenomics analysis of the morphological aspects and bacterial composition of broiler feces.}, journal = {Poultry science}, volume = {102}, number = {2}, pages = {102401}, pmid = {36565637}, issn = {1525-3171}, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Chickens/genetics ; *Gastrointestinal Microbiome ; Bacteria/genetics ; Feces/microbiology ; Firmicutes ; }, abstract = {In this descriptive study, we used metagenomics to analyze the relationship between the morphological aspects of chicken feces and its respective bacterial compositions. The microbiota composition was determined by sequencing the V4 region of the 16S rRNA genes collected from fresh broiler feces at 19 d old. In total, 48 samples were collected and divided into 8 groups of 6 samples each. The morphological changes studied were feed passage (FP) and reddish mucus (RM). Each was classified into 3 levels of intensity: 1 (slight), 2 (moderate), or 3 (intense). Thus, the 8 groups studied were feed passage (FP-1; FP-2; FP-3), reddish mucus (RM-1; RM-2; RM-3), normal ileal feces (NIF), and cecal discharge (CD). The alpha diversity (Shannon's index) revealed that the CD group showed greater diversity, and was significantly different from FP-2, FP-3, and RM-1. The beta diversity showed that the CD group samples were more homogeneous than the ileal feces groups. The relative abundance analysis revealed that Firmicutes and Proteobacteria were the most abundant phyla in the ileal feces groups. In CD, Firmicutes and Bacteroidetes were the most abundant. The relative abundance at the genus level revealed 136 different bacterial genera. In the ileal feces groups, the two most abundant genera were Lactobacillus and Escherichia/Shigella, except in the FP-1 and RM-2 groups, which had the opposite order. Unlike the others, the CD group had a higher abundance of Bacteroides and Faecalibacterium. When comparing the NIF group with the others, significant changes were found in the fecal microbiota, with nine genera for the FP groups, 19 for the RM groups, and 61 when compared to CD. The results of the present study suggest that evaluation of fecal morphology is a fundamental task that makes it possible to act quickly and assertively, as the morphological aspects of the feces may be related to the composition and structure of fecal microbiota.}, } @article {pmid36565548, year = {2023}, author = {Wang, R and Cai, Y and Lu, W and Zhang, R and Shao, R and Yau, SY and Stubbs, B and McIntyre, RS and Su, KP and Xu, G and Qi, L and So, KF and Lin, K}, title = {Exercise effect on the gut microbiota in young adolescents with subthreshold depression: A randomized psychoeducation-controlled Trial.}, journal = {Psychiatry research}, volume = {319}, number = {}, pages = {115005}, doi = {10.1016/j.psychres.2022.115005}, pmid = {36565548}, issn = {1872-7123}, mesh = {Humans ; Adolescent ; *Depression/therapy ; *Gastrointestinal Microbiome ; Exercise ; }, abstract = {This 3-month randomized psychoeducation-controlled trial (RCT) of exercise was undertaken in young adolescents with subthreshold depression to examine the impact on gut microbiota. Participants (aged 12-14 years) were randomly assigned to an exercise or a psychoeducation-controlled group. The exercise intervention arm took moderate-intensity exercise, comprised of 30 min of running per day, 4 days a week for 3 months. Psychoeducation intervention consisted of 6 sessions of group activity including gaming, reading, and singing. The gut microbiota was assessed by metagenomic sequencing. After 3-month moderate-intensity exercise, the intervention group increased the relative abundance of Coprococcus, Blautia, Dorea, Tyzzerella at the genus level, as well as Tyzzerella nexilis, Ruminococcus obeum at species level when compared to the psychoeducation-controlled group. Moreover, EggNOG analyses showed that the defense and signal transduction mechanism were highly enriched after the active intervention, and changes were correlated with improvements in depressive symptoms measured by Chinese Patient Depression Questionnaire 9. The KEGG pathway of neurodegenerative diseases was depleted in the microbiome in young adolescents with subthreshold depression after exercise intervention. This 3-month RCT suggests that at both the genus and species levels, aerobic group exercise intervention improved in depressive symptoms and revealed changes in gut microbiota suggesting beneficial effects.}, } @article {pmid36564805, year = {2022}, author = {Li, X and Li, R and Ji, B and Zhao, L and Wang, J and Yan, T}, title = {Integrative metagenomic and metabolomic analyses reveal the role of gut microbiota in antibody-mediated renal allograft rejection.}, journal = {Journal of translational medicine}, volume = {20}, number = {1}, pages = {614}, pmid = {36564805}, issn = {1479-5876}, mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Gastrointestinal Microbiome/genetics ; Dysbiosis ; Antibodies ; Allografts ; Graft Rejection ; }, abstract = {BACKGROUND: Antibody-mediated rejection (AMR) remains one of the major barriers for graft survival after kidney transplantation. Our previous study suggested a gut microbiota dysbiosis in kidney transplantation recipients with AMR. However, alternations in gut microbial function and structure at species level have not been identified. In the present study, we investigated the metagenomic and metabolic patterns of gut microbiota in AMR patients to provide a comprehensive and in-depth understanding of gut microbiota dysbiosis in AMR.

METHODS: We enrolled 60 kidney transplantation recipients, 28 showed AMR and 32 were non-AMR controls with stable post-transplant renal functions. Shotgun sequencing and untargeted LC/MS metabolomic profiling of fecal samples were performed in kidney transplantation recipients with AMR and controls.

RESULTS: Totally, we identified 311 down-regulated and 27 up-regulated gut microbial species associated with AMR after kidney transplantation, resulting in the altered expression levels of 437 genes enriched in 22 pathways, of which 13 were related to metabolism. Moreover, 32 differential fecal metabolites were found in recipients with AMR. Among them, alterations in 3b-hydroxy-5-cholenoic acid, L-pipecolic acid, taurocholate, and 6k-PGF1alpha-d4 directly correlated with changes in gut microbial species and functions. Specific differential fecal species and metabolites were strongly associated with clinical indexes (Cr, BUN, etc.), and could distinguish the recipients with AMR from controls as potential biomarkers.

CONCLUSIONS: Altogether, our findings provided a comprehensive and in-depth understanding of the correlation between AMR and gut microbiota, which is important for the etiological and diagnostic study of AMR after kidney transplantation.}, } @article {pmid36564713, year = {2022}, author = {Liu, Y and Zhu, J and Wang, H and Lu, W and Lee, YK and Zhao, J and Zhang, H}, title = {Machine learning framework for gut microbiome biomarkers discovery and modulation analysis in large-scale obese population.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {850}, pmid = {36564713}, issn = {1471-2164}, mesh = {Humans ; *Gastrointestinal Microbiome ; Obesity ; Feces/microbiology ; Biomarkers ; Machine Learning ; }, abstract = {BACKGROUND: The gut microbiome has proven to be an important factor affecting obesity; however, it remains a challenge to identify consistent biomarkers across geographic locations and perform precisely targeted modulation for obese individuals.

RESULTS: This study proposed a systematic machine learning framework and applied it to 870 human stool metagenomes across five countries to obtain comprehensive regional shared biomarkers and conduct a personalized modulation analysis. In our pipeline, a heterogeneous ensemble feature selection diagram is first developed to determine an optimal subset of biomarkers through the aggregation of multiple techniques. Subsequently, a deep reinforcement learning method was established to alter the targeted composition to the desired healthy target. In this manner, we can realize personalized modulation by counterfactual inference. Consequently, a total of 42 species were identified as regional shared biomarkers, and they showed good performance in distinguishing obese people from the healthy group (area under curve (AUC) =0.85) when demonstrated on validation datasets. In addition, by pooling all counterfactual explanations, we found that Akkermansia muciniphila, Faecalibacterium prausnitzii, Prevotella copri, Bacteroides dorei, Bacteroides eggerthii, Alistipes finegoldii, Alistipes shahii, Eubacterium sp. _CAG_180, and Roseburia hominis may be potential broad-spectrum targets with consistent modulation in the multi-regional obese population.

CONCLUSIONS: This article shows that based on our proposed machine-learning framework, we can obtain more comprehensive and accurate biomarkers and provide modulation analysis for the obese population. Moreover, our machine-learning framework will also be very useful for other researchers to further obtain biomarkers and perform counterfactual modulation analysis in different diseases.}, } @article {pmid36564666, year = {2023}, author = {Minkina, T and Sushkova, S and Delegan, Y and Bren, A and Mazanko, M and Kocharovskaya, Y and Filonov, A and Rajput, VD and Mandzhieva, S and Rudoy, D and Prazdnova, EV and Elena, V and Zelenkova, G and Ranjan, A}, title = {Effect of chicken manure on soil microbial community diversity in poultry keeping areas.}, journal = {Environmental geochemistry and health}, volume = {45}, number = {12}, pages = {9303-9319}, pmid = {36564666}, issn = {1573-2983}, support = {075-15-2019-1880//Government of the Russian Federation/ ; }, mesh = {Animals ; *Soil ; Chickens ; Manure ; Poultry ; Soil Microbiology ; Bacteria/genetics ; *Microbiota ; }, abstract = {The poultry industry is generating a significant amount of waste from chicken droppings that are abundant in microbes as well as macro- and micronutrients suitable for manure. It has the potential to improve the microbial activity and nutrient dynamics in the soil, ultimately improving soil fertility. The present study aimed to investigate the effect of chicken droppings manure (CDM) on the diversity of the soil microbiome in the free walking chicken's area located in Stefanidar, Rostov Region, Russia. The data obtained were compared with 16 s rRNA from control samples located not far from the chicken's free-walking area, but not in direct contact with the droppings. Effect of CDM on the physicochemical characteristics of the soil and changes in its microbial diversity were assessed by employing the metagenomic approaches and 16 s rRNA-based taxonomic assessment. The alpha and beta diversity indices revealed that the application of the CDM significantly improved the soil microbial diversity. The 16S taxonomical analysis confirmed Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Planctomycetes as abundant bacterial phylum. It also revealed the increase in the total number of the individual operational taxonomic unit (OTU) species, a qualitative indicator of the rich microbial community. The alpha diversity confirmed that the significant species richness of the soil is associated with the CDM treatment. The increased OTUs represent the qualitative indicator of a community that has been studied up to the depth of 5-20 cm of the CDM treatment range. These findings suggested that CDM-mediated microbial richness are believed to confer the cycling of carbon, nitrogen, and sulfur, along with key soil enzymes such as dehydrogenases and catalase carbohydrate-active enzymes. Hence, the application of CDM could improve soil fertility by nutrient cycling caused by changes in soil microbial dynamics, and it could also be a cost-effective sustainable means of improving soil health.}, } @article {pmid36564496, year = {2022}, author = {Allioux, M and Yvenou, S and Merkel, A and Cozannet, M and Aubé, J and Pommellec, J and Le Romancer, M and Lavastre, V and Guillaume, D and Alain, K}, title = {A metagenomic insight into the microbiomes of geothermal springs in the Subantarctic Kerguelen Islands.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {22243}, pmid = {36564496}, issn = {2045-2322}, support = {P30 CA016086/CA/NCI NIH HHS/United States ; }, mesh = {Metagenome ; *Hot Springs/microbiology ; Metagenomics/methods ; Islands ; Archaea ; *Microbiota/genetics ; Phylogeny ; }, abstract = {The Kerguelen Islands, located in the southern part of the Indian Ocean, are very isolated geographically. The microbial diversity and communities present on the island, especially associated to geothermal springs, have never been analyzed with high-throughput sequencing methods. In this article, we performed the first metagenomics analysis of microorganisms present in Kerguelen hot springs. From four hot springs, we assembled metagenomes and recovered 42 metagenome-assembled genomes, mostly associated with new putative taxa based on phylogenomic analyses and overall genome relatedness indices. The 42 MAGs were studied in detail and showed putative affiliations to 13 new genomic species and 6 new genera of Bacteria or Archaea according to GTDB. Functional potential of MAGs suggests the presence of thermophiles and hyperthermophiles, as well as heterotrophs and primary producers possibly involved in the sulfur cycle, notably in the oxidation of sulfur compounds. This paper focused on only four of the dozens of hot springs in the Kerguelen Islands and should be considered as a preliminary study of the microorganisms inhabiting the hot springs of these isolated islands. These results show that more efforts should be made towards characterization of Kerguelen Islands ecosystems, as they represent a reservoir of unknown microbial lineages.}, } @article {pmid36564466, year = {2022}, author = {Fachrul, M and Méric, G and Inouye, M and Pamp, SJ and Salim, A}, title = {Assessing and removing the effect of unwanted technical variations in microbiome data.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {22236}, pmid = {36564466}, issn = {2045-2322}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Swine ; *Microbiota/genetics ; Metagenome ; Freezing ; Bacteroidetes ; Feces ; }, abstract = {Varying technologies and experimental approaches used in microbiome studies often lead to irreproducible results due to unwanted technical variations. Such variations, often unaccounted for and of unknown source, may interfere with true biological signals, resulting in misleading biological conclusions. In this work, we aim to characterize the major sources of technical variations in microbiome data and demonstrate how in-silico approaches can minimize their impact. We analyzed 184 pig faecal metagenomes encompassing 21 specific combinations of deliberately introduced factors of technical and biological variations. Using the novel Removing Unwanted Variations-III-Negative Binomial (RUV-III-NB), we identified several known experimental factors, specifically storage conditions and freeze-thaw cycles, as likely major sources of unwanted variation in metagenomes. We also observed that these unwanted technical variations do not affect taxa uniformly, with freezing samples affecting taxa of class Bacteroidia the most, for example. Additionally, we benchmarked the performances of different correction methods, including ComBat, ComBat-seq, RUVg, RUVs, and RUV-III-NB. While RUV-III-NB performed consistently robust across our sensitivity and specificity metrics, most other methods did not remove unwanted variations optimally. Our analyses suggest that a careful consideration of possible technical confounders is critical during experimental design of microbiome studies, and that the inclusion of technical replicates is necessary to efficiently remove unwanted variations computationally.}, } @article {pmid36564415, year = {2022}, author = {Wu, L and Xie, X and Li, Y and Liang, T and Zhong, H and Yang, L and Xi, Y and Zhang, J and Ding, Y and Wu, Q}, title = {Gut microbiota as an antioxidant system in centenarians associated with high antioxidant activities of gut-resident Lactobacillus.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {102}, pmid = {36564415}, issn = {2055-5008}, mesh = {Aged, 80 and over ; Young Adult ; Humans ; *Gastrointestinal Microbiome ; Antioxidants ; Lactobacillus ; Centenarians ; Metagenome ; }, abstract = {The gut microbiota plays an important role in human health and longevity, and the gut microbiota of centenarians shows unique characteristics. Nowadays, most microbial research on longevity is usually limited to the bioinformatics level, lacking validating information on culturing functional microorganisms. Here, we combined metagenomic sequencing and large-scale in vitro culture to reveal the unique gut microbial structure of the world's longevity town-Jiaoling, China, centenarians and people of different ages. Functional strains were isolated and screened in vitro, and the possible relationship between gut microbes and longevity was explored and validated in vivo. 247 healthy Cantonese natives of different ages participated in the study, including 18 centenarians. Compared with young adults, the gut microbiota of centenarians exhibits higher microbial diversity, xenobiotics biodegradation and metabolism, oxidoreductases, and multiple species (the potential probiotics Lactobacillus, Akkermansia, the methanogenic Methanobrevibacter, gut butyrate-producing members Roseburia, and SCFA-producing species uncl Clostridiales, uncl Ruminococcaceae) known to be beneficial to host metabolism. These species are constantly changing with age. We also isolated 2055 strains from these samples by large-scale in vitro culture, most of which were detected by metagenomics, with clear complementarity between the two approaches. We also screened an age-related gut-resident Lactobacillus with independent intellectual property rights, and its metabolite (L-ascorbic acid) and itself have good antioxidant effects. Our findings underscore the existence of age-related trajectories in the human gut microbiota, and that distinct gut microbiota and gut-resident as antioxidant systems may contribute to health and longevity.}, } @article {pmid36563106, year = {2023}, author = {Chai, X and Wang, J and Li, H and Gao, C and Li, S and Wei, C and Huang, J and Tian, Y and Yuan, J and Lu, J and Gao, D and Zheng, Y and Huang, C and Zhou, J and Shi, G and Ke, A and Liu, F and Fan, J and Cai, J}, title = {Intratumor microbiome features reveal antitumor potentials of intrahepatic cholangiocarcinoma.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2156255}, pmid = {36563106}, issn = {1949-0984}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; *Gastrointestinal Microbiome ; *Microbiota/genetics ; Bacteria/genetics ; *Cholangiocarcinoma/genetics/pathology ; Bile Ducts, Intrahepatic/pathology ; *Bile Duct Neoplasms/genetics/pathology ; }, abstract = {Intrahepatic cholangiocarcinoma (ICC) is a rare malignancy with a high prevalence in China. This study aimed to characterize the ICC tissues' bacterial metagenomics signature and explore its antitumor potential for cancer. In this study, 16S rRNA sequencing was carried out on 99 tissues to characterize the features of intratumoral microbiota, followed by single-cell RNA sequencing (scRNA-seq) and multilevel validation. The presence of microbial DNA in tissues was determined using staining, fluorescence in situ hybridization (FISH), and transmission electron microscopy (TEM). A Gram-positive aerobic bacterium, identified as Staphylococcus capitis, was cultured from fresh tissues. Meanwhile, scRNA-seq showed that intratumoral bacteria could be present in multiple cell types. Using 16S rRNA sequencing, we identified a total of 2,320,287 high-quality reads corresponding to 4,594 OTU (operational taxonomic units) sequences. The most abundant bacterial orders include Burkholderiales, Pseudomonadales, Xanthomonadales, Bacillales and Clostridiales. Alpha and Beta diversity analysis revealed specific features in different tissues. In addition, the content of Paraburkholderia fungorum was significantly higher in the paracancerous tissues and negatively correlated with CA199 (Carbohydrate antigen199) levels. The results of in vitro and in vivo experiments suggest that P. fungorum possesses an antitumor activity against tumors. Metabolomics and transcriptomics showed that P. fungorum could inhibit tumor growth through alanine, aspartate and glutamate metabolism. We determined the characteristic profile of the intratumoral microbiota and the antitumor effect of P. fungorum in ICC.}, } @article {pmid36562201, year = {2023}, author = {Dreisbach, C and Alhusen, J and Prescott, S and Dudley, D and Trinchieri, G and Siega-Riz, AM}, title = {Metagenomic characterization of the maternal prenatal gastrointestinal microbiome by pregravid BMI.}, journal = {Obesity (Silver Spring, Md.)}, volume = {31}, number = {2}, pages = {412-422}, pmid = {36562201}, issn = {1930-739X}, support = {F31 NR017821/NR/NINR NIH HHS/United States ; }, mesh = {Pregnancy ; Humans ; Female ; Overweight/complications ; Body Mass Index ; *Gastrointestinal Microbiome ; Obesity/epidemiology ; *Diabetes, Gestational ; }, abstract = {OBJECTIVE: The incidence of women entering into pregnancy with BMI indicating overweight or obesity is rising with concurrent increases in adverse complications such as gestational diabetes. Although several studies have examined the compositional changes to the microbiome across BMI classifications, there has been no investigation regarding changes in microbial function during pregnancy.

METHODS: A total of 105 gastrointestinal microbiome biospecimens were used in this analysis. Biospecimens were sequenced by using the Illumina NovaSeq 6000 shotgun metagenomics platform.

RESULTS: Findings indicate an enrichment in microbiota from the phylum Firmicutes across all pregravid BMI groups with a decrease in α diversity in groups with BMI indicating obesity or overweight compared with a group with BMI indicating normal weight (p = 0.02). More specifically, women with BMI indicating obesity or overweight had enrichment in Bifidobacterium bifidum and B. adolescentis. Women with BMI > 25 kg/m[2] had a higher abundance of microbiota that support biotin synthesis and regulate epithelial cells in the lower gastrointestinal tract. These epithelial cells are responsible for host adaptability to dietary lipid variation and caloric absorption.

CONCLUSIONS: Our analysis suggests that there are differences in microbial composition and function between BMI groups. Future research should consider how these changes contribute to specific clinical outcomes during pregnancy.}, } @article {pmid36559640, year = {2022}, author = {Postiglione, A and Prigioniero, A and Zuzolo, D and Tartaglia, M and Scarano, P and Maisto, M and Ranauda, MA and Sciarrillo, R and Thijs, S and Vangronsveld, J and Guarino, C}, title = {Quercus ilex Phyllosphere Microbiome Environmental-Driven Structure and Composition Shifts in a Mediterranean Contex.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {24}, pages = {}, pmid = {36559640}, issn = {2223-7747}, abstract = {The intra- and interdomain phyllosphere microbiome features of Quercus ilex L. in a Mediterranean context is reported. We hypothesized that the main driver of the phyllosphere microbiome might be the season and that atmospheric pollutants might have a co-effect. Hence, we investigated the composition of epiphytic bacteria and fungi of leaves sampled in urban and natural areas (in Southern Italy) in summer and winter, using microscopy and metagenomic analysis. To assess possible co-effects on the composition of the phyllosphere microbiome, concentrations of particulate matter and polycyclic aromatic hydrocarbons (PAHs) were determined from sampled leaves. We found that environmental factors had a significative influence on the phyllosphere biodiversity, altering the taxa relative abundances. Ascomycota and Firmicutes were higher in summer and in urban areas, whereas a significant increase in Proteobacteria was observed in the winter season, with higher abundance in natural areas. Network analysis suggested that OTUs belonging to Acidobacteria, Cytophagia, unkn. Firmicutes(p), Actinobacteria are keystone of the Q. ilex phyllosphere microbiome. In addition, 83 genes coding for 5 enzymes involved in PAH degradation pathways were identified. Given that the phyllosphere microbiome can be considered an extension of the ecosystem services offered by trees, our results can be exploited in the framework of Next-Generation Biomonitoring.}, } @article {pmid36558391, year = {2022}, author = {Feng, C and Zhang, W and Zhang, T and He, Q and Kwok, LY and Tan, Y and Zhang, H}, title = {Heat-Killed Bifidobacterium bifidum B1628 May Alleviate Dextran Sulfate Sodium-Induced Colitis in Mice, and the Anti-Inflammatory Effect Is Associated with Gut Microbiota Modulation.}, journal = {Nutrients}, volume = {14}, number = {24}, pages = {}, pmid = {36558391}, issn = {2072-6643}, support = {32001711, 31972083//National Natural Science Foundation of China/ ; 2021ZD0014//Inner Mongolia Science and Technology Major Projects/ ; MOF and MARA//China Agriculture Research System/ ; }, mesh = {Animals ; Mice ; Anti-Inflammatory Agents/pharmacology ; *Bifidobacterium bifidum/metabolism ; *Colitis/therapy/drug therapy ; Colon/metabolism ; Cytokines/metabolism ; Dextran Sulfate/adverse effects ; Disease Models, Animal ; Dysbiosis/pathology ; *Gastrointestinal Microbiome ; Hot Temperature ; *Inflammatory Bowel Diseases/pathology ; Interleukin-13 ; Mice, Inbred C57BL ; Tumor Necrosis Factor-alpha ; }, abstract = {Inflammatory bowel disease (IBD) is a chronic inflammatory disease associated with gut dysbiosis. This study aimed to investigate the effects of heat-killed Bifidobacterium bifidum B1628 (HB1628) in dextran sulfate sodium (DSS)-induced colitis in mice. The following three mouse groups were included (n = eight per group): NC (normal control), DSS (colitis), and HB1628 (colitis and postbiotic). The mice in the DSS group showed significant weight loss and histological damage, developed bloody diarrhea, scored high in the disease activity index (DAI), and exhibited increases in pro-inflammatory cytokines (interleukin [IL]-1β, IL-6, and tumor necrosis factor [TNF]-α) and decreases in an anti-inflammatory cytokine (IL-13) in the serum. These changes were accompanied by gut microbiota modulation in colitis mice (decreases in Rikenellaceae and Eubacterium; increases in Peptostreptococcaceae, Bacteroides vulgatus, and Parasutterella excrementihominis). The HB1628 group had lower DAIs, histology scores, and serum levels of pro-inflammatory cytokines (IL-1β and TNF-α), but higher levels of an anti-inflammatory cytokine (IL-13), compared with the DSS group, suggesting a less severe inflammatory state after the HB1628 intervention. Additionally, HB1628 improved DSS-induced gut dysbiosis, which is evidenced by increases in intestinal beneficial bacteria, such as Lactobacillus, and decreases in known unfavorable taxa in IBD, e.g., Porphyromonadaceae, Subdoligranulum, Lachnospiraceae bacterium 3_1_46FAA, and Alistipes indistinctus. Functional metagenomics revealed three significantly enriched metabolic pathways in the HB1628 group (namely, the aerobic respiration I [cytochrome c] pathway and the superpathways of L-phenylalanine biosynthesis and L-tryptophan biosynthesis, respectively). In conclusion, our results showed that HB1628 effectively improved the inflammation state and tissue damage in DSS-induced colitis mice, and the symptom relief effect was accompanied by obvious gut microbiota remodulation.}, } @article {pmid36558359, year = {2022}, author = {Bustamante, JM and Dawson, T and Loeffler, C and Marfori, Z and Marchesi, JR and Mullish, BH and Thompson, CC and Crandall, KA and Rahnavard, A and Allegretti, JR and Cummings, BP}, title = {Impact of Fecal Microbiota Transplantation on Gut Bacterial Bile Acid Metabolism in Humans.}, journal = {Nutrients}, volume = {14}, number = {24}, pages = {}, pmid = {36558359}, issn = {2072-6643}, support = {MC_PC_12025/MRC_/Medical Research Council/United Kingdom ; MR/R000875/1/MRC_/Medical Research Council/United Kingdom ; R21 AT010956/AT/NCCIH NIH HHS/United States ; R21AT010956/NH/NIH HHS/United States ; }, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Feces/microbiology ; Bacteria/genetics ; Bile Acids and Salts/analysis ; }, abstract = {Fecal microbiota transplantation (FMT) is a promising therapeutic modality for the treatment and prevention of metabolic disease. We previously conducted a double-blind, randomized, placebo-controlled pilot trial of FMT in obese metabolically healthy patients in which we found that FMT enhanced gut bacterial bile acid metabolism and delayed the development of impaired glucose tolerance relative to the placebo control group. Therefore, we conducted a secondary analysis of fecal samples collected from these patients to assess the potential gut microbial species contributing to the effect of FMT to improve metabolic health and increase gut bacterial bile acid metabolism. Fecal samples collected at baseline and after 4 weeks of FMT or placebo treatment underwent shotgun metagenomic analysis. Ultra-high-performance liquid chromatography-mass spectrometry was used to profile fecal bile acids. FMT-enriched bacteria that have been implicated in gut bile acid metabolism included Desulfovibrio fairfieldensis and Clostridium hylemonae. To identify candidate bacteria involved in gut microbial bile acid metabolism, we assessed correlations between bacterial species abundance and bile acid profile, with a focus on bile acid products of gut bacterial metabolism. Bacteroides ovatus and Phocaeicola dorei were positively correlated with unconjugated bile acids. Bifidobacterium adolescentis, Collinsella aerofaciens, and Faecalibacterium prausnitzii were positively correlated with secondary bile acids. Together, these data identify several candidate bacteria that may contribute to the metabolic benefits of FMT and gut bacterial bile acid metabolism that requires further functional validation.}, } @article {pmid36555624, year = {2022}, author = {Levi Mortera, S and Marzano, V and Vernocchi, P and Matteoli, MC and Guarrasi, V and Gardini, S and Del Chierico, F and Rapini, N and Deodati, A and Fierabracci, A and Cianfarani, S and Putignani, L}, title = {Functional and Taxonomic Traits of the Gut Microbiota in Type 1 Diabetes Children at the Onset: A Metaproteomic Study.}, journal = {International journal of molecular sciences}, volume = {23}, number = {24}, pages = {}, pmid = {36555624}, issn = {1422-0067}, mesh = {Adolescent ; Humans ; Child ; Aged ; *Diabetes Mellitus, Type 1 ; *Gastrointestinal Microbiome/physiology ; RNA, Ribosomal, 16S/genetics ; *Insulin-Secreting Cells ; Insulin, Regular, Human ; Insulin ; }, abstract = {Type 1 diabetes (T1D) is a chronic autoimmune metabolic disorder with onset in pediatric/adolescent age, characterized by insufficient insulin production, due to a progressive destruction of pancreatic β-cells. Evidence on the correlation between the human gut microbiota (GM) composition and T1D insurgence has been recently reported. In particular, 16S rRNA-based metagenomics has been intensively employed in the last decade in a number of investigations focused on GM representation in relation to a pre-disease state or to a response to clinical treatments. On the other hand, few works have been published using alternative functional omics, which is more suitable to provide a different interpretation of such a relationship. In this work, we pursued a comprehensive metaproteomic investigation on T1D children compared with a group of siblings (SIBL) and a reference control group (CTRL) composed of aged matched healthy subjects, with the aim of finding features in the T1D patients' GM to be related with the onset of the disease. Modulated metaproteins were found either by comparing T1D with CTRL and SIBL or by stratifying T1D by insulin need (IN), as a proxy of β-cells damage, showing some functional and taxonomic traits of the GM, possibly related to the disease onset at different stages of severity.}, } @article {pmid36555615, year = {2022}, author = {Šerá, J and Huynh, F and Ly, F and Vinter, Š and Kadlečková, M and Krátká, V and Máčalová, D and Koutný, M and Wallis, C}, title = {Biodegradable Polyesters and Low Molecular Weight Polyethylene in Soil: Interrelations of Material Properties, Soil Organic Matter Substances, and Microbial Community.}, journal = {International journal of molecular sciences}, volume = {23}, number = {24}, pages = {}, pmid = {36555615}, issn = {1422-0067}, support = {IGA/FT/2021/009//Tomas Bata University in Zlín/ ; }, mesh = {*Polyesters ; *Soil ; Plastics ; Polyethylene ; Molecular Weight ; Polymers ; Bacteria/genetics ; Microbial Consortia ; Soil Microbiology ; }, abstract = {Conventional and also biodegradable polymer microplastics have started to be broadly present in the environment, if they end up in soil, they may influence both abiotic and biotic soil properties. In this study, the interactions of polyethylene wax together with three biodegradable polyesters PLA, PHB and PBAT with a soil matrix were investigated over a 1-year incubation period. Soil organic matter content was measured using UV-VIS, the microbial biomass amount was measured using qPCR, the mineralisation of polymers was measured using UGA 3000, the surface of polymers was observed with SEM, live/dead microorganisms were determined by fluorescent microscopy and microbial consortia diversity was analyzed using NGS. The amount of humic substances was generally higher in incubations with slowly degrading polyesters, but the effect was temporary. The microbial biomass grew during the incubations; the addition of PHB enhanced fungal biomass whereas PE wax enhanced bacterial biomass. Fungal microbial consortia diversity was altered in incubations with PHB and PBAT. Interestingly, these two polyesters were also covered in biofilm, probably fungal. No such trend was observed in a metagenomic analysis of bacteria, although, bacterial biofilm was probably formed on the PE520 surface. Different methods confirmed the effect of certain polymers on the soil environment.}, } @article {pmid36555488, year = {2022}, author = {Filardo, S and Di Pietro, M and De Angelis, M and Brandolino, G and Porpora, MG and Sessa, R}, title = {In-Silico Functional Metabolic Pathways Associated to Chlamydia trachomatis Genital Infection.}, journal = {International journal of molecular sciences}, volume = {23}, number = {24}, pages = {}, pmid = {36555488}, issn = {1422-0067}, support = {C26A15PC5N//University of Rome "Sapienza"/ ; }, mesh = {Female ; Humans ; Chlamydia trachomatis ; Vagina/metabolism ; *Chlamydia Infections/epidemiology ; *Microbiota ; Metabolic Networks and Pathways ; }, abstract = {The advent of high-throughput technologies, such as 16s rDNA sequencing, has significantly contributed to expanding our knowledge of the microbiota composition of the genital tract during infections such as Chlamydia trachomatis. The growing body of metagenomic data can be further exploited to provide a functional characterization of microbial communities via several powerful computational approaches. Therefore, in this study, we investigated the predicted metabolic pathways of the cervicovaginal microbiota associated with C. trachomatis genital infection in relation to the different Community State Types (CSTs), via PICRUSt2 analysis. Our results showed a more rich and diverse mix of predicted metabolic pathways in women with a CST-IV microbiota as compared to all the other CSTs, independently from infection status. C. trachomatis genital infection further modified the metabolic profiles in women with a CST-IV microbiota and was characterized by increased prevalence of the pathways for the biosynthesis of precursor metabolites and energy, biogenic amino-acids, nucleotides, and tetrahydrofolate. Overall, predicted metabolic pathways might represent the starting point for more precisely designed future metabolomic studies, aiming to investigate the actual metabolic pathways characterizing C. trachomatis genital infection in the cervicovaginal microenvironment.}, } @article {pmid36554758, year = {2022}, author = {Song, D and Huo, T and Zhang, Z and Cheng, L and Wang, L and Ming, K and Liu, H and Li, M and Du, X}, title = {Metagenomic Analysis Reveals the Response of Microbial Communities and Their Functions in Lake Sediment to Environmental Factors.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {24}, pages = {}, pmid = {36554758}, issn = {1660-4601}, mesh = {Humans ; *Lakes/chemistry ; Chlorophyll A ; Bacteria/genetics/metabolism ; *Microbiota ; China ; Geologic Sediments/chemistry ; }, abstract = {Jingpo Lake is the largest mountain barrier lake in China and plays a key role in breeding, power generation, and providing a source of drinking water. Microbes are important participants in the formation of lake resources and energy cycles. However, the ecological protection of Jingpo Lake has faced serious challenges in recent years. In this study, we investigate the responses of the microbial community's composition of sediments at five locations to an environmental gradient representing water quality and water-depth changes using a metagenomic sequence. We found that the diversity and composition of the microbiota sediments were altered spatially and correlated with the physicochemical factors of water samples. In the microbial community, relatively lower Chao1, alternating conditional expectations, and Shannon and Simpson indices were found at the shallowest location with higher total phosphorus and chlorophyll a. Furthermore, the Kyoto Encyclopedia of Genes and Genomes analysis revealed that the metabolism function was the most abundant functional classification in Jingpo Lake. The levels of total phosphorus, chlorophyll a and pH were positively correlated with the abundance of Flavobacterium and the bacterial functions of the carbohydrate metabolism and amino acid metabolism. In conclusion, our results reveal the physical and chemical characteristics, as well as the microbial community characteristics, of Jingpo Lake, which provides new insights for studying the relationship between environmental factors and the bacterial community distribution of freshwater ecosystems, in addition to also providing a theoretical basis for the environmental monitoring and protection of the lake.}, } @article {pmid36554499, year = {2022}, author = {Dania, MI and Faraji, B and Wachira, J}, title = {Micronutrient Biosynthesis Potential of Spontaneous Grain Fermentation Microbiomes.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {24}, pages = {}, pmid = {36554499}, issn = {1660-4601}, support = {U54 MD013376/MD/NIMHD NIH HHS/United States ; UL1 GM118973/GM/NIGMS NIH HHS/United States ; 5UL1GM118973/GM/NIGMS NIH HHS/United States ; 5U54MD013376/NH/NIH HHS/United States ; }, mesh = {Humans ; Fermentation ; Micronutrients/metabolism ; Phylogeny ; Bacteria ; *Microbiota ; Edible Grain ; *Trace Elements/metabolism ; }, abstract = {Fermented foods play an important role in the human diet and particularly so in under-resourced environments where cold preservation is not attainable due to irregular supply of electricity. Fermented foods are reported to support gut health by contributing probiotics. The purpose of this study was to investigate the microbial diversity and metabolic potential of spontaneous millet fermentation. The literature in the field was reviewed and analyses were conducted on publicly available Sequence Read Archive (SRA) datasets. Quality analysis was performed with FastQC, and operational taxonomic units (OTUs) were generated using Quantitative Insights Into Microbial Ecology (QIIME2) and Divisive Amplicon Denoising Algorithm (DADA2) pipelines with Greengenes as the reference database. Metagenomics and pathways analysis were performed with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2). Statistical analysis and visualization were accomplished with Statistical Analysis of Metagenomic Profiles (STAMP). At the family taxonomic level, there were differences in the relative abundances of the dominant taxa of bacteria that are involved in the spontaneous fermentation of millet namely Lactobacillaceae, Burkholderiaceae, Streptococcaceae, Leuconostocaceae, and Acetobacteraceae. Clostridiaceae was the dominant family in one dataset. The incidence of Lactobacillaceae and Bifidobacteriaceae suggest the probiotic characteristics of fermented millet. The datasets were collected with fermentations that were mediated by autochthonous microorganisms and the presence of some potential pathogens such as Enterobacteriaceae, Clostridiaceae, Aeromonadaceae, Microbacteiaceae, Pseudomonadaceae, and Neisseriaceae which suggest the need for standardization of fermentation approaches. The genomes show the potential to synthesize metabolites such as essential amino acids and vitamins, suggesting that the respective fermented foods can be further optimized to enhance nutritional benefits.}, } @article {pmid36553546, year = {2022}, author = {Terrón-Camero, LC and Gordillo-González, F and Salas-Espejo, E and Andrés-León, E}, title = {Comparison of Metagenomics and Metatranscriptomics Tools: A Guide to Making the Right Choice.}, journal = {Genes}, volume = {13}, number = {12}, pages = {}, pmid = {36553546}, issn = {2073-4425}, mesh = {*Bacteria/genetics ; Archaea/genetics ; Software ; *Microbiota/genetics ; Metagenome/genetics ; }, abstract = {The study of microorganisms is a field of great interest due to their environmental (e.g., soil contamination) and biomedical (e.g., parasitic diseases, autism) importance. The advent of revolutionary next-generation sequencing techniques, and their application to the hypervariable regions of the 16S, 18S or 23S ribosomal subunits, have allowed the research of a large variety of organisms more in-depth, including bacteria, archaea, eukaryotes and fungi. Additionally, together with the development of analysis software, the creation of specific databases (e.g., SILVA or RDP) has boosted the enormous growth of these studies. As the cost of sequencing per sample has continuously decreased, new protocols have also emerged, such as shotgun sequencing, which allows the profiling of all taxonomic domains in a sample. The sequencing of hypervariable regions and shotgun sequencing are technologies that enable the taxonomic classification of microorganisms from the DNA present in microbial communities. However, they are not capable of measuring what is actively expressed. Conversely, we advocate that metatranscriptomics is a "new" technology that makes the identification of the mRNAs of a microbial community possible, quantifying gene expression levels and active biological pathways. Furthermore, it can be also used to characterise symbiotic interactions between the host and its microbiome. In this manuscript, we examine the three technologies above, and discuss the implementation of different software and databases, which greatly impact the obtaining of reliable results. Finally, we have developed two easy-to-use pipelines leveraging Nextflow technology. These aim to provide everything required for an average user to perform a metagenomic analysis of marker genes with QIMME2 and a metatranscriptomic study using Kraken2/Bracken.}, } @article {pmid36552852, year = {2022}, author = {Zargari Marandi, R and Jørgensen, M and Ilett, EE and Nørgaard, JC and Noguera-Julian, M and Paredes, R and Lundgren, JD and Sengeløv, H and MacPherson, CR}, title = {Pre-Transplant Prediction of Acute Graft-versus-Host Disease Using the Gut Microbiome.}, journal = {Cells}, volume = {11}, number = {24}, pages = {}, pmid = {36552852}, issn = {2073-4409}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Transplantation, Homologous ; *Graft vs Host Disease ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Bacteria ; }, abstract = {Gut microbiota is thought to influence host responses to allogeneic hematopoietic stem cell transplantation (aHSCT). Recent evidence points to this post-transplant for acute graft-versus-host disease (aGvHD). We asked whether any such association might be found pre-transplant and conducted a metagenome-wide association study (MWAS) to explore. Microbial abundance profiles were estimated using ensembles of Kaiju, Kraken2, and DeepMicrobes calls followed by dimensionality reduction. The area under the curve (AUC) was used to evaluate classification of the samples (aGvHD vs. none) using an elastic net to test the relevance of metagenomic data. Clinical data included the underlying disease (leukemia vs. other hematological malignancies), recipient age, and sex. Among 172 aHSCT patients of whom 42 developed aGVHD post transplantation, a total of 181 pre-transplant tool samples were analyzed. The top performing model predicting risk of aGVHD included a reduced species profile (AUC = 0.672). Beta diversity (37% in Jaccard's Nestedness by mean fold change, p < 0.05) was lower in those developing aGvHD. Ten bacterial species including Prevotella and Eggerthella genera were consistently found to associate with aGvHD in indicator species analysis, as well as relief and impurity-based algorithms. The findings support the hypothesis on potential associations between gut microbiota and aGvHD based on a data-driven approach to MWAS. This highlights the need and relevance of routine stool collection for the discovery of novel biomarkers.}, } @article {pmid36550785, year = {2023}, author = {Ye, D and Huang, J and Wu, J and Xie, K and Gao, X and Yan, K and Zhang, P and Tao, Y and Li, Y and Zang, S and Rong, X and Li, J and Guo, J}, title = {Integrative metagenomic and metabolomic analyses reveal gut microbiota-derived multiple hits connected to development of gestational diabetes mellitus in humans.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2154552}, pmid = {36550785}, issn = {1949-0984}, mesh = {Humans ; Pregnancy ; Female ; *Diabetes, Gestational/microbiology ; *Gastrointestinal Microbiome ; Blood Glucose/metabolism ; Metagenome ; Dopamine/analysis ; Metabolomics ; Bacteria/genetics/metabolism ; }, abstract = {Gestational diabetes mellitus (GDM) is characterized by the development of hyperglycemia and insulin resistance during the second or third trimester of pregnancy, associated with considerable risks to both the mother and developing fetus. Although emerging evidence suggests an association between the altered gut microbiota and GDM, remarkably little is known about the microbial and metabolic mechanisms that link the dysbiosis of the gut microbiota to the development of GDM. In this study, a metagenome-wide association study and serum metabolomics profiling were performed in a cohort of pregnant women with GDM and pregnant women with normal glucose tolerance (NGT). We identified gut microbial alterations associated with GDM and linked to the changes in circulating metabolites. Blood metabolite profiles revealed that GDM patients exhibited a marked increase in 2-hydroxybutyric acid and L-alpha-aminobutyric acid, but a decrease in methionine sulfoxide, allantoin, and dopamine and dopaminergic synapse, when compared with those in NGT controls. Short-chain fatty acid-producing genera, including Faecalibacterium, Prevotella, and Streptococcus, and species Bacteroides coprophilus, Eubacterium siraeum, Faecalibacterium prausnitzii, Prevotella copri, and Prevotella stercorea, were significantly reduced in GDM patients relative to those in NGT controls. Bacterial co-occurrence network analysis revealed that pro-inflammatory bacteria were over-represented as the core species in GDM patients. These microbial and metabolic signatures are closely associated with clinical parameters of glucose metabolism in GDM patients and NGT controls. In conclusion, we identified circulating dopamine insufficiency, imbalanced production of SCFAs, and excessive metabolic inflammation as gut microbiota-driven multiple parallel hits linked to GDM development. This work might explain in part the mechanistic link between altered gut microbiota and GDM pathogenesis, and suggest that gut microbiota may serve as a promising target to intervene in GDM.}, } @article {pmid36550399, year = {2022}, author = {Hu, X and Haas, JG and Lathe, R}, title = {The electronic tree of life (eToL): a net of long probes to characterize the microbiome from RNA-seq data.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {317}, pmid = {36550399}, issn = {1471-2180}, support = {MR/P011349/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {RNA-Seq ; *Microbiota/genetics ; Bacteria/genetics ; Archaea ; Metagenome ; *Viruses/genetics ; RNA, Ribosomal/genetics ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Microbiome analysis generally requires PCR-based or metagenomic shotgun sequencing, sophisticated programs, and large volumes of data. Alternative approaches based on widely available RNA-seq data are constrained because of sequence similarities between the transcriptomes of microbes/viruses and those of the host, compounded by the extreme abundance of host sequences in such libraries. Current approaches are also limited to specific microbial groups. There is a need for alternative methods of microbiome analysis that encompass the entire tree of life.

RESULTS: We report a method to specifically retrieve non-human sequences in human tissue RNA-seq data. For cellular microbes we used a bioinformatic 'net', based on filtered 64-mer sequences designed from small subunit ribosomal RNA (rRNA) sequences across the Tree of Life (the 'electronic tree of life', eToL), to comprehensively (98%) entrap all non-human rRNA sequences present in the target tissue. Using brain as a model, retrieval of matching reads, re-exclusion of human-related sequences, followed by contig building and species identification, is followed by confirmation of the abundance and identity of the corresponding species groups. We provide methods to automate this analysis. The method reduces the computation time versus metagenomics by a factor of >1000. A variant approach is necessary for viruses. Again, because of significant matches between viral and human sequences, a 'stripping' approach is essential. Contamination during workup is a potential problem, and we discuss strategies to circumvent this issue. To illustrate the versatility of the method we report the use of the eToL methodology to unambiguously identify exogenous microbial and viral sequences in human tissue RNA-seq data across the entire tree of life including Archaea, Bacteria, Chloroplastida, basal Eukaryota, Fungi, and Holozoa/Metazoa, and discuss the technical and bioinformatic challenges involved.

CONCLUSIONS: This generic methodology is likely to find wide application in microbiome analysis including diagnostics.}, } @article {pmid36549320, year = {2023}, author = {Liou, JM and Jiang, XT and Chen, CC and Luo, JC and Bair, MJ and Chen, PY and Chou, CK and Fang, YJ and Chen, MJ and Chen, CC and Lee, JY and Yang, TH and Yu, CC and Kuo, CC and Chiu, MC and Chen, CY and Shun, CT and Hu, WH and Tsai, MH and Hsu, YC and Tseng, CH and Chang, CY and Lin, JT and El-Omar, EM and Wu, MS and , }, title = {Second-line levofloxacin-based quadruple therapy versus bismuth-based quadruple therapy for Helicobacter pylori eradication and long-term changes to the gut microbiota and antibiotic resistome: a multicentre, open-label, randomised controlled trial.}, journal = {The lancet. Gastroenterology & hepatology}, volume = {8}, number = {3}, pages = {228-241}, doi = {10.1016/S2468-1253(22)00384-3}, pmid = {36549320}, issn = {2468-1253}, mesh = {Adult ; Male ; Humans ; Female ; Middle Aged ; Young Adult ; Anti-Bacterial Agents/adverse effects ; Bismuth/adverse effects ; Levofloxacin/therapeutic use ; *Helicobacter pylori ; Metronidazole/adverse effects ; Clarithromycin/adverse effects ; Esomeprazole/therapeutic use/adverse effects ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; Proton Pump Inhibitors/therapeutic use ; Drug Therapy, Combination ; Australia ; *Helicobacter Infections/drug therapy ; }, abstract = {BACKGROUND: Levofloxacin-based therapy or bismuth-based quadruple therapy are the recommended second-line regimens for Helicobacter pylori eradication after failure of clarithromycin-based therapy. However, resistance to levofloxacin has increased in the past decade. Furthermore, little is known about the long-term effects of H pylori eradication on the antibiotic resistome. In this study, we compared these second-line eradication therapies for efficacy, tolerability, and short-term and long-term effects on the gut microbiota, antibiotic resistome, and metabolic parameters.

METHODS: We did a multicentre, open-label, parallel group, randomised controlled trial at eight hospitals in Taiwan. Adult patients (age ≥20 years) with persistent H pylori infection after first-line clarithromycin-based therapy were randomly assigned (1:1, permuted block sizes of four) to receive levofloxacin-based sequential quadruple therapy for 14 days (EAML14; esomeprazole 40 mg and amoxicillin 1 g for 7 days, followed by esomeprazole 40 mg, metronidazole 500 mg, and levofloxacin 250 mg for 7 days, all twice-daily) or bismuth-based quadruple therapy for 10 days (BQ10; esomeprazole 40 mg twice daily, bismuth tripotassium dicitrate 300 mg four times a day, tetracycline 500 mg four times a day, and metronidazole 500 mg three times a day). All investigators were masked to the randomisation sequence. The primary endpoint was H pylori eradication rate measured by [13]C urea breath test 6 weeks after second-line treatment according to both intention-to-treat (ITT) and per-protocol analysis. The microbiota composition and antibiotic resistome of faecal samples collected at baseline (before treatment) and at 2 weeks, 8 weeks, and 1 year after eradication therapy was profiled by shotgun metagenomic sequencing and 16S rRNA gene sequencing. The frequency of adverse effects and changes in the gut microbiota and antibiotic resistome were assessed in all participants with available data. The trial is complete and registered with ClinicalTrails.gov, NCT03148366.

FINDINGS: Between Feb 25, 2015, and Dec 11, 2020, 560 patients were randomly assigned to receive EAML14 or BQ10 (n=280 per group; 261 [47%] men and 299 [53%] women). Mean age was 55·9 years (SD 12·7) in the EAML14 group and 54·9 years (12·3) in the BQ10 group. Eradication of H pylori was achieved in 246 (88%) of 280 participants in the EAML14 group and 245 (88%) of 280 in the BQ10 group according to ITT analysis (risk difference -0·4%, 95% CI -5·8 to 5·1; p=0·90). In the per-protocol analysis, 246 (90%) of 273 participants in the EAML14 group and 245 (93%) of 264 participants in the BQ10 group achieved H pylori eradication (risk difference 2·7%, 95% CI -0·2 to 7·4; p=0·27). Transient perturbation of faecal microbiota diversity at week 2 was largely restored to basal state 1 year after EAML14 or BQ10. Diversity recovery was slower with BQ10, and recovery in species abundance was partial after both therapies. On shotgun sequencing, we observed significant increases in total resistome after EAML14 (p=0·0002) and BQ10 (p=4·3 × 10[-10]) at week 2, which were restored to pretreatment level by week 8. The resistance rates of Escherichia coli and Klebsiella pneumonia to levofloxacin, ciprofloxacin, ampicillin (ampicillin-sulbactam for K pneumonia), and various cephalosporins were significantly increased in the EAML14 group compared with in the BQ10 group at week 2, which were restored to pretreatment levels and showed no significant differences at week 8 and 1 year. The frequency of any adverse effects was significantly higher after BQ10 therapy (211 [77%] of 273 participants) than after EAML14 therapy (134 [48%] of 277; p<0·0001).

INTERPRETATION: We found no evidence of superiority between levofloxacin-based quadruple therapy and bismuth-based quadruple therapy in the second-line treatment of H pylori infection. The transient increase in the antibiotic resistome and perturbation of faecal microbiota diversity were largely restored to pretreatment state from 2 months to 1 year after eradication therapy.

FUNDING: The Ministry of Science and Technology of Taiwan, the Ministry of Health and Welfare of Taiwan, National Taiwan University Hospital, Taipei Veteran General Hospital, and the Australian Federal Government through the St George and Sutherland Medical Research Foundation.

TRANSLATION: For the Chinese translation of the abstract see Supplementary Materials section.}, } @article {pmid36549300, year = {2023}, author = {Zhu, Y and Dwidar, M and Nemet, I and Buffa, JA and Sangwan, N and Li, XS and Anderson, JT and Romano, KA and Fu, X and Funabashi, M and Wang, Z and Keranahalli, P and Battle, S and Tittle, AN and Hajjar, AM and Gogonea, V and Fischbach, MA and DiDonato, JA and Hazen, SL}, title = {Two distinct gut microbial pathways contribute to meta-organismal production of phenylacetylglutamine with links to cardiovascular disease.}, journal = {Cell host & microbe}, volume = {31}, number = {1}, pages = {18-32.e9}, pmid = {36549300}, issn = {1934-6069}, support = {R21 CA267711/CA/NCI NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; R01 HL103866/HL/NHLBI NIH HHS/United States ; S10 OD016346/OD/NIH HHS/United States ; R01 HL160747/HL/NHLBI NIH HHS/United States ; }, mesh = {Mice ; Animals ; *Cardiovascular Diseases ; *Gastrointestinal Microbiome ; Glutamine ; }, abstract = {Recent studies show gut microbiota-dependent metabolism of dietary phenylalanine into phenylacetic acid (PAA) is critical in phenylacetylglutamine (PAGln) production, a metabolite linked to atherosclerotic cardiovascular disease (ASCVD). Accordingly, microbial enzymes involved in this transformation are of interest. Using genetic manipulation in selected microbes and monocolonization experiments in gnotobiotic mice, we identify two distinct gut microbial pathways for PAA formation; one is catalyzed by phenylpyruvate:ferredoxin oxidoreductase (PPFOR) and the other by phenylpyruvate decarboxylase (PPDC). PPFOR and PPDC play key roles in gut bacterial PAA production via oxidative and non-oxidative phenylpyruvate decarboxylation, respectively. Metagenomic analyses revealed a significantly higher abundance of both pathways in gut microbiomes of ASCVD patients compared with controls. The present studies show a role for these two divergent microbial catalytic strategies in the meta-organismal production of PAGln. Given the numerous links between PAGln and ASCVD, these findings will assist future efforts to therapeutically target PAGln formation in vivo.}, } @article {pmid36546449, year = {2023}, author = {Fontaine, SS and Kohl, KD}, title = {The microbiome buffers tadpole hosts from heat stress: a hologenomic approach to understand host-microbe interactions under warming.}, journal = {The Journal of experimental biology}, volume = {226}, number = {1}, pages = {}, pmid = {36546449}, issn = {1477-9145}, mesh = {Animals ; Larva ; Host Microbial Interactions ; *Microbiota ; *Thermotolerance ; }, abstract = {Phenotypic plasticity is an important strategy that animals employ to respond and adjust to changes in their environment. Plasticity may occur via changes in host gene expression or through functional changes in their microbiomes, which contribute substantially to host physiology. Specifically, the presence and function of host-associated microbes can impact how animals respond to heat stress. We previously demonstrated that 'depleted' tadpoles, with artificially disrupted microbiomes, are less tolerant to heat than 'colonized' tadpoles, with more natural microbiomes. However, the mechanisms behind these effects are unclear. Here, we compared gene expression profiles of the tadpole gut transcriptome, and tadpole gut microbial metagenome, between colonized and depleted tadpoles under cool or warm conditions. Our goal was to identify differences in host and microbial responses to heat between colonized and depleted tadpoles that might explain their observed differences in heat tolerance. We found that depleted tadpoles exhibited a much stronger degree of host gene expression plasticity in response to heat, while the microbiome of colonized tadpoles was significantly more heat sensitive. These patterns indicate that functional changes in the microbiome in response to heat may allow for a dampened host response, ultimately buffering hosts from the deleterious effects of heat stress. We also identified several specific host and microbial pathways that could be contributing to increased thermal tolerance in colonized tadpoles including amino acid metabolism, vitamin biosynthesis and ROS scavenging pathways. Our results demonstrate that the microbiome influences host plasticity and the response of hosts to environmental stressors.}, } @article {pmid36544282, year = {2023}, author = {Bai, X and Xu, Q and Zhang, W and Wang, C}, title = {The Gut-Eye Axis: Correlation Between the Gut Microbiota and Autoimmune Dry Eye in Individuals With Sjögren Syndrome.}, journal = {Eye & contact lens}, volume = {49}, number = {1}, pages = {1-7}, doi = {10.1097/ICL.0000000000000953}, pmid = {36544282}, issn = {1542-233X}, mesh = {Humans ; *Sjogren's Syndrome/complications ; *Gastrointestinal Microbiome ; *Autoimmune Diseases/complications/therapy ; Dysbiosis/complications ; *Dry Eye Syndromes/etiology/therapy ; }, abstract = {The impact of gut microbiota on human health, autoimmunity, and disease occurrence has long been recognized since the advancement of metagenomic sequencing technology has enabled a new level of perspective on the human microbiome. Emerging findings also suggest the existence of a gut-eye axis, wherein gut dysbiosis may be a crucial factor affecting the onset and progression of multiple ocular diseases. Sjögren syndrome (SS) is a chronic autoimmune disease mainly affecting the exocrine glands, primarily the lacrimal gland in the eye, resulting in severe dry eye. Although there are currently various treatments for environmental dry eye, the efficacy for SS-related autoimmune dry eye is limited, and new and more effective therapies still need to be explored. The latest studies have demonstrated that the gut microbiota plays a key role in the pathogenesis of autoimmune dry eye. This review describes the effect of gut microbiota on the ocular surface of autoimmune dry eye; introduces the presumable pathways forming the "gut dysbiosis-ocular surface-lacrimal gland axis"; discusses the advantages of restoring intestinal microecology to treat dry eye by fecal microbiota transplantation or probiotics, which are expected to provide perspectives into the correlation between the gut microbiome and dry eye; enhance our understanding of the pathogenesis in autoimmune dry eye; and be useful in the development of future interventions of dry eye by regulating the gut microbiota.}, } @article {pmid36543914, year = {2022}, author = {Chioma, OS and Mallott, EK and Chapman, A and Van Amburg, JC and Wu, H and Shah-Gandhi, B and Dey, N and Kirkland, ME and Blanca Piazuelo, M and Johnson, J and Bernard, GR and Bodduluri, SR and Davison, S and Haribabu, B and Bordenstein, SR and Drake, WP}, title = {Gut microbiota modulates lung fibrosis severity following acute lung injury in mice.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1401}, pmid = {36543914}, issn = {2399-3642}, support = {P20GM125504/GM/NIGMS NIH HHS/United States ; P20 GM125504/GM/NIGMS NIH HHS/United States ; T32AR059039-10/AR/NIAMS NIH HHS/United States ; K24 HL127301/HL/NHLBI NIH HHS/United States ; K12 HL 143956-4/HL/NHLBI NIH HHS/United States ; T32 AR059039/AR/NIAMS NIH HHS/United States ; R56 HL149129/HL/NHLBI NIH HHS/United States ; 1R56HL149129-01A1/HL/NHLBI NIH HHS/United States ; K12 HL143956/HL/NHLBI NIH HHS/United States ; K24 HL127301-01/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Humans ; Mice ; *Acute Lung Injury ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Interleukin-17 ; Mice, Inbred C57BL ; *Pulmonary Fibrosis/metabolism/pathology ; Fibroblasts/metabolism/microbiology ; }, abstract = {Independent studies demonstrate the significance of gut microbiota on the pathogenesis of chronic lung diseases; yet little is known regarding the role of the gut microbiota in lung fibrosis progression. Here we show, using the bleomycin murine model to quantify lung fibrosis in C57BL/6 J mice housed in germ-free, animal biosafety level 1 (ABSL-1), or animal biosafety level 2 (ABSL-2) environments, that germ-free mice are protected from lung fibrosis, while ABSL-1 and ABSL-2 mice develop mild and severe lung fibrosis, respectively. Metagenomic analysis reveals no notable distinctions between ABSL-1 and ABSL-2 lung microbiota, whereas greater microbial diversity, with increased Bifidobacterium and Lactobacilli, is present in ABSL-1 compared to ABSL-2 gut microbiota. Flow cytometric analysis reveals enhanced IL-6/STAT3/IL-17A signaling in pulmonary CD4 + T cells of ABSL-2 mice. Fecal transplantation of ABSL-2 stool into germ-free mice recapitulated more severe fibrosis than transplantation of ABSL-1 stool. Lactobacilli supernatant reduces collagen 1 A production in IL-17A- and TGFβ1-stimulated human lung fibroblasts. These findings support a functional role of the gut microbiota in augmenting lung fibrosis severity.}, } @article {pmid36543896, year = {2022}, author = {Tramice, A and Paris, D and Manca, A and Guevara Agudelo, FA and Petrosino, S and Siracusa, L and Carbone, M and Melck, D and Raymond, F and Piscitelli, F}, title = {Analysis of the oral microbiome during hormonal cycle and its alterations in menopausal women: the "AMICA" project.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {22086}, pmid = {36543896}, issn = {2045-2322}, mesh = {Female ; Humans ; *Luteinizing Hormone ; Follicle Stimulating Hormone ; Menopause ; Menstrual Cycle ; *Microbiota ; }, abstract = {The maintenance of human health is dependent on a symbiotic relationship between humans and associated bacteria. The diversity and abundance of each habitat's signature microbes vary widely among body areas and among them the oral microbiome plays a key role. Significant changes in the oral cavity, predominantly at salivary and periodontal level, have been associated with changes in estrogen levels. However, whether the oral microbiome is affected by hormonal level alterations is understudied. Hence the main objective pursued by AMICA project was to characterize the oral microbiome (saliva) in healthy women through: profiling studies using "omics" technologies (NMR-based metabolomics, targeted lipidomics by LC-MS, metagenomics by NGS); SinglePlex ELISA assays; glycosidase activity analyses and bioinformatic analysis. For this purpose, thirty-nine medically healthy women aged 26-77 years (19 with menstrual cycle and 20 in menopause) were recruited. Participants completed questionnaires assessing detailed medical and medication history and demographic characteristics. Plasmatic and salivary levels of sexual hormones were assessed (FSH, estradiol, LH and progesteron) at day 3 and 14 for women with menstrual cycle and only once for women in menopause. Salivary microbiome composition was assessed through meta-taxonomic 16S sequencing and overall, the salivary microbiome of most women remained relatively stable throughout the menstrual cycle and in menopause. Targeted lipidomics and untargeted metabolomics profiling were assessed through the use of LC-MS and NMR spectroscopy technologies, respectively and significant changes in terms of metabolites were identified in saliva of post-menopausal women in comparison to cycle. Moreover, glycosyl hydrolase activities were screened and showed that the β-D-hexosaminidase activity was the most present among those analyzed. Although this study has not identified significant alterations in the composition of the oral microbiome, multiomics analysis have revealed a strong correlation between 2-AG and α-mannosidase. In conclusion, the use of a multidisciplinary approach to investigate the oral microbiome of healthy women provided some indication about microbiome-derived predictive biomarkers that could be used in the future for developing new strategies to help to re-establish the correct hormonal balance in post-menopausal women.}, } @article {pmid36539569, year = {2023}, author = {Shi, F and Liu, G and Lin, Y and Guo, CL and Han, J and Chu, ESH and Shi, C and Li, Y and Zhang, H and Hu, C and Liu, R and He, S and Guo, G and Chen, Y and Zhang, X and Coker, OO and Wong, SH and Yu, J and She, J}, title = {Altered gut microbiome composition by appendectomy contributes to colorectal cancer.}, journal = {Oncogene}, volume = {42}, number = {7}, pages = {530-540}, pmid = {36539569}, issn = {1476-5594}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; Dysbiosis/microbiology ; Appendectomy/adverse effects ; Longitudinal Studies ; *Colorectal Neoplasms/genetics/microbiology ; }, abstract = {Appendectomy impacts the homeostasis of gut microbiome in patients. We aimed to study the role of appendectomy in colorectal cancer (CRC) risk through causing gut microbial dysbiosis. Population-based longitudinal study (cohort 1, n = 129,155) showed a 73.0% increase in CRC risk among appendectomy cases throughout 20 years follow-up (Adjusted sub-distribution hazard ratio (SHR) 1.73, 95% CI 1.49-2.01, P < 0.001). Shotgun metagenomic sequencing was performed on fecal samples from cohort 2 (n = 314). Gut microbial dysbiosis in appendectomy subjects was observed with significant enrichment of 7 CRC-promoting bacteria (Bacteroides vulgatus, Bacteroides fragilis, Veillonella dispar, Prevotella ruminicola, Prevotella fucsa, Prevotella dentalis, Prevotella denticola) and depletion of 5 beneficial commensals (Blautia sp YL58, Enterococcus hirae, Lachnospiraceae bacterium Choco86, Collinsella aerofaciens, Blautia sp SC05B48). Microbial network analysis showed increased correlation strengths among enriched bacteria and their enriched oncogenic pathways in appendectomy subjects compared to controls. Of which, B. fragilis was the centrality in the network of the enriched bacteria. We further confirmed that appendectomy promoted colorectal tumorigenesis in mice by causing gut microbial dysbiosis and impaired intestinal barrier function. Collectively, this study revealed appendectomy-induced microbial dysbiosis characterized by enriched CRC-promoting bacteria and depleted beneficial commensals, signifying that the gut microbiome may play a crucial role in CRC development induced by appendectomy.}, } @article {pmid36539432, year = {2022}, author = {Zhou, J and Zhang, Q and Zhao, Y and Zou, Y and Chen, M and Zhou, S and Wang, Z}, title = {The relationship of Megamonas species with nonalcoholic fatty liver disease in children and adolescents revealed by metagenomics of gut microbiota.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {22001}, pmid = {36539432}, issn = {2045-2322}, mesh = {Humans ; Adolescent ; Child ; *Non-alcoholic Fatty Liver Disease/pathology ; *Gastrointestinal Microbiome/genetics ; Firmicutes ; Liver/metabolism ; }, abstract = {Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease in children and adolescents. The gut microbiota plays an important role in the pathophysiology of NAFLD through the gut-liver axis. Therefore, we aimed to investigate the genus and species of gut microbiota and their functions in children and adolescents with NAFLD. From May 2017 to July 2018, a total of 58 children and adolescents, including 27 abnormal weight (AW) (obese) NAFLD patients, 16 AW non-NAFLD children, and 15 healthy children, were enrolled in this study at Shenzhen Children's Hospital. All of them underwent magnetic resonance spectroscopy (MRS) to quantify the liver fat fraction. Stool samples were collected and analysed with metagenomics. According to body mass index (BMI) and MRS proton density fat fraction (MRS-PDFF), we divided the participants into BMI groups, including the AW group (n = 43) and the Lean group (n = 15); MRS groups, including the NAFLD group (n = 27) and the Control group (n = 31); and BMI-MRS 3 groups, including NAFLD_AW (AW children with NAFLD) (n = 27), Ctrl_AW (n = 16) (AW children without NAFLD) and Ctrl_Lean (n = 15). There was no difference in sex or age among those groups (p > 0.05). In the BMI groups, at the genus level, Dialister, Akkermansia, Odoribacter, and Alistipes exhibited a significant decrease in AW children compared with the Lean group. At the species level, Megamonas hypermegale was increased in the AW group, while Akkermansia muciniphila, Dialister invisus, Alistipes putredinis, Bacteroides massiliensis, Odoribacter splanchnicus, and Bacteroides thetaiotaomicron were decreased in AW children, compared to the Lean group. Compared with the Control group, the genus Megamonas, the species of Megamonas hypermegale and Megamonas rupellensis, increased in the NAFLD group. Furthermore, the genus Megamonas was enriched in the NAFLD_AW group, while Odoribacter, Alistipes, Dialister, and Akkermansia were depleted compared with the Ctrl_Lean or Ctrl_AW group at the genus level. Megamonas hypermegale and Megamonas rupellensis exhibited a significant increase in NAFLD_AW children compared with the Ctrl_Lean or Ctrl_AW group at the species level. Compared with healthy children, the pathways of P461-PWY contributed by the genus Megamonas were significantly increased in NAFLD_AW. We found that compared to healthy children, the genus Megamonas was enriched, while Megamonas hypermegale and Megamonas rupellensis were enriched at the species level in children and adolescents with NAFLD. This indicates that the NAFLD status and/or diet associated with NAFLD patients might lead to the enrichment of the genus Megamonas or Megamonas species.}, } @article {pmid36537058, year = {2022}, author = {Ul-Haq, A and Seo, H and Jo, S and Park, H and Kim, S and Lee, Y and Lee, S and Jeong, JH and Song, HY}, title = {Characterization of Fecal Microbiomes of Osteoporotic Patients in Korea.}, journal = {Polish journal of microbiology}, volume = {71}, number = {4}, pages = {601-613}, pmid = {36537058}, issn = {2544-4646}, mesh = {Humans ; Bacteria ; *Microbiota ; *Gastrointestinal Microbiome ; Feces/chemistry ; *Osteoporosis ; RNA, Ribosomal, 16S/genetics ; Biomarkers ; Republic of Korea ; }, abstract = {An imbalanced gut microbiome has been linked to a higher risk of many bone-related diseases. The objective of this study was to discover biomarkers of osteoporosis (OP). So, we collected 76 stool samples (60 human controls and 16 OP patients), extracted DNA, and performed 16S ribosomal ribonucleic acid (rRNA) gene-based amplicon sequencing. Among the taxa with an average taxonomic composition greater than 1%, only the Lachnospira genus showed a significant difference between the two groups. The Linear Discriminant Effect Size analysis and qPCR experiments indicated the Lachnospira genus as a potential biomarker of OP. Moreover, a total of 11 metabolic pathways varied between the two groups. Our study concludes that the genus Lachnospira is potentially crucial for diagnosing and treating osteoporosis. The findings of this study might help researchers better understand OP from a microbiome perspective. This research might develop more effective diagnostic and treatment methods for OP in the future.}, } @article {pmid36536072, year = {2023}, author = {Camargo, AP and de Souza, RSC and Jose, J and Gerhardt, IR and Dante, RA and Mukherjee, S and Huntemann, M and Kyrpides, NC and Carazzolle, MF and Arruda, P}, title = {Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot.}, journal = {The ISME journal}, volume = {17}, number = {3}, pages = {354-370}, pmid = {36536072}, issn = {1751-7370}, mesh = {*Ecosystem ; Brazil ; Soil Microbiology ; Biodiversity ; *Microbiota ; Bacteria/genetics/metabolism ; Plants/metabolism ; Soil/chemistry ; Phosphorus/metabolism ; Nitrogen/metabolism ; }, abstract = {The substrates of the Brazilian campos rupestres, a grassland ecosystem, have extremely low concentrations of phosphorus and nitrogen, imposing restrictions to plant growth. Despite that, this ecosystem harbors almost 15% of the Brazilian plant diversity, raising the question of how plants acquire nutrients in such a harsh environment. Here, we set out to uncover the taxonomic profile, the compositional and functional differences and similarities, and the nutrient turnover potential of microbial communities associated with two plant species of the campos rupestres-dominant family Velloziaceae that grow over distinct substrates (soil and rock). Using amplicon sequencing data, we show that, despite the pronounced composition differentiation, the plant-associated soil and rock communities share a core of highly efficient colonizers that tend to be highly abundant and is enriched in 21 bacterial families. Functional investigation of metagenomes and 522 metagenome-assembled genomes revealed that the microorganisms found associated to plant roots are enriched in genes involved in organic compound intake, and phosphorus and nitrogen turnover. We show that potential for phosphorus transport, mineralization, and solubilization are mostly found within bacterial families of the shared microbiome, such as Xanthobacteraceae and Bryobacteraceae. We also detected the full repertoire of nitrogen cycle-related genes and discovered a lineage of Isosphaeraceae that acquired nitrogen-fixing potential via horizontal gene transfer and might be also involved in nitrification via a metabolic handoff association with Binataceae. We highlight that plant-associated microbial populations in the campos rupestres harbor a genetic repertoire with potential to increase nutrient availability and that the microbiomes of biodiversity hotspots can reveal novel mechanisms of nutrient turnover.}, } @article {pmid36533929, year = {2023}, author = {Rojas, CA and Holekamp, KE and Viladomat Jasso, M and Souza, V and Eisen, JA and Theis, KR}, title = {Taxonomic, Genomic, and Functional Variation in the Gut Microbiomes of Wild Spotted Hyenas Across 2 Decades of Study.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0096522}, pmid = {36533929}, issn = {2379-5077}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Hyaenidae/genetics ; RNA, Ribosomal, 16S/genetics ; *Carnivora/genetics ; Metagenomics ; }, abstract = {The gut microbiome provides vital functions for mammalian hosts, yet research on its variability and function across adult life spans and multiple generations is limited in large mammalian carnivores. Here, we used 16S rRNA gene and metagenomic high-throughput sequencing to profile the bacterial taxonomic composition, genomic diversity, and metabolic function of fecal samples collected from 12 wild spotted hyenas (Crocuta crocuta) residing in the Masai Mara National Reserve, Kenya, over a 23-year period spanning three generations. The metagenomic data came from four of these hyenas and spanned two 2-year periods. With these data, we determined the extent to which host factors predicted variation in the gut microbiome and identified the core microbes present in the guts of hyenas. We also investigated novel genomic diversity in the mammalian gut by reporting the first metagenome-assembled genomes (MAGs) for hyenas. We found that gut microbiome taxonomic composition varied temporally, but despite this, a core set of 14 bacterial genera were identified. The strongest predictors of the microbiome were host identity and age, suggesting that hyenas possess individualized microbiomes and that these may change with age during adulthood. The gut microbiome functional profiles of the four adult hyenas were also individual specific and were associated with prey abundance, indicating that the functions of the gut microbiome vary with host diet. We recovered 149 high-quality MAGs from the hyenas' guts; some MAGs were classified as taxa previously reported for other carnivores, but many were novel and lacked species-level matches to genomes in existing reference databases. IMPORTANCE There is a gap in knowledge regarding the genomic diversity and variation of the gut microbiome across a host's life span and across multiple generations of hosts in wild mammals. Using two types of sequencing approaches, we found that although gut microbiomes were individualized and temporally variable among hyenas, they correlated similarly to large-scale changes in the ecological conditions experienced by their hosts. We also recovered 149 high-quality MAGs from the hyena gut, greatly expanding the microbial genome repertoire known for hyenas, carnivores, and wild mammals in general. Some MAGs came from genera abundant in the gastrointestinal tracts of canid species and other carnivores, but over 80% of MAGs were novel and from species not previously represented in genome databases. Collectively, our novel body of work illustrates the importance of surveying the gut microbiome of nonmodel wild hosts, using multiple sequencing methods and computational approaches and at distinct scales of analysis.}, } @article {pmid36527826, year = {2023}, author = {Lv, Y and Lou, Y and Liu, A and Cheng, Q and Yang, G and Xu, C and Luo, Y and Lou, J and Yu, J and Fang, Y and Zhao, H and Peng, K and Ni, Y and Chen, J}, title = {The impact of exclusive enteral nutrition on the gut microbiome and bile acid metabolism in pediatric Crohn's disease.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {42}, number = {2}, pages = {116-128}, doi = {10.1016/j.clnu.2022.11.018}, pmid = {36527826}, issn = {1532-1983}, mesh = {Child ; Humans ; *Bile Acids and Salts/metabolism ; *Crohn Disease/diet therapy/etiology/metabolism/microbiology ; *Enteral Nutrition ; Firmicutes/isolation & purification ; *Gastrointestinal Microbiome ; Leukocyte L1 Antigen Complex/analysis ; Remission Induction ; Dysbiosis/complications/metabolism/microbiology ; Feces/chemistry/microbiology ; }, abstract = {BACKGROUND: Gut dysbiosis and associated bile acid (BA) metabolism play an important role in the pathogenesis of Crohn's disease (CD). We investigated the impacts of the exclusive enteral nutrition treatment (EEN) on the gut microbiome (GM) and BAs metabolism for patients with CD.

METHODS: Targeted metabolomics analysis and metagenomics analysis were performed in feces to investigate the BA and GM changes of patients before and after 2-months EEN therapy. The Pediatric Crohn's Disease Activity Index (PCDAI) and fecal calprotectin were used to evaluate the severity and mucosal inflammation of CD.

RESULTS: A total of 27 newly diagnosed pediatric patients with CD and 27 healthy controls were recruited in this study. Both GM structure and the secondary BA metabolism were significantly impaired in patients, which could return towards normal levels after EEN treatment. The most abundant taxa Firmicutes and 11 BAs were found closely associated with the PCDAI score and fecal calprotectin. Meanwhile, the close interactions between Firmicute bacteria and BAs might contribute to the remission of CD after EEN treatment. The qPCR data further confirmed that the relative expressions of Firmicutes phylum, and genus Flavonifractor and Clostridium V were improved after EEN treatment.

CONCLUSIONS: Firmicutes bacteria and the balance of primary and secondary BA compositions in the gut were closely associated with the health status of CD disease indicated by the PCDAI score and fecal calprotectin. Understanding the recovery process of gut microbiome and BA metabolism will help us to explore the potential mechanisms of EEN therapy.}, } @article {pmid36527813, year = {2023}, author = {Jan, TR and Lin, CS and Wang, SY and Yang, WY}, title = {Cytokines and cecal microbiome modulations conferred by a dual vaccine in Salmonella-infected layers.}, journal = {Poultry science}, volume = {102}, number = {2}, pages = {102373}, pmid = {36527813}, issn = {1525-3171}, mesh = {Humans ; Animals ; Cytokines ; Salmonella enteritidis ; RNA, Ribosomal, 16S ; Chickens/genetics ; *Salmonella Vaccines ; *Microbiota ; Vaccines, Attenuated ; *Salmonella Infections, Animal/prevention & control ; *Poultry Diseases/prevention & control ; }, abstract = {Zoonotic Salmonella infection is a critical and challenging issue for public health. Since human infections are mainly associated with consuming contaminated chicken products, strategies to reduce Salmonella carriage and shedding are essential. Here we investigate the mechanisms of the live attenuated Salmonella vaccine (AviPro Salmonella Duo) against Salmonella Enteritidis (SE) infection. We focused on inflammatory-related cytokine expressions and cecal microbiota modulations in specific-pathogen-free (SPF) and field layers. Forty-eight 2-day-old SPF layers were randomly allotted into S.SEvc, S.SEc, S.Vc, and S.Ct groups in trial 1. The equal number of filed layers at 25 wk were allocated into SEvc, SEc, Vc, and Ct groups in trial 2. Each group contained 12 layers. Groups were further assigned for vaccination (S.Vc and Vc groups), SE challenge (S.SEc and SEc groups), vaccination and the following SE challenge (S.SEvc and SEvc groups), or the placebo treatment (S.Ct and Ct groups). Cecal tissues and contents of layers on day 14 post-SE-challenges were collected for cytokine mRNA expression and 16S rRNA metagenomic analyses. We found that SE challenges significantly upregulated expressions of IFNγ, IL-1β, IL-12β, and NFκB1A in SPF layers. The vaccine notably counteracted the levels of IFNα, IFNγ, and NFκB1A activated by SE attacks. The vaccination, SE challenge, and their combination did not significantly affect alpha diversities but promoted dissimilarities in microbial communities between groups. Eubacterium_coprostanoligenes and Faecalibacterium_prausnitzii were identified as contributory taxa in the cecal microbiota of SE-challenged and vaccinated SPF layers. A significantly higher abundance of Faecalibacterium_prausnitzii in the ceca further correlated with the vaccination conferred protection against SE infection. In contrast, Oscillibacter_valericigenes and Mediterraneibacter_glycyrrhizinilyticus were featured taxa in Salmonella-infected field layers. Megamonas_hypermegale and Megamonas_rupellensis were identified as featured taxa in vaccinated field layers compared to SE-infected layers. To conclude, applying a dual Salmonella vaccine in this study modulated expressions of inflammatory-related cytokines and the cecal microbiome in layers, contributing to protection against SE infection. The feature microbes are promising for developing predictive indices and as antibiotic alternatives added to feed to reduce the risk of Salmonella shedding and contamination.}, } @article {pmid36527793, year = {2023}, author = {Du, H and Chen, B and Fu, W and Yang, F and Lv, X and Tan, Y and Xi, X and Wang, L and Xu, Y}, title = {Composition and function of viruses in sauce-flavor baijiu fermentation.}, journal = {International journal of food microbiology}, volume = {387}, number = {}, pages = {110055}, doi = {10.1016/j.ijfoodmicro.2022.110055}, pmid = {36527793}, issn = {1879-3460}, mesh = {Fermentation ; Bacteria/genetics/metabolism ; *Microbiota/genetics ; Food ; *Bacteriophages/genetics ; }, abstract = {Viruses are highly abundant in nature, associated with quality and safety of traditional fermented foods. However, the overall viral diversity and function are still poorly understood in food microbiome. Traditional baijiu fermentation is an ideal model system to examine the diversity and function of viruses owing to easy access, stable operation, and domesticated microbial community. Equipped with cutting-edge viral metagenomics, we investigated the viral community in the fermented grain and fermentation environment, as well as their contribution to baijiu fermentation. Viral communities in the fermented grains and fermentation environment are highly similar. The dominant viruses were bacteriophages, mainly including the order Caudovirales and the family Inoviridae. Furtherly, association network analysis showed that viruses and bacteria were significantly negatively correlated (P < 0.01). Viral diversity could significantly influence bacterial and fungal succession (P < 0.05). Moreover, we proved that starter phages could significantly inhibit the growth of Bacillus licheniformis in the logarithmic growth stage (P < 0.05) under culture condition. Based on the functional annotations, viruses and bacteria both showed high distribution of genes related to amino acid and carbohydrate metabolism. In addition, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes were also identified in viruses, indicating that viruses were involved in the decomposition of complex polysaccharides during fermentation. Our results revealed that viruses could crucially affect microbial community and metabolism during traditional fermentation.}, } @article {pmid36526191, year = {2023}, author = {Barbosa, FAS and Brait, LAS and Coutinho, FH and Ferreira, CM and Moreira, EF and de Queiroz Salles, L and Meirelles, PM}, title = {Ecological landscape explains aquifers microbial structure.}, journal = {The Science of the total environment}, volume = {862}, number = {}, pages = {160822}, doi = {10.1016/j.scitotenv.2022.160822}, pmid = {36526191}, issn = {1879-1026}, mesh = {Humans ; *Groundwater/chemistry ; Bacteria/metabolism ; Water Quality ; Gram-Negative Bacteria ; *Microbiota ; }, abstract = {Aquifers have significant social, economic, and ecological importance. They supply 30 % of the freshwater for human consumption worldwide, including agricultural and industrial use. Despite aquifers' importance, the relationships between aquifer categories and their inhabiting microbial communities are still unknown. Characterizing variations within microbial communities' function and taxonomy structure at different aquifers could give a panoramic view of patterns that may enable the detection and prediction of environmental impact caused by multiple sources. Using publicly available shotgun metagenomic datasets, we examined whether soil properties, land use, and climate variables would have a more significant influence on the taxonomy and functional structure of the microbial communities than the ecological landscapes of the aquifer (i.e., Karst, Porous, Saline, Geyser, and Porous Contaminated). We found that these categories are stronger predictors of microbial communities' structure than geographical localization. In addition, our results show that microbial richness and dominance patterns are the opposite of those found in multicellular life, where extreme habitats harbour richer functional and taxonomic microbial communities. We found that low-abundant and recently described candidate taxa, such as the chemolithoautotrophic genus Candidatus Altiarcheum and the Candidate phylum Parcubacteria, are the main contributors to aquifer microbial communities' dissimilarities. Genes related to gram-negative bacteria proteins, cell wall structures, and phage activity were the primary contributors to aquifer microbial communities' dissimilarities among the aquifers' ecological landscapes. The results reported in the present study highlight the utility of using ecological landscapes for investigating aquifer microbial communities. In addition, we suggest that functions played by recently described and low abundant bacterial groups need further investigation once they might affect water quality, geochemical cycles, and the effects of anthropogenic disturbances such as pollution and climatic events on aquifers.}, } @article {pmid36526186, year = {2023}, author = {Nie, S and Mo, S and Gao, T and Yan, B and Shen, P and Kashif, M and Zhang, Z and Li, J and Jiang, C}, title = {Coupling effects of nitrate reduction and sulfur oxidation in a subtropical marine mangrove ecosystem with Spartina alterniflora invasion.}, journal = {The Science of the total environment}, volume = {862}, number = {}, pages = {160930}, doi = {10.1016/j.scitotenv.2022.160930}, pmid = {36526186}, issn = {1879-1026}, mesh = {*Ecosystem ; *Wetlands ; Nitrates/metabolism ; Introduced Species ; Poaceae/metabolism ; Nitrogen/analysis ; Sulfur/metabolism ; China ; }, abstract = {The mangrove ecosystem has a high nitrate reduction capacity, which significantly alleviates severe nitrogen pollution. However, current research on nitrate reduction mechanisms in the mangrove ecosystem is limited. Furthermore, Spartina alterniflora invasion has disrupted the balance of the mangrove ecosystem and the effect of S. alterniflora on nitrate reduction has not yet been fully elucidated. Nitrate reduction was comprehensively investigated in a subtropical mangrove ecosystem in this study, which has been invaded by S. alterniflora for 40 years. Results showed that S. alterniflora significantly increased the relative and absolute abundance of nitrate reduction genes, especially nirS (nitrite reductase), in the mangrove ecosystem. Dissimilatory nitrate reduction to ammonium was the main pathway of nitrate reduction in the mangrove ecosystem. Nitrate reduction was mainly performed by Desulfobacterales and occurred in the shallow layers (0-10 cm) of mangrove sediments. A strong positive correlation was found between nitrate reduction and sulfur oxidation (especially sulfide oxidation), and the sulfide content was significantly positively correlated with the relative abundance of nitrate reduction genes. Moreover, 207 metagenomic assembled genomes (MAGs) were constructed, including 50 MAGs with high numbers (≥ 10) of nitrate reduction genes. This finding indicates that the dominant microbes had strong nitrate reduction potential in mangrove sediments. Our findings highlight the impact of S. alterniflora invasion on nitrate reduction in a subtropical marine mangrove ecosystem. This study provides new insights into our understanding of nitrogen pollution control and contributes to the exploration of new nitrogen-degrading microbes in mangrove ecosystems.}, } @article {pmid36524338, year = {2023}, author = {Lee, W and Kim, MH and Park, J and Kim, YJ and Kim, E and Heo, EJ and Kim, SH and Kim, G and Shin, H and Kim, SH and Kim, HY}, title = {Seasonal Changes in the Microbial Communities on Lettuce (Lactuca sativa L.) in Chungcheong-do, South Korea.}, journal = {Journal of microbiology and biotechnology}, volume = {33}, number = {2}, pages = {219-227}, pmid = {36524338}, issn = {1738-8872}, mesh = {*Lactuca/microbiology ; Seasons ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenome ; Bacteria ; }, abstract = {Lettuce is one of the most consumed vegetables worldwide. However, it has potential risks associated with pathogenic bacterial contamination because it is usually consumed raw. In this study, we investigated the changes in the bacterial community on lettuce (Lactuca sativa L.) in Chungcheong-do, South Korea, and the prevalence of foodborne pathogens on lettuce in different seasons using 16S rRNA gene-based sequencing. Our data revealed that the Shannon diversity index showed the same tendency in term of the number of OTUs, with the index being greatest for summer samples in comparison to other seasons. Moreover, the microbial communities were significantly different between the four seasons. The relative abundance of Actinobacteriota varied according to the season. Family Micrococcaceae was most dominant in all samples except summer, and Rhizobiaceae was predominant in the microbiome of the summer sample. At the genus level, the relative abundance of Bacillus was greatest in spring samples, whereas Pseudomonas was greatest in winter samples. Potential pathogens, such as Staphylococcus and Clostridium, were detected with low relative abundance in all lettuce samples. We also performed metagenome shotgun sequencing analysis on the selected summer and winter samples, which were expected to be contaminated with foodborne pathogens, to support 16S rRNA gene-based sequencing dataset. Moreover, we could detect seasonal biomarkers and microbial association networks of microbiota on lettuce samples. Our results suggest that seasonal characteristics of lettuce microbial communities, which include diverse potential pathogens, can be used as basic data for food safety management to predict and prevent future outbreaks.}, } @article {pmid36523460, year = {2022}, author = {Baeza, JA}, title = {Mitochondrial genomes assembled from non-invasive eDNA metagenomic scat samples in the endangered Amur tiger Panthera tigris altaica.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e14428}, pmid = {36523460}, issn = {2167-8359}, mesh = {Animals ; *Tigers/genetics ; *Genome, Mitochondrial/genetics ; Endangered Species ; Metagenomics ; Metagenome ; }, abstract = {The Amur or Siberian tiger Panthera tigris altaica (Temminck, 1844) is currently restricted to a small region of its original geographical range in northwestern Asia and is considered 'endangered' by the IUCN Red List of Threatened Species. This solitary, territorial, and large top predator is in major need of genomic resources to inform conservation management strategies. This study formally tested if complete mitochondrial genomes of P. tigris altaica can be assembled from non-enriched metagenomic libraries generated from scat eDNA samples using the Illumina sequencing platform and open-access bioinformatics pipelines. The mitogenome of P. tigris altaica was assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 322.7x to 17.6x in four different scat eDNA samples. A nearly complete mitochondrial genome (101x) was retrieved from a fifth scat eDNA sample. The complete or nearly complete mitochondrial genomes of P. tigris altaica were AT-rich and composed of 13 protein coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Synteny observed in all assembled mitogenomes was identical to that reported before for P. tigris altaica and other felids. A phylogenomic analysis based on all PCGs demonstrated that the mitochondrial genomes assembled from scat eDNA reliably identify the sequenced samples as belonging to P. tigris and distinguished the same samples from closely and distantly related congeneric species. This study demonstrates that it is viable to retrieve accurate whole and nearly complete mitochondrial genomes of P. tigris altaica (and probably other felids) from scat eDNA samples without library enrichment protocols and using open-access bioinformatics workflows. This new genomic resource represents a new tool to support conservation strategies (bio-prospecting and bio-monitoring) in this iconic cat.}, } @article {pmid36522829, year = {2023}, author = {Shimomura, Y and Zha, L and Komukai, S and Narii, N and Sobue, T and Kitamura, T and Shiba, S and Mizutani, S and Yamada, T and Sawada, N and Yachida, S}, title = {Mediation effect of intestinal microbiota on the relationship between fiber intake and colorectal cancer.}, journal = {International journal of cancer}, volume = {152}, number = {9}, pages = {1752-1762}, doi = {10.1002/ijc.34398}, pmid = {36522829}, issn = {1097-0215}, mesh = {Male ; Humans ; Middle Aged ; Female ; *Colorectal Neoplasms/diagnosis ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; *Gemella ; Fusobacterium nucleatum ; }, abstract = {Higher fiber intake has been associated with a lower risk of colorectal cancer (CRC) and has been shown to protect against CRC based on probable evidence. Recent studies revealed a possible mechanism whereby the interaction between intestinal microbiota and fiber intake mediates CRC risk. However, the specific intestinal bacteria and the amount of these bacteria involved in this mechanism are not fully known. Therefore, this single-center study aimed to determine whether specific intestinal bacteria mediated the relationship between fiber intake and CRC risk. We enrolled patients who received colonoscopy at National Cancer Center Hospital. This cross-sectional study included 180 patients with clinically diagnosed CRC and 242 controls. We conducted a causal mediation analysis to assess the natural indirect effect and natural direct effect of specific intestinal bacteria on association between fiber intake and CRC risk. The median age was 64 (interquartile range, 54-70) years, and 58% of the participants were males. We used metagenomics for profiling gut microbiomes. The relative abundance of each species in each sample was calculated. Among the candidate, Fusobacterium nucleatum and Gemella morbillorum had a significant natural indirect effect based on their highest fiber intake compared to the lowest fiber intake, with a risk difference (95% confidence interval, proportion of mediation effect) of -0.06 [-0.09 to -0.03, 23%] and -0.03 [-0.06 to -0.01, 10.5%], respectively. Other bacteria did not display natural indirect effects. In conclusion, Fusobacterium nucleatum and Gemella morbillorum were found to mediate the relationship between fiber intake and CRC risk.}, } @article {pmid36522762, year = {2022}, author = {Olías-Molero, AI and Botías, P and Cuquerella, M and García-Cantalejo, J and Barcia, E and Torrado, S and Torrado, JJ and Alunda, JM}, title = {Leishmania infantum infection does not affect the main composition of the intestinal microbiome of the Syrian hamster.}, journal = {Parasites & vectors}, volume = {15}, number = {1}, pages = {468}, pmid = {36522762}, issn = {1756-3305}, support = {PR87/19-22646//Proyectos Santander/Complutense/ ; }, mesh = {Cricetinae ; Dogs ; Male ; Animals ; *Leishmania infantum ; Mesocricetus ; *Gastrointestinal Microbiome ; *Leishmaniasis, Visceral/parasitology ; *Leishmaniasis/parasitology ; Immunoglobulin G ; }, abstract = {BACKGROUND: Visceral leishmaniasis (VL) is the most severe form of all leishmanial infections and is caused by infection with protozoa of Leishmania donovani and Leishmania infantum. This parasitic disease occurs in over 80 countries and its geographic distribution is on the rise. Although the interaction between the intestinal microbiome and the immune response has been established in several pathologies, it has not been widely studied in leishmaniasis. The Syrian hamster is the most advanced laboratory model for developing vaccines and new drugs against VL. In the study reported here, we explored the relationship between the intestinal microbiome and infection with L. infantum in this surrogate host.

METHODS: Male Syrian hamsters (120-140 g) were inoculated with 10[8] promastigotes of a canine-derived L. infantum strain or left as uninfected control animals. Infection was maintained for 19 weeks (endpoint) and monitored by an immunoglobulin G (IgG) enyzme-linked immunosorbent assay throughout the experiment. Individual faecal samples, obtained at weeks 16, 18 and 19 post-inoculation, were analysed to determine the 16S metagenomic composition (the operational taxonomic units [OTUs] of the intestinal microbiome and the comparison between groups were FDR (false discovery rate)-adjusted).

RESULTS: Leishmania infantum infection elicited moderate clinical signs and lesions and a steady increase in specific anti-Leishmania serum IgG. The predominant phyla (Firmicutes + Bacteriodetes: > 90%), families (Muribaculaceae + Lachnospiraceae + Ruminococcaceae: 70-80%) and genera found in the uninfected hamsters showed no significant variations throughout the experiment. Leishmania infantum infection provoked a slightly higher-albeit non-significant-value for the Firmicutes/Bacteriodetes ratio but no notable differences were found in the relative abundance or diversity of phyla and families. The microbiome of the infected hamsters was enriched in CAG-352, whereas Lachnospiraceae UCG-004, the [Eubacterium] ventriosum group and Allobaculum were less abundant.

CONCLUSIONS: The lack of extensive significant differences between hamsters infected and uninfected with L. infantum in the higher taxa (phyla, families) and the scarce variation found, which was restricted to genera with a low relative abundance, suggest that there is no clear VL infection-intestinal microbiome axis in hamsters. Further studies are needed (chronic infections, co-abundance analyses, intestinal sampling, functional analysis) to confirm these findings and to determine more precisely the possible relationship between microbiome composition and VL infection.}, } @article {pmid36522631, year = {2022}, author = {Rojas-Jaimes, J and Lindo-Seminario, D and Correa-Núñez, G and Diringer, B}, title = {Characterization of the bacterial microbiome of Amblyomma scalpturatum and Amblyomma ovale collected from Tapirus terrestris and Amblyomma sabanerae collected from Chelonoidis denticulata, Madre de Dios- Peru.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {305}, pmid = {36522631}, issn = {1471-2180}, mesh = {Animals ; Humans ; Male ; Amblyomma ; Peru ; *Ticks/microbiology ; Animals, Wild ; *Turtles ; *Microbiota ; Brazil ; }, abstract = {BACKGROUND: Ticks are arthropods that can host and transmit pathogens to wild animals, domestic animals, and even humans. The microbiome in ticks is an endosymbiotic, pathogenic and is yet to be fully understood.

RESULTS: Adult male Amblyomma scalpturatum (A. scalpturatum) and Amblyomma ovale (A. ovale) ticks were collected from Tapirus terrestris (T. terrestris) captured in the rural area of San Lorenzo Village, and males Amblyomma sabanerae were collected from Chelonoidis denticulate (C. denticulate) of the Gamita Farm in the Amazon region of Madre de Dios, Peru. The Chao1 and Shannon-Weaver analyses indicated a greater bacterial richness and diversity in male A. sabanerae (Amblyomma sabanerae; 613.65-2.03) compared to male A. scalpturatum and A. ovale (A. scalpturatum and A. ovale; 102.17-0.40). Taxonomic analyses identified 478 operational taxonomic units representing 220 bacterial genera in A. sabanerae and 86 operational taxonomic units representing 28 bacterial genera in A. scalpturatum and A. ovale. Of the most prevalent genera was Francisella (73.2%) in A. sabanerae, and Acinetobacter (96.8%) in A. scalpturatum and A. ovale to be considered as the core microbiome of A. sabanerae and A. scalpturatum/A. ovale respectively.

CONCLUSIONS: We found a high bacterial diversity in male of A. sabanerae collected from C. denticulata showed prevalence of Francisella and prevalence of Acinetobacter in male A. scalpturatum and A. ovale collected from T. terrestris. The greatest bacterial diversity and richness was found in males A. sabanerae. This is the first bacterial metagenomic study performed in A. scalpturatum/A. ovale and A. sabanerae collected from T. terrestris and C. denticulata in the Peruvian jungle.}, } @article {pmid36522388, year = {2022}, author = {Villoslada-Blanco, P and Pérez-Matute, P and Íñiguez, M and Recio-Fernández, E and Jansen, D and De Coninck, L and Close, L and Blanco-Navarrete, P and Metola, L and Ibarra, V and Alba, J and Matthijnssens, J and Oteo, JA}, title = {Impact of HIV infection and integrase strand transfer inhibitors-based treatment on the gut virome.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {21658}, pmid = {36522388}, issn = {2045-2322}, mesh = {Humans ; *HIV Infections/drug therapy ; Virome ; *HIV Integrase Inhibitors/pharmacology/therapeutic use ; Dysbiosis/drug therapy ; *Bacteriophages ; *Viruses ; Integrases ; *HIV Integrase ; }, abstract = {Viruses are the most abundant components of the human gut microbiome with a significant impact on health and disease. The effects of human immunodeficiency virus (HIV) infection on gut virome has been scarcely analysed. Several studies suggested that integrase strand transfers inhibitors (INSTIs) are associated with a healthier gut. Thus, the objective of this work was to evaluate the effects of HIV infection and INSTIs on gut virome composition. 26 non-HIV-infected volunteers, 15 naive HIV-infected patients and 15 INSTIs-treated HIV-infected patients were recruited and their gut virome composition was analysed using shotgun sequencing. Bacteriophages were the most abundant and diverse viruses present in gut. HIV infection was accompanied by a decrease in phage richness which was reverted after INSTIs-based treatment. β-diversity of phages revealed that samples from HIV-infected patients clustered separately from those belonging to the control group. Differential abundant analysis showed an increase in phages belonging to Caudoviricetes class in the naive group and a decrease of Malgrandaviricetes class phages in the INSTIs-treated group compared to the control group. Besides, it was observed that INSTIs-based treatment was not able to reverse the increase of lysogenic phages associated with HIV infection or to modify the decrease observed on the relative abundance of Proteobacteria-infecting phages. Our study describes for the first time the impact of HIV and INSTIs on gut virome and demonstrates that INSTIs-based treatments are able to partially restore gut dysbiosis at the viral level, which opens several opportunities for new studies focused on microbiota-based therapies.}, } @article {pmid36522100, year = {2023}, author = {Ke, Y and Sun, W and Jing, Z and Zhao, Z and Xie, S}, title = {Seasonal variations of microbial community and antibiotic resistome in a suburb drinking water distribution system in a northern Chinese city.}, journal = {Journal of environmental sciences (China)}, volume = {127}, number = {}, pages = {714-725}, doi = {10.1016/j.jes.2022.07.001}, pmid = {36522100}, issn = {1001-0742}, mesh = {Humans ; Anti-Bacterial Agents ; *Drinking Water ; Genes, Bacterial ; *Microbiota ; Seasons ; China ; }, abstract = {Antibiotic resistance genes (ARGs) are an emerging issue for drinking water safety. However, the seasonal variation of ARGs in drinking water distribution systems (DWDS) is still unclear. This work revealed the tempo-spatial changes of microbial community, ARGs, mobile genetic elements (MGEs) co-occurring with ARGs, ARG hosts in DWDS bulk water by means of metagenome assembly. The microbial community and antibiotic resistome varied with sampling season and site. Temperature, ammonia, chlorite and total plate count (TPC) drove the variations of microbial community structure. Moreover, environmental parameters (total organic carbon (TOC), chlorite, TPC and hardness) shifted antibiotic resistome. ARGs and MGEs co-occurring with ARGs showed higher relative abundance in summer and autumn, which might be attributed to detached pipe biofilm. In particular, ARG-bacitracin and plasmid were the predominant ARG and MGE, respectively. ARG hosts changed with season and site and were more diverse in summer and autumn. In winter and spring, Limnohabitans and Mycobacterium were the major ARG hosts as well as the dominant genera in microbial community. In addition, in summer and autumn, high relative abundance of Achromobacter and Stenotrophomonas were the hosts harboring many kinds of ARGs and MGEs at site in a residential zone (0.4 km from the water treatment plant). Compared with MGEs, microbial community had a greater contribution to the variation of antibiotic resistome. This work gives new insights into the dynamics of ARGs in full-scale DWDS and the underlying factors.}, } @article {pmid36520393, year = {2023}, author = {Štursová, M and López-Mondéjar, R and Baldrian, P}, title = {Investigating the Bacterial and Fungal Communities Involved in Dead Biomass Degradation in Forest Soils.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2605}, number = {}, pages = {157-168}, pmid = {36520393}, issn = {1940-6029}, mesh = {*Mycobiome ; Soil/chemistry ; Biomass ; Soil Microbiology ; Fungi/metabolism ; Forests ; Bacteria/metabolism ; }, abstract = {Stable isotope probing (SIP) provides the opportunity to label decomposer microorganisms that build their biomass on a specific substrate. In combination with high-throughput sequencing, SIP allows for the identification of microbial community members involved in a particular decomposition process. Further information can be gained (in SIP experiments) through gene-targeted metagenomics and metatranscriptomics, opening the possibility to describe the pool of genes catalyzing specific decomposition reactions in situ and to identify the diversity of genes that are expressed. When combined with gene descriptions of fungal and/or bacterial isolates from the same environment, specific biochemical reactions involved in decomposition can be linked to individual microbial taxa. Here, we describe the use of these methods to explore the decomposer community of fungi and bacteria in forest litter and soil.}, } @article {pmid36519933, year = {2023}, author = {Conti, A and Casagrande Pierantoni, D and Robert, V and Corte, L and Cardinali, G}, title = {MinION Sequencing of Yeast Mock Communities To Assess the Effect of Databases and ITS-LSU Markers on the Reliability of Metabarcoding Analysis.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0105222}, pmid = {36519933}, issn = {2165-0497}, mesh = {Humans ; *Saccharomyces cerevisiae/genetics ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; DNA, Ribosomal/genetics ; *Microbiota ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Microbial communities play key roles both for humans and the environment. They are involved in ecosystem functions, maintaining their stability, and provide important services, such as carbon cycle and nitrogen cycle. Acting both as symbionts and as pathogens, description of the structure and composition of these communities is important. Metabarcoding uses ribosomal DNA (rDNA) (eukaryotic) or rRNA gene (prokaryotic) sequences for identification of species present in a site and measuring their abundance. This procedure requires several technical steps that could be source of bias producing a distorted view of the real community composition. In this work, we took advantage of an innovative "long-read" next-generation sequencing (NGS) technology (MinION) amplifying the DNA spanning from the internal transcribed spacer (ITS) to large subunit (LSU) that can be read simultaneously in this platform, providing more information than "short-read" systems. The experimental system consisted of six fungal mock communities composed of species present at various relative amounts to mimic natural situations characterized by predominant and low-frequency species. The influence of the sequencing platform (MinION and Illumina MiSeq) and the effect of different reference databases and marker sequences on metagenomic identification of species were evaluated. The results showed that the ITS-based database provided more accurate species identification than LSU. Furthermore, a procedure based on a preliminary identification with standard reference databases followed by the production of custom databases, including only the best outputs of the first step, is proposed. This additional step improved the estimate of species proportion of the mock communities and reduced the number of ghost species not really present in the simulated communities. IMPORTANCE Metagenomic analyses are fundamental in many research areas; therefore, improvement of methods and protocols for the description of microbial communities becomes more and more necessary. Long-read sequencing could be used for reducing biases due to the multicopy nature of rDNA sequences and short-read limitations. However, these novel technologies need to be assessed and standardized with controlled experiments, such as mock communities. The interest behind this work was to evaluate how long reads performed identification and quantification of species mixed in precise proportions and how the choice of database affects such analyses. Development of a pipeline that mitigates the effect of the barcoding sequences and the impact of the reference database on metagenomic analyses can help microbiome studies go one step further.}, } @article {pmid36519836, year = {2023}, author = {Douglas, GM and Kim, S and Langille, MGI and Shapiro, BJ}, title = {Efficient computation of contributional diversity metrics from microbiome data with FuncDiv.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {1}, pages = {}, pmid = {36519836}, issn = {1367-4811}, support = {//National Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Microbiota ; Metagenomics ; Software ; }, abstract = {MOTIVATION: Microbiome datasets with taxa linked to the functions (e.g. genes) they encode are becoming more common as metagenomics sequencing approaches improve. However, these data are challenging to analyze due to their complexity. Summary metrics, such as the alpha and beta diversity of taxa contributing to each function (i.e. contributional diversity), represent one approach to investigate these data, but currently there are no straightforward methods for doing so.

RESULTS: We addressed this gap by developing FuncDiv, which efficiently performs these computations. Contributional diversity metrics can provide novel insights that would be impossible to identify without jointly considering taxa and functions.

FuncDiv is distributed under a GNU Affero General Public License v3.0 and is available at https://github.com/gavinmdouglas/FuncDiv.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36519129, year = {2022}, author = {Li, W and Li, H and Wang, S and Han, K and Liu, Y and An, Z and Wu, H and Li, J and Song, J and Wu, W}, title = {Regional pattern and signatures of gut microbiota in rural residents with coronary heart disease: A metagenomic analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1007161}, pmid = {36519129}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics ; *Microbiota ; *Coronary Disease ; }, abstract = {Coronary heart disease (CHD) is tightly associated with gut microbiota, but microbiota heterogeneity limits the application of microbial biomarkers and personalized interventions demand regional-specific features. The purpose of this study was to comprehensively characterize the regional pattern of gut microbiota in rural residents with CHD and assess the predictive value and clinical correlations of local microbial signatures. We profiled the gut microbiota by shotgun metagenomic sequencing from 19 CHD and 19 healthy residents in rural Xinxiang, China, and tested the physiological parameters. The results indicated that microbial diversity, as well as KEGG orthology (KO) and carbohydrate-active enzymes (CAZymes) functions, deserved no significant disparities between CHD and healthy residents. The relative abundance of Bacteroidetes phylum was significantly lower and unclassified Lachnospiraceae genus, and Eubacterium rectale species were markedly higher in CHD residents compared with the healthy control. Co-occurrence network revealed a more diverse and scattered ecology in CHD residents. LEfSe identified 39 potential biomarkers and butanoate metabolism and glycosyltransferases families were the enhanced KO and CAZymes in CHD residents, respectively. Twenty key signatures were determined by the random forest algorithm and most of them belonged to the Clostridium cluster. These key signatures harbored a superior accuracy of 83.9% to distinguish CHD and healthy residents and, fasting serum insulin, diastolic blood pressure, and body mass index were the top three clinical parameters influencing the gut bacterial community. Furthermore, we also found that low-density lipoprotein and waist circumference had significantly positive correlations with the members of the Clostridium cluster. These findings expand our knowledge in the regional-specific pattern of gut microbiota for rural CHD residents and highlight the non-invasive diagnostic value and clinical correlations of microbial signatures.}, } @article {pmid36518262, year = {2022}, author = {Liu, L and Wu, P and Chen, F and Zhou, J and Guo, A and Shi, K and Zhang, Q}, title = {Multi-omics analyses reveal that the gut microbiome and its metabolites promote milk fat synthesis in Zhongdian yak cows.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e14444}, pmid = {36518262}, issn = {2167-8359}, mesh = {Animals ; Female ; Cattle ; *Milk/chemistry ; *Gastrointestinal Microbiome ; Multiomics ; Metabolomics ; Firmicutes ; Myristic Acids/analysis ; }, abstract = {BACKGROUND: Yak cows produce higher quality milk with higher concentrations of milk fat than dairy cows. Recently, studies have found the yak milk yield and milk fat percentage have decreased significantly over the past decade, highlighting the urgency for yak milk improvement. Therefore, we aimed to analyze how the gut microbiome impacts milk fat synthesis in Zhongdian yak cows.

METHODS: We collected milk samples from Zhongdian yak cows and analyzed the milk fat percentage, selecting five Zhongdian yak cows with a very high milk fat percentage (>7%, 8.70 ± 1.89%, H group) and five Zhongdian yak cows with a very low milk fat percentage (<5%, 4.12 ± 0.43%, L group), and then obtained gut samples of these ten Zhongdian yak cows through rectal palpation. Gut metagenomics, metabolomics, and conjoint metagenomics and metabolomics analyses were performed on these samples, identifying taxonomic changes, functional changes, and changes in gut microbes-metabolite interactions within the milk fat synthesis-associated Zhongdian yak cows gut microbiome, to identify potential regulatory mechanisms of milk fat at the gut microbiome level in Zhongdian yak cows.

RESULTS: The metagenomics analysis revealed Firmicutes and Proteobacteria were significantly more abundant in the gut of the high-milk fat Zhongdian yak cows. These bacteria are involved in the biosynthesis of unsaturated fatty acids and amino acids, leading to greater efficiency in converting energy to milk fat. The metabolomics analysis showed that the elevated gut metabolites in high milk fat percentage Zhongdian yak cows were mainly enriched in lipid and amino acid metabolism. Using a combined metagenomic and metabolomics analysis, positive correlations between Firmicutes (Desulfocucumis, Anaerotignum, Dolosiccus) and myristic acid, and Proteobacteria (Catenovulum, Comamonas, Rubrivivax, Marivita, Succinimouas) and choline were found in the gut of Zhongdian yak cows. These interactions may be the main contributors to methanogen inhibition, producing less methane leading to higher-efficient milk fat production.

CONCLUSIONS: A study of the gut microbe, gut metabolites, and milk fat percentage of Zhongdian yak cows revealed that the variations in milk fat percentage between yak cows may be caused by the gut microbes and their metabolites, especially Firmicutes-myristic acid and Proteobacteria-choline interactions, which are important to milk fat synthesis. Our study provides new insights into the functional roles of the gut microbiome in producing small molecule metabolites and contributing to milk performance traits in yak cows.}, } @article {pmid36517824, year = {2022}, author = {Miao, Q and Liang, T and Pei, N and Liu, C and Pan, J and Li, N and Wang, Q and Chen, Y and Chen, Y and Ma, Y and Jin, W and Zhang, Y and Su, Y and Yao, Y and Huang, Y and Zhou, C and Bao, R and Xu, X and Chen, W and Hu, B and Li, J}, title = {Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing.}, journal = {Respiratory research}, volume = {23}, number = {1}, pages = {345}, pmid = {36517824}, issn = {1465-993X}, support = {SHDC2020CR2031B//Clinical Research Plan of Shanghai Hospital Development Center/ ; }, mesh = {Humans ; Metagenomics/methods ; *Microbiota/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; *Mycobacterium tuberculosis ; *Respiratory Tract Infections/diagnosis ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: The application of clinical mNGS for diagnosing respiratory infections improves etiology diagnosis, however at the same time, it brings new challenges as an unbiased sequencing method informing all identified microbiomes in the specimen.

METHODS: Strategy evaluation and metagenomic analysis were performed for the mNGS data generated between March 2017 and October 2019. Diagnostic strengths of four specimen types were assessed to pinpoint the more appropriate type for mNGS diagnosis of respiratory infections. Microbiome complexity was revealed between patient cohorts and infection types. A bioinformatic pipeline resembling diagnosis results was built based upon multiple bioinformatic parameters.

RESULTS: The positive predictive values (PPVs) for mNGS diagnosing of non-mycobacterium, Nontuberculous Mycobacteria (NTM), and Aspergillus were obviously higher in bronchoalveolar lavage fluid (BALF) demonstrating the potency of BALF in mNGS diagnosis. Lung tissues and sputum were acceptable for diagnosis of the Mycobacterium tuberculosis (MTB) infections. Interestingly, significant taxonomy differences were identified in sufficient BALF specimens, and unique bacteriome and virome compositions were found in the BALF specimens of tumor patients. Our pipeline showed comparative diagnostic strength with the clinical microbiological diagnosis.

CONCLUSIONS: To achieve reliable mNGS diagnosis result, BALF specimens for suspicious common infections, and lung tissues and sputum for doubtful MTB infections are recommended to avoid the false results given by the complexed respiratory microbiomes. Our developed bioinformatic pipeline successful helps mNGS data interpretation and reduces manual corrections for etiology diagnosis.}, } @article {pmid36517072, year = {2023}, author = {Kim, H and Kim, ES and Cho, JH and Song, M and Cho, JH and Kim, S and Keum, GB and Kwak, J and Doo, H and Pandey, S and Park, SH and Lee, JH and Jung, H and Hur, TY and Kim, JK and Oh, KK and Kim, HB and Lee, JH}, title = {Exploring the Microbial Community and Functional Characteristics of the Livestock Feces Using the Whole Metagenome Shotgun Sequencing.}, journal = {Journal of microbiology and biotechnology}, volume = {33}, number = {1}, pages = {51-60}, pmid = {36517072}, issn = {1738-8872}, mesh = {Animals ; Swine ; Livestock ; Metagenome ; Chickens ; *Microbiota ; *Foodborne Diseases/microbiology ; Feces/microbiology ; }, abstract = {The foodborne illness is the important public health concerns, and the livestock feces are known to be one of the major reservoirs of foodborne pathogens. Also, it was reported that 45.5% of foodborne illness outbreaks have been associated with the animal products contaminated with the livestock feces. In addition, it has been known that the persistence of a pathogens depends on many potential virulent factors including the various virulent genes. Therefore, the first step to understanding the public health risk of livestock feces is to identify and describe microbial communities and potential virulent genes that contribute to bacterial pathogenicity. We used the whole metagenome shotgun sequencing to evaluate the prevalence of foodborne pathogens and to characterize the virulence associated genes in pig and chicken feces. Our data showed that the relative abundance of potential foodborne pathogens, such as Bacillus cereus was higher in chickens than pigs at the species level while the relative abundance of foodborne pathogens including Campylobacter coli was only detected in pigs. Also, the microbial functional characteristics of livestock feces revealed that the gene families related to "Biofilm formation and quorum sensing" were highly enriched in pigs than chicken. Moreover, the variety of gene families associated with "Resistance to antibiotics and toxic compounds" were detected in both animals. These results will help us to prepare the scientific action plans to improve awareness and understanding of the public health risks of livestock feces.}, } @article {pmid36516158, year = {2022}, author = {Ruaud, A and Pfister, N and Ley, RE and Youngblut, ND}, title = {Interpreting tree ensemble machine learning models with endoR.}, journal = {PLoS computational biology}, volume = {18}, number = {12}, pages = {e1010714}, pmid = {36516158}, issn = {1553-7358}, mesh = {Humans ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Machine Learning ; Metagenome ; *Microbiota ; }, abstract = {Tree ensemble machine learning models are increasingly used in microbiome science as they are compatible with the compositional, high-dimensional, and sparse structure of sequence-based microbiome data. While such models are often good at predicting phenotypes based on microbiome data, they only yield limited insights into how microbial taxa may be associated. We developed endoR, a method to interpret tree ensemble models. First, endoR simplifies the fitted model into a decision ensemble. Then, it extracts information on the importance of individual features and their pairwise interactions, displaying them as an interpretable network. Both the endoR network and importance scores provide insights into how features, and interactions between them, contribute to the predictive performance of the fitted model. Adjustable regularization and bootstrapping help reduce the complexity and ensure that only essential parts of the model are retained. We assessed endoR on both simulated and real metagenomic data. We found endoR to have comparable accuracy to other common approaches while easing and enhancing model interpretation. Using endoR, we also confirmed published results on gut microbiome differences between cirrhotic and healthy individuals. Finally, we utilized endoR to explore associations between human gut methanogens and microbiome components. Indeed, these hydrogen consumers are expected to interact with fermenting bacteria in a complex syntrophic network. Specifically, we analyzed a global metagenome dataset of 2203 individuals and confirmed the previously reported association between Methanobacteriaceae and Christensenellales. Additionally, we observed that Methanobacteriaceae are associated with a network of hydrogen-producing bacteria. Our method accurately captures how tree ensembles use features and interactions between them to predict a response. As demonstrated by our applications, the resultant visualizations and summary outputs facilitate model interpretation and enable the generation of novel hypotheses about complex systems.}, } @article {pmid36515546, year = {2023}, author = {Chen, C and Zhang, Y and Yao, X and Li, S and Wang, G and Huang, Y and Yang, Y and Zhang, A and Liu, C and Zhu, D and Li, H and Yan, Q and Ma, W}, title = {Characterizations of the Gut Bacteriome, Mycobiome, and Virome in Patients with Osteoarthritis.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0171122}, pmid = {36515546}, issn = {2165-0497}, mesh = {Humans ; *Mycobiome ; Virome ; *Microbiota ; *Gastrointestinal Microbiome ; *Viruses/genetics ; Bacteria/genetics ; }, abstract = {The gut microbiota plays an essential role in the regulation of the immune system and the etiology of human autoimmune diseases. However, a holistic understanding of the gut bacteriome, mycobiome, and virome in patients with osteoarthritis (OA) remains lacking. Here, we explored the gut microbiotas of 44 OA patients and 46 healthy volunteers via deep whole-metagenome shotgun sequencing of their fecal samples. The gut bacteriome and mycobiome were analyzed using a reference-based strategy. Gut viruses were identified from the metagenomic assembled contigs, and the gut virome was profiled based on 6,567 nonredundant viral operational taxonomic units (vOTUs). We revealed that the gut microbiome (including bacteriome, mycobiome, and virome) of OA patients is fundamentally altered, characterized by a panel of 279 differentially abundant bacterial species, 10 fungal species, and 627 vOTUs. The representative OA-enriched bacteria included Anaerostipes hadrus (GENOME147149), Prevotella sp900313215 (GENOME08259), Eubacterium_E hallii (GENOME000299), and Blautia A (GENOME001004), while Bacteroides plebeius A (GENOME239725), Roseburia inulinivorans (GENOME 001770), Dialister sp900343095 (GENOME075103), Phascolarctobacterium faecium (GENOME233517), and several members of Faecalibacterium and Prevotella were depleted in OA patients. Fungi such as Debaryomyces fabryi (GenBank accession no. GCA_003708665), Candida parapsilosis (GCA_000182765), and Apophysomyces trapeziformis (GCA_000696975) were enriched in the OA gut microbiota, and Malassezia restricta (GCA_003290485), Aspergillus fumigatus (GCA_003069565), and Mucor circinelloides (GCA_010203745) were depleted. The OA-depleted viruses spanned Siphoviridae (95 vOTUs), Myoviridae (70 vOTUs), and Microviridae (5 vOTUs), while 30 Siphoviridae vOTUs were enriched in OA patients. Functional analysis of the gut bacteriome and virome also uncovered their functional signatures in relation to OA. Moreover, we demonstrated that the OA-associated gut bacterial and viral signatures are tightly interconnected, suggesting that they may impact disease together. Finally, we showed that the multikingdom signatures are effective in discriminating the OA patients from healthy controls, suggesting the potential of gut microbiota for the prediction of OA and related diseases. Our results delineated the fecal bacteriome, mycobiome, and virome landscapes of the OA microbiota and provided biomarkers that will aid in future mechanistic and clinical intervention studies. IMPORTANCE The gut microbiome of OA patients was completely altered compared to that in healthy individuals, including 279 differentially abundant bacterial species, 10 fungal species and 627 viral operational taxonomic units (vOTUs). Functional analysis of the gut bacteriome and virome also revealed their functional signatures in relation to OA. We found that OA-associated gut bacterial and viral signatures were tightly interconnected, indicating that they may affect the disease together. The OA patients can be discriminated effectively from healthy controls using the multikingdom signatures, suggesting the potential of gut microbiota for the prediction of OA and related diseases.}, } @article {pmid36513659, year = {2022}, author = {Isaac, S and Flor-Duro, A and Carruana, G and Puchades-Carrasco, L and Quirant, A and Lopez-Nogueroles, M and Pineda-Lucena, A and Garcia-Garcera, M and Ubeda, C}, title = {Microbiome-mediated fructose depletion restricts murine gut colonization by vancomycin-resistant Enterococcus.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7718}, pmid = {36513659}, issn = {2041-1723}, mesh = {Mice ; Animals ; Vancomycin/pharmacology ; Fructose/pharmacology ; *Vancomycin-Resistant Enterococci/genetics ; *Microbiota ; Anti-Bacterial Agents/pharmacology ; Bacteria ; *Gram-Positive Bacterial Infections/microbiology ; }, abstract = {Multidrug-resistant organisms (MDRO) are a major threat to public health. MDRO infections, including those caused by vancomycin-resistant Enterococcus (VRE), frequently begin by colonization of the intestinal tract, a crucial step that is impaired by the intestinal microbiota. However, the specific members of the microbiota that suppress MDRO colonization and the mechanisms of such protection are largely unknown. Here, using metagenomics and mouse models that mimic the patients' exposure to antibiotics, we identified commensal bacteria associated with protection against VRE colonization. We further found a consortium of five strains that was sufficient to restrict VRE gut colonization in antibiotic treated mice. Transcriptomics in combination with targeted metabolomics and in vivo assays indicated that the bacterial consortium inhibits VRE growth through nutrient depletion, specifically by reducing the levels of fructose, a carbohydrate that boosts VRE growth in vivo. Finally, in vivo RNA-seq analysis of each strain of the consortium in combination with ex vivo and in vivo assays demonstrated that a single bacterium (Olsenella sp.) could recapitulate the effect of the consortium. Our results indicate that nutrient depletion by specific commensals can reduce VRE intestinal colonization, which represents a novel non-antibiotic based strategy to prevent infections caused by this multidrug-resistant organism.}, } @article {pmid36511842, year = {2023}, author = {Lebedeva, OP and Popov, VN and Syromyatnikov, MY and Starkova, NN and Maslov, AY and Kozarenko, ON and Gryaznova, MV}, title = {Female reproductive tract microbiome and early miscarriages.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {131}, number = {2}, pages = {61-76}, pmid = {36511842}, issn = {1600-0463}, support = {22-24-00802//Russian Science Foundation/ ; }, mesh = {Pregnancy ; Female ; Humans ; *Abortion, Spontaneous/etiology ; *Microbiota ; Prognosis ; Bacteria ; Vagina/microbiology ; }, abstract = {Miscarriage is one of the main causes of reproductive loss, which can lead to a number of physical and psychological complications and other long-term consequences. However, the role of vaginal and uterine microbiome in such complications is poorly understood. To review the published data on the function of the female reproductive tract microbiome in the pathogenesis of early miscarriages. The articles published over the past 20 years and deposited in PubMed, Google Academy, Scopus, Elibrary, ResearchGate, and EBSCO databases were analyzed. The review presents new data on the impact of the vaginal and uterine microbiome on the local immunity, including defense against sexually transmitted infections, and its association with other factors of miscarriages. The studies on the microbiome of non-pregnant women with recurrent miscarriages in the anamnesis, patients undergoing IVF, and pregnant women with miscarriages, as well as new directions in the microbiome research are discussed. The majority of studies have demonstrated that the dominant species of the vaginal and uterine microbiome in patients with early miscarriages are non-Lactobacillus bacteria. As many of these bacteria have not previously been detected by cultural studies and their role in obstetric complications is not well defined, further research on the female reproductive tract microbiome, including the microbiome of the cervix uteri, is needed to develop new approaches for the prognosis and prevention of miscarriages.}, } @article {pmid36511663, year = {2023}, author = {Wang, L and Li, Q and Li, C and Wu, C and Chen, F and Chen, X and Zhang, F}, title = {Nitrate Nitrogen and pH Correlate with Changes in Rhizosphere Microbial Community Assemblages during Invasion of Ambrosia artemisiifolia and Bidens pilosa.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0364922}, pmid = {36511663}, issn = {2165-0497}, mesh = {Nitrates ; Ambrosia ; *Bidens ; Rhizosphere ; Nitrogen ; Introduced Species ; Soil/chemistry ; Plants ; *Microbiota ; Hydrogen-Ion Concentration ; Soil Microbiology ; }, abstract = {The rhizosphere of invasive plants presumably develops different soil microbial assemblages compared with native plants, which may hinder or promote their invasion. However, to date, no studies have clearly explored rhizosphere microbial community assemblages during invasion. The invasive species Ambrosia artemisiifolia L. and Bidens pilosa L. are widely distributed in China and are known to reduce local biodiversity and cause agricultural losses. Monoculture of A. artemisiifolia or B. pilosa, a mixture of each invasive and native species, and monoculture of native species were established to simulate different degrees of invasion. Metagenomic sequencing techniques were used to test microbial community structure and function. The aim was to explore the drivers of the assembly of peculiar functional microbes in the rhizosphere soil of invasive species during the long-term invasive-native species interaction. Compared with the native species, the relative abundance of 34 microbial genera was higher in the rhizosphere soil of the invasive species. The NO3-N concentration in the rhizosphere soil from the A. artemisiifolia and B. pilosa monocultures was lower than that from monocultures of the three native plants, whereas pH followed the opposite trend. The NO3-N concentration was significantly and negatively correlated with Sporichthya, Afipia, Actinokineospora, and Pseudolabrys. pH was positively correlated with Bradyrhizobium, Actinoplanes, Micromonospora, Steroidobacter, Burkholderia, and Labilithrix. The differences in soil microbes, NO3-N concentrations, and pH between native and invasive species suggest that the rhizosphere soil microbial assemblages may vary. The reduced NO3-N concentration and increased pH corelated with changes in rhizosphere microbial community during A. artemisiifolia and B. pilosa invasion. IMPORTANCE Soil microbial communities play a vital role in the growth of invasive plants. Invasive species may shape peculiar functional microbes in the rhizosphere soil of an invasive species to benefit its growth. However, the drivers of the assembly of soil microbial communities in the rhizosphere soil of invasive species remain unclear. Our study established the relationship between soil microbial communities and soil chemical properties during invasion by A. artemisiifolia and B. pilosa. Additionally, it showed that the presence of the invasive plants correlated with changes in NO3-N and pH, as well as in rhizosphere microbial community assemblage. Furthermore, the study provided important insights into the difference in the microbial community assembly between native and invasive plant species.}, } @article {pmid36510248, year = {2022}, author = {Jurburg, SD and Buscot, F and Chatzinotas, A and Chaudhari, NM and Clark, AT and Garbowski, M and Grenié, M and Hom, EFY and Karakoç, C and Marr, S and Neumann, S and Tarkka, M and van Dam, NM and Weinhold, A and Heintz-Buschart, A}, title = {The community ecology perspective of omics data.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {225}, pmid = {36510248}, issn = {2049-2618}, mesh = {*Ecology/methods ; *Metagenomics/methods ; Metabolomics/methods ; }, abstract = {The measurement of uncharacterized pools of biological molecules through techniques such as metabarcoding, metagenomics, metatranscriptomics, metabolomics, and metaproteomics produces large, multivariate datasets. Analyses of these datasets have successfully been borrowed from community ecology to characterize the molecular diversity of samples (ɑ-diversity) and to assess how these profiles change in response to experimental treatments or across gradients (β-diversity). However, sample preparation and data collection methods generate biases and noise which confound molecular diversity estimates and require special attention. Here, we examine how technical biases and noise that are introduced into multivariate molecular data affect the estimation of the components of diversity (i.e., total number of different molecular species, or entities; total number of molecules; and the abundance distribution of molecular entities). We then explore under which conditions these biases affect the measurement of ɑ- and β-diversity and highlight how novel methods commonly used in community ecology can be adopted to improve the interpretation and integration of multivariate molecular data. Video Abstract.}, } @article {pmid36509943, year = {2023}, author = {Li, W and Ma, ZS}, title = {The Upper Respiratory Tract Microbiome Network Impacted by SARS-CoV-2.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1428-1437}, pmid = {36509943}, issn = {1432-184X}, mesh = {Animals ; Humans ; SARS-CoV-2/genetics ; *COVID-19 ; *Chiroptera ; *Microbiota/genetics ; Bacteria/genetics ; Respiratory System ; }, abstract = {The microbiome of upper respiratory tract (URT) acts as a gatekeeper to respiratory health of the host. However, little is still known about the impacts of SARS-CoV-2 infection on the microbial species composition and co-occurrence correlations of the URT microbiome, especially the relationships between SARS-CoV-2 and other microbes. Here, we characterized the URT microbiome based on RNA metagenomic-sequencing datasets from 1737 nasopharyngeal samples collected from COVID-19 patients. The URT-microbiome network consisting of bacteria, archaea, and RNA viruses was built and analyzed from aspects of core/periphery species, cluster composition, and balance between positive and negative interactions. It is discovered that the URT microbiome in the COVID-19 patients is enriched with Enterobacteriaceae, a gut associated family containing many pathogens. These pathogens formed a dense cooperative guild that seemed to suppress beneficial microbes collectively. Besides bacteria and archaea, 72 eukaryotic RNA viruses were identified in the URT microbiome of COVID-19 patients. Only five of these viruses were present in more than 10% of all samples, including SARS-CoV-2 and a bat coronavirus (i.e., BatCoV BM48-31) not detected in humans by routine means. SARS-CoV-2 was inhibited by a cooperative alliance of 89 species, but seems to cooperate with BatCoV BM48-31 given their statistically significant, positive correlations. The presence of cooperative bat-coronavirus partner of SARS-CoV-2 (BatCoV BM48-31), which was previously discovered in bat but not in humans to the best of our knowledge, is puzzling and deserves further investigation given their obvious implications. Possible microbial translocation mechanism from gut to URT also deserves future studies.}, } @article {pmid36509053, year = {2023}, author = {Oldenburg, CE and Hinterwirth, A and Dah, C and Millogo, O and Coulibaly, B and Ouedraogo, M and Sié, A and Chen, C and Zhong, L and Ruder, K and Lebas, E and Nyatigo, F and Arnold, BF and O'Brien, KS and Doan, T}, title = {Gut Microbiome among Children with Uncomplicated Severe Acute Malnutrition in a Randomized Controlled Trial of Azithromycin versus Amoxicillin.}, journal = {The American journal of tropical medicine and hygiene}, volume = {108}, number = {1}, pages = {206-211}, pmid = {36509053}, issn = {1476-1645}, mesh = {Child ; Humans ; Infant ; Azithromycin/therapeutic use ; Amoxicillin/therapeutic use ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents/therapeutic use ; *Severe Acute Malnutrition ; *Malnutrition ; }, abstract = {Antibiotics are routinely used as part of the management of severe acute malnutrition and are known to reduce gut microbial diversity in non-malnourished children. We evaluated gut microbiomes in children participating in a randomized controlled trial (RCT) of azithromycin versus amoxicillin for severe acute malnutrition. Three hundred one children aged 6 to 59 months with uncomplicated severe acute malnutrition (mid-upper arm circumference < 11.5 cm and/or weight-for-height Z-score < -3 without clinical complications) were enrolled in a 1:1 RCT of single-dose azithromycin versus a 7-day course of amoxicillin (standard of care). Of these, 109 children were randomly selected for microbiome evaluation at baseline and 8 weeks. Rectal swabs were processed with metagenomic DNA sequencing. We compared alpha diversity (inverse Simpson's index) at 8 weeks and evaluated relative abundance of microbial taxa using DESeq2. Of 109 children enrolled in the microbiome study, 95 were followed at 8 weeks. We found no evidence of a difference in alpha diversity between the azithromycin and amoxicillin groups at 8 weeks controlling for baseline diversity (mean difference -0.6, 95% CI -1.8 to 0.6, P = 0.30). Gut microbiomes did not diversify during the study. Differentially abundant genera at the P < 0.01 level included Salmonella spp. and Shigella spp., both of which were overabundant in the azithromycin compared with amoxicillin groups. We found no evidence to support an overall difference in gut microbiome diversity between azithromycin and amoxicillin among children with uncomplicated severe acute malnutrition, but potentially pathogenic bacteria that can cause invasive diarrhea were more common in the azithromycin group. Trial Registration: ClinicalTrials.gov NCT03568643.}, } @article {pmid36508259, year = {2023}, author = {Cheng, K and Ning, Z and Li, L and Zhang, X and Serrana, JM and Mayne, J and Figeys, D}, title = {MetaLab-MAG: A Metaproteomic Data Analysis Platform for Genome-Level Characterization of Microbiomes from the Metagenome-Assembled Genomes Database.}, journal = {Journal of proteome research}, volume = {22}, number = {2}, pages = {387-398}, pmid = {36508259}, issn = {1535-3907}, mesh = {Humans ; Metagenome ; Proteomics ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Computational Biology ; Metagenomics ; }, abstract = {The studies of microbial communities have drawn increased attention in various research fields such as agriculture, environment, and human health. Recently, metaproteomics has become a powerful tool to interpret the roles of the community members by investigating the expressed proteins of the microbes. However, analyzing the metaproteomic data sets at genome resolution is still challenging because of the lack of efficient bioinformatics tools. Here we develop MetaLab-MAG, a specially designed tool for the characterization of microbiomes from metagenome-assembled genomes databases. MetaLab-MAG was evaluated by analyzing various human gut microbiota data sets and performed comparably or better than searching the gene catalog protein database directly. MetaLab-MAG can quantify the genome-level microbiota compositions and supports both label-free and isobaric labeling-based quantification strategies. MetaLab-MAG removes the obstacles of metaproteomic data analysis and provides the researchers with in-depth and comprehensive information from the microbiomes.}, } @article {pmid36507666, year = {2023}, author = {Diao, Z and Lai, H and Han, D and Yang, B and Zhang, R and Li, J}, title = {Validation of a Metagenomic Next-Generation Sequencing Assay for Lower Respiratory Pathogen Detection.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0381222}, pmid = {36507666}, issn = {2165-0497}, mesh = {Humans ; Metagenome ; *Respiratory Tract Infections/diagnosis ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; }, abstract = {Lower respiratory infection (LRI) is the most fatal communicable disease, with only a few pathogens identified. Metagenomic next-generation sequencing (mNGS), as an unbiased, hypothesis-free, and culture-independent method, theoretically enables the detection of all pathogens in a single test. In this study, we developed and validated a DNA-based mNGS method for the diagnosis of LRIs from bronchoalveolar lavage fluid (BALF). We prepared simulated in silico data sets and published raw data sets from patients to evaluate the performance of our in-house bioinformatics pipeline and compared it with the popular metagenomics pipeline Kraken2-Bracken. In addition, a series of biological microbial communities were used to comprehensively validate the performance of our mNGS assay. Sixty-nine clinical BALF samples were used for clinical validation to determine the accuracy. The in-house bioinformatics pipeline validation showed a recall of 88.03%, precision of 99.14%, and F1 score of 92.26% via single-genome simulated data. Mock in silico microbial community and clinical metagenomic data showed that the in-house pipeline has a stricter cutoff value than Kraken2-Bracken, which could prevent false-positive detection by the bioinformatics pipeline. The validation for the whole mNGS pipeline revealed that overwhelming human DNA, long-term storage at 4°C, and repeated freezing-thawing reduced the analytical sensitivity of the assay. The mNGS assay showed a sensitivity of 95.18% and specificity of 91.30% for pathogen detection from BALF samples. This study comprehensively demonstrated the analytical performance of this laboratory-developed mNGS assay for pathogen detection from BALF, which contributed to the standardization of this technology. IMPORTANCE To our knowledge, this study is the first to comprehensively validate the mNGS assay for the diagnosis of LRIs from BALF. This study exhibited a ready-made example for clinical laboratories to prepare reference materials and develop comprehensive validation schemes for their in-house mNGS assays, which would accelerate the standardization of mNGS testing.}, } @article {pmid36507660, year = {2023}, author = {Zheng, J and Liang, JL and Jia, P and Feng, SW and Lu, JL and Luo, ZH and Ai, HX and Liao, B and Li, JT and Shu, WS}, title = {Diverse Methylmercury (MeHg) Producers and Degraders Inhabit Acid Mine Drainage Sediments, but Few Taxa Correlate with MeHg Accumulation.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0073622}, pmid = {36507660}, issn = {2379-5077}, mesh = {*Methylmercury Compounds/analysis ; Bacteria/genetics ; Phylogeny ; Metagenome ; Firmicutes/genetics ; }, abstract = {Methylmercury (MeHg) is a notorious neurotoxin, and its production and degradation in the environment are mainly driven by microorganisms. A variety of microbial MeHg producers carrying the gene pair hgcAB and degraders carrying the merB gene have been separately reported in recent studies. However, surprisingly little attention has been paid to the simultaneous investigation of the diversities of microbial MeHg producers and degraders in a given habitat, and no studies have been performed to explore to what extent these two contrasting microbial groups correlate with MeHg accumulation in the habitat of interest. Here, we collected 86 acid mine drainage (AMD) sediments from an area spanning approximately 500,000 km[2] in southern China and profiled the sediment-borne putative MeHg producers and degraders using genome-resolved metagenomics. 46 metagenome-assembled genomes (MAGs) containing hgcAB and 93 MAGs containing merB were obtained, including those from various taxa without previously known MeHg-metabolizing microorganisms. These diverse MeHg-metabolizing MAGs were formed largely via multiple independent horizontal gene transfer (HGT) events. The putative MeHg producers from Deltaproteobacteria and Firmicutes as well as MeHg degraders from Acidithiobacillia were closely correlated with MeHg accumulation in the sediments. Furthermore, these three taxa, in combination with two abiotic factors, explained over 60% of the variance in MeHg accumulation. Most of the members of these taxa were characterized by their metabolic potential for nitrogen fixation and copper tolerance. Overall, these findings improve our understanding of the ecology of MeHg-metabolizing microorganisms and likely have implications for the development of management strategies for the reduction of MeHg accumulation in the AMD sediments. IMPORTANCE Microorganisms are the main drivers of MeHg production and degradation in the environment. However, little attention has been paid to the simultaneous investigation of the diversities of microbial MeHg producers and degraders in a given habitat. We used genome-resolved metagenomics to reveal the vast phylogenetic and metabolic diversities of putative MeHg producers and degraders in AMD sediments. Our results show that the diversity of MeHg-metabolizing microorganisms (particularly MeHg degraders) in AMD sediments is much higher than was previously recognized. Via multiple linear regression analysis, we identified both microbial and abiotic factors affecting MeHg accumulation in AMD sediments. Despite their great diversity, only a few taxa of MeHg-metabolizing microorganisms were closely correlated with MeHg accumulation. This work underscores the importance of using genome-resolved metagenomics to survey MeHg-metabolizing microorganisms and provides a framework for the illumination of the microbial basis of MeHg accumulation via the characterization of physicochemical properties, MeHg-metabolizing microorganisms, and the correlations between them.}, } @article {pmid36503863, year = {2023}, author = {Singh, G and Agrawal, H and Bednarek, P}, title = {Specialized metabolites as versatile tools in shaping plant-microbe associations.}, journal = {Molecular plant}, volume = {16}, number = {1}, pages = {122-144}, doi = {10.1016/j.molp.2022.12.006}, pmid = {36503863}, issn = {1752-9867}, mesh = {*Plants/metabolism ; Adaptation, Physiological ; Genomics ; *Microbiota ; }, abstract = {Plants are rich repository of a large number of chemical compounds collectively referred to as specialized metabolites. These compounds are of importance for adaptive processes including responses against changing abiotic conditions and interactions with various co-existing organisms. One of the strikingly affirmed functions of these specialized metabolites is their involvement in plants' life-long interactions with complex multi-kingdom microbiomes including both beneficial and harmful microorganisms. Recent developments in genomic and molecular biology tools not only help to generate well-curated information about regulatory and structural components of biosynthetic pathways of plant specialized metabolites but also to create and screen mutant lines defective in their synthesis. In this review, we have comprehensively surveyed the function of these specialized metabolites and discussed recent research findings demonstrating the responses of various microbes on tested mutant lines having defective biosynthesis of particular metabolites. In addition, we attempt to provide key clues about the impact of these metabolites on the assembly of the plant microbiome by summarizing the major findings of recent comparative metagenomic analyses of available mutant lines under customized and natural microbial niches. Subsequently, we delineate benchmark initiatives that aim to engineer or manipulate the biosynthetic pathways to produce specialized metabolites in heterologous systems but also to diversify their immune function. While denoting the function of these metabolites, we also discuss the critical bottlenecks associated with understanding and exploiting their function in improving plant adaptation to the environment.}, } @article {pmid36503356, year = {2022}, author = {Sauceda, C and Bayne, C and Sudqi, K and Gonzalez, A and Dulai, PS and Knight, R and Gonzalez, DJ and Gonzalez, CG}, title = {Stool multi-omics for the study of host-microbe interactions in inflammatory bowel disease.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2154092}, pmid = {36503356}, issn = {1949-0984}, support = {U34 DK126626/DK/NIDDK NIH HHS/United States ; R01 DK131005/DK/NIDDK NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; T32 DK007202/DK/NIDDK NIH HHS/United States ; T32 GM007752/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Host Microbial Interactions ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Multiomics ; *Inflammatory Bowel Diseases/genetics ; }, abstract = {Inflammatory Bowel Disease (IBD) is a chronic immune-mediated inflammatory disease of the gastrointestinal tract that is a growing public burden. Gut microbes and their interactions with hosts play a crucial role in disease pathogenesis and progression. These interactions are complex, spanning multiple physiological systems and data types, making comprehensive disease assessment difficult, and often overwhelming single-omic capabilities. Stool-based multi-omics is a promising approach for characterizing host-gut microbiome interactions using deep integration of technologies such as 16S rRNA sequencing, shotgun metagenomics, meta-transcriptomics, metabolomics, and metaproteomics. The wealth of information generated through multi-omic studies is poised to usher in advancements in IBD research and precision medicine. This review highlights historical and recent findings from stool-based muti-omic studies that have contributed to unraveling IBD's complexity. Finally, we discuss common pitfalls, issues, and limitations, and how future pipelines should address them to standardize multi-omics in IBD research and beyond.}, } @article {pmid36501007, year = {2022}, author = {Coimbra, VOR and Crovesy, L and Ribeiro-Alves, M and Faller, ALK and Mattos, F and Rosado, EL}, title = {Gut Microbiota Profile in Adults Undergoing Bariatric Surgery: A Systematic Review.}, journal = {Nutrients}, volume = {14}, number = {23}, pages = {}, pmid = {36501007}, issn = {2072-6643}, mesh = {Humans ; RNA, Ribosomal, 16S ; *Bariatric Surgery/methods ; *Gastric Bypass/methods ; *Gastrointestinal Microbiome ; Gastrectomy/methods ; Bacteria/genetics ; *Obesity, Morbid/surgery ; Treatment Outcome ; }, abstract = {Gut microbiota (GM) after bariatric surgery (BS) has been considered as a factor associated with metabolic improvements and weight loss. In this systematic review, we evaluate changes in the GM, characterized by 16S rRNA and metagenomics techniques, in obese adults who received BS. The PubMed, Scopus, Web of Science, and LILACS databases were searched. Two independent reviewers analyzed articles published in the last ten years, using Rayyan QCRI. The initial search resulted in 1275 documents, and 18 clinical trials were included after the exclusion criteria were applied. The predominance of intestinal bacteria phyla varied among studies; however, most of them reported a greater amount of Bacteroidetes (B), Proteobacteria (P), and diversity (D) after BS. Firmicutes (F), B, and the (F/B) ratio was inconsistent, increasing or decreasing after Roux-en-Y gastric bypass (RYGB) and sleeve gastrectomy (SG) were conducted, compared to before surgery. There was a reduction in the relative proportion of F. Moreover, a higher proportion of Actinobacteria (A) was observed after RYGB was conducted. However, the same was not identified when SG procedures were applied. Genera abundance and bacteria predominance varied according to the surgical procedure, with limited data regarding the impact on phyla. The present study was approved by PROSPERO, under registration number CRD42020209509.}, } @article {pmid36499044, year = {2022}, author = {Fang, Z and Chen, Y and Li, Y and Sun, L and Deng, Q and Wang, J and Gooneratne, R}, title = {Oleic Acid Facilitates Cd Excretion by Increasing the Abundance of Burkholderia in Cd-Exposed Mice.}, journal = {International journal of molecular sciences}, volume = {23}, number = {23}, pages = {}, pmid = {36499044}, issn = {1422-0067}, support = {32172215//National Natural Science Foundation of China/ ; 31701706//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Mice ; Animals ; Cadmium/toxicity ; *Burkholderia ; Oleic Acid/pharmacology ; *Gastrointestinal Microbiome ; Feces ; }, abstract = {As a global pollutant, cadmium (Cd) can easily enter the body through food chains, threatening human health. Most Cd is initially absorbed in the gut, with the gut microbiota playing a pivotal role in reducing Cd absorption and accumulation. This study assessed the effects of three fatty acids on Cd accumulation and toxicity in Cd-exposed mice. The results showed that oleic acid (OA) was the most effective in facilitating Cd excretion in mice among these fatty acids. The use of OA led to reduced Cd accumulation in the organs and increased Cd content in the feces. The metagenomic analysis of the gut microbiota showed that the genus Burkholderia was the most significantly restored by OA in Cd-exposed mice. Burkholderia cepacia, as the type species for the genus Burkholderia, also exhibited strong Cd tolerance after treatment with OA. Furthermore, the electron microscopy analysis showed that most of the Cd was adsorbed on the surface of B. cepacia, where the extracellular polymeric substances (EPSs) secreted by B. cepacia play a key role, displaying a strong capacity for Cd adsorption. The peak at 2355 cm[-1] and the total sulfhydryl group content of EPSs showed significant increases following co-treatment with Cd and OA. The results demonstrated the potential roles that gut Burkholderia may play in OA-mediated Cd excretion in mice.}, } @article {pmid36496062, year = {2023}, author = {Mazzoli, A and Porzio, AD and Gatto, C and Crescenzo, R and Nazzaro, M and Spagnuolo, MS and Baccigalupi, L and Ricca, E and Amoresano, A and Fontanarosa, C and Bernacchioni, C and Donati, C and Iossa, S and Cigliano, L}, title = {Skeletal muscle insulin resistance and adipose tissue hypertrophy persist beyond the reshaping of gut microbiota in young rats fed a fructose-rich diet.}, journal = {The Journal of nutritional biochemistry}, volume = {113}, number = {}, pages = {109247}, doi = {10.1016/j.jnutbio.2022.109247}, pmid = {36496062}, issn = {1873-4847}, mesh = {Rats ; Animals ; *Insulin Resistance ; *Gastrointestinal Microbiome ; Fructose/adverse effects/metabolism ; Diet ; Adipose Tissue/metabolism ; Insulin/metabolism ; Hypertrophy/metabolism ; Muscle, Skeletal/metabolism ; }, abstract = {To investigate whether short term fructose-rich diet induces changes in the gut microbiota as well as in skeletal muscle and adipose tissue physiology and verify whether they persist even after fructose withdrawal, young rats of 30 d of age were fed for 3 weeks a fructose-rich or control diet. At the end of the 3-weeks period, half of the rats from each group were maintained for further 3 weeks on a control diet. Metagenomic analysis of gut microbiota and short chain fatty acids levels (faeces and plasma) were investigated. Insulin response was evaluated at the whole-body level and both in skeletal muscle and epididymal adipose tissue, together with skeletal muscle mitochondrial function, oxidative stress, and lipid composition. In parallel, morphology and physiological status of epididymal adipose tissue was also evaluated. Reshaping of gut microbiota and increased content of short chain fatty acids was elicited by the fructose diet and abolished by switching back to control diet. On the other hand, most metabolic changes elicited by fructose-rich diet in skeletal muscle and epididymal adipose tissue persisted after switching to control diet. Increased dietary fructose intake even on a short-time basis elicits persistent changes in the physiology of metabolically relevant tissues, such as adipose tissue and skeletal muscle, through mechanisms that go well beyond the reshaping of gut microbiota. This picture delineates a harmful situation, in particular for the young populations, posed at risk of metabolic modifications that may persist in their adulthood.}, } @article {pmid36481500, year = {2023}, author = {Sharma, P and Nadda, AK and Kumar, S}, title = {Microbial community profiling in bio-stimulated municipal solid waste for effective removal of organic pollutants containing endocrine disrupting chemicals.}, journal = {Microbiological research}, volume = {267}, number = {}, pages = {127273}, doi = {10.1016/j.micres.2022.127273}, pmid = {36481500}, issn = {1618-0623}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Endocrine Disruptors/analysis ; *Environmental Pollutants/analysis ; *Microbiota ; Solid Waste/analysis ; }, abstract = {The study was aimed to improve the degradation of organic pollutants in municipal solid waste (MSW) through the bio-stimulation process. The results showed that the physico-chemical properties of MSW (control) had a high value of pH (9.2 ± 0.02); total suspended solids (TSS: 1547 ± 23 mg/kg[-1]), and total dissolved solids (TDS:76 ± 0.67 mg/kg[-1]). After the biostimulation process (biostimulated MSW), the physico-chemical parameters of MSW were reduced as pH (7.1 ± 0.01); TSS (41 ± 0.01 mg/kg[-1]), and TDS (789 ± 03 mg/kg[-1]). Furthermore, the major organic pollutants detected from MSW by gas chromatography-mass spectroscopy (GC-MS) analysis at different retention time (RT) were hexadecane (RT-8.79); pentadecane (RT-9.36); and hexasiloxane (RT-9.43) while these organic pollutants were degraded after the biostimulation process. The whole-genome metagenome sequencing size (%) analyses showed major groups of bacteria (40.82%) followed by fungi (0.05%), virus (0.0032%), and archaea (0.0442%) in MSW. The species richness and evenness of the microbial community were decreased substantially due to the biostimulation treatment. The total number of genes in the biostimulated MSW (PS-3_11267) sample were 465302 whereas the number of genes in the control MSW (PS-4_11268) sample were 256807. Furthermore, the biostimulated MSW (PS-3_11267) aligned the reads to bacteria (19502525), fungi (40030), virus (3339), and archaea (12759) genomes whereas the control sample (PS-4_11268) aligned the reads to bacteria (17057259), fungi (19148), virus (1335), and archaea (18447) genomes. Moreover, the relative abundance at genus level in biostimulated MSW (PS-3_11267) (Ochrobactrum and Phenylobacterium), phylum; (Proteobacteria and Actinobacteria), and species (Chthoniobacter flavus and Vulgatibacter incomptus) level was the most abundant. The results provided valuable information regarding the degradation of organic pollutants in MSW by microbial communities through biostimulation for the prevention of soil pollution and health protection.}, } @article {pmid36481466, year = {2023}, author = {Xu, Y and You, G and Yin, J and Zhang, M and Peng, D and Xu, J and Yang, S and Hou, J}, title = {Salt tolerance evolution facilitates antibiotic resistome in soil microbiota: Evidences from dissemination evaluation, hosts identification and co-occurrence exploration.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {317}, number = {}, pages = {120830}, doi = {10.1016/j.envpol.2022.120830}, pmid = {36481466}, issn = {1873-6424}, mesh = {Humans ; *Genes, Bacterial ; Salt Tolerance ; Anti-Bacterial Agents/pharmacology ; Soil ; *Microbiota ; Soil Microbiology ; }, abstract = {Salinity is considered as one of the vital factors affecting the profiles of antibiotic resistance genes (ARGs) in soils, whereby its roles in shaping the antibiotic resistome were still poorly understood. Here, metagenomic analysis was conducted to track the ARGs distributions and dissemination in soils during salt accumulation and desalinization processes. Neutral-salt accumulation for 45 and 90 days significantly increased the relative abundances of ARGs and mobile genetic elements (MGEs) carrying antibiotic resistance contigs (ARCs). The ARGs within antibiotic efflux and target protection families primarily carried by Streptomyces, Nocardioides, Rhodanobacter and Monashia were largely enriched by salinity. The ARGs subtypes of the resistance-nodulation-division (RND) family, ATP-binding cassette (ABC) family, rRNA methyltransferase and other efflux were closely associated with MGEs, contributing to the enrichment of ARGs. Moreover, the ARGs subtypes and transposons were genetically linked with the salt-tolerance mechanisms of organic osmolyte transporters and K[+] uptake proteins on the same ARC, demonstrating the coselection of ARGs and halotolerant genes. Furthermore, the antibiotic resistome could recover to a normal state after the prolonged incubation by alleviating salt stress. Nevertheless, the acquisition of ARGs by opportunistic pathogens after salt treatment was increased, serving to prioritize further efforts on the health risks correlated with resistance propagation and human exposure in saline soils.}, } @article {pmid36481142, year = {2023}, author = {Song, A and Peng, J and Si, Z and Xu, D and Sun, M and Zhang, J and Wang, S and Wang, E and Bi, J and Chong, F and Fan, F}, title = {Metagenomics reveals the increased antibiotics resistome through prokaryote rather than virome after overuse of rare earth element compounds.}, journal = {The Science of the total environment}, volume = {863}, number = {}, pages = {160704}, doi = {10.1016/j.scitotenv.2022.160704}, pmid = {36481142}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/toxicity ; Virome ; Nitrates ; Ecosystem ; *Metals, Rare Earth ; Metals ; Genes, Bacterial ; Soil ; Metagenomics ; }, abstract = {Rare earth elements (REE) are extensively exploited in the agricultural ecosystems due to their various beneficial roles on plant growth. However, the ecotoxicological effects and environmental risk of REE are poorly assessed. Here, we investigated the effects of lanthanum and cerium nitrate on soil prokaryote and viral metal resistance genes (MRGs) and antibiotics resistance genes (ARGs) using a metagenomic-based approach. We found that relative abundances of prokaryote phyla Bacteroidetes and Chloroflexi decreased with increasing of both REE compounds. In addition, low level REE nitrate (0.05 and 0.1 mmol kg[-1] soil) inhibited the viral family Phycodanaviridae, Rudiviridae, Schitoviridae, whereas high level (0.16 and 0.32 mmol kg[-1] soil) REE nitrate suppressed the viral family Herelleviridae, Iridoviridae, Podoviridae. ARGs were not significantly affected by low level of REE nitrate. However, high level of both REEs nitrate increased the abundances of dominant prokaryote genes resisting to most of the drug classes, such as aminoglycoside, elfamycin, fluoroquinolone, macrolide, rifamycin. Abundance of MRGs in prokaryote did not change consistently with REE nitrate compound type and input rate. MRGs were only partially detected in the virome in some of the treatments, while ARGs was not detected in virome. Together, we demonstrated that overuse of REE nitrate in agriculture would increase the risk of dissemination of ARGs through prokaryotes but not virus, although viral community was substantially shifted.}, } @article {pmid36480164, year = {2023}, author = {Engelberts, JP and Robbins, SJ and Herbold, CW and Moeller, FU and Jehmlich, N and Laffy, PW and Wagner, M and Webster, NS}, title = {Metabolic reconstruction of the near complete microbiome of the model sponge Ianthella basta.}, journal = {Environmental microbiology}, volume = {25}, number = {3}, pages = {646-660}, pmid = {36480164}, issn = {1462-2920}, support = {294343/ERC_/European Research Council/International ; }, mesh = {Animals ; *Porifera/microbiology ; Phylogeny ; Archaea/metabolism ; *Microbiota ; Symbiosis/physiology ; }, abstract = {Many marine sponges host highly diverse microbiomes that contribute to various aspects of host health. Although the putative function of individual groups of sponge symbionts has been increasingly described, the extreme diversity has generally precluded in-depth characterization of entire microbiomes, including identification of syntrophic partnerships. The Indo-Pacific sponge Ianthella basta is emerging as a model organism for symbiosis research, hosting only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium and a range of other low abundance or transitory taxa. Here, we retrieved metagenome assembled genomes (MAGs) representing >90% of I. basta's microbial community, facilitating the metabolic reconstruction of the sponge's near complete microbiome. Through this analysis, we identified metabolic complementarity between microbes, including vitamin sharing, described the importance of low abundance symbionts, and characterized a novel microbe-host attachment mechanism in the Alphaproteobacterium. We further identified putative viral sequences, highlighting the role viruses can play in maintaining symbioses in I. basta through the horizontal transfer of eukaryotic-like proteins, and complemented this data with metaproteomics to identify active metabolic pathways in bacteria, archaea, and viruses. This data provide the framework to adopt I. basta as a model organism for studying host-microbe interactions and provide a basis for in-depth physiological experiments.}, } @article {pmid36477304, year = {2023}, author = {Richardson, L and Allen, B and Baldi, G and Beracochea, M and Bileschi, ML and Burdett, T and Burgin, J and Caballero-Pérez, J and Cochrane, G and Colwell, LJ and Curtis, T and Escobar-Zepeda, A and Gurbich, TA and Kale, V and Korobeynikov, A and Raj, S and Rogers, AB and Sakharova, E and Sanchez, S and Wilkinson, DJ and Finn, RD}, title = {MGnify: the microbiome sequence data analysis resource in 2023.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D753-D759}, pmid = {36477304}, issn = {1362-4962}, mesh = {Genomics/methods ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Software ; *Sequence Analysis/methods ; }, abstract = {The MGnify platform (https://www.ebi.ac.uk/metagenomics) facilitates the assembly, analysis and archiving of microbiome-derived nucleic acid sequences. The platform provides access to taxonomic assignments and functional annotations for nearly half a million analyses covering metabarcoding, metatranscriptomic, and metagenomic datasets, which are derived from a wide range of different environments. Over the past 3 years, MGnify has not only grown in terms of the number of datasets contained but also increased the breadth of analyses provided, such as the analysis of long-read sequences. The MGnify protein database now exceeds 2.4 billion non-redundant sequences predicted from metagenomic assemblies. This collection is now organised into a relational database making it possible to understand the genomic context of the protein through navigation back to the source assembly and sample metadata, marking a major improvement. To extend beyond the functional annotations already provided in MGnify, we have applied deep learning-based annotation methods. The technology underlying MGnify's Application Programming Interface (API) and website has been upgraded, and we have enabled the ability to perform downstream analysis of the MGnify data through the introduction of a coupled Jupyter Lab environment.}, } @article {pmid36476562, year = {2022}, author = {Liu, Y and Zhang, Z and Ji, M and Hu, A and Wang, J and Jing, H and Liu, K and Xiao, X and Zhao, W}, title = {Comparison of prokaryotes between Mount Everest and the Mariana Trench.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {215}, pmid = {36476562}, issn = {2049-2618}, mesh = {*Metagenomics ; *Bicycling ; }, abstract = {BACKGROUND: Mount Everest and the Mariana Trench represent the highest and deepest places on Earth, respectively. They are geographically separated, with distinct extreme environmental parameters that provide unique habitats for prokaryotes. Comparison of prokaryotes between Mount Everest and the Mariana Trench will provide a unique perspective to understanding the composition and distribution of environmental microbiomes on Earth.

RESULTS: Here, we compared prokaryotic communities between Mount Everest and the Mariana Trench based on shotgun metagenomic analysis. Analyzing 25 metagenomes and 1176 metagenome-assembled genomes showed distinct taxonomic compositions between Mount Everest and the Mariana Trench, with little taxa overlap, and significant differences in genome size, GC content, and predicted optimal growth temperature. However, community metabolic capabilities exhibited striking commonality, with > 90% of metabolic modules overlapping among samples of Mount Everest and the Mariana Trench, with the only exception for CO2 fixations (photoautotrophy in Mount Everest but chemoautotrophy in the Mariana Trench). Most metabolic pathways were common but performed by distinct taxa in the two extreme habitats, even including some specialized metabolic pathways, such as the versatile degradation of various refractory organic matters, heavy metal metabolism (e.g., As and Se), stress resistance, and antioxidation. The metabolic commonality indicated the overall consistent roles of prokaryotes in elemental cycling and common adaptation strategies to overcome the distinct stress conditions despite the intuitively huge differences in Mount Everest and the Mariana Trench.

CONCLUSION: Our results, the first comparison between prokaryotes in the highest and the deepest habitats on Earth, may highlight the principles of prokaryotic diversity: although taxa are habitat-specific, primary metabolic functions could be always conserved. Video abstract.}, } @article {pmid36476129, year = {2023}, author = {Zhao, L and Luo, JL and Ali, MK and Spiekerkoetter, E and Nicolls, MR}, title = {The Human Respiratory Microbiome: Current Understandings and Future Directions.}, journal = {American journal of respiratory cell and molecular biology}, volume = {68}, number = {3}, pages = {245-255}, pmid = {36476129}, issn = {1535-4989}, support = {R01 HL095686/HL/NHLBI NIH HHS/United States ; R01 HL158714/HL/NHLBI NIH HHS/United States ; R01 HL138473/HL/NHLBI NIH HHS/United States ; R01 HL141105/HL/NHLBI NIH HHS/United States ; I01 BX005628/BX/BLRD VA/United States ; }, mesh = {Humans ; Lung/microbiology ; *Asthma ; *Pulmonary Disease, Chronic Obstructive/microbiology ; *Microbiota ; *Cystic Fibrosis/microbiology ; }, abstract = {Microorganisms colonize the human body. The lungs and respiratory tract, previously believed to be sterile, harbor diverse microbial communities and the genomes of bacteria (bacteriome), viruses (virome), and fungi (mycobiome). Recent advances in amplicon and shotgun metagenomic sequencing technologies and data-analyzing methods have greatly aided the identification and characterization of microbial populations from airways. The respiratory microbiome has been shown to play roles in human health and disease and is an area of rapidly emerging interest in pulmonary medicine. In this review, we provide updated information in the field by focusing on four lung conditions, including asthma, chronic obstructive pulmonary disease, cystic fibrosis, and idiopathic pulmonary fibrosis. We evaluate gut, oral, and upper airway microbiomes and how they contribute to lower airway flora. The discussion is followed by a systematic review of the lower airway microbiome in health and disease. We conclude with promising research avenues and implications for evolving therapeutics.}, } @article {pmid36475916, year = {2023}, author = {Xu, R and Li, Q and Wang, H and Su, Y and Zhu, W}, title = {Reduction of Redox Potential Exerts a Key Role in Modulating Gut Microbial Taxa and Function by Dietary Supplementation of Pectin in a Pig Model.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0328322}, pmid = {36475916}, issn = {2165-0497}, mesh = {Swine ; Animals ; Pectins ; *Gastrointestinal Microbiome/physiology ; Feces/microbiology ; *Microbiota ; Dietary Supplements ; Oxidation-Reduction ; }, abstract = {Pectin exists in a vast range of plants and has a long history of acting as a functional food additive with potential prebiotic effects on intestinal health. However, knowledge of how pectin regulates gut microbial communities is still insufficient and limited. Here, metatranscriptome sequencing revealed that a pectin-enriched diet (PEC) decreased the abundances of fungal keystone taxa (e.g., amino acid-producing Kazachstania spp.) and their genes involved in oxidative phosphorylation, while it increased the abundance of sulfate-reducing Desulfovibrio spp., and methane-producing Methanobrevibacter spp. in colon microbiomes. Furthermore, we first confirmed that PEC decreased fecal redox potential in a fistula pig model, which could be supported by the enrichment of antioxidants (e.g., inosine) in feces. Fecal metagenome analysis disclosed that certain microbial taxa promoted inosine biosynthesis from pectin degradation, including Prevotella, which plays an essential role in pectin biodegradation. Overall, these results demonstrate that pectin decreases the redox potential in pig hindgut to modulate microbial composition and functions, and specific microorganisms generate reducing agents in the course of pectin degradation to decrease redox potential of microbial ecosystem. IMPORTANCE Collective studies indicate that pectin degradation promotes extensive microorganisms that can be involved in pectin degradation directly or indirectly, or benefit from the altered physiological conditions caused by pectin ingestions. Our study focuses on effects of pectin on gut microbial taxa and functions, as well as its interactions with altered environmental features. Our results demonstrate pectin-induced proreducing shifts on colon microbial taxa and functions, and first confirm that pectin decreases hindgut redox potential, which is an important environmental feature that can modulate microbial communities. These results infer that there is bidirectional regulation between microbiota and redox potential during pectin degradation. In general, this investigation proposes new insights into the pectin-modulating gut microbial ecosystem and also provides new perspectives for targeting modulation of gut microbiota.}, } @article {pmid36475872, year = {2023}, author = {Queiroz, LL and Lacorte, GA and Isidorio, WR and Landgraf, M and de Melo Franco, BDG and Pinto, UM and Hoffmann, C}, title = {High Level of Interaction between Phages and Bacteria in an Artisanal Raw Milk Cheese Microbial Community.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0056422}, pmid = {36475872}, issn = {2379-5077}, mesh = {Humans ; Animals ; *Cheese/analysis ; Milk/microbiology ; *Bacteriophages/genetics ; Bacteria/genetics ; *Lactobacillales ; *Microbiota/genetics ; }, abstract = {Microbial starter cultures are used in the production of many cheeses around the world, such as Parmigiano-Reggiano, in Italy, Époisses, in France, and Canastra, in Brazil, providing many of the unique features of these cheeses. Bacteriophages (phages) are ubiquitous and well known to modulate the structure of bacterial communities, and recent data indicate that cheeses contain a high abundance of naturally occurring phages. Here, we analyze the viral and bacterial metagenomes of Canastra cheese: a traditional artisanal Brazilian cheese produced using an endogenous starter culture and raw milk. Over 1,200 viral operational taxonomic units were recovered using both isolated viral-like particles and complete metagenomic DNA. Common viral families identified included Siphoviridae and Myoviridae, with 40% of putative phage genomes unidentified at the family level of classification. We observed very high phage diversity, which varied greatly across different cheese producers, with 28% of phage genomes detected in only one producer. Several metagenome-assembled genomes were recovered for lactic acid-producing bacteria, as well as nonstarter bacterial species, and we identified several phage-bacterium interactions, at the strain level of resolution, varying across distinct cheese producers. We postulate that at least one bacterial strain detected could be endogenous and unique to the Canastra cheese-producing region in Brazil and that its growth seems to be modulated by autochthonous phages present in this artisanal production system. This phage-host relationship is likely to influence the fermentation dynamics and ultimately the sensorial profile of these cheeses, with implications for other similar cheese production systems around the world. IMPORTANCE Our work demonstrated a dynamic yet stable microbial ecosystem during cheese production using an endogenous starter culture. This was observed across several distinct producers and was marked by genomic evidence of continued phage-bacterium interactions, such as the presence of bacterial defense mechanisms. Furthermore, we provide evidence of unique microbial signatures for each individual cheese producer studied in the region, a fact that may have profound consequences on product traceability. This was the first effort to describe and understand the bacteriophage composition and ecological dynamics within the Brazilian Canastra cheese production system. The study of this prototypical backslopping production system provides a solid background for further mechanistic studies of the production of many cheeses around the world.}, } @article {pmid36475774, year = {2023}, author = {Bogomolnaya, L and Talamantes, M and Rocha, J and Nagarajan, A and Zhu, W and Spiga, L and Winter, MG and Konganti, K and Adams, LG and Winter, S and Andrews-Polymenis, H}, title = {Taxonomic and Metagenomic Analyses Define the Development of the Microbiota in the Chick.}, journal = {mBio}, volume = {14}, number = {1}, pages = {e0244422}, pmid = {36475774}, issn = {2150-7511}, support = {R01 AI118807/AI/NIAID NIH HHS/United States ; R01 DK134692/DK/NIDDK NIH HHS/United States ; R21 AI166263/AI/NIAID NIH HHS/United States ; R21 AI171537/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Chickens/microbiology ; Isoleucine ; *Microbiota ; Salmonella typhimurium/metabolism ; Cecum/microbiology ; Amino Acids, Branched-Chain/metabolism ; Valine/metabolism ; *Salmonella Infections, Animal/microbiology ; *Poultry Diseases/microbiology ; }, abstract = {Chicks are ideal to follow the development of the intestinal microbiota and to understand how a pathogen perturbs this developing population. Taxonomic/metagenomic analyses captured the development of the chick microbiota in unperturbed chicks and in chicks infected with Salmonella enterica serotype Typhimurium (STm) during development. Taxonomic analysis suggests that colonization by the chicken microbiota takes place in several waves. The cecal microbiota stabilizes at day 12 posthatch with prominent Gammaproteobacteria and Clostridiales. Introduction of S. Typhimurium at day 4 posthatch disrupted the expected waves of intestinal colonization. Taxonomic and metagenomic shotgun sequencing analyses allowed us to identify species present in uninfected chicks. Untargeted metabolomics suggested different metabolic activities in infected chick microbiota. This analysis and gas chromatography-mass spectrometry on ingesta confirmed that lactic acid in cecal content coincides with the stable presence of enterococci in STm-infected chicks. Unique metabolites, including 2-isopropylmalic acid, an intermediate in the biosynthesis of leucine, were present only in the cecal content of STm-infected chicks. The metagenomic data suggested that the microbiota in STm-infected chicks contained a higher abundance of genes, from STm itself, involved in branched-chain amino acid synthesis. We generated an ilvC deletion mutant (STM3909) encoding ketol-acid-reductoisomerase, a gene required for the production of l-isoleucine and l-valine. ΔilvC mutants are disadvantaged for growth during competitive infection with the wild type. Providing the ilvC gene in trans restored the growth of the ΔilvC mutant. Our integrative approach identified biochemical pathways used by STm to establish a colonization niche in the chick intestine during development. IMPORTANCE Chicks are an ideal model to follow the development of the intestinal microbiota and to understand how a pathogen perturbs this developing population. Using taxonomic and metagenomic analyses, we captured the development of chick microbiota to 19 days posthatch in unperturbed chicks and in chicks infected with Salmonella enterica serotype Typhimurium (STm). We show that normal development of the microbiota takes place in waves and is altered in the presence of a pathogen. Metagenomics and metabolomics suggested that branched-chain amino acid biosynthesis is especially important for Salmonella growth in the infected chick intestine. Salmonella mutants unable to make l-isoleucine and l-valine colonize the chick intestine poorly. Restoration of the pathway for biosynthesis of these amino acids restored the colonizing ability of Salmonella. Integration of multiple analyses allowed us to correctly identify biochemical pathways used by Salmonella to establish a niche for colonization in the chick intestine during development.}, } @article {pmid36475759, year = {2023}, author = {Chen, BY and Lin, WZ and Li, YL and Bi, C and Du, LJ and Liu, Y and Zhou, LJ and Liu, T and Xu, S and Shi, CJ and Zhu, H and Wang, YL and Sun, JY and Liu, Y and Zhang, WC and Zhang, Z and Zhang, HL and Zhu, YQ and Duan, SZ}, title = {Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0195622}, pmid = {36475759}, issn = {2165-0497}, mesh = {Humans ; *Mycobiome ; *Gastrointestinal Microbiome/physiology ; *Microbiota ; *Hypertension ; Mouth ; Feces/microbiology ; Fungi/genetics ; }, abstract = {The mycobiome is an essential constituent of the human microbiome and is associated with various diseases. However, the role of oral and gut fungi in hypertension (HTN) remains largely unexplored. In this study, saliva, subgingival plaques, and feces were collected from 36 participants with HTN and 24 healthy controls for metagenomic sequencing. The obtained sequences were analyzed using the Kraken2 taxonomic annotation pipeline to assess fungal composition and diversity. Correlations between oral and gut fungi and clinic parameters, between fungi within the same sample types, and between different sample types were identified by Spearman's correlation analysis. Overall, the subgingival fungal microbiome had substantially higher alpha diversity than the salivary and fecal fungal microbiomes. The fungal microbiomes of the three sample types displayed distinct beta diversity from each other. Oral fungi but not gut fungi in HTN had beta diversity significantly different from that of controls. Among the fungi shared in the oral cavity and gut, Exophiala was the genus with the most notable changes. Exophiala spinifera was the most abundant salivary species in HTN. Some fungal species directly correlated with blood pressure, including gut Exophiala xenobiotica and Exophiala mesophila. The markedly impaired ecological cocorrelation networks of oral and gut fungi in HTN suggested compromised association among fungal species. Most fungi were shared in the oral cavity and gut, and their correlations suggested the potential interplays between oral and gut fungi. In conclusion, the oral cavity and intestine have unique fungal ecological environments. The fungal enrichment and ecology in HTN, the correlations between oral and gut fungi, and the associations between oral and gut fungi and clinical parameters suggest an important role that the fungal microbiome may play in HTN. IMPORTANCE Our study fills the gap in human studies investigating the oral and gut fungal microbiota in association with blood pressure. It characterizes the diversity and composition of the oral and gut fungal microbiome in human subjects, elucidates the dysbiosis of fungal ecology in a hypertensive population, and establishes oral-gut fungal correlations and fungus-clinical parameter correlations. Targeting fungi in the oral cavity and/or gut may provide novel strategies for the prevention and treatment of hypertension.}, } @article {pmid36474348, year = {2022}, author = {Mukhopadhyay, S and Lee, JJ and Hartman, E and Woodford, E and Dhudasia, MB and Mattei, LM and Daniel, SG and Wade, KC and Underwood, MA and Bittinger, K}, title = {Preterm infants at low risk for early-onset sepsis differ in early fecal microbiome assembly.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2154091}, pmid = {36474348}, issn = {1949-0984}, support = {K23 HD088753/HD/NICHD NIH HHS/United States ; UL1 TR001878/TR/NCATS NIH HHS/United States ; }, mesh = {Infant, Newborn ; Humans ; *Infant, Premature ; Cohort Studies ; *Gastrointestinal Microbiome ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antibiotics are administered near-universally to very low birth weight (VLBW) infants after birth for suspected early-onset sepsis (EOS). We previously identified a phenotypic group of VLBW infants, referred to as low-risk for EOS (LRE), whose risk of EOS is low enough to avoid routine antibiotic initiation. In this cohort study, we compared 18 such infants with 30 infants categorized as non-LRE to determine if the lower risk of pathogen transmission at birth is accompanied by differences in microbiome acquisition and development. We did shotgun metagenomic sequencing of 361 fecal samples obtained serially. LRE infants had a higher human-to-bacterial DNA ratio than non-LRE infants in fecal samples on days 1-3 after birth, confirming lower bacterial acquisition among LRE infants. The microbial diversity and composition in samples from days 4-7 differed between the groups with a predominance of Staphylococcus epidermidis in LRE infants and Enterobacteriaceae sp. in non-LRE infants. Compositional differences were congruent with the distribution of virulence factors and antibiotic resistant genes. After the first week, the overall composition was similar, but changes in relative abundance for several taxa with increasing age differed between groups. Of the nine late-onset bacteremia episodes, eight occurred in non-LRE infants. Species isolated from the blood culture was detected in the pre-antibiotic fecal samples of the infant for all episodes, though these species were also found in infants without bacteremia. In conclusion, LRE infants present a distinct pattern of microbiome development that is aligned with their low risk for EOS. Further investigation to determine the impact of these differences on later outcomes such as late-onset bacteremia is warranted.}, } @article {pmid36473884, year = {2022}, author = {Goodarzi, Z and Asad, S and Mehrshad, M}, title = {Genome-resolved insight into the reservoir of antibiotic resistance genes in aquatic microbial community.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {21047}, pmid = {36473884}, issn = {2045-2322}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Microbiota ; }, abstract = {Aquatic microbial communities are an important reservoir of antibiotic resistance genes (ARGs). However, distribution and diversity of different ARG categories in environmental microbes with different ecological strategies is not yet well studied. Despite the potential exposure of the southern part of the Caspian Sea to the release of antibiotics, little is known about its natural resistome profile. We used a combination of Hidden Markov model (HMM), homology alignment and a deep learning approach for comprehensive screening of the diversity and distribution of ARGs in the Caspian Sea metagenomes at genome resolution. Detected ARGs were classified into five antibiotic resistance categories including prevention of access to target (44%), modification/protection of targets (30%), direct modification of antibiotics (22%), stress resistance (3%), and metal resistance (1%). The 102 detected ARG containing metagenome-assembled genomes of the Caspian Sea were dominated by representatives of Acidimicrobiia, Gammaproteobacteria, and Actinobacteria classes. Comparative analysis revealed that the highly abundant, oligotrophic, and genome streamlined representatives of taxa Acidimicrobiia and Actinobacteria modify the antibiotic target via mutation to develop antibiotic resistance rather than carrying extra resistance genes. Our results help with understanding how the encoded resistance categories of each genome are aligned with its ecological strategies.}, } @article {pmid36472532, year = {2022}, author = {Moraitou, M and Forsythe, A and Fellows Yates, JA and Brealey, JC and Warinner, C and Guschanski, K}, title = {Ecology, Not Host Phylogeny, Shapes the Oral Microbiome in Closely Related Species.}, journal = {Molecular biology and evolution}, volume = {39}, number = {12}, pages = {}, pmid = {36472532}, issn = {1537-1719}, mesh = {Animals ; Gorilla gorilla ; Phylogeny ; Dental Calculus ; *Hominidae ; *Microbiota/genetics ; }, abstract = {Host-associated microbiomes are essential for a multitude of biological processes. Placed at the contact zone between external and internal environments, the little-studied oral microbiome has important roles in host physiology and health. Here, we investigate the roles of host evolutionary relationships and ecology in shaping the oral microbiome in three closely related gorilla subspecies (mountain, Grauer's, and western lowland gorillas) using shotgun metagenomics of 46 museum-preserved dental calculus samples. We find that the oral microbiomes of mountain gorillas are functionally and taxonomically distinct from the other two subspecies, despite close evolutionary relationships and geographic proximity with Grauer's gorillas. Grauer's gorillas show intermediate bacterial taxonomic and functional, and dietary profiles. Altitudinal differences in gorilla subspecies ranges appear to explain these patterns, suggesting a close connection between dental calculus microbiomes and the environment, likely mediated through diet. This is further supported by the presence of gorilla subspecies-specific phyllosphere/rhizosphere taxa in the oral microbiome. Mountain gorillas show a high abundance of nitrate-reducing oral taxa, which may promote adaptation to a high-altitude lifestyle by modulating blood pressure. Our results suggest that ecology, rather than evolutionary relationships and geographic distribution, shape the oral microbiome in these closely related species.}, } @article {pmid36472419, year = {2022}, author = {Coker, J and Zhalnina, K and Marotz, C and Thiruppathy, D and Tjuanta, M and D'Elia, G and Hailu, R and Mahosky, T and Rowan, M and Northen, TR and Zengler, K}, title = {A Reproducible and Tunable Synthetic Soil Microbial Community Provides New Insights into Microbial Ecology.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0095122}, pmid = {36472419}, issn = {2379-5077}, support = {T32 GM007198/GM/NIGMS NIH HHS/United States ; }, mesh = {*Soil ; Reproducibility of Results ; Soil Microbiology ; Plant Roots ; *Microbiota ; Plants/microbiology ; }, abstract = {Microbial soil communities form commensal relationships with plants to promote the growth of both parties. The optimization of plant-microbe interactions to advance sustainable agriculture is an important field in agricultural research. However, investigation in this field is hindered by a lack of model microbial community systems and efficient approaches for building these communities. Two key challenges in developing standardized model communities are maintaining community diversity over time and storing/resuscitating these communities after cryopreservation, especially considering the different growth rates of organisms. Here, a model synthetic community (SynCom) of 16 soil microorganisms commonly found in the rhizosphere of diverse plant species, isolated from soil surrounding a single switchgrass plant, has been developed and optimized for in vitro experiments. The model soil community grows reproducibly between replicates and experiments, with a high community α-diversity being achieved through growth in low-nutrient media and through the adjustment of the starting composition ratios for the growth of individual organisms. The community can additionally be cryopreserved with glycerol, allowing for easy replication and dissemination of this in vitro system. Furthermore, the SynCom also grows reproducibly in fabricated ecosystem devices (EcoFABs), demonstrating the application of this community to an existing in vitro plant-microbe system. EcoFABs allow reproducible research in model plant systems, offering the precise control of environmental conditions and the easy measurement of plant microbe metrics. Our results demonstrate the generation of a stable and diverse microbial SynCom for the rhizosphere that can be used with EcoFAB devices and can be shared between research groups for maximum reproducibility. IMPORTANCE Microbes associate with plants in distinct soil communities to the benefit of both the soil microbes and the plants. Interactions between plants and these microbes can improve plant growth and health and are therefore a field of study in sustainable agricultural research. In this study, a model community of 16 soil bacteria has been developed to further the reproducible study of plant-soil microbe interactions. The preservation of the microbial community has been optimized for dissemination to other research settings. Overall, this work will advance soil microbe research through the optimization of a robust, reproducible model community.}, } @article {pmid36470490, year = {2023}, author = {Xiong, W and Wang, S and Jin, Y and Wu, Z and Liu, D and Su, H}, title = {Insights into nitrogen and phosphorus metabolic mechanisms of algal-bacterial aerobic granular sludge via metagenomics: Performance, microbial community and functional genes.}, journal = {Bioresource technology}, volume = {369}, number = {}, pages = {128442}, doi = {10.1016/j.biortech.2022.128442}, pmid = {36470490}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; Nitrogen ; Phosphorus ; Extracellular Polymeric Substance Matrix ; Metagenomics ; Bioreactors/microbiology ; Bacteria/genetics ; *Microbiota ; Waste Disposal, Fluid ; Denitrification ; Aerobiosis ; }, abstract = {Aiming to propose the potential mechanism for the enhancement of nitrogen (N) and phosphorus (P) removal of algal-bacterial aerobic granular sludge (A-AGS), metagenomic analysis was applied to identify the metabolic pathways. The results showed that chemical oxygen demand, ammonia nitrogen, total N, and total P removal of A-AGS could reach to 94.5%, 97.5%, 78.1%, and 88.5%, respectively. Algae enriched the content of extracellular polymeric substance, which significantly promoted the formation of A-AGS. Further investigations in functional genes suggested that nitrification process (amo, nxr, hao, etc.), denitrification process (nir, nap, nor, etc.), and polyphosphate accumulation (ppk, ppk2, etc.) were enhanced greatly in A-AGS. Notably, genus Thauera was the dominant source of functional genes, which penetrated both in N and P metabolism. The higher N and P removal performance in A-AGS could be attributed to synergistic effect between bacteria and microalgae, which may provide the basic for the application in wastewater treatment.}, } @article {pmid36469554, year = {2022}, author = {Zhao, C and Goldman, M and Smith, BJ and Pollard, KS}, title = {Genotyping Microbial Communities with MIDAS2: From Metagenomic Reads to Allele Tables.}, journal = {Current protocols}, volume = {2}, number = {12}, pages = {e604}, pmid = {36469554}, issn = {2691-1299}, support = {R01 HL160862/HL/NHLBI NIH HHS/United States ; T32 GM067547/GM/NIGMS NIH HHS/United States ; }, mesh = {*Metagenome/genetics ; Genotype ; Alleles ; *Microbiota/genetics ; Nucleotides ; }, abstract = {The Metagenomic Intra-Species Diversity Analysis System 2 (MIDAS2) is a scalable pipeline that identifies single nucleotide variants and gene copy number variants in metagenomes using comprehensive reference databases built from public microbial genome collections (metagenotyping). MIDAS2 is the first metagenotyping tool with functionality to control metagenomic read mapping filters and to customize the reference database to the microbial community, features that improve the precision and recall of detected variants. In this article we present four basic protocols for the most common use cases of MIDAS2, along with supporting protocols for installation and use. In addition, we provide in-depth guidance on adjusting command line parameters, editing the reference database, optimizing hardware utilization, and understanding the metagenotyping results. All the steps of metagenotyping, from raw sequencing reads to population genetic analysis, are demonstrated with example data in two downloadable sequencing libraries of single-end metagenomic reads representing a mixture of multiple bacterial species. This set of protocols empowers users to accurately genotype hundreds of species in thousands of samples, providing rich genetic data for studying the evolution and strain-level ecology of microbial communities. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Species prescreening Basic Protocol 2: Download MIDAS reference database Basic Protocol 3: Population single nucleotide variant calling Basic Protocol 4: Pan-genome copy number variant calling Support Protocol 1: Installing MIDAS2 Support Protocol 2: Command line inputs Support Protocol 3: Metagenotyping with a custom collection of genomes Support Protocol 4: Metagenotyping with advanced parameters.}, } @article {pmid36468852, year = {2022}, author = {Velez-Cortes, F and Wang, H}, title = {Characterization and Spatial Mapping of the Human Gut Metasecretome.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0071722}, pmid = {36468852}, issn = {2379-5077}, support = {R01 AI132403/AI/NIAID NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; R21 AI146817/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Bacteria/genetics ; Bacterial Proteins/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Phylogeny ; }, abstract = {Bacterially secreted proteins play an important role in microbial physiology and ecology in many environments, including the mammalian gut. While gut microbes have been extensively studied over the past decades, little is known about the proteins that they secrete into the gastrointestinal tract. In this study, we developed and applied a computational pipeline to a comprehensive catalog of human-associated metagenome-assembled genomes in order to predict and analyze the bacterial metasecretome of the human gut, i.e., the collection of proteins secreted out of the cytoplasm by human gut bacteria. We identified the presence of large and diverse families of secreted carbohydrate-active enzymes and assessed their phylogenetic distributions across different taxonomic groups, which revealed an enrichment in Bacteroidetes and Verrucomicrobia. By mapping secreted proteins to available metagenomic data from endoscopic sampling of the human gastrointestinal tract, we specifically pinpointed regions in the upper and lower intestinal tract along the lumen and mucosa where specific glycosidases are secreted by resident microbes. The metasecretome analyzed in this study constitutes the most comprehensive list of secreted proteins produced by human gut bacteria reported to date and serves as a useful resource for the microbiome research community. IMPORTANCE Bacterially secreted proteins are necessary for the proper functioning of bacterial cells and communities. Secreted proteins provide bacterial cells with the ability to harvest resources from the exterior, import these resources into the cell, and signal to other bacteria. In the human gut microbiome, these actions impact host health and allow the maintenance of a healthy gut bacterial community. We utilized computational tools to identify the major components of human gut bacterially secreted proteins and determined their spatial distribution in the gastrointestinal tract. Our analysis of human gut bacterial secreted proteins will allow a better understanding of the impact of gut bacteria on human health and represents a step toward identifying new protein functions with interesting applications in biomedicine and industry.}, } @article {pmid36468273, year = {2023}, author = {Hino, A and Fukushima, K and Kusakabe, S and Ueda, T and Sudo, T and Fujita, J and Motooka, D and Takeda, AK and Shinozaki, NO and Watanabe, S and Yokota, T and Shibayama, H and Nakamura, S and Hosen, N}, title = {Prolonged gut microbial alterations in post-transplant survivors of allogeneic haematopoietic stem cell transplantation.}, journal = {British journal of haematology}, volume = {201}, number = {4}, pages = {725-737}, doi = {10.1111/bjh.18574}, pmid = {36468273}, issn = {1365-2141}, mesh = {Humans ; *Gastrointestinal Microbiome ; Dysbiosis/complications ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Patient Discharge ; *Graft vs Host Disease/microbiology ; *Bronchiolitis Obliterans Syndrome ; }, abstract = {Dysbiosis of the gut microbiota has been reported to increase early complications after allogeneic haematopoietic stem cell transplantation (allo-HSCT). However, it remains unclear whether gut microbial alterations persist during late complications, such as chronic graft-versus-host disease (cGVHD) or secondary cancers. Here, we analysed the gut microbiota of 59 patients who survived for 1-21.7 years (median, 6.4 years) after allo-HSCT. Long-term survivors showed lower gut microbial diversity than the age- and sex-matched healthy controls. This decreased diversity was reflected in the reduced abundance of the butyrate-producing bacteria. Patients with a history of grade 3 acute graft-versus-host disease (aGVHD) exhibited higher Veillonella abundance than patients with a history of grade 1-2 or non-aGVHD cases. The abundance of Faecalibacterium showed no decrease only in limited cGVHD cases. Additionally, the microbial structure in the secondary cancer group was significantly different (p < 0.05) from that in the non-secondary cancer group. This study is the first to show that microbial dysbiosis is present over a 10-year lifetime after discharge following allo-HSCT. Our results suggest that these prolonged gut microbial alterations may be associated with the development and exacerbation of late complications in post-transplant survivors.}, } @article {pmid36467737, year = {2022}, author = {Jeon, J and Kang, S and Hur, JK and Rho, M}, title = {Metagenomic characterization of sphingomyelinase C in the microbiome of humans and environments.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1015706}, pmid = {36467737}, issn = {2235-2988}, mesh = {Humans ; *Metagenome ; Sphingomyelin Phosphodiesterase/genetics ; Metagenomics ; *Microbiota ; Genomics ; }, abstract = {Bacterial sphingomyelinases (SMases) hydrolyze sphingomyelin and play an important role in membrane dynamics and the host immune system. While the number of sequenced genomes and metagenomes is increasing, a limited number of experimentally validated SMases have been reported, and the genomic diversity of SMases needs to be elucidated extensively. This study investigated the sequence and structural characteristics of SMases in bacterial genomes and metagenomes. Using previously identified SMases, such as the β-toxin of Staphylococcus aureus, we identified 276 putative SMases and 15 metagenomic SMases by a sequence homology search. Among the predicted metagenomic SMases, six non-redundant metagenomic SMases (M-SMase1-6) were selected for further analysis. The predicted SMases were confirmed to contain highly conserved residues in the central metal-binding site; however, the edge metal-binding site showed high diversity according to the taxon. In addition, protein structure modeling of metagenomic SMases confirmed structural conservation of the central metal-binding site and variance of the edge metal-binding site. From the activity assay on M-SMase2 and M-SMase5, we found that they displayed sphingomyelinase activity compared to Bacillus cereus SMase. This study elucidates a comprehensive genomic characterization of SMases and provides insight into the sequence-structure-activity relationship.}, } @article {pmid36464731, year = {2022}, author = {Ruscheweyh, HJ and Milanese, A and Paoli, L and Karcher, N and Clayssen, Q and Keller, MI and Wirbel, J and Bork, P and Mende, DR and Zeller, G and Sunagawa, S}, title = {Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {212}, pmid = {36464731}, issn = {2049-2618}, mesh = {Swine ; Cattle ; Animals ; RNA, Ribosomal, 16S/genetics ; *Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; Soil ; }, abstract = {BACKGROUND: Taxonomic profiling is a fundamental task in microbiome research that aims to detect and quantify the relative abundance of microorganisms in biological samples. Available methods using shotgun metagenomic data generally depend on the deposition of sequenced and taxonomically annotated genomes, usually from cultures of isolated strains, in reference databases (reference genomes). However, the majority of microorganisms have not been cultured yet. Thus, a substantial fraction of microbial community members remains unaccounted for during taxonomic profiling, particularly in samples from underexplored environments. To address this issue, we developed the mOTU profiler, a tool that enables reference genome-independent species-level profiling of metagenomes. As such, it supports the identification and quantification of both "known" and "unknown" species based on a set of select marker genes.

RESULTS: We present mOTUs3, a command line tool that enables the profiling of metagenomes for >33,000 species-level operational taxonomic units. To achieve this, we leveraged the reconstruction of >600,000 draft genomes, most of which are metagenome-assembled genomes (MAGs), from diverse microbiomes, including soil, freshwater systems, and the gastrointestinal tract of ruminants and other animals, which we found to be underrepresented by reference genomes. Overall, two thirds of all species-level taxa lacked a reference genome. The cumulative relative abundance of these newly included taxa was low in well-studied microbiomes, such as the human body sites (6-11%). By contrast, they accounted for substantial proportions (ocean, freshwater, soil: 43-63%) or even the majority (pig, fish, cattle: 60-80%) of the relative abundance across diverse non-human-associated microbiomes. Using community-developed benchmarks and datasets, we found mOTUs3 to be more accurate than other methods and to be more congruent with 16S rRNA gene-based methods for taxonomic profiling. Furthermore, we demonstrate that mOTUs3 increases the resolution of well-known microbial groups into species-level taxa and helps identify new differentially abundant taxa in comparative metagenomic studies.

CONCLUSIONS: We developed mOTUs3 to enable accurate species-level profiling of metagenomes. Compared to other methods, it provides a more comprehensive view of prokaryotic community diversity, in particular for currently underexplored microbiomes. To facilitate comparative analyses by the research community, it is released with >11,000 precomputed profiles for publicly available metagenomes and is freely available at: https://github.com/motu-tool/mOTUs . Video Abstract.}, } @article {pmid36464700, year = {2022}, author = {Cohen, Y and Borenstein, E}, title = {The microbiome's fiber degradation profile and its relationship with the host diet.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {266}, pmid = {36464700}, issn = {1741-7007}, support = {2435/19//Israel Science Foundation/ ; }, mesh = {Humans ; Dietary Fiber ; Diet ; *Gastrointestinal Microbiome ; *Microbiota ; Metagenome ; }, abstract = {BACKGROUND: The relationship between the gut microbiome and diet has been the focus of numerous recent studies. Such studies aim to characterize the impact of diet on the composition of the microbiome, as well as the microbiome's ability to utilize various compounds in the diet and produce metabolites that may be beneficial for the host. Consumption of dietary fibers (DFs)-polysaccharides that cannot be broken down by the host's endogenous enzymes and are degraded primarily by members of the microbiome-is known to have a profound effect on the microbiome. Yet, a comprehensive characterization of microbiome compositional and functional shifts in response to the consumption of specific DFs is still lacking.

RESULTS: Here, we introduce a computational framework, coupling metagenomic sequencing with careful annotation of polysaccharide degrading enzymes and DF structures, for inferring the metabolic ability of a given microbiome sample to utilize a broad catalog of DFs. We demonstrate that the inferred fiber degradation profile (IFDP) generated by our framework accurately reflects the dietary habits of various hosts across four independent datasets. We further demonstrate that IFDPs are more tightly linked to the host diet than commonly used taxonomic and functional microbiome-based profiles. Finally, applying our framework to a set of ~700 metagenomes that represents large human population cohorts from 9 different countries, we highlight intriguing global patterns linking DF consumption habits with microbiome capacities.

CONCLUSIONS: Combined, our findings serve as a proof-of-concept for the use of DF-specific analysis for providing important complementary information for better understanding the relationship between dietary habits and the gut microbiome.}, } @article {pmid36463395, year = {2022}, author = {Zhu, LT and Huang, HN and Avellán-Llaguno, RD and Qin, Y and An, XL and Su, JQ and Huang, Q and Zhu, YG}, title = {Diverse functional genes harboured in extracellular vesicles from environmental and human microbiota.}, journal = {Journal of extracellular vesicles}, volume = {11}, number = {12}, pages = {e12292}, pmid = {36463395}, issn = {2001-3078}, mesh = {Humans ; *Microbiota/genetics ; *Extracellular Vesicles/genetics ; Metagenome/genetics ; Metagenomics ; Feces ; }, abstract = {Exchange of mobile functional genes within microbiota benefits the microbial community. However, the status of the mobile gene pool in environment is still largely unclear, impeding the understanding on the process of gene transfer in natural microbial communities. The release of extracellular vesicles (EVs) by diverse organisms has been proposed to be a vital way in the complex networks of interactions between microbes and their habitats. In this study, we hypothesized that microbial EVs encapsulating functional DNA are widely distributed in the environmental matrix. The prevalence, source and DNA cargoes of EVs in three types of typical microbial habitats were studied. High abundance of EVs comparable to the bacterial concentration was found in human faeces, wastewater and soil. Metagenomic analysis showed the diverse and differential taxonomy of EVs-associated DNA compared to source microbiome. An array of efficient EVs producing species was identified. A wide variety of mobile genes including glycoside hydrolase family 25 were enriched. Antibiotic resistance genes co-localizing with mobile genetic elements were abundant in the EVs. This study provides novel insights into the prevalent EVs as a reservoir for the mobile functional genes in the natural environment.}, } @article {pmid36462818, year = {2023}, author = {Bloomfield, SJ and Zomer, AL and O'Grady, J and Kay, GL and Wain, J and Janecko, N and Palau, R and Mather, AE}, title = {Determination and quantification of microbial communities and antimicrobial resistance on food through host DNA-depleted metagenomics.}, journal = {Food microbiology}, volume = {110}, number = {}, pages = {104162}, doi = {10.1016/j.fm.2022.104162}, pmid = {36462818}, issn = {1095-9998}, mesh = {Animals ; *Anti-Bacterial Agents ; RNA, Ribosomal, 16S/genetics ; Drug Resistance, Bacterial/genetics ; DNA ; *Microbiota ; Seafood ; Salmon ; }, abstract = {Food products carry bacteria unless specifically sterilised. These bacteria can be pathogenic, commensal or associated with food spoilage, and may also be resistant to antimicrobials. Current methods for detecting bacteria on food rely on culturing for specific bacteria, a time-consuming process, or 16S rRNA metabarcoding that can identify different taxa but not their genetic content. Directly sequencing metagenomes of food is inefficient as its own DNA vastly outnumbers the bacterial DNA present. We optimised host DNA depletion enabling efficient sequencing of food microbiota, thereby increasing the proportion of non-host DNA sequenced 13-fold (mean; range: 1.3-40-fold) compared to untreated samples. The method performed best on chicken, pork and leafy green samples which had high mean prokaryotic read proportions post-depletion (0.64, 0.74 and 0.74, respectively), with lower mean prokaryotic read proportions in salmon (0.50) and prawn samples (0.19). We show that bacterial compositions and concentrations of antimicrobial resistance (AMR) genes differed by food type, and that salmon metagenomes were influenced by the production/harvesting method. The approach described in this study is an efficient and effective method of identifying and quantifying the predominant bacteria and AMR genes on food.}, } @article {pmid36461382, year = {2022}, author = {Valentino, V and Sequino, G and Cobo-Díaz, JF and Álvarez-Ordóñez, A and De Filippis, F and Ercolini, D}, title = {Evidence of virulence and antibiotic resistance genes from the microbiome mapping in minimally processed vegetables producing facilities.}, journal = {Food research international (Ottawa, Ont.)}, volume = {162}, number = {Pt B}, pages = {112202}, doi = {10.1016/j.foodres.2022.112202}, pmid = {36461382}, issn = {1873-7145}, mesh = {Virulence ; *Vegetables ; Anti-Bacterial Agents ; Drug Resistance, Microbial/genetics ; *Microbiota/genetics ; }, abstract = {Daily consumption of fresh vegetables is highly recommended by international health organizations, because of their high content of nutrients. However, fresh vegetables might harbour several pathogenic microorganisms or contribute to spread antibiotic resistance, thus representing a hazard for consumers. In addition, little is known about the transmission routes of the residential microbiome from the food handling environment to vegetables. Therefore, we collected environmental and food samples from three manufactures producing fresh vegetables to estimate the relevance of the built environment microbiome on that of the finished products. Our results show that food contact surfaces sampled after routine cleaning and disinfection procedures host a highly diverse microbiome, including pathogens such as the enterotoxigenic Bacillus cereus sensu stricto. In addition, we provide evidence of the presence of a wide range of antibiotic resistance and virulence genes on food contact surfaces associated with multiple taxa, thus supporting the hypothesis that selection of resistant and pathogenic taxa might occur on sanitized surfaces. This study also highlights the potential of microbiome mapping routinely applied in food industries monitoring programs to ensure food safety.}, } @article {pmid36461373, year = {2022}, author = {Hou, Y and Zhang, Z and Cui, Y and Peng, C and Fan, Y and Tan, C and Wang, Q and Liu, Z and Gong, J}, title = {Pu-erh tea and theabrownin ameliorate metabolic syndrome in mice via potential microbiota-gut-liver-brain interactions.}, journal = {Food research international (Ottawa, Ont.)}, volume = {162}, number = {Pt B}, pages = {112176}, doi = {10.1016/j.foodres.2022.112176}, pmid = {36461373}, issn = {1873-7145}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Liver ; *Metabolic Syndrome ; Brain ; Obesity ; Tea ; }, abstract = {Metabolic syndrome (MS) is a common metabolic disorder characterized by obesity, insulin resistance, cardiovascular disease and gut microbiota dysbiosis. Pu-erh tea and its ingredient theabrownin have known functions on the reduction of body weight gain and fat accumulation. However, few studies systematicly analyze the different contributions and mechanisms of their anti-metabolic syndrome functions through multi-omics combination analysis. Here, we used metagenomics, transcriptomics and metabolomics technology to investigate the anti-metabolic syndrome mechanism of Pu-erh tea and theabrownin in MS mice. Our results suggested that Pu-erh tea and theabrownin interventions could improve the physiological functions of liver, jejunum and adipose tissues in MS mice. Hepatic transcriptome revealed that both interventions could regulate the circadian rhythm pathway. Glycerophospholipid and linoleic acid metabolism were also modulated by both interventions through serum and brain metabolome analysis. Faecal metagenome demonstrated that both interventions could increase the relative abundance of Clostridiales bacterium 42_27, Blautia coccoides and Firmicutes bacterium ASF500, but decrease the relative abundance of Brevundimonas vesicularis. Otherwise, compared with Pu-erh tea, theabrownin markedly upregulated the levels of hepatic antioxidants (i.e., SOD, GSH), prominently downregulated hepatic inflammatory factors (i.e., IL-1, IL-6, TNF-α) and malondialdehyde oxidant, but modestly reduced obesity-associated short-chain fatty acids in faeces in MS mice. Taken together, our data provided insights into the homogeneous and heterogeneous natural biological functions of theabrownin and Pu-erh tea in the treatment of metabolic syndrome.}, } @article {pmid36461096, year = {2022}, author = {Wang, G and Wang, X and Ma, Y and Cai, S and Yang, L and Fan, Y and Zeng, X and Qiao, S}, title = {Lactobacillus reuteri improves the development and maturation of fecal microbiota in piglets through mother-to-infant microbe and metabolite vertical transmission.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {211}, pmid = {36461096}, issn = {2049-2618}, mesh = {Animals ; Swine ; Female ; Pregnancy ; Humans ; *Limosilactobacillus reuteri ; Mothers ; Feces ; *Microbiota ; *Body Fluids ; Clostridiaceae ; }, abstract = {BACKGROUND: The immature neonatal fecal microbiota substantially impacts the development of gut health and greatly increases the risk of disease. Developing effective strategies to modulate the development of neonatal fecal microbiota has great significance. Herein, we investigated whether the maternal dietary supplementation and oral administration of Lactobacillus reuteri could effectively promote the development and maturation of the fecal microbiome in piglets from birth to weaning.

RESULTS: Metagenomic analysis of colostrum showed that maternal dietary L. reuteri supplementation influenced the overall microbiota composition, decreased the abundance of the phylum Proteobacteria and increased that of the species Bifidobacterium choerinum. KEGG pathway analysis revealed that maternal L. reuteri supplementation enriched the lysine biosynthesis and glycolysis/gluconeogenesis pathways and downregulated the bacterial invasion of epithelial cells in the colostrum. In addition, L. reuteri supplementation significantly altered the metabolite features and modules in umbilical cord blood serum based on metabolomics. Further, a significant covariation was observed between these differential metabolites and the species in colostrum. Maternal dietary L. reuteri supplementation also significantly influenced the microbiota composition and increased the meconium abundance of beneficial bacteria (such as Romboutsia, Lactobacillus, Blautia, Butyricicoccus, and Ruminococcus), some of which were markedly associated with several differential metabolites in umbilical cord blood serum between two groups. Notably, both the maternal dietary supplementation and oral intake of L. reuteri had strong impacts on the overall microbial composition and maturation of fecal microbiota in piglets during early life, and these effects were dependent on the growth stage. Oral administration of L. reuteri promoted diarrhea resistance in neonates, while maternal supplementation of L. reuteri enhanced the abilities of antioxidants and decreased inflammation. Moreover, the administration of L. reuteri via both methods in combination improved the growth performances of piglets.

CONCLUSION: Overall, our data demonstrated that L. reuteri had the ability to modulate the composition of fecal microbiota in newborn piglets by influencing the microbial community and functional composition in the colostrum and by altering several key metabolites in the umbilical cord blood serum. Also, both the maternal dietary supplementation and oral administration of L. reuteri effectively promoted the development and maturation of the fecal microbiome in piglets during early life. Both the maternal dietary supplementation and oral administration of L. reuteri in combination optimized the growth performances of piglets. Video Abstract.}, } @article {pmid36457116, year = {2022}, author = {Salazar, C and Giménez, M and Riera, N and Parada, A and Puig, J and Galiana, A and Grill, F and Vieytes, M and Mason, CE and Antelo, V and D'Alessandro, B and Risso, J and Iraola, G}, title = {Human microbiota drives hospital-associated antimicrobial resistance dissemination in the urban environment and mirrors patient case rates.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {208}, pmid = {36457116}, issn = {2049-2618}, mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; Sewage ; Drug Resistance, Bacterial/genetics ; *Microbiota/genetics ; Hospitals ; *Cross Infection ; Carbapenems ; }, abstract = {BACKGROUND: The microbial community composition of urban environments is primarily determined by human activity. The use of metagenomics to explore how microbial communities are shaped in a city provides a novel input that can improve decisions on public health measures, architectural design, and urban resilience. Of note, the sewage system in a city acts as a complex reservoir of bacteria, pharmaceuticals, and antimicrobial resistant (AMR) genes that can be an important source of epidemiological information. Hospital effluents are rich in patient-derived bacteria and can thus readily become a birthplace and hotspot reservoir for antibiotic resistant pathogens which are eventually incorporated into the environment. Yet, the scope to which nosocomial outbreaks impact the urban environment is still poorly understood.

RESULTS: In this work, we extensively show that different urban waters from creeks, beaches, sewage spillways and collector pipes enclose discrete microbial communities that are characterized by a differential degree of contamination and admixture with human-derived bacteria. The abundance of human bacteria correlates with the abundance of AMR genes in the environment, with beta-lactamases being the top-contributing class to distinguish low vs. highly-impacted urban environments. Indeed, the abundance of beta-lactamase resistance and carbapenem resistance determinants in the urban environment significantly increased in a 1-year period. This was in line with a pronounced increase of nosocomial carbapenem-resistant infections reported during the same period that was mainly driven by an outbreak-causing, carbapenemase-producing Klebsiella pneumoniae (KPC) ST-11 strain. Genome-resolved metagenomics of urban waters before and after this outbreak, coupled with high-resolution whole-genome sequencing, confirmed the dissemination of the ST-11 strain and a novel KPC megaplasmid from the hospital to the urban environment. City-wide analysis showed that geospatial dissemination of the KPC megaplasmid in the urban environment inversely depended on the sewage system infrastructure.

CONCLUSIONS: We show how urban metagenomics and outbreak genomic surveillance can be coupled to generate relevant information for infection control, antibiotic stewardship, and pathogen epidemiology. Our results highlight the need to better characterize and understand how human-derived bacteria and antimicrobial resistance disseminate in the urban environment to incorporate this information in the development of effluent treatment infrastructure and public health policies. Video Abstract.}, } @article {pmid36457108, year = {2022}, author = {Shen, J and McFarland, AG and Blaustein, RA and Rose, LJ and Perry-Dow, KA and Moghadam, AA and Hayden, MK and Young, VB and Hartmann, EM}, title = {An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {206}, pmid = {36457108}, issn = {2049-2618}, support = {BAA FY2018-OADS-01 Contract 02915/CC/CDC HHS/United States ; }, mesh = {Workflow ; *Metagenomics ; Environmental Monitoring ; *Microbiota/genetics ; Delivery of Health Care ; }, abstract = {BACKGROUND: Effective surveillance of microbial communities in the healthcare environment is increasingly important in infection prevention. Metagenomics-based techniques are promising due to their untargeted nature but are currently challenged by several limitations: (1) they are not powerful enough to extract valid signals out of the background noise for low-biomass samples, (2) they do not distinguish between viable and nonviable organisms, and (3) they do not reveal the microbial load quantitatively. An additional practical challenge towards a robust pipeline is the inability to efficiently allocate sequencing resources a priori. Assessment of sequencing depth is generally practiced post hoc, if at all, for most microbiome studies, regardless of the sample type. This practice is inefficient at best, and at worst, poor sequencing depth jeopardizes the interpretation of study results. To address these challenges, we present a workflow for metagenomics-based environmental surveillance that is appropriate for low-biomass samples, distinguishes viability, is quantitative, and estimates sequencing resources.

RESULTS: The workflow was developed using a representative microbiome sample, which was created by aggregating 120 surface swabs collected from a medical intensive care unit. Upon evaluating and optimizing techniques as well as developing new modules, we recommend best practices and introduce a well-structured workflow. We recommend adopting liquid-liquid extraction to improve DNA yield and only incorporating whole-cell filtration when the nonbacterial proportion is large. We suggest including propidium monoazide treatment coupled with internal standards and absolute abundance profiling for viability assessment and involving cultivation when demanding comprehensive profiling. We further recommend integrating internal standards for quantification and additionally qPCR when we expect poor taxonomic classification. We also introduce a machine learning-based model to predict required sequencing effort from accessible sample features. The model helps make full use of sequencing resources and achieve desired outcomes. Video Abstract CONCLUSIONS: This workflow will contribute to more accurate and robust environmental surveillance and infection prevention. Lessons gained from this study will also benefit the continuing development of methods in relevant fields.}, } @article {pmid36457105, year = {2022}, author = {Panwar, P and Williams, TJ and Allen, MA and Cavicchioli, R}, title = {Population structure of an Antarctic aquatic cyanobacterium.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {207}, pmid = {36457105}, issn = {2049-2618}, mesh = {Antarctic Regions ; *Cyanobacteria/genetics ; Lakes ; *Microbiota ; Nitrogen ; }, abstract = {BACKGROUND: Ace Lake is a marine-derived, stratified lake in the Vestfold Hills of East Antarctica with an upper oxic and lower anoxic zone. Cyanobacteria are known to reside throughout the water column. A Synechococcus-like species becomes the most abundant member in the upper sunlit waters during summer while persisting annually even in the absence of sunlight and at depth in the anoxic zone. Here, we analysed ~ 300 Gb of Ace Lake metagenome data including 59 Synechococcus-like metagenome-assembled genomes (MAGs) to determine depth-related variation in cyanobacterial population structure. Metagenome data were also analysed to investigate viruses associated with this cyanobacterium and the host's capacity to defend against or evade viruses.

RESULTS: A single Synechococcus-like species was found to exist in Ace Lake, Candidatus Regnicoccus frigidus sp. nov., consisting of one phylotype more abundant in the oxic zone and a second phylotype prevalent in the oxic-anoxic interface and surrounding depths. An important aspect of genomic variation pertained to nitrogen utilisation, with the capacity to perform cyanide assimilation and asparagine synthesis reflecting the depth distribution of available sources of nitrogen. Both specialist (host specific) and generalist (broad host range) viruses were identified with a predicted ability to infect Ca. Regnicoccus frigidus. Host-virus interactions were characterised by a depth-dependent distribution of virus type (e.g. highest abundance of specialist viruses in the oxic zone) and host phylotype capacity to defend against (e.g. restriction-modification, retron and BREX systems) and evade viruses (cell surface proteins and cell wall biosynthesis and modification enzymes).

CONCLUSION: In Ace Lake, specific environmental factors such as the seasonal availability of sunlight affects microbial abundances and the associated processes that the microbial community performs. Here, we find that the population structure for Ca. Regnicoccus frigidus has evolved differently to the other dominant phototroph in the lake, Candidatus Chlorobium antarcticum. The geography (i.e. Antarctica), limnology (e.g. stratification) and abiotic (e.g. sunlight) and biotic (e.g. microbial interactions) factors determine the types of niches that develop in the lake. While the lake community has become increasingly well studied, metagenome-based studies are revealing that niche adaptation can take many paths; these paths need to be determined in order to make reasonable predictions about the consequences of future ecosystem perturbations. Video Abstract.}, } @article {pmid36457010, year = {2022}, author = {Liu, L and Yang, Y and Deng, Y and Zhang, T}, title = {Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {209}, pmid = {36457010}, issn = {2049-2618}, mesh = {Metagenome/genetics ; Metagenomics ; *Nanopores ; RNA, Ribosomal, 16S/genetics ; Sewage ; *Microbiota/genetics ; Prophages ; }, abstract = {BACKGROUND: The accurate and comprehensive analyses of genome-resolved metagenomics largely depend on the reconstruction of reference-quality (complete and high-quality) genomes from diverse microbiomes. Closing gaps in draft genomes have been approaching with the inclusion of Nanopore long reads; however, genome quality improvement requires extensive and time-consuming high-accuracy short-read polishing.

RESULTS: Here, we introduce NanoPhase, an open-source tool to reconstruct reference-quality genomes from complex metagenomes using only Nanopore long reads. Using Kit 9 and Q20+ chemistries, we first evaluated the feasibility of NanoPhase using a ZymoBIOMICS gut microbiome standard (including 21 strains), then sequenced the complex activated sludge microbiome and reconstructed 275 MAGs with median completeness of ~ 90%. As a result, NanoPhase improved the MAG contiguity (median MAG N50: 735 Kb, 44-86X compared to conventional short-read-based methods) while maintaining high accuracy, allowing for a full and accurate investigation of target microbiomes. Additionally, leveraging these high-contiguity reference-quality genomes, we identified 165 prophages within 111 MAGs, with 5 as active prophages, indicating the prophage was a neglected source of genetic diversity within microbial populations and influencer in shaping microbial composition in the activated sludge microbiome.

CONCLUSIONS: Our results demonstrated that NanoPhase enables reference-quality genome reconstruction from complex metagenomes directly using only Nanopore long reads. Furthermore, besides the 16S rRNA genes and biosynthetic gene clusters, the generated high-accuracy and high-contiguity MAGs improved the host identification of critical mobile genetic elements, e.g., prophage, serving as a genomic blueprint to investigate the microbial potential and ecology in the activated sludge ecosystem. Video Abstract.}, } @article {pmid36455775, year = {2023}, author = {Dell'Anno, F and Joaquim van Zyl, L and Trindade, M and Buschi, E and Cannavacciuolo, A and Pepi, M and Sansone, C and Brunet, C and Ianora, A and de Pascale, D and Golyshin, PN and Dell'Anno, A and Rastelli, E}, title = {Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {317}, number = {}, pages = {120772}, doi = {10.1016/j.envpol.2022.120772}, pmid = {36455775}, issn = {1873-6424}, mesh = {Biodegradation, Environmental ; *Petroleum/analysis ; Bacteria/genetics/metabolism ; *Metals, Heavy/metabolism ; *Polycyclic Aromatic Hydrocarbons/metabolism ; Hydrocarbons/metabolism ; *Microbiota ; Geologic Sediments/microbiology ; }, abstract = {Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustainable strategy. Here, we hypothesized that the heavily polluted coastal area facing the Sarno River mouth, which discharges >3 tons of polycyclic aromatic hydrocarbons (PAHs) and ∼15 tons of heavy metals (HMs) into the sea annually, hosts unique microbiomes including marine bacteria useful for PAHs and HMs bioremediation. We thus enriched the microbiome of marine sediments, contextually selecting for HM-resistant bacteria. The enriched mixed bacterial culture was subjected to whole-DNA sequencing, metagenome-assembled-genomes (MAGs) annotation, and further sub-culturing to obtain the major bacterial species as pure strains. We obtained two novel isolates corresponding to the two most abundant MAGs (Alcanivorax xenomutans strain-SRM1 and Halomonas alkaliantarctica strain-SRM2), and tested their ability to degrade PAHs and remove HMs. Both strains exhibited high PAHs degradation (60-100%) and HMs removal (21-100%) yield, and we described in detail >60 genes in their MAGs to unveil the possible genetic basis for such abilities. Most promising yields (∼100%) were obtained towards naphthalene, pyrene and lead. We propose these novel bacterial strains and related genetic repertoire to be further exploited for effective bioremediation of marine environments contaminated with both PAHs and HMs.}, } @article {pmid36453930, year = {2022}, author = {Wang, Z and Yang, T and Mei, X and Wang, N and Li, X and Yang, Q and Dong, C and Jiang, G and Lin, J and Xu, Y and Shen, Q and Jousset, A and Banerjee, S}, title = {Bio-Organic Fertilizer Promotes Pear Yield by Shaping the Rhizosphere Microbiome Composition and Functions.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0357222}, pmid = {36453930}, issn = {2165-0497}, mesh = {Fertilizers/analysis ; *Pyrus ; Rhizosphere ; Soil/chemistry ; *Microbiota ; Bacteria ; Soil Microbiology ; }, abstract = {Bio-organic fertilizers (BOF) containing both organic amendments and beneficial microorganisms have been consistently shown to improve soils fertility and yield. However, the exact mechanisms which link amendments and yields remain disputed, and the complexity of bio-organic fertilizers may work in parallel in several ways. BOF may directly improve yield by replenishing soil nutrients or introducing beneficial microbial genes or indirectly by altering the soil microbiome to enrich native beneficial microorganisms. In this work, we aim to disentangle the relative contributions of direct and indirect effects on pear yield. We treated pear trees with either chemical fertilizer or organic fertilizer with/without the plant-beneficial bacterium Bacillus velezensis SQR9. We then assessed, in detail, soil physicochemical and biological properties (metagenome sequencing) as well as pear yield. We then evaluated the relative importance of direct and indirect effects of soil amendments on pear yield. Both organic treatments increased plant yield by up to 20%, with the addition of bacteria tripling the increase driven by organic fertilizer alone. This increase could be linked to alterations in soil physicochemical properties, bacterial community function, and metabolism. Supplementation of organic fertilizer SQR9 increased rhizosphere microbiome richness and functional diversity. Fertilizer-sensitive microbes and functions responded as whole guilds. Pear yield was most positively associated with the Mitsuaria- and Actinoplanes-dominated ecological clusters and with gene clusters involved in ion transport and secondary metabolite biosynthesis. Together, these results suggested that bio-organic fertilizers mainly act indirectly on plant yield by creating soil chemical properties which promote a plant-beneficial microbiome. IMPORTANCE Bio-organic fertilization is a widely used, eco-friendly, sustainable approach to increasing plant productivity in the agriculture and fruit industries. However, it remains unclear whether the promotion of fruit productivity is related to specific changes in microbial inoculants, the resident microbiome, and/or the physicochemical properties of rhizosphere soils. We found that bio-organic fertilizers alter soil chemical properties, thus manipulating specific microbial taxa and functions within the rhizosphere microbiome of pear plants to promote yield. Our work unveils the ecological mechanisms which underlie the beneficial impacts of bio-organic fertilizers on yield promotion in fruit orchards, which may help in the design of more efficient biofertilizers to promote sustainable fruit production.}, } @article {pmid36453905, year = {2022}, author = {Han, S and Zhuang, J and Pan, Y and Wu, W and Ding, K}, title = {Different Characteristics in Gut Microbiome between Advanced Adenoma Patients and Colorectal Cancer Patients by Metagenomic Analysis.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0159322}, pmid = {36453905}, issn = {2165-0497}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms ; Intestines ; Bacteria/genetics ; Feces/microbiology ; Firmicutes ; *Adenoma/genetics/microbiology ; }, abstract = {The occurrence and development of colorectal cancer (CRC) and advanced adenoma (AA) are closely related to the gut microbiome, and AA has a high cancerization progression rate to CRC. Current studies have revealed that bacteriological analysis cannot identify CRC from AA. The objective was to explore microbial targets that could identify CRC and AA from a microecological perspective and to figure out the best way to identify CRC based on fecal microbes. The metagenomic sequencing data were used to describe the gut microbiome profile and analyze the differences between microbial abundance and microbial single nucleotide polymorphism (SNP) characteristics in AA and CRC patients. It was found that there were no significant differences in the diversity between the two groups. The abundance of bacteria (e.g., Firmicutes, Clostridia, and Blautia), fungi (Hypocreales), archaea (Methanosarcina, Methanoculleus, and Methanolacinia), and viruses (Alphacoronavirus, Sinsheimervirus, and Gammaretrovirus) differed between AA and CRC patients. Multiple machine-learning algorithms were used to establish prediction models, aiming to identify CRC and AA. The accuracy of the random forest (RF) model based on the gut microbiome was 86.54%. Nevertheless, the accuracy of SNP was 92.31% in identifying CRC from AA. In conclusion, using microbial SNP was the best method to identify CRC, it was superior to using the gut microbiome, and it could provide new targets for CRC screening. IMPORTANCE There are differences in characteristic microorganisms between AA and CRC. However, current studies have indicated that bacteriological analysis cannot identify CC from AA, and thus, we wondered if there were some other targets that could be used to identify CRC from AA in the gut microbiome. The differences of SNPs in the gut microbiota of intraindividuals were significantly smaller than those of interindividuals. In addition, compared with intestinal microbes, SNP was less affected by time with certain stability. It was discovered that microbial SNP was better than the gut microbiome for identifying CRC from AA. Therefore, screening characteristic microbial SNP could provide a new research direction for identifying CRC from AA.}, } @article {pmid36453887, year = {2022}, author = {Zhang, W and Han, N and Zhang, T and Qiang, Y and Peng, X and Li, X and Kan, B}, title = {The Spatial Features and Temporal Changes in the Gut Microbiota of a Healthy Chinese Population.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0131022}, pmid = {36453887}, issn = {2165-0497}, mesh = {Adult ; Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; East Asian People ; *Microbiota ; Feces/microbiology ; }, abstract = {In this study, we aimed to understand the characteristics of the gut microbial composition in a healthy Chinese population and to evaluate if they differed across different regions. In addition, we aimed to understand the changes in the gut microbial composition over time. We collected 239 fecal samples from healthy Chinese adults living in four regions and performed a 1-year time cohort study in a small population in Beijing. The Chinese gut microbiota share 34 core bacterial genera and 39 core bacterial species, which exist in all collected samples. Several disease-related microorganisms (DRMs), virulence factors, and antibiotic resistance genes were found in one or more healthy Chinese samples. Differences in gut microbiota were observed in samples from different regions, locations, individuals, and time points. Compared to other factors, time was associated with a lower degree of change in the gut microbiota. Our findings revealed spatial and temporal changes in the gut microbiota of healthy Chinese individuals. Compared to fecal microbiomes of 152 samples in the publicly released the Human Microbiome Project (HMP) project from the United States, samples in this study have higher variability in the fecal microbiome, with higher richness, Shannon diversity indices, and Pielou evenness indexes, at both the genus and species levels. The microbiota data obtained in this study will provide a detailed basis for further understanding the composition of the gut microbiota in the healthy Chinese population. IMPORTANCE China accounts for approximately 1/5th of the world's total population. Differences in environment, ethnicity, and living habits could impart unique features to the structure of the gut microbiota of Chinese individuals. In 2016, we started to investigate healthy Chinese people and their gut microbiomes. Phase I results for 16S rRNA amplicons have been released. However, owing to the limitations of 16S rRNA amplicon sequencing, the gut microbiome of a healthy Chinese population could not be examined thoroughly at the species level, and the detailed changes in the gut microbiota over time need to be investigated. To address these knowledge gaps, we started a phase II study and investigated the basis for variations in the gut microbiome composition in a healthy Chinese population at the species level using shotgun metagenomics technology. In the phase II study, we also conducted a time scale analysis of fecal samples from healthy Chinese subjects, as a pioneered study, which quantitatively clarified the changes in the gut microbiota at both the spatial and temporal levels and elucidated the distribution pattern of DRMs in healthy Chinese individuals.}, } @article {pmid36451083, year = {2022}, author = {Sun, J and Qiu, Z and Egan, R and Ho, H and Li, Y and Wang, Z}, title = {Persistent memory as an effective alternative to random access memory in metagenome assembly.}, journal = {BMC bioinformatics}, volume = {23}, number = {1}, pages = {513}, pmid = {36451083}, issn = {1471-2105}, support = {DE-AC02-05CH11231//Biological and Environmental Research/ ; }, mesh = {*Metagenome ; Metagenomics ; *Microbiota ; Software ; Computational Biology ; }, abstract = {BACKGROUND: The assembly of metagenomes decomposes members of complex microbe communities and allows the characterization of these genomes without laborious cultivation or single-cell metagenomics. Metagenome assembly is a process that is memory intensive and time consuming. Multi-terabyte sequences can become too large to be assembled on a single computer node, and there is no reliable method to predict the memory requirement due to data-specific memory consumption pattern. Currently, out-of-memory (OOM) is one of the most prevalent factors that causes metagenome assembly failures.

RESULTS: In this study, we explored the possibility of using Persistent Memory (PMem) as a less expensive substitute for dynamic random access memory (DRAM) to reduce OOM and increase the scalability of metagenome assemblers. We evaluated the execution time and memory usage of three popular metagenome assemblers (MetaSPAdes, MEGAHIT, and MetaHipMer2) in datasets up to one terabase. We found that PMem can enable metagenome assemblers on terabyte-sized datasets by partially or fully substituting DRAM. Depending on the configured DRAM/PMEM ratio, running metagenome assemblies with PMem can achieve a similar speed as DRAM, while in the worst case it showed a roughly two-fold slowdown. In addition, different assemblers displayed distinct memory/speed trade-offs in the same hardware/software environment.

CONCLUSIONS: We demonstrated that PMem is capable of expanding the capacity of DRAM to allow larger metagenome assembly with a potential tradeoff in speed. Because PMem can be used directly without any application-specific code modification, these findings are likely to be generalized to other memory-intensive bioinformatics applications.}, } @article {pmid36450914, year = {2022}, author = {Miller, JH and Simpson, C}, title = {When did mammoths go extinct?.}, journal = {Nature}, volume = {612}, number = {7938}, pages = {E1-E3}, pmid = {36450914}, issn = {1476-4687}, mesh = {Animals ; *Metagenomics ; *Mammoths/genetics ; Biota ; }, } @article {pmid36450879, year = {2023}, author = {Deepthi, M and Arvind, K and Saxena, R and Pulikkan, J and Sharma, VK and Grace, T}, title = {Exploring variation in the fecal microbial communities of Kasaragod Dwarf and Holstein crossbred cattle.}, journal = {Antonie van Leeuwenhoek}, volume = {116}, number = {1}, pages = {53-65}, pmid = {36450879}, issn = {1572-9699}, mesh = {Female ; Animals ; Cattle ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Feces ; *Gastrointestinal Microbiome/genetics ; Alcaligenes/genetics ; }, abstract = {The gut microbiota and its impact on health and nutrition in animals, including cattle has been of intense interest in recent times. Cattle, in particular indigenous varieties like Kasaragod Dwarf cow, have not received the due consideration given to other non-native cattle breeds, and the composition of their fecal microbiome is yet to be established. This study applied 16S rRNA high-throughput sequencing of fecal samples and compared the Kasaragod Dwarf with the highly prevalent Holstein crossbred cattle. Variation in their microbial composition was confirmed by marker gene-based taxonomic analysis. Principle Coordinate Analysis (PCoA) showed the distinct microbial architecture of the two cattle types. While the two cattle types possess unique signature taxa, in Kasaragod Dwarf cattle, many of the identified genera, including Anaerovibrio, Succinivibrio, Roseburia, Coprococcus, Paludibacter, Sutterella, Coprobacillus, and Ruminobacter, have previously been shown to be present in higher abundance in animals with higher feed efficiency. This is the first report of Kasaragod Dwarf cattle fecal microbiome profiling. Our findings highlight the predominance of specific taxa potentially associated with different fermentation products and feed efficiency phenotypes in Kasaragod Dwarf cattle compared to Holstein crossbred cattle.}, } @article {pmid36448813, year = {2022}, author = {Patin, NV and Goodwin, KD}, title = {Long-Read Sequencing Improves Recovery of Picoeukaryotic Genomes and Zooplankton Marker Genes from Marine Metagenomes.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0059522}, pmid = {36448813}, issn = {2379-5077}, mesh = {Animals ; *Metagenome/genetics ; Zooplankton/genetics ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Genome, Microbial ; }, abstract = {Long-read sequencing offers the potential to improve metagenome assemblies and provide more robust assessments of microbial community composition and function than short-read sequencing. We applied Pacific Biosciences (PacBio) CCS (circular consensus sequencing) HiFi shotgun sequencing to 14 marine water column samples and compared the results with those for short-read metagenomes from the corresponding environmental DNA samples. We found that long-read metagenomes varied widely in quality and biological information. The community compositions of the corresponding long- and short-read metagenomes were frequently dissimilar, suggesting higher stochasticity and/or bias associated with PacBio sequencing. Long reads provided few improvements to the assembly qualities, gene annotations, and prokaryotic metagenome-assembled genome (MAG) binning results. However, only long reads produced high-quality eukaryotic MAGs and contigs containing complete zooplankton marker gene sequences. These results suggest that high-quality long-read metagenomes can improve marine community composition analyses and provide important insight into eukaryotic phyto- and zooplankton genetics, but the benefits may be outweighed by the inconsistent data quality. IMPORTANCE Ocean microbes provide critical ecosystem services, but most remain uncultivated. Their communities can be studied through shotgun metagenomic sequencing and bioinformatic analyses, including binning draft microbial genomes. However, most sequencing to date has been done using short-read technology, which rarely yields genome sequences of key microbes like SAR11. Long-read sequencing can improve metagenome assemblies but is hampered by technological shortcomings and high costs. In this study, we compared long- and short-read sequencing of marine metagenomes. We found a wide range of long-read metagenome qualities and minimal improvements to microbiome analyses. However, long reads generated draft genomes of eukaryotic algal species and provided full-length marker gene sequences of zooplankton species, including krill and copepods. These results suggest that long-read sequencing can provide greater genetic insight into the wide diversity of eukaryotic phyto- and zooplankton that interact as part of and with the marine microbiome.}, } @article {pmid36448791, year = {2022}, author = {Ryu, SW and Kim, JS and Oh, BS and Choi, WJ and Yu, SY and Bak, JE and Park, SH and Kang, SW and Lee, J and Jung, WY and Lee, JS and Lee, JH}, title = {Gut Microbiota Eubacterium callanderi Exerts Anti-Colorectal Cancer Activity.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0253122}, pmid = {36448791}, issn = {2165-0497}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Eubacterium ; *Colorectal Neoplasms/therapy ; Bacteria ; }, abstract = {The gut microbiota (GM) is associated with colorectal cancer (CRC) development. However, studies demonstrating the role of GM in CRC are limited to metagenomic analyses. These studies lack direct evidence proving that the candidate strains are involved in CRC, and isolated probiotics for bacteriotherapy. Therefore, to identify novel GM with anti-CRC activity, we previously isolated gut bacteria from the feces of healthy individuals, screened the isolated GM's anti-CRC activity, and discovered that cell-free supernatants of GM isolates demonstrated antiproliferative activity against CRC cells. Here, our study identified one of them as Eubacterium callanderi and chose it for further study because the genus Eubacterium has been suggested to contribute to various aspects of gut health; however, the functions are unknown. First, we confirmed that E. callanderi cell-free supernatant (EcCFS) exerted antiproliferative activity-by inducing apoptosis and cell cycle arrest-that was dose-dependent and specific to cancer cell lines. Next, we discovered that EcCFS active molecules were heat stable and protease insensitive. High-performance liquid chromatography analysis revealed that EcCFS contained high butyrate concentrations possessing anticancer activity. Additionally, gas chromatography-mass spectrometry analysis of the aqueous phase of ethyl acetate-extracted EcCFS and an antiproliferation assay of the aqueous phase and 4-aminobutanoic acid (GABA) suggested that GABA is a possible anti-CRC agent. Finally, in the CT26 allograft mouse model, E. callanderi oral administration and EcCFS peri-tumoral injection inhibited tumor growth in vivo. Therefore, our study reveals that E. callanderi has an anti-CRC effect and suggests that it may be a potential candidate for developing probiotics to control CRC. IMPORTANCE The gut microbiota has been reported to be involved in colorectal cancer, as suggested by metagenomic analysis. However, metagenomic analysis has limitations, such as bias in the analysis and the absence of bacterial resources for follow-up studies. Therefore, we attempted to discover gut microorganisms that are related to colorectal cancer using the culturomics method. In this study, we discovered that Eubacterium callanderi possesses anti-colorectal cancer activity in vitro and in vivo, suggesting that E. callanderi could be used in bacteriotherapy for colorectal cancer treatment.}, } @article {pmid36448268, year = {2023}, author = {Lu, Y and Lv, Y and Zhang, Y and Liu, Q and Xu, X and Xiao, X and Xu, J}, title = {Metatranscriptomes reveal the diverse responses of Thaumarchaeota ecotypes to environmental variations in the northern slope of the South China Sea.}, journal = {Environmental microbiology}, volume = {25}, number = {2}, pages = {410-427}, doi = {10.1111/1462-2920.16289}, pmid = {36448268}, issn = {1462-2920}, mesh = {*Ecotype ; Phylogeny ; *Archaea/metabolism ; Water/metabolism ; Carbon/metabolism ; Nitrogen/metabolism ; Seawater ; }, abstract = {Thaumarchaeota are among the most abundant prokaryotes in the ocean, playing important roles in carbon and nitrogen cycling. Marine Thaumarchaeota ecotypes exhibit depth-related diversification and seasonal changes. However, transcriptomic activities concerning niche partitioning among thaumarchaeal ecotypes remain unclear. Here, we examined the variations in the distribution and transcriptomic activity of marine Thaumarchaeota ecotypes. Three primary ecotypes were identified: a Nitrosopumilus-like clade; a Nitrosopelagicus-like water column A (WCA) clade, thriving in epipelagic water; and a water column B (WCB) clade, dominant in deep water. Depth-related partitioning of the three ecotypes and the seasonal variability of the WCA and WCB ecotypes were observed. Nutrient concentrations, chlorophyll α and salinity were the primary environmental factors. The relative abundance of the WCA ecotype and its transcript abundance of amoA gene were positively correlated with chlorophyll α and salinity, while the WCB ecotype was positively correlated with nitrate and phosphate. Based on high-quality metagenome-assembled genomes, transcriptomic analysis revealed that the three ecotypes exhibited various co-occurring expression patterns of the elemental cycling genes in the nitrogen, carbon, phosphorus, and sulfur cycles. Our results provide transcriptomic evidence of the niche differentiation of marine Thaumarchaeota ecotypes, highlighting the diverse roles of ecotypes and WCA subclades in biogeochemical cycles.}, } @article {pmid36445553, year = {2022}, author = {Bora, SS and Naorem, RS and Hazarika, DJ and Dasgupta, A and Churaman, A and Gogoi, M and Barooah, M}, title = {Agricultural Land Use Influences Bacteriophage Community Diversity, Richness, and Heterogeneity.}, journal = {Current microbiology}, volume = {80}, number = {1}, pages = {10}, pmid = {36445553}, issn = {1432-0991}, mesh = {*Bacteriophages/genetics ; Agriculture ; Soil ; Biodiversity ; Tea ; }, abstract = {The last two decades have witnessed a large-scale conversion of crop cultivation areas into small and mid-sized tea plantations in Assam, India. Agricultural land-use pattern positively or negatively influences native hydrology and above- and belowground biodiversity. Very little is known about the effect of agricultural land-use patterns on the soil virus (especially, bacteriophage) community structure and function. This metagenomic-based study evaluated the rhizosphere viral community structure of three interlinked cultivation areas, viz., mixed cropping area (coded as CP1), tea-seed orchard (CP2), and monocropping tea cultivation (CP3). The bacteriophages belonged to four major classes with the dominance of Malgrandaviricetes (CP1: 79.37%; CP2: 64.62%; CP3: 4.85%) followed by Caudoviricetes (CP1: 20.49%; CP2: 35.22%; CP3: 90.29%), Faserviricetes (CP1: 0.03%; CP2: 0.08%; CP3: 3.88%), and Tectiliviricetes (CP1: 0.12%; CP2: 0.07%; CP3: 0.97%). Microviruses dominated the phage population in both CP1 and CP2, representing 79.35% and 64.59% of total bacteriophage abundance. Both CP1 and CP2 had higher bacteriophage richness (species richness, R in CP1: 65; R in CP2: 66) and lower evenness (Pielou's evenness index, J in CP1: 0.531; J in CP2: 0.579) compared to the CP3 (R: 30; J: 0.902). Principal component analysis of edaphic soil factors and bacteriophage community structure showed a reverse-proportional correlation between the levels of Al saturation, and exchangeable Al[3+] ions with that of soil pH, and bacteriophage abundance. Our study indicates that monocropping tea cultivation soil bears less viral richness, abundance, and heterogeneity.}, } @article {pmid36445165, year = {2022}, author = {Jaiswal, S and Aneja, B and Jagannadham, J and Pandey, B and Chhokar, RS and Gill, SC and Ahlawat, OP and Kumar, A and Angadi, UB and Rai, A and Tiwari, R and Iquebal, MA and Kumar, D}, title = {Unveiling the Wheat Microbiome under Varied Agricultural Field Conditions.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0263322}, pmid = {36445165}, issn = {2165-0497}, mesh = {*Triticum/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Soil/chemistry ; Crops, Agricultural/microbiology ; Bacteria/genetics ; Soil Microbiology ; }, abstract = {Wheat being the important staple food crop plays a significant role in nutritional security. A wide variety of microbial communities beneficial to plants and contributing to plant health and production are found in the rhizosphere. The wheat microbiome encompasses an extensive variety of microbial species playing a key role in sustaining the physiology of the crop, nutrient uptake, and biotic/abiotic stress resilience. This report presents wheat microbiome analysis under six different farm practices, namely, organic (Org), timely sown (TS), wheat after pulse crop (WAPC), temperature-controlled phenotyping facility (TCPF), maize-wheat cropping system (MW), and residue burnt field (Bur), using 16S rRNA sequencing methodology. The soil samples collected from either side of the wheat row were mixed to get a final sample set for DNA extraction under each condition. After the data preprocessing, microbial community analysis was performed, followed by functional analysis and annotation. An abundance of the phylum Proteobacteria was observed, followed by Acidobacteria, Actinobacteria, and Gemmatimonadetes in the majority of the samples, while relative abundance was found to vary at the genus level. Analysis against the Carbohydrate-Active Enzymes (CAZy) database showed a high number of glycoside hydrolase genes in the TS, TCPF, and WAPC samples, while the Org, MW, and Bur samples predominantly had glycosyltransferase genes and carbohydrate esterase genes were in the lowest numbers. Also, the Org and TCPF samples showed lower diversity, while rare and abundant species ranged from 12 to 25% and 20 to 32% of the total bacterial species in all the sets, respectively. These variations indicate that the different cropping sequence had a significant impact on soil microbial diversity and community composition, which characterizes its economic and environmental value as a sustainable agricultural approach to maintaining food security and ecosystem health. IMPORTANCE This investigation examined the wheat microbiome under six different agricultural field conditions to understand the role of cropping pattern on soil microbial diversity. This study also elaborated the community composition, which has importance in economic (role of beneficial community leading to higher production) and environmental (role of microbial diversity/community in safeguarding the soil health, etc.) arenas. This could lead to a sustainable farming approach for food security and improved ecosystem health. Also, the majority of the microbes are unculturable; hence, technology-based microcultivation will be a potential approach for harnessing other cultured microorganisms, leading to unique species for commercial production. The outcome of this research-accelerated work can provide an idea to the scientists/breeders/agronomists/pathologists under the mentioned field conditions regarding their influence over their crops.}, } @article {pmid36445161, year = {2022}, author = {Sylvain, FÉ and Leroux, N and Normandeau, É and Holland, A and Bouslama, S and Mercier, PL and Luis Val, A and Derome, N}, title = {Genomic and Environmental Factors Shape the Active Gill Bacterial Community of an Amazonian Teleost Holobiont.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0206422}, pmid = {36445161}, issn = {2165-0497}, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Gills/chemistry/microbiology ; Fishes/genetics/microbiology ; *Microbiota/physiology ; Water ; Genomics ; Bacteria/genetics ; }, abstract = {Fish bacterial communities provide functions critical for their host's survival in contrasting environments. These communities are sensitive to environmental-specific factors (i.e., physicochemical parameters, bacterioplankton), and host-specific factors (i.e., host genetic background). The relative contribution of these factors shaping Amazonian fish bacterial communities is largely unknown. Here, we investigated this topic by analyzing the gill bacterial communities of 240 wild flag cichlids (Mesonauta festivus) from 4 different populations (genetic clusters) distributed across 12 sites in 2 contrasting water types (ion-poor/acidic black water and ion-rich/circumneutral white water). Transcriptionally active gill bacterial communities were characterized by a 16S rRNA metabarcoding approach carried on RNA extractions. They were analyzed using comprehensive data sets from the hosts genetic background (Genotyping-By-Sequencing), the bacterioplankton (16S rRNA) and a set of 34 environmental parameters. Results show that the taxonomic structure of 16S rRNA gene transcripts libraries were significantly different between the 4 genetic clusters and also between the 2 water types. However, results suggest that the contribution of the host's genetic background was relatively weak in comparison to the environment-related factors in structuring the relative abundance of different active gill bacteria species. This finding was also confirmed by a mixed-effects modeling analysis, which indicated that the dissimilarity between the taxonomic structure of bacterioplanktonic communities possessed the best explicative power regarding the dissimilarity between gill bacterial communities' structure, while pairwise fixation indexes (FST) from the hosts' genetic data only had a weak explicative power. We discuss these results in terms of bacterial community assembly processes and flag cichlid fish ecology. IMPORTANCE Host-associated microbial communities respond to factors specific to the host physiology, genetic backgrounds, and life history. However, these communities also show different degrees of sensitivity to environment-dependent factors, such as abiotic physico-chemical parameters and ecological interactions. The relative importance of host- versus environment-associated factors in shaping teleost bacterial communities is still understudied and is paramount for their conservation and aquaculture. Here, we studied the relative importance of host- and environment-associated factors structuring teleost bacterial communities using gill samples from a wild Amazonian teleost model (Mesonauta festivus) sampled in contrasting habitats along a 1500 km section of the Amazonian basin, thus ensuring high genetic diversity. Results showed that the contribution of the host's genetic background was weak compared to environment-related bacterioplanktonic communities in shaping gill bacterial assemblages, thereby suggesting that our understanding of teleost microbiome assembly could benefit from further studies focused on the ecological interplay between host-associated and free-living communities.}, } @article {pmid36445112, year = {2022}, author = {Sánchez-Navarro, R and Nuhamunada, M and Mohite, OS and Wasmund, K and Albertsen, M and Gram, L and Nielsen, PH and Weber, T and Singleton, CM}, title = {Long-Read Metagenome-Assembled Genomes Improve Identification of Novel Complete Biosynthetic Gene Clusters in a Complex Microbial Activated Sludge Ecosystem.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0063222}, pmid = {36445112}, issn = {2379-5077}, mesh = {*Metagenome/genetics ; Sewage ; Multigene Family/genetics ; *Microbiota/genetics ; Genome, Bacterial/genetics ; }, abstract = {Microorganisms produce a wide variety of secondary/specialized metabolites (SMs), the majority of which are yet to be discovered. These natural products play multiple roles in microbiomes and are important for microbial competition, communication, and success in the environment. SMs have been our major source of antibiotics and are used in a range of biotechnological applications. In silico mining for biosynthetic gene clusters (BGCs) encoding the production of SMs is commonly used to assess the genetic potential of organisms. However, as BGCs span tens to over 200 kb, identifying complete BGCs requires genome data that has minimal assembly gaps within the BGCs, a prerequisite that was previously only met by individually sequenced genomes. Here, we assess the performance of the currently available genome mining platform antiSMASH on 1,080 high-quality metagenome-assembled bacterial genomes (HQ MAGs) previously produced from wastewater treatment plants (WWTPs) using a combination of long-read (Oxford Nanopore) and short-read (Illumina) sequencing technologies. More than 4,200 different BGCs were identified, with 88% of these being complete. Sequence similarity clustering of the BGCs implies that the majority of this biosynthetic potential likely encodes novel compounds, and few BGCs are shared between genera. We identify BGCs in abundant and functionally relevant genera in WWTPs, suggesting a role of secondary metabolism in this ecosystem. We find that the assembly of HQ MAGs using long-read sequencing is vital to explore the genetic potential for SM production among the uncultured members of microbial communities. IMPORTANCE Cataloguing secondary metabolite (SM) potential using genome mining of metagenomic data has become the method of choice in bioprospecting for novel compounds. However, accurate biosynthetic gene cluster (BGC) detection requires unfragmented genomic assemblies, which have been technically difficult to obtain from metagenomes until very recently with new long-read technologies. Here, we determined the biosynthetic potential of activated sludge (AS), the microbial community used in resource recovery and wastewater treatment, by mining high-quality metagenome-assembled genomes generated from long-read data. We found over 4,000 BGCs, including BGCs in abundant process-critical bacteria, with no similarity to the BGCs of characterized products. We show how long-read MAGs are required to confidently assemble complete BGCs, and we determined that the AS BGCs from different studies have very little overlap, suggesting that AS is a rich source of biosynthetic potential and new bioactive compounds.}, } @article {pmid36443458, year = {2022}, author = {Shaffer, JP and Nothias, LF and Thompson, LR and Sanders, JG and Salido, RA and Couvillion, SP and Brejnrod, AD and Lejzerowicz, F and Haiminen, N and Huang, S and Lutz, HL and Zhu, Q and Martino, C and Morton, JT and Karthikeyan, S and Nothias-Esposito, M and Dührkop, K and Böcker, S and Kim, HW and Aksenov, AA and Bittremieux, W and Minich, JJ and Marotz, C and Bryant, MM and Sanders, K and Schwartz, T and Humphrey, G and Vásquez-Baeza, Y and Tripathi, A and Parida, L and Carrieri, AP and Beck, KL and Das, P and González, A and McDonald, D and Ladau, J and Karst, SM and Albertsen, M and Ackermann, G and DeReus, J and Thomas, T and Petras, D and Shade, A and Stegen, J and Song, SJ and Metz, TO and Swafford, AD and Dorrestein, PC and Jansson, JK and Gilbert, JA and Knight, R and , }, title = {Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity.}, journal = {Nature microbiology}, volume = {7}, number = {12}, pages = {2128-2150}, pmid = {36443458}, issn = {2058-5276}, support = {R01 DK102932/DK/NIDDK NIH HHS/United States ; R01 GM107550/GM/NIGMS NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; U01 AI124316/AI/NIAID NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; R01 HL134887/HL/NHLBI NIH HHS/United States ; RF1 AG058942/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; *Microbiota/genetics ; Metagenome ; Metagenomics ; Earth, Planet ; Soil ; }, abstract = {Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth's environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.}, } @article {pmid36442206, year = {2022}, author = {Zhang, K and Paul, KC and Jacobs, JP and Chou, HL and Duarte Folle, A and Del Rosario, I and Yu, Y and Bronstein, JM and Keener, AM and Ritz, B}, title = {Parkinson's Disease and the Gut Microbiome in Rural California.}, journal = {Journal of Parkinson's disease}, volume = {12}, number = {8}, pages = {2441-2452}, pmid = {36442206}, issn = {1877-718X}, support = {P30 ES007048/ES/NIEHS NIH HHS/United States ; R01 ES010544/ES/NIEHS NIH HHS/United States ; K01 AG072044/AG/NIA NIH HHS/United States ; P50 NS038367/NS/NINDS NIH HHS/United States ; P01 ES016732/ES/NIEHS NIH HHS/United States ; U54 ES012078/ES/NIEHS NIH HHS/United States ; R01 ES031106/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Parkinson Disease ; *Gastrointestinal Microbiome/genetics ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; California ; }, abstract = {BACKGROUND: Increasing evidence connects the gut microbiome to Parkinson's disease (PD) etiology, but little is known about microbial contributions to PD progression and its clinical features.

OBJECTIVE: We aim to explore the association between the gut microbiome with PD, and the microbial association with PD-specific clinical features.

METHODS: In a community-based case-control study of 96 PD patients and 74 controls, microbiome data were obtained from 16S rRNA gene sequencing of fecal samples, and analyzed for microbial diversity, taxa abundance, and predicted functional pathways that differed in PD patients and controls, and their association with PD-specific features (disease duration, motor subtypes, L-DOPA daily dose, and motor function).

RESULTS: PD patients' gut microbiome showed lower species diversity (p = 0.04) and were compositionally different (p = 0.002) compared to controls but had a higher abundance of three phyla (Proteobacteria, Verrucomicrobiota, Actinobacteria) and five genera (Akkermansia, Enterococcus, Hungatella, and two Ruminococcaceae) controlling for sex, race, age, and sequencing platform. Also, 35 Metacyc pathways were predicted to be differentially expressed in PD patients including biosynthesis, compound degradation/utilization/assimilation, generation of metabolites and energy, and glycan pathways. Additionally, the postural instability gait dysfunction subtype was associated with three phyla and the NAD biosynthesis pathway. PD duration was associated with the Synergistota phylum, six genera, and the aromatic compound degradation pathways. Two genera were associated with motor function.

CONCLUSION: PD patients differed from controls in gut microbiome composition and its predicted metagenome. Clinical features were also associated with bacterial taxa and altered metabolic pathways of interest for PD progression.}, } @article {pmid36442156, year = {2022}, author = {van Dongen, KCW and Ioannou, A and Wesseling, S and Beekmann, K and Belzer, C}, title = {Differences in gut microbial fructoselysine degradation activity between breast-fed and formula-fed infants.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {1}, pages = {}, pmid = {36442156}, issn = {1574-6941}, mesh = {Adult ; Female ; Humans ; Infant ; *Gastrointestinal Microbiome ; Breast Feeding ; Infant Formula ; Milk, Human/microbiology ; Feces/microbiology ; }, abstract = {The Amadori product fructoselysine is formed upon heating of food products and is abundantly present in infant formula while being almost absent in breast milk. The human gut microbiota can degrade fructoselysine for which interindividual differences have been described for adults. The aim of this study is to compare functional differences in microbial fructoselysine degradation between breast-fed and formula-fed infants, in view of their different diets and resulting different fructoselysine exposures. First, a publicly available metagenomic dataset with metagenome-assembled genomes (MAGs) from infant fecal samples was analyzed and showed that query genes involved in fructoselysine degradation (frlD/yhfQ) were abundantly present in multiple bacterial taxa in the fecal samples, with a higher prevalence in the formula-fed infants. Next, fecal samples collected from exclusively breast-fed and formula-fed infants were anaerobically incubated with fructoselysine. Both groups degraded fructoselysine, however the fructoselysine degradation activity was significantly higher by fecal samples from formula-fed infants. Overall, this study provides evidence that infant formula feeding, leading to increased dietary fructoselysine exposure, seems to result in an increased fructoselysine degradation activity in the gut microbiota of infants. This indicates that the infant gut microbiota adapts towards dietary fructoselysine exposure.}, } @article {pmid36439214, year = {2022}, author = {Qian, B and Zhang, K and Li, Y and Sun, K}, title = {Update on gut microbiota in cardiovascular diseases.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1059349}, pmid = {36439214}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Cardiovascular Diseases ; *Hypertension ; Bile Acids and Salts ; *Heart Failure ; }, abstract = {In recent years, due to the development and widespread utilization of metagenomic sequencing and metabolomics, the relationship between gut microbiota and human cardiovascular diseases (CVDs) has received extensive attention. A growing number of studies have shown a strong relationship between gut microbiota and CVDs, such as coronary atherosclerosis, hypertension (HTN) and heart failure (HF). It has also been revealed that intestinal flora-related metabolites, such as trimethylamine-N-oxide (TMAO), short-chain fatty acids (SCFA) and bile acids (BAs), are also related to the development, prevention, treatment and prognosis of CVDs. In this review, we presented and summarized the recent findings on the relationship between gut microbiota and CVDs, and concluded several currently known gut microbiota-related metabolites and the occurrence and development of CVDs.}, } @article {pmid36437083, year = {2022}, author = {Zhang, X and Zhou, JJ and Zhou, M and Luo, XZ and Yan, XJ and Liu, YD and Li, W}, title = {[Metagenomic and Metatranscriptomic Analysis of Nitrogen Removal Functional Microbial Community of Petrochemical Wastewater Biological Treatment Systems].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {43}, number = {11}, pages = {5115-5122}, doi = {10.13227/j.hjkx.202112283}, pmid = {36437083}, issn = {0250-3301}, mesh = {Humans ; *Wastewater ; Nitrogen ; Ammonia ; Denitrification ; China ; *Microbiota/genetics ; Sewage ; }, abstract = {Petrochemicals are one of the pillar industries of China. Despite this, the treatment of petrochemical wastewater has long been seen as a massive challenge in the field of water pollution control, hindering the high-quality and sustainable development of the petrochemical industry. The majority of petrochemical enterprises and zones are located near rivers or seas, so their wastewater discharges can easily cause watershed or regional water ecological risks. Specifically, nitrogen pollution in petrochemical wastewater poses a significant threat to water ecological safety and human health. Sludge samples were collected from a petrochemical wastewater A/O nitrogen removal process line in a chemical industry zone in Shanghai. Metagenomic and metatranscriptomic methods were used to analyze the community structure of microorganisms, the functional characteristics of nitrogen removal bacteria, and the key nitrogen metabolism pathways in different sludges during the period when effluent water quality was stable and fluctuating. During the study, it was found that the nitrite and nitrate removal was relatively stable in this process, but ammonia oxidation fluctuated easily. In the study of microbial communities, it was found to be a nitrification-denitrification pathway that primarily removed nitrogen from the A/O process, and no genes related to ANAMMOX were detected. Approximately 90% of the functional genes responsible for removing nitrogen were responsible for denitrification, whereas only 0.17% of them were involved in the conversion of ammonia nitrogen in the nitrification process. Moreover, the abundance of ammonia-oxidizing bacteria in the process was extremely low, and the main genus was Nitrosomonas. It is likely that this is the main cause of fluctuations in ammonia nitrogen concentration in effluent due to water quality shocks in the process line.}, } @article {pmid36436705, year = {2023}, author = {Lamoureux, C and Rézig, S and Le Bars, H and Le Divenah, F and Tandé, D and Vélo-Suarez, L and Badell, E and Brisse, S and Héry-Arnaud, G and Beauruelle, C}, title = {Corynebacterium ulcerans as filamentous branching rods.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {29}, number = {5}, pages = {600-601}, doi = {10.1016/j.cmi.2022.11.016}, pmid = {36436705}, issn = {1469-0691}, mesh = {Humans ; Corynebacterium ; *Corynebacterium Infections/microbiology ; *Diphtheria/microbiology ; Diphtheria Toxin ; }, } @article {pmid36436665, year = {2023}, author = {Chen, X and Wang, J and Pan, C and Feng, L and Chen, S and Xie, S}, title = {Metagenomic insights into the influence of thallium spill on sediment microbial community.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {317}, number = {}, pages = {120660}, doi = {10.1016/j.envpol.2022.120660}, pmid = {36436665}, issn = {1873-6424}, mesh = {Thallium/toxicity ; Genes, Bacterial ; Bacteria/genetics ; *Metals, Heavy/analysis ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; }, abstract = {Thallium (Tl) is an extremely toxic metal. The release of Tl into the natural environment can pose a potential threat to organisms. So far, information about the impact of Tl on indigenous microorganisms is still very limited. In addition, there has been no report on how sudden Tl spill influences the structure and function of the microbial community. Therefore, this study explored the response of river sediment microbiome to a Tl spill. Residual T1 in the sediment significantly decreased bacterial community diversity. The increase in the abundance of Bacteroidetes in all Tl- impacted sediments suggested the advantage of Bacteroidetes to resist Tl pressure. Under T1 stress, microbial genes related to carbon fixation and gene cysH participating in assimilatory sulfate reduction were down-regulated, while genes related to nitrogen cycling were up-regulated. After T1 spill, increase in both metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) was observed in Tl-impacted sediments. Moreover, the abundance of MRGs and ARGs was significantly correlated with sediment Tl concentration, implying the positive effect of Tl contamination on the proliferation of these resistance genes. Procrustes analysis suggested a significant congruence between profiles of MRGs and bacterial communities. Through LEfSe and co-occurrence network analysis, Trichococcus, Polaromonas, and Arenimonas were identified to be tolerant and resistant to Tl pollution. The colocalization analysis of contigs indicated the co-effects of selection and transfer for MRGs/ARGs were important reasons for the increase in the microbial resistance in Tl-impacted sediments. This study added new insights into the effect of Tl spill on microbial community and highlighted the role of heavy metal spill in the increase of both heavy metal and antibiotic resistance genes.}, } @article {pmid36434943, year = {2023}, author = {He, X and Li, Z and Li, X and Zhao, H and Hu, Y and Han, W and Wang, C and Yin, C and Chen, Y}, title = {The fecal microbiota of gravidas with fetal growth restriction newborns characterized by metagenomic sequencing.}, journal = {Current research in translational medicine}, volume = {71}, number = {1}, pages = {103354}, doi = {10.1016/j.retram.2022.103354}, pmid = {36434943}, issn = {2452-3186}, mesh = {Pregnancy ; Female ; Infant, Newborn ; Humans ; Fetal Growth Retardation/genetics/pathology ; Placenta ; Case-Control Studies ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; }, abstract = {BACKGROUND: Fetal growth restriction (FGR) is a complex obstetric complication with various causes and of great harm. However, the specific pathogenesis of FGR is unclear, which limits its effective treatment. Gut microbiota dysbiosis was found to be important in pathogenesis of various diseases. However, its role in FGR development remains unclear and needs to be clarified.

METHODS: In our case-control study, we recruited eight FGR and eight control female participants and collected their fecal samples in third trimester before delivery. We performed metagenomic sequencing and bioinformatic analysis to compare the gut microbiota composition and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways between the two groups.

RESULTS: Our results showed that totally 20 gut microbes were significantly different between two groups (p<0•05), and the correlation analysis found that g__Roseomonas and g__unclassified_f__Propionibacteriaceae were significantly positive correlated with both maternal body mass index (BMI) before delivery, placental weight, and neonatal birth weight (BW) percentile (all p<0•05), while g__Marinisporobacter and g__Sphingomonas were significantly negative correlated with both neonatal BMI and neonatal BW percentile (all p<0•05). Through KEGG pathway analysis, we found that the abundance of the Nitrogen metabolism pathway decreased significantly (p<0•05) whereas the abundance of the Amoebiasis pathway increased significantly in the FGR group (p<0•05).

CONCLUSION: In this study, we demonstrated that the occurrence of FGR is associated with the change of gut microbiota of pregnant women.}, } @article {pmid36434287, year = {2022}, author = {Debnath, T and Deb, S and Das, SK}, title = {Influence of Geochemistry in the Tropical Hot Springs on Microbial Community Structure and Function.}, journal = {Current microbiology}, volume = {80}, number = {1}, pages = {4}, pmid = {36434287}, issn = {1432-0991}, support = {D.O.No. BT/BI/04/058/2002 VOL-II//Department of Biotechnology/ ; }, mesh = {*Hot Springs/microbiology ; Phylogeny ; *Microbiota/genetics ; Archaea/genetics ; Bacteria/genetics ; *Chloroflexi ; }, abstract = {Thermophiles inhabiting high temperatures are considered primitive microorganisms on early Earth. In this regard, several works have demonstrated microbial community composition in geothermal environments. Despite that, studies on hot springs located in the Indian subcontinent viz., Surajkund in the district Hazaribag, Jharkhand; Bakreshwar in the district Birbhum, West Bengal; Tantloi in the district Dumka, and Sidpur in the district Pakur, Jharkhand are scanty. Nonetheless, the metagenomic analysis of these hot springs showed significant differences in the predominant phyla corresponding to geochemical properties. The Chloroflexi, Proteobacteria, Actinobacteria, Deinococcus-Thermus, and Firmicutes were dominant phyla in all the samples. In contrast, Meiothermus was more in comparatively low-temperature hot springs. In addition, archaeal phyla, Euryarchaeota, Candidatus Bathyarchaeota, and Crenarchaeota were predominant in all samples. The canonical correspondence analysis (CCA) showed the abundance of Deinococcus, Thermus, Pyrobaculum, Kocuria, and Geodermatophilus positively correlated with the aqueous concentration of sulfate, fluoride, and argon in relatively high-temperature (≥ 72 °C) hot springs. However, at a lower temperature (≤ 63 °C), Thermodesulfovibrio, Caldilinea, Chloroflexus, Meiothermus, and Tepidimonas are positively correlated with the concentration of zinc, iron, and dissolved oxygen. Further, hierarchical clustering exhibits variations in its functional attributes depending on the temperature gradients. Metagenome analysis predicted carbon, methane, sulfur, and nitrogen metabolism genes, indicating a wide range of bacteria and archaea habitation in these hot springs. In addition, identified several genes encode polyketide biosynthesis pathways. The present study described the microbial community composition and function in the tropical hot springs and their relationship with the environmental variables.}, } @article {pmid36432504, year = {2022}, author = {Benítez-Guerrero, T and Vélez-Ixta, JM and Juárez-Castelán, CJ and Corona-Cervantes, K and Piña-Escobedo, A and Martínez-Corona, H and De Sales-Millán, A and Cruz-Narváez, Y and Gómez-Cruz, CY and Ramírez-Lozada, T and Acosta-Altamirano, G and Sierra-Martínez, M and Zárate-Segura, PB and García-Mena, J}, title = {Gut Microbiota Associated with Gestational Health Conditions in a Sample of Mexican Women.}, journal = {Nutrients}, volume = {14}, number = {22}, pages = {}, pmid = {36432504}, issn = {2072-6643}, support = {SECTEI/249/2019-CM-SECTEI/109/2020-CM-SECTEI/124/2021, Convocatoria 2019, Proyectos Científicos, Tecnológicos y/o de Innovación para la atención a problemas específicos de la Ciudad de México relacionados con la investigación y atención de enfermedades cr//Secretaría de Ciencia, Tecnología e Innovación de la CDMX/ ; CONACyT-163235 INFR-2011-01//Consejo Nacional de Ciencia y Tecnología/ ; CONACyT-302670-2019-Apoyos para Adquisición y Mantenimiento de Infraestructura en Insti-tuciones y laboratorios de Investigación Especializada.//Consejo Nacional de Ciencia y Tecnología/ ; }, mesh = {Pregnancy ; Humans ; Female ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/analysis ; *Diabetes, Gestational ; Dysbiosis/microbiology ; Feces/microbiology ; Fatty Acids, Volatile/metabolism ; Bacteria ; *Pre-Eclampsia ; }, abstract = {Gestational diabetes (GD), pre-gestational diabetes (PD), and pre-eclampsia (PE) are morbidities affecting gestational health which have been associated with dysbiosis of the mother's gut microbiota. This study aimed to assess the extent of change in the gut microbiota diversity, short-chain fatty acids (SCFA) production, and fecal metabolites profile in a sample of Mexican women affected by these disorders. Fecal samples were collected from women with GD, PD, or PE in the third trimester of pregnancy, along with clinical and biochemical data. Gut microbiota was characterized by high-throughput DNA sequencing of V3-16S rRNA gene libraries; SCFA and metabolites were measured by High-Pressure Liquid Chromatography (HPLC) and (Fourier Transform Ion Cyclotron Mass Spectrometry (FT-ICR MS), respectively, in extracts prepared from feces. Although the results for fecal microbiota did not show statistically significant differences in alfa diversity for GD, PD, and PE concerning controls, there was a difference in beta diversity for GD versus CO, and a high abundance of Proteobacteria, followed by Firmicutes and Bacteroidota among gestational health conditions. DESeq2 analysis revealed bacterial genera associated with each health condition; the Spearman's correlation analyses showed selected anthropometric, biochemical, dietary, and SCFA metadata associated with specific bacterial abundances, and although the HPLC did not show relevant differences in SCFA content among the studied groups, FT-ICR MS disclosed the presence of interesting metabolites of complex phenolic, valeric, arachidic, and caprylic acid nature. The major conclusion of our work is that GD, PD, and PE are associated with fecal bacterial microbiota profiles, with distinct predictive metagenomes.}, } @article {pmid36430609, year = {2022}, author = {Tilocca, B and Soggiu, A and Iavarone, F and Greco, V and Putignani, L and Ristori, MV and Macari, G and Spina, AA and Morittu, VM and Ceniti, C and Piras, C and Bonizzi, L and Britti, D and Urbani, A and Figeys, D and Roncada, P}, title = {The Functional Characteristics of Goat Cheese Microbiota from a One-Health Perspective.}, journal = {International journal of molecular sciences}, volume = {23}, number = {22}, pages = {}, pmid = {36430609}, issn = {1422-0067}, support = {AIM1879147 - 2 (Bruno Tilocca)//Attraction International Mobility-AIM, PON-FSE/ ; }, mesh = {Animals ; *Cheese/analysis ; Goats/genetics ; RNA, Ribosomal, 16S/genetics ; *One Health ; Bacteria/genetics ; *Microbiota/genetics ; }, abstract = {Goat cheese is an important element of the Mediterranean diet, appreciated for its health-promoting features and unique taste. A pivotal role in the development of these characteristics is attributed to the microbiota and its continuous remodeling over space and time. Nevertheless, no thorough study of the cheese-associated microbiota using two metaomics approaches has previously been conducted. Here, we employed 16S rRNA gene sequencing and metaproteomics to explore the microbiota of a typical raw goat milk cheese at various ripening timepoints and depths of the cheese wheel. The 16S rRNA gene-sequencing and metaproteomics results described a stable microbiota ecology across the selected ripening timepoints, providing evidence for the microbiologically driven fermentation of goat milk products. The important features of the microbiota harbored on the surface and in the core of the cheese mass were highlighted in both compositional and functional terms. We observed the rind microbiota struggling to maintain the biosafety of the cheese through competition mechanisms and/or by preventing the colonization of the cheese by pathobionts of animal or environmental origin. The core microbiota was focused on other biochemical processes, supporting its role in the development of both the health benefits and the pleasant gustatory nuances of goat cheese.}, } @article {pmid36430244, year = {2022}, author = {Assalin, HB and De Almeida, KCG and Guadagnini, D and Santos, A and Teixeira, CJ and Bordin, S and Rocha, GZ and Saad, MJA}, title = {Proton Pump Inhibitor Pantoprazole Modulates Intestinal Microbiota and Induces TLR4 Signaling and Fibrosis in Mouse Liver.}, journal = {International journal of molecular sciences}, volume = {23}, number = {22}, pages = {}, pmid = {36430244}, issn = {1422-0067}, support = {2014/50907-5; 2019/03196-0; 2020/06397-3//São Paulo Research Foundation/ ; INCT Obesidade e Diabetes CNPq (465693/2014-8)//National Council for Scientific and Technological Development/ ; }, mesh = {Mice ; Humans ; Animals ; Toll-Like Receptor 4/therapeutic use ; *Gastrointestinal Microbiome ; Pantoprazole/pharmacology ; Proton Pump Inhibitors/pharmacology/therapeutic use ; Lipopolysaccharides/pharmacology ; Mice, Inbred C57BL ; *Non-alcoholic Fatty Liver Disease/drug therapy/etiology ; Fibrosis ; }, abstract = {Proton pump inhibitors (PPIs) are one of the most prescribed drugs around the world. PPIs induce microbiota modulation such as obesity both in humans and in animal models. However, since PPIs can induce microbiota modulation despite the absence of a high-fat diet or weight gain, it is an interesting model to correlate microbiota modulation with the establishment of non-alcoholic fatty liver disease (NAFLD). We investigated the effect of pantoprazole treatment on TLR4 signaling and liver histology in C57BL/6J mice for 60 days, trying to correlate microbiota modulation with some aspects of liver injury. We performed glucose (GTT) and insulin (ITT) tolerance tests, serum lipopolysaccharide (LPS) dosage, liver histology, liver and intestine extraction for Western blot and qPCR. Fecal microbiota were investigated via metagenomics. Chronic treatment with pantoprazole induced microbiota modulation and impaired ileum barrier integrity, without an association with insulin resistance. Furthermore, increased circulating LPS and increased Toll-like receptor 4 (TLR4) and TGFβ downstream signaling may have an important role in the development of the observed liver microvesicular steatosis and fibrosis. Finally, this model of PPI-induced changes in microbiota might be useful to investigate liver microvesicular steatosis and fibrosis.}, } @article {pmid36430229, year = {2022}, author = {Mathebela, P and Damane, BP and Mulaudzi, TV and Mkhize-Khwitshana, ZL and Gaudji, GR and Dlamini, Z}, title = {Influence of the Microbiome Metagenomics and Epigenomics on Gastric Cancer.}, journal = {International journal of molecular sciences}, volume = {23}, number = {22}, pages = {}, pmid = {36430229}, issn = {1422-0067}, support = {23108//Department of Surgery, University of Pretoria, the South African Medical Research Council (SAMRC)/ ; 138139//the National Research Foundation (NRF)/ ; }, mesh = {Humans ; Metagenomics ; Dysbiosis/microbiology ; *Stomach Neoplasms/genetics/microbiology ; Epigenomics ; Neoplasm Recurrence, Local ; *Microbiota/genetics ; *Helicobacter pylori/genetics ; Carcinogenesis/pathology ; }, abstract = {Gastric cancer (GC) is one of the major causes of cancer deaths worldwide. The disease is seldomly detected early and this limits treatment options. Because of its heterogeneous and complex nature, the disease remains poorly understood. The literature supports the contribution of the gut microbiome in the carcinogenesis and chemoresistance of GC. Drug resistance is the major challenge in GC therapy, occurring as a result of rewired metabolism. Metabolic rewiring stems from recurring genetic and epigenetic factors affecting cell development. The gut microbiome consists of pathogens such as H. pylori, which can foster both epigenetic alterations and mutagenesis on the host genome. Most of the bacteria implicated in GC development are Gram-negative, which makes it challenging to eradicate the disease. Gram-negative bacterium co-infections with viruses such as EBV are known as risk factors for GC. In this review, we discuss the role of microbiome-induced GC carcinogenesis. The disease risk factors associated with the presence of microorganisms and microbial dysbiosis are also discussed. In doing so, we aim to emphasize the critical role of the microbiome on cancer pathological phenotypes, and how microbiomics could serve as a potential breakthrough in determining effective GC therapeutic targets. Additionally, consideration of microbial dysbiosis in the GC classification system might aid in diagnosis and treatment decision-making, taking the specific pathogen/s involved into account.}, } @article {pmid36430197, year = {2022}, author = {Cuomo, P and Capparelli, R and Alifano, M and Iannelli, A and Iannelli, D}, title = {Gut Microbiota Host-Gene Interaction.}, journal = {International journal of molecular sciences}, volume = {23}, number = {22}, pages = {}, pmid = {36430197}, issn = {1422-0067}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2 ; Host Microbial Interactions ; *Microbiota ; Anti-Bacterial Agents ; }, abstract = {Studies carried out in the last ten years have shown that the metabolites made up from the gut microbiota are essential for multiple functions, such as the correct development of the immune system of newborns, interception of pathogens, and nutritional enrichment of the diet. Therefore, it is not surprising that alteration of the gut microbiota is the starting point of gastrointestinal infection, obesity, type 2 diabetes, inflammatory bowel disease, colorectal cancer, and lung cancer. Diet changes and antibiotics are the major factors damaging the gut microbiota. Early exposure of the newborns to antibiotics may prevent their correct development of the immune system, exposing them to pathogen infections, allergies, and chronic inflammatory diseases. We already know much on how host genes, microbiota, and the environment interact, owing to experiments in several model animals, especially in mice; advances in molecular technology; microbiota transplantation; and comparative metagenomic analysis. However, much more remains to be known. Longitudinal studies on patients undergoing to therapy, along with the identification of bacteria prevalent in responding patients may provide valuable data for improving therapies.}, } @article {pmid36430182, year = {2022}, author = {Santonocito, S and Ferlito, S and Polizzi, A and Ronsivalle, V and Sclafani, R and Valletta, A and Lo Giudice, A and Cavalcanti, R and Spagnuolo, G and Isola, G}, title = {Therapeutic and Metagenomic Potential of the Biomolecular Therapies against Periodontitis and the Oral Microbiome: Current Evidence and Future Perspectives.}, journal = {International journal of molecular sciences}, volume = {23}, number = {22}, pages = {}, pmid = {36430182}, issn = {1422-0067}, mesh = {Humans ; *Periodontitis/microbiology ; Metagenome ; Metagenomics ; *Microbiota ; Periodontium/metabolism ; Dysbiosis/therapy ; }, abstract = {The principles of periodontal therapy are based on the control of microbial pathogens and host factors that contribute to biofilm dysbiosis, with the aim of modulating the progression of periodontitis and periodontal tissue destruction. It is currently known how differently each individual responds to periodontal treatment, depending on both the bacterial subtypes that make up the dysbiotic biofilm and interindividual variations in the host inflammatory response. This has allowed the current variety of approaches for the management of periodontitis to be updated by defining the goals of target strategies, which consist of reducing the periodontopathogenic microbial flora and/or modulating the host-mediated response. Therefore, this review aims to update the current variety of approaches for the management of periodontitis based on recent target therapies. Recently, encouraging results have been obtained from several studies exploring the effects of some targeted therapies in the medium- and long-term. Among the most promising target therapies analyzed and explored in this review include: cell-based periodontal regeneration, mediators against bone resorption, emdogain (EMD), platelet-rich plasma, and growth factors. The reviewed evidence supports the hypothesis that the therapeutic combination of epigenetic modifications of periodontal tissues, interacting with the dysbiotic biofilm, is a key step in significantly reducing the development and progression of disease in periodontal patients and improving the therapeutic response of periodontal patients. However, although studies indicate promising results, these need to be further expanded and studied to truly realize the benefits that targeted therapies could bring in the treatment of periodontitis.}, } @article {pmid36427959, year = {2022}, author = {Payami, H}, title = {The many genomes of Parkinson's disease.}, journal = {International review of neurobiology}, volume = {167}, number = {}, pages = {59-80}, doi = {10.1016/bs.irn.2022.07.007}, pmid = {36427959}, issn = {2162-5514}, mesh = {Humans ; *Parkinson Disease/genetics ; *Microbiota ; }, abstract = {Genetic component of Parkinson's disease, once firmly believed non-existent, involves the human genome, mitochondrial genome, and the microbiome. Understanding the genomics of PD requires identification of PD-relevant genes and learning how they interact within the hologenome and with their environment. This chapter is an evidence-based perspective of a geneticist on how far we have come in this endeavor. The contemporary scientific society started with a naive and simplistic view of PD, evolved to accept that Parkinson's disease is probably the most complex disease there is, the progress we have made in discovering the genes and elucidating their functions, and now assembling the parts to create the whole.}, } @article {pmid36427112, year = {2022}, author = {Huang, S and Liu, D and Chen, M and Xi, G and Yang, P and Jia, C and Mao, D}, title = {Effects of Bacillus subtilis subsp. on the microbial community and aroma components of flue-cured tobacco leaves based on metagenome analysis.}, journal = {Archives of microbiology}, volume = {204}, number = {12}, pages = {726}, pmid = {36427112}, issn = {1432-072X}, mesh = {*Metagenome ; Nicotiana ; Odorants ; Bacillus subtilis/genetics ; *Microbiota ; Plant Leaves ; }, abstract = {To improve the sensory quality of aged flue-cured tobacco (FCT), Bacillus subtilis subsp, H11 was inoculated on aged FCT leaves named Pingdingshan DCFB. The metagenome and thecharacteristic aroma substances of aged FCT with different fermentation times (0 h, 12 h, 24 h, and 36 h) were systematically analyzed. The results showed that the content of aroma components and sensory quality of aged FCT were significantly improved when the strain was treated at 35 °C with 25% moisture for 24 h. The inoculation of H11 had a strong influence on the microbial composition and metabolism of the aged FCT leaf surface. Five microorganisms Pantoea (35.04%, 20.12-56.95%), Enterobacter (22.16, 13.60-39.82%), Pseudomonas (12.12, 3.13-26.17%), Terribacillus (8.00%, 4.65-13.01%) and Bacillus (6.54%, 0.67-16.96%) accounted for the largest proportion during the process of fermentation. The content of most neutral flavor components such as ketones and aldehydes in FCT after fermentation was higher than that priorto fermentation. After 24 h fermentation, 3-furfural, 5-methylfurfural, dihydrokiwi lactone and megalotrienone increased by 71.42%, 49.19%, 21.09%, and 10.56%, respectively. Correlation analysis between groups showed that Pseudomonas was significantly correlated with (E, E)-2, 4-heptadienal (P < 0.05), Franconibacter was correlated with damascus ketone (P < 0.05), and Terribacillus was related to the production of β-citral (P < 0.05). GH9 may be involved in the formation of damasone (P < 0.05), and 4-cyclopentene-1, 3-dione was significantly correlated with glycoside hydrolase family 5 (GH5) (P < 0.05). The correlation between 4-oxyisophorone and GH31, GH103, GH73, and GH3 was significant (P < 0.05). Microorganisms and GHs may play important roles in FCT fermentation.}, } @article {pmid36427064, year = {2022}, author = {Silva, JB and Centurion, VB and Duarte, AWF and Galazzi, RM and Arruda, MAZ and Sartoratto, A and Rosa, LH and Oliveira, VM}, title = {Unravelling the genetic potential for hydrocarbon degradation in the sediment microbiome of Antarctic islands.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {1}, pages = {}, doi = {10.1093/femsec/fiac143}, pmid = {36427064}, issn = {1574-6941}, mesh = {RNA, Ribosomal, 16S/genetics ; Antarctic Regions ; Hydrocarbons/metabolism ; *Microbiota/genetics ; Soil Microbiology ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Islands ; *Polycyclic Aromatic Hydrocarbons/metabolism ; }, abstract = {Hydrocarbons may have a natural or anthropogenic origin and serve as a source of carbon and energy for microorganisms in Antarctic soils. Herein, 16S rRNA gene and shotgun sequencing were employed to characterize taxonomic diversity and genetic potential for hydrocarbon degradation of the microbiome from sediments of sites located in two Antarctic islands subjected to different temperatures, geochemical compositions, and levels of presumed anthropogenic impact, named: Crater Lake/Deception Island (pristine area), Whalers Bay and Fumarole Bay/Deception Island (anthropogenic-impacted area), and Hannah Point/Livingston Island (anthropogenic-impacted area). Hydrocarbon concentrations were measured for further correlation analyses with biological data. The majority of the hydrocarbon-degrading genes were affiliated to the most abundant bacterial groups of the microbiome: Proteobacteria and Actinobacteria. KEGG annotation revealed 125 catabolic genes related to aromatic hydrocarbon (styrene, toluene, ethylbenzene, xylene, naphthalene, and polycyclic hydrocarbons) and aliphatic (alkanes and cycloalkanes) pathways. Only aliphatic hydrocarbons, in low concentrations, were detected in all areas, thus not characterizing the areas under study as anthropogenically impacted or nonimpacted. The high richness and abundance of hydrocarbon-degrading genes suggest that the genetic potential of the microbiome from Antarctic sediments for hydrocarbon degradation is driven by natural hydrocarbon occurrence.}, } @article {pmid36424722, year = {2023}, author = {Heo, M and Park, YS and Yoon, H and Kim, NE and Kim, K and Shin, CM and Kim, N and Lee, DH}, title = {Potential of Gut Microbe-Derived Extracellular Vesicles to Differentiate Inflammatory Bowel Disease Patients from Healthy Controls.}, journal = {Gut and liver}, volume = {17}, number = {1}, pages = {108-118}, pmid = {36424722}, issn = {2005-1212}, mesh = {Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Inflammatory Bowel Diseases/diagnosis/microbiology ; Feces ; *Extracellular Vesicles ; }, abstract = {BACKGROUND/AIMS: This study aimed to evaluate the potential of the stool microbiome and gut microbe-derived extracellular vesicles (EVs) to differentiate between patients with inflammatory bowel disease (IBD) and healthy controls, and to predict relapse in patients with IBD.

METHODS: Metagenomic profiling of the microbiome and bacterial EVs in stool samples of controls (n=110) and patients with IBD (n=110) was performed using 16S rRNA sequencing and then compared. Patients with IBD were divided into two enterotypes based on their microbiome, and the cumulative risk of relapse was evaluated.

RESULTS: There was a significant difference in the composition of the stool microbiome and gut microbe-derived EVs between patients with IBD and controls. The alpha diversity of the microbiome in patients with IBD was significantly lower than that in controls, while the beta diversity also differed significantly between the two groups. These findings were more prominent in gut microbe-derived EVs than in the stool microbiome. The survival curve tended to be different for enterotypes based on the gut microbe-derived EVs; however, this difference was not statistically significant (log-rank test, p=0.166). In the multivariable analysis, elevated fecal calprotectin (>250 mg/kg) was the only significant risk factor associated with relapse (adjusted hazard ratio, 3.147; 95% confidence interval, 1.545 to 6.408; p=0.002).

CONCLUSIONS: Analysis of gut microbe-derived EVs is better at differentiating patients with IBD from healthy controls than stool microbiome analysis.}, } @article {pmid36424179, year = {2023}, author = {Simon, MC and Sina, C and Ferrario, PG and Daniel, H and , }, title = {Gut Microbiome Analysis for Personalized Nutrition: The State of Science.}, journal = {Molecular nutrition & food research}, volume = {67}, number = {1}, pages = {e2200476}, doi = {10.1002/mnfr.202200476}, pmid = {36424179}, issn = {1613-4133}, mesh = {Humans ; *Gastrointestinal Microbiome ; Nutritional Status ; Diet ; *Microbiota ; Metagenome ; }, abstract = {Whereas most concepts of personalized nutrition (PN) in the past, included genotyping, recent years have brought new approaches that include microbiome analysis to optimize recommendations for diet and lifestyle changes. The new approach, offered by companies, that microbiome analysis provides a real benefit to either more concise recommendations or for increased compliance to PN, is largely lacking scientific validation. Although the microbiome field shows enormous proliferation, it has some major flaws that make its use in the public health domain currently critical. Starting with the quality and representative character of the stool samples, its processing and analysis as well as assembly of metagenome data and the interpretation. Moreover, there is still no consensus of what constitutes a "normal/healthy" microbiome, nor what features characterize a dysbiotic microbiome. And, based on hundreds of individual parameters and environmental factors, the intestinal microbiome shows a huge variability and consequently changing one factor-such as food intake-is likely to have a limited impact in achieving optimized health. The present review intends to summarize the state of consolidated knowledge on human gut microbiome in the context of diet and disease, its key features, and its influencing factors as well as its "add-on" quality for PN offers.}, } @article {pmid36423788, year = {2023}, author = {Kappel, BA and De Angelis, L and Puetz, A and Ballanti, M and Menghini, R and Marx, N and Federici, M}, title = {Antibiotic-induced gut microbiota depletion exacerbates host hypercholesterolemia.}, journal = {Pharmacological research}, volume = {187}, number = {}, pages = {106570}, doi = {10.1016/j.phrs.2022.106570}, pmid = {36423788}, issn = {1096-1186}, mesh = {Animals ; Humans ; Mice ; *Anti-Bacterial Agents/adverse effects ; Cholesterol/metabolism ; Firmicutes ; *Gastrointestinal Microbiome/drug effects ; *Hypercholesterolemia/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Hypercholesterolemia is a major driver of atherosclerosis, thus contributing to high morbidity and mortality worldwide. Gut microbiota have been identified as modulator of blood lipids including cholesterol levels. Few studies have already linked certain bacteria and microbial mechanisms to host cholesterol. However, in particular mouse models revealed conflicting results depending on genetics and experimental protocol. To gain further insights into the relationship between intestinal bacteria and host cholesterol metabolism, we first performed fecal 16S rRNA targeted metagenomic sequencing in a human cohort (n = 24) naïve for cholesterol lowering drugs. Here, we show alterations in the gut microbiota composition of hypercholesterolemic patients with depletion of Bifidobacteria, expansion of Clostridia and increased Firmicutes/Bacteroidetes ratio. To test whether pharmacological intervention in gut microbiota impacts host serum levels of cholesterol, we treated hypercholesterolemic Apolipoprotein E knockout with oral largely non-absorbable antibiotics. Antibiotics increased serum cholesterol, but only when mice were fed normal chow diet and cholesterol was measured in the random fed state. These elevations in cholesterol already occurred few days after treatment initiation and were reversible after stopping antibiotics with re-acquisition of intestinal bacteria. Gene expression analyses pointed to increased intestinal cholesterol uptake mediated by antibiotics in the fed state. Non-targeted serum metabolomics suggested that diminished plant sterol levels and reduced bile acid cycling were involved microbial mechanisms. In conclusion, our work further enlightens the link between gut microbiota and host cholesterol metabolism. Pharmacological disruption of the gut flora by antibiotics was able to exacerbate serum cholesterol and may impact cardiovascular disease.}, } @article {pmid36423125, year = {2022}, author = {Ogunbayo, AE and Mogotsi, MT and Sondlane, H and Nkwadipo, KR and Sabiu, S and Nyaga, MM}, title = {Metagenomic Analysis of Respiratory RNA Virome of Children with and without Severe Acute Respiratory Infection from the Free State, South Africa during COVID-19 Pandemic Reveals Higher Diversity and Abundance in Summer Compared with Winter Period.}, journal = {Viruses}, volume = {14}, number = {11}, pages = {}, pmid = {36423125}, issn = {1999-4915}, mesh = {Child ; Animals ; Humans ; Virome ; South Africa/epidemiology ; *COVID-19 ; Seasons ; RNA ; Pandemics ; *Respiratory Tract Infections ; *Pneumonia ; *Viruses/genetics ; Respiratory System ; }, abstract = {Viral respiratory infections contribute to significant morbidity and mortality in children. Currently, there are limited reports on the composition and abundance of the normal commensal respiratory virome in comparison to those in severe acute respiratory infections (SARIs) state. This study characterised the respiratory RNA virome in children ≤ 5 years with (n = 149) and without (n = 139) SARI during the summer and winter of 2020/2021 seasons in South Africa. Nasopharyngeal swabs were, collected, pooled, enriched for viral RNA detection, sequenced using Illumina MiSeq, and analysed using the Genome Detective bioinformatic tool. Overall, Picornaviridae, Paramoxyviridae, Pneumoviridae, Picobirnaviridae, Totiviridae, and Retroviridae families were the most abundant viral population in both groups across both seasons. Human rhinovirus and endogenous retrovirus K113 were detected in most pools, with exclusive detection of Pneumoviridae in SARI pools. Generally, higher viral diversity/abundance was seen in children with SARI and in the summer pools. Several plant/animal viruses, eukaryotic viruses with unclear pathogenicity including a distinct rhinovirus A type, were detected. This study provides remarkable data on the respiratory RNA virome in children with and without SARI with a degree of heterogeneity of known viruses colonizing their respiratory tract. The implication of the detected viruses in the dynamics/progression of SARI requires further investigations.}, } @article {pmid36422845, year = {2022}, author = {Ul-Haq, A and Lee, KA and Seo, H and Kim, S and Jo, S and Ko, KM and Moon, SJ and Kim, YS and Choi, JR and Song, HY and Kim, HS}, title = {Characteristic alterations of gut microbiota in uncontrolled gout.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {60}, number = {12}, pages = {1178-1190}, pmid = {36422845}, issn = {1976-3794}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Uric Acid ; Bacteria/genetics ; *Gout/drug therapy ; }, abstract = {Microbiome research has been on the rise recently for a more in-depth understanding of gout. Meanwhile, there is a need to understand the gut microbiome related to uric acid-lowering drug resistance. In this study, 16S rRNA gene-based microbiota analysis was performed for a total of 65 stool samples from 17 healthy controls and 48 febuxostat-treated gout patients (including 28 controlled subjects with decreased uric acid levels and 20 uncontrolled subjects with non-reduced uric acid levels). Alpha diversity of bacterial community decreased in the healthy control, controlled, and uncontrolled groups. In the case of beta diversity, the bacterial community was significantly different among groups (healthy control, controlled, and uncontrolled groups). Taxonomic biomarker analysis revealed the increased population of g-Bifidobacterium in healthy controls and g-Prevotella in uncontrolled patients. PCR further confirmed this result at the species level. Additionally, functional metagenomics predictions led to the exploration of various functional biomarkers, including purine metabolism. The results of this study can serve as a basis for developing potential new strategies for diagnosing and treating gout from microbiome prospects.}, } @article {pmid36420990, year = {2022}, author = {Núñez-Sánchez, MA and Herisson, FM and Keane, JM and García-González, N and Rossini, V and Pinhiero, J and Daly, J and Bustamante-Garrido, M and Hueston, CM and Patel, S and Canela, N and Herrero, P and Claesson, MJ and Melgar, S and Nally, K and Caplice, NM and Gahan, CGM}, title = {Microbial bile salt hydrolase activity influences gene expression profiles and gastrointestinal maturation in infant mice.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2149023}, pmid = {36420990}, issn = {1949-0984}, mesh = {Female ; Humans ; Mice ; Animals ; *Transcriptome ; *Gastrointestinal Microbiome ; Amidohydrolases/genetics/metabolism ; Gastrointestinal Tract/microbiology ; Bacteria/genetics ; Basic Helix-Loop-Helix Transcription Factors/metabolism ; }, abstract = {The mechanisms by which early microbial colonizers of the neonate influence gut development are poorly understood. Bacterial bile salt hydrolase (BSH) acts as a putative colonization factor that influences bile acid signatures and microbe-host signaling pathways and we considered whether this activity can influence infant gut development. In silico analysis of the human neonatal gut metagenome confirmed that BSH enzyme sequences are present as early as one day postpartum. Gastrointestinal delivery of cloned BSH to immature gnotobiotic mice accelerated shortening of the colon and regularized gene expression profiles, with monocolonised mice more closely resembling conventionally raised animals. In situ expression of BSH decreased markers of cell proliferation (Ki67, Hes2 and Ascl2) and strongly increased expression of ALPI, a marker of cell differentiation and barrier function. These data suggest an evolutionary paradigm whereby microbial BSH activity potentially influences bacterial colonization and in-turn benefits host gastrointestinal maturation.}, } @article {pmid36419280, year = {2023}, author = {Liao, J and Dou, Y and Yang, X and An, S}, title = {Soil microbial community and their functional genes during grassland restoration.}, journal = {Journal of environmental management}, volume = {325}, number = {Pt A}, pages = {116488}, doi = {10.1016/j.jenvman.2022.116488}, pmid = {36419280}, issn = {1095-8630}, mesh = {*Soil ; Grassland ; *Microbiota ; Nitrification ; Carbon ; }, abstract = {Soil microbial functional genes are linked with carbon (C) as well as nitrogen (N) cycling processes, and their relative abundances are strongly affected by ecosystem managements. Yet, soil microbial community compositions and their C, N cycling genes' abundance in temperate grasslands remain poorly studied. Here, the Illumina MiSeq sequencing (16 S rRNA gene and internal transcribed spacer [ITS]) and meta-genomic GeoChip sequencing technologies were used to explore the alterations of microbial compositions and functional genes in the topsoil (0-10 cm) following grassland restoration. Grassland restoration increased the relative abundances of the copiotrophs (such as Actinobacteria, Proteobacteria, Bacteroidetes), but reduced the oligotrophs (including Acidobacteria, Chloroflexi, Planctomycetes), suggesting that microorganisms shifted from oligotrophic to copiotrophic groups during grassland restoration. The changes in microbial eco-strategies were also supported by the meta-genomic GeoChip sequencing data. In the early restoration years, the microbial functional genes were dominant with recalcitrant C degradation (pgu, glx, lig, mnp), C fixation (accA, aclB, acsA, rbcL), N fixation (nifH), and nitrification (amoA, hao) related genes. In the later restoration years, the microbial functional genes were dominant with labile C degradation (amyA, amyX, apu, sga, abfA), and denitrification (nosZ, nirS, narG, napA) related genes. The changes in microbial functional genes were mainly related to soil biotic factors (microbial biomass C and N, as well as C- and N-acquiring enzymes). Finally, we made a framework illustrating the changes in microbial eco-strategies and soil C, N cycling processes. This is the first attempt to link microbial functional genes with microbial eco-strategies by incorporating soil microbial meta-genomic information during grassland restoration.}, } @article {pmid36419034, year = {2022}, author = {Li, P and Luo, H and Ji, B and Nielsen, J}, title = {Machine learning for data integration in human gut microbiome.}, journal = {Microbial cell factories}, volume = {21}, number = {1}, pages = {241}, pmid = {36419034}, issn = {1475-2859}, support = {NNF15OC0016798//Novo Nordisk Foundation Center for Basic Metabolic Research/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Metagenomics ; Dysbiosis ; Machine Learning ; }, abstract = {Recent studies have demonstrated that gut microbiota plays critical roles in various human diseases. High-throughput technology has been widely applied to characterize the microbial ecosystems, which led to an explosion of different types of molecular profiling data, such as metagenomics, metatranscriptomics and metabolomics. For analysis of such data, machine learning algorithms have shown to be useful for identifying key molecular signatures, discovering potential patient stratifications, and particularly for generating models that can accurately predict phenotypes. In this review, we first discuss how dysbiosis of the intestinal microbiota is linked to human disease development and how potential modulation strategies of the gut microbial ecosystem can be used for disease treatment. In addition, we introduce categories and workflows of different machine learning approaches, and how they can be used to perform integrative analysis of multi-omics data. Finally, we review advances of machine learning in gut microbiome applications and discuss related challenges. Based on this we conclude that machine learning is very well suited for analysis of gut microbiome and that these approaches can be useful for development of gut microbe-targeted therapies, which ultimately can help in achieving personalized and precision medicine.}, } @article {pmid36417437, year = {2022}, author = {Osborn, LJ and Schultz, K and Massey, W and DeLucia, B and Choucair, I and Varadharajan, V and Banerjee, R and Fung, K and Horak, AJ and Orabi, D and Nemet, I and Nagy, LE and Wang, Z and Allende, DS and Willard, BB and Sangwan, N and Hajjar, AM and McDonald, C and Ahern, PP and Hazen, SL and Brown, JM and Claesen, J}, title = {A gut microbial metabolite of dietary polyphenols reverses obesity-driven hepatic steatosis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {48}, pages = {e2202934119}, pmid = {36417437}, issn = {1091-6490}, support = {R01 DK120679/DK/NIDDK NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; S10 OD023436/OD/NIH HHS/United States ; R01 DK130227/DK/NIDDK NIH HHS/United States ; P30 CA043703/CA/NCI NIH HHS/United States ; T32 GM088088/GM/NIGMS NIH HHS/United States ; P50 AA024333/AA/NIAAA NIH HHS/United States ; R01 AI153173/AI/NIAID NIH HHS/United States ; U01 AA026938/AA/NIAAA NIH HHS/United States ; }, mesh = {Humans ; Mice ; Animals ; Polyphenols/pharmacology ; *Gastrointestinal Microbiome/physiology ; *Fatty Liver/prevention & control ; Obesity/metabolism ; Diet, High-Fat/adverse effects ; Flavonoids/pharmacology ; }, abstract = {The molecular mechanisms by which dietary fruits and vegetables confer cardiometabolic benefits remain poorly understood. Historically, these beneficial properties have been attributed to the antioxidant activity of flavonoids. Here, we reveal that the host metabolic benefits associated with flavonoid consumption hinge, in part, on gut microbial metabolism. Specifically, we show that a single gut microbial flavonoid catabolite, 4-hydroxyphenylacetic acid (4-HPAA), is sufficient to reduce diet-induced cardiometabolic disease (CMD) burden in mice. The addition of flavonoids to a high fat diet heightened the levels of 4-HPAA within the portal plasma and attenuated obesity, and continuous delivery of 4-HPAA was sufficient to reverse hepatic steatosis. The antisteatotic effect was shown to be associated with the activation of AMP-activated protein kinase α (AMPKα). In a large survey of healthy human gut metagenomes, just over one percent contained homologs of all four characterized bacterial genes required to catabolize flavonols into 4-HPAA. Our results demonstrate the gut microbial contribution to the metabolic benefits associated with flavonoid consumption and underscore the rarity of this process in human gut microbial communities.}, } @article {pmid36416806, year = {2022}, author = {Pavloudi, C and Zafeiropoulos, H}, title = {Deciphering the community structure and the functional potential of a hypersaline marsh microbial mat community.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {12}, pages = {}, doi = {10.1093/femsec/fiac141}, pmid = {36416806}, issn = {1574-6941}, support = {MIS 5017160//RECONNECT/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria ; Metagenome ; Metagenomics ; Phylogeny ; }, abstract = {Microbial mats are vertically stratified communities of microorganisms characterized by pronounced physiochemical gradients allowing for high species diversity and a wide range of metabolic capabilities. High Throughput Sequencing has the potential to reveal the biodiversity and function of such ecosystems in the cycling of elements. The present study combines 16S rRNA amplicon sequencing and shotgun metagenomics on a hypersaline marsh in Tristomo bay (Karpathos, Greece). Samples were collected in July 2018 and November 2019 from microbial mats, deeper sediment, aggregates observed in the water overlying the sediment, as well as sediment samples with no apparent layering. Metagenomic samples' coassembly and binning revealed 250 bacterial and 39 archaeal metagenome-assembled genomes, with completeness estimates higher than 70% and contamination less than 5%. All MAGs had KEGG Orthology terms related to osmoadaptation, with the 'salt in' strategy ones being prominent. Halobacteria and Bacteroidetes were the most abundant taxa in the mats. Photosynthesis was most likely performed by purple sulphur and nonsulphur bacteria. All samples had the capacity for sulphate reduction, dissimilatory arsenic reduction, and conversion of pyruvate to oxaloacetate. Overall, both sequencing methodologies resulted in similar taxonomic compositions and revealed that the formation of the microbial mat in this marsh exhibits seasonal variation.}, } @article {pmid36416760, year = {2022}, author = {Kircher, B and Woltemate, S and Gutzki, F and Schlüter, D and Geffers, R and Bähre, H and Vital, M}, title = {Predicting butyrate- and propionate-forming bacteria of gut microbiota from sequencing data.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2149019}, pmid = {36416760}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Butyrates/metabolism ; Propionates/metabolism ; RNA, Ribosomal, 16S/genetics ; Fatty Acids, Volatile/metabolism ; Bacteria ; }, abstract = {The bacteria-derived short-chain fatty acids (SCFAs) butyrate and propionate play important (distinct) roles in health and disease, and understanding the ecology of respective bacteria on a community-wide level is a top priority in microbiome research. Applying sequence data (metagenomics and 16S rRNA gene) to predict SCFAs production in vitro and in vivo, a clear split between butyrate- and propionate-forming bacteria was detected with only very few taxa exhibiting pathways for the production of both SCFAs. After in vitro growth of fecal communities from distinct donors (n = 8) on different substrates (n = 7), abundances of bacteria exhibiting pathways correlated with respective SCFA concentrations, in particular in the case of butyrate. For propionate, correlations were weaker, indicating that its production is less imprinted into the core metabolism compared with butyrate-forming bacteria. Longitudinal measurements in vivo (n = 5 time-points from 20 subjects) also revealed a correlation between abundances of pathway-carrying bacteria and concentrations of the two SCFAs. Additionally, lower bacterial cell concentrations, together with higher stool moisture, promoted overall bacterial activity (measured by flow cytometry and coverage patterns of metagenome-assembled genomes) that led to elevated SCFA concentrations with over-proportional levels of butyrate. Predictions on pathway abundances based on 16S rRNA gene data using our in-house database worked well, yielding similar results as metagenomic-based analyses. Our study indicates that stimulating growth of butyrate- and propionate-producing bacteria directly leads to more production of those compounds, which is governed by two functionally distinct bacterial groups facilitating the development of precision intervention strategies targeting either metabolite.}, } @article {pmid36414646, year = {2022}, author = {Perez-Fernandez, CA and Wilburn, P and Davila, A and DiRuggiero, J}, title = {Adaptations of endolithic communities to abrupt environmental changes in a hyper-arid desert.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {20022}, pmid = {36414646}, issn = {2045-2322}, support = {80NSSC19K0470//National Aeronautics and Space Administration (NASA)/ ; NNX15AP18G//National Aeronautics and Space Administration (NASA)/ ; }, mesh = {*Desert Climate ; Acclimatization ; *Microbiota/genetics ; Metagenome ; Sodium Chloride ; Water ; }, abstract = {The adaptation mechanisms of microbial communities to natural perturbations remain unexplored, particularly in extreme environments. The extremophilic communities of halite (NaCl) nodules from the hyper-arid core of the Atacama Desert are self-sustained and represent a unique opportunity to study functional adaptations and community dynamics with changing environmental conditions. We transplanted halite nodules to different sites in the desert and investigated how their taxonomic, cellular, and biochemical changes correlated with water availability, using environmental data modeling and metagenomic analyses. Salt-in strategists, mainly represented by haloarchaea, significantly increased in relative abundance at sites characterized by extreme dryness, multiple wet/dry cycles, and colder conditions. The functional analysis of metagenome-assembled genomes (MAGs) revealed site-specific enrichments in archaeal MAGs encoding for the uptake of various compatible solutes and for glycerol utilization. These findings suggest that opportunistic salt-in strategists took over the halite communities at the driest sites. They most likely benefited from compounds newly released in the environment by the death of microorganisms least adapted to the new conditions. The observed changes were consistent with the need to maximize cellular bioenergetics when confronted with lower water availability and higher salinity, providing valuable information on microbial community adaptations and resilience to climate change.}, } @article {pmid36413016, year = {2022}, author = {France, M and Ma, B and Ravel, J}, title = {Persistence and In Vivo Evolution of Vaginal Bacterial Strains over a Multiyear Time Period.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0089322}, pmid = {36413016}, issn = {2379-5077}, support = {UH2AI083264//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01NR015495//HHS | NIH | National Institute of Nursing Research (NINR)/ ; }, mesh = {Female ; Humans ; *Vagina/microbiology ; Bacteria/genetics ; *Microbiota/genetics ; Lactobacillus/genetics ; Metagenome/genetics ; }, abstract = {It is not clear whether the bacterial strains that comprise our microbiota are mostly long-term colonizers or transient residents. Studies have demonstrated decades-long persistence of bacterial strains within the gut, but persistence at other body sites has yet to be determined. The vaginal microbiota (VMB) is often dominated by Lactobacillus, although it is also commonly comprised of a more diverse set of other facultative and obligate anaerobes. Longitudinal studies have demonstrated that these communities can be stable over several menstrual cycles or can fluctuate temporally in species composition. We sought to determine whether the bacterial strains that comprise the VMB were capable of persisting over longer time periods. We performed shotgun metagenomics on paired samples from 10 participants collected 1 and 2 years apart. The resulting sequences were de novo assembled and binned into high-quality metagenome assembled genomes. Persistent strains were identified based on the sequence similarity between the genomes present at the two time points and were found in the VMB of six of the participants, three of which had multiple persistent strains. The VMB of the remaining four participants was similar in species composition at the two time points but was comprised of different strains. For the persistent strains, we were able to identify the mutations that were fixed in the populations over the observed time period, giving insight into the evolution of these bacteria. These results indicate that bacterial strains can persist in the vagina for extended periods of time, providing an opportunity for them to evolve in the host microenvironment. IMPORTANCE The stability of strains within the vaginal microbiota is largely uncharacterized. Should these strains be capable of persisting for extended periods of time, they could evolve within their host in response to selective pressures exerted by the host or by other members of the community. Here, we present preliminary findings demonstrating that bacterial strains can persist in the vagina for at least 1 year. We further characterized in vivo evolution of the persistent strains. Several participants were also found to not have persistent strains, despite having a vaginal microbiota (VMB) with similar species composition at the two time points. Our observations motivate future studies that collect samples from more participants, at more time points, and over even longer periods of time. Understanding which strains persist, what factors drive their persistence, and what selective pressures they face will inform the development and delivery of rationally designed live biotherapeutics for the vagina.}, } @article {pmid36411639, year = {2022}, author = {Singh, N and Singh, V and Rai, SN and Mishra, V and Vamanu, E and Singh, MP}, title = {Deciphering the gut microbiome in neurodegenerative diseases and metagenomic approaches for characterization of gut microbes.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {156}, number = {}, pages = {113958}, doi = {10.1016/j.biopha.2022.113958}, pmid = {36411639}, issn = {1950-6007}, mesh = {Humans ; Metagenomics ; *Gastrointestinal Microbiome/genetics ; *Neurodegenerative Diseases ; Metagenome ; Central Nervous System ; }, abstract = {The central nervous system has essential role in the regulation of the physiological condition of the human body. Gut microbes cause several types of gastrointestinal diseases like ulcer stomach and intestine and irritable bowel syndrome. Microbes present in the human gut can affect brain function by the release of neuroactive metabolites such as neurotransmitters, hormones, and other compounds. Gut microbial-derived metabolites also have an important role in neurological diseases such as Alzheimer's disease, Parkinson's disease, etc. Vital communication between the gut microbes and the central nervous system is known as the microbiota-gut-brain axis. It provides a communication pathway between the gut and brain which is made up of the vagus nerve, immune system components, and neuroendocrine. Disturbance in gut microbiota composition can alter the central nervous system and enteric nervous system functions. Metagenomics has been employed for the identification, and characterization of gut microbes and microbial-derived metabolites. This review is focused on the gut microbes-brain relationship and the role of gut microbes in neurodegenerative diseases. This study is also focused on major metagenomic approaches and their role in gut microbes characterization.}, } @article {pmid36411435, year = {2022}, author = {Miles, AM and McArt, JAA and Lima, SF and Neves, RC and Ganda, E}, title = {The association of hyperketonemia with fecal and rumen microbiota at time of diagnosis in a case-control cohort of early lactation cows.}, journal = {BMC veterinary research}, volume = {18}, number = {1}, pages = {411}, pmid = {36411435}, issn = {1746-6148}, support = {This work is/was supported by the USDA National Institute of Food and Agriculture and Hatch Appropriations under Project #PEN04752 Accession #1023328.//U.S. Department of Agriculture/ ; }, mesh = {Female ; Cattle ; Pregnancy ; Animals ; Rumen/metabolism ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Milk/metabolism ; *Cattle Diseases/diagnosis ; *Ketosis/veterinary ; Lactation ; 3-Hydroxybutyric Acid ; *Microbiota ; }, abstract = {BACKGROUND: Many dairy cows experience a state of energy deficit as they transition from late gestation to early lactation. The aims of this study were to 1) determine if the development of hyperketonemia in early lactation dairy cows is indicated by their gut microbiome, and 2) to identify microbial features which may inform health status. We conducted a prospective nested case-control study in which cows were enrolled 14 to 7 days before calving and followed through their first 14 days in milk (DIM). Hyperketonemic cows (HYK, n = 10) were classified based on a blood β-hydroxybutyrate (BHB) concentration 1.2 mmol/L within their first 14 DIM. For each HYK cow, two non-HYK (CON, n = 20) cows were matched by parity and 3 DIM, with BHB < 1.2 mmol/L. Daily blood BHB measures were used to confirm CON cows maintained their healthy status; some CON cows displayed BHB 1.2 mmol/L after matching and these cows were reclassified as control-HYK (C-HYK, n = 9). Rumen and fecal samples were collected on the day of diagnosis or matching and subjected to 16S rRNA profiling.

RESULTS: No differences in taxa abundance, or alpha and beta diversity, were observed among CON, C-HYK, and HYK health groups for fecal microbiomes. Similar microbiome composition based on beta diversity analysis was detected for all health statuses, however the rumen microbiome of CON and HYK cows were found to be significantly different. Interestingly, highly similar microbiome composition was observed among C-HYK cow rumen and fecal microbiomes, suggesting that these individual animals which initially appear healthy with late onset of hyperketonemia were highly similar to each other. These C-HYK cows had significantly lower abundance of Ruminococcus 2 in their rumen microbiome compared to CON and HYK groups. Multinomial regressions used to compute log-fold changes in microbial abundance relative to health status were not found to have predictive value, therefore were not useful to identify the role of certain microbial features in predicting health status.

CONCLUSIONS: Lower relative abundance of Ruminococcus 2 in C-HYK cow rumens was observed, suggesting these cows may be less efficient at degrading cellulose although the mechanistic role of Ruminococcus spp. in rumen metabolism is not completely understood. Substantial differences in fecal or rumen microbiomes among cows experiencing different levels of energy deficit were not observed, suggesting that hyperketonemia may not be greatly influenced by gut microbial composition, and vice versa. Further studies using higher resolution -omics approaches like meta-transcriptomics or meta-proteomics are needed to decipher the exact mechanisms at play.}, } @article {pmid36411314, year = {2023}, author = {}, title = {Rapid mining of (meta)genomic biodiversity by repurposing CRISPRi for positive selection.}, journal = {Nature biotechnology}, volume = {41}, number = {5}, pages = {620-621}, pmid = {36411314}, issn = {1546-1696}, mesh = {*Biodiversity ; *Genomics ; Mining ; }, } @article {pmid36403657, year = {2023}, author = {Hamidou Soumana, I and Ryu, MH and Leitao Filho, FS and Yang, J and Orach, J and Nislow, C and Leung, JM and Rider, CF and Carlsten, C}, title = {Exposure to diesel exhaust alters the functional metagenomic composition of the airway microbiome in former smokers.}, journal = {Environmental research}, volume = {216}, number = {Pt 4}, pages = {114826}, doi = {10.1016/j.envres.2022.114826}, pmid = {36403657}, issn = {1096-0953}, mesh = {Humans ; Vehicle Emissions/toxicity/analysis ; Smokers ; *Air Pollution/analysis ; Metagenome ; *Microbiota ; *Air Pollutants/analysis ; }, abstract = {The lung microbiome plays a crucial role in airway homeostasis, yet we know little about the effects of exposures such as air pollution therein. We conducted a controlled human exposure study to assess the impact of diesel exhaust (DE) on the human airway microbiome. Twenty-four participants (former smokers with mild to moderate COPD (N = 9), healthy former smokers (N = 7), and control healthy never smokers (N = 8)) were exposed to DE (300 μg/m[3] PM2.5) and filtered air (FA) for 2 h in a randomized order, separated by a 4-week washout. Endobronchial brushing samples were collected 24 h post-exposure and sequenced for the 16S microbiome, which was analyzed using QIIME2 and PICRUSt2 to examine diversity and metabolic functions, respectively. DE exposure altered airway microbiome metabolic functions in spite of statistically stable microbiome diversity. Affected functions included increases in: superpathway of purine deoxyribonucleosides degradation (pathway differential abundance 743.9, CI 95% 201.2 to 1286.6), thiazole biosynthesis I (668.5, CI 95% 139.9 to 1197.06), and L-lysine biosynthesis II (666.5, CI 95% 73.3 to 1257.7). There was an exposure-by-age effect, such that menaquinone biosynthesis superpathways were the most enriched function in the microbiome of participants aged >60, irrespective of smoking or health status. Moreover, exposure-by-phenotype analysis showed metabolic alterations in former smokers after DE exposure. These observations suggest that DE exposure induced substantial changes in the metabolic functions of the airway microbiome despite the absence of diversity changes.}, } @article {pmid36403441, year = {2023}, author = {Lu, P and Shi, H and Tao, J and Jin, J and Wang, S and Zheng, Q and Liu, P and Xiang, B and Chen, Q and Xu, Y and Li, Z and Tan, J and Cao, P}, title = {Metagenomic insights into the changes in the rhizosphere microbial community caused by the root-knot nematode Meloidogyne incognita in tobacco.}, journal = {Environmental research}, volume = {216}, number = {Pt 4}, pages = {114848}, doi = {10.1016/j.envres.2022.114848}, pmid = {36403441}, issn = {1096-0953}, mesh = {Animals ; *Tylenchoidea/physiology ; Nicotiana ; Rhizosphere ; Ammonia ; Urease/metabolism ; Plant Diseases ; Plant Roots/metabolism ; *Microbiota ; Bacteria/genetics ; Soil ; }, abstract = {Root-knot nematode (RKN) disease is a destructive soil disease that affects crop health and causes huge losses in crop production. To explore the relationships between soil environments, rhizobacterial communities, and plant health, rhizosphere bacterial communities were analyzed using metagenomic sequencing in tobacco samples with different grades of RKN disease. The results showed that the community structure and function of the plant rhizosphere were significantly correlated to the RKN disease. RKN density and urease content were key factors affecting the rhizosphere bacterial community. Urease accelerated the catabolism of urea and led to the production of high concentrations of ammonia, which directly suppressed the development of RKNs or by improving the nutritional and growth status of microorganisms that were antagonistic to RKNs. Further experiments showed that the suppression role of ammonia should be attributed to the direct inhibition of NH3. The bacterial members that were positively correlated with RKN density, contained many plant cell wall degrading enzymes, which might destroy plant cell walls and promote the colonization of RKN in tobacco roots. The analysis of metatranscriptome and metabolism demonstrated the role of these cell wall degrading enzymes. This study offers a comprehensive insight into the relationships between RKNs, bacteria, and soil environmental factors and provides new ideas for the biological control of RKNs.}, } @article {pmid36402183, year = {2023}, author = {Wei, C and Sun, D and Yuan, W and Li, L and Dai, C and Chen, Z and Zeng, X and Wang, S and Zhang, Y and Jiang, S and Wu, Z and Liu, D and Jiang, L and Peng, S}, title = {Metagenomics revealing molecular profiles of microbial community structure and metabolic capacity in Bamucuo lake, Tibet.}, journal = {Environmental research}, volume = {217}, number = {}, pages = {114847}, doi = {10.1016/j.envres.2022.114847}, pmid = {36402183}, issn = {1096-0953}, mesh = {Tibet ; *Lakes ; Bacteria/genetics/metabolism ; *Microbiota ; Soil Microbiology ; Soil ; Water ; }, abstract = {Microorganisms play critical ecological roles in the global biogeochemical cycles. However, extensive information on the microbial communities in Qinghai-Tibet Plateau (QTP), which is the highest plateau in the world, is still lacking, particularly in high elevation locations above 4500 m. Here, we performed a survey of th e soil and water microbial communities in Bamucuo Lake, Tibet, by using shotgun metagenomic methods. In the soil and water samples, we reconstructed 75 almost complete metagenomic assembly genomes, and 74 of the metagenomic assembly genomes from the water sample represented novel species. Proteobacteria and Actinobacteria were found to be the dominant bacterial phyla, while Euryarchaeota was the dominant archaeal phylum. The largest virus, Pandoravirus salinus, was found in the soil microbial community. We concluded that the microorganisms in Bamucuo Lake are most likely to fix carbon mainly through the 3-hydroxypropionic bi-cycle pathway. This study, for the first time, characterized the microbial community composition and metabolic capacity in QTP high-elevation locations with 4555 m, confirming that QTP is a vast and valuable resource pool, in which many microorganisms can be used to develop new bioactive substances and new antibiotics to which pathogenic microorganisms have not yet developed resistance.}, } @article {pmid36401832, year = {2023}, author = {Zhao, F and Ma, T and Zhang, X and Zhao, Q and Zhu, K and Cao, J and Liu, Z and Shen, X and Li, C}, title = {Holothuria leucospilota Polysaccharides Improve Immunity and the Gut Microbiota in Cyclophosphamide-Treated Immunosuppressed Mice.}, journal = {Molecular nutrition & food research}, volume = {67}, number = {8}, pages = {e2200317}, doi = {10.1002/mnfr.202200317}, pmid = {36401832}, issn = {1613-4133}, mesh = {Mice ; Female ; Animals ; *Holothuria ; *Gastrointestinal Microbiome ; Cyclophosphamide/adverse effects ; Immunosuppressive Agents ; Polysaccharides/chemistry ; Immunologic Factors ; }, abstract = {SCOPE: Immunosuppression is one of the major risk factors for a series of diseases, such as tumor, rheumatoid arthritis, and microbial infection. Various natural products have attracted wide attention due to their immunomodulatory activities. Herein, the study investigates the regulation of Holothuria leucospilota polysaccharides (HLP) in immunosuppressed mice.

METHODS AND RESULTS: Eight-week-old female BALB/c mice are injected intraperitoneally with cyclophosphamide (80 mg kg[-1] body weight day[-1]) to establish the immunosuppressive model. After 12 days of HLP treatment, the immune organ indexes, serum cytokines, and immunoglobulin levels are significantly increased in immunosuppressed mice (p < 0.05). Real-time fluorescent quantitative polymerase chain reaction and western blotting analysis find that HLP improves the immune factors, T-cell markers, and Toll-like receptors (TLR) pathway-related proteins expression. Simultaneously, HLP significantly increases the short-chain fatty acids concentration and regulates the gut microbiota composition (p < 0.05). Furthermore, the metagenomics analysis shows that HLP increases the levels of functional genes involved in amino acid metabolism, carbohydrate metabolism, and growth activity of the gut microbiota.

CONCLUSION: HLP intervention improves the mice's immune function, and the beneficial effects are closely associated with intestinal homeostasis regulation and TLR pathway activation. This study suggests the potential for HLP as prebiotics in novel immunopotentiators development.}, } @article {pmid36401059, year = {2023}, author = {Gao, Y and Wang, H and Hu, Y and Li, J and Xu, W and Zhao, L and Su, X and Han, J and Li, T and Fang, X and Liu, L}, title = {Whole-genome metagenomic analysis of the oral microbiota in patients with obstructive sleep apnea.}, journal = {Sleep & breathing = Schlaf & Atmung}, volume = {27}, number = {4}, pages = {1383-1398}, pmid = {36401059}, issn = {1522-1709}, support = {QNC19054//Youth Program for Military Medicine of Chinese PLA General Hospital/ ; 19BJZ34//Military Health Care Project/ ; LB20211A010013//Army Equipment Construction Applied Research Project/ ; }, mesh = {Humans ; Novobiocin ; *Sleep Apnea, Obstructive/diagnosis/therapy ; Cholesterol, LDL ; Lipids ; Continuous Positive Airway Pressure ; *Microbiota/genetics ; }, abstract = {PURPOSE: The oral microbiota is closely associated with systemic health, but few studies have investigated the oral microbiota in patients with obstructive sleep apnea (OSA). This study aimed to identify the variation of oral microbiota among patients with severe OSA, and the change of oral microbiota after treatment with continuous positive airway pressure (CPAP).

METHODS: Participants were enrolled in the study from November 2020 to August 2021. Sleep parameters using full nocturnal polysomnography (PSG) were collected on healthy controls, patients with severe OSA, and patients with severe OSA after CPAP treatment for 3 months. Oral samples were also collected by rubbing disposable medical sterile swabs on the buccal mucosa. Routine blood tests and biochemical indicators were measured using the fully automated biochemical analyzer. Oral microbial composition of oral samples were determined using whole-genome metagenomic analysis in all participants. Correlations were analyzed between the oral microbiota and blood lipids.

RESULTS: Study enrollment included 14 participants, 7 healthy controls and 7 patients with severe OSA. At the species level, the relative abundances of Prevotella, Alloprevotella, Bacteroides, Veillonella_tobetsuensis, Candidatus saccharimonas, and Leptotrichia in the groups with severe OSA were significantly lower than those in the healthy controls (P both < 0.05). The abundances of Capnocytophaga, Veillonella, Bacillus_anthracis, Eikenella, and Kingella were significantly higher whereas the abundances of Gordonia and Streptococcus were significantly lower in the group with severe OSA compared to the severe OSA-CPAP group (P < 0.05 for both). According to the Kyoto Encyclopedia of Genes and Genomes (KEGG), 4 pathways changed in the group with severe OSA compared with healthy controls (P both < 0.05). Pathways related to Novobiocin biosynthesis, 2-Oxocarboxylic acid metabolism, and Histidine metabolism were enriched in the patients with severe OSA. Nine pathways showed significant differences with regard to the relative abundances of phenylalanine metabolism; alanine, aspartate, and glutamate metabolism; one carbon pool by folate; monobactam biosynthesis; 2-oxocarboxylic acid metabolism; arginine biosynthesis and vitamin B6 metabolism; novobiocin biosynthesis; and arginine and proline metabolism, which were significantly higher in the group with severe OSA compared to the severe OSA-CPAP group (P both < 0.05). The Spearman correlation analysis between blood lipid parameters and oral microbiota components showed that negative correlations were observed between total cholesterol and Streptomyces (r =  - 0.893, P = 0.007), and high-density lipoprotein cholesterol (HDL-C) and Gordonia (r = - 0.821, P = 0.023); positive correlations were observed between HDL-C and Candidatus saccharimonas (r = 0.929, P = 0.003), and low-density lipoprotein cholesterol (LDL-C) and Capnocytophaga (r = 0.893, P = 0.007).

CONCLUSION: There was an apparent discrepancy of the oral microbiota and metabolic pathways between the group with severe OSA and controls, and CPAP significantly changed oral microbial abundance and metabolic pathways in patients with severe OSA. Correlation analysis showed that these oral bacteria were strongly correlated with the blood lipids level.}, } @article {pmid36400919, year = {2022}, author = {Scorrano, G and Nielsen, SH and Vetro, DL and Sawafuji, R and Mackie, M and Margaryan, A and Fotakis, AK and Martínez-Labarga, C and Fabbri, PF and Allentoft, ME and Carra, M and Martini, F and Rickards, O and Olsen, JV and Pedersen, MW and Cappellini, E and Sikora, M}, title = {Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1262}, pmid = {36400919}, issn = {2399-3642}, mesh = {Humans ; Animals ; *Proteomics ; Dental Calculus ; Diet ; Genomics ; *Microbiota/genetics ; }, abstract = {Recent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and genetic diversity of our species. Here we present a multi-omics study, integrating metagenomic and proteomic analyses of dental calculus, and human ancient DNA analysis of the petrous bones of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified Villabruna cluster. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analysis of dental calculus showed a diet rich in animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of this approach in the study of prehistoric humans and will enable future research to reach a more holistic understanding of the population dynamics and ecology.}, } @article {pmid36400841, year = {2022}, author = {Lin, Q and Xavier, BB and Alako, BTF and Mitchell, AL and Rajakani, SG and Glupczynski, Y and Finn, RD and Cochrane, G and Malhotra-Kumar, S}, title = {Screening of global microbiomes implies ecological boundaries impacting the distribution and dissemination of clinically relevant antimicrobial resistance genes.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1217}, pmid = {36400841}, issn = {2399-3642}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Bayes Theorem ; *Microbiota/genetics ; Genes, Bacterial ; }, abstract = {Understanding the myriad pathways by which antimicrobial-resistance genes (ARGs) spread across biomes is necessary to counteract the global menace of antimicrobial resistance. We screened 17939 assembled metagenomic samples covering 21 biomes, differing in sequencing quality and depth, unevenly across 46 countries, 6 continents, and 14 years (2005-2019) for clinically crucial ARGs, mobile colistin resistance (mcr), carbapenem resistance (CR), and (extended-spectrum) beta-lactamase (ESBL and BL) genes. These ARGs were most frequent in human gut, oral and skin biomes, followed by anthropogenic (wastewater, bioreactor, compost, food), and natural biomes (freshwater, marine, sediment). Mcr-9 was the most prevalent mcr gene, spatially and temporally; blaOXA-233 and blaTEM-1 were the most prevalent CR and BL/ESBL genes, but blaGES-2 and blaTEM-116 showed the widest distribution. Redundancy analysis and Bayesian analysis showed ARG distribution was non-random and best-explained by potential host genera and biomes, followed by collection year, anthropogenic factors and collection countries. Preferential ARG occurrence, and potential transmission, between characteristically similar biomes indicate strong ecological boundaries. Our results provide a high-resolution global map of ARG distribution and importantly, identify checkpoint biomes wherein interventions aimed at disrupting ARGs dissemination are likely to be most effective in reducing dissemination and in the long term, the ARG global burden.}, } @article {pmid36400799, year = {2022}, author = {Tong, Z and Zhou, X and Chu, Y and Zhang, T and Zhang, J and Zhao, X and Wang, Z and Ding, R and Meng, Q and Yu, J and Wang, J and Kang, Y}, title = {Implications of oral streptococcal bacteriophages in autism spectrum disorder.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {91}, pmid = {36400799}, issn = {2055-5008}, mesh = {Humans ; *Autism Spectrum Disorder/complications/microbiology ; *Streptococcus Phages ; *Gastrointestinal Microbiome ; Mouth/microbiology ; *Bacteriophages/genetics ; }, abstract = {Growing evidence suggests altered oral and gut microbiota in autism spectrum disorder (ASD), but little is known about the alterations and roles of phages, especially within the oral microbiota in ASD subjects. We enrolled ASD (n = 26) and neurotypical subjects (n = 26) with their oral hygiene controlled, and the metagenomes of both oral and fecal samples (n = 104) are shotgun-sequenced and compared. We observe extensive and diverse oral phageome comparable to that of the gut, and clear signals of mouth-to-gut phage strain transfer within individuals. However, the overall phageomes of the two sites are widely different and show even less similarity in the oral communities between ASD and control subjects. The ASD oral phageome exhibits significantly reduced abundance and alpha diversity, but the Streptococcal phages there are atypically enriched, often dominating the community. The over-representation of Streptococcal phages is accompanied by enriched oral Streptococcal virulence factors and Streptococcus bacteria, all exhibiting a positive correlation with the severity of ASD clinical manifestations. These changes are not observed in the parallel sampling of the gut flora, suggesting a previously unknown oral-specific association between the excessive Streptococcal phage enrichment and ASD pathogenesis. The findings provide new evidence for the independent microbiome-mouth-brain connection, deepen our understanding of how the growth dynamics of bacteriophages and oral microbiota contribute to ASD, and point to novel effective therapeutics.}, } @article {pmid36400152, year = {2023}, author = {Xi, C and Li, A and Lai, J and Huang, X and Zhang, P and Yan, S and Jiao, M and Huang, H and Hu, S}, title = {Brain-gut microbiota multimodal predictive model in patients with bipolar depression.}, journal = {Journal of affective disorders}, volume = {323}, number = {}, pages = {140-152}, doi = {10.1016/j.jad.2022.11.026}, pmid = {36400152}, issn = {1573-2517}, mesh = {Humans ; *Bipolar Disorder/diagnostic imaging/drug therapy ; Quetiapine Fumarate/therapeutic use ; *Gastrointestinal Microbiome ; Brain/diagnostic imaging ; Gray Matter ; Magnetic Resonance Imaging/methods ; }, abstract = {BACKGROUND: The "microbiota-gut-brain axis" which bridges the brain and gut microbiota is involved in the pathological mechanisms of bipolar disorder (BD), but rare is known about the exact association patterns and the potential for clinical diagnosis and treatment outcome prediction.

METHODS: At baseline, fecal samples and resting-state MRI data were collected from 103 BD depression patients and 39 healthy controls (HCs) for metagenomic sequencing and network-based functional connectivity (FC), grey matter volume (GMV) analyses. All patients then received 4-weeks quetiapine treatment and were further classified as responders and non-responders. Based on pre-treatment datasets, the correlation networks were established between gut microbiota and neuroimaging measures and the multimodal kernal combination support vector machine (SVM) classifiers were constructed to distinguish BD patients from HCs, and quetiapine responders from non-responders.

RESULTS: The multi-modal pre-treatment characteristics of quetiapine responders, were closer to the HCs compared to non-responders. And the correlation network analyses found the substantial correlations existed in HC between the Anaerotruncus_ unclassified，Porphyromonas_asaccharolytica，Actinomyces_graevenitzii et al. and the functional connectomes involved default mode network (DMN),somatomotor (SM), visual, limbic and basal ganglia networks were disrupted in BD. Moreover, in terms of the multimodal classifier, it reached optimized area under curve (AUC-ROC) at 0.9517 when classified BD from HC, and also acquired 0.8292 discriminating quetiapine responders from non-responders, which consistently better than even using the best unique modality.

LIMITATIONS: Lack post-treatment and external validation datasets; size of HCs is modest.

CONCLUSIONS: Multi-modalities of combining pre-treatment gut microbiota with neuroimaging endophenotypes might be a superior approach for accurate diagnosis and quetiapine efficacy prediction in BD.}, } @article {pmid36399503, year = {2023}, author = {Zheng, J and Hu, B and Zhang, X and Ge, Q and Yan, Y and Akresi, J and Piyush, V and Huang, L and Yin, Y}, title = {dbCAN-seq update: CAZyme gene clusters and substrates in microbiomes.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D557-D563}, pmid = {36399503}, issn = {1362-4962}, support = {R01 GM140370/GM/NIGMS NIH HHS/United States ; R21 AI171952/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Humans ; Carbohydrates ; Metagenome/genetics ; *Microbiota/genetics ; Multigene Family ; Polysaccharides/metabolism ; Enzymes/genetics ; Bacteria/enzymology ; Environmental Microbiology ; }, abstract = {Carbohydrate Active EnZymes (CAZymes) are significantly important for microbial communities to thrive in carbohydrate rich environments such as animal guts, agricultural soils, forest floors, and ocean sediments. Since 2017, microbiome sequencing and assembly have produced numerous metagenome assembled genomes (MAGs). We have updated our dbCAN-seq database (https://bcb.unl.edu/dbCAN_seq) to include the following new data and features: (i) ∼498 000 CAZymes and ∼169 000 CAZyme gene clusters (CGCs) from 9421 MAGs of four ecological (human gut, human oral, cow rumen, and marine) environments; (ii) Glycan substrates for 41 447 (24.54%) CGCs inferred by two novel approaches (dbCAN-PUL homology search and eCAMI subfamily majority voting) (the two approaches agreed on 4183 CGCs for substrate assignments); (iii) A redesigned CGC page to include the graphical display of CGC gene compositions, the alignment of query CGC and subject PUL (polysaccharide utilization loci) of dbCAN-PUL, and the eCAMI subfamily table to support the predicted substrates; (iv) A statistics page to organize all the data for easy CGC access according to substrates and taxonomic phyla; and (v) A batch download page. In summary, this updated dbCAN-seq database highlights glycan substrates predicted for CGCs from microbiomes. Future work will implement the substrate prediction function in our dbCAN2 web server.}, } @article {pmid36399496, year = {2023}, author = {Terlouw, BR and Blin, K and Navarro-Muñoz, JC and Avalon, NE and Chevrette, MG and Egbert, S and Lee, S and Meijer, D and Recchia, MJJ and Reitz, ZL and van Santen, JA and Selem-Mojica, N and Tørring, T and Zaroubi, L and Alanjary, M and Aleti, G and Aguilar, C and Al-Salihi, SAA and Augustijn, HE and Avelar-Rivas, JA and Avitia-Domínguez, LA and Barona-Gómez, F and Bernaldo-Agüero, J and Bielinski, VA and Biermann, F and Booth, TJ and Carrion Bravo, VJ and Castelo-Branco, R and Chagas, FO and Cruz-Morales, P and Du, C and Duncan, KR and Gavriilidou, A and Gayrard, D and Gutiérrez-García, K and Haslinger, K and Helfrich, EJN and van der Hooft, JJJ and Jati, AP and Kalkreuter, E and Kalyvas, N and Kang, KB and Kautsar, S and Kim, W and Kunjapur, AM and Li, YX and Lin, GM and Loureiro, C and Louwen, JJR and Louwen, NLL and Lund, G and Parra, J and Philmus, B and Pourmohsenin, B and Pronk, LJU and Rego, A and Rex, DAB and Robinson, S and Rosas-Becerra, LR and Roxborough, ET and Schorn, MA and Scobie, DJ and Singh, KS and Sokolova, N and Tang, X and Udwary, D and Vigneshwari, A and Vind, K and Vromans, SPJM and Waschulin, V and Williams, SE and Winter, JM and Witte, TE and Xie, H and Yang, D and Yu, J and Zdouc, M and Zhong, Z and Collemare, J and Linington, RG and Weber, T and Medema, MH}, title = {MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D603-D610}, pmid = {36399496}, issn = {1362-4962}, support = {F32 AT011475/AT/NCCIH NIH HHS/United States ; R01 AI155694/AI/NIAID NIH HHS/United States ; U24 AT010811/AT/NCCIH NIH HHS/United States ; }, mesh = {*Genomics ; *Genome ; Multigene Family ; Biosynthetic Pathways/genetics ; }, abstract = {With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.}, } @article {pmid36398862, year = {2022}, author = {Fouladi, F and Bulik-Sullivan, EC and Glenny, EM and Thornton, LM and Reed, KK and Thomas, S and Kleiman, S and Watters, A and Oakes, J and Huh, EY and Tang, Q and Liu, J and Djukic, Z and Harper, L and Trillo-Ordoñez, Y and Sun, S and Blakely, I and Mehler, PS and Fodor, AA and Tarantino, LM and Bulik, CM and Carroll, IM}, title = {Reproducible changes in the anorexia nervosa gut microbiota following inpatient therapy remain distinct from non-eating disorder controls.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2143217}, pmid = {36398862}, issn = {1949-0984}, support = {R01 MH119084/MH/NIMH NIH HHS/United States ; R01 MH105684/MH/NIMH NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; R01 MH118278/MH/NIMH NIH HHS/United States ; R01 MH120170/MH/NIMH NIH HHS/United States ; R01 MH124871/MH/NIMH NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; T32 DK007737/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Anorexia Nervosa/therapy ; Inpatients ; Feces ; *Microbiota ; }, abstract = {The composition of the gut microbiota in patients with anorexia nervosa (AN), and the ability of this microbial community to influence the host, remains uncertain. To achieve a broader understanding of the role of the intestinal microbiota in patients with AN, we collected fecal samples before and following clinical treatment at two geographically distinct eating disorder units (Center of Excellence for Eating Disorders [UNC-CH] and ACUTE Center for Eating Disorders [Denver Health]). Gut microbiotas were characterized in patients with AN, before and after inpatient treatment, and in non-eating disorder (non-ED) controls using shotgun metagenomic sequencing. The impact of inpatient treatment on the AN gut microbiota was remarkably consistent between eating disorder units. Although weight in patients with AN showed improvements, AN microbiotas post-treatment remained distinct from non-ED controls. Additionally, AN gut microbiotas prior to treatment exhibited more fermentation pathways and a lower ability to degrade carbohydrates than non-ED controls. As the intestinal microbiota can influence nutrient metabolism, our data highlight the complex microbial communities in patients with AN as an element needing further attention post inpatient treatment. Additionally, this study defines the effects of renourishment on the AN gut microbiota and serves as a platform to develop precision nutrition approaches to potentially mitigate impediments to recovery.}, } @article {pmid36394327, year = {2022}, author = {Mann, E and Shekarriz, S and Surette, MG}, title = {Human Gut Metagenomes Encode Diverse GH156 Sialidases.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {23}, pages = {e0175522}, pmid = {36394327}, issn = {1098-5336}, mesh = {Humans ; Glycoside Hydrolases/genetics ; *Metagenome ; *Neuraminidase/genetics/metabolism ; Polysaccharides ; Sialic Acids/metabolism ; Gastrointestinal Microbiome ; }, abstract = {The intestinal lining is protected by a mucous barrier composed predominantly of complex carbohydrates. Gut microbes employ diverse glycoside hydrolases (GHs) to liberate mucosal sugars as a nutrient source to facilitate host colonization. Intensive catabolism of mucosal glycans, however, may contribute to barrier erosion, pathogen encroachment, and inflammation. Sialic acid is an acidic sugar featured at terminal positions of host glycans. Characterized sialidases from the microbiome belong to the GH33 family, according to CAZy (Carbohydrate-Active enZYmes Database). In 2018 a functional metagenomics screen using thermal spring DNA uncovered the founding member of the GH156 sialidase family, the presence of which has yet to be reported in the context of the human microbiome. A subset of GH156 sequences from the CAZy database containing key sialidase residues was used to build a hidden Markov model. HMMsearch against public databases revealed ~10× more putative GH156 sialidases than currently cataloged by CAZy. Represented phyla include Bacteroidota, Verrucomicrobiota, and Firmicutes_A from human microbiomes, all of which play notable roles in carbohydrate fermentation. Analyses of metagenomic data sets revealed that GH156s are frequently encoded in metagenomes, with a greater variety and abundance of GH156 genes observed in traditional hunter-gatherer or agriculturalist societies than in industrialized societies, particularly relative to individuals with inflammatory bowel disease (IBD). Nineteen GH156s were recombinantly expressed and assayed for sialidase activity. The five GH156 sialidases identified here share limited sequence identity to each other or the founding GH156 family member and are representative of a large subset of the family. IMPORTANCE Sialic acids occupy terminal positions of human glycans where they act as receptors for microbes, toxins, and immune signaling molecules. Microbial enzymes that remove sialic acids, sialidases, are abundant in the human microbiome where they may contribute to shaping the microbiota community structure or contribute to pathology. Furthermore, sialidases have proven to hold therapeutic potential for cancer therapy. Here, we examined the sequence space of a sialidase family of enzymes, GH156, previously unknown in the human gut environment. Our analyses suggest that human populations with disparate dietary practices harbor distinct varieties and abundances of GH156-encoding genes. Furthermore, we demonstrate the sialidase activity of 5 gut-derived GH156s. These results expand the diversity of sialidases that may contribute to host glycan degradation, and these sequences may have biotechnological or clinical utility.}, } @article {pmid36394321, year = {2022}, author = {Shetty, SA and Stege, PB and Hordijk, J and Gijsbers, E and Dierikx, CM and van Duijkeren, E and Franz, E and Willems, RJL and Paganelli, FL and Fuentes, S}, title = {Species-Specific Patterns of Gut Metabolic Modules in Dutch Individuals with Different Dietary Habits.}, journal = {mSphere}, volume = {7}, number = {6}, pages = {e0051222}, pmid = {36394321}, issn = {2379-5042}, mesh = {Adult ; Humans ; *Diet, Vegetarian ; Diet ; Diet, Vegan ; *Microbiota ; Feeding Behavior ; }, abstract = {Diet is an important determinant of the human gut microbiome. Here, we analyzed fecal metagenomes of Dutch adults following omnivorous, pescatarian, vegan, and vegetarian diets. We compared the taxonomic composition of individuals from our study with publicly available gut metagenomes from westernized and non-westernized societies. We observed that, despite long-term transition to diets rich in plant fibers (vegan or vegetarian), the microbiomes of these were typical of westernized populations, and similar in composition to omnivores. Although there were no major differences in metabolic modules, we identified differences in the species that contributed to particular functions, such as carbohydrate degradation and short-chain fatty acid metabolism. Overall, this study shows functional redundancy of the microbiomes among westernized populations, which is independent of long-term individual dietary habits. IMPORTANCE Diet is an important modulator of the human gut microbiome, which is susceptible to increased consumption of plant fibers in vegan or vegetarian lifestyles. To investigate this, we compared the gut microbiome of Dutch adults following omnivorous, pescatarian, vegan and vegetarian diets. We did not observe major differences in the gut microbiome composition and function between individuals with different dietary habits. However, we observed differences in the species that contribute to the core functions of the gut microbiome. Our study thus emphasizes the need to better understand the species-specific functional changes associated with dietary habits in the human gut microbiome.}, } @article {pmid36394280, year = {2022}, author = {Thompson, KN and Oulhote, Y and Weihe, P and Wilkinson, JE and Ma, S and Zhong, H and Li, J and Kristiansen, K and Huttenhower, C and Grandjean, P}, title = {Effects of Lifetime Exposures to Environmental Contaminants on the Adult Gut Microbiome.}, journal = {Environmental science & technology}, volume = {56}, number = {23}, pages = {16985-16995}, doi = {10.1021/acs.est.2c03185}, pmid = {36394280}, issn = {1520-5851}, mesh = {Adult ; Humans ; *Gastrointestinal Microbiome ; *Fluorocarbons ; *Environmental Pollutants/analysis ; *Polychlorinated Biphenyls/analysis ; *Hydrocarbons, Chlorinated ; *Mercury ; Hazardous Substances ; }, abstract = {Emerging experimental evidence indicates that toxicant-induced alterations in gut microbiota composition and activity may affect host homeostasis. However, data from human studies are scarce; to our knowledge, no previous studies have quantified the association of lifetime exposure to environmental chemicals, across multiple time points, with the composition of the adult gut microbiome. Here we studied 124 individuals born in the Faroe Islands in 1986-1987 who were followed approximately every seven years from birth through age 28 years. Organochlorine compounds, including polychlorinated biphenyls (PCBs) and pesticides, perfluoroalkyl substances (PFAS), and mercury (Hg), were measured in cord blood and longitudinally in participants' blood. At age 28, the gut microbiome was assessed using shotgun metagenomic sequencing. Historical contaminant exposures had little direct effect on the adult gut microbiome, while a small number of fastidious anaerobes were weakly linked to recent PFAS/PFOS exposures at age 28. In this cohort, our findings suggest no lasting effects of early life exposures on adult gut microbial composition, but proximal exposures may contribute to gut microbiome alterations. The methods developed and used for this investigation may help in future identification of small but lasting impacts of environmental toxicant exposure on the gut microbiome.}, } @article {pmid36389176, year = {2022}, author = {Chen, H and Tang, N and Ye, Q and Yu, X and Yang, R and Cheng, H and Zhang, G and Zhou, X}, title = {Alternation of the gut microbiota in metabolically healthy obesity: An integrated multiomics analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1012028}, pmid = {36389176}, issn = {2235-2988}, mesh = {Metagenomics ; Bacteroides ; *Gastrointestinal Microbiome ; Humans ; Obesity/complications ; *Obesity, Metabolically Benign/complications ; Mice ; Animals ; }, abstract = {BACKGROUND: Although the gut microbiota may be involved in obesity onset and progression, the exact association of the gut microbiota in metabolically healthy obesity (MHO) remains largely unknown.

METHODS: An integrated paired-sample metagenomic analysis was conducted to investigate the gut microbial network and biomarkers of microbial species from the MHO and healthy non-obese subjects in the GMrepo database. Further explorations were performed in the MHO mice model using a multiomics analysis to detect changes in the composition and function of the intestinal microbiome and associated metabolites.

RESULTS: In the human study, 314 matched metagenomic data were qualified for the final analysis. We identified seven significantly changed species possibly involved in MHO pathogenesis (MHO-enriched: Bacteroides vulgatus, Megamonas sp; MHO-depleted: Butyrivibrio crossotus, Faecalibacterium prausnitzii, Bacteroides cellulosilyticus; Eubacterium siraeum; Bacteroides massiliensis). In the murine study, we found 79 significantly-changed species which may have possible associations with the MHO phenotype. The depletion of Bacteroides cellulosilyticus was commonly recognized in the human and murine MHO phenotype. Consistent with the metagenomic data, liquid chromatography-mass spectrometry (LC/MS) revealed significantly changed gut metabolites, which may promote MHO pathogenesis by altering the amino acids and lipid metabolic pathways. In the microbe-metabolites interaction analysis, we identified certain fatty acids (Dodecanedioic acid, Arachidic Acid, Mevalonic acid, etc.) that were significantly correlated with the MHO-enriched or depleted species.

CONCLUSION: This study provides insights into identifying specific microbes and metabolites that may involve in the development of obesity without metabolic disorders. Future modalities for MHO intervention may be further validated by targeting these bacteria and metabolites.}, } @article {pmid36389165, year = {2022}, author = {Li, Z and Yu, X and Guo, H and Lee, T and Hu, J}, title = {A maximum-type microbial differential abundance test with application to high-dimensional microbiome data analyses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {988717}, pmid = {36389165}, issn = {2235-2988}, support = {U54 MD000538/MD/NIMHD NIH HHS/United States ; R33 AG057382/AG/NIA NIH HHS/United States ; }, mesh = {*Data Analysis ; *Microbiota ; High-Throughput Nucleotide Sequencing ; Computer Simulation ; }, abstract = {BACKGROUND: High-throughput metagenomic sequencing technologies have shown prominent advantages over traditional pathogen detection methods, bringing great potential in clinical pathogen diagnosis and treatment of infectious diseases. Nevertheless, how to accurately detect the difference in microbiome profiles between treatment or disease conditions remains computationally challenging.

RESULTS: In this study, we propose a novel test for identifying the difference between two high-dimensional microbiome abundance data matrices based on the centered log-ratio transformation of the microbiome compositions. The test p-value can be calculated directly with a closed-form solution from the derived asymptotic null distribution. We also investigate the asymptotic statistical power against sparse alternatives that are typically encountered in microbiome studies. The proposed test is maximum-type equal-covariance-assumption-free (MECAF), making it widely applicable to studies that compare microbiome compositions between conditions. Our simulation studies demonstrated that the proposed MECAF test achieves more desirable power than competing methods while having the type I error rate well controlled under various scenarios. The usefulness of the proposed test is further illustrated with two real microbiome data analyses. The source code of the proposed method is freely available at https://github.com/Jiyuan-NYU-Langone/MECAF.

CONCLUSIONS: MECAF is a flexible differential abundance test and achieves statistical efficiency in analyzing high-throughput microbiome data. The proposed new method will allow us to efficiently discover shifts in microbiome abundances between disease and treatment conditions, broadening our understanding of the disease and ultimately improving clinical diagnosis and treatment.}, } @article {pmid36380056, year = {2022}, author = {Zhang, C and Shi, Y and Burch, M and Olthoff, B and Ericsson, AC and Franklin, CL}, title = {Transfer efficiency and impact on disease phenotype of differing methods of gut microbiota transfer.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {19621}, pmid = {36380056}, issn = {2045-2322}, support = {U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Mice ; Animals ; *Gastrointestinal Microbiome/genetics ; Fecal Microbiota Transplantation/methods ; *Colitis/chemically induced/genetics ; Phenotype ; *Microbiota ; Dextran Sulfate/adverse effects ; Disease Models, Animal ; Mice, Inbred C57BL ; }, abstract = {To test causal relationships between complex gut microbiota (GM) and host outcomes, researchers frequently transfer GM between donor and recipient mice via embryo transfer (ET) rederivation, cross-fostering (CF), and co-housing. In this study, we assess the influence of the transfer method and the differences in baseline donor and recipient microbiota richness, on transfer efficiency. Additionally, recipient mice were subjected to DSS-induced chronic colitis to determine whether disease severity was affected by GM transfer efficiency or features within the GM. We found that the recipient's genetic background, the baseline richness of donor and recipient GM, and the transfer method all influenced the GM transfer efficiency. Recipient genetic background and GM both had significant effects on DSS colitis severity and, unexpectedly, the transfer method was strongly associated with differential disease severity regardless of the other factors.}, } @article {pmid36378489, year = {2022}, author = {Gupta, VK and Bakshi, U and Chang, D and Lee, AR and Davis, JM and Chandrasekaran, S and Jin, YS and Freeman, MF and Sung, J}, title = {TaxiBGC: a Taxonomy-Guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0092522}, pmid = {36378489}, issn = {2379-5077}, support = {R35 GM133475/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Metagenome/genetics ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Computational Biology ; Multigene Family/genetics ; }, abstract = {Biosynthetic gene clusters (BGCs) in microbial genomes encode bioactive secondary metabolites (SMs), which can play important roles in microbe-microbe and host-microbe interactions. Given the biological significance of SMs and the current profound interest in the metabolic functions of microbiomes, the unbiased identification of BGCs from high-throughput metagenomic data could offer novel insights into the complex chemical ecology of microbial communities. Currently available tools for predicting BGCs from shotgun metagenomes have several limitations, including the need for computationally demanding read assembly, predicting a narrow breadth of BGC classes, and not providing the SM product. To overcome these limitations, we developed taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC), a command-line tool for predicting experimentally characterized BGCs (and inferring their known SMs) in metagenomes by first pinpointing the microbial species likely to harbor them. We benchmarked TaxiBGC on various simulated metagenomes, showing that our taxonomy-guided approach could predict BGCs with much-improved performance (mean F1 score, 0.56; mean PPV score, 0.80) compared with directly identifying BGCs by mapping sequencing reads onto the BGC genes (mean F1 score, 0.49; mean PPV score, 0.41). Next, by applying TaxiBGC on 2,650 metagenomes from the Human Microbiome Project and various case-control gut microbiome studies, we were able to associate BGCs (and their SMs) with different human body sites and with multiple diseases, including Crohn's disease and liver cirrhosis. In all, TaxiBGC provides an in silico platform to predict experimentally characterized BGCs and their SM production potential in metagenomic data while demonstrating important advantages over existing techniques. IMPORTANCE Currently available bioinformatics tools to identify BGCs from metagenomic sequencing data are limited in their predictive capability or ease of use to even computationally oriented researchers. We present an automated computational pipeline called TaxiBGC, which predicts experimentally characterized BGCs (and infers their known SMs) in shotgun metagenomes by first considering the microbial species source. Through rigorous benchmarking techniques on simulated metagenomes, we show that TaxiBGC provides a significant advantage over existing methods. When demonstrating TaxiBGC on thousands of human microbiome samples, we associate BGCs encoding bacteriocins with different human body sites and diseases, thereby elucidating a possible novel role of this antibiotic class in maintaining the stability of microbial ecosystems throughout the human body. Furthermore, we report for the first time gut microbial BGC associations shared among multiple pathologies. Ultimately, we expect our tool to facilitate future investigations into the chemical ecology of microbial communities across diverse niches and pathologies.}, } @article {pmid36377936, year = {2022}, author = {Chen, J and Li, Z and Wang, X and Fan, B and Deng, F and D Yu, H and Ze, X and Zhu, L and Yin, Y and Chen, Y and Zhao, J and Yang, Y and Wang, X}, title = {Isomaltooligosaccharides Sustain the Growth of Prevotella Both In Vitro and in Animal Models.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0262121}, pmid = {36377936}, issn = {2165-0497}, mesh = {Humans ; Animals ; Mice ; Aged ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Feces/microbiology ; Prevotella/genetics ; Carbohydrates ; Models, Animal ; Starch ; }, abstract = {The human digestive tract is colonized by trillions of bacterial cells that play important roles in human health and diseases. It is well known that dietary habits are associated with human microbiota enterotypes. However, the factors that determine the enterotype still remain elusive. In this study, it was first examined, via in vitro batch fermentation, how different carbohydrates affect the Bacteroides and Prevotella enterotypes. Among the 11 substrates (fructo-, galacto-, xylo-, manno-, and isomalto-oligosaccharides [IMO] and lactulose, raffinose, starch, inulin [INU], mannitol, and xylitol) tested, IMO, INU, and starch were found to sustain the growth of Prevotella through batch fermentation. The development of the Prevotella and Bacteroides enterotypes was further simulated in chemostats using fecal samples. IMO coupled with faster dilution rates and lower pH were required to sustain the growth of Prevotella copri in the chemostat based on 16S rRNA gene and metagenomic sequencing. Meanwhile, starch with relatively lower dilution rates and higher pH was required to support the development of the Bacteroides enterotype. Amylo-α-1,6-glucosidase, pectin, and xylan lyases were the carbohydrate-active enzymes associated with the Prevotella enterotype. The Bacteroides enterotype was associated with more diversified carbohydrate-active enzymes. Consistently, since honey contains high isomaltose content, mice fed IMO and honey displayed an increased relative abundance of Prevotella in the colon. In conclusion, both in vitro systems and a mouse model were used to demonstrate that IMO maintains the Prevotella enterotype. This result provides insight into the nutritional requirements underlying gut enterotype formation. IMPORTANCE The Prevotella enterotype type is a human traditional enterotype with high dietary fiber intake, which is related to healthy ageing and Parkinson's disease development. Manipulations of the dwelled gut microbes by dietary isomalto-oligosaccharides efficiently sustained Prevotella type enterotypes, indicating that it can be used in the improvement of elderly health by increasing the gut transit time.}, } @article {pmid36377901, year = {2022}, author = {Wicaksono, WA and Egamberdieva, D and Berg, C and Mora, M and Kusstatscher, P and Cernava, T and Berg, G}, title = {Function-Based Rhizosphere Assembly along a Gradient of Desiccation in the Former Aral Sea.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0073922}, pmid = {36377901}, issn = {2379-5077}, mesh = {Humans ; *Rhizosphere ; Desiccation ; Bacteria/genetics ; Archaea/genetics ; *Microbiota/genetics ; Soil ; Plants ; }, abstract = {The desiccation of the Aral Sea represents one of the largest human-made environmental regional disasters. The salt- and toxin-enriched dried-out basin provides a natural laboratory for studying ecosystem functioning and rhizosphere assembly under extreme anthropogenic conditions. Here, we investigated the prokaryotic rhizosphere communities of the native pioneer plant Suaeda acuminata (C.A.Mey.) Moq. in comparison to bulk soil across a gradient of desiccation (5, 10, and 40 years) by metagenome and amplicon sequencing combined with quantitative PCR (qPCR) analyses. The rhizosphere effect was evident due to significantly higher bacterial abundances but less diversity in the rhizosphere compared to bulk soil. Interestingly, in the highest salinity (5 years of desiccation), rhizosphere functions were mainly provided by archaeal communities. Along the desiccation gradient, we observed a significant change in the rhizosphere microbiota, which was reflected by (i) a decreasing archaeon-bacterium ratio, (ii) replacement of halophilic archaea by specific plant-associated bacteria, i.e., Alphaproteobacteria and Actinobacteria, and (iii) an adaptation of specific, potentially plant-beneficial biosynthetic pathways. In general, both bacteria and archaea were found to be involved in carbon cycling and fixation, as well as methane and nitrogen metabolism. Analysis of metagenome-assembled genomes (MAGs) showed specific signatures for production of osmoprotectants, assimilatory nitrate reduction, and transport system induction. Our results provide evidence that rhizosphere assembly by cofiltering specific taxa with distinct traits is a mechanism which allows plants to thrive under extreme conditions. Overall, our findings highlight a function-based rhizosphere assembly, the importance of plant-microbe interactions in salinated soils, and their exploitation potential for ecosystem restoration approaches. IMPORTANCE The desertification of the Aral Sea basin in Uzbekistan and Kazakhstan represents one of the most serious anthropogenic environmental disasters of the last century. Since the 1960s, the world's fourth-largest inland body of water has been constantly shrinking, which has resulted in an extreme increase of salinity accompanied by accumulation of many hazardous and carcinogenic substances, as well as heavy metals, in the dried-out basin. Here, we investigated bacterial and archaeal communities in the rhizosphere of pioneer plants by combining classic molecular methods with amplicon sequencing as well as metagenomics for functional insights. By implementing a desiccation gradient, we observed (i) remarkable differences in the archaeon-bacterium ratio of plant rhizosphere samples, (ii) replacement of archaeal indicator taxa during succession, and (iii) the presence of specific, potentially plant-beneficial biosynthetic pathways in archaea present during the early stages. In addition, our results provide hitherto-undescribed insights into the functional redundancy between plant-associated archaea and bacteria.}, } @article {pmid36377900, year = {2022}, author = {McGonigle, JM and Bernau, JA and Bowen, BB and Brazelton, WJ}, title = {Metabolic Potential of Microbial Communities in the Hypersaline Sediments of the Bonneville Salt Flats.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0084622}, pmid = {36377900}, issn = {2379-5077}, mesh = {*Calcium Sulfate/metabolism ; Bacteria/genetics ; Archaea/genetics ; Sodium Chloride/metabolism ; *Microbiota/genetics ; Sodium Chloride, Dietary/metabolism ; }, abstract = {The Bonneville Salt Flats (BSF) appear to be entirely desolate when viewed from above, but they host rich microbial communities just below the surface salt crust. In this study, we investigated the metabolic potential of the BSF microbial ecosystem. The predicted and measured metabolic activities provide new insights into the ecosystem functions of evaporite landscapes and are an important analog for potential subsurface microbial ecosystems on ancient and modern Mars. Hypersaline and evaporite systems have been investigated previously as astrobiological analogs for Mars and other salty celestial bodies, but these studies have generally focused on aquatic systems and cultivation-dependent approaches. Here, we present an ecosystem-level examination of metabolic pathways within the shallow subsurface of evaporites. We detected aerobic and anaerobic respiration as well as methanogenesis in BSF sediments. Metagenome-assembled genomes of diverse bacteria and archaea encode a remarkable diversity of metabolic pathways, including those associated with carbon fixation, carbon monoxide oxidation, acetogenesis, methanogenesis, sulfide oxidation, denitrification, and nitrogen fixation. These results demonstrate the potential for multiple energy sources and metabolic pathways in BSF and highlight the possibility for vibrant microbial ecosystems in the shallow subsurface of evaporites. IMPORTANCE The Bonneville Salt Flats is a unique ecosystem created from 10,000 years of desiccation and serves as an important natural laboratory for the investigation of the habitability of salty, halite, and gypsum-rich environments. Here, we show that gypsum-rich mineral deposits host a surprising diversity of organisms and appear to play a key role in stimulating the microbial cycling of sulfur and nitrogen compounds. This work highlights how diverse microbial communities within the shallow subsurface sediments are capable of maintaining an active and sustainable ecosystem, even though the surface salt crust appears to be completely devoid of life.}, } @article {pmid36376937, year = {2022}, author = {Liang, X and Fu, Y and Cao, WT and Wang, Z and Zhang, K and Jiang, Z and Jia, X and Liu, CY and Lin, HR and Zhong, H and Miao, Z and Gou, W and Shuai, M and Huang, Y and Chen, S and Zhang, B and Chen, YM and Zheng, JS}, title = {Gut microbiome, cognitive function and brain structure: a multi-omics integration analysis.}, journal = {Translational neurodegeneration}, volume = {11}, number = {1}, pages = {49}, pmid = {36376937}, issn = {2047-9158}, support = {R01 HD038700/HD/NICHD NIH HHS/United States ; R24 HD050924/HD/NICHD NIH HHS/United States ; R01 HD030880/HD/NICHD NIH HHS/United States ; R01-DK104371/DK/NIDDK NIH HHS/United States ; R01-HD30880/NH/NIH HHS/United States ; P30 AG066615/AG/NIA NIH HHS/United States ; R01-HD38700/NH/NIH HHS/United States ; R01 DK104371/DK/NIDDK NIH HHS/United States ; R01 AG065357/AG/NIA NIH HHS/United States ; DK056350/NH/NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; Case-Control Studies ; Cognition ; Brain/diagnostic imaging ; }, abstract = {BACKGROUND: Microbiome-gut-brain axis may be involved in the progression of age-related cognitive impairment and relevant brain structure changes, but evidence from large human cohorts is lacking. This study was aimed to investigate the associations of gut microbiome with cognitive impairment and brain structure based on multi-omics from three independent populations.

METHODS: We included 1430 participants from the Guangzhou Nutrition and Health Study (GNHS) with both gut microbiome and cognitive assessment data available as a discovery cohort, of whom 272 individuals provided fecal samples twice before cognitive assessment. We selected 208 individuals with baseline microbiome data for brain magnetic resonance imaging during the follow-up visit. Fecal 16S rRNA and shotgun metagenomic sequencing, targeted serum metabolomics, and cytokine measurements were performed in the GNHS. The validation analyses were conducted in an Alzheimer's disease case-control study (replication study 1, n = 90) and another community-based cohort (replication study 2, n = 1300) with cross-sectional dataset.

RESULTS: We found protective associations of specific gut microbial genera (Odoribacter, Butyricimonas, and Bacteroides) with cognitive impairment in both the discovery cohort and the replication study 1. Result of Bacteroides was further validated in the replication study 2. Odoribacter was positively associated with hippocampal volume (β, 0.16; 95% CI 0.06-0.26, P = 0.002), which might be mediated by acetic acids. Increased intra-individual alterations in gut microbial composition were found in participants with cognitive impairment. We also identified several serum metabolites and inflammation-associated metagenomic species and pathways linked to impaired cognition.

CONCLUSIONS: Our findings reveal that specific gut microbial features are closely associated with cognitive impairment and decreased hippocampal volume, which may play an important role in dementia development.}, } @article {pmid36376589, year = {2023}, author = {Chivian, D and Jungbluth, SP and Dehal, PS and Wood-Charlson, EM and Canon, RS and Allen, BH and Clark, MM and Gu, T and Land, ML and Price, GA and Riehl, WJ and Sneddon, MW and Sutormin, R and Zhang, Q and Cottingham, RW and Henry, CS and Arkin, AP}, title = {Metagenome-assembled genome extraction and analysis from microbiomes using KBase.}, journal = {Nature protocols}, volume = {18}, number = {1}, pages = {208-238}, pmid = {36376589}, issn = {1750-2799}, mesh = {*Metagenome ; Phylogeny ; Genome, Bacterial ; *Microbiota/genetics ; Bacteria/genetics ; Metagenomics ; }, abstract = {Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. To realize the hope of capturing Earth's microbial genetic complement and to facilitate the investigation of the functional roles of specific lineages in a given ecosystem, technologies that accelerate the recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high-quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). Overall, these steps take about a day to obtain extracted genomes when starting from smaller environmental shotgun read libraries, or up to about a week from larger libraries. In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAGs, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq and others. While portions of such capabilities are available individually from other resources, the combination of the intuitive usability, data interoperability and integration of tools in a freely available computational resource makes KBase a powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended with additional MAG recovery and analysis tools, via the KBase software development kit (SDK).}, } @article {pmid36376318, year = {2022}, author = {Wallen, ZD and Demirkan, A and Twa, G and Cohen, G and Dean, MN and Standaert, DG and Sampson, TR and Payami, H}, title = {Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6958}, pmid = {36376318}, issn = {2041-1723}, support = {R01 ES032440/ES/NIEHS NIH HHS/United States ; T32 NS095775/NS/NINDS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Parkinson Disease/genetics ; Dysbiosis/genetics ; Metagenomics/methods ; Metagenome/genetics ; }, abstract = {Parkinson's disease (PD) may start in the gut and spread to the brain. To investigate the role of gut microbiome, we conducted a large-scale study, at high taxonomic resolution, using uniform standardized methods from start to end. We enrolled 490 PD and 234 control individuals, conducted deep shotgun sequencing of fecal DNA, followed by metagenome-wide association studies requiring significance by two methods (ANCOM-BC and MaAsLin2) to declare disease association, network analysis to identify polymicrobial clusters, and functional profiling. Here we show that over 30% of species, genes and pathways tested have altered abundances in PD, depicting a widespread dysbiosis. PD-associated species form polymicrobial clusters that grow or shrink together, and some compete. PD microbiome is disease permissive, evidenced by overabundance of pathogens and immunogenic components, dysregulated neuroactive signaling, preponderance of molecules that induce alpha-synuclein pathology, and over-production of toxicants; with the reduction in anti-inflammatory and neuroprotective factors limiting the capacity to recover. We validate, in human PD, findings that were observed in experimental models; reconcile and resolve human PD microbiome literature; and provide a broad foundation with a wealth of concrete testable hypotheses to discern the role of the gut microbiome in PD.}, } @article {pmid36375448, year = {2023}, author = {Webster, MT and Beaurepaire, A and Neumann, P and Stolle, E}, title = {Population Genomics for Insect Conservation.}, journal = {Annual review of animal biosciences}, volume = {11}, number = {}, pages = {115-140}, doi = {10.1146/annurev-animal-122221-075025}, pmid = {36375448}, issn = {2165-8110}, mesh = {Animals ; Humans ; *Ecosystem ; *Conservation of Natural Resources/methods ; Metagenomics ; Endangered Species ; Biodiversity ; Insecta/genetics ; }, abstract = {Insects constitute vital components of ecosystems. There is alarming evidence for global declines in insect species diversity, abundance, and biomass caused by anthropogenic drivers such as habitat degradation or loss, agricultural practices, climate change, and environmental pollution. This raises important concerns about human food security and ecosystem functionality and calls for more research to assess insect population trends and identify threatened species and the causes of declines to inform conservation strategies. Analysis of genetic diversity is a powerful tool to address these goals, but so far animal conservation genetics research has focused strongly on endangered vertebrates, devoting less attention to invertebrates, such as insects, that constitute most biodiversity. Insects' shorter generation times and larger population sizes likely necessitate different analytical methods and management strategies. The availability of high-quality reference genome assemblies enables population genomics to address several key issues. These include precise inference of past demographic fluctuations and recent declines, measurement of genetic load levels, delineation of evolutionarily significant units and cryptic species, and analysis of genetic adaptation to stressors. This enables identification of populations that are particularly vulnerable to future threats, considering their potential to adapt and evolve. We review the application of population genomics to insect conservation and the outlook for averting insect declines.}, } @article {pmid36372753, year = {2022}, author = {Zhuang, SQ and Mao, YX and Deng, FC and Luo, YY and Shi, WY and Li, X and Cao, YQ and Xu, JC and Tang, S}, title = {[Comparative analysis of metagenomic and 16S rDNA sequencing in gut microbiota of healthy elderly].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {56}, number = {11}, pages = {1618-1624}, doi = {10.3760/cma.j.cn112150-20211222-01177}, pmid = {36372753}, issn = {0253-9624}, support = {DQGG0401//National Research Program for Key Issues in Air Pollution Control, China/ ; 2020YSRF_03//Young Scholar Scientific Research Foundation of National Institute of Environmental Health, China CDC/ ; }, mesh = {Male ; Female ; Humans ; Aged ; *Gastrointestinal Microbiome/genetics ; DNA, Ribosomal/genetics ; Feces ; Sequence Analysis, DNA ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Objective: To explore the differences in subsequent analysis between metagenomic and 16Sr DNA sequencing in compositionally characterizing gut microbiota of healthy elderly. Methods: By using a panel study design, five monthly repeated measurements were performed among 76 healthy older people in Jinan City, Shandong Province. Their fecal samples were collected, and genomic DNA was extracted and analyzed through metagenomic and 16Sr DNA sequencing to compare the composition and diversity of gut microbiota. The correlation between species abundance and α diversity was analyzed by Pearson correlation analysis, and the correlation between species abundance and β diversity was determined by Procrustes analysis. Results: The age of 76 participants was (65.07±2.75), and the body mass index was (25.03±2.40) kg/m[2]. There were 38 males and 38 females. A total of 345 fecal samples were obtained from five monthly repeated measurements. Compared with 16S rDNA sequencing, metagenomic sequencing showed more annotated species at each level. The difference in the number of two sequencing species increased with the decrease of the level. Although there were significant differences in species richness between the two sequencing methods. Their species richness was highly correlated at both phylum (r=0.88, P<0.001) and genus (r=0.77, P<0.001) levels. Bacteroidetes and Firmicutes were the common dominant species. Gut microbiota diversity analysis further showed that there was a significantly positive correlation between α diversity (r=0.70, P<0.001) and β diversities (M[2]=0.84, P<0.05) in the two groups. Conclusion: The annotation efficiency of metagenomic sequencing is much higher than that of 16S rDNA sequencing. The two sequencing methods are consistent in phylum abundance as well as α diversity.}, } @article {pmid36371463, year = {2022}, author = {Farda, B and Vaccarelli, I and Ercole, C and Djebaili, R and Del Gallo, M and Pellegrini, M}, title = {Exploring structure, microbiota, and metagenome functions of epigean and hypogean black deposits by microscopic, molecular and bioinformatic approaches.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {19405}, pmid = {36371463}, issn = {2045-2322}, mesh = {*Metagenome ; RNA, Ribosomal, 16S/genetics/metabolism ; Computational Biology ; *Microbiota/genetics ; Bacteria ; Phylogeny ; Archaea/genetics ; }, abstract = {This study revealed how Bacteria and Archaea communities and their metabolic functions differed between two groups of black deposits identified in gorge and cave environments. Scanning electron microscopy coupled with energy dispersive spectroscopy was used to analyse the presence of microbial biosignatures and the elemental composition of samples. Metabarcoding of the V3-V4 regions of 16S rRNA was used to investigate Bacteria and Archaea communities. Based on 16S rRNA sequencing results, PICRUSt software was used to predict metagenome functions. Micrographs showed that samples presented microbial biosignatures and microanalyses highlighted Mn concretions and layers on Al-Si surfaces. The 16S rRNA metabarcoding alpha-diversity metrics showed similar Simpson's and Shannon indices and different values of the Chao-1 index. The amplicon sequence variants (ASVs) analysis at the different taxonomic levels showed a diverse genera composition. However, the communities of all samples shared the presence of uncultured ASVs belonging to the Gemmatales family (Phylogenesis: Gemmataceae; Planctomycetes; Planctomycetota; Bacteria). The predicted metagenome functions analysis revealed diverse metabolic profiles of the Cave and Gorge groups. Genes coding for essential Mn metabolism were present in all samples. Overall, the findings on structure, microbiota, and predicted metagenome functions showed a similar microbial contribution to epigean and hypogean black deposits Mn metabolism.}, } @article {pmid36369227, year = {2022}, author = {Meslier, V and Quinquis, B and Da Silva, K and Plaza Oñate, F and Pons, N and Roume, H and Podar, M and Almeida, M}, title = {Benchmarking second and third-generation sequencing platforms for microbial metagenomics.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {694}, pmid = {36369227}, issn = {2052-4463}, support = {R01 DE024463/DE/NIDCR NIH HHS/United States ; }, mesh = {High-Throughput Nucleotide Sequencing/methods ; Metagenome ; *Metagenomics/methods ; *Microbiota/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Shotgun metagenomic sequencing is a common approach for studying the taxonomic diversity and metabolic potential of complex microbial communities. Current methods primarily use second generation short read sequencing, yet advances in third generation long read technologies provide opportunities to overcome some of the limitations of short read sequencing. Here, we compared seven platforms, encompassing second generation sequencers (Illumina HiSeq 300, MGI DNBSEQ-G400 and DNBSEQ-T7, ThermoFisher Ion GeneStudio S5 and Ion Proton P1) and third generation sequencers (Oxford Nanopore Technologies MinION R9 and Pacific Biosciences Sequel II). We constructed three uneven synthetic microbial communities composed of up to 87 genomic microbial strains DNAs per mock, spanning 29 bacterial and archaeal phyla, and representing the most complex and diverse synthetic communities used for sequencing technology comparisons. Our results demonstrate that third generation sequencing have advantages over second generation platforms in analyzing complex microbial communities, but require careful sequencing library preparation for optimal quantitative metagenomic analysis. Our sequencing data also provides a valuable resource for testing and benchmarking bioinformatics software for metagenomics.}, } @article {pmid36368924, year = {2022}, author = {Du, C and Zhou, X and Zhang, K and Huang, S and Wang, X and Zhou, S and Chen, Y}, title = {Inactivation of the MSTN gene expression changes the composition and function of the gut microbiome in sheep.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {273}, pmid = {36368924}, issn = {1471-2180}, mesh = {Sheep ; Male ; Female ; Animals ; *Myostatin/genetics ; *Gastrointestinal Microbiome ; Meat ; Gene Expression ; }, abstract = {BACKGROUND: Myostatin (MSTN) negatively regulates the muscle growth in animals and MSTN deficient sheep have been widely reported previously. The goal of this study was to explore how MSTN inactivation influences their gut microbiota composition and potential functions.

RESULTS: We compared the slaughter parameters and meat quality of 3 MSTN-edited male sheep and 3 wild-type male sheep, and analyzed the gut microbiome of the MSTN-edited sheep (8 female and 8 male sheep) and wild-type sheep (8 female and 8 male sheep) through metagenomic sequencing. The results showed that the body weight, carcass weight and eye muscle area of MSTN-edited sheep were significantly higher, but there were no significant differences in the meat quality indexes. At the microbial level, the alpha diversity was significantly higher in the MSTN-edited sheep (P < 0.05), and the microbial composition was significantly different by PCoA analysis in the MSTN-edited and wild-type sheep. The abundance of Firmicutes significantly increased and Bacteroidota significantly decreased in the MSTN-edited sheep. At genus level, the abundance of Flavonifractor, Subdoligranulum, Ruthenibacterium, Agathobaculum, Anaerotignum, Oribacterium and Lactobacillus were significantly increased in the MSTN-edited sheep (P < 0.05). Further analysis of functional differences was found that the carotenoid biosynthesis was significantly increased and the peroxisome, apoptosis, ferroptosis, N-glycan biosynthesis, thermogenesis, and adipocytokines pathways were decreased in the MSTN-edited sheep (P < 0.05). Moreover, carbohydrate-active enzymes (CAZymes) results certified the abundance of the GH13_39, GH4, GH137, GH71 and PL17 were upregulated, and the GT41 and CBM20 were downregulated in the MSTN-edited sheep (P < 0.05).

CONCLUSIONS: Our study suggested that MSTN inactivation remarkably influenced the composition and potential function of hindgut microbial communities of the sheep, and significantly promoted growth performance without affecting meat quality.}, } @article {pmid36368923, year = {2022}, author = {Rosenboom, I and Scheithauer, T and Friedrich, FC and Pörtner, S and Hollstein, L and Pust, MM and Sifakis, K and Wehrbein, T and Rosenhahn, B and Wiehlmann, L and Chhatwal, P and Tümmler, B and Davenport, CF}, title = {Wochenende - modular and flexible alignment-based shotgun metagenome analysis.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {748}, pmid = {36368923}, issn = {1471-2164}, mesh = {Humans ; *Metagenome ; Metagenomics/methods ; Software ; *Microbiota/genetics ; Genome, Human ; Sequence Analysis, DNA/methods ; Algorithms ; }, abstract = {BACKGROUND: Shotgun metagenome analysis provides a robust and verifiable method for comprehensive microbiome analysis of fungal, viral, archaeal and bacterial taxonomy, particularly with regard to visualization of read mapping location, normalization options, growth dynamics and functional gene repertoires. Current read classification tools use non-standard output formats, or do not fully show information on mapping location. As reference datasets are not perfect, portrayal of mapping information is critical for judging results effectively.

RESULTS: Our alignment-based pipeline, Wochenende, incorporates flexible quality control, trimming, mapping, various filters and normalization. Results are completely transparent and filters can be adjusted by the user. We observe stringent filtering of mismatches and use of mapping quality sharply reduces the number of false positives. Further modules allow genomic visualization and the calculation of growth rates, as well as integration and subsequent plotting of pipeline results as heatmaps or heat trees. Our novel normalization approach additionally allows calculation of absolute abundance profiles by comparison with reads assigned to the human host genome.

CONCLUSION: Wochenende has the ability to find and filter alignments to all kingdoms of life using both short and long reads, and requires only good quality reference genomes. Wochenende automatically combines multiple available modules ranging from quality control and normalization to taxonomic visualization. Wochenende is available at https://github.com/MHH-RCUG/nf_wochenende .}, } @article {pmid36368555, year = {2023}, author = {Wang, B and Song, L and Li, W and Hou, L and Li, J and Xu, X and Sheng, G}, title = {Distribution and migration of antibiotic resistance genes, as well as their correlation with microbial communities in swine farm and its surrounding environments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {316}, number = {Pt 2}, pages = {120618}, doi = {10.1016/j.envpol.2022.120618}, pmid = {36368555}, issn = {1873-6424}, mesh = {Swine ; Animals ; Farms ; *Anti-Bacterial Agents/analysis ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; *Microbiota ; Manure/analysis ; Soil/chemistry ; Bacteria/genetics ; Water/analysis ; }, abstract = {The prevalence and correlation of antibiotic resistance genes (ARGs) in pig farm wastewater treatment plants (WWTPs) and surrounding environment were investigated using metagenomics and real time quantitative PCR (q-PCR). The hosts of ARGs were also studied in this study. The abundance of ARGs decreased significantly in the anoxic/oxic (A/O) process and disinfection tank of WWTPs. New ARGs emerged in wastewater that passed though the anaerobic reactor. The abundances of ARGs in the soils and water near pig farm were 10- and 35-fold higher than those in the control, respectively. The abundance of ARGs in wells near pig farm were an order of magnitude higher than that in the control. Similarly, a high abundance of ARGs was detected in swine manure. After composting, most of the ARGs were eliminated, but sul1 increased 10.5-fold. A high-throughput analysis revealed that the pig farm altered the microbial community structure in the surrounding environment, with 52% and 37% of the operational taxonomic units (OTUs) endemic to the soil and water samples near pig farm in comparison with these data in the control, respectively. The phyla Proteobacteria, Choroflexi, and Actinobacteriota dominated the water and soil samples. In addition, three pathogenic genera were found in the surrounding soil and water samples. A metagenomic analysis identified 14 types of ARGs (>1%), with the highest proportion of multidrug ARGs at 47%. A total of 28 subtypes of ARGs were detected (>1%), with macB the most prevalent. The correlation analysis revealed that several key phyla, including Proteobacteria, Actinobacteria and Acidobacteria, were the main potential hosts and posed a positive correlation with the ARGs. Efflux pumps (60-66%) were the primary resistance mechanism, and each resistance mechanism was distributed in similar proportions in the microbial community.}, } @article {pmid36367700, year = {2022}, author = {Mallawaarachchi, V and Lin, Y}, title = {Accurate Binning of Metagenomic Contigs Using Composition, Coverage, and Assembly Graphs.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {29}, number = {12}, pages = {1357-1376}, doi = {10.1089/cmb.2022.0262}, pmid = {36367700}, issn = {1557-8666}, mesh = {*Metagenomics/methods ; Metagenome/genetics ; *Microbiota/genetics ; Algorithms ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenomics enables the recovery of various genetic materials from different species, thus providing valuable insights into microbial communities. Metagenomic binning group sequences belong to different organisms, which is an important step in the early stages of metagenomic analysis pipelines. The classic pipeline followed in metagenomic binning is to assemble short reads into longer contigs and then bin these resulting contigs into groups representing different taxonomic groups in the metagenomic sample. Most of the currently available binning tools are designed to bin metagenomic contigs, but they do not make use of the assembly graphs that produce such assemblies. In this study, we propose MetaCoAG, a metagenomic binning tool that uses assembly graphs with the composition and coverage information of contigs. MetaCoAG estimates the number of initial bins using single-copy marker genes, assigns contigs into bins iteratively, and adjusts the number of bins dynamically throughout the binning process. We show that MetaCoAG significantly outperforms state-of-the-art binning tools by producing similar or more high-quality bins than the second-best binning tool on both simulated and real datasets. To the best of our knowledge, MetaCoAG is the first stand-alone contig-binning tool that directly makes use of the assembly graph information along with other features of the contigs.}, } @article {pmid36367339, year = {2023}, author = {Raghwani, J and Faust, CL and François, S and Nguyen, D and Marsh, K and Raulo, A and Hill, SC and Parag, KV and Simmonds, P and Knowles, SCL and Pybus, OG}, title = {Seasonal dynamics of the wild rodent faecal virome.}, journal = {Molecular ecology}, volume = {32}, number = {17}, pages = {4763-4776}, pmid = {36367339}, issn = {1365-294X}, support = {/WT_/Wellcome Trust/United Kingdom ; 220414/WT_/Wellcome Trust/United Kingdom ; 851550/ERC_/European Research Council/International ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Virome ; Seasons ; Cross-Sectional Studies ; Animals, Wild ; Arvicolinae ; Murinae ; }, abstract = {Viral discovery studies in wild animals often rely on cross-sectional surveys at a single time point. As a result, our understanding of the temporal stability of wild animal viromes remains poorly resolved. While studies of single host-virus systems indicate that host and environmental factors influence seasonal virus transmission dynamics, comparable insights for whole viral communities in multiple hosts are lacking. Utilizing noninvasive faecal samples from a long-term wild rodent study, we characterized viral communities of three common European rodent species (Apodemus sylvaticus, A. flavicollis and Myodes glareolus) living in temperate woodland over a single year. Our findings indicate that a substantial fraction of the rodent virome is seasonally transient and associated with vertebrate or bacteria hosts. Further analyses of one of the most common virus families, Picornaviridae, show pronounced temporal changes in viral richness and evenness, which were associated with concurrent and up to ~3-month lags in host density, ambient temperature, rainfall and humidity, suggesting complex feedbacks from the host and environmental factors on virus transmission and shedding in seasonal habitats. Overall, this study emphasizes the importance of understanding the seasonal dynamics of wild animal viromes in order to better predict and mitigate zoonotic risks.}, } @article {pmid36364902, year = {2022}, author = {Liang, T and Li, D and Zunong, J and Li, M and Amaerjiang, N and Xiao, H and Khattab, NM and Vermund, SH and Hu, Y}, title = {Interplay of Lymphocytes with the Intestinal Microbiota in Children with Nonalcoholic Fatty Liver Disease.}, journal = {Nutrients}, volume = {14}, number = {21}, pages = {}, pmid = {36364902}, issn = {2072-6643}, support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; 2022-1G-4262//Capital's Funds for Health Improvement and Research/ ; 7202009//Beijing Natural Science Foundation/ ; 82073574//National Natural Science Foundation of China/ ; }, mesh = {Child ; Humans ; *Non-alcoholic Fatty Liver Disease/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; Verrucomicrobia ; Lymphocytes ; Liver ; }, abstract = {Abnormally high lymphocyte counts are seen in persons with nonalcoholic fatty liver disease (NAFLD). Gut microbiota dysbiosis is a risk factor for NAFLD. We assessed the gut microbiota of 63 healthy children and 63 children with NAFLD using 16S rRNA gene and metagenomic sequencing to explore the relationships. Compared with healthy children (HC group), the Bacteroidetes, Verrucomicrobia, and Akkermansia were less abundant, while the Actinobacteria were more abundant in children with NAFLD (FLD group). To understand the effect of lymphocytes on the gut microbiota of children with NAFLD, we compared the microbiota of 41 children with NAFLD and high numbers of lymphocytes (FLD_HL group) and 22 children with NAFLD and low numbers of lymphocytes (FLD_LL group). The abundances of Bacteroidetes, Verrucobacterium, and Akkermansia increased and Actinobacteria decreased in the FLD_LL group compared to the FLD_HL group. Akkermansia was negatively correlated with lymphocyte count. NAFLD may disturb the gut microbiota in children through reducing the abundance of Akkermansia and increasing the abundance of proinflammatory bacteria, such as Escherichia-Shigella. Conclusions: High lymphocyte counts are associated with disturbances of gut microbiota and emergence of opportunistic pathogens in children with NAFLD.}, } @article {pmid36364873, year = {2022}, author = {Barber, C and Sabater, C and Ávila-Gálvez, MÁ and Vallejo, F and Bendezu, RA and Guérin-Deremaux, L and Guarner, F and Espín, JC and Margolles, A and Azpiroz, F}, title = {Effect of Resistant Dextrin on Intestinal Gas Homeostasis and Microbiota.}, journal = {Nutrients}, volume = {14}, number = {21}, pages = {}, pmid = {36364873}, issn = {2072-6643}, support = {//Roquette Frères (France)/ ; PID2021-122295OB-I00//Ministerio de Ciencia e Innovación, Spain/ ; PID2019-103914RB-I00//Ministerio de Ciencia e Innovación, Spain/ ; AGL2016-78311-R//Ministerio de Ciencia e Innovación, Spain/ ; FJC2019-042125-I//Ministerio de Ciencia e Innovación, Spain/ ; }, mesh = {Humans ; *Dextrins/pharmacology ; *Microbiota ; Intestines ; Prebiotics ; Feces ; Homeostasis ; }, abstract = {Previous studies have shown that a resistant dextrin soluble fibre has prebiotic properties with related health benefits on blood glucose management and satiety. Our aim was to demonstrate the effects of continuous administration of resistant dextrin on intestinal gas production, digestive sensations, and gut microbiota metabolism and composition. Healthy subjects (n = 20) were given resistant dextrin (14 g/d NUTRIOSE[®], Roquette Frères, Lestrem, France) for four weeks. Outcomes were measured before, at the beginning, end, and two weeks after administration: anal evacuations of gas during daytime; digestive perception, girth, and gas production in response to a standard meal; sensory and digestive responses to a comfort meal; volume of colonic biomass by magnetic resonance; taxonomy and metabolic functions of fecal microbiota by shotgun sequencing; metabolomics in urine. Dextrin administration produced an initial increase in intestinal gas production and gas-related sensations, followed by a subsequent decrease, which magnified after discontinuation. Dextrin enlarged the volume of colonic biomass, inducing changes in microbial metabolism and composition with an increase in short chain fatty acids-producing species and modulation of bile acids and biotin metabolism. These data indicate that consumption of a soluble fibre induces an adaptative response of gut microbiota towards fermentative pathways with lower gas production.}, } @article {pmid36364844, year = {2022}, author = {Lin, H and Chen, J and Ma, S and An, R and Li, X and Tan, H}, title = {The Association between Gut Microbiome and Pregnancy-Induced Hypertension: A Nested Case-Control Study.}, journal = {Nutrients}, volume = {14}, number = {21}, pages = {}, pmid = {36364844}, issn = {2072-6643}, support = {81773535//National Natural Science Foundation of China/ ; 2018SK2061//Key Research and Development Program of Hunan Province/ ; }, mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology ; Case-Control Studies ; *Hypertension, Pregnancy-Induced ; Blood Pressure/physiology ; Bacteria/genetics ; }, abstract = {(1) Background: Pregnancy-induced hypertension (PIH) is associated with obvious microbiota dysbiosis in the third trimester of pregnancy. However, the mechanisms behind these changes remain unknown. Therefore, this study aimed to explore the relationship between the gut microbiome in early pregnancy and PIH occurrence. (2) Methods: A nested case-control study design was used based on the follow-up cohort. Thirty-five PIH patients and thirty-five matched healthy pregnant women were selected as controls. The gut microbiome profiles were assessed in the first trimester using metagenomic sequencing. (3) Results: Diversity analyses showed that microbiota diversity was altered in early pregnancy. At the species level, eight bacterial species were enriched in healthy controls: Alistipes putredinis, Bacteroides vulgatus, Ruminococcus torques, Oscillibacter unclassified, Akkermansia muciniphila, Clostridium citroniae, Parasutterella excrementihominis and Burkholderiales bacterium_1_1_47. Conversely, Eubacterium rectale, and Ruminococcus bromii were enriched in PIH patients. The results of functional analysis showed that the changes in these different microorganisms may affect the blood pressure of pregnant women by affecting the metabolism of vitamin K2, sphingolipid, lipid acid and glycine. (4) Conclusion: Microbiota dysbiosis in PIH patients begins in the first trimester of pregnancy, and this may be associated with the occurrence of PIH. Bacterial pathway analyses suggest that the gut microbiome might lead to the development of PIH through the alterations of function modules.}, } @article {pmid36364726, year = {2022}, author = {Xiao, F and Gao, X and Hu, H and Le, J and Chen, Y and Shu, X and Liang, Z and Xu, Y and Wang, Y and Zhang, T}, title = {Exclusive Enteral Nutrition Exerts Anti-Inflammatory Effects through Modulating Microbiota, Bile Acid Metabolism, and Immune Activities.}, journal = {Nutrients}, volume = {14}, number = {21}, pages = {}, pmid = {36364726}, issn = {2072-6643}, support = {81900474//National Natural Science Foundation of China/ ; 81870373//National Natural Science Foundation of China/ ; 19140904300//Shanghai Science and Technology Committee/ ; ZDSYS20200811143757022//Shenzhen Key Laboratory Foundation/ ; 802-012677//Peacock Talent Programs Research Start-up Grant/ ; }, mesh = {*Enteral Nutrition ; Anti-Inflammatory Agents ; Crohn Disease ; Bacteria ; Bile Acids and Salts ; Leukocytes, Mononuclear ; Mice ; Animals ; *Microbiota ; Remission Induction ; }, abstract = {Exclusive enteral nutrition (EEN) can induce remission in patients with pediatric Crohn's disease (CD). This study aims to depict EEN's modification of bile acid (BA) metabolism in pediatric CD and explores the effect of the EEN-enriched BA in inhibiting the inflammatory response. The twelve enrolled pediatric CD patients showed BA dysmetabolism, represented by decreased levels of fecal secondary and unconjugated BAs as determined by UPLC-TQMS, which were accompanied by gut microbiota dysbiosis and reduced BA-metabolizing bacteria including Eubacterium and Ruminococcus genera, assessed by shotgun metagenomic sequencing. EEN treatment induced remission in these patients at eight weeks, and nine patients remained in stable remission for longer than 48 weeks. EEN improved BA dysmetabolism, with some enriched BAs, including hyocholic acid (HCA), α-muricholic acid (αMCA), strongly associated with decreased severity of CD symptoms. These BAs were significantly correlated with the increased abundance of certain bacteria, including Clostridium innocuum and Hungatella hathewayi, which express 3β-hydroxysteroid dehydrogenase and 5β-reductase. HCA could suppress TNF-α production by CD4+ T cells in the peripheral blood mononuclear cells (PBMCs) of CD patients. Moreover, intraperitoneal injection of HCA could attenuate dextran sulfate sodium (DSS)-induced mouse colitis. Our data suggests that BA modification may contribute to the EEN-induced remission of pediatric CD.}, } @article {pmid36364328, year = {2022}, author = {Baćmaga, M and Wyszkowska, J and Borowik, A and Kucharski, J}, title = {Effects of Tebuconazole Application on Soil Microbiota and Enzymes.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {21}, pages = {}, pmid = {36364328}, issn = {1420-3049}, support = {30.610.006-110//University of Warmia and Mazury in Olsztyn, Faculty of Agriculture and Forestry, Department of Soil Science and Microbiology/ ; 010/RID/2018/19//Minister of Education and Science in the range of the program entitled "Regional Initiative of Excellence" for the years 2019-2023/ ; }, mesh = {*Soil/chemistry ; Soil Microbiology ; *Microbiota ; Triazoles/pharmacology ; Bacteria ; RNA, Ribosomal, 16S ; }, abstract = {Identification of pesticide impact on the soil microbiome is of the utmost significance today. Diagnosing the response of bacteria to tebuconazole, used for plant protection, may help isolate the most active bacteria applicable in the bioaugmentation of soils contaminated with this preparation. Bearing in mind the above, a study was undertaken to test the effect of tebuconazole on the diversity of bacteria at all taxonomic levels and on the activity of soil enzymes. It was conducted by means of standard and metagenomic methods. Its results showed that tebuconazole applied in doses falling within the ranges of good agricultural practice did not significantly disturb the biological homeostasis of soil and did not diminish its fertility. Tebuconazole was found to stimulate the proliferation of organotrophic bacteria and fungi, and also the activities of soil enzymes responsible for phosphorus, sulfur, and carbon metabolism. It did not impair the activity of urease responsible for urea hydrolysis, or cause any significant changes in the structure of bacterial communities. All analyzed soil samples were mainly populated by bacteria from the phylum Proteobacteria, Actinobacteria, Firmicutes, Gemmatimonadetes, Acidobacteria, Planctomycetes, and Chloroflexi. Bacteria from the genera Kaistobacter, Arthrobacter, and Streptomyces predominated in the soils contaminated with tebuconazole, whereas these from the Gemmata genus were inactivated by this preparation.}, } @article {pmid36362265, year = {2022}, author = {Nirmalkar, K and Qureshi, F and Kang, DW and Hahn, J and Adams, JB and Krajmalnik-Brown, R}, title = {Shotgun Metagenomics Study Suggests Alteration in Sulfur Metabolism and Oxidative Stress in Children with Autism and Improvement after Microbiota Transfer Therapy.}, journal = {International journal of molecular sciences}, volume = {23}, number = {21}, pages = {}, pmid = {36362265}, issn = {1422-0067}, support = {GR37996//Finch Therapuetics, MA, USA and Arizona Board of regents/ ; }, mesh = {Child ; Humans ; *Autistic Disorder ; RNA, Ribosomal, 16S/genetics/metabolism ; *Autism Spectrum Disorder/genetics/therapy/metabolism ; *Microbiota ; Metagenomics ; Oxidative Stress ; Sulfur ; }, abstract = {Links between gut microbiota and autism spectrum disorder (ASD) have been explored in many studies using 16S rRNA gene amplicon and shotgun sequencing. Based on these links, microbiome therapies have been proposed to improve gastrointestinal (GI) and ASD symptoms in ASD individuals. Previously, our open-label microbiota transfer therapy (MTT) study provided insight into the changes in the gut microbial community of children with ASD after MTT and showed significant and long-term improvement in ASD and GI symptoms. Using samples from the same study, the objective of this work was to perform a deeper taxonomic and functional analysis applying shotgun metagenomic sequencing. Taxonomic analyses revealed that ASD Baseline had many bacteria at lower relative abundances, and their abundance increased after MTT. The relative abundance of fiber consuming and beneficial microbes including Prevotella (P. dentalis, P. enoeca, P. oris, P. meloninogenica), Bifidobacterium bifidum, and a sulfur reducer Desulfovibrio piger increased after MTT-10wks in children with ASD compared to Baseline (consistent at genus level with the previous 16S rRNA gene study). Metabolic pathway analysis at Baseline compared to typically developing (TD) children found an altered abundance of many functional genes but, after MTT, they became similar to TD or donors. Important functional genes that changed included: genes encoding enzymes involved in folate biosynthesis, sulfur metabolism and oxidative stress. These results show that MTT treatment not only changed the relative abundance of important genes involved in metabolic pathways, but also seemed to bring them to a similar level to the TD controls. However, at a two-year follow-up, the microbiota and microbial genes shifted into a new state, distinct from their levels at Baseline and distinct from the TD group. Our current findings suggest that microbes from MTT lead to initial improvement in the metabolic profile of children with ASD, and major additional changes at two years post-treatment. In the future, larger cohort studies, mechanistic in vitro experiments and metatranscriptomics studies are recommended to better understand the role of these specific microbes, functional gene expression, and metabolites relevant to ASD.}, } @article {pmid36362150, year = {2022}, author = {Sterling, KG and Dodd, GK and Alhamdi, S and Asimenios, PG and Dagda, RK and De Meirleir, KL and Hudig, D and Lombardi, VC}, title = {Mucosal Immunity and the Gut-Microbiota-Brain-Axis in Neuroimmune Disease.}, journal = {International journal of molecular sciences}, volume = {23}, number = {21}, pages = {}, pmid = {36362150}, issn = {1422-0067}, support = {R01 NS105783/NS/NINDS NIH HHS/United States ; U54 GM104944/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Immunity, Mucosal ; *Gastrointestinal Microbiome/physiology ; *Enteric Nervous System/physiology ; *Parkinson Disease ; Brain/physiology ; }, abstract = {Recent advances in next-generation sequencing (NGS) technologies have opened the door to a wellspring of information regarding the composition of the gut microbiota. Leveraging NGS technology, early metagenomic studies revealed that several diseases, such as Alzheimer's disease, Parkinson's disease, autism, and myalgic encephalomyelitis, are characterized by alterations in the diversity of gut-associated microbes. More recently, interest has shifted toward understanding how these microbes impact their host, with a special emphasis on their interactions with the brain. Such interactions typically occur either systemically, through the production of small molecules in the gut that are released into circulation, or through signaling via the vagus nerves which directly connect the enteric nervous system to the central nervous system. Collectively, this system of communication is now commonly referred to as the gut-microbiota-brain axis. While equally important, little attention has focused on the causes of the alterations in the composition of gut microbiota. Although several factors can contribute, mucosal immunity plays a significant role in shaping the microbiota in both healthy individuals and in association with several diseases. The purpose of this review is to provide a brief overview of the components of mucosal immunity that impact the gut microbiota and then discuss how altered immunological conditions may shape the gut microbiota and consequently affect neuroimmune diseases, using a select group of common neuroimmune diseases as examples.}, } @article {pmid36361709, year = {2022}, author = {Torres-Sánchez, A and Ruiz-Rodríguez, A and Ortiz, P and Moreno, MA and Ampatzoglou, A and Gruszecka-Kosowska, A and Monteoliva-Sánchez, M and Aguilera, M}, title = {Exploring Next Generation Probiotics for Metabolic and Microbiota Dysbiosis Linked to Xenobiotic Exposure: Holistic Approach.}, journal = {International journal of molecular sciences}, volume = {23}, number = {21}, pages = {}, pmid = {36361709}, issn = {1422-0067}, support = {PI20/01278//Instituto de Salud Carlos III/ ; IE_2019-198//FEDER Project Infrastructure/ ; }, mesh = {Animals ; Humans ; Dysbiosis/therapy ; Xenobiotics ; *Probiotics/therapeutic use ; *Microbiota ; *Gastrointestinal Microbiome ; }, abstract = {Variation of gut microbiota in metabolic diseases seems to be related to dysbiosis induced by exposure to multiple substances called Microbiota Disrupting Chemicals (MDCs), which are present as environmental and dietary contaminants. Some recent studies have focused on elucidating the alterations of gut microbiota taxa and their metabolites as a consequence of xenobiotic exposures to find possible key targets involved in the severity of the host disease triggered. Compilation of data supporting the triad of xenobiotic-microbiota-metabolic diseases would subsequently allow such health misbalances to be prevented or treated by identifying beneficial microbe taxa that could be Next Generation Probiotics (NGPs) with metabolic enzymes for MDC neutralisation and mitigation strategies. In this review, we aim to compile the available information and reports focused on variations of the main gut microbiota taxa in metabolic diseases associated with xenobiotic exposure and related microbial metabolite profiles impacting the host health status. We performed an extensive literature search using SCOPUS, Web of Science, and PubMed databases. The data retrieval and thorough analyses highlight the need for more combined metagenomic and metabolomic studies revealing signatures for xenobiotics and triggered metabolic diseases. Moreover, metabolome and microbiome compositional taxa analyses allow further exploration of how to target beneficial NGP candidates according to their alleged variability abundance and potential therapeutic significance. Furthermore, this holistic approach has identified limitations and the need of future directions to expand and integrate key knowledge to design appropriate clinical and interventional studies with NGPs. Apart from human health, the beneficial microbes and metabolites identified could also be proposed for various applications under One Health, such as probiotics for animals, plants and environmental bioremediation.}, } @article {pmid36357577, year = {2023}, author = {Krukowski, H and Valkenburg, S and Madella, AM and Garssen, J and van Bergenhenegouwen, J and Overbeek, SA and Huys, GRB and Raes, J and Glorieux, G}, title = {Gut microbiome studies in CKD: opportunities, pitfalls and therapeutic potential.}, journal = {Nature reviews. Nephrology}, volume = {19}, number = {2}, pages = {87-101}, pmid = {36357577}, issn = {1759-507X}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Renal Insufficiency, Chronic/metabolism ; Dysbiosis/microbiology ; }, abstract = {Interest in gut microbiome dysbiosis and its potential association with the development and progression of chronic kidney disease (CKD) has increased substantially in the past 6 years. In parallel, the microbiome field has matured considerably as the importance of host-related and environmental factors is increasingly recognized. Past research output in the context of CKD insufficiently considered the myriad confounding factors that are characteristic of the disease. Gut microbiota-derived metabolites remain an interesting therapeutic target to decrease uraemic (cardio)toxicity. However, future studies on the effect of dietary and biotic interventions will require harmonization of relevant readouts to enable an in-depth understanding of the underlying beneficial mechanisms. High-quality standards throughout the entire microbiome analysis workflow are also of utmost importance to obtain reliable and reproducible results. Importantly, investigating the relative composition and abundance of gut bacteria, and their potential association with plasma uraemic toxins levels is not sufficient. As in other fields, the time has come to move towards in-depth quantitative and functional exploration of the patient's gut microbiome by relying on confounder-controlled quantitative microbial profiling, shotgun metagenomics and in vitro simulations of microorganism-microorganism and host-microorganism interactions. This step is crucial to enable the rational selection and monitoring of dietary and biotic intervention strategies that can be deployed as a personalized intervention in CKD.}, } @article {pmid36357393, year = {2022}, author = {Su, Q and Liu, Q and Lau, RI and Zhang, J and Xu, Z and Yeoh, YK and Leung, TWH and Tang, W and Zhang, L and Liang, JQY and Yau, YK and Zheng, J and Liu, C and Zhang, M and Cheung, CP and Ching, JYL and Tun, HM and Yu, J and Chan, FKL and Ng, SC}, title = {Faecal microbiome-based machine learning for multi-class disease diagnosis.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6818}, pmid = {36357393}, issn = {2041-1723}, mesh = {Humans ; *COVID-19/diagnosis ; Feces ; Machine Learning ; *Microbiota ; Post-Acute COVID-19 Syndrome ; }, abstract = {Systemic characterisation of the human faecal microbiome provides the opportunity to develop non-invasive approaches in the diagnosis of a major human disease. However, shared microbial signatures across different diseases make accurate diagnosis challenging in single-disease models. Herein, we present a machine-learning multi-class model using faecal metagenomic dataset of 2,320 individuals with nine well-characterised phenotypes, including colorectal cancer, colorectal adenomas, Crohn's disease, ulcerative colitis, irritable bowel syndrome, obesity, cardiovascular disease, post-acute COVID-19 syndrome and healthy individuals. Our processed data covers 325 microbial species derived from 14.3 terabytes of sequence. The trained model achieves an area under the receiver operating characteristic curve (AUROC) of 0.90 to 0.99 (Interquartile range, IQR, 0.91-0.94) in predicting different diseases in the independent test set, with a sensitivity of 0.81 to 0.95 (IQR, 0.87-0.93) at a specificity of 0.76 to 0.98 (IQR 0.83-0.95). Metagenomic analysis from public datasets of 1,597 samples across different populations observes comparable predictions with AUROC of 0.69 to 0.91 (IQR 0.79-0.87). Correlation of the top 50 microbial species with disease phenotypes identifies 363 significant associations (FDR < 0.05). This microbiome-based multi-disease model has potential clinical application in disease diagnostics and treatment response monitoring and warrants further exploration.}, } @article {pmid36357382, year = {2022}, author = {Liu, Y and Elworth, RAL and Jochum, MD and Aagaard, KM and Treangen, TJ}, title = {De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6799}, pmid = {36357382}, issn = {2041-1723}, support = {P01 AI152999/AI/NIAID NIH HHS/United States ; R01 DK128187/DK/NIDDK NIH HHS/United States ; R01 HD091731/HD/NICHD NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; T32 HL098069/HL/NHLBI NIH HHS/United States ; R01 NR014792/NR/NINR NIH HHS/United States ; T32 HD098068/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; Biomass ; *Microbiota/genetics ; Metagenomics/methods ; Metagenome ; Specimen Handling ; }, abstract = {Computational analysis of host-associated microbiomes has opened the door to numerous discoveries relevant to human health and disease. However, contaminant sequences in metagenomic samples can potentially impact the interpretation of findings reported in microbiome studies, especially in low-biomass environments. Contamination from DNA extraction kits or sampling lab environments leaves taxonomic "bread crumbs" across multiple distinct sample types. Here we describe Squeegee, a de novo contamination detection tool that is based upon this principle, allowing the detection of microbial contaminants when negative controls are unavailable. On the low-biomass samples, we compare Squeegee predictions to experimental negative control data and show that Squeegee accurately recovers putative contaminants. We analyze samples of varying biomass from the Human Microbiome Project and identify likely, previously unreported kit contamination. Collectively, our results highlight that Squeegee can identify microbial contaminants with high precision and thus represents a computational approach for contaminant detection when negative controls are unavailable.}, } @article {pmid36357381, year = {2022}, author = {Liu, Q and Su, Q and Zhang, F and Tun, HM and Mak, JWY and Lui, GC and Ng, SSS and Ching, JYL and Li, A and Lu, W and Liu, C and Cheung, CP and Hui, DSC and Chan, PKS and Chan, FKL and Ng, SC}, title = {Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6806}, pmid = {36357381}, issn = {2041-1723}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *COVID-19 ; Metagenomics/methods ; Feces/microbiology ; Post-Acute COVID-19 Syndrome ; }, abstract = {Our knowledge of the role of the gut microbiome in acute coronavirus disease 2019 (COVID-19) and post-acute COVID-19 is rapidly increasing, whereas little is known regarding the contribution of multi-kingdom microbiota and host-microbial interactions to COVID-19 severity and consequences. Herein, we perform an integrated analysis using 296 fecal metagenomes, 79 fecal metabolomics, viral load in 1378 respiratory tract samples, and clinical features of 133 COVID-19 patients prospectively followed for up to 6 months. Metagenomic-based clustering identifies two robust ecological clusters (hereafter referred to as Clusters 1 and 2), of which Cluster 1 is significantly associated with severe COVID-19 and the development of post-acute COVID-19 syndrome. Significant differences between clusters could be explained by both multi-kingdom ecological drivers (bacteria, fungi, and viruses) and host factors with a good predictive value and an area under the curve (AUC) of 0.98. A model combining host and microbial factors could predict the duration of respiratory viral shedding with 82.1% accuracy (error ± 3 days). These results highlight the potential utility of host phenotype and multi-kingdom microbiota profiling as a prognostic tool for patients with COVID-19.}, } @article {pmid36354350, year = {2022}, author = {Zhong, J and Wu, D and Zeng, Y and Wu, G and Zheng, N and Huang, W and Li, Y and Tao, X and Zhu, W and Sheng, L and Shen, X and Zhang, W and Zhu, R and Li, H}, title = {The Microbial and Metabolic Signatures of Patients with Stable Coronary Artery Disease.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0246722}, pmid = {36354350}, issn = {2165-0497}, mesh = {Humans ; *Coronary Artery Disease ; *Gastrointestinal Microbiome ; Metabolome ; Metagenomics ; Lipid Metabolism ; }, abstract = {Growing evidence indicates an association between gut dysbiosis and coronary artery disease (CAD). However, the underlying mechanisms relevant to stable CAD (SCAD) pathogenesis, based on microbe-host metabolism interactions, are poorly explored. Here, we constructed a quasi-paired cohort based on the metabolic background of metagenomic samples by the propensity score matching (PSM) principle. Compared to healthy controls (HCs), gut microbiome disturbances were observed in SCAD patients, accompanied by differences in serum metabolome, mainly including elevated acylcarnitine and decreased unsaturated fatty acids in SCAD patients, which implicated the reduced cardiac fatty acid oxidation. Moreover, we identified Ralstonia pickettii as the core strain responsible for impaired microbial homeostasis in SCAD patientsm and may be partly responsible for the decrease of host unsaturated fatty acid levels. These findings highlight the importance of unsaturated fatty acids, R. pickettii, and their interaction in the pathogenesis of SCAD. IMPORTANCE Stable coronary artery disease (SCAD) is an early stage of CAD development. It is important to understand the pathogenesis of SCAD and find out the possible prevention and control targets for delaying the progression of CAD. We observed reduced levels of unsaturated fatty acids (USFAs) in SCAD patients. However, the reduced USFAs may be related to Ralstonia Pickettii, which was the core strain responsible for the impaired gut microbial function in SCAD patients, and further affected the host's cardiovascular health by altering amino acids, vitamin B metabolism, and LPS biosynthesis. These findings not only emphasized the importance of USFAs for cardiovascular health, but also R. Pickettii for maintaining microbial function homeostasis. More importantly, our study revealed, for the first time, that enriched R. Pickettii might be responsible for the reduced USFAs in SCAD patients, which adds new evidence on the role of altered gut microbiota for SCAD formation.}, } @article {pmid36352504, year = {2022}, author = {Tremblay, J and Schreiber, L and Greer, CW}, title = {High-resolution shotgun metagenomics: the more data, the better?.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {6}, pages = {}, doi = {10.1093/bib/bbac443}, pmid = {36352504}, issn = {1477-4054}, mesh = {Humans ; Sequence Analysis, DNA/methods ; *Metagenomics/methods ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; }, abstract = {In shotgun metagenomics (SM), the state-of-the-art bioinformatic workflows are referred to as high-resolution shotgun metagenomics (HRSM) and require intensive computing and disk storage resources. While the increase in data output of the latest iteration of high-throughput DNA sequencing systems can allow for unprecedented sequencing depth at a minimal cost, adjustments in HRSM workflows will be needed to properly process these ever-increasing sequence datasets. One potential adaptation is to generate so-called shallow SM datasets that contain fewer sequencing data per sample as compared with the more classic high coverage sequencing. While shallow sequencing is a promising avenue for SM data analysis, detailed benchmarks using real-data are lacking. In this case study, we took four public SM datasets, one massive and the others moderate in size and subsampled each dataset at various levels to mimic shallow sequencing datasets of various sequencing depths. Our results suggest that shallow SM sequencing is a viable avenue to obtain sound results regarding microbial community structures and that high-depth sequencing does not bring additional elements for ecological interpretation. More specifically, results obtained by subsampling as little as 0.5 M sequencing clusters per sample were similar to the results obtained with the largest subsampled dataset for human gut and agricultural soil datasets. For an Antarctic dataset, which contained only a few samples, 4 M sequencing clusters per sample was found to generate comparable results to the full dataset. One area where ultra-deep sequencing and maximizing the usage of all data was undeniably beneficial was in the generation of metagenome-assembled genomes.}, } @article {pmid36352436, year = {2022}, author = {Guo, Q and Li, L and Wang, C and Huang, Y and Ma, F and Cong, S and Tan, J and Yao, L and Chen, A and Zheng, L}, title = {Comprehensive virome analysis of the viral spectrum in paediatric patients diagnosed with Mycoplasma pneumoniae pneumonia.}, journal = {Virology journal}, volume = {19}, number = {1}, pages = {181}, pmid = {36352436}, issn = {1743-422X}, mesh = {Child ; Humans ; Infant ; Child, Preschool ; Mycoplasma pneumoniae/genetics ; Virome ; *Coinfection ; *Pneumonia, Mycoplasma/diagnosis/epidemiology ; *Viruses/genetics ; *Respiratory Tract Infections ; *Respiratory Syncytial Virus, Human ; }, abstract = {BACKGROUND: Among hospitalized children suffering from community-acquired pneumonia, Mycoplasma pneumoniae (MP) is one of the most common pathogens. MP often exists as a co-infection with bacteria or viruses, which can exacerbate the clinical symptoms. We investigated the pathogen spectrum in MP-positive and MP-negative samples from hospitalized children with respiratory tract infections in Beijing, China.

METHOD: This study included 1038 samples of nasopharyngeal aspirates obtained between April, 2017 and March, 2018 from hospitalized children under 6 years of age with respiratory tract infections. To explore the impact of MP infection on the composition of the pathogen spectrum, 185 nasopharyngeal aspirates (83 MP-positive/102 MP-negative) were randomly selected for next-generation sequencing and comprehensive metagenomics analysis. Real-time PCR was used to detect and verify common respiratory viruses.

RESULTS: Of the 1038 samples, 454 (43.7%) were infected with MP. In children < 6 years of age, the MP infection rate gradually increased with age, with the highest rate of 74.2% in 5-6-year-olds. The results of metagenomics analysis revealed 11 human, animal and plant virus families, and bacteriophages, including common respiratory viruses, enteroviruses and anelloviruses. The virus family with the highest number of reads in both MP-positive and MP-negative samples was the Pneumoviridae, and the number of reads for human respiratory syncytial virus (HRSV) in MP-positive samples was higher than that in MP-negative samples. Among the 83 MP-positive samples, 47 (56.63%) were co-infected with viruses, the most common of which was influenza virus (IFV). The durations of hospitalization and fever were higher in patients with MP co-infection than MP single infection, but the difference was not statistically significant.

CONCLUSION: The viral family with the highest number of reads in both groups was Pneumoviridae, and the number of reads matched to HRSV in MP-positive samples was much higher than MP-negative samples. Co-infection of MP and IFV infection were the most cases.}, } @article {pmid36351942, year = {2022}, author = {Bianco, K and de Farias, BO and Gonçalves-Brito, AS and Alves do Nascimento, AP and Magaldi, M and Montenegro, K and Flores, C and Oliveira, S and Monteiro, MA and Spisso, BF and Pereira, MU and Ferreira, RG and Albano, RM and Cardoso, AM and Clementino, MM}, title = {Mobile resistome of microbial communities and antimicrobial residues from drinking water supply systems in Rio de Janeiro, Brazil.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {19050}, pmid = {36351942}, issn = {2045-2322}, mesh = {Animals ; Humans ; *Drinking Water/microbiology ; Brazil ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; *Environmental Pollutants ; Genes, Bacterial ; }, abstract = {Antibiotic resistance genes (ARGs) are widespread in the environment due to the overuse of antibiotics and other pollutants, posing a threat to human and animal health. In this study, we evaluated antimicrobial residues, bacterial diversity and ARGs in two important watersheds, Guandu and São João, that supply drinking water to Rio de Janeiro city, Brazil. In addition, tap water samples were collected from three different cities in Rio de Janeiro State, including the metropolitan area of Rio de Janeiro city. Clarithromycin, sulfamethoxazole and azithromycin were found in untreated water and drinking water in all samples. A greater abundance of Proteobacteria was observed in Guandu and São João watersheds, with most of the sequences belonging to the Gammaproteobacteria class. A plasmidome-focused metagenomics approach revealed 4881 (Guandu), 3705 (São João) and 3385 (drinking water) ARGs mainly associated with efflux systems. The genes encoding metallo-β-lactamase enzymes (blaAIM, blaGIM, blaIMP, and blaVIM) were detected in the two watersheds and in drinking water samples. Moreover, we demonstrated the presence of the colistin resistance genes mcr-3 and mcr-4 (both watersheds) and mcr-9 (drinking water and Guandu) for the first time in Brazil. Our data emphasize the importance of introducing measures to reduce the disposal of antibiotics and other pollutants capable of promoting the occurrence and spread of the microbial resistome on aquatic environments and predicting possible negative impacts on human health.}, } @article {pmid36349836, year = {2023}, author = {Yuan, ZA and Zhong, LQ and Du, HR and Feng, JN and Liu, XX and Yuan, HY and Guo, JH and Liu, P and Zhang, MH}, title = {Effects of vegetation type differences induced by human disturbance on the nutrition strategy and gut microbiota of Siberian roe deer.}, journal = {Molecular ecology}, volume = {32}, number = {10}, pages = {2534-2550}, doi = {10.1111/mec.16775}, pmid = {36349836}, issn = {1365-294X}, mesh = {Humans ; Animals ; *Deer/physiology ; *Gastrointestinal Microbiome/genetics ; Forests ; Diet/veterinary ; *Microbiota ; }, abstract = {The Siberian roe deer (Capreolus pygargus) is a widely distributed ungulate in northeast China. Due to a series of human disturbance activities such as large-scale forest cutting, deforestation and reclamation, road construction in the past, the appearance and internal structure of forest vegetation in the habitat of Siberian roe have changed significantly. At the same time, Siberian roe population had a series of ecological adaptation responses in the face of such habitat changes. Therefore, two typical vegetation types with differences were selected in the Muling Forest, China. We used nutritional ecology and microbial metagenomic analysis techniques to compare the nutritional selection strategy and the structure and functional characteristics of faecal microbiota of Siberian roe groups in two vegetation types. The results showed that the α diversity of dietary and gut microbes of deer in Natural Forest was higher than that in Plantation Forest. However, the gut microbes of the Plantation Forest group contained more unique enzymes in the functional pathways of carbon metabolism and biosynthesis of amino acids. This study suggests that habitat type is associated with plant community composition, and contributes to changes in the intake proportions of major macronutrients by altering the availability, quality, and composition of certain edible plants. Feeding behaviour may be an important regulatory factor of gut microbiota structure and function of deer. The metabolic function of gut microbiota to different nutrients may affect the microbial community structure. Therefore, our results suggest that the gut microbes of Siberian roe may have coevolved with their diets, and reflect the adaptability of deer populations to environmental changes (e.g., vegetation type). Our study provides new insights into how spatial heterogeneity affects nutrition and microecosystems by describing the interactions among the environment, diet, and symbiotic gut microbes in wild ungulates.}, } @article {pmid36346444, year = {2023}, author = {Palmer, B and Lawson, D and Lipson, DA}, title = {Years After a Fire, Biocrust Microbial Communities are Similar to Unburned Communities in a Coastal Grassland.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {1028-1044}, pmid = {36346444}, issn = {1432-184X}, mesh = {Ecosystem ; Grassland ; *Microbiota ; *Fires ; Bacteria/genetics ; Chlorophyll ; Soil ; }, abstract = {Microbial communities are integral for ecosystem processes and their taxonomic composition and function may be altered by a disturbance such as fire. Biocrusts are composed of macroscopic and microscopic organisms and are important for a variety of ecosystem functions, such as nutrient cycling and erosion control. We sought to understand if biocrust community composition and function were altered 1 year after a prescribed fire and 6 years after a wildfire in a coastal California grassland on San Clemente Island. We used shotgun metagenomic sequencing and measurements of chlorophyll content, exopolysaccharide production related to soil stability, and nitrogen fixation. There were no differences in the community composition between unburned samples and the samples burned in the prescribed fire and wildfire. Chlorophyll content differed between the prescribed fire and the controls; however, there were no measured differences in exopolysaccharide production, and nitrogen fixation. However, the wildfire and their respective unburned samples had different functions based on the gene annotations. We compiled one Actinobacteria metagenome-assembled genome from the shotgun sequences which had genes for oxidative and heat stress tolerance. These results suggest that the biocrust community can reach a community composition and function similar to the unburned biocrusts within a year after a prescribed burn and 6 years after a wildfire. However, legacy effects of the wildfire may present themselves in the differences between functional gene sequences. Due to their ability to match the undisturbed community composition and function within years and without intervention, future restoration work should consider the biocrusts in their restoration plans as they may provide valuable ecosystem functions after a disturbance.}, } @article {pmid36346384, year = {2022}, author = {Williams, RBH}, title = {Adapt or perish.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36346384}, issn = {2050-084X}, mesh = {*Metagenomics ; *Microbiota ; }, abstract = {Microbial communities in wastewater treatment plants provide insights into the development and mechanisms of antimicrobial resistance.}, } @article {pmid36346230, year = {2022}, author = {Goggans, ML and Bilbrey, EA and Quiroz-Moreno, CD and Francis, DM and Jacobi, SK and Kovac, J and Cooperstone, JL}, title = {Short-Term Tomato Consumption Alters the Pig Gut Microbiome toward a More Favorable Profile.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0250622}, pmid = {36346230}, issn = {2165-0497}, mesh = {Humans ; Animals ; Swine ; *Gastrointestinal Microbiome/genetics ; *Solanum lycopersicum ; Feces ; Diet ; Bacteroidetes ; Firmicutes ; Vegetables ; }, abstract = {Diets rich in fruits and vegetables have been shown to exert positive effects on the gut microbiome. However, little is known about the specific effect of individual fruits or vegetables on gut microbe profiles. This study aims to elucidate the effects of tomato consumption on the gut microbiome, as tomatoes account for 22% of vegetable consumption in Western diets, and their consumption has been associated with positive health outcomes. Using piglets as a physiologically relevant model of human metabolism, 20 animals were assigned to either a control or a tomato powder-supplemented diet (both macronutrient matched and isocaloric) for 14 days. The microbiome was sampled rectally at three time points: day 0 (baseline), day 7 (midpoint), and day 14 (end of study). DNA was sequenced using shotgun metagenomics, and reads were annotated using MG-RAST. There were no differences in body weight or feed intake between our two treatment groups. There was a microbial shift which included a higher ratio of Bacteroidota to Bacillota (formerly known as Bacteroidetes and Firmicutes, respectively) and higher alpha-diversity in tomato-fed animals, indicating a shift to a more desirable phenotype. Analyses at both the phylum and genus levels showed global microbiome profile changes (permutational multivariate analysis of variance [PERMANOVA], P ≤ 0.05) over time but not with tomato consumption. These data suggest that short-term tomato consumption can beneficially influence the gut microbial profile, warranting further investigation in humans. IMPORTANCE The composition of the microorganisms in the gut is a contributor to overall health, prompting the development of strategies to alter the microbiome composition. Studies have investigated the role of the diet on the microbiome, as it is a major modifiable risk factor contributing to health; however, little is known about the causal effects of consumption of specific foods on the gut microbiota. A more complete understanding of how individual foods impact the microbiome will enable more evidence-based dietary recommendations for long-term health. Tomatoes are of interest as the most consumed nonstarchy vegetable and a common source of nutrients and phytochemicals across the world. This study aimed to elucidate the effect of short-term tomato consumption on the microbiome, using piglets as a physiologically relevant model to humans. We found that tomato consumption can positively affect the gut microbial profile, which warrants further investigation in humans.}, } @article {pmid36343820, year = {2023}, author = {Li, H and Xia, W and Liu, X and Wang, X and Liu, G and Chen, H and Zhu, L and Li, D}, title = {Food provisioning results in functional, but not compositional, convergence of the gut microbiomes of two wild Rhinopithecus species: Evidence of functional redundancy in the gut microbiome.}, journal = {The Science of the total environment}, volume = {858}, number = {Pt 2}, pages = {159957}, doi = {10.1016/j.scitotenv.2022.159957}, pmid = {36343820}, issn = {1879-1026}, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Presbytini ; Bacteria ; Feces ; }, abstract = {The consumption of similar diets has led to the convergence of gut microbial compositions and functions across phylogenetically distinct animals. However, given the functional redundancy in gut microbiomes, it remains unclear whether synchrony occurs in their functions only and not in their composition, even within phylogenetically close animals consuming a similar diet. In this study, we collected fresh fecal samples from a Rhinopithecus roxellana population in April 2021 (before food provisioning) and June and December 2021 (after food provisioning) and used high-throughput sequencing methods (full-length 16S rRNA gene sequencing and metagenomes) to investigate changes in the gut microbiome due to food provisioning. Combining the results from our previous studies on a wild Rhinopithecus bieti population, we found that the artificial food provisions (e.g., apples, carrots, and peanuts) affected the gut microbiome, and synchrony occurred only in its functions and antibiotic resistance gene community in both Rhinopithecus species, reflecting its ecological functional redundancy. Given the current findings (e.g., depletion in probiotic microbes, dysbiosis in the gut microbial community, and changes in the antibiotic resistance gene profile), anthropogenic disturbances (e.g., food provisioning) would have potential negative effects on host health. Therefore, human activity in animal conservation should be rethought from the standpoint of gut microbial diversity.}, } @article {pmid36343772, year = {2023}, author = {Perez-Garcia, J and González-Carracedo, M and Espuela-Ortiz, A and Hernández-Pérez, JM and González-Pérez, R and Sardón-Prado, O and Martin-Gonzalez, E and Mederos-Luis, E and Poza-Guedes, P and Corcuera-Elosegui, P and Callero, A and Sánchez-Machín, I and Korta-Murua, J and Pérez-Pérez, JA and Villar, J and Pino-Yanes, M and Lorenzo-Diaz, F}, title = {The upper-airway microbiome as a biomarker of asthma exacerbations despite inhaled corticosteroid treatment.}, journal = {The Journal of allergy and clinical immunology}, volume = {151}, number = {3}, pages = {706-715}, doi = {10.1016/j.jaci.2022.09.041}, pmid = {36343772}, issn = {1097-6825}, mesh = {Humans ; *Anti-Asthmatic Agents/therapeutic use ; RNA, Ribosomal, 16S ; Administration, Inhalation ; *Asthma/drug therapy ; *Microbiota ; Adrenal Cortex Hormones/therapeutic use ; Biomarkers ; }, abstract = {BACKGROUND: The response to inhaled corticosteroids (ICS) in asthma is affected by the interplay of several factors. Among these, the role of the upper-airway microbiome has been scarcely investigated. We aimed to evaluate the association between the salivary, pharyngeal, and nasal microbiome with asthma exacerbations despite receipt of ICS.

METHODS: Samples from 250 asthma patients from the Genomics and Metagenomics of Asthma Severity (GEMAS) study treated with ICS were analyzed. Control/case subjects were defined by the absence/presence of asthma exacerbations in the past 6 months despite being treated with ICS. The bacterial microbiota was profiled by sequencing the V3-V4 region of the 16S rRNA gene. Differences between groups were assessed by PERMANOVA and regression models adjusted for potential confounders. A false discovery rate (FDR) of 5% was used to correct for multiple comparisons. Classification models of asthma exacerbations despite ICS treatment were built with machine learning approaches based on clinical, genetic, and microbiome data.

RESULTS: In nasal and saliva samples, case subjects had lower bacterial diversity (Richness, Shannon, and Faith indices) than control subjects (.007 ≤ P ≤ .037). Asthma exacerbations accounted for 8% to 9% of the interindividual variation of the salivary and nasal microbiomes (.003 ≤ P ≤ .046). Three, 4, and 11 bacterial genera from the salivary, pharyngeal, and nasal microbiomes were differentially abundant between groups (4.09 × 10[-12] ≤ FDR ≤ 0.047). Integrating clinical, genetic, and microbiome data showed good discrimination for the development of asthma exacerbations despite receipt of ICS (AUCtraining: 0.82 and AUCvalidation: 0.77).

CONCLUSION: The diversity and composition of the upper-airway microbiome are associated with asthma exacerbations despite ICS treatment. The salivary microbiome has a potential application as a biomarker of asthma exacerbations despite receipt of ICS.}, } @article {pmid36343662, year = {2022}, author = {Lee, JW and Cowley, ES and Wolf, PG and Doden, HL and Murai, T and Caicedo, KYO and Ly, LK and Sun, F and Takei, H and Nittono, H and Daniel, SL and Cann, I and Gaskins, HR and Anantharaman, K and Alves, JMP and Ridlon, JM}, title = {Formation of secondary allo-bile acids by novel enzymes from gut Firmicutes.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2132903}, pmid = {36343662}, issn = {1949-0984}, support = {R25 CA057699/CA/NCI NIH HHS/United States ; T15 LM007359/LM/NLM NIH HHS/United States ; R01 CA204808/CA/NCI NIH HHS/United States ; T32 GM140935/GM/NIGMS NIH HHS/United States ; R01 GM134423/GM/NIGMS NIH HHS/United States ; R03 AI147127/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Bile Acids and Salts ; Firmicutes/metabolism ; Phylogeny ; *Gastrointestinal Microbiome ; Lithocholic Acid/metabolism ; Deoxycholic Acid/metabolism ; }, abstract = {The gut microbiome of vertebrates is capable of numerous biotransformations of bile acids, which are responsible for intestinal lipid digestion and function as key nutrient-signaling molecules. The human liver produces bile acids from cholesterol predominantly in the A/B-cis orientation in which the sterol rings are "kinked", as well as small quantities of A/B-trans oriented "flat" stereoisomers known as "primary allo-bile acids". While the complex multi-step bile acid 7α-dehydroxylation pathway has been well-studied for conversion of "kinked" primary bile acids such as cholic acid (CA) and chenodeoxycholic acid (CDCA) to deoxycholic acid (DCA) and lithocholic acid (LCA), respectively, the enzymatic basis for the formation of "flat" stereoisomers allo-deoxycholic acid (allo-DCA) and allo-lithocholic acid (allo-LCA) by Firmicutes has remained unsolved for three decades. Here, we present a novel mechanism by which Firmicutes generate the "flat" bile acids allo-DCA and allo-LCA. The BaiA1 was shown to catalyze the final reduction from 3-oxo-allo-DCA to allo-DCA and 3-oxo-allo-LCA to allo-LCA. Phylogenetic and metagenomic analyses of human stool samples indicate that BaiP and BaiJ are encoded only in Firmicutes and differ from membrane-associated bile acid 5α-reductases recently reported in Bacteroidetes that indirectly generate allo-LCA from 3-oxo-Δ[4]-LCA. We further map the distribution of baiP and baiJ among Firmicutes in human metagenomes, demonstrating an increased abundance of the two genes in colorectal cancer (CRC) patients relative to healthy individuals.}, } @article {pmid36343281, year = {2023}, author = {Moutsoglou, DM and Tatah, J and Prisco, SZ and Prins, KW and Staley, C and Lopez, S and Blake, M and Teigen, L and Kazmirczak, F and Weir, EK and Kabage, AJ and Guan, W and Khoruts, A and Thenappan, T}, title = {Pulmonary Arterial Hypertension Patients Have a Proinflammatory Gut Microbiome and Altered Circulating Microbial Metabolites.}, journal = {American journal of respiratory and critical care medicine}, volume = {207}, number = {6}, pages = {740-756}, pmid = {36343281}, issn = {1535-4970}, support = {R01 HL162927/HL/NHLBI NIH HHS/United States ; T32 HL144472/HL/NHLBI NIH HHS/United States ; UL1 TR002494/TR/NCATS NIH HHS/United States ; T32 HL144472/GF/NIH HHS/United States ; F32 HL154533/HL/NHLBI NIH HHS/United States ; F32 HL154533/GF/NIH HHS/United States ; K08 HL140100/HL/NHLBI NIH HHS/United States ; R01 HL158795/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Pulmonary Arterial Hypertension ; Dysbiosis ; Phylogeny ; Familial Primary Pulmonary Hypertension ; Inflammation ; *Vascular Diseases ; Bile Acids and Salts ; }, abstract = {Rationale: Inflammation drives pulmonary arterial hypertension (PAH). Gut dysbiosis causes immune dysregulation and systemic inflammation by altering circulating microbial metabolites; however, little is known about gut dysbiosis and microbial metabolites in PAH. Objectives: To characterize the gut microbiome and microbial metabolites in patients with PAH. Methods: We performed 16S ribosomal RNA gene and shotgun metagenomics sequencing on stool from patients with PAH, family control subjects, and healthy control subjects. We measured markers of inflammation, gut permeability, and microbial metabolites in plasma from patients with PAH, family control subjects, and healthy control subjects. Measurements and Main Results: The gut microbiome was less diverse in patients with PAH. Shannon diversity index correlated with measures of pulmonary vascular disease but not with right ventricular function. Patients with PAH had a distinct gut microbial signature at the phylogenetic level, with fewer copies of gut microbial genes that produce antiinflammatory short-chain fatty acids (SCFAs) and secondary bile acids and lower relative abundances of species encoding these genes. Consistent with the gut microbial changes, patients with PAH had relatively lower plasma concentrations of SCFAs and secondary bile acids. Patients with PAH also had enrichment of species with the microbial genes that encoded the proinflammatory microbial metabolite trimethylamine. The changes in the gut microbiome and circulating microbial metabolites between patients with PAH and family control subjects were not as substantial as the differences between patients with PAH and healthy control subjects. Conclusions: Patients with PAH have proinflammatory gut dysbiosis, in which lower circulating SCFAs and secondary bile acids may facilitate pulmonary vascular disease. These findings support investigating modulation of the gut microbiome as a potential treatment for PAH.}, } @article {pmid36342154, year = {2022}, author = {Li, J and Dong, C and Lai, Q and Wang, G and Shao, Z}, title = {Frequent Occurrence and Metabolic Versatility of Marinifilaceae Bacteria as Key Players in Organic Matter Mineralization in Global Deep Seas.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0086422}, pmid = {36342154}, issn = {2379-5077}, mesh = {Animals ; *Lignin/metabolism ; *Bacteria/genetics ; Oceans and Seas ; Metagenome ; Bacteroidetes/genetics ; Plants/genetics ; Carbon/metabolism ; }, abstract = {Transfer of animal and plant detritus of both terrestrial and marine origins to the deep sea occurs on a global scale. Microorganisms play an important role in mineralizing them therein, but these are yet to be identified in situ. To observe key bacteria involved, we conducted long-term in situ incubation and found that members of the family Marinifilaceae (MF) occurred as some of the most predominant bacteria thriving on the new inputs of plant and animal biomasses in the deep sea in both marginal and oceanic areas. This taxon is diverse and ubiquitous in marine environments. A total of 11 MAGs belonging to MF were retrieved from metagenomic data and diverged into four subgroups in the phylogenomic tree. Based on metagenomic and metatranscriptomic analyses, we described the metabolic features and in situ metabolizing activities of different subgroups. The MF-2 subgroup, which dominates plant detritus-enriched cultures, specializes in polysaccharide degradation and lignin oxidation and has high transcriptional activities of related genes in situ. Intriguingly, members of this subgroup encode a nitrogen fixation pathway to compensate for the shortage of nitrogen sources inside the plant detritus. In contrast, other subgroups dominating the animal tissue-supported microbiomes are distinguished from MF-2 with regard to carbon and nitrogen metabolism and exhibit high transcriptional activity for proteolysis in situ. Despite these metabolic divergences of MF lineages, they show high in situ transcriptional activities for organic fermentation and anaerobic respiration (reductions of metal and/or dimethyl sulfoxide). These results highlight the role of previously unrecognized Marinifilaceae bacteria in organic matter mineralization in marine environments by coupling carbon and nitrogen cycling with metal and sulfur. IMPORTANCE Microbial mineralization of organic matter has a significant impact on the global biogeochemical cycle. This report confirms the role of Marinifilaceae in organic degradation in the oceans, with a contribution to ocean carbon cycling that has previously been underestimated. It was the dominant taxon thriving on plant and animal biomasses in our in situ incubator, as well as in whale falls and wood falls. At least 9 subgroups were revealed, and they were widely distributed in oceans globally but predominant in organic-matter-rich environments, with an average relative abundance of 8.3%. Different subgroups display a preference for the degradation of different macromolecules (polysaccharides, lignin, and protein) and adapt to their environments via special metabolic mechanisms.}, } @article {pmid36342125, year = {2022}, author = {Alegria Terrazas, R and Robertson-Albertyn, S and Corral, AM and Escudero-Martinez, C and Kapadia, R and Balbirnie-Cumming, K and Morris, J and Hedley, PE and Barret, M and Torres-Cortes, G and Paterson, E and Baggs, EM and Abbott, J and Bulgarelli, D}, title = {Defining Composition and Function of the Rhizosphere Microbiota of Barley Genotypes Exposed to Growth-Limiting Nitrogen Supplies.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0093422}, pmid = {36342125}, issn = {2379-5077}, support = {BB/S002871/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Rhizosphere ; *Hordeum/microbiology ; Nitrogen ; Plant Roots ; *Microbiota/genetics ; Soil ; Genotype ; }, abstract = {The microbiota populating the rhizosphere, the interface between roots and soil, can modulate plant growth, development, and health. These microbial communities are not stochastically assembled from the surrounding soil, but their composition and putative function are controlled, at least partially, by the host plant. Here, we use the staple cereal barley as a model to gain novel insights into the impact of differential applications of nitrogen, a rate-limiting step for global crop production, on the host genetic control of the rhizosphere microbiota. Using a high-throughput amplicon sequencing survey, we determined that nitrogen availability for plant uptake is a factor promoting the selective enrichment of individual taxa in the rhizosphere of wild and domesticated barley genotypes. Shotgun sequencing and metagenome-assembled genomes revealed that this taxonomic diversification is mirrored by a functional specialization, manifested by the differential enrichment of multiple Gene Ontology terms, of the microbiota of plants exposed to nitrogen conditions limiting barley growth. Finally, a plant soil feedback experiment revealed that host control of the barley microbiota underpins the assembly of a phylogenetically diverse group of bacteria putatively required to sustain plant performance under nitrogen-limiting supplies. Taken together, our observations indicate that under nitrogen conditions limiting plant growth, host-microbe and microbe-microbe interactions fine-tune the host genetic selection of the barley microbiota at both taxonomic and functional levels. The disruption of these recruitment cues negatively impacts plant growth. IMPORTANCE The microbiota inhabiting the rhizosphere, the thin layer of soil surrounding plant roots, can promote the growth, development, and health of their host plants. Previous research indicated that differences in the genetic composition of the host plant coincide with variations in the composition of the rhizosphere microbiota. This is particularly evident when looking at the microbiota associated with input-demanding modern cultivated varieties and their wild relatives, which have evolved under marginal conditions. However, the functional significance of these differences remains to be fully elucidated. We investigated the rhizosphere microbiota of wild and cultivated genotypes of the global crop barley and determined that nutrient conditions limiting plant growth amplify the host control on microbes at the root-soil interface. This is reflected in a plant- and genotype-dependent functional specialization of the rhizosphere microbiota, which appears to be required for optimal plant growth. These findings provide novel insights into the significance of the rhizosphere microbiota for plant growth and sustainable agriculture.}, } @article {pmid36342051, year = {2022}, author = {Jiang, H and Cao, HW and Chai, ZX and Chen, XY and Zhang, CF and Zhu, Y and Xin, JW}, title = {Dynamic alterations in yak (Bos grunniens) rumen microbiome in response to seasonal variations in diet.}, journal = {Physiological genomics}, volume = {54}, number = {12}, pages = {514-525}, doi = {10.1152/physiolgenomics.00112.2022}, pmid = {36342051}, issn = {1531-2267}, mesh = {Animals ; Cattle ; RNA, Ribosomal, 16S/genetics ; *Rumen ; *Microbiota/physiology ; Diet ; Bacteroidetes/genetics ; Cellulose ; }, abstract = {Rumen microorganisms play important roles in the healthy growth of yaks. This study investigated changes in yak rumen microbiome during natural grazing at the warm seasons and supplementary feeding at cold seasons. High-throughput sequencing of 16S rRNA and metagenome analysis were conducted to investigate the structures and functions of yak rumen microbial communities. The results indicated that Bacteroidetes and Firmicutes were the most abundant phyla. In addition, Bacteroidetes might play a more important role than Firmicutes during the supplementary feeding stage (spring and winter), but less during natural grazing stage (summer and autumn). KEGG analysis showed that the amino sugar and nucleotide sugar metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, starch and sucrose metabolism, and fructose and mannose metabolism were the main pathways in the microbial community, which were significantly different between seasons. The carbohydrate-active enzymes (CAZyme) annotation revealed that cellulose was an important carbon source for microorganisms in yak rumen. Glycoside hydrolases (GHs) were the most abundant class of CAZymes, followed by glycosyl transferases (GTs), which were important to digestion of oil, cellulose, and hemicellulose in food. These results contribute to the understanding of microbial components and functions in yak rumen.}, } @article {pmid36341458, year = {2022}, author = {Yang, J and Qin, S and Zhang, H}, title = {Precise strategies for selecting probiotic bacteria in treatment of intestinal bacterial dysfunctional diseases.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1034727}, pmid = {36341458}, issn = {1664-3224}, mesh = {Pregnancy ; Female ; Humans ; *Probiotics/therapeutic use ; Bacteria ; *Microbiota ; *Intestinal Diseases ; *Bacterial Infections ; }, abstract = {Abundant microbiota resides in the organs of the body, which utilize the nutrition and form a reciprocal relationship with the host. The composition of these microbiota changes under different pathological conditions, particularly in response to stress and digestive diseases, making the microbial composition and health of the hosts body interdependent. Probiotics are living microorganisms that have demonstrated beneficial effects on physical health and as such are used as supplements to ameliorate symptoms of various digestive diseases by optimizing microbial composition of the gut and restore digestive balance. However, the supplementary effect does not achieve the expected result. Therefore, a targeted screening strategy on probiotic bacteria is crucial, owing to the presence of several bacterial strains. Core bacteria work effectively in maintaining microbiological homeostasis and stabilization in the gastrointestinal tract. Some of the core bacteria can be inherited and acquired from maternal pregnancy and delivery; others can be acquired from contact with the mother, feces, and the environment. Knowing the genera and functions of the core bacteria could be vital in the isolation and selection of probiotic bacteria for supplementation. In addition, other supporting strains of probiotic bacteria are also needed. A comprehensive strategy for mining both core and supporting bacteria before its clinical use is needed. Using metagenomics or other methods of estimation to discern the typically differentiated strains of bacteria is another important strategy to treat dysbiosis. Hence, these two factors are significant to carry out targeted isolation and selection of the functional strains to compose the resulting probiotic preparation for application in both research and clinical use. In conclusion, precise probiotic supplementation, by screening abundant strains of bacteria and isolating specific probiotic strains, could rapidly establish the core microbiota needed to confer resilience, particularly in bacterial dysfunctional diseases. This approach can help identify distinct bacteria which can be used to improve supplementation therapies.}, } @article {pmid36341405, year = {2022}, author = {Wang, X and Xiong, K and Huang, F and Huang, J and Liu, Q and Duan, N and Ruan, H and Jiang, H and Zhu, Y and Lin, L and Song, Y and Zhao, M and Zheng, L and Ye, P and Qian, Y and Hu, Q and Yan, F and Wang, W}, title = {A metagenome-wide association study of the gut microbiota in recurrent aphthous ulcer and regulation by thalidomide.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1018567}, pmid = {36341405}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Stomatitis, Aphthous ; Thalidomide/therapeutic use ; Dysbiosis/complications ; Metagenome ; }, abstract = {Recurrent aphthous ulcer (RAU), one of the most common diseases in humans, has an unknown etiology and is difficult to treat. Thalidomide is an important immunomodulatory and antitumor drug and its effects on the gut microbiota still remain unclear. We conducted a metagenomic sequencing study of fecal samples from a cohort of individuals with RAU, performed biochemical assays of cytokines, immunoglobulins and antimicrobial peptides in serum and saliva, and investigated the regulation effects of thalidomide administration and withdrawal. Meanwhile we constructed the corresponding prediction models. Our metagenome-wide association results indicated that gut dysbacteriosis, microbial dysfunction and immune imbalance occurred in RAU patients. Thalidomide regulated gut dysbacteriosis in a species-specific manner and had different sustainable effects on various probiotics and pathogens. A previously unknown association between gut microbiota alterations and RAU was found, and the specific roles of thalidomide in modulating the gut microbiota and immunity were determined, suggesting that RAU may be affected by targeting gut dysbacteriosis and modifying immune imbalance. In-depth insights into sophisticated networks consisting of the gut microbiota and host cells may lead to the development of emerging treatments, including prebiotics, probiotics, synbiotics, and postbiotics.}, } @article {pmid36334202, year = {2023}, author = {Tian, L and Wang, L and Zhang, X and Huang, X and Wang, F and Zhu, S and Li, X and Guan, Y}, title = {Multi-omics analysis on seasonal variations of the biofilm microbial community in a full-scale pre-denitrification biofilter.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {9}, pages = {24284-24298}, pmid = {36334202}, issn = {1614-7499}, support = {21-1-4-sf-11-nsh//science and technology program for public wellbeing of qingdao/ ; }, mesh = {*Denitrification ; Bioreactors/microbiology ; Seasons ; Multiomics ; Proteomics ; *Microbiota ; Biofilms ; Nitrogen ; }, abstract = {The seasonal variations of biofilm communities in a municipal wastewater treatment plant were investigated using multi-omics techniques. The abundance of the main phyla of microorganisms varied with summer (July 2019) and winter (January 2019) samples considerably, the Bacteroidetes enriched in winter and Chloroflexi in summer. The results of metaproteomic and metagenomic showed that most of the functional microorganisms belonged to the Betaproteobacteria class, and the enrichment of Flavobacteria class in winter guaranteed the stability of denitrification performance to some extent. Seasonal variations affected the proteomic expression profiling, a total of 2835 differentially expressed proteins identified were significantly enriched in quorum sensing, two-component system, ribosome, benzoate degradation, butanoate metabolism, tricarboxylic acid cycle (TCA cycle), and cysteine and methionine metabolism pathways. With the expression of nitrogen metabolic proteins decreases in winter, the overall expression of denitrification-related enzymes in winter was much lower than that in summer, the nitrogen metabolism pathway varied significantly. Seasonal variations also induced the alteration of the biofilm metabolite profile; a total of 66 differential metabolites, 8 potential biomarkers, and 8 perturbed metabolic pathways such as TCA cycle were detected. It was found that most of the perturbed pathways are directly related to nitrogen metabolism, and several amino acids and organic acids associated with the TCA cycle were significantly perturbed, the accumulation of TCA cycle intermediates, ornithine, and L-histidine in winter might be conducive to resisting cold temperatures. Furthermore, the correlation between biofilm microbial communities and metabolites was identified by the combined analysis of metabolomic and metaproteomic. The differences of microbial community structure, function, and metabolism between winter and summer in a full-scale pre-denitrification biofilter were revealed for the first time, strengthening our understanding of the microbial ecology of biofilm communities.}, } @article {pmid36334119, year = {2023}, author = {Zhao, F and Guo, Z and Kwok, LY and Zhao, Z and Wang, K and Li, Y and Sun, Z and Zhao, J and Zhang, H}, title = {Bifidobacterium lactis Probio-M8 improves bone metabolism in patients with postmenopausal osteoporosis, possibly by modulating the gut microbiota.}, journal = {European journal of nutrition}, volume = {62}, number = {2}, pages = {965-976}, pmid = {36334119}, issn = {1436-6215}, support = {2021ZD0014//Inner Mongolia Science and Technology Major Projects/ ; }, mesh = {Female ; Humans ; *Bifidobacterium animalis ; *Gastrointestinal Microbiome ; *Osteoporosis, Postmenopausal/drug therapy ; Calcitriol ; Calcium ; *Probiotics ; }, abstract = {PURPOSE: Postmenopausal osteoporosis (PMO) is usually managed by conventional drug treatment. However, prolonged use of these drugs cause side effects. Gut microbiota may be a potential target for treatment of PMO. This work was a three-month intervention trial aiming to evaluate the added effect of probiotics as adjunctive treatment for PMO.

METHODS: Forty patients with PMO were randomized into probiotic (n = 20; received Bifidobacterium animalis subsp. lactis Probio-M8 [Probio-M8], calcium, calcitriol) and placebo (n = 20; received placebo material, calcium, calcitriol) groups. The bone mineral density of patients was measured at month 0 (0 M; baseline) and month 3 (3 M; after three-month intervention). Blood and fecal samples were collected 0 M and 3 M. Only 15 and 12 patients from Probio-M8 and placebo groups, respectively, provided complete fecal samples for gut microbiota analysis.

RESULTS: No significant change was observed in the bone mineral density of patients at 3 M. Co-administering Probio-M8 improved the bone metabolism, reflected by an increased vitamin D3 level and decreased PTH and procalcitonin levels in serum at 3 M. Fecal metagenomic analysis revealed modest changes in the gut microbiome in both groups at 3 M. Interestingly, Probio-M8 co-administration affected the gut microbial interactive correlation network, particularly the short-chain fatty acid-producing bacteria. Probio-M8 co-administration significantly increased genes encoding some carbohydrate metabolism pathways (including ABC transporters, the phosphotransferase system, and fructose and mannose metabolism) and a choline-phosphate cytidylyltransferase.

CONCLUSIONS: Co-administering Probio-M8 with conventional drugs/supplements was more efficacious than conventional drugs/supplements alone in managing PMO. Our study shed insights into the beneficial mechanism of probiotic adjunctive treatment.

Chinese Clinical Trial Registry (identifier number: ChiCTR1800019268).}, } @article {pmid36333950, year = {2023}, author = {Hammer, TJ and Easton-Calabria, A and Moran, NA}, title = {Microbiome assembly and maintenance across the lifespan of bumble bee workers.}, journal = {Molecular ecology}, volume = {32}, number = {3}, pages = {724-740}, pmid = {36333950}, issn = {1365-294X}, support = {R35 GM131738/GM/NIGMS NIH HHS/United States ; R35GM131738/NH/NIH HHS/United States ; 2018-08156//National Institute of Food and Agriculture/ ; }, mesh = {Humans ; Bees/genetics ; Animals ; Longevity/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; }, abstract = {How a host's microbiome changes over its lifespan can influence development and ageing. As these temporal patterns have only been described in detail for a handful of hosts, an important next step is to compare microbiome succession more broadly and investigate why it varies. Here we characterize the temporal dynamics and stability of the bumble bee worker gut microbiome. Bumble bees have simple and host-specific gut microbiomes, and their microbial dynamics may influence health and pollination services. We used 16S rRNA gene sequencing, quantitative PCR and metagenomics to characterize gut microbiomes over the lifespan of Bombus impatiens workers. We also sequenced gut transcriptomes to examine host factors that may control the microbiome. At the community level, microbiome assembly is highly predictable and similar to patterns of primary succession observed in the human gut. However, at the strain level, partitioning of bacterial variants among colonies suggests stochastic colonization events similar to those observed in flies and nematodes. We also find strong differences in temporal dynamics among symbiont species, suggesting ecological differences among microbiome members in colonization and persistence. Finally, we show that both the gut microbiome and host transcriptome-including expression of key immunity genes-stabilize, as opposed to senesce, with age. We suggest that in highly social groups such as bumble bees, maintenance of both microbiomes and immunity contribute to inclusive fitness, and thus remain under selection even in old age. Our findings provide a foundation for exploring the mechanisms and functional outcomes of bee microbiome succession.}, } @article {pmid36333419, year = {2022}, author = {Sieber, G and Beisser, D and Rothenberger, JL and Shah, M and Schumann, M and Sures, B and Boenigk, J}, title = {Microbial community shifts induced by plastic and zinc as substitutes of tire abrasion.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {18684}, pmid = {36333419}, issn = {2045-2322}, mesh = {*Plastics ; Microplastics ; Zinc/chemistry ; Fresh Water ; *Microbiota ; }, abstract = {Aquatic environments serve as a sink for anthropogenic discharges. A significant part of the discharge is tire wear, which is increasingly being released into the environment, causing environmental disasters due to their longevity and the large number of pollutants they contain. Main components of tires are plastic and zinc, which therefore can be used as substitutes for tire abrasion to study the effect on microbial life. We investigate environmentally realistic concentrations of plastic and zinc on a freshwater microeukaryotic community using high-throughput sequencing of the 18S V9 region over a 14-day exposure period. Apart from a generally unchanged diversity upon exposure to zinc and nanoplastics, a change in community structure due to zinc is evident, but not due to nanoplastics. Evidently, nanoplastic particles hardly affect the community, but zinc exposure results in drastic functional abundance shifts concerning the trophic mode. Phototrophic microorganisms were almost completely diminished initially, but photosynthesis recovered. However, the dominant taxa performing photosynthesis changed from bacillariophytes to chlorophytes. While phototrophic organisms are decreasing in the presence of zinc, the mixotrophic fraction initially benefitted and the heterotrophic fraction were benefitting throughout the exposure period. In contrast to lasting changes in taxon composition, the functional community composition is initially strongly imbalanced after application of zinc but returns to the original state.}, } @article {pmid36330877, year = {2023}, author = {Wang, P and Yuan, Q and Wang, X and Hu, B and Wang, C}, title = {Metagenomic insight into the distribution of metal resistance genes within cascade reservoir waters: Synergic impacts of geographic variation and anthropogenic pollution.}, journal = {Environmental research}, volume = {216}, number = {Pt 3}, pages = {114682}, doi = {10.1016/j.envres.2022.114682}, pmid = {36330877}, issn = {1096-0953}, mesh = {*Metagenomics ; Rivers ; Metals ; Water Quality ; *Microbiota ; China ; Environmental Monitoring ; }, abstract = {Metal resistance genes (MRGs) are potential bio-indicators to diagnose contamination stress on riverine ecosystems. Within reservoir systems, river damming weakens hydrodynamic condition and enriches metal contaminants. But, little is known about the synergic impacts of geographic variation and anthropogenic pollution on MRGs. In this study, the abundance, composition and microbes of MRGs in four cascade reservoirs along the Jinsha River, southwestern China were investigated via high-throughput metagenomics. The results showed significant enrichment of chromium, cadmium and lead in Ludila and Xiluodu reservoirs with moderate ecological risks based on the criteria of drinking water quality and aquatic life protection. Nevertheless, at watershed scale, these metals played little role in up-regulating MRGs abundance owing to the limited toxic stress on microbes. Accordingly, geographic variation showed stronger impacts on MRGs composition than metals as revealed by the distance-decay relationship (Pearson correlation, rgeo = 0.24-0.57, rmetal = 0.10-0.41) and co-occurrence network (Node degree to MRGs subtype, ngeo = 180, nmetal = 6). River damming, as an artificial isolation of geographic space, significantly affected MRGs composition. The longer operation history, smaller storage capacity and higher regulation frequency caused the higher dissimilarity of MRGs composition between the reservoir's upstream and downstream areas. In conclusion, the metal pollution level is a prerequisite regulating MRGs; while under the lowly-polluted conditions, geographic variation had stronger impacts on MRGs than metal pollution via altered assembly of microbial communities. This study provides an important guidance for the future environmental management and ecological protection of river-reservoir ecosystems.}, } @article {pmid36329213, year = {2022}, author = {Zaman, S and Gohar, M and Kanwal, H and Chaudhary, A and Imran, M}, title = {Impact of Probiotic Geotrichum candidum QAUGC01 on Health, Productivity, and Gut Microbial Diversity of Dairy Cattle.}, journal = {Current microbiology}, volume = {79}, number = {12}, pages = {376}, pmid = {36329213}, issn = {1432-0991}, mesh = {Dietary Supplements/analysis ; *Probiotics/analysis ; Milk ; Rumen/microbiology ; *Gastrointestinal Microbiome ; Diet/veterinary ; Female ; Cattle ; Bacteria/genetics ; Lactation ; Animals ; Geotrichum ; Animal Feed/analysis ; }, abstract = {Gut microbial diversity is a determinant of animal productivity and health. Probiotic supplementation in feed has been known to modulate the gut microbial diversity resulting in better feed utilization and resistance against diseases. The current study was designed to determine the probiotic potential of Geotrichum candidum QAUGC01 (VHDP00000000) in Sahiwal-Friesian crossbred dairy cows and its impact on gut microbial diversity, health, and productivity. To evaluate health and productivity, growth performance, determination of blood parameters, serum biochemistry, feed efficiency, milk yield & composition, and nutrients digestibility was determined and compared between control and experimental groups. Moreover, at the end of the experiment, the gut microbial diversity was evaluated through MiSeq (Illumina) sequencing of bacterial and fungal/yeast DNA in dung samples of both control and experimental cows. Inspite of a significant reduction in dry matter intake the increase in feed efficiency and milk yield was observed in experimental cows with normal hematological and serum biochemical profile. The increase in anaerobic bacterial count and decrease in the shredding of pathogenic flora was observed in experimental cows. Metagenomic analysis revealed Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes to be the four dominating phyla among bacteria and, Ascomycota followed by Basidiomycota and Neocallimastigomycota among the fungal population in both groups. The diversity of the core microbiome revealed high bacterial and Fungal Alpha diversity in the experimental group than in control via the Shannon index. This study provided insights into the safe use of G. candidum as a probiotic, to improve growth performance, health, productivity and gut microbial diversity of dairy cattle.}, } @article {pmid36327953, year = {2022}, author = {Ehlers, L and Netz, LAW and Reiner, J and Berlin, P and Bannert, K and Bastian, M and Zechner, D and Lamprecht, G and Jaster, R}, title = {Effects of Bile Duct Ligation and Ghrelin Treatment on the Colonic Barrier and Microbiome of Mice.}, journal = {Pharmacology}, volume = {107}, number = {11-12}, pages = {564-573}, doi = {10.1159/000527142}, pmid = {36327953}, issn = {1423-0313}, mesh = {Mice ; Animals ; Ghrelin/pharmacology/therapeutic use ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S/genetics ; Bile Ducts/surgery ; *Cholestasis/microbiology/pathology ; Liver/pathology ; *Microbiota ; Weight Loss ; Solvents ; Disease Models, Animal ; }, abstract = {INTRODUCTION: Cholestatic liver disease (CLD) is associated with intestinal barrier dysfunction. The peptide hormone ghrelin may exert both hepatoprotective and barrier-strengthening effects. Here, we have evaluated these effects under the conditions of experimental cholestasis.

METHODS: C57BL/6J mice with bile duct ligation (BDL) or sham surgery were treated with ghrelin or solvent for 9 days. Liver injury was assessed by histological and laboratory analyses. Paracellular macromolecule permeability and transmural electrical resistance (TMER) of colonic tissues were measured using a Ussing chamber. Expression of tight junction (TJ) genes was quantified by real-time PCR. Amplicon metagenomic sequencing was employed to analyze bacterial 16S rRNA from colonic stool samples.

RESULTS: Mice with BDL exhibited weight loss and signs of severe liver injury. These changes were unaffected by ghrelin treatment. FITC-4-kDa-dextran flux was increased and TMER decreased after BDL. Treatment with ghrelin tended to reduce these effects. Furthermore, application of ghrelin was associated with higher mRNA levels of claudin-4, occludin, and ZO-1 in colonic tissues of mice with BDL. Reduced alpha-diversity of the microbiome was observed in solvent-treated mice with BDL but not in ghrelin-treated animals.

CONCLUSION: Ghrelin treatment did not improve weight loss and liver damage but increased gene expression of colonic TJ proteins and restored the alpha-diversity of the microbiome. Since protective effects of ghrelin might be masked by the severity of the model, we suggest follow-up studies in models of milder CLD.}, } @article {pmid36327844, year = {2023}, author = {Yi, X and Wen, P and Liang, JL and Jia, P and Yang, TT and Feng, SW and Liao, B and Shu, WS and Li, JT}, title = {Phytostabilization mitigates antibiotic resistance gene enrichment in a copper mine tailings pond.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt B}, pages = {130255}, doi = {10.1016/j.jhazmat.2022.130255}, pmid = {36327844}, issn = {1873-3336}, mesh = {*Copper/toxicity ; *Ponds ; Soil Microbiology ; Drug Resistance, Microbial/genetics ; Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Mining-impacted environments are distributed globally and have become increasingly recognized as hotspots of antibiotic resistance genes (ARGs). However, there are currently no reports on treatment technologies to deal with such an important environmental problem. To narrow this knowledge gap, we implemented a phytostabilization project in an acidic copper mine tailings pond and employed metagenomics to explore ARG characteristics in the soil samples. Our results showed that phytostabilization decreased the total ARG abundance in 0-10 cm soil layer by 75 %, which was companied by a significant decrease in ARG mobility, and a significant increase in ARG diversity and microbial diversity. Phytostabilization was also found to drastically alter the ARG host composition and to significantly reduce the total abundance of virulence factor genes of ARG hosts. Soil nutrient status, heavy metal toxicity and SO4[2-] concentration were important physicochemical factors to affect the total ARG abundance, while causal mediation analysis showed that their effects were largely mediated by the changes in ARG mobility and microbial diversity. The increase in ARG diversity associated with phytostabilization was mainly mediated by a small subgroup of ARG hosts, most of which could not be classified at the genus level and deserve further research in the future.}, } @article {pmid36325032, year = {2022}, author = {Kinsella, CM and Deijs, M and Becker, C and Broekhuizen, P and van Gool, T and Bart, A and Schaefer, AS and van der Hoek, L}, title = {Host prediction for disease-associated gastrointestinal cressdnaviruses.}, journal = {Virus evolution}, volume = {8}, number = {2}, pages = {veac087}, pmid = {36325032}, issn = {2057-1577}, abstract = {Metagenomic techniques have facilitated the discovery of thousands of viruses, yet because samples are often highly biodiverse, fundamental data on the specific cellular hosts are usually missing. Numerous gastrointestinal viruses linked to human or animal diseases are affected by this, preventing research into their medical or veterinary importance. Here, we developed a computational workflow for the prediction of viral hosts from complex metagenomic datasets. We applied it to seven lineages of gastrointestinal cressdnaviruses using 1,124 metagenomic datasets, predicting hosts of four lineages. The Redondoviridae, strongly associated to human gum disease (periodontitis), were predicted to infect Entamoeba gingivalis, an oral pathogen itself involved in periodontitis. The Kirkoviridae, originally linked to fatal equine disease, were predicted to infect a variety of parabasalid protists, including Dientamoeba fragilis in humans. Two viral lineages observed in human diarrhoeal disease (CRESSV1 and CRESSV19, i.e. pecoviruses and hudisaviruses) were predicted to infect Blastocystis spp. and Endolimax nana respectively, protists responsible for millions of annual human infections. Our prediction approach is adaptable to any virus lineage and requires neither training datasets nor host genome assemblies. Two host predictions (for the Kirkoviridae and CRESSV1 lineages) could be independently confirmed as virus-host relationships using endogenous viral elements identified inside host genomes, while a further prediction (for the Redondoviridae) was strongly supported as a virus-host relationship using a case-control screening experiment of human oral plaques.}, } @article {pmid36322790, year = {2023}, author = {Battat, R and Scherl, EJ and Lukin, D and Charilaou, P and Mahtani, P and Gerber, J and Gandara, JA and , and Dündar, F and Zumbo, P and Betel, D and Guo, CJ and Longman, RS}, title = {Increased Primary Bile Acids with Ileocolonic Resection Impact Ileal Inflammation and Gut Microbiota in Inflammatory Bowel Disease.}, journal = {Journal of Crohn's & colitis}, volume = {17}, number = {5}, pages = {795-803}, pmid = {36322790}, issn = {1876-4479}, support = {R01 DK120985/DK/NIDDK NIH HHS/United States ; R01 DK128257/DK/NIDDK NIH HHS/United States ; UL1 TR002384/TR/NCATS NIH HHS/United States ; UL1TR002384/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/surgery/microbiology ; Inflammation ; *Ileitis/surgery/microbiology ; Colectomy ; Bile Acids and Salts ; }, abstract = {BACKGROUND: Most Crohn's disease [CD] patients require surgery. Ileitis recurs after most ileocolectomies and is a critical determinant for outcomes. The impacts of ileocolectomy-induced bile acid [BA] perturbations on intestinal microbiota and inflammation are unknown. We characterized the relationships between ileocolectomy, stool BAs, microbiota and intestinal inflammation in inflammatory bowel disease [IBD].

METHODS: Validated IBD clinical and endoscopic assessments were prospectively collected. Stool primary and secondary BA concentrations were compared based on ileocolectomy and ileitis status. Primary BA thresholds for ileitis were evaluated. Metagenomic sequencing was use to profile microbial composition and function. Relationships between ileocolectomy, BAs and microbiota were assessed.

RESULTS: In 166 patients, elevated primary and secondary BAs existed with ileocolectomy. With ileitis, only primary BAs [795 vs 398 nmol/g, p = 0.009] were higher compared to without ileitis. The optimal primary BA threshold [≥228 nmol/g] identified ileitis on multivariable analysis [odds ratio = 2.3, p = 0.04]. Microbial diversity, Faecalibacterium prausnitzii and O-acetylhomoserine aminocarboxypropyltransferase [MetY] were decreased with elevated primary BAs. Amongst ileocolectomy patients, only those with elevated primary BAs had diversity, F. prausnitzii and MetY reductions. Those with both ileocolectomy and intermediate [p = 0.002] or high [≥228 nmol/g, p = 9.1e-11]] primary BA concentrations had reduced F. prausnitzii compared to without ileocolectomy. Those with ileocolectomy and low [<29.2 nmol/g] primary BA concentrations had similar F. prausnitzii to those without ileocolectomy [p = 0.13]. MetY was reduced with ileitis [p = 0.02].

CONCLUSIONS: Elevated primary BAs were associated with ileitis, and reduced microbial diversity, F. prausnitzii abundance and enzymatic abundance of MetY [acetate and l-methionine-producing enzyme expressed by F. prausnitzii], and were the only factors associated with these findings after ileocolectomy.}, } @article {pmid36322250, year = {2022}, author = {Salamon, D and Zapała, B and Krawczyk, A and Potasiewicz, A and Nikiforuk, A and Stój, A and Gosiewski, T}, title = {Comparison of iSeq and MiSeq as the two platforms for 16S rRNA sequencing in the study of the gut of rat microbiome.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {22}, pages = {7671-7681}, pmid = {36322250}, issn = {1432-0614}, support = {2021/43/D/NZ5/00469//Narodowe Centrum Nauki/ ; 1/CX/CSRD VA/United States ; 1/CX/CSRD VA/United States ; }, mesh = {Rats ; Animals ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; DNA, Bacterial/genetics ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Amplicon-based next-generation sequencing (NGS) of the 16S ribosomal RNA (16S) regions is a culture-free method used to identify and analyze Procaryota occurring within a given sample. The prokaryotic 16S rRNA gene contains conserved regions and nine variable regions (V1-V9) frequently used for phylogenetic classification of genus or species in diverse microbial populations. This work compares the accuracy and efficacy of two platforms, iSeq and MiSeq from Illumina, used in sequencing 16S rRNA. The most important similarities and differences of 16S microbiome sequencing in 20 fecal rat samples were described. Genetic libraries were prepared according to 16S Metagenomic Sequencing Library Preparation (Illumina) for the V3 and V4 regions of the 16S. The species richness obtained using iSeq technology was lower compared to MiSeq. At the second taxonomy level (L2), the abundance of taxa was comparable for both platforms. At the L7, the taxa abundance was significantly different, and the number of taxa was higher for the MiSeq. The alpha diversity was lower for iSeq than for MiSeq, starting from the order to the species level. The beta diversity estimation revealed statistically significant differences in microbiota diversity starting from the class level to the species level in samples sequenced on two investigated platforms. This work disclosed that the iSeq platform could be used to evaluate the bacterial profile of the samples to characterize the overall profile. The MiSeq System seems to be better for a detailed analysis of the differences in the microbiota composition. KEY POINTS: • iSeq platform allows to shorten the sequencing time three times compared to the MiSeq. • iSeq can only be used for an initial and quick microbiome assessment. • MiSeq is better for a detailed analysis of the differences in the microbiota composition.}, } @article {pmid36321901, year = {2022}, author = {Zhang, XX and Lv, QB and Yan, QL and Zhang, Y and Guo, RC and Meng, JX and Ma, H and Qin, SY and Zhu, QH and Li, CQ and Liu, R and Liu, G and Li, SH and Sun, DB and Ni, HB}, title = {A Catalog of over 5,000 Metagenome-Assembled Microbial Genomes from the Caprinae Gut Microbiota.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0221122}, pmid = {36321901}, issn = {2165-0497}, mesh = {Sheep ; Animals ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics/metabolism ; Genome, Bacterial ; Metagenomics ; Genome, Microbial ; Ruminants ; }, abstract = {Most microbiome studies regarding the ruminant digestive tract have focused on the rumen microbiota, whereas only a few studies were performed on investigating the gut microbiota of ruminants, which limits our understanding of this important component. Herein, the gut microbiota of 30 Caprinae animals (sheep and goats) from six provinces in China was characterized using ultradeep (>100 Gbp per sample) metagenome shotgun sequencing. An inventory of Caprinae gut microbial species containing 5,046 metagenomic assembly genomes (MAGs) was constructed. Particularly, 2,530 of the genomes belonged to uncultured candidate species. These genomes largely expanded the genomic repository of the current microbes in the Caprinae gut. Several enzymes and biosynthetic gene clusters encoded by these Caprinae gut species were identified. In summary, our study extends the gut microbiota characteristics of Caprinae and provides a basis for future studies on animal production and animal health. IMPORTANCE We constructed a microbiota catalog containing 5,046 MAGs from Caprinae gut from six regions of China. Most of the MAGs do not overlap known databases and appear to be potentially new species. We also characterized the functional spectrum of these MAGs and analyzed the differences between different regions. Our study enriches the understanding of taxonomic, functional, and metabolic diversity of Caprinae gut microbiota. We are confident that the manuscript will be of utmost interest to a wide range of readers and be widely applied in future research.}, } @article {pmid36321893, year = {2022}, author = {Wu, Y and Jha, R and Li, A and Liu, H and Zhang, Z and Zhang, C and Zhai, Q and Zhang, J}, title = {Probiotics (Lactobacillus plantarum HNU082) Supplementation Relieves Ulcerative Colitis by Affecting Intestinal Barrier Functions, Immunity-Related Gene Expression, Gut Microbiota, and Metabolic Pathways in Mice.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0165122}, pmid = {36321893}, issn = {2165-0497}, mesh = {Humans ; Animals ; Mice ; *Colitis, Ulcerative/chemically induced/therapy ; *Gastrointestinal Microbiome ; *Lactobacillus plantarum ; *Colitis/chemically induced ; Colon/metabolism ; *Probiotics/therapeutic use ; Metabolic Networks and Pathways ; Gene Expression ; Disease Models, Animal ; }, abstract = {Probiotics can effectively improve ulcerative colitis (UC), but the mechanism is still unclear. Here, shotgun metagenome and transcriptome analyses were performed to explore the therapeutic effect and the mechanism of the probiotic Lactobacillus plantarum HNU082 (Lp082) on UC. The results showed that Lp082 treatment significantly ameliorated dextran sulfate sodium (DSS)-induced UC in mice, which was manifested as increases in body weight, water intake, food intake, and colon length and decreases in disease activity index (DAI), immune organ index, inflammatory factors, and histopathological scores after Lp082 intake. An in-depth study discovered that Lp082 could improve the intestinal mucosal barrier and relieve inflammation by cooptimizing the biological barrier, chemical barrier, mechanical barrier, and immune barrier. Specifically, Lp082 rebuilt the biological barrier by regulating the intestinal microbiome and increasing the production of short-chain fatty acids (SCFAs). Lp082 improved the chemical barrier by reducing intercellular cell adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule (VCAM) and increasing goblet cells and mucin2. Lp082 ameliorated the mechanical barrier by increasing zonula occludens-1 (ZO-1), zonula occludens-2 (ZO-2), and occludin while decreasing claudin-1 and claudin-2. Lp082 optimized the immune barrier by reducing the content of interleukin-1β (IL-1β), IL-6, tumor necrosis factor-α (TNF-α), myeloperoxidase (MPO), and interferon-γ (IFN-γ) and increasing IL-10, transforming growth factor-β1 (TGF-β1), and TGF-β2, inhibiting the NF-κB signaling pathway. Taken together, probiotic Lp082 can play a protective role in a DSS-induced colitis mouse model by protecting the intestinal mucosal barrier, attenuating the inflammatory response, and regulating microbial imbalance. This study provides support for the development of probiotic-based microbial products as an alternative treatment strategy for UC. IMPORTANCE Many studies have focused on the therapeutic effect of probiotics on ulcerative colitis (UC), but few studies have paid attention to the mechanism of probiotics, especially the therapeutic effect. This study suggests that Lp082 has a therapeutic effect on colitis in mice. Its mechanisms of action include protecting the mucosal barrier and actively modulating the gut microbiome, modulating inflammatory pathways, and reducing neutrophil infiltration. Our study enriches the mechanism and provides a new prospect for probiotics in the treatment of colitis, helps to deepen the understanding of the intestinal mucosal barrier, and provides guidance for the future probiotic treatment of human colitis.}, } @article {pmid36319439, year = {2023}, author = {Deng, F and Chen, Y and Sun, QS and Lin, ZB and Min, Y and Zhao, BC and Huang, ZB and Liu, WF and Li, C and Hu, JJ and Liu, KX}, title = {Gut microbiota dysbiosis is associated with sepsis-induced cardiomyopathy in patients: A case-control study.}, journal = {Journal of medical virology}, volume = {95}, number = {1}, pages = {e28267}, doi = {10.1002/jmv.28267}, pmid = {36319439}, issn = {1096-9071}, mesh = {Humans ; *Gastrointestinal Microbiome ; Case-Control Studies ; Dysbiosis/complications ; *Cardiomyopathies/etiology ; *Bacteriophages ; Bacteria/genetics ; *Sepsis/complications ; }, abstract = {BACKGROUND: Myocardial injury is a major complication of sepsis and a key factor affecting prognosis. Therefore, early and accurate diagnosis and timely management of sepsis-induced cardiomyopathy (SICM) are of great significance for the prevention and treatment of sepsis. The gut microbiota has been shown to be closely associated with sepsis or myocardial injury, but the association between the gut microbiota and SICM is not fully understood. This study aimed to explore the link between gut microbiota composition and SICM.

METHODS: A case-control and single-center study of clinical features and gut microbiota profiles by Metagenome and Virome was conducted in SICM patients (n = 15) and sepsis-uninduced cardiomyopathy patients (SNICM, n = 16).

RESULTS: Compared with SNICM patients, SICM patients showed significant myocardial injury and higher 28-day mortality, SOFA scores, lactate levels, and infection levels on admission. Meanwhile, differences in the composition of gut bacteria, archaea, fungi, and viruses were analyzed between the two groups. Differential gut bacteria or viruses were found to have a good predictive effect on SICM. Furthermore, gut bacteria and viruses that differed between the two groups were strongly related. The abundance of Cronobacter and Cronobacter phage was higher in the SICM group than in the SNICM group, and the receiver operating characteristic curve showed that Cronobacter and Cronobacter phage both had a good predictive effect on SICM.

CONCLUSIONS: SICM patients may have specific gut microbiota signatures, and Cronobacter and Cronobacter phages have a good ability to identify and diagnose SICM.}, } @article {pmid36318623, year = {2022}, author = {Karakan, T and Gundogdu, A and Alagözlü, H and Ekmen, N and Ozgul, S and Tunali, V and Hora, M and Beyazgul, D and Nalbantoglu, OU}, title = {Artificial intelligence-based personalized diet: A pilot clinical study for irritable bowel syndrome.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2138672}, pmid = {36318623}, issn = {1949-0984}, mesh = {Humans ; *Irritable Bowel Syndrome/microbiology ; *Gastrointestinal Microbiome ; Artificial Intelligence ; RNA, Ribosomal, 16S ; Diet ; }, abstract = {We enrolled consecutive IBS-M patients (n = 25) according to Rome IV criteria. Fecal samples were obtained from all patients twice (pre-and post-intervention) and high-throughput 16S rRNA sequencing was performed. Six weeks of personalized nutrition diet (n = 14) for group 1 and a standard IBS diet (n = 11) for group 2 were followed. AI-based diet was designed based on optimizing a personalized nutritional strategy by an algorithm regarding individual gut microbiome features. The IBS-SSS evaluation for pre- and post-intervention exhibited significant improvement (p < .02 and p < .001 for the standard IBS diet and personalized nutrition groups, respectively). While the IBS-SSS evaluation changed to moderate from severe in 78% (11 out of 14) of the personalized nutrition group, no such change was observed in the standard IBS diet group. A statistically significant increase in the Faecalibacterium genus was observed in the personalized nutrition group (p = .04). Bacteroides and putatively probiotic genus Propionibacterium were increased in the personalized nutrition group. The change (delta) values in IBS-SSS scores (before-after) in personalized nutrition and standard IBS diet groups are significantly higher in the personalized nutrition group. AI-based personalized microbiome modulation through diet significantly improves IBS-related symptoms in patients with IBS-M. Further large-scale, randomized placebo-controlled trials with long-term follow-up (durability) are needed.}, } @article {pmid36318246, year = {2023}, author = {Lei, B and Xu, Y and Lei, Y and Li, C and Zhou, P and Wang, L and Yang, Q and Li, X and Li, F and Liu, C and Cui, C and Chen, T and Ni, W and Hu, S}, title = {CRAMdb: a comprehensive database for composition and roles of microbiome in animals.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D700-D707}, pmid = {36318246}, issn = {1362-4962}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; Fungi/genetics ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Databases, Factual ; }, abstract = {CRAMdb (a database for composition and roles of animal microbiome) is a comprehensive resource of curated and consistently annotated metagenomes for non-human animals. It focuses on the composition and roles of the microbiome in various animal species. The main goal of the CRAMdb is to facilitate the reuse of animal metagenomic data, and enable cross-host and cross-phenotype comparisons. To this end, we consistently annotated microbiomes (including 16S, 18S, ITS and metagenomics sequencing data) of 516 animals from 475 projects spanning 43 phenotype pairs to construct the database that is equipped with 9430 bacteria, 278 archaea, 2216 fungi and 458 viruses. CRAMdb provides two main contents: microbiome composition data, illustrating the landscape of the microbiota (bacteria, archaea, fungi, and viruses) in various animal species, and microbiome association data, revealing the relationships between the microbiota and various phenotypes across different animal species. More importantly, users can quickly compare the composition of the microbiota of interest cross-host or body site and the associated taxa that differ between phenotype pairs cross-host or cross-phenotype. CRAMdb is freely available at (http://www.ehbio.com/CRAMdb).}, } @article {pmid36318011, year = {2022}, author = {Gil, JC and Hird, SM}, title = {Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0238422}, pmid = {36318011}, issn = {2165-0497}, mesh = {Animals ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Geese ; Multiomics ; *Microbiota/genetics ; Metagenomics/methods ; Canada ; }, abstract = {16S rRNA amplicon sequences are predominantly used to identify the taxonomic composition of a microbiome, but they can also be used to generate simulated metagenomes to circumvent costly empirical shotgun sequencing. The effectiveness of using "simulated metagenomes" (shotgun metagenomes simulated from 16S rRNA amplicons using a database of full genomes closely related to the amplicons) in nonmodel systems is poorly known. We sought to determine the accuracy of simulated metagenomes in a nonmodel organism, the Canada goose (Branta canadensis), by comparing metagenomes and metatranscriptomes to simulated metagenomes derived from 16S amplicon sequencing. We found significant differences between the metagenomes, metatranscriptomes, and simulated metagenomes when comparing enzymes, KEGG orthologies (KO), and metabolic pathways. The simulated metagenomes accurately identified the majority (>70%) of the total enzymes, KOs, and pathways. The simulated metagenomes accurately identified the majority of the short-chain fatty acid metabolic pathways crucial to folivores. When narrowed in scope to specific genes of interest, the simulated metagenomes overestimated the number of antimicrobial resistance genes and underestimated the number of genes related to the breakdown of plant matter. Our results suggest that simulated metagenomes should not be used in lieu of empirical sequencing when studying the functional potential of a nonmodel organism's microbiome. Regarding the function of the Canada goose microbiome, we found unexpected amounts of fermentation pathways, and we found that a few taxa are responsible for large portions of the functional potential of the microbiome. IMPORTANCE The taxonomic composition of a microbiome is predominately identified using amplicon sequencing of 16S rRNA genes, but as a single marker, it cannot identify functions (genes). Metagenome and metatranscriptome sequencing can determine microbiome function but can be cost prohibitive. Therefore, computational methods have been developed to generate simulated metagenomes derived from 16S rRNA sequences and databases of full-length genomes. Simulated metagenomes can be an effective alternative to empirical sequencing, but accuracy depends on the genomic database used and whether the database contains organisms closely related to the 16S sequences. These tools are effective in well-studied systems, but the accuracy of these predictions in a nonmodel system is less known. Using a nonmodel bird species, we characterized the function of the microbiome and compared the accuracy of 16S-derived simulated metagenomes to sequenced metagenomes. We found that the simulated metagenomes reflect most but not all functions of empirical metagenome sequencing.}, } @article {pmid36317886, year = {2022}, author = {Zaramela, LS and Tjuanta, M and Moyne, O and Neal, M and Zengler, K}, title = {synDNA-a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0044722}, pmid = {36317886}, issn = {2379-5077}, mesh = {*Metagenome/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Plasmids ; DNA ; }, abstract = {Microbiome studies have the common goal of determining which microbial taxa are present, respond to specific conditions, or promote phenotypic changes in the host. Most of these studies rely on relative abundance measurements to drive conclusions. Inherent limitations of relative values are the inability to determine whether an individual taxon is more or less abundant and the magnitude of this change between the two samples. These limitations can be overcome by using absolute abundance quantifications, which can allow for a more complete understanding of community dynamics by measuring variations in total microbial loads. Obtaining absolute abundance measurements is still technically challenging. Here, we developed synthetic DNA (synDNA) spike-ins that enable precise and cost-effective absolute quantification of microbiome data by adding defined amounts of synDNAs to the samples. We designed 10 synDNAs with the following features: 2,000-bp length, variable GC content (26, 36, 46, 56, or 66% GC), and negligible identity to sequences found in the NCBI database. Dilution pools were generated by mixing the 10 synDNAs at different concentrations. Shotgun metagenomic sequencing showed that the pools of synDNAs with different percentages of GC efficiently reproduced the serial dilution, showing high correlation (r = 0.96; R[2] ≥ 0.94) and significance (P < 0.01). Furthermore, we demonstrated that the synDNAs can be used as DNA spike-ins to generate linear models and predict with high accuracy the absolute number of bacterial cells in complex microbial communities. IMPORTANCE The synDNAs designed in this study enable accurate and reproducible measurements of absolute amount and fold changes of bacterial species in complex microbial communities. The method proposed here is versatile and promising as it can be applied to bacterial communities or genomic features like genes and operons, in addition to being easily adaptable by other research groups at a low cost. We also made the synDNAs' sequences and the plasmids available to encourage future application of the proposed method in the study of microbial communities.}, } @article {pmid36316342, year = {2022}, author = {Alessandri, G and Fontana, F and Mancabelli, L and Lugli, GA and Tarracchini, C and Argentini, C and Longhi, G and Viappiani, A and Milani, C and Turroni, F and van Sinderen, D and Ventura, M}, title = {Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {88}, pmid = {36316342}, issn = {2055-5008}, mesh = {Humans ; Infant ; Child ; *Gastrointestinal Microbiome ; Ecosystem ; Bacteria/genetics ; Biodiversity ; Metagenomics ; }, abstract = {In vitro gut cultivation models provide host-uncoupled, fast, and cost-efficient solutions to investigate the effects of intrinsic and extrinsic factors impacting on both composition and functionality of the intestinal microbial ecosystem. However, to ensure the maintenance and survival of gut microbial players and preserve their functions, these systems require close monitoring of several variables, including oxygen concentration, pH, and temperature, as well as the use of a culture medium satisfying the microbial nutritional requirements. In this context, in order to identify the macro- and micro-nutrients necessary for in vitro cultivation of the infant gut microbiota, a meta-analysis based on 1669 publicly available shotgun metagenomic samples corresponding to fecal samples of healthy, full-term infants aged from a few days to three years was performed to define the predominant species characterizing the "infant-like" gut microbial ecosystem. A subsequent comparison of growth performances was made using infant fecal samples that contained the most abundant bacterial taxa of the infant gut microbiota, when cultivated on 18 different culture media. This growth analysis was performed by means of flow cytometry-based bacterial cell enumeration and shallow shotgun sequencing, which allowed the formulation of an optimized growth medium, i.e., Infant Gut Super Medium (IGSM), which maintains and sustains the infant gut microbial biodiversity under in vitro growth conditions. Furthermore, this formulation was used to evaluate the in vitro effect of two drugs commonly used in pediatrics, i.e., acetaminophen and simethicone, on the taxonomic composition of the infant gut microbiota.}, } @article {pmid36314746, year = {2022}, author = {Gobert, A and Evers, MS and Morge, C and Sparrow, C and Delafont, V}, title = {Comparison of DNA purification methods for high-throughput sequencing of fungal communities from wine fermentation.}, journal = {MicrobiologyOpen}, volume = {11}, number = {5}, pages = {e1321}, pmid = {36314746}, issn = {2045-8827}, mesh = {*Wine/analysis/microbiology ; Fermentation ; *Mycobiome ; High-Throughput Nucleotide Sequencing ; DNA ; DNA, Fungal/genetics ; }, abstract = {High-throughput sequencing approaches, which target a taxonomically discriminant locus, allow for in-depth insight into microbial communities' compositions. Although microorganisms are historically investigated by cultivation on artificial culture media, this method presents strong limitations, since only a limited proportion of microorganisms can be grown in vitro. This pitfall appears even more limiting in enological and winemaking processes, during which a wide range of molds, yeasts, and bacteria are observed at the different stages of the fermentation course. Such an understanding of those dynamic communities and how they impact wine quality therefore stands as a major challenge for the future of enology. As of now, although high-throughput sequencing has already allowed for the investigation of fungal communities, there is no available comparative study focusing on the performance of microbial deoxyribonucleic acid (DNA) extraction in enological matrixes. This study aims to provide a comparison of five selected extraction methods, assayed on both must and fermenting must, as well as on finished wine. These procedures were evaluated according to their extraction yields, the purity of their extracted DNA, and the robustness of downstream molecular analyses, including polymerase chain reaction and high-throughput sequencing of fungal communities. Altogether, two out of the five assessed microbial DNA extraction methods (DNeasy PowerSoil Pro Kit and E.Z.N.A.® Food DNA Kit) appeared suitable for robust evaluations of the microbial communities in wine samples. Consequently, this study provides robust tools for facilitated upcoming studies to further investigate microbial communities during winemaking using high-throughput sequencing.}, } @article {pmid36310860, year = {2022}, author = {Zhang, Y and Niazi, SA and Yang, Y and Wang, Y and Cao, X and Liu, Y and Li, Y and Zhou, Q}, title = {Smoking by altering the peri-implant microbial community structure compromises the responsiveness to treatment.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1040765}, pmid = {36310860}, issn = {2235-2988}, mesh = {Humans ; Smoking/adverse effects ; *Peri-Implantitis ; Smokers ; *Microbiota ; Prostheses and Implants ; }, abstract = {Smoking is an essential risk factor for peri-implant diseases. It also hampers the clinical outcomes of peri-implant therapies. Nonetheless, the effect of smoking can go undetected until the emergence of clinical signs. Bacterial-induced inflammation is responsible for the initiation and progression of peri-implant diseases. We hypothesize that smoking impacts the peri-implant microbiome even in status of clinical health, putting it into a sub-healthy condition that responds poorly to peri-implant treatments. To validate this, peri-implant plaque samples from 18 participants including 10 smokers (S) and 8 non-smokers (NS), who had received implant prostheses were analyzed using metagenomic shotgun sequencing. The results showed that in addition to taxonomical and functional differences, the local stability in the S group was also shown to be much higher than that in the NS group, indicating greater stubbornness of the peri-implant microbiome associated with smoking. Besides, the topological structures were also distinct between the two groups. The highly connected species interacted more preferentially with each other in the S group (eigenvector centralization, 0.0273 in S and 0.0183 in NS), resulting in a greater tendency of forming small-world modules (modularity, 0.714 in S and 0.582 in NS). While in the NS group, inter-species correlations were more evenly distributed (clustering coefficient, 0.532 in S and 0.666 in NS). These alterations overall explained the greater stubbornness of the peri-implant microbiome associated with smoking, which may cause poor responsiveness to peri-implant therapies. From a microbial perspective, this may be a potential reason why smoking impacts negatively on the outcome of peri-implant treatments.}, } @article {pmid36306091, year = {2023}, author = {Jameson, E and Taubert, M and Angel, R and Coyotzi, S and Chen, Y and Eyice, Ö and Schäfer, H and Murrell, JC and Neufeld, JD and Dumont, MG}, title = {DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {261-282}, pmid = {36306091}, issn = {1940-6029}, mesh = {RNA, Ribosomal, 16S/genetics/chemistry ; Carbon Isotopes/chemistry ; Isotope Labeling/methods ; *DNA/chemistry ; *Proteins/chemistry ; Biomarkers ; RNA, Messenger ; }, abstract = {Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of [13]C, [18]O, or [15]N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labelled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labelled populations by targeted gene analysis. Such approaches usually involved fingerprint-based analyses or sequencing clone libraries containing 16S rRNA genes or functional marker gene amplicons. Although molecular fingerprinting remains a valuable approach for rapid confirmation of isotope labelling, recent advances in sequencing technology mean that it is possible to obtain affordable and comprehensive amplicon profiles, or even metagenomes and metatranscriptomes from SIP experiments. Not only can the abundance of microbial groups be inferred from metagenomes, but researchers can bin, assemble, and explore individual genomes to build hypotheses about the metabolic capabilities of labelled microorganisms. Analysis of labelled mRNA is a more recent advance that can provide independent metatranscriptome-based analysis of active microorganisms. The power of metatranscriptomics is that mRNA abundance often correlates closely with the corresponding activity of encoded enzymes, thus providing insight into microbial metabolism at the time of sampling. Together, these advances have improved the sensitivity of SIP methods and allowed using labelled substrates at environmentally relevant concentrations. Particularly as methods improve and costs continue to drop, we expect that the integration of SIP with multiple omics-based methods will become prevalent components of microbial ecology studies, leading to further breakthroughs in our understanding of novel microbial populations and elucidation of the metabolic function of complex microbial communities. In this chapter, we provide protocols for obtaining labelled DNA, RNA, and proteins that can be used for downstream omics-based analyses.}, } @article {pmid36306082, year = {2023}, author = {Thakor, A and Cheng, J and Charles, TC}, title = {Isolation of Genes Encoding Carbon Metabolism Pathways from Complex Microbial Communities.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {115-123}, pmid = {36306082}, issn = {1940-6029}, mesh = {*Carbon/metabolism ; Escherichia coli/genetics/metabolism ; *Microbiota ; Metagenome ; Metagenomics ; Fermentation ; }, abstract = {The ability to produce high-value products using bacteria will increasingly rely on continued research to make large-scale bacterial fermentation cost-efficient. Engineering bacteria to use alternate carbon sources as feedstock provides an opportunity to reduce production costs. Using inexpensive carbon sources from various forms of waste provides an opportunity to substantially reduce feedstock costs. Functional carbon metabolism pathways can be identified by the introduction of metagenomic libraries into the organism of interest followed by screening for the desired phenotype. We present here a method to transfer metagenomic libraries from E. coli to Pseudomonas alloputida, followed by screening for use of galactose as a sole carbon source.}, } @article {pmid36306077, year = {2023}, author = {Weiland-Bräuer, N and Saleh, L and Schmitz, RA}, title = {Functional Metagenomics as a Tool to Tap into Natural Diversity of Valuable Biotechnological Compounds.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {23-49}, pmid = {36306077}, issn = {1940-6029}, mesh = {*Ecosystem ; *Metagenomics ; Metagenome ; Biotechnology ; Biodiversity ; }, abstract = {The marine ecosystem covers more than 70% of the world's surface, and oceans represent a source of varied types of organisms due to the diversified environment. Consequently, the marine environment is an exceptional depot of novel bioactive natural products, with structural and chemical features generally not found in terrestrial habitats. Here, in particular, microbes represent a vast source of unknown and probably new physiological characteristics. They have evolved during extended evolutionary processes of physiological adaptations under various environmental conditions and selection pressures. However, to date, the biodiversity of marine microbes and the versatility of their bioactive compounds and metabolites have not been fully explored. Thus, metagenomic tools are required to exploit the untapped marine microbial diversity and their bioactive compounds. This chapter focuses on function-based marine metagenomics to screen for bioactive molecules of value for biotechnology. Functional metagenomic strategies are described, including sampling in the marine environment, constructing marine metagenomic large-insert libraries, and examples on function-based screens for quorum quenching and anti-biofilm activities.}, } @article {pmid36306076, year = {2023}, author = {Hollensteiner, J and Wemheuer, F and Schneider, D and Pfeiffer, B and Wemheuer, B}, title = {Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a Universal cDNA as Universal Template for Marker Gene Studies.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {13-21}, pmid = {36306076}, issn = {1940-6029}, mesh = {DNA, Complementary/genetics ; RNA, Ribosomal, 16S/genetics ; *DNA/genetics ; *Microbiota ; Sequence Analysis, DNA ; Metagenomics/methods ; Phylogeny ; }, abstract = {Microbial communities play an important role in marine ecosystem processes. Although the number of studies targeting marker genes such as the 16S rRNA gene has increased during the last years, the vast majority of marine diversity are rather unexplored. Moreover, most studies focused on the entire microbial community and thus do not assess the active fraction of the microbial community. Here, we describe a detailed protocol for the simultaneous extraction of DNA and RNA from marine water samples and the generation of cDNA from the isolated RNA that can be used as a universal template in various marker gene studies.}, } @article {pmid36306075, year = {2023}, author = {Simon, C and Daniel, R}, title = {Construction of Small-Insert and Large-Insert Metagenomic Libraries.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {1-12}, pmid = {36306075}, issn = {1940-6029}, mesh = {Gene Library ; *Metagenomics/methods ; *Metagenome ; Biodiversity ; Plasmids/genetics ; }, abstract = {The vast majority of the Earth's biological diversity are hidden in uncultured and yet uncharacterized microbial genomes. The construction of metagenomic libraries is one cultivation-independent molecular approach to assess this unexplored genetic reservoir. High numbers of novel biocatalysts have been identified by function-based or sequence-based screening of metagenomic libraries derived from various environments. Here, we describe detailed protocols for the construction of metagenomic small-insert and large-insert libraries in plasmids and fosmids, respectively, from environmental DNA.}, } @article {pmid36305395, year = {2022}, author = {Ju, Y and Wang, X and Wang, Y and Li, C and Yue, L and Chen, F}, title = {[Application of metagenomic and culturomic technologies in fecal microbiota transplantation: a review].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {38}, number = {10}, pages = {3594-3605}, doi = {10.13345/j.cjb.220573}, pmid = {36305395}, issn = {1872-2075}, mesh = {Humans ; *Fecal Microbiota Transplantation ; Metagenomics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Bacteria ; }, abstract = {Fecal microbiota transplantation (FMT) refers to using the intestinal microorganisms present in the feces or processed feces from healthy people for treating various types of diseases, such as digestive and metabolic diseases. The rapid development of metagenomic and culturomic technologies in gut microbiome analysis provides powerful tools for the FMT research and its clinical applications. Metagenomics technologies comprehensively revealed the diversity and functions of gut microbiota under health and disease conditions, while culturomics technologies helped isolation and identification of "unculturable" bacteria in the human gut under conventional culture conditions. The combination of these two technologies not only enabled us better understand the FMT regularities of cause and effect in clinical practices, but also effectively promoted its applications. Considering the above advantages, this article summarized the applications of metagenomics and culturomics technologies in FMT and prospected its future development trend.}, } @article {pmid36302811, year = {2022}, author = {Aalam, SMM and Crasta, DN and Roy, P and Miller, AL and Gamb, SI and Johnson, S and Till, LM and Chen, J and Kashyap, P and Kannan, N}, title = {Genesis of fecal floatation is causally linked to gut microbial colonization in mice.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {18109}, pmid = {36302811}, issn = {2045-2322}, support = {P30 DK084567/DK/NIDDK NIH HHS/United States ; R01 DK114007/DK/NIDDK NIH HHS/United States ; }, mesh = {Mice ; Humans ; Animals ; *Gastrointestinal Microbiome ; Feces/microbiology ; Fecal Microbiota Transplantation ; Metagenomics ; Bacteria/genetics ; }, abstract = {The origin of fecal floatation phenomenon remains poorly understood. Following our serendipitous discovery of differences in buoyancy of feces from germ-free and conventional mice, we characterized microbial and physical properties of feces from germ-free and gut-colonized (conventional and conventionalized) mice. The gut-colonization associated differences were assessed in feces using DNA, bacterial-PCR, scanning electron microscopy, FACS, thermogravimetry and pycnometry. Based on the differences in buoyancy of feces, we developed levô in fimo test (LIFT) to distinguish sinking feces (sinkers) of germ-free mice from floating feces (floaters) of gut-colonized mice. By simultaneous tracking of microbiota densities and gut colonization kinetics in fecal transplanted mice, we provide first direct evidence of causal relationship between gut microbial colonization and fecal floatation. Rare discordance in LIFT and microbiota density indicated that enrichment of gasogenic gut colonizers may be necessary for fecal floatation. Finally, fecal metagenomics analysis of 'floaters' from conventional and syngeneic fecal transplanted mice identified colonization of > 10 gasogenic bacterial species including highly prevalent B. ovatus, an anaerobic commensal bacteria linked with flatulence and intestinal bowel diseases. The findings reported here will improve our understanding of food microbial biotransformation and gut microbial regulators of fecal floatation in human health and disease.}, } @article {pmid36301254, year = {2023}, author = {Safari-Alighiarloo, N and Emami, Z and Rezaei-Tavirani, M and Alaei-Shahmiri, F and Razavi, S}, title = {Gut Microbiota and Their Associated Metabolites in Diabetes: A Cross Talk Between Host and Microbes-A Review.}, journal = {Metabolic syndrome and related disorders}, volume = {21}, number = {1}, pages = {3-15}, doi = {10.1089/met.2022.0049}, pmid = {36301254}, issn = {1557-8518}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2 ; Dysbiosis ; Metabolomics/methods ; Metabolome ; }, abstract = {Dysbiosis of the gut microbiota's composition and function is important in developing insulin resistance and diabetes. Diabetes has also been linked to changes in the circulating and fecal metabolites. Evidence suggests the associations between the gut microbiota and the aberrant diabetes-related metabolome. Metabolites play a crucial role in the host-microbiota interactions. Researchers have used a combination of metagenomic and metabolomic approaches to investigate the relationships between gut microbial dysbiosis and metabolic abnormalities in diabetes. We summarized current discoveries on the associations between the gut microbiota and metabolites in type 1 diabetes, type 2 diabetes, and gestational diabetes mellitus in the scoping review. According to research, the gut microbiota changes might involve in the development of diabetes through modulating the host's metabolic pathways such as immunity, energy metabolism, lipid metabolism, and amino acid metabolism. These results add to our understanding of the interplay between the host and gut microbiota metabolism.}, } @article {pmid36300928, year = {2022}, author = {Chen, J and Zeng, P and Gong, L and Zhang, X and Ling, Z and Bi, K and Shi, F and Wang, K and Zhang, Q and Jiang, J and Zhang, Y and Uede, T and El-Omar, EM and Diao, H}, title = {Osteopontin Exacerbates High-Fat Diet-Induced Metabolic Disorders in a Microbiome-Dependent Manner.}, journal = {mBio}, volume = {13}, number = {6}, pages = {e0253122}, pmid = {36300928}, issn = {2150-7511}, mesh = {Animals ; Humans ; Mice ; Diet, High-Fat ; *Gastrointestinal Microbiome ; *Metabolic Diseases ; Mice, Inbred C57BL ; Obesity ; Osteopontin/pharmacology/therapeutic use ; Microbiota ; }, abstract = {The gut microbiome is involved in metabolic disorders. Osteopontin (OPN), as a key cytokine, contributes to various inflammation-related diseases. The underlying role of OPN in the microbiome remains poorly understood. Here, we investigated whether OPN could modulate metabolic disorders by affecting gut microbiota. In our present study, we found that the expression of OPN was elevated in individuals with obesity compared to that observed in healthy controls. There was a positive correlation between plasma OPN levels and body mass index (BMI) in humans. Moreover, OPN significantly exacerbated lipid accumulation and metabolic disorders in high-fat diet (HFD)-fed mice. Importantly, OPN significantly aggravated HFD-induced gut dysbiosis with a key signature profile. Fecal microbiota transplantation also supported the role of OPN in HFD-induced metabolic disorders in a microbiota-dependent manner. Moreover, the microbiome shift of OPN-deficient mice would be compensated to resemble those of wild-type mice by feeding with either OPN-containing milk or recombinant OPN protein in vivo. Furthermore, metagenomic analysis showed that OPN induced a higher abundance of Dorea and a lower abundance of Lactobacillus, which were positively and negatively correlated with body weight, respectively. Indeed, the abundance of Dorea was significantly decreased after Lactobacillus administration, suggesting that OPN may regulate the intestinal abundance of Dorea by reducing the colonization of Lactobacillus. We further confirmed that OPN decreased the adhesion of Lactobacillus to intestinal epithelial cells through the Notch signaling pathway. This study suggested that OPN could exacerbate HFD-induced metabolic dysfunctions through the OPN-induced alteration of the gut microbiome. Therefore, OPN could be a potential therapeutic target for metabolic syndrome. IMPORTANCE Gut microbiota are involved in metabolic disorders. However, microbiome-based therapeutic interventions are not always effective, which might be due to interference of the host factors. Here, we identified a strong positive correlation between OPN levels and BMI in humans. Next, we confirmed that OPN could aggravate high-fat diet-induced metabolic disorders in mice. Importantly, we found that fecal microbiota transplantation from OPN-deficient mice significantly alleviated metabolic disorders in WT mice. OPN directly induces the remodeling of the gut microbiota both in vitro and in vivo. These findings indicate that OPN could contribute to metabolic disorders by inducing an alteration of gut microbiota. OPN regulated the relative abundance of Lactobacillus by decreasing the adhesion of Lactobacillus to intestinal epithelial cells through the Notch signaling pathway. These data identify OPN as a potential pharmaceutical target for weight control and for the treatment of metabolic disorders.}, } @article {pmid36299622, year = {2022}, author = {Gao, Y and Sohn, MB and Wang, J}, title = {Editorial: Gut virome and human health.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1043256}, pmid = {36299622}, issn = {2235-2988}, mesh = {Humans ; *Virome ; Metagenomics ; *Viruses/genetics ; }, } @article {pmid36297000, year = {2022}, author = {Rey-Mariño, A and Francino, MP}, title = {Nutrition, Gut Microbiota, and Allergy Development in Infants.}, journal = {Nutrients}, volume = {14}, number = {20}, pages = {}, pmid = {36297000}, issn = {2072-6643}, support = {PID2019-105969GB-I00//Ministry of Science and Innovation, Spain/ ; 816303//European Commission/ ; }, mesh = {Infant ; Humans ; *Gastrointestinal Microbiome ; *Hypersensitivity/etiology ; *Microbiota ; Metagenomics ; Diet ; }, abstract = {The process of gut microbiota development in infants is currently being challenged by numerous factors associated with the contemporary lifestyle, including diet. A thorough understanding of all aspects of microbiota development will be necessary for engineering strategies that can modulate it in a beneficial direction. The long-term consequences for human development and health of alterations in the succession pattern that forms the gut microbiota are just beginning to be explored and require much further investigation. Nevertheless, it is clear that gut microbiota development in infancy bears strong associations with the risk for allergic disease. A useful understanding of microbial succession in the gut of infants needs to reveal not only changes in taxonomic composition but also the development of functional capacities through time and how these are related to diet and various environmental factors. Metagenomic and metatranscriptomic studies have started to produce insights into the trends of functional repertoire and gene expression change within the first year after birth. This understanding is critical as during this period the most substantial development of the gut microbiota takes place and the relations between gut microbes and host immunity are established. However, further research needs to focus on the impact of diet on these changes and on how diet can be used to counteract the challenges posed by modern lifestyles to microbiota development and reduce the risk of allergic disease.}, } @article {pmid36296361, year = {2022}, author = {Goodman, AZ and Papudeshi, B and Doane, MP and Mora, M and Kerr, E and Torres, M and Nero Moffatt, J and Lima, L and Nosal, AP and Dinsdale, E}, title = {Epidermal Microbiomes of Leopard Sharks (Triakis semifasciata) Are Consistent across Captive and Wild Environments.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296361}, issn = {2076-2607}, abstract = {Characterizations of shark-microbe systems in wild environments have outlined patterns of species-specific microbiomes; however, whether captivity affects these trends has yet to be determined. We used high-throughput shotgun sequencing to assess the epidermal microbiome belonging to leopard sharks (Triakis semifasciata) in captive (Birch Aquarium, La Jolla California born and held permanently in captivity), semi-captive (held in captivity for <1 year in duration and scheduled for release; Scripps Institute of Oceanography, San Diego, CA, USA) and wild environments (Moss Landing and La Jolla, CA, USA). Here, we report captive environments do not drive epidermal microbiome compositions of T. semifasciata to significantly diverge from wild counterparts as life-long captive sharks maintain a species-specific epidermal microbiome resembling those associated with semi-captive and wild populations. Major taxonomic composition shifts observed were inverse changes of top taxonomic contributors across captive duration, specifically an increase of Pseudoalteromonadaceae and consequent decrease of Pseudomonadaceae relative abundance as T. semifasciata increased duration in captive conditions. Moreover, we show captivity did not lead to significant losses in microbial α-diversity of shark epidermal communities. Finally, we present a novel association between T. semifasciata and the Muricauda genus as Metagenomes associated genomes revealed a consistent relationship across captive, semi-captive, and wild populations. Since changes in microbial communities is often associated with poor health outcomes, our report illustrates that epidermally associated microbes belonging to T. semifasciata are not suffering detrimental impacts from long or short-term captivity. Therefore, conservation programs which house sharks in aquariums are providing a healthy environment for the organisms on display. Our findings also expand on current understanding of shark epidermal microbiomes, explore the effects of ecologically different scenarios on benthic shark microbe associations, and highlight novel associations that are consistent across captive gradients.}, } @article {pmid36296177, year = {2022}, author = {Leite, MFA and van den Broek, SWEB and Kuramae, EE}, title = {Current Challenges and Pitfalls in Soil Metagenomics.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296177}, issn = {2076-2607}, abstract = {Soil microbial communities are essential components of agroecological ecosystems that influence soil fertility, nutrient turnover, and plant productivity. Metagenomics data are increasingly easy to obtain, but studies of soil metagenomics face three key challenges: (1) accounting for soil physicochemical properties; (2) incorporating untreated controls; and (3) sharing data. Accounting for soil physicochemical properties is crucial for better understanding the changes in soil microbial community composition, mechanisms, and abundance. Untreated controls provide a good baseline to measure changes in soil microbial communities and separate treatment effects from random effects. Sharing data increases reproducibility and enables meta-analyses, which are important for investigating overall effects. To overcome these challenges, we suggest establishing standard guidelines for the design of experiments for studying soil metagenomics. Addressing these challenges will promote a better understanding of soil microbial community composition and function, which we can exploit to enhance soil quality, health, and fertility.}, } @article {pmid36293448, year = {2022}, author = {Malicka, M and Magurno, F and Piotrowska-Seget, Z}, title = {Phenol and Polyaromatic Hydrocarbons Are Stronger Drivers Than Host Plant Species in Shaping the Arbuscular Mycorrhizal Fungal Component of the Mycorrhizosphere.}, journal = {International journal of molecular sciences}, volume = {23}, number = {20}, pages = {}, pmid = {36293448}, issn = {1422-0067}, support = {2017/25/N/NZ8/01676//National Science Centre, Poland/ ; }, mesh = {*Mycorrhizae/physiology ; Soil Microbiology ; Phenol ; *Glomeromycota ; Soil/chemistry ; Plants/genetics ; Hydrocarbons ; *Polycyclic Aromatic Hydrocarbons ; DNA, Ribosomal/genetics ; *Microbiota ; Plant Roots/microbiology ; }, abstract = {Changes in soil microbial communities in response to hydrocarbon pollution are critical indicators of disturbed ecosystem conditions. A core component of these communities that is functionally adjusted to the life-history traits of the host and environmental factors consists of arbuscular mycorrhizal fungi (AMF). AMF communities associated with Poa trivialis and Phragmites australis growing at a phenol and polynuclear aromatic hydrocarbon (PAH)-contaminated site and at an uncontaminated site were compared based on LSU rDNA sequencing. Dissimilarities in species composition and community structures indicated soil pollution as the main factor negatively affecting the AMF diversity. The AMF communities at the contaminated site were dominated by fungal generalists (Rhizophagus, Funneliformis, Claroideoglomus, Paraglomus) with wide ecological tolerance. At the control site, the AMF communities were characterized by higher taxonomic and functional diversity than those exposed to the contamination. The host plant identity was the main driver distinguishing the two AMF metacommunities. The AMF communities at the uncontaminated site were represented by Polonospora, Paraglomus, Oehlia, Nanoglomus, Rhizoglomus, Dominikia, and Microdominikia. Polonosporaceae and Paraglomeraceae were particularly dominant in the Ph. australis mycorrhizosphere. The high abundance of early diverging AMF could be due to the use of primers able to detect lineages such as Paraglomeracae that have not been recognized by previously used 18S rDNA primers.}, } @article {pmid36293097, year = {2022}, author = {Escuder-Rodríguez, JJ and DeCastro, ME and Saavedra-Bouza, A and Becerra, M and González-Siso, MI}, title = {Insights on Microbial Communities Inhabiting Non-Volcanic Hot Springs.}, journal = {International journal of molecular sciences}, volume = {23}, number = {20}, pages = {}, pmid = {36293097}, issn = {1422-0067}, support = {ED431C 2020/08//Xunta de Galicia/ ; RTI2018-099249-B-I00//MINISTERIO DE CIENCIA, INNOVACIÓN Y UNIVERSIDADES/ ; }, mesh = {Bacteria/metabolism ; Biodiversity ; *Hot Springs/microbiology ; *Microbiota ; Peptide Hydrolases/metabolism ; Phylogeny ; Sulfur/metabolism ; }, abstract = {The northwest of Spain has an abundance of non-volcanic hot springs that, until recently, had only been used for thermalism activities. One of such hot springs, Muiño da Veiga, has now been explored using metagenomics to study the microbial community that inhabits these high-temperature circumneutral continental waters. Sequencing of the metagenome allowed the characterization of its composition, diversity, metabolic connections and potential as a source for thermozymes, as well as its ability to assemble MAGs. A diverse microbial community dominated by Bacteria domain members was revealed, particularly from the early-branching Aquificales group. The most abundant genus was Sulfurihydrogenibium, known for its implication in sulfur cycling and for forming mats that enable novel niches. The variety of primary producers with autotrophic pathways (and specifically the sulfur oxidizing pathway) expands the range of available nutrients, and the increase in biomass forms thicker mats, resulting in more available niches and broader microbial diversity. Nonetheless, certain metabolic pathways were attributed to less abundant members of the microbial community, reinforcing the idea that the rare biosphere plays important roles in the network of interactions present in an ecosystem and acts as genetic reservoirs. In addition, three of the assembled MAGs represent novel microbial diversity found in this hot spring. Moreover, the presence of enzymes and microorganisms with possible biotechnological applications was confirmed, including proteases, lipases and cell-wall degrading enzymes, pointing to the potential for the hot spring as a source for thermozymes.}, } @article {pmid36293066, year = {2022}, author = {Vanstokstraeten, R and Mackens, S and Callewaert, E and Blotwijk, S and Emmerechts, K and Crombé, F and Soetens, O and Wybo, I and Vandoorslaer, K and Mostert, L and De Geyter, D and Muyldermans, A and Blockeel, C and Piérard, D and Demuyser, T}, title = {Culturomics to Investigate the Endometrial Microbiome: Proof-of-Concept.}, journal = {International journal of molecular sciences}, volume = {23}, number = {20}, pages = {}, pmid = {36293066}, issn = {1422-0067}, mesh = {Pregnancy ; Humans ; Female ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenomics/methods ; Bacteria ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {The microbiome of the reproductive tract has been associated with (sub)fertility and it has been suggested that dysbiosis reduces success rates and pregnancy outcomes. The endometrial microbiome is of particular interest given the potential impact on the embryo implantation. To date, all endometrial microbiome studies have applied a metagenomics approach. A sequencing-based technique, however, has its limitations, more specifically in adequately exploring low-biomass settings, such as intra-uterine/endometrial samples. In this proof-of-concept study, we demonstrate the applicability of culturomics, a high-throughput culturing approach, to investigate the endometrial microbiome. Ten subfertile women undergoing diagnostic hysteroscopy and endometrial biopsy, as part of their routine work-up at Brussels IVF, were included after their informed consent. Biopsies were used to culture microbiota for up to 30 days in multiple aerobic and anaerobic conditions. Subsequent WASPLab[®]-assisted culturomics enabled a standardized methodology. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) or 16S rRNA sequencing was applied to identify all of bacterial and fungal isolates. Eighty-three bacterial and two fungal species were identified. The detected species were in concordance with previously published metagenomics-based endometrial microbiota analyses as 77 (91%) of them belonged to previously described genera. Nevertheless, highlighting the added value of culturomics to identify most isolates at the species level, 53 (62.4%) of the identified species were described in the endometrial microbiota for the first time. This study shows the applicability and added value of WASPLab[®]-assisted culturomics to investigate the low biomass endometrial microbiome at a species level.}, } @article {pmid36293010, year = {2022}, author = {Ferrandi, EE and Bassanini, I and Bertuletti, S and Riva, S and Tognoli, C and Vanoni, M and Monti, D}, title = {Functional Characterization and Synthetic Application of Is2-SDR, a Novel Thermostable and Promiscuous Ketoreductase from a Hot Spring Metagenome.}, journal = {International journal of molecular sciences}, volume = {23}, number = {20}, pages = {}, pmid = {36293010}, issn = {1422-0067}, support = {CN00000033, PNRR MUR -M4C2 -D. D. n.1034, 17.06.2022//National Biodiversity Future Center/ ; }, mesh = {*Hot Springs ; Metagenome ; *Short Chain Dehydrogenase-Reductases ; Hydroxysteroid Dehydrogenases/genetics ; Ketones ; Steroids ; Water ; Cholic Acid ; Pharmaceutical Preparations ; Solvents ; Substrate Specificity ; }, abstract = {In a metagenome mining-based search of novel thermostable hydroxysteroid dehydrogenases (HSDHs), enzymes that are able to selectively oxidize/reduce steroidal compounds, a novel short-chain dehydrogenase/reductase (SDR), named Is2-SDR, was recently discovered. This enzyme, found in an Icelandic hot spring metagenome, shared a high sequence similarity with HSDHs, but, unexpectedly, showed no activity in the oxidation of the tested steroid substrates, e.g., cholic acid. Despite that, Is2-SDR proved to be a very active and versatile ketoreductase, being able to regio- and stereoselectively reduce a diversified panel of carbonylic substrates, including bulky ketones, α- and β-ketoesters, and α-diketones of pharmaceutical relevance. Further investigations showed that Is2-SDR was indeed active in the regio- and stereoselective reduction of oxidized steroid derivatives, and this outcome was rationalized by docking analysis in the active site model. Moreover, Is2-SDR showed remarkable thermostability, with an apparent melting temperature (TM) around 75 °C, as determined by circular dichroism analysis, and no significant decrease in catalytic activity, even after 5 h at 80 °C. A broad tolerance to both water-miscible and water-immiscible organic solvents was demonstrated as well, thus, confirming the potential of this new biocatalyst for its synthetic application.}, } @article {pmid36292799, year = {2022}, author = {Bhattacharya, C and Tierney, BT and Ryon, KA and Bhattacharyya, M and Hastings, JJA and Basu, S and Bhattacharya, B and Bagchi, D and Mukherjee, S and Wang, L and Henaff, EM and Mason, CE}, title = {Supervised Machine Learning Enables Geospatial Microbial Provenance.}, journal = {Genes}, volume = {13}, number = {10}, pages = {}, pmid = {36292799}, issn = {2073-4425}, support = {U01 DA053941/DA/NIDA NIH HHS/United States ; R01 AI125416/AI/NIAID NIH HHS/United States ; R21 EB031466/EB/NIBIB NIH HHS/United States ; R01 AI151059/AI/NIAID NIH HHS/United States ; R21 AI129851/AI/NIAID NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; Metagenome ; *Microbiota/genetics ; Supervised Machine Learning ; Cities ; }, abstract = {The recent increase in publicly available metagenomic datasets with geospatial metadata has made it possible to determine location-specific, microbial fingerprints from around the world. Such fingerprints can be useful for comparing microbial niches for environmental research, as well as for applications within forensic science and public health. To determine the regional specificity for environmental metagenomes, we examined 4305 shotgun-sequenced samples from the MetaSUB Consortium dataset-the most extensive public collection of urban microbiomes, spanning 60 different cities, 30 countries, and 6 continents. We were able to identify city-specific microbial fingerprints using supervised machine learning (SML) on the taxonomic classifications, and we also compared the performance of ten SML classifiers. We then further evaluated the five algorithms with the highest accuracy, with the city and continental accuracy ranging from 85-89% to 90-94%, respectively. Thereafter, we used these results to develop Cassandra, a random-forest-based classifier that identifies bioindicator species to aid in fingerprinting and can infer higher-order microbial interactions at each site. We further tested the Cassandra algorithm on the Tara Oceans dataset, the largest collection of marine-based microbial genomes, where it classified the oceanic sample locations with 83% accuracy. These results and code show the utility of SML methods and Cassandra to identify bioindicator species across both oceanic and urban environments, which can help guide ongoing efforts in biotracing, environmental monitoring, and microbial forensics (MF).}, } @article {pmid36292745, year = {2022}, author = {Sánchez-Pellicer, P and Navarro-Moratalla, L and Núñez-Delegido, E and Agüera-Santos, J and Navarro-López, V}, title = {How Our Microbiome Influences the Pathogenesis of Alopecia Areata.}, journal = {Genes}, volume = {13}, number = {10}, pages = {}, pmid = {36292745}, issn = {2073-4425}, mesh = {Humans ; *Alopecia Areata/genetics ; RNA, Ribosomal, 16S/genetics ; *Autoimmune Diseases/genetics ; *Microbiota ; }, abstract = {Alopecia areata is a multifactorial autoimmune-based disease with a complex pathogenesis. As in all autoimmune diseases, genetic predisposition is key. The collapse of the immune privilege of the hair follicle leading to scalp loss is a major pathogenic event in alopecia areata. The microbiota considered a bacterial ecosystem located in a specific area of the human body could somehow influence the pathogenesis of alopecia areata, as it occurs in other autoimmune diseases. Moreover, the Next Generation Sequencing of the 16S rRNA bacterial gene and the metagenomic methodology have provided an excellent characterization of the microbiota. The aim of this narrative review is to examine the published literature on the cutaneous and intestinal microbiota in alopecia areata to be able to establish a pathogenic link. In this review, we summarize the influence of the microbiota on the development of alopecia areata. We first introduce the general pathogenic mechanisms that cause alopecia areata to understand the influence that the microbiota may exert and then we summarize the studies that have been carried out on what type of gut and skin microbiota is found in patients with this disease.}, } @article {pmid36292643, year = {2022}, author = {Li, M and Tyx, RE and Rivera, AJ and Zhao, N and Satten, GA}, title = {What Can We Learn about the Bias of Microbiome Studies from Analyzing Data from Mock Communities?.}, journal = {Genes}, volume = {13}, number = {10}, pages = {}, pmid = {36292643}, issn = {2073-4425}, support = {R01 GM116065/GM/NIGMS NIH HHS/United States ; R01 GM141074/GM/NIGMS NIH HHS/United States ; R21 AI154236/AI/NIAID NIH HHS/United States ; U24 OD023382/OD/NIH HHS/United States ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenomics/methods ; Bacteria/genetics ; Bias ; }, abstract = {It is known that data from both 16S and shotgun metagenomics studies are subject to biases that cause the observed relative abundances of taxa to differ from their true values. Model community analyses, in which the relative abundances of all taxa in the sample are known by construction, seem to offer the hope that these biases can be measured. However, it is unclear whether the bias we measure in a mock community analysis is the same as we measure in a sample in which taxa are spiked in at known relative abundance, or if the biases we measure in spike-in samples is the same as the bias we would measure in a real (e.g., biological) sample. Here, we consider these questions in the context of 16S rRNA measurements on three sets of samples: the commercially available Zymo cells model community; the Zymo model community mixed with Swedish Snus, a smokeless tobacco product that is virtually bacteria-free; and a set of commercially available smokeless tobacco products. Each set of samples was subject to four different extraction protocols. The goal of our analysis is to determine whether the patterns of bias observed in each set of samples are the same, i.e., can we learn about the bias in the commercially available smokeless tobacco products by studying the Zymo cells model community?}, } @article {pmid36291654, year = {2022}, author = {Fang, C and Zuo, K and Fu, Y and Zhu, X and Li, J and Zhong, J and Xu, L and Yang, X}, title = {Aggravated Gut Microbiota and Metabolomic Imbalances Are Associated with Hypertension Patients Comorbid with Atrial Fibrillation.}, journal = {Biomolecules}, volume = {12}, number = {10}, pages = {}, pmid = {36291654}, issn = {2218-273X}, mesh = {Humans ; *Atrial Fibrillation ; *Gastrointestinal Microbiome ; *Hypertension ; Stearic Acids ; Arachidonic Acids ; Linoleic Acids ; Palmitic Acids ; Oleic Acids ; }, abstract = {Disordered gut microbiota (GM) as the co-contributor of atrial fibrillation (AF) and hypertension (HTN) might be associated with AF risk in HTN. This study aimed to explore the altered GM community and metabolic patterns between 27 HTN patients with AF (HTN-AF) and 27 non-AF HTN patients through fecal metagenomic and serum metabolomic analysis. Compared to non-AF HTN patients, significant microbial alterations (p = 0.004), including increased microbial diversity (p < 0.05), shifted enterotype dominated by Prevotella to Bacteroides, and abundant disease-linked genera Ruminococcus, Streptococcus, Veillonella, Dorea, and Enterococcus, were observed in HTN-AF patients. A species-based random forest prediction model was associated with the risk of AF occurrence in HTN patients. Furthermore, GM metabolic profiles dramatically differed between HTN and HTN-AF patients, especially the imbalance of saturated and unsaturated fatty acids. In HTN-AF patients, circulating palmitic acid and arachidonic acid levels were significantly elevated, while the levels of tetracosahexaenoic acid, oleic acid, linoleic acid, and stearic acid were decreased (p < 0.001, VIP > 1), mediating 85.99% of gut microbial indirect effects on AF (p < 0.001). Thus, our findings preliminarily indicated that exacerbated dysbiosis of GM and relevant metabolites was associated with high AF susceptibility and might be a potential target for AF prediction and prevention in HTN.}, } @article {pmid36291597, year = {2022}, author = {Miao, Q and Zhang, X and Wang, Y and Li, X and Wang, Z and Tian, L and Qu, L and Wei, Y}, title = {Characterization of Novel Pectinolytic Enzymes Derived from the Efficient Lignocellulose Degradation Microbiota.}, journal = {Biomolecules}, volume = {12}, number = {10}, pages = {}, pmid = {36291597}, issn = {2218-273X}, mesh = {*Polygalacturonase/metabolism ; Lignin/metabolism ; *Microbiota/genetics ; Metagenomics ; }, abstract = {Diverse pectinolytic enzymes are widely applied in the food, papermaking, and other industries, and they account for more than 25% of the global industrial enzyme demands. Efficient lignocellulose degradation microbiota are reservoirs of pectinolytic enzymes and other lignocellulose-degrading genes. Metagenomics has been widely used to discover new pectinolytic enzymes. Here, we used a metagenomic strategy to characterize pectinolytic genes from one efficient lignocellulose-degrading microbiota derived from pulp and paper wastewater treatment microbiota. A total of 23 predicted full-length GH28 and PL1 family pectinolytic genes were selectively cloned and expressed in Escherichia coli, and 5 of the expressed proteins had pectinolytic activities. Among them, the characterization of one pectinolytic enzyme, PW-pGH28-3, which has a 58.4% identity with an exo-polygalacturonase gene of Aquipluma nitroreducens, was further investigated. The optimal pH and optimal temperature of PW-pGH28-3 were 8.0 and 40 °C, respectively, and its pectinolytic activity at the optimal condition was 13.5 ± 1.1 U/mg protein. Bioinformatics analyses and structural modeling suggest that PW-pGH28-3 is a novel secretory exo-polygalacturonase, which is confirmed by its hydrolysates of polygalacturonic acid. The detection of PW-pGH28-3 and other pectinolytic genes showed that efficient lignocellulose degradation microbiota could provide potential efficient pectinolytic enzymes for industrial application. In the future, improving metagenomic screening efficiency would discover efficient lignocellulose-degrading enzymes and lead to the sustainable and green utilization of lignocellulose.}, } @article {pmid36291121, year = {2022}, author = {Mishra, AK and Sudalaimuthuasari, N and Hazzouri, KM and Saeed, EE and Shah, I and Amiri, KMA}, title = {Tapping into Plant-Microbiome Interactions through the Lens of Multi-Omics Techniques.}, journal = {Cells}, volume = {11}, number = {20}, pages = {}, pmid = {36291121}, issn = {2073-4409}, mesh = {*Plant Roots/metabolism ; Genome-Wide Association Study ; *Microbiota ; Soil/chemistry ; Plants/metabolism ; Pheromones/metabolism ; }, abstract = {This review highlights the pivotal role of root exudates in the rhizosphere, especially the interactions between plants and microbes and between plants and plants. Root exudates determine soil nutrient mobilization, plant nutritional status, and the communication of plant roots with microbes. Root exudates contain diverse specialized signaling metabolites (primary and secondary). The spatial behavior of these metabolites around the root zone strongly influences rhizosphere microorganisms through an intimate compatible interaction, thereby regulating complex biological and ecological mechanisms. In this context, we reviewed the current understanding of the biological phenomenon of allelopathy, which is mediated by phytotoxic compounds (called allelochemicals) released by plants into the soil that affect the growth, survival, development, ecological infestation, and intensification of other plant species and microbes in natural communities or agricultural systems. Advances in next-generation sequencing (NGS), such as metagenomics and metatranscriptomics, have opened the possibility of better understanding the effects of secreted metabolites on the composition and activity of root-associated microbial communities. Nevertheless, understanding the role of secretory metabolites in microbiome manipulation can assist in designing next-generation microbial inoculants for targeted disease mitigation and improved plant growth using the synthetic microbial communities (SynComs) tool. Besides a discussion on different approaches, we highlighted the advantages of conjugation of metabolomic approaches with genetic design (metabolite-based genome-wide association studies) in dissecting metabolome diversity and understanding the genetic components of metabolite accumulation. Recent advances in the field of metabolomics have expedited comprehensive and rapid profiling and discovery of novel bioactive compounds in root exudates. In this context, we discussed the expanding array of metabolomics platforms for metabolome profiling and their integration with multivariate data analysis, which is crucial to explore the biosynthesis pathway, as well as the regulation of associated pathways at the gene, transcript, and protein levels, and finally their role in determining and shaping the rhizomicrobiome.}, } @article {pmid36289209, year = {2022}, author = {Kim, CY and Ma, J and Lee, I}, title = {HiFi metagenomic sequencing enables assembly of accurate and complete genomes from human gut microbiota.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6367}, pmid = {36289209}, issn = {2041-1723}, mesh = {Humans ; *Metagenome/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; Nucleotides ; }, abstract = {Advances in metagenomic assembly have led to the discovery of genomes belonging to uncultured microorganisms. Metagenome-assembled genomes (MAGs) often suffer from fragmentation and chimerism. Recently, 20 complete MAGs (cMAGs) have been assembled from Oxford Nanopore long-read sequencing of 13 human fecal samples, but with low nucleotide accuracy. Here, we report 102 cMAGs obtained by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing of five human fecal samples, whose initial circular contigs were selected for complete prokaryotic genomes using our bioinformatics workflow. Nucleotide accuracy of the final cMAGs was as high as that of Illumina sequencing. The cMAGs could exceed 6 Mbp and included complete genomes of diverse taxa, including entirely uncultured RF39 and TANB77 orders. Moreover, cMAGs revealed that regions hard to assemble by short-read sequencing comprised mostly genomic islands and rRNAs. HiFi metagenomic sequencing will facilitate cataloging accurate and complete genomes from complex microbial communities, including uncultured species.}, } @article {pmid36289064, year = {2022}, author = {Nzabarushimana, E and Tang, H}, title = {Functional profile of host microbiome indicates Clostridioides difficile infection.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2135963}, pmid = {36289064}, issn = {1949-0984}, support = {R01 AI143254/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Clostridioides difficile/genetics ; *Gastrointestinal Microbiome ; *Clostridium Infections/therapy ; Fecal Microbiota Transplantation/methods ; *Microbiota ; Anti-Bacterial Agents/therapeutic use ; Treatment Outcome ; }, abstract = {Clostridioides difficile infection (CDI) is a gastro-intestinal (GI) infection that illustrates how perturbations in symbiotic host-microbiome interactions render the GI tract vulnerable to the opportunistic pathogens. CDI also serves as an example of how such perturbations could be reversed via gut microbiota modulation mechanisms, especially fecal microbiota transplantation (FMT). However, microbiome-mediated diagnosis of CDI remains understudied. Here, we evaluated the diagnostic capabilities of the fecal microbiome on the prediction of CDI. We used the metagenomic sequencing data from ten previous studies, encompassing those acquired from CDI patients treated by FMT, CDI-negative patients presenting other intestinal health conditions, and healthy volunteers taking antibiotics. We designed a hybrid species/function profiling approach that determines the abundances of microbial species in the community contributing to its functional profile. These functionally informed taxonomic profiles were then used for classification of the microbial samples. We used logistic regression (LR) models using these features, which showed high prediction accuracy (with an average AUC≥0.91), substantiating that the species/function composition of the gut microbiome has a robust diagnostic prediction of CDI. We further assessed the confounding impact of antibiotic therapy on CDI prediction and found that it is distinguishable from the CDI impact. Finally, we devised a log-odds score computed from the output of the LR models to quantify the likelihood of CDI in a gut microbiome sample and applied it to evaluating the effectiveness of FMT based on post-FMT microbiome samples. The results showed that the gut microbiome of patients exhibited a gradual but steady improvement after receiving successful FMT, indicating the restoration of the normal microbiome functions.}, } @article {pmid36288838, year = {2022}, author = {Fransson, E and Gudnadottir, U and Hugerth, LW and Itzel, EW and Hamsten, M and Boulund, F and Pennhag, A and Du, J and Schuppe-Koistinen, I and Brusselaers, N and Engstrand, L}, title = {Cohort profile: the Swedish Maternal Microbiome project (SweMaMi) - assessing the dynamic associations between the microbiome and maternal and neonatal adverse events.}, journal = {BMJ open}, volume = {12}, number = {10}, pages = {e065825}, pmid = {36288838}, issn = {2044-6055}, mesh = {Infant ; Pregnancy ; Infant, Newborn ; Female ; Humans ; Child ; Sweden/epidemiology ; *Premature Birth ; Pregnancy Trimester, Third ; Cohort Studies ; *Microbiota ; }, abstract = {PURPOSE: The Swedish Maternal Microbiome (SweMaMi) project was initiated to better understand the dynamics of the microbiome in pregnancy, with longitudinal microbiome sampling, shotgun metagenomics, extensive questionnaires and health registry linkage.

PARTICIPANTS: Pregnant women were recruited before the 20th gestational week during 2017-2021 in Sweden. In total, 5439 pregnancies (5193 unique women) were included. For 3973 pregnancies (73%), samples were provided at baseline, and for 3141 (58%) at all three timepoints (second and third trimester and postpartum). In total, 38 591 maternal microbiome samples (vaginal, faecal and saliva) and 3109 infant faecal samples were collected. Questionnaires were used to collect information on general, reproductive and mental health, diet and lifestyle, complemented by linkage to the nationwide health registries, also used to follow up the health of the offspring (up to age 10).

FINDINGS TO DATE: The cohort is fairly representative for the total Swedish pregnant population (data from 2019), with 41% first-time mothers. Women with university level education, born in Sweden, with normal body mass index, not using tobacco-products and aged 30-34 years were slightly over-represented.

FUTURE PLANS: The sample and data collection were finalised in November 2021. The next steps are the characterisation of the microbial DNA and linkage to the health and demographic information from the questionnaires and registries. The role of the microbiome on maternal and neonatal outcomes and early-childhood diseases will be explored (including preterm birth, miscarriage) and the role and interaction of other risk factors and confounders (including endometriosis, polycystic ovarian syndrome, diet, drug use). This is currently among the largest pregnancy cohorts in the world with longitudinal design and detailed and standardised microbiome sampling enabling follow-up of both mothers and children. The findings are expected to contribute greatly to the field of reproductive health focusing on pregnancy and neonatal outcomes.}, } @article {pmid36288294, year = {2023}, author = {Narayana, JK and Aliberti, S and Mac Aogáin, M and Jaggi, TK and Ali, NABM and Ivan, FX and Cheng, HS and Yip, YS and Vos, MIG and Low, ZS and Lee, JXT and Amati, F and Gramegna, A and Wong, SH and Sung, JJY and Tan, NS and Tsaneva-Atanasova, K and Blasi, F and Chotirmall, SH}, title = {Microbial Dysregulation of the Gut-Lung Axis in Bronchiectasis.}, journal = {American journal of respiratory and critical care medicine}, volume = {207}, number = {7}, pages = {908-920}, pmid = {36288294}, issn = {1535-4970}, mesh = {Animals ; Mice ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Lung/microbiology ; *Bronchiectasis/drug therapy ; *Microbiota ; }, abstract = {Rationale: Emerging data support the existence of a microbial "gut-lung" axis that remains unexplored in bronchiectasis. Methods: Prospective and concurrent sampling of gut (stool) and lung (sputum) was performed in a cohort of n = 57 individuals with bronchiectasis and subjected to bacteriome (16S rRNA) and mycobiome (18S Internal Transcribed Spacer) sequencing (total, 228 microbiomes). Shotgun metagenomics was performed in a subset (n = 15; 30 microbiomes). Data from gut and lung compartments were integrated by weighted similarity network fusion, clustered, and subjected to co-occurrence analysis to evaluate gut-lung networks. Murine experiments were undertaken to validate specific Pseudomonas-driven gut-lung interactions. Results: Microbial communities in stable bronchiectasis demonstrate a significant gut-lung interaction. Multibiome integration followed by unsupervised clustering reveals two patient clusters, differing by gut-lung interactions and with contrasting clinical phenotypes. A high gut-lung interaction cluster, characterized by lung Pseudomonas, gut Bacteroides, and gut Saccharomyces, is associated with increased exacerbations and greater radiological and overall bronchiectasis severity, whereas the low gut-lung interaction cluster demonstrates an overrepresentation of lung commensals, including Prevotella, Fusobacterium, and Porphyromonas with gut Candida. The lung Pseudomonas-gut Bacteroides relationship, observed in the high gut-lung interaction bronchiectasis cluster, was validated in a murine model of lung Pseudomonas aeruginosa infection. This interaction was abrogated after antibiotic (imipenem) pretreatment in mice confirming the relevance and therapeutic potential of targeting the gut microbiome to influence the gut-lung axis. Metagenomics in a subset of individuals with bronchiectasis corroborated our findings from targeted analyses. Conclusions: A dysregulated gut-lung axis, driven by lung Pseudomonas, associates with poorer clinical outcomes in bronchiectasis.}, } @article {pmid36288274, year = {2022}, author = {France, MT and Brown, SE and Rompalo, AM and Brotman, RM and Ravel, J}, title = {Identification of shared bacterial strains in the vaginal microbiota of related and unrelated reproductive-age mothers and daughters using genome-resolved metagenomics.}, journal = {PloS one}, volume = {17}, number = {10}, pages = {e0275908}, pmid = {36288274}, issn = {1932-6203}, support = {R01 AI116799/AI/NIAID NIH HHS/United States ; R01 NR015495/NR/NINR NIH HHS/United States ; R01 AI060892/AI/NIAID NIH HHS/United States ; }, mesh = {Child ; Humans ; Female ; Adolescent ; *Microbiota/genetics ; Vagina/microbiology ; Reproduction ; Bacteria/genetics ; Metagenomics ; }, abstract = {It has been suggested that the human microbiome might be vertically transmitted from mother to offspring and that early colonizers may play a critical role in development of the immune system. Studies have shown limited support for the vertical transmission of the intestinal microbiota but the derivation of the vaginal microbiota remains largely unknown. Although the vaginal microbiota of children and reproductive age women differ in composition, the vaginal microbiota could be vertically transmitted. To determine whether there was any support for this hypothesis, we examined the vaginal microbiota of daughter-mother pairs from the Baltimore metropolitan area (ages 14-27, 32-51; n = 39). We assessed whether the daughter's microbiota was similar in composition to their mother's using metataxonomics. Permutation tests revealed that while some pairs did have similar vaginal microbiota, the degree of similarity did not exceed that expected by chance. Genome-resolved metagenomics was used to identify shared bacterial strains in a subset of the families (n = 22). We found a small number of bacterial strains that were shared between mother-daughter pairs but identified more shared strains between individuals from different families, indicating that vaginal bacteria may display biogeographic patterns. Earlier-in-life studies are needed to demonstrate vertical transmission of the vaginal microbiota.}, } @article {pmid36287644, year = {2023}, author = {Walsh, LH and Coakley, M and Walsh, AM and O'Toole, PW and Cotter, PD}, title = {Bioinformatic approaches for studying the microbiome of fermented food.}, journal = {Critical reviews in microbiology}, volume = {49}, number = {6}, pages = {693-725}, doi = {10.1080/1040841X.2022.2132850}, pmid = {36287644}, issn = {1549-7828}, mesh = {*Microbiota/genetics ; Metagenome ; Computational Biology/methods ; *Fermented Foods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {High-throughput DNA sequencing-based approaches continue to revolutionise our understanding of microbial ecosystems, including those associated with fermented foods. Metagenomic and metatranscriptomic approaches are state-of-the-art biological profiling methods and are employed to investigate a wide variety of characteristics of microbial communities, such as taxonomic membership, gene content and the range and level at which these genes are expressed. Individual groups and consortia of researchers are utilising these approaches to produce increasingly large and complex datasets, representing vast populations of microorganisms. There is a corresponding requirement for the development and application of appropriate bioinformatic tools and pipelines to interpret this data. This review critically analyses the tools and pipelines that have been used or that could be applied to the analysis of metagenomic and metatranscriptomic data from fermented foods. In addition, we critically analyse a number of studies of fermented foods in which these tools have previously been applied, to highlight the insights that these approaches can provide.}, } @article {pmid36286976, year = {2022}, author = {Starikova, EV and Galeeva, JS and Andreev, DN and Sokolov, PS and Fedorov, DE and Manolov, AI and Pavlenko, AV and Klimina, KM and Veselovsky, VA and Zaborovsky, AV and Evdokimov, VV and Andreev, NG and Devkota, MK and Fomenko, AK and Khar'kovskii, VA and Asadulin, PO and Kucher, SA and Cheremushkina, AS and Yanushevich, OO and Maev, IV and Krikheli, NI and Levchenko, OV and Ilina, EN and Govorun, VM}, title = {[Composition of oropharyngeal microbiota in patients with COVID-19 of different pneumonia severity].}, journal = {Terapevticheskii arkhiv}, volume = {94}, number = {8}, pages = {963-972}, doi = {10.26442/00403660.2022.08.201780}, pmid = {36286976}, issn = {0040-3660}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *COVID-19 ; *Microbiota ; Oropharynx/microbiology ; Lung ; }, abstract = {AIM: To identify features of the taxonomic composition of the oropharyngeal microbiota of COVID-19 patients with different disease severity.

MATERIALS AND METHODS: The study group included 156 patients hospitalized with confirmed diagnosis of COVID-19 in the clinical medical center of Yevdokimov Moscow State University of Medicine and Dentistry between April and June 2021. There were 77 patients with mild pneumonia according to CT (CT1) and 79 patients with moderate to severe pneumonia (CT2 and CT3). Oropharyngeal swabs were taken when the patient was admitted to the hospital. Total DNA was isolated from the samples, then V3V4 regions of the 16s rRNA gene were amplified, followed by sequencing using Illumina HiSeq 2500 platform. DADA2 algorithm was used to obtain amplicon sequence variants (ASV).

RESULTS: When comparing the microbial composition of the oropharynx of the patients with different forms of pneumonia, we have identified ASVs associated with the development of both mild and severe pneumonia outside hospital treatment. Based on the results obtained, ASVs associated with a lower degree of lung damage belong predominantly to the class of Gram-negative Firmicutes (Negativicutes), to various classes of Proteobacteria, as well as to the order Fusobacteria. In turn, ASVs associated with a greater degree of lung damage belong predominantly to Gram-positive classes of Firmicutes Bacilli and Clostridia. While being hospitalized, patients with severe pneumonia demonstrated negative disease dynamics during treatment significantly more often.

CONCLUSION: We have observed differences in the taxonomic composition of the oropharyngeal microbiota in patients with different forms of pneumonia developed outside hospital treatment against COVID-19. Such differences might be due to the presumed barrier function of the oropharyngeal microbiota, which reduces the risk of virus titer increase.}, } @article {pmid36283165, year = {2022}, author = {Papakonstantinou, A and Nuciforo, P and Borrell, M and Zamora, E and Pimentel, I and Saura, C and Oliveira, M}, title = {The conundrum of breast cancer and microbiome - A comprehensive review of the current evidence.}, journal = {Cancer treatment reviews}, volume = {111}, number = {}, pages = {102470}, doi = {10.1016/j.ctrv.2022.102470}, pmid = {36283165}, issn = {1532-1967}, mesh = {Humans ; Female ; *Breast Neoplasms ; *Microbiota ; Bacteria ; *Gastrointestinal Microbiome ; }, abstract = {Disturbance of the microbial balance of a habitat can have detrimental effects on the health of the individual and, in addition, polymorphic microbiomes were recently suggested as emerging cancer hallmarks. Modern sequencing and metagenomics techniques have allowed characterization of intratumoral microbiome composition even in tissues such as the breast. We conducted a comprehensive literature review on different aspects related to the microbial landscape of the breast tissue and breast tumors, as well as its relation to systemic therapy. Emerging data suggest varying microbiome composition intratumorally compared to the normal breast tissue and other tumor types. Differences in the microbes present in normal breast and cancerous lesions of the breast have also been described, as well as potential correlation between microbiome composition and breast cancer subtype and stage. The interplay between gut and breast microbiome is not well understood although bacterial allocation through mesenteric lymph nodes has been suggested as a possible pathway. Moreover, gut bacteria with estrogen metabolizing properties are of special interest in the context of breast cancer and available knowledge and reported studies are hereby described. The relationship of gut microbiome and cancer therapy is another aspect of interest and available data are presented. Notwithstanding, the field of microbiome in the context of breast cancer is starting to evolve and a number of questions arise, with the gut-breast-cancer therapy axis in the center.}, } @article {pmid36282811, year = {2022}, author = {Garrido-Sanz, L and Àngel Senar, M and Piñol, J}, title = {Drastic reduction of false positive species in samples of insects by intersecting the default output of two popular metagenomic classifiers.}, journal = {PloS one}, volume = {17}, number = {10}, pages = {e0275790}, pmid = {36282811}, issn = {1932-6203}, mesh = {Animals ; *Metagenomics/methods ; *Metagenome ; High-Throughput Nucleotide Sequencing/methods ; DNA ; Insecta/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The use of high-throughput sequencing to recover short DNA reads of many species has been widely applied on biodiversity studies, either as amplicon metabarcoding or shotgun metagenomics. These reads are assigned to taxa using classifiers. However, for different reasons, the results often contain many false positives. Here we focus on the reduction of false positive species attributable to the classifiers. We benchmarked two popular classifiers, BLASTn followed by MEGAN6 (BM) and Kraken2 (K2), to analyse shotgun sequenced artificial single-species samples of insects. To reduce the number of misclassified reads, we combined the output of the two classifiers in two different ways: (1) by keeping only the reads that were attributed to the same species by both classifiers (intersection approach); and (2) by keeping the reads assigned to some species by any classifier (union approach). In addition, we applied an analytical detection limit to further reduce the number of false positives species. As expected, both metagenomic classifiers used with default parameters generated an unacceptably high number of misidentified species (tens with BM, hundreds with K2). The false positive species were not necessarily phylogenetically close, as some of them belonged to different orders of insects. The union approach failed to reduce the number of false positives, but the intersection approach got rid of most of them. The addition of an analytic detection limit of 0.001 further reduced the number to ca. 0.5 false positive species per sample. The misidentification of species by most classifiers hampers the confidence of the DNA-based methods for assessing the biodiversity of biological samples. Our approach to alleviate the problem is straightforward and significantly reduced the number of reported false positive species.}, } @article {pmid36280853, year = {2022}, author = {Muscatt, G and Hilton, S and Raguideau, S and Teakle, G and Lidbury, IDEA and Wellington, EMH and Quince, C and Millard, A and Bending, GD and Jameson, E}, title = {Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {181}, pmid = {36280853}, issn = {2049-2618}, support = {MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; EP/L016494/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; BB/T009152/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L025892/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M017982/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Rhizosphere ; Soil Microbiology ; Plant Roots/microbiology ; *Microbiota/genetics ; Soil/chemistry ; Bacteria/genetics ; *RNA Viruses/genetics ; *Bacteriophages/genetics ; *Brassica napus ; DNA ; }, abstract = {BACKGROUND: The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions.

RESULTS: Here, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape (Brassica napus L.). By recovering 1059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of "Kill-the-Winner" dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots, and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of "viral priming," which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation.

CONCLUSIONS: Overall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil, and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability. Video Abstract.}, } @article {pmid36279912, year = {2023}, author = {Krishnaswamy, VG and Mani, K and Senthil Kumar, P and Rangasamy, G and Sridharan, R and Rethnaraj, C and Amirtha Ganesh, SS and Kalidas, S and Palanisamy, V and Chellama, NJ and Chowdula, S and Parthasarathy, V and Rajendran, S}, title = {Prevalence of differential microbiome in healthy, diseased and nipped colonies of corals, Porites lutea in the Gulf of Kachchh, north-west coast of India.}, journal = {Environmental research}, volume = {216}, number = {Pt 2}, pages = {114622}, doi = {10.1016/j.envres.2022.114622}, pmid = {36279912}, issn = {1096-0953}, mesh = {Animals ; *Anthozoa/microbiology ; Prevalence ; Coral Reefs ; *Microbiota ; Bacteria/genetics ; }, abstract = {Coral reefs are constantly subjected to multiple stresses like diseases and fish predation, which can profoundly influence the coral microbiome. This study investigated the differences in bacterial community structure of healthy, white syndrome affected and blenny nipped coral colonies of Porites lutea, collected from the coral reefs of Gulf of Kachchh, north-west coast of India. Present study observed that the stressed coral colonies harbored more OTUs and contained higher diversity values compared to healthy corals colonies. Similarly, beta diversity analysis indicated the dissimilarities among the three coral samples analyzed. Though the taxonomy analysis indicated bacterial phyla like Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria among the entire coral samples studied, there was a variation in their relative abundances. Huge variations were observed in the relative dominance at the bacterial genera level. About 13phyla and 11 genera was identified in healthy coral. The PBN sample was found to contain Proteobacteria, Cyanobacteria, Verrucomicrobia, and Lentisphaerae as dominant phyla and Endozoicomonas, Dyella, Woeseia, and Winogradskyella as dominant genera. The PWS sample contained Proteobacteria, Lentisphaerae, Spirochaetes, and Tenericutes as dominant phyla and Endozoicomonas, Arcobacter, Sunxiuqinia, and Carboxylicivirgia as dominant genera. Among the healthy samples, sequences belonging to Uncultured Rhodospirillaceae were dominant, while Woeseia and sequences belonging to Uncultured Rhodovibrionaceae were dominant among the blenny nipped white syndrome infected corals. Although any previously established pathogen was not identified, present study revealed the presence of a potentially pathogenic bacterium, Arcobacter, among the diseased corals. It also demonstrated a dynamic microbiome among the Porites lutea colonies on subjecting to various stresses.}, } @article {pmid36279751, year = {2022}, author = {Bellerba, F and Serrano, D and Harriet, J and Pozzi, C and Segata, N and NabiNejad, A and Piperni, E and Gnagnarella, P and Macis, D and Aristarco, V and Accornero, CA and Manghi, P and Gonzaga, AG and Biffi, R and Bottiglieri, L and Trovato, C and Zampino, MG and Corso, F and Bellocco, R and Raimondi, S and Rescigno, M and Gandini, S}, title = {Colorectal cancer, Vitamin D and microbiota: A double-blind Phase II randomized trial (ColoViD) in colorectal cancer patients.}, journal = {Neoplasia (New York, N.Y.)}, volume = {34}, number = {}, pages = {100842}, pmid = {36279751}, issn = {1476-5586}, mesh = {Humans ; Female ; Male ; Vitamin D ; Vitamins/therapeutic use ; Dietary Supplements ; *Colorectal Neoplasms/drug therapy ; *Microbiota ; }, abstract = {BACKGROUND: Several studies suggest a role of gut microbiota in colorectal cancer (CRC) initiation and progression. Vitamin D (vitD) blood levels are also inversely correlated with CRC risk and prognosis. However, these factors' interplay remains unknown.

METHODS: 74 CRC patients after standard treatment were randomized to 1-year 2000 IU/day vitD or placebo.  Baseline and post-treatment fecal microbiota for shotgun metagenomics sequencing was collected. Coda-lasso and Principal Component Analysis were used to select and summarize treatment-associated taxa and pathways. Associations between vitD and taxa/pathways were investigated with logistic regression. Mediation analysis was performed to study if treatment-associated taxa mediated the effect of supplementation on 25(OH)D levels. Cox proportional-hazards model was used for disease-free survival (DFS).

RESULTS: 60 patients were analyzed. Change in alpha diversity (Shannon: p = 0.77; Simpson: p = 0.63) and post-treatment beta diversity (p = 0.70) were comparable between arms. Post-treatment abundances of 63 taxa and 32 pathways differed between arms. The 63 taxa also mediated the effect of supplementation on 25(OH)D (p = 0.02). There were sex differences in vitD levels, microbiota and pathways. Pathways of essential amino acids' biosynthesis were more abundant in supplemented women. Fusobacterium nucleatum presence at baseline was associated with worse DFS (p = 0.02). Those achieving vitD sufficiency (25(OH)D≥30 ng/ml) had lower post-treatment abundances (p = 0.05). Women were more likely to have F. nucleatum post-treatment (p = 0.02).

CONCLUSIONS: VitD supplementation may contribute shaping the gut microbiota and the microbiota may partially mediate the effect of supplementation on 25(OH)D. The observed sex-specific differences highlight the necessity of including sex/gender as a variable in microbiome studies.}, } @article {pmid36278460, year = {2022}, author = {Suryaletha, K and Savithri, AV and Nayar, SA and Asokan, S and Rajeswary, D and Thomas, S}, title = {Demystifying Bacteriocins of Human Microbiota by Genome Guided Prospects: An Impetus to Rekindle the Antimicrobial Research.}, journal = {Current protein & peptide science}, volume = {23}, number = {12}, pages = {811-822}, pmid = {36278460}, issn = {1875-5550}, mesh = {Humans ; *Bacteriocins/genetics/pharmacology ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; Bacteria/genetics ; }, abstract = {The human microbiome is a reservoir of potential bacteriocins that can counteract multidrug resistant bacterial pathogens. Unlike antibiotics, bacteriocins selectively inhibit a spectrum of competent bacteria and are said to safeguard gut commensals, reducing the chance of dysbiosis. Bacteriocinogenic probiotics or bacteriocins of human origin will be more pertinent in human physiological conditions for therapeutic applications to act against invading pathogens. Recent advancement in the omics approach enables the mining of diverse and novel bacteriocins by identifying biosynthetic gene clusters from the human microbial genome, pangenome or shotgun metagenome, which is a breakthrough in the discovery line of novel bacteriocins. This review summarizes the most recent trends and therapeutic potential of bacteriocins of human microbial origin, the advancement in the in silico algorithms and databases in the discovery of novel bacteriocin, and how to bridge the gap between the discovery of bacteriocin genes from big datasets and their in vitro production. Besides, the later part of the review discussed the various impediments in their clinical applications and possible solution to bring them into the frontline therapeutics to control infections, thereby meeting the challenges of global antimicrobial resistance.}, } @article {pmid36275026, year = {2022}, author = {Abdelbary, MMH and Hatting, M and Bott, A and Dahlhausen, A and Keller, D and Trautwein, C and Conrads, G}, title = {The oral-gut axis: Salivary and fecal microbiome dysbiosis in patients with inflammatory bowel disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1010853}, pmid = {36275026}, issn = {2235-2988}, mesh = {Mice ; Animals ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Inflammatory Bowel Diseases/microbiology ; *Microbiota ; Bacteria ; Escherichia ; Inflammation/complications ; Cytokines/genetics ; }, abstract = {Inflammatory bowel disease (IBD) is a group of chronic inflammatory disorders that fall into two main categories: Crohn's disease (CD) and ulcerative colitis (UC). The gastrointestinal tract extends from the mouth to the anus and harbors diverse bacterial communities. Several sequencing-based studies have identified an intestinal enrichment of oral-associated bacteria and demonstrated their ability to induce intestinal inflammation in mice, suggesting that intestinal pathobionts originate from the oral cavity, particularly members of the genus Streptococcus. This study aimed to investigate the composition of the salivary and fecal microbiome of IBD patients (n = 14) compared to healthy controls (n = 12) and to determine the abundance of common bacterial taxa in both niches. Metagenomic DNA was extracted from saliva and fecal samples, and the 16S rRNA gene was targeted for sequencing. Our results revealed that the overall microbial composition of saliva was significantly altered in the IBD patients compared to the control subjects (p = 0.038). At the genus level, Veillonella and Prevotella were highly abundant in IBD (median: 25.4% and 22.2%, respectively) compared to the control group (17.9% and 13.4%, respectively). In contrast, Neisseria, Streptococcus, Haemophilus, and Fusobacterium were associated with a healthy gut state. Regarding the fecal microbiome, the IBD group had a significantly higher abundance of Clostridium sensu stricto 1 and Escherichia-Shigella (both comprising pathogenic bacteria) compared with the control group. Members of both bacterial groups have previously been shown to positively correlate with intestinal inflammation and high expression of pro-inflammatory cytokines that disrupt intestinal barrier integrity. In addition, we demonstrate that the increased abundance of Clostridium sensu stricto 1 and Escherichia-Shigella has also been associated with significant upregulation of certain metabolic pathways in the feces of the IBD group, including bacterial invasion of epithelial cells. Streptococcus was the only common genus detected in both the salivary and fecal microbiome and represented the oral-gut axis in our study. Using culture-based methods, we isolated 57 and 91 Streptococcus strains from saliva as well as 40 and 31 strains from fecal samples of the controls and IBD patients, respectively. The phylogenetic tree of streptococci based on sodA sequences revealed several patient-specific clusters comprising salivary and fecal streptococcal isolates from the same patient and belonging to the same species, suggesting that the oral cavity is an endogenous reservoir for intestinal strains.}, } @article {pmid36274442, year = {2022}, author = {Tims, S and Marsaux, C and Pinto, A and Daly, A and Karall, D and Kuhn, M and Santra, S and Roeselers, G and Knol, J and MacDonald, A and Scholl-Bürgi, S}, title = {Altered gut microbiome diversity and function in patients with propionic acidemia.}, journal = {Molecular genetics and metabolism}, volume = {137}, number = {3}, pages = {308-322}, doi = {10.1016/j.ymgme.2022.09.012}, pmid = {36274442}, issn = {1096-7206}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Propionic Acidemia ; Propionates ; Feces/microbiology ; Butyrates ; }, abstract = {Propionic acidemia (PA) is an inherited metabolic disorder of propionate metabolism, where the gut microbiota may play a role in pathophysiology and therefore, represent a relevant therapeutic target. Little is known about the gut microbiota composition and activity in patients with PA. Although clinical practice varies between metabolic treatment centers, management of PA requires combined dietary and pharmaceutical treatments, both known to affect the gut microbiota. This study aimed to characterize the gut microbiota and its metabolites in fecal samples of patients with PA compared with healthy controls from the same household. Eight patients (aged 3-14y) and 8 controls (4-31y) were recruited from Center 1 (UK) and 7 patients (11-33y) and 6 controls (15-54y) from Center 2 (Austria). Stool samples were collected 4 times over 3 months, alongside data on dietary intakes and medication usage. Several microbial taxa differed between patients with PA and controls, particularly for Center 1, e.g., Proteobacteria levels were increased, whereas butyrate-producing genera, such as Roseburia and Faecalibacterium, were decreased. Most measured microbial metabolites were lower in patients with PA, and butyrate was particularly depleted in patients from Center 1. Furthermore, microbiota profile of these patients showed the lowest compositional and functional diversity, and lowest stability over 3 months. As the first study to map the gut microbiota of patients with PA, this work represents an important step forward for developing new therapeutic strategies to further improve PA clinical status. New dietary strategies should consider microbial propionate production as well as butyrate production and microbiota stability.}, } @article {pmid36274162, year = {2022}, author = {Focardi, A and Moore, LR and Raina, JB and Seymour, JR and Paulsen, IT and Tetu, SG}, title = {Plastic leachates impair picophytoplankton and dramatically reshape the marine microbiome.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {179}, pmid = {36274162}, issn = {2049-2618}, mesh = {Plastics/chemistry ; Polyvinyl Chloride ; *Water Pollutants, Chemical/chemistry ; *Microbiota/genetics ; Zinc ; Water ; }, abstract = {BACKGROUND: Each year, approximately 9.5 million metric tons of plastic waste enter the ocean with the potential to adversely impact all trophic levels. Until now, our understanding of the impact of plastic pollution on marine microorganisms has been largely restricted to the microbial assemblages that colonize plastic particles. However, plastic debris also leaches considerable amounts of chemical additives into the water, and this has the potential to impact key groups of planktonic marine microbes, not just those organisms attached to plastic surfaces.

RESULTS: To investigate this, we explored the population and genetic level responses of a marine microbial community following exposure to leachate from a common plastic (polyvinyl chloride) or zinc, a specific plastic additive. Both the full mix of substances leached from polyvinyl chloride (PVC) and zinc alone had profound impacts on the taxonomic and functional diversity of our natural planktonic community. Microbial primary producers, both prokaryotic and eukaryotic, which comprise the base of the marine food web, were strongly impaired by exposure to plastic leachates, showing significant declines in photosynthetic efficiency, diversity, and abundance. Key heterotrophic taxa, such as SAR11, which are the most abundant planktonic organisms in the ocean, also exhibited significant declines in relative abundance when exposed to higher levels of PVC leachate. In contrast, many copiotrophic bacteria, including members of the Alteromonadales, dramatically increased in relative abundance under both exposure treatments. Moreover, functional gene and genome analyses, derived from metagenomes, revealed that PVC leachate exposure selects for fast-adapting, motile organisms, along with enrichment in genes usually associated with pathogenicity and an increased capacity to metabolize organic compounds leached from PVC.

CONCLUSIONS: This study shows that substances leached from plastics can restructure marine microbial communities with the potential for significant impacts on trophodynamics and biogeochemical cycling. These findings substantially expand our understanding of the ways by which plastic pollution impact life in our oceans, knowledge which is particularly important given that the burden of plastic pollution in the marine environment is predicted to continue to rise. Video Abstract.}, } @article {pmid36273894, year = {2022}, author = {Sato, Y and Takebe, H and Oishi, K and Yasuda, J and Kumagai, H and Hirooka, H and Yoshida, T}, title = {Identification of 146 Metagenome-assembled Genomes from the Rumen Microbiome of Cattle in Japan.}, journal = {Microbes and environments}, volume = {37}, number = {4}, pages = {}, pmid = {36273894}, issn = {1347-4405}, mesh = {Cattle ; Animals ; *Metagenome ; Rumen ; Japan ; Bacteria/metabolism ; Phylogeny ; *Microbiota ; Cellulose/metabolism ; Metagenomics ; }, abstract = {The rumen contains a complex microbial ecosystem that degrades plant materials, such as cellulose and hemicellulose. We herein reconstructed 146 nonredundant, rumen-specific metagenome-assembled genomes (MAGs), with ≥50% completeness and <10% contamination, from cattle in Japan. The majority of MAGs were potentially novel strains, encoding various enzymes related to plant biomass degradation and volatile fatty acid production. The MAGs identified in the present study may be valuable resources to enhance the resolution of future taxonomical and functional studies based on metagenomes and metatranscriptomes.}, } @article {pmid36273241, year = {2023}, author = {Larkin, AA and Hagstrom, GI and Brock, ML and Garcia, NS and Martiny, AC}, title = {Basin-scale biogeography of Prochlorococcus and SAR11 ecotype replication.}, journal = {The ISME journal}, volume = {17}, number = {2}, pages = {185-194}, pmid = {36273241}, issn = {1751-7370}, support = {T32 AI141346/AI/NIAID NIH HHS/United States ; }, mesh = {*Ecotype ; *Prochlorococcus ; Seawater/microbiology ; Indian Ocean ; Metagenome ; }, abstract = {Establishing links between microbial diversity and environmental processes requires resolving the high degree of functional variation among closely related lineages or ecotypes. Here, we implement and validate an improved metagenomic approach that estimates the spatial biogeography and environmental regulation of ecotype-specific replication patterns (RObs) across ocean regions. A total of 719 metagenomes were analyzed from meridional Bio-GO-SHIP sections in the Atlantic and Indian Ocean. Accounting for sequencing bias and anchoring replication estimates in genome structure were critical for identifying physiologically relevant biological signals. For example, ecotypes within the dominant marine cyanobacteria Prochlorococcus exhibited distinct diel cycles in RObs that peaked between 19:00-22:00. Additionally, both Prochlorococcus ecotypes and ecotypes within the highly abundant heterotroph Pelagibacter (SAR11) demonstrated systematic biogeographies in RObs that differed from spatial patterns in relative abundance. Finally, RObs was significantly regulated by nutrient stress and temperature, and explained by differences in the genomic potential for nutrient transport, energy production, cell wall structure, and replication. Our results suggest that our new approach to estimating replication is reflective of gross population growth. Moreover, this work reveals that the interaction between adaptation and environmental change drives systematic variability in replication patterns across ocean basins that is ecotype-specific, adding an activity-based dimension to our understanding of microbial niche space.}, } @article {pmid36273146, year = {2022}, author = {Sato, Y and Wippler, J and Wentrup, C and Ansorge, R and Sadowski, M and Gruber-Vodicka, H and Dubilier, N and Kleiner, M}, title = {Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {178}, pmid = {36273146}, issn = {2049-2618}, mesh = {Animals ; Bacteria/genetics ; *Microbial Consortia ; Phylogeny ; Sulfates ; Sulfur ; *Symbiosis ; *Annelida/microbiology ; }, abstract = {BACKGROUND: Many animals live in intimate associations with a species-rich microbiome. A key factor in maintaining these beneficial associations is fidelity, defined as the stability of associations between hosts and their microbiota over multiple host generations. Fidelity has been well studied in terrestrial hosts, particularly insects, over longer macroevolutionary time. In contrast, little is known about fidelity in marine animals with species-rich microbiomes at short microevolutionary time scales, that is at the level of a single host population. Given that natural selection acts most directly on local populations, studies of microevolutionary partner fidelity are important for revealing the ecological and evolutionary processes that drive intimate beneficial associations within animal species.

RESULTS: In this study on the obligate symbiosis between the gutless marine annelid Olavius algarvensis and its consortium of seven co-occurring bacterial symbionts, we show that partner fidelity varies across symbiont species from strict to absent over short microevolutionary time. Using a low-coverage sequencing approach that has not yet been applied to microbial community analyses, we analysed the metagenomes of 80 O. algarvensis individuals from the Mediterranean and compared host mitochondrial and symbiont phylogenies based on single-nucleotide polymorphisms across genomes. Fidelity was highest for the two chemoautotrophic, sulphur-oxidizing symbionts that dominated the microbial consortium of all O. algarvensis individuals. In contrast, fidelity was only intermediate to absent in the sulphate-reducing and spirochaetal symbionts with lower abundance. These differences in fidelity are likely driven by both selective and stochastic forces acting on the consistency with which symbionts are vertically transmitted.

CONCLUSIONS: We hypothesize that variable degrees of fidelity are advantageous for O. algarvensis by allowing the faithful transmission of their nutritionally most important symbionts and flexibility in the acquisition of other symbionts that promote ecological plasticity in the acquisition of environmental resources. Video Abstract.}, } @article {pmid36271396, year = {2022}, author = {Wen, T and Xie, P and Penton, CR and Hale, L and Thomashow, LS and Yang, S and Ding, Z and Su, Y and Yuan, J and Shen, Q}, title = {Specific metabolites drive the deterministic assembly of diseased rhizosphere microbiome through weakening microbial degradation of autotoxin.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {177}, pmid = {36271396}, issn = {2049-2618}, mesh = {Rhizosphere ; Soil Microbiology ; Citrulline ; alpha-Tocopherol ; *Microbiota ; *Fusarium ; Bacteria/genetics ; Soil ; Sugars ; Galactitol ; }, abstract = {BACKGROUND: Process and function that underlie the assembly of a rhizosphere microbial community may be strongly linked to the maintenance of plant health. However, their assembly processes and functional changes in the deterioration of soilborne disease remain unclear. Here, we investigated features of rhizosphere microbiomes related to Fusarium wilt disease and assessed their assembly by comparison pair of diseased/healthy sequencing data. The untargeted metabolomics was employed to explore potential community assembly drivers, and shotgun metagenome sequencing was used to reveal the mechanisms of metabolite-mediated process after soil conditioning.

RESULTS: Results showed the deterministic assembly process associated with diseased rhizosphere microbiomes, and this process was significantly correlated to five metabolites (tocopherol acetate, citrulline, galactitol, octadecylglycerol, and behenic acid). Application of the metabolites resulted in a deterministic assembly of microbiome with the high morbidity of watermelon. Furthermore, metabolite conditioning was found to weaken the function of autotoxin degradation undertaken by specific bacterial group (Bradyrhizobium, Streptomyces, Variovorax, Pseudomonas, and Sphingomonas) while promoting the metabolism of small-molecule sugars and acids initiated from another bacterial group (Anaeromyxobacter, Bdellovibrio, Conexibacter, Flavobacterium, and Gemmatimonas). Video Abstract CONCLUSION: These findings strongly suggest that shifts in a metabolite-mediated microbial community assembly process underpin the deterministic establishment of soilborne Fusarium wilt disease and reveal avenues for future research focusing on ameliorating crop loss due to this pathogen.}, } @article {pmid36270766, year = {2024}, author = {Ali, MJ}, title = {Fungal microbiome (mycobiome) and virome of the lacrimal sac in patients with PANDO: the lacriome paper 5.}, journal = {The British journal of ophthalmology}, volume = {108}, number = {2}, pages = {317-322}, doi = {10.1136/bjo-2022-322433}, pmid = {36270766}, issn = {1468-2079}, mesh = {Humans ; *Dacryocystorhinostomy ; *Lacrimal Duct Obstruction ; *Mycobiome/genetics ; *Nasolacrimal Duct ; Prospective Studies ; Virome/genetics ; }, abstract = {PURPOSE: To study the fungal microbiome (mycobiome) and the virome of the lacrimal sacs in patients with primary acquired nasolacrimal duct obstruction (PANDO).

METHODS: A prospective study was performed on 10 consecutive samples of the lacrimal sac contents obtained from patients with PANDO. The samples were obtained from the lacrimal sacs under endoscopy guidance and immediately transported on ice to the laboratory. Following DNA extraction and library preparation, a whole shotgun metagenome sequencing was performed on the Illumina platform (NOVASEQ 6000). The fungal internal transcript spacer analysis was performed using the PIPITS v2.7 . The viral taxonomy profiling was performed using Kraken2 against the virus database.

RESULTS: The taxonomic hit distribution across the lacrimal sac samples showed rich fungal diversity (4 phyla, 12 classed, 21 families and 26 genera). The major phyla were Ascomycota and Basidiomycota, and the key genera identified were Alternaria, Hyphopichia, Malassezia, Aspergillus and Epicoccum. The virome analysis identified 13 phyla, 15 classes and 27 families. The viruses were commonly from the families Poxviridae, Retroviridae, Siphoviridae and Myoviridae, Poxviridae being the most prevalent family. The BeAn 58058 virus, a member of the Poxviridae family, was the most abundant in all the samples.

CONCLUSION: The present study is the first whole metagenome sequencing exclusively of the fungal microbiome and virome from the lacrimal sacs of patients with PANDO. The lacrimal sacs harbour diverse fungal and viral communities with distinct ecosystem dynamics. Further studies of their functions and interactions with the hosts would provide valuable insights.}, } @article {pmid36270683, year = {2022}, author = {Mahapatra, S and Mohanty, S and Mishra, R and Prasad, P}, title = {An overview of cancer and the human microbiome.}, journal = {Progress in molecular biology and translational science}, volume = {191}, number = {1}, pages = {83-139}, doi = {10.1016/bs.pmbts.2022.07.007}, pmid = {36270683}, issn = {1878-0814}, mesh = {Humans ; *Microbiota ; Symbiosis ; *Neoplasms ; }, abstract = {Mutual beneficial associations with the microbial consortia are an essential requisite of human life. Microbial communities have both a symbiotic and a pathogenic standpoint, which portrays a context-dependent scenario of the human microbiome. The symbiotic assemblage works to develop indispensable functions of the human body such as immune system, digestive system, defense against colonization by pathobionts and their toxins, etc. Furthermore, any deviation in the resource utilization by the symbionts due to host factors comprising lifestyle changes, diet, drugs, immunocompromised states, and co-morbidities could perturb beneficial microbes communities and promote the invasion by opportunistic pathogens thus, disrupting the homeostatic state. Microbial infestations have proved to be carcinogenic but this does not spontaneously establish a cancer hallmark, rather they initiate a cascade of events that disturbs the normal cellular activities finally these defective machineries invade distant sites of the body, submitting to a devastative transformed internal milieu. Significant technological and system biology advances have been made in elucidating a lucid but complex basis of such microbe-associated malignancies. This chapter discusses the recent advances, without compromising the concepts of the inception studies, including a brief version of the microbial status in cancer generation, mechanistic approaches adapted, therapeutic interventions, system biology approaches with special mention on the study design gaps, challenges in addressing the drawbacks and finally with a perspective of the future targeted studies, has been a focus of this piece of work.}, } @article {pmid36270682, year = {2022}, author = {Ahrodia, T and Das, S and Bakshi, S and Das, B}, title = {Structure, functions, and diversity of the healthy human microbiome.}, journal = {Progress in molecular biology and translational science}, volume = {191}, number = {1}, pages = {53-82}, doi = {10.1016/bs.pmbts.2022.07.003}, pmid = {36270682}, issn = {1878-0814}, mesh = {Humans ; *Microbiota ; Bacteria/genetics ; Metagenome ; *Gastrointestinal Microbiome ; Archaea ; }, abstract = {Taxonomic composition and functional potency of microbes associated with different parts of the human body have largely been explored by culture-independent metagenome sequencing. The diverse microbiota living throughout the human body is made up of thousands of microbial taxa from all three domains of life: Archaea, Bacteria, and Eukarya. Microbial load and functional potency in different body sites are well distinct and have minimal resemblance at higher taxonomic levels between the two habitats. The highest microbial load, diversity, and functional potency including biosynthesis of essential nutrients, chemical modifications of dietary components, and sources of immunomodulatory molecules, are found in the gut microbiome. However, the inter-individual diversity and dynamics of the human microbiome in a given body habitat vary greatly over time. Both environmental factors and host genetics contribute significantly to shaping microbial community structure and its stability. A basic understanding of native microbial compositions and their functional potency and stability in different parts of healthy humans living across geography will help us to identify disease-specific microbiota and develop potential microbiome-based therapeutics. Here, we updated our current understanding of the diversity, dynamics, and functional potency of microbiomes associated with different parts of the human body.}, } @article {pmid36270681, year = {2022}, author = {Ghosh, TS and Das, M}, title = {Emerging tools for understanding the human microbiome.}, journal = {Progress in molecular biology and translational science}, volume = {191}, number = {1}, pages = {29-51}, doi = {10.1016/bs.pmbts.2022.06.027}, pmid = {36270681}, issn = {1878-0814}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Microbiota ; Metagenome ; Metagenomics/methods ; Computational Biology/methods ; }, abstract = {Recent advances in sequencing technologies, experimental protocols and approaches in data generation and analysis have enabled us to investigate the human microbiome at an unprecedented level of resolution. The current chapter aims to provide an understanding of the different computational and bioinformatic strategies adopted to answer the different questions of a typical microbiome investigation and how the upstream DNA sequencing methodologies can affect this. The chapter enlist the state-of-the-art in metagenomic data analysis along with the available strategies to perform an integrated investigation of the human microbiome along with other data layers.}, } @article {pmid36270377, year = {2023}, author = {Evariste, L and Mouchet, F and Pinelli, E and Flahaut, E and Gauthier, L and Barret, M}, title = {Gut microbiota impairment following graphene oxide exposure is associated to physiological alterations in Xenopus laevis tadpoles.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 2}, pages = {159515}, doi = {10.1016/j.scitotenv.2022.159515}, pmid = {36270377}, issn = {1879-1026}, mesh = {Animals ; *Gastrointestinal Microbiome ; Larva ; *Graphite/toxicity ; Xenopus laevis ; *Microbiota ; Bacteria/genetics ; }, abstract = {Graphene-based nanomaterials such as graphene oxide (GO) possess unique properties triggering high expectations for the development of technological applications. Thus, GO is likely to be released in aquatic ecosystems. It is essential to evaluate its ecotoxicological potential to ensure a safe use of these nanomaterials. In amphibians, previous studies highlighted X. laevis tadpole growth inhibitions together with metabolic disturbances and genotoxic effects following GO exposure. As GO is known to exert bactericidal effects whereas the gut microbiota constitutes a compartment involved in host homeostasis regulation, it is important to determine if this microbial compartment constitutes a toxicological pathway involved in known GO-induced host physiological impairments. This study investigates the potential link between gut microbial communities and host physiological alterations. For this purpose, X. laevis tadpoles were exposed during 12 days to GO. Growth rate was monitored every 2 days and genotoxicity was assessed through enumeration of micronucleated erythrocytes. Genomic DNA was also extracted from the whole intestine to quantify gut bacteria and to analyze the community composition. GO exposure led to a dose dependent growth inhibition and genotoxic effects were detected following exposure to low doses. A transient decrease of the total bacteria was noticed with a persistent shift in the gut microbiota structure in exposed animals. Genotoxic effects were associated to gut microbiota remodeling characterized by an increase of the relative abundance of Bacteroides fragilis. The growth inhibitory effects would be associated to a shift in the Firmicutes/Bacteroidetes ratio while metagenome inference suggested changes in metabolic pathways and upregulation of detoxification processes. This work indicates that the gut microbiota compartment is a biological compartment of interest as it is integrative of host physiological alterations and should be considered for ecotoxicological studies as structural or functional impairments could lead to later life host fitness loss.}, } @article {pmid36268225, year = {2022}, author = {Khorsand, B and Asadzadeh Aghdaei, H and Nazemalhosseini-Mojarad, E and Nadalian, B and Nadalian, B and Houri, H}, title = {Overrepresentation of Enterobacteriaceae and Escherichia coli is the major gut microbiome signature in Crohn's disease and ulcerative colitis; a comprehensive metagenomic analysis of IBDMDB datasets.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1015890}, pmid = {36268225}, issn = {2235-2988}, mesh = {Humans ; *Colitis, Ulcerative ; *Crohn Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Escherichia coli ; Siderophores ; Lipopolysaccharides ; *Inflammatory Bowel Diseases/microbiology ; Feces/microbiology ; *Escherichia coli Infections ; Sulfur ; Nitrogen ; }, abstract = {OBJECTIVES: A number of converging strands of research suggest that the intestinal Enterobacteriaceae plays a crucial role in the development and progression of inflammatory bowel disease (IBD), however, the changes in the abundance of Enterobacteriaceae species and their related metabolic pathways in Crohn's disease (CD) and ulcerative colitis (UC) compared to healthy people are not fully explained by comprehensive comparative metagenomics analysis. In the current study, we investigated the alternations of the Enterobacterales population in the gut microbiome of patients with CD and UC compared to healthy subjects.

METHODS: Metagenomic datasets were selected from the Integrative Human Microbiome Project (HMP2) through the Inflammatory Bowel Disease Multi'omics Database (IBDMDB). We performed metagenome-wide association studies on fecal samples from 191 CD patients, 132 UC patients, and 125 healthy controls (HCs). We used the metagenomics dataset to study bacterial community structure, relative abundance, differentially abundant bacteria, functional analysis, and Enterobacteriaceae-related biosynthetic pathways.

RESULTS: Compared to the gut microbiome of HCs, six Enterobacteriaceae species were significantly elevated in both CD and UC patients, including Escherichia coli, Klebsiella variicola, Klebsiella quasipneumoniae, Klebsiella pneumoniae, Proteus mirabilis, Citrobacter freundii, and Citrobacter youngae, while Klebsiella oxytoca, Morganella morganii, and Citrobacter amalonaticus were uniquely differentially abundant and enriched in the CD cohort. Four species were uniquely differentially abundant and enriched in the UC cohort, including Citrobacter portucalensis, Citrobacter pasteurii, Citrobacter werkmanii, and Proteus hauseri. Our analysis also showed a dramatically increased abundance of E. coli in their intestinal bacterial community. Biosynthetic pathways of aerobactin siderophore, LPS, enterobacterial common antigen, nitrogen metabolism, and sulfur relay systems encoded by E. coli were significantly elevated in the CD samples compared to the HCs. Menaquinol biosynthetic pathways were associated with UC that belonged to K. pneumoniae strains.

CONCLUSIONS: In conclusion, compared with healthy people, the taxonomic and functional composition of intestinal bacteria in CD and UC patients was significantly shifted to Enterobacteriaceae species, mainly E. coli and Klebsiella species.}, } @article {pmid36265810, year = {2022}, author = {Carson, TL and Buro, AW and Miller, D and Peña, A and Ard, JD and Lampe, JW and Yi, N and Lefkowitz, E and William, VP and Morrow, C and Wilson, L and Barnes, S and Demark-Wahnefried, W}, title = {Rationale and study protocol for a randomized controlled feeding study to determine the structural- and functional-level effects of diet-specific interventions on the gut microbiota of non-Hispanic black and white adults.}, journal = {Contemporary clinical trials}, volume = {123}, number = {}, pages = {106968}, pmid = {36265810}, issn = {1559-2030}, support = {R01 CA253219/CA/NCI NIH HHS/United States ; T32 CA090314/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Male ; Humans ; Female ; *Gastrointestinal Microbiome ; White People ; Feces/microbiology ; Diet ; Bacteria/genetics ; Randomized Controlled Trials as Topic ; }, abstract = {BACKGROUND: Colorectal cancer (CRC), the third leading cause of cancer-related deaths in the US, has been associated with an overrepresentation or paucity of several microbial taxa in the gut microbiota, but causality has not been established. Black men and women have among the highest CRC incidence and mortality rates of any racial/ethnic group. This study will examine the impact of the Dietary Approaches to Stop Hypertension (DASH) diet on gut microbiota and fecal metabolites associated with CRC risk.

METHODS: A generally healthy sample of non-Hispanic Black and white adults (n = 112) is being recruited to participate in a parallel-arm randomized controlled feeding study. Participants are randomized to receive the DASH diet or a standard American diet for a 28-day period. Fecal samples are collected weekly throughout the study to analyze changes in the gut microbiota using 16 s rRNA and selected metagenomics. Differences in bacterial alpha and beta diversity and taxa that have been associated with CRC (Bacteroides, Fusobacterium, Clostridium, Lactobacillus, Bifidobacterium, Ruminococcus, Porphyromonas, Succinivibrio) are being evaluated. Covariate measures include body mass index, comorbidities, medication history, physical activity, stress, and demographic characteristics.

CONCLUSION: Our findings will provide preliminary evidence for the DASH diet as an approach for cultivating a healthier gut microbiota across non-Hispanic Black and non-Hispanic White adults. These results can impact clinical, translational, and population-level approaches for modification of the gut microbiota to reduce risk of chronic diseases including CRC.

TRIAL REGISTRATION: This study was registered on ClinicalTrials.gov, identifier NCT04538482, on September 4, 2020 (https://clinicaltrials.gov/ct2/show/NCT04538482).}, } @article {pmid36264997, year = {2022}, author = {Li, Y and Shi, M and Zhang, B and Wu, J and Wang, Y and Li, M and Wu, Y and Hu, X and Hu, D and Huang, Z and Wronski, T}, title = {Effects of different weaning times on the stress response and the intestinal microbiota composition of female forest musk deer (Moschus berezovskii) and their fawns.}, journal = {PloS one}, volume = {17}, number = {10}, pages = {e0276542}, pmid = {36264997}, issn = {1932-6203}, mesh = {Humans ; Animals ; Female ; *Gastrointestinal Microbiome/genetics ; *Deer/physiology ; Weaning ; Hydrocortisone ; Forests ; Receptors, Cholinergic ; Receptor Protein-Tyrosine Kinases ; }, abstract = {The effects of mother-infant separation (i.e., weaning) on the physiology, psychology and nutrition of mammalian infants have attracted much attention. Forest musk deer (FMD) is a first-class protected species in China and listed endangered in the IUCN Red List. The captive breeding population is not only an important source for restocking of wild resources, but also a necessary way to supply the market with legal musk. So far, there is no scientific basis for the appropriate separation time of FMD females and their infants. Therefore, we used metagenome sequencing and enzyme-linked immunosorbent assays to study changes in the fecal cortisol concentration, as well as the intestinal microbiome composition and function of females and fawns at three different separation times, i.e., after 80 days, 90 days and 100 days. The results showed that the increment of the cortisol concentration in female FMD increased with increasing lactation time. The increment of cortisol concentration in infant FMD was highest in the 80 days weaning group, but there was no significant difference between the 90 days and the 100 days separation time. Based on the annotation results of COG, KEGG and CAZy databases, the abundance of different functions annotated by the intestinal microbiome of mothers and fawns of the 90 days weaning group changed slightly after separation. Based on the above results, the separation of mother and infant FMD is recommended after 90 days, i.e., the separation time that triggered the lowest rate of weaning stress and that supported a relatively stable gastro-intestinal physiology.}, } @article {pmid36264306, year = {2022}, author = {Amin, AB and Zhang, L and Zhang, J and Mao, S}, title = {Fermented soybean meal modified the rumen microbiome to enhance the yield of milk components in Holstein cows.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {22}, pages = {7627-7642}, pmid = {36264306}, issn = {1432-0614}, support = {2021YFF1000703-01//National Key research and Development Program of China/ ; }, mesh = {Animals ; Cattle ; Female ; Pregnancy ; Acetates/metabolism ; Animal Feed ; Diet/veterinary ; Dietary Supplements ; Fermentation ; *Fermented Foods ; Lactation ; Methionine/metabolism ; *Microbiota ; Milk Proteins/metabolism/pharmacology ; Propionates/metabolism ; RNA, Ribosomal, 16S/metabolism ; Rumen/microbiology ; Glycine max/metabolism ; }, abstract = {The study was conducted to evaluate the rumen microbiota as well as the milk composition and milk component yields of Holstein cows supplemented with fermented soybean meal (FSBM). Eighteen Holstein cows in their 2nd parity with 54.38 ± 11.12 SD days in milking (DIM) were divided into two dietary groups (CON and TRT) of nine cows per group. The cows in the TRT group received 300 g of FSBM per cow per day in addition to the conventional diet, while each cow in the CON group was supplemented with 350 g of soybean meal (SBM) in their diet daily throughout the 28-day feeding trial. Rumen bacterial composition was detected via 16S rRNA sequencing, and the functional profiles of bacterial communities were predicted. Milk composition, milk yield, as well as rumen fermentation parameters, and serum biochemistry were also recorded. The inclusion of FSBM into the diets of Holstein cows increased the milk urea nitrogen (MUN), milk protein yield, fat corrected milk (FCM), and milk fat yield while the milk somatic cell count (SCC) was decreased. In the rumen, the relative abundances of Fibrobacterota, and Spirochaetota phyla were increased in the TRT group, while the percentage of Proteobacteria was lower. In addition, the supplementation of FSBM to Holstein cows increased the acetate percentage, rumen pH, and acetate to propionate ratio, while the proportion of propionate and propionate % was observed to decrease in the TRT group. The KEGG pathway and functional prediction revealed an upregulation in the functional genes associated with the biosynthesis of amino acids in the TRT group. This enrichment in functional genes resulted in an improved synthesis of several essential amino acids including lysine, methionine, and branch chain amino acids (BCAA) which might be responsible for the increased milk protein yield. Future studies should employ shotgun metagenomics, transcriptomics, and metabolomics technology to investigate the effects of FSBM on other rumen microbiomes and milk protein synthesis in the mammary gland in Holstein cows. KEY POINTS: • The supplementation of fermented soybean meal (FSBM) to Holstein cows modified the proportion of rumen bacteria. • Predicted metabolic pathways and functional genes of rumen bacteria revealed an enrichment in pathway and genes associated with biosynthesis of amino acids in the group fed FSBM. • The cows supplemented with FSBM record an improved rumen fermentation. • Cows supplemented with FSBM recorded an increased yield of milk protein and milk fat.}, } @article {pmid36264141, year = {2022}, author = {Rühlemann, MC and Wacker, EM and Ellinghaus, D and Franke, A}, title = {MAGScoT: a fast, lightweight and accurate bin-refinement tool.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {24}, pages = {5430-5433}, pmid = {36264141}, issn = {1367-4811}, support = {//German Research Foundation/ ; SFB 1182//Collaborative Research Center 1182: Origin and Function of Metaorganisms/ ; //DFG Research Unit 5042/ ; }, mesh = {*Algorithms ; Metagenomics ; Metagenome ; *Microbiota ; }, abstract = {MOTIVATION: Recovery of metagenome-assembled genomes (MAGs) from shotgun metagenomic data is an important task for the comprehensive analysis of microbial communities from variable sources. Single binning tools differ in their ability to leverage specific aspects in MAG reconstruction, the use of ensemble binning refinement tools is often time consuming and computational demand increases with community complexity. We introduce MAGScoT, a fast, lightweight and accurate implementation for the reconstruction of highest-quality MAGs from the output of multiple genome-binning tools.

RESULTS: MAGScoT outperforms popular bin-refinement solutions in terms of quality and quantity of MAGs as well as computation time and resource consumption.

MAGScoT is available via GitHub (https://github.com/ikmb/MAGScoT) and as an easy-to-use Docker container (https://hub.docker.com/repository/docker/ikmb/magscot).

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36261869, year = {2022}, author = {Lourenço, TGB and de Oliveira, AM and Tsute Chen, G and Colombo, APV}, title = {Oral-gut bacterial profiles discriminate between periodontal health and diseases.}, journal = {Journal of periodontal research}, volume = {57}, number = {6}, pages = {1227-1237}, doi = {10.1111/jre.13059}, pmid = {36261869}, issn = {1600-0765}, support = {00239/2016-7//National Council for Scientific and Technological Development (CNPq)/ ; 001//Coordination of Improvement of Higher Education Personnel (CAPES)/ ; E-26/202.256/2019; E-26/201.162/2014//Foundation for Research Financial Support in the State of Rio de Janeiro (FAPERJ)/ ; E-26/201.162/2014//Foundation for Research Financial Support in the State of Rio de Janeiro (FAPERJ)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Periodontitis/diagnosis/microbiology ; Aggregatibacter actinomycetemcomitans/genetics ; *Periodontal Diseases/microbiology ; }, abstract = {OBJECTIVE: This investigation explored oral-gut microbial signatures with potential to distinguish among periodontal conditions.

BACKGROUND DATA: The interplay between the oral and gut microbiomes may be a critical pathway linking periodontal diseases and systemic inflammatory disorders. The mechanisms by which oral microorganisms translocate to the gut and cause microbial dysbiosis, favoring an inflammatory state, are still unknown. As a first approach, characterization of oral-gut microbial profiles associated with periodontal health and diseases can provide insights on such mechanisms of etiology and pathogenesis.

METHODS: Fecal and saliva samples from individuals with periodontal health (PH, 8), gingivitis (GG, 17), and periodontitis (PD, 24) were analyzed for their microbial composition by 16S rRNA gene sequencing. Microbial taxa were compared and correlated to periodontal parameters. Multivariate discriminant analysis (MDA) was carried out to identify profiles related to health and disease.

RESULTS: Few significant differences in oral-gut taxa were detected among clinical groups, although increase in fecal Fusobacterium nucleatum ss vincentii and salivary Aggregatibacter actinomycetemcomitans, Parvimonas micra, and Fretibacterium sp. HMT358 were strongly correlated with deep pockets and inflammation (p < .01). Over 50% of the fecal microbiota comprised microorganisms shared between oral and gut sites, whereas oral taxa were detected in approximately 9%, particularly enriched in GG fecal samples (p = .04). Trends for lower fecal richness and higher salivary diversity in PD compared to PH were observed. MDA was able to classify correctly 82% of the patients into the clinical groups. Main classifiers of periodontitis were high BMI, older age, and enrichment of oral-fecal Leptotrichia sp. HMT4, Peptostreptococcus stomatis, Dialister invisus, and a novel Lautropia sp. HMTC89-like organism.

CONCLUSION: Within the limitations of an exploratory investigation, specific profiles of oral-gut taxa, including known and potential novel organisms, combined with social-demographic features were able to discriminate individuals with periodontal diseases in this study population.}, } @article {pmid36261508, year = {2023}, author = {Lin, L and Lai, Z and Yang, H and Zhang, J and Qi, W and Xie, F and Mao, S}, title = {Genome-centric investigation of bile acid metabolizing microbiota of dairy cows and associated diet-induced functional implications.}, journal = {The ISME journal}, volume = {17}, number = {1}, pages = {172-184}, pmid = {36261508}, issn = {1751-7370}, mesh = {Animals ; Female ; Cattle ; *Bile Acids and Salts ; *Microbiota ; Metagenome ; Intestines/microbiology ; Diet ; }, abstract = {Although the importance of bile acid (BA)-related microbial strains and enzymes is increasingly recognized for monogastric animals, a lack of knowledge about BA metabolism in dairy cows limits functional applications aimed at the targeted modulation of microbe-host interactions for animal production and health. In the present study, 108 content samples from six intestinal regions of dairy cows were used for shotgun metagenomic sequencing. Overall, 372 high-quality metagenome-assembled genomes (MAGs) were involved in BA deconjugation, oxidation, and dehydroxylation pathways. Furthermore, the BA-metabolizing microbiome predominately occurred in the large intestine, resulting in the accumulation of secondary unconjugated BAs. Comparative genomic analysis revealed that the bile salt hydrolase (BSH)-carrying microbial populations managed with the selective environment of the dairy cow intestine by adopting numerous host mucin glycan-degrading abilities. A sequence similarity network analysis classified 439 BSH homologs into 12 clusters and identified different clusters with diverse evolution, taxonomy, signal peptides, and ecological niches. Our omics data further revealed that the strains of Firmicutes bacterium CAG-110 processed the increased abundance of BSHs from Cluster 1, coinciding with the changes in the colon cholic acid concentration after grain introduction, and were intricately related to intestinal inflammation. This study is the first to use a genome-centric approach and whole intestine-targeted metabolomics to reveal microbial BA metabolism and its diet-induced functional implications in dairy cows. These findings provide insight into the manipulation of intestinal microorganisms for improving host health.}, } @article {pmid36261472, year = {2022}, author = {Lam, TJ and Ye, Y}, title = {Meta-analysis of microbiome association networks reveal patterns of dysbiosis in diseased microbiomes.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {17482}, pmid = {36261472}, issn = {2045-2322}, support = {R01 AI108888/AI/NIAID NIH HHS/United States ; R01 AI143254/AI/NIAID NIH HHS/United States ; R21 CA143254/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Dysbiosis/microbiology ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Microbial Interactions ; }, abstract = {The human gut microbiome is composed of a diverse and dynamic population of microbial species which play key roles in modulating host health and physiology. While individual microbial species have been found to be associated with certain disease states, increasing evidence suggests that higher-order microbial interactions may have an equal or greater contribution to host fitness. To better understand microbial community dynamics, we utilize networks to study interactions through a meta-analysis of microbial association networks between healthy and disease gut microbiomes. Taking advantage of the large number of metagenomes derived from healthy individuals and patients with various diseases, together with recent advances in network inference that can deal with sparse compositional data, we inferred microbial association networks based on co-occurrence of gut microbial species and made the networks publicly available as a resource (GitHub repository named GutNet). Through our meta-analysis of inferred networks, we were able to identify network-associated features that help stratify between healthy and disease states such as the differentiation of various bacterial phyla and enrichment of Proteobacteria interactions in diseased networks. Additionally, our findings show that the contributions of taxa in microbial associations are disproportionate to their abundances and that rarer taxa of microbial species play an integral part in shaping dynamics of microbial community interactions. Network-based meta-analysis revealed valuable insights into microbial community dynamics between healthy and disease phenotypes. We anticipate that the healthy and diseased microbiome association networks we inferred will become an important resource for human-related microbiome research.}, } @article {pmid36259734, year = {2022}, author = {Zhao, D and Zhang, S and Kumar, S and Zhou, H and Xue, Q and Sun, W and Zhou, J and Xiang, H}, title = {Comparative Genomic Insights into the Evolution of Halobacteria-Associated "Candidatus Nanohaloarchaeota".}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0066922}, pmid = {36259734}, issn = {2379-5077}, mesh = {*Euryarchaeota ; Phylogeny ; Halobacterium ; Archaea ; Genomics ; *Microbiota ; }, abstract = {Members of the phylum "Candidatus Nanohaloarchaeota," a representative lineage within the DPANN superphylum, are characterized by their nanosized cells and symbiotic lifestyle with Halobacteria. However, the development of the symbiosis remains unclear. Here, we propose two novel families, "Candidatus Nanoanaerosalinaceae" and "Candidatus Nanohalalkaliarchaeaceae" in "Ca. Nanohaloarchaeota," represented by five dereplicated metagenome-assembled genomes obtained from hypersaline sediments or related enrichment cultures of soda-saline lakes. Phylogenetic analyses reveal that the two novel families are placed at the root of the family "Candidatus Nanosalinaceae," including the cultivated taxa. The two novel families prefer hypersaline sediments, and the acid shift of predicted proteomes indicates a "salt-in" strategy for hypersaline adaptation. They contain a lower proportion of putative horizontal gene transfers from Halobacteria than "Ca. Nanosalinaceae," suggesting a weaker association with Halobacteria. Functional prediction and historical events reconstruction disclose that they exhibit divergent potentials in carbohydrate and organic acid metabolism and environmental responses. Globally, comparative genomic analyses based on the new families enrich the taxonomic and functional diversity of "Ca. Nanohaloarchaeota" and provide insights into the evolutionary process of "Ca. Nanohaloarchaeota" and their symbiotic relationship with Halobacteria. IMPORTANCE The DPANN superphylum is a group of archaea widely distributed in various habitats. They generally have small cells and have a symbiotic lifestyle with other archaea. The archaeal symbiotic interaction is vital to understanding microbial communities. However, the formation and evolution of the symbiosis between the DPANN lineages and other diverse archaea remain unclear. Based on phylogeny, habitat distribution, hypersaline adaptation, host prediction, functional potentials, and historical events of "Ca. Nanohaloarchaeota," a representative phylum within the DPANN superphylum, we report two novel families representing intermediate stages, and we infer the evolutionary process of "Ca. Nanohaloarchaeota" and their Halobacteria-associated symbiosis. Altogether, this research helps in understanding the evolution of symbiosis in "Ca. Nanohaloarchaeota" and provides a model for the evolution of other DPANN lineages.}, } @article {pmid36258280, year = {2023}, author = {Al-Emran, HM and Rahman, S and Hasan, MS and Ul Alam, R and Islam, OK and Anwar, A and Jahid, MIK and Hossain, A}, title = {Microbiome analysis revealing microbial interactions and secondary bacterial infections in COVID-19 patients comorbidly affected by Type 2 diabetes.}, journal = {Journal of medical virology}, volume = {95}, number = {1}, pages = {e28234}, pmid = {36258280}, issn = {1096-9071}, mesh = {Humans ; Aged ; *COVID-19/complications/epidemiology/microbiology ; SARS-CoV-2 ; *Diabetes Mellitus, Type 2/complications ; *Coinfection/complications ; *Microbiota ; Bacteria/genetics ; *Bacterial Infections/epidemiology/complications ; Microbial Interactions ; }, abstract = {The mortality of coronavirus disease 2019 (COVID-19) disease is very high among the elderly or individuals having comorbidities such as obesity, cardiovascular diseases, lung infections, hypertension, and/or diabetes. Our study characterizes the metagenomic features in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-infected patients with or without type 2 diabetes, to identify the microbial interactions associated with its fatal consequences.This study compared the baseline nasopharyngeal microbiome of SARS-CoV-2-infected diabetic and nondiabetic patients with controls adjusted for age and gender. The metagenomics based on next-generation sequencing was performed using Ion GeneStudio S5 Series and the data were analyzed by the Vegan-package in R. All three groups possessed significant bacterial diversity and dissimilarity indexes (p < 0.05). Spearman's correlation coefficient network analysis illustrated 183 significant positive correlations and 13 negative correlations of pathogenic bacteria (r = 0.6-1.0, p < 0.05), and 109 positive correlations between normal flora and probiotic bacteria (r > 0.6, p < 0.05). The SARS-CoV-2 diabetic group exhibited a significant increase in pathogens and secondary infection-causing bacteria (p < 0.05) with a simultaneous decrease of normal flora (p < 0.05). The dysbiosis of the bacterial community might be linked with severe consequences of COVID-19-infected diabetic patients, although a few probiotic strains inhibited numerous pathogens in the same pathological niches. This study suggested that the promotion of normal flora and probiotics through dietary supplementation and excessive inflammation reduction by preventing secondary infections might lead to a better outcome for those comorbid patients.}, } @article {pmid36257972, year = {2023}, author = {Rogers, TJ and Buongiorno, J and Jessen, GL and Schrenk, MO and Fordyce, JA and de Moor, JM and Ramírez, CJ and Barry, PH and Yücel, M and Selci, M and Cordone, A and Giovannelli, D and Lloyd, KG}, title = {Chemolithoautotroph distributions across the subsurface of a convergent margin.}, journal = {The ISME journal}, volume = {17}, number = {1}, pages = {140-150}, pmid = {36257972}, issn = {1751-7370}, mesh = {*Geologic Sediments/chemistry ; Phylogeny ; Metagenomics/methods ; Bacteria/genetics/metabolism ; *Microbiota ; Carbon/metabolism ; Sulfur/metabolism ; }, abstract = {Subducting oceanic crusts release fluids rich in biologically relevant compounds into the overriding plate, fueling subsurface chemolithoautotrophic ecosystems. To understand the impact of subsurface geochemistry on microbial communities, we collected fluid and sediments from 14 natural springs across a ~200 km transect across the Costa Rican convergent margin and performed shotgun metagenomics. The resulting 404 metagenome-assembled genomes (MAGs) cluster into geologically distinct regions based on MAG abundance patterns: outer forearc-only (25% of total relative abundance), forearc/arc-only (38% of total relative abundance), and delocalized (37% of total relative abundance) clusters. In the outer forearc, Thermodesulfovibrionia, Candidatus Bipolaricaulia, and Firmicutes have hydrogenotrophic sulfate reduction and Wood-Ljungdahl (WL) carbon fixation pathways. In the forearc/arc, Anaerolineae, Ca. Bipolaricaulia, and Thermodesulfovibrionia have sulfur oxidation, nitrogen cycling, microaerophilic respiration, and WL, while Aquificae have aerobic sulfur oxidation and reverse tricarboxylic acid carbon fixation pathway. Transformation-based canonical correspondence analysis shows that MAG distribution corresponds to concentrations of aluminum, iron, nickel, dissolved inorganic carbon, and phosphate. While delocalized MAGs appear surface-derived, the subsurface chemolithoautotrophic, metabolic, and taxonomic landscape varies by the availability of minerals/metals and volcanically derived inorganic carbon. However, the WL pathway persists across all samples, suggesting that this versatile, energy-efficient carbon fixation pathway helps shape convergent margin subsurface ecosystems.}, } @article {pmid36257428, year = {2023}, author = {Semedo, M and Song, B}, title = {Sediment metagenomics reveals the impacts of poultry industry wastewater on antibiotic resistance and nitrogen cycling genes in tidal creek ecosystems.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 2}, pages = {159496}, doi = {10.1016/j.scitotenv.2022.159496}, pmid = {36257428}, issn = {1879-1026}, mesh = {Animals ; *Wastewater/analysis ; Metagenomics ; Poultry ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; *Microbiota ; Anti-Bacterial Agents/pharmacology/analysis ; Nitrogen/analysis ; }, abstract = {The intensification of the poultry industry may lead to the increased spread of antibiotic resistance genes (ARGs) in the environment. However, the impacts of wastewater discharge from poultry processing plants on the sediment resistome are relatively unexplored. Furthermore, its relationships with important biogeochemical pathways, such as the N cycle, are virtually unknown. The overall objective of this study was to examine the abundance and diversity of antibiotic resistance and N cycling genes in sediment microbial communities impacted by poultry industry wastewater. We performed a metagenomic investigation of sediments in an impacted and a reference tidal creek. We also quantified the abundance of the clinical class 1 integron-integrase gene (intI1) through qPCR as a secondary marker of anthropogenic contamination. Abundance and diversity of ARGs were substantially higher in the impacted tidal creek, especially near the wastewater discharge. Abundances of ARGs conferring resistance to macrolides, tetracyclines, and streptogramins were also higher in the impacted creek than the reference creek. From the N cycling genes detected in the metagenomes, nrfA, the genetic marker for dissimilatory nitrate reduction to ammonia (DNRA), had the strongest positive relationship with the total abundance of ARGs, which may indicate an increased potential of eutrophication in ARG-impacted ecosystems due to nitrogen retention. This study demonstrates that wastewater discharge from a poultry processing plant can increase the spread of ARGs, which may result in negative impacts on ecosystem health.}, } @article {pmid36255324, year = {2022}, author = {Miranda-Carrazco, A and Navarro-Noya, YE and Govaerts, B and Verhulst, N and Dendooven, L}, title = {Nitrogen Fertilizer Application Alters the Root Endophyte Bacterial Microbiome in Maize Plants, but Not in the Stem or Rhizosphere Soil.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0178522}, pmid = {36255324}, issn = {2165-0497}, mesh = {*Soil/chemistry ; Endophytes ; Nitrogen ; Zea mays/microbiology ; Fertilizers ; Rhizosphere ; Bacteria/genetics ; *Microbiota ; Crops, Agricultural ; Soil Microbiology ; }, abstract = {Plant-associated microorganisms that affect plant development, their composition, and their functionality are determined by the host, soil conditions, and agricultural practices. How agricultural practices affect the rhizosphere microbiome has been well studied, but less is known about how they might affect plant endophytes. In this study, the metagenomic DNA from the rhizosphere and endophyte communities of root and stem of maize plants was extracted and sequenced with the "diversity arrays technology sequencing," while the bacterial community and functionality (organized by subsystems from general to specific functions) were investigated in crops cultivated with or without tillage and with or without N fertilizer application. Tillage had a small significant effect on the bacterial community in the rhizosphere, but N fertilizer had a highly significant effect on the roots, but not on the rhizosphere or stem. The relative abundance of many bacterial species was significantly different in the roots and stem of fertilized maize plants, but not in the unfertilized ones. The abundance of N cycle genes was affected by N fertilization application, most accentuated in the roots. How these changes in bacterial composition and N genes composition might affect plant development or crop yields has still to be unraveled. IMPORTANCE We investigated the bacterial community structure in the rhizosphere, root, and stem of maize plants cultivated under different agricultural techniques, i.e., with or without N fertilization, and with or without tillage. We found that the bacterial community was defined mostly by the plant compartment and less by agricultural techniques. In the roots, N fertilizer application affected the bacterial community structure, the microbiome functionality, and the abundance of genes involved in the N cycle, but the effect in the rhizosphere and stem was much smaller. Contrary, tillage did not affect the maize microbiome. This study enriches our knowledge about the plant-microbiome system and how N fertilization application affected it.}, } @article {pmid36252903, year = {2023}, author = {Sun, Y and Guo, J and Wei, F and Chen, X and Li, M and Li, C and Xia, S and Zhang, G and You, W and Cong, X and Yu, T and Wang, S}, title = {Microbial functional communities and the antibiotic resistome profile in a high-selenium ecosystem.}, journal = {Chemosphere}, volume = {311}, number = {Pt 1}, pages = {136858}, doi = {10.1016/j.chemosphere.2022.136858}, pmid = {36252903}, issn = {1879-1298}, mesh = {*Selenium/pharmacology/analysis ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; *Microbiota ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Soil ; Soil Microbiology ; Genes, Bacterial ; }, abstract = {Enshi City, in the Hubei Province of China, is known as the world capital of selenium with the most abundant selenium resource. An important selenium hyperaccumulator plant, Cardamine violifolia, was found to naturally grow in this high-selenium ecosystem. However, relatively little is known about the impact of the selenium levels on microbial community and functional shifts in C. violifolia rhizosphere. Here, we tested the hypothesis that underground microbial diversity and function vary along a selenium gradient, including antibiotic resistance genes (ARGs). Comprehensive metagenomic analyses, such as taxonomic investigation, functional detection, and ARG annotation, showed that selenium, mercury, cadmium, lead, arsenic, and available phosphorus and potassium were correlated with microbial diversity and function. Thaumarchaeota was exclusively dominant in the highest selenium concentration of mine outcrop, and Rhodanobacter and Nitrospira were predominant in the high-selenium ecosystem. The plant C. violifolia enriched a high concentration of selenium in the rhizosphere compared to those in the bulk soil, and it recruited Variovorax and Polaromonas in its rhizosphere. Microbial abundance showed a trend of increasing first and then decreasing from low to high selenium concentrations. Annotation of ARGs showed that the multidrug resistance genes adeF, mtrA, and poxtA, the aminoglycoside resistance gene rpsL, and the sulfonamide resistant gene sul2 were enriched in the high-selenium system. It was discovered that putative antibiotic resistant bacteria displayed obvious differences in the farmland and the soils with various selenium concentrations, indicating that a high-selenium ecosystem harbors the specific microbes with a higher capacity to enrich or resist selenium, toxic metals, or antibiotics. Taken together, these results reveal the effects of selenium concentration and the selenium hyperaccumulator plant C. violifolia on shaping the microbial functional community and ARGs. Metalloid selenium-inducible antibiotic resistance is worth paying attention to in future.}, } @article {pmid36252326, year = {2022}, author = {de Diego, GA and Penas-Steinhardt, A and Ferro, JP and Palacio, MJ and Ossana, NA and Eissa, BL and Belforte, F}, title = {Impact of exposure to arsenic on the bacterial microbiota associated with river biofilms in the Pampas region.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {252}, number = {}, pages = {106319}, doi = {10.1016/j.aquatox.2022.106319}, pmid = {36252326}, issn = {1879-1514}, mesh = {Humans ; *Arsenic/toxicity ; RNA, Ribosomal, 16S/genetics ; *Water Pollutants, Chemical/toxicity ; *Microbiota ; Bacteria/genetics ; Biofilms ; Water ; }, abstract = {Freshwater contamination by arsenic (As) is a worldwide problem. It may be found in Pampean streams of Argentina at concentrations higher than those recommended by international organizations and stipulated by national regulations. Exposure to high As concentrations causes serious consequences to both human health and the environment. The general objective of this work was to evaluate the effect of As on the biofilm microbiota structure from Naveira stream, Luján, Province of Buenos Aires (Coordinates: 34º34'02″ S 59º03'51″ W). The biofilm collected was cultivated in glass aquaria at different As III concentrations (0, 0.2 and 20 mg / L), inside incubation chambers under controlled conditions (16 h light: 8 h dark and 24 ± 1 °C) and constant aeration for 31 d, with partial water renewal every 9 d. We amplified the hypervariable regions V3 and V4 of the bacterial 16S rRNA gene from biofilm bacterial community samples to determine the diversity and abundance of the different taxa. The taxonomic composition of each sample, the alpha diversity of each treatment and the main metabolic pathways were analyzed. Principal Component Analysis of the present phyla and a Linear Discriminant Analysis of the metabolic pathways was also performed. Significant changes were observed in relation to the taxonomic composition of the bacterial community after exposure to the metalloid. However, this effect was not observed at the low concentration used (0.2 mg / L), which is the one that corresponds to ecologically relevant levels. The significantly affected phyla were Verrucomicrobiota, Acidobacteriota, Patescibacteria, Hydrogenedentes and WPS-2. The relative abundances of the Verrucomicrobiota, WPS-2 and Patescibacteria groups were notably decreased in the treatment with high As, while the Acidobacteria group was increased in both treatments with As. The stream samples showed greater bacterial diversity than those grown in the laboratory without As. Finally, it was possible to characterize the metabolic profile of the biofilm developed under natural conditions in the leaves of the aquatic plant Elodea canadensis in the Naveira stream. In addition, results showed that biosynthesis-related pathways were more abundant at the high As concentration treatment (20 mg / L).}, } @article {pmid36251393, year = {2022}, author = {Giri, S and Uehara, O and Takada, A and Paudel, D and Morikawa, T and Arakawa, T and Nagasawa, T and Abiko, Y and Furuichi, Y}, title = {The effect of Porphyromonas gingivalis on the gut microbiome of mice in relation to aging.}, journal = {Journal of periodontal research}, volume = {57}, number = {6}, pages = {1256-1266}, doi = {10.1111/jre.13062}, pmid = {36251393}, issn = {1600-0765}, mesh = {Mice ; Animals ; *Porphyromonas gingivalis ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; Tumor Necrosis Factor-alpha ; Mice, Inbred C57BL ; Aging ; RNA, Messenger ; }, abstract = {BACKGROUND AND OBJECTIVE: The translocation of oral bacteria, including Porphyromonas gingivalis, to the gut has been shown to alter gut microbiome. However, the effect of P. gingivalis on gut microbiome in relation to aging has not been demonstrated. We hypothesize that P. gingivalis has more detrimental effect on gut environment with increased age. The objective of this study is to investigate the effect of P. gingivalis on gut environment using aged mice.

MATERIALS AND METHODS: C57BL/6J mice aged 4 weeks (young) or 76 weeks (old) were divided into four groups: control-young, control-old, P. gingivalis-administered young, and P. gingivalis-administered old. P. gingivalis was orally administered thrice weekly for 5 weeks. At 30 days after the last P. gingivalis administration, 16S rRNA sequencing was performed to study the gut microbiome. The mRNA and protein expression of intestinal junctional barrier molecules and the levels of the inflammatory cytokines IL-1β and TNF-α in the serum were evaluated.

RESULTS: Significant differences in the gut microbiomes between the groups, in terms of taxonomic abundance, bacterial diversity, and predicted metagenome function, were observed. A significant reduction in the alpha diversity and in the abundance of beneficial bacteria, such as Akkermansia and Clostridiaceae, in the P. gingivalis-administered old mice was observed. The mRNA and protein levels of Claudin-1 and Claudin-2 in the intestine were significantly elevated, while E-cadherin was significantly downregulated in the P. gingivalis-administered old mice, as were the serum levels of IL-1β and TNF-α.

CONCLUSION: The effect of P. gingivalis on the gut environment is more pronounced in old mice than in young mice.}, } @article {pmid36250060, year = {2022}, author = {Monshizadeh, M and Zomorodi, S and Mortensen, K and Ye, Y}, title = {Revealing bacteria-phage interactions in human microbiome through the CRISPR-Cas immune systems.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {933516}, pmid = {36250060}, issn = {2235-2988}, support = {R01 AI108888/AI/NIAID NIH HHS/United States ; R01 AI143254/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; CRISPR-Cas Systems ; Humans ; Immune System ; *Microbiota/genetics ; }, abstract = {The human gut microbiome is composed of a diverse consortium of microorganisms. Relatively little is known about the diversity of the bacteriophage population and their interactions with microbial organisms in the human microbiome. Due to the persistent rivalry between microbial organisms (hosts) and phages (invaders), genetic traces of phages are found in the hosts' CRISPR-Cas adaptive immune system. Mobile genetic elements (MGEs) found in bacteria include genetic material from phage and plasmids, often resultant from invasion events. We developed a computational pipeline (BacMGEnet), which can be used for inference and exploratory analysis of putative interactions between microbial organisms and MGEs (phages and plasmids) and their interaction network. Given a collection of genomes as the input, BacMGEnet utilizes computational tools we have previously developed to characterize CRISPR-Cas systems in the genomes, which are then used to identify putative invaders from publicly available collections of phage/prophage sequences. In addition, BacMGEnet uses a greedy algorithm to summarize identified putative interactions to produce a bacteria-MGE network in a standard network format. Inferred networks can be utilized to assist further examination of the putative interactions and for discovery of interaction patterns. Here we apply the BacMGEnet pipeline to a few collections of genomic/metagenomic datasets to demonstrate its utilities. BacMGEnet revealed a complex interaction network of the Phocaeicola vulgatus pangenome with its phage invaders, and the modularity analysis of the resulted network suggested differential activities of the different P. vulgatus' CRISPR-Cas systems (Type I-C and Type II-C) against some phages. Analysis of the phage-bacteria interaction network of human gut microbiome revealed a mixture of phages with a broad host range (resulting in large modules with many bacteria and phages), and phages with narrow host range. We also showed that BacMGEnet can be used to infer phages that invade bacteria and their interactions in wound microbiome. We anticipate that BacMGEnet will become an important tool for studying the interactions between bacteria and their invaders for microbiome research.}, } @article {pmid36248884, year = {2022}, author = {Gill, T and Stauffer, P and Asquith, M and Laderas, T and Martin, TM and Davin, S and Schleisman, M and Ramirez, C and Ogle, K and Lindquist, I and Nguyen, J and Planck, SR and Shaut, C and Diamond, S and Rosenbaum, JT and Karstens, L}, title = {Axial spondyloarthritis patients have altered mucosal IgA response to oral and fecal microbiota.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {965634}, pmid = {36248884}, issn = {1664-3224}, support = {R01 EY029266/EY/NEI NIH HHS/United States ; P30 EY010572/EY/NEI NIH HHS/United States ; K01 DK116706/DK/NIDDK NIH HHS/United States ; T32 HL083808/HL/NHLBI NIH HHS/United States ; T15 LM007088/LM/NLM NIH HHS/United States ; }, mesh = {Amino Acids ; *Axial Spondyloarthritis ; Clostridiales/genetics ; Feces/chemistry ; *Gastrointestinal Microbiome/genetics ; Humans ; Immunoglobulin A/analysis ; Propionates ; RNA, Ribosomal, 16S/analysis/genetics ; }, abstract = {Axial spondyloarthritis (axSpA) is an inflammatory arthritis involving the spine and the sacroiliac joint with extra-articular manifestations in the eye, gut, and skin. The intestinal microbiota has been implicated as a central environmental component in the pathogenesis of various types of spondyloarthritis including axSpA. Additionally, alterations in the oral microbiota have been shown in various rheumatological conditions, such as rheumatoid arthritis (RA). Therefore, the aim of this study was to investigate whether axSpA patients have an altered immunoglobulin A (IgA) response in the gut and oral microbial communities. We performed 16S rRNA gene (16S) sequencing on IgA positive (IgA[+]) and IgA negative (IgA[-]) fractions (IgA-SEQ) from feces (n=17 axSpA; n=14 healthy) and saliva (n=14 axSpA; n=12 healthy), as well as on IgA-unsorted fecal and salivary samples. PICRUSt2 was used to predict microbial metabolic potential in axSpA patients and healthy controls (HCs). IgA-SEQ analyses revealed enrichment of several microbes in the fecal (Akkermansia, Ruminococcaceae, Lachnospira) and salivary (Prevotellaceae, Actinobacillus) microbiome in axSpA patients as compared with HCs. Fecal microbiome from axSpA patients showed a tendency towards increased alpha diversity in IgA[+] fraction and decreased diversity in IgA[-] fraction in comparison with HCs, while the salivary microbiome exhibits a significant decrease in alpha diversity in both IgA[+] and IgA[-] fractions. Increased IgA coating of Clostridiales Family XIII in feces correlated with disease severity. Inferred metagenomic analysis suggests perturbation of metabolites and metabolic pathways for inflammation (oxidative stress, amino acid degradation) and metabolism (propanoate and butanoate) in axSpA patients. Analyses of fecal and salivary microbes from axSpA patients reveal distinct populations of immunoreactive microbes compared to HCs using the IgA-SEQ approach. These bacteria were not identified by comparing their relative abundance alone. Predictive metagenomic analysis revealed perturbation of metabolites/metabolic pathways in axSpA patients. Future studies on these immunoreactive microbes may lead to better understanding of the functional role of IgA in maintaining microbial structure and human health.}, } @article {pmid36244970, year = {2022}, author = {Thomann, AK and Wüstenberg, T and Wirbel, J and Knoedler, LL and Thomann, PA and Zeller, G and Ebert, MP and Lis, S and Reindl, W}, title = {Depression and fatigue in active IBD from a microbiome perspective-a Bayesian approach to faecal metagenomics.}, journal = {BMC medicine}, volume = {20}, number = {1}, pages = {366}, pmid = {36244970}, issn = {1741-7015}, mesh = {Amino Acids ; Bayes Theorem ; Depression ; Fatigue ; Feces/microbiology ; Glycosaminoglycans ; Humans ; *Inflammatory Bowel Diseases ; Metagenomics ; *Microbiota ; Pectins ; }, abstract = {BACKGROUND: Extraintestinal symptoms are common in inflammatory bowel diseases (IBD) and include depression and fatigue. These are highly prevalent especially in active disease, potentially due to inflammation-mediated changes in the microbiota-gut-brain axis. The aim of this study was to investigate the associations between structural and functional microbiota characteristics and severity of fatigue and depressive symptoms in patients with active IBD.

METHODS: We included clinical data of 62 prospectively enrolled patients with IBD in an active disease state. Patients supplied stool samples and completed the questionnaires regarding depression and fatigue symptoms. Based on taxonomic and functional metagenomic profiles of faecal gut microbiota, we used Bayesian statistics to investigate the associative networks and triangle motifs between bacterial genera, functional modules and symptom severity of self-reported fatigue and depression.

RESULTS: Associations with moderate to strong evidence were found for 3 genera (Odoribacter, Anaerotruncus and Alistipes) and 3 functional modules (pectin, glycosaminoglycan and central carbohydrate metabolism) with regard to depression and for 4 genera (Intestinimonas, Anaerotruncus, Eubacterium and Clostridiales g.i.s) and 2 functional modules implicating amino acid and central carbohydrate metabolism with regard to fatigue.

CONCLUSIONS: This study provides the first evidence of association triplets between microbiota composition, function and extraintestinal symptoms in active IBD. Depression and fatigue were associated with lower abundances of short-chain fatty acid producers and distinct pathways implicating glycan, carbohydrate and amino acid metabolism. Our results suggest that microbiota-directed therapeutic approaches may reduce fatigue and depression in IBD and should be investigated in future research.}, } @article {pmid36244438, year = {2023}, author = {Pacholak, A and Zgoła-Grześkowiak, A and Kaczorek, E}, title = {Dynamics of microbial communities during biotransformation of nitrofurantoin.}, journal = {Environmental research}, volume = {216}, number = {Pt 2}, pages = {114531}, doi = {10.1016/j.envres.2022.114531}, pmid = {36244438}, issn = {1096-0953}, mesh = {Humans ; *Nitrofurantoin/chemistry/metabolism/pharmacology ; Biotransformation ; Biodegradation, Environmental ; Biodiversity ; *Microbiota ; Microbial Consortia ; }, abstract = {The purpose of this research was to investigate the biodegradation of nitrofurantoin (NFT), a typical nitrofuran antibiotic of potential carcinogenic properties, by two microbial communities derived from distinct environmental niches - mountain stream (NW) and seaport water (SS). The collected environmental samples represent the reserve of the protected area with no human intervention and the contaminated area that concentrates intense human activities. The structure, composition, and diversity of the communities were analyzed at three timepoints during NFT biodegradation. Comamonadaceae (43.2%) and Pseudomonadaceae (19.6%) were the most abundant families in the initial NW sample. The top families in the initial SS sample included Aeromonadaceae (31.4%) and Vibrionaceae (25.3%). The proportion of the most abundant families in both consortia was remarkably reduced in all samples treated with NFT. The biodiversity significantly increased in both consortia treated with NFT suggesting that NFT significantly alters community structure in the aquatic systems. In this study, NFT removal efficiency and transformation products were also studied. The biodegradation rate decreased with the increasing initial NFT concentration. Biodegradation followed similar pathways for both consortia and led to the formation of transformation products: 1-aminohydantoin, semicarbazide (SEM), and hydrazine (HYD). SEM and HYD were detected for the first time as NFT biotransformation products. This study demonstrates that the structure of the microbial community may be directly correlated with the presence of NFT. Enchanced biodiversity of the microbial community does not have to be correlated with increase in functional capacity, such as the ability to biodegradation because higher biodiversity corresponded to lower biodegradation. Our findings provide new insights into the effect of NFT contamination on aquatic microbiomes. The study also increases our understanding of the environmental impact of nitrofuran residues and their biodegradation.}, } @article {pmid36243881, year = {2022}, author = {Sola, L and Quadu, E and Bortolazzo, E and Bertoldi, L and Randazzo, CL and Pizzamiglio, V and Solieri, L}, title = {Insights on the bacterial composition of Parmigiano Reggiano Natural Whey Starter by a culture-dependent and 16S rRNA metabarcoding portrait.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {17322}, pmid = {36243881}, issn = {2045-2322}, mesh = {Amino Acids, Branched-Chain ; Bacteria/genetics ; *Food Microbiology ; Galactose ; *Lactobacillus/genetics ; Purines ; RNA, Ribosomal, 16S/genetics ; Whey ; Whey Proteins ; }, abstract = {Natural whey starters (NWS) are undefined bacterial communities produced daily from whey of the previous cheese-making round, by application of high temperature. As a result, in any dairy plant, NWS are continuously evolving, undefined mixtures of several strains and/or species of lactic acid bacteria, whose composition and performance strongly depend on the selective pressure acting during incubation. While NWS is critical to assure consistency to cheese-making process, little is known about the composition, functional features, and plant-to-plant fluctuations. Here, we integrated 16S rRNA metabarcoding and culture-dependent methods to profile bacterial communities of 10 NWS sampled in the production area of Parmigiano Reggiano cheese. 16S rRNA metabarcoding analysis revealed two main NWS community types, namely NWS type-H and NWS type-D. Lactobacillus helveticus was more abundant in NWS type-H, whilst Lactobacillus delbrueckii/St. thermophilus in NWS type-D, respectively. Based on the prediction of metagenome functions, NWS type-H samples were enriched in functional pathways related to galactose catabolism and purine metabolism, while NWS type-D in pathways related to aromatic and branched chain amino acid biosynthesis, which are flavor compound precursors. Culture-dependent approaches revealed low cultivability of individual colonies as axenic cultures and high genetic diversity in the pool of cultivable survivors. Co-culturing experiments showed that fermentative performance decreases by reducing the bacterial complexity of inoculum, suggesting that biotic interactions and cross-feeding relationships could take place in NWS communities, assuring phenotypic robustness. Even though our data cannot directly predict these ecological interactions, this study provides the basis for experiments targeted at understanding how selective regime affects composition, bacterial interaction, and fermentative performance in NWS.}, } @article {pmid36243451, year = {2022}, author = {Thompson, TP and Megaw, J and Kelly, SA and Hopps, J and Gilmore, BF}, title = {Microbial communities of halite deposits and other hypersaline environments.}, journal = {Advances in applied microbiology}, volume = {120}, number = {}, pages = {1-32}, doi = {10.1016/bs.aambs.2022.06.001}, pmid = {36243451}, issn = {0065-2164}, mesh = {Archaea/genetics ; Glycerol ; Metagenomics ; *Microbiota ; Phylogeny ; *Sodium Chloride ; }, abstract = {Large regions of Earth's surface are underlain by salt deposits that evaporated from ancient oceans and are populated by extreme halophilic microbes. While the microbiology of ancient evaporites has been well studied, the ecology of halite deposits and more recently formed NaCl "salticle" stalactite structures (speleothems) in a Triassic halite mine are less well characterized. The microbiome of Kilroot Salt Mine was profiled using conventional and enhanced culturing techniques. From this, 89 halophilic archaeal isolates from six known genera, and 55 halophilic or halotolerant bacterial isolates from 18 genera were obtained. Culture-independent metagenomic approaches also revealed that culturing techniques were inadvertently biased toward specific taxa, and the need for optimized isolation procedures are required to enhance cultivation diversity. Speleothems formed from saturated brines are unique structures that have the potential to entomb haloarchaea cells for thousands of years within fluid inclusions. The presence of such fluid inclusions, alongside the high abundance of genes related to glycerol metabolism, biofilm formation, and persister cell formation is highly suggestive of an environmental niche that could promote longevity and survivability. Finally, previous studies reporting the discovery of novel biocatalysts from the Kilroot mine microbiome, suggests that this environment may be an untapped source of chemical diversity with high biodiscovery potential.}, } @article {pmid36243187, year = {2022}, author = {Yun, Y and Su, T and Gui, Z and Tian, X and Chen, Y and Cao, Y and Yang, S and Xie, J and Anwar, N and Li, M and Li, G and Ma, T}, title = {Stress-responses of microbes in oil reservoir under high tetracycline exposure and their environmental risks.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {315}, number = {}, pages = {120355}, doi = {10.1016/j.envpol.2022.120355}, pmid = {36243187}, issn = {1873-6424}, mesh = {*Oil and Gas Fields ; Genes, Bacterial ; RNA, Ribosomal, 16S ; Tetracycline ; Anti-Bacterial Agents/analysis ; *Microbiota ; }, abstract = {As the groundwater ecosystem is connected with surface, antibiotics and antibiotic resistance genes (ARGs) in aquatic environments will gradually infiltrate into the deep environment, posing a potential threat to groundwater ecosystem. However, knowledge on the environmental risk of antibiotics and ARGs in groundwater ecosystem and their ecological process still remains unexplored. In this study, lab-scale oil reservoirs under high tetracycline stress were performed to evaluate the dynamics of microbial communities, ARGs and potential functions by using 16S rRNA gene sequencing and metagenomics analysis. Although the presence of antibiotics remarkably reduced the microbial abundance and diversity in a short term, but remain stable or even increased after a long-term incubation. Antibiotic stress caused a greater diversity and abundance of ARGs, and higher numbers of ARGs-related species with the capacity to transfer ARGs to other microbes through horizontal gene transfer. Thus, a much more frequent associations of microbial community at both node- and network-level and a selective pressure on enrichment of antibiotic resistant bacteria related to "anaerobic n-alkane degradation" and "methylotrophic methanogenesis" were observed. It is important to emphasize that high antibiotic stress could also prevent some microbes related to "Sulfate reduction", "Fe(II) oxidation", "Nitrate reduction", and "Xylene and Toluene degradation". This study provides an insight into the long-term stress-responses of microbial communities and functions in oil reservoir under tetracycline exposure, which may help to elucidate the effect of antibiotic stress on biogeochemical cycling with microbial involvement in groundwater ecosystem.}, } @article {pmid36242065, year = {2022}, author = {Chen, X and Tang, K and Zhang, M and Liu, S and Chen, M and Zhan, P and Fan, W and Chen, CA and Zhang, Y}, title = {Genome-centric insight into metabolically active microbial population in shallow-sea hydrothermal vents.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {170}, pmid = {36242065}, issn = {2049-2618}, mesh = {Cytochromes/genetics/metabolism ; *Epsilonproteobacteria/genetics ; Formates/metabolism ; *Gammaproteobacteria/genetics/metabolism ; Humans ; Hydrogen/metabolism ; *Hydrothermal Vents/microbiology ; *Microbiota ; Oxidoreductases ; Oxygen/metabolism ; Phylogeny ; Sulfur/metabolism ; }, abstract = {BACKGROUND: Geothermal systems have contributed greatly to both our understanding of the functions of extreme life and the evolutionary history of life itself. Shallow-sea hydrothermal systems are ecological intermediates of deep-sea systems and terrestrial springs, harboring unique and complexed ecosystems, which are well-lit and present physicochemical gradients. The microbial communities of deep-sea and terrestrial geothermal systems have been well-studied at the population genome level, yet little is known about the communities inhabiting the shallow-sea hydrothermal systems and how they compare to those inhabiting other geothermal systems.

RESULTS: Here, we used genome-resolved metagenomic and metaproteomic approaches to probe into the genetic potential and protein expression of microorganisms from the shallow-sea vent fluids off Kueishantao Island. The families Nautiliaceae and Campylobacteraceae within the Epsilonbacteraeota and the Thiomicrospiraceae within the Gammaproteobacteria were prevalent in vent fluids over a 3-year sampling period. We successfully reconstructed the in situ metabolic modules of the predominant populations within the Epsilonbacteraeota and Gammaproteobacteria by mapping the metaproteomic data back to metagenome-assembled genomes. Those active bacteria could use the reductive tricarboxylic acid cycle or Calvin-Benson-Bassham cycle for autotrophic carbon fixation, with the ability to use reduced sulfur species, hydrogen or formate as electron donors, and oxygen as a terminal electron acceptor via cytochrome bd oxidase or cytochrome bb3 oxidase. Comparative metagenomic and genomic analyses revealed dramatic differences between submarine and terrestrial geothermal systems, including microbial functional potentials for carbon fixation and energy conversion. Furthermore, shallow-sea hydrothermal systems shared many of the major microbial genera that were first isolated from deep-sea and terrestrial geothermal systems, while deep-sea and terrestrial geothermal systems shared few genera.

CONCLUSIONS: The metabolic machinery of the active populations within Epsilonbacteraeota and Gammaproteobacteria at shallow-sea vents can mirror those living at deep-sea vents. With respect to specific taxa and metabolic potentials, the microbial realm in the shallow-sea hydrothermal system presented ecological linkage to both deep-sea and terrestrial geothermal systems. Video Abstract.}, } @article {pmid36241909, year = {2022}, author = {He, X and Wang, X and Fan, G and Li, F and Wu, W and Wang, Z and Fu, M and Wei, X and Ma, S and Ma, X}, title = {Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {17239}, pmid = {36241909}, issn = {2045-2322}, mesh = {Animals ; Arvicolinae/genetics ; Feces ; Metagenomics ; Phylogeny ; Rodentia/genetics ; Tibet ; *Virome ; *Viruses/genetics ; }, abstract = {Rodents are natural reservoirs of diverse zoonotic viruses and widely distributed on the Tibetan Plateau. A comprehensive understanding of the virome in local rodent species could provide baseline of viral content and assist in efforts to reduce the risk for future emergence of rodent related zoonotic diseases. A total of 205 tissue and fecal samples from 41 wild Qinghai voles were collected. Metagenomic analyses were performed to outline the characteristics of the viromes, and phylogenetic analyses were used to identify the novel viral genomes. The virome distribution among five tissues (liver, lung, spleen, small intestine with content and feces) was also compared. We identified sequences related to 46 viral families. Novel viral genomes from distinct evolutionary lineages with known viruses were characterized for their genomic and evolutionary characteristics, including Hepatovirus, Hepacivirus, Rotavirus, and Picobirnavirus. Further analyses revealed that the core virome harbored by rodent internal tissues were quite different from the virome found in intestine and fecal samples. These findings provide an overview of the viromes in wild Qinghai voles, which are unique and the most common rodent species in the eastern Tibetan Plateau. A high diversity of viruses is likely present in rodent species in this area.}, } @article {pmid36240919, year = {2023}, author = {Lozada, M and Diéguez, MC and García, PE and Dionisi, HM}, title = {Microbial communities associated with kelp detritus in temperate and subantarctic intertidal sediments.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 1}, pages = {159392}, doi = {10.1016/j.scitotenv.2022.159392}, pmid = {36240919}, issn = {1879-1026}, mesh = {*Kelp ; Ecosystem ; RNA, Ribosomal, 16S ; *Macrocystis ; *Microbiota/physiology ; Alginates ; }, abstract = {Kelp forests, among the most productive ecosystems on Earth, cover large areas of the South Atlantic coast. Sediment heterotrophic bacteria have a pivotal role in the degradation of kelp biomass, however, the response of sediment microbial communities to periodic kelp biomass inputs is mostly unknown. Here, we show that kelp biomass induced rapid changes in overlying water chemistry and shifts in sediment microbial communities, which differed in the experimental systems containing Macrocystis pyrifera (M) and Undaria pinnatifida (U) with sediments of the respective regions. We observed results compatible with the degradation of labile, high molecular weight compounds into smaller and more refractory compounds towards the end of the incubations. The capability of microbial communities to degrade alginate, the major component of kelp cell walls, significantly increased with respect to controls after kelp biomass addition (Absorbance at 235 nm 1.2 ± 0.3 and 1.0 ± 0.2 for M and U, respectively, controls <0.2, t = 4 days). Shifts in microbial community structure (based on 16S rRNA gene amplicon sequencing) were tightly related to the kelp treatment and, to a lesser extent, to the sediment provenance (Principal Coordinates Analysis, 80 % of variation explained in the first two axes). Dissolved oxygen, pH, salinity, alginolytic potential, Absorbance at 235 and 600 nm, total N, total C, and SUVA index correlated significantly with community structure. Differentially abundant populations between kelp-amended treatments and controls included members of the Flavobacteriia class (Algibacter and Polaribacter), and Gammaproteobacteria (Psychromonas and Marinomonas), among others. Metagenomes of M and U-amended sediments contained sequences from 18 of the 19 enzyme families related to alginate or fucoidan degradation. Specific taxonomic groups were associated with enzyme classes targeting different substrates, suggesting niche differentiation. This work expands our knowledge on the patterns of microbial assemblages from intertidal sediments in response to kelp biomass inputs.}, } @article {pmid36239777, year = {2023}, author = {Tian, C and Lv, Y and Yang, Z and Zhang, R and Zhu, Z and Ma, H and Li, J and Zhang, Y}, title = {Microbial Community Structure and Metabolic Potential at the Initial Stage of Soil Development of the Glacial Forefields in Svalbard.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {933-946}, pmid = {36239777}, issn = {1432-184X}, support = {41676177//National Natural Science Foundation of China/ ; 41921006//National Natural Science Foundation of China/ ; 41676175//National Natural Science Foundation of China/ ; 41676188//National Natural Science Foundation of China/ ; SL2020MS022//Oceanic Interdisciplinary Program of Shanghai Jiao Tong University/ ; 21TQ1400201//Shanghai Pilot Program for Basic Research of Shanghai Jiao Tong University/ ; }, mesh = {*Soil/chemistry ; Svalbard ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota/genetics ; Ice Cover/microbiology ; Soil Microbiology ; }, abstract = {Microbial communities have been identified as the primary inhabitants of Arctic forefields. However, the metabolic potential of microbial communities in these newly exposed soils remains underexplored due to limited access. Here, we sampled the very edge of the glacial forefield in Svalbard and performed the 16S rRNA genes and metagenomic analysis to illustrate the ecosystem characteristics. Burkholderiales and Micrococcales were the dominant bacterial groups at the initial stage of soil development of glacial forefields. 214 metagenome-assembled genomes were recovered from glacier forefield microbiome datasets, including only 2 belonging to archaea. Analysis of these metagenome-assembled genomes revealed that 41% of assembled genomes had the genetic potential to use nitrate and nitrite as electron acceptors. Metabolic pathway reconstruction for these microbes suggested versatility for sulfide and thiosulfate oxidation, H2 and CO utilization, and CO2 fixation. Our results indicate the importance of anaerobic processes in elemental cycling in the glacial forefields. Besides, a range of genes related to adaption to low temperature and other stresses were detected, which revealed the presence of diverse mechanisms of adaption to the extreme environment of Svalbard. This research provides ecological insight into the initial stage of the soil developed during the retreating of glaciers.}, } @article {pmid36239393, year = {2022}, author = {Hickl, O and Queirós, P and Wilmes, P and May, P and Heintz-Buschart, A}, title = {binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {6}, pages = {}, pmid = {36239393}, issn = {1477-4054}, support = {PRIDE/11823097//National Research Fund/ ; ERC-CoG 863664/ERC_/European Research Council/International ; }, mesh = {*Metagenome ; Metagenomics/methods ; Algorithms ; Cluster Analysis ; *Microbiota/genetics ; }, abstract = {The reconstruction of genomes is a critical step in genome-resolved metagenomics and for multi-omic data integration from microbial communities. Here, we present binny, a binning tool that produces high-quality metagenome-assembled genomes (MAG) from both contiguous and highly fragmented genomes. Based on established metrics, binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods and finds unique genomes that could not be detected by other methods. binny uses k-mer-composition and coverage by metagenomic reads for iterative, nonlinear dimension reduction of genomic signatures as well as subsequent automated contig clustering with cluster assessment using lineage-specific marker gene sets. When compared with seven widely used binning algorithms, binny provides substantial amounts of uniquely identified MAGs and almost always recovers the most near-complete ($\gt 95\%$ pure, $\gt 90\%$ complete) and high-quality ($\gt 90\%$ pure, $\gt 70\%$ complete) genomes from simulated datasets from the Critical Assessment of Metagenome Interpretation initiative, as well as substantially more high-quality draft genomes, as defined by the Minimum Information about a Metagenome-Assembled Genome standard, from a real-world benchmark comprised of metagenomes from various environments than any other tested method.}, } @article {pmid36233330, year = {2022}, author = {Zhang, Y and Ma, C and Han, Y and Jin, H and Luo, H and Hao, X and Li, M}, title = {Integrative Analysis of the Nasal Microbiota and Serum Metabolites in Bovines with Respiratory Disease by 16S rRNA Sequencing and Gas Chromatography/Mass Selective Detector-Based Metabolomics.}, journal = {International journal of molecular sciences}, volume = {23}, number = {19}, pages = {}, pmid = {36233330}, issn = {1422-0067}, support = {31960036//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Cattle ; *Cattle Diseases ; Chromatography, Gas ; Lactic Acid ; Metabolomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Respiration Disorders ; *Respiratory Tract Diseases/veterinary ; Sarcosine ; }, abstract = {Bovine respiratory disease (BRD) continues to pose a serious threat to the cattle industry, resulting in substantial economic losses. As a multifactorial disease, pathogen infection and respiratory microbial imbalance are important causative factors in the occurrence and development of BRD. Integrative analyses of 16S rRNA sequencing and metabolomics allow comprehensive identification of the changes in microbiota and metabolism associated with BRD, making it possible to determine which pathogens are responsible for the disease and to develop new therapeutic strategies. In our study, 16S rRNA sequencing and metagenomic analysis were used to describe and compare the composition and diversity of nasal microbes in healthy cattle and cattle with BRD from different farms in Yinchuan, Ningxia, China. We found a significant difference in nasal microbial diversity between diseased and healthy bovines; notably, the relative abundance of Mycoplasma bovis and Pasteurella increased. This indicated that the composition of the microbial community had changed in diseased bovines compared with healthy ones. The data also strongly suggested that the reduced relative abundance of probiotics, including Pasteurellales and Lactobacillales, in diseased samples contributes to the susceptibility to bovine respiratory disease. Furthermore, serum metabolomic analysis showed altered concentrations of metabolites in BRD and that a significant decrease in lactic acid and sarcosine may impair the ability of bovines to generate energy and an immune response to pathogenic bacteria. Based on the correlation analysis between microbial diversity and the metabolome, lactic acid (2TMS) was positively correlated with Gammaproteobacteria and Bacilli and negatively correlated with Mollicutes. In summary, microbial communities and serum metabolites in BRD were characterized by integrative analysis. This study provides a reference for monitoring biomarkers of BRD, which will be critical for the prevention and treatment of BRD in the future.}, } @article {pmid36233028, year = {2022}, author = {Kato, T and Kagawa, M and Suda, W and Tsuboi, Y and Inoue-Suzuki, S and Kikuchi, J and Hattori, M and Ohta, T and Ohno, H}, title = {Integrated Multi-Omics Analysis Reveals Differential Effects of Fructo-Oligosaccharides (FOS) Supplementation on the Human Gut Ecosystem.}, journal = {International journal of molecular sciences}, volume = {23}, number = {19}, pages = {}, pmid = {36233028}, issn = {1422-0067}, support = {not applicable//Japan Aerospace Exploration Agency/ ; }, mesh = {Fructose/pharmacology ; Humans ; Immunoglobulin A/metabolism ; *Microbiota ; *Oligosaccharides/metabolism/pharmacology ; Prebiotics ; }, abstract = {Changes in the gut ecosystem, including the microbiome and the metabolome, and the host immune system after fructo-oligosaccharide (FOS) supplementation were evaluated. The supplementation of FOS showed large inter-individual variability in the absolute numbers of fecal bacteria and an increase in Bifidobacterium. The fecal metabolome analysis revealed individual variability in fructose utilization in response to FOS supplementation. In addition, immunoglobulin A(IgA) tended to increase upon FOS intake, and peripheral blood monocytes significantly decreased upon FOS intake and kept decreasing in the post-FOS phase. Further analysis using a metagenomic approach showed that the differences could be at least in part due to the differences in gene expressions of enzymes that are involved in the fructose metabolism pathway. While the study showed individual differences in the expected health benefits of FOS supplementation, the accumulation of "personalized" knowledge of the gut ecosystem with its genetic expression may enable effective instructions on prebiotic consumption to optimize health benefits for individuals in the future.}, } @article {pmid36232990, year = {2022}, author = {Kobayashi, T and Iwaki, M and Nakajima, A and Nogami, A and Yoneda, M}, title = {Current Research on the Pathogenesis of NAFLD/NASH and the Gut-Liver Axis: Gut Microbiota, Dysbiosis, and Leaky-Gut Syndrome.}, journal = {International journal of molecular sciences}, volume = {23}, number = {19}, pages = {}, pmid = {36232990}, issn = {1422-0067}, mesh = {Dysbiosis/complications ; Endotoxins/metabolism ; Fructose/metabolism ; *Gastrointestinal Microbiome ; Humans ; Liver/metabolism ; *Non-alcoholic Fatty Liver Disease/metabolism ; }, abstract = {Global lifestyle changes have led to an increased incidence of non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH), requiring further in-depth research to understand the mechanisms and develop new therapeutic strategies. In particular, high-fat and high-fructose diets have been shown to increase intestinal permeability, which can expose the liver to endotoxins. Indeed, accumulating evidence points to a link between these liver diseases and the intestinal axis, including dysbiosis of the gut microbiome and leaky-gut syndrome. Here, we review the mechanisms contributing to these links between the liver and small intestine in the pathogenesis of NAFLD/NASH, focusing on the roles of intestinal microbiota and their metabolites to influence enzymes essential for proper liver metabolism and function. Advances in next-generation sequencing technology have facilitated analyses of the metagenome, providing new insights into the roles of the intestinal microbiota and their functions in physiological and pathological mechanisms. This review summarizes recent research linking the gut microbiome to liver diseases, offering new research directions to elucidate the detailed mechanisms and novel targets for treatment and prevention.}, } @article {pmid36232865, year = {2022}, author = {Sun, P and Zhu, H and Li, X and Shi, W and Guo, Y and Du, X and Zhang, L and Su, L and Qin, C}, title = {Comparative Metagenomics and Metabolomes Reveals Abnormal Metabolism Activity Is Associated with Gut Microbiota in Alzheimer's Disease Mice.}, journal = {International journal of molecular sciences}, volume = {23}, number = {19}, pages = {}, pmid = {36232865}, issn = {1422-0067}, mesh = {*Alzheimer Disease/pathology ; Amino Acids, Aromatic ; Animals ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Metabolome ; Mice ; Neurotransmitter Agents ; Vitamins ; }, abstract = {A common symptom in Alzheimer's disease (AD) is cognitive decline, of which the potential pathogenesis remains unclear. In order to understand the mechanism of gut microbiota in AD, it is necessary to clarify the relationship between gut microbiota and metabolites. Behavioral tests, pathological examination, metagenomics, and metabolomics were applied to analyze the difference of gut microbiota and metabolome between APP[swe]/PS1[ΔE9] (PAP) mice with cognitive decline and age-matched controls, and their possible correlations. Our results showed that PAP mice and health mice had different structures of the bacterial communities in the gut. The abundances and diversities of the bacterial communities in health mice were higher than in PAP mice by metagenomics analysis. The abundances of Libanicoccus massiliensis, Paraprevotella clara, and Lactobacillus amylovorus were significantly increased in PAP mice, while the abundances of Turicibacter sanguinis, Dubosiella newyorkensis, and Prevotella oris were greatly reduced. Furthermore, PAP mice possessed peculiar metabolic phenotypes in stool, serum, and hippocampus relative to WT mice, as is demonstrated by alterations in neurotransmitters metabolism, lipid metabolism, aromatic amino acids metabolism, energy metabolism, vitamin digestion and absorption, and bile metabolism. Microbiota-host metabolic correlation analysis suggests that abnormal metabolism in stool, serum, and hippocampus of PAP mice may be modulated by the gut microbiota, especially T. sanguinis, D. newyorkensis, and P. oris. Therefore, abnormal metabolism activity is associated with gut microbiota in Alzheimer's disease mice. Our results imply that modifying host metabolism through targeting gut microbiota may be a novel and viable strategy for the prevention and treatment of AD in the future.}, } @article {pmid36619855, year = {2021}, author = {Puetz, LC and Delmont, TO and Aizpurua, O and Guo, C and Zhang, G and Katajamaa, R and Jensen, P and Gilbert, MTP}, title = {Gut Microbiota Linked with Reduced Fear of Humans in Red Junglefowl Has Implications for Early Domestication.}, journal = {Advanced genetics (Hoboken, N.J.)}, volume = {2}, number = {4}, pages = {2100018}, pmid = {36619855}, issn = {2641-6573}, abstract = {Domestication of animals can lead to profound phenotypic modifications within short evolutionary time periods, and for many species behavioral selection is likely at the forefront of this process. Animal studies have strongly implicated that the gut microbiome plays a major role in host behavior and cognition through the microbiome-gut-brain axis. Consequently, herein, it is hypothesized that host gut microbiota may be one of the earliest phenotypes to change as wild animals were domesticated. Here, the gut microbiome community in two selected lines of red junglefowl that are selected for either high or low fear of humans up to eight generations is examined. Microbiota profiles reveal taxonomic differences in gut bacteria known to produce neuroactive compounds between the two selection lines. Gut-brain module analysis by means of genome-resolved metagenomics identifies enrichment in the microbial synthesis and degradation potential of metabolites associated with fear extinction and reduces anxiety-like behaviors in low fear fowls. In contrast, high fear fowls are enriched in gut-brain modules from the butyrate and glutamate pathways, metabolites associated with fear conditioning. Overall, the results identify differences in the composition and functional potential of the gut microbiota across selection lines that may provide insights into the mechanistic explanations of the domestication process.}, } @article {pmid36755065, year = {2021}, author = {Armbrecht, L and Eisenhofer, R and Utge, J and Sibert, EC and Rocha, F and Ward, R and Pierella Karlusich, JJ and Tirichine, L and Norris, R and Summers, M and Bowler, C}, title = {Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {66}, pmid = {36755065}, issn = {2730-6151}, abstract = {Sedimentary ancient DNA (sedaDNA) analyses are increasingly used to reconstruct marine ecosystems. The majority of marine sedaDNA studies use a metabarcoding approach (extraction and analysis of specific DNA fragments of a defined length), targeting short taxonomic marker genes. Promising examples are 18S-V9 rRNA (~121-130 base pairs, bp) and diat-rbcL (76 bp), targeting eukaryotes and diatoms, respectively. However, it remains unknown how 18S-V9 and diat-rbcL derived compositional profiles compare to metagenomic shotgun data, the preferred method for ancient DNA analyses as amplification biases are minimised. We extracted DNA from five Santa Barbara Basin sediment samples (up to ~11 000 years old) and applied both a metabarcoding (18S-V9 rRNA, diat-rbcL) and a metagenomic shotgun approach to (i) compare eukaryote, especially diatom, composition, and (ii) assess sequence length and database related biases. Eukaryote composition differed considerably between shotgun and metabarcoding data, which was related to differences in read lengths (~112 and ~161 bp, respectively), and overamplification of short reads in metabarcoding data. Diatom composition was influenced by reference bias that was exacerbated in metabarcoding data and characterised by increased representation of Chaetoceros, Thalassiosira and Pseudo-nitzschia. Our results are relevant to sedaDNA studies aiming to accurately characterise paleo-ecosystems from either metabarcoding or metagenomic data.}, } @article {pmid37124704, year = {2021}, author = {Chiba, Y and Oiki, S and Zhao, Y and Nagano, Y and Urayama, SI and Hagiwara, D}, title = {Splitting of RNA-dependent RNA polymerase is common in Narnaviridae: Identification of a type II divided RdRp from deep-sea fungal isolates.}, journal = {Virus evolution}, volume = {7}, number = {2}, pages = {veab095}, pmid = {37124704}, issn = {2057-1577}, abstract = {Until recently, it was accepted that RNA-dependent RNA polymerase (RdRp) is the only essential gene for non-retro RNA viruses and is encoded by a single open reading frame (ORF) in their genomes. However, divided RdRps that are coded by two ORFs were discovered in fungal RNA viruses in a few independent reports. This discovery showed higher plasticity of viral RdRp than was expected. Among these divided RdRps, the division site was common; specifically, the first part of the RdRp contains motifs F, A, and B, whereas the latter part possesses motifs C and D. These RdRps are designated as type I divided RdRp and have been limited to viruses in a specific clade of Narnaviridae. In this study, to further understand the plasticity of RdRp, we explored viruses from deep sea-derived fungal strains as an untapped resource with a focus on Aspergillus section Versicolores. Seven strains were found to be infected by a total of 13 viruses, and the viral RNA genomes were determined by fragmented and primer-ligated double-stranded RNA sequencing technology. Among them, six strains belong to Narnaviridae. One of the strains, Aspergillus tennesseensis narnavirus 1, which infects an Aspergillus tennesseensis, has a divided RdRp with a new division site (referred to as type II divided RdRp). A couple of sequences for possible type II divided RdRps were also detected in public metagenomic data sets. Our findings reveal that different types of divisions in RdRp are present in the virosphere, and two types of RdRp splitting occurred independently within Narnaviridae.}, } @article {pmid36747039, year = {2021}, author = {Alejandre-Colomo, C and Francis, B and Viver, T and Harder, J and Fuchs, BM and Rossello-Mora, R and Amann, R}, title = {Cultivable Winogradskyella species are genomically distinct from the sympatric abundant candidate species.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {51}, pmid = {36747039}, issn = {2730-6151}, support = {AM 73/9-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; AM 73/9-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; AM 73/9-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; AM 73/9-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Winogradskyella is a genus within the phylum Bacteroidetes with a clear marine origin. Most members of this genus have been found associated with marine animals and algae, but also with inorganic surfaces such as sand. In this study, we analyzed genomes of eleven species recently isolated from surface seawater samples from the North Sea during a single spring algae bloom. Corresponding metagenomes yielded a single Candidatus species for this genus. All species in culture, with the exception of W. ursingii, affiliated with a Winogradskyella lineage characterized by large genomes (~4.3 ± 0.4 Mb), with high complexity in their carbohydrate and protein degradation genes. Specifically, the polysaccharide utilization loci (PULs) were diverse within each individual strain, indicating large substrate versatility. Although present in the North Sea, the abundances of these strains were at, or below, the detection limit of the metagenomes. In contrast, the single species, classified as Candidatus W. atlantica, to which all North Sea MAGs belonged, affiliated with a lineage in which the cultivated representatives showed small genomes of ~3.0-3.5 Mb, with the MAGs having ~2.3 Mb. In Ca. W. atlantica, genome streamlining has apparently resulted in the loss of biosynthesis pathways for several amino acids including arginine, methionine, leucine and valine, and the PUL loci were reduced to a single one for utilizing laminarin. This as-yet uncultivated species seems to capitalize on sporadically abundant substrates that are released by algae blooms, mainly laminarin. We also suggest that this streamlined genome might be responsible for the lack of growth on plates for this Candidatus species, in contrast to growth of the less abundant but coexisting members of the genus.}, } @article {pmid36717704, year = {2021}, author = {Busi, SB and de Nies, L and Habier, J and Wampach, L and Fritz, JV and Heintz-Buschart, A and May, P and Halder, R and de Beaufort, C and Wilmes, P}, title = {Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {8}, pmid = {36717704}, issn = {2730-6151}, support = {ATTRACT/A09/03//Fonds National de la Recherche Luxembourg (National Research Fund)/ ; CORE/C15/SR/10404839//Fonds National de la Recherche Luxembourg (National Research Fund)/ ; PRIDE17/11823097//Fonds National de la Recherche Luxembourg (National Research Fund)/ ; AFR PHD-2013-5824125//Fonds National de la Recherche Luxembourg (National Research Fund)/ ; CORE Junior/14/BM/8066232//Fonds National de la Recherche Luxembourg (National Research Fund)/ ; CRSII5_180241//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; FZT 118//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Caesarean section delivery (CSD) disrupts mother-to-neonate transmission of specific microbial strains and functional repertoires as well as linked immune system priming. Here we investigate whether differences in microbiome composition and impacts on host physiology persist at 1 year of age. We perform high-resolution, quantitative metagenomic analyses of the gut microbiomes of infants born by vaginal delivery (VD) or by CSD, from immediately after birth through to 1 year of life. Several microbial populations show distinct enrichments in CSD-born infants at 1 year of age including strains of Bacteroides caccae, Bifidobacterium bifidum and Ruminococcus gnavus, whereas others are present at higher levels in the VD group including Faecalibacterium prausnitizii, Bifidobacterium breve and Bifidobacterium kashiwanohense. The stimulation of healthy donor-derived primary human immune cells with LPS isolated from neonatal stool samples results in higher levels of tumour necrosis factor alpha (TNF-α) in the case of CSD extracts over time, compared to extracts from VD infants for which no such changes were observed during the first year of life. Functional analyses of the VD metagenomes at 1 year of age demonstrate a significant increase in the biosynthesis of the natural antibiotics, carbapenem and phenazine. Concurrently, we find antimicrobial resistance (AMR) genes against several classes of antibiotics in both VD and CSD. The abundance of AMR genes against synthetic (including semi-synthetic) agents such as phenicol, pleuromutilin and diaminopyrimidine are increased in CSD children at day 5 after birth. In addition, we find that mobile genetic elements, including phages, encode AMR genes such as glycopeptide, diaminopyrimidine and multidrug resistance genes. Our results demonstrate persistent effects at 1 year of life resulting from birth mode-dependent differences in earliest gut microbiome colonisation.}, } @article {pmid37118004, year = {2021}, author = {Zhang, X and Zhong, H and Li, Y and Shi, Z and Ren, H and Zhang, Z and Zhou, X and Tang, S and Han, X and Lin, Y and Yang, F and Wang, D and Fang, C and Fu, Z and Wang, L and Zhu, S and Hou, Y and Xu, X and Yang, H and Wang, J and Kristiansen, K and Li, J and Ji, L}, title = {Sex- and age-related trajectories of the adult human gut microbiota shared across populations of different ethnicities.}, journal = {Nature aging}, volume = {1}, number = {1}, pages = {87-100}, pmid = {37118004}, issn = {2662-8465}, mesh = {Humans ; Female ; Adult ; Male ; *Gastrointestinal Microbiome/genetics ; Feces ; *Microbiota ; Ethnicity ; Metagenomics ; }, abstract = {Lifelong sex- and age-related trajectories of the human gut microbiota remain largely unexplored. Using metagenomics, we derived the gut microbial composition of 2,338 adults (26-76 years) from a Han Chinese population-based cohort where metabolic health, hormone levels and aspects of their lifestyles were also recorded. In this cohort, and in three independent cohorts distributed across China, Israel and the Netherlands, we observed sex differences in the gut microbial composition and a shared age-related decrease in sex-dependent differences in gut microbiota. Compared to men, the gut microbiota of premenopausal women exhibited higher microbial diversity and higher abundances of multiple species known to have beneficial effects on host metabolism. We also found consistent sex-independent, age-related gut microbial characteristics across all populations, with the presence of members of the oral microbiota being the strongest indicator of older chronological age. Our findings highlight the existence of sex- and age-related trajectories in the human gut microbiota that are shared between populations of different ethnicities and emphasize the pivotal links between sex hormones, gut microbiota and host metabolism.}, } @article {pmid36231339, year = {2022}, author = {Xu, P and Chen, X and Li, K and Meng, R and Pu, Y}, title = {Metagenomic Analysis of Microbial Alliances for Efficient Degradation of PHE: Microbial Community Structure and Reconstruction of Metabolic Network.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {19}, pages = {}, pmid = {36231339}, issn = {1660-4601}, mesh = {Bacteria ; Biodegradation, Environmental ; Metabolic Networks and Pathways/genetics ; *Microbiota ; *Phenanthrenes/metabolism ; *Polycyclic Aromatic Hydrocarbons/analysis ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Polycyclic aromatic hydrocarbons are a widespread organic pollutant worldwide. In this study, a highly efficient phenanthrene (PHE)-degrading microbial community was enriched from oil extraction soil, which could degrade 500 mg/L PHE within 4 days. Using 16S rRNA sequencing, the dominant bacteria in this community at the phylum level were found to be Proteobacteria, Actinobacteria, and Firmicutes. Metagenomic annotation of genes revealed the metabolic pathways and the contribution of different bacteria to the degradation process. Pseudomonadaceae contributed multiple functional genes in the degradation process. This study revealed the functional genes, metabolic pathways, and microbial interactions of the microbial community, which are expected to provide guidance for practical management.}, } @article {pmid36231135, year = {2022}, author = {Chan, LC and Zhang, Y and Kuang, X and Koohi-Moghadam, M and Wu, H and Lam, TYC and Chiou, J and Wen, C}, title = {Captopril Alleviates Chondrocyte Senescence in DOCA-Salt Hypertensive Rats Associated with Gut Microbiome Alteration.}, journal = {Cells}, volume = {11}, number = {19}, pages = {}, pmid = {36231135}, issn = {2073-4409}, mesh = {Acetates ; Animals ; Antihypertensive Agents ; Captopril/adverse effects ; Chondrocytes ; *Desoxycorticosterone Acetate/adverse effects ; Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; *Hypertension ; RNA, Ribosomal, 16S ; Rats ; }, abstract = {Gut microbiota is the key controller of healthy aging. Hypertension and osteoarthritis (OA) are two frequently co-existing age-related pathologies in older adults. Both are associated with gut microbiota dysbiosis. Hereby, we explore gut microbiome alteration in the Deoxycorticosterone acetate (DOCA)-induced hypertensive rat model. Captopril, an anti-hypertensive medicine, was chosen to attenuate joint damage. Knee joints were harvested for radiological and histological examination; meanwhile, fecal samples were collected for 16S rRNA and shotgun sequencing. The 16S rRNA data was annotated using Qiime 2 v2019.10, while metagenomic data was functionally profiled with HUMAnN 2.0 database. Differential abundance analyses were adopted to identify the significant bacterial genera and pathways from the gut microbiota. DOCA-induced hypertension induced p16INK4a+ senescent cells (SnCs) accumulation not only in the aorta and kidney (p < 0.05) but also knee joint, which contributed to articular cartilage degradation and subchondral bone disturbance. Captopril removed the p16INK4a + SnCs from different organs, partially lowered blood pressure, and mitigated cartilage damage. Meanwhile, these alterations were found to associate with the reduction of Escherichia-Shigella levels in the gut microbiome. As such, gut microbiota dysbiosis might emerge as a metabolic link in chondrocyte senescence induced by DOCA-triggered hypertension. The underlying molecular mechanism warrants further investigation.}, } @article {pmid36231116, year = {2022}, author = {Zeng, Y and Liang, JQ}, title = {Nasal Microbiome and Its Interaction with the Host in Childhood Asthma.}, journal = {Cells}, volume = {11}, number = {19}, pages = {}, pmid = {36231116}, issn = {2073-4409}, mesh = {*Asthma ; Child ; Dysbiosis ; Humans ; Infant ; *Microbiota ; Respiratory System ; *Respiratory Tract Infections ; }, abstract = {Childhood asthma is a major chronic non-communicable disease in infants and children, often triggered by respiratory tract infections. The nasal cavity is a reservoir for a broad variety of commensal microbes and potential pathogens associated with respiratory illnesses including asthma. A healthy nasal microenvironment has protective effects against respiratory tract infections. The first microbial colonisation in the nasal region is initiated immediately after birth. Subsequently, colonisation by nasal microbiota during infancy plays important roles in rapidly establishing immune homeostasis and the development and maturation of the immune system. Dysbiosis of microbiota residing in the mucosal surfaces, such as the nasopharynx and guts, triggers immune modulation, severe infection, and exacerbation events. Nasal microbiome dysbiosis is related to the onset of symptomatic infections. Dynamic interactions between viral infections and the nasal microbiota in early life affect the later development of respiratory infections. In this review, we summarise the existing findings related to nasal microbiota colonisation, dynamic variations, and host-microbiome interactions in childhood health and respiratory illness with a particular examination of asthma. We also discuss our current understanding of biases produced by environmental factors and technical concerns, the importance of standardised research methods, and microbiome modification for the prevention or treatment of childhood asthma. This review lays the groundwork for paying attention to an essential but less emphasized topic and improves the understanding of the overall composition, dynamic changes, and influence of the nasal microbiome associated with childhood asthma.}, } @article {pmid36229545, year = {2022}, author = {Gounot, JS and Chia, M and Bertrand, D and Saw, WY and Ravikrishnan, A and Low, A and Ding, Y and Ng, AHQ and Tan, LWL and Teo, YY and Seedorf, H and Nagarajan, N}, title = {Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6044}, pmid = {36229545}, issn = {2041-1723}, mesh = {Asian People/genetics ; *Bacteriocins/genetics ; Cross-Sectional Studies ; Genome, Human ; Humans ; Metagenome/genetics ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Despite extensive efforts to address it, the vastness of uncharacterized 'dark matter' microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population-specific biases in genomic reference databases can further compound this problem. Leveraging advances in hybrid assembly (using short and long reads) and Hi-C technologies in a cross-sectional survey, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4497 medium and high-quality metagenome assembled genomes, 1708 of which were missing in short-read only analysis and with >28× N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3413 strains unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of strains were unrepresented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36-88%) unrepresented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies.}, } @article {pmid36229418, year = {2022}, author = {Wei, G and Zhang, G and Li, M and Liu, C and Wei, F and Wang, Y and Huang, Z and Chen, Z and Zheng, Y and Chen, S and Dong, L}, title = {Core rhizosphere microbiome of Panax notoginseng and its associations with belowground biomass and saponin contents.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {6238-6251}, doi = {10.1111/1462-2920.16245}, pmid = {36229418}, issn = {1462-2920}, mesh = {Rhizosphere ; *Panax notoginseng/microbiology ; Soil Microbiology ; Biomass ; *Saponins ; Plant Roots/microbiology ; *Microbiota/genetics ; }, abstract = {The core rhizosphere microbiome is critical for plant fitness. However, its contribution to the belowground biomass and saponin contents of Panax notoginseng remains unclear. High-throughput sequencing of amplicon and metagenome was performed to obtain the microbiome profiles and functional traits in P. notoginseng rhizosphere across a large spatial scale. We obtained 639 bacterial and 310 fungal core OTUs, which were mainly affected by soil pH and organic matter (OM). The core taxa were grouped into four ecological clusters (i.e. high pH, low pH, high OM and low OM) for sharing similar habitat preferences. Furthermore, structural equation modelling (SEM) and correlation analyses revealed that the diversity and composition of core microbiomes, as well as the metagenome-derived microbial functions, were related to belowground biomass and saponin contents. Key microbial genera related to the two plant indicators were also identified. In short, this study explored the main driving environmental factors of core microbiomes in the P. notoginseng rhizosphere and revealed that the core microbiomes and microbial functions potentially contributed to the belowground biomass and saponin contents of the plant. This work may enhance our understanding of interactions between microbes and perennial plants and improve our ability to manage root microbiota for the sustainable production of herbal medicine.}, } @article {pmid36228621, year = {2022}, author = {Tang, B and Tang, L and He, W and Jiang, X and Hu, C and Li, Y and Zhang, Y and Pang, K and Lei, Y and Li, S and Liu, S and Wang, S and Yang, M and Li, Z and Zhao, F and Yang, S}, title = {Correlation of gut microbiota and metabolic functions with the antibody response to the BBIBP-CorV vaccine.}, journal = {Cell reports. Medicine}, volume = {3}, number = {10}, pages = {100752}, pmid = {36228621}, issn = {2666-3791}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; COVID-19 Vaccines ; Antibody Formation ; *COVID-19 ; Fatty Acids, Volatile/metabolism ; }, abstract = {Increasing evidence indicates that gut microbiota may play a key role in vaccination immunity. Here, we investigate whether the human gut microbiota and metabolic function correlate with the BBIBP-CorV vaccine response. A total of 207 participants who received the BBIBP-CorV vaccine are enrolled. The gut microbiome and metabolic functions are investigated using metagenomic sequencing and metabolomic assays. We find that BBIBP-CorV vaccination is accompanied by altered microbiome composition and functional pathways, and the gut microbiome and its functional profiles correlate with the vaccine response. The levels of short-chain fatty acids (SCFAs) are much higher in the high antibody response group compared to the low response group, and several SCFAs display a positive correlation with the antibody response. Our study highlights that the gut microbiome and its function is associated with the BBIBP-CorV vaccine response, providing evidence for further exploration of microbiome modulation to improve COVID-19 vaccine efficacy.}, } @article {pmid36228567, year = {2022}, author = {Le Sayec, M and Xu, Y and Laiola, M and Gallego, FA and Katsikioti, D and Durbidge, C and Kivisild, U and Armes, S and Lecomte, M and Fança-Berthon, P and Fromentin, E and Plaza Oñate, F and Cruickshank, JK and Rodriguez-Mateos, A}, title = {The effects of Aronia berry (poly)phenol supplementation on arterial function and the gut microbiome in middle aged men and women: Results from a randomized controlled trial.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {41}, number = {11}, pages = {2549-2561}, doi = {10.1016/j.clnu.2022.08.024}, pmid = {36228567}, issn = {1532-1983}, mesh = {Male ; Middle Aged ; Humans ; Female ; *Photinia/chemistry ; Pulse Wave Analysis ; *Gastrointestinal Microbiome ; Phenol/pharmacology ; Blood Pressure ; Phenols/pharmacology ; Double-Blind Method ; Dietary Supplements ; Plant Extracts/pharmacology ; Butyrates ; }, abstract = {BACKGROUND AND AIMS: Berry (poly)phenol consumption has been associated with cardioprotective benefits, however little is known on the role the gut microbiome may play on such health benefits. Our objective was to investigate the effects of aronia berry (poly)phenol consumption on cardiometabolic health and gut microbiome richness and composition in prehypertensive middle-aged men and women.

METHODS: A total of 102 prehypertensive participants were included in a parallel 12-week randomized double-blind placebo-controlled trial. Volunteers were randomly allocated to daily consume an encapsulated (poly)phenol-rich aronia berry extract (Aronia, n = 51) or a matched maltodextrin placebo (Control, n = 51). Blood pressure (BP) and arterial function (office and 24 h), endothelial function (measured as flow-mediated dilation), serum biochemistry (including blood lipids), plasma and urine (poly)phenol metabolites as well as gut microbiome composition through shotgun metagenomic sequencing were monitored over the study period. Relationships between vascular outcomes, (poly)phenol metabolites and gut microbiome were investigated using an integrated multi-levels approach.

RESULTS: A significant improvement in arterial indices measured as augmentation index (AIx) and pulse wave velocity (PWV) was found in the Aronia compared to Control group (awake Δ PWV = -0.24 m/s; 95% CI: -0.79, -0.01 m/s, P < 0.05; 24 h peripheral Δ AIx = -6.8; -11.2, -2.3, %, P = 0.003; 24 h central Δ AIx = -3.3; -5.5, -1.0, %, P = 0.006). No changes in BP, endothelial function or blood lipids were found following the intervention. Consumption of aronia (poly)phenols led to a significant increase in gut microbiome gene richness and in the abundance of butyrate-producing species such as Lawsonibacter asaccharolyticus and Intestinimonas butyriciproducens species, compared to Control group. Results from an approach including metabolomic, metagenomic and clinical outcomes highlighted associations between aronia-derived phenolic metabolites, arterial stiffness, and gut microbiome.

CONCLUSIONS: Aronia berry (poly)phenol consumption improved arterial function in prehypertensive middle-aged individuals, possibly via modulation of gut microbiome richness and composition based on the associations observed between these parameters.

CLINICAL TRIAL REGISTRY: The National Institutes of Health (NIH)-randomized trial records held on the NIH ClinicalTrials.gov website (NCT03434574). Aronia Berry Consumption on Blood Pressure.}, } @article {pmid36226871, year = {2022}, author = {Tian, P and Wu, L and Kudo, M and Hayashi, M and Qin, L and Gao, M and Xu, A and Liu, T}, title = {TangNaiKang, herbal formulation, alleviates obesity in diabetic SHR/cp rats through modulation of gut microbiota and related metabolic functions.}, journal = {Pharmaceutical biology}, volume = {60}, number = {1}, pages = {2002-2010}, pmid = {36226871}, issn = {1744-5116}, mesh = {Animals ; Body Weight ; Cholesterol/pharmacology ; DNA, Ribosomal/pharmacology ; *Diabetes Mellitus/drug therapy ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Fatty Acids, Volatile ; *Gastrointestinal Microbiome ; Obesity/drug therapy/metabolism ; Rats ; Rats, Inbred SHR ; Rats, Inbred WKY ; Triglycerides ; }, abstract = {CONTEXT: Tangnaikang (TNK) is a Chinese herbal formulation that has lipid-lowering effects, but its effect on reducing obesity has not been studied.

OBJECTIVE: To observe the effect of TNK on obesity and explore its effect on gut microbiota of obese rats.

MATERIALS AND METHODS: The SHR/NDmcr-cp rats were divided into three groups: (1) 3.24 g/kg TNK (High TNK), (2) 1.62 g/kg TNK (Low TNK), and (3) an untreated control (CON). Wistar-Kyoto rats were used as normal controls (WKY). After 8 weeks of TNK oral administration, body weight, abdominal circumference, triglycerides (TC) and total cholesterol (CHO) were measured. Gut microbiota diversity was studied by 16S rDNA sequencing, and metagenomes analysis was conducted to determine alteration in functional gene expression.

RESULTS: The body weight (496.60 ± 6.0 g vs. 523.40 ± 5.6 g), abdomen circumference (24.00 ± 0.11 cm vs. 24.87 ± 0.25 cm), TC (3.04 ± 0.16 mmol/L vs. 4.97 ± 0.21 mmol/L), CHO (2.42 ± 0.15 mmol/L vs. 2.84 ± 0.09 mmol/L) of rats in the High TNK group were decreased significantly (all p < 0.05). TNK administration regulates intestinal flora, up-regulates Eisenbergiella and down-regulates Clostridium_sensu_stricto_1, which is beneficial to the production of short-chain fatty acids (SCFAs). Metagenomes analysis shows that TNK is closely related to the fatty acid synthesis pathway.

DISCUSSION AND CONCLUSIONS: TNK can regulate gut microbiota to reduce obesity, which may be related to fatty acid metabolism. Our research supports the clinical application of TNK preparation and provides a new perspective for the treatment of obesity.}, } @article {pmid36225905, year = {2022}, author = {Han, Y and Xu, J and Yan, Y and Zhao, X}, title = {Dynamics of the gut microbiota in rats after hypobaric hypoxia exposure.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e14090}, pmid = {36225905}, issn = {2167-8359}, mesh = {Rats ; Animals ; *Gastrointestinal Microbiome/genetics ; Hypoxia/microbiology ; Feces/microbiology ; Bacteria, Anaerobic ; Fatty Acids, Volatile ; }, abstract = {BACKGROUND: Gut microbiota plays an important role in host health and is influenced by multiple factors. Hypobaric hypoxia usually existing at high altitude conditions can adversely affect normal physiological functions. However, the dynamic changes of gut microbiota influenced by hypobaric hypoxia have not been elucidated.

METHODS: In this study, we collected fecal samples from seven rats at 14 time points from entering the hypobaric chamber (eight time points) to leaving the chamber (six time points) and five rats served as normoxic controls. Metagenome sequencing was performed on all samples and the dynamics of taxa and functions were analyzed.

RESULTS: We found that the α-diversity was changed in the first 5 days after entering or leaving the hypobaric chamber. The β-diversity analysis revealed that gut microbiota structure was significantly separated among 14 time points. After entering the chamber, the relative abundance of Bacteroides decreased and the most abundant genus turned into Prevotella. The abundance of Firmicutes and Bacteroidetes showed an opposite trend and both have a significant change within 5 days after entering or leaving the hypobaric hypoxia chamber. Some obligate anaerobic bacteria belonging to Desulfovibrio and Alistipes were significantly enriched after entering the chamber for 5 weeks, whereas Probiotics like Bifidobacterium and Lactococcus, and short-chain fatty acids producers like Butyrivibrio and Pseudobutyrivibrio were significantly enriched after leaving the chamber for 3 weeks. Microbial functions like 'Two-component regulatory system', 'beta-carotene biosynthesis' and 'Fatty acid biosynthesis' were significantly enriched after entering the chamber for 5 weeks. Hypobaric hypoxia conditions could deeply affect the diversity and structure of gut microbiota. The alterations of abundance of dominant taxa (Firmicutes and Bacteroidetes), increased anaerobes and decreased probiotics induced by hypobaric hypoxia conditions might affect the host health.}, } @article {pmid36225234, year = {2022}, author = {Herman, MA and Irazoqui, JE and Samuel, BS and Vega, N}, title = {Editorial: C. elegans host-microbiome interactions: From medical to ecological and evolutionary model.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1035545}, pmid = {36225234}, issn = {2235-2988}, support = {DP2 DK116645/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; *Caenorhabditis elegans ; Dysbiosis ; Humans ; *Microbiota ; }, } @article {pmid36224660, year = {2022}, author = {Sanders, JG and Yan, W and Mjungu, D and Lonsdorf, EV and Hart, JA and Sanz, CM and Morgan, DB and Peeters, M and Hahn, BH and Moeller, AH}, title = {A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {212}, pmid = {36224660}, issn = {1474-760X}, support = {R01 AI050529/AI/NIAID NIH HHS/United States ; R35 GM138284/GM/NIGMS NIH HHS/United States ; T32 AI145821/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; *Genome, Bacterial ; Genomics ; Metagenome ; *Microbiota/genetics ; Pan troglodytes/genetics ; Phylogeny ; Workflow ; }, abstract = {Earth's environments harbor complex consortia of microbes that affect processes ranging from host health to biogeochemical cycles. Understanding their evolution and function is limited by an inability to isolate genomes in a high-throughput manner. Here, we present a workflow for bacterial whole-genome sequencing using open-source labware and the OpenTrons robotics platform, reducing costs to approximately $10 per genome. We assess genomic diversity within 45 gut bacterial species from wild-living chimpanzees and bonobos. We quantify intraspecific genomic diversity and reveal divergence of homologous plasmids between hosts. This enables population genetic analyses of bacterial strains not currently possible with metagenomic data alone.}, } @article {pmid36224545, year = {2022}, author = {Espinoza, JL and Dupont, CL}, title = {VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes.}, journal = {BMC bioinformatics}, volume = {23}, number = {1}, pages = {419}, pmid = {36224545}, issn = {1471-2105}, support = {P01 AI118687/AI/NIAID NIH HHS/United States ; R01 AI170111/AI/NIAID NIH HHS/United States ; 1R01AI170111-01/NH/NIH HHS/United States ; }, mesh = {*Archaea/genetics ; Bacteria/genetics ; Cluster Analysis ; Ecosystem ; Eukaryota/genetics ; Genome, Viral ; Humans ; *Metagenome ; Metagenomics/methods ; }, abstract = {BACKGROUND: With the advent of metagenomics, the importance of microorganisms and how their interactions are relevant to ecosystem resilience, sustainability, and human health has become evident. Cataloging and preserving biodiversity is paramount not only for the Earth's natural systems but also for discovering solutions to challenges that we face as a growing civilization. Metagenomics pertains to the in silico study of all microorganisms within an ecological community in situ, however, many software suites recover only prokaryotes and have limited to no support for viruses and eukaryotes.

RESULTS: In this study, we introduce the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite developed to recover genomes from all domains. To our knowledge, VEBA is the first end-to-end metagenomics suite that can directly recover, quality assess, and classify prokaryotic, eukaryotic, and viral genomes from metagenomes. VEBA implements a novel iterative binning procedure and hybrid sample-specific/multi-sample framework that yields more genomes than any existing methodology alone. VEBA includes a consensus microeukaryotic database containing proteins from existing databases to optimize microeukaryotic gene modeling and taxonomic classification. VEBA also provides a unique clustering-based dereplication strategy allowing for sample-specific genomes and genes to be directly compared across non-overlapping biological samples. Finally, VEBA is the only pipeline that automates the detection of candidate phyla radiation bacteria and implements the appropriate genome quality assessments. VEBA's capabilities are demonstrated by reanalyzing 3 existing public datasets which recovered a total of 948 MAGs (458 prokaryotic, 8 eukaryotic, and 482 viral) including several uncharacterized organisms and organisms with no public genome representatives.

CONCLUSIONS: The VEBA software suite allows for the in silico recovery of microorganisms from all domains of life by integrating cutting edge algorithms in novel ways. VEBA fully integrates both end-to-end and task-specific metagenomic analysis in a modular architecture that minimizes dependencies and maximizes productivity. The contributions of VEBA to the metagenomics community includes seamless end-to-end metagenomics analysis but also provides users with the flexibility to perform specific analytical tasks. VEBA allows for the automation of several metagenomics steps and shows that new information can be recovered from existing datasets.}, } @article {pmid36223744, year = {2022}, author = {Di Gesù, CM and Matz, LM and Bolding, IJ and Fultz, R and Hoffman, KL and Gammazza, AM and Petrosino, JF and Buffington, SA}, title = {Maternal gut microbiota mediate intergenerational effects of high-fat diet on descendant social behavior.}, journal = {Cell reports}, volume = {41}, number = {2}, pages = {111461}, pmid = {36223744}, issn = {2211-1247}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; R01 HD109095/HD/NICHD NIH HHS/United States ; T32 AG067952/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; *Diet, High-Fat/adverse effects ; Dysbiosis ; Female ; *Gastrointestinal Microbiome ; Male ; Mice ; Pregnancy ; Social Behavior ; }, abstract = {Dysbiosis of the maternal gut microbiome during pregnancy is associated with adverse neurodevelopmental outcomes. We previously showed that maternal high-fat diet (MHFD) in mice induces gut dysbiosis, social dysfunction, and underlying synaptic plasticity deficits in male offspring (F1). Here, we reason that, if HFD-mediated changes in maternal gut microbiota drive offspring social deficits, then MHFD-induced dysbiosis in F1 female MHFD offspring would likewise impair F2 social behavior. Metataxonomic sequencing reveals reduced microbial richness among female F1 MHFD offspring. Despite recovery of microbial richness among MHFD-descendant F2 mice, they display social dysfunction. Post-weaning Limosilactobacillus reuteri treatment increases the abundance of short-chain fatty acid-producing taxa and rescues MHFD-descendant F2 social deficits. L. reuteri exerts a sexually dimorphic impact on gut microbiota configuration, increasing discriminant taxa between female cohorts. Collectively, these results show multigenerational impacts of HFD-induced dysbiosis in the maternal lineage and highlight the potential of maternal microbiome-targeted interventions for neurodevelopmental disorders.}, } @article {pmid36223712, year = {2022}, author = {Fan, L and Zhu, X and Sun, S and Yu, C and Huang, X and Ness, R and Dugan, LL and Shu, L and Seidner, DL and Murff, HJ and Fodor, AA and Azcarate-Peril, MA and Shrubsole, MJ and Dai, Q}, title = {Ca:Mg ratio, medium-chain fatty acids, and the gut microbiome.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {41}, number = {11}, pages = {2490-2499}, pmid = {36223712}, issn = {1532-1983}, support = {UL1 TR000445/TR/NCATS NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; R01 DK110166/DK/NIDDK NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; UL1 RR024975/RR/NCRR NIH HHS/United States ; R01 CA202936/CA/NCI NIH HHS/United States ; R01 CA149633/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Coconut Oil ; Calcium ; Maltose ; Magnesium ; Fatty Acids/metabolism ; Ketone Bodies ; Sucrose ; Fructose ; Glucose ; }, abstract = {BACKGROUND & AIMS: Ketogenic medium-chain fatty acids (MCFAs) with profound health benefits are commonly found in dairy products, palm kernel oil and coconut oil. We hypothesize that magnesium (Mg) supplementation leads to enhanced gut microbial production of MCFAs and, in turn, increased circulating MCFAs levels.

METHODS: We tested this hypothesis in the Personalized Prevention of Colorectal Cancer Trial (PPCCT) (NCT01105169), a double-blind 2 × 2 factorial randomized controlled trial enrolling 240 participants. Six 24-h dietary recalls were performed for all participants at the baseline and during the intervention period. Based on the baseline 24-h dietary recalls, the Mg treatment used a personalized dose of Mg supplementation that would reduce the calcium (Ca): Mg intake ratio to around 2.3. We measured plasma MCFAs, sugars, ketone bodies and tricarboxylic acid cycle (TCA cycle) metabolites using the Metabolon's global Precision Metabolomics™ LC-MS platform. Whole-genome shotgun metagenomics (WGS) sequencing was performed to assess microbiota in stool samples, rectal swabs, and rectal biopsies.

RESULTS: Personalized Mg treatment (mean dose 205.58 mg/day with a range from 77.25 to 389.55 mg/day) significantly increased the plasma levels of C7:0, C8:0, and combined C7:0 and C8:0 by 18.45%, 25.28%, and 24.20%, respectively, compared to 14.15%, 10.12%, and 12.62% decreases in the placebo arm. The effects remain significant after adjusting for age, sex, race and baseline level (P = 0.0126, P = 0.0162, and P = 0.0031, respectively) and FDR correction at 0.05 (q = 0.0324 for both C7:0 and C8:0). Mg treatment significantly reduced the plasma level of sucrose compared to the placebo arm (P = 0.0036 for multivariable-adjusted and P = 0.0216 for additional FDR correction model) whereas alterations in daily intakes of sucrose, fructose, glucose, maltose and C8:0 from baseline to the end of trial did not differ between two arms. Mediation analysis showed that combined C7:0 and C8:0 partially mediated the effects of Mg treatment on total and individual ketone bodies (P for indirect effect = 0.0045, 0.0043, and 0.03, respectively). The changes in plasma levels of C7:0 and C8:0 were significantly and positively correlated with the alterations in stool microbiome α diversity (r = 0.51, p = 0.0023 and r = 0.34, p = 0.0497, respectively) as well as in stool abundance for the signatures of MCFAs-related microbiota with acyl-ACP thioesterase gene producing C7:0 (r = 0.46, p = 0.0067) and C8:0 (r = 0.49, p = 0.003), respectively, following Mg treatment.

CONCLUSIONS: Optimizing Ca:Mg intake ratios to around 2.3 through 12-week personalized Mg supplementation leads to increased circulating levels of MCFAs (i.e. C7:0 and C8:0), which is attributed to enhanced production from gut microbial fermentation and, maybe, sucrose consumption.}, } @article {pmid36223010, year = {2022}, author = {Lüth, T and Graspeuntner, S and Neumann, K and Kirchhoff, L and Masuch, A and Schaake, S and Lupatsii, M and Tse, R and Griesinger, G and Trinh, J and Rupp, J}, title = {Improving analysis of the vaginal microbiota of women undergoing assisted reproduction using nanopore sequencing.}, journal = {Journal of assisted reproduction and genetics}, volume = {39}, number = {11}, pages = {2659-2667}, pmid = {36223010}, issn = {1573-7330}, support = {J10_2020//Universität zu Lübeck/ ; }, mesh = {Female ; Humans ; RNA, Ribosomal, 16S/genetics ; *Nanopore Sequencing ; Prospective Studies ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Reproduction ; }, abstract = {PURPOSE: Subclinical alterations of the vaginal microbiome have been described to be associated with female infertility and may serve as predictors for failure of in vitro fertilization treatment. While large prospective studies to delineate the role of microbial composition are warranted, integrating microbiome information into clinical management depends on economical and practical feasibility, specifically on a short duration from sampling to final results. The currently most used method for microbiota analysis is either metagenomics sequencing or amplicon-based microbiota analysis using second-generation methods such as sequencing-by-synthesis approaches (Illumina), which is both expensive and time-consuming. Thus, additional approaches are warranted to accelerate the usability of the microbiome as a marker in clinical praxis.

METHODS: Herein, we used a set of ten selected vaginal swabs from women undergoing assisted reproduction, comparing and performing critical optimization of nanopore-based microbiota analysis with the results from MiSeq-based data as a quality reference.

RESULTS: The analyzed samples carried varying community compositions, as shown by amplicon-based analysis of the V3V4 region of the bacterial 16S rRNA gene by MiSeq sequencing. Using a stepwise procedure to optimize adaptation, we show that a close approximation of the microbial composition can be achieved within a reduced time frame and at a minimum of costs using nanopore sequencing.

CONCLUSIONS: Our work highlights the potential of a nanopore-based methodical setup to support the feasibility of interventional studies and contribute to the development of microbiome-based clinical decision-making in assisted reproduction.}, } @article {pmid36222702, year = {2022}, author = {Xu, S and Liu, Y and Zhang, Z and Xu, Y and Qi, Z}, title = {Distributional Pattern of Bacteria, Protists, and Diatoms in Ocean according to Water Depth in the Northern South China Sea.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0275921}, pmid = {36222702}, issn = {2165-0497}, mesh = {*Diatoms/genetics ; Water ; Biodiversity ; Eukaryota ; Bacteria/genetics ; *Microbiota/genetics ; China ; Oceans and Seas ; }, abstract = {Ocean microbiomes provide insightful details about the condition of water and the global impact of marine ecosystems. A fine-scale analysis of ocean microbes may shed light on the dynamics and function of the ocean microbiome community. In this study, we evaluated the changes in the community and function of marine bacteria, protists, and diatoms corresponding to different ocean depths using next-generation sequencing methods. We found that diatoms displayed a potential water-depth pattern in species richness (alpha diversity) and community composition (beta diversity). However, for bacteria and protists, there was no significant relationship between water depth and species richness. This may be related to the biological characteristics of diatoms. The photosynthesis of diatoms and their distribution may be associated with the fluctuating light regime in the underwater climate. Moreover, salinity displayed negative effects on the abundance of some diatom and bacterial groups, which indicates that salinity may be one of the factors restricting ocean microorganism diversity. In addition, compared to the global ocean microbiome composition, function, and antibiotic resistance genes, a water depth pattern due to the fine-scale region was not observed in this study. IMPORTANCE Fine-scale analysis of ocean microbes provides insights into the dynamics and functions of the ocean microbiome community. Here, using amplicon and metagenome sequencing methods, we found that diatoms in the northern South China Sea displayed a potential water-depth pattern in species richness and community composition, which may be related to their biological characteristics. The potential effects of the differences in geographic sites mainly occurred in the diatom and bacterial communities. Moreover, given the correlation between the environmental factors and relative abundance of antibiotic resistance genes (ARGs), the study of ocean ARG distribution patterns should integrate the potential effects of environmental factors.}, } @article {pmid36221927, year = {2023}, author = {Holmes, IA and Grundler, MC}, title = {Phylogenetically under-dispersed gut microbiomes are not correlated with host genomic heterozygosity in a genetically diverse reptile community.}, journal = {Molecular ecology}, volume = {32}, number = {1}, pages = {258-274}, pmid = {36221927}, issn = {1365-294X}, support = {T32 AI145821/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; *Microbiota ; Genomics ; Reptiles/genetics ; }, abstract = {While key elements of fitness in vertebrate animals are impacted by their microbiomes, the host genetic characteristics that factor into microbiome composition are not fully understood. Here, we correlate host genomic heterozygosity and gut microbiome phylogenetic diversity across a community of reptiles in southwestern New Mexico to test hypotheses about the behaviour of host genes that drive microbiome assembly. We find that microbiome communities are phylogenetically under-dispersed relative to random expectations, and that host heterozygosity is not correlated with microbiome diversity. Our analyses reinforce results from functional genomic work that identify conserved host immune and nonimmune genes as key players in microbiome assembly, rather than gene families that rely on heterozygosity for their function.}, } @article {pmid36220843, year = {2022}, author = {West, KA and Yin, X and Rutherford, EM and Wee, B and Choi, J and Chrisman, BS and Dunlap, KL and Hannibal, RL and Hartono, W and Lin, M and Raack, E and Sabino, K and Wu, Y and Wall, DP and David, MM and Dabbagh, K and DeSantis, TZ and Iwai, S}, title = {Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {17034}, pmid = {36220843}, issn = {2045-2322}, support = {R44 DA043954/DA/NIDA NIH HHS/United States ; }, mesh = {*Autism Spectrum Disorder/genetics ; Bacteria/genetics ; Child ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; *Microbiota ; }, abstract = {Observational studies have shown that the composition of the human gut microbiome in children diagnosed with Autism Spectrum Disorder (ASD) differs significantly from that of their neurotypical (NT) counterparts. Thus far, reported ASD-specific microbiome signatures have been inconsistent. To uncover reproducible signatures, we compiled 10 publicly available raw amplicon and metagenomic sequencing datasets alongside new data generated from an internal cohort (the largest ASD cohort to date), unified them with standardized pre-processing methods, and conducted a comprehensive meta-analysis of all taxa and variables detected across multiple studies. By screening metadata to test associations between the microbiome and 52 variables in multiple patient subsets and across multiple datasets, we determined that differentially abundant taxa in ASD versus NT children were dependent upon age, sex, and bowel function, thus marking these variables as potential confounders in case-control ASD studies. Several taxa, including the strains Bacteroides stercoris t__190463 and Clostridium M bolteae t__180407, and the species Granulicatella elegans and Massilioclostridium coli, exhibited differential abundance in ASD compared to NT children only after subjects with bowel dysfunction were removed. Adjusting for age, sex and bowel function resulted in adding or removing significantly differentially abundant taxa in ASD-diagnosed individuals, emphasizing the importance of collecting and controlling for these metadata. We have performed the largest (n = 690) and most comprehensive systematic analysis of ASD gut microbiome data to date. Our study demonstrated the importance of accounting for confounding variables when designing statistical comparative analyses of ASD- and NT-associated gut bacterial profiles. Mitigating these confounders identified robust microbial signatures across cohorts, signifying the importance of accounting for these factors in comparative analyses of ASD and NT-associated gut profiles. Such studies will advance the understanding of different patient groups to deliver appropriate therapeutics by identifying microbiome traits germane to the specific ASD phenotype.}, } @article {pmid36219973, year = {2022}, author = {Muñoz-García, A and Arbeli, Z and Boyacá-Vásquez, V and Vanegas, J}, title = {Metagenomic and genomic characterization of heavy metal tolerance and resistance genes in the rhizosphere microbiome of Avicennia germinans in a semi-arid mangrove forest in the tropics.}, journal = {Marine pollution bulletin}, volume = {184}, number = {}, pages = {114204}, doi = {10.1016/j.marpolbul.2022.114204}, pmid = {36219973}, issn = {1879-3363}, mesh = {*Avicennia/genetics ; Wetlands ; Rhizosphere ; Metagenomics ; Cadmium ; *Metals, Heavy/toxicity ; *Microbiota ; }, abstract = {Mangroves are often exposed to heavy metals that accumulate in the food chain, generate toxicity to mangrove plants and affect microbial diversity. This study determined the abundance of genes associated with resistance and tolerance to heavy metals in the rhizosphere microbiome of Avicennia germinans from a semi-arid mangrove of La Guajira-Colombia by metagenomics and genomics approach. Twenty-eight genes associated with tolerance and 49 genes related to resistance to heavy metals were detected. Genes associated with tolerance and resistance to Cu, especially cusA and copA, were the most abundant. The highest number of genes for tolerance and resistance were for Zn and Co, respectively. The isolate Vibrio fluvialis showed the ability to tolerate Cu, Ni, Zn, and Cd. This work used a complementary approach of metagenomics and genomics to characterize the potential of mangrove microorganisms to tolerate and resist heavy metals and the influence of salinity on their abundance.}, } @article {pmid36216056, year = {2023}, author = {Yi, W and Ji, Y and Gao, H and Luo, S and Pan, R and Song, J and He, Y and Li, Y and Wu, Y and Yan, S and Liang, Y and Sun, X and Jin, X and Mei, L and Cheng, J and Su, H}, title = {Effects of urban particulate matter on gut microbiome and partial schizophrenia-like symptoms in mice: Evidence from shotgun metagenomic and metabolomic profiling.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 1}, pages = {159305}, doi = {10.1016/j.scitotenv.2022.159305}, pmid = {36216056}, issn = {1879-1026}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Particulate Matter/toxicity ; *Schizophrenia ; Dizocilpine Maleate/pharmacology ; Phosphorylcholine/pharmacology ; Feces ; Estriol ; Estrogens ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Epidemiological evidence reported that particulate matter (PM) was associated with increased schizophrenia (SCZ) risk. Disturbance of gut microbiome was involved in SCZ. However, it remains unclear whether PM induces SCZ-like symptoms and how gut microbiome regulates them. Therefore, a multi-omics animal experiment was conducted to verify how urban PM induces SCZ-like behavior and altered gut microbiota and metabolic pathways.

METHODS: Using a completely random design, mice were divided into three groups: PM group, control group and MK801 group, which received daily tracheal instillation of PM solution, sterile PBS solution and intraperitoneal injection of MK801 (establish SCZ model), respectively. After a 14-day intervention, feces were collected for multi-omics testing (shotgun metagenomic sequencing and untargeted metabolomic profiling), followed by open field test, tail suspension test, and passive avoidance test. Besides, fecal microbiome of PM group and control group were transplanted into "pseudo-sterile" mice, then behavioral tests were conducted.

RESULTS: Similar to MK801 group, mice in PM group showed SCZ-like symptoms, including increased spontaneous activity, excitability, anxiety and decreased learning and spatial memory. PM exposure significantly increased the relative abundance of Verrucomicrobia and decreased that of Fibrobacteres et al. The metabolism pathways of estrogen signaling (estriol, 16-glucuronide-estriol and 21-desoxycortisol) and choline metabolism (phosphocholine) were significantly altered by PM exposure. Verrucomicrobia was negatively correlated with the level of estriol, which was correlated with decreased learning and spatial memory. Fibrobacteres and Deinococcus-Thermus were positively correlated with the level of phosphocholine, which was correlated with increased spontaneous activity, excitability and anxiety. Fecal microbiome transplantation from PM group mice reproduced excitability and anxiety symptoms.

CONCLUSIONS: Exposure to PM may affect composition of gut microbiome and alterations of estrogen signaling pathway and choline metabolism pathway, which were associated with partial SCZ-like behaviors. But whether gut microbiome regulates these metabolic pathways and behaviors remains to be determined.}, } @article {pmid36216053, year = {2023}, author = {Yang, X and Ni, K and Shi, Y and Yi, X and Ji, L and Wei, S and Jiang, Y and Zhang, Y and Cai, Y and Ma, Q and Tang, S and Ma, L and Ruan, J}, title = {Metagenomics reveals N-induced changes in carbon-degrading genes and microbial communities of tea (Camellia sinensis L.) plantation soil under long-term fertilization.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 2}, pages = {159231}, doi = {10.1016/j.scitotenv.2022.159231}, pmid = {36216053}, issn = {1879-1026}, mesh = {Soil/chemistry ; Carbon/analysis ; *Camellia sinensis/metabolism ; Soil Microbiology ; Metagenomics ; *Microbiota ; Nitrogen/analysis ; Tea ; *Chitinases ; *Cellulases ; Fertilization ; }, abstract = {Soil organic carbon (SOC) is an important C pool of the global ecosystem and is affected by various agricultural practices including fertilization. Excessive nitrogen (N) application is an important field management measure in tea plantation systems. However, the mechanism underlying the impact of N fertilization on SOC, especially the microscopic mechanism remain unclear. The present study explored the effects of N fertilization on C-cycling genes, SOC-degrading enzymes and microbes expressing these enzymes by using a metagenomic approach in a tea plantation under long-term fertilization with different N rates. Results showed that N application significantly changed the abundance of C-cycling genes, SOC-degrading enzymes, especially those associated with labile and recalcitrant C degradation. In addition, the beta-glucosidase and chitinase-expressing microbial communities showed a significant difference under different N rates. At the phylum level, microbial taxa involved in C degradation were highly similar and abundant, while at the genus level, only specific taxa performed labile and recalcitrant C degradation; these SOC-degrading microbes were significantly enriched under N application. Redundancy analysis (RDA) revealed that the soil and pruned litter properties greatly influenced the SOC-degrading communities; pH and DOC of the soil and biomass and total polyphenol (TP) of the pruned litter exerted significant effects. Additionally, the random forest (RF) algorithm revealed that soil pH and dominant taxa efficiently predicted the beta-glucosidase abundance, while soil pH and DOC, pruned litter TP, and the highly abundant microbial taxa efficiently predicted chitinase abundance. Our study indicated that long-term N fertilization exerted a significant positive effect on SOC-degrading enzymes and microbes expressing these enzymes, resulting in potential impact on soil C storage in a perennial tea plantation ecosystem.}, } @article {pmid36214570, year = {2022}, author = {Utter, DR and Cavanaugh, CM and Borisy, GG}, title = {Genome-Centric Dynamics Shape the Diversity of Oral Bacterial Populations.}, journal = {mBio}, volume = {13}, number = {6}, pages = {e0241422}, pmid = {36214570}, issn = {2150-7511}, support = {R01 DE030136/DE/NIDCR NIH HHS/United States ; UL1 TR001102/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; Bacteria/genetics ; Metagenome ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; }, abstract = {Two major viewpoints have been put forward for how microbial populations change, differing in whether adaptation is driven principally by gene-centric or genome-centric processes. Longitudinal sampling at microbially relevant timescales, i.e., days to weeks, is critical for distinguishing these mechanisms. Because of its significance for both microbial ecology and human health and its accessibility and high level of curation, we used the oral microbiota to study bacterial intrapopulation genome dynamics. Metagenomes were generated by shotgun sequencing of total community DNA from the healthy tongues of 17 volunteers at four to seven time points obtained over intervals of days to weeks. We obtained 390 high-quality metagenome-assembled genomes (MAGs) defining population genomes from 55 genera. The vast majority of genes in each MAG were tightly linked over the 2-week sampling window, indicating that the majority of the population's genomes were temporally stable at the MAG level. MAG-defined populations were composed of up to 5 strains, as determined by single-nucleotide-variant frequencies. Although most were stable over time, individual strains carrying over 100 distinct genes that rose from low abundance to dominance in a population over a period of days were detected. These results indicate a genome-wide as opposed to a gene-level process of population change. We infer that genome-wide selection of ecotypes is the dominant mode of adaptation in the oral populations over short timescales. IMPORTANCE The oral microbiome represents a microbial community of critical relevance to human health. Recent studies have documented the diversity and dynamics of different bacteria to reveal a rich, stable ecosystem characterized by strain-level dynamics. However, bacterial populations and their genomes are neither monolithic nor static; their genomes are constantly evolving to lose, gain, or alter their functional potential. To better understand how microbial genomes change in complex communities, we used culture-independent approaches to reconstruct the genomes (MAGs) for bacterial populations that approximated different species, in 17 healthy donors' mouths over a 2-week window. Our results underscored the importance of strain-level dynamics, which agrees with and expands on the conclusions of previous research. Altogether, these observations reveal patterns of genomic dynamics among strains of oral bacteria occurring over a matter of days.}, } @article {pmid36212846, year = {2022}, author = {Camacho, A and Rochera, C and Picazo, A}, title = {Effect of experimentally increased nutrient availability on the structure, metabolic activities, and potential microbial functions of a maritime Antarctic microbial mat.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {900158}, pmid = {36212846}, issn = {1664-302X}, abstract = {The role of competitive interactions based on resource utilisation was explored in a phototrophic microbial mat from Byers Peninsula (Maritime Antarctica). Shotgun metagenomic profiling of the mat showed a taxonomic and functionally diverse microbial community. The heterotrophic bacterial community was dominated by Proteobacteria, where genera typically found in polar habitats, such as Janthinobacterium, Pseudomonas, and Polaromonas, were highly prevalent. Cyanobacteria played the main role as primary producers, accompanied by diatoms and chlorophytes. To test the potential effects of the inorganic nutrient (N and P) availability on this community, a fully factorial nitrate and phosphorus addition experiment was conducted in situ. The mat exhibited a functional and structural response to the nutrient amendments. Compared to the undisturbed mat, phosphorus fertilisation favoured the growth of (non-heterocystous) cyanobacteria relative to that of diatoms, as indicated by changes in the carotenoid pigment biomarkers. Although no mat accretion was visible, fertilisation improved the phototrophic activity, and, mainly, when P was amended, the production of exopolymeric substances was favoured, whereas further changes in the vertical distribution of primary production activity were observed as well. Illumina amplicon sequencing of the 16S rRNA gene also demonstrated changes in the relative abundance of heterotrophic prokaryotes, which were detectable from the phylum to the genus level and mainly related to the amendment of nitrogen. Predictions made on the functional skills of these shifted prokaryotic communities indicated changes in abundance selecting taxa with a metabolic adaptation to the new nutrient scenarios. They mainly consisted of the enhancement of ecological strategies and metabolic regulatory mechanisms related to the uptake and metabolising of either nitrogen or phosphorus, regulated by its availability whether in a balanced way or not. This study is a pioneer in demonstrating how shifts in the regional dynamic of nutrients might alter the metabolic equilibrium of these initially considered homeostatic benthic communities. They can be accordingly considered as taxonomically diverse microbiomes with a functional repertoire still inclined to respond to the biogeochemical alteration of nutrient cycles, although occurring in a cold extreme environment where biological activity is partially restricted by environmental harshness.}, } @article {pmid36210425, year = {2022}, author = {Klimenko, ES and Belkova, NL and Romanitsa, AI and Pogodina, AV and Rychkova, LV and Darenskaya, MA}, title = {Differences in Gut Microbiota Composition and Predicted Metabolic Functions: a Pilot Study of Adolescents with Normal Weight and Obesity.}, journal = {Bulletin of experimental biology and medicine}, volume = {173}, number = {5}, pages = {628-632}, pmid = {36210425}, issn = {1573-8221}, mesh = {Adolescent ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Obesity/genetics ; Phylogeny ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Understanding the principles underlying the stability and sustainability of the gut microbiome of adolescents with normal weight and obesity will make it possible to implement a personalized approach to the correction of metabolic disorders. The article presents the results of a pilot study of the diversity and metabolic potential of the gut microbiome in adolescents with normal body weight and obesity. Biological material was studied using metagenomic sequencing of the V3-V4 variable regions of the 16S rRNA gene. In all adolescents with normal weight, similar degree of the phylogenetic relationship between the bacterial taxa of the community was demonstrated. In contrast, obese adolescents were characterized by the presence of phylogenetically distinct taxa in the gut microbiota. However, even with differences in taxonomic composition, the gut microbial community can compensate for the absence of certain taxonomic groups by implementing the necessary metabolic functions using other phylogenetically close taxa.}, } @article {pmid36210003, year = {2022}, author = {Wasana, WP and Senevirathne, A and Nikapitiya, C and Lee, JS and Kang, DH and Kwon, KK and Oh, C and De Zoysa, M}, title = {Probiotic effects of Pseudoalteromonas ruthenica: Antibacterial, immune stimulation and modulation of gut microbiota composition.}, journal = {Fish & shellfish immunology}, volume = {131}, number = {}, pages = {229-243}, doi = {10.1016/j.fsi.2022.09.070}, pmid = {36210003}, issn = {1095-9947}, mesh = {Animals ; *Gastrointestinal Microbiome ; Zebrafish ; *Probiotics/pharmacology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {This study aimed to characterise and evaluate the probiotic properties of a newly isolated marine bacterium, strain S6031. The isolated strain was identified as Pseudoalteromonas ruthenica. In vivo experiments were conducted with P. ruthenica-immersed larvae and P. ruthenica-enriched Artemia fed to adult zebrafish. Disease tolerance of larval zebrafish against Edwardsiella piscicida was demonstrated by 66.34% cumulative per cent survival (CPS) in the P. ruthenica-exposed group, which was higher than the CPS of the control (46.67%) at 72 h post challenge (hpc). Heat-stressed larvae had 55% CPS in the P. ruthenica-immersed group, while the control had 30% CPS at 60 hpc. Immune-stress response gene transcripts (muc5.1, muc5.2, muc5.3, alpi2, alpi3, hsp70, and hsp90a) were induced, while pro-inflammatory genes (tnfα, il1b, and il6) were downregulated in P. ruthenica-immersed larvae compared to the control. This trend was confirmed by low pro-inflammatory and high stress-responsive protein expression levels in P. ruthenica-exposed larvae. Adult zebrafish had higher CPS (27.2%) in the P. ruthenica-fed group than the control (9.52%) upon E. piscicida challenge, suggesting increased disease tolerance. Histological analysis demonstrated modulation of goblet cell density and average villus height in the P. ruthenica-supplemented group. Metagenomics analysis clearly indicated modulation of alpha diversity indices and the relative abundance of Proteobacteria in the P. ruthenica-supplemented zebrafish gut. Furthermore, increased Firmicutes colonisation and reduced Bacteroidetes abundance in the gut were observed upon P. ruthenica supplementation. Additionally, this study confirmed the concentration-dependent increase of colony dispersion and macrophage uptake upon mucin treatment. In summary, P. ruthenica possesses remarkable functional properties as a probiotic that enhances host defence against diseases and thermal stress.}, } @article {pmid36209779, year = {2023}, author = {Ritchie, G and Strodl, E and Parham, S and Bambling, M and Cramb, S and Vitetta, L}, title = {An exploratory study of the gut microbiota in major depression with anxious distress.}, journal = {Journal of affective disorders}, volume = {320}, number = {}, pages = {595-604}, doi = {10.1016/j.jad.2022.10.001}, pmid = {36209779}, issn = {1573-2517}, mesh = {Humans ; Male ; Female ; Young Adult ; Adult ; Middle Aged ; *Depressive Disorder, Major/psychology ; *Gastrointestinal Microbiome/genetics ; Depression/diagnosis ; RNA, Ribosomal, 16S/genetics ; Anxiety/diagnosis ; }, abstract = {OBJECTIVES: To explore differences in the diversity and composition of the gut microbiome between major depressive disorder (MDD) with and without anxious distress.

METHODS: The study comprised 117 participants (79 female, 36 male, 2 other, mean age 38.2 ± 13.4 years) with a current major depressive episode (MDE) with (n = 63) and without (n = 54) the anxious distress specifier. A clinical psychologist administered the structured clinical interview for the DSM-5-RV to confirm a diagnosis of depression. Participants provided stool samples which were immediately frozen and stored at -80 °C. These samples were analysed using the Illumina 16S Metagenomics sequencing protocol in which the sequencing primers target the V3 and V4 regions of the 16S rRNA gene. Participants also completed mental health questionnaires to assess severity of depression (BDI-II), generalized anxiety (GAD-7), and stress (PSS).

RESULTS: There were no significant group differences in α-diversity (Shannon's diversity Index; Simpson Index), richness (ACE; Chao1), (Pielou's) evenness, or beta diversity (Bray-Curtis dissimilarity index and weighted UniFrac distance) of gut bacteria. Significant group differences in the relative abundance of gut microbiota however were observed at each taxonomical level, including across 15 genera and 18 species.

LIMITATIONS: This was an exploratory study that needs to be replicated across larger samples and compared with a healthy control group.

CONCLUSIONS: The research contributes to knowledge of the depressive gut microbial profile unique to the anxious distress subtype of MDD.}, } @article {pmid36209079, year = {2022}, author = {Zhao, L and Wang, C and Peng, S and Zhu, X and Zhang, Z and Zhao, Y and Zhang, J and Zhao, G and Zhang, T and Heng, X and Zhang, L}, title = {Pivotal interplays between fecal metabolome and gut microbiome reveal functional signatures in cerebral ischemic stroke.}, journal = {Journal of translational medicine}, volume = {20}, number = {1}, pages = {459}, pmid = {36209079}, issn = {1479-5876}, mesh = {Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Ischemic Stroke ; Metabolome ; Metabolomics ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Integrative analysis approaches of metagenomics and metabolomics have been widely developed to understand the association between disease and the gut microbiome. However, the different profiling patterns of different metabolic samples in the association analysis make it a matter of concern which type of sample is the most closely associated with gut microbes and disease. To address this lack of knowledge, we investigated the association between the gut microbiome and metabolomic profiles of stool, urine, and plasma samples from ischemic stroke patients and healthy subjects.

METHODS: We performed metagenomic sequencing (feces) and untargeted metabolomics analysis (feces, plasma, and urine) from ischemic stroke patients and healthy volunteers. Differential analyses were conducted to find key differential microbiota and metabolites for ischemic stroke. Meanwhile, Spearman's rank correlation and linear regression analyses were used to study the association between microbiota and metabolites of different metabolic mixtures.

RESULTS: Untargeted metabolomics analysis shows that feces had the most abundant features and identified metabolites, followed by urine and plasma. Feces had the highest number of differential metabolites between ischemic stroke patients and the healthy group. Based on the association analysis between metagenomics and metabolomics of fecal, urine, and plasma, fecal metabolome showed the strongest association with the gut microbiome. There are 1073, 191, and 81 statistically significant pairs (P < 0.05) in the correlation analysis for fecal, urine, and plasma metabolome. Fecal metabolites explained the variance of alpha-diversity of the gut microbiome up to 31.1%, while urine and plasma metabolites only explained the variance of alpha-diversity up to 13.5% and 10.6%. Meanwhile, there were more significant differential metabolites in feces than urine and plasma associated with the stroke marker bacteria.

CONCLUSIONS: The systematic association analysis between gut microbiome and metabolomics reveals that fecal metabolites show the strongest association with the gut microbiome, followed by urine and plasma. The findings would promote the association study between the gut microbiome and fecal metabolome to explore key factors that are associated with diseases. We also provide a user-friendly web server and a R package to facilitate researchers to conduct the association analysis of gut microbiome and metabolomics.}, } @article {pmid36208825, year = {2022}, author = {Dong, ZX and Tang, QH and Li, WL and Wang, ZW and Li, XJ and Fu, CM and Li, D and Qian, K and Tian, WL and Guo, J}, title = {Honeybee (Apis mellifera) resistance to deltamethrin exposure by Modulating the gut microbiota and improving immunity.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {314}, number = {}, pages = {120340}, doi = {10.1016/j.envpol.2022.120340}, pmid = {36208825}, issn = {1873-6424}, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome ; Bacteria ; *Pesticides ; *Environmental Pollutants ; Defensins ; }, abstract = {Honeybees (Apis mellifera) are important economic insects and play important roles in pollination and maintenance of ecological balance. However, the use of pesticides has posed a substantial threat to bees in recent years, with the more widely used deltamethrin being the most harmful. In this study, we found that deltamethrin exposure significantly reduced bee survival in a dose-dependent manner (p = 0.025). In addition, metagenomic sequencing further revealed that DM exposure significantly reduced the diversity of the bee gut microbiota (Chao1, p < 0.0001; Shannon, p < 0.0001; Simpson, p < 0.0001) and decreased the relative abundance of core species of the gut microbiota. Importantly, in studies of GF-bees, we found that the colonization of important gut bacteria such as Gilliamella apicola and Lactobacillus kunkeei significantly increased bee resistance to DM (survival rate increased from 16.7 to 66.7%). Interestingly, we found that the immunity-genes Defensin-2 and Toll were significantly upregulated in bees after the colonization of gut bacteria. These results suggest that gut bacteria may protect against DM stress by improving host immunity. Our findings provide an important rationale for protecting honeybees from pollutants from the perspective of gut microbes.}, } @article {pmid36208631, year = {2022}, author = {Afrizal, A and Jennings, SAV and Hitch, TCA and Riedel, T and Basic, M and Panyot, A and Treichel, N and Hager, FT and Wong, EO and Wolter, B and Viehof, A and von Strempel, A and Eberl, C and Buhl, EM and Abt, B and Bleich, A and Tolba, R and Blank, LM and Navarre, WW and Kiessling, F and Horz, HP and Torow, N and Cerovic, V and Stecher, B and Strowig, T and Overmann, J and Clavel, T}, title = {Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities.}, journal = {Cell host & microbe}, volume = {30}, number = {11}, pages = {1630-1645.e25}, doi = {10.1016/j.chom.2022.09.011}, pmid = {36208631}, issn = {1934-6069}, mesh = {Mice ; Animals ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Bacteria ; Metagenome ; Intestines ; Disease Models, Animal ; Mammals/genetics ; }, abstract = {Microbiome research needs comprehensive repositories of cultured bacteria from the intestine of mammalian hosts. We expanded the mouse intestinal bacterial collection (www.dsmz.de/miBC) to 212 strains, all publicly available and taxonomically described. This includes strain-level diversity, small-sized bacteria, and previously undescribed taxa (one family, 10 genera, and 39 species). This collection enabled metagenome-educated prediction of synthetic communities (SYNs) that capture key functional differences between microbiomes, notably identifying communities associated with either resistance or susceptibility to DSS-induced colitis. Additionally, nine species were used to amend the Oligo-Mouse Microbiota (OMM)12 model, yielding the OMM19.1 model. The added strains compensated for phenotype differences between OMM12 and specific pathogen-free mice, including body composition and immune cells in the intestine and associated lymphoid tissues. Ready-to-use OMM stocks are available for future studies. In conclusion, this work improves our knowledge of gut microbiota diversity in mice and enables functional studies via the modular use of isolates.}, } @article {pmid36207493, year = {2023}, author = {Nobu, MK and Nakai, R and Tamazawa, S and Mori, H and Toyoda, A and Ijiri, A and Suzuki, S and Kurokawa, K and Kamagata, Y and Tamaki, H}, title = {Unique H2-utilizing lithotrophy in serpentinite-hosted systems.}, journal = {The ISME journal}, volume = {17}, number = {1}, pages = {95-104}, pmid = {36207493}, issn = {1751-7370}, mesh = {Autotrophic Processes ; *Hydrogen ; *Microbiota ; Glycine ; Oxidoreductases ; }, abstract = {Serpentinization of ultramafic rocks provides molecular hydrogen (H2) that can support lithotrophic metabolism of microorganisms, but also poses extremely challenging conditions, including hyperalkalinity and limited electron acceptor availability. Investigation of two serpentinization-active systems reveals that conventional H2-/CO2-dependent homoacetogenesis is thermodynamically unfavorable in situ due to picomolar CO2 levels. Through metagenomics and thermodynamics, we discover unique taxa capable of metabolism adapted to the habitat. This included a novel deep-branching phylum, "Ca. Lithacetigenota", that exclusively inhabits serpentinite-hosted systems and harbors genes encoding alternative modes of H2-utilizing lithotrophy. Rather than CO2, these putative metabolisms utilize reduced carbon compounds detected in situ presumably serpentinization-derived: formate and glycine. The former employs a partial homoacetogenesis pathway and the latter a distinct pathway mediated by a rare selenoprotein-the glycine reductase. A survey of microbiomes shows that glycine reductases are diverse and nearly ubiquitous in serpentinite-hosted environments. "Ca. Lithacetigenota" glycine reductases represent a basal lineage, suggesting that catabolic glycine reduction is an ancient bacterial innovation by Terrabacteria for gaining energy from geogenic H2 even under hyperalkaline, CO2-poor conditions. Unique non-CO2-reducing metabolisms presented here shed light on potential strategies that extremophiles may employ for overcoming a crucial obstacle in serpentinization-associated environments, features potentially relevant to primordial lithotrophy in early Earth.}, } @article {pmid36207335, year = {2022}, author = {Tao, J and Wang, W and Weissman, JL and Zhang, Y and Chen, S and Zhu, Y and Zhang, C and Hou, S}, title = {Size-fractionated microbiome observed during an eight-month long sampling in Jiaozhou Bay and the Yellow Sea.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {605}, pmid = {36207335}, issn = {2052-4463}, support = {Nos. 42141003//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Bays/microbiology ; China ; Genome, Microbial ; Metagenome ; *Microbiota ; Oceans and Seas ; }, abstract = {Jiaozhou Bay is a typical semi-enclosed bay with a temperate climate imposed by strong anthropogenic influence. To investigate microbial biodiversity and ecosystem services in this highly dynamic coastal environment, we conducted a monthly microbial survey spanning eight months at two stations in the bay and the open Yellow Sea starting in April 2015. This report provides a comprehensive inventory of amplicon sequences and environmental microbial genomes from this survey. In total, 2,543 amplicon sequence variants were obtained with monthly relative abundance profiles in three size fractions (>2.7 μm, 2.7-0.7 μm, and 0.7-0.22 μm). Shotgun metagenomes yielded 915 high-quality metagenome-assembled genomes with ≥50% completeness and ≤5% contamination. These environmental genomes comprise 27 bacterial and 5 archaeal phyla. We expect this comprehensive dataset will facilitate a better understanding of coastal microbial ecology.}, } @article {pmid36206369, year = {2022}, author = {Braga, LPP and Orland, C and Emilson, EJS and Fitch, AA and Osterholz, H and Dittmar, T and Basiliko, N and Mykytczuk, NCS and Tanentzap, AJ}, title = {Viruses direct carbon cycling in lake sediments under global change.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {41}, pages = {e2202261119}, pmid = {36206369}, issn = {1091-6490}, mesh = {Amino Sugars/metabolism ; Bacteria/genetics/metabolism ; Carbon/metabolism ; Carbon Cycle ; *Greenhouse Gases/metabolism ; Lakes/microbiology ; *Viruses/genetics/metabolism ; Water/metabolism ; }, abstract = {Global change is altering the vast amount of carbon cycled by microbes between land and freshwater, but how viruses mediate this process is poorly understood. Here, we show that viruses direct carbon cycling in lake sediments, and these impacts intensify with future changes in water clarity and terrestrial organic matter (tOM) inputs. Using experimental tOM gradients within sediments of a clear and a dark boreal lake, we identified 156 viral operational taxonomic units (vOTUs), of which 21% strongly increased with abundances of key bacteria and archaea, identified via metagenome-assembled genomes (MAGs). MAGs included the most abundant prokaryotes, which were themselves associated with dissolved organic matter (DOM) composition and greenhouse gas (GHG) concentrations. Increased abundances of virus-like particles were separately associated with reduced bacterial metabolism and with shifts in DOM toward amino sugars, likely released by cell lysis rather than higher molecular mass compounds accumulating from reduced tOM degradation. An additional 9.6% of vOTUs harbored auxiliary metabolic genes associated with DOM and GHGs. Taken together, these different effects on host dynamics and metabolism can explain why abundances of vOTUs rather than MAGs were better overall predictors of carbon cycling. Future increases in tOM quantity, but not quality, will change viral composition and function with consequences for DOM pools. Given their importance, viruses must now be explicitly considered in efforts to understand and predict the freshwater carbon cycle and its future under global environmental change.}, } @article {pmid36204250, year = {2022}, author = {Shen, Z and Thomashow, LS and Ou, Y and Tao, C and Wang, J and Xiong, W and Liu, H and Li, R and Shen, Q and Kowalchuk, GA}, title = {Shared Core Microbiome and Functionality of Key Taxa Suppressive to Banana Fusarium Wilt.}, journal = {Research (Washington, D.C.)}, volume = {2022}, number = {}, pages = {9818073}, pmid = {36204250}, issn = {2639-5274}, abstract = {Microbial contributions to natural soil suppressiveness have been reported for a range of plant pathogens and cropping systems. To disentangle the mechanisms underlying suppression of banana Panama disease caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc4), we used amplicon sequencing to analyze the composition of the soil microbiome from six separate locations, each comprised of paired orchards, one potentially suppressive and one conducive to the disease. Functional potentials of the microbiomes from one site were further examined by shotgun metagenomic sequencing after soil suppressiveness was confirmed by greenhouse experiments. Potential key antagonists involved in disease suppression were also isolated, and their activities were validated by a combination of microcosm and pot experiments. We found that potentially suppressive soils shared a common core community with relatively low levels of F. oxysporum and relatively high proportions of Myxococcales, Pseudomonadales, and Xanthomonadales, with five genera, Anaeromyxobacter, Kofleria, Plesiocystis, Pseudomonas, and Rhodanobacter being significantly enriched. Further, Pseudomonas was identified as a potential key taxon linked to pathogen suppression. Metagenomic analysis showed that, compared to the conducive soil, the microbiome in the disease suppressive soil displayed a significantly greater incidence of genes related to quorum sensing, biofilm formation, and synthesis of antimicrobial compounds potentially active against Foc4. We also recovered a higher frequency of antagonistic Pseudomonas isolates from disease suppressive experimental field sites, and their protective effects against banana Fusarium wilt disease were demonstrated under greenhouse conditions. Despite differences in location and soil conditions, separately located suppressive soils shared common characteristics, including enrichment of Myxococcales, Pseudomonadales, and Xanthomonadales, and enrichment of specific Pseudomonas populations with antagonistic activity against the pathogen. Moreover, changes in functional capacity toward an increase in quorum sensing, biofilm formation, and antimicrobial compound synthesizing involve in disease suppression.}, } @article {pmid36203793, year = {2022}, author = {Clinton, NA and Hameed, SA and Agyei, EK and Jacob, JC and Oyebanji, VO and Jabea, CE}, title = {Crosstalk between the Intestinal Virome and Other Components of the Microbiota, and Its Effect on Intestinal Mucosal Response and Diseases.}, journal = {Journal of immunology research}, volume = {2022}, number = {}, pages = {7883945}, pmid = {36203793}, issn = {2314-7156}, mesh = {*Bacteriophages ; *Gastrointestinal Microbiome ; Intestinal Mucosa ; *Microbiota ; Virome ; *Viruses ; }, abstract = {In recent years, there has been ample evidence illustrating the effect of microbiota on gut immunity, homeostasis, and disease. Most of these studies have engaged more efforts in understanding the role of the bacteriome in gut mucosal immunity and disease. However, studies on the virome and its influence on gut mucosal immunity and pathology are still at infancy owing to limited metagenomic tools. Nonetheless, the existing studies on the virome have largely been focused on the bacteriophages as these represent the main component of the virome with little information on endogenous retroviruses (ERVs) and eukaryotic viruses. In this review, we describe the gut virome, and its role in gut mucosal response and disease progression. We also explore the crosstalk between the virome and other microorganisms in the gut mucosa and elaborate on how these interactions shape the gut mucosal immunity going from bacteriophages through ERVs to eukaryotic viruses. Finally, we elucidate the potential contribution of this crosstalk in the pathogenesis of inflammatory bowel diseases and colon cancer.}, } @article {pmid36202244, year = {2023}, author = {Zou, C and Wang, M and Chen, Y and Qin, Y and Zhao, Y and Qiao, L and Zhu, S and Chen, T and Yuan, Y}, title = {Effects of different cathodic potentials on performance, microbial community structure and function for bioelectrochemical-stimulated dechlorination of 2,4,6-trichlorophenol in sediments.}, journal = {Environmental research}, volume = {216}, number = {Pt 1}, pages = {114477}, doi = {10.1016/j.envres.2022.114477}, pmid = {36202244}, issn = {1096-0953}, mesh = {*Chlorophenols/chemistry ; *Microbiota ; Electrodes ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; }, abstract = {Bioelectrochemical systems with biocathodes constitute a promising means to enhance the biological dechlorination of 2,4,6-trichlorophenol (2,4,6-TCP) in constructed wetland (CW) sediments. However, the effect of different cathodic potentials on the structure and function of 2,4,6-TCP-reducing biocathode communities in CW sediments is largely unknown. Here, we evaluated the performance and microbial community structure of 2,4,6-TCP-reducing biocathode systems at different cathodic potentials (- 0.5, - 0.7, - 0.9, and - 1.1 V vs. saturated calomel electrode). The dechlorination efficiency of 2,4,6-TCP with the biocathode relatively increased by 16.02%-33.17% compared to that in the open circuit. The highest 2,4,6-TCP dechlorination efficiency (92.34 ± 0.86%) was observed at - 0.7 V in sediment, which may be due to the highest abundance of functional genera (e.g., Pseudomonas, Spirochaeta) at - 0.7 V. Metagenomic analysis provided new insights into the metabolic potential of microorganisms in CW sediments and suggested possible 2,4,6-TCP conversion pathways in sediments. 2,4,6-TCP was gradually dechlorinated to form 4-chlorophenol, followed by a ring-opening step via the activities of chlorophenol reductive dehalogenase and oxygenase (e.g., cprA, tfdB). Interestingly, micro-electrical stimulation enhanced the expression of chlorophenol reductive dehalogenase (cprA). Therefore, our findings at the molecular and gene expression levels provide insights into the effects of different cathodic potentials on the performance and community structure of 2,4,6-TCP-reducing biocathode systems in CW sediments.}, } @article {pmid36201636, year = {2022}, author = {Su, Q and Liu, Q and Zhang, L and Xu, Z and Liu, C and Lu, W and Ching, JY and Li, A and Mak, JWY and Lui, GCY and Ng, SSS and Chow, KM and Hui, DS and Chan, PK and Chan, FKL and Ng, SC}, title = {Antibiotics and probiotics impact gut antimicrobial resistance gene reservoir in COVID-19 patients.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2128603}, pmid = {36201636}, issn = {1949-0984}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; *COVID-19/complications ; Drug Resistance, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; *Probiotics/therapeutic use ; SARS-CoV-2/genetics ; Tetracyclines ; Vancomycin ; Post-Acute COVID-19 Syndrome ; *COVID-19 Drug Treatment ; }, abstract = {Dysbiosis of gut microbiota is well-described in patients with coronavirus 2019 (COVID-19), but the dynamics of antimicrobial resistance genes (ARGs) reservoir, known as resistome, is less known. Here, we performed longitudinal fecal metagenomic profiling of 142 patients with COVID-19, characterized the dynamics of resistome from diagnosis to 6 months after viral clearance, and reported the impact of antibiotics or probiotics on the ARGs reservoir. Antibiotic-naive patients with COVID-19 showed increased abundance and types, and higher prevalence of ARGs compared with non-COVID-19 controls at baseline. Expansion in resistome was mainly driven by tetracycline, vancomycin, and multidrug-resistant genes and persisted for at least 6 months after clearance of SARS-CoV-2. Patients with expanded resistome exhibited increased prevalence of Klebsiella sp. and post-acute COVID-19 syndrome. Antibiotic treatment resulted in further increased abundance of ARGs whilst oral probiotics (synbiotic formula, SIM01) significantly reduced the ARGs reservoir in the gut microbiota of COVID-19 patients during the acute infection and recovery phase. Collectively, these findings shed new insights on the dynamic of ARGs reservoir in COVID-19 patients and the potential role of microbiota-directed therapies in reducing the burden of accumulated ARGs.}, } @article {pmid36200987, year = {2023}, author = {Wang, B and Du, P and Huang, S and He, D and Chen, J and Wen, X and Yang, J and Xian, S and Cheng, Z}, title = {Comparison of the caecal microbial community structure and physiological indicators of healthy and infection Eimeria tenella chickens during peak of oocyst shedding.}, journal = {Avian pathology : journal of the W.V.P.A}, volume = {52}, number = {1}, pages = {51-61}, doi = {10.1080/03079457.2022.2133681}, pmid = {36200987}, issn = {1465-3338}, mesh = {Animals ; *Eimeria tenella/genetics ; Chickens/microbiology ; *Poultry Diseases/microbiology ; Oocysts/physiology ; *Coccidiosis/parasitology/veterinary ; *Microbiota ; }, abstract = {Eimeria tenella (E. tenella), an important intestinal parasite of chicken caeca, causes coccidiosis and brings large economic losses to the poultry industry annually. Gut microorganismal alterations directly affect the health of the body. To understand how E. tenella affects its host, we analysed the changes in caecal microbial diversity and the physiological and morphological changes during the peak of oocyst shedding. Infected and healthy chickens differed significantly in caecal pathology and blood indicators. At the genus level, the abundances of Faecalibacterium, Clostridium, Lachnoclostridium, Gemmiger, Flavonifractor, Pseudoflavonifractor and Oscillibacter were significantly decreased in the infected samples, whereas Escherichia, Nocardia and Chlamydia were significantly increased. Functional gene pathways related to replication, recombination and repair, and transcription were significantly decreased, and functional genes related to metabolism were highly significantly reduced in the infected samples. Furthermore, in the infected samples, E. tenella reduced the haemoglobin levels and red blood cell counts, greatly reduced the beneficial bacteria and increased the potentially pathogenic bacteria. This study provides a research basis for further understanding the pathogenic mechanisms of E. tenella and provides insight for potential new drug development.RESEARCH HIGHLIGHTS First simultaneous description of caecal microbiota and physiological indicators during E. tenella infection.Metagenomics used to explore functional properties of chicken caecal microbiota during E. tenella infection.Caecal microbial compositions and functional genes altered significantly after infection.Blood indicators and caecal morphology were significantly altered in the infected group.}, } @article {pmid36198385, year = {2022}, author = {Bamola, VD and Dubey, D and Samanta, P and Kedia, S and Ahuja, V and Madempudi, RS and Neelamraju, J and Chaudhry, R}, title = {Role of a probiotic strain in the modulation of gut microbiota and cytokines in inflammatory bowel disease.}, journal = {Anaerobe}, volume = {78}, number = {}, pages = {102652}, doi = {10.1016/j.anaerobe.2022.102652}, pmid = {36198385}, issn = {1095-8274}, mesh = {Humans ; *Gastrointestinal Microbiome ; Cytokines ; *Probiotics/therapeutic use ; Bifidobacterium ; *Inflammatory Bowel Diseases/therapy ; Tumor Necrosis Factor-alpha ; }, abstract = {OBJECTIVE: To assess the effect of a probiotic strain Bacillus clausii UBBC-07 on gut microbiota and cytokines in IBD patients.

METHOD: Patients were randomly allocated to either placebo or probiotic Bacillus clausii UBBC-07 for four weeks along with the standard medical treatment (SMT). Enrolled patients were evaluated before and after intervention for presence of the given probiotic, change in gut microbiota, change in serum cytokines, serotonin and dopamine, symptoms of disease, physical, behavioral and psychological parameters.

RESULTS: Probiotic strain Bacillus clausii UBBC-07 showed good survival in IBD patients in the treatment group (p < 0.01) without any reported adverse event. Metagenomic analysis showed that the given probiotic strain was able to modulate the gut microbiota in treated group. Phylum Firmicutes was increased and phylum Bacteroidetes was decreased in the probiotic treated group. A significant increase was observed in the abundance of anaerobic bacterial genera Lactobacillus, Bifidobacterium and Faecalibacterium in the probiotic treated group (p < 0.01) as compared to placebo group. Significant increase was observed in IL-10 (p < 0.05) and variable decrease in the secretion of IL-1β, TNF- α, IL-6, IL -17 and IL -23 in probiotic treated group. In the treatment group a significant decrease in the symptoms of IBD and improvement in the psychological parameter to various degrees was noted.

CONCLUSION: These results indicated that probiotic strain B clausii UBBC-07 affected the gut microbiota and cytokine secretion and shown efficacy in IBD patients.}, } @article {pmid36198381, year = {2023}, author = {Chen, F and Li, S and Guo, R and Song, F and Zhang, Y and Wang, X and Huo, X and Lv, Q and Ullah, H and Wang, G and Ma, Y and Yan, Q and Ma, X}, title = {Meta-analysis of fecal viromes demonstrates high diagnostic potential of the gut viral signatures for colorectal cancer and adenoma risk assessment.}, journal = {Journal of advanced research}, volume = {49}, number = {}, pages = {103-114}, pmid = {36198381}, issn = {2090-1224}, mesh = {Humans ; Virome ; *Gastrointestinal Microbiome ; *Viruses ; *Adenoma/diagnosis ; Risk Assessment ; Biomarkers ; *Colorectal Neoplasms/diagnosis/microbiology ; }, abstract = {INTRODUCTION: Viruses have been reported as inducers of tumorigenesis. Little studies have explored the impact of the gut virome on the progression of colorectal cancer. However, there is still a problem with the repeatability of viral signatures across multiple cohorts.

OBJECTIVES: The present study aimed to reveal the repeatable gut vial signatures of colorectal cancer and adenoma patients and decipher the potential of viral markers in disease risk assessment for diagnosis.

METHODS: 1,282 available fecal metagenomes from 9 published studies for colorectal cancer and adenoma were collected. A gut viral catalog was constructed via a reference-independent approach. Viral signatures were identified by cross-cohort meta-analysis and used to build predictive models based on machine learning algorithms. New fecal samples were collected to validate the generalization of predictive models.

RESULTS: The gut viral composition of colorectal cancer patients was drastically altered compared with healthy, as evidenced by changes in some Siphoviridae and Myoviridae viruses and enrichment of Microviridae, whereas the virome variation in adenoma patients was relatively low. Cross-cohort meta-analysis identified 405 differential viruses for colorectal cancer, including several phages of Porphyromonas, Fusobacterium, and Hungatella that were enriched in patients and some control-enriched Ruminococcaceae phages. In 9 discovery cohorts, the optimal risk assessment model obtained an average cross-cohort area under the curve of 0.830 for discriminating colorectal cancer patients from controls. This model also showed consistently high accuracy in 2 independent validation cohorts (optimal area under the curve, 0.906). Gut virome analysis of adenoma patients identified 88 differential viruses and achieved an optimal area under the curve of 0.772 for discriminating patients from controls.

CONCLUSION: Our findings demonstrate the gut virome characteristics in colorectal cancer and adenoma and highlight gut virus-bacterial synergy in the progression of colorectal cancer. The gut viral signatures may be new targets for colorectal cancer treatment. In addition, high repeatability and predictive power of the prediction models suggest the potential of gut viral biomarkers in non-invasive diagnostic tests of colorectal cancer and adenoma.}, } @article {pmid36197791, year = {2023}, author = {Brennan, GL}, title = {Sequencing our way to more accurate community abundance.}, journal = {Molecular ecology resources}, volume = {23}, number = {1}, pages = {13-15}, pmid = {36197791}, issn = {1755-0998}, support = {//Georgina L. Brennan Marie Skłodowska-Curie Individual Fellowship/ ; }, mesh = {*Biodiversity ; *Metagenomics/methods ; Metagenome ; Ecology ; Oceans and Seas ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Over the last two decades, there has been a huge increase in our understanding of microbial diversity, structure and composition enabled by high-throughput sequencing technologies. Yet, it is unclear how the number of sequences translates to the number of cells or species within the community. In some cases, additional observational data may be required to ensure relative abundance patterns from sequence reads are biologically meaningful. The goal of DNA-based methods for biodiversity assessments is to obtain robust community abundance data, simultaneously, from environmental samples. In this issue of Molecular Ecology Resources, Pierella Karlusich et al. (2022) describe a new method for quantifying phytoplankton cell abundance. Using Tara Oceans data sets, the authors propose the photosynthetic gene psbO for reporting accurate relative abundance of the entire phytoplankton community from metagenomic data. The authors demonstrate higher correlations with traditional optical methods (including microscopy and flow cytometry), using their new method, improving upon molecular abundance assessments using multicopy marker genes. Furthermore, to facilitate application of their approach, the authors curated a psbO gene database for accessible taxonomic queries. This is an important step towards improving species abundance estimates from molecular data and eventually reporting of absolute species abundance, enhancing our understanding of community dynamics.}, } @article {pmid36195901, year = {2022}, author = {Kelly, JB and Carlson, DE and Low, JS and Thacker, RW}, title = {Novel trends of genome evolution in highly complex tropical sponge microbiomes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {164}, pmid = {36195901}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Evolution, Molecular ; *Lipopolysaccharides ; Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; Phylogeny ; Steroids ; Sterols ; }, abstract = {BACKGROUND: Tropical members of the sponge genus Ircinia possess highly complex microbiomes that perform a broad spectrum of chemical processes that influence host fitness. Despite the pervasive role of microbiomes in Ircinia biology, it is still unknown how they remain in stable association across tropical species. To address this question, we performed a comparative analysis of the microbiomes of 11 Ircinia species using whole-metagenomic shotgun sequencing data to investigate three aspects of bacterial symbiont genomes-the redundancy in metabolic pathways across taxa, the evolution of genes involved in pathogenesis, and the nature of selection acting on genes relevant to secondary metabolism.

RESULTS: A total of 424 new, high-quality bacterial metagenome-assembled genomes (MAGs) were produced for 10 Caribbean Ircinia species, which were evaluated alongside 113 publicly available MAGs sourced from the Pacific species Ircinia ramosa. Evidence of redundancy was discovered in that the core genes of several primary metabolic pathways could be found in the genomes of multiple bacterial taxa. Across hosts, the metagenomes were depleted in genes relevant to pathogenicity and enriched in eukaryotic-like proteins (ELPs) that likely mimic the hosts' molecular patterning. Finally, clusters of steroid biosynthesis genes (CSGs), which appear to be under purifying selection and undergo horizontal gene transfer, were found to be a defining feature of Ircinia metagenomes.

CONCLUSIONS: These results illustrate patterns of genome evolution within highly complex microbiomes that illuminate how associations with hosts are maintained. The metabolic redundancy within the microbiomes could help buffer the hosts from changes in the ambient chemical and physical regimes and from fluctuations in the population sizes of the individual microbial strains that make up the microbiome. Additionally, the enrichment of ELPs and depletion of LPS and cellular motility genes provide a model for how alternative strategies to virulence can evolve in microbiomes undergoing mixed-mode transmission that do not ultimately result in higher levels of damage (i.e., pathogenicity) to the host. Our last set of results provides evidence that sterol biosynthesis in Ircinia-associated bacteria is widespread and that these molecules are important for the survival of bacteria in highly complex Ircinia microbiomes. Video Abstract.}, } @article {pmid36193874, year = {2022}, author = {Yang, Z and Chen, Z and Lin, X and Yao, S and Xian, M and Ning, X and Fu, W and Jiang, M and Li, N and Xiao, X and Feng, M and Lian, Z and Yang, W and Ren, X and Zheng, Z and Zhao, J and Wei, N and Lu, W and Roponen, M and Schaub, B and Wong, GWK and Su, Z and Wang, C and Li, J}, title = {Rural environment reduces allergic inflammation by modulating the gut microbiota.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2125733}, pmid = {36193874}, issn = {1949-0984}, mesh = {Animals ; Bacteria/genetics ; Dust ; Endotoxins ; *Gastrointestinal Microbiome ; *Hypersensitivity/microbiology/prevention & control ; Immunoglobulin E ; Inflammation ; Mice ; Ovalbumin ; }, abstract = {Rural environments and microbiota are linked to a reduction in the prevalence of allergies. However, the mechanism underlying the reduced allergies modulated by rural residency is unclear. Here, we assessed gut bacterial composition and metagenomics in urban and rural children in the EuroPrevall-INCO cohort. Airborne dusts, including mattress and rural henhouse dusts, were profiled for bacterial and fungal composition by amplicon sequencing. Mice were repeatedly exposed to intranasal dust extracts and evaluated for their effects on ovalbumin (OVA)-induced allergic airway inflammation, and gut microbiota restoration was validated by fecal microbiota transplant (FMT) from dust-exposed donor mice. We found that rural children had fewer allergies and unique gut microbiota with fewer Bacteroides and more Prevotella. Indoor dusts in rural environments harbored higher endotoxin level and diversity of bacteria and fungi, whereas indoor urban dusts were enriched with Aspergillus and contained elevated pathogenic bacteria. Intranasal administration of rural dusts before OVA sensitization reduced respiratory eosinophils and blood IgE level in mice and also led to a recovery of gut bacterial diversity and Ruminiclostridium in the mouse model. FMT restored the protective effect by reducing OVA-induced lung eosinophils in recipient mice. Together, these results support a cause-effect relationship between exposure to dust microbiota and allergy susceptibility in children and mice. Specifically, rural environmental exposure modulated the gut microbiota, which was essential in reducing allergy in children from Southern China. Our findings support the notion that the modulation of gut microbiota by exposure to rural indoor dust may improve allergy prevention.}, } @article {pmid36192998, year = {2022}, author = {Ruiz-Rico, M and Renwick, S and Vancuren, SJ and Robinson, AV and Gianetto-Hill, C and Allen-Vercoe, E and Barat, JM}, title = {Influence of free and immobilized chitosan on a defined human gut microbial ecosystem.}, journal = {Food research international (Ottawa, Ont.)}, volume = {161}, number = {}, pages = {111890}, doi = {10.1016/j.foodres.2022.111890}, pmid = {36192998}, issn = {1873-7145}, mesh = {Bacteroidetes/metabolism ; *Chitosan/metabolism ; Clostridium ; Ecosystem ; *Gastrointestinal Microbiome ; Gastrointestinal Tract ; Humans ; }, abstract = {In this work, the influence of different forms of presentation of chitosan in the human gut microbiota with a defined bacterial community was evaluated. First, the susceptibility of individual gut bacterial isolates against chitosan was studied within a concentration range between 0.125 and 1 mg/mL. Then, the impact of chitosan (0.25 and 1 mg/mL) on a defined human gut microbial ecosystem was studied by metagenomic and metabonomic analyses. The results showed that chitosan in its free form had a high impact on individual isolates with a minimum inhibitory concentration below 1 mg/mL for most of the strains studied. In comparison, chitosan immobilized in the different carriers displayed a diverse effect on gut microbiota. The most susceptible strains were Agathobacter rectalis strain 16-6-I 1 FAA, Clostridium spiroforme strain 16-6-I 21 FAA and Mediterraneibacter faecis strain 16-6-I 30 FAA. The impact of the different modes of presentation of chitosan was strain-specific and species-specific when compared to results obtained from analysis of other strains within the genera Agathobacter, Clostridium and Mediterraneibacter, and therefore a study using a defined ecosystem was needed to extrapolate the results. Significant decreases in defined community richness and diversity and changes in metabolic profile were observed after exposure to free chitosan. Free chitosan produced significant reductions in the abundance of the genera Lachnoclostridium, Anaerotignum, Blautia, Enterococcus, Eubacterium and Ruthenibacterium together with a slight decrease of the production of SCFAs, among other fermentation by-products. The immobilized chitosan significantly alleviated the impact caused by the antimicrobial polymer and significantly increased the relative abundance of the Bacteroidetes phylum compared to free chitosan. These results suggest the significance of assessing the impact of new ingredients and materials included in food on the human gut microbiota with models that simulate the gastrointestinal environment, such as in vitro bioreactor systems.}, } @article {pmid36192803, year = {2022}, author = {Ma, S and Shungin, D and Mallick, H and Schirmer, M and Nguyen, LH and Kolde, R and Franzosa, E and Vlamakis, H and Xavier, R and Huttenhower, C}, title = {Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {208}, pmid = {36192803}, issn = {1474-760X}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R24DK110499/DK/NIDDK NIH HHS/United States ; P30DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases ; *Microbiota ; }, abstract = {Microbiome studies of inflammatory bowel diseases (IBD) have achieved a scale for meta-analysis of dysbioses among populations. To enable microbial community meta-analyses generally, we develop MMUPHin for normalization, statistical meta-analysis, and population structure discovery using microbial taxonomic and functional profiles. Applying it to ten IBD cohorts, we identify consistent associations, including novel taxa such as Acinetobacter and Turicibacter, and additional exposure and interaction effects. A single gradient of dysbiosis severity is favored over discrete types to summarize IBD microbiome population structure. These results provide a benchmark for characterization of IBD and a framework for meta-analysis of any microbial communities.}, } @article {pmid36190138, year = {2022}, author = {Weissman, JL and Peras, M and Barnum, TP and Fuhrman, JA}, title = {Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0074522}, pmid = {36190138}, issn = {2379-5077}, mesh = {Humans ; *Metagenome/genetics ; Benchmarking ; Codon Usage ; *Microbiota/genetics ; }, abstract = {Trait inference from mixed-species assemblages is a central problem in microbial ecology. Frequently, sequencing information from an environment is available, but phenotypic measurements from individual community members are not. With the increasing availability of molecular data for microbial communities, bioinformatic approaches that map metagenome to (meta)phenotype are needed. Recently, we developed a tool, gRodon, that enables the prediction of the maximum growth rate of an organism from genomic data on the basis of codon usage patterns. Our work and that of other groups suggest that such predictors can be applied to mixed-species communities in order to derive estimates of the average community-wide maximum growth rate. Here, we present an improved maximum growth rate predictor designed for metagenomes that corrects a persistent GC bias in the original gRodon model for metagenomic prediction. We benchmark this predictor with simulated metagenomic data sets to show that it has superior performance on mixed-species communities relative to earlier models. We go on to provide guidance on data preprocessing and show that calling genes from assembled contigs rather than directly from reads dramatically improves performance. Finally, we apply our predictor to large-scale metagenomic data sets from marine and human microbiomes to illustrate how community-wide growth prediction can be a powerful approach for hypothesis generation. Altogether, we provide an updated tool with clear guidelines for users about the uses and pitfalls of metagenomic prediction of the average community-wide maximal growth rate. IMPORTANCE Microbes dominate nearly every known habitat, and therefore tools to survey the structure and function of natural microbial communities are much needed. Metagenomics, in which the DNA content of an entire community of organisms is sequenced all at once, allows us to probe the genetic diversity contained in a habitat. Yet, mapping metagenomic information to the actual traits of community members is a difficult and largely unsolved problem. Here, we present and validate a tool that allows users to predict the average maximum growth rate of a microbial community directly from metagenomic data. Maximum growth rate is a fundamental characteristic of microbial species that can give us a great deal of insight into their ecological role, and by applying our community-level predictor to large-scale metagenomic data sets from marine and human-associated microbiomes, we show how community-wide growth prediction can be a powerful approach for hypothesis generation.}, } @article {pmid36189350, year = {2022}, author = {Sakai, SA and Aoshima, M and Sawada, K and Horasawa, S and Yoshikawa, A and Fujisawa, T and Kadowaki, S and Denda, T and Matsuhashi, N and Yasui, H and Goto, M and Yamazaki, K and Komatsu, Y and Nakanishi, R and Nakamura, Y and Bando, H and Hamaya, Y and Kageyama, SI and Yoshino, T and Tsuchihara, K and Yamashita, R}, title = {Fecal microbiota in patients with a stoma decreases anaerobic bacteria and alters taxonomic and functional diversities.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {925444}, pmid = {36189350}, issn = {2235-2988}, mesh = {Bacteria, Anaerobic/genetics/metabolism ; *Colorectal Neoplasms/microbiology/surgery ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Humans ; Methane ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Colorectal cancer (CRC) is one of the most common malignant diseases. Generally, stoma construction is performed following surgery for the resection of the primary tumor in patients with CRC. The association of CRC with the gut microbiota has been widely reported, and the gut microbiota is known to play an important role in the carcinogenesis, progression, and treatment of CRC. In this study, we compared the microbiota of patients with CRC between with and without a stoma using fecal metagenomic sequencing data from SCRUM-Japan MONSTAR-SCREEN, a joint industry-academia cancer research project in Japan. We found that the composition of anaerobes was reduced in patients with a stoma. In particular, the abundance of Alistipes, Akkermansia, Intestinimonas, and methane-producing archaea decreased. We also compared gene function (e.g., KEGG Orthology and KEGG pathway) and found that gene function for methane and short-chain fatty acids (SCFAs) production was underrepresented in patients with a stoma. Furthermore, a stoma decreased Shannon diversity based on taxonomic composition but increased that of the KEGG pathway. These results suggest that the feces of patients with a stoma have a reduced abundance of favorable microbes for cancer immunotherapy. In conclusion, we showed that a stoma alters the taxonomic and functional profiles in feces and may be a confounding factor in fecal microbiota analysis.}, } @article {pmid36189343, year = {2022}, author = {Lv, LJ and Li, SH and Wen, JY and Wang, GY and Li, H and He, TW and Lv, QB and Xiao, MC and Duan, HL and Chen, MC and Yi, ZT and Yan, QL and Yin, AH}, title = {Deep metagenomic characterization of gut microbial community and function in preeclampsia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {933523}, pmid = {36189343}, issn = {2235-2988}, mesh = {Bacitracin ; *Bacteriocins ; Biomarkers ; Chlorophyll ; Dysbiosis ; Feces/microbiology ; Female ; Folic Acid ; Humans ; Metagenome ; *Microbiota ; *Porphyrins ; *Pre-Eclampsia ; Pregnancy ; Pyridoxal Phosphate ; RNA, Ribosomal, 16S/genetics ; Rhamnose ; Riboflavin ; }, abstract = {Preeclampsia (PE) is a pregnancy complication characterized by severe hypertension and multiple organ damage. Gut microbiota has been linked to PE by previous amplicon sequencing studies. To resolve the PE gut microbiota in a higher taxonomy resolution, we performed shotgun metagenomic sequencing on the fecal samples from 40 early-onset PE and 37 healthy pregnant women. We recovered 1,750 metagenome-assembled genomes (representing 406 species) from the metagenomic dataset and profiled their abundances. We found that PE gut microbiota had enriched in some species belonging to Blautia, Pauljensenia, Ruminococcus, and Collinsella and microbial functions such as the bacitracin/lantibiotics transport system, maltooligosaccharide transport system, multidrug efflux pump, and rhamnose transport system. Conversely, the gut microbiome of healthy pregnant women was enriched in species of Bacteroides and Phocaeicola and microbial functions including the porphyrin and chlorophyll metabolism, pyridoxal-P biosynthesis, riboflavin metabolism, and folate biosynthesis pathway. PE diagnostic potential of gut microbial biomarkers was developed using both species and function profile data. These results will help to explore the relationships between gut bacteria and PE and provide new insights into PE early warning.}, } @article {pmid36189246, year = {2022}, author = {Santiago-Rodriguez, TM and Hollister, EB}, title = {Unraveling the viral dark matter through viral metagenomics.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1005107}, pmid = {36189246}, issn = {1664-3224}, mesh = {Computational Biology ; Genome, Viral ; Metagenomics ; *Microbiota ; *Viruses/genetics ; }, abstract = {Viruses are part of the microbiome and have essential roles in immunology, evolution, biogeochemical cycles, health, and disease progression. Viruses influence a wide variety of systems and processes, and the continued discovery of novel viruses is anticipated to reveal new mechanisms influencing the biology of diverse environments. While the identity and roles of viruses continue to be discovered and understood through viral metagenomics, most of the sequences in virome datasets cannot be attributed to known viruses or may be only distantly related to species already described in public sequence databases, at best. Such viruses are known as the viral dark matter. Ongoing discoveries from the viral dark matter have provided insights into novel viruses from a variety of environments, as well as their potential in immunological processes, virus evolution, health, disease, therapeutics, and surveillance. Increased understanding of the viral dark matter will continue with a combination of cultivation, microscopy, sequencing, and bioinformatic efforts, which are discussed in the present review.}, } @article {pmid36188134, year = {2022}, author = {Tran, DM and Huynh, TU and Nguyen, TH and Do, TO and Nguyen, QV and Nguyen, AD}, title = {Metagenomic next-generation sequencing of the microbiome dataset from the surface water sample collected from Serepok River in Yok Don National Park, Vietnam.}, journal = {Data in brief}, volume = {45}, number = {}, pages = {108614}, pmid = {36188134}, issn = {2352-3409}, abstract = {The Central Highlands region is considered as the center with the highest biodiversity in Vietnam because it has the majority of national parks such as Yok Don, Chu Yang Sin, Bidoup-Nui Ba, Ta Dung, Chu Mon Ray, and Kon Ka Kinh and nature reserves such as Ngoc Linh, Kon Chu Rang, Ea So, Nam Ka, and Nam Nung with different ecosystems [1]. Of the national parks and nature reserves, Yok Don has the most different ecosystem. Yok Don is the second biggest national park, and it is the only national park that conserves dry deciduous dipterocarp forests in Vietnam [2]. Presently, the decrease in forest area and global warming have led to the continuous reduction in microbial resources in this region. Thus, a dataset of the soil microbiome in this region has been established to explore microbial resources for conservation and further application in sustainable agricultural production in this region [3]; however, to the best of our knowledge, a dataset of water microbiome remains unknown. This work presented a microbiome dataset from surface water samples collected from Serepok River in Yok Don National Park, Vietnam. Metagenomic next-generation sequencing was used to characterize microbial communities in the sample. The raw sequence in this work was uploaded in Fastq format on NCBI, which can be accessed at https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA853090. This metagenome dataset can provide valuable information on surface water microbial communities and their functionality. It can also be used for further studies on the conservation and application of indigenous microbial resources for sustainable crop production in this region.}, } @article {pmid36184671, year = {2022}, author = {Armbrecht, L and Weber, ME and Raymo, ME and Peck, VL and Williams, T and Warnock, J and Kato, Y and Hernández-Almeida, I and Hoem, F and Reilly, B and Hemming, S and Bailey, I and Martos, YM and Gutjahr, M and Percuoco, V and Allen, C and Brachfeld, S and Cardillo, FG and Du, Z and Fauth, G and Fogwill, C and Garcia, M and Glüder, A and Guitard, M and Hwang, JH and Iizuka, M and Kenlee, B and O'Connell, S and Pérez, LF and Ronge, TA and Seki, O and Tauxe, L and Tripathi, S and Zheng, X}, title = {Ancient marine sediment DNA reveals diatom transition in Antarctica.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5787}, pmid = {36184671}, issn = {2041-1723}, mesh = {Antarctic Regions ; DNA, Ancient ; *Diatoms/genetics ; Ecosystem ; Eukaryota ; Geologic Sediments ; }, abstract = {Antarctica is one of the most vulnerable regions to climate change on Earth and studying the past and present responses of this polar marine ecosystem to environmental change is a matter of urgency. Sedimentary ancient DNA (sedaDNA) analysis can provide such insights into past ecosystem-wide changes. Here we present authenticated (through extensive contamination control and sedaDNA damage analysis) metagenomic marine eukaryote sedaDNA from the Scotia Sea region acquired during IODP Expedition 382. We also provide a marine eukaryote sedaDNA record of ~1 Mio. years and diatom and chlorophyte sedaDNA dating back to ~540 ka (using taxonomic marker genes SSU, LSU, psbO). We find evidence of warm phases being associated with high relative diatom abundance, and a marked transition from diatoms comprising <10% of all eukaryotes prior to ~14.5 ka, to ~50% after this time, i.e., following Meltwater Pulse 1A, alongside a composition change from sea-ice to open-ocean species. Our study demonstrates that sedaDNA tools can be expanded to hundreds of thousands of years, opening the pathway to the study of ecosystem-wide marine shifts and paleo-productivity phases throughout multiple glacial-interglacial cycles.}, } @article {pmid36184305, year = {2023}, author = {Lockwood, MB and Chlipala, GE and Maeinschein-Cline, M and DeVon, HA and Lichvar, AB and Samra, MK and Park, CG and Campara, M and Doorenbos, AZ and Tussing-Humphreys, LM and Spaggiari, M and Bronas, UG and Steel, JL and Green, SS}, title = {Pain Interference in End Stage Kidney Disease is Associated with Changes in Gut Microbiome Features Before and After Kidney Transplantation.}, journal = {Pain management nursing : official journal of the American Society of Pain Management Nurses}, volume = {24}, number = {1}, pages = {68-77}, pmid = {36184305}, issn = {1532-8635}, support = {U01 DK123787/DK/NIDDK NIH HHS/United States ; K23 NR018482/NR/NINR NIH HHS/United States ; K24 AT011995/AT/NCCIH NIH HHS/United States ; UL1 TR002003/TR/NCATS NIH HHS/United States ; L30 NR020114/NR/NINR NIH HHS/United States ; }, mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Gastrointestinal Microbiome/genetics ; *Kidney Failure, Chronic ; Feces ; Pain ; Inflammation ; }, abstract = {BACKGROUND: Pain, a common debilitating symptom among kidney transplant recipients (KTRs), is among the most common and undertreated symptoms after kidney transplantation.

AIMS: Characterize associations between gut microbiome features and pain interference before and after kidney transplantation.

DESIGN: Longitudinal, repeated measures study, collecting fecal specimens and pain interference data pretransplant and 3 months posttransplant.

SETTING: Participants were recruited at the kidney transplant clinic at the University of Illinois Hospital & Health Sciences System.

PARTICIPANTS/SUBJECTS: 19 living donor kidney transplant recipients.

METHODS: We assessed fecal microbial community structure with shotgun metagenomic sequencing; we used pain interference scores derived from the Patient-Reported Outcomes Measurement Information System-57.

RESULTS: We measured a reduction in the Shannon diversity index in both groups after transplantation but observed no significant differences between groups at either time point. We did observe significant differences in fecal microbial Bray-Curtis similarity index among those reporting pain interference pre- transplant versus no pain interference at 3-months posttransplant (R = .306, p = .022), and between pain interference groups at posttransplant (R = .249, p = .041). Pairwise models showed significant differences between groups posttransplant in relative abundances of several taxa, including a 5-fold reduction.ßin Akkermansia among those with pain interference and a higher relative abundance of taxa associated with chronic inflammation in those with pain interference posttransplant. Functional gene analysis identified two features that were significantly enriched in those with pain interference, including a peptide transport system gene.

CONCLUSIONS: Gut microbiota community structure differs between groups with and without pain interference at 3 months after kidney transplantation. Several taxa involved in intestinal barrier integrity and chronic inflammation were associated with posttransplant pain.}, } @article {pmid36182984, year = {2022}, author = {Öztürk, Hİ and Demirci, T and Akın, N and Oğul, A}, title = {Elucidation of the initial bacterial community of Ezine PDO cheese using next-generation sequencing.}, journal = {Archives of microbiology}, volume = {204}, number = {10}, pages = {656}, pmid = {36182984}, issn = {1432-072X}, mesh = {Animals ; *Cheese/microbiology ; Food Microbiology ; High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; Milk/microbiology ; Streptococcus thermophilus/genetics ; }, abstract = {This study aims to reveal initial bacterial consortia of Ezine PDO cheeses comprehensively by following a metagenomic approach. A total of 8 artisanal Ezine cheese samples were collected from the Bayramiç and Ezine districts of Çanakkale province of Turkey. Ezine cheese was found to contain Firmicutes, Bacteroidetes, and Proteobacteria phyla dominantly. Streptococcus, Lactococcus, and Lactobacillus genera dominated the microbiota with relative abundances of 4.47-56.07%, 7.33-20.34%, and 1.21-25.12%, respectively, followed by Bacteroides and Prevotella genera. Excluding two cheese samples obtained from the Ezine district, the most dominant species was Streptococcus thermophilus (8.24-54.34%). It was also found in greater proportions in the cheeses of the Bayramiç district. Unexpectedly, Lactobacillus graminis (11.50-23.63%) was the most abundant species in two samples collected from the Ezine district. However, lower bacterial diversity was determined in the samples collected from the Bayramiç district. The lowest species richness was 129 OTU-species in the cheeses from the Bayramiç district while the highest species richness was 267 OTU-species in cheeses from the Ezine district. In addition, the Simpson index was the highest in cheeses from the Ezine district, where different species were evenly distributed. Permutational multivariate analysis of variance tests also confirmed that the differences in the structure of bacterial consortia in cheeses from two different districts were statistically significant. This study will provide pioneer data for further investigations on the role of complex bacterial composition in maintaining and improving the quality and safety of Ezine cheese.}, } @article {pmid36182913, year = {2022}, author = {Tian, J and Hou, X and Ge, M and Xu, H and Yu, B and Liu, J and Shao, R and Holmes, EC and Lei, C and Shi, M}, title = {The diversity and evolutionary relationships of ticks and tick-borne bacteria collected in China.}, journal = {Parasites & vectors}, volume = {15}, number = {1}, pages = {352}, pmid = {36182913}, issn = {1756-3305}, support = {20142BBG70097//"Medical youth top talent project of Hubei" Fellowship and Science and Technology Project of Jiangxi/ ; FL170100022//Australian Research Council Australia Laureate Fellowship/ ; KQTD20200820145822023//Shenzhen Science and Technology Program/ ; 2019ZT08Y464//Guangdong Province "Pearl River Talent Plan" Innovation and Entrepreneurship Team Project/ ; }, mesh = {Animals ; *Borrelia/genetics ; Coxiella/genetics ; DNA, Mitochondrial/genetics ; Humans ; *Ixodes/microbiology ; *Rickettsia/genetics ; *Tick-Borne Diseases/epidemiology/microbiology ; }, abstract = {BACKGROUND: Ticks (order Ixodida) are ectoparasites, vectors and reservoirs of many infectious agents affecting humans and domestic animals. However, the lack of information on tick genomic diversity leaves significant gaps in the understanding of the evolution of ticks and associated bacteria.

RESULTS: We collected > 20,000 contemporary and historical (up to 60 years of preservation) tick samples representing a wide range of tick biodiversity across diverse geographic regions in China. Metagenomic sequencing was performed on individual ticks to obtain the complete or near-complete mitochondrial (mt) genome sequences from 46 tick species, among which mitochondrial genomes of 23 species were recovered for the first time. These new mt genomes data greatly expanded the diversity of many tick groups and revealed five cryptic species. Utilizing the same metagenomic sequence data we identified divergent and abundant bacteria in Haemaphysalis, Ixodes, Dermacentor and Carios ticks, including nine species of pathogenetic bacteria and potentially new species within the genus Borrelia. We also used these data to explore the evolutionary relationship between ticks and their associated bacteria, revealing a pattern of long-term co-divergence relationship between ticks and Rickettsia and Coxiella bacteria.

CONCLUSIONS: In sum, our study provides important new information on the genetic diversity of ticks based on an analysis of mitochondrial DNA as well as on the prevalence of tick-borne pathogens in China. It also sheds new light on the long-term evolutionary and ecological relationships between ticks and their associated bacteria.}, } @article {pmid36182683, year = {2022}, author = {Neugent, ML and Kumar, A and Hulyalkar, NV and Lutz, KC and Nguyen, VH and Fuentes, JL and Zhang, C and Nguyen, A and Sharon, BM and Kuprasertkul, A and Arute, AP and Ebrahimzadeh, T and Natesan, N and Xing, C and Shulaev, V and Li, Q and Zimmern, PE and Palmer, KL and De Nisco, NJ}, title = {Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome.}, journal = {Cell reports. Medicine}, volume = {3}, number = {10}, pages = {100753}, pmid = {36182683}, issn = {2666-3791}, support = {R01 DK131267/DK/NIDDK NIH HHS/United States ; }, mesh = {Female ; Humans ; Postmenopause ; *Urinary Tract Infections/drug therapy ; Estrogens ; *Microbiota/genetics ; Lactobacillus ; *Anti-Infective Agents ; }, abstract = {Postmenopausal women are severely affected by recurrent urinary tract infection (rUTI). The urogenital microbiome is a key component of the urinary environment. However, changes in the urogenital microbiome underlying rUTI susceptibility are unknown. Here, we perform shotgun metagenomics and advanced culture on urine from a controlled cohort of postmenopausal women to identify urogenital microbiome compositional and function changes linked to rUTI susceptibility. We identify candidate taxonomic biomarkers of rUTI susceptibility in postmenopausal women and an enrichment of lactobacilli in postmenopausal women taking estrogen hormone therapy. We find robust correlations between Bifidobacterium and Lactobacillus and urinary estrogens in women without urinary tract infection (UTI) history. Functional analyses reveal distinct metabolic and antimicrobial resistance gene (ARG) signatures associated with rUTI. Importantly, we find that ARGs are enriched in the urogenital microbiomes of women with rUTI history independent of current UTI status. Our data suggest that rUTI and estrogen shape the urogenital microbiome in postmenopausal women.}, } @article {pmid36182642, year = {2023}, author = {Lin, CH and Lai, HC and Wu, MS}, title = {Gut-oriented disease modifying therapy for Parkinson's disease.}, journal = {Journal of the Formosan Medical Association = Taiwan yi zhi}, volume = {122}, number = {1}, pages = {9-18}, doi = {10.1016/j.jfma.2022.09.010}, pmid = {36182642}, issn = {0929-6646}, mesh = {Humans ; *Parkinson Disease/therapy ; *Gastrointestinal Microbiome/physiology ; *Enteric Nervous System/metabolism ; }, abstract = {Neuropathology studies have shown that the pathognomonic feature of Parkinson's disease (PD), one of the most common neurodegenerative disorders, may start from the gut enteric nervous system and then spread to the central dopaminergic neurons through the gut-brain axis. With the advent of metagenomic sequencing and metabolomic analysis, a plethora of evidence has revealed different gut microbiomes and gut metabolites in patients with PD compared with unaffected controls. Currently, although dopaminergic treatments and deep brain stimulation can provide some symptomatic benefits for motor symptoms of the disease, their long-term use is problematic. A mechanism-targeted therapy to halt the neurodegeneration is lacking. The recently observed gut microenvironmental changes in the early stages of the disease play a vital role in the PD pathogenesis. Patients whose disease begins in the gut may benefit most from interventions that target the gut microenvironments. In this review, we will summarize the current studies demonstrating multifunctional roles of gut microbiota in the gut-brain axis of PD and the currently available evidence for targeting the gut microbiota as a novel approach to potential disease-modifying therapy in PD.}, } @article {pmid36181699, year = {2023}, author = {Hu, M and Le, Y and Sardans, J and Yan, R and Zhong, Y and Sun, D and Tong, C and Peñuelas, J}, title = {Moderate salinity improves the availability of soil P by regulating P-cycling microbial communities in coastal wetlands.}, journal = {Global change biology}, volume = {29}, number = {1}, pages = {276-288}, doi = {10.1111/gcb.16465}, pmid = {36181699}, issn = {1365-2486}, support = {SGR2017-1005//Catalan Government/ ; CIVP20A6621//Fundación Ramón Areces/ ; 42171102//National Natural Science Foundation of China/ ; 2021J01177//Natural Science Foundation of Fujian Province/ ; PID2020-115770RB-I00//Spanish Government/ ; }, mesh = {*Wetlands ; Soil ; Salinity ; *Microbiota ; Fresh Water ; }, abstract = {Accelerated sea-level rise is expected to cause the salinization of freshwater wetlands, but the responses to salinity of the availability of soil phosphorus (P) and of microbial genes involved in the cycling of P remain unexplored. We conducted a field experiment to investigate the effects of salinity on P cycling by soil microbial communities and their regulatory roles on P availability in coastal freshwater and brackish wetlands. Salinity was positively correlated with P availability, with higher concentrations of labile P but lower concentrations of moderately labile P in the brackish wetland. The diversity and richness of microbial communities involved in P cycling were higher in the brackish wetland than the freshwater wetland. Salinity substantially altered the composition of the P-cycling microbial community, in which those of the brackish wetland were separated from those of the freshwater wetland. Metagenomic sequence analysis indicated that functional genes involved in the solubilization of inorganic P and the subsequent transport and regulation of P were more abundant in coastal soils. The relative abundances of most of the target genes differed between the wetlands, with higher abundances of P-solubilization (gcd and ppa) and -mineralization (phoD, phy, and ugpQ) genes and lower abundances of P-transport genes (pstB, ugpA, ugpB, ugpE, and pit) in the brackish wetland. A significant positive correlation between the concentration of labile P and the abundances of the target genes suggested that salinity may, at least in part, improve P availability by regulating the P-cycling microbial community. Our results suggest that the P-cycling microbial community abundance and P availability respond positively to moderate increases in salinity by promoting the microbial solubilization and mineralization of soil P. Changes in microbial communities and microbially mediated P cycling may represent microbial strategies to adapt to moderate salinity levels, which in turn control soil function and nutrient balance.}, } @article {pmid36181381, year = {2022}, author = {Ma, X and Brinker, E and Cao, W and Graff, EC and Wang, X}, title = {Effect of mineral oil as a lubricant to collect feces from cats for microbiome studies.}, journal = {Journal of veterinary internal medicine}, volume = {36}, number = {6}, pages = {1974-1980}, pmid = {36181381}, issn = {1939-1676}, support = {//Alabama Agriculture Experiment Station/ ; //Auburn University College of Veterinary Medicine Animal Health and Disease Research/ ; 180254//Auburn University Intramural Grant Program/ ; EC22-023//EveryCat Health Foundation/ ; 1928770//National Science Foundation/ ; 1018100//USDA National Institute of Food and Agriculture/ ; }, mesh = {Male ; Cats ; Animals ; *Mineral Oil ; Lubricants ; Cohort Studies ; Feces ; *Microbiota ; DNA ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Fecal specimens are critical for disease screening, diagnosis, and gut microbiome research. For domestic cats, lubricants are often necessary to obtain a sufficient quantity of sample. However, the effect of lubrication on feline microbiome analysis has not been assessed.

OBJECTIVES: To evaluate if lubrication using mineral oil during cat feces sample collection affects the DNA extraction, metagenomic sequencing yield, and the microbial composition and diversity in subsequent gut microbiome analyses.

ANIMALS: Eight 6-year-old male, neutered, domestic short-haired cats housed in a research facility.

METHODS: Cohort study. The gut microbiomes were investigated for fecal sample collection with and without lubrication using whole-genome shotgun metagenomic sequencing.

RESULTS: Fecal specimens were collected using a fecal loop under sedation without lubrication and with mineral oil lubrication. There were no significant differences between the 2 groups in the microbial DNA yield in ng/mg fecal sample (75.75 [25.8-125.7] vs 60.72 [33.49-87.95], P = .95), metagenomic sequencing yield in Gbp (10.31 [6.29-14.32] vs 13.53 [12.04-15.02], P = .2), proportion of host contamination (0.1 [0.02-0.18] vs 0.15 [0-0.3], P = .84), relative taxonomy abundance (P > .8), or the number of microbial genes covered (408 132 [341 556-474 708] vs 425 697 [358 505-492 889], P = .31).

Fecal sampling with mineral oil lubrication did not change the microbial DNA extraction yield, metagenomic sequencing yield, level of host contamination, the microbial composition and diversity in subsequent gut microbiome analyses. Here we reported a proven cat-friendly protocol for fecal sample collection in clinical and research setting for gut microbiome analyses.}, } @article {pmid36179670, year = {2022}, author = {Narunsky-Haziza, L and Sepich-Poore, GD and Livyatan, I and Asraf, O and Martino, C and Nejman, D and Gavert, N and Stajich, JE and Amit, G and González, A and Wandro, S and Perry, G and Ariel, R and Meltser, A and Shaffer, JP and Zhu, Q and Balint-Lahat, N and Barshack, I and Dadiani, M and Gal-Yam, EN and Patel, SP and Bashan, A and Swafford, AD and Pilpel, Y and Knight, R and Straussman, R}, title = {Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions.}, journal = {Cell}, volume = {185}, number = {20}, pages = {3789-3806.e17}, pmid = {36179670}, issn = {1097-4172}, support = {DP1 AT010885/AT/NCCIH NIH HHS/United States ; HHSN261201500003C/CA/NCI NIH HHS/United States ; HHSN261201400008C/CA/NCI NIH HHS/United States ; U24 CA248454/CA/NCI NIH HHS/United States ; HHSN261201500003I/CA/NCI NIH HHS/United States ; P50 DA026306/DA/NIDA NIH HHS/United States ; U24 DK131617/DK/NIDDK NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; F30 CA243480/CA/NCI NIH HHS/United States ; R01 DA026334/DA/NIDA NIH HHS/United States ; P01 DA012065/DA/NIDA NIH HHS/United States ; R00 AA020235/AA/NIAAA NIH HHS/United States ; P30 MH062512/MH/NIMH NIH HHS/United States ; }, mesh = {DNA, Fungal/analysis ; Fungi/genetics ; Humans ; *Mycobiome ; *Neoplasms ; }, abstract = {Cancer-microbe associations have been explored for centuries, but cancer-associated fungi have rarely been examined. Here, we comprehensively characterize the cancer mycobiome within 17,401 patient tissue, blood, and plasma samples across 35 cancer types in four independent cohorts. We report fungal DNA and cells at low abundances across many major human cancers, with differences in community compositions that differ among cancer types, even when accounting for technical background. Fungal histological staining of tissue microarrays supported intratumoral presence and frequent spatial association with cancer cells and macrophages. Comparing intratumoral fungal communities with matched bacteriomes and immunomes revealed co-occurring bi-domain ecologies, often with permissive, rather than competitive, microenvironments and distinct immune responses. Clinically focused assessments suggested prognostic and diagnostic capacities of the tissue and plasma mycobiomes, even in stage I cancers, and synergistic predictive performance with bacteriomes.}, } @article {pmid36179649, year = {2022}, author = {Liu, J and Wang, J and Zhou, Y and Han, H and Liu, W and Li, D and Li, F and Cao, D and Lei, Q}, title = {Integrated omics analysis reveals differences in gut microbiota and gut-host metabolite profiles between obese and lean chickens.}, journal = {Poultry science}, volume = {101}, number = {11}, pages = {102165}, pmid = {36179649}, issn = {1525-3171}, mesh = {Animals ; *Chickens ; *Gastrointestinal Microbiome ; Obesity/genetics/veterinary ; Abdominal Fat/metabolism ; Adipose Tissue/metabolism ; }, abstract = {Abdominal fat is the major adipose tissue in chickens. In chicken, the deposition of abdominal fat affects meat yield and quality. Previous reports suggest that gut microbiota composition and function are associated with lipid metabolism. In this study, we used comparative metagenomics and metabolomics analysis to determine the gut microbiota and gut-host metabolite profiles in Shouguang (SG; a Chinese chicken breed with low-fat deposition) and Luqin (LQ; a fatty-type chicken breed with a fast growth rate) chickens. The results showed that LQ chickens had higher body weight, eviscerated yield, abdominal fat yield, abdominal fat ratio, and triglyceride (TG) content in the breast muscle than SG chickens. Untargeted metabolomics analyses showed a total of 11 liver metabolites, 19 plasma metabolites, and 30 cecal metabolites differentially enriched in LQ and SG chickens based on variable importance in the projection (VIP) ≥ 1 and P ≤ 0.05. These metabolites are involved in lipid and amino acid metabolism. The relative abundance of bacteria in the microbiota differed significantly between the 2 chicken breeds. The functional prediction of microbiota abundant in LQ chickens was starch and lactose degradation. Erysipelatoclostridium was abundant in LQ chickens and significantly positively correlated to palmitoyl ethanolamide (PEA), a key regulator of lipid metabolism. Our findings revealed differences in liver and plasma metabolites between chicken breeds with different adipose deposition capacities. Long-chain acylcarnitines might be important markers of adipose deposition differences in chickens. The cecum's microbial communities and metabolome profiles significantly differed between LQ and SG chickens. However, the relationship between cecal microbiota and their metabolites and liver and plasma metabolites is not thoroughly understood. Future research will focus on relating tissue metabolite changes to intestinal microbiota and their effects on body fat deposition.}, } @article {pmid36179077, year = {2022}, author = {Douglas, GM and Hayes, MG and Langille, MGI and Borenstein, E}, title = {Integrating phylogenetic and functional data in microbiome studies.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {22}, pages = {5055-5063}, pmid = {36179077}, issn = {1367-4811}, mesh = {Phylogeny ; *Microbiota/genetics ; Metagenomics ; Software ; }, abstract = {MOTIVATION: Microbiome functional data are frequently analyzed to identify associations between microbial functions (e.g. genes) and sample groups of interest. However, it is challenging to distinguish between different possible explanations for variation in community-wide functional profiles by considering functions alone. To help address this problem, we have developed POMS, a package that implements multiple phylogeny-aware frameworks to more robustly identify enriched functions.

RESULTS: The key contribution is an extended balance-tree workflow that incorporates functional and taxonomic information to identify functions that are consistently enriched in sample groups across independent taxonomic lineages. Our package also includes a workflow for running phylogenetic regression. Based on simulated data we demonstrate that these approaches more accurately identify gene families that confer a selective advantage compared with commonly used tools. We also show that POMS in particular can identify enriched functions in real-world metagenomics datasets that are potential targets of strong selection on multiple members of the microbiome.

These workflows are freely available in the POMS R package at https://github.com/gavinmdouglas/POMS.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36178961, year = {2022}, author = {Jung, TH and Hwang, HJ and Han, KS}, title = {Correlation of attention deficit hyperactivity disorder with gut microbiota according to the dietary intake of Korean elementary school students.}, journal = {PloS one}, volume = {17}, number = {9}, pages = {e0275520}, pmid = {36178961}, issn = {1932-6203}, mesh = {Animals ; *Attention Deficit Disorder with Hyperactivity/epidemiology ; Butyrates ; Eating ; Fatty Acids, Volatile ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Republic of Korea/epidemiology ; Students ; }, abstract = {We investigated the impact of dietary patterns on the gut microbiota and concentration of short-chain fatty acids in the feces of Korean elementary school students. The dietary intake and ADHD assessment of 40 Korean elementary school students were analyzed using a dish-based semi-quantitative food frequency questionnaire. Analysis of gut microbiota and short-chain fatty acids composition were performed using the real-time polymerase chain reaction, metagenomics, and gas chromatography methods. The dietary patterns of participants were divided into four groups: healthy, processed food, fish and shellfish, and meat. The participants were also divided into two groups according to their ADHD scores: 0-30, control group; over 30, ADHD group. The ADHD score of the processed food group was significantly higher than that of the healthy group. The processed food and ADHD groups showed significantly higher abundance of harmful bacteria, such as the Enterobacter, Escherichia coli, and Clostridium strains, and markedly lower abundance of beneficial bacteria, such as the Bifidobacterium and Ruminococcus strains, than the control group. The heat maps of metagenomics indicated that each group was separated into distinct clusters, and the processed food and ADHD groups showed significantly lower α-diversity of gut microbiota than the control group. In these groups, the concentration of acetate or butyrate in the feces was significantly lower than that in the control group. These results may indicate that imbalanced diets can disturb the colonic microbial balance and are likely to become a potential risk factor for the prevalence of ADHD.}, } @article {pmid36175462, year = {2022}, author = {Morozova, MV and Borisova, MA and Snytnikova, OA and Achasova, KM and Litvinova, EA and Tsentalovich, YP and Kozhevnikova, EN}, title = {Colitis-associated intestinal microbiota regulates brain glycine and host behavior in mice.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {16345}, pmid = {36175462}, issn = {2045-2322}, mesh = {Animals ; Brain ; Choline ; *Colitis ; *Fabaceae ; Female ; *Gastrointestinal Microbiome ; Glycine ; Inflammation ; *Inflammatory Bowel Diseases ; Male ; Mice ; Receptors, N-Methyl-D-Aspartate ; }, abstract = {Inflammatory bowel diseases (IBD) are chronic and relapsing inflammatory disorders of the gastrointestinal tract with complex etiology and no strategies for complete cure. IBD are often complicated by mental disorders like anxiety and depression, indicating substantial shifts in the microbiota gut-brain axis. However, the mechanisms connecting IBD to mental diseases are still under debate. Here we use Muc2 knockout mouse model of chronic colitis to uncouple the effects of the intestinal microbiota on host behavior from chronic inflammation in the gut. Muc2 knockout male mice exhibit high exploratory activity, reduced anxiety-related behaviors, impaired sensorimotor gating, and altered social preference towards males and females. Microbial transfer to wild-type mice via littermate co-housing shows that colitis-associated microbiota rather than inflammation per se defines behavioral features in Muc2 colitis model. Metagenomic profiling and combination of antibiotic treatments revealed that bacterial species Akkermansia muciniphila is associated with the behavioral phenotype in mutants, and that its intestinal abundance correlates with social preference towards males. Metabolomic analysis together with pharmacological inhibition of Gly and NMDA receptors helped us to determine that brain glycine is responsible for the behavioral phenotype in Muc2 mice. Blood and brain metabolic profiles suggest that microbiota-dependent changes in choline metabolism might be involved in regulation of central glycine neurotransmission. Taken together, our data demonstrates that colitis-associated microbiota controls anxiety, sensorimotor gating and social behavior via metabolic regulation of the brain glycinergic system, providing new venues to combat neurological complications of IBD.}, } @article {pmid36175428, year = {2022}, author = {Peters, SL and Borges, AL and Giannone, RJ and Morowitz, MJ and Banfield, JF and Hettich, RL}, title = {Experimental validation that human microbiome phages use alternative genetic coding.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5710}, pmid = {36175428}, issn = {2041-1723}, support = {R01 GM103600/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteriophages/genetics ; Chromatography, Liquid ; Codon, Terminator ; Glutamine ; Humans ; *Microbiota/genetics ; Proteomics ; Tandem Mass Spectrometry ; }, abstract = {Previous bioinformatic analyses of metagenomic data have indicated that bacteriophages can use genetic codes different from those of their host bacteria. In particular, reassignment of stop codon TAG to glutamine (a variation known as 'genetic code 15') has been predicted. Here, we use LC-MS/MS-based metaproteomics of human fecal samples to provide experimental evidence of the use of genetic code 15 in two crAss-like phages. Furthermore, the proteomic data from several phage structural proteins supports the reassignment of the TAG stop codon to glutamine late in the phage infection cycle. Thus, our work experimentally validates the expression of genetic code 15 in human microbiome phages.}, } @article {pmid36174929, year = {2023}, author = {Cheng, WY and Liu, WX and Ding, Y and Wang, G and Shi, Y and Chu, ESH and Wong, S and Sung, JJY and Yu, J}, title = {High Sensitivity of Shotgun Metagenomic Sequencing in Colon Tissue Biopsy by Host DNA Depletion.}, journal = {Genomics, proteomics & bioinformatics}, volume = {21}, number = {6}, pages = {1195-1205}, pmid = {36174929}, issn = {2210-3244}, mesh = {Animals ; *Colon/microbiology/pathology ; Mice ; Humans ; *Metagenomics/methods ; Biopsy ; Sequence Analysis, DNA/methods ; Bacteria/genetics/classification/isolation & purification ; Gastrointestinal Microbiome/genetics ; DNA, Bacterial/genetics ; Metagenome/genetics ; High-Throughput Nucleotide Sequencing/methods ; DNA/genetics ; Phylogeny ; }, abstract = {The high host genetic background of tissue biopsies hinders the application of shotgun metagenomic sequencing in characterizing the tissue microbiota. We proposed an optimized method that removed host DNA from colon biopsies and examined the effect on metagenomic analysis. Human or mouse colon biopsies were divided into two groups, with one group undergoing host DNA depletion and the other serving as the control. Host DNA was removed through differential lysis of mammalian and bacterial cells before sequencing. The impact of host DNA depletion on microbiota was compared based on phylogenetic diversity analyses and regression analyses. Removing host DNA enhanced bacterial sequencing depth and improved species discovery, increasing bacterial reads by 2.46 ± 0.20 folds while reducing host reads by 6.80% ± 1.06%. Moreover, 2.40 times more of bacterial species were detected after host DNA depletion. This was confirmed from mouse colon tissues, increasing bacterial reads by 5.46 ± 0.42 folds while decreasing host reads by 10.2% ± 0.83%. Similarly, significantly more bacterial species were detected in the mouse colon tissue upon host DNA depletion (P < 0.001). Furthermore, an increased microbial richness was evident in the host DNA-depleted samples compared with non-depleted controls in human colon biopsies and mouse colon tissues (P < 0.001). Our optimized method of host DNA depletion improves the sensitivity of shotgun metagenomic sequencing in bacteria detection in the biopsy, which may yield a more accurate taxonomic profile of the tissue microbiota and identify bacteria that are important for disease initiation or progression.}, } @article {pmid36174355, year = {2022}, author = {Centurion, VB and Campanaro, S and Basile, A and Treu, L and Oliveira, VM}, title = {Microbiome structure in biofilms from a volcanic island in Maritime Antarctica investigated by genome-centric metagenomics and metatranscriptomics.}, journal = {Microbiological research}, volume = {265}, number = {}, pages = {127197}, doi = {10.1016/j.micres.2022.127197}, pmid = {36174355}, issn = {1618-0623}, mesh = {Antarctic Regions ; Biofilms ; Metagenome ; *Metagenomics/methods ; *Microbiota/genetics ; Reactive Oxygen Species ; }, abstract = {Antarctica is the coldest and driest continent on Earth, characterized by polyextreme environmental conditions, where species adapted form complex networks of interactions. Microbial communities growing in these harsh environments can form biofilms that help the associated species to survive and thrive. A rich body of knowledge describes environmental biofilm communities; however, most studies have focused on dominant community members rather than functional complexity and metabolic potential. To overcome these limitations, the present study used genome-centric metagenomics to describe two biofilm samples subjected to different temperature collected in Deception Island, Maritime Antarctica. The results unraveled a complex biofilm microbiome represented by 180 metagenome-assembled genomes. The potential metabolic interactions were investigated using metabolic flux balance analysis and revealed that purple bacteria are the community members with the highest correlations with other bacteria. Due to their predicted mixotrophic behavior, they may play a crucial role in the microbiome, likely supporting the heterotrophic species in biofilms. Metatranscriptomics results revealed that the chaperone system and proteins counteracting ROS and toxic compounds have a major role in maintaining bacterial cell homeostasis in sediments of volcanic origin.}, } @article {pmid36171758, year = {2022}, author = {Chai, J and Liu, X and Usdrowski, H and Deng, F and Li, Y and Zhao, J}, title = {Geography, niches, and transportation influence bovine respiratory microbiome and health.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {961644}, pmid = {36171758}, issn = {2235-2988}, mesh = {Animals ; Bacteria/genetics ; Cattle ; *Cattle Diseases/microbiology ; Geography ; Lung ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {Bovine respiratory disease (BRD), one of the most common and infectious diseases in the beef industry, is associated with the respiratory microbiome and stressors of transportation. The impacts of the bovine respiratory microbiota on health and disease across different geographic locations and sampling niches are poorly understood, resulting in difficult identification of BRD causes. In this study, we explored the effects of geography and niches on the bovine respiratory microbiome and its function by re-analyzing published metagenomic datasets and estimated the main opportunistic pathogens that changed after transportation. The results showed that diversity, composition, structure, and function of the bovine nasopharyngeal microbiota were different across three worldwide geographic locations. The lung microbiota also showed distinct microbial composition and function compared with nasopharyngeal communities from different locations. Although different signature microbiota for each geographic location were identified, a module with co-occurrence of Mycoplasma species was observed in all bovine respiratory communities regardless of geography. Moreover, transportation, especially long-distance shipping, could increase the relative abundance of BRD-associated pathogens. Lung microbiota from BRD calves shaped clusters dominated with different pathogens. In summary, geography, sampling niches, and transportation are important factors impacting the bovine respiratory microbiome and disease, and clusters of lung microbiota by different bacterial species may explain BRD pathogenesis, suggesting the importance of a deeper understanding of bovine respiratory microbiota in health.}, } @article {pmid36171634, year = {2022}, author = {Carda-Diéguez, M and Moazzez, R and Mira, A}, title = {Functional changes in the oral microbiome after use of fluoride and arginine containing dentifrices: a metagenomic and metatranscriptomic study.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {159}, pmid = {36171634}, issn = {2049-2618}, mesh = {Adult ; Ammonia ; Arginine/therapeutic use ; Bacteria/genetics ; Cariostatic Agents/therapeutic use ; *Dental Caries/prevention & control ; *Dental Plaque ; *Dentifrices/therapeutic use ; Double-Blind Method ; Fluorides/therapeutic use ; Humans ; Metagenome/genetics ; *Microbiota/genetics ; *Periodontitis ; Phosphates/therapeutic use ; Tooth Remineralization ; Toothpastes ; }, abstract = {BACKGROUND: Tooth decay is one of the most prevalent diseases worldwide, and efficient tooth brushing with a fluoride-containing dentifrice is considered fundamental to caries prevention. Fluoride-containing dentifrices have been extensively studied in relation to enamel resistance to demineralization. Arginine (Arg) has also been proposed as a promising prebiotic to promote pH buffering through ammonia production. Here, we present the first metagenomic (DNA sequencing of the whole microbial community) and metatranscriptomic (RNAseq of the same community) analyses of human dental plaque to evaluate the effect of brushing with fluoride (Fl) and a Fl+Arg containing dentifrices on oral microbial composition and activity. Fifty-three patients were enrolled in a longitudinal clinical intervention study with two arms, including 26 caries-active and 27 caries-free adults. After a minimum 1-week washout period, dental plaque samples were collected at this post-washout baseline, 3 months after the use of a 1450-ppm fluoride dentifrice, and after 6 months of using a 1450-ppm fluoride with 1.5% arginine dentifrice.

RESULTS: There was a shift in both the composition and activity of the plaque microbiome after 3 months of brushing with the fluoride-containing toothpaste compared to the samples collected at the 1-week post-washout period, both for caries-active and caries-free sites. Although several caries-associated bacteria were reduced, there was also an increase in several health- and periodontitis-associated bacteria. Over 400 genes changed proportion in the metagenome, and between 180 and 300 genes changed their expression level depending on whether caries-free or caries-active sites were analyzed. The metagenome and metatranscriptome also changed after the subjects brushed with the Fl+Arg dentifrice. There was a further decrease of both caries- and periodontitis-associated organisms. In both caries-free and caries-active sites, a decrease of genes from the arginine biosynthesis pathway was also observed, in addition to an increase in the expression of genes associated with the arginine deiminase pathway, which catabolizes arginine into ammonia, thereby buffering acidic pH. Bacterial richness and diversity were not affected by either of the two treatments in the two arms of the study.

CONCLUSIONS: Our data demonstrate that long-term use of both assayed dentifrices changes the bacterial composition and functional profiles of human dental plaque towards a healthier microbial community, both in caries-free and caries-active sites. This observation was especially apparent for the Fl+Arg dentifrice. Thus, we conclude that the preventive benefits of tooth brushing go beyond the physical removal of dental plaque and that the active ingredients formulated within dentifrices have a positive effect not only on enamel chemistry but also on the metabolism of oral microbial populations. Video Abstract.}, } @article {pmid36171387, year = {2022}, author = {Lu, J and Rincon, N and Wood, DE and Breitwieser, FP and Pockrandt, C and Langmead, B and Salzberg, SL and Steinegger, M}, title = {Metagenome analysis using the Kraken software suite.}, journal = {Nature protocols}, volume = {17}, number = {12}, pages = {2815-2839}, pmid = {36171387}, issn = {1750-2799}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; U24 CA180922/CA/NCI NIH HHS/United States ; R35 GM139602/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Metagenome ; Software ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenomic experiments expose the wide range of microscopic organisms in any microbial environment through high-throughput DNA sequencing. The computational analysis of the sequencing data is critical for the accurate and complete characterization of the microbial community. To facilitate efficient and reproducible metagenomic analysis, we introduce a step-by-step protocol for the Kraken suite, an end-to-end pipeline for the classification, quantification and visualization of metagenomic datasets. Our protocol describes the execution of the Kraken programs, via a sequence of easy-to-use scripts, in two scenarios: (1) quantification of the species in a given metagenomics sample; and (2) detection of a pathogenic agent from a clinical sample taken from a human patient. The protocol, which is executed within 1-2 h, is targeted to biologists and clinicians working in microbiome or metagenomics analysis who are familiar with the Unix command-line environment.}, } @article {pmid36170451, year = {2022}, author = {Rozman, V and Mohar Lorbeg, P and Treven, P and Accetto, T and Golob, M and Zdovc, I and Bogovič Matijašić, B}, title = {Lactic acid bacteria and bifidobacteria deliberately introduced into the agro-food chain do not significantly increase the antimicrobial resistance gene pool.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2127438}, pmid = {36170451}, issn = {1949-0984}, mesh = {Anti-Bacterial Agents/pharmacology ; Bifidobacterium/genetics ; Drug Resistance, Bacterial/genetics ; Food Chain ; *Gastrointestinal Microbiome ; Gene Pool ; Humans ; *Lactobacillales/genetics ; Tetracyclines ; }, abstract = {Lactic acid bacteria (LAB) and bifidobacteria may serve as reservoirs of antimicrobial resistance, but the risk posed by strains intentionally introduced into the agro-food chain has not yet been thoroughly investigated. The aim of our study was to evaluate whether probiotics, starter and protective cultures, and feed additives represent a risk to human health. In addition to commercial strains of LAB and bifidobacteria, isolates from human milk or colostrum, intestinal mucosa or feces, and fermented products were analyzed. Phenotypic susceptibility data of 474 strains showed that antimicrobial resistance was more common in intestinal isolates than in commercial strains. Antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) were characterized in the whole genome sequences of 1114 strains using comparative genomics. Intrinsic ARGs were abundant in enterococci, bifidobacteria, and lactococci but were considered non-risky due to the absence of MGEs. The results revealed that 13.8% of commercial strains contained acquired ARGs, most frequently for tetracycline. We associated 75.5% of the acquired ARGs with known or novel MGEs, and their potential for transmission was assessed by examining metagenomic sequences. We confirmed that ARGs and MGEs were not as abundant or diverse in commercial strains as in human intestinal isolates or isolates from human milk, suggesting that strains intentionally introduced into the agro-food chain do not pose a significant threat. However, attention should be paid especially to individual probiotic strains containing elements that have been shown to have high potential for transferability in the gut microbiota.Abbreviations: ARG, antimicrobial resistance gene; ICE, integrative and conjugative element; IME, integrative and mobilizable element; LAB, lactic acid bacteria; MDR, multidrug resistance; MIC, minimum inhibitory concentration; MGE, mobile genetic element; TRRPP, tetracycline-resistant ribosomal protection protein; WGS, whole genome sequences.}, } @article {pmid36169892, year = {2022}, author = {Wani, AK and Akhtar, N and Singh, R and Chopra, C and Kakade, P and Borde, M and Al-Khayri, JM and Suprasanna, P and Zimare, SB}, title = {Prospects of advanced metagenomics and meta-omics in the investigation of phytomicrobiome to forecast beneficial and pathogenic response.}, journal = {Molecular biology reports}, volume = {49}, number = {12}, pages = {12165-12179}, pmid = {36169892}, issn = {1573-4978}, mesh = {*Metagenomics/methods ; *Microbiota/genetics ; Rhizosphere ; Metabolomics/methods ; Plants/genetics ; }, abstract = {Microorganisms dwell in diverse plant niches as non-axenic biotic components that are beneficial as well pathogenic for the host. They improve nutrients-uptake, stress tolerance, phytohormone synthesis, and strengthening the defense system through phyllosphere, rhizosphere, and endosphere. The negative consequences of the microbial communities are largely in the form of diseases characterized by certain symptoms such as gall, cankers, rots etc. Uncultivable and unspecified nature of different phytomicrobiomes communities is a challenge in the management of plant disease, a leading cause for the loss of the plant products. Metagenomics has opened a new gateway for the exploration of microorganisms that are hitherto unknown, enables investigation of the functional aspect of microbial gene products through metatranscriptomics and metabolomics. Metagenomics offers advantages of characterizing previously unknown microorganisms from extreme environments like hot springs, glaciers, deep seas, animal gut etc. besides bioprospecting gene products such as Taq polymerase, bor encoded indolotryptoline, hydrolases, and polyketides. This review provides a detailed account of the phytomicrobiome networks and highlights the importance and limitations of metagenomics and other meta-omics approaches for the understanding of plant microbial diversity with special focus on the disease control and its management.}, } @article {pmid36169826, year = {2023}, author = {Huo, Q and Li, R and Chen, C and Wang, C and Long, T and Liu, X}, title = {Study on potential microbial community to the waste water treatment from bauxite desilication process.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {6}, pages = {15438-15453}, pmid = {36169826}, issn = {1614-7499}, mesh = {Aluminum Oxide ; Wastewater ; Bacteria/genetics ; *Microbiota/genetics ; *Water Purification ; }, abstract = {Discharging waste water from the bauxite desilication process will bring potential environmental risk from the residual ions and organic compounds, especially hydrolyzed polyacrylamide. Characterization of the microbial community diversity in waste water plays an important role in the biological treatment of waste water. In this study, eight waste water samples from five flotation plants in China were investigated. The microbial community and functional profiles within the waste water were analyzed by a metagenomic sequencing method and associated with geochemical properties. The results revealed that Proteobacteria and Firmicutes were the dominant bacterial phyla. Both phylogenetical and clusters of orthologous groups' analyses indicated that Tepidicella, Paracoccus, Pseudomonas, and Exiguobacterium could be the dominant bacterial genera in the waste water from bauxite desilication process for their abilities to biodegrade complex organic compounds. The results of the microbial community diversity and functional gene compositions analyses provided a beneficial orientation for the biotreatment of waste water, as well as regenerative using of water resources. Besides, this study revealed that waste water from bauxite desilication process was an ideal ecosystem to find novel microorganisms, such as efficient strains for bio-desilication and bio-desulfurization of bauxite.}, } @article {pmid36169685, year = {2022}, author = {Lin, S and Li, Q and Xu, Z and Chen, Z and Tao, Y and Tong, Y and Wang, T and Chen, S and Wang, P}, title = {Detection of the role of intestinal flora and tryptophan metabolism involved in antidepressant-like actions of crocetin based on a multi-omics approach.}, journal = {Psychopharmacology}, volume = {239}, number = {11}, pages = {3657-3677}, pmid = {36169685}, issn = {1432-2072}, support = {81703688//the National Natural Science Foundation of China/ ; 2022C03050//the key research and development project of Zhejiang Provinc/ ; 2017YFE0130100//key projects of international scientific and technological innovation cooperation between governments/ ; LQ22H280014//Zhejiang Provincial Natural Science Foundation of China under Grant/ ; 21ywb80//Taizhou Social development science and technology program/ ; }, mesh = {Animals ; Mice ; *Tryptophan/metabolism ; Receptors, Aryl Hydrocarbon/metabolism ; Serotonin/metabolism ; Depression/metabolism ; Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism ; *Gastrointestinal Microbiome ; Kynurenic Acid/metabolism ; Serotonin Plasma Membrane Transport Proteins/metabolism ; Occludin/metabolism/pharmacology ; Arachidonic Acid/metabolism/pharmacology ; Antidepressive Agents/pharmacology/therapeutic use/metabolism ; Hippocampus ; Inflammation/metabolism ; Cytokines/metabolism ; Mitogen-Activated Protein Kinases/metabolism ; Arginine/pharmacology ; Stress, Psychological/drug therapy ; }, abstract = {RATIONALE: Depression is a serious mood disorder, and crocetin has a variety of pharmacological activities, including antidepressant effect. The alterations of intestinal flora have a significant correlation with depression, and crocetin can alter the composition of intestinal flora in mice with depression-like behaviors.

OBJECTIVE: This study investigated the underlying antidepressant mechanisms of crocetin through multi-omics coupled with biochemical technique validation.

METHODS: Chronic unpredictable stress (CUMS) was used to induce mice model of depression to evaluate the antidepressant effect of crocetin through behavioral tests, and the metagenomic and metabolomic were used to explore the potential mechanisms involved. In order to verify its underlying mechanism, western blot (WB), Elisa, immune histological and HPLC techniques were used to detect the level of inflammatory cytokines and the level of metabolites/proteins related to tryptophan metabolism in crocetin-treated mice.

RESULTS: Crocetin ameliorated depression-like behaviors and increased mobility in depressive mice induced by CUMS. Metagenomic results showed that crocetin regulated the structure of intestinal flora, as well as significantly regulated the function gene related to derangements in energy metabolism and amino acid metabolism in mice with depression-like behaviors. Metabolomic results showed that the tryptophan metabolism, arginine metabolism and arachidonic acid metabolism played an essential role in exerting antidepressant-like effect of crocetin. According to multi-omics approaches and validation results, tryptophan metabolism and inflammation were identified and validated as valuable biological processes involved in the antidepressant effects of crocetin. Crocetin regulated the tryptophan metabolism in mice with depression-like behaviors, including increased aryl hydrocarbon receptor (AhR) expression, reduced indoleamine 2,3-dioxygenase 1 (IDO1) and serotonin transporter (SERT) expression in the hippocampus, elevated the content of 5-HT, kynurenic acid in serum and 5-HT, tryptophan in hippocampus. In addition, crocetin also attenuated inflammation in mice with depression-like behaviors, which presented with reducing the production of inflammatory cytokines in serum and colon. Meanwhile, crocetin up-regulated the expression of zonula occludens 1 (ZO-1) and occludin in ileum and colon to repair the intestinal barrier for preventing inflammation transfer.

CONCLUSION: Our findings clarify that crocetin exerted antidepressant effects through its anti-inflammation, repairment of intestinal barrier, modulatory on the intestinal flora and metabolic disorders, which further regulated tryptophan metabolism and impacted mitogen-activated protein kinase (MAPK) signaling pathway to enhance neural plasticity, thereby protect neural.}, } @article {pmid36169030, year = {2022}, author = {Simpson, JB and Redinbo, MR}, title = {Multi-omic analysis of host-microbial interactions central to the gut-brain axis.}, journal = {Molecular omics}, volume = {18}, number = {10}, pages = {896-907}, doi = {10.1039/d2mo00205a}, pmid = {36169030}, issn = {2515-4184}, support = {P30 CA016086/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Host Microbial Interactions ; Brain ; *Gastrointestinal Microbiome/physiology ; Neurotransmitter Agents ; Brain-Gut Axis ; }, abstract = {The gut microbiota impact numerous aspects of human physiology, including the central nervous system (CNS). Emerging work is now focusing on the microbial factors underlying the bi-directional communication network linking host and microbial systems within the gastrointestinal tract to the CNS, the "gut-brain axis". Neurotransmitters are key coordinators of this network, and their dysregulation has been linked to numerous neurological disease states. As the bioavailability of neurotransmitters is modified by gut microbes, it is critical to unravel the influence of the microbiota on neurotransmitters in the context of the gut-brain axis. Here we review foundational studies that defined molecular relationships between the microbiota, neurotransmitters, and the gut-brain axis. We examine links between the gut microbiome, behavior, and neurological diseases, as well as microbial influences on neurotransmitter bioavailability and physiology. Finally, we review multi-omics technologies uniquely applicable to this area, including high-throughput genetics, modern metabolomics, structure-guided metagenomics, targeted proteomics, and chemogenetics. Interdisciplinary studies will continue to drive the discovery of molecular mechanisms linking the gut microbiota to clinical manifestations of neurobiology.}, } @article {pmid36167925, year = {2022}, author = {Kim, DW and Ahn, JH and Cha, CJ}, title = {Biodegradation of plastics: mining of plastic-degrading microorganisms and enzymes using metagenomics approaches.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {60}, number = {10}, pages = {969-976}, pmid = {36167925}, issn = {1976-3794}, mesh = {Biodegradation, Environmental ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Plastics/metabolism ; }, abstract = {Plastic pollution exacerbated by the excessive use of synthetic plastics and its recalcitrance has been recognized among the most pressing global threats. Microbial degradation of plastics has gained attention as a possible eco-friendly countermeasure, as several studies have shown microbial metabolic capabilities as potential degraders of various synthetic plastics. However, still defined biochemical mechanisms of biodegradation for the most plastics remain elusive, because the widely used culture-dependent approach can access only a very limited amount of the metabolic potential in each microbiome. A culture-independent approach, including metagenomics, is becoming increasingly important in the mining of novel plastic-degrading enzymes, considering its more expanded coverage on the microbial metabolism in microbiomes. Here, we described the advantages and drawbacks associated with four different metagenomics approaches (microbial community analysis, functional metagenomics, targeted gene sequencing, and whole metagenome sequencing) for the mining of plastic-degrading microorganisms and enzymes from the plastisphere. Among these approaches, whole metagenome sequencing has been recognized among the most powerful tools that allow researchers access to the entire metabolic potential of a microbiome. Accordingly, we suggest strategies that will help to identify plastisphere-enriched sequences as de novo plastic-degrading enzymes using the whole metagenome sequencing approach. We anticipate that new strategies for metagenomics approaches will continue to be developed and facilitate to identify novel plastic-degrading microorganisms and enzymes from microbiomes.}, } @article {pmid36167684, year = {2022}, author = {Seong, HJ and Roux, S and Hwang, CY and Sul, WJ}, title = {Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {157}, pmid = {36167684}, issn = {2049-2618}, mesh = {*Bacteriophages/genetics ; DNA ; DNA Methylation/genetics ; Metagenome/genetics ; Metagenomics ; Methyltransferases/genetics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life.

RESULTS: We reconstructed 15,056 viral, 252 prokaryotic, 56 giant viral, and 6 eukaryotic metagenome-assembled genomes from northwest Pacific Ocean seawater samples using short- and long-read sequencing approaches. These metagenome-derived genomes mostly represented novel taxa, and recruited a majority of reads. Thanks to single-molecule real-time (SMRT) sequencing technology, base modification could also be detected for these genomes. This showed that DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark.

CONCLUSIONS: Overall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome. Video Abstract.}, } @article {pmid36166104, year = {2023}, author = {Liu, H and Wu, W and Luo, Y}, title = {Oral and intravenous iron treatment alter the gut microbiome differentially in dialysis patients.}, journal = {International urology and nephrology}, volume = {55}, number = {3}, pages = {759-767}, pmid = {36166104}, issn = {1573-2584}, support = {Sz2019016//Provincial special matching funds of Shanxi Provincial People's Hospital/ ; }, mesh = {Humans ; Iron ; *Gastrointestinal Microbiome ; Renal Dialysis ; Ferric Oxide, Saccharated ; *Renal Insufficiency, Chronic ; *Anemia ; }, abstract = {OBJECTIVE: Chronic kidney disease (CKD) is often complicated by anemia, which seriously affects the quality-of-life and prognosis of patients. These patients usually need iron replacement therapy. Oral iron affects the composition and abundance of intestinal flora by increasing intestinal iron concentration.

METHODS: We undertook an interventional study to investigate the effects of oral versus intravenous iron therapy on the gut microbiota. Oral ferrous succinate tablets (n = 14) or intravenous iron sucrose (n = 14) was administered to anemic maintenance hemodialysis (MHD) patients for 2 months.

RESULTS: Oral and intravenous iron treatments had different effects on gut microbial composition and diversity. After oral iron treatment, the α-diversity was decreased, while at the phylum level, the abundance of Firmicutes was reduced and the abundance of Bacteroides was increased. At the genus level, the abundance of Blautia and Coprococcus was decreased, and the abundance of Bacteroidetes was increased. Oral iron therapy was associated with a higher abundance of Lactobacillus compared with that measured in intravenous iron-treated patients. According to metagenome function prediction analysis, oral iron increased the metabolic processes of phenylalanine, valine, leucine, and isoleucine. These changes may increase uremic toxin levels, thereby increasing the progression of renal disease.

CONCLUSION: Iron therapy affects the diversity and composition of gut flora in MHD patients. Oral iron affects the number of bacteria and increases amino acid metabolism compared with intravenous iron. These results indicate that intravenous iron may be more appropriate for MHD patients.}, } @article {pmid36165830, year = {2022}, author = {Afzal, S and Singh, NK}, title = {Effect of zinc and iron oxide nanoparticles on plant physiology, seed quality and microbial community structure in a rice-soil-microbial ecosystem.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {314}, number = {}, pages = {120224}, doi = {10.1016/j.envpol.2022.120224}, pmid = {36165830}, issn = {1873-6424}, mesh = {Soil/chemistry ; *Oryza/metabolism ; *Zinc Oxide/chemistry ; Zinc ; Soil Microbiology ; Nitrites ; Lignin ; Ammonia ; Rhizosphere ; *Soil Pollutants/analysis ; *Microbiota ; Nitrogen ; Plant Physiological Phenomena ; Seeds/chemistry ; Carbon ; Micronutrients ; Streptomycin ; Magnetic Iron Oxide Nanoparticles ; Sulfates ; Chitin ; }, abstract = {In this study, we assessed the impact of zinc oxide (ZnO) and iron oxide (FeO) (<36 nm) nanoparticles (NPs) as well as their sulphate salt (bulk) counterpart (0, 25, 100 mg/kg) on rice growth and seed quality as well as the microbial community in the rhizosphere environment of rice. During the rice growing season 2021-22, all experiments were conducted in a greenhouse (temperature: day 30 °C; night 20 °C; relative humidity: 70%; light period: 16 h/8 h, day/night) in rice field soil. Results showed that low concentrations of FeO and ZnO NPs (25 mg/kg) promoted rice growth (height (29%, 16%), pigment content (2%, 3%)) and grain quality parameters such as grains per spike (8%, 9%), dry weight of grains (12%, 14%) respectively. As compared to the control group, the Zn (2%) and Fe (5%) accumulations at their respective low concentrations of NP treatments showed stimulation. Interestingly, our results showed that at low concentration of both the NPs the soil microbes had more diversity and richness than those in the bulk treated and control soil group. Although a number of phyla were affected by the presence of NPs, the strongest effects were observed for change in the abundance of the three phyla for Proteobacteria, Actinobacteria, and Planctomycetes. The rhizosphere environment was notably enriched with potential streptomycin producers, carbon and nitrogen fixers, and lignin degraders with regard to functional groups of microorganisms. However, microbial communities mainly responsible for chitin degradation, ammonia oxidation, and nitrite reduction were found to be decreased. The results from this study highlight significant changes in several plant-based endpoints, as well as the rhizosphere soil microorganisms. It further adds information to our understanding of the nanoscale-specific impacts of important micronutrient oxides on both rice and its associated soil microbiome.}, } @article {pmid36165828, year = {2022}, author = {Bertucci, A and Hoede, C and Dassié, E and Gourves, PY and Suin, A and Le Menach, K and Budzinski, H and Daverat, F}, title = {Impact of environmental micropollutants and diet composition on the gut microbiota of wild european eels (Anguilla anguilla).}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {314}, number = {}, pages = {120207}, doi = {10.1016/j.envpol.2022.120207}, pmid = {36165828}, issn = {1873-6424}, mesh = {Animals ; *Anguilla ; *Gastrointestinal Microbiome ; Environmental Biomarkers ; *Arsenic ; Hexachlorocyclohexane ; Persistent Organic Pollutants ; *Metals, Heavy ; Diet ; *Water Pollutants, Chemical/toxicity ; }, abstract = {In fish, the gut microbiome plays a crucial role in homeostasis and health and is affected by several organic and inorganic environmental contaminants. Amphidromous fish are sentinel species, particularly exposed to these stressors. We used whole metagenome sequencing to characterize the gut microbiome of wild European eels (Anguilla anguilla) at a juvenile stage captured from three sites with contrasted pollution levels in term of heavy metals and persistent organic pollutants. The objectives were to identify what parameters could alter the gut microbiome of this catadromous fish and to explore the potential use of microbiota as bioindicators of environment quality. We identified a total of 1079 microbial genera. Overall, gut microbiome was dominated by Proteobacteria, Firmicutes and Actinobacteria. Alpha and beta diversity were different amongst sites and could be explained by a reduced number of environmental and biological factors, specifically the relative abundance of fish preys in eels' diet, PCB101, γHCH (lindane), transnonachlor and arsenic. Furthermore, we identified a series of indicator taxa with differential abundance between the three sites. Changes in the microbial communities in the gut caused by environmental pollutants were previously undocumented in European eels. Our results indicate that microbiota might represent another route by which pollutants affect the health of these aquatic sentinel organisms.}, } @article {pmid36165045, year = {2022}, author = {Shareefdeen, H and Hill, C}, title = {The gut virome in health and disease: new insights and associations.}, journal = {Current opinion in gastroenterology}, volume = {38}, number = {6}, pages = {549-554}, pmid = {36165045}, issn = {1531-7056}, mesh = {Bacteria ; *Bacteriophages ; *COVID-19 ; Humans ; Infant, Newborn ; Metagenomics ; *Microbiota ; Virome ; *Viruses ; }, abstract = {PURPOSE OF REVIEW: Recent years have seen great strides made in the field of viral metagenomics. Many studies have reported alterations in the virome in different disease states. The vast majority of the human intestinal virome consists of bacteriophages, viruses that infect bacteria. The dynamic relationship between gut bacterial populations and bacteriophages is influenced by environmental factors that also impact host health and disease. In this review, we focus on studies highlighting the dynamics of the gut virome and fluctuations associated with disease states.

RECENT FINDINGS: Novel correlations have been identified between the human gut virome and diseases such as obesity, necrotizing enterocolitis and severe acute respiratory syndrome coronavirus 2 infection. Further associations between the virome and cognition, diet and geography highlight the complexity of factors that can influence the dynamic relationship between gut bacteria, bacteriophages and health.

SUMMARY: Here, we highlight some novel associations between the virome and health that will be the foundation for future studies in this field. The future development of microbiome-based interventions, identification of biomarkers, and novel therapeutics will require a thorough understanding of the gut virome and its dynamics.}, } @article {pmid36164761, year = {2022}, author = {Hooi, SL and Dwiyanto, J and Rasiti, H and Toh, KY and Wong, RKM and Lee, JWJ}, title = {A case report of improvement on ADHD symptoms after fecal microbiota transplantation with gut microbiome profiling pre- and post-procedure.}, journal = {Current medical research and opinion}, volume = {38}, number = {11}, pages = {1977-1982}, doi = {10.1080/03007995.2022.2129232}, pmid = {36164761}, issn = {1473-4877}, mesh = {Female ; Humans ; Young Adult ; Adult ; Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; *Clostridioides difficile ; *Attention Deficit Disorder with Hyperactivity/therapy ; *Clostridium Infections ; Feces ; }, abstract = {BACKGROUND: Recent studies demonstrate the association of the gut microbiome in regulating interactions between the central nervous system and intestinal function. Individuals with attention-deficit hyperactivity disorder (ADHD) have been shown to have unique gut microbial signature, with depletion of beneficial commensal microbes. Fecal microbiota transplant (FMT) restores the imbalanced gut microbiome and may replete missing microbes to increase production of hormones and neurotransmitters regulating human behavior and cognition.

RESEARCH DESIGN & METHODS: Here, we present an interesting case of a 22-year-old woman treated with FMT primarily to treat recurrent Clostridioides difficile infection, which coincidentally alleviated her ADHD symptoms. We also present the pre- and post-FMT gut microbiota profiles conducted using shotgun metagenomic sequencing on the patient's fecal samples to thereby highlight potential microbial-associated mechanisms associated with the relief of ADHD symptoms.

RESULTS & CONCLUSIONS: Our case report provides preliminary evidence regarding the use of FMT in a patient with C. difficile and ADHD. We speculate that gut microbiome modulation, in particular the gain or loss of specific microbial species and pathways involving the metabolism of SCFAs, tryptophan and GABA, may merit further exploration as a potential therapeutic strategy for ADHD.}, } @article {pmid36163498, year = {2022}, author = {Beck, LC and Masi, AC and Young, GR and Vatanen, T and Lamb, CA and Smith, R and Coxhead, J and Butler, A and Marsland, BJ and Embleton, ND and Berrington, JE and Stewart, CJ}, title = {Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants.}, journal = {Nature microbiology}, volume = {7}, number = {10}, pages = {1525-1535}, pmid = {36163498}, issn = {2058-5276}, support = {/WT_/Wellcome Trust/United Kingdom ; 221745/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents ; Bifidobacterium/genetics ; *Bifidobacterium bifidum ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; *Probiotics ; }, abstract = {The development of the gut microbiome from birth plays important roles in short- and long-term health, but factors influencing preterm gut microbiome development are poorly understood. In the present study, we use metagenomic sequencing to analyse 1,431 longitudinal stool samples from 123 very preterm infants (<32 weeks' gestation) who did not develop intestinal disease or sepsis over a study period of 10 years. During the study period, one cohort had no probiotic exposure whereas two cohorts were given different probiotic products: Infloran (Bifidobacterium bifidum and Lactobacillus acidophilus) or Labinic (B. bifidum, B. longum subsp. infantis and L. acidophilus). Mothers' own milk, breast milk fortifier, antibiotics and probiotics were significantly associated with the gut microbiome, with probiotics being the most significant factor. Probiotics drove microbiome transition into different preterm gut community types (PGCTs), each enriched in a different Bifidobacterium sp. and significantly associated with increased postnatal age. Functional analyses identified stool metabolites associated with PGCTs and, in preterm-derived organoids, sterile faecal supernatants impacted intestinal, organoid monolayer, gene expression in a PGCT-specific manner. The present study identifies specific influencers of gut microbiome development in very preterm infants, some of which overlap with those impacting term infants. The results highlight the importance of strain-specific differences in probiotic products and their impact on host interactions in the preterm gut.}, } @article {pmid36163472, year = {2022}, author = {Pinto, G and Shetty, SA and Zoetendal, EG and Gonçalves, RFS and Pinheiro, AC and Almeida, C and Azeredo, J and Smidt, H}, title = {An in vitro fermentation model to study the impact of bacteriophages targeting Shiga toxin-encoding Escherichia coli on the colonic microbiota.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {74}, pmid = {36163472}, issn = {2055-5008}, mesh = {*Bacteriophages/genetics ; Coliphages/genetics ; Colon ; *Escherichia coli Infections/microbiology/prevention & control ; Fermentation ; Humans ; *Microbiota ; Shiga Toxin ; *Shiga-Toxigenic Escherichia coli ; }, abstract = {Lytic bacteriophages are considered safe for human consumption as biocontrol agents against foodborne pathogens, in particular in ready-to-eat foodstuffs. Phages could, however, evolve to infect different hosts when passing through the gastrointestinal tract (GIT). This underlines the importance of understanding the impact of phages towards colonic microbiota, particularly towards bacterial families usually found in the colon such as the Enterobacteriaceae. Here we propose in vitro batch fermentation as model for initial safety screening of lytic phages targeting Shiga toxin-producing Escherichia coli (STEC). As inoculum we used faecal material of three healthy donors. To assess phage safety, we monitored fermentation parameters, including short chain fatty acid production and gas production/intake by colonic microbiota. We performed shotgun metagenomic analysis to evaluate the outcome of phage interference with colonic microbiota composition and functional potential. During the 24 h incubation, concentrations of phage and its host were also evaluated. We found the phage used in this study, named E. coli phage vB_EcoS_Ace (Ace), to be safe towards human colonic microbiota, independently of the donors' faecal content used. This suggests that individuality of donor faecal microbiota did not interfere with phage effect on the fermentations. However, the model revealed that the attenuated STEC strain used as phage host perturbed the faecal microbiota as based on metagenomic analysis, with potential differences in metabolic output. We conclude that the in vitro batch fermentation model used in this study is a reliable safety screening for lytic phages intended to be used as biocontrol agents.}, } @article {pmid36161902, year = {2022}, author = {Li, ML and Wang, S and Xu, P and Tian, HY and Bai, M and Zhang, YP and Shao, Y and Xiong, ZJ and Qi, XG and Cooper, DN and Zhang, G and Zhu, HH and Wu, DD}, title = {Functional genomics analysis reveals the evolutionary adaptation and demographic history of pygmy lorises.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {40}, pages = {e2123030119}, pmid = {36161902}, issn = {1091-6490}, mesh = {*Adaptation, Biological/genetics ; Animals ; *Biological Evolution ; Demography ; Hibernation ; *Lorisidae/genetics ; Metagenomics ; Metalloendopeptidases/genetics ; }, abstract = {Lorises are a group of globally threatened strepsirrhine primates that exhibit many unusual physiological and behavioral features, including a low metabolic rate, slow movement, and hibernation. Here, we assembled a chromosome-level genome sequence of the pygmy loris (Xanthonycticebus pygmaeus) and resequenced whole genomes from 50 pygmy lorises and 6 Bengal slow lorises (Nycticebus bengalensis). We found that many gene families involved in detoxification have been specifically expanded in the pygmy loris, including the GSTA gene family, with many newly derived copies functioning specifically in the liver. We detected many genes displaying evolutionary convergence between pygmy loris and koala, including PITRM1. Significant decreases in PITRM1 enzymatic activity in these two species may have contributed to their characteristic low rate of metabolism. We also detected many evolutionarily convergent genes and positively selected genes in the pygmy loris that are involved in muscle development. Functional assays demonstrated the decreased ability of one positively selected gene, MYOF, to up-regulate the fast-type muscle fiber, consistent with the lower proportion of fast-twitch muscle fibers in the pygmy loris. The protein product of another positively selected gene in the pygmy loris, PER2, exhibited weaker binding to the key circadian core protein CRY, a finding that may be related to this species' unusual circadian rhythm. Finally, population genomics analysis revealed that these two extant loris species, which coexist in the same habitat, have exhibited an inverse relationship in terms of their demography over the past 1 million years, implying strong interspecies competition after speciation.}, } @article {pmid36161453, year = {2022}, author = {Lugli, GA and Fontana, F and Tarracchini, C and Mancabelli, L and Milani, C and Turroni, F and Ventura, M}, title = {Exploring the biodiversity of Bifidobacterium asteroides among honey bee microbiomes.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {5666-5679}, pmid = {36161453}, issn = {1462-2920}, mesh = {Bees ; Animals ; Phylogeny ; *Bifidobacterium/genetics ; *Microbiota/genetics ; Metagenome ; }, abstract = {Bifidobacterium asteroides is considered the ancestor of the genus Bifidobacterium, which has evolved in close touch with the hindgut of social insects. However, recent studies revealed high intraspecies biodiversity within this taxon, uncovering the putative existence of multiple bifidobacterial species, thus, suggesting its reclassification. Here, a genomic investigation of 98 B. asteroides-related genomes retrieved from public repositories and reconstructed from metagenomes of the hindgut of Apis mellifera and Apis cerana was performed to shed light on the genetic variability of this taxon. Phylogenetic and genomic analyses revealed the existence of eight clusters, of which five have been recently characterized with a representative type strain of the genus and three were represented by putative novel bifidobacterial species inhabiting the honeybee gut. Then, the dissection of 366 shotgun metagenomes of honeybee guts revealed a pattern of seven B. asteroides-related taxa within A. mellifera that co-exist with the host, while A. cerana microbiome was characterized by the predominance of one of the novel species erroneously classified as B. asteroides. A further glycobiome analysis unveiled a conserved repertoire of glycosyl hydrolases (GHs) reflecting degradative abilities towards a broad range of simple carbohydrates together with genes encoding specific GHs of each B. asteroides-related taxa.}, } @article {pmid36159864, year = {2022}, author = {Qiu, Q and Deng, J and Deng, H and Yao, D and Yan, Y and Ye, S and Shang, X and Deng, Y and Han, L and Zheng, G and Roy, B and Chen, Y and Han, L and Huang, R and Fang, X and Lu, C}, title = {Association of the characteristics of the blood metabolome and gut microbiome with the outcome of methotrexate therapy in psoriasis.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {937539}, pmid = {36159864}, issn = {1664-3224}, mesh = {Fatty Acids ; *Gastrointestinal Microbiome/physiology ; Humans ; Lipids ; Metabolome ; Methotrexate/therapeutic use ; Prospective Studies ; *Psoriasis/drug therapy ; RNA, Ribosomal, 16S ; }, abstract = {Metabolic status and gut microecology are implicated in psoriasis. Methotrexate (MTX) is usually the first-line treatment for this disease. However, the relationship between MTX and host metabolic status and the gut microbiota is unclear. This study aimed to characterize the features of blood metabolome and gut microbiome in patients with psoriasis after treatment with MTX. Serum and stool samples were collected from 15 patients with psoriasis. Untargeted liquid chromatography-mass spectrometry and metagenomics sequencing were applied to profile the blood metabolome and gut microbiome, respectively. We found that the response to MTX varied according to metabolomic and metagenomic features at baseline; for example, patients who had high levels of serum nutrient molecular and more enriched gut microbiota had a poor response. After 16 weeks of MTX, we observed a reduction in microbial activity pathways, and patients with a good response showed more microbial activity and less biosynthesis of serum fatty acid. We also found an association between the serum metabolome and the gut microbiome before intervention with MTX. Carbohydrate metabolism, transporter systems, and protein synthesis within microbes were associated with host metabolic clusters of lipids, benzenoids, and organic acids. These findings suggest that the metabolic status of the blood and the gut microbiome is involved in the effectiveness of MTX in psoriasis, and that inhibition of symbiotic intestinal microbiota may be one of the mechanisms of action of MTX. Prospective studies in larger sample sizes are needed to confirm these findings.}, } @article {pmid36155528, year = {2022}, author = {Liang, F and Chen, CY and Li, YP and Ke, YC and Ho, EP and Jeng, CF and Lin, CH and Chen, SK}, title = {Early Dysbiosis and Dampened Gut Microbe Oscillation Precede Motor Dysfunction and Neuropathology in Animal Models of Parkinson's Disease.}, journal = {Journal of Parkinson's disease}, volume = {12}, number = {8}, pages = {2423-2440}, doi = {10.3233/JPD-223431}, pmid = {36155528}, issn = {1877-718X}, mesh = {Humans ; Mice ; Animals ; Infant ; *Parkinson Disease ; alpha-Synuclein/metabolism ; *Gastrointestinal Microbiome/physiology ; Dysbiosis ; Disease Models, Animal ; }, abstract = {BACKGROUND: Studies have shown different gut microbiomes in patients with Parkinson's disease (PD) compared to unaffected controls. However, when the gut microbiota shift toward dysbiosis in the PD process remains unclear.

OBJECTIVE: We aim to investigate the changes in gut microbiota, locomotor function, and neuropathology longitudinally in PD rodent models.

METHODS: Fecal microbiota were longitudinally assessed by sequencing the V4-V5 region of the 16S ribosomal RNA gene in a human mutant α-synuclein over-expressing mouse model of PD, SNCA p.A53T mice, and the non-transgenic littermate controls. The locomotor function, neuronal integrity, and α-synuclein expression in the different brain regions were compared between groups. Human fecal microbiota communities from 58 patients with PD and 46 unaffected controls were also analyzed using metagenomic sequencing for comparison.

RESULTS: Compared to non-transgenic littermate controls, the altered gut microbiota of the SNCA p.A53T mice can be detected as early as 2 months old, and the diurnal oscillation of the gut microbiome was dampened throughout PD progression starting from 4 months old. However, neuropathology changes and motor deficits were observed starting at 6 months old. Similar changes in altered gut microbiota were also observed in another PD genetic mouse model carrying the LRRK2 p.G2019S mutation at 2 months old. Among the commonly enriched gut microbiota in both PD genetic mouse models, the abundance of Parabateroides Merdae and Ruminococcus torques were also increased in human PD patients compared to controls.

CONCLUSION: These findings revealed the altered gut microbiota communities and oscillations preceding the occurrence of neuropathy and motor dysfunction in the PD process.}, } @article {pmid36155191, year = {2023}, author = {Nagata, N and Takeuchi, T and Masuoka, H and Aoki, R and Ishikane, M and Iwamoto, N and Sugiyama, M and Suda, W and Nakanishi, Y and Terada-Hirashima, J and Kimura, M and Nishijima, T and Inooka, H and Miyoshi-Akiyama, T and Kojima, Y and Shimokawa, C and Hisaeda, H and Zhang, F and Yeoh, YK and Ng, SC and Uemura, N and Itoi, T and Mizokami, M and Kawai, T and Sugiyama, H and Ohmagari, N and Ohno, H}, title = {Human Gut Microbiota and Its Metabolites Impact Immune Responses in COVID-19 and Its Complications.}, journal = {Gastroenterology}, volume = {164}, number = {2}, pages = {272-288}, pmid = {36155191}, issn = {1528-0012}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *COVID-19 ; Cross-Sectional Studies ; SARS-CoV-2 ; Feces/chemistry ; Immunity ; Cytokines ; Vitamin B 6/analysis ; }, abstract = {BACKGROUND & AIMS: We investigate interrelationships between gut microbes, metabolites, and cytokines that characterize COVID-19 and its complications, and we validate the results with follow-up, the Japanese 4D (Disease, Drug, Diet, Daily Life) microbiome cohort, and non-Japanese data sets.

METHODS: We performed shotgun metagenomic sequencing and metabolomics on stools and cytokine measurements on plasma from 112 hospitalized patients with SARS-CoV-2 infection and 112 non-COVID-19 control individuals matched by important confounders.

RESULTS: Multiple correlations were found between COVID-19-related microbes (eg, oral microbes and short-chain fatty acid producers) and gut metabolites (eg, branched-chain and aromatic amino acids, short-chain fatty acids, carbohydrates, neurotransmitters, and vitamin B6). Both were also linked to inflammatory cytokine dynamics (eg, interferon γ, interferon λ3, interleukin 6, CXCL-9, and CXCL-10). Such interrelationships were detected highly in severe disease and pneumonia; moderately in the high D-dimer level, kidney dysfunction, and liver dysfunction groups; but rarely in the diarrhea group. We confirmed concordances of altered metabolites (eg, branched-chain amino acids, spermidine, putrescine, and vitamin B6) in COVID-19 with their corresponding microbial functional genes. Results in microbial and metabolomic alterations with severe disease from the cross-sectional data set were partly concordant with those from the follow-up data set. Microbial signatures for COVID-19 were distinct from diabetes, inflammatory bowel disease, and proton-pump inhibitors but overlapping for rheumatoid arthritis. Random forest classifier models using microbiomes can highly predict COVID-19 and severe disease. The microbial signatures for COVID-19 showed moderate concordance between Hong Kong and Japan.

CONCLUSIONS: Multiomics analysis revealed multiple gut microbe-metabolite-cytokine interrelationships in COVID-19 and COVID-19related complications but few in gastrointestinal complications, suggesting microbiota-mediated immune responses distinct between the organ sites. Our results underscore the existence of a gut-lung axis in COVID-19.}, } @article {pmid36154277, year = {2022}, author = {Herrera, G and Arboleda, JC and Pérez-Jaramillo, JE and Patarroyo, MA and Ramírez, JD and Muñoz, M}, title = {Microbial Interdomain Interactions Delineate the Disruptive Intestinal Homeostasis in Clostridioides difficile Infection.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0050222}, pmid = {36154277}, issn = {2165-0497}, mesh = {Humans ; *Clostridioides difficile/genetics ; *Clostridium Infections/microbiology ; *Microbiota ; Bacteria ; Anti-Bacterial Agents ; Homeostasis ; Virulence Factors/genetics ; *Anti-Infective Agents ; Butyrates ; }, abstract = {Clostridioides difficile infection (CDI) creates an imbalance in the intestinal microbiota due to the interaction of the components making up this ecosystem, but little is known about the impact of this disease on other microbial members. This work has thus been aimed at evaluating the taxonomic composition, potential gene-associated functions, virulence factors, and antimicrobial resistance profiles of gut microbiomes. A total of 48 DNA samples obtained from patients with health care facility-acquired (HCFO) and community-onset (CO) diarrhea were distributed in the following four groups according to CDI status: HCFO/+ (n = 13), HCFO/- (n = 8), CO/+ (n = 13), and CO/- (n = 14). These samples were subjected to shotgun metagenomics sequencing. Although the CDI groups' microbiota had microbiome alterations, the greatest imbalance was observed in the in the HCFO+/- groups, with an increase in common pathogens and phage populations, as well as a decrease in beneficial microorganisms that leads to a negative impact on some intestinal homeostasis-related metabolic processes. A reduction in the relative abundance of butyrate metabolism-associated genes was also detected in the HCFO groups (P < 0.01), with an increase in some virulence factors and antibiotic-resistance markers. A set of 51 differentially abundant species in the groups with potential association to CDI enabled its characterization, leading to their spatial separation by onset. Strong correlations between phages and some archaeal and bacterial phyla were identified. This highlighted the need to study the microbiota's various components since their imbalance is multifactorial, with some pathogens contributing to a greater or lesser extent because of their interaction with the ecosystem they inhabit. IMPORTANCE Clostridioides difficile infection represents a serious public health problem in different countries due to its high morbi-mortality and the high costs it represents for health care systems. Studies have shown the impact of this infection on intestinal microbiome homeostasis, mainly on bacterial populations. Our research provides evidence of the impact of CDI at both the compositional (bacteria, archaea, and viruses), and functional levels, allowing us to understand that the alterations of the microbiota occur systemically and are caused by multiple perturbations generated by different members of the microbiota as well as by some pathogens that take advantage of the imbalance to proliferate. Likewise, the 51 differentially abundant species in the study groups with potential association to CDI found in this study could help us envisage future treatments against this and other inflammatory diseases, improving future therapeutic options for patients.}, } @article {pmid36152674, year = {2022}, author = {Corander, J and Hanage, WP and Pensar, J}, title = {Causal discovery for the microbiome.}, journal = {The Lancet. Microbe}, volume = {3}, number = {11}, pages = {e881-e887}, pmid = {36152674}, issn = {2666-5247}, support = {T32 AI007535/AI/NIAID NIH HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; Metagenomics/methods ; Causality ; Metagenome ; }, abstract = {Measurement and manipulation of the microbiome is generally considered to have great potential for understanding the causes of complex diseases in humans, developing new therapies, and finding preventive measures. Many studies have found significant associations between the microbiome and various diseases; however, Koch's classical postulates remind us about the importance of causative reasoning when considering the relationship between microbes and a disease manifestation. Although causal discovery in observational microbiome data faces many challenges, methodological advances in causal structure learning have improved the potential of data-driven prediction of causal effects in large-scale biological systems. In this Personal View, we show the capability of existing methods for inferring causal effects from metagenomic data, and we highlight ways in which the introduction of causal structures that are more flexible than existing structures offers new opportunities for causal reasoning. Our observations suggest that microbiome research can further benefit from tools developed in the past 5 years in causal discovery and learn from their applications elsewhere.}, } @article {pmid36151459, year = {2023}, author = {Yamamoto, M and Takaki, Y and Kashima, H and Tsuda, M and Tanizaki, A and Nakamura, R and Takai, K}, title = {In situ electrosynthetic bacterial growth using electricity generated by a deep-sea hydrothermal vent.}, journal = {The ISME journal}, volume = {17}, number = {1}, pages = {12-20}, pmid = {36151459}, issn = {1751-7370}, mesh = {*Hydrothermal Vents/microbiology ; Phylogeny ; Metagenomics ; *Microbiota/genetics ; Bacteria ; Electricity ; }, abstract = {Electroautotrophic microorganisms have attracted great attention since they exhibit a new type of primary production. Here, in situ electrochemical cultivation was conducted using the naturally occurring electromotive forces at a deep-sea hydrothermal vent. The voltage and current generation originating from the resulting microbial activity was observed for 12 days of deployment, with fluctuation in response to tidal cycles. A novel bacterium belonging to the genus Thiomicrorhabdus dominated the microbial community specifically enriched on the cathode. Metagenomic analysis provided the draft genome of the bacterium and the gene repertoire indicated that the bacterium has the potential for thio-autotrophic growth, which is a typical physiological feature of the members of the genus, while the bacterium had a unique gene cluster encoding multi-heme cytochrome c proteins responsible for extracellular electron transfer. Herein, we propose this bacterium as a new species, specifically enriched during electricity generation, as 'Candidatus Thiomicrorhabdus electrophagus'. This finding suggests the natural occurrence of electrosynthetic microbial populations using the geoelectricity in deep-sea hydrothermal environments.}, } @article {pmid36151458, year = {2023}, author = {Maciel-Guerra, A and Baker, M and Hu, Y and Wang, W and Zhang, X and Rong, J and Zhang, Y and Zhang, J and Kaler, J and Renney, D and Loose, M and Emes, RD and Liu, L and Chen, J and Peng, Z and Li, F and Dottorini, T}, title = {Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock.}, journal = {The ISME journal}, volume = {17}, number = {1}, pages = {21-35}, pmid = {36151458}, issn = {1751-7370}, mesh = {Animals ; Humans ; Anti-Bacterial Agents ; *Anti-Infective Agents ; Chickens/microbiology ; Escherichia coli/genetics ; Genes, Bacterial ; Livestock/microbiology ; *Microbiota ; *Soil Microbiology ; Drug Resistance, Bacterial ; }, abstract = {A debate is currently ongoing as to whether intensive livestock farms may constitute reservoirs of clinically relevant antimicrobial resistance (AMR), thus posing a threat to surrounding communities. Here, combining shotgun metagenome sequencing, machine learning (ML), and culture-based methods, we focused on a poultry farm and connected slaughterhouse in China, investigating the gut microbiome of livestock, workers and their households, and microbial communities in carcasses and soil. For both the microbiome and resistomes in this study, differences are observed across environments and hosts. However, at a finer scale, several similar clinically relevant antimicrobial resistance genes (ARGs) and similar associated mobile genetic elements were found in both human and broiler chicken samples. Next, we focused on Escherichia coli, an important indicator for the surveillance of AMR on the farm. Strains of E. coli were found intermixed between humans and chickens. We observed that several ARGs present in the chicken faecal resistome showed correlation to resistance/susceptibility profiles of E. coli isolates cultured from the same samples. Finally, by using environmental sensing these ARGs were found to be correlated to variations in environmental temperature and humidity. Our results show the importance of adopting a multi-domain and multi-scale approach when studying microbial communities and AMR in complex, interconnected environments.}, } @article {pmid36151114, year = {2022}, author = {Dekkers, KF and Sayols-Baixeras, S and Baldanzi, G and Nowak, C and Hammar, U and Nguyen, D and Varotsis, G and Brunkwall, L and Nielsen, N and Eklund, AC and Bak Holm, J and Nielsen, HB and Ottosson, F and Lin, YT and Ahmad, S and Lind, L and Sundström, J and Engström, G and Smith, JG and Ärnlöv, J and Orho-Melander, M and Fall, T}, title = {An online atlas of human plasma metabolite signatures of gut microbiome composition.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5370}, pmid = {36151114}, issn = {2041-1723}, mesh = {Biomarkers ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolome ; Metabolomics/methods ; Middle Aged ; Uremic Toxins ; }, abstract = {Human gut microbiota produce a variety of molecules, some of which enter the bloodstream and impact health. Conversely, dietary or pharmacological compounds may affect the microbiota before entering the circulation. Characterization of these interactions is an important step towards understanding the effects of the gut microbiota on health. In this cross-sectional study, we used deep metagenomic sequencing and ultra-high-performance liquid chromatography linked to mass spectrometry for a detailed characterization of the gut microbiota and plasma metabolome, respectively, of 8583 participants invited at age 50 to 64 from the population-based Swedish CArdioPulmonary bioImage Study. Here, we find that the gut microbiota explain up to 58% of the variance of individual plasma metabolites and we present 997 associations between alpha diversity and plasma metabolites and 546,819 associations between specific gut metagenomic species and plasma metabolites in an online atlas (https://gutsyatlas.serve.scilifelab.se/). We exemplify the potential of this resource by presenting novel associations between dietary factors and oral medication with the gut microbiome, and microbial species strongly associated with the uremic toxin p-cresol sulfate. This resource can be used as the basis for targeted studies of perturbation of specific metabolites and for identification of candidate plasma biomarkers of gut microbiota composition.}, } @article {pmid36149894, year = {2022}, author = {Zhang, L and Chen, L and Yu, XA and Duvallet, C and Isazadeh, S and Dai, C and Park, S and Frois-Moniz, K and Duarte, F and Ratti, C and Alm, EJ and Ling, F}, title = {MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes.}, journal = {PLoS computational biology}, volume = {18}, number = {9}, pages = {e1010472}, pmid = {36149894}, issn = {1553-7358}, mesh = {*COVID-19 ; *Gastrointestinal Microbiome/genetics ; Humans ; Pandemics ; Population Density ; Sewage ; Wastewater ; }, abstract = {The metagenome embedded in urban sewage is an attractive new data source to understand urban ecology and assess human health status at scales beyond a single host. Analyzing the viral fraction of wastewater in the ongoing COVID-19 pandemic has shown the potential of wastewater as aggregated samples for early detection, prevalence monitoring, and variant identification of human diseases in large populations. However, using census-based population size instead of real-time population estimates can mislead the interpretation of data acquired from sewage, hindering assessment of representativeness, inference of prevalence, or comparisons of taxa across sites. Here, we show that taxon abundance and sub-species diversisty in gut-associated microbiomes are new feature space to utilize for human population estimation. Using a population-scale human gut microbiome sample of over 1,100 people, we found that taxon-abundance distributions of gut-associated multi-person microbiomes exhibited generalizable relationships with respect to human population size. Here and throughout this paper, the human population size is essentially the sample size from the wastewater sample. We present a new algorithm, MicrobiomeCensus, for estimating human population size from sewage samples. MicrobiomeCensus harnesses the inter-individual variability in human gut microbiomes and performs maximum likelihood estimation based on simultaneous deviation of multiple taxa's relative abundances from their population means. MicrobiomeCensus outperformed generic algorithms in data-driven simulation benchmarks and detected population size differences in field data. New theorems are provided to justify our approach. This research provides a mathematical framework for inferring population sizes in real time from sewage samples, paving the way for more accurate ecological and public health studies utilizing the sewage metagenome.}, } @article {pmid36147601, year = {2022}, author = {Zhou, Z and Lv, H and Lv, J and Shi, Y and Huang, H and Chen, L and Shi, D}, title = {Alterations of gut microbiota in cirrhotic patients with spontaneous bacterial peritonitis: A distinctive diagnostic feature.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {999418}, pmid = {36147601}, issn = {2235-2988}, mesh = {Bacteria/genetics ; Dysbiosis/diagnosis/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Limosilactobacillus reuteri ; Liver Cirrhosis/complications/diagnosis ; *Peritonitis/diagnosis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Spontaneous bacterial peritonitis (SBP) is a severe infection in cirrhotic patients that requires early diagnosis to improve the long-term outcome. Alterations in the gut microbiota have been shown to correlate with the development and progression of liver cirrhosis. However, the relationship between SBP and gut microbiota remains unknown.

METHODS: In this study, we applied 16S rRNA pyrosequencing of feces to ascertain possible links between the gut microbiota and SBP. We recruited 30 SBP patients, 30 decompensated cirrhotic patients without SBP (NSBP) and 30 healthy controls. Metagenomic functional prediction of bacterial taxa was achieved using PICRUSt.

RESULTS: The composition of the gut microbiota in the SBP patients differed remarkably from that in the NSBP patients and healthy individuals. The microbial richness was significantly decreased, while the diversity was increased in the SBP patients. Thirty-four bacterial taxa containing 15 species, mainly pathogens such as Klebsiella pneumoniae, Serratia marcescens and Prevotella oris, were dominant in the SBP group, while 42 bacterial taxa containing 16 species, especially beneficial species such as Faecalibacterium prausnitzii, Methanobrevibacter smithii and Lactobacillus reuteri, were enriched in the NSBP group. Notably, we found that 18 gene functions of gut microbiota were different between SBP patients and NSBP patients, which were associated with energy metabolism and functional substance metabolism. Five optimal microbial markers were determined using a random forest model, and the combination of Lactobacillus reuteri, Rothia mucilaginosa, Serratia marcescens, Ruminococcus callidus and Neisseria mucosa achieved an area under the curve (AUC) value of 0.8383 to distinguish SBP from decompensated cirrhosis.

CONCLUSIONS: We described the obvious dysbiosis of gut microbiota in SBP patients and demonstrated the potential of microbial markers as noninvasive diagnostic tools for SBP at an early stage.}, } @article {pmid36146871, year = {2022}, author = {Sasivimolrattana, T and Chantratita, W and Sensorn, I and Chaiwongkot, A and Oranratanaphan, S and Bhattarakosol, P}, title = {Human Virome in Cervix Controlled by the Domination of Human Papillomavirus.}, journal = {Viruses}, volume = {14}, number = {9}, pages = {}, pmid = {36146871}, issn = {1999-4915}, mesh = {*Alphapapillomavirus ; *Cervix Uteri/virology ; *Coinfection ; DNA, Viral/genetics ; Female ; Humans ; Papillomaviridae/genetics ; *Papillomavirus Infections ; Uterine Cervical Neoplasms ; *Virome/genetics ; Viruses ; }, abstract = {Although other co-viral infections could also be considered influencing factors, cervical human papillomavirus (HPV) infection is the main cause of cervical cancer. Metagenomics have been employed in the NGS era to study the microbial community in each habitat. Thus, in this investigation, virome capture sequencing was used to examine the virome composition in the HPV-infected cervix. Based on the amount of HPV present in each sample, the results revealed that the cervical virome of HPV-infected individuals could be split into two categories: HPV-dominated (HD; ≥60%) and non-HPV-dominated (NHD; <60%). Cervical samples contained traces of several human viral species, including the molluscum contagiosum virus (MCV), human herpesvirus 4 (HHV4), torque teno virus (TTV), and influenza A virus. When compared to the HD group, the NHD group had a higher abundance of several viruses. Human viral diversity appears to be influenced by HPV dominance. This is the first proof that the diversity of human viruses in the cervix is impacted by HPV abundance. However, more research is required to determine whether human viral variety and the emergence of cancer are related.}, } @article {pmid36146789, year = {2022}, author = {Busse, L and Tisza, M and DiRuggiero, J}, title = {Viruses Ubiquity and Diversity in Atacama Desert Endolithic Communities.}, journal = {Viruses}, volume = {14}, number = {9}, pages = {}, pmid = {36146789}, issn = {1999-4915}, support = {80NSSC19K0470/NASA/NASA/United States ; NNX15AP18G/NASA/NASA/United States ; }, mesh = {Calcium Carbonate ; Calcium Sulfate ; Desert Climate ; *Microbiota ; *Viruses/genetics ; }, abstract = {Viruses are key players in the environment, and recent metagenomic studies have revealed their diversity and genetic complexity. Despite progress in understanding the ecology of viruses in extreme environments, viruses' dynamics and functional roles in dryland ecosystems, which cover about 45% of the Earth's land surfaces, remain largely unexplored. This study characterizes virus sequences in the metagenomes of endolithic (within rock) microbial communities ubiquitously found in hyper-arid deserts. Taxonomic classification and network construction revealed the presence of novel and diverse viruses in communities inhabiting calcite, gypsum, and ignimbrite rocks. Viral genome maps show a high level of protein diversity within and across endolithic communities and the presence of virus-encoded auxiliary metabolic genes. Phage-host relationships were predicted by matching tRNA, CRISPR spacer, and protein sequences in the viral and microbial metagenomes. Primary producers and heterotrophic bacteria were found to be putative hosts to some viruses. Intriguingly, viral diversity was not correlated with microbial diversity across rock substrates.}, } @article {pmid36146775, year = {2022}, author = {Hesse, RD and Roach, M and Kerr, EN and Papudeshi, B and Lima, LFO and Goodman, AZ and Hoopes, L and Scott, M and Meyer, L and Huveneers, C and Dinsdale, EA}, title = {Phage Diving: An Exploration of the Carcharhinid Shark Epidermal Virome.}, journal = {Viruses}, volume = {14}, number = {9}, pages = {}, pmid = {36146775}, issn = {1999-4915}, support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Bacteriophages/genetics ; *Diving ; Ecosystem ; Epidermis ; Metagenomics ; *Sharks ; *Virome ; }, abstract = {The epidermal microbiome is a critical element of marine organismal immunity, but the epidermal virome of marine organisms remains largely unexplored. The epidermis of sharks represents a unique viromic ecosystem. Sharks secrete a thin layer of mucus which harbors a diverse microbiome, while their hydrodynamic dermal denticles simultaneously repel environmental microbes. Here, we sampled the virome from the epidermis of three shark species in the family Carcharhinidae: the genetically and morphologically similar Carcharhinus obscurus (n = 6) and Carcharhinus galapagensis (n = 10) and the outgroup Galeocerdo cuvier (n = 15). Virome taxonomy was characterized using shotgun metagenomics and compared with a suite of multivariate analyses. All three sharks retain species-specific but highly similar epidermal viromes dominated by uncharacterized bacteriophages which vary slightly in proportional abundance within and among shark species. Intraspecific variation was lower among C. galapagensis than among C. obscurus and G. cuvier. Using both the annotated and unannotated reads, we were able to determine that the Carcharhinus galapagensis viromes were more similar to that of G. cuvier than they were to that of C. obscurus, suggesting that behavioral niche may be a more prominent driver of virome than host phylogeny.}, } @article {pmid36145068, year = {2022}, author = {Pang, L and Zhi, Q and Jian, W and Liu, Z and Lin, H}, title = {The Oral Microbiome Impacts the Link between Sugar Consumption and Caries: A Preliminary Study.}, journal = {Nutrients}, volume = {14}, number = {18}, pages = {}, pmid = {36145068}, issn = {2072-6643}, support = {81903345//National Natural Science Foundation of China/ ; }, mesh = {Adolescent ; Candida albicans ; *Dental Caries/etiology ; Dietary Sugars/adverse effects ; Humans ; Lactobacillus ; *Microbiota ; Phosphotransferases ; Streptococcus mutans ; Sugars ; }, abstract = {BACKGROUND: The excessive and frequent intake of refined sugar leads to caries. However, the relationship between the amount of sugar intake and the risk of caries is not always consistent. Oral microbial profile and function may impact the link between them. This study aims to identify the plaque microbiota characteristics of caries subjects with low (CL) and high (CH) sugar consumption, and of caries-free subjects with low (FL) and high sugar (FH) consumption.

METHODS: A total of 40 adolescents were enrolled in the study, and supragingival plaque samples were collected and subjected to metagenomic analyses. The caries status, sugar consumption, and oral-health behaviors of the subjects were recorded.

RESULTS: The results indicate that the CL group showed a higher abundance of several cariogenic microorganisms Lactobacillus, A. gerencseriae, A. dentails, S. mutans, C. albicans, S. wiggsiae and P. acidifaciens. C. gingivalis, and P. gingivalis, which were enriched in the FH group. In terms of gene function, the phosphotransferase sugar uptake system, phosphotransferase system, and several two-component responses-regulator pairs were enriched in the CL group.

CONCLUSION: Overall, our data suggest the existence of an increased cariogenic microbial community and sugar catabolism potential in the CL group, and a healthy microbial community in the FH group, which had self-stabilizing functional potential.}, } @article {pmid36144417, year = {2022}, author = {Esposito, AM and Esposito, MM and Ptashnik, A}, title = {Phylogenetic Diversity of Animal Oral and Gastrointestinal Viromes Useful in Surveillance of Zoonoses.}, journal = {Microorganisms}, volume = {10}, number = {9}, pages = {}, pmid = {36144417}, issn = {2076-2607}, abstract = {Great emphasis has been placed on bacterial microbiomes in human and animal systems. In recent years, advances in metagenomics have allowed for the detection and characterization of more and more native viral particles also residing in these organisms. The digestive tracts of animals and humans-from the oral cavity, to the gut, to fecal excretions-have become one such area of interest. Next-generation sequencing and bioinformatic analyses have uncovered vast phylogenetic virome diversity in companion animals, such as dogs and cats, as well as farm animals and wildlife such as bats. Zoonotic and arthropod-borne illnesses remain major causes of worldwide outbreaks, as demonstrated by the devastating COVID-19 pandemic. This highlights the increasing need to identify and study animal viromes to prevent such disastrous cross-species transmission outbreaks in the coming years. Novel viruses have been uncovered in the viromes of multiple organisms, including birds, bats, cats, and dogs. Although the exact consequences for public health have not yet become clear, many analyses have revealed viromes dominated by RNA viruses, which can be the most problematic to human health, as these genomes are known for their high mutation rates and immune system evasion capabilities. Furthermore, in the wake of worldwide disruption from the COVID-19 pandemic, it is evident that proper surveillance of viral biodiversity is crucial. For instance, gut viral metagenomic analysis in dogs has shown close relationships between the highly abundant canine coronavirus and human coronavirus strains 229E and NL63. Future studies and vigilance could potentially save many lives.}, } @article {pmid36142786, year = {2022}, author = {Mayorga, L and Serrano-Gómez, G and Xie, Z and Borruel, N and Manichanh, C}, title = {Intercontinental Gut Microbiome Variances in IBD.}, journal = {International journal of molecular sciences}, volume = {23}, number = {18}, pages = {}, pmid = {36142786}, issn = {1422-0067}, support = {PI20/00130//Instituto de Salud Carlos III/ ; 812969/MCCC_/Marie Curie/United Kingdom ; PI17/00614//Instituto de Salud Carlos III/ ; }, mesh = {Biomarkers ; *Colitis, Ulcerative/diagnosis ; *Crohn Disease/diagnosis ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; *Inflammatory Bowel Diseases ; }, abstract = {The development of biomarkers for inflammatory bowel disease (IBD) diagnosis would be relevant in a generalized context. However, intercontinental investigation on these microbial biomarkers remains scarce. We examined taxonomic microbiome variations in IBD using published DNA shotgun metagenomic data. For this purpose, we used sequenced data from our previous Spanish Crohn's disease (CD) and ulcerative colitis (UC) cohort, downloaded sequence data from a Chinese CD cohort, and downloaded taxonomic and functional profiling tables from a USA CD and UC cohort. At the global level, geographical location and disease phenotype were the main explanatory covariates of microbiome variations. In healthy controls (HC) and UC, geography turned out to be the most important factor, while disease intestinal location was the most important one in CD. Disease severity correlated with lower alpha-diversity in UC but not in CD. Across geography, alpha-diversity was significantly different independently of health status, except for CD. Despite recruitment from different countries and with different disease severity scores, CD patients may harbor a very similar microbial taxonomic profile. Our study pointed out that geographic location, disease activity status, and other environmental factors are important contributing factors in microbiota changes in IBD. We therefore strongly recommend taking these factors into consideration for future IBD studies to obtain globally valid and reproducible biomarkers.}, } @article {pmid36142684, year = {2022}, author = {Gladkov, GV and Kimeklis, AK and Afonin, AM and Lisina, TO and Orlova, OV and Aksenova, TS and Kichko, AA and Pinaev, AG and Andronov, EE}, title = {The Structure of Stable Cellulolytic Consortia Isolated from Natural Lignocellulosic Substrates.}, journal = {International journal of molecular sciences}, volume = {23}, number = {18}, pages = {}, pmid = {36142684}, issn = {1422-0067}, support = {18-16-00073//Russian Science Foundation/ ; }, mesh = {Bacteria/metabolism ; Cellulose/metabolism ; *Lignin/metabolism ; *Microbial Consortia ; }, abstract = {Recycling plant matter is one of the challenges facing humanity today and depends on efficient lignocellulose degradation. Although many bacterial strains from natural substrates demonstrate cellulolytic activities, the CAZymes (Carbohydrate-Active enZYmes) responsible for these activities are very diverse and usually distributed among different bacteria in one habitat. Thus, using microbial consortia can be a solution to rapid and effective decomposition of plant biomass. Four cellulolytic consortia were isolated from enrichment cultures from composting natural lignocellulosic substrates-oat straw, pine sawdust, and birch leaf litter. Enrichment cultures facilitated growth of similar, but not identical cellulose-decomposing bacteria from different substrates. Major components in all consortia were from Proteobacteria, Actinobacteriota and Bacteroidota, but some were specific for different substrates-Verrucomicrobiota and Myxococcota from straw, Planctomycetota from sawdust and Firmicutes from leaf litter. While most members of the consortia were involved in the lignocellulose degradation, some demonstrated additional metabolic activities. Consortia did not differ in the composition of CAZymes genes, but rather in axillary functions, such as ABC-transporters and two-component systems, usually taxon-specific and associated with CAZymes. Our findings show that enrichment cultures can provide reproducible cellulolytic consortia from various lignocellulosic substrates, the stability of which is ensured by tight microbial relations between its components.}, } @article {pmid36142289, year = {2022}, author = {Graziano, S and Caldara, M and Gullì, M and Bevivino, A and Maestri, E and Marmiroli, N}, title = {A Metagenomic and Gene Expression Analysis in Wheat (T. durum) and Maize (Z. mays) Biofertilized with PGPM and Biochar.}, journal = {International journal of molecular sciences}, volume = {23}, number = {18}, pages = {}, pmid = {36142289}, issn = {1422-0067}, support = {818431//European Union/ ; }, mesh = {Charcoal/chemistry ; Fertilizers/analysis ; Gene Expression ; Plant Roots ; Soil/chemistry ; Soil Microbiology ; *Triticum/genetics ; Water/metabolism ; *Zea mays/metabolism ; }, abstract = {Commodity crops, such as wheat and maize, are extremely dependent on chemical fertilizers, a practice contributing greatly to the increase in the contaminants in soil and water. Promising solutions are biofertilizers, i.e., microbial biostimulants that when supplemented with soil stimulate plant growth and production. Moreover, the biofertilizers can be fortified when (i) provided as multifunctional consortia and (ii) combined with biochar with a high cargo capacity. The aim of this work was to determine the molecular effects on the soil microbiome of different biofertilizers and delivery systems, highlight their physiological effects and merge the data with statistical analyses. The measurements of the physiological parameters (i.e., shoot and root biomass), transcriptomic response of genes involved in essential pathways, and characterization of the rhizosphere population were analyzed. The results demonstrated that wheat and maize supplemented with different combinations of selected microbial consortia and biochar have a positive effect on plant growth in terms of shoot and root biomass; the treatments also had a beneficial influence on the biodiversity of the indigenous rhizo-microbial community, reinforcing the connection between microbes and plants without further spreading contaminants. There was also evidence at the transcriptional level of crosstalk between microbiota and plants.}, } @article {pmid36142138, year = {2022}, author = {Borroni, D and Paytuví-Gallart, A and Sanseverino, W and Gómez-Huertas, C and Bonci, P and Romano, V and Giannaccare, G and Rechichi, M and Meduri, A and Oliverio, GW and Rocha-de-Lossada, C and On Behalf Of Lucy Consortium, }, title = {Exploring the Healthy Eye Microbiota Niche in a Multicenter Study.}, journal = {International journal of molecular sciences}, volume = {23}, number = {18}, pages = {}, pmid = {36142138}, issn = {1422-0067}, mesh = {Cross-Sectional Studies ; DNA ; *Health Promotion ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {PURPOSE: This study aims to explore and characterize healthy eye microbiota.

METHODS: Healthy subjects older than 18 years were selected for this descriptive cross-sectional study. Samples were collected with an eSwab with 1 mL of Liquid Amies Medium (Copan Brescia, Italy). Following DNA extraction, libraries preparation, and amplification, PCR products were purified and end-repaired for barcode ligation. Libraries were pooled to a final concentration of 26 pM. Template preparation was performed with Ion Chef according to Ion 510, Ion 520, and Ion 530 Kit-Chef protocol. Sequencing of the amplicon libraries was carried out on a 520 or 530 chip using the Ion Torrent S5 system (Thermo Fisher; Waltham, MA, USA). Raw reads were analyzed with GAIA (v 2.02).

RESULTS: Healthy eye microbiota is a low-diversity microbiome. The vast majority of the 137 analyzed samples were highly enriched with Staphylococcus, whereas only in a few of them, other genera such as Bacillus, Pseudomonas, and Corynebacterium predominate. We found an average of 88 genera with an average Shannon index of 0.65.

CONCLUSION: We identified nine different ECSTs. A better understanding of healthy eye microbiota has the potential to improve disease diagnosis and personalized regimens to promote health.}, } @article {pmid36140732, year = {2022}, author = {D'Argenio, V and Veneruso, I and Gong, C and Cecarini, V and Bonfili, L and Eleuteri, AM}, title = {Gut Microbiome and Mycobiome Alterations in an In Vivo Model of Alzheimer's Disease.}, journal = {Genes}, volume = {13}, number = {9}, pages = {}, pmid = {36140732}, issn = {2073-4425}, mesh = {*Alzheimer Disease/metabolism ; Animals ; Biomarkers ; Dysbiosis ; Ecosystem ; *Gastrointestinal Microbiome ; Mice ; *Mycobiome ; }, abstract = {Gut microbiota has emerged as an important key regulator of health and disease status. Indeed, gut microbial dysbiosis has been identified in an increasing number of diseases, including neurodegenerative disorders. Accordingly, microbial alterations have been reported also in Alzheimer's disease (AD), suggesting possible pathogenetic mechanisms contributing to the development of specific AD hallmarks and exacerbating metabolic alterations and neuroinflammation. The identification of these mechanisms is crucial to develop novel, targeted therapies and identify potential biomarkers for diagnostic purposes. Thus, the possibility to have AD in vivo models to study this microbial ecosystem represents a great opportunity for translational applications. Here, we characterized both gut microbiome and mycobiome of 3xTg-AD mice, one of the most widely used AD models, to identify specific microbial alterations with respect to the wild-type counterpart. Interestingly, we found a significant reduction of the Coprococcus and an increased abundance of Escherichia_Shigella and Barnesiella genera in the AD mice compatible with a pro-inflammatory status and the development of AD-related pathogenetic features. Moreover, the fungal Dipodascaceae family was significantly increased, thus suggesting a possible contribution to the metabolic alterations found in AD. Our data point out the strict connection between bacterial dysbiosis and AD and, even if further studies are required to clarify the underlining mechanisms, it clearly indicates the need for extensive metagenomic studies over the bacterial counterpart.}, } @article {pmid36138466, year = {2022}, author = {Keller-Costa, T and Kozma, L and Silva, SG and Toscan, R and Gonçalves, J and Lago-Lestón, A and Kyrpides, NC and Nunes da Rocha, U and Costa, R}, title = {Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {151}, pmid = {36138466}, issn = {2049-2618}, mesh = {Animals ; Ankyrins ; *Anthozoa/microbiology ; Chitin ; *Chitinases ; *Gammaproteobacteria ; Metagenomics/methods ; *Microbiota/genetics ; Oxygen ; Phylogeny ; Protein Serine-Threonine Kinases ; *Rhodobacteraceae ; Symbiosis ; }, abstract = {BACKGROUND: The role of bacterial symbionts that populate octocorals (Cnidaria, Octocorallia) is still poorly understood. To shed light on their metabolic capacities, we examined 66 high-quality metagenome-assembled genomes (MAGs) spanning 30 prokaryotic species, retrieved from microbial metagenomes of three octocoral species and seawater.

RESULTS: Symbionts of healthy octocorals were affiliated with the taxa Endozoicomonadaceae, Candidatus Thioglobaceae, Metamycoplasmataceae, unclassified Pseudomonadales, Rhodobacteraceae, unclassified Alphaproteobacteria and Ca. Rhabdochlamydiaceae. Phylogenomics inference revealed that the Endozoicomonadaceae symbionts uncovered here represent two species of a novel genus unique to temperate octocorals, here denoted Ca. Gorgonimonas eunicellae and Ca. Gorgonimonas leptogorgiae. Their genomes revealed metabolic capacities to thrive under suboxic conditions and high gene copy numbers of serine-threonine protein kinases, type 3-secretion system, type-4 pili, and ankyrin-repeat proteins, suggesting excellent capabilities to colonize, aggregate, and persist inside their host. Contrarily, MAGs obtained from seawater frequently lacked symbiosis-related genes. All Endozoicomonadaceae symbionts harbored endo-chitinase and chitin-binging protein-encoding genes, indicating that they can hydrolyze the most abundant polysaccharide in the oceans. Other symbionts, including Metamycoplasmataceae and Ca. Thioglobaceae, may assimilate the smaller chitin oligosaccharides resulting from chitin breakdown and engage in chitin deacetylation, respectively, suggesting possibilities for substrate cross-feeding and a role for the coral microbiome in overall chitin turnover. We also observed sharp differences in secondary metabolite production potential between symbiotic lineages. Specific Proteobacteria taxa may specialize in chemical defense and guard other symbionts, including Endozoicomonadaceae, which lack such capacity.

CONCLUSION: This is the first study to recover MAGs from dominant symbionts of octocorals, including those of so-far unculturable Endozoicomonadaceae, Ca. Thioglobaceae and Metamycoplasmataceae symbionts. We identify a thus-far unanticipated, global role for Endozoicomonadaceae symbionts of corals in the processing of chitin, the most abundant natural polysaccharide in the oceans and major component of the natural zoo- and phytoplankton feed of octocorals. We conclude that niche partitioning, metabolic specialization, and adaptation to low oxygen conditions among prokaryotic symbionts likely contribute to the plasticity and adaptability of the octocoral holobiont in changing marine environments. These findings bear implications not only for our understanding of symbiotic relationships in the marine realm but also for the functioning of benthic ecosystems at large. Video Abstract.}, } @article {pmid36138352, year = {2022}, author = {Liu, G and Zhang, BF and Chang, J and Hu, XL and Li, C and Xu, TT and Liu, SQ and Hu, DF}, title = {Population genomics reveals moderate genetic differentiation between populations of endangered Forest Musk Deer located in Shaanxi and Sichuan.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {668}, pmid = {36138352}, issn = {1471-2164}, support = {31872962//National Natural Science Foundation of China/ ; 2019HB2096001006//The Biodiversity Survey, Monitoring and Assessment Project (2019-2023) of the Ministry of Ecology and Environment/ ; }, mesh = {Animals ; China ; *Deer/genetics ; *Endangered Species ; Forests ; *Genetics, Population ; Metagenomics ; Nucleotides ; Phylogeny ; }, abstract = {BACKGROUND: Many endangered species exist in small, genetically depauperate, or inbred populations, hence promoting genetic differentiation and reducing long-term population viability. Forest Musk Deer (Moschus berezovskii) has been subject to illegal hunting for hundreds of years due to the medical and commercial values of musk, resulting in a significant decline in population size. However, it is still unclear to what extent the genetic exchange and inbreeding levels are between geographically isolated populations. By using whole-genome data, we reconstructed the demographic history, evaluated genetic diversity, and characterized the population genetic structure of Forest Musk Deer from one wild population in Sichuan Province and two captive populations from two ex-situ centers in Shaanxi Province.

RESULTS: SNP calling by GATK resulted in a total of 44,008,662 SNPs. Principal component analysis (PCA), phylogenetic tree (NJ tree), ancestral component analysis (ADMIXTURE) and the ABBA-BABA test separated Sichuan and Shaanxi Forest Musk Deer as two genetic clusters, but no obvious genetic differentiation was observed between the two captive populations. The average pairwise FST value between the populations in Sichuan and Shaanxi ranged from 0.05-0.07, suggesting a low to moderate genetic differentiation. The mean heterozygous SNPs rate was 0.14% (0.11%-0.15%) for Forest Musk Deer at the genomic scale, and varied significantly among three populations (Chi-square = 1.22, p < 0.05, Kruskal-Wallis Test), with the Sichuan population having the lowest (0.11%). The nucleotide diversity of three populations varied significantly (p < 0.05, Kruskal-Wallis Test), with the Sichuan population having the lowest genetic θπ (1.69 × 10[-3]).

CONCLUSIONS: Genetic diversity of Forest Musk Deer was moderate at the genomic scale compared with other endangered species. Genetic differentiation between populations in Sichuan and Shaanxi may not only result from historical biogeographical factors but also be associated with contemporary human disturbances. Our findings provide scientific aid for the conservation and management of Forest Musk Deer. They can extend the proposed measures at the genomic level to apply to other musk deer species worldwide.}, } @article {pmid36137486, year = {2022}, author = {Afridi, MS and Fakhar, A and Kumar, A and Ali, S and Medeiros, FHV and Muneer, MA and Ali, H and Saleem, M}, title = {Harnessing microbial multitrophic interactions for rhizosphere microbiome engineering.}, journal = {Microbiological research}, volume = {265}, number = {}, pages = {127199}, doi = {10.1016/j.micres.2022.127199}, pmid = {36137486}, issn = {1618-0623}, mesh = {Crops, Agricultural ; *Microbiota ; Plant Roots ; *Rhizosphere ; Soil ; Soil Microbiology ; }, abstract = {The rhizosphere is a narrow and dynamic region of plant root-soil interfaces, and it's considered one of the most intricate and functionally active ecosystems on the Earth, which boosts plant health and alleviates the impact of biotic and abiotic stresses. Improving the key functions of the microbiome via engineering the rhizosphere microbiome is an emerging tool for improving plant growth, resilience, and soil-borne diseases. Recently, the advent of omics tools, gene-editing techniques, and sequencing technology has allowed us to unravel the entangled webs of plant-microbes interactions, enhancing plant fitness and tolerance to biotic and abiotic challenges. Plants secrete signaling compounds with low molecular weight into the rhizosphere, that engage various species to generate a massive deep complex array. The underlying principle governing the multitrophic interactions of the rhizosphere microbiome is yet unknown, however, some efforts have been made for disease management and agricultural sustainability. This review discussed the intra- and inter- microbe-microbe and microbe-animal interactions and their multifunctional roles in rhizosphere microbiome engineering for plant health and soil-borne disease management. Simultaneously, it investigates the significant impact of immunity utilizing PGPR and cover crop strategy in increasing rhizosphere microbiome functions for plant development and protection using omics techniques. The ecological engineering of rhizosphere plant interactions could be used as a potential alternative technology for plant growth improvement, sustainable disease control management, and increased production of economically significant crops.}, } @article {pmid36135710, year = {2022}, author = {Tan, Y and Du, H and Zhang, H and Fang, C and Jin, G and Chen, S and Wu, Q and Zhang, Y and Zhang, M and Xu, Y}, title = {Geographically Associated Fungus-Bacterium Interactions Contribute to the Formation of Geography-Dependent Flavor during High-Complexity Spontaneous Fermentation.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0184422}, pmid = {36135710}, issn = {2165-0497}, mesh = {Humans ; Fermentation ; *Bacteria/metabolism ; *Microbiota/physiology ; Fungi/physiology ; Geography ; }, abstract = {Fermented foods often have attractive flavor characteristics to meet various human demands. An ever-challenging target is the production of fermented foods with equal flavor profiles outside the product's origin. However, the formation of geography-dependent flavor in high-complexity fermentations remains poorly understood. Here, taking Chinese liquor (baijiu) fermentation as an example, we collected 403 samples from 9 different locations in China across a latitude range of 27°N to 37°N. We revealed and validated the geography-dependent flavor formation patterns by using culture-independent (metabolomics, metagenomics, and metatranscriptomics) and culture-dependent tools. We found that the baijiu microbiomes along with their metabolites were flavor related and geography dependent. The geographical characteristics were determined mainly by 20 to 40 differentiated chemical markers in metabolites and the latitude-dependent fungal structure of the microbiome. About 48 to 156 core microbiota members out of 735 bacterial genera and 290 fungal genera contributed to the chemical markers. The contributions of both fungi and bacteria were greater than those from either bacteria or fungi alone. Representatively, we revealed that dynamic interdependent interactions between yeasts and Lactobacillus facilitated the metabolism of heterocyclic flavor chemicals such as 2-acetylpyrrole, 2,3,5-trimethylpyrazine, and 2-acetylfuran. Moreover, we found that the intraspecific genomic diversity and microbial structure were two biotic factors that contributed to dynamic microbiome assembly. Based on the assembly pattern, adjusting the composition and distribution of initial species was one option to regulate the formation of diverse flavor characteristics. Our study provided a rationale for developing a microbiome design to achieve a defined flavor goal. IMPORTANCE People consume many spontaneously fermented foods and beverages with different flavors on a daily basis. One crucial and hotly discussed question is how to reproduce fermented food flavor without geographical limitations to meet diverse human demands. The constantly enriched knowledge of the microbial contribution to fermented flavor offers valuable insights into flavor biotechnological development. However, we still have a poor understanding of what factors limit the reproduction of fermented flavor outside the product's origin in high-complexity spontaneous fermentations. Here, taking baijiu fermentation as an example, we revealed that geography-dependent flavor was contributed mainly by fungus-bacterium cooperative metabolism. The distinct initial microbial composition, distribution, and intraspecific genomic diversity limited reproducible microbial interactions and metabolism in different geographical areas. The abundant microbial resources and predicted fungus-bacterium interactions found in baijiu fermentation enable us to design a synthetic microbial community to reproduce desired flavor profiles in the future.}, } @article {pmid36135388, year = {2022}, author = {Peroumal, D and Sahu, SR and Kumari, P and Utkalaja, BG and Acharya, N}, title = {Commensal Fungus Candida albicans Maintains a Long-Term Mutualistic Relationship with the Host To Modulate Gut Microbiota and Metabolism.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0246222}, pmid = {36135388}, issn = {2165-0497}, mesh = {Mice ; Animals ; *Candida albicans/genetics ; *Gastrointestinal Microbiome/physiology ; Symbiosis ; Obesity ; Hormones ; Body Weight ; DNA, Ribosomal ; }, abstract = {Candida albicans survives as a commensal fungus in the gastrointestinal tract, and that its excessive growth causes infections in immunosuppressed individuals is widely accepted. However, any mutualistic relationship that may exist between C. albicans and the host remains undetermined. Here, we showed that a long-term feeding of C. albicans does not cause any noticeable infections in the mouse model. Our 16S and 18S ribosomal DNA (rDNA) sequence analyses suggested that C. albicans colonizes in the gut and modulates microbiome dynamics, which in turn mitigates high-fat-diet-induced uncontrolled body weight gain and metabolic hormonal imbalances. Interestingly, adding C. albicans to a nonobesogenic diet stimulated the appetite-regulated hormones and helped the mice maintain a healthy body weight. In concert, our results suggest a mutualism between C. albicans and the host, contrary to the notion that C. albicans is always an adversary and indicating it can instead be a bona fide admirable companion of the host. Finally, we discuss its potential translational implication as a probiotic, especially in obese people or people dependent on high-fat calorie intakes to manage obesity associated complications. IMPORTANCE Candida albicans is mostly considered an opportunistic pathogen that causes fetal systemic infections. However, this study demonstrates that in its commensal state, it maintains a long-term mutualistic relationship with the host and regulates microbial dynamics in the gut and host physiology. Thus, we concluded that C. albicans is not always an adversary but rather can be a bona fide admirable companion of the host. More importantly, as several genomic knockout strains of C. albicans were shown to be avirulent, such candidate strains may be explored further as preferable probiotic isolates to control obesity.}, } @article {pmid36131174, year = {2023}, author = {Su, C and Zhou, X and Lu, P and Dai, X and Chen, Z and Liang, B and Tian, Y and Chen, M}, title = {Role of coke media strategy in an adsorption-biological coupling technology for wastewater treatment performance, microbial community, and metabolic pathways features.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {5}, pages = {13469-13482}, pmid = {36131174}, issn = {1614-7499}, mesh = {Wastewater ; Waste Disposal, Fluid/methods ; *Coke ; Adsorption ; Bioreactors ; Nitrification ; *Microbiota ; Nitrogen/metabolism ; *Water Purification ; Carbon ; Phosphorus ; Metabolic Networks and Pathways ; Phosphates ; Denitrification ; Sewage/microbiology ; }, abstract = {With the increase of wastewater discharge, the requirement of wastewater treatment technology is gradually increased. How to treat wastewater economically, while making the treatment process short, easy to manage and low running cost, is the focus of attention. Adsorption-biological coupling technology could make adsorption and biodegradation complement each other, which has coupled accumulation effect. In this study, with coke as the adsorbent, the efficiency of the adsorption-biological coupling reactor on the treatment of total phosphorus (TP), chemical oxygen demand (COD), and ammonia nitrogen (NH3-N) in domestic wastewater under different influent modes was investigated. Meanwhile, microbial community and metabolic pathways analysis of the reactor were carried out. Results showed that when the influent modes of the coupling reactor was once a day and the daily sewage treatment capacity was 2 L, the treatment efficiency of TP, COD, and NH3-N was the best. The removal rate of TP and NH3-N was 87.96% and 96.14%, respectively. The dominant phylum was Proteobacteria (39.84-44.49%), and the dominant genus was Sphingomonas (4.27-7.16%), and Gemmatimonas (1.27-3.58%). According to the metagenomic analysis, carbon metabolism process was evenly distributed in U (upper), M (middle), and L (lower) layers of the coupling reactor. Phosphate metabolism was mainly in the U layer at first, then in the M and L layers gradually. Carbon metabolism and phosphate metabolism provided sufficient energy for microbial degradation of pollutants. Nitrogen removal in the reactor mainly happened in the S and Z layers by nitrification (M00528) and denitrification (M00529), respectively.}, } @article {pmid36130883, year = {2023}, author = {Kato-Kogoe, N and Kamiya, K and Sakaguchi, S and Omori, M and Komori, E and Kudo, A and Nakamura, S and Nakano, T and Ueno, T and Tamaki, J and Hoshiga, M}, title = {Salivary Microbiota Associated with Peripheral Microvascular Endothelial Dysfunction.}, journal = {Journal of atherosclerosis and thrombosis}, volume = {30}, number = {7}, pages = {820-833}, pmid = {36130883}, issn = {1880-3873}, mesh = {Humans ; Aged ; Saliva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Hyperemia ; *Atherosclerosis ; }, abstract = {AIMS: Oral health is associated with atherosclerotic cardiovascular disease (ACVD). We previously identified the salivary microbiota characteristics of patients with ACVD. However, whether salivary microbiota is characteristic under impaired vascular endothelial function before ACVD onset remains unclear. Therefore, we aimed to evaluate the characteristics of salivary microbiota associated with peripheral microvascular endothelial dysfunction.

METHODS: We collected saliva samples from 172 community-dwelling elderly individuals without a history of ACVD and performed 16S rRNA metagenomic analysis. We assessed the peripheral microvascular endothelial function using reactive hyperemia index (RHI) and compared the salivary microbiota in the groups with normal (RHI ≥ 2.10), borderline, and abnormal (RHI ＜1.67) peripheral endothelial function. Furthermore, we applied machine learning techniques to evaluate whether salivary microbiota could discriminate between individuals with normal and abnormal endothelial function.

RESULTS: The number of operational taxonomic units (OTUs) was higher in the abnormal group than in the normal group (p=0.037), and differences were found in the overall salivary microbiota structure (unweighted UniFrac distances, p=0.038). The linear discriminant analysis (LDA) effect size (LEfSe) algorithm revealed several significantly differentially abundant bacterial genera between the two groups. An Extra Trees classifier model was built to discriminate between groups with normal and abnormal vascular endothelial function based on the microbial composition at the genus level (AUC=0.810).

CONCLUSIONS: The salivary microbiota in individuals with endothelial dysfunction was distinct from that in individuals with normal endothelial function, indicating that the salivary microbiota may be related to endothelial function.}, } @article {pmid36128620, year = {2022}, author = {Li, Y and Sun, H and Huang, Y and Yin, A and Zhang, L and Han, J and Lyu, Y and Xu, X and Zhai, Y and Sun, H and Wang, P and Zhao, J and Sun, S and Dong, H and Zhu, F and Wang, Q and Augusto Rohde, L and Xie, X and Sun, X and Xiong, L}, title = {Gut metagenomic characteristics of ADHD reveal low Bacteroides ovatus-associated host cognitive impairment.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2125747}, pmid = {36128620}, issn = {1949-0984}, mesh = {Animals ; *Attention Deficit Disorder with Hyperactivity/microbiology ; Bacteroides ; Cognition ; *Cognitive Dysfunction ; *Gastrointestinal Microbiome/physiology ; Humans ; Rats ; }, abstract = {Attention-deficit/hyperactivity disorder (ADHD) is a highly heterogeneous psychiatric disorder that can have three phenotypical presentations: inattentive (I-ADHD), hyperactive-impulsive (HI-ADHD), and combined (C-ADHD). Environmental factors correlated with the gut microbiota community have been implicated in the development of ADHD. However, whether different ADHD symptomatic presentations are associated with distinct microbiota compositions and whether patients could benefit from the correction of aberrant bacterial colonization are still largely unclear. We carried out metagenomic shotgun analysis with 207 human fecal samples to characterize the gut microbial profiles of patients with ADHD grouped according to their phenotypical presentation. Then, we transplanted the candidate low-abundance bacteria identified in patient subgroups into ADHD rats and evaluated ADHD-associated behaviors and neuronal activation in these rats. Patients with C-ADHD had a different gut microbial composition from that of healthy controls (HCs) (p = .02), but not from that of I-ADHD patients. Eight species became progressively attenuated or enriched when comparing the compositions of HCs to those of I-ADHD and C-ADHD; in particular, the abundance of Bacteroides ovatus was depleted in patients with C-ADHD. In turn, Bacteroides ovatus supplementation ameliorated spatial working memory deficits and reversed θ electroencephalogram rhythm alterations in ADHD rats. In addition, Bacteroides ovatus induced enhanced neuronal activation in the hippocampal CA1 subregion. These findings indicate that gut microbial characteristics that are unique to patients with C-ADHD may be masked when considering a more heterogeneous group of patients. We link the gut microbiota to brain function in an ADHD animal model, suggesting the relevance of testing a potential bacteria-based intervention for some aspects of ADHD.}, } @article {pmid36126709, year = {2023}, author = {Loiola, M and Silva, AET and Krull, M and Barbosa, FA and Galvão, EH and Patire, VF and Cruz, ICS and Barros, F and Hatje, V and Meirelles, PM}, title = {Mangrove microbial community recovery and their role in early stages of forest recolonization within shrimp ponds.}, journal = {The Science of the total environment}, volume = {855}, number = {}, pages = {158863}, doi = {10.1016/j.scitotenv.2022.158863}, pmid = {36126709}, issn = {1879-1026}, mesh = {Animals ; *Ecosystem ; Ponds ; Forests ; Wetlands ; Soil/chemistry ; Crustacea ; *Microbiota ; }, abstract = {Shrimp farming is blooming worldwide, posing a severe threat to mangroves and its multiple goods and ecosystem services. Several studies reported the impacts of aquaculture on mangrove biotic communities, including microbiomes. However, little is known about how mangrove soil microbiomes would change in response to mangrove forest recolonization. Using genome-resolved metagenomics, we compared the soil microbiome of mangrove forests (both with and without the direct influence of shrimp farming effluents) with active shrimp farms and mangroves under a recolonization process. We found that the structure and composition of active shrimp farms microbial communities differ from the control mangrove forests, mangroves under the impact of the shrimp farming effluents, and mangroves under recolonization. Shrimp farming ponds microbiomes have lower microbial diversity and are dominated by halophilic microorganisms, presenting high abundance of multiple antibiotic resistance genes. On the other hand, control mangrove forests, impacted mangroves (exposed to the shrimp farming effluents), and recolonization ponds were more diverse, with a higher abundance of genes related to carbon mobilization. Our data also indicated that the microbiome is recovering in the mangrove recolonization ponds, performing vital metabolic functions and functionally resembling microbiomes found in those soils of neighboring control mangrove forests. Despite highlighting the damage caused by the habitat changes in mangrove soil microbiome community and functioning, our study sheds light on these systems incredible recovery capacity. Our study shows the importance of natural mangrove forest recovery, enhancing ecosystem services by the soil microbial communities even in a very early development stage of mangrove forest, thus encouraging mangrove conservation and restoration efforts worldwide.}, } @article {pmid36126379, year = {2022}, author = {Roessler, J and Leistner, DM and Landmesser, U and Haghikia, A}, title = {Modulatory role of gut microbiota in cholesterol and glucose metabolism: Potential implications for atherosclerotic cardiovascular disease.}, journal = {Atherosclerosis}, volume = {359}, number = {}, pages = {1-12}, doi = {10.1016/j.atherosclerosis.2022.08.018}, pmid = {36126379}, issn = {1879-1484}, mesh = {*Atherosclerosis ; *Cardiovascular Diseases/metabolism ; Cholesterol/metabolism ; *Gastrointestinal Microbiome ; Glucose/metabolism ; Humans ; }, abstract = {Accumulating evidence suggests an important role of gut microbiota in physiological processes of host metabolism as well as cardiometabolic disease. Recent advances in metagenomic and metabolomic research have led to discoveries of novel pathways in which intestinal microbial metabolism of dietary nutrients is linked to metabolic profiles and cardiovascular disease risk. A number of metaorganismal circuits have been identified by microbiota transplantation studies and experimental models using germ-free rodents. Many of these pathways involve gut microbiota-related bioactive metabolites that impact host metabolism, in particular lipid and glucose homeostasis, partly via specific host receptors. In this review, we summarize the current knowledge of how the gut microbiome can impact cardiometabolic phenotypes and provide an overview of recent advances of gut microbiome research. Finally, the potential of modulating intestinal microbiota composition and/or targeting microbiota-related pathways for novel preventive and therapeutic strategies in cardiometabolic and cardiovascular diseases will be discussed.}, } @article {pmid36125585, year = {2022}, author = {Aydin, S and Erözden, AA and Tavşanlı, N and Müdüroğlu, A and Çalışkan, M and Kara, İ}, title = {Anthocyanin Addition to Kefir: Metagenomic Analysis of Microbial Community Structure.}, journal = {Current microbiology}, volume = {79}, number = {11}, pages = {327}, pmid = {36125585}, issn = {1432-0991}, support = {38774//Istanbul Üniversitesi/ ; }, mesh = {Anthocyanins ; Fermentation ; *Kefir/microbiology ; *Microbiota ; Streptococcus thermophilus ; }, abstract = {The addition of anthocyanin to kefir for the production of more functional and bio-diversified kefir beverages has the potential to increase kefir's healthful activities. In the present study, anthocyanin extracts, obtained from black carrots, were added into kefir mixture during the fermentation process in different concentrations (1% and 5%, w/v). These kefir samples were then analyzed in terms of their microbiological qualities by metagenomic analysis. The results of the analyses show that the addition of anthocyanin has significant impacts on the community structure of kefir microbiome which in turn directly affects the expected health impacts of the beverage. Kefir with no anthocyanin included predominantly probiotic bacteria such as Lactococcus lactis (34%) and Lactobacillus kefiri (34%). On the other hand, kefir with 1% anthocyanin demonstrated a more balanced distribution of probiotic species like Lb. kefiri (17%), Leuconostoc mesenteroides (9%), and Lc. lactis (5%) at similar abundance rates. 5% anthocyanin kefir demonstrated the highest polarity in the community with a strong dominance of probiotic Lb. kefiri (72%), and distinctly less abundant bacteria such as Streptococcus salivarius subsp. thermophilus (3%). These findings provide that fortification with anthocyanins can be utilized to enhance the quality, composition, and beneficial functions of kefir.}, } @article {pmid36123651, year = {2022}, author = {Li, Q and Vehik, K and Li, C and Triplett, E and Roesch, L and Hu, YJ and Krischer, J}, title = {A robust and transformation-free joint model with matching and regularization for metagenomic trajectory and disease onset.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {661}, pmid = {36123651}, issn = {1471-2164}, support = {P30 CA021765/CA/NCI NIH HHS/United States ; U24 DK097771/DK/NIDDK NIH HHS/United States ; CA21765/CA/NCI NIH HHS/United States ; U24DK097771/DK/NIDDK NIH HHS/United States ; }, mesh = {Cohort Studies ; Feces ; Humans ; *Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {BACKGROUND: To identify operational taxonomy units (OTUs) signaling disease onset in an observational study, a powerful strategy was selecting participants by matched sets and profiling temporal metagenomes, followed by trajectory analysis. Existing trajectory analyses modeled individual OTU or microbial community without adjusting for the within-community correlation and matched-set-specific latent factors.

RESULTS: We proposed a joint model with matching and regularization (JMR) to detect OTU-specific trajectory predictive of host disease status. The between- and within-matched-sets heterogeneity in OTU relative abundance and disease risk were modeled by nested random effects. The inherent negative correlation in microbiota composition was adjusted by incorporating and regularizing the top-correlated taxa as longitudinal covariate, pre-selected by Bray-Curtis distance and elastic net regression. We designed a simulation pipeline to generate true biomarkers for disease onset and the pseudo biomarkers caused by compositionality. We demonstrated that JMR effectively controlled the false discovery and pseudo biomarkers in a simulation study generating temporal high-dimensional metagenomic counts with random intercept or slope. Application of the competing methods in the simulated data and the TEDDY cohort showed that JMR outperformed the other methods and identified important taxa in infants' fecal samples with dynamics preceding host disease status.

CONCLUSION: Our method JMR is a robust framework that models taxon-specific trajectory and host disease status for matched participants without transformation of relative abundance, improving the power of detecting disease-associated microbial features in certain scenarios. JMR is available in R package mtradeR at https://github.com/qianli10000/mtradeR.}, } @article {pmid36123312, year = {2022}, author = {Perez-Molphe-Montoya, E and Küsel, K and Overholt, WA}, title = {Redefining the phylogenetic and metabolic diversity of phylum Omnitrophota.}, journal = {Environmental microbiology}, volume = {24}, number = {11}, pages = {5437-5449}, doi = {10.1111/1462-2920.16170}, pmid = {36123312}, issn = {1462-2920}, mesh = {RNA, Ribosomal, 16S/genetics/metabolism ; Phylogeny ; *Ecosystem ; *Metagenome ; Bacteria ; }, abstract = {The candidate phylum Omnitrophica-recently termed Omnitrophota, and originally known as OP3-is an understudied bacterial clade that has primarily been found in aquatic ecosystems. To characterize the diversity and ecology of this phylum, we reconstructed 55 Omnitrophota metagenome-assembled genomes (MAGs) from a well-characterized groundwater system within central Germany and placed them within the context of publicly available genomes. Seven clades were identified, four of which contained novel genomes obtained from our groundwater system. All clades exhibited the capacity for type IV pili, type II secretion systems, glycogen storage, and carbohydrate degradation. Only the characterized Cand. Omnitrophus magneticus genome exhibited functions associated with magnetosome construction. Clades were characterized by sets of traits rather than unique pathways, which were then used to infer ecological strategies. These lifestyles consisted of mixotrophs, obligate fermenters, and versatile respiratory heterotrophs. Patterns in 16S rRNA gene amplicons from a 6 years, monthly sampled groundwater time-series dataset reflected the persistent and widespread occurrence of Clade 7 Wood-Ljungdahl utilizing mixotrophs and highlight this group as a core member of the groundwater community. Overall, this study uncovered, characterized, and contextualized the metabolic and phylogenetic diversity within phylum Omnitrophota, and predicts that environmental populations may mediate both nitrogen and sulfur cycling, along with organic matter production and degradation within aquatic ecosystems.}, } @article {pmid36122838, year = {2023}, author = {Thompson, DS and Fu, C and Gandhi, T and Fowler, JC and Frueh, BC and Weinstein, BL and Petrosino, J and Hadden, JK and Carlson, M and Coarfa, C and Madan, A}, title = {Differential co-expression networks of the gut microbiota are associated with depression and anxiety treatment resistance among psychiatric inpatients.}, journal = {Progress in neuro-psychopharmacology & biological psychiatry}, volume = {120}, number = {}, pages = {110638}, pmid = {36122838}, issn = {1878-4216}, support = {U54 HG004973/HG/NHGRI NIH HHS/United States ; P42 ES027725/ES/NIEHS NIH HHS/United States ; R25 GM056929/GM/NIGMS NIH HHS/United States ; R25 GM069234/GM/NIGMS NIH HHS/United States ; P50 MD015496/MD/NIMHD NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Depression ; Inpatients ; Anxiety ; Biomarkers ; }, abstract = {BACKGROUND: Comorbid anxiety and depression are common and are associated with greater disease burden than either alone. Our recent efforts have identified an association between gut microbiota dysfunction and severity of anxiety and depression. In this follow-up, we applied Differential Co-Expression Analysis (DiffCoEx) to identify potential gut microbiota biomarker(s) candidates of treatment resistance among psychiatric inpatients.

METHODS: In a sample of convenience, 100 psychiatric inpatients provided clinical data at admission and discharge; fecal samples were collected early during the hospitalization. Whole genome shotgun sequencing methods were used to process samples. DiffCoEx was used to identify clusters of microbial features significantly different based on treatment resistance status. Once overlapping features were identified, a knowledge-mining tool was used to review the literature using a list of microbial species/pathways and a select number of medical subject headlines (MeSH) terms relevant for depression, anxiety, and brain-gut-axis dysregulation. Network analysis used overlapping features to identify microbial interactions that could impact treatment resistance.

RESULTS: DiffCoEx analyzed 10,403 bacterial features: 43/44 microbial features associated with depression treatment resistance overlapped with 43/114 microbial features associated with anxiety treatment resistance. Network analysis resulted in 8 biological interactions between 16 bacterial species. Clostridium perfringens evidenced the highest connection strength (0.95). Erysipelotrichaceae bacterium 6_1_45 has been most widely examined, is associated with inflammation and dysbiosis, but has not been associated with depression or anxiety.

CONCLUSION: DiffCoEx potentially identified gut bacteria biomarker candidates of depression and anxiety treatment-resistance. Future efforts in psychiatric microbiology should examine the mechanistic relationship of identified pro-inflammatory species, potentially contributing to a biomarker-based algorithm for treatment resistance.}, } @article {pmid36121227, year = {2022}, author = {Ramos-Tapia, I and Nuñez, R and Salinas, C and Salinas, P and Soto, J and Paneque, M}, title = {Study of Wetland Soils of the Salar de Atacama with Different Azonal Vegetative Formations Reveals Changes in the Microbiota Associated with Hygrophile Plant Type on the Soil Surface.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0053322}, pmid = {36121227}, issn = {2165-0497}, mesh = {Bacteria/genetics ; *Microbiota/genetics ; Phylogeny ; Plants ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; *Wetlands ; }, abstract = {Salar de Atacama is located approximately 55 km south of San Pedro de Atacama in the Antofagasta region, Chile. The high UV irradiation and salt concentration and extreme drought make Salar de Atacama an ideal site to search for novel soil microorganisms with unique properties. Here, we used a metataxonomic approach (16S rRNA V3-V4) to identify and characterize the soil microbiota associated with different surface azonal vegetation formations, including strict hygrophiles (Baccharis juncea, Juncus balticus, and Schoenoplectus americanus), transitional hygrophiles (Distichlis spicata, Lycium humile, and Tessaria absinthioides), and their various combinations. We detected compositional differences among the soil surface microbiota associated with each plant formation in the sampling area. There were changes in soil microbial phylogenetic diversity from the strict to the transitional hygrophiles. Moreover, we found alterations in the abundance of bacterial phyla and genera. Halobacteriota and Actinobacteriota might have facilitated water uptake by the transitional hygrophiles. Our findings helped to elucidate the microbiota of Salar de Atacama and associate them with the strict and transitional hygrophiles indigenous to the region. These findings could be highly relevant to future research on the symbiotic relationships between microbiota and salt-tolerant plants in the face of climate change-induced desertification. IMPORTANCE The study of the composition and diversity of the wetland soil microbiota associated with hygrophilous plants in a desert ecosystem of the high Puna in northern Chile makes it an ideal approach to search for novel extremophilic microorganisms with unique properties. These microorganisms are adapted to survive in ecological niches, such as those with high UV irradiation, extreme drought, and high salt concentration; they can be applied in various fields, such as biotechnology and astrobiology, and industries, including the pharmaceutical, food, agricultural, biofuel, cosmetic, and textile industries. These microorganisms can also be used for ecological conservation and restoration. Extreme ecosystems are a unique biological resource and biodiversity hot spots that play a crucial role in maintaining environmental sustainability. The findings could be highly relevant to future research on the symbiotic relationships between microbiota and extreme-environment-tolerant plants in the face of climate change-induced desertification.}, } @article {pmid36121163, year = {2022}, author = {Fierer, N and Holland-Moritz, H and Alexiev, A and Batther, H and Dragone, NB and Friar, L and Gebert, MJ and Gering, S and Henley, JB and Jech, S and Kibby, EM and Melie, T and Patterson, WB and Peterson, E and Schutz, K and Stallard-Olivera, E and Sterrett, J and Walsh, C and Mansfeldt, C}, title = {A Metagenomic Investigation of Spatial and Temporal Changes in Sewage Microbiomes across a University Campus.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0065122}, pmid = {36121163}, issn = {2379-5077}, support = {T32 GM008759/GM/NIGMS NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Sewage/microbiology ; Wastewater ; Universities ; *Microbiota/genetics ; Metagenome/genetics ; Bacteria/genetics ; }, abstract = {Wastewater microbial communities are not static and can vary significantly across time and space, but this variation and the factors driving the observed spatiotemporal variation often remain undetermined. We used a shotgun metagenomic approach to investigate changes in wastewater microbial communities across 17 locations in a sewer network, with samples collected from each location over a 3-week period. Fecal material-derived bacteria constituted a relatively small fraction of the taxa found in the collected samples, highlighting the importance of environmental sources to the sewage microbiome. The prokaryotic communities were highly variable in composition depending on the location within the sampling network, and this spatial variation was most strongly associated with location-specific differences in sewage pH. However, we also observed substantial temporal variation in the composition of the prokaryotic communities at individual locations. This temporal variation was asynchronous across sampling locations, emphasizing the importance of independently considering both spatial and temporal variation when assessing the wastewater microbiome. The spatiotemporal patterns in viral community composition closely tracked those of the prokaryotic communities, allowing us to putatively identify the bacterial hosts of some of the dominant viruses in these systems. Finally, we found that antibiotic resistance gene profiles also exhibit a high degree of spatiotemporal variability, with most of these genes unlikely to be derived from fecal bacteria. Together, these results emphasize the dynamic nature of the wastewater microbiome, the challenges associated with studying these systems, and the utility of metagenomic approaches for building a multifaceted understanding of these microbial communities and their functional attributes. IMPORTANCE Sewage systems harbor extensive microbial diversity, including microbes derived from both human and environmental sources. Studies of the sewage microbiome are useful for monitoring public health and the health of our infrastructure, but the sewage microbiome can be highly variable in ways that are often unresolved. We sequenced DNA recovered from wastewater samples collected over a 3-week period at 17 locations in a single sewer system to determine how these communities vary across time and space. Most of the wastewater bacteria, and the antibiotic resistance genes they harbor, were not derived from human feces, but human usage patterns did impact how the amounts and types of bacteria and bacterial genes we found in these systems varied over time. Likewise, the wastewater communities, including both bacteria and their viruses, varied depending on location within the sewage network, highlighting the challenges and opportunities in efforts to monitor and understand the sewage microbiome.}, } @article {pmid36121066, year = {2022}, author = {Shi, T and Zhang, T and Wang, X and Wang, X and Shen, W and Guo, X and Liu, Y and Li, Z and Jiang, Y}, title = {Metagenomic Analysis of in Vitro Ruminal Fermentation Reveals the Role of the Copresent Microbiome in Plant Biomass Degradation.}, journal = {Journal of agricultural and food chemistry}, volume = {70}, number = {38}, pages = {12095-12106}, doi = {10.1021/acs.jafc.2c03522}, pmid = {36121066}, issn = {1520-5118}, mesh = {Animals ; Biomass ; Fatty Acids, Volatile/metabolism ; Fermentation ; *Metagenome ; *Microbiota ; Pectins/metabolism ; Rumen/metabolism ; Xylans/metabolism ; }, abstract = {In vitro ruminal fermentation is considered an efficient way to degrade crop residue. To better understand the microbial communities and their functions during in vitro ruminal fermentation, the microbiome and short chain fatty acid (SCFA) production were investigated using the metagenomic sequencing and rumen simulation technique (RUSITEC) system. A total of 1677 metagenome-assembled genomes (MAGs) were reconstructed, and 298 MAGs were found copresenting in metagenomic data of the current work and 58 previously ruminal representative samples. Additionally, the domains related to pectin and xylan degradation were overrepresented in the copresent MAGs compared with total MAGs. Among the copresent MAGs, we obtained 14 MAGs with SCFA-synthesis-related genes positively correlated with SCFA concentrations. The MAGs obtained from this study enable a better understanding of dominant microbial communities across in vivo and in vitro ruminal fermentation and show promise for pointing out directions for further research on in vitro ruminal fermentation.}, } @article {pmid36119925, year = {2022}, author = {Prasetiyono, BWHE and Widiyanto, W and Pandupuspitasari, NS}, title = {Gut Microbiota Profiles in Dairy Cattle from Highland and Coastal Regions Using Shotgun Metagenomic Approach.}, journal = {BioMed research international}, volume = {2022}, number = {}, pages = {3659052}, pmid = {36119925}, issn = {2314-6141}, mesh = {Animals ; Cattle ; Firmicutes ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {There is significant difference in milk production of highland and coastal regions in Indonesia of which the latter is critically low. The recent studies indicate a possibility of improving the milk yield and quality by manipulating the gut microbiota, for which profiling and abundance of gut microbiota in these divergent regions need to be addressed. The present study was the first of its kind to explore the dairy cattle gut microbiota diversity, abundance, and functional annotation of the two divergent Indonesian regions, the highland and coastal regions, by shotgun metagenomic approach. Unfavorable environmental conditions such as type of forage grass in coastal regions and high temperature remain a limiting factor; however, the improvement through manipulating the gut microbiota was not considered until recently to improve the quality and quantity of coastal region dairy cattle. The application of recent advance technologies can help achieve this goal on sustainable basis. The results show Bacteroidetes in higher abundance in coastal region (FPP) than in highland (Salatiga) while Firmicutes were higher in Salatiga. Furthermore, a collective physiology of the community was found by annotating the sequences against KEGG, eggNOG, and CAZy databases. To identify the role in pathways, an mPATH analysis was performed to have insight into the microbiota community in different metabolic pathways. The identified targets can be used as prebiotic and/or probiotic to improve the average milk yield of coastal region dairy cattle by manipulating the dairy feed with desired microbes.}, } @article {pmid36116499, year = {2022}, author = {Singh, A and Varma, A and Prasad, R and Porwal, S}, title = {Bioprospecting uncultivable microbial diversity in tannery effluent contaminated soil using shotgun sequencing and bio-reduction of chromium by indigenous chromate reductase genes.}, journal = {Environmental research}, volume = {215}, number = {Pt 2}, pages = {114338}, doi = {10.1016/j.envres.2022.114338}, pmid = {36116499}, issn = {1096-0953}, mesh = {Bacteria/genetics ; Biodegradation, Environmental ; Bioprospecting ; Chromium/analysis ; Cytosine ; DNA ; Guanine ; *Nucleic Acids ; Oxidoreductases ; Phylogeny ; Soil/chemistry ; *Soil Pollutants/analysis/toxicity ; }, abstract = {The tannery industry generates a consequential threat to the environment by producing a large amount of potentially toxic metal-containing waste. Bioremediation has been a promising approach for treating potentially toxic metals, but the efficiency of remediation in microbes is one of the factors limiting their application in tanneries waste treatment. The motivation behind the present work was to explore the microbial diversity and chromate reductase genes present in the tannery effluent-contaminated soil using metagenomics approach. The use of shotgun sequencing enabled the identification of operational parameters that influence microbiome composition and their ability to reduce Chromium (Cr) concentration. The Cr concentration in Kanpur tannery effluent contaminated soil sample was 700 ppm which is many folds than the approved permissible limit by World Health Organisation (WHO) for Cr is 100 ppm. Metagenomic Deoxyribo Nucleic Acid (DNA) was extracted to explore taxonomic community structure, phylogenetic linkages, and functional profile. With a Guanine-Cytosine (GC) abundance of 54%, total of 45,163,604 high-quality filtered reads were obtained. Bacteria (83%), Archaebacteria (14%), and Viruses (3%) were discovered in the structural biodiversity. Bacteria were classified to phylum level, with Proteobacteria (52%) being the dominant population, followed by Bacteriodetes (15%), Chloroflexi (15%), Spirochaetes (7%), Thermotogae (5%), Actinobacteria (4%), and Firmicutes (1%). The OXR genes were cloned and checked for their efficiency to reduce Cr concentration. Insitu validation of OXR8 gene showed a reduction of Cr concentration from 700 ppm to 24 ppm in 72 h (96.51% reduction). The results of this study suggests that there is a huge reservoir of microbes and chromate reductase genes which are unexplored yet.}, } @article {pmid36116269, year = {2022}, author = {Gül, F and Karadayı, S and Yurdabakan, Z and Özbek, T and Karadayı, B}, title = {Investigating changes in salivary microbiota due to dental treatment: A metagenomic analysis study for forensic purposes.}, journal = {Forensic science international}, volume = {340}, number = {}, pages = {111447}, doi = {10.1016/j.forsciint.2022.111447}, pmid = {36116269}, issn = {1872-6283}, mesh = {Adolescent ; Adult ; Bacteria/genetics ; *Dental Caries ; Humans ; Metagenomics/methods ; *Microbiota/genetics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; Young Adult ; }, abstract = {The advent of next generation sequencing techniques as well as the existing traditional culture methods has enabled metagenomic studies on the usability of microbiomes for the forensic identification of individuals to gain momentum. However, before the utilization of microbiomes as a potential technique for real forensic case resolutions, it is necessary to understand the stability of the microbiota compositions in an individual's biological samples and the factors responsible for their variations. In the present study, we compared the microbiota compositions present in the saliva of individuals with active dental caries before and after treatment from a forensic and clinical perspective using an approach based on the sequencing of all the variable regions (V1-V9) of the bacterial 16 S rRNA gene. For this purpose, 10 individuals were included in the study comprising of 8 individuals between the ages of 18-50 years with at least 3 deep dentin caries as patients and 2 healthy individuals without any dental or gingival diseases as controls. Saliva samples were collected from the patients at two timepoints, before and after treatment, as well as from the healthy individuals (before and after control) at an interval of 1 month. The collected 20 saliva samples were subjected to metagenomic analysis using the MinION device, which was developed by Oxford Nanopore Technologies (ONT Oxford, UK). Bioinformatic analyses were performed on the obtained data and the results were evaluated using statistical comparison methods and alpha/beta diversity analyses within the scope of the study objective. On evaluation using the distance metrics, it was observed that the microbial compositions in the saliva of individuals with active caries remained relatively stable after treatment. However, the relative abundance levels of bacteria of 28 genera and species showed statistically significant differences before and after treatment (p < 0.05). As a result, although the composition of salivary microbiome remained relatively stable after caries treatment, there were significant changes in many types of bacteria, especially at the species level, between the BT and AT samples. Our results provide a framework for further forensic and clinical investigations regarding the factors that affect human salivary microbiome diversity.}, } @article {pmid36115596, year = {2022}, author = {Guman, MSS and Hoozemans, JB and Haal, S and de Jonge, PA and Aydin, Ö and Lappa, D and Meijnikman, AS and Westerink, F and Acherman, Y and Bäckhed, F and de Brauw, M and Nielsen, J and Nieuwdorp, M and Groen, AK and Gerdes, VEA}, title = {Adipose Tissue, Bile Acids, and Gut Microbiome Species Associated With Gallstones After Bariatric Surgery.}, journal = {Journal of lipid research}, volume = {63}, number = {11}, pages = {100280}, pmid = {36115596}, issn = {1539-7262}, mesh = {Humans ; *Gallstones/etiology/surgery ; *Gastrointestinal Microbiome/genetics ; Bile Acids and Salts ; Longitudinal Studies ; *Bariatric Surgery/adverse effects ; Adipose Tissue ; Bacteria ; }, abstract = {Several risk factors are associated with gallstone disease after bariatric surgery, but the underlying pathophysiological mechanisms of gallstone formation are unclear. We hypothesize that gallstone formation after bariatric surgery is induced by different pathways compared with gallstone formation in the general population, since postoperative formation occurs rapidly in patients who did not develop gallstones in preceding years. To identify both pathophysiological and potentially protective mechanisms against postoperative gallstone formation, we compared the preoperative fasting metabolome, fecal microbiome, and liver and adipose tissue transcriptome obtained before or during bariatric surgery of obese patients with and without postoperative gallstones. In total, 88 patients were selected from the BARIA longitudinal cohort study. Within this group, 32 patients had postoperative gallstones within 2 years. Gut microbiota metagenomic analyses showed group differences in abundance of 41 bacterial species, particularly abundance of Lactobacillaceae and Enterobacteriaceae in patients without gallstones. Subcutaneous adipose tissue transcriptomic analyses revealed four genes that were suppressed in gallstone patients compared with patients without gallstones. These baseline gene expression and gut microbiota composition differences might relate to protective mechanisms against gallstone formation after bariatric surgery. Moreover, baseline fasting blood samples of patients with postoperative gallstones showed increased levels of several bile acids. Overall, we revealed different genes and bacteria associated with gallstones than those previously reported in the general population, supporting the hypothesis that gallstone formation after bariatric surgery follows a different trajectory. Further research is necessary to confirm the involvement of the bile acids, adipose tissue activity, and microbial species observed here.}, } @article {pmid36115554, year = {2022}, author = {Perez-Marron, J and Sanders, C and Gomez, E and Escopete, S and Owerkowicz, T and Orwin, PM}, title = {Community and shotgun metagenomic analysis of Alligator mississippiensis oral cavity and GI tracts reveal complex ecosystems and potential reservoirs of antibiotic resistance.}, journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology}, volume = {274}, number = {}, pages = {111319}, doi = {10.1016/j.cbpa.2022.111319}, pmid = {36115554}, issn = {1531-4332}, mesh = {*Alligators and Crocodiles/genetics ; Animals ; *Colorectal Neoplasms ; Drug Resistance, Microbial ; Humans ; Metagenomics/methods ; *Microbiota/genetics ; Mouth/microbiology ; }, abstract = {We report here the community structure and functional analysis of the microbiome of the Alligator mississippiensis GI tract from the oral cavity through the entirety of the digestive tract. Although many vertebrate microbiomes have been studied in recent years, the archosaur microbiome has only been given cursory attention. In the oral cavity we used amplicon-based community analysis to examine the structure of the oral microbiome during alligator development. We found a community that diversified over time and showed many of the hallmarks we would expect of a stable oral community. This is a bit surprising given the rapid turnover of alligator teeth but suggests that the stable gumline microbes are able to rapidly colonize the emerging teeth. As we move down the digestive tract, we were able to use both long and short read sequencing approaches to evaluate the community using a shotgun metagenomics approach. Long read sequencing was applied to samples from the stomach/duodenum, and the colorectal region, revealing a fairly uniform and low complexity community made up primarily of proteobacteria at the top of the gut and much more diversity in the colon. We used deep short read sequencing to further interrogate this colorectal community. The two sequencing approaches were concordant with respect to community structure but substantially more detail was available in the short read data, in spite of high levels of host DNA contamination. Using both approaches we were able to show that the colorectal community is a potential reservoir for antibiotic resistance, human pathogens such as Clostridiodes difficile and a possible source of novel antimicrobials or other useful secondary metabolites.}, } @article {pmid36113855, year = {2022}, author = {Isaac, AL and Tritto, M and Colwell, RR and Armstrong, DG}, title = {Metagenomics of diabetic foot ulcer undergoing treatment with total contact casting: a case study.}, journal = {Journal of wound care}, volume = {31}, number = {Sup9}, pages = {S45-S49}, doi = {10.12968/jowc.2022.31.Sup9.S45}, pmid = {36113855}, issn = {0969-0700}, support = {R01 DK124789/DK/NIDDK NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; *Diabetes Mellitus/drug therapy ; *Diabetic Foot/microbiology ; Humans ; *Microbiota/genetics ; Tetracyclines ; Wound Healing ; }, abstract = {OBJECTIVE: Diabetic foot ulcers (DFUs) are characterised by the presence of many microbes, some of which may not be identified by traditional culture techniques. Total contact casting (TCC) remains the gold-standard for offloading, yet little is known about the microbiome of wounds that progress from hard-to-heal to closed within a TCC.

METHOD: A patient with a DFU underwent weekly treatment with TCC to closure. Samples for next-generation sequencing (NGS) and bioinformatics analysis of tissue samples were collected during each visit. Detection, identification, characterisation of the microbial community and abundance of microbes in each sample were compared.

RESULTS: Abundance of microbes, identified by species and strain, changed with each treatment visit. By the final week of treatment, species diversity of the wound microbiome had decreased significantly, highlighted by an observed decrease in the number of total microorganisms present. Resistance genes for tetracyclines were detected in the first sample, but not in subsequent samples.

CONCLUSION: The results of this study suggest dynamic microbiological changes associated with DFUs as they progress to healing within a TCC. As NGS becomes more readily available, further studies will be helpful to gain an improved understanding of the significance of the wound microbiome in patients with DFUs.}, } @article {pmid36113426, year = {2022}, author = {, and , }, title = {Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course.}, journal = {Cell}, volume = {185}, number = {19}, pages = {3467-3486.e16}, pmid = {36113426}, issn = {1097-4172}, support = {R01 NS087226/NS/NINDS NIH HHS/United States ; R01 NS098023/NS/NINDS NIH HHS/United States ; R01 NS124882/NS/NINDS NIH HHS/United States ; R35 NS111644/NS/NINDS NIH HHS/United States ; }, mesh = {Fatty Acids, Volatile ; *Gastrointestinal Microbiome ; Humans ; Interferon-beta ; *Multiple Sclerosis ; Phytic Acid ; Pyruvates ; }, abstract = {Changes in gut microbiota have been associated with several diseases. Here, the International Multiple Sclerosis Microbiome Study (iMSMS) studied the gut microbiome of 576 MS patients (36% untreated) and genetically unrelated household healthy controls (1,152 total subjects). We observed a significantly increased proportion of Akkermansia muciniphila, Ruthenibacterium lactatiformans, Hungatella hathewayi, and Eisenbergiella tayi and decreased Faecalibacterium prausnitzii and Blautia species. The phytate degradation pathway was over-represented in untreated MS, while pyruvate-producing carbohydrate metabolism pathways were significantly reduced. Microbiome composition, function, and derived metabolites also differed in response to disease-modifying treatments. The therapeutic activity of interferon-β may in part be associated with upregulation of short-chain fatty acid transporters. Distinct microbial networks were observed in untreated MS and healthy controls. These results strongly support specific gut microbiome associations with MS risk, course and progression, and functional changes in response to treatment.}, } @article {pmid36113358, year = {2022}, author = {Wojciechowski, S and Majchrzak-Górecka, M and Biernat, P and Odrzywołek, K and Pruss, Ł and Zych, K and Jan Majta, and Milanowska-Zabel, K}, title = {Machine learning on the road to unlocking microbiota's potential for boosting immune checkpoint therapy.}, journal = {International journal of medical microbiology : IJMM}, volume = {312}, number = {7}, pages = {151560}, doi = {10.1016/j.ijmm.2022.151560}, pmid = {36113358}, issn = {1618-0607}, mesh = {Humans ; *Microbiota ; *Gastrointestinal Microbiome ; Treatment Outcome ; Machine Learning ; Dysbiosis ; }, abstract = {The intestinal microbiota is a complex and diverse ecological community that fulfills multiple functions and substantially impacts human health. Despite its plasticity, unfavorable conditions can cause perturbations leading to so-called dysbiosis, which have been connected to multiple diseases. Unfortunately, understanding the mechanisms underlying the crosstalk between those microorganisms and their host is proving to be difficult. Traditionally used bioinformatic tools have difficulties to fully exploit big data generated for this purpose by modern high throughput screens. Machine Learning (ML) may be a potential means of solving such problems, but it requires diligent application to allow for drawing valid conclusions. This is especially crucial as gaining insight into the mechanistic basis of microbial impact on human health is highly anticipated in numerous fields of study. This includes oncology, where growing amounts of studies implicate the gut ecosystems in both cancerogenesis and antineoplastic treatment outcomes. Based on these reports and first signs of clinical benefits related to microbiota modulation in human trials, hopes are rising for the development of microbiome-derived diagnostics and therapeutics. In this mini-review, we're inspecting analytical approaches used to uncover the role of gut microbiome in immune checkpoint therapy (ICT) with the use of shotgun metagenomic sequencing (SMS) data.}, } @article {pmid36112078, year = {2023}, author = {Stothart, MR and McLoughlin, PD and Poissant, J}, title = {Shallow shotgun sequencing of the microbiome recapitulates 16S amplicon results and provides functional insights.}, journal = {Molecular ecology resources}, volume = {23}, number = {3}, pages = {549-564}, doi = {10.1111/1755-0998.13713}, pmid = {36112078}, issn = {1755-0998}, support = {D20EQ-051//Morris Animal Foundation/ ; 2016-06459//Natural Sciences and Engineering Research Council of Canada/ ; 2019-04388//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; Horses/genetics ; RNA, Ribosomal, 16S/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; Metagenome ; Bacteria ; Metagenomics/methods ; }, abstract = {Prevailing 16S rRNA gene-amplicon methods for characterizing the bacterial microbiome of wildlife are economical, but result in coarse taxonomic classifications, are subject to primer and 16S copy number biases, and do not allow for direct estimation of microbiome functional potential. While deep shotgun metagenomic sequencing can overcome many of these limitations, it is prohibitively expensive for large sample sets. Here we evaluated the ability of shallow shotgun metagenomic sequencing to characterize taxonomic and functional patterns in the faecal microbiome of a model population of feral horses (Sable Island, Canada). Since 2007, this unmanaged population has been the subject of an individual-based, long-term ecological study. Using deep shotgun metagenomic sequencing, we determined the sequencing depth required to accurately characterize the horse microbiome. In comparing conventional vs. high-throughput shotgun metagenomic library preparation techniques, we validate the use of more cost-effective laboratory methods. Finally, we characterize similarities between 16S amplicon and shallow shotgun characterization of the microbiome, and demonstrate that the latter recapitulates biological patterns first described in a published amplicon data set. Unlike for amplicon data, we further demonstrate how shallow shotgun metagenomic data provide useful insights regarding microbiome functional potential which support previously hypothesized diet effects in this study system.}, } @article {pmid36111438, year = {2022}, author = {Wu, Y and Li, A and Liu, H and Zhang, Z and Zhang, C and Ma, C and Zhang, L and Zhang, J}, title = {Lactobacillus plantarum HNU082 alleviates dextran sulfate sodium-induced ulcerative colitis in mice through regulating gut microbiome.}, journal = {Food & function}, volume = {13}, number = {19}, pages = {10171-10185}, doi = {10.1039/d2fo02303b}, pmid = {36111438}, issn = {2042-650X}, mesh = {Animals ; Claudin-1/metabolism ; Claudin-2/metabolism ; *Colitis/metabolism ; *Colitis, Ulcerative/pathology ; Colon/metabolism ; Dextran Sulfate/adverse effects ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Humans ; Intercellular Adhesion Molecule-1/metabolism ; Interleukin-10/metabolism ; Interleukin-6/metabolism ; *Lactobacillus plantarum/metabolism ; Mice ; Mice, Inbred C57BL ; NF-kappa B/metabolism ; Peroxidase/metabolism ; RNA, Messenger/metabolism ; Transforming Growth Factor beta1/metabolism ; Transforming Growth Factor beta2/adverse effects/metabolism ; Tumor Necrosis Factor-alpha/metabolism ; }, abstract = {Probiotics have shown good efficacy in the prevention of ulcerative colitis (UC), but the specific mechanism remains unclear. Therefore, shotgun metagenomic and transcriptome analyses were performed to explore the preventive effect of a potential probiotic Lactobacillus plantarum HNU082 (Lp082) on UC and its specific mechanism. The results showed that Lp082 intervention ameliorated dextran sulfate sodium (DSS)-induced UC in mice, which was manifested in the increase in body weight, water intake, food intake, and colon length and the decrease in the DAI index, immune organ index, inflammatory factors and histopathological scores after Lp082 intake. The mechanism is deeply studied and it is discovered that Lp082 improves the intestinal mucosal barrier by co-optimizing biological barriers, chemical barriers, mechanical barriers, and immune barriers. Specifically, Lp082 improved the biological barrier by increasing the diversity, optimizing the species composition and the structure of the gut microbiota, increasing bacteria producing short chain fatty acids (SCFAs), and activating microbial metabolic pathways producing SCFAs so as to enhance the content of SCFAs. Lp082 optimized the chemical barrier by decreasing the mRNA expression of ICAM-1 and VCAM and by increasing the content of goblet cells and the mRNA expression and immunofluorescent protein content of mucin2. Lp082 ameliorated the mechanical barrier by decreasing the mRNA expression of claudin-1 and claudin-2, and by increasing the mRNA expression of ZO-1 and ZO-2 and the immunofluorescent protein content of ZO-1. Lp082 also optimized the immune barrier by increasing the mRNA expression of IL-10, TGF-β1, and TGF-β2 and by decreasing the mRNA expression and protein contents of IL-6, tumour necrosis factor-alpha (TNF-α) and myeloperoxidase (MPO). In addition, Lp082 can also regulate the metabolic pathways of inflammation and disease in mice, and notably, Lp082 inhibits the NF-κB signaling pathway by inhibiting NF-κB signaling molecules to alleviate UC. In conclusion, improving gut microbiota dysbiosis, protecting the intestinal mucosal barrier, regulating inflammatory and disease pathways, and affecting neutrophil infiltration are the potential mechanisms of probiotic Lp082 in alleviating UC. Our study enriches the mechanism and provides a new prospect for Lactobacillus plantarum HNU082 in the prevention of colitis, provides support for the development of probiotic-based microbial products as an alternative prevention strategy for UC, and provides guidance for the future probiotic prevention of human colitis.}, } @article {pmid36109646, year = {2022}, author = {Kang, JTL and Teo, JJY and Bertrand, D and Ng, A and Ravikrishnan, A and Yong, M and Ng, OT and Marimuthu, K and Chen, SL and Chng, KR and Gan, YH and Nagarajan, N}, title = {Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects.}, journal = {Nature microbiology}, volume = {7}, number = {10}, pages = {1516-1524}, pmid = {36109646}, issn = {2058-5276}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; *Carbapenem-Resistant Enterobacteriaceae/genetics ; Escherichia coli/genetics ; *Gastrointestinal Microbiome ; Humans ; Klebsiella pneumoniae/genetics ; beta-Lactamases/genetics/metabolism ; }, abstract = {Long-term colonization of the gut microbiome by carbapenemase-producing Enterobacteriaceae (CPE) is a growing area of public health concern as it can lead to community transmission and rapid increase in cases of life-threatening CPE infections. Here, leveraging the observation that many subjects are decolonized without interventions within a year, we used longitudinal shotgun metagenomics (up to 12 timepoints) for detailed characterization of ecological and evolutionary dynamics in the gut microbiome of a cohort of CPE-colonized subjects and family members (n = 46; 361 samples). Subjects who underwent decolonization exhibited a distinct ecological shift marked by recovery of microbial diversity, key commensals and anti-inflammatory pathways. In addition, colonization was marked by elevated but unstable Enterobacteriaceae abundances, which exhibited distinct strain-level dynamics for different species (Escherichia coli and Klebsiella pneumoniae). Finally, comparative analysis with whole-genome sequencing data from CPE isolates (n = 159) helped identify substrain variation in key functional genes and the presence of highly similar E. coli and K. pneumoniae strains with variable resistance profiles and plasmid sharing. These results provide an enhanced view into how colonization by multi-drug-resistant bacteria associates with altered gut ecology and can enable transfer of resistance genes, even in the absence of overt infection and antibiotic usage.}, } @article {pmid36109637, year = {2022}, author = {Ianiro, G and Punčochář, M and Karcher, N and Porcari, S and Armanini, F and Asnicar, F and Beghini, F and Blanco-Míguez, A and Cumbo, F and Manghi, P and Pinto, F and Masucci, L and Quaranta, G and De Giorgi, S and Sciumè, GD and Bibbò, S and Del Chierico, F and Putignani, L and Sanguinetti, M and Gasbarrini, A and Valles-Colomer, M and Cammarota, G and Segata, N}, title = {Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases.}, journal = {Nature medicine}, volume = {28}, number = {9}, pages = {1913-1923}, pmid = {36109637}, issn = {1546-170X}, support = {R01 CA230551/CA/NCI NIH HHS/United States ; U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents ; *Clostridium Infections/microbiology/therapy ; Fecal Microbiota Transplantation/methods ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Treatment Outcome ; }, abstract = {Fecal microbiota transplantation (FMT) is highly effective against recurrent Clostridioides difficile infection and is considered a promising treatment for other microbiome-related disorders, but a comprehensive understanding of microbial engraftment dynamics is lacking, which prevents informed applications of this therapeutic approach. Here, we performed an integrated shotgun metagenomic systematic meta-analysis of new and publicly available stool microbiomes collected from 226 triads of donors, pre-FMT recipients and post-FMT recipients across eight different disease types. By leveraging improved metagenomic strain-profiling to infer strain sharing, we found that recipients with higher donor strain engraftment were more likely to experience clinical success after FMT (P = 0.017) when evaluated across studies. Considering all cohorts, increased engraftment was noted in individuals receiving FMT from multiple routes (for example, both via capsules and colonoscopy during the same treatment) as well as in antibiotic-treated recipients with infectious diseases compared with antibiotic-naïve patients with noncommunicable diseases. Bacteroidetes and Actinobacteria species (including Bifidobacteria) displayed higher engraftment than Firmicutes except for six under-characterized Firmicutes species. Cross-dataset machine learning predicted the presence or absence of species in the post-FMT recipient at 0.77 average AUROC in leave-one-dataset-out evaluation, and highlighted the relevance of microbial abundance, prevalence and taxonomy to infer post-FMT species presence. By exploring the dynamics of microbiome engraftment after FMT and their association with clinical variables, our study uncovered species-specific engraftment patterns and presented machine learning models able to predict donors that might optimize post-FMT specific microbiome characteristics for disease-targeted FMT protocols.}, } @article {pmid36109636, year = {2022}, author = {Schmidt, TSB and Li, SS and Maistrenko, OM and Akanni, W and Coelho, LP and Dolai, S and Fullam, A and Glazek, AM and Hercog, R and Herrema, H and Jung, F and Kandels, S and Orakov, A and Thielemann, R and von Stetten, M and Van Rossum, T and Benes, V and Borody, TJ and de Vos, WM and Ponsioen, CY and Nieuwdorp, M and Bork, P}, title = {Drivers and determinants of strain dynamics following fecal microbiota transplantation.}, journal = {Nature medicine}, volume = {28}, number = {9}, pages = {1902-1912}, pmid = {36109636}, issn = {1546-170X}, mesh = {*Clostridium Infections/therapy ; Fecal Microbiota Transplantation ; Feces ; *Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract ; Humans ; *Microbiota ; }, abstract = {Fecal microbiota transplantation (FMT) is a therapeutic intervention for inflammatory diseases of the gastrointestinal tract, but its clinical mode of action and subsequent microbiome dynamics remain poorly understood. Here we analyzed metagenomes from 316 FMTs, sampled pre and post intervention, for the treatment of ten different disease indications. We quantified strain-level dynamics of 1,089 microbial species, complemented by 47,548 newly constructed metagenome-assembled genomes. Donor strain colonization and recipient strain resilience were mostly independent of clinical outcomes, but accurately predictable using LASSO-regularized regression models that accounted for host, microbiome and procedural variables. Recipient factors and donor-recipient complementarity, encompassing entire microbial communities to individual strains, were the main determinants of strain population dynamics, providing insights into the underlying processes that shape the post-FMT gut microbiome. Applying an ecology-based framework to our findings indicated parameters that may inform the development of more effective, targeted microbiome therapies in the future, and suggested how patient stratification can be used to enhance donor microbiota colonization or the displacement of recipient microbes in clinical practice.}, } @article {pmid36109557, year = {2022}, author = {Jung, J and Bugenyi, AW and Lee, MR and Choi, YJ and Song, KD and Lee, HK and Son, YO and Lee, DS and Lee, SC and Son, YJ and Heo, J}, title = {High-quality metagenome-assembled genomes from proximal colonic microbiomes of synbiotic-treated korean native black pigs reveal changes in functional capacity.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {14595}, pmid = {36109557}, issn = {2045-2322}, mesh = {Animals ; Female ; Health Promotion ; Metagenome ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sus scrofa/genetics ; Swine ; *Synbiotics ; }, abstract = {Synbiotics are feed supplements with the potential to promote health and productivity in pigs partly, through modulation of the intestinal microbiome. Our study used shotgun sequencing and 16S rRNA gene sequencing techniques to characterize the effect of a synbiotic containing three Lactobacillus species and a fructo-oligosaccharide on the proximal colonic microbiome of 4- to 7-month-old Korean native black gilts. With shotgun sequencing we constructed unique metagenome-assembled genomes of gut microbiota in Native Black Pig for the first time, which we then used for downstream analysis. Results showed that synbiotic treatment did not alter microbial diversity and evenness within the proximal colons, but altered composition of some members of the Lactobacillaceae, Enterococcaceae and Streptococcaceae families. Functional analysis of the shotgun sequence data revealed 8 clusters of orthologous groups (COGs) that were differentially represented in the proximal colonic microbiomes of synbiotic-treated Jeju black pigs relative to controls. In conclusion, our results show that administering this synbiotic causes changes in the functional capacity of the proximal colonic microbiome of the Korean native black pig. This study improves our understanding of the potential impact of synbiotics on the colonic microbiome of Korean native black pigs.}, } @article {pmid36108841, year = {2023}, author = {Sharma, U and Rawat, D and Mukherjee, P and Farooqi, F and Mishra, V and Sharma, RS}, title = {Ecological life strategies of microbes in response to antibiotics as a driving factor in soils.}, journal = {The Science of the total environment}, volume = {854}, number = {}, pages = {158791}, doi = {10.1016/j.scitotenv.2022.158791}, pmid = {36108841}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents ; Soil/chemistry ; Soil Microbiology ; Bacteria ; *Microbiota ; }, abstract = {Antibiotics as a selection pressure driving the evolution of soil microbial communities is not well understood. Since microbial functions govern ecosystem services, an ecological framework is required to understand and predict antibiotic-induced functional and structural changes in microbial communities. Therefore, metagenomic studies explaining the impacts of antibiotics on soil microbial communities were mined, and alterations in microbial taxa were analyzed through an ecological lens using Grimes's Competitor-Stress tolerator-Ruderal (CSR) model. We propose considering antibiotics as the primary abiotic factor mentioned in the CSR model and classifying non-susceptible microbial taxa as degraders, resistant, and resilient groups analogous to competitors, stress tolerators, and ruderal strategists, respectively. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were among the phyla harboring most members with antibiotic-resistant groups. However, some antibiotic-resistant microbes in these phyla could not only tolerate but also subsist solely on antibiotics, while others degraded antibiotics as a part of secondary metabolism. Irrespective of their taxonomic affiliation, microbes with each life strategy displayed similar phenotypic characteristics. Therefore, it is recommended to consider microbial functional traits associated with each life strategy while analyzing the ecological impacts of antibiotics. Also, potential ecological crises posed by antibiotics through changes in microbial community and ecosystem functions were visualized. Applying ecological theory to understand and predict antibiotics-induced changes in microbial communities will also provide better insight into microbial behavior in the background of emerging contaminants and help develop a robust ecological classification system of microbes.}, } @article {pmid36108783, year = {2022}, author = {Atim, SA and Ashraf, S and Belij-Rammerstorfer, S and Ademun, AR and Vudriko, P and Nakayiki, T and Niebel, M and Shepherd, J and Balinandi, S and Nakanjako, G and Abaasa, A and Johnson, PCD and Odongo, S and Esau, M and Bahati, M and Kaleebu, P and Lutwama, JJ and Masembe, C and Lambe, T and Thomson, EC and Tweyongyere, R}, title = {Risk factors for Crimean-Congo Haemorrhagic Fever (CCHF) virus exposure in farming communities in Uganda.}, journal = {The Journal of infection}, volume = {85}, number = {6}, pages = {693-701}, pmid = {36108783}, issn = {1532-2742}, support = {MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 107743/WT_/Wellcome Trust/United Kingdom ; MC_UU_00027/1/MRC_/Medical Research Council/United Kingdom ; 102789/Z/13/A/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Female ; Animals ; Humans ; Cattle ; Dogs ; *Hemorrhagic Fever Virus, Crimean-Congo ; *Hemorrhagic Fever, Crimean/epidemiology ; Uganda/epidemiology ; Cross-Sectional Studies ; *Ticks ; Goats ; Risk Factors ; Agriculture ; }, abstract = {BACKGROUND: Crimean-Congo Haemorrhagic Fever (CCHF) is an emerging human-health threat causing sporadic outbreaks in livestock farming communities. However, the full extent and the risks associated with exposure of such communities has not previously been well-described.

METHODS: We collected blood samples from 800 humans, 666 cattle, 549 goats and 32 dogs in districts within and outside Ugandan cattle corridor in a cross-sectional survey, and tested for CCHFV-specific IgG antibodies using Enzyme-Linked Immunosorbent Assays. Sociodemographic and epidemiological data were recorded using structured questionnaire. Ticks were collected to identify circulating nairoviruses by metagenomic sequencing.

RESULTS: CCHFV seropositivity was in 221/800 (27·6%) in humans, 612/666 (91·8%) in cattle, 413/549 (75·2%) in goats and 18/32 (56·2%) in dogs. Human seropositivity was associated with livestock farming (AOR=5·68, p<0·0001), age (AOR=2·99, p=0·002) and collecting/eating engorged ticks (AOR=2·13, p=0·004). In animals, seropositivity was higher in cattle versus goats (AOR=2·58, p<0·0001), female sex (AOR=2·13, p=0·002) and heavy tick infestation (>50 ticks: AOR=3·52, p=0·004). CCHFV was identified in multiple tick pools of Rhipicephalus appendiculatus.

INTERPRETATION: The very high CCHF seropositivity especially among livestock farmers and multiple regional risk factors associated exposures, including collecting/eating engorged ticks previously unrecognised, highlights need for further surveillance and sensitisation and control policies against the disease.}, } @article {pmid36108613, year = {2022}, author = {Li, L and Mac Aogáin, M and Xu, T and Jaggi, TK and Chan, LLY and Qu, J and Wei, L and Liao, S and Cheng, HS and Keir, HR and Dicker, AJ and Tan, KS and De Yun, W and Koh, MS and Ong, TH and Lim, AYH and Abisheganaden, JA and Low, TB and Hassan, TM and Long, X and Wark, PAB and Oliver, B and Drautz-Moses, DI and Schuster, SC and Tan, NS and Fang, M and Chalmers, JD and Chotirmall, SH}, title = {Neisseria species as pathobionts in bronchiectasis.}, journal = {Cell host & microbe}, volume = {30}, number = {9}, pages = {1311-1327.e8}, doi = {10.1016/j.chom.2022.08.005}, pmid = {36108613}, issn = {1934-6069}, support = {SCAF/17/03/CSO_/Chief Scientist Office/United Kingdom ; }, mesh = {Animals ; *Bronchiectasis/epidemiology ; Humans ; Metagenome ; Mice ; *Microbiota ; Neisseria/genetics ; }, abstract = {Neisseria species are frequently identified in the bronchiectasis microbiome, but they are regarded as respiratory commensals. Using a combination of human cohorts, next-generation sequencing, systems biology, and animal models, we show that bronchiectasis bacteriomes defined by the presence of Neisseria spp. associate with poor clinical outcomes, including exacerbations. Neisseria subflava cultivated from bronchiectasis patients promotes the loss of epithelial integrity and inflammation in primary epithelial cells. In vivo animal models of Neisseria subflava infection and metabolipidome analysis highlight immunoinflammatory functional gene clusters and provide evidence for pulmonary inflammation. The murine metabolipidomic data were validated with human Neisseria-dominant bronchiectasis samples and compared with disease in which Pseudomonas-, an established bronchiectasis pathogen, is dominant. Metagenomic surveillance of Neisseria across various respiratory disorders reveals broader importance, and the assessment of the home environment in bronchiectasis implies potential environmental sources of exposure. Thus, we identify Neisseria species as pathobionts in bronchiectasis, allowing for improved risk stratification in this high-risk group.}, } @article {pmid36108099, year = {2022}, author = {Paul, LJ and Ericsson, AC and Andrews, FM and McAdams, Z and Keowen, ML and St Blanc, MP and Banse, HE}, title = {Dietary and management factors influence the equine gastric microbiome.}, journal = {Journal of the American Veterinary Medical Association}, volume = {260}, number = {S3}, pages = {S111-S120}, doi = {10.2460/javma.22.07.0277}, pmid = {36108099}, issn = {1943-569X}, mesh = {Horses ; Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Stomach Ulcer/veterinary ; Gastric Mucosa/pathology ; *Horse Diseases/pathology ; Diet/veterinary ; }, abstract = {OBJECTIVE: The purpose of this study was to characterize the relationship of diet and management factors with the glandular gastric mucosal microbiome. We hypothesize that the gastric mucosal microbial community is influenced by diet and management factors. Our specific objective is to characterize the gastric mucosal microbiome in relation to these factors.

ANIMALS: 57 client-owned horses in the southern Louisiana region with and without equine glandular gastric disease.

PROCEDURES: Diet and management data were collected via a questionnaire. Gastroscopy was used for evaluation of equine gastric ulcer syndrome and collection of glandular mucosal pinch biopsies. 16S rRNA amplicon sequencing was used for microbiome analysis. Similarity and diversity indices and sequence read counts of individual taxa were compared between diet and management factors.

RESULTS: Differences were detected in association with offering hay, type of hay, sweet feed, turnout, and stalling. Offering hay and stalling showed differences in similarity indices, whereas hay type, sweet feed, and turnout showed differences in similarity and diversity indices. Offering hay, hay type, and sweet feed were also associated with differences in individual sequence read counts.

CLINICAL RELEVANCE: This study provides preliminary characterization of the complex relationship between the glandular gastric microbiome and diet/management factors. The ideal microbiome to promote a healthy glandular gastric environment remains unknown.}, } @article {pmid36108023, year = {2022}, author = {Suzuki, TA and Fitzstevens, JL and Schmidt, VT and Enav, H and Huus, KE and Mbong Ngwese, M and Grießhammer, A and Pfleiderer, A and Adegbite, BR and Zinsou, JF and Esen, M and Velavan, TP and Adegnika, AA and Song, LH and Spector, TD and Muehlbauer, AL and Marchi, N and Kang, H and Maier, L and Blekhman, R and Ségurel, L and Ko, G and Youngblut, ND and Kremsner, P and Ley, RE}, title = {Codiversification of gut microbiota with humans.}, journal = {Science (New York, N.Y.)}, volume = {377}, number = {6612}, pages = {1328-1332}, pmid = {36108023}, issn = {1095-9203}, support = {/WT_/Wellcome Trust/United Kingdom ; R35 GM128716/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteria/classification/genetics ; Child ; *Gastrointestinal Microbiome/genetics ; *Host Microbial Interactions ; Humans ; Metagenome ; Oxygen/metabolism ; }, abstract = {The gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. The question is whether such specificity arises from a shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification of host and microbiota, we analyzed paired gut metagenomes and human genomes for 1225 individuals in Europe, Asia, and Africa, including mothers and their children. Between and within countries, a parallel evolutionary history was evident for humans and their gut microbes. Moreover, species displaying the strongest codiversification independently evolved traits characteristic of host dependency, including reduced genomes and oxygen and temperature sensitivity. These findings all point to the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease phenotypes.}, } @article {pmid36107142, year = {2022}, author = {Luu, LDW and Singh, H and Castaño-Rodríguez, N and Leach, ST and Riordan, SM and Tedla, N and Krishnan, U and Kaakoush, NO}, title = {Changes to the upper gastrointestinal microbiotas of children with reflux oesophagitis and oesophageal metaplasia.}, journal = {Microbial genomics}, volume = {8}, number = {9}, pages = {}, pmid = {36107142}, issn = {2057-5858}, mesh = {Bacteria/genetics ; Child ; Cytokines ; *Esophagitis, Peptic/drug therapy ; *Gastrointestinal Microbiome ; Humans ; Metaplasia/drug therapy ; *Microbiota/genetics ; Prospective Studies ; Proton Pump Inhibitors/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Retrospective Studies ; *Upper Gastrointestinal Tract ; }, abstract = {Little is known of the relationships among paediatric upper gastrointestinal microbiotas, and the impact of medication use and disease on their diversity. Here, we investigated the diversity of three microbiotas in the upper gastrointestinal tract of paediatric patients in relation to each other and to host factors. Oral, oesophageal and gastric microbiotas from a prospective paediatric cohort (n=54) were profiled using the 16S rRNA gene and ITS2 amplicon sequencing. 16S rRNA gene amplicon sequencing of oesophageal biopsies from a retrospective paediatric cohort (n=96) and shotgun metagenomics data from oesophageal brushings (n=88) were employed for genomic signature validation. Bacterial diversity and composition showed substantial differences across oral, oesophageal and gastric fluid samples that were not replicated for fungi, and the presence of reflux led to increased homogeneity in the bacterial component of these three microbiotas. The oral and oesophageal microbiotas were associated with age, sex, history of oesophageal atresia and presence of oesophageal metaplasia, with the latter characterized by Prevotella enrichment. Proton pump inhibitor use was associated with increased oral bacterial richness in the gastric fluid, and this correlated with increased levels of gastric pro-inflammatory cytokines. Profiling of oesophageal biopsies from a retrospective paediatric cohort confirmed an increased Prevotella prevalence in samples with metaplasia. Analysis of metagenome-derived oesophageal Prevotella melaninogenica genomes identified strain-specific features that were significantly increased in prevalence in samples with metaplasia. Prevotella enrichment is a signature associated with paediatric oesophageal metaplasia, and proton pump inhibitor use substantially alters the paediatric gastric microenvironment.}, } @article {pmid36106575, year = {2023}, author = {Huang, YW and Wang, WH and Lan, MY}, title = {Analysing sinonasal microbiota of fungal rhinosinusitis by next-generation sequencing.}, journal = {Clinical otolaryngology : official journal of ENT-UK ; official journal of Netherlands Society for Oto-Rhino-Laryngology & Cervico-Facial Surgery}, volume = {48}, number = {2}, pages = {313-320}, doi = {10.1111/coa.13980}, pmid = {36106575}, issn = {1749-4486}, support = {MOST1102628B075020//Ministry of Science and Technology, Taiwan/ ; V109 C080//Taipei Veterans General Hospital/ ; V111C007//Taipei Veterans General Hospital/ ; }, mesh = {Humans ; Prospective Studies ; *Microbiota/genetics ; Bacteria/genetics ; Streptococcus ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {OBJECTIVES: Fungal rhinosinusitis is an inflammatory disease of the nose that may lead to life-threatening complications. This study compared the bacterial and fungal microbiomes between patients with invasive fungal rhinosinusitis (IFRS) and non-IFRS (NIFRS).

DESIGN: This was a prospective study including 18 IFRS and NIFRS patients. Fungal and bacterial microbiomes from surgical specimens were sequenced from amplicons of the internal transcribed spacer 1 (ITS1) region and the V3-V4 region of the 16S locus, respectively. Microbiomes were generated using the Illumina MiSeq System 2 x 301 base pair chemistry with a paired-end protocol.

SETTING: Tertiary medical centre.

RESULTS: Targeted metagenomics identified Aspergillus spp. as the predominant fungus in both IFRS and NIFRS patients. Based on phylum and genera level diversity, and abundance differences, significant differences of operational taxonomic units (OTUs) (Fusobacterium, Prevotella, Pseudomonas, Neisseria and Streptococcus) were more abundant in NIFRS compared with IFRS patients.

CONCLUSIONS: This is the first study to analyse bacterial and fungal microbiomes in patients with IFRS and NIFRS via ITS1 and 16S genomics sequencing. Bacterial microbiomes from patients with IFRS demonstrated dysbiosis (alterations in diversity and abundance) compared to those from patients with NIFRS.}, } @article {pmid36105149, year = {2022}, author = {Chen, S and Niu, C and Lv, W}, title = {Multi-omics insights reveal the remodeling of gut mycobiome with P. gingivalis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {937725}, pmid = {36105149}, issn = {2235-2988}, mesh = {Animals ; Feces/microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; Mice ; *Mycobiome ; Porphyromonas gingivalis ; }, abstract = {As a keystone periodontal pathogen, Porphyromonas gingivalis (P. gingivalis) was suggested to be involved in the progression of systemic diseases by altering the intestinal microecology. However, studies concerning gut microbiome have focused entirely on the bacterial component, while the fungal community (gut mycobiome) has been overlooked. In this study, we aimed to characterize the alteration of gut mycobiome profile with P. gingivalis administration using mice fecal samples. Metagenomic analysis showed a distinct composition pattern of mycobiome and significant difference of beta diversity between control and the P. gingivalis group. Some fungal species were differentially characterized with P. gingivalis administration, among which Pyricularia pennisetigena and Alternaria alternata showed positive correlation with P. gingivalis. KEGG functional analyses revealed that three pathways, namely, "pentose and glucuronate interconversions", "metabolic pathways", and "two-component system", were statistically enriched with P. gingivalis administration. Moreover, the alteration of gut mycobiome was also closely related with serum metabolites, especially lipid and tryptophan metabolic pathways. Taken together, this study demonstrated the alteration of fungal composition and function with P. gingivalis administration for the first time, and investigated the fungi-bacterial interaction and fungi-metabolite interaction preliminarily, providing a whole insight into gut mycobiome remodeling with oral pathobiont through multi-omics analyses.}, } @article {pmid36104920, year = {2022}, author = {Li, T and Li, R and Cao, Y and Tao, C and Deng, X and Ou, Y and Liu, H and Shen, Z and Li, R and Shen, Q}, title = {Soil antibiotic abatement associates with the manipulation of soil microbiome via long-term fertilizer application.}, journal = {Journal of hazardous materials}, volume = {439}, number = {}, pages = {129704}, doi = {10.1016/j.jhazmat.2022.129704}, pmid = {36104920}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents/pharmacology ; *Fertilizers/analysis ; Genes, Bacterial ; Manure/microbiology ; *Microbiota ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The effects of different fertilization on microbial communities and resistome in agricultural soils with a history of fresh manure application remains largely unclear. Here, soil antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and microbial communities were deciphered using metagenomics approach from a long-term field experiment with different fertilizer inputs. A total of 541 ARG subtypes were identified, with Multidrug, Macrolides-Lincosamides-Streptogramins (MLS), and Bacitracin resistance genes as the most universal ARG types. The abundance of ARGs detected in manure (2.52 ARGs/16 S rRNA) treated soils was higher than chemical fertilizer (2.42 ARGs/16 S rRNA) or compost (2.37 ARGs/16 S rRNA) amended soils. The higher abundance of MGEs and the enrichment of Proteobacteria were observed in manure treated soils than in chemical fertilizer or compost amended soils. Proteobacter and Actinobacter were recognized as the main potential hosts of ARGs revealed by network analysis. Further soil pH was identified as the key driver in determining the composition of both microbial community and resistome. The present study investigated the mechanisms driving the microbial community, MGEs and ARG profiles of long-term fertilized soils with ARGs contamination, and our findings could support strategies to manage the dissemination of soil ARGs.}, } @article {pmid36104726, year = {2022}, author = {Calabrese, FM and Ameur, H and Nikoloudaki, O and Celano, G and Vacca, M and Junior, WJ and Manzari, C and Vertè, F and Di Cagno, R and Pesole, G and De Angelis, M and Gobbetti, M}, title = {Metabolic framework of spontaneous and synthetic sourdough metacommunities to reveal microbial players responsible for resilience and performance.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {148}, pmid = {36104726}, issn = {2049-2618}, mesh = {*Bread/analysis ; Edible Grain ; Fermentation ; Food Microbiology ; *Microbiota/genetics ; }, abstract = {BACKGROUND: In nature, microbial communities undergo changes in composition that threaten their resiliency. Here, we interrogated sourdough, a natural cereal-fermenting metacommunity, as a dynamic ecosystem in which players are subjected to continuous environmental and spatiotemporal stimuli.

RESULTS: The inspection of spontaneous sourdough metagenomes and transcriptomes revealed dominant, subdominant and satellite players that are engaged in different functional pathways. The highest microbial richness was associated with the highest number of gene copies per pathway. Based on meta-omics data collected from 8 spontaneous sourdoughs and their identified microbiota, we de novo reconstructed a synthetic microbial community SDG. We also reconstructed SMC-SD43 from scratch using the microbial composition of its spontaneous sourdough equivalent for comparison. The KEGG number of dominant players in the SDG was not affected by depletion of a single player, whereas the subdominant and satellite species fluctuated, revealing unique contributions. Compared to SMC-SD43, SDG exhibited broader transcriptome redundancy. The invariant volatilome profile of SDG after in situ long-term back slopping revealed its stability. In contrast, SMC-SD43 lost many taxon members. Dominant, subdominant and satellite players together ensured gene and transcript redundancy.

CONCLUSIONS: Our study demonstrates how, by starting from spontaneous sourdoughs and reconstructing these communities synthetically, it was possible to unravel the metabolic contributions of individual players. For resilience and good performance, the sourdough metacommunity must include dominant, subdominant and satellite players, which together ensure gene and transcript redundancy. Overall, our study changes the paradigm and introduces theoretical foundations for directing food fermentations. Video Abstract.}, } @article {pmid36100971, year = {2022}, author = {Xiao, C and Wang, JT and Su, C and Miao, Z and Tang, J and Ouyang, Y and Yan, Y and Jiang, Z and Fu, Y and Shuai, M and Gou, W and Xu, F and Yu, EY and Liang, Y and Liang, X and Tian, Y and Wang, J and Huang, F and Zhang, B and Wang, H and Chen, YM and Zheng, JS}, title = {Associations of dietary diversity with the gut microbiome, fecal metabolites, and host metabolism: results from 2 prospective Chinese cohorts.}, journal = {The American journal of clinical nutrition}, volume = {116}, number = {4}, pages = {1049-1058}, pmid = {36100971}, issn = {1938-3207}, support = {R01 HD038700/HD/NICHD NIH HHS/United States ; R01 HD030880/HD/NICHD NIH HHS/United States ; R01-HD30880/GF/NIH HHS/United States ; R24 HD050924/HD/NICHD NIH HHS/United States ; R01 DK104371/DK/NIDDK NIH HHS/United States ; }, mesh = {Bile Acids and Salts ; China ; Ecosystem ; Feces/chemistry ; *Gastrointestinal Microbiome ; Humans ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Dietary diversity is essential for human health. The gut ecosystem provides a potential link between dietary diversity, host metabolism, and health, yet this mechanism is poorly understood.

OBJECTIVES: Here, we aimed to investigate the relation between dietary diversity and the gut environment as well as host metabolism from a multiomics perspective.

METHODS: Two independent longitudinal Chinese cohorts (a discovery and a validation cohort) were included in the present study. Dietary diversity was evaluated with FFQs. In the discovery cohort (n = 1916), we performed shotgun metagenomic and 16S ribosomal ribonucleic acid (rRNA) sequencing to profile the gut microbiome. We used targeted metabolomics to quantify fecal and serum metabolites. The associations between dietary diversity and the microbial composition were replicated in the validation cohort (n = 1320).

RESULTS: Dietary diversity was positively associated with α diversity of the gut microbiota. We identified dietary diversity-related gut environment features, including the microbial structure (β diversity), 68 microbial genera, 18 microbial species, 8 functional pathways, and 13 fecal metabolites. We further found 332 associations of dietary diversity and related gut environment features with circulating metabolites. Both the dietary diversity and diversity-related features were inversely correlated with 4 circulating secondary bile acids. Moreover, 16 mediation associations were observed among dietary diversity, diversity-related features, and the 4 secondary bile acids.

CONCLUSIONS: These results suggest that high dietary diversity is associated with the gut microbial environment. The identified key microbes and metabolites may serve as hypotheses to test for preventing metabolic diseases.}, } @article {pmid36100957, year = {2022}, author = {Jia, L and Weng, S and Wu, J and Tian, X and Zhang, Y and Wang, X and Wang, J and Yan, D and Wang, W and Fang, F and Zhu, Z and Qiu, C and Zhang, W and Xu, Y and Wan, Y}, title = {Preexisting antibodies targeting SARS-CoV-2 S2 cross-react with commensal gut bacteria and impact COVID-19 vaccine induced immunity.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2117503}, pmid = {36100957}, issn = {1949-0984}, mesh = {Animals ; Antibodies, Monoclonal ; Antibodies, Viral ; *COVID-19/prevention & control ; COVID-19 Vaccines ; Escherichia coli ; *Gastrointestinal Microbiome ; Humans ; Mice ; SARS-CoV-2 ; *Viral Vaccines ; }, abstract = {The origins of preexisting SARS-CoV-2 cross-reactive antibodies and their potential impacts on vaccine efficacy have not been fully clarified. In this study, we demonstrated that S2 was the prevailing target of the preexisting S protein cross-reactive antibodies in both healthy human and SPF mice. A dominant antibody epitope was identified on the connector domain of S2 (1147-SFKEELDKYFKNHT-1160, P144), which could be recognized by preexisting antibodies in both human and mouse. Through metagenomic sequencing and fecal bacteria transplant, we demonstrated that the generation of S2 cross-reactive antibodies was associated with commensal gut bacteria. Furthermore, six P144 reactive monoclonal antibodies were isolated from naïve SPF mice and were proven to cross-react with commensal gut bacteria collected from both human and mouse. A variety of cross-reactive microbial proteins were identified using LC-MS, of which E. coli derived HSP60 and HSP70 proteins were confirmed to be able to bind to one of the isolated monoclonal antibodies. Mice with high levels of preexisting S2 cross-reactive antibodies mounted higher S protein specific binding antibodies, especially against S2, after being immunized with a SARS-CoV-2 S DNA vaccine. Similarly, we found that levels of preexisting S2 and P144-specific antibodies correlated positively with RBD binding antibody titers after two doses of inactivated SARS-CoV-2 vaccination in human. Collectively, our study revealed an alternative origin of preexisting S2-targeted antibodies and disclosed a previously neglected aspect of the impact of gut microbiota on host anti-SARS-CoV-2 immunity.}, } @article {pmid36100953, year = {2022}, author = {Bai, X and Sun, Y and Li, Y and Li, M and Cao, Z and Huang, Z and Zhang, F and Yan, P and Wang, L and Luo, J and Wu, J and Fan, D and Chen, H and Zhi, M and Lan, P and Zeng, Z and Wu, X and Miao, Y and Zuo, T}, title = {Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {147}, pmid = {36100953}, issn = {2049-2618}, mesh = {Adult ; Archaea ; Bacteria/genetics ; Diet ; Ethnicity ; *Gastrointestinal Microbiome/genetics ; Geography ; Humans ; *Urbanization ; }, abstract = {BACKGROUND AND AIMS: The human gut is home to a largely underexplored microbiome component, the archaeome. Little is known of the impact of geography, urbanization, ethnicity, and diet on the gut archaeome in association with host health. We aim to delineate the variation of the human gut archaeome in healthy individuals and its association with environmental factors and host homeostasis.

METHODS: Using metagenomic sequencing, we characterized the fecal archaeomes of 792 healthy adult subjects from 5 regions in China, spanning 6 ethnicities (Han, Zang, Miao, Bai, Dai, and Hani), consisting of both urban and rural residents for each ethnicity. In addition, we sampled 119 host variables (including lifestyle, diet, and blood parameters) and interrogated the influences of those factors, individually and combined, on gut archaeome variations.

RESULTS: Population geography had the strongest impact on the gut archaeome composition, followed by urbanization, dietary habit, and ethnicity. Overall, the metadata had a cumulative effect size of 11.0% on gut archaeome variation. Urbanization decreased both the α-diversity (intrinsic microbial diversity) and the β-diversity (inter-individual dissimilarities) of the gut archaeome, and the archaea-to-bacteria ratios in feces, whereas rural residents were enriched for Methanobrevibacter smithii in feces. Consumption of buttered milk tea (a characteristic diet of the rural Zang population) was associated with increased abundance of M. smithii. M. smithii was at the central hub of archaeal-bacterial interactions in the gut microecology, where it was positively correlated with the abundances of a multitude of short chain fatty acid (SCFA)-producing bacteria (including Roseburia faecis, Collinsella aerofaciens, and Prevotella copri). Moreover, a decreased abundance of M. smithii was associated with increased human blood levels of cholinesterase in the urban population, coinciding with the increasing prevalence of noncommunicable diseases (such as dementia) during urbanization.

CONCLUSIONS: Our data highlight marked contributions of environmental and host factors (geography, urbanization, ethnicity, and habitual diets) to gut archaeome variations across healthy individuals, and underscore the impact of urbanization on the gut archaeome in association with host health in modern society. Video Abstract.}, } @article {pmid36099099, year = {2022}, author = {Ninomiya, K and Paudel, D and Uehara, O and Morikawa, T and Islam, ST and Khurelchuluun, A and Ariwansa, D and Yoshida, K and Matsuoka, H and Hajime, H and Kayoko, F and Nakamura, K and Abiko, Y}, title = {Effect of Systemic Administration of Amitriptyline on Oral Microbes in Rats.}, journal = {In vivo (Athens, Greece)}, volume = {36}, number = {5}, pages = {2134-2142}, pmid = {36099099}, issn = {1791-7549}, mesh = {*Amitriptyline/pharmacology ; Animals ; Antidepressive Agents ; *Gastrointestinal Microbiome ; Rats ; Rats, Sprague-Dawley ; }, abstract = {BACKGROUND/AIM: Amitriptyline is a major tricyclic antidepressant that is also used to relieve chronic orofacial pain. Recently, alterations in gut flora due to various antidepressants have been demonstrated. However, it remains unknown how antidepressants affect the oral environment, including microbiota and innate immunity. The aim of this study was to investigate the effects of amitriptyline on oral microflora and antimicrobial peptides.

MATERIALS AND METHODS: Sprague-Dawley rats were intraperitoneally injected with amitriptyline for 2 weeks. The DNA extracted from the oral swabs were used to perform 16SrRNA sequencing to evaluate the oral microbiome. Quantitative RT-PCR was performed to evaluate the mRNA levels of antimicrobial peptides in the buccal tissues.

RESULTS: No significant differences in salivary flow rates were observed between the amitriptyline and control groups. Taxonomic analysis showed significant alterations in bacteria such as Corynebacterium, Rothia, and Porphyromonas due to amitriptyline administration. The beta diversity showed significant differences between the amitriptyline and control groups. Additionally, the predicted metagenome functions were significantly different between the two groups. The mRNA expression levels of antimicrobial peptides in the amitriptyline group were significantly higher as compared to controls.

CONCLUSION: Systemic administration of amitriptyline may affect the oral environment, including oral microbes and innate immunity in the oral mucosa.}, } @article {pmid36098925, year = {2022}, author = {Sharma, R and Patil, C and Majeed, J and Kumar, S and Aggarwal, G}, title = {Next-generation sequencing in the biodiversity conservation of endangered medicinal plants.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {49}, pages = {73795-73808}, pmid = {36098925}, issn = {1614-7499}, mesh = {Biodiversity ; Computational Biology ; Genomics ; High-Throughput Nucleotide Sequencing ; *Plants, Medicinal/genetics ; }, abstract = {Medicinal plants have been used as traditional herbal medicines in the treatment of various types of diseases. However, the increased demand for these plants highlights the importance of conservation specifically for endangered species. Significant advancements in next-generation sequencing (NGS) technologies have accelerated medicinal plant research while reducing costs and time demands. NGS systems enable high-throughput whole genome sequencing as well as direct RNA sequencing and transcriptome analysis. The sequence data sets created can be used in a variety of areas of study, including biodiversity conservation, comparative genomics, transcriptomic analysis, single cell mining, metagenomics, epigenetics, molecular marker discovery, multi genome sequencing, and so on. Commercial sequencing service providers are constantly working to improve technologies to address bioinformatics problems in NGS data analysis. Several genome sequencing projects on medicinal plants have been completed recently and a few more are in the works. In some medicinal plants, massive NGS-based data has been developed. In the present review, we have attempted to briefly discuss advancements in NGS technology on medicinally essential plants in India. The review will also provide ideas for applying NGS technologies for exploring genomes of various endangered medicinal plants whose genome sequences are not normally available and thus provides valuable insights for the conservation of these vulnerable species.}, } @article {pmid36097140, year = {2023}, author = {Koonin, EV and Krupovic, M and Dolja, VV}, title = {The global virome: How much diversity and how many independent origins?.}, journal = {Environmental microbiology}, volume = {25}, number = {1}, pages = {40-44}, doi = {10.1111/1462-2920.16207}, pmid = {36097140}, issn = {1462-2920}, mesh = {*Virome ; Phylogeny ; *Viruses/genetics ; Metagenomics ; Virion ; Genome, Viral ; }, abstract = {Viruses are considered to be the most abundant biological entities on earth. They also display striking genetic diversity as emphatically demonstrated by the recent advances of metagenomics and metatranscriptomics. But what are the limits of this diversity, that is, how many virus species in the earth virome? By combining the available estimates of the number of prokaryote species with those of the virome size, we obtain back-of-the-envelope estimates of the total number of distinct virus species, which come out astronomically large, from about 10[7] to about 10[9] . The route of virus origins apparently involved non-viral replicators capturing and exapting various cellular proteins to become virus capsid subunits. How many times in the history of life has this happened? In other words, how many realms of viruses, the highest rank taxa that are supposed to be monophyletic, comprise the global virome? We argue that viruses emerged on a number (even if far from astronomical) independent occasions, so the number of realms will considerably increase from the current 6, by splitting some of the current realms, giving the realm status to some of the currently unclassified groups of viruses and discovery of new distinct groups.}, } @article {pmid36096891, year = {2022}, author = {Li, T and Zhang, Z and Ma, Y and Song, Y and Yang, G and Han, X and Zhang, X}, title = {Nitrogen deposition experiment mimicked with NH4NO3 overestimates the effect on soil microbial community composition and functional potential in the Eurasian steppe.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {49}, pmid = {36096891}, issn = {2524-6372}, support = {32071547//National Natural Science Foundation of China/ ; 32071547//National Natural Science Foundation of China/ ; 32071547//National Natural Science Foundation of China/ ; 32071547//National Natural Science Foundation of China/ ; 32071547//National Natural Science Foundation of China/ ; 32071547//National Natural Science Foundation of China/ ; 32071547//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The nitrogenous compound deposited from the atmosphere to the soil is complex, but most field experiments mimic nitrogen deposition with the acid NH4NO3 alone. Thus, whether the acid and non-acid nitrogenous compounds have similar effects on biodiversity and ecosystem functions remains understudied. We mimicked nitrogen deposition with acidic NH4NO3 and (NH4)2SO4, and non-acidic urea, slow-released urea and NH4HCO3 in a temperate steppe, and quantified soil microbial taxonomic and functional gene composition with amplicon sequencing and shotgun metagenomics, respectively.

RESULTS: While NH4NO3 and (NH4)2SO4 significantly altered the soil microbial taxonomic and functional composition as well as their carbon decomposition potential, the other three compounds had smaller effects.

CONCLUSION: Our results suggested that previous nitrogen deposition experiments mimicked with NH4NO3 or (NH4)2SO4 alone may have overestimated the effect on biodiversity and ecosystem functions in the Eurasian steppe and similar ecosystems affected by mainly nonacidic nitrogen deposition.}, } @article {pmid36095141, year = {2022}, author = {Wu, YY and Gou, W and Yan, Y and Liu, CY and Yang, Y and Chen, D and Xie, K and Jiang, Z and Fu, Y and Zhu, HL and Zheng, JS and Chen, YM}, title = {Gut microbiota and acylcarnitine metabolites connect the beneficial association between equol and adiposity in adults: a prospective cohort study.}, journal = {The American journal of clinical nutrition}, volume = {116}, number = {6}, pages = {1831-1841}, doi = {10.1093/ajcn/nqac252}, pmid = {36095141}, issn = {1938-3207}, mesh = {Adult ; Female ; Humans ; Male ; Adiposity ; Carnitine ; Equol/urine ; *Gastrointestinal Microbiome ; *Isoflavones/pharmacology ; Obesity ; Prospective Studies ; Middle Aged ; }, abstract = {BACKGROUND: Many studies have investigated the effects of soy isoflavones on weight control, but few have focused on the role of equol, a gut-derived metabolite of daidzein with greater bioavailability than other soy isoflavones.

OBJECTIVES: This study examined the association of equol production with obesity and explored the mediating roles of equol-related gut microbiota and microbial carnitine metabolites.

METHODS: This 6.6-y prospective study included 2958 Chinese adults (2011 females and 947 males) aged 60.6 ± 6.0 y (mean ± SD) at baseline. Urinary equol and isoflavones were measured using HPLC-tandem MS. BMI, percentage fat mass (%FM), and serum triglycerides (TGs) were assessed every 3 y. Metagenomics sequencing and assessment of carnitine metabolites in feces were performed in a subsample of 897 participants.

RESULTS: Urinary equol, but not daidzein and genistein, was independently and inversely associated with the obesity-related indicators of BMI, %FM, and a biomarker (TGs). Equol producers (EPs) had lower odds of adiposity conditions and a reduced risk of 6.6-y obesity progression than non-EPs among total participants. Gut microbial analyses indicated that EPs had higher microbiome species richness (P = 3.42 × 10-5) and significantly different β-diversity of gut microbiota compared with the non-EP group (P = 0.001), with 20 of 162 species differing significantly. EPs (compared with non-EPs) had higher abundances of Alistipes senegalensis and Coprococcus catus but lower abundances of Ruminococcus gnavus (false discovery rate <0.05). Among the 7 determined fecal acylcarnitine metabolites, palmitoylcarnitine, oleylcarnitine 18:1, and stearylcarnitine were inversely associated with EPs but positively correlated with obesity conditions and progression. Path analyses indicated that the beneficial association between equol and obesity might be mediated by gut microbiota and decreased production of 3 acylcarnitines in feces.

CONCLUSIONS: This study suggests a beneficial association between equol and obesity, mediated by the gut microbiome and acylcarnitines, in adults.This trial was registered at clinicaltrials.gov as NCT03179657.}, } @article {pmid36093695, year = {2023}, author = {Raghavan, K and Dedeepiya, VD and Yamamoto, N and Ikewaki, N and Sonoda, T and Iwasaki, M and Kandaswamy, RS and Senthilkumar, R and Preethy, S and Abraham, SJK}, title = {Benefits of Gut Microbiota Reconstitution by Beta 1,3-1,6 Glucans in Subjects with Autism Spectrum Disorder and Other Neurodegenerative Diseases.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {94}, number = {s1}, pages = {S241-S252}, pmid = {36093695}, issn = {1875-8908}, mesh = {Humans ; *Gastrointestinal Microbiome ; alpha-Synuclein ; Glucans ; *Autism Spectrum Disorder/therapy/microbiology ; *Neurodegenerative Diseases/therapy ; }, abstract = {BACKGROUND: Aureobasidium pullulans (black yeast) AFO-202 strain-produced beta glucan, Nichi Glucan, has been shown to improve the behavior and sleep pattern along with an increase in α-synuclein and melatonin in children with autism spectrum disorder (ASD).

OBJECTIVE: In this randomized pilot clinical study, we have evaluated the gut microbiota of subjects with ASD after consumption of Nichi Glucan.

METHODS: Eighteen subjects with ASD were randomly allocated: six subjects in the control group (Group 1): conventional treatment comprising remedial behavioral therapies and L-carnosine 500 mg per day, and 12 subjects (Group 2) underwent supplementation with Nichi Glucan 0.5 g twice daily along with the conventional treatment for 90 days.

RESULTS: Whole genome metagenome (WGM) sequencing of the stool samples at baseline and after intervention showed that among genera of relevance, the abundance of Enterobacteriaceae was decreased almost to zero in Group 2 after intervention, whereas it increased from 0.36% to 0.85% in Group 1. The abundance of Bacteroides increased in Group 1, whereas it decreased in Group 2. The abundance of Prevotella increased while the abundance of Lactobacillus decreased in both Group 1 and Group 2. Among species, a decrease was seen in Escherichia coli, Akkermansia muciniphila CAG:154, Blautia spp., Coprobacillus sp., and Clostridium bolteae CAG:59, with an increase of Faecalibacterium prausnitzii and Prevotella copri, which are both beneficial.

CONCLUSION: AFO-202 beta 1,3-1,6 glucan, in addition to balancing the gut microbiome in children with ASD and its role in effective control of curli-producing Enterobacteriaceae that leads to α-synuclein misfolding and accumulation, may have a prophylactic role in Parkinson's and Alzheimer's diseases as well.}, } @article {pmid36093194, year = {2022}, author = {Shi, X and Gao, B and Srivastava, A and Izzi, Z and Abdalla, Y and Shen, W and Raj, D}, title = {Alterations of gut microbial pathways and virulence factors in hemodialysis patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {904284}, pmid = {36093194}, issn = {2235-2988}, support = {U01 DK099914/DK/NIDDK NIH HHS/United States ; R01 DK125256/DK/NIDDK NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Metagenome ; Metagenomics ; Renal Dialysis ; Virulence Factors/genetics ; }, abstract = {Alterations in gut microbiota might contribute to uremic toxicity and immune dysregulation in patients with end-stage renal disease. Hemodialysis patients are prone to infection and higher mortality following sepsis. The virulence factors in the gut metagenome have not been well studied in hemodialysis patients, which could be employed by microorganisms to successfully thrive and flourish in their hosts. In this study, we performed shotgun metagenomics sequencing on fecal DNA collected from 16 control subjects and 24 hemodialysis patients. Our analysis shows that a number of microbial species, metabolic pathways, antibiotic resistance, and virulence factors were significantly altered in hemodialysis patients compared with controls. In particular, erythromycin resistance methylase, pyridoxamine 5-phosphate oxidase, and streptothricin-acetyl-transferase were significantly increased in hemodialysis patients. The findings in our study laid a valuable foundation to further elucidate the causative role of virulence factors in predisposing HD patients to infection and to develop treatment strategies to reduce the genetic capacities of antibiotic resistance and virulence factors in HD patients.}, } @article {pmid36089219, year = {2023}, author = {Li, W and Wang, L and Li, X and Zheng, X and Cohen, MF and Liu, YX}, title = {Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes.}, journal = {Genomics, proteomics & bioinformatics}, volume = {21}, number = {6}, pages = {1182-1194}, pmid = {36089219}, issn = {2210-3244}, mesh = {*Metagenomics/methods ; *Bacterial Proteins/genetics/metabolism ; *Phylogeny ; *Microbiota/genetics ; Copper/metabolism ; Metagenome/genetics ; Escherichia coli/genetics/metabolism ; Genetic Variation/genetics ; }, abstract = {Exploring the natural diversity of functional genes/proteins from environmental DNA in high throughput remains challenging. In this study, we developed a sequence-based functional metagenomics procedure for mining the diversity of copper (Cu) resistance gene copA in global microbiomes, by combining the metagenomic assembly technology, local BLAST, evolutionary trace analysis (ETA), chemical synthesis, and conventional functional genomics. In total, 87 metagenomes were collected from a public database and subjected to copA detection, resulting in 93,899 hits. Manual curation of 1214 hits of high confidence led to the retrieval of 517 unique CopA candidates, which were further subjected to ETA. Eventually, 175 novel copA sequences of high quality were discovered. Phylogenetic analysis showed that almost all these putative CopA proteins were distantly related to known CopA proteins, with 55 sequences from totally unknown species. Ten novel and three known copA genes were chemically synthesized for further functional genomic tests using the Cu-sensitive Escherichia coli (ΔcopA). The growth test and Cu uptake determination showed that five novel clones had positive effects on host Cu resistance and uptake. One recombinant harboring copA-like 15 (copAL15) successfully restored Cu resistance of the host with a substantially enhanced Cu uptake. Two novel copA genes were fused with the gfp gene and expressed in E. coli for microscopic observation. Imaging results showed that they were successfully expressed and their proteins were localized to the membrane. The results here greatly expand the diversity of known CopA proteins, and the sequence-based procedure developed overcomes biases in length, screening methods, and abundance of conventional functional metagenomics.}, } @article {pmid36089141, year = {2022}, author = {Zheng, M and Shao, S and Chen, Y and Chen, B and Wang, M}, title = {Metagenomics analysis of microbial community distribution in large-scale and step-by-step purification system of swine wastewater.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {313}, number = {}, pages = {120137}, doi = {10.1016/j.envpol.2022.120137}, pmid = {36089141}, issn = {1873-6424}, mesh = {Ammonia/analysis ; Animals ; Bacteria/genetics ; *Chlorella ; *Environmental Pollutants/analysis ; Metagenomics ; *Microbiota ; Nitrogen/analysis ; Sewage/chemistry ; Swine ; Wastewater/chemistry ; *Water Purification/methods ; }, abstract = {Biological treatment is one of the most widely used methods to treat swine wastewater in wastewater treatment plants. The microbial community plays an important role in the swine slurry treatment system. However, limited information is available regarding the correlation between pollutant concentration and dominant microbial community in swine wastewater. This work aimed to study the profiling of microbial communities and their abundance in the 40 M[3]/day large-scale and step-by-step treatment pools of swine wastewater. Metagenome sequencing was applied to study the changes of microbial community structure in biochemical reaction pools. The results showed that in the heavily polluted pools, it was mainly Proteobacteria, Cyanobacteria, Chlorella and other strains that could tolerate high concentration of ammonia nitrogen to remove nitrogen and absorb chemical oxygen demand (COD). In the moderately polluted pools, Nitrospirae, Actinobacteria and other strains further cooperated to purify swine wastewater. In the later stage, the emergence of Brachionus indicated the reduction of water pollution. The dominant microbes and their abundance changed with the purification of swine wastewater in different stages. Moreover, the dominant microflora of swine wastewater treatment pools at all levels reflected little difference in phylum classification level, while in genus classification level, the dominant microflora manifested great difference. Findings demonstrated that the microorganisms maintained ecological balance and absorbed the nutrients in the swine wastewater treatment pools, so as to play the role of purifying sewage. Therefore, the stepwise purification of swine wastewater can be realized by adding bacteria and microalgae of different genera.}, } @article {pmid36089127, year = {2022}, author = {Wang, Z and Zhang, W and Xing, X and Li, X and Zheng, D and Bao, H and Xing, L}, title = {Effects of ferroferric oxide on propionate methanogenesis in sequencing batch reactors: Microbial community structure and metagenomic analysis.}, journal = {Bioresource technology}, volume = {363}, number = {}, pages = {127909}, doi = {10.1016/j.biortech.2022.127909}, pmid = {36089127}, issn = {1873-2976}, mesh = {Acetates ; Adenosine Triphosphatases ; Anaerobiosis ; Bacteria/genetics ; Bioreactors/microbiology ; Humic Substances ; Metagenomics ; Methane ; *Microbiota ; NAD ; Oxides ; *Propionates ; Riboflavin ; Wastewater/microbiology ; }, abstract = {This study investigated the effects of ferroferric oxide (Fe3O4) on propionate methanogenesis in anaerobic sequencing batch reactor (ASBR). Compared to ASBRC (without Fe3O4 addition), the addition of 10 g/L Fe3O4 (ASBRFe) decreased the maximum methane production rate by 69.6 % when propionate was used as the sole substrate. The addition of Fe3O4 reduced the contents of humic substances, riboflavin and nicotinamide adenine dinucleotide in extracellular polymeric substances. Therefore, Fe3O4 inhibited interspecies electron transfer of microorganisms through electronic mediators. Microbial community analysis revealed that Fe3O4 addition increased the relative abundance of acetate oxidizing bacterium (Mesotoga), but decreased the abundance of hydrogenotrophic methanogen (Methanobacterium). Further metagenomics analysis indicated that Fe3O4 increased the abundance of acetate oxidation genes and decreased that of hydrogenotrophic methanogenesis, quorum sensing and V/A-type ATPase genes. Thus, Fe3O4 reduced propionate methanogenesis during anaerobic digestion. The overall results indicate that Fe3O4 addition inhibits methanogenesis for treatment of propionate-contaminated wastewater in ASBR.}, } @article {pmid36088366, year = {2022}, author = {Liu, MC and Zhang, JT and Chen, JJ and Zhu, Y and Fu, BK and Hu, ZY and Fang, LQ and Zhang, XA and Liu, W}, title = {A global dataset of microbial community in ticks from metagenome study.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {560}, pmid = {36088366}, issn = {2052-4463}, support = {81825019//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Microbiota/genetics ; Systematic Reviews as Topic ; *Ticks/microbiology ; }, abstract = {Ticks are important vectors of various zoonotic pathogens that can infect animals and humans, and most documented tick-borne pathogens have a strong bias towards microorganisms with strong disease phenotypes. The recent development of next-generation sequencing (NGS) has enabled the study of microbial communities, referred to as microbiome. Herein, we undertake a systematic review of published literature to build a comprehensive global dataset of microbiome determined by NGS in field-collected ticks. The dataset comprised 4418 records from 76 literature involving geo-referenced occurrences for 46 species of ticks and 219 microorganism families, revealing a total of 83 emerging viruses identified from 24 tick species belonging to 6 tick genera since 1980. The viral, bacterial and eukaryotic composition was compared regarding the tick species, their live stage and types of the specimens, or the geographic location. The data can assist the further investigation of ecological, biogeographical and epidemiological features of the tick-borne disease.}, } @article {pmid36086955, year = {2022}, author = {Mancabelli, L and Milani, C and Fontana, F and Lugli, GA and Tarracchini, C and Viappiani, A and Ciociola, T and Ticinesi, A and Nouvenne, A and Meschi, T and Turroni, F and Ventura, M}, title = {Untangling the link between the human gut microbiota composition and the severity of the symptoms of the COVID-19 infection.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {6453-6462}, pmid = {36086955}, issn = {1462-2920}, mesh = {Humans ; *Gastrointestinal Microbiome ; *COVID-19 ; SARS-CoV-2 ; Dysbiosis/microbiology ; Pandemics ; Bacteria/genetics ; }, abstract = {Recent pandemic infection caused by SARS-CoV-2 (COVID-19) led the scientific community to investigate the possible causes contributing to the physiopathology of this disease. In this context, analyses of the intestinal microbiota highlighted possible correlation between host-associated bacterial communities and development of the COVID-19. Nevertheless, a detailed investigation of the role of the human microbiota in the severity of the symptoms of this disease is still lacking. This study performed a comprehensive meta-analysis of 323 faecal samples from public and novel Italian data sets based on the shotgun metagenomic approach. In detail, the comparative analyses revealed possible differences in the microbial biodiversity related to the individual health status, highlighting a species richness decrease in COVID-19 patients with a severe prognosis. Moreover, healthy subjects resulted characterized by a higher abundance of protective and health-supporting bacterial species, while patients affected by COVID-19 disease displayed a significant increase of opportunistic pathogen bacteria involved in developing putrefactive dysbiosis. Furthermore, prediction of the microbiome functional capabilities suggested that individuals affected by COVID-19 subsist in an unbalanced metabolism characterized by an overrepresentation of enzymes involved in the protein metabolism at the expense of carbohydrates oriented pathways, which can impact on disease severity and in excessive systemic inflammation.}, } @article {pmid36086900, year = {2023}, author = {Bell, KL and Turo, KJ and Lowe, A and Nota, K and Keller, A and Encinas-Viso, F and Parducci, L and Richardson, RT and Leggett, RM and Brosi, BJ and Burgess, KS and Suyama, Y and de Vere, N}, title = {Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding.}, journal = {Molecular ecology}, volume = {32}, number = {23}, pages = {6345-6362}, pmid = {36086900}, issn = {1365-294X}, support = {2021-67012-35153//USDA-NIFA/ ; BB/CSP1720/1//Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {*Ecosystem ; *DNA Barcoding, Taxonomic/methods ; Pollen/genetics ; Plants/genetics ; DNA ; Pollination/genetics ; }, abstract = {Anthropogenic activities are triggering global changes in the environment, causing entire communities of plants, pollinators and their interactions to restructure, and ultimately leading to species declines. To understand the mechanisms behind community shifts and declines, as well as monitoring and managing impacts, a global effort must be made to characterize plant-pollinator communities in detail, across different habitat types, latitudes, elevations, and levels and types of disturbances. Generating data of this scale will only be feasible with rapid, high-throughput methods. Pollen DNA metabarcoding provides advantages in throughput, efficiency and taxonomic resolution over traditional methods, such as microscopic pollen identification and visual observation of plant-pollinator interactions. This makes it ideal for understanding complex ecological networks and their responses to change. Pollen DNA metabarcoding is currently being applied to assess plant-pollinator interactions, survey ecosystem change and model the spatiotemporal distribution of allergenic pollen. Where samples are available from past collections, pollen DNA metabarcoding has been used to compare contemporary and past ecosystems. New avenues of research are possible with the expansion of pollen DNA metabarcoding to intraspecific identification, analysis of DNA in ancient pollen samples, and increased use of museum and herbarium specimens. Ongoing developments in sequencing technologies can accelerate progress towards these goals. Global ecological change is happening rapidly, and we anticipate that high-throughput methods such as pollen DNA metabarcoding are critical for understanding the evolutionary and ecological processes that support biodiversity, and predicting and responding to the impacts of change.}, } @article {pmid36085351, year = {2022}, author = {Dai, D and Dai, F and Chen, J and Jin, M and Li, M and Hu, D and Liu, Z and Zhang, Z and Xu, F and Chen, WH}, title = {Integrated multi-omics reveal important roles of gut contents in intestinal ischemia-reperfusion induced injuries in rats.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {938}, pmid = {36085351}, issn = {2399-3642}, mesh = {Animals ; *Gastrointestinal Microbiome ; Ischemia ; Metabolomics ; Rats ; Reperfusion ; *Reperfusion Injury ; }, abstract = {Intestinal ischemia-reperfusion (IIR) is a life-threatening clinical event with damaging signals whose origin and contents are unclear. Here we observe that IIR significantly affect the metabolic profiles of most organs by unbiased organ-wide metabolic analysis of gut contents, blood, and fifteen organs in rats (n = 29). Remarkably, correlations between gut content metabolic profiles and those of other organs are the most significant. Gut contents are also the only ones to show dynamic correlations during IIR. Additionally, according to targeted metabolomics analysis, several neurotransmitters are considerably altered in the gut during IIR, and displayed noteworthy correlations with remote organs. Likewise, metagenomics analysis (n = 35) confirm the effects of IIR on gut microbiota, and identify key species fundamental to the changes in gut metabolites, particularly neurotransmitters. Our multi-omics results establish key roles of gut contents in IIR induced remote injury and provide clues for future exploration.}, } @article {pmid36083005, year = {2022}, author = {Chen, J and Zhang, X}, title = {dICC: distance-based intraclass correlation coefficient for metagenomic reproducibility studies.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {21}, pages = {4969-4971}, pmid = {36083005}, issn = {1367-4811}, support = {R01 GM144351/GM/NIGMS NIH HHS/United States ; }, mesh = {Reproducibility of Results ; *Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {SUMMARY: Due to the sparsity and high dimensionality, microbiome data are routinely summarized into pairwise distances capturing the compositional differences. Many biological insights can be gained by analyzing the distance matrix in relation to some covariates. A microbiome sampling method that characterizes the inter-sample relationship more reproducibly is expected to yield higher statistical power. Traditionally, the intraclass correlation coefficient (ICC) has been used to quantify the degree of reproducibility for a univariate measurement using technical replicates. In this work, we extend the traditional ICC to distance measures and propose a distance-based ICC (dICC). We derive the asymptotic distribution of the sample-based dICC to facilitate statistical inference. We illustrate dICC using a real dataset from a metagenomic reproducibility study.

dICC is implemented in the R CRAN package GUniFrac.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36082501, year = {2023}, author = {Özdemir, A and Yozgat, A and Işgın-Atıcı, K and Avcı, E and Yıldız, BD and Gündoğdu, A and Nalbantoğlu, U and Turhan, T and Doğruman-Al, F and Büyüktuncer, Z}, title = {Potential associations between alterations in gut microbiome and obesity-related traits after the bariatric surgery.}, journal = {Journal of human nutrition and dietetics : the official journal of the British Dietetic Association}, volume = {36}, number = {3}, pages = {981-996}, doi = {10.1111/jhn.13087}, pmid = {36082501}, issn = {1365-277X}, mesh = {Humans ; *Obesity, Morbid/surgery ; *Gastrointestinal Microbiome ; *Bariatric Surgery ; Diet ; Cholesterol ; }, abstract = {BACKGROUND: This study aimed to examine the effects of both obesity and bariatric surgery on gut microbiome, dietary intake, as well as metabolic and inflammatory parameters.

METHODS: All participants (15 with morbid obesity who had bariatric surgery, 8 with morbid obesity and 11 non-obese) were followed up for a 6-month period with interviews at baseline (M0), at the end of 3 (M3) and 6 months (M6). Dietary assessment was done, and blood and faecal samples were collected.

RESULTS: Dietary energy and nutrient intakes as well as serum glucose levels, total cholesterol, low-density lipoprotein (LDL)-cholesterol and high sensitivity C-reactive protein (hs-CRP) levels decreased after surgery (p < 0.05, for each). Participants with morbid obesity had higher levels of Firmicutes and lower levels of Bacteroidetes at M0 compared to non-obese participants. The abundances of Bacteroidetes increased (p = 0.02), whereas that of Firmicutes decreased (p > 0.05) after the surgery, leading to a significant decrease in Firmicutes/Bacteroidetes ratio (p = 0.01). At sub-phylum level, the abundances of Lactobacillus and Bifidobacterium decreased, whereas those of Akkermansia increased after the surgery (p < 0.01, for each). Although participants who were morbidly obese had a distinct profile according to ß-diversity indices at M0, it became similar with the profile of non-obese participants (p > 0.05) at M3 and M6. Similarly, α-diversity indices were lower in subjects with morbid obesity at M0, but became similar to levels in non-obese controls at M6.

CONCLUSION: This study confirmed that bariatric surgery has substantial impacts on gut microbiome's composition and diversity, as well as anthropometrical measurements and biochemical parameters, which were associated with the alterations in dietary intake patterns.}, } @article {pmid36081364, year = {2022}, author = {Molina Ortiz, JP and Read, MN and McClure, DD and Holmes, A and Dehghani, F and Shanahan, ER}, title = {High throughput genome scale modeling predicts microbial vitamin requirements contribute to gut microbiome community structure.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2118831}, pmid = {36081364}, issn = {1949-0984}, mesh = {Animals ; Bacteroides/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics/methods ; Mice ; Phylogeny ; Vitamins ; }, abstract = {Human gut microbiome structure and emergent metabolic outputs impact health outcomes. However, what drives such community characteristics remains underexplored. Here, we rely on high throughput genomic reconstruction modeling, to infer the metabolic attributes and nutritional requirements of 816 gut strains, via a framework termed GEMNAST. This has been performed in terms of a group of human vitamins to examine the role vitamin exchanges have at different levels of community organization. We find that only 91 strains can satisfy their vitamin requirements (prototrophs) while the rest show various degrees of auxotrophy/specialization, highlighting their dependence on external sources, such as other members of the microbial community. Further, 79% of the strains in our sample were mapped to 11 distinct vitamin requirement profiles with low phylogenetic consistency. Yet, we find that human gut microbial community enterotype indicators display marked metabolic differences. Prevotella strains display a metabolic profile that can be complemented by strains from other genera often associated with the Prevotella enterotype and agrarian diets, while Bacteroides strains occupy a prototrophic profile. Finally, we identify pre-defined interaction modules (IMs) of gut species from human and mice predicted to be driven by, or highly independent of vitamin exchanges. Our analysis provides mechanistic grounding to gut microbiome stability and to co-abundance-based observations, a fundamental step toward understanding emergent processes that influence health outcomes. Further, our work opens a path to future explorations in the field through applications of GEMNAST to additional nutritional dimensions.}, } @article {pmid36079806, year = {2022}, author = {Liu, L and Chen, X and Liu, L and Qin, H}, title = {Clostridium butyricum Potentially Improves Immunity and Nutrition through Alteration of the Microbiota and Metabolism of Elderly People with Malnutrition in Long-Term Care.}, journal = {Nutrients}, volume = {14}, number = {17}, pages = {}, pmid = {36079806}, issn = {2072-6643}, support = {81972221, 81730102 and 31970111//National Natural Science Foundation of China/ ; }, mesh = {Aged ; *Clostridium butyricum ; Fatty Acids, Volatile/metabolism ; Humans ; Long-Term Care ; *Malnutrition ; *Microbiota ; Single-Blind Method ; Vitamins ; }, abstract = {Recent research advances examining the gut microbiome and its association with human health have indicated that microbiota-targeted intervention is a promising means for health modulation. In this study, elderly people in long-term care (aged 83.2 ± 5.3 year) with malnutrition (MNA-SF score ≤ 7) were recruited in a community hospital for a 12-week randomized, single-blind clinical trial with Clostridium butyricum. Compared with the basal fluctuations of the control group, an altered gut microbiome was observed in the intervention group, with increased (p < 0.05) Coprobacillus species, Carnobacterium divergens, and Corynebacterium_massiliense, and the promoted growth of the beneficial organisms Akketmanse muciniphila and Alistipes putredinis. A concentrated profile of 14 increased Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs (KOs) that were enriched in cofactor/vitamin production and carbohydrate metabolism pathways were discovered; the genes were found to be correlated (p < 0.05) with an elevated abundance of plasma metabolites and short-chain fatty acids (SCFAs), unsaturated medium- to long-chain fatty acids (MFA, LFA), carnitines, and amino acids, thus suggesting a coordinated ameliorated metabolism. Proinflammatory factor interferon-gamma (IFN-γ) levels decreased (p < 0.05) throughout the intervention, while the gut barrier tight junction protein, occludin, rose in abundance (p = 0.059), and the sensitive nutrition biomarker prealbumin improved, in contrast to the opposite changes in control. Based on our results obtained during a relatively short intervention time, C. butyricum might have great potential for improving nutrition and immunity in elderly people in long-term care with malnutrition through the alteration of gut microbiota, increasing the abundance of beneficial bacteria and activating the metabolism in SCFA and cofactor/vitamin production, bile acid metabolism, along with efficient energy generation.}, } @article {pmid36076344, year = {2023}, author = {Xu, H and Qian, Y and Jia, S and Shi, Z and Zhong, Q}, title = {Comparative analysis of subgingival microbiota in patients with mild, moderate, and severe chronic periodontitis.}, journal = {Oral diseases}, volume = {29}, number = {7}, pages = {2865-2877}, doi = {10.1111/odi.14373}, pmid = {36076344}, issn = {1601-0825}, support = {20184Y0244//Shanghai Municipal Health and Family Planning Commission/ ; }, mesh = {Humans ; *Chronic Periodontitis/therapy ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Gingival Crevicular Fluid ; *Microbiota/genetics ; }, abstract = {In this study, we explored the suspected pathogens of chronic periodontitis at different stages of occurrence and development. We collected 100 gingival crevicular fluid samples, 27, 27, and 26 from patients with mild, moderate, and severe chronic periodontitis, respectively, and 20 from healthy individuals. Pathogens were detected using a 16S rRNA metagenomic approach. Quantitative Insights in Microbial Ecology, Mothur, and other software were used to analyze the original data, draw relative abundance histograms and heat maps, and calculate flora abundance and diversity indexes. We identified 429 operational taxonomic units, covering 13 phyla, 20 classes, 32 orders, 66 families, and 123 genera from the four groups of samples. Each group showed microbial diversity, and the number of new species of bacterial flora in the gingival crevicular fluid samples gradually increased from the healthy to the severe chronic periodontitis group. There was a significant difference in the relative abundance of the core flora at the phylum, class, order, family, and genus classification levels. Our data indicated a certain correlation between the changes in the subgingival microbial structure and the occurrence and development of chronic periodontitis, which might be able to provide a reference for the diagnosis, treatment and prevention of chronic periodontitis.}, } @article {pmid36076153, year = {2022}, author = {Guo, Y and Song, B and Li, A and Wu, Q and Huang, H and Li, N and Yang, Y and Adams, JM and Yang, L}, title = {Higher pH is associated with enhanced co-occurrence network complexity, stability and nutrient cycling functions in the rice rhizosphere microbiome.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {6200-6219}, doi = {10.1111/1462-2920.16185}, pmid = {36076153}, issn = {1462-2920}, mesh = {Rhizosphere ; *Oryza ; Soil Microbiology ; *Microbiota/genetics ; Soil ; Nutrients ; Hydrogen-Ion Concentration ; }, abstract = {The rice rhizosphere microbiota is crucial for crop yields and nutrient use efficiency. However, little is known about how co-occurrence patterns, keystone taxa and functional gene assemblages relate to soil pH in the rice rhizosphere soils. Using shotgun metagenome analysis, the rice rhizosphere microbiome was investigated across 28 rice fields in east-central China. At higher pH sites, the taxonomic co-occurrence network of rhizosphere soils was more complex and compact, as defined by higher average degree, graph density and complexity. Network stability was greatest at medium pH (6.5 < pH < 7.5), followed by high pH (7.5 < pH). Keystone taxa were more abundant at higher pH and correlated significantly with key ecosystem functions. Overall functional genes involved in C, N, P and S cycling were at a higher relative abundance in higher pH rhizosphere soils, excepting C degradation genes (e.g. key genes involved in starch, cellulose, chitin and lignin degradation). Our results suggest that the rice rhizosphere soil microbial network is more complex and stable at higher pH, possibly indicating increased efficiency of nutrient cycling. These observations may indicate routes towards more efficient soil management and understanding of the potential effects of soil acidification on the rice rhizosphere system.}, } @article {pmid36076058, year = {2022}, author = {Ravi, A and Troncoso-Rey, P and Ahn-Jarvis, J and Corbin, KR and Harris, S and Harris, H and Aydin, A and Kay, GL and Le Viet, T and Gilroy, R and Pallen, MJ and Page, AJ and O'Grady, J and Warren, FJ}, title = {Hybrid metagenome assemblies link carbohydrate structure with function in the human gut microbiome.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {932}, pmid = {36076058}, issn = {2399-3642}, support = {BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG1860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012512/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10343/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BS/E/F/000PR10346/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10348/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10349/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10352/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/genetics/metabolism ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Starch/metabolism ; }, abstract = {Complex carbohydrates that escape small intestinal digestion, are broken down in the large intestine by enzymes encoded by the gut microbiome. This is a symbiotic relationship between microbes and host, resulting in metabolic products that influence host health and are exploited by other microbes. However, the role of carbohydrate structure in directing microbiota community composition and the succession of carbohydrate-degrading microbes, is not fully understood. In this study we evaluate species-level compositional variation within a single microbiome in response to six structurally distinct carbohydrates in a controlled model gut using hybrid metagenome assemblies. We identified 509 high-quality metagenome-assembled genomes (MAGs) belonging to ten bacterial classes and 28 bacterial families. Bacterial species identified as carrying genes encoding starch binding modules increased in abundance in response to starches. The use of hybrid metagenomics has allowed identification of several uncultured species with the functional potential to degrade starch substrates for future study.}, } @article {pmid36075807, year = {2023}, author = {Zysset-Burri, DC and Morandi, S and Herzog, EL and Berger, LE and Zinkernagel, MS}, title = {The role of the gut microbiome in eye diseases.}, journal = {Progress in retinal and eye research}, volume = {92}, number = {}, pages = {101117}, doi = {10.1016/j.preteyeres.2022.101117}, pmid = {36075807}, issn = {1873-1635}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Central Serous Chorioretinopathy ; *Microbiota ; *Uveitis ; *Macular Degeneration ; *Retinal Artery Occlusion ; }, abstract = {The gut microbiome is a complex ecosystem of microorganisms and their genetic entities colonizing the gastrointestinal tract. When in balanced composition, the gut microbiome is in symbiotic interaction with its host and maintains intestinal homeostasis. It is involved in essential functions such as nutrient metabolism, inhibition of pathogens and regulation of immune function. Through translocation of microbes and their metabolites along the epithelial barrier, microbial dysbiosis induces systemic inflammation that may lead to tissue destruction and promote the onset of various diseases. Using whole-metagenome shotgun sequencing, several studies have shown that the composition and associated functional capacities of the gut microbiome are associated with age-related macular degeneration, retinal artery occlusion, central serous chorioretinopathy and uveitis. In this review, we provide an overview of the current knowledge about the gut microbiome in eye diseases, with a focus on interactions between the microbiome, specific microbial-derived metabolites and the immune system. We explain how these interactions may be involved in the pathogenesis of age-related macular degeneration, retinal artery occlusion, central serous chorioretinopathy and uveitis and guide the development of new therapeutic approaches by microbiome-altering interventions for these diseases.}, } @article {pmid36075413, year = {2022}, author = {Prado, T and Brandão, ML and Fumian, TM and Freitas, L and Chame, M and Leomil, L and Magalhães, MGP and Degrave, WMS and Leite, JPG and Miagostovich, MP}, title = {Virome analysis in lakes of the South Shetland Islands, Antarctica - 2020.}, journal = {The Science of the total environment}, volume = {852}, number = {}, pages = {158537}, doi = {10.1016/j.scitotenv.2022.158537}, pmid = {36075413}, issn = {1879-1026}, mesh = {Humans ; Lakes ; Antarctic Regions ; Virome ; Prospective Studies ; *Viruses/genetics ; *RNA Viruses ; *Microbiota ; Islands ; }, abstract = {Polar freshwater ecosystems are characterized by a distinct microbiota. However, little is known about viral diversity and abundance, especially regarding the ecology of RNA viruses. We used shotgun metagenomic analysis on samples from Antarctic ecosystems, and report here the characterization of the virome fraction, from different lakes located in the South Shetland Islands (Penguin, Ardley, Deception and King George Island) in the Peninsula Antarctica, in the summer season 2020. DNA viruses (99.4 %) prevailed over RNA viruses (0.6 %) in the lake samples. Six viral orders were identified in the metagenomic libraries: Caudovirales (dsDNA), which was prevalent in most lakes; Picornavirales (ssRNA+); Sobelivirales (ssRNA+); Tolivirales (ssRNA+); Petitvirales (ssDNA) and Baphyvirales (ssDNA), including eight viral families (Herelleviridae, Siphoviridae, Myoviridae, Microviridae, Marnaviridae, Bacilladnaviridae, Barnaviridae and Tombusviridae) and several other, mainly non-classified ssRNA[(+)] viruses in the lakes of Ardley Island. Bacteriophages (dsDNA) (Herelleviridae family) infecting the phylum Firmicutes and Siphoviridae were predominant in most lakes evaluated. Functional analysis demonstrated a prevalence of unknown proteins (68 %) in the virome. Our prospective study provides virome analysis data from different lakes in the South Shetland Islands, Antarctica, opening exploratory lines for future research related to the biodiversity and viral ecology in this extreme ecosystem.}, } @article {pmid36075400, year = {2022}, author = {Fan, X and Deng, H and Qiu, J and Ji, H and Shen, X}, title = {Antibiotics-induced depression in mice via the microbiota-gut-brain axis.}, journal = {Journal of affective disorders}, volume = {318}, number = {}, pages = {152-158}, doi = {10.1016/j.jad.2022.08.059}, pmid = {36075400}, issn = {1573-2517}, mesh = {Adrenocorticotropic Hormone ; Animals ; Anti-Bacterial Agents/adverse effects ; Brain-Derived Neurotrophic Factor ; Brain-Gut Axis ; Corticosterone ; *Depression/etiology ; Disease Models, Animal ; Dysbiosis ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred C57BL ; NF-kappa B/metabolism ; Norepinephrine ; Serotonin ; Stress, Psychological/complications ; }, abstract = {BACKGROUND: Intestinal dysbacteriosis is associated with depression. This study aimed to establish an antibiotics-induced depression mouse model and explore the mechanism of antibiotic-induced depression.

METHODS: C57BL/6 J mice were treated with antibiotics to prepare the antibiotic-induced depression mouse model. Behavioral tests and depression-related bio-markers were examined. To understand the abundance of different bacteria in intestinal flora and screen out the predominant bacterial species, metagenomic analysis of feces was carried out. Finally, we detected the expression of NF-κB-p65 and p-NF-κB-p65 in PFC and the hippocampus using Western blot.

RESULTS: Mixtures A and B caused depression-like behavior in mice. Norepinephrine, 5-hydroxytryptamine, and brain-derived neurotrophic factor in hippocampus and PFC of antibiotic-induced depression mice significantly decreased. The serum adrenocorticotropic hormone and corticosterone concentrations increased. The abundance values of Bacteroides thetaiotaomicron, Klebsiella oxytoca, and Klebsiella aerogenes in antibiotic-induced depression mice significantly increased, and the characteristic KO genes and metabolic pathways in antibiotic-induced depression mice were significantly different with in CUMS depression mice (the positive control) and normal mice. The relative levels of p-NF-κB-p65 in antibiotics-induced depression mice were significantly higher than in normal mice.

LIMITATIONS: How dysbacteriosis induces inflammation in the central nervous system is unclear.

CONCLUSIONS: Specific antibiotic mixture can cause depression-like behavior and changes of depression-related bio-markers in mice. The antibiotic-induced depression mice display changes in the species and metabolism of intestinal bacterial flora. The activation of NF-κB inflammatory signaling pathway in the central nervous system may act as one of the mechanisms in the development of antibiotic-induced depression.}, } @article {pmid36073806, year = {2022}, author = {Hakim, D and Wandro, S and Zengler, K and Zaramela, LS and Nowinski, B and Swafford, A and Zhu, Q and Song, SJ and Gonzalez, A and McDonald, D and Knight, R}, title = {Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0075822}, pmid = {36073806}, issn = {2379-5077}, support = {DP1 AT010885/AT/NCCIH NIH HHS/United States ; U24 CA248454/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Algorithms ; Staphylococcus aureus/genetics ; Metagenome ; Metagenomics/methods ; *Microbiota ; }, abstract = {Assigning taxonomy remains a challenging topic in microbiome studies, due largely to ambiguity of reads which overlap multiple reference genomes. With the Web of Life (WoL) reference database hosting 10,575 reference genomes and growing, the percentage of ambiguous reads will only increase. The resulting artifacts create both the illusion of co-occurrence and a long tail end of extraneous reference hits that confound interpretation. We introduce genome cover, the fraction of reference genome overlapped by reads, to distinguish these artifacts. We show how to dynamically predict genome cover by read count and examine our model in Staphylococcus aureus monoculture. Our modeling cleanly separates both S. aureus and true contaminants from the false artifacts of reference overlap. We next introduce saturated genome cover, the true fraction of a reference genome overlapped by sample contents. Genome cover may not saturate for low abundance or low prevalence bacteria. We assuage this worry with examination of a large human fecal data set. By compositing the metric across like samples, genome cover saturates even for rare species. We note that it is a threshold on saturated genome cover, not genome cover itself, which indicates a spurious reference hit or distant relative. We present Zebra, a method to compute and threshold the genome cover metric across like samples, a recurrence to estimate genome cover and confirm saturation, and provide guidance for choosing cover thresholds in real world scenarios. Standalone genome cover and integration into Woltka are available: https://github.com/biocore/zebra_filter, https://github.com/qiyunzhu/woltka. IMPORTANCE Taxonomic assignment, assigning sequences to specific taxonomic units, is a crucial processing step in microbiome analyses. Issues in taxonomic assignment affect interpretation of what microbes are present in each sample and may be associated with specific environmental or clinical conditions. Assigning importance to a particular taxon relies strongly on independence of assigned counts. The false inclusion of thousands of correlated taxa makes interpretation ambiguous, leading to underconstrained results which cannot be reproduced. The importance sometimes attached to implausible artifacts such as anthrax or bubonic plague is especially problematic. We show that the Zebra filter retrieves only the nearest relatives of sample contents enabling more reproducible and biologically plausible interpretation of metagenomic data.}, } @article {pmid36073802, year = {2022}, author = {Li, C and Hao, L and Lü, F and Duan, H and Zhang, H and He, P}, title = {Syntrophic Acetate-Oxidizing Microbial Consortia Enriched from Full-Scale Mesophilic Food Waste Anaerobic Digesters Showing High Biodiversity and Functional Redundancy.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0033922}, pmid = {36073802}, issn = {2379-5077}, mesh = {Humans ; Microbial Consortia/genetics ; Ammonia/metabolism ; Anaerobiosis ; Food ; RNA, Ribosomal, 16S/genetics ; *Refuse Disposal ; Bacteria/genetics ; Oxidation-Reduction ; *Euryarchaeota/genetics ; Acetates/metabolism ; }, abstract = {Syntrophic acetate oxidation (SAO) coupled with hydrogenotrophic methanogenesis (HM) plays a vital role in the anaerobic digestion of protein-rich feedstocks such as food wastes. However, current knowledge of the biodiversity and genetic potential of the involved microbial participants, especially syntrophic acetate-oxidizing bacteria (SAOB), is limited due to the low abundance of these microorganisms and challenges in their isolation. The intent of this study was to enrich and identify potential SAOB. Therefore, we conducted continuous acetate feeding under high ammonia concentrations using two separate inoculum consortia of microorganisms that originated from full-scale mesophilic food waste digesters, which lasted for more than 200 days. Using 16S rRNA gene amplicon and metagenomic analyses, we observed a convergence of the experimental microbial communities during the enrichment regarding taxonomic composition and metabolic functional composition. Stable carbon isotope analyses of biogas indicated that SAO-HM was the dominant methanogenic pathway during the enrichment process. The hydrogenotrophic methanogen Methanoculleus dominated the archaeal community. The enriched SAO community featured high biodiversity and metabolic functional redundancy. By analyzing the metagenome-assembled genomes, the known SAOB Syntrophaceticus schinkii and six uncultured populations were identified to have the genetic potential to perform SAO through the conventional reversed Wood-Ljungdahl pathway, while another six bacteria were found to encode the reversed Wood-Ljungdahl pathway combined with a glycine cleavage system as novel SAOB candidates. These results showed that the food waste anaerobic digesters harbor diverse SAOB and highlighted the importance of the glycine cleavage system for acetate oxidation. IMPORTANCE Syntrophic acetate oxidation to CO2 and H2, together with hydrogenotrophic methanogenesis, contributes to much of the carbon flux in the anaerobic digestion of organic wastes, especially at high ammonia concentrations. A deep understanding of the biodiversity, metabolic genetic potential, and ecology of the SAO community can help to improve biomethane production from wastes for clean energy production. Here, we enriched the SAO-HM functional guild obtained from full-scale food waste anaerobic digesters and recorded dynamic changes in community taxonomic composition and functional profiles. By reconstructing the metabolic pathways, diverse known and novel bacterial members were found to have SAO potential via the reversed Wood-Ljungdahl (WL) pathway alone, or via the reversed WL pathway with a glycine cleavage system (WLP-GCS), and those catalyzing WLP-GCS showed higher microbial abundance. This study revealed the biodiversity and metabolic functional redundancy of SAOB in full-scale anaerobic digester systems and provided inspiration for further genome-centric studies.}, } @article {pmid36073352, year = {2022}, author = {Grouzdev, D and Gaisin, V and Lunina, O and Krutkina, M and Krasnova, E and Voronov, D and Baslerov, R and Sigalevich, P and Savvichev, A and Gorlenko, V}, title = {Microbial communities of stratified aquatic ecosystems of Kandalaksha Bay (White Sea) shed light on the evolutionary history of green and brown morphotypes of Chlorobiota.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {10}, pages = {}, doi = {10.1093/femsec/fiac103}, pmid = {36073352}, issn = {1574-6941}, mesh = {Bays ; *Chlorobi/genetics ; *Microbiota/genetics ; Photosynthesis ; Phylogeny ; Water ; }, abstract = {Anoxygenic photoautotrophic metabolism of green sulfur bacteria of the family Chlorobiaceae played a significant role in establishing the Earth's biosphere. Two known major ecological forms of these phototrophs differ in their pigment composition and, therefore, in color: the green and brown forms. The latter form often occurs in low-light environments and is specialized to harvest blue light, which can penetrate to the greatest depth in the water column. In the present work, metagenomic sequencing was used to investigate the natural population of brown Chl. phaeovibrioides ZM in a marine stratified Zeleny Mys lagoon in the Kandalaksha Bay (the White Sea) to supplement the previously obtained genomes of brown Chlorobiaceae. The genomes of brown and green Chlorobiaceae were investigated using comparative genome analysis and phylogenetic and reconciliation analysis to reconstruct the evolution of these ecological forms. Our results support the suggestion that the last common ancestor of Chlorobiaceae belonged to the brown form, i.e. it was adapted to the conditions of low illumination. However, despite the vertical inheritance of these characteristics, among modern Chlorobiaceae populations, the genes responsible for synthesizing the pigments of the brown form are subject to active horizontal transfer.}, } @article {pmid36073311, year = {2022}, author = {McLean, AR and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Site-tropism of streptococci in the oral microbiome.}, journal = {Molecular oral microbiology}, volume = {37}, number = {6}, pages = {229-243}, pmid = {36073311}, issn = {2041-1014}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE027958/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Streptococcus/genetics ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics ; Mouth/microbiology ; Tropism ; Phylogeny ; }, abstract = {A detailed understanding of where bacteria localize is necessary to advance microbial ecology and microbiome-based therapeutics. The site-specialist hypothesis predicts that most microbes in the human oral cavity have a primary habitat type within the mouth where they are most abundant. We asked whether this hypothesis accurately describes the distribution of the members of the genus Streptococcus, a clinically relevant taxon that dominates most oral sites. Prior analysis of 16S rRNA gene sequencing data indicated that some oral Streptococcus clades are site-specialists while others may be generalists. However, within complex microbial populations composed of numerous closely related species and strains, such as the oral streptococci, genome-scale analysis is necessary to provide the resolution to discriminate closely related taxa with distinct functional roles. Here, we assess whether individual species within this genus are specialists using publicly available genomic sequence data that provide species-level resolution. We chose a set of high-quality representative genomes for human oral Streptococcus species. Onto these genomes, we mapped shotgun metagenomic sequencing reads from supragingival plaque, tongue dorsum, and other sites in the oral cavity. We found that every abundant Streptococcus species in the healthy human oral cavity showed strong site-tropism and that even closely related species such as S. mitis, S. oralis, and S. infantis specialized in different sites. These findings indicate that closely related bacteria can have distinct habitat distributions in the absence of dispersal limitation and under similar environmental conditions and immune regimes. Substantial overlap between the core genes of these three species suggests that site-specialization is determined by subtle differences in genomic content.}, } @article {pmid36070704, year = {2022}, author = {Wanapaisan, P and Chuansangeam, M and Nopnipa, S and Mathuranyanon, R and Nonthabenjawan, N and Ngamsombat, C and Thientunyakit, T and Muangpaisan, W}, title = {Association between Gut Microbiota with Mild Cognitive Impairment and Alzheimer's Disease in a Thai Population.}, journal = {Neuro-degenerative diseases}, volume = {22}, number = {2}, pages = {43-54}, doi = {10.1159/000526947}, pmid = {36070704}, issn = {1660-2862}, mesh = {Humans ; Aged ; *Alzheimer Disease/diagnosis ; *Gastrointestinal Microbiome ; Southeast Asian People ; *Cognitive Dysfunction/complications ; Neuroimaging ; }, abstract = {BACKGROUND: Mild cognitive impairment (MCI) and Alzheimer's disease (AD) are common in older adults. Much recent work has implicated the connection between the gut and the brain via bidirectional communication of the gastrointestinal tract and the central nervous system through biochemical signaling. Altered gut microbiota composition has shown controversial results based on geographic location, age, diet, physical activity, psychological status, underlying diseases, medication, and drug use.

OBJECTIVES: This study aimed to investigate the relationships of gut microbiota with MCI and AD.

METHODS: 16S metagenome profiles from stool collection of participant groups (normal; n = 20, MCI; n = 12, AD; n = 20) were analyzed. The diagnosis of cognitive conditions was made by standard criteria consisting of clinical interviews, physical examinations, cognitive assessments, laboratory examinations, and neuroimaging by both structural neuroimaging and amyloid positron emission tomography scans. Correlations between medical factors with food frequency and the fecal microbiome were elucidated.

RESULTS: A significant difference at the operational taxonomic unit level was observed. The significantly higher abundance of bacteria in nondementia patients belonged to the Clostridiales order, including Clostridium sensu stricto 1 (p < 0.0001), Fusicatenibacter (p = 0.0007), Lachnospiraceae (p = 0.001), Agathobacter (p = 0.021), and Fecalibacterium (p < 0.0001). In contrast, Escherichia-Shigella (p = 0.0002), Bacteroides (p = 0.0014), Holdemanella (p < 0.0001), Romboutsia (p = 0.001), and Megamonas (p = 0.047) were the dominant genera in the AD group. Left and right hippocampus and right amygdala volumes were significantly decreased in the AD group (p < 0.001) and significantly correlated with the groups of bacteria that were significantly different between groups.

CONCLUSION: There was a relationship between the composition of the gut microbiome and neurodegenerative disorders, including MCI and AD. Reduction of Clostridiaceae and increases in Enterobacteriaceae and Bacteroides were associated with persons with MCI and AD, consistent with previous studies. The altered gut microbiome could be potentially targeted for the early diagnosis of dementia and the reduction of AD risk.}, } @article {pmid36069455, year = {2022}, author = {Maringanti, VS and Bucci, V and Gerber, GK}, title = {MDITRE: Scalable and Interpretable Machine Learning for Predicting Host Status from Temporal Microbiome Dynamics.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0013222}, pmid = {36069455}, issn = {2379-5077}, support = {R01 GM130777/GM/NIGMS NIH HHS/United States ; 1R01GM130777//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Machine Learning ; Software ; Metagenomics/methods ; }, abstract = {Longitudinal microbiome data sets are being generated with increasing regularity, and there is broad recognition that these studies are critical for unlocking the mechanisms through which the microbiome impacts human health and disease. However, there is a dearth of computational tools for analyzing microbiome time-series data. To address this gap, we developed an open-source software package, Microbiome Differentiable Interpretable Temporal Rule Engine (MDITRE), which implements a new highly efficient method leveraging deep-learning technologies to derive human-interpretable rules that predict host status from longitudinal microbiome data. Using semi-synthetic and a large compendium of publicly available 16S rRNA amplicon and metagenomics sequencing data sets, we demonstrate that in almost all cases, MDITRE performs on par with or better than popular uninterpretable machine learning methods, and orders-of-magnitude faster than the prior interpretable technique. MDITRE also provides a graphical user interface, which we show through case studies can be used to derive biologically meaningful interpretations linking patterns of microbiome changes over time with host phenotypes. IMPORTANCE The human microbiome, or collection of microbes living on and within us, changes over time. Linking these changes to the status of the human host is crucial to understanding how the microbiome influences a variety of human diseases. Due to the large scale and complexity of microbiome data, computational methods are essential. Existing computational methods for linking changes in the microbiome to the status of the human host are either unable to scale to large and complex microbiome data sets or cannot produce human-interpretable outputs. We present a new computational method and software package that overcomes the limitations of previous methods, allowing researchers to analyze larger and more complex data sets while producing easily interpretable outputs. Our method has the potential to enable new insights into how changes in the microbiome over time maintain health or lead to disease in humans and facilitate the development of diagnostic tests based on the microbiome.}, } @article {pmid36069454, year = {2022}, author = {Pandolfo, M and Telatin, A and Lazzari, G and Adriaenssens, EM and Vitulo, N}, title = {MetaPhage: an Automated Pipeline for Analyzing, Annotating, and Classifying Bacteriophages in Metagenomics Sequencing Data.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0074122}, pmid = {36069454}, issn = {2379-5077}, support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R506552/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *Bacteriophages/genetics ; Reproducibility of Results ; Metagenomics/methods ; *Microbiota/genetics ; *Viruses ; }, abstract = {Phages are the most abundant biological entities on the planet, and they play an important role in controlling density, diversity, and network interactions among bacterial communities through predation and gene transfer. To date, a variety of bacteriophage identification tools have been developed that differ in the phage mining strategies used, input files requested, and results produced. However, new users attempting bacteriophage analysis can struggle to select the best methods and interpret the variety of results produced. Here, we present MetaPhage, a comprehensive reads-to-report pipeline that streamlines the use of multiple phage miners and generates an exhaustive report. The report both summarizes and visualizes the key findings and enables further exploration of key results via interactive filterable tables. The pipeline is implemented in Nextflow, a widely adopted workflow manager that enables an optimized parallelization of tasks in different locations, from local server to the cloud; this ensures reproducible results from containerized packages. MetaPhage is designed to enable scalability and reproducibility; also, it can be easily expanded to include new miners and methods as they are developed in this continuously growing field. MetaPhage is freely available under a GPL-3.0 license at https://github.com/MattiaPandolfoVR/MetaPhage. IMPORTANCE Bacteriophages (viruses that infect bacteria) are the most abundant biological entities on earth and are increasingly studied as members of the resident microbiota community in many environments, from oceans to soils and the human gut. Their identification is of great importance to better understand complex bacterial dynamics and microbial ecosystem function. A variety of metagenome bacteriophage identification tools have been developed that differ in the phage mining strategies used, input files requested, and results produced. To facilitate the management and the execution of such a complex workflow, we developed MetaPhage (MP), a comprehensive reads-to-report pipeline that streamlines the use of multiple phage miners and generates an exhaustive report. The pipeline is implemented in Nextflow, a widely adopted workflow manager that enables an optimized parallelization of tasks. MetaPhage is designed to enable scalability and reproducibility and offers an installation-free, dependency-free, and conflict-free workflow execution.}, } @article {pmid36069449, year = {2022}, author = {Shi, C and Beller, L and Wang, L and Rosales Rosas, A and De Coninck, L and Héry, L and Mousson, L and Pagès, N and Raes, J and Delang, L and Vega-Rúa, A and Failloux, AB and Matthijnssens, J}, title = {Bidirectional Interactions between Arboviruses and the Bacterial and Viral Microbiota in Aedes aegypti and Culex quinquefasciatus.}, journal = {mBio}, volume = {13}, number = {5}, pages = {e0102122}, pmid = {36069449}, issn = {2150-7511}, mesh = {Humans ; Animals ; Female ; *Culex ; *Aedes ; *Arboviruses ; *Zika Virus ; *Zika Virus Infection ; Mosquito Vectors ; *West Nile virus ; *Viruses ; *Microbiota ; Bacteria ; Sucrose ; Water ; }, abstract = {Mosquitoes are important vectors for many arboviruses. It is becoming increasingly clear that various symbiotic microorganisms (including bacteria and insect-specific viruses; ISVs) in mosquitoes have the potential to modulate the ability of mosquitoes to transmit arboviruses. In this study, we compared the bacteriome and virome (both eukaryotic viruses and bacteriophages) of female adult Aedes aegypti and Culex quinquefasciatus mosquitoes fed with sucrose/water, blood, or blood spiked with Zika virus (ZIKV) or West Nile virus (WNV), respectively. Furthermore, we investigated associations between the microbiota and vector competence. We show that the influence of arboviruses on the mosquito microbiome-and vice versa-is distinct for each combination of arbovirus/mosquito species. The presence of ZIKV resulted in a temporarily increased Aedes ISV diversity. However, this effect was distinct for different ISVs: some ISVs decreased following the blood meal (Aedes aegypti totivirus), whereas other ISVs increased only when the blood contained ZIKV (Guadeloupe mosquito virus). Also, the diversity of the Aedes bacteriome depended on the diet and the presence of ZIKV, with a lower diversity observed for mosquitoes receiving blood without ZIKV. In Cx. quinquefasciatus, some ISVs increased in WNV-infected mosquitoes (Guadeloupe Culex tymo-like virus). Particularly, the presence of Wenzhou sobemo-like virus 3 (WSLV3) was associated with the absence of infectious WNV in mosquito heads, suggesting that WSLV3 might affect vector competence for WNV. Distinct profiles of bacteriophages were identified in Culex mosquitoes depending on diet, despite the lack of clear changes in the bacteriome. Overall, our data demonstrate a complex three-way interaction among arboviruses, resident microbiota, and the host, which is distinct for different arbovirus-mosquito combinations. A better understanding of these interactions may lead to the identification of microbiota able to suppress the ability of arbovirus transmission to humans, and hence improved arbovirus control measures. IMPORTANCE In this study, we first utilized the single mosquito microbiome analysis, demonstrating a complex three-way interaction among arboviruses, resident microbiota, and the host, which is distinct for different arbovirus-mosquito combinations. Some of the previously described "core virus" increased in the mosquitos receiving viral blood meal, like Guadeloupe mosquito virus and Guadeloupe Culex tymo-like virus, suggesting their potential roles in ZIKV and WNV infection. Notably, Wenzhou sobemo-like virus 3 was associated with the absence of infectious WNV in heads of Culex mosquitoes, which might affect vector competence for WNV. A better understanding of these interactions will lead to the identification of microbiota able to suppress the ability of arbovirus transmission to humans, and hence improved arbovirus control measures.}, } @article {pmid36068270, year = {2022}, author = {Ke, S and Weiss, ST and Liu, YY}, title = {Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5235}, pmid = {36068270}, issn = {2041-1723}, support = {U19 AI095219/AI/NIAID NIH HHS/United States ; U01 HL089856/HL/NHLBI NIH HHS/United States ; RF1 AG067744/AG/NIA NIH HHS/United States ; R01 AI141529/AI/NIAID NIH HHS/United States ; R01 HD093761/HD/NICHD NIH HHS/United States ; UH3 OD023268/OD/NIH HHS/United States ; }, mesh = {*COVID-19 ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome/genetics ; *Microbiota ; SARS-CoV-2/genetics ; }, abstract = {Coronavirus disease 2019 (COVID-19), primarily a respiratory disease caused by infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is often accompanied by gastrointestinal symptoms. However, little is known about the relation between the human microbiome and COVID-19, largely due to the fact that most previous studies fail to provide high taxonomic resolution to identify microbes that likely interact with SARS-CoV-2 infection. Here we used whole-metagenome shotgun sequencing data together with assembly and binning strategies to reconstruct metagenome-assembled genomes (MAGs) from 514 COVID-19 related nasopharyngeal and fecal samples in six independent cohorts. We reconstructed a total of 11,584 medium-and high-quality microbial MAGs and obtained 5403 non-redundant MAGs (nrMAGs) with strain-level resolution. We found that there is a significant reduction of strain richness for many species in the gut microbiome of COVID-19 patients. The gut microbiome signatures can accurately distinguish COVID-19 cases from healthy controls and predict the progression of COVID-19. Moreover, we identified a set of nrMAGs with a putative causal role in the clinical manifestations of COVID-19 and revealed their functional pathways that potentially interact with SARS-CoV-2 infection. Finally, we demonstrated that the main findings of our study can be largely validated in three independent cohorts. The presented results highlight the importance of incorporating the human gut microbiome in our understanding of SARS-CoV-2 infection and disease progression.}, } @article {pmid36068230, year = {2022}, author = {Li, JT and Jia, P and Wang, XJ and Ou, SN and Yang, TT and Feng, SW and Lu, JL and Fang, Z and Liu, J and Liao, B and Shu, WS and Liang, JL}, title = {Metagenomic and metatranscriptomic insights into sulfate-reducing bacteria in a revegetated acidic mine wasteland.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {71}, pmid = {36068230}, issn = {2055-5008}, mesh = {Bacteria ; *Metagenome ; *Metagenomics ; Phylogeny ; Sulfates/metabolism ; }, abstract = {The widespread occurrence of sulfate-reducing microorganisms (SRMs) in temporarily oxic/hypoxic aquatic environments indicates an intriguing possibility that SRMs can prevail in constantly oxic/hypoxic terrestrial sulfate-rich environments. However, little attention has been given to this possibility, leading to an incomplete understanding of microorganisms driving the terrestrial part of the global sulfur (S) cycle. In this study, genome-centric metagenomics and metatranscriptomics were employed to explore the diversity, metabolic potential, and gene expression profile of SRMs in a revegetated acidic mine wasteland under constantly oxic/hypoxic conditions. We recovered 16 medium- to high-quality metagenome-assembled genomes (MAGs) containing reductive dsrAB. Among them, 12 and four MAGs belonged to Acidobacteria and Deltaproteobacteria, respectively, harboring three new SRM genera. Comparative genomic analysis based on seven high-quality MAGs (completeness >90% and contamination <10%; including six acidobacterial and one deltaproteobacterial) and genomes of three additional cultured model species showed that Acidobacteria-related SRMs had more genes encoding glycoside hydrolases, oxygen-tolerant hydrogenases, and cytochrome c oxidases than Deltaproteobacteria-related SRMs. The opposite pattern was observed for genes encoding superoxide reductases and thioredoxin peroxidases. Using VirSorter, viral genome sequences were found in five of the 16 MAGs and in all three cultured model species. These prophages encoded enzymes involved in glycoside hydrolysis and antioxidation in their hosts. Moreover, metatranscriptomic analysis revealed that 15 of the 16 SRMs reported here were active in situ. An acidobacterial MAG containing a prophage dominated the SRM transcripts, expressing a large number of genes involved in its response to oxidative stress and competition for organic matter.}, } @article {pmid36068216, year = {2022}, author = {Nishijima, S and Nagata, N and Kiguchi, Y and Kojima, Y and Miyoshi-Akiyama, T and Kimura, M and Ohsugi, M and Ueki, K and Oka, S and Mizokami, M and Itoi, T and Kawai, T and Uemura, N and Hattori, M}, title = {Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5252}, pmid = {36068216}, issn = {2041-1723}, mesh = {Bacteria ; *Bacteriophages/genetics ; Humans ; Metagenome ; Metagenomics ; *Virome/genetics ; }, abstract = {Indigenous bacteriophage communities (virome) in the human gut have a huge impact on the structure and function of gut bacterial communities (bacteriome), but virome variation at a population scale is not fully investigated yet. Here, we analyse the gut dsDNA virome in the Japanese 4D cohort of 4198 deeply phenotyped individuals. By assembling metagenomic reads, we discover thousands of high-quality phage genomes including previously uncharacterised phage clades with different bacterial hosts than known major ones. The distribution of host bacteria is a strong determinant for the distribution of phages in the gut, and virome diversity is highly correlated with anti-viral defence mechanisms of the bacteriome, such as CRISPR-Cas and restriction-modification systems. We identify 97 various intrinsic/extrinsic factors that significantly affect the virome structure, including age, sex, lifestyle, and diet, most of which showed consistent associations with both phages and their predicted bacterial hosts. Among the metadata categories, disease and medication have the strongest effects on the virome structure. Overall, these results present a basis to understand the symbiotic communities of bacteria and their viruses in the human gut, which will facilitate the medical and industrial applications of indigenous viruses.}, } @article {pmid36068003, year = {2022}, author = {Ahn, HK and Kim, K and Park, J and Kim, KH}, title = {Urinary microbiome profile in men with genitourinary malignancies.}, journal = {Investigative and clinical urology}, volume = {63}, number = {5}, pages = {569-576}, pmid = {36068003}, issn = {2466-054X}, support = {NRF-2018R1C1B6007564//National Research Foundation of Korea/ ; }, mesh = {Bacteria ; Humans ; Male ; *Microbiota/genetics ; *Prostatic Neoplasms/pathology ; RNA, Ribosomal, 16S/genetics ; *Urinary Bladder Neoplasms/pathology ; *Urinary Tract ; }, abstract = {PURPOSE: Recent advances in molecular biology technology have allowed identification of microbial communities in the urinary tract, and urinary microbiome is associated with various urological diseases. In this study, we aimed to characterize the urinary microbiome of genitourinary malignancies.

MATERIALS AND METHODS: Metagenomic analysis of urinary DNA was performed in 85 patients including 30 with bladder cancer (BC), 27 with prostate cancer (PC), 12 with renal cancer (RC), and 16 with non-cancer (NC). 16S rRNA gene sequencing was conducted after amplification of the V3-V4 region.

RESULTS: PC and RC had significantly lower Shannon index than BC, and beta diversity showed significantly different microbiome composition between four groups. We identified six genera of Cutibacterium, Peptoniphilus, Sphingomonas, Staphylococcus, Micrococcus, and Moraxella, which showed significantly different abundance between the four groups. When each of the malignancies were compared to NC at the species level, Micrococcus sp. was significantly increased in BC. We also identified 12 and five species with increased populations in PC and RC, respectively. Of these, Cutibacterium acnes, Cutibacterium granulosum, Peptoniphilus lacydonensis, and Tessaracoccus were significantly increased in both PC and RC.

CONCLUSIONS: Urinary microbiome composition was different depending on the type of genitourinary malignancies, and we identified bacteria that are significantly associated with each type of malignancy. Specifically, several bacterial species were associated both PC and RC, suggesting that PC and RC share a similar pathogenesis-related urinary microbiome.}, } @article {pmid36065055, year = {2022}, author = {Ong, CT and Ross, EM and Boe-Hansen, G and Turni, C and Hayes, BJ and Fordyce, G and Tabor, AE}, title = {Adaptive sampling during sequencing reveals the origins of the bovine reproductive tract microbiome across reproductive stages and sexes.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {15075}, pmid = {36065055}, issn = {2045-2322}, mesh = {Animals ; Australia ; Cattle ; Female ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Pregnancy ; }, abstract = {Cattle enterprises are one of the major livestock production systems globally and are forecasted to have stable growth in the next decade. To facilitate sustainable live weight production, optimal reproductive performance is essential. Microbial colonisation in the reproductive tract has been demonstrated as one of the factors contributing to bovine reproductive performance. Studies also implied that reproductive metagenomes are different at each stage of the estrous cycle. This study applied Oxford Nanopore Technologies' adaptive long-read sequencing to profile the bovine reproductive microbiome collected from tropical cattle in northern Queensland, Australia. The microbiome samples were collected from cattle of different sexes, reproductive status and locations to provide a comprehensive view of the bovine reproductive microbiome in northern Australian cattle. Ascomycota, Firmicutes and Proteobacteria were abundant phyla identified in the bovine reproductive metagenomes of Australian cattle regardless of sexes, reproductive status and location. The species level taxonomical investigation suggested that gastrointestinal metagenome and the surrounding environment were potentially the origins of the bovine reproductive metagenome. Functional profiles further affirmed this implication, revealing that the reproductive metagenomes of the prepubertal and postpartum animals were dominated by microorganisms that catabolise dietary polysaccharides as an energy substrate while that of the pregnant animals had the function of harvesting energy from aromatic compounds. Bovine reproductive metagenome investigations can be employed to trace the origins of abnormal metagenomes, which is beneficial for disease prevention and control. Additionally, our results demonstrated different reproductive metagenome diversities between cattle from two different locations. The variation in diversity within one location can serve as the indicator of abnormal reproductive metagenome, but between locations inferences cannot be made. We suggest establishing localised metagenomic indices that can be used to infer abnormal reproductive metagenomes which contribute to abortion or sub-fertility.}, } @article {pmid36063723, year = {2022}, author = {Li, Y and Yu, Y and Wu, X and Liu, B and Ma, H and Zhao, X and Cao, S and Ding, S and Li, T and Wang, X and Wang, P and Xu, X and Zhao, J and Liu, Y and Lan, C and Wang, J and Chen, L and Zeng, Q}, title = {Specially designed yogurt supplemented with combination of pro- and prebiotics relieved constipation in mice and humans.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {103-104}, number = {}, pages = {111802}, doi = {10.1016/j.nut.2022.111802}, pmid = {36063723}, issn = {1873-1244}, mesh = {Humans ; Mice ; Animals ; *Prebiotics ; Yogurt ; Quality of Life ; Constipation/therapy ; *Gastrointestinal Microbiome ; }, abstract = {OBJECTIVE: Functional constipation is a gastrointestinal disorder that affects millions of people and is correlated with gut microbiome dysbiosis. The currently available treatments are ineffective; therefore, novel treatment schemes targeting the gut microbiome are desired. The aim of this study was to assess the effects of yogurt supplemented with seven probiotic strains and six types of dietary fibers on functional constipation.

METHODS: In the mouse study, mice with induced constipation were administered the yogurt once a day for 1 wk, with fecal parameters and intestinal transit rate measured. In the clinical study, participants with constipation (N = 86) were given the yogurt once daily (200 g) for 4 wk. Fecal and blood samples along with Patient Assessment of Constipation-symptoms and Patient Assessment of Constipation-Quality of Life Scale questionnaires were collected to evaluate the safety and efficacy of the yogurt. Shotgun metagenomic sequencing was performed to analyze fecal samples of both mice and humans.

RESULTS: We found that constipated mice had different gut microbiomes compared with those in healthy controls; yogurt treatment significantly relieved constipation-related symptoms and resulted in shifts in the microbiome. Yogurt also relieved symptoms of antibiotic-induced constipation in mice and restored the gut microbiome to a certain extent. In the clinical trial with 86 patients, yogurt administration significantly improved constipation symptoms and showed no serious adverse effects (was generally considered safe). However, subsequent metagenomic profiling of the gut microbiome did not reveal significant changes in the microbial composition, in contrast to the results in mice. We hypothesize that the differences in dosage between mice and humans may attribute to such discrepancies, and microbiome changes may not be necessary for improvements of constipation symptoms in humans.

CONCLUSION: Results from this study showed that yogurt can potentially be used for the treatment of constipation.}, } @article {pmid36063685, year = {2022}, author = {Bhosle, A and Wang, Y and Franzosa, EA and Huttenhower, C}, title = {Progress and opportunities in microbial community metabolomics.}, journal = {Current opinion in microbiology}, volume = {70}, number = {}, pages = {102195}, doi = {10.1016/j.mib.2022.102195}, pmid = {36063685}, issn = {1879-0364}, support = {R24 DK110499/DK/NIDDK NIH HHS/United States ; U19 AI110820/AI/NIAID NIH HHS/United States ; }, mesh = {*Metabolomics ; *Microbiota ; Metabolome/physiology ; Metagenomics ; }, abstract = {The metabolome lies at the interface of host-microbiome crosstalk. Previous work has established links between chemically diverse microbial metabolites and a myriad of host physiological processes and diseases. Coupled with scalable and cost-effective technologies, metabolomics is thus gaining popularity as a tool for characterization of microbial communities, particularly when combined with metagenomics as a window into microbiome function. A systematic interrogation of microbial community metabolomes can uncover key microbial compounds, metabolic capabilities of the microbiome, and also provide critical mechanistic insights into microbiome-linked host phenotypes. In this review, we discuss methods and accompanying resources that have been developed for these purposes. The accomplishments of these methods demonstrate that metabolomes can be used to functionally characterize microbial communities, and that microbial properties can be used to identify and investigate chemical compounds.}, } @article {pmid36059453, year = {2022}, author = {Li, L and Yang, K and Li, C and Zhang, H and Yu, H and Chen, K and Yang, X and Liu, L}, title = {Metagenomic shotgun sequencing and metabolomic profiling identify specific human gut microbiota associated with diabetic retinopathy in patients with type 2 diabetes.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {943325}, pmid = {36059453}, issn = {1664-3224}, mesh = {Case-Control Studies ; *Diabetes Mellitus, Type 2/metabolism ; *Diabetic Retinopathy/genetics/metabolism ; *Gastrointestinal Microbiome/genetics ; Humans ; Lysine ; }, abstract = {BACKGROUND: Diabetic retinopathy (DR) is a common microvascular complication of diabetes mellitus (DM) and is one of the leading causes of blindness among DM patients. However, the molecular mechanism involving DR remains unclear.

METHODS: A case-control study with age-, sex-, and duration-matched diabetic patients and controls was conducted, which included 15 type 2 DM (T2DM) patients with DR and 15 T2DM patients without DR. Shotgun sequencing and non-targeted metabolomic profiling analyses of fecal samples were performed, and comprehensive bioinformatics analyses were conducted.

RESULTS: Using metagenomic analyses, we identified 293,460 unique genes in the non-DR group, while that in the DR group was 283,235, and the number of overlapping genes was 1,237,914. Regarding phylum levels, Actinobacteria decreased but Bacteroidetes increased in the DR group when compared with those in the control group. Regarding genus levels, Bifidobacterium and Lactobacillus decreased. Cellular processes, environmental information processes, and metabolism-related pathways were found at higher levels in the gut microbiome of DR patients. Using metabolomic analyses, we found 116 differentially expressed metabolites with a positive ion model and 168 differentially expressed metabolites with a negative ion model between the two groups. Kyoto Encyclopedia of Genes and Genomes annotation revealed six pathways with different levels between DR and diabetic controls, namely, cellular processes, environmental information processing, genetic information processing, human diseases, organismal systems and metabolism. Moreover, lysine biosynthesis and lysine degradation were enriched using a positive model, but histidine metabolism and β-alanine metabolism were enriched using a negative model.

CONCLUSIONS: Together, the metagenomic profiles of DR patients indicated different gut microbiota compositions and characteristic fecal metabolic phenotypes in DR patients. Our findings of microbial pathways therefore provided potential etiological and therapeutic targets for DR patients.}, } @article {pmid36057234, year = {2022}, author = {Li, R and Zhu, L and Wang, Y and Zhu, YG}, title = {Metagenomic insights into environmental risk of field microplastics in an urban river.}, journal = {Water research}, volume = {223}, number = {}, pages = {119018}, doi = {10.1016/j.watres.2022.119018}, pmid = {36057234}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; Genes, Bacterial ; *Microbiota ; *Microplastics ; Plastics ; Virulence Factors ; Water ; }, abstract = {Microplastics (MPs) are emerging as anthropogenic vectors for the colonization and transportation of microbial communities in aquatic ecosystems. However, the composition of the microbiome and its environmental risk on field MPs at watershed scale has rarely been explored. Here, geographical distributions of microbiome, antibiotic resistance genes (ARGs) and virulence factors (VFs) on field MPs at watershed scale were characterized and their potential environmental risks were evaluated based on the data from metagenomic analyzes. The succession of microbial communities on MPs was observed along the watershed, and some ARGs and VFs were significantly enriched on MPs in urban region in comparison with rural region. Potential environmental risk of MPs conducted by Projection Pursuit Regression model in midstream (peri-urban region) and downstream (urban region) were significantly higher than that in upstream (rural region), and exhibit close relationships with MPs concentration and water velocity. Furthermore, our source tracking results demonstrated that the microbiome, ARGs and VFs in urban region MPs were largely derived from rural region MPs. Our results caution us that special attention should be paid to the risks posed by MPs in urban water bodies, and highlight the threat of MPs from rural upstream areas.}, } @article {pmid36056907, year = {2022}, author = {von Takach, B and Ranjard, L and Burridge, CP and Cameron, SF and Cremona, T and Eldridge, MDB and Fisher, DO and Frankenberg, S and Hill, BM and Hohnen, R and Jolly, CJ and Kelly, E and MacDonald, AJ and Moussalli, A and Ottewell, K and Phillips, BL and Radford, IJ and Spencer, PBS and Trewella, GJ and Umbrello, LS and Banks, SC}, title = {Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads.}, journal = {Molecular ecology}, volume = {31}, number = {21}, pages = {5468-5486}, pmid = {36056907}, issn = {1365-294X}, mesh = {Animals ; *Metagenomics ; Bufo marinus/genetics ; Predatory Behavior ; *Marsupialia/genetics ; Australia/epidemiology ; }, abstract = {Mammal declines across northern Australia are one of the major biodiversity loss events occurring globally. There has been no regional assessment of the implications of these species declines for genomic diversity. To address this, we conducted a species-wide assessment of genomic diversity in the northern quoll (Dasyurus hallucatus), an Endangered marsupial carnivore. We used next generation sequencing methods to genotype 10,191 single nucleotide polymorphisms (SNPs) in 352 individuals from across a 3220-km length of the continent, investigating patterns of population genomic structure and diversity, and identifying loci showing signals of putative selection. We found strong heterogeneity in the distribution of genomic diversity across the continent, characterized by (i) biogeographical barriers driving hierarchical population structure through long-term isolation, and (ii) severe reductions in diversity resulting from population declines, exacerbated by the spread of introduced toxic cane toads (Rhinella marina). These results warn of a large ongoing loss of genomic diversity and associated adaptive capacity as mammals decline across northern Australia. Encouragingly, populations of the northern quoll established on toad-free islands by translocations appear to have maintained most of the initial genomic diversity after 16 years. By mapping patterns of genomic diversity within and among populations, and investigating these patterns in the context of population declines, we can provide conservation managers with data critical to informed decision-making. This includes the identification of populations that are candidates for genetic management, the importance of remnant island and insurance/translocated populations for the conservation of genetic diversity, and the characterization of putative evolutionarily significant units.}, } @article {pmid36056757, year = {2023}, author = {Kharofa, J and Apewokin, S and Alenghat, T and Ollberding, NJ}, title = {Metagenomic analysis of the fecal microbiome in colorectal cancer patients compared to healthy controls as a function of age.}, journal = {Cancer medicine}, volume = {12}, number = {3}, pages = {2945-2957}, pmid = {36056757}, issn = {2045-7634}, mesh = {Humans ; *Colorectal Neoplasms/genetics ; Metagenome ; Metagenomics ; Fusobacterium nucleatum ; Carcinogenesis/genetics ; *Microbiota ; }, abstract = {BACKGROUND AND AIMS: Colorectal cancer (CRC) incidence is increasing in young patients without a clear etiology. Emerging data have implicated the fecal microbiome in CRC carcinogenesis. However, its impact on young onset CRC is poorly defined.

METHODS: We performed a meta-analysis of fecal metagenomics sequencing data from n = 692 patients with CRC and n = 602 healthy controls from eleven studies to evaluate features of the fecal metagenome associated with CRC. We hypothesized that known carcinogenic virulence factors (colibactin, fadA) and species abundance may be differentially enriched in young CRC patients relative to older CRC patients and controls.

RESULTS: Summary odds ratios (OR) for CRC were increased with the presence of colibactin (OR 1.92 95% CI 1.08-3.38), fadA (OR 4.57 95% CI 1.63-12.85), and F. nucleatum (OR 6.93 95% CI 3.01-15.96) in meta-analysis models adjusted for age, gender, and body mass index. The OR for CRC for the presence of E.coli was 2.02 (0.92-4.45). An increase in the prevalence of Fusobacterium nucleatum (OR = 1.40 [1.18; 1.65]) and Escherichia coli (OR = 1.14 [1.02; 1.28]) per 10-year increase in age was observed in models including samples from both CRC and healthy controls. Species relative abundance was differentially enriched in young CRC patients for five species-Intestinimonas butyriciproducens, Holdemania filiformis, Firimicutues bacterium CAG 83, Bilophilia wadsworthia, and Alistipes putredinis.

CONCLUSION: In this study, we observed strong associations with CRC status for colibactin, fadA, and Fusobacterium nucleatum with CRC relative to controls. In addition, we identified several microbial species differentially enriched in young colorectal cancer patients. Studies targeting the young CRC patients are warranted to elucidate underlying preclinical mechanisms.}, } @article {pmid36056619, year = {2022}, author = {Gill, SP and Learman, DR and Annis, ML and Woolnough, DA}, title = {Freshwater mussels and host fish gut microbe community composition shifts after agricultural contaminant exposure.}, journal = {Journal of applied microbiology}, volume = {133}, number = {6}, pages = {3645-3658}, pmid = {36056619}, issn = {1365-2672}, support = {F16AP00639//U.S. Fish and Wildlife Service/ ; }, mesh = {Animals ; Female ; *Gastrointestinal Microbiome ; *Bivalvia ; Fresh Water ; Seafood ; *Bass ; *Water Pollutants, Chemical ; }, abstract = {AIMS: We examined the effects of a mixture of contaminants found in agricultural watersheds on the gut microbiota and physiology of both the freshwater mussel Lampsilis cardium, and L. cardium host fish Micropterus salmoides.

METHODS AND RESULTS: Lampsilis cardium and M. salmoides were exposed to three concentrations of agricultural contaminants for 60 days (observing behaviour daily) before being sampled for gut microbiota analyses. DNA was extracted from the gut samples, amplified via PCR, and sequenced using the Illumina Mi-Seq platform. Only L. cardium guts had differing microbiota across treatments, with an increase in potentially pathogenic Aeromonas. We also provide novel evidence of a core microbiota within L. cardium and M. salmoides. In terms of physiology, female L. cardium exhibited a decrease in movement and marsupial gill display in contaminant exposures.

CONCLUSIONS: Exposure to contaminants from agricultural watersheds may affect population recruitment within freshwater mussel communities over time. Specifically, increased pathogenic micro-organisms and altered behaviour can reduce the likelihood of glochidia dispersal.

This study supports emerging research that contaminants found in agricultural watersheds may be a factor in freshwater mussel population declines. It also provides novel evidence that unionids have a core gut microbiota.}, } @article {pmid36055570, year = {2022}, author = {Ullah, N and Kakakhel, MA and Khan, I and Gul Hilal, M and Lajia, Z and Bai, Y and Sajjad, W and Yuxi, L and Ullah, H and Almohaimeed, HM and Al-Sarraj, F and Assiri, R and Aggad, WS and Alharbi, NA and Alshehri, AM and Liu, G and Sun, H and Zhang, C}, title = {Structural and compositional segregation of the gut microbiota in HCV and liver cirrhotic patients: A clinical pilot study.}, journal = {Microbial pathogenesis}, volume = {171}, number = {}, pages = {105739}, doi = {10.1016/j.micpath.2022.105739}, pmid = {36055570}, issn = {1096-1208}, mesh = {Bacteria/genetics ; Dysbiosis/microbiology ; Enterobacteriaceae/genetics ; *Gastrointestinal Microbiome ; Hepacivirus/genetics ; *Hepatitis C/complications ; Humans ; Liver Cirrhosis ; *Liver Diseases ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Gut microbial dysbiosis during the development of Hepatitis C virus and liver-related diseases is not well studied. Nowadays, HCV and liver cirrhosis are the major concerns that cause gut bacterial alteration, which leads to dysbiosis. For this purpose, the present study was aimed at correlating the gut bacterial community of the control group in comparison to HCV and liver cirrhotic patients. A total of 23 stool samples were collected, including control (9), liver cirrhotic (8), and HCV (6). The collected samples were subjected to 16 S rRNA Illumina gene sequencing. In comparison with control, a significant gut bacterial alteration was observed in the progression of HCV and liver cirrhosis. Overall, Firmicutes were significantly abundant in the whole study. No significant difference was observed in the alpha diversity of the control and patient studies. Additionally, the beta diversity based on non-metric multidimensional scaling (NMDS) has a significant difference (p = 0.005) (ANOSIM R[2] = 0.14) in all groups. The discriminative results based on the LEfSe tool revealed that the HCV-infected patients had higher Enterobacteriaceae and Enterobacterial, as well as Lactobacillus and Bacilli in comparison than the liver-cirrhotic patients. These taxa were significantly different from the control group (p < 0.05). Regarding prospects, a detailed analysis of the function through metagenomics and transcriptomics is needed.}, } @article {pmid36055158, year = {2022}, author = {Beura, S and Kundu, P and Das, AK and Ghosh, A}, title = {Metagenome-scale community metabolic modelling for understanding the role of gut microbiota in human health.}, journal = {Computers in biology and medicine}, volume = {149}, number = {}, pages = {105997}, doi = {10.1016/j.compbiomed.2022.105997}, pmid = {36055158}, issn = {1879-0534}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Inflammatory Bowel Diseases/metabolism ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Metabolic activities of the microbial population are important to maintain the balance of almost all the ecosystems on earth. In the human gut environment, these microbial communities play essential roles in digestion and help to maintain biochemical homeostasis by synthesizing several vital metabolic compounds. Imbalance in the microbial abundance and community structure in the human gut microbiota leads to different diseases and metabolic disorders. Studying the metabolic interplay between the microbial consortia within the host environment is the key to exploring the cause behind the development of various diseases condition. However, mapping the entire biochemical characteristic of human gut microbiota may not be feasible only through experimental approaches. Therefore, the advanced systems biology approach, i.e., metagenome-scale community metabolic modelling, is introduced for understanding the metabolic role and interaction pattern of the entire microbiome. This in silico method directly uses the metagenomic information to model the microbial communities, which mimic the metabolic behavior of the human gut microbiome. This review discusses the recent development of metagenome-scale community metabolic model reconstruction tools and their application in studying the inter-link between the human gut microbiome and health. The application of the community metabolic models to study the metabolic profile of the human gut microbiome has also been investigated. Alteration of the metabolic fluxes associated with different biochemical activities in type 1 diabetics, type 2 diabetics, inflammatory bowel diseases (IBD), gouty arthritis, colorectal cancer (CRC), etc., has also been assessed with the metagenome-scale models. Thus, modelling the microbial communities combined with advanced experimental design may lead to novel therapeutic approaches like personalized microbiome modelling for treating human disease.}, } @article {pmid36055123, year = {2022}, author = {Nandi, SK and Basu, S and Bhattacharjya, A and Dey Ghosh, R and Bose, CK and Mukhopadhyay, S and Bhattacharya, R}, title = {Interplay of gut microbiome, fatty acids, and the endocannabinoid system in regulating development, progression, immunomodulation, and chemoresistance of cancer.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {103-104}, number = {}, pages = {111787}, doi = {10.1016/j.nut.2022.111787}, pmid = {36055123}, issn = {1873-1244}, mesh = {Humans ; *Gastrointestinal Microbiome ; Endocannabinoids/pharmacology ; Fatty Acids/pharmacology ; Drug Resistance, Neoplasm ; Fatty Acids, Volatile/metabolism ; Immunomodulation ; Immunity ; *Fatty Acids, Omega-3/pharmacology ; *Neoplasms/drug therapy ; Tumor Microenvironment ; }, abstract = {The roles of gut microorganisms in cancer are diverse. Studies on metagenomics and bioinformatics have documented diverse microbial etiology in different tumors. Evidence supports that a commensal microbiome could provide a promising strategy to treat and prevent cancer through interference in several biologic processes, such as host cell survival and death, host immune function, inflammation, oncogenic signaling, and several hormone receptor signaling and detoxification pathways. The cumulative evidence recommends that metabolites of commensal gut microorganisms (e.g., short-chain fatty acids, omega-3 and -6 fatty acids) play an important role in cancer prevention, with a robust antiproliferative effect of omega-3 fatty acids. Intriguingly, the endocannabinoid system (omega-3 and -6 fatty acid-derived neurotransmitter of the body) shows diverse effects on cancer prevention and oncogenesis depending on the context of the tumor microenvironment. Thus, an interplay of gut microorganisms with their fatty acid metabolites and the endocannabinoid system play an important role in the development, progression, immunomodulation, and chemoresistance of cancer. In this review, we highlight aspects of the current knowledge of and interactions between the microbiome with fatty acids and the host endocannabinoid system. We also document their effect on host immunomodulation and chemoresistance, and discuss how these insights might translate into future development of microbiome-targeted therapeutic interventions.}, } @article {pmid36054683, year = {2023}, author = {Fan, L and Chen, J and Pan, L and Xin, X and Geng, B and Yang, L and Wang, Q and Ma, W and Lou, Y and Bian, J and Cui, X and Li, J and Wang, L and Chen, Z and Wang, W and Cui, C and Li, S and Gao, Q and Song, Q and Deng, Y and Fan, J and Yu, J and Zhang, H and Li, Y and Cai, J}, title = {Alterations of Gut Microbiome, Metabolome, and Lipidome in Takayasu Arteritis.}, journal = {Arthritis & rheumatology (Hoboken, N.J.)}, volume = {75}, number = {2}, pages = {266-278}, doi = {10.1002/art.42331}, pmid = {36054683}, issn = {2326-5205}, mesh = {Humans ; *Takayasu Arteritis/drug therapy ; *Gastrointestinal Microbiome/genetics ; Lipidomics ; Inflammation ; Metabolome ; *Behcet Syndrome ; *Cardiovascular Diseases ; }, abstract = {OBJECTIVE: Mounting evidence has linked microbiome and metabolome to systemic autoimmunity and cardiovascular diseases (CVDs). Takayasu arteritis (TAK) is a rare disease that shares features of immune-related inflammatory diseases and CVDs, about which there is relatively limited information. This study was undertaken to characterize gut microbial dysbiosis and its crosstalk with phenotypes in TAK.

METHODS: To address the discriminatory signatures, we performed shotgun sequencing of fecal metagenome across a discovery cohort (n = 97) and an independent validation cohort (n = 75) including TAK patients, healthy controls, and controls with Behçet's disease (BD). Interrogation of untargeted metabolomics and lipidomics profiling of plasma and fecal samples were also used to refine features mediating associations between microorganisms and TAK phenotypes.

RESULTS: A combined model of bacterial species, including unclassified Escherichia, Veillonella parvula, Streptococcus parasanguinis, Dorea formicigenerans, Bifidobacterium adolescentis, Lachnospiraceae bacterium 7 1 58FAA, Escherichia coli, Streptococcus salivarius, Klebsiella pneumoniae, Bifidobacterium longum, and Lachnospiraceae Bacterium 5 1 63FAA, distinguished TAK patients from controls with areas under the curve (AUCs) of 87.8%, 85.9%, 81.1%, and 71.1% in training, test, and validation sets including healthy or BD controls, respectively. Diagnostic species were directly or indirectly (via metabolites or lipids) correlated with TAK phenotypes of vascular involvement, inflammation, discharge medication, and prognosis. External validation against publicly metagenomic studies (n = 184) on hypertension, atrial fibrillation, and healthy controls, confirmed the diagnostic accuracy of the model for TAK.

CONCLUSION: This study first identifies the discriminatory gut microbes in TAK. Dysbiotic microbes are also linked to TAK phenotypes directly or indirectly via metabolic and lipid modules. Further explorations of the microbiome-metagenome interface in TAK subtype prediction and pathogenesis are suggested.}, } @article {pmid36053854, year = {2023}, author = {Xia, Y and Zhou, W and Du, Y and Wang, Y and Zhu, M and Zhao, Y and Wu, Z and Zhang, W}, title = {Difference of microbial community and gene composition with saccharification function between Chinese nongxiangxing daqu and jiangxiangxing daqu.}, journal = {Journal of the science of food and agriculture}, volume = {103}, number = {2}, pages = {637-647}, doi = {10.1002/jsfa.12175}, pmid = {36053854}, issn = {1097-0010}, support = {No.2018YFE0127400//the National Key R&D Program of China/ ; }, mesh = {Fermentation ; Bacteria/genetics ; *Microbiota ; *Bacillus/genetics ; China ; Alcoholic Beverages/analysis ; }, abstract = {BACKGROUND: The saccharification function of daqu is usually characterized by two indicators: saccharification power and liquefaction power. Daqu provides diverse microbial saccharifying enzymes for hydrolyzing carbohydrate in Baijiu fermenting grain. Obviously, the composition of microbial communities and enzymatic genes in different types of daqu cultured at varied temperatures is different. However, these differences in saccharification function are not fully understood.

RESULTS: The findings suggested that the saccharification power and liquefaction power of jiangxiangxing daqu were lower than those of nongxiangxing daqu throughout the production process. We employed metagenomics to find evidence that a mode of multiple saccharifying enzymes involving amylase, cellulase and hemicellulase originating from various microbes exists in daqu. Moreover, a totality of 541 related differential genes were obtained, some of which, annotated to genera of Aspergillus, Lactobacillus and Weissella, were significantly enriched (P < 0.05) in nongxiangxing daqu, while others, annotated to thermophilic genera of Virgibacillus, Bacillus, Kroppenstedtia and Saccharopolyspora, showed a higher relative abundance in jiangxiangxing daqu (P < 0.05).

CONCLUSION: Various microbial communities of daqu showed diverse saccharification capacity during cultivation of different parameters. These findings are helpful in comprehending the saccharification functional genes of daqu. © 2022 Society of Chemical Industry.}, } @article {pmid36050658, year = {2022}, author = {Karpinets, TV and Wu, X and Solley, T and El Alam, MB and Sims, TT and Yoshida-Court, K and Lynn, E and Ahmed-Kaddar, M and Biegert, G and Yue, J and Song, X and Sun, H and Petrosino, JF and Mezzari, MP and Okhuysen, P and Eifel, PJ and Jhingran, A and Lin, LL and Schmeler, KM and Ramondetta, L and Ajami, N and Jenq, RR and Futreal, A and Zhang, J and Klopp, AH and Colbert, LE}, title = {Metagenomes of rectal swabs in larger, advanced stage cervical cancers have enhanced mucus degrading functionalities and distinct taxonomic structure.}, journal = {BMC cancer}, volume = {22}, number = {1}, pages = {945}, pmid = {36050658}, issn = {1471-2407}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; T32 CA101642/CA/NCI NIH HHS/United States ; P30CA016672/NH/NIH HHS/United States ; CA101642-14/NH/NIH HHS/United States ; }, mesh = {Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolic Networks and Pathways ; Metagenome ; Mucus ; *Uterine Cervical Neoplasms ; }, abstract = {BACKGROUND: Gut microbiome community composition differs between cervical cancer (CC) patients and healthy controls, and increased gut diversity is associated with improved outcomes after treatment. We proposed that functions of specific microbial species adjoining the mucus layer may directly impact the biology of CC.

METHOD: Metagenomes of rectal swabs in 41 CC patients were examined by whole-genome shotgun sequencing to link taxonomic structures, molecular functions, and metabolic pathway to patient's clinical characteristics.

RESULTS: Significant association of molecular functions encoded by the metagenomes was found with initial tumor size and stage. Profiling of the molecular function abundances and their distributions identified 2 microbial communities co-existing in each metagenome but having distinct metabolism and taxonomic structures. Community A (Clostridia and Proteobacteria predominant) was characterized by high activity of pathways involved in stress response, mucus glycan degradation and utilization of degradation byproducts. This community was prevalent in patients with larger, advanced stage tumors. Conversely, community B (Bacteroidia predominant) was characterized by fast growth, active oxidative phosphorylation, and production of vitamins. This community was prevalent in patients with smaller, early-stage tumors.

CONCLUSIONS: In this study, enrichment of mucus degrading microbial communities in rectal metagenomes of CC patients was associated with larger, more advanced stage tumors.}, } @article {pmid36050292, year = {2022}, author = {Zeng, S and Patangia, D and Almeida, A and Zhou, Z and Mu, D and Paul Ross, R and Stanton, C and Wang, S}, title = {A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5139}, pmid = {36050292}, issn = {2041-1723}, support = {MR/W016184/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Child ; Child, Preschool ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Age-specific reference genomes of the human gut microbiome can provide higher resolution for metagenomic analyses including taxonomic classification, strain-level genomic investigation and functional characterization. We present the Early-Life Gut Genomes (ELGG) catalog with 32,277 genomes representing 2172 species from 6122 fecal metagenomes collected from children under 3 years old spanning delivery mode, gestational age, feeding pattern, and geography. The ELGG substantially expanded the phylogenetic diversity by 38% over the isolate microbial genomes, and the genomic landscape of the early-life microbiome by increasing recruitment of metagenomic reads to 82.8%. More than 60% of the ELGG species lack an isolate representative. The conspecific genomes of the most abundant species from children differed in gene diversity and functions compared to adults. The ELGG genomes encode over 80 million protein sequences, forming the Early-Life Gut Proteins (ELGP) catalog with over four million protein clusters, 29.5% of which lacked functional annotations. The ELGG and ELGP references provided new insights into the early-life human gut microbiome and will facilitate studies to understand the development and mechanisms of disturbances of the human gut microbiome in early life.}, } @article {pmid36049506, year = {2022}, author = {Das, N and Bhuyan, B and Pandey, P}, title = {Correlation of soil microbiome with crude oil contamination drives detection of hydrocarbon degrading genes which are independent to quantity and type of contaminants.}, journal = {Environmental research}, volume = {215}, number = {Pt 1}, pages = {114185}, doi = {10.1016/j.envres.2022.114185}, pmid = {36049506}, issn = {1096-0953}, mesh = {Anthracenes/analysis/metabolism ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Hydrocarbons ; *Microbiota ; Naphthalenes/analysis/metabolism ; *Petroleum/analysis ; *Phenanthrenes/analysis ; Pyrenes/metabolism ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {The impacts of crude oil contamination on soil microbial populations were explored in seven different polluted areas near oil and gas drilling sites and refineries of Assam, India. Using high-throughput sequencing techniques, the functional genes and metabolic pathways involved in the bioconversion of crude oil contaminants by the indigenous microbial community were explored. Total petroleum hydrocarbon (TPH) concentrations in soil samples ranged from 1109.47 to 75,725.33 mg/kg, while total polyaromatic hydrocarbon (PAH) concentrations ranged from 0.780 to 560.05 mg/kg. Pyrene, benzo[a]anthracene, naphthalene, phenanthrene, and anthracene had greater quantities than the maximum permitted limits, suggesting a greater ecological risk, in comparison to other polyaromatic hydrocarbons. According to the metagenomic data analysis, the bacterial phyla Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroides were the most prevalent among all polluted areas. The most prominent hydrocarbon degraders in the contaminated sites included Burkholderia, Mycobacterium, Polaromonas, and Pseudomonas. However, the kinds of pollutants and their concentrations did not correlate with the abundances of respective degrading genes for all polluted locations, as some of the sites with little to low PAH contamination had significant abundances of corresponding functional genes for degradation. Thus, the findings of this study imply that the microbiome of hydrocarbon-contaminated areas, which are biologically involved in the degradation process, has various genes, operons and catabolic pathways that are independent of the presence of a specific kind of contaminant.}, } @article {pmid36049483, year = {2022}, author = {Gao, J and Zhao, X and Hu, S and Huang, Z and Hu, M and Jin, S and Lu, B and Sun, K and Wang, Z and Fu, J and Weersma, RK and He, X and Zhou, H}, title = {Gut microbial DL-endopeptidase alleviates Crohn's disease via the NOD2 pathway.}, journal = {Cell host & microbe}, volume = {30}, number = {10}, pages = {1435-1449.e9}, doi = {10.1016/j.chom.2022.08.002}, pmid = {36049483}, issn = {1934-6069}, mesh = {Acetylmuramyl-Alanyl-Isoglutamine/chemistry/metabolism ; Animals ; *Colitis ; *Crohn Disease/metabolism ; Endopeptidases ; *Gastrointestinal Microbiome ; Ligands ; Mice ; Nod2 Signaling Adaptor Protein/genetics ; Peptidoglycan/metabolism ; }, abstract = {The pattern-recognition receptor NOD2 senses bacterial muropeptides to regulate host immunity and maintain homeostasis. Loss-of-function mutations in NOD2 are associated with Crohn's disease (CD), but how the variations in microbial factors influence NOD2 signaling and host pathology is elusive. We demonstrate that the Firmicutes peptidoglycan remodeling enzyme, DL-endopeptidase, increased the NOD2 ligand level in the gut and impacted colitis outcomes. Metagenomic analyses of global cohorts (n = 857) revealed that DL-endopeptidase gene abundance decreased globally in CD patients and negatively correlated with colitis. Fecal microbiota from CD patients with low DL-endopeptidase activity predisposed mice to colitis. Administering DL-endopeptidase, but not an active site mutant, alleviated colitis via the NOD2 pathway. Therapeutically restoring NOD2 ligands with a DL-endopeptidase-producing Lactobacillus salivarius strain or mifamurtide, a clinical analog of muramyl dipeptide, exerted potent anti-colitis effects. Our study suggests that the depletion of DL-endopeptidase contributes to CD pathogenesis through NOD2 signaling, providing a therapeutically modifiable target.}, } @article {pmid36048399, year = {2022}, author = {Zhu, M and Wang, C and Yang, S and Du, X and Zhu, Y and Zhang, T and Lv, Y and Zhao, W}, title = {Alterations in Gut Microbiota Profiles of Mice Infected with Echinococcus granulosus sensu lato Microbiota Profiles of Mice Infected with E. granulosus s.l.}, journal = {Acta parasitologica}, volume = {67}, number = {4}, pages = {1594-1602}, pmid = {36048399}, issn = {1896-1851}, support = {No.81860366//the National Natural Science Foundation of China/ ; No.32060805//the National Natural Science Foundation of China/ ; No. 2021BEG03088//Key Technology Research and Development Program of Shandong/ ; 2019AAC03264//he Natural Science Foundation of Ningxia/ ; 2020AAC02039//the Natural Science Foundation of Ningxia Hui Autonomous Region/ ; }, mesh = {Animals ; Humans ; Mice ; *Echinococcus granulosus/genetics ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Echinococcosis/parasitology ; *Microbiota ; Genotype ; }, abstract = {OBJECTIVE: Cystic echinococcosis is a kind of parasitic disease that seriously endangers human and animal health. At present, its prevention and treatment still do not achieve the desired results. The aims of this study were to explore the effect of CE on intestinal microflora in mice.

METHODS: In this study, 16S rRNA metagenome sequencing and bioinformatics were used to analyze the intestinal flora of mice infected with E. granulosus s.l. Changes in intestinal microbial community abundance were investigated and the differences in microbial populations of mice infected with E. granulosus s.l. were screened.

RESULTS: Our results show that at the phylum level, nine abundant taxa were identified, the relative abundance of Firmicutes and Proteobacteria were enriched in infected mice, whereas Bacteroidetes and Patescibacteria were enriched in control mice (P < 0.01). At the class level, 13 abundant taxa were identified, the relative abundance of Bacilli was enriched in control mice, but decreased in infected mice (P < 0.01). At the order level, 15 abundant taxa were identified, the relative abundance of Lactobacillales was enriched in control mice, but decreased in infected mice (P < 0.01). At the family level, 28 abundant taxa were identified, enriched bacteria in the infected mice was Streptococcaceae, while the enriched bacteria in the control group was Lactobacillaceae (P < 0.01). At the genus level, 79 abundant taxa were identified, enriched bacteria in the infected mice was Streptococcus, while the enriched bacteria in the control group was uncultured_bacterium_f_Eggerthellaceae (P < 0.01). At the species level, 80 abundant taxa were identified, enriched bacteria in the infected mice was uncultured_bacterium_g_Streptococcus, while the enriched bacteria in the control group was uncultured_bacterium_f_Eggerthellaceae (P < 0.01). 39 KEGG pathways were identified that were differentially enriched between the infected and control mice.

CONCLUSION: This study comprehensively demonstrates the differential intestinal microbiota of infected mice and analyzes the metabolic pathways related to the specific microbiota. This could provide new targets and research direction for the treatment and prevention of diseases caused by E. granulosus s.l.}, } @article {pmid36045603, year = {2022}, author = {Lindstedt, K and Buczek, D and Pedersen, T and Hjerde, E and Raffelsberger, N and Suzuki, Y and Brisse, S and Holt, K and Samuelsen, Ø and Sundsfjord, A}, title = {Detection of Klebsiella pneumoniae human gut carriage: a comparison of culture, qPCR, and whole metagenomic sequencing methods.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2118500}, pmid = {36045603}, issn = {1949-0984}, mesh = {Adult ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; *Klebsiella Infections/diagnosis ; Klebsiella pneumoniae/genetics ; }, abstract = {Klebsiella pneumoniae is an important opportunistic healthcare-associated pathogen and major contributor to the global spread of antimicrobial resistance. Gastrointestinal colonization with K. pneumoniae is a major predisposing risk factor for infection and forms an important hub for the dispersal of resistance. Current culture-based detection methods are time consuming, give limited intra-sample abundance and strain diversity information, and have uncertain sensitivity. Here we investigated the presence and abundance of K. pneumoniae at the species and strain level within fecal samples from 103 community-based adults by qPCR and whole metagenomic sequencing (WMS) compared to culture-based detection. qPCR demonstrated the highest sensitivity, detecting K. pneumoniae in 61.2% and 75.8% of direct-fecal and culture-enriched sweep samples, respectively, including 52/52 culture-positive samples. WMS displayed lower sensitivity, detecting K. pneumoniae in 71.2% of culture-positive fecal samples at a 0.01% abundance cutoff, and was inclined to false positives in proportion to the relative abundance of other Enterobacterales present. qPCR accurately quantified K. pneumoniae to 16 genome copies/reaction while WMS could estimate relative abundance to at least 0.01%. Quantification by both methods correlated strongly with each other (Spearman's rho = 0.91). WMS also supported accurate intra-sample K. pneumoniae sequence type (ST)-level diversity detection from fecal microbiomes to 0.1% relative abundance, agreeing with the culture-based detected ST in 16/19 samples. Our results show that qPCR and WMS are sensitive and reliable tools for detection, quantification, and strain analysis of K. pneumoniae from fecal samples with potential to support infection control and enhance insights in K. pneumoniae gastrointestinal ecology.}, } @article {pmid36045431, year = {2022}, author = {Meng, Y and Li, S and Zhang, C and Zheng, H}, title = {Strain-level profiling with picodroplet microfluidic cultivation reveals host-specific adaption of honeybee gut symbionts.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {140}, pmid = {36045431}, issn = {2049-2618}, mesh = {Animals ; Bacteria/genetics ; Bees ; Bifidobacterium/genetics ; Metagenome ; *Microbiota ; *Microfluidics ; Symbiosis ; }, abstract = {BACKGROUND: Symbiotic gut microbes have a rich genomic and metabolic pool and are closely related to hosts' health. Traditional sequencing profiling masks the genomic and phenotypic diversity among strains from the same species. Innovative droplet-based microfluidic cultivation may help to elucidate the inter-strain interactions. A limited number of bacterial phylotypes colonize the honeybee gut, while individual strains possess unique genomic potential and critical capabilities, which provides a particularly good model for strain-level analyses.

RESULTS: Here, we construct a droplet-based microfluidic platform and generated ~ 6 × 10[8] droplets encapsulated with individual bacterial cells from the honeybee gut and cultivate in different media. Shotgun metagenomic analysis reveals significant changes in community structure after droplet-based cultivation, with certain species showing higher strain-level diversity than in gut samples. We obtain metagenome-assembled genomes, and comparative analysis reveal a potential novel cluster from Bifidobacterium in the honeybee. Interestingly, Lactobacillus panisapium strains obtained via droplet cultivation from Apis mellifera contain a unique set of genes encoding L-arabinofuranosidase, which is likely important for the survival of bacteria in competitive environments.

CONCLUSIONS: By encapsulating single bacteria cells inside microfluidic droplets, we exclude potential interspecific competition for the enrichment of rare strains by shotgun sequencing at high resolution. The comparative genomic analysis reveals underlying mechanisms for host-specific adaptations, providing intriguing insights into microbe-microbe interactions. The current approach may facilitate the hunting for elusive bacteria and paves the way for large-scale studies of more complex animal microbial communities. Video Abstract.}, } @article {pmid36044594, year = {2022}, author = {Swarte, JC and Li, Y and Hu, S and Björk, JR and Gacesa, R and Vich Vila, A and Douwes, RM and Collij, V and Kurilshikov, A and Post, A and Klaassen, MAY and Eisenga, MF and Gomes-Neto, AW and Kremer, D and Jansen, BH and Knobbe, TJ and Berger, SP and Sanders, JF and Heiner-Fokkema, MR and Porte, RJ and Cuperus, FJC and de Meijer, VE and Wijmenga, C and Festen, EAM and Zhernakova, A and Fu, J and Harmsen, HJM and Blokzijl, H and Bakker, SJL and Weersma, RK}, title = {Gut microbiome dysbiosis is associated with increased mortality after solid organ transplantation.}, journal = {Science translational medicine}, volume = {14}, number = {660}, pages = {eabn7566}, doi = {10.1126/scitranslmed.abn7566}, pmid = {36044594}, issn = {1946-6242}, mesh = {Dysbiosis ; *Gastrointestinal Microbiome/genetics ; *Hematopoietic Stem Cell Transplantation ; Humans ; *Organ Transplantation ; Virulence Factors ; }, abstract = {Organ transplantation is a life-saving treatment for patients with end-stage disease, but survival rates after transplantation vary considerably. There is now increasing evidence that the gut microbiome is linked to the survival of patients undergoing hematopoietic cell transplant, yet little is known about the role of the gut microbiome in solid organ transplantation. We analyzed 1370 fecal samples from 415 liver and 672 renal transplant recipients using shotgun metagenomic sequencing to assess microbial taxonomy, metabolic pathways, antibiotic resistance genes, and virulence factors. To quantify taxonomic and metabolic dysbiosis, we also analyzed 1183 age-, sex-, and body mass index-matched controls from the same population. In addition, a subset of 78 renal transplant recipients was followed longitudinally from pretransplantation to 24 months after transplantation. Our data showed that both liver and kidney transplant recipients suffered from gut dysbiosis, including lower microbial diversity, increased abundance of unhealthy microbial species, decreased abundance of important metabolic pathways, and increased prevalence and diversity of antibiotic resistance genes and virulence factors. These changes were found to persist up to 20 years after transplantation. Last, we demonstrated that the use of immunosuppressive drugs was associated with the observed dysbiosis and that the extent of dysbiosis was associated with increased mortality after transplantation. This study represents a step toward potential microbiome-targeted interventions that might influence the outcomes of recipients of solid organ transplantation.}, } @article {pmid36044481, year = {2022}, author = {Mtshali, K and Khumalo, ZTH and Kwenda, S and Arshad, I and Thekisoe, OMM}, title = {Exploration and comparison of bacterial communities present in bovine faeces, milk and blood using 16S rRNA metagenomic sequencing.}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0273799}, pmid = {36044481}, issn = {1932-6203}, mesh = {Animals ; Bacteria/genetics ; Bacteroidetes/genetics ; Cattle ; Feces/microbiology ; Female ; *Microbiota/genetics ; *Milk/microbiology ; RNA, Ribosomal, 16S/genetics ; South Africa ; }, abstract = {Cattle by-products like faeces, milk and blood have many uses among rural communities; aiding to facilitate everyday household activities and occasional rituals. Ecologically, the body sites from which they are derived consist of distinct microbial communities forming a complex ecosystem of niches. We aimed to explore and compare the faecal, milk and blood microbiota of cows through 16S rRNA sequencing. All downstream analyses were performed using applications in R Studio (v3.6.1). Alpha-diversity metrics showed significant differences between faeces and blood; faeces and milk; but non-significant between blood and milk using Kruskal-Wallis test, P < 0,05. The beta-diversity metrics on Principal Coordinate Analysis and Non-Metric Dimensional Scaling significantly clustered samples by type (PERMANOVA test, P < 0,05). The overall analysis revealed a total of 30 phyla, 74 classes, 156 orders, 243 families and 408 genera. Firmicutes, Bacteroidota and Proteobacteria were the most abundant phyla overall. A total of 58 genus-level taxa occurred concurrently between the body sites. The important taxa could be categorized into four potentially pathogenic clusters i.e. arthropod-borne; food-borne and zoonotic; mastitogenic; and metritic and abortigenic. A number of taxa were significantly differentially abundant (DA) between sites based on the Wald test implemented in DESeq2 package. Majority of the DA taxa (i.e. Romboutsia, Paeniclostridium, Monoglobus, Akkermansia, Turicibacter, Bacteroides, Candidatus_Saccharimonas, UCG-005 and Prevotellaceae_UCG-004) were significantly enriched in faeces in comparison to milk and blood, except for Anaplasma which was greatly enriched in blood and was in turn the largest microbial genus in the entire analysis. This study provides insights into the microbial community composition of the sampled body sites and its extent of overlapping. It further highlights the potential risk of disease occurrence and transmission between the animals and the community of Waaihoek in KwaZulu-Natal, Republic of South Africa pertaining to their unsanitary practices associated with the use of cattle by-products.}, } @article {pmid36041613, year = {2022}, author = {Li, Q and Tian, L and Cai, X and Wang, Y and Mao, Y}, title = {Plastisphere showing unique microbiome and resistome different from activated sludge.}, journal = {The Science of the total environment}, volume = {851}, number = {Pt 2}, pages = {158330}, doi = {10.1016/j.scitotenv.2022.158330}, pmid = {36041613}, issn = {1879-1026}, mesh = {*Sewage/microbiology ; Polyvinyl Chloride ; Genes, Bacterial ; Microplastics ; Plastics ; *Microbiota ; Anti-Bacterial Agents/pharmacology ; Tetracycline ; Wastewater/microbiology ; }, abstract = {Plastisphere (the biofilm on microplastics) in wastewater treatment plants (WWTPs) may enrich pathogens and antibiotic resistance genes (ARGs) which can cause risks to the ecological environment by discharging into receiving waters. However, the microbiome and resistome of plastisphere in activated sludge (AS) systems remain inconclusive. Here, metagenome was applied to investigate the microbial composition, functions and ARGs of the Polyvinyl chloride (PVC) plastisphere in lab-scale reactors, and revealed the effects of tetracycline (TC) and/or Cu(II) pressures on them. The results indicated that the plastisphere provided a new niche for microbiota showing unique functions distinct from the AS. Particularly, various potentially pathogenic bacteria tended to enrich in PVC plastisphere. Moreover, various ARGs were detected in plastisphere and AS, but the plastisphere had more potential ARGs hosts and a stronger correlation with ARGs. The ARGs abundances increased after exposure to TC and/or Cu(II) pressures, especially tetracycline resistance genes (TRGs), and the results further showed that TRGs with different resistance mechanisms were separately enriched in plastisphere and AS. Furthermore, the exogenous pressures from Cu(II) or/and TC also enhanced the association of potential pathogens with TRGs in PVC plastisphere. The findings contribute to assessing the potential risks of spreading pathogens and ARGs through microplastics in WWTPs.}, } @article {pmid36041519, year = {2022}, author = {Shi, F and Almerick T Boncan, D and Wan, HT and Chan, TF and Zhang, EL and Lai, KP and Wong, CK}, title = {Hepatic metabolism gene expression and gut microbes in offspring, subjected to in-utero PFOS exposure and postnatal diet challenges.}, journal = {Chemosphere}, volume = {308}, number = {Pt 1}, pages = {136196}, doi = {10.1016/j.chemosphere.2022.136196}, pmid = {36041519}, issn = {1879-1298}, mesh = {Body Weight ; Carbohydrates ; Diet, High-Fat ; Fatty Acids, Volatile/metabolism ; Female ; *Gastrointestinal Microbiome ; Gene Expression ; Humans ; Lipid Metabolism ; Lipids ; Liver/metabolism ; Polysaccharides/metabolism ; *Prenatal Exposure Delayed Effects/metabolism ; Sucrose/metabolism ; Vitamins/metabolism/pharmacology ; }, abstract = {We examined the changes in hepatic metabolic gene expression and gut microbiota of offspring exposed to PFOS in-utero. At GD17.5, our data showed that PFOS exposure decreased fetal bodyweights and hepatic metabolic gene expressions but increased relative liver mass and lipid accumulation. At PND21, in-utero high-dose PFOS-exposed offspring exhibited significantly greater bodyweight (catch-up-growth), associated with significant induction of hepatic metabolic gene expression. In addition, 16SrRNA-sequencing of the cecal samples revealed an increase in carbohydrate catabolism but a reduction in microbial polysaccharide synthesis and short-chain fatty acid (SCFA) metabolism. From PND21-80, a postnatal diet-challenge for the offspring was conducted. At PND80 under a normal diet, in-utero high-dose PFOS-exposed offspring maintained the growth "catch-up" effect. In contrast, in a high-fat-diet, the bodyweight of in-utero high-dose PFOS-exposed adult offspring were significantly lesser than the corresponding low-dose and control groups. Even though in the high-fat-diet, the in-utero PFOS-exposed adult offspring showed significant upregulation of hepatic metabolic genes, the lower bodyweight suggests that they had difficulty utilizing high-fat nutrients. Noteworthy, the metagenomic data showed a significant reduction in the biosynthesis of microbial polysaccharides, vitamin B, and SCFAs in the PFOS-exposed adult offspring. Furthermore, the observed effects were significantly reduced in the PFOS-exposed adult offspring with the high-fat diet but supplemented with sucrose. Our study demonstrated that in-utero PFOS exposure caused inefficient fat metabolism and increased the risk of hepatic steatosis in offspring.}, } @article {pmid36037841, year = {2022}, author = {Zhang, Q and Zhao, L and Zhang, J and Liu, W and Cai, S and Chen, L and Cai, T and Ji, XM}, title = {Nitrogen contribution and microbial community of size-fractionated anammox sludge in continuous stirred-tank reactors.}, journal = {Bioresource technology}, volume = {362}, number = {}, pages = {127857}, doi = {10.1016/j.biortech.2022.127857}, pmid = {36037841}, issn = {1873-2976}, mesh = {Anaerobic Ammonia Oxidation ; Anaerobiosis ; Bioreactors ; Denitrification ; *Microbiota ; Nitrogen ; Oxidation-Reduction ; *Sewage ; }, abstract = {In this study, the microbial diversity of size-fractionated anammox sludge in a well-mixed system and their contribution to nitrogen transformation were investigated. Results showed that small granules (0.2-1.0 mm) contributed to the major part of the nitrogen removal rate (56 %) due to its largest mixed liquor volatile suspended solids (1240 ± 80 mg·L[-1]). However, large granules (>1.0 mm) possessed the highest relative abundances of Ca. Kuenenia stuttgartiensis and specific anammox activity, representing 49.34 % and 24.45 ± 0.01 mg-N·g[-1]-mixed liquor volatile suspended solids·h[-1], respectively. The microbial diversity decreased as the increase of granular size, resulting in microbial community shifting to a simpler model. Metagenomic analysis showed that fine sludge might be the potential major for NO/N2O production in the mature well-mixed system under inorganic conditions. This study provides guidance for the evaluation of nitrogen contribution by anammox size-fractionated sludge and the inhibition of the potential NO/N2O emission in anammox processes.}, } @article {pmid36036910, year = {2022}, author = {Chang, CJ and Somohano, K and Zemsky, C and Uhlemann, AC and Liebmann, J and Cioffi, GA and Al-Aswad, LA and Lynch, SV and Winn, BJ}, title = {Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome.}, journal = {Investigative ophthalmology & visual science}, volume = {63}, number = {9}, pages = {32}, pmid = {36036910}, issn = {1552-5783}, support = {P30 EY002162/EY/NEI NIH HHS/United States ; }, mesh = {Antihypertensive Agents/therapeutic use ; *Dry Eye Syndromes/drug therapy/metabolism ; *Glaucoma/drug therapy/metabolism ; Humans ; *Microbiota ; Ophthalmic Solutions/therapeutic use ; RNA, Ribosomal, 16S/genetics/metabolism ; Tears/metabolism ; }, abstract = {PURPOSE: To investigate the ocular surface microbiome of patients with unilateral or asymmetric glaucoma being treated with topical ophthalmic medications in one eye and to determine whether microbial community changes were related to measures of ocular surface disease.

METHODS: V3-V4 16S rRNA sequencing was conducted on ocular surface swabs collected from both eyes of 17 subjects: 10 patients with asymmetric/unilateral glaucoma using topical glaucoma therapy on only one eye and seven age-matched, healthy controls with no history of ocular disease or eyedrop use. Samples were categorized into three groups: patients' glaucomatous eye treated with eyedrops, patients' contralateral eye without eyedrops, and healthy control eyes. Comparisons were made for microbial diversity and composition, with differences in composition tested for association with ocular surface disease measures including tear meniscus height, tear break-up time, and Dry Eye Questionnaire.

RESULTS: Samples obtained from the patients' treated and untreated eyes both had significantly greater alpha-diversity and relative abundance of gram-negative organisms compared to healthy controls. The microbial composition of patient eyes was associated with decreased tear meniscus height and tear break-up time, whereas metagenomic predictions, based on 16S rRNA data, suggested increased synthesis of lipopolysaccharide.

CONCLUSIONS: The ocular surface microbiome of patients taking unilateral preserved glaucoma drops is characterized by a highly diverse array of gram-negative bacteria that is significantly different from the predominantly gram-positive microbes detected on healthy control eyes. These compositional differences were associated with decreased tear film measures and distinct inferred protein synthesis pathways, suggesting a potential link between microbial alterations and ocular surface inflammation.}, } @article {pmid36036626, year = {2022}, author = {Li, C and Tang, M and Li, X and Zhou, X}, title = {Community Dynamics in Structure and Function of Honey Bee Gut Bacteria in Response to Winter Dietary Shift.}, journal = {mBio}, volume = {13}, number = {5}, pages = {e0113122}, pmid = {36036626}, issn = {2150-7511}, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome/physiology ; Seasons ; Tryptophan ; Bacteria/genetics ; Diet ; Ethanol ; Phenylalanine ; Lactates ; Pyruvates ; }, abstract = {Temperate honey bees (Apis mellifera) are challenged by low temperatures and abrupt dietary shifts associated with behavioral changes during winter. Case studies have revealed drastic turnover in the gut microbiota of winter bees, highlighted by the seasonal dominance of a non-core bacterium Bartonella. However, neither biological consequence nor underlying mechanism of this microbial turnover is clear. In particular, we ask whether such changes in gut profile are related to winter dietary shift and possibly beneficial to host and associated gut microbiome? Here, we integrated evidences from genomics, metagenomics, and metabolomics in three honey bee subspecies maintained at the same locality of northern China to profile both diversity and functional variations in gut bacteria across seasons. Our results showed that winter dominance of Bartonella was shared in all tested honey bee lineages. This seasonal change was likely a consequence of winter dietary shifts characterized by greatly reduced pollen consumption and accumulation of metabolic waste due to restricted excretion. Bartonella showed expanded genomic capacity in utilizing more diverse energy substrates, such as converting metabolic wastes lactate and ethanol into pyruvate, an energy source for self-utilization and possibly also for host and other symbionts. Furthermore, Bartonella was the only bacterium capable of both producing and secreting tryptophan and phenylalanine, whose metabolic products were detected in bee guts, even though all gut bacteria lacked relevant digestion enzymes. These results thus suggested a possible mechanism where the gut bacteria might benefit the host by supplementing them with essential amino acids lacking in a protein shortage diet. IMPORTANCE The abilities to survive winter and to adapt to major food changes are key traits that have enabled successful range expansion of the honey bees from the tropic to temperate climate. Our results highlighted a new possibility that gut bacteria may have played an important role in host survival of the severe winter condition. The non-core bacterium Bartonella is not only more adaptive to the winter diet but is also equipped with the capacity to provide the host with essential nutrients and important metabolic substrates. This overall host-bacterium profile is probably favored by natural selection, resulting in a consistent winter gut strategy across varied honey bee lineages. Conversely, when the hosts start to forage again, core bacteria maintained at low abundance during winter returned to their typical dominant status, thus completing the annual gut turnover. Our study suggests a new hypothesis where seasonal gut variations may improve the fitness of the honey bee, allowing them to explore more diverse climates.}, } @article {pmid36032108, year = {2022}, author = {He, L and Chen, R and Zhang, B and Zhang, S and Khan, BA and Zhu, D and Wu, Z and Xiao, C and Chen, B and Chen, F and Hou, K}, title = {Fecal microbiota transplantation treatment of autoimmune-mediated type 1 diabetes mellitus.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {930872}, pmid = {36032108}, issn = {1664-3224}, mesh = {Adolescent ; *Diabetes Mellitus, Type 1 ; Fecal Microbiota Transplantation ; Feces ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; }, abstract = {UNLABELLED: Type 1 diabetes mellitus (T1DM) is an autoimmune-mediated disease characterized by a reduced or absolute lack of insulin secretion and often associated with a range of vascular and neurological complications for which there is a lack of effective treatment other than lifestyle interventions and pharmacological treatments such as insulin injections. Studies have shown that the gut microbiota is involved in mediating the onset and development of many fecal and extrafecal diseases, including autoimmune T1DM. In recent years, many cases of gut microbiota transplantation for diseases of the bowel and beyond have been reported worldwide, and this approach has been shown to be safe and effective. Here, we conducted an experimental treatment study in two adolescent patients diagnosed with autoimmune T1DM for one year. Patients received one to three rounds of normal fecal microbiota transplants (FMT) and were followed for up to 30 weeks. Clinical outcomes were measured, including biochemical indices, medication regimen, and dosage adjustment. Fecal microbiota metagenomic sequencing after transplantation provides a reference for more reasonable and effective microbiota transplantation protocols to treat autoimmune T1DM. Our results suggest that FMT is an effective treatment for autoimmune T1DM.

CLINICAL TRIAL REGISTRATION: http://www.chictr.org.cn, identifier ChiCTR2100045789.}, } @article {pmid36031409, year = {2022}, author = {Li, J and Jin, J and Li, S and Zhong, Y and Jin, Y and Zhang, X and Xia, B and Zhu, Y and Guo, R and Sun, X and Guo, J and Hu, F and Xiao, W and Huang, F and Ye, H and Li, R and Zhou, Y and Xiang, X and Yao, H and Yan, Q and Su, L and Wu, L and Luo, T and Liu, Y and Guo, X and Qin, J and Qi, H and He, J and Wang, J and Li, Z}, title = {Tonsillar Microbiome-Derived Lantibiotics Induce Structural Changes of IL-6 and IL-21 Receptors and Modulate Host Immunity.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {9}, number = {30}, pages = {e2202706}, pmid = {36031409}, issn = {2198-3844}, support = {U1903210//National Natural Science Foundation of China/ ; 81901648//National Natural Science Foundation of China/ ; 81801618//National Natural Science Foundation of China/ ; 81771743//National Natural Science Foundation of China/ ; 32141004//National Natural Science Foundation of China/ ; Z191100006619109//Beijing Municipal Science & Technology Commission/ ; PKU2021LCXQ008//Clinical Medicine Plus X-Young Scholars Project of Peking University, supported by "the Fundamental Research Funds for the Central Universities/ ; XDB29020000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; Z191100006619114//Beijing Science and Technology Program/ ; 0094/2018/A3//Macao Science and Technology Fund/ ; }, mesh = {Animals ; Humans ; Mice ; *Arthritis, Rheumatoid/drug therapy/metabolism ; *Bacteriocins/therapeutic use ; Interleukin-6/metabolism ; *Microbiota ; *Receptors, Interleukin-21/metabolism ; T-Lymphocytes, Helper-Inducer/metabolism ; *Palatine Tonsil/microbiology ; *Receptors, Interleukin-6/metabolism ; }, abstract = {Emerging evidence emphasizes the functional impacts of host microbiome on the etiopathogenesis of autoimmune diseases, including rheumatoid arthritis (RA). However, there are limited mechanistic insights into the contribution of microbial biomolecules especially microbial peptides toward modulating immune homeostasis. Here, by mining the metagenomics data of tonsillar microbiome, a deficiency of the encoding genes of lantibiotic peptides salivaricins in RA patients is identified, which shows strong correlation with circulating immune cells. Evidence is provided that the salivaricins exert immunomodulatory effects in inhibiting T follicular helper (Tfh) cell differentiation and interleukin-21 (IL-21) production. Mechanically, salivaricins directly bind to and induce conformational changes of IL-6 and IL-21 receptors, thereby inhibiting the bindings of IL-6 and IL-21 to their receptors and suppressing the downstream signaling pathway. Finally, salivaricin administration exerts both prophylactic and therapeutic effects against experimental arthritis in a murine model of RA. Together, these results provide a mechanism link of microbial peptides-mediated immunomodulation.}, } @article {pmid36031136, year = {2022}, author = {Zheng, Y and Wang, P and Yang, X and Zhao, L and Ren, L and Li, J}, title = {Metagenomics insight into bioaugmentation mechanism of Propionibacterium acidipropionici during anaerobic acidification of kitchen waste.}, journal = {Bioresource technology}, volume = {362}, number = {}, pages = {127843}, doi = {10.1016/j.biortech.2022.127843}, pmid = {36031136}, issn = {1873-2976}, mesh = {Anaerobiosis ; Coenzyme A/metabolism ; Hydrogen-Ion Concentration ; Metagenomics ; *Propionates/metabolism ; Propionibacteriaceae ; *Propionibacterium/genetics/metabolism ; }, abstract = {In the present study, a biochemical strategy for improving propionic acid production from kitchen waste acidification by bioaugmentation with Propionibacterium acidipropionici (P. acidipropionici) was investigated. When the inoculum of P. acidipropionici was 30% (w/w) of the seeding sludge, the propionic acid production increased by 79.57%. Further, bioaugmentation improved the relative abundance of Firmicute and Actinobacteria. The results of metagenomic analysis further reveal that the ATP-binding cassette (ABC) transporters and all related pathways of Propanoate metabolism (ko00640) were enriched when P. acidipropionici was added. For Propanoate metabolism, most functional genes involved in the conversion from Glycolysis / Gluconeogenesis (ko00010) to Propanoyl-CoA and conversion from Propanoyl-CoA to propionic acid were enhanced after bioaugmentation with P. acidipropionici, thereby promoting propionic acid production. As such, bioaugmentation with P. acidipropionici was effective in the anaerobic acidification of kitchen waste for propionic acid production.}, } @article {pmid36029916, year = {2022}, author = {Kundu, P and Mondal, S and Ghosh, A}, title = {Bacterial species metabolic interaction network for deciphering the lignocellulolytic system in fungal cultivating termite gut microbiota.}, journal = {Bio Systems}, volume = {221}, number = {}, pages = {104763}, doi = {10.1016/j.biosystems.2022.104763}, pmid = {36029916}, issn = {1872-8324}, mesh = {Animals ; Bacteria ; *Gastrointestinal Microbiome ; Glycoside Hydrolases/metabolism ; *Isoptera/metabolism/microbiology ; *Termitomyces ; }, abstract = {Fungus-cultivating termite Odontotermes badius developed a mutualistic association with Termitomyces fungi for the plant material decomposition and providing a food source for the host survival. The mutualistic relationship sifted the microbiome composition of the termite gut and Termitomyces fungal comb. Symbiotic bacterial communities in the O. badius gut and fungal comb have been studied extensively to identify abundant bacteria and their lignocellulose degradation capabilities. Despite several metagenomic studies, the species-wide metabolic interaction patterns of bacterial communities in termite gut and fungal comb remains unclear. The bacterial species metabolic interaction network (BSMIN) has been constructed with 230 bacteria identified from the O. badius gut and fungal comb microbiota. The network portrayed the metabolic map of the entire microbiota and highlighted several inter-species biochemical interactions like cross-feeding, metabolic interdependency, and competition. Further, the reconstruction and analysis of the bacterial influence network (BIN) quantified the positive and negative pairwise influences in the termite gut and fungal comb microbial communities. Several key macromolecule degraders and fermentative microbial entities have been identified by analyzing the BIN. The mechanistic interplay between these influential microbial groups and the crucial glycoside hydrolases (GH) enzymes produced by the macromolecule degraders execute the community-wide functionality of lignocellulose degradation and subsequent fermentation. The metabolic interaction pattern between the nine influential microbial species has been determined by considering them growing in a synthetic microbial community. Competition (30%), parasitism (47%), and mutualism (17%) were predicted to be the major mode of metabolic interaction in this synthetic microbial community. Further, the antagonistic metabolic effect was found to be very high in the metabolic-deprived condition, which may disrupt the community functionality. Thus, metabolic interactions of the crucial bacterial species and their GH enzyme cocktail identified from the O. badius gut and fungal comb microbiota may provide essential knowledge for developing a synthetic microcosm with efficient lignocellulolytic machinery.}, } @article {pmid36029249, year = {2022}, author = {Zeng, W and Gautam, A and Huson, DH}, title = {DeepToA: an ensemble deep-learning approach to predicting the theater of activity of a microbiome.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {20}, pages = {4670-4676}, doi = {10.1093/bioinformatics/btac584}, pmid = {36029249}, issn = {1367-4811}, mesh = {Algorithms ; *Deep Learning ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Sequence Analysis, DNA ; }, abstract = {MOTIVATION: Metagenomics is the study of microbiomes using DNA sequencing. A microbiome consists of an assemblage of microbes that is associated with a 'theater of activity' (ToA). An important question is, to what degree does the taxonomic and functional content of the former depend on the (details of the) latter? Here, we investigate a related technical question: Given a taxonomic and/or functional profile estimated from metagenomic sequencing data, how to predict the associated ToA? We present a deep-learning approach to this question. We use both taxonomic and functional profiles as input. We apply node2vec to embed hierarchical taxonomic profiles into numerical vectors. We then perform dimension reduction using clustering, to address the sparseness of the taxonomic data and thus make the problem more amenable to deep-learning algorithms. Functional features are combined with textual descriptions of protein families or domains. We present an ensemble deep-learning framework DeepToA for predicting the ToA of amicrobial community, based on taxonomic and functional profiles. We use SHAP (SHapley Additive exPlanations) values to determine which taxonomic and functional features are important for the prediction.

RESULTS: Based on 7560 metagenomic profiles downloaded from MGnify, classified into 10 different theaters of activity, we demonstrate that DeepToA has an accuracy of 98.30%. We show that adding textual information to functional features increases the accuracy.

Our approach is available at http://ab.inf.uni-tuebingen.de/software/deeptoa.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36029242, year = {2022}, author = {Solari, SM and Young, RB and Marcelino, VR and Forster, SC}, title = {expam-high-resolution analysis of metagenomes using distance trees.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {20}, pages = {4814-4816}, pmid = {36029242}, issn = {1367-4811}, mesh = {*Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Software ; }, abstract = {SUMMARY: Shotgun metagenomic sequencing provides the capacity to understand microbial community structure and function at unprecedented resolution; however, the current analytical methods are constrained by a focus on taxonomic classifications that may obfuscate functional relationships. Here, we present expam, a tree-based, taxonomy agnostic tool for the identification of biologically relevant clades from shotgun metagenomic sequencing.

expam is an open-source Python application released under the GNU General Public Licence v3.0. expam installation instructions, source code and tutorials can be found at https://github.com/seansolari/expam.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36028255, year = {2023}, author = {Badran, M and Khalyfa, A and Ericsson, AC and Puech, C and McAdams, Z and Bender, SB and Gozal, D}, title = {Gut microbiota mediate vascular dysfunction in a murine model of sleep apnoea: effect of probiotics.}, journal = {The European respiratory journal}, volume = {61}, number = {1}, pages = {}, pmid = {36028255}, issn = {1399-3003}, support = {R01 HL130984/HL/NHLBI NIH HHS/United States ; R56 HL140548/HL/NHLBI NIH HHS/United States ; RF1 AG061824/AG/NIA NIH HHS/United States ; }, mesh = {Mice ; Animals ; *Gastrointestinal Microbiome/physiology ; Disease Models, Animal ; RNA, Ribosomal, 16S ; Mice, Inbred C57BL ; *Sleep Apnea, Obstructive/complications/therapy ; *Probiotics ; Hypoxia ; *Coronary Artery Disease/therapy/complications ; }, abstract = {BACKGROUND: Obstructive sleep apnoea (OSA) is a chronic prevalent condition characterised by intermittent hypoxia (IH), and is associated with endothelial dysfunction and coronary artery disease (CAD). OSA can induce major changes in gut microbiome diversity and composition, which in turn may induce the emergence of OSA-associated morbidities. However, the causal effects of IH-induced gut microbiome changes on the vasculature remain unexplored. Our objective was to assess if vascular dysfunction induced by IH is mediated through gut microbiome changes.

METHODS: Faecal microbiota transplantation (FMT) was conducted on C57BL/6J naïve mice for 6 weeks to receive either IH or room air (RA) faecal slurry with or without probiotics (VSL#3). In addition to 16S rRNA amplicon sequencing of their gut microbiome, FMT recipients underwent arterial blood pressure and coronary artery and aorta function testing, and their trimethylamine N-oxide (TMAO) and plasma acetate levels were determined. Finally, C57BL/6J mice were exposed to IH, IH treated with VSL#3 or RA for 6 weeks, and arterial blood pressure and coronary artery function assessed.

RESULTS: Gut microbiome taxonomic profiles correctly segregated IH from RA in FMT mice and the normalising effect of probiotics emerged. Furthermore, IH-FMT mice exhibited increased arterial blood pressure and TMAO levels, and impairments in aortic and coronary artery function (p<0.05) that were abrogated by probiotic administration. Lastly, treatment with VSL#3 under IH conditions did not attenuate elevations in arterial blood pressure or CAD.

CONCLUSIONS: Gut microbiome alterations induced by chronic IH underlie, at least partially, the typical cardiovascular disturbances of sleep apnoea and can be mitigated by concurrent administration of probiotics.}, } @article {pmid36028202, year = {2022}, author = {Wang, J and Xiao, J and Zhu, Z and Wang, S and Zhang, L and Fan, Z and Deng, Y and Hu, Z and Peng, F and Shen, S and Deng, F}, title = {Diverse viromes in polar regions: A retrospective study of metagenomic data from Antarctic animal feces and Arctic frozen soil in 2012-2014.}, journal = {Virologica Sinica}, volume = {37}, number = {6}, pages = {883-893}, pmid = {36028202}, issn = {1995-820X}, mesh = {Animals ; *Soil ; Ecosystem ; Retrospective Studies ; Antarctic Regions ; Phylogeny ; Virome ; Cold Climate ; *Viruses ; Feces ; Metagenomics ; }, abstract = {Antarctica and the Arctic are the coldest places, containing a high diversity of microorganisms, including viruses, which are important components of polar ecosystems. However, owing to the difficulties in obtaining access to animal and environmental samples, the current knowledge of viromes in polar regions is still limited. To better understand polar viromes, this study performed a retrospective analysis using metagenomic sequencing data of animal feces from Antarctica and frozen soil from the Arctic collected during 2012-2014. The results reveal diverse communities of DNA and RNA viruses from at least 23 families from Antarctic animal feces and 16 families from Arctic soils. Although the viral communities from Antarctica and the Arctic show a large diversity, they have genetic similarities with known viruses from different ecosystems and organisms with similar viral proteins. Phylogenetic analysis of Microviridae, Parvoviridae, and Larvidaviridae was further performed, and complete genomic sequences of two novel circular replication-associated protein (rep)-encoding single-stranded (CRESS) DNA viruses closely related to Circoviridae were identified. These results reveal the high diversity, complexity, and novelty of viral communities from polar regions, and suggested the genetic similarity and functional correlations of viromes between the Antarctica and Arctic. Variations in viral families in Arctic soils, Arctic freshwater, and Antarctic soils are discussed. These findings improve our understanding of polar viromes and suggest the importance of performing follow-up in-depth investigations of animal and environmental samples from Antarctica and the Arctic, which would reveal the substantial role of these viruses in the global viral community.}, } @article {pmid36026526, year = {2022}, author = {Palmnäs-Bédard, MSA and Costabile, G and Vetrani, C and Åberg, S and Hjalmarsson, Y and Dicksved, J and Riccardi, G and Landberg, R}, title = {The human gut microbiota and glucose metabolism: a scoping review of key bacteria and the potential role of SCFAs.}, journal = {The American journal of clinical nutrition}, volume = {116}, number = {4}, pages = {862-874}, pmid = {36026526}, issn = {1938-3207}, mesh = {Adult ; *Diabetes Mellitus, Type 2/drug therapy ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Glucose/metabolism ; Humans ; Prospective Studies ; Verrucomicrobia/metabolism ; }, abstract = {The gut microbiota plays a fundamental role in human nutrition and metabolism and may have direct implications for type 2 diabetes and associated preconditions. An improved understanding of relations between human gut microbiota and glucose metabolism could lead to novel opportunities for type 2 diabetes prevention, but human observational studies reporting on such findings have not been extensively reviewed. Here, we review the literature on associations between gut microbiota and markers and stages of glucose dysregulation and insulin resistance in healthy adults and in adults with metabolic disease and risk factors. We present the current evidence for identified key bacteria and their potential roles in glucose metabolism independent of overweight, obesity, and metabolic drugs. We provide support for SCFAs mediating such effects and discuss the role of diet, as well as metabolites derived from diet and gut microbiota interactions. From 5983 initially identified PubMed records, 45 original studies were eligible and reviewed. α Diversity and 45 bacterial taxa were associated with selected outcomes. Six taxa were most frequently associated with glucose metabolism: Akkermansia muciniphila, Bifidobacterium longum, Clostridium leptum group, Faecalibacterium prausnitzii, and Faecalibacterium (inversely associated) and Dorea (directly associated). For Dorea and A. muciniphila, associations were independent of metabolic drugs and body measures. For A. muciniphila and F. prausnitzii, limited evidence supported SCFA mediation of potential effects on glucose metabolism. We conclude that observational studies applying metagenomics sequencing to identify species-level relations are warranted, as are studies accounting for confounding factors and investigating SCFA and postprandial glucose metabolism. Such advances in the field will, together with mechanistic and prospective studies and investigations into diet-gut microbiota interactions, have the potential to bring critical insight into roles of gut microbiota and microbial metabolites in human glucose metabolism and to contribute toward the development of novel prevention strategies for type 2 diabetes, including precision nutrition.}, } @article {pmid36016275, year = {2022}, author = {Cholleti, H and de Jong, J and Blomström, AL and Berg, M}, title = {Characterization of Pipistrellus pygmaeus Bat Virome from Sweden.}, journal = {Viruses}, volume = {14}, number = {8}, pages = {}, pmid = {36016275}, issn = {1999-4915}, mesh = {Animals ; *Chiroptera ; Genome, Viral ; Humans ; Mammals ; Phylogeny ; *Picornaviridae/genetics ; *Plant Viruses/genetics ; *RNA Viruses/genetics ; Sweden ; Virome ; }, abstract = {Increasing amounts of data indicate that bats harbor a higher viral diversity relative to other mammalian orders, and they have been recognized as potential reservoirs for pathogenic viruses, such as the Hendra, Nipah, Marburg, and SARS-CoV viruses. Here, we present the first viral metagenomic analysis of Pipistrellus pygmaeus from Uppsala, Sweden. Total RNA was extracted from the saliva and feces of individual bats and analyzed using Illumina sequencing. The results identified sequences related to 51 different viral families, including vertebrate, invertebrate, and plant viruses. These viral families include Coronaviridae, Picornaviridae, Dicistroviridae, Astroviridae, Hepeviridae, Reoviridae, Botourmiaviridae, Lispviridae, Totiviridae, Botoumiaviridae, Parvoviridae, Retroviridae, Adenoviridae, and Partitiviridae, as well as different unclassified viruses. We further characterized three near full-length genome sequences of bat coronaviruses. A phylogenetic analysis showed that these belonged to alphacoronaviruses with the closest similarity (78-99% at the protein level) to Danish and Finnish bat coronaviruses detected in Pipistrellus and Myotis bats. In addition, the full-length and the near full-length genomes of picornavirus were characterized. These showed the closest similarity (88-94% at the protein level) to bat picornaviruses identified in Chinese bats. Altogether, the results of this study show that Swedish Pipistrellus bats harbor a great diversity of viruses, some of which are closely related to mammalian viruses. This study expands our knowledge on the bat population virome and improves our understanding of the evolution and transmission of viruses among bats and to other species.}, } @article {pmid36014890, year = {2022}, author = {Burakova, I and Smirnova, Y and Gryaznova, M and Syromyatnikov, M and Chizhkov, P and Popov, E and Popov, V}, title = {The Effect of Short-Term Consumption of Lactic Acid Bacteria on the Gut Microbiota in Obese People.}, journal = {Nutrients}, volume = {14}, number = {16}, pages = {}, pmid = {36014890}, issn = {2072-6643}, support = {project FZGW-2020-0001 (unique number of the register of State tasks 075001X39782002)//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {Bacteria ; *Gastrointestinal Microbiome ; Humans ; *Lactobacillales ; *Limosilactobacillus fermentum ; Obesity/microbiology/therapy ; *Probiotics/therapeutic use ; }, abstract = {Obesity is a problem of modern health care that causes the occurrence of many concomitant diseases: arterial hypertension, diabetes mellitus, non-alcoholic fatty liver disease, and cardiovascular diseases. New strategies for the treatment and prevention of obesity are being developed that are based on using probiotics for modulation of the gut microbiota. Our study aimed to evaluate the bacterial composition of the gut of obese patients before and after two weeks of lactic acid bacteria (Lactobacillus acidophilus, Lactiplantibacillus plantarum, Limosilactobacillus fermentum, and Lactobacillus delbrueckii) intake. The results obtained showed an increase in the number of members of the phylum Actinobacteriota in the group taking nutritional supplements, while the number of phylum Bacteroidota decreased in comparison with the control group. There has also been an increase in potentially beneficial groups: Bifidobacterium, Blautia, Eubacterium, Anaerostipes, Lactococcus, Lachnospiraceae ND3007, Streptococcus, Escherichia-Shigella, and Lachnoclostridium. Along with this, a decrease in the genera was demonstrated: Faecalibacterium, Pseudobutyrivibrio, Subdoligranulum, Faecalibacterium, Clostridium sensu stricto 1 and 2, Catenibacterium, Megasphaera, Phascolarctobacterium, and the Oscillospiraceae NK4A214 group, which contribute to the development of various metabolic disorders. Modulation of the gut microbiota by lactic acid bacteria may be one of the ways to treat obesity.}, } @article {pmid36014042, year = {2022}, author = {Sbaoui, Y and Ezaouine, A and Toumi, M and Farkas, R and Kbaich, MA and Habbane, M and El Mouttaqui, S and Kadiri, FZ and El Messal, M and Tóth, E and Bennis, F and Chegdani, F}, title = {Effect of Climate on Bacterial and Archaeal Diversity of Moroccan Marine Microbiota.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {36014042}, issn = {2076-2607}, abstract = {The Moroccan coast is characterized by a diversity of climate, reflecting a great richness and diversity of fauna and flora. By this, marine microbiota plays a fundamental role in many biogeochemical processes, environmental modifications, and responses to temperature changes. To date, no exploration by high-throughput techniques has been carried out on the characterization of the Moroccan marine microbiota. The objective of this work is to study the diversity and metabolic functions of MMM from the Moroccan coast (Atlantic and Mediterranean) according to the water source (WS) and the type of climate (CT) using the approach high-throughput sequencing of the 16SrRNA gene. Four water samples of twelve sampling sites from the four major climates along the Moroccan coastline were collected, and prokaryotic DNA was extracted. V4 region of 16S rRNA gene was amplified, and the product PCR was sequenced by Illumina Miseq. The β-diversity and α-diversity indices were determined to assess the species richness and evenness. The obtained results were analyzed by Mothur and R software. A total of twenty-eight Bacterial phyla and twelve Archaea were identified from the samples. Proteobacteria, Bacteroidetes, and Cyanobacteria are the three key bacterial phyla, and the Archaeal phyla identified are: Euryarchaeota, Nanoarchaeaeota, Crenarchaeota, Hydrothermarchaeota, Asgardaeota, Diapherotrites, and Thaumarchaeota in the Moroccan coastline and the four climates studied. The whole phylum are involved in marine biogeochemical cycles, and through their functions they participate in the homeostasis of the ocean in the presence of pollutants or stressful biotic and abiotic factors. In conclusion, the obtained results reported sufficient deepness of sequencing to cover the majority of Archaeal and Bacterial genera in each site. We noticed a strong difference in microbiota diversity, abundance, and taxonomy inter- and intra-climates and water source without significant differences in function. To better explore this diversity, other omic approaches can be applied such as the metagenomic shotgun, and transcriptomic approaches allowing a better characterization of the Moroccan marine microbiota and to understand the mechanisms of its adaptation and its impacts in/on the ecosystem.}, } @article {pmid36014039, year = {2022}, author = {Pérez, V and Liu, Y and Hengst, MB and Weyrich, LS}, title = {A Case Study for the Recovery of Authentic Microbial Ancient DNA from Soil Samples.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {36014039}, issn = {2076-2607}, support = {1211515//FONDECYT/ ; 1201692//FONDECYT/ ; 1181773//FONDECYT/ ; 74190093//ANID-International Postdoctoral Research fellowship-ANID/ ; FT180100407//Australian Research Council Future Fellowship/ ; }, abstract = {High Throughput DNA Sequencing (HTS) revolutionized the field of paleomicrobiology, leading to an explosive growth of microbial ancient DNA (aDNA) studies, especially from environmental samples. However, aDNA studies that examine environmental microbes routinely fail to authenticate aDNA, examine laboratory and environmental contamination, and control for biases introduced during sample processing. Here, we surveyed the available literature for environmental aDNA projects—from sample collection to data analysis—and assessed previous methodologies and approaches used in the published microbial aDNA studies. We then integrated these concepts into a case study, using shotgun metagenomics to examine methodological, technical, and analytical biases during an environmental aDNA study of soil microbes. Specifically, we compared the impact of five DNA extraction methods and eight bioinformatic pipelines on the recovery of microbial aDNA information in soil cores from extreme environments. Our results show that silica-based methods optimized for aDNA research recovered significantly more damaged and shorter reads (<100 bp) than a commercial kit or a phenol−chloroform method. Additionally, we described a stringent pipeline for data preprocessing, efficiently decreasing the representation of low-complexity and duplicated reads in our datasets and downstream analyses, reducing analytical biases in taxonomic classification.}, } @article {pmid36012686, year = {2022}, author = {Ajiboye, TT and Ayangbenro, AS and Babalola, OO}, title = {Functional Diversity of Microbial Communities in the Soybean (Glycine max L.) Rhizosphere from Free State, South Africa.}, journal = {International journal of molecular sciences}, volume = {23}, number = {16}, pages = {}, pmid = {36012686}, issn = {1422-0067}, support = {UID123634; UID132595//National Research Foundation/ ; }, mesh = {*Fabaceae ; *Microbiota/genetics ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; South Africa ; Glycine max/genetics ; }, abstract = {The plant microbiome is involved in enhancing nutrient acquisition, plant growth, stress tolerance, and reducing chemical inputs. The identification of microbial functional diversity offers the chance to evaluate and engineer them for various agricultural processes. Using a shotgun metagenomics technique, this study examined the functional diversity and metabolic potentials of microbial communities in the rhizosphere of soybean genotype link 678. The dominant genera are Geobacter, Nitrobacter, Burkholderia, Candidatus, Bradyrhizobium and Streptomyces. Twenty-one functional categories were present, with fourteen of the functions being dominant in all samples. The dominant functions include carbohydrates, fatty acids, lipids and isoprenoids, amino acids and derivatives, sulfur metabolism, and nitrogen metabolism. A Kruskal-Wallis test was used to test samples' diversity differences. There was a significant difference in the alpha diversity. ANOSIM was used to analyze the similarities of the samples and there were significant differences between the samples. Phosphorus had the highest contribution of 64.3% and was more prominent among the soil properties that influence the functional diversity of the samples. Given the functional groups reported in this study, soil characteristics impact the functional role of the rhizospheric microbiome of soybean.}, } @article {pmid36009744, year = {2022}, author = {Zhang, SD and Lin, GH and Han, JR and Lin, YW and Wang, FQ and Lu, DC and Xie, JX and Zhao, JX}, title = {Digestive Tract Morphology and Gut Microbiota Jointly Determine an Efficient Digestive Strategy in Subterranean Rodents: Plateau Zokor.}, journal = {Animals : an open access journal from MDPI}, volume = {12}, number = {16}, pages = {}, pmid = {36009744}, issn = {2076-2615}, support = {31760622//National Natural Science Foundation of China/ ; }, abstract = {Rodents' lifestyles vary in different environments, and to adapt to various lifestyles specific digestion strategies have been developed. Among these strategies, the morphology of the digestive tracts and the gut microbiota are considered to play the most important roles in such adaptations. However, how subterranean rodents adapt to extreme environments through regulating gut microbial diversity and morphology of the digestive tract has yet to be fully studied. Here, we conducted the comparisons of the gastrointestinal morphology, food intake, food assimilation, food digestibility and gut microbiota of plateau zokor Eospalax baileyi in Qinghai-Tibet Plateau and laboratory rats Rattus norvegicus to further understand the survival strategy in a typical subterranean rodent species endemic to the Qinghai-Tibet Plateau. Our results revealed that plateau zokor evolved an efficient foraging strategy with low food intake, high food digestibility, and ultimately achieved a similar amount of food assimilation to laboratory rats. The length and weight of the digestive tract of the plateau zokor was significantly higher than the laboratory rat. Particularly, the weight and length of the large intestine and cecum in plateau zokor is three times greater than that of the laboratory rat. Microbiome analysis showed that genus (i.e., Prevotella, Oscillospira, CF231, Ruminococcus and Bacteroides), which are usually associated with cellulose degradation, were significantly enriched in laboratory rats, compared to plateau zokor. However, prediction of metagenomic function revealed that both plateau zokor and laboratory rats shared the same functions in carbohydrate metabolism and energy metabolism. The higher digestibility of crude fiber in plateau zokor was mainly driven by the sizes of cecum and cecum tract, as well as those gut microbiota which associated with cellulose degradation. Altogether, our results highlight that both gut microbiota and the morphology of the digestive tract are vital to the digestion in wild rodents.}, } @article {pmid36009027, year = {2022}, author = {Błażejewska, A and Zalewska, M and Grudniak, A and Popowska, M}, title = {A Comprehensive Study of the Microbiome, Resistome, and Physical and Chemical Characteristics of Chicken Waste from Intensive Farms.}, journal = {Biomolecules}, volume = {12}, number = {8}, pages = {}, pmid = {36009027}, issn = {2218-273X}, mesh = {Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Animals ; Anti-Bacterial Agents/pharmacology ; *Chickens ; Farms ; Genes, Bacterial ; Manure ; *Microbiota/genetics ; }, abstract = {The application of chicken waste to farmland could be detrimental to public health. It may contribute to the dissemination of antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) from feces and their subsequent entry into the food chain. The present study analyzes the metagenome and resistome of chicken manure and litter obtained from a commercial chicken farm in Poland. ARB were isolated, identified, and screened for antibiogram fingerprints using standard microbiological and molecular methods. The physicochemical properties of the chicken waste were also determined. ARGs, integrons, and mobile genetic elements (MGE) in chicken waste were analyzed using high-throughput SmartChip qPCR. The results confirm the presence of many ARGs, probably located in MGE, which can be transferred to other bacteria. Potentially pathogenic or opportunistic microorganisms and phytopathogens were isolated. More than 50% of the isolated strains were classified as being multi-drug resistant, and the remainder were resistant to at least one antibiotic class; these pose a real risk of entering the groundwater and contaminating the surrounding environment. Our results indicate that while chicken manure can be sufficient sources of the nutrients essential for plant growth, its microbiological aspects make this material highly dangerous to the environment.}, } @article {pmid36009014, year = {2022}, author = {Fang, C and Zuo, K and Jiao, K and Zhu, X and Fu, Y and Zhong, J and Xu, L and Yang, X}, title = {PAGln, an Atrial Fibrillation-Linked Gut Microbial Metabolite, Acts as a Promoter of Atrial Myocyte Injury.}, journal = {Biomolecules}, volume = {12}, number = {8}, pages = {}, pmid = {36009014}, issn = {2218-273X}, mesh = {*Atrial Fibrillation ; Calcium-Calmodulin-Dependent Protein Kinase Type 2/metabolism ; *Gastrointestinal Microbiome ; Humans ; Myocytes, Cardiac/metabolism ; Ryanodine Receptor Calcium Release Channel/metabolism ; }, abstract = {Phenylacetylglutamine (PAGln), a gut microbiota (GM)-derived metabolite, is associated with cardiovascular disease. Studies have shown that disordered GM participated in the progression of atrial fibrillation (AF), but the relationship between PAGln and AF is unclear. This study investigated the characteristics of PAGln in AF patients and its impact on atrial myocytes. Based on our previous metagenomic data, the relative abundance of porA, a critical bacterial enzyme for PAGln synthesis, exhibited an increased tendency in AF. In an independent cohort consisting of 42 controls without AF and 92 AF patients, plasma PAGln levels were higher in AF patients than in controls (p < 0.001) by immunoassay. Notably, PAGln exerted a predictive potential of AF with an AUC of 0.774 (p < 0.001), and a predictive model constructed based on the PAGln and Taiwan AF score further improved the predictive potential. Furthermore, a positive correlation was determined between PAGln and LA diameter. Subsequently, the effect of PAGln intervention was examined on HL-1 cells in vitro, revealing that PAGln increased apoptosis, reactive oxygen species (ROS) production, CaMKII and RyR2 activation and decreased cell viability. In conclusion, increased PAGln was associated with AF, and PAGln might contribute to the AF pathogenesis by promoting oxidative stress and apoptosis in atrial myocytes.}, } @article {pmid36005400, year = {2022}, author = {Uehara, M and Inoue, T and Kominato, M and Hase, S and Sasaki, E and Toyoda, A and Sakakibara, Y}, title = {Intraintestinal Analysis of the Functional Activity of Microbiomes and Its Application to the Common Marmoset Intestine.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0052022}, pmid = {36005400}, issn = {2379-5077}, mesh = {Animals ; Humans ; Callithrix/genetics ; *Microbiota/genetics ; Metagenome ; Intestines ; *Gastrointestinal Microbiome/genetics ; }, abstract = {The intestinal microbiome is closely related to host health, and metatranscriptomic analysis can be used to assess the functional activity of microbiomes by quantifying microbial gene expression levels, helping elucidate the interactions between the microbiome and the environment. However, the functional changes in the microbiome along the host intestinal tract remain unknown, and previous analytical methods have limitations, such as potentially overlooking unknown genes due to dependence on existing databases. The objective of this study is to develop a computational pipeline combined with next-generation sequencing for spatial covariation analysis of the functional activity of microbiomes at multiple intestinal sites (biogeographic locations) within the same individual. This method reconstructs a reference metagenomic sequence across multiple intestinal sites and integrates the metagenome and metatranscriptome, allowing the gene expression levels of the microbiome, including unknown bacterial genes, to be compared among multiple sites. When this method was applied to metatranscriptomic analysis in the intestinal tract of common marmosets, a New World monkey, the reconstructed metagenome covered most of the expressed genes and revealed that the differences in microbial gene expression among the cecum, transverse colon, and feces were more dynamic and sensitive to environmental shifts than the abundances of the genes. In addition, metatranscriptomic profiling at three intestinal sites of the same individual enabled covariation analysis incorporating spatial relevance, accurately predicting the function of a total of 10,856 unknown genes. Our findings demonstrate that our proposed analytical method captures functional changes in microbiomes at the gene resolution level. IMPORTANCE We developed an analysis method that integrates metagenomes and metatranscriptomes from multiple intestinal sites to elucidate how microbial function varies along the intestinal tract. This method enables spatial covariation analysis of the functional activity of microbiomes and accurate identification of gene expression changes among intestinal sites, including changes in the expression of unknown bacterial genes. Moreover, we applied this method to the investigation of the common marmoset intestine, which is anatomically and pharmacologically similar to that of humans. Our findings indicate the expression pattern of the microbiome varies in response to changes in the internal environment along the intestinal tract, and this microbial change may affect the intestinal environment.}, } @article {pmid36001521, year = {2023}, author = {Shen, Y and Zhu, J and Deng, Z and Lu, W and Wang, H}, title = {EnsDeepDP: An Ensemble Deep Learning Approach for Disease Prediction Through Metagenomics.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {20}, number = {2}, pages = {986-998}, doi = {10.1109/TCBB.2022.3201295}, pmid = {36001521}, issn = {1557-9964}, mesh = {Humans ; Metagenomics ; *Deep Learning ; Algorithms ; Machine Learning ; *Microbiota/genetics ; }, abstract = {A growing number of studies show that the human microbiome plays a vital role in human health and can be a crucial factor in predicting certain human diseases. However, microbiome data are often characterized by the limited samples and high-dimensional features, which pose a great challenge for machine learning methods. Therefore, this paper proposes a novel ensemble deep learning disease prediction method that combines unsupervised and supervised learning paradigms. First, unsupervised deep learning methods are used to learn the potential representation of the sample. Afterwards, the disease scoring strategy is developed based on the deep representations as the informative features for ensemble analysis. To ensure the optimal ensemble, a score selection mechanism is constructed, and performance boosting features are engaged with the original sample. Finally, the composite features are trained with gradient boosting classifier for health status decision. For case study, the ensemble deep learning flowchart has been demonstrated on six public datasets extracted from the human microbiome profiling. The results show that compared with the existing algorithms, our framework achieves better performance on disease prediction.}, } @article {pmid36000841, year = {2022}, author = {Cen, L and Chang, Y and Bedree, JK and Ma, Y and Zhong, Q and Utter, DR and Dong, PT and Lux, R and Bor, B and Liu, J and McLean, JS and Le, S and He, X}, title = {Exploitation of a Bacterium-Encoded Lytic Transglycosylase by a Human Oral Lytic Phage To Facilitate Infection.}, journal = {Journal of virology}, volume = {96}, number = {17}, pages = {e0106322}, pmid = {36000841}, issn = {1098-5514}, support = {R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 GM110243/GM/NIGMS NIH HHS/United States ; R01 AI087946/AI/NIAID NIH HHS/United States ; S10 OD023603/OD/NIH HHS/United States ; F31 DE026057/DE/NIDCR NIH HHS/United States ; R01 DE030943/DE/NIDCR NIH HHS/United States ; R01 AI132818/AI/NIAID NIH HHS/United States ; R01 DE031274/DE/NIDCR NIH HHS/United States ; }, mesh = {*Actinomycetaceae/enzymology/virology ; Bacteriophage Receptors/metabolism ; *Bacteriophages/enzymology/genetics/physiology ; *Glycosyltransferases/genetics/metabolism ; Host Specificity ; Humans ; Microbiota ; Mouth/microbiology/virology ; Mutation ; Peptidoglycan/metabolism ; Plankton/virology ; Viral Proteins/genetics/metabolism ; }, abstract = {Bacteriophages (phages) are an integral part of the human oral microbiome. Their roles in modulating bacterial physiology and shaping microbial communities have been discussed but remain understudied due to limited isolation and characterization of oral phage. Here, we report the isolation of LC001, a lytic phage targeting human oral Schaalia odontolytica (formerly known as Actinomyces odontolyticus) strain XH001. We showed that LC001 attached to and infected surface-grown, but not planktonic, XH001 cells, and it displayed remarkable host specificity at the strain level. Whole-genome sequencing of spontaneous LC001-resistant, surface-grown XH001 mutants revealed that the majority of the mutants carry nonsense or frameshift mutations in XH001 gene APY09_05145 (renamed ltg-1), which encodes a putative lytic transglycosylase (LT). The mutants are defective in LC001 binding, as revealed by direct visualization of the significantly reduced attachment of phage particles to the XH001 spontaneous mutants compared that to the wild type. Meanwhile, targeted deletion of ltg-1 produced a mutant that is defective in LC001 binding and resistant to LC001 infection even as surface-grown cells, while complementation of ltg-1 in the mutant background restored the LC001-sensitive phenotype. Intriguingly, similar expression levels of ltg-1 were observed in surface-grown and planktonic XH001, which displayed LC001-binding and nonbinding phenotypes, respectively. Furthermore, the overexpression of ltg-1 failed to confer an LC001-binding and -sensitive phenotype to planktonic XH001. Thus, our data suggested that rather than directly serving as a phage receptor, ltg-1-encoded LT may increase the accessibility of phage receptor, possibly via its enzymatic activity, by cleaving the peptidoglycan structure for better receptor exposure during peptidoglycan remodeling, a function that can be exploited by LC001 to facilitate infection. IMPORTANCE The evidence for the presence of a diverse and abundant phage population in the host-associated oral microbiome came largely from metagenomic analysis or the observation of virus-like particles within saliva/plaque samples, while the isolation of oral phage and investigation of their interaction with bacterial hosts are limited. Here, we report the isolation of LC001, the first lytic phage targeting oral Schaalia odontolytica. Our study suggested that LC001 may exploit the host bacterium-encoded lytic transglycosylase function to gain access to the receptor, thus facilitating its infection.}, } @article {pmid36000725, year = {2022}, author = {Guo, C and Yang, M and Jiang, B and Ye, C and Luo, L and Liu, Y and Huang, H and Mei, X and Zhu, Y and Deng, W and Du, F and He, X and Zhu, Y and Zhu, S}, title = {Moisture Controls the Suppression of Panax notoginseng Root Rot Disease by Indigenous Bacterial Communities.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0041822}, pmid = {36000725}, issn = {2379-5077}, mesh = {*Panax notoginseng/microbiology ; Soil Microbiology ; Plant Roots/microbiology ; Bacteria/genetics ; Soil ; }, abstract = {Harnessing indigenous soil microbial suppression is an emerging strategy for managing soilborne plant diseases. Soil moisture is a vital factor in soil microbiomes, but its role in the regulation of microbial suppression is poorly understood. Here, we investigated the correlation of root rot disease of Panax notoginseng with rhizosphere microbial communities mediated by soil moisture gradients from 55% to 100% field capacity (FC); then, we captured the disease-suppressive and disease-inductive microbiomes and validated their functions by a culture experiment with synthetic microbiotas containing keystone species. We found that proper soil moisture at 75% to 95% FC could maintain a disease-suppressive microbiome to alleviate root rot disease. However, extremely low or high soil moistures (>95% FC or <75% FC) could aggravate root rot disease by depleting the disease-suppressive microbiome while enriching the disease-inductive microbiome. Both the low-soil-moisture-enriched pathogen Monographella cucumerina and the high-soil-moisture-enriched pathogen Ilyonectria destructans could synergize with different disease-inductive microbiomes to aggravate disease. Metagenomic data confirmed that low- and high-moisture conditions suppressed antibiotic biosynthesis genes but enriched pathogenicity-related genes, resulting in a change in the soil state from disease suppressive to inductive. This study highlights the importance of soil moisture when indigenous microbial suppression is harnessed for disease control. IMPORTANCE Soilborne diseases pose a major problem in high-intensity agricultural systems due to the imbalance of microbial communities in soil, resulting in the buildup of soilborne pathogens. Harnessing indigenous soil microbial suppression is an emerging strategy for overcoming soilborne plant diseases. In this study, we showed that soil moisture is a key factor in balancing microbiome effects on root rot disease. Proper soil moisture management represent an effective approach to maintain microbial disease resistance by enriching disease-suppressive microbiomes. Conversely, moisture stresses may enrich for a disease-inductive microbiome and aid accumulation of host-specific soilborne pathogens threatening crop production. This work could provide a new strategy for sustainable control of soilborne diseases by enriching the indigenous disease-suppressive microbiome through soil moisture management.}, } @article {pmid36000724, year = {2022}, author = {Vieira, J and Jesudasen, S and Bringhurst, L and Sui, HY and McIver, L and Whiteson, K and Hanselmann, K and O'Toole, GA and Richards, CJ and Sicilian, L and Neuringer, I and Lai, PS}, title = {Supplemental Oxygen Alters the Airway Microbiome in Cystic Fibrosis.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0036422}, pmid = {36000724}, issn = {2379-5077}, support = {K23 ES023700/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Cystic Fibrosis/drug therapy ; *Hyperoxia ; *Microbiota/genetics ; Lung/microbiology ; Bacteria ; *Staphylococcal Infections ; Pseudomonas aeruginosa ; Oxygen/therapeutic use ; }, abstract = {Features of the airway microbiome in persons with cystic fibrosis (pwCF) are correlated with disease progression. Microbes have traditionally been classified for their ability to tolerate oxygen. It is unknown whether supplemental oxygen, a common medical intervention, affects the airway microbiome of pwCF. We hypothesized that hyperoxia significantly impacts the pulmonary microbiome in cystic fibrosis. In this study, we cultured spontaneously expectorated sputum from pwCF in artificial sputum medium under 21%, 50%, and 100% oxygen conditions using a previously validated model system that recapitulates microbial community composition in uncultured sputum. Culture aliquots taken at 24, 48, and 72 h, along with uncultured sputum, underwent shotgun metagenomic sequencing with absolute abundance values obtained with the use of spike-in bacteria. Raw sequencing files were processed using the bioBakery pipeline to determine changes in taxonomy, predicted function, antimicrobial resistance genes, and mobile genetic elements. Hyperoxia reduced absolute microbial load, species richness, and diversity. Hyperoxia reduced absolute abundance of specific microbes, including facultative anaerobes such as Rothia and some Streptococcus species, with minimal impact on canonical CF pathogens such as Pseudomonas aeruginosa and Staphylococcus aureus. The effect size of hyperoxia on predicted functional pathways was stronger than that on taxonomy. Large changes in microbial cooccurrence networks were noted. Hyperoxia exposure perturbs airway microbial communities in a manner well tolerated by key pathogens. Supplemental oxygen use may enable the growth of lung pathogens and should be further studied in the clinical setting. IMPORTANCE The airway microbiome in persons with cystic fibrosis (pwCF) is correlated with lung function and disease severity. Supplemental oxygen use is common in more advanced CF, yet its role in perturbing airway microbial communities is unknown. By culturing sputum samples from pwCF under normal and elevated oxygen conditions, we found that increased oxygen led to reduced total numbers and diversity of microbes, with relative sparing of common CF pathogens such as Pseudomonas aeruginosa and Staphylococcus aureus. Supplemental oxygen use may enable the growth of lung pathogens and should be further studied in the clinical setting.}, } @article {pmid35999570, year = {2022}, author = {Madrigal, P and Singh, NK and Wood, JM and Gaudioso, E and Hernández-Del-Olmo, F and Mason, CE and Venkateswaran, K and Beheshti, A}, title = {Machine learning algorithm to characterize antimicrobial resistance associated with the International Space Station surface microbiome.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {134}, pmid = {35999570}, issn = {2049-2618}, support = {U01 DA053941/DA/NIDA NIH HHS/United States ; R01 AI151059/AI/NIAID NIH HHS/United States ; }, mesh = {Algorithms ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Humans ; Machine Learning ; Metagenomics/methods ; *Microbiota/genetics ; *Spacecraft ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) has a detrimental impact on human health on Earth and it is equally concerning in other environments such as space habitat due to microgravity, radiation and confinement, especially for long-distance space travel. The International Space Station (ISS) is ideal for investigating microbial diversity and virulence associated with spaceflight. The shotgun metagenomics data of the ISS generated during the Microbial Tracking-1 (MT-1) project and resulting metagenome-assembled genomes (MAGs) across three flights in eight different locations during 12 months were used in this study. The objective of this study was to identify the AMR genes associated with whole genomes of 226 cultivable strains, 21 shotgun metagenome sequences, and 24 MAGs retrieved from the ISS environmental samples that were treated with propidium monoazide (PMA; viable microbes).

RESULTS: We have analyzed the data using a deep learning model, allowing us to go beyond traditional cut-offs based only on high DNA sequence similarity and extending the catalog of AMR genes. Our results in PMA treated samples revealed AMR dominance in the last flight for Kalamiella piersonii, a bacteria related to urinary tract infection in humans. The analysis of 226 pure strains isolated from the MT-1 project revealed hundreds of antibiotic resistance genes from many isolates, including two top-ranking species that corresponded to strains of Enterobacter bugandensis and Bacillus cereus. Computational predictions were experimentally validated by antibiotic resistance profiles in these two species, showing a high degree of concordance. Specifically, disc assay data confirmed the high resistance of these two pathogens to various beta-lactam antibiotics.

CONCLUSION: Overall, our computational predictions and validation analyses demonstrate the advantages of machine learning to uncover concealed AMR determinants in metagenomics datasets, expanding the understanding of the ISS environmental microbiomes and their pathogenic potential in humans. Video Abstract.}, } @article {pmid35998206, year = {2022}, author = {Li, J and George Markowitz, RH and Brooks, AW and Mallott, EK and Leigh, BA and Olszewski, T and Zare, H and Bagheri, M and Smith, HM and Friese, KA and Habibi, I and Lawrence, WM and Rost, CL and Lédeczi, Á and Eeds, AM and Ferguson, JF and Silver, HJ and Bordenstein, SR}, title = {Individuality and ethnicity eclipse a short-term dietary intervention in shaping microbiomes and viromes.}, journal = {PLoS biology}, volume = {20}, number = {8}, pages = {e3001758}, pmid = {35998206}, issn = {1545-7885}, support = {P30 DK058404/DK/NIDDK NIH HHS/United States ; R01 DK117144/DK/NIDDK NIH HHS/United States ; T32 HG008341/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Ethnicity ; Feces ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; *Microbiota/genetics ; Virome ; }, abstract = {Many diseases linked with ethnic health disparities associate with changes in microbial communities in the United States, but the causes and persistence of ethnicity-associated microbiome variation are not understood. For instance, microbiome studies that strictly control for diet across ethnically diverse populations are lacking. Here, we performed multiomic profiling over a 9-day period that included a 4-day controlled vegetarian diet intervention in a defined geographic location across 36 healthy Black and White females of similar age, weight, habitual diets, and health status. We demonstrate that individuality and ethnicity account for roughly 70% to 88% and 2% to 10% of taxonomic variation, respectively, eclipsing the effects a short-term diet intervention in shaping gut and oral microbiomes and gut viromes. Persistent variation between ethnicities occurs for microbial and viral taxa and various metagenomic functions, including several gut KEGG orthologs, oral carbohydrate active enzyme categories, cluster of orthologous groups of proteins, and antibiotic-resistant gene categories. In contrast to the gut and oral microbiome data, the urine and plasma metabolites tend to decouple from ethnicity and more strongly associate with diet. These longitudinal, multiomic profiles paired with a dietary intervention illuminate previously unrecognized associations of ethnicity with metagenomic and viromic features across body sites and cohorts within a single geographic location, highlighting the importance of accounting for human microbiome variation in research, health determinants, and eventual therapies. Trial Registration: ClinicalTrials.gov ClinicalTrials.gov Identifier: NCT03314194.}, } @article {pmid35995802, year = {2022}, author = {Craddock, HA and Godneva, A and Rothschild, D and Motro, Y and Grinstein, D and Lotem-Michaeli, Y and Narkiss, T and Segal, E and Moran-Gilad, J}, title = {Phenotypic correlates of the working dog microbiome.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {66}, pmid = {35995802}, issn = {2055-5008}, mesh = {Animals ; Dogs ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; *Microbiota ; Working Dogs ; }, abstract = {Dogs have a key role in law enforcement and military work, and research with the goal of improving working dog performance is ongoing. While there have been intriguing studies from lab animal models showing a potential connection between the gut microbiome and behavior or mental health there is a dearth of studies investigating the microbiome-behavior relationship in working dogs. The overall objective of this study was to characterize the microbiota of working dogs and to determine if the composition of the microbiota is associated with behavioral and performance outcomes. Freshly passed stools from each working canine (Total n = 134) were collected and subject to shotgun metagenomic sequencing using Illumina technology. Behavior, performance, and demographic metadata were collected. Descriptive statistics and prediction models of behavioral/phenotypic outcomes using gradient boosting classification based on Xgboost were used to study associations between the microbiome and outcomes. Regarding machine learning methodology, only microbiome features were used for training and predictors were estimated in cross-validation. Microbiome markers were statistically associated with motivation, aggression, cowardice/hesitation, sociability, obedience to one trainer vs many, and body condition score (BCS). When prediction models were developed based on machine learning, moderate predictive power was observed for motivation, sociability, and gastrointestinal issues. Findings from this study suggest potential gut microbiome markers of performance and could potentially advance care for working canines.}, } @article {pmid35995413, year = {2023}, author = {Wang, G and Li, S and Yan, Q and Guo, R and Zhang, Y and Chen, F and Tian, X and Lv, Q and Jin, H and Ma, X and Ma, Y}, title = {Optimization and evaluation of viral metagenomic amplification and sequencing procedures toward a genome-level resolution of the human fecal DNA virome.}, journal = {Journal of advanced research}, volume = {48}, number = {}, pages = {75-86}, pmid = {35995413}, issn = {2090-1224}, mesh = {Humans ; Reproducibility of Results ; *Virome ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; *Viruses/genetics ; DNA, Viral/genetics ; }, abstract = {INTRODUCTION: Viruses in the human gut have been linked to health and disease. Deciphering the gut virome is dependent on metagenomic sequencing of the virus-like particles (VLPs) purified from the fecal specimens. A major limitation of conventional viral metagenomic sequencing is the low recoverability of viral genomes from the metagenomic dataset.

OBJECTIVES: To develop an optimal method for viral amplification and metagenomic sequencing for maximizing the recovery of viral genomes.

METHODS: We performed parallel virus enrichment and DNA extraction to generate ∼ 30 viral DNA samples from each of 5 fresh fecal specimens and conducted the experiments including 1) optimizing the cycle number for high-fidelity enzyme-based PCR amplification, 2) evaluating the reproducibility of the optimally whole viral metagenomic experimental process, 3) evaluating the reliability of multiple displacement amplification (MDA), 4) testing the capability of long-read sequencing for improving viral metagenomic assembly, and 5) comparing the differences between viral metagenomic and bulk metagenomic approaches.

RESULTS: Our results revealed that the optimal cycle number for PCR amplification is 15. We verified the reliability of MDA and the effectiveness of long-read sequencing. Based on our optimized results, we generated 151 high-quality viruses using the dataset combined from short-read and long-read sequencing. Genomic analysis of these viruses found that most (60.3%) of them were previously unknown and showed a remarkable diversity of viral functions, especially the existence of 206 viral auxiliary metabolic genes. Finally, we uncovered significant differences in the efficiency and coverage of viral identification between viral metagenomic and bulk metagenomic approaches.

CONCLUSIONS: Our study demonstrates the potential of optimized experiment and sequencing strategies in uncovering viral genomes from fecal specimens, which will facilitate future research about the genome-level characterization of complex viral communities.}, } @article {pmid35993719, year = {2022}, author = {Baker, JL}, title = {Using Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0049122}, pmid = {35993719}, issn = {2379-5077}, support = {K99 DE029228/DE/NIDCR NIH HHS/United States ; K99-DE029228//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; }, mesh = {Humans ; Sequence Analysis, DNA/methods ; *Nanopore Sequencing/methods ; Saliva ; Genome, Bacterial/genetics ; *Microbiota/genetics ; Bacteria/genetics ; }, abstract = {Obtaining complete, high-quality reference genomes is essential to the study of any organism. Recent advances in nanopore sequencing, as well as genome assembly and analysis methods, have made it possible to obtain complete bacterial genomes from metagenomic (i.e., multispecies) samples, including those from the human microbiome. In this study, methods are presented to obtain complete bacterial genomes from human saliva using complementary Oxford Nanopore (ONT) and Illumina sequencing. Applied to 3 human saliva samples, these methods resulted in 11 complete bacterial genomes: 3 Saccharibacteria clade G6 (also known as Ca. Nanogingivalaceae HMT-870), 1 Saccharibacteria clade G1 HMT-348, 2 Rothia mucilaginosa, 2 Actinomyces graevenitzii, 1 Mogibacterium diversum, 1 Lachnospiraceae HMT-096, and 1 Lancefieldella parvula; and one circular chromosome of Ruminococcaceae HMT-075 (which likely has at least 2 chromosomes). The 4 Saccharibacteria genomes, as well as the Actinomyces graeventizii genomes, represented the first complete genomes from their respective bacterial taxa. Aside from the complete genomes, the assemblies contained 147 contigs of over 500,000 bp each and thousands of smaller contigs, together representing a myriad of additional draft genomes including many which are likely nearly complete. The complete genomes enabled highly accurate pangenome analysis, which identified unique and missing features of each genome compared to its closest relatives with complete genomes available in public repositories. These features provide clues as to the lifestyle and ecological role of these bacteria within the human oral microbiota, which will be particularly useful in designing future studies of the taxa that have never been isolated or cultivated. IMPORTANCE Obtaining complete and accurate genomes is crucial to the study of any organism. Previously, obtaining complete genomes of bacteria, including those of the human microbiome, frequently required isolation of the organism, as well as low-throughput, manual sequencing methods to resolve repeat regions. Advancements in long-read sequencing technologies, including Oxford Nanopore (ONT), have made it possible to obtain complete, closed bacterial genomes from metagenomic samples. This study reports methods to obtain complete genomes from the human oral microbiome using complementary ONT and Illumina sequencing of saliva samples. Eleven complete genomes were obtained from 3 human saliva samples, with genomes of Saccharibacteria HMT-870, Saccharibacteria HMT-348, and Actinomyces graeventzii being the first complete genomes from their respective taxa. Obtaining complete bacterial genomes in a high-throughput manner will help illuminate the metabolic and ecological roles of important members of the human microbiota, particularly those that have remained recalcitrant to isolation and cultivation.}, } @article {pmid35993708, year = {2022}, author = {Miranda, K and Weigel, BL and Fogarty, EC and Veseli, IA and Giblin, AE and Eren, AM and Pfister, CA}, title = {The Diversity and Functional Capacity of Microbes Associated with Coastal Macrophytes.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0059222}, pmid = {35993708}, issn = {2379-5077}, mesh = {*Metagenome/genetics ; *Microbiota ; Rhizosphere ; Nitrogen/metabolism ; Sulfur/metabolism ; }, abstract = {Coastal marine macrophytes exhibit some of the highest rates of primary productivity in the world. They have been found to host a diverse set of microbes, many of which may impact the biology of their hosts through metabolisms that are unique to microbial taxa. Here, we characterized the metabolic functions of macrophyte-associated microbial communities using metagenomes collected from 2 species of kelp (Laminaria setchellii and Nereocystis luetkeana) and 3 marine angiosperms (Phyllospadix scouleri, P. serrulatus, and Zostera marina), including the rhizomes of two surfgrass species (Phyllospadix spp.), the seagrass Zostera marina, and the sediments surrounding P. scouleri and Z. marina. Using metagenomic sequencing, we describe 63 metagenome-assembled genomes (MAGs) that potentially benefit from being associated with macrophytes and may contribute to macrophyte fitness through their metabolic activity. Host-associated metagenomes contained genes for the use of dissolved organic matter from hosts and vitamin (B1, B2, B7, B12) biosynthesis in addition to a range of nitrogen and sulfur metabolisms that recycle dissolved inorganic nutrients into forms more available to the host. The rhizosphere of surfgrass and seagrass contained genes for anaerobic microbial metabolisms, including nifH genes associated with nitrogen fixation, despite residing in a well-mixed and oxygenated environment. The range of oxygen environments engineered by macrophytes likely explains the diversity of both oxidizing and reducing microbial metabolisms and contributes to the functional capabilities of microbes and their influences on carbon and nitrogen cycling in nearshore ecosystems. IMPORTANCE Kelps, seagrasses, and surfgrasses are ecosystem engineers on rocky shorelines, where they show remarkably high levels of primary production. Through analysis of their associated microbial communities, we found a variety of microbial metabolisms that may benefit the host, including nitrogen metabolisms, sulfur oxidation, and the production of B vitamins. In turn, these microbes have the genetic capabilities to assimilate the dissolved organic compounds released by their macrophyte hosts. We describe a range of oxygen environments associated with surfgrass, including low-oxygen microhabitats in their rhizomes that host genes for nitrogen fixation. The tremendous productivity of coastal seaweeds and seagrasses is likely due in part to the activities of associated microbes, and an increased understanding of these associations is needed.}, } @article {pmid35991836, year = {2022}, author = {Hu, J and Yang, J and Chen, L and Meng, X and Zhang, X and Li, W and Li, Z and Huang, G}, title = {Alterations of the Gut Microbiome in Patients With Pituitary Adenoma.}, journal = {Pathology oncology research : POR}, volume = {28}, number = {}, pages = {1610402}, pmid = {35991836}, issn = {1532-2807}, mesh = {*Adenoma ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics ; *Pituitary Neoplasms ; }, abstract = {Pituitary adenoma (PA) includes invasive pituitary adenoma (IPA) and noninvasive pituitary adenoma (NIPA), which are associated with the endocrine system. The gut microbiome plays an important role in human metabolism, but the association between the gut microbiome and pituitary adenoma remains unclear. A total of 44 subjects were enrolled in this study. Of these, 29 PA patients were further divided into IPA patients (n = 13) and NIPA patients (n = 16), while 15 healthy age-matched subjects were defined as control subjects. We collected faecal samples and characterized the gut microbial profiles by metagenomic sequencing using the Illumina X-ten platform. PLS-DA showed different microbial clusters among the three groups, and slightly different microbial ecological networks were observed. LEfSe analysis revealed significant alterations in the microbial community among PA patients. In particular, the enrichment of Clostridium innocuum, along with the reduced abundance of Oscillibacter sp. 57_20 and Fusobacterium mortiferum, were observed both in the IPA and NIPA groups compared to the control group. Moreover, PA patients could be effectively classified based on these bacteria using a support vector machine algorithm. In summary, this study demonstrated significant differences in the gut microbiome between PA patients and healthy controls. Future mechanistic experiments are needed to determine whether such alterations are a cause or consequence of pituitary adenoma.}, } @article {pmid35989412, year = {2022}, author = {Thakur, SS and Lone, AR and Yellaboina, S and Tambat, S and Yadav, AN and Jain, SK and Yadav, S}, title = {Metagenomic Insights into the Gut Microbiota of Eudrilus eugeniae (Kinberg) and Its Potential Roles in Agroecosystem.}, journal = {Current microbiology}, volume = {79}, number = {10}, pages = {295}, pmid = {35989412}, issn = {1432-0991}, mesh = {*Actinobacteria/genetics ; Animals ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; *Microbiota ; *Oligochaeta/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; Soil ; }, abstract = {Gut microbiomes, a consortium of microorganisms that live in the animal gut, are highly engineered microbial communities. It makes a major contribution to digestive health, metabolism management, and the development of a strong immune system in the host. The present study was taken up to answer the long-running question about the existence of truly indigenous microflora of the epigeic earthworm gut. This is due to the general difficulties of culturing many of the microorganisms found in soil or earthworms' gut. Keeping this fact in a view, the metagenomics approach using 16S rRNA marker gene incorporated with amplicon-based sequencing was used to explore microbiota of commercially overriding, diversely fed epigeic earthworm Eudrilus eugeniae (Kinberg) in three varied habitats viz., artificial soil (AS), organic agricultural farm soil (OAFS) and conventional agriculture farm soil (CAFS). There are predominant bacteria that belong to different phyla such as Proteobacteria (29.72-76.81%), Actinobacteria (11.06-34.42%), Firmicutes (6.02-19.81%), and Bacteroidetes (2.40-9.22%) present in the gut of E. eugeniae. The alpha diversity (Observed species, Chao1, ACE, Shannon, Simpson, and Fisher alpha) indices showed that OAFS had significantly higher alpha diversity than AS and CAFS groups. The core microbiota analysis showed that OAFS and AS groups had a relatively similar bacterial panel in comparison to the CAFS group. Various statistical tools i.e. MetagenomeSeq, LEfSe, and Random Forest analysis were performed and the findings demonstrated prevalence of the most significant bacterial genera; Aeromonas, Gaiella, and Burkholderia in CAFS group. Nonetheless, in AS and OAFS groups, the common existence of Anaerosporobacter and Aquihabitans were found respectively. Metagenomic functional prediction revealed that earthworms' gut microbial communities were actively involved in multiple organic and xenobiotics compound degradation-related pathways. This is the first research to use high-throughput 16S rRNA gene amplicon sequencing to show the gut microbiota of E. eugeniae in diverse agricultural systems. The findings suggest the configuration of the gut microbiota of earthworms and its potential role in the soil ecosystem depends on the microbial communities of the soil.}, } @article {pmid35988549, year = {2022}, author = {Alcazar, CG and Paes, VM and Shao, Y and Oesser, C and Miltz, A and Lawley, TD and Brocklehurst, P and Rodger, A and Field, N}, title = {The association between early-life gut microbiota and childhood respiratory diseases: a systematic review.}, journal = {The Lancet. Microbe}, volume = {3}, number = {11}, pages = {e867-e880}, pmid = {35988549}, issn = {2666-5247}, support = {/WT_/Wellcome Trust/United Kingdom ; WT101169MA/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Infant ; Humans ; Infant, Newborn ; Child, Preschool ; Child ; Adolescent ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Bacteria/genetics ; *Asthma/epidemiology ; *Respiration Disorders/complications ; *Respiratory Tract Infections/epidemiology ; }, abstract = {Data from animal models suggest a role of early-life gut microbiota in lung immune development, and in establishing susceptibility to respiratory infections and asthma in humans. This systematic review summarises the association between infant (ages 0-12 months) gut microbiota composition measured by genomic sequencing, and childhood (ages 0-18 years) respiratory diseases (ie, respiratory infections, wheezing, or asthma). Overall, there was evidence that low α-diversity and relative abundance of particular gut-commensal bacteria genera (Bifidobacterium, Faecalibacterium, Ruminococcus, and Roseburia) are associated with childhood respiratory diseases. However, results were inconsistent and studies had important limitations, including insufficient characterisation of bacterial taxa to species level, heterogeneous outcome definitions, residual confounding, and small sample sizes. Large longitudinal studies with stool sampling during the first month of life and shotgun metagenomic approaches to improve bacterial and fungal taxa resolution are needed. Standardising follow-up times and respiratory disease definitions and optimising causal statistical approaches might identify targets for primary prevention of childhood respiratory diseases.}, } @article {pmid35988536, year = {2022}, author = {Azimi, M and Keshavarz Shahbaz, S and Mansourabadi, AH and Mohamed Khosroshahi, L and Pourkalhor, S and Rezakhani, M and Masoumi, F}, title = {Intestinal Microbiota: Novel Personalized Cancer Immunotherapy in Colorectal Cancer.}, journal = {International archives of allergy and immunology}, volume = {183}, number = {11}, pages = {1147-1165}, doi = {10.1159/000525695}, pmid = {35988536}, issn = {1423-0097}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/therapy/diagnosis/pathology ; Dysbiosis/therapy ; *Microbiota ; Immunotherapy ; }, abstract = {The human colon harbors a diverse array of microorganisms that play fundamental roles in colorectal cancer (CRC). Increasing evidence indicates that dysbiosis of the intestinal microbiome has been associated with the development of CRC. Interaction between host genetics, intestinal microbiota, and lifestyle is well-indicated in the influence, prevention, and treatment of CRC. Various microbiome compositions have reported anticancer and/or anti-inflammatory properties. The presence of our microbiota is integral to our development, but a change in its composition can often lead to adverse effects, increasing the propensity for serious diseases like cancers. Recently, molecular detection and metabolomic techniques have increased our knowledge of the role of microbiota in promoting tumorigenesis. Dietary interventions may be appropriate to regulate the growth of beneficial microbiota in the gut. Metagenomic approaches along with immunology and metabolomics will obvious a new path for the treatment of CRC. In this study, we summarized recent advances in understanding the mechanisms involved in microbiota-related colorectal carcinoma, based on evidence from immunotherapy studies.}, } @article {pmid35987213, year = {2022}, author = {Suez, J and Cohen, Y and Valdés-Mas, R and Mor, U and Dori-Bachash, M and Federici, S and Zmora, N and Leshem, A and Heinemann, M and Linevsky, R and Zur, M and Ben-Zeev Brik, R and Bukimer, A and Eliyahu-Miller, S and Metz, A and Fischbein, R and Sharov, O and Malitsky, S and Itkin, M and Stettner, N and Harmelin, A and Shapiro, H and Stein-Thoeringer, CK and Segal, E and Elinav, E}, title = {Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance.}, journal = {Cell}, volume = {185}, number = {18}, pages = {3307-3328.e19}, doi = {10.1016/j.cell.2022.07.016}, pmid = {35987213}, issn = {1097-4172}, mesh = {Adult ; Animals ; Aspartame/pharmacology ; Blood Glucose ; Humans ; Mice ; *Microbiota ; *Non-Nutritive Sweeteners/analysis/pharmacology ; Saccharin/pharmacology ; }, abstract = {Non-nutritive sweeteners (NNS) are commonly integrated into human diet and presumed to be inert; however, animal studies suggest that they may impact the microbiome and downstream glycemic responses. We causally assessed NNS impacts in humans and their microbiomes in a randomized-controlled trial encompassing 120 healthy adults, administered saccharin, sucralose, aspartame, and stevia sachets for 2 weeks in doses lower than the acceptable daily intake, compared with controls receiving sachet-contained vehicle glucose or no supplement. As groups, each administered NNS distinctly altered stool and oral microbiome and plasma metabolome, whereas saccharin and sucralose significantly impaired glycemic responses. Importantly, gnotobiotic mice conventionalized with microbiomes from multiple top and bottom responders of each of the four NNS-supplemented groups featured glycemic responses largely reflecting those noted in respective human donors, which were preempted by distinct microbial signals, as exemplified by sucralose. Collectively, human NNS consumption may induce person-specific, microbiome-dependent glycemic alterations, necessitating future assessment of clinical implications.}, } @article {pmid35986714, year = {2023}, author = {Luo, M and Ji, Y and Warton, D and Yu, DW}, title = {Extracting abundance information from DNA-based data.}, journal = {Molecular ecology resources}, volume = {23}, number = {1}, pages = {174-189}, pmid = {35986714}, issn = {1755-0998}, support = {QYZDY-SSW-SMC024//Key Research Program of Frontier Sciences, CAS/ ; //University of Chinese Academy of Sciences/ ; //Kunming Institute of Zoology/ ; GREKF19-01//State Key Laboratory of Genetic Resources and Evolution/ ; GREKF20-01//State Key Laboratory of Genetic Resources and Evolution/ ; GREKF21-01//State Key Laboratory of Genetic Resources and Evolution/ ; //University of East Anglia/ ; SMC024//Chinese Academy of Sciences/ ; sCom//idiv.de/ ; XDA20050202//Strategic Priority Research Program, Chinese Academy of Sciences/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Metagenomics/methods ; DNA/genetics ; Biodiversity ; }, abstract = {The accurate extraction of species-abundance information from DNA-based data (metabarcoding, metagenomics) could contribute usefully to diet analysis and food-web reconstruction, the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the inference of false positives and negatives. However, multiple sources of bias and noise in sampling and processing combine to inject error into DNA-based data sets. To understand how to extract abundance information, it is useful to distinguish two concepts. (i) Within-sample across-species quantification describes relative species abundances in one sample. (ii) Across-sample within-species quantification describes how the abundance of each individual species varies from sample to sample, such as over a time series, an environmental gradient or different experimental treatments. First, we review the literature on methods to recover across-species abundance information (by removing what we call "species pipeline biases") and within-species abundance information (by removing what we call "pipeline noise"). We argue that many ecological questions can be answered with just within-species quantification, and we therefore demonstrate how to use a "DNA spike-in" to correct for pipeline noise and recover within-species abundance information. We also introduce a model-based estimator that can be used on data sets without a physical spike-in to approximate and correct for pipeline noise.}, } @article {pmid35986393, year = {2022}, author = {Yang, L and Chen, J}, title = {A comprehensive evaluation of microbial differential abundance analysis methods: current status and potential solutions.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {130}, pmid = {35986393}, issn = {2049-2618}, support = {R01 GM144351/GM/NIGMS NIH HHS/United States ; R21 HG011662/HG/NHGRI NIH HHS/United States ; }, mesh = {Computer Simulation ; Data Analysis ; *Microbiota ; }, abstract = {BACKGROUND: Differential abundance analysis (DAA) is one central statistical task in microbiome data analysis. A robust and powerful DAA tool can help identify highly confident microbial candidates for further biological validation. Numerous DAA tools have been proposed in the past decade addressing the special characteristics of microbiome data such as zero inflation and compositional effects. Disturbingly, different DAA tools could sometimes produce quite discordant results, opening to the possibility of cherry-picking the tool in favor of one's own hypothesis. To recommend the best DAA tool or practice to the field, a comprehensive evaluation, which covers as many biologically relevant scenarios as possible, is critically needed.

RESULTS: We performed by far the most comprehensive evaluation of existing DAA tools using real data-based simulations. We found that DAA methods explicitly addressing compositional effects such as ANCOM-BC, Aldex2, metagenomeSeq (fitFeatureModel), and DACOMP did have improved performance in false-positive control. But they are still not optimal: type 1 error inflation or low statistical power has been observed in many settings. The recent LDM method generally had the best power, but its false-positive control in the presence of strong compositional effects was not satisfactory. Overall, none of the evaluated methods is simultaneously robust, powerful, and flexible, which makes the selection of the best DAA tool difficult. To meet the analysis needs, we designed an optimized procedure, ZicoSeq, drawing on the strength of the existing DAA methods. We show that ZicoSeq generally controlled for false positives across settings, and the power was among the highest. Application of DAA methods to a large collection of real datasets revealed a similar pattern observed in simulation studies.

CONCLUSIONS: Based on the benchmarking study, we conclude that none of the existing DAA methods evaluated can be applied blindly to any real microbiome dataset. The applicability of an existing DAA method depends on specific settings, which are usually unknown a priori. To circumvent the difficulty of selecting the best DAA tool in practice, we design ZicoSeq, which addresses the major challenges in DAA and remedies the drawbacks of existing DAA methods. ZicoSeq can be applied to microbiome datasets from diverse settings and is a useful DAA tool for robust microbiome biomarker discovery. Video Abstract.}, } @article {pmid35986253, year = {2022}, author = {Berckx, F and Nguyen, TV and Bandong, CM and Lin, HH and Yamanaka, T and Katayama, S and Wibberg, D and Blom, J and Kalinowski, J and Tateno, M and Simbahan, J and Liu, CT and Brachmann, A and Pawlowski, K}, title = {A tale of two lineages: how the strains of the earliest divergent symbiotic Frankia clade spread over the world.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {602}, pmid = {35986253}, issn = {1471-2164}, mesh = {*Frankia/genetics ; *Magnoliopsida/genetics ; Metagenome ; Nitrogen Fixation ; Phylogeny ; Plants/genetics ; Symbiosis/genetics ; }, abstract = {It is currently assumed that around 100 million years ago, the common ancestor to the Fabales, Fagales, Rosales and Cucurbitales in Gondwana, developed a root nodule symbiosis with a nitrogen-fixing bacterium. The symbiotic trait evolved first in Frankia cluster-2; thus, strains belonging to this cluster are the best extant representatives of this original symbiont. Most cluster-2 strains could not be cultured to date, except for Frankia coriariae, and therefore many aspects of the symbiosis are still elusive. Based on phylogenetics of cluster-2 metagenome-assembled genomes (MAGs), it has been shown that the genomes of strains originating in Eurasia are highly conserved. These MAGs are more closely related to Frankia cluster-2 in North America than to the single genome available thus far from the southern hemisphere, i.e., from Papua New Guinea.To unravel more biodiversity within Frankia cluster-2 and predict routes of dispersal from Gondwana, we sequenced and analysed the MAGs of Frankia cluster-2 from Coriaria japonica and Coriaria intermedia growing in Japan, Taiwan and the Philippines. Phylogenetic analyses indicate there is a clear split within Frankia cluster-2, separating a continental from an island lineage. Presumably, these lineages already diverged in Gondwana.Based on fossil data on the host plants, we propose that these two lineages dispersed via at least two routes. While the continental lineage reached Eurasia together with their host plants via the Indian subcontinent, the island lineage spread towards Japan with an unknown host plant.}, } @article {pmid35986094, year = {2022}, author = {Li, Z and Wang, X and Zhang, Y and Yu, Z and Zhang, T and Dai, X and Pan, X and Jing, R and Yan, Y and Liu, Y and Gao, S and Li, F and Huang, Y and Tian, J and Yao, J and Xing, X and Shi, T and Ning, J and Yao, B and Huang, H and Jiang, Y}, title = {Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates.}, journal = {The ISME journal}, volume = {16}, number = {12}, pages = {2775-2787}, pmid = {35986094}, issn = {1751-7370}, mesh = {Animals ; *Rumen/microbiology ; Phylogeny ; Biomass ; *Ciliophora/genetics ; Genomics ; Bacteria/genetics ; Fungi ; }, abstract = {Understanding the biodiversity and genetics of gut microbiomes has important implications for host physiology and industrial enzymes, whereas most studies have been focused on bacteria and archaea, and to a lesser extent on fungi and viruses. One group, still underexplored and elusive, is ciliated protozoa, despite its importance in shaping microbiota populations. Integrating single-cell sequencing and an assembly-and-identification pipeline, we acquired 52 high-quality ciliate genomes of 22 rumen morphospecies from 11 abundant morphogenera. With these genomes, we resolved the taxonomic and phylogenetic framework that revised the 22 morphospecies into 19 species spanning 13 genera and reassigned the genus Dasytricha from Isotrichidae to a new family Dasytrichidae. Comparative genomic analyses revealed that extensive horizontal gene transfers and gene family expansion provided rumen ciliate species with a broad array of carbohydrate-active enzymes (CAZymes) to degrade all major kinds of plant and microbial carbohydrates. In particular, the genomes of Diplodiniinae and Ophryoscolecinae species encode as many CAZymes as gut fungi, and ~80% of their degradative CAZymes act on plant cell-wall. The activities of horizontally transferred cellulase and xylanase of ciliates were experimentally verified and were 2-9 folds higher than those of the inferred corresponding bacterial donors. Additionally, the new ciliate dataset greatly facilitated rumen metagenomic analyses by allowing ~12% of the metagenomic sequencing reads to be classified as ciliate sequences.}, } @article {pmid35985261, year = {2022}, author = {Jha, V and Bombaywala, S and Purohit, H and Dafale, NA}, title = {Differential colonization and functioning of microbial community in response to phosphate levels.}, journal = {Journal of environmental management}, volume = {321}, number = {}, pages = {115856}, doi = {10.1016/j.jenvman.2022.115856}, pmid = {35985261}, issn = {1095-8630}, mesh = {Metagenome ; Metagenomics ; *Microbiota/genetics ; Phosphates ; Proteobacteria/genetics ; Soil Microbiology ; }, abstract = {Microbes play a major role in phosphate cycling and regulate its availability in various environments. The metagenomic study highlights the microbial community divergence and interplay of phosphate metabolism functional genes in response to phosphate rich (100 mgL[-1]), limiting (25 mgL[-1]), and stressed (5 mgL[-1]) conditions at lab-scale bioreactor. Total five core phyla were found responsive toward different phosphate (Pi) levels. However, major variations were observed in Proteobacteria and Actinobacteria with 33-81% and 5-56% relative abundance, respectively. Canonical correspondence analysis reflects the colonization of Sinorhizobium (0.8-4%), Mesorhizobium (1-4%), Rhizobium (0.5-3%) in rich condition whereas, Pseudomonas (1-2%), Rhodococcus (0.2-2%), Flavobacterium (0.2-1%) and Streptomyces (0.3-4%) colonized in limiting and stress condition. The functional profiling demonstrates that Pi limiting and stress condition subjected biomass were characterized by abundant PQQ-Glucose dehydrogenase, alkaline phosphatase, 5'-nucleotidase, and phospholipases C genes. The finding implies that the major abundant genera belonging to phosphate solubilization enriched in limiting/stressed conditions decide the functional turnover by modulating the metabolic flexibility for Pi cycling. The study gives a better insight into intrinsic ecological responsiveness mediated by microbial communities in different Pi conditions that would help to design the microbiome according to the soil phosphate condition. Furthermore, this information assists in sustainably maintaining the ecological balance by omitting excessive chemical fertilizers and eutrophication.}, } @article {pmid35983330, year = {2022}, author = {de la Haba, RR and Antunes, A and Hedlund, BP}, title = {Editorial: Extremophiles: Microbial genomics and taxogenomics.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {984632}, pmid = {35983330}, issn = {1664-302X}, } @article {pmid35982311, year = {2022}, author = {Le, HH and Lee, MT and Besler, KR and Comrie, JMC and Johnson, EL}, title = {Characterization of interactions of dietary cholesterol with the murine and human gut microbiome.}, journal = {Nature microbiology}, volume = {7}, number = {9}, pages = {1390-1403}, pmid = {35982311}, issn = {2058-5276}, support = {R35 GM138281/GM/NIGMS NIH HHS/United States ; S10 OD018516/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteroides ; Cholesterol ; Cholesterol, Dietary ; Dietary Fats ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Microbiota ; Sulfotransferases ; }, abstract = {Consumption of dietary lipids, such as cholesterol, modulates the gut microbiome with consequences for host health through the production of microbiome-derived metabolites. Despite the implications for host metabolism, a limited number of specific interactions of the gut microbiome with diet-derived lipids have been characterized. This is partially because obtaining species-level resolution of the responsible taxa can be challenging and additional approaches are needed to identify health-relevant metabolites produced from cholesterol-microbiome interactions. Here we performed bio-orthogonal labelling sort sequence spectrometry, a click chemistry based workflow, to profile cholesterol-specific host-microbe interactions. Mice were exposed to an alkyne-functionalized variant of cholesterol and 16S ribosomal RNA gene amplicon sequencing of faecal samples identified diet-derived cholesterol-interacting microbes from the genera Bacteroides, Bifidobacterium, Enterococcus and Parabacteroides. Shotgun metagenomic analysis provided species-level resolution of diet-derived cholesterol-interacting microbes with enrichment of bile acid-like and sulfotransferase-like activities. Using untargeted metabolomics, we identify that cholesterol is converted to cholesterol sulfate in a Bacteroides-specific manner via the enzyme BT_0416. Mice monocolonized with Bacteroides thetaiotaomicron lacking Bt_0416 showed altered host cholesterol and cholesterol sulfate compared with wild-type mice, identifying a previously uncharacterized microbiome-transformation of cholesterol and a mechanism for microbiome-dependent contributions to host phenotype. Moreover, identification of a cholesterol-responsive sulfotransferase in Bacteroides suggests diet-dependent mechanisms for altering microbiome-specific cholesterol metabolism. Overall, our work identifies numerous cholesterol-interacting microbes with implications for more precise microbiome-conscious regulation of host cholesterol homeostasis.}, } @article {pmid35980774, year = {2022}, author = {Kim, SY and Park, E and Lim, WJ and In Kim, S and Jeon, SW and Chang, Y and Ryu, S and Kim, HL and Kim, HN}, title = {Association Between Gut Microbiota and Depressive Symptoms: A Cross-Sectional Population-Based Study in South Korea.}, journal = {Psychosomatic medicine}, volume = {84}, number = {7}, pages = {757-765}, doi = {10.1097/PSY.0000000000001111}, pmid = {35980774}, issn = {1534-7796}, mesh = {Adult ; Cross-Sectional Studies ; Depression/epidemiology/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/genetics ; Republic of Korea/epidemiology ; }, abstract = {OBJECTIVE: This study aimed to investigate the association between gut microbiota and depressive symptoms in a large population cohort of Korean adults.

METHODS: Overall, 1238 participants were included in the study. Participants were categorized into depressed or non-depressed groups, based on the depressive symptoms reported on the Center for Epidemiologic Studies Rating Scale for Depression, with a cutoff score of 16, and their fecal microbiota was profiled using 16S ribosomal RNA gene sequencing. Several alpha and beta diversity measures were also estimated. The association between depressive symptoms and gut microbiota was analyzed using generalized linear models. The inferred function of the metagenomes was compared between the two groups.

RESULTS: There were no consistent differences in alpha and beta diversity between the depressed and non-depressed groups. However, the continuous measure of depressive symptoms was inversely associated with one of four measures of alpha diversity (Shannon's diversity, p = .021). We also found a substantial difference between the depressed and non-depressed groups in the Bray-Curtis dissimilarity among the four beta diversity indices (p = .004). Participants whose depressive symptoms exceeded a clinical cutoff score had a lower relative abundance of the genus Faecalibacterium when compared with controls (coefficient = -0.025, q = 0.047). However, the depressed group had a significantly higher abundance of the genus Oscillospira than did the non-depressed group (coefficient = 0.002, q = 0.023).

CONCLUSIONS: Our findings contribute to the identification of potential relationships between the gut microbiota and depressive symptoms and provide useful insights for developing microbiota-based interventions for patients with depressive symptoms.}, } @article {pmid35979944, year = {2022}, author = {Hempel, CA and Wright, N and Harvie, J and Hleap, JS and Adamowicz, SJ and Steinke, D}, title = {Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments.}, journal = {Nucleic acids research}, volume = {50}, number = {16}, pages = {9279-9293}, pmid = {35979944}, issn = {1362-4962}, mesh = {*Metagenomics/methods ; *Microbiota/genetics ; Sequence Analysis, RNA ; High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Metagenomics and total RNA sequencing (total RNA-Seq) have the potential to improve the taxonomic identification of diverse microbial communities, which could allow for the incorporation of microbes into routine ecological assessments. However, these target-PCR-free techniques require more testing and optimization. In this study, we processed metagenomics and total RNA-Seq data from a commercially available microbial mock community using 672 data-processing workflows, identified the most accurate data-processing tools, and compared their microbial identification accuracy at equal and increasing sequencing depths. The accuracy of data-processing tools substantially varied among replicates. Total RNA-Seq was more accurate than metagenomics at equal sequencing depths and even at sequencing depths almost one order of magnitude lower than those of metagenomics. We show that while data-processing tools require further exploration, total RNA-Seq might be a favorable alternative to metagenomics for target-PCR-free taxonomic identifications of microbial communities and might enable a substantial reduction in sequencing costs while maintaining accuracy. This could be particularly an advantage for routine ecological assessments, which require cost-effective yet accurate methods, and might allow for the incorporation of microbes into ecological assessments.}, } @article {pmid35978381, year = {2022}, author = {Chiciudean, I and Russo, G and Bogdan, DF and Levei, EA and Faur, L and Hillebrand-Voiculescu, A and Moldovan, OT and Banciu, HL}, title = {Competition-cooperation in the chemoautotrophic ecosystem of Movile Cave: first metagenomic approach on sediments.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {44}, pmid = {35978381}, issn = {2524-6372}, abstract = {BACKGROUND: Movile Cave (SE Romania) is a chemoautotrophically-based ecosystem fed by hydrogen sulfide-rich groundwater serving as a primary energy source analogous to the deep-sea hydrothermal ecosystems. Our current understanding of Movile Cave microbiology has been confined to the sulfidic water and its proximity, as most studies focused on the water-floating microbial mat and planktonic accumulations likely acting as the primary production powerhouse of this unique subterranean ecosystem. By employing comprehensive genomic-resolved metagenomics, we questioned the spatial variation, chemoautotrophic abilities, ecological interactions and trophic roles of Movile Cave's microbiome thriving beyond the sulfidic-rich water.

RESULTS: A customized bioinformatics pipeline led to the recovery of 106 high-quality metagenome-assembled genomes from 7 cave sediment metagenomes. Assemblies' taxonomy spanned 19 bacterial and three archaeal phyla with Acidobacteriota, Chloroflexota, Proteobacteria, Planctomycetota, Ca. Patescibacteria, Thermoproteota, Methylomirabilota, and Ca. Zixibacteria as prevalent phyla. Functional gene analyses predicted the presence of CO2 fixation, methanotrophy, sulfur and ammonia oxidation in the explored sediments. Species Metabolic Coupling Analysis of metagenome-scale metabolic models revealed the highest competition-cooperation interactions in the sediments collected away from the water. Simulated metabolic interactions indicated autotrophs and methanotrophs as major donors of metabolites in the sediment communities. Cross-feeding dependencies were assumed only towards 'currency' molecules and inorganic compounds (O2, PO4[3-], H[+], Fe[2+], Cu[2+]) in the water proximity sediment, whereas hydrogen sulfide and methanol were assumedly traded exclusively among distant gallery communities.

CONCLUSIONS: These findings suggest that the primary production potential of Movile Cave expands way beyond its hydrothermal waters, enhancing our understanding of the functioning and ecological interactions within chemolithoautotrophically-based subterranean ecosystems.}, } @article {pmid35974020, year = {2022}, author = {Feng, P and Yang, J and Zhao, S and Ling, Z and Han, R and Wu, Y and Salama, ES and Kakade, A and Khan, A and Jin, W and Zhang, W and Jeon, BH and Fan, J and Liu, M and Mamtimin, T and Liu, P and Li, X}, title = {Human supplementation with Pediococcus acidilactici GR-1 decreases heavy metals levels through modifying the gut microbiota and metabolome.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {63}, pmid = {35974020}, issn = {2055-5008}, mesh = {Animals ; Copper ; *Gastrointestinal Microbiome ; Humans ; Metabolome ; *Metals, Heavy ; Mice ; *Pediococcus acidilactici ; *Probiotics ; }, abstract = {Exposure to heavy metals (HMs) is a threat to human health. Although probiotics can detoxify HMs in animals, their effectiveness and mechanism of action in humans have not been studied well. Therefore, we conducted this randomized, double-blind, controlled trial on 152 occupational workers from the metal industry, an at-risk human population, to explore the effectiveness of probiotic yogurt in reducing HM levels. Participants were randomly assigned to two groups: one consumed probiotic yogurt containing the HM-resistant strain Pediococcus acidilactici GR-1 and the other consumed conventional yogurt for 12 weeks. Analysis of metal contents in the blood revealed that the consumption of probiotic yogurt resulted in a higher and faster decrease in copper (34.45%) and nickel (38.34%) levels in the blood than the consumption of conventional yogurt (16.41% and 27.57%, respectively). Metagenomic and metabolomic studies identified a close correlation between gut microbiota (GM) and host metabolism. Significantly enriched members of Blautia and Bifidobacterium correlated positively with the antioxidant capacities of GM and host. Further murine experiments confirmed the essential role of GM and protective effect of GR-1 on the antioxidative role of the intestine against copper. Thus, the use of probiotic yogurt may be an effective and affordable approach for combating toxic metal exposure through the protection of indigenous GM in humans.ClinicalTrials.gov identifier: ChiCTR2100053222.}, } @article {pmid35972440, year = {2023}, author = {Hellmann, J and Ta, A and Ollberding, NJ and Bezold, R and Lake, K and Jackson, K and Dirksing, K and Bonkowski, E and Haslam, DB and Denson, LA}, title = {Patient-Reported Outcomes Correlate With Microbial Community Composition Independent of Mucosal Inflammation in Pediatric Inflammatory Bowel Disease.}, journal = {Inflammatory bowel diseases}, volume = {29}, number = {2}, pages = {286-296}, pmid = {35972440}, issn = {1536-4844}, support = {P30 DK078392/DK/NIDDK NIH HHS/United States ; T32 ES010957/ES/NIEHS NIH HHS/United States ; T32 DK007727/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Child ; Prospective Studies ; *Inflammatory Bowel Diseases/diagnosis ; *Colitis, Ulcerative/diagnosis ; *Crohn Disease/diagnosis ; *Microbiota ; Feces ; Leukocyte L1 Antigen Complex/metabolism ; Inflammation ; Abdominal Pain ; Patient Reported Outcome Measures ; }, abstract = {BACKGROUND: Inflammatory bowel diseases (IBDs) involve an aberrant host response to intestinal microbiota causing mucosal inflammation and gastrointestinal symptoms. Patient-reported outcomes (PROs) are increasingly important in clinical care and research. Our aim was to examine associations between PROs and fecal microbiota in patients 0 to 22 years of age with IBD.

METHODS: A longitudinal, prospective, single-center study tested for associations between microbial community composition via shotgun metagenomics and PROs including stool frequency and rectal bleeding in ulcerative colitis (UC) and abdominal pain and stool frequency in Crohn's disease (CD). Mucosal inflammation was assessed with fecal calprotectin. A negative binomial mixed-effects model including clinical characteristics and fecal calprotectin tested for differentially abundant species and metabolic pathways by PROs.

RESULTS: In 70 CD patients with 244 stool samples, abdominal pain correlated with increased relative abundance of Haemophilus and reduced Clostridium spp. There were no differences relative to calprotectin level. In 23 UC patients with 76 samples, both rectal bleeding and increased stool frequency correlated with increased Klebsiella and reduced Bacteroides spp. Conversely, UC patients with lower calprotectin had reduced Klebsiella. Both UC and CD patients with active symptoms exhibited less longitudinal microbial community stability. No differences in metabolic pathways were observed in CD. Increased sulfoglycolysis and ornithine biosynthesis correlated with symptomatic UC.

CONCLUSIONS: Microbial community composition correlated with PROs in both CD and UC. Metabolic pathways differed relative to PROs in UC, but not CD. Data suggest that microbiota may contribute to patient symptoms in IBD, in addition to effects of mucosal inflammation.}, } @article {pmid35972231, year = {2022}, author = {Cui, J and Ramesh, G and Wu, M and Jensen, ET and Crago, O and Bertoni, AG and Gao, C and Hoffman, KL and Sheridan, PA and Wong, KE and Wood, AC and Chen, YI and Rotter, JI and Petrosino, JF and Rich, SS and Goodarzi, MO}, title = {Butyrate-Producing Bacteria and Insulin Homeostasis: The Microbiome and Insulin Longitudinal Evaluation Study (MILES).}, journal = {Diabetes}, volume = {71}, number = {11}, pages = {2438-2446}, pmid = {35972231}, issn = {1939-327X}, support = {P30 ES030285/ES/NIEHS NIH HHS/United States ; UL1 TR001420/TR/NCATS NIH HHS/United States ; UL1 TR001881/TR/NCATS NIH HHS/United States ; P30 DK063491/DK/NIDDK NIH HHS/United States ; R01 DK109588/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Insulin ; *Insulin Resistance ; *Diabetes Mellitus, Type 2 ; Blood Glucose/analysis ; Insulin, Regular, Human ; Homeostasis ; *Microbiota ; Butyrates ; }, abstract = {Gut microbiome studies have documented depletion of butyrate-producing taxa in type 2 diabetes. We analyzed associations between butyrate-producing taxa and detailed measures of insulin homeostasis, whose dysfunction underlies diabetes in 224 non-Hispanic Whites and 129 African Americans, all of whom completed an oral glucose tolerance test. Stool microbiome was assessed by whole-metagenome shotgun sequencing with taxonomic profiling. We examined associations among 36 butyrate-producing taxa (n = 7 genera and 29 species) and insulin sensitivity, insulin secretion, disposition index, insulin clearance, and prevalence of dysglycemia (prediabetes plus diabetes, 46% of cohort), adjusting for age, sex, BMI, and race. The genus Coprococcus was associated with higher insulin sensitivity (β = 0.14; P = 0.002) and disposition index (β = 0.12; P = 0.012) and a lower rate of dysglycemia (odds ratio [OR] 0.91; 95% CI 0.85-0.97; P = 0.0025). In contrast, Flavonifractor was associated with lower insulin sensitivity (β = -0.13; P = 0.004) and disposition index (β = -0.11; P = 0.04) and higher prevalence of dysglycemia (OR 1.22; 95% CI 1.08-1.38; P = 0.0013). Species-level analyses found 10 bacteria associated with beneficial directions of effects and two bacteria with adverse associations on insulin homeostasis and dysglycemia. Although most butyrate producers analyzed appear to be metabolically beneficial, this is not the case for all such bacteria, suggesting that microbiome-directed therapeutic measures to prevent or treat diabetes should be targeted to specific butyrate-producing taxa rather than all butyrate producers.}, } @article {pmid35969797, year = {2022}, author = {DeWoody, JA and Jeon, JY and Bickham, JW and Heenkenda, EJ and Janjua, S and Lamka, GF and Mularo, AJ and Black, A and Brüniche-Olsen, A and Willoughby, JR}, title = {The Threatened Species Imperative: Conservation assessments would benefit from population genomic insights.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {35}, pages = {e2210685119}, pmid = {35969797}, issn = {1091-6490}, mesh = {Animals ; Biodiversity ; *Conservation of Natural Resources ; *Endangered Species ; *Metagenomics ; }, } @article {pmid35968974, year = {2022}, author = {Swaney, MH and Sandstrom, S and Kalan, LR}, title = {Cobamide Sharing Is Predicted in the Human Skin Microbiome.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0067722}, pmid = {35968974}, issn = {2379-5077}, support = {R35GM137828//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32AI055397//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; U19AI142720//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; U19 AI142720/AI/NIAID NIH HHS/United States ; R35 GM137828/GM/NIGMS NIH HHS/United States ; T32 AI055397/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Bacteria/genetics ; *Cobamides ; *Microbiota/genetics ; Vitamin B 12 ; Vitamins ; *Skin/microbiology ; }, abstract = {The skin microbiome is a key player in human health, with diverse functions ranging from defense against pathogens to education of the immune system. While recent studies have begun to shed light on the valuable role that skin microorganisms have in maintaining the skin barrier, a detailed understanding of the complex interactions that shape healthy skin microbial communities is limited. Cobamides, the vitamin B12 class of cofactor, are essential for organisms across the tree of life. Because this vitamin is only produced by a limited fraction of prokaryotes, cobamide sharing is predicted to mediate community dynamics within microbial communities. Here, we provide the first large-scale metagenomic assessment of cobamide biosynthesis and utilization in the skin microbiome. We show that while numerous and diverse taxa across the major bacterial phyla on the skin encode cobamide-dependent enzymes, relatively few species encode de novo cobamide biosynthesis. We show that cobamide producers and users are integrated into the network structure of microbial communities across the different microenvironments of the skin and that changes in microbiome community structure and diversity are associated with the abundance of cobamide producers in the Corynebacterium genus, for both healthy and diseased skin states. Finally, we find that de novo cobamide biosynthesis is enriched only in Corynebacterium species associated with hosts, including those prevalent on human skin. We confirm that the cofactor is produced in excess through quantification of cobamide production by human skin-associated species isolated in the laboratory. Taken together, our results reveal the potential for cobamide sharing within skin microbial communities, which we hypothesize mediates microbiome community dynamics and host interactions. IMPORTANCE The skin microbiome is essential for maintaining skin health and function. However, the microbial interactions that dictate microbiome structure, stability, and function are not well understood. Here, we investigate the biosynthesis and use of cobamides, a cofactor needed by many organisms but only produced by select prokaryotes, within the human skin microbiome. We found that while a large proportion of skin taxa encode cobamide-dependent enzymes, only a select few encode de novo cobamide biosynthesis. Further, the abundance of cobamide-producing Corynebacterium species is associated with skin microbiome diversity and structure, and within this genus, de novo biosynthesis is enriched in host-associated species compared to environment-associated species. These findings identify cobamides as a potential mediator of skin microbiome dynamics and skin health.}, } @article {pmid35967853, year = {2022}, author = {Sheng, S and Yan, S and Chen, J and Zhang, Y and Wang, Y and Qin, Q and Li, W and Li, T and Huang, M and Ding, S and Tang, L}, title = {Gut microbiome is associated with metabolic syndrome accompanied by elevated gamma-glutamyl transpeptidase in men.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {946757}, pmid = {35967853}, issn = {2235-2988}, mesh = {Adult ; *Gastrointestinal Microbiome/physiology ; Genome-Wide Association Study ; Humans ; Male ; *Metabolic Syndrome/blood/complications/physiopathology ; Polyamines ; *gamma-Glutamyltransferase/blood ; }, abstract = {It is predicted that by 2035, metabolic syndrome (MS) will be found in nearly more than half of our adult population, seriously affecting the health of our body. MS is usually accompanied by the occurrence of abnormal liver enzymes, such as elevated gamma-glutamyl transpeptidase (GGT). More and more studies have shown that the gut microbiota is involved in MS; however, the correlation between gut microbiota and MS with elevated GGT has not been studied comprehensively. Especially, there are few reports about its role in the physical examination of the population of men with MS and elevated GGT. By using the whole-genome shotgun sequencing technology, we conducted a genome-wide association study of the gut microbiome in 66 participants diagnosed as having MS accompanied by high levels of GGT (case group) and 66 participants with only MS and normal GGT level (control group). We found that the number of gut microbial species was reduced in participants in the case group compared to that of the control group. The overall microbial composition between the two groups is of significant difference. The gut microbiota in the case group is characterized by increased levels of "harmful bacteria" such as Megamonas hypermegale, Megamonas funiformis, Megamonas unclassified, Klebsiella pneumoniae, and Fusobacterium mortiferum and decreased levels of "beneficial bacteria" such as Faecalibacterium prausnitzii, Eubacterium eligens, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bacteroides dorei, and Alistipes putredinis. Moreover, the pathways of POLYAMSYN-PWY, ARG+POLYAMINE-SYN, PWY-6305, and GOLPDLCAT-PWY were also increased in the case group, which may play a role in the elevation of GGT by producing amine, polyamine, putrescine, and endogenous alcohol. Taken together, there are apparent changes in the composition of the gut microbiome in men with MS and abnormal GGT levels, and it is high time to discover specific gut microbiome as a potential therapeutic target in that population. More in-depth studies of relevant mechanism could offer some new methods for the treatment of MS with elevated GGT.}, } @article {pmid35967852, year = {2022}, author = {Ma, Y and Luo, M and Deng, Y and Yang, X and Wang, X and Chen, G and Qin, Z and Deng, Y and Nan, M and Chen, Y and Wang, P and Wei, H and Han, L and Fang, X and Liu, Z}, title = {Antibiotic-Induced Primary Biles Inhibit SARS-CoV-2 Endoribonuclease Nsp15 Activity in Mouse Gut.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {896504}, pmid = {35967852}, issn = {2235-2988}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Bile Acids and Salts/physiology ; *COVID-19/physiopathology ; *Endoribonucleases/antagonists & inhibitors/metabolism/physiology ; *Gastrointestinal Microbiome/physiology ; Mice ; *SARS-CoV-2 ; *Viral Nonstructural Proteins/antagonists & inhibitors/metabolism/physiology ; *COVID-19 Drug Treatment ; }, abstract = {The gut microbiome profile of COVID-19 patients was found to correlate with a viral load of SARS-CoV-2, COVID-19 severity, and dysfunctional immune responses, suggesting that gut microbiota may be involved in anti-infection. In order to investigate the role of gut microbiota in anti-infection against SARS-CoV-2, we established a high-throughput in vitro screening system for COVID-19 therapeutics by targeting the endoribonuclease (Nsp15). We also evaluated the activity inhibition of the target by substances of intestinal origin, using a mouse model in an attempt to explore the interactions between gut microbiota and SARS-CoV-2. The results unexpectedly revealed that antibiotic treatment induced the appearance of substances with Nsp15 activity inhibition in the intestine of mice. Comprehensive analysis based on functional profiling of the fecal metagenomes and endoribonuclease assay of antibiotic-enriched bacteria and metabolites demonstrated that the Nsp15 inhibitors were the primary bile acids that accumulated in the gut as a result of antibiotic-induced deficiency of bile acid metabolizing microbes. This study provides a new perspective on the development of COVID-19 therapeutics using primary bile acids.}, } @article {pmid35967333, year = {2022}, author = {Xing, C and Du, Y and Duan, T and Nim, K and Chu, J and Wang, HY and Wang, RF}, title = {Interaction between microbiota and immunity and its implication in colorectal cancer.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {963819}, pmid = {35967333}, issn = {1664-3224}, support = {R01 CA101795/CA/NCI NIH HHS/United States ; R01 CA246547/CA/NCI NIH HHS/United States ; U54 CA210181/CA/NCI NIH HHS/United States ; }, mesh = {*Colitis/metabolism ; *Colorectal Neoplasms/metabolism ; *Gastrointestinal Microbiome ; Humans ; Inflammation/complications ; *Microbiota ; }, abstract = {Colorectal cancer (CRC) is one of the leading causes of cancer-related death in the world. Besides genetic causes, colonic inflammation is one of the major risk factors for CRC development, which is synergistically regulated by multiple components, including innate and adaptive immune cells, cytokine signaling, and microbiota. The complex interaction between CRC and the gut microbiome has emerged as an important area of current CRC research. Metagenomic profiling has identified a number of prominent CRC-associated bacteria that are enriched in CRC patients, linking the microbiota composition to colitis and cancer development. Some microbiota species have been reported to promote colitis and CRC development in preclinical models, while a few others are identified as immune modulators to induce potent protective immunity against colitis and CRC. Mechanistically, microbiota regulates the activation of different immune cell populations, inflammation, and CRC via crosstalk between innate and adaptive immune signaling pathways, including nuclear factor kappa B (NF-κB), type I interferon, and inflammasome. In this review, we provide an overview of the potential interactions between gut microbiota and host immunity and how their crosstalk could synergistically regulate inflammation and CRC, thus highlighting the potential roles and mechanisms of gut microbiota in the development of microbiota-based therapies to prevent or alleviate colitis and CRC.}, } @article {pmid35966925, year = {2022}, author = {Hui, M and Wang, A and Cheng, J and Sha, Z}, title = {Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13758}, pmid = {35966925}, issn = {2167-8359}, mesh = {Humans ; Animals ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; *Decapoda ; Crustacea/genetics ; Bacteria/genetics ; *Gammaproteobacteria/genetics ; *Microbiota/genetics ; }, abstract = {Shrimps of the family Alvinocarididae, endemic species to deep sea chemosynthetic ecosystems, harbor epibiotic microbes on gills which probably play important roles in the survival of the shrimps. Among them, Alvinocaris longirostris and Shinkaicaris leurokolos occupy different ecological niches within the same hydrothermal vent in Okinawa Trough, and A. longirostris also exists in a methane seep of the South China Sea. In this study, full-length 16S rRNA sequences of the gill associated bacteria of two alvinocaridid species from different chemosynthetically ecological niches were first captured by single-molecule real-time sequencing. Totally, 120,792 optimized circular consensus sequences with ∼1,450 bp in length were obtained and clustered into 578 operational taxonomic units. Alpha diversity analysis showed seep A. longirostris had the highest species richness and evenness (average Chao1 = 213.68, Shannon = 3.39). Beta diversity analysis revealed that all samples were clearly divided into three groups, and microbial community of A. longirostris from seep and vent were more related than the other comparisons. By permutational multivariate analysis of variance, the most significant community compositional variance was detected between seep A. longirostris and vent S. leurokolos (R [2] = 0.731, P = 0.001). The taxon tags were further classified into 21 phyla, 40 classes, 89 orders, 124 families and 135 genera. Overall, the microbial communities were dominated by Campylobacteria and Gammaproteobacteria. Alphaproteobacteria, Bacteroidia, Verrucomicrobiae, Bacilli and other minor groups were also detected at lower abundance. Taxonomic groups recovered from the vent S. leurokolos samples were only dominated by Sulfurovaceae (94.06%). In comparison, gill-associated microbiota of vent A. longirostris consisted of more diverse sulfur-oxidizing bacteria, including Sulfurovaceae (69.21%), Thiotrichaceae (6.77%) and a putative novel Gammaproteobacteria group (14.37%), while in seep A. longirostris, Gammaproteobacteria un-group (44.01%) constituted the major component, following the methane-oxidizing bacteria Methylomonadaceae (19.38%), and Sulfurovaceae (18.66%). Therefore, the gill associated bacteria composition and abundance of alvinocaridid shrimps are closely related to the habitat heterogeneity and the selection of microbiota by the host. However, the interaction between these alvinocaridid shrimps and the epibiotic communities requires further study based on metagenome sequencing and fluorescence in situ hybridization.}, } @article {pmid35966074, year = {2022}, author = {Sugino, KY and Hernandez, TL and Barbour, LA and Kofonow, JM and Frank, DN and Friedman, JE}, title = {A maternal higher-complex carbohydrate diet increases bifidobacteria and alters early life acquisition of the infant microbiome in women with gestational diabetes mellitus.}, journal = {Frontiers in endocrinology}, volume = {13}, number = {}, pages = {921464}, pmid = {35966074}, issn = {1664-2392}, support = {P30 DK048520/DK/NIDDK NIH HHS/United States ; R01 DK101659/DK/NIDDK NIH HHS/United States ; R01 DK128416/DK/NIDDK NIH HHS/United States ; }, mesh = {Bifidobacterium ; *Diabetes, Gestational/metabolism ; Diet ; Female ; Glucose ; Glycerol ; Humans ; Infant ; Insulin ; *Microbiota ; Pregnancy ; }, abstract = {Gestational diabetes mellitus (GDM) is associated with considerable imbalances in intestinal microbiota that may underlie pathological conditions in both mothers and infants. To more definitively identify these alterations, we evaluated the maternal and infant gut microbiota through the shotgun metagenomic analysis of a subset of stool specimens collected from a randomized, controlled trial in diet-controlled women with GDM. The women were fed either a CHOICE diet (60% complex carbohydrate/25% fat/15% protein, n=18) or a conventional diet (CONV, 40% complex carbohydrate/45% fat/15% protein, n=16) from 30 weeks' gestation through delivery. In contrast to other published studies, we designed the study to minimize the influence of other dietary sources by providing all meals, which were eucaloric and similar in fiber content. At 30 and 37 weeks' gestation, we collected maternal stool samples; performed the fasting measurements of glucose, glycerol, insulin, free fatty acids, and triglycerides; and administered an oral glucose tolerance test (OGTT) to measure glucose clearance and insulin response. Infant stool samples were collected at 2 weeks, 2 months, and 4-5 months of age. Maternal glucose was controlled to conventional targets in both diets, with no differences in Homeostatic Model Assessment of Insulin Resistance (HOMA-IR). No differences in maternal alpha or beta diversity between the two diets from baseline to 37 weeks' gestation were observed. However, women on CHOICE diet had higher levels of Bifidobacteriaceae, specifically Bifidobacterium adolescentis, compared with women on CONV. Species-level taxa varied significantly with fasting glycerol, fasting glucose, and glucose AUC after the OGTT challenge. Maternal diet significantly impacted the patterns of infant colonization over the first 4 months of life, with CHOICE infants showing increased microbiome alpha diversity (richness), greater Clostridiaceae, and decreased Enterococcaceae over time. Overall, these results suggest that an isocaloric GDM diet containing greater complex carbohydrates with reduced fat leads to an ostensibly beneficial effect on the maternal microbiome, improved infant gut microbiome diversity, and reduced opportunistic pathogens capable of playing a role in obesity and immune system development. These results highlight the critical role a maternal diet has in shaping the maternal and infant microbiome in women with GDM.}, } @article {pmid35965344, year = {2022}, author = {Rossi, A and Morlino, MS and Gaspari, M and Basile, A and Kougias, P and Treu, L and Campanaro, S}, title = {Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {125}, pmid = {35965344}, issn = {2049-2618}, mesh = {Anaerobiosis ; Archaea/genetics ; Metagenome/genetics ; *Microbiota ; Virus Activation ; *Viruses/genetics ; }, abstract = {BACKGROUND: The viral community has the potential to influence the structure of the microbiome and thus the yield of the anaerobic digestion process. However, the virome composition in anaerobic digestion is still under-investigated. A viral induction experiment was conducted on separate batches undergoing a series of DNA-damaging stresses, in order to coerce temperate viruses to enter the lytic cycle.

RESULTS: The sequencing of the metagenome revealed a viral community almost entirely composed of tailed bacteriophages of the order Caudovirales. Following a binning procedure 1,092 viral and 120 prokaryotic genomes were reconstructed, 64 of which included an integrated prophage in their sequence. Clustering of coverage profiles revealed the presence of species, both viral and microbial, sharing similar reactions to shocks. A group of viral genomes, which increase under organic overload and decrease under basic pH, uniquely encode the yopX gene, which is involved in the induction of temperate prophages. Moreover, the in-silico functional analysis revealed an enrichment of sialidases in viral genomes. These genes are associated with tail proteins and, as such, are hypothesised to be involved in the interaction with the host. Archaea registered the most pronounced changes in relation to shocks and featured behaviours not shared with other species. Subsequently, data from 123 different samples of the global anaerobic digestion database was used to determine coverage profiles of host and viral genomes on a broader scale.

CONCLUSIONS: Viruses are key components in anaerobic digestion environments, shaping the microbial guilds which drive the methanogenesis process. In turn, environmental conditions are pivotal in shaping the viral community and the rate of induction of temperate viruses. This study provides an initial insight into the complexity of the anaerobic digestion virome and its relation with the microbial community and the diverse environmental parameters. Video Abstract.}, } @article {pmid35965333, year = {2022}, author = {Broman, E and Izabel-Shen, D and Rodríguez-Gijón, A and Bonaglia, S and Garcia, SL and Nascimento, FJA}, title = {Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {126}, pmid = {35965333}, issn = {2049-2618}, mesh = {Carbon ; *Microbiota/genetics ; Nitrogen ; Oxygen ; *Salinity ; }, abstract = {BACKGROUND: Microorganisms in the seafloor use a wide range of metabolic processes, which are coupled to the presence of functional genes within their genomes. Aquatic environments are heterogenous and often characterized by natural physiochemical gradients that structure these microbial communities potentially changing the diversity of functional genes and its associated metabolic processes. In this study, we investigated spatial variability and how environmental variables structure the diversity and composition of benthic functional genes and metabolic pathways across various fundamental environmental gradients. We analyzed metagenomic data from sediment samples, measured related abiotic data (e.g., salinity, oxygen and carbon content), covering 59 stations spanning 1,145 km across the Baltic Sea.

RESULTS: The composition of genes and microbial communities were mainly structured by salinity plus oxygen, and the carbon to nitrogen (C:N) ratio for specific metabolic pathways related to nutrient transport and carbon metabolism. Multivariate analyses indicated that the compositional change in functional genes was more prominent across environmental gradients compared to changes in microbial taxonomy even at genus level, and indicate functional diversity adaptation to local environments. Oxygen deficient areas (i.e., dead zones) were more different in gene composition when compared to oxic sediments.

CONCLUSIONS: This study highlights how benthic functional genes are structured over spatial distances and by environmental gradients and resource availability, and suggests that changes in, e.g., oxygenation, salinity, and carbon plus nitrogen content will influence functional metabolic pathways in benthic habitats. Video Abstract.}, } @article {pmid35965269, year = {2023}, author = {Lima, LFO and Alker, AT and Papudeshi, B and Morris, MM and Edwards, RA and de Putron, SJ and Dinsdale, EA}, title = {Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {392-407}, pmid = {35965269}, issn = {1432-184X}, mesh = {Animals ; *Anthozoa/microbiology ; Ecosystem ; Metagenome ; Coral Reefs ; Bacteria/genetics/metabolism ; *Microbiota/genetics ; Seawater/microbiology ; }, abstract = {The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here, we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. The analysis was conducted using metagenomes and metagenome-assembled genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs. The microbial community structure in the coral SML varied according to the local environment, both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and those that are related to higher levels of microbial activity, competition, and stress response. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome, potentially increasing holobiont resilience to environmental changes and disease.}, } @article {pmid35962889, year = {2022}, author = {Oliveira, MET and Paulino, GVB and Dos Santos Júnior, ED and da Silva Oliveira, FA and Melo, VMM and Ursulino, JS and de Aquino, TM and Shetty, AK and Landell, MF and Gitaí, DLG}, title = {Multi-omic Analysis of the Gut Microbiome in Rats with Lithium-Pilocarpine-Induced Temporal Lobe Epilepsy.}, journal = {Molecular neurobiology}, volume = {59}, number = {10}, pages = {6429-6446}, pmid = {35962889}, issn = {1559-1182}, support = {311553/2018-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 313769/2018-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 312889/2021-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 315895/2021-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Animals ; *Epilepsy/metabolism ; *Epilepsy, Temporal Lobe/metabolism ; *Gastrointestinal Microbiome ; Lithium ; Pilocarpine ; Rats ; }, abstract = {Evidence supports that the gut microbiota and bacteria-dependent metabolites influence the maintenance of epileptic brain activity. However, the alterations in the gut microbiota between epileptic versus healthy individuals are poorly understood. We used a multi-omic approach to evaluate the changes in the composition of gut metagenome as well in the fecal metabolomic profile in rats before and after being submitted to status epilepticus (SE)-induced temporal lobe epilepsy (TLE). The 16S ribosomal RNA (rRNA) sequencing of fecal samples coupled to bioinformatic analysis revealed taxonomic, compositional, and functional shifts in epileptic rats. The species richness (Chao1 index) was significantly lower in the post-TLE group, and the β-diversity analysis revealed clustering separated from the pre-TLE group. The taxonomic abundance analysis showed a significant increase of phylum Desulfobacterota and a decrease of Patescibacteria in the post-TLE group. The DESEq2 and LEfSe analysis resulted in 18 genera significantly enriched between post-TLE and pre-TLE groups at the genus level. We observed that epileptic rats present a peculiar metabolic phenotype, including a lower concentration of D-glucose and L-lactic acid and a higher concentration of L-glutamic acid and glycine. The microbiota-host metabolic correlation analysis showed that the genera differentially abundant in post-TLE rats are associated with the altered metabolites, especially the proinflammatory Desulfovibrio and Marvinbryantia, which were enriched in epileptic animals and positively correlated with these excitatory neurotransmitters and carbohydrate metabolites. Therefore, our data revealed a correlation between dysbacteriosis in epileptic animals and fecal metabolites that are known to be relevant for maintaining epileptic brain activity by enhancing chronic inflammation, an excitatory-inhibitory imbalance, and/or a metabolic disturbance. These data are promising and suggest that targeting the gut microbiota could provide a novel avenue for preventing and treating acquired epilepsy. However, the causal relationship between these microbial/metabolite components and the SRS occurrence still needs further exploration.}, } @article {pmid35959379, year = {2022}, author = {Yan, H and Qin, Q and Yan, S and Chen, J and Yang, Y and Li, T and Gao, X and Ding, S}, title = {Comparison Of The Gut Microbiota In Different Age Groups In China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {877914}, pmid = {35959379}, issn = {2235-2988}, mesh = {Aged ; Bacteroides ; Bacteroides fragilis ; Bacteroidetes ; *Bifidobacterium longum ; Clostridiales ; Escherichia coli/genetics ; Feces/microbiology ; Firmicutes ; *Gastrointestinal Microbiome ; Humans ; Lipopolysaccharides ; }, abstract = {Aging is now the most profound risk factor for almost all non-communicable diseases. Studies have shown that probiotics play a specific role in fighting aging. We used metagenomic sequencing to study the changes in gut microbes in different age groups and found that aging had the most significant effect on subjects' gut microbe structure. Our study divided the subjects (n=614) into two groups by using 50 years as the age cut-off point for the grouping. Compared with the younger group, several species with altered abundance and specific functional pathways were found in the older group. At the species level, the abundance of Bacteroides fragilis, Bifidobacterium longum, Clostridium bolteae, Escherichia coli, Klebsiella pneumoniae, and Parabacteroides merdae were increased in older individuals. They were positively correlated to the pathways responsible for lipopolysaccharide (LPS) biosynthesis and the degradation of short-chain fatty acids (SCFAs). On the contrary, the levels of Barnesiella intestinihominis, Megamonas funiformis, and Subdoligranulum unclassified were decreased in the older group, which negatively correlated with the above pathways (p-value<0.05). Functional prediction revealed 92 metabolic pathways enriched in the older group significantly higher than those in the younger group (p-value<0.05), especially pathways related to LPS biosynthesis and the degradation of SCFAs. Additionally, we established a simple non-invasive model of aging, nine species (Bacteroides fragilis, Barnesiella intestinihominis, Bifidobacterium longum, Clostridium bolteae, Escherichia coli, Klebsiella pneumoniae, Megamonas funiformis, Parabacteroides merdae, and Subdoligranulum unclassified) were selected to construct the model. The area under the receiver operating curve (AUC) of the model implied that supplemented probiotics might influence aging. We discuss the features of the aging microbiota that make it more amenable to pre-and probiotic interventions. We speculate these metabolic pathways of gut microbiota can be associated with the immune status and inflammation of older adults. Health interventions that promote a diverse microbiome could influence the health of older adults.}, } @article {pmid35958146, year = {2022}, author = {Summers, S and Pek, YS and Vinod, DP and McDougald, D and Todd, PA and Birch, WR and Rice, SA}, title = {Bacterial biofilm colonization and succession in tropical marine waters are similar across different types of stone materials used in seawall construction.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {928877}, pmid = {35958146}, issn = {1664-302X}, abstract = {Seawalls are important in protecting coastlines from currents, erosion, sea-level rise, and flooding. They are, however, associated with reduced biodiversity, due to their steep orientation, lack of microhabitats, and the materials used in their construction. Hence, there is considerable interest in modifying seawalls to enhance the settlement and diversity of marine organisms, as microbial biofilms play a critical role facilitating algal and invertebrate colonization. We assessed how different stone materials, ranging from aluminosilicates to limestone and concrete, affect biofilm formation. Metagenomic assessment of marine microbial communities indicated no significant impact of material on microbial diversity, irrespective of the diverse surface chemistry and topography. Based on KEGG pathway analysis, surface properties appeared to influence the community composition and function during the initial stages of biofilm development, but this effect disappeared by Day 31. We conclude that marine biofilms converged over time to a generic marine biofilm, rather than the underlying stone substrata type playing a significant role in driving community composition.}, } @article {pmid35956844, year = {2022}, author = {Chen, Z and Liu, B and Gong, Z and Huang, H and Gong, Y and Xiao, W}, title = {Metagenomics Approach to the Intestinal Microbiome Structure and Abundance in High-Fat-Diet-Induced Hyperlipidemic Rat Fed with (-)-Epigallocatechin-3-Gallate Nanoparticles.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {15}, pages = {}, pmid = {35956844}, issn = {1420-3049}, support = {2021NK2010//Major Science and Technology Project of Hunan Province/ ; 2021NK2016//The Key R&D Program of Hunan Province/ ; 2020NK4244//Hunan innovative province construction project Funding/ ; 21B0782//Excellent youth project of Hunan education department/ ; }, mesh = {Animals ; *Catechin/analogs & derivatives/chemistry ; Cholesterol ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; *Hyperlipidemias/drug therapy/etiology ; Metagenomics ; Molecular Docking Simulation ; *Nanoparticles/chemistry ; Rats ; Spectroscopy, Fourier Transform Infrared ; }, abstract = {The effects of nanoparticles (NPs) on microbiota homeostasis and their physiological relevance are still unclear. Herein, we compared the modulation and consequent pharmacological effects of oral administration of (-)-epigallocatechin-3-gallate (EGCG)-loaded β-cyclodextrin (β-CD) NPs (EGCG@β-CD NPs) and EGCG on gut microbiota. EGCG@β-CD NPs were prepared using self-assembly and their influence on the intestinal microbiome structure was analyzed using a metagenomics approach. The "Encapsulation efficiency (EE), particle size, polydispersity index (PDI), zeta potential" of EGCG@β-CD NPs were recorded as 98.27 ± 0.36%, 124.6 nm, 0.313 and -24.3 mV, respectively. Surface morphology of EGCG@β-CD NPs was observed as spherical. Fourier-transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD) and molecular docking studies confirmed that EGCG could be well encapsulated in β-CD and formed as EGCG@β-CD NPs. After being continuously administered EGCG@β-CD NPs for 8 weeks, the serum cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) and liver malondialdehyde (MDA) levels in the rats were significantly decreased, while the levels of catalase (CAT) and apolipoprotein-A1 (apo-A1) in the liver increased significantly in the hyperlipidemia model of rats, when compared to the high-fat-diet group. Furthermore, metagenomic analysis revealed that the ratio of Verrucomicrobia/Bacteroidetes was altered and Bacteroidetes decreased in the high-fat diet +200 mg/kg·bw EGCG@β-CD NPs group, while the abundance of Verrucomicrobia was significantly increased, especially Akkermansia muciniphila in rat feces. EGCG@β-CD NPs could be a promising EGCG delivery strategy to modulate the gut microbiota, enhancing its employment in the prevention of hyperlipidemia.}, } @article {pmid35956358, year = {2022}, author = {Bischoff, SC and Nguyen, NK and Seethaler, B and Beisner, J and Kügler, P and Stefan, T}, title = {Gut Microbiota Patterns Predicting Long-Term Weight Loss Success in Individuals with Obesity Undergoing Nonsurgical Therapy.}, journal = {Nutrients}, volume = {14}, number = {15}, pages = {}, pmid = {35956358}, issn = {2072-6643}, support = {01GI1122H//Federal Ministry of Education and Research/ ; }, mesh = {Adult ; *Gastrointestinal Microbiome ; Humans ; Obesity/microbiology/therapy ; Prospective Studies ; Weight Loss ; *Weight Reduction Programs ; }, abstract = {Background: The long-term success of nonsurgical weight reduction programs is variable; thus, predictors of outcome are of major interest. We hypothesized that the intestinal microbiota known to be linked with diet and obesity contain such predictive elements. Methods: Metagenome analysis by shotgun sequencing of stool DNA was performed in a cohort of 15 adults with obesity (mean body mass index 43.1 kg/m[2]) who underwent a one-year multidisciplinary weight loss program and another year of follow-up. Eight individuals were persistently successful (mean relative weight loss 18.2%), and seven individuals were not successful (0.2%). The relationship between relative abundancies of bacterial genera/species and changes in relative weight loss or body mass index was studied using three different statistical modeling methods. Results: When combining the predictor variables selected by the applied statistical modeling, we identified seven bacterial genera and eight bacterial species as candidates for predicting success of weight loss. By classification of relative weight-loss predictions for each patient using 2-5 term models, 13 or 14 out of 15 individuals were predicted correctly. Conclusions: Our data strongly suggest that gut microbiota patterns allow individual prediction of long-term weight loss success. Prediction accuracy seems to be high but needs confirmation by larger prospective trials.}, } @article {pmid35955951, year = {2022}, author = {Anzalone, A and Mosca, A and Dimaria, G and Nicotra, D and Tessitori, M and Privitera, GF and Pulvirenti, A and Leonardi, C and Catara, V}, title = {Soil and Soilless Tomato Cultivation Promote Different Microbial Communities That Provide New Models for Future Crop Interventions.}, journal = {International journal of molecular sciences}, volume = {23}, number = {15}, pages = {}, pmid = {35955951}, issn = {1422-0067}, support = {"Investigation of phytopathological problems of the main Sicilian pro-ductive contexts and eco-sustainable defense strategies_ (PIA.CE.RI. 2020-2022)//University of Catania/ ; WATER4AGRIFOOD", n. ARS01_00825//PON "RICERCA E INNOVAZIONE" 2014 - 2020, Azione II/ ; }, mesh = {*Ascomycota ; Bacteria/genetics ; *Solanum lycopersicum/microbiology ; *Microbiota ; Plant Roots/microbiology ; Rhizosphere ; Soil ; Soil Microbiology ; }, abstract = {The cultivation of soilless tomato in greenhouses has increased considerably, but little is known about the assembly of the root microbiome compared to plants grown in soil. To obtain such information, we constructed an assay in which we traced the bacterial and fungal communities by amplicon-based metagenomics during the cultivation chain from nursery to greenhouse. In the greenhouse, the plants were transplanted either into agricultural soil or into coconut fiber bags (soilless). At the phylum level, bacterial and fungal communities were primarily constituted in all microhabitats by Proteobacteria and Ascomycota, respectively. The results showed that the tomato rhizosphere microbiome was shaped by the substrate or soil in which the plants were grown. The microbiome was different particularly in terms of the bacterial communities. In agriculture, enrichment has been observed in putative biological control bacteria of the genera Pseudomonas and Bacillus and in potential phytopathogenic fungi. Overall, the study describes the different shaping of microbial communities in the two cultivation methods.}, } @article {pmid35954712, year = {2022}, author = {Laue, HE and Shen, Y and Bloomquist, TR and Wu, H and Brennan, KJM and Cassoulet, R and Wilkie, E and Gillet, V and Desautels, AS and Abdelouahab, N and Bellenger, JP and Burris, HH and Coull, BA and Weisskopf, MG and Zhang, W and Takser, L and Baccarelli, AA}, title = {In Utero Exposure to Caffeine and Acetaminophen, the Gut Microbiome, and Neurodevelopmental Outcomes: A Prospective Birth Cohort Study.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {15}, pages = {}, pmid = {35954712}, issn = {1660-4601}, support = {R01ES027845/ES/NIEHS NIH HHS/United States ; R01 ES027845/ES/NIEHS NIH HHS/United States ; P30ES009089/ES/NIEHS NIH HHS/United States ; P30 ES013508/ES/NIEHS NIH HHS/United States ; T32 CA134286/CA/NCI NIH HHS/United States ; R21ES02841/ES/NIEHS NIH HHS/United States ; R21 ES024841/ES/NIEHS NIH HHS/United States ; P30 ES000002/ES/NIEHS NIH HHS/United States ; UH3 OD023275/OD/NIH HHS/United States ; P30 ES009089/ES/NIEHS NIH HHS/United States ; K23ES022242/ES/NIEHS NIH HHS/United States ; K23 ES022242/ES/NIEHS NIH HHS/United States ; }, mesh = {Acetaminophen/adverse effects ; Bacteria/genetics ; Birth Cohort ; Caffeine/adverse effects ; Cohort Studies ; Female ; *Gastrointestinal Microbiome ; Humans ; Pregnancy ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Pregnant individuals are exposed to acetaminophen and caffeine, but it is unknown how these exposures interact with the developing gut microbiome. We aimed to determine whether acetaminophen and/or caffeine relate to the childhood gut microbiome and whether features of the gut microbiome alter the relationship between acetaminophen/caffeine and neurodevelopment. Forty-nine and 85 participants provided meconium and stool samples at 6-7, respectively, for exposure and microbiome assessment. Fecal acetaminophen and caffeine concentrations were quantified, and fecal DNA underwent metagenomic sequencing. Caregivers and study staff assessed the participants' motor and cognitive development using standardized scales. Prenatal exposures had stronger associations with the childhood microbiome than concurrent exposures. Prenatal acetaminophen exposure was associated with a trend of lower gut bacterial diversity in childhood [β = -0.17 Shannon Index, 95% CI: (-0.31, -0.04)] and was marginally associated with differences in the relative abundances of features of the gut microbiome at the phylum (Firmicutes, Actinobacteria) and gene pathway levels. Among the participants with a higher relative abundance of Proteobacteria, prenatal exposure to acetaminophen and caffeine was associated with lower scores on WISC-IV subscales. Acetaminophen during bacterial colonization of the naïve gut is associated with lasting alterations in childhood microbiome composition. Future studies may inform our understanding of downstream health effects.}, } @article {pmid35953888, year = {2022}, author = {Simpson, JB and Sekela, JJ and Graboski, AL and Borlandelli, VB and Bivins, MM and Barker, NK and Sorgen, AA and Mordant, AL and Johnson, RL and Bhatt, AP and Fodor, AA and Herring, LE and Overkleeft, H and Lee, JR and Redinbo, MR}, title = {Metagenomics combined with activity-based proteomics point to gut bacterial enzymes that reactivate mycophenolate.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2107289}, pmid = {35953888}, issn = {1949-0984}, support = {T32 GM135095/GM/NIGMS NIH HHS/United States ; K23 AI124464/AI/NIAID NIH HHS/United States ; T32 DK007750/DK/NIDDK NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; P30 CA016086/CA/NCI NIH HHS/United States ; R01 GM137286/GM/NIGMS NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; }, mesh = {Flavin Mononucleotide ; *Gastrointestinal Microbiome/physiology ; Glucuronides ; Humans ; Immunosuppressive Agents ; Mycophenolic Acid/therapeutic use ; Proteomics ; }, abstract = {Mycophenolate mofetil (MMF) is an important immunosuppressant prodrug prescribed to prevent organ transplant rejection and to treat autoimmune diseases. MMF usage, however, is limited by severe gastrointestinal toxicity that is observed in approximately 45% of MMF recipients. The active form of the drug, mycophenolic acid (MPA), undergoes extensive enterohepatic recirculation by bacterial β-glucuronidase (GUS) enzymes, which reactivate MPA from mycophenolate glucuronide (MPAG) within the gastrointestinal tract. GUS enzymes demonstrate distinct substrate preferences based on their structural features, and gut microbial GUS enzymes that reactivate MPA have not been identified. Here, we compare the fecal microbiomes of transplant recipients receiving MMF to healthy individuals using shotgun metagenomic sequencing. We find that neither microbial composition nor the presence of specific structural classes of GUS genes are sufficient to explain the differences in MPA reactivation measured between fecal samples from the two cohorts. We next employed a GUS-specific activity-based chemical probe and targeted metaproteomics to identify and quantify the GUS proteins present in the human fecal samples. The identification of specific GUS enzymes was improved by using the metagenomics data collected from the fecal samples. We found that the presence of GUS enzymes that bind the flavin mononucleotide (FMN) is significantly correlated with efficient MPA reactivation. Furthermore, structural analysis identified motifs unique to these FMN-binding GUS enzymes that provide molecular support for their ability to process this drug glucuronide. These results indicate that FMN-binding GUS enzymes may be responsible for reactivation of MPA and could be a driving force behind MPA-induced GI toxicity.}, } @article {pmid35953616, year = {2023}, author = {Teker, HT and Ceylani, T}, title = {Intermittent fasting supports the balance of the gut microbiota composition.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {26}, number = {1}, pages = {51-57}, pmid = {35953616}, issn = {1618-1905}, mesh = {Rats ; Animals ; Male ; *Gastrointestinal Microbiome ; Intermittent Fasting ; Rats, Wistar ; Intestines/microbiology ; Bacteria/genetics ; }, abstract = {There is a growing body of detailed research demonstrating that intermittent fasting is essentially a cleansing activity in terms of health. Especially since its applications that exceed 16 h trigger autophagy, it continues its effect on all tissue and organ systems after the regeneration movement that starts at the cellular level. Similarly, it continues to be better understood with each passing day that the gut microbiota (GM) has many positive effects on all tissue and organ systems. Although the GM is affected by many different parameters, dietary habits are reported to be the most effective factor. Therefore, it is important to investigate the effects of different preferred fasting practices on the GM, which has numerous health benefits. Pointing out this situation, this study aims to determine the effects of 18-h intermittent fasting for 5 weeks on the shaping of GM. A 12-month-old male Wistar rat was chosen as the model organism in the study. At the end of the application, the metagenome was applied to the cecum content of the intestinal tissue collected from the sacrificed animals. Intermittent fasting practice led to an increase in alpha diversity, which expresses a significant bacterial diversity, the stabilization of Firmicutes and Bacteroidetes ratios (F/B), and the reshaping of the values with the highest prevalence in all stages of the classification, especially in the family, genus, and species care. Analysis results showed that the preferred intermittent fasting program helps balance the GM composition. This study is an important example showing the strong positive link between intermittent fasting and GM.}, } @article {pmid35953094, year = {2023}, author = {Kong, C and Liang, L and Liu, G and Du, L and Yang, Y and Liu, J and Shi, D and Li, X and Ma, Y}, title = {Integrated metagenomic and metabolomic analysis reveals distinct gut-microbiome-derived phenotypes in early-onset colorectal cancer.}, journal = {Gut}, volume = {72}, number = {6}, pages = {1129-1142}, doi = {10.1136/gutjnl-2022-327156}, pmid = {35953094}, issn = {1468-3288}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/diagnosis ; *Microbiota ; Phenotype ; Choline ; }, abstract = {OBJECTIVE: The incidence of early-onset colorectal cancer (EO-CRC) is steadily increasing. Here, we aimed to characterise the interactions between gut microbiome, metabolites and microbial enzymes in EO-CRC patients and evaluate their potential as non-invasive biomarkers for EO-CRC.

DESIGN: We performed metagenomic and metabolomic analyses, identified multiomics markers and constructed CRC classifiers for the discovery cohort with 130 late-onset CRC (LO-CRC), 114 EO-CRC subjects and age-matched healthy controls (97 LO-Control and 100 EO-Control). An independent cohort of 38 LO-CRC, 24 EO-CRC, 22 LO-Controls and 24 EO-Controls was analysed to validate the results.

RESULTS: Compared with controls, reduced alpha-diversity was apparent in both, LO-CRC and EO-CRC subjects. Although common variations existed, integrative analyses identified distinct microbiome-metabolome associations in LO-CRC and EO-CRC. Fusobacterium nucleatum enrichment and short-chain fatty acid depletion, including reduced microbial GABA biosynthesis and a shift in acetate/acetaldehyde metabolism towards acetyl-CoA production characterises LO-CRC. In comparison, multiomics signatures of EO-CRC tended to be associated with enriched Flavonifractor plauti and increased tryptophan, bile acid and choline metabolism. Notably, elevated red meat intake-related species, choline metabolites and KEGG orthology (KO) pldB and cbh gene axis may be potential tumour stimulators in EO-CRC. The predictive model based on metagenomic, metabolomic and KO gene markers achieved a powerful classification performance for distinguishing EO-CRC from controls.

CONCLUSION: Our large-sample multiomics data suggest that altered microbiome-metabolome interplay helps explain the pathogenesis of EO-CRC and LO-CRC. The potential of microbiome-derived biomarkers as promising non-invasive tools could be used for the accurate detection and distinction of individuals with EO-CRC.}, } @article {pmid35951476, year = {2022}, author = {Bhardwaj, K and Garg, A and Pandey, AD and Sharma, H and Kumar, M and Vrati, S}, title = {Insights into the human gut virome by sampling a population from the Indian subcontinent.}, journal = {The Journal of general virology}, volume = {103}, number = {8}, pages = {}, doi = {10.1099/jgv.0.001774}, pmid = {35951476}, issn = {1465-2099}, mesh = {Animals ; *Bacteriophages ; Genome, Viral ; Humans ; Metagenomics ; Virome/genetics ; *Viruses/genetics ; }, abstract = {Gut virome plays an important role in human physiology but remains poorly understood. This study reports an investigation of the human gut DNA-virome of a previously unexplored ethnic population through metagenomics of faecal samples collected from individuals residing in Northern India. Analysis shows that, similar to the populations investigated earlier, majority of the identified virome belongs to bacteriophages and a smaller fraction (<20 %) consists of viruses that infect animals, archaea, protists, multiple domains or plants. However, crAss-like phages, in this population, are dominated by the genera VI, VII and VIII. Interestingly, it also reveals the presence of a virus family, Sphaerolipoviridae, which has not been detected in the human gut earlier. Viral families, Siphoviridae, Myoviridae, Podoviridae, Microviridae, Herelleviridae and Phycodnaviridae are detected in all of the analysed individuals, which supports the existence of a core virome. Lysogeny-associated genes were found in less than 10 % of the assembled genomes and a negative correlation was observed in the richness of bacterial and free-viral species, suggesting that the dominant lifestyle of gut phage is not lysogenic. This is in contrast to some of the earlier studies. Further, several hundred high-quality viral genomes were recovered. Detailed characterization of these genomes would be useful for understanding the biology of these viruses and their significance in human physiology.}, } @article {pmid35951007, year = {2022}, author = {Natola, L and Seneviratne, SS and Irwin, D}, title = {Population genomics of an emergent tri-species hybrid zone.}, journal = {Molecular ecology}, volume = {31}, number = {20}, pages = {5356-5367}, doi = {10.1111/mec.16650}, pmid = {35951007}, issn = {1365-294X}, mesh = {Animals ; Birds ; British Columbia ; *Gene Flow ; Genome/genetics ; Hybridization, Genetic ; *Metagenomics ; }, abstract = {Isolating barriers that drive speciation are commonly studied in the context of two-species hybrid zones. There is, however, evidence that more complex introgressive relationships are common in nature. Here, we use field observations and genomic analysis, including the sequencing and assembly of a novel reference genome, to study an emergent hybrid zone involving two colliding hybrid zones of three woodpecker species: red-breasted, red-naped, and yellow-bellied sapsuckers (Sphyrapicus ruber, S. nuchalis, and S. varius). Surveys of the area surrounding Prince George, British Columbia, Canada, show that all three species are sympatric, and Genotyping-by-Sequencing identifies hybrids from each species pair and birds with ancestry from all three species. Observations of phenotypes and genotypes of mated pairs provide evidence for assortative mating, though there is some heterospecific pairing. Hybridization is more extensive in this tri-species hybrid zone than in two di-species hybrid zones. However, there is no evidence of a hybrid swarm and admixture is constrained to contact zones, so we classify this region as a tension zone and invoke selection against hybrids as a likely mechanism maintaining species boundaries. Analysis of sapsucker age classes does not show disadvantages in hybrid survival to adulthood, so we speculate the selection upholding the tension zone may involve hybrid fecundity. Gene flow among all sapsuckers in di-species hybrid zones suggests introgression probably occurred before the formation of this tri-species hybrid zone, and might result from bridge hybridization, vagrancies, or other three-species interactions.}, } @article {pmid35950862, year = {2022}, author = {Ortiz Sanjuán, JM and Manzanilla, EG and Cabrera-Rubio, R and Crispie, F and Cotter, PD and Garrido, JJ and Argüello, H}, title = {Using Shotgun Sequencing to Describe the Changes Induced by In-Feed Zinc Oxide and Apramycin in the Microbiomes of Pigs One Week Postweaning.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0159722}, pmid = {35950862}, issn = {2165-0497}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Diarrhea/microbiology ; Escherichia coli ; *Gastrointestinal Microbiome ; Nebramycin/analogs & derivatives ; Swine ; *Zinc Oxide/pharmacology/therapeutic use ; }, abstract = {Postweaning diarrhea (PWD) is a relevant problem associated with early weaning on pig farms. For decades, in-feed antibiotics and therapeutic zinc oxide (ZnO) have been widely used to prevent PWD in piglets. The European Union is banning both strategies in 2022 due to antimicrobial resistance and environmental contamination concerns, respectively. Understanding the effects of these products on the pig microbiome is crucial for correcting potential microbial disbalances that would prompt PWD. Using shotgun sequencing, three trials were carried out to explore the impact of in-feed apramycin and ZnO, combined with different farm hygiene protocols, on the fecal microbiomes of piglets 7 days postweaning. In trial 1, 28-day-old piglets were allocated to one of three groups: control diet (Ct), Ct + ZnO (Zn), and Ct + apramycin (Ab). In trials 2 and 3, piglets were allocated to the same treatments, but the trials also included different cleaning protocols, achieving different hygiene levels. In-feed treatments impacted the richness, diversity, and relative abundance of the piglets' microbiome more than hygiene. Pigs in the Ct group showed higher species richness than pigs in the Ab and Zn groups. A clustering analysis evidenced a link between Enterobacteriaceae in the Ct group; Lactobacillaceae and Veillonellaceae mainly in the Ct group; and Bacteroidaceae, Ruminococcaceae, Oscillospiraceae, Acidaminococcaceae, and Lactobacillaceae in the Ab and Zn groups. Functional data analysis revealed a higher abundance of virulence genes in the Ct group microbiomes and heavy metal and antimicrobial resistance-related functions in the Zn treatment group. The results demonstrate that alternatives to Ab and ZnO should balance the microbial abundance and stimulate the growth of commensals to outcompete potential pathogens. IMPORTANCE Weaning is a critical period for piglets, during which potentially harmful bacteria such as Escherichia coli can increase in abundance in the intestine, creating digestive problems and diarrhea. In-feed antibiotics, the most frequent administration route for antibiotics in livestock, and therapeutic doses of zinc oxide (ZnO) help to control diarrhea but prompt secondary problems such as antimicrobial resistance and soil pollution from heavy metals. Understanding how these strategies impact the gut microbiota is crucial for establishing health biomarkers and designing successful replacement strategies. Using shotgun sequencing, this study compares the microbiota of pigs after early weaning when treated with in-feed antibiotics, ZnO, or treatment-free diets to describe differences that could define the susceptibility to infections, providing the basis for future research on improving intestinal resilience through microbiota-based strategies.}, } @article {pmid35946140, year = {2023}, author = {do Amaral, GCLS and Hassan, MA and Sloniak, MC and Pannuti, CM and Romito, GA and Villar, CC}, title = {Effects of antimicrobial mouthwashes on the human oral microbiome: Systematic review of controlled clinical trials.}, journal = {International journal of dental hygiene}, volume = {21}, number = {1}, pages = {128-140}, doi = {10.1111/idh.12617}, pmid = {35946140}, issn = {1601-5037}, mesh = {Adult ; Humans ; *Anti-Infective Agents/pharmacology/therapeutic use ; *Anti-Infective Agents, Local/therapeutic use ; Chlorhexidine/therapeutic use ; *Dental Plaque/drug therapy ; *Microbiota ; Mouthwashes/therapeutic use ; Phylogeny ; Controlled Clinical Trials as Topic ; }, abstract = {OBJECTIVES: This review aimed to assess the impact of mouthwashes on the composition of the human oral microbiome.

METHOD: An electronic search algorithm was adapted to MEDLINE-PubMed, Scopus, Embase and ISI Web of Science, and reference lists of relevant sources were manually searched. Inclusion criteria were controlled clinical trials published in English whose population were adult individuals who rinse with antimicrobial mouthwashes and that analysed changes in the oral microbiome by metataxonomy, metagenomics or phylogenetic microarray. Identified studies were screened and assessed following the PRISMA guidelines, and results were compiled into qualitative synthesis of the evidence.

RESULTS: Five controlled clinical studies were included. These studies found associations between the daily use of mouthwashes and changes in the oral microbiome, but the nature of the effect varied according to the mouthwash. Chlorhexidine (CHX) rinses lowered microbial diversity. While 7-day use of CHX led to increases in the abundance of Neisseria, Streptococcus and Granulicatella and a decrease in the abundance of Actinomyces, its prolonged use led to widespread reductions in several genera and species. Cetylpyridinium chloride-containing mouthwashes specifically lowered the abundance of gingivitis-associated genera. In contrast, N-acetyl cysteine-based mouthwashes did not promote changes in the oral microbiome.

CONCLUSIONS: Despite substantial heterogeneity, we found evidence to support the hypothesis that CHX and CPC mouthwashes promote changes in oral microbial structure and/or reductions in community diversity that favour the resolution of dysbiosis. However, future large population-based studies of adequate duration are needed to fully understand the extent to which antimicrobial mouthwashes modulate the microbiome.}, } @article {pmid35945942, year = {2022}, author = {Liao, LB and Chen, XX and Xiang, J and Zhang, NN and Wang, ET and Shi, FS}, title = {Zanthoxylum bungeanum root-rot associated shifts in microbiomes of root endosphere, rhizosphere, and soil.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13808}, pmid = {35945942}, issn = {2167-8359}, mesh = {Soil ; *Zanthoxylum ; Rhizosphere ; Bacteria ; Soil Microbiology ; Plant Roots/microbiology ; *Microbiota/genetics ; Trees ; }, abstract = {Root-rot disease has lead to serious reduction in yields and jeopardized the survival of the economically and ecologically important Zanthoxylum bungeanum trees cultured in Sichuan Province. In order to investigate the interaction between the microbiome and the root-rot disease, a metagenomic analysis was performed to characterize the microbial communities and functions in Z. bungeanum root endosphere, rhizosphere and bulk soil with/without root-rot disease. Soil physicochemical properties, microbial population size and enzyme activities were also analyzed for finding their interactions with the root-rot disease. As results, lower total nitrogen (TN) and available phosphorus (AP) contents but higher pH in rhizosphere and bulk soil, as well as lower substrate-induced respiration (SIR) and higher protease activity in bulk soil of diseased trees were found, in comparison with that of healthy trees. Microbial diversity and community composition were changed by root-rot disease in the endosphere, but not in rhizosphere and bulk soils. The endophytic microbiome of diseased trees presented higher Proteobacteria abundance and lower abundances of Bacteroidetes, Firmicutes and dominant fungal phyla. The relative abundances of nitrogen cycle- and carbon cycle-related genes in endophytic microbiomes were different between the diseased and healthy trees. Based on ANOSIM and PCoA, functional profiles (KEGG and CAZy) of microbiomes in rhizosphere and bulk soil shifted significantly between the diseased and healthy trees. In addition, soil pH, TN, AP, SIR, invertase and protease were estimated as the main factors influencing the shifts of taxonomic and functional groups in microbiomes of rhizosphere and bulk soil. Conclusively, the imbalance of root and soil microbial function groups might lead to shifts in the root endosphere-rhizosphere microenvironment, which in turn resulted in Z. bungeanum root-rot.}, } @article {pmid35945559, year = {2022}, author = {Gómez, M and Martinez, D and Muñoz, M and Ramírez, JD}, title = {Aedes aegypti and Ae. albopictus microbiome/virome: new strategies for controlling arboviral transmission?.}, journal = {Parasites & vectors}, volume = {15}, number = {1}, pages = {287}, pmid = {35945559}, issn = {1756-3305}, mesh = {*Aedes ; Animals ; *Arboviruses/genetics ; Humans ; Mosquito Vectors ; Virome ; *Zika Virus/genetics ; *Zika Virus Infection ; }, abstract = {Aedes aegypti and Aedes albopictus are the main vectors of highly pathogenic viruses for humans, such as dengue (DENV), chikungunya (CHIKV), and Zika (ZIKV), which cause febrile, hemorrhagic, and neurological diseases and remain a major threat to global public health. The high ecological plasticity, opportunistic feeding patterns, and versatility in the use of urban and natural breeding sites of these vectors have favored their dispersal and adaptation in tropical, subtropical, and even temperate zones. Due to the lack of available treatments and vaccines, mosquito population control is the most effective way to prevent arboviral diseases. Resident microorganisms play a crucial role in host fitness by preventing or enhancing its vectorial ability to transmit viral pathogens. High-throughput sequencing and metagenomic analyses have advanced our understanding of the composition and functionality of the microbiota of Aedes spp. Interestingly, shotgun metagenomics studies have established that mosquito vectors harbor a highly conserved virome composed of insect-specific viruses (ISV). Although ISVs are not infectious to vertebrates, they can alter different phases of the arboviral cycle, interfering with transmission to the human host. Therefore, this review focuses on the description of Ae. aegypti and Ae. albopictus as vectors susceptible to infection by viral pathogens, highlighting the role of the microbiota-virome in vectorial competence and its potential in control strategies for new emerging and re-emerging arboviruses.}, } @article {pmid35945331, year = {2022}, author = {Chen, Y and Xia, Z and Li, H}, title = {Comparative analysis of the fecal bacterial communities of hawksbill sea turtles (Eretmochelys imbricata) and green sea turtles (Chelonia mydas).}, journal = {FEMS microbiology letters}, volume = {369}, number = {1}, pages = {}, doi = {10.1093/femsle/fnac073}, pmid = {35945331}, issn = {1574-6968}, mesh = {Animals ; Bacteroidetes ; Feces ; *Gastrointestinal Microbiome ; *Microbiota ; Sugars ; *Turtles ; }, abstract = {Hawksbill sea turtles (Eretmochelys imbricata) are important for maintaining healthy coral reef ecosystems currently qualify as "critically endangered" by the IUCN. Their gut microbiota is closely linked to host nutrition and health, however, the gut microbiota of hawksbill sea turtles from a natural reserve remains unclear. Therefore, exploring their microbial community structure in a natural reserve may provide valuable information on strategies for protecting this species. In this study, we investigated hawksbill sea turtle fecal microbial communities from a natural reserve using 16S metagenomics and compared the gut microbiota from fecal samples of hawksbill and green sea turtles (Chelonia mydas). The results indicated that the structure of fecal microbial communities was significantly different between hawksbill and green sea turtles. In hawksbill sea turtles, the three dominant phyla were Bacteroidetes, Firmicutes, and Fusobacteria, whereas the fecal microbial communities of green sea turtles were mainly composed of Firmicutes, Bacteroidetes, and Proteobacteria. Among the hawksbill sea turtle fecal microbes, the predominant genera were Cetobacterium and Rikenell, whereas in green sea turtles, the predominant genera were Bacteroides and Paludibacter. In addition, predictive metagenomic analysis indicated that sugar catabolism was enriched in green sea turtle fecal microbiota, whereas pathways related to secondary metabolite production were enriched in hawksbill sea turtle fecal microbiota. Our study provides preliminary data on the fecal microbiota features of sea turtles from the natural reserve, which may contribute to the management of the food requirements and long-term conservation of hawksbill sea turtles.}, } @article {pmid35944355, year = {2022}, author = {Dhondge, HV and Barvkar, VT and Paul, D and Dastager, SG and Pable, AA and Nadaf, AB}, title = {Exploring the core microbiota in scented rice (Oryza sativa L.) rhizosphere through metagenomics approach.}, journal = {Microbiological research}, volume = {263}, number = {}, pages = {127157}, doi = {10.1016/j.micres.2022.127157}, pmid = {35944355}, issn = {1618-0623}, mesh = {India ; Metagenomics ; *Microbiota/genetics ; *Oryza/microbiology ; Proline/metabolism ; Rhizosphere ; Soil Microbiology ; }, abstract = {Rice is a major food crop cultivated around the globe. Specially scented rice varieties are of commercial importance but they are low-yielding. The rhizospheric microflora plays a significant role in improving yield and aroma. However, the core microbiome of the scented rice rhizosphere is comparatively less explored. Here, we analyzed the core microbiome associated with the rhizosphere of the scented (Ambemohar-157 and Dehradun basmati) in comparison with non-scented rice (Kolam and Arize 6444 Gold) cultivated at two different geoclimatic zones of India (Maharashtra and Uttarakhand) using the metagenomics approach. The alpha and beta diversity analysis showed that the microbial communities associated with scented and non-scented varieties significantly changes with respect to richness, diversity, and evenness. The taxonomic profiling revealed the variation in composition, diversity, and abundance of the microbiome in terms of phyla and genera associated with scented rice varieties over non-scented. The cluster analysis distinguishes the microbial communities based on their geographical positions. The core microbiome analysis revealed that scented rice rhizosphere shelters distinct and unique microbiota. 28.6 % of genera were exclusively present only in the scented rice rhizosphere. The putative functional gene annotation revealed the high abundance of genes related to the biosynthesis of 2-acetyl-1-pyrroline (2AP) precursors in scented rice. The precursor feeding analysis revealed proline as a preferred substrate by 2AP synthesizing bacteria. The 2AP precursor proline and proline metabolism genes showed a positive correlation. The scented rice-specific rhizobacteria pointed out in this study can be used as bio-inoculants for enhancing aroma, yield, and sustainable rice cultivation.}, } @article {pmid35944043, year = {2022}, author = {Yang, Z and Zhang, Y and Stubbe-Espejel, A and Zhao, Y and Liu, M and Li, J and Zhao, Y and Tong, G and Liu, N and Qi, L and Hutchins, A and Lin, S and Li, Y}, title = {Vaginal microbiota and personal risk factors associated with HPV status conversion-A new approach to reduce the risk of cervical cancer?.}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0270521}, pmid = {35944043}, issn = {1932-6203}, mesh = {*Alphapapillomavirus ; Female ; Humans ; *Microbiota ; Papillomaviridae/genetics ; *Papillomavirus Infections ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; *Uterine Cervical Neoplasms/epidemiology/microbiology/prevention & control ; Vagina/microbiology ; }, abstract = {Vaginal microbiota (VMB) is associated with changes in Human papilloma virus (HPV) status, which consequently influences the risk of cervical cancer. This association was often confounded by personal risk factors. This pilot research aimed to explore the relationship between vaginal microbiota, personal risk factors and their interactions with HPV status conversion to identify the vaginal microbiota that was associated with HPV clearance under heterogeneous personal risk factors. A total of 38 women participated by self-collecting a cervicovaginal mucus (CVM) sample that was sent for metagenomics sequencing. Most of the participants also filled in personal risk factors questionnaire through an eHealth platform and authorized the use of their previous HPV genotyping results stored in this eHealth platform. Based on the two HPV results, the participants were grouped into three cohorts, namely HPV negative, HPV persistent infection, and HPV status conversion. The relative abundance of VMB and personal factors were compared among these three cohorts. A correlation investigation was performed between VMB and the significant personal factors to characterize a robustness of the panel for HPV status change using R programming. At baseline, 12 participants were HPV-negative, and 22 were HPV-positive. Within one year, 18 women remained HPV-positive, 12 were HPV-negative and 4 participants showed HPV clearance. The factors in the eHealth questionnaire were systematically evaluated which identified several factors significantly associated with persistent HPV infection, including age, salary, history of reproductive tract infection, and the total number of sexual partners. Concurrent vaginal microbiome samples suggest that a candidate biomarker panel consisting of Lactobacillus gasseri, Streptococcus agalactiae, and Timona prevotella bacteria, which may be associated with HPV clearance. This pilot study indicates a stable HPV status-related vaginal microbe environment. To establish a robust biomarker panel for clinical use, larger cohorts will be recruited into follow-up studies.}, } @article {pmid35943661, year = {2022}, author = {Ma, W and Drew, DA and Staller, K}, title = {The Gut Microbiome and Colonic Motility Disorders: A Practical Framework for the Gastroenterologist.}, journal = {Current gastroenterology reports}, volume = {24}, number = {10}, pages = {115-126}, pmid = {35943661}, issn = {1534-312X}, support = {K01 DK120742/DK/NIDDK NIH HHS/United States ; K23 DK120945/DK/NIDDK NIH HHS/United States ; K01DK120742/DK/NIDDK NIH HHS/United States ; K23DK120945/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Humans ; Dysbiosis ; Fecal Microbiota Transplantation ; *Gastroenterologists ; *Gastrointestinal Microbiome/physiology ; *Irritable Bowel Syndrome/etiology/therapy ; Constipation ; Diarrhea ; Metagenome ; }, abstract = {PURPOSE OF REVIEW: Colonic motility disorders may be influenced by the gut microbiota, which plays a role in modulating sensory and motor function. However, existing data are inconsistent, possibly due to complex disease pathophysiology, fluctuation in symptoms, and difficulty characterizing high-resolution taxonomic composition and function of the gut microbiome.

RECENT FINDINGS: Increasingly, human studies have reported associations between gut microbiome features and colonic motility disorders, such as irritable bowel syndrome and constipation. Several microbial metabolites have been identified as regulators of colonic motility in animal models. Modulation of the gut microbiota via dietary intervention, probiotics, and fecal microbiota transplant is a promising avenue for treatment for these diseases. An integration of longitudinal multi-omics data will facilitate further understanding of the causal effects of dysbiosis on disease. Further understanding of the microbiome-driven mechanisms underlying colonic motility disorders may be leveraged to develop personalized, microbiota-based approaches for disease prevention and treatment.}, } @article {pmid35943262, year = {2022}, author = {Laanbroek, HJ and Cassman, NA and Keijzer, RM and Kuramae, EE}, title = {The Stochastic Assembly of Nitrobacter winogradskyi-Selected Microbiomes with Heterotrophs from Sewage Sludge or Grassland Soil.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {17}, pages = {e0078322}, pmid = {35943262}, issn = {1098-5336}, mesh = {Bacteria/genetics ; Bioreactors/microbiology ; Carbon ; Grassland ; *Microbiota ; Nitrification ; Nitrites ; Nitrobacter/genetics ; Nitrogen ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; *Sewage/microbiology ; Soil ; }, abstract = {Chemolitho-autotrophic microorganisms like the nitrite-oxidizing Nitrobacter winogradskyi create an environment for heterotrophic microorganisms that profit from the production of organic compounds. It was hypothesized that the assembly of a community of heterotrophic microorganisms around N. winogradskyi depends on the ecosystem from which the heterotrophs are picked. To test this hypothesis, pure cultures of N. winogradskyi were grown in continuously nitrite-fed bioreactors in a mineral medium free of added organic carbon that had been inoculated with diluted sewage sludge or with a suspension from a grassland soil. Samples for chemical and 16S rRNA gene amplicon analyses were taken after each volume change in the bioreactor. At the end of the enrichment runs, samples for shotgun metagenomics were also collected. Already after two volume changes, the transformations in community structure became less dynamic. The enrichment of heterotrophs from both sewage and soil was highly stochastic and yielded different dominant genera in most of the enrichment runs that were independent of the origin of the inoculum. Hence, the hypothesis had to be refuted. Notwithstanding the large variation in taxonomic community structure among the enrichments, the functional compositions of the communities were statistically not different between soil- and sludge-based enrichments. IMPORTANCE In the process of aerobic nitrification, nitrite-oxidizing bacteria together with ammonia-oxidizing microorganisms convert mineral nitrogen from its most reduced appearance, i.e., ammonium, into its most oxidized form, i.e., nitrate. Because the form of mineral nitrogen has large environmental implications, nitrite-oxidizing bacteria such as Nitrobacter winogradskyi play a central role in the global biogeochemical nitrogen cycle. In addition to this central role, the autotrophic nitrite-oxidizing bacteria also play a fundamental role in the global carbon cycle. They form the basis of heterotrophic food webs, in which the assimilated carbon is recycled. Little is known about the heterotrophic microorganisms that participate in these food webs, let alone their assembly in different ecosystems. This study showed that the assembly of microbial food webs by N. winogradskyi was a highly stochastic process and independent of the origin of the heterotrophic microorganisms, but the functional characteristics of the different food webs were similar.}, } @article {pmid35943155, year = {2022}, author = {Moya-Gonzálvez, EM and Peña-Gil, N and Rubio-Del-Campo, A and Coll-Marqués, JM and Gozalbo-Rovira, R and Monedero, V and Rodríguez-Díaz, J and Yebra, MJ}, title = {Infant Gut Microbial Metagenome Mining of α-l-Fucosidases with Activity on Fucosylated Human Milk Oligosaccharides and Glycoconjugates.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0177522}, pmid = {35943155}, issn = {2165-0497}, mesh = {Animals ; *Blood Group Antigens/analysis/metabolism ; Fucose/analysis/chemistry/metabolism ; *Gastrointestinal Microbiome ; Glycoconjugates/analysis/metabolism ; Humans ; Infant ; Infant, Newborn ; Mammals/genetics/metabolism ; Metagenome ; Milk, Human/chemistry/metabolism ; Oligosaccharides/analysis/chemistry/metabolism ; Polysaccharides ; alpha-L-Fucosidase/chemistry/genetics/metabolism ; }, abstract = {The gastrointestinal microbiota members produce α-l-fucosidases that play key roles in mucosal, human milk, and dietary oligosaccharide assimilation. Here, 36 open reading frames (ORFs) coding for putative α-l-fucosidases belonging to glycosyl hydrolase family 29 (GH29) were identified through metagenome analysis of breast-fed infant fecal microbiome. Twenty-two of those ORFs showed a complete coding sequence with deduced amino acid sequences displaying the highest degree of identity with α-l-fucosidases from Bacteroides thetaiotaomicron, Bacteroides caccae, Phocaeicola vulgatus, Phocaeicola dorei, Ruminococcus gnavus, and Streptococcus parasanguinis. Based on sequence homology, 10 α-l-fucosidase genes were selected for substrate specificity characterization. The α-l-fucosidases Fuc18, Fuc19A, Fuc35B, Fuc39, and Fuc1584 showed hydrolytic activity on α1,3/4-linked fucose present in Lewis blood antigens and the human milk oligosaccharide (HMO) 3-fucosyllactose. In addition, Fuc1584 also hydrolyzed fucosyl-α-1,6-N-acetylglucosamine (6FN), a component of the core fucosylation of N-glycans. Fuc35A and Fuc193 showed activity on α1,2/3/4/6 linkages from H type-2, Lewis blood antigens, HMOs and 6FN. Fuc30 displayed activity only on α1,6-linked l-fucose, and Fuc5372 showed a preference for α1,2 linkages. Fuc2358 exhibited a broad substrate specificity releasing l-fucose from all the tested free histo-blood group antigens, HMOs, and 6FN. This latest enzyme also displayed activity in glycoconjugates carrying lacto-N-fucopentaose II (Le[a]) and lacto-N-fucopentaose III (Le[x]) and in the glycoprotein mucin. Fuc18, Fuc19A, and Fuc39 also removed l-fucose from neoglycoproteins and human α-1 acid glycoprotein. These results give insight into the great diversity of α-l-fucosidases from the infant gut microbiota, thus supporting the hypothesis that fucosylated glycans are crucial for shaping the newborn microbiota composition. IMPORTANCE α-l-Fucosyl residues are frequently present in many relevant glycans, such as human milk oligosaccharides (HMOs), histo-blood group antigens (HBGAs), and epitopes on cell surface glycoconjugate receptors. These fucosylated glycans are involved in a number of mammalian physiological processes, including adhesion of pathogens and immune responses. The modulation of l-fucose content in such processes may provide new insights and knowledge regarding molecular interactions and may help to devise new therapeutic strategies. Microbial α-l-fucosidases are exoglycosidases that remove α-l-fucosyl residues from free oligosaccharides and glycoconjugates and can be also used in transglycosylation reactions to synthesize oligosaccharides. In this work, α-l-fucosidases from the GH29 family were identified and characterized from the metagenome of fecal samples of breastfed infants. These enzymes showed different substrate specificities toward HMOs, HBGAs, naturally occurring glycoproteins, and neoglycoproteins. These novel glycosidase enzymes from the breast-fed infant gut microbiota, which resulted in a good source of α-l-fucosidases, have great biotechnological potential.}, } @article {pmid35941765, year = {2022}, author = {Singh, V and Son, H and Lee, G and Lee, S and Unno, T and Shin, JH}, title = {Role, relevance, and possibilities of in vitro fermentation models in human dietary, and gut-microbial studies.}, journal = {Biotechnology and bioengineering}, volume = {119}, number = {11}, pages = {3044-3061}, doi = {10.1002/bit.28206}, pmid = {35941765}, issn = {1097-0290}, mesh = {Animals ; Colon ; Diet ; Fatty Acids, Volatile/metabolism ; Fermentation ; Humans ; *Microbiota ; *Prebiotics ; }, abstract = {Dietary studies play a crucial role in determining the health-benefiting effects of most food substances, including prebiotics, probiotics, functional foods, and bioactive compounds. Such studies involve gastrointestinal digestion and colonic fermentation of dietary substances. In colonic fermentation, any digested food is further metabolized in the gut by the residing colonic microbiota, causing a shift in the gut microenvironment and production of various metabolites, such as short-chain fatty acids. These diet-induced shifts in the microbial community and metabolite production, which can be assessed through in vitro fermentation models using a donor's fecal microbiota, are well known to impact the health of the host. Although in vivo or animal experiments are the gold standard in dietary studies, recent advancements using different in vitro systems, like artificial colon (ARCOL), mini bioreactor array (MBRA), TNO in vitro model of the colon (TIM), Simulator of the Human Intestinal Microbial Ecosystem (SHIME), M-SHIME, Copenhagen MiniGut, and Dynamic Gastrointestinal Simulator, make it easy to study the dietary impact in terms of the gut microbiota and metabolites. Such a continuous in vitro system can have multiple compartments corresponding to different parts of the colon, that is, proximal, transverse, and distal colon, making the findings physiologically more significant. Furthermore, postfermentation samples can be analyzed using metagenomic, metabolomic, quantitative-polymerase chain reaction, and flow-cytometry approaches. Moreover, studies have shown that in vitro results are in accordance with the in vivo findings, supporting their relevance in dietary studies and giving confidence that shifts in metabolites are only due to microbes. This review meticulously describes the recent advancements in various fermentation models and their relevance in dietary studies.}, } @article {pmid35941112, year = {2022}, author = {Martino, C and Zaramela, LS and Gao, B and Embree, M and Tarasova, J and Parker, SJ and Wang, Y and Chu, H and Chen, P and Lee, KC and Galzerani, DD and Gengatharan, JM and Lekbua, A and Neal, M and Knight, R and Tsukamoto, H and Metallo, CM and Schnabl, B and Zengler, K}, title = {Acetate reprograms gut microbiota during alcohol consumption.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {4630}, pmid = {35941112}, issn = {2041-1723}, support = {R01 CA234245/CA/NCI NIH HHS/United States ; I01 BX004594/BX/BLRD VA/United States ; I01 BX001991/BX/BLRD VA/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; R37 AA020703/AA/NIAAA NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; IK6 BX004205/BX/BLRD VA/United States ; U01 AA026939/AA/NIAAA NIH HHS/United States ; P30 CA014195/CA/NCI NIH HHS/United States ; }, mesh = {Acetates/pharmacology ; Alcohol Drinking/adverse effects ; Animals ; Ethanol/metabolism ; *Gastrointestinal Microbiome ; *Liver Diseases ; Mice ; Mice, Inbred C57BL ; }, abstract = {Liver damage due to chronic alcohol use is among the most prevalent liver diseases. Alcohol consumption frequency is a strong factor of microbiota variance. Here we use isotope labeled [1-[13]C] ethanol, metagenomics, and metatranscriptomics in ethanol-feeding and intragastric mouse models to investigate the metabolic impacts of alcohol consumption on the gut microbiota. First, we show that although stable isotope labeled [1-[13]C] ethanol contributes to fatty acid pools in the liver, plasma, and cecum contents of mice, there is no evidence of ethanol metabolism by gut microbiota ex vivo under anaerobic conditions. Next, we observe through metatranscriptomics that the gut microbiota responds to ethanol-feeding by activating acetate dissimilation, not by metabolizing ethanol directly. We demonstrate that blood acetate concentrations are elevated during ethanol consumption. Finally, by increasing systemic acetate levels with glyceryl triacetate supplementation, we do not observe any impact on liver disease, but do induce similar gut microbiota alterations as chronic ethanol-feeding in mice. Our results show that ethanol is not directly metabolized by the gut microbiota, and changes in the gut microbiota linked to ethanol are a side effect of elevated acetate levels. De-trending for these acetate effects may be critical for understanding gut microbiota changes that cause alcohol-related liver disease.}, } @article {pmid35940813, year = {2022}, author = {Rahmeh, R and Akbar, A and Alomirah, H and Kishk, M and Al-Ateeqi, A and Al-Milhm, S and Shajan, A and Akbar, B and Al-Merri, S and Alotaibi, M and Esposito, A}, title = {Camel milk microbiota: A culture-independent assessment.}, journal = {Food research international (Ottawa, Ont.)}, volume = {159}, number = {}, pages = {111629}, doi = {10.1016/j.foodres.2022.111629}, pmid = {35940813}, issn = {1873-7145}, mesh = {Animals ; Bacteria/genetics ; Camelus ; Humans ; *Microbiota/genetics ; Milk/microbiology ; *Mycobiome ; }, abstract = {Camel milk is renowned for its nutritional value and its therapeutic properties. It is considered a promising alternative to bovine milk due to its higher nutritional benefits, hypoallergenic characteristics and greater digestibility in the human gastrointestinal system. This study reports camel milk's bacterial and fungal microbiota, and the effect of geographical location and season on its bacterial community. We sequenced the V3-V4 regions of the16S rRNA gene for bacteria and the internal transcribed spacer (ITS) for fungi. A total of 134 samples of dromedary raw camel milk were collected from south, north and middle Kuwait during two seasons. Raw camel milk showed a diversified bacterial community, with 1196 genera belonging to 33 phyla. The four most predominant phyla of bacteria were Proteobacteria, Firmicutes, Actinobacteria and Bacteroidota. The core microbiota of raw camel milk, represented by the dominant genera shared by the majority of samples, was constituted by the genera Schlegelella, Paenibacillus, Lactobacillus, unclassified Comamonadaceae, Pediococcus, Moraxella, Acinetobacter, Staphylococcus, Enterococcus, Pseudomonas, Streptococcus, unclassified Micrococcaceae, Rothia, unclassified Sphingomonadaceae, unclassified Neisseriaceae and Sphingomonas. The fungal population was assessed in 14 raw camel milk samples, and comprised 87 genera belonging to 3 phyla. The genera Penicillium, Cladosporium, Candida, Aspergillus, Alternaria and Fusarium, dominated the fungal community. These findings shed light on raw camel milk's core bacterial and fungal microbiome. The geographical location and the season had a significant impact on the diversity and composition of camel milk microbiome.}, } @article {pmid35939616, year = {2022}, author = {Wang, J and Qie, J and Zhu, D and Zhang, X and Zhang, Q and Xu, Y and Wang, Y and Mi, K and Pei, Y and Liu, Y and Ji, G and Liu, X}, title = {The landscape in the gut microbiome of long-lived families reveals new insights on longevity and aging - relevant neural and immune function.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2107288}, pmid = {35939616}, issn = {1949-0984}, mesh = {Aged ; Aged, 80 and over ; Aging ; Bacteria/genetics ; Brain-Derived Neurotrophic Factor/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Immunity ; Longevity ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Human longevity has a strong familial and genetic component. Dynamic characteristics of the gut microbiome during aging associated with longevity, neural, and immune function remained unknown. Here, we aim to reveal the synergistic changes in gut microbiome associated with decline in neural and immune system with aging and further obtain insights into the establishment of microbiome homeostasis that can benefit human longevity. Based on 16S rRNA and metagenomics sequencing data for 32 longevity families including three generations, centenarians, elderly, and young groups, we found centenarians showed increased diversity of gut microbiota, severely damaged connection among bacteria, depleted in microbial-associated essential amino acid function, and increased abundance of anti-inflammatory bacteria in comparison to young and elderly groups. Some potential probiotic species, such as Desulfovibrio piger, Gordonibacter pamelaeae, Odoribacter splanchnicus, and Ruminococcaceae bacterium D5 were enriched with aging, which might possibly support health maintenance. The level of Amyloid-β (Aβ) and brain-derived neurotrophic factor (BDNF) related to neural function showed increased and decreased with aging, respectively. The elevated level of inflammatory factors was observed in centenarians compared with young and elderly groups. The enriched Bacteroides fragilis in centenarians might promote longevity through up-regulating anti-inflammatory factor IL-10 expression to mediate the critical balance between health and disease. Impressively, the associated analysis for gut microbiota with the level of Aβ, BDNF, and inflammatory factors suggests Bifidobacterium pseudocatenulatum could be a particularly beneficial bacteria in the improvement of impaired neural and immune function. Our results provide a rationale for targeting the gut microbiome in future clinical applications of aging-related diseases and extending life span.Abbreviations: 16S rRNA: 16S ribosomal RNA; MAGs: Metagenome-assembled genomes; ASVs: Amplicon sequence variants; DNA: Deoxyribonucleic acid; FDR: False discovery rate: KEGG: Kyoto Encyclopedia of Genes and Genomes; PCoA: Principal coordinates analysis; PCR: Polymerase chain reaction; PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States; Aβ: Amyloid-β (Aβ); BDNF: Brain-derived neurotrophic factor.}, } @article {pmid35938729, year = {2022}, author = {Du, S and Zhang, Y and Shen, JP and Hu, HW and Zhang, J and Shu, C and He, JZ}, title = {Alteration of Manure Antibiotic Resistance Genes via Soil Fauna Is Associated with the Intestinal Microbiome.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0052922}, pmid = {35938729}, issn = {2379-5077}, mesh = {Animals ; Humans ; *Gastrointestinal Microbiome/genetics ; Soil ; Manure/analysis ; Anti-Bacterial Agents/analysis ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Larva/genetics ; }, abstract = {Livestock wastes contain high levels of antibiotic resistance genes (ARGs) and a variety of human-related pathogens. Bioconversion of livestock manure using larvae of the beetle Protaetia brevitarsis is an effective technique for waste reduction and value creation; however, the fate of manure ARGs during gut passage and interaction with the gut microbiome of P. brevitarsis remains unclear. To investigate this, we fed P. brevitarsis with dry chicken manure for 6 days and measured bacterial community dynamics and ARG abundance and diversity along the P. brevitarsis gut tract using high-throughput quantitative PCR and metagenomics approaches. The diversity of ARGs was significantly lower in larval midgut, hindgut, and frass than in raw chicken manure, and around 80% of pathogenicity-related genes (PRGs) exhibited reduced abundance. Network analysis demonstrated that Bacteroidetes and Firmicutes were the key bacterial phyla associated with ARG reduction. Metagenomic analysis further indicated that ARGs, mobile genetic elements (MGEs), and PRGs were simultaneously attenuated in the hindgut, implicating a decreased likelihood for horizontal gene transfer (HGT) of ARGs among bacteria and pathogens during manure bioconversion. Our findings demonstrated that the attenuation of ARGs is strongly associated with the variation of the gut microbiome of P. brevitarsis, providing insights into mechanisms of risk mitigation of ARG dissemination during manure bioconversion. IMPORTANCE Saprophagous fauna like the oriental edible beetle (P. brevitarsis) plays a fundamental role in converting organic wastes into biofertilizer. Accumulating evidence has shown that soil fauna can reduce the abundance of ARGs, although the underlying mechanism of ARG reduction is still unclear. In our previous research, we found a large reduction of ARGs in vegetable roots and leaves from frass compared with raw manure, providing a promising biofertilizer for soil-vegetable systems. Therefore, in this study, temporal dynamic changes in the microbiomes of the donor (chicken manure) and host (P. brevitarsis) were investigated, and we found a close association between the gut microbiome and the alteration of ARGs. These results shed new light on how the insect gut microbiome can mitigate manure-borne ARGs and provide insights into the bioconversion process via a typical member of the saprophagous fauna, P. brevitarsis.}, } @article {pmid35937693, year = {2022}, author = {Fu, Y and Wu, J and Wang, D and Li, T and Shi, X and Li, L and Zhu, M and Zhang, Z and Yu, X and Dai, Q}, title = {Metagenomic profiling of ocular surface microbiome changes in Demodex blepharitis patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {922753}, pmid = {35937693}, issn = {2235-2988}, mesh = {*Acinetobacter ; Bacteria/genetics ; *Blepharitis/epidemiology/pathology ; Humans ; Meibomian Glands/pathology ; *Microbiota/genetics ; Proteobacteria ; }, abstract = {PURPOSE: To compare the ocular surface and meibum microbial communities of humans with Demodex Blepharitis (DB) and healthy controls.

METHODS: Conjunctival sac and meibum samples from 25 DB patients and 11 healthy controls were analyzed using metagenomic next-generation sequencing (mNGS).

RESULTS: The alpha-diversity of the conjunctival sac microbiome of the DB group (observed, Chao1, ACE) was lower than that of the control group, whereas all meibum diversity indicators were similar. In conjunctival samples, the relative abundance (RA) of the phylum Proteobacteria was significantly higher (p=0.023), and the RA of both phyla Actinobacteria and Firmicutes was significantly lower (p=0.002, 0.025, respectively) in the DB group than that in the control group. In meibum samples, the RA of the phyla Proteobacteria and Actinobacteria were similar, whereas that of the phylum Firmicutes was significantly lower in the DB group (p=0.019) than that in the control group. Linear discriminant analysis with effect size measurement of the conjunctival and meibum microbiomes showed that Sphingobium sp. YG1 and Acinetobacter guillouiae were enriched in the DB group. Sphingobium sp. YG1, Acinetobacter guillouiae and Pseudomonas putida in the DB group were related to more severe ocular surface clinical parameters. Discriminative genera's principal coordinate analysis separated all control and DB microbiomes into two distinct clusters.

CONCLUSIONS: Proteobacteria's increased prevalence may indicate ocular microbial community instability. The species Sphingobium sp. YG1 and Acinetobacter guillouiae are potentially pathogenic bacterial biomarkers in DB. Demodex infection mainly affects the ocular surface microbiome rather than penetrating deeper into the meibomian gland.}, } @article {pmid35935588, year = {2022}, author = {Yang, Q and Xu, Y and Shen, L and Pan, Y and Huang, J and Ma, Q and Yu, C and Chen, J and Chen, Y and Chen, M}, title = {Guanxinning Tablet Attenuates Coronary Atherosclerosis via Regulating the Gut Microbiota and Their Metabolites in Tibetan Minipigs Induced by a High-Fat Diet.}, journal = {Journal of immunology research}, volume = {2022}, number = {}, pages = {7128230}, pmid = {35935588}, issn = {2314-7156}, mesh = {Animals ; *Coronary Artery Disease ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Swine ; Swine, Miniature ; Tablets/pharmacology ; Tibet ; Tumor Necrosis Factor-alpha/pharmacology ; }, abstract = {Coronary atherosclerosis (CA) is a chronic and evolving inflammatory disease characterized by the build-up of atherosclerotic plaque in the wall of coronary arteries. Guanxinning tablet (GXNT) is a novel Chinese medicine formula, which has been clinically used to treat coronary heart disease for many years. However, the potential mechanism for treating CA remains unclear. Thus, the study was aimed at investigating the therapeutic effect of GXNT on CA and further explore the underlying mechanisms from the perspective of gut microbiota. Following the establishment of a CA model in Tibetan minipigs, GXNT was orally administrated. We simultaneously detected blood lipid levels, observed ventricular function using ultrasound examination, measured platelet aggregation, and checked changes in inflammatory factors, oxidative stress factors, and vascular endothelial injury-related indexes applying ELISA assays. Histopathological changes of coronary artery tissue were subsequently evaluated using Sudan IV staining, HE staining, Oil red "O" staining, and immunohistochemistry assays. Finally, alterations of the gut microbiota and microbial metabolites were detected using metagenomic sequencing and targeted metabolomics, respectively. The results have suggested that GXNT could regulate dyslipidemia, improve heart function, and inhibit the levels of ox-LDL, CRP, TNF-α, IL-1β, SOD, MDA, vWF, and ET-1, as well as platelet aggregation. Additionally, histopathological findings revealed that GXNT could reduce lipid deposition, alleviate AS lesions, and restrain the expressions of NF-κB, TNF-α, and MMP-9. Furthermore, the composition of the gut microbiota was altered. Specifically, GXNT could upregulate the relative abundance of Prevotellaceae and Prevotella and downregulate the abundance of Proteobacteria, Enterobacteriaceae, and Escherichia. As for microbial metabolites, GXNT could increase fecal propionic acid, butyric acid, and LCA-3S and decrease fecal TMA-related metabolites, CDCA, and serum TMAO. In sum, the results showed that GXNT had a satisfactory anti-CA effect, and the mechanism was closely associated with modulating gut microbiota and related metabolites.}, } @article {pmid35934074, year = {2022}, author = {Lou, D and Zhang, X and Cao, Y and Zhou, Z and Liu, C and Kuang, G and Tan, J and Zhu, L}, title = {A novel NADP(H)-dependent 3α-HSDH from the intestinal microbiome of Ursus thibetanus.}, journal = {International journal of biological macromolecules}, volume = {219}, number = {}, pages = {159-165}, doi = {10.1016/j.ijbiomac.2022.07.252}, pmid = {35934074}, issn = {1879-0003}, mesh = {Animals ; Bile Acids and Salts ; Escherichia coli/genetics/metabolism ; *Gastrointestinal Microbiome ; Glutathione ; Glycochenodeoxycholic Acid ; Hydroxysteroid Dehydrogenases/metabolism ; Ions ; NADP ; Peptide Hydrolases ; Recombinant Proteins/metabolism ; Transferases ; *Ursidae/metabolism ; }, abstract = {3α-HSDHs have a crucial role in the bioconversion of steroids, and have been widely applied in the detection of total bile acid (TBA). In this study, we report a novel NADP(H)-dependent 3α-HSDH (named Sc 3α-HSDH) cloned from the intestinal microbiome of Ursus thibetanus. Sc 3α-HSDH was solubly expressed in E. coli (BL21) as a recombinant glutathione-S-transferase (GST)-tagged protein and freed from its GST-fusion by cleavage using the PreScission protease. Sc 3α-HSDH is a new member of the short-chain dehydrogenases/reductase superfamily (SDRs) with a typical α/β folding pattern, based on protein three-dimensional models predicted by AlphaFold. The best activity of Sc 3α-HSDH occurred at pH 8.5 and the temperature optima was 55 °C, indicating that Sc 3α-HSDH is not an extremozyme. The catalytic efficiencies (kcat/Km) of Sc 3α-HSDH catalyzing the oxidation reaction with the substrates, glycochenodeoxycholic acid (GCDCA) and glycoursodeoxycholic acid (GUDCA), were 183.617 and 34.458 s[-1] mM[-1], respectively. In addition, multiple metal ions can enhance the activity of Sc 3α-HSDH when used at concentrations ranging from 2 % to 42 %. The results also suggest that the metagenomic approach is an efficient method for identifying novel enzymes.}, } @article {pmid35933411, year = {2022}, author = {Zhang, H and Wang, M and Wang, H and Chen, H and Cao, L and Zhong, Z and Lian, C and Zhou, L and Li, C}, title = {Metagenome sequencing and 768 microbial genomes from cold seep in South China Sea.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {480}, pmid = {35933411}, issn = {2052-4463}, support = {42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42076091//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42076091//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Archaea/genetics ; Bacteria/genetics ; *Genome, Microbial ; Geologic Sediments/microbiology ; *Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cold seep microbial communities are fascinating ecosystems on Earth which provide unique models for understanding the living strategies in deep-sea distinct environments. In this study, 23 metagenomes were generated from samples collected in the Site-F cold seep field in South China Sea, including the sea water closely above the invertebrate communities, the cold seep fluids, the fluids under the invertebrate communities and the sediment column around the seep vent. By binning tools, we retrieved a total of 768 metagenome assembled genome (MAGs) that were estimated to be >60% complete. Of the MAGs, 61 were estimated to be >90% complete, while an additional 105 were >80% complete. Phylogenomic analysis revealed 597 bacterial and 171 archaeal MAGs, of which nearly all were distantly related to known cultivated isolates. In the 768 MAGs, the abundant Bacteria in phylum level included Proteobacteria, Desulfobacterota, Bacteroidota, Patescibacteria and Chloroflexota, while the abundant Archaea included Asgardarchaeota, Thermoplasmatota, and Thermoproteota. These results provide a dataset available for further interrogation of deep-sea microbial ecology.}, } @article {pmid35931735, year = {2022}, author = {Kim, K and Lee, S and Park, SC and Kim, NE and Shin, C and Lee, SK and Jung, Y and Yoon, D and Kim, H and Kim, S and Hwang, GS and Won, S}, title = {Role of an unclassified Lachnospiraceae in the pathogenesis of type 2 diabetes: a longitudinal study of the urine microbiome and metabolites.}, journal = {Experimental & molecular medicine}, volume = {54}, number = {8}, pages = {1125-1132}, pmid = {35931735}, issn = {2092-6413}, mesh = {Acetoacetates ; *Diabetes Mellitus, Type 2/complications ; Glycated Hemoglobin ; Humans ; Longitudinal Studies ; *Microbiota ; Prospective Studies ; }, abstract = {Recent investigations have revealed that the human microbiome plays an essential role in the occurrence of type 2 diabetes (T2D). However, despite the importance of understanding the involvement of the microbiota throughout the body in T2D, most studies have focused specifically on the intestinal microbiota. Extracellular vesicles (EVs) have been recently found to provide important evidence regarding the mechanisms of T2D pathogenesis, as they act as key messengers between intestinal microorganisms and the host. Herein, we explored microorganisms potentially associated with T2D by tracking changes in microbiota-derived EVs from patient urine samples collected three times over four years. Mendelian randomization analysis was conducted to evaluate the causal relationships among microbial organisms, metabolites, and clinical measurements to provide a comprehensive view of how microbiota can influence T2D. We also analyzed EV-derived metagenomic (N = 393), clinical (N = 5032), genomic (N = 8842), and metabolite (N = 574) data from a prospective longitudinal Korean community-based cohort. Our data revealed that GU174097_g, an unclassified Lachnospiraceae, was associated with T2D (β = -189.13; p = 0.00006), and it was associated with the ketone bodies acetoacetate and 3-hydroxybutyrate (r = -0.0938 and -0.0829, respectively; p = 0.0022 and 0.0069, respectively). Furthermore, a causal relationship was identified between acetoacetate and HbA1c levels (β = 0.0002; p = 0.0154). GU174097_g reduced ketone body levels, thus decreasing HbA1c levels and the risk of T2D. Taken together, our findings indicate that GU174097_g may lower the risk of T2D by reducing ketone body levels.}, } @article {pmid35931074, year = {2022}, author = {Podlesny, D and Durdevic, M and Paramsothy, S and Kaakoush, NO and Högenauer, C and Gorkiewicz, G and Walter, J and Fricke, WF}, title = {Identification of clinical and ecological determinants of strain engraftment after fecal microbiota transplantation using metagenomics.}, journal = {Cell reports. Medicine}, volume = {3}, number = {8}, pages = {100711}, pmid = {35931074}, issn = {2666-3791}, mesh = {*Clostridium Infections/therapy ; Dysbiosis/therapy ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; }, abstract = {Fecal microbiota transplantation (FMT) is a promising therapeutic approach for microbiota-associated pathologies, but our understanding of the post-FMT microbiome assembly process and its ecological and clinical determinants is incomplete. Here we perform a comprehensive fecal metagenome analysis of 14 FMT trials, involving five pathologies and >250 individuals, and determine the origins of strains in patients after FMT. Independently of the underlying clinical condition, conspecific coexistence of donor and recipient strains after FMT is uncommon and donor strain engraftment is strongly positively correlated with pre-FMT recipient microbiota dysbiosis. Donor strain engraftment was enhanced through antibiotic pretreatment and bowel lavage and dependent on donor and recipient ɑ-diversity; strains from relatively abundant species were more likely and from predicted oral, oxygen-tolerant, and gram-positive species less likely to engraft. We introduce a general mechanistic framework for post-FMT microbiome assembly in alignment with ecological theory, which can guide development of optimized, more targeted, and personalized FMT therapies.}, } @article {pmid35930838, year = {2022}, author = {Roslund, MI and Parajuli, A and Hui, N and Puhakka, R and Grönroos, M and Soininen, L and Nurminen, N and Oikarinen, S and Cinek, O and Kramná, L and Schroderus, AM and Laitinen, OH and Kinnunen, T and Hyöty, H and Sinkkonen, A and , }, title = {A Placebo-controlled double-blinded test of the biodiversity hypothesis of immune-mediated diseases: Environmental microbial diversity elicits changes in cytokines and increase in T regulatory cells in young children.}, journal = {Ecotoxicology and environmental safety}, volume = {242}, number = {}, pages = {113900}, doi = {10.1016/j.ecoenv.2022.113900}, pmid = {35930838}, issn = {1090-2414}, mesh = {Bacteria/genetics ; Biodiversity ; Child, Preschool ; Cytokines ; Double-Blind Method ; Humans ; *Interleukin-10 ; *Interleukin-17 ; Sand ; T-Lymphocytes, Regulatory ; }, abstract = {BACKGROUND: According to the biodiversity hypothesis of immune-mediated diseases, lack of microbiological diversity in the everyday living environment is a core reason for dysregulation of immune tolerance and - eventually - the epidemic of immune-mediated diseases in western urban populations. Despite years of intense research, the hypothesis was never tested in a double-blinded and placebo-controlled intervention trial.

OBJECTIVE: We aimed to perform the first placebo-controlled double-blinded test that investigates the effect of biodiversity on immune tolerance.

METHODS: In the intervention group, children aged 3-5 years were exposed to playground sand enriched with microbially diverse soil, or in the placebo group, visually similar, but microbially poor sand colored with peat (13 participants per treatment group). Children played twice a day for 20 min in the sandbox for 14 days. Sand, skin and gut bacterial, and blood samples were taken at baseline and after 14 days. Bacterial changes were followed for 28 days. Sand, skin and gut metagenome was determined by high throughput sequencing of bacterial 16 S rRNA gene. Cytokines were measured from plasma and the frequency of blood regulatory T cells was defined as a percentage of total CD3 +CD4 + T cells.

RESULTS: Bacterial richness (P < 0.001) and diversity (P < 0.05) were higher in the intervention than placebo sand. Skin bacterial community, including Gammaproteobacteria, shifted only in the intervention treatment to resemble the bacterial community in the enriched sand (P < 0.01). Mean change in plasma interleukin-10 (IL-10) concentration and IL-10 to IL-17A ratio supported immunoregulation in the intervention treatment compared to the placebo treatment (P = 0.02). IL-10 levels (P = 0.001) and IL-10 to IL-17A ratio (P = 0.02) were associated with Gammaproteobacterial community on the skin. The change in Treg frequencies was associated with the relative abundance of skin Thermoactinomycetaceae 1 (P = 0.002) and unclassified Alphaproteobacteria (P < 0.001). After 28 days, skin bacterial community still differed in the intervention treatment compared to baseline (P < 0.02).

CONCLUSIONS: This is the first double-blinded placebo-controlled study to show that daily exposure to microbial biodiversity is associated with immune modulation in humans. The findings support the biodiversity hypothesis of immune-mediated diseases. We conclude that environmental microbiota may contribute to child health, and that adding microbiological diversity to everyday living environment may support immunoregulation.}, } @article {pmid35930195, year = {2022}, author = {Ceylani, T and Teker, HT}, title = {The effect of young blood plasma administration on gut microbiota in middle-aged rats.}, journal = {Archives of microbiology}, volume = {204}, number = {9}, pages = {541}, pmid = {35930195}, issn = {1432-072X}, support = {BAP-21-TBMY-4901-07//Muş Alparslan Üniversitesi/ ; }, mesh = {Animals ; Bacteria/genetics ; Dysbiosis/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Metagenome ; Plasma ; Rats ; }, abstract = {Numerous in-depth studies continue to reveal the many benefits of gut microbiota and young blood plasma administration. Dysbiosis, which occurs in the intestinal microbiota, especially in the aging process, is associated with many metabolic and cognitive disorders. Therefore, many studies aim to reverse the dysbiosis that occurs. There are also studies showing that young blood plasma application reverses the effects of aging at the level of many tissues and organs. Today, while research continues to reveal all the benefits of young blood plasma application in terms of health, blood plasma centers are also being established. In this study, we aimed to reveal the impact of young blood plasma, administered for 1 month, on the intestinal microbiota of middle-aged rats. After detailed metagenome analysis, alpha diversity indices demonstrated greater bacterial richness in the microbiota of plasma-administered rats compared with control rats. In addition, the Firmicutes/Bacteroidetes ratio was significantly diminished in plasma group microbiota, confirming possible rejuvenation properties of young plasma. Furthermore, increased counts of Bifidobacterium longum, Coprococcus catus, and Romboutsia ilealis species were measured in plasma-administered rats. The study revealed many fluctuations in different bacterial taxonomic units of the microbiota that could be valuable in future research on blood-based anti-aging treatments.}, } @article {pmid35930018, year = {2022}, author = {Zhang, X and Ren, H and Zhao, C and Shi, Z and Qiu, L and Yang, F and Zhou, X and Han, X and Wu, K and Zhong, H and Li, Y and Li, J and Ji, L}, title = {Metagenomic analysis reveals crosstalk between gut microbiota and glucose-lowering drugs targeting the gastrointestinal tract in Chinese patients with type 2 diabetes: a 6 month, two-arm randomised trial.}, journal = {Diabetologia}, volume = {65}, number = {10}, pages = {1613-1626}, pmid = {35930018}, issn = {1432-0428}, mesh = {Acarbose/therapeutic use ; Blood Glucose/metabolism ; China ; *Diabetes Mellitus, Type 2 ; Ecosystem ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/metabolism ; Glipizide/therapeutic use ; Glucagon-Like Peptide 1/therapeutic use ; Glucose ; Humans ; Hypoglycemic Agents/pharmacology ; Research ; Vildagliptin/therapeutic use ; }, abstract = {AIMS/HYPOTHESIS: The use of oral glucose-lowering drugs, particularly those designed to target the gut ecosystem, is often observed in association with altered gut microbial composition or functional capacity in individuals with type 2 diabetes. The gut microbiota, in turn, plays crucial roles in the modulation of drug efficacy. We aimed to assess the impacts of acarbose and vildagliptin on human gut microbiota and the relationships between pre-treatment gut microbiota and therapeutic responses.

METHODS: This was a randomised, open-labelled, two-arm trial in treatment-naive type 2 diabetes patients conducted in Beijing between December 2016 and December 2017. One hundred participants with overweight/obesity and newly diagnosed type 2 diabetes were recruited from the Pinggu Hospital and randomly assigned to the acarbose (n=50) or vildagliptin (n=50) group using sealed envelopes. The treatment period was 6 months. Blood, faecal samples and visceral fat data from computed tomography images were collected before and after treatments to measure therapeutic outcomes and gut microbiota. Metagenomic datasets from a previous type 2 diabetes cohort receiving acarbose or glipizide for 3 months were downloaded and processed. Statistical analyses were applied to identify the treatment-related changes in clinical variables, gut microbiota and associations.

RESULTS: Ninety-two participants were analysed. After 6 months of acarbose (n=44) or vildagliptin (n=48) monotherapy, both groups achieved significant reductions in HbA1c (from 60 to 46 mmol/mol [from 7.65% to 6.40%] in the acarbose group and from 59 to 44 mmol/mol [from 7.55% to 6.20%] in the vildagliptin group) and visceral fat areas (all adjusted p values for pre-post comparisons <0.05). Both arms showed drug-specific and shared changes in relative abundances of multiple gut microbial species and pathways, especially the common reductions in Bacteroidetes species. Three months and 6 months of acarbose-induced changes in microbial composition were highly similar in type 2 diabetes patients from the two independent studies. Vildagliptin treatment significantly enhanced fasting active glucagon-like peptide-1 (GLP-1) levels. Baseline gut microbiota, rather than baseline GLP-1 levels, were strongly associated with GLP-1 response to vildagliptin, and to a lesser extent with GLP-1 response to acarbose.

CONCLUSIONS/INTERPRETATION: This study reveals common microbial responses in type 2 diabetes patients treated with two glucose-lowering drugs targeting the gut differently and acceptable performance of baseline gut microbiota in classifying individuals with different GLP-1 responses to vildagliptin. Our findings highlight bidirectional interactions between gut microbiota and glucose-lowering drugs.

TRIAL REGISTRATION: ClinicalTrials.gov NCT02999841 FUNDING: National Key Research and Development Project: 2016YFC1304901.}, } @article {pmid35929783, year = {2022}, author = {Sampara, P and Luo, Y and Lin, X and Ziels, RM}, title = {Integrating Genome-Resolved Metagenomics with Trait-Based Process Modeling to Determine Biokinetics of Distinct Nitrifying Communities within Activated Sludge.}, journal = {Environmental science & technology}, volume = {56}, number = {16}, pages = {11670-11682}, pmid = {35929783}, issn = {1520-5851}, mesh = {Bacteria/genetics ; Bioreactors/microbiology ; Metagenomics ; *Microbiota ; Nitrification ; Nitrites ; Nitrogen ; Oxidation-Reduction ; *Sewage/microbiology ; }, abstract = {Conventional bioprocess models for wastewater treatment are based on aggregated bulk biomass concentrations and do not incorporate microbial physiological diversity. Such a broad aggregation of microbial functional groups can fail to predict ecosystem dynamics when high levels of physiological diversity exist within trophic guilds. For instance, functional diversity among nitrite-oxidizing bacteria (NOB) can obfuscate engineering strategies for their out-selection in activated sludge (AS), which is desirable to promote energy-efficient nitrogen removal. Here, we hypothesized that different NOB populations within AS can have different physiological traits that drive process performance, which we tested by estimating biokinetic growth parameters using a combination of highly replicated respirometry, genome-resolved metagenomics, and process modeling. A lab-scale AS reactor subjected to a selective pressure for over 90 days experienced resilience of NOB activity. We recovered three coexisting Nitrospira population genomes belonging to two sublineages, which exhibited distinct growth strategies and underwent a compositional shift following the selective pressure. A trait-based process model calibrated at the NOB genus level better predicted nitrite accumulation than a conventional process model calibrated at the NOB guild level. This work demonstrates that trait-based modeling can be leveraged to improve our prediction, control, and design of functionally diverse microbiomes driving key environmental biotechnologies.}, } @article {pmid35928983, year = {2022}, author = {Hakimjavadi, H and George, SH and Taub, M and Dodds, LV and Sanchez-Covarrubias, AP and Huang, M and Pearson, JM and Slomovitz, BM and Kobetz, EN and Gharaibeh, R and Sowamber, R and Pinto, A and Chamala, S and Schlumbrecht, MP}, title = {The vaginal microbiome is associated with endometrial cancer grade and histology.}, journal = {Cancer research communications}, volume = {2}, number = {6}, pages = {447-455}, pmid = {35928983}, issn = {2767-9764}, support = {P30 CA240139/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Female ; *Endometrial Neoplasms/genetics ; Vagina/microbiology ; Hysterectomy ; *Microbiota/genetics ; *Carcinoma ; }, abstract = {The human microbiome has been strongly correlated with disease pathology and outcomes, yet remains relatively underexplored in patients with malignant endometrial disease. In this study, vaginal microbiome samples were prospectively collected at the time of hysterectomy from 61 racially and ethnically diverse patients from three disease conditions: 1) benign gynecologic disease (controls, n=11), 2) low-grade endometrial carcinoma (n=30), and 3) high-grade endometrial carcinoma (n=20). Extracted DNA underwent shotgun metagenomics sequencing, and microbial α and β diversities were calculated. Hierarchical clustering was used to describe community state types (CST), which were then compared by microbial diversity and grade. Differential abundance was calculated, and machine learning utilized to assess the predictive value of bacterial abundance to distinguish grade and histology. Both α- and β-diversity were associated with patient tumor grade. Four vaginal CST were identified that associated with grade of disease. Different histologies also demonstrated variation in CST within tumor grades. Using supervised clustering algorithms, critical microbiome markers at the species level were used to build models that predicted benign vs carcinoma, high-grade carcinoma versus benign, and high-grade versus low-grade carcinoma with high accuracy. These results confirm that the vaginal microbiome segregates not just benign disease from endometrial cancer, but is predictive of histology and grade. Further characterization of these findings in large, prospective studies is needed to elucidate their potential clinical applications.}, } @article {pmid35927305, year = {2022}, author = {Kim, N and Gim, JA and Lee, BJ and Choi, BI and Yoon, HS and Kim, SH and Joo, MK and Park, JJ and Kim, C}, title = {Crosstalk between mucosal microbiota, host gene expression, and sociomedical factors in the progression of colorectal cancer.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {13447}, pmid = {35927305}, issn = {2045-2322}, mesh = {*Adenoma/genetics/microbiology ; Bacteria/genetics ; *Colorectal Neoplasms/pathology ; *Gastrointestinal Microbiome/genetics ; Gene Expression ; Humans ; Intestinal Mucosa/pathology ; *Microbiota/genetics ; }, abstract = {Various omics-based biomarkers related to the occurrence, progression, and prognosis of colorectal cancer (CRC) have been identified. In this study, we attempted to identify gut microbiome-based biomarkers and detect their association with host gene expression in the initiation and progression of CRC by integrating analysis of the gut mucosal metagenome, RNA sequencing, and sociomedical factors. We performed metagenome and RNA sequencing on colonic mucosa samples from 13 patients with advanced CRC (ACRC), 10 patients with high-risk adenoma (HRA), and 7 normal control (NC) individuals. All participants completed a questionnaire on sociomedical factors. The interaction and correlation between changes in the microbiome and gene expression were assessed using bioinformatic analysis. When comparing HRA and NC samples, which can be considered to represent the process of tumor initiation, 28 genes and five microbiome species were analyzed with correlation plots. When comparing ACRC and HRA samples, which can be considered to represent the progression of CRC, seven bacterial species and 21 genes were analyzed. When comparing ACRC and NC samples, 16 genes and five bacterial species were analyzed, and four correlation plots were generated. A network visualizing the relationship between bacterial and host gene expression in the initiation and progression of CRC indicated that Clostridium spiroforme and Tyzzerella nexilis were hub bacteria in the development and progression of CRC. Our study revealed the interactions of and correlation between the colonic mucosal microbiome and host gene expression to identify potential roles of the microbiome in the initiation and progression of CRC. Our results provide gut microbiome-based biomarkers that may be potential diagnostic markers and therapeutic targets in patients with CRC.}, } @article {pmid35922873, year = {2022}, author = {Gaire, TN and Odland, C and Zhang, B and Ray, T and Doster, E and Nerem, J and Dee, S and Davies, P and Noyes, N}, title = {The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {118}, pmid = {35922873}, issn = {2049-2618}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; *Coinfection ; Metagenomics ; *Microbiota/genetics ; *Porcine Reproductive and Respiratory Syndrome/drug therapy ; *Porcine respiratory and reproductive syndrome virus/genetics ; Swine ; }, abstract = {BACKGROUND: Antimicrobials are used in food-producing animals for purposes of preventing, controlling, and/or treating infections. In swine, a major driver of antimicrobial use is porcine reproductive and respiratory syndrome (PRRS), which is caused by a virus that predisposes infected animals to secondary bacterial infections. Numerous antimicrobial protocols are used to treat PRRS, but we have little insight into how these treatment schemes impact antimicrobial resistance (AMR) dynamics within the fecal microbiome of commercial swine. The aim of this study was to determine whether different PRRS-relevant antimicrobial treatment protocols were associated with differences in the fecal microbiome and resistome of growing pigs. To accomplish this, we used a metagenomics approach to characterize and compare the longitudinal wean-to-market resistome and microbiome of pigs challenged with PRRS virus and then exposed to different antimicrobial treatments, and a group of control pigs not challenged with PRRS virus and having minimal antimicrobial exposure. Genomic DNA was extracted from pen-level composite fecal samples from each treatment group and subjected to metagenomic sequencing and microbiome-resistome bioinformatic and statistical analysis. Microbiome-resistome profiles were compared over time and between treatment groups.

RESULTS: Fecal microbiome and resistome compositions both changed significantly over time, with a dramatic and stereotypic shift between weaning and 9 days post-weaning (dpw). Antimicrobial resistance gene (ARG) richness and diversity were significantly higher at earlier time points, while microbiome richness and diversity were significantly lower. The post-weaning shift was characterized by transition from a Bacteroides-dominated enterotype to Lactobacillus- and Streptococcus-dominated enterotypes. Both the microbiome and resistome stabilized by 44 dpw, at which point the trajectory of microbiome-resistome maturation began to diverge slightly between the treatment groups, potentially due to physical clustering of the pigs. Challenge with PRRS virus seemed to correspond to the re-appearance of many very rare and low-abundance ARGs within the feces of challenged pigs. Despite very different antimicrobial exposures after challenge with PRRS virus, resistome composition remained largely similar between the treatment groups. Differences in ARG abundance between the groups were mostly driven by temporal changes in abundance that occurred prior to antimicrobial exposures, with the exception of ermG, which increased in the feces of treated pigs, and was significantly more abundant in the feces of these pigs compared to the pigs that did not receive post-PRRS antimicrobials.

CONCLUSIONS: The fecal microbiome-resistome of growing pigs exhibited a stereotypic trajectory driven largely by weaning and physiologic aging of the pigs. Events such as viral illness, antimicrobial exposures, and physical grouping of the pigs exerted significant yet relatively minor influence over this trajectory. Therefore, the AMR profile of market-age pigs is the culmination of the life history of the individual pigs and the populations to which they belong. Disease status alone may be a significant driver of AMR in market-age pigs, and understanding the interaction between disease processes and antimicrobial exposures on the swine microbiome-resistome is crucial to developing effective, robust, and reproducible interventions to control AMR. Video Abstract.}, } @article {pmid35922588, year = {2022}, author = {Wang, Y and Xu, J and Chen, H and Yu, J and Xu, X and Sun, L and Xu, X and Yu, C and Xu, F and Huang, J and Jiao, X and Zhang, Y}, title = {A balanced gut microbiota is essential to maintain health in captive sika deer.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {17}, pages = {5659-5674}, pmid = {35922588}, issn = {1432-0614}, mesh = {Animals ; Bacteria ; Bifidobacterium ; *Deer ; *Gastrointestinal Microbiome ; Humans ; Lactobacillus ; Metagenomics ; *Microbiota ; }, abstract = {Certain animals harbor a high proportion of pathogens, particular the zoonotic pathogens, in their gut microbiome but are usually asymptomic; however, their carried pathogens may seriously threaten the public health. By understanding how the microbiome overcomes the negative effects of pathogens to maintain host health, we can develop novel solutions to control animal-mediated pathogen transmission including identification and application of beneficial microbes. Here, we analyzed the gut microbiota of 10 asymptomic captive sika deer individuals by full-length 16S rDNA sequencing. Twenty-nine known pathogens capable of infecting humans were identified, and the accumulated proportions of the identified pathogens were highly variable among individuals (2.33 to 39.94%). The relative abundances of several beneficial bacteria, including Lactobacillus and Bifidobacterium, were found to be positively correlated with the relative abundances of accumulated pathogens. Whole-genome metagenomic analysis revealed that the beneficial- and pathogenic-associated functions, such as genes involved in the synthesis of short chain fatty acids and virulence factors, were also positively correlated in the microbiome, indicating that the beneficial and pathogenic functions were maintained at a relatively balanced ratio. Furthermore, the bacteriophages that target the identified pathogens were found to be positively correlated with the pathogenic content in the microbiome. Several high-quality genomes of beneficial bacteria affiliated with Lactobacillus and Bifidobacterium and bacteriophages were recovered from the metagenomic data. Overall, this study provides novel insights into the interplay between beneficial and pathogenic content to ensure maintenance of a healthy gut microbiome, and also contributes to discovery of novel beneficial microbes and functions that control pathogens. KEY POINTS: • Certain asymptomic captive sika deer individuals harbor relatively high amounts of zoonotic pathogens. • The beneficial microbes and the beneficial functions are balanced with the pathogenic contents in the gut microbiome. • Several high-quality genomes of beneficial bacteria and bacteriophages are recovered by metagenomics.}, } @article {pmid35920823, year = {2022}, author = {Aishwarya, S and Gunasekaran, K}, title = {Meta-analysis of the microbial biomarkers in the gut-lung crosstalk in COVID-19, community-acquired pneumonia and Clostridium difficile infections.}, journal = {Letters in applied microbiology}, volume = {75}, number = {5}, pages = {1293-1306}, pmid = {35920823}, issn = {1472-765X}, mesh = {Humans ; *Clostridioides difficile ; *COVID-19 ; *Gastrointestinal Microbiome ; *Clostridium Infections/microbiology ; Dysbiosis ; Lung ; Biomarkers ; }, abstract = {Respiratory infections are the leading causes of mortality and the current pandemic COVID-19 is one such trauma that imposed catastrophic devastation to the health and economy of the world. Unravelling the correlations and interplay of the human microbiota in the gut-lung axis would offer incredible solutions to the underlying mystery of the disease progression. The study compared the microbiota profiles of six samples namely healthy gut, healthy lung, COVID-19 infected gut, COVID-19 infected lungs, Clostridium difficile infected gut and community-acquired pneumonia infected lungs. The metagenome data sets were processed, normalized, classified and the rarefaction curves were plotted. The microbial biomarkers for COVID-19 infections were identified as the abundance of Candida and Escherichia in lungs with Ruminococcus in the gut. Candida and Staphylococcus could play a vital role as putative prognostic biomarkers of community-acquired pneumonia whereas abundance of Faecalibacterium and Clostridium is associated with the C. difficile infections in gut. A machine learning random forest classifier applied to the data sets efficiently classified the biomarkers. The study offers an extensive and incredible understanding of the existence of gut-lung axis during dysbiosis of two anatomically different organs.}, } @article {pmid35917175, year = {2022}, author = {Tchitchek, N and Nguekap Tchoumba, O and Pires, G and Dandou, S and Campagne, J and Churlaud, G and Fourcade, G and Hoffmann, TW and Strozzi, F and Gaal, C and Bonny, C and Le Chatelier, E and Erlich, SD and Sokol, H and Klatzmann, D}, title = {Low-dose IL-2 shapes a tolerogenic gut microbiota that improves autoimmunity and gut inflammation.}, journal = {JCI insight}, volume = {7}, number = {17}, pages = {}, pmid = {35917175}, issn = {2379-3708}, mesh = {Animals ; *Autoimmune Diseases ; Autoimmunity ; Dextran Sulfate/toxicity ; *Gastrointestinal Microbiome ; Humans ; Inflammation/therapy ; Interleukin-2/pharmacology ; Mice ; Mice, Inbred C57BL ; Mice, Inbred NOD ; }, abstract = {Gut microbiota dysbiosis is associated with inflammatory bowel diseases and with cardiometabolic, neurological, and autoimmune diseases. Gut microbiota composition has a direct effect on the immune system, and vice versa, and it has a particular effect on Treg homeostasis. Low-dose IL-2 (IL-2LD) stimulates Tregs and is a promising treatment for autoimmune and inflammatory diseases. We aimed to evaluate the impact of IL-2LD on gut microbiota and correlatively on the immune system. We used 16S ribosomal RNA profiling and metagenomics to characterize gut microbiota of mice and humans treated or not with IL-2LD. We performed fecal microbiota transplantation (FMT) from IL-2LD-treated to naive recipient mice and evaluated its effects in models of gut inflammation and diabetes. IL-2LD markedly affected gut microbiota composition in mice and humans. Transfer of an IL-2-tuned microbiota by FMT protected C57BL/6J mice from dextran sulfate sodium-induced colitis and prevented diabetes in NOD mice. Metagenomic analyses highlighted a role for several species affected by IL-2LD and for microbial pathways involved in the biosynthesis of amino acids, short-chain fatty acids, and L-arginine. Our results demonstrate that IL-2LD induced changes in gut microbiota that are involved in the immunoregulatory effects of IL-2LD and suggest a crosstalk between Tregs and gut microbiota. These results provide potentially novel insight for understanding the mode of action of Treg-directed therapies.}, } @article {pmid35916669, year = {2022}, author = {FitzGerald, J and Patel, S and Eckenberger, J and Guillemard, E and Veiga, P and Schäfer, F and Walter, J and Claesson, MJ and Derrien, M}, title = {Improved gut microbiome recovery following drug therapy is linked to abundance and replication of probiotic strains.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2094664}, pmid = {35916669}, issn = {1949-0984}, mesh = {Anti-Bacterial Agents/therapeutic use ; *Cultured Milk Products ; Feces ; *Gastrointestinal Microbiome ; Humans ; *Probiotics/pharmacology/therapeutic use ; }, abstract = {Probiotics have been used for decades to alleviate the negative side-effects of oral antibiotics, but our mechanistic understanding on how they work is so far incomplete. Here, we performed a metagenomic analysis of the fecal microbiota in participants who underwent a 14-d Helicobacter pylori eradication therapy with or without consumption of a multi-strain probiotic intervention (L. paracasei CNCM I-1518, L. paracasei CNCM I-3689, L. rhamnosus CNCM I-3690, and four yogurt strains) in a randomized, double-blinded, controlled clinical trial. Using a strain-level analysis for detection and metagenomic determination of replication rate, ingested strains were detected and replicated transiently in fecal samples and in the gut during and following antibiotic administration. Consumption of the fermented milk product led to a significant, although modest, improvement in the recovery of microbiota composition. Stratification of participants into two groups based on the degree to which their microbiome recovered showed i) a higher fecal abundance of the probiotic L. paracasei and L. rhamnosus strains and ii) an elevated replication rate of one strain (L. paracasei CNCMI-1518) in the recovery group. Collectively, our findings show a small but measurable benefit of a fermented milk product on microbiome recovery after antibiotics, which was linked to the detection and replication of specific probiotic strains. Such functional insight can form the basis for the development of probiotic-based intervention aimed to protect gut microbiome from drug treatments.}, } @article {pmid35916407, year = {2022}, author = {Ma, R and Zhao, M and Wang, H and Hou, R and Qin, K and Qian, Y and Zhang, H and Zhou, Y and Wu, W and Gu, J and Wang, X and Shen, Q and Liu, S and Liu, J and Bi, W and Yu, X and Yang, S and Feng, F and Li, Z and Zhang, L and Lan, G and Chen, C and Xue, F and Wang, Y and Chong, H and Hong, Y and Ji, L and Liu, Y and Qi, D and Shan, T and Zhang, W}, title = {Virome of Giant Panda-Infesting Ticks Reveals Novel Bunyaviruses and Other Viruses That Are Genetically Close to Those from Giant Pandas.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0203422}, pmid = {35916407}, issn = {2165-0497}, mesh = {Animals ; Ecosystem ; *Orthobunyavirus ; *Ticks ; *Ursidae ; Virome/genetics ; *Viruses/genetics ; }, abstract = {Tick infestations have been reported as one of the factors threatening the health of giant pandas, but studies of viral pathogens carried by ticks feeding on the blood of giant pandas are limited. To assess whether blood-sucking ticks of giant pandas can carry viral pathogens and if so, whether the viruses in ticks are associated with those previously detected in giant panda hosts, we determined the viromes of ticks detached from giant pandas in a field stocking area in Sichuan Province, southwest China. Using viral metagenomics we identified 32 viral species in ticks, half of which (including anellovirus [n = 9], circovirus [n = 3], and gemycircularvirus [n = 4]) showed homology to viruses carried by giant pandas and their associated host species (such as red pandas and mosquitoes) in the same living domain. Remarkably, several viruses in this study phylogenetically assigned as bunyavirus, hepe-like virus, and circovirus were detected with relatively high abundance, but whether these newly identified tick-associated viruses can replicate in ticks and then transmit to host animals during a blood meal will require further investigation. These findings further expand our understanding of the role of giant panda-infesting ticks in the local ecosystem, especially related to viral acquisition and transmission, and lay a foundation to assess the risk for giant panda exposure to tick-borne viruses. IMPORTANCE Ticks rank only second to mosquitoes as blood-feeding arthropods, capable of spreading pathogens (including viruses, bacteria, and parasites) to hosts during a blood meal. To better understand the relationship between viruses carried by ticks and viruses that have been reported in giant pandas, it is necessary to analyze the viromes of giant panda-parasitic blood-sucking ticks. This study collected 421 ticks on the body surface of giant pandas in Sichuan Province, China. We characterized the extensive genetic diversity of viruses harbored by these ticks and reported frequent communication of viruses between giant pandas and their ticks. While most of the virome discovered here are nonpathogenic viruses from giant pandas and potentially tick-specific viruses, we revealed some possible tick-borne viruses, represented by novel bunyaviruses. This research contributes to the literature because currently there are few studies on the virome of giant panda-infesting ticks.}, } @article {pmid35915372, year = {2022}, author = {Limberg, J and Egan, CE and Mora, HA and Putzel, G and Stamatiou, AT and Ullmann, TM and Moore, MD and Stefanova, D and Thiesmeyer, JW and Finnerty, BM and Beninato, T and McKenzie, K and Robitsek, RJ and Chan, J and Zarnegar, R and Fahey, TJ}, title = {Metagenomic Sequencing of the Gallbladder Microbiome: Bacterial Diversity Does Not Vary by Surgical Pathology.}, journal = {Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract}, volume = {26}, number = {11}, pages = {2282-2291}, pmid = {35915372}, issn = {1873-4626}, mesh = {Humans ; Female ; Adult ; Middle Aged ; Male ; Gallbladder/surgery ; *Pathology, Surgical ; *Cholecystitis, Acute ; *Gallbladder Diseases ; *Microbiota/genetics ; Bacteria/genetics ; }, abstract = {INTRODUCTION: Alterations in the microbiome contribute to the pathogenesis of many gastrointestinal diseases. However, the composition of the microbiome in gallbladder disease is not well described.

METHODS: We aimed to characterize the biliary microbiome in cholecystectomy patients. Bile and biliary stones were collected at cholecystectomy for a variety of surgical indications between 2017 and 2019. DNA was extracted and metagenomic sequencing was performed with subsequent taxonomic classification using Kraken2. The fraction of bacterial to total DNA reads, relative abundance of bacterial species, and overall species diversity were compared between pathologies and demographics.

RESULTS: A total of 74 samples were obtained from 49 patients: 46 bile and 28 stones, with matched pairs from 25 patients. The mean age was 48 years, 76% were female, 29% were Hispanic, and 29% of patients had acute cholecystitis. The most abundant species were Klebsiella pneumoniae, Staphylococcus aureus, and Streptococcus pasteurianus. The bacterial fraction in bile and stone samples was higher in acute cholecystitis compared to other non-infectious pathologies (p < 0.05). Neither the diversity nor differential prevalence of specific bacterial species varied significantly between infectious and other non-infectious gallbladder pathologies. Multivariate analysis of the non-infectious group revealed that patients over 40 years of age had increased bacterial fractions (p < 0.05).

CONCLUSIONS: Metagenomic sequencing permits characterization of the gallbladder microbiome in cholecystectomy patients. Although a higher prevalence of bacteria was seen in acute cholecystitis, species and diversity were similar regardless of surgical indication. Additional study is required to determine how the microbiome can contribute to the development of symptomatic gallbladder disease.}, } @article {pmid35914737, year = {2023}, author = {Liu, Y and Lau, HC and Cheng, WY and Yu, J}, title = {Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment.}, journal = {Genomics, proteomics & bioinformatics}, volume = {21}, number = {1}, pages = {84-96}, pmid = {35914737}, issn = {2210-3244}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/diagnosis/etiology/therapy ; *Microbiota ; Biomarkers ; Carcinogenesis ; }, abstract = {Colorectal cancer (CRC) is one of the most frequently diagnosed cancers and the leading cause of cancer-associated deaths. Epidemiological studies have shown that both genetic and environmental risk factors contribute to the development of CRC. Several metagenomic studies of CRC have identified gut dysbiosis as a fundamental risk factor in the evolution of colorectal malignancy. Although enormous efforts and substantial progresses have been made in understanding the relationship between human gut microbiome and CRC, the precise mechanisms involved remain elusive. Recent data have shown a direct causative role of the gut microbiome in DNA damage, inflammation, and drug resistance in CRC, suggesting that modulation of gut microbiome could act as a powerful tool in CRC prevention and therapy. Here, we provide an overview of the relationship between gut microbiome and CRC, and explore relevant mechanisms of colorectal tumorigenesis. We next highlight the potential of bacterial species as clinical biomarkers, as well as their roles in therapeutic response. Factors limiting the clinical translation of gut microbiome and strategies for resolving current challenges are further discussed.}, } @article {pmid35913193, year = {2022}, author = {Zheng, X and Dai, X and Zhu, Y and Yang, J and Jiang, H and Dong, H and Huang, L}, title = {(Meta)Genomic Analysis Reveals Diverse Energy Conservation Strategies Employed by Globally Distributed Gemmatimonadota.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0022822}, pmid = {35913193}, issn = {2379-5077}, mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Bacteria ; Genomics ; *Microbiota/genetics ; }, abstract = {Gemmatimonadota is a phylum-level lineage distributed widely but rarely reported. Only six representatives of Gemmatimonadota have so far been isolated and cultured in laboratory. The physiology, ecology, and evolutionary history of this phylum remain unknown. The 16S rRNA gene survey of our salt lake and deep-sea sediments, and Earth Microbiome Project (EMP) samples, reveals that Gemmatimonadota exist in diverse environments globally. In this study, we retrieved 17 metagenome-assembled genomes (MAGs) from salt lake sediments (12 MAGs) and deep-sea sediments (5 MAGs). Analysis of these MAGs and the nonredundant MAGs or genomes from public databases reveals Gemmatimonadota can degrade various complex organic substrates, and mainly employ heterotrophic pathways (e.g., glycolysis and tricarboxylic acid [TCA] cycle) for growth via aerobic respiration. And the processes of sufficient energy being stored in glucose through gluconeogenesis, followed by the synthesis of more complex compounds, are prevalent in Gemmatimonadota. A highly expandable pangenome for Gemmatimonadota has been observed, which presumably results from their adaptation to thriving in diverse environments. The enrichment of the Na[+]/H[+] antiporter in the SG8-23 order represents their adaptation to salty habitats. Notably, we identified a novel lineage of the SG8-23 order, which is potentially anoxygenic phototrophic. This lineage is not closely related to the phototrophs in the order of Gemmatimonadales. The two orders differ distinctly in the gene organization and phylogenetic relationship of their photosynthesis gene clusters, indicating photosystems in Gemmatimonadota have evolved in two independent routes. IMPORTANCE The phylum Gemmatimonadota is widely distributed in various environments. However, their physiology, ecology and evolutionary history remain unknown, primary due to the limited cultured isolates and available genomes. We were intrigued to find out how widespread this phylum is, and how it can thrive under diverse conditions. Our results here expand the knowledge of the genetic and metabolic diversity of Gemmatimonadota, and shed light on the diverse energy conservation strategies (i.e., oxidative phosphorylation, substrate phosphorylation, and photosynthetic phosphorylation) responsible for their global distribution. Moreover, gene organization and phylogenetic analysis of photosynthesis gene clusters in Gemmatimonadota provide a valuable insight into the evolutionary history of photosynthesis.}, } @article {pmid35913189, year = {2022}, author = {Frouin, E and Lecoeuvre, A and Armougom, F and Schrenk, MO and Erauso, G}, title = {Comparative Metagenomics Highlight a Widespread Pathway Involved in Catabolism of Phosphonates in Marine and Terrestrial Serpentinizing Ecosystems.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0032822}, pmid = {35913189}, issn = {2379-5077}, mesh = {*Organophosphonates ; Metagenomics ; *Microbiota/genetics ; Phosphorus ; Methane ; }, abstract = {Serpentinizing hydrothermal systems result from water circulating into the subsurface and interacting with mantle-derived rocks notably near mid-ocean ridges or continental ophiolites. Serpentinization and associated reactions produce alkaline fluids enriched in molecular hydrogen, methane, and small organic molecules that are assumed to feed microbial inhabitants. In this study, we explored the relationships linking serpentinization to associated microbial communities by comparative metagenomics of serpentinite-hosted systems, basalt-hosted vents, and hot springs. The shallow Prony bay hydrothermal field (PBHF) microbiome appeared to be more related to those of ophiolitic sites than to the Lost City hydrothermal field (LCHF) microbiome, probably because of the meteoric origin of its fluid, like terrestrial alkaline springs. This study emphasized the ubiquitous importance of a set of genes involved in the catabolism of phosphonates and highly enriched in all serpentinizing sites compared to other ecosystems. Because most of the serpentinizing systems are depleted in inorganic phosphate, the abundance of genes involved in the carbon-phosphorus lyase pathway suggests that the phosphonates constitute a source of phosphorus in these ecosystems. Additionally, hydrocarbons such as methane, released upon phosphonate catabolism, may contribute to the overall budget of organic molecules in serpentinizing systems. IMPORTANCE This first comparative metagenomic study of serpentinite-hosted environments provides an objective framework to understand the functioning of these peculiar ecosystems. We showed a taxonomic similarity between the PBHF and other terrestrial serpentinite-hosted ecosystems. At the same time, the LCHF microbial community was closer to deep basalt-hosted hydrothermal fields than continental ophiolites, despite the influence of serpentinization. This study revealed shared functional capabilities among serpentinite-hosted ecosystems in response to environmental stress, the metabolism of abundant dihydrogen, and the metabolism of phosphorus. Our results are consistent with the generalized view of serpentinite environments but provide deeper insight into the array of factors that may control microbial activities in these ecosystems. Moreover, we show that metabolism of phosphonate is widespread among alkaline serpentinizing systems and could play a crucial role in phosphorus and methane biogeochemical cycles. This study opens a new line of investigation of the metabolism of reduced phosphorus compounds in serpentinizing environments.}, } @article {pmid35913177, year = {2022}, author = {Tao, S and Zou, H and Li, J and Wei, H}, title = {Landscapes of Enteric Virome Signatures in Early-Weaned Piglets.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0169822}, pmid = {35913177}, issn = {2165-0497}, mesh = {Animals ; Bacteria/genetics ; Diarrhea/microbiology/veterinary ; *Gastrointestinal Microbiome/genetics ; Mice ; Swine ; *Virome/genetics ; Weaning ; }, abstract = {Diarrhea caused by early-weaning-induced stress can increase mortality rates and reduce growth performance of piglets, seriously harming the livestock industry. To date, studies on the gut microbiome of early-weaned piglets have focused almost exclusively on bacteria, while studies on their gut virome are extremely lacking. Here, we used metagenomic and metatranscriptomic sequencing combined with bioinformatic analysis techniques to preliminarily characterize the intestinal virome of early-weaned piglets at different biological classification levels. The alpha diversity of enteroviruses was generally elevated in early-weaned piglets with diarrhea, compared to healthy piglets, whereas the two groups of piglets showed no significant difference in beta diversity. In addition, the species compositions of the gut virome were similar between healthy piglets and piglets with diarrhea, while their respective dominant species were somewhat different. We also identified 58 differential DNA viruses and 16 differential RNA viruses between the two groups of piglets at all biological taxonomic levels. Of these, 1 (family Dhakavirus) and 6 (phylum Artverviricota, class Revtraviricetes, order Ortervirales, family Retroviridae, genus Gammaretrovirus, and species Kirsten murine sarcoma virus) specific viruses disappeared from the intestines of healthy piglets and piglets with diarrhea, respectively. Moreover, we found that some DNA and RNA viruses formed strong correlations among themselves or between them. IMPORTANCE This study systematically reveals the biological diversity, structure, and composition of intestinal DNA and RNA virus profiles in early-weaned piglets. Furthermore, characteristics of differences in gut viromes between early-weaned healthy piglets and piglets with diarrhea were also elucidated. Importantly, some potential biomarkers for early-weaned piglets with diarrhea were identified. These findings fill a gap for the early-weaned piglet gut virome and lay the foundation for the development of strategies to target enteroviruses for the prevention and treatment of early-weaning-induced piglet diarrhea.}, } @article {pmid35913151, year = {2022}, author = {Call, TB and Davis, EK and Bean, JD and Lemmon, SG and Chaston, JM}, title = {Bacterial Metabolism and Transport Genes Are Associated with the Preference of Drosophila melanogaster for Dietary Yeast.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {16}, pages = {e0072022}, pmid = {35913151}, issn = {1098-5336}, support = {R15 GM140388/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; Diet ; Drosophila ; *Drosophila melanogaster/microbiology ; Glucose/metabolism ; *Microbiota/genetics ; Thiamine/metabolism ; }, abstract = {Many animal traits are influenced by their associated microorganisms ("microbiota"). To expand our understanding of the relationship between microbial genotype and host phenotype, we report an analysis of the influence of the microbiota on the dietary preference of the fruit fly Drosophila melanogaster. First, we confirmed through experiments on flies reared bacteria-free ("axenic") or in monoassociation with two different strains of bacteria that the microbiota significantly influences fruit fly dietary preference across a range of ratios of dietary yeast:dietary glucose. Then, focusing on microbiota-dependent changes in fly dietary preference for yeast (DPY), we performed a metagenome-wide association (MGWA) study to define microbial species specificity for this trait and to predict bacterial genes that influence it. In a subsequent mutant analysis, we confirmed that disrupting a subset of the MGWA-predicted genes influences fly DPY, including for genes involved in thiamine biosynthesis and glucose transport. Follow-up tests revealed that the bacterial influence on fly DPY did not depend on bacterial modification of the glucose or protein content of the fly diet, suggesting that the bacteria mediate their effects independent of the fly diet or through more specific dietary changes than broad ratios of protein and glucose. Together, these findings provide additional insight into bacterial determinants of host nutrition and behavior by revealing specific genetic disruptions that influence D. melanogaster DPY. IMPORTANCE Associated microorganisms ("microbiota") impact the physiology and behavior of their hosts, and defining the mechanisms underlying these interactions is a major gap in the field of host-microbe interactions. This study expands our understanding of how the microbiota can influence dietary preference for yeast (DPY) of a model host, Drosophila melanogaster. First, we show that fly preferences for a range of different dietary yeast:dietary glucose ratios vary significantly with the identity of the microbes that colonize the fruit flies. We then performed a metagenome-wide association study to identify candidate bacterial genes that contributed to some of these bacterial influences. We confirmed that disrupting some of the predicted genes, including genes involved in glucose transport and thiamine biosynthesis, resulted in changes to fly DPY and show that the influence of two of these genes is not through changes in dietary ratios of protein to glucose. Together, these efforts expand our understanding of the bacterial genetic influences on a feeding behavior of a model animal host.}, } @article {pmid35911731, year = {2022}, author = {Huang, J and Zheng, X and Kang, W and Hao, H and Mao, Y and Zhang, H and Chen, Y and Tan, Y and He, Y and Zhao, W and Yin, Y}, title = {Metagenomic and metabolomic analyses reveal synergistic effects of fecal microbiota transplantation and anti-PD-1 therapy on treating colorectal cancer.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {874922}, pmid = {35911731}, issn = {1664-3224}, mesh = {Animals ; Bacteroides ; *Colorectal Neoplasms/etiology/therapy ; Fecal Microbiota Transplantation/adverse effects ; *Gastrointestinal Microbiome ; Metagenome ; Mice ; }, abstract = {Anti-PD-1 immunotherapy has saved numerous lives of cancer patients; however, it only exerts efficacy in 10-15% of patients with colorectal cancer. Fecal microbiota transplantation (FMT) is a potential approach to improving the efficacy of anti-PD-1 therapy, whereas the detailed mechanisms and the applicability of this combination therapy remain unclear. In this study, we evaluated the synergistic effect of FMT with anti-PD-1 in curing colorectal tumor-bearing mice using a multi-omics approach. Mice treated with the combination therapy showed superior survival rate and tumor control, compared to the mice received anti-PD-1 therapy or FMT alone. Metagenomic analysis showed that composition of gut microbiota in tumor-bearing mice treated with anti-PD-1 therapy was remarkably altered through receiving FMT. Particularly, Bacteroides genus, including FMT-increased B. thetaiotaomicron, B. fragilis, and FMT-decreased B. ovatus might contribute to the enhanced efficacy of anti-PD-1 therapy. Furthermore, metabolomic analysis upon mouse plasma revealed several potential metabolites that upregulated after FMT, including punicic acid and aspirin, might promote the response to anti-PD-1 therapy via their immunomodulatory functions. This work broadens our understanding of the mechanism by which FMT improves the efficacy of anti-PD-1 therapy, which may contribute to the development of novel microbiota-based anti-cancer therapies.}, } @article {pmid35908467, year = {2022}, author = {Zhao, F and Wang, C and Song, S and Fang, C and Zhou, G and Li, C and Kristiansen, K}, title = {Casein and red meat proteins differentially affect the composition of the gut microbiota in weaning rats.}, journal = {Food chemistry}, volume = {397}, number = {}, pages = {133769}, doi = {10.1016/j.foodchem.2022.133769}, pmid = {35908467}, issn = {1873-7072}, mesh = {Animals ; Caseins/metabolism ; Cattle ; Diet ; Dietary Proteins/metabolism ; *Gastrointestinal Microbiome ; Humans ; Meat ; Meat Proteins ; Rats ; *Red Meat ; Weaning ; }, abstract = {Casein and meat are food sources providing high-quality animal proteins for human consumption. However, little is known concerning potentially different effects of these animal protein sources during early stages of life. In the present study, casein and red meat proteins (beef and pork) were fed to young postweaning rats for 14 days based on the AIN-93G diet formula. Casein and red meat protein-based diets did not differentially affect the overall growth performance. However, they discriminately modulated the abundances of different potentially beneficial bacteria belonging to genus Lactobacillus. Intake of the casein-based diet increased the intestinal abundance of Lactococcus lactis with a pronounced potential for galactose utilization via the Tag6P pathway, and it also resulted in lower amounts of toxic ammonia in the rat cecum compared to red meat protein-based diets. We observed no adverse effects on colonic tissue in response to any of the protein-based diets based on histological observations.}, } @article {pmid35907589, year = {2022}, author = {Stevenson, SJR and Lee, KC and Handley, KM and Angert, ER and White, WL and Clements, KD}, title = {Substrate degradation pathways, conserved functions and community composition of the hindgut microbiota in the herbivorous marine fish Kyphosus sydneyanus.}, journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology}, volume = {272}, number = {}, pages = {111283}, doi = {10.1016/j.cbpa.2022.111283}, pmid = {35907589}, issn = {1531-4332}, mesh = {Animals ; Fatty Acids, Volatile/pharmacology ; Fishes/genetics ; *Gastrointestinal Microbiome ; *Microbiota ; *Perciformes/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Symbiotic gut microbiota in the herbivorous marine fish Kyphosus sydneyanus play an important role in digestion by converting refractory algal carbohydrate into short-chain fatty acids. Here we characterised community composition using both 16S rRNA gene amplicon sequencing and shotgun-metagenome sequencing. Sequencing was carried out on lumen and mucosa samples (radial sections) from three axial sections taken from the hindgut of wild-caught fish. Both lumen and mucosa communities displayed distinct distributions along the hindgut, likely an effect of the differing selection pressures within these hindgut locations, as well as considerable variation among individual fish. In contrast, metagenomic sequences displayed a high level of functional similarity between individual fish and gut sections in the relative abundance of genes (based on sequencing depth) that encoded enzymes involved in algal-derived substrate degradation. These results suggest that the host gut environment selects for functional capacity in symbionts rather than taxonomic identity. Functional annotation of the enzymes encoded by the gut microbiota was carried out to infer the metabolic pathways used by the gut microbiota for the degradation of important dietary substrates: mannitol, alginate, laminarin, fucoidan and galactan (e.g. agar and carrageenan). This work provides the first evidence of the genomic potential of K. sydneyanus hindgut microbiota to convert highly refractory algal carbohydrates into metabolically useful short-chain fatty acids.}, } @article {pmid35906397, year = {2022}, author = {Sugden, S and Holert, J and Cardenas, E and Mohn, WW and Stein, LY}, title = {Microbiome of the freshwater sponge Ephydatia muelleri shares compositional and functional similarities with those of marine sponges.}, journal = {The ISME journal}, volume = {16}, number = {11}, pages = {2503-2512}, pmid = {35906397}, issn = {1751-7370}, mesh = {Animals ; DNA Restriction-Modification Enzymes/genetics ; Fresh Water ; *Microbiota/genetics ; Phylogeny ; *Porifera/microbiology ; RNA, Ribosomal, 16S/genetics ; Transposases/genetics ; Vitamin B 12 ; Water ; }, abstract = {Sponges are known for hosting diverse communities of microbial symbionts, but despite persistent interest in the sponge microbiome, most research has targeted marine sponges; freshwater sponges have been the focus of less than a dozen studies. Here, we used 16 S rRNA gene amplicon sequencing and shotgun metagenomics to characterize the microbiome of the freshwater sponge Ephydatia muelleri and identify potential indicators of sponge-microbe mutualism. Using samples collected from the Sooke, Nanaimo, and Cowichan Rivers on Vancouver Island, British Columbia, we show that the E. muelleri microbiome is distinct from the ambient water and adjacent biofilms and is dominated by Sediminibacterium, Comamonas, and unclassified Rhodospirillales. We also observed phylotype-level differences in sponge microbiome taxonomic composition among different rivers. These differences were not reflected in the ambient water, suggesting that other environmental or host-specific factors may drive the observed geographic variation. Shotgun metagenomes and metagenome-assembled genomes further revealed that freshwater sponge-associated bacteria share many genomic similarities with marine sponge microbiota, including an abundance of defense-related proteins (CRISPR, restriction-modification systems, and transposases) and genes for vitamin B12 production. Overall, our results provide foundational information on the composition and function of freshwater sponge-associated microbes, which represent an important yet underappreciated component of the global sponge microbiome.}, } @article {pmid35906393, year = {2022}, author = {Bay, V and Gür, S and Bayraktar, O}, title = {Plant-derived tormentic acid alters the gut microbiota of the silkworm (Bombyx mori).}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {13005}, pmid = {35906393}, issn = {2045-2322}, mesh = {Animals ; Bacteria/genetics ; *Bombyx/microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; Triterpenes ; }, abstract = {In recent years, phytochemicals have started to attract more attention due to their contribution to health and bioactivity. Microorganisms in the intestines of organisms contribute to the processing, function, and biotransformation of these substances. The silkworm (Bombyx mori) is one of the organisms used for the biotransformation of phytochemicals due to its controlled reproduction and liability to microbial manipulation. In this study, a bioactive compound, tormentic acid (TA), extracted from Sarcopoterium spinosum was used in the silkworm diet, and the alterations of intestinal microbiota of the silkworm were assessed. To do this, silkworms were fed on a diet with various tormentic acid content, and 16S metagenomic analysis was performed to determine the alterations in the gut microbiota profile of these organisms. Diet with different TA content did not cause a change in the bacterial diversity of the samples. A more detailed comparison between different feeding groups indicated increased abundance of bacteria associated with health, i.e., Intestinibacter spp., Flavonifractor spp., Senegalimassilia spp., through the utilization of bioactive substances such as flavonoids. In conclusion, it might be said that using TA as a supplementary product might help ameliorate the infected gut, promote the healthy gut, and relieve the undesirable effects of medicines on the gastrointestinal system.}, } @article {pmid35906296, year = {2022}, author = {Marx, V}, title = {Why the ocean virome matters.}, journal = {Nature methods}, volume = {19}, number = {8}, pages = {924-927}, pmid = {35906296}, issn = {1548-7105}, mesh = {*Bacteriophages ; Metagenomics ; *Microbiota ; Oceans and Seas ; Virome ; }, abstract = {Expeditions are delivering data wealth about our planet’s oceans, including its microbes. Some labs are now diving deep into the ocean virome.}, } @article {pmid35906254, year = {2022}, author = {Coker, MO and Lebeaux, RM and Hoen, AG and Moroishi, Y and Gilbert-Diamond, D and Dade, EF and Palys, TJ and Madan, JC and Karagas, MR}, title = {Metagenomic analysis reveals associations between salivary microbiota and body composition in early childhood.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {13075}, pmid = {35906254}, issn = {2045-2322}, support = {US Environmental Protection Agency RD83459901/EPA/EPA/United States ; P20 ES018175/ES/NIEHS NIH HHS/United States ; R01 DE028154/DE/NIDCR NIH HHS/United States ; R01 LM012723/LM/NLM NIH HHS/United States ; P01 ES022832/ES/NIEHS NIH HHS/United States ; NLM R01LM012723/NH/NIH HHS/United States ; P20 GM104416/GM/NIGMS NIH HHS/United States ; NIEHS UH3OD023275/NH/NIH HHS/United States ; NIDCR R01DE028154/NH/NIH HHS/United States ; UH3 OD023275/OD/NIH HHS/United States ; T32 AI007519/AI/NIAID NIH HHS/United States ; }, mesh = {Body Composition ; Body Mass Index ; Body Weight ; Child, Preschool ; Cohort Studies ; Humans ; *Microbiota/genetics ; }, abstract = {Several studies have shown that body mass index is strongly associated with differences in gut microbiota, but the relationship between body weight and oral microbiota is less clear especially in young children. We aimed to evaluate if there is an association between child growth and the saliva microbiome. We hypothesized that associations between growth and the saliva microbiome would be moderate, similarly to the association between growth and the gut microbiome. For 236 toddlers participating in the New Hampshire Birth Cohort Study, we characterized the association between multiple longitudinal anthropometric measures of body height, body weight and body mass. Body Mass Index (BMI) z-scores were calculated, and dual-energy x-ray absorptiometry (DXA) was used to estimate body composition. Shotgun metagenomic sequencing of saliva samples was performed to taxonomically and functionally profile the oral microbiome. We found that within-sample diversity was inversely related to body mass measurements while community composition was not associated. Although the magnitude of associations were small, some taxa were consistently associated with growth and modified by sex. Certain taxa were associated with decreased weight or growth (including Actinomyces odontolyticus and Prevotella melaninogenica) or increased growth (such as Streptococcus mitis and Corynebacterium matruchotii) across anthropometric measures. Further exploration of the functional significance of this relationship will enhance our understanding of the intersection between weight gain, microbiota, and energy metabolism and the potential role of these relationships on the onset of obesity-associated diseases in later life.}, } @article {pmid35905873, year = {2022}, author = {Ebrahimian, F and De Bernardini, N and Tsapekos, P and Treu, L and Zhu, X and Campanaro, S and Karimi, K and Angelidaki, I}, title = {Effect of pressure on biomethanation process and spatial stratification of microbial communities in trickle bed reactors under decreasing gas retention time.}, journal = {Bioresource technology}, volume = {361}, number = {}, pages = {127701}, doi = {10.1016/j.biortech.2022.127701}, pmid = {35905873}, issn = {1873-2976}, mesh = {Biofuels ; Bioreactors ; *Euryarchaeota ; Hydrogen ; Methane ; *Microbiota/genetics ; }, abstract = {The current study investigated the effect of elevating gas pressure on biomethanation in trickle-bed reactors (TBRs). The increased pressure led to successful biomethanation (CH4 > 90 %) at a gas retention time (GRT) of 21 min, due to the improved transfer rates of H2 and CO2. On the contrary, the non-pressurized TBR performance was reduced at GRTs shorter than 40 min. Metagenomic analysis revealed that the microbial populations collected from the lower and middle parts of the reactor under the same GRT were more homogeneous compared with those developed in the upper layer. Comparison with previous experiments suggest that microbial stratification is mainly driven by the nutrient provision strategy. Methanobacterium species was the most dominant methanogen and it was mainly associated with the bottom and middle parts of TBRs. Overall, the increased pressure did not affect markedly the microbial composition, while the GRT was the most important parameter shaping the microbiomes.}, } @article {pmid35905860, year = {2023}, author = {Qiu, B and Xi, Y and Liu, F and Li, Y and Xie, X and Guo, J and Guo, S and Wu, Y and Wu, L and Liang, T and Ding, Y and Zhang, J and Wu, Q and Liu, H}, title = {Gut Microbiome Is Associated With the Response to Chemoradiotherapy in Patients With Non-small Cell Lung Cancer.}, journal = {International journal of radiation oncology, biology, physics}, volume = {115}, number = {2}, pages = {407-418}, doi = {10.1016/j.ijrobp.2022.07.032}, pmid = {35905860}, issn = {1879-355X}, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung ; Chemoradiotherapy ; Fatty Acids ; *Gastrointestinal Microbiome ; *Lung Neoplasms ; RNA, Ribosomal, 16S ; }, abstract = {PURPOSE: To explore the dynamic change of gut microbiota and its predictive role in progression-free survival (PFS) in non-small cell lung cancer (NSCLC) after concurrent chemoradiotherapy (CCRT).

METHODS AND MATERIALS: Forty-one patients with NSCLC in 2 phase 2 trials (NCT02573506 and NCT03006575) were analyzed. A total of 102 fecal samples were collected at 3 time points (T0, before CCRT; T1, 2 weeks after the initiation of CCRT; and T2, the end of CCRT). Gut microbiota composition and functionality were analyzed by 16S rRNA gene sequencing and shotgun metagenomics, respectively. Alpha diversity, taxonomic composition, and KEGG functional pathways were compared between patients in the long-PFS group (PFS ≥11.0 months) and short-PFS group (PFS <11.0 months). A random forest classifier was constructed to identify microbial signature related to PFS. Clinical and microbial factors potentially predictive of PFS were assessed in the univariate and multivariate Cox regression analysis.

RESULTS: The abundance of Bacteroidota and Proteobacteria increased, while the abundance of Firmicutes decreased after CCRT. Shannon index (P = .006) and PD index (P = .022) were significantly higher in the long-PFS group than for those in the short-PFS group at T1. The PFS-prediction microbial signature at T1 included unclassified members of the Lanchospiraceae spp., such as NK4A136 and UCG-003 groups, Dorea sp., various strains from within the Eubacterium hallii and E. siraeum groups, and an unclassified member of the Muribaculaceae, which yielded an area under the ROC curve of 0.87. These discriminatory genera mostly belong to phylum Firmicutes/family Clostridia. Multivariate analysis indicated PD index (HR = 8.036, P = .016) and the abundance of Dorea sp. at T1 (HR = 4.186, P = .043) were independent predictors of PFS. The KEGG pathways at T1 overrepresented in the long-PFS group included fatty acid metabolism, fatty acid biosynthesis, and arginine biosynthesis. Those overrepresented in the short-PFS group included lipopolysaccharide biosynthesis, ascorbate and aldarate metabolism, and biosynthesis of vancomycin group antibiotics.

CONCLUSIONS: Gut microbiota composition and functionality at 2 weeks after the initiation of CCRT were associated with PFS in NSCLC. Further research is needed to confirm these results.}, } @article {pmid35902439, year = {2022}, author = {Li, G and Jiang, Y and Li, Q and An, D and Bao, M and Lang, L and Han, L and Huang, X and Jiang, C}, title = {Comparative and functional analyses of fecal microbiome in Asian elephants.}, journal = {Antonie van Leeuwenhoek}, volume = {115}, number = {9}, pages = {1187-1202}, pmid = {35902439}, issn = {1572-9699}, support = {31270001//National Natural Science Foundation of China/ ; 31460005//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacteroidetes/genetics ; *Elephants/genetics/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; *Microbiota ; }, abstract = {Asian elephant is large herbivorous animal with elongated hindgut. To explore fecal microbial community composition with various ages, sex and diets, and their role in plant biomass degrading and nutrition conversation. We generated 119 Gb by metagenome sequencing from 10 different individual feces and identified 5.3 million non-redundant genes. The comprehensive analysis established that the Bacteroidetes, Firmicutes and Proteobacteria constituted the most dominant phyla in overall fecal samples. In different individuals, the alpha diversity of the fecal microbiota in female was lower than male, and the alpha diversity of the fecal microbiota in older was higher than younger, and the fecal microbial diversity was the most complex in wild elephant. But the predominant population compositions were similar to each other. Moreover, the newborn infant elephant feces assembled and maintained a diverse but host-specific fecal microbial population. The discovery speculated that Asian elephant maybe have start to building microbial populations before birth. Meanwhile, these results illustrated that host phylogeny, diets, ages and sex are significant factors for fecal microbial community composition. Therefore, we put forward the process of Asian elephant fecal microbial community composition that the dominant populations were built first under the guidance of phylogeny, and then shaped gradually a unique and flexible gut microbial community structure under the influences of diet, age and sex. This study found also that the Bacteroidetes were presumably the main drivers of plant fiber-degradation. A large of secondary metabolite biosynthetic gene clusters, and genes related to enediyne biosynthesis were found and showed that the Asian elephant fecal microbiome harbored a diverse and abundant genetic resource. A picture of antibiotic resistance genes (ARGs) reservoirs of fecal microbiota in Asian elephants was provided. Surprisingly, there was such wide range of ARGs in newborn infant elephant. Further strengthening our speculation that the fetus of Asian elephant has colonized prototypical fecal microbiota before birth. However, it is necessary to point out that the data give a first inside into the gut microbiota of Asian elephants but too few individuals were studied to draw general conclusions for differences among wild and captured elephants, female and male or different ages. Further studies are required. Additionally, the cultured actinomycetes from Asian elephant feces also were investigated, which the feces of Asian elephants could be an important source of actinomycetes.}, } @article {pmid35901372, year = {2023}, author = {Frankot, MA and O'Hearn, CM and Blancke, AM and Rodriguez, B and Pechacek, KM and Gandhi, J and Hu, G and Martens, KM and Vonder Haar, C}, title = {Acute gut microbiome changes after traumatic brain injury are associated with chronic deficits in decision-making and impulsivity in male rats.}, journal = {Behavioral neuroscience}, volume = {137}, number = {1}, pages = {15-28}, pmid = {35901372}, issn = {1939-0084}, support = {U54 GM104942/GM/NIGMS NIH HHS/United States ; P20 GM121322/GM/NIGMS NIH HHS/United States ; R01 NS110905/NS/NINDS NIH HHS/United States ; P20 GM103434/GM/NIGMS NIH HHS/United States ; }, mesh = {Rats ; Male ; Animals ; *Gastrointestinal Microbiome ; Rats, Long-Evans ; *Brain Injuries, Traumatic/complications/microbiology ; Impulsive Behavior ; *Gambling ; }, abstract = {The mechanisms underlying chronic psychiatric-like impairments after traumatic brain injury (TBI) are currently unknown. The goal of the present study was to assess the role of diet and the gut microbiome in psychiatric symptoms after TBI. Rats were randomly assigned to receive a high-fat diet (HFD) or calorie-matched low-fat diet (LFD). After 2 weeks of free access, rats began training on the rodent gambling task (RGT), a measure of risky decision-making and motor impulsivity. After training, rats received a bilateral frontal TBI or a sham procedure and continued postinjury testing for 10 weeks. Fecal samples were collected before injury and 3-, 30-, and 60 days postinjury to evaluate the gut microbiome. HFD altered the microbiome, but ultimately had low-magnitude effects on behavior and did not modify functional outcomes after TBI. Injury-induced functional deficits were far more robust; TBI substantially decreased optimal choice and increased suboptimal choice and motor impulsivity on the RGT. TBI also affected the microbiome, and a model comparison approach revealed that bacterial diversity measured 3 days postinjury was predictive of chronic psychiatric-like deficits on the RGT. A functional metagenomic analysis identified changes to dopamine and serotonin synthesis pathways as a potential candidate mechanism. Thus, the gut may be a potential acute treatment target for psychiatric symptoms after TBI, as well as a biomarker for injury and deficit severity. However, further research will be needed to confirm and extend these findings. (PsycInfo Database Record (c) 2023 APA, all rights reserved).}, } @article {pmid35897801, year = {2022}, author = {Tian, Y and Rimal, B and Gui, W and Koo, I and Yokoyama, S and Perdew, GH and Patterson, AD}, title = {Early Life Short-Term Exposure to Polychlorinated Biphenyl 126 in Mice Leads to Metabolic Dysfunction and Microbiota Changes in Adulthood.}, journal = {International journal of molecular sciences}, volume = {23}, number = {15}, pages = {}, pmid = {35897801}, issn = {1422-0067}, support = {R01 ES028288 (ADP) and R35 ES028244 (GHP)//National Institutes of Health Grants/ ; Project PEN047702 and Accession number 1009993//USDA National Institute of Food and Federal Appropriations/ ; R35 ES028244/ES/NIEHS NIH HHS/United States ; R01 ES028288/ES/NIEHS NIH HHS/United States ; S10 OD021750/OD/NIH HHS/United States ; }, mesh = {Animals ; *Environmental Pollutants/toxicity ; *Gastrointestinal Microbiome/genetics ; Mice ; *Microbiota ; *Polychlorinated Biphenyls/toxicity ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {Early life exposure to environmental pollutants may have long-term consequences and harmful impacts on health later in life. Here, we investigated the short- and long-term impact of early life 3,3',4,4',5-pentacholorobiphenyl (PCB 126) exposure (24 μg/kg body weight for five days) in mice on the host and gut microbiota using 16S rRNA gene sequencing, metagenomics, and [1]H NMR- and mass spectrometry-based metabolomics. Induction of Cyp1a1, an aryl hydrocarbon receptor (AHR)-responsive gene, was observed at 6 days and 13 weeks after PCB 126 exposure consistent with the long half-life of PCB 126. Early life, Short-Term PCB 126 exposure resulted in metabolic abnormalities in adulthood including changes in liver amino acid and nucleotide metabolism as well as bile acid metabolism and increased hepatic lipogenesis. Interestingly, early life PCB 126 exposure had a greater impact on bacteria in adulthood at the community structure, metabolic, and functional levels. This study provides evidence for an association between early life environmental pollutant exposure and increased risk of metabolic disorders later in life and suggests the microbiome is a key target of environmental chemical exposure.}, } @article {pmid35895627, year = {2022}, author = {Calle-Tobón, A and Pérez-Pérez, J and Forero-Pineda, N and Chávez, OT and Rojas-Montoya, W and Rúa-Uribe, G and Gómez-Palacio, A}, title = {Local-scale virome depiction in Medellín, Colombia, supports significant differences between Aedes aegypti and Aedes albopictus.}, journal = {PloS one}, volume = {17}, number = {7}, pages = {e0263143}, pmid = {35895627}, issn = {1932-6203}, mesh = {*Aedes/classification/virology ; Animals ; Colombia ; *Insect Viruses/genetics ; Mosquito Vectors/virology ; *RNA Viruses/genetics ; *Virome/genetics ; Wolbachia/genetics ; }, abstract = {Aedes spp. comprise the primary group of mosquitoes that transmit arboviruses such as dengue, Zika, and chikungunya viruses to humans, and thus these insects pose a significant burden on public health worldwide. Advancements in next-generation sequencing and metagenomics have expanded our knowledge on the richness of RNA viruses harbored by arthropods such as Ae. aegypti and Ae. albopictus. Increasing evidence suggests that vector competence can be modified by the microbiome (comprising both bacteriome and virome) of mosquitoes present in endemic zones. Using an RNA-seq-based metataxonomic approach, this study determined the virome structure, Wolbachia presence and mitochondrial diversity of field-caught Ae. aegypti and Ae. albopictus mosquitoes in Medellín, Colombia, a municipality with a high incidence of mosquito-transmitted arboviruses. The two species are sympatric, but their core viromes differed considerably in richness, diversity, and abundance; although the community of viral species identified was large and complex, the viromes were dominated by few virus species. BLAST searches of assembled contigs suggested that at least 17 virus species (16 of which are insect-specific viruses [ISVs]) infect the Ae. aegypti population. Dengue virus 3 was detected in one sample and it was the only pathogenic virus detected. In Ae. albopictus, up to 11 ISVs and one plant virus were detected. Therefore, the virome composition appears to be species-specific. The bacterial endosymbiont Wolbachia was identified in all Ae. albopictus samples and in some Ae. aegypti samples collected after 2017. The presence of Wolbachia sp. in Ae. aegypti was not related to significant changes in the richness, diversity, or abundance of this mosquito's virome, although it was related to an increase in the abundance of Aedes aegypti To virus 2 (Metaviridae). The mitochondrial diversity of these mosquitoes suggested that the Ae. aegypti population underwent a change that started in the second half of 2017, which coincides with the release of Wolbachia-infected mosquitoes in Medellín, indicating that the population of wMel-infected mosquitoes released has introduced new alleles into the wild Ae. aegypti population of Medellín. However, additional studies are required on the dispersal speed and intergenerational stability of wMel in Medellín and nearby areas as well as on the introgression of genetic variants in the native mosquito population.}, } @article {pmid35892598, year = {2022}, author = {Zhang, T and Wu, X and Yuan, H and Huang, S and Park, S}, title = {Mitigation of Memory Impairment with Fermented Fucoidan and λ-Carrageenan Supplementation through Modulating the Gut Microbiota and Their Metagenome Function in Hippocampal Amyloid-β Infused Rats.}, journal = {Cells}, volume = {11}, number = {15}, pages = {}, pmid = {35892598}, issn = {2073-4409}, mesh = {Acetylcholinesterase/metabolism ; *Alzheimer Disease/metabolism ; Amyloid beta-Peptides/metabolism ; Animals ; Brain-Derived Neurotrophic Factor/metabolism ; Carrageenan/metabolism ; Dietary Supplements ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Hippocampus/metabolism ; Insulin/metabolism ; Memory Disorders/complications ; Metagenome ; Polysaccharides ; Rats ; }, abstract = {Attenuating acetylcholinesterase and insulin/insulin-like growth factor-1 signaling in the hippocampus is associated with Alzheimer's disease (AD) development. Fucoidan and carrageenan are brown and red algae, respectively, with potent antibacterial, anti-inflammatory, antioxidant and antiviral activities. This study examined how low-molecular-weight (MW) and high-MW fucoidan and λ-carrageenan would improve memory impairment in Alzheimer's disease-induced rats caused by an infusion of toxic amyloid-β(Aβ). Fucoidan and λ-carrageenan were dissected into low-MW by Luteolibacter&nbsp;algae and Pseudoalteromonas&nbsp;carrageenovora. Rats receiving an Aβ(25-35) infusion in the CA1 region of the hippocampus were fed dextrin (AD-Con), 1% high-MW fucoidan (AD-F-H), 1% low-MW fucoidan (AD-F-L), 1% high-MW λ-carrageenan (AD-C-H), and 1% low-MW λ-carrageenan (AD-C-L) for six weeks. Rats to receive saline infusion (Normal-Con) had an AD-Con diet. The AD-F-L group showed an improved memory function, which manifested as an enhanced Y-maze spontaneous alternation test, water maze, and passive avoidance tests, similar to the Normal-Con group. AD-F-L also potentiated hippocampal insulin signaling and increased the expression of ciliary neurotrophic factor (CNTF) and brain-derived neurotrophic factor (BDNF) in the hippocampus. AD-C-L improved the memory function mainly by increasing the BDNF content. AD-F-H and AD-C-H did not improve the memory function. Compared to AD-Con, the ascending order of AD-C-H, AD-F-H, AD-C-L, and AD-F-L increased insulin signaling by enhancing the pSTAT3®pAkt®pGSK-3β pathway. AD-F-L improved glucose tolerance the most. Compared to AD-CON, the AD-F-L treatment increased the serum acetate concentrations and compensated for the defect of cerebral glucose metabolism. AD-Con increased Clostridium, Terrisporobacter and Sporofaciens compared to Normal-Con, and AD-F-L and AD-C-L increased Akkermentia. In conclusion, AD-F-L and AD-C-L alleviated the memory function in the rats with induced AD symptoms by modulating.}, } @article {pmid35891376, year = {2022}, author = {Cannon, JL and Seabolt, MH and Xu, R and Montmayeur, A and Suh, SH and Diez-Valcarce, M and Bucardo, F and Becker-Dreps, S and Vinjé, J}, title = {Gut Microbiome Changes Occurring with Norovirus Infection and Recovery in Infants Enrolled in a Longitudinal Birth Cohort in Leon, Nicaragua.}, journal = {Viruses}, volume = {14}, number = {7}, pages = {}, pmid = {35891376}, issn = {1999-4915}, support = {K24 AI141744/AI/NIAID NIH HHS/United States ; R01 AI127845/AI/NIAID NIH HHS/United States ; R01AI127845/AI/NIAID NIH HHS/United States ; none/CC/CDC HHS/United States ; K24AI141744/AI/NIAID NIH HHS/United States ; }, mesh = {Birth Cohort ; *Caliciviridae Infections ; Cohort Studies ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Nicaragua/epidemiology ; *Norovirus/genetics ; }, abstract = {Noroviruses are associated with one fifth of diarrheal illnesses globally and are not yet preventable with vaccines. Little is known about the effects of norovirus infection on infant gut microbiome health, which has a demonstrated role in protecting hosts from pathogens and a possible role in oral vaccine performance. In this study, we characterized infant gut microbiome changes occurring with norovirus-associated acute gastroenteritis (AGE) and the extent of recovery. Metagenomic sequencing was performed on the stools of five infants participating in a longitudinal birth cohort study conducted in León, Nicaragua. Taxonomic and functional diversities of gut microbiomes were profiled at time points before, during, and after norovirus infection. Initially, the gut microbiomes resembled those of breastfeeding infants, rich in probiotic species. When disturbed by AGE, Gammaproteobacteria dominated, particularly Pseudomonas species. Alpha diversity increased but the genes involved in carbohydrate metabolism and glycan biosynthesis decreased. After the symptoms subsided, the gut microbiomes rebounded with their taxonomic and functional communities resembling those of the pre-infection microbiomes. In this study, during disruptive norovirus-associated AGE, the gut microbiome was temporarily altered, returning to a pre-infection composition a median of 58 days later. Our study provides new insights for developing probiotic treatments and furthering our understanding of the role that episodes of AGE have in shaping the infant gut microbiome, their long-term outcomes, and implications for oral vaccine effectiveness.}, } @article {pmid35891346, year = {2022}, author = {French, RK and Filion, A and Niebuhr, CN and Holmes, EC}, title = {Metatranscriptomic Comparison of Viromes in Endemic and Introduced Passerines in New Zealand.}, journal = {Viruses}, volume = {14}, number = {7}, pages = {}, pmid = {35891346}, issn = {1999-4915}, mesh = {Animals ; *Bird Diseases/epidemiology ; Introduced Species ; New Zealand/epidemiology ; *Passeriformes ; *Songbirds ; Virome ; }, abstract = {New Zealand/Aotearoa has many endemic passerine birds vulnerable to emerging infectious diseases. Yet little is known about viruses in passerines, and in some countries, including New Zealand, the virome of wild passerines has been only scarcely researched. Using metatranscriptomic sequencing we characterised the virome of New Zealand endemic and introduced species of passerine. Accordingly, we identified 34 possible avian viruses from cloacal swabs of 12 endemic and introduced bird species not showing signs of disease. These included a novel siadenovirus, iltovirus, and avastrovirus in the Eurasian blackbird (Turdus merula, an introduced species), song thrush (Turdus philomelos, introduced) and silvereye/tauhou (Zosterops lateralis, introduced), respectively. This is the first time novel viruses from these genera have been identified in New Zealand, likely reflecting prior undersampling. It also represents the first identification of an iltovirus and siadenovirus in blackbirds and thrushes globally. These three viruses were only found in introduced species and may pose a risk to endemic species if they were to jump species boundaries, particularly the iltoviruses and siadenoviruses that have a prior history of disease associations. Further virus study and surveillance are needed in New Zealand avifauna, particularly in Turdus populations and endemic species.}, } @article {pmid35889831, year = {2022}, author = {Sharon, I and Quijada, NM and Pasolli, E and Fabbrini, M and Vitali, F and Agamennone, V and Dötsch, A and Selberherr, E and Grau, JH and Meixner, M and Liere, K and Ercolini, D and de Filippo, C and Caderni, G and Brigidi, P and Turroni, S}, title = {The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept.}, journal = {Nutrients}, volume = {14}, number = {14}, pages = {}, pmid = {35889831}, issn = {2072-6643}, mesh = {Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/methods ; *Microbiota ; Sequence Analysis, DNA ; }, abstract = {The core microbiome, which refers to a set of consistent microbial features across populations, is of major interest in microbiome research and has been addressed by numerous studies. Understanding the core microbiome can help identify elements that lead to dysbiosis, and lead to treatments for microbiome-related health states. However, defining the core microbiome is a complex task at several levels. In this review, we consider the current state of core human microbiome research. We consider the knowledge that has been gained, the factors limiting our ability to achieve a reliable description of the core human microbiome, and the fields most likely to improve that ability. DNA sequencing technologies and the methods for analyzing metagenomics and amplicon data will most likely facilitate higher accuracy and resolution in describing the microbiome. However, more effort should be invested in characterizing the microbiome's interactions with its human host, including the immune system and nutrition. Other components of this holobiontic system should also be emphasized, such as fungi, protists, lower eukaryotes, viruses, and phages. Most importantly, a collaborative effort of experts in microbiology, nutrition, immunology, medicine, systems biology, bioinformatics, and machine learning is probably required to identify the traits of the core human microbiome.}, } @article {pmid35889746, year = {2022}, author = {Dore, MP and Sau, R and Niolu, C and Abbondio, M and Tanca, A and Bibbò, S and Loria, M and Pes, GM and Uzzau, S}, title = {Metagenomic Changes of Gut Microbiota following Treatment of Helicobacter pylori Infection with a Simplified Low-Dose Quadruple Therapy with Bismuth or Lactobacillus reuteri.}, journal = {Nutrients}, volume = {14}, number = {14}, pages = {}, pmid = {35889746}, issn = {2072-6643}, mesh = {Anti-Bacterial Agents/pharmacology ; Bismuth/pharmacology/therapeutic use ; Drug Therapy, Combination ; *Gastrointestinal Microbiome ; *Helicobacter Infections/drug therapy/microbiology ; *Helicobacter pylori ; Humans ; *Limosilactobacillus reuteri ; Metronidazole/therapeutic use ; Proton Pump Inhibitors ; RNA, Ribosomal, 16S ; Rabeprazole/pharmacology/therapeutic use ; Tetracycline/pharmacology/therapeutic use ; Treatment Outcome ; }, abstract = {BACKGROUND: Probiotic supplementation to antibiotic regimens against Helicobacter pylori infection has been proposed to improve eradication rate and to decrease detrimental effects on gut microbiota.

AIMS: To evaluate microbiota modifications due to a low-dose quadruple therapy with bismuth or Lactobacillus reuteri.

METHODS: Forty-six patients infected with H. pylori were prospectively enrolled in a single-centre, randomized controlled trial to receive b.i.d. with meals for 10 days low-dose quadruple therapy consisting of rabeprazole 20 mg and bismuth (two capsules of Pylera[®] plus 250 mg each of tetracycline and metronidazole), or the same dose of rabeprazole and antibiotics plus Gastrus[®] (L. reuteri), one tablet twice-a-day for 27 days. Stool samples were collected at the enrolment, at the end and 30-40 days after the treatment. Gut microbiota composition was investigated with 16S rRNA gene sequencing.

RESULTS: Eradication rate was by ITT 78% in both groups, and by PP analysis 85.7% and 95.5% for Gastrus[®] and bismuth group, respectively. Alpha and beta diversity decreased at the end of treatment and was associated with a reduction of bacterial genera beneficial for gut homeostasis, which was rescued 30-40 days later in both groups, suggesting a similar impact of the two regimens in challenging bacterial community complexity.

CONCLUSIONS: Low-dose bismuth quadruple therapy proved to be effective with lower costs and amount of antibiotics and bismuth. Gastrus[®] might be an option for patients with contraindications to bismuth. L. reuteri was unable to significantly counteract dysbiosis induced by antibiotics. How to administer probiotics to prevent gut microbiota alterations remains an open question.}, } @article {pmid35889742, year = {2022}, author = {Anderson, EM and Rozowsky, JM and Fazzone, BJ and Schmidt, EA and Stevens, BR and O'Malley, KA and Scali, ST and Berceli, SA}, title = {Temporal Dynamics of the Intestinal Microbiome Following Short-Term Dietary Restriction.}, journal = {Nutrients}, volume = {14}, number = {14}, pages = {}, pmid = {35889742}, issn = {2072-6643}, support = {T32 GM008721/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics/metabolism ; Diet, Protein-Restricted ; Dysbiosis ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; }, abstract = {Short-term dietary restriction has been proposed as an intriguing pre-operative conditioning strategy designed to attenuate the surgical stress response and improve outcomes. However, it is unclear how this nutritional intervention influences the microbiome, which is known to modulate the systemic condition. Healthy individuals were recruited to participate in a four-day, 70% protein-restricted, 30% calorie-restricted diet, and stool samples were collected at baseline, after the restricted diet, and after resuming normal food intake. Taxonomy and functional pathway analysis was performed via shotgun metagenomic sequencing, prevalence filtering, and differential abundance analysis. High prevalence species were altered by the dietary intervention but quickly returned to baseline after restarting a regular diet. Composition and functional changes after the restricted diet included the decreased relative abundance of commensal bacteria and a catabolic phenotype. Notable species changes included Faecalibacterium prausnitzii and Roseburia intestinalis, which are major butyrate producers within the colon and are characteristically decreased in many disease states. The macronutrient components of the diet might have influenced these changes. We conclude that short-term dietary restriction modulates the ecology of the gut microbiome, with this modulation being characterized by a relative dysbiosis.}, } @article {pmid35888639, year = {2022}, author = {Sokolovs-Karijs, O and Brīvība, M and Saksis, R and Sumeraga, G and Girotto, F and Erts, R and Osīte, J and Krūmiņa, A}, title = {An Overview of Adenoid Microbiome Using 16S rRNA Gene Sequencing-Based Metagenomic Analysis.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {58}, number = {7}, pages = {}, pmid = {35888639}, issn = {1648-9144}, mesh = {*Adenoids/chemistry/microbiology ; Bacteria/genetics ; Child ; Genes, rRNA ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/analysis/genetics ; Veillonella ; }, abstract = {Background and Objectives: the upper respiratory tract harbors the highest bacterial density in the whole respiratory system. Adenoids, which are located in the nasopharynx, are a major site of bacterial colonies in the upper airways. Our goal was to use culture-independent molecular techniques to identify the breadth of bacterial diversity in the adenoid vegetations of children suffering from chronic rhinosinusitis and obstructive sleep apnea. Materials and methods: in total, 21 adenoid samples were investigated using amplification and sequencing of the V3-V4 hypervariable region of the bacterial 16S rRNA gene. Results: among the most common bacterial species found were Veillonella atypica, Fusobactrium nucelatum, Shaalia odontolytica, and Moraxella catarrhalis. Veillonella atypica and Fusbacteriumnucelatum dominated the microbiome in all 21 samples, attributing to more than 60% of all detected genetic material. Conclusions: since both Veillonella atypica and Fusobacterium nucleatum are, predominantly, oral cavity and dental microorganisms, our findings may suggest oral microbiome migration deeper into the oropharynx and nasopharynx where these bacteria colonize adenoid vegetations.}, } @article {pmid35886216, year = {2022}, author = {Grace-Farfaglia, P and Frazier, H and Iversen, MD}, title = {Essential Factors for a Healthy Microbiome: A Scoping Review.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {14}, pages = {}, pmid = {35886216}, issn = {1660-4601}, mesh = {Diet ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome/physiology ; Humans ; Metagenome ; *Microbiota ; }, abstract = {Recent discoveries of the purpose and potential of microbial interactions with humans have broad implications for our understanding of metabolism, immunity, the host−microbe genetic interactions. Bioavailability and bioaccessibility of phytonutrients in foods not only enrich microbial diversity in the lower human gastrointestinal tract (GIT) but also direct the functioning of the metagenome of the microbiota. Thus, healthy choices must include foods that contain nutrients that satisfy both the needs of humans and their microbes. Physical activity interventions at a moderate level of intensity have shown positive effects on metabolism and the microbiome, while intense training (>70% VO2max) reduces diversity in the short term. The microbiome of elite endurance athletes is a robust producer of short-chain fatty acids. A lifestyle lacking activity is associated with the development of chronic disease, and experimental conditions simulating weightlessness in humans demonstrate loss of muscle mass occurring in conjunction with a decline in gut short-chain fatty acid (SCFA) production and the microbes that produce them. This review summarizes evidence addressing the relationship between the intestinal microbiome, diet, and physical activity. Data from the studies reviewed suggest that food choices and physical fitness in developed countries promote a resource “curse” dilemma for the microbiome and our health.}, } @article {pmid35882315, year = {2022}, author = {Zhang, S and Xiao, M and Liang, C and Chui, C and Wang, N and Shi, J and Liu, L}, title = {Multivariate insights into enhanced biogas production in thermophilic dry anaerobic co-digestion of food waste with kitchen waste or garden waste: Process properties, microbial communities and metagenomic analyses.}, journal = {Bioresource technology}, volume = {361}, number = {}, pages = {127684}, doi = {10.1016/j.biortech.2022.127684}, pmid = {35882315}, issn = {1873-2976}, mesh = {Anaerobiosis ; Biofuels ; Bioreactors/microbiology ; Food ; Gardens ; Methane/metabolism ; *Microbiota ; *Refuse Disposal/methods ; Sewage/microbiology ; }, abstract = {Multisubstrate synergetic anaerobic co-digestion can effectively overcome low efficiency of food waste (FW) mono-digestion. This study investigated the effect of supplementing FW with kitchen waste (KW) or garden waste (GW) on thermophilic dry anaerobic co-digestion. FW-KW and FW-GW co-digestion enhanced biogas production by 24.69 % and 44.96 % at organic loading rate (OLR) of 3 g VS L[-1] d[-1], and increased OLR tolerance from 3 to 4 g VS L[-1] d[-1] through mitigating ammonia nitrogen inhibition and volatile fatty acids accumulation. Co-digestion enriched the dominant hydrolytic bacteria Defluviitoga, resulting in an acceleration of substrate hydrolysis. FW-KW co-digestion improved biogas production by increasing gene abundance related to key enzymes in methanogenesis pathways and promoting the conversion of intermediate products into methane. FW-GW co-digestion enhanced biogas production by enriching ABC transporters-associated genes, leading to efficient substrate utilization. This study provides a promising approach for FW treatment with multivariate insights into thermophilic dry anaerobic co-digestion.}, } @article {pmid35880887, year = {2022}, author = {Holman, DB and Kommadath, A and Tingley, JP and Abbott, DW}, title = {Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0238022}, pmid = {35880887}, issn = {2165-0497}, mesh = {Animals ; Archaea/genetics ; Bacteria ; Carbohydrates ; *Gastrointestinal Microbiome/genetics ; Mammals/genetics ; *Metagenome ; Metagenomics/methods ; Swine ; }, abstract = {Pigs are among the most numerous and intensively farmed food-producing animals in the world. The gut microbiome plays an important role in the health and performance of swine and changes rapidly after weaning. Here, fecal samples were collected from pigs at 7 different times points from 7 to 140 days of age. These swine fecal metagenomes were used to assemble 1,150 dereplicated metagenome-assembled genomes (MAGs) that were at least 90% complete and had less than 5% contamination. These MAGs represented 472 archaeal and bacterial species, and the most widely distributed MAGs were the uncultured species Collinsella sp002391315, Sodaliphilus sp004557565, and Prevotella sp000434975. Weaning was associated with a decrease in the relative abundance of 69 MAGs (e.g., Escherichia coli) and an increase in the relative abundance of 140 MAGs (e.g., Clostridium sp000435835, Oliverpabstia intestinalis). Genes encoding for the production of the short-chain fatty acids acetate, butyrate, and propionate were identified in 68.5%, 18.8%, and 8.3% of the MAGs, respectively. Carbohydrate-active enzymes associated with the degradation of arabinose oligosaccharides and mixed-linkage glucans were predicted to be most prevalent among the MAGs. Antimicrobial resistance genes were detected in 327 MAGs, including 59 MAGs with tetracycline resistance genes commonly associated with pigs, such as tet(44), tet(Q), and tet(W). Overall, 82% of the MAGs were assigned to species that lack cultured representatives indicating that a large portion of the swine gut microbiome is still poorly characterized. The results here also demonstrate the value of MAGs in adding genomic context to gut microbiomes. IMPORTANCE Many of the bacterial strains found in the mammalian gut are difficult to culture and isolate due to their various growth and nutrient requirements that are frequently unknown. Here, we assembled strain-level genomes from short metagenomic sequences, so-called metagenome-assembled genomes (MAGs), that were derived from fecal samples collected from pigs at multiple time points. The genomic context of a number of antimicrobial resistance genes commonly detected in swine was also determined. In addition, our study connected taxonomy with potential metabolic functions such as carbohydrate degradation and short-chain fatty acid production.}, } @article {pmid35875611, year = {2022}, author = {Liang, H and Jo, JH and Zhang, Z and MacGibeny, MA and Han, J and Proctor, DM and Taylor, ME and Che, Y and Juneau, P and Apolo, AB and McCulloch, JA and Davar, D and Zarour, HM and Dzutsev, AK and Brownell, I and Trinchieri, G and Gulley, JL and Kong, HH}, title = {Predicting cancer immunotherapy response from gut microbiomes using machine learning models.}, journal = {Oncotarget}, volume = {13}, number = {}, pages = {876-889}, pmid = {35875611}, issn = {1949-2553}, mesh = {Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Immunotherapy ; Machine Learning ; *Melanoma/therapy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cancer immunotherapy has significantly improved patient survival. Yet, half of patients do not respond to immunotherapy. Gut microbiomes have been linked to clinical responsiveness of melanoma patients on immunotherapies; however, different taxa have been associated with response status with implicated taxa inconsistent between studies. We used a tumor-agnostic approach to find common gut microbiome features of response among immunotherapy patients with different advanced stage cancers. A combined meta-analysis of 16S rRNA gene sequencing data from our mixed tumor cohort and three published immunotherapy gut microbiome datasets from different melanoma patient cohorts found certain gut bacterial taxa correlated with immunotherapy response status regardless of tumor type. Using multivariate selbal analysis, we identified two separate groups of bacterial genera associated with responders versus non-responders. Statistical models of gut microbiome community features showed robust prediction accuracy of immunotherapy response in amplicon sequencing datasets and in cross-sequencing platform validation with shotgun metagenomic datasets. Results suggest baseline gut microbiome features may be predictive of clinical outcomes in oncology patients on immunotherapies, and some of these features may be generalizable across different tumor types, patient cohorts, and sequencing platforms. Findings demonstrate how machine learning models can reveal microbiome-immunotherapy interactions that may ultimately improve cancer patient outcomes.}, } @article {pmid35874661, year = {2022}, author = {Rodrigues, VF and Elias-Oliveira, J and Pereira, ÍS and Pereira, JA and Barbosa, SC and Machado, MSG and Carlos, D}, title = {Akkermansia muciniphila and Gut Immune System: A Good Friendship That Attenuates Inflammatory Bowel Disease, Obesity, and Diabetes.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {934695}, pmid = {35874661}, issn = {1664-3224}, mesh = {*Akkermansia ; Animals ; Chronic Disease ; *Diabetes Mellitus/microbiology ; Gastrointestinal Microbiome ; Humans ; Immune System ; *Inflammatory Bowel Diseases/microbiology ; Mice ; *Obesity/microbiology ; }, abstract = {Akkermansia muciniphila is a Gram-negative anaerobic mucus-layer-degrading bacterium that colonizes the intestinal mucosa of humans and rodents. Metagenomic data have shown an inverse correlation between the abundance of A. muciniphila and diseases such as inflammatory bowel disease (IBD), obesity, and diabetes. Thus, in recent decades, the potential of this bacterium as an immunomodulatory probiotic for autoimmune and chronic inflammatory diseases has been explored in experimental models. Corroborating these human correlation data, it has been reported that A. muciniphila slows down the development and progression of diabetes, obesity, and IBD in mice. Consequently, clinical studies with obese and diabetic patients are being performed, and the preliminary results are very promising. Therefore, this mini review highlights the main findings regarding the beneficial roles of A. muciniphila and its action mechanisms in autoimmune and chronic inflammatory diseases.}, } @article {pmid35870224, year = {2022}, author = {Kuhnert, E and Collemare, J}, title = {A genomic journey in the secondary metabolite diversity of fungal plant and insect pathogens: from functional to population genomics.}, journal = {Current opinion in microbiology}, volume = {69}, number = {}, pages = {102178}, doi = {10.1016/j.mib.2022.102178}, pmid = {35870224}, issn = {1879-0364}, mesh = {Animals ; Genome, Fungal ; Genomics ; Insecta ; *Metagenomics ; *Plant Diseases/microbiology ; Plants ; }, abstract = {Fungal pathogens produce a broad array of secondary metabolites (SMs), which allow the fungus to thrive in its natural habitat and gain competitive advantage. Analysis of the genetically encoded blueprints for SM assembly highlighted that only a small portion of the SMs these fungi are capable of producing are known, and even fewer have been investigated for their natural function. Using molecular tools, a lot of progress has been made recently in identifying the blueprint products and linking them to their ecological purpose such as the peptide virulence factor fusaoctaxin A released by Fusarium graminearum during infection of wheat or the F. oxysporum polyketide bikaverin that provides competitive advantage against bacteria in tomato. In addition, population genomics have given particularly important insights into the species-specific plasticity of the SM blueprint arsenal, showcasing the ongoing evolution and adaptation of fungal pathogens. This approach holds promise in inferring roles in pathogenicity of many more fungal SMs.}, } @article {pmid35870206, year = {2022}, author = {Su, H and Wu, C and Han, P and Liu, Z and Liang, M and Zhang, Z and Wang, Z and Guo, G and He, X and Pang, J and Wang, C and Weng, S and He, J}, title = {The microbiome and its association with antibiotic resistance genes in the hadal biosphere at the Yap Trench.}, journal = {Journal of hazardous materials}, volume = {439}, number = {}, pages = {129543}, doi = {10.1016/j.jhazmat.2022.129543}, pmid = {35870206}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology ; Archaea/genetics ; Bacteria ; Drug Resistance, Microbial/genetics ; *Microbiota/genetics ; }, abstract = {The hadal biosphere, the deepest part of the ocean, is known as the least-explored aquatic environment and hosts taxonomically diverse microbial communities. However, the microbiome and its association with antibiotic resistance genes (ARGs) in the hadal ecosystem remain unknown. Here, we profiled the microbiome diversity and ARG occurrence in seawater and sediments of the Yap Trench (YT) using metagenomic sequencing. Within the prokaryote (bacteria and archaea) lineages, the main components of bacteria were Gammaproteobacteria (77.76 %), Firmicutes (8.36 %), and Alphaproteobacteria (2.25 %), whereas the major components of archaea were Nitrososphaeria (6.51 %), Nanoarchaeia (0.42 %), and Thermoplasmata (0.25 %), respectively. Taxonomy of viral contigs showed that the classified viral communities in YT seawater and sediments were dominated by Podoviridae (45.96 %), Siphoviridae (29.41 %), and Myoviridae (24.63 %). A large majority of viral contigs remained uncharacterized and exhibited endemicity. A total of 48 ARGs encoding resistance to 12 antibiotic classes were identified and their hosts were bacteria and viruses. Novel ARG subtypes mexFYTV-1, mexFYTV-2, mexFYTV-3, vanRYTV-1, vanSYTV-1 (carried by unclassified viruses), and bacAYTB-1 (carried by phylum Firmicutes) were detected in seawater samples. Overall, our findings imply that the hadal environment of the YT is a repository of viral and ARG diversity.}, } @article {pmid35868082, year = {2022}, author = {Chen, F and Fan, B and Wang, C and Qian, J and Wang, B and Tang, X and Qin, Z and Chen, Y and Bin Liang, and Liu, W and Wang, A and Ye, Y and Wang, Y}, title = {Weak electro-stimulation promotes microbial uranium removal: Efficacy and mechanisms.}, journal = {Journal of hazardous materials}, volume = {439}, number = {}, pages = {129622}, doi = {10.1016/j.jhazmat.2022.129622}, pmid = {35868082}, issn = {1873-3336}, mesh = {Bacteria/metabolism ; Biodegradation, Environmental ; Oxidation-Reduction ; *Uranium/chemistry ; Wastewater ; *Water Pollutants, Radioactive/chemistry ; }, abstract = {Removal and recovery of uranium from uranium-mine wastewater is beneficial to environmental protection and resource preservation. Reduction of soluble hexavalent U (U(VI)) to insoluble tetravalent uranium (U(IV)) by microbes is a plausible approach for this purpose, but its practical implementation has long been restricted by its intrinsic drawbacks. The electro-stimulated microbial process offers promise in overcoming these drawbacks. However, its applicability in real wastewater has not been evaluated yet, and its U(VI) removal mechanisms remain poorly understood. Herein, we report that introducing a weak electro-stimulation considerably boosted microbial U(VI) removal activities in both synthetic and real wastewater. The U(VI) removal has proceeded via U(VI)-to-U(IV) reduction in the biocathode, and the electrochemical characterization demonstrates the crucial role of the electroactive biofilm. Microbial community analysis shows that the broad biodiversity of the cathode biofilm is capable of U(VI) reduction, and the molecular ecological network indicates that synthetic metabolisms among electroactive and metal-reducing bacteria play major roles in electro-microbial-mediated uranium removal. Metagenomic sequencing elucidates that the electro-stimulated U(VI) bioreduction may proceed via e-pili, extracellular electron shuttles, periplasmic and outer membrane cytochrome, and thioredoxin pathways. These findings reveal the potential and mechanism of the electro-stimulated U(VI) bioreduction system for the treatment of U-bearing wastewater.}, } @article {pmid35867822, year = {2022}, author = {Hu, Y and Satten, GA and Hu, YJ}, title = {LOCOM: A logistic regression model for testing differential abundance in compositional microbiome data with false discovery rate control.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {30}, pages = {e2122788119}, pmid = {35867822}, issn = {1091-6490}, support = {R01 GM116065/GM/NIGMS NIH HHS/United States ; R01 GM141074/GM/NIGMS NIH HHS/United States ; }, mesh = {Logistic Models ; Metagenomics/methods ; *Microbiota/genetics ; Sequence Analysis ; }, abstract = {Compositional analysis is based on the premise that a relatively small proportion of taxa are differentially abundant, while the ratios of the relative abundances of the remaining taxa remain unchanged. Most existing methods use log-transformed data, but log-transformation of data with pervasive zero counts is problematic, and these methods cannot always control the false discovery rate (FDR). Further, high-throughput microbiome data such as 16S amplicon or metagenomic sequencing are subject to experimental biases that are introduced in every step of the experimental workflow. McLaren et al. [eLife 8, e46923 (2019)] have recently proposed a model for how these biases affect relative abundance data. Motivated by this model, we show that the odds ratios in a logistic regression comparing counts in two taxa are invariant to experimental biases. With this motivation, we propose logistic compositional analysis (LOCOM), a robust logistic regression approach to compositional analysis, that does not require pseudocounts. Inference is based on permutation to account for overdispersion and small sample sizes. Traits can be either binary or continuous, and adjustment for confounders is supported. Our simulations indicate that LOCOM always preserved FDR and had much improved sensitivity over existing methods. In contrast, analysis of composition of microbiomes (ANCOM) and ANCOM with bias correction (ANCOM-BC)/ANOVA-Like Differential Expression tool (ALDEx2) had inflated FDR when the effect sizes were small and large, respectively. Only LOCOM was robust to experimental biases in every situation. The flexibility of our method for a variety of microbiome studies is illustrated by the analysis of data from two microbiome studies. Our R package LOCOM is publicly available.}, } @article {pmid35864536, year = {2022}, author = {Jiang, Q and Lin, L and Xie, F and Jin, W and Zhu, W and Wang, M and Qiu, Q and Li, Z and Liu, J and Mao, S}, title = {Metagenomic insights into the microbe-mediated B and K2 vitamin biosynthesis in the gastrointestinal microbiome of ruminants.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {109}, pmid = {35864536}, issn = {2049-2618}, mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Rumen/metabolism ; Ruminants/metabolism ; Vitamin B 12/metabolism ; Vitamins ; }, abstract = {BACKGROUND: B and K2 vitamins, essential nutrients in host metabolism, can be synthesized by the rumen microbiome in ruminants and subsequently absorbed by the host. However, the B and K2 vitamin biosynthesis by the whole gastrointestinal microbiome and their abundances in different dietary strategies are largely unknown. Here, we reanalyzed our previous large-scale metagenomic data on the gastrointestinal microbiome of seven ruminant species and recruited 17,425 nonredundant microbial genomes from published datasets to gain a comprehensive understanding of the microbe-mediated B and K2 vitamin biosynthesis in ruminants.

RESULTS: We identified 1,135,807 genes and 167 enzymes involved in B and K2 vitamin biosynthesis. Our results indicated that the total abundances of B and K2 vitamin biosynthesis were dominant in the stomach microbiome, while the biosynthesis of thiamine, niacin, and pyridoxine was more abundant in the large intestine. By examining 17,425 nonredundant genomes, we identified 2366 high-quality genomes that were predicted to de novo biosynthesize at least one vitamin. Genomic analysis suggested that only 2.7% of these genomes can synthesize five or more vitamins, and nearly half of genomes can synthesize only one vitamin. Moreover, we found that most genomes possessed cobalamin transporters or cobalamin-dependent enzymes to consume cobalamin directly, and only a few microbial genomes possessed a complete cobalamin biosynthesis pathway. Based on these genomic data, we examined the effect of the high-grain (HG) diet on the vitamin biosynthesis of the rumen microbiome of dairy cattle. We revealed that most vitamin biosynthesis was enhanced in the HG group, while only cobalamin synthesis was inhibited in the HG group, indicating that dietary fiber is vital for cobalamin biosynthesis.

CONCLUSIONS: We primarily provided a gene catalog and 2366 microbial genomes involved in B and K2 vitamin biosynthesis in ruminants. Our findings demonstrated the regional heterogeneity and dietary effect of vitamin biosynthetic potential in the ruminant gastrointestinal microbiome and interpreted the biosynthesis mechanisms of these microbes and their physiological adaptability. This study expands our understanding of microbe-mediated vitamin biosynthesis in ruminants and may provide novel targets for manipulation to improve the production of these essential vitamins. Video abstract.}, } @article {pmid35864173, year = {2023}, author = {Tian, C and Pang, J and Bu, C and Wu, S and Bai, H and Li, Y and Guo, Q and Siddique, KHM}, title = {The Microbiomes in Lichen and Moss Biocrust Contribute Differently to Carbon and Nitrogen Cycles in Arid Ecosystems.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {497-508}, pmid = {35864173}, issn = {1432-184X}, support = {2016YFE0203400//National Key Research and Development Program of China/ ; 2017YFC0504703//National Key Research and Development Program of China/ ; 41971131//National Natural Scientific Foundation of China/ ; }, mesh = {Ecosystem ; *Lichens ; Carbon ; Nitrates ; Soil/chemistry ; *Bryophyta ; Nitrogen Fixation ; *Microbiota ; Soil Microbiology ; Nitrogen/chemistry ; }, abstract = {Biological soil crusts (biocrusts) are distributed in arid and semiarid regions across the globe. Microorganisms are an essential component in biocrusts. They add and accelerate critical biochemical processes. However, little is known about the functional genes and metabolic processes of microbiomes in lichen and moss biocrust. This study used shotgun metagenomic sequencing to compare the microbiomes of lichen-dominated and moss-dominated biocrust and reveal the microbial genes and metabolic pathways involved in carbon and nitrogen cycling. The results showed that Actinobacteria, Bacteroidetes, and Acidobacteria were more abundant in moss biocrust than lichen biocrust, while Proteobacteria and Cyanobacteria were more abundant in lichen biocrust than moss biocrust. The relative abundance of carbohydrate-active enzymes and enzymes associated with carbon and nitrogen metabolism differed significantly between microbiomes of the two biocrust types. However, in the microbial communities of both biocrust types, respiration pathways dominated over carbon fixation pathways. The genes encoding carbon monoxide dehydrogenase were more abundant than those encoding ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo) involved in carbon fixation. Similarly, metabolic N-pathway diversity was dominated by nitrogen reduction, followed by denitrification, with nitrogen fixation the lowest proportion. Gene diversity involved in N cycling differed between the microbiomes of the two biocrust types. Assimilatory nitrate reduction genes had higher relative abundance in lichen biocrust, whereas dissimilatory nitrate reduction genes had higher relative abundance in moss biocrust. As dissolved organic carbon and soil organic carbon are considered the main drivers of the community structure in the microbiome of biocrust, these results indicate that biocrust type has a pivotal role in microbial diversity and related biogeochemical cycling.}, } @article {pmid35863030, year = {2022}, author = {Rhoades, NS and Cinco, IR and Hendrickson, SM and Slifka, MK and Messaoudi, I}, title = {Taxonomic and Functional Shifts in the Perinatal Gut Microbiome of Rhesus Macaques.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0081422}, pmid = {35863030}, issn = {2165-0497}, support = {P51 OD011092/OD/NIH HHS/United States ; }, mesh = {Adult ; Animals ; Butyrates ; Feces ; Female ; Folic Acid ; *Gastrointestinal Microbiome/physiology ; Humans ; Infant, Newborn ; Macaca mulatta/genetics/metabolism ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; Starch ; }, abstract = {Pregnancy and the postpartum period result in some of the most dramatic metabolic, hormonal, and physiological changes that can be experienced by an otherwise healthy adult. The timing and magnitude of these changes is key for both maternal and fetal health. One of the factors believed to critically modulate these physiological changes is the maternal gut microbiome. However, the dynamic changes in this community during the perinatal period remain understudied. Clinical studies can be complicated by confounding variables like diet and other drivers of heterogeneity in the human microbiome. Therefore, in this study, we conducted a longitudinal analysis of the fecal microbiome obtained during the pregnancy and postpartum periods in 26 captive rhesus macaques using 16S rRNA gene amplicon sequencing and shotgun metagenomics. Shifts at both the taxonomic and functional potential level were detected when comparing pregnancy to postpartum samples. Taxonomically, Alloprevotella, Actinobacillus, and Anaerovibrio were enriched in the gut microbiome during pregnancy, while Treponema, Lachnospiraceae, and Methanosphaera were more abundant postpartum. Functionally, the gut microbiome during pregnancy was associated with increased abundance in pathways involving the production of the short-chain fatty acid (SCFA) butyrate, while pathways associated with starch degradation and folate transformation were more abundant during the postpartum period. These data demonstrate dramatic changes in the maternal gut microbiome even in the absence of dietary changes and suggest that rhesus macaques could provide a valuable model to determine how changes in the microbiome correlate to other physiological changes in pregnancy. IMPORTANCE Pregnancy and the postpartum period are characterized by a myriad of metabolic and physiological adaptations needed to support fetal growth and maternal health. The maternal gut microbiome is believed to play a key role during this period but remains underexplored. Here, we report significant shifts in the taxonomic landscape and functional potential of the gut microbiome in 26 pregnant rhesus macaques during the transition from pregnancy to the postpartum period, despite shared dietary and environmental exposures. Increased abundance of pathways involved in the production of the short-chain fatty acid butyrate could play a critical role in modulating the maternal immune system and regulating fetal tolerance. On the other hand, increased abundance of pathways associated with starch degradation and folate transformation during the postpartum period could be important for meeting the metabolic demands of breastfeeding and neonatal growth.}, } @article {pmid35863004, year = {2022}, author = {Zhang, L and Wang, Z and Zhang, X and Zhao, L and Chu, J and Li, H and Sun, W and Yang, C and Wang, H and Dai, W and Yan, S and Chen, X and Xu, D}, title = {Alterations of the Gut Microbiota in Patients with Diabetic Nephropathy.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0032422}, pmid = {35863004}, issn = {2165-0497}, mesh = {Bacteroides ; Clostridiales ; *Diabetes Mellitus, Type 2/microbiology ; *Diabetic Nephropathies/microbiology/pathology ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Diabetic nephropathy (DN) is the primary cause of end-stage renal disease. Accumulating studies have implied a critical role for the gut microbiota in diabetes mellitus (DM) and DN. However, the precise roles and regulatory mechanisms of the gut microbiota in the pathogenesis of DN remain largely unclear. In this study, metagenomics sequencing was performed using fecal samples from healthy controls (CON) and type 2 diabetes mellitus (T2DM) patients with or without DN. Fresh fecal samples from 15 T2DM patients without DN, 15 DN patients, and 15 age-, gender-, and body mass index (BMI)-matched healthy controls were collected. The compositions and potential functions of the gut microbiota were estimated. Although no difference of gut microbiota α and β diversity was observed between the CON, T2DM, and DN groups, the relative abundances of butyrate-producing bacteria (Clostridium, Eubacterium, and Roseburia intestinalis) and potential probiotics (Lachnospira and Intestinibacter) were significantly reduced in T2DM and DN patients. Besides, Bacteroides stercoris was significantly enriched in fecal samples from patients with DN. Moreover, Clostridium sp. 26_22 was negatively associated with serum creatinine (P < 0.05). DN patients could be accurately distinguished from CON by Clostridium sp. CAG_768 (area under the curve [AUC] = 0.941), Bacteroides propionicifaciens (AUC = 0.905), and Clostridium sp. CAG_715 (AUC = 0.908). DN patients could be accurately distinguished from T2DM patients by Pseudomonadales, Fusobacterium varium, and Prevotella sp. MSX73 (AUC = 0.889). Regarding the potential bacterial functions of the gut microbiota, the citrate cycle, base excision repair, histidine metabolism, lipoic acid metabolism, and bile acid biosynthesis were enriched in DN patients, while selenium metabolism and branched-chain amino acid biosynthesis were decreased in DN patients. IMPORTANCE Gut microbiota imbalance is found in fecal samples from DN patients, in which Roseburia intestinalis is significantly decreased, while Bacteroides stercoris is increased. There is a significant correlation between gut microbiota imbalance and clinical indexes related to lipid metabolism, glucose metabolism, and renal function. The gut microbiota may be predictive factors for the development and progression of DN, although further studies are warranted to illustrate their regulatory mechanisms.}, } @article {pmid35862824, year = {2022}, author = {Schultz, J and Modolon, F and Rosado, AS and Voolstra, CR and Sweet, M and Peixoto, RS}, title = {Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0036722}, pmid = {35862824}, issn = {2379-5077}, mesh = {Animals ; *Anthozoa ; Bacteria/genetics ; *Microbiota/genetics ; Metagenome ; Biotechnology ; }, abstract = {The vast majority of environmental microbes have not yet been cultured, and most of the knowledge on coral-associated microbes (CAMs) has been generated from amplicon sequencing and metagenomes. However, exploring cultured CAMs is key for a detailed and comprehensive characterization of the roles of these microbes in shaping coral health and, ultimately, for their biotechnological use as, for example, coral probiotics and other natural products. Here, the strategies and technologies that have been used to access cultured CAMs are presented, while advantages and disadvantages associated with each of these strategies are discussed. We highlight the existing gaps and potential improvements in culture-dependent methodologies, indicating several possible alternatives (including culturomics and in situ diffusion devices) that could be applied to retrieve the CAM "dark matter" (i.e., the currently undescribed CAMs). This study provides the most comprehensive synthesis of the methodologies used to recover the cultured coral microbiome to date and draws suggestions for the development of the next generation of CAM culturomics.}, } @article {pmid35862823, year = {2022}, author = {Loureiro, C and Galani, A and Gavriilidou, A and Chaib de Mares, M and van der Oost, J and Medema, MH and Sipkema, D}, title = {Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0035722}, pmid = {35862823}, issn = {2379-5077}, mesh = {Animals ; *Porifera/genetics ; Metagenome ; *Microbiota/genetics ; Bacteria/genetics ; *Biological Products/metabolism ; }, abstract = {Marine sponges and their microbial symbiotic communities are rich sources of diverse natural products (NPs) that often display biological activity, yet little is known about the global distribution of NPs and the symbionts that produce them. Since the majority of sponge symbionts remain uncultured, it is a challenge to characterize their NP biosynthetic pathways, assess their prevalence within the holobiont, and measure the diversity of NP biosynthetic gene clusters (BGCs) across sponge taxa and environments. Here, we explore the microbial biosynthetic landscapes of three high-microbial-abundance (HMA) sponges from the Atlantic Ocean and the Mediterranean Sea. This data set reveals striking novelty, with <1% of the recovered gene cluster families (GCFs) showing similarity to any characterized BGC. When zooming in on the microbial communities of each sponge, we observed higher variability of specialized metabolic and taxonomic profiles between sponge species than within species. Nonetheless, we identified conservation of GCFs, with 20% of sponge GCFs being shared between at least two sponge species and a GCF core comprised of 6% of GCFs shared across all species. Within this functional core, we identified a set of widespread and diverse GCFs encoding nonribosomal peptide synthetases that are potentially involved in the production of diversified ether lipids, as well as GCFs putatively encoding the production of highly modified proteusins. The present work contributes to the small, yet growing body of data characterizing NP landscapes of marine sponge symbionts and to the cryptic biosynthetic potential contained in this environmental niche. IMPORTANCE Marine sponges and their microbial symbiotic communities are a rich source of diverse natural products (NPs). However, little is known about the sponge NP global distribution landscape and the symbionts that produce them. Here, we make use of recently developed tools to perform untargeted mining and comparative analysis of sponge microbiome metagenomes of three sponge species in the first study considering replicate metagenomes of multiple sponge species. We present an overview of the biosynthetic diversity across these sponge holobionts, which displays extreme biosynthetic novelty. We report not only the conservation of biosynthetic and taxonomic diversity but also a core of conserved specialized metabolic pathways. Finally, we highlight several novel GCFs with unknown ecological function, and observe particularly high biosynthetic potential in Acidobacteriota and Latescibacteria symbionts. This study paves the way toward a better understanding of the marine sponge holobionts' biosynthetic potential and the functional and ecological role of sponge microbiomes.}, } @article {pmid35862821, year = {2022}, author = {Lidbury, IDEA and Raguideau, S and Borsetto, C and Murphy, ARJ and Bottrill, A and Liu, S and Stark, R and Fraser, T and Goodall, A and Jones, A and Bending, GD and Tibbet, M and Hammond, JP and Quince, C and Scanlan, DJ and Pandhal, J and Wellington, EMH}, title = {Stimulation of Distinct Rhizosphere Bacteria Drives Phosphorus and Nitrogen Mineralization in Oilseed Rape under Field Conditions.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0002522}, pmid = {35862821}, issn = {2379-5077}, support = {BB/L026074/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T009152/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Brassica napus ; Rhizosphere ; Bacteria/genetics ; *Microbiota/genetics ; Plants ; Soil ; }, abstract = {Advances in DNA sequencing technologies have drastically changed our perception of the structure and complexity of the plant microbiome. By comparison, our ability to accurately identify the metabolically active fraction of soil microbiota and its specific functional role in augmenting plant health is relatively limited. Important ecological interactions being performed by microbes can be investigated by analyzing the extracellular protein fraction. Here, we combined a unique protein extraction method and an iterative bioinformatics pipeline to capture and identify extracellular proteins (metaexoproteomics) synthesized in the rhizosphere of Brassica spp. We first validated our method in the laboratory by successfully identifying proteins related to a host plant (Brassica rapa) and its bacterial inoculant, Pseudomonas putida BIRD-1. This identified numerous rhizosphere specific proteins linked to the acquisition of plant-derived nutrients in P. putida. Next, we analyzed natural field-soil microbial communities associated with Brassica napus L. (oilseed rape). By combining metagenomics with metaexoproteomics, 1,885 plant, insect, and microbial proteins were identified across bulk and rhizosphere samples. Metaexoproteomics identified a significant shift in the metabolically active fraction of the soil microbiota responding to the presence of B. napus roots that was not apparent in the composition of the total microbial community (metagenome). This included stimulation of rhizosphere-specialized bacteria, such as Gammaproteobacteria, Betaproteobacteria, and Flavobacteriia, and the upregulation of plant beneficial functions related to phosphorus and nitrogen mineralization. Our metaproteomic assessment of the "active" plant microbiome at the field-scale demonstrates the importance of moving beyond metagenomics to determine ecologically important plant-microbe interactions underpinning plant health. IMPORTANCE Plant-microbe interactions are critical to ecosystem function and crop production. While significant advances have been made toward understanding the structure of the plant microbiome, learning about its full functional role is still in its infancy. This is primarily due to an incomplete ability to determine in situ plant-microbe interactions actively operating under field conditions. Proteins are the functional entities of the cell. Therefore, their identification and relative quantification within a microbial community provide the best proxy for which microbes are the most metabolically active and which are driving important plant-microbe interactions. Here, we provide the first metaexoproteomics assessment of the plant microbiome using field-grown oilseed rape as the model crop species, identifying key taxa responsible for specific ecological interactions. Gaining a mechanistic understanding of the plant microbiome is central to developing engineered plant microbiomes to improve sustainable agricultural approaches and reduce our reliance on nonrenewable resources.}, } @article {pmid35862818, year = {2022}, author = {Fang, Y and Liu, J and Yang, J and Wu, G and Hua, Z and Dong, H and Hedlund, BP and Baker, BJ and Jiang, H}, title = {Compositional and Metabolic Responses of Autotrophic Microbial Community to Salinity in Lacustrine Environments.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0033522}, pmid = {35862818}, issn = {2379-5077}, mesh = {*Bacteria/genetics ; Salinity ; *Microbiota/genetics ; Autotrophic Processes ; Proteobacteria ; Carbon Cycle ; }, abstract = {The compositional and physiological responses of autotrophic microbiotas to salinity in lakes remain unclear. In this study, the community composition and carbon fixation pathways of autotrophic microorganisms in lacustrine sediments with a salinity gradient (82.6 g/L to 0.54 g/L) were investigated by using metagenomic analysis. A total of 117 metagenome-assembled genomes (MAGs) with carbon fixation potentially belonging to 20 phyla were obtained. The abundance of these potential autotrophs increased significantly with decreasing salinity, and the variation of sediment autotrophic microbial communities was mainly affected by salinity, pH, and total organic carbon. Notably, along the decreasing salinity gradient, the dominant lineage shifted from Desulfobacterota to Proteobacteria. Meanwhile, the dominant carbon fixation pathway shifted from the Wood-Lungdahl pathway to the less-energy-efficient Calvin-Benson-Bassham cycle, with glycolysis shifting from the Embden-Meyerhof-Parnas pathway to the less-exergonic Entner-Doudoroff pathway. These results suggest that the physiological efficiency of autotrophic microorganisms decreased when the environmental salinity became lower. Metabolic inference of these MAGs revealed that carbon fixation may be coupled to the oxidation of reduced sulfur compounds and ferrous iron, dissimilatory nitrate reduction at low salinity, and dissimilatory sulfate reduction in hypersaline sediments. These results extend our understanding of metabolic versatility and niche diversity of autotrophic microorganisms in saline environments and shed light on the response of autotrophic microbiomes to salinity. These findings are of great significance for understanding the impact of desalination caused by climate warming on the carbon cycle of saline lake ecosystems. IMPORTANCE The Qinghai-Tibetan lakes are experiencing water increase and salinity decrease due to climate warming. However, little is known about how the salinity decrease will affect the composition of autotrophic microbial populations and their carbon fixation pathways. In this study, we used genome-resolved metagenomics to interpret the dynamic changes in the autotrophic microbial community and metabolic pathways along a salinity gradient. The results showed that desalination drove the shift of the dominant microbial lineage from Desulfobacterota to Proteobacteria, enriched autotrophs with lower physiological efficiency pathways, and enhanced coupling between the carbon cycle and other element cycles. These results can predict the future response of microbial communities to lake desalination and improve our understanding of the effect of climate warming on the carbon cycle in saline aquatic ecosystems.}, } @article {pmid35862686, year = {2022}, author = {Bhar, S and Singh, R and Pinna, NK and Bose, T and Dutta, A and Mande, SS}, title = {Sensing Host Health: Insights from Sensory Protein Signature of the Metagenome.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {15}, pages = {e0059622}, pmid = {35862686}, issn = {1098-5336}, mesh = {Biomarkers ; *Diabetes Mellitus, Type 2 ; Dysbiosis ; Humans ; Metagenome ; *Microbiota ; }, abstract = {The human microbiota, which comprises an ensemble of taxonomically and functionally diverse but often mutually cooperating microorganisms, benefits its host by shaping the host immunity, energy harvesting, and digestion of complex carbohydrates as well as production of essential nutrients. Dysbiosis in the human microbiota, especially the gut microbiota, has been reported to be linked to several diseases and metabolic disorders. Recent studies have further indicated that tracking these dysbiotic variations could potentially be exploited as biomarkers of disease states. However, the human microbiota is not geography agnostic, and hence a taxonomy-based (microbiome) biomarker for disease diagnostics has certain limitations. In comparison, (microbiome) function-based biomarkers are expected to have a wider applicability. Given that (i) the host physiology undergoes certain changes in the course of a disease and (ii) host-associated microbial communities need to adapt to this changing microenvironment of their host, we hypothesized that signatures emanating from the abundance of bacterial proteins associated with the signal transduction system (herein referred to as sensory proteins [SPs]) might be able to distinguish between healthy and diseased states. To test this hypothesis, publicly available metagenomic data sets corresponding to three diverse health conditions, namely, colorectal cancer, type 2 diabetes mellitus, and schizophrenia, were analyzed. Results demonstrated that SP signatures (derived from host-associated metagenomic samples) indeed differentiated among healthy individual and patients suffering from diseases of various severities. Our finding was suggestive of the prospect of using SP signatures as early biomarkers for diagnosing the onset and progression of multiple diseases and metabolic disorders. IMPORTANCE The composition of the human microbiota, a collection of host-associated microbes, has been shown to differ among healthy and diseased individuals. Recent studies have investigated whether tracking these variations could be exploited for disease diagnostics. It has been noted that compared to microbial taxonomies, the ensemble of functional proteins encoded by microbial genes are less likely to be affected by changes in ethnicity and dietary preferences. These functions are expected to help the microbe adapt to changing environmental conditions. Thus, healthy individuals might harbor a different set of genes than diseased individuals. To test this hypothesis, we analyzed metagenomes from healthy and diseased individuals for signatures of a particular group of proteins called sensory proteins (SP), which enable the bacteria to sense and react to changes in their microenvironment. Results demonstrated that SP signatures indeed differentiate among healthy individuals and those suffering from diseases of various severities.}, } @article {pmid35862660, year = {2022}, author = {Swarthout, JM and Fuhrmeister, ER and Hamzah, L and Harris, AR and Ahmed, MA and Gurley, ES and Satter, SM and Boehm, AB and Pickering, AJ}, title = {Differential Overlap in Human and Animal Fecal Microbiomes and Resistomes in Rural versus Urban Bangladesh.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {14}, pages = {e0075922}, pmid = {35862660}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Bangladesh ; Chickens/genetics ; Escherichia coli/genetics ; Genes, Bacterial ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Rural Population ; }, abstract = {Low- and middle-income countries (LMICs) bear the largest mortality burden of antibiotic-resistant infections. Small-scale animal production and free-roaming domestic animals are common in many LMICs, yet data on zoonotic exchange of gut bacteria and antibiotic resistance genes (ARGs) in low-income communities are sparse. Differences between rural and urban communities with regard to population density, antibiotic use, and cohabitation with animals likely influence the frequency of transmission of gut bacterial communities and ARGs between humans and animals. Here, we determined the similarity in gut microbiomes, using 16S rRNA gene amplicon sequencing, and resistomes, using long-read metagenomics, between humans, chickens, and goats in a rural community compared to an urban community in Bangladesh. Gut microbiomes were more similar between humans and chickens in the rural (where cohabitation is more common) than the urban community, but there was no difference for humans and goats in the rural versus the urban community. Human and goat resistomes were more similar in the urban community, and ARG abundance was higher in urban animals than rural animals. We identified substantial overlap of ARG alleles in humans and animals in both settings. Humans and chickens had more overlapping ARG alleles than humans and goats. All fecal hosts from the urban community and rural humans carried ARGs on chromosomal contigs classified as potentially pathogenic bacteria, including Escherichia coli, Campylobacter jejuni, Clostridioides difficile, and Klebsiella pneumoniae. These findings provide insight into the breadth of ARGs circulating within human and animal populations in a rural compared to urban community in Bangladesh. IMPORTANCE While the development of antibiotic resistance in animal gut microbiomes and subsequent transmission to humans has been demonstrated in intensive farming environments and high-income countries, evidence of zoonotic exchange of antibiotic resistance in LMIC communities is lacking. This research provides genomic evidence of overlap of antibiotic resistance genes between humans and animals, especially in urban communities, and highlights chickens as important reservoirs of antibiotic resistance. Chicken and human gut microbiomes were more similar in rural Bangladesh, where cohabitation is more common. Incorporation of long-read metagenomics enabled characterization of bacterial hosts of resistance genes, which has not been possible in previous culture-independent studies using only short-read sequencing. These findings highlight the importance of developing strategies for combatting antibiotic resistance that account for chickens being reservoirs of ARGs in community environments, especially in urban areas.}, } @article {pmid35862452, year = {2022}, author = {Szabo, RE and Pontrelli, S and Grilli, J and Schwartzman, JA and Pollak, S and Sauer, U and Cordero, OX}, title = {Historical contingencies and phage induction diversify bacterioplankton communities at the microscale.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {30}, pages = {e2117748119}, pmid = {35862452}, issn = {1091-6490}, mesh = {Aquatic Organisms ; *Bacteria/classification ; *Bacteriophages ; Chitin/metabolism ; *Microbiota ; *Seawater/microbiology/virology ; }, abstract = {In many natural environments, microorganisms decompose microscale resource patches made of complex organic matter. The growth and collapse of populations on these resource patches unfold within spatial ranges of a few hundred micrometers or less, making such microscale ecosystems hotspots of heterotrophic metabolism. Despite the potential importance of patch-level dynamics for the large-scale functioning of heterotrophic microbial communities, we have not yet been able to delineate the ecological processes that control natural populations at the microscale. Here, we address this challenge by characterizing the natural marine communities that assembled on over 1,000 individual microscale particles of chitin, the most abundant marine polysaccharide. Using low-template shotgun metagenomics and imaging, we find significant variation in microscale community composition despite the similarity in initial species pools across replicates. Chitin-degrading taxa that were rare in seawater established large populations on a subset of particles, resulting in a wide range of predicted chitinolytic abilities and biomass at the level of individual particles. We show, through a mathematical model, that this variability can be attributed to stochastic colonization and historical contingencies affecting the tempo of growth on particles. We find evidence that one biological process leading to such noisy growth across particles is differential predation by temperate bacteriophages of chitin-degrading strains, the keystone members of the community. Thus, initial stochasticity in assembly states on individual particles, amplified through ecological interactions, may have significant consequences for the diversity and functionality of systems of microscale patches.}, } @article {pmid35861776, year = {2023}, author = {Chattopadhyay, I and Lu, W and Manikam, R and Malarvili, MB and Ambati, RR and Gundamaraju, R}, title = {Can metagenomics unravel the impact of oral bacteriome in human diseases?.}, journal = {Biotechnology & genetic engineering reviews}, volume = {39}, number = {1}, pages = {85-117}, doi = {10.1080/02648725.2022.2102877}, pmid = {35861776}, issn = {2046-5556}, mesh = {Female ; Humans ; Pregnancy ; *Dental Caries ; *Periodontal Diseases/microbiology ; Porphyromonas gingivalis ; *Microbiota ; *Arthritis, Rheumatoid ; }, abstract = {Oral microbial ecosystems are vital in maintaining the health of the oral cavity and the entire body. Oral microbiota is associated with the progression of oral diseases such as dental caries, periodontal diseases, head and neck cancer, and several systemic diseases such as cardiovascular disease, rheumatoid arthritis, adverse pregnancy outcomes, diabetes, lung infection, colorectal cancer, and pancreatic cancer. Buccal mucosa, tongue dorsum, hard palate, saliva, palatine tonsils, throat, keratinized gingiva, supra-gingival plaque, subgingival plaque, dentures, and lips are microbial habitats of the oral cavity. Porphyromonas gingivalis may have a role in the development of periodontal diseases, oral cancer, diabetes, and atherosclerotic disease. Fusobacterium nucleatum showed a higher abundance in periodontal diseases, oral and colon cancer, adverse pregnancy outcomes, diabetes, and rheumatoid arthritis. The higher abundance of Prevotella intermedia is typical in periodontal diseases, rheumatoid arthritis, and adverse pregnancy outcome. S. salivarius displayed higher abundance in both dental caries and OSCC. Oral bacteria may influence systemic diseases through inflammation by releasing pro inflammatory cytokines. Identification of oral bacteria using culture-dependent approaches and next-generation sequencing-based metagenomic approaches is believed to significantly identify the therapeutic targets and non-invasive diagnostic indicators in different human diseases. Oral bacteria in saliva could be exploited as a non-invasive diagnostic indicator for the early detection of oral and systemic disorders. Other therapeutic approaches such as the use of probiotics, green tea polyphenol, cold atmospheric plasma (CAP) therapy, antimicrobial photodynamic therapy, and antimicrobial peptides are used to inhibit the growth of biofilm formation by oral bacteria.}, } @article {pmid35860041, year = {2022}, author = {Zhang, J and Xu, M and Zou, X and Chen, J}, title = {Structural and functional characteristics of soil microbial community in a Pinus massoniana forest at different elevations.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13504}, pmid = {35860041}, issn = {2167-8359}, mesh = {*Pinus ; Soil/chemistry ; Fungi/genetics ; Forests ; Bacteria/genetics ; Archaea/genetics ; *Microbiota/genetics ; Amino Acids ; }, abstract = {Shifts in forest soil microbial communities over altitudinal gradients have long been attracting scientific interest. The distribution patterns of different soil microbial communities along altitudinal gradients in subtropical mountain forest ecosystems remain unclear. To better understand the changes in soil microbial communities along an altitude gradient, we used Illumina MiSeq metagenome sequencing technology to survey the soil microbial communities in a Pinus massoniana forest at four elevations (Mp1000, Mp1200, Mp1400, Mp1600) and in a tea garden in Guizhou Leigong Mountain in Southwestern China. We observed that the richness of bacteria, fungi, and viruses in the soil microbial community changed in a unimodal pattern with increasing elevation while that of Archaea first increased significantly, then decreased, and finally increased again. Euryarchaeota and Thaumarchaeota were the predominant Archaea, Proteobacteria and Acidobacteria were the predominant bacterial groups, Ascomycota and Basidiomycota were the predominant fungal groups, and Myoviridae, Podoviridae, and Siphoviridae were the predominant virus groups. Amino acid transport and metabolism, energy production and conversion, signal transduction mechanisms, and DNA replication, restructuring and repair were the predominant categories as per NOG function gene-annotation. Carbohydrate metabolism, global and overview map, amino acid metabolism, and energy metabolism were predominant categories in the KEGG pathways. Glycosyl transferase and glycoside hydrolase were predominant categories among carbohydrate enzyme-functional genes. Cluster, redundancy, and co-occurring network analyses showed obvious differences in the composition, structure, and function of different soil microbial communities along the altitudinal gradient studied. Our findings indicate that the different soil microbial communities along the altitudinal gradient have different distribution patterns, which may provide a better understanding of the mechanisms that determine microbial life in a mid-subtropical mountain forest ecosystem.}, } @article {pmid35859219, year = {2022}, author = {Bharti, M and Nagar, S and Khurana, H and Negi, RK}, title = {Metagenomic insights to understand the role of polluted river Yamuna in shaping the gut microbial communities of two invasive fish species.}, journal = {Archives of microbiology}, volume = {204}, number = {8}, pages = {509}, pmid = {35859219}, issn = {1432-072X}, mesh = {Animals ; *Carps ; Humans ; Introduced Species ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Rivers ; Water ; }, abstract = {The gastrointestinal microbial community plays a crucial role in host health, immunity, protection, development and provides nutrients to the host. The rising human-induced pollution and heavy metal contamination in all aquatic systems globally has led us to explore the gut microbial diversity of two exotic invasive fish Cyprinus carpio (Linnaeus, 1858) and Oreochromis niloticus (Linnaeus,1857) from river Yamuna, India. These fishes are aquatic bioindicators with high demographic resilience. Exploring these associations would pave the way for addressing problems that inhabitant fishes are facing due to the increasing pollution load in the River Yamuna. Based on 16S rRNA gene amplicon sequencing, our results deliver comparative information on the gut microbiome of these fishes and highlight connotations between the microbiome of gut and water samples. The gut of C. carpio and O. niloticus was dominated by phyla Proteobacteria whereas Bacteroidetes dominated the water sample. Microbial communities showed predicted roles such as pathogenicity (Escherichia-Shigella, Aeromonas veronii, Vibrio cholerae, Streptococcus iniae, Flavobacterium columnare, Klebsiella pneumoniae, Mycobacterium sp.), probiotic applications (Bacillus velezensis, Lactobacillus plantarum, Enterococcus faecalis, Bifidobacterium longum, Lactococcus lactis, Leuconostoc falkenbergense) and involvement in sewage and organic matter decomposition (Nitrosomonas sp., Methanosaeta harundinacea, Dechloromonas agitata, Thauera humireducens, Zoogloea ramigera). Heavy metal degrading members (Leucobacter chromiireducens, Pseudomonas fluorescens, P. aeruginosa, Klebsiella pneumoniae, and Micrococcus luteus) were detected in gut microbiome samples thus supporting the notion that fish shapes its gut microbiota with changing ecology. Functional profiling showed that microbial communities are specialized in metabolic functions thus reflecting the dietary profile of these invasive fishes.}, } @article {pmid35858888, year = {2022}, author = {Killinger, BJ and Whidbey, C and Sadler, NC and DeLeon, AJ and Munoz, N and Kim, YM and Wright, AT}, title = {Activity-based protein profiling identifies alternating activation of enzymes involved in the bifidobacterium shunt pathway or mucin degradation in the gut microbiome response to soluble dietary fiber.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {60}, pmid = {35858888}, issn = {2055-5008}, support = {P41 GM103493/GM/NIGMS NIH HHS/United States ; R21 ES029319/ES/NIEHS NIH HHS/United States ; R56 ES030220/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Bacteria ; Bifidobacterium/metabolism ; Carrier Proteins/metabolism ; Dietary Fiber ; Feces/microbiology ; *Gastrointestinal Microbiome ; Mice ; Mucins/metabolism/pharmacology ; Sugars/metabolism/pharmacology ; }, abstract = {While deprivation of dietary fiber has been associated with adverse health outcomes, investigations concerning the effect of dietary fiber on the gut microbiome have been largely limited to compositional sequence-based analyses or utilize a defined microbiota not native to the host. To extend understanding of the microbiome's functional response to dietary fiber deprivation beyond correlative evidence from sequence-based analyses, approaches capable of measuring functional enzymatic activity are needed. In this study, we use an activity-based protein profiling (ABPP) approach to identify sugar metabolizing and transport proteins in native mouse gut microbiomes that respond with differential activity to the deprivation or supplementation of the soluble dietary fibers inulin and pectin. We found that the microbiome of mice subjected to a high fiber diet high in soluble fiber had increased functional activity of multiple proteins, including glycoside hydrolases, polysaccharide lyases, and sugar transport proteins from diverse taxa. The results point to an increase in activity of the Bifidobacterium shunt metabolic pathway in the microbiome of mice fed high fiber diets. In those subjected to a low fiber diet, we identified a shift from the degradation of dietary fibers to that of gut mucins, in particular by the recently isolated taxon "Musculibacterium intestinale", which experienced dramatic growth in response to fiber deprivation. When combined with metabolomics and shotgun metagenomics analyses, our findings provide a functional investigation of dietary fiber metabolism in the gut microbiome and demonstrates the power of a combined ABPP-multiomics approach for characterizing the response of the gut microbiome to perturbations.}, } @article {pmid35857470, year = {2022}, author = {Wada, N and Hsu, MT and Tandon, K and Hsiao, SS and Chen, HJ and Chen, YH and Chiang, PW and Yu, SP and Lu, CY and Chiou, YJ and Tu, YC and Tian, X and Chen, BC and Lee, DC and Yamashiro, H and Bourne, DG and Tang, SL}, title = {High-resolution spatial and genomic characterization of coral-associated microbial aggregates in the coral Stylophora pistillata.}, journal = {Science advances}, volume = {8}, number = {27}, pages = {eabo2431}, pmid = {35857470}, issn = {2375-2548}, abstract = {Bacteria commonly form aggregates in a range of coral species [termed coral-associated microbial aggregates (CAMAs)], although these structures remain poorly characterized despite extensive efforts studying the coral microbiome. Here, we comprehensively characterize CAMAs associated with Stylophora pistillata and quantify their cell abundance. Our analysis reveals that multiple Endozoicomonas phylotypes coexist inside a single CAMA. Nanoscale secondary ion mass spectrometry imaging revealed that the Endozoicomonas cells were enriched with phosphorus, with the elemental compositions of CAMAs different from coral tissues and endosymbiotic Symbiodiniaceae, highlighting a role in sequestering and cycling phosphate between coral holobiont partners. Consensus metagenome-assembled genomes of the two dominant Endozoicomonas phylotypes confirmed their metabolic potential for polyphosphate accumulation along with genomic signatures including type VI secretion systems allowing host association. Our findings provide unprecedented insights into Endozoicomonas-dominated CAMAs and the first direct physiological and genomic linked evidence of their biological role in the coral holobiont.}, } @article {pmid35857094, year = {2022}, author = {Rau, J and Werner, D and Beer, M and Höper, D and Kampen, H}, title = {The microbial RNA metagenome of Aedes albopictus (Diptera: Culicidae) from Germany.}, journal = {Parasitology research}, volume = {121}, number = {9}, pages = {2587-2599}, pmid = {35857094}, issn = {1432-1955}, mesh = {*Aedes ; Animals ; Female ; Humans ; Introduced Species ; Male ; Metagenome ; Mosquito Vectors ; RNA ; *Zika Virus ; *Zika Virus Infection ; }, abstract = {Aedes albopictus is a highly invasive mosquito species that has become widespread across the globe. In addition, it is an efficient vector of numerous pathogens of medical and veterinary importance, including dengue, chikungunya and Zika viruses. Among others, the vector potential of mosquitoes is influenced by their microbiome. However, this influence is very dynamic and can vary between individuals and life stages. To obtain a rough overview on the microbiome of Ae. albopictus populations in Germany, pooled female and pooled male individuals from seven German locations were investigated by total RNA sequencing. The mosquito specimens had been collected as larvae in the field and processed immediately after adult emergence, i.e. without females having fed on blood. RNA fragments with high degrees of identity to a large number of viruses and microorganisms were identified, including, for example, Wolbachia pipientis and Acinetobacter baumannii, with differences between male and female mosquitoes. Knowledge about the natural occurrence of microorganisms in mosquitoes may be translated into new approaches to vector control, for example W. pipientis can be exploited to manipulate mosquito reproduction and vector competence. The study results show how diverse the microbiome of Ae. albopictus can be, and the more so needs to be adequately analysed and interpreted.}, } @article {pmid35852333, year = {2022}, author = {Mackelprang, R and Vaishampayan, P and Fisher, K}, title = {Adaptation to Environmental Extremes Structures Functional Traits in Biological Soil Crust and Hypolithic Microbial Communities.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0141921}, pmid = {35852333}, issn = {2379-5077}, mesh = {Soil/chemistry ; Desert Climate ; *Cyanobacteria ; *Microbiota ; Metagenome ; *Bryophyta/physiology ; }, abstract = {Biological soil crusts (biocrusts) are widespread in drylands and deserts. At the microhabitat scale, they also host hypolithic communities that live under semitranslucent stones. Both environmental niches experience exposure to extreme conditions such as high UV radiation, desiccation, temperature fluctuations, and resource limitation. However, hypolithic communities are somewhat protected from extremes relative to biocrust communities. Conditions are otherwise similar, so comparing them can answer outstanding questions regarding adaptations to environmental extremes. Using metagenomic sequencing, we assessed the functional potential of dryland soil communities and identified the functional underpinnings of ecological niche differentiation in biocrusts versus hypoliths. We also determined the effect of the anchoring photoautotroph (moss or cyanobacteria). Genes and pathways differing in abundance between biocrusts and hypoliths indicate that biocrust communities adapt to the higher levels of UV radiation, desiccation, and temperature extremes through an increased ability to repair damaged DNA, sense and respond to environmental stimuli, and interact with other community members and the environment. Intracellular competition appears to be crucial to both communities, with biocrust communities using the Type VI Secretion System (T6SS) and hypoliths favoring a diversity of antibiotics. The dominant primary producer had a reduced effect on community functional potential compared with niche, but an abundance of genes related to monosaccharide, amino acid, and osmoprotectant uptake in moss-dominated communities indicates reliance on resources provided to heterotrophs by mosses. Our findings indicate that functional traits in dryland communities are driven by adaptations to extremes and we identify strategies that likely enable survival in dryland ecosystems. IMPORTANCE Biocrusts serve as a keystone element of desert and dryland ecosystems, stabilizing soils, retaining moisture, and serving as a carbon and nitrogen source in oligotrophic environments. Biocrusts cover approximately 12% of the Earth's terrestrial surface but are threatened by climate change and anthropogenic disturbance. Given their keystone role in ecosystem functioning, loss will have wide-spread consequences. Biocrust microbial constituents must withstand polyextreme environmental conditions including high UV exposure, desiccation, oligotrophic conditions, and temperature fluctuations over short time scales. By comparing biocrust communities with co-occurring hypolithic communities (which inhabit the ventral sides of semitranslucent stones and are buffered from environmental extremes), we identified traits that are likely key adaptations to extreme conditions. These include DNA damage repair, environmental sensing and response, and intracellular competition. Comparison of the two niches, which differ primarily in exposure levels to extreme conditions, makes this system ideal for understanding how functional traits are structured by the environment.}, } @article {pmid35852145, year = {2022}, author = {Bolliri, C and Fontana, A and Cereda, E and Barichella, M and Cilia, R and Ferri, V and Caronni, S and Calandrella, D and Morelli, L and Pezzoli, G}, title = {Gut Microbiota in Monozygotic Twins Discordant for Parkinson's Disease.}, journal = {Annals of neurology}, volume = {92}, number = {4}, pages = {631-636}, doi = {10.1002/ana.26454}, pmid = {35852145}, issn = {1531-8249}, mesh = {Bile Acids and Salts ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; *Parkinson Disease/genetics/pathology ; Twins, Monozygotic ; }, abstract = {Differences in gut microbiota between Parkinson's disease patients and controls seem to depend on multiple-frequently unmeasured-confounders. Monozygotic twins offer a unique model for controlling several factors responsible for interpersonal variation in gut microbiota. Fecal samples from 20 monozygotic twin pairs (n = 40) discordant for Parkinson's disease were studied (metagenomic shotgun analysis). Paired data analysis detected minimal differences in bacterial taxa abundance at species level (Bacteroides pectinophilus [p = 0.037], Bifidobacterium pseudocatenulatum [p = 0.050], and Bifidobacterium catenulatum [p = 0.025]) and in predicted metabolic pathways (primary bile acid biosynthesis [p = 0.037]). Additional studies are warranted to understand the role of gut microbiota in the pathogenesis of Parkinson's disease. ANN NEUROL 2022;92:631-636.}, } @article {pmid35851765, year = {2022}, author = {Wang, Y and Zhang, Y and Lane, NE and Wu, J and Yang, T and Li, J and He, H and Wei, J and Zeng, C and Lei, G}, title = {Population-based metagenomics analysis reveals altered gut microbiome in sarcopenia: data from the Xiangya Sarcopenia Study.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {13}, number = {5}, pages = {2340-2351}, pmid = {35851765}, issn = {2190-6009}, support = {2019RS2010//Science and Technology Program of Hunan Province/ ; 2021Q14//Youth Science Foundation of Xiangya Hospital/ ; 2020LNJJ03//Project Program of National Clinical Research Center for Geriatric Disorders/ ; U21A20352//National Natural Science Foundation of China/ ; 82072502//National Natural Science Foundation of China/ ; 81902265//National Natural Science Foundation of China/ ; 81930071//National Natural Science Foundation of China/ ; }, mesh = {Bacteroides ; Clostridiaceae ; Clostridiales ; Desulfovibrio ; Female ; Furaldehyde ; *Gastrointestinal Microbiome/genetics ; Humans ; Middle Aged ; Phenylalanine ; RNA, Ribosomal, 16S/genetics ; *Sarcopenia/diagnosis/epidemiology ; Staurosporine ; Tryptophan ; Tyrosine ; alpha-Linolenic Acid ; }, abstract = {BACKGROUND: Several studies have examined gut microbiota and sarcopenia using 16S ribosomal RNA amplicon sequencing; however, this technique may not be able to identify altered specific species and functional capacities of the microbes. We performed shotgun metagenomic sequencing to compare the gut microbiome composition and function between individuals with and without sarcopenia.

METHODS: Participants were from a community-based observational study conducted among the residents of rural areas in China. Appendicular skeletal muscle mass was assessed using direct segmental multi-frequency bioelectrical impedance and grip strength using a Jamar Hydraulic Hand dynamometer. Physical performance was evaluated using the Short Physical Performance Battery, 5-time chair stand test and gait speed with the 6 m walk test. Sarcopenia and its severity were diagnosed according to the Asian Working Group for Sarcopenia 2019 algorithm. The gut microbiome was profiled by shotgun metagenomic sequencing to determine the microbial composition and function. A gut microbiota-based model for classification of sarcopenia was constructed using the random forest model, and its performance was assessed using the area under receiver-operating characteristic curve (AUC).

RESULTS: The study sample included 1417 participants (women: 58.9%; mean age: 63.3 years; sarcopenia prevalence: 10.0%). β-diversity indicated by Bray-Curtis distance (genetic level: P = 0.004; taxonomic level of species: P = 0.020), but not α-diversity indicated by Shannon index (genetic level: P = 0.962; taxonomic level of species: P = 0.922), was significantly associated with prevalent sarcopenia. After adjusting for potential confounders, participants with sarcopenia had higher relative abundance of Desulfovibrio piger (P = 0.003, Q = 0.090), Clostridium symbiosum (P < 0.001, Q = 0.035), Hungatella effluvii (P = 0.003, Q = 0.090), Bacteroides fluxus (P = 0.002, Q = 0.089), Absiella innocuum (P = 0.002, Q = 0.072), Coprobacter secundus (P = 0.002, Q = 0.085) and Clostridium citroniae (P = 0.001, Q = 0.060) than those without sarcopenia. The relative abundance of six species (Desulfovibrio piger, Clostridium symbiosum, Hungatella effluvii, Bacteroides fluxus, Absiella innocuum, and Clostridium citroniae) was also positively associated with sarcopenia severity. A differential species-based model was constructed to separate participants with sarcopenia from controls. The value of the AUC was 0.852, suggesting that model has a decent discriminative performance. Desulfovibrio piger ranked the highest in this model. Functional annotation analysis revealed that the phenylalanine, tyrosine, and tryptophan biosynthesis were depleted (P = 0.006, Q = 0.071), while alpha-Linolenic acid metabolism (P = 0.008, Q = 0.094), furfural degradation (P = 0.001, Q = 0.029) and staurosporine biosynthesis (P = 0.006, Q = 0.072) were enriched in participants with sarcopenia. Desulfovibrio piger was significantly associated with staurosporine biosynthesis (P < 0.001).

CONCLUSIONS: This large population-based observational study provided empirical evidence that alterations in the gut microbiome composition and function were observed among individuals with sarcopenia.}, } @article {pmid35850395, year = {2022}, author = {Szakács, S and Koók, L and Nemestóthy, N and Bélafi-Bakó, K and Bakonyi, P}, title = {Studying microbial fuel cells equipped with heterogeneous ion exchange membranes: Electrochemical performance and microbial community assessment of anodic and membrane-surface biofilms.}, journal = {Bioresource technology}, volume = {360}, number = {}, pages = {127628}, doi = {10.1016/j.biortech.2022.127628}, pmid = {35850395}, issn = {1873-2976}, mesh = {*Bioelectric Energy Sources/microbiology ; Biofilms ; Electrodes ; Ion Exchange ; Membranes, Artificial ; *Microbiota ; Oxygen ; }, abstract = {In this study, microbial fuel cells deploying heterogeneous ion exchange membranes were assessed. The behavior of the cells as a function of the membrane applied was evaluated in terms of maximal current density, electron recovery efficiency and energy production rate (up to 427.5 mA, 47.7 % and 660 J m[-2]h[-1], respectively) at different substrate (acetate) feedings (2.15 - 8.6 mM). System performance was characterized in the light of oxygen and acetate crossovers. The effect of membranes (in relation to the oxygen mass transfer coefficient, kO) on the microbial diversity of anodic and membrane-surface biofilms was investigated. Based on the relative abundance of bacterial orders, the two populations could be distinguished and membranes with larger kO tended to promote more the air-tolerant microbes in the biofouling layer. This indicates that membrane kO has a direct effect on membrane foulant microbial composition, and thus, on the expected time-stability of the membrane.}, } @article {pmid35846764, year = {2022}, author = {Zhang, D and Zheng, M and Zhang, Y and Feng, G and Peng, C and Li, C and Li, Y and Zhang, H and Li, N and Xiao, P}, title = {Multiple Novel Mosquito-Borne Zoonotic Viruses Revealed in Pangolin Virome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {874003}, pmid = {35846764}, issn = {2235-2988}, mesh = {*Alphavirus/genetics ; Animals ; China ; Chlorocebus aethiops ; *Culicidae ; *Encephalitis Virus, Japanese/genetics ; Humans ; Pangolins ; Phylogeny ; Vero Cells ; Virome ; }, abstract = {Swab samples were collected from 34 pangolins in Guangxi Province, China. Metavirome sequencing and bioinformatics approaches were undertaken to determine the abundant viral sequences in the viromes. The results showed that the viral sequences belong to 24 virus taxonomic families. To verify the results, PCR combined with phylogenetic analysis was conducted. Some viral sequences including Japanese encephalitis virus (JEV), Getah virus (GETV), and chikungunya virus (CHIKV) were detected. On the basis of the metavirome analysis, seven segments belonging to JEV were further identified through PCR amplification. Sequence comparison showed that, among seven sequences, JEV-China/P2020E-1 displayed the highest nucleotide (80.6%), with the JEV isolated in South Korea, 1988, and all of which belonging to genotype III. Seven CHIKV sequences were detected, with the highest homology (80.6%) to the Aedes africanus in Côte d'Ivoire, 1993. Moreover, passage from BHK-21 to Vero cells makes the newly isolated CHIKV-China/P2020-1 more contagious. In addition, the newly verified GETV sequences shared 86.4% identity with the 1955 GETV isolated from Malaysia. Some sudden and recurrent viruses have also been observed from the virome of pangolin in Guangxi Province, China; hence, dissemination tests will be implemented in the future.}, } @article {pmid35846388, year = {2022}, author = {Abuzahrah, SS and Baeshen, MN and Alkaladi, A and Bataweel, NM and Alhejen, AM and Abdelkader, H}, title = {Exploring the taxonomic and functional diversity of marine benthic micro-Eukaryotes along the Red Sea coast of Jeddah city.}, journal = {Saudi journal of biological sciences}, volume = {29}, number = {8}, pages = {103342}, pmid = {35846388}, issn = {1319-562X}, abstract = {BACKGROUNDS: Diverse marine habitats along Jeddah's Red Sea coast support rich biodiversity. Few studies have been done on its diverse communities, especially its microbial counterparts. Metagenomic analysis of marine benthic micro-eukaryotic communities was performed for the first time on the Red Sea coast of Jeddah. This research looks into their community structure and metabolic potential.

METHODS: Next-generation sequencing was used to examine the micro-eukaryotic communities of seven sedimentary soil samples from four Jeddah coast locations. After isolating DNA from seven benthic sedimentary soil samples, the 18S rDNA V4 regions were amplified and sequenced on the Illumina MiSeq. It was also verified using an Agilent Technologies 2100 Bioanalyzer with a DNA 1000 chip (Agilent Technologies, Fisher Scientific). A standard curve of fluorescence readings generated by qPCR quantification using the Illumina library was achieved using the GS FLX library. Metagenomic data analysis was used to evaluate the microbial communities' biochemical and enzymatic allocations in studied samples.

RESULTS: Blast analysis showed that the top ten phyla were Annelida, Eukaryota, Diatomea, Porifera, Phragmoplastophyta, Arthropoda, Dinoflagellata, Xenacoelomorpha Nematoda, and uncultured. Annelida was also found in the highest percentage (93%), in the sample M followed by Porifera (64%), the most abundant in the control sample then Eukaryotes (61%), Phragmatoplastophyta (55%), Arthropoda, and Diatomea (the least common) (32%). community diversity analysis: using Shannon and inverse Simpson indices showed sediment composition to be effective. Also, PICRUST2 indicated that the most abundant pathways were pyruvate fermentation to isobutanol, pyrimidine deoxyribonucleotide phosphorylation, adenosine ribonucleotide de novo biosynthesis, guanosine ribonucleotide de novo biosynthesis, NAD salvage pathway I, the super pathway of glyoxylate bypass and aerobic respiration I (cytochrome c).

CONCLUSION: Results showed that high throughput metagenomics could reveal species diversity and estimate gene profiles. Environmental factors appear to be more important than geographic variation in determining the structure of these microbial communities. This study provides the first report of marine benthic micro-eukaryotic communities found on the Red Sea coast of Jeddah and will serve as a good platform for future research.}, } @article {pmid35841748, year = {2022}, author = {Walker, ME and Simpson, JB and Redinbo, MR}, title = {A structural metagenomics pipeline for examining the gut microbiome.}, journal = {Current opinion in structural biology}, volume = {75}, number = {}, pages = {102416}, pmid = {35841748}, issn = {1879-033X}, support = {P30 CA016086/CA/NCI NIH HHS/United States ; R01 GM135218/GM/NIGMS NIH HHS/United States ; R01 GM137286/GM/NIGMS NIH HHS/United States ; T32 GM008570/GM/NIGMS NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Metagenome ; *Metagenomics ; Proteomics ; }, abstract = {Metagenomic sequencing data provide a rich resource from which to expand our understanding of differential protein functions involved in human health. Here, we outline a pipeline that combines microbial whole genome sequencing with protein structure data to yield a structural metagenomics-informed atlas of microbial enzyme families of interest. Visualizing metagenomics data through a structural lens facilitates downstream studies including targeted inhibition and probe-based proteomics to define at the molecular level how different enzyme orthologs impact in vivo function. Application of this pipeline to gut microbial enzymes like glucuronidases, TMA lyases, and bile salt hydrolases is expected to pinpoint their involvement in health and disease and may aid in the development of therapeutics that target specific enzymes within the microbiome.}, } @article {pmid35841645, year = {2022}, author = {Chen, YC and Yu, YH}, title = {Bacillus licheniformis-fermented products and enramycin differentially modulate microbiota and antibiotic resistome in the cecal digesta of broilers.}, journal = {Poultry science}, volume = {101}, number = {9}, pages = {102010}, pmid = {35841645}, issn = {1525-3171}, mesh = {Aminocoumarins ; Animal Feed/analysis ; Animals ; Anti-Bacterial Agents/pharmacology ; *Bacillus licheniformis ; Bacteria ; Cecum/microbiology ; Chickens ; Diet/veterinary ; Dietary Supplements/analysis ; Lincosamides ; Male ; *Microbiota ; Peptides ; }, abstract = {Since antibiotic resistance is a global health issues, the use of antibiotics in animal feed for growth promotion has been restricted in many countries. Bacillus licheniformis probiotic is a potential alternative to antibiotics for increasing poultry performance. Through metagenomic sequencing, this study investigated the effects of B. licheniformis-fermented products (BLFPs) and enramycin on the microbial community composition and antibiotic resistance gene (ARG) distribution in the cecal digesta of broilers at the age of 35 d. In total, 144 one-day-old male broiler chicks (Ross 308) were randomly assigned to 4 dietary treatments as follows: basal diet (control [C] group), basal diet plus 10 mg/kg enramycin (E group), basal diet plus 1 g/kg BLFPs (L group), and basal diet plus 3 g/kg BLFPs (H group), with 6 replicate cages per treatment group and 6 birds per cage. The results indicated that the cecal alpha diversity (richness and evenness) of bacterial species was higher in the H group than in the C group. Principal coordinate analysis of microbiota and the ARG composition indicated clear differences among the cecal samples of the groups. In the cecal digesta, the abundance of active bacteria associated with probiotic properties, such as Lactobacillus crispatus and Akkermansia muciniphila, was higher in the H group than in the other groups. Enramycin treatment promoted the expression of peptide (bcrA), glycopeptide (vanRI), and lincosamide (lsaE) resistance genes but inhibited the expression of aminocoumarin (parY) and pleuromutilin (TaeA) resistance genes. BLFP (1 and 3 g/kg) treatment suppressed the expression of aminoglycoside (ANT(6)-Ib), streptogramin (vatB), and peptide (ugd) resistance genes but enhanced the expression of macrolide (efrA) and aminocoumarin (novA) resistance genes. The abundance of peptide resistance genes in Bacteroides spp. was lower in the H group than in the C group. The abundance of lincosamide resistance genes in Lactobacillus spp. was higher in the E group than in the other groups. These results demonstrated that differential changes in the structure of 3 g/kg BLFPs and enramycin-induced cecal microbial communities accompany changes in the abundance of bacterial hosts carrying specific ARGs in the cecal microbiota of broilers.}, } @article {pmid35841078, year = {2022}, author = {Li, P and Liu, J and Saleem, M and Li, G and Luan, L and Wu, M and Li, Z}, title = {Reduced chemodiversity suppresses rhizosphere microbiome functioning in the mono-cropped agroecosystems.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {108}, pmid = {35841078}, issn = {2049-2618}, mesh = {Carbon ; DNA ; *Microbiota/genetics ; Plant Roots/microbiology ; Plants ; Rhizosphere ; Soil ; Soil Microbiology ; *Streptomyces ; }, abstract = {BACKGROUND: Rhizodeposits regulate rhizosphere interactions, processes, nutrient and energy flow, and plant-microbe communication and thus play a vital role in maintaining soil and plant health. However, it remains unclear whether and how alteration in belowground carbon allocation and chemodiversity of rhizodeposits influences microbiome functioning in the rhizosphere ecosystems. To address this research gap, we investigated the relationship of rhizosphere carbon allocation and chemodiversity with microbiome biodiversity and functioning during peanut (Arachis hypogaea) continuous mono-cropping. After continuously labeling plants with [13]CO2, we studied the chemodiversity and composition of rhizodeposits, along with the composition and diversity of active rhizosphere microbiome using metabolomic, amplicon, and shotgun metagenomic sequencing approaches based on DNA stable-isotope probing (DNA-SIP).

RESULTS: Our results indicated that enrichment and depletion of rhizodeposits and active microbial taxa varied across plant growth stages and cropping durations. Specifically, a gradual decrease in the rhizosphere carbon allocation, chemodiversity, biodiversity and abundance of plant-beneficial taxa (such as Gemmatimonas, Streptomyces, Ramlibacter, and Lysobacter), and functional gene pathways (such as quorum sensing and biosynthesis of antibiotics) was observed with years of mono-cropping. We detected significant and strong correlations between rhizodeposits and rhizosphere microbiome biodiversity and functioning, though these were regulated by different ecological processes. For instance, rhizodeposits and active bacterial communities were mainly governed by deterministic and stochastic processes, respectively. Overall, the reduction in carbon deposition and chemodiversity during peanut continuous mono-cropping tended to suppress microbial biodiversity and its functions in the rhizosphere ecosystem.

CONCLUSIONS: Our results, for the first time, provide the evidence underlying the mechanism of rhizosphere microbiome malfunctioning in mono-cropped systems. Our study opens new avenues to deeply disentangle the complex plant-microbe interactions from the perspective of rhizodeposits chemodiversity and composition and will serve to guide future microbiome research for improving the functioning and services of soil ecosystems. Video abstract.}, } @article {pmid35840779, year = {2022}, author = {Conteville, LC and Vicente, ACP}, title = {A plasmid network from the gut microbiome of semi-isolated human groups reveals unique and shared metabolic and virulence traits.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {12102}, pmid = {35840779}, issn = {2045-2322}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics ; Plasmids/genetics ; Virulence/genetics ; }, abstract = {The plasmids in gut microbiomes have the potential to contribute to the microbiome community, as well as human health and physiology. Nevertheless, this niche remains poorly explored. In general, most microbiome studies focus on urban-industrialized groups, but here, we studied semi-isolated groups from South America and Africa, which would represent a link between ancestral and modern human groups. Based on open metagenomic data, we characterized the set of plasmids, including their genes and functions, from the gut microbiome of the Hadza, Matses, Tunapuco, and Yanomami, semi-isolated groups with a hunter, gather or subsistence lifestyle. Unique plasmid clusters and gene functions for each human group were identified. Moreover, a dozen plasmid clusters circulating in other niches worldwide are shared by these distinct groups. In addition, novel and unique plasmids harboring resistance (encompassing six antibiotic classes and multiple metals) and virulence (as type VI secretion systems) genes were identified. Functional analysis revealed pathways commonly associated with urban-industrialized groups, such as lipopolysaccharide biosynthesis that was characterized in the Hadza gut plasmids. These results demonstrate the richness of plasmids in semi-isolated human groups' gut microbiome, which represents an important source of information with biotechnological/pharmaceutical potential, but also on the spread of resistance/virulence genes to semi-isolated groups.}, } @article {pmid35840731, year = {2022}, author = {Cárdenas, A and Raina, JB and Pogoreutz, C and Rädecker, N and Bougoure, J and Guagliardo, P and Pernice, M and Voolstra, CR}, title = {Greater functional diversity and redundancy of coral endolithic microbiomes align with lower coral bleaching susceptibility.}, journal = {The ISME journal}, volume = {16}, number = {10}, pages = {2406-2420}, pmid = {35840731}, issn = {1751-7370}, support = {OSR-2017-CRG6-3400-02//King Abdullah University of Science and Technology (KAUST)/ ; }, mesh = {Animals ; *Anthozoa ; Coral Bleaching ; Coral Reefs ; Metagenomics ; *Microbiota ; Symbiosis ; }, abstract = {The skeleton of reef-building coral harbors diverse microbial communities that could compensate for metabolic deficiencies caused by the loss of algal endosymbionts, i.e., coral bleaching. However, it is unknown to what extent endolith taxonomic diversity and functional potential might contribute to thermal resilience. Here we exposed Goniastrea edwardsi and Porites lutea, two common reef-building corals from the central Red Sea to a 17-day long heat stress. Using hyperspectral imaging, marker gene/metagenomic sequencing, and NanoSIMS, we characterized their endolithic microbiomes together with [15]N and [13]C assimilation of two skeletal compartments: the endolithic band directly below the coral tissue and the deep skeleton. The bleaching-resistant G. edwardsi was associated with endolithic microbiomes of greater functional diversity and redundancy that exhibited lower N and C assimilation than endoliths in the bleaching-sensitive P. lutea. We propose that the lower endolithic primary productivity in G. edwardsi can be attributed to the dominance of chemolithotrophs. Lower primary production within the skeleton may prevent unbalanced nutrient fluxes to coral tissues under heat stress, thereby preserving nutrient-limiting conditions characteristic of a stable coral-algal symbiosis. Our findings link coral endolithic microbiome structure and function to bleaching susceptibility, providing new avenues for understanding and eventually mitigating reef loss.}, } @article {pmid35840409, year = {2022}, author = {Morandi, S and Cremonesi, P and Arioli, S and Stocco, G and Silvetti, T and Biscarini, F and Castiglioni, B and Greco, Ç and D'Ascanio, V and Mora, D and Brasca, M}, title = {Effect of using mycotoxin-detoxifying agents in dairy cattle feed on natural whey starter biodiversity.}, journal = {Journal of dairy science}, volume = {105}, number = {8}, pages = {6513-6526}, doi = {10.3168/jds.2022-21793}, pmid = {35840409}, issn = {1525-3198}, mesh = {Animal Feed/analysis ; Animals ; Biodiversity ; Cattle ; *Cheese/analysis ; DNA, Bacterial/analysis ; Food Microbiology ; *Lactobacillus helveticus ; *Mycotoxins/analysis ; Whey/chemistry ; Whey Proteins/analysis ; }, abstract = {Natural whey cultures (NWC) are undefined multiple-strain bacterial starter communities that can be affected by even small changes along the entire dairy chain. We applied a multidisciplinary approach to investigate how the addition of 2 mycotoxin-detoxifying agents [sodium smectite and lignocellulose-based material (B1); leonardite and betaine (B2)] to cow diets modified the microbiota of the NWC in manufacture of a Grana-like cheese. Microbiological and flow cytometry analyses showed that the content and viability of lactic acid bacteria (LAB) and the total whey microbiota were not affected by the detoxifying agents, and Streptococcus thermophilus, Lactobacillus helveticus, and Limosilactobacillus fermentum were the dominant taxa. Random amplified polymorphic DNA-PCR fingerprinting and metagenomic analysis highlighted differences in the bacterial community of the NWC and in the relative abundance of Bacteroidetes that increased when B1 and B2 were included in the diet. Two of 6 St. thermophilus biotypes were detected only in control samples; conversely, none of the Lb. helveticus biotypes found in control samples were isolated from B1 and B2. In vitro tests showed that the 2 binders did not significantly affect the development of St. thermophilus, but they stimulated the growth of Lb. helveticus strains recovered only from B1 and B2 NWC. The addition of binders in cow feed can affect the LAB biotypes present in NWC.}, } @article {pmid35839908, year = {2022}, author = {Tao, J and Chen, Q and Chen, S and Lu, P and Chen, Y and Jin, J and Li, J and Xu, Y and He, W and Long, T and Deng, X and Yin, H and Li, Z and Fan, J and Cao, P}, title = {Metagenomic insight into the microbial degradation of organic compounds in fermented plant leaves.}, journal = {Environmental research}, volume = {214}, number = {Pt 1}, pages = {113902}, doi = {10.1016/j.envres.2022.113902}, pmid = {35839908}, issn = {1096-0953}, mesh = {Cellulose ; Lignin ; *Metagenome ; *Metagenomics ; Microbial Consortia ; Plant Leaves ; }, abstract = {Microbial degradation of organic compounds is an environmentally benign and energy efficient part in product processing. Fermentation of plant leaves involves enzymatic actions of many microorganisms. However, microbes and enzymes discovered from natural degradation communities were still limited by cultural methods. In this study, we used a metagenomics sequence-guided strategy to identify the microbes and enzymes involved in compound degradation and explore the potential synergy among community members in fermented tobacco leaves. The results showed that contents of protein, starch, pectin, lignin, and cellulose varied in fermented leaves from different growing sites. The different compound contents were closely related to taxonomic composition and functional profiles of foliar microbial communities. Microbial communities showed significant correlations with protein, lignin, and cellulose. Vital species for degradations of protein (Bacillus cereus and Terribacillus aidingensis), lignin (Klebsiella pneumoniae and Pantoea ananatis) and cellulose (Pseudomonas putida and Sphingomonas sp. Leaf20) were identified and relating hydrolytic enzymes were annotated. Further, twenty-two metagenome-assembled genomes (MAGs) were assembled from metagenomes and six potential cellulolytic genomes were used to reconstruct the cellulose-degrading process, revealing the potential metabolic cooperation related to cellulose degradation. Our work should deepen the understanding of microbial roles in plant fermentation and provide a new viewpoint for applying microbial consortia to convert plant organic components to small molecules.}, } @article {pmid35838255, year = {2022}, author = {Arias, MB and Hartle-Mougiou, K and Taboada, S and Vogler, AP and Riesgo, A and Elfekih, S}, title = {Unveiling biogeographical patterns in the worldwide distributed Ceratitis capitata (medfly) using population genomics and microbiome composition.}, journal = {Molecular ecology}, volume = {31}, number = {18}, pages = {4866-4883}, doi = {10.1111/mec.16616}, pmid = {35838255}, issn = {1365-294X}, mesh = {Animals ; *Ceratitis capitata/genetics/microbiology ; Metagenomics ; *Microbiota/genetics ; Microsatellite Repeats ; South Africa ; }, abstract = {Invasive species are among the most important, growing threats to food security and agricultural systems. The Mediterranean medfly, Ceratitis capitata, is one of the most damaging representatives of a group of rapidly expanding species in the family Tephritidae, due to their wide host range and high invasiveness potential. Here, we used restriction site-associated DNA sequencing (RADseq) to investigate the population genomic structure and phylogeographical history of medflies collected from six sampling sites, including Africa (South Africa), the Mediterranean (Spain, Greece), Latin America (Guatemala, Brazil) and Australia. A total of 1907 single nucleotide polymorphisms (SNPs) were used to identify two genetic clusters separating native and introduced ranges, consistent with previous findings. In the introduced range, all individuals were assigned to one genetic cluster except for those in Brazil, which showed introgression of an additional genetic cluster that also appeared in South Africa, and which could not be previously identified using microsatellite markers. Moreover, we assessed the microbial composition variations in medfly populations from selected sampling sites using amplicon sequencing of the 16S ribosomal RNA (V4 region). Microbiome composition and structure were highly similar across geographical regions and host plants, and only the Brazilian specimens showed increased diversity levels and a unique composition of its microbiome compared to other sampling sites. The unique SNP patterns and microbiome features in the Brazilian specimens could point to a direct migration route from Africa with subsequent adaptation of the microbiota to the specific conditions present in Brazil. These findings significantly improve our understanding of the evolutionary history of the global medfly invasions and their adaptation to newly colonized environments.}, } @article {pmid35837874, year = {2022}, author = {Wilcox, TM and Jensen, MR}, title = {Drawing a line in the sand: Environmental DNA population genomics.}, journal = {Molecular ecology resources}, volume = {22}, number = {7}, pages = {2455-2457}, doi = {10.1111/1755-0998.13686}, pmid = {35837874}, issn = {1755-0998}, mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/methods ; *DNA, Environmental/genetics ; Ecology ; Ecosystem ; Environmental Monitoring/methods ; Metagenomics/methods ; *Turtles ; }, abstract = {Environmental DNA (eDNA) sampling uses genetic material in the environment to infer species presence sight-unseen. The method has rapidly become a powerful tool for monitoring biodiversity. However, biological diversity, as per the Convention on Biological Diversity definition of "diversity within species, between species and of ecosystems" is more inclusive than most eDNA studies cover: The vast majority focus only on between-species and ecosystem-level biodiversity. However, a tantalizing prospect, as illustrated by Farrell et al. (2022) in this issue of Molecular Ecology Resources, is that we might also be able to unlock information about individual and population-level diversity via population genomic analysis of these environmental samples. Farrell et al. (2022) found that targeted samples of beach sand contained genetic material not just informative about sea turtle presence, but also indicated the presence of pathogens and genome-wide mitochondrial and nuclear sequences that could accurately infer individual turtle source population. Moving from proof-of-concept to robust, population genomic inference will require a growth of genomic resources for nonmodel organisms and careful study design considerations, some of which have already been pioneered by related fields.}, } @article {pmid35837785, year = {2022}, author = {Medina, V and Rosso, BE and Soria, M and Gutkind, GO and Pagano, EA and Zavala, JA}, title = {Feeding on soybean crops changed gut bacteria diversity of the southern green stinkbug (Nezara viridula) and reduced negative effects of some associated bacteria.}, journal = {Pest management science}, volume = {78}, number = {11}, pages = {4608-4617}, doi = {10.1002/ps.7080}, pmid = {35837785}, issn = {1526-4998}, support = {//Fondo para la Investigación Científica y Tecnológica/ ; //Ministerio de Ciencia, Tecnología e Innovación Productiva/ ; }, mesh = {Animals ; Crops, Agricultural ; Cysteine ; *Cysteine Proteases ; Enterobacteriaceae ; *Gastrointestinal Microbiome ; *Heteroptera ; Lipids ; Nymph ; Glycine max ; }, abstract = {BACKGROUND: The southern green stinkbug (Nezara viridula) is a mayor pest of soybean. However, the mechanism underlying stinkbug resistance to soybean defenses is yet ignored. Although gut bacteria could play an essential role in tolerating plant defenses, most studies testing questions related to insect-plant-bacteria interactions have been performed in laboratory condition. Here we performed experiments in laboratory and field conditions with N. viridula and its gut bacteria, studying gut lipid peroxidaxion levels and cysteine activity in infected and unifected nymphs, testing the hypothesis that feeding on field-grown soybean decreases bacterial abundance in stinkbugs.

RESULTS: Gut bacterial abundance and infection ratio were higher in N. viridula adults reared in laboratory than in those collected from soybean crops, suggesting that stinkbugs in field conditions may modulate gut bacterial colonization. Manipulating gut microbiota by infecting stinkbugs with Yokenella sp. showed that these bacteria abundance decreased in field conditions, and negatively affected stinkbugs performance and were more aggressive in laboratory rearing than in field conditions. Infected nymphs that fed on soybean pods had lower mortality, higher mass and shorter development period than those reared in the laboratory, and suggested that field conditions helped nymphs to recover from Yokenella sp. infection, despite of increased lipid peroxidation and decreased cysteine proteases activity in nymphs' guts.

CONCLUSIONS: Our results demonstrated that feeding on field-grown soybean reduced bacterial abundance and infection in guts of N. viridula and highlighted the importance to test functional activities or pathogenicity of microbes under realistic field conditions prior to establish conclusions on three trophic interactions. © 2022 Society of Chemical Industry.}, } @article {pmid35836413, year = {2022}, author = {Milke, F and Sanchez-Garcia, S and Dlugosch, L and McNichol, J and Fuhrman, J and Simon, M and Wagner-Döbler, I}, title = {Composition and Biogeography of Planktonic Pro- and Eukaryotic Communities in the Atlantic Ocean: Primer Choice Matters.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {895875}, pmid = {35836413}, issn = {1664-302X}, abstract = {Basin-scale biogeographic observations of marine pelagic pro- and eukaryotic communities are necessary to understand forces driving community composition and for providing a baseline to monitor global change. Deep sequencing of rRNA genes provides community composition at high resolution; yet, it is unclear how the choice of primers affects biogeographic patterns. Here, we re-amplified 16S rRNA genes from DNA sampled during R/V Polarstern Cruise ANT28-5 over a latitudinal transect across the Atlantic Ocean from 52°S to 47°N using universal V4-V5 primers and compared the results with those obtained previously with V5-V6 bacteria-specific primers. For validation of our results, we inferred community composition based on 16S rRNA genes of metagenomes from the same stations and single amplified genomes (SAGs) from the Global Ocean Reference Genome (GORG) database. We found that the universal V4-V5 primers retrieved SAR11 clades with similar relative proportions as those found in the GORG database while the V5-V6 primers recovered strongly diverging clade abundances. We confirmed an inverse bell-shaped distance-decay relationship and a latitudinal diversity gradient that did not decline linearly with absolute latitude in the Atlantic Ocean. Patterns were modified by sampling depth, sequencing depth, choice of primers, and abundance filtering. Especially richness patterns were not robust to methodological change. This study offers a detailed picture of the Atlantic Ocean microbiome using a universal set of PCR primers that allow for the conjunction of biogeographical patterns among organisms from different domains of life.}, } @article {pmid35834536, year = {2022}, author = {Cheng, JE and Su, P and Zhang, ZH and Zheng, LM and Wang, ZY and Hamid, MR and Dai, JP and Du, XH and Chen, LJ and Zhai, ZY and Kong, XT and Liu, Y and Zhang, DY}, title = {Metagenomic analysis of the dynamical conversion of photosynthetic bacterial communities in different crop fields over different growth periods.}, journal = {PloS one}, volume = {17}, number = {7}, pages = {e0262517}, pmid = {35834536}, issn = {1932-6203}, mesh = {Bacteria ; Crops, Agricultural ; High-Throughput Nucleotide Sequencing ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Soil Microbiology ; }, abstract = {Photosynthetic bacteria are beneficial to plants, but knowledge of photosynthetic bacterial community dynamics in field crops during different growth stages is scarce. The factors controlling the changes in the photosynthetic bacterial community during plant growth require further investigation. In this study, 35 microbial community samples were collected from the seedling, flowering, and mature stages of tomato, cucumber, and soybean plants. 35 microbial community samples were assessed using Illumina sequencing of the photosynthetic reaction center subunit M (pufM) gene. The results revealed significant alpha diversity and community structure differences among the three crops at the different growth stages. Proteobacteria was the dominant bacterial phylum, and Methylobacterium, Roseateles, and Thiorhodococcus were the dominant genera at all growth stages. PCoA revealed clear differences in the structure of the microbial populations isolated from leaf samples collected from different crops at different growth stages. In addition, a dissimilarity test revealed significant differences in the photosynthetic bacterial community among crops and growth stages (P<0.05). The photosynthetic bacterial communities changed during crop growth. OTUs assigned to Methylobacterium were present in varying abundances among different sample types, which we speculated was related to the function of different Methylobacterium species in promoting plant growth development and enhancing plant photosynthetic efficiency. In conclusion, the dynamics observed in this study provide new research ideas for the detailed assessments of the relationship between photosynthetic bacteria and different growth stages of plants.}, } @article {pmid35834499, year = {2022}, author = {McKeen, S and Roy, NC and Mullaney, JA and Eriksen, H and Lovell, A and Kussman, M and Young, W and Fraser, K and Wall, CR and McNabb, WC}, title = {Adaptation of the infant gut microbiome during the complementary feeding transition.}, journal = {PloS one}, volume = {17}, number = {7}, pages = {e0270213}, pmid = {35834499}, issn = {1932-6203}, mesh = {Feces ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant Nutritional Physiological Phenomena ; Metagenome ; Pilot Projects ; }, abstract = {The infant gut microbiome progresses in composition and function during the introduction of solid foods throughout the first year of life. The purpose of this study was to characterize changes in healthy infant gut microbiome composition, metagenomic functional capacity, and associated metabolites over the course of the complementary feeding period. Fecal samples were obtained at three 'snapshot' timepoints from infants participating in the 'Nourish to Flourish' pilot study: before the introduction of solid foods at approximately 4 months of age, after introducing solid foods at 9 months of age, and after continued diet diversification at 12 months of age. KEGG and taxonomy assignments were correlated with LC-MS metabolomic profiles to identify patterns of co-abundance. The composition of the microbiome diversified during the first year of life, while the functional capacity present in the gut microbiome remained stable. The introduction of solid foods between 4 and 9 months of age corresponded to a larger magnitude of change in relative abundance of sequences assigned to KEGG pathways and taxonomic assignments, as well as to stronger correlations with metabolites, compared to the magnitude of changes and number of correlations seen during continued diet diversification between 9 and 12 months of age. Changes in aqueous fecal metabolites were more strongly correlated with KEGG pathway assignments, while changes in lipid metabolites associated with taxonomic assignments, particularly between 9 and 12 months of age. This study establishes trends in microbiome composition and functional capacity occurring during the complementary feeding period and identifies potential metabolite targets for future investigations.}, } @article {pmid35834269, year = {2022}, author = {Qiao, H and Tan, XR and Li, H and Li, JY and Chen, XZ and Li, YQ and Li, WF and Tang, LL and Zhou, GQ and Zhang, Y and Liang, YL and He, QM and Zhao, Y and Huang, SY and Gong, S and Li, Q and Ye, ML and Chen, KL and Sun, Y and Ma, J and Liu, N}, title = {Association of Intratumoral Microbiota With Prognosis in Patients With Nasopharyngeal Carcinoma From 2 Hospitals in China.}, journal = {JAMA oncology}, volume = {8}, number = {9}, pages = {1301-1309}, pmid = {35834269}, issn = {2374-2445}, mesh = {Adolescent ; Adult ; Aged ; Biomarkers ; China/epidemiology ; Cohort Studies ; Female ; Hospitals ; Humans ; Male ; *Microbiota ; Middle Aged ; Nasopharyngeal Carcinoma/pathology ; *Nasopharyngeal Neoplasms/pathology ; Neoplasm Recurrence, Local/pathology ; Neoplasm Staging ; Nucleotides ; Prognosis ; RNA, Ribosomal, 16S ; Retrospective Studies ; Young Adult ; }, abstract = {IMPORTANCE: Microbiota-tumor interactions have qualified microbiota as a promising prognostic biomarker in various types of cancers. Although the nasopharynx acts as a crucial niche of the upper respiratory tract microbiome, whether the intratumoral microbiota exists and its clinical significance in nasopharyngeal carcinoma (NPC) remain uncertain.

OBJECTIVE: To evaluate the clinical significance of intratumoral microbiota for individual prognostication in patients with NPC.

This retrospective cohort study included NPC biopsy samples from 2 hospitals: Sun Yat-sen University Cancer Center (Guangzhou, China) and Zhejiang Cancer Hospital (Hangzhou, China) between January 2004 and November 2016, with follow-up through November 2020. A total of 802 patients were included according to the following criteria: with histologically proven NPC, without distant metastasis at initial diagnosis, had not received antitumor treatment before biopsy sampling, aged between 18 and 70 years, with complete medical records and regular follow-up, without a history of cancer, and successfully extracted enough DNA for experiments.

MAIN OUTCOMES AND MEASURES: The primary end point was disease-free survival, and the secondary end points included distant metastasis-free survival and overall survival. To assess the existence and load of intratumoral microbiota in 96 patients with NPC with or without tumor relapse, 16S rRNA sequencing and quantitative polymerase chain reaction were used. The associations between intratumoral bacterial load and clinical outcome were evaluated in 241 fresh-frozen NPC samples (training cohort) and validated in paraffin-embedded NPC samples of internal (n = 233) and external (n = 232) validation cohorts. Metagenomic and transcriptome analyses were performed to ascertain the origin and underlying mechanism of intratumoral bacteria.

RESULTS: A total of 802 patients with NPC (mean [SD] age, 46.2 [10.6] years; 594 [74.1%] male) were enrolled. Microbiota presented within NPC tumor tissues, among which Corynebacterium and Staphylococcus predominated. Patients with a high bacterial load in the training cohort had inferior rates of disease-free survival (hazard ratio [HR], 2.90; 95% CI, 1.72-4.90; P < .001), distant metastasis-free survival (HR, 3.18; 95% CI, 1.58-6.39; P < .001), and overall survival (HR, 3.41; 95% CI, 1.90-6.11, P < .001) than those with a low bacterial load, a finding that was validated by the internal and external validation cohorts. Single-nucleotide variant analysis revealed that the nasopharyngeal microbiota was the main origin of NPC intratumoral bacteria. Transcriptome and digital pathology analyses demonstrated that a higher intratumoral bacterial load was negatively associated with T-lymphocyte infiltration.

CONCLUSIONS AND RELEVANCE: Intratumoral bacterial load was a robust prognostic tool for patients with NPC in this cohort study, indicating potential guidance for treatment decisions in patients at different levels of risk of malignant progression.}, } @article {pmid35834135, year = {2022}, author = {Pereira, LB and Gambarini, VMO and de Menezes, AB and Ottoboni, LMM and Vicentini, R}, title = {Influence of Sugarcane Variety on Rhizosphere Microbiota Under Irrigated and Water-Limiting Conditions.}, journal = {Current microbiology}, volume = {79}, number = {9}, pages = {246}, pmid = {35834135}, issn = {1432-0991}, support = {2015/00408-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2016/08994-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2014/05929-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 140547/2014-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Bacteria ; Edible Grain ; *Microbiota/genetics ; Plant Roots/microbiology ; Rhizosphere ; *Saccharum/microbiology ; Soil Microbiology ; Water/metabolism ; }, abstract = {Drought is one of the main problems linked to climate change that is faced by agriculture, affecting various globally important crops, including sugarcane. Environmentally sustainable strategies have been sought to mitigate the effects of climate change on crops. Among them, the use of beneficial microorganisms offers a promising approach. However, it is still necessary to understand the mechanisms that regulate plant-microorganism interactions, in normal situations and under stress. In this work, the rhizosphere metagenomes of two sugarcane varieties, one resistant and the other susceptible to drought, were compared under normal conditions and under water-limiting conditions. The results showed that for the drought-resistant sugarcane variety, bacteria belonging to the order Sphingomonadales and the family Xanthomonadaceae presented increased activities in terms of mobility, colonization, and cell growth. In contrast, the rhizosphere associated with the drought-sensitive variety exhibited increases of bacteria belonging to the family Polyangiaceae, and the genus Streptomyces, with modifications in DNA metabolism and ribosome binding proteins. The results pointed to variation in the rhizosphere microbiota that was modulated by the host plant genotype, revealing potential bacterial candidates that could be recruited to assist plants during water-limiting conditions.}, } @article {pmid35832425, year = {2022}, author = {Zeng, Q and Zhao, M and Wang, F and Li, Y and Li, H and Zheng, J and Chen, X and Zhao, X and Ji, L and Gao, X and Liu, C and Wang, Y and Cheng, S and Xu, J and Pan, B and Sun, J and Li, Y and Li, D and He, Y and Zheng, L}, title = {Integrating Choline and Specific Intestinal Microbiota to Classify Type 2 Diabetes in Adults: A Machine Learning Based Metagenomics Study.}, journal = {Frontiers in endocrinology}, volume = {13}, number = {}, pages = {906310}, pmid = {35832425}, issn = {1664-2392}, mesh = {Adult ; Betaine/metabolism ; Choline/metabolism ; Cross-Sectional Studies ; *Diabetes Mellitus, Type 2 ; *Gastrointestinal Microbiome/genetics ; Glucose ; Humans ; Machine Learning ; Metagenomics ; Methylamines/metabolism ; *Prediabetic State ; }, abstract = {Emerging evidence is examining the precise role of intestinal microbiota in the pathogenesis of type 2 diabetes. The aim of this study was to investigate the association of intestinal microbiota and microbiota-generated metabolites with glucose metabolism systematically in a large cross-sectional study in China. 1160 subjects were divided into three groups based on their glucose level: normal glucose group (n=504), prediabetes group (n=394), and diabetes group (n=262). Plasma concentrations of TMAO, choline, betaine, and carnitine were measured. Intestinal microbiota was measured in a subgroup of 161 controls, 144 prediabetes and 56 diabetes by using metagenomics sequencing. We identified that plasma choline [Per SD of log-transformed change: odds ratio 1.36 (95 confidence interval 1.16, 1.58)] was positively, while betaine [0.77 (0.66, 0.89)] was negatively associated with diabetes, independently of TMAO. Individuals with diabetes could be accurately distinguished from controls by integrating data on choline, and certain microbiota species, as well as traditional risk factors (AUC=0.971). KOs associated with the carbohydrate metabolism pathway were enhanced in individuals with high choline level. The functional shift in the carbohydrate metabolism pathway in high choline group was driven by species Ruminococcus lactaris, Coprococcus catus and Prevotella copri. We demonstrated the potential ability for classifying diabetic population by choline and specific species, and provided a novel insight of choline metabolism linking the microbiota to impaired glucose metabolism and diabetes.}, } @article {pmid35822382, year = {2022}, author = {Lin, Y and Li, J and Li, Y}, title = {[Metagenome-wide association of gut microbiome features in children with moderate-severe house dust mite allergic rhinitis].}, journal = {Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology head and neck surgery}, volume = {36}, number = {7}, pages = {533-539}, pmid = {35822382}, issn = {2096-7993}, mesh = {Animals ; Child ; Child, Preschool ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; *Microbiota ; Pyroglyphidae ; *Rhinitis, Allergic ; *Rhinitis, Allergic, Perennial ; }, abstract = {Objective:To draw a distinct gut microbiota pattern of children with moderate-severe dust mite-induced allergic rhinitis（DAR） and healthy children. Methods:3-10 years old moderate-severe DAR children（68 cases） and healthy children（38 cases） were involved in this study. General information was collected through questionnaires, and fecal samples were collected for metagenomic sequencing. MetaPhlAn3 was used to generate the microbiota composition abundance in detail, and Alpha and Beta diversity changes were calculated. The difference in species abundance at different taxonomic levels were compared. Differences in functional pathways were compared by LEfSe analysis. Results:The diversity of gut microbiota in children with moderate-severe DAR didn't change significantly compared with healthy children. A total of 37 microbial communities or species with significant abundance difference were found, mainly included Lachnoclostridium, Prevotella, Blautia wexlerae, Prevotella copri, Eubacterium eligens, Eubacterium sp CAG 180, etc. However, the metabolism functions of gut microbiota in children with moderate-severe DAR changed compared with healthy children. Various of fatty acids anabolism enhanced in DAR children. Conclusion:Compared with healthy children, there was no significant difference in gut microbial diversity in moderate-severe DAR children. The abundance of a series of specific microbe species had a marked alteration in DAR, accompanied with changes in certain microbial functional pathways.}, } @article {pmid35819612, year = {2022}, author = {Tremblay, ÉD and Bilodeau, GJ}, title = {Biomonitoring of Fungal and Oomycete Plant Pathogens by Using Metabarcoding.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2536}, number = {}, pages = {309-346}, pmid = {35819612}, issn = {1940-6029}, mesh = {*Biological Monitoring ; DNA Primers/genetics ; Ecosystem ; *Oomycetes/genetics ; Plants ; }, abstract = {Fungal and oomycete plant pathogens are responsible for the devastation of various ecosystems such as forest and crop species worldwide. In an effort to protect such natural resources for food, lumber, etc., early detection of non-indigenous phytopathogenic fungi in new areas is a key approach in managing threats at their source of introduction. A workflow was developed using high-throughput sequencing (HTS), more specifically metabarcoding, a method for rapid and higher throughput species screening near high-risk areas, and over larger geographical spaces. Biomonitoring of fungal and oomycete entities of plant pathogens (e.g., airborne spores) regained from environmental samples and their processing by metabarcoding is thoroughly described here. The amplicon-based approach goes from DNA and sequencing library preparation using custom-designed polymerase chain reaction (PCR) fusion primers that target the internal transcribed spacer 1 (ITS1) from fungi and oomycetes and extends to multiplex HTS with the Ion Torrent platform. In addition, a brief and simplified overview of the bioinformatics analysis pipeline and other available tools required to process amplicon sequences is also included. The raw data obtained and processed enable users to select a bioinformatics pipeline in order to directly perform biodiversity, presence/absence, geographical distribution, and abundance analyses through the tools suggested, which allows for accelerated identification of phytopathogens of interest.}, } @article {pmid35819600, year = {2022}, author = {Vettraino, AM and Luchi, N}, title = {A Rapid Method for Extracting High-Quality DNA from Soils.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2536}, number = {}, pages = {103-107}, pmid = {35819600}, issn = {1940-6029}, mesh = {DNA/genetics ; DNA, Bacterial/genetics ; Metagenomics/methods ; *Soil/chemistry ; *Soil Microbiology ; }, abstract = {Metagenomics offers the possibility to study the microbial community of soils at large scale, allowing the characterization also of unculturable microorganisms. Availability of high-quality DNA is a prerequisite of this approach. However, since soils have highly heterogeneous physicochemical properties, several parameters need to be considered for the development of the best molecular practices. A method for isolation of high-molecular-weight and good-quality metagenomic DNA from different soil samples is described here. The protocol combines physical and chemical strategies to ensure efficient cell lysis and precipitation of humic impurities-free DNA suitable for downstream processing for metagenomics study.}, } @article {pmid35819265, year = {2022}, author = {Rubiola, S and Macori, G and Civera, T and Fanning, S and Mitchell, M and Chiesa, F}, title = {Comparison Between Full-Length 16S rRNA Metabarcoding and Whole Metagenome Sequencing Suggests the Use of Either Is Suitable for Large-Scale Microbiome Studies.}, journal = {Foodborne pathogens and disease}, volume = {19}, number = {7}, pages = {495-504}, doi = {10.1089/fpd.2022.0027}, pmid = {35819265}, issn = {1556-7125}, mesh = {High-Throughput Nucleotide Sequencing/methods ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {Since the number of studies of the microbial communities related to food and food-associated matrices almost completely reliant on next-generation sequencing techniques is rising, evaluations of these high-throughput methods are critical. Currently, the two most used sequencing methods to profile the microbiota of complex samples, including food and food-related matrices, are the 16S ribosomal RNA (rRNA) metabarcoding and the whole metagenome sequencing (WMS), both of which are powerful tools for the monitoring of foodborne pathogens and the investigation of the microbiome. Herein, the microbial profiles of 20 bulk tank milk filters from different dairy farms were investigated using both the full-length 16S (FL-16S) rRNA metabarcoding, a third-generation sequencing method whose application in food and food-related matrices is yet in its infancy, and the WMS, to evaluate the correlation and the reliability of these two methods to explore the microbiome of food-related matrices. Metabarcoding and metagenomic data were generated on a MinION platform (Oxford Nanopore Technologies) and on a Illumina NovaSeq 6000 platform, respectively. Our findings support the greater resolution of WMS in terms of both increased detection of bacterial taxa and enhanced detection of diversity; in contrast, FL-16S rRNA metabarcoding has proven to be a promising, less expensive, and more practical tool to profile most abundant taxa. The significant correlation of the two technologies both in terms of taxa diversity and richness, together with the similar profiles defined for both highly abundant taxa and core microbiomes, including Acinetobacter, Bacillus, and Escherichia genera, highlights the possible application of both methods for different purposes. This study allowed the first comparison of FL-16S rRNA sequencing and WMS to investigate the microbial composition of a food-related matrix, pointing out the advantageous use of FL-16S rRNA to identify dominant microorganisms and the superior power of WMS for the taxonomic detection of low abundant microorganisms and to perform functional analysis of the microbial communities.}, } @article {pmid35818005, year = {2022}, author = {Garfias-Gallegos, D and Zirión-Martínez, C and Bustos-Díaz, ED and Arellano-Fernández, TV and Lovaco-Flores, JA and Espinosa-Jaime, A and Avelar-Rivas, JA and Sélem-Mójica, N}, title = {Metagenomics Bioinformatic Pipeline.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2512}, number = {}, pages = {153-179}, pmid = {35818005}, issn = {1940-6029}, mesh = {Computational Biology/methods ; Metagenome ; *Metagenomics/methods ; *Microbiota ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {Microbial communities' taxonomic and functional diversity has been broadly studied since sequencing technologies enabled faster and cheaper data obtainment. Nevertheless, the programming skills needed and the amount of software available may be overwhelming to someone trying to analyze these data. Here, we present a comprehensive and straightforward pipeline that takes shotgun metagenomics data through the needed steps to obtain valuable results. The raw data goes through a quality control process, metagenomic assembly, binning (the obtention of single genomes from a metagenome), taxonomic assignment, and taxonomic diversity analysis and visualization.}, } @article {pmid35817360, year = {2022}, author = {Rodriguez-Diaz, C and Taminiau, B and García-García, A and Cueto, A and Robles-Díaz, M and Ortega-Alonso, A and Martín-Reyes, F and Daube, G and Sanabria-Cabrera, J and Jimenez-Perez, M and Isabel Lucena, M and Andrade, RJ and García-Fuentes, E and García-Cortes, M}, title = {Microbiota diversity in nonalcoholic fatty liver disease and in drug-induced liver injury.}, journal = {Pharmacological research}, volume = {182}, number = {}, pages = {106348}, doi = {10.1016/j.phrs.2022.106348}, pmid = {35817360}, issn = {1096-1186}, mesh = {Bacteria ; *Chemical and Drug Induced Liver Injury/metabolism ; *Gastrointestinal Microbiome ; Humans ; Liver/metabolism ; Liver Cirrhosis/metabolism ; Metagenome ; *Non-alcoholic Fatty Liver Disease/metabolism ; }, abstract = {The gut microbiota could play a significant role in the progression of nonalcoholic fatty liver disease (NAFLD); however, its relevance in drug-induced liver injury (DILI) remains unexplored. Since the two hepatic disorders may share damage pathways, we analysed the metagenomic profile of the gut microbiota in NAFLD, with or without significant liver fibrosis, and in DILI, and we identified the main associated bacterial metabolic pathways. In the NAFLD group, we found a decrease in Alistipes, Barnesiella, Eisenbergiella, Flavonifractor, Fusicatenibacter, Gemminger, Intestinimonas, Oscillibacter, Parasutterella, Saccharoferementans and Subdoligranulum abundances compared with those in both the DILI and control groups. Additionally, we detected an increase in Enterobacter, Klebsiella, Sarcina and Turicibacter abundances in NAFLD, with significant liver fibrosis, compared with those in NAFLD with no/mild liver fibrosis. The DILI group exhibited a lower microbial bacterial richness than the control group, and lower abundances of Acetobacteroides, Blautia, Caloramator, Coprococcus, Flavobacterium, Lachnospira, Natronincola, Oscillospira, Pseudobutyrivibrio, Shuttleworthia, Themicanus and Turicibacter compared with those in the NAFLD and control groups. We found seven bacterial metabolic pathways that were impaired only in DILI, most of which were associated with metabolic biosynthesis. In the NAFLD group, most of the differences in the bacterial metabolic pathways found in relation to those in the DILI and control groups were related to fatty acid and lipid biosynthesis. In conclusion, we identified a distinct bacterial profile with specific bacterial metabolic pathways for each type of liver disorder studied. These differences can provide further insight into the physiopathology and development of NAFLD and DILI.}, } @article {pmid35812740, year = {2022}, author = {Jeffery, NW and Lehnert, SJ and Kess, T and Layton, KKS and Wringe, BF and Stanley, RRE}, title = {Application of Omics Tools in Designing and Monitoring Marine Protected Areas For a Sustainable Blue Economy.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {886494}, pmid = {35812740}, issn = {1664-8021}, abstract = {A key component of the global blue economy strategy is the sustainable extraction of marine resources and conservation of marine environments through networks of marine protected areas (MPAs). Connectivity and representativity are essential factors that underlie successful implementation of MPA networks, which can safeguard biological diversity and ecosystem function, and ultimately support the blue economy strategy by balancing ocean use with conservation. New "big data" omics approaches, including genomics and transcriptomics, are becoming essential tools for the development and maintenance of MPA networks. Current molecular omics techniques, including population-scale genome sequencing, have direct applications for assessing population connectivity and for evaluating how genetic variation is represented within and among MPAs. Effective baseline characterization and long-term, scalable, and comprehensive monitoring are essential for successful MPA management, and omics approaches hold great promise to characterize the full range of marine life, spanning the microbiome to megafauna across a range of environmental conditions (shallow sea to the deep ocean). Omics tools, such as eDNA metabarcoding can provide a cost-effective basis for biodiversity monitoring in large and remote conservation areas. Here we provide an overview of current omics applications for conservation planning and monitoring, with a focus on metabarcoding, metagenomics, and population genomics. Emerging approaches, including whole-genome sequencing, characterization of genomic architecture, epigenomics, and genomic vulnerability to climate change are also reviewed. We demonstrate that the operationalization of omics tools can enhance the design, monitoring, and management of MPAs and thus will play an important role in a modern and comprehensive blue economy strategy.}, } @article {pmid35810633, year = {2022}, author = {Wang, S and Wang, J and Liu, Z and Zhang, B}, title = {Unraveling diverse survival strategies of microorganisms to vanadium stress in aquatic environments.}, journal = {Water research}, volume = {221}, number = {}, pages = {118813}, doi = {10.1016/j.watres.2022.118813}, pmid = {35810633}, issn = {1879-2448}, mesh = {Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Metagenomics ; *Microbiota ; *Vanadium/analysis ; }, abstract = {Worldwide vanadium contamination is posing serious risks to ecosystems. Although abilities of microbial communities to cope with vanadium stress using specific survival strategies have been reported, little is known regarding their relative importance and the underlying detoxification/tolerance mechanisms. Herein, we investigated the potential survival strategies of microbial communities and associated pathways in aquatic environments based on geochemistry and molecular biology. High vanadium content was observed for both water (12.6 ± 1.15 mg/L) and sediment (1.18 × 10[3] ± 10.4 mg/kg) in the investigated polluted stream. Co-occurrence network investigation implied that microbial communities showed cooperative interactions to adapt to the vanadium-polluted condition. Vanadium was also characterized as one of the vital factors shaping the community structure via redundancy analysis and structural equation models. Based on the metagenomic technology, three survival strategies including denitrification pathway, electron transfer, and metal resistance in innate microbes under the vanadium stress were revealed, with comprehensively summarized vanadium detoxification/tolerance genes. Remarkable role of electron transfer genes and the prevalent existence of resistance genes during detoxifying vanadium were highlighted. Overall, these findings provide novel insights into survival strategies under the vanadium contamination in aquatic environments, which can be of great significance for the identification, isolation, and application of vanadium reducing bacteria in vanadium bioremediation.}, } @article {pmid35810602, year = {2022}, author = {Ma, Q and Gao, F and Zhou, L and Fan, Y and Zhao, B and Xi, W and Wang, C and Zhu, F and Ma, X and Wang, W and Wang, Y}, title = {Characterizing serum amino acids in schizophrenic patients: Correlations with gut microbes.}, journal = {Journal of psychiatric research}, volume = {153}, number = {}, pages = {125-133}, doi = {10.1016/j.jpsychires.2022.07.006}, pmid = {35810602}, issn = {1879-1379}, mesh = {Amino Acids ; Arginine ; *Gastrointestinal Microbiome/physiology ; Glutamine ; Humans ; Leucine ; Methionine ; *Schizophrenia ; }, abstract = {Amino acid abnormalities have been suggested to be a key pathophysiological mechanism in schizophrenia (SZ). Recently, gut microbes were found to be critically involved in mental and metabolic diseases. However, the relationship between serum amino acid levels and gut microbes in SZ is rarely studied. Here, we analyzed serum amino acid levels in 76 untreated SZ patients and 79 healthy controls (HC). Serum levels of 10 amino acids were significantly altered in patients with SZ. We further classified the cut-off values for serum arginine, leucine, glutamine, and methionine levels to distinguish SZ patients from controls. These classifiers were shown to be effective in another validation cohort (49 SZ and 48 HC). The correlation between serum amino acids and clinical symptoms and cognitive functions was also analyzed. Arginine, leucine, glutamine, and methionine levels were significantly correlated with clinical symptoms and cognitive impairments in SZ patients. By metagenome shotgun sequencing of fecal samples, we found that patients with SZ with a low level of serum amino acids have higher richness and evenness of the gut microbiota. At the genus level, the abundances of Mitsuokella and Oscillibacter are significantly abnormal. At the mOTU level, 15 mOTUs in the low-level SZ group were significantly different from the HC group. In addition, Mitsuokella multacida was correlated with glutamine and methionine, respectively. Our research revealed that alterations in serum amino acid levels are critically related to changes in gut microbiota composition in SZ patients. These findings may shed light on new strategies for the diagnosis and treatment of SZ.}, } @article {pmid35810517, year = {2022}, author = {Zou, Z and Li, S and Wu, J and Guo, S and Zhang, Y and Huang, M and Valsami-Jones, E and Lynch, I and Liu, X and Wang, J and Zou, J}, title = {Effects of nanopolystyrene addition on nitrogen fertilizer fate, gaseous loss of N from the soil, and soil microbial community composition.}, journal = {Journal of hazardous materials}, volume = {438}, number = {}, pages = {129509}, doi = {10.1016/j.jhazmat.2022.129509}, pmid = {35810517}, issn = {1873-3336}, mesh = {Ammonia ; *Brassica ; Fertilizers/analysis ; Gases ; *Microbiota ; Nitrogen/analysis ; Nitrous Oxide ; Plastics ; Soil ; Soil Microbiology ; }, abstract = {Nanoplastics and microplastics are the degradation products of plastics waste and have become a dominant pollutant in the environment. However, little is known about the ecological impacts of nanoplastic particles in the agroecosystem. We conducted a mesocosm experiment to examine nanopolystyrene effects on fertilizer nitrogen (N) fate, N gaseous losses and soil microbial communities using Chinese cabbage (Brassica Campestris ssp.) as the model plant. The two-factorial experiment was designed as the addition of [15]N-labeled urea exposed without and with ~50 nm nanopolystyrene (0, 0.05%, and 0.1%). Nanopolystyrene addition had a detectable effect on soil mineral N content. The [15]N uptake of plants was reduced in aboveground biomass but enhanced in roots with increasing nanopolystyrene concentration. Nanopolystyrene addition decreased soil nitrous oxide and ammonia emissions by 27% and 37%, respectively. Nanopolystyrene addition consistently reduced the abundance of ammonia oxidizer genes but showed contrasting effects on denitrifying genes. Metagenomic sequencing data revealed no significant effects of nanopolystyrene on the N-cycle pathway, while it significantly altered the composition of bacterial and fungal communities. This study provided the first insights into the nanopolystyrene induced linkage of root growth with more root N uptake and less gaseous N losses and the associated changes in the microbial community.}, } @article {pmid35810346, year = {2022}, author = {Hrapovic, N and Richard, T and Messaraa, C and Li, X and Abbaspour, A and Fabre, S and Mavon, A and Andersson, B and Khmaladze, I}, title = {Clinical and metagenomic profiling of hormonal acne-prone skin in different populations.}, journal = {Journal of cosmetic dermatology}, volume = {21}, number = {11}, pages = {6233-6242}, doi = {10.1111/jocd.15225}, pmid = {35810346}, issn = {1473-2165}, support = {//Oriflame Cosmetics AB/ ; }, mesh = {Female ; Humans ; Pilot Projects ; Skin/metabolism ; *Acne Vulgaris/metabolism ; Bacteria/genetics ; *Microbiota ; }, abstract = {INTRODUCTION: Acne is one of the most common skin concerns of unknown etiology, often connected to the menstrual cycle in women, and possibly to the microbial profile and function.

OBJECTIVE: We aimed to investigate how hormonal fluctuation affects hormonal acne-prone skin in different populations in relation to skin clinical parameters and microbial profiles.

METHODS: We evaluated skin features by using biophysical and topographical tools. For microbial profiling, we sequenced facial skin microbiota and associated the findings with the skin clinical parameters during the different phases of the menstrual cycle.

RESULTS: We identified differences between and within hormonal phases in women of Chinese and Caucasian origin. Changes were discovered in transepidermal water loss (TEWL), sebum level, hydration level, and pore volume. The most abundant identifiable genera in both ethnicities were Cutibacterium, Staphylococcus, and Streptococcus, without any significant abundant differences within the menstrual cycle. Interestingly, 11 bacterial metabolic pathways were downregulated in Chinese compared to Caucasian skin during the follicular phase. The majority of these pathways were associated with skin redox balance, perhaps indicating a weaker oxidative stress response in Chinese versus Caucasian skin. Novosphingobium taxa were increased in the Chinese skin microbiome, which has been reported to protect skin from pollution-mediated oxidative stress.

CONCLUSION: Thus, this pilot study explored some of the clinical and metagenomic changes in acne-prone skin, and provide guidance to tailor-personalized skin care regimes during the menstrual cycle. Also, the skin redox status in acne-prone skin, provides more opportunity to tailor-personalized skin care regimes.}, } @article {pmid35807903, year = {2022}, author = {Xu, AA and Kennedy, LK and Hoffman, K and White, DL and Kanwal, F and El-Serag, HB and Petrosino, JF and Jiao, L}, title = {Dietary Fatty Acid Intake and the Colonic Gut Microbiota in Humans.}, journal = {Nutrients}, volume = {14}, number = {13}, pages = {}, pmid = {35807903}, issn = {2072-6643}, support = {R01 CA172880/CA/NCI NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; P30 DK56338/NH/NIH HHS/United States ; I01 CX001430/CX/CSRD VA/United States ; CIN13-413/VA/VA/United States ; R01CA172880,/NH/NIH HHS/United States ; P30 CA022453/CA/NCI NIH HHS/United States ; }, mesh = {Adenosine Deaminase ; Animals ; Bacteria/genetics ; Cross-Sectional Studies ; Diet, High-Fat/adverse effects ; Dietary Fats ; Fatty Acids/chemistry ; Fatty Acids, Monounsaturated ; *Gastrointestinal Microbiome ; Humans ; Intercellular Signaling Peptides and Proteins ; RNA, Ribosomal, 16S/genetics ; *Trans Fatty Acids ; }, abstract = {A high-fat diet has been associated with systemic diseases in humans and alterations in gut microbiota in animal studies. However, the influence of dietary fatty acid intake on gut microbiota in humans has not been well studied. In this cross-sectional study, we examined the association between intake of total fatty acids (TFAs), saturated fatty acids (SFAs), trans fatty acids (TrFAs), monounsaturated fatty acids (MUFAs), polyunsaturated fatty acids (PUFAs), n3-FAs, and n6-FAs, and the community composition and structure of the adherent colonic gut microbiota. We obtained 97 colonic biopsies from 34 participants with endoscopically normal colons. Microbial DNA was used to sequence the 16S rRNA V4 region. The DADA2 and SILVA database were used for amplicon sequence variant assignment. Dietary data were collected using the Block food frequency questionnaire. The biodiversity and the relative abundance of the bacterial taxa by higher vs. lower fat intake were compared using the Mann−Whitney test followed by multivariable negative binomial regression model. False discovery rate−adjusted p-values (q value) < 0.05 indicated statistical significance. The beta diversity of gut bacteria differed significantly by intake of all types of fatty acids. The relative abundance of Sutterella was significantly higher with higher intake of TFAs, MUFAs, PUFAs, and n6-FAs. The relative abundance of Tyzzerella and Fusobacterium was significantly higher with higher intake of SFAs. Tyzzerella was also higher with higher intake of TrFA. These observations were confirmed by multivariate analyses. Dietary fat intake was associated with bacterial composition and structure. Sutterella, Fusobacterium, and Tyzzerella were associated with fatty acid intake.}, } @article {pmid35806099, year = {2022}, author = {Sabater, C and Calvete-Torre, I and Ruiz, L and Margolles, A}, title = {Arabinoxylan and Pectin Metabolism in Crohn's Disease Microbiota: An In Silico Study.}, journal = {International journal of molecular sciences}, volume = {23}, number = {13}, pages = {}, pmid = {35806099}, issn = {1422-0067}, support = {AGL2016-78311-R//Ministry of Economy, Industry and Competitiveness/ ; }, mesh = {*Crohn Disease/drug therapy ; Dysbiosis ; Humans ; *Microbiota ; Pectins ; Xylans ; }, abstract = {Inflammatory bowel disease is a chronic disorder including ulcerative colitis and Crohn's disease (CD). Gut dysbiosis is often associated with CD, and metagenomics allows a better understanding of the microbial communities involved. The objective of this study was to reconstruct in silico carbohydrate metabolic capabilities from metagenome-assembled genomes (MAGs) obtained from healthy and CD individuals. This computational method was developed as a mean to aid rationally designed prebiotic interventions to rebalance CD dysbiosis, with a focus on metabolism of emergent prebiotics derived from arabinoxylan and pectin. Up to 1196 and 1577 MAGs were recovered from CD and healthy people, respectively. MAGs of Akkermansia muciniphila, Barnesiella viscericola DSM 18177 and Paraprevotella xylaniphila YIT 11841 showed a wide range of unique and specific enzymes acting on arabinoxylan and pectin. These glycosidases were also found in MAGs recovered from CD patients. Interestingly, these arabinoxylan and pectin degraders are predicted to exhibit metabolic interactions with other gut microbes reduced in CD. Thus, administration of arabinoxylan and pectin may ameliorate dysbiosis in CD by promoting species with key metabolic functions, capable of cross-feeding other beneficial species. These computational methods may be of special interest for the rational design of prebiotic ingredients targeting at CD.}, } @article {pmid35803374, year = {2022}, author = {Xu, M and Huang, XH and Shen, XX and Chen, HQ and Li, C and Jin, GQ and Cao, JS and Xue, ZX}, title = {Metagenomic insights into the spatiotemporal responses of antibiotic resistance genes and microbial communities in aquaculture sediments.}, journal = {Chemosphere}, volume = {307}, number = {Pt 1}, pages = {135596}, doi = {10.1016/j.chemosphere.2022.135596}, pmid = {35803374}, issn = {1879-1298}, mesh = {Animals ; Anti-Bacterial Agents/analysis/pharmacology ; Aquaculture ; China ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; *Metals, Heavy/analysis ; *Microbiota ; }, abstract = {The dissemination of antibiotic resistance genes (ARGs) in aquaculture systems is a potential threat to environmental safety and human health. However, the spatiotemporal distribution pattern of ARGs and key factors associated with their dissemination in aquaculture sediments remain unclear. In this study, ARGs, mobile genetic elements, microbial community composition, heavy metal contents, and nutrient contents of samples collected from a whole culture cycle of fish in a representative aquaculture farm were characterized. The distribution patterns of nine subtypes of ARGs (tetW, tetM, tetA, ermC, ermB, sul1, sul2, floR, and qnrS) showed clear spatiotemporal differences. The absolute abundance of ARGs in aquaculture sediments was higher in winter and in rivers of the aquaculture farm. Proteobacteria was the dominant phylum in all sediment samples. The results of network and redundancy analyses confirmed that the Dechloromonas, Candidatus Accumulibacter, Smithella, Geobacter, and Anaeromyxobacter belonging to Proteobacteria were positively correlated with ARGs, suggesting that these microbial species are potential hosts of corresponding ARGs. Our study highlights that the microbial community is the determining factor for ARG dissemination. Strategies for inhibiting these potential hosts of ARGs should be developed based on controllable factors.}, } @article {pmid35803340, year = {2022}, author = {Ma, S and Qiao, L and Liu, X and Zhang, S and Zhang, L and Qiu, Z and Yu, C}, title = {Microbial community succession in soils under long-term heavy metal stress from community diversity-structure to KEGG function pathways.}, journal = {Environmental research}, volume = {214}, number = {Pt 2}, pages = {113822}, doi = {10.1016/j.envres.2022.113822}, pmid = {35803340}, issn = {1096-0953}, mesh = {Bacteria ; Gold/analysis/metabolism/pharmacology ; *Metals, Heavy/analysis/toxicity ; *Microbiota ; Soil/chemistry ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Currently, understanding the structure and function of the microbial community is the key step in artificially constructing microbial communities to control soil heavy metal pollution. Abundant/rare microbial communities play different roles in different levels of concentrations. However, the correlation between heavy metals and rare/abundant subgroups is poorly understood. In this study, we used a metagenomics approach to comprehensively investigate the evolutionary changes in microbial diversity, structure, and function under different heavy metal concentration stress in soils surrounding gold tailings. The results show that the main pollutants were Pb, As, and Zn. Indigenous microorganisms have different responses to heavy metal concentrations. Bacteria are the main components of indigenous microorganisms, mainly including Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria. With the increase of heavy metal pollution, the relative abundance of Proteobacteria increased, and that of Actinobacteria decreased. Archaea was significantly inhibited by heavy metal stress and was more sensitive to heavy metal concentration. The response of fungi to heavy metal concentration was not obvious. The results of KEGG pathways showed that carbon fixation was inhibited with increasing heavy metal concentrations, while nitrogen metabolism was in contrast. Abundant subcommunity had a greater correlation mainly with metal resistance mechanisms, and rare subcommunity plays a key role for soil nutrient cycling such as N, S cycling in soils contaminated. Overall, this study provides a comprehensive analysis of the effects of heavy metal stress at different concentrations on microorganisms in farmland around gold tailings and reveals the relationship between heavy metals on KEGG pathways.}, } @article {pmid35803007, year = {2022}, author = {Polo, C and Hernández, M and García-Seco, T and Fernández, V and Briones, V and Diez-Guerrier, A and Abad, D and Rodríguez-Lázaro, D and Domínguez, L and Pérez-Sancho, M}, title = {Exploiting 16S rRNA-based metagenomics to reveal neglected microorganisms associated with infertility in breeding bulls in Spanish extensive herds.}, journal = {Research in veterinary science}, volume = {150}, number = {}, pages = {52-57}, doi = {10.1016/j.rvsc.2022.04.019}, pmid = {35803007}, issn = {1532-2661}, mesh = {Animals ; Bacteria/genetics ; Breeding ; Cattle ; *Cattle Diseases/epidemiology/genetics ; *Infertility/genetics/veterinary ; Male ; Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bovine infectious infertility represents a problem due to the high impact on animal production and, in many cases, in public health. A lack of information on the characteristics of the bacterial population of the bovine reproductive system can hamper a comprehensive understanding of reproductive pathologies and the role that the microbiome could play. A metagenomic study based on the V3-V4 hypervariable region of the bacterial 16S rRNA gene was performed in 1029 preputial samples from bulls raised in an extensive regimen in Spain (944 from herds with low fertility rates -case group-, and 85 samples from reproductively healthy herds -control group-). The most representative phyla as well as the most 10 abundant bacterial families and their abundance did not show significant differences in both case and control groups. Similarly, the (alpha and beta) diversity of the bacterial populations was similar in both type of herds: the Shannon and Simpson indices show a high diversity of species, while the Bray-Curtis dissimilarity index did not show relevant differences in the bacterial communities. A deeper analysis of the operational taxonomic units showed the presence of one genera, Mycoplasma spp. significantly associated with fertility problems. Our study highlights the promising potential that the application of sequencing techniques (e.g. 16S rRNA-based metagenomics) possesses in examining bovine infertility, as they are able to reveal different pathogens that could go unnoticed using diagnostic approaches for only the main known pathogens.}, } @article {pmid35802409, year = {2022}, author = {Edwards, A and Soares, A and Debbonaire, A and Edwards Rassner, SM}, title = {Before you go: a packing list for portable DNA sequencing of microbiomes and metagenomes.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {7}, pages = {}, doi = {10.1099/mic.0.001220}, pmid = {35802409}, issn = {1465-2080}, mesh = {High-Throughput Nucleotide Sequencing ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; }, } @article {pmid35802345, year = {2022}, author = {Kim, K and Lee, Y and Won, S}, title = {Relative contributions of the host genome, microbiome, and environment to the metabolic profile.}, journal = {Genes & genomics}, volume = {44}, number = {9}, pages = {1081-1089}, pmid = {35802345}, issn = {2092-9293}, mesh = {Humans ; *Metabolic Syndrome/genetics ; Metabolome ; *Microbiota/genetics ; Polymorphism, Single Nucleotide ; Prospective Studies ; }, abstract = {BACKGROUND: Metabolic syndrome is as a well-known risk factor for cardiovascular disease, which is associated with both genetic and environmental factors. Recently, the microbiome composition has been shown to affect the development of metabolic syndrome. Thus, it is expected that the complex interplay among host genetics, the microbiome, and environmental factors could affect metabolic syndrome.

OBJECTIVE: To evaluate the relative contributions of genetic, microbiome, and environmental factors to metabolic syndrome using statistical approaches.

METHODS: Data from the prospective Korean Association REsource project cohort (N = 8476) were used in this study, including single-nucleotide polymorphisms, phenotypes and lifestyle factors, and the urine-derived microbial composition. The effect of each data source on metabolic phenotypes was evaluated using a heritability estimation approach and a prediction model separately. We further experimented with various types of metagenomic relationship matrices to estimate the phenotypic variance explained by the microbiome.

RESULTS: With the heritability estimation, five of the 11 metabolic phenotypes were significantly associated with metagenome-wide similarity. We found significant heritability for fasting glucose (4.8%), high-density lipoprotein cholesterol (4.9%), waist-hip ratio (7.7%), and waist circumference (5.6%). Microbiome compositions provided more accurate estimations than genetic factors for the same sample size. In the prediction model, the contribution of each source to the prediction accuracy varied for each phenotype.

CONCLUSION: The effects of host genetics, the metagenome, and environmental factors on metabolic syndrome were minimal. Our statistical analysis suffers from a small sample size, and the measurement error is expected to be substantial. Further analysis is necessary to quantify the effects with better accuracy.}, } @article {pmid35801409, year = {2022}, author = {Hertz, FB and Holm, JB and Pallejá, A and Björnsdóttir, MK and Mikkelsen, LS and Brandsborg, E and Frimodt-Møller, N}, title = {Vaginal microbiome following orally administered probiotic.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {130}, number = {10}, pages = {605-611}, pmid = {35801409}, issn = {1600-0463}, mesh = {Female ; Gardnerella vaginalis ; Humans ; *Microbiota ; *Probiotics ; Vagina/microbiology ; *Vaginosis, Bacterial ; }, abstract = {Here, we present a longitudinal shotgun sequencing metagenomics study of 16 healthy, Danish women in the reproductive age. The aim of the study was to investigate whether lactobacilli, orally consumed, had any impact on the vaginal microbiome and its functional potential. The 16 women aged 19-45 years were recruited from Copenhagen, Denmark. One baseline vaginal sample (Day 0) and two study samples (Days 25-30 and Days 55-60, respectively), were sampled. The vaginal samples were analyzed by shotgun metagenomics. We detected 26 species in the vaginal microbiota of the 16 women, of which six belonged to the Lactobacillus genus. We observed three vaginal microbiome clusters mainly dominated by Gardnerella vaginalis, Lactobacillus iners, or Lactobacillus crispatus. The oral probiotic had no detectable effect on either the composition or the functional potential of the vaginal microbiota. Most of the study subjects (11 out of 16 women) exhibited only minor changes in the vaginal microbiome during the treatment with probiotics. Any compositional changes could not be associated to the probiotic treatment. Future studies may benefit from an increased number of participants, and administration of the probiotics during conditions with bacterial imbalance (e.g., during/after antibiotic treatment) or the use of different Lactobacillus spp. known to colonize the vagina.}, } @article {pmid35800388, year = {2022}, author = {Fang, B and Li, Q and Wan, Z and OuYang, Z and Zhang, Q}, title = {Exploring the Association Between Cervical Microbiota and HR-HPV Infection Based on 16S rRNA Gene and Metagenomic Sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {922554}, pmid = {35800388}, issn = {2235-2988}, mesh = {Bacteria/genetics ; Cervix Uteri/microbiology ; Female ; Genes, rRNA ; Humans ; *Microbiota/genetics ; *Papillomavirus Infections ; RNA, Ribosomal, 16S/genetics ; Vagina/microbiology ; }, abstract = {The relationship between the cervico-vaginal microbiome and high-risk human papillomavirus (HR-HPV) is well observed. However, there is a lack of adequate research regarding the cervical microbiota in HR-HPV infection. Most published research results have used 16S rRNA gene sequencing technology; this technology only focuses on marker sequences, resulting in incomplete gene information acquisition. Metagenomic sequencing technology can effectively compensate for the deficiency of 16S rRNA gene sequencing, thus improving the analysis of microbiota function. Cervical swab samples from 20 females with HR-HPV infection and 20 uninfected (Control) women were analyzed through 16S rRNA gene and metagenomic sequencing. Our results indicated that the composition and function of the cervical microbiota of HR-HPV infection differed notably from that of control women. Compared with control women, Firmicutes was decreased during HR-HPV infection, whereas Actinobacteria was increased. At the genus level, Lactobacillus was enriched in control women, while levels of Gardnerella and Bifidobacterium were lower. At the species level, Lactobacillus crispatus, L. jensenii, and L. helveticus were enriched in control women; these were the top three species with biomarker significance between the two groups. Eight pathways and four KEGG orthologies of the cervical microbiota of statistical differences were identified between the HR-HPV infection and control women. Collectively, our study described the cervical microbiota and its potential function during HR-HPV infection. Biomarkers of cervical microbiota and the changed bacterial metabolic pathways and metabolites can help clarify the pathogenic mechanism of HR-HPV infection, making them promising targets for clinical treatment and intervention for HR-HPV infection and cervical carcinoma.}, } @article {pmid35800387, year = {2022}, author = {Hong, RP and Hou, YY and Xu, XJ and Lang, JD and Jin, YF and Zeng, XF and Zhang, X and Tian, G and You, X}, title = {The Difference of Gut Microbiota and Their Correlations With Urinary Organic Acids Between Autistic Children With and Without Atopic Dermatitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {886196}, pmid = {35800387}, issn = {2235-2988}, mesh = {Aconitic Acid/analysis ; Adipates/analysis ; *Autistic Disorder ; Child ; Clostridiales ; *Dermatitis, Atopic/complications/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Autism is a kind of biologically based neurodevelopmental condition, and the coexistence of atopic dermatitis (AD) is not uncommon. Given that the gut microbiota plays an important role in the development of both diseases, we aimed to explore the differences of gut microbiota and their correlations with urinary organic acids between autistic children with and without AD. We enrolled 61 autistic children including 36 with AD and 25 without AD. The gut microbiota was sequenced by metagenomic shotgun sequencing, and the diversity, compositions, and functional pathways were analyzed further. Urinary organic acids were assayed by gas chromatography-mass spectrometry, and univariate/multivariate analyses were applied. Spearman correlation analysis was conducted to explore their relationships. In our study, AD individuals had more prominent gastrointestinal disorders. The alpha diversity of the gut microbiota was lower in the AD group. LEfSe analysis showed a higher abundance of Anaerostipes caccae, Eubacterium hallii, and Bifidobacterium bifidum in AD individuals, with Akkermansia muciniphila, Roseburia intestinalis, Haemophilus parainfluenzae, and Rothia mucilaginosa in controls. Meanwhile, functional profiles showed that the pathway of lipid metabolism had a higher proportion in the AD group, and the pathway of xenobiotics biodegradation was abundant in controls. Among urinary organic acids, adipic acid, 3-hydroxyglutaric acid, tartaric acid, homovanillic acid, 2-hydroxyphenylacetic acid, aconitic acid, and 2-hydroxyhippuric acid were richer in the AD group. However, only adipic acid remained significant in the multivariate analysis (OR = 1.513, 95% CI [1.042, 2.198], P = 0.030). In the correlation analysis, Roseburia intestinalis had a negative correlation with aconitic acid (r = -0.14, P = 0.02), and the latter was positively correlated with adipic acid (r = 0.41, P = 0.006). Besides, the pathway of xenobiotics biodegradation seems to inversely correlate with adipic acid (r = -0.42, P = 0.18). The gut microbiota plays an important role in the development of AD in autistic children, and more well-designed studies are warranted to explore the underlying mechanism.}, } @article {pmid35800027, year = {2022}, author = {Palmer, M and Sutcliffe, I and Venter, SN and Hedlund, BP}, title = {It is time for a new type of type to facilitate naming the microbial world.}, journal = {New microbes and new infections}, volume = {47}, number = {}, pages = {100991}, pmid = {35800027}, issn = {2052-2975}, abstract = {Since January 1, 2001, the only acceptable nomenclatural type for species under the International Code of Nomenclature of Prokaryotes (ICNP) has been pure cultures. Here, we argue that this requirement is discordant with the more inclusive nature of nomenclatural types accepted under other codes of nomenclature and posit that the unique rigidity of the ICNP has failed to serve the broad research community and has stifled progress. This case is based on the axiom that many archaea and bacteria are interdependent in nature and therefore difficult, if not impossible, to grow, preserve, and distribute as pure cultures. As such, a large proportion of Earth's biodiversity cannot be named under the current system, which limits our ability to communicate about microbial diversity within and beyond the microbiology research community. Genome sequence data are now encouraged for valid publication of new taxa in microbial systematics journals, and metagenome-assembled genomes and single cell-amplified genomes are being generated rapidly from every biome on Earth. Thus, genome sequences are available for both cultivated and uncultivated microorganisms and can readily serve as a new category of nomenclatural type, allowing for a unified nomenclature for all archaea and bacteria, whether or not they are available as pure cultures. Ideally this would be under a single code of nomenclature but, as we review here, the newly established SeqCode will operate in parallel with the ICNP as a first step toward this goal.}, } @article {pmid35799498, year = {2022}, author = {Vasileiadis, S and Perruchon, C and Scheer, B and Adrian, L and Steinbach, N and Trevisan, M and Plaza-Bolaños, P and Agüera, A and Chatzinotas, A and Karpouzas, DG}, title = {Nutritional inter-dependencies and a carbazole-dioxygenase are key elements of a bacterial consortium relying on a Sphingomonas for the degradation of the fungicide thiabendazole.}, journal = {Environmental microbiology}, volume = {24}, number = {11}, pages = {5105-5122}, doi = {10.1111/1462-2920.16116}, pmid = {35799498}, issn = {1462-2920}, mesh = {*Sphingomonas/genetics/metabolism ; Thiabendazole/metabolism ; *Fungicides, Industrial/metabolism ; *Dioxygenases/metabolism ; Biodegradation, Environmental ; Bacteria/genetics/metabolism ; Carbazoles/metabolism ; Vitamin B 12/metabolism ; }, abstract = {Thiabendazole (TBZ), is a persistent fungicide/anthelminthic and a serious environmental threat. We previously enriched a TBZ-degrading bacterial consortium and provided first evidence for a Sphingomonas involvement in TBZ transformation. Here, using a multi-omic approach combined with DNA-stable isotope probing (SIP) we verified the key degrading role of Sphingomonas and identify potential microbial interactions governing consortium functioning. SIP and amplicon sequencing analysis of the heavy and light DNA fraction of cultures grown on [13] C-labelled versus [12] C-TBZ showed that 66% of the [13] C-labelled TBZ was assimilated by Sphingomonas. Metagenomic analysis retrieved 18 metagenome-assembled genomes with the dominant belonging to Sphingomonas, Sinobacteriaceae, Bradyrhizobium, Filimonas and Hydrogenophaga. Meta-transcriptomics/-proteomics and non-target mass spectrometry suggested TBZ transformation by Sphingomonas via initial cleavage by a carbazole dioxygenase (car) to thiazole-4-carboxamidine (terminal compound) and catechol or a cleaved benzyl ring derivative, further transformed through an ortho-cleavage (cat) pathway. Microbial co-occurrence and gene expression networks suggested strong interactions between Sphingomonas and a Hydrogenophaga. The latter activated its cobalamin biosynthetic pathway and Sphingomonas its cobalamin salvage pathway to satisfy its B12 auxotrophy. Our findings indicate microbial interactions aligning with the 'black queen hypothesis' where Sphingomonas (detoxifier, B12 recipient) and Hydrogenophaga (B12 producer, enjoying detoxification) act as both helpers and beneficiaries.}, } @article {pmid35799219, year = {2022}, author = {Sinha, A and Li, Y and Mirzaei, MK and Shamash, M and Samadfam, R and King, IL and Maurice, CF}, title = {Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {105}, pmid = {35799219}, issn = {2049-2618}, support = {170921//CIHR/Canada ; }, mesh = {Animals ; Bacteria/genetics ; *Bacteriophages/genetics ; *Colitis/therapy ; *Colitis, Ulcerative/microbiology/therapy ; *Gastrointestinal Microbiome ; Inflammation ; *Inflammatory Bowel Diseases/microbiology ; Mice ; }, abstract = {BACKGROUND: Inflammatory bowel diseases (IBDs) including Crohn's disease (CD) and ulcerative colitis (UC) are characterized by chronic and debilitating gut inflammation. Altered bacterial communities of the intestine are strongly associated with IBD initiation and progression. The gut virome, which is primarily composed of bacterial viruses (bacteriophages, phages), is thought to be an important factor regulating and shaping microbial communities in the gut. While alterations in the gut virome have been observed in IBD patients, the contribution of these viruses to alterations in the bacterial community and heightened inflammatory responses associated with IBD patients remains largely unknown.

RESULTS: Here, we performed in vivo microbial cross-infection experiments to follow the effects of fecal virus-like particles (VLPs) isolated from UC patients and healthy controls on bacterial diversity and severity of experimental colitis in human microbiota-associated (HMA) mice. Shotgun metagenomics confirmed that several phages were transferred to HMA mice, resulting in treatment-specific alterations in the gut virome. VLPs from healthy and UC patients also shifted gut bacterial diversity of these mice, an effect that was amplified during experimental colitis. VLPs isolated from UC patients specifically altered the relative abundance of several bacterial taxa previously implicated in IBD progression. Additionally, UC VLP administration heightened colitis severity in HMA mice, as indicated by shortened colon length and increased pro-inflammatory cytokine production. Importantly, this effect was dependent on intact VLPs.

CONCLUSIONS: Our findings build on recent literature indicating that phages are dynamic regulators of bacterial communities in the gut and implicate the intestinal virome in modulating intestinal inflammation and disease. Video Abstract.}, } @article {pmid35796792, year = {2022}, author = {Westaway, JAF and Huerlimann, R and Kandasamy, Y and Miller, CM and Norton, R and Watson, D and Infante-Vilamil, S and Rudd, D}, title = {Exploring the long-term colonisation and persistence of probiotic-prophylaxis species on the gut microbiome of preterm infants: a pilot study.}, journal = {European journal of pediatrics}, volume = {181}, number = {9}, pages = {3389-3400}, pmid = {35796792}, issn = {1432-1076}, mesh = {Aftercare ; Cross-Sectional Studies ; *Enterocolitis, Necrotizing/prevention & control ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Patient Discharge ; Pilot Projects ; *Probiotics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Preterm infants suffer from a higher incidence of acute diseases such as necrotising enterocolitis and sepsis. This risk can be mitigated through probiotic prophylaxis during admission. This reduction in risk is likely the result of acute modulation of the gut microbiome induced by probiotic species, which has been observed to occur up until discharge. We aimed to determine if this modulation, and the associated probiotic species, persisted beyond discharge. We conducted both a cross-sectional analysis (n = 18), at ~ 18 months of age, and a longitudinal analysis (n = 6), from admission to 18 months of the gut microbiome of preterm infants using both shotgun metagenomics and 16S rRNA profiling respectively. The 16S amplicon sequencing revealed that the microbial composition of the probiotic-supplemented infants changed dramatically over time, stabilising at discharge. However, species from the probiotic Infloran[®], as well as positive modulatory effects previously associated with supplementation, do not appear to persist beyond discharge and once prophylaxis has stopped. Conclusions: Although differences exist between supplemented and non-supplemented groups, the implications of these differences remain unclear. Additionally, despite a lack of long-term colonisation, the presence of probiotics during early neonatal life may still have modulatory effects on the microbiome assembly and immune system training. What is Known: • Evidence suggests modulation of the microbiome occurs during probiotic prophylaxis, which may support key taxa that exert positive immunological benefits. • Some evidence suggests that this modulation can persist post-prophylaxis. What is New: • We present support for long-term modulation in association with probiotic prophylaxis in a cohort of infants from North Queensland Australia. • We also observed limited persistence of the probiotic species post-discharge.}, } @article {pmid35794664, year = {2022}, author = {Xu, Y and Milburn, O and Beiersdorfer, T and Du, L and Akinbi, H and Haslam, DB}, title = {Antibiotic exposure prevents acquisition of beneficial metabolic functions in the preterm infant gut microbiome.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {103}, pmid = {35794664}, issn = {2049-2618}, support = {UL1 TR001425/TR/NCATS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; Child, Preschool ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; *Microbiota ; }, abstract = {BACKGROUND: Aberrations in the preterm microbiome following antibiotic therapy have been reported in previous studies. The objective of this study was to probe potential underlying mechanisms between this observation and susceptibility to adverse prematurity-related outcomes.

RESULTS: Metagenomic shotgun sequencing was performed on 133 stool and 253 skin samples collected at 1 and 3 weeks of age from 68 infants born at <36 weeks postmenstrual age and birth weight <2000 g. After accounting for gestational age and maternal antibiotics, the distribution of organisms in all samples and the corresponding metabolic pathway abundance were compared between infants exposed to postnatal antibiotics and antibiotics-naïve infants. In antibiotic-naïve infants, gestational and postnatal age imparted similar trajectories on maturation of the microbial community and associated metabolic functional capacity, with postnatal age exerting greater contribution. Antibiotic exposure was associated with reversal in maturation trajectory from the first week to the third week of age (p< 0.001). Butyrate-producing genera, including Clostridium and Blautia, were significantly more abundant in antibiotic-naïve neonates at 3 weeks postnatal age. Correspondingly, metabolic pathways required for short-chain fatty acid synthesis were significantly increased in antibiotic-naïve infants, but not in antibiotic-exposed neonates, at 3 weeks after birth.

CONCLUSIONS: Early brief antibiotic exposure markedly disrupts developmental trajectory of the neonatal microbiome and its corresponding functional capacity. Our findings may provide a mechanistic explanation for the known associations between antibiotic use and adverse outcomes in preterm infants. Video Abstract.}, } @article {pmid35794633, year = {2022}, author = {Kanukollu, S and Remus, R and Rücker, AM and Buchen-Tschiskale, C and Hoffmann, M and Kolb, S}, title = {Methanol utilizers of the rhizosphere and phyllosphere of a common grass and forb host species.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {35}, pmid = {35794633}, issn = {2524-6372}, support = {KO 2912/9-1//deutsche forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: Managed grasslands are global sources of atmospheric methanol, which is one of the most abundant volatile organic compounds in the atmosphere and promotes oxidative capacity for tropospheric and stratospheric ozone depletion. The phyllosphere is a favoured habitat of plant-colonizing methanol-utilizing bacteria. These bacteria also occur in the rhizosphere, but their relevance for methanol consumption and ecosystem fluxes is unclear. Methanol utilizers of the plant-associated microbiota are key for the mitigation of methanol emission through consumption. However, information about grassland plant microbiota members, their biodiversity and metabolic traits, and thus key actors in the global methanol budget is largely lacking.

RESULTS: We investigated the methanol utilization and consumption potentials of two common plant species (Festuca arundinacea and Taraxacum officinale) in a temperate grassland. The selected grassland exhibited methanol formation. The detection of [13]C derived from [13]C-methanol in 16S rRNA of the plant microbiota by stable isotope probing (SIP) revealed distinct methanol utilizer communities in the phyllosphere, roots and rhizosphere but not between plant host species. The phyllosphere was colonized by members of Gamma- and Betaproteobacteria. In the rhizosphere, [13]C-labelled Bacteria were affiliated with Deltaproteobacteria, Gemmatimonadates, and Verrucomicrobiae. Less-abundant [13]C-labelled Bacteria were affiliated with well-known methylotrophs of Alpha-, Gamma-, and Betaproteobacteria. Additional metagenome analyses of both plants were consistent with the SIP results and revealed Bacteria with methanol dehydrogenases (e.g., MxaF1 and XoxF1-5) of known but also unusual genera (i.e., Methylomirabilis, Methylooceanibacter, Gemmatimonas, Verminephrobacter). [14]C-methanol tracing of alive plant material revealed divergent potential methanol consumption rates in both plant species but similarly high rates in the rhizosphere and phyllosphere.

CONCLUSIONS: Our study revealed the rhizosphere as an overlooked hotspot for methanol consumption in temperate grasslands. We further identified unusual new but potentially relevant methanol utilizers besides well-known methylotrophs in the phyllosphere and rhizosphere. We did not observe a plant host-specific methanol utilizer community. Our results suggest that our approach using quantitative SIP and metagenomics may be useful in future field studies to link gross methanol consumption rates with the rhizosphere and phyllosphere microbiome.}, } @article {pmid35793793, year = {2022}, author = {Lee, JY and Mitchell, HD and Burnet, MC and Wu, R and Jenson, SC and Merkley, ED and Nakayasu, ES and Nicora, CD and Jansson, JK and Burnum-Johnson, KE and Payne, SH}, title = {Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics.}, journal = {Journal of proteome research}, volume = {21}, number = {8}, pages = {2023-2035}, pmid = {35793793}, issn = {1535-3907}, mesh = {*Microbiota/genetics ; Peptides/analysis/genetics ; Proteome/genetics ; *Proteomics/methods ; RNA, Ribosomal, 16S/genetics ; Soil ; }, abstract = {Metaproteomics has been increasingly utilized for high-throughput characterization of proteins in complex environments and has been demonstrated to provide insights into microbial composition and functional roles. However, significant challenges remain in metaproteomic data analysis, including creation of a sample-specific protein sequence database. A well-matched database is a requirement for successful metaproteomics analysis, and the accuracy and sensitivity of PSM identification algorithms suffer when the database is incomplete or contains extraneous sequences. When matched DNA sequencing data of the sample is unavailable or incomplete, creating the proteome database that accurately represents the organisms in the sample is a challenge. Here, we leverage a de novo peptide sequencing approach to identify the sample composition directly from metaproteomic data. First, we created a deep learning model, Kaiko, to predict the peptide sequences from mass spectrometry data and trained it on 5 million peptide-spectrum matches from 55 phylogenetically diverse bacteria. After training, Kaiko successfully identified organisms from soil isolates and synthetic communities directly from proteomics data. Finally, we created a pipeline for metaproteome database generation using Kaiko. We tested the pipeline on native soils collected in Kansas, showing that the de novo sequencing model can be employed as an alternative and complementary method to construct the sample-specific protein database instead of relying on (un)matched metagenomes. Our pipeline identified all highly abundant taxa from 16S rRNA sequencing of the soil samples and uncovered several additional species which were strongly represented only in proteomic data.}, } @article {pmid35792945, year = {2022}, author = {Quintanilla-Mena, MA and Olvera-Novoa, MA and Sánchez-Tapia, IA and Lara-Pérez, LA and Rivas-Reyes, I and Gullian-Klanian, M and Patiño-Suárez, MV and Puch-Hau, CA}, title = {The digestive tract sections of the sea cucumber Isostichopus badionotus reveal differences in composition, diversity, and functionality of the gut microbiota.}, journal = {Archives of microbiology}, volume = {204}, number = {8}, pages = {463}, pmid = {35792945}, issn = {1432-072X}, support = {2015-01-1551//Consejo Nacional de Ciencia y Tecnología/ ; }, mesh = {Animals ; Firmicutes/genetics ; *Gastrointestinal Microbiome ; Gastrointestinal Tract ; RNA, Ribosomal, 16S/genetics ; *Sea Cucumbers ; }, abstract = {For the first time, this study analyses the composition and diversity of the gut microbiota of Isostichopus badionotus in captivity, using high-throughput 16S rRNA sequencing, and predicts the metagenomic functions of the microbiota. The results revealed a different composition of the gut microbiota for the foregut (FG) and midgut (MG) compared to the hindgut (HG), with a predominance of Proteobacteria, followed by Actinobacteria, Bacteroidetes, and Firmicutes. The FG and MG demonstrated a greater bacterial diversity compared to the HG. In addition, a complex network of interactions was observed at the genus level and identified some strains with probiotic and bioremediation potentials, such as Acinetobacter, Ruegeria, Streptococcus, Lactobacillus, Pseudomonas, Enterobacter, Aeromonas, Rhodopseudomonas, Agarivorans, Bacillus, Enterococcus, Micrococcus, Bifidobacterium, and Shewanella. Predicting metabolic pathways revealed that the bacterial composition in each section of the intestine participates in different physiological processes such as metabolism, genetic and environmental information processing, organismal systems, and cellular processes. Understanding and manipulating microbe--host-environment interactions and their associated functional capacity could substantially contribute to achieving more sustainable aquaculture systems for I. badionotus.}, } @article {pmid35792328, year = {2022}, author = {Zhang, L and Gong, X and Chen, Z and Zhou, Y}, title = {Genome-centric metagenomics analysis revealed the metabolic function of abundant microbial communities in thermal hydrolysis-assisted thermophilic anaerobic digesters under propionate stress.}, journal = {Bioresource technology}, volume = {360}, number = {}, pages = {127574}, doi = {10.1016/j.biortech.2022.127574}, pmid = {35792328}, issn = {1873-2976}, mesh = {Anaerobiosis ; Bacteria/genetics/metabolism ; Bioreactors/microbiology ; Hydrolysis ; *Metagenomics ; Methane/metabolism ; Methanosarcina/metabolism ; *Microbiota/genetics ; Propionates/metabolism ; }, abstract = {The ecological roles of microbial communities and how they interact with each other in thermal hydrolysis process (THP) assisted thermophilic anaerobic digestion (THP-AD) reactors remain largely unknown, especially under propionate stress. Two thermophilic THP-AD reactors had methane yield of 240-248 mL/g VSadded, but accumulated approximately 2000 mg/L propionate. Genome-centric metagenomics analysis showed that 68 metagenome-assembled genomes (MAGs) were recovered, 32 MAGs of which were substantially enriched. Firmicutes spp. dominated the enriched microbial community, including hydrolytic/fermentative bacteria and syntrophs. Methanogenic activities were mainly mediated by Methanosarcina sp. and Methanothermobacter spp. In addition to hydrogenotrophic methanogens, Thermodesulfovibrio sp. could also be a vital H2 scavenger, contributing to maintaining low H2 partial pressure in the bioreactors. The remarkable accumulation of propionate could be likely attributed to the weak syntrophic propionate-oxidizing activity or its absence. These findings advanced our knowledge about the mutualistic symbiosis of carbon metabolism in thermophilic THP-AD reactors.}, } @article {pmid35791570, year = {2022}, author = {Wang, ZH and Jiang, XJ}, title = {[Contrasting Responses of the Microbial Community Structure and Functional Traits to Soil pH in Purple Soils].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {43}, number = {7}, pages = {3876-3883}, doi = {10.13227/j.hjkx.202111055}, pmid = {35791570}, issn = {0250-3301}, mesh = {Humans ; *Microbiota ; Nitrogen ; Phylogeny ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {To clarify the effect of pH on the structure and functional traits of soil microbial communities in purple soils, three purple upland soils developed from the same parent material that differed in pH were selected as the research objects, and metagenomic shotgun sequencing was used to investigate the structure and functional traits of the microbial communities among different pH soils. The shotgun sequencing identified a total of 89 phyla, 222 classes, 527 orders, 1009 families, 2769 genera, and 14354 species in these soils. Regardless of the phylogenetic classification level, the microbial community structures of these three purple soils with different pHs were significantly different. RDA results corroborated the highly significant difference in the microbial community structures among the three purple soils with different pHs, and the soil properties tested here all had significant correlations with soil microbial community structure, in which the soil pH had the greatest effect (R[2]=0.9985, P=0.001). However, the results of investigating the microbial community functions revealed that the main metabolic processes of the three purple soils were all involved in unknown functions, global and overview maps, amino acid metabolism, carbohydrate metabolism, ammonia assimilation, etc. There was almost no significant difference in the relative abundance of microbes in the three purple soils annotated with the same function regardless of the COG/KEGG functional database and nitrogen cycling functional database, indicating that the overall function trait of soil microbial community was relatively conservative and not easily affected by environmental factors.}, } @article {pmid35790781, year = {2022}, author = {Leviatan, S and Shoer, S and Rothschild, D and Gorodetski, M and Segal, E}, title = {An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3863}, pmid = {35790781}, issn = {2041-1723}, mesh = {*Cancer Vaccines ; Ecosystem ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome/genetics ; Metagenomics ; }, abstract = {The gut is the richest ecosystem of microbes in the human body and has great influence on our health. Despite many efforts, the set of microbes inhabiting this environment is not fully known, limiting our ability to identify microbial content and to research it. In this work, we combine new microbial metagenomic assembled genomes from 51,052 samples, with previously published genomes to produce a curated set of 241,118 genomes. Based on this set, we procure a new and improved human gut microbiome reference set of 3594 high quality species genomes, which successfully matches 83.65% validation samples' reads. This improved reference set contains 310 novel species, including one that exists in 19% of validation samples. Overall, this study provides a gut microbial genome reference set that can serve as a valuable resource for further research.}, } @article {pmid35788780, year = {2022}, author = {Hernández-Guzmán, M and Pérez-Hernández, V and Gómez-Acata, S and Jiménez-Bueno, N and Verhulst, N and Muñoz-Arenas, LC and Navarro-Noya, YE and Luna-Guido, ML and Dendooven, L}, title = {Application of young maize plant residues alters the microbiome composition and its functioning in a soil under conservation agriculture: a metagenomics study.}, journal = {Archives of microbiology}, volume = {204}, number = {8}, pages = {458}, pmid = {35788780}, issn = {1432-072X}, mesh = {Agriculture ; Archaea/genetics ; Cellulose ; Metagenomics ; *Microbiota/genetics ; Soil ; *Zea mays ; }, abstract = {To increase our knowledge on how application of organic material alters soil microbial populations and functionality, shotgun metagenomic sequencing was used to determine the microbial communities and their potential functionality in an arable soil amended with young maize plants (Zea mays L.) in a laboratory experiment after 3 days. The relative abundance of bacterial and viral groups was strongly affected by organic material application, whereas that of the archaeal, protist and fungal groups was less affected. Cellulose degraders with copiotrophic lifestyle (e.g., Betaproteobacteria) were enriched in the amended soil, whereas the groups with slow growing oligotrophic and chemolithoautotrophic metabolism within Bacteria and Archaea were greater in the unamended than in the amended soil. The soil viral structure and richness were also affected. Caudovirales was the dominant viral family, with members of Siphoviridae enriched in the amended soil and members of Myoviridae in the unamended soil. More specialized metabolic traits related to both the degradation of complex C compounds and denitrification related genes were enriched in the young maize plant amended soil than in the unamended soil, whereas nitrification related genes were enriched in the latter. Copiotrophic life-style bacterial groups were enriched in the amended soil, whereas oligotrophic life-style bacterial groups in the unamended soil. Many bacterial and viral phylotypes were affected by the application of young maize plants, but the number of soil fungi, archaea and protists affected was smaller. Metabolic functionality was affected by the application of organic material as the relative abundance of genes involved in the denitrification process was higher in the maize plant amended soil than in the unamended soil and those involved in the nitrification process was higher in the unamended soil.}, } @article {pmid35788394, year = {2022}, author = {Wei, Y and Chang, L and Liu, G and Wang, X and Yang, Y and Hashimoto, K}, title = {Long-lasting beneficial effects of maternal intake of sulforaphane glucosinolate on gut microbiota in adult offspring.}, journal = {The Journal of nutritional biochemistry}, volume = {109}, number = {}, pages = {109098}, doi = {10.1016/j.jnutbio.2022.109098}, pmid = {35788394}, issn = {1873-4847}, mesh = {Adult Children ; Female ; *Gastrointestinal Microbiome/physiology ; Glucosinolates ; Humans ; Interleukin-6 ; Isothiocyanates ; Lipopolysaccharides ; Male ; Oximes ; Pregnancy ; Sulfoxides ; Tumor Necrosis Factor-alpha ; }, abstract = {Mounting evidence suggests the impact of maternal diet on the health of offspring. We reported that maternal diet of sulforaphane glucosinolate (SGS) could prevent behavioral abnormalities in offspring after maternal immune activation. The present study was designed to investigate whether the dietary intake of SGS during pregnancy and lactation influences the composition of gut microbiota in the offspring. The dietary intake of SGS during pregnancy and lactation caused significant changes in the α-diversity and β-diversity of gut microbiota in 3-week-old offspring (SGS-3W group) and 10-week-old offspring (SGS-10W group). The LEfSe algorithm identified several microbes as important phylotypes in the SGS-3W or SGS-10W groups. Predictive functional metagenomes showed that the maternal intake of SGS caused several KEGG pathways alterations with respect to the genetic information processing and metabolism. Furthermore, the plasma levels of interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) in the SGS-10W group after the injection of lipopolysaccharide (LPS: 0.5 mg/kg) were significantly lower than those of the CON-10W group. It is noteworthy that there were positive correlations between the relative abundance of the genus Blautia and IL-6 (or TNF-α) in adult offspring. Moreover, there were sex differences of gut microbiota composition in offspring. In conclusion, these data suggest that the dietary intake of SGS during pregnancy and lactation might produce long-lasting beneficial effects in adult offspring through the persistent modulation of gut microbiota. It is likely that the modulation of gut microbiota by maternal nutrition may confer resilience versus vulnerability to stress-related psychiatric disorders in the offspring.}, } @article {pmid35788347, year = {2022}, author = {Nagata, N and Nishijima, S and Miyoshi-Akiyama, T and Kojima, Y and Kimura, M and Aoki, R and Ohsugi, M and Ueki, K and Miki, K and Iwata, E and Hayakawa, K and Ohmagari, N and Oka, S and Mizokami, M and Itoi, T and Kawai, T and Uemura, N and Hattori, M}, title = {Population-level Metagenomics Uncovers Distinct Effects of Multiple Medications on the Human Gut Microbiome.}, journal = {Gastroenterology}, volume = {163}, number = {4}, pages = {1038-1052}, doi = {10.1053/j.gastro.2022.06.070}, pmid = {35788347}, issn = {1528-0012}, mesh = {*Anti-Infective Agents ; Cross-Sectional Studies ; Fatty Acids, Volatile/pharmacology ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {BACKGROUND & AIMS: Medication is a major determinant of human gut microbiome structure, and its overuse increases the risks of morbidity and mortality. However, effects of certain commonly prescribed drugs and multiple medications on the gut microbiome are still underinvestigated.

METHODS: We performed shotgun metagenomic analysis of fecal samples from 4198 individuals in the Japanese 4D (Disease, Drug, Diet, Daily life) microbiome project. A total of 759 drugs were profiled, and other metadata, such as anthropometrics, lifestyles, diets, physical activities, and diseases, were prospectively collected. Second fecal samples were collected from 243 individuals to assess the effects of drug initiation and discontinuation on the microbiome.

RESULTS: We found that numerous drugs across different treatment categories influence the microbiome; more than 70% of the drugs we profiled had not been examined before. Individuals exposed to multiple drugs, polypharmacy, showed distinct gut microbiome structures harboring significantly more abundant upper gastrointestinal species and several nosocomial pathobionts due to additive drug effects. Polypharmacy was also associated with microbial functions, including the reduction of short-chain fatty acid metabolism and increased bacterial stress responses. Even nonantibiotic drugs were significantly correlated with an increased antimicrobial resistance potential through polypharmacy. Notably, a 2-time points dataset revealed the alteration and recovery of the microbiome in response to drug initiation and cessation, corroborating the observed drug-microbe associations in the cross-sectional cohort.

CONCLUSION: Our large-scale metagenomics unravels extensive and disruptive impacts of individual and multiple drug exposures on the human gut microbiome, providing a drug-microbe catalog as a basis for a deeper understanding of the role of the microbiome in drug efficacy and toxicity.}, } @article {pmid35788345, year = {2022}, author = {Gao, R and Wu, C and Zhu, Y and Kong, C and Zhu, Y and Gao, Y and Zhang, X and Yang, R and Zhong, H and Xiong, X and Chen, C and Xu, Q and Qin, H}, title = {Integrated Analysis of Colorectal Cancer Reveals Cross-Cohort Gut Microbial Signatures and Associated Serum Metabolites.}, journal = {Gastroenterology}, volume = {163}, number = {4}, pages = {1024-1037.e9}, doi = {10.1053/j.gastro.2022.06.069}, pmid = {35788345}, issn = {1528-0012}, mesh = {*Adenoma/diagnosis ; China ; *Colorectal Neoplasms/diagnosis/metabolism ; Feces ; *Gastrointestinal Microbiome ; Humans ; Metabolomics/methods ; Serotonin ; }, abstract = {BACKGROUND & AIMS: Studies have reported abnormal gut microbiota or circulating metabolome associated with colorectal cancer (CRC), but it remains a challenge to capture the CRC-relevant features consistent across geographic regions. This is particularly the problem for metabolic traits of CRC because the analyses generally use different platforms and laboratory methods, which poses a barrier to cross-dataset examination. In light of this, we sought to elucidate the microbial and metabolic signatures of CRC with broad population relevance.

METHODS: In this integrated metagenomic (healthy controls [HC], n = 91; colorectal adenoma [CRA], n = 63; CRC, n = 71) and metabolomic (HC, n = 34; CRA, n = 31; CRC, n = 35) analysis, CRC-associated features and microbe-metabolite correlations were first identified from a Shanghai cohort. A gut microbial panel was trained in the in-house cohort and cross-validated in 7 published metagenomic datasets of CRC. The in-house metabolic connections to the cross-cohort microbial signatures were used as evidence to infer serum metabolites with potentially external relevance. In addition, a combined microbe-metabolite panel was produced for diagnosing CRC or adenoma.

RESULTS: CRC-associated alterations were identified in the gut microbiome and serum metabolome. A composite microbe-metabolite diagnostic panel was developed and yielded an area under the curve of 0.912 for adenoma and 0.994 for CRC. We showed that many CRC-associated metabolites were linked to cross-cohort gut microbiome signatures of the disease, including CRC-enriched leucylalanine, serotonin, and imidazole propionate; and CRC-depleted perfluorooctane sulfonate, 2-linoleoylglycerol (18:2), and sphingadienine.

CONCLUSIONS: We generated cross-cohort metagenomic signatures of CRC, some of which linked to in-house CRC-associated serum metabolites. The microbial and metabolic shifts may have wide population relevance.}, } @article {pmid35787295, year = {2022}, author = {Zeng, J and Tu, Q and Yu, X and Qian, L and Wang, C and Shu, L and Liu, F and Liu, S and Huang, Z and He, J and Yan, Q and He, Z}, title = {PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {101}, pmid = {35787295}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Databases, Factual ; Metagenome/genetics ; *Microbiota ; *Phosphorus ; }, abstract = {BACKGROUND: Phosphorus (P) is one of the most essential macronutrients on the planet, and microorganisms (including bacteria and archaea) play a key role in P cycling in all living things and ecosystems. However, our comprehensive understanding of key P cycling genes (PCGs) and microorganisms (PCMs) as well as their ecological functions remains elusive even with the rapid advancement of metagenome sequencing technologies. One of major challenges is a lack of a comprehensive and accurately annotated P cycling functional gene database.

RESULTS: In this study, we constructed a well-curated P cycling database (PCycDB) covering 139 gene families and 10 P metabolic processes, including several previously ignored PCGs such as pafA encoding phosphate-insensitive phosphatase, ptxABCD (phosphite-related genes), and novel aepXVWPS genes for 2-aminoethylphosphonate transporters. We achieved an annotation accuracy, positive predictive value (PPV), sensitivity, specificity, and negative predictive value (NPV) of 99.8%, 96.1%, 99.9%, 99.8%, and 99.9%, respectively, for simulated gene datasets. Compared to other orthology databases, PCycDB is more accurate, more comprehensive, and faster to profile the PCGs. We used PCycDB to analyze P cycling microbial communities from representative natural and engineered environments and showed that PCycDB could apply to different environments.

CONCLUSIONS: We demonstrate that PCycDB is a powerful tool for advancing our understanding of microbially driven P cycling in the environment with high coverage, high accuracy, and rapid analysis of metagenome sequencing data. The PCycDB is available at https://github.com/ZengJiaxiong/Phosphorus-cycling-database . Video Abstract.}, } @article {pmid35784064, year = {2022}, author = {Schmidt, A and Schneider, C and Decker, P and Hohberg, K and Römbke, J and Lehmitz, R and Bálint, M}, title = {Shotgun metagenomics of soil invertebrate communities reflects taxonomy, biomass, and reference genome properties.}, journal = {Ecology and evolution}, volume = {12}, number = {6}, pages = {e8991}, pmid = {35784064}, issn = {2045-7758}, abstract = {Metagenomics - shotgun sequencing of all DNA fragments from a community DNA extract - is routinely used to describe the composition, structure, and function of microorganism communities. Advances in DNA sequencing and the availability of genome databases increasingly allow the use of shotgun metagenomics on eukaryotic communities. Metagenomics offers major advances in the recovery of biomass relationships in a sample, in comparison to taxonomic marker gene-based approaches (metabarcoding). However, little is known about the factors which influence metagenomics data from eukaryotic communities, such as differences among organism groups, the properties of reference genomes, and genome assemblies.We evaluated how shotgun metagenomics records composition and biomass in artificial soil invertebrate communities at different sequencing efforts. We generated mock communities of controlled biomass ratios from 28 species from all major soil mesofauna groups: mites, springtails, nematodes, tardigrades, and potworms. We shotgun sequenced these communities and taxonomically assigned them with a database of over 270 soil invertebrate genomes.We recovered over 95% of the species, and observed relatively high false-positive detection rates. We found strong differences in reads assigned to different taxa, with some groups (e.g., springtails) consistently attracting more hits than others (e.g., enchytraeids). Original biomass could be predicted from read counts after considering these taxon-specific differences. Species with larger genomes, and with more complete assemblies, consistently attracted more reads than species with smaller genomes. The GC content of the genome assemblies had no effect on the biomass-read relationships. Results were similar among different sequencing efforts.The results show considerable differences in taxon recovery and taxon specificity of biomass recovery from metagenomic sequence data. The properties of reference genomes and genome assemblies also influence biomass recovery, and they should be considered in metagenomic studies of eukaryotes. We show that low- and high-sequencing efforts yield similar results, suggesting high cost-efficiency of metagenomics for eukaryotic communities. We provide a brief roadmap for investigating factors which influence metagenomics-based eukaryotic community reconstructions. Understanding these factors is timely as accessibility of DNA sequencing and momentum for reference genomes projects show a future where the taxonomic assignment of DNA from any community sample becomes a reality.}, } @article {pmid35782152, year = {2022}, author = {Kayani, MUR and Zaidi, SSA and Feng, R and Yu, K and Qiu, Y and Yu, X and Chen, L and Huang, L}, title = {Genome-Resolved Characterization of Structure and Potential Functions of the Zebrafish Stool Microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {910766}, pmid = {35782152}, issn = {2235-2988}, mesh = {Animals ; Feces ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Microbiota ; Zebrafish ; }, abstract = {Zebrafish have been used as a model organism for more than 50 years and are considered an excellent model for studying host-microbiome interactions. However, this largely depends on our understanding of the zebrafish gut microbiome itself. Despite advances in sequencing and data analysis methods, the zebrafish gut microbiome remains highly understudied. This study performed the de novo metagenome assembly and recovery of the metagenome-assembled genomes (MAGs) through genome binning (and refinement) of the contigs assembled from the zebrafish stool. The results indicate that majority of the MAGs had excellent quality i.e. high completeness (≥90%) and low contamination levels (≤5%). MAGs mainly belong to the taxa that are known to be members of the core zebrafish stool microbiome, including the phylum Proteobacteria, Fusobacteriota, and Actinobacteriota. However, most of the MAGs remained unclassified at the species level and reflected previously unexplored microbial taxa and their potential novelty. These MAGs also contained genes with predicted functions associated with diverse metabolic pathways that included carbohydrate, amino acid, and lipid metabolism pathways. Lastly, we performed a comparative analysis of Paucibacter MAGs and reference genomes that highlighted the presence of novel Paucibacter species and enriched metabolic potential in the recovered MAGs.}, } @article {pmid35782115, year = {2022}, author = {Moussa, DG and Ahmad, P and Mansour, TA and Siqueira, WL}, title = {Current State and Challenges of the Global Outcomes of Dental Caries Research in the Meta-Omics Era.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {887907}, pmid = {35782115}, issn = {2235-2988}, support = {//CIHR/Canada ; }, mesh = {*Dental Caries ; Genome-Wide Association Study ; Humans ; Metabolomics/methods ; Metagenomics ; *Microbiota/genetics ; }, abstract = {Despite significant healthcare advances in the 21[st] century, the exact etiology of dental caries remains unsolved. The past two decades have witnessed a tremendous growth in our understanding of dental caries amid the advent of revolutionary omics technologies. Accordingly, a consensus has been reached that dental caries is a community-scale metabolic disorder, and its etiology is beyond a single causative organism. This conclusion was based on a variety of microbiome studies following the flow of information along the central dogma of biology from genomic data to the end products of metabolism. These studies were facilitated by the unprecedented growth of the next- generation sequencing tools and omics techniques, such as metagenomics and metatranscriptomics, to estimate the community composition of oral microbiome and its functional potential. Furthermore, the rapidly evolving proteomics and metabolomics platforms, including nuclear magnetic resonance spectroscopy and/or mass spectrometry coupled with chromatography, have enabled precise quantification of the translational outcomes. Although the majority supports 'conserved functional changes' as indicators of dysbiosis, it remains unclear how caries dynamics impact the microbiota functions and vice versa, over the course of disease onset and progression. What compounds the situation is the host-microbiota crosstalk. Genome-wide association studies have been undertaken to elucidate the interaction of host genetic variation with the microbiome. However, these studies are challenged by the complex interaction of host genetics and environmental factors. All these complementary approaches need to be orchestrated to capture the key players in this multifactorial disease. Herein, we critically review the milestones in caries research focusing on the state-of-art singular and integrative omics studies, supplemented with a bibliographic network analysis to address the oral microbiome, the host factors, and their interactions. Additionally, we highlight gaps in the dental literature and shed light on critical future research questions and study designs that could unravel the complexities of dental caries, the most globally widespread disease.}, } @article {pmid35780677, year = {2022}, author = {Feng, L and Xiao, C and Luo, Y and Qiao, Y and Chen, D}, title = {The fate of antibiotic resistance genes, microbial community, and potential pathogens in the maricultural sediment by live seaweeds and oxytetracycline.}, journal = {Journal of environmental management}, volume = {318}, number = {}, pages = {115597}, doi = {10.1016/j.jenvman.2022.115597}, pmid = {35780677}, issn = {1095-8630}, mesh = {Anti-Bacterial Agents/analysis/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microbiota ; *Oxytetracycline/analysis/pharmacology ; *Seaweed ; *Ulva/genetics ; }, abstract = {Three common seaweeds including Ulva fasciata, Codium cylindricum and Ishige okamurai were used for the remediation of maricultural wastewater and sediment in the presence/absence of trace level of oxytetracycline (OTC) in lab-scale experiments. Higher NO3[-]-N and PO4[3-]-P removal rates were achieved due to the presence of seaweeds, and trace OTC also had a positive effect on NO3[-]-N removal. A slight variation of 2.10-2.15% were observed in the total relative abundances of antibiotic resistance genes (ARGs) of different sediment samples after one-month operation. However, the variation of ARGs profiles by the co-existence of different seaweeds and OTC was in the descending order of Ishige okamurai > Codium cylindricum > Ulva fasciata, which was in accordance with the variation of microbial hosts at genus level. The abundance of dominant tetracycline resistance genes promoted by the co-existence of different seaweeds and OTC in compared with the presence of single seaweed or OTC via metagenomic sequencing and qPCR analysis, and the co-existence of Ishige okamurai and OTC exhibited the largest impact. The potential pathogens were more sensitive to the co-existence of seaweed and OTC than single seaweeds. Meanwhile, a variety of ARGs were enriched in the pathogens, and the dominant pathogenic bacteria of Vibrio had 133 Vibrio species with 28 subtypes of ARGs. The variation of ARGs profiles in the sediment were strongly related with the dominant phyla Proteobacteria, Actinobacteria, Firmicutes, Planctomycetes and Cyanobacteria. Besides, Nitrate level exhibited more significant effect on ∑ARGs, ARGs resistant to vancomycin and streptogramin_a, while phosphate level exhibited more positively significant effect on ARGs resistant to fosmidomycin, ATFBT and cephalosporin.}, } @article {pmid35780499, year = {2022}, author = {Shen, Y and Yu, F and Zhang, D and Zou, Q and Xie, M and Chen, X and Yuan, L and Lou, B and Xie, G and Wang, R and Yang, X and Chen, W and Wang, Q and Feng, B and Teng, Y and Dong, Y and Huang, L and Bao, J and Han, D and Liu, C and Wu, W and Liu, X and Fan, L and Timko, MP and Zheng, S and Chen, Y}, title = {Dynamic Alterations in the Respiratory Tract Microbiota of Patients with COVID-19 and its Association with Microbiota in the Gut.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {9}, number = {27}, pages = {e2200956}, pmid = {35780499}, issn = {2198-3844}, support = {82072377//National Natural Science Foundation of China/ ; 81971919//National Natural Science Foundation of China/ ; }, mesh = {Biomarkers ; *COVID-19 ; Defensins ; Enterococcus ; Gastrointestinal Tract ; Humans ; Leukocytes, Mononuclear ; *Microbiota ; Respiratory System ; }, abstract = {The role of respiratory tract microbes and the relationship between respiratory tract and gut microbiomes in coronavirus disease 2019 (COVID-19) remain uncertain. Here, the metagenomes of sputum and fecal samples from 66 patients with COVID-19 at three stages of disease progression are sequenced. Respiratory tract, gut microbiome, and peripheral blood mononuclear cell (PBMC) samples are analyzed to compare the gut and respiratory tract microbiota of intensive care unit (ICU) and non-ICU (nICU) patients and determine relationships between respiratory tract microbiome and immune response. In the respiratory tract, significantly fewer Streptococcus, Actinomyces, Atopobium, and Bacteroides are found in ICU than in nICU patients, while Enterococcus and Candida increase. In the gut, significantly fewer Bacteroides are found in ICU patients, while Enterococcus increases. Significant positive correlations exist between relative microbiota abundances in the respiratory tract and gut. Defensin-related pathways in PBMCs are enhanced, and respiratory tract Streptococcus is reduced in patients with COVID-19. A respiratory tract-gut microbiota model identifies respiratory tract Streptococcus and Atopobium as the most prominent biomarkers distinguishing between ICU and nICU patients. The findings provide insight into the respiratory tract and gut microbial dynamics during COVID-19 progression, considering disease severity, potentially contributing to diagnosis, and treatment strategies.}, } @article {pmid35780470, year = {2022}, author = {Jaya, FR and Tanner, JC and Whitehead, MR and Doughty, P and Keogh, JS and Moritz, CC and Catullo, RA}, title = {Population genomics and sexual signals support reproductive character displacement in Uperoleia (Anura: Myobatrachidae) in a contact zone.}, journal = {Molecular ecology}, volume = {31}, number = {17}, pages = {4527-4543}, pmid = {35780470}, issn = {1365-294X}, mesh = {Animals ; *Anura/genetics ; Female ; Male ; *Metagenomics ; Phylogeography ; Reproduction/genetics ; Sympatry ; }, abstract = {When closely related species come into contact via range expansion, both may experience reduced fitness as a result of the interaction. Selection is expected to favour traits that minimize costly interspecies reproductive interactions (such as mismating) via a phenomenon called reproductive character displacement (RCD). Research on RCD frequently assumes secondary contact between species, but the geographical history of species interactions is often unknown. Population genomic data permit tests of geographical hypotheses about species origins and secondary contact through range expansion. We used population genomic data from single nucleotide polymorphisms (SNPs), mitochondrial sequence data, advertisement call data and morphological data to investigate a species complex of toadlets (Uperoleia borealis, U. crassa, U. inundata) from northern Australia. Although the three species of frogs were morphologically indistinguishable in our analysis, we determined that U. crassa and U. inundata form a single species (synonymized here) based on an absence of genomic divergence. SNP data identified the phylogeographical origin of U. crassa as the Top End, with subsequent westward invasion into the range of U. borealis in the Kimberley. We identified six F1 hybrids, all of which had the U. borealis mitochondrial haplotype, suggesting unidirectional hybridization. Consistent with the RCD hypothesis, U. borealis and U. crassa sexual signals differ more in sympatry than in allopatry. Hybrid males have intermediate calls, which probably reduces attractiveness to females. Integrating population genomic data, mitochondrial sequencing, morphology and behavioural approaches provides an unusually detailed collection of evidence for reproductive character displacement following range expansion and secondary contact.}, } @article {pmid35780445, year = {2022}, author = {Chen, Y and Xia, Z and Li, H}, title = {Metagenomic comparison of gut communities between hawksbills (Eretmochelys imbricata) and green sea turtles (Chelonia mydas).}, journal = {Archives of microbiology}, volume = {204}, number = {8}, pages = {450}, pmid = {35780445}, issn = {1432-072X}, support = {2020ZDZX1050//Department of Education of Guangdong Province/ ; 2020SC0302019//the Science and Technology Planning Project of Huizhou City/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Firmicutes ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics ; *Turtles/genetics ; }, abstract = {The gut microbiota is closely linked to host nutrition, immunity, and health. Here, metagenomic analysis was conducted to elucidate the taxonomic and functional diversity of gut communities from hawksbills and green sea turtles. In terms of diversity and abundance, the gut microbiota of herbivorous green sea turtles showed a higher bacterial diversity and richness than that of hawksbills. Firmicutes dominated in all groups; however, the phylum Proteobacteria showed a higher relative abundance in hawksbills. Several metabolic pathways displayed broad prevalence and high relative abundances in the two sea turtle populations. Antibiotic resistance genes (ARGs) responsible for resistance to glycopeptide and tetracycline were the most abundant in all samples. In ARGs, the subtype macB was the most abundant in the two different sea turtle populations; however, evgS, bcrA, and efrA were more abundant in the green sea turtles, while in the hawksbills, tetT and tetB(P) were more abundant. Among mobile genetic elements (MGEs), the abundance of 16 MGE types showed a significant difference between the two sea turtle populations. MGE type transposase and plasmid were the most abundant in the two sea turtle populations. Additionally, gene functions were enriched in carbohydrate esterases, glycoside hydrolases, and polysaccharide lyases in the green sea turtles, whereas genes related to glycosyltransferases and auxiliary activities were highly abundant in hawksbills. These metagenomic profiles provide further insights into the microbial diversities of the two types of sea turtles and provide valuable information for future conservation efforts.}, } @article {pmid35778624, year = {2022}, author = {Wei, C and Gu, W and Tian, R and Xu, F and Han, Y and Ji, Y and Li, T and Zhu, Y and Lang, P and Wu, W}, title = {Comparative analysis of the structure and function of rhizosphere microbiome of the Chinese medicinal herb Alisma in different regions.}, journal = {Archives of microbiology}, volume = {204}, number = {7}, pages = {448}, pmid = {35778624}, issn = {1432-072X}, support = {82073958//National Natural Science Foundation of China/ ; 81673534//Innovative Research Group Project of the National Natural Science Foundation of China/ ; ZDXM-3-24//Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization/ ; 2019//Qing Lan Project/ ; SYSD2020248//Suzhou Science and Technology Development Plan/ ; }, mesh = {*Alisma/chemistry/genetics ; Bacteria/genetics ; *Microbiota/genetics ; *Plants, Medicinal ; Rhizosphere ; *Triterpenes ; }, abstract = {Rhizoma Alismatis, a commonly used traditional Chinese medicine, is the dried tuber of Alisma orientale and Alisma A. plantago-aquatica, mainly cultivated in Fujian and Sichuan provinces (China), respectively. Studies have shown that the rhizosphere microbiome is a key factor determining quality of Chinese medicinal plants. Here we applied metagenomics to investigate the rhizosphere microbiome of Alisma in Fujian and Sichuan, focusing on its structure and function and those genes involved in protostane triterpenes biosynthesis. The dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes. Compared with Fujian, the rhizosphere of Sichuan has a greater α diversity and stronger microbial interactions but significantly lower relative abundance of archaea. Microbes with disease-suppressing functions were more abundant in Sichuan than Fujian, but vice versa for those with IAA-producing functions. Gemmatimonas, Anaeromyxobacter, and Pseudolabrys were the main contributors to the potential functional difference in two regions. Genes related to protostane triterpenes biosynthesis were enriched in Fujian. Steroidobacter, Pseudolabrys, Nevskia, and Nitrospira may contribute to the accumulation of protostane triterpenes in Alisma. This work fills a knowledge gap of Alisma's rhizosphere microbiome, providing a valuable reference for studying its beneficial microorganisms.}, } @article {pmid35777903, year = {2022}, author = {Tian, T and Mao, Q and Xie, J and Wang, Y and Shao, WH and Zhong, Q and Chen, JJ}, title = {Multi-omics data reveals the disturbance of glycerophospholipid metabolism caused by disordered gut microbiota in depressed mice.}, journal = {Journal of advanced research}, volume = {39}, number = {}, pages = {135-145}, pmid = {35777903}, issn = {2090-1224}, mesh = {Animals ; Fatty Acids, Volatile/metabolism ; Firmicutes/metabolism ; *Gastrointestinal Microbiome ; Glycerophospholipids ; Lipid Metabolism ; Mice ; Tryptophan/metabolism ; }, abstract = {INTRODUCTION: Although researchers have done intensive research on depression, its pathogenesis is still not fully explained. More and more evidence suggests that gut microbiota is closely related to the onset of depression; but its specific functional ways are not clearly identified.

OBJECTIVES: The purpose of our work was to find out how the gut microbiota was involved in the onset of depression, and to identify the potential ways to link the gut and brain in mice with depressive-like behaviors (DLB).

METHODS: We used the chronic restraint stress (CRS)-induced depression model here. Gut microbiota compositions in fecal samples, lipid metabolism (in fecal, serum and hippocampus samples) and neurotransmitters in hippocampus samples were detected.

RESULTS: We found that the 7 of 13 differential genera that significantly correlated with DLB belonged to phylum Firmicutes. The differential lipid metabolites in fecal samples mainly belonged to glycerophospholipids (GP) and fatty acids (FA) metabolism, and three important "metabolite type-bacterial taxa" correlated pairs were identified: "FA/GP-Firmicutes", "FA/GP-Akkermansia", and "FA/GP-Bifidobacterium". The key differential lipid metabolites significantly correlated with DLB mainly belonged to FA and GP, and the DLB-related metagenomic genes were consistently enriched in GP metabolism and FA metabolism. Three significantly changed short-chain fatty acids (SCFAs) were significantly correlated with the majority of differential genera. Meanwhile, we found that the differential lipid metabolites in serum and hippocampus samples were mainly mapped into the GP metabolism, and there were four differential neurotransmitters from the tryptophan pathway in hippocampus samples.

CONCLUSION: Together, our findings could provide novel insights into the role of "microbiota-gut-brain" (MGB) axis in depression, and indicate that the gut microbiota might have a vital role in the onset of DLB by affecting the peripheral/central GP metabolism and tryptophan pathway. The "Firmicutes-SCFAs-GP metabolism-Tryptophan pathway" might be a possible way to link the gut and brain in depressed mice.}, } @article {pmid35777538, year = {2022}, author = {Ma, S and Liu, H}, title = {Effects of 3D-printed bulking agent on microbial community succession and carbohydrate-active enzymes genes during swine manure composting.}, journal = {Chemosphere}, volume = {306}, number = {}, pages = {135513}, doi = {10.1016/j.chemosphere.2022.135513}, pmid = {35777538}, issn = {1879-1298}, mesh = {Animals ; Carbohydrates ; *Composting/methods ; Manure/microbiology ; *Microbiota ; Printing, Three-Dimensional ; Soil ; Swine ; }, abstract = {The bulking agent plays an important role in aerobic composting, but their shape, porosity, and homogeneity need to be optimized. In the present work, a bulking agent with a uniform shape was prepared by 3D printing to explore its influence on physicochemical parameters, microbial community succession, and gene abundance of carbohydrate-active enzymes (CAZymes) in swine manure aerobic composting. The results showed that adding 3D-printed bulking agents can increase maximum temperature, prolong the thermophilic period, and improve the degradation rate of volatile solids, which was attributed to ameliorative air permeability by the porous 3D-printed bulking agent. The abundances of some pathogenic bacteria decreased and CAZymes genes increased respectively in response to the addition of the 3D-printed bulking agent, implying it has a certain positive effect on improving the safety of compost products and promoting the degradation of organic matter. In summary, the 3D-printed bulking agent has good application potential in laboratory-scale aerobic composting.}, } @article {pmid35777321, year = {2022}, author = {Hauptfeld, E and Pelkmans, J and Huisman, TT and Anocic, A and Snoek, BL and von Meijenfeldt, FAB and Gerritse, J and van Leeuwen, J and Leurink, G and van Lit, A and van Uffelen, R and Koster, MC and Dutilh, BE}, title = {A metagenomic portrait of the microbial community responsible for two decades of bioremediation of poly-contaminated groundwater.}, journal = {Water research}, volume = {221}, number = {}, pages = {118767}, doi = {10.1016/j.watres.2022.118767}, pmid = {35777321}, issn = {1879-2448}, mesh = {Biodegradation, Environmental ; *Groundwater ; Metagenome ; *Microbiota ; *Water Pollutants, Chemical/analysis ; }, abstract = {Biodegradation of pollutants is a sustainable and cost-effective solution to groundwater pollution. Here, we investigate microbial populations involved in biodegradation of poly-contaminants in a pipeline for heavily contaminated groundwater. Groundwater moves from a polluted park to a treatment plant, where an aerated bioreactor effectively removes the contaminants. While the biomass does not settle in the reactor, sediment is collected afterwards and used to seed the new polluted groundwater via a backwash cycle. The pipeline has successfully operated since 1999, but the biological components in the reactor and the contaminated park groundwater have never been described. We sampled seven points along the pipeline, representing the entire remediation process, and characterized the changing microbial communities using genome-resolved metagenomic analysis. We assembled 297 medium- and high-quality metagenome-assembled genome sequences representing on average 46.3% of the total DNA per sample. We found that the communities cluster into two distinct groups, separating the anaerobic communities in the park groundwater from the aerobic communities inside the plant. In the park, the community is dominated by members of the genus Sulfuricurvum, while the plant is dominated by generalists from the order Burkholderiales. Known aromatic compound biodegradation pathways are four times more abundant in the plant-side communities compared to the park-side. Our findings provide a genome-resolved portrait of the microbial community in a highly effective groundwater treatment system that has treated groundwater with a complex contamination profile for two decades.}, } @article {pmid35777297, year = {2022}, author = {Guo, W and Guo, XJ and Xu, LN and Shao, LW and Zhu, BC and Liu, H and Wang, YJ and Gao, KY}, title = {Effect of whole-plant corn silage treated with lignocellulose-degrading bacteria on growth performance, rumen fermentation, and rumen microflora in sheep.}, journal = {Animal : an international journal of animal bioscience}, volume = {16}, number = {7}, pages = {100576}, doi = {10.1016/j.animal.2022.100576}, pmid = {35777297}, issn = {1751-732X}, mesh = {Animals ; Bacteria/metabolism ; Citrates/pharmacology ; Diet/veterinary ; Dietary Fiber/metabolism ; Digestion ; Fermentation ; *Gastrointestinal Microbiome ; Glucosides/pharmacology ; Hydrolases/metabolism/pharmacology ; Lignin/metabolism ; Male ; Rumen/metabolism ; Sheep ; *Silage/analysis ; Zea mays/chemistry ; }, abstract = {Lignification of cellulose limits the effective utilisation of fibre in plant cell wall. Lignocellulose-degrading bacteria secrete enzymes that decompose lignin and have the potential to improve fibre digestibility. Therefore, this study aimed to investigate the effect of whole-plant corn silage inoculated with lignocellulose-degrading bacteria on the growth performance, rumen fermentation, and rumen microbiome in sheep. Twelve 2-month-old male hybrid sheep (Dorper ♂ × small-tailed Han ♀) were randomly assigned into two dietary groups (n = 6): (1) untreated whole-plant corn silage (WPCS) and (2) WPCS inoculated with bacterial inoculant (WPCSB). Whole-plant corn silage inoculated with bacterial inoculant had higher in situ NDF digestibility than WPCS. Sheep in the WPCSB group had significantly higher average daily gain, DM intake, and feed conversion rate than those in the WPCS group (P < 0.05). Furthermore, higher volatile fatty acid concentrations were detected in WPCSB rumen samples, leading to lower ruminal pH (P < 0.05). The WPCSB group showed higher abundance of Bacteroidetes and lower abundance of Firmicutes in the rumen microbiome than the WPCS group (P < 0.05). Multiple differential genera were identified, with Prevotella being the most dominant genus and more abundant in WPCSB samples. Moreover, the enriched functional attributes, including those associated with glycolysis/gluconeogenesis and citrate cycle, were more actively expressed in the WPCSB samples than in the WPCS samples. Additionally, certain glucoside hydrolases that hydrolyse the side chains of hemicelluloses and pectins were also actively expressed in the WPCSB microbiome. These findings suggested that WPCSB increased NDF digestibility in three ways: (1) by increasing the relative abundance of the most abundant genera, (2) by recruiting more functional features involved in glycolysis/gluconeogenesis and citrate cycle pathways, and (3) by increasing the relative abundance and/or expression activity of the glucoside hydrolases involved in hemicellulose and pectin metabolism. Our findings provide novel insights into the microbial mechanisms underlying improvement in the growth performance of sheep/ruminants. However, the biological mechanisms cannot be fully elucidated using only metagenomics tools; therefore, a combined multi-omics approach will be used in subsequent studies.}, } @article {pmid35774405, year = {2022}, author = {Horne, RG and Freedman, SB and Johnson-Henry, KC and Pang, XL and Lee, BE and Farion, KJ and Gouin, S and Schuh, S and Poonai, N and Hurley, KF and Finkelstein, Y and Xie, J and Williamson-Urquhart, S and Chui, L and Rossi, L and Surette, MG and Sherman, PM}, title = {Intestinal Microbial Composition of Children in a Randomized Controlled Trial of Probiotics to Treat Acute Gastroenteritis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {883163}, pmid = {35774405}, issn = {2235-2988}, mesh = {Child ; Child, Preschool ; Feces/microbiology ; *Gastroenteritis/drug therapy ; *Gastrointestinal Microbiome ; Humans ; Intestines ; *Microbiota ; *Probiotics/therapeutic use ; RNA, Ribosomal, 16S/genetics ; }, abstract = {UNLABELLED: Compositional analysis of the intestinal microbiome in pre-schoolers is understudied. Effects of probiotics on the gut microbiota were evaluated in children under 4-years-old presenting to an emergency department with acute gastroenteritis. Included were 70 study participants (n=32 placebo, n=38 probiotics) with stool specimens at baseline (day 0), day 5, and after a washout period (day 28). Microbiota composition and deduced functions were profiled using 16S ribosomal RNA sequencing and predictive metagenomics, respectively. Probiotics were detected at day 5 of administration but otherwise had no discernable effects, whereas detection of bacterial infection (P<0.001) and participant age (P<0.001) had the largest effects on microbiota composition, microbial diversity, and deduced bacterial functions. Participants under 1 year had lower bacterial diversity than older aged pre-schoolers; compositional changes of individual bacterial taxa were associated with maturation of the gut microbiota. Advances in age were associated with differences in gut microbiota composition and deduced microbial functions, which have the potential to impact health later in life.

CLINICAL TRIAL REGISTRATION: www.ClinicalTrials.gov, identifier: NCT01853124.}, } @article {pmid35774395, year = {2022}, author = {Lee, SH and Park, HK and Kang, CD and Choi, DH and Park, SC and Park, JM and Nam, SJ and Chae, GB and Lee, KY and Cho, H and Lee, SJ}, title = {High Dose Intramuscular Vitamin D3 Supplementation Impacts the Gut Microbiota of Patients With Clostridioides Difficile Infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {904987}, pmid = {35774395}, issn = {2235-2988}, mesh = {Bacteria/genetics ; Cholecalciferol ; *Clostridioides difficile ; *Clostridium Infections/microbiology ; Dietary Supplements ; *Gastrointestinal Microbiome ; Humans ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Vancomycin ; Vitamin D ; *Vitamin D Deficiency/microbiology ; }, abstract = {BACKGROUND AND AIM: Current therapeutic strategies for Clostridioides difficile infections (CDI), including oral vancomycin, metronidazole and fecal microbial transplantation, have limited efficacy and treatment failure may occur in as many as one- third of cases. Recent studies have reported that lower concentrations of 25-hydroxyvitamin D are associated with CDI severity and recurrence. However, there have been no studies on microbiota composition after the administration of vitamin D in patients with CDI. Therefore, our study aimed to compare the microbiota composition between the two groups, including eight CDI-positive patients with vitamin D supplementation and ten CDI-positive patients without vitamin D supplementation by using 16S rRNA microbial profiling.

METHODS: Twenty subjects were enrolled in this prospective randomized controlled study. One subject dropped out due to lack of contact with the guardian after discharge and one subject dropped out due to withdrawal of consent. Thus, 18 patients with CDI and vitamin D insufficiency (vitamin D level < 17 ng/mL) were divided into two groups: CDI with vitamin D supplementation (n = 8) and CDI without vitamin D supplementation (control: n = 10). Subjects with vitamin D insufficiency were randomized to receive 200,000 IU intramuscular cholecalciferol whereas patients in the control group received only oral vancomycin. Stool samples were obtained twice before vancomycin was administered and eight weeks after treatment; the V3-V4 16S rRNA metagenomic sequencing was performed using EzBioCloud.

RESULTS: The alpha diversity of the gut microbiota in the recovery state was significantly higher than that in the CDI state. Analysis of bacterial relative abundance showed significantly lower Proteobacteria and higher Lachnospiraceae, Ruminococcaceae, Akkermansiaceae, and Bifidobacteriaceae in the recovery state. When comparing the control and vitamin D treatment groups after eight weeks, increase in alpha diversity and, abundance of Lachnospiraceae, and Ruminococcaceae exhibited the same trend in both groups. A significant increase in Bifidobacteriaceae and Christensenellaceae was observed in the vitamin D group; Proteobacteria abundance was significantly lower in the vitamin D treatment group after eight weeks than that in the control group.

CONCLUSION: Our study confirmed that the increase in the abundance of beneficial bacteria such as Bifidobacteriaceae, and Christensenellaceae were prominently evident during recovery after administration of a high dose of cholecalciferol. These findings indicate that vitamin D administration may be useful in patients with CDI, and further studies with larger sample sizes are required.}, } @article {pmid35773309, year = {2022}, author = {Bajagai, YS and Petranyi, F and J Yu, S and Lobo, E and Batacan, R and Kayal, A and Horyanto, D and Ren, X and M Whitton, M and Stanley, D}, title = {Phytogenic supplement containing menthol, carvacrol and carvone ameliorates gut microbiota and production performance of commercial layers.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {11033}, pmid = {35773309}, issn = {2045-2322}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Chickens ; Cyclohexane Monoterpenes ; Cymenes ; Dietary Supplements/analysis ; Female ; *Gastrointestinal Microbiome ; Menthol/pharmacology ; }, abstract = {Consumer push towards open and free-range production systems makes biosecurity on farms challenging, leading to increased disease and animal welfare issues. Phytogenic products are increasingly becoming a viable alternative for the use of antibiotics in livestock production. Here we present a study of the effects of commercial phytogenic supplement containing menthol, carvacrol and carvone on intestinal microbiota of layer hens, microbial functional capacity, and intestinal morphology. A total of 40,000 pullets were randomly assigned to two sides of the experimental shed. Growth performance, mortality, egg production and egg quality parameters were recorded throughout the trial period (18-30 weeks of age). Microbial community was investigated using 16S amplicon sequencing and functional difference using metagenomic sequencing. Phytogen supplemented birds had lower mortality and number of dirty eggs, and their microbial communities showed reduced richness. Although phytogen showed the ability to control the range of poultry pathogens, its action was not restricted to pathogenic taxa, and it involved functional remodelling the intestinal community towards increased cofactor production, heterolactic fermentation and salvage and recycling of metabolites. The phytogen did not alter the antimicrobial resistance profile or the number of antibiotic resistance genes. The study indicates that phytogenic supplementation can mimic the action of antibiotics in altering the gut microbiota and be used as their alternative in industry-scale layer production.}, } @article {pmid35769000, year = {2022}, author = {Shang, J and Tang, X and Guo, R and Sun, Y}, title = {Accurate identification of bacteriophages from metagenomic data using Transformer.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {4}, pages = {}, pmid = {35769000}, issn = {1477-4054}, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; Metagenome ; Metagenomics/methods ; *Microbiota ; }, abstract = {MOTIVATION: Bacteriophages are viruses infecting bacteria. Being key players in microbial communities, they can regulate the composition/function of microbiome by infecting their bacterial hosts and mediating gene transfer. Recently, metagenomic sequencing, which can sequence all genetic materials from various microbiome, has become a popular means for new phage discovery. However, accurate and comprehensive detection of phages from the metagenomic data remains difficult. High diversity/abundance, and limited reference genomes pose major challenges for recruiting phage fragments from metagenomic data. Existing alignment-based or learning-based models have either low recall or precision on metagenomic data.

RESULTS: In this work, we adopt the state-of-the-art language model, Transformer, to conduct contextual embedding for phage contigs. By constructing a protein-cluster vocabulary, we can feed both the protein composition and the proteins' positions from each contig into the Transformer. The Transformer can learn the protein organization and associations using the self-attention mechanism and predicts the label for test contigs. We rigorously tested our developed tool named PhaMer on multiple datasets with increasing difficulty, including quality RefSeq genomes, short contigs, simulated metagenomic data, mock metagenomic data and the public IMG/VR dataset. All the experimental results show that PhaMer outperforms the state-of-the-art tools. In the real metagenomic data experiment, PhaMer improves the F1-score of phage detection by 27%.}, } @article {pmid35768947, year = {2022}, author = {Jing, H and Xiao, X and Zhang, Y and Li, Z and Jian, H and Luo, Y and Han, Z}, title = {Composition and Ecological Roles of the Core Microbiome along the Abyssal-Hadal Transition Zone Sediments of the Mariana Trench.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0198821}, pmid = {35768947}, issn = {2165-0497}, mesh = {Archaea/genetics ; *Bacteria/genetics/metabolism ; *Microbiota/genetics ; Nitrogen/metabolism ; Oceans and Seas ; }, abstract = {The unique geological features of hadal trenches are known to influence both the structure and ecological function of microbial communities. It is also well known that heterotrophs and chemoautotrophs dominate the hadal and abyssal pelagic zones, respectively. Here, a metagenomic investigation was conducted on sediment samples obtained from the abyssal-hadal transition zone in the Mariana Trench to gain a better understanding of the general diversity and potential function of the core microbiome in this zone. A high level of cosmopolitanism existed in the core microbiome referred from a high community similarity among different stations. Niche differentiation along the fine-scale of different sediment layers was observed, especially for major archaeal groups, largely due to sediment depth and the source of organic matter. A prevalence of nitrogen biogeochemical cycles driven by various nitrifying groups with the capability of dark carbon fixation in the abyssal-hadal biosphere was also demonstrated. The predominance of heterotrophic over chemolithoautotrophic pathways in this transition zone was found, and a high abundance of genes related to respiration and carbon fixation (i.e., the intact Calvin and rTCA cycles) were detected as well, which might reflect the intensive microbial activities known to occur in this deep biosphere. The presence of those metabolic processes and associated microbes were reflected by functional and genetic markers generated from the metagenomic data in the current study. However, their roles and contributions to the nitrogen/carbon biogeochemical cycles and flux in the abyssal-hadal transition zone still need further analysis. IMPORTANCE The Mariana Trench is the deepest oceanic region on earth, its microbial ecological exploration has become feasible with the rapid progress of submersible and metagenomic sequencing. We investigated the community compositions and metabolic functions of the core microbiome along the abyssal-hadal transition zone of the Mariana Trench, although most studies by far were focused on the pelagic zone. We found a predominance of heterotrophic groups and related metabolic pathways, which were closely associated with nitrogen biogeochemical cycles driven by various nitrifying groups with the capability of dark carbon fixation.}, } @article {pmid35768736, year = {2023}, author = {Fernando, DG and Saravia, FL and Atkinson, SN and Barron, M and Kirby, JR and Kindel, TL}, title = {A single, peri-operative antibiotic can persistently alter the post-operative gut microbiome after Roux-en-Y gastric bypass.}, journal = {Surgical endoscopy}, volume = {37}, number = {2}, pages = {1476-1486}, pmid = {35768736}, issn = {1432-2218}, support = {K08 HL140000/HL/NHLBI NIH HHS/United States ; R21 AG075501/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Female ; Adult ; Middle Aged ; Male ; *Gastric Bypass ; *Gastrointestinal Microbiome/physiology ; Anti-Bacterial Agents ; Clindamycin ; Prospective Studies ; RNA, Ribosomal, 16S ; *Obesity, Morbid/surgery ; }, abstract = {INTRODUCTION: Roux-en-Y gastric bypass (RYGB) significantly alters the gut microbiome and may be a mechanism for post-operative cardiovascular disease improvement. We have previously found an association between the class of peri-operative, intravenous antibiotic administered at the time of RYGB and the resolution rate of hypertension suggesting the gut microbiome as a mechanism. In this study, we performed a prospective study of RYGB to determine if a single intravenous antibiotic could alter the gastrointestinal microbial composition.

METHODS: Patients undergoing RYGB were randomized to a single, peri-operative antibiotic of intravenous cefazolin (n = 8) or clindamycin (n = 8). Stool samples were collected from four-time points: 2 weeks pre-op (- 2w), 2 days pre-op (- 2d), 2 weeks post-op (+ 2w) and 3 months post-op (+ 3m). Stool samples were processed for genomic DNA followed by Illumina 16S rRNA gene sequencing and shotgun metagenomic sequencing (MGS).

RESULTS: A total of 60 stool samples (- 2w, n = 16; - 2d, n = 15; + 2w, n = 16; + 3m, n = 13) from 16 patients were analyzed. 87.5% of patients were female with an average age of 48.6 ± 12.2 years and pre-operative BMI of 50.9 ± 23.3 kg/m[2]. RYGB induced statistically significant differences in alpha and beta diversity. There were statistically significant differences in alpha diversity at + 2w and beta diversity at + 3m due to antibiotic treatment. MGS revealed significantly distinct gut microbiota with 11 discriminatory metagenomic assembled genomes driven by antibiotic treatment at 3 months post-op, including increased Bifidobacterium spp. with clindamycin.

CONCLUSION: RYGB induces significant changes in the gut microbiome at 2 weeks that are maintained 3 months after surgery. However, the single peri-operative dose of antibiotic administered at the time of RYGB induces unique and persisting changes to the gut microbiome that are antibiotic-specific. Increased Bifidobacterium spp. with clindamycin administration may improve the metabolic efficacy of RYGB when considering gut-microbiome driven mechanisms for blood pressure resolution.}, } @article {pmid35768643, year = {2022}, author = {Ojima, MN and Jiang, L and Arzamasov, AA and Yoshida, K and Odamaki, T and Xiao, J and Nakajima, A and Kitaoka, M and Hirose, J and Urashima, T and Katoh, T and Gotoh, A and van Sinderen, D and Rodionov, DA and Osterman, AL and Sakanaka, M and Katayama, T}, title = {Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides.}, journal = {The ISME journal}, volume = {16}, number = {9}, pages = {2265-2279}, pmid = {35768643}, issn = {1751-7370}, support = {R01 DK030292/DK/NIDDK NIH HHS/United States ; }, mesh = {*Bifidobacterium/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant ; Milk, Human/chemistry ; Oligosaccharides ; }, abstract = {Bifidobacteria are among the first colonizers of the infant gut, and human milk oligosaccharides (HMOs) in breastmilk are instrumental for the formation of a bifidobacteria-rich microbiota. However, little is known about the assembly of bifidobacterial communities. Here, by applying assembly theory to a community of four representative infant-gut associated Bifidobacterium species that employ varied strategies for HMO consumption, we show that arrival order and sugar consumption phenotypes significantly affected community formation. Bifidobacterium bifidum and Bifidobacterium longum subsp. infantis, two avid HMO consumers, dominate through inhibitory priority effects. On the other hand, Bifidobacterium breve, a species with limited HMO-utilization ability, can benefit from facilitative priority effects and dominates by utilizing fucose, an HMO degradant not utilized by the other bifidobacterial species. Analysis of publicly available breastfed infant faecal metagenome data showed that the observed trends for B. breve were consistent with our in vitro data, suggesting that priority effects may have contributed to its dominance. Our study highlights the importance and history dependency of initial community assembly and its implications for the maturation trajectory of the infant gut microbiota.}, } @article {pmid35768476, year = {2022}, author = {Yabuuchi, S and Oiki, S and Minami, S and Takase, R and Watanabe, D and Hashimoto, W}, title = {Enhanced propagation of Granulicatella adiacens from human oral microbiota by hyaluronan.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {10948}, pmid = {35768476}, issn = {2045-2322}, mesh = {Bacteria/metabolism ; *Carnobacteriaceae/metabolism ; Glycosaminoglycans/metabolism ; Humans ; Hyaluronic Acid/metabolism ; *Microbiota ; Streptococcus/metabolism ; }, abstract = {Host determinants for formation/composition of human oral microbiota remain to be clarified, although microorganisms entering the mouth cannot necessarily colonize the oral environment. Here we show that human oral-abundant bacteria degraded host glycosaminoglycans (GAGs) in saliva and gingiva, and certain bacteria significantly grew on hyaluronan (HA), a kind of GAGs. Microbial communities from teeth or gingiva of healthy donors assimilated HA. Metagenomic analysis of human oral microbiota under different carbon sources revealed HA-driven Granulicatella growth. HA-degrading bacterial strains independently isolated from teeth and gingiva were identified as Granulicatella adiacens producing extracellular 130 kDa polysaccharide lyase as a HA-degrading enzyme encoded in a peculiar GAG genetic cluster containing genes for isomerase KduI and dehydrogenase DhuD. These findings demonstrated that GAGs are one of the host determinants for formation/composition of oral microbiota not only for colonization but also for the adaptation to the host niche. Especially, HA enhanced the G. adiacens propagation.}, } @article {pmid35766975, year = {2022}, author = {Jackson, EW and Wilhelm, RC and Buckley, DH and Hewson, I}, title = {The RNA virome of echinoderms.}, journal = {The Journal of general virology}, volume = {103}, number = {6}, pages = {}, doi = {10.1099/jgv.0.001772}, pmid = {35766975}, issn = {1465-2099}, mesh = {Animals ; Biodiversity ; Echinodermata/genetics ; Phylogeny ; *RNA ; Sequence Analysis, DNA ; *Virome/genetics ; }, abstract = {Echinoderms are a phylum of marine invertebrates that include model organisms, keystone species, and animals commercially harvested for seafood. Despite their scientific, ecological, and economic importance, there is little known about the diversity of RNA viruses that infect echinoderms compared to other invertebrates. We screened over 900 transcriptomes and viral metagenomes to characterize the RNA virome of 38 echinoderm species from all five classes (Crinoidea, Holothuroidea, Asteroidea, Ophiuroidea and Echinoidea). We identified 347 viral genome fragments that were classified to genera and families within nine viral orders - Picornavirales, Durnavirales, Martellivirales, Nodamuvirales, Reovirales, Amarillovirales, Ghabrivirales, Mononegavirales, and Hepelivirales. We compared the relative viral representation across three life stages (embryo, larvae, adult) and characterized the gene content of contigs which encoded complete or near-complete genomes. The proportion of viral reads in a given transcriptome was not found to significantly differ between life stages though the majority of viral contigs were discovered from transcriptomes of adult tissue. This study illuminates the biodiversity of RNA viruses from echinoderms, revealing the occurrence of viral groups in natural populations.}, } @article {pmid35766965, year = {2022}, author = {van Heck, JIP and Gacesa, R and Stienstra, R and Fu, J and Zhernakova, A and Harmsen, HJM and Weersma, RK and Joosten, LAB and Tack, CJ}, title = {The Gut Microbiome Composition Is Altered in Long-standing Type 1 Diabetes and Associates With Glycemic Control and Disease-Related Complications.}, journal = {Diabetes care}, volume = {45}, number = {9}, pages = {2084-2094}, doi = {10.2337/dc21-2225}, pmid = {35766965}, issn = {1935-5548}, mesh = {Cross-Sectional Studies ; *Diabetes Mellitus, Type 1/complications ; *Gastrointestinal Microbiome/genetics ; Glycated Hemoglobin ; Glycemic Control ; Humans ; }, abstract = {OBJECTIVE: People with type 1 diabetes are at risk for developing micro- and macrovascular complications. Little is known about the gut microbiome in long-standing type 1 diabetes. We explored differences in the gut microbiome of participants with type 1 diabetes compared with healthy control subjects and associated the gut microbiome with diabetes-related complications.

RESEARCH DESIGN AND METHODS: Microbiome data of 238 participants with type 1 diabetes with an average disease duration of 28 ± 15 years were compared with 2,937 age-, sex-, and BMI-matched individuals. Clinical characteristics and fecal samples were collected, and metagenomic shotgun sequencing was performed. Microbial taxonomy was associated with type 1 diabetes-related characteristics and vascular complications.

RESULTS: No significant difference in the α-diversity of the gut microbiome was found between participants with type 1 diabetes and healthy control subjects. However, 43 bacterial taxa were significantly depleted in type 1 diabetes, while 37 bacterial taxa were significantly enriched. HbA1c and disease duration explained a significant part of the variation in the gut microbiome (R2 > 0.008, false discovery rate [FDR] <0.05), and HbA1c was significantly associated with the abundance of several microbial species. Additionally, both micro- and macrovascular complications explained a significant part of the variation in the gut microbiome (R2 > 0.0075, FDR < 0.05). Nephropathy was strongly associated with several microbial species. Macrovascular complications displayed similar associations with nephropathy.

CONCLUSIONS: Our data show that the gut microbiome is altered in people with (long-standing) type 1 diabetes and is associated with glycemic control and diabetes-related complications. As a result of the cross-sectional design, the causality of these relationships remains to be determined.}, } @article {pmid35766483, year = {2022}, author = {Avuthu, N and Guda, C}, title = {Meta-Analysis of Altered Gut Microbiota Reveals Microbial and Metabolic Biomarkers for Colorectal Cancer.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0001322}, pmid = {35766483}, issn = {2165-0497}, mesh = {Biomarkers ; *Colorectal Neoplasms/diagnosis ; Dysbiosis/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Reproducibility of Results ; }, abstract = {Colorectal cancer (CRC) is the second leading cause of cancer mortality worldwide. The dysbiotic gut microbiota and its metabolite secretions play a significant role in CRC development and progression. In this study, we identified microbial and metabolic biomarkers applicable to CRC using a meta-analysis of metagenomic datasets from diverse geographical regions. We used LEfSe, random forest (RF), and co-occurrence network methods to identify microbial biomarkers. Geographic dataset-specific markers were identified and evaluated using area under the ROC curve (AUC) scores and random effect size. Co-occurrence networks analysis showed a reduction in the overall microbial associations and the presence of oral pathogenic microbial clusters in CRC networks. Analysis of predicted metabolites from CRC datasets showed the enrichment of amino acids, cadaverine, and creatine in CRC, which were positively correlated with CRC-associated microbes (Peptostreptococcus stomatis, Gemella morbillorum, Bacteroides fragilis, Parvimonas spp., Fusobacterium nucleatum, Solobacterium moorei, and Clostridium symbiosum), and negatively correlated with control-associated microbes. Conversely, butyrate, nicotinamide, choline, tryptophan, and 2-hydroxybutanoic acid showed positive correlations with control-associated microbes (P < 0.05). Overall, our study identified a set of global CRC biomarkers that are reproducible across geographic regions. We also reported significant differential metabolites and microbe-metabolite interactions associated with CRC. This study provided significant insights for further investigations leading to the development of noninvasive CRC diagnostic tools and therapeutic interventions. IMPORTANCE Several studies showed associations between gut dysbiosis and CRC. Yet, the results are not conclusive due to cohort-specific associations that are influenced by genomic, dietary, and environmental stimuli and associated reproducibility issues with various analysis approaches. Emerging evidence suggests the role of microbial metabolites in modulating host inflammation and DNA damage in CRC. However, the experimental validations have been hindered by cost, resources, and cumbersome technical expertise required for metabolomic investigations. In this study, we performed a meta-analysis of CRC microbiota data from diverse geographical regions using multiple methods to achieve reproducible results. We used a computational approach to predict the metabolomic profiles using existing CRC metagenomic datasets. We identified a reliable set of CRC-specific biomarkers from this analysis, including microbial and metabolite markers. In addition, we revealed significant microbe-metabolite associations through correlation analysis and microbial gene families associated with dysregulated metabolic pathways in CRC, which are essential in understanding the vastly sporadic nature of CRC development and progression.}, } @article {pmid35765950, year = {2022}, author = {Van Brussel, K and Wang, X and Shi, M and Carrai, M and Feng, S and Li, J and Holmes, EC and Beatty, JA and Barrs, VR}, title = {The enteric virome of cats with feline panleukopenia differs in abundance and diversity from healthy cats.}, journal = {Transboundary and emerging diseases}, volume = {69}, number = {5}, pages = {e2952-e2966}, pmid = {35765950}, issn = {1865-1682}, mesh = {Animals ; *Bocavirus/genetics ; *Calicivirus, Feline ; *Cat Diseases ; Cats ; *Feline Panleukopenia/epidemiology ; Feline Panleukopenia Virus/genetics ; Mammals ; *Parvoviridae ; Virome ; *Viruses ; }, abstract = {Feline panleukopenia (FPL) is a severe, often fatal disease caused by feline panleukopenia virus (FPV). How infection with FPV might impact the composition of the entire eukaryotic enteric virome in cats has not been characterized. We used meta-transcriptomic and viral particle enrichment metagenomic approaches to characterize the enteric viromes of 23 cats naturally infected with FPV (FPV-cases) and 36 age-matched healthy shelter cats (healthy controls). Sequencing reads from mammalian infecting viral families largely belonged to the Coronaviridae, Parvoviridae and Astroviridae. The most abundant viruses among the healthy control cats were feline coronavirus, Mamastrovirus 2 and Carnivore bocaparvovirus 3 (feline bocavirus), with frequent coinfections of all three. Feline chaphamaparvovirus was only detected in healthy controls (6 out of 36, 16.7%). Among the FPV-cases, in addition to FPV, the most abundant viruses were Mamastrovirus 2, feline coronavirus and C. bocaparvovirus 4 (feline bocaparvovirus 2). The latter and feline bocaparvovirus 3 were detected significantly more frequently in FPV-cases than in healthy controls. Feline calicivirus was present in a higher proportion of FPV-cases (11 out of 23, 47.8%) compared to healthy controls (5 out of 36, 13.9%, p = 0.0067). Feline kobuvirus infections were also common among FPV-cases (9 out of 23, 39.1%) and were not detected in any healthy controls (p < .0001). While abundant in both groups, astroviruses were more frequently present in FPV-cases (19 out of 23, 82.6%) than in healthy controls (18 out of 36, p = .0142). The differences in eukaryotic virome composition revealed here indicate that further investigations are warranted to determine associations between enteric viral co-infections on clinical disease severity in cats with FPL.}, } @article {pmid35765106, year = {2022}, author = {Urbaniak, C and Morrison, MD and Thissen, JB and Karouia, F and Smith, DJ and Mehta, S and Jaing, C and Venkateswaran, K}, title = {Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {100}, pmid = {35765106}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Humans ; *Malassezia ; Metagenome ; Metagenomics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: The International Space Station (ISS) is a unique and complex built environment with the ISS surface microbiome originating from crew and cargo or from life support recirculation in an almost entirely closed system. The Microbial Tracking 1 (MT-1) project was the first ISS environmental surface study to report on the metagenome profiles without using whole-genome amplification. The study surveyed the microbial communities from eight surfaces over a 14-month period. The Microbial Tracking 2 (MT-2) project aimed to continue the work of MT-1, sampling an additional four flights from the same locations, over another 14 months.

METHODS: Eight surfaces across the ISS were sampled with sterile wipes and processed upon return to Earth. DNA extracted from the processed samples (and controls) were treated with propidium monoazide (PMA) to detect intact/viable cells or left untreated and to detect the total DNA population (free DNA/compromised cells/intact cells/viable cells). DNA extracted from PMA-treated and untreated samples were analyzed using shotgun metagenomics. Samples were cultured for bacteria and fungi to supplement the above results.

RESULTS: Staphylococcus sp. and Malassezia sp. were the most represented bacterial and fungal species, respectively, on the ISS. Overall, the ISS surface microbiome was dominated by organisms associated with the human skin. Multi-dimensional scaling and differential abundance analysis showed significant temporal changes in the microbial population but no spatial differences. The ISS antimicrobial resistance gene profiles were however more stable over time, with no differences over the 5-year span of the MT-1 and MT-2 studies. Twenty-nine antimicrobial resistance genes were detected across all samples, with macrolide/lincosamide/streptogramin resistance being the most widespread. Metagenomic assembled genomes were reconstructed from the dataset, resulting in 82 MAGs. Functional assessment of the collective MAGs showed a propensity for amino acid utilization over carbohydrate metabolism. Co-occurrence analyses showed strong associations between bacterial and fungal genera. Culture analysis showed the microbial load to be on average 3.0 × 10[5] cfu/m[2] CONCLUSIONS: Utilizing various metagenomics analyses and culture methods, we provided a comprehensive analysis of the ISS surface microbiome, showing microbial burden, bacterial and fungal species prevalence, changes in the microbiome, and resistome over time and space, as well as the functional capabilities and microbial interactions of this unique built microbiome. Data from this study may help to inform policies for future space missions to ensure an ISS surface microbiome that promotes astronaut health and spacecraft integrity. Video Abstract.}, } @article {pmid35763072, year = {2022}, author = {Wang, Z and Zhang, Z and Lu, C and Zhou, J and Wang, Z and Han, J and Su, X}, title = {Effects of Sporisorium reiliana polysaccharides and Phoenix dactylifera monosaccharides on the gut microbiota and serum metabolism in mice with fructose-induced hyperuricemia.}, journal = {Archives of microbiology}, volume = {204}, number = {7}, pages = {436}, pmid = {35763072}, issn = {1432-072X}, support = {ZS20190105//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products/ ; Y202146257//General Project of Zhejiang Provincial Department of Education/ ; }, mesh = {Animals ; Fructose/adverse effects ; *Gastrointestinal Microbiome ; *Hyperuricemia/chemically induced/drug therapy ; Mice ; Monosaccharides ; *Phoeniceae ; Polysaccharides ; Uric Acid ; }, abstract = {In recent decades, the prevalence of hyperuricemia has increased, and dietary fructose is an important risk factor for the development of this disease. This study investigated and compared the effects of Sphacelotheca reiliana polysaccharides and Phoenix dactylifera monosaccharides on a series of physiological and biochemical indicators and on the metagenomes and serum metabolites in mice with hyperuricemia caused by a high-fructose diet. S. reiliana polysaccharides inhibited uric acid biosynthesis and promoted uric acid excretion, thereby alleviating the hyperuricemia phenotype. In addition, hyperuricemia was closely related to the gut microbiota. After treatment with S. reiliana polysaccharides, the abundances of Bacteroidetes and Proteobacteria in the mouse intestines were decreased, the expression of genes involved in glycolysis/gluconeogenesis metabolic pathways and purine metabolism was downregulated, and the dysfunction of the gut microbiota was alleviated. With regard to serum metabolism, the abundance of hippuric acid, uridine, kynurenic acid, propionic acid and arachidonoyl decreased, and the abundances of serum metabolites in inflammatory pathways involved in kidney injury and gout, such as bile acid metabolism, purine metabolism and tryptophan metabolism pathways, decreased. P. dactylifera monosaccharides aggravated hyperuricemia. This research provides a valuable reference for the development of sugar applications.}, } @article {pmid35762794, year = {2022}, author = {Roguet, A and Newton, RJ and Eren, AM and McLellan, SL}, title = {Guts of the Urban Ecosystem: Microbial Ecology of Sewer Infrastructure.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0011822}, pmid = {35762794}, issn = {2379-5077}, support = {R01 AI091829/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Anti-Bacterial Agents ; Bacteria/genetics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; United States ; *Wastewater ; }, abstract = {Microbes have inhabited the oceans and soils for millions of years and are uniquely adapted to their habitat. In contrast, sewer infrastructure in modern cities dates back only ~150 years. Sewer pipes transport human waste and provide a view into public health, but the resident organisms that likely modulate these features are relatively unexplored. Here, we show that the bacterial assemblages sequenced from untreated wastewater in 71 U.S. cities were highly coherent at a fine sequence level, suggesting that urban infrastructure separated by great spatial distances can give rise to strikingly similar communities. Within the overall microbial community structure, temperature had a discernible impact on the distribution patterns of closely related amplicon sequence variants, resulting in warm and cold ecotypes. Two bacterial genera were dominant in most cities regardless of their size or geographic location; on average, Arcobacter accounted for 11% and Acinetobacter 10% of the entire community. Metagenomic analysis of six cities revealed these highly abundant resident organisms carry clinically important antibiotic resistant genes blaCTX-M, blaOXA, and blaTEM. In contrast, human fecal bacteria account for only ~13% of the community; therefore, antibiotic resistance gene inputs from human sources to the sewer system could be comparatively small, which will impact measurement capabilities when monitoring human populations using wastewater. With growing awareness of the metabolic potential of microbes within these vast networks of pipes and the ability to examine the health of human populations, it is timely to increase our understanding of the ecology of these systems. IMPORTANCE Sewer infrastructure is a relatively new habitat comprised of thousands of kilometers of pipes beneath cities. These wastewater conveyance systems contain large reservoirs of microbial biomass with a wide range of metabolic potential and are significant reservoirs of antibiotic resistant organisms; however, we lack an adequate understanding of the ecology or activity of these communities beyond wastewater treatment plants. The striking coherence of the sewer microbiome across the United States demonstrates that the sewer environment is highly selective for a particular microbial community composition. Therefore, results from more in-depth studies or proven engineering controls in one system could be extrapolated more broadly. Understanding the complex ecology of sewer infrastructure is critical for not only improving our ability to treat human waste and increasing the sustainability of our cities but also to create scalable and effective sewage microbial observatories, which are inevitable investments of the future to monitor health in human populations.}, } @article {pmid35762661, year = {2022}, author = {Pfenninger, M and Foucault, Q}, title = {Population Genomic Time Series Data of a Natural Population Suggests Adaptive Tracking of Fluctuating Environmental Changes.}, journal = {Integrative and comparative biology}, volume = {62}, number = {6}, pages = {1812-1826}, doi = {10.1093/icb/icac098}, pmid = {35762661}, issn = {1557-7023}, mesh = {Animals ; *Metagenomics ; Time Factors ; *Physical Conditioning, Animal ; Gene Frequency ; Selection, Genetic ; Genomics/methods ; Adaptation, Physiological/genetics ; }, abstract = {Natural populations are constantly exposed to fluctuating environmental changes that negatively affect their fitness in unpredictable ways. While theoretical models show the possibility of counteracting these environmental changes through rapid evolutionary adaptations, there have been few empirical studies demonstrating such adaptive tracking in natural populations. Here, we analyzed environmental data, fitness-related phenotyping and genomic time-series data sampled over 3 years from a natural Chironomus riparius (Diptera, Insecta) population to address this question. We show that the population's environment varied significantly on the time scale of the sampling in many selectively relevant dimensions, independently of each other. Similarly, phenotypic fitness components evolved significantly on the same temporal scale (mean 0.32 Haldanes), likewise independent from each other. The allele frequencies of 367,446 SNPs across the genome showed evidence of positive selection. Using temporal correlation of spatially coherent allele frequency changes revealed 35,574 haplotypes with more than one selected SNP. The mean selection coefficient for these haplotypes was 0.30 (s.d. = 0.68). The frequency changes of these haplotypes clustered in 46 different temporal patterns, indicating concerted, independent evolution of many polygenic traits. Nine of these patterns were strongly correlated with measured environmental variables. Enrichment analysis of affected genes suggested the implication of a wide variety of biological processes. Thus, our results suggest overall that the natural population of C. riparius tracks environmental change through rapid polygenic adaptation in many independent dimensions. This is further evidence that natural selection is pervasive at the genomic level and that evolutionary and ecological time scales may not differ at all, at least in some organisms.}, } @article {pmid35761577, year = {2022}, author = {Kothe, CI and Mohellibi, N and Renault, P}, title = {Revealing the microbial heritage of traditional Brazilian cheeses through metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {157}, number = {}, pages = {111265}, doi = {10.1016/j.foodres.2022.111265}, pmid = {35761577}, issn = {1873-7145}, mesh = {Animals ; Biodiversity ; Brazil ; *Cheese/analysis ; Food Microbiology ; *Lactobacillales/genetics ; *Lactococcus lactis/genetics ; Metagenomics ; Streptococcus thermophilus/genetics ; Yeasts ; }, abstract = {Brazilian artisanal cheeses date from the first Portuguese settlers and evolved via local factors, resulting in unique products that are now part of the patrimony and identity of different Brazilian regions. In this study, we combined several culture-independent approaches, including 16S/ITS metagenetics, assembly- and deep profiling-metagenomics to characterize the originality of the microbiota of five varieties of Brazilian artisanal cheeses from the South and Southeast regions of Brazil. Their core microbiota contained mainly lactic acid bacteria (LAB), of which Lactococcus lactis subsp. lactis was the most frequent, followed by Streptococcus thermophilus in the South region. Moreover, several samples from the Southeast region contained, as dominant LAB, two other food Streptococci belonging to a new species of the salivarius group and S. infantarius. Rinds of samples from the Southeast region were dominated by the halotolerant bacterium Corynebacterium variabile, and the yeasts Diutina catenulata, followed by Debaryomyces hansenii and Kodamaea ohmeri. Rinds from the South region contained mainly LAB due to their short ripening time, and the predominant yeast was D. hansenii. Phylogenomic analysis based on L. lactis metagenome-assembled genomes (MAGs) showed that most Brazilian strains are closely related and form a different clade from those whose genomes are available at this time, indicating that they belong to a specific group. Lastly, functional analysis showed that S. infantarius acquired a ∼ 26 kb DNA fragment from S. thermophilus starter strains that carry the LacSZ system, allowing fast lactose assimilation, an adaptation advantage for growth in milk. Finally, our study identified several areas of concern, such as the presence of somatic cell DNA and high levels of antibiotic resistance genes in several cheese microbiota, suggesting that milk from diseased animals may still be used occasionally. Overall, the data from this study highlight the potential value of the traditional and artisanal cheese production network in Brazil, and provide a metagenomic-based scheme to help manage this resource safely.}, } @article {pmid35761554, year = {2022}, author = {Sequino, G and Valentino, V and Villani, F and De Filippis, F}, title = {Omics-based monitoring of microbial dynamics across the food chain for the improvement of food safety and quality.}, journal = {Food research international (Ottawa, Ont.)}, volume = {157}, number = {}, pages = {111242}, doi = {10.1016/j.foodres.2022.111242}, pmid = {35761554}, issn = {1873-7145}, mesh = {*Food Chain ; Food Safety ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {The diffusion of high-throughput sequencing has dramatically changed the study of food microbial ecology. Amplicon-based description of the microbial community may be routinary implemented in the food industry to understand how the processing parameters and the raw material quality may affect the microbial community of the final product, as well as how the community changes during the shelf-life. In addition, application of shotgun metagenomics may represent an invaluable resource to understand the functional potential of the microbial community, identifying the presence of spoilage-associated activities or genes related to pathogenesis. Finally, retrieving Metagenome-Assembled Genomes (MAGs) of relevant species may be useful for strain-tracking along the food chain and in case of food poisoning outbreaks. This review gives an overview of the possible applications of sequencing-based approaches in the study of food microbial ecology, highlighting limitations that still prevent the spreading of these techniques to the food industry.}, } @article {pmid35761265, year = {2022}, author = {Wynendaele, E and Debunne, N and Janssens, Y and De Spiegeleer, A and Verbeke, F and Tack, L and Van Welden, S and Goossens, E and Knappe, D and Hoffmann, R and Van De Wiele, C and Laukens, D and Van Eenoo, P and Vereecke, L and Van Immerseel, F and De Wever, O and De Spiegeleer, B}, title = {The quorum sensing peptide EntF* promotes colorectal cancer metastasis in mice: a new factor in the host-microbiome interaction.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {151}, pmid = {35761265}, issn = {1741-7007}, mesh = {Amino Acids ; Animals ; *Colorectal Neoplasms ; Humans ; Mice ; *Microbiota/physiology ; Peptides ; Quorum Sensing/physiology ; }, abstract = {BACKGROUND: Colorectal cancer, one of the most common malignancies worldwide, is associated with a high mortality rate, mainly caused by metastasis. Comparative metagenome-wide association analyses of healthy individuals and cancer patients suggest a role for the human intestinal microbiota in tumor progression. However, the microbial molecules involved in host-microbe communication are largely unknown, with current studies mainly focusing on short-chain fatty acids and amino acid metabolites as potential mediators. Quorum sensing peptides are not yet considered in this context since their presence in vivo and their ability to affect host cells have not been reported so far.

RESULTS: Here, we show that EntF*, a metabolite of the quorum sensing peptide EntF produced by Enterococcus faecium, is naturally present in mice bloodstream. Moreover, by using an orthotopic mouse model, we show that EntF* promotes colorectal cancer metastasis in vivo, with metastatic lesions in liver and lung tissues. In vitro tests suggest that EntF* regulates E-cadherin expression and consequently the epithelial-mesenchymal transition, via the CXCR4 receptor. In addition, alanine-scanning analysis indicates that the first, second, sixth, and tenth amino acid of EntF* are critical for epithelial-mesenchymal transition and tumor metastasis.

CONCLUSION: Our work identifies a new class of molecules, quorum sensing peptides, as potential regulators of host-microbe interactions. We prove, for the first time, the presence of a selected quorum sensing peptide metabolite in a mouse model, and we demonstrate its effects on colorectal cancer metastasis. We believe that our work represents a starting point for future investigations on the role of microbiome in colorectal cancer metastasis and for the development of novel bio-therapeutics in other disease areas.}, } @article {pmid35761090, year = {2022}, author = {Banciu, HL and Gridan, IM and Zety, AV and Baricz, A}, title = {Asgard archaea in saline environments.}, journal = {Extremophiles : life under extreme conditions}, volume = {26}, number = {2}, pages = {21}, pmid = {35761090}, issn = {1433-4909}, support = {PN-III-P4-ID-PCE-2020-1559//Ministry of Research, Innovation and Digitization, CNCS/CCCDI - UEFISCDI/ ; }, mesh = {*Archaea ; Eukaryotic Cells/metabolism ; *Genome, Archaeal ; Metagenome ; Phylogeny ; }, abstract = {Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.}, } @article {pmid35760913, year = {2022}, author = {Liu, Y and Ji, M and Yu, T and Zaugg, J and Anesio, AM and Zhang, Z and Hu, S and Hugenholtz, P and Liu, K and Liu, P and Chen, Y and Luo, Y and Yao, T}, title = {A genome and gene catalog of glacier microbiomes.}, journal = {Nature biotechnology}, volume = {40}, number = {9}, pages = {1341-1348}, pmid = {35760913}, issn = {1546-1696}, mesh = {*Ice Cover/chemistry ; *Microbiota/genetics ; Snow/chemistry ; }, abstract = {Glaciers represent a unique inventory of microbial genetic diversity and a record of evolution. The Tibetan Plateau contains the largest area of low-latitude glaciers and is particularly vulnerable to global warming. By sequencing 85 metagenomes and 883 cultured isolates from 21 Tibetan glaciers covering snow, ice and cryoconite habitats, we present a specialized glacier microbial genome and gene catalog to archive glacial genomic and functional diversity. This comprehensive Tibetan Glacier Genome and Gene (TG2G) catalog includes 883 genomes and 2,358 metagenome-assembled genomes, which represent 968 candidate species spanning 30 phyla. The catalog also contains over 25 million non-redundant protein-encoding genes, the utility of which is demonstrated by the exploration of secondary metabolite biosynthetic potentials, virulence factor identification and global glacier metagenome comparison. The TG2G catalog is a valuable resource that enables enhanced understanding of the structure and functions of Tibetan glacial microbiomes.}, } @article {pmid35760036, year = {2023}, author = {Troci, A and Rausch, P and Waschina, S and Lieb, W and Franke, A and Bang, C}, title = {Long-Term Dietary Effects on Human Gut Microbiota Composition Employing Shotgun Metagenomics Data Analysis.}, journal = {Molecular nutrition & food research}, volume = {67}, number = {24}, pages = {e2101098}, doi = {10.1002/mnfr.202101098}, pmid = {35760036}, issn = {1613-4133}, support = {//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Feces ; Diet ; *Microbiota ; Metagenome ; Metagenomics/methods ; }, abstract = {SCOPE: The gut microbiome regulates various metabolic pathways in the host and its dysbiosis is involved in the pathogenesis of diverse diseases. One of the major factors triggering gut microbiome establishment is diet. This study aims to unravel interactions and changes between diet and gut microbiome over a period of 3 years.

METHODS AND RESULTS: This study investigates the relation between diet and the microbiome of 75 individuals over a 3-year time period. Shotgun metagenomic sequencing is performed to profile gut microbial composition and function. This study shows that there are significant changes in gut microbiome taxonomy and functional composition between two time points. Whereas microbial taxonomy is found to be highly individualized, overall microbial functions stay relatively stable. Moreover, in silico metabolic modeling of microbial communities indicates that changes in dietary intake of medium-chain saturated fatty acids is accompanied by an altered utilization of amino acids by the gut microbiome.

CONCLUSION: The study design allows us to validate functional stability within the gut microbiome of healthy subjects over a 3-year period. However, enduring changes in nutrition such as increased alcohol consumption or decreased intake of vegetables come along with enhanced microbial functions that are associated with disease etiology.}, } @article {pmid35759425, year = {2022}, author = {Muthappa, DM and Lamba, S and Sivasankaran, SK and Naithani, A and Rogers, N and Srikumar, S and Macori, G and Scannell, AGM and Fanning, S}, title = {16S rRNA Based Profiling of Bacterial Communities Colonizing Bakery-Production Environments.}, journal = {Foodborne pathogens and disease}, volume = {19}, number = {7}, pages = {485-494}, doi = {10.1089/fpd.2022.0014}, pmid = {35759425}, issn = {1556-7125}, mesh = {*Bacteria/genetics ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Conventional culture-based techniques are largely inadequate in elucidating the microbiota contained in an environment, due to low recovery within a complex bacterial community. This limitation has been mitigated by the use of next-generation sequencing (NGS)-based approaches thereby facilitating the identification and classification of both culturable and uncultivable microorganisms. Amplicon targeted NGS methods, such as 16S ribosomal RNA (16S rRNA) and shotgun metagenomics, are increasingly being applied in various settings such as in food production environments to decipher the microbial consortium therein. Even though multiple food matrices/food production environments have been studied, the low-moisture environment associated with bakery food production remains to be investigated. To address this knowledge gap, in this study, we investigated the microbiome associated with two bakery production sites (designated as A and B) located in Ireland using 16S rRNA-amplicon-based sequencing. Amplicons corresponding to a hypervariable region contained within the 16S rRNA gene were amplified from DNA samples purified from environmental swabs and ingredients collected at both sites at various stages (preparation, production, postproduction, and storage) across the bakery production chain, over three seasons (winter, spring, and summer). These amplicons were sequenced, and data were analyzed using the mothur pipeline and visualized using MicrobiomeAnalyst and a series of R packages. The top seven bacterial phyla identified at both sites were composed of Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Deinococcus-Thermus, Patescibacteria, and Verrucomicrobia. In addition, the phyla Tenericutes (Mycoplasmatota) and Acidobacteria were observed only in samples taken at site B. Different bacterial compositions were identified at each stage of production. These same bacteria were also found to be present in the final processed food suggesting the influence of the environment on the food matrix. This study is the first demonstration of the utility of 16S rRNA amplicon-based sequencing to describe the microbiota associated with bakery processing environments.}, } @article {pmid35758682, year = {2022}, author = {Li, Y and Cao, L and Ye, M and Xu, R and Chen, X and Ma, Y and Tian, RR and Liu, FL and Zhang, P and Kuang, YQ and Zheng, YT and Zhang, C}, title = {Plasma Virome Reveals Blooms and Transmission of Anellovirus in Intravenous Drug Users with HIV-1, HCV, and/or HBV Infections.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0144722}, pmid = {35758682}, issn = {2165-0497}, mesh = {*Anelloviridae ; *Drug Users ; *HIV Infections/complications ; *HIV-1/genetics ; Hepacivirus/genetics ; *Hepatitis B/complications/epidemiology ; Hepatitis B virus/genetics ; *Hepatitis C/epidemiology ; Humans ; Phylogeny ; *Substance Abuse, Intravenous/complications/epidemiology ; Virome ; }, abstract = {Intravenous drug users (IDUs) are a high-risk group for HIV-1, hepatitis C virus (HCV), and hepatitis B virus (HBV) infections, which are the leading causes of death in IDUs. However, the plasma virome of IDUs and how it is influenced by above viral infections remain unclear. Using viral metagenomics, we determined the plasma virome of IDUs and its association with HIV-1, HCV, and/or HBV infections. Compared with healthy individuals, IDUs especially those with major viral infections had higher viral abundance and diversity. Anelloviridae dominated plasma virome. Coinfections of multiple anelloviruses were common, and anelloviruses from the same genus tended to coexist together. In this study, 4,487 anellovirus ORF1 sequences were identified, including 1,620 (36.1%) with less than 69% identity to any known sequences, which tripled the current number. Compared with healthy controls (HC), more anellovirus sequences were observed in neg-IDUs, and HIV-1, HCV, and/or HBV infections further expanded the sequence number in IDUs, which was characterized by the emergence of novel divergent taxons and blooms of resident anelloviruses. Pegivirus was mainly identified in infected IDUs. Five main pegivirus transmission clusters (TCs) were identified by phylogenetic analysis, suggesting a transmission link. Similar anellovirus profiles were observed in IDUs within the same TC, suggesting transmission of anellome among IDUs. Our data suggested that IDUs suffered higher plasma viral burden especially anelloviruses, which was associated with HIV-1, HCV, and/or HBV infections. Blooms in abundance and unprecedented diversity of anellovirus highlighted active evolution and replication of this virus in blood circulation, and an uncharacterized role it may engage with the host. IMPORTANCE Virome is associated with immune status and determines or influences disease progression through both pathogenic and resident viruses. Increased viral burden in IDUs especially those with major viral infections indicated the suboptimal immune status and high infection risks of these population. Blooms in abundance and unprecedented diversity of anellovirus highlighted its active evolution and replication in the blood circulation, and sensitive response to other viral infections. In addition, transmission cluster analysis revealed the transmission link of pegivirus among IDUs, and the individuals with transmission links shared similar anellome profiles. In-depth monitoring of the plasma virome in high-risk populations is not only needed for surveillance for emerging viruses and transmission networks of major and neglected bloodborne viruses, but also important for a better understanding of commensal viruses and their role it may engage with immune system.}, } @article {pmid35753210, year = {2022}, author = {Tsai, IJ}, title = {The teenage years of yeast population genomics - trace history, admixing and getting wilder.}, journal = {Current opinion in genetics & development}, volume = {75}, number = {}, pages = {101942}, doi = {10.1016/j.gde.2022.101942}, pmid = {35753210}, issn = {1879-0380}, mesh = {Biological Evolution ; *Metagenomics ; *Saccharomyces cerevisiae/genetics ; }, abstract = {Population genomics studies the evolutionary processes that shape intraspecies genetic variations. In this review, I explore the insights into yeast population genomics that have emerged from recent advances in sequencing. Genomes of the model Saccharomyces cerevisiae and many new yeast species from around the world are being used to address various aspects of population biology, including geographical origin, the level of introgression, domestication signatures, and outcrossing frequency. New long-read sequencing has enabled a greater capacity to quantify these variations at a finer resolution from complete de novo genomes at the population scale to phasing subgenomes of different origins. These resources provide a platform to dissect the relationship between phenotypes across environmental niches.}, } @article {pmid35752737, year = {2022}, author = {Jangid, A and Fukuda, S and Seki, M and Suzuki, Y and Taylor, TD and Ohno, H and Prakash, T}, title = {Gut microbiota alternation under the intestinal epithelium-specific knockout of mouse Piga gene.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {10812}, pmid = {35752737}, issn = {2045-2322}, mesh = {Animals ; *Escherichia coli Infections/microbiology ; *Escherichia coli O157 ; *Gastrointestinal Microbiome ; Intestinal Mucosa/microbiology ; Intestines/microbiology ; Mice ; }, abstract = {Crosstalk between the gut microbiota and intestinal epithelium shapes the gut environment and profoundly influences the intestinal immune homeostasis. Glycosylphosphatidylinositol anchored proteins (GPI - APs) contribute to a variety of gut-associated immune functions, including microbial surveillance and defense, and epithelial cell polarity. Properly polarised epithelial cells are essential for the establishment of the barrier function of gut epithelia. The Piga gene is one among seven genes that encode for an enzyme which is involved in the first step of GPI-anchor biosynthesis. This is the first study reporting a knockout of the intestinal epithelial cell-specific Piga gene (Piga-/-) and its association with the gut microbiota in mice using a whole metagenome shotgun-based sequencing approach. An overall reduced microbiota diversity has been observed in the Piga-/- group as compared to the control group (ANOVA p = 0.34). The taxonomic biomarkers, namely: Gammaproteobacteria (class), Enterobacterales (order), Enterobacteriaceae (family), Escherichia (genus), Proteus (genus) and Escherichia coli (species), increased more in the Piga-/- mice as compared to in the control group. Further, the pathogenic E. coli strains, namely E. coli O157:H7 str. EDL 933 (EHEC), E. coli CFT073 (UPEC) and E. coli 536 (UPEC), were found in the Piga-/- mice which also harbored virulence factor transporters. In addition, the taxa responsible for short chain fatty acid production were decreased in the Piga-/- group. The Piga-/- mice gut harbored an increased number of microbial functions responsible for the survival of pathogens in the inflamed gut environment. Our observations clearly indicate that the Piga-/- mice gut might have an overall enhancement in pathogenic behaviour and reduced capabilities beneficial to health.}, } @article {pmid35752638, year = {2022}, author = {Lemos, LN and de Carvalho, FM and Santos, FF and Valiatti, TB and Corsi, DC and de Oliveira Silveira, AC and Gerber, A and Guimarães, APC and de Oliveira Souza, C and Brasiliense, DM and Maia Castelo-Branco, DSC and Anzai, EK and Bessa-Neto, FO and de Melo, GM and de Souza, GH and Ferraz, LFC and de Nazaré Miranda Bahia, M and Mattos, MS and da Silva, RGB and Veiga, R and Simionatto, S and Monteiro, WAP and de Oliveira Lima, WA and Kiffer, CRV and Cayô, R and Gales, AC and de Vasconcelos, ATR}, title = {Large Scale Genome-Centric Metagenomic Data from the Gut Microbiome of Food-Producing Animals and Humans.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {366}, pmid = {35752638}, issn = {2052-4463}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; Cattle ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; Metagenomics ; Swine ; }, abstract = {The One Health concept is a global strategy to study the relationship between human and animal health and the transfer of pathogenic and non-pathogenic species between these systems. However, to the best of our knowledge, no data based on One Health genome-centric metagenomics are available in public repositories. Here, we present a dataset based on a pilot-study of 2,915 metagenome-assembled genomes (MAGs) of 107 samples from the human (N = 34), cattle (N = 28), swine (N = 15) and poultry (N = 30) gut microbiomes. Samples were collected from the five Brazilian geographical regions. Of the draft genomes, 1,273 were high-quality drafts (≥90% of completeness and ≤5% of contamination), and 1,642 were medium-quality drafts (≥50% of completeness and ≤10% of contamination). Taxonomic predictions were based on the alignment and concatenation of single-marker genes, and the most representative phyla were Bacteroidota, Firmicutes, and Proteobacteria. Many of these species represent potential pathogens that have already been described or potential new families, genera, and species with potential biotechnological applications. Analyses of this dataset will highlight discoveries about the ecology and functional role of pathogens and uncultivated Archaea and Bacteria from food-producing animals and humans. Furthermore, it also represents an opportunity to describe new species from underrepresented taxonomic groups.}, } @article {pmid35751943, year = {2022}, author = {Lee, SA and Kim, M and Esterhuizen, M and Le, VV and Kang, M and Ko, SR and Oh, HM and Kim, YJ and Ahn, CY}, title = {An acceleration of carotenoid production and growth of Haematococcus lacustris induced by host-microbiota network interaction.}, journal = {Microbiological research}, volume = {262}, number = {}, pages = {127097}, doi = {10.1016/j.micres.2022.127097}, pmid = {35751943}, issn = {1618-0623}, mesh = {Acceleration ; Bacteria/genetics ; Biomass ; Carotenoids ; *Chlorophyta ; *Microbiota ; }, abstract = {Haematococcus lacustris is a chlamydomonadalean with high biotechnological interest owing to its capacity to produce astaxanthin, a valuable secondary carotenoid with extraordinary antioxidation properties. However, its prolonged growth has limited its utility commercially. Thus, rapid growth to attain high densities of H. lacustris cells optimally producing astaxanthin is an essential biotechnological target to facilitate profitable commercialisation. Our study focused on characterising the bacterial communities associated with the alga's phycosphere by metagenomics. Subsequently, we altered the bacterial consortia in combined co-culture with key beneficial bacteria to optimise the growth of H. lacustris. The algal biomass increased by up to 2.1-fold in co-cultures, leading to a 1.6-fold increase in the astaxanthin yield. This study attempted to significantly improve the H. lacustris growth rate and biomass yield via Next-Generation Sequencing analysis and phycosphere bacterial augmentation, highlighting the possibility to overcome the hurdles associated with astaxanthin production by H. lacustris at a commercial scale.}, } @article {pmid35751094, year = {2022}, author = {Fritsch, DA and Jackson, MI and Wernimont, SM and Feld, GK and MacLeay, JM and Brejda, JJ and Cochrane, CY and Gross, KL}, title = {Microbiome function underpins the efficacy of a fiber-supplemented dietary intervention in dogs with chronic large bowel diarrhea.}, journal = {BMC veterinary research}, volume = {18}, number = {1}, pages = {245}, pmid = {35751094}, issn = {1746-6148}, mesh = {Animals ; Diarrhea/veterinary ; Diet/veterinary ; Dietary Fiber/therapeutic use ; *Dog Diseases/drug therapy ; Dogs ; Feces ; Indoles ; Inflammation/veterinary ; *Microbiota ; Prospective Studies ; }, abstract = {BACKGROUND: Chronic large bowel diarrhea is a common occurrence in pet dogs. While nutritional intervention is considered the primary therapy, the metabolic and gut microfloral effects of fiber and polyphenol-enriched therapeutic foods are poorly understood.

METHODS: This prospective clinical study enrolled 31 adult dogs from private veterinary practices with chronic, active large bowel diarrhea. Enrolled dogs received a complete and balanced dry therapeutic food containing a proprietary fiber bundle for 56 days. Metagenomic and metabolomic profiling were performed on fecal samples at Days 1, 2, 3, 14, 28, and 56; metabolomic analysis was conducted on serum samples taken at Days 1, 2, 3, 28, and 56.

RESULTS: The dietary intervention improved clinical signs and had a clear effect on the gut microfloral metabolic output of canines with chronic diarrhea, shifting gut metabolism from a predominantly proteolytic to saccharolytic fermentative state. Microbial metabolism of tryptophan to beneficial indole postbiotics and the conversion of plant-derived phenolics into bioavailable postbiotics were observed. The intervention altered the endocannabinoid, polyunsaturated fatty acid, and sphingolipid profiles, suggesting a modulation in gastrointestinal inflammation. Changes in membrane phospholipid and collagen signatures were indicative of improved gut function and possible alleviation of the pathophysiology related to chronic diarrhea.

CONCLUSIONS: In dogs with chronic diarrhea, feeding specific dietary fibers increased gut saccharolysis and bioavailable phenolic and indole-related compounds, while suppressing putrefaction. These changes were associated with improved markers of gut inflammation and stool quality.}, } @article {pmid35751044, year = {2022}, author = {Maeda, Y and Motooka, D and Kawasaki, T and Oki, H and Noda, Y and Adachi, Y and Niitsu, T and Okamoto, S and Tanaka, K and Fukushima, K and Amiya, S and Hara, R and Oguro-Igashira, E and Matsuki, T and Hirata, H and Takeda, Y and Kida, H and Kumanogoh, A and Nakamura, S and Takeda, K}, title = {Longitudinal alterations of the gut mycobiota and microbiota on COVID-19 severity.}, journal = {BMC infectious diseases}, volume = {22}, number = {1}, pages = {572}, pmid = {35751044}, issn = {1471-2334}, support = {20fk0108265//Japan Agency for Medical Research and Development/ ; 18gm1010005//AMED-CREST grants/ ; }, mesh = {*COVID-19 ; Enterococcus ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; SARS-CoV-2 ; }, abstract = {BACKGROUND: The impact of SARS-CoV-2 infection on the gut fungal (mycobiota) and bacterial (microbiota) communities has been elucidated individually. This study analyzed both gut mycobiota and microbiota and their correlation in the COVID-19 patients with severe and mild conditions and follow-up to monitor their alterations after recovery.

METHODS: We analyzed the gut mycobiota and microbiota by bacterial 16S and fungal ITS1 metagenomic sequencing of 40 severe patients, 38 mild patients, and 30 healthy individuals and reanalyzed those of 10 patients with severe COVID-19 approximately 6 months after discharge.

RESULTS: The mycobiota of the severe and mild groups showed lower diversity than the healthy group, and in some, characteristic patterns dominated by a single fungal species, Candida albicans, were detected. Lower microbial diversity in the severe group was observed, but no differences in its diversity or community structure were detected between the mild and healthy groups. The microbiota of the severe group was characterized by an increase in Enterococcus and Lactobacillus, and a decrease in Faecalibacterium and Bacteroides. The abundance of Candida was positively correlated with that of Enterococcus in patients with COVID-19. After the recovery of severe patients, alteration of the microbiota remained, but the mycobiota recovered its diversity comparable to that of mild and healthy groups.

CONCLUSION: In mild cases, the microbiota is stable during SARS-CoV-2 infection, but in severe cases, alterations persist for 6 months after recovery.}, } @article {pmid35751037, year = {2022}, author = {Li, J and Zhao, Q and Huang, JP and Jia, JY and Zhu, TF and Hong, T and Su, J}, title = {The functional microbiota of on- and off-year moso bamboo (Phyllostachys edulis) influences the development of the bamboo pest Pantana phyllostachysae.}, journal = {BMC plant biology}, volume = {22}, number = {1}, pages = {307}, pmid = {35751037}, issn = {1471-2229}, mesh = {Animals ; Gene Expression Regulation, Plant ; Larva ; *Microbiota ; *Moths ; Plant Leaves ; Poaceae ; }, abstract = {BACKGROUND: Development of Pantana phyllostachysae, a moso bamboo pest, is affected by its diet. Understanding the mechanism underlying the different insect-resistant capacities of on- and off-year moso bamboo fed by P. phyllostachysae is crucial for managing pest outbreaks. As microbes were proven to influence plant immunity, we compared gut microbial communities of P. phyllostachysae with different diets by metabarcoding sequencing. By using sterilization assay, microbes were removed from leaf surfaces, and thus we confirmed that microbes inhabiting moso bamboo leaves impact the weight of P. phyllostachysae larva. Furthermore, the gut microbial communities of P. phyllostachysae fed on on- and off-year bamboo leaves were compared, to identify the functional microbial communities that impact the interaction between bamboo leaves and P. phyllostachysae.

RESULTS: We found that species from orders Lactobacillales and Rickettsiales are most effective within functional microbiota. Functional prediction revealed that gut microbes of larva fed on on-year leaves were related to naphthalene degradation, while those fed on off-year leaves were related to biosynthesis of ansamycins, polyketide sugar unit biosynthesis, metabolism of xenobiotics, and tetracycline biosynthesis. Most functional microbes are beneficial to the development of larva that feed on on-year bamboo leaves, but damage the balance of intestinal microenvironment and immune systems of those larva that feed on off-year leaves.

CONCLUSIONS: This work developed an efficient strategy for microbiome research of Lepidopteran insects and provided insights into microbiota related to the interaction between host plants and P. phyllostachysae. We provided microbial candidates for the ecological control of P. phyllostachysae according to the function of effective microbiota.}, } @article {pmid35750913, year = {2022}, author = {Rout, AK and Dehury, B and Parida, PK and Sarkar, DJ and Behera, B and Das, BK and Rai, A and Behera, BK}, title = {Taxonomic profiling and functional gene annotation of microbial communities in sediment of river Ganga at Kanpur, India: insights from whole-genome metagenomics study.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {54}, pages = {82309-82323}, pmid = {35750913}, issn = {1614-7499}, mesh = {Rivers/chemistry ; Metagenomics ; Catalase ; Geologic Sediments/chemistry ; Molecular Sequence Annotation ; Xenobiotics ; *Microbiota ; Bacteria/genetics ; Nitrogen/analysis ; Hydrolases ; Plastics ; Methane ; Coloring Agents/analysis ; Chlorobenzenes/analysis ; Sulfur ; *Environmental Pollutants/analysis ; Benzoates/analysis ; Aminobenzoates/analysis ; Mixed Function Oxygenases ; }, abstract = {The perennial river Ganga is recognized as one of India's largest rivers of India, but due to continuous anthropogenic activities, the river's ecosystem is under threat. Next-generation sequencing technology has transformed metagenomics in the exploration of microbiome and their imperative function in diverse aquatic ecosystems. In this study, we have uncovered the structure of community microbiome and their functions in sediments of river Ganga at Kanpur, India, at three polluted stretches through a high-resolution metagenomics approach using Illumina HiSeq 2500. Among the microbes, bacteria dominate more than 82% in the three polluted sediment samples of river Ganga. Pseudomonadota (alpha, beta, and gamma) is the major phylum of bacteria that dominates in three sediment samples. Genes involved in degradation of xenobiotic compounds involving nitrotoluene, benzoate, aminobenzoate, chlorocyclohexane, and chlorobenzene were significantly enriched in the microbiome of polluted stretches. Pathway analysis using KEGG database revealed a higher abundance of genes involved in energy metabolism such as oxidative phosphorylation, nitrogen, methane, sulfur, and carbon fixation pathways in the sediment metagenome data from the river Ganga. A higher abundance of pollutant degrading enzymes like 4-hydroxybenzoate 3-monooxygenase, catalase-peroxidase, and altronate hydrolase in the polluted microbiome indicates their role in degradation of plastics and dyes. Overall, our study has provided bacterial diversity and their dynamics in community structure and function from polluted river microbiome, which is expected to open up better avenues for exploration of novel functional genes/enzymes with potential application in health and bioremediation.}, } @article {pmid35750322, year = {2022}, author = {Kelly, MS and Bunyavanich, S and Phipatanakul, W and Lai, PS}, title = {The Environmental Microbiome, Allergic Disease, and Asthma.}, journal = {The journal of allergy and clinical immunology. In practice}, volume = {10}, number = {9}, pages = {2206-2217.e1}, pmid = {35750322}, issn = {2213-2201}, support = {R01 AI147028/AI/NIAID NIH HHS/United States ; U01 AI110397/AI/NIAID NIH HHS/United States ; U19 AI136053/AI/NIAID NIH HHS/United States ; U01 AI160082/AI/NIAID NIH HHS/United States ; K23 ES023700/ES/NIEHS NIH HHS/United States ; R01 AI144119/AI/NIAID NIH HHS/United States ; K24 AI106822/AI/NIAID NIH HHS/United States ; R01 AI118833/AI/NIAID NIH HHS/United States ; R38 HL150212/HL/NHLBI NIH HHS/United States ; }, mesh = {*Asthma/complications ; Environmental Exposure/adverse effects ; Humans ; *Hypersensitivity/epidemiology/etiology ; *Microbiota ; }, abstract = {The environmental microbiome represents the entirety of the microbes and their metabolites that we encounter in our environments. A growing body of evidence supports the role of the environmental microbiome in risk for and severity of allergic diseases and asthma. The environmental microbiome represents a ubiquitous, lifelong exposure to non-self antigens. During the critical window between birth and 1 year of life, interactions between our early immune system and the environmental microbiome have 2 consequences: our individual microbiome is populated by environmental microbes, and our immune system is trained regarding which antigens to tolerate. During this time, a diversity of exposures appears largely protective, dramatically decreasing the risk of developing allergic diseases and asthma. As we grow older, our interactions with the environmental microbiome change. While it continues to exert influence over the composition of the human microbiome, the environmental microbiome becomes increasingly a source for antigenic stimulation and infection. The same microbial exposure protective against disease development may exacerbate disease severity. Although much has been learned about the importance of the environmental microbiome in allergic disease, much more remains to be understood about these complicated interactions between our environment, our microbiome, our immune system, and disease.}, } @article {pmid35750287, year = {2023}, author = {Dong, C and Yang, Y and Wang, Y and Hu, X and Wang, Q and Gao, F and Sun, S and Liu, Q and Li, L and Liu, J and Tang, Y and Zhang, S and Wu, C and Zhu, H}, title = {Gut microbiota combined with metabolites reveals unique features of acute myocardial infarction patients different from stable coronary artery disease.}, journal = {Journal of advanced research}, volume = {46}, number = {}, pages = {101-112}, pmid = {35750287}, issn = {2090-1224}, mesh = {Humans ; *Coronary Artery Disease/metabolism/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Myocardial Infarction ; Biomarkers ; }, abstract = {INTRODUCTION: Acute myocardial infarction (AMI) accounts for the majority of deaths caused by coronary artery disease (CAD). Early warning of AMI, especially for patients with stable coronary artery disease (sCAD), is urgently needed. Our previous study showed that alterations in the gut microbiota were correlated with CAD severity.

OBJECTIVES: Herein, we tried to discover accurate and convenient biomarkers for AMI by combination of gut microbiota and fecal/blood/urinary metabolomics.

METHODS: We recruited 190 volunteers including 93 sCAD patients, 49 AMI patients, and 48 subjects with normal coronary artery (NCA), and measured their blood biochemical parameters, 16S rRNA-based gut microbiota and NMR-based fecal/blood/urinary metabolites. We further selected 20 subjects from each group and analyzed their gut microbiota by whole-metagenome shotgun sequencing.

RESULTS: Multi-omic analyses revealed that AMI patients exhibited specific changes in gut microbiota and serum/urinary/fecal metabolites as compared to subjects with sCAD or NCA. Fourteen bacterial genera and 30 metabolites (11 in feces, 10 in blood, 9 in urine) were closely related to AMI phenotypes and could accurately distinguish AMI patients from sCAD patients. Some species belonging to Alistipes, Streptococcus, Ruminococcus, Lactobacillus and Faecalibacterium were effective to distinguish AMI from sCAD and their predictive ability was confirmed in an independent cohort of CAD patients. We further selected nine indicators including 4 bacterial genera, 3 fecal and 2 urinary metabolites as a noninvasive biomarker set which can distinguish AMI from sCAD with an AUC of 0.932.

CONCLUSION: Combination of gut microbiota and fecal/urinary metabolites provided a set of potential useful and noninvasive predictive biomarker for AMI from sCAD.}, } @article {pmid35749534, year = {2022}, author = {Gaio, D and DeMaere, MZ and Anantanawat, K and Eamens, GJ and Falconer, L and Chapman, TA and Djordjevic, S and Darling, AE}, title = {Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig.}, journal = {PloS one}, volume = {17}, number = {6}, pages = {e0270372}, pmid = {35749534}, issn = {1932-6203}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Dysbiosis ; Female ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Phylogeny ; *Probiotics ; Swine ; Weaning ; }, abstract = {Intensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Orally administered antibiotics are well known to cause dysbiosis. To counteract dysbiotic effects, numerous studies in the past two decades sought to understand whether probiotics are a valid tool to help re-establish a healthy gut microbial community after antibiotic treatment. Although dysbiotic effects of antibiotics are well investigated, little is known about the effects of intramuscular antibiotic treatment on the gut microbiome and a few studies attempted to study treatment effects using phylogenetic diversity analysis techniques. In this study we sought to determine the effects of two probiotic- and one intramuscularly administered antibiotic treatment on the developing gut microbiome of post-weaning piglets between their 3rd and 9th week of life. Shotgun metagenomic sequences from over 800 faecal time-series samples derived from 126 post-weaning piglets and 42 sows were analysed in a phylogenetic framework. Differences between individual hosts such as breed, litter, and age, were found to be important contributors to variation in the community composition. Host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The post-weaning pig gut microbiome appeared to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life. Treatment effects of the antibiotic and probiotic treatments were found but were subtle and included a higher representation of Mollicutes associated with intramuscular antibiotic treatment, and an increase of Lactobacillus associated with probiotic treatment. The discovery of correlations between experimental factors and microbial community composition is more commonly addressed with OTU-based methods and rarely analysed via phylogenetic diversity measures. The latter method, although less intuitive than the former, suffers less from library size normalization biases, and it proved to be instrumental in this study for the discovery of correlations between microbiome composition and host-, and treatment factors.}, } @article {pmid35749527, year = {2022}, author = {Apiwatsiri, P and Pupa, P and Sirichokchatchawan, W and Sawaswong, V and Nimsamer, P and Payungporn, S and Hampson, DJ and Prapasarakul, N}, title = {Metagenomic analysis of the gut microbiota in piglets either challenged or not with enterotoxigenic Escherichia coli reveals beneficial effects of probiotics on microbiome composition, resistome, digestive function and oxidative stress responses.}, journal = {PloS one}, volume = {17}, number = {6}, pages = {e0269959}, pmid = {35749527}, issn = {1932-6203}, mesh = {Animals ; *Enterotoxigenic Escherichia coli ; *Escherichia coli Infections/prevention & control/veterinary ; *Gastrointestinal Microbiome ; *Microbiota ; Oxidative Stress ; *Probiotics/pharmacology ; Swine ; *Swine Diseases ; Weaning ; }, abstract = {This study used metagenomic analysis to investigate the gut microbiota and resistome in piglets that were or were not challenged with enterotoxigenic Escherichia coli (ETEC) and had or had not received dietary supplementation with microencapsulated probiotics. The 72 piglets belonged to six groups that were either non-ETEC challenged (groups 1-3) or ETEC challenged (receiving 5ml of 109 CFU/ml pathogenic ETEC strain L3.2 one week following weaning at three weeks of age: groups 4-6). On five occasions at 2, 5, 8, 11, and 14 days of piglet age, groups 2 and 5 were supplemented with 109 CFU/ml of multi-strain probiotics (Lactiplantibacillus plantarum strains 22F and 25F, and Pediococcus acidilactici 72N) while group 4 received 109 CFU/ml of P. acidilactici 72N. Group 3 received 300mg/kg chlortetracycline in the weaner diet to mimic commercial conditions. Rectal faecal samples were obtained for metagenomic and resistome analysis at 2 days of age, and at 12 hours and 14 days after the timing of post-weaning challenge with ETEC. The piglets were all euthanized at 42 days of age. The piglets in groups 2 and 5 were enriched with several desirable microbial families, including Lactobacillaceae, Lachnospiraceae and Ruminococcaceae, while piglets in group 3 had increases in members of the Bacteroidaceae family and exhibited an increase in tetW and tetQ genes. Group 5 had less copper and multi-biocide resistance. Mobile genetic elements IncQ1 and IncX4 were the most prevalent replicons in antibiotic-fed piglets. Only groups 6 and 3 had the integrase gene (intl) class 2 and 3 detected, respectively. The insertion sequence (IS) 1380 was prevalent in group 3. IS3 and IS30, which are connected to dietary intake, were overrepresented in group 5. Furthermore, only group 5 showed genes associated with detoxification, with enrichment of genes associated with oxidative stress, glucose metabolism, and amino acid metabolism compared to the other groups. Overall, metagenomic analysis showed that employing a multi-strain probiotic could transform the gut microbiota, reduce the resistome, and boost genes associated with food metabolism.}, } @article {pmid35743947, year = {2022}, author = {Doytchinov, VV and Dimov, SG}, title = {Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {6}, pages = {}, pmid = {35743947}, issn = {2075-1729}, support = {70-25-72 from 03.08.2021//NATIONAL CENTER FOR POLAR STUDIES - SOFIA UNIVERSITY "ST. KLIMENT OHRIDSKI"/ ; }, abstract = {Antarctica represents a unique environment, both due to the extreme meteorological and geological conditions that govern it and the relative isolation from human influences that have kept its environment largely undisturbed. However, recent trends in climate change dictate an unavoidable change in the global biodiversity as a whole, and pristine environments, such as Antarctica, allow us to study and monitor more closely the effects of the human impact. Additionally, due to its inaccessibility, Antarctica contains a plethora of yet uncultured and unidentified microorganisms with great potential for useful biological activities and production of metabolites, such as novel antibiotics, proteins, pigments, etc. In recent years, amplicon-based next-generation sequencing (NGS) has allowed for a fast and thorough examination of microbial communities to accelerate the efforts of unknown species identification. For these reasons, in this review, we present an overview of the archaea, bacteria, and fungi present on the Antarctic continent and the surrounding area (maritime Antarctica, sub-Antarctica, Southern Sea, etc.) that have recently been identified using amplicon-based NGS methods.}, } @article {pmid35741032, year = {2022}, author = {Islam, SMS and Ryu, HM and Sohn, S}, title = {Tetragenococcus halophilus Alleviates Intestinal Inflammation in Mice by Altering Gut Microbiota and Regulating Dendritic Cell Activation via CD83.}, journal = {Cells}, volume = {11}, number = {12}, pages = {}, pmid = {35741032}, issn = {2073-4409}, mesh = {Animals ; Anti-Inflammatory Agents/pharmacology ; *Colitis/drug therapy ; *Colitis, Ulcerative/drug therapy ; Dendritic Cells ; Dextran Sulfate/pharmacology ; Enterococcaceae ; *Gastrointestinal Microbiome ; Inflammation ; Mice ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Ulcerative colitis (UC) is one of the major subtypes of inflammatory bowel disease with unknown etiology. Probiotics have recently been introduced as a treatment for UC. Tetragenococcus halophilus (T. halophilus) is a lactic acid-producing bacterium that survives in environments with high salt concentrations, though little is known about its immunomodulatory function as a probiotic. The purpose of this study is to determine whether T. halophilus exerts an anti-inflammatory effect on intestinal inflammation in mice. Colitis was induced in C57BL/6J mice by feeding 4% DSS in drinking water for 7 days. T. halophilus was orally administered with DSS. Anti-inflammatory functions were subsequently evaluated by flow cytometry, qRT-PCT, and ELISA. Gut microbial composition was analyzed by 16S rRNA metagenomic analysis. DSS-induced colitis mice treated with T. halophilus showed less weight loss and significantly suppressed colonic shortening compared to DSS-induced colitis mice. T. halophilus significantly reduced the frequency of the dendritic cell activation molecule CD83 in peripheral blood leukocytes and intestinal epithelial lymphocytes. Frequencies of CD8+NK1.1+ cells decreased in mice with colitis after T. halophilus treatment and IL-1β levels were also reduced. Alteration of gut microbiota was observed in mice with colitis after administration of T. halophilus. These results suggest T. halophilus is effective in alleviating DSS-induced colitis in mice by altering immune regulation and gut microbiome compositions.}, } @article {pmid35739766, year = {2022}, author = {Yang, Y and Li, T and Liu, P and Li, H and Hu, F}, title = {The formation of specific bacterial communities contributes to the enrichment of antibiotic resistance genes in the soil plastisphere.}, journal = {Journal of hazardous materials}, volume = {436}, number = {}, pages = {129247}, doi = {10.1016/j.jhazmat.2022.129247}, pmid = {35739766}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; *Microbiota/genetics ; Microplastics ; Plastics ; Polyethylene/pharmacology ; *Soil ; }, abstract = {Soil serves as a major reservoir of both antibiotic resistance genes (ARGs) and microplastics. However, the characteristics of the antibiotic resistome in the soil plastisphere remain largely unknown. In this study, we used metagenomic approaches to reveal the changing patterns of ARGs and the bacterial community and their associations in response to three types of microplastics (light density polyethylene, LDPE; polypropylene, PP; polystyrene, PS) using particles 550 µm or 75 µm in diameter. The total ARG abundances significantly increased in the plastisphere and varied across plastic types. The LDPE plastisphere had the highest ARG total abundance and lowest Shannon diversity index, indicating that this plastic had the most severe negative impact on soil bacterial diversity. The PP plastisphere contained higher relative abundances of the pathogenic bacteria Acinetobacter johnsonii and Escherichia coli, demonstrating the higher pathogenic risk of the microbial communities enriched in the plastisphere. Specifically, multidrug resistance genes (ceoB and MuxB) co-existed with more than four microbial taxa, increasing the potential risk of ARG spread in pathogenic bacteria. These findings implied that the plastisphere acts as a hotspot for acquiring and spreading antibiotic resistance and may have long-term negative effects on the soil ecosystem and human health.}, } @article {pmid35739659, year = {2022}, author = {Li, YJ and Chuang, CH and Cheng, WC and Chen, SH and Chen, WL and Lin, YJ and Lin, CY and Shih, YH}, title = {A metagenomics study of hexabromocyclododecane degradation with a soil microbial community.}, journal = {Journal of hazardous materials}, volume = {430}, number = {}, pages = {128465}, doi = {10.1016/j.jhazmat.2022.128465}, pmid = {35739659}, issn = {1873-3336}, mesh = {Humans ; *Hydrocarbons, Brominated/analysis ; Metagenomics ; *Microbiota ; Soil ; *Soil Pollutants ; }, abstract = {Hexabromocyclododecanes (HBCDs) are globally prevalent and persistent organic pollutants (POPs) listed by the Stockholm Convention in 2013. They have been detected in many environmental media from waterbodies to Plantae and even in the human body. Due to their highly bioaccumulative characterization, they pose an urgent public health issue. Here, we demonstrate that the indigenous microbial community in the agricultural soil in Taiwan could decompose HBCDs with no additional carbon source incentive. The degradation kinetics reached 0.173 day[-1] after the first treatment and 0.104 day[-1] after second exposure. With additional C-sources, the rate constants decreased to 0.054-0.097 day[-1]. The hydroxylic debromination metabolites and ring cleavage long-chain alkane metabolites were identified to support the potential metabolic pathways utilized by the soil microbial communities. The metagenome established by Nanopore sequencing showed significant compositional alteration in the soil microbial community after the HBCD treatment. After ranking, comparing relative abundances, and performing network analyses, several novel bacterial taxa were identified to contribute to HBCD biotransformation, including Herbaspirillum, Sphingomonas, Brevundimonas, Azospirillum, Caulobacter, and Microvirga, through halogenated / aromatic compound degradation, glutathione-S-transferase, and hydrolase activity. We present a compelling and applicable approach combining metagenomics research, degradation kinetics, and metabolomics strategies, which allowed us to decipher the natural attenuation and remediation mechanisms of HBCDs.}, } @article {pmid35739345, year = {2022}, author = {Sumithra, TG and Sharma, SRK and Gayathri, S and Ebeneezar, S and Reshma, KJ and Anikuttan, KK and Narasimapallavan, GI and Rameshkumar, P and Sakthivel, M and Prabu, DL and Tamilmani, G and Vijayagopal, P and Gopalakrishnan, A}, title = {Comparative evaluation of fish larval preservation methods on microbiome profiles to aid in metagenomics research.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {12}, pages = {4719-4735}, pmid = {35739345}, issn = {1432-0614}, support = {BT/AAQ/3/SP29267/2018 dated 11/05/2020.//Department of Biotechnology, Ministry of Science and Technology, Government of India/ ; }, mesh = {Animals ; Ethanol ; Fishes ; Larva ; Metagenome ; *Metagenomics/methods ; *Microbiota/genetics ; Reproducibility of Results ; }, abstract = {Applications of microbiome research through metagenomics promise to generate microbiome manipulation strategies for improved larval survival in aquaculture. However, existing lacunae on the effects of sample preservation methods in metagenome profiles hinder the successful application of this technique. In this context, four preservation methods were scrutinized to identify reliable methods for fish larval microbiome research. The results showed that a total of ten metagenomics metrics, including DNA yield, taxonomic and functional microbiome profiles, and diversity measures, were significantly (P < 0.05) influenced by the preservation method. Activity ranking based on the performance and reproducibility showed that three methods, namely immediate direct freezing, room temperature preservation in absolute ethanol, and preservation at - 20 °C in lysis, storage, and transportation buffer, could be recommended for larval microbiome research. Furthermore, as there was an apparent deviation of the microbiome profiles of ethanol preserved samples at room temperature, the other methods are preferred. Detailed analysis showed that this deviation was due to the bias towards Vibrionales and Rhodobacterales. The microbial taxa responsible for the dissimilarity across different methods were identified. Altogether, the paper sheds light on the preservation protocols of fish larval microbiome research for the first time. The results can help in cross-comparison of future and past larval microbiome studies. Furthermore, this is the first report on the activity ranking of preservation methods based on metagenomics metrics. Apart from methodological perspectives, the paper provides for the first time certain insights into larval microbial profiles of Rachycentron canadum, a potential marine aquaculture species. KEY POINTS: • First report on effects of preservation methods on fish larval microbiome profiles. • First report on activity ranking of preservation methods based on metagenomics metrics. • Storage methods influenced DNA yield, taxonomic and functional microbiome profiles.}, } @article {pmid35732881, year = {2022}, author = {Imai, Y and Lee, SW and Sakaguchi, S and Kato-Kogoe, N and Taniguchi, K and Omori, M and Tanaka, R and Honda, K and Osumi, W and Nakano, T and Ueno, T and Uchiyama, K}, title = {Comparison of the gastric microbiome in Billroth I and Roux-en-Y reconstructions after distal gastrectomy.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {10594}, pmid = {35732881}, issn = {2045-2322}, mesh = {Anastomosis, Roux-en-Y ; Gastrectomy ; Gastroenterostomy ; *Gastrointestinal Microbiome ; Humans ; Postoperative Complications/surgery ; *Stomach Neoplasms/surgery ; Treatment Outcome ; }, abstract = {The changes in gastric microbiota following reconstruction after gastrectomy have not been reported. This study aimed to compare the gastric microbiota following Billroth I and Roux-en-Y reconstructions after distal gastrectomy. We enrolled 71 gastrectomized patients with gastric cancer; 31 and 40 underwent Billroth I and Roux-en-Y reconstructions, respectively. During upper gastrointestinal endoscopy, gastric fluid was collected immediately before and 6 months after distal gastrectomy. Deoxyribonucleic acid isolated from each sample was evaluated using 16S ribosomal ribonucleic acid metagenomic analysis. Analysis revealed that the gastric microbiota's species richness (expressed as the alpha diversity) was significantly lower after than before distal gastrectomy (operational taxonomic units, p = 0.001; Shannon index, p = 0.03). The interindividual diversity (beta diversity) was significantly different before and after distal gastrectomy (unweighted UniFrac distances, p = 0.04; weighted UniFrac distances, p = 0.001; Bray-Curtis, p = 0.001). Alpha and beta diversity were not significantly different between Billroth I and Roux-en-Y reconstructions (observed operational taxonomic units, p = 0.58; Shannon index, p = 0.95; unweighted UniFrac distances, p = 0.65; weighted UniFrac distances, p = 0.67; Bray-Curtis, p = 0.63). Our study demonstrated significant differences in gastric microbiota diversity, composition, and community before and after distal gastrectomy but no difference between Billroth I and Roux-en-Y reconstruction after distal gastrectomy.}, } @article {pmid35730934, year = {2022}, author = {Morris, MM and Kimbrel, JA and Geng, H and Tran-Gyamfi, MB and Yu, ET and Sale, KL and Lane, TW and Mayali, X}, title = {Bacterial Community Assembly, Succession, and Metabolic Function during Outdoor Cultivation of Microchloropsis salina.}, journal = {mSphere}, volume = {7}, number = {4}, pages = {e0023122}, pmid = {35730934}, issn = {2379-5042}, mesh = {*Biofuels ; Biomass ; Metagenome ; *Microbiota ; Symbiosis ; }, abstract = {Outdoor cultivation of microalgae has promising potential for renewable bioenergy, but there is a knowledge gap on the structure and function of the algal microbiome that coinhabits these ecosystems. Here, we describe the assembly mechanisms, taxonomic structure, and metabolic potential of bacteria associated with Microchloropsis salina cultivated outdoors. Open mesocosms were inoculated with algal cultures that were either free of bacteria or coincubated with one of two different strains of alga-associated bacteria and were sampled across five time points taken over multiple harvesting rounds of a 40-day experiment. Using quantitative analyses of metagenome-assembled genomes (MAGs), we tracked bacterial community compositional abundance and taxon-specific functional capacity involved in algal-bacterial interactions. One of the inoculated bacteria (Alteromonas sp.) persisted and dispersed across mesocosms, whereas the other inoculated strain (Phaeobacter gallaeciensis) disappeared by day 17 while a taxonomically similar but functionally distinct Phaeobacter strain became established. The inoculated strains were less abundant than 6 numerically dominant newly recruited taxa with functional capacities for mutualistic or saprophytic lifestyles, suggesting a generalist approach to persistence. This includes a highly abundant unclassified Rhodobacteraceae species that fluctuated between 25% and 77% of the total community. Overall, we did not find evidence for priority effects exerted by the distinct inoculum conditions; all mesocosms converged with similar microbial community compositions by the end of the experiment. Instead, we infer that the 15 total populations were retained due to host selection, as they showed high metabolic potential for algal-bacterial interactions such as recycling alga-produced carbon and nitrogen and production of vitamins and secondary metabolites associated with algal growth and senescence, including B vitamins, tropodithietic acid, and roseobacticides. IMPORTANCE Bacteria proliferate in nutrient-rich aquatic environments, including engineered algal biofuel systems, where they remineralize photosynthates, exchange secondary metabolites with algae, and can influence system output of biomass or oil. Despite this, knowledge on the microbial ecology of algal cultivation systems is lacking, and the subject is worthy of investigation. Here, we used metagenomics to characterize the metabolic capacities of the predominant bacteria associated with the biofuel-relevant microalga Microchloropsis salina and to predict testable metabolic interactions between algae and manipulated communities of bacteria. We identified a previously undescribed and uncultivated organism that dominated the community. Collectively, the microbial community may interact with the alga in cultivation via exchange of secondary metabolites which could affect algal success, which we demonstrate as a possible outcome from controlled experiments with metabolically analogous isolates. These findings address the scalability of lab-based algal-bacterial interactions through to cultivation systems and more broadly provide a framework for empirical testing of genome-based metabolic predictions.}, } @article {pmid35729161, year = {2022}, author = {Zhang, L and Jonscher, KR and Zhang, Z and Xiong, Y and Mueller, RS and Friedman, JE and Pan, C}, title = {Islet autoantibody seroconversion in type-1 diabetes is associated with metagenome-assembled genomes in infant gut microbiomes.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3551}, pmid = {35729161}, issn = {2041-1723}, support = {R01 AT011618/AT/NCCIH NIH HHS/United States ; }, mesh = {Autoantibodies ; Child ; *Diabetes Mellitus, Type 1/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Metagenome/genetics ; Metagenomics/methods ; *Microbiota ; Seroconversion ; }, abstract = {The immune system of some genetically susceptible children can be triggered by certain environmental factors to produce islet autoantibodies (IA) against pancreatic β cells, which greatly increases their risk for Type-1 diabetes. An environmental factor under active investigation is the gut microbiome due to its important role in immune system education. Here, we study gut metagenomes that are de-novo-assembled in 887 at-risk children in the Environmental Determinants of Diabetes in the Young (TEDDY) project. Our results reveal a small set of core protein families, present in >50% of the subjects, which account for 64% of the sequencing reads. Time-series binning generates 21,536 high-quality metagenome-assembled genomes (MAGs) from 883 species, including 176 species that hitherto have no MAG representation in previous comprehensive human microbiome surveys. IA seroconversion is positively associated with 2373 MAGs and negatively with 1549 MAGs. Comparative genomics analysis identifies lipopolysaccharides biosynthesis in Bacteroides MAGs and sulfate reduction in Anaerostipes MAGs as functional signatures of MAGs with positive IA-association. The functional signatures in the MAGs with negative IA-association include carbohydrate degradation in lactic acid bacteria MAGs and nitrate reduction in Escherichia MAGs. Overall, our results show a distinct set of gut microorganisms associated with IA seroconversion and uncovered the functional genomics signatures of these IA-associated microorganisms.}, } @article {pmid35727547, year = {2022}, author = {Cowart, DA and Murphy, KR and Cheng, CC}, title = {Environmental DNA from Marine Waters and Substrates: Protocols for Sampling and eDNA Extraction.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2498}, number = {}, pages = {225-251}, pmid = {35727547}, issn = {1940-6029}, mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/methods ; *DNA, Environmental/genetics ; Ecosystem ; Environmental Monitoring/methods ; Metagenomics/methods ; }, abstract = {Environmental DNA (eDNA) analysis has emerged in recent years as a powerful tool for the detection, monitoring, and characterization of aquatic metazoan communities, including vulnerable species. The rapid rate of adopting the eDNA approach across diverse habitats and taxonomic groups attests to its value for a wide array of investigative goals, from understanding natural or changing biodiversity to informing on conservation efforts at local and global scales. Regardless of research objectives, eDNA workflows commonly include the following essential steps: environmental sample acquisition, processing and preservation of samples, and eDNA extraction, followed by eDNA sequencing library preparation, high-capacity sequencing and sequence data analysis, or other methods of genetic detection. In this chapter, we supply instructional details for the early steps in the workflow to facilitate researchers considering adopting eDNA analysis to address questions in marine environments. Specifically, we detail sampling, preservation, extraction, and quantification protocols for eDNA originating from marine water, shallow substrates, and deeper sediments. eDNA is prone to degradation and loss, and to contamination through improper handling; these factors crucially influence the outcome and validity of an eDNA study. Thus, we also provide guidance on avoiding these pitfalls. Following extraction, purified eDNA is often sequenced on massively parallel sequencing platforms for comprehensive faunal diversity assessment using a metabarcoding or metagenomic approach, or for the detection and quantification of specific taxa by qPCR methods. These components of the workflow are project-specific and thus not included in this chapter. Instead, we briefly touch on the preparation of eDNA libraries and discuss comparisons between sequencing approaches to aid considerations in project design.}, } @article {pmid35727019, year = {2022}, author = {Sun, S and Wang, H and Howard, AG and Zhang, J and Su, C and Wang, Z and Du, S and Fodor, AA and Gordon-Larsen, P and Zhang, B}, title = {Loss of Novel Diversity in Human Gut Microbiota Associated with Ongoing Urbanization in China.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0020022}, pmid = {35727019}, issn = {2379-5077}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 HD030880/HD/NICHD NIH HHS/United States ; R01 DK104371/DK/NIDDK NIH HHS/United States ; R01 AG065357/AG/NIA NIH HHS/United States ; P2C HD050924/HD/NICHD NIH HHS/United States ; D43 TW009077/TW/FIC NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Urbanization ; Bacteria/genetics ; *Microbiota ; Metagenome/genetics ; }, abstract = {Recent rapid and large-scale urbanization has had a profound impact on human lifestyles and is associated with an increased risk of many diseases. Recent studies have revealed large differences in the human gut microbiota across populations in countries at different stages of urbanization. However, few studies have analyzed the impact of ongoing urbanization within the same geographic region. In this study, we sampled 214 participants in communities of different urbanization levels within two provinces of China and reconstructed draft prokaryotic genomes with metagenome sequences. The genomes were clustered into 447 species-level operational taxonomic units (OTUs), among which 196 did not have genomes in public reference databases according to the GTDB-Tk pipeline. The novel OTUs comprised 19.1% abundance in rural participants and 16.0% in urban participants, increasing the proportion of classified reads from 47.6% to 65.3% across all samples. Among the unknown OTUs, 26 OTUs present in rural samples were absent in urban participants, while 70 unknown OTUs were more abundant in rural than urban participants, suggesting potential loss and growth suppression of novel human symbionts during urbanization. Moreover, there were a higher number of genes, especially transporters, identified in genomes assembled from urban samples. This change in gene functionality indicates that urbanization not only altered the community structure of the human gut microbiota but also impacted its functional capacity. Taken together, these data show a dramatic change in the microbiota with urbanization and suggest the importance of cataloging microbial diversity from rural populations while these communities still exist. IMPORTANCE Previous studies have reported the differences in human gut microbiota across populations of different urbanization levels, but most of the studies focused on populations across different geographic regions. In this study, we analyzed the impact of ongoing urbanization in neighborhoods within the same geographic region. By assembling shotgun metagenome sequences, we reconstructed prokaryotic genomes from human gut microbiota and found that the novel bacterial OTUs were less abundant and less prevalent in urban participants than in rural participants, indicating potential loss and suppression of novel human symbionts during urbanization. Genes, including transporters and antibiotic resistance genes, were enriched in genomes of urban origins, suggesting change in functional potential of the microbiota. These findings suggest the significant influence of urbanization on human gut microbiota and the necessity of exploring the microbial diversity of rural populations.}, } @article {pmid35726918, year = {2022}, author = {Brumfield, KD and Leddy, M and Usmani, M and Cotruvo, JA and Tien, CT and Dorsey, S and Graubics, K and Fanelli, B and Zhou, I and Registe, N and Dadlani, M and Wimalarante, M and Jinasena, D and Abayagunawardena, R and Withanachchi, C and Huq, A and Jutla, A and Colwell, RR}, title = {Microbiome Analysis for Wastewater Surveillance during COVID-19.}, journal = {mBio}, volume = {13}, number = {4}, pages = {e0059122}, pmid = {35726918}, issn = {2150-7511}, support = {R01 ES030317/ES/NIEHS NIH HHS/United States ; }, mesh = {*COVID-19/epidemiology ; COVID-19 Testing ; Humans ; *Microbiota ; RNA, Viral/analysis/genetics ; SARS-CoV-2/genetics ; Wastewater ; Wastewater-Based Epidemiological Monitoring ; }, abstract = {Wastewater surveillance (WS), when coupled with advanced molecular techniques, offers near real-time monitoring of community-wide transmission of SARS-CoV-2 and allows assessing and mitigating COVID-19 outbreaks, by evaluating the total microbial assemblage in a community. Composite wastewater samples (24 h) were collected weekly from a manhole between December 2020 and November 2021 in Maryland, USA. RT-qPCR results showed concentrations of SARS-CoV-2 RNA recovered from wastewater samples reflected incidence of COVID-19 cases. When a drastic increase in COVID-19 was detected in February 2021, samples were selected for microbiome analysis (DNA metagenomics, RNA metatranscriptomics, and targeted SARS-CoV-2 sequencing). Targeted SARS-CoV-2 sequencing allowed for detection of important genetic mutations, such as spike: K417N, D614G, P681H, T716I, S982A, and D1118H, commonly associated with increased cell entry and reinfection. Microbiome analysis (DNA and RNA) provided important insight with respect to human health-related factors, including detection of pathogens and their virulence/antibiotic resistance genes. Specific microbial species comprising the wastewater microbiome correlated with incidence of SARS-CoV-2 RNA, suggesting potential association with SARS-CoV-2 infection. Climatic conditions, namely, temperature, were related to incidence of COVID-19 and detection of SARS-CoV-2 in wastewater, having been monitored as part of an environmental risk score assessment carried out in this study. In summary, the wastewater microbiome provides useful public health information, and hence, a valuable tool to proactively detect and characterize pathogenic agents circulating in a community. In effect, metagenomics of wastewater can serve as an early warning system for communicable diseases, by providing a larger source of information for health departments and public officials. IMPORTANCE Traditionally, testing for COVID-19 is done by detecting SARS-CoV-2 in samples collected from nasal swabs and/or saliva. However, SARS-CoV-2 can also be detected in feces of infected individuals. Therefore, wastewater samples can be used to test all individuals of a community contributing to the sewage collection system, i.e., the infrastructure, such as gravity pipes, manholes, tanks, lift stations, control structures, and force mains, that collects used water from residential and commercial sources and conveys the flow to a wastewater treatment plant. Here, we profile community wastewater collected from a manhole, detect presence of SARS-CoV-2, identify genetic mutations of SARS-CoV-2, and perform COVID-19 risk score assessment of the study area. Using metagenomics analysis, we also detect other microorganisms (bacteria, fungi, protists, and viruses) present in the samples. Results show that by analyzing all microorganisms present in wastewater, pathogens circulating in a community can provide an early warning for contagious diseases.}, } @article {pmid35726867, year = {2022}, author = {Choo, C and Mahurkar-Joshi, S and Dong, TS and Lenhart, A and Lagishetty, V and Jacobs, JP and Labus, JS and Jaffe, N and Mayer, EA and Chang, L}, title = {Colonic mucosal microbiota is associated with bowel habit subtype and abdominal pain in patients with irritable bowel syndrome.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {323}, number = {2}, pages = {G134-G143}, pmid = {35726867}, issn = {1522-1547}, support = {R21 DK104078/DK/NIDDK NIH HHS/United States ; P30 DK041301/DK/NIDDK NIH HHS/United States ; P50 DK064539/DK/NIDDK NIH HHS/United States ; IK2 CX001717/CX/CSRD VA/United States ; UL1 TR001881/TR/NCATS NIH HHS/United States ; }, mesh = {Abdominal Pain/etiology ; Constipation ; Diarrhea ; Feces ; Habits ; Humans ; Intestinal Mucosa/pathology ; *Irritable Bowel Syndrome ; *Microbiota ; Prevotella ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Mucosal microbiota differ significantly from fecal microbiota and may play a different role in the pathophysiology of irritable bowel syndrome (IBS). The aims of this study were to determine if the composition of mucosal microbiota differed between IBS, or IBS bowel habit (BH) subtypes, and healthy controls (HCs). Sigmoid colon mucosal biopsies were obtained from 97 Rome-positive patients with IBS (28% IBS-constipation, 38% IBS-diarrhea, 24% IBS-mixed, and 10% IBS-unsubtyped) and 54 HCs, from which DNA was extracted. 16S rRNA gene sequencing and microbial composition analysis were performed. Group differences in α and β diversity and taxonomic level differences were determined using linear regression while controlling for confounding variables. IBS BH subtype was associated with microbial α diversity (P = 0.0003) with significant differences seen in the mucosal microbiota of IBS-constipation versus IBS-diarrhea (P = 0.046). There were no significant differences in α or β diversity in the mucosal microbiota of IBS versus HCs (P = 0.29 and 0.93, respectively), but metagenomic profiling suggested functional differences. The relative abundance of Prevotella_9 copri within IBS was significantly correlated with increased abdominal pain (r = 0.36, P = 0.0003), which has not been previously reported in IBS. Significant differences in the mucosal microbiota were present within IBS BH subtypes but not between IBS and HCs, supporting the possibility of IBS BH subtype-specific pathogenesis. Increased Prevotella copri may contribute to symptoms in patients with IBS.NEW & NOTEWORTHY Gut mucosal microbiota differs significantly from fecal microbiota in irritable bowel syndrome (IBS) and may play a different role in its pathophysiology. Investigation of colonic mucosal microbiota in the largest cohort of patients with IBS and healthy controls accounting for confounding variables, including diet demonstrated significant differences in mucosal microbiota between IBS bowel habit subtypes but not between IBS and healthy controls. In addition, the study reported gut microbiota is associated with abdominal pain in patients with IBS.}, } @article {pmid35725732, year = {2022}, author = {Odrzywolek, K and Karwowska, Z and Majta, J and Byrski, A and Milanowska-Zabel, K and Kosciolek, T}, title = {Deep embeddings to comprehend and visualize microbiome protein space.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {10332}, pmid = {35725732}, issn = {2045-2322}, mesh = {Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Proteins/genetics ; }, abstract = {Understanding the function of microbial proteins is essential to reveal the clinical potential of the microbiome. The application of high-throughput sequencing technologies allows for fast and increasingly cheaper acquisition of data from microbial communities. However, many of the inferred protein sequences are novel and not catalogued, hence the possibility of predicting their function through conventional homology-based approaches is limited, which indicates the need for further research on alignment-free methods. Here, we leverage a deep-learning-based representation of proteins to assess its utility in alignment-free analysis of microbial proteins. We trained a language model on the Unified Human Gastrointestinal Protein catalogue and validated the resulting protein representation on the bacterial part of the SwissProt database. Finally, we present a use case on proteins involved in SCFA metabolism. Results indicate that the deep learning model manages to accurately represent features related to protein structure and function, allowing for alignment-free protein analyses. Technologies that contextualize metagenomic data are a promising direction to deeply understand the microbiome.}, } @article {pmid35724776, year = {2022}, author = {Chang, J and van Veen, JA and Tian, C and Kuramae, EE}, title = {A review on the impact of domestication of the rhizosphere of grain crops and a perspective on the potential role of the rhizosphere microbial community for sustainable rice crop production.}, journal = {The Science of the total environment}, volume = {842}, number = {}, pages = {156706}, doi = {10.1016/j.scitotenv.2022.156706}, pmid = {35724776}, issn = {1879-1026}, mesh = {Crop Production ; Crops, Agricultural/microbiology ; Domestication ; Edible Grain ; *Microbiota ; *Mycorrhizae ; *Oryza/microbiology ; Plant Roots/microbiology ; Rhizosphere ; Soil Microbiology ; }, abstract = {The rhizosphere-associated microbiome impacts plant performance and tolerance to abiotic and biotic stresses. Despite increasing recognition of the enormous functional role of the rhizomicrobiome on the survival of wild plant species growing under harsh environmental conditions, such as nutrient, water, temperature, and pathogen stresses, the utilization of the rhizosphere microbial community in domesticated rice production systems has been limited. Better insight into how this role of the rhizomicrobiome for the performance and survival of wild plants has been changed during domestication and development of present domesticated crops, may help to assess the potential of the rhizomicrobial community to improve the sustainable production of these crops. Here, we review the current knowledge of the effect of domestication on the microbial rhizosphere community of rice and other crops by comparing its diversity, structure, and function in wild versus domesticated species. We also examine the existing information on the impact of the plant on their physico-chemical environment. We propose that a holobiont approach should be explored in future studies by combining detailed analysis of the dynamics of the physicochemical microenvironment surrounding roots to systematically investigate the microenvironment-plant-rhizomicrobe interactions during rice domestication, and suggest focusing on the use of beneficial microbes (arbuscular mycorrhizal fungi and Nitrogen fixers), denitrifiers and methane consumers to improve the sustainable production of rice.}, } @article {pmid35723062, year = {2022}, author = {Chitcharoen, S and Sivapornnukul, P and Payungporn, S}, title = {Revolutionized virome research using systems microbiology approaches.}, journal = {Experimental biology and medicine (Maywood, N.J.)}, volume = {247}, number = {13}, pages = {1135-1147}, pmid = {35723062}, issn = {1535-3699}, mesh = {Metagenomics ; *Microbiota ; Virome/genetics ; *Viruses/genetics ; }, abstract = {Currently, both pathogenic and commensal viruses are continuously being discovered and acknowledged as ubiquitous components of microbial communities. The advancements of systems microbiological approaches have changed the face of virome research. Here, we focus on viral metagenomic approach to study virus community and their interactions with other microbial members as well as their hosts. This review also summarizes challenges, limitations, and benefits of the current virome approaches. Potentially, the studies of virome can be further applied in various biological and clinical fields.}, } @article {pmid35720380, year = {2022}, author = {Patterson, GT and Osorio, EY and Peniche, A and Dann, SM and Cordova, E and Preidis, GA and Suh, JH and Ito, I and Saldarriaga, OA and Loeffelholz, M and Ajami, NJ and Travi, BL and Melby, PC}, title = {Pathologic Inflammation in Malnutrition Is Driven by Proinflammatory Intestinal Microbiota, Large Intestine Barrier Dysfunction, and Translocation of Bacterial Lipopolysaccharide.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {846155}, pmid = {35720380}, issn = {1664-3224}, support = {K08 DK113114/DK/NIDDK NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; T32 AI007526/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria ; Cecum/microbiology ; *Gastrointestinal Diseases ; *Gastrointestinal Microbiome ; Inflammation ; *Intestinal Diseases ; Lipopolysaccharides ; *Malnutrition ; Mice ; Weight Loss ; }, abstract = {Acute malnutrition, or wasting, is implicated in over half of all deaths in children under five and increases risk of infectious disease. Studies in humans and preclinical models have demonstrated that malnutrition is linked to an immature intestinal microbiota characterized by increased prevalence of Enterobacteriaceae. Observational studies in children with moderate acute malnutrition (MAM) have also observed heightened systemic inflammation and increased circulating bacterial lipopolysaccharides (LPS; endotoxin). However, the mechanisms that underpin the systemic inflammatory state and endotoxemia, and their pathophysiological consequences, remain uncertain. Understanding these pathophysiological mechanisms is necessary to design targeted treatments that will improve the unacceptable rate of failure or relapse that plague current approaches. Here we use a mouse model of MAM to investigate the mechanisms that promote inflammation in the malnourished host. We found that mice with MAM exhibited increased systemic inflammation at baseline, increased translocation of bacteria and bacterial LPS, and an exaggerated response to inflammatory stimuli. An exaggerated response to bacterial LPS was associated with increased acute weight loss. Remarkably, intestinal inflammation and barrier dysfunction was found in the cecum and colon. The cecum showed a dysbiotic microbiota with expansion of Gammaproteobacteria and some Firmicutes, and contraction of Bacteroidetes. These changes were paralleled by an increase in fecal LPS bioactivity. The inflammatory phenotype and weight loss was modulated by oral administration of non-absorbable antibiotics that altered the proportion of cecal Gammaproteobacteria. We propose that the heightened inflammation of acute malnutrition is the result of changes in the intestinal microbiota, intestinal barrier dysfunction in the cecum and colon, and increased systemic exposure to LPS.}, } @article {pmid35719363, year = {2022}, author = {Xue, J and Dominguez Rieg, JA and Thomas, L and White, JR and Rieg, T}, title = {Intestine-Specific NHE3 Deletion in Adulthood Causes Microbial Dysbiosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {896309}, pmid = {35719363}, issn = {2235-2988}, support = {I01 BX004968/BX/BLRD VA/United States ; R01 DK110621/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Animals ; Bacteroidetes ; Dysbiosis/microbiology ; Firmicutes ; *Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases/microbiology ; Intestines/microbiology ; Mice ; Sodium-Hydrogen Exchanger 3/genetics ; }, abstract = {In the intestine, the Na[+]/H[+] exchanger 3 (NHE3) plays a critical role for Na[+] and fluid absorption. NHE3 deficiency predisposes patients to inflammatory bowel disease (IBD). In mice, selective deletion of intestinal NHE3 causes various local and systemic pathologies due to dramatic changes in the intestinal environment, which can influence microbiota colonization. By using metagenome shotgun sequencing, we determined the effect of inducible intestinal epithelial cell-specific deletion of NHE3 (NHE3[IEC-KO]) in adulthood on the gut microbiome in mice. Compared with control mice, NHE3[IEC-KO] mice show a significantly different gut microbiome signature, with an unexpected greater diversity. At the phylum level, NHE3[IEC-KO] mice showed a significant expansion in Proteobacteria and a tendency for lower Firmicutes/Bacteroidetes (F/B) ratio, an indicator of dysbiosis. At the family level, NHE3[IEC-KO] mice showed significant expansions in Bacteroidaceae, Rikenellaceae, Tannerellaceae, Flavobacteriaceae and Erysipelotrichaceae, but had contractions in Lachnospiraceae, Prevotellaceae and Eubacteriaceae. At the species level, after removing those with lowest occurrence and abundance, we identified 23 species that were significantly expanded (several of which are established pro-inflammatory pathobionts); whereas another 23 species were found to be contracted (some of which are potential anti-inflammatory probiotics) in NHE3[IEC-KO] mice. These results reveal that intestinal NHE3 deletion creates an intestinal environment favoring the competitive advantage of inflammophilic over anti-inflammatory species, which is commonly featured in conventional NHE3 knockout mice and patients with IBD. In conclusion, our study emphasizes the importance of intestinal NHE3 for gut microbiota homeostasis, and provides a deeper understanding regarding interactions between NHE3, dysbiosis, and IBD.}, } @article {pmid35719350, year = {2022}, author = {Shin, J and Li, T and Zhu, L and Wang, Q and Liang, X and Li, Y and Wang, X and Zhao, S and Li, L and Li, Y}, title = {Obese Individuals With and Without Phlegm-Dampness Constitution Show Different Gut Microbial Composition Associated With Risk of Metabolic Disorders.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {859708}, pmid = {35719350}, issn = {2235-2988}, mesh = {Bacteria/genetics ; *Diabetes Mellitus, Type 2/complications ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Obesity/complications/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Obesity is conventionally considered a risk factor for multiple metabolic diseases, such as dyslipidemia, type 2 diabetes, hypertension, and cardiovascular disease (CVD). However, not every obese patient will progress to metabolic disease. Phlegm-dampness constitution (PDC), one of the nine TCM constitutions, is considered a high-risk factor for obesity and its complications. Alterations in the gut microbiota have been shown to drive the development and progression of obesity and metabolic disease, however, key microbial changes in obese patients with PDC have a higher risk for metabolic disorders remain elusive.

METHODS: We carried out fecal 16S rRNA gene sequencing in the present study, including 30 obese subjects with PDC (PDC), 30 individuals without PDC (non-PDC), and 30 healthy controls with balanced constitution (BC). Metagenomic functional prediction of bacterial taxa was achieved using PICRUSt.

RESULTS: Obese individuals with PDC had higher BMI, waist circumference, hip circumference, and altered composition of their gut microbiota compared to non-PDC obese individuals. At the phylum level, the gut microbiota was characterized by increased abundance of Bacteroidetes and decreased levels of Firmicutes and Firmicutes/Bacteroidetes ratio. At the genus level, Faecalibacterium, producing short-chain fatty acid, achieving anti-inflammatory effects and strengthening intestinal barrier functions, was depleted in the PDC group, instead, Prevotella was enriched. Most PDC-associated bacteria had a stronger correlation with clinical indicators of metabolic disorders rather than more severe obesity. The PICRUSt analysis demonstrated 70 significantly different microbiome community functions between the two groups, which were mainly involved in carbohydrate and amino acid metabolism, such as promoting Arachidonic acid metabolism, mineral absorption, and Lipopolysaccharide biosynthesis, reducing Arginine and proline metabolism, flavone and flavonol biosynthesis, Glycolysis/Gluconeogenesis, and primary bile acid biosynthesis. Furthermore, a disease classifier based on microbiota was constructed to accurately discriminate PDC individuals from all obese people.

CONCLUSION: Our study shows that obese individuals with PDC can be distinguished from non-PDC obese individuals based on gut microbial characteristics. The composition of the gut microbiome altered in obese with PDC may be responsible for their high risk of metabolic diseases.}, } @article {pmid35719339, year = {2022}, author = {Xi, Y and Liu, F and Qiu, B and Li, Y and Xie, X and Guo, J and Wu, L and Liang, T and Wang, D and Wang, J and Chen, M and Xue, L and Ding, Y and Zhang, J and Wu, Q and Liu, H}, title = {Analysis of Gut Microbiota Signature and Microbe-Disease Progression Associations in Locally Advanced Non-Small Cell Lung Cancer Patients Treated With Concurrent Chemoradiotherapy.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {892401}, pmid = {35719339}, issn = {2235-2988}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; *Carcinoma, Non-Small-Cell Lung/drug therapy/genetics ; Chemoradiotherapy ; *Diabetes Mellitus, Type 2 ; Disease Progression ; Fatty Acids ; *Gastrointestinal Microbiome/genetics ; Humans ; *Lung Neoplasms/drug therapy/genetics ; Retrospective Studies ; }, abstract = {PURPOSE: To evaluate the association of gut microbiome signature and disease progression in locally advanced non-small cell lung cancer (LA-NSCLC) patients treated with concurrent chemoradiotherapy (CCRT) by fecal metagenome analysis.

METHODS: Metagenome-wide association studies on baseline fecal samples from 18 LA-NSCLC patients before CCRT and 13 controls from healthy first-degree relatives were performed. Among the 18 LA-NSCLC patients, six patients were defined as the long progression-free survival (long-PFS) group (PFS≥11 months) while another 12 were in the short-PFS group (PFS<11 months). Alpha diversity, taxonomic composition, and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways were compared between groups.

RESULTS: The Firmicutes/Bacteroidetes value of long-PFS group was higher than those of short-PFS (p=0.073) and healthy individual groups (p=0.009). Meanwhile, long-PFS group had significantly higher diversities in Fungi, Archaea, and Viruses than short-PFS group. The KEGG pathways overrepresented in short-PFS group included fructose and mannose metabolism (p=0.028), streptomycin biosynthesis (p=0.028), acarbose and validamycin biosynthesis (p=0.013), ribosome biogenesis in eukaryotes (p=0.035), biosynthesis of vancomycin group antibiotics (p=0.004), apoptosis-fly (p=0.044), and tetracycline biosynthesis (p=0.044), while those overrepresented in long-PFS group included fatty acid biosynthesis (p=0.035), fatty acid metabolism (p=0.008), vancomycin resistance (p=0.008), longevity regulating pathway-worm (p=0.028), type II diabetes mellitus (p=0.004), and viral carcinogenesis (p=0.003). Further analysis of antibiotic resistome demonstrated that the short-PFS group had a trend with more antibiotic resistance genes than healthy control (p=0.070) and long-PFS groups (p=0.218). The vancomycin resistance sequences were significantly enriched in the long-PFS group compared to the short-PFS group (p=0.006).

CONCLUSIONS: The baseline gut microbiome composition and functionality might be associated with PFS in LA-NSCLC treated with CCRT. The outcome of CCRT might be modulated through bacterial metabolic pathways. The antibiotic resistance genes might play a role in disease progression and provide potential information on the relationship between the use of antibiotics and treatment efficacy of CCRT in LA-NSCLC.}, } @article {pmid35719330, year = {2022}, author = {Li, Y and Yang, Y and Ma, L and Liu, J and An, Q and Zhang, C and Yin, G and Cao, Z and Pan, H}, title = {Comparative Analyses of Antibiotic Resistance Genes in Jejunum Microbiota of Pigs in Different Areas.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {887428}, pmid = {35719330}, issn = {2235-2988}, mesh = {Animals ; *Anti-Bacterial Agents/analysis/pharmacology ; China ; Drug Resistance, Microbial ; Genes, Bacterial/genetics ; Jejunum ; *Microbiota ; Swine ; }, abstract = {Antibiotic resistance genes (ARGs) are emerging environmental contaminants that threaten human and animal health. Intestinal microbiota may be an important ARGs repository, and intensive animal farming is a likely contributor to the environmental burden of ARGs. Using metagenomic sequencing, we investigated the structure, function, and drug resistance of the jejunal microbial community in Landrace (LA, Kunming), Saba (SB, Kunming), Dahe (DH, Qujing), and Diannan small-ear piglets (DS, Xishuangbanna) from different areas in Yunnan Province, China. Remarkable differences in jejunal microbial diversity among the different pig breeds, while the microbial composition of pig breeds in close areas tends to be similar. Functional analysis showed that there were abundant metabolic pathways and carbohydrate enzymes in all samples. In total, 32,487 ARGs were detected in all samples, which showed resistance to 38 categories of drugs. The abundance of ARGs in jejunum was not significantly different between LA and SB from the same area, but significantly different between DS, DH and LA or SB from different areas. Therefore, the abundance of ARGs was little affected by pig breeds and microorganism community structure, but it was closely related to geographical location. In addition, as a probiotic, Lactobacillus amylovorus is also an important ARGs producing bacterium. Our results revealed the antibiotic exposure and intestinal microbial resistance of farms in the study areas, which could provide basic knowledge and potential strategies for rational use of antibiotics and reducing the risk of ARGs transmission in animal husbandry.}, } @article {pmid35718910, year = {2022}, author = {Wang, S and Li, B and Mao, H and Zhu, M and Zhang, X and Xiang, X and Wang, Z}, title = {[Effects of rice wheat intervention on intestinal microflora of rats based on metagenomics].}, journal = {Wei sheng yan jiu = Journal of hygiene research}, volume = {51}, number = {3}, pages = {449-455}, doi = {10.19813/j.cnki.weishengyanjiu.2022.03.018}, pmid = {35718910}, issn = {1000-8020}, mesh = {Animals ; Carbohydrates ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Glycoside Hydrolases ; Lipids ; Male ; Metagenomics ; *Oryza ; Rats ; Rats, Sprague-Dawley ; Triticum ; }, abstract = {OBJECTIVE: To investigate the effects of rice on intestinal microflora in rats.

METHODS: Thirty 4-week-old male SD rats were randomly divided into control group, rice group and wheat group according to body weight. The control group was fed with AIN-93 diet, the rice group and the wheat group was fed with the AIN-93 diet which the carbohydrate was replaced with rice and wheat, respectively, for 4 weeks. At the end of the experiment, lipid related biochemical indexes were determined, and the contents of the distal colon(feces) of rats were collected for macro factor detection.

RESULTS: From the beginning to the end of feeding, there was no difference in weight gain among the groups. After the end of the experiment, there was no difference among lipid-related indicators and blood glucose. α diversity showed that there was no difference in the diversity of intestinal microbiota between the rice and wheat groups, and the gene abundance analysis of intestinal microbiota in the wheat group showed that the gene abundance of intestinal microbiota was lower. The difference analysis of intestinal microbiota result showed that compared with the rice group, the wheat group was composed of higher proportion of verrucomicrophyla and lower proportion of Bacteroidetes. Lefse analysis showed that the surface group was enriched with Akkermansia Muciniphila, Bifidobacterium animalis, and a variety of beneficial bacteria such as Faecalibaculum rodentium and Intestinimonas butyriciproducens, while Prevotella copri was rich in the rice group. Glycoside hydrolases 8, glycoside hydrolases 16, glycoside hydrolases 99 and glycosyl transferase family 56.

CONCLUSION: Rice or wheat as different carbohydrate sources have different effects on the composition of intestinal microflora and carbohydrate-related active enzymes in rats.}, } @article {pmid35718835, year = {2022}, author = {Bao, S and Wang, H and Li, W and Ji, L and Wang, X and Shen, Q and Yang, S and Zhou, C and Zhang, W}, title = {Dynamic alterations of the mice gut virome after Coxsackievirus B3 infection.}, journal = {Journal of medical virology}, volume = {94}, number = {10}, pages = {4959-4969}, doi = {10.1002/jmv.27946}, pmid = {35718835}, issn = {1096-9071}, mesh = {Animals ; *Coxsackievirus Infections ; *Enterovirus Infections ; Humans ; Mice ; *Microviridae ; Phylogeny ; Virome ; }, abstract = {The gut microbiome plays an essential role in the human health and dysbiosis has been implicated in numerous diseases. Coxsackievirus B3 infects millions of humans yearly and yet limited research has explored dynamic alterations of the gut virome after infection. Here, we established the mouse model of Coxsackievirus B3 infection and collected fecal samples at several time points to investigate alterations of the gut virome using viral metagenomic analysis. We found that the mice virome was dominated by Caudovirales and Microviridae, and phylogenetic analyses showed that both Caudovirales and Microviridae had high diversity. The gut virome had significant variations with the increase of Caudovirales and the decrease of Microviridae after infection. We proposed that Caudovirales and Microviridae may be biomarkers for the Coxsackievirus infection process. This study provides a reference for the dynamic changes of the gut virome after human Enterovirus infection, which may help guide the rational drug use in clinical treatment and provide new ideas for preventing Enterovirus infection.}, } @article {pmid35718758, year = {2022}, author = {Jia, H and Lyu, W and Hirota, K and Saito, E and Miyoshi, M and Hohjoh, H and Furukawa, K and Saito, K and Haritani, M and Taguchi, A and Hasebe, Y and Kato, H}, title = {Eggshell membrane modulates gut microbiota to prevent murine pre-cachexia through suppression of T helper cell differentiation.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {13}, number = {4}, pages = {2088-2101}, pmid = {35718758}, issn = {2190-6009}, support = {18K11095//Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {Animals ; *Cachexia/prevention & control ; Cell Differentiation ; Diet ; *Egg Shell ; *Gastrointestinal Microbiome ; Inflammation ; Interleukin-10 ; Male ; Mice ; Mice, Inbred C57BL ; Proteomics ; *T-Lymphocytes, Helper-Inducer/cytology ; }, abstract = {BACKGROUND: Cachexia is a life-threatening condition observed in several pathologies, such as cancer or chronic diseases. Interleukin 10 (Il10) gene transfer is known to improve cachexia by downregulating Il6. Here, we used an IL10-knockout mouse model to simulate cachexia and investigate the effects of eggshell membrane (ESM), a resistant protein, on general pre-cachexia symptoms, which is particularly important for the development of cachexia therapeutics.

METHODS: Five-week-old male C57BL6/J mice were fed an AIN-93G powdered diet (WT), and 5-week-old male B6.129P2-Il10 < tm1Cgn>/J (IL10[-/-]) mice were fed either the AIN-93G diet (KO) or an 8% ESM-containing diet (KOE) for 28 weeks. The tissue weight and levels of anaemia-, blood glucose-, lipid metabolism-, and muscular and colonic inflammation-related biochemical markers were measured. Transcriptomic analysis on liver and colon mucus and proteomic analysis on skeletal muscle were performed. Ingenuity Pathway Analysis was used to identify molecular pathways and networks. Caecal short-chain fatty acids (SCFAs) were identified using HPLC, and caecal bacteria DNA were subjected to metagenomic analysis. Flow cytometry analysis was performed to measure the CD4[+] IL17[+] T cells in mesenteric lymph nodes.

RESULTS: The body weight, weight of gastrocnemius muscle and fat tissues, colon weight/length ratio, plasma HDL and NEFA, muscular PECAM-1 levels (P < 0.01), plasma glucose and colonic mucosal myeloperoxidase activity (P < 0.05) and T helper (Th) 17 cell abundance (P = 0.071) were improved in KOE mice over KO mice. Proteomic analysis indicated the protective role of ESM in muscle weakness and maintenance of muscle formation (>1.5-fold). Transcriptomic analysis revealed that ESM supplementation suppressed the LPS/IL1-mediated inhibition of RXR function pathway in the liver and downregulated the colonic mucosal expression of chemokines and Th cell differentiation-related markers (P < 0.01) by suppressing the upstream BATF pathway. Analysis of the intestinal microenvironment revealed that ESM supplementation ameliorated the microbial alpha diversity and the abundance of microbiota associated with the degree of inflammation (P < 0.05) and increased the level of total organic acids, particularly of SCFAs such as butyrate (2.3-fold), which could inhibit Th1 and Th17 production.

CONCLUSIONS: ESM supplementation ameliorated the chief symptoms of cachexia, including anorexia, lean fat tissue mass, skeletal muscle wasting and reduced physical function. ESM also improved colon and skeletal muscle inflammation, lipid metabolism and microbial dysbiosis. These results along with the suppressed differentiation of Th cells could be associated with the beneficial intestinal microenvironment and, subsequently, attenuation of pre-cachexia. Our findings provide insights into the potential of ESM in complementary interventions for pre-cachexia prevention.}, } @article {pmid35717483, year = {2023}, author = {Moroishi, Y and Gui, J and Nadeau, KC and Morrison, HG and Madan, J and Karagas, MR}, title = {A prospective study of the infant gut microbiome in relation to vaccine response.}, journal = {Pediatric research}, volume = {93}, number = {3}, pages = {725-731}, pmid = {35717483}, issn = {1530-0447}, support = {UH3 OD023275/OD/NIH HHS/United States ; P42 ES007373/ES/NIEHS NIH HHS/United States ; R21 ES020936/ES/NIEHS NIH HHS/United States ; P01 ES022832/ES/NIEHS NIH HHS/United States ; UG3 OD023275/OD/NIH HHS/United States ; P20 GM104416/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Infant ; *Gastrointestinal Microbiome/genetics ; Prospective Studies ; Cohort Studies ; RNA, Ribosomal, 16S/genetics ; *Tetanus ; Tetanus Toxoid ; Feces ; Immunoglobulin G ; Polysaccharides ; }, abstract = {BACKGROUND: The establishment of the gut microbiome plays a key symbiotic role in the developing immune system; however, its influence on vaccine response is yet uncertain. We prospectively investigated the composition and diversity of the early-life gut microbiome in relation to infant antibody response to two routinely administered vaccines.

METHODS: Eighty-three infants enrolled in the New Hampshire Birth Cohort Study were included in the analysis. We collected blood samples at 12 months of age and assayed the isolated serum to quantify total IgG and measured antibody to pneumococcal capsular polysaccharide and tetanus toxoid. Stool samples were collected from infants at 6 weeks of age and sequenced using 16S rRNA, and a subset of 61 samples were sequenced using shotgun metagenomics sequencing.

RESULTS: We observed differences in beta diversity for 16S 6-week stool microbiota and pneumococcal and tetanus IgG antibody responses. Metagenomics analyses identified species and metabolic pathways in 6-week stool associated with tetanus antibody response, in particular, negative associations with the relative abundance of Aeriscardovia aeriphila species and positive associations with the relative abundance of species associated with CDP-diacylglycerol biosynthesis pathways.

CONCLUSIONS: The early gut microbiome composition may influence an infant's vaccine response.

IMPACT: Early intestinal microbiome acquisition plays a critical role in immune maturation and in both adaptive and innate immune response in infancy. We identified associations between early life microbiome composition and response to two routinely administered vaccines-pneumococcal capsular polysaccharide and tetanus toxoid-measured at approximately 1 year of age. Our findings highlight the potential impact of the gut microbiome on infant immune response that may open up opportunities for future interventions.}, } @article {pmid35716556, year = {2022}, author = {Guan, Y and Xue, X and Jia, J and Li, X and Xing, H and Wang, Z}, title = {Metagenomic assembly and binning analyses the prevalence and spread of antibiotic resistome in water and fish gut microbiomes along an environmental gradient.}, journal = {Journal of environmental management}, volume = {318}, number = {}, pages = {115521}, doi = {10.1016/j.jenvman.2022.115521}, pmid = {35716556}, issn = {1095-8630}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Gastrointestinal Microbiome ; Genes, Bacterial ; *Microbiota ; Prevalence ; Water ; }, abstract = {The pristine river and urban river show an environmental gradient caused by anthropogenic impacts such as wastewater treatment plants and domestic wastewater discharges. Here, metagenomic and binning analyses unveiled antibiotic resistance genes (ARGs) profiles, their co-occurrence with metal resistance genes (MRGs) and mobile genetic elements (MGEs), and their host bacteria in water and Hemiculter leucisculus samples of the river. Results showed that the decrease of ARG abundances from pristine to anthropogenic regions was attributed to the reduction of the relative abundance of multidrug resistance genes in water microbiomes along the environmental gradient. Whereas anthropogenic impact contributed to the enrichment of ARGs in fish gut microbiomes. From pristine to anthropogenic water samples, the dominant host bacteria shifted from Pseudomonas to Actinobacteria. Potential pathogens Vibrio parahaemolyticus, Enterobacter kobei, Aeromonas veronii and Microcystis aeruginosa_C with multiple ARGs were retrieved from fish gut microbes in lower reach of Ba River. The increasing trends in the proportion of the contigs carrying ARGs (ARCs) concomitant with plasmids along environmental gradient indicated that plasmids act as efficient mobility vehicles to enhance the spread of ARGs under anthropogenic pressures. Moreover, the higher co-occurrence of ARGs and MRGs on plasmids revealed that anthropogenic impacts accelerated the co-transfer potential of ARGs and MRGs and the enrichment of ARGs. Partial least squares path modeling revealed anthropogenic contamination could shape fish gut antibiotic resistome mainly via affecting ARG host bacteria in water microbiomes, following by ARGs co-occurrence with MGEs and MRGs in gut microbiomes. This study enhanced our understanding of the mechanism of the anthropogenic activities on the transmission of antibiotic resistome in river ecosystem and emphasized the risk of ARGs and pathogens transferring from an aquatic environment to fish guts.}, } @article {pmid35715703, year = {2022}, author = {Lan, Y and Sun, J and Chen, C and Wang, H and Xiao, Y and Perez, M and Yang, Y and Kwan, YH and Sun, Y and Zhou, Y and Han, X and Miyazaki, J and Watsuji, TO and Bissessur, D and Qiu, JW and Takai, K and Qian, PY}, title = {Endosymbiont population genomics sheds light on transmission mode, partner specificity, and stability of the scaly-foot snail holobiont.}, journal = {The ISME journal}, volume = {16}, number = {9}, pages = {2132-2143}, pmid = {35715703}, issn = {1751-7370}, support = {42176110//National Natural Science Foundation of China (National Science Foundation of China)/ ; 18K06401//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {Animals ; *Hydrothermal Vents/microbiology ; Metagenomics ; Phylogeny ; Snails/physiology ; Symbiosis/genetics ; }, abstract = {The scaly-foot snail (Chrysomallon squamiferum) inhabiting deep-sea hydrothermal vents in the Indian Ocean relies on its sulphur-oxidising gammaproteobacterial endosymbionts for nutrition and energy. In this study, we investigate the specificity, transmission mode, and stability of multiple scaly-foot snail populations dwelling in five vent fields with considerably disparate geological, physical and chemical environmental conditions. Results of population genomics analyses reveal an incongruent phylogeny between the endosymbiont and mitochondrial genomes of the scaly-foot snails in the five vent fields sampled, indicating that the hosts obtain endosymbionts via horizontal transmission in each generation. However, the genetic homogeneity of many symbiont populations implies that vertical transmission cannot be ruled out either. Fluorescence in situ hybridisation of ovarian tissue yields symbiont signals around the oocytes, suggesting that vertical transmission co-occurs with horizontal transmission. Results of in situ environmental measurements and gene expression analyses from in situ fixed samples show that the snail host buffers the differences in environmental conditions to provide the endosymbionts with a stable intracellular micro-environment, where the symbionts serve key metabolic functions and benefit from the host's cushion. The mixed transmission mode, symbiont specificity at the species level, and stable intracellular environment provided by the host support the evolutionary, ecological, and physiological success of scaly-foot snail holobionts in different vents with unique environmental parameters.}, } @article {pmid35715496, year = {2022}, author = {Shell, WA and Rehan, SM}, title = {Comparative metagenomics reveals expanded insights into intra- and interspecific variation among wild bee microbiomes.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {603}, pmid = {35715496}, issn = {2399-3642}, mesh = {Agriculture ; Animals ; Bees ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Plants ; }, abstract = {The holobiont approach proposes that species are most fully understood within the context of their associated microbiomes, and that both host and microbial community are locked in a mutual circuit of co-evolutionary selection. Bees are an ideal group for this approach, as they comprise a critical group of pollinators that contribute to both ecological and agricultural health worldwide. Metagenomic analyses offer comprehensive insights into an organism's microbiome, diet, and viral load, but remain largely unapplied to wild bees. Here, we present metagenomic data from three species of carpenter bees sampled from around the globe, representative of the first ever carpenter bee core microbiome. Machine learning, co-occurrence, and network analyses reveal that wild bee metagenomes are unique to host species. Further, we find that microbiomes are likely strongly affected by features of their local environment, and feature evidence of plant pathogens previously known only in honey bees. Performing the most comprehensive comparative analysis of bee microbiomes to date we discover that microbiome diversity is inversely proportional to host species social complexity. Our study helps to establish some of the first wild bee hologenomic data while offering powerful empirical insights into the biology and health of vital pollinators.}, } @article {pmid35715385, year = {2022}, author = {Gronniger, JL and Wang, Z and Brandt, GR and Ward, CS and Tsementzi, D and Mu, H and Gu, J and Johnson, ZI and Konstantinidis, KT and Hunt, DE}, title = {Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables.}, journal = {Environmental microbiology}, volume = {24}, number = {9}, pages = {4167-4177}, doi = {10.1111/1462-2920.16086}, pmid = {35715385}, issn = {1462-2920}, mesh = {Metagenome ; *Microbiota/genetics ; Oceans and Seas ; Phytoplankton ; }, abstract = {Disturbances, here defined as events that directly alter microbial community composition, are commonly studied in host-associated and engineered systems. In spite of global change both altering environmental averages and increasing extreme events, there has been relatively little research into the causes, persistence and population-level impacts of disturbance in the dynamic coastal ocean. Here, we utilize 3 years of observations from a coastal time series to identify disturbances based on the largest week-over-week changes in the microbiome (i.e. identifying disturbance as events that alter the community composition). In general, these microbiome disturbances were not clearly linked to specific environmental factors and responsive taxa largely differed, aside from SAR11, which generally declined. However, several disturbance metagenomes identified increased phage-associated genes, suggesting that unexplained community shifts might be caused by increased mortality. Furthermore, a category 1 hurricane, the only event that would likely be classified a priori as an environmental disturbance, was not an outlier in microbiome composition, but did enhance a bloom in seasonally abundant phytoplankton. Thus, as extreme environmental changes intensify, assumptions of what constitutes a disturbance should be re-examined in the context of ecological history and microbiome responses.}, } @article {pmid35714435, year = {2022}, author = {Borker, SS and Thakur, A and Khatri, A and Kumar, R}, title = {Quality assessment, safety evaluation, and microbiome analysis of night-soil compost from Lahaul valley of northwestern Himalaya.}, journal = {Waste management (New York, N.Y.)}, volume = {149}, number = {}, pages = {42-52}, doi = {10.1016/j.wasman.2022.06.003}, pmid = {35714435}, issn = {1879-2456}, mesh = {Animals ; Bacteria/genetics ; Cattle ; *Composting ; Food ; Humans ; *Metals, Heavy ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Refuse Disposal ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The Himalayan dry toilet system prevalent in the northwestern Himalaya is a traditional practice of converting human faeces into a compost-like soil amendment. The current study evaluated night-soil compost (NSC) for agricultural use by assessing the compost quality, safety, and microbiome properties. Based on the fertility and clean indices determined by the fertility and heavy metal parameters, NSC was categorized as good quality compost with high fertilizing potential and moderate concentration of heavy metals. With respect to pathogens, the faecal coliform levels in the NSC were categorized as safe according to the U.S. Environmental Protection Agency standards. The bacterial community structure based on 16S rRNA gene amplicons revealed a diverse taxonomy with 14 phyla and 54 genera in NSC. Compared to publicly available 16S rRNA gene amplicon data, NSC exhibited predominant phyla (Proteobacteria, Bacteriodetes, Actinobacteria, and Firmicutes) similar to human faeces, cattle manure, food waste compost, vermicompost, and activated sludge. However, statistically, NSC was distinct at the genus level from all other groups. Additionally, pathogenic bacteria with antimicrobial resistance (AMR) genes in the NSC metagenome were determined by performing a standalone BLASTN against the PATRIC database. The analysis revealed 139 pathogenic strains with most pathogens susceptible to antibiotics, indicating lower AMR in the predicted strains. The phytotoxicity of NSC with Pisum sativum var. AS-10 seeds showed a germination index of > 85%, indicating NSC's non-harmful effects on seed germination and root growth. Overall, NSC from Himalayan dry toilets can be used as a soil amendment for food and non-food plants.}, } @article {pmid35713407, year = {2022}, author = {Shaffer, JP and Carpenter, CS and Martino, C and Salido, RA and Minich, JJ and Bryant, M and Sanders, K and Schwartz, T and Humphrey, G and Swafford, AD and Knight, R}, title = {A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities.}, journal = {BioTechniques}, volume = {73}, number = {1}, pages = {34-46}, pmid = {35713407}, issn = {1940-9818}, support = {R01 DK102932/DK/NIDDK NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; U01 AI124316/AI/NIAID NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; R01 HL134887/HL/NHLBI NIH HHS/United States ; RF1 AG058942/AG/NIA NIH HHS/United States ; }, mesh = {Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenomics/methods ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Microbial communities contain a broad phylogenetic diversity of organisms; however, the majority of methods center on describing bacteria and archaea. Fungi are important symbionts in many ecosystems and are potentially important members of the human microbiome, beyond those that can cause disease. To expand our analysis of microbial communities to include data from the fungal internal transcribed spacer (ITS) region, five candidate DNA extraction kits were compared against our standardized protocol for describing bacteria and archaea using 16S rRNA gene amplicon- and shotgun metagenomics sequencing. The results are presented considering a diverse panel of host-associated and environmental sample types and comparing the cost, processing time, well-to-well contamination, DNA yield, limit of detection and microbial community composition among protocols. Across all criteria, the MagMAX Microbiome kit was found to perform best. The PowerSoil Pro kit performed comparably but with increased cost per sample and overall processing time. The Zymo MagBead, NucleoMag Food and Norgen Stool kits were included.}, } @article {pmid35713100, year = {2023}, author = {Dixit, S and Kumar, S and Sharma, R and Banakar, PS and Singh, M and Keshri, A and Tyagi, AK}, title = {Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review.}, journal = {Animal biotechnology}, volume = {34}, number = {7}, pages = {3187-3205}, doi = {10.1080/10495398.2022.2078979}, pmid = {35713100}, issn = {1532-2378}, mesh = {Animals ; *Rumen/metabolism ; Farms ; Multiomics ; *Microbiota ; Diet/veterinary ; Animal Feed ; }, abstract = {Continuous improvement in the living standards of developing countries, calls for an urgent need of high quality meat and dairy products. The farm animals have a micro-ecosystem in gastro-intestinal tract, comprising of a wide variety of flora and fauna which converts roughages and agricultural byproducts as well as nutrient rich concentrate sources into the useful products such as volatile fatty acids and microbial crude proteins. The microbial diversity changes according to composition of the feed, host species/breed and host's individual genetic makeup. From culture methods to next-generation sequencing technologies, the knowledge has emerged a lot to know-how of microbial world viz. their identification, enzymatic activities and metabolites which are the keys of ruminant's successful existence. The structural composition of ruminal community revealed through metagenomics can be elaborated by metatranscriptomics and metabolomics through deciphering their functional role in metabolism and their responses to the external and internal stimuli. These highly sophisticated analytical tools have made possible to correlate the differences in the feed efficiency, nutrients utilization and methane emissions to their rumen microbiome. The comprehensively understood rumen microbiome will enhance the knowledge in the fields of animal nutrition, biotechnology and climatology through deciphering the significance of each and every domain of residing microbial entity. The present review undertakes the recent investigations regarding rumen multi-omics viz. taxonomic and functional potential of microbial populations, host-diet-microbiome interactions and correlation with metabolic dynamics.}, } @article {pmid35711426, year = {2022}, author = {Hua, H and Meydan, C and Afshin, EE and Lili, LN and D'Adamo, CR and Rickard, N and Dudley, JT and Price, ND and Zhang, B and Mason, CE}, title = {A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {889702}, pmid = {35711426}, issn = {1664-3224}, mesh = {DNA, Bacterial/genetics ; Feces/microbiology ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Specimen Handling/methods ; }, abstract = {While a range of methods for stool collection exist, many require complicated, self-directed protocols and stool transfer. In this study, we introduce and validate a novel, wipe-based approach to fecal sample collection and stabilization for metagenomics analysis. A total of 72 samples were collected across four different preservation types: freezing at -20°C, room temperature storage, a commercial DNA preservation kit, and a dissolvable wipe used with DESS (dimethyl sulfoxide, ethylenediaminetetraacetic acid, sodium chloride) solution. These samples were sequenced and analyzed for taxonomic abundance metrics, bacterial metabolic pathway classification, and diversity analysis. Overall, the DESS wipe results validated the use of a wipe-based capture method to collect stool samples for microbiome analysis, showing an R[2] of 0.96 for species across all kingdoms, as well as exhibiting a maintenance of Shannon diversity (3.1-3.3) and species richness (151-159) compared to frozen samples. Moreover, DESS showed comparable performance to the commercially available preservation kit (R[2] of 0.98), and samples consistently clustered by subject across each method. These data support that the DESS wipe method can be used for stable, room temperature collection and transport of human stool specimens.}, } @article {pmid35710760, year = {2022}, author = {Escudero-Martinez, C and Coulter, M and Alegria Terrazas, R and Foito, A and Kapadia, R and Pietrangelo, L and Maver, M and Sharma, R and Aprile, A and Morris, J and Hedley, PE and Maurer, A and Pillen, K and Naclerio, G and Mimmo, T and Barton, GJ and Waugh, R and Abbott, J and Bulgarelli, D}, title = {Identifying plant genes shaping microbiota composition in the barley rhizosphere.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3443}, pmid = {35710760}, issn = {2041-1723}, support = {BB/S002871/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/genetics ; Genes, Plant/genetics ; *Hordeum/genetics ; *Microbiota/genetics ; Plant Roots/genetics ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; }, abstract = {A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here, we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plant's capacity of shaping rhizosphere microbes.}, } @article {pmid35710651, year = {2022}, author = {Zhou, L and Huang, S and Gong, J and Xu, P and Huang, X}, title = {500 metagenome-assembled microbial genomes from 30 subtropical estuaries in South China.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {310}, pmid = {35710651}, issn = {2052-4463}, mesh = {China ; Estuaries ; *Genome, Microbial ; *Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {As a unique geographical transition zone, the estuary is considered as a model environment to decipher the diversity, functions and ecological processes of microbial communities, which play important roles in the global biogeochemical cycle. Here we used surface water metagenomic sequencing datasets to construct metagenome-assembled genomes (MAGs) from 30 subtropical estuaries at a large scale along South China. In total, 500 dereplicated MAGs with completeness ≥ 50% and contamination ≤ 10% were obtained, among which more than one-thirds (n = 207 MAGs) have a completeness ≥ 70%. These MAGs are dominated by taxa assigned to the phylum Proteobacteria (n = 182 MAGs), Bacteroidota (n = 110) and Actinobacteriota (n = 104). These draft genomes can be used to study the diversity, phylogenetic history and metabolic potential of microbiota in the estuary, which should help improve our understanding of the structure and function of these microorganisms and how they evolved and adapted to extreme conditions in the estuarine ecosystem.}, } @article {pmid35710629, year = {2022}, author = {Oyserman, BO and Flores, SS and Griffioen, T and Pan, X and van der Wijk, E and Pronk, L and Lokhorst, W and Nurfikari, A and Paulson, JN and Movassagh, M and Stopnisek, N and Kupczok, A and Cordovez, V and Carrión, VJ and Ligterink, W and Snoek, BL and Medema, MH and Raaijmakers, JM}, title = {Disentangling the genetic basis of rhizosphere microbiome assembly in tomato.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3228}, pmid = {35710629}, issn = {2041-1723}, support = {U01 GM110706/GM/NIGMS NIH HHS/United States ; }, mesh = {Iron/metabolism ; *Solanum lycopersicum/metabolism ; *Microbiota/genetics ; Plant Breeding ; Plants/metabolism ; Rhizosphere ; }, abstract = {Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, we map the molecular features of the rhizosphere microbiome as quantitative traits of a diverse hybrid population of wild and domesticated tomato. Gene content analysis of prioritized tomato quantitative trait loci suggests a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31 Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the water channel aquaporin SlTIP2.3. Within metagenome-assembled genomes of root-associated Streptomyces and Cellvibrio, we identify bacterial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associates with specific tomato QTLs. By integrating 'microbiomics' and quantitative plant genetics, we pinpoint putative plant and reciprocal rhizobacterial traits underlying microbiome assembly, thereby providing a first step towards plant-microbiome breeding programs.}, } @article {pmid35709584, year = {2022}, author = {Ferrocino, I and Rantsiou, K and Cocolin, L}, title = {Microbiome and -omics application in food industry.}, journal = {International journal of food microbiology}, volume = {377}, number = {}, pages = {109781}, doi = {10.1016/j.ijfoodmicro.2022.109781}, pmid = {35709584}, issn = {1879-3460}, mesh = {Food Industry ; Microbiological Techniques ; *Microbiota ; }, abstract = {The enormous potential of multi-omics approaches to unravel microbiome-related links between food quality, sustainability and safety still requires experimental work and extensive data integration to increase knowledge and understand the biological and ecological processes involved in the assembly and dynamics of microbial communities along the production chains. Data spanning from DNA sequences to transcripts and metabolites need to be integrated in order to be translated at industrial level and literature showed several successful examples. The application of microbiome studies in food systems has shown the potential to improve food quality. Nevertheless, classical microbiological methods are still highly relevant even if isolation and characterization of strains in pure culture is often laborious and time-consuming and requires the use of several specific growth media that take into the account microbial growth characteristics as well as food characteristics. Studies on microbiomes have become a popular topic in the food industry since it can be used as a tool to improve quality and safety in the food chain.}, } @article {pmid35707175, year = {2022}, author = {Koedooder, C and Landou, E and Zhang, F and Wang, S and Basu, S and Berman-Frank, I and Shaked, Y and Rubin-Blum, M}, title = {Metagenomes of Red Sea Subpopulations Challenge the Use of Marker Genes and Morphology to Assess Trichodesmium Diversity.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {879970}, pmid = {35707175}, issn = {1664-302X}, abstract = {Trichodesmium are filamentous cyanobacteria of key interest due to their ability to fix carbon and nitrogen within an oligotrophic marine environment. Their blooms consist of a dynamic assemblage of subpopulations and colony morphologies that are hypothesized to occupy unique niches. Here, we assessed the poorly studied diversity of Trichodesmium in the Red Sea, based on metagenome-assembled genomes (MAGs) and hetR gene-based phylotyping. We assembled four non-redundant MAGs from morphologically distinct Trichodesmium colonies (tufts, dense and thin puffs). Trichodesmium thiebautii (puffs) and Trichodesmium erythraeum (tufts) were the dominant species within these morphotypes. While subspecies diversity is present for both T. thiebautii and T. erythraeum, a single T. thiebautii genotype comprised both thin and dense puff morphotypes, and we hypothesize that this phenotypic variation is likely attributed to gene regulation. Additionally, we found the rare non-diazotrophic clade IV and V genotypes, related to Trichodesmium nobis and Trichodesmium miru, respectively that likely occurred as single filaments. The hetR gene phylogeny further indicated that the genotype in clade IV could represent the species Trichodesmium contortum. Importantly, we show the presence of hetR paralogs in Trichodesmium, where two copies of the hetR gene were present within T. thiebautii genomes. This may lead to the overestimation of Trichodesmium diversity as one of the copies misidentified T. thiebautii as Trichodesmium aureum. Taken together, our results highlight the importance of re-assessing Trichodesmium taxonomy while showing the ability of genomics to capture the complex diversity and distribution of Trichodesmium populations.}, } @article {pmid35705745, year = {2023}, author = {Song, L and Wang, Y and Zhang, R and Yang, S}, title = {Microbial Mediation of Carbon, Nitrogen, and Sulfur Cycles During Solid Waste Decomposition.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {311-324}, pmid = {35705745}, issn = {1432-184X}, support = {52000016//National Natural Science Foundation of China/ ; 51578642//National Natural Science Foundation of China/ ; }, mesh = {*Solid Waste/analysis ; Nitrogen/analysis ; Carbon ; RNA, Ribosomal, 16S/genetics ; Carbon Dioxide ; Bacteria/genetics ; Archaea/genetics ; *Microbiota ; Sulfur ; Waste Disposal Facilities ; }, abstract = {Landfills are a unique "terrestrial ecosystem" and serve as a significant carbon sink. Microorganisms convert biodegradable substances in municipal solid waste (MSW) to CH4, CO2, and microbial biomass, consisting of the carbon cycling in landfills. Microbial-mediated N and S cycles are also the important biogeochemical process during MSW decomposition, resulting in N2O and H2S emission, respectively. Meanwhile, microbial-mediated N and S cycles affect carbon cycling. How microbial community structure and function respond to C, N, and S cycling during solid waste decomposition, however, are not well-characterized. Here, we show the response of bacterial and archaeal community structure and functions to C, N, and S cycling during solid waste decomposition in a long-term (265 days) operation laboratory-scale bioreactor through 16S rRNA-based pyrosequencing and metagenomics analysis. Bacterial and archaeal community composition varied during solid waste decomposition. Aerobic respiration was the main pathway for CO2 emission, while anaerobic C fixation was the main pathway in carbon fixation. Methanogenesis and denitrification increased during solid waste decomposition, suggesting increasing CH4 and N2O emission. In contract, fermentation decreased along solid waste decomposition. Interestingly, Clostridiales were abundant and showed potential for several pathways in C, N, and S cycling. Archaea were involved in many pathways of C and N cycles. There is a shift between bacteria and archaea involvement in N2 fixation along solid waste decomposition that bacteria Clostridiales and Bacteroidales were initially dominant and then Methanosarcinales increased and became dominant in methanogenic phase. These results provide extensive microbial mediation of C, N, and S cycling profiles during solid waste decomposition.}, } @article {pmid35705722, year = {2022}, author = {Di Chiacchio, IM and Gómez-Abenza, E and Paiva, IM and de Abreu, DJM and Rodríguez-Vidal, JF and Carvalho, EEN and Carvalho, SM and Solis-Murgas, LD and Mulero, V}, title = {Bee pollen in zebrafish diet affects intestinal microbiota composition and skin cutaneous melanoma development.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9998}, pmid = {35705722}, issn = {2045-2322}, mesh = {Animals ; Bees ; Diet ; *Gastrointestinal Microbiome ; *Melanoma/etiology ; Pollen ; *Skin Neoplasms/etiology ; Zebrafish ; Melanoma, Cutaneous Malignant ; }, abstract = {Bee pollen is recommended as dietary supplement due to immunostimulating functions including antioxidant, anti-inflammatory and anti-carcinogenic properties. Nevertheless, the effectiveness of such properties is still not well understood. As diet can be associated with animal performance, microbiota modulation and potentially factor for cancer, this study aimed to analyze if bee pollen could influence growth, gut microbial and skin cutaneous melanoma development in zebrafish. Control diets based on commercial flakes and Artemia were compared with the same diet supplemented with bee pollen. Fish weight gain, increased length, intestinal bacteria metagenomics analysis, serum amyloid A gene expression and cutaneous melanoma transplantation assays were performed. Bee pollen affected microbiota composition and melanoma development. Differential abundance revealed higher abundance in the control group for Aeromonadaceae family, Aeromonas and Pseudomonas genus, A. sobria, A. schubertii, A. jandaei and P. alcaligenes species compared with pollen diet group. Pollen group presented higher abundance for Chromobacterium genus and for Gemmobacter aquaticus, Flavobacterium succinicans and Bifidobacterium breve compared with control group. Unexpectedly, fish fed with bee pollen showed higher tumor growth rate and larger tumor size than control group. This is the first study to report intestinal microbial changes and no protective cancer properties after bee pollen administration.}, } @article {pmid35705309, year = {2022}, author = {Prekrasna, I and Pavlovska, M and Miryuta, N and Dzhulai, A and Dykyi, E and Convey, P and Kozeretska, I and Bedernichek, T and Parnikoza, I}, title = {Antarctic Hairgrass Rhizosphere Microbiomes: Microscale Effects Shape Diversity, Structure, and Function.}, journal = {Microbes and environments}, volume = {37}, number = {2}, pages = {}, pmid = {35705309}, issn = {1347-4405}, mesh = {*Actinobacteria/genetics ; Antarctic Regions ; Bacteria/genetics ; Lignin ; *Microbiota/genetics ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The rhizosphere microbiome of the native Antarctic hairgrass Deschampsia antarctica from the central maritime Antarctic was investigated using 16S RNA metagenomics and compared to those of the second native Antarctic plant Colobanthus quitensis and closely related temperate D. cespitosa. The rhizosphere microbial communities of D. antarctica and D. cespitosa had high taxon richness, while that of C. quitensis had markedly lower diversity. The majority of bacteria in the rhizosphere communities of the hairgrass were affiliated to Proteobacteria, Bacteroidetes, and Actinobacteria. The rhizosphere of C. quitensis was dominated by Actinobacteria. All microbial communities included high proportions of unique amplicon sequence variants (ASVs) and there was high heterogeneity between samples at the ASV level. The soil parameters examined did not explain this heterogeneity. Bacteria belonging to Actinobacteria, Bacteroidetes, and Proteobacteria were sensitive to fluctuations in the soil surface temperature. The values of the United Soil Surface Temperature Influence Index (UTII, I[t]i) showed that variations in most microbial communities from Galindez Island were associated with microscale variations in temperature. Metabolic predictions in silico using PICRUSt 2.0, based on the taxonomically affiliated part of the microbiomes, showed similarities with the rhizosphere community of D. antarctica in terms of the predicted functional repertoire. The results obtained indicate that these communities are involved in the primary processes of soil development (particularly the degradation of lignin and lignin-derived compounds) in the central maritime Antarctic and may be beneficial for the growth of Antarctic vascular plants. However, due to the limitations associated with interpreting PICRUSt 2.0 outputs, these predictions need to be verified experimentally.}, } @article {pmid35703559, year = {2022}, author = {Churcheward, B and Millet, M and Bihouée, A and Fertin, G and Chaffron, S}, title = {MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0043222}, pmid = {35703559}, issn = {2379-5077}, mesh = {Workflow ; *Metagenomics/methods ; Metagenome/genetics ; *Microbiota ; Genome, Microbial ; }, abstract = {Metagenome-assembled genomes (MAGs) represent individual genomes recovered from metagenomic data. MAGs are extremely useful to analyze uncultured microbial genomic diversity, as well as to characterize associated functional and metabolic potential in natural environments. Recent computational developments have considerably improved MAG reconstruction but also emphasized several limitations, such as the nonbinning of sequence regions with repetitions or distinct nucleotidic composition. Different assembly and binning strategies are often used; however, it still remains unclear which assembly strategy, in combination with which binning approach, offers the best performance for MAG recovery. Several workflows have been proposed in order to reconstruct MAGs, but users are usually limited to single-metagenome assembly or need to manually define sets of metagenomes to coassemble prior to genome binning. Here, we present MAGNETO, an automated workflow dedicated to MAG reconstruction, which includes a fully-automated coassembly step informed by optimal clustering of metagenomic distances, and implements complementary genome binning strategies, for improving MAG recovery. MAGNETO is implemented as a Snakemake workflow and is available at: https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto. IMPORTANCE Genome-resolved metagenomics has led to the discovery of previously untapped biodiversity within the microbial world. As the development of computational methods for the recovery of genomes from metagenomes continues, existing strategies need to be evaluated and compared to eventually lead to standardized computational workflows. In this study, we compared commonly used assembly and binning strategies and assessed their performance using both simulated and real metagenomic data sets. We propose a novel approach to automate coassembly, avoiding the requirement for a priori knowledge to combine metagenomic information. The comparison against a previous coassembly approach demonstrates a strong impact of this step on genome binning results, but also the benefits of informing coassembly for improving the quality of recovered genomes. MAGNETO integrates complementary assembly-binning strategies to optimize genome reconstruction and provides a complete reads-to-genomes workflow for the growing microbiome research community.}, } @article {pmid35703536, year = {2022}, author = {Wang, H and Shankar, V and Jiang, X}, title = {Compositional and Functional Changes in Microbial Communities of Composts Due to the Composting-Related Factors and the Presence of Listeria monocytogenes.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0184521}, pmid = {35703536}, issn = {2165-0497}, support = {P20 GM109094/GM/NIGMS NIH HHS/United States ; P20 GM146584/GM/NIGMS NIH HHS/United States ; }, mesh = {*Composting ; *Listeria monocytogenes/genetics ; *Microbiota ; Soil ; Soil Microbiology ; }, abstract = {Listeria monocytogenes is a leading foodborne pathogen that can contaminate fresh produce in farm environment, resulting in deadly outbreaks. Composts contain a diversity of microorganisms, and some of them may be compost-adapted competitive exclusion microorganisms against L. monocytogenes. To understand interactions between compost microflora and the pathogen, both dairy- and poultry-wastes based composts (n = 12) were inoculated with L. monocytogenes, and then analyzed by next-generation sequencing approaches along with culturing methods. DNA extraction and enumeration of L. monocytogenes were performed at 0 and 72 h post-incubation at room temperature. The major bacterial phyla were identified as Firmicutes (23%), Proteobacteria (23%), Actinobacteria (19%), Chloroflexi (13%), Bacteroidetes (12%), Gemmatimonadetes (2%), and Acidobacteria (2%). The top three indicator genera enriched in different compost types were identified by LEfSe with LDA score > 2. The interactions between L. monocytogenes and indigenous microflora were limited as no significant changes in the dominant microbial members in compost ecosystem, but some discriminatory species such as Bacillus, Geobacillus, and Brevibacterium were identified by Random Forest analysis. Besides, changes in metabolic pathways and the increased abundance of bacteriocins category in the compost samples containing L. monocytogenes after 72 h postinoculation were revealed by metatranscriptomic sequencing. Taken together, the compost-related factors such as compost types, composting stages, and the collection farms are major drivers that affect compost microbial compositions, and the analysis of compost metagenome implied that interactions between L. monocytogenes and compost microflora may include competition for nutrients and the presence of antimicrobials. IMPORTANCE Listeria monocytogenes has been recognized as the etiological agent causing foodborne disease outbreaks, with fresh produce as vulnerable for contamination at even preharvest stage. Owing to the richness in microbial community, compost may mediate suppression of pathogens. In this study, the impact of compost-related factors and L. monocytogenes intrusion on dynamic changes in compost microbiome was investigated by next generation sequencing techniques. The compost-related factors such as compost types, composting stages, and the collection farms are major drivers that affect compost microbiome. The interactions between L. monocytogenes and compost microflora may include the competition for nutrients and the presence of antimicrobials produced by native compost microorganisms as potential competitive exclusion microorganisms. Findings from this study are important for the composting industry to understand the composition and functionality of microbial community in their products and help developing organic fertilizers fortified with anti-L. monocytogenes competitive exclusion microorganisms.}, } @article {pmid35702025, year = {2022}, author = {Chelluboina, B and Kieft, K and Breister, A and Anantharaman, K and Vemuganti, R}, title = {Gut virome dysbiosis following focal cerebral ischemia in mice.}, journal = {Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism}, volume = {42}, number = {9}, pages = {1597-1602}, pmid = {35702025}, issn = {1559-7016}, support = {R01 NS101960/NS/NINDS NIH HHS/United States ; R35 GM143024/GM/NIGMS NIH HHS/United States ; IK6 BX005690/BX/BLRD VA/United States ; R01 NS109459/NS/NINDS NIH HHS/United States ; R01 NS099531/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Bacteria ; *Bacteriophages ; *Brain Ischemia ; Dysbiosis ; *Gastrointestinal Microbiome ; Metagenomics ; Mice ; Virome ; *Viruses/genetics ; }, abstract = {Stroke leads to gut bacterial dysbiosis that impacts the post-stroke outcome. The gut microbiome also contains a high abundance of viruses which might play a crucial role in disease progression and recovery by modulating the metabolism of both host and host's gut bacteria. We presently analyzed the virome composition (viruses and phages) by shotgun metagenomics in the fecal samples obtained at 1 day of reperfusion following transient focal ischemia in adult mice. Viral genomes, viral auxiliary metabolic genes, and viral protein networks were compared between stroke and sham conditions (stroke vs sham, exclusive to sham and exclusive to stroke). Following focal ischemia, abundances of 2 viral taxa decreased, and 5 viral taxa increased compared with the sham. Furthermore, the abundance of Clostridia-like phages and Erysipelatoclostridiaceae-like phages were altered in the stroke compared with the sham cohorts. This is the first report to show that the gut virome responds acutely to stroke.}, } @article {pmid35699469, year = {2022}, author = {Low, A and Lee, JKY and Gounot, JS and Ravikrishnan, A and Ding, Y and Saw, WY and Tan, LWL and Moong, DKN and Teo, YY and Nagarajan, N and Seedorf, H}, title = {Mutual Exclusion of Methanobrevibacter Species in the Human Gut Microbiota Facilitates Directed Cultivation of a Candidatus Methanobrevibacter Intestini Representative.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0084922}, pmid = {35699469}, issn = {2165-0497}, mesh = {Feces ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Methanobrevibacter/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Methanogenic Archaea (methanogens) are a phylogenetically diverse group of microorganisms and are considered to be the most abundant archaeal representatives in the human gut. However, the gut methanogen diversity of human populations in many global regions remains poorly investigated. Here, we report the abundance and diversity of gut methanogenic Archaea in a multi-ethnic cohort of healthy Singaporeans by using a concerted approach of metagenomic sequencing, 16S rRNA gene amplicon sequencing, and quantitative PCR. Our results indicate a mutual exclusion of Methanobrevibacter species, i.e., the highly prevalent Methanobrevibacter smithii and the less prevalent Candidatus Methanobrevibacter intestini in more than 80% of the samples when using an amplicon sequencing-based approach. Leveraging on this finding, we were able to select a fecal sample to isolate a representative strain, TLL-48-HuF1, for Candidatus Methanobrevibacter intestini. The analyzed physiological parameters of M. smithii DSM 861[T] and strain TLL-48-HuF1 suggest high similarity of the two species. Comparative genome analysis and the mutual exclusion of the Methanobrevibacter species indicate potentially different niche adaptation strategies in the human host, which may support the designation of Candidatus M. intestini as a novel species. IMPORTANCE Methanogens are important hydrogen consumers in the gut and are associated with differing host health. Here, we determine the prevalence and abundance of archaeal species in the guts of a multi-ethnic cohort of healthy Singapore residents. While Methanobrevibacter smithii is the most prevalent and abundant methanogen in the human gut of local subjects, the recently proposed Candidatus Methanobrevibacter intestini is the abundant methanogen in a minority of individuals that harbor them. The observed potential mutual exclusion of M. smithii and Ca. M. intestini provides further support to the proposal that the two physiologically similar strains may belong to different Methanobrevibacter species.}, } @article {pmid35699432, year = {2022}, author = {Tlais, AZA and Lemos Junior, WJF and Filannino, P and Campanaro, S and Gobbetti, M and Di Cagno, R}, title = {How Microbiome Composition Correlates with Biochemical Changes during Sauerkraut Fermentation: a Focus on Neglected Bacterial Players and Functionalities.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0016822}, pmid = {35699432}, issn = {2165-0497}, mesh = {Bacteria/genetics ; *Brassica/chemistry/metabolism/microbiology ; Fermentation ; Food Microbiology ; *Microbiota ; }, abstract = {This study provided a new perspective on the bacterial community succession during sauerkraut fermentation, and on resulting metabolic functions. While culture-dependent methods confirmed the key role of the well-known core microbiome species, metagenomic approach (shotgun) revealed Secundilactobacillus malefermentans as a species of the core microbiome, especially during the last weeks of fermentation. Although the potentiality of S. malefermentans has not yet fully explored, it held core functional genes usually attributed to others lactic acid bacteria driving sauerkraut fermentation. Based on our results it is arguable that S. malefermentans might have a key a role during sauerkraut fermentation carried out at low temperature. Under our experimental conditions, the profile of phenolic compounds changed throughout sauerkraut fermentation. The amount of free phenolics, including free phenolic acids, increased at the beginning of the fermentation, whereas the conversion of phenolic acids into microbial derivatives was consistent during the last part of the sauerkraut fermentation. We pioneered correlating changes in the phenolics profile to changes in the microbiome, although the framework presented is still fragmentary. Annotated genes linked to the phenolic compounds metabolism (VprA and padA) were found in many core species during the whole process. A high metabolic potential for phenolics bioconversion emerged for lactobacilli and Pediococcus spp. through correlation analysis between microbiome composition and phenolics profile. IMPORTANCE Our study was not limited to describe the succession pattern of the microbial community during sauerkraut fermentation, but also revealed how some neglected bacterial players belong to the core species during sauerkrauts processing, especially at low temperature. Such species might have a role as potential starters to optimize the fermentation processes and to obtain sauerkrauts with improved and standardized nutritional and sensory features. Furthermore, our correlations between microbiome composition and phenolics profile might also represent new references for sauerkraut biotechnology, aiming to identify new metabolic drivers of potential sauerkraut functionalities. Finally, sauerkraut ecosystem is a tractable model, although with high level of complexity, and resultant ecological information might be extended to other plant ecosystems.}, } @article {pmid35698614, year = {2022}, author = {Li, Y and Bi, Y and Yang, L and Jin, K}, title = {Comparative study on intestinal microbiome composition and function in young and adult Hainan gibbons (Nomascus hainanus).}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13527}, pmid = {35698614}, issn = {2167-8359}, mesh = {Animals ; Hylobates ; *Gastrointestinal Microbiome/genetics ; *Hylobatidae ; *Microbiota ; Firmicutes ; Bacteroidetes ; }, abstract = {The Hainan gibbon is one of the most endangered primates in the world, with a small population size, narrow distribution range, and high inbreeding risk, which retains the risk of species extinction. To explore the composition and functional differences of the intestinal microbiome of Hainan gibbons at different ages, the faecal microbiomes of young and adult Hainan gibbons were analysed using metagenome sequencing. The results showed that the dominant phyla in the intestinal tract of young and adult Hainan gibbons were Firmicutes and Bacteroidetes, and the dominant genus was Prevotella. Linear discriminant analysis effect size analysis showed that Firmicutes, Ruminococcus, Clostridium, and Butyrivibrio were significantly more abundant in adults than in young, whereas Bacteroidetes, Proteobacteria, Prevotella, and Bacteroides were significantly more abundant in young than in adults. In terms of gene function, the adult Hainan gibbon intestinal microbiome generally harboured a higher abundance of genes related to metabolic processes, such as carbohydrate, amino acid, and nucleotide metabolism. This may be due to adaptive advantages for adult Hainan gibbons, such as stable and mature intestinal microbiome composition, which allows them to utilise diverse foods efficiently. In summary, this study helps understand the dynamic changes in the intestinal microbiome of young and adult Hainan gibbons and plays a key role in the health monitoring and rejuvenation of their population.}, } @article {pmid35696554, year = {2022}, author = {Han, Y and Quan, X and Chuang, Y and Liang, Q and Li, Y and Yuan, Z and Bian, Y and Wei, L and Wang, J and Zhao, Y}, title = {A multi-omics analysis for the prediction of neurocognitive disorders risk among the elderly in Macao.}, journal = {Clinical and translational medicine}, volume = {12}, number = {6}, pages = {e909}, pmid = {35696554}, issn = {2001-1326}, mesh = {Aged ; *Gastrointestinal Microbiome ; Humans ; Macau ; Metagenomics/methods ; Neurocognitive Disorders ; *Proteomics/methods ; }, abstract = {BACKGROUND: Due to the increasing ageing population, neurocognitive disorders (NCDs) have been a global public health issue, and its prevention and early diagnosis are crucial. Our previous study demonstrated that there is a significant correlation between specific populations and NCDs, but the biological characteristics of the vulnerable group predispose to NCDs are unclear. The purpose of this study is to investigate the predictors for the vulnerable group by a multi-omics analysis.

METHODS: Multi-omics approaches, including metagenomics, metabolomic and proteomic, were used to detect gut microbiota, faecal metabolites and urine exosome of 8 normal controls and 13 vulnerable elders after a rigorous screening of 400 elders in Macao. The multi-omics data were analysed using R and Bioconductor. The two-sided Wilcoxon's rank-sum test, Kruskal-Wallis rank sum test and the linear discriminant analysis effective size were applied to investigate characterized features. Moreover, a 2-year follow-up was conducted to evaluate cognitive function change of the elderly.

RESULTS: Compared with the control elders, the metagenomics of gut microbiota showed that Ruminococcus gnavus, Lachnospira eligens, Escherichia coli and Desulfovibrio piger were increased significantly in the vulnerable group. Carboxylates, like alpha-ketoglutaric acid and d-saccharic acid, and levels of vitamins had obvious differences in the faecal metabolites. There was a distinct decrease in the expression of eukaryotic translation initiation factor 2 subunit 1 (eIF2α) and amine oxidase A (MAO-A) according to the proteomic results of the urine exosomes. Moreover, the compound annual growth rate of neurocognitive scores was notably decreased in vulnerable elders.

CONCLUSIONS: The multi-omics characteristics of disturbed glyoxylate and dicarboxylate metabolism (bacteria), vitamin digestion and absorption and tricarboxylic acid cycle in vulnerable elders can serve as predictors of NCDs risk among the elderly of Macao. Intervention with them may be effective therapeutic approaches for NCDs, and the underlying mechanisms merit further exploration.}, } @article {pmid35695679, year = {2022}, author = {Bouzid, F and Gtif, I and Alfadhli, S and Charfeddine, S and Ghorbel, W and Abdelhédi, R and Benmarzoug, R and Abid, L and Bouayed Abdelmoula, N and Elloumi, I and Masmoudi, S and Rebai, A and Kharrat, N}, title = {A potential oral microbiome signature associated with coronary artery disease in Tunisia.}, journal = {Bioscience reports}, volume = {42}, number = {7}, pages = {}, pmid = {35695679}, issn = {1573-4935}, mesh = {Bacteria/genetics ; *Coronary Artery Disease/genetics ; Humans ; Metagenome ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Streptococcus ; Tunisia/epidemiology ; }, abstract = {The coronary artery disease (CAD) is a chronic inflammatory disease involving genetic as well as environmental factors. Recent evidence suggests that the oral microbiome has a significant role in triggering atherosclerosis. The present study assessed the oral microbiome composition variation between coronary patients and healthy subjects in order to identify a potential pathogenic signature associated with CAD. We performed metagenomic profiling of salivary microbiomes by 16S ribosomal RNA (rRNA) next-generation sequencing. Oral microbiota profiling was performed for 30 individuals including 20 patients with CAD and ten healthy individuals without carotid plaques or previous stroke or myocardial infarction. We found that oral microbial communities in patients and healthy controls are represented by similar global core oral microbiome. The predominant taxa belonged to Firmicutes (genus Streptococcus, Veillonella, Granulicatella, Selenomonas), Proteobacteria (genus Neisseria, Haemophilus), Actinobacteria (genus Rothia), Bacteroidetes (genus Prevotella, Porphyromonas), and Fusobacteria (genus Fusobacterium, Leptotrichia). More than 60% relative abundance of each sample for both CAD patients and controls is represented by three major genera including Streptococcus (24.97 and 26.33%), Veillonella (21.43 and 19.91%), and Neisseria (14.23 and 15.33%). Using penalized regression analysis, the bacterial genus Eikenella was involved as the major discriminant genus for both status and Syntax score of CAD. We also reported a significant negative correlation between Syntax score and Eikenella abundance in coronary patients' group (Spearman rho = -0.68, P=0.00094). In conclusion, the abundance of Eikenella in oral coronary patient samples compared with controls could be a prominent pathological indicator for the development of CAD.}, } @article {pmid35695567, year = {2022}, author = {Tinker, K and Lipus, D and Gardiner, J and Stuckman, M and Gulliver, D}, title = {The Microbial Community and Functional Potential in the Midland Basin Reveal a Community Dominated by Both Thiosulfate and Sulfate-Reducing Microorganisms.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0004922}, pmid = {35695567}, issn = {2165-0497}, mesh = {*Hydrogen Sulfide ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sulfates/chemistry ; Thiosulfates ; Water ; }, abstract = {The Permian Basin is the highest producing oil and gas reservoir in the United States. Hydrocarbon resources in this region are often accessed by unconventional extraction methods, including horizontal drilling and hydraulic fracturing. Despite the importance of the Permian Basin, there is no publicly available microbiological data from this region. We completed an analysis of Permian produced water samples to understand the dynamics present in hydraulically fractured wells in this region. We analyzed produced water samples taken from 10 wells in the Permian region of the Midland Basin using geochemical measurements, 16S rRNA gene sequencing, and metagenomic sequencing. Compared to other regions, we found that Permian Basin produced water was characterized by higher sulfate and lower total dissolved solids (TDS) concentrations, with a median of 1,110 mg/L and 107,000 mg/L. Additionally, geochemical measurements revealed the presence of frac hits, or interwell communication events where an established well is affected by the pumping of fracturing fluid into a new well. The occurrence of frac hits was supported by correlations between the microbiome and the geochemical parameters. Our 16S rRNA gene sequencing identified a produced water microbiome characterized by anaerobic, halophilic, and sulfur reducing taxa. Interestingly, sulfate and thiosulfate reducing taxa including Halanaerobium, Orenia, Marinobacter, and Desulfohalobium were the most prevalent microbiota in most wells. We further investigated the metabolic potential of microorganisms in the Permian Basin with metagenomic sequencing. We recovered 15 metagenome assembled genomes (MAGs) from seven different samples representing 6 unique well sites. These MAGs corroborated the high presence of sulfate and thiosulfate reducing genes across all wells, especially from key taxa including Halanaerobium and Orenia. The observed microbiome composition and metabolic capabilities in conjunction with the high sulfate concentrations demonstrate a high potential for hydrogen sulfide production in the Permian Basin. Additionally, evidence of frac hits suggests the possibility for the exchange of microbial cells and/or genetic information between wells. This exchange would increase the likelihood of hydrogen sulfide production and has implications for the oil and gas industry. IMPORTANCE The Permian Basin is the largest producing oil and gas region in the United States and plays a critical role supplying national energy needs. Previous work in other basins has demonstrated that the geochemistry and microbiology of hydrocarbon regions can have a major impact on well infrastructure and production. Despite that, little work has been done to understand the complex dynamics present in the Permian Basin. This study characterizes and analyzes 10 unique wells and one groundwater sample in the Permian Basin using geochemical and microbial techniques. Across all wells we found a high number of classic and thiosulfate reducers, suggesting that hydrogen sulfide production may be especially prevalent in the Permian Basin. Additionally, our analysis revealed a biogeochemical signal impacted by the presence of frac hits, or interwell communication events where an established well is affected by the pumping of fracturing fluid into a new well. This information can be utilized by the oil and gas industry to improve oil recovery efforts and minimize commercial and environmental costs.}, } @article {pmid35695430, year = {2022}, author = {Fansler, RT and Zhu, W}, title = {Mind the Gap: Bridging the Divide from Sequencing Data to Empiric Phenotypes in the Human Gut Microbiota.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0020722}, pmid = {35695430}, issn = {2379-5077}, support = {R01 DK134692/DK/NIDDK NIH HHS/United States ; R35 GM147470/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; Polysaccharides ; *Microbiota ; Genomics ; }, abstract = {The gut microbiome exerts a powerful influence on human health and disease. Elucidating the underlying mechanisms of the microbiota's influence is hindered by the immense complexity of the gut microbial community and the glycans they forage. Despite a wealth of genomic and metagenomic sequencing information, there remains a lack of informative phenotypic measurements. Pudlo NA, Urs K, Crawford R, Pirani A, et al. (mSystems 7: e00947-21, 2022, https://doi.org/10.1128/msystems.00947-21) decode this complexity by introducing a scalable assay to measure specific carbohydrate utilization in the dominant microbiota phylum Bacteroidetes. The results reveal a mosaic structure of glycan utilization, both genetic and functional, underpinning niche construction in the human gastrointestinal tract. This Commentary highlights the significance of their findings in connection to the field's growing appreciation for competition, cooperation, and horizontal gene transfer in shaping the highly complex microbial community.}, } @article {pmid35691354, year = {2022}, author = {Silveira, DD and Farooq, AJ and Wallace, SJ and Lapolli, FR and Nivala, J and Weber, KP}, title = {Structural and functional spatial dynamics of microbial communities in aerated and non-aerated horizontal flow treatment wetlands.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 4}, pages = {156600}, doi = {10.1016/j.scitotenv.2022.156600}, pmid = {35691354}, issn = {1879-1026}, mesh = {*Environmental Pollutants ; *Microbiota ; RNA, Ribosomal, 16S ; Waste Disposal, Fluid/methods ; *Water Purification/methods ; Wetlands ; }, abstract = {A multiphasic study using structural and functional analyses was employed to investigate the spatial dynamics of the microbial community within five horizontal subsurface flow treatment wetlands (TWs) of differing designs in Germany. The TWs differed in terms of the depth of media saturation, presence of plants (Phragmites australis), and aeration. In addition to influent and effluent water samples, internal samples were taken at different locations (12.5 %, 25 %, 50 %, and 75 % of the fractional distance along the flow path) within each system. 16S rRNA sequencing was used for the investigation of microbial community structure and was compared to microbial community function and enumeration data. The microbial community structure in the unaerated systems was similar, but different from the aerated TW profiles. Spatial positioning along the flow path explained the majority of microbial community dynamics/differences within this study. This was mainly attributed to the availability of nutrients closer to the inlet which also regulated the fixed biofilm/biomass densities. As the amount of fixed biofilm decreased from the inlet to the TW outlets, structural diversity increased, suggesting different microbial communities were present to handle the more easily utilized/degraded pollutants near the inlet vs. the more difficult to degrade and recalcitrant pollutants closer to the outlets. This study also confirmed that effluent water samples do not accurately describe the microbial communities responsible for water treatment inside a TW, highlighting the importance of using internal samples for investigating microbial communities in TWs. The results of this study reinforce an existing knowledge gap regarding the potential for TW design modifications which incorporate microbial community spatial dynamics (heterogeneity). It is suggested that utilizing step-feeding could allow for improved water treatment within the same areal footprint, and modifications enhancing co-metabolic processes could assist in improving the treatment of more difficult to degrade or recalcitrant compounds such as micropollutants.}, } @article {pmid35690059, year = {2022}, author = {Wilmanski, T and Kornilov, SA and Diener, C and Conomos, MP and Lovejoy, JC and Sebastiani, P and Orwoll, ES and Hood, L and Price, ND and Rappaport, N and Magis, AT and Gibbons, SM}, title = {Heterogeneity in statin responses explained by variation in the human gut microbiome.}, journal = {Med (New York, N.Y.)}, volume = {3}, number = {6}, pages = {388-405.e6}, pmid = {35690059}, issn = {2666-6340}, support = {U19 AG023122/AG/NIA NIH HHS/United States ; }, mesh = {Cross-Sectional Studies ; *Diabetes Mellitus, Type 2/drug therapy ; *Gastrointestinal Microbiome/genetics ; Humans ; *Hydroxymethylglutaryl-CoA Reductase Inhibitors/adverse effects ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Statins remain one of the most prescribed medications worldwide. While effective in decreasing atherosclerotic cardiovascular disease risk, statin use is associated with adverse effects for a subset of patients, including disrupted metabolic control and increased risk of type 2 diabetes.

METHODS: We investigated the potential role of the gut microbiome in modifying patient responses to statin therapy across two independent cohorts (discovery n = 1,848, validation n = 991). Microbiome composition was assessed in these cohorts using stool 16S rRNA amplicon and shotgun metagenomic sequencing, respectively. Microbiome associations with markers of statin on-target and adverse effects were tested via a covariate-adjusted interaction analysis framework, utilizing blood metabolomics, clinical laboratory tests, genomics, and demographics data.

FINDINGS: The hydrolyzed substrate for 3-hydroxy-3-methylglutarate-coenzyme-A (HMG-CoA) reductase, HMG, emerged as a promising marker for statin on-target effects in cross-sectional cohorts. Plasma HMG levels reflected both statin therapy intensity and known genetic markers for variable statin responses. Through exploring gut microbiome associations between blood-derived measures of statin effectiveness and adverse metabolic effects of statins, we find that heterogeneity in statin responses was consistently associated with variation in the gut microbiome across two independent cohorts. A Bacteroides-enriched and diversity-depleted gut microbiome was associated with more intense statin responses, both in terms of on-target and adverse effects.

CONCLUSIONS: With further study and refinement, gut microbiome monitoring may help inform precision statin treatment.

FUNDING: This research was supported by the M.J. Murdock Charitable Trust, WRF, NAM Catalyst Award, and NIH grant U19AG023122 awarded by the NIA.}, } @article {pmid35689701, year = {2022}, author = {Imai, T and Inoue, R and Nishida, A and Yokota, Y and Morishima, S and Kawahara, M and Kusada, H and Tamaki, H and Andoh, A}, title = {Features of the gut prokaryotic virome of Japanese patients with Crohn's disease.}, journal = {Journal of gastroenterology}, volume = {57}, number = {8}, pages = {559-570}, pmid = {35689701}, issn = {1435-5922}, mesh = {Bacteria/genetics ; *Crohn Disease/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Japan ; RNA, Ribosomal, 16S/genetics ; Virome/genetics ; }, abstract = {BACKGROUND/AIMS: The gut virome is mainly composed of bacteriophages and influences gut homeostasis and pathogenic conditions. In this study, we analyzed the gut prokaryotic virome in Japanese patients with Crohn's disease (CD).

MATERIALS/METHODS: We collected 19 fecal samples from CD patients and 16 samples from healthy controls. The gut bacteriome was analyzed by 16S rRNA gene sequencing and the virome was profiled by shotgun metagenomic sequencing.

RESULTS: Despite no differences in richness and evenness, there was a significant difference in the overall structure of the gut virome between CD patients and controls (P = 0.013). CrAssphage and Staphylococcus virus, belonging to the order Caudovirales, were dominant in the gut virome of controls and CD patients. The abundance of crAssphage was significantly greater in CD patients than controls (P = 0.021). Lactococcus, Enterococcus and Lactobacillus phages were present only in CD patients, while Xanthomonas and Escherichia phages were unique to the controls. In the gut bacteriome of CD patients, richness and evenness were significantly lower, and a significant difference in the overall structure was observed between groups (P = 0.014). The gut bacteriome of CD patients was characterized by a decrease of the genera Faecalibacterium, Roseburia, and Ruminococcus and an increase of the family Enterobacteriaceae. There were more significant correlations between viruses and bacteria in CD patients than controls.

CONCLUSIONS: The gut virome of CD patients was distinct from that of healthy controls in a Japanese population. An altered gut virome may be one of the factors associated with the bacterial dysbiosis of CD.}, } @article {pmid35689184, year = {2022}, author = {Van der Jeugt, F and Maertens, R and Steyaert, A and Verschaffelt, P and De Tender, C and Dawyndt, P and Mesuere, B}, title = {UMGAP: the Unipept MetaGenomics Analysis Pipeline.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {433}, pmid = {35689184}, issn = {1471-2164}, support = {1164420N//Agentschap voor Innovatie door Wetenschap en Technologie/ ; 1174621N//Agentschap voor Innovatie door Wetenschap en Technologie/ ; 1512619N//Agentschap voor Innovatie door Wetenschap en Technologie/ ; 12I5220N//Agentschap voor Innovatie door Wetenschap en Technologie/ ; }, mesh = {Algorithms ; Bacteria/genetics ; *Metagenomics ; Sequence Analysis, DNA ; Software ; *Viruses/genetics ; }, abstract = {BACKGROUND: Shotgun metagenomics yields ever richer and larger data volumes on the complex communities living in diverse environments. Extracting deep insights from the raw reads heavily depends on the availability of fast, accurate and user-friendly biodiversity analysis tools.

RESULTS: Because environmental samples may contain strains and species that are not covered in reference databases and because protein sequences are more conserved than the genes encoding them, we explore the alternative route of taxonomic profiling based on protein coding regions translated from the shotgun metagenomics reads, instead of directly processing the DNA reads. We therefore developed the Unipept MetaGenomics Analysis Pipeline (UMGAP), a highly versatile suite of open source tools that are implemented in Rust and support parallelization to achieve optimal performance. Six preconfigured pipelines with different performance trade-offs were carefully selected, and benchmarked against a selection of state-of-the-art shotgun metagenomics taxonomic profiling tools.

CONCLUSIONS: UMGAP's protein space detour for taxonomic profiling makes it competitive with state-of-the-art shotgun metagenomics tools. Despite our design choices of an extra protein translation step, a broad spectrum index that can identify both archaea, bacteria, eukaryotes and viruses, and a highly configurable non-monolithic design, UMGAP achieves low runtime, manageable memory footprint and high accuracy. Its interactive visualizations allow for easy exploration and comparison of complex communities.}, } @article {pmid35688988, year = {2022}, author = {Yi, X and Liang, JL and Su, JQ and Jia, P and Lu, JL and Zheng, J and Wang, Z and Feng, SW and Luo, ZH and Ai, HX and Liao, B and Shu, WS and Li, JT and Zhu, YG}, title = {Globally distributed mining-impacted environments are underexplored hotspots of multidrug resistance genes.}, journal = {The ISME journal}, volume = {16}, number = {9}, pages = {2099-2113}, pmid = {35688988}, issn = {1751-7370}, support = {42077117//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Drug Resistance, Multiple/genetics ; *Genes, Bacterial ; *Genes, MDR ; Humans ; Metagenome ; *Mining ; Phylogeny ; }, abstract = {Mining is among the human activities with widest environmental impacts, and mining-impacted environments are characterized by high levels of metals that can co-select for antibiotic resistance genes (ARGs) in microorganisms. However, ARGs in mining-impacted environments are still poorly understood. Here, we conducted a comprehensive study of ARGs in such environments worldwide, taking advantage of 272 metagenomes generated from a global-scale data collection and two national sampling efforts in China. The average total abundance of the ARGs in globally distributed studied mine sites was 1572 times per gigabase, being rivaling that of urban sewage but much higher than that of freshwater sediments. Multidrug resistance genes accounted for 40% of the total ARG abundance, tended to co-occur with multimetal resistance genes, and were highly mobile (e.g. on average 16% occurring on plasmids). Among the 1848 high-quality metagenome-assembled genomes (MAGs), 85% carried at least one multidrug resistance gene plus one multimetal resistance gene. These high-quality ARG-carrying MAGs considerably expanded the phylogenetic diversity of ARG hosts, providing the first representatives of ARG-carrying MAGs for the Archaea domain and three bacterial phyla. Moreover, 54 high-quality ARG-carrying MAGs were identified as potential pathogens. Our findings suggest that mining-impacted environments worldwide are underexplored hotspots of multidrug resistance genes.}, } @article {pmid35686590, year = {2022}, author = {Jiang, S and Nie, J and Chen, YX and Wang, XY and Chen, F}, title = {Structure and Composition of Candidate Phyla Radiation in Supragingival Plaque of Caries Patients.}, journal = {The Chinese journal of dental research}, volume = {25}, number = {2}, pages = {107-118}, doi = {10.3290/j.cjdr.b3086339}, pmid = {35686590}, issn = {1867-5646}, mesh = {Bacteria ; Capnocytophaga ; *Dental Caries ; Dental Caries Susceptibility ; *Dental Deposits ; *Dental Plaque/microbiology ; Humans ; *Microbiota ; Mouth/microbiology ; }, abstract = {OBJECTIVE: To investigate the composition and abundance of candidate phyla radiation (CPR) in the oral cavity in caries patients and a healthy population.

METHODS: The raw macrogenomic sequencing data for a total of 88 subjects were downloaded from the National Centre for Biotechnology Sequence Read Archive (NCBI SRA) public database according to the public data usage specifications. Trimmomatic (Department for Metabolic Networks, Potsdam, Germany) and Bowtie 2 (University of Maryland, College Park, MD, USA) were used to quality control and dehost the host sequences. Species annotation was made using Kraken2 (Johns Hopkins University, Baltimore, MD, USA) and Bracken (Johns Hopkins University) based on the reference database. According to the results of the species annotation, the species-significant differences and species correlation of caries and healthy oral microbiota in species composition and microbiota diversity were analysed to study the distribution and abundance differences of CPR in the oral environment.

RESULTS: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria were the main components. The relative abundance of TM7 (Candidatus Saccharibacteria) and GN02 (Candidatus Gracilibacteria) of CPR is second only to the aforementioned five bacteria, indicating that CPR is an important part of the oral microbiota. TM7 and GN02 were common to both the caries patients and healthy patients and were detected in all samples, suggesting that CPR is the 'core microbiome'. There was a correlation between CPR and a variety of oral microbiota, among which the positive correlation with Capnocytophaga was the strongest, suggesting that Capnocytophaga might be the potential host bacteria of CPR.

CONCLUSION: CPR is an indispensable part of the oral microbiota. It is the 'core microflora' of the oral cavity and may play an important role in the stability and function of the oral microecological environment. Capnocytophaga may be the potential host bacteria of CPR.}, } @article {pmid35685549, year = {2022}, author = {Fang, C and Zuo, K and Zhang, W and Zhong, J and Li, J and Xu, L and Yang, X}, title = {Association between Gut Microbiota Dysbiosis and the CHA2DS2-VASc Score in Atrial Fibrillation Patients.}, journal = {International journal of clinical practice}, volume = {2022}, number = {}, pages = {7942605}, pmid = {35685549}, issn = {1742-1241}, mesh = {*Atrial Fibrillation/complications ; Dysbiosis/complications ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Risk Assessment ; Risk Factors ; *Stroke/complications ; *Thromboembolism/etiology ; }, abstract = {BACKGROUND: In our previous studies, we found a disordered taxonomic composition and function of gut microbiota (GM) in atrial fibrillation (AF) patients. However, direct evidence about the association between dysbiotic microbiota and thromboembolic risk in AF is lacking.

AIMS: In this study, we analyzed the interaction of GM and related functional patterns in AF with different CHA2DS2-VASc scores to assess its potential as a biomarker for predicting stroke risk. Patients and Methods. The CHA2DS2-VASc score was used for thromboembolic risk stratification in AF according to American Heart Association (AHA) guidelines. We investigated the taxonomic and functional annotation of GM based on metagenomic data from 50 AF patients (32 with high thromboembolic risk (CHA2DS2-VASc score ≥2 (males) or CHA2DS2-VASc score ≥3 (females)) and 18 individuals with low thromboembolic risk (CHA2DS2-VASc score <2 (males) or CHA2DS2-VASc score <3 (females))).

RESULTS: The gut microbial diversity, composition, and function in AF were different in high and low CHA2DS2-VASc score groups. In high thromboembolic risk group, the abundance of Prevotella, Lachnospiraceae, and Eubacterium rectale, related to the production of short-chain fatty acids and anti-inflammatory were reduced (all P < 0.05). Furthermore, annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG), a database of genes and genomes, the KEGG orthology-based scoring approach exhibited a significant association with thromboembolic risk in AF patients.

CONCLUSIONS: Imbalance of GM and microbial dysfunction are involved in aggravated thromboembolic risk of AF.}, } @article {pmid35684099, year = {2022}, author = {Gold, MS and Quinn, PJ and Campbell, DE and Peake, J and Smart, J and Robinson, M and O'Sullivan, M and Vogt, JK and Pedersen, HK and Liu, X and Pazirandeh-Micol, E and Heine, RG}, title = {Effects of an Amino Acid-Based Formula Supplemented with Two Human Milk Oligosaccharides on Growth, Tolerability, Safety, and Gut Microbiome in Infants with Cow's Milk Protein Allergy.}, journal = {Nutrients}, volume = {14}, number = {11}, pages = {}, pmid = {35684099}, issn = {2072-6643}, mesh = {Amino Acids ; Animals ; Cattle ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant Formula ; Male ; *Milk Hypersensitivity ; Milk, Human ; Oligosaccharides ; }, abstract = {This open-label, non-randomized, multicenter trial (Registration: NCT03661736) aimed to assess if an amino acid-based formula (AAF) supplemented with two human milk oligosaccharides (HMO) supports normal growth and is well tolerated in infants with a cow's milk protein allergy (CMPA). Term infants aged 1-8 months with moderate-to-severe CMPA were enrolled. The study formula was an AAF supplemented with 2'-fucosyllactose (2'-FL) and lacto-N-neotetraose (LNnT). Infants were fed the study formula for 4 months and were offered to remain on the formula until 12 months of age. Tolerance and safety were assessed throughout the trial. Out of 32 infants (mean age 18.6 weeks; 20 (62.5%) male), 29 completed the trial. During the 4-month principal study period, the mean weight-for-age Z score (WAZ) increased from -0.31 at the baseline to +0.28 at the 4-months' follow-up. Linear and head growth also progressed along the WHO child growth reference, with a similar small upward trend. The formula was well tolerated and had an excellent safety profile. When comparing the microbiome at the baseline to the subsequent visits, there was a significant on-treatment enrichment in HMO-utilizing bifidobacteria, which was associated with a significant increase in fecal short-chain fatty acids. In addition, we observed a significant reduction in the abundance of fecal Proteobacteria, suggesting that the HMO-supplemented study formula partially corrected the gut microbial dysbiosis in infants with CMPA.}, } @article {pmid35681493, year = {2022}, author = {Das De, T and Sharma, P and Tevatiya, S and Chauhan, C and Kumari, S and Yadav, P and Singla, D and Srivastava, V and Rani, J and Hasija, Y and Pandey, KC and Kajla, M and Dixit, R}, title = {Bidirectional Microbiome-Gut-Brain-Axis Communication Influences Metabolic Switch-Associated Responses in the Mosquito Anopheles culicifacies.}, journal = {Cells}, volume = {11}, number = {11}, pages = {}, pmid = {35681493}, issn = {2073-4409}, mesh = {Animals ; *Anopheles ; Bacteria/genetics ; Brain/metabolism ; Cell Communication ; Female ; *Gastrointestinal Microbiome/physiology ; }, abstract = {The periodic ingestion of a protein-rich blood meal by adult female mosquitoes causes a drastic metabolic change in their innate physiological status, which is referred to as a 'metabolic switch'. While understanding the neural circuits for host-seeking is modestly attended, how the gut 'metabolic switch' modulates brain functions, and resilience to physiological homeostasis, remains unexplored. Here, through a comparative brain RNA-Seq study, we demonstrate that the protein-rich diet induces the expression of brain transcripts related to mitochondrial function and energy metabolism, possibly causing a shift in the brain's engagement to manage organismal homeostasis. A dynamic mRNA expression pattern of neuro-signaling and neuro-modulatory genes in both the gut and brain likely establishes an active gut-brain communication. The disruption of this communication through decapitation does not affect the modulation of the neuro-modulator receptor genes in the gut. In parallel, an unusual and paramount shift in the level of neurotransmitters (NTs), from the brain to the gut after blood feeding, further supports the idea of the gut's ability to serve as a 'second brain'. After blood-feeding, a moderate enrichment of the gut microbial population, and altered immunity in the gut of histamine receptor-silenced mosquitoes, provide initial evidence that the gut-microbiome plays a crucial role in gut-brain-axis communication. Finally, a comparative metagenomics evaluation of the gut microbiome highlighted that blood-feeding enriches the family members of the Morganellaceae and Pseudomonadaceae bacterial communities. The notable observation of a rapid proliferation of Pseudomonas bacterial sp. and tryptophan enrichment in the gut correlates with the suppression of appetite after blood-feeding. Additionally, altered NTs dynamics of naïve and aseptic mosquitoes provide further evidence that gut-endosymbionts are key modulators for the synthesis of major neuroactive molecules. Our data establish a new conceptual understanding of microbiome-gut-brain-axis communication in mosquitoes.}, } @article {pmid35680904, year = {2022}, author = {Bruce, SA and Aytur, SA and Andam, CP and Bucci, JP}, title = {Metagenomics to characterize sediment microbial biodiversity associated with fishing exposure within the Stellwagen Bank National Marine Sanctuary.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9499}, pmid = {35680904}, issn = {2045-2322}, mesh = {Biodiversity ; *Biological Products ; Ecosystem ; Geologic Sediments ; Hunting ; Metagenomics ; *Microbiota/genetics ; }, abstract = {Microbes in marine sediments constitute a large percentage of the global marine ecosystem and function to maintain a healthy food web. In continental shelf habitats such as the Gulf of Maine (GoM), relatively little is known of the microbial community abundance, biodiversity, and natural product potential. This report is the first to provide a time-series assessment (2017-2020) of the sediment microbial structure in areas open and closed to fishing within the Stellwagen Bank National Marine Sanctuary (SBNMS). A whole metagenome sequencing (WMS) approach was used to characterize the sediment microbial community. Taxonomic abundance was calculated across seven geographic sites with 14 individual sediment samples collected during the summer and fall seasons. Bioinformatics analyses identified more than 5900 different species across multiple years. Non-metric multidimensional scaling methods and generalized linear models demonstrated that species richness was inversely associated with fishing exposure levels and varied by year. Additionally, the discovery of 12 unique biosynthetic gene clusters (BGCs) collected across sites confirmed the potential for medically relevant natural product discovery in the SBNMS. This study provides a practical assessment of how fishing exposure and temporal trends may affect microbial community structure in a coastal marine sanctuary.}, } @article {pmid35680554, year = {2023}, author = {Kuhl, LP and Marostica, PJC and Macedo, AJ and Kuhl, G and Siebert, M and Manica, D and Sekine, L and Schweiger, C}, title = {High microbiome variability in pediatric tracheostomy cannulas in patients with similar clinical characteristics.}, journal = {Brazilian journal of otorhinolaryngology}, volume = {89}, number = {2}, pages = {254-263}, pmid = {35680554}, issn = {1808-8686}, mesh = {RNA, Ribosomal, 16S/genetics ; *Tracheostomy ; Cannula ; *Microbiota/genetics ; Brazil ; }, abstract = {OBJECTIVES: To evaluate the bacterial microbiome found in tracheostomy cannulas of a group of children diagnosed with glossoptosis secondary to Robin Sequence (RS), and its clinical implications.

METHODS: Pediatric patients were enrolled in the study at the time of the cannula change in the hospital. During this procedure, the removed cannula was collected and stored for amplicon sequencing of 16s rRNA. DNA extraction was performed using DNeasy PowerBiofilm Kit (QIAGEN® ‒ Cat nº 24000-50) while sequencing was performed with the S5 (Ion S5™ System, Thermo Fisher Scientific), following Brazilian Microbiome Project (BMP) protocol.

RESULTS: All 12 patients included in the study were using tracheostomy uncuffed cannulas of the same brand, had tracheostomy performed for over 1-year and had used the removed cannula for approximately 3-months. Most abundant genera found were Aggregatibacter, Pseudomonas, Haemophilus, Neisseria, Staphylococcus, Fusobacterium, Moraxella, Streptococcus, Alloiococcus, and Capnocytophaga. Individual microbiome of each individual was highly variable, not correlating to any particular clinical characteristic.

CONCLUSION: The microbiome of tracheostomy cannulas is highly variable, even among patients with similar clinical characteristics, making it challenging to determine a standard for normality.}, } @article {pmid35680095, year = {2022}, author = {Rehner, J and Schmartz, GP and Groeger, L and Dastbaz, J and Ludwig, N and Hannig, M and Rupf, S and Seitz, B and Flockerzi, E and Berger, T and Reichert, MC and Krawczyk, M and Meese, E and Herr, C and Bals, R and Becker, SL and Keller, A and Müller, R and , }, title = {Systematic Cross-biospecimen Evaluation of DNA Extraction Kits for Long- and Short-read Multi-metagenomic Sequencing Studies.}, journal = {Genomics, proteomics & bioinformatics}, volume = {20}, number = {2}, pages = {405-417}, pmid = {35680095}, issn = {2210-3244}, mesh = {Humans ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Feces ; High-Throughput Nucleotide Sequencing/methods ; DNA/genetics ; DNA, Bacterial/genetics ; }, abstract = {High-quality DNA extraction is a crucial step in metagenomic studies. Bias by different isolation kits impairs the comparison across datasets. A trending topic is, however, the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with diseases. We thus collected bile, stool, saliva, plaque, sputum, and conjunctival swab samples and performed DNA extraction with three commercial kits. For each combination of the specimen type and DNA extraction kit, 20-gigabase (Gb) metagenomic data were generated using short-read sequencing. While profiles of the specimen types showed close proximity to each other, we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction kits. No kit outperformed all selected kits on every specimen. We reached consistently good results using the Qiagen QiAamp DNA Microbiome Kit. Depending on the specimen, our data indicate that over 10 Gb of sequencing data are required to achieve sufficient resolution, but DNA-based identification is superior to identification by mass spectrometry. Finally, long-read nanopore sequencing confirmed the results (correlation coefficient > 0.98). Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.}, } @article {pmid35678705, year = {2022}, author = {Sun, J and Prabhu, A and Aroney, STN and Rinke, C}, title = {Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials.}, journal = {Microbial genomics}, volume = {8}, number = {6}, pages = {}, pmid = {35678705}, issn = {2057-5858}, mesh = {Animals ; *Coleoptera/metabolism ; Larva/metabolism ; *Microbiota/genetics ; Plastics/metabolism ; Polystyrenes/metabolism ; }, abstract = {Plastics are inexpensive and widely used organic polymers, but their high durability hinders biodegradation. Polystyrene, including extruded polystyrene (also known as styrofoam), is among the most commonly produced plastics worldwide and is recalcitrant to microbial degradation. In this study, we assessed changes in the gut microbiome of superworms (Zophobas morio) reared on bran, polystyrene or under starvation conditions over a 3 weeks period. Superworms on all diets were able to complete their life cycle to pupae and imago, although superworms reared on polystyrene had minimal weight gains, resulting in lower pupation rates compared to bran reared worms. The change in microbial gut communities from baseline differed considerably between diet groups, with polystyrene and starvation groups characterized by a loss of microbial diversity and the presence of opportunistic pathogens. Inferred microbial functions enriched in the polystyrene group included transposon movements, membrane restructuring and adaptations to oxidative stress. We detected several encoded enzymes with reported polystyrene and styrene degradation abilities, supporting previous reports of polystyrene-degrading bacteria in the superworm gut. By recovering metagenome-assembled genomes (MAGs) we linked phylogeny and functions and identified genera including Pseudomonas, Rhodococcus and Corynebacterium that possess genes associated with polystyrene degradation. In conclusion, our results provide the first metagenomic insights into the metabolic pathways used by the gut microbiome of superworms to degrade polystyrene. Our results also confirm that superworms can survive on polystyrene feed, but this diet has considerable negative impacts on host gut microbiome diversity and health.}, } @article {pmid35676509, year = {2022}, author = {Gharechahi, J and Sarikhan, S and Han, JL and Ding, XZ and Salekdeh, GH}, title = {Functional and phylogenetic analyses of camel rumen microbiota associated with different lignocellulosic substrates.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {46}, pmid = {35676509}, issn = {2055-5008}, mesh = {Animals ; Camelus/microbiology ; Lignin ; *Microbiota/genetics ; Phylogeny ; *Rumen/microbiology ; }, abstract = {Rumen microbiota facilitates nutrition through digestion of recalcitrant lignocellulosic substrates into energy-accessible nutrients and essential metabolites. Despite the high similarity in rumen microbiome structure, there might be distinct functional capabilities that enable different ruminant species to thrive on various lignocellulosic substrates as feed. Here, we applied genome-centric metagenomics to explore phylogenetic diversity, lignocellulose-degrading potential and fermentation metabolism of biofilm-forming microbiota colonizing 11 different plant substrates in the camel rumen. Diversity analysis revealed significant variations in the community of rumen microbiota colonizing different substrates in accordance with their varied physicochemical properties. Metagenome reconstruction recovered genome sequences of 590 bacterial isolates and one archaeal lineage belonging to 20 microbial phyla. A comparison to publicly available reference genomes and rumen metagenome-assembled genomes revealed that most isolates belonged to new species with no well-characterized representatives. We found that certain low abundant taxa, including members of Verrucomicrobiota, Planctomycetota and Fibrobacterota, possessed a disproportionately large number of carbohydrate active enzymes per Mb of genome, implying their high metabolic potential to contribute to the rumen function. In conclusion, we provided a detailed picture of the diversity and functional significance of rumen microbiota colonizing feeds of varying lignocellulose composition in the camel rumen. A detailed analysis of 591 metagenome-assembled genomes revealed a network of interconnected microbiota and highlighted the key roles of certain taxonomic clades in rumen function, including those with minimal genomes (e.g., Patescibacteria). The existence of a diverse array of gene clusters encoding for secondary metabolites unveiled the specific functions of these biomolecules in shaping community structure of rumen microbiota.}, } @article {pmid35676296, year = {2022}, author = {Suarez, C and Sedlacek, CJ and Gustavsson, DJI and Eiler, A and Modin, O and Hermansson, M and Persson, F}, title = {Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {47}, pmid = {35676296}, issn = {2055-5008}, mesh = {Anaerobic Ammonia Oxidation ; Bacteria/genetics ; Biofilms ; Bioreactors/microbiology ; *Microbiota ; *Nitrites ; }, abstract = {The resistance and resilience provided by functional redundancy, a common feature of microbial communities, is not always advantageous. An example is nitrite oxidation in partial nitritation-anammox (PNA) reactors designed for nitrogen removal in wastewater treatment, where suppression of nitrite oxidizers like Nitrospira is sought. In these ecosystems, biofilms provide microhabitats with oxygen gradients, allowing the coexistence of aerobic and anaerobic bacteria. We designed a disturbance experiment where PNA biofilms, treating water from a high-rate activated sludge process, were constantly or intermittently exposed to anaerobic sidestream wastewater, which has been proposed to inhibit nitrite oxidizers. With increasing sidestream exposure we observed decreased abundance, alpha-diversity, functional versatility, and hence functional redundancy, among Nitrospira in the PNA biofilms, while the opposite patterns were observed for anammox bacteria within Brocadia. At the same time, species turnover was observed for aerobic ammonia-oxidizing Nitrosomonas populations. The different exposure regimens were associated with metagenomic assembled genomes of Nitrosomonas, Nitrospira, and Brocadia, encoding genes related to N-cycling, substrate usage, and osmotic stress response, possibly explaining the three different patterns by niche differentiation. These findings imply that disturbances can be used to manage the functional redundancy of biofilm microbiomes in a desirable direction, which should be considered when designing operational strategies for wastewater treatment.}, } @article {pmid35676264, year = {2022}, author = {Chen, L and Zhao, N and Cao, J and Liu, X and Xu, J and Ma, Y and Yu, Y and Zhang, X and Zhang, W and Guan, X and Yu, X and Liu, Z and Fan, Y and Wang, Y and Liang, F and Wang, D and Zhao, L and Song, M and Wang, J}, title = {Short- and long-read metagenomics expand individualized structural variations in gut microbiomes.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3175}, pmid = {35676264}, issn = {2041-1723}, mesh = {*Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Metabolome/genetics ; Metagenome ; Metagenomics ; *Nanopores ; }, abstract = {In-depth profiling of genetic variations in the gut microbiome is highly desired for understanding its functionality and impacts on host health and disease. Here, by harnessing the long read advantage provided by Oxford Nanopore Technology (ONT), we characterize fine-scale genetic variations of structural variations (SVs) in hundreds of gut microbiomes from healthy humans. ONT long reads dramatically improve the quality of metagenomic assemblies, enable reliable detection of a large, expanded set of structural variation types (notably including large insertions and inversions). We find SVs are highly distinct between individuals and stable within an individual, representing gut microbiome fingerprints that shape strain-level differentiations in function within species, complicating the associations to metabolites and host phenotypes such as blood glucose. In summary, our study strongly emphasizes that incorporating ONT reads into metagenomic analyses expands the detection scope of genetic variations, enables profiling strain-level variations in gut microbiome, and their intricate correlations with metabolome.}, } @article {pmid35675542, year = {2022}, author = {Peters, BA and Lin, J and Qi, Q and Usyk, M and Isasi, CR and Mossavar-Rahmani, Y and Derby, CA and Santoro, N and Perreira, KM and Daviglus, ML and Kominiarek, MA and Cai, J and Knight, R and Burk, RD and Kaplan, RC}, title = {Menopause Is Associated with an Altered Gut Microbiome and Estrobolome, with Implications for Adverse Cardiometabolic Risk in the Hispanic Community Health Study/Study of Latinos.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0027322}, pmid = {35675542}, issn = {2379-5077}, support = {R01 MD011389/MD/NIMHD NIH HHS/United States ; N01HC65236/HL/NHLBI NIH HHS/United States ; N01HC65234/HL/NHLBI NIH HHS/United States ; N01HC65237/HL/NHLBI NIH HHS/United States ; U01 HL146204/HL/NHLBI NIH HHS/United States ; K01 HL160146/HL/NHLBI NIH HHS/United States ; N01HC65235/HL/NHLBI NIH HHS/United States ; P30 DK111022/DK/NIDDK NIH HHS/United States ; N01HC65233/HL/NHLBI NIH HHS/United States ; }, mesh = {Female ; Male ; Humans ; *Gastrointestinal Microbiome ; Public Health ; Menopause ; Gonadal Steroid Hormones ; Hispanic or Latino ; *Cardiovascular Diseases ; }, abstract = {Menopause is a pivotal period during which loss of ovarian hormones increases cardiometabolic risk and may also influence the gut microbiome. However, the menopause-microbiome relationship has not been examined in a large study, and its implications for cardiometabolic disease are unknown. In the Hispanic Community Health Study/Study of Latinos, a population with high burden of cardiometabolic risk factors, shotgun metagenomic sequencing was performed on stool from 2,300 participants (295 premenopausal women, 1,027 postmenopausal women, and 978 men), and serum metabolomics was available on a subset. Postmenopausal women trended toward lower gut microbiome diversity and altered overall composition compared to premenopausal women, while differing less from men, in models adjusted for age and other demographic/behavioral covariates. Differentially abundant taxa for post- versus premenopausal women included Bacteroides sp. strain Ga6A1, Prevotella marshii, and Sutterella wadsworthensis (enriched in postmenopause) and Escherichia coli-Shigella spp., Oscillibacter sp. strain KLE1745, Akkermansia muciniphila, Clostridium lactatifermentans, Parabacteroides johnsonii, and Veillonella seminalis (depleted in postmenopause); these taxa similarly differed between men and women. Postmenopausal women had higher abundance of the microbial sulfate transport system and decreased abundance of microbial β-glucuronidase; these functions correlated with serum progestin metabolites, suggesting involvement of postmenopausal gut microbes in sex hormone retention. In postmenopausal women, menopause-related microbiome alterations were associated with adverse cardiometabolic profiles. In summary, in a large U.S. Hispanic/Latino population, menopause is associated with a gut microbiome more similar to that of men, perhaps related to the common condition of a low estrogen/progesterone state. Future work should examine similarity of results in other racial/ethnic groups. IMPORTANCE The menopausal transition, marked by declining ovarian hormones, is recognized as a pivotal period of cardiometabolic risk. Gut microbiota metabolically interact with sex hormones, but large population studies associating menopause with the gut microbiome are lacking. Our results from a large study of Hispanic/Latino women and men suggest that the postmenopausal gut microbiome in women is slightly more similar to the gut microbiome in men and that menopause depletes specific gut pathogens and decreases the hormone-related metabolic potential of the gut microbiome. At the same time, gut microbes may participate in sex hormone reactivation and retention in postmenopausal women. Menopause-related gut microbiome changes were associated with adverse cardiometabolic risk in postmenopausal women, indicating that the gut microbiome contributes to changes in cardiometabolic health during menopause.}, } @article {pmid35675435, year = {2022}, author = {Leung, H and Long, X and Ni, Y and Qian, L and Nychas, E and Siliceo, SL and Pohl, D and Hanhineva, K and Liu, Y and Xu, A and Nielsen, HB and Belda, E and Clément, K and Loomba, R and Li, H and Jia, W and Panagiotou, G}, title = {Risk assessment with gut microbiome and metabolite markers in NAFLD development.}, journal = {Science translational medicine}, volume = {14}, number = {648}, pages = {eabk0855}, pmid = {35675435}, issn = {1946-6242}, support = {U01 DK130190/DK/NIDDK NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; U01 AA029019/AA/NIAAA NIH HHS/United States ; R01 DK124318/DK/NIDDK NIH HHS/United States ; U01 DK061734/DK/NIDDK NIH HHS/United States ; P01 HL147835/HL/NHLBI NIH HHS/United States ; R01 DK121378/DK/NIDDK NIH HHS/United States ; R01 DK106419/DK/NIDDK NIH HHS/United States ; }, mesh = {Biomarkers ; *Gastrointestinal Microbiome ; Humans ; *Non-alcoholic Fatty Liver Disease/pathology ; Prospective Studies ; Risk Assessment ; }, abstract = {A growing body of evidence suggests interplay between the gut microbiota and the pathogenesis of nonalcoholic fatty liver disease (NAFLD). However, the role of the gut microbiome in early detection of NAFLD is unclear. Prospective studies are necessary for identifying reliable, microbiome markers for early NAFLD. We evaluated 2487 individuals in a community-based cohort who were followed up 4.6 years after initial clinical examination and biospecimen sampling. Metagenomic and metabolomic characterizations using stool and serum samples taken at baseline were performed for 90 participants who progressed to NAFLD and 90 controls who remained NAFLD free at the follow-up visit. Cases and controls were matched for gender, age, body mass index (BMI) at baseline and follow-up, and 4-year BMI change. Machine learning models integrating baseline microbial signatures (14 features) correctly classified participants (auROCs of 0.72 to 0.80) based on their NAFLD status and liver fat accumulation at the 4-year follow up, outperforming other prognostic clinical models (auROCs of 0.58 to 0.60). We confirmed the biological relevance of the microbiome features by testing their diagnostic ability in four external NAFLD case-control cohorts examined by biopsy or magnetic resonance spectroscopy, from Asia, Europe, and the United States. Our findings raise the possibility of using gut microbiota for early clinical warning of NAFLD development.}, } @article {pmid35672613, year = {2022}, author = {Berntson, L and Öman, A and Engstrand, L and Dicksved, J}, title = {A Pilot Study Investigating Faecal Microbiota After Two Dietary Interventions in Children with Juvenile Idiopathic Arthritis.}, journal = {Current microbiology}, volume = {79}, number = {7}, pages = {215}, pmid = {35672613}, issn = {1432-0991}, support = {R-657931//Reumatikerförbundet/ ; R-744331//Reumatikerförbundet/ ; R-848441//Reumatikerförbundet/ ; }, mesh = {Adolescent ; *Arthritis, Juvenile/therapy ; Child ; Feces/microbiology ; Humans ; *Microbiota/genetics ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {There is evidence for an impact of the gut microbiota on the immune system, which has consequences for inflammatory diseases. Exclusive enteral nutrition (EEN) and the specific carbohydrate diet (SCD) have been demonstrated as effective anti-inflammatory treatments for children with Crohn's disease. We have previously shown an anti-inflammatory effect from these nutritional treatments in children with juvenile idiopathic arthritis (JIA). The aim of this study was to investigate if improved clinical symptoms after EEN or SCD treatment in children with JIA could be linked to changes in faecal microbiota. We included sixteen patients with JIA (age 7-17 years), six for treatment with EEN and ten with SCD. EEN was given for 3-5 weeks and SCD for 4-5 weeks, with clinical and laboratory status assessed before and after treatment. Faecal samples were analysed for microbiota diversity and composition using 16S rRNA gene sequencing. Analyses of the faecal microbiota showed an effect on the overall composition with both interventions; the most striking result was a decreased relative abundance of the genus Faecalibacterium from EEN and of Bifidobacterium from SCD. The α-diversity decreased significantly from SCD (P = 0.04), but not from EEN (P = 0.22). Despite the study cohorts being small, both EEN and SCD were shown to impact the faecal microbiota. Future larger studies with a focus on metagenomics or metabolomics could possibly reveal a link and clarify the clinical effects of those nutritional regimens.}, } @article {pmid35672441, year = {2022}, author = {Amandito, R and Malik, A and Rohsiswatmo, R}, title = {Metagenomic profiles of the early life microbiome of Indonesian inpatient neonates and their influence on clinical characteristics.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9413}, pmid = {35672441}, issn = {2045-2322}, mesh = {Feces/microbiology ; Female ; Humans ; Indonesia ; Infant ; Infant, Newborn ; *Infant, Premature ; Inpatients ; Meconium/microbiology ; *Microbiota/genetics ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Determining the initial normal neonatal gut microbiome is challenging. The debate regarding the sterile fetal environment is still ongoing. Therefore, studying and comparing normal and dysbiotic microbiomes requires the elucidation of both the fetal and infant microbiomes. Factors influencing the normal microbiome also include regional and genetic factors specific to different countries. Determining the normal microbiome population in our center and their association with the clinical conditions of infants is helpful as a tool for both the prevention and treatment of related diseases during neonatal care. Here, we employed metagenomic sequencing to characterize meconium and the subsequent early-life gut microbiome of preterm neonates in Jakarta, Indonesia. Microbiome diversity and complexity was higher in the meconium and on day 4 than on day 7. At the genus level, the most abundant genus overall was unidentified Enterobacteriaceae, with meconium samples dominated by Ureaplasma, day 4 fecal samples dominated by Staphylococcus, and day 7 samples dominated by Clostridiales, while at the phylum level the most abundant was Proteobacteria and Firmicutes. Perinatal factors of PROM and mother's diet influenced the meconium microbiome, while day 4 and day 7 microbiome was associated with bacteremia and early administration of antibiotics. One of our sample sets was derived from triplets, and they had varying diversity despite being triplets. These data are valuable for understanding the formation of a healthy microbiome specific to neonates and devising a strategy to improve both the gut health and related clinical outcomes of the neonate.}, } @article {pmid35671624, year = {2022}, author = {Zenga, J and Atkinson, S and Yen, T and Massey, B and Stadler, M and Bruening, J and Peppard, W and Reuben, M and Hayward, M and Mesich, B and Buchan, B and Ledeboer, N and Sanchez, JL and Fraser, R and Lin, CW and Holtz, ML and Awan, M and Wong, SJ and Puram, SV and Salzman, N}, title = {A phase 2 trial of a topical antiseptic bundle in head and neck cancer surgery: Effects on surgical site infection and the oral microbiome.}, journal = {EBioMedicine}, volume = {81}, number = {}, pages = {104099}, pmid = {35671624}, issn = {2352-3964}, support = {UG1 CA189823/CA/NCI NIH HHS/United States ; UL1 TR001436/TR/NCATS NIH HHS/United States ; }, mesh = {*Anti-Infective Agents, Local/therapeutic use ; *Head and Neck Neoplasms/surgery ; Humans ; *Microbiota ; Preoperative Care ; Surgical Wound Infection/chemically induced/prevention & control ; }, abstract = {BACKGROUND: Head and neck cancer (HNC) surgery remains an important component of management but is associated with a high rate of surgical site infection (SSI). We aimed to assess the safety and efficacy of a topical mucosal antiseptic bundle in preventing SSI and evaluate microbial predictors of infection through a genomic sequencing approach.

METHODS: This study was an open-label, single-arm, single-center, phase 2 trial of a topical mucosal antiseptic bundle in patients with HNC undergoing aerodigestive tract resection and reconstruction. Patients underwent topical preparation of the oral mucosa with povidone-iodine (PI) and chlorhexidine gluconate (CHG) pre- and intra-operatively followed by oral tetracycline ointment every 6 hours for 2 days post-operatively. The primary outcome was change in bacterial bioburden at the oral surgical site. Secondary outcomes included safety, SSI, and microbial predictors of infection.

FINDINGS: Of 27 patients screened between January 8, 2021, and May 14, 2021, 26 were enrolled and 25 completed the study. There were no antiseptic-related adverse events. The topical mucosal antiseptic bundle significantly decreased oral bacterial colony-forming units from pre-operative levels (log10 mean difference 4·03, 95%CI 3·13-4·;92). There were three SSI (12%) within 30 days. In correlative genomic studies, a distinct set of amplicon sequence variants in the post-operative microbiome was associated with SSI. Further, despite no instance of post-operative orocervical fistula, metagenomic sequence mapping revealed the oral cavity as the origin of the infectious organism in two of the three SSI.

INTERPRETATION: The bacterial strains which subsequently caused SSI were frequently identified in the pre-operative oral cavity. Accordingly, a topical antiseptic bundle decreased oral bacterial bioburden throughout the peri-operative period and was associated with a low rate of SSI, supporting further study of topical antisepsis in HNC surgery.

FUNDING: Alliance Oncology.}, } @article {pmid35668255, year = {2022}, author = {Yang, H and Huang, Y and Li, K and Zhu, P and Wang, Y and Li, X and Meng, Q and Niu, Q and Wang, S and Li, Q}, title = {Lignocellulosic depolymerization induced by ionic liquids regulating composting habitats based on metagenomics analysis.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {50}, pages = {76298-76309}, pmid = {35668255}, issn = {1614-7499}, support = {No. 41861124004//National Natural Science Foundation of China/ ; No. 21878057//National Natural Science Foundation of China/ ; }, mesh = {*Actinobacteria/genetics/metabolism ; Bacteria/genetics/metabolism ; Cellulose ; *Composting ; *Ionic Liquids ; Lignin/metabolism ; Manure/microbiology ; Metagenomics ; *Microbiota ; Soil ; }, abstract = {The application of ionic liquids with sawdust and fresh dairy manure was studied in composting. The degradation of organic matter (OM), dissolved organic matter (DOM), and lignocellulose was analyzed. The DOM decreased by 14.25 mg/g and 11.11 mg/g in experimental group (ILs) and control group (CK), respectively. OM decreased by 7.32% (CK) and 8.91% (ILs), respectively. The degradation rates of hemicellulose, lignin, and cellulose in ILs (56.62%, 42.01%, and 23.97%) were higher than in CK (38.39%, 39.82%, and 16.04%). Microbial community and carbohydrate-active enzymes (CAZymes) were analyzed based on metagenomics. Metagenomic analysis results showed that ionic liquids enriched Actinobacteria and Proteobacteria in composting. Compared with CK, the total abundance values of GH11, GH6, AA6, and AA3_2 in ILs increased by 13.98%, 10.12%, 11.21%, and 13.68%, respectively. Ionic liquids can improve the lignocellulosic degradation by regulating the environmental physicochemical parameters (temperature, pH, C/N) to promote the growth of Actinobacteria and Proteobacteria and carbohydrate-active enzymes (CAZymes) abundance. Therefore, ionic liquids are a promising additive in lignocellulosic waste composting.}, } @article {pmid35667424, year = {2022}, author = {Bose, H and Sahu, RP and Sar, P}, title = {Impact of arsenic on microbial community structure and their metabolic potential from rice soils of West Bengal, India.}, journal = {The Science of the total environment}, volume = {841}, number = {}, pages = {156486}, doi = {10.1016/j.scitotenv.2022.156486}, pmid = {35667424}, issn = {1879-1026}, mesh = {Archaea ; *Arsenic/analysis ; Bacteria/metabolism ; *Microbiota ; *Oryza/genetics ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Paddy soil is a heterogenous ecosystem that harbours diverse microbial communities critical for maintaining ecosystem sustainability and crop yield. Considering the importance of soil in crop production and recent reports on its contamination with arsenic (As) across the South East Asia, its microbial community composition and biogeochemical functions remained inadequately studied. We have characterized the microbial communities of rice soil from eleven paddy fields of As-contaminated sites from West Bengal (India), through metagenomics and amplicon sequencing. 16S rRNA gene sequencing showed considerable bacterial diversity [over 0.2 million Operational Taxonomic Units (OTUs)] and abundance (upto 1.6 × 10[7] gene copies/g soil). Existence of a core-microbiome (261 OTUs conserved out of a total 141,172 OTUs) across the samples was noted. Most of the core-microbiome members were also found to represent the abundant taxa of the soil. Statistical analyses suggested that the microbial communities were highly constrained by As, Fe K, N, PO4[3-], SO4[2-] and organic carbon (OC). Members of Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Planctomycetes and Thaumarchaeota constituted the core-microbiome. Co-occurrence network analysis displayed significant interaction among diverse anaerobic, SO4[2-] and NO3[-] reducing, cellulose and other organic matter or C1 compound utilizing, fermentative and aerobic/facultative anaerobic bacteria and archaea. Correlation analysis suggested that taxa which were positively linked with soil parameters that maintain soil health and productivity (e.g., N, K, PO4[3-] and Fe) were adversely impacted by increasing As concentration. Shotgun metagenomics highlighted major metabolic pathways controlling the C (3-hydroxypropionate bicycle), N (Denitrification, dissimilatory NO3[-] reduction to ammonium), and S (assimilatory SO4[2-] reduction and sulfide oxidation) cycling, As homeostasis (methylation and reduction) and plant growth promotion (polyphosphate hydrolysis and auxin biosynthesis). All these major biogeochemical processes were found to be catalyzed by the members of most abundant/core-community.}, } @article {pmid35667265, year = {2022}, author = {Han, DS and Wu, WK and Liu, PY and Yang, YT and Hsu, HC and Kuo, CH and Wu, MS and Wang, TG}, title = {Differences in the gut microbiome and reduced fecal butyrate in elders with low skeletal muscle mass.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {41}, number = {7}, pages = {1491-1500}, doi = {10.1016/j.clnu.2022.05.008}, pmid = {35667265}, issn = {1532-1983}, mesh = {Aged ; Animals ; Butyrates ; Fatty Acids, Volatile/metabolism ; Feces ; *Gastrointestinal Microbiome/physiology ; Humans ; Muscle, Skeletal/physiology ; *Sarcopenia ; }, abstract = {BACKGROUND AND AIMS: Despite animal studies revealing a causal link between the gut microbiota and skeletal muscle mass, the role of the gut microbiome and its metabolites in humans having low muscle mass remains unclear.

METHODS: Eighty-eight subjects older than 65 years were measured for sarcopenia-related parameters, including body composition, grip strength, gait speed and flexibility. Participants were divided into normal muscle mass group (NM, n = 52) and low muscle mass group (LM, n = 36) and fresh fecal samples were collected for metagenome and short chain fatty acids (SCFAs) analysis.

RESULTS: The richness and evenness of gut microbiota diversity were significantly decreased in the subjects with low muscle mass, including observed ASVs, Shannon and Chao 1 index. A significant difference of gut microbiota profile was noted between NM group and LM group. The Firmicutes/Bacteroidetes ratio was significantly reduced in the LM group. A significant decrease in the abundance of a SCFA-producer, Marvinbryantia spp., whereas a remarkable enrichment of a flavonoid degrader, Flavonifractor spp., was observed in the LM elders. Comparing with the NM group, the fecal butyrate significantly diminished in the LM group and correlated with skeletal muscle mass index.

CONCLUSIONS: This is the first study that demonstrates the reduced fecal butyrate in elders with low muscle mass and highlights the associated gut microbiome changes. The identified gut microbial features and fecal butyrate level may serve as potential biomarkers for early detection of sarcopenic patients.}, } @article {pmid35666311, year = {2022}, author = {Hede, N and Khandeparker, L}, title = {Ecological Impacts of Aged Freshwater Biofilms on Estuarine Microbial Communities Elucidated Through Microcosm Experiments: A Microbial Invasion Perspective.}, journal = {Current microbiology}, volume = {79}, number = {7}, pages = {210}, pmid = {35666311}, issn = {1432-0991}, support = {GAP 2429//ballast water management program, india (ministry of shipping and dg shipping)/ ; PSC 0105//csir funded ocean finder program/ ; }, mesh = {Bacteria/genetics ; Biofilms ; Fresh Water/microbiology ; *Microbiota ; *Vibrio cholerae ; Water ; }, abstract = {Inadvertent introductions of alien species via biofilms as a vector released through ballast water are of environmental importance, yet their consequences are not much known. In the present study, biofilm communities developed in an inland freshwater port under in situ and dark conditions were subjected to long-term dark incubations. Subsequently, the impact of these aged biofilms as vectors on estuarine water column communities were evaluated using microcosm experiments in the laboratory. Variations in biofilm and planktonic microbial communities were quantified using quantitative PCR.Upon prolonged dark incubation, a shift in bacterial diversity with an increase in tolerant bacterial communities better adapted to stress was observed. Actinobacteria were the dominant taxa in both aged biofilms upon dark incubations. The laboratory studies indicated that on exposure of these biofilms to estuarine water, resuscitation of Vibrio alginolyticus, V. parahaemolyticus, and V. cholerae from a dormant state existing in these biofilms to culturable form was observed. Moreover, the results revealed that both the biofilm types can pose a threat to the environment, but the degree of risk can be attributed to the imbalance caused by significant changes in the surrounding estuarine microbial communities. Consequently, this may result in either proliferation or decline of some genera with different metabolic potential and resuscitation of pathogenic forms not present earlier, thereby influencing the ecology of the environment. Quantifying these effects in the field using biofilm metagenomes with an emphasis on virulent species and understanding traits that enable them to adapt to changing environments is a way forward.}, } @article {pmid35663881, year = {2022}, author = {Vidal, P and Martínez-Martínez, M and Fernandez-Lopez, L and Roda, S and Méndez-García, C and Golyshina, OV and Guallar, V and Peláez, AI and Ferrer, M}, title = {Metagenomic Mining for Esterases in the Microbial Community of Los Rueldos Acid Mine Drainage Formation.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {868839}, pmid = {35663881}, issn = {1664-302X}, abstract = {Acid mine drainage (AMD) systems are extremely acidic and are metal-rich formations inhabited by relatively low-complexity communities of acidophiles whose enzymes remain mostly uncharacterized. Indeed, enzymes from only a few AMD sites have been studied. The low number of available cultured representatives and genome sequences of acidophiles inhabiting AMDs makes it difficult to assess the potential of these environments for enzyme bioprospecting. In this study, using naïve and in silico metagenomic approaches, we retrieved 16 esterases from the α/β-hydrolase fold superfamily with the closest match from uncultured acidophilic Acidobacteria, Actinobacteria (Acidithrix, Acidimicrobium, and Ferrimicrobium), Acidiphilium, and other Proteobacteria inhabiting the Los Rueldos site, which is a unique AMD formation in northwestern Spain with a pH of ∼2. Within this set, only two polypeptides showed high homology (99.4%), while for the rest, the pairwise identities ranged between 4 and 44.9%, suggesting that the diversity of active polypeptides was dominated not by a particular type of protein or highly similar clusters of proteins, but by diverse non-redundant sequences. The enzymes exhibited amino acid sequence identities ranging from 39 to 99% relative to homologous proteins in public databases, including those from other AMDs, thus indicating the potential novelty of proteins associated with a specialized acidophilic community. Ten of the 16 hydrolases were successfully expressed in Escherichia coli. The pH for optimal activity ranged from 7.0 to 9.0, with the enzymes retaining 33-68% of their activities at pH 5.5, which was consistent with the relative frequencies of acid residues (from 54 to 67%). The enzymes were the most active at 30-65°C, retaining 20-61% of their activity under the thermal conditions characterizing Los Rueldos (13.8 ± 0.6°C). The analysis of the substrate specificity revealed the capacity of six hydrolases to efficiently degrade (up to 1,652 ± 75 U/g at pH 8.0 and 30°C) acrylic- and terephthalic-like [including bis(2-hydroxyethyl)-terephthalate, BHET] esters, and these enzymes could potentially be of use for developing plastic degradation strategies yet to be explored. Our assessment uncovers the novelty and potential biotechnological interest of enzymes present in the microbial populations that inhibit the Los Rueldos AMD system.}, } @article {pmid35661258, year = {2022}, author = {Brandau, L and Jacksch, S and Weis, S and Schnell, S and Egert, M}, title = {Minority report: small-scale metagenomic analysis of the non-bacterial kitchen sponge microbiota.}, journal = {Archives of microbiology}, volume = {204}, number = {7}, pages = {363}, pmid = {35661258}, issn = {1432-072X}, support = {13FH197PX6//Bundesministerium für Bildung und Forschung/ ; }, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; Metagenome ; Metagenomics ; *Microbiota/genetics ; Phylogeny ; *Porifera/genetics ; }, abstract = {Kitchen sponges are particularly well known to harbor a high number and diversity of bacteria, including pathogens. Viruses, archaea, and eukaryotes in kitchen sponges, however, have not been examined in detail so far. To increase knowledge on the non-bacterial kitchen sponge microbiota and its potential hygienic relevance, we investigated five used kitchen sponges by means of metagenomic shot-gun sequencing. Viral particles were sought to be enriched by a filter step during DNA extraction from the sponges. Data analysis revealed that ~ 2% of the sequences could be assigned to non-bacterial taxa. Each sponge harbored different virus (phage) species, while the present archaea were predominantly affiliated with halophilic taxa. Among the eukaryotic taxa, besides harmless algae, or amoebas, mainly DNA from food-left-overs was found. The presented work offers new insights into the complex microbiota of used kitchen sponges and contributes to a better understanding of their hygienic relevance.}, } @article {pmid35660864, year = {2022}, author = {Béchade, B and Hu, Y and Sanders, JG and Cabuslay, CS and Łukasik, P and Williams, BR and Fiers, VJ and Lu, R and Wertz, JT and Russell, JA}, title = {Turtle ants harbor metabolically versatile microbiomes with conserved functions across development and phylogeny.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {8}, pages = {}, doi = {10.1093/femsec/fiac068}, pmid = {35660864}, issn = {1574-6941}, mesh = {Animals ; *Ants ; Bacteria/genetics ; Dietary Fiber ; *Gastrointestinal Microbiome ; Nitrogen ; Phylogeny ; Symbiosis ; }, abstract = {Gut bacterial symbionts can support animal nutrition by facilitating digestion and providing valuable metabolites. However, changes in symbiotic roles between immature and adult stages are not well documented, especially in ants. Here, we explored the metabolic capabilities of microbiomes sampled from herbivorous turtle ant (Cephalotes sp.) larvae and adult workers through (meta)genomic screening and in vitro metabolic assays. We reveal that larval guts harbor bacterial symbionts with impressive metabolic capabilities, including catabolism of plant and fungal recalcitrant dietary fibers and energy-generating fermentation. Additionally, several members of the specialized adult gut microbiome, sampled downstream of an anatomical barrier that dams large food particles, show a conserved potential to depolymerize many dietary fibers. Symbionts from both life stages have the genomic capacity to recycle nitrogen and synthesize amino acids and B-vitamins. With help of their gut symbionts, including several bacteria likely acquired from the environment, turtle ant larvae may aid colony digestion and contribute to colony-wide nitrogen, B-vitamin and energy budgets. In addition, the conserved nature of the digestive capacities among adult-associated symbionts suggests that nutritional ecology of turtle ant colonies has long been shaped by specialized, behaviorally-transferred gut bacteria with over 45 million years of residency.}, } @article {pmid35660621, year = {2022}, author = {He, J and Zhang, N and Shen, X and Muhammad, A and Shao, Y}, title = {Deciphering environmental resistome and mobilome risks on the stone monument: A reservoir of antimicrobial resistance genes.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 3}, pages = {156443}, doi = {10.1016/j.scitotenv.2022.156443}, pmid = {35660621}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {Antimicrobial resistance (AMR) in the environment has attracted increasing attention as an emerging global threat to public health. Stone is an essential ecosystem in nature and also an important material for human society, having architectural and aesthetic values. However, little is known about the AMR in stone ecosystems, particularly in the stone monument, where antimicrobials are often applied against biodeterioration. Here, we provide the first detailed metagenomic study of AMR genes across different types of biodeteriorated stone monuments, which revealed abundant and diverse AMR genes conferring resistance to drugs (antibiotics), biocides, and metals. Totally, 132 AMR subtypes belonging to 27 AMR types were detected including copper-, rifampin-, and aminocoumarins-resistance genes, of which diversity was mainly explained by the spatial turnover (replacement of genes between samples) rather than nestedness (loss of nested genes between samples). Source track analysis confirms that stone resistomes are likely driven by anthropogenic activities across stone heritage areas. We also detected various mobile genetic elements (namely mobilome, e.g., prophages, plasmids, and insertion sequences) that could accelerate replication and horizontal transfer of AMR genes. Host-tracking analysis further identified multiple biodeterioration-related bacterial genera such as Pseudonocardia, Sphingmonas, and Streptomyces as the major hosts of resistome. Taken together, these findings highlight that stone microbiota is one of the natural reservoirs of antimicrobial-resistant hazards, and the diverse resistome and mobilome carried by active biodeteriogens may improve their adaptation on stone and even deactivate the antimicrobials applied against biodeterioration. This enhanced knowledge may also provide novel and specific avenues for environmental management and stone heritage protection.}, } @article {pmid35659906, year = {2022}, author = {Ducarmon, QR and Zwittink, RD and Willems, RPJ and Verhoeven, A and Nooij, S and van der Klis, FRM and Franz, E and Kool, J and Giera, M and Vandenbroucke-Grauls, CMJE and Fuentes, S and Kuijper, EJ}, title = {Gut colonisation by extended-spectrum β-lactamase-producing Escherichia coli and its association with the gut microbiome and metabolome in Dutch adults: a matched case-control study.}, journal = {The Lancet. Microbe}, volume = {3}, number = {6}, pages = {e443-e451}, doi = {10.1016/S2666-5247(22)00037-4}, pmid = {35659906}, issn = {2666-5247}, mesh = {Adult ; Anti-Bacterial Agents/pharmacology ; Bacteria/metabolism ; Case-Control Studies ; Cross-Sectional Studies ; *Escherichia coli/genetics ; Ethnicity ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolome ; beta-Lactamases/genetics ; }, abstract = {BACKGROUND: Gut colonisation by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli is a risk factor for developing overt infection. The gut microbiome can provide colonisation resistance against enteropathogens, but it remains unclear whether it confers resistance against ESBL-producing E coli. We aimed to identify a potential role of the microbiome in controlling colonisation by this antibiotic-resistant bacterium.

METHODS: For this matched case-control study, we used faeces from 2751 individuals in a Dutch cross-sectional population study (PIENTER-3) to culture ESBL-producing bacteria. Of these, we selected 49 samples that were positive for an ESBL-producing E coli (ESBL-positive) and negative for several variables known to affect microbiome composition. These samples were matched 1:1 to ESBL-negative samples on the basis of individuals' age, sex, having been abroad or not in the past 6 months, and ethnicity. Shotgun metagenomic sequencing was done and taxonomic species composition and functional annotations (ie, microbial metabolism and carbohydrate-active enzymes) were determined. Targeted quantitative metabolic profiling (proton nuclear magnetic resonance spectroscopy) was done to investigate metabolomic profiles and combinations of univariate (t test and Wilcoxon test), multivariate (principal coordinates analysis, permutational multivariate analysis of variance, and partial least-squares discriminant analysis) and machine-learning approaches (least absolute shrinkage and selection operator and random forests) were used to analyse all the molecular data.

FINDINGS: No differences in diversity parameters or in relative abundance were observed between ESBL-positive and ESBL-negative groups based on bacterial species-level composition. Machine-learning approaches using microbiota composition did not accurately predict ESBL status (area under the receiver operating characteristic curve [AUROC]=0·41) when using either microbiota composition or any of the functional profiles. The metabolome also did not differ between ESBL groups, as assessed by various methods including random forest (AUROC=0·61).

INTERPRETATION: By combining multiomics and machine-learning approaches, we conclude that asymptomatic gut carriage of ESBL-producing E coli is not associated with an altered microbiome composition or function. This finding might suggest that microbiome-mediated colonisation resistance against ESBL-producing E coli is not as relevant as it is against other enteropathogens and antibiotic-resistant bacteria.

FUNDING: None.}, } @article {pmid35658830, year = {2022}, author = {Kastl, A and Zong, W and Gershuni, VM and Friedman, ES and Tanes, C and Boateng, A and Mitchell, WJ and O'Connor, K and Bittinger, K and Terry, NA and Bales, C and Albenberg, L and Wu, GD}, title = {Dietary fiber-based regulation of bile salt hydrolase activity in the gut microbiota and its relevance to human disease.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2083417}, pmid = {35658830}, issn = {1949-0984}, support = {P30 DK050306/DK/NIDDK NIH HHS/United States ; T32 AI118684/AI/NIAID NIH HHS/United States ; }, mesh = {Amidohydrolases/metabolism ; Animals ; Bile Acids and Salts ; Dietary Fiber ; *Gastrointestinal Microbiome/physiology ; Humans ; Mice ; }, abstract = {Complications of short bowel syndrome (SBS) include malabsorption and bacterial overgrowth, requiring prolonged dependence on parenteral nutrition (PN). We hypothesized that the intolerance of whole food in some SBS patients might be due to the effect of dietary fiber on the gut microbiome. Shotgun metagenomic sequencing and targeted metabolomics were performed using biospecimens collected from 55 children with SBS and a murine dietary fiber model. Bioinformatic analyses were performed on these datasets as well as from a healthy human dietary intervention study. Compared to healthy controls, the gut microbiota in SBS had lower diversity and increased Proteobacteria, a pattern most pronounced in children on PN and inversely correlated with whole food consumption. Whole food intake correlated with increased glycoside hydrolases (GH) and bile salt hydrolases (BSH) with reduced fecal conjugated bile acids suggesting that dietary fiber regulates BSH activity via GHs. Mechanistic evidence supporting this notion was generated via fecal and plasma bile acid profiling in a healthy human fiber-free dietary intervention study as well as in a dietary fiber mouse experiment. Gaussian mixture modeling of fecal bile acids was used to identify three clinically relevant SBS phenotypes. Dietary fiber is associated with bile acid deconjugation likely via an interaction between gut microbiota BSHs and GHs in the small intestine, which may lead to whole food intolerance in patients with SBS. This mechanism not only has potential utility in clinical phenotyping and targeted therapeutics in SBS based on bile acid metabolism but may have relevance to other intestinal disease states.}, } @article {pmid35657425, year = {2023}, author = {Meena, M and Yadav, G and Sonigra, P and Nagda, A and Mehta, T and Swapnil, P and Harish, and Marwal, A and Kumar, S}, title = {Multifarious Responses of Forest Soil Microbial Community Toward Climate Change.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {49-74}, pmid = {35657425}, issn = {1432-184X}, mesh = {*Ecosystem ; Climate Change ; Soil/chemistry ; Forests ; *Microbiota ; Nitrogen/analysis ; Soil Microbiology ; Carbon ; }, abstract = {Forest soils are a pressing subject of worldwide research owing to the several roles of forests such as carbon sinks. Currently, the living soil ecosystem has become dreadful as a consequence of several anthropogenic activities including climate change. Climate change continues to transform the living soil ecosystem as well as the soil microbiome of planet Earth. The majority of studies have aimed to decipher the role of forest soil bacteria and fungi to understand and predict the impact of climate change on soil microbiome community structure and their ecosystem in the environment. In forest soils, microorganisms live in diverse habitats with specific behavior, comprising bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are influenced by biotic interactions and nutrient accessibility. Soil microbiome also drives multiple crucial steps in the nutrient biogeochemical cycles (carbon, nitrogen, phosphorous, and sulfur cycles). Soil microbes help in the nitrogen cycle through nitrogen fixation during the nitrogen cycle and maintain the concentration of nitrogen in the atmosphere. Soil microorganisms in forest soils respond to various effects of climate change, for instance, global warming, elevated level of CO2, drought, anthropogenic nitrogen deposition, increased precipitation, and flood. As the major burning issue of the globe, researchers are facing the major challenges to study soil microbiome. This review sheds light on the current scenario of knowledge about the effect of climate change on living soil ecosystems in various climate-sensitive soil ecosystems and the consequences for vegetation-soil-climate feedbacks.}, } @article {pmid35655185, year = {2022}, author = {Ziko, L and AbdelRaheem, O and Nabil, M and Aziz, RK and Siam, R}, title = {Bioprospecting the microbiome of Red Sea Atlantis II brine pool for peptidases and biosynthetic genes with promising antibacterial activity.}, journal = {Microbial cell factories}, volume = {21}, number = {1}, pages = {109}, pmid = {35655185}, issn = {1475-2859}, mesh = {Anti-Bacterial Agents/pharmacology ; Bioprospecting ; *Enterococcus faecium ; Humans ; Indian Ocean ; *Microbiota ; Peptide Hydrolases ; Salts ; }, abstract = {BACKGROUND: The search for novel antimicrobial agents is crucial as antibiotic-resistant pathogens continue to emerge, rendering the available antibiotics no longer effective. Likewise, new anti-cancer drugs are needed to combat the emergence of multi-drug resistant tumors. Marine environments are wealthy sources for natural products. Additionally, extreme marine environments are interesting niches to search for bioactive natural compounds. In the current study, a fosmid library of metagenomic DNA isolated from Atlantis II Deep Lower Convective Layer (ATII LCL), was functionally screened for antibacterial activity as well as anticancer effects.

RESULTS: Two clones exhibited antibacterial effects against the marine Bacillus Cc6 strain, namely clones 102-5A and 88-1G and they were further tested against eleven other challenging strains, including six safe relatives of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter  spp.), a safe relative to Mycobacterium tuberculosis and four resistant clinical isolates. Clone 88-1G resulted in clear zones of inhibition against eight bacterial strains, while clone 102-5A resulted in zones of inhibition against five bacterial strains. The whole cell lysates of clone 88-1G showed 15% inhibition of Mtb ClpP protease -Mycobacterium tuberculosis drug target-, while whole cell lysates of clone 102-5A showed 19% inhibition of Mtb ClpP protease. Whole cell lysates from the selected clones exhibited anticancer effects against MCF-7 breast cancer cells (cell viability at 50% v/v was 46.2% ± 9.9 for 88-1G clone and 38% ± 7 for 102-5A clone), U2OS osteosarcoma cells (cell viability at 50% v/v was 64.6% ± 12.3 for 88-1G clone and 28.3% ± 1.7 for 102-5A clone) and 1BR hTERT human fibroblast cells (cell viability at 50% v/v was 74.4% ± 5.6 for 88-1G clone and 57.6% ± 8.9 for 102-5A clone). Sequencing of 102-5A and 88-1G clones, and further annotation detected putative proteases and putative biosynthetic genes in clones 102-5A and 88-1G, respectively.

CONCLUSIONS: The ATII LCL metagenome hosts putative peptidases and biosynthetic genes that confer antibiotic and anti-cancer effects. The tested clones exhibited promising antibacterial activities against safe relative strains to ESKAPE pathogens and Mycobacterium tuberculosis. Thus, searching the microbial dark matter of extreme environments is a promising approach to identify new molecules with pharmaceutical potential use.}, } @article {pmid35655063, year = {2022}, author = {Bourquin, M and Busi, SB and Fodelianakis, S and Peter, H and Washburne, A and Kohler, TJ and Ezzat, L and Michoud, G and Wilmes, P and Battin, TJ}, title = {The microbiome of cryospheric ecosystems.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3087}, pmid = {35655063}, issn = {2041-1723}, mesh = {Climate Change ; *Microbiota/genetics ; *Permafrost ; Phylogeny ; Snow ; }, abstract = {The melting of the cryosphere is among the most conspicuous consequences of climate change, with impacts on microbial life and related biogeochemistry. However, we are missing a systematic understanding of microbiome structure and function across cryospheric ecosystems. Here, we present a global inventory of the microbiome from snow, ice, permafrost soils, and both coastal and freshwater ecosystems under glacier influence. Combining phylogenetic and taxonomic approaches, we find that these cryospheric ecosystems, despite their particularities, share a microbiome with representatives across the bacterial tree of life and apparent signatures of early and constrained radiation. In addition, we use metagenomic analyses to define the genetic repertoire of cryospheric bacteria. Our work provides a reference resource for future studies on climate change microbiology.}, } @article {pmid35654877, year = {2022}, author = {Stockdale, SR and Harrington, RS and Shkoporov, AN and Khokhlova, EV and Daly, KM and McDonnell, SA and O'Reagan, O and Nolan, JA and Sheehan, D and Lavelle, A and Draper, LA and Shanahan, F and Ross, RP and Hill, C}, title = {Metagenomic assembled plasmids of the human microbiome vary across disease cohorts.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9212}, pmid = {35654877}, issn = {2045-2322}, mesh = {Humans ; *Inflammatory Bowel Diseases/genetics/microbiology ; Metagenome ; Metagenomics ; *Microbiota ; Plasmids/genetics ; }, abstract = {We compiled a human metagenome assembled plasmid (MAP) database and interrogated differences across multiple studies that were originally designed to investigate the composition of the human microbiome across various lifestyles, life stages and events. This was performed as plasmids enable bacteria to rapidly expand their functional capacity through mobilisation, yet their contribution to human health and disease is poorly understood. We observed that inter-sample β-diversity differences of plasmid content (plasmidome) could distinguish cohorts across a multitude of conditions. We also show that reduced intra-sample plasmidome α-diversity is consistent amongst patients with inflammatory bowel disease (IBD) and Clostridioides difficile infections. We also show that faecal microbiota transplants can restore plasmidome diversity. Overall plasmidome diversity, specific plasmids, and plasmid-encoded functions can all potentially act as biomarkers of IBD or its severity. The human plasmidome is an overlooked facet of the microbiome and should be integrated into investigations regarding the role of the microbiome in promoting health or disease. Including MAP databases in analyses will enable a greater understanding of the roles of plasmid-encoded functions within the gut microbiome and will inform future human metagenome analyses.}, } @article {pmid35654195, year = {2022}, author = {Beale, DJ and Bissett, A and Nilsson, S and Bose, U and Nelis, JLD and Nahar, A and Smith, M and Gonzalez-Astudillo, V and Braun, C and Baddiley, B and Vardy, S}, title = {Perturbation of the gut microbiome in wild-caught freshwater turtles (Emydura macquarii macquarii) exposed to elevated PFAS levels.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 3}, pages = {156324}, doi = {10.1016/j.scitotenv.2022.156324}, pmid = {35654195}, issn = {1879-1026}, mesh = {Animals ; *Environmental Pollutants ; *Fluorocarbons ; Fresh Water ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Turtles/metabolism ; }, abstract = {Per- and polyfluoroalkyl substances (PFAS) are environmentally persistent and pervasive. Understanding the toxicity of PFAS to wildlife is difficult, both due to the complexity of biotic and abiotic perturbations in the taxa under study and the practical and ethical problems associated with studying the impacts of environmental pollutants on free living wildlife. One avenue of inquiry into the effects of environmental pollutants, such as PFAS, is assessing the impact on the host gut microbiome. Here we show the microbial composition and biochemical functional outputs from the gut microbiome of sampled faeces from euthanised and necropsied wild-caught freshwater turtles (Emydura macquarii macquarii) exposed to elevated PFAS levels. The microbial community composition was profiled by 16S rRNA gene sequencing using a Nanopore MinION and the biochemical functional outputs of the gut microbiome were profiled using a combination of targeted central carbon metabolism metabolomics using liquid chromatography coupled to a triple quadrupole mass spectrometer (LC-QqQ-MS) and untargeted metabolomics using liquid chromatography coupled to a quadrupole time of flight mass spectrometer (LC-QToF-MS). Total PFAS was measured in the turtle serum using standard methods. These preliminary data demonstrated a 60-fold PFAS increase in impacted turtles compared to the sampled aquatic environment. The microbiome community was also impacted in the PFAS exposed turtles, with the ratio of Firmicutes-to-Bacteroidetes rising from 1.4 at the reference site to 5.5 at the PFAS impacted site. This ratio increase is indicative of host stress and dysfunction of the gut microbiome that was correlated with the biochemical metabolic function data, metabolites observed that are indications of stress and inflammation in the gut microbiome. Utilising the gut microbiome of sampled faeces collected from freshwater turtles provides a non-destructive avenue for investigating the impacts of PFAS in native wildlife, and provides an avenue to explore other contaminants in higher-order taxa within the environment.}, } @article {pmid35654160, year = {2022}, author = {Guan, Y and Hou, T and Li, X and Feng, L and Wang, Z}, title = {Metagenomic insights into comparative study of nitrogen metabolic potential and microbial community between primitive and urban river sediments.}, journal = {Environmental research}, volume = {212}, number = {Pt D}, pages = {113592}, doi = {10.1016/j.envres.2022.113592}, pmid = {35654160}, issn = {1096-0953}, mesh = {Bacteria/genetics/metabolism ; China ; Denitrification ; Geologic Sediments/chemistry ; *Microbiota ; *Nitrogen/analysis ; Nitrogen Dioxide ; }, abstract = {As a result of anthropogenic pollution, the nitrogen nutrients load in urban rivers has increased, potentially raising the risk of river eutrophication. Here, we studied how anthropogenic impacts alter nitrogen metabolism in river sediments by comparing the metagenomic function of microbial communities between relatively primitive and human-disturbed sediments. The contents of organic matter (OM), total nitrogen (TN), NO3[-]-N and NO2[-]-N were higher in primitive site than in polluted sites, which might be due to vegetation density, sediment type, hydrology, etc. Whereas, NH4[+]-N content was higher in midstream and downstream, indicating that nitrogen loading increased in the anthropogenic regions and subsequently leading higher NH4[+]-N. Hierarchical cluster analyses revealed significant changes in the community structure and functional potential between the primitive and human-affected sites. Metagenomic analysis demonstrated that Demequina, Streptomyces, Rubrobacter and Dechloromonas were the predominant denitrifiers. Ardenticatena and Dechloromonas species were the most important contributors to dissimilatory nitrate reduction. Furthermore, anthropogenic pollution significantly increased their abundance, and resulting in a decrease in NO3[-], NO2[-]-N and an increase in NH4[+]-N contents. Additionally, the SOX metabolism of Dechloromonas and Sulfuritalea may involve in the sulfur-dependent autotrophic denitrification process by coupling the conversion of thiosulfate to sulfate with the reduction of NO3[-]-N to N2. From pristine to anthropogenic pollution sediments, the major nitrifying bacteria harboring Hao transitioned from Nitrospira to Nitrosomonas. This study sheds light on the consequences of anthropogenic activities on nitrogen metabolism in river sediments, allowing for better management of nitrogen pollution and eutrophication in river.}, } @article {pmid35651033, year = {2022}, author = {Hou, Q and Wang, Y and Cai, W and Ni, H and Zhao, H and Zhang, Z and Liu, Z and Liu, J and Zhong, J and Guo, Z}, title = {Metagenomic and physicochemical analyses reveal microbial community and functional differences between three types of low-temperature Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {156}, number = {}, pages = {111167}, doi = {10.1016/j.foodres.2022.111167}, pmid = {35651033}, issn = {1873-7145}, mesh = {Bacteria ; Fermentation ; *Metagenome ; Metagenomics ; *Microbiota ; Temperature ; }, abstract = {Complex microbes of different types of low-temperature Daqu (LTD) play an important role in the formation of flavors and qualities of light-flavor Baijiu during fermentation. However, characterizing the taxonomic and functional diversity of microbiota in three types of LTD (Houhuo, Hongxin, Qingcha) remains a major challenge. The present study combined metagenomic sequencing with culture-based methods and physicochemical analysis to compare the three LTD microbiota and elucidate their function in LFB brewing. The results revealed a high diversity of microbes in LTD, with 1286 genera and 4157 species detected across all studied samples. Bacteria and fungi were the main microbes in LTD, with a bacterial to fungal relative abundance ratio of above 4:1. Bacillus (21.18%) and Bacillus licheniformis (17.45%) were the most abundant microbes in the LTD microbiota at the genus and species levels, respectively. Culture-dependent analysis found the highest abundances of bacteria, fungi, and lactic acid bacteria in Houhuo, while the metagenomic-based microbiota found that the relative abundance of bacteria and fungi were highest in Houhuo and Hongxin among the three types of LTD, respectively. The different production temperatures of LTD had little effect on its microbial variety, but obviously impacted the microbiota structure and metagenomic function of LTD. Although the microbiota of the three types of LTD shared a high commonality, each had specific microbiota and functional metagenomic features, suggesting their different but complementary roles in the LFB fermentation process. The representative dominant microbes in Houhuo were mostly involved in metabolic pathways associated with the production of flavor substances in liquor. In contrast, the enriched microbes in Qingcha and Hongxin were not only capable of producing specific flavor substances but also had a strong ability to degrade macromolecular substances in raw materials, promoting microbial growth. This study has greatly enriched our knowledge of the effect of LTD fermentation temperature on its quality, providing practical and interesting information for future improvement of LTD and light-flavor Baijiu products.}, } @article {pmid35650232, year = {2022}, author = {Poor, AP and Moreno, LZ and Monteiro, MS and Matajira, CEC and Dutra, MC and Leal, DF and Silva, APS and Gomes, VTM and Barbosa, MRF and Sato, MIZ and Moreno, AM}, title = {Vaginal microbiota signatures in healthy and purulent vulvar discharge sows.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9106}, pmid = {35650232}, issn = {2045-2322}, mesh = {Animals ; Bacteria/genetics ; Female ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Swine ; *Vagina/microbiology ; Vulva ; }, abstract = {Purulent vulvar discharges, primarily caused by genito-urinary tract infections, are an important source of economic loss for swine producers due to sow culling and mortality. However, the agents that compose the vaginal microbiota of sows and their changes during infections are not well understood. The first goal of this study was to characterize and compare the vaginal bacterial content of healthy (HE, n = 40) and purulent vulvar discharge sows (VD, n = 270) by a culture-dependent method and MALDI-TOF MS identification. Secondly, we performed 16S rRNA targeted metagenomic approach (n = 72) to compare the vaginal microbiota between these groups. We found a wide variety of bacteria, with Proteobacteria, Firmicutes, and Bacteroidota being the most abundant phyla in both groups, as well as Escherichia-Shigella, Streptococcus, and Bacteroides at the genus level. Most agents identified in the sequencing method also grew in the culture-dependent method, showing the viability of these bacteria. Alpha diversity did not differ between HE and VD sows, regarding sample richness and diversity, but a beta-diversity index showed a different microbiota composition between these groups in two tested herds. ANCOM analysis revealed that Bacteroides pyogenes were more abundant in VD females and can be a marker for this group. Other agents also require attention, such as the Streptococcus dysgalactiae and Staphylococcus hyicus found in remarkably greater relative abundance in VD sows. Network analysis revealed important positive correlations between some potentially pathogenic genera, such as between Escherichia-Shigella, Trueperella, Streptococcus, Corynebacterium, and Prevotella, which did not occur in healthy sows. We conclude that the alteration of the vaginal microbiota between healthy and purulent vulvar discharge sows, although not extreme, could be due to the increase in the relative abundance of specific agents and to associations between potentially pathogenic bacteria.}, } @article {pmid35643020, year = {2022}, author = {Smith, SE and Huang, W and Tiamani, K and Unterer, M and Khan Mirzaei, M and Deng, L}, title = {Emerging technologies in the study of the virome.}, journal = {Current opinion in virology}, volume = {54}, number = {}, pages = {101231}, doi = {10.1016/j.coviro.2022.101231}, pmid = {35643020}, issn = {1879-6265}, mesh = {*Bacteriophages/genetics ; Metagenome ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Virome ; *Viruses/genetics ; }, abstract = {Despite the growing interest in the microbiome in recent years, the study of the virome, the major part of which is made up of bacteriophages, is relatively underdeveloped compared with their bacterial counterparts. This is due in part to the lack of a universally conserved marker such as the 16S rRNA gene. For this reason, the development of metagenomic approaches was a major milestone in the study of the viruses in the microbiome or virome. However, it has become increasingly clear that these wet-lab methods have not yet been able to detect the full range of viruses present, and our understanding of the composition of the virome remains incomplete. In recent years, a range of new technologies has been developed to further our understanding. Direct RNA-Seq technologies bypass the need for cDNA synthesis, thus avoiding biases subjected to this step, which further expands our understanding of RNA viruses. The new generation of amplification methods could solve the low biomass issue relevant to most virome samples while reducing the error rate and biases caused by whole genome amplification. The application of long-read sequencing to virome samples can resolve the shortcomings of short-read sequencing in generating complete viral genomes and avoid the biases introduced by the assembly. Novel experimental methods developed to measure viruses' host range can help overcome the challenges of assigning hosts to many phages, specifically unculturable ones.}, } @article {pmid35642928, year = {2022}, author = {Liu, Q and Zuo, T and Lu, W and Yeoh, YK and Su, Q and Xu, Z and Tang, W and Yang, K and Zhang, F and Lau, LHS and Lui, RNS and Chin, ML and Wong, R and Cheung, CP and Zhu, W and Chan, PKS and Chan, FKL and Lui, GC and Ng, SC}, title = {Longitudinal Evaluation of Gut Bacteriomes and Viromes after Fecal Microbiota Transplantation for Eradication of Carbapenem-Resistant Enterobacteriaceae.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0151021}, pmid = {35642928}, issn = {2379-5077}, mesh = {Animals ; Mice ; Fecal Microbiota Transplantation ; *Carbapenem-Resistant Enterobacteriaceae ; Virome ; Escherichia coli ; Pilot Projects ; *Bacteriophages ; }, abstract = {Understanding the role of fecal microbiota transplantation (FMT) in the decolonization of multidrug-resistant organisms (MDRO) is critical. Specifically, little is known about virome changes in MDRO-infected subjects treated with FMT. Using shotgun metagenomic sequencing, we characterized longitudinal dynamics of the gut virome and bacteriome in three recipients who successfully decolonized carbapenem-resistant Enterobacteriaceae (CRE), including Klebsiella spp. and Escherichia coli, after FMT. We observed large shifts of the fecal bacterial microbiota resembling a donor-like community after transfer of a fecal microbiota dominated by the genus Ruminococcus. We found a substantial expansion of Klebsiella phages after FMT with a concordant decrease of Klebsiella spp. and striking increase of Escherichia phages in CRE E. coli carriers after FMT. We also observed the CRE elimination and similar evolution of Klebsiella phage in mice, which may play a role in the collapse of the Klebsiella population after FMT. In summary, our pilot study documented bacteriome and virome alterations after FMT which mediate many of the effects of FMT on the gut microbiome community. IMPORTANCE Fecal microbiota transplantation (FMT) is an effective treatment for multidrug-resistant organisms; however, introducing a complex mixture of microbes also has unknown consequences for landscape features of gut microbiome. We sought to understand bacteriome and virome alterations in patients undergoing FMT to treat infection with carbapenem-resistant Enterobacteriaceae. This finding indicates that transkingdom interactions between the virome and bacteriome communities may have evolved in part to support efficient FMT for treating CRE.}, } @article {pmid35642922, year = {2022}, author = {Hoskinson, C and Zheng, K and Gabel, J and Kump, A and German, R and Podicheti, R and Marino, N and Stiemsma, LT}, title = {Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0148921}, pmid = {35642922}, issn = {2379-5077}, mesh = {Animals ; Humans ; Female ; Dysbiosis/diagnosis ; *Microbiota/genetics ; Breast ; Bacteria/genetics ; *Breast Neoplasms/diagnosis ; *Mammary Neoplasms, Animal ; *Precancerous Conditions ; }, abstract = {Microbiota studies have reported changes in the microbial composition of the breast upon cancer development. However, results are inconsistent and limited to the later phases of cancer development (after diagnosis). We analyzed and compared the resident bacterial taxa of histologically normal breast tissue (healthy, H, n = 49) with those of tissues donated prior to (prediagnostic, PD, n = 15) and after (adjacent normal, AN, n = 49, and tumor, T, n = 46) breast cancer diagnosis (n total = 159). DNA was isolated from tissue samples and submitted for Illumina MiSeq paired-end sequencing of the V3-V4 region of the 16S gene. To infer bacterial function in breast cancer, we predicted the functional bacteriome from the 16S sequencing data using PICRUSt2. Bacterial compositional analysis revealed an intermediary taxonomic signature in the PD tissue relative to that of the H tissue, represented by shifts in Bacillaceae, Burkholderiaceae, Corynebacteriaceae, Streptococcaceae, and Staphylococcaceae. This compositional signature was enhanced in the AN and T tissues. We also identified significant metabolic reprogramming of the microbiota of the PD, AN, and T tissue compared with the H tissue. Further, preliminary correlation analysis between host transcriptome profiling and microbial taxa and genes in H and PD tissues identified altered associations between the human host and mammary microbiota in PD tissue compared with H tissue. These findings suggest that compositional shifts in bacterial abundance and metabolic reprogramming of the breast tissue microbiota are early events in breast cancer development that are potentially linked with cancer susceptibility. IMPORTANCE The goal of this study was to determine the role of resident breast tissue bacteria in breast cancer development. We analyzed breast tissue bacteria in healthy breast tissue and breast tissue donated prior to (precancerous) and after (postcancerous) breast cancer diagnosis. Compared to healthy tissue, the precancerous and postcancerous breast tissues demonstrated differences in the amounts of breast tissue bacteria. In addition, breast tissue bacteria exhibit different functions in pre-cancerous and post-cancerous breast tissues relative to healthy tissue. These differences in function are further emphasized by altered associations of the breast tissue bacteria with gene expression in the human host prior to cancer development. Collectively, these analyses identified shifts in bacterial abundance and metabolic function (dysbiosis) prior to breast tumor diagnosis. This dysbiosis may serve as a therapeutic target in breast cancer prevention.}, } @article {pmid35642511, year = {2022}, author = {Weigel, BL and Miranda, KK and Fogarty, EC and Watson, AR and Pfister, CA}, title = {Functional Insights into the Kelp Microbiome from Metagenome-Assembled Genomes.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0142221}, pmid = {35642511}, issn = {2379-5077}, mesh = {Humans ; Metagenome/genetics ; *Kelp/genetics ; Dissolved Organic Matter ; Nitrates/metabolism ; Phylogeny ; *Microbiota/genetics ; Bacteria ; Vitamins/metabolism ; }, abstract = {Eukaryotic organisms evolved in a microbial world and often have intimate associations with diverse bacterial groups. Kelp, brown macroalgae in the order Laminariales, play a vital role in coastal ecosystems, yet we know little about the functional role of the microbial symbionts that cover their photosynthetic surfaces. Here, we reconstructed 79 bacterial metagenome-assembled genomes (MAGs) from blades of the bull kelp, Nereocystis luetkeana, allowing us to determine their metabolic potential and functional roles. Despite the annual life history of bull kelp, nearly half of the bacterial MAGs were detected across multiple years. Diverse members of the kelp microbiome, spanning 6 bacterial phyla, contained genes for transporting and assimilating dissolved organic matter (DOM), which is secreted by kelp in large quantities and likely fuels the metabolism of these heterotrophic bacteria. Bacterial genomes also contained alginate lyase and biosynthesis genes, involved in polysaccharide degradation and biofilm formation, respectively. Kelp-associated bacterial genomes contained genes for dissimilatory nitrate reduction and urea hydrolysis, likely providing a reduced source of nitrogen to the host kelp. The genome of the most abundant member of the kelp microbiome and common macroalgal symbiont, Granulosicoccus, contained a full suite of genes for synthesizing cobalamin (vitamin B12), suggesting that kelp-associated bacteria have the potential to provide their host kelp with vitamins. Finally, kelp-associated Granulosicoccus contained genes that typify the aerobic anoxygenic phototrophic bacteria, including genes for bacteriochlorophyll synthesis and photosystem II reaction center proteins, making them the first known photoheterotrophic representatives of this genus. IMPORTANCE Kelp (brown algae in the order Laminariales) are foundational species that create essential habitat in temperate and arctic coastal marine ecosystems. These photosynthetic giants host millions of microbial taxa whose functions are relatively unknown, despite their potential importance for host-microbe interactions and nutrient cycling in kelp forest ecosystems. We reconstructed bacterial genomes from metagenomic samples collected from blades of the bull kelp, Nereocystis luetkeana, allowing us to determine the functional gene content of specific members of the kelp microbiome. These bacterial genomes spanned 6 phyla and 19 families and included common alga-associated microbial symbionts such as Granulosicoccus. Key functions encoded in kelp-associated bacterial genomes included dissolved organic matter assimilation, alginate metabolism, vitamin B12 biosynthesis, and nitrogen reduction from nitrate and urea to ammonium, potentially providing the host kelp with vitamins and reduced nitrogen.}, } @article {pmid35641653, year = {2022}, author = {Marrocco, F and Delli Carpini, M and Garofalo, S and Giampaoli, O and De Felice, E and Di Castro, MA and Maggi, L and Scavizzi, F and Raspa, M and Marini, F and Tomassini, A and Nicolosi, R and Cason, C and Trettel, F and Miccheli, A and Iebba, V and D'Alessandro, G and Limatola, C}, title = {Short-chain fatty acids promote the effect of environmental signals on the gut microbiome and metabolome in mice.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {517}, pmid = {35641653}, issn = {2399-3642}, mesh = {Animals ; Fatty Acids, Volatile ; Formates ; *Gastrointestinal Microbiome ; Metabolome ; Mice ; *Microbiota ; }, abstract = {Gut microorganisms and the products of their metabolism thoroughly affect host brain development, function and behavior. Since alterations of brain plasticity and cognition have been demonstrated upon motor, sensorial and social enrichment of the housing conditions, we hypothesized that gut microbiota and metabolome could be altered by environmental stimuli, providing part of the missing link among environmental signals and brain effects. In this preliminary study, metagenomic and metabolomic analyses of mice housed in different environmental conditions, standard and enriched, identify environment-specific microbial communities and metabolic profiles. We show that mice housed in an enriched environment have distinctive microbiota composition with a reduction in gut bacterial richness and biodiversity and are characterized by a metabolomic fingerprint with the increase of formate and acetate and the decrease of bile salts. We demonstrate that mice treated with a mixture of formate and acetate recapitulate some of the brain plasticity effects modulated by environmental enrichment, such as hippocampal neurogenesis, neurotrophin production, short-term plasticity and cognitive behaviors, that can be further exploited to decipher the mechanisms involved in experience-dependent brain plasticity.}, } @article {pmid35641510, year = {2022}, author = {Yeoh, YK and Sun, Y and Ip, LYT and Wang, L and Chan, FKL and Miao, Y and Ng, SC}, title = {Prevotella species in the human gut is primarily comprised of Prevotella copri, Prevotella stercorea and related lineages.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9055}, pmid = {35641510}, issn = {2045-2322}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Microbiota ; Prevotella/genetics/metabolism ; }, abstract = {Prevotella species in the human gut microbiome are primarily comprised of Prevotella copri, and its diversity and function were recently investigated in detail. Much less is known about other Prevotella species in the human gut. Here, we examined the composition of Prevotella species in human guts by mapping publicly available gut metagenomes to a dereplicated set of metagenome-assembled genomes (MAGs) representing Prevotella lineages found in human guts. In most human cohorts, P. copri is the most relatively abundant species (e.g. up to 14.3% relative abundance in Tangshan, China). However, more than half of the metagenome reads in several cohorts mapped to Prevotella MAGs representing P. stercorea and several other species sister to P. stercorea and P. copri. Analyses of genes encoded in these genomes indicated that P. stercorea and related lineages lacked many hemicellulose degrading enzymes and were thus less likely to metabolise hemicelluloses compared with P. copri and copri-related lineages. Instead, P. stercorea genomes possess several carbohydrate esterases that may be involved in releasing ester modifications from carbohydrates to facilitate their degradation. These findings reveal unexplored Prevotella diversity in the human gut and indicate possible niche partitions among these related species.}, } @article {pmid35638779, year = {2022}, author = {Attai, H and Wilde, J and Liu, R and Chopyk, J and Garcia, AG and Allen-Vercoe, E and Pride, D}, title = {Bacteriophage-Mediated Perturbation of Defined Bacterial Communities in an In Vitro Model of the Human Gut.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0113522}, pmid = {35638779}, issn = {2165-0497}, mesh = {Animals ; Bacteria ; *Bacteriophages ; Bacteroidetes ; Feces/microbiology ; Gastrointestinal Tract/microbiology ; Humans ; Mice ; *Microbiota ; *Viruses ; }, abstract = {The study of bacteriophage communities reproducing in the gastrointestinal tract is limited by the quality of model systems supporting experimental manipulation in vitro. Traditionally, studies aiming to experimentally address phage-bacteria dynamics have utilized gnotobiotic mice inoculated with defined bacterial communities. While mouse models simulate complex interactions between microbes and their host, they also forestall the study of phage-bacteria dynamics in isolation of host factors. Here, we established a method for manipulating phage-bacteria dynamics using an in vitro chemostat bioreactor model of the distal human gut. We create defined communities representing a subset of bacteria in the feces of two human individuals, cultivated these communities in chemostat bioreactors, developed methods to purify the autochthonous viromes associated with each cultured community, and trialed a system for transmitting live or heat-killed viruses between chemostat bioreactors to decipher outcomes of virus-mediated perturbation. We found that allochthonous viromes were detectable via metagenomic sequencing against the autochthonous virome background and that shifts in bacterial community diversity and composition were detectable in relation to time posttreatment. These microbiome composition changes spanned multiple phyla, including Bacteroidetes, Firmicutes, and Actinobacteria. We also found that compositional changes occurred when using live viruses regardless of whether intrasubject or intersubject viruses were used as the perturbation agents. Our results supported the use of chemostat bioreactors as a platform for studying complex bacteria-phage dynamics in vitro. IMPORTANCE Bacteriophages are relatively ubiquitous in the environment and are highly abundant in the human microbiome. Phages can be commonly transmitted between close contacts, but the impact that such transmissions may have on their bacteria counterparts in our microbiomes is unknown. We developed a chemostat cultivation system to simulate individual-specific features of human distal gut microbiota that can be used to transmit phages between ecosystems and measure their impacts on the microbiota. We used this system to transfer phage communities between chemostats that represented different human subjects. We found that there were significant effects on overall microbiota diversity and changes in the relative abundances of Bacteroidetes, Firmicutes, and Actinobacteria, when intersubject perturbations were performed, compared to intrasubject perturbations. These changes were observed when perturbations were performed using live phages, but not when heat-killed phages were used, and they support the use of chemostat systems for studying complex human bacteria-phage dynamics.}, } @article {pmid35638605, year = {2022}, author = {Dillard, BA and Chung, AK and Gunderson, AR and Campbell-Staton, SC and Moeller, AH}, title = {Humanization of wildlife gut microbiota in urban environments.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35638605}, issn = {2050-084X}, support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Animals, Wild ; Bacteria/genetics ; Cities ; *Gastrointestinal Microbiome ; Humans ; *Lizards ; Urbanization ; }, abstract = {Urbanization is rapidly altering Earth's environments, demanding investigation of the impacts on resident wildlife. Here, we show that urban populations of coyotes (Canis latrans), crested anole lizards (Anolis cristatellus), and white-crowned sparrows (Zonotrichia leucophrys) acquire gut microbiota constituents found in humans, including gut bacterial lineages associated with urbanization in humans. Comparisons of urban and rural wildlife and human populations revealed significant convergence of gut microbiota among urban populations relative to rural populations. All bacterial lineages overrepresented in urban wildlife relative to rural wildlife and differentially abundant between urban and rural humans were also overrepresented in urban humans relative to rural humans. Remarkably, the bacterial lineage most overrepresented in urban anoles was a Bacteroides sequence variant that was also the most significantly overrepresented in urban human populations. These results indicate parallel effects of urbanization on human and wildlife gut microbiota and suggest spillover of bacteria from humans into wildlife in cities.}, } @article {pmid35637503, year = {2022}, author = {Ning, Y and Hu, M and Gong, Y and Huang, R and Xu, K and Chen, S and Zhang, F and Liu, Y and Chen, F and Chang, Y and Zhao, G and Li, C and Zhou, R and Lammi, MJ and Guo, X and Wang, X}, title = {Comparative analysis of the gut microbiota composition between knee osteoarthritis and Kashin-Beck disease in Northwest China.}, journal = {Arthritis research & therapy}, volume = {24}, number = {1}, pages = {129}, pmid = {35637503}, issn = {1478-6362}, mesh = {China/epidemiology ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; *Kashin-Beck Disease/genetics ; *Osteoarthritis, Knee/genetics ; }, abstract = {BACKGROUND: Osteoarthritis (OA) and Kashin-Beck disease (KBD) both are two severe osteochondral disorders. In this study, we aimed to compare the gut microbiota structure between OA and KBD patients.

METHODS: Fecal samples collected from OA and KBD patients were used to characterize the gut microbiota using 16S rDNA gene sequencing. To identify whether gut microbial changes at the species level are associated with the genes or functions of the gut bacteria between OA and KBD groups, metagenomic sequencing of fecal samples from OA and KBD subjects was performed.

RESULTS: The OA group was characterized by elevated Epsilonbacteraeota and Firmicutes levels. A total of 52 genera were identified to be significantly differentially abundant between the two groups. The genera Raoultella, Citrobacter, Flavonifractor, g__Lachnospiraceae_UCG-004, and Burkholderia-Caballeronia-Paraburkholderia were more abundant in the OA group. The KBD group was characterized by higher Prevotella_9, Lactobacillus, Coprococcus_2, Senegalimassilia, and Holdemanella. The metagenomic sequencing showed that the Subdoligranulum_sp._APC924/74, Streptococcus_parasanguinis, and Streptococcus_salivarius were significantly increased in abundance in the OA group compared to those in the KBD group, and the species Prevotella_copri, Prevotella_sp._CAG:386, and Prevotella_stercorea were significantly decreased in abundance in the OA group compared to those in the KBD group by using metagenomic sequencing.

CONCLUSION: Our study provides a comprehensive landscape of the gut microbiota between OA and KBD patients and provides clues for better understanding the mechanisms underlying the pathogenesis of OA and KBD.}, } @article {pmid35637399, year = {2022}, author = {Salih, H and Karaynir, A and Yalcin, M and Oryasin, E and Holyavkin, C and Basbulbul, G and Bozdogan, B}, title = {Metagenomic analysis of wastewater phageome from a University Hospital in Turkey.}, journal = {Archives of microbiology}, volume = {204}, number = {6}, pages = {353}, pmid = {35637399}, issn = {1432-072X}, mesh = {*Bacteriophages/genetics ; Ecosystem ; Hospitals ; Humans ; *Podoviridae/genetics ; Turkey ; Virome ; Wastewater ; }, abstract = {Phage DNA analysis gives opportunity to understand living ecosystem of the environment where the samples are taken. In the present study, we analyzed phage DNA obtained from wastewater sample of university hospital sewage. After filtration, long high-speed centrifugation was done to collect phages. DNA was extracted from pellet by phenol chloroform extraction and used for NGS sequencing. The host profile, taxonomic and functional analyses were performed using MG-RAST, and ResFinder program was used for resistance gene detection. High amounts of reads belong to bacteriophage groups (~ 95%) from our DNA sample were obtained and all bacteriophage reads were found belonging to Caudovirales order and Myoviridae (56%), Siphoviridae (43%), and Podoviridae (0.02%) families. The most common host genera were Escherichia (88.20%), Salmonella (5.49%) and Staphylococcus (5.19%). SEED subsystems hits were mostly structural parts and KEGG Orthology hits were nucleotide- and carbohydrate metabolism-related genes. No anti-microbial resistance genes were detected. Our bacteriophage DNA purification method is favorable for phage metagenomic studies. Dominance of coliphages may explain infrequent Podoviridae. Dominancy of structural genes and auxiliary genes is probably due to abundance of lytic phages in our sample. Absence of antibiotic resistance genes even in hospital environment phages indicates that phages are not important carrier of resistance genes.}, } @article {pmid35636700, year = {2022}, author = {Alma'abadi, A and Behzad, H and Alarawi, M and Conchouso, D and Saito, Y and Hosokawa, M and Nishikawa, Y and Kogawa, M and Takeyama, H and Mineta, K and Gojobori, T}, title = {Identification of lipolytic enzymes using high-throughput single-cell screening and sorting of a metagenomic library.}, journal = {New biotechnology}, volume = {70}, number = {}, pages = {102-108}, doi = {10.1016/j.nbt.2022.05.006}, pmid = {35636700}, issn = {1876-4347}, mesh = {Enzymes ; Gene Library ; Lipase/genetics/metabolism ; Metagenome ; *Metagenomics ; *Microbiota ; }, abstract = {The demand for novel, robust microbial biocatalysts for use in industrial and pharmaceutical applications continues to increase rapidly. As a result, there is a need to develop advanced tools and technologies to exploit the vast metabolic potential of unculturable microorganisms found in various environments. Single-cell and functional metagenomics studies can explore the enzymatic potential of entire microbial communities in a given environment without the need to culture the microorganisms. This approach has contributed substantially to the discovery of unique microbial genes for industrial and medical applications. Functional metagenomics involves the extraction of microbial DNA directly from environmental samples, constructing expression libraries comprising the entire microbial genome, and screening of the libraries for the presence of desired phenotypes. In this study, lipolytic enzymes from the Red Sea were targeted. A high-throughput single-cell microfluidic platform combined with a laser-based fluorescent screening bioassay was employed to discover new genes encoding lipolytic enzymes. Analysis of the metagenomic library led to the identification of three microbial genes encoding lipases based on their functional similarity and sequence homology to known lipases. The results demonstrated that microfluidics is a robust technology that can be used for screening in functional metagenomics. The results also indicate that the Red Sea is a promising, under-investigated source of new genes and gene products.}, } @article {pmid35633118, year = {2022}, author = {Tham, KC and Lefferdink, R and Duan, K and Lim, SS and Wong, XFCC and Ibler, E and Wu, B and Abu-Zayed, H and Rangel, SM and Del Duca, E and Chowdhury, M and Chima, M and Kim, HJ and Lee, B and Guttman-Yassky, E and Paller, AS and Common, JEA}, title = {Distinct skin microbiome community structures in congenital ichthyosis.}, journal = {The British journal of dermatology}, volume = {187}, number = {4}, pages = {557-570}, pmid = {35633118}, issn = {1365-2133}, support = {P30 AR075049/AR/NIAMS NIH HHS/United States ; }, mesh = {Adult ; Humans ; *Ichthyosiform Erythroderma, Congenital ; *Ichthyosis/genetics ; *Ichthyosis, Lamellar/genetics ; Lipids ; *Microbiota/genetics ; Skin/pathology ; }, abstract = {BACKGROUND: The ichthyoses are rare genetic keratinizing disorders that share the characteristics of an impaired epidermal barrier and increased risk of microbial infections. Although ichthyotic diseases share a T helper (Th) 17 cell immune signature, including increased expression of antimicrobial peptides, the skin microbiota of ichthyoses is virtually unexplored.

OBJECTIVES: To analyse the metagenome profile of skin microbiome for major congenital ichthyosis subtypes.

METHODS: Body site-matched skin surface samples were collected from the scalp, upper arm and upper buttocks of 16 healthy control participants and 22 adult patients with congenital forms of ichthyosis for whole metagenomics sequencing analysis.

RESULTS: Taxonomic profiling showed significant shifts in bacteria and fungi abundance and sporadic viral increases across ichthyosis subtypes. Cutibacterium acnes and Malassezia were significantly reduced across body sites, consistent with skin barrier disruption and depletion of lipids. Microbial richness was reduced, with specific increases in Staphylococcus and Corynebacterium genera, as well as shifts in fungal species, including Malassezia. Malassezia globosa was reduced at all body sites, whereas M. sympodialis was reduced in the ichthyotic upper arm and upper buttocks. Malassezia slooffiae, by contrast, was strikingly increased at all body sites in participants with congenital ichthyosiform erythroderma (CIE) and lamellar ichthyosis (LI). A previously undescribed Trichophyton species was also detected as sporadically colonizing the skin of patients with CIE, LI and epidermolytic ichthyosis subtypes.

CONCLUSIONS: The ichthyosis skin microbiome is significantly altered from healthy skin with specific changes predominating among ichthyosis subtypes. Skewing towards the Th17 pathway may represent a response to the altered microbial colonization in ichthyosis. What is already known about this topic? The skin microbiome of congenital ichthyoses is largely unexplored. Microbes play an important role in pathogenesis, as infections are common. The relative abundances of staphylococci and corynebacteria is increased in the cutaneous microbiome of patients with Netherton syndrome, but extension of these abundances to all congenital ichthyoses is unexplored. What does this study add? A common skin microbiome signature was observed across congenital ichthyoses. Distinct microbiome features were associated with ichthyosis subtypes. Changes in microbiome may contribute to T helper 17 cell immune polarization. What is the translational message? These data provide the basis for comparison of the microbiome with lipidomic and transcriptomic alterations in these forms of ichthyosis and consideration of correcting the dysbiosis as a therapeutic intervention.}, } @article {pmid35632601, year = {2022}, author = {Litov, AG and Zueva, AI and Tiunov, AV and Van Thinh, N and Belyaeva, NV and Karganova, GG}, title = {Virome of Three Termite Species from Southern Vietnam.}, journal = {Viruses}, volume = {14}, number = {5}, pages = {}, pmid = {35632601}, issn = {1999-4915}, mesh = {Animals ; Ecosystem ; Forests ; *Isoptera ; *RNA Viruses ; Vietnam ; Virome ; }, abstract = {Modern metagenomic approaches enable the effective discovery of novel viruses in previously unexplored organisms. Termites are significant ecosystem converters and influencers. As with the majority of tropical forest insects, termites are studied insufficiently, and termite virome remains especially understudied. Here, we studied the virome of lichenophagous and mycophagous termites (Hospitalitermes bicolor, Macrotermes carbonarius and Odontotermes wallonensis) collected in the Cat Tien National Park (Vietnam). We assembled four full genomes of novel viruses related to Solemoviridae, Lispiviridae, Polycipiviridae and Kolmioviridae. We also found several contigs with relation to Chuviridae and Deltaflexiviridae that did not correspond to complete virus genomes. All the novel viruses clustered phylogenetically with previously identified viruses of the termites. Deltaflexi-like contigs were identified in the fungi-cultivating M. carbonarius and showed homology with viruses recently discovered in the edible basidiomycete mushrooms.}, } @article {pmid35627235, year = {2022}, author = {Silva, I and Alves, M and Malheiro, C and Silva, ARR and Loureiro, S and Henriques, I and González-Alcaraz, MN}, title = {Short-Term Responses of Soil Microbial Communities to Changes in Air Temperature, Soil Moisture and UV Radiation.}, journal = {Genes}, volume = {13}, number = {5}, pages = {}, pmid = {35627235}, issn = {2073-4425}, mesh = {Bacteria/genetics ; DNA, Ribosomal ; *Microbiota ; *Soil/chemistry ; Temperature ; Ultraviolet Rays ; Water ; }, abstract = {We analyzed the effects on a soil microbial community of short-term alterations in air temperature, soil moisture and ultraviolet radiation and assessed the role of invertebrates (species Enchytraeus crypticus) in modulating the community's response to these factors. The reference soil, Lufa 2.2, was incubated for 48 h, with and without invertebrates, under the following conditions: standard (20 °C + 50% water holding capacity (WHC)); increased air temperature (15-25 °C or 20-30 °C + 50% WHC); flood (20 °C + 75% WHC); drought (20 °C + 25% WHC); and ultraviolet radiation (UV) (20 °C + 50% WHC + UV). BIOLOG EcoPlates and 16S rDNA sequencing (Illumina) were used to assess the microbial community's physiological profile and the bacterial community's structure, respectively. The bacterial abundance (estimated by 16S rDNA qPCR) did not change. Most of the conditions led to an increase in microbial activity and a decrease in diversity. The structure of the bacterial community was particularly affected by higher air temperatures (20-30 °C, without E. crypticus) and floods (with E. crypticus). Effects were observed at the class, genera and OTU levels. The presence of invertebrates mostly resulted in the attenuation of the observed effects, highlighting the importance of considering microbiome-invertebrate interactions. Considering future climate changes, the effects described here raise concern. This study provides fundamental knowledge to develop effective strategies to mitigate these negative outcomes. However, long-term studies integrating biotic and abiotic factors are needed.}, } @article {pmid35624491, year = {2022}, author = {Arora, J and Kinjo, Y and Šobotník, J and Buček, A and Clitheroe, C and Stiblik, P and Roisin, Y and Žifčáková, L and Park, YC and Kim, KY and Sillam-Dussès, D and Hervé, V and Lo, N and Tokuda, G and Brune, A and Bourguignon, T}, title = {The functional evolution of termite gut microbiota.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {78}, pmid = {35624491}, issn = {2049-2618}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Isoptera ; Metagenome ; Phylogeny ; Soil ; }, abstract = {BACKGROUND: Termites primarily feed on lignocellulose or soil in association with specific gut microbes. The functioning of the termite gut microbiota is partly understood in a handful of wood-feeding pest species but remains largely unknown in other taxa. We intend to fill this gap and provide a global understanding of the functional evolution of termite gut microbiota.

RESULTS: We sequenced the gut metagenomes of 145 samples representative of the termite diversity. We show that the prokaryotic fraction of the gut microbiota of all termites possesses similar genes for carbohydrate and nitrogen metabolisms, in proportions varying with termite phylogenetic position and diet. The presence of a conserved set of gut prokaryotic genes implies that essential nutritional functions were present in the ancestor of modern termites. Furthermore, the abundance of these genes largely correlated with the host phylogeny. Finally, we found that the adaptation to a diet of soil by some termite lineages was accompanied by a change in the stoichiometry of genes involved in important nutritional functions rather than by the acquisition of new genes and pathways.

CONCLUSIONS: Our results reveal that the composition and function of termite gut prokaryotic communities have been remarkably conserved since termites first appeared ~ 150 million years ago. Therefore, the "world's smallest bioreactor" has been operating as a multipartite symbiosis composed of termites, archaea, bacteria, and cellulolytic flagellates since its inception. Video Abstract.}, } @article {pmid35620087, year = {2022}, author = {Li, X and Guo, R and Zou, X and Yao, Y and Lu, L}, title = {The First Cbk-Like Phage Infecting Erythrobacter, Representing a Novel Siphoviral Genus.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {861793}, pmid = {35620087}, issn = {1664-302X}, abstract = {Erythrobacter is an important and widespread bacterial genus in the ocean. However, our knowledge about their phages is still rare. Here, a novel lytic phage vB_EliS-L02, infecting Erythrobacter litoralis DSM 8509, was isolated and purified from Sanggou Bay seawater, China. Morphological observation revealed that the phage belonged to Cbk-like siphovirus, with a long prolate head and a long tail. The host range test showed that phage vB_EliS-L02 could only infect a few strains of Erythrobacter, demonstrating its potential narrow-host range. The genome size of vB_EliS-L02 was 150,063 bp with a G+C content of 59.43%, encoding 231 putative open reading frames (ORFs), but only 47 were predicted to be functional domains. Fourteen auxiliary metabolic genes were identified, including phoH that may confer vB_EliS-L02 the advantage of regulating phosphate uptake and metabolism under a phosphate-limiting condition. Genomic and phylogenetic analyses indicated that vB_EliS-L02 was most closely related to the genus Lacusarxvirus with low similarity (shared genes < 30%, and average nucleotide sequence identity < 70%), distantly from other reported phages, and could be grouped into a novel viral genus cluster, in this study as Eliscbkvirus. Meanwhile, the genus Eliscbkvirus and Lacusarxvirus stand out from other siphoviral genera and could represent a novel subfamily within Siphoviridae, named Dolichocephalovirinae-II. Being a representative of an understudied viral group with manifold adaptations to the host, phage vB_EliS-L02 could improve our understanding of the virus-host interactions and provide reference information for viral metagenomic analysis in the ocean.}, } @article {pmid35618944, year = {2023}, author = {Lau, NS and Ting, SY and Sam, KK and M, J and Wong, SC and Wu, X and Waiho, K and Fazhan, H and Shu-Chien, AC}, title = {Comparative Analyses of Scylla olivacea Gut Microbiota Composition and Function Suggest the Capacity for Polyunsaturated Fatty Acid Biosynthesis.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {575-588}, pmid = {35618944}, issn = {1432-184X}, mesh = {Animals ; *Brachyura ; *Gastrointestinal Microbiome ; Fatty Acids, Unsaturated/metabolism ; Diet ; Lipid Metabolism ; }, abstract = {Although numerous studies in aquatic organisms have linked lipid metabolism with intestinal bacterial structure, the possibility of the gut microbiota participating in the biosynthesis of beneficial long-chain polyunsaturated fatty acid (LC-PUFA) remains vague. We profiled the gut microbiota of the mud crab Scylla olivacea fed with either a LC-PUFA rich (FO) or a LC-PUFA-poor but C18-PUFA substrate-rich (LOCO) diet. Additionally, a diet with a similar profile as LOCO but with the inclusion of an antibiotic, oxolinic acid (LOCOAB), was also used to further demarcate the possibility of LC-PUFA biosynthesis in gut microbiota. Compared to diet FO treatment, crabs fed diet LOCO contained a higher proportion of Proteobacteria, notably two known taxonomy groups with PUFA biosynthesis capacity, Vibrio and Shewanella. Annotation of metagenomic datasets also revealed enrichment in the KEGG pathway of unsaturated fatty acid biosynthesis and polyketide synthase-like system sequences with this diet. Intriguingly, diet LOCOAB impeded the presence of Vibrio and Shewanella and with it, the function of unsaturated fatty acid biosynthesis. However, there was an increase in the function of short-chain fatty acid production, accompanied by a shift towards the abundance of phyla Bacteroidota and Spirochaetota. Collectively, these results exemplified bacterial communities and their corresponding PUFA biosynthesis pathways in the microbiota of an aquatic crustacean species.}, } @article {pmid35618126, year = {2022}, author = {Huang, G and Qu, Q and Wang, M and Huang, M and Zhou, W and Wei, F}, title = {Global landscape of gut microbiome diversity and antibiotic resistomes across vertebrates.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 2}, pages = {156178}, doi = {10.1016/j.scitotenv.2022.156178}, pmid = {35618126}, issn = {1879-1026}, mesh = {Animals ; Anti-Bacterial Agents ; Bacteria ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Vertebrates ; }, abstract = {Multiple factors influence gut microbiome diversity in vertebrate hosts. Most previous studies have only investigated specific factors and certain host species or taxa. However, a comprehensive assessment of the relative contributions of individual factors towards gut microbial diversity within a broader evolutionary context remains lacking. Here, 2202 16S rRNA gene sequencing samples of gut bacterial communities collected from 452 host species across seven classes were analyzed together to understand the factors broadly affecting vertebrate gut microbiomes across hosts with different diets, threatened status, captivity status, and habitat environmental factors. Among wild vertebrates, diet was most significantly associated with gut microbiome alpha diversity, while host phylogeny and diet were significantly associated with beta diversity, consistent with a previous study. Host threatened status and habitat environmental factors (e.g., geography and climate) were also associated with gut bacterial community beta diversity. Subsequent ecological modeling revealed a strong association between stochastic assembly processes and patterns of gut bacterial diversity among free-ranging vertebrates. In addition, metagenomic analysis of gut microbiomes from 62 captive vertebrates and sympatric humans revealed similar diversity and resistome profiles despite differences in host phylogeny, diet, and threatened status. These results thus suggest that captivity diminishes the effects of host phylogeny, diet, and threatened status on the diversity of vertebrate gut bacterial communities. The most overrepresented antibiotic resistant genes (ARGs) observed in these samples are involved in resistance to β-lactams, aminoglycosides, and tetracycline. These results also revealed potential horizontal transfers of ARGs between captive animals and humans, thereby jointly threatening public health and vertebrate conservation. Together, this study provides a comprehensive overview of the diversity and resistomes of vertebrate gut microbiomes. These combined analyses will help guide future vertebrate conservation via the rational manipulation of microbial diversity and reducing antibiotic usage.}, } @article {pmid35614211, year = {2022}, author = {Zhang, Y and Bhosle, A and Bae, S and McIver, LJ and Pishchany, G and Accorsi, EK and Thompson, KN and Arze, C and Wang, Y and Subramanian, A and Kearney, SM and Pawluk, A and Plichta, DR and Rahnavard, A and Shafquat, A and Xavier, RJ and Vlamakis, H and Garrett, WS and Krueger, A and Huttenhower, C and Franzosa, EA}, title = {Discovery of bioactive microbial gene products in inflammatory bowel disease.}, journal = {Nature}, volume = {606}, number = {7915}, pages = {754-760}, pmid = {35614211}, issn = {1476-4687}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AT009708/AT/NCCIH NIH HHS/United States ; R01 DK127171/DK/NIDDK NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; }, mesh = {*Bacterial Proteins/analysis/genetics ; Chronic Disease ; *Gastrointestinal Microbiome/genetics ; *Genes, Microbial ; Humans ; *Inflammatory Bowel Diseases/microbiology ; Metagenomics ; Proteomics ; Reproducibility of Results ; Transcriptome ; }, abstract = {Microbial communities and their associated bioactive compounds[1-3] are often disrupted in conditions such as the inflammatory bowel diseases (IBD)[4]. However, even in well-characterized environments (for example, the human gastrointestinal tract), more than one-third of microbial proteins are uncharacterized and often expected to be bioactive[5-7]. Here we systematically identified more than 340,000 protein families as potentially bioactive with respect to gut inflammation during IBD, about half of which have not to our knowledge been functionally characterized previously on the basis of homology or experiment. To validate prioritized microbial proteins, we used a combination of metagenomics, metatranscriptomics and metaproteomics to provide evidence of bioactivity for a subset of proteins that are involved in host and microbial cell-cell communication in the microbiome; for example, proteins associated with adherence or invasion processes, and extracellular von Willebrand-like factors. Predictions from high-throughput data were validated using targeted experiments that revealed the differential immunogenicity of prioritized Enterobacteriaceae pilins and the contribution of homologues of von Willebrand factors to the formation of Bacteroides biofilms in a manner dependent on mucin levels. This methodology, which we term MetaWIBELE (workflow to identify novel bioactive elements in the microbiome), is generalizable to other environmental communities and human phenotypes. The prioritized results provide thousands of candidate microbial proteins that are likely to interact with the host immune system in IBD, thus expanding our understanding of potentially bioactive gene products in chronic disease states and offering a rational compendium of possible therapeutic compounds and targets.}, } @article {pmid35614182, year = {2022}, author = {Iwańska, O and Latoch, P and Suchora, M and Pidek, IA and Huber, M and Bubak, I and Kopik, N and Kovalenko, M and Gąsiorowski, M and Armache, JP and Starosta, AL}, title = {Lake microbiome and trophy fluctuations of the ancient hemp rettery.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {8846}, pmid = {35614182}, issn = {2045-2322}, mesh = {*Cannabis/genetics ; Geologic Sediments/microbiology ; Lakes/microbiology ; Metagenome ; *Microbiota/genetics ; }, abstract = {Lake sediments not only store the long-term ecological information including pollen and microfossils but are also a source of sedimentary DNA (sedDNA). Here, by the combination of traditional multi-proxy paleolimnological methods with the whole-metagenome shotgun-sequencing of sedDNA we were able to paint a comprehensive picture of the fluctuations in trophy and bacterial diversity and metabolism of a small temperate lake in response to hemp retting, across the past 2000 years. Hemp retting (HR), a key step in hemp fibre production, was historically carried out in freshwater reservoirs and had a negative impact on the lake ecosystems. In Lake Slone, we identified two HR events, during the late stage of the Roman and Early Medieval periods and correlated these to the increased trophy and imbalanced lake microbiome. The metagenomic analyses showed a higher abundance of Chloroflexi, Planctomycetes and Bacteroidetes and a functional shift towards anaerobic metabolism, including degradation of complex biopolymers such as pectin and cellulose, during HR episodes. The lake eutrophication during HR was linked to the allochthonous, rather than autochthonous carbon supply-hemp straws. We also showed that the identification of HR based on the palynological analysis of hemp pollen may be inconclusive and we suggest the employment of the fibre count analysis as an additional and independent proxy.}, } @article {pmid35613310, year = {2022}, author = {Luo, T and Guo, Z and Liu, D and Guo, Z and Wu, Q and Li, Q and Lin, R and Chen, P and Ou, C and Chen, M}, title = {Deficiency of PSRC1 accelerates atherosclerosis by increasing TMAO production via manipulating gut microbiota and flavin monooxygenase 3.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2077602}, pmid = {35613310}, issn = {1949-0984}, mesh = {Animals ; *Atherosclerosis/genetics/microbiology ; Bacteria/genetics/metabolism ; *Gastrointestinal Microbiome/physiology ; *Methylamines/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Mixed Function Oxygenases/metabolism ; *Oxygenases/metabolism ; *Phosphoproteins/deficiency ; Plaque, Atherosclerotic/metabolism/microbiology ; }, abstract = {Maladaptive inflammatory and immune responses are responsible for intestinal barrier integrity and function dysregulation. Proline/serine-rich coiled-coil protein 1 (PSRC1) critically contributes to the immune system, but direct data on the gut microbiota and the microbial metabolite trimethylamine N-oxide (TMAO) are lacking. Here, we investigated the impact of PSRC1 deletion on TMAO generation and atherosclerosis. We first found that PSRC1 deletion in apoE[-/-] mice accelerated atherosclerotic plaque formation, and then the gut microbiota and metabolites were detected using metagenomics and untargeted metabolomics. Our results showed that PSRC1 deficiency enriched trimethylamine (TMA)-producing bacteria and functional potential for TMA synthesis and accordingly enhanced plasma betaine and TMAO production. Furthermore, PSRC1 deficiency resulted in a proinflammatory colonic phenotype that was significantly associated with the dysregulated bacteria. Unexpectedly, hepatic RNA-seq indicated upregulated flavin monooxygenase 3 (FMO3) expression following PSRC1 knockout. Mechanistically, PSRC1 overexpression inhibited FMO3 expression in vitro, while an ERα inhibitor rescued the downregulation. Consistently, PSRC1-knockout mice exhibited higher plasma TMAO levels with a choline-supplemented diet, which was gut microbiota dependent, as evidenced by antibiotic treatment. To investigate the role of dysbiosis induced by PSRC1 deletion in atherogenesis, apoE[-/-] mice were transplanted with the fecal microbiota from either apoE[-/-] or PSRC1[-/-]apoE[-/-] donor mice. Mice that received PSRC1-knockout mouse feces showed an elevation in TMAO levels, as well as plaque lipid deposition and macrophage accumulation, which were accompanied by increased plasma lipid levels and impaired hepatic cholesterol transport. Overall, we identified PSRC1 as an atherosclerosis-protective factor, at least in part, attributable to its regulation of TMAO generation via a multistep pathway. Thus, PSRC1 holds great potential for manipulating the gut microbiome and alleviating atherosclerosis.}, } @article {pmid35612791, year = {2022}, author = {Fong, SB and Boyer, E and Bonnaure-Mallet, M and Meuric, V}, title = {Microbiota in Periodontitis: Advances in the Omic Era.}, journal = {Advances in experimental medicine and biology}, volume = {1373}, number = {}, pages = {19-43}, pmid = {35612791}, issn = {0065-2598}, mesh = {Bacteria/genetics ; Biofilms ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota/genetics ; *Periodontitis/microbiology ; }, abstract = {The complexity of the oral microbiome continues to astound researchers even with the advancement of multi-disciplinary strategies being used to study these microorganisms in relation to the human body. There is extensive literature available that explains how oral bacterial communities exist within the biofilm and maintains a balance with the host immune system, but when this balance is tipped disease can occur. The purpose of this review is to highlight the subgingival microbial compositions during health and periodontal disease using next generation sequencing techniques, as well as determining the types of functional activities that partake during these states. The subgingival microbiota is a fluid structure that can adapt accordingly to the environment and the identification of signature biomarkers may aid in the assessment of risk and disease severity in an individual to complement clinical diagnosis in the future.}, } @article {pmid35608941, year = {2022}, author = {Otake-Kasamoto, Y and Kayama, H and Kishikawa, T and Shinzaki, S and Tashiro, T and Amano, T and Tani, M and Yoshihara, T and Li, B and Tani, H and Liu, L and Hayashi, A and Okuzaki, D and Motooka, D and Nakamura, S and Okada, Y and Iijima, H and Takeda, K and Takehara, T}, title = {Lysophosphatidylserines derived from microbiota in Crohn's disease elicit pathological Th1 response.}, journal = {The Journal of experimental medicine}, volume = {219}, number = {7}, pages = {}, pmid = {35608941}, issn = {1540-9538}, support = {//Core Research for Evolutional Science and TechnologyPRIME/ ; 19gm1010004//Japan Agency for Medical Research and Development/ ; //Osaka University Graduate School of Medicine/ ; //Immunology Frontier Research Center/ ; 17H04159//Grant-in-Aid for Scientific Research/ ; }, mesh = {Animals ; *Colitis/pathology ; *Crohn Disease/etiology ; Dysbiosis/complications ; Humans ; Inflammation/pathology ; Intestinal Mucosa/metabolism ; Lysophospholipids ; Mice ; *Microbiota ; Th1 Cells/metabolism ; }, abstract = {Microbiota alteration and IFN-γ-producing CD4+ T cell overactivation are implicated in Crohn's disease (CD) pathogenesis. However, it remains unclear how dysbiosis enhances Th1 responses, leading to intestinal inflammation. Here, we identified key metabolites derived from dysbiotic microbiota that induce enhanced Th1 responses and exaggerate colitis in mouse models. Patients with CD showed elevated lysophosphatidylserine (LysoPS) concentration in their feces, accompanied by a higher relative abundance of microbiota possessing a gene encoding the phospholipid-hydrolyzing enzyme phospholipase A. LysoPS induced metabolic reprogramming, thereby eliciting aberrant effector responses in both human and mouse IFN-γ-producing CD4+ T cells. Administration of LysoPS into two mouse colitis models promoted large intestinal inflammation. LysoPS-induced aggravation of colitis was impaired in mice lacking P2ry10 and P2ry10b, and their CD4+ T cells were hyporesponsive to LysoPS. Thus, our findings elaborate on the mechanism by which metabolites elevated in patients with CD harboring dysbiotic microbiota promote Th1-mediated intestinal pathology.}, } @article {pmid35608350, year = {2022}, author = {Tong, X and Yu, X and Du, Y and Su, F and Liu, Y and Li, H and Liu, Y and Mu, K and Liu, Q and Li, H and Zhu, J and Xu, H and Xiao, F and Li, Y}, title = {Peripheral Blood Microbiome Analysis via Noninvasive Prenatal Testing Reveals the Complexity of Circulating Microbial Cell-Free DNA.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0041422}, pmid = {35608350}, issn = {2165-0497}, mesh = {*Cell-Free Nucleic Acids/genetics ; *Epstein-Barr Virus Infections ; Female ; Herpesvirus 4, Human ; Humans ; *Microbiota/genetics ; *Noninvasive Prenatal Testing ; Pregnancy ; Retrospective Studies ; }, abstract = {While circulating cell-free DNA (cfDNA) is becoming a powerful marker for noninvasive identification of infectious pathogens in liquid biopsy specimens, a microbial cfDNA baseline in healthy individuals is urgently needed for the proper interpretation of microbial cfDNA sequencing results in clinical metagenomics. Because noninvasive prenatal testing (NIPT) shares many similarities with the sequencing protocol of metagenomics, we utilized the standard low-pass whole-genome-sequencing-based NIPT to establish a microbial cfDNA baseline in healthy people. Sequencing data from a total of 107,763 peripheral blood samples of healthy pregnant women undergoing NIPT screening were retrospectively collected and reanalyzed for microbiome DNA screening. It was found that more than 95% of exogenous cfDNA was from bacteria, 3% from eukaryotes, and 0.4% from viruses, indicating the gut/environment origins of many microorganisms. Overall and regional abundance patterns were well illustrated, with huge regional diversity and complexity, and unique interspecies and symbiotic relationships were observed for TORCH organisms (Toxoplasma gondii, others [Treponema pallidum {causing syphilis}, hepatitis B virus {HBV}, and human parvovirus B19 {HPV-B19} ], rubella virus, cytomegalovirus [CMV], and herpes simplex virus [HSV]) and another common virus, Epstein-Barr virus (EBV). To sum up, our study revealed the complexity of the baseline circulating microbial cfDNA and showed that microbial cfDNA sequencing results need to be interpreted in a more comprehensive manner. IMPORTANCE While circulating cell-free DNA (cfDNA) has been becoming a powerful marker for noninvasive identification of infectious pathogens in liquid biopsy specimens, a baseline for microbial cfDNA in healthy individuals is urgently needed for the proper interpretation of microbial cfDNA sequencing results in clinical metagenomics. Standard low-pass whole-genome-sequencing-based NIPT shares many similarities with the sequencing protocol for metagenomics and could provide a microbial cfDNA baseline in healthy people; thus, a reference cfDNA data set of the human microbiome was established with sequencing data from a total of 107,763 peripheral blood samples of healthy pregnant women undergoing NIPT screening. Our study revealed the complexity of circulating microbial cfDNA and indicated that microbial cfDNA sequencing results need to be interpreted in a more comprehensive manner, especially with regard to geographic patterns and coexistence networks.}, } @article {pmid35605852, year = {2022}, author = {Zhang, J and Fu, Q and Huang, Y and Fan, Y and Liang, M and Chen, H and Yu, S}, title = {Negative impacts of sea-level rise on soil microbial involvement in carbon metabolism.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 2}, pages = {156087}, doi = {10.1016/j.scitotenv.2022.156087}, pmid = {35605852}, issn = {1879-1026}, mesh = {Carbon/analysis ; Ecosystem ; *Microbiota ; Sea Level Rise ; *Soil ; Soil Microbiology ; }, abstract = {Sea-level rise has been threatening the terrestrial ecosystem functioning of coastal islands, of which the most important component is carbon (C) cycling. However, metagenomic and metabolomic evidence documenting salt intrusion effects on molecular biological processes of C cycling are still lacking. Here, we investigated microbial communities, metagenomic taxonomy and function, and metabolomic profiles in the marine-terrestrial transition zone of low- and high-tide, and low- and high-land areas based on distances of 0 m, 50 m, 100 m, and 200 m, respectively, to the water-land junction of Neilingding Island. Our results showed that soil salinity (EC) was the dominant driver controlling bacterial abundance and community composition and metagenomic taxonomy and function. The metabolomic profiling at the low-tide site was significantly different from that of other sites. The low-tide site had greater abundance of Proteobacteria and Bacteroidetes (1.6-3.7 fold), especially Gammaproteobacteria, but lower abundance (62-83%) of Acidobacteria and Chloroflexi, compared with other three sites. The metagenomic functional genes related to carbohydrate metabolism decreased at the low-tide site by 15.2%, including the metabolism of aminosugars, di- and oligo-saccharides, glycoside hydrolases, and monosaccharides, leading to significant decreases in 21 soil metabolites, such as monosaccharide (l-gulose), disaccharide (sucrose and turanose), and oligosaccharides (stachyose and maltotetraose). Our study demonstrates that elevated salinity due to sea-level rise may suppress C-cycling genes and their metabolites, therefore having negative impacts on microbial metabolism of organic matter.}, } @article {pmid35604174, year = {2022}, author = {Zhang, Z and Nie, S and Sang, Y and Mo, S and Li, J and Kashif, M and Su, G and Yan, B and Jiang, C}, title = {Effects of Spartina alterniflora Invasion on Nitrogen Fixation and Phosphorus Solubilization in a Subtropical Marine Mangrove Ecosystem.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0068221}, pmid = {35604174}, issn = {2165-0497}, mesh = {*Ecosystem ; Introduced Species ; Nitrogen Fixation ; *Phosphorus ; Poaceae/physiology ; Wetlands ; }, abstract = {Nitrogen fixation (NF) and phosphorus solubilization (PS) play a key role in maintaining the stability of mangrove ecosystems. In China, the invasion of Spartina alterniflora has brought a serious threat to the mangrove ecosystem. However, systematic research on NF and PS in mangrove sediments has not been conducted, and limited studies have focused on the response of NF and PS to S. alterniflora invasion, particularly at different sediment depths. In the present study, shotgun metagenomics and quantitative PCR were used to study the 0- to 100-cm sediment profile of the mangrove ecosystem in the Beibu Gulf of China. Results showed that the PS potential of mangrove sediments was primarily caused by enzymes encoded by phoA, phoD, ppx, ppa, and gcd genes. S. alterniflora changed environmental factors, such as total nitrogen, total phosphorus, and total organic carbon, and enhanced the potential of NF and PS in sediments. Moreover, most microorganisms involved in NF or PS (NFOPSMs) responded positively to the invasion of S. alterniflora. Cd, available iron, and salinity were the key environmental factors that affected the distribution of NF and PS genes (NFPSGs) and NFOPSMs. A strong coupling effect was observed between NF and PS in the mangrove ecosystem. S. alterniflora invasion enhanced the coupling of NF and PS and the interaction of microorganisms involved in NF and PS (NFAPSM), thereby promoting the turnover of NP and improving sediment quality. Finally, 108 metagenome-assembled genomes involved in NF or PS were reconstructed to further evaluate NFOPSMs. IMPORTANCE This study revealed the efficient nutrient cycling mechanism of mangroves. Positive coupling effects were observed in sediment quality, NF and PS processes, and NFOPSMs with the invasion of S. alterniflora. This research contributed to the understanding of the effects of S. alterniflora invasion on the subtropical mangrove ecosystem and provided theoretical guidance for mangrove protection, restoration, and soil management. Additionally, novel NFOPSMs provided a reference for the development of marine biological fertilizers.}, } @article {pmid35604118, year = {2022}, author = {Cornet, L and Cleenwerck, I and Praet, J and Leonard, RR and Vereecken, NJ and Michez, D and Smagghe, G and Baurain, D and Vandamme, P}, title = {Phylogenomic Analyses of Snodgrassella Isolates from Honeybees and Bumblebees Reveal Taxonomic and Functional Diversity.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0150021}, pmid = {35604118}, issn = {2379-5077}, mesh = {Animals ; Bees ; Phylogeny ; *Neisseriaceae/genetics ; *Microbiota ; }, abstract = {Snodgrassella is a genus of Betaproteobacteria that lives in the gut of honeybees (Apis spp.) and bumblebees (Bombus spp). It is part of a conserved microbiome that is composed of a few core phylotypes and is essential for bee health and metabolism. Phylogenomic analyses using whole-genome sequences of 75 Snodgrassella strains from 4 species of honeybees and 14 species of bumblebees showed that these strains formed a monophyletic lineage within the Neisseriaceae family, that Snodgrassella isolates from Asian honeybees diverged early from the other species in their evolution, that isolates from honeybees and bumblebees were well separated, and that this genus consists of at least seven species. We propose to formally name two new Snodgrassella species that were isolated from bumblebees: i.e., Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov. Possible evolutionary scenarios for 107 species- or group-specific genes revealed very limited evidence for horizontal gene transfer. Functional analyses revealed the importance of small proteins, defense mechanisms, amino acid transport and metabolism, inorganic ion transport and metabolism and carbohydrate transport and metabolism among these 107 specific genes. IMPORTANCE The microbiome of honeybees (Apis spp.) and bumblebees (Bombus spp.) is highly conserved and represented by few phylotypes. This simplicity in taxon composition makes the bee's microbiome an emergent model organism for the study of gut microbial communities. Since the description of the Snodgrassella genus, which was isolated from the gut of honeybees and bumblebees in 2013, a single species (i.e., Snodgrassella alvi), has been named. Here, we demonstrate that this genus is actually composed of at least seven species, two of which (Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov.) are formally described and named in the present publication. We also report the presence of 107 genes specific to Snodgrassella species, showing notably the importance of small proteins and defense mechanisms in this genus.}, } @article {pmid35601103, year = {2022}, author = {Que, T and Pang, X and Huang, H and Chen, P and Wei, Y and Hua, Y and Liao, H and Wu, J and Li, S and Wu, A and He, M and Ruan, X and Hu, Y}, title = {Comparative Gut Microbiome in Trachypithecus leucocephalus and Other Primates in Guangxi, China, Based on Metagenome Sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {872841}, pmid = {35601103}, issn = {2235-2988}, mesh = {Animals ; Calcium Carbonate ; China ; *Colobinae ; *Gastrointestinal Microbiome/genetics ; Metagenome ; }, abstract = {The Trachypithecus leucocephalus (white-headed langur) is a highly endangered, karst-endemic primate species, inhabiting the karst limestone forest in Guangxi, Southwest China. How white-headed langurs adapted to karst limestone and special dietary remains unclear. It is the first time to study the correlation between the gut microbiome of primates and special dietary, and environment in Guangxi. In the study, 150 fecal samples are collected from nine primates in Guangxi, China. Metagenomic sequencing is used to analyze and compare the gut microbiome composition and diversity between white-headed langurs and other primates. Our results indicate that white-headed langurs has a higher diversity of microbiome than other primates, and the key microbiome are phylum Firmicutes, class Clostridia, family Lachnospiraceae, and genera Clostridiates and Ruminococcus, which are related to the digestion and degradation of cellulose. Ten genera are significantly more abundant in white-headed langurs and François' langur than in other primates, most of which are high-temperature microbiome. Functional analysis reveals that energy synthesis-related pathways and sugar metabolism-related pathways are less abundant in white-headed langurs and François' langur than in other primates. This phenomenon could be an adaptation mechanism of leaf-eating primates to low-energy diet. The gut microbiome of white-headed langurs is related to diet and karst limestone environment. This study could serve as a reference to design conservation breeding, manage conservation units, and determine conservation priorities.}, } @article {pmid35598686, year = {2022}, author = {Delik, A and Dinçer, S and Ülger, Y and Akkız, H and Karaoğullarından, Ü}, title = {Metagenomic identification of gut microbiota distribution on the colonic mucosal biopsy samples in patients with non-alcoholic fatty liver disease.}, journal = {Gene}, volume = {833}, number = {}, pages = {146587}, doi = {10.1016/j.gene.2022.146587}, pmid = {35598686}, issn = {1879-0038}, mesh = {Biopsy ; *Gastrointestinal Microbiome/genetics ; Humans ; *Liver Neoplasms/complications ; *Non-alcoholic Fatty Liver Disease/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) is known to be the most common liver disease in the world, and there are currently no approved pharmacological treatments to prevent or treat this condition. In addition to being associated with an increased risk of hepatocellular carcinoma and cirrhosis, NAFLD has now become the leading cause of liver failure-associated transplantation. The 16S rRNA gene which conserved regions can serve as universal primer binding sites for PCR amplification of gene fragments, while hypervariable regions contain significant sequence diversity useful for prokaryotic identification purposes. 16S rRNA gene sequences can be use by researchers to identify prokaryotic taxonomy found in clinical samples. As a result of increasing microbiota studies with developing technological developments, the role of intestinal microbiota in the pathogenesis of NAFLD is revealed in an important way. In this study, it was aimed to determine the clinical prognostic importance of gut microbiota in the pathogenesis of NAFLD and to determine the microbial composition with intestinal mucosal biopsy samples in NAFLD patients.

MATERIAL AND METHOD: We included 20 patients diagnosed with NAFLD as a result of liver function tests, histological, ultrasonographic, biopsy evidence and 20 normal control groups created under exclusion criteria in this study. The healthy control group of the same age and gender as the patients were determined to be equal, and the age, gender, BMI, insulin resistance, AST, ALT levels of the individuals were recorded for analysis. İntestinal mucosal biopsy samples were taken from the individuals included in the study under sterile conditions. Microbial results were obtained as a result of 16S rRNA amplicon metagenomic processes. The region of approximately 1500 bp covering the V1-V9 region of the 16S rRNA gene was targeted to detect microbial diversity. The amplified regions were sequenced using next-generation sequencing. Operational Taxonomic Unit (OTU) value was obtained with bioinformatics software with the obtained sequence data. The analysis of the recorded parameters was done with the SPSS.19 statistical program.

RESULTS: In the designed study, 16 phyla, 28 class, 56 order, 128 family, 415 genera, 1041 species microorganisms were analyzed taxonomically in a total of 40 individuals. In our study, Intestinal microbial diversity is lower in NAFLD patients compared to control group individuals. In addition, gram-negative bacteria were found to be more dominant in NAFLD patients. As a phylum, Proteobacteria increased in NAFLD group, Bacteroidetes and Actinobacteria in control group, while Firmicutes had equal distribution in both groups. BMI OR = 6.37, 95 %CI (0.39-0.40) p value was 0.001 in laboratory data, whereas Proteobacteria OR = 1.754, 95% CI (0.901-3.416), p value 0.05 in microbial profile.

CONCLUSION: The 16S rRNA metagenomic study of intestinal microbiota using colonic mucosal biopsy samples in NAFLD disease was the first study in the Turkish population, and important data were obtained for other studies. In the data obtained, we think Proteobacteria, Ruminococcaceae, Escherichia coli and Bacilli are very important in both diagnostic and treatment options as a microbial profile in NAFLD.}, } @article {pmid35597403, year = {2022}, author = {Kim, DW and Jeong, HS and Kim, E and Lee, H and Choi, CH and Lee, SJ}, title = {Oral delivery of stem-cell-loaded hydrogel microcapsules restores gut inflammation and microbiota.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {347}, number = {}, pages = {508-520}, doi = {10.1016/j.jconrel.2022.05.028}, pmid = {35597403}, issn = {1873-4995}, mesh = {Animals ; Capsules ; Hydrogels/pharmacology ; Inflammation ; *Inflammatory Bowel Diseases/drug therapy ; *Mesenchymal Stem Cells ; Mice ; *Microbiota ; }, abstract = {Mesenchymal stem cells (MSCs) are an attractive candidate for the treatment of inflammatory bowel disease (IBD), but their poor delivery rate to an inflamed colon is a major factor hampering the clinical potential of stem cell therapies. Moreover, there remains a formidable hurdle to overcome with regard to survival and homing in to injured sites. Here, we develop a strategy utilizing monodisperse hydrogel microcapsules with a thin intermediate oil layer prepared by a triple-emulsion drop-based microfluidic approach as an in-situ oral delivering carrier. The oral delivery of stem-cell-loaded hydrogel microcapsules (SC-HM) enhances MSC survival and retention in the hostile stomach environment due to the intermediate oil layer and low value of the overall stiffness, facilitating programmable cell release during gastrointestinal peristalsis. SC-HM is shown to induce tissue repair, reduce the colonic macrophage infiltration responsible for the secretion of the pro-inflammatory factors, and significantly mitigate the severity of IBD in a mouse model, where MSCs released by SC-HM successfully accumulate at the colonic crypt. Moreover, a metagenomics analysis reveals that SC-HM ameliorates the dysbiosis of specific bacterial genera, including Bacteroides acidifaciens, Lactobacillus (L.) gasseri, Lactobacillus reuteri, and L. intestinalis, implying optimization of the microorganism's composition and abundance. These findings demonstrate that SC-HM is a potential IBD treatment candidate.}, } @article {pmid35596862, year = {2022}, author = {Parida, PK and Behera, BK and Dehury, B and Rout, AK and Sarkar, DJ and Rai, A and Das, BK and Mohapatra, T}, title = {Community structure and function of microbiomes in polluted stretches of river Yamuna in New Delhi, India, using shotgun metagenomics.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {47}, pages = {71311-71325}, pmid = {35596862}, issn = {1614-7499}, mesh = {ATP-Binding Cassette Transporters ; *Atrazine ; Benzene ; Benzoates ; Carbon ; Catalase ; Environmental Biomarkers ; Environmental Monitoring/methods ; Fatty Acids ; Metagenomics/methods ; Methane ; *Microbiota ; Mixed Function Oxygenases ; Nitrogen ; Sulfates ; Sulfur ; Water ; Xenobiotics ; }, abstract = {The large population residing in the northern region of India surrounding Delhi mostly depends on water of River Yamuna, a tributary of mighty Ganga for agriculture, drinking and various religious activities. However, continuous anthropogenic activities mostly due to pollution mediated by rapid urbanization and industrialization have profoundly affected river microflora and their function thus its health. In this study, potential of whole-genome metagenomics was exploited to unravel the novel consortia of microbiome and their functional potential in the polluted sediments of the river at Delhi. Analysis of high-quality metagenome data from Illumina NextSeq500 revealed substantial differences in composition of microbiota at different sites dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Chloroflexi phyla. The presence of highly dominant anaerobic bacteria like Dechloromonas aromatica (benzene reducing and denitrifying), Rhodopseudomonas palustris (organic matter reducing), Syntrophus aciditrophicus (fatty acid reducing) and Syntrophobacter fumaroxidans (sulphate reducing) in the polluted river Yamuna signifies the impact of unchecked pollution in declining health of the river ecosystem. A decline in abundance of phages was also noticed along the downstream river Yamuna. Mining of mycobiome reads uncovered plethora of fungal communities (i.e. Nakaseomyces, Aspergillus, Schizosaccharomyces and Lodderomyces) in the polluted stretches due to the availability of higher organic carbon and total nitrogen (%) could be decoded as promising bioindicators of river trophic status. Pathway analysis through KEGG revealed higher abundance of genes involved in energy metabolism (nitrogen and sulphur), methane metabolism, degradation of xenobiotics (Nitrotoluene, Benzoate and Atrazine), two-component system (atoB, cusA and silA) and membrane transport (ABC transporters). Catalase-peroxidase and 4-hydroxybenzoate 3-monooxygenase were the most enriched pollution degrading enzymes in the polluted study sites of river Yamuna. Overall, our results provide crucial insights into microbial dynamics and their function in response to high pollution and could be insightful to the ongoing remediation strategies to clean river Yamuna.}, } @article {pmid35595870, year = {2022}, author = {Shi, H and Nelson, JW and Phillips, S and Petrosino, JF and Bryan, RM and Durgan, DJ}, title = {Alterations of the gut microbial community structure and function with aging in the spontaneously hypertensive stroke prone rat.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {8534}, pmid = {35595870}, issn = {2045-2322}, support = {R01HL134838/HL/NHLBI NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01NS102594/NS/NINDS NIH HHS/United States ; DK56338/NH/NIH HHS/United States ; R01 HL134838/HL/NHLBI NIH HHS/United States ; R01 NS102594/NS/NINDS NIH HHS/United States ; 16SDG29970000/AHA/American Heart Association-American Stroke Association/United States ; T32 GM008231/GM/NIGMS NIH HHS/United States ; T32 GM008231/NH/NIH HHS/United States ; }, mesh = {Aging ; Animals ; Blood Pressure/physiology ; Dysbiosis ; *Gastrointestinal Microbiome ; *Hypertension ; Rats ; Rats, Inbred SHR ; Rats, Inbred WKY ; *Stroke ; Tryptophan ; }, abstract = {Gut dysbiosis, a pathological imbalance of bacteria, has been shown to contribute to the development of hypertension (HT), systemic- and neuro-inflammation, and blood-brain barrier (BBB) disruption in spontaneously hypertensive stroke prone rats (SHRSP). However, to date individual species that contribute to HT in the SHRSP model have not been identified. One potential reason, is that nearly all studies of the SHRSP gut microbiota have analyzed samples from rats with established HT. The goal of this study was to examine the SHRSP gut microbiota before, during, and after the onset of hypertension, and in normotensive WKY control rats over the same age range. We hypothesized that we could identify key microbes involved in the development of HT by comparing WKY and SHRSP microbiota during the pre-hypertensive state and longitudinally. Systolic blood pressure (SBP) was measured by tail-cuff plethysmography and fecal microbiota analyzed by16S rRNA gene sequencing. SHRSP showed significant elevations in SBP, as compared to WKY, beginning at 8 weeks of age (p < 0.05 at each time point). Bacterial community structure was significantly different between WKY and SHRSP as early as 4 weeks of age, and remained different throughout the study (p = 0.001-0.01). At the phylum level we observed significantly reduced Firmicutes and Deferribacterota, and elevated Bacteroidota, Verrucomicrobiota, and Proteobacteria, in pre-hypertensive SHRSP, as compared to WKY. At the genus level we identified 18 bacteria whose relative abundance was significantly different in SHRSP versus WKY at the pre-hypertensive ages of 4 or 6 weeks. In an attempt to further refine bacterial candidates that might contribute to the SHRSP phenotype, we compared the functional capacity of WKY versus SHRSP microbial communities. We identified significant differences in amino acid metabolism. Using untargeted metabolomics we found significant reductions in metabolites of the tryptophan-kynurenine pathway and increased indole metabolites in SHRSP versus WKY plasma. Overall, we provide further evidence that gut dysbiosis contributes to hypertension in the SHRSP model, and suggest for the first time the potential involvement of tryptophan metabolizing microbes.}, } @article {pmid35595857, year = {2022}, author = {Gao, S and Khan, MI and Kalsoom, F and Liu, Z and Chen, Y and Chen, Z}, title = {Role of gene regulation and inter species interaction as a key factor in gut microbiota adaptation.}, journal = {Archives of microbiology}, volume = {204}, number = {6}, pages = {342}, pmid = {35595857}, issn = {1432-072X}, mesh = {Acclimatization ; Adaptation, Physiological/genetics ; Animals ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics ; }, abstract = {Gut microbiota is a class of microbial flora present in various eukaryotic multicellular complex animals such as human beings. Their community's growth and survival are greatly influenced by various factors such as host-pathogen, pathogen-environment and genetic regulation. Modern technologies like metagenomics have particularly extended our capacity to uncover the microbial treasures in challenging conditions like communities surviving at high altitude. Molecular characterizations by newly developed sequencing tools have shown that this complex interaction greatly influences microbial adaptation to the environment. Literature shows that gut microbiota alters the genetic expression and switches to an alternative pathway under the influence of unfavorable conditions. The remarkable adaptability of microbial genetic regulatory networks enables them to survive and expand in tough and energy-limited conditions. Variable prevalence of species in various regions has strengthened this initial evidence. In view of the interconnection of the world in the form of a global village, this phenomenon must be explored more clearly. In this regard, recently there has been significant addition of knowledge to the field of microbial adaptation. This review summarizes and shed some light on mechanisms of microbial adaptation via gene regulation and species interaction in gut microbiota.}, } @article {pmid35595739, year = {2022}, author = {Price, JT and Vwalika, B and France, M and Ravel, J and Ma, B and Mwape, H and Rittenhouse, KJ and De Paris, K and Hobbs, M and Nelson, JA and Kasaro, MP and Stringer, EM and Stringer, JSA}, title = {HIV-associated vaginal microbiome and inflammation predict spontaneous preterm birth in Zambia.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {8573}, pmid = {35595739}, issn = {2045-2322}, support = {K01 TW010857/TW/FIC NIH HHS/United States ; P30 AI50410; T32 HD075731; K01 TW010857; D43 TW009340; R21DK123674; R01HL148672/NH/NIH HHS/United States ; OPP1033514/GATES/Bill & Melinda Gates Foundation/United States ; 6361/Gerber/The Gerber Foundation/United States ; OPP1189217/GATES/Bill & Melinda Gates Foundation/United States ; }, mesh = {Bacteria, Anaerobic ; Female ; Gardnerella ; *HIV Infections/complications ; Humans ; Infant, Newborn ; Inflammation/complications ; *Microbiota/genetics ; Pregnancy ; *Premature Birth ; Vagina ; Zambia/epidemiology ; }, abstract = {A Lactobacillus-deficient, anaerobe-rich vaginal microbiome has been associated with local inflammation and spontaneous preterm birth (sPTB), but few studies have assessed this association in the setting of HIV. We performed metagenomic sequencing and inflammatory marker assays on vaginal swabs collected in pregnancy. We grouped samples into 7 metagenomic clusters (mgClust) using the non-redundant VIRGO catalogue, and derived inflammatory scores by factor analysis. Of 221 participants, median Shannon diversity index (SDI) was highest in HIV+ with detectable viral load (1.31, IQR: 0.85-1.66; p < 0.001) and HIV+ with undetectable virus (1.17, IQR: 0.51-1.66; p = 0.01) compared to HIV- (0.74, IQR: 0.35-1.26). Inflammatory scores positively correlated with SDI (+ 0.66, 95%CI 0.28, 1.03; p = 0.001), highest among anaerobe-rich mgClust2-mgClust6. HIV was associated with predominance of anaerobe-rich mgClust5 (17% vs. 6%; p = 0.02) and mgClust6 (27% vs. 11%; p = 0.002). Relative abundance of a novel Gardnerella metagenomic subspecies > 50% predicted sPTB (RR 2.6; 95%CI: 1.1, 6.4) and was higher in HIV+ (23% vs. 10%; p = 0.001). A novel Gardnerella metagenomic subspecies more abundant in women with HIV predicted sPTB. The risk of sPTB among women with HIV may be mediated by the vaginal microbiome and inflammation, suggesting potential targets for prevention.}, } @article {pmid35594632, year = {2022}, author = {Liu, Q and Zhang, X and Li, Z and Chen, Y and Yin, Y and Lu, Z and Ouyang, M and Chen, L}, title = {Maternal diets have effects on intestinal mucosal flora and susceptibility to colitis of offspring mice during early life.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {99-100}, number = {}, pages = {111672}, doi = {10.1016/j.nut.2022.111672}, pmid = {35594632}, issn = {1873-1244}, mesh = {Animals ; Female ; Humans ; Mice ; Rats ; *Colitis/etiology ; Diet/adverse effects ; Diet, High-Fat ; *Gastrointestinal Microbiome/physiology ; *Inflammatory Bowel Diseases/etiology ; Maternal Nutritional Physiological Phenomena ; Mice, Inbred C57BL ; }, abstract = {OBJECTIVES: Intestinal flora is considered closely related to the occurrence of inflammatory bowel disease (IBD). This study aimed to discover whether diverse diet conditions during early life lead to different intestinal flora structure and impact different susceptibility to IBD.

METHODS: We performed a randomized, controlled trial to investigate the relationship between maternal diet, intestinal flora, and susceptibility of IBD in offspring mice. We treated the maternal mice with different dietary conditions (maternal high fat, high protein, or normal diet, and offspring continued maternal diets or changed to normal diet), and then extracted bacterial meta-genomic DNA from the intestinal mucosa of the offspring during the early life and adult stages. We amplified and sequenced the conserved gene v3-v4 of the bacterial 16 S ribosomal RNA. After dextran sulphate sodium intervention, we evaluated the susceptibility to intestinal inflammation with hematoxylin and eosin stains and disease activity index scores.

RESULTS: The number of species and alpha diversity of weaning mice (3 wk old) fed a maternal high-protein diet were significantly lower than those of the control diet group (P < 0.05). Among adult (8 wk old) offspring rats, the alpha diversity of mice that continued on a high-protein diet remained significantly decreased (P < 0.05). In addition, 12 kinds of weak bacteria were found in weaning mice fed a maternal high-protein diet compared with the control group. Offspring that continued in the maternal high-protein group had increased disease activity index and pathologic scores after weaning.

CONCLUSIONS: In general, our study shows that a maternal high-protein diet during early life can negatively regulate the intestinal flora diversity of offspring mice. A high-protein diet during early life led to higher susceptibility of IBD in offspring rats.}, } @article {pmid35593171, year = {2022}, author = {Galanis, A and Vardakas, P and Reczko, M and Harokopos, V and Hatzis, P and Skoulakis, EMC and Pavlopoulos, GA and Patalano, S}, title = {Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey.}, journal = {Molecular ecology resources}, volume = {22}, number = {7}, pages = {2506-2523}, doi = {10.1111/1755-0998.13626}, pmid = {35593171}, issn = {1755-0998}, support = {798082//H2020 Marie Skłodowska-Curie Actions/ ; MIS 5002562//European Regional Development Fund/ ; //Hellenic Ministry of Rural Development and Food/ ; //Fondation Santé/ ; }, mesh = {Animals ; Bacteria/genetics ; Bees/genetics ; DNA ; *Gastrointestinal Microbiome ; *Honey ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {Honeybees (Apis mellifera) continue to succumb to human and environmental pressures despite their crucial role in providing essential ecosystem services. Owing to their foraging and honey production activities, honeybees form complex relationships with species across all domains, such as plants, viruses, bacteria and other hive pests, making honey a valuable biomonitoring tool for assessing their ecological niche. Thus, the application of honey shotgun metagenomics (SM) has paved the way for a detailed description of the species honeybees interact with. Nevertheless, SM bioinformatics tools and DNA extraction methods rely on resources not necessarily optimized for honey. In this study, we compared five widely used taxonomic classifiers using simulated species communities commonly found in honey. We found that Kraken 2 with a threshold of 0.5 performs best in assessing species distribution. We also optimized a simple NaOH-based honey DNA extraction methodology (Direct-SM), which profiled species seasonal variability similarly to an established column-based DNA extraction approach (SM). Both approaches produce results consistent with melissopalinology analysis describing the botanical landscape surrounding the apiary. Interestingly, we detected a strong stability of the bacteria constituting the core and noncore gut microbiome across seasons, pointing to the potential utility of honey for noninvasive assessment of bee microbiota. Finally, the Direct-SM approach to detect Varroa correlates well with the biomonitoring of mite infestation observed in hives. These observations suggest that Direct-SM methodology has the potential to comprehensively describe honeybee ecological niches and can be tested as a building block for large-scale studies to assess bee health in the field.}, } @article {pmid35589762, year = {2022}, author = {Szóstak, N and Szymanek, A and Havránek, J and Tomela, K and Rakoczy, M and Samelak-Czajka, A and Schmidt, M and Figlerowicz, M and Majta, J and Milanowska-Zabel, K and Handschuh, L and Philips, A}, title = {The standardisation of the approach to metagenomic human gut analysis: from sample collection to microbiome profiling.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {8470}, pmid = {35589762}, issn = {2045-2322}, mesh = {DNA ; Humans ; Metagenome ; *Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; }, abstract = {In recent years, the number of metagenomic studies increased significantly. Wide range of factors, including the tremendous community complexity and variability, is contributing to the challenge in reliable microbiome community profiling. Many approaches have been proposed to overcome these problems making hardly possible to compare results of different studies. The significant differences between procedures used in metagenomic research are reflected in a variation of the obtained results. This calls for the need for standardisation of the procedure, to reduce the confounding factors originating from DNA isolation, sequencing and bioinformatics analyses in order to ensure that the differences in microbiome composition are of a true biological origin. Although the best practices for metagenomics studies have been the topic of several publications and the main aim of the International Human Microbiome Standard (IHMS) project, standardisation of the procedure for generating and analysing metagenomic data is still far from being achieved. To highlight the difficulties in the standardisation of metagenomics methods, we thoroughly examined each step of the analysis of the human gut microbiome. We tested the DNA isolation procedure, preparation of NGS libraries for next-generation sequencing, and bioinformatics analysis, aimed at identifying microbial taxa. We showed that the homogenisation time is the leading factor impacting sample diversity, with the recommendation for a shorter homogenisation time (10 min). Ten minutes of homogenisation allows for better reflection of the bacteria gram-positive/gram-negative ratio, and the obtained results are the least heterogenous in terms of beta-diversity of samples microbial composition. Besides increasing the homogenisation time, we observed further potential impact of the library preparation kit on the gut microbiome profiling. Moreover, our analysis revealed that the choice of the library preparation kit influences the reproducibility of the results, which is an important factor that has to be taken into account in every experiment. In this study, a tagmentation-based kit allowed for obtaining the most reproducible results. We also considered the choice of the computational tool for determining the composition of intestinal microbiota, with Kraken2/Bracken pipeline outperforming MetaPhlAn2 in our in silico experiments. The design of an experiment and a detailed establishment of an experimental protocol may have a serious impact on determining the taxonomic profile of the intestinal microbiome community. Results of our experiment can be helpful for a wide range of studies that aim to better understand the role of the gut microbiome, as well as for clinical purposes.}, } @article {pmid35588986, year = {2022}, author = {Murali, A and Giri, V and Cameron, HJ and Sperber, S and Zickgraf, FM and Haake, V and Driemert, P and Walk, T and Kamp, H and Rietjens, IM and van Ravenzwaay, B}, title = {Investigating the gut microbiome and metabolome following treatment with artificial sweeteners acesulfame potassium and saccharin in young adult Wistar rats.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {165}, number = {}, pages = {113123}, doi = {10.1016/j.fct.2022.113123}, pmid = {35588986}, issn = {1873-6351}, mesh = {Animals ; Bile Acids and Salts ; Body Weight ; Feces/chemistry ; Female ; *Gastrointestinal Microbiome ; Male ; Metabolome ; Metabolomics ; Rats ; Rats, Wistar ; Saccharin ; Sweetening Agents/analysis ; Thiazines ; }, abstract = {To elucidate if artificial sweeteners modify fecal bacterial composition and the fecal and plasma metabolomes, Wistar rats from both sexes were treated for 28 days with acesulfame potassium (40 and 120 mg/kg body weight) and saccharin (20 and 100 mg/kg body weight). Targeted MS-based metabolome profiling (plasma and feces) and fecal 16S gene sequencing were conducted. Both sweeteners exhibited only minor effects on the fecal metabolome and microbiota. Saccharin treatment significantly altered amino acids, lipids, energy metabolism and specifically, bile acids in the plasma metabolome. Additionally, sex-specific differences were observed for conjugated primary and secondary bile acids. Acesulfame potassium treated male rats showed larger alterations in glycine conjugated primary and secondary bile-acids than females. Other changes in the plasma metabolome were more profound for saccharin than acesulfame potassium, for both sexes. Changes in conjugated bile-acids in plasma, which are often associated with microbiome changes, and the absence of similarly large changes in microbiota suggest an adaptative change of the latter, rather than toxicity. Further studies with a high resolution 16S sequencing data and/or metagenomics approach, with particular emphasis on bile acids, will be required to explore the mechanisms driving this metabolic outcome of saccharin in Wistar rats.}, } @article {pmid35587930, year = {2022}, author = {Benyedem, H and Lekired, A and Mhadhbi, M and Dhibi, M and Romdhane, R and Chaari, S and Rekik, M and Ouzari, HI and Hajji, T and Darghouth, MA}, title = {First insights into the microbiome of Tunisian Hyalomma ticks gained through next-generation sequencing with a special focus on H. scupense.}, journal = {PloS one}, volume = {17}, number = {5}, pages = {e0268172}, pmid = {35587930}, issn = {1932-6203}, mesh = {Animals ; Cattle ; *Francisella/genetics ; High-Throughput Nucleotide Sequencing ; *Ixodidae/genetics/microbiology ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Rickettsia/genetics ; *Ticks/genetics ; }, abstract = {Ticks are one of the most important vectors of several pathogens affecting humans and animals. In addition to pathogens, ticks carry diverse microbiota of symbiotic and commensal microorganisms. In this study, we have investigated the first Tunisian insight into the microbial composition of the most dominant Hyalomma species infesting Tunisian cattle and explored the relative contribution of tick sex, life stage, and species to the diversity, richness and bacterial species of tick microbiome. In this regard, next generation sequencing for the 16S rRNA (V3-V4 region) of tick bacterial microbiota and metagenomic analysis were established. The analysis of the bacterial diversity reveals that H. marginatum and H. excavatum have greater diversity than H. scupense. Furthermore, microbial diversity and composition vary according to the tick's life stage and sex in the specific case of H. scupense. The endosymbionts Francisella, Midichloria mitochondrii, and Rickettsia were shown to be the most prevalent in Hyalomma spp. Rickettsia, Francisella, Ehrlichia, and Erwinia are the most common zoonotic bacteria found in Hyalomma ticks. Accordingly, Hyalomma ticks could represent potential vectors for these zoonotic bacterial agents.}, } @article {pmid35587374, year = {2022}, author = {Kohl, KD and Dieppa-Colón, E and Goyco-Blas, J and Peralta-Martínez, K and Scafidi, L and Shah, S and Zawacki, E and Barts, N and Ahn, Y and Hedayati, S and Secor, SM and Rowe, MP}, title = {Gut Microbial Ecology of Five Species of Sympatric Desert Rodents in Relation to Herbivorous and Insectivorous Feeding Strategies.}, journal = {Integrative and comparative biology}, volume = {62}, number = {2}, pages = {237-251}, doi = {10.1093/icb/icac045}, pmid = {35587374}, issn = {1557-7023}, support = {IOS-1942587//National Science Foundation/ ; }, mesh = {Animals ; Chitin ; Dipodomys ; *Gastrointestinal Microbiome ; Herbivory ; *Microbiota ; Peromyscus ; Rodentia ; }, abstract = {The gut microbial communities of mammals provide numerous benefits to their hosts. However, given the recent development of the microbiome field, we still lack a thorough understanding of the variety of ecological and evolutionary factors that structure these communities across species. Metabarcoding is a powerful technique that allows for multiple microbial ecology questions to be investigated simultaneously. Here, we employed DNA metabarcoding techniques, predictive metagenomics, and culture-dependent techniques to inventory the gut microbial communities of several species of rodent collected from the same environment that employ different natural feeding strategies [granivorous pocket mice (Chaetodipus penicillatus); granivorous kangaroo rats (Dipodomys merriami); herbivorous woodrats (Neotoma albigula); omnivorous cactus mice (Peromyscus eremicus); and insectivorous grasshopper mice (Onychomys torridus)]. Of particular interest were shifts in gut microbial communities in rodent species with herbivorous and insectivorous diets, given the high amounts of indigestible fibers and chitinous exoskeleton in these diets, respectively. We found that herbivorous woodrats harbored the greatest microbial diversity. Granivorous pocket mice and kangaroo rats had the highest abundances of the genus Ruminococcus and highest predicted abundances of genes related to the digestion of fiber, representing potential adaptations in these species to the fiber content of seeds and the limitations to digestion given their small body size. Insectivorous grasshopper mice exhibited the greatest inter-individual variation in the membership of their microbiomes, and also exhibited the highest predicted abundances of chitin-degrading genes. Culture-based approaches identified 178 microbial isolates (primarily Bacillus and Enterococcus), with some capable of degrading cellulose and chitin. We observed several instances of strain-level diversity in these metabolic capabilities across isolates, somewhat highlighting the limitations and hidden diversity underlying DNA metabarcoding techniques. However, these methods offer power in allowing the investigation of several questions concurrently, thus enhancing our understanding of gut microbial ecology.}, } @article {pmid35585555, year = {2022}, author = {Deng, K and Shuai, M and Zhang, Z and Jiang, Z and Fu, Y and Shen, L and Zheng, JS and Chen, YM}, title = {Temporal relationship among adiposity, gut microbiota, and insulin resistance in a longitudinal human cohort.}, journal = {BMC medicine}, volume = {20}, number = {1}, pages = {171}, pmid = {35585555}, issn = {1741-7015}, mesh = {Adiposity ; Cohort Studies ; *Gastrointestinal Microbiome ; Humans ; *Insulin Resistance ; Obesity/epidemiology ; }, abstract = {BACKGROUND: The temporal relationship between adiposity and gut microbiota was unexplored. Whether some gut microbes lie in the pathways from adiposity to insulin resistance is less clear. Our study aims to reveal the temporal relationship between adiposity and gut microbiota and investigate whether gut microbiota may mediate the association of adiposity with insulin resistance in a longitudinal human cohort study.

METHODS: We obtained repeated-measured gut shotgun metagenomic and anthropometric data from 426 Chinese participants over ~3 years of follow-up. Cross-lagged path analysis was used to examine the temporal relationship between BMI and gut microbial features. The associations between the gut microbes and insulin resistance-related phenotypes were examined using a linear mixed-effect model. We examined the mediation effect of gut microbes on the association between adiposity and insulin resistance-related phenotypes. Replication was performed in the HMP cohort.

RESULTS: Baseline BMI was prospectively associated with levels of ten gut microbial species. Among them, results of four species (Adlercreutzia equolifaciens, Parabacteroides unclassified, Lachnospiraceae bacterium 3 1 57FAA CT1, Lachnospiraceae bacterium 7 1 58FAA) were replicated in the independent HMP cohort. Lachnospiraceae bacterium 3 1 57FAA CT1 was inversely associated with HOMA-IR and fasting insulin. Lachnospiraceae bacterium 3 1 57FAA CT1 mediated the association of overweight/obesity with HOMA-IR (FDR<0.05). Furthermore, Lachnospiraceae bacterium 3 1 57FAA CT1 was positively associated with the butyrate-producing pathway PWY-5022 (p < 0.001).

CONCLUSIONS: Our study identified one potentially beneficial microbe Lachnospiraceae bacterium 3 1 57FAA CT1, which might mediate the effect of adiposity on insulin resistance. The identified microbes are helpful for the discovery of novel therapeutic targets, as to mitigate the impact of adiposity on insulin resistance.}, } @article {pmid35585088, year = {2022}, author = {Yan, J and Liao, C and Taylor, BP and Fontana, E and Amoretti, LA and Wright, RJ and Littmann, ER and Dai, A and Waters, N and Peled, JU and Taur, Y and Perales, MA and Siranosian, BA and Bhatt, AS and van den Brink, MRM and Pamer, EG and Schluter, J and Xavier, JB}, title = {A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {219}, pmid = {35585088}, issn = {2052-4463}, support = {U01 AI124275/AI/NIAID NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; R56 AI137269/AI/NIAID NIH HHS/United States ; K08 HL143189/HL/NHLBI NIH HHS/United States ; R01 AI137269/AI/NIAID NIH HHS/United States ; }, mesh = {*Feces/microbiology ; *Hematopoietic Stem Cell Transplantation ; Humans ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Hospitalized patients receiving hematopoietic cell transplants provide a unique opportunity to study the human gut microbiome. We previously compiled a large-scale longitudinal dataset of fecal microbiota and associated metadata, but we had limited that analysis to taxonomic composition of bacteria from 16S rRNA gene sequencing. Here we augment those data with shotgun metagenomics. The compilation amounts to a nested subset of 395 samples compiled from different studies at Memorial Sloan Kettering. Shotgun metagenomics describes the microbiome at the functional level, particularly in antimicrobial resistances and virulence factors. We provide accession numbers that link each sample to the paired-end sequencing files deposited in a public repository, which can be directly accessed by the online services of PATRIC to be analyzed without the users having to download or transfer the files. Then, we show how shotgun sequencing enables the assembly of genomes from metagenomic data. The new data, combined with the metadata published previously, enables new functional studies of the microbiomes of patients with cancer receiving bone marrow transplantation.}, } @article {pmid35584918, year = {2022}, author = {He, T and Zhu, C and Li, Z and Ai, L and Hu, D and Wang, C and Li, F and Yang, X and Lv, H and Chen, W and Qian, H and Tan, W and Wang, C}, title = {Virome analysis of ticks in Zhoushan Archipelago, China.}, journal = {The Journal of veterinary medical science}, volume = {84}, number = {6}, pages = {847-854}, pmid = {35584918}, issn = {1347-7439}, mesh = {Animals ; China/epidemiology ; *Phlebovirus ; Phylogeny ; *Tick-Borne Diseases/veterinary ; *Ticks ; Virome/genetics ; *Viruses/genetics ; }, abstract = {Ticks are an important group of arthropod vectors. Ticks pose a profound risk to public health by transmitting many types of microorganisms that are human and animal pathogens. With the development of next-generation sequencing (NGS) technology and viral metagenomics, numerous novel viruses have been discovered in ticks and tick-related hosts. To fully understand the virus spectrum in ticks in the Zhoushan Archipelago of Zhejiang province in China, ticks were collected from Qushan Island, Zhoushan Island, and Daishan Island in the Zhoushan Archipelago in June 2016. NGS performed to investigate the diversity of tick-associated viruses identified 21 viral sequences. Twelve were pathogenic to humans and animals. Trough verification by polymerase chain reaction (PCR) revealed the existence of three tick-associated viruses with extensive homology with Dabieshan, MG22, and Odaw virus. Other NGS-detected sequences that could not be amplified by PCR were highly homologous (92-100%) with known pathogenic viruses that included hepatitis B virus, papillomavirus, and human mastadenovirus C. This is the first study to systematically apply high throughput sequencing technology to explore the spectrum of viruses carried by ticks in the Zhoushan Archipelago. The findings are fundamental knowledge of the diversity of tick-associated viruses in this region and will inform strategies to monitor and prevent the spread of tick-borne diseases.}, } @article {pmid35584752, year = {2022}, author = {Singh, R and Pal, DB and Alkhanani, MF and Almalki, AH and Areeshi, MY and Haque, S and Srivastava, N}, title = {Prospects of soil microbiome application for lignocellulosic biomass degradation: An overview.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 1}, pages = {155966}, doi = {10.1016/j.scitotenv.2022.155966}, pmid = {35584752}, issn = {1879-1026}, mesh = {*Biofuels ; Biomass ; Lignin/metabolism ; *Microbiota ; Soil ; }, abstract = {Sustainable and practically viable biofuels production technology using lignocellulosic biomass is still seeking its way of implementation owing to some major issues involved therein. Unavailability of efficient microbial sources for the degradation of cellulosic biomass is one of the major roadblocks in biomass to biofuels production technology. In this context, utilization of microbiomes to degrade lignocellulaosic biomass is emerging as a rapid and effective approach that can fulfill the requirements of biomass based biofuels production technology. Therefore, the present review is targeted to explore soil metagenomic approach to improve the lignocellulosic biomass degradation processing for the cost-effective and eco-friendly application. Soil microbiomes consist of rich microbial community along with high probability of cellulolytic microbes, and can be identified by culture independent metagenomics method which can be structurally and functionally explored via genomic library. Therefore, in depth analysis and discussion have also been made via structural & functional metagenomics tools along with their contribution to genomic library. Additionally, the present review highlights currently existing bottlenecks along with their feasible solutions. This review will help to understand the basic research as well as industrial concept for the process improvement based on soil microbiome mediated lignocellulosic biomass degradation, and this may likely to implement for the low-cost commercial biofuels production technology.}, } @article {pmid35584271, year = {2022}, author = {Han, W and Tang, H and Ye, Y}, title = {Locality-Sensitive Hashing-Based k-Mer Clustering for Identification of Differential Microbial Markers Related to Host Phenotype.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {29}, number = {7}, pages = {738-751}, pmid = {35584271}, issn = {1557-8666}, support = {R01 AI108888/AI/NIAID NIH HHS/United States ; R01 AI143254/AI/NIAID NIH HHS/United States ; }, mesh = {Cluster Analysis ; Metagenome ; *Metagenomics/methods ; *Microbiota/genetics ; Phenotype ; }, abstract = {Microbial organisms play important roles in many aspects of human health and diseases. Encouraged by the numerous studies that show the association between microbiomes and human diseases, computational and machine learning methods have been recently developed to generate and utilize microbiome features for prediction of host phenotypes such as disease versus healthy cancer immunotherapy responder versus nonresponder. We have previously developed a subtractive assembly approach, which focuses on extraction and assembly of differential reads from metagenomic data sets that are likely sampled from differential genomes or genes between two groups of microbiome data sets (e.g., healthy vs. disease). In this article, we further improved our subtractive assembly approach by utilizing groups of k-mers with similar abundance profiles across multiple samples. We implemented a locality-sensitive hashing (LSH)-enabled approach (called kmerLSHSA) to group billions of k-mers into k-mer coabundance groups (kCAGs), which were subsequently used for the retrieval of differential kCAGs for subtractive assembly. Testing of the kmerLSHSA approach on simulated data sets and real microbiome data sets showed that, compared with the conventional approach that utilizes all genes, our approach can quickly identify differential genes that can be used for building promising predictive models for microbiome-based host phenotype prediction. We also discussed other potential applications of LSH-enabled clustering of k-mers according to their abundance profiles across multiple microbiome samples.}, } @article {pmid35583811, year = {2022}, author = {Zhao, F and Wang, C and Song, S and Fang, C and Kristiansen, K and Li, C}, title = {Intake of a Chicken Protein-Based or Soy Protein-Based Diet Differentially Affects Growth Performance, Absorptive Capacity, and Gut Microbiota in Young Rats.}, journal = {Molecular nutrition & food research}, volume = {66}, number = {13}, pages = {e2101124}, doi = {10.1002/mnfr.202101124}, pmid = {35583811}, issn = {1613-4133}, support = {//Ministry of Science and Technology (10000 Talent Project)/ ; CARS-35//Ministry of Agriculture and Rural Affairs of the People's Republic of China/ ; 31471600//National Natural Science Foundation of China/ ; 21KJB550008//Jiangsu Provincial Department of Education/ ; PADP//Jiangsu Provincial Department of Education/ ; }, mesh = {Animals ; Cecum ; Chickens ; Diet ; *Gastrointestinal Microbiome ; Rats ; Soybean Proteins/pharmacology ; }, abstract = {SCOPE: Both plant and animal products provide protein for human demands. However, the effect of protein sources on the physiological responses and the composition and functions of the gut microbiota during the early stage of life have received little attention.

METHODS AND RESULTS: In the present study, chicken protein and soy protein are fed to young weaning rats for 14 days based on the AIN-93G diet formulation. The growth performance is recorded, and the morphology of the small intestine is analyzed to estimate the absorptive capacity. Shotgun metagenomic sequencing is applied to analyze the cecal microbiota. The chicken protein-based diet (CHPD) enhances growth performance and absorptive capacity in young rats compared to the soy protein-based diet (SPD). The CHPD maintains higher levels of Lactobacillus species, associated with glutathione synthesis.

CONCLUSION: The CHPD seems favorable for young growing rats in relation to growth performance and absorptive capacity, correlated with changes in the composition and functional potential of the gut microbiota.}, } @article {pmid35579684, year = {2022}, author = {Johny, TK and Puthusseri, RM and Saidumohamed, BE and Sheela, UB and Puthusseri, SP and Sasidharan, RS and Bhat, SG}, title = {Appraisal of cytotoxicity and acrylamide mitigation potential of L-asparaginase SlpA from fish gut microbiome.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {9-10}, pages = {3583-3598}, pmid = {35579684}, issn = {1432-0614}, support = {MOES/10-MLR/2/2007//Centre for Marine Living Resources and Ecology- Ministry of Earth Sciences, Government of India/ ; MOES/10-MLRTD/03/2013//Centre for Marine Living Resources and Ecology- Ministry of Earth Sciences, Government of India/ ; }, mesh = {Acrylamide/metabolism ; Animals ; *Antineoplastic Agents/pharmacology ; Asparaginase/genetics/metabolism ; Asparagine/metabolism ; *Gastrointestinal Microbiome ; Glutaminase ; }, abstract = {L-asparaginase catalyzes the hydrolysis of L-asparagine to L-aspartic acid and ammonia. It has application in the treatment of acute lymphoblastic leukemia in children, as well as in other malignancies, in addition to its role as a food processing aid for the mitigation of acrylamide formation in the baking industry. Its use in cancer chemotherapy is limited due to problems such as its intrinsic glutaminase activity and associated side effects, leading to an increased interest in the search for novel L-asparaginases without L-glutaminase activity. This study reports the cloning and expression of an L-asparaginase contig obtained from whole metagenome shotgun sequencing of Sardinella longiceps gut microbiota. Purified recombinant glutaminase-free L-asparaginase SlpA was a 74 kDa homodimer, with maximal activity at pH 8 and 30 °C. Km and Vmax of SlpA were determined to be 3.008 mM and 0.014 mM/min, respectively. SlpA displayed cytotoxic activity against K-562 (chronic myeloid leukemia) and MCF-7 (breast cancer) cell lines with IC50 values of 0.3443 and 2.692 U/mL, respectively. SlpA did not show any cytotoxic activity against normal lymphocytes and was proved to be hemocompatible. Pre-treatment of biscuit and bread dough with different concentrations of SlpA resulted in a clear, dose-dependent reduction of acrylamide formation during baking. KEY POINTS: • Cloned and expressed L-asparaginase (SlpA) from fish gut microbiota • Purified SlpA displayed good cytotoxicity against K-562 and MCF-7 cell lines • SlpA addition caused a significant reduction of acrylamide formation during baking.}, } @article {pmid35579554, year = {2022}, author = {Sim, M and Lee, J and Wy, S and Park, N and Lee, D and Kwon, D and Kim, J}, title = {Generation and application of pseudo-long reads for metagenome assembly.}, journal = {GigaScience}, volume = {11}, number = {}, pages = {}, pmid = {35579554}, issn = {2047-217X}, mesh = {High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Metagenomic assembly using high-throughput sequencing data is a powerful method to construct microbial genomes in environmental samples without cultivation. However, metagenomic assembly, especially when only short reads are available, is a complex and challenging task because mixed genomes of multiple microorganisms constitute the metagenome. Although long read sequencing technologies have been developed and have begun to be used for metagenomic assembly, many metagenomic studies have been performed based on short reads because the generation of long reads requires higher sequencing cost than short reads.

RESULTS: In this study, we present a new method called PLR-GEN. It creates pseudo-long reads from metagenomic short reads based on given reference genome sequences by considering small sequence variations existing in individual genomes of the same or different species. When applied to a mock community data set in the Human Microbiome Project, PLR-GEN dramatically extended short reads in length of 101 bp to pseudo-long reads with N50 of 33 Kbp and 0.4% error rate. The use of these pseudo-long reads generated by PLR-GEN resulted in an obvious improvement of metagenomic assembly in terms of the number of sequences, assembly contiguity, and prediction of species and genes.

CONCLUSIONS: PLR-GEN can be used to generate artificial long read sequences without spending extra sequencing cost, thus aiding various studies using metagenomes.}, } @article {pmid35579429, year = {2022}, author = {Devi, P and Maurya, R and Mehta, P and Shamim, U and Yadav, A and Chattopadhyay, P and Kanakan, A and Khare, K and Vasudevan, JS and Sahni, S and Mishra, P and Tyagi, A and Jha, S and Budhiraja, S and Tarai, B and Pandey, R}, title = {Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0231121}, pmid = {35579429}, issn = {2165-0497}, mesh = {*Achromobacter denitrificans/genetics ; Bacillus cereus ; *COVID-19 ; *Coinfection ; Humans ; *Microbiota/genetics ; Phylogeny ; Prospective Studies ; SARS-CoV-2/genetics ; Severity of Illness Index ; }, abstract = {The modulators of severe COVID-19 have emerged as the most intriguing features of SARS-CoV-2 pathogenesis. This is especially true as we are encountering variants of concern (VOC) with increased transmissibility and vaccination breakthroughs. Microbial co-infections are being investigated as one of the crucial factors for exacerbation of disease severity and complications of COVID-19. A key question remains whether early transcriptionally active microbial signature/s in COVID-19 patients can provide a window for future disease severity susceptibility and outcome? Using complementary metagenomics sequencing approaches, respiratory virus oligo panel (RVOP) and Holo-seq, our study highlights the possible functional role of nasopharyngeal early resident transcriptionally active microbes in modulating disease severity, within recovered patients with sub-phenotypes (mild, moderate, severe) and mortality. The integrative analysis combines patients' clinical parameters, SARS-CoV-2 phylogenetic analysis, microbial differential composition, and their functional role. The clinical sub-phenotypes analysis led to the identification of transcriptionally active bacterial species associated with disease severity. We found significant transcript abundance of Achromobacter xylosoxidans and Bacillus cereus in the mortality, Leptotrichia buccalis in the severe, Veillonella parvula in the moderate, and Actinomyces meyeri and Halomonas sp. in the mild COVID-19 patients. Additionally, the metabolic pathways, distinguishing the microbial functional signatures between the clinical sub-phenotypes, were also identified. We report a plausible mechanism wherein the increased transcriptionally active bacterial isolates might contribute to enhanced inflammatory response and co-infections that could modulate the disease severity in these groups. Current study provides an opportunity for potentially using these bacterial species for screening and identifying COVID-19 patient sub-groups with severe disease outcome and priority medical care. IMPORTANCE COVID-19 is invariably a disease of diverse clinical manifestation, with multiple facets involved in modulating the progression and outcome. In this regard, we investigated the role of transcriptionally active microbial co-infections as possible modulators of disease pathology in hospital admitted SARS-CoV-2 infected patients. Specifically, can there be early nasopharyngeal microbial signatures indicative of prospective disease severity? Based on disease severity symptoms, the patients were segregated into clinical sub-phenotypes: mild, moderate, severe (recovered), and mortality. We identified significant presence of transcriptionally active isolates, Achromobacter xylosoxidans and Bacillus cereus in the mortality patients. Importantly, the bacterial species might contribute toward enhancing the inflammatory responses as well as reported to be resistant to common antibiotic therapy, which together hold potential to alter the disease severity and outcome.}, } @article {pmid35575585, year = {2022}, author = {Kawser, AQMR and Foysal, MJ and Chua, EG and Ali, MH and Mannan, A and Siddik, MAB and Paul, SI and Rahman, MM and Tay, A}, title = {Microbiome data reveal significant differences in the bacterial diversity in freshwater rohu (Labeo rohita) across the supply chain in Dhaka, Bangladesh.}, journal = {Letters in applied microbiology}, volume = {75}, number = {4}, pages = {813-823}, pmid = {35575585}, issn = {1472-765X}, support = {//University of Western Australia/ ; }, mesh = {Animals ; Bacteria/genetics ; Bangladesh ; *Cyprinidae ; Fresh Water ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The present study aimed to characterize and compare the skin and gut microbial communities of rohu at various post-harvest stages of consumption using quantitative real-time polymerase chain reaction and 16S rRNA-based amplicon sequencing. Real-time PCR amplification detected higher copy numbers for coliform bacteria-Escherichia coli, Salmonella enterica and Shigella spp. in the marketed fish-compared to fresh and frozen samples. The 16S rRNA data revealed higher alpha diversity measurements in the skin of fish from different retail markets of Dhaka city. Beta ordination revealed distinct clustering of bacterial OTUs for the skin and gut samples from three different groups. At the phylum level, Proteobacteria was most abundant in all groups except the Fusobacteria in the control fish gut. Although Aeromonas was found ubiquitous in all types of samples, diverse bacterial genera were identified in the marketed fish samples. Nonetheless, low species richness was observed for the frozen fish. Most of the differentially abundant bacteria in the skin samples of marketed fish are opportunistic human pathogens enriched at different stages of postharvest handling and processing. Therefore, considering the microbial contamination in the aquatic environment in Bangladesh, post-harvest handling should be performed with proper methods and care to minimize bacterial transmission into fish.}, } @article {pmid35574962, year = {2022}, author = {Goh, CE and Bohn, B and Marotz, C and Molinsky, R and Roy, S and Paster, BJ and Chen, CY and Rosenbaum, M and Yuzefpolskaya, M and Colombo, PC and Desvarieux, M and Papapanou, PN and Jacobs, DR and Knight, R and Demmer, RT}, title = {Nitrite Generating and Depleting Capacity of the Oral Microbiome and Cardiometabolic Risk: Results from ORIGINS.}, journal = {Journal of the American Heart Association}, volume = {11}, number = {10}, pages = {e023038}, pmid = {35574962}, issn = {2047-9980}, support = {R01 DK102932/DK/NIDDK NIH HHS/United States ; R21 DE022422/DE/NIDCR NIH HHS/United States ; T32 HL007779/HL/NHLBI NIH HHS/United States ; R00 DE018739/DE/NIDCR NIH HHS/United States ; T32 HL007779/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Bacteria/genetics/metabolism ; *Cardiovascular Diseases/diagnosis/epidemiology/genetics ; Female ; Humans ; Male ; *Microbiota ; Nitrates/metabolism ; Nitric Oxide/metabolism ; Nitrites ; Nitrogen ; Nitrogen Dioxide/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {Background The enterosalivary nitrate-nitrite-nitric oxide (NO3-NO2-NO) pathway generates NO following oral microbiota-mediated production of salivary nitrite, potentially linking the oral microbiota to reduced cardiometabolic risk. Nitrite depletion by oral bacteria may also be important for determining the net nitrite available systemically. We examine if higher abundance of oral microbial genes favoring increased oral nitrite generation and decreased nitrite depletion is associated with a better cardiometabolic profile cross-sectionally. Methods and Results This study includes 764 adults (mean [SD] age 32 [9] years, 71% women) enrolled in ORIGINS (Oral Infections, Glucose Intolerance, and Insulin Resistance Study). Microbial DNA from subgingival dental plaques underwent 16S rRNA gene sequencing; PICRUSt2 was used to estimate functional gene profiles. To represent the different components and pathways of nitrogen metabolism in bacteria, predicted gene abundances were operationalized to create summary scores by (1) bacterial nitrogen metabolic pathway or (2) biochemical product (NO2, NO, or ammonia [NH3]) formed by the action of the bacterial reductases encoded. Finally, nitrite generation-to-depletion ratios of gene abundances were created from the above summary scores. A composite cardiometabolic Z score was created from cardiometabolic risk variables, with higher scores associated with worse cardiometabolic health. We performed multivariable linear regression analysis with cardiometabolic Z score as the outcome and the gene abundance summary scores and ratios as predictor variables, adjusting for sex, age, race, and ethnicity in the simple adjusted model. A 1 SD higher NO versus NH3 summary ratio was inversely associated with a -0.10 (false discovery rate q=0.003) lower composite cardiometabolic Z score in simple adjusted models. Higher NH3 summary score (suggestive of nitrite depletion) was associated with higher cardiometabolic risk, with a 0.06 (false discovery rate q=0.04) higher composite cardiometabolic Z score. Conclusions Increased net capacity for nitrite generation versus depletion by oral bacteria, assessed through a metagenome estimation approach, is associated with lower levels of cardiometabolic risk.}, } @article {pmid35574681, year = {2022}, author = {Li, F and Jiang, L and Pan, S and Jiang, S and Fan, Y and Jiang, C and Gao, C and Leng, Y}, title = {Multi-omic Profiling Reveals that Intra-abdominal-Hypertension-Induced Intestinal Damage Can Be Prevented by Microbiome and Metabolic Modulations with 5-Hydroxyindoleacetic Acid as a Diagnostic Marker.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0120421}, pmid = {35574681}, issn = {2379-5077}, mesh = {Rats ; Animals ; *Intra-Abdominal Hypertension ; Hydroxyindoleacetic Acid ; Critical Illness ; Multiomics ; Tryptophan/pharmacology ; *Microbiota ; *Sepsis ; *Hypertension ; }, abstract = {Emerging evidence shows that modulation of the microbiome can suppress intra-abdominal hypertension (IAH)-induced intestinal barrier damage through the regulation of amino acid (AA) biosynthesis. Here, we investigated the protective effects of orally gavaged Lactobacillus acidophilus L-92 (L92) and a mixture of AA in rats with induced IAH. The results showed that both L92 and AA pretreatments effectively mitigated IAH-induced intestinal damage. Interestingly, L92 but not AA prevented metagenomic changes induced by IAH. Bacteroides fragilis, Bacteroides eggerthii, Bacteroides ovatus, Faecalibacterium prausnitzii, Prevotella, and extensively altered functional pathways were associated with L92-mediated host protection. Metabolomic profiling revealed that tryptophan metabolism was involved in both L92- and AA-mediated gut protection. The tryptophan metabolite 5-hydroxyindoleacetic acid (5-HIAA) is a sensitive biomarker for IAH in rats and patients with either gut-derived sepsis (n = 41) or all-source sepsis (n = 293). In conclusion, we show that microbiome and metabolic modulations can effectively prevent IAH-induced intestinal damage and that 5-HIAA is a potential metabolic marker for IAH and sepsis. IMPORTANCE Gut protection through modulation of the microbiome for critically ill patients has been gaining much attention recently. Intra-abdominal hypertension (IAH) is a prevailing clinical feature of acute gastrointestinal injuries in critically ill patients, characterized by nonspecific intestinal barrier damage. Prolonged IAH can induce or aggravate the development of sepsis and multiorgan dysfunctions. Therefore, the prevention of IAH-induced damage in rats through microbiome and metabolic interventions by commercially available L92 and AA treatments and the identification of 5-HIAA as an important marker for IAH/sepsis have important clinical implications for the treatment and early diagnosis of critically ill patients.}, } @article {pmid35573175, year = {2022}, author = {Ghosh, A and Saha, R and Bhadury, P}, title = {Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13169}, pmid = {35573175}, issn = {2167-8359}, mesh = {*Water ; Wetlands ; *Microbiota/genetics ; Metagenome/genetics ; Bacteria/genetics ; Firmicutes/genetics ; }, abstract = {Estuaries are one of the most productive ecosystems and their productivity is maintained by resident microbial communities. Recent alterations driven by climate change have further escalated these stressors leading to the propagation of traits such as antibiotic resistance and heavy metal resistance in microbial communities. Surface water samples from eleven stations along the Thakuran and Matla estuaries of the Sundarbans Biosphere Reserve (SBR) of Sundarbans mangrove located in South Asia were sampled in monsoon (June) 2019 to elucidate resident microbial communities based on Nanopore sequencing. Metagenomic analyses revealed the widespread dominance of Proteobacteria across all the stations along with a high abundance of Firmicutes. Other phyla, including Euryarchaeota, Thaumarchaeota, Actinobacteria, Bacteroidetes and Cyanobacteria showed site-specific trends in abundance. Further taxonomic affiliations showed Gammaproteobacteria and Alphaproteobacteria to be dominant classes with high abundances of Bacilli in SBR_Stn58 and SBR_Stn113. Among the eukaryotic communities, the most abundant classes included Prasinophyceae, Saccharyomycetes and Sardariomycetes. Functional annotation showed metabolic activities such as carbohydrate, amino acid, nitrogen and phosphorus metabolisms to be uniformly distributed across all the studied stations. Pathways such as stress response, sulphur metabolism and motility-associated genes appeared in low abundances in SBR. Functional traits such as antibiotic resistance showed overwhelming dominance of genes involved in multidrug resistance along with widespread resistance towards commonly used antibiotics including Tetracycline, glycopeptide and aminoglycoside. Metal resistance genes including arsenic, nickel and copper were found in comparable abundances across the studied stations. The prevalence of ARG and MRG might indicate presence of pollutants and hint toward deteriorating ecosystem health status of Sundarbans mangrove.}, } @article {pmid35572506, year = {2022}, author = {Porto, BN}, title = {Insights Into the Role of the Lung Virome During Respiratory Viral Infections.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {885341}, pmid = {35572506}, issn = {1664-3224}, mesh = {Child ; Humans ; Lung ; Metagenomics ; Virome ; *Virus Diseases ; *Viruses/genetics ; }, abstract = {The virome constitutes the viral component of the microbiome and it consists of the genomes of all the viruses that inhabit a particular region of the human body, including those that cause acute, persistent or latent infection, and retroviral elements integrated to host chromosomes. The human virome is composed by eukaryotic viruses, bacteriophages and archaeal viruses. The understanding of the virome composition and role on human health has been delayed by the absence of specific tools and techniques to accurately characterize viruses. However, more recently, advanced methods for viral diagnostics, such as deep sequencing and metagenomics, have allowed a better understanding of the diverse viral species present in the human body. Previous studies have shown that the respiratory virome modulates the host immunity and that, since childhood, the human lung is populated by viruses for whom there is no disease association. Whether these viruses are potentially pathogenic and the reason for their persistence remain elusive. Increased respiratory viral load can cause exacerbation of chronic pulmonary diseases, including COPD, cystic fibrosis, and asthma. Moreover, the presence of resident viral populations may contribute to the pathogenesis of community-acquired respiratory virus infections. In this mini review, I will discuss the recent progress on our understanding of the human lung virome and summarize the up-to-date knowledge on the relationships among community-acquired respiratory viruses, the lung virome and the immune response to better understand disease pathophysiology and the factors that may lead to viral persistence.}, } @article {pmid35572406, year = {2022}, author = {Diao, Z and Han, D and Zhang, R and Li, J}, title = {Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections.}, journal = {Journal of advanced research}, volume = {38}, number = {}, pages = {201-212}, pmid = {35572406}, issn = {2090-1224}, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Respiratory Tract Infections/diagnosis ; }, abstract = {Metagenomic next-generation sequencing (mNGS) has changed the diagnosis landscape of lower respiratory tract infections (LRIs). With the development of newer sequencing assays, it is now possible to assess all microorganisms in a sample using a single mNGS analysis. The applications of mNGS for LRIs span a wide range of areas including LRI diagnosis, airway microbiome analyses, human host response analyses, and prediction of drug resistance. mNGS is currently in an exciting transitional period; however, before implementation in a clinical setting, there are several barriers to overcome, such as the depletion of human nucleic acid, discrimination between colonization and infection, high costs, and so on. Aim of Review: In this review, we summarize the potential applications and challenges of mNGS in the diagnosis of LRIs to promote the integration of mNGS into the management of patients with respiratory tract infections in a clinical setting. Key Scientific Concepts of Review: Once its analytical validation, clinical validation and clinical utility been demonstrated, mNGS will become an important tool in the field of infectious disease diagnosis.}, } @article {pmid35568852, year = {2022}, author = {Keburiya, LK and Smolnikova, VY and Priputnevich, TV and Muravieva, VV and Gordeev, AB and Trofimov, DY and Shubina, ES and Kochetkova, TO and Rogacheva, MS and Kalinina, EA and Sukhikh, GT}, title = {Does the uterine microbiota affect the reproductive outcomes in women with recurrent implantation failures?.}, journal = {BMC women's health}, volume = {22}, number = {1}, pages = {168}, pmid = {35568852}, issn = {1472-6874}, mesh = {Embryo Implantation ; *Embryo Transfer ; Female ; Fertilization in Vitro ; Humans ; *Microbiota ; Pregnancy ; Pregnancy Rate ; }, abstract = {BACKGROUND: Inefficiency of in vitro fertilization (IVF) programs can be caused by implantation failures. The uterine microbiota can influence the implantation process. However, it still remains unclear whether opportunistic microorganisms detected in the endometrium have a negative impact on the implantation success. The aim of our study was to evaluate the influence of the uterine microbiota on the embryo implantation success in patients undergoing assisted reproductive technologies.

METHODS: The study included 130 women diagnosed with infertility. The patients were divided into three groups: group I included women with the first IVF attempt (n = 39); group II included patients with recurrent implantation failure following embryo transfer with ovarian stimulation (n = 27); group III consisted of women with recurrent implantation failure following frozen-thawed embryo transfer (n = 64). We performed microbiological examination of the embryo transfer catheter which was removed from the uterine cavity after embryo transfer; cervical discharge of all the patients was studied as well. Thirty patients were selected for metagenomic sequencing.

RESULTS: The study showed that the uterine cavity is not free of microorganisms. A total of 44 species of microorganisms were detected: 26 species of opportunistic organisms and 18 species of commensals (14 species of lactobacilli and 4 species of bifidobacteria). Obligate anaerobic microorganisms and Gardnerella vaginalis were detected more frequently in group I compared to group III (strict anaerobes-15.4 and 1.6%; G. vaginalis-12.8 and 1.6%, respectively) (p < 0.05). However, this fact did not have a negative influence on the pregnancy rate: it was 51.3% in group I, it was 29.6% and 35.9% in women with recurrent implantation failures, respectively.

CONCLUSION: Opportunistic microorganisms which were revealed in low or moderate titers (10[3]-10[5] CFU/ml) in the uterine cavity and cervical canal did not affect the pregnancy rate in the women in the study groups. The microflora of the uterine cavity and cervical canal differed in qualitative composition in 87.9% of patients, therefore, we can suggest that the uterine cavity may form its own microbiota. The microbiota of the uterine cavity is characterized by fewer species diversity compared to the microbiota of the cervical canal.}, } @article {pmid35568730, year = {2022}, author = {Lebeaux, RM and Madan, JC and Nguyen, QP and Coker, MO and Dade, EF and Moroishi, Y and Palys, TJ and Ross, BD and Pettigrew, MM and Morrison, HG and Karagas, MR and Hoen, AG}, title = {Impact of antibiotics on off-target infant gut microbiota and resistance genes in cohort studies.}, journal = {Pediatric research}, volume = {92}, number = {6}, pages = {1757-1766}, pmid = {35568730}, issn = {1530-0447}, support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; R01 LM012723/LM/NLM NIH HHS/United States ; P20 ES018175/ES/NIEHS NIH HHS/United States ; P01 ES022832/ES/NIEHS NIH HHS/United States ; P20 GM104416/GM/NIGMS NIH HHS/United States ; UH3 OD023275/OD/NIH HHS/United States ; T32 AI007519/AI/NIAID NIH HHS/United States ; }, mesh = {Child ; Humans ; Infant ; Child, Preschool ; Anti-Bacterial Agents/adverse effects ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Cohort Studies ; Escherichia coli ; }, abstract = {BACKGROUND: Young children are frequently exposed to antibiotics, with the potential for collateral consequences to the gut microbiome. The impact of antibiotic exposures to off-target microbes (i.e., bacteria not targeted by treatment) and antibiotic resistance genes (ARGs) is poorly understood.

METHODS: We used metagenomic sequencing data from paired stool samples collected prior to antibiotic exposure and at 1 year from over 200 infants and a difference-in-differences approach to assess the relationship between subsequent exposures and the abundance or compositional diversity of microbes and ARGs while adjusting for covariates.

RESULTS: By 1 year, the abundance of multiple species and ARGs differed by antibiotic exposure. Compared to infants never exposed to antibiotics, Bacteroides vulgatus relative abundance increased by 1.72% (95% CI: 0.19, 3.24) while Bacteroides fragilis decreased by 1.56% (95% CI: -4.32, 1.21). Bifidobacterium species also exhibited opposing trends. ARGs associated with exposure included class A beta-lactamase gene CfxA6. Among infants attending day care, Escherichia coli and ARG abundance were both positively associated with antibiotic use.

CONCLUSION: Novel findings, including the importance of day care attendance, were identified through considering microbiome data at baseline and post-intervention. Thus, our study design and approach have important implications for future studies evaluating the unintended impacts of antibiotics.

IMPACT: The impact of antibiotic exposure to off-target microbes and antibiotic resistance genes in the gut is poorly defined. We quantified these impacts in two cohort studies using a difference-in-differences approach. Novel to microbiome studies, we used pre/post-antibiotic data to emulate a randomized controlled trial. Compared to infants unexposed to antibiotics between baseline and 1 year, the relative abundance of multiple off-target species and antibiotic resistance genes was altered. Infants who attended day care and were exposed to antibiotics within the first year had a higher abundance of Escherichia coli and antibiotic resistance genes; a novel finding warranting further investigation.}, } @article {pmid35566348, year = {2022}, author = {Madubuike, H and Ferry, N}, title = {Characterisation of a Novel Acetyl Xylan Esterase (BaAXE) Screened from the Gut Microbiota of the Common Black Slug (Arion ater).}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {9}, pages = {}, pmid = {35566348}, issn = {1420-3049}, mesh = {Acetylesterase ; Animals ; *Gastrointestinal Microbiome ; *Gastropoda/metabolism ; Substrate Specificity ; Xylans/chemistry ; }, abstract = {Acetyl xylan esterases (AXEs) are enzymes capable of hydrolysing the acetyl bonds in acetylated xylan, allowing for enhanced activity of backbone-depolymerizing enzymes. Bioprospecting novel AXE is essential in designing enzyme cocktails with desired characteristics targeting the complete breakdown of lignocellulose. In this article, we report the characterisation of a novel AXE identified as Gene_id_40363 in the metagenomic library analysed from the gut microbiota of the common black slug. The conserved domain description was identified with an NCBI BLASTp search using the translated nucleotide sequence as a query. The activity of the recombinant enzyme was tested on various synthetic substrates and acetylated substrates. The protein sequence matched the conserved domain described as putative hydrolase and aligned closely to an uncharacterized esterase from Buttiauxella agrestis, hence the designation as BaAXE. BaAXE showed low sequence similarity among characterized CE family proteins with an available 3D structure. BaAXE was active on 4-nitrophenyl acetate, reporting a specific activity of 78.12 U/mg and a Km value of 0.43 mM. The enzyme showed optimal activity at 40 °C and pH 8 and showed high thermal stability, retaining over 40% activity after 2 h of incubation from 40 °C to 100 °C. BaAXE hydrolysed acetyl bonds, releasing acetic acid from acetylated xylan and β-D-glucose pentaacetate. BaAXE has great potential for biotechnological applications harnessing its unique characteristics. In addition, this proves the possibility of bioprospecting novel enzymes from understudied environments.}, } @article {pmid35565868, year = {2022}, author = {Yu, X and Xing, Y and Liu, H and Chang, Y and You, Y and Dou, Y and Liu, B and Wang, Q and Ma, D and Chen, L and Tong, X}, title = {Effects of a Formula with scGOS/lcFOS (9:1) and Glycomacropeptide (GMP) Supplementation on the Gut Microbiota of Very Preterm Infants.}, journal = {Nutrients}, volume = {14}, number = {9}, pages = {}, pmid = {35565868}, issn = {2072-6643}, support = {NO. S160004//Natural Science Foundation of Beijing/ ; 2021YFC2700700//National Key Research and Development Program of China/ ; No. BYSYLXHG2019005//Peking University Third Hospital Research Fund for outstanding overseas returnees/ ; }, mesh = {Caseins ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant Formula ; Infant, Newborn ; Infant, Premature ; Oligosaccharides/pharmacology ; Peptide Fragments ; Prebiotics/analysis ; }, abstract = {Microbial colonization of very preterm (VPT) infants is detrimentally affected by the complex interplay of physiological, dietary, medical, and environmental factors. The aim of this study was to evaluate the effects of an infant formula containing the specific prebiotic mixture of scGOS/lcFOS (9:1) and glycomacropeptide (GMP) on the composition and function of VPT infants' gut microbiota. Metagenomic analysis was performed on the gut microbiota of VPT infants sampled at four time points: 24 h before the trial and 7, 14, and 28 days after the trial. Functional profiling was aggregated into gut and brain modules (GBMs) and gut metabolic modules (GMMs) based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Enterococcus faecium, Escherichia coli, Klebsiella aerogenes, and Klebsiella pneumoniae were dominant species in both the test group and the control group. After the 4-week intervention, the abundance of Bifidobacterium in the test group was significantly increased. We found two GBMs (quinolinic acid synthesis and kynurenine degradation) and four GMMs (glutamine degradation, glyoxylate bypass, dissimilatory nitrate reduction, and preparatory phase of glycolysis) were significantly enriched in the test group, respectively. The results of this study suggested that formula enriched with scGOS/lcFOS (9:1) and GPM is beneficial to the intestinal microecology of VPT infants.}, } @article {pmid35565725, year = {2022}, author = {Hernandez, AR and Kemp, KM and Burke, SN and Buford, TW and Carter, CS}, title = {Influence of Aging, Macronutrient Composition and Time-Restricted Feeding on the Fischer344 x Brown Norway Rat Gut Microbiota.}, journal = {Nutrients}, volume = {14}, number = {9}, pages = {}, pmid = {35565725}, issn = {2072-6643}, support = {RF1 AG060977/AG/NIA NIH HHS/United States ; K12GM088010/NH/NIH HHS/United States ; T32HD071866/NH/NIH HHS/United States ; RF1AG060977//National Institute of Health/ ; K02AG062498/NH/NIH HHS/United States ; R01AG054538/NH/NIH HHS/United States ; P2CHD086851/NH/NIH HHS/United States ; }, mesh = {Aging ; Animals ; Cytokines ; *Gastrointestinal Microbiome ; *Neurodegenerative Diseases ; Nutrients ; Rats ; }, abstract = {Both ketogenic diets (KD) and time-restricted feeding (TRF) regimens have the ability to influence several parameters of physical health, including gut microbiome composition and circulating cytokine concentration. Moreover, both of these dietary interventions prevent common impairments associated with the aging process. However, significantly altering macronutrient intake, which is required for a KD, may be unappealing to individuals and decrease compliance to dietary treatments. In contrast to a KD, TRF allows individuals to continue eating the foods they are used to, and only requires a change in the time of day at which they eat. Therefore, we investigated both a KD and a diet with a more Western-like macronutrient profile in the context of TRF, and compared both diets to animals allowed access to standard chow ad libitum in young adult and aged rats. While limited effects on cytokine levels were observed, both methods of microbiome analysis (16S sequencing and metagenomics) indicate that TRF and KDs significantly altered the gut microbiome in aged rats. These changes were largely dependent on changes to feeding paradigm (TRF vs. ad libitum) alone regardless of macronutrient content for many gut microbiota, but there were also macronutrient-specific changes. Specifically, functional analysis indicates significant differences in several pathways, including those involved in the tricarboxylic acid (TCA) cycle, carbohydrate metabolism and neurodegenerative disease. These data indicate that age- and disease-related gut dysbiosis may be ameliorated through the use of TRF with both standard diets and KDs.}, } @article {pmid35562600, year = {2023}, author = {Greene, LK and McKenney, EA and Gasper, W and Wrampelmeier, C and Hayer, S and Ehmke, EE and Clayton, JB}, title = {Gut Site and Gut Morphology Predict Microbiome Structure and Function in Ecologically Diverse Lemurs.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1608-1619}, pmid = {35562600}, issn = {1432-184X}, support = {PRFB 1906416//Directorate for Biological Sciences/ ; }, mesh = {Animals ; *Lemur ; Retrospective Studies ; *Lemuridae ; *Microbiota ; *Strepsirhini ; }, abstract = {Most studies of wildlife gut microbiotas understandably rely on feces to approximate consortia along the gastrointestinal tract. We therefore compared microbiome structure and predicted metagenomic function in stomach, small intestinal, cecal, and colonic samples from 52 lemurs harvested during routine necropsies. The lemurs represent seven genera (Cheirogaleus, Daubentonia, Varecia, Hapalemur, Eulemur, Lemur, Propithecus) characterized by diverse feeding ecologies and gut morphologies. In particular, the hosts variably depend on fibrous foodstuffs and show correlative morphological complexity in their large intestines. Across host lineages, microbiome diversity, variability, membership, and function differed between the upper and lower gut, reflecting regional tradeoffs in available nutrients. These patterns related minimally to total gut length but were modulated by fermentation capacity (i.e., the ratio of small to large intestinal length). Irrespective of feeding strategy, host genera with limited fermentation capacity harbored more homogenized microbiome diversity along the gut, whereas those with expanded fermentation capacity harbored cecal and colonic microbiomes with greater diversity and abundant fermentative Ruminococcaceae taxa. While highlighting the value of curated sample repositories for retrospective comparisons, our results confirm that the need to survive on fibrous foods, either routinely or in hypervariable environments, can shape the morphological and microbial features of the lower gut.}, } @article {pmid35561922, year = {2022}, author = {Xie, H and Chen, Z and Feng, X and Wang, M and Luo, Y and Wang, Y and Xu, P}, title = {L-theanine exuded from Camellia sinensis roots regulates element cycling in soil by shaping the rhizosphere microbiome assembly.}, journal = {The Science of the total environment}, volume = {837}, number = {}, pages = {155801}, doi = {10.1016/j.scitotenv.2022.155801}, pmid = {35561922}, issn = {1879-1026}, mesh = {*Camellia sinensis/chemistry ; Glutamates ; *Microbiota/genetics ; Plant Roots/metabolism ; RNA, Ribosomal, 16S/analysis ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; Tea/metabolism ; }, abstract = {Root exudate metabolites are a key medium for the interaction between plants and soil microbiota. L-theanine is a unique non-protein amino acid critical for the flavor and potential health benefits of tea products; however, its biological function in tea plants is not well understood. As L-theanine is mainly synthesized in the roots of tea plants, we hypothesized that L-theanine could affect the function of the rhizosphere microbiota by modulating microbial assembly. In the present study, L-theanine was detected in the exudates of tea plant roots using liquid chromatography-mass spectrometry. Additionally, 16S rRNA gene sequencing revealed that L-theanine significantly altered the structure of the rhizosphere microbiota and selectively shaped rhizosphere microbial assembly. Moreover, metagenomic data showed that L-theanine affected the abundance of genes encoding element cycling in soil. Interestingly, the denitrification and complete nitrification pathways were significantly inhibited by L-theanine by decreasing the narH, napA, and napB genes abundance. These findings provide new insights into the biological function of L-theanine, as well as the implications of interactions between tea plant root exudates and the rhizosphere microbiome.}, } @article {pmid35561657, year = {2022}, author = {Doerksen, T and Christensen, T and Lu, A and Noll, L and Bai, J and Henningson, J and Palinski, R}, title = {Assessment of porcine Rotavirus-associated virome variations in pigs with enteric disease.}, journal = {Veterinary microbiology}, volume = {270}, number = {}, pages = {109447}, doi = {10.1016/j.vetmic.2022.109447}, pmid = {35561657}, issn = {1873-2542}, mesh = {Animals ; Diarrhea/epidemiology/veterinary ; Feces ; Genotype ; Humans ; Mammals ; Phylogeny ; *Rotavirus/genetics ; *Rotavirus Infections/epidemiology/veterinary ; Swine ; *Swine Diseases/epidemiology ; Virome ; }, abstract = {Enteric disease is the predominant cause of morbidity and mortality in young mammals including pigs. Viral species involved in porcine enteric disease complex (PEDC) include rotaviruses, coronaviruses, picornaviruses, astroviruses and pestiviruses among others. The virome of three groups of swine samples submitted to the Kansas State University Veterinary Diagnostic Laboratory for routine testing were assessed, namely, a Rotavirus A positive (RVA) group, a Rotavirus co-infection (RV) group and a Rotavirus Negative (RV Neg) group. All groups were designated by qRT-PCR test results for Porcine Rotavirus A, B, C and H such that samples positive for RVA only went in the RVA group, samples positive for > 1 rotavirus went in the RV group and samples negative for all were grouped in the RVNeg group. All of the animals had clinical enteric disease resulting in scours and swollen joints/lameness, enlarged heart and/or a cough. All samples were metagenomic sequenced and analyzed for viral species composition that identified 14 viral species and eight bacterial viruses/phages. Sapovirus and Escherichia coli phages were found at a high prevalence in RVA and RV samples but were found at low or no prevalence in the RVNeg samples. Picobirnavirus was identified at a high proportion and prevalence in RVNeg and RV samples but at a low prevalence in the RVA group. Non-rotaviral diversity was highest in RVA samples followed by RV then RV Neg samples. A sequence analysis of the possible host of Picobirnaviruses revealed fungi as the most likely host. Various sequences were extracted from the sample reads and a phylogenetic update was provided showing a high prevalence of G9 and P[23] RVA genotypes. These data are important for pathogen surveillance and control measures.}, } @article {pmid35559844, year = {2021}, author = {Meier, MJ and Nguyen, KC and Crosthwait, J and Kawata, A and Rigden, M and Leingartner, K and Wong, A and Holloway, A and Shwed, PS and Beaudette, L and Navarro, M and Wade, M and Tayabali, AF}, title = {Low dose antibiotic ingestion potentiates systemic and microbiome changes induced by silver nanoparticles.}, journal = {NanoImpact}, volume = {23}, number = {}, pages = {100343}, doi = {10.1016/j.impact.2021.100343}, pmid = {35559844}, issn = {2452-0748}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; DNA, Ribosomal/pharmacology ; Eating ; Mammals ; *Metal Nanoparticles/chemistry ; Mice ; *Microbiota ; Silver/chemistry ; }, abstract = {Changes in the mammalian gut microbiome are linked to the impairment of immunological function and numerous other pathologies. Antimicrobial silver nanoparticles (AgNPs) are incorporated into numerous consumer products (e.g., clothing, cosmetics, food packaging), which may directly impact the gut microbiome through ingestion. The human health impact of chronic AgNP ingestion is still uncertain, but evidence from exposure to other antimicrobials provides a strong rationale to assess AgNP effects on organ function, immunity, metabolism, and gut-associated microbiota. To investigate this, mice were gavaged daily for 5 weeks with saline, AgNPs, antibiotics (ciprofloxacin and metronidazole), or AgNPs combined with antibiotics. Animals were weighed daily, assessed for glucose tolerance, organ function, tissue and blood cytokine and leukocyte levels. At the end of the study, we used 16S rDNA amplicon and whole-metagenome shotgun sequencing to assess changes in the gut microbiome. In mice exposed to both AgNPs and antibiotics, silver was found in the stomach, and small and large intestines, but negligible amounts were present in other organs examined. Mice exposed to AgNPs alone showed minimal tissue silver levels. Antibiotics, but not AgNPs, altered glucose metabolism. Mice given AgNPs and antibiotics together demonstrated slower weight gain, reduced peripheral lymphocytes, and elevated splenic, but not circulatory markers of inflammation. 16S rDNA profiling of cecum and feces and metagenomic sequencing of fecal DNA demonstrated that combined AgNP-antibiotic treatment also significantly altered the structure and function of the gut microbiota, including depletion of the indicator species Akkermansia muciniphila. This study provides evidence for possible biological effects from repeated ingestion of AgNP-containing consumer products when antibiotics are also being used and raises concern that an impaired gut microbiome (e.g., through antibiotic use) can potentiate the harm from chemical exposures such as AgNPs.}, } @article {pmid35551951, year = {2022}, author = {Ariaeenejad, S and Kavousi, K and Afshar Jahanshahi, D and Sheykh Abdollahzadeh Mamaghani, A and Ghasemitabesh, R and Moosavi-Movahedi, AA and Hosseini Salekdeh, G}, title = {Enzymatically triggered delignification through a novel stable laccase: A mixed in-silico /in-vitro exploration of a complex environmental microbiota.}, journal = {International journal of biological macromolecules}, volume = {211}, number = {}, pages = {328-341}, doi = {10.1016/j.ijbiomac.2022.05.039}, pmid = {35551951}, issn = {1879-0003}, mesh = {Biomass ; Laccase/chemistry/genetics ; *Lignin/chemistry ; *Microbiota ; Saccharomyces cerevisiae ; }, abstract = {Laccases have been broadly applied as a multitasking biocatalyst in various industries, but their applications tend to be limited by easy deactivation, lack of adequate stability, and susceptibility under complex conditions. Identifying stable laccase as a green-biocatalyst is crucial for developing cost-effective biorefining processes. In this direction, we attempted in-silico screening a stable metagenome-derived laccase (PersiLac1) from tannery wastewater in a complex environment. The laccase exhibited high thermostability, retaining 53.19% activity after 180 min at 70 °C, and it was stable in a wide range of pH (4.0-9.0). After 33 days of storage at 50°C, pH 6.0, the enzyme retained 71.65% of its activity. Various metal ions, inhibitors, and organic solvents showed that PersiLac1 has a stable structure. The stable PersiLac1 could successfully remove lignin and phenolic from quinoa husk and rice straw. In the separate hydrolysis and fermentation process (SHF) after 72 h, hydrolysis was obtained 100% and 73.4% for quinoa husk and rice straw, and fermentation by the S. cerevisiae was be produced 41.46 g/L and 27.75g/L ethanol, respectively. Results signified that the novel lignin-degrading enzyme was confirmed to have great potential for industrial application as a green-biocatalyst based on enzymatically triggered to delignification and detoxify lignocellulosic biomass.}, } @article {pmid35551905, year = {2022}, author = {Li, J and Liang, Q and Huang, F and Liao, Y and Zhao, W and Yang, J and Wen, X and Li, X and Chen, T and Guo, S and Liang, J and Wei, L and Liang, L}, title = {Metagenomic Profiling of the Ocular Surface Microbiome in Patients After Allogeneic Hematopoietic Stem Cell Transplantation.}, journal = {American journal of ophthalmology}, volume = {242}, number = {}, pages = {144-155}, doi = {10.1016/j.ajo.2022.04.026}, pmid = {35551905}, issn = {1879-1891}, mesh = {Dysbiosis ; *Graft vs Host Disease/diagnosis ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Humans ; Male ; *Microbiota ; Prospective Studies ; }, abstract = {PURPOSE: To investigate the characteristics of the ocular surface microbiome in patients after allogeneic hematopoietic stem cell transplantation (allo-HSCT) and the associations between the microbial dysbiosis and chronic ocular graft-versus-host disease (oGVHD).

DESIGN: Prospective cohort study.

METHODS: Ocular surface samples from 48 healthy subjects and 76 patients after allo-HSCT, including 50 patients with chronic oGVHD and 26 patients without oGVHD, were collected. Species-level composition of the ocular surface microbiome was surveyed via metagenomic shotgun sequencing. OGVHD was diagnosed and graded according to the International Chronic Ocular GVHD Consensus Group criteria.

RESULTS: The α-diversity of the microbiota was significantly decreased in patients after allo-HSCT. Nevertheless, we detected more types of viral species in the allo-HSCT group than the healthy group, especially anelloviruses. The mismatch of donor-recipient sex was only negatively associated with the α-diversity in male but not female recipients. Moreover, the microbiome of patients with oGVHD was distinct from patients without oGVHD. Gordonia bronchialis and Pseudomonas parafulva were enriched in patients with oGVHD and positively associated with International Chronic Ocular GVHD score.

CONCLUSIONS: This study suggests that the ocular surface microbiome after allo-HSCT is characterized by a loss of diversity. Furthermore, the microbial dysbiosis at the ocular surface is associated with the status and severity of chronic oGVHD. These results lay the groundwork for future investigations of the potential microbial mechanism for oGVHD.}, } @article {pmid35551553, year = {2022}, author = {Elbon, CE and LeCleir, GR and Tuttle, MJ and Jurgensen, SK and Demas, TG and Keller, CJ and Stewart, T and Buchan, A}, title = {Microbiomes and Planctomycete diversity in large-scale aquaria habitats.}, journal = {PloS one}, volume = {17}, number = {5}, pages = {e0267881}, pmid = {35551553}, issn = {1932-6203}, mesh = {*Ammonium Compounds/metabolism ; Anaerobiosis ; Bacteria ; Bioreactors/microbiology ; *Microbiota/genetics ; Nitrites/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Planctomycetes ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {In commercial large-scale aquaria, controlling levels of nitrogenous compounds is essential for macrofauna health. Naturally occurring bacteria are capable of transforming toxic nitrogen species into their more benign counterparts and play important roles in maintaining aquaria health. Nitrification, the microbially-mediated transformation of ammonium and nitrite to nitrate, is a common and encouraged process for management of both commercial and home aquaria. A potentially competing microbial process that transforms ammonium and nitrite to dinitrogen gas (anaerobic ammonium oxidation [anammox]) is mediated by some bacteria within the phylum Planctomycetes. Anammox has been harnessed for nitrogen removal during wastewater treatment, as the nitrogenous end product is released into the atmosphere rather than in aqueous discharge. Whether anammox bacteria could be similarly utilized in commercial aquaria is an open question. As a first step in assessing the viability of this practice, we (i) characterized microbial communities from water and sand filtration systems for four habitats at the Tennessee Aquarium and (ii) examined the abundance and anammox potential of Planctomycetes using culture-independent approaches. 16S rRNA gene amplicon sequencing revealed distinct, yet stable, microbial communities and the presence of Planctomycetes (~1-15% of library reads) in all sampled habitats. Preliminary metagenomic analyses identified the genetic potential for multiple complete nitrogen metabolism pathways. However, no known genes diagnostic for the anammox reaction were found in this survey. To better understand the diversity of this group of bacteria in these systems, a targeted Planctomycete-specific 16S rRNA gene-based PCR approach was used. This effort recovered amplicons that share <95% 16S rRNA gene sequence identity to previously characterized Planctomycetes, suggesting novel strains within this phylum reside within aquaria.}, } @article {pmid35550809, year = {2022}, author = {Zhu, J and Chen, G and Zhou, J and Zeng, Y and Cheng, K and Cai, Z}, title = {Dynamic patterns of quorum sensing signals in phycospheric microbes during a marine algal bloom.}, journal = {Environmental research}, volume = {212}, number = {Pt C}, pages = {113443}, doi = {10.1016/j.envres.2022.113443}, pmid = {35550809}, issn = {1096-0953}, mesh = {Bacteria/metabolism ; Eutrophication ; *Microbiota ; Phytoplankton/genetics ; *Quorum Sensing ; }, abstract = {In the marine environment, the interactions among various species based on chemical signals play critical roles in influencing microbial structure and function. Quorum sensing (QS), the well-known signal-dependent communication autoinducer, is an important regulator in complex microbial communities. Here, we explored the QS gene profiles of phycosphere bacteria during a microcosmic phytoplankton bloom using metagenomic sequence data. More than fifteen subtypes of QS systems and 211,980 non-redundant amino acid sequences were collected and classified for constructing a hierarchical quorum-sensing database. The abundance of the various QS subtypes varied at different bloom stages and showed a strong correlation with phycosphere microorganisms. This suggested that QS is involved in regulating the phycosphere microbial succession during an algal bloom. A neutral community model revealed that the QS functional gene community assemblies were driven by stochastic processes. Co-occurrence model analysis showed that the QS gene networks of phycospheric microbes had similar topological structure and functional composition, which is a potential cornerstone for maintaining signal communication and population stabilization among microorganisms. Overall, QS systems have a strong relationship with the development of algal blooms and participate in regulating algal-associated microbial communities as chemical signals. This research reveals the chemical and ecological behavior of algal symbiotic bacteria and expands the current understanding of microbial dynamics in marine algal blooms.}, } @article {pmid35549618, year = {2022}, author = {Chen, L and Zheng, T and Yang, Y and Chaudhary, PP and Teh, JPY and Cheon, BK and Moses, D and Schuster, SC and Schlundt, J and Li, J and Conway, PL}, title = {Integrative multiomics analysis reveals host-microbe-metabolite interplays associated with the aging process in Singaporeans.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2070392}, pmid = {35549618}, issn = {1949-0984}, mesh = {Adult ; Aged ; Aging ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Metabolome ; Metagenomics ; Singapore ; Young Adult ; }, abstract = {The age-associated alterations in microbiomes vary across populations due to the influence of genetics and lifestyles. To the best of our knowledge, the microbial changes associated with aging have not yet been investigated in Singapore adults. We conducted shotgun metagenomic sequencing of fecal and saliva samples, as well as fecal metabolomics to characterize the gut and oral microbial communities of 62 healthy adult male Singaporeans, including 32 young subjects (age, 23.1 ± 1.4 years) and 30 elderly subjects (age, 69.0 ± 3.5 years). We identified 8 gut and 13 oral species that were differentially abundant in elderly compared to young subjects. By combining the gut and oral microbiomes, 25 age-associated oral-gut species connections were identified. Moreover, oral bacteria Acidaminococcus intestine and Flavonifractor plautii were less prevalent/abundant in elderly gut samples than in young gut samples, whereas Collinsella aerofaciens and Roseburia hominis showed the opposite trends. These results indicate the varied gut-oral communications with aging. Subsequently, we expanded the association studies on microbiome, metabolome and host phenotypic parameters. In particular, Eubacterium eligens increased in elderly compared to young subjects, and was positively correlated with triglycerides, which implies that the potential role of E. eligens in lipid metabolism is altered during the aging process. Our results demonstrated aging-associated changes in the gut and oral microbiomes, as well as the connections between metabolites and host-microbe interactions, thereby deepening the understanding of alterations in the human microbiome during the aging process in a Singapore population.}, } @article {pmid35548466, year = {2022}, author = {Feng, R and Zhang, T and Kayani, MUR and Wang, Z and Shen, Y and Su, KL and Bielike, K and Chen, L}, title = {Patients with Primary and Secondary Bile Duct Stones Harbor Distinct Biliary Microbial Composition and Metabolic Potential.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {881489}, pmid = {35548466}, issn = {2235-2988}, mesh = {Bacteria/genetics ; *Gallstones/genetics/microbiology ; Humans ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {INTRODUCTION: Cholelithiasis has a high incidence worldwide and limited treatment options due to its poorly understood pathogenesis. Furthermore, the role of biliary microbiota in cholelithiasis remains understudied. To address these questions, we performed microbial sequencing from biliary samples from primary bile duct stone (PBDS) and secondary bile duct stone (SBDS) patients.

RESULTS: We analyzed in total 45 biliary samples, including those from cholelithiasis patients with PBDS or SBDS and people with other digestive diseases. 16S rRNA sequencing showed the bacteria family Alcaligenaceae increased in relative abundance in the lithiasis group compared with the non-lithiasis group. In addition, the PBDS group showed significantly lower bacterial diversity than SBDS, with Propionibacteriaceae, Sphingomonadaceae, and Lactobacillaceae as the most significant bacteria families decreased in relative abundance. We further performed whole metagenomic shotgun sequencing (wMGS) and found increased ability of biofilm synthesis and the ability to sense external stimuli in PBDS based on functional annotation of mapped reads. From genome-resolved analysis of the samples, we identified 36 high-quality draft bacterial genome sequences with completion ≥70% and contamination ≤10%. Most of these genomes were classified into Proteobacteria, Firmicutes, or Actinobacteria.

CONCLUSIONS: Our findings indicated that there is a subtle impact on biliary microbiome from cholelithiasis while the difference is more pronounced between the PBDS and SBDS. It was revealed that the diversity of biliary microbiota in PBDS is lower, while some metabolic pathways are up-regulated, including those linked to higher incidence of different types of cancer, providing new insights for the understanding of cholelithiasis with different origin.}, } @article {pmid35546409, year = {2022}, author = {Liu, S and Moon, CD and Zheng, N and Huws, S and Zhao, S and Wang, J}, title = {Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {76}, pmid = {35546409}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Genomics ; *Metagenome/genetics ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Although there is now an extensive understanding of the diversity of microbial life on earth through culture-independent metagenomic DNA sequence analyses, the isolation and cultivation of microbes remains critical to directly study them and confirm their metabolic and physiological functions, and their ecological roles. The majority of environmental microbes are as yet uncultured however; therefore, bringing these rare or poorly characterized groups into culture is a priority to further understand microbiome functions. Moreover, cultivated isolates may find utility in a range of applications, such as new probiotics, biocontrol agents, and agents for industrial processes. The growing abundance of metagenomic and meta-transcriptomic sequence information from a wide range of environments provides more opportunities to guide the isolation and cultivation of microbes of interest. In this paper, we discuss a range of successful methodologies and applications that have underpinned recent metagenome-guided isolation and cultivation of microbe efforts. These approaches include determining specific culture conditions to enrich for taxa of interest, to more complex strategies that specifically target the capture of microbial species through antibody engineering and genome editing strategies. With the greater degree of genomic information now available from uncultivated members, such as via metagenome-assembled genomes, the theoretical understanding of their cultivation requirements will enable greater possibilities to capture these and ultimately gain a more comprehensive understanding of the microbiomes. Video Abstract.}, } @article {pmid35545448, year = {2022}, author = {Chen, DW and Garud, NR}, title = {Rapid evolution and strain turnover in the infant gut microbiome.}, journal = {Genome research}, volume = {32}, number = {6}, pages = {1124-1136}, pmid = {35545448}, issn = {1549-5469}, support = {R25 MH109172/MH/NIMH NIH HHS/United States ; T32 GM139790/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Feces ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Metagenomics ; Mothers ; }, abstract = {Although the ecological dynamics of the infant gut microbiome have been intensely studied, relatively little is known about evolutionary dynamics in the infant gut microbiome. Here we analyze longitudinal fecal metagenomic data from more than 700 infants and their mothers over the first year of life and find that the evolutionary dynamics in infant gut microbiomes are distinct from those of adults. We find evidence for more than a 10-fold increase in the rate of evolution and strain turnover in the infant gut compared with healthy adults, with the mother-infant transition at delivery being a particularly dynamic period in which gene loss dominates. Within a few months after birth, these dynamics stabilize, and gene gains become increasingly frequent as the microbiome matures. We furthermore find that evolutionary changes in infants show signatures of being seeded by a mixture of de novo mutations and transmissions of pre-evolved lineages from the broader family. Several of these evolutionary changes occur in parallel across infants, highlighting candidate genes that may play important roles in the development of the infant gut microbiome. Our results point to a picture of a volatile infant gut microbiome characterized by rapid evolutionary and ecological change in the early days of life.}, } @article {pmid35545042, year = {2022}, author = {Russell, A and Copio, JN and Shi, Y and Kang, S and Franklin, CL and Ericsson, AC}, title = {Reduced housing density improves statistical power of murine gut microbiota studies.}, journal = {Cell reports}, volume = {39}, number = {6}, pages = {110783}, pmid = {35545042}, issn = {2211-1247}, support = {U42 OD010918/OD/NIH HHS/United States ; U42 RR014821/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Housing ; Mice ; Mice, Inbred C57BL ; }, abstract = {The gut microbiome of humans and animals is critical to host health. Mice are used to investigate the microbiome and its influences; however, the predictive value of such studies is hindered by cage effects due to coprophagy. Our objectives were to evaluate the influence of cage density on the statistical power to detect treatment-dependent effects of a selective pressure on microbiome composition. C57BL/6 mice were separated into groups of 2 or 4 mice per cage and then assigned to groups receiving enrofloxacin, broad-spectrum antibiotics, or control. Fecal samples were collected at weeks 0, 1, and 4, along with contents of the jejunum and cecum. Bacterial DNA analysis examined microbiome richness, diversity, and variability within and between cages. Statistical analyses reveal that reduced housing density consistently results in comparable susceptibility to antibiotics, reduced cage effects, and increased statistical power to detect treatment-associated effects, justifying the practice of reduced housing density.}, } @article {pmid35544980, year = {2022}, author = {Patil, MP and Woo, HE and Lee, IC and Nakashita, S and Kim, K and Kim, JO and Kim, K}, title = {A microcosm study of microbial community profiles during sediment remediation using pyrolyzed oyster shells.}, journal = {Journal of environmental management}, volume = {316}, number = {}, pages = {115229}, doi = {10.1016/j.jenvman.2022.115229}, pmid = {35544980}, issn = {1095-8630}, mesh = {Animals ; Bacteria/genetics ; Geologic Sediments/microbiology ; *Microbiota ; *Ostreidae/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The accumulation of organic and inorganic components in sediments leads to a deterioration in the environment and an imbalance in the coastal ecosystem. Currently, capping is the most effective technology for remediating polluted sediment and restoring ecosystems. A microcosm experiment was designed using pyrolyzed oyster shell (POS). These were mixed in with coastal sediment or added as a capping layer. The results showed that POS effectively decreased pollutants, including PO4-P and NH4-N. Metagenomics analysis was performed using 16S rRNA gene sequencing and the most abundant phyla identified in the POS treated and untreated sediments were Proteobacteria, followed by Firmicutes, Bacteroidetes, Chloroflexi, Fusobacteria, Nitrospirae, and Spirochaetes. The relative abundance of Proteobacteria members of the Class Gammaproteobacteria significantly increased, but Deltaproteobacteria gradually decreased throughout the experiment in POS-covered sediment. This suggests that the POS effectively promoted a shift from anaerobic to facultative anaerobic or aerobic microbial communities in the sediment. Dominant species of facultative anaerobic or microaerophilic bacteria from the order Chromatiales and phylum Nitrospirae were observed in the POS-covered sediment. Based on these study results, it can be concluded that POS is an effective covering material for sediment remediation and restores the microbial communities in sediments.}, } @article {pmid35544149, year = {2021}, author = {Yuki, Y and Nojima, M and Hosono, O and Tanaka, H and Kimura, Y and Satoh, T and Imoto, S and Uematsu, S and Kurokawa, S and Kashima, K and Mejima, M and Nakahashi-Ouchida, R and Uchida, Y and Marui, T and Yoshikawa, N and Nagamura, F and Fujihashi, K and Kiyono, H}, title = {Oral MucoRice-CTB vaccine for safety and microbiota-dependent immunogenicity in humans: a phase 1 randomised trial.}, journal = {The Lancet. Microbe}, volume = {2}, number = {9}, pages = {e429-e440}, doi = {10.1016/S2666-5247(20)30196-8}, pmid = {35544149}, issn = {2666-5247}, mesh = {Animals ; *COVID-19 ; COVID-19 Vaccines ; *Cholera ; Diarrhea ; Humans ; Immunogenicity, Vaccine ; Immunoglobulin A ; Immunoglobulin G ; Male ; *Microbiota ; SARS-CoV-2 ; *Vaccines ; }, abstract = {BACKGROUND: There are an estimated 1·3-4·0 million cases of cholera and 20 000-140 000 cholera-related deaths worldwide each year. The rice-based cholera toxin B subunit (CTB) vaccine, MucoRice-CTB, is an oral candidate vaccine that does not require a cold chain, has shown efficacy in animal models, and could be of benefit in places where there is a paucity of medical infrastructure. We aim to assess the safety, tolerability, and immunogenicity of MucoRice-CTB in humans.

METHODS: We did a double-blind, randomised, placebo-controlled, dose-escalation, phase 1 study at one centre in Tokyo, Japan. Eligible participants were healthy adult men with measurable serum and faecal antibodies against CTB at screening. Participants were excluded if they had allergy to rice; history of cholera or travellers' diarrhoea; poorly controlled constipation; abnormal results on hepatic, renal, or haematological screening tests; use of any over-the-counter drugs within 7 days before first administration; inability to use a medically acceptable means of contraception; or other reasons by medical judgment of the investigator. Three dose cohorts of participants were randomly assigned by block to receive oral MucoRice-CTB (1 g, 3 g, or 6 g) or placebo (1 g, 3 g, or 6 g), once every 2 weeks for 8 weeks (for a total of 4 doses). The dose groups were performed sequentially, and each dose cohort was completed before the higher dose cohort began. All medical staff, participants, and most trial staff were masked to treatment allocation. The primary outcomes were safety and tolerability, measured by 12-lead electrocardiogram; vital signs; haematology, biochemistry, and urinalysis; rice protein-specific serum IgE antibody concentration; and monitoring of adverse events. Participants were assessed at baseline and at 1, 2, 4, 6, 8, and 16 weeks after the first administration of vaccine or placebo. The safety analysis set included all participants enrolled in the trial who received at least one dose of the study drug or placebo and were compliant with good clinical practice. The full analysis population included all participants enrolled in the trial who received at least one dose of the study drug and for whom any data were obtained after the start of study drug administration. Meta-genomic analysis of study participants was performed using bacterial DNA from faecal samples before vaccination. This trial is registered with UMIN.ac.jp, UMIN000018001.

FINDINGS: Between June 23, 2015, and May 31, 2016, 226 participants were recruited and assessed for eligibility. 166 participants were excluded based on health condition or schedule. We then randomly selected 60 male volunteers aged 20-40 years who were enrolled and assigned to MucoRice-CTB (10 participants assigned to 1 g, 10 participants assigned to 3 g, and 10 participants assigned to 6 g), or placebo (10 participants assigned to 1 g, 10 participants assigned to 3 g, and 10 participants assigned to 6 g). All participants received at least one dose of study drug or placebo and were included in the safety analyses. Two participants given MucoRice-CTB 3 g and one participant given MucoRice-CTB 6 g were lost to follow-up and excluded from the efficacy analysis. Serum CTB-specific IgG and IgA antibody concentrations in participants who received 6 g MucoRice-CTB increased significantly in both a time-dependent and dose-dependent manner compared with those in the placebo groups (p for interaction=0·002 for IgG, p=0·004 for IgA). Genome analysis of subjects' faeces before vaccination revealed that compared to non-responders, responders had a gut microbiota of higher diversity with the presence of Escherichia coli and Shigella spp. 28 (93%) of 30 participants who received MucoRice-CTB at any dose had at least one adverse event during the study period, compared with 30 (100%) of 30 participants given placebo. Grade 3 or higher adverse events were reported in four participants in the MucoRice-CTB group (5 events) and four participants in the placebo group (10 events). The most common serious adverse event was haemoglobin decreased (2 events in 2 participants in the pooled MucoRice-CTB group, 2 events in 2 participants in the placebo group; all grade 3).

INTERPRETATION: Participants given MucoRice-CTB showed increased CTB-specific serum IgG and IgA antibody concentrations without inducing serious adverse events, indicating that MucoRice-CTB could be a safe and potent vaccine to prevent diarrhoeal disease. MucoRice-CTB induced neutralising antibodies against diarrhoeal toxins in a gut microbiota-dependent manner. A similar phase 1 trial will be done with participants of other ethnicities to substantiate our findings.

FUNDING: Translational Research Acceleration Network Program of Japan Agency for Medical Research and Development; Ministry of Education, Culture, Sports, Science and Technology, Japan; Science and Technology Research Partnership for Sustainable Development; Grant-in-Aid for Scientific Research (S) (18H05280) (to H K) from the Japan Society for the Promotion of Science (JSPS); Grant-in-Aid for Young Scientists (B) (16K16144) (to Y K) from JSPS; Grant-in-Aid for Young Scientists (18K18148) (to Y K) from JSPS; Grant from International Joint Usage/Research Center (K3002), the Institute of Medical Science, University of Tokyo.}, } @article {pmid35544065, year = {2022}, author = {Tsitsiklis, A and Osborne, CM and Kamm, J and Williamson, K and Kalantar, K and Dudas, G and Caldera, S and Lyden, A and Tan, M and Neff, N and Soesanto, V and Harris, JK and Ambroggio, L and Maddux, AB and Carpenter, TC and Reeder, RW and Locandro, C and Simões, EAF and Leroue, MK and Hall, MW and Zuppa, AF and Carcillo, J and Meert, KL and Sapru, A and Pollack, MM and McQuillen, PS and Notterman, DA and Dean, JM and Zinter, MS and Wagner, BD and DeRisi, JL and Mourani, PM and Langelier, CR}, title = {Lower respiratory tract infections in children requiring mechanical ventilation: a multicentre prospective surveillance study incorporating airway metagenomics.}, journal = {The Lancet. Microbe}, volume = {3}, number = {4}, pages = {e284-e293}, pmid = {35544065}, issn = {2666-5247}, support = {UG1 HD050096/HD/NICHD NIH HHS/United States ; UG1 HD063108/HD/NICHD NIH HHS/United States ; R01 HL155418/HL/NHLBI NIH HHS/United States ; K23 HL138461/HL/NHLBI NIH HHS/United States ; UG1 HD034116/HD/NICHD NIH HHS/United States ; U01 HD049934/HD/NICHD NIH HHS/United States ; UG1 HD049981/HD/NICHD NIH HHS/United States ; K23 HL146936/HL/NHLBI NIH HHS/United States ; UG1 HD049983/HD/NICHD NIH HHS/United States ; UG1 HD083170/HD/NICHD NIH HHS/United States ; UG1 HD083166/HD/NICHD NIH HHS/United States ; R01 HL124103/HL/NHLBI NIH HHS/United States ; UG1 HD083171/HD/NICHD NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Child ; Cohort Studies ; Critical Illness ; Haemophilus influenzae ; Humans ; Metagenomics ; Moraxella catarrhalis ; Prospective Studies ; Respiration, Artificial ; *Respiratory Syncytial Virus, Human ; *Respiratory Tract Infections/diagnosis ; United States ; }, abstract = {BACKGROUND: Lower respiratory tract infections (LRTI) are a leading cause of critical illness and mortality in mechanically ventilated children; however, the pathogenic microbes frequently remain unknown. We combined traditional diagnostics with metagenomic next generation sequencing (mNGS) to evaluate the cause of LRTI in critically ill children.

METHODS: We conducted a prospective, multicentre cohort study of critically ill children aged 31 days to 17 years with respiratory failure requiring mechanical ventilation (>72 h) in the USA. By combining bacterial culture and upper respiratory viral PCR testing with mNGS of tracheal aspirate collected from all patients within 24 h of intubation, we determined the prevalence, age distribution, and seasonal variation of viral and bacterial respiratory pathogens detected by either method in children with or without LRTI.

FINDINGS: Between Feb 26, 2015, and Dec 31, 2017, of the 514 enrolled patients, 397 were eligible and included in the study (276 children with LRTI and 121 with no evidence of LRTI). A presumptive microbiological cause was identified in 255 (92%) children with LRTI, with respiratory syncytial virus (127 [46%]), Haemophilus influenzae (70 [25%]), and Moraxella catarrhalis (65 [24%]) being most prevalent. mNGS identified uncommon pathogens including Ureaplasma parvum and Bocavirus. Co-detection of viral and bacterial pathogens occurred in 144 (52%) patients. Incidental carriage of potentially pathogenic microbes occurred in 82 (68%) children without LRTI, with rhinovirus (30 [25%]) being most prevalent. Respiratory syncytial virus (p<0·0001), H influenzae (p=0·0006), and M catarrhalis (p=0·0002) were most common in children younger than 5 years. Viral and bacterial LRTI occurred predominantly during winter months.

INTERPRETATION: These findings demonstrate that respiratory syncytial virus, H influenzae, and M catarrhalis contribute disproportionately to severe paediatric LRTI, co-infections are common, and incidental carriage of potentially pathogenic microbes occurs frequently. Further, we provide a framework for future epidemiological and emerging pathogen surveillance studies, highlighting the potential for metagenomics to enhance clinical diagnosis.

FUNDING: US National Institutes of Health and CZ Biohub.}, } @article {pmid35543338, year = {2022}, author = {Wang, S and Wei, L and Gao, Y and Rong, Y and Zha, Z and Lyu, Y and Feng, Z}, title = {Novel amikacin resistance genes identified from human gut microbiota by functional metagenomics.}, journal = {Journal of applied microbiology}, volume = {133}, number = {2}, pages = {898-907}, doi = {10.1111/jam.15615}, pmid = {35543338}, issn = {1365-2672}, support = {KYYZ2021//Fundamental Research Funds for the Central Universities/ ; 31770049//National Natural Science Foundation of China/ ; }, mesh = {*Amikacin/pharmacology ; Aminoglycosides/pharmacology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Kanamycin ; Methyltransferases/genetics ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/genetics ; }, abstract = {AIMS: The aim of this study was to evaluate the diversity and potential for horizontal transfer of amikacin resistance genes from the human gut.

METHODS AND RESULTS: A library of human faecal microbiota was constructed and subjected to functional screening for amikacin resistance. In total, five amikacin resistance genes that conferred relatively high amikacin resistance, with minimum inhibitory concentrations (MICs) ranging from 64 to >512, were identified from the library, including a novel aminoglycoside acetyltransferase gene and a 16S rRNA methyltransferase (MTase) gene, labelled aac (6')-Iao and rmtI, respectively. AAC(6')-Iao showed the highest identity of 48% to AAC(6')-Ian from a clinical isolate Serratia marcescens, whereas RmtI shared the closest amino acid identity of 32% with ArmA from Klebsiella pneumonia. The MICs of these five subclones to six commonly used aminoglycosides were determined. Susceptibility analysis indicated that RmtI was associated with high resistance phenotype to 4,6-disubstituted 2-DOS aminoglycosides, whereas AAC(6')-Iao conferred resistance to amikacin and kanamycin. In addition, kinetic parameters of AAC(6')-Iao were determined, suggesting a strong catalytic effect on amikacin and kanamycin.

CONCLUSIONS: Antibiotic resistance genes with low identity to known sequences can be uncovered by functional metagenomics. In addition, the diversity and prevalence of amikacin resistance genes merit further investigation in extended habitats, especially the 16S rRNA MTase gene that might have been underestimated in previous cognition.

Two novel amikacin resistance genes were identified in this study, including a 16S rRNA methyltransferase gene rmtI and an aminoglycoside acetyltransferase gene aac(6')-Iao. This work would contribute to the in-depth study of the diversity and horizontal transfer potential of amikacin resistance genes in the microbiome of the human gut.}, } @article {pmid35538082, year = {2022}, author = {Shin, J and Noh, JR and Choe, D and Lee, N and Song, Y and Cho, S and Kang, EJ and Go, MJ and Ha, SK and Kim, JH and Kim, YH and Kim, KS and Kim, BC and Lee, CH and Cho, BK}, title = {Comprehensive 16S rRNA and metagenomic data from the gut microbiome of aging and rejuvenation mouse models.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {197}, pmid = {35538082}, issn = {2052-4463}, support = {2019M3A9F3065867//National Research Foundation of Korea (NRF)/ ; 2018M3A9H3024759//National Research Foundation of Korea (NRF)/ ; }, mesh = {*Aging/genetics ; Animals ; Disease Models, Animal ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Mice ; *RNA, Ribosomal, 16S/genetics ; Rejuvenation ; }, abstract = {The gut microbiota is associated with the health and longevity of the host. A few methods, such as fecal microbiota transplantation and oral administration of probiotics, have been applied to alter the gut microbiome and promote healthy aging. The changes in host microbiomes still remain poorly understood. Here, we characterized both the changes in gut microbial communities and their functional potential derived from colon samples in mouse models during aging. We achieved this through four procedures including co-housing, serum injection, parabiosis, and oral administration of Akkermansia muciniphila as probiotics using bacterial 16 S rRNA sequencing and shotgun metagenomic sequencing. The dataset comprised 16 S rRNA sequencing (36,249,200 paired-end reads, 107 sequencing data) and metagenomic sequencing data (307,194,369 paired-end reads, 109 sequencing data), characterizing the taxonomy of bacterial communities and their functional potential during aging and rejuvenation. The generated data expand the resources of the gut microbiome related to aging and rejuvenation and provide a useful dataset for research on developing therapeutic strategies to achieve healthy active aging.}, } @article {pmid35536051, year = {2022}, author = {Seitz, VA and McGivern, BB and Daly, RA and Chaparro, JM and Borton, MA and Sheflin, AM and Kresovich, S and Shields, L and Schipanski, ME and Wrighton, KC and Prenni, JE}, title = {Variation in Root Exudate Composition Influences Soil Microbiome Membership and Function.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {11}, pages = {e0022622}, pmid = {35536051}, issn = {1098-5336}, support = {P30 CA046934/CA/NCI NIH HHS/United States ; P30CA046934//CU | Anschutz Medical Campus, University of Colorado (CU Anschutz)/ ; }, mesh = {Exudates and Transudates ; *Microbiota/physiology ; Plant Growth Regulators/metabolism ; Plant Roots/metabolism ; Plants/genetics ; RNA, Ribosomal, 16S/genetics/metabolism ; Rhizosphere ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {Root exudation is one of the primary processes that mediate interactions between plant roots, microorganisms, and the soil matrix, yet the mechanisms by which exudation alters microbial metabolism in soils have been challenging to unravel. Here, utilizing distinct sorghum genotypes, we characterized the chemical heterogeneity between root exudates and the effects of that variability on soil microbial membership and metabolism. Distinct exudate chemical profiles were quantified and used to formulate synthetic root exudate treatments: a high-organic-acid treatment (HOT) and a high-sugar treatment (HST). To parse the response of the soil microbiome to different exudate regimens, laboratory soil reactors were amended with these root exudate treatments as well as a nonexudate control. Amplicon sequencing of the 16S rRNA gene illustrated distinct microbial diversity patterns and membership in response to HST, HOT, or control amendments. Exometabolite changes reflected these microbial community changes, and we observed enrichment of organic and amino acids, as well as possible phytohormones in the HST relative to the HOT and control. Linking the metabolic capacity of metagenome-assembled genomes in the HST to the exometabolite patterns, we identified microorganisms that could produce these phytohormones. Our findings emphasize the tractability of high-resolution multiomics tools to investigate soil microbiomes, opening the possibility of manipulating native microbial communities to improve specific soil microbial functions and enhance crop production. IMPORTANCE Decrypting the chemical interactions between plant roots and the soil microbiome is a gateway for future manipulation and management of the rhizosphere, a soil compartment critical to promoting plant fitness and yields. Our experimental results demonstrate how soil microbial community and genomic diversity is influenced by root exudates of differing chemical compositions and how changes in this microbiome result in altered production of plant-relevant metabolites. Together, these findings demonstrate the tractability of high-resolution multiomics tools to investigate soil microbiomes and provide new information on plant-soil environments useful for the development of efficient and precise microbiota management strategies in agricultural systems.}, } @article {pmid35536037, year = {2022}, author = {Hu, C and Beyda, ND and Garey, KW}, title = {A Vancomycin HPLC Assay for Use in Gut Microbiome Research.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0168821}, pmid = {35536037}, issn = {2165-0497}, support = {U01 AI124290/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents ; Chromatography, High Pressure Liquid/methods ; *Gastrointestinal Microbiome ; Humans ; Reproducibility of Results ; *Vancomycin/pharmacokinetics ; }, abstract = {The human microbiome project has revolutionized our understanding of the interaction between commensal microbes and human health. By far, the biggest perturbation of the microbiome involves use of broad-spectrum antibiotics excreted in the gut. Thus, pharmacodynamics of microbiome changes in relation to drug exposure pharmacokinetics is an emerging field. However, reproducibility studies are necessary to develop the field. A simple and fast high-performance liquid chromatography-photodiode array detector (HPLC) method was validated for quantitative fecal vancomycin analysis. Reproducibility of results were tested based on sample storage time, homogeneity of antibiotic within stool, and concentration consistency after lyophilization. The HPLC method enabled the complete elution of vancomycin within ~4.2 min on the reversed-phase C18 column under the isocratic elution mode, with excellent recovery (85% to 110%) over a 4-log, quantitative range (0.4-100 μg/mL). Relative standard derivations (RSD) of intra-day and inter-day results ranged from 0.4% to 5.4%. Using sample stool aliquots of various weights consistently demonstrated similar vancomycin concentrations (mean RSD: 6%; range: 2-16%). After correcting for water concentrations, vancomycin concentrations obtained after lyophilization were similar to the concentrations obtained from the original samples (RSD less than 10%). These methodologies establish sample condition standards for a quantitative HPLC to enable vancomycin pharmacokinetic studies with the human microbiome. IMPORTANCE Research on antibiotic effect on the gut microbiome is an emerging field with standardization of research methods needed. In this study, a simple and fast high-performance liquid chromatography method was validated for quantitative fecal vancomycin analysis. Reproducibility of results were tested to standardize storage time, homogeneity of antibiotic within stool, and concentration consistency after lyophilization. These methodologies establish sample condition standards for a quantitative HPLC to enable vancomycin pharmacokinetic studies with the human microbiome.}, } @article {pmid35536006, year = {2022}, author = {Oliver, A and Xue, Z and Villanueva, YT and Durbin-Johnson, B and Alkan, Z and Taft, DH and Liu, J and Korf, I and Laugero, KD and Stephensen, CB and Mills, DA and Kable, ME and Lemay, DG}, title = {Association of Diet and Antimicrobial Resistance in Healthy U.S. Adults.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0010122}, pmid = {35536006}, issn = {2150-7511}, support = {F32 HD093185/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Diet ; Dietary Fiber ; Drug Resistance, Bacterial/genetics ; *Gastrointestinal Microbiome ; Humans ; Phylogeny ; }, abstract = {Antimicrobial resistance (AMR) represents a significant source of morbidity and mortality worldwide, with expectations that AMR-associated consequences will continue to worsen throughout the coming decades. Since resistance to antibiotics is encoded in the microbiome, interventions aimed at altering the taxonomic composition of the gut might allow us to prophylactically engineer microbiomes that harbor fewer antibiotic resistant genes (ARGs). Diet is one method of intervention, and yet little is known about the association between diet and antimicrobial resistance. To address this knowledge gap, we examined diet using the food frequency questionnaire (FFQ; habitual diet) and 24-h dietary recalls (Automated Self-Administered 24-h [ASA24[®]] tool) coupled with an analysis of the microbiome using shotgun metagenome sequencing in 290 healthy adult participants of the United States Department of Agriculture (USDA) Nutritional Phenotyping Study. We found that aminoglycosides were the most abundant and prevalent mechanism of AMR in these healthy adults and that aminoglycoside-O-phosphotransferases (aph3-dprime) correlated negatively with total calories and soluble fiber intake. Individuals in the lowest quartile of ARGs (low-ARG) consumed significantly more fiber in their diets than medium- and high-ARG individuals, which was concomitant with increased abundances of obligate anaerobes, especially from the family Clostridiaceae, in their gut microbiota. Finally, we applied machine learning to examine 387 dietary, physiological, and lifestyle features for associations with antimicrobial resistance, finding that increased phylogenetic diversity of diet was associated with low-ARG individuals. These data suggest diet may be a potential method for reducing the burden of AMR. IMPORTANCE Antimicrobial resistance (AMR) represents a considerable burden to health care systems, with the public health community largely in consensus that AMR will be a major cause of death worldwide in the coming decades. Humans carry antibiotic resistance in the microbes that live in and on us, collectively known as the human microbiome. Diet is a powerful method for shaping the human gut microbiome and may be a tractable method for lessening antibiotic resistance, and yet little is known about the relationship between diet and AMR. We examined this relationship in healthy individuals who contained various abundances of antibiotic resistance genes and found that individuals who consumed diverse diets that were high in fiber and low in animal protein had fewer antibiotic resistance genes. Dietary interventions may be useful for lessening the burden of antimicrobial resistance and might ultimately motivate dietary guidelines which will consider how nutrition can reduce the impact of infectious disease.}, } @article {pmid35536001, year = {2022}, author = {Higginson, EE and Sayeed, MA and Pereira Dias, J and Shetty, V and Ballal, M and Srivastava, SK and Willis, I and Qadri, F and Dougan, G and Mutreja, A}, title = {Microbiome Profiling of Enterotoxigenic Escherichia coli (ETEC) Carriers Highlights Signature Differences between Symptomatic and Asymptomatic Individuals.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0015722}, pmid = {35536001}, issn = {2150-7511}, support = {/WT_/Wellcome Trust/United Kingdom ; 106158/Z/14/Z//Wellcome Trust (WT)/ ; }, mesh = {Adult ; Bacteria/genetics ; Child ; Diarrhea/microbiology ; *Enterotoxigenic Escherichia coli/genetics ; *Escherichia coli Infections/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; }, abstract = {Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrhea in children in low- and middle-income countries (LMICs). However, large-scale pathogen burden studies in children have identified ETEC in the guts of both symptomatic patients and controls. The factors that influence this balance are poorly understood, but it is postulated that the gut microbiome may play a role in either resistance or progression to disease. In this study, we profiled the microbiomes of children and adults from Bangladesh who were asymptomatically or symptomatically infected with ETEC. Symptomatic patients had significantly higher numbers of sequenced reads mapping to both E. coli and two ETEC toxins, suggesting higher bacterial burden. They were also significantly more likely to be coinfected with enteroaggregative E. coli (EAEC) and had higher proportions of other Gammaproteobacteria, including Klebsiella, Salmonella, and Haemophilus. Colonization with ETEC was also associated with increased prevalence of antimicrobial resistance (AMR) genes, most notably those of the β-lactamase class. Taxonomic profiles were distinctly different between all groups in both species richness and composition, although the direction of these changes was different in adults and children. As seen previously, children with high E. coli burdens also had higher proportions of Streptococcus spp., while healthy children were more heavily colonized by Bifidobacterium spp. Our study provides insight into the microbiome changes that occur upon infection with ETEC in an endemic setting and provides rationale for future studies investigating how the microbiome may protect or predispose individuals to symptomatic infections with gastrointestinal pathogens. IMPORTANCE Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrhea in children in low- and middle-income countries. However, these bacteria are often identified in both patients and healthy controls. We do not yet understand why only some people get sick, but it has been suggested that the gut microbiome might play a role. In this study, we used metagenomic sequencing to profile the gut microbiomes of individuals in Bangladesh, with or without a symptomatic ETEC infection. In general, individuals with high levels of ETEC also harbored other pathogenic E. coli strains, higher proportions of Gammaproteobacteria such as Salmonella and Klebsiella, and a higher burden of antimicrobial resistance genes in their guts. Healthy children, in contrast, had higher levels of bifidobacteria. These data confirm that the composition of the gut microbiome is different between symptomatic and asymptomatic people and provides important preliminary information on the impact of the gut microbiome in intestinal infections.}, } @article {pmid35535499, year = {2022}, author = {Nguyen, TTM and Mai, VH and Kim, HS and Kim, D and Seo, M and An, YJ and Park, S}, title = {Real-Time Monitoring of Host-Gut Microbial Interspecies Interaction in Anticancer Drug Metabolism.}, journal = {Journal of the American Chemical Society}, volume = {144}, number = {19}, pages = {8529-8535}, doi = {10.1021/jacs.1c10998}, pmid = {35535499}, issn = {1520-5126}, mesh = {*Antineoplastic Agents/metabolism/pharmacology ; Bacteria/metabolism ; Fluorouracil/pharmacology ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {Gut microbiome can affect drug metabolism considerably, leading to modified drug response. However, quantitative estimation of host vs. microbial contributions in a living host-gut microbiome system has been challenging. Using the interspecies system of Caenorhabditis elegans and gut bacteria, we developed a real-time approach for monitoring their metabolic interaction in vivo during anticancer drug 5-fluorouracil (5-FU) metabolism. The fluorine NMR-based approach yielded the quantitative contributions to the host 5-FU metabolism made by human gut-microbial species of variable genetic backgrounds. It also experimentally confirmed a bacterial gene-metabolism relationship. Differential 5-FU catabolism among bacterial substrains and the contributions to the host metabolism, unobservable by conventional 16S rRNA metagenomic sequencing, were also found. The metabolic contributions could be correlated with phenotypic developmental toxicity of 5-FU to the host fed with different substrains. Our convenient platform should help to reveal heterogeneity in host-gut microbiome interactions for many drugs in a living symbiotic system.}, } @article {pmid35534630, year = {2022}, author = {Feng, X and Cheng, H and Portik, D and Li, H}, title = {Metagenome assembly of high-fidelity long reads with hifiasm-meta.}, journal = {Nature methods}, volume = {19}, number = {6}, pages = {671-674}, pmid = {35534630}, issn = {1548-7105}, support = {R01 HG010040/HG/NHGRI NIH HHS/United States ; U01 HG010971/HG/NHGRI NIH HHS/United States ; }, mesh = {Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Microbiota/genetics ; Sequence Analysis, DNA ; Software ; }, abstract = {De novo assembly of metagenome samples is a common approach to the study of microbial communities. Current metagenome assemblers developed for short sequence reads or noisy long reads were not optimized for accurate long reads. We thus developed hifiasm-meta, a metagenome assembler that exploits the high accuracy of recent data. Evaluated on seven empirical datasets, hifiasm-meta reconstructed tens to hundreds of complete circular bacterial genomes per dataset, consistently outperforming other metagenome assemblers.}, } @article {pmid35533856, year = {2022}, author = {Long, S and Liu, X and Chen, J and Zhao, L and Pavlostathis, SG}, title = {Effect of tetracycline on bio-electrochemically assisted anaerobic methanogenic systems: Process performance, microbial community structure, and functional genes.}, journal = {The Science of the total environment}, volume = {837}, number = {}, pages = {155756}, doi = {10.1016/j.scitotenv.2022.155756}, pmid = {35533856}, issn = {1879-1026}, mesh = {Anaerobiosis ; Anti-Bacterial Agents/metabolism/pharmacology ; Bacteria/metabolism ; Bioreactors/microbiology ; Methane/metabolism ; *Microbiota ; Propionates/metabolism ; Tetracycline/pharmacology ; *Wastewater/microbiology ; }, abstract = {Bio-electrochemically assisted anaerobic methanogenic systems (An-BES) are highly effective in wastewater treatment for methane production and degradation of toxic compounds. However, information on the treatment of antibiotic-bearing wastewater in An-BES is still very limited. This study therefore investigated the effect of tetracycline (TC) on the performance, microbial community, as well as functional and antibiotic resistance genes of An-BES. TC at 1 and 5 mg/L inhibited methane production by less than 4.8% compared to the TC-free control. At 10 mg/L TC, application of 0.5 and 1.0 V decreased methane production by 14 and 9.6%, respectively. Under the effect of 1-10 mg/L TC, application of 1.0 V resulted in a decrease of current from 42.3 to 2.8 mA. TC was mainly removed by adsorption; its removal extent increased by 19.5 and 32.9% with application of 0.5 and 1.0 V, respectively. At 1.0 V, current output was not recovered with the addition of granular activated carbon, which completely removed TC by adsorption. Metagenomic analysis showed that propionate oxidizing bacteria and methanogens were more abundant in electrode biofilms than in suspended culture. Antibiotic resistance genes (ARGs) were less abundant in biofilms than in suspended culture, regardless of whether voltage was applied or not. Application of 1.0 V resulted in the enrichment of Geobacter in the anode and Methanobacterium in the cathode. TC inhibited exoelectrogens, propionate oxidizing bacteria, and the methylmalonyl CoA pathway, leading to a decrease of current output, COD consumption, and methane production. These findings deepen our understanding of the inhibitory effect of TC in An-BES towards efficient bioenergy recovery from antibiotic-bearing wastewater, as well as the response of functional microorganisms to TC in such systems.}, } @article {pmid35533800, year = {2022}, author = {Bessède, E and Mégraud, F}, title = {Microbiota and gastric cancer.}, journal = {Seminars in cancer biology}, volume = {86}, number = {Pt 3}, pages = {11-17}, doi = {10.1016/j.semcancer.2022.05.001}, pmid = {35533800}, issn = {1096-3650}, mesh = {Humans ; Mice ; Animals ; *Stomach Neoplasms/etiology ; *Helicobacter Infections/complications/microbiology/pathology ; *Epstein-Barr Virus Infections/complications ; Herpesvirus 4, Human ; *Helicobacter pylori/genetics ; *Microbiota ; }, abstract = {The discovery of Helicobacter pylori in 1982 drew to an end the stomach being considered as a sterile organ. Later, the progress in molecular methods, especially Next Generation Sequencing and metagenomics, has highlighted the fact that a diverse microbiota including five major phyla could also be present in the stomach. However, when present, H. pylori is the essential species and it influences the other bacterial communities in terms of richness and evenness. It is now well accepted that H. pylori is the main risk factor for gastric cancer, especially the strains harboring the cag pathogenicity island and the CagA oncoprotein, but the need for other factors from the host and the environment can explain the important difference between those infected and those developing gastric cancer. Several studies showed a difference between the gastric microbiota of patients at various stages of development of gastric premalignant and malignant lesions, showing globally a reduced microbial diversity and an increase in the presence of intestinal commensals, especially with nitrosative functions. Other studies showed an increase in oral microbiota. These data suggest that the gastric microbiota other than H. pylori may play a role in the last steps of gastric carcinogenesis. It must also be noted that in a limited number of cases, a virus: the Epstein Barr Virus is responsible for the evolution toward gastric cancer, while in others the mycobiota also needs to be explored. Finally, the use of mice models allowed an exploration of the role of different gastric microbiota in addition to H. pylori.}, } @article {pmid35533355, year = {2022}, author = {Satjarak, A and Graham, LE and Trest, MT and Zedler, J and Knack, JJ and Arancibia-Avila, P}, title = {Nitrogen fixation and other biogeochemically important features of Atacama Desert giant horsetail plant microbiomes inferred from metagenomic contig analysis.}, journal = {Annals of botany}, volume = {130}, number = {1}, pages = {65-75}, pmid = {35533355}, issn = {1095-8290}, mesh = {*Equisetum ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Nitrogen Fixation ; Plants/genetics ; }, abstract = {BACKGROUND AND AIMS: Canyon stream beds in the hyperarid Atacama Desert surprisingly harbour magnificent groves of endemic giant horsetail wetland plants, Equisetum xylochaetum. Our previous metagenomic study of eukaryotes closely associated with this plant indicated that the microbiome included prokaryotes that might likewise influence host success and environment. We explored this possibility by using the metagenomic sequence to characterize prokaryote taxa and functional genes present in the microbiome of E. xylochaetum sampled from remote sites differing in the degree of anthropogenic disturbance. We focused on biogeochemical functions known to be important in wetland ecosystems.

METHODS: To ensure that analyses were conducted on microbes most closely associated with plants, we extracted DNA from well-washed plant organs whose microbial biofilms were revealed with scanning electron microscopy. To assess the benefits of longer sequences for taxonomic and gene classifications, results of analyses performed using contigs were compared with those obtained with unassembled reads. We employed methods widely used to estimate genomic coverage of single taxa for genomic analysis to infer relative abundances of taxa and functional genes.

KEY RESULTS: Key functional bacterial genera (e.g. Hydrogenophaga, Sulfuritalea and Rhodoferax) inferred from taxonomic and functional gene analysis of contigs - but not unassembled reads - to occur on surfaces of (or within) plants at relatively high abundance (>50× genomic coverage) indicated roles in nitrogen, sulfur and other mineral cycling processes. Comparison between sites revealed impacts on biogeochemical functions, e.g. reduced levels of the nifH gene marker under disturbance. Vanadium nitrogenases were more important than molybdenum nitrogenases, indicated by both functional genes and taxa such as Rhodomicrobium and Phaeospirillum inferred from contigs but not unassembled reads.

CONCLUSIONS: Our contig-based metagenomic analyses revealed that microbes performing key wetland biogeochemical functions occur as tightly adherent biofilms on the plant body, not just in water or sediments, and that disturbance reduces such functions, providing arguments for conservation efforts.}, } @article {pmid35532211, year = {2022}, author = {Odintsova, VE and Klimenko, NS and Tyakht, AV}, title = {Approximation of a Microbiome Composition Shift by a Change in a Single Balance Between Two Groups of Taxa.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0015522}, pmid = {35532211}, issn = {2379-5077}, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenomics/methods ; Metagenome ; Social Group ; }, abstract = {Linking microbiome composition obtained from metagenomic or 16S rRNA sequencing to various factors poses a real challenge. The compositional approach to such data is well described: a so-called isometric log-ratio (ILR) transform provides correct treatment of relative abundances. Most existing compositional methods differ in the particular choice of the transform. Although this choice does not influence the prediction of a model, it determines the subset of balances between groups of microbial taxa subsequently used for interpreting the composition shifts. We propose a method to interpret these shifts independently of the initial choice of ILR coordinates by the nearest single-balance shift. We describe here application of the method to regression, classification, and principal balance analysis of compositional data. Analytical treatment and cross-validation show that the approach provides the least-squares estimate of a single-balance shift associated with a factor with possible adjustment for covariates. As for classification and principal balance analysis, the nearest balance method provides results comparable to other compositional tools. Its advantages are the absence of assumptions about the number of taxa included in the balance and its low computational cost. The method is implemented in the R package NearestBalance. IMPORTANCE The method proposed here extends the range of compositional methods providing interpretation of classical statistical tools applied to data converted to the ILR coordinates. It provides a strictly optimal solution in several special cases. The approach is universally applicable to compositional data of any nature, including microbiome data sets.}, } @article {pmid35532210, year = {2022}, author = {Kadlečková, D and Tachezy, R and Erban, T and Deboutte, W and Nunvář, J and Saláková, M and Matthijnssens, J}, title = {The Virome of Healthy Honey Bee Colonies: Ubiquitous Occurrence of Known and New Viruses in Bee Populations.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0007222}, pmid = {35532210}, issn = {2379-5077}, mesh = {Animals ; Bees ; Virome ; Ecosystem ; Australia ; *RNA Viruses ; *Varroidae ; *Bacteriophages ; }, abstract = {Honey bees are globally important pollinators threatened by many different pathogens, including viruses. We investigated the virome of honey bees collected at the end of the beekeeping season (August/September) in Czechia, a Central European country. Samples were examined in biological replicates to assess the homogeneity, stability, and composition of the virome inside a single hive. By choice of healthy workers from colonies, where Varroa destructor was under control, we could identify ubiquitous bee viruses. Deformed wing virus (DWV) was highly prevalent, even though the bees were healthy, without any noticeable disease signs. The overall virome composition (consisting of honey bee-, plant-, and bacterium-infecting viruses) was driven primarily by the hive and its location. However, honey bee-specific viruses showed an uneven distribution within the same hive. In addition, our results point to an unusual cooccurrence between two rhabdoviruses and reveal the presence of five distinct lineages of Lake Sinai viruses (LSVs) clustering with other LSV strains described globally. Comparison of our results with the virome of Australian honey bees, the last truly Varroa- and DWV-free population, showed a strong difference with respect to DWV and a set of diverse members of the Picornavirales, of which the latter were absent in our samples. We hypothesize that the occurrence of DWV introduced by Varroa strongly affects the virome structure despite the mite being under control. IMPORTANCE The Western honey bee, Apis mellifera, is a vital part of our ecosystem as well as cultural heritage. Annual colony losses endanger beekeeping. In this study, we examined healthy bees from the heart of Central Europe, where honey bee colonies have been commonly affected by varroosis over 5 decades. Our virome analysis showed the presence of ubiquitous viruses in colonies where the mite Varroa destructor was under control and no honey bee disease signs were observed. Compared to previous studies, an important part of our study was the analysis of multiple replicates from individual hives. Our overall results indicate that the virome structure (including bee-infecting viruses, plant-infecting viruses, and bacteriophages) is stable within hives; however, the bee-infecting viruses varied largely within interhive replicates, suggesting variation of honey bee viruses within individual bees. Of interest was the striking difference between the viromes of our 39 pools and 9 pools of honey bee viromes previously analyzed in Australia. It could be suggested that Varroa not only affects DWV spread in bee colonies but also affects diverse members of the Picornavirales, which were strongly decreased in Czech bees compared to the Varroa- and DWV-naive Australian bees.}, } @article {pmid35526726, year = {2022}, author = {Kinoshita, Y and Niwa, H and Uchida-Fujii, E and Nukada, T and Ueno, T}, title = {Simultaneous Daily Fecal Microbiota Transplantation Fails to Prevent Metronidazole-Induced Dysbiosis of Equine Gut Microbiota.}, journal = {Journal of equine veterinary science}, volume = {114}, number = {}, pages = {104004}, doi = {10.1016/j.jevs.2022.104004}, pmid = {35526726}, issn = {0737-0806}, mesh = {Animals ; *Dysbiosis/chemically induced/veterinary ; Fecal Microbiota Transplantation/methods/veterinary ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Horse Diseases/chemically induced ; Horses ; Metronidazole ; }, abstract = {Antimicrobial administration can lead to imbalances of gastrointestinal microbiota, called dysbiosis. Dysbiosis sometimes results in diarrhea and enteritis in horses. Fecal microbiota transplantation (FMT) is used to treat affected horses, but whether it is effective as a prophylactic approach for dysbiosis in horses receiving antimicrobials remains unknown. The aim of this study was to assess the efficacy of simultaneous FMT against metronidazole-induced dysbiosis in horses. Changes in the ratios of bacterial families, determined by metagenomic analysis, were similar between the metronidazole-treated group and the simultaneous metronidazole- and FMT-treated group, notably in the Clostridiaceae, Ruminococcaceae, and Enterobacteriaceae. Differences in fecal bacterial compositions were due mainly to metronidazole administration (P = .0003), but not to FMT (P = .3136). Simultaneous FMT at 500 g of donor feces in 1 L of suspension once a day did not inhibit metronidazole-induced dysbiosis. The results show that the FMT protocol needs to be improved to prevent metronidazole-induced gut dysbiosis in horses.}, } @article {pmid35526643, year = {2022}, author = {Drovetski, SV and Schmidt, BK and Lai, JE and Gross, MS and Hladik, ML and Matterson, KO and Karouna-Renier, NK}, title = {Exposure to crop production alters cecal prokaryotic microbiota, inflates virulome and resistome in wild prairie grouse.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {306}, number = {}, pages = {119418}, doi = {10.1016/j.envpol.2022.119418}, pmid = {35526643}, issn = {1873-6424}, mesh = {Animals ; Chickens ; Crop Production ; *Grassland ; *Microbiota ; Quail ; }, abstract = {Chemically intensive crop production depletes wildlife food resources, hinders animal development, health, survival, and reproduction, and it suppresses wildlife immune systems, facilitating emergence of infectious diseases with excessive mortality rates. Gut microbiota is crucial for wildlife's response to environmental stressors. Its composition and functionality are sensitive to diet changes and environmental pollution associated with modern crop production. In this study we use shotgun metagenomics (median 8,326,092 sequences/sample) to demonstrate that exposure to modern crop production detrimentally affects cecal microbiota of sharp-tailed grouse (Tympanuchus phasianellus: 9 exposed, 18 unexposed and greater prairie chickens (T. cupido; 11, 11). Exposure to crop production had greater effect on microbiota richness (t = 6.675, P < 0.001) and composition (PERMANOVA r[2] = 0.212, P = 0.001) than did the host species (t = 4.762, P < 0.001; r[2] = 0.070, P = 0.001) or their interaction (t = 3.449; r[2] = 0.072, both P = 0.001), whereas sex and age had no effect. Although microbiota richness was greater in exposed (T. cupido chao1 = 152.8 ± 20.5; T. phasianellus 115.3 ± 17.1) than in unexposed (102.9 ± 15.1 and 101.1 ± 17.2, respectively) birds, some beneficial bacteria dropped out of exposed birds' microbiota or declined and were replaced by potential pathogens. Exposed birds also had higher richness and load of virulome (mean ± standard deviation; T. cupido 24.8 ± 10.0 and 10.1 ± 5.5, respectively; T. phasianellus 13.4 ± 6.8/4.9 ± 2.8) and resistome (T. cupido 46.8 ± 11.7/28.9 ± 10.2, T. phasianellus 38.3 ± 16.7/18.9 ± 14.2) than unexposed birds (T. cupido virulome: 14.2 ± 13.5, 4.5 ± 4.2; T. cupido resistome: 31.6 ± 20.2 and 13.1 ± 12.0; T. phasianellus virulome: 5.2 ± 4.7 and 1.4 ± 1.5; T. phasianellus resistome: 13.7 ± 16.1 and 4.0 ± 6.4).}, } @article {pmid35526357, year = {2022}, author = {Parente, E and Zotta, T and Ricciardi, A}, title = {FoodMicrobionet v4: A large, integrated, open and transparent database for food bacterial communities.}, journal = {International journal of food microbiology}, volume = {372}, number = {}, pages = {109696}, doi = {10.1016/j.ijfoodmicro.2022.109696}, pmid = {35526357}, issn = {1879-3460}, mesh = {*Bacteria/genetics ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {With the availability of high-throughput sequencing techniques our knowledge of the structure and dynamics of food microbial communities has made a quantum leap. However, this knowledge is dispersed in a large number of papers and hard data are only partly available through powerful on-line databases and tools such as QIITA, MGnify and the Integrated Microbial Next Generation Sequencing platform, whose annotation is not optimized for foods. Here, we present the 4th iteration of FoodMicrobionet, a database of the composition of bacterial microbial communities of foods and food environments. With 180 studies and 10,151 samples belonging to 8 major food groups FoodMicrobionet 4.1.2 is arguably the largest and best annotated database on food bacterial communities. This version includes 1684 environmental samples and 8467 food samples, belonging to 16 L1 categories and 196 L6 categories of the EFSA FoodEx2 classification and is approximately 4 times larger than previous version (3.1, https://doi.org/10.1016/j.ijfoodmicro.2019.108249). As a representative case study among the many potential applications of FoodMicrobionet, we confirm that taxonomic assignment at the genus level can be performed confidently for the majority of amplicon sequence variants using the most commonly used 16S RNA gene target regions (V1-V3, V3-V4, V4), with best results with higher quality sequences and longer fragment lengths, but that care should be exercised in confirming the assignment at species level. Both FoodMicrobionet and related data and software conform to FAIR (findable, accessible, interoperable, reusable/reproducible) criteria for scientific data and software and are freely available on public repositories (GitHub, Mendeley data). Even if FoodMicrobionet does not have the sophistication of QIITA, IMNGS and MGnify, we feel that this iteration, due to its size and diversity, provides a valuable asset for both the scientific community and industrial and regulatory stakeholders.}, } @article {pmid35525356, year = {2022}, author = {Zhang, Y and Zhang, S and Yuan, Y and Li, Y and Zhu, R and Yang, Y and Xing, S and Wang, Y and Wu, Y and Liao, X and Mi, J}, title = {Metagenomic assembly reveals the circadian oscillations of the microbiome and antibiotic resistance genes in a model of laying hens.}, journal = {The Science of the total environment}, volume = {836}, number = {}, pages = {155692}, doi = {10.1016/j.scitotenv.2022.155692}, pmid = {35525356}, issn = {1879-1026}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Chickens/genetics ; Drug Resistance, Microbial/genetics ; Female ; Genes, Bacterial ; *Metagenome ; *Microbiota ; }, abstract = {The increasing risks of antibiotic resistance genes (ARGs) in livestock feces have attracted global attention. However, how the rhythmic activity of ARGs changes in fecal microbiota remains largely unclear. In our study, we collected 52 fresh fecal samples every 6 h over 72 h from laying hens and characterized circadian oscillations of bacteria and ARGs using an approach based on assembled metagenome shotgun sequencing. We found that 14% of commensal bacterial taxonomic units fluctuated over 24 h. A total of 33 out of 281 ARGs and 17 of 574 mobile genetic elements (MGEs) featured rhythmic patterns in feces. lnuC and ANT(6)H-lb were the two most abundant ARGs with circadian oscillation identified from feces, and they increased during the day and decreased at night. Acetate, butyrate, propionate, and 78 out of 392 MetaCyc pathways relating to short-chain fatty acid (SCFA) metabolism featured circadian oscillations. Assessment of the above ARG-other element connections revealed that 17 ARGs presented strong correlations with 7 MGEs, and 2 SCFAs (acetate and propanoate) and bacterial species in feces. Structural equation model (SEM) analysis showed that ARGs were directly affected by microbial β-diversity and MGEs. These results showed a comprehensive map of ARGs over 24 h and revealed circadian oscillations of ARGs, which are influenced by key bacterial species, MGEs, and metabolites. Together, our findings advance comprehension of circadian oscillations of ARGs in the fecal microbiota and provide a reference for ARGs control and management.}, } @article {pmid35525218, year = {2022}, author = {Geng, H and Wang, F and Yan, C and Ma, S and Zhang, Y and Qin, Q and Tian, Z and Liu, R and Chen, H and Zhou, B and Yuan, R}, title = {Rhizosphere microbial community composition and survival strategies in oligotrophic and metal(loid) contaminated iron tailings areas.}, journal = {Journal of hazardous materials}, volume = {436}, number = {}, pages = {129045}, doi = {10.1016/j.jhazmat.2022.129045}, pmid = {35525218}, issn = {1873-3336}, mesh = {Bacteria/genetics ; Iron/analysis ; Metals/analysis ; *Microbiota ; Mining ; Plants ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {In this study, the metal(loid) fractions in two alkaline iron tailings areas with similar physico-chemical properties and the enrichment ability of dominant plants in these areas were investigated. Additionally, high-throughput sequencing and metagenome analysis were used to examine the rhizosphere microbial community structures and their strategies and potential for carbon fixation, nitrogen metabolism, and metal(loid) resistance in mining areas. Results showed that Salsola collina, Setaria viridis, and Xanthium sibiricum have strong enrichment capacity for As, and the maximum transport factor for Mn can reach 4.01. The richness and diversity of bacteria were the highest in rhizosphere tailings, and the dominant phyla were Proteobacteria, Actinobacteria, Ascomycota, and Thaumarchaeota. The key taxa present in rhizosphere tailings were generally metal(loid) resistant, especially Sphingomonas, Pseudomonas, Nocardioides, and Microbacterium. The reductive citrate cycle was the main carbon fixation pathway of microorganisms in tailings. Rhizosphere microorganisms have evolved a series of survival strategies and can adapt to oligotrophic and metal(loid) polluted mining environments. The results of this study provide a basis for the potential application of plant-microbial in situ remediation of alkaline tailings.}, } @article {pmid35524899, year = {2022}, author = {You, HS and Lee, SH and Lee, YJ and Lee, H and Kang, SS and Hyun, SH}, title = {Next-Generation Sequencing Results Vary Between Cultured and Uncultured Microbes.}, journal = {Current microbiology}, volume = {79}, number = {6}, pages = {187}, pmid = {35524899}, issn = {1432-0991}, support = {PA-I000001//korean national police agency/ ; }, mesh = {Bacteria/genetics ; Firmicutes ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Next-generation sequencing (NGS) technology has led to innovations in environmental metagenomics and investigations involving humans and microbes. However, it is necessary to analyze the components that will affect analysis of the method upon processing a large amount of information. In particular, the processing method after sample collection affects the NGS results, and it is necessary to check for inaccurate results. Here, we show that the microbial communities obtained from fingertip samples differ from those obtained from fingertips remaining on mobile phones and desks, when cultured or not for 24 h. We also confirmed changes in microbial communities in fingertip samples from desks incubated for 2, 4, 8, 16, and 24 h. Samples of prints from mobile phones that are considerably vulnerable to external factors were not analyzed. Ratios of Firmicutes and Bacillus were, respectively, increased in cultures at the phylum and species levels. Collectively, we identified bacterial species that can aid in determining whether a sample has been cultured. In addition, although microbial communities differed depending on sample types, we confirmed changes after culture for 4 and 8 h. However, since this study is a sample limited to three types, it is necessary to analyze other types of samples in the same way and check whether they are applicable to all types. This strategy can verify the suitability of samples for deriving informative results from cultured or uncultured bacterial communities.}, } @article {pmid35521214, year = {2022}, author = {Filardo, S and Scalese, G and Virili, C and Pontone, S and Di Pietro, M and Covelli, A and Bedetti, G and Marinelli, P and Bruno, G and Stramazzo, I and Centanni, M and Sessa, R and Severi, C}, title = {The Potential Role of Hypochlorhydria in the Development of Duodenal Dysbiosis: A Preliminary Report.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {854904}, pmid = {35521214}, issn = {2235-2988}, mesh = {*Achlorhydria/pathology ; Dysbiosis/microbiology ; Gastric Mucosa/microbiology ; *Helicobacter Infections/microbiology ; *Helicobacter pylori/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In recent years, the role of gastric and duodenal microbiota has acquired increasing importance in the homeostasis of the host, although, to date, most evidence concern the faecal microbiota. Indeed, the gastric, and duodenal microbiota are challenging to study, due to gastric acid, bile, digestive enzymes, and rapid transit time. Specifically, the gastric acid environment may influence their bacterial composition since the acid barrier protects against orally ingested microorganisms and leads to their inactivation before reaching the intestine. The aim of this study was to assess a correlation between intragastric pH and gastric as well as intestinal microbiota of patients with histologic gastric alterations. pH was measured in the gastric juice and the bacterial composition in gastric and duodenal biopsies and faecal samples, was investigated via 16s rRNA gene sequencing. The main result is the direct correlation of duodenal microbiota biodiversity, via alpha diversity measures, with intragastric pH values. In particular, patients with hypochlorhydria showed increased duodenal microbiota biodiversity, higher intragastric pH values being prevalent in patients with chronic atrophic gastritis. Lastly, the latter was also strongly associated to the presence of oral bacteria, like Rothia mucilaginosa, Streptococcus salivarius and Granulicatella adiacens, in the duodenal microbiota. In conclusions, our results suggest a low-acid gastric environment as a contributive factor for duodenal dysbiosis, potentially leading to the development of pathological conditions of the gastrointestinal tract.}, } @article {pmid35515981, year = {2022}, author = {Cobos, M and Estela, SL and Rodríguez, HN and Castro, CG and Grandez, M and Castro, JC}, title = {Soil microbial diversity and functional profiling of a tropical rainforest of a highly dissected low hill from the upper Itaya river basin revealed by analysis of shotgun metagenomics sequencing data.}, journal = {Data in brief}, volume = {42}, number = {}, pages = {108205}, pmid = {35515981}, issn = {2352-3409}, abstract = {The tropical rainforest of a highly dissected low hill from the upper Itaya river basin belongs to the western Amazonia region. Some investigations on the biodiversity of these rainforests were more focused on animals and plants diversity. The soils of this region are composed of moderately fertile sediments deposited recently from the initiation of the Andean orogenesis in the Miocene until now. However, scientific information about the soil microbial and functional diversity is still missing. This report presents shotgun metagenomics sequencing data from soils of this rainforest type. A composite loamy soil sample was collected from a primary forest, and metagenomic DNA was purified with standardized methods. Furthermore, libraries were prepared and paired-end sequenced on the Illumina NextSeq 550 platform. Raw Illumina paired-end reads have been uploaded and analysed in the Metagenomics RAST server (MG-RAST). The raw sequence data in fastq format is available at NCBI's Sequence Read Archive (SRA) with accession number SRX12846710.}, } @article {pmid35515005, year = {2022}, author = {Sheehy, L and Cutler, J and Weedall, GD and Rae, R}, title = {Microbiome Analysis of Malacopathogenic Nematodes Suggests No Evidence of a Single Bacterial Symbiont Responsible for Gastropod Mortality.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {878783}, pmid = {35515005}, issn = {1664-3224}, mesh = {Animals ; *Microbiota ; *Nematoda ; *Rhabditoidea/microbiology ; Snails ; Soil ; }, abstract = {Nematodes and bacteria are prevalent in soil ecosystems, and some have evolved symbiotic relationships. In some cases, symbionts carry out highly specialized functions: a prime example being entomopathogenic nematodes (EPNs), which vector bacteria (Xenorhabdus or Photorhabdus) into insect hosts, killing them to provide a food source for the nematodes. It is thought that the commercially available malacopathogenic (kills slugs and snails) biocontrol nematode Phasmarhabditis hermaphrodita vectors a bacterium (Moraxella osloensis) into slugs to kill them. To investigate this further we used a metagenomic approach to profile the bacteria present in the commercial strain of P. hermaphrodita, a wild strain of P. hermaphrodita and two other Phasmarhabditis species (P. californica and P. neopapillosa), after they had killed their slug host (Deroceras invadens). We show that these nematodes do not exclusively associate with one bacterium but a range of species, with members of the phyla Pseudomonadota, Bacillota, Actinobacteriota and Bacteroidota the most prevalent. The commercial strain of P. hermaphrodita had the least diverse bacterial community. Furthermore, we found that the bacterium P. hermaphrodita has been cultured on for 25 years is not the expected species M. osloensis but is Psychrobacter spp. and the only strain of the Phasmarhabditis species to associate with Psychrobacter spp. was the commercial strain of P. hermaphrodita. In summary, we found no evidence to show that P. hermaphrodita rely exclusively on one bacterium to cause host mortality but found variable and diverse bacterial communities associated with these nematodes in their slug hosts.}, } @article {pmid35512372, year = {2022}, author = {Yakimovich, KM and Quarmby, LM}, title = {A metagenomic study of the bacteria in snow algae microbiomes.}, journal = {Canadian journal of microbiology}, volume = {68}, number = {7}, pages = {507-520}, doi = {10.1139/cjm-2021-0313}, pmid = {35512372}, issn = {1480-3275}, mesh = {Bacteria/genetics ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The bacterial communities found in snow algae blooms have been described in terms of their 16S rRNA gene community profiles, but little information exists on their metabolic potential. Previously, we reported that several bacterial taxa are common across snow algae blooms in the southwestern mountains of the Coast Range in British Columbia, Canada. Here, we further this work by reporting a partial bacterial metagenome from the same snow algal microbiomes. Using shotgun metagenomic data, we constructed metagenomically assembled bacterial genomes (MAGs). Of the total 54 binned MAGs, 28 were bacterial and estimated to be at least 50% complete based on single copy core genes. The 28 MAGs fell into five classes: Actinomycetia, Alphaproteobacteria, Bacteroidia, Betaproteobacteria, and Gammaproteobacteria. All MAGs were assigned to a class, 27 to an order, 25 to a family, 18 to a genus, and none to species. MAGs showed the potential to support algal growth by synthesizing B-vitamins and growth hormones. There was also widespread adaptation to the low oxygen environment of biofilms, including synthesis of high-affinity terminal oxidases and anaerobic pathways for cobalamin synthesis. Also notable were the absence of N2 fixation, and the presence of incomplete denitrification pathways suggestive of NO signalling within the microbiome.}, } @article {pmid35511760, year = {2022}, author = {Nagy, A and Abdallah, F and El Damaty, HM and Tariq, A and Merwad, AMA and Alhatlani, BY and Elsohaby, I}, title = {Genetic characterization of upper respiratory tract virome from nonvaccinated Egyptian cow-calf operations.}, journal = {PloS one}, volume = {17}, number = {5}, pages = {e0267036}, pmid = {35511760}, issn = {1932-6203}, mesh = {Animals ; Cattle ; *Cattle Diseases/epidemiology ; Female ; *Herpesvirus 1, Bovine/genetics ; *Herpesvirus 5, Bovine ; Phylogeny ; *Respiratory Tract Diseases ; Virome ; *Viruses/genetics ; }, abstract = {Bovine respiratory disease (BRD) is the costliest complex disease affecting the cattle industry worldwide, with significant economic losses. BRD pathogenesis involves several interactions between microorganisms, such as bacteria and viruses, and management factors. The present study aimed to characterize the nasal virome from 43 pooled nasal swab samples collected from Egyptian nonvaccinated cow-calf operations with acute BRD from January to February 2020 using metagenomic sequencing. Bovine herpesvirus-1 (BHV-1), first detection of bovine herpesvirus-5 (BHV-5), and first detection of bovine parvovirus-3 (BPV-3) were the most commonly identified in Egyptian cattle. Moreover, phylogenetic analysis of glycoprotein B revealed that the BHV-1 isolate is closely related to the Cooper reference strain (genotype 1.1), whereas the BHV-5 isolate is closely related to the reference virus GenBank NP_954920.1. In addition, the whole-genome sequence of BPV-3 showed 93.02% nucleotide identity with the reference virus GenBank AF406967.1. In this study, several DNA viruses, such as BHV-1 and first detection BHV-5, and BPV-3, were detected and may have an association with the BRD in Egyptian cattle. Therefore, further research, including investigating more samples from different locations to determine the prevalence of detected viruses and their contributions to BRD in cattle in Egypt, is needed.}, } @article {pmid35511486, year = {2022}, author = {Hu, S and Mok, J and Gowans, M and Ong, DEH and Hartono, JL and Lee, JWJ}, title = {Oral Microbiome of Crohn's Disease Patients With and Without Oral Manifestations.}, journal = {Journal of Crohn's & colitis}, volume = {16}, number = {10}, pages = {1628-1636}, pmid = {35511486}, issn = {1876-4479}, support = {A-0002940-00-0//National University of Singapore/ ; }, mesh = {Humans ; *Crohn Disease/diagnosis ; Dysbiosis ; *Oral Ulcer ; *Dental Caries ; Feces ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND AND AIMS: Microbiome dysbiosis is associated with inflammatory destruction in Crohn's disease [CD]. Although gut microbiome dysbiosis is well established in CD, the oral microbiome is comparatively under-studied. This study aims to characterize the oral microbiome of CD patients with/without oral manifestations.

METHODS: Patients with CD were recruited with age-, gender- and race-matched controls. Potential confounders such as dental caries and periodontal condition were recorded. The oral microbiome was collected using saliva samples. Microbial DNA was extracted and sequenced using shotgun sequencing. Metagenomic taxonomic and functional profiles were generated and analysed.

RESULTS: The study recruited 41 patients with CD and 24 healthy controls. Within the CD subjects, 39.0% had oral manifestations with the majority presenting with cobblestoning and/or oral ulcers. Principal coordinate analysis demonstrated distinct oral microbiome profiles between subjects with and without CD, with four key variables responsible for overall oral microbiome variance: [1] diagnosis of CD, [2] concomitant use of steroids, [3] concomitant use of azathioprine and 4] presence of oral ulcers. Thirty-two significant differentially abundant microbial species were identified, with the majority associated with the diagnosis of CD. A predictive model based on differences in the oral microbiome found that the oral microbiome has strong discriminatory function to distinguish subjects with and without CD [AUROC 0.84]. Functional analysis found that an increased representation of microbial enzymes [n = 5] in the butyrate pathway was positively associated with the presence of oral ulcers.

CONCLUSIONS: The oral microbiome can aid in the diagnosis of CD and its composition was associated with oral manifestations.}, } @article {pmid35510767, year = {2022}, author = {Mei, R and Liu, WT}, title = {Meta-Omics-Supervised Characterization of Respiration Activities Associated with Microbial Immigrants in Anaerobic Sludge Digesters.}, journal = {Environmental science & technology}, volume = {56}, number = {10}, pages = {6689-6698}, doi = {10.1021/acs.est.2c01029}, pmid = {35510767}, issn = {1520-5851}, mesh = {Anaerobiosis ; Bioreactors ; *Emigrants and Immigrants ; Humans ; Methane/metabolism ; *Microbiota ; Nitrates ; RNA, Ribosomal, 16S/genetics ; Respiration ; Sewage/chemistry ; Sulfates ; }, abstract = {Immigration has been recently recognized as an important ecological process that affects the microbial community structure in diverse ecosystems. However, the fate of microbial immigrants in the new environment and their involvement in the local biochemical network remain unclear. In this study, we performed meta-omics-supervised characterization of immigrants' activities in anaerobic sludge digesters. Metagenomic analyses revealed that immigrants from the feed sludge accounted for the majority of populations capable of anaerobic respiration in a digester. Electron acceptors that were predicted to be respired, including nitrate, nitrite, sulfate, and elemental sulfur, were added to digester sludge in batch tests. Consumption of up to 91% of the added electron acceptors was observed within the experiment period. 16S rRNA sequencing detected populations that were stimulated by the electron acceptors, largely overlapping with respiration-capable immigrants identified by metagenomic analysis. Metatranscriptomic analysis of the batch tests provided additional evidence for upregulated expression of respiration genes and concomitant suppressed expression of methanogenesis. Anaerobic respiration activity was further evaluated in full-scale digesters in nine wastewater treatment plants. Although nitrate and sulfate respiration were ubiquitous, the expression level of respiration genes was generally 2-3 orders of magnitude lower than the expression of methanogenesis in most digesters, suggesting marginal ecological roles by immigrants in full-scale digester ecosystems.}, } @article {pmid35508019, year = {2022}, author = {Kinasz, CT and Kreusch, MG and Bendia, AG and Pellizari, VH and Duarte, RTD}, title = {Taxonomic and functional diversity from Antarctic ice-tephra microbial community: ecological insights and potential for bioprospection.}, journal = {Anais da Academia Brasileira de Ciencias}, volume = {94}, number = {suppl 1}, pages = {e20210621}, doi = {10.1590/0001-3765202220210621}, pmid = {35508019}, issn = {1678-2690}, mesh = {Antarctic Regions ; Carbon ; *Cyanobacteria ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Antarctic active volcanoes can disperse pyroclastic minerals at long distances, transporting nutrients and microorganisms to the surrounding glacial environment. The sedimented volcanic materials - called tephras - may interact with glacier ice and produce a unique environment for microbial life. This study aimed to describe the microbial community structure of an Antarctic glacier ice with tephra layers in terms of its taxonomic and functional diversity. Ice samples from Collins Glacier (King George Island) containing tephra layers of Deception Island volcano were analyzed by a whole shotgun metagenomic approach. Taxonomic analysis revealed a highly diverse community dominated by phyla Bacteroidetes, Cyanobacteria and Proteobacteria. The dominant genera were Chitinophaga (13%), Acidobacterium (8%), and Cyanothece (4%), being all of these known to include psychrotolerant and psychrophilic strains. Functional diversity analysis revealed almost complete carbon, nitrogen and sulfur biogeochemical cycles. Carbohydrate metabolism of the ice-tephra community uses both organic and inorganic carbon inputs, where photosynthesis plays an important role through CO2 fixation. Our results also demonstrate a biotechnological potential for this glacial community, with functional annotations for styrene degradation and carotenoid pigment genes. Future metatranscriptomic studies shall further reveal the active strategies and the biotechnology potential of extremophiles from this unique ice-tephra microbial community.}, } @article {pmid35505248, year = {2022}, author = {Worby, CJ and Schreiber, HL and Straub, TJ and van Dijk, LR and Bronson, RA and Olson, BS and Pinkner, JS and Obernuefemann, CLP and Muñoz, VL and Paharik, AE and Azimzadeh, PN and Walker, BJ and Desjardins, CA and Chou, WC and Bergeron, K and Chapman, SB and Klim, A and Manson, AL and Hannan, TJ and Hooton, TM and Kau, AL and Lai, HH and Dodson, KW and Hultgren, SJ and Earl, AM}, title = {Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women.}, journal = {Nature microbiology}, volume = {7}, number = {5}, pages = {630-639}, pmid = {35505248}, issn = {2058-5276}, support = {R37 AI048689/AI/NIAID NIH HHS/United States ; R01 AI165915/AI/NIAID NIH HHS/United States ; T32 GM139774/GM/NIGMS NIH HHS/United States ; R01 DK121822/DK/NIDDK NIH HHS/United States ; T32 GM007067/GM/NIGMS NIH HHS/United States ; U01 AI095542/AI/NIAID NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; 2019083/DDCF_/Doris Duke Charitable Foundation/United States ; }, mesh = {Dysbiosis ; Escherichia coli ; *Escherichia coli Infections/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Leukocytes, Mononuclear ; *Urinary Tract Infections/microbiology ; }, abstract = {Recurrent urinary tract infections (rUTIs) are a major health burden worldwide, with history of infection being a significant risk factor. While the gut is a known reservoir for uropathogenic bacteria, the role of the microbiota in rUTI remains unclear. We conducted a year-long study of women with (n = 15) and without (n = 16) history of rUTI, from whom we collected urine, blood and monthly faecal samples for metagenomic and transcriptomic interrogation. During the study 24 UTIs were reported, with additional samples collected during and after infection. The gut microbiome of individuals with a history of rUTI was significantly depleted in microbial richness and butyrate-producing bacteria compared with controls, reminiscent of other inflammatory conditions. However, Escherichia coli gut and bladder populations were comparable between cohorts in both relative abundance and phylogroup. Transcriptional analysis of peripheral blood mononuclear cells revealed expression profiles indicative of differential systemic immunity between cohorts. Altogether, these results suggest that rUTI susceptibility is in part mediated through the gut-bladder axis, comprising gut dysbiosis and differential immune response to bacterial bladder colonization, manifesting in symptoms.}, } @article {pmid35504350, year = {2022}, author = {Wang, X and Liu, X and Xiao, S and Zhang, Z and Wu, L and Cheng, Y and Tan, Y and Zhang, G and Jiang, C}, title = {Comparison of gut microbiota compositions and corresponding genetic and metabolic features between guttate and plaque psoriasis by metagenomic sequencing.}, journal = {Microbial pathogenesis}, volume = {167}, number = {}, pages = {105560}, doi = {10.1016/j.micpath.2022.105560}, pmid = {35504350}, issn = {1096-1208}, mesh = {*Epstein-Barr Virus Infections ; *Gastrointestinal Microbiome/genetics ; Herpesvirus 4, Human ; Humans ; Metagenomics ; *Psoriasis ; }, abstract = {BACKGROUND: Guttate psoriasis (GP) and psoriasis plaques (PP) are common subtypes of psoriasis. Previous studies have fully researched the association between psoriasis and gut microbiota. However, the differences in gut microbiota between GPs and PPs are still unknown.

METHODS: Fecal samples were collected from 30 psoriatic patients (15 GP and 15 PP) and 15 healthy subjects. Metagenomic sequencing was then used to compare gut microbiota compositions and corresponding genetic and metabolic features between GP and PP.

RESULTS: We found that the genus Megamonas was increased in PP and reduced in GP. The genus Eubacterium was increased in GP and decreased in PP. Ten KEGG pathway were significantly enriched in GP: bacterial secretion system, ribosome, sphingolipid signaling pathway, steroid hormone biosynthesis, complement and coagulation cascades, proteoglycans in cancer, FOXO signaling pathway, cGMP-PKG signaling pathway, insulin resistance, and Epstein-Barr virus infection. Ten metabolites were significantly differentially abundant between GP and PP. Among them, thiamine, biotin, butylamine, phenylethylamine, folic acid, 1,2-propanediol, and 4-aminobutyrate were enriched in PP and l-glutamate, l-glutamine, and propanoate were enriched in GP.

CONCLUSIONS: These results provide a theoretical basis for the microbiome-guided stratification of patients with psoriasis.}, } @article {pmid35504169, year = {2022}, author = {Tian, Z and Zhuang, X and Zhuo, S and Zhu, Y and Hu, S and Zhao, M and Tang, C and Zhang, Z and Li, X and Ma, R and Zeng, Z and Feng, R and Chen, M}, title = {Dietary inflammatory potential mediated gut microbiota and metabolite alterations in Crohn's disease: A fire-new perspective.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {41}, number = {6}, pages = {1260-1271}, doi = {10.1016/j.clnu.2022.04.014}, pmid = {35504169}, issn = {1532-1983}, mesh = {Bacteria ; *Crohn Disease ; Diet/adverse effects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Inflammation/microbiology ; }, abstract = {BACKGROUND & AIMS: Pro-inflammatory diet interacting with gut microbiome might trigger for Crohn's disease (CD). We aimed to investigate the relationship between dietary inflammatory potential and microflora/metabolites change and their link with CD.

METHODS: The dietary inflammatory potential was assessed using a dietary inflammatory index (DII) based on the Food Frequency Questionnaire from 150 new-onset CD patients and 285 healthy controls (HCs). We selected 41 CD patients and 89 HCs who had not received medication for metagenomic and targeted metabolomic sequencing to profile their gut microbial composition as well as fecal and serum metabolites. DII scores were classified into quartiles to investigate associations among different variables.

RESULTS: DII scores of CD patients were significantly higher than HCs (0.56 ± 1.20 vs 0.23 ± 1.02, p = 0.017). With adjustment for confounders, a higher DII score was significantly associated with higher risk of CD (OR: 1.420; 95% CI: 1.049, 1.923, p = 0.023). DII score also was positively correlated with disease activity (p = 0.001). Morganella morganii and Veillonella parvula were increased while Coprococcus eutactus was decreased in the pro-inflammatory diets group, as well as in CD. DII-related bacteria were associated with disease activity and inflammatory markers in CD patients. Among the metabolic change, pro-inflammatory diet induced metabolites change were largely involved in amino acid metabolic pathways that were also observed in CD.

CONCLUSIONS: Pro-inflammatory diet might be associated with increased risk and disease activity of CD. Diet with high DII potentially involves in CD by mediating alterations in gut microbiota and metabolites.}, } @article {pmid35504157, year = {2022}, author = {Hegarty, B and Dai, Z and Raskin, L and Pinto, A and Wigginton, K and Duhaime, M}, title = {A snapshot of the global drinking water virome: Diversity and metabolic potential vary with residual disinfectant use.}, journal = {Water research}, volume = {218}, number = {}, pages = {118484}, doi = {10.1016/j.watres.2022.118484}, pmid = {35504157}, issn = {1879-2448}, mesh = {Bacteria/genetics ; Chlorine ; *Disinfectants/pharmacology ; *Drinking Water ; Metagenomics ; Virome ; *Viruses/genetics ; *Water Purification ; }, abstract = {Viruses are important drivers of microbial community ecology and evolution, influencing microbial mortality, metabolism, and horizontal gene transfer. However, the effects of viruses remain largely unknown in many environments, including in drinking water systems. Drinking water metagenomic studies have offered a whole community perspective of bacterial impacts on water quality, but have not yet considered the influences of viruses. In this study, we address this gap by mining viral DNA sequences from publicly available drinking water metagenomes from distribution systems in six countries around the world. These datasets provide a snapshot of the taxonomic diversity and metabolic potential of the global drinking water virome; and provide an opportunity to investigate the effects of geography, climate, and drinking water treatment practices on viral diversity. Both environmental conditions and differences in sample processing were found to influence the viral composition. Using free chlorine as the residual disinfectant was associated with clear differences in viral taxonomic diversity and metabolic potential, with significantly fewer viral populations and less even viral community structures than observed in distribution systems without residual disinfectant. Additionally, drinking water viruses carry antibiotic resistance genes (ARGs), as well as genes to survive oxidative stress and nitrogen limitation. Through this study, we have demonstrated that viral communities are diverse across drinking water systems and vary with the use of residual disinfectant. Our findings offer directions for future research to develop a more robust understanding of how virus-bacteria interactions in drinking water distribution systems affect water quality.}, } @article {pmid35503723, year = {2022}, author = {Pronk, LJU and Medema, MH}, title = {Whokaryote: distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure.}, journal = {Microbial genomics}, volume = {8}, number = {5}, pages = {}, pmid = {35503723}, issn = {2057-5858}, mesh = {Bacteria/genetics ; Eukaryota/genetics ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Metagenomics has become a prominent technology to study the functional potential of all organisms in a microbial community. Most studies focus on the bacterial content of these communities, while ignoring eukaryotic microbes. Indeed, many metagenomics analysis pipelines silently assume that all contigs in a metagenome are prokaryotic, likely resulting in less accurate annotation of eukaryotes in metagenomes. Early detection of eukaryotic contigs allows for eukaryote-specific gene prediction and functional annotation. Here, we developed a classifier that distinguishes eukaryotic from prokaryotic contigs based on foundational differences between these taxa in terms of gene structure. We first developed Whokaryote, a random forest classifier that uses intergenic distance, gene density and gene length as the most important features. We show that, with an estimated recall, precision and accuracy of 94, 96 and 95 %, respectively, this classifier with features grounded in biology can perform almost as well as the classifiers EukRep and Tiara, which use k-mer frequencies as features. By retraining our classifier with Tiara predictions as an additional feature, the weaknesses of both types of classifiers are compensated; the result is Whokaryote+Tiara, an enhanced classifier that outperforms all individual classifiers, with an F1 score of 0.99 for both eukaryotes and prokaryotes, while still being fast. In a reanalysis of metagenome data from a disease-suppressive plant endospheric microbial community, we show how using Whokaryote+Tiara to select contigs for eukaryotic gene prediction facilitates the discovery of several biosynthetic gene clusters that were missed in the original study. Whokaryote (+Tiara) is wrapped in an easily installable package and is freely available from https://github.com/LottePronk/whokaryote.}, } @article {pmid35503575, year = {2023}, author = {Dick, JM and Tan, J}, title = {Chemical Links Between Redox Conditions and Estimated Community Proteomes from 16S rRNA and Reference Protein Sequences.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1338-1355}, pmid = {35503575}, issn = {1432-184X}, mesh = {RNA, Ribosomal, 16S/genetics ; *Proteome ; *Microbiota/genetics ; Metagenome ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Environmental influences on community structure are often assessed through multivariate analyses in order to relate microbial abundances to separately measured physicochemical variables. However, genes and proteins are themselves chemical entities; in combination with genome databases, differences in microbial abundances directly encode for chemical variability. We predicted that the carbon oxidation state of estimated community proteomes, obtained by combining taxonomic abundances from published 16S rRNA gene sequencing datasets with reference microbial proteomes from the NCBI Reference Sequence (RefSeq) database, would reflect environmental oxidation-reduction conditions. Analysis of multiple datasets confirms the geobiochemical predictions for environmental redox gradients in hydrothermal systems, stratified lakes and marine environments, and shale gas wells. The geobiochemical signal is largest for the steep redox gradients associated with hydrothermal systems and between injected water and produced fluids from shale gas wells, demonstrating that microbial community composition can be a chemical proxy for environmental redox gradients. Although estimates of oxidation state from 16S amplicon and metagenomic sequences are correlated, the 16S-based estimates show stronger associations with redox gradients in some environments.}, } @article {pmid35502903, year = {2022}, author = {Brealey, JC and Lecaudey, LA and Kodama, M and Rasmussen, JA and Sveier, H and Dheilly, NM and Martin, MD and Limborg, MT}, title = {Microbiome "Inception": an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0067922}, pmid = {35502903}, issn = {2150-7511}, mesh = {Animals ; Bacteria/genetics ; *Cestoda/genetics ; Dysbiosis ; *Gastrointestinal Microbiome/physiology ; *Microbiota ; *Parasites ; }, abstract = {The concept of a holobiont, a host organism and its associated microbial communities, encapsulates the vital role the microbiome plays in the normal functioning of its host. Parasitic infections can disrupt this relationship, leading to dysbiosis. However, it is increasingly recognized that multicellular parasites are themselves holobionts. Intestinal parasites share space with the host gut microbiome, creating a system of nested microbiomes within the primary host. However, how the parasite, as a holobiont, interacts with the host holobiont remains unclear, as do the consequences of these interactions for host health. Here, we used 16S amplicon and shotgun metagenomics sequencing to characterize the microbiome of the intestinal cestode Eubothrium and its effect on the gut microbiome of its primary host, Atlantic salmon. Our results indicate that cestode infection is associated with salmon gut dysbiosis by acting as a selective force benefiting putative pathogens and potentially introducing novel bacterial species to the host. Our results suggest that parasitic cestodes may themselves be holobionts nested within the microbial community of their holobiont host, emphasizing the importance of also considering microbes associated with parasites when studying intestinal parasitic infections. IMPORTANCE The importance of the parasite microbiome is gaining recognition. Of particular concern is understanding how these parasite microbiomes influence host-parasite interactions and parasite interactions with the vertebrate host microbiome as part of a system of nested holobionts. However, there are still relatively few studies focusing on the microbiome of parasitic helminths in general and almost none on cestodes in particular, despite the significant burden of disease caused by these parasites globally. Our study provides insights into a system of significance to the aquaculture industry, cestode infections of Atlantic salmon and, more broadly, expands our general understanding of parasite-microbiome-host interactions and introduces a new element, the microbiome of the parasite itself, which may play a critical role in modulating the host microbiome, and, therefore, the host response, to parasite infection.}, } @article {pmid35501923, year = {2022}, author = {Parker, A and Romano, S and Ansorge, R and Aboelnour, A and Le Gall, G and Savva, GM and Pontifex, MG and Telatin, A and Baker, D and Jones, E and Vauzour, D and Rudder, S and Blackshaw, LA and Jeffery, G and Carding, SR}, title = {Fecal microbiota transfer between young and aged mice reverses hallmarks of the aging gut, eye, and brain.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {68}, pmid = {35501923}, issn = {2049-2618}, support = {BB/CCG1860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N000250/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Aging ; Animals ; Brain ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/physiology ; Inflammation/pathology ; Mice ; }, abstract = {BACKGROUND: Altered intestinal microbiota composition in later life is associated with inflammaging, declining tissue function, and increased susceptibility to age-associated chronic diseases, including neurodegenerative dementias. Here, we tested the hypothesis that manipulating the intestinal microbiota influences the development of major comorbidities associated with aging and, in particular, inflammation affecting the brain and retina.

METHODS: Using fecal microbiota transplantation, we exchanged the intestinal microbiota of young (3 months), old (18 months), and aged (24 months) mice. Whole metagenomic shotgun sequencing and metabolomics were used to develop a custom analysis workflow, to analyze the changes in gut microbiota composition and metabolic potential. Effects of age and microbiota transfer on the gut barrier, retina, and brain were assessed using protein assays, immunohistology, and behavioral testing.

RESULTS: We show that microbiota composition profiles and key species enriched in young or aged mice are successfully transferred by FMT between young and aged mice and that FMT modulates resulting metabolic pathway profiles. The transfer of aged donor microbiota into young mice accelerates age-associated central nervous system (CNS) inflammation, retinal inflammation, and cytokine signaling and promotes loss of key functional protein in the eye, effects which are coincident with increased intestinal barrier permeability. Conversely, these detrimental effects can be reversed by the transfer of young donor microbiota.

CONCLUSIONS: These findings demonstrate that the aging gut microbiota drives detrimental changes in the gut-brain and gut-retina axes suggesting that microbial modulation may be of therapeutic benefit in preventing inflammation-related tissue decline in later life. Video abstract.}, } @article {pmid35501856, year = {2022}, author = {Mesnage, R and Bowyer, RCE and El Balkhi, S and Saint-Marcoux, F and Gardere, A and Ducarmon, QR and Geelen, AR and Zwittink, RD and Tsoukalas, D and Sarandi, E and Paramera, EI and Spector, T and Steves, CJ and Antoniou, MN}, title = {Impacts of dietary exposure to pesticides on faecal microbiome metabolism in adult twins.}, journal = {Environmental health : a global access science source}, volume = {21}, number = {1}, pages = {46}, pmid = {35501856}, issn = {1476-069X}, support = {MR/N01183X/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Dietary Exposure/analysis ; *Herbicides/analysis ; Humans ; *Insecticides/analysis ; *Microbiota ; Organophosphorus Compounds ; *Pesticide Residues/analysis ; *Pesticides ; Vegetables/chemistry ; }, abstract = {BACKGROUND: Dietary habits have a profound influence on the metabolic activity of gut microorganisms and their influence on health. Concerns have been raised as to whether the consumption of foodstuffs contaminated with pesticides can contribute to the development of chronic disease by affecting the gut microbiome. We performed the first pesticide biomonitoring survey of the British population, and subsequently used the results to perform the first pesticide association study on gut microbiome composition and function from the TwinsUK registry.

METHODS: Dietary exposure of 186 common insecticide, herbicide, or fungicide residues and the faecal microbiome in 65 twin pairs in the UK was investigated. We evaluated if dietary habits, geographic location, or the rural/urban environment, are associated with the excretion of pesticide residues. The composition and metabolic activity of faecal microbiota was evaluated using shotgun metagenomics and metabolomics respectively. We performed a targeted urine metabolomics analysis in order to evaluate whether pesticide urinary excretion was also associated with physiological changes.

RESULTS: Pyrethroid and/or organophosphorus insecticide residues were found in all urine samples, while the herbicide glyphosate was found in 53% of individuals. Food frequency questionnaires showed that residues from organophosphates were higher with increased consumption of fruit and vegetables. A total of 34 associations between pesticide residue concentrations and faecal metabolite concentrations were detected. Glyphosate excretion was positively associated with an overall increased bacterial species richness, as well as to fatty acid metabolites and phosphate levels. The insecticide metabolite Br2CA, reflecting deltamethrin exposure, was positively associated with the phytoestrogens enterodiol and enterolactone, and negatively associated with some N-methyl amino acids. Urine metabolomics performed on a subset of samples did not reveal associations with the excretion of pesticide residues.

CONCLUSIONS: The consumption of conventionally grown fruit and vegetables leads to higher ingestion of pesticides with unknown long-term health consequences. Our results highlight the need for future dietary intervention studies to understand effects of pesticide exposure on the gut microbiome and possible health consequences.}, } @article {pmid35501694, year = {2022}, author = {Jiang, C and Zhu, S and Feng, J and Shui, W}, title = {Slope aspect affects the soil microbial communities in karst tiankeng negative landforms.}, journal = {BMC ecology and evolution}, volume = {22}, number = {1}, pages = {54}, pmid = {35501694}, issn = {2730-7182}, mesh = {Bacteria ; Biodiversity ; Humans ; *Microbiota ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {BACKGROUND: Karst tiankeng is a large-scale negative surface terrain, and slope aspects affect the soil conditions, vegetation and microbial flora in the tiankeng. However, the influence of the slope aspect on the soil microbial community in tiankeng has not been elucidated.

METHODS: In this study, metagenomic sequencing technology was used to analyze the soil microbial community structure and functional potentials on the shady and sunny slopes of karst tiankeng.

RESULTS: The Shannon-Wiener diversity of microbial communities on shady slope (SHS) was significantly higher than that on sunny slope (SUS). Although the composition of dominant phyla on shady slope (SHS) and sunny slope (SUS) was similar, there were significant differences in beta-diversity. The linear discriminate analysis (LDA) results showed that biomarkers mainly belongs to Actinobacteria, Chloroflexi and Proteobacteria. Functional pathways and CAZy (Carbohydrate-Active Enzymes) genes also had a remarkable response to slope aspect change. LEfSe results indicated several biomarker pathways in sunny slope involved in human disease. Moreover, the abundance of CAZy genes was higher in shady slope and had stronger ability in decomposing litter. The microbial communities were mainly correlation with the vegetation characteristics (species richness and coverage) and soil properties (SOC and pH).

CONCLUSIONS: These results indicate slope aspect has a pronounced influence on microbial community composition, structure and function at karst tiankeng. In the future, the conservation of karst tiankeng biodiversity should pay more attention to topographical factors.}, } @article {pmid35501656, year = {2022}, author = {Klimenko, ES and Belkova, NL and Romanitsa, AI and Pogodina, AV and Rychkova, LV}, title = {Diversity and Metabolic Potential of the Gut Microbiome in Adolescents with Functional Bowel Disorder.}, journal = {Bulletin of experimental biology and medicine}, volume = {172}, number = {6}, pages = {681-685}, pmid = {35501656}, issn = {1573-8221}, mesh = {Adolescent ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The article presents the results of a pilot study of the diversity and metabolic potential of the gut microbiome in adolescents with various forms of functional bowel disorder. The participants were the patients of the Clinic of Research Center for Family Health and Human Reproduction Problems. Biological material was studied using metagenomic sequencing of V3-V4 variable regions of the 16S rRNA gene. We showed that the composition of the minor component of the intestinal microbiome in adolescents with functional bowel disorder differs from that in the healthy subjects (control). Different types of transit disturbances in functional bowel disorder also differ from each other. According to the metabolic potential, adolescents can be divided into two groups irrespective of the pathophysiological manifestations: for one group, a more intensive metabolism in amino acid and lipid biosynthesis pathways was predicted than for the other.}, } @article {pmid35501417, year = {2022}, author = {Levy-Booth, DJ and Navas, LE and Fetherolf, MM and Liu, LY and Dalhuisen, T and Renneckar, S and Eltis, LD and Mohn, WW}, title = {Discovery of lignin-transforming bacteria and enzymes in thermophilic environments using stable isotope probing.}, journal = {The ISME journal}, volume = {16}, number = {8}, pages = {1944-1956}, pmid = {35501417}, issn = {1751-7370}, support = {STPGP 506595-17//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; SIP004//Genome British Columbia/ ; }, mesh = {Bacteria/genetics/metabolism ; *Gammaproteobacteria/metabolism ; Isotopes/metabolism ; Lignin/metabolism ; *Microbiota ; Tandem Mass Spectrometry ; }, abstract = {Characterizing microorganisms and enzymes involved in lignin biodegradation in thermal ecosystems can identify thermostable biocatalysts. We integrated stable isotope probing (SIP), genome-resolved metagenomics, and enzyme characterization to investigate the degradation of high-molecular weight, [13]C-ring-labeled synthetic lignin by microbial communities from moderately thermophilic hot spring sediment (52 °C) and a woody "hog fuel" pile (53 and 62 °C zones). [13]C-Lignin degradation was monitored using IR-GCMS of [13]CO2, and isotopic enrichment of DNA was measured with UHLPC-MS/MS. Assembly of 42 metagenomic libraries (72 Gb) yielded 344 contig bins, from which 125 draft genomes were produced. Fourteen genomes were significantly enriched with [13]C from lignin, including genomes of Actinomycetes (Thermoleophilaceae, Solirubrobacteraceae, Rubrobacter sp.), Firmicutes (Kyrpidia sp., Alicyclobacillus sp.) and Gammaproteobacteria (Steroidobacteraceae). We employed multiple approaches to screen genomes for genes encoding putative ligninases and pathways for aromatic compound degradation. Our analysis identified several novel laccase-like multi-copper oxidase (LMCO) genes in [13]C-enriched genomes. One of these LMCOs was heterologously expressed and shown to oxidize lignin model compounds and minimally transformed lignin. This study elucidated bacterial lignin depolymerization and mineralization in thermal ecosystems, establishing new possibilities for the efficient valorization of lignin at elevated temperature.}, } @article {pmid35501347, year = {2022}, author = {Gao, S and Paez-Espino, D and Li, J and Ai, H and Liang, J and Luo, Z and Zheng, J and Chen, H and Shu, W and Huang, L}, title = {Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {2389}, pmid = {35501347}, issn = {2041-1723}, mesh = {Acids ; *Biodiversity ; Metagenome/genetics ; Mining ; *Viruses/genetics ; }, abstract = {Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our knowledge of viral biogeographic patterns and the corresponding drivers is still limited. Here, we perform metagenomic deep sequencing on 90 acid mine drainage (AMD) sediments sampled across Southern China and examine the biogeography of viruses in this extreme environment. The results demonstrate that prokaryotic communities dictate viral taxonomic and functional diversity, abundance and structure, whereas other factors especially latitude and mean annual temperature also impact viral populations and functions. In silico predictions highlight lineage-specific virus-host abundance ratios and richness-dependent virus-host interaction structure. Further functional analyses reveal important roles of environmental conditions and horizontal gene transfers in shaping viral auxiliary metabolic genes potentially involved in phosphorus assimilation. Our findings underscore the importance of both abiotic and biotic factors in predicting the taxonomic and functional biogeographic dynamics of viruses in the AMD sediments.}, } @article {pmid35500534, year = {2022}, author = {Mirza, AI and Zhu, F and Knox, N and Forbes, JD and Bonner, C and Van Domselaar, G and Bernstein, CN and Graham, M and Marrie, RA and Hart, J and Yeh, EA and Arnold, DL and Bar-Or, A and O'Mahony, J and Zhao, Y and Hsiao, W and Banwell, B and Waubant, E and Tremlett, H}, title = {The metabolic potential of the paediatric-onset multiple sclerosis gut microbiome.}, journal = {Multiple sclerosis and related disorders}, volume = {63}, number = {}, pages = {103829}, doi = {10.1016/j.msard.2022.103829}, pmid = {35500534}, issn = {2211-0356}, mesh = {Adolescent ; Canada ; Child ; Female ; *Gastrointestinal Microbiome ; Glatiramer Acetate ; Humans ; Male ; *Multiple Sclerosis ; Starch ; }, abstract = {BACKGROUND: The aim of this study was to examine the gut microbiome's metabolic potential in paediatric-onset MS patients (symptom onset <18 years).

METHODS: We included 17 MS participants and 20 controls similar for sex, age, race, and stool consistency from the Canadian Paediatric Demyelinating Disease Network study. Stool-derived gut metagenome gene abundances were used to estimate relative abundances and turnover scores of individual microbial metabolites and the composition and diversity of carbohydrate-active enzymes (CAZymes). MS participants and controls were compared using the Wilcoxon rank-sum test, as were the disease-modifying drug (DMD) exposed and naïve MS participants.

RESULTS: The median age(s) at MS symptom onset=16.1 years (interquartile range [IQR]=1.7), and at stool sample procurement=16.9/15.8 years (IQR=2.0/1.4), for the MS participants/controls. Most MS and control participants were girls (80-82%). Five (29%) of the MS participants had never been exposed to a DMD pre-stool sample and 12 (71%) had (7 to beta-interferon and 5 glatiramer acetate). While the relative abundance of metabolites did not differ between MS participants and controls, turnover scores did. MS participants had a greater potential to metabolize lipopolysaccharides than controls (score difference=1.6E-04, p = 0.034) but lower potential to metabolize peptidoglycan molecules and starch (score differences<2.2E-02, p<0.040). Further, although CAZymes diversity did not differ (p>0.050), starch-degrading subfamilies were underrepresented in MS participants versus controls (relative abundance differences >-0.34, p<0.040) and in the DMD exposed verses DMD naïve MS participants (relative abundance differences>-0.20, p<0.049).

CONCLUSION: Paediatric-onset MS participants had an altered gut microbiome-related metabolic potential compared to controls, including higher breakdown of lipopolysaccharide molecules, but lower resistant starch metabolism.}, } @article {pmid35499324, year = {2022}, author = {Yang, Q and Cahn, JKB and Piel, J and Song, YF and Zhang, W and Lin, HW}, title = {Marine Sponge Endosymbionts: Structural and Functional Specificity of the Microbiome within Euryspongia arenaria Cells.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0229621}, pmid = {35499324}, issn = {2165-0497}, mesh = {Animals ; Lipase/genetics ; *Microbiota ; Phylogeny ; *Porifera/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Sponge microbiomes are typically profiled by analyzing the community DNA of whole tissues, which does not distinguish the taxa residing within sponge cells from extracellular microbes. To uncover the endosymbiotic microbiome, we separated the sponge cells to enrich the intracellular microbes. The intracellular bacterial community of sponge Euryspongia arenaria was initially assessed by amplicon sequencing, which indicated that it hosts three unique phyla not found in the extracellular and bulk tissue microbiomes. These three phyla account for 66% of the taxonomically known genera in the intracellular microbiome. The shotgun metagenomic analysis extended the taxonomic coverage to viruses and eukaryotes, revealing the most abundant signature taxa specific to the intracellular microbiome. Functional KEGG pathway annotation demonstrated that the endosymbiotic microbiome hosted the greatest number of unique gene orthologs. The pathway profiles distinguished the intra- and extracellular microbiomes from the tissue and seawater microbiomes. Carbohydrate-active enzyme analysis further discriminated each microbiome based on their representative and dominant enzyme families. One pathway involved in digestion system and family esterase had a consistently higher level in intracellular microbiome and could statistically differentiate the intracellular microbiome from the others, suggesting that triacylglycerol lipases could be the key functional component peculiar to the endosymbionts. The identified higher abundance of lipase-related eggNOG categories further supported the lipid-hydrolyzing metabolism of endosymbiotic microbiota. Pseudomonas members, reported as lipase-producing bacteria, were only in the endosymbiotic microbiome, meanwhile Pseudomonas also showed a greater abundance intracellularly. Our study aided a comprehensive sponge microbiome that demonstrated the taxonomic and functional specificity of endosymbiotic microbiota. IMPORTANCE Sponges host abundant microbial symbionts that can produce an impressive number of novel bioactive metabolites. However, knowledge on intracellular (endosymbiotic) microbiota is scarce. We characterize the composition and function of the endosymbiotic microbiome by separation of sponge cells and enrichment of intracellular microbes. We uncover a noteworthy number of taxa exclusively in the endosymbiotic microbiome. We unlock the unique pathways and enzymes of endosymbiotic taxa. This study achieves a more comprehensive sponge microbial community profile, which demonstrates the structural and functional specificity of the endosymbiotic microbiome. Our findings not only open the possibility to reveal the low abundant and the likely missed microbiota when directly sequencing the sponge bulk tissues, but also warrant future in-depth exploration within single sponge cells.}, } @article {pmid35499050, year = {2022}, author = {Wu, Y and Zheng, Y and Wang, S and Chen, Y and Tao, J and Chen, Y and Chen, G and Zhao, H and Wang, K and Dong, K and Hu, F and Feng, Y and Zheng, H}, title = {Genetic divergence and functional convergence of gut bacteria between the Eastern honey bee Apis cerana and the Western honey bee Apis mellifera.}, journal = {Journal of advanced research}, volume = {37}, number = {}, pages = {19-31}, pmid = {35499050}, issn = {2090-1224}, mesh = {Animals ; Bacteria/genetics ; Bees/genetics ; Chromatography, Liquid ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Tandem Mass Spectrometry ; }, abstract = {INTRODUCTION: The functional relevance of intra-species diversity in natural microbial communities remains largely unexplored. The guts of two closely related honey bee species, Apis cerana and A. mellifera, are colonised by a similar set of core bacterial species composed of host-specific strains, thereby providing a good model for an intra-species diversity study.

OBJECTIVES: We aim to assess the functional relevance of intra-species diversity of A. cerana and A. mellifera gut microbiota.

METHODS: Honey bee workers were collected from four regions of China. Their gut microbiomes were investigated by shotgun metagenomic sequencing, and the bacterial compositions were compared at the species level. A cross-species colonisation assay was conducted, with the gut metabolomes being characterised by LC-MS/MS.

RESULTS: Comparative analysis showed that the strain composition of the core bacterial species was host-specific. These core bacterial species presented distinctive functional profiles between the hosts. However, the overall functional profiles of the A. cerana and A. mellifera gut microbiomes were similar; this was further supported by the consistency of the honey bees' gut metabolome, as the gut microbiota of different honey bee species showed rather similar metabolic profiles in the cross-species colonisation assay. Moreover, this experiment also demonstrated that the gut microbiota of A. cerana and A. mellifera could cross colonise between the two honey bee species.

CONCLUSION: Our findings revealed functional differences in most core gut bacteria between the guts of A. cerana and A. mellifera, which may be associated with their inter-species diversity. However, the functional profiles of the overall gut microbiomes between the two honey bee species converge, probably as a result of the overlapping ecological niches of the two species. Our findings provide critical insights into the evolution and functional roles of the mutualistic microbiota of honey bees and reveal that functional redundancy could stabilise the gene content diversity at the strain-level within the gut community.}, } @article {pmid35499044, year = {2022}, author = {Wu, C and Zhao, Y and Zhang, Y and Yang, Y and Su, W and Yang, Y and Sun, L and Zhang, F and Yu, J and Wang, Y and Guo, P and Zhu, B and Wu, S}, title = {Gut microbiota specifically mediates the anti-hypercholesterolemic effect of berberine (BBR) and facilitates to predict BBR's cholesterol-decreasing efficacy in patients.}, journal = {Journal of advanced research}, volume = {37}, number = {}, pages = {197-208}, pmid = {35499044}, issn = {2090-1224}, mesh = {Animals ; Bacteria ; *Berberine/pharmacology/therapeutic use ; Cholesterol/pharmacology ; *Gastrointestinal Microbiome ; Humans ; *Hyperlipidemias/drug therapy ; Mice ; }, abstract = {INTRODUCTION: Gut microbiota has been implicated in the pharmacological activities of many natural products. As an effective hypolipidemic agent, berberine (BBR)'s clinical application is greatly impeded by the obvious inter-individual response variation. To date, little evidence exists on the causality between gut microbes and its therapeutic effects, and the linkage of bacteria alterations to the inter-individual response variation.

OBJECTIVES: This study aims to confirm the causal role of the gut microbiota in BBR's anti-hyperlipidemic effect and identify key bacteria that can predict its effectiveness.

METHODS: The correlation between gut microbiota and BBR's inter-individual response variation was studied in hyperlipidemic patients. The causal role of gut microbes in BBR's anti-hyperlipidemic effects was subsequently assessed by altered administration routes, co-treatment with antibiotics, fecal microbiota transplantation, and metagenomic analysis.

RESULTS: Three-month clinical study showed that BBR was effectively to decrease serum lipids but displayed an obvious response variation. The cholesterol-lowering but not triglyceride-decreasing effect of BBR was closely related to its modulation on gut microbiota. Interestingly, the baseline levels of Alistipes and Blautia could accurately predict its anti-hypercholesterolemic efficiency in the following treatment. Causality experiments in mice further confirmed that the gut microbiome is both necessary and sufficient to mediate the lipid-lowering effect of BBR. The absence of Blautia substantially abolished BBR's cholesterol-decreasing efficacy.

CONCLUSION: The gut microbiota is necessary and sufficient for BBR's hyperlipidemia-ameliorating effect. The baseline composition of gut microbes can be an effective predictor for its pharmacotherapeutic efficacy, providing a novel way to achieve personalized therapy.}, } @article {pmid35497193, year = {2022}, author = {Bakir-Gungor, B and Hacılar, H and Jabeer, A and Nalbantoglu, OU and Aran, O and Yousef, M}, title = {Inflammatory bowel disease biomarkers of human gut microbiota selected via different feature selection methods.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13205}, pmid = {35497193}, issn = {2167-8359}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/diagnosis ; *Crohn Disease/diagnosis ; *Colitis, Ulcerative/diagnosis ; Biomarkers ; }, abstract = {The tremendous boost in next generation sequencing and in the "omics" technologies makes it possible to characterize the human gut microbiome-the collective genomes of the microbial community that reside in our gastrointestinal tract. Although some of these microorganisms are considered to be essential regulators of our immune system, the alteration of the complexity and eubiotic state of microbiota might promote autoimmune and inflammatory disorders such as diabetes, rheumatoid arthritis, Inflammatory bowel diseases (IBD), obesity, and carcinogenesis. IBD, comprising Crohn's disease and ulcerative colitis, is a gut-related, multifactorial disease with an unknown etiology. IBD presents defects in the detection and control of the gut microbiota, associated with unbalanced immune reactions, genetic mutations that confer susceptibility to the disease, and complex environmental conditions such as westernized lifestyle. Although some existing studies attempt to unveil the composition and functional capacity of the gut microbiome in relation to IBD diseases, a comprehensive picture of the gut microbiome in IBD patients is far from being complete. Due to the complexity of metagenomic studies, the applications of the state-of-the-art machine learning techniques became popular to address a wide range of questions in the field of metagenomic data analysis. In this regard, using IBD associated metagenomics dataset, this study utilizes both supervised and unsupervised machine learning algorithms, (i) to generate a classification model that aids IBD diagnosis, (ii) to discover IBD-associated biomarkers, (iii) to discover subgroups of IBD patients using k-means and hierarchical clustering approaches. To deal with the high dimensionality of features, we applied robust feature selection algorithms such as Conditional Mutual Information Maximization (CMIM), Fast Correlation Based Filter (FCBF), min redundancy max relevance (mRMR), Select K Best (SKB), Information Gain (IG) and Extreme Gradient Boosting (XGBoost). In our experiments with 100-fold Monte Carlo cross-validation (MCCV), XGBoost, IG, and SKB methods showed a considerable effect in terms of minimizing the microbiota used for the diagnosis of IBD and thus reducing the cost and time. We observed that compared to Decision Tree, Support Vector Machine, Logitboost, Adaboost, and stacking ensemble classifiers, our Random Forest classifier resulted in better performance measures for the classification of IBD. Our findings revealed potential microbiome-mediated mechanisms of IBD and these findings might be useful for the development of microbiome-based diagnostics.}, } @article {pmid35493727, year = {2022}, author = {Li, M and Wang, C and Guo, Q and Xu, C and Xie, Z and Tan, J and Wu, S and Wang, P and Guo, J and Fang, Z and Zhu, S and Duan, L and Jiang, X and Zhu, H}, title = {More Positive or More Negative? Metagenomic Analysis Reveals Roles of Virome in Human Disease-Related Gut Microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {846063}, pmid = {35493727}, issn = {2235-2988}, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; *Diabetes Mellitus, Type 2 ; *Gastrointestinal Microbiome/genetics ; Humans ; *Irritable Bowel Syndrome ; *Microbiota ; Virome/genetics ; *Viruses/genetics ; }, abstract = {Viruses are increasingly viewed as vital components of the human gut microbiota, while their roles in health and diseases remain incompletely understood. Here, we first sequenced and analyzed the 37 metagenomic and 18 host metabolomic samples related to irritable bowel syndrome (IBS) and found that some shifted viruses between IBS and controls covaried with shifted bacteria and metabolites. Especially, phages that infect beneficial lactic acid bacteria depleted in IBS covaried with their hosts. We also retrieved public whole-genome metagenomic datasets of another four diseases (type 2 diabetes, Crohn's disease, colorectal cancer, and liver cirrhosis), totaling 438 samples including IBS, and performed uniform analysis of the gut viruses in diseases. By constructing disease-specific co-occurrence networks, we found viruses actively interacting with bacteria, negatively correlated with possible dysbiosis-related and inflammation-mediating bacteria, increasing the connectivity between bacteria modules, and contributing to the robustness of the networks. Functional enrichment analysis showed that phages interact with bacteria through predation or expressing genes involved in the transporter and secretion system, metabolic enzymes, etc. We further built a viral database to facilitate systematic functional classification and explored the functions of viral genes on interacting with bacteria. Our analyses provided a systematic view of the gut virome in the disease-related microbial community and suggested possible positive roles of viruses concerning gut health.}, } @article {pmid35493492, year = {2022}, author = {Thiam, M and Wang, Q and Barreto Sánchez, AL and Zhang, J and Ding, J and Wang, H and Zhang, Q and Zhang, N and Wang, J and Li, Q and Wen, J and Zhao, G}, title = {Heterophil/Lymphocyte Ratio Level Modulates Salmonella Resistance, Cecal Microbiota Composition and Functional Capacity in Infected Chicken.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {816689}, pmid = {35493492}, issn = {1664-3224}, mesh = {Animals ; Bacteroidetes ; *Chickens ; Lymphocytes ; *Microbiota/genetics ; Propionates ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Salmonella enteritidis ; Valerates ; }, abstract = {The gastrointestinal microbiota plays a vital role in ensuring the maintenance of host health through interactions with the immune system. The Heterophil/Lymphocyte (H/L) ratio reflects poultry's robustness and immune system status. Chickens with low H/L ratio are superior to the chickens with high H/L ratio in survival, immune response, and resistance to Salmonella infection, but the underlying mechanisms remain unclear. This study aimed to identify microorganisms associated with resistance to Salmonella Enteritidis infection in chickens based on the H/L ratio. The 16S rRNA and metagenomic analysis were conducted to examine microbiome and functional capacity between the 2 groups, and Short Chain Fatty Acids (SCFAs) and histopathology were conducted to explore the potential difference between susceptible and resistant groups at 7 and 21 days post-infection (dpi). The microbiome exploration revealed that low H/L ratio chickens, compared to high H/L ratio chickens, displayed a significantly higher abundance of Proteobacteria (Escherichia coli) and Bacteroidetes (Bacteroides plebeius) at 7 and 21 dpi, respectively. Anaerostipes (r = 0.63) and Lachnoclostridium (r = 0.63) were identified as bacterial genus significantly correlated with H/L (P < 0.001). Interestingly, Bacteroides was significantly and positively correlated with bodyweight post-infection (r = 0.72), propionate (r = 0.78) and valerate (r = 0.82) contents, while Salmonella was significantly and negatively correlated with bodyweight post-infection (r = - 0.67), propionate (r = - 0.61) and valerate (r = - 0.65) contents (P < 0.001). Furthermore, the comparative analysis of the functional capacity of cecal microbiota of the chickens with high and low H/L ratio revealed that the chickens with low H/L ratio possess more enriched immune pathways, lower antibiotic resistance genes and virulence factors compared to the chickens with high H/L ratio. These results suggest that the chickens with low H/L ratio are more resistant to Salmonella Enteritidis, and it is possible that the commensal Proteobacteria and Bacteroidetes are involved in this resistance against Salmonella infection. These findings provide valuable resources for selecting and breeding disease-resistant chickens.}, } @article {pmid35491162, year = {2022}, author = {Goto, M and Kobira, Y and Kaneko, S and Arima, H and Michihara, A and Azuma, K and Higashi, T and Motoyama, K and Watanabe, H and Maruyama, T and Kadowaki, D and Otagiri, M and Iohara, D and Hirayama, F and Anraku, M}, title = {The Effects of Sacran, a Sulfated Polysaccharide, on Gut Microbiota Using Chronic Kidney Disease Model Rats.}, journal = {Biological & pharmaceutical bulletin}, volume = {45}, number = {5}, pages = {576-582}, doi = {10.1248/bpb.b21-00897}, pmid = {35491162}, issn = {1347-5215}, mesh = {Animals ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Polysaccharides/pharmacology/therapeutic use ; Rats ; *Renal Insufficiency, Chronic/drug therapy ; Sulfates/therapeutic use ; }, abstract = {The aim of this study was to investigate the beneficial effects of sacran, a sulfated polysaccharide, on renal damage and intestinal microflora, in 5/6 nephrectomy rats as a model for chronic kidney disease (CKD). 5/6 Nephrectomy rats were divided into sacran treated and non-treated groups and examined for lethality after 4 weeks. The 5/6 nephrectomy rats were also divided into three groups: sacran treated, non-treated and AST-120 treated groups, and treated orally in a concentration-dependent manner for 4 weeks. Renal function was estimated by biochemical and histopathological analyses. Metagenomic analysis of feces from each group after 4 weeks was also performed and changes in intestinal microflora were compared. The administration of sacran to CKD rats at ≥19 mg/d increased their survival. In addition, the sacran-treated group improved CKD-related parameters in a concentration-dependent manner, and the inhibitory effect of 40 mg/d of sacran was comparable to that of AST-120. The changes in the intestinal microflora of the sacran treated group were positively correlated with an increase in the number of Lactobacillus species, which are known to be rich in beneficial bacteria, and the increment of this beneficial bacteria was negatively correlated with the concentration of indoxyl sulfate, a uremic toxin, in plasma. These results strongly suggest that the oral administration of sacran could contribute to the stabilization of intestinal microflora in CKD rats and to the reduction of oxidative stress as well as the inhibition of progression of CKD.}, } @article {pmid35489611, year = {2022}, author = {Saqr, A and Carlson, B and Staley, C and Rashidi, A and Al-Kofahi, M and Kaiser, T and Holtan, S and MacMillan, M and Young, JA and Jurdi, NE and Weisdorf, D and Khoruts, A and Jacobson, PA}, title = {Reduced Enterohepatic Recirculation of Mycophenolate and Lower Blood Concentrations Are Associated with the Stool Bacterial Microbiome after Hematopoietic Cell Transplantation.}, journal = {Transplantation and cellular therapy}, volume = {28}, number = {7}, pages = {372.e1-372.e9}, doi = {10.1016/j.jtct.2022.04.018}, pmid = {35489611}, issn = {2666-6367}, support = {P30 CA077598/CA/NCI NIH HHS/United States ; UL1 TR002494/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Bacteria/metabolism ; Enzyme Inhibitors ; Glucuronidase ; Glucuronides ; *Graft vs Host Disease/chemically induced ; *Hematopoietic Stem Cell Transplantation ; Humans ; Immunosuppressive Agents/therapeutic use ; *Microbiota ; Mycophenolic Acid/therapeutic use ; }, abstract = {Mycophenolate mofetil (MMF) is an important immunosuppressant used after allogeneic hematopoietic cell transplantation (HCT). MMF has a narrow therapeutic index, and blood concentrations of mycophenolic acid (MPA), the active component of MMF, are highly variable. Low MPA concentrations are associated with the risk of graft-versus-host disease (GVHD), whereas high concentrations are associated with toxicity. Reasons for variability are not well known and may include the presence of β-glucuronidase-producing bacteria in the gastrointestinal tract, which enhance MPA enterohepatic recirculation (EHR) by transforming MPA metabolites formed in the liver back to MPA. This study was conducted to determine whether individuals with high MPA EHR have a greater abundance of β-glucuronidase-producing bacteria in their stool and higher MPA concentrations compared with those with low EHR. We conducted a pharmacomicrobiomics study in 20 adult HCT recipients receiving a myeloablative or reduced-intensity preparative regimen. Participants received MMF 1 g i.v. every 8 hours with tacrolimus. Intensive pharmacokinetic sampling of MMF was conducted before hospital discharge; total MPA, MPA glucuronide (MPAG), and acyl-glucuronide metabolite (acylMPAG) were measured. EHR was defined as the ratio of MPA area under the concentration-versus-time curve (AUC)4-8 to MPA AUC0-8. Differences in stool microbiome diversity and composition, determined by shotgun metagenomic sequencing, were compared above and below the median EHR (22%; range, 5% to 44%). The median EHR was 12% in the low EHR group and 29% in the high EHR group. MPA troughs, MPA AUC4-8, and acyl-glucuronide metabolite (acylMPAG) AUC4-8/AUC0-8 ratio were greater in the high EHR group compared with the low EHR group (1.53 μg/mL versus .28 μg/mL [P = .0001], 7.33 hour·μg/mL versus 1.79 hour·μg/mL [P = .0003], and .33 hour·μg/mL versus .24 hour·μg/mL [P = .0007], respectively). MPA AUC0-8 was greater in the high EHR group than in the low EHR group, and the difference trended toward significance (22.8 hour·μg/mL versus 15.3 hour·μg/mL; P = .06). Bacteroides vulgatus, Bacteroides stercoris, and Bacteroides thetaiotaomicron were 1.2- to 2.4-fold more abundant (P = .039, .024, and .046, respectively) in the high EHR group. MPA EHR was positively correlated with B. vulgatus (⍴ = .58; P ≤ .01) and B. thetaiotaomicron (⍴ = .46; P < .05) and negatively correlated with Blautia hydrogenotrophica (⍴ = -.53; P < .05). Therapeutic MPA troughs were achieved in 80% of patients in the high EHR group but in no patients in the low EHR group. There was a trend toward differences in MPA AUC0-8 and MPA concentration at steady-state (μg/mL) between the high EHR group versus the low EHR group (P = .06). MPA EHR was variable. Patients with high MPA EHR had greater abundance of Bacteroides species in stool and higher MPA exposure compared with patients with low MPA EHR. Therefore, Bacteroides may be protective against poor outcomes, such as graft-versus-host disease, in some patients but may increase the risk of MPA adverse effects in others. These data need to be confirmed and studied after oral MMF therapy.}, } @article {pmid35489490, year = {2022}, author = {Sanseverino, I and Gómez, L and Navarro, A and Cappelli, F and Niegowska, M and Lahm, A and Barbiere, M and Porcel-Rodríguez, E and Valsecchi, S and Pedraccini, R and Crosta, S and Lettieri, T}, title = {Holistic approach to chemical and microbiological quality of aquatic ecosystems impacted by wastewater effluent discharges.}, journal = {The Science of the total environment}, volume = {835}, number = {}, pages = {155388}, doi = {10.1016/j.scitotenv.2022.155388}, pmid = {35489490}, issn = {1879-1026}, mesh = {Bacteria ; Environmental Monitoring/methods ; *Microbiota ; Rivers/chemistry ; Waste Disposal, Fluid/methods ; Wastewater/chemistry ; *Water Pollutants, Chemical/analysis ; *Water Purification ; }, abstract = {Wastewater treatment plants (WWTPs) collect wastewater from various sources and use different treatment processes to reduce the load of pollutants in the environment. Since the removal of many chemical pollutants and bacteria by WWTPs is incomplete, they constitute a potential source of contaminants. The continuous release of contaminants through WWTP effluents can compromise the health of the aquatic ecosystems, even if they occur at very low concentrations. The main objective of this work was to characterize, over a period of four months, the treatment steps starting from income to the effluent and 5 km downstream to the receiving river. In this context, the efficiency removal of chemical pollutants (e.g. hormones and pharmaceuticals, including antibiotics) and bacteria was assessed in a WWTP case study by using a holistic approach. It embraces different chemical and biological-based methods, such as pharmaceutical analysis by HPLC-MSMS, growth rate inhibition in algae, ligand binding estrogen receptor assay, microbial community study by 16S and shotgun sequencing along with relative quantification of resistance genes by quantitative polymerase chain reaction. Although both, chemical and biological-based methods showed a significant reduction of the pollutant burden in effluent and surface waters compared to the influent of the WWTP, no complete removal of pollutants, pathogens and antibiotic resistance genes was observed.}, } @article {pmid35489450, year = {2022}, author = {Dai, C and Wu, H and Wang, X and Zhao, K and Lu, Z}, title = {Network and meta-omics reveal the cooperation patterns and mechanisms in an efficient 1,4-dioxane-degrading microbial consortium.}, journal = {Chemosphere}, volume = {301}, number = {}, pages = {134723}, doi = {10.1016/j.chemosphere.2022.134723}, pmid = {35489450}, issn = {1879-1298}, mesh = {Bacteria/metabolism ; Biodegradation, Environmental ; *Dioxanes/metabolism ; Humans ; *Microbial Consortia/genetics ; Xanthobacter ; }, abstract = {1,4-Dioxane is an emerging wastewater contaminant with probable human carcinogenicity. Our current understanding of microbial interactions during 1,4-dioxane biodegradation process in mixed cultures is limited. Here, we applied metagenomic, metatranscriptomic and co-occurrence network analyses to unraveling the microbial cooperation between degrader and non-degraders in an efficient 1,4-dioxane-degrading microbial consortium CH1. A 1,4-dioxane-degrading bacterium, Ancylobacter polymorphus ZM13, was isolated from CH1 and had a potential of being one of the important degraders due to its high relative abundance, highly expressed monooxygenase genes tmoABCDEF and high betweenness centrality of networks. The strain ZM13 cooperated obviously with 6 bacterial genera in the network, among which Xanthobacter and Mesorhizobium could be involved in the intermediates metabolism with responsible genes encoding alcohol dehydrogenase (adh), aldehyde dehydrogenase (aldh), glycolate oxidase (glcDEF), glyoxylate carboligase (gcl), malate synthase (glcB) and 2-isopropylmalate synthase (leuA) differentially high-expressed. Also, 1,4-dioxane facilitated the shift of biodiversity and function of CH1, and those cooperators cooperated with ZM13 in the way of providing amino acids or fatty acids, as well as relieving environmental stresses to promote biodegradation. These results provide new insights into our understandings of the microbial interactions during 1,4-dioxane degradation, and have important implications for predicting microbial cooperation and constructing efficient and stable synthetic 1,4-dioxane-degrading consortia for practical remediation.}, } @article {pmid35485976, year = {2023}, author = {Jiang, Y and Balaban, M and Zhu, Q and Mirarab, S}, title = {DEPP: Deep Learning Enables Extending Species Trees using Single Genes.}, journal = {Systematic biology}, volume = {72}, number = {1}, pages = {17-34}, pmid = {35485976}, issn = {1076-836X}, support = {R35 GM142725/GM/NIGMS NIH HHS/United States ; }, mesh = {Phylogeny ; *Deep Learning ; RNA, Ribosomal, 16S/genetics ; Algorithms ; *Microbiota/genetics ; }, abstract = {Placing new sequences onto reference phylogenies is increasingly used for analyzing environmental samples, especially microbiomes. Existing placement methods assume that query sequences have evolved under specific models directly on the reference phylogeny. For example, they assume single-gene data (e.g., 16S rRNA amplicons) have evolved under the GTR model on a gene tree. Placement, however, often has a more ambitious goal: extending a (genome-wide) species tree given data from individual genes without knowing the evolutionary model. Addressing this challenging problem requires new directions. Here, we introduce Deep-learning Enabled Phylogenetic Placement (DEPP), an algorithm that learns to extend species trees using single genes without prespecified models. In simulations and on real data, we show that DEPP can match the accuracy of model-based methods without any prior knowledge of the model. We also show that DEPP can update the multilocus microbial tree-of-life with single genes with high accuracy. We further demonstrate that DEPP can combine 16S and metagenomic data onto a single tree, enabling community structure analyses that take advantage of both sources of data. [Deep learning; gene tree discordance; metagenomics; microbiome analyses; neural networks; phylogenetic placement.].}, } @article {pmid35484634, year = {2022}, author = {Duncan, A and Barry, K and Daum, C and Eloe-Fadrosh, E and Roux, S and Schmidt, K and Tringe, SG and Valentin, KU and Varghese, N and Salamov, A and Grigoriev, IV and Leggett, RM and Moulton, V and Mock, T}, title = {Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {67}, pmid = {35484634}, issn = {2049-2618}, mesh = {Atlantic Ocean ; Chlorophyll A ; Eukaryota/genetics ; *Metagenome/genetics ; *Microbiota/genetics ; Phylogeny ; Phytoplankton/genetics ; }, abstract = {BACKGROUND: Phytoplankton communities significantly contribute to global biogeochemical cycles of elements and underpin marine food webs. Although their uncultured genomic diversity has been estimated by planetary-scale metagenome sequencing and subsequent reconstruction of metagenome-assembled genomes (MAGs), this approach has yet to be applied for complex phytoplankton microbiomes from polar and non-polar oceans consisting of microbial eukaryotes and their associated prokaryotes.

RESULTS: Here, we have assembled MAGs from chlorophyll a maximum layers in the surface of the Arctic and Atlantic Oceans enriched for species associations (microbiomes) with a focus on pico- and nanophytoplankton and their associated heterotrophic prokaryotes. From 679 Gbp and estimated 50 million genes in total, we recovered 143 MAGs of medium to high quality. Although there was a strict demarcation between Arctic and Atlantic MAGs, adjacent sampling stations in each ocean had 51-88% MAGs in common with most species associations between Prasinophytes and Proteobacteria. Phylogenetic placement revealed eukaryotic MAGs to be more diverse in the Arctic whereas prokaryotic MAGs were more diverse in the Atlantic Ocean. Approximately 70% of protein families were shared between Arctic and Atlantic MAGs for both prokaryotes and eukaryotes. However, eukaryotic MAGs had more protein families unique to the Arctic whereas prokaryotic MAGs had more families unique to the Atlantic.

CONCLUSION: Our study provides a genomic context to complex phytoplankton microbiomes to reveal that their community structure was likely driven by significant differences in environmental conditions between the polar Arctic and warm surface waters of the tropical and subtropical Atlantic Ocean. Video Abstract.}, } @article {pmid35484230, year = {2022}, author = {Edwinson, AL and Yang, L and Peters, S and Hanning, N and Jeraldo, P and Jagtap, P and Simpson, JB and Yang, TY and Kumar, P and Mehta, S and Nair, A and Breen-Lyles, M and Chikkamenahalli, L and Graham, RP and De Winter, B and Patel, R and Dasari, S and Kashyap, P and Griffin, T and Chen, J and Farrugia, G and Redinbo, MR and Grover, M}, title = {Gut microbial β-glucuronidases regulate host luminal proteases and are depleted in irritable bowel syndrome.}, journal = {Nature microbiology}, volume = {7}, number = {5}, pages = {680-694}, pmid = {35484230}, issn = {2058-5276}, support = {R01 GM135218/GM/NIGMS NIH HHS/United States ; R03 DK120745/DK/NIDDK NIH HHS/United States ; R01 GM137286/GM/NIGMS NIH HHS/United States ; R01 DK127998/DK/NIDDK NIH HHS/United States ; K23 DK103911/DK/NIDDK NIH HHS/United States ; P30 DK084567/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bilirubin ; Endopeptidases ; Escherichia coli ; *Gastrointestinal Microbiome/physiology ; Glucuronidase/genetics ; Humans ; *Irritable Bowel Syndrome ; Mice ; Serine Proteases/genetics ; }, abstract = {Intestinal proteases mediate digestion and immune signalling, while increased gut proteolytic activity disrupts the intestinal barrier and generates visceral hypersensitivity, which is common in irritable bowel syndrome (IBS). However, the mechanisms controlling protease function are unclear. Here we show that members of the gut microbiota suppress intestinal proteolytic activity through production of unconjugated bilirubin. This occurs via microbial β-glucuronidase-mediated conversion of bilirubin conjugates. Metagenomic analysis of faecal samples from patients with post-infection IBS (n = 52) revealed an altered gut microbiota composition, in particular a reduction in Alistipes taxa, and high gut proteolytic activity driven by specific host serine proteases compared with controls. Germ-free mice showed 10-fold higher proteolytic activity compared with conventional mice. Colonization with microbiota samples from high proteolytic activity IBS patients failed to suppress proteolytic activity in germ-free mice, but suppression of proteolytic activity was achieved with colonization using microbiota from healthy donors. High proteolytic activity mice had higher intestinal permeability, a higher relative abundance of Bacteroides and a reduction in Alistipes taxa compared with low proteolytic activity mice. High proteolytic activity IBS patients had lower fecal β-glucuronidase activity and end-products of bilirubin deconjugation. Mice treated with unconjugated bilirubin and β-glucuronidase-overexpressing E. coli significantly reduced proteolytic activity, while inhibitors of microbial β-glucuronidases increased proteolytic activity. Together, these data define a disease-relevant mechanism of host-microbial interaction that maintains protease homoeostasis in the gut.}, } @article {pmid35484115, year = {2022}, author = {Pan, S and Zhu, C and Zhao, XM and Coelho, LP}, title = {A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {2326}, pmid = {35484115}, issn = {2041-1723}, mesh = {Algorithms ; *Metagenome/genetics ; Metagenomics/methods ; *Microbiota/genetics ; Neural Networks, Computer ; }, abstract = {Metagenomic binning is the step in building metagenome-assembled genomes (MAGs) when sequences predicted to originate from the same genome are automatically grouped together. The most widely-used methods for binning are reference-independent, operating de novo and enable the recovery of genomes from previously unsampled clades. However, they do not leverage the knowledge in existing databases. Here, we introduce SemiBin, an open source tool that uses deep siamese neural networks to implement a semi-supervised approach, i.e. SemiBin exploits the information in reference genomes, while retaining the capability of reconstructing high-quality bins that are outside the reference dataset. Using simulated and real microbiome datasets from several different habitats from GMGCv1 (Global Microbial Gene Catalog), including the human gut, non-human guts, and environmental habitats (ocean and soil), we show that SemiBin outperforms existing state-of-the-art binning methods. In particular, compared to other methods, SemiBin returns more high-quality bins with larger taxonomic diversity, including more distinct genera and species.}, } @article {pmid35483672, year = {2022}, author = {Malmstrom, CM and Martin, MD and Gagnevin, L}, title = {Exploring the Emergence and Evolution of Plant Pathogenic Microbes Using Historical and Paleontological Sources.}, journal = {Annual review of phytopathology}, volume = {60}, number = {}, pages = {187-209}, doi = {10.1146/annurev-phyto-021021-041830}, pmid = {35483672}, issn = {1545-2107}, mesh = {Animals ; Archaea ; Bacteria ; *Fungi ; Humans ; *Microbiota ; Plants ; }, abstract = {Biotechnological advances now permit broad exploration of past microbial communities preserved in diverse substrates. Despite biomolecular degradation, high-throughput sequencing of preserved materials can yield invaluable genomic and metagenomic data from the past. This line of research has expanded from its initial human- and animal-centric foci to include plant-associated microbes (viruses, archaea, bacteria, fungi, and oomycetes), for which historical, archaeological, and paleontological data illuminate past epidemics and evolutionary history. Genetic mechanisms underlying the acquisition of microbial pathogenicity, including hybridization, polyploidization, and horizontal gene transfer, can now be reconstructed, as can gene-for-gene coevolution with plant hosts. Epidemiological parameters, such as geographic origin and range expansion, can also be assessed. Building on published case studies with individual phytomicrobial taxa, the stage is now set for broader, community-wide studies of preserved plant microbiomes to strengthen mechanistic understanding of microbial interactions and plant disease emergence.}, } @article {pmid35482264, year = {2022}, author = {Paranhos, AGO and Pereira, AR and da Fonseca, YA and de Queiroz Silva, S and de Aquino, SF}, title = {Tylosin in anaerobic reactors: degradation kinetics, effects on methane production and on the microbial community.}, journal = {Biodegradation}, volume = {33}, number = {3}, pages = {283-300}, pmid = {35482264}, issn = {1572-9729}, support = {2510001557612017-21//National Health Fundation - FUNASA/ ; 423101/2018-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; APQ-02701-18//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; }, mesh = {Anaerobiosis ; Biodegradation, Environmental ; Bioreactors/microbiology ; Kinetics ; Methane/metabolism ; *Microbiota ; *Tylosin/pharmacology ; }, abstract = {Tylosin eliminated in animal waste, during therapeutic treatment, can be efficiently removed in anaerobic systems. The present study investigated the influence of tylosin concentration and assessed its degradation kinetics and the microorganisms involved in each stage of its anaerobic digestion (hydrolysis/acidogenesis; acetogenesis; methanogenesis). The results showed a stimulating effect on methane production with increasing tylosin concentration in the poultry litter up to 80 mg kg[-1] tylosin (232.9 NL CH4 kg SV[-1]). As for tylosin degradation, greater removal of antibiotics was observed in the methanogenic phase (88%), followed by acetogenic (84%) and hydrolytic/acidogenic (76%) phases. The higher rate of tylosin degradation obtained in the methanogenic step, is mainly related to the co-metabolic effect exerted by the presence of acetate and its degradation by acetoclastic methanogens. Indeed, metagenomic analyses suggested a syntrophic action between archaea of the genus Methanobacterium, and bacteria such as Clostridium and Flexilinea, which seemed decisive for tylosin degradation.}, } @article {pmid35477737, year = {2022}, author = {Wang, H and Yang, GX and Hu, Y and Lam, P and Sangha, K and Siciliano, D and Swenerton, A and Miller, R and Tilley, P and Von Dadelszen, P and Kalyan, S and Tang, P and Patel, MS}, title = {Comprehensive human amniotic fluid metagenomics supports the sterile womb hypothesis.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6875}, pmid = {35477737}, issn = {2045-2322}, support = {130494//CIHR/Canada ; }, mesh = {Amniotic Fluid ; Female ; Humans ; Metagenomics ; *Microbiota/genetics ; *Nucleic Acids ; Uterus ; }, abstract = {As metagenomic approaches for detecting infectious agents have improved, each tissue that was once thought to be sterile has been found to harbor a variety of microorganisms. Controversy still exists over the status of amniotic fluid, which is part of an immunologically privileged zone that is required to prevent maternal immune system rejection of the fetus. Due to this privilege, the exclusion of microbes has been proposed to be mandatory, leading to the sterile womb hypothesis. Since nucleic acid yields from amniotic fluid are very low, contaminating nucleic acid found in water, reagents and the laboratory environment frequently confound attempts to address this hypothesis. Here we present metagenomic criteria for microorganism detection and a metagenomic method able to be performed with small volumes of starting material, while controlling for exogenous contamination, to circumvent these and other pitfalls. We use this method to show that human mid-gestational amniotic fluid has no detectable virome or microbiome, supporting the sterile womb hypothesis.}, } @article {pmid35477306, year = {2022}, author = {Kwan, SY and Sabotta, CM and Joon, A and Wei, P and Petty, LE and Below, JE and Wu, X and Zhang, J and Jenq, RR and Hawk, ET and McCormick, JB and Fisher-Hoch, SP and Beretta, L}, title = {Gut Microbiome Alterations Associated with Diabetes in Mexican Americans in South Texas.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0003322}, pmid = {35477306}, issn = {2379-5077}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; P50 CA217674/CA/NCI NIH HHS/United States ; UL1 TR000371/TR/NCATS NIH HHS/United States ; UL1 TR003167/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Butyrates ; *Diabetes Mellitus, Type 2/epidemiology ; Enterobacteriaceae ; *Gastrointestinal Microbiome/genetics ; Mexican Americans/genetics ; Prospective Studies ; Texas/ethnology ; }, abstract = {Mexican Americans have a high prevalence of diabetes and burden of diabetes-related complications, highlighting the need for novel preventive strategies and noninvasive predictors of diabetes risk tailored to this population. Changes in the gut microbiome have the potential to predict diabetes. Here, we aimed to identify alterations in the gut microbiome associated with diabetes in the high-risk population of Mexican Americans in South Texas. Stool samples were collected from 216 subjects from the population-based Cameron County Hispanic Cohort. Among them, 75 had type 2 diabetes. Taxonomic and functional profiling of the stool samples were assessed by 16S and shotgun metagenomic sequencing, and the influence of genetic factors was explored. The gut microbiome of subjects with diabetes was enriched with proinflammatory Proteobacteria members (Enterobacteriaceae, Escherichia-Shigella) and depleted of butyrate-producing Clostridiales members (Faecalibacterium prausnitzii, Peptostreptococcaceae, and Clostridium sensu stricto 1). The accompanying metagenomic changes in subjects with diabetes suggested dysregulated amino acid metabolism, reduced galacturonate and glucuronate catabolism (correlating with Faecalibacterium prausnitzii abundance), and enriched heme biosynthesis (correlating with Enterobacteriaceae abundance). Polymorphism rs7129790 near MMP27 was strongly associated with high Proteobacteria abundance and was more frequent in this cohort and in individuals of Mexican ancestry than in Europeans. In conclusion, Mexican Americans in South Texas with diabetes display distinct gut microbiome and metagenomic signatures. These signatures may have utility in risk modeling and disease prevention in this high-risk population. IMPORTANCE The gut microbiome composition varies across ethnicities and geographical locations, yet studies on diabetes-associated microbiome changes specific to high-risk Mexican Americans are lacking. Here, we aimed to identify specific alterations associated with diabetes in this population, as well as host genetic factors that may explain increased disease susceptibility in this ethnic group. Using samples from a population-based cohort of Mexican Americans with a high prevalence of obesity and diabetes, we confirmed findings from studies on other ethnicities that suggested promotion of a chronic proinflammatory environment, loss of butyrate production, and compromised intestinal barrier integrity. High abundance of proinflammatory Proteobacteria was associated with a polymorphism that was more frequent in this cohort and in individuals of Mexican ancestry than in Europeans. Validation of microbiome-based risk models for diabetes should be evaluated in prospective cohort studies.}, } @article {pmid35477134, year = {2022}, author = {Kairmi, SH and Taha-Abdelaziz, K and Yitbarek, A and Sargolzaei, M and Spahany, H and Astill, J and Shojadoost, B and Alizadeh, M and Kulkarni, RR and Parkinson, J and Sharif, S}, title = {Effects of therapeutic levels of dietary antibiotics on the cecal microbiome composition of broiler chickens.}, journal = {Poultry science}, volume = {101}, number = {6}, pages = {101864}, pmid = {35477134}, issn = {1525-3171}, mesh = {Animal Feed/analysis ; Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria ; Cecum/microbiology ; Chickens ; Diet/veterinary ; Dietary Supplements/analysis ; *Enteritis/veterinary ; *Microbiota ; }, abstract = {Dietary antibiotics, including antibiotic growth promoters (AGPs), have been commonly used to improve health and growth of poultry. The present study investigated the effects of therapeutic doses of dietary antibiotics, including bacitracin methylene disalicylate (BMD), penicillin G potassium (PP) and an ionophore (salinomycin, SA), on the cecal microbiome of chickens. BMD and SA treatments were given as dietary supplements from d 1 to 35 of age. The SAPP (salinomycin+ penicillin G potassium) group was given SA as a dietary supplement from d 1 to 35 of age and PP was added to drinking water from d 19 to 24 of age to simulate common practices for control of necrotic enteritis in broilers. The cecal contents were collected from all treatment groups on d 10, 24, and 35 of age and DNA was extracted for metagenomic analysis of the cecal microbiome. The results revealed that dietary or water supplementation of therapeutic levels of antibiotics and ionophores to chickens significantly altered the cecal microbial homeostasis during different stages of the chicken life. The alpha diversity analysis showed that BMD, SA, and SAPP treatments decreased diversity and evenness of the cecal microbiome of treated chickens on d 10 of age. Species richness was also reduced on d 35 following treatment with BMD. Beta diversity analyses revealed that SAPP and BMD induced significant changes in the relative abundance of Gram-positive and -negative bacteria on d 10, while no significant differences were observed on d 24. On d 35, the non-treated control group had higher relative abundance of unclassified Gram-positive and -negative bacteria compared to SA, SAPP, and BMD treatment groups. Overall, despite their beneficial role in controlling necrotic enteritis outbreaks, the findings of this study highlight the potential negative effects of dietary supplementation of therapeutic levels of antibiotics on the gut microbiome and suggest that adjusting gut bacteria may be required to restore microbial richness and diversity of the gut microbiome following treatment with these antibiotics.}, } @article {pmid35476894, year = {2022}, author = {Lee, CC and Liang, F and Lee, IC and Lu, TH and Shan, YY and Jeng, CF and Zou, YF and Yu, HT and Chen Alen, SK}, title = {External light-dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells.}, journal = {EMBO reports}, volume = {23}, number = {6}, pages = {e52316}, pmid = {35476894}, issn = {1469-3178}, mesh = {Animals ; Circadian Rhythm ; *Gastrointestinal Microbiome ; Light ; Mice ; Photoperiod ; RNA, Ribosomal, 16S/metabolism ; *Retinal Ganglion Cells/metabolism ; Rod Opsins/genetics/metabolism ; }, abstract = {Gut microbiota are involved in many physiological functions such as metabolism, brain development, and neurodegenerative diseases. Many microbes in the digestive tract do not maintain a constant level of their relative abundance but show daily oscillations under normal conditions. Recent evidence indicates that chronic jetlag, constant darkness, or deletion of the circadian core gene can alter the composition of gut microbiota and dampen the daily oscillation of gut microbes. However, the neuronal circuit responsible for modulating gut microbiota remained unclear. Using genetic mouse models and 16s rRNA metagenomic analysis, we find that light-dark cycle information transmitted by the intrinsically photosensitive retinal ganglion cells (ipRGCs) is essential for daily oscillations of gut microbes under temporal restricted high-fat diet conditions. Furthermore, aberrant light exposure such as dim light at night (dLAN) can alter the composition, relative abundance, and daily oscillations of gut microbiota. Together, our results indicate that external light-dark cycle information can modulate gut microbiota in the direction from the brain to the gut via the sensory system.}, } @article {pmid35475684, year = {2022}, author = {Rubin, IMC and Mollerup, S and Broholm, C and Knudsen, SB and Baker, A and Helms, M and Holm, MKA and Kallemose, T and Westh, H and Dahl Knudsen, J and Pinholt, M and Petersen, AM}, title = {No Effect of Lactobacillus rhamnosus GG on Eradication of Colonization by Vancomycin-Resistant Enterococcus faecium or Microbiome Diversity in Hospitalized Adult Patients.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0234821}, pmid = {35475684}, issn = {2165-0497}, mesh = {Adult ; Aged ; Child ; *Enterococcus faecium ; *Gram-Positive Bacterial Infections/drug therapy ; Humans ; *Lacticaseibacillus rhamnosus ; *Microbiota ; *Probiotics/therapeutic use ; Vancomycin/pharmacology/therapeutic use ; *Vancomycin-Resistant Enterococci ; }, abstract = {The purpose of this trial was to evaluate the efficacy of a 4-week supplementation of Lactobacillus rhamnosus GG (LGG) in eliminating the gastrointestinal carrier state of vancomycin-resistant Enterococcus faecium (VREfm) in hospitalized adults. The primary outcome of the study was the number of patients with cleared VREfm colonization after the 4-week intervention. Secondary outcomes were clearance of VREfm colonization at weeks 8, 16, and 24, number of VREfm infections (isolated from nonintestinal foci), and changes in fecal microbiome diversity after the intervention. The trial was a multicenter, randomized, double-blind, placebo-controlled trial in hospitalized adult VREfm carriers. Patients were enrolled and randomized to receive 60 billion CFU of LGG daily or placebo for 4 weeks. For a subgroup of patients, rectal swabs for VREfm were collected also at 8, 16, and 24 weeks and analyzed using shotgun metagenomics. Patients ingesting a minimum of 50% of the probiotic during the 4-week intervention were included in subsequent outcome analyses (48 of 81 patients). Twelve of 21 patients in the LGG group (57%) compared to 15 of 27 patients in the placebo group (56%) cleared their VREfm carriage. Eighteen patients completed the entire 24-week intervention with the same minimum compliancy. Of these, almost 90% in both groups cleared their VREfm carriage. We found a statistically significant difference between VREfm clearers and nonclearers regarding metronidazole and vancomycin usage as well as length of hospitalization after inclusion. The microbiome analyses revealed no significant difference in alpha diversity between the LGG and the placebo group. Beta diversity differed between the groups and the different time points. This study did not show an effect of LGG in eradication of VREfm after a 4-week intervention. IMPORTANCE Whereas other studies exploring the effect of L. rhamnosus in clearing VREfm from the intestine included children and adults, with a wider age range, our study consisted of a geriatric patient cohort. The natural clearance of VREfm in this study was almost 60% after 4 weeks, thus much higher than described previously. Also, this study characterizes the microbiome of VREfm patients in detail. This article showed no effect of the probiotic L. rhamnosus in clearing VREfm from the intestine of patients.}, } @article {pmid35473500, year = {2022}, author = {Jiang, C and Sun, XR and Feng, J and Zhu, SF and Shui, W}, title = {Metagenomic analysis reveals the different characteristics of microbial communities inside and outside the karst tiankeng.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {115}, pmid = {35473500}, issn = {1471-2180}, mesh = {Humans ; Metagenome ; *Microbiota ; Nitrogen ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {BACKGROUND: Karst tiankengs serve as a reservoir of biodiversity in the degraded karst landscape areas. However, the microbial diversity of karst tiankengs is poorly understood. Here, we investigated the composition and function of the microbial community in a karst tiankeng.

RESULTS: We found that habitat differences inside and outside the karst tiankeng changed the composition and structure of the soil microbial communities, and the dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi and Acidobacteria. The Shannon-Wiener diversity of microbial communities inside and outside the tiankeng was significantly different, and it was higher inside the tiankeng (IT). Venn and LEfSe analysis found that the soil microbial communities inside the tiankeng had 640 more endemic species and 39 more biomarker microbial clades than those identified outside of the tiankeng (OT)..Functional prediction indicated that soil microorganisms in outside the tiankeng had a high potential for carbohydrate metabolism, translation and amino acid metabolism. There were biomarker pathways associated with several of human diseases at both IT and OT sites. Except for auxiliary activities (AA), other CAZy classes had higher abundance at IT sites, which can readily convert litter and fix carbon and nitrogen, thereby supporting the development of underground forests. The differences in microbial communities were mainly related to the soil water content and soil total nitrogen.

CONCLUSIONS: Our results provide a metagenomic overview of the karst tiankeng system and provide new insights into habitat conservation and biodiversity restoration in the area.}, } @article {pmid35469423, year = {2022}, author = {Yin, J and Zhang, Z and Guo, Y and Chen, Y and Xu, Y and Chen, W and Shao, Y and Yu, Y and Zhu, L and Chen, L and Ruan, L}, title = {Precision Probiotics in Agroecosystems: Multiple Strategies of Native Soil Microbiotas for Conquering the Competitor Ralstonia solanacearum.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0115921}, pmid = {35469423}, issn = {2379-5077}, mesh = {RNA, Ribosomal, 16S/genetics ; *Ralstonia solanacearum/genetics ; *Microbiota/genetics ; *Probiotics/pharmacology ; Soil ; *Solanum lycopersicum ; }, abstract = {Ralstonia solanacearum (Rs), a soilborne phytopathogen, causes bacterial wilt disease in a broad range of hosts. Common approaches, for example, the direct reduction of the pathogen using classic single broad-spectrum probiotics, suffer from poor colonization efficiency, interference by resident microbiota, and nonnative-microorganism invasion. The soil microbiota plays an important role in plant health. Revealing the intrinsic linkage between the microbiome and the occurrence of disease and then applying it to agroecosystems for the precise control of soilborne diseases should be an effective strategy. Here, we surveyed the differences in the microbiome between healthy and diseased soils used for tomato planting across six climatic regions in China by using 16S rRNA amplicon and metagenomic sequencing. The roles of species associated with disease symptoms were further validated. Healthy soil possessed more diverse bacterial communities and more potential plant probiotics than diseased soil. Healthy soil simultaneously presented multiple strategies, including specifically antagonizing Rs, decreasing the gene expression of the type III secretion system of Rs, and competing for nutrition with Rs. Bacteria enriched in diseased samples promoted the progression of tomato bacterial wilt by strengthening the chemotaxis of pathogens. Therefore, Rs and its collaborators should be jointly combatted for disease suppression. Our research provides integrated insights into a multifaceted strategy for the biocontrol of tomato bacterial wilt based on the individual network of local microbiota. IMPORTANCE In the current work, the relationship between the soil microbiota and tomato bacterial wilt on a large scale offered us a comprehensive understanding of the disease. The delicate strategy of the microbiota in soil used for growing tomatoes to conquer the strong competitor, Rs, was revealed by microbiome research. The collaborators of Rs that coexist in a common niche with Rs strengthened our understanding of the pathogenesis of bacterial wilt. Bacteria enriched in healthy soil that antagonized pathogens with high specificity provide a novel view for ecofriendly probiotics mining. Our study offers new perspectives on soilborne-pathogen biocontrol in agroecosystems by decoding the rule of the natural ecosystem.}, } @article {pmid35469377, year = {2022}, author = {Pathak, B and Khataniar, A and Das, B and Upadhyaya, S and Medhi, A and Bhuyan, PK and Buragohain, AK and Borah, D}, title = {Spatio-temporal diversity of biological aerosols over Northeast India: a metagenomic approach.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {42}, pages = {64096-64111}, pmid = {35469377}, issn = {1614-7499}, support = {ECR/2016/00132//Department of Science and Technology's Science and Engineering Research Board (DST-SERB), Govt. of India/ ; }, mesh = {Aerosols/analysis ; Bacteria/genetics ; *Environmental Monitoring ; India ; Metagenome ; Metagenomics ; *Particulate Matter ; Seasons ; }, abstract = {Northeast India is considered as one of the major biodiversity hotspots in the world, but the region is underexplored for their microbial biodiversity. Extensive characterization of biological aerosol (bioaerosol) samples collected from various locations of Northeast India was carried out for all four seasons in a year. These were characterized in terms of their constituents, such as pollens, fungal spores, animal debris, and non-biological components, and particulate matters, such as inhalable, thoracic, and alveolic, and finally, the bacterial diversity was determined by DNA-based metagenomic approach. The non-biological (non-viable) component of aerosols is found to vary from 30 to 89% in the pre-monsoon season, which coexists with pollens (4-20%), animal debris (1-24%), and fungal spores (1-17%). The highest number of culturable microbial populations in terms of CFU count was observed in the pre-monsoon samples (i.e., 125.24-632.45 CFU/m[3]), and the lowest CFU was observed in monsoon season (i.e., 20.83-319.0 CFU/m[3]). The metagenomic approach with the samples collected during pre-monsoon season showed a total of bacterial 184 OTUs (operational taxonomic units) with 28,028 abundance count comprising 7 major phylum, 6 classes, 10 orders, 15 families, 13 genus, and 8 species of bacteria. The species-level distribution clearly shows the presence of Gammaproteobacteria (52%) most abundantly, followed by Bacilli (21%), Alphaproteobacteria (14%), Betaproteobacteria (5%), Flavobacteria (5%), and Sphingobacteria (3%). It is the first report from the entire Northeast India to uncover spatio-temporal distribution of biological components and bacterial diversity in aerosol samples through a DNA-based metagenomic approach.}, } @article {pmid35468809, year = {2022}, author = {He, L and Huang, X and Zhang, G and Yuan, L and Shen, E and Zhang, L and Zhang, XH and Zhang, T and Tao, L and Ju, F}, title = {Distinctive signatures of pathogenic and antibiotic resistant potentials in the hadal microbiome.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {19}, pmid = {35468809}, issn = {2524-6372}, support = {2018YFE0110500//national key research and development program of china/ ; 51908467//national natural science foundation of china/ ; 31970129//national natural science foundation of china/ ; 31800128//national natural science foundation of china/ ; LR20C010001//natural science foundation of zhejiang province/ ; }, abstract = {BACKGROUND: Hadal zone of the deep-sea trenches accommodates microbial life under extreme energy limitations and environmental conditions, such as low temperature, high pressure, and low organic matter down to 11,000 m below sea level. However, microbial pathogenicity, resistance, and adaptation therein remain unknown. Here we used culture-independent metagenomic approaches to explore the virulence and antibiotic resistance in the hadal microbiota of the Mariana Trench.

RESULTS: The results indicate that the 10,898 m Challenger Deep bottom sediment harbored prosperous microbiota with contrasting signatures of virulence factors and antibiotic resistance, compared with the neighboring but shallower 6038 m steep wall site and the more nearshore 5856 m Pacific basin site. Virulence genes including several famous large translocating virulence genes (e.g., botulinum neurotoxins, tetanus neurotoxin, and Clostridium difficile toxins) were uniquely detected in the trench bottom. However, the shallower and more nearshore site sediment had a higher abundance and richer diversity of known antibiotic resistance genes (ARGs), especially for those clinically relevant ones (e.g., fosX, sul1, and TEM-family extended-spectrum beta-lactamases), revealing resistance selection under anthropogenic stresses. Further analysis of mobilome (i.e., the collection of mobile genetic elements, MGEs) suggests horizontal gene transfer mediated by phage and integrase as the major mechanism for the evolution of Mariana Trench sediment bacteria. Notably, contig-level co-occurring and taxonomic analysis shows emerging evidence for substantial co-selection of virulence genes and ARGs in taxonomically diverse bacteria in the hadal sediment, especially for the Challenger Deep bottom where mobilized ARGs and virulence genes are favorably enriched in largely unexplored bacteria.

CONCLUSIONS: This study reports the landscape of virulence factors, antibiotic resistome, and mobilome in the sediment and seawater microbiota residing hadal environment of the deepest ocean bottom on earth. Our work unravels the contrasting and unique features of virulence genes, ARGs, and MGEs in the Mariana Trench bottom, providing new insights into the eco-environmental and biological processes underlying microbial pathogenicity, resistance, and adaptative evolution in the hadal environment.}, } @article {pmid35467501, year = {2022}, author = {Zhu, Y and Ma, L and Wei, W and Li, X and Chang, Y and Pan, Z and Gao, H and Yang, R and Bi, Y and Ding, L}, title = {Metagenomics analysis of cultured mucosal bacteria from colorectal cancer and adjacent normal mucosal tissues.}, journal = {Journal of medical microbiology}, volume = {71}, number = {4}, pages = {}, doi = {10.1099/jmm.0.001523}, pmid = {35467501}, issn = {1473-5644}, mesh = {Bacteria/genetics ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/microbiology ; Metagenomics ; }, abstract = {Introduction. Colorectal cancer (CRC) is one of the most common cancers worldwide. Multiple risk factors are involved in CRC development, including age, genetics, lifestyle, diet and environment. Of these, the role of the gut microbiota in cancer biology is increasingly recognized.Hypothesis/Gap Statement. Micro-organisms have been widely detected in stool samples, but few mucosal samples have been detected and sequenced in depth.Aim. Analysis of cultured mucosal bacteria from colorectal cancer and adjacent normal mucosal tissues with metagenomics sequencing.Methodology. Twenty-eight paired tumour and non-tumour tissues from 14 patients undergoing surgery for CRC were analysed. We removed the influence of eukaryotic cells via culture. The composition of mucosal microbiota in intestinal mucosa were detected and analysed with metagenomic sequencing.Results. Compared with non-cultured mucosal sample, 80 % bacteria species could be detected after culture. Moreover, after culture, additional 30 % bacteria could be detected, compared with non-cultured samples. Since after culture it was difficult to estimate the original abundance of microbiome, we focused on the identification of the CRC tissue-specific species. There were 298 bacterial species, which could only be cultured and detected in CRC tissues. Myroides odoratimimus and Cellulophaga baltica could be isolated from all the tumour samples of 14 CRC patients, suggesting that these species may be related to tumour occurrence and development. Further functional analysis indicated that bacteria from CRC tissues showed more active functions, including basic metabolism, signal transduction and survival activities.Conclusion. We used a new method based on culture to implement information on prokaryotic taxa, and related functions, which samples were from colorectal tissues. This method is suitable for removing eukaryotic contamination and detecting micro-organisms from other tissues.}, } @article {pmid35467389, year = {2022}, author = {Ma, X and Brinker, E and Graff, EC and Cao, W and Gross, AL and Johnson, AK and Zhang, C and Martin, DR and Wang, X}, title = {Whole-Genome Shotgun Metagenomic Sequencing Reveals Distinct Gut Microbiome Signatures of Obese Cats.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0083722}, pmid = {35467389}, issn = {2165-0497}, mesh = {Animals ; Bacteria/genetics ; Cats ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Mice ; Obesity/genetics/microbiology/veterinary ; Overweight/genetics ; Weight Loss/genetics ; }, abstract = {Overweight and obesity are growing health problems in domestic cats, increasing the risks of insulin resistance, lipid dyscrasias, neoplasia, cardiovascular disease, and decreasing longevity. The signature of obesity in the feline gut microbiota has not been studied at the whole-genome metagenomic level. We performed whole-genome shotgun metagenomic sequencing in the fecal samples of eight overweight/obese and eight normal cats housed in the same research environment. We obtained 271 Gbp of sequences and generated a 961-Mbp de novo reference contig assembly, with 1.14 million annotated microbial genes. In the obese cat microbiome, we discovered a significant reduction in microbial diversity (P < 0.01) and Firmicutes abundance (P = 0.005), as well as decreased Firmicutes/Bacteroidetes ratios (P = 0.02), which is the inverse of obese human/mouse microbiota. Linear discriminant analysis and quantitative PCR (qPCR) validation revealed significant increases of Bifidobacterium sp., Olsenella provencensis, Dialister sp.CAG:486, and Campylobacter upsaliensis as the hallmark of obese microbiota among 400 enriched species, whereas 1,525 bacterial species have decreased abundance in the obese microbiome. Phascolarctobacterium succinatutens and an uncharacterized Erysipelotrichaceae bacterium are highly abundant (>0.05%) in the normal gut with over 400-fold depletion in the obese microbiome. Fatty acid synthesis-related pathways are significantly overrepresented in the obese compared with the normal cat microbiome. In conclusion, we discovered dramatically decreased microbial diversity in obese cat gut microbiota, suggesting potential dysbiosis. A panel of seven significantly altered, highly abundant species can serve as a microbiome indicator of obesity. Our findings in the obese cat microbiome composition, abundance, and functional capacities provide new insights into feline obesity. IMPORTANCE Obesity affects around 45% of domestic cats, and licensed drugs for treating feline obesity are lacking. Physical exercise and calorie restrictions are commonly used for weight loss but with limited efficacy. Through comprehensive analyses of normal and obese cat gut bacteria flora, we identified dramatic shifts in the obese gut microbiome, including four bacterial species significantly enriched and two species depleted in the obese cats. The key bacterial community and functional capacity alterations discovered from this study will inform new weight management strategies for obese cats, such as evaluations of specific diet formulas that alter the microbiome composition, and the development of prebiotics and probiotics that promote the increase of beneficial species and the depletion of obesity-associated species. Interestingly, these bacteria identified in our study were also reported to affect the weight loss success in human patients, suggesting translational potential in human obesity.}, } @article {pmid35463645, year = {2022}, author = {Dong, Z and Lv, W and Zhang, C and Chen, S}, title = {Correlation Analysis of Gut Microbiota and Serum Metabolome With Porphyromonas gingivalis-Induced Metabolic Disorders.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {858902}, pmid = {35463645}, issn = {2235-2988}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Metabolic Diseases/etiology ; Metabolome ; Mice ; Mice, Inbred C57BL ; Porphyromonas gingivalis ; }, abstract = {Periodontitis has been demonstrated to increase the risk of metabolic syndrome (MetS), but the underlying mechanism remains unclear. Recent studies have indicated periodontopathic bacteria such as Porphyromonas gingivalis could induce gut microbiota (GM) dysbiosis and aggravate metabolic disorders. However, the effects of microbial metabolites have barely been evaluated. Here, we investigated the alteration of serum metabolome with P. gingivalis-induced metabolic disorders, and explored the correlations of GM and serum metabolites. In this study, we orally administered P. gingivalis ATCC33277 to C57BL/6 mice and performed metagenomic sequencing and untargeted metabolomics with fecal samples and serum collection. In vivo experiments showed a higher proportion of fat mass and worse glucose tolerance in P. gingivalis-administered mice, accompanied with an increase of adipose inflammation and gut permeability, which was similar to HFD-induced obese mice. Metagenomic sequencing indicated a compositional and functional alteration of GM. Untargeted metabolomics revealed an alteration of metabolites in P. gingivalis-administered mice, and most of them were engaged in metabolic pathways, such as tryptophan metabolism and choline metabolism. Correlation analysis between GM and serum metabolome indicated strong relativity with P. gingivalis administration. These results demonstrated some specific microbiota-derived metabolites in the pathogenesis of P. gingivalis-induced metabolic disorders, providing promising targets for the development of novel treatment strategies for MetS.}, } @article {pmid35460847, year = {2022}, author = {Liu, Z and Dong, WT and Wei, WF and Huo, JH and Wang, WM}, title = {Exploring the mechanism of Qinbaiqingfei-concentrate pills in the treatment of Mycoplasma pneumoniae pneumonia from the perspective of intestinal microbiota and mucosal immunity.}, journal = {Journal of ethnopharmacology}, volume = {293}, number = {}, pages = {115308}, doi = {10.1016/j.jep.2022.115308}, pmid = {35460847}, issn = {1872-7573}, mesh = {Animals ; *Drugs, Chinese Herbal/therapeutic use ; *Gastrointestinal Microbiome ; *Immunity, Mucosal ; Immunoglobulin A, Secretory ; Interleukin-10 ; Interleukin-4 ; Mycoplasma pneumoniae ; NF-kappa B/metabolism ; *Pneumonia, Mycoplasma/drug therapy ; Rats ; Tumor Necrosis Factor-alpha ; }, abstract = {Traditional Chinese medicine categorizes Mycoplasma pneumoniae pneumonia as "lung heat", and treatment with heat clear and detoxify. Traditional Chinese medicine believes that the lungs and intestines come from the same source, and the intestine is related to pneumonia. This is the same as the gut-lung axis theory. Qinbaiqingfei concentrate pills (QBs) were modified based on Cough San in the ancient medical book Medical Awareness. It clears lung heat, moisturizes the lungs and dredges collaterals, and has a good ability to treat Mycoplasma pneumoniae.

AIM OF THE STUDY: A rat model of Mycoplasma pneumoniae was established. From the aspect of intestinal flora and mucosal immunity, the potential mechanism of the QBs was researched.

MATERIALS AND METHODS: First, the content of Mycoplasma pneumoniae in lung tissue and the levels of the inflammatory factors IL-4, IL-10, TNF-α and INF-γ were detected. To determine the expression of NF-kB related proteins in lung tissue, which can understand the ability in treating disease. Next, metagenomic sequencing was performed to detect changes in short-chain fatty acids, proving the ability of the drug to regulate intestinal microecology. Finally, HDAC, LPS, SIgA, etc. were detected to facilitate the correlation of the overall experimental indicators.

RESULTS: QBs reduces the levels of IL-4, IL-10, TNF-α and INF-γ in the serum by inhibiting the expression of MyD88, IKKα, IκBα, and NF-κB p65 in lung tissue. In addition, QBs restores the ratio of gram-negative bacteria to gram-positive bacteria in the intestine, restores the secretion of acetic acid, propionic acid, butyric acid, isobutyric acid and isovaleric acid, and promotes the secretion of NF-κB p65 and SIgA by HDAC1/3. The result is that the lung tissue is repaired and the proliferation of Mycoplasma pneumoniae is inhibited.

CONCLUSIONS: From the "gut-lung axis", a new research perspective was discovered. QBs intervened in the intestines and lungs to treat Mycoplasma pneumoniae.}, } @article {pmid35460297, year = {2022}, author = {Geraerts, M and Vangestel, C and Artois, T and Fernandes, JMO and Jorissen, MWP and Chocha Manda, A and Danadu Mizani, C and Smeets, K and Snoeks, J and Sonet, G and Tingbao, Y and Van Steenberge, M and Vreven, E and Lunkayilakio Wamuini, S and Vanhove, MPM and Huyse, T}, title = {Population genomics of introduced Nile tilapia Oreochromis niloticus (Linnaeus, 1758) in the Democratic Republic of the Congo: Repeated introductions since colonial times with multiple sources.}, journal = {Molecular ecology}, volume = {31}, number = {12}, pages = {3304-3322}, doi = {10.1111/mec.16479}, pmid = {35460297}, issn = {1365-294X}, mesh = {Animals ; Aquaculture ; *Cichlids/genetics ; Democratic Republic of the Congo ; Introduced Species ; Metagenomics ; }, abstract = {During colonial times, Nile tilapia Oreochromis niloticus (Linnaeus, 1758) was introduced into non-native parts of the Congo Basin (Democratic Republic of the Congo, DRC) for the first time. Currently, it is the most farmed cichlid in the DRC, and is present throughout the Congo Basin. Although Nile tilapia has been reported as an invasive species, documentation of historical introductions into this basin and its consequences are scant. Here, we study the genetic consequences of these introductions by genotyping 213 Nile tilapia from native and introduced regions, focusing on the Congo Basin. Additionally, 48 specimens from 16 other tilapia species were included to test for hybridization. Using RAD sequencing (27,611 single nucleotide polymorphisms), we discovered genetic admixture with other tilapia species in several morphologically identified Nile tilapia from the Congo Basin, reflecting their ability to interbreed and the potential threat they pose to the genetic integrity of native tilapias. Nile tilapia populations from the Upper Congo and those from the Middle-Lower Congo are strongly differentiated. The former show genetic similarity to Nile tilapia from the White Nile, while specimens from the Benue Basin and Lake Kariba are similar to Nile tilapia from the Middle-Lower Congo, suggesting independent introductions using different sources. We conclude that the presence of Nile tilapia in the Congo Basin results from independent introductions, reflecting the dynamic aquaculture history, and that their introduction probably leads to genetic interactions with native tilapias, which could lower their fitness. We therefore urge avoiding further introductions of Nile tilapia in non-native regions and to use native tilapias in future aquaculture efforts.}, } @article {pmid35458219, year = {2022}, author = {Franck, M and de Toro-Martín, J and V Varin, T and Garneau, V and Pilon, G and Roy, D and Couture, P and Couillard, C and Marette, A and Vohl, MC}, title = {Gut Microbial Signatures of Distinct Trimethylamine N-Oxide Response to Raspberry Consumption.}, journal = {Nutrients}, volume = {14}, number = {8}, pages = {}, pmid = {35458219}, issn = {2072-6643}, support = {MRT-168045//CIHR/ ; not applicable//WA Red Raspberry Commission (WRRC)/ ; }, mesh = {Bacteria ; *Gastrointestinal Microbiome ; Humans ; Methylamines ; *Rubus/metabolism ; }, abstract = {The aim of this exploratory study was to evaluate the gut microbial signatures of distinct trimethylamine N-oxide (TMAO) responses following raspberry consumption. Investigations were carried out in 24 subjects at risk of developing metabolic syndrome who received 280 g/day of frozen raspberries for 8 weeks. Blood and stool samples were collected at weeks 0 and 8. Inter-individual variability in plasma TMAO levels was analyzed, 7 subjects were excluded due to noninformative signals and 17 subjects were kept for analysis and further stratified according to their TMAO response. Whole-metagenome shotgun sequencing analysis was used to determine the impact of raspberry consumption on gut microbial composition. Before the intervention, the relative abundance of Actinobacteriota was significantly higher in participants whose TMAO levels increased after the intervention (p = 0.03). The delta TMAO (absolute differences of baseline and week 8 levels) was positively associated with the abundance of gut bacteria such as Bilophila wadsworthia (p = 0.02; r[2] = 0.37), from the genus Granulicatella (p = 0.03; r[2] = 0.48) or the Erysipelotrichia class (p = 0.03; r[2] = 0.45). Changes in the gut microbial ecology induced by raspberry consumption over an 8-week period presumably impacted quaternary amines-utilizing activity and thus plasma TMAO levels.}, } @article {pmid35456888, year = {2022}, author = {Tsiantas, K and Konteles, SJ and Kritsi, E and Sinanoglou, VJ and Tsiaka, T and Zoumpoulakis, P}, title = {Effects of Non-Polar Dietary and Endogenous Lipids on Gut Microbiota Alterations: The Role of Lipidomics.}, journal = {International journal of molecular sciences}, volume = {23}, number = {8}, pages = {}, pmid = {35456888}, issn = {1422-0067}, support = {T2EDK- 03847//European Union and Greek national funds (European Social Fund - ESF) - Operational Program Competitiveness, Entrepreneurship and Innovation/ ; }, mesh = {Carotenoids/pharmacology ; Dietary Fats/pharmacology ; *Gastrointestinal Microbiome ; Lipidomics ; Sterols/pharmacology ; }, abstract = {Advances in sequencing technologies over the past 15 years have led to a substantially greater appreciation of the importance of the gut microbiome to the health of the host. Recent outcomes indicate that aspects of nutrition, especially lipids (exogenous or endogenous), can influence the gut microbiota composition and consequently, play an important role in the metabolic health of the host. Thus, there is an increasing interest in applying holistic analytical approaches, such as lipidomics, metabolomics, (meta)transcriptomics, (meta)genomics, and (meta)proteomics, to thoroughly study the gut microbiota and any possible interplay with nutritional or endogenous components. This review firstly summarizes the general background regarding the interactions between important non-polar dietary (i.e., sterols, fat-soluble vitamins, and carotenoids) or amphoteric endogenous (i.e., eicosanoids, endocannabinoids-eCBs, and specialized pro-resolving mediators-SPMs) lipids and gut microbiota. In the second stage, through the evaluation of a vast number of dietary clinical interventions, a comprehensive effort is made to highlight the role of the above lipid categories on gut microbiota and vice versa. In addition, the present status of lipidomics in current clinical interventions as well as their strengths and limitations are also presented. Indisputably, dietary lipids and most phytochemicals, such as sterols and carotenoids, can play an important role on the development of medical foods or nutraceuticals, as they exert prebiotic-like effects. On the other hand, endogenous lipids can be considered either prognostic indicators of symbiosis or dysbiosis or even play a role as specialized mediators through dietary interventions, which seem to be regulated by gut microbiota.}, } @article {pmid35456018, year = {2022}, author = {Henry, C and Bassignani, A and Berland, M and Langella, O and Sokol, H and Juste, C}, title = {Modern Metaproteomics: A Unique Tool to Characterize the Active Microbiome in Health and Diseases, and Pave the Road towards New Biomarkers-Example of Crohn's Disease and Ulcerative Colitis Flare-Ups.}, journal = {Cells}, volume = {11}, number = {8}, pages = {}, pmid = {35456018}, issn = {2073-4409}, mesh = {Biomarkers/metabolism ; *Colitis, Ulcerative/diagnosis ; *Crohn Disease/diagnosis ; Feces ; Humans ; *Microbiota ; }, abstract = {Thanks to the latest developments in mass spectrometry, software and standards, metaproteomics is emerging as the vital complement of metagenomics, to make headway in understanding the actual functioning of living and active microbial communities. Modern metaproteomics offers new possibilities in the area of clinical diagnosis. This is illustrated here, for the still highly challenging diagnosis of intestinal bowel diseases (IBDs). Using bottom-up proteomics, we analyzed the gut metaproteomes of the same twenty faecal specimens processed either fresh or after a two-month freezing period. We focused on metaproteomes of microbial cell envelopes since it is an outstanding way of capturing host and host-microbe interaction signals. The protein profiles of pairs of fresh and frozen-thawed samples were closely related, making feasible deferred analysis in a distant diagnosis centre. The taxonomic and functional landscape of microbes in diverse IBD phenotypes-active ulcerative colitis, or active Crohn's disease either with ileo-colonic or exclusive colonic localization-differed from each other and from the controls. Based on their specific peptides, we could identify proteins that were either strictly overrepresented or underrepresented in all samples of one clinical group compared to all samples of another group, paving the road for promising additional diagnostic tool for IBDs.}, } @article {pmid35452382, year = {2022}, author = {Hua, X and Cao, Y and Morgan, DM and Miller, K and Chin, SM and Bellavance, D and Khalili, H}, title = {Longitudinal analysis of the impact of oral contraceptive use on the gut microbiome.}, journal = {Journal of medical microbiology}, volume = {71}, number = {4}, pages = {}, doi = {10.1099/jmm.0.001512}, pmid = {35452382}, issn = {1473-5644}, mesh = {Child, Preschool ; Contraceptives, Oral/pharmacology ; Estradiol ; Female ; *Gastrointestinal Microbiome ; Gonadal Steroid Hormones ; Humans ; Testosterone ; }, abstract = {Introduction. Evidence has linked exogenous and endogenous sex hormones with the human microbiome.Hypothesis/Gap statement. The longitudinal effects of oral contraceptives (OC) on the human gut microbiome have not previously been studied.Aim. We sought to examine the longitudinal impact of OC use on the taxonomic composition and metabolic functions of the gut microbiota and endogenous sex steroid hormones after initiation of OC use.Methodology. We recruited ten healthy women who provided blood and stool samples prior to OC use, 1 month and 6 months after starting OC. We measured serum levels of sex hormones, including estradiol, progesterone, sex hormone-binding globulin (SHBG), and total testosterone. Shotgun metagenomic sequencing was performed on DNA extracted from faecal samples. Species and metabolic pathway abundances were determined using MetaPhlAn2 and HUMAnN2. Multivariate association with linear models was used to identify microbial species and metabolic pathways associated with OC use and endogenous levels of sex hormones.Results. The percentage variance of the microbial community explained by individual factors ranged from 9.9 % for age to 2.7 % for time since initiation of OC use. We observed no changes in the diversity or composition of the gut microbiome following OC initiation. However, the relative abundance of the biosynthesis pathways of peptidoglycan, amino acids (lysine, threonine, methionine, and tryptophan), and the NAD salvage pathway increased after OC initiation. In addition, serum levels of estradiol and SHBG were positively associated with Eubacterium ramulus, a flavonoid-degrading bacterium. Similarly, microbes involving biosynthesis of l-lysine, l-threonine, and l-methionine were significantly associated with lower estradiol, SHBG, and higher levels of total testosterone.Conclusion. Our study provides the first piece of evidence supporting the association between exogenous and endogenous sex hormones and gut microbiome composition and function.}, } @article {pmid35452151, year = {2022}, author = {Lu, JL and Jia, P and Feng, SW and Wang, YT and Zheng, J and Ou, SN and Wu, ZH and Liao, B and Shu, WS and Liang, JL and Li, JT}, title = {Remarkable effects of microbial factors on soil phosphorus bioavailability: A country-scale study.}, journal = {Global change biology}, volume = {28}, number = {14}, pages = {4459-4471}, doi = {10.1111/gcb.16213}, pmid = {35452151}, issn = {1365-2486}, mesh = {Acid Phosphatase ; Carbon ; Ecosystem ; Nitrogen ; *Phosphorus ; *Soil ; Soil Microbiology ; }, abstract = {Low soil phosphorus (P) bioavailability causes the widespread occurrence of P-limited terrestrial ecosystems around the globe. Exploring the factors influencing soil P bioavailability at large spatial scales is critical for managing these ecosystems. However, previous studies have mostly focused on abiotic factors. In this study, we explored the effects of microbial factors on soil P bioavailability of terrestrial ecosystems using a country-scale sampling effort. Our results showed that soil microbial biomass carbon (MBC) and acid phosphatase were important predictors of soil P bioavailability of agro- and natural ecosystems across China although they appeared less important than total soil P. The two microbial factors had a positive effect on soil P bioavailability of both ecosystem types and were able to mediate the effects of several abiotic factors (e.g., mean annual temperature). Meanwhile, we revealed that soil phytase could affect soil P bioavailability at the country scale via ways similar to those of soil MBC and acid phosphatase, a pattern being more pronounced in agroecosystems than in natural ecosystems. Moreover, we obtained evidence for the positive effects of microbial genes encoding these enzymes on soil P bioavailability at the country scale although their effect sizes varied between the two ecosystem types. Taken together, this study demonstrated the remarkable effects of microbial factors on soil P bioavailability at a large spatial scale, highlighting the importance to consider microbial factors in managing the widespread P-limited terrestrial ecosystems.}, } @article {pmid35450835, year = {2022}, author = {Hurst, R and Meader, E and Gihawi, A and Rallapalli, G and Clark, J and Kay, GL and Webb, M and Manley, K and Curley, H and Walker, H and Kumar, R and Schmidt, K and Crossman, L and Eeles, RA and Wedge, DC and Lynch, AG and Massie, CE and , and Yazbek-Hanna, M and Rochester, M and Mills, RD and Mithen, RF and Traka, MH and Ball, RY and O'Grady, J and Brewer, DS and Wain, J and Cooper, CS}, title = {Microbiomes of Urine and the Prostate Are Linked to Human Prostate Cancer Risk Groups.}, journal = {European urology oncology}, volume = {5}, number = {4}, pages = {412-419}, doi = {10.1016/j.euo.2022.03.006}, pmid = {35450835}, issn = {2588-9311}, support = {C5047/A22530/CRUK_/Cancer Research UK/United Kingdom ; BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10349/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG1860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/00044600/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/genetics ; Humans ; Male ; *Microbiota/genetics ; Prostate/pathology ; *Prostatic Neoplasms/pathology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Bacteria play a suspected role in the development of several cancer types, and associations between the presence of particular bacteria and prostate cancer have been reported.

OBJECTIVE: To provide improved characterisation of the prostate and urine microbiome and to investigate the prognostic potential of the bacteria present.

Microbiome profiles were interrogated in sample collections of patient urine (sediment microscopy: n = 318, 16S ribosomal amplicon sequencing: n = 46; and extracellular vesicle RNA-seq: n = 40) and cancer tissue (n = 204).

Microbiomes were assessed using anaerobic culture, population-level 16S analysis, RNA-seq, and whole genome DNA sequencing.

RESULTS AND LIMITATIONS: We demonstrate an association between the presence of bacteria in urine sediments and higher D'Amico risk prostate cancer (discovery, n = 215 patients, p < 0.001; validation, n = 103, p < 0.001, χ[2] test for trend). Characterisation of the bacterial community led to the (1) identification of four novel bacteria (Porphyromonas sp. nov., Varibaculum sp. nov., Peptoniphilus sp. nov., and Fenollaria sp. nov.) that were frequently found in patient urine, and (2) definition of a patient subgroup associated with metastasis development (p = 0.015, log-rank test). The presence of five specific anaerobic genera, which includes three of the novel isolates, was associated with cancer risk group, in urine sediment (p = 0.045, log-rank test), urine extracellular vesicles (p = 0.039), and cancer tissue (p = 0.035), with a meta-analysis hazard ratio for disease progression of 2.60 (95% confidence interval: 1.39-4.85; p = 0.003; Cox regression). A limitation is that functional links to cancer development are not yet established.

CONCLUSIONS: This study characterises prostate and urine microbiomes, and indicates that specific anaerobic bacteria genera have prognostic potential.

PATIENT SUMMARY: In this study, we investigated the presence of bacteria in patient urine and the prostate. We identified four novel bacteria and suggest a potential prognostic utility for the microbiome in prostate cancer.}, } @article {pmid35449461, year = {2022}, author = {Kaelin, EA and Rodriguez, C and Hall-Moore, C and Hoffmann, JA and Linneman, LA and Ndao, IM and Warner, BB and Tarr, PI and Holtz, LR and Lim, ES}, title = {Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants.}, journal = {Nature microbiology}, volume = {7}, number = {5}, pages = {653-662}, pmid = {35449461}, issn = {2058-5276}, support = {R01 DK122029/DK/NIDDK NIH HHS/United States ; R01 HD092311/HD/NICHD NIH HHS/United States ; R00 DK107923/DK/NIDDK NIH HHS/United States ; UH3 AI083265/AI/NIAID NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; UH2 AI083265/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/genetics ; *Enterocolitis, Necrotizing/microbiology ; Feces/microbiology ; Female ; Humans ; Infant ; Infant, Newborn ; *Infant, Newborn, Diseases ; Infant, Premature ; Pregnancy ; *Premature Birth ; Virome/genetics ; }, abstract = {Necrotizing enterocolitis (NEC) is a serious consequence of preterm birth and is often associated with gut bacterial microbiome alterations. However, little is known about the development of the gut virome in preterm infants, or its role in NEC. Here, using metagenomic sequencing, we characterized the DNA gut virome of 9 preterm infants who developed NEC and 14 gestational age-matched preterm infants who did not. Infants were sampled longitudinally before NEC onset over the first 11 weeks of life. We observed substantial interindividual variation in the gut virome between unrelated preterm infants, while intraindividual variation over time was significantly less. We identified viral and bacterial signatures in the gut that preceded NEC onset. Specifically, we observed a convergence towards reduced viral beta diversity over the 10 d before NEC onset, which was driven by specific viral signatures and accompanied by specific viral-bacterial interactions. Our results indicate that bacterial and viral perturbations precede the sudden onset of NEC. These findings suggest that early life virome signatures in preterm infants may be implicated in NEC.}, } @article {pmid35449389, year = {2022}, author = {Koo, H and Morrow, CD}, title = {Early indicators of microbial strain dysbiosis in the human gastrointestinal microbial community of certain healthy humans and hospitalized COVID-19 patients.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6562}, pmid = {35449389}, issn = {2045-2322}, mesh = {*COVID-19 ; Dysbiosis ; Feces ; *Gastrointestinal Microbiome ; Hospitalization ; Humans ; }, abstract = {Dysbiosis in the human gastrointestinal microbial community could functionally impact microbial metabolism and colonization resistance to pathogens. To further elucidate the indicators of microbial strain dysbiosis, we have developed an analytic method that detects patterns of presence/absence of selected KEGG metabolic pathways for a selected strain (PKS). Using a metagenomic data set consisting of multiple high-density fecal samples from six normal individuals, we found three had unique PKS for important gut commensal microbes, Bacteroides vulgatus and Bacteroides uniformis, at all sample times examined. Two individuals had multiple shared PKS clusters of B. vulgatus or B. uniformis over time. Analysis of a data set of high-density fecal samples from eight COVID-19 hospitalized patients taken over a short period revealed that two patients had shared PKS clusters for B. vulgatus and one shared cluster for B. uniformis. Our analysis demonstrates that while the majority of normal individuals with no B. vulgatus or B. uniformis strain change over time have unique PKS, in some healthy humans and patients hospitalized with COVID-19, we detected shared PKS clusters at the different times suggesting a slowing down of the intrinsic rates of strain variation that could eventually lead to a dysbiosis in the microbial strain community.}, } @article {pmid35449330, year = {2022}, author = {Zhang, J and Zhang, Q and Zhang, Z and Zhou, Z and Lu, T and Sun, L and Qian, H}, title = {Evaluation of phoxim toxicity on aquatic and zebrafish intestinal microbiota by metagenomics and 16S rRNA gene sequencing analysis.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {42}, pages = {63017-63027}, pmid = {35449330}, issn = {1614-7499}, support = {21976161//National Natural Science Foundation of China/ ; 21777144//National Natural Science Foundation of China/ ; 22176176//Innovative Research Group Project of the National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Genes, rRNA ; Metagenomics ; *Microbiota ; Organophosphorus Compounds ; Organothiophosphorus Compounds ; *Pesticides ; RNA, Ribosomal, 16S/genetics ; Zebrafish/genetics ; }, abstract = {Phoxim is one of the main organophosphorus pesticides used in agricultural production. However, little information is known about how it affects the aquatic microbial community and the intestinal microbiota of fish. Herein, we utilized shotgun metagenomics and 16S rRNA gene sequencing to reveal the aquatic eco-risk of phoxim. Seven days of phoxim exposure significantly changed the composition of aquatic microbial community, obliterated the interactions between microorganisms, and thus reduced the complexity and stability of the microbial community. During long-time exposure (i.e., 14 days), most of the ecological functions were restored due to the redundancy of the microbial community. However, phoxim exposure promoted the dissemination of elfamycin resistance gene. The zebrafish gut microbial community also recovered from a temporary ecological disorder of aquatic microbiota, but phoxim continually affected zebrafish growth and swimming behavior. Overall, our results demonstrated that phoxim exposure significantly changed the structure and function of the microbial community and displayed a negative impact on freshwater ecosystems in a short exposure time.}, } @article {pmid35446845, year = {2022}, author = {Giliberti, R and Cavaliere, S and Mauriello, IE and Ercolini, D and Pasolli, E}, title = {Host phenotype classification from human microbiome data is mainly driven by the presence of microbial taxa.}, journal = {PLoS computational biology}, volume = {18}, number = {4}, pages = {e1010066}, pmid = {35446845}, issn = {1553-7358}, mesh = {*Bacteria/genetics ; Humans ; Metagenome/genetics ; *Microbiota/genetics ; Phenotype ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Machine learning-based classification approaches are widely used to predict host phenotypes from microbiome data. Classifiers are typically employed by considering operational taxonomic units or relative abundance profiles as input features. Such types of data are intrinsically sparse, which opens the opportunity to make predictions from the presence/absence rather than the relative abundance of microbial taxa. This also poses the question whether it is the presence rather than the abundance of particular taxa to be relevant for discrimination purposes, an aspect that has been so far overlooked in the literature. In this paper, we aim at filling this gap by performing a meta-analysis on 4,128 publicly available metagenomes associated with multiple case-control studies. At species-level taxonomic resolution, we show that it is the presence rather than the relative abundance of specific microbial taxa to be important when building classification models. Such findings are robust to the choice of the classifier and confirmed by statistical tests applied to identifying differentially abundant/present taxa. Results are further confirmed at coarser taxonomic resolutions and validated on 4,026 additional 16S rRNA samples coming from 30 public case-control studies.}, } @article {pmid35446234, year = {2022}, author = {Mujagic, Z and Kasapi, M and Jonkers, DM and Garcia-Perez, I and Vork, L and Weerts, ZZRM and Serrano-Contreras, JI and Zhernakova, A and Kurilshikov, A and Scotcher, J and Holmes, E and Wijmenga, C and Keszthelyi, D and Nicholson, JK and Posma, JM and Masclee, AA}, title = {Integrated fecal microbiome-metabolome signatures reflect stress and serotonin metabolism in irritable bowel syndrome.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2063016}, pmid = {35446234}, issn = {1949-0984}, support = {MR/S004033/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Feces/chemistry ; *Gastrointestinal Microbiome/physiology ; Humans ; *Irritable Bowel Syndrome/metabolism ; Metabolome ; *Microbiota ; Serotonin/metabolism ; }, abstract = {To gain insight into the complex microbiome-gut-brain axis in irritable bowel syndrome (IBS), several modalities of biological and clinical data must be combined. We aimed to identify profiles of fecal microbiota and metabolites associated with IBS and to delineate specific phenotypes of IBS that represent potential pathophysiological mechanisms. Fecal metabolites were measured using proton nuclear magnetic resonance ([1]H-NMR) spectroscopy and gut microbiome using shotgun metagenomic sequencing (MGS) in a combined dataset of 142 IBS patients and 120 healthy controls (HCs) with extensive clinical, biological and phenotype information. Data were analyzed using support vector classification and regression and kernel t-SNE. Microbiome and metabolome profiles could distinguish IBS and HC with an area-under-the-receiver-operator-curve of 77.3% and 79.5%, respectively, but this could be improved by combining microbiota and metabolites to 83.6%. No significant differences in predictive ability of the microbiome-metabolome data were observed between the three classical, stool pattern-based, IBS subtypes. However, unsupervised clustering showed distinct subsets of IBS patients based on fecal microbiome-metabolome data. These clusters could be related plasma levels of serotonin and its metabolite 5-hydroxyindoleacetate, effects of psychological stress on gastrointestinal (GI) symptoms, onset of IBS after stressful events, medical history of previous abdominal surgery, dietary caloric intake and IBS symptom duration. Furthermore, pathways in metabolic reaction networks were integrated with microbiota data, that reflect the host-microbiome interactions in IBS. The identified microbiome-metabolome signatures for IBS, associated with altered serotonin metabolism and unfavorable stress response related to GI symptoms, support the microbiota-gut-brain link in the pathogenesis of IBS.}, } @article {pmid35444277, year = {2022}, author = {Raina, JB and Lambert, BS and Parks, DH and Rinke, C and Siboni, N and Bramucci, A and Ostrowski, M and Signal, B and Lutz, A and Mendis, H and Rubino, F and Fernandez, VI and Stocker, R and Hugenholtz, P and Tyson, GW and Seymour, JR}, title = {Chemotaxis shapes the microscale organization of the ocean's microbiome.}, journal = {Nature}, volume = {605}, number = {7908}, pages = {132-138}, pmid = {35444277}, issn = {1476-4687}, mesh = {Bacteria ; *Chemotaxis ; Dissolved Organic Matter ; *Microbiota ; Oceans and Seas ; Phytoplankton/metabolism ; Seawater/microbiology ; }, abstract = {The capacity of planktonic marine microorganisms to actively seek out and exploit microscale chemical hotspots has been widely theorized to affect ocean-basin scale biogeochemistry[1-3], but has never been examined comprehensively in situ among natural microbial communities. Here, using a field-based microfluidic platform to quantify the behavioural responses of marine bacteria and archaea, we observed significant levels of chemotaxis towards microscale hotspots of phytoplankton-derived dissolved organic matter (DOM) at a coastal field site across multiple deployments, spanning several months. Microscale metagenomics revealed that a wide diversity of marine prokaryotes, spanning 27 bacterial and 2 archaeal phyla, displayed chemotaxis towards microscale patches of DOM derived from ten globally distributed phytoplankton species. The distinct DOM composition of each phytoplankton species attracted phylogenetically and functionally discrete populations of bacteria and archaea, with 54% of chemotactic prokaryotes displaying highly specific responses to the DOM derived from only one or two phytoplankton species. Prokaryotes exhibiting chemotaxis towards phytoplankton-derived compounds were significantly enriched in the capacity to transport and metabolize specific phytoplankton-derived chemicals, and displayed enrichment in functions conducive to symbiotic relationships, including genes involved in the production of siderophores, B vitamins and growth-promoting hormones. Our findings demonstrate that the swimming behaviour of natural prokaryotic assemblages is governed by specific chemical cues, which dictate important biogeochemical transformation processes and the establishment of ecological interactions that structure the base of the marine food web.}, } @article {pmid35444255, year = {2022}, author = {Li, Z and Lai, J and Zhang, P and Ding, J and Jiang, J and Liu, C and Huang, H and Zhen, H and Xi, C and Sun, Y and Wu, L and Wang, L and Gao, X and Li, Y and Fu, Y and Jie, Z and Li, S and Zhang, D and Chen, Y and Zhu, Y and Lu, S and Lu, J and Wang, D and Zhou, H and Yuan, X and Li, X and Pang, L and Huang, M and Yang, H and Zhang, W and Brix, S and Kristiansen, K and Song, X and Nie, C and Hu, S}, title = {Multi-omics analyses of serum metabolome, gut microbiome and brain function reveal dysregulated microbiota-gut-brain axis in bipolar depression.}, journal = {Molecular psychiatry}, volume = {27}, number = {10}, pages = {4123-4135}, pmid = {35444255}, issn = {1476-5578}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bipolar Disorder/metabolism ; Brain-Gut Axis ; Metabolome ; *Microbiota ; Brain/metabolism ; }, abstract = {The intricate processes of microbiota-gut-brain communication in modulating human cognition and emotion, especially in the context of mood disorders, have remained elusive. Here we performed faecal metagenomic, serum metabolomics and neuroimaging studies on a cohort of 109 unmedicated patients with depressed bipolar disorder (BD) patients and 40 healthy controls (HCs) to characterise the microbial-gut-brain axis in BD. Across over 12,000 measured metabolic features, we observed a large discrepancy (73.54%) in the serum metabolome between BD patients and HCs, spotting differentially abundant microbial-derived neuroactive metabolites including multiple B-vitamins, kynurenic acid, gamma-aminobutyric acid and short-chain fatty acids. These metabolites could be linked to the abundance of gut microbiota presented with corresponding biosynthetic potentials, including Akkermansia muciniphila, Citrobacter spp. (Citrobacter freundii and Citrobacter werkmanii), Phascolarctobacterium spp., Yersinia spp. (Yersinia frederiksenii and Yersinia aleksiciae), Enterobacter spp. (Enterobacter cloacae and Enterobacter kobei) and Flavobacterium spp. Based on functional neuroimaging, BD-related neuroactive microbes and metabolites were discovered as potential markers associated with BD-typical features of functional connectivity of brain networks, hinting at aberrant cognitive function, emotion regulation, and interoception. Our study combines gut microbiota and neuroactive metabolites with brain functional connectivity, thereby revealing potential signalling pathways from the microbiota to the gut and the brain, which may have a role in the pathophysiology of BD.}, } @article {pmid35444202, year = {2022}, author = {Busi, SB and Bourquin, M and Fodelianakis, S and Michoud, G and Kohler, TJ and Peter, H and Pramateftaki, P and Styllas, M and Tolosano, M and De Staercke, V and Schön, M and de Nies, L and Marasco, R and Daffonchio, D and Ezzat, L and Wilmes, P and Battin, TJ}, title = {Genomic and metabolic adaptations of biofilms to ecological windows of opportunity in glacier-fed streams.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {2168}, pmid = {35444202}, issn = {2041-1723}, mesh = {Biodiversity ; Biofilms ; Ecosystem ; *Ice Cover ; *Microbiota/genetics ; Rivers/microbiology ; }, abstract = {In glacier-fed streams, ecological windows of opportunity allow complex microbial biofilms to develop and transiently form the basis of the food web, thereby controlling key ecosystem processes. Using metagenome-assembled genomes, we unravel strategies that allow biofilms to seize this opportunity in an ecosystem otherwise characterized by harsh environmental conditions. We observe a diverse microbiome spanning the entire tree of life including a rich virome. Various co-existing energy acquisition pathways point to diverse niches and the exploitation of available resources, likely fostering the establishment of complex biofilms during windows of opportunity. The wide occurrence of rhodopsins, besides chlorophyll, highlights the role of solar energy capture in these biofilms while internal carbon and nutrient cycling between photoautotrophs and heterotrophs may help overcome constraints imposed by oligotrophy in these habitats. Mechanisms potentially protecting bacteria against low temperatures and high UV-radiation are also revealed and the selective pressure of this environment is further highlighted by a phylogenomic analysis differentiating important components of the glacier-fed stream microbiome from other ecosystems. Our findings reveal key genomic underpinnings of adaptive traits contributing to the success of complex biofilms to exploit environmental opportunities in glacier-fed streams, which are now rapidly changing owing to global warming.}, } @article {pmid35443766, year = {2022}, author = {Satjarak, A and Golinski, GK and Trest, MT and Graham, LE}, title = {Microbiome and related structural features of Earth's most archaic plant indicate early plant symbiosis attributes.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6423}, pmid = {35443766}, issn = {2045-2322}, mesh = {*Bryophyta/genetics ; *Embryophyta/genetics ; Humans ; *Microbiota/genetics ; *Mycorrhizae ; Phylogeny ; Plants/microbiology ; Symbiosis ; }, abstract = {Origin of earliest land plants from ancestral algae dramatically accelerated the evolution of Earth's terrestrial ecosystems, in which microbial symbioses have played key roles. Recent molecular diversification analyses identify the rare, geographically-limited moss Takakia as Earth's most archaic modern land plant. Despite occupying a phylogenetic position pivotal for understanding earliest plants, Takakia microbial associations are poorly known. Here, we describe symbiosis-related structural features and contig-based metagenomic data that illuminate the evolutionary transition from streptophyte algae to early embryophytes. We observed that T. lepidozioides shares with streptophyte algae secretion of microbe-harboring mucilage and bacterial taxa such as Rhizobium and genes indicating nitrogen fixation. We find that Takakia root-analogs produce lateral mucilage organs that are more complex than generally understood, having structural analogies to angiosperm lateral roots adapted for N-fixation symbioses, including presence of intracellular microbes. We also find structural and metagenomic evidence for mycorrhiza-like species of glomalean fungi (including Rhizophagus irregularis) not previously known for mosses, as well as ascomycete fungi (e.g. Rhizoscyphus ericae) that associate with other early-diverging plants. Because Takakia is the oldest known modern plant genus, this study of plants of a remote locale not strongly influenced by human activities may indicate microbiome features of early land plants.}, } @article {pmid35443009, year = {2022}, author = {Lin, PC and Yang, YSH and Lin, SC and Lu, MC and Tsai, YT and Lu, SC and Chen, SH and Chen, SY}, title = {Clinical significance and intestinal microbiota composition in immunocompromised children with norovirus gastroenteritis.}, journal = {PloS one}, volume = {17}, number = {4}, pages = {e0266876}, pmid = {35443009}, issn = {1932-6203}, mesh = {*Caliciviridae Infections/epidemiology ; Child ; Feces ; *Gastroenteritis ; *Gastrointestinal Microbiome/genetics ; Genotype ; Humans ; Infant ; *Norovirus/genetics ; RNA, Viral ; }, abstract = {BACKGROUND: Norovirus (NoV) infection is common in pediatric patients with immunodeficiency and is more likely to cause severe disease. Objective Our study aims to figure out the clinical differences and distribution of intestinal microbiota in immunocompromised children with NoV gastroenteritis.

METHODS: Pediatric patients admitted to Shang-Ho Hospital with diagnosis of acute gastroenteritis including different immune status were enrolled and their medical records were reviewed. NoV gastroenteritis was validated using RT-PCR molecular methods. Viral shedding period was determined by real-time RT-PCR assays. Intestinal microbiota enrichment analysis was carried out by next generation sequencing after fecal DNA extraction and subsequent Linear Discriminant Analysis (LDA) Effect Size (LEfSe) method.

RESULTS: Significantly higher frequency of diarrhea [mean, (IQR), 3.8 (3-5) /day] and longer viral shedding time [mean, IQR, 8.5 (5-13) days] was found in immunocompromised NoV infections than in immunocompetent patients without NoV infections (p = 0.013*) and immunocompetent patients with NoV infections (p = 0.030**). The fever prevalence was significantly lower in immunocompromised NoV infections than in different immune or infection status. Intestinal microbiota metagenomics analysis showed no significant community richness difference while the LEfSe analysis showed a significant difference in commensal richness at the phylum level, the family level, and the genus level in patients under different immune status.

CONCLUSION: We evaluated the clinical significances and microbiota composition in immunocompromised children with norovirus gastroenteritis. This will further facilitate studies of the interaction between the intestinal microbiota in such patients with precise determination of their bacterial infection control and probiotic supplements strategy.}, } @article {pmid35441283, year = {2022}, author = {Xiao, M and Lu, B and Ding, R and Liu, X and Wu, X and Li, Y and Liu, X and Qiu, L and Zhang, Z and Xie, J and Chen, Y and Zhang, D and Dong, L and Zhang, M and Peng, J and Yang, H and Kudihna, T and Xu, Y and Li, T and Yi, C and Zhu, L}, title = {Metatranscriptomic analysis of host response and vaginal microbiome of patients with severe COVID-19.}, journal = {Science China. Life sciences}, volume = {65}, number = {7}, pages = {1473-1476}, pmid = {35441283}, issn = {1869-1889}, mesh = {*COVID-19 ; Female ; Humans ; Metagenomics ; *Microbiota/genetics ; }, } @article {pmid35440728, year = {2022}, author = {González-Dávila, P and Schwalbe, M and Danewalia, A and Dalile, B and Verbeke, K and Mahata, SK and El Aidy, S}, title = {Catestatin selects for colonization of antimicrobial-resistant gut bacterial communities.}, journal = {The ISME journal}, volume = {16}, number = {8}, pages = {1873-1882}, pmid = {35440728}, issn = {1751-7370}, support = {I01 BX003934/BX/BLRD VA/United States ; }, mesh = {Animals ; *Anti-Infective Agents ; Chromogranin A/genetics/metabolism/pharmacology ; *Gastrointestinal Microbiome ; Mice ; Mice, Knockout ; Peptide Fragments/genetics/metabolism ; Peptides ; }, abstract = {The gut microbiota is in continuous interaction with the innermost layer of the gut, namely the epithelium. One of the various functions of the gut epithelium, is to keep the microbes at bay to avoid overstimulation of the underlying mucosa immune cells. To do so, the gut epithelia secrete a variety of antimicrobial peptides, such as chromogranin A (CgA) peptide catestatin (CST: hCgA352-372). As a defense mechanism, gut microbes have evolved antimicrobial resistance mechanisms to counteract the killing effect of the secreted peptides. To this end, we treated wild-type mice and CST knockout (CST-KO) mice (where only the 63 nucleotides encoding CST have been deleted) with CST for 15 consecutive days. CST treatment was associated with a shift in the diversity and composition of the microbiota in the CST-KO mice. This effect was less prominent in WT mice. Levels of the microbiota-produced short-chain fatty acids, in particular, butyrate and acetate were significantly increased in CST-treated CST-KO mice but not the WT group. Both CST-treated CST-KO and WT mice showed a significant increase in microbiota-harboring phosphoethanolamine transferase-encoding genes, which facilitate their antimicrobial resistance. Finally, we show that CST was degraded by Escherichia coli via an omptin-protease and that the abundance of this gene was significantly higher in metagenomic datasets collected from patients with Crohn's disease but not with ulcerative colitis. Overall, this study illustrates how the endogenous antimicrobial peptide, CST, shapes the microbiota composition in the gut and primes further research to uncover the role of bacterial resistance to CST in disease states such as inflammatory bowel disease.}, } @article {pmid35440708, year = {2022}, author = {Bai-Tong, SS and Thoemmes, MS and Weldon, KC and Motazavi, D and Kitsen, J and Hansen, S and Furst, A and Geng, B and Song, SJ and Gilbert, JA and Bode, L and Dorrestein, PC and Knight, R and Leibel, SA and Leibel, SL}, title = {The impact of maternal asthma on the preterm infants' gut metabolome and microbiome (MAP study).}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6437}, pmid = {35440708}, issn = {2045-2322}, mesh = {*Asthma ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Metabolome ; *Microbiota ; Pilot Projects ; Prospective Studies ; }, abstract = {Preterm infants are at a greater risk for the development of asthma and atopic disease, which can lead to lifelong negative health consequences. This may be due, in part, to alterations that occur in the gut microbiome and metabolome during their stay in the Neonatal Intensive Care Unit (NICU). To explore the differential roles of family history (i.e., predisposition due to maternal asthma diagnosis) and hospital-related environmental and clinical factors that alter microbial exposures early in life, we considered a unique cohort of preterm infants born ≤ 34 weeks gestational age from two local level III NICUs, as part of the MAP (Microbiome, Atopic disease, and Prematurity) Study. From MAP participants, we chose a sub-cohort of infants whose mothers had a history of asthma and matched gestational age and sex to infants of mothers without a history of asthma diagnosis (control). We performed a prospective, paired metagenomic and metabolomic analysis of stool and milk feed samples collected at birth, 2 weeks, and 6 weeks postnatal age. Although there were clinical factors associated with shifts in the diversity and composition of stool-associated bacterial communities, maternal asthma diagnosis did not play an observable role in shaping the infant gut microbiome during the study period. There were significant differences, however, in the metabolite profile between the maternal asthma and control groups at 6 weeks postnatal age. The most notable changes occurred in the linoleic acid spectral network, which plays a role in inflammatory and immune pathways, suggesting early metabolomic changes in the gut of preterm infants born to mothers with a history of asthma. Our pilot study suggests that a history of maternal asthma alters a preterm infants' metabolomic pathways in the gut, as early as the first 6 weeks of life.}, } @article {pmid35440670, year = {2022}, author = {Zuo, W and Wang, B and Bai, X and Luan, Y and Fan, Y and Michail, S and Sun, F}, title = {16S rRNA and metagenomic shotgun sequencing data revealed consistent patterns of gut microbiome signature in pediatric ulcerative colitis.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6421}, pmid = {35440670}, issn = {2045-2322}, support = {R01 HD081197/HD/NICHD NIH HHS/United States ; R01 GM120624/GM/NIGMS NIH HHS/United States ; HD081197/NH/NIH HHS/United States ; R01 GM131407/GM/NIGMS NIH HHS/United States ; GM120624/NH/NIH HHS/United States ; GM131407/NH/NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Child ; *Colitis, Ulcerative/genetics ; Dysbiosis/genetics ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Dysbiosis of human gut microbiota has been reported in association with ulcerative colitis (UC) in both children and adults using either 16S rRNA gene or shotgun sequencing data. However, these studies used either 16S rRNA or metagenomic shotgun sequencing but not both. We sequenced feces samples from 19 pediatric UC and 23 healthy children ages between 7 to 21 years using both 16S rRNA and metagenomic shotgun sequencing. The samples were analyzed using three different types of data: 16S rRNA genus level abundance, microbial species and pathway abundance profiles. We demonstrated that (a) the alpha diversity of pediatric UC cases is lower than that of healthy controls; (b) the beta diversity within children with UC is more variable than within the healthy children; (c) several microbial families including Akkermansiaceae, Clostridiaceae, Eggerthellaceae, Lachnospiraceae, and Oscillospiraceae, contain species that are depleted in pediatric UC compared to controls; (d) a few associated species unique to pediatric UC, but not adult UC, were also identified, e.g. some species in the Christensenellaceae family were found to be depleted and some species in the Enterobacteriaceae family were found to be enriched in pediatric UC; and (e) both 16S rRNA and shotgun sequencing data can predict pediatric UC status with area under the receiver operating characteristic curve (AUROC) of close to 0.90 based on cross validation. We showed that 16S rRNA data yielded similar results as shotgun data in terms of alpha diversity, beta diversity, and prediction accuracy. Our study demonstrated that pediatric UC subjects harbor a dysbiotic and less diverse gut microbial population with distinct differences from healthy children. We also showed that 16S rRNA data yielded accurate disease prediction results in comparison to shotgun data, which can be more expensive and laborious. These conclusions were confirmed in an independent data set of 7 pediatric UC cases and 8 controls.}, } @article {pmid35440640, year = {2022}, author = {Li, C and Luan, Z and Zhao, Y and Chen, J and Yang, Y and Wang, C and Jing, Y and Qi, S and Li, Z and Guo, H and Xu, W and Zhao, B and Wu, C and Wang, S and Yang, Y and Sun, G}, title = {Deep insights into the gut microbial community of extreme longevity in south Chinese centenarians by ultra-deep metagenomics and large-scale culturomics.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {28}, pmid = {35440640}, issn = {2055-5008}, mesh = {Aged, 80 and over ; Bacteria/genetics ; Centenarians ; China ; Health Promotion ; Humans ; Longevity ; *Metagenomics/methods ; *Microbiota ; Young Adult ; }, abstract = {The gut microbes play important roles in human longevity and the gut microbiota profile of centenarians shows some unique features from young adults. Nowadays, most microbial studies on longevity are commonly based on metagenomic sequencing which may lose information about the functional microbes with extremely low abundance. Here, we combined in-depth metagenomic sequencing and large-scale culturomics to reveal the unique gut microbial structure of a Chinese longevity population, and to explore the possible relationship between intestinal microbes and longevity. Twenty-five healthy Hainan natives were enrolled in the study, including 12 centenarians and 13 senior neighbors. An average of 51.1 Gb raw sequencing data were obtained from individual fecal sample. We assembled 1778 non-redundant metagenomic assembled genomes (MAGs), 33.46% of which cannot be classified into known species. Comparison with the ordinary people in Hainan province, the longevous cohort displayed significantly decreased abundance of butyrate-producing bacteria and largely increased proportion of Escherichia coli, Desulfovibrio piger and Methanobrevibacter smithii. These species showed a constant change with aging. We also isolated 8,030 strains from these samples by large-scale culturomics, most of which belonged to 203 known species as identified by MALDI-TOF. Surprisingly, only 42.17% of the isolated species were also detected by metagenomics, indicating obvious complementarity between these two approaches. Combination of two complement methods, in-depth metagenomic sequencing and culturomics, provides deeper insights into the longevity-related gut microbiota. The uniquely enriched gut microbes in Hainan extreme decades population may help to promote health and longevity.}, } @article {pmid35440042, year = {2022}, author = {Wolf, PG and Cowley, ES and Breister, A and Matatov, S and Lucio, L and Polak, P and Ridlon, JM and Gaskins, HR and Anantharaman, K}, title = {Diversity and distribution of sulfur metabolic genes in the human gut microbiome and their association with colorectal cancer.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {64}, pmid = {35440042}, issn = {2049-2618}, support = {T32 CA057699/CA/NCI NIH HHS/United States ; T15 LM007359/LM/NLM NIH HHS/United States ; R01 CA204808/CA/NCI NIH HHS/United States ; T32 GM008692/GM/NIGMS NIH HHS/United States ; T32 GM140935/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria ; *Carcinoma ; *Colorectal Neoplasms/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Sulfates/metabolism ; Sulfur/metabolism ; Taurine/metabolism ; }, abstract = {BACKGROUND: Recent evidence implicates microbial sulfidogenesis as a potential trigger of colorectal cancer (CRC), highlighting the need for comprehensive knowledge of sulfur metabolism within the human gut. Microbial sulfidogenesis produces genotoxic hydrogen sulfide (H2S) in the human colon using inorganic (sulfate) and organic (taurine/cysteine/methionine) substrates; however, the majority of studies have focused on sulfate reduction using dissimilatory sulfite reductases (Dsr).

RESULTS: Here, we show that genes for microbial sulfur metabolism are more abundant and diverse than previously observed and are statistically associated with CRC. Using ~ 17,000 bacterial genomes from publicly available stool metagenomes, we studied the diversity of sulfur metabolic genes in 667 participants across different health statuses: healthy, adenoma, and carcinoma. Sulfidogenic genes were harbored by 142 bacterial genera and both organic and inorganic sulfidogenic genes were associated with carcinoma. Significantly, the anaerobic sulfite reductase (asr) genes were twice as abundant as dsr, demonstrating that Asr is likely a more important contributor to sulfate reduction in the human gut than Dsr. We identified twelve potential pathways for reductive taurine metabolism and discovered novel genera harboring these pathways. Finally, the prevalence of metabolic genes for organic sulfur indicates that these understudied substrates may be the most abundant source of microbially derived H2S.

CONCLUSIONS: Our findings significantly expand knowledge of microbial sulfur metabolism in the human gut. We show that genes for microbial sulfur metabolism in the human gut are more prevalent than previously known, irrespective of health status (i.e., in both healthy and diseased states). Our results significantly increase the diversity of pathways and bacteria that are associated with microbial sulfur metabolism in the human gut. Overall, our results have implications for understanding the role of the human gut microbiome and its potential contributions to the pathogenesis of CRC. Video abstract.}, } @article {pmid35439563, year = {2022}, author = {Wang, K and Qaisar, M and Chen, B and Xiao, J and Cai, J}, title = {Metagenomic analysis of microbial community and metabolic pathway of simultaneous sulfide and nitrite removal process exposed to divergent hydraulic retention times.}, journal = {Bioresource technology}, volume = {354}, number = {}, pages = {127186}, doi = {10.1016/j.biortech.2022.127186}, pmid = {35439563}, issn = {1873-2976}, mesh = {Bacteria/genetics/metabolism ; Bioreactors ; Denitrification ; Metabolic Networks and Pathways ; Metagenomics ; *Microbiota ; *Nitrites/metabolism ; Nitrogen/metabolism ; Sulfides/metabolism ; }, abstract = {The role of hydraulic retention time (HRT) on S[0] production was assessed through metagenomics analyses. Considering comprehensive performance for the tested HRTs (0.25-13.33 h), the optimal HRT was 1 h, while respective sulfide and nitrite loading rate could reach 6.84 kg S/(m[3]·d) and 1.95 kg N/(m[3]·d), and total S[0] yield was 0.36 kg S/(kg (VSS)·d). Bacterial community richness decreased along the shortening of HRT. Microbacterium, Sulfurimonas, Sulfurovum, Paracoccus and Thauera were highly abundant bacteria. During sulfur metabolism, high expression of sqr gene was the main reason of maintaining high desulfurization load, while lacking soxB caused the continuous increase of S[0]. Regarding nitrogen metabolism, the rapid decrease of nitrite transporter prevented nitrite to enter in cells, which caused a rapid decrease of nitrite removal under extreme HRT. Adjusting HRT is an effective way to enhance S[0] production for the application of the simultaneous sulfide and nitrite removal process.}, } @article {pmid35437888, year = {2022}, author = {Latz, MAC and Grujcic, V and Brugel, S and Lycken, J and John, U and Karlson, B and Andersson, A and Andersson, AF}, title = {Short- and long-read metabarcoding of the eukaryotic rRNA operon: Evaluation of primers and comparison to shotgun metagenomics sequencing.}, journal = {Molecular ecology resources}, volume = {22}, number = {6}, pages = {2304-2318}, doi = {10.1111/1755-0998.13623}, pmid = {35437888}, issn = {1755-0998}, support = {NV-03728-17//Naturvårdsverket/ ; 34442//Villum Fonden/ ; }, mesh = {DNA Primers/genetics ; *Eukaryota/genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; *rRNA Operon/genetics ; }, abstract = {High-throughput sequencing-based analysis of microbial diversity has evolved vastly over the last decade. Currently, the go-to method for studying microbial eukaryotes is short-read metabarcoding of variable regions of the 18S rRNA gene with <500 bp amplicons. However, there is a growing interest in applying long-read sequencing of amplicons covering the rRNA operon for improving taxonomic resolution. For both methods, the choice of primers is crucial. It determines if community members are covered, if they can be identified at a satisfactory taxonomic level, and if the obtained community profile is representative. Here, we designed new primers targeting 18S and 28S rRNA based on 177,934 and 21,072 database sequences, respectively. The primers were evaluated in silico along with published primers on reference sequence databases and marine metagenomics data sets. We further evaluated a subset of the primers for short- and long-read sequencing on environmental samples in vitro and compared the obtained community profile with primer-unbiased metagenomic sequencing. Of the short-read pairs, a new V6-V8 pair and the V4_Balzano pair used with a simplified PCR protocol provided good results in silico and in vitro. Fewer differences were observed between the long-read primer pairs. The long-read amplicons and ITS1 alone provided higher taxonomic resolution than V4. Together, our results represent a reference and guide for selection of robust primers for research on and environmental monitoring of microbial eukaryotes.}, } @article {pmid35437874, year = {2022}, author = {Guo, Y and Liu, C and Zhao, X and Zhang, X and Wu, Q and Wang, Z and Lu, J}, title = {Changes in gut microbiota, metabolite SCFAs, and GPR43 expression in obese diabetic mice after sleeve gastrectomy.}, journal = {Journal of applied microbiology}, volume = {133}, number = {2}, pages = {555-568}, doi = {10.1111/jam.15583}, pmid = {35437874}, issn = {1365-2672}, support = {19ZR1456000//National Natural Science Foundation of Shanghai/ ; 20ZR1456600//National Natural Science Foundation of Shanghai/ ; }, mesh = {Animals ; *Diabetes Mellitus, Experimental/surgery ; *Fatty Acids, Volatile/metabolism ; Gastrectomy/methods ; *Gastrointestinal Microbiome ; Mice ; Mice, Obese ; Obesity/genetics/surgery ; *Receptors, G-Protein-Coupled/genetics ; }, abstract = {AIMS: To evaluate changes in short-chain fatty acid levels and G protein-coupled receptor 43 expression and distribution in gut microbiota and explore their relationships in obese diabetic mice after sleeve gastrectomy.

METHODS AND RESULTS: Diet-induced obese mice and obese diabetic ob/ob mice were established. Changes in glucose metabolism, lipid metabolism, gut microbiota, metabolite short-chain fatty acids, and G protein-coupled receptor 43 expressions were assessed in both models 10 weeks postoperatively. Mice that underwent sleeve gastrectomy exhibited sustained weight loss and reduced glucose, insulin, leptin, and cholesterol levels. Metagenomic sequencing revealed significant characteristic alterations in gut microbiota after sleeve gastrectomy, which were correlated with changes in faecal short-chain fatty acid levels. Postoperatively, G protein-coupled receptor 43 expression in the colon tissue was upregulated in both models, whereas its expression in the adipose tissue was downregulated in the diet-induced obese mouse model.

CONCLUSIONS: Metabolic improvement in obese and diabetic mice after sleeve gastrectomy is associated with alterations in gut microbiota, short-chain fatty acid levels, and G protein-coupled receptor 43 expressions.

Our findings reveal a possible mechanism through which sleeve gastrectomy improves obesity and diabetes via changes in bacteria producing short-chain fatty acids and G protein-coupled receptor 43.}, } @article {pmid35436900, year = {2022}, author = {Song, J and Li, T and Zheng, Z and Fu, W and Long, Z and Shi, N and Han, Y and Zhang, L and Yu, Y and Fang, H}, title = {Carbendazim shapes microbiome and enhances resistome in the earthworm gut.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {63}, pmid = {35436900}, issn = {2049-2618}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Benzimidazoles ; Carbamates ; *Fungicides, Industrial ; Genes, Bacterial ; *Microbiota/genetics ; *Oligochaeta ; Soil/chemistry ; }, abstract = {BACKGROUND: It is worrisome that several pollutants can enhance the abundance of antibiotic resistance genes (ARGs) in the environment, including agricultural fungicides. As an important bioindicator for environmental risk assessment, earthworm is still a neglected focus that the effects of the fungicide carbendazim (CBD) residues on the gut microbiome and resistome are largely unknown. In this study, Eisenia fetida was selected to investigate the effects of CBD in the soil-earthworm systems using shotgun metagenomics and qPCR methods.

RESULTS: CBD could significantly perturb bacterial community and enrich specific bacteria mainly belonging to the phylum Actinobacteria. More importantly, CBD could serve as a co-selective agent to elevate the abundance and diversity of ARGs, particularly for some specific types (e.g., multidrug, glycopeptide, tetracycline, and rifamycin resistance genes) in the earthworm gut. Additionally, host tracking analysis suggested that ARGs were mainly carried in some genera of the phyla Actinobacteria and Proteobacteria. Meanwhile, the level of ARGs was positively relevant to the abundance of mobile genetic elements (MGEs) and some representative co-occurrence patterns of ARGs and MGEs (e.g., cmx-transposase and sul1-integrase) were further found on the metagenome-assembled contigs in the CBD treatments.

CONCLUSIONS: It can be concluded that the enhancement effect of CBD on the resistome in the earthworm gut may be attributed to its stress on the gut microbiome and facilitation on the ARGs dissemination mediated by MGEs, which may provide a novel insight into the neglected ecotoxicological risk of the widely used agrochemicals on the gut resistome of earthworm dwelling in soil. Video abstract.}, } @article {pmid35436715, year = {2022}, author = {Liu, Z and Wei, Y and Li, J and Ding, GC}, title = {Integrating 16S rRNA amplicon metagenomics and selective culture for developing thermophilic bacterial inoculants to enhance manure composting.}, journal = {Waste management (New York, N.Y.)}, volume = {144}, number = {}, pages = {357-365}, doi = {10.1016/j.wasman.2022.04.013}, pmid = {35436715}, issn = {1879-2456}, mesh = {*Agricultural Inoculants/genetics ; *Composting ; Manure/microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Soil ; }, abstract = {Composting is an important method for treating and recycling organic waste, and the use of microbial inoculants can increase the efficiency of composting. Herein, we illustrate an approach that integrate 16S rRNA amplicon metagenomics and selective culture of thermophilic bacteria for the development of inoculants to improve manure composting. The 16S rRNA amplicon sequencing analysis revealed that Firmicutes and Actinobacteria were dominant in the composting mixture, and that different microbial hubs succeeded during the thermophilic stage. All isolated thermophilic bacteria were affiliated with the order Bacillales, such as Geobacillus, Bacillus, and Aeribacillus. These isolated thermophilic bacteria were grouped into 11 phylotypes, which shared ＞99% sequence identity to 0.15% to 5.32% of 16S rRNA reads by the amplicon sequencing. Three of these phylotypes transiently enriched during the thermophilic stage. Six thermophilic bacteria were selected from the three phylotypes to obtain seven microbial inoculants. Five out of seven of the microbial inoculants enhanced the thermophilic stage of composting by 16.9% to 52.2%. Three-dimensional excitation emission matrix analysis further revealed that two inoculants (Thermoactinomyces intermedius and Ureibacillus thermophilus) stimulated humification. Additionally, the 16S rRNA amplicon sequencing analysis revealed that inoculation with thermophilic bacteria enhanced the succession of the microbial community during composting. In conclusion, 16S rRNA amplicon metagenomics is a useful tool for the development of microbial inoculants to enhance manure composting.}, } @article {pmid35435739, year = {2022}, author = {Verbanic, S and Deacon, JM and Chen, IA}, title = {The Chronic Wound Phageome: Phage Diversity and Associations with Wounds and Healing Outcomes.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0277721}, pmid = {35435739}, issn = {2165-0497}, support = {DP2 GM123457/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; Humans ; Metagenomics ; *Microbiota ; Virome ; *Viruses/genetics ; Wound Healing ; }, abstract = {Two leading impediments to chronic wound healing are polymicrobial infection and biofilm formation. Recent studies have characterized the bacterial fraction of these microbiomes and have begun to elucidate compositional correlations to healing outcomes. However, the factors that drive compositional shifts are still being uncovered. The virome may play an important role in shaping bacterial community structure and function. Previous work on the skin virome determined that it was dominated by bacteriophages, viruses that infect bacteria. To characterize the virome, we enrolled 20 chronic wound patients presenting at an outpatient wound care clinic in a microbiome survey, collecting swab samples from healthy skin and chronic wounds (diabetic, venous, arterial, or pressure) before and after a single, sharp debridement procedure. We investigated the virome using a virus-like particle enrichment procedure, shotgun metagenomic sequencing, and a k-mer-based, reference-dependent taxonomic classification method. Taxonomic composition, diversity, and associations with covariates are presented. We find that the wound virome is highly diverse, with many phages targeting known pathogens, and may influence bacterial community composition and functionality in ways that impact healing outcomes. IMPORTANCE Chronic wounds are an increasing medical burden. These wounds are known to be rich in microbial content, including both bacteria and bacterial viruses (phages). The viruses may play an important role in shaping bacterial community structure and function. We analyzed the virome and bacterial composition of 20 patients with chronic wounds. The viruses found in wounds are highly diverse compared to normal skin, unlike the bacterial composition, where diversity is decreased. These data represent an initial look at this relatively understudied component of the chronic wound microbiome and may help inform future phage-based interventions.}, } @article {pmid35435701, year = {2022}, author = {Podowski, JC and Paver, SF and Newton, RJ and Coleman, ML}, title = {Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0237921}, pmid = {35435701}, issn = {2150-7511}, mesh = {*Ammonia/metabolism ; Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; *Ecosystem ; Genome ; Lakes/microbiology ; Nitrification ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; Rhodopsins, Microbial ; }, abstract = {Microbial nitrification is a critical process governing nitrogen availability in aquatic systems. Freshwater nitrifiers have received little attention, leaving many unanswered questions about their taxonomic distribution, functional potential, and ecological interactions. Here, we reconstructed genomes to infer the metabolism and ecology of free-living picoplanktonic nitrifiers across the Laurentian Great Lakes, a connected series of five of Earth's largest lakes. Surprisingly, ammonia-oxidizing bacteria (AOB) related to Nitrosospira dominated over ammonia-oxidizing archaea (AOA) at nearly all stations, with distinct ecotypes prevailing in the transparent, oligotrophic upper lakes compared to Lakes Erie and Ontario. Unexpectedly, one ecotype of Nitrosospira encodes proteorhodopsin, which could enhance survival under conditions where ammonia oxidation is inhibited or substrate limited. Nitrite-oxidizing bacteria (NOB) "Candidatus Nitrotoga" and Nitrospira fluctuated in dominance, with the latter prevailing in deeper, less-productive basins. Genome reconstructions reveal highly reduced genomes and features consistent with genome streamlining, along with diverse adaptations to sunlight and oxidative stress and widespread capacity for organic nitrogen use. Our findings expand the known functional diversity of nitrifiers and establish their ecological genomics in large lake ecosystems. By elucidating links between microbial biodiversity and biogeochemical cycling, our work also informs ecosystem models of the Laurentian Great Lakes, a critical freshwater resource experiencing rapid environmental change. IMPORTANCE Microorganisms play critical roles in Earth's nitrogen cycle. In lakes, microorganisms called nitrifiers derive energy from reduced nitrogen compounds. In doing so, they transform nitrogen into a form that can ultimately be lost to the atmosphere by a process called denitrification, which helps mitigate nitrogen pollution from fertilizer runoff and sewage. Despite their importance, freshwater nitrifiers are virtually unexplored. To understand their diversity and function, we reconstructed genomes of freshwater nitrifiers across some of Earth's largest freshwater lakes, the Laurentian Great Lakes. We discovered several new species of nitrifiers specialized for clear low-nutrient waters and distinct species in comparatively turbid Lake Erie. Surprisingly, one species may be able to harness light energy by using a protein called proteorhodopsin, despite the fact that nitrifiers typically live in deep dark water. Our work reveals the unique biodiversity of the Great Lakes and fills key gaps in our knowledge of an important microbial group, the nitrifiers.}, } @article {pmid35434230, year = {2022}, author = {Tran, DM and Nguyen, TH and Huynh, TU and Do, TO and Nguyen, QV and Nguyen, AD}, title = {Analysis of endophytic microbiome dataset from roots of black pepper (Piper nigrum L.) cultivated in the Central Highlands region, Vietnam using 16S rRNA gene metagenomic next-generation sequencing.}, journal = {Data in brief}, volume = {42}, number = {}, pages = {108108}, pmid = {35434230}, issn = {2352-3409}, abstract = {Vietnam is the most prominent black pepper producer and exporter in the world. In 2020, the cultivated area of black pepper in Vietnam was 132.000 hectares and its production was 270.000 tons, in which the Central Highlands region took about 70% of both the cultivated area and production [1]. Hence, this region is thought to be the capital of black pepper cultivation and production in Vietnam. Numerous researches have investigated biodiversity and collected various beneficial endophytic bacteria from this plant in this region; however, traditional methods only were used to isolate such bacteria [2], [3], [4], [5]. Therefore, these studies have a limitation to providing insight into the profiles of the endophytic microorganism dataset in the black pepper plant. Most recently, our work based on the 16S rRNA gene amplicon sequencing revealed an insight into profiles of microbial diversity and its functionality from the sample collected from a forest in this region; however, that work was just focused on soil microbiome dataset from the dry deciduous dipterocarp forest in Yok Don national park [6]. To our knowledge, a dataset of endophytic microbiome of black pepper plant cultivated in the Central Highlands remains unclear. This report presents a dataset of the endophytic microbiome from a representative sample combined from five different root samples of black pepper (Vinh Linh local variety) cultivated in the Central Highlands of Vietnam using 16S rRNA gene metagenomic next-generation sequencing. The dataset in this work can provide information on the endophytic microbial diversity and its functionality. It can also be useful for developing cultivation techniques by applying endophytic microbial genetic resources for sustainable black pepper production in the Central Highlands, Vietnam, towards the nutrient need in different stages of development and growth.}, } @article {pmid35433497, year = {2022}, author = {Wang, Y and Gao, X and Lv, J and Zeng, Y and Li, Q and Wang, L and Zhang, Y and Gao, W and Wang, J}, title = {Gut Microbiome Signature Are Correlated With Bone Mineral Density Alterations in the Chinese Elders.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {827575}, pmid = {35433497}, issn = {2235-2988}, mesh = {Aged ; Bone Density/genetics ; China ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; *Osteoporosis/genetics ; RNA, Ribosomal, 16S/genetics ; *Vitamin D Deficiency ; }, abstract = {OBJECTIVE: Osteoporosis (OP), clinically featured with a low bone mineral density (BMD) and high risk of bone fracture, has become a major risk factor of disability and death in the elders, especially in postmenopausal women. The gut microbiome (GM) is thought to be implicated in bone metabolism. Herein, we clarified the composition signature and gene functional profile of GM in older people with normal and low BMD.

DESIGN AND METHODS: A total of 455 participants underwent the BMD measurement and biochemical detection. GM analysis was further performed on 113 cases of postmenopausal women and men aged over 50, including both 16S rRNA and metagenomic sequencing.

RESULTS: Generally, the BMD value was significantly lower in the older age groups, especially in the postmenopausal women. Consistently, we observed obvious vitamin D deficiency or insufficiency in females (compared to the male, P < 0.0001). The results from 16S rRNA sequencing revealed higher numbers of OTUs and diversity indexes in females than in males. The abundance in composition of Firmicutes and Clostridiales were correlated with the BMD values in females. LEfSe analysis discovered several enriched bacteria taxons in OP and normal control (NC) subgroups. A positive correlation between the number of genes and BMD values was observed in females based on metagenomic sequencing analysis. Furthermore, we identified the connecting modules among the GM composition - gene functional signature - BMD value/T score in both females and males.

CONCLUSIONS: This study provides evidences upon which to understand the mechanisms of the effects of GM on bone health, consequently revealing the physiology status and potential diagnostic/therapeutic targets based on GM for OP and postmenopausal osteoporosis (PMOP). Besides, the status of vitamin D deficiency or insufficiency need to be concerned and improved in the Chinese people.}, } @article {pmid35432264, year = {2022}, author = {Dong, Y and Zheng, K and Zou, X and Liang, Y and Liu, Y and Li, X and Shao, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M}, title = {Characterization and Genomic Analysis of the First Podophage Infecting Shewanella, Representing a Novel Viral Cluster.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {853973}, pmid = {35432264}, issn = {1664-302X}, abstract = {Shewanella is a common bacterial genus in marine sediments and deep seas, with a variety of metabolic abilities, suggesting its important roles in the marine biogeochemical cycles. In this study, a novel lytic Shewanella phage, vB_SInP-X14, was isolated from the surface coastal waters of Qingdao, China. The vB_SInP-X14 contains a linear, double-strand 36,396-bp with the G + C content of 44.1% and harbors 40 predicted open reading frames. Morphological, growth, and genomic analysis showed that it is the first isolated podovirus infecting Shewanella, with a short propagation time (40 min), which might be resulted from three lytic-related genes. Phylogenetic analysis suggested that vB_SInP-X14 could represent a novel viral genus, named Bocovirus, with four isolated but not classified phages. In addition, 14 uncultured viral genomes assembled from the marine metagenomes could provide additional support to establish this novel viral genus. This study reports the first podovirus infecting Shewanella, establishes a new interaction system for the study of virus-host interactions, and also provides new reference genomes for the marine viral metagenomic analysis.}, } @article {pmid35431236, year = {2022}, author = {Jeong, S and Huang, LK and Tsai, MJ and Liao, YT and Lin, YS and Hu, CJ and Hsu, YH}, title = {Cognitive Function Associated with Gut Microbial Abundance in Sucrose and S-Adenosyl-L-Methionine (SAMe) Metabolic Pathways.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {87}, number = {3}, pages = {1115-1130}, doi = {10.3233/JAD-215090}, pmid = {35431236}, issn = {1875-8908}, mesh = {*Alzheimer Disease/metabolism ; Cognition ; *Cognitive Dysfunction/psychology ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolic Networks and Pathways ; RNA, Ribosomal, 16S/genetics/metabolism ; S-Adenosylmethionine ; Sucrose ; }, abstract = {BACKGROUND: Differential abundance of gut microbiota has found to be associated with Alzheimer's disease (AD). However, the relative abundance of gut microbiota between dementia and mild cognitive impairment (MCI) in AD is not well studied.

OBJECTIVE: We attempted to identify differentially enriched gut microbes and their metabolic pathways in AD patients with dementia comparing to AD patients with MCI.

METHODS: Fecal samples were collected at Shuang Ho Hospital, Taipei Medical University, Taiwan and analyzed by whole metagenomic sequencing technique. For normal controls without AD (NC), 16S rRNA sequencing was obtained from the Taiwan Microbiome Database. A total of 48 AD (38 dementia and 10 MCI defined by cognitive function scores) and 50 NC were included. Microbiome alpha and beta diversities were estimated. Differentially enriched microbes were identified with HAllA, MaAsLin, DESeq2, and LEfSe statistical modeling approaches.

RESULTS: We found significantly increased abundance of Firmicutes but decreased abundance of Bacteroidetes at phylum level in AD compared to NC. In AD patients, cognitive function scores were negatively associated with abundance of Blautia hydrogenotrophica (Firmicutes), Anaerotruncus colihominis (Firmicutes), and Gordonibacter pamelaeae (Actinobacteria). In addition, microbial abundance in the sucrose and S-Adenosyl-L-methionine (SAMe) metabolic pathways was more enriched in AD with MCI than AD with dementia and significantly associated with higher cognitive function scores.

CONCLUSION: Gut microbe community diversity was similar in AD patients regardless of MCI or dementia status. However, differential analyses probed in lower-level taxa and metabolic pathways suggested that specific gut microbes in Firmicutes and Actinobacteria might involve in cognitive decline.}, } @article {pmid35430893, year = {2022}, author = {Zheng, PF and Wei, Z and Zhou, Y and Li, Q and Qi, Z and Diao, X and Wang, Y}, title = {Genomic Evidence for the Recycling of Complex Organic Carbon by Novel Thermoplasmatota Clades in Deep-Sea Sediments.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0007722}, pmid = {35430893}, issn = {2379-5077}, mesh = {*Carbon/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Archaea/genetics ; Genomics ; *Microbiota/genetics ; Organic Chemicals/metabolism ; }, abstract = {Thermoplasmatota have been widely reported in a variety of ecosystems, but their distribution and ecological role in marine sediments are still elusive. Here, we obtained four draft genomes affiliated with the former RBG-16-68-12 clade, which is now considered a new order, "Candidatus Yaplasmales," of the Thermoplasmatota phylum in sediments from the South China Sea. The phylogenetic trees based on the 16S rRNA genes and draft genomes showed that "Ca. Yaplasmales" archaea are composed of three clades: A, B, and C. Among them, clades A and B are abundantly distributed (up to 10.86%) in the marine anoxic sediment layers (>10-cm depth) of six of eight cores from 1,200- to 3,400-m depths. Metabolic pathway reconstructions indicated that all clades of "Ca. Yaplasmales" have the capacity for alkane degradation by predicted alkyl-succinate synthase. Clade A of "Ca. Yaplasmales" might be mixotrophic microorganisms for the identification of the complete Wood-Ljungdahl pathway and putative genes involved in the degradation of aromatic and halogenated organic compounds. Clades B and C were likely heterotrophic, especially with the potential capacity of the spermidine/putrescine and aromatic compound degradation, as suggested by a significant negative correlation between the concentrations of aromatic compounds and the relative abundances of clade B. The sulfide-quinone oxidoreductase and pyrophosphate-energized membrane proton pump were encoded by all genomes of "Ca. Yaplasmales," serving as adaptive strategies for energy production. These findings suggest that "Ca. Yaplasmales" might synergistically transform benthic pollutant and detrital organic matter, possibly playing a vital role in the marine and terrestrial sedimentary carbon cycle. IMPORTANCE Deep oceans receive large amounts of complex organic carbon and anthropogenic pollutants. The deep-sea sediments of the continental slopes serve as the biggest carbon sink on Earth. Particulate organic carbons and detrital proteins accumulate in the sediment. The microbially mediated recycling of complex organic carbon is still largely unknown, which is an important question for carbon budget in global oceans and maintenance of the deep-sea ecosystem. In this study, we report the prevalence (up to 10.86% of the microbial community) of archaea from a novel order of Thermoplasmatota, "Ca. Yaplasmales," in six of eight cores from 1,200- to 3,400-m depths in the South China Sea. We provide genomic evidence of "Ca. Yaplasmales" in the anaerobic microbial degradation of alkanes, aliphatic and monoaromatic hydrocarbons, and halogenated organic compounds. Our study identifies the key archaeal players in anoxic marine sediments, which are probably critical in recycling the complex organic carbon in global oceans.}, } @article {pmid35430593, year = {2022}, author = {Dove, NC and Taş, N and Hart, SC}, title = {Ecological and genomic responses of soil microbiomes to high-severity wildfire: linking community assembly to functional potential.}, journal = {The ISME journal}, volume = {16}, number = {7}, pages = {1853-1863}, pmid = {35430593}, issn = {1751-7370}, support = {DEAC05-00OR22725//U.S. Department of Energy (DOE)/ ; EAR-1331939//National Science Foundation (NSF)/ ; }, mesh = {Ecosystem ; *Fires ; Genomics ; *Microbiota ; Soil ; *Wildfires ; }, abstract = {Increasing wildfire severity, which is common throughout the western United States, can have deleterious effects on plant regeneration and large impacts on carbon (C) and nitrogen (N) cycling rates. Soil microbes are pivotal in facilitating these elemental cycles, so understanding the impact of increasing fire severity on soil microbial communities is critical. Here, we assess the long-term impact of high-severity fires on the soil microbiome. We find that high-severity wildfires result in a multi-decadal (>25 y) recovery of the soil microbiome mediated by concomitant differences in aboveground vegetation, soil chemistry, and microbial assembly processes. Our results depict a distinct taxonomic and functional successional pattern of increasing selection in post-fire soil microbial communities. Changes in microbiome composition corresponded with changes in microbial functional potential, specifically altered C metabolism and enhanced N cycling potential, which related to rates of potential decomposition and inorganic N availability, respectively. Based on metagenome-assembled genomes, we show that bacterial genomes enriched in our earliest site (4 y since fire) harbor distinct traits such as a robust stress response and a high potential to degrade pyrogenic, polyaromatic C that allow them to thrive in post-fire environments. Taken together, these results provide a biological basis for previously reported process rate measurements and explain the temporal dynamics of post-fire biogeochemistry, which ultimately constrains ecosystem recovery.}, } @article {pmid35430490, year = {2022}, author = {Zhou, Y and Liu, M and Yang, J}, title = {Recovering metagenome-assembled genomes from shotgun metagenomic sequencing data: Methods, applications, challenges, and opportunities.}, journal = {Microbiological research}, volume = {260}, number = {}, pages = {127023}, doi = {10.1016/j.micres.2022.127023}, pmid = {35430490}, issn = {1618-0623}, mesh = {High-Throughput Nucleotide Sequencing ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Reference genomes are essential for analyzing the metabolic and functional potentials of microbiomes. However, microbial genome resources are limited because most of microorganisms are difficult to culture. Genome binning is a culture-independent approach that can recover a vast number of microbial genomes from short-read high throughput shotgun metagenomic sequencing data. In this review, we summarize methods commonly used for reconstructing metagenome-assembled genomes (MAGs) to provide a reference for researchers to choose propriate software programs among the numerous and complicated tools and pipelines that are available for these analyses. In addition, we discuss application prospects, challenges, and opportunities for recovering MAGs from metagenomic sequencing data.}, } @article {pmid35429147, year = {2022}, author = {Yukawa-Muto, Y and Kamiya, T and Fujii, H and Mori, H and Toyoda, A and Sato, I and Konishi, Y and Hirayama, A and Hara, E and Fukuda, S and Kawada, N and Ohtani, N}, title = {Distinct responsiveness to rifaximin in patients with hepatic encephalopathy depends on functional gut microbial species.}, journal = {Hepatology communications}, volume = {6}, number = {8}, pages = {2090-2104}, pmid = {35429147}, issn = {2471-254X}, mesh = {Ammonia/metabolism ; Animals ; Bacteria ; Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome ; *Hepatic Encephalopathy/drug therapy ; Humans ; Liver Cirrhosis/complications ; Mice ; *Rifaximin/therapeutic use ; Urease/metabolism ; }, abstract = {Hepatic encephalopathy (HE) is the neuropsychiatric complication of liver cirrhosis (LC). The influence of gut microbiota on HE pathogenesis has been suggested but not precisely elucidated. Here, we investigate how the gut microbial profile changed in patients with HE to clarify the functional gut microbial species associated with HE. We focused on their responses to rifaximin (RFX), a nonabsorbable antibiotic used in HE therapy. Feces samples were collected from patients with decompensated LC (all HE), patients with compensated LC, and healthy controls, and fecal gut microbial profiles were compared using 16S ribosomal RNA gene amplicon and metagenomic sequencing. The linear discriminant analysis effect size was used to identify specific species. Urease-positive Streptococcus salivarius, which can produce ammonia, was identified as the most significantly abundant gut microbiota in the HE group, and its ability to elevate the levels of blood ammonia as well as brain glutamine was experimentally verified in mice. Urease-negative Ruminococcus gnavus was also identified as a significantly abundant species in patients with RFX-nonresponsive HE after RFX administration. Interestingly, R. gnavus enhanced urease activity of recombinant urease itself, implying that R. gnavus could amplify ammonia production of surrounding urease-positive microbiota. Furthermore, the sensitivity of S. salivarius and R. gnavus to RFX depended on conjugated secondary bile acid levels, suggesting a therapeutic potential of the combined use of secondary bile acid levels with RFX for enhancing the efficacy of RFX. This study identified specific gut bacterial species abundant in patients with HE and verified their functions linked to HE pathophysiology. Targeting these bacteria could be a potentially effective strategy to treat HE.}, } @article {pmid35421499, year = {2022}, author = {Haque, S and Srivastava, N and Pal, DB and Alkhanani, MF and Almalki, AH and Areeshi, MY and Naidu, R and Gupta, VK}, title = {Functional microbiome strategies for the bioremediation of petroleum-hydrocarbon and heavy metal contaminated soils: A review.}, journal = {The Science of the total environment}, volume = {833}, number = {}, pages = {155222}, doi = {10.1016/j.scitotenv.2022.155222}, pmid = {35421499}, issn = {1879-1026}, mesh = {Biodegradation, Environmental ; Humans ; Hydrocarbons ; *Metals, Heavy/analysis ; *Microbiota ; *Petroleum/metabolism ; Soil/chemistry ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Petroleum hydrocarbons and heavy metals are the two major soil contaminants that are released into the environment in the forms of industrial effluents. These contaminants exert serious impacts on human health and the sustainability of the environment. In this context, remediation of these pollutants via a biological approach can be effective, low-cost, and eco-friendly approach. The implementation of microorganisms and metagenomics are regarded as the advanced solution for remediating such pollutants. Further, microbiomes can overcome this issue via adopting specific structural, functional and metabolic pathways involved in the microbial community to degrade these pollutants. Genomic sequencing and library can effectively channelize the degradation of these pollutants via microbiomes. Nevertheless, more advanced technology and reliable strategies are required to develop. The present review provides insights into the role of microbiomes to effectively remediate/degrade petroleum hydrocarbons and heavy metals in contaminated soil. The possible degradation mechanisms of these pollutants have also been discussed in detail along with their existing limitations. Finally, prospects of the bioremediation strategies using microbiomes are discussed.}, } @article {pmid35421490, year = {2022}, author = {Hu, J and Liu, G and Li, H and Luo, H and Zhang, R}, title = {Synergistic effect of bioanode and biocathode on nitrobenzene removal: Microbial community structure and functions.}, journal = {The Science of the total environment}, volume = {833}, number = {}, pages = {155190}, doi = {10.1016/j.scitotenv.2022.155190}, pmid = {35421490}, issn = {1879-1026}, mesh = {*Bioelectric Energy Sources ; Electricity ; Electrodes ; Glucose ; *Microbiota ; Nitrobenzenes/metabolism ; }, abstract = {This study aimed to reveal the synergistic effect of bioanode and biocathode on nitrobenzene (NB) removal with different microbial community structures and functions. Single-chamber bioelectrochemical reactors were constructed and operated with different initial concentrations of NB and glucose as the substrate. With the synergistic effect of biocathode and bioanode, NB was completely removed within 8 h at a kinetic rate constant of 0.8256 h[-1], and high conversion rate from NB to AN (92%) was achieved within 18 h. The kinetic rate constant of NB removal was linearly correlated with the maximum current density and total coulombs (R[2] > 0.95). Increase of glucose and NB concentrations had significantly positive and negative effects, respectively, on the NB removal kinetics (R[2] > 0.97 and R[2] > 0.93, respectively). Geobacter sp. and Enterococcus sp. dominated in the bioanode and biocathode, respectively. The presence of Klebsiella pneumoniae in the bioanode was beneficial for Geobacter species to produce electricity and to alleviate the NB inhibition. As one of the dominant species at the biocathode, Methanobacterium formicicum has the ability of nitroaromatics degradation according to KEGG analysis, which played a crucial role for NB reduction. Fermentative bacteria converted glucose into volatile fatty acids or H2, to provide energy sources to other species (e.g., Geobacter sulfurreducens and Methanobacterium formicicum). The information from this study is useful to optimize the bioelectrocatalytic system for nitroaromatic compound removal.}, } @article {pmid35421353, year = {2022}, author = {Dsouza, M and Menon, R and Crossette, E and Bhattarai, SK and Schneider, J and Kim, YG and Reddy, S and Caballero, S and Felix, C and Cornacchione, L and Hendrickson, J and Watson, AR and Minot, SS and Greenfield, N and Schopf, L and Szabady, R and Patarroyo, J and Smith, W and Harrison, P and Kuijper, EJ and Kelly, CP and Olle, B and Bobilev, D and Silber, JL and Bucci, V and Roberts, B and Faith, J and Norman, JM}, title = {Colonization of the live biotherapeutic product VE303 and modulation of the microbiota and metabolites in healthy volunteers.}, journal = {Cell host & microbe}, volume = {30}, number = {4}, pages = {583-598.e8}, doi = {10.1016/j.chom.2022.03.016}, pmid = {35421353}, issn = {1934-6069}, mesh = {*Clostridioides difficile ; *Clostridium Infections/microbiology/therapy ; Fecal Microbiota Transplantation/methods ; Healthy Volunteers ; Humans ; *Microbiota ; }, abstract = {Manipulation of the gut microbiota via fecal microbiota transplantation (FMT) has shown clinical promise in diseases such as recurrent Clostridioides difficile infection (rCDI). However, the variable nature of this approach makes it challenging to describe the relationship between fecal strain colonization, corresponding microbiota changes, and clinical efficacy. Live biotherapeutic products (LBPs) consisting of defined consortia of clonal bacterial isolates have been proposed as an alternative therapeutic class because of their promising preclinical results and safety profile. We describe VE303, an LBP comprising 8 commensal Clostridia strains under development for rCDI, and its early clinical development in healthy volunteers (HVs). In a phase 1a/b study in HVs, VE303 is determined to be safe and well-tolerated at all doses tested. VE303 strains optimally colonize HVs if dosed over multiple days after vancomycin pretreatment. VE303 promotes the establishment of a microbiota community known to provide colonization resistance.}, } @article {pmid35417481, year = {2022}, author = {Lyalina, S and Stepanauskas, R and Wu, F and Sanjabi, S and Pollard, KS}, title = {Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community.}, journal = {PloS one}, volume = {17}, number = {4}, pages = {e0261795}, pmid = {35417481}, issn = {1932-6203}, support = {R21 AI108953/AI/NIAID NIH HHS/United States ; R21 AI134037/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Humans ; Mammals/genetics ; Metagenome ; Metagenomics ; Mice ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Laboratory mice are widely studied as models of mammalian biology, including the microbiota. However, much of the taxonomic and functional diversity of the mouse gut microbiome is missed in current metagenomic studies, because genome databases have not achieved a balanced representation of the diverse members of this ecosystem. Towards solving this problem, we used flow cytometry and low-coverage sequencing to capture the genomes of 764 single cells from the stool of three laboratory mice. From these, we generated 298 high-coverage microbial genome assemblies, which we annotated for open reading frames and phylogenetic placement. These genomes increase the gene catalog and phylogenetic breadth of the mouse microbiota, adding 135 novel species with the greatest increase in diversity to the Muribaculaceae and Bacteroidaceae families. This new diversity also improves the read mapping rate, taxonomic classifier performance, and gene detection rate of mouse stool metagenomes. The novel microbial functions revealed through our single-cell genomes highlight previously invisible pathways that may be important for life in the murine gastrointestinal tract.}, } @article {pmid35416715, year = {2022}, author = {Yang, C and Su, Q and Tang, M and Luo, S and Zheng, H and Zhang, X and Zhou, X}, title = {Amplicon Sequencing of Single-Copy Protein-Coding Genes Reveals Accurate Diversity for Sequence-Discrete Microbiome Populations.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0210521}, pmid = {35416715}, issn = {2165-0497}, mesh = {Animals ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {An in-depth understanding of microbial function and the division of ecological niches requires accurate delineation and identification of microbes at a fine taxonomic resolution. Microbial phylotypes are typically defined using a 97% small subunit (16S) rRNA threshold. However, increasing evidence has demonstrated the ubiquitous presence of taxonomic units of distinct functions within phylotypes. These so-called sequence-discrete populations (SDPs) have used to be mainly delineated by disjunct sequence similarity at the whole-genome level. However, gene markers that could accurately identify and quantify SDPs are lacking in microbial community studies. Here, we developed a pipeline to screen single-copy protein-coding genes that could accurately characterize SDP diversity via amplicon sequencing of microbial communities. Fifteen candidate marker genes were evaluated using three criteria (extent of sequence divergence, phylogenetic accuracy, and conservation of primer regions) and the selected genes were subject to test the efficiency in differentiating SDPs within Gilliamella, a core honeybee gut microbial phylotype, as a proof-of-concept. The results showed that the 16S V4 region failed to report accurate SDP diversities due to low taxonomic resolution and changing copy numbers. In contrast, the single-copy genes recommended by our pipeline were able to successfully quantify Gilliamella SDPs for both mock samples and honeybee guts, with results highly consistent with those of metagenomics. The pipeline developed in this study is expected to identify single-copy protein coding genes capable of accurately quantifying diverse bacterial communities at the SDP level. IMPORTANCE Microbial communities can be distinguished by discrete genetic and ecological characteristics. These sequence-discrete populations are foundational for investigating the composition and functional structures of microbial communities at high resolution. In this study, we screened for reliable single-copy protein-coding marker genes to identify sequence-discrete populations through our pipeline. Using marker gene amplicon sequencing, we could accurately and efficiently delineate the population diversity in microbial communities. These results suggest that single copy protein-coding genes can be an accurate, quantitative, and economical alternative for characterizing population diversity. Moreover, the feasibility of a gene as marker for any bacterial population identification can be quickly evaluated by the pipeline proposed here.}, } @article {pmid35416402, year = {2022}, author = {Zhong, C and Nesbø, CL and von Gunten, K and Zhang, Y and Shao, X and Jin, R and Konhauser, KO and Goss, GG and Martin, JW and He, Y and Qian, PY and Lanoil, BD and Alessi, DS}, title = {Complex impacts of hydraulic fracturing return fluids on soil microbial community respiration, structure and functional potentials.}, journal = {Environmental microbiology}, volume = {24}, number = {9}, pages = {4108-4123}, doi = {10.1111/1462-2920.16009}, pmid = {35416402}, issn = {1462-2920}, mesh = {*Hydraulic Fracking ; *Microbiota/genetics ; Respiration ; Soil ; Soil Microbiology ; Wastewater/chemistry ; Water ; *Water Pollutants, Chemical/analysis ; }, abstract = {The consequences of soils exposed to hydraulic fracturing (HF) return fluid, often collectively termed flowback and produced water (FPW), are poorly understood, even though soils are a common receptor of FPW spills. Here, we investigate the impacts on soil microbiota exposed to FPW collected from the Montney Formation of western Canada. We measured soil respiration, microbial community structure and functional potentials under FPW exposure across a range of concentrations, exposure time and soil types (luvisol and chernozem). We find that soil type governs microbial community response upon FPW exposure. Within each soil, FPW exposure led to reduced biotic soil respiration, and shifted microbial community structure and functional potentials. We detect substantially higher species richness and more unique functional genes in FPW-exposed soils than in FPW-unexposed soils, with metagenome-assembled genomes (e.g. Marinobacter persicus) from luvisol soil exposed to concentrated FPW being most similar to genomes from HF/FPW sites. Our data demonstrate the complex impacts of microbial communities following FPW exposure and highlight the site-specific effects in evaluation of spills and agricultural reuse of FPW on the normal soil functions.}, } @article {pmid35415828, year = {2022}, author = {Salam, LB}, title = {Metagenomic insights into the microbial community structure and resistomes of a tropical agricultural soil persistently inundated with pesticide and animal manure use.}, journal = {Folia microbiologica}, volume = {67}, number = {5}, pages = {707-719}, pmid = {35415828}, issn = {1874-9356}, mesh = {Aminoglycosides ; Animals ; Anti-Bacterial Agents/pharmacology ; Cadmium ; Chromium ; Cobalt ; Colistin ; Copper ; *Disinfectants ; Genes, Bacterial ; Glycopeptides ; Lincosamides ; Macrolides ; Manure/microbiology ; *Mercury ; Metagenomics ; *Microbiota/genetics ; Nickel ; *Pesticides/pharmacology ; *Selenium ; Soil/chemistry ; Soil Microbiology ; Streptogramins ; Tungsten ; Zinc ; beta-Lactamases/genetics ; }, abstract = {Persistent use of pesticides and animal manure in agricultural soils inadvertently introduced heavy metals and antibiotic/antibiotic resistance genes (ARGs) into the soil with deleterious consequences. The microbiome and heavy metal and antibiotic resistome of a pesticide and animal manure inundated agricultural soil (SL6) obtained from a vegetable farm at Otte, Eiyenkorin, Kwara State, Nigeria, was deciphered via shotgun metagenomics and functional annotation of putative ORFs (open reading frames). Structural metagenomics of SL6 microbiome revealed 29 phyla, 49 classes, 94 orders, 183 families, 366 genera, 424 species, and 260 strains with the preponderance of the phyla Proteobacteria (40%) and Actinobacteria (36%), classes Actinobacteria (36%), Alphaproteobacteria (18%), and Gammaproteobacteria (17%), and genera Kocuria (16%), Sphingobacterium (11%), and Brevundimonas (10%), respectively. Heavy metal resistance genes annotation conducted using Biocide and Metal Resistance Gene Database (BacMet) revealed the detection of genes responsible for the uptake, transport, detoxification, efflux, and regulation of copper, cadmium, zinc, nickel, chromium, cobalt, selenium, tungsten, mercury, and several others. ARG annotation using the Antibiotic Resistance Gene-annotation (ARG-ANNOT) revealed ARGs for 11 antibiotic classes with the preponderance of β-lactamases, mobilized colistin resistance determinant (mcr-1), macrolide-lincosamide-streptogramin (MLS), glycopeptide, and aminoglycoside resistance genes, among others. The persistent use of pesticide and animal manure is strongly believed to play a major role in the proliferation of heavy metal and antibiotic resistance genes in the soil. This study revealed that agricultural soils inundated with pesticide and animal manure use are potential hotspots for ARG spread and may accentuate the spread of multidrug resistant clinical pathogens.}, } @article {pmid35414589, year = {2022}, author = {Shalon, N and Relman, DA and Yaffe, E}, title = {Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors.}, journal = {Genome research}, volume = {32}, number = {5}, pages = {986-1003}, pmid = {35414589}, issn = {1549-5469}, support = {R01 AI147023/AI/NIAID NIH HHS/United States ; }, mesh = {Genotype ; Humans ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Plasmids/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Mobile genetic elements with circular genomes play a key role in the evolution of microbial communities. Their circular genomes correspond to circular walks in metagenome graphs, and yet, assemblies derived from natural microbial communities produce graphs riddled with spurious cycles, complicating the accurate reconstruction of circular genomes. We present DomCycle, an algorithm that reconstructs likely circular genomes based on the identification of so-called "dominant" graph cycles. In the implementation, we leverage paired reads to bridge assembly gaps and scrutinize cycles through a nucleotide-level analysis, making the approach robust to misassembly artifacts. We validated the approach using simulated and real sequencing data. Application of DomCycle to 32 publicly available DNA shotgun sequence data sets from diverse natural environments led to the reconstruction of hundreds of circular mobile genomes. Clustering revealed 20 highly prevalent and cryptic plasmids that have clonal population structures with recent common ancestors. This method facilitates the study of microbial communities that evolve through horizontal gene transfer.}, } @article {pmid35414107, year = {2022}, author = {Martínez-Álvaro, M and Auffret, MD and Duthie, CA and Dewhurst, RJ and Cleveland, MA and Watson, M and Roehe, R}, title = {Bovine host genome acts on rumen microbiome function linked to methane emissions.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {350}, pmid = {35414107}, issn = {2399-3642}, support = {BB/N01720X/1, BB/N016742/1, BB/S006567/1, BB/S006680/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Animals ; Archaea/genetics ; Cattle ; Metagenome ; Methane ; *Microbiota/genetics ; *Rumen ; }, abstract = {Our study provides substantial evidence that the host genome affects the comprehensive function of the microbiome in the rumen of bovines. Of 1,107/225/1,141 rumen microbial genera/metagenome assembled uncultured genomes (RUGs)/genes identified from whole metagenomics sequencing, 194/14/337 had significant host genomic effects (heritabilities ranging from 0.13 to 0.61), revealing that substantial variation of the microbiome is under host genomic control. We found 29/22/115 microbial genera/RUGs/genes host-genomically correlated (|0.59| to |0.93|) with emissions of the potent greenhouse gas methane (CH4), highlighting the strength of a common host genomic control of specific microbial processes and CH4. Only one of these microbial genes was directly involved in methanogenesis (cofG), whereas others were involved in providing substrates for archaea (e.g. bcd and pccB), important microbial interspecies communication mechanisms (ABC.PE.P), host-microbiome interaction (TSTA3) and genetic information processes (RP-L35). In our population, selection based on abundances of the 30 most informative microbial genes provided a mitigation potential of 17% of mean CH4 emissions per generation, which is higher than for selection based on measured CH4 using respiration chambers (13%), indicating the high potential of microbiome-driven breeding to cumulatively reduce CH4 emissions and mitigate climate change.}, } @article {pmid35413940, year = {2022}, author = {Shan, T and Yang, S and Wang, H and Wang, H and Zhang, J and Gong, G and Xiao, Y and Yang, J and Wang, X and Lu, J and Zhao, M and Yang, Z and Lu, X and Dai, Z and He, Y and Chen, X and Zhou, R and Yao, Y and Kong, N and Zeng, J and Ullah, K and Wang, X and Shen, Q and Deng, X and Zhang, J and Delwart, E and Tong, G and Zhang, W}, title = {Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {60}, pmid = {35413940}, issn = {2049-2618}, mesh = {Animals ; Animals, Wild ; Birds ; Cloaca ; Phylogeny ; *RNA Viruses/genetics ; Virome/genetics ; *Viruses/genetics ; }, abstract = {BACKGROUND: Wild birds may harbor and transmit viruses that are potentially pathogenic to humans, domestic animals, and other wildlife.

RESULTS: Using the viral metagenomic approach, we investigated the virome of cloacal swab specimens collected from 3182 birds (the majority of them wild species) consisting of > 87 different species in 10 different orders within the Aves classes. The virus diversity in wild birds was higher than that in breeding birds. We acquired 707 viral genomes from 18 defined families and 4 unclassified virus groups, with 265 virus genomes sharing < 60% protein sequence identities with their best matches in GenBank comprising new virus families, genera, or species. RNA viruses containing the conserved RdRp domain with no phylogenetic affinity to currently defined virus families existed in different bird species. Genomes of the astrovirus, picornavirus, coronavirus, calicivirus, parvovirus, circovirus, retrovirus, and adenovirus families which include known avian pathogens were fully characterized. Putative cross-species transmissions were observed with viruses in wild birds showing > 95% amino acid sequence identity to previously reported viruses in domestic poultry. Genomic recombination was observed for some genomes showing discordant phylogenies based on structural and non-structural regions. Mapping the next-generation sequencing (NGS) data respectively against the 707 genomes revealed that these viruses showed distribution pattern differences among birds with different habitats (breeding or wild), orders, and sampling sites but no significant differences between birds with different behavioral features (migratory and resident).

CONCLUSIONS: The existence of a highly diverse virome highlights the challenges in elucidating the evolution, etiology, and ecology of viruses in wild birds. Video Abstract.}, } @article {pmid35413802, year = {2022}, author = {Schlebusch, S and Graham, RMA and Jennison, AV and Lassig-Smith, MM and Harris, PNA and Lipman, J and Ó Cuív, P and Paterson, DL}, title = {Standard rectal swabs as a surrogate sample for gut microbiome monitoring in intensive care.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {99}, pmid = {35413802}, issn = {1471-2180}, mesh = {Anti-Bacterial Agents ; Critical Care ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The purpose of this study was to investigate the use of routinely available rectal swabs as a surrogate sample type for testing the gut microbiome and monitoring antibiotic effects on key gut microorganisms, of patients hospitalised in an intensive care unit. A metagenomic whole genome sequencing approach was undertaken to determine the diversity of organisms as well as resistance genes and to compare findings between the two sampling techniques.

RESULTS: No significant difference was observed in overall diversity between the faeces and rectal swabs and sampling technique was not demonstrated to predict microbial community variation. More human DNA was present in the swabs and some differences were observed only for a select few anaerobes and bacteria also associated with skin and/or the female genitourinary system, possibly reflecting sampling site or technique. Antibiotics and collections at different times of admission were both considered significant influences on microbial community composition alteration. Detection of antibiotic resistance genes between rectal swabs and faeces were overall not significantly different, although some variations were detected with a potential association with the number of human sequence reads in a sample.

CONCLUSION: Testing the gut microbiome using standard rectal swab collection techniques currently used for multi-resistant organism screening has been demonstrated to have utility in gut microbiome monitoring in intensive care. The use of information from this article, in terms of methodology as well as near equivalence demonstrated between rectal swabs and faeces will be able to support and potentially facilitate the introduction into clinical practice.}, } @article {pmid35413521, year = {2022}, author = {Li, L and Xiao, Y and Wang, C and Olsen, RH and Meng, H and Shi, L}, title = {Exploring the resistome, virulome, mobilome and microbiome along pork production chain using metagenomics.}, journal = {International journal of food microbiology}, volume = {371}, number = {}, pages = {109674}, doi = {10.1016/j.ijfoodmicro.2022.109674}, pmid = {35413521}, issn = {1879-3460}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Genes, Bacterial ; Metagenomics ; *Microbiota ; *Pork Meat ; *Red Meat ; Swine ; beta-Lactamases/genetics ; }, abstract = {In order to understand and minimize microbial contaminants spread from animal to raw pork products, we explored the diversity of antibiotic resistance genes (ARGs), virulence factors (VFs), mobile genetic elements (MGEs) and the bacterial community composition in feces of pigs, processing areas as well as the end pork products in a large-scale pig slaughterhouse in China using metagenomics. The abundance and diversity of microbial community was higher in arrival and slaughtering room area and decreased sharply in the end pork products. Furthermore, the relative abundance of some clinically relevant pathogens and opportunity pathogens were greater in the end pork products and cutter samples. We identified 1412 subtypes of ARGs related to 30 antibiotic classes, in which ARGs related to multidrug resistance and β-lactamase were dominant. Resistance determinants to clinically critical important antibiotics, including sequences related to mcr, optrA, poxtA, tetX and β-lactamase genes (i.e. blaOXA, blaVIM, blaIMP, blaGES, blaNDM, blaKPC and blaSME) were detected. More than 42 general virulence features, mainly adherence, secretion system, iron uptake, toxin, antiphagocytosis and immune evasion, were identified. A total of 1922 types of MGEs, mainly plasmids were observed. Most of the ARGs are predicted to be associated with MGEs. The prevalence of ARGs, VFs and MGEs decreased over subsequential processing steps. Most of the remaining ARGs, VFs and MGEs in end pork products were also present on other samples, indicating the flow of these genes through the production line. These results broaden our understanding of the global ARGs, VFs and MGEs diversity along the pork production chain, with the suggestion of implementing improved control measures to reduce the risk of spread of pathogenic bacteria and their associated resistome, virulome and mobilome from animal to the food chain and the surrounding environment.}, } @article {pmid35413454, year = {2022}, author = {Hua, M and Duan, A and Li, Q and Yue, J and Liu, X and Yuan, L and Liu, J and Chen, C}, title = {Alteration of microbiota and immune response of mice gavaged with Klebsiella oxytoca.}, journal = {Microbes and infection}, volume = {24}, number = {6-7}, pages = {104977}, doi = {10.1016/j.micinf.2022.104977}, pmid = {35413454}, issn = {1769-714X}, mesh = {Animals ; Cytokines ; Immunity ; *Klebsiella Infections/microbiology ; Klebsiella oxytoca/genetics ; Mice ; *Microbiota ; }, abstract = {Interactions between the microbiota and immune system play a vital role in the host homeostasis. Increasing studies have investigated environmental perturbations affecting the microbiota. However, studies also are needed to model how an organ-specific immune response affects the microbiota to understand the dynamic changes between the immune system and microbiota. We constructed a murine Klebsiella oxytoca infection model, in which mice were gavaged with K. oxytoca, and the microbiota and immune responses of both the digestive tract and respiratory tract were compared for 1-2 weeks after infection. Metagenomic and cytokine analysis of the samples displayed a delayed colonization of K. oxytoca, but an early immune response in the respiratory tract, as compared with that in the digestive tract, suggested niche-specific characteristics of bacterial colonization and the corresponding immune response. Furthermore, we constructed an interaction map of K. oxytoca in both the digestive tract and respiratory tract that furthers our understanding of the host-microbe biology in K. oxytoca-infected hosts.}, } @article {pmid35412096, year = {2022}, author = {Passarini, MRZ and Ottoni, JR and Costa, PEDS and Hissa, DC and Falcão, RM and Melo, VMM and Balbino, VQ and Mendonça, LAR and Lima, MGS and Coutinho, HDM and Verde, LCL}, title = {Fungal community diversity of heavy metal contaminated soils revealed by metagenomics.}, journal = {Archives of microbiology}, volume = {204}, number = {5}, pages = {255}, pmid = {35412096}, issn = {1432-072X}, support = {DCR-0024-01438.01.00/12//funcap/ ; }, mesh = {Biodegradation, Environmental ; Metagenomics ; *Metals, Heavy/metabolism ; *Mycobiome ; Soil ; Soil Microbiology ; *Soil Pollutants/metabolism ; }, abstract = {The inappropriate disposal of toxic compounds generated by industrial activity has been impacting the environment considerably. Microbial communities inhabiting contaminated sites may represent interesting ecological alternatives for the decontamination of environments. The present work aimed to investigate the fungal diversity and its functionality contained in stream sediments with industrial waste contaminated with heavy metals by using metagenomic approach. A total of 12 fungal orders were retrieved from datasets and, at phylum level, Ascomycota was the most abundant, followed by Basidiomycota, Chytridiomycota and Blastocladiomycota. Higher abundance of sequences was encountered within the less contaminated site, while the lower abundance was found in the sample with the higher contamination with lead. Gene sequences related to DNA repair and heavy metals biosorption processes were found in the four samples analyzed. The genera Aspergillus and Chaetomium, and Saccharomycetales order were highly present within all samples, showing their potential to be used for bioremediation studies. The present work demonstrated the importance of using the metagenomic approach to understand the dynamics and the possible metabolic pathways associated with fungal communities related to environmental samples containing heavy metals, as well as evidenced the importance of improving culturomics techniques for isolating strains with potential application in bioremediation processes of environments contaminated with heavy metals.}, } @article {pmid35410034, year = {2022}, author = {Campobasso, CP and Mastroianni, G and Feola, A and Mascolo, P and Carfora, A and Liguori, B and Zangani, P and Dell'Annunziata, F and Folliero, V and Petrillo, A and Della Pepa, ME and Martora, F and Galdiero, M}, title = {MALDI-TOF Mass Spectrometry Analysis and Human Post-Mortem Microbial Community: A Pilot Study.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {7}, pages = {}, pmid = {35410034}, issn = {1660-4601}, mesh = {Humans ; Metagenomics ; *Microbiota ; Pilot Projects ; Reproducibility of Results ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; }, abstract = {Introduction: The human post-mortem microbiome (HPM) plays a major role in the decomposition process. Successional changes in post-mortem bacterial communities have been recently demonstrated using high throughput metagenomic sequencing techniques, showing great potential as a post-mortem interval (PMI) predictor. The aim of this study is to verify the application of the mass spectrometry technique, better known as MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry), as a cheap and quick method for microbe taxonomic identification and for studying the PM microbiome. Methods: The study was carried out on 18 human bodies, ranging from 4 months to 82 years old and with a PMI range from 24 h up to 15 days. The storage time interval in the coolers was included in the final PMI estimates. Using the PMI, the sample study was divided into three main groups: seven cases with a PMI < 72 h; six cases with a PMI of 72−168 h and five cases with a PMI > 168 h. For each body, microbiological swabs were sampled from five external anatomical sites (eyes, ears, nose, mouth, and rectum) and four internal organs (brain, spleen, liver, and heart). Results: The HPM became increasingly different from the starting communities over time in the internal organs as well as at skin sites; the HPM microbiome was mostly dominated by Firmicutes and Proteobacteria phyla; and a PM microbial turnover existed during decomposition, evolving with the PMI. Conclusions: MALDI-TOF is a promising method for PMI estimation, given its sample handling, good reproducibility, and high speed and throughput. Although several intrinsic and extrinsic factors can affect the structure of the HPM, MALDI-TOF can detect the overall microbial community turnover of most prevalent phyla during decomposition. Limitations are mainly related to its sensitivity due to the culture-dependent method and bias in the identification of new isolates.}, } @article {pmid35409199, year = {2022}, author = {Li, QC and Wang, B and Zeng, YH and Cai, ZH and Zhou, J}, title = {The Microbial Mechanisms of a Novel Photosensitive Material (Treated Rape Pollen) in Anti-Biofilm Process under Marine Environment.}, journal = {International journal of molecular sciences}, volume = {23}, number = {7}, pages = {}, pmid = {35409199}, issn = {1422-0067}, support = {41976126//National Natural Science Foundation of China/ ; 2020B1515120012//Guangdong Basic and Applied Basic Research Foundation/ ; }, mesh = {*Biofilms ; *Biofouling/prevention & control ; Oxidants/pharmacology ; Pollen ; Seawater/microbiology ; }, abstract = {Marine biofouling is a worldwide problem in coastal areas and affects the maritime industry primarily by attachment of fouling organisms to solid immersed surfaces. Biofilm formation by microbes is the main cause of biofouling. Currently, application of antibacterial materials is an important strategy for preventing bacterial colonization and biofilm formation. A natural three-dimensional carbon skeleton material, TRP (treated rape pollen), attracted our attention owing to its visible-light-driven photocatalytic disinfection property. Based on this, we hypothesized that TRP, which is eco-friendly, would show antifouling performance and could be used for marine antifouling. We then assessed its physiochemical characteristics, oxidant potential, and antifouling ability. The results showed that TRP had excellent photosensitivity and oxidant ability, as well as strong anti-bacterial colonization capability under light-driven conditions. Confocal laser scanning microscopy showed that TRP could disperse pre-established biofilms on stainless steel surfaces in natural seawater. The biodiversity and taxonomic composition of biofilms were significantly altered by TRP (p < 0.05). Moreover, metagenomics analysis showed that functional classes involved in the antioxidant system, environmental stress, glucose−lipid metabolism, and membrane-associated functions were changed after TRP exposure. Co-occurrence model analysis further revealed that TRP markedly increased the complexity of the biofilm microbial network under light irradiation. Taken together, these results demonstrate that TRP with light irradiation can inhibit bacterial colonization and prevent initial biofilm formation. Thus, TRP is a potential nature-based green material for marine antifouling.}, } @article {pmid35409014, year = {2022}, author = {Jones, KA and Richard, AJ and Salbaum, JM and Newman, S and Carmouche, R and Webb, S and Bruce-Keller, AJ and Stephens, JM and Campagna, SR}, title = {Cross-Omics Analysis of Fenugreek Supplementation Reveals Beneficial Effects Are Caused by Gut Microbiome Changes Not Mammalian Host Physiology.}, journal = {International journal of molecular sciences}, volume = {23}, number = {7}, pages = {}, pmid = {35409014}, issn = {1422-0067}, support = {R01 AT010279/AT/NCCIH NIH HHS/United States ; NIH 2P30DK072476/NH/NIH HHS/United States ; NIH8 1P30GM118430-02/NH/NIH HHS/United States ; R01AT010279/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; Cholesterol ; *Diabetes Mellitus, Type 2/drug therapy ; Dietary Supplements ; *Gastrointestinal Microbiome ; Mammals ; Mice ; Plant Extracts/pharmacology/therapeutic use ; *Trigonella ; }, abstract = {Herbal remedies are increasing in popularity as treatments for metabolic conditions such as obesity and Type 2 Diabetes. One potential therapeutic option is fenugreek seeds (Trigonella foenum-graecum), which have been used for treating high cholesterol and Type 2 diabetes. A proposed mechanism for these benefits is through alterations in the microbiome, which impact mammalian host metabolic function. This study used untargeted metabolomics to investigate the fenugreek-induced alterations in the intestinal, liver, and serum profiles of mice fed either a 60% high-fat or low-fat control diet each with or without fenugreek supplementation (2% w/w) for 14 weeks. Metagenomic analyses of intestinal contents found significant alterations in the relative composition of the gut microbiome resulting from fenugreek supplementation. Specifically, Verrucomicrobia, a phylum containing beneficial bacteria which are correlated with health benefits, increased in relative abundance with fenugreek. Metabolomics partial least squares discriminant analysis revealed substantial fenugreek-induced changes in the large intestines. However, it was observed that while the magnitude of changes was less, significant modifications were present in the liver tissues resulting from fenugreek supplementation. Further analyses revealed metabolic processes affected by fenugreek and showed broad ranging impacts in multiple pathways, including carnitine biosynthesis, cholesterol and bile acid metabolism, and arginine biosynthesis. These pathways may play important roles in the beneficial effects of fenugreek.}, } @article {pmid35406140, year = {2022}, author = {Leeuwendaal, NK and Stanton, C and O'Toole, PW and Beresford, TP}, title = {Fermented Foods, Health and the Gut Microbiome.}, journal = {Nutrients}, volume = {14}, number = {7}, pages = {}, pmid = {35406140}, issn = {2072-6643}, support = {6555//Teagasc - The Irish Agriculture and Food Development Authority/ ; }, mesh = {Diet ; Fermentation ; *Fermented Foods ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Fermented foods have been a part of human diet for almost 10,000 years, and their level of diversity in the 21st century is substantial. The health benefits of fermented foods have been intensively investigated; identification of bioactive peptides and microbial metabolites in fermented foods that can positively affect human health has consolidated this interest. Each fermented food typically hosts a distinct population of microorganisms. Once ingested, nutrients and microorganisms from fermented foods may survive to interact with the gut microbiome, which can now be resolved at the species and strain level by metagenomics. Transient or long-term colonization of the gut by fermented food strains or impacts of fermented foods on indigenous gut microbes can therefore be determined. This review considers the primary food fermentation pathways and microorganisms involved, the potential health benefits, and the ability of these foodstuffs to impact the gut microbiome once ingested either through compounds produced during the fermentation process or through interactions with microorganisms from the fermented food that are capable of surviving in the gastro-intestinal transit. This review clearly shows that fermented foods can affect the gut microbiome in both the short and long term, and should be considered an important element of the human diet.}, } @article {pmid35404958, year = {2022}, author = {Grazioli, F and Siarheyeu, R and Alqassem, I and Henschel, A and Pileggi, G and Meiser, A}, title = {Microbiome-based disease prediction with multimodal variational information bottlenecks.}, journal = {PLoS computational biology}, volume = {18}, number = {4}, pages = {e1010050}, pmid = {35404958}, issn = {1553-7358}, mesh = {*Gastrointestinal Microbiome ; Humans ; Machine Learning ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Scientific research is shedding light on the interaction of the gut microbiome with the human host and on its role in human health. Existing machine learning methods have shown great potential in discriminating healthy from diseased microbiome states. Most of them leverage shotgun metagenomic sequencing to extract gut microbial species-relative abundances or strain-level markers. Each of these gut microbial profiling modalities showed diagnostic potential when tested separately; however, no existing approach combines them in a single predictive framework. Here, we propose the Multimodal Variational Information Bottleneck (MVIB), a novel deep learning model capable of learning a joint representation of multiple heterogeneous data modalities. MVIB achieves competitive classification performance while being faster than existing methods. Additionally, MVIB offers interpretable results. Our model adopts an information theoretic interpretation of deep neural networks and computes a joint stochastic encoding of different input data modalities. We use MVIB to predict whether human hosts are affected by a certain disease by jointly analysing gut microbial species-relative abundances and strain-level markers. MVIB is evaluated on human gut metagenomic samples from 11 publicly available disease cohorts covering 6 different diseases. We achieve high performance (0.80 < ROC AUC < 0.95) on 5 cohorts and at least medium performance on the remaining ones. We adopt a saliency technique to interpret the output of MVIB and identify the most relevant microbial species and strain-level markers to the model's predictions. We also perform cross-study generalisation experiments, where we train and test MVIB on different cohorts of the same disease, and overall we achieve comparable results to the baseline approach, i.e. the Random Forest. Further, we evaluate our model by adding metabolomic data derived from mass spectrometry as a third input modality. Our method is scalable with respect to input data modalities and has an average training time of < 1.4 seconds. The source code and the datasets used in this work are publicly available.}, } @article {pmid35404122, year = {2022}, author = {Hu, Y and Irinyi, L and Hoang, MTV and Eenjes, T and Graetz, A and Stone, EA and Meyer, W and Schwessinger, B and Rathjen, JP}, title = {Inferring Species Compositions of Complex Fungal Communities from Long- and Short-Read Sequence Data.}, journal = {mBio}, volume = {13}, number = {2}, pages = {e0244421}, pmid = {35404122}, issn = {2150-7511}, support = {FT180100024//Australian Research Council/ ; GNT1121936//Department of Health | National Health and Medical Research Council (NHMRC)/ ; HSF_17_04//Hermon Slade Foundation/ ; }, mesh = {Bacteria/genetics ; Fungi/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; *Microbiota/genetics ; *Mycobiome ; }, abstract = {The kingdom Fungi is highly diverse in morphology and ecosystem function. Yet fungi are challenging to characterize as they can be difficult to culture and morphologically indistinct. Overall, their description and analysis lag far behind other microbes such as bacteria. Classification of species via high-throughput sequencing is increasingly becoming the norm for pathogen detection, microbiome studies, and environmental monitoring. With the rapid development of sequencing technologies, however, standardized procedures for taxonomic assignment of long sequence reads have not yet been well established. Focusing on nanopore sequencing technology, we compared classification and community composition analysis pipelines using shotgun and amplicon sequencing data generated from mock communities comprising 43 fungal species. We show that regardless of the sequencing methodology used, the highest accuracy of species identification was achieved by sequence alignment against a fungal-specific database. During the assessment of classification algorithms, we found that applying cutoffs to the query coverage of each read or contig significantly improved the classification accuracy and community composition analysis without major data loss. We also generated draft genome assemblies for three fungal species from nanopore data which were absent from genome databases. Our study improves sequence-based classification and estimation of relative sequence abundance using real fungal community data and provides a practical guide for the design of metagenomics analyses focusing on fungi. IMPORTANCE Our study is unique in that it provides an in-depth comparative study of a real-life complex fungal community analyzed with multiple long- and short-read sequencing approaches. These technologies and their application are currently of great interest to diverse biologists as they seek to characterize the community compositions of microbiomes. Although great progress has been made on bacterial community compositions, microbial eukaryotes such as fungi clearly lag behind. Our study provides a detailed breakdown of strategies to improve species identification with immediate relevance to real-world studies. We find that real-life data sets do not always behave as expected, distinct from reports based on simulated data sets.}, } @article {pmid35402307, year = {2022}, author = {Mudrik-Zohar, H and Carasso, S and Gefen, T and Zalmanovich, A and Katzir, M and Cohen, Y and Paitan, Y and Geva-Zatorsky, N and Chowers, M}, title = {Microbiome Characterization of Infected Diabetic Foot Ulcers in Association With Clinical Outcomes: Traditional Cultures Versus Molecular Sequencing Methods.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {836699}, pmid = {35402307}, issn = {2235-2988}, mesh = {*Diabetes Mellitus ; *Diabetic Foot/complications/microbiology ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Infected diabetic foot ulcers (IDFU) are a major complication of diabetes mellitus. These potentially limb-threatening ulcers are challenging to treat due to impaired wound healing characterizing diabetic patients and the complex microbial environment of these ulcers.

AIM: To analyze the microbiome of IDFU in association with clinical outcomes.

METHODS: Wound biopsies from IDFU were obtained from hospitalized patients and were analyzed using traditional microbiology cultures, 16S rRNA sequencing and metagenomic sequencing. Patients' characteristics, culture-based results and sequencing data were analyzed in association with clinical outcomes.

RESULTS: A total of 31 patients were enrolled. Gram-negative bacteria dominated the IDFU samples (79%, 59% and 54% of metagenomics, 16S rRNA and cultures results, respectively, p<0.001). 16S rRNA and metagenomic sequencing detected significantly more anaerobic bacteria, as compared to conventional cultures (59% and 76%, respectively vs. 26% in cultures, p=0.001). Culture-based results showed that Staphylococcus aureus was more prevalent among patients who were treated conservatively (p=0.048). In metagenomic analysis, the Bacteroides genus was more prevalent among patients who underwent amputation (p<0.001). Analysis of metagenomic-based functional data showed that antibiotic resistance genes and genes related to biofilm production and to bacterial virulent factors were more prevalent in IDFU that resulted in amputation (p<0.001).

CONCLUSION: Sequencing tools uncover the complex biodiversity of IDFU and emphasize the high prevalence of anaerobes and Gram-negative bacteria in these ulcers. Furthermore, sequencing results highlight possible associations among certain genera, species, and bacterial functional genes to clinical outcomes.}, } @article {pmid35402298, year = {2022}, author = {Li, K and Zeng, Z and Liu, J and Pei, L and Wang, Y and Li, A and Kulyar, MF and Shahzad, M and Mehmood, K and Li, J and Qi, D}, title = {Effects of Short-Chain Fatty Acid Modulation on Potentially Diarrhea-Causing Pathogens in Yaks Through Metagenomic Sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {805481}, pmid = {35402298}, issn = {2235-2988}, mesh = {Animals ; Bacteria/genetics ; Cattle ; Clostridiales ; Diarrhea/microbiology ; Fatty Acids, Volatile ; Feces ; *Gastrointestinal Microbiome ; *Metagenomics ; }, abstract = {Short-chain fatty acids (SCFA) are principal nutrient substrates of intestinal epithelial cells that regulate the epithelial barrier in yaks. Until now, metagenomics sequencing has not been reported in diarrheal yaks. Scarce information is available regarding the levels of fecal SCFA and diarrhea in yaks. So, our study aims to identify the potential pathogens that cause the emerging diarrhea and explore the potential relationship of short-chain fatty acids in this issue. We estimated diarrhea rate in yaks after collecting an equal number of fecal samples from affected animals. Metagenomics sequencing and quantitative analysis of SCFA were performed, which revealed 15%-25% and 5%-10% prevalence of diarrhea in yak's calves and adults, respectively. Violin box plot also showed a higher degree of dispersion in gene abundance distribution of diarrheal yaks, as compared to normal yaks. We found 366,163 significant differential abundance genes in diarrheal yaks, with 141,305 upregulated and 224,858 downregulated genes compared with normal yaks via DESeq analysis. Metagenomics binning analysis indicated the higher significance of bin 33 (Bacteroidales) (p < 0.05) in diarrheal animals, while bin 10 (p < 0.0001), bin 30 (Clostridiales) (p < 0.05), bin 51 (Lactobacillales) (p < 0.05), bin 8 (Lachnospiraceae) (p < 0.05), and bin 47 (Bacteria) (p < 0.05) were significantly higher in normal yaks. At different levels, a significant difference in phylum (n = 4), class (n = 8), oder (n = 8), family (n = 16), genus (n = 17), and species (n = 30) was noticed, respectively. Compared with healthy yaks, acetic acid (p < 0.01), propionic acid (p < 0.01), butyric acid (p < 0.01), isobutyric acid (p < 0.01), isovaleric acid (p < 0.05), and caproic acid (p < 0.01) were all observed significantly at a lower rate in diarrheal yaks. In conclusion, besides the increased Staphylococcus aureus, Babesia ovata, Anaplasma phagocytophilum, Bacteroides fluxus, viruses, Klebsiella pneumonia, and inflammation-related bacteria, the decrease of SCFA caused by the imbalance of intestinal microbiota was potentially observed in diarrheal yaks.}, } @article {pmid35400171, year = {2022}, author = {You, X and Dadwal, UC and Lenburg, ME and Kacena, MA and Charles, JF}, title = {Murine Gut Microbiome Meta-analysis Reveals Alterations in Carbohydrate Metabolism in Response to Aging.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0124821}, pmid = {35400171}, issn = {2379-5077}, support = {R01 AG060621/AG/NIA NIH HHS/United States ; R01 AG046246/AG/NIA NIH HHS/United States ; P30 AR070253/AR/NIAMS NIH HHS/United States ; R01 AG046257/AG/NIA NIH HHS/United States ; T32 AR065971/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Aging ; Carbohydrate Metabolism ; Fatty Acids, Volatile/analysis ; }, abstract = {Compositional and functional alterations to the gut microbiota during aging are hypothesized to potentially impact our health. Thus, determining aging-specific gut microbiome alterations is critical for developing microbiome-based strategies to improve health and promote longevity in the elderly. In this study, we performed a meta-analysis of publicly available 16S rRNA gene sequencing data from studies investigating the effect of aging on the gut microbiome in mice. Aging reproducibly increased gut microbial alpha diversity and shifted the microbial community structure in mice. We applied the bioinformatic tool PICRUSt2 to predict microbial metagenome function and established a random forest classifier to differentiate between microbial communities from young and old hosts and to identify aging-specific metabolic features. In independent validation data sets, this classifier achieved an area under the receiver operating characteristic curve (AUC) of 0.75 to 0.97 in differentiating microbiomes from young and old hosts. We found that 50% of the most important predicted aging-specific metabolic features were involved in carbohydrate metabolism. Furthermore, fecal short-chain fatty acid (SCFA) concentrations were significantly decreased in old mice, and the expression of the SCFA receptor Gpr41 in the colon was significantly correlated with the relative abundances of gut microbes and microbial carbohydrate metabolic pathways. In conclusion, this study identified aging-specific alterations in the composition and function of the gut microbiome and revealed a potential relationship between aging, microbial carbohydrate metabolism, fecal SCFA, and colonic Gpr41 expression. IMPORTANCE Aging-associated microbial alteration is hypothesized to play an important role in host health and longevity. However, investigations regarding specific gut microbes or microbial functional alterations associated with aging have had inconsistent results. We performed a meta-analysis across 5 independent studies to investigate the effect of aging on the gut microbiome in mice. Our analysis revealed that aging increased gut microbial alpha diversity and shifted the microbial community structure. To determine if we could reliably differentiate the gut microbiomes from young and old hosts, we established a random forest classifier based on predicted metagenome function and validated its performance against independent data sets. Alterations in microbial carbohydrate metabolism and decreased fecal short-chain fatty acid (SCFA) concentrations were key features of aging and correlated with host colonic expression of the SCFA receptor Gpr41. This study advances our understanding of the impact of aging on the gut microbiome and proposes a hypothesis that alterations in gut microbiota-derived SCFA-host GPR41 signaling are a feature of aging.}, } @article {pmid35398852, year = {2022}, author = {Nagasue, T and Hirano, A and Torisu, T and Umeno, J and Shibata, H and Moriyama, T and Kawasaki, K and Fujioka, S and Fuyuno, Y and Matsuno, Y and Esaki, M and Kitazono, T}, title = {The Compositional Structure of the Small Intestinal Microbial Community via Balloon-Assisted Enteroscopy.}, journal = {Digestion}, volume = {103}, number = {4}, pages = {308-318}, doi = {10.1159/000524023}, pmid = {35398852}, issn = {1421-9867}, mesh = {Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; Intestine, Small ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {INTRODUCTION: An association has been found between human-gut microbiota and various diseases (e.g., metabolic disease) by analyzing fecal or colonic microbiota. Despite the importance of the small intestinal microbiota, sampling difficulties prevent its full analysis. We investigated the composition and metagenomic functions of microbiota along the small intestine and compared them with the microbiota from feces and from other gastrointestinal (GI) sites.

METHODS: Mucosal samples from the six GI sites (stomach, duodenum, distal jejunum, proximal ileum, terminal ileum, and rectum) were collected under balloon-assisted enteroscopy. Fecal samples were collected from all participants. The microbial structures and metagenomic functions of the small intestinal mucosal microbiota were compared with those from feces and other GI sites using 16S ribosomal RNA gene sequencing.

RESULTS: We analyzed 133 samples from 29 participants. Microbial beta diversity analysis showed that the jejunum and ileum differed significantly from the lower GI tract and the feces (p < 0.001). Jejunal and duodenal microbiotas formed similar clusters. Wide clusters spanning the upper and lower GI tracts were observed with the ileal microbiota, which differed significantly from the jejunal microbiota (p < 0.001). Veillonella and Streptococcus were abundant in the jejunum but less so in the lower GI tract and feces. The metagenomic functions associated with nutrient metabolism differed significantly between the small intestine and the feces.

CONCLUSIONS: The fact that the compositional structures of small intestinal microbiota differed from those of fecal and other GI microbiotas reveals that analyzing the small intestinal microbiota is necessary for association studies on metabolic diseases and gut microbiota.}, } @article {pmid35398777, year = {2022}, author = {Zhang, Z and Jiao, Q and Zhang, Y and Liu, B and Wang, Y and Li, J}, title = {OTUCD: Unsupervised GCN based metagenomics non-overlapping community detection.}, journal = {Computational biology and chemistry}, volume = {98}, number = {}, pages = {107670}, doi = {10.1016/j.compbiolchem.2022.107670}, pmid = {35398777}, issn = {1476-928X}, mesh = {Algorithms ; Humans ; Metagenome ; *Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Metagenomics is a discipline that studies the genetic material of all tiny organisms in the biological environment. In recent years, the interaction between metagenomic microbial communities, the transfer of horizontal genes, and the dynamic changes of microbial ecosystems have attracted more and more attention. It is of great significance to use the community detection algorithm to divide the metagenomic microbes into modules, and it has a positive guiding role for the follow-up research on human, drug, microbial interaction study and drug prediction and development. At present, there are challenges in mining the effective information hidden in large-scale microbial sequence data. The non-linear characteristics and non-scalability of microbial sequence data still bother people. This paper proposes an end-to-end unsupervised GCN learning model OTUCD (Operational Classification Unit Community Detection), which divides large-scale metagenomic sequence data into potential gene modules. We construct an OTU network, and then performs subsequent nonoverlapping community detection task with graph convolutional networks. Experimental scores show that the community detection effect of this method is better than other latest metagenomic algorithms.}, } @article {pmid35398400, year = {2022}, author = {Do, TT and Nolan, S and Hayes, N and O'Flaherty, V and Burgess, C and Brennan, F and Walsh, F}, title = {Metagenomic and HT-qPCR analysis reveal the microbiome and resistome in pig slurry under storage, composting, and anaerobic digestion.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {305}, number = {}, pages = {119271}, doi = {10.1016/j.envpol.2022.119271}, pmid = {35398400}, issn = {1873-6424}, mesh = {Anaerobiosis ; Animals ; Anti-Bacterial Agents/pharmacology ; *Composting ; Manure/analysis ; Metagenome ; *Microbiota/genetics ; Nitrogen/analysis ; Swine ; }, abstract = {Direct application of pig slurry to agricultural land, as a means of nutrient recycling, introduces pathogens, antibiotic resistant bacteria, or genes, to the environment. With global environmental sustainability policies mandating a reduction in synthetic fertilisation and a commitment to a circular economy it is imperative to find effective on-farm treatments of slurry that maximises its fertilisation value and minimises risk to health and the environment. We assessed and compared the effect of storage, composting, and anaerobic digestion (AD) on pig slurry microbiome, resistome and nutrient content. Shotgun metagenomic sequencing and HT-qPCR arrays were implemented to understand the dynamics across the treatments. Our results identified that each treatment methods have advantages and disadvantages in removal pollutants or increasing nutrients. The data suggests that storage and composting are optimal for the removal of human pathogens and anaerobic digestion for the reduction in antibiotic resistance (AMR) genes and mobile genetic elements. The nitrogen content is increased in storage and AD, while reduced in composting. Thus, depending on the requirement for increased or reduced nitrogen the optimum treatment varies. Combining the results indicates that composting provides the greatest gain by reducing risk to human health and the environment. Network analysis revealed reducing Proteobacteria and Bacteroidetes while increasing Firmicutes will reduce the AMR content. KEGG analysis identified no significant change in the pathways across all treatments. This novel study provides a data driven decision tree to determine the optimal treatment for best practice to minimise pathogen, AMR and excess or increasing nutrient transfer from slurry to environment.}, } @article {pmid35398320, year = {2022}, author = {Ghazi, AR and Münch, PC and Chen, D and Jensen, J and Huttenhower, C}, title = {Strain Identification and Quantitative Analysis in Microbial Communities.}, journal = {Journal of molecular biology}, volume = {434}, number = {15}, pages = {167582}, doi = {10.1016/j.jmb.2022.167582}, pmid = {35398320}, issn = {1089-8638}, support = {R24 DK110499/DK/NIDDK NIH HHS/United States ; U19 AI110820/AI/NIAID NIH HHS/United States ; }, mesh = {Metagenome ; *Metagenomics/methods ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Microbiology has long studied the ways in which subtle genetic differences between closely related microbial strains can have profound impacts on their phenotypes and those of their surrounding environments and communities. Despite the growth in high-throughput microbial community profiling, however, such strain-level differences remain challenging to detect. Once detected, few quantitative approaches have been well-validated for associating strain variants from microbial communities with phenotypes of interest, such as medication usage, treatment efficacy, host environment, or health. First, the term "strain" itself is not used consistently when defining a highly-resolved taxonomic or genomic unit from within a microbial community. Second, computational methods for identifying such strains directly from shotgun metagenomics are difficult, with several possible reference- and assembly-based approaches available, each with different sensitivity/specificity tradeoffs. Finally, statistical challenges exist in using any of the resulting strain profiles for downstream analyses, which can include strain tracking, phylogenetic analysis, or genetic association studies. We provide an in depth discussion of recently available computational tools that can be applied for this task, as well as statistical models and gaps in performing and interpreting any of these three main types of studies using strain-resolved shotgun metagenomic profiling of microbial communities.}, } @article {pmid35398082, year = {2022}, author = {Djouina, M and Vignal, C and Dehaut, A and Caboche, S and Hirt, N and Waxin, C and Himber, C and Beury, D and Hot, D and Dubuquoy, L and Launay, D and Duflos, G and Body-Malapel, M}, title = {Oral exposure to polyethylene microplastics alters gut morphology, immune response, and microbiota composition in mice.}, journal = {Environmental research}, volume = {212}, number = {Pt B}, pages = {113230}, doi = {10.1016/j.envres.2022.113230}, pmid = {35398082}, issn = {1096-0953}, mesh = {Animals ; Biomarkers ; Immunity ; Mice ; *Microbiota ; Microplastics/toxicity ; Plastics ; Polyethylene/toxicity ; *Water Pollutants, Chemical/analysis ; }, abstract = {The ubiquitous and growing presence of microplastics (MPs) in all compartments of the environment raises concerns about their possible harmful effects on human health. Human exposure to MPs occurs largely through ingestion. Polyethylene (PE) is widely employed for reusable bags and food packaging and found to be present in drinking water and food. It is also one of the major polymers detected in human stool. The aim of this study was to characterize the effects of intestinal exposure to PE MPs on gut homeostasis. Mice were orally exposed for 6 weeks to PE microbeads of 2 different sizes, 36 and 116 μm, that correspond to those found in human stool. They were administrated either individually or as a mixture at a dose of 100 μg/g of food. Both PE microbead sizes were detected in mouse stool. Different parameters related to major intestinal functions were compared between control mice, mice exposed to each type of microbead, or co-exposed to the 2 types of microbeads. Intestinal disturbances were observed after individual exposure to each size of PE microbead, and the most marked deleterious effects were found in co-exposed mice. At the histomorphological level, crypt depth was increased throughout the intestinal tissues. Significant variations of gene expression related to epithelial, permeability, and inflammatory biomarkers were quantified. Defective recruitment of some intestinal immune cells was observed from the proximal portion of the small intestine to the colon. Several bacterial taxa at the order level were found to be affected by exposure to the MPs by metagenomic analysis of cecal microbiota. These results show that ingestion of PE microbeads induces significant alterations of crucial intestinal markers in mice and underscores the need to further study the health impact of MP exposure in humans.}, } @article {pmid35397610, year = {2022}, author = {Strehlow, BW and Schuster, A and Francis, WR and Canfield, DE}, title = {Metagenomic data for Halichondria panicea from Illumina and nanopore sequencing and preliminary genome assemblies for the sponge and two microbial symbionts.}, journal = {BMC research notes}, volume = {15}, number = {1}, pages = {135}, pmid = {35397610}, issn = {1756-0500}, support = {16518//Villum Fonden/ ; }, mesh = {Animals ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics ; *Microbiota ; *Nanopore Sequencing ; *Porifera/genetics ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: These data were collected to generate a novel reference metagenome for the sponge Halichondria panicea and its microbiome for subsequent differential expression analyses.

DATA DESCRIPTION: These data include raw sequences from four separate sequencing runs of the metagenome of a single individual of Halichondria panicea-one Illumina MiSeq (2 × 300 bp, paired-end) run and three Oxford Nanopore Technologies (ONT) long-read sequencing runs, generating 53.8 and 7.42 Gbp respectively. Comparing assemblies of Illumina, ONT and an Illumina-ONT hybrid revealed the hybrid to be the 'best' assembly, comprising 163 Mbp in 63,555 scaffolds (N50: 3084). This assembly, however, was still highly fragmented and only contained 52% of core metazoan genes (with 77.9% partial genes), so it was also not complete. However, this sponge is an emerging model species for field and laboratory work, and there is considerable interest in genomic sequencing of this species. Although the resultant assemblies from the data presented here are suboptimal, this data note can inform future studies by providing an estimated genome size and coverage requirements for future sequencing, sharing additional data to potentially improve other suboptimal assemblies of this species, and outlining potential limitations and pitfalls of the combined Illumina and ONT approach to novel genome sequencing.}, } @article {pmid35396347, year = {2022}, author = {Magnuson, E and Altshuler, I and Fernández-Martínez, MÁ and Chen, YJ and Maggiori, C and Goordial, J and Whyte, LG}, title = {Active lithoautotrophic and methane-oxidizing microbial community in an anoxic, sub-zero, and hypersaline High Arctic spring.}, journal = {The ISME journal}, volume = {16}, number = {7}, pages = {1798-1808}, pmid = {35396347}, issn = {1751-7370}, support = {CGSD2-534189-2019//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; 272792//Fonds de Recherche du Québec - Nature et Technologies (Quebec Fund for Research in Nature and Technology)/ ; }, mesh = {Anaerobiosis ; Archaea/genetics/metabolism ; Gases/metabolism ; Geologic Sediments/microbiology ; *Methane/metabolism ; *Microbiota ; Oxidation-Reduction ; Oxygen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfates/metabolism ; Sulfides/metabolism ; }, abstract = {Lost Hammer Spring, located in the High Arctic of Nunavut, Canada, is one of the coldest and saltiest terrestrial springs discovered to date. It perennially discharges anoxic (<1 ppm dissolved oxygen), sub-zero (~-5 °C), and hypersaline (~24% salinity) brines from the subsurface through up to 600 m of permafrost. The sediment is sulfate-rich (1 M) and continually emits gases composed primarily of methane (~50%), making Lost Hammer the coldest known terrestrial methane seep and an analog to extraterrestrial habits on Mars, Europa, and Enceladus. A multi-omics approach utilizing metagenome, metatranscriptome, and single-amplified genome sequencing revealed a rare surface terrestrial habitat supporting a predominantly lithoautotrophic active microbial community driven in part by sulfide-oxidizing Gammaproteobacteria scavenging trace oxygen. Genomes from active anaerobic methane-oxidizing archaea (ANME-1) showed evidence of putative metabolic flexibility and hypersaline and cold adaptations. Evidence of anaerobic heterotrophic and fermentative lifestyles were found in candidate phyla DPANN archaea and CG03 bacteria genomes. Our results demonstrate Mars-relevant metabolisms including sulfide oxidation, sulfate reduction, anaerobic oxidation of methane, and oxidation of trace gases (H2, CO2) detected under anoxic, hypersaline, and sub-zero ambient conditions, providing evidence that similar extant microbial life could potentially survive in similar habitats on Mars.}, } @article {pmid35394234, year = {2022}, author = {Ayiti, OE and Ayangbenro, AS and Babalola, OO}, title = {Relationship between nitrifying microorganisms and other microorganisms residing in the maize rhizosphere.}, journal = {Archives of microbiology}, volume = {204}, number = {5}, pages = {246}, pmid = {35394234}, issn = {1432-072X}, support = {UID123634//National Research Foundation South Africa/ ; UID132595//National Research Foundation South Africa/ ; }, mesh = {*Microbiota ; *Rhizosphere ; Soil/chemistry ; Soil Microbiology ; Zea mays/microbiology ; }, abstract = {The microbial network of rhizosphere is unique as a result of root exudate. Insights into the relationship that exists with the energy metabolic functional groups will help in biofertilizer production. We hypothesize that there exists a relationship between nitrifying microorganisms and other energy metabolic functional microbial groups in the maize rhizosphere across different growth stages. Nucleospin soil DNA extraction kit was used to extract DNA from soil samples collected from maize rhizosphere. The 16S metagenomics sequencing was carried out on Illumina Miseq. The sequence obtained was analyzed on MG-RAST. Nitrospira genera were the most abundant in the nitrifying community. Nitrifying microorganisms were more than each of the studied functional groups except for nitrogen-fixing bacteria. Also, majority of the microorganisms were noticed at the fruiting stage and there was variation in the microbial structure across different growth stages. The result showed that there exists a substantial amount of both negative and positive correlation within the nitrifying microorganisms, and between them and other energy metabolic functional groups. The knowledge obtained from this study will help improve the growth and development of maize through modification of the rhizosphere microbial community structure.}, } @article {pmid35392807, year = {2022}, author = {Raineri, S and Sherriff, JA and Thompson, KSJ and Jones, H and Pfluger, PT and Ilott, NE and Mellor, J}, title = {Pharmacologically induced weight loss is associated with distinct gut microbiome changes in obese rats.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {91}, pmid = {35392807}, issn = {1471-2180}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacteroides ; Female ; *Gastrointestinal Microbiome ; Inflammation ; Obesity/microbiology ; Rats ; Rats, Wistar ; Weight Loss ; }, abstract = {BACKGROUND: Obesity, metabolic disease and some psychiatric conditions are associated with changes to relative abundance of bacterial species and specific genes in the faecal microbiome. Little is known about the impact of pharmacologically induced weight loss on distinct microbiome species and their respective gene programs in obese individuals.

METHODOLOGY: Using shotgun metagenomics, the composition of the microbiome was obtained for two cohorts of obese female Wistar rats (n = 10-12, total of 82) maintained on a high fat diet before and after a 42-day treatment with a panel of four investigatory or approved anti-obesity drugs (tacrolimus/FK506, bupropion, naltrexone and sibutramine), alone or in combination.

RESULTS: Only sibutramine treatment induced consistent weight loss and improved glycaemic control in the obese rats. Weight loss was associated with reduced food intake and changes to the faecal microbiome in multiple microbial taxa, genes, and pathways. These include increased β-diversity, increased relative abundance of multiple Bacteroides species, increased Bacteroides/Firmicutes ratio and changes to abundance of genes and species associated with obesity-induced inflammation, particularly those encoding components of the flagellum and its assembly.

CONCLUSIONS: Sibutramine-induced weight loss in obese rats is associated with improved metabolic health, and changes to the faecal microbiome consistent with a reduction in obesity-induced bacterially-driven inflammation.}, } @article {pmid35392799, year = {2022}, author = {Behzad, H and Ohyanagi, H and Alharbi, B and Ibarra, M and Alarawi, M and Saito, Y and Duarte, CM and Bajic, V and Mineta, K and Gojobori, T}, title = {A cautionary signal from the Red Sea on the impact of increased dust activity on marine microbiota.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {277}, pmid = {35392799}, issn = {1471-2164}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Dust/analysis ; Indian Ocean ; Metagenomics ; *Microbiota ; }, abstract = {BACKGROUND: Global climate change together with growing desertification is leading to increased dust emissions to the atmosphere, drawing attention to possible impacts on marine ecosystems receiving dust deposition. Since microorganisms play important roles in maintaining marine homeostasis through nutrient cycling and carbon flow, detrimental changes in the composition of marine microbiota in response to increased dust input could negatively impact marine health, particularly so in seas located within the Global Dust Belt. Due to its strategic location between two deserts and unique characteristics, the Red Sea provides an attractive semi-enclosed "megacosm" to examine the impacts of large dust deposition on the vastly diverse microbiota in its exceptionally warm oligotrophic waters.

RESULTS: We used culture-independent metagenomic approaches to assess temporal changes in the Red Sea microbiota in response to two severe sandstorms, one originated in the Nubian Desert in the summer 2016 and a second one originated in the Libyan Desert in the spring 2017. Despite differences in sandstorm origin and meteorological conditions, both sandstorms shifted bacterial and Archaeal groups in a similar mode. In particular, the relative abundance of autotrophic bacteria declined while those of heterotrophic bacteria, particularly Bacteroidetes, and Archaea increased. The changes peaked within six days from the start of sandstorms, and the community recovered the original assemblage within one month.

CONCLUSION: Our results suggest that increased dust emission with expanding desertification could lead to undesirable impacts in ocean function, enhancing heterotrophic processes while reducing autotrophic ones, thereby affecting the marine food web in seas receiving dust deposition.}, } @article {pmid35390655, year = {2022}, author = {Cao, L and Liao, Y and Su, C and Tang, L and Qi, Z and Wei, L and Wu, J and Gao, S}, title = {Effects of PFOA on the physicochemical properties of anaerobic granular sludge: Performance evaluation, microbial community and metagenomic analysis.}, journal = {Journal of environmental management}, volume = {313}, number = {}, pages = {114936}, doi = {10.1016/j.jenvman.2022.114936}, pmid = {35390655}, issn = {1095-8630}, mesh = {Anaerobiosis ; Bioreactors ; Caprylates ; Fluorocarbons ; *Microbiota ; *Sewage ; Waste Disposal, Fluid ; }, abstract = {The impact of perfluorooctanoic acid (PFOA) on the anaerobic granular sludge was evaluated through a sequential batch experiment. Results showed that PFOA inhibited the chemical oxygen demand (COD) removal rate of the sludge and the dosage of 100 mg/L PFOA was more obvious. However, this negative effect would gradually weaken with the adaptation of microorganisms. For the 50 mg/L PFOA experimental group, the proteins content in the extracellular polymeric substances (EPS) of the anaerobic granular sludge increased from 1.53 mg/g to 3.65 mg/g. Meanwhile, PFOA inhibited the 2-(p-iodophenyl)-3-(p-nitrophenyl)-5-phenyltetrazolium chloride (INT) activity of the anaerobic granular sludge. Furthermore, 100 mg/L PFOA reduced the relative abundance of Proteobacteria by 5.99% and Longilinea by 1.11%. 100 mg/L PFOA mainly restricted COD removal by affecting the glycolysis process, with the abundances of glucokinase and pyruvate kinase reduced by 8% and 28.1%, respectively. Compared with the control group, the relative abundance of the methyl-coenzyme M reductase alpha subunit increased by 84%, respectively, under 100 mg/L PFOA.}, } @article {pmid35390349, year = {2022}, author = {Voigt, AY and Emiola, A and Johnson, JS and Fleming, ES and Nguyen, H and Zhou, W and Tsai, KY and Fink, C and Oh, J}, title = {Skin Microbiome Variation with Cancer Progression in Human Cutaneous Squamous Cell Carcinoma.}, journal = {The Journal of investigative dermatology}, volume = {142}, number = {10}, pages = {2773-2782.e16}, pmid = {35390349}, issn = {1523-1747}, support = {R01 AR078634/AR/NIAMS NIH HHS/United States ; U19 AI142733/AI/NIAID NIH HHS/United States ; P30 CA034196/CA/NCI NIH HHS/United States ; K22 AI119231/AI/NIAID NIH HHS/United States ; U54 NS105539/NS/NINDS NIH HHS/United States ; R21 AR075174/AR/NIAMS NIH HHS/United States ; DP2 GM126893/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents ; *Carcinoma, Squamous Cell/pathology ; Humans ; *Keratosis, Actinic/pathology ; *Microbiota ; *Skin Neoplasms/pathology ; }, abstract = {The skin microbiome plays a critical role in skin homeostasis and disorders. UVR is the major cause of nonmelanoma skin cancer, but other risk factors, including immune suppression, chronic inflammation, and antibiotic usage, suggest the microbiome as an additional, unexplored risk factor and potential disease biomarker. The overarching goal was to study the skin microbiome in squamous cell carcinoma (SCC) and premalignant actinic keratosis compared with that in healthy skin to identify skin cancer‒associated changes in the skin microbiome. We performed a high-resolution analysis of shotgun metagenomes of actinic keratosis and SCC in healthy skin, revealing the microbial community shifts specific to actinic keratosis and SCC. Most prominently, the relative abundance of pathobiont Staphylococcus aureus was increased at the expense of commensal Cutibacterium acnes in SCC compared with that in healthy skin, and enrichment of functional pathways in SCC reflected this shift. Notably, C. acnes associated with lesional versus healthy skin differed at the strain level, suggesting the specific functional changes associated with its depletion in SCC. Our study revealed a transitional microbial dysbiosis from healthy skin to actinic keratosis to SCC, supporting further investigation of the skin microbiome for use as a biomarker and providing hypotheses for studies investigating how these microbes might influence skin cancer progression.}, } @article {pmid35389162, year = {2022}, author = {Dunn, CM and Jeffries, MA}, title = {The Microbiome in Osteoarthritis: a Narrative Review of Recent Human and Animal Model Literature.}, journal = {Current rheumatology reports}, volume = {24}, number = {5}, pages = {139-148}, pmid = {35389162}, issn = {1534-6307}, support = {K08AR070891/AR/NIAMS NIH HHS/United States ; K08 AR070891/AR/NIAMS NIH HHS/United States ; R01AR076440/AR/NIAMS NIH HHS/United States ; I01 BX004882/BX/BLRD VA/United States ; R33 AR078075/AR/NIAMS NIH HHS/United States ; P20GM125528/GM/NIGMS NIH HHS/United States ; R61AR078075/AR/NIAMS NIH HHS/United States ; I01 CX002494/CX/CSRD VA/United States ; P20 GM125528/GM/NIGMS NIH HHS/United States ; R61 AR078075/AR/NIAMS NIH HHS/United States ; R01 AR076440/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Humans ; *Microbiota ; Models, Animal ; *Osteoarthritis, Knee ; *Probiotics/therapeutic use ; }, abstract = {PURPOSE OF THE REVIEW: The microbiome has recently emerged as a powerful contributor to health and illness in chronic, systemic disorders. Furthermore, new microbiome niches beyond traditional gut locations are frequently being described. Over the past 5 years, numerous pivotal studies have demonstrated associations between changes in various microbiome niches and the development of osteoarthritis (OA). Herein, we review the most impactful recent literature, including microbiome associations with disease and the potential therapeutic value of microbiome manipulation.

RECENT FINDINGS: The gut microbiome of human OA patients is enriched in specific bacterial clades, most notably Streptococcus, which correlates with OA pain, Firmicutes, and others. Most studies have focused on knee OA, although one publication demonstrated positive associations with 3 gut microbiome clades in hand OA. OA can be easily distinguished from RA by evaluating differences in oral microbiome composition. Most studies have also demonstrated a reduction in richness of the gut microbiome (alpha diversity) associated with OA. Several studies have identified bacterial signatures within human knee and hip cartilage, synovial fluid, and synovial tissue and have described changes in these patterns occurring with the development of OA. In animal models of OA, high-fat diet-induced obesity has been the most well-studied OA risk factor associated with changes in the microbiome, with numerous bacterial clades changed within the gut microbiome and associated with OA. Also in animal models, various oral supplementations, including dietary fiber, probiotics including Lactobacillus species, and cecal microbiome transplantation have all shown improvements in OA histopathology or cartilage healing. Microbiome changes are strongly associated with the OA disease process and with individual OA risk factors related to both the gut microbiome and the microbial DNA patterns in the joint. Microbiome-directed interventions have the potential to prevent or reduce the progression of OA. Future studies should investigate the mechanistic underpinnings of these microbiome associations and further define the therapeutic potential of microbiome augmentation.}, } @article {pmid35388735, year = {2022}, author = {Davies, M and Galazzo, G and van Hattem, JM and Arcilla, MS and Melles, DC and de Jong, MD and Schultsz, C and Wolffs, P and McNally, A and Schaik, WV and Penders, J}, title = {Enterobacteriaceae and Bacteroidaceae provide resistance to travel-associated intestinal colonization by multi-drug resistant Escherichia coli.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2060676}, pmid = {35388735}, issn = {1949-0984}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria ; Bacteroidaceae ; Diarrhea/drug therapy ; Enterobacteriaceae/genetics ; *Enterobacteriaceae Infections/microbiology ; Escherichia coli/genetics ; *Gastrointestinal Microbiome ; Humans ; Travel ; beta-Lactamases/genetics/pharmacology ; }, abstract = {Previous studies have shown high acquisition risks of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) among international travelers visiting antimicrobial resistance (AMR) hotspots. Although antibiotic use and travelers' diarrhea have shown to influence the ESBL-E acquisition risk, it remains largely unknown whether successful colonization of ESBL-E during travel is associated with the composition, functional capacity and resilience of the traveler's microbiome. The microbiome of pre- and post-travel fecal samples from 190 international travelers visiting Africa or Asia was profiled using whole metagenome shotgun sequencing. A metagenomics species concept approach was used to determine the microbial composition, population diversity and functional capacity before travel and how it is altered longitudinally. Eleven travelers were positive for ESBL-E before travel and removed from the analysis. Neither the microbial richness (Chao1), diversity (effective Shannon) and community structure (Bray-Curtis dissimilarity) in pretravel samples nor the longitudinal change of these metrics during travel were predictive for ESBL-E acquisition. A zero-inflated two-step beta-regression model was used to determine how the longitudinal change in both prevalence and abundance of each taxon was related to ESBL acquisition. There were detected increases in both the prevalence and abundance of Citrobacter freundii and two members of the genus Bacteroides, in association with remaining uncolonized by ESBL-E. These results highlight the potential of these individual microbes as a microbial consortium to prevent the acquisition of ESBL-E. The ability to alter a person's colonization resistance to a bacterium could be key to intervention strategies that aim to minimize the spread of MDR bacteria.}, } @article {pmid35387878, year = {2022}, author = {Bai, X and Wei, H and Liu, W and Coker, OO and Gou, H and Liu, C and Zhao, L and Li, C and Zhou, Y and Wang, G and Kang, W and Ng, EK and Yu, J}, title = {Cigarette smoke promotes colorectal cancer through modulation of gut microbiota and related metabolites.}, journal = {Gut}, volume = {71}, number = {12}, pages = {2439-2450}, pmid = {35387878}, issn = {1468-3288}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology ; *Cigarette Smoking/adverse effects ; Mice, Inbred C57BL ; Carcinogenesis ; *Colorectal Neoplasms/microbiology ; }, abstract = {OBJECTIVE: Cigarette smoking is a major risk factor for colorectal cancer (CRC). We aimed to investigate whether cigarette smoke promotes CRC by altering the gut microbiota and related metabolites.

DESIGN: Azoxymethane-treated C57BL/6 mice were exposed to cigarette smoke or clean air 2 hours per day for 28 weeks. Shotgun metagenomic sequencing and liquid chromatography mass spectrometry were parallelly performed on mice stools to investigate alterations in microbiota and metabolites. Germ-free mice were transplanted with stools from smoke-exposed and smoke-free control mice.

RESULTS: Mice exposed to cigarette smoke had significantly increased tumour incidence and cellular proliferation compared with smoke-free control mice. Gut microbial dysbiosis was observed in smoke-exposed mice with significant differential abundance of bacterial species including the enrichment of Eggerthella lenta and depletion of Parabacteroides distasonis and Lactobacillus spp. Metabolomic analysis showed increased bile acid metabolites, especially taurodeoxycholic acid (TDCA) in the colon of smoke-exposed mice. We found that E. lenta had the most positive correlation with TDCA in smoke-exposed mice. Moreover, smoke-exposed mice manifested enhanced oncogenic MAPK/ERK (mitogen-activated protein kinase/extracellular signal‑regulated protein kinase 1/2) signalling (a downstream target of TDCA) and impaired gut barrier function. Furthermore, germ-free mice transplanted with stools from smoke-exposed mice (GF-AOMS) had increased colonocyte proliferation. Similarly, GF-AOMS showed increased abundances of gut E. lenta and TDCA, activated MAPK/ERK pathway and impaired gut barrier in colonic epithelium.

CONCLUSION: The gut microbiota dysbiosis induced by cigarette smoke plays a protumourigenic role in CRC. The smoke-induced gut microbiota dysbiosis altered gut metabolites and impaired gut barrier function, which could activate oncogenic MAPK/ERK signalling in colonic epithelium.}, } @article {pmid35387876, year = {2022}, author = {Yang, J and Hou, L and Wang, J and Xiao, L and Zhang, J and Yin, N and Yao, S and Cheng, K and Zhang, W and Shi, Z and Wang, J and Jiang, H and Huang, N and You, Y and Lin, M and Shang, R and Wei, Y and Zhao, Y and Zhao, F}, title = {Unfavourable intrauterine environment contributes to abnormal gut microbiome and metabolome in twins.}, journal = {Gut}, volume = {71}, number = {12}, pages = {2451-2462}, pmid = {35387876}, issn = {1468-3288}, mesh = {Infant, Newborn ; Pregnancy ; Infant ; Female ; Humans ; *Gastrointestinal Microbiome ; Dysbiosis ; Cysteine/pharmacology ; RNA, Ribosomal, 16S/genetics ; Metabolome ; Feces/microbiology ; }, abstract = {OBJECTIVE: Fetal growth restriction (FGR) is a devastating pregnancy complication that increases the risk of perinatal mortality and morbidity. This study aims to determine the combined and relative effects of genetic and intrauterine environments on neonatal microbial communities and to explore selective FGR-induced gut microbiota disruption, metabolic profile disturbances and possible outcomes.

DESIGN: We profiled and compared the gut microbial colonisation of 150 pairs of twin neonates who were classified into four groups based on their chorionicity and discordance of fetal birth weight. Gut microbiota dysbiosis and faecal metabolic alterations were determined by 16S ribosomal RNA and metagenomic sequencing and metabolomics, and the long-term effects were explored by surveys of physical and neurocognitive development conducted after 2~3 years of follow-up.

RESULTS: Adverse intrauterine environmental factors related to selective FGR dominate genetics in their effects of elevating bacterial diversity and altering the composition of early-life gut microbiota, and this effect is positively related to the severity of selective FGR in twins. The influence of genetic factors on gut microbes diminishes in the context of selective FGR. Gut microbiota dysbiosis in twin neonates with selective FGR and faecal metabolic alterations features decreased abundances of Enterococcus and Acinetobacter and downregulated methionine and cysteine levels. Correlation analysis indicates that the faecal cysteine level in early life is positively correlated with the physical and neurocognitive development of infants.

CONCLUSION: Dysbiotic microbiota profiles and pronounced metabolic alterations are associated with selective FGR affected by adverse intrauterine environments, emphasising the possible effects of dysbiosis on long-term neurobehavioural development.}, } @article {pmid35383822, year = {2022}, author = {Aguilar-Lopez, M and Wetzel, C and MacDonald, A and Ho, TTB and Donovan, SM}, title = {Metagenomic profile of the fecal microbiome of preterm infants consuming mother's own milk with bovine milk-based fortifier or infant formula: a cross-sectional study.}, journal = {The American journal of clinical nutrition}, volume = {116}, number = {2}, pages = {435-445}, pmid = {35383822}, issn = {1938-3207}, support = {K23 HL150300/HL/NHLBI NIH HHS/United States ; }, mesh = {Breast Feeding ; Cesarean Section ; Cross-Sectional Studies ; Female ; Humans ; Infant ; Infant Formula/chemistry ; Infant, Newborn ; Infant, Premature ; *Microbiota ; *Milk, Human/chemistry ; Mothers ; Pregnancy ; }, abstract = {BACKGROUND: Preterm (PT) infants harbor a different gut microbiome than full-term infants. Multiple factors affect gut microbial colonization of PT infants, including low gestational age, high rates of Cesarean section, exposure to antibiotics, and diet. Human milk, whether it's mother's own milk (MOM) or donor human milk, is the preferred feeding mode for PT infants but needs to be fortified to achieve adequate nutrient content. Infant formulas are introduced at later stages if human milk is insufficient or unavailable. How these dietary exposures affect the gut microbiome of PT infants is poorly understood.

OBJECTIVES: The goal of this study was to evaluate the metagenomic potential of the fecal microbiome of PT infants consuming MOM with bovine milk-based fortifier compared with PT formula alone.

METHODS: Forty-two stool samples, from 27 infants consuming MOM or formula (21 samples in each group) were included. Twelve infants had repeated sampling (2-3 samples). Shotgun genomic DNA sequencing was performed and analyzed using MetaPhlAn and HUMAnN2. Multivariate regression analysis, adjusting by the repeated sampling, was used to identify the features that differed between PT infants consuming MOM compared with formula.

RESULTS: The primary function of the fecal microbiome of PT infants was characterized by a high abundance of biosynthesis pathways. A set of core features was identified; these belonged to pathways for amino acid metabolism and vitamin K-2 biosynthesis. Five pathways significantly differed between the MOM and formula group. Pathways for fatty acid and carbohydrate degradation were significantly higher in the MOM group. Taxonomically, members of the phylum Actinobacteria and the genus Bifidobacterium were higher in PT infants exposed to MOM.

CONCLUSIONS: This study provides insight into the influence of feeding MOM compared with infant formula on the structure and function of the fecal microbiome of PT infants.}, } @article {pmid35382951, year = {2022}, author = {Orbe-Orihuela, YC and Godoy-Lozano, EE and Lagunas-Martínez, A and Castañeda-Márquez, AC and Murga-Garrido, S and Díaz-Benítez, CE and Ochoa-Leyva, A and Cornejo-Granados, F and Cruz, M and Estrada, K and Bermúdez-Morales, VH and Sanchez-Flores, A and Burguete-García, AI}, title = {Association of Gut Microbiota with Dietary-dependent Childhood Obesity.}, journal = {Archives of medical research}, volume = {53}, number = {4}, pages = {407-415}, doi = {10.1016/j.arcmed.2022.03.007}, pmid = {35382951}, issn = {1873-5487}, mesh = {Body Mass Index ; Carbohydrates ; Child ; Cross-Sectional Studies ; Diet ; *Gastrointestinal Microbiome ; Humans ; *Pediatric Obesity/epidemiology/etiology ; }, abstract = {AIM: To evaluate the taxonomic profile of the gut microbiota using metagenomics and the association with diet-dependent childhood obesity.

METHODS: A cross-sectional study of a subsample of 46 children was conducted. The children were classified as normal-weight, overweight, and obese according to their age and sex and the World Health Organization (WHO) guidelines. Dietary patterns were determined through principal component analysis. The profile of the human gut microbiota was determined by bioinformatic analysis using whole metagenome shotgun sequencing. The association of gut microbiota and z-BMI, waist circumference and hip circumference, and the possible modifying effect of diet were analyzed using multiple regression models.

RESULTS: Children with an abundance of Holdemania spp. and high protein and complex carbohydrate consumption had a lower z-BMI (β -19.06, p = 0.011), waist circumference (β -171.92, p = 0.003), and hip circumference (β -157.57, p = 0.004). In contrast, observed a positive association between Coprococcus catus and the low intake of this dietary pattern with hip circumference (β 147.87, p = 0.025). Furthermore, the presence of Bilophila spp. and Paraprevotella xylaniphila with high saturated fat and simple carbohydrate consumption we observed a positive association between z-BMI (β 47.5, p = 0.002), hip circumference (β 44.54, p = 0.025), and waist circumference (β 44.34, p = 0.004).

CONCLUSION: We suggest that the synergism between diet and the profile of children's gut microbiota can be a factor that could be associated with the development of obesity and its complications in childhood.}, } @article {pmid35381769, year = {2022}, author = {Bamola, VD and Kapardar, R and Lal, B and Sharma, A and Chaudhry, R}, title = {A metagenomic assessment of gut microbiota in Indian colon cancer patients.}, journal = {Journal of cancer research and therapeutics}, volume = {18}, number = {1}, pages = {96-102}, doi = {10.4103/0973-1482.341139}, pmid = {35381769}, issn = {1998-4138}, mesh = {*Colonic Neoplasms ; Dysbiosis ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Gut microbiota plays an important role in the development of different diseases including colorectal cancer. The geography, lifestyle, and dietary habits of Indians are different from Western world, thus microbiome studies of Western population could not be extrapolated to their Indian counterparts.

METHOD: Therefore, we have conducted a study on gut microbiota in Indian healthy subjects and patients of colon cancer using 16S ribosomal RNA Amplicon sequencing. Operational taxonomic units were calculated for different bacterial taxon including phylum, class, order, family, and genus level.

RESULTS: Observed results indicated a considerable difference in the bacterial diversity in both the groups. Phylum Firmicutes was significantly dominated in both the groups followed by Bacteroidetes, Actinobacteria, and Proteobacteria which clearly indicates the dominance of phylum Firmicutes in Indian population. Phylum Firmicutes and Actinobacteria were significantly abundant in the healthy group while phylum Bacteroidetes in the colon cancer group. Bacterial genera Megamonas, Megasphaera, Mitsuokella, and Streptococcus were significantly abundant in the healthy group and Veillonella, Prevotella, and Eubacterium in the colon cancer group. Bacterial genus Bradyrhizobium was present in the healthy group and Alistipes, Coprococcus, Dorea, and Rhodococcus were present in the colon cancer group but absent in the healthy group.

CONCLUSION: There was a considerable difference in bacterial diversity in both the study groups indicating dysbiosis in the colon cancer group.}, } @article {pmid35378331, year = {2022}, author = {Gonzalez, CG and Mills, RH and Kordahi, MC and Carrillo-Terrazas, M and Secaira-Morocho, H and Widjaja, CE and Tsai, MS and Mittal, Y and Yee, BA and Vargas, F and Weldon, K and Gauglitz, JM and Delaroque, C and Sauceda, C and Rossitto, LA and Ackermann, G and Humphrey, G and Swafford, AD and Siegel, CA and Buckey, JC and Raffals, LE and Sadler, C and Lindholm, P and Fisch, KM and Valaseck, M and Suriawinata, A and Yeo, GW and Ghosh, P and Chang, JT and Chu, H and Dorrestein, P and Zhu, Q and Chassaing, B and Knight, R and Gonzalez, DJ and Dulai, PS}, title = {The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {14}, number = {1}, pages = {35-53}, pmid = {35378331}, issn = {2352-345X}, support = {U34 DK126626/DK/NIDDK NIH HHS/United States ; R01 AI123202/AI/NIAID NIH HHS/United States ; R21 DK119724/DK/NIDDK NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 AI141630/AI/NIAID NIH HHS/United States ; T32 DK007202/DK/NIDDK NIH HHS/United States ; T32 GM007752/GM/NIGMS NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; P01 AI132122/AI/NIAID NIH HHS/United States ; R01 AI129973/AI/NIAID NIH HHS/United States ; TL1 TR001443/TR/NCATS NIH HHS/United States ; UG3 TR003355/TR/NCATS NIH HHS/United States ; R01 AI155696/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Colitis, Ulcerative/therapy ; Humans ; *Hyperbaric Oxygenation ; Interleukin-10 ; Mice ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND & AIMS: Hyperbaric oxygen therapy (HBOT) is a promising treatment for moderate-to-severe ulcerative colitis. However, our current understanding of the host and microbial response to HBOT remains unclear. This study examined the molecular mechanisms underpinning HBOT using a multi-omic strategy.

METHODS: Pre- and post-intervention mucosal biopsies, tissue, and fecal samples were collected from HBOT phase 2 clinical trials. Biopsies and fecal samples were subjected to shotgun metaproteomics, metabolomics, 16s rRNA sequencing, and metagenomics. Tissue was subjected to bulk RNA sequencing and digital spatial profiling (DSP) for single-cell RNA and protein analysis, and immunohistochemistry was performed. Fecal samples were also used for colonization experiments in IL10[-/-] germ-free UC mouse models.

RESULTS: Proteomics identified negative associations between HBOT response and neutrophil azurophilic granule abundance. DSP identified an HBOT-specific reduction of neutrophil STAT3, which was confirmed by immunohistochemistry. HBOT decreased microbial diversity with a proportional increase in Firmicutes and a secondary bile acid lithocholic acid. A major source of the reduction in diversity was the loss of mucus-adherent taxa, resulting in increased MUC2 levels post-HBOT. Targeted database searching revealed strain-level associations between Akkermansia muciniphila and HBOT response status. Colonization of IL10[-/-] with stool obtained from HBOT responders resulted in lower colitis activity compared with non-responders, with no differences in STAT3 expression, suggesting complementary but independent host and microbial responses.

CONCLUSIONS: HBOT reduces host neutrophil STAT3 and azurophilic granule activity in UC patients and changes in microbial composition and metabolism in ways that improve colitis activity. Intestinal microbiota, especially strain level variations in A muciniphila, may contribute to HBOT non-response.}, } @article {pmid35377222, year = {2022}, author = {Tarracchini, C and Fontana, F and Lugli, GA and Mancabelli, L and Alessandri, G and Turroni, F and Ventura, M and Milani, C}, title = {Investigation of the Ecological Link between Recurrent Microbial Human Gut Communities and Physical Activity.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0042022}, pmid = {35377222}, issn = {2165-0497}, mesh = {Bacteria/genetics ; Butyrates ; Exercise ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; }, abstract = {Emerging evidence has shown an association between the composition of intestinal microbial communities and host physical activity, suggesting that modifications of the gut microbiota composition may support training, performance, and post-exercise recovery of the host. Nevertheless, investigation of differences in the gut microbiota between athletes and individuals with reduced physical activity is still lacking. In this study, we performed a meta-analysis of 207 publicly available shotgun metagenomics sequencing data of fecal samples from athletes and healthy non-athletes. Accordingly, analysis of species-level fecal microbial profiles revealed three recurring compositional patterns, named HPC1 to 3, that characterize the host based on their commitment to physical activity. Interestingly, the gut microbiome of athletes showed a higher abundance of anti-inflammatory, health-promoting bacteria than that of non-athletic individuals. Moreover, the bacterial species profiled in the gut of professional athletes are short-fatty acid producers, which potentially improve energy production, and therefore sports performances. Intriguingly, microbial interaction network analyses suggested that exercise-induced microbiota adaptation involves the whole microbial community structure, resulting in a complex microbe-microbe interplay driven by positive relationships among the predicted butyrate-producing community members. IMPORTANCE Through metagenomic analyses, this work revealed that athletes have a gut-associated microbial community enriched in butyrate-producing species compared with non-athletes. This evidence can support the existence of a two-way association between the host's lifestyle and the gut microbiota composition, with potential intriguing athletic performance outcomes.}, } @article {pmid35372133, year = {2022}, author = {Pan, L and Wu, F and Cai, Q and Xu, Z and Hu, H and Tang, T and Yue, R and Hou, Y and Zhang, X and Fang, Y and Huang, X and Kang, Y}, title = {Whole Genome Profiling of Lung Microbiome in Solid Organ Transplant Recipients Reveals Virus Involved Microecology May Worsen Prognosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {863399}, pmid = {35372133}, issn = {2235-2988}, mesh = {Cytomegalovirus/genetics ; Humans ; Lung ; *Microbiota/genetics ; *Organ Transplantation/adverse effects ; Retrospective Studies ; }, abstract = {Solid organ transplantation (SOT) is the final therapeutic option for recipients with end-stage organ failure, and its long-term success is limited by infections and chronic allograft dysfunction. Viral infection in SOT recipients is considered an important factor affecting prognosis. In this study, we retrospectively analyzed 43 cases of respiratory infections in SOT recipients using metagenomic next-generation sequencing (mNGS) for bronchoalveolar lavage fluid (BALF). At least one virus was detected in 26 (60.5%) recipients, while 17 (39.5%) were virus-negative. Among virus-positive recipients, cytomegalovirus (CMV) was detected in 14 (32.6%), Torque teno virus (TTV) was detected in 9 (20.9%), and other viruses were detected in 6 (14.0%). Prognostic analysis showed that the mortality of the virus-positive group was higher than that of the virus-negative group regardless whether it is the main cause of infection. Analysis of different types of viruses showed that the mortality of the CMV-positive group was significantly higher than that of the CMV-negative group, but no significant difference was observed in other type of virus groups. The diversity analysis of the lung microbiome showed that there was a significant difference between the virus-positive group and the negative group, in particular, the significant differences in microorganisms such as Pneumocystis jirovecii (PJP) and Moraxella osloensiswere detected. Moreover, in the presence of CMV, Pneumocystis jirovecii, Veillonella parvula, and other species showed dramatic changes in the lung of SOT patients, implying that high degree of co-infection between CMV and Pneumocystis jirovecii may occur. Taken together, our study shows that the presence of virus is associated with worse prognosis and dramatically altered lung microbiota in SOT recipients.}, } @article {pmid35372129, year = {2022}, author = {Greenbaum, J and Lin, X and Su, KJ and Gong, R and Shen, H and Shen, J and Xiao, HM and Deng, HW}, title = {Integration of the Human Gut Microbiome and Serum Metabolome Reveals Novel Biological Factors Involved in the Regulation of Bone Mineral Density.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {853499}, pmid = {35372129}, issn = {2235-2988}, support = {P20 GM109036/GM/NIGMS NIH HHS/United States ; R01 AG061917/AG/NIA NIH HHS/United States ; R01 AR069055/AR/NIAMS NIH HHS/United States ; U19 AG055373/AG/NIA NIH HHS/United States ; }, mesh = {Biological Factors ; Bone Density ; Female ; *Gastrointestinal Microbiome ; Humans ; Metabolome ; *Microbiota ; }, abstract = {While the gut microbiome has been reported to play a role in bone metabolism, the individual species and underlying functional mechanisms have not yet been characterized. We conducted a systematic multi-omics analysis using paired metagenomic and untargeted serum metabolomic profiles from a large sample of 499 peri- and early post-menopausal women to identify the potential crosstalk between these biological factors which may be involved in the regulation of bone mineral density (BMD). Single omics association analyses identified 22 bacteria species and 17 serum metabolites for putative association with BMD. Among the identified bacteria, Bacteroidetes and Fusobacteria were negatively associated, while Firmicutes were positively associated. Several of the identified serum metabolites including 3-phenylpropanoic acid, mainly derived from dietary polyphenols, and glycolithocholic acid, a secondary bile acid, are metabolic byproducts of the microbiota. We further conducted a supervised integrative feature selection with respect to BMD and constructed the inter-omics partial correlation network. Although still requiring replication and validation in future studies, the findings from this exploratory analysis provide novel insights into the interrelationships between the gut microbiome and serum metabolome that may potentially play a role in skeletal remodeling processes.}, } @article {pmid35372117, year = {2022}, author = {Xiong, Z and Peng, K and Song, S and Zhu, Y and Gu, J and Huang, C and Li, X}, title = {Cerebral Intraparenchymal Hemorrhage Changes Patients' Gut Bacteria Composition and Function.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {829491}, pmid = {35372117}, issn = {2235-2988}, mesh = {Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Hemorrhage/genetics ; Humans ; Metagenome ; Metagenomics ; }, abstract = {Gut bacteria consists of 150 times more genes than humans that are vital for health. Several studies revealed that gut bacteria are associated with disease status and influence human behavior and mentality. Whether human brain injury alters the gut bacteria is yet unclear, we tested 20 fecal samples from patients with cerebral intraparenchymal hemorrhage and corresponding healthy controls through metagenomic shotgun sequencing. The composition of patients' gut bacteria changed significantly at the phylum level; Verrucomicrobiota was the specific phylum colonized in the patients' gut. The functional alteration was observed in the patients' gut bacteria, including high metabolic activity for nutrients or neuroactive compounds, strong antibiotic resistance, and less virulence factor diversity. The changes in the transcription and metabolism of differential species were more evident than those of the non-differential species between groups, which is the primary factor contributing to the functional alteration of patients with cerebral intraparenchymal hemorrhage.}, } @article {pmid35369727, year = {2022}, author = {Zhu, Q and Huang, S and Gonzalez, A and McGrath, I and McDonald, D and Haiminen, N and Armstrong, G and Vázquez-Baeza, Y and Yu, J and Kuczynski, J and Sepich-Poore, GD and Swafford, AD and Das, P and Shaffer, JP and Lejzerowicz, F and Belda-Ferre, P and Havulinna, AS and Méric, G and Niiranen, T and Lahti, L and Salomaa, V and Kim, HC and Jain, M and Inouye, M and Gilbert, JA and Knight, R}, title = {Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0016722}, pmid = {35369727}, issn = {2379-5077}, support = {RG/13/13/30194/BHF_/British Heart Foundation/United Kingdom ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; U24 CA248454/CA/NCI NIH HHS/United States ; RG/18/13/33946/BHF_/British Heart Foundation/United Kingdom ; CH/12/2/29428/BHF_/British Heart Foundation/United Kingdom ; K12 GM068524/GM/NIGMS NIH HHS/United States ; F30 CA243480/CA/NCI NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Phylogeny ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Ecology ; }, abstract = {We introduce the operational genomic unit (OGU) method, a metagenome analysis strategy that directly exploits sequence alignment hits to individual reference genomes as the minimum unit for assessing the diversity of microbial communities and their relevance to environmental factors. This approach is independent of taxonomic classification, granting the possibility of maximal resolution of community composition, and organizes features into an accurate hierarchy using a phylogenomic tree. The outputs are suitable for contemporary analytical protocols for community ecology, differential abundance, and supervised learning while supporting phylogenetic methods, such as UniFrac and phylofactorization, that are seldom applied to shotgun metagenomics despite being prevalent in 16S rRNA gene amplicon studies. As demonstrated in two real-world case studies, the OGU method produces biologically meaningful patterns from microbiome data sets. Such patterns further remain detectable at very low metagenomic sequencing depths. Compared with taxonomic unit-based analyses implemented in currently adopted metagenomics tools, and the analysis of 16S rRNA gene amplicon sequence variants, this method shows superiority in informing biologically relevant insights, including stronger correlation with body environment and host sex on the Human Microbiome Project data set and more accurate prediction of human age by the gut microbiomes of Finnish individuals included in the FINRISK 2002 cohort. We provide Woltka, a bioinformatics tool to implement this method, with full integration with the QIIME 2 package and the Qiita web platform, to facilitate adoption of the OGU method in future metagenomics studies. IMPORTANCE Shotgun metagenomics is a powerful, yet computationally challenging, technique compared to 16S rRNA gene amplicon sequencing for decoding the composition and structure of microbial communities. Current analyses of metagenomic data are primarily based on taxonomic classification, which is limited in feature resolution. To solve these challenges, we introduce operational genomic units (OGUs), which are the individual reference genomes derived from sequence alignment results, without further assigning them taxonomy. The OGU method advances current read-based metagenomics in two dimensions: (i) providing maximal resolution of community composition and (ii) permitting use of phylogeny-aware tools. Our analysis of real-world data sets shows that it is advantageous over currently adopted metagenomic analysis methods and the finest-grained 16S rRNA analysis methods in predicting biological traits. We thus propose the adoption of OGUs as an effective practice in metagenomic studies.}, } @article {pmid35369657, year = {2021}, author = {Shah, NB and Nigwekar, SU and Kalim, S and Lelouvier, B and Servant, F and Dalal, M and Krinsky, S and Fasano, A and Tolkoff-Rubin, N and Allegretti, AS}, title = {The Gut and Blood Microbiome in IgA Nephropathy and Healthy Controls.}, journal = {Kidney360}, volume = {2}, number = {8}, pages = {1261-1274}, pmid = {35369657}, issn = {2641-7650}, mesh = {Case-Control Studies ; Dysbiosis/complications ; *Gastrointestinal Microbiome/genetics ; *Glomerulonephritis, IGA/complications ; Humans ; *Microbiota ; }, abstract = {BACKGROUND: IgA nephropathy (IgAN) has been associated with gut dysbiosis, intestinal membrane disruption, and translocation of bacteria into blood. Our study aimed to understand the association of gut and blood microbiomes in patients with IgAN in relation to healthy controls.

METHODS: We conducted a case-control study with 20 patients with progressive IgAN, matched with 20 healthy controls, and analyzed bacterial DNA quantitatively in blood using 16S PCR and qualitatively in blood and stool using 16S metagenomic sequencing. We conducted between-group comparisons as well as comparisons between the blood and gut microbiomes.

RESULTS: Higher median 16S bacterial DNA in blood was found in the IgAN group compared with the healthy controls group (7410 versus 6030 16S rDNA copies/μl blood, P=0.04). α- and β-Diversity in both blood and stool was largely similar between the IgAN and healthy groups. In patients with IgAN, in comparison with healthy controls, we observed higher proportions of the class Coriobacteriia and species of the genera Legionella, Enhydrobacter, and Parabacteroides in blood, and species of the genera Bacteroides, Escherichia-Shigella, and some Ruminococcus in stool. Taxa distribution were markedly different between the blood and stool samples of each subject in both IgAN and healthy groups, without any significant correlation between corresponding gut and blood phyla.

CONCLUSIONS: Important bacterial taxonomic differences, quantitatively in blood and qualitatively in both blood and stool samples, that were detected between IgAN and healthy groups warrant further investigation into their roles in the pathogenesis of IgAN. Although gut bacterial translocation into blood may be one of the potential sources of the blood microbiome, marked taxonomic differences between gut and blood samples in each subject in both groups confirms that the blood microbiome does not directly reflect the gut microbiome. Further research is needed into other possible sites of origin and internal regulation of the blood microbiome.}, } @article {pmid35368152, year = {2022}, author = {Hsu, CL and Zhang, X and Jiang, L and Lang, S and Hartmann, P and Pride, D and Fouts, DE and Stärkel, P and Schnabl, B}, title = {Intestinal virome in patients with alcohol use disorder and after abstinence.}, journal = {Hepatology communications}, volume = {6}, number = {8}, pages = {2058-2069}, pmid = {35368152}, issn = {2471-254X}, support = {T32 DK007202/NH/NIH HHS/United States ; K12 HD85036/NH/NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 AA026939/NH/NIH HHS/United States ; R37 AA020703/NH/NIH HHS/United States ; R01 AA24726/NH/NIH HHS/United States ; R37 AA020703/AA/NIAAA NIH HHS/United States ; }, mesh = {*Alcoholism ; Bacteria/genetics ; *Bacteriophages/genetics ; *Gastrointestinal Microbiome ; Humans ; Intestines ; *Liver Diseases, Alcoholic ; Metagenomics ; Virome ; }, abstract = {Alcohol use is a leading cause of chronic liver disease worldwide, and changes in the microbiome associated with alcohol use contribute to patients' risk for liver disease progression. Less is known about the effects of alcohol use on the intestinal viral microbiome (virome) and interactions between bacteriophages and their target bacteria. We studied changes in the intestinal virome of 62 clinically well-characterized patients with alcohol use disorder (AUD) during active alcohol use and after 2 weeks of alcohol abstinence, by extracting virus-like particles and performing metagenomic sequencing. We observed decreased abundance of Propionibacterium, Lactobacillus, and Leuconostoc phages in patients with active AUD when compared with controls, whereas after 2 weeks of alcohol abstinence, patients with AUD demonstrated an increase in the abundance of Propionibacterium, Lactobacillus, and Leuconostoc phages. The intestinal virome signature was also significantly different in patients with AUD with progressive liver disease, with increased abundance of phages targeting Enterobacteria and Lactococcus species phages compared with patients with AUD with nonprogressive liver disease. By performing moderation analyses, we found that progressive liver disease is associated with changes in interactions between some bacteriophages and their respective target bacteria. In summary, active alcohol use and alcohol-associated progressive liver disease are associated with changes in the fecal virome, some of which are partially reversible after a short period of abstinence. Progression of alcohol-associated liver disease is associated with changes in bacteriophage-bacteria interactions.}, } @article {pmid35367886, year = {2022}, author = {Zhang, Y and Cui, R and Shi, G and Dai, Y and Dong, J and Wu, Q and Zhang, H and Dai, J}, title = {Dioxin-like polychlorinated biphenyl 126 (PCB126) disrupts gut microbiota-host metabolic dysfunction in mice via aryl hydrocarbon receptor activation.}, journal = {Ecotoxicology and environmental safety}, volume = {236}, number = {}, pages = {113448}, doi = {10.1016/j.ecoenv.2022.113448}, pmid = {35367886}, issn = {1090-2414}, mesh = {Animals ; *Dioxins ; *Environmental Pollutants/toxicity ; *Gastrointestinal Microbiome ; Male ; Mice ; Mice, Inbred C57BL ; *Polychlorinated Biphenyls/toxicity ; *Polychlorinated Dibenzodioxins/toxicity ; Receptors, Aryl Hydrocarbon/genetics/metabolism ; }, abstract = {Exposure to environmental pollutants, including dioxin-like pollutants, can cause numerous health issues. A common exposure route to pollutants is through contaminated foods, and thus the gastrointestinal system and gut microbiota are often exposed to high amounts of pollutants. Multiple studies have focused on the imbalance in intestinal microbiota composition caused by dioxin-like pollutants. Here, we examined the effects of polychlorinated biphenyl 126 (PCB126) on the composition and functions of gut microbes through metagenomic sequencing, and explored the correlations between microflora dysbiosis and aryl hydrocarbon receptor (AHR) signaling. Adult male wild-type and Ahr[-/-] mice with a C57BL/6 background were weekly exposed to 50 μg/kg body weight of PCB126 for 8 weeks. Results showed that PCB126 had the opposite effect on gut microbiota composition and diversity in the wild-type and Ahr[-/-] mice. Functional prediction found that PCB126 exposure mainly altered carbon metabolism and signal regulatory pathways in wild-type mice but impacted DNA replication and lipopolysaccharide biosynthesis in Ahr[-/-] mice. In wild-type mice, PCB126 exposure induced liver injury, decreased serum lipid content, and delayed gastrointestinal motility, which were significantly correlated to several specific bacterial taxa, such as Helicobacter. Following AHR knockout, however, the holistic effects of PCB126 on the host were lessened or abolished. These results suggest that PCB126 may disrupt host metabolism and gut microbiota dynamics via AHR activation. Overall, our findings provide new insight into the complex interactions between host metabolism and gut microbiota, which may contribute to grouped assessment of environmental pollutants in the future.}, } @article {pmid35367655, year = {2022}, author = {Zhou, YY and Zhang, X and Pan, LY and Zhang, WW and Chen, F and Hu, SS and Jiang, HY}, title = {Fecal microbiota in pediatric depression and its relation to bowel habits.}, journal = {Journal of psychiatric research}, volume = {150}, number = {}, pages = {113-121}, doi = {10.1016/j.jpsychires.2022.03.037}, pmid = {35367655}, issn = {1879-1379}, mesh = {Adult ; Child ; *Depression ; Dysbiosis ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Habits ; Humans ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Although gut microbiota dysbiosis has been observed in the fecal samples of depressive adult patients, the detailed structure and composition of microbiota in pediatric depression remain unclear. To enhance our understanding of gut microbiota structure in depressive children, as well as the relationship between gut microbiota and bowel habits, we performed 16S rRNA sequencing to evaluate the gut microbial population in a cohort of 171 children (101 depressive patients and 70 controls) aged 12-18 years. Further analysis consisting of 30 drug-naive patients and 23 controls was performed to validate the results. Compared to controls, we found markedly decreased microbial richness and diversity, a distinct metagenomic composition with reduced short-chain fatty acid-producing bacteria (associated with healthy status), and overgrowth of bacteria such as Escherichia-Shigella and Flavonifractor in pediatric depression. Further analyses limited to drug-naive patients found similar results. Notably, we also observed that several taxa may be involved in the pathogenesis of disordered bowel habits in pediatric depression. Our findings suggest could inform future pediatric depression interventions specifically targeting the bacteria associated with bowel movements.}, } @article {pmid35366955, year = {2022}, author = {Li, PD and Zhu, ZR and Zhang, Y and Xu, J and Wang, H and Wang, Z and Li, H}, title = {The phyllosphere microbiome shifts toward combating melanose pathogen.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {56}, pmid = {35366955}, issn = {2049-2618}, mesh = {Bacteria/genetics ; *Melanosis ; *Microbiota ; Plant Leaves/microbiology ; Rhizosphere ; }, abstract = {BACKGROUND: Plants can recruit beneficial microbes to enhance their ability to defend against pathogens. However, in contrast to the intensively studied roles of the rhizosphere microbiome in suppressing plant pathogens, the collective community-level change and effect of the phyllosphere microbiome in response to pathogen invasion remains largely elusive.

RESULTS: Here, we integrated 16S metabarcoding, shotgun metagenomics and culture-dependent methods to systematically investigate the changes in phyllosphere microbiome between infected and uninfected citrus leaves by Diaporthe citri, a fungal pathogen causing melanose disease worldwide. Multiple microbiome features suggested a shift in phyllosphere microbiome upon D. citri infection, highlighted by the marked reduction of community evenness, the emergence of large numbers of new microbes, and the intense microbial network. We also identified the microbiome features from functional perspectives in infected leaves, such as enriched microbial functions for iron competition and potential antifungal traits, and enriched microbes with beneficial genomic characteristics. Glasshouse experiments demonstrated that several bacteria associated with the microbiome shift could positively affect plant performance under D. citri challenge, with reductions in disease index ranging from 65.7 to 88.4%. Among them, Pantoea asv90 and Methylobacterium asv41 identified as "recruited new microbes" in the infected leaves, exhibited antagonistic activities to D. citri both in vitro and in vivo, including inhibition of spore germination and/or mycelium growth. Sphingomonas spp. presented beneficial genomic characteristics and were found to be the main contributor for the functional enrichment of iron complex outer membrane receptor protein in the infected leaves. Moreover, Sphingomonas asv20 showed a stronger suppression ability against D. citri in iron-deficient conditions than iron-sufficient conditions, suggesting a role of iron competition during their antagonistic action.

CONCLUSIONS: Overall, our study revealed how phyllosphere microbiomes differed between infected and uninfected citrus leaves by melanose pathogen, and identified potential mechanisms for how the observed microbiome shift might have helped plants cope with pathogen pressure. Our findings provide novel insights into understanding the roles of phyllosphere microbiome responses during pathogen challenge. Video abstract.}, } @article {pmid35365687, year = {2022}, author = {Xie, Z and Yu, Z and Li, Y and Wang, G and Liu, X and Tang, C and Lian, T and Adams, J and Liu, J and Liu, J and Herbert, SJ and Jin, J}, title = {Soil microbial metabolism on carbon and nitrogen transformation links the crop-residue contribution to soil organic carbon.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {14}, pmid = {35365687}, issn = {2055-5008}, mesh = {Carbon ; *Microbiota ; Nitrogen ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {The beneficial effect of crop residue amendment on soil organic carbon (SOC) stock and stability depends on the functional response of soil microbial communities. Here we synchronized microbial metagenomic analysis, nuclear magnetic resonance and plant-[15]N labeling technologies to gain understanding of how microbial metabolic processes affect SOC accumulation in responses to differences in N supply from residues. Residue amendment brought increases in the assemblage of genes involved in C-degradation profiles from labile to recalcitrant C compounds as well as N mineralization. The N mineralization genes were correlated with the C and N accumulation in the particulate and mineral-associated C pools, and plant-derived aliphatic forms of SOC. Thus, the combined C and N metabolic potential of the microbial community transforms residue into persistent organic compounds, thereby increasing C and N sequestration in stable SOC pools. This study emphasizes potential microbially mediated mechanisms by which residue N affects C sequestration in soils.}, } @article {pmid35365192, year = {2022}, author = {Papaiakovou, M and Littlewood, DTJ and Doyle, SR and Gasser, RB and Cantacessi, C}, title = {Worms and bugs of the gut: the search for diagnostic signatures using barcoding, and metagenomics-metabolomics.}, journal = {Parasites & vectors}, volume = {15}, number = {1}, pages = {118}, pmid = {35365192}, issn = {1756-3305}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/T020733/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract ; Metabolomics ; Metagenomics ; *Microbiota ; }, abstract = {Gastrointestinal (GI) helminth infections cause significant morbidity in both humans and animals worldwide. Specific and sensitive diagnosis is central to the surveillance of such infections and to determine the effectiveness of treatment strategies used to control them. In this article, we: (i) assess the strengths and limitations of existing methods applied to the diagnosis of GI helminth infections of humans and livestock; (ii) examine high-throughput sequencing approaches, such as targeted molecular barcoding and shotgun sequencing, as tools to define the taxonomic composition of helminth infections; and (iii) discuss the current understanding of the interactions between helminths and microbiota in the host gut. Stool-based diagnostics are likely to serve as an important tool well into the future; improved diagnostics of helminths and their environment in the gut may assist the identification of biomarkers with the potential to define the health/disease status of individuals and populations, and to identify existing or emerging anthelmintic resistance.}, } @article {pmid35362813, year = {2022}, author = {Sharma, P and Singh, SP}, title = {Identification and profiling of microbial community from industrial sludge.}, journal = {Archives of microbiology}, volume = {204}, number = {4}, pages = {234}, pmid = {35362813}, issn = {1432-072X}, mesh = {Metagenome ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Sewage/microbiology ; }, abstract = {The purpose of this study is to identify microbial communities in pulp and paper industry sludge and their metagenomic profiling on the basis of; phylum, class, order, family, genus and species level. Results revealed that the dominant phyla in 16S rRNA Illumina Miseq analysis inside sludge were Anaerolinea, Pseudomonas, Clostridia, Bacteriodia, Gammaproteobacteria, Spirochetia, Deltaproteobacteria, Spirochaetaceae, Prolixibacteraceae and some unknown microbial strains are also dominant. Metagenomics is a molecular biology-based technology that uses bioinformatics to evaluate huge gene sequences extracted from environmental samples to assess the composition and function of microbiota. The results of metabarcoding of the V3-V4 16S rRNA regions acquired from paired-end Illumina MiSeq sequencing were used to analyze bacterial communities and structure. The present work demonstrates the potential approach to sludge treatment in the open environment via the naturally adapted microorganism, which could be an essential addition to the disposal site. In summary, these investigations indicate that the indigenous microbial community is an acceptable bioresource for remediation or detoxification following secondary treatment. This research aims at understanding the structure of microbial communities and their diversity (%) in highly contaminated sludge to perform in situ bioremediation.}, } @article {pmid35362479, year = {2022}, author = {Wensel, CR and Pluznick, JL and Salzberg, SL and Sears, CL}, title = {Next-generation sequencing: insights to advance clinical investigations of the microbiome.}, journal = {The Journal of clinical investigation}, volume = {132}, number = {7}, pages = {}, pmid = {35362479}, issn = {1558-8238}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; 27140/CRUK_/Cancer Research UK/United Kingdom ; R35 GM130151/GM/NIGMS NIH HHS/United States ; A27140/CRUK_/Cancer Research UK/United Kingdom ; R01 CA196845/CA/NCI NIH HHS/United States ; R56 DK107726/DK/NIDDK NIH HHS/United States ; }, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; }, abstract = {Next-generation sequencing (NGS) technology has advanced our understanding of the human microbiome by allowing for the discovery and characterization of unculturable microbes with prediction of their function. Key NGS methods include 16S rRNA gene sequencing, shotgun metagenomic sequencing, and RNA sequencing. The choice of which NGS methodology to pursue for a given purpose is often unclear for clinicians and researchers. In this Review, we describe the fundamentals of NGS, with a focus on 16S rRNA and shotgun metagenomic sequencing. We also discuss pros and cons of each methodology as well as important concepts in data variability, study design, and clinical metadata collection. We further present examples of how NGS studies of the human microbiome have advanced our understanding of human disease pathophysiology across diverse clinical contexts, including the development of diagnostics and therapeutics. Finally, we share insights as to how NGS might further be integrated into and advance microbiome research and clinical care in the coming years.}, } @article {pmid35361114, year = {2022}, author = {Rudar, J and Porter, TM and Wright, M and Golding, GB and Hajibabaei, M}, title = {LANDMark: an ensemble approach to the supervised selection of biomarkers in high-throughput sequencing data.}, journal = {BMC bioinformatics}, volume = {23}, number = {1}, pages = {110}, pmid = {35361114}, issn = {1471-2105}, support = {RGPIN-2020-05733//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Algorithms ; Biomarkers ; *High-Throughput Nucleotide Sequencing ; Machine Learning ; Support Vector Machine ; }, abstract = {BACKGROUND: Identification of biomarkers, which are measurable characteristics of biological datasets, can be challenging. Although amplicon sequence variants (ASVs) can be considered potential biomarkers, identifying important ASVs in high-throughput sequencing datasets is challenging. Noise, algorithmic failures to account for specific distributional properties, and feature interactions can complicate the discovery of ASV biomarkers. In addition, these issues can impact the replicability of various models and elevate false-discovery rates. Contemporary machine learning approaches can be leveraged to address these issues. Ensembles of decision trees are particularly effective at classifying the types of data commonly generated in high-throughput sequencing (HTS) studies due to their robustness when the number of features in the training data is orders of magnitude larger than the number of samples. In addition, when combined with appropriate model introspection algorithms, machine learning algorithms can also be used to discover and select potential biomarkers. However, the construction of these models could introduce various biases which potentially obfuscate feature discovery.

RESULTS: We developed a decision tree ensemble, LANDMark, which uses oblique and non-linear cuts at each node. In synthetic and toy tests LANDMark consistently ranked as the best classifier and often outperformed the Random Forest classifier. When trained on the full metabarcoding dataset obtained from Canada's Wood Buffalo National Park, LANDMark was able to create highly predictive models and achieved an overall balanced accuracy score of 0.96 ± 0.06. The use of recursive feature elimination did not impact LANDMark's generalization performance and, when trained on data from the BE amplicon, it was able to outperform the Linear Support Vector Machine, Logistic Regression models, and Stochastic Gradient Descent models (p ≤ 0.05). Finally, LANDMark distinguishes itself due to its ability to learn smoother non-linear decision boundaries.

CONCLUSIONS: Our work introduces LANDMark, a meta-classifier which blends the characteristics of several machine learning models into a decision tree and ensemble learning framework. To our knowledge, this is the first study to apply this type of ensemble approach to amplicon sequencing data and we have shown that analyzing these datasets using LANDMark can produce highly predictive and consistent models.}, } @article {pmid35360922, year = {2022}, author = {Kaiser, T and Jahansouz, C and Staley, C}, title = {Network-based approaches for the investigation of microbial community structure and function using metagenomics-based data.}, journal = {Future microbiology}, volume = {17}, number = {}, pages = {621-631}, doi = {10.2217/fmb-2021-0219}, pmid = {35360922}, issn = {1746-0921}, mesh = {Host Microbial Interactions ; *Metagenomics/methods ; *Microbiota ; }, abstract = {Network-based approaches offer a powerful framework to evaluate microbial community organization and function as it relates to a variety of environmental processes. Emerging studies are exploring network theory as a method for data integration that is likely to be critical for the integration of 'omics' data using systems biology approaches. Intricacies of network theory and methodological and computational complexities in network construction, however, impede the use of these tools for translational science. We provide a perspective on the methods of network construction, interpretation and emerging uses for these techniques in understanding host-microbiota interactions.}, } @article {pmid35358556, year = {2022}, author = {Wang, PH and Chen, YL and Wu, TY and Wu, YW and Wang, TY and Shih, CJ and Wei, ST and Lai, YL and Liu, CX and Chiang, YR}, title = {Omics and mechanistic insights into di-(2-ethylhexyl) phthalate degradation in the O2-fluctuating estuarine sediments.}, journal = {Chemosphere}, volume = {299}, number = {}, pages = {134406}, doi = {10.1016/j.chemosphere.2022.134406}, pmid = {35358556}, issn = {1879-1298}, mesh = {Biodegradation, Environmental ; *Diethylhexyl Phthalate/metabolism ; *Phthalic Acids/metabolism ; Thauera ; }, abstract = {Di-(2-ethylhexyl) phthalate (DEHP) represents the most used phthalate plasticizer with an annual production above the millions of tons worldwide. Due to its inadequate disposal, outstanding chemical stability, and extremely low solubility (3 mg/L), endocrine-disrupting DEHP often accumulates in urban estuarine sediments at concentrations above the predicted no-effect concentration (20-100 mg/kg). Our previous study suggested that microbial DEHP degradation in estuarine sediments proceeds synergistically where DEHP side-chain hydrolysis to form phthalic acid represents a bottleneck. Here, we resolved this bottleneck and deconstructed the microbial synergy in O2-fluctuating estuarine sediments. Metagenomic analysis and RNA sequencing suggested that orthologous genes encoding extracellular DEHP hydrolase NCU65476 in Acidovorax sp. strain 210-6 are often flanked by the co-expressed composite transposon and are widespread in aquatic environments worldwide. Therefore, we developed a turbidity-based microplate assay to characterize NCU65476. The optimized assay conditions (with 1 mM Ca[2+] and pH 6.0) increased the DEHP hydrolysis rate by a factor of 10. Next, we isolated phthalic acid-degrading Hydrogenophaga spp. and Thauera chlorobenzoica from Guandu estuarine sediment to study the effect of O2(aq) on their metabolic synergy with strain 210-6. The results of co-culture experiments suggested that after DEHP side-chain hydrolysis by strain 210-6, phthalic acid can be degraded by Hydrogenophaga sp. when O2(aq) is above 1 mg/L or degraded by Thauera chlorobenzoica anaerobically. Altogether, our data demonstrates that DEHP could be degraded synergistically in estuarine sediments via divergent pathways responding to O2 availability. The optimized conditions for NCU65476 could facilitate the practice of DEHP bioremediation in estuarine sediments.}, } @article {pmid35355372, year = {2022}, author = {Lugli, GA and Longhi, G and Mancabelli, L and Alessandri, G and Tarracchini, C and Fontana, F and Turroni, F and Milani, C and van Sinderen, D and Ventura, M}, title = {Tap water as a natural vehicle for microorganisms shaping the human gut microbiome.}, journal = {Environmental microbiology}, volume = {24}, number = {9}, pages = {3912-3923}, pmid = {35355372}, issn = {1462-2920}, mesh = {Bacteria/genetics ; *Drinking Water ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Fresh potable water is an indispensable drink which humans consume daily in substantial amounts. Nonetheless, very little is known about the composition of the microbial community inhabiting drinking water or its impact on our gut microbiota. In the current study, an exhaustive shotgun metagenomics analysis of the tap water microbiome highlighted the occurrence of a highly genetic biodiversity of the microbial communities residing in fresh water and the existence of a conserved core tap water microbiota largely represented by novel microbial species, representing microbial dark matter. Furthermore, genome reconstruction of this microbial dark matter from water samples unveiled homologous sequences present in the faecal microbiome of humans from various geographical locations. Accordingly, investigation of the faecal microbiota content of a subject that daily consumed tap water for 3 years provides proof for horizontal transmission and colonization of water bacteria in the human gut.}, } @article {pmid35354850, year = {2022}, author = {Tilahun, Y and Pinango, JQ and Johnson, F and Lett, C and Smith, K and Gipson, T and McCallum, M and Hoyt, P and Tritt, A and Yadav, A and Elshahed, M and Wang, Z}, title = {Transcript and blood-microbiome analysis towards a blood diagnostic tool for goats affected by Haemonchus contortus.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {5362}, pmid = {35354850}, issn = {2045-2322}, mesh = {Animals ; Goats ; *Haemonchiasis/veterinary ; *Haemonchus/genetics ; Hematologic Tests ; Male ; *Microbiota/genetics ; }, abstract = {The Alpine goat (Capra aegagrus hircus) is parasitized by the barber pole worm (Haemonchus contortus). Hematological parameters from transcript and metagenome analysis in the host are reflective of infestation. We explored comparisons between blood samples of control, infected, infected zoledronic acid-treated, and infected antibody (anti-γδ T cells) treated wethers under controlled conditions. Seven days post-inoculation (dpi), we identified 7,627 transcripts associated with the different treatment types. Microbiome measurements at 7 dpi revealed fewer raw read counts across all treatments and a less diverse microbial flora than at 21 dpi. This study identifies treatment specific transcripts and an increase in microflora abundance and diversity as wethers age. Further, F/B ratio reflect health, based on depression or elevation above thresholds defined by the baseline of non-infected controls. Forty Alpine wethers were studied where blood samples were collected from five goats in four treatment groups on 7 dpi and 21 dpi. Transcript and microbiome profiles were obtained using the Partek Flow (St. Louis, Missouri, USA) software suites pipelines. Inflammation comparisons were based on the Firmicutes/Bacteriodetes ratios that are calculated as well as the reduction of microbial diversity.}, } @article {pmid35354069, year = {2022}, author = {Liu, Y and Méric, G and Havulinna, AS and Teo, SM and Åberg, F and Ruuskanen, M and Sanders, J and Zhu, Q and Tripathi, A and Verspoor, K and Cheng, S and Jain, M and Jousilahti, P and Vázquez-Baeza, Y and Loomba, R and Lahti, L and Niiranen, T and Salomaa, V and Knight, R and Inouye, M}, title = {Early prediction of incident liver disease using conventional risk factors and gut-microbiome-augmented gradient boosting.}, journal = {Cell metabolism}, volume = {34}, number = {5}, pages = {719-730.e4}, pmid = {35354069}, issn = {1932-7420}, support = {BRC-1215-20014/DH_/Department of Health/United Kingdom ; UL1 TR001442/TR/NCATS NIH HHS/United States ; P42 ES010337/ES/NIEHS NIH HHS/United States ; RG/18/13/33946/BHF_/British Heart Foundation/United Kingdom ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 DK124318/DK/NIDDK NIH HHS/United States ; U01 DK061734/DK/NIDDK NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R01 DK121378/DK/NIDDK NIH HHS/United States ; RG/13/13/30194/BHF_/British Heart Foundation/United Kingdom ; R01 DK106419/DK/NIDDK NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Liver Diseases ; Metagenomics ; *Microbiota ; Prospective Studies ; Risk Factors ; }, abstract = {The gut microbiome has shown promise as a predictive biomarker for various diseases. However, the potential of gut microbiota for prospective risk prediction of liver disease has not been assessed. Here, we utilized shallow shotgun metagenomic sequencing of a large population-based cohort (N > 7,000) with ∼15 years of follow-up in combination with machine learning to investigate the predictive capacity of gut microbial predictors individually and in conjunction with conventional risk factors for incident liver disease. Separately, conventional and microbial factors showed comparable predictive capacity. However, microbiome augmentation of conventional risk factors using machine learning significantly improved the performance. Similarly, disease-free survival analysis showed significantly improved stratification using microbiome-augmented models. Investigation of predictive microbial signatures revealed previously unknown taxa for liver disease, as well as those previously associated with hepatic function and disease. This study supports the potential clinical validity of gut metagenomic sequencing to complement conventional risk factors for prediction of liver diseases.}, } @article {pmid35353011, year = {2022}, author = {Jaffe, AL and Fuster, M and Schoelmerich, MC and Chen, LX and Colombet, J and Billard, H and Sime-Ngando, T and Banfield, JF}, title = {Long-Term Incubation of Lake Water Enables Genomic Sampling of Consortia Involving Planctomycetes and Candidate Phyla Radiation Bacteria.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0022322}, pmid = {35353011}, issn = {2379-5077}, mesh = {Humans ; *Planctomycetes ; Lakes/microbiology ; Metagenomics ; Phylogeny ; Bacteria ; Genomics ; *Microbiota ; Water/metabolism ; }, abstract = {Microbial communities in lakes can profoundly impact biogeochemical processes through their individual activities and collective interactions. However, the complexity of these communities poses challenges, particularly for studying rare organisms such as Candidate Phyla Radiation bacteria (CPR) and enigmatic entities such as aster-like nanoparticles (ALNs). Here, a reactor was inoculated with water from Lake Fargette, France, and maintained under dark conditions at 4°C for 31 months and enriched for ALNs, diverse Planctomycetes, and CPR bacteria. We reconstructed draft genomes and predicted metabolic traits for 12 diverse Planctomycetes and 9 CPR bacteria, some of which are likely representatives of undescribed families or genera. One CPR genome representing the little-studied lineage "Candidatus Peribacter" was curated to completion (1.239 Mbp) and unexpectedly encodes the full gluconeogenesis pathway. Metatranscriptomic data indicate that some planctomycetes and CPR bacteria were active under the culture conditions, accounting for ∼30% and ∼1% of RNA reads mapping to the genome set, respectively. We also reconstructed genomes and obtained transmission electron microscope images for numerous viruses, including one with a >300-kbp genome and several predicted to infect Planctomycetes. Together, our analyses suggest that freshwater Planctomycetes are central players in a subsystem that includes ALNs, symbiotic CPR bacteria, and viruses. IMPORTANCE Laboratory incubations of natural microbial communities can aid in the study of member organisms and their networks of interaction. This is particularly important for understudied lineages for which key elements of basic biology are still emerging. Using genomics and microscopy, we found that members of the bacterial lineage Planctomycetes may be central players in a subset of a freshwater lake microbiome that includes other bacteria, archaea, viruses, and mysterious entities, called aster-like nanoparticles (ALNs), whose origin is unknown. Our results help constrain the possible origins of ALNs and provide insight into possible interactions within a complex lake ecosystem.}, } @article {pmid35352015, year = {2022}, author = {Speth, DR and Yu, FB and Connon, SA and Lim, S and Magyar, JS and Peña-Salinas, ME and Quake, SR and Orphan, VJ}, title = {Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily.}, journal = {The ISME journal}, volume = {16}, number = {7}, pages = {1750-1764}, pmid = {35352015}, issn = {1751-7370}, support = {019.153LW.039//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 51250//John Templeton Foundation (JTF)/ ; DE-SC0016469//DOE | Office of Science (SC)/ ; }, mesh = {Geologic Sediments/microbiology ; *Hydrothermal Vents/microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physicochemical data and 16S rRNA gene amplicons to characterize the sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 30% of those currently known, showing the microbial community in Auka hydrothermal sediments is highly diverse. 16S rRNA gene amplicon screening of 224 sediment samples across the vent field indicates that the MAGs retrieved from a single site are representative of the microbial community in the vent field sediments. Metabolic reconstruction of a vent-specific, deeply branching clade within the Desulfobacterota suggests these organisms metabolize sulfur using novel octaheme cytochrome-c proteins related to hydroxylamine oxidoreductase. Community-wide comparison between Auka MAGs and MAGs from Guaymas Basin revealed a remarkable 20% species-level overlap, suggestive of long-distance species transfer over 400 km and subsequent sediment colonization. Optimal growth temperature prediction on the Auka MAGs, and thousands of reference genomes, shows that thermophily is a trait that has evolved frequently. Taken together, our Auka vent field results offer new perspectives on our understanding of hydrothermal vent microbiology.}, } @article {pmid35350209, year = {2022}, author = {De Maio, N and Kalaghatgi, P and Turakhia, Y and Corbett-Detig, R and Minh, BQ and Goldman, N}, title = {Maximum likelihood pandemic-scale phylogenetics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {35350209}, issn = {2692-8205}, support = {R35 GM128932/GM/NIGMS NIH HHS/United States ; }, abstract = {Phylogenetics plays a crucial role in the interpretation of genomic data[1]. Phylogenetic analyses of SARS-CoV-2 genomes have allowed the detailed study of the virus's origins[2], of its international[3,4] and local[4-9] spread, and of the emergence[10] and reproductive success[11] of new variants, among many applications. These analyses have been enabled by the unparalleled volumes of genome sequence data generated and employed to study and help contain the pandemic[12]. However, preferred model-based phylogenetic approaches including maximum likelihood and Bayesian methods, mostly based on Felsenstein's 'pruning' algorithm[13,14], cannot scale to the size of the datasets from the current pandemic[4,15], hampering our understanding of the virus's evolution and transmission[16]. We present new approaches, based on reworking Felsenstein's algorithm, for likelihood-based phylogenetic analysis of epidemiological genomic datasets at unprecedented scales. We exploit near-certainty regarding ancestral genomes, and the similarities between closely related and densely sampled genomes, to greatly reduce computational demands for memory and time. Combined with new methods for searching amongst candidate evolutionary trees, this results in our MAPLE ('MAximum Parsimonious Likelihood Estimation') software giving better results than popular approaches such as FastTree 2[17], IQ-TREE 2[18], RAxML-NG[19] and UShER[15]. Our approach therefore allows complex and accurate probabilistic phylogenetic analyses of millions of microbial genomes, extending the reach of genomic epidemiology. Future epidemiological datasets are likely to be even larger than those currently associated with COVID-19, and other disciplines such as metagenomics and biodiversity science are also generating huge numbers of genome sequences[20-22]. Our methods will permit continued use of preferred likelihood-based phylogenetic analyses.}, } @article {pmid35349787, year = {2022}, author = {Olsson, LM and Boulund, F and Nilsson, S and Khan, MT and Gummesson, A and Fagerberg, L and Engstrand, L and Perkins, R and Uhlén, M and Bergström, G and Tremaroli, V and Bäckhed, F}, title = {Dynamics of the normal gut microbiota: A longitudinal one-year population study in Sweden.}, journal = {Cell host & microbe}, volume = {30}, number = {5}, pages = {726-739.e3}, doi = {10.1016/j.chom.2022.03.002}, pmid = {35349787}, issn = {1934-6069}, mesh = {Bacteria/genetics ; Bifidobacterium/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Sweden ; }, abstract = {Temporal dynamics of the gut microbiota potentially limit the identification of microbial features associated with health status. Here, we used whole-genome metagenomic and 16S rRNA gene sequencing to characterize the intra- and inter-individual variations of gut microbiota composition and functional potential of a disease-free Swedish population (n = 75) over one year. We found that 23% of the total compositional variance was explained by intra-individual variation. The degree of intra-individual compositional variability was negatively associated with the abundance of Faecalibacterium prausnitzii (a butyrate producer) and two Bifidobacterium species. By contrast, the abundance of facultative anaerobes and aerotolerant bacteria such as Escherichia coli and Lactobacillus acidophilus varied extensively, independent of compositional stability. The contribution of intra-individual variance to the total variance was greater for functional pathways than for microbial species. Thus, reliable quantification of microbial features requires repeated samples to address the issue of intra-individual variations of the gut microbiota.}, } @article {pmid35348284, year = {2022}, author = {Griswold, CK}, title = {A dynamic ancestral graph model and GPU-based simulation of a community based on metagenomic sampling.}, journal = {Molecular ecology resources}, volume = {22}, number = {6}, pages = {2429-2442}, doi = {10.1111/1755-0998.13613}, pmid = {35348284}, issn = {1755-0998}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; //Canadian Foundation for Innovation/ ; }, mesh = {Biota ; *Metagenome ; *Metagenomics ; Selection, Genetic ; }, abstract = {In this paper, we present an ancestral graph model of the evolution of a guild in an ecological community. The model is based on a metagenomic sampling design in that a random sample is taken at the community, as opposed the taxon, level and species are discovered by genetic sequencing. The specific implementation of the model envisions an ecological guild that was founded by colonization at some point in the past that then potentially undergoes diversification by natural selection. Within the graph, species emerge and evolve through the diversification process and their densities in the graph are dynamic and governed by both ecological drift and random genetic drift, as well as differential viability. We employ the 3% sequence divergence rule at a marker locus to identify operational taxonomic units. We then explore approaches to see whether there are indirect signals of the diversification process, including population genetic and ecological approaches. In terms of population genetics, we study the joint site frequency spectrum of OTUs, as well its associated statistics. In terms of ecology, we study the species (or OTU) abundance distribution. For both, we observe deviations from neutrality, which indicates that there may be signals of diversifying selection in metagenomic studies under certain conditions. The model is available as a GPU-based computer program in C/C++ and using OpenCL, with the long-term goal of adding functionality iteratively to model large-scale eco-evolutionary processes for metagenomic data.}, } @article {pmid35346845, year = {2022}, author = {Chen, J and Wang, M and Zhang, P and Li, H and Qu, K and Xu, R and Guo, N and Zhu, H}, title = {Cordycepin alleviated metabolic inflammation in Western diet-fed mice by targeting intestinal barrier integrity and intestinal flora.}, journal = {Pharmacological research}, volume = {178}, number = {}, pages = {106191}, doi = {10.1016/j.phrs.2022.106191}, pmid = {35346845}, issn = {1096-1186}, mesh = {Animals ; Deoxyadenosines ; Diet, High-Fat/adverse effects ; Diet, Western/adverse effects ; *Gastrointestinal Microbiome ; Inflammation/complications/drug therapy ; Lipopolysaccharides/pharmacology ; Mice ; Mice, Inbred C57BL ; Obesity/metabolism ; }, abstract = {Metabolic inflammation is a crucial factor in the pathogenesis of obesity and promotes related complications. Accumulating evidence has indicated that regulating intestinal integrity and the gut microbiota may be new treatment strategies for metabolic inflammation and obesity. Cordycepin has been reported to improve obesity, but the mechanism is not yet clear. Here, we showed that cordycepin considerably alleviated systemic inflammation while reducing body weight gain and metabolic disorders in Western diet (WD)-fed mice. Further investigations showed that cordycepin significantly ameliorated WD-induced damage to the intestinal barrier and decreased the leakage of lipopolysaccharide (LPS) into the blood in mice by suppressing intestinal inflammation, oxidative stress damage, and decreasing intestinal epithelial cell apoptosis and pyroptosis. In addition, by using metagenomic sequencing, we found that cordycepin could also regulate the homeostasis of intestinal flora, including selectively increasing the abundance of Akkermansia muciniphila and reducing the production of fecal LPS. Besides, we demonstrated that the intestinal flora partially mediated the beneficial effects of cordycepin on improving intestinal barrier function, and obesity-related symptoms in WD-fed mice by a fecal microbiota transplantation experiment. Hence, our findings provided new insights into the role of cordycepin in improving metabolic inflammation and obesity from the perspective of regulating the intestinal barrier function and intestinal flora, and further provided data support for the utility of cordycepin in the treatment of obesity and its complications.}, } @article {pmid35346469, year = {2022}, author = {Liu, Y and Zhang, F}, title = {Changes of antibiotic resistance genes and gut microbiota after the ingestion of goat milk.}, journal = {Journal of dairy science}, volume = {105}, number = {6}, pages = {4804-4817}, doi = {10.3168/jds.2021-21325}, pmid = {35346469}, issn = {1525-3198}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Eating ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Goats ; Male ; Mice ; Milk ; }, abstract = {Antibiotic resistance genes, as newly emerging contaminants, have become a serious challenge to public health through the food chain. The gut of humans and animals is an important reservoir for the development and dissemination of antibiotic resistance genes because of the great abundance and diversity of intestinal microbiota. In the present study, we evaluated the influence of goat milk on the diversity and abundance of antibiotic resistance genes and gut microbial communities, especially pathogenic bacteria. Male mice were used, 12 for each of the 2 groups: a control group that received sterile distilled water and a treated group that received goat milk, and gut microbiota and antibiotic resistance genes were compared in these groups using metagenomic analysis. The results revealed that ingestion of goat milk decreased the diversity and abundance of antibiotic resistance genes in the mice gut. The relative abundance of fluoroquinolone, peptide, macrolide, and β-lactam resistance genes in the total microbial genes significantly decreased after the intervention. Goat milk intake also significantly reduced the abundance of pathogenic bacteria, such as Clostridium bolteae, Clostridium symbiosum, Helicobacter cinaedi, and Helicobacter bilis. Therefore, goat milk intake might decrease the transfer potential of antibiotic resistance gene to pathogenic bacteria in the gut. In addition, bacteria with multiple resistance mechanisms accounted for approximately 4.5% of total microbial communities in the control group, whereas it was not detectable in the goat milk group, indicating the total inhibition by goat milk intake. This study highlights the influence of goat milk on antibiotic resistome and microbial communities in the gut, and provides a new insight into the function of goat milk for further study.}, } @article {pmid35346308, year = {2022}, author = {Söder, J and Wernersson, S and Höglund, K and Hagman, R and Lindåse, S and Dicksved, J}, title = {Composition and short-term stability of gut microbiota in lean and spontaneously overweight healthy Labrador retriever dogs.}, journal = {Acta veterinaria Scandinavica}, volume = {64}, number = {1}, pages = {8}, pmid = {35346308}, issn = {1751-0147}, mesh = {Animals ; *Dog Diseases ; Dogs ; Feces ; *Gastrointestinal Microbiome/genetics ; Male ; Obesity/veterinary ; Overweight/veterinary ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: The gut microbiota and its metabolic end-products act in close collaboration with the nutrient metabolism of the animal. A relationship between excess adiposity and alterations in gut microbiota composition has been identified in humans and rodents, but data are scarce for overweight dogs. This study compared composition and temporal variations of gut microbiota in healthy lean and spontaneously overweight dogs. The analysis was based on three individual fresh faeces samples from each dog during a 10-day period. Twenty-seven healthy and intact male Labrador retriever dogs were included, 12 of which were classified as lean (body condition score (BCS) 4-5 on a 9-point scale) and 15 as overweight (BCS 6-8). Gut microbiota was analysed by Illumina sequencing of the V3-V4 region of the 16S rRNA gene.

RESULTS: Lean and overweight groups of dogs were not separated by principal coordinate analysis (PCoA), analysis of similarity (one-way ANOSIM, P = 0.99) or species indicator analysis (IndVal) using operational taxonomic units (OTU) data. Gut microbial taxa at phylum, family or genus level did not differ between lean and overweight dogs in mixed-model repeated measures analyses. Short-term stability, evaluated by similarity index, did not differ between lean and overweight dogs over the 10-day period. Pooled Firmicutes/Bacteroidetes (F/B) ratio was 3.1 ± 3.7 in overweight dogs and 2.1 ± 1.2 in lean dogs (P = 0.83). Individual dogs, irrespective of body condition (lean or overweight), displayed variation in mean alpha diversity (Chao-1 index range 122-245, Shannon index range 2.6-3.6) and mean similarity index (range 44-85%).

CONCLUSIONS: Healthy lean and spontaneously overweight Labrador retriever dogs had comparable gut microbiota composition and short-term stability over a 10-day sampling period. There were no alterations in microbial diversity or in relative abundance of specific taxa at phylum, family or genus level in overweight compared to lean dogs. Our findings suggest that there are few detectable differences in gut microbiota composition between healthy spontaneously overweight and lean dogs by the current method. Future application of metagenomic or metabolomic techniques could be used to investigate microbial genes or microbial end-products that may differ even when microbiota compositional analyses fail to detect a significant difference between lean and overweight dogs.}, } @article {pmid35345588, year = {2022}, author = {Gilroy, R and Leng, J and Ravi, A and Adriaenssens, EM and Oren, A and Baker, D and La Ragione, RM and Proudman, C and Pallen, MJ}, title = {Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic diversity.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13084}, pmid = {35345588}, issn = {2167-8359}, support = {BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10351/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Horses ; Metagenome/genetics ; Metagenomics ; *Microbiota ; Bacteria/genetics ; Archaea/genetics ; Mammals ; *Bacteriophages ; }, abstract = {BACKGROUND: The horse plays crucial roles across the globe, including in horseracing, as a working and companion animal and as a food animal. The horse hindgut microbiome makes a key contribution in turning a high fibre diet into body mass and horsepower. However, despite its importance, the horse hindgut microbiome remains largely undefined. Here, we applied culture-independent shotgun metagenomics to thoroughbred equine faecal samples to deliver novel insights into this complex microbial community.

RESULTS: We performed metagenomic sequencing on five equine faecal samples to construct 123 high- or medium-quality metagenome-assembled genomes from Bacteria and Archaea. In addition, we recovered nearly 200 bacteriophage genomes. We document surprising taxonomic diversity, encompassing dozens of novel or unnamed bacterial genera and species, to which we have assigned new Candidatus names. Many of these genera are conserved across a range of mammalian gut microbiomes.

CONCLUSIONS: Our metagenomic analyses provide new insights into the bacterial, archaeal and bacteriophage components of the horse gut microbiome. The resulting datasets provide a key resource for future high-resolution taxonomic and functional studies on the equine gut microbiome.}, } @article {pmid35344714, year = {2022}, author = {Li, MX and Li, MY and Lei, JX and Wu, YZ and Li, ZH and Chen, LM and Zhou, CL and Su, JY and Huang, GX and Huang, XQ and Zheng, XB}, title = {Huangqin decoction ameliorates DSS-induced ulcerative colitis: Role of gut microbiota and amino acid metabolism, mTOR pathway and intestinal epithelial barrier.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {100}, number = {}, pages = {154052}, doi = {10.1016/j.phymed.2022.154052}, pmid = {35344714}, issn = {1618-095X}, mesh = {Amino Acids/metabolism ; Animals ; *Colitis/chemically induced/drug therapy/metabolism ; *Colitis, Ulcerative/chemically induced/drug therapy/metabolism ; Colon/pathology ; Dextran Sulfate/adverse effects ; Disease Models, Animal ; *Drugs, Chinese Herbal/therapeutic use ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred C57BL ; Scutellaria baicalensis/chemistry ; TOR Serine-Threonine Kinases/metabolism ; }, abstract = {BACKGROUND: The clinical treatment of ulcerative colitis (UC) is limited. A traditional Chinese medicinal formula, Huangqin decoction (HQD), is chronicled in Shang Han Lun and is widely used to ameliorate gastrointestinal disorders, such as UC; however, its mechanism is yet to be clarified.

PURPOSE: The present study aimed to investigate the effect of HQD on 7-day colitis induced by 3% dextran sulfate sodium (DSS) in mice and further explore the inhibitory effect of metabolites on DSS-damaged FHC cells.

METHODS: The therapeutic efficacy of HQD was evaluated in a well-established DSS-induced colitis mice model. The clinical symptoms were analyzed, and biological samples were collected for microscopic examination, metabolomics, metagenomics, and the evaluation of the epithelial barrier function. The mechanism of metabolites regulated by HQD was evaluated in the DSS-induced FHC cell damage model. The samples were collected to detect the physiological functions of the cells.

RESULTS: HQD suppressed the inflammation of DSS-induced colitis in vivo, attenuated DSS-induced clinical manifestations, reversed colon length reduction, and reduced histological injury. After HQD treatment, the DSS-induced gut dysbiosis was modulated, and the gut microbiota achieved a new equilibrium state. In addition, HQD activated the mTOR signaling pathway by upregulating amino acid metabolism. Significant phosphorylation of S6 and 4E-BP1 ameliorated intestinal epithelial barrier dysfunction. Moreover, HQD-regulated metabolites protected the epithelial barrier integrity by inhibiting DSS-induced apoptosis of FHC cells and regulating the proteins affecting apoptosis and cell-cell junction.

CONCLUSIONS: These findings indicated that the mechanism of HQD was related to regulating the gut microbiota and amino acid metabolism, activating the mTOR signaling pathway, and protecting the intestinal mucosal barrier integrity.}, } @article {pmid35344623, year = {2022}, author = {Li, C and Liao, H and Xu, L and Wang, C and He, N and Wang, J and Li, X}, title = {The adjustment of life history strategies drives the ecological adaptations of soil microbiota to aridity.}, journal = {Molecular ecology}, volume = {31}, number = {10}, pages = {2920-2934}, doi = {10.1111/mec.16445}, pmid = {35344623}, issn = {1365-294X}, mesh = {Ecosystem ; Glucosidases ; *Life History Traits ; *Microbiota/genetics ; Soil ; Soil Microbiology ; }, abstract = {Soil microbiota increase their fitness to local habitats by adjusting their life history strategies. Yet, how such adjustments drive their ecological adaptations in xeric grasslands remains elusive. In this study, shifts in the traits that potentially represent microbial life history strategies were studied along two aridity gradients with different climates using metagenomic and trait-based approaches. The results indicated that resource acquisition (e.g., higher activities of β-d-glucosidase and N-acetyl-β-d-glucosidase, higher degradation rates of cellulose and chitin, as well as genes involved in cell motility, biodegradation, transportation and competition) and growth yield (e.g., higher biomass and respiration) strategies were depleted at higher aridity. However, maintenance of cellular and high growth potential (e.g., higher metabolic quotients and genes related to DNA replication, transcription, translation, central carbon metabolism and biosynthesis) and stress tolerance (e.g., genes involved in DNA damage repair, cation transportation, sporulation and osmolyte biosynthesis) strategies were enriched at higher aridity. This implied that microbiota have lower growth yields but are probably well primed for rapid responses to pulses of rainfall in more arid soils, whereas those in less arid soils may have stronger resource acquisition and growth yield abilities. By integrating a large amount of evidence from taxonomic, metagenomic, genomic and biochemical investigations, this study demonstrates that the ecological adaptations of soil microbiota to aridity made by adjusting and optimizing their life history strategies are universal in xeric grasslands and provides an underlying mechanistic understanding of soil microbial responses to climate changes.}, } @article {pmid35344283, year = {2022}, author = {Testerman, T and Li, Z and Galuppo, B and Graf, J and Santoro, N}, title = {Insights from shotgun metagenomics into bacterial species and metabolic pathways associated with NAFLD in obese youth.}, journal = {Hepatology communications}, volume = {6}, number = {8}, pages = {1962-1974}, pmid = {35344283}, issn = {2471-254X}, support = {R01 DK114504/DK/NIDDK NIH HHS/United States ; R18 DK113403/DK/NIDDK NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolic Networks and Pathways/genetics ; Metagenomics ; *Non-alcoholic Fatty Liver Disease/genetics ; Obesity/complications ; }, abstract = {Nonalcoholic fatty liver disease (NAFLD) is the most common form of liver disease and is often the precursor for more serious liver conditions such as nonalcoholic steatohepatitis and cirrhosis. Although the gut microbiome has been implicated in the development of NAFLD, the strong association of obesity with NAFLD and its effect on microbiome structure has made interpreting study outcomes difficult. In the present study, we examined the taxonomic and functional differences between the microbiomes of youth with obesity and with and without NAFLD. Shotgun metagenome sequencing was performed to profile the microbiomes of 36 subjects, half of whom were diagnosed with NAFLD using abdominal magnetic resonance imaging. Beta diversity analysis showed community-wide differences between the groups (p = 0.002). Specific taxonomic differences included increased relative abundances of the species Fusicatenibacter saccharivorans (p = 0.042), Romboutsia ilealis (p = 0.046), and Actinomyces sp. ICM47 (p = 0.0009), and a decrease of Bacteroides thetaiotamicron (p = 0.0002), in the NAFLD group as compared with the non-NAFLD group. At the phylum level, Bacteroidetes (p < 0.0001) was decreased in the NAFLD group. Functionally, branched-chain amino acid (p = 0.01343) and aromatic amino acid (p = 0.01343) synthesis pathways had increased relative abundances in the NAFLD group along with numerous energy use pathways, including pyruvate fermentation to acetate (p = 0.01318). Conclusion: Community-wide differences were noted based on NAFLD status, and individual bacterial species along with specific metabolic pathways were identified as potential drivers of these differences. The results of the present study support the idea that the NAFLD phenotype displays a differentiated microbial and functional signature from the obesity phenotype.}, } @article {pmid35343798, year = {2022}, author = {Kaelin, EA and Skidmore, PT and Łaniewski, P and Holland, LA and Chase, DM and Herbst-Kralovetz, MM and Lim, ES}, title = {Cervicovaginal DNA Virome Alterations Are Associated with Genital Inflammation and Microbiota Composition.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0006422}, pmid = {35343798}, issn = {2379-5077}, support = {R00 DK107923/DK/NIDDK NIH HHS/United States ; R01 HD092311/HD/NICHD NIH HHS/United States ; }, mesh = {Female ; Humans ; *Uterine Cervical Neoplasms ; Virome ; *Papillomavirus Infections/microbiology ; Pilot Projects ; Cervix Uteri/microbiology ; Inflammation ; *Microbiota ; DNA ; *Bacteriophages ; Tumor Microenvironment ; }, abstract = {While the link between the cervicovaginal bacterial microbiome, human papillomavirus (HPV) infection, and cervical cancer is recognized (P. Łaniewski, D. Barnes, A. Goulder, H. Cui, et al., Sci. Rep. 8:7593, 2018, http://dx.doi.org/10.1038/s41598-018-25879-7; A. Mitra, D. A. MacIntyre, Y. S. Lee, A. Smith, et al., Sci. Rep. 5:16865, 2015, http://dx.doi.org/10.1038/srep16865; A. Mitra, D. A. MacIntyre, J. R. Marchesi, Y. S. Lee, et al., Microbiome 4:58, 2016, http://dx.doi.org/10.1186/s40168-016-0203-0; J. Norenhag, J. Du, M. Olovsson, H. Verstraelen, et al., BJOG, 127:171-180, 2020, http://dx.doi.org/10.1111/1471-0528.15854; E. O. Dareng, B. Ma, A. O. Famooto, S. N. Adebamowo, et al., Epidemiol. Infect. 144:123-137, 2016, http://dx.doi.org/10.1017/S0950268815000965; A. Audirac-Chalifour, K. Torres-Poveda, M. Bahena-Roman, J. Tellez-Sosa et al., PLoS One 11:e0153274, 2016, http://dx.doi.org/10.1371/journal.pone.0153274; M. Di Paola, C. Sani, A. M. Clemente, A. Iossa, et al., Sci. Rep. 7:10200, 2017, http://dx.doi.org/10.1038/s41598-017-09842-6), the role of the cervicovaginal virome remains poorly understood. In this pilot study, we conducted metagenomic next-generation sequencing of cervicovaginal lavage specimens to investigate the relationship between the cervicovaginal DNA virome, bacterial microbiome, genital inflammation, and HPV infection. Specific virome alterations were associated with features of the local microenvironment related to HPV persistence and progression to cervical cancer. Cervicovaginal viromes clustered distinctly by genital inflammation state. Genital inflammation was associated with decreased virome richness and alpha diversity and an increased abundance of Anelloviridae species from the genus Alphatorquevirus. Lactobacillus bacteriophages were closely associated with increased Lactobacillus abundance, consistent with phage-host relationships. Interestingly, bacteria-bacteriophage transkingdom interactions were linked to genital inflammation and showed specific interactions with bacterial vaginosis-associated bacteria, including Gardnerella, Prevotella, and Sneathia. Taken together, our results reveal prominent virome interactions with features of the cervicovaginal microenvironment that are associated with HPV and cervical cancer. These findings expand our understanding of the cervicovaginal host-microbiome interactions in women's health. IMPORTANCE HPV infection is an established risk factor for cervical cancer. However, more broadly, the role of the cervicovaginal virome in cervical cancer progression is not well understood. Here, we identified cervicovaginal DNA virome alterations associated with local microenvironment factors (vaginal microbiota and genital inflammation) that influence HPV persistence and progression to cervical cancer. These findings indicate that the cervicovaginal virome plays an important role in women's health.}, } @article {pmid35343797, year = {2022}, author = {Busby, TJ and Miller, CR and Moran, NA and Van Leuven, JT}, title = {Global Composition of the Bacteriophage Community in Honey Bees.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0119521}, pmid = {35343797}, issn = {2379-5077}, support = {P20 GM104420/GM/NIGMS NIH HHS/United States ; }, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics ; Bacteria/genetics ; *Microbiota ; Plants ; }, abstract = {The microbial communities in animal digestive systems are critical for host development and health. They stimulate the immune system during development, synthesize important chemical compounds like hormones, aid in digestion, competitively exclude pathogens, etc. Compared to the bacterial and fungal components of the microbiome, we know little about the temporal and spatial dynamics of bacteriophage communities in animal digestive systems. Recently, the bacteriophages of the honey bee gut were characterized in two European bee populations. Most of the bacteriophages described in these two reports were novel, harbored many metabolic genes in their genomes, and had a community structure that suggests coevolution with their bacterial hosts. To describe the conservation of bacteriophages in bees and begin to understand their role in the bee microbiome, we sequenced the virome of Apis mellifera from Austin, TX, and compared bacteriophage compositions among three locations around the world. We found that most bacteriophages from Austin are novel, sharing no sequence similarity with anything in public repositories. However, many bacteriophages are shared among the three bee viromes, indicating specialization of bacteriophages in the bee gut. Our study, along with the two previous bee virome studies, shows that the bee gut bacteriophage community is simple compared to that of many animals, consisting of several hundred types of bacteriophages that primarily infect four of the dominant bacterial phylotypes in the bee gut. IMPORTANCE Viruses that infect bacteria (bacteriophages) are abundant in the microbial communities that live on and in plants and animals. However, our knowledge of the structure, dynamics, and function of these viral communities lags far behind our knowledge of their bacterial hosts. We sequenced the first bacteriophage community of honey bees from the United States and compared the U.S. honey bee bacteriophage community to those of samples from Europe. Our work is an important characterization of an economically critical insect species and shows how bacteriophage communities can contain highly conserved individuals and be highly variable in composition across a wide geographic range.}, } @article {pmid35343768, year = {2022}, author = {Lotankar, M and Mokkala, K and Houttu, N and Koivuniemi, E and Sørensen, N and Nielsen, HB and Munukka, E and Lahti, L and Laitinen, K}, title = {Distinct Diet-Microbiota-Metabolism Interactions in Overweight and Obese Pregnant Women: a Metagenomics Approach.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0089321}, pmid = {35343768}, issn = {2165-0497}, mesh = {Cross-Sectional Studies ; Diet ; Feces ; Female ; Humans ; Inflammation/metabolism ; Metagenomics ; *Microbiota ; Obesity ; *Overweight/complications/metabolism ; Pregnancy ; Pregnant Women ; }, abstract = {Diet and gut microbiota are known to modulate metabolic health. Our aim was to apply a metagenomics approach to investigate whether the diet-gut microbiota-metabolism and inflammation relationships differ in pregnant overweight and obese women. This cross-sectional study was conducted in overweight (n = 234) and obese (n = 152) women during early pregnancy. Dietary quality was measured by a validated index of diet quality (IDQ). Gut microbiota taxonomic composition and species diversity were assessed by metagenomic profiling (Illumina HiSeq platform). Markers for glucose metabolism (glucose, insulin) and low-grade inflammation (high sensitivity C-reactive protein [hsCRP], glycoprotein acetylation [GlycA]) were analyzed from blood samples. Higher IDQ scores were positively associated with a higher gut microbiota species diversity (r = 0.273, P = 0.007) in obese women, but not in overweight women. Community composition (beta diversity) was associated with the GlycA level in the overweight women (P = 0.04) but not in the obese. Further analysis at the species level revealed a positive association between the abundance of species Alistipes finegoldii and the GlycA level in overweight women (logfold change = 4.74, P = 0.04). This study has been registered at ClinicalTrials.gov under registration no. NCT01922791 (https://clinicaltrials.gov/ct2/show/NCT01922791). IMPORTANCE We observed partially distinct diet-gut microbiota-metabolism and inflammation responses in overweight and obese pregnant women. In overweight women, gut microbiota community composition and the relative abundance of A. finegoldii were associated with an inflammatory status. In obese women, a higher dietary quality was related to a higher gut microbiota diversity and a healthy inflammatory status.}, } @article {pmid35342733, year = {2022}, author = {Domínguez, FF and Crisanto, MEV and Castro, RLS and Rojas, LV and Cuba, VMB and Santos, GRS and Ramos, CAL and Mialhe, E}, title = {Metagenomic analysis of the intestinal microbiome in goats on cactus and Salicornia-based diets.}, journal = {Open veterinary journal}, volume = {12}, number = {1}, pages = {61-68}, pmid = {35342733}, issn = {2218-6050}, mesh = {Animals ; Bacteroidetes/genetics ; *Cactaceae/genetics ; *Chenopodiaceae/genetics ; Diet/veterinary ; *Gastrointestinal Microbiome/genetics ; Goats ; RNA, Ribosomal, 16S/genetics ; Soil ; }, abstract = {BACKGROUND: The Peruvian coast is characterized by its arid and saline soils, the cactus being an alternative for arid soils and Salicornia for saline soils. Therefore, it is necessary to develop nutrition based on the intestinal microbiota in goats.

AIM: To identify the intestinal microbiota in goats through a metagenomic analysis.

METHODS: In this study, goats and kids were randomly selected and fed cacti and Salicornia as potential forage species compared to native grass to study the changes in the microbiota using massive sequencing using the 16S rRNA gene as a marker.

RESULTS: The sequencing results showed the taxonomic levels of Bacteroidetes and Firmicutes at the phylum level as the most abundant in creole goats' microbiome, varying from 18% to 36% and 47% to 66%, respectively. At the genus level, variants of the genus Ruminococcaceae stand out, related to cellulose degradation, as the most dominant in all samples, followed by Christensenellaceae, Rikenellaceae, and Prevotellaceae. Also, the genus Akkermansia appeared in greater abundance in kids fed with cactus, being necessary for being related to the intestinal mucosa's health and avoiding the adhesion of pathogens to the intestinal epithelium.

CONCLUSION: These microbiota changes based on diets with high fiber content are necessary to understand the adaptation of this species to favorable dietary changes.}, } @article {pmid35342556, year = {2022}, author = {Van Dam, AR and Covas Orizondo, JO and Lam, AW and McKenna, DD and Van Dam, MH}, title = {Metagenomic clustering reveals microbial contamination as an essential consideration in ultraconserved element design for phylogenomics with insect museum specimens.}, journal = {Ecology and evolution}, volume = {12}, number = {3}, pages = {e8625}, pmid = {35342556}, issn = {2045-7758}, support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; }, abstract = {Phylogenomics via ultraconserved elements (UCEs) has led to improved phylogenetic reconstructions across the tree of life. However, inadvertently incorporating non-targeted DNA into the UCE marker design will lead to misinformation being incorporated into subsequent analyses. To date, the effectiveness of basic metagenomic filtering strategies has not been assessed in arthropods. Designing markers from museum specimens requires careful consideration of methods due to the high levels of microbial contamination typically found in such specimens. We investigate if contaminant sequences are carried forward into a UCE marker set we developed from insect museum specimens using a standard bioinformatics pipeline. We find that the methods currently employed by most researchers do not exclude contamination from the final set of targets. Lastly, we highlight several paths forward for reducing contamination in UCE marker design.}, } @article {pmid35342048, year = {2022}, author = {Chen, SJ and Chen, CC and Liao, HY and Wu, YW and Liou, JM and Wu, MS and Kuo, CH and Lin, CH}, title = {Alteration of Gut Microbial Metabolites in the Systemic Circulation of Patients with Parkinson's Disease.}, journal = {Journal of Parkinson's disease}, volume = {12}, number = {4}, pages = {1219-1230}, doi = {10.3233/JPD-223179}, pmid = {35342048}, issn = {1877-718X}, mesh = {Bile Acids and Salts ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Indoles ; *Parkinson Disease/diagnosis ; }, abstract = {BACKGROUND: Emerging evidence suggests that gut dysbiosis contributes to Parkinson's disease (PD) by signaling through microbial metabolites. Hippuric acid (HA), indole derivatives, and secondary bile acids are among the most common gut metabolites.

OBJECTIVE: To examine the relationship of systemic concentrations of these microbial metabolites associated with changes of gut microbiota, PD status, and severity of PD.

METHODS: We enrolled 56 patients with PD and 43 age- and sex-matched healthy participants. Motor and cognitive severity were assessed with Movement Disorder Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) part III motor score and the Mini-Mental State Examination (MMSE), respectively. Plasma concentrations of targeted gut metabolites were measured with liquid chromatography-tandem mass spectrometry. Gut microbiota was analyzed with shotgun metagenomic sequencing.

RESULTS: Compared with controls, PD patients had significantly higher plasma levels of HA, indole-3-propionic acid (IPA), deoxycholic acid (DCA), and glycodeoxycholic acid (GDCA). After adjustment for age and sex in a multivariate logistic regression analysis, plasma levels of HA (odds ratio [OR] 3.21, p < 0.001), IPA (OR 2.59, p = 0.031), and GDCA (OR 2.82, p = 0.036) were associated with positive PD status. Concentrations of these gut metabolites did not correlate with MDS-UPDRS part III score or MMSE after adjustment for confounders. Microbial metabolite levels were associated with the relative abundance of pro-inflammatory gut bacteria.

CONCLUSION: Aberrant gut microbial metabolites of HA, indole derivatives and secondary bile acids associated with specific gut microbiota changes were observed in patients with PD.}, } @article {pmid35340143, year = {2022}, author = {Zuo, K and Zhang, J and Fang, C and Wang, YX and Liu, LF and Liu, Y and Liu, Z and Wang, YJ and Shi, L and Tian, Y and Yin, XD and Liu, XP and Liu, XQ and Zhong, JC and Li, KB and Li, J and Yang, XC}, title = {[Metagenomic data-analysis reveals enrichment of lipopolysaccharide synthesis in the gut microbiota of atrial fibrillation patients].}, journal = {Zhonghua xin xue guan bing za zhi}, volume = {50}, number = {3}, pages = {249-256}, doi = {10.3760/cma.j.cn112148-20210106-00015}, pmid = {35340143}, issn = {0253-3758}, support = {81970271//National Natural Science Foundation of China/ ; }, mesh = {Aged ; *Atrial Fibrillation/complications ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Humans ; Lipopolysaccharides ; Male ; Middle Aged ; Prospective Studies ; }, abstract = {Objective: To investigate the functional changes of key gut microbiota (GM) that produce lipopolysaccharide (LPS) in atrial fibrillation (AF) patients and to explore their potential role in the pathogenesis of AF. Methods: This was a prospective cross-sectional study. Patients with AF admitted to Beijing Chaoyang Hospital of Capital Medical University were enrolled from March 2016 to December 2018. Subjects with matched genetic backgrounds undergoing physical examination during the same period were selected as controls. Clinical baseline data and fecal samples were collected. Bacterial DNA was extracted and metagenomic sequencing was performed by using Illumina Novaseq. Based on metagenomic data, the relative abundances of KEGG Orthology (KO), enzymatic genes and species that harbored enzymatic genes were acquired. The key features were selected via the least absolute shrinkage and selection operator (LASSO) analysis. The role of GM-derived LPS biosynthetic feature in the development of AF was assessed by receiver operating characteristic (ROC) curve, partial least squares structural equation modeling (PLS-SEM) and logistic regression analysis. Results: Fifty nonvalvular AF patients (mean age: 66.0 (57.0, 71.3), 32 males(64%)) were enrolled as AF group. Fifty individuals (mean age 55.0 (50.5, 57.5), 41 males(82%)) were recruited as controls. Compared with the controls, AF patients showed a marked difference in the GM genes underlying LPS-biosynthesis, including 20 potential LPS-synthesis KO, 7 LPS-biosynthesis enzymatic genes and 89 species that were assigned as taxa harbored nine LPS-enzymatic genes. LASSO regression analysis showed that 5 KO, 3 enzymatic genes and 9 species could be selected to construct the KO, enzyme and species scoring system. Genes enriched in AF group included 2 KO (K02851 and K00972), 3 enzymatic genes (LpxH, LpxC and LpxK) and 7 species (Intestinibacter bartlettii、Ruminococcus sp. JC304、Coprococcus catus、uncultured Eubacterium sp.、Eubacterium sp. CAG:251、Anaerostipes hadrus、Dorea longicatena). ROC curve analysis revealed the predictive capacity of differential GM-derived LPS signatures to distinguish AF patients in terms of above KO, enzymatic and species scores: area under curve (AUC)=0.957, 95%CI: 0.918-0.995, AUC=0.940, 95%CI 0.889-0.991, AUC=0.972, 95%CI 0.948-0.997. PLS-SEM showed that changes in lipopolysaccharide-producing bacteria could be involved in the pathogenesis of AF. The key KO mediated 35.17% of the total effect of key bacteria on AF. After incorporating the clinical factors of AF, the KO score was positively associated with the significantly increased risk of AF (OR<0.001, 95%CI:<0.001-0.021, P<0.001). Conclusion: Microbes involved in LPS synthesis are enriched in the gut of AF patients, accompanied with up-regulated LPS synthesis function by encoding the LPS-enzymatic biosynthesis gene.}, } @article {pmid35338351, year = {2022}, author = {El Saie, A and Fu, C and Grimm, SL and Robertson, MJ and Hoffman, K and Putluri, V and Ambati, CSR and Putluri, N and Shivanna, B and Coarfa, C and Pammi, M}, title = {Metabolome and microbiome multi-omics integration from a murine lung inflammation model of bronchopulmonary dysplasia.}, journal = {Pediatric research}, volume = {92}, number = {6}, pages = {1580-1589}, pmid = {35338351}, issn = {1530-0447}, support = {R01 CA220297/CA/NCI NIH HHS/United States ; P42 ES027725/ES/NIEHS NIH HHS/United States ; R01 CA216426/CA/NCI NIH HHS/United States ; R03 HD098482/HD/NICHD NIH HHS/United States ; R21 HD091718/HD/NICHD NIH HHS/United States ; P50 MD015496/MD/NIMHD NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Infant, Newborn ; Humans ; Mice ; *Bronchopulmonary Dysplasia/etiology ; *Hyperoxia/complications/metabolism ; Animals, Newborn ; Dysbiosis ; Lipopolysaccharides/metabolism ; Multiomics ; Infant, Premature ; Lung/metabolism ; *Pneumonia/metabolism ; *Microbiota ; Inflammation/metabolism ; Metabolome ; Disease Models, Animal ; }, abstract = {BACKGROUND: Respiratory tract microbial dysbiosis can exacerbate inflammation and conversely inflammation may cause dysbiosis. Dysbiotic microbiome metabolites may lead to bronchopulmonary dysplasia (BPD). Hyperoxia and lipopolysaccharide (LPS) interaction alters lung microbiome and metabolome, mediating BPD lung injury sequence.

METHODS: C57BL6/J mice were exposed to 21% (normoxia) or 70% (hyperoxia) oxygen during postnatal days (PND) 1-14. Pups were injected with LPS (6 mg/kg) or equal PBS volume, intraperitoneally on PND 3, 5, and 7. At PND14, the lungs were collected for microbiome and metabolomic analyses (n = 5/group).

RESULTS: Microbiome alpha and beta diversity were similar between groups. Metabolic changes included hyperoxia 31 up/18 down, LPS 7 up/4 down, exposure interaction 8. Hyperoxia increased Intestinimonas abundance, whereas LPS decreased Clostridiales, Dorea, and Intestinimonas; exposure interaction affected Blautia. Differential co-expression analysis on multi-omics data identified exposure-altered modules. Hyperoxia metabolomics response was integrated with a published matching transcriptome, identifying four induced genes (ALDOA, GAA, NEU1, RENBP), which positively correlated with BPD severity in a published human newborn cohort.

CONCLUSIONS: We report hyperoxia and LPS lung microbiome and metabolome signatures in a clinically relevant BPD model. We identified four genes correlating with BPD status in preterm infants that are promising targets for therapy and prevention.

IMPACT: Using multi-omics, we identified and correlated key biomarkers of hyperoxia and LPS on murine lung micro-landscape and examined their potential clinical implication, which shows strong clinical relevance for future research. Using a double-hit model of clinical relevance to bronchopulmonary dysplasia, we are the first to report integrated metabolomic/microbiome landscape changes and identify novel disease biomarker candidates.}, } @article {pmid35337386, year = {2022}, author = {Podlesny, D and Arze, C and Dörner, E and Verma, S and Dutta, S and Walter, J and Fricke, WF}, title = {Metagenomic strain detection with SameStr: identification of a persisting core gut microbiota transferable by fecal transplantation.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {53}, pmid = {35337386}, issn = {2049-2618}, mesh = {Adult ; *Clostridium Infections/therapy ; Fecal Microbiota Transplantation ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics ; Treatment Outcome ; }, abstract = {BACKGROUND: The understanding of how microbiomes assemble, function, and evolve requires metagenomic tools that can resolve microbiota compositions at the strain level. However, the identification and tracking of microbial strains in fecal metagenomes is challenging and available tools variably classify subspecies lineages, which affects their applicability to infer microbial persistence and transfer.

RESULTS: We introduce SameStr, a bioinformatic tool that identifies shared strains in metagenomes by determining single-nucleotide variants (SNV) in species-specific marker genes, which are compared based on a maximum variant profile similarity. We validated SameStr on mock strain populations, available human fecal metagenomes from healthy individuals and newly generated data from recurrent Clostridioides difficile infection (rCDI) patients treated with fecal microbiota transplantation (FMT). SameStr demonstrated enhanced sensitivity to detect shared dominant and subdominant strains in related samples (where strain persistence or transfer would be expected) when compared to other tools, while being robust against false-positive shared strain calls between unrelated samples (where neither strain persistence nor transfer would be expected). We applied SameStr to identify strains that are stably maintained in fecal microbiomes of healthy adults over time (strain persistence) and that successfully engraft in rCDI patients after FMT (strain engraftment). Taxonomy-dependent strain persistence and engraftment frequencies were positively correlated, indicating that a specific core microbiota of intestinal species is adapted to be competitive both in healthy microbiomes and during post-FMT microbiome assembly. We explored other use cases for strain-level microbiota profiling, as a metagenomics quality control measure and to identify individuals based on the persisting core gut microbiota.

CONCLUSION: SameStr provides for a robust identification of shared strains in metagenomic sequence data with sufficient specificity and sensitivity to examine strain persistence, transfer, and engraftment in human fecal microbiomes. Our findings identify a persisting healthy adult core gut microbiota, which should be further studied to shed light on microbiota contributions to chronic diseases. Video abstract.}, } @article {pmid35336180, year = {2022}, author = {Caudill, MT and Brayton, KA}, title = {The Use and Limitations of the 16S rRNA Sequence for Species Classification of Anaplasma Samples.}, journal = {Microorganisms}, volume = {10}, number = {3}, pages = {}, pmid = {35336180}, issn = {2076-2607}, support = {R01AI136832/NH/NIH HHS/United States ; //Achievement Rewards for College Scientists (ARCS) Foundation/ ; }, abstract = {With the advent of cheaper, high-throughput sequencing technologies, the ability to survey biodiversity in previously unexplored niches and geographies has expanded massively. Within Anaplasma, a genus containing several intra-hematopoietic pathogens of medical and economic importance, at least 25 new species have been proposed since the last formal taxonomic organization. Given the obligate intracellular nature of these bacteria, none of these proposed species have been able to attain formal standing in the nomenclature per the International Code of Nomenclature of Prokaryotes rules. Many novel species' proposals use sequence data obtained from targeted or metagenomic PCR studies of only a few genes, most commonly the 16S rRNA gene. We examined the utility of the 16S rRNA gene sequence for discriminating Anaplasma samples to the species level. We find that while the genetic diversity of the genus Anaplasma appears greater than appreciated in the last organization of the genus, caution must be used when attempting to resolve to a species descriptor from the 16S rRNA gene alone. Specifically, genomically distinct species have similar 16S rRNA gene sequences, especially when only partial amplicons of the 16S rRNA are used. Furthermore, we provide key bases that allow classification of the formally named species of Anaplasma.}, } @article {pmid35334900, year = {2022}, author = {Mennella, JA and Li, Y and Bittinger, K and Friedman, ES and Zhao, C and Li, H and Wu, GD and Trabulsi, JC}, title = {The Macronutrient Composition of Infant Formula Produces Differences in Gut Microbiota Maturation That Associate with Weight Gain Velocity and Weight Status.}, journal = {Nutrients}, volume = {14}, number = {6}, pages = {}, pmid = {35334900}, issn = {2072-6643}, support = {R01HD072307/NH/NIH HHS/United States ; R01 HD072307/HD/NICHD NIH HHS/United States ; P30 DK050306/DK/NIDDK NIH HHS/United States ; R03 HD094908/HD/NICHD NIH HHS/United States ; Investigator Initiated//Mead Johnson (United States)/ ; R03HD94908/NH/NIH HHS/United States ; P30 DK050306/NH/NIH HHS/United States ; }, mesh = {Animals ; Cattle ; Child ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant Formula ; Nutrients ; *Pediatric Obesity ; Weight Gain ; }, abstract = {This proof-of-principle study analyzed fecal samples from 30 infants who participated in a randomized controlled trial on the effects of the macronutrient composition of infant formula on growth and energy balance. In that study, infants randomized to be fed cow milk formula (CMF) had faster weight-gain velocity during the first 4 months and higher weight-for-length Z scores up to 11.5 months than those randomized to an isocaloric extensive protein hydrolysate formula (EHF). Here we examined associations among infant formula composition, gut microbial composition and maturation, and children's weight status. Fecal samples collected before and monthly up to 4.5 months after randomization were analyzed by shotgun metagenomic sequencing and targeted metabolomics. The EHF group had faster maturation of gut microbiota than the CMF group, and increased alpha diversity driven by Clostridia taxa. Abundance of Ruminococcus gnavus distinguished the two groups after exclusive feeding of the assigned formula for 3 months. Abundance of Clostridia at 3-4 months negatively correlated with prior weight-gain velocity and body weight phenotypes when they became toddlers. Macronutrient differences between the formulas likely led to the observed divergence in gut microbiota composition that was associated with differences in transient rapid weight gain, a well-established predictor of childhood obesity and other comorbidities.}, } @article {pmid35333990, year = {2022}, author = {Sugiyama, N and Uehara, O and Morikawa, T and Paudel, D and Ebata, K and Hiraki, D and Harada, F and Yoshida, K and Kato, S and Nagasawa, T and Miura, H and Abiko, Y and Furuichi, Y}, title = {Gut flora alterations due to lipopolysaccharide derived from Porphyromonas gingivalis.}, journal = {Odontology}, volume = {110}, number = {4}, pages = {673-681}, pmid = {35333990}, issn = {1618-1255}, support = {20H03867//Grant-in-Aid for Scientific Research (B)/ ; }, mesh = {Animals ; Dysbiosis ; *Gastrointestinal Microbiome ; Interleukin-6 ; Lipopolysaccharides/pharmacology ; Mice ; Mice, Inbred C57BL ; *Porphyromonas gingivalis ; RNA, Ribosomal, 16S ; Tumor Necrosis Factor-alpha ; }, abstract = {Gut dysbiosis induces 'leaky gut,' a condition associated with diabetes, NASH, and various auto-immune diseases. Porphyromonas gingivalis is a periodontopathic bacterium which causes periodontal tissue breakdown, and often enters the systemic blood flow. Oral administration of P. gingivalis induced gut dysbiosis in mice model, but no systemic administration of P. gingivalis has been reported thus far. In the present study, we investigated the effect of P. gingivalis-derived lipopolysaccharide (Pg-LPS) on the intestinal flora of our established mouse model. Eight-week-old C57BL/6J mice were intraperitoneally administered Pg-LPS. Three months later, DNA was extracted from stool, and RNA from the small and large intestines. After euthanizing the mice, pathological sections of the intestinal tract were prepared and stained with hematoxylin and eosin (H&E). Tumor necrosis factor alpha (TNF-α), interleukin (IL)-1β, and IL-6 expression levels were evaluated using quantitative PCR. 16S rRNA gene PCR amplicon analysis data were acquired using NGS. Microbial diversity and composition were analyzed using Quantitative Insights into Microbial Ecology 2. Furthermore, alterations in microbial function were performed by PICRUSt2. No significant inflammatory changes were observed in the H&E. No significant differences in the mRNA levels of IL-1β, IL-6, and TNF-α were observed between the groups. Pg-LPS administration decreased the abundance of Allobacterium in the gut. A predictive metagenomic analysis by PICRUSt2 and STAMP showed that 47 pathways increased and 17 pathways decreased after Pg-LPS administration. Systemic application of periodontal pathogens may cause changes in the intestinal flora which may affect the physiological functions of the intestinal tract.}, } @article {pmid35332832, year = {2022}, author = {Crits-Christoph, A and Hallowell, HA and Koutouvalis, K and Suez, J}, title = {Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2055944}, pmid = {35332832}, issn = {1949-0984}, support = {DP5 OD029603/OD/NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Genes, Bacterial ; Humans ; Metagenomics ; *Microbiota/genetics ; }, abstract = {A global rise in antimicrobial resistance among pathogenic bacteria has proved to be a major public health threat, with the rate of multidrug-resistant bacterial infections increasing over time. The gut microbiome has been studied as a reservoir of antibiotic resistance genes (ARGs) that can be transferred to bacterial pathogens via horizontal gene transfer (HGT) of conjugative plasmids and mobile genetic elements (the gut resistome). Advances in metagenomic sequencing have facilitated the identification of resistome modulators, including live microbial therapeutics such as probiotics and fecal microbiome transplantation that can either expand or reduce the abundances of ARG-carrying bacteria in the gut. While many different gut microbes encode for ARGs, they are not uniformly distributed across, or transmitted by, various members of the microbiome, and not all are of equal clinical relevance. Both experimental and theoretical approaches in microbial ecology have been applied to understand differing frequencies of ARG horizontal transfer between commensal microbes as well as between commensals and pathogens. In this commentary, we assess the evidence for the role of commensal gut microbes in encoding antimicrobial resistance genes, the degree to which they are shared both with other commensals and with pathogens, and the host and environmental factors that can impact resistome dynamics. We further discuss novel sequencing-based approaches for identifying ARGs and predicting future transfer events of clinically relevant ARGs from commensals to pathogens.}, } @article {pmid35332724, year = {2022}, author = {Wang, Y and Zhang, J and Ling, ZX and Deng, SL}, title = {[Dynamic Microbial Shifts and Functional Analysis of Saliva Microbial Communities with Caries Children].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {53}, number = {2}, pages = {242-249}, pmid = {35332724}, issn = {1672-173X}, mesh = {Child ; *Dental Caries ; Dental Caries Susceptibility ; Humans ; *Microbiota/genetics ; Saliva ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVE: To observe the dynamic changes in the salivary microbiota of children with dental caries and those who were caries-free and to analyze the functional differences in the oral microecology of the two groups during the course of sugar metabolism and the synthesis and transport of multiple amino acids.

METHODS: Ten children with dental caries and 10 caries-free children were enrolled. We employed Illumina metagenomics technology to analyze the composition and function of salivary microbiome in children with and without caries. Six months later, PacBio single-molecule long-read sequencing technology was used to analyze the changes over time in the oral microbial communities of the two groups. We studied the patterns of change in the oral microbial communities under diseased or healthy conditions and attempted to offer a comprehensive interpretation of children's oral microbiota in terms of its composition and functions.

RESULTS: The composition of the oral microbiota of children with or without dental caries changed significantly over time. At the phylum level, changing trends in the salivary microbial communities of children with dental caries were in line with those in caries-free children. In these microbial communities, increased proportions of Firmicutes and decreased proportions of Actinobacteria and Bacteroidetes were found in the two groups. At the genus level, however, the two groups showed significantly different changes of the salivary microbial communities. Upward trends in the abundance of Lactobacillus, Methylobacterium, and Megasphaera were found in the caries group, while the abundance of these genera in the caries-free group showed downward trends. At the species level, L. fermentum, L. gasseri, L. oris, S. downei, and some other species belonging to the genus Lactobacillus showed upward trends in the saliva of children with caries, while they consistently stayed at a relative low level of abundance in caries-free children. The abundance of S. gordonii and S. mutans decreased to a certain extent in children with dental caries, but the abundance of S. gordonii and S. mutans in caries-free children were always at a low level. Species such as S. mutans and C. gracilis were positively correlated to the sum of decayed, missing and filled teeth (dmft), while N. flavescens was negatively correlated to dmft. gltA, icd, and mqo, the key genes related to tricarboxylic acid (TCA) cycle, gudB, a glutamate synthesis-related gene, and argAB/C/J, arginine synthesis-related genes, were significantly increased in caries-free children. In addition, the abundance of the NADH dehydrogenase-related gene nuoB/C/D/E/H/I/J/K/L/M in the electron transport chain increased significantly in caries-free children.

CONCLUSION: Dynamic changes were found in the oral microbiota of children with or without caries. The trends of microbial shifts over time were associated with the oral health status. Oxidative phosphorylation and the synthesis and transport of amino acids such as glutamate and arginine in the oral microecology were more active in caries-free children.}, } @article {pmid35331330, year = {2022}, author = {Liu, B and Sträuber, H and Saraiva, J and Harms, H and Silva, SG and Kasmanas, JC and Kleinsteuber, S and Nunes da Rocha, U}, title = {Machine learning-assisted identification of bioindicators predicts medium-chain carboxylate production performance of an anaerobic mixed culture.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {48}, pmid = {35331330}, issn = {2049-2618}, mesh = {Anaerobiosis ; Bioreactors ; *Caproates ; Caprylates ; Environmental Biomarkers ; Machine Learning ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The ability to quantitatively predict ecophysiological functions of microbial communities provides an important step to engineer microbiota for desired functions related to specific biochemical conversions. Here, we present the quantitative prediction of medium-chain carboxylate production in two continuous anaerobic bioreactors from 16S rRNA gene dynamics in enriched communities.

RESULTS: By progressively shortening the hydraulic retention time (HRT) from 8 to 2 days with different temporal schemes in two bioreactors operated for 211 days, we achieved higher productivities and yields of the target products n-caproate and n-caprylate. The datasets generated from each bioreactor were applied independently for training and testing machine learning algorithms using 16S rRNA genes to predict n-caproate and n-caprylate productivities. Our dataset consisted of 14 and 40 samples from HRT of 8 and 2 days, respectively. Because of the size and balance of our dataset, we compared linear regression, support vector machine and random forest regression algorithms using the original and balanced datasets generated using synthetic minority oversampling. Further, we performed cross-validation to estimate model stability. The random forest regression was the best algorithm producing more consistent results with median of error rates below 8%. More than 90% accuracy in the prediction of n-caproate and n-caprylate productivities was achieved. Four inferred bioindicators belonging to the genera Olsenella, Lactobacillus, Syntrophococcus and Clostridium IV suggest their relevance to the higher carboxylate productivity at shorter HRT. The recovery of metagenome-assembled genomes of these bioindicators confirmed their genetic potential to perform key steps of medium-chain carboxylate production.

CONCLUSIONS: Shortening the hydraulic retention time of the continuous bioreactor systems allows to shape the communities with desired chain elongation functions. Using machine learning, we demonstrated that 16S rRNA amplicon sequencing data can be used to predict bioreactor process performance quantitatively and accurately. Characterizing and harnessing bioindicators holds promise to manage reactor microbiota towards selection of the target processes. Our mathematical framework is transferrable to other ecosystem processes and microbial systems where community dynamics is linked to key functions. The general methodology used here can be adapted to data types of other functional categories such as genes, transcripts, proteins or metabolites. Video Abstract.}, } @article {pmid35327556, year = {2022}, author = {Sanchez-Cid, C and Tignat-Perrier, R and Franqueville, L and Delaurière, L and Schagat, T and Vogel, TM}, title = {Sequencing Depth Has a Stronger Effect than DNA Extraction on Soil Bacterial Richness Discovery.}, journal = {Biomolecules}, volume = {12}, number = {3}, pages = {}, pmid = {35327556}, issn = {2218-273X}, mesh = {Bacteria/genetics ; DNA ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; *Soil ; }, abstract = {Although Next-Generation Sequencing techniques have increased our access to the soil microbiome, each step of soil metagenomics presents inherent biases that prevent the accurate definition of the soil microbiome and its ecosystem function. In this study, we compared the effects of DNA extraction and sequencing depth on bacterial richness discovery from two soil samples. Four DNA extraction methods were used, and sequencing duplicates were generated for each DNA sample. The V3-V4 region of the 16S rRNA gene was sequenced to determine the taxonomical richness measured by each method at the amplicon sequence variant (ASV) level. Both the overall functional richness and antibiotic resistance gene (ARG) richness were evaluated by metagenomics sequencing. Despite variable DNA extraction methods, sequencing depth had a greater influence on bacterial richness discovery at both the taxonomical and functional levels. Sequencing duplicates from the same sample provided access to different portions of bacterial richness, and this was related to differences in the sequencing depth. Thus, the sequencing depth introduced biases in the comparison of DNA extraction methods. An optimisation of the soil metagenomics workflow is needed in order to sequence at a sufficient and equal depth. This would improve the accuracy of metagenomic comparisons and soil microbiome profiles.}, } @article {pmid35325312, year = {2022}, author = {Borjigin, Q and Zhang, B and Yu, X and Gao, J and Zhang, X and Qu, J and Ma, D and Hu, S and Han, S}, title = {Metagenomics study to compare the taxonomic composition and metabolism of a lignocellulolytic microbial consortium cultured in different carbon conditions.}, journal = {World journal of microbiology & biotechnology}, volume = {38}, number = {5}, pages = {78}, pmid = {35325312}, issn = {1573-0972}, support = {31760353//National Natural Science Foundation of China/ ; 32060434//National Natural Science Foundation of China/ ; 2020MS03086//Natural Science Foundation of Inner Mongolia/ ; 2018ZD02//Natural Science Foundation of Inner Mongolia/ ; CARS-02-63//Earmarked Fund for China Agriculture Research System/ ; 25204120//Innovative Research Group Project of the National Natural Science Foundation of China/ ; }, mesh = {Bacteria/metabolism ; Carbon/metabolism ; Metagenomics ; *Microbial Consortia/genetics ; *Sphingobacterium ; }, abstract = {A lignocellulolytic microbial consortium holds promise for the in situ biodegradation of crop straw and the comprehensive and effective utilization of agricultural waste. In this study, we applied metagenomics technology to comprehensively explore the metabolic functional potential and taxonomic diversity of the microbial consortia CS (cultured on corn stover) and FP (cultured on filter paper). Analyses of the data on metagenomics taxonomic affiliations revealed considerable differences in the taxonomic composition and carbohydrate-active enzymes profile of the microbial consortia CS and FP. Pseudomonas, Dysgonomonas and Sphingobacterium in CS and Cellvibrio and Pseudomonas in FP had a much wider distribution of lignocellulose degradative ability. The genes for more lignocellulose degradative enzymes were detected when the relatively simple substrate filter paper was used as the carbon source. Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analyses revealed considerable levels of similarity, and carbohydrate metabolic and amino acid metabolic pathways were the most enriched in CS and FP, respectively. The mechanism used by the two microbial consortia to degrade lignocellulose was similar, but the annotation of quantity of genes indicated that they are diverse and vary greatly. These data underlie the interactions between microorganisms and the synergism of enzymes during the degradative process of lignocellulose under different substrates and suggest the development of potential microbial resources.}, } @article {pmid35324742, year = {2022}, author = {Kim, H and Park, YH and Yang, JE and Kim, HS and Kim, SC and Oh, EJ and Moon, J and Cho, W and Shin, W and Yu, C}, title = {Analysis of Major Bacteria and Diversity of Surface Soil to Discover Biomarkers Related to Soil Health.}, journal = {Toxics}, volume = {10}, number = {3}, pages = {}, pmid = {35324742}, issn = {2305-6304}, support = {2019R1I1A2A01057002//National Research Foundation of Korea (NRF)/ ; 2019R1A61A03033167//National Research Foundation of Korea (NRF)/ ; 2020002480005//Korean Ministry of Environment as" Development of soil Health Assessment System for Con-taminated and Remediated Soil' project/ ; 2019002820004//Korea Ministry of Environment through the strategic EcoSSSoil Project, KEITI (Korea Environ-mental Industry and Technology Institute)/ ; }, abstract = {The discovery of biomarkers for assessing soil health requires the exploration of organisms that can explain the core functions of soil and identification of species with major roles in these functions. However, identifying specific keystone markers within the soil microbiota is challenging. Next-generation sequencing (NGS)-based molecular-biological methods have revealed information on soil biodiversity; however, whether this biodiversity is related to soil health remains unclear. In this study, we performed NGS on grassland surface soil to compare the prokaryotic and eukaryotic genetic diversity to determine the chemical soil quality and examined markers associated with soil health. Microorganisms associated with the nitrogen cycle, bioremediation, plant pathogenicity, antibiotic production, and material degradation showed potential for use as markers. To propose a framework for soil health assessment, we not only used traditional indicators, such as chemical and physical measures, but also assessed metagenomics data of soil by land use to identify the major factors influencing the microbial structure in soil. Moreover, major keystone species were identified. Furthermore, the microbial genetic diversity of generally healthy surface soil, such as forests, farmland, and parks, was determined. These findings provide basic data for exploring soil health-related biomarkers.}, } @article {pmid35323827, year = {2022}, author = {Boeckman, JX and Sprayberry, S and Korn, AM and Suchodolski, JS and Paulk, C and Genovese, K and Rech, RR and Giaretta, PR and Blick, AK and Callaway, T and Gill, JJ}, title = {Effect of chronic and acute enterotoxigenic E. coli challenge on growth performance, intestinal inflammation, microbiome, and metabolome of weaned piglets.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {5024}, pmid = {35323827}, issn = {2045-2322}, support = {T35 OD010991/OD/NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Diarrhea/prevention & control/veterinary ; *Enterotoxigenic Escherichia coli ; *Escherichia coli Infections/prevention & control ; Inflammation ; Leukocyte L1 Antigen Complex ; Metabolome ; *Microbiota ; Swine ; *Swine Diseases/prevention & control ; Weaning ; }, abstract = {Post-weaning enteropathies in swine caused by pathogenic E. coli, such as post-weaning diarrhea (PWD) or edema disease (ED), remain a significant problem for the swine industry. Reduction in the use of antibiotics over concerns of antibiotic resistance and public health concerns, necessitate the evaluation of effective antibiotic alternatives to prevent significant loss of livestock and/or reductions in swine growth performance. For this purpose, an appropriate piglet model of pathogenic E. coli enteropathy is required. In this study, we attempted to induce clinical signs of post-weaning disease in a piglet model using a one-time acute or lower daily chronic dose of a pathogenic E. coli strain containing genes for both heat stable and labile toxins, as well as Shiga toxin. The induced disease state was monitored by determining fecal shedding and colonization of the challenge strain, animal growth performance, cytokine levels, fecal calprotectin, histology, fecal metabolomics, and fecal microbiome shifts. The most informative analyses were colonization and shedding of the pathogen, serum cytokines, metabolomics, and targeted metagenomics to determine dysbiosis. Histopathological changes of the gastrointestinal (GI) tract and tight junction leakage as measured by fecal calprotectin concentrations were not observed. Chronic dosing was similar to the acute regimen suggesting that a high dose of pathogen, as used in many studies, may not be necessary. The piglet disease model presented here can be used to evaluate alternative PWD treatment options.}, } @article {pmid35323045, year = {2022}, author = {Kieft, K and Anantharaman, K}, title = {Deciphering Active Prophages from Metagenomes.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0008422}, pmid = {35323045}, issn = {2379-5077}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; Prophages/genetics ; Metagenome ; Lysogeny ; *Bacteriophages/genetics ; *Microbiota ; }, abstract = {Temperate phages (prophages) are ubiquitous in nature and persist as dormant components of host cells (lysogenic stage) before activating and lysing the host (lytic stage). Actively replicating prophages contribute to central community processes, such as enabling bacterial virulence, manipulating biogeochemical cycling, and driving microbial community diversification. Recent advances in sequencing technology have allowed for the identification and characterization of diverse phages, yet no approaches currently exist for identifying if a prophage has activated. Here, we present PropagAtE (Prophage Activity Estimator), an automated software tool for estimating if a prophage is in the lytic or lysogenic stage of infection. PropagAtE uses statistical analyses of prophage-to-host read coverage ratios to decipher actively replicating prophages, irrespective of whether prophages were induced or spontaneously activated. We demonstrate that PropagAtE is fast, accurate, and sensitive, regardless of sequencing depth. Application of PropagAtE to prophages from 348 complex metagenomes from human gut, murine gut, and soil environments identified distinct spatial and temporal prophage activation signatures, with the highest proportion of active prophages in murine gut samples. In infants treated with antibiotics or infants without treatment, we identified active prophage populations correlated with specific treatment groups. Within time series samples from the human gut, 11 prophage populations, some encoding the sulfur metabolism gene cysH or a rhuM-like virulence factor, were consistently present over time but not active. Overall, PropagAtE will facilitate accurate representations of viruses in microbiomes by associating prophages with their active roles in shaping microbial communities in nature. IMPORTANCE Viruses that infect bacteria are key components of microbiomes and ecosystems. They can kill and manipulate microorganisms, drive planetary-scale processes and biogeochemical cycling, and influence the structures of entire food networks. Prophages are viruses that can exist in a dormant state within the genome of their host (lysogenic stage) before activating in order to replicate and kill the host (lytic stage). Recent advances have allowed for the identification of diverse viruses in nature, but no approaches exist for characterizing prophages and their stages of infection (prophage activity). We develop and benchmark an automated approach, PropagAtE, to identify the stages of infection of prophages from genomic data. We provide evidence that active prophages vary in identity and abundance across multiple environments and scales. Our approach will enable accurate and unbiased analyses of viruses in microbiomes and ecosystems.}, } @article {pmid35323040, year = {2022}, author = {Pettigrew, MM and Kwon, J and Gent, JF and Kong, Y and Wade, M and Williams, DJ and Creech, CB and Evans, S and Pan, Q and Walter, EB and Martin, JM and Gerber, JS and Newland, JG and Hofto, ME and Staat, MA and Fowler, VG and Chambers, HF and Huskins, WC and , }, title = {Comparison of the Respiratory Resistomes and Microbiota in Children Receiving Short versus Standard Course Treatment for Community-Acquired Pneumonia.}, journal = {mBio}, volume = {13}, number = {2}, pages = {e0019522}, pmid = {35323040}, issn = {2150-7511}, support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; UM1 AI104681/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; Child ; Child, Preschool ; *Community-Acquired Infections/drug therapy ; Humans ; Infant ; *Microbiota ; *Pneumonia/drug therapy ; beta-Lactams/therapeutic use ; }, abstract = {Pediatric community-acquired pneumonia (CAP) is often treated with 10 days of antibiotics. Shorter treatment strategies may be effective and lead to less resistance. The impact of duration of treatment on the respiratory microbiome is unknown. Data are from children (n = 171), ages 6 to 71 months, enrolled in the SCOUT-CAP trial (NCT02891915). Children with CAP were randomized to a short (5 days) versus standard (10 days) beta-lactam treatment strategy. Throat swabs were collected at enrollment and the end of the study and used for shotgun metagenomic sequencing. The number of beta-lactam and multidrug efflux resistance genes per prokaryotic cell (RGPC) was significantly lower in children receiving the short compared to standard treatment strategy at the end of the study (Wilcoxon rank sum test, P < 0.05 for each). Wilcoxon effect sizes were small for beta-lactam (r: 0.15; 95% confidence interval [CI], 0.01 to 0.29) and medium for multidrug efflux RGPC (r: 0.23; 95% CI, 0.09 to 0.37). Analyses comparing the resistome at the beginning and end of the trial indicated that in contrast to the standard strategy group, the resistome significantly differed in children receiving the short course strategy. Relative abundances of commensals such as Neisseria subflava were higher in children receiving the standard strategy, and Prevotella species and Veillonella parvula were higher in children receiving the short course strategy. We conclude that children receiving 5 days of beta-lactam therapy for CAP had a significantly lower abundance of antibiotic resistance determinants than those receiving standard 10-day treatment. These data provide an additional rationale for reductions in antibiotic use when feasible. IMPORTANCE Antibiotic resistance is a major threat to public health. Treatment strategies involving shorter antibiotic courses have been proposed as a strategy to lower the potential for antibiotic resistance. We examined relationships between the duration of antibiotic treatment and its impact on resistance genes and bacteria in the respiratory microbiome using data from a randomized controlled trial of beta-lactam therapy for pediatric pneumonia. The randomized design provides reliable evidence of the effectiveness of interventions and minimizes the potential for confounding. Children receiving 5 days of therapy for pneumonia had a lower prevalence of two different types of resistance genes than did those receiving the 10-day treatment. Our data also suggest that children receiving longer durations of therapy have a greater abundance of antibiotic resistance genes for a longer period of time than do children receiving shorter durations of therapy. These data provide an additional rationale for reductions in antibiotic use.}, } @article {pmid35320603, year = {2022}, author = {Kohler, TJ and Fodelianakis, S and Michoud, G and Ezzat, L and Bourquin, M and Peter, H and Busi, SB and Pramateftaki, P and Deluigi, N and Styllas, M and Tolosano, M and de Staercke, V and Schön, M and Brandani, J and Marasco, R and Daffonchio, D and Wilmes, P and Battin, TJ}, title = {Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function.}, journal = {Global change biology}, volume = {28}, number = {12}, pages = {3846-3859}, pmid = {35320603}, issn = {1365-2486}, mesh = {Bacteria/genetics ; Climate Change ; Ecosystem ; *Ice Cover/microbiology ; *Microbiota ; Phylogeny ; Water ; }, abstract = {The shrinking of glaciers is among the most iconic consequences of climate change. Despite this, the downstream consequences for ecosystem processes and related microbiome structure and function remain poorly understood. Here, using a space-for-time substitution approach across 101 glacier-fed streams (GFSs) from six major regions worldwide, we investigated how glacier shrinkage is likely to impact the organic matter (OM) decomposition rates of benthic biofilms. To do this, we measured the activities of five common extracellular enzymes and estimated decomposition rates by using enzyme allocation equations based on stoichiometry. We found decomposition rates to average 0.0129 (% d[-1]), and that decreases in glacier influence (estimated by percent glacier catchment coverage, turbidity, and a glacier index) accelerates decomposition rates. To explore mechanisms behind these relationships, we further compared decomposition rates with biofilm and stream water characteristics. We found that chlorophyll-a, temperature, and stream water N:P together explained 61% of the variability in decomposition. Algal biomass, which is also increasing with glacier shrinkage, showed a particularly strong relationship with decomposition, likely indicating their importance in contributing labile organic compounds to these carbon-poor habitats. We also found high relative abundances of chytrid fungi in GFS sediments, which putatively parasitize these algae, promoting decomposition through a fungal shunt. Exploring the biofilm microbiome, we then sought to identify bacterial phylogenetic clades significantly associated with decomposition, and found numerous positively (e.g., Saprospiraceae) and negatively (e.g., Nitrospira) related clades. Lastly, using metagenomics, we found evidence of different bacterial classes possessing different proportions of EEA-encoding genes, potentially informing some of the microbial associations with decomposition rates. Our results, therefore, present new mechanistic insights into OM decomposition in GFSs by demonstrating that an algal-based "green food web" is likely to increase in importance in the future and will promote important biogeochemical shifts in these streams as glaciers vanish.}, } @article {pmid35320047, year = {2022}, author = {Beller, L and Deboutte, W and Vieira-Silva, S and Falony, G and Tito, RY and Rymenans, L and Yinda, CK and Vanmechelen, B and Van Espen, L and Jansen, D and Shi, C and Zeller, M and Maes, P and Faust, K and Van Ranst, M and Raes, J and Matthijnssens, J}, title = {The virota and its transkingdom interactions in the healthy infant gut.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {13}, pages = {e2114619119}, pmid = {35320047}, issn = {1091-6490}, mesh = {Bacteria ; *Bacteriophages ; *Gastrointestinal Microbiome ; Humans ; Infant ; *Microbiota ; *Viruses ; }, abstract = {SignificanceMicrobes colonizing the infant gut during the first year(s) of life play an important role in immune system development. We show that after birth the (nearly) sterile gut is rapidly colonized by bacteria and their viruses (phages), which often show a strong cooccurrence. Most viruses infecting the infant do not cause clinical signs and their numbers strongly increase after day-care entrance. The infant diet is clearly reflected by identification of plant-infecting viruses, whereas fungi and parasites are not part of a stable gut microbiota. These temporal high-resolution baseline data about the gut colonization process will be valuable for further investigations of pathogenic viruses, dynamics between phages and their bacterial host, as well as studies investigating infants with a disturbed microbiota.}, } @article {pmid35319433, year = {2022}, author = {Gardner, CM and Gerhard, WA and Redfern, LK and Gunsch, CK}, title = {Evaluation of developing maize microbiomes and associations among nitrogen cyclers and key fungal taxa.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {3}, pages = {}, doi = {10.1099/mic.0.001155}, pmid = {35319433}, issn = {1465-2080}, mesh = {Humans ; *Microbiota/genetics ; *Mycorrhizae ; Nitrogen ; Soil Microbiology ; Zea mays ; }, abstract = {More sustainable approaches to agriculture are urgently needed to protect existing resources and optimize crop yields and to provide food for a growing global human population. More sustainable agricultural practices that utilize plant-microbe relationships across cultivation are urgently needed. The main objectives of this study were to track the prokaryotic and fungal microbiomes associated with key growth stages of developing maize to evaluate the relationships among nitrogen cycling bacteria and major fungal genera including those known to contain arbuscular mycorrhizal fungi and other important taxa. Prokaryotic and fungal microbiomes associated with bulk soils, rhizosphere soils and tissues of developing maize were characterized using Illumina MiSeq sequencing. Similarities in microbiome diversity and abundance were compared to sample metadata to explore the influence of external factors on microbiome development. Correlations among target fungal taxa, bulk bacteria and nitrogen cycling bacteria were determined using non-parametric Spearman correlations. Important maize-associated fungal taxa were detected in all samples across growth stages, with Fusarium, Penicillium and Aspergillus fungi comprising up to 4.21, 4.26 and 0.28% of all fungal genera, respectively. Thirteen statistically significant correlations between nitrogen cycling genera and targeted fungal genera were also identified (rS≥0.70 or rS≤-0.70; P<0.05). This study is the first to note a strong positive association among several nitrifying bacteria and Fusarium (R=0.71; P=0.0046), Aspergillus (R=0.71; P=0.0055) and Cladosporium spcies (R=0.74; P=0.0038), suggesting the levels of soil nitrate, nitrite or nitrification intermediates may have large roles in the proliferation of important maize-associated fungi.}, } @article {pmid35318755, year = {2023}, author = {Peimbert, M and Alcaraz, LD}, title = {Where environmental microbiome meets its host: Subway and passenger microbiome relationships.}, journal = {Molecular ecology}, volume = {32}, number = {10}, pages = {2602-2618}, doi = {10.1111/mec.16440}, pmid = {35318755}, issn = {1365-294X}, mesh = {Humans ; *Railroads ; *Microbiota/genetics ; Metagenome ; Cities ; Bacteria/genetics ; }, abstract = {Subways are urban transport systems with high capacity. Every day around the world, there are more than 150 million subway passengers. Since 2013, thousands of microbiome samples from various subways worldwide have been sequenced. Skin bacteria and environmental organisms dominate the subway microbiomes. The literature has revealed common bacterial groups in subway systems; even so, it is possible to identify cities by their microbiome. Low frequency bacteria are responsible for specific bacterial fingerprints of each subway system. Furthermore, daily subway commuters leave their microbial clouds and interact with other passengers. Microbial exchange is quite fast; the hand microbiome changes within minutes, and after cleaning the handrails, the bacteria are re-established within minutes. To investigate new taxa and metabolic pathways of subway microbial communities, several high-quality metagenomic-assembled genomes (MAG) have been described. Subways are harsh environments unfavorable for microorganism growth. However, recent studies have observed a wide diversity of viable and metabolically active bacteria. Understanding which bacteria are living, dormant, or dead allows us to propose realistic ecological interactions. Questions regarding the relationship between humans and the subway microbiome, particularly the microbiome effects on personal and public health, remain unanswered. This review summarizes our knowledge of subway microbiomes and their relationship with passenger microbiomes.}, } @article {pmid35318388, year = {2022}, author = {Skipper, PJA and Skipper, LK and Dixon, RA}, title = {A metagenomic analysis of the bacterial microbiome of limestone, and the role of associated biofilms in the biodeterioration of heritage stone surfaces.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {4877}, pmid = {35318388}, issn = {2045-2322}, mesh = {Bacteria/genetics ; Biofilms ; Calcium Carbonate ; *Metagenomics ; *Microbiota/genetics ; }, abstract = {There is growing concern surrounding the aesthetic and physical effects of microbial biofilms on heritage buildings and monuments. Carboniferous stones, such as limestone and marble, are soluble in weak acid solutions and therefore particularly vulnerable to biocorrosion. This paper aims to determine the differences and commonalities between the microbiome of physically damaged and undamaged Lincolnshire limestone, an area of research which has not been previously studied. A lack of information about the core microbiome has resulted in conflicting claims in the literature regarding the biodeteriorative potential of many microorganisms. To address this, we used metagenomics alongside traditional microbiological techniques to produce an in-depth analysis of differences between the bacterial microbiomes found on deteriorated and undamaged external limestone surfaces. We demonstrate there is a core microbiome on Lincolnshire limestone present on both damaged and undamaged surfaces. In addition to the core microbiome, significant differences were found between species isolated from undamaged compared to damaged surfaces. Isolated species were characterised for biofilm formation and biodeteriorative processes, resulting in the association of species with biodeterioration that had not been previously described. Additionally, we have identified a previously undescribed method of biofilm-associated biomechanical damage. This research adds significant new understanding to the field, aiding decision making in conservation of stone surfaces.}, } @article {pmid35318044, year = {2022}, author = {Chia, M and Naim, ANM and Tay, ASL and Lim, K and Chew, KL and Yow, SJ and Chen, J and Common, JEA and Nagarajan, N and Tham, EH}, title = {Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their caregivers.}, journal = {The Journal of allergy and clinical immunology}, volume = {150}, number = {4}, pages = {894-908}, doi = {10.1016/j.jaci.2022.01.031}, pmid = {35318044}, issn = {1097-6825}, mesh = {Adult ; Caregivers ; Child ; *Dermatitis, Atopic/pathology ; Enterotoxins ; Humans ; *Microbiota ; Neoplasm Recurrence, Local ; Quality of Life ; Skin/pathology ; Staphylococcus aureus ; }, abstract = {BACKGROUND: Atopic dermatitis (AD) is a common chronic skin condition in children (15-20%) that can significantly impair their quality of life. As a result of its relapsing nature and enrichment of Staphylococcus aureus during flares, clinical management can include eradicating S aureus from the skin of children; however, this does not extend to their healthy caregivers, who are potential reservoirs.

OBJECTIVE: Our aim was to understand skin microbiome sharing and microbial features in children with AD and their healthy adult caregivers.

METHODS: We utilized whole-metagenome profiling at 4 body sites (volar forearm, antecubital fossae, cheeks, and lesions) in combination with sequencing of S aureus isolates to characterize a cohort of children with AD and their healthy caregivers (n = 30 families) compared to matched pairs from control households (n = 30 families).

RESULTS: Metagenomic analysis revealed distinct microbiome configurations in the nonlesional skin of AD children and their healthy caregivers versus controls, which were sufficient to accurately predict case-control status (area under the receiver operating characteristic curve > 0.8). These differences were accompanied by significant microbiome similarity between children and their caregivers, indicating that microbiome sharing may play a role in recurrent disease flares. Whole-genome comparisons with high-quality S aureus isolate genomes (n = 55) confirmed significant strain sharing between AD children and their caregivers and AD-specific enrichment of strains expressing enterotoxins Q and K/K2.

CONCLUSION: Our results highlight the distinctive skin microbiome features of healthy caregivers for children with AD and support their inclusion in strategies for the treatment of recurrent pediatric AD.}, } @article {pmid35317857, year = {2022}, author = {Murakami, T and Takeuchi, N and Mori, H and Hirose, Y and Edwards, A and Irvine-Fynn, T and Li, Z and Ishii, S and Segawa, T}, title = {Metagenomics reveals global-scale contrasts in nitrogen cycling and cyanobacterial light-harvesting mechanisms in glacier cryoconite.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {50}, pmid = {35317857}, issn = {2049-2618}, mesh = {*Cyanobacteria/genetics ; Ecosystem ; *Ice Cover/microbiology ; Metagenomics ; Nitrogen/metabolism ; Phycoerythrin/metabolism ; }, abstract = {BACKGROUND: Cryoconite granules are mineral-microbial aggregates found on glacier surfaces worldwide and are hotspots of biogeochemical reactions in glacier ecosystems. However, despite their importance within glacier ecosystems, the geographical diversity of taxonomic assemblages and metabolic potential of cryoconite communities around the globe remain unclear. In particular, the genomic content of cryoconite communities on Asia's high mountain glaciers, which represent a substantial portion of Earth's ice masses, has rarely been reported. Therefore, in this study, to elucidate the taxonomic and ecological diversities of cryoconite bacterial consortia on a global scale, we conducted shotgun metagenomic sequencing of cryoconite acquired from a range of geographical areas comprising Polar (Arctic and Antarctic) and Asian alpine regions.

RESULTS: Our metagenomic data indicate that compositions of both bacterial taxa and functional genes are particularly distinctive for Asian cryoconite. Read abundance of the genes responsible for denitrification was significantly more abundant in Asian cryoconite than the Polar cryoconite, implying that denitrification is more enhanced in Asian glaciers. The taxonomic composition of Cyanobacteria, the key primary producers in cryoconite communities, also differs between the Polar and Asian samples. Analyses on the metagenome-assembled genomes and fluorescence emission spectra reveal that Asian cryoconite is dominated by multiple cyanobacterial lineages possessing phycoerythrin, a green light-harvesting component for photosynthesis. In contrast, Polar cryoconite is dominated by a single cyanobacterial species Phormidesmis priestleyi that does not possess phycoerythrin. These findings suggest that the assemblage of cryoconite bacterial communities respond to regional- or glacier-specific physicochemical conditions, such as the availability of nutrients (e.g., nitrate and dissolved organic carbon) and light (i.e., incident shortwave radiation).

CONCLUSIONS: Our genome-resolved metagenomics provides the first characterization of the taxonomic and metabolic diversities of cryoconite from contrasting geographical areas, highlighted by the distinct light-harvesting approaches of Cyanobacteria and nitrogen utilization between Polar and Asian cryoconite, and implies the existence of environmental controls on the assemblage of cryoconite communities. These findings deepen our understanding of the biodiversity and biogeochemical cycles of glacier ecosystems, which are susceptible to ongoing climate change and glacier decline, on a global scale. Video abstract.}, } @article {pmid35316680, year = {2022}, author = {He, C and Liu, J and Wang, R and Li, Y and Zheng, Q and Jiao, F and He, C and Shi, Q and Xu, Y and Zhang, R and Thomas, H and Batt, J and Hill, P and Lewis, M and Maclntyre, H and Lu, L and Zhang, Q and Tu, Q and Shi, T and Chen, F and Jiao, N}, title = {Metagenomic evidence for the microbial transformation of carboxyl-rich alicyclic molecules: A long-term macrocosm experiment.}, journal = {Water research}, volume = {216}, number = {}, pages = {118281}, doi = {10.1016/j.watres.2022.118281}, pmid = {35316680}, issn = {1879-2448}, mesh = {Bacteria/genetics/metabolism ; *Diatoms/genetics ; Dissolved Organic Matter ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Phytoplankton/genetics/metabolism ; }, abstract = {Carboxyl-rich alicyclic molecules (CRAMs) widely exist in the ocean and constitute the central part of the refractory dissolved organic matter (RDOM) pool. Although a consensus has been reached that microbial activity forms CRAMs, the detailed molecular mechanisms remain largely unexplored. To better understand the underlying genetic mechanisms driving the microbial transformation of CRAM, a long-term macrocosm experiment spanning 220 days was conducted in the Aquatron Tower Tank at Dalhousie University, Halifax, Canada, with the supply of diatom-derived DOM as a carbon source. The DOM composition, community structure, and metabolic pathways were characterised using multi-omics approaches. The addition of diatom lysate introduced a mass of labile DOM into the incubation seawater, which led to a low degradation index (IDEG) and refractory molecular lability boundary (RMLB) on days 1 and 18. The molecular compositions of the DOM molecules in the later incubation period (from day 120 to day 220) were more similar in composition to those on day 0, suggesting a rapid turnover of phytoplankton debris by microbial communities. Taxonomically, while Alpha proteobacteria dominated during the entire incubation period, Gamma proteobacteria became more sensitive and abundant than the other bacterial groups on days 1 and 18. Recalcitrant measurements such as IDEG and RMLB were closely related to the DOM molecules, bacterial community, and Kyoto encyclopaedia of Genes and Genomes (KEGG) modules, suggesting close associations between RDOM accumulation and microbial metabolism. KEGG modules that showed strong positive correlation with CRAMs were identified using a microbial ecological network approach. The identified KEGG modules produced the substrates, such as the acetyl-CoA or 3‑hydroxy-3-methylglutaryl-CoA, which could participate in the mevalonate pathway to generate the precursor of CRAM analogues, isopentenyl-PP, suggesting a potential generation pathway of CRAM analogues in bacteria and archaea. This study revealed the potential genetic and molecular processes involved in the microbial origin of CRAM analogues, and thus indicated a vital ecological role of bacteria and archaea in RDOM production. This study also offered new perspectives on the carbon sequestration in the ocean.}, } @article {pmid35315566, year = {2022}, author = {Zhou, D and Li, N and Yang, F and Zhang, H and Bai, Z and Dong, Y and Li, M and Zhu, W and Fei, Z and Xiao, P and Sun, X and Lu, Z}, title = {Soil causes gut microbiota to flourish and total serum IgE levels to decrease in mice.}, journal = {Environmental microbiology}, volume = {24}, number = {9}, pages = {3898-3911}, doi = {10.1111/1462-2920.15979}, pmid = {35315566}, issn = {1462-2920}, mesh = {Amino Acids ; Animals ; Dinitrofluorobenzene ; Fatty Acids, Volatile ; *Gastrointestinal Microbiome/genetics ; Immunoglobulin E ; Mice ; Soil/chemistry ; Type III Secretion Systems ; }, abstract = {Traditional farm environments induce protection from allergic diseases. In this study, farm environmental factors were classified into three categories, environmental microbes, soil, and organic matter. To explore the impact of soil and environmental microorganisms on gut microbiota and immune function, mice were fed sterilized soil and inhaling microbes, soil microbes, or non-sterilized soil. Metagenomic sequencing results showed the intake of sterile soil, that is, inhaling a small amount of soil microbes in the air increased gut microbial diversity and the abundance of type III secretion system (T3SS) genes, and decreased serum immune IgE levels induced by 2-4-dinitrofluorobenzene (DNFB). The intake of soil microbes increased the abundance of genes involved in the metabolism of short-chain fatty acids and amino acid biosynthesis. Meanwhile, the intake of soil increased gut microbial diversity, the abundance of T3SS genes and related infectious elements, and genes associated with the metabolism of short-chain fatty acids and amino acid biosynthesis, and decreased serum IgE levels. Therefore, soil may be useful as a potential 'prebiotic' promoting the reproduction and growth of some intestinal microorganisms that harbour bacterial secretion system genes, especially those of T3SS, whose abundance was positively and significantly correlated with innate immune function of mice.}, } @article {pmid35315560, year = {2022}, author = {Adler, A and Poirier, S and Pagni, M and Maillard, J and Holliger, C}, title = {Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter.}, journal = {Environmental microbiology}, volume = {24}, number = {4}, pages = {2136-2156}, pmid = {35315560}, issn = {1462-2920}, mesh = {Bacteria/genetics ; *Betaproteobacteria/genetics ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Sewage/microbiology ; }, abstract = {Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragmented and incomplete genomes. Here, the metagenomes of four samples of aerobic granular sludge bioreactors containing Candidatus (Ca.) Accumulibacter, a phosphate-accumulating organism of interest for wastewater treatment, were sequenced with both PacBio and Illumina. Different strategies of genome assembly and binning were investigated, including published protocols and a binning procedure adapted to the binning of long contigs (MuLoBiSC). Multiple criteria were considered to select the best strategy for Ca. Accumulibacter, whose multiple strains in every sample represent a challenging microdiversity. In this case, the best strategy relies on long-read only assembly and a custom binning procedure including MuLoBiSC in metaWRAP. Several high-quality Ca. Accumulibacter MAGs, including a novel species, were obtained independently from different samples. Comparative genomic analysis showed that MAGs retrieved in different samples harbour genomic rearrangements in addition to accumulation of point mutations. The microdiversity of Ca. Accumulibacter, likely driven by mobile genetic elements, causes major difficulties in recovering MAGs, but it is also a hallmark of the panmictic lifestyle of these bacteria.}, } @article {pmid35314706, year = {2022}, author = {Zhou, YL and Mara, P and Cui, GJ and Edgcomb, VP and Wang, Y}, title = {Microbiomes in the Challenger Deep slope and bottom-axis sediments.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {1515}, pmid = {35314706}, issn = {2041-1723}, mesh = {*Bacteria/metabolism ; Geologic Sediments ; Heterotrophic Processes ; Metagenome/genetics ; *Microbiota/genetics ; Water/metabolism ; }, abstract = {Hadal trenches are the deepest and most remote regions of the ocean. The 11-kilometer deep Challenger Deep is the least explored due to the technical challenges of sampling hadal depths. It receives organic matter and heavy metals from the overlying water column that accumulate differently across its V-shaped topography. Here, we collected sediments across the slope and bottom-axis of the Challenger Deep that enable insights into its in situ microbial communities. Analyses of 586 metagenome-assembled genomes retrieved from 37 metagenomes show distinct diversity and metabolic capacities between bottom-axis and slope sites. 26% of prokaryotic 16S rDNA reads in metagenomes were novel, with novelty increasing with water and sediment depths. These predominantly heterotrophic microbes can recycle macromolecules and utilize simple and complex hydrocarbons as carbon sources. Metagenome and metatranscriptome data support reduction and biotransformation of arsenate for energy gain in sediments that present a two-fold greater accumulation of arsenic compared to non-hadal sites. Complete pathways for anaerobic ammonia oxidation are predominantly identified in genomes recovered from bottom-axis sediments compared to slope sites. Our results expand knowledge of microbially-mediated elemental cycling in hadal sediments, and reveal differences in distribution of processes involved in nitrogen loss across the trench.}, } @article {pmid35312212, year = {2022}, author = {Nguyen, STT and Vardeh, DP and Nelson, TM and Pearson, LA and Kinsela, AS and Neilan, BA}, title = {Bacterial community structure and metabolic potential in microbialite-forming mats from South Australian saline lakes.}, journal = {Geobiology}, volume = {20}, number = {4}, pages = {546-559}, pmid = {35312212}, issn = {1472-4669}, mesh = {Australia ; *Cyanobacteria/genetics ; Geologic Sediments/chemistry ; Lakes/microbiology ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; South Australia ; }, abstract = {Microbialites are sedimentary rocks created in association with benthic microorganisms. While they harbour complex microbial communities, Cyanobacteria perform critical roles in sediment stabilisation and accretion. Microbialites have been described from permanent and ephemeral saline lakes in South Australia; however, the microbial communities that generate and inhabit these biogeological structures have not been studied in detail. To address this knowledge gap, we investigated the composition, diversity and metabolic potential of bacterial communities from different microbialite-forming mats and surrounding sediments in five South Australian saline coastal lakes using 16S rRNA gene sequencing and predictive metagenome analyses. While Proteobacteria and Bacteroidetes were the dominant phyla recovered from the mats and sediments, Cyanobacteria were significantly more abundant in the mat samples. Interestingly, at lower taxonomic levels, the mat communities were vastly different across the five lakes. Comparative analysis of putative mat and sediment metagenomes via PICRUSt2 revealed important metabolic pathways driving the process of carbonate precipitation, including cyanobacterial oxygenic photosynthesis, ureolysis and nitrogen fixation. These pathways were highly conserved across the five examined lakes, although they appeared to be performed by distinct groups of bacterial taxa found in each lake. Stress response, quorum sensing and circadian clock were other important pathways predicted by the in silico metagenome analysis. The enrichment of CRISPR/Cas and phage shock associated genes in these cyanobacteria-rich communities suggests that they may be under selective pressure from viral infection. Together, these results highlight that a very stable ecosystem function is maintained by distinctly different communities in microbialite-forming mats in the five South Australian lakes and reinforce the concept that 'who' is in the community is not as critical as their net metabolic capacity.}, } @article {pmid35311904, year = {2022}, author = {Wang, Y and Guan, LL}, title = {Translational multi-omics microbiome research for strategies to improve cattle production and health.}, journal = {Emerging topics in life sciences}, volume = {6}, number = {2}, pages = {201-213}, doi = {10.1042/ETLS20210257}, pmid = {35311904}, issn = {2397-8554}, mesh = {Animals ; Cattle ; Metagenomics ; Methane ; *Microbiota ; Milk ; *Rumen ; }, abstract = {Cattle microbiome plays a vital role in cattle growth and performance and affects many economically important traits such as feed efficiency, milk/meat yield and quality, methane emission, immunity and health. To date, most cattle microbiome research has focused on metataxonomic and metagenomic characterization to reveal who are there and what they may do, preventing the determination of the active functional dynamics in vivo and their causal relationships with the traits. Therefore, there is an urgent need to combine other advanced omics approaches to improve microbiome analysis to determine their mode of actions and host-microbiome interactions in vivo. This review will critically discuss the current multi-omics microbiome research in beef and dairy cattle, aiming to provide insights on how the information generated can be applied to future strategies to improve production efficiency, health and welfare, and environment-friendliness in cattle production through microbiome manipulations.}, } @article {pmid35311577, year = {2022}, author = {Shiroma, H and Shiba, S and Erawijantari, PP and Takamaru, H and Yamada, M and Sakamoto, T and Kanemitsu, Y and Mizutani, S and Soga, T and Saito, Y and Shibata, T and Fukuda, S and Yachida, S and Yamada, T}, title = {Surgical Treatment for Colorectal Cancer Partially Restores Gut Microbiome and Metabolome Traits.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0001822}, pmid = {35311577}, issn = {2379-5077}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/genetics ; Metabolome ; *Adenoma ; Carcinogenesis ; }, abstract = {Accumulating evidence indicates that the gut microbiome and metabolites are associated with colorectal cancer (CRC). However, the influence of surgery for CRC treatment on the gut microbiome and metabolites and how it relates to CRC risk in postoperative CRC patients remain partially understood. Here, we collected 170 fecal samples from 85 CRC patients pre- and approximately 1 year postsurgery and performed shotgun metagenomic sequencing and capillary electrophoresis-time of flight mass spectrometry-based metabolomics analyses to characterize alterations between pre- and postsurgery. We determined that the relative abundance of 114 species was altered postsurgery (P < 0.005). CRC-associated species, such as Fusobacterium nucleatum, were decreased postsurgery. On the other hand, Clostridium scindens, carcinogenesis-associated deoxycholate (DCA)-producing species, and its biotransformed genes (bai operon) were increased postsurgery. The concentration of 60 fecal metabolites was also altered postsurgery (P < 0.005). Two bile acids, cholate and DCA, were increased postsurgery. We developed methods to estimate postoperative CRC risk based on the gut microbiome and metabolomic compositions using a random forest machine-learning algorithm that classifies large adenoma or early-stage CRC and healthy controls from publicly available data sets. We applied methods to preoperative samples and then compared the estimated CRC risk between the two groups according to the presence of large adenoma or tumors 5 years postsurgery (P < 0.05). Overall, our results show that the gut microbiome and metabolites dynamically change from pre- to postsurgery. In postoperative CRC patients, potential CRC risk derived from gut microbiome and metabolites still remains, which indicates the importance of follow-up assessments. IMPORTANCE The gut microbiome and metabolites are associated with CRC progression and carcinogenesis. Postoperative CRC patients are reported to be at an increased CRC risk; however, how gut microbiome and metabolites are related to CRC risk in postoperative patients remains only partially understood. In this study, we investigated the influence of surgical CRC treatment on the gut microbiome and metabolites. We found that the CRC-associated species Fusobacterium nucleatum was decreased postsurgery, whereas carcinogenesis-associated DCA and its producing species and genes were increased postsurgery. We developed methods to estimate postoperative CRC risk based on the gut microbiome and metabolomic compositions. We applied methods to compare the estimated CRC risk between two groups according to the presence of large adenoma or tumors after 5 years postsurgery. To our knowledge, this study is the first report on differences between pre- and postsurgery using metagenomics and metabolomics data analysis. Our methods might be used for CRC risk assessment in postoperative patients.}, } @article {pmid35311446, year = {2022}, author = {Ranaivo, H and Thirion, F and Béra-Maillet, C and Guilly, S and Simon, C and Sothier, M and Van Den Berghe, L and Feugier-Favier, N and Lambert-Porcheron, S and Dussous, I and Roger, L and Roume, H and Galleron, N and Pons, N and Le Chatelier, E and Ehrlich, SD and Laville, M and Doré, J and Nazare, JA}, title = {Increasing the diversity of dietary fibers in a daily-consumed bread modifies gut microbiota and metabolic profile in subjects at cardiometabolic risk.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2044722}, pmid = {35311446}, issn = {1949-0984}, mesh = {Bread/analysis ; *Cardiovascular Diseases ; Dietary Fiber/analysis ; *Gastrointestinal Microbiome ; Humans ; Metabolome ; }, abstract = {Some cardiometabolic risk factors such as dyslipidemia and insulin resistance are known to be associated with low gut microbiota richness. A link between gut microbiota richness and the diversity of consumed dietary fibers (DF) has also been reported. We introduced a larger diversity of consumed DF by using a daily consumed bread in subjects at cardiometabolic risk and assessed the impacts on the composition and functions of gut microbiota as well as on cardiometabolic profile. Thirty-nine subjects at cardiometabolic risk were included in a double-blind, randomized, cross-over, twice 8-week study, and consumed daily 150 g of standard bread or enriched with a 7-dietary fiber mixture (5.55 g and 16.05 g of fibers, respectively). Before and after intervention, stool samples were collected for gut microbiota analysis from species determination down to gene-level abundance using shotgun metagenomics, and cardiometabolic profile was assessed. Multi-fiber bread consumption significantly decreased Bacteroides vulgatus, whereas it increased Parabacteroides distasonis, Fusicatenibacter saccharivorans, an unclassified Acutalibacteraceae and an unclassified Eisenbergiella (q < 0.1). The fraction of gut microbiota carrying the gene coding for five families/subfamilies of glycoside hydrolases (CAZymes) were also increased and negatively correlated with peaks and total/incremental area under curve (tAUC/iAUC) of postprandial glycemia and insulinemia. Compared to control bread, multi-fiber bread decreased total cholesterol (-0.42 mM; q < 0.01), LDL cholesterol (-0.36 mM; q < 0.01), insulin (-2.77 mIU/l; q < 0.05), and HOMA (-0.78; q < 0.05). In conclusion, increasing the diversity of DF in a daily consumed product modifies gut microbiota composition and function and could be a relevant nutritional tool to improve cardiometabolic profile.}, } @article {pmid35310842, year = {2022}, author = {Di Guglielmo, MD and Franke, KR and Robbins, A and Crowgey, EL}, title = {Impact of Early Feeding: Metagenomics Analysis of the Infant Gut Microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {816601}, pmid = {35310842}, issn = {2235-2988}, support = {P30 GM114736/GM/NIGMS NIH HHS/United States ; U54 GM104941/GM/NIGMS NIH HHS/United States ; }, mesh = {Breast Feeding ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Infant Formula ; Metagenomics ; *Microbiota ; }, abstract = {BACKGROUND: Different feeding regimens in infancy alter the gastrointestinal (gut) microbial environment. The fecal microbiota in turn influences gastrointestinal homeostasis including metabolism, immune function, and extra-/intra-intestinal signaling. Advances in next generation sequencing (NGS) have enhanced our ability to study the gut microbiome of breast-fed (BF) and formula-fed (FF) infants with a data-driven hypothesis approach.

METHODS: Next generation sequencing libraries were constructed from fecal samples of BF (n=24) and FF (n=10) infants and sequenced on an Illumina HiSeq 2500. Taxonomic classification of the NGS data was performed using the Sunbeam/Kraken pipeline and a functional analysis at the gene level was performed using publicly available algorithms, including BLAST, and custom scripts. Differentially represented genera, genes, and NCBI Clusters of Orthologous Genes (COG) were determined between cohorts using count data and R (statistical packages edgeR and DESeq2).

RESULTS: Thirty-nine genera were found to be differentially represented between the BF and FF cohorts (FDR ≤ 0.01) including Parabacteroides, Enterococcus, Haemophilus, Gardnerella, and Staphylococcus. A Welch t-test of the Shannon diversity index for BF and FF samples approached significance (p=0.061). Bray-Curtis and Jaccard distance analyses demonstrated clustering and overlap in each analysis. Sixty COGs were significantly overrepresented and those most significantly represented in BF vs. FF samples showed dichotomy of categories representing gene functions. Over 1,700 genes were found to be differentially represented (abundance) between the BF and FF cohorts.

CONCLUSIONS: Fecal samples analyzed from BF and FF infants demonstrated differences in microbiota genera. The BF cohort includes greater presence of beneficial genus Bifidobacterium. Several genes were identified as present at different abundances between cohorts indicating differences in functional pathways such as cellular defense mechanisms and carbohydrate metabolism influenced by feeding. Confirmation of gene level NGS data via PCR and electrophoresis analysis revealed distinct differences in gene abundances associated with important biologic pathways.}, } @article {pmid35310160, year = {2022}, author = {Irazoqui, JM and Eberhardt, MF and Adjad, MM and Amadio, AF}, title = {Identification of key microorganisms in facultative stabilization ponds from dairy industries, using metagenomics.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e12772}, pmid = {35310160}, issn = {2167-8359}, mesh = {*Wastewater ; Ponds ; Dairying ; *Microbiota/genetics ; Genome, Microbial ; }, abstract = {Wastewater stabilization ponds are a natural form of wastewater treatment. Their low operation and maintenance costs have made them popular, especially in developing countries. In these systems, effluents are retained for long periods of time, allowing the microbial communities present in the ponds to degrade the organic matter present, using both aerobic and anaerobic processes. Even though these systems are widespread in low income countries, there are no studies about the microorganisms present in them and how they operate. In this study, we analised the microbial communities of two serial full-scale stabilization ponds systems using whole genome shotgun sequencing. First, a taxonomic profiling of the reads was performed, to estimate the microbial diversity. Then, the reads of each system were assembled and binned, allowing the reconstruction of 110 microbial genomes. A functional analysis of the genomes allowed us to find how the main metabolic pathways are carried out, and we propose several organisms that would be key to this kind of environment, since they play an important role in these metabolic pathways. This study represents the first genome-centred approach to understand the metabolic processes in facultative ponds. A better understanding of these microbial communities and how they stabilize the effluents of dairy industries is necessary to improve them and to minimize the environmental impact of dairy industries wastewater.}, } @article {pmid35309369, year = {2022}, author = {Fan, Y and Gao, Y and Ma, Q and Yang, Z and Zhao, B and He, X and Yang, J and Yan, B and Gao, F and Qian, L and Wang, W and Zhu, F and Ma, X}, title = {Multi-Omics Analysis Reveals Aberrant Gut-Metabolome-Immune Network in Schizophrenia.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {812293}, pmid = {35309369}, issn = {1664-3224}, mesh = {Bacteria ; Cytokines ; *Gastrointestinal Microbiome ; Humans ; Metabolome ; *Schizophrenia ; }, abstract = {Schizophrenia (SCZ) is associated with several immune dysfunctions, including elevated levels of pro-inflammatory cytokines. Microorganisms and their metabolites have been found to regulate the immune system, and that intestinal microbiota is significantly disturbed in schizophrenic patients. To systematically investigate aberrant gut-metabolome-immune network in schizophrenia, we performed an integrative analysis of intestinal microbiota, serum metabolome, and serum inflammatory cytokines in 63 SCZ patients and 57 healthy controls using a multi-omics strategy. Eighteen differentially abundant metabolite clusters were altered in patients displayed higher cytokine levels, with a significant increase in pro-inflammatory metabolites and a significant decrease in anti-inflammatory metabolites (such as oleic acid and linolenic acid). The bacterial co-abundance groups in the gut displayed more numerous and stronger correlations with circulating metabolites than with cytokines. By integrating these data, we identified that certain bacteria might affect inflammatory cytokines by modulating host metabolites, such as amino acids and fatty acids. A random forest model was constructed based on omics data, and seven serum metabolites significantly associated with cytokines and α-diversity of intestinal microbiota were able to accurately distinguish the cases from the controls with an area under the receiver operating characteristic curve of 0.99. Our results indicated aberrant gut-metabolome-immune network in SCZ and gut microbiota may influence immune responses by regulating host metabolic processes. These findings suggest a mechanism by which microbial-derived metabolites regulated inflammatory cytokines and insights into the diagnosis and treatment of mental disorders from the microbial-immune system in the future.}, } @article {pmid35304940, year = {2022}, author = {Arora-Williams, K and Holder, C and Secor, M and Ellis, H and Xia, M and Gnanadesikan, A and Preheim, SP}, title = {Abundant and persistent sulfur-oxidizing microbial populations are responsive to hypoxia in the Chesapeake Bay.}, journal = {Environmental microbiology}, volume = {24}, number = {5}, pages = {2315-2332}, pmid = {35304940}, issn = {1462-2920}, mesh = {*Bays ; Maryland ; *Microbiota/genetics ; Oxidation-Reduction ; Oxygen ; RNA, Ribosomal, 16S/genetics ; Sulfur ; *Sulfur-Reducing Bacteria ; Virginia ; Water ; }, abstract = {The number, size and severity of aquatic low-oxygen dead zones are increasing worldwide. Microbial processes in low-oxygen environments have important ecosystem-level consequences, such as denitrification, greenhouse gas production and acidification. To identify key microbial processes occurring in low-oxygen bottom waters of the Chesapeake Bay, we sequenced both 16S rRNA genes and shotgun metagenomic libraries to determine the identity, functional potential and spatiotemporal distribution of microbial populations in the water column. Unsupervised clustering algorithms grouped samples into three clusters using water chemistry or microbial communities, with extensive overlap of cluster composition between methods. Clusters were strongly differentiated by temperature, salinity and oxygen. Sulfur-oxidizing microorganisms were found to be enriched in the low-oxygen bottom water and predictive of hypoxic conditions. Metagenome-assembled genomes demonstrate that some of these sulfur-oxidizing populations are capable of partial denitrification and transcriptionally active in a prior study. These results suggest that microorganisms capable of oxidizing reduced sulfur compounds are a previously unidentified microbial indicator of low oxygen in the Chesapeake Bay and reveal ties between the sulfur, nitrogen and oxygen cycles that could be important to capture when predicting the ecosystem response to remediation efforts or climate change.}, } @article {pmid35302439, year = {2022}, author = {Gehrig, JL and Portik, DM and Driscoll, MD and Jackson, E and Chakraborty, S and Gratalo, D and Ashby, M and Valladares, R}, title = {Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data.}, journal = {Microbial genomics}, volume = {8}, number = {3}, pages = {}, pmid = {35302439}, issn = {2057-5858}, mesh = {Humans ; Metagenome/genetics ; Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {A long-standing challenge in human microbiome research is achieving the taxonomic and functional resolution needed to generate testable hypotheses about the gut microbiota's impact on health and disease. With a growing number of live microbial interventions in clinical development, this challenge is renewed by a need to understand the pharmacokinetics and pharmacodynamics of therapeutic candidates. While short-read sequencing of the bacterial 16S rRNA gene has been the standard for microbiota profiling, recent improvements in the fidelity of long-read sequencing underscores the need for a re-evaluation of the value of distinct microbiome-sequencing approaches. We leveraged samples from participants enrolled in a phase 1b clinical trial of a novel live biotherapeutic product to perform a comparative analysis of short-read and long-read amplicon and metagenomic sequencing approaches to assess their utility for generating clinical microbiome data. Across all methods, overall community taxonomic profiles were comparable and relationships between samples were conserved. Comparison of ubiquitous short-read 16S rRNA amplicon profiling to long-read profiling of the 16S-ITS-23S rRNA amplicon showed that only the latter provided strain-level community resolution and insight into novel taxa. All methods identified an active ingredient strain in treated study participants, though detection confidence was higher for long-read methods. Read coverage from both metagenomic methods provided evidence of active-ingredient strain replication in some treated participants. Compared to short-read metagenomics, approximately twice the proportion of long reads were assigned functional annotations. Finally, compositionally similar bacterial metagenome-assembled genomes (MAGs) were recovered from short-read and long-read metagenomic methods, although a greater number and more complete MAGs were recovered from long reads. Despite higher costs, both amplicon and metagenomic long-read approaches yielded added microbiome data value in the form of higher confidence taxonomic and functional resolution and improved recovery of microbial genomes compared to traditional short-read methodologies.}, } @article {pmid35300964, year = {2022}, author = {Sharma, P and Singh, SP and Iqbal, HMN and Tong, YW}, title = {Omics approaches in bioremediation of environmental contaminants: An integrated approach for environmental safety and sustainability.}, journal = {Environmental research}, volume = {211}, number = {}, pages = {113102}, doi = {10.1016/j.envres.2022.113102}, pmid = {35300964}, issn = {1096-0953}, mesh = {Biodegradation, Environmental ; *Environmental Pollutants/metabolism ; Genomics/methods ; Humans ; Metabolomics/methods ; *Microbiota ; Proteomics/methods ; }, abstract = {Non-degradable pollutants have emerged as a result of industrialization, population growth, and lifestyle changes, endangering human health and the environment. Bioremediation is the process of clearing hazardous contaminants with the help of microorganisms, and cost-effective approach. The low-cost and environmentally acceptable approach to removing environmental pollutants from ecosystems is microbial bioremediation. However, to execute these different bioremediation approaches successfully, this is imperative to have a complete understanding of the variables impacting the development, metabolism, dynamics, and native microbial communities' activity in polluted areas. The emergence of new technologies like next-generation sequencing, protein and metabolic profiling, and advanced bioinformatic tools have provided critical insights into microbial communities and underlying mechanisms in environmental contaminant bioremediation. These omics approaches are meta-genomics, meta-transcriptomics, meta-proteomics, and metabolomics. Moreover, the advancements in these technologies have greatly aided in determining the effectiveness and implementing microbiological bioremediation approaches. At Environmental Protection Agency (EPA)-The government placed special emphasis on exploring how molecular and "omic" technologies may be used to determine the nature, behavior, and functions of the intrinsic microbial communities present at pollution containment systems. Several omics techniques are unquestionably more informative and valuable in elucidating the mechanism of the process and identifying the essential player's involved enzymes and their regulatory elements. This review provides an overview and description of the omics platforms that have been described in recent reports on omics approaches in bioremediation and that demonstrate the effectiveness of integrated omics approaches and their novel future use.}, } @article {pmid35300688, year = {2022}, author = {Cui, J and Hou, S and Liu, B and Yang, M and Wei, L and Du, S and Li, S}, title = {Species composition and overall diversity are significantly correlated between the tongue coating and gastric fluid microbiomes in gastritis patients.}, journal = {BMC medical genomics}, volume = {15}, number = {1}, pages = {60}, pmid = {35300688}, issn = {1755-8794}, mesh = {*Gastritis/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; RNA, Ribosomal, 16S ; Tongue/microbiology ; }, abstract = {BACKGROUND: In traditional Chinese medicine, it is believed that the "tongue coating is produced by fumigation of stomach gas", and that tongue coating can reflect the health status of humans, especially stomach health. Therefore, studying the relationship between the microbiome of the tongue coating and the gastric fluid is of great significance for understanding the biological basis of tongue diagnosis.

METHODS: This paper detected the microbiomes of the tongue coating and the gastric fluid in 35 gastritis patients using metagenomic sequencing technology, systematically constructed the microbial atlas of tongue coating and gastric juice, and first described the similar characteristics between the two sites.

RESULTS: There was a significant correlation between tongue coating and gastric juice in terms of microbial species composition and overall diversity. In terms of species composition, it was found that the two sites were dominated by five phyla, namely, Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria and Proteobacteria, and that most of the gastric microbial species could be detected from the patient's own tongue coating. In terms of overall diversity, a significant correlation was found between the alpha diversity of the tongue coating microbiome and the gastric juice microbiome. Furthermore, in terms of abundance, 4 classes, 2 orders, 4 families, 18 genera and 46 species were found to significantly correlate between the tongue coating and the gastric fluid.

CONCLUSIONS: The results provide microbiome-based scientific evidence for tongue diagnosis, and offer a new perspective for understanding the biological basis of tongue diagnosis.}, } @article {pmid35300678, year = {2022}, author = {Xiong, X and Liu, X and Wang, Z and Xu, Q and Xu, J and Rao, Y}, title = {Identifying biomarkers of the gut bacteria, bacteriophages and serum metabolites associated with three weaning periods in piglets.}, journal = {BMC veterinary research}, volume = {18}, number = {1}, pages = {104}, pmid = {35300678}, issn = {1746-6148}, mesh = {Animals ; Bacteria/genetics ; *Bacteriophages ; Biomarkers/metabolism ; *Gastrointestinal Microbiome/genetics ; Swine ; Weaning ; }, abstract = {BACKGROUND: The establishment of the piglet gut microbiome has a prolonged influence on host health, as it sets the stage for establishment of the adult swine microbiome. Substantial changes in host metabolism and immunity around the time of weaning may be accompanied by alterations in the gut microbiome. In this study, we systematically evaluated differences in the gut microbiome and host metabolites among three weaning periods using shotgun metagenomic sequencing and untargeted metabolomic profiling in piglets.

RESULTS: We identified that P. copri was the most significantly different species among three weaning periods, and was the key bacterial species for mitigating piglet adaptation during the weaning transition, while Bacillus_phage_BCD7, the only differential bacteriophages, was significantly and positively correlated with P. copri enriched in day 28 group. Additionally, P. copri and Bacillus_phage_BCD7 was significantly correlated with the shifts of functional capacities of the gut microbiome and several CAZymes in day 28 group. Furthermore, the altered metabolites we observed were enriched in pathways matched to the functional capacity of the gut microbiome e.g., aminoacyl-tRNA biosynthesis.

CONCLUSION: The results from this study indicate that the bacteria-phage interactions and host-microbial interactions during the weaning transition impact host metabolism, leading to beneficial host changes among three weaning periods.}, } @article {pmid35298549, year = {2022}, author = {Juhász, Á and Molnár-Nagy, V and Bata, Z and Tso, KH and Mayer, Z and Posta, K}, title = {Alternative to ZnO to establish balanced intestinal microbiota for weaning piglets.}, journal = {PloS one}, volume = {17}, number = {3}, pages = {e0265573}, pmid = {35298549}, issn = {1932-6203}, mesh = {Animal Feed ; Animals ; Diarrhea/prevention & control/veterinary ; Dietary Supplements ; *Gastrointestinal Microbiome ; Prebiotics ; Swine ; Weaning ; *Zinc Oxide/pharmacology ; }, abstract = {A wide range of phytobiotic feed additives are available on the market claiming to have beneficial effects on the growth of the host animal and to promote the development of a balanced microflora. The present study investigated the effects of the phytobiotic-prebiotic mixture of curcumin, wheat germ, and chicory on the growth performance and on the intestinal microflora composition of weaning piglets. Post weaning diarrhea causes significant losses for the producers, most commonly it is prevented by feeding high doses of zinc oxide (ZnO). The effect of a phytobiotic-prebiotic feed additive (1 kg T-1) was compared to a positive control (3.1 kg T-1 ZnO) and to a negative control (no feed supplement) in an in vivo animal trial. There was no significant difference in the final body weight and average daily gain of the trial and positive control groups, and both groups showed significantly (P<0.05) better results than the negative control. The feed conversion ratio of the phytobiotic-prebiotic supplemented group was significantly improved (P<0.05) compared to both controls. Both phytobiotic-prebiotic mixture and ZnO were able to significantly reduce (P<0.05) the amount of coliforms after weaning, even though ZnO reduced the amount of coliforms more efficiently than the trial feed additive, it also reduced the amount of potentially beneficial bacteria. Metagenomic data also corroborated the above conclusion. In the trial and positive control groups, the relative abundance of Enterobacteriaceae decreased by 85 and 88% between 3 weeks and 6 weeks of age, while in the negative control group a slight increase occurred. Lactobacillaceae were more abundant in the trial group (29.98%) than in the positive (8.67%) or in the negative (22.45%) control groups at 6 weeks of age. In summary, this study demonstrated that a phytobiotic-prebiotic feed additive may be a real alternative to ZnO for the prevention of post weaning diarrhea and promote the development of a balanced gut system.}, } @article {pmid35298370, year = {2022}, author = {Cuscó, A and Pérez, D and Viñes, J and Fàbregas, N and Francino, O}, title = {Novel canine high-quality metagenome-assembled genomes, prophages and host-associated plasmids provided by long-read metagenomics together with Hi-C proximity ligation.}, journal = {Microbial genomics}, volume = {8}, number = {3}, pages = {}, pmid = {35298370}, issn = {2057-5858}, mesh = {Animals ; Bacteria/genetics ; Dogs ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; Plasmids/genetics ; Prophages/genetics ; }, abstract = {The human gut microbiome has been extensively studied, yet the canine gut microbiome is still largely unknown. The availability of high-quality genomes is essential in the fields of veterinary medicine and nutrition to unravel the biological role of key microbial members in the canine gut environment. Our aim was to evaluate nanopore long-read metagenomics and Hi-C (high-throughput chromosome conformation capture) proximity ligation to provide high-quality metagenome-assembled genomes (HQ MAGs) of the canine gut environment. By combining nanopore long-read metagenomics and Hi-C proximity ligation, we retrieved 27 HQ MAGs and 7 medium-quality MAGs of a faecal sample of a healthy dog. Canine MAGs (CanMAGs) improved genome contiguity of representatives from the animal and human MAG catalogues - short-read MAGs from public datasets - for the species they represented: they were more contiguous with complete ribosomal operons and at least 18 canonical tRNAs. Both canine-specific bacterial species and gut generalists inhabit the dog's gastrointestinal environment. Most of them belonged to Firmicutes, followed by Bacteroidota and Proteobacteria. We also assembled one Actinobacteriota and one Fusobacteriota MAG. CanMAGs harboured antimicrobial-resistance genes (ARGs) and prophages and were linked to plasmids. ARGs conferring resistance to tetracycline were most predominant within CanMAGs, followed by lincosamide and macrolide ones. At the functional level, carbohydrate transport and metabolism was the most variable within the CanMAGs, and mobilome function was abundant in some MAGs. Specifically, we assigned the mobilome functions and the associated mobile genetic elements to the bacterial host. The CanMAGs harboured 50 bacteriophages, providing novel bacterial-host information for eight viral clusters, and Hi-C proximity ligation data linked the six potential plasmids to their bacterial host. Long-read metagenomics and Hi-C proximity ligation are likely to become a comprehensive approach to HQ MAG discovery and assignment of extra-chromosomal elements to their bacterial host. This will provide essential information for studying the canine gut microbiome in veterinary medicine and animal nutrition.}, } @article {pmid35296830, year = {2022}, author = {Walsh, CAJ and Momigliano, P and Boussarie, G and Robbins, WD and Bonnin, L and Fauvelot, C and Kiszka, JJ and Mouillot, D and Vigliola, L and Manel, S}, title = {Genomic insights into the historical and contemporary demographics of the grey reef shark.}, journal = {Heredity}, volume = {128}, number = {4}, pages = {225-235}, pmid = {35296830}, issn = {1365-2540}, mesh = {Animals ; Coral Reefs ; Gene Flow ; Metagenomics ; Population Density ; *Sharks/genetics ; }, abstract = {Analyses of genetic diversity can shed light on both the origins of biodiversity hotspots, as well as the conservation status of species that are impacted by human activities. With these objectives, we assembled a genomic dataset of 14,935 single nucleotide polymorphisms from 513 grey reef sharks (Carcharhinus amblyrhynchos) sampled across 17 locations in the tropical Indo-Pacific. We analysed geographic variation in genetic diversity, estimated ancient and contemporary effective population size (Ne) across sampling locations (using coalescent and linkage disequilibrium methods) and modelled the history of gene flow between the Coral Triangle and the Coral Sea. Genetic diversity decreased with distance away from the Coral Triangle and north-western Australia, implying that C. amblyrhynchos may have originated in this region. Increases in Ne were detected across almost all sampling locations 40,000-90,000 generations ago (approximately 0.6-1.5 mya, given an estimated generation time of 16.4 years), suggesting a range expansion around this time. More recent, secondary increases in Ne were inferred for the Misool and North Great Barrier Reef sampling locations, but joint modelling did not clarify whether these were due to population growth, migration, or both. Despite the greater genetic diversity and ancient Ne observed at sites around Australia and the Coral Triangle, remote reefs around north-western New Caledonia had the highest contemporary Ne, demonstrating the importance of using multiple population size assessment methods. This study provides insight into both the past and present demographics of C. amblyrhynchos and contributes to our understanding of evolution in marine biodiversity hotspots.}, } @article {pmid35296712, year = {2022}, author = {Schaefer, L and Hernandez, H and Coats, RA and Yu, Z and Pflugfelder, SC and Britton, RA and de Paiva, CS}, title = {Gut-derived butyrate suppresses ocular surface inflammation.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {4512}, pmid = {35296712}, issn = {2045-2322}, support = {EY026893/NH/NIH HHS/United States ; F32 EY007001/EY/NEI NIH HHS/United States ; T32 EY007001/EY/NEI NIH HHS/United States ; EY007001/EY/NEI NIH HHS/United States ; R01 EY026893/EY/NEI NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Butyrates/metabolism/pharmacology ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Inflammation/drug therapy/metabolism ; Mice ; Monocarboxylic Acid Transporters/metabolism ; Tears/metabolism ; }, abstract = {Dry eye is a common ocular inflammatory disorder characterized by tear film instability and reduced tear production. There is increasing evidence that homeostasis of the ocular surface is impacted by the intestinal microbiome. We are interested in investigating the potential role of microbially produced small molecules in mediating the interaction between the intestinal microbiota and the ocular surface. One such molecule is butyrate, a short-chain fatty acid (SCFA) produced by certain members of the gut microbiota through fermentation of dietary fiber. Here we show that SCFA transporter SLC5A8 is expressed in vivo in murine conjunctival and corneal epithelium. Pre-treatment of in vitro corneal epithelial cultures or bone marrow-derived dendritic cells (BMDCs) with phenylbutyrate (PBA) reduces lipopolysaccharide-induced pro-inflammatory Tnf expression. Corneal epithelial cultures and BMDCs isolated from Slc5a8 knockout mice are unable to respond to PBA pre-treatment, suggesting that SLC5A8 is required for the protective effect of PBA. The treatment of mice undergoing desiccating stress (DS) with oral tributyrin, a prodrug form of butyrate, reduces inflammation at the ocular surface in vivo, and this effect partially requires SLC5A8. Finally, expression analysis on conjunctival tissue isolated from mice subjected to DS with and without tributyrin treatment revealed that treatment downregulated genes involved in Type I interferon signaling. Together these data support our hypothesis that SCFAs produced in the gut participate in the maintenance of ocular surface homeostasis.}, } @article {pmid35294588, year = {2022}, author = {Guarin, TC and Li, L and Pagilla, KR}, title = {Microbial community characterization in advanced water reclamation for potable reuse.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {7}, pages = {2763-2773}, pmid = {35294588}, issn = {1432-0614}, mesh = {Bacteria/genetics ; *Drinking Water/microbiology ; *Microbiota ; *Ozone ; RNA, Ribosomal, 16S/genetics ; *Water Purification ; }, abstract = {This study investigated the microbial community structure and composition across two treatment steps used in advanced water reclamation for potable reuse applications, namely Coagulation/Flocculation/Clarification/Granular Media Filtration (CFCGMF) and Ozone-Biological Activated Carbon filtration (O3/BAC). The study examined the richness, variations, and similarities of the microorganisms involved at each treatment step to better understand the role of ecology and the dynamics on unit process performance and the microbial community developed within it. The bacterial microbiomes at each treatment step were independently characterized using 16S metagenomic sequencing. Combining both treatment steps, a total of 3801 species were detected. From the total species detected, 38% and 98% were identified at CFCGMF and O3/BAC, respectively. The most abundant phyla were Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes in both treatment steps. The identified species were classified based on their preferences to free-living style (59%) vs attached-living style (22%) showing a relatively low richness in the BAC media, but higher diversities. At the taxonomic class level, Betaproteobacteria was the predominant in both system processes. Additionally, a list of eight genera were identified as potential bacterial pathogens present in both process effluents. They are Aeromonas, Clostridium, Enterobacter, Escherichia, Flavobacterium, Legionella, Mycobacterium, and Pseudomonas. CFCGMF effluent yielded less pathogenic bacteria than both the ozone and BAC filter effluent from the O3/BAC process unit; their relative abundance accounted for about 2% and 8% for CFCGMF and O3/BAC, respectively. Detailed studies to characterize the microbial communities are crucial in interpreting the mechanisms and synergies between processes performance and microorganisms by identifying the needs and best practices to ensure public health protection. Key points • Microbial communities of two treatment processes are characterized using 16S rRNA sequencing. • Organisms that can tolerate ozone and form biofilms define microbial community in subsequent biofilters. • In relatively low abundances, potential pathogenic bacteria are detected in the treated water.}, } @article {pmid35293806, year = {2022}, author = {Wang, L and Cheng, X and Bai, L and Gao, M and Kang, G and Cao, X and Huang, H}, title = {Positive Interventional Effect of Engineered Butyrate-Producing Bacteria on Metabolic Disorders and Intestinal Flora Disruption in Obese Mice.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0114721}, pmid = {35293806}, issn = {2165-0497}, mesh = {Animals ; Bacteria/genetics/metabolism ; Butyrates/adverse effects/metabolism ; *Gastrointestinal Microbiome/physiology ; Glucose/adverse effects ; *Metabolic Diseases ; Mice ; Mice, Inbred C57BL ; Mice, Obese ; Obesity/therapy ; }, abstract = {The substantially increased prevalence of obesity and obesity-related diseases has generated considerable concern. Currently, synthetic biological strategies have played an essential role in preventing and treating chronic diseases such as obesity. A growing number of symbiotic bacteria used as vectors for genetic engineering have been applied to create living therapeutics. In this study, using Bacillus subtilis as a cellular chassis, we constructed the engineered butyrate-producing strain BsS-RS06551 with a butyrate yield of 1.5 g/liter. A mouse model of obesity induced by a high-fat diet (HFD) was established to study the long-term intervention effects of this butyrate-producing bacteria on obesity. Combined with phenotypic assay results, we found that BsS-RS06551 could effectively retard body weight gain induced by a high-fat diet and visceral fat accumulation of mice, whereas it could improve glucose tolerance and insulin tolerance, reducing liver damage. We explored the BsS-RS06551 mechanism of action on host function and changes in intestinal flora by integrating multiple omics profiling, including untargeted metabolomics and metagenomics. The results showed that 24 major differential metabolites were involved in the metabolic regulation of BsS-RS06551 to prevent obesity in mice, including bile acid metabolism, branch chain amino acids, aromatic amino acids, and other metabolic pathways. Continuous ingestion of BsS-RS06551 could regulate gut microbiota composition and structure and enhance intestinal flora metabolic function abundance, which was closely related to host interactions. Our results demonstrated that engineered butyrate-producing bacteria had potential as an effective strategy to prevent obesity. IMPORTANCE Obesity is a chronic metabolic disease with an imbalance between energy intake and energy expenditure, and obesity-related metabolic diseases have become increasingly common. There is an urgent need to develop effective interventions for the prevention and treatment of obesity. This study showed that long-term consumption of BsS-RS06551 had a significant inhibitory effect on obesity induced by a high-fat diet and was more potent in inhibiting obesity than prebiotic inulin. In addition, this study showed a beneficial effect on host glucose, lipid metabolism, and gut microbe composition. Considering its colonization potential, this engineered bacteria provided a new strategy for the effective and convenient treatment of obesity in the long term.}, } @article {pmid35293804, year = {2022}, author = {Kang, Y and Tian, L and Gu, X and Chen, Y and Ma, X and Lin, S and Li, Z and Lou, Y and Zheng, M}, title = {Characterization of the Ocular Surface Microbiome in Keratitis Patients after Repeated Ophthalmic Antibiotic Exposure.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0216221}, pmid = {35293804}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Microbial ; Humans ; *Keratitis/drug therapy/microbiology ; *Microbiota ; Pseudomonas ; Pseudomonas aeruginosa ; }, abstract = {In human medicine, antibiotics have been widely used to treat microbial infections. The extensive use of antibiotics is a leading cause of antibiotic resistance. Currently, the influence of the use of antibiotics on the ocular surface microbiome in the course of keratitis treatment remains to be explored in depth. We performed metagenomic analyses in a cohort of 26 healthy controls (HCs), 28 keratitis patients (KPs) who received antibiotics [KP (abx+) group], and 12 KPs who were antibiotic naive [KP (abx-) group]. We identified that the dissimilarities in microbial community structure (Bray-Curtis and Jaccard analyses) between the KP (abx+) group and the HC group were greater than those between the KP (abx-) group and the HC group. Pseudomonas lactis, P. aeruginosa, Pseudomonas sp. FDAARGOS_380, Pseudomonas sp. J380, Corynebacterium simulans, Streptococcus pyogenes, Finegoldia magna, and Aspergillus oryzae had no statistically significant differences between the KP (abx+) and KP (abx-) groups but did have statistically significant differences between the KP (abx+) and HC groups and between the KP (abx-) and HC groups. Among them, Pseudomonas lactis, P. aeruginosa, Pseudomonas sp. FDAARGOS_380, and Pseudomonas sp. J380 were identified as possible hosts carrying multidrug-resistant genes. The total abundance and number of antibiotic resistance genes (ARGs) were greater in the KP (abx+) group than in the HC and KP (abx-) groups. The functional profile analysis of ocular surface microbiota revealed that pathogenesis-related functional pathways and virulence functions were enriched in KPs. In conclusion, our results show that empirical antibiotic treatment in KPs leads to increases in the antibiotic resistance of ocular surface microbiota. IMPORTANCE Treatment for keratitis is based on appropriate antimicrobial therapy. A direct correlation between antibiotic use and the extent of antibiotic resistance has been reported. Therefore, knowledge of the antibiotic resistance patterns of ocular surface microbial flora in KPs is important for clinical treatment. To the best of our knowledge, this is the first study to use metagenomic approaches to investigate the associations between ophthalmic antibiotic use and the ocular surface microbiome of KPs. Monitoring the microbiota and antibiotic resistome profiles for the ocular surface has huge potential to help ophthalmologists choose the appropriate antibiotics and will thereby improve the efficacy of treatment regimens, which has important implications for reducing the development of antibiotic resistance of the ocular surface to a certain extent.}, } @article {pmid35293551, year = {2022}, author = {Berbert, L and Santos, A and Magro, DO and Guadagnini, D and Assalin, HB and Lourenço, LH and Martinez, CAR and Saad, MJA and Coy, CSR}, title = {Metagenomics analysis reveals universal signatures of the intestinal microbiota in colorectal cancer, regardless of regional differences.}, journal = {Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas}, volume = {55}, number = {}, pages = {e11832}, pmid = {35293551}, issn = {1414-431X}, mesh = {*Colorectal Neoplasms/pathology ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The human gut microbiota is a complex and dynamic community of microorganisms living in our intestines and has emerged as an important factor for colorectal adenocarcinoma (CRC). The purpose of our study was to investigate the microbiota composition in Brazilian CRC patients compared with a local control population (CTL) to find out which changes could be considered universal or regional features in CRC microbiota. Fecal samples were obtained from 28 CRC and 23 CTL individuals. The 16S rRNA gene was used for metagenomic analysis. In addition to the anthropometric variables, the clinical stage (TNM 2018) was considered. Patients with CRC had a significant increase in alpha diversity and a higher percentage of genus Prevotella and a decreased proportion of Megamonas and Ruminococcus. Additionally, the proportion of Faecalibacterium prausnitzii was associated with a better prognosis in the first stages of CRC, and Fusobacterium nucleatum proved to be an important marker of colorectal carcinogenesis and tumor aggressiveness. Although regional differences influence the composition of the microbiota, in the case of CRC, the microhabitat created by the tumor seems to be a major factor. Our results contribute to a better understanding of the carcinogenic process, and even in different environments, some factors appear to be characteristic of the microbiota of patients with CRC.}, } @article {pmid35292384, year = {2022}, author = {Tang, L and Su, C and Fan, C and Li, R and Wang, Y and Gao, S and Chen, M}, title = {Long-term effect of perfluorooctanoic acid on the anammox system based on metagenomics: Performance, sludge characteristic and microbial community dynamic.}, journal = {Bioresource technology}, volume = {351}, number = {}, pages = {127002}, doi = {10.1016/j.biortech.2022.127002}, pmid = {35292384}, issn = {1873-2976}, mesh = {*Ammonium Compounds ; Anaerobic Ammonia Oxidation ; Anaerobiosis ; Bioreactors ; Caprylates ; Denitrification ; Fluorocarbons ; Metagenomics ; *Microbiota ; Nitrogen/metabolism ; Oxidation-Reduction ; Sewage ; }, abstract = {The effects of PFOA on the nitrogen removal performance, microbial community and functional genes of anaerobic ammonium oxidation (anammox) sludge in an anaerobic baffled reactor (ABR) were investigated. The removal efficiencies of ammonia nitrogen (NH4[+]-N) and nitrite (NO2[-]-N) decreased from 93.90 ± 3.64% and 98.6 ± 1.84% to 77.81 ± 6.86% and 77.96 ± 1.88% when PFOA increased from 5 mg/L to 50 mg/L, respectively. X-ray photoelectron spectra analysis of the anammox sludge showed the presence of both C-F and CaF2 forms of F. Metagenomics analysis of the anammox sludge in the first compartment illustrated that the relative abundance of Ca.Brocadia and Ca.Kuenenia decreased from 22.21% and 5.61% to 2.11% and 2.84% at 50 mg/L PFOA compared with that without PFOA. In addition, the nitrogen metabolism pathway showed that adding 50 mg/L PFOA decreased the expression of HzsB, HzsC, and Hdh (anammox genes) by 0.096%, 0.05% and 0.062%, respectively.}, } @article {pmid35289939, year = {2022}, author = {Todberg, T and Egeberg, A and Zachariae, C and Sørensen, N and Pedersen, O and Skov, L}, title = {Patients with psoriasis have a dysbiotic taxonomic and functional gut microbiota.}, journal = {The British journal of dermatology}, volume = {187}, number = {1}, pages = {89-98}, doi = {10.1111/bjd.21245}, pmid = {35289939}, issn = {1365-2133}, support = {20,000 DKK//Grosserer Fogts Foundation/ ; 450,000 DKK//Kongelig Hofbuntmager Aage Bangs Fond/ ; 25,000 DKK//Liv Bryhns Foundation/ ; 45,000 DKK//Robert and Kirsten Wehnerts Foundation/ ; N/A//The LEO Foundation/ ; //The Novo Nordisk Foundation Center for Basic Metabolic Research./ ; }, mesh = {Case-Control Studies ; Dysbiosis ; *Gastrointestinal Microbiome/genetics ; Humans ; Longitudinal Studies ; *Psoriasis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Accumulating evidence supports the findings of an altered gut microbiota in patients with autoimmune disease. However, existing studies on the role of the gut microbiota in patients with psoriasis have demonstrated conflicting results and have mainly been based on 16s rRNA gene sequencing analysis.

OBJECTIVES: To examine whether the gut microbiota of patients with psoriasis was altered in composition and functional potentials compared with healthy controls, and as a second approach compared with healthy cohabitant partners. A further aim was to investigate relationships to disease severity, and seasonal impact on the gut microbiota.

METHODS: In a case-control study, 126 faecal samples were collected from a sample of 53 systemically untreated patients with plaque psoriasis; 52 healthy controls matched for age, sex and body mass index; and 21 cohabitant partners. A subpopulation of 18 patients with psoriasis and 19 healthy controls continued in a longitudinal study, where four to six faecal samples were collected over 9-12 months. The gut microbiota was characterized using shotgun metagenomic sequencing analysis.

RESULTS: A significantly lower richness (P = 0·007) and difference in community composition (P = 0·01) of metagenomic species was seen in patients with psoriasis compared with healthy controls, and patients with psoriasis had a lower microbial diversity than their partners (P = 0·04). Additionally, the functional richness was decreased in patients with psoriasis compared with healthy controls (P = 0·01) and partners (P = 0·05). Increased disease severity was correlated with alterations in taxonomy and function, with a slight tendency towards a lower richness of metagenomic species, albeit not significant (P = 0·08). The seasonal analysis showed no shifts in community composition in healthy controls or in patients with psoriasis.

CONCLUSIONS: The findings of a different gut microbiota in composition and functional potentials between patients with psoriasis and healthy controls support a linkage between the gut microbiota and psoriasis. These findings need to be validated in larger studies, and a potential causal relationship between the gut microbiota and psoriasis still needs to be shown.}, } @article {pmid35289671, year = {2022}, author = {de Sousa, LP and Guerreiro-Filho, O and Mondego, JMC}, title = {The Rhizosphere Microbiomes of Five Species of Coffee Trees.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0044422}, pmid = {35289671}, issn = {2165-0497}, mesh = {*Coffea ; Coffee/chemistry ; *Mycobiome ; Rhizosphere ; Trees ; }, abstract = {Coffee is one of the most important commodities in the global market. Of the 130 species of Coffea, only Coffea arabica and Coffea canephora are actually cultivated on a large scale. Despite the economic and social importance of coffee, little research has been done on the coffee tree microbiome. To assess the structure and function of the rhizosphere microbiome, we performed a deep shotgun metagenomic sequencing of the rhizospheres of five different species, C. arabica, C. canephora, Coffea stenophylla, Coffea racemosa, and Coffea liberica. Our findings indicated that C. arabica and C. stenophylla have different microbiomes, while no differences were detected between the other Coffea species. The core rhizosphere microbiome comprises genera such as Streptomyces, Mycobacterium, Bradyrhizobium, Burkholderia, Sphingomonas, Penicillium, Trichoderma, and Rhizophagus, several of which are potential plant-beneficial microbes. Streptomyces and mycorrhizal fungi dominate the microbial communities. The concentration of sucrose in the rhizosphere seems to influence fungal communities, and the concentration of caffeine/theobromine has little effect on the microbiome. We also detected a possible relationship between drought tolerance in Coffea and known growth-promoting microorganisms. The results provide important information to guide future studies of the coffee tree microbiome to improve plant production and health. IMPORTANCE The microbiome has been identified as a fundamental factor for the maintenance of plant health, helping plants to fight diseases and the deleterious effects of abiotic stresses. Despite this, in-depth studies of the microbiome have been limited to a few species, generally with a short life cycle, and perennial species have mostly been neglected. The coffee tree microbiome, on the other hand, has gained interest in recent years as Coffea trees are perennial tropical species of enormous importance, especially for developing countries. A better understanding of the microorganisms associated with coffee trees can help to mitigate the deleterious effects of climate change on the crop, improving plant health and making the system more sustainable.}, } @article {pmid35289669, year = {2022}, author = {Poulsen, CS and Ekstrøm, CT and Aarestrup, FM and Pamp, SJ}, title = {Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0009022}, pmid = {35289669}, issn = {2165-0497}, mesh = {Animals ; Bacteria/genetics ; Bias ; DNA ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Microbiota/genetics ; Sequence Analysis, DNA/methods ; Swine ; }, abstract = {Metagenomics is increasingly used to describe microbial communities in biological specimens. Ideally, the steps involved in the processing of the biological specimens should not change the microbiome composition in a way that it could lead to false interpretations of inferred microbial community composition. Common steps in sample preparation include sample collection, storage, DNA isolation, library preparation, and DNA sequencing. Here, we assess the effect of three library preparation kits and two DNA sequencing platforms. Of the library preparation kits, one involved a PCR step (Nextera), and two were PCR free (NEXTflex and KAPA). We sequenced the libraries on Illumina HiSeq and NextSeq platforms. As example microbiomes, two pig fecal samples and two sewage samples of which aliquots were stored at different storage conditions (immediate processing and storage at -80°C) were assessed. All DNA isolations were performed in duplicate, totaling 80 samples, excluding controls. We found that both library preparation and sequencing platform had systematic effects on the inferred microbial community composition. The different sequencing platforms introduced more variation than library preparation and freezing the samples. The results highlight that all sample processing steps need to be considered when comparing studies. Standardization of sample processing is key to generating comparable data within a study, and comparisons of differently generated data, such as in a meta-analysis, should be performed cautiously. IMPORTANCE Previous research has reported effects of sample storage conditions and DNA isolation procedures on metagenomics-based microbiome composition; however, the effect of library preparation and DNA sequencing in metagenomics has not been thoroughly assessed. Here, we provide evidence that library preparation and sequencing platform introduce systematic biases in the metagenomic-based characterization of microbial communities. These findings suggest that library preparation and sequencing are important parameters to keep consistent when aiming to detect small changes in microbiome community structure. Overall, we recommend that all samples in a microbiome study are processed in the same way to limit unwanted variations that could lead to false conclusions. Furthermore, if we are to obtain a more holistic insight from microbiome data generated around the world, we will need to provide more detailed sample metadata, including information about the different sample processing procedures, together with the DNA sequencing data at the public repositories.}, } @article {pmid35288695, year = {2022}, author = {Smith, M and Dai, A and Ghilardi, G and Amelsberg, KV and Devlin, SM and Pajarillo, R and Slingerland, JB and Beghi, S and Herrera, PS and Giardina, P and Clurman, A and Dwomoh, E and Armijo, G and Gomes, ALC and Littmann, ER and Schluter, J and Fontana, E and Taur, Y and Park, JH and Palomba, ML and Halton, E and Ruiz, J and Jain, T and Pennisi, M and Afuye, AO and Perales, MA and Freyer, CW and Garfall, A and Gier, S and Nasta, S and Landsburg, D and Gerson, J and Svoboda, J and Cross, J and Chong, EA and Giralt, S and Gill, SI and Riviere, I and Porter, DL and Schuster, SJ and Sadelain, M and Frey, N and Brentjens, RJ and June, CH and Pamer, EG and Peled, JU and Facciabene, A and van den Brink, MRM and Ruella, M}, title = {Gut microbiome correlates of response and toxicity following anti-CD19 CAR T cell therapy.}, journal = {Nature medicine}, volume = {28}, number = {4}, pages = {713-723}, pmid = {35288695}, issn = {1546-170X}, support = {R01 CA226983/CA/NCI NIH HHS/United States ; P01 CA214278/CA/NCI NIH HHS/United States ; P01 CA023766/CA/NCI NIH HHS/United States ; R01 HL147584/HL/NHLBI NIH HHS/United States ; R01 CA219871/CA/NCI NIH HHS/United States ; R01 HL125571/HL/NHLBI NIH HHS/United States ; K99 CA212302/CA/NCI NIH HHS/United States ; K08 CA194256/CA/NCI NIH HHS/United States ; R01 CA228358/CA/NCI NIH HHS/United States ; R00 CA212302/CA/NCI NIH HHS/United States ; K08 HL143189/HL/NHLBI NIH HHS/United States ; R01 HL123340/HL/NHLBI NIH HHS/United States ; R01 CA206012/CA/NCI NIH HHS/United States ; R01 CA228308/CA/NCI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; P01 AG052359/AG/NIA NIH HHS/United States ; }, mesh = {Antigens, CD19 ; *Gastrointestinal Microbiome ; Humans ; Immunotherapy, Adoptive/adverse effects ; *Neurotoxicity Syndromes/etiology ; Prospective Studies ; *Receptors, Chimeric Antigen ; Retrospective Studies ; }, abstract = {Anti-CD19 chimeric antigen receptor (CAR) T cell therapy has led to unprecedented responses in patients with high-risk hematologic malignancies. However, up to 60% of patients still experience disease relapse and up to 80% of patients experience CAR-mediated toxicities, such as cytokine release syndrome or immune effector cell-associated neurotoxicity syndrome. We investigated the role of the intestinal microbiome on these outcomes in a multicenter study of patients with B cell lymphoma and leukemia. We found in a retrospective cohort (n = 228) that exposure to antibiotics, in particular piperacillin/tazobactam, meropenem and imipenem/cilastatin (P-I-M), in the 4 weeks before therapy was associated with worse survival and increased neurotoxicity. In stool samples from a prospective cohort of CAR T cell recipients (n = 48), the fecal microbiome was altered at baseline compared to healthy controls. Stool sample profiling by 16S ribosomal RNA and metagenomic shotgun sequencing revealed that clinical outcomes were associated with differences in specific bacterial taxa and metabolic pathways. Through both untargeted and hypothesis-driven analysis of 16S sequencing data, we identified species within the class Clostridia that were associated with day 100 complete response. We concluded that changes in the intestinal microbiome are associated with clinical outcomes after anti-CD19 CAR T cell therapy in patients with B cell malignancies.}, } @article {pmid35288138, year = {2022}, author = {Shen, J and Luo, Y and Tao, Q and White, PJ and Sun, G and Li, M and Luo, J and He, Y and Li, B and Li, Q and Xu, Q and Cai, Y and Li, H and Wang, C}, title = {The exacerbation of soil acidification correlates with structural and functional succession of the soil microbiome upon agricultural intensification.}, journal = {The Science of the total environment}, volume = {828}, number = {}, pages = {154524}, doi = {10.1016/j.scitotenv.2022.154524}, pmid = {35288138}, issn = {1879-1026}, mesh = {Hydrogen-Ion Concentration ; *Microbiota/genetics ; *Oryza ; Protons ; Soil/chemistry ; Soil Microbiology ; *Streptomyces ; Triticum ; }, abstract = {Agricultural intensification driven by land-use changes has caused continuous and cumulative soil acidification (SA) throughout the global agroecosystem. Microorganisms mediate acid-generating reactions; however, the microbial mechanisms responsible for exacerbating SA feedback remain largely unknown. To determine the microbial community composition and putative function associated with SA, we conducted a metagenomic analysis of soils across a chronosequence that has elapsed since the conversion of rice-wheat (RW) to rice-vegetable (RV) rotations. Compared to RW rotations, soil pH decreased by 0.50 and 1.56 units (p < 0.05) in response to 10-year and 20-year RV rotations, respectively. Additionally, acid saturation ratios were increased by 7.3% and 36.2% (p < 0.05), respectively. The loss of microbial beta-diversity was a key element that contributed to the exacerbation of SA in the RV. Notably, the 20-year RV-enriched microbial taxa were more hydrogen (H[+])-, aluminium (Al[3+])-, and nitrate nitrogen (NO3[-]-N) -dependent and contained more genera exhibiting dehydrogenation functions than did RW-enriched taxa. "M00115, M00151, M00417, and M00004" and "M00531 and M00135" that are the "proton-pumping" and "proton-consuming" gene modules, respectively, were linked to the massive recruitment of acid-dependent biomarkers in 20-year RV soils, particularly Rhodanobacter, Gemmatirosa, Sphingomonas, and Streptomyces. Collectively, soils in long-term RV rotations were highly acidified and acid-sensitive, as the enrichment of microbial dehydrogenation genes allowing for soil buffering capacity is more vulnerable to H[+] loading and consequently promotes the colonization of more acid-tolerant and acidogenic microbes, and ultimately provide new clues for researchers to elucidate the interaction between SA and the soil microbiome.}, } @article {pmid35287721, year = {2022}, author = {Gregory, AC and Gerhardt, K and Zhong, ZP and Bolduc, B and Temperton, B and Konstantinidis, KT and Sullivan, MB}, title = {MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {49}, pmid = {35287721}, issn = {2049-2618}, support = {T32 AI112542/AI/NIAID NIH HHS/United States ; }, mesh = {Child ; Humans ; Metagenome/genetics ; *Microbiota/genetics ; Nucleotides ; Virome ; *Viruses/genetics ; }, abstract = {BACKGROUND: Microbes and their viruses are hidden engines driving Earth's ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter-(macrodiversity) and intra-(microdiversity) population variation, analytical tools to do so remain scattered or under-developed.

RESULTS: Here, we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro- and microdiversity levels. Macrodiversity estimates include population abundances and α- and β-diversity. Microdiversity calculations include identification of single nucleotide polymorphisms, novel codon-constrained linkage of SNPs, nucleotide diversity (π and θ), and selective pressures (pN/pS and Tajima's D) within and fixation indices (FST) between populations. MetaPop will also identify genes with distinct codon usage. Following rigorous validation, we applied MetaPop to the gut viromes of autistic children that underwent fecal microbiota transfers and their neurotypical peers. The macrodiversity results confirmed our prior findings for viral populations (microbial shotgun metagenomes were not available) that diversity did not significantly differ between autistic and neurotypical children. However, by also quantifying microdiversity, MetaPop revealed lower average viral nucleotide diversity (π) in autistic children. Analysis of the percentage of genomes detected under positive selection was also lower among autistic children, suggesting that higher viral π in neurotypical children may be beneficial because it allows populations to better "bet hedge" in changing environments. Further, comparisons of microdiversity pre- and post-FMT in autistic children revealed that the delivery FMT method (oral versus rectal) may influence viral activity and engraftment of microdiverse viral populations, with children who received their FMT rectally having higher microdiversity post-FMT. Overall, these results show that analyses at the macro level alone can miss important biological differences.

CONCLUSIONS: These findings suggest that standardized population and genetic variation analyses will be invaluable for maximizing biological inference, and MetaPop provides a convenient tool package to explore the dual impact of macro- and microdiversity across microbial communities. Video abstract.}, } @article {pmid35286304, year = {2022}, author = {Kalmar, L and Gupta, S and Kean, IRL and Ba, X and Hadjirin, N and Lay, EM and de Vries, SPW and Bateman, M and Bartlet, H and Hernandez-Garcia, J and Tucker, AW and Restif, O and Stevens, MP and Wood, JLN and Maskell, DJ and Grant, AJ and Holmes, MA}, title = {HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities.}, journal = {PLoS genetics}, volume = {18}, number = {3}, pages = {e1009776}, pmid = {35286304}, issn = {1553-7404}, support = {MR/N002660/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents ; *Anti-Infective Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Metagenomics ; *Microbiota ; Swine ; }, abstract = {Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a comprehensive laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli. The bioinformatics pipeline code is available at https://github.com/lkalmar/HAM-ART.}, } @article {pmid35285696, year = {2022}, author = {Song, W and Liu, J and Qin, W and Huang, J and Yu, X and Xu, M and Stahl, D and Jiao, N and Zhou, J and Tu, Q}, title = {Functional Traits Resolve Mechanisms Governing the Assembly and Distribution of Nitrogen-Cycling Microbial Communities in the Global Ocean.}, journal = {mBio}, volume = {13}, number = {2}, pages = {e0383221}, pmid = {35285696}, issn = {2150-7511}, support = {2019YFA0606700//National Key Research and Development Program of China/ ; 2020YFA0607600//National Key Research and Development Program of China/ ; 2017YFA0604300//National Key Research and Development Program of China/ ; 31971446//National Natural Science Foundation of China (NSFC)/ ; 92051110//National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Metagenome ; *Microbiota ; *Nitrogen ; Nitrogen Cycle ; Oceans and Seas ; }, abstract = {Microorganisms drive much of the marine nitrogen (N) cycle, which jointly controls the primary production in the global ocean. However, our understanding of the microbial communities driving the global ocean N cycle remains fragmented. Focusing on "who is doing what, where, and how?", this study draws a clear picture describing the global biogeography of marine N-cycling microbial communities by utilizing the Tara Oceans shotgun metagenomes. The marine N-cycling communities are highly variable taxonomically but relatively even at the functional trait level, showing clear functional redundancy properties. The functional traits and taxonomic groups are shaped by the same set of geo-environmental factors, among which, depth is the major factor impacting marine N-cycling communities, differentiating mesopelagic from epipelagic communities. Latitudinal diversity gradients and distance-decay relationships are observed for taxonomic groups, but rarely or weakly for functional traits. The composition of functional traits is strongly deterministic as revealed by null model analysis, while a higher degree of stochasticity is observed for taxonomic composition. Integrating multiple lines of evidence, in addition to drawing a biogeographic picture of marine N-cycling communities, this study also demonstrated an essential microbial ecological theory-determinism governs the assembly of microbial communities performing essential biogeochemical processes; the environment selects functional traits rather than taxonomic groups; functional redundancy underlies stochastic taxonomic community assembly. IMPORTANCE A critical question in microbial ecology is how the complex microbial communities are formed in natural ecosystems with the existence of thousands different species, thereby performing essential ecosystem functions and maintaining ecosystem stability. Previous studies disentangling the community assembly mechanisms mainly focus on microbial taxa, ignoring the functional traits they carry. By anchoring microbial functional traits and their carrying taxonomic groups involved in nitrogen cycling processes, this study demonstrated an important mechanism associated with the complex microbial community assembly. Evidence shows that the environment selects functional traits rather than taxonomic groups, and functional redundancy underlies stochastic taxonomic community assembly. This study is expected to provide valuable mechanistic insights into the complex microbial community assembly in both natural and artificial ecosystems.}, } @article {pmid35282279, year = {2022}, author = {Amillano-Cisneros, JM and Hernández-Rosas, PT and Gomez-Gil, B and Navarrete-Ramírez, P and Ríos-Durán, MG and Martínez-Chávez, CC and Johnston-Monje, D and Martínez-Palacios, CA and Raggi, L}, title = {Loss of gut microbial diversity in the cultured, agastric fish, Mexican pike silverside (Chirostoma estor: Atherinopsidae).}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13052}, pmid = {35282279}, issn = {2167-8359}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Esocidae/genetics ; RNA, Ribosomal, 16S/genetics ; Fishes/genetics ; Bacteria/genetics ; }, abstract = {Teleost fish are the most diverse group of extant vertebrates and have varied digestive anatomical structures and strategies, suggesting they also possess an array of different host-microbiota interactions. Differences in fish gut microbiota have been shown to affect host development, the process of gut colonization, and the outcomes of gene-environment or immune system-microbiota interactions. There is generally a lack of studies on the digestive mechanisms and microbiota of agastric short-intestine fish however, meaning that we do not understand how changes in gut microbial diversity might influence the health of these types of fish. To help fill these gaps in knowledge, we decided to study the Mexican pike silverside (Chirostoma estor) which has a simplified alimentary canal (agastric, short-intestine, 0.7 gut relative length) to observe the diversity and metabolic potential of its intestinal microbiota. We characterized gut microbial populations using high-throughput sequencing of the V3 region in bacterial 16S rRNA genes while searching for population shifts resulting associated with fish development in different environments and cultivation methods. Microbiota samples were taken from the digesta, anterior and posterior intestine (the three different intestinal components) of fish that grew wild in a lake, that were cultivated in indoor tanks, or that were raised in outdoor ponds. Gut microbial diversity was significantly higher in wild fish than in cultivated fish, suggesting a loss of diversity when fish are raised in controlled environments. The most abundant phyla observed in these experiments were Firmicutes and Proteobacteria, particularly of the genera Mycoplasma, Staphylococcus, Spiroplasma, and Aeromonas. Of the 14,161 OTUs observed in this experiment, 133 were found in all groups, and 17 of these, belonging to Acinetobacter, Aeromonas, Pseudomonas, and Spiroplasma genera, were found in all samples suggesting the existence of a core C. estor microbiome. Functional metagenomic prediction of bacterial ecological functions using PICRUSt2 suggested that different intestinal components select for functionally distinct microbial populations with variation in pathways related to the metabolism of amino acids, vitamins, cofactors, and energy. Our results provide, for the first time, information on the bacterial populations present in an agastric, short-gut teleost with commercial potential and show that controlled cultivation of this fish reduces the diversity of its intestinal microbiota.}, } @article {pmid35281451, year = {2022}, author = {Gao, R and Xia, K and Wu, M and Zhong, H and Sun, J and Zhu, Y and Huang, L and Wu, X and Yin, L and Yang, R and Chen, C and Qin, H}, title = {Alterations of Gut Mycobiota Profiles in Adenoma and Colorectal Cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {839435}, pmid = {35281451}, issn = {2235-2988}, mesh = {*Adenoma ; *Colorectal Neoplasms/microbiology ; Dysbiosis/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Accumulating evidence indicates that gut microbiota dysbiosis contributes to colorectal cancer and adenoma. However, a few studies revealed the altered gut mycobiota architecture in colorectal cancer. The present study characterized the gut mycobiota profiles in adenoma and colorectal cancer patients by metagenomic sequencing. Malassezia restricta increased, while Leucoagaricus_sp_SymCcos and fungal_sp_ARF18 significantly decreased in adenoma. Phanerochaete_chrysosporium, Lachancea_waltii, and Aspergillus_rambellii were the top 3 fungi that were significantly enriched in colorectal cancer, while Candida_versatilis, Pseudocercospora_pini_densiflorae, and Candida_sp_JCM_15000 were dominant in the healthy controls. Thirteen fungi, ranked as critical biomarkers in diagnosing colorectal cancer, showed positive associations among all samples. Lachancea_waltii and Phanerochaete_chrysosporium showed the most significant association within CRC. The values of area under the receiver-operating characteristics curve (AUROC) of selected 13 mycobiota were 0.926 in the training model and 0.757 in the 10-fold validation model. Our study provided a reliable investigation of the alterations of gut mycobiota in the development of colorectal cancer and established a convincing diagnostic model for colorectal cancer, which might improve the treatment strategy for colorectal cancer in the future.}, } @article {pmid35281446, year = {2022}, author = {Huang, J and Wei, S and Jiang, C and Xiao, Z and Liu, J and Peng, W and Zhang, B and Li, W}, title = {Involvement of Abnormal Gut Microbiota Composition and Function in Doxorubicin-Induced Cardiotoxicity.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {808837}, pmid = {35281446}, issn = {2235-2988}, mesh = {Animals ; Apoptosis ; *Cardiotoxicity/drug therapy/etiology/metabolism ; Doxorubicin/toxicity ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred C57BL ; Oxidative Stress ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVES: Doxorubicin (Dox), a chemotherapeutic anthracycline agent for the treatment of a variety of malignancies, has a limitation in clinical application for dose-dependent cardiotoxicity. The purpose of this study was to explore the relationship between the composition/function of the gut microbiota and Dox-induced cardiotoxicity (DIC).

METHODS: C57BL/6J mice were injected intraperitoneally with 15 mg/kg of Dox, with or without antibiotics (Abs) administration. The M-mode echocardiograms were performed to assess cardiac function. The histopathological analysis was conducted by H&E staining and TUNEL kit assay. The serum levels of creatine kinase (CK), CK-MB (CK-MB), lactic dehydrogenase (LDH), and cardiac troponin T (cTnT) were analyzed by an automatic biochemical analyzer. 16S rRNA gene and metagenomic sequencing of fecal samples were used to explore the gut microbiota composition and function.

KEY FINDINGS: Dox caused left ventricular (LV) dilation and reduced LV contractility. The levels of cardiomyocyte apoptosis and myocardial enzymes were elevated in Dox-treated mice compared with the control (Con) group. 16S rRNA gene sequencing results revealed significant differences in microbial composition between the two groups. In the Dox group, the relative abundances of Allobaculum, Muribaculum, and Lachnoclostridium were significantly decreased, whereas Faecalibaculum, Dubosiella, and Lachnospiraceae were significantly increased compared with the Con group at the genus level. Functional enrichment with Cluster of orthologous groups of proteins (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the Dox mice displayed different clusters of cellular processes and metabolism from the Con mice. The different species and their functions between the two groups were associated with the clinical factors of cardiac enzymes. Moreover, depletion of the gut microbiota could alleviate Dox-induced myocardial injury and cardiomyocyte apoptosis.

CONCLUSIONS: The study here shows that composition imbalance and functional changes of the gut microbiota can be one of the etiological mechanisms underlying DIC. The gut microbiota may serve as new targets for the treatment of cardiotoxicity and cardiovascular diseases.}, } @article {pmid35281043, year = {2022}, author = {Cheng, M and Liu, H and Han, M and Li, SC and Bu, D and Sun, S and Hu, Z and Yang, P and Wang, R and Liu, Y and Chen, F and Peng, J and Peng, H and Song, H and Xia, Y and Chu, L and Zhou, Q and Guan, F and Wu, J and Tan, G and Ning, K}, title = {Microbiome Resilience and Health Implications for People in Half-Year Travel.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {848994}, pmid = {35281043}, issn = {1664-3224}, mesh = {Carbohydrates ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Travel entail change in geography and diet, both of which are known as determinant factors in shaping the human gut microbiome. Additionally, altered gut microbiome modulates immunity, bringing about health implications in humans. To explore the effects of the mid-term travel on the gut microbiome, we generated 16S rRNA gene and metagenomic sequencing data from longitudinal samples collected over six months. We monitored dynamic trajectories of the gut microbiome variation of a Chinese volunteer team (VT) in their whole journey to Trinidad and Tobago (TAT). We found gut microbiome resilience that VT's gut microbial compositions gradually transformed to the local TAT's enterotypes during their six-month stay in TAT, and then reverted to their original enterotypes after VT's return to Beijing in one month. Moreover, we identified driven species in this bi-directional plasticity that could play a role in immunity modulation, as exemplified by Bacteroides dorei that attenuated atherosclerotic lesion formation and effectively suppressed proinflammatory immune response. Another driven species P. copri could play a crucial role in rheumatoid arthritis pathogenesis, a chronic autoimmune disease. Carbohydrate-active enzymes are often implicated in immune and host-pathogen interactions, of which glycoside hydrolases were found decreased but glycosyltransferases and carbohydrate esterases increased during the travel; these functions were then restored after VT' returning to Beijing. Furthermore, we discovered these microbial changes and restoration were mediated by VT people's dietary changes. These findings indicate that half-year travel leads to change in enterotype and functional patterns, exerting effects on human health. Microbial intervention by dietary guidance in half-year travel would be conducive to immunity modulation for maintaining health.}, } @article {pmid35279076, year = {2022}, author = {Garber, AI and Armbruster, CR and Lee, SE and Cooper, VS and Bomberger, JM and McAllister, SM}, title = {SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {202}, pmid = {35279076}, issn = {1471-2164}, support = {CFF BOMBER18G0/NH/NIH HHS/United States ; U01AI124302/NH/NIH HHS/United States ; UL1 TR000005/TR/NCATS NIH HHS/United States ; T32HL129949/NH/NIH HHS/United States ; R33HL137077/NH/NIH HHS/United States ; CFF RDP BOMBER19R0/NH/NIH HHS/United States ; R01HL12377/NH/NIH HHS/United States ; }, mesh = {Bacteria/genetics ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; Software ; }, abstract = {BACKGROUND: Shotgun sequencing of cultured microbial isolates/individual eukaryotes (whole-genome sequencing) and microbial communities (metagenomics) has become commonplace in biology. Very often, sequenced samples encompass organisms spanning multiple domains of life, necessitating increasingly elaborate software for accurate taxonomic classification of assembled sequences.

RESULTS: While many software tools for taxonomic classification exist, SprayNPray offers a quick and user-friendly, semi-automated approach, allowing users to separate contigs by taxonomy (and other metrics) of interest. Easy installation, usage, and intuitive output, which is amenable to visual inspection and/or further computational parsing, will reduce barriers for biologists beginning to analyze genomes and metagenomes. This approach can be used for broad-level overviews, preliminary analyses, or as a supplement to other taxonomic classification or binning software. SprayNPray profiles contigs using multiple metrics, including closest homologs from a user-specified reference database, gene density, read coverage, GC content, tetranucleotide frequency, and codon-usage bias.

CONCLUSIONS: The output from this software is designed to allow users to spot-check metagenome-assembled genomes, identify, and remove contigs from putative contaminants in isolate assemblies, identify bacteria in eukaryotic assemblies (and vice-versa), and identify possible horizontal gene transfer events.}, } @article {pmid35278679, year = {2022}, author = {Wani, AK and Roy, P and Kumar, V and Mir, TUG}, title = {Metagenomics and artificial intelligence in the context of human health.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {100}, number = {}, pages = {105267}, doi = {10.1016/j.meegid.2022.105267}, pmid = {35278679}, issn = {1567-7257}, mesh = {Artificial Intelligence ; DNA ; Humans ; *Metagenomics/methods ; *Microbiota/genetics ; Sequence Analysis, DNA ; }, abstract = {Human microbiome is ubiquitous, dynamic, and site-specific consortia of microbial communities. The pathogenic nature of microorganisms within human tissues has led to an increase in microbial studies. Characterization of genera, like Streptococcus, Cutibacterium, Staphylococcus, Bifidobacterium, Lactococcus and Lactobacillus through culture-dependent and culture-independent techniques has been reported. However, due to the unique environment within human tissues, it is difficult to culture these microorganisms making their molecular studies strenuous. MGs offer a gateway to explore and characterize hidden microbial communities through a culture-independent mode by direct DNA isolation. By function and sequence-based MGs, Scientists can explore the mechanistic details of numerous microbes and their interaction with the niche. Since the data generated from MGs studies is highly complex and multi-dimensional, it requires accurate analytical tools to evaluate and interpret the data. Artificial intelligence (AI) provides the luxury to automatically learn the data dimensionality and ease its complexity that makes the disease diagnosis and disease response easy, accurate and timely. This review provides insight into the human microbiota and its exploration and expansion through MG studies. The review elucidates the significance of MGs in studying the changing microbiota during disease conditions besides highlighting the role of AI in computational analysis of MG data.}, } @article {pmid35277583, year = {2022}, author = {Park, JY and Seo, H and Kang, CS and Shin, TS and Kim, JW and Park, JM and Kim, JG and Kim, YK}, title = {Dysbiotic change in gastric microbiome and its functional implication in gastric carcinogenesis.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {4285}, pmid = {35277583}, issn = {2045-2322}, mesh = {Carcinogenesis ; Dysbiosis ; *Gastritis ; *Gastrointestinal Microbiome/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; *Stomach Neoplasms ; }, abstract = {Although there is a growing interest in the role of gastric microbiome on the development of gastric cancer, the exact mechanism is largely unknown. We aimed to investigate the changes of gastric microbiome during gastric carcinogenesis, and to predict the functional potentials of the microbiome involved in the cancer development. The gastric microbiome was analyzed using gastric juice samples from 88 prospectively enrolled patients, who were classified into gastritis, gastric adenoma, or early/advanced gastric cancer group. Differences in microbial diversity and composition were analyzed with 16S rRNA gene profiling, using next-generation sequencing method. Metagenomic biomarkers were selected using logistic regression models, based on relative abundances at genus level. We used Tax4Fun to predict possible functional pathways of gastric microbiome involved in the carcinogenesis. The microbial diversity continuously decreased in its sequential process of gastric carcinogenesis, from gastritis to gastric cancer. The microbial composition was significantly different among the four groups of each disease status, as well as between the cancer group and non-cancer group. Gastritis group was differently enriched with genera Akkermansia and Lachnospiraceae NK4A136 Group, whereas the cancer group was enriched with Lactobacillus and Veillonella. Predictive analysis of the functional capacity of the microbiome suggested enrichment or depletion of several functional pathways related to carcinogenesis in the cancer group. There are significant changes in the diversity and composition of gastric microbiome during the gastric carcinogenesis process. Gastric cancer was characterized with microbial dysbiosis, along with functional changes potentially favoring carcinogenesis.}, } @article {pmid35277009, year = {2022}, author = {Hiraishi, K and Zhao, F and Kurahara, LH and Li, X and Yamashita, T and Hashimoto, T and Matsuda, Y and Sun, Z and Zhang, H and Hirano, K}, title = {Lactulose Modulates the Structure of Gut Microbiota and Alleviates Colitis-Associated Tumorigenesis.}, journal = {Nutrients}, volume = {14}, number = {3}, pages = {}, pmid = {35277009}, issn = {2072-6643}, support = {21K11699//KAKENHI/ ; }, mesh = {Animals ; Carcinogenesis ; *Colitis/chemically induced/drug therapy/pathology ; Dextran Sulfate/pharmacology ; *Gastrointestinal Microbiome ; Lactulose/pharmacology ; Mice ; }, abstract = {Lactulose, a galactose-fructose disaccharide, is made from the milk sugar lactose by heating or isomerization processes. Lactulose is proposed to modulate gut microbiota and thus expected to be beneficial in treating inflammatory bowel disease. In the present study, we investigated the therapeutic effect of lactulose on gastrointestinal inflammation and inflammation-related tumorigenesis in a mouse model of colorectal cancer as well as its effect on gut microbiota composition. Azoxymethane (AOM)/dextran sulfate sodium (DSS) model was used in this study. Lactulose treatment was performed by feeding 2% lactulose for 14 weeks. Stool samples collected at 4 time points were used for metagenomic analysis of the microbiota. Pathological analysis was performed 21 weeks after AOM injection. AOM/DSS increased the macrophage counts, inflammatory cytokine expression, colorectal tumorigenesis, and imbalance in gut microbiota composition, as evidenced by increased pathogen abundance (e.g., Escherichia and Clostridium). Lactulose significantly inhibited the inflammatory events, and ameliorated inflammation and tumorigenesis. The composition of the intestinal microbiota was also restored upon lactulose treatment, and lactulose reduced pathogen abundance and increased the abundance of Muribaculum and Lachnospiraceae. Meanwhile, the pathways related to Crohn's disease were downregulated after lactulose treatment. Our findings suggest that lactulose restores the structure and composition of the intestinal microbiota, mitigates inflammation, and suppresses inflammatory tumorigenesis.}, } @article {pmid35276896, year = {2022}, author = {Byerley, LO and Gallivan, KM and Christopher, CJ and Taylor, CM and Luo, M and Dowd, SE and Davis, GM and Castro, HF and Campagna, SR and Ondrak, KS}, title = {Gut Microbiome and Metabolome Variations in Self-Identified Muscle Builders Who Report Using Protein Supplements.}, journal = {Nutrients}, volume = {14}, number = {3}, pages = {}, pmid = {35276896}, issn = {2072-6643}, support = {2P20GM103424 and UL1TR003096/NH/NIH HHS/United States ; none//American Public University System/ ; }, mesh = {Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Metabolome/genetics ; *Microbiota/genetics ; Muscles ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Muscle builders frequently consume protein supplements, but little is known about their effect on the gut microbiota. This study compared the gut microbiome and metabolome of self-identified muscle builders who did or did not report consuming a protein supplement. Twenty-two participants (14 males and 8 females) consumed a protein supplement (PS), and seventeen participants (12 males and 5 females) did not (No PS). Participants provided a fecal sample and completed a 24-h food recall (ASA24). The PS group consumed significantly more protein (118 ± 12 g No PS vs. 169 ± 18 g PS, p = 0.02). Fecal metabolome and microbiome were analyzed by using untargeted metabolomics and 16S rRNA gene sequencing, respectively. Metabolomic analysis identified distinct metabolic profiles driven by allantoin (VIP score = 2.85, PS 2.3-fold higher), a catabolic product of uric acid. High-protein diets contain large quantities of purines, which gut microbes degrade to uric acid and then allantoin. The bacteria order Lactobacillales was higher in the PS group (22.6 ± 49 No PS vs. 136.5 ± 38.1, PS (p = 0.007)), and this bacteria family facilitates purine absorption and uric acid decomposition. Bacterial genes associated with nucleotide metabolism pathways (p < 0.001) were more highly expressed in the No PS group. Both fecal metagenomic and metabolomic analyses revealed that the PS group’s higher protein intake impacted nitrogen metabolism, specifically altering nucleotide degradation.}, } @article {pmid35273319, year = {2022}, author = {Burgess, BT and Irvine, RL and Russello, MA}, title = {Population genomics of Sitka black-tailed deer supports invasive species management and ecological restoration on islands.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {223}, pmid = {35273319}, issn = {2399-3642}, mesh = {Animals ; Biodiversity ; *Deer/genetics ; *Introduced Species ; Islands ; Metagenomics ; }, abstract = {Invasive mammals represent a critical threat to island biodiversity; eradications can result in ecological restoration yet may fail in the absence of key population parameters. Over-browsing by invasive Sitka black-tailed deer (Odocoileus hemionus sitkensis) is causing severe ecological and cultural impacts across the Haida Gwaii archipelago (Canada). Previous eradication attempts demonstrate forest regeneration upon deer removal, but reinvasion reverses conservation gains. Here we use restriction-site associated DNA sequencing (12,947 SNPs) to investigate connectivity and gene flow of invasive deer (n = 181) across 15 islands, revealing little structure throughout Haida Gwaii and identifying the large, central island of Moresby (>2600 km[2]) as the greatest source of migrants. As a result, the archipelago itself should be considered the primary eradication unit, with the exception of geographically isolated islands like SGang Gwaay. Thus, limiting eradications to isolated islands combined with controlled culling and enhanced biosecurity may be the most effective strategies for achieving ecological restoration goals.}, } @article {pmid35273169, year = {2022}, author = {Cai, YY and Huang, FQ and Lao, X and Lu, Y and Gao, X and Alolga, RN and Yin, K and Zhou, X and Wang, Y and Liu, B and Shang, J and Qi, LW and Li, J}, title = {Integrated metagenomics identifies a crucial role for trimethylamine-producing Lachnoclostridium in promoting atherosclerosis.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {11}, pmid = {35273169}, issn = {2055-5008}, mesh = {Animals ; *Atherosclerosis ; Choline ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; Methylamines ; Mice ; }, abstract = {Microbial trimethylamine (TMA)-lyase activity promotes the development of atherosclerosis by generating of TMA, the precursor of TMA N-oxide (TMAO). TMAO is well documented, but same can not be said of TMA-producing bacteria. This work aimed to identify TMA-producing genera in human intestinal microbiota. We retrieved the genomes of human-associated microorganisms from the Human Microbiome Project database comprising 1751 genomes, Unified Human Gastrointestinal Genome collection consisting 4644 gut prokaryotes, recapitulated 4930 species-level genome bins and public gut metagenomic data of 2134 individuals from 11 populations. By sequence searching, 216 TMA-lyase-containing species from 102 genera were found to contain the homologous sequences of cntA/B, yeaW/X, and/or cutC/D. We identified 13 strains from 5 genera with cntA sequences, and 30 strains from 14 genera with cutC showing detectable relative abundance in healthy individuals. Lachnoclostridium (p = 2.9e-05) and Clostridium (p = 5.8e-04), the two most abundant cutC-containing genera, were found to be much higher in atherosclerotic patients compared with healthy persons. Upon incubation with choline (substrate), L. saccharolyticum effectively transformed it to TMA at a rate higher than 98.7% while that for C. sporogenes was 63.8-67.5% as detected by liquid chromatography-triple quadrupole mass spectrometry. In vivo studies further showed that treatment of L. saccharolyticum and choline promoted a significant increase in TMAO level in the serum of ApoE[-/-] mice with obvious accumulation of aortic plaque in same. This study discloses the significance and efficiency of the gut bacterium L. saccharolyticum in transforming choline to TMA and consequently promoting the development of atherosclerosis.}, } @article {pmid35272716, year = {2022}, author = {Eberhard, FE and Klimpel, S and Guarneri, AA and Tobias, NJ}, title = {Exposure to Trypanosoma parasites induces changes in the microbiome of the Chagas disease vector Rhodnius prolixus.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {45}, pmid = {35272716}, issn = {2049-2618}, mesh = {Animals ; *Chagas Disease ; Insect Vectors/microbiology/parasitology ; *Microbiota/genetics ; *Parasites ; *Rhodnius/parasitology ; *Trypanosoma cruzi/genetics ; }, abstract = {BACKGROUND: The causative agent of Chagas disease, Trypanosoma cruzi, and its nonpathogenic relative, Trypanosoma rangeli, are transmitted by haematophagous triatomines and undergo a crucial ontogenetic phase in the insect's intestine. In the process, the parasites interfere with the host immune system as well as the microbiome present in the digestive tract potentially establishing an environment advantageous for development. However, the coherent interactions between host, pathogen and microbiota have not yet been elucidated in detail. We applied a metagenome shotgun sequencing approach to study the alterations in the microbiota of Rhodnius prolixus, a major vector of Chagas disease, after exposure to T. cruzi and T. rangeli focusing also on the functional capacities present in the intestinal microbiome of the insect.

RESULTS: The intestinal microbiota of R. prolixus was dominated by the bacterial orders Enterobacterales, Corynebacteriales, Lactobacillales, Clostridiales and Chlamydiales, whereas the latter conceivably originated from the blood used for pathogen exposure. The anterior and posterior midgut samples of the exposed insects showed a reduced overall number of organisms compared to the control group. However, we also found enriched bacterial groups after exposure to T. cruzi as well as T rangeli. While the relative abundance of Enterobacterales and Corynebacteriales decreased considerably, the Lactobacillales, mainly composed of the genus Enterococcus, developed as the most abundant taxonomic group. This applies in particular to vectors challenged with T. rangeli and at early timepoints after exposure to vectors challenged with T. cruzi. Furthermore, we were able to reconstruct four metagenome-assembled genomes from the intestinal samples and elucidate their unique metabolic functionalities within the triatomine microbiome, including the genome of a recently described insect symbiont, Candidatus Symbiopectobacterium, and the secondary metabolites producing bacteria Kocuria spp.

CONCLUSIONS: Our results facilitate a deeper understanding of the processes that take place in the intestinal tract of triatomine vectors during colonisation by trypanosomal parasites and highlight the influential aspects of pathogen-microbiota interactions. In particular, the mostly unexplored metabolic capacities of the insect vector's microbiome are clearer, underlining its role in the transmission of Chagas disease. Video Abstract.}, } @article {pmid35272699, year = {2022}, author = {Bates, KA and Sommer, U and Hopkins, KP and Shelton, JMG and Wierzbicki, C and Sergeant, C and Tapley, B and Michaels, CJ and Schmeller, DS and Loyau, A and Bosch, J and Viant, MR and Harrison, XA and Garner, TWJ and Fisher, MC}, title = {Microbiome function predicts amphibian chytridiomycosis disease dynamics.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {44}, pmid = {35272699}, issn = {2049-2618}, support = {MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Anura/genetics/microbiology ; *Chytridiomycota/genetics ; *Microbiota/genetics ; *Mycoses/microbiology/veterinary ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The fungal pathogen Batrachochytrium dendrobatidis (Bd) threatens amphibian biodiversity and ecosystem stability worldwide. Amphibian skin microbial community structure has been linked to the clinical outcome of Bd infections, yet its overall functional importance is poorly understood.

METHODS: Microbiome taxonomic and functional profiles were assessed using high-throughput bacterial 16S rRNA and fungal ITS2 gene sequencing, bacterial shotgun metagenomics and skin mucosal metabolomics. We sampled 56 wild midwife toads (Alytes obstetricans) from montane populations exhibiting Bd epizootic or enzootic disease dynamics. In addition, to assess whether disease-specific microbiome profiles were linked to microbe-mediated protection or Bd-induced perturbation, we performed a laboratory Bd challenge experiment whereby 40 young adult A. obstetricans were exposed to Bd or a control sham infection. We measured temporal changes in the microbiome as well as functional profiles of Bd-exposed and control animals at peak infection.

RESULTS: Microbiome community structure and function differed in wild populations based on infection history and in experimental control versus Bd-exposed animals. Bd exposure in the laboratory resulted in dynamic changes in microbiome community structure and functional differences, with infection clearance in all but one infected animal. Sphingobacterium, Stenotrophomonas and an unclassified Commamonadaceae were associated with wild epizootic dynamics and also had reduced abundance in laboratory Bd-exposed animals that cleared infection, indicating a negative association with Bd resistance. This was further supported by microbe-metabolite integration which identified functionally relevant taxa driving disease outcome, of which Sphingobacterium and Bd were most influential in wild epizootic dynamics. The strong correlation between microbial taxonomic community composition and skin metabolome in the laboratory and field is inconsistent with microbial functional redundancy, indicating that differences in microbial taxonomy drive functional variation. Shotgun metagenomic analyses support these findings, with similar disease-associated patterns in beta diversity. Analysis of differentially abundant bacterial genes and pathways indicated that bacterial environmental sensing and Bd resource competition are likely to be important in driving infection outcomes.

CONCLUSIONS: Bd infection drives altered microbiome taxonomic and functional profiles across laboratory and field environments. Our application of multi-omics analyses in experimental and field settings robustly predicts Bd disease dynamics and identifies novel candidate biomarkers of infection. Video Abstract.}, } @article {pmid35272051, year = {2022}, author = {Zhou, F and Gan, R and Zhang, F and Ren, C and Yu, L and Si, Y and Huang, Z}, title = {PHISDetector: A Tool to Detect Diverse In Silico Phage-host Interaction Signals for Virome Studies.}, journal = {Genomics, proteomics & bioinformatics}, volume = {20}, number = {3}, pages = {508-523}, pmid = {35272051}, issn = {2210-3244}, mesh = {Humans ; *Bacteriophages/genetics ; Virome ; Prophages/genetics ; Bacteria/genetics ; *Microbiota ; }, abstract = {Phage-microbe interactions are appealing systems to study coevolution, and have also been increasingly emphasized due to their roles in human health, disease, and the development of novel therapeutics. Phage-microbe interactions leave diverse signals in bacterial and phage genomic sequences, defined as phage-host interaction signals (PHISs), which include clustered regularly interspaced short palindromic repeats (CRISPR) targeting, prophage, and protein-protein interaction signals. In the present study, we developed a novel tool phage-host interaction signal detector (PHISDetector) to predict phage-host interactions by detecting and integrating diverse in silico PHISs, and scoring the probability of phage-host interactions using machine learning models based on PHIS features. We evaluated the performance of PHISDetector on multiple benchmark datasets and application cases. When tested on a dataset of 758 annotated phage-host pairs, PHISDetector yields the prediction accuracies of 0.51 and 0.73 at the species and genus levels, respectively, outperforming other phage-host prediction tools. When applied to on 125,842 metagenomic viral contigs (mVCs) derived from 3042 geographically diverse samples, a detection rate of 54.54% could be achieved. Furthermore, PHISDetector could predict infecting phages for 85.6% of 368 multidrug-resistant (MDR) bacteria and 30% of 454 human gut bacteria obtained from the National Institutes of Health (NIH) Human Microbiome Project (HMP). The PHISDetector can be run either as a web server (http://www.microbiome-bigdata.com/PHISDetector/) for general users to study individual inputs or as a stand-alone version (https://github.com/HIT-ImmunologyLab/PHISDetector) to process massive phage contigs from virome studies.}, } @article {pmid35271887, year = {2022}, author = {Balinandi, S and Hayer, J and Cholleti, H and Wille, M and Lutwama, JJ and Malmberg, M and Mugisha, L}, title = {Identification and molecular characterization of highly divergent RNA viruses in cattle, Uganda.}, journal = {Virus research}, volume = {313}, number = {}, pages = {198739}, doi = {10.1016/j.virusres.2022.198739}, pmid = {35271887}, issn = {1872-7492}, mesh = {Animals ; Cattle ; *Cattle Diseases/epidemiology ; *Coltivirus ; *Flaviviridae ; Humans ; Phylogeny ; *RNA Viruses/genetics ; *Reoviridae/genetics ; Uganda/epidemiology ; }, abstract = {The risk for the emergence of novel viral zoonotic diseases in animals and humans in Uganda is high given its geographical location with high biodiversity. We aimed to identify and characterize viruses in 175 blood samples from cattle selected in Uganda using molecular approaches. We identified 8 viral species belonging to 4 families (Flaviviridae, Peribunyaviridae, Reoviridae and Rhabdoviridae) and 6 genera (Hepacivirus, Pestivirus, Orthobunyavirus, Coltivirus, Dinovernavirus and Ephemerovirus). Four viruses were highly divergent and tetantively named Zikole virus (Family: Flaviviridae), Zeboroti virus (Family: Reoviridae), Zebtine virus (Family: Rhabdoviridae) and Kokolu virus (Family: Rhabdoviridae). In addition, Bovine Hepacivirus, Obodhiang virus, Aedes pseudoscutellaris reovirus and Schmallenberg virus were identified for the first time in Ugandan cattle. We report 8 viral species belonging to 4 viral families including divergent ones in the blood of cattle in Uganda. Hence, cattle may be reservoir hosts for likely emergence of novel viruses with pathogenic potential to cause zoonotic diseases in different species with serious public health implications.}, } @article {pmid35271802, year = {2022}, author = {Cai, J and Sun, L and Gonzalez, FJ}, title = {Gut microbiota-derived bile acids in intestinal immunity, inflammation, and tumorigenesis.}, journal = {Cell host & microbe}, volume = {30}, number = {3}, pages = {289-300}, pmid = {35271802}, issn = {1934-6069}, support = {Z01 BC005562/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Bile Acids and Salts ; Carcinogenesis ; *Gastrointestinal Microbiome ; Humans ; Inflammation ; Prospective Studies ; }, abstract = {Inflammatory bowel disease (IBD) and colorectal cancer (CRC) are heterogeneous intestinal diseases that threaten the health of an increasing number of individuals as their lifestyles become westernized. New insights have been discovered with the development of various omics techniques, revealing that gut-microbiota-derived metabolites play important roles in maintaining intestinal homeostasis and modulating the progression of intestinal diseases from both metabolic and immunological perspectives. Clinical metagenomic and metabolomic studies have revealed links between microbial bile acid (BA) metabolism and IBD and CRC progression. Several BA-derived metabolites were recently been demonstrated to play a role in intestinal immunity, providing fresh insights into how BAs affect the course of IBD and CRC. In this review, we discuss recent studies on the involvement of gut microbiota-derived BAs in intestinal immunity, inflammation, and tumorigenesis along with human omics data to provide prospective insights into future prevention and treatment of IBD and CRC.}, } @article {pmid35268611, year = {2022}, author = {Kabaivanova, L and Hubenov, V and Dimitrova, L and Simeonov, I and Wang, H and Petrova, P}, title = {Archaeal and Bacterial Content in a Two-Stage Anaerobic System for Efficient Energy Production from Agricultural Wastes.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {5}, pages = {}, pmid = {35268611}, issn = {1420-3049}, support = {Grant KP-06-IP-CHINA/3//Bulgarian National Science Fund/ ; 2021YFE0102700//Intergovernmental International Science and Technology Innovation Cooperation Key project of the National Key R&D Program of China/ ; }, mesh = {Anaerobiosis ; *Archaea/metabolism/genetics ; *Methane/metabolism ; *Hydrogen/metabolism ; *Biofuels ; Bacteria/metabolism/genetics ; Bioreactors/microbiology ; Agriculture/methods ; Triticum/metabolism ; Biodegradation, Environmental ; Microbial Consortia/physiology ; }, abstract = {Anaerobic digestion (AD) is a microbially-driven process enabling energy production. Microorganisms are the core of anaerobic digesters and play an important role in the succession of hydrolysis, acidogenesis, acetogenesis, and methanogenesis processes. The diversity of participating microbial communities can provide new information on digester performance for biomass valorization and biofuel production. In this study anaerobic systems were used, operating under mesophilic conditions that realized biodegradation processes of waste wheat straw pretreated with NaOH-a renewable source for hydrogen and methane production. These processes could be managed and optimized for hydrogen and methane separately but combining them in a two-stage system can lead to higher yields and a positive energy balance. The aim of the study was to depict a process of biohydrogen production from lignocellulosic waste followed by a second one leading to the production of biomethane. Archaeal and bacterial consortia in a two-stage system operating with wheat straw were identified for the first time and the role of the most important representatives was elucidated. The mixed cultures were identified by the molecular-biological methods of metagenomics. The results showed that biohydrogen generation is most probably due to the presence of Proteiniphilum saccharofermentans, which was 28.2% to 45.4% of the microbial community in the first and the second bioreactor, respectively. Archaeal representatives belonging to Methanobacterium formicicum (0.71% of the community), Methanosarcina spelaei (0.03%), Methanothrix soehngenii (0.012%), and Methanobacterium beijingense (0.01%) were proven in the methane-generating reactor. The correlation between substrate degradation and biogas accumulation was calculated, together with the profile of fatty acids as intermediates produced during the processes. The hydrogen concentration in the biogas reached 14.43%, and the Methane concentration was 69%. Calculations of the energy yield during the two-stage process showed 1195.89 kWh·t[-1] compared to a 361.62 kWh·t[-1] cumulative yield of energy carrier for a one-stage process.}, } @article {pmid35266795, year = {2022}, author = {Barbosa da Costa, N and Hébert, MP and Fugère, V and Terrat, Y and Fussmann, GF and Gonzalez, A and Shapiro, BJ}, title = {A Glyphosate-Based Herbicide Cross-Selects for Antibiotic Resistance Genes in Bacterioplankton Communities.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0148221}, pmid = {35266795}, issn = {2379-5077}, mesh = {*Herbicides/pharmacology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Bacteria ; Aquatic Organisms ; Glyphosate ; }, abstract = {Agrochemicals often contaminate freshwater bodies, affecting microbial communities that underlie aquatic food webs. For example, the herbicide glyphosate has the potential to indirectly select for antibiotic-resistant bacteria. Such cross-selection could occur if the same genes (encoding efflux pumps, for example) confer resistance to both glyphosate and antibiotics. To test for cross-resistance in natural aquatic bacterial communities, we added a glyphosate-based herbicide (GBH) to 1,000-liter mesocosms filled with water from a pristine lake. Over 57 days, we tracked changes in bacterial communities with shotgun metagenomic sequencing and annotated metagenome-assembled genomes (MAGs) for the presence of known antibiotic resistance genes (ARGs), plasmids, and resistance mutations in the enzyme targeted by glyphosate (enolpyruvyl-shikimate-3-phosphate synthase; EPSPS). We found that high doses of GBH significantly increased ARG frequency and selected for multidrug efflux pumps in particular. The relative abundance of MAGs after a high dose of GBH was predictable based on the number of ARGs in their genomes (17% of variation explained) and, to a lesser extent, by resistance mutations in EPSPS. Together, these results indicate that GBHs can cross-select for antibiotic resistance in natural freshwater bacteria. IMPORTANCE Glyphosate-based herbicides (GBHs) such as Roundup formulations may have the unintended consequence of selecting for antibiotic resistance genes (ARGs), as demonstrated in previous experiments. However, the effects of GBHs on ARGs remain unknown in natural aquatic communities, which are often contaminated with pesticides from agricultural runoff. Moreover, the resistance provided by ARGs compared to canonical mutations in the glyphosate target enzyme, EPSPS, remains unclear. Here, we performed a freshwater mesocosm experiment showing that a GBH strongly selects for ARGs, particularly multidrug efflux pumps. These selective effects were evident after just a few days, and the ability of bacteria to survive and thrive after GBH stress was predictable by the number of ARGs in their genomes and, to a lesser extent, by mutations in EPSPS. Intensive GBH application may therefore have the unintended consequence of selecting for ARGs in natural freshwater communities.}, } @article {pmid35266150, year = {2022}, author = {Carrell, AA and Lawrence, TJ and Cabugao, KGM and Carper, DL and Pelletier, DA and Lee, JH and Jawdy, SS and Grimwood, J and Schmutz, J and Hanson, PJ and Shaw, AJ and Weston, DJ}, title = {Habitat-adapted microbial communities mediate Sphagnum peatmoss resilience to warming.}, journal = {The New phytologist}, volume = {234}, number = {6}, pages = {2111-2125}, pmid = {35266150}, issn = {1469-8137}, mesh = {Carbon ; Ecosystem ; Metagenome ; *Microbiota ; *Sphagnopsida/physiology ; Temperature ; }, abstract = {Sphagnum peatmosses are fundamental members of peatland ecosystems, where they contribute to the uptake and long-term storage of atmospheric carbon. Warming threatens Sphagnum mosses and is known to alter the composition of their associated microbiome. Here, we use a microbiome transfer approach to test if microbiome thermal origin influences host plant thermotolerance. We leveraged an experimental whole-ecosystem warming study to collect field-grown Sphagnum, mechanically separate the associated microbiome and then transfer onto germ-free laboratory Sphagnum for temperature experiments. Host and microbiome dynamics were assessed with growth analysis, Chla fluorescence imaging, metagenomics, metatranscriptomics and 16S rDNA profiling. Microbiomes originating from warming field conditions imparted enhanced thermotolerance and growth recovery at elevated temperatures. Metagenome and metatranscriptome analyses revealed that warming altered microbial community structure in a manner that induced the plant heat shock response, especially the HSP70 family and jasmonic acid production. The heat shock response was induced even without warming treatment in the laboratory, suggesting that the warm-microbiome isolated from the field provided the host plant with thermal preconditioning. Our results demonstrate that microbes, which respond rapidly to temperature alterations, can play key roles in host plant growth response to rapidly changing environments.}, } @article {pmid35265196, year = {2022}, author = {Hu, W and Chen, ZM and Li, XX and Lu, L and Yang, GH and Lei, ZX and You, LJ and Cui, XB and Lu, SC and Zhai, ZY and Zeng, ZY and Chen, Y and Huang, SL and Gong, W}, title = {Faecal microbiome and metabolic signatures in rectal neuroendocrine tumors.}, journal = {Theranostics}, volume = {12}, number = {5}, pages = {2015-2027}, pmid = {35265196}, issn = {1838-7640}, mesh = {*Gastrointestinal Microbiome ; Humans ; Metabolome ; Metabolomics/methods ; Metagenome ; Metagenomics ; *Microbiota ; *Neuroendocrine Tumors ; Tumor Microenvironment ; }, abstract = {Background: The prevalence of rectal neuroendocrine tumors (RNET) has increased substantially over the past decades. Little is known on mechanistic alteration in the pathogenesis of such disease. We postulate that perturbations of human gut microbiome-metabolome interface influentially affect the development of RNET. The study aims to characterize the composition and function of faecal microbiome and metabolites in RNET individuals. Methods: We performed deep shotgun metagenomic sequencing and untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomic profiling of faecal samples from the discovery cohort (18 RNET patients, 40 controls), and validated the microbiome and metabolite-based classifiers in an independent cohort (15 RNET participants, 19 controls). Results: We uncovered a dysbiotic gut ecological microenvironment in RNET patients, characterized by aberrant depletion and attenuated connection of microbial species, and abnormally aggregated lipids and lipid-like molecules. Functional characterization based on our in-house and Human Project Unified Metabolic Analysis Network 2 (HUMAnN2) pipelines further indicated a nutrient deficient gut microenvironment in RNET individuals, evidenced by diminished activities such as energy metabolism, vitamin biosynthesis and transportation. By integrating these data, we revealed 291 robust associations between representative differentially abundant taxonomic species and metabolites, indicating a tight interaction of gut microbiome with metabolites in RNET pathogenesis. Finally, we identified a cluster of gut microbiome and metabolite-based signatures, and replicated them in an independent cohort, showing accurate prediction of such neoplasm from healthy people. Conclusions: Our current study is the first to comprehensively characterize the perturbed interface of gut microbiome and metabolites in RNET patients, which may provide promising targets for microbiome-based diagnostics and therapies for this disorder.}, } @article {pmid35265049, year = {2021}, author = {Bouhia, Y and Hafidi, M and Ouhdouch, Y and El Boukhari, MEM and El Fels, L and Zeroual, Y and Lyamlouli, K}, title = {Microbial Community Succession and Organic Pollutants Removal During Olive Mill Waste Sludge and Green Waste Co-composting.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {814553}, pmid = {35265049}, issn = {1664-302X}, abstract = {Olive mill wastewater sludge (OMWS) is the main by-product of the olive industry. OMWS is usually dumped in landfills without prior treatment and may cause several eco-environmental hazards due to its high toxicity, which is mainly attributed to polyphenols and lipids. OMWS is rich in valuable biocompounds, which makes it highly desirable for valorization by composting. However, there is a need to understand how microbial communities evolve during OMWS composting with respect to physicochemical changes and the dynamics of pollutant degradation. In this study, we addressed the relationship between microbial community, physicochemical variations and pollutants degradation during the co-composting of OMWS and green wastes using metagenomic- and culture-dependent approaches. The results showed that in raw OMWS, Pichia was the most represented genus with almost 53% of the total identified fungal population. Moreover, the bacteria that dominated were Zymobacter palmae (20%) and Pseudomonas sp. (19%). The addition of green waste to OMWS improved the actinobacterial diversity of the mixture and enhanced the degradation of lipids (81.3%) and polyphenols (84.54%). Correlation analysis revealed that Actinobacteria and fungi (Candida sp., Galactomyces sp., and Pichia manshurica) were the microorganisms that had the greatest influence on the composting process. Overall, these findings provide for the first time some novel insights into the microbial dynamics during OMWS composting and may contribute to the development of tailored inoculum for process optimization.}, } @article {pmid35264618, year = {2022}, author = {New, FN and Baer, BR and Clark, AG and Wells, MT and Brito, IL}, title = {Collective effects of human genomic variation on microbiome function.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {3839}, pmid = {35264618}, issn = {2045-2322}, support = {DP2 HL141007/HL/NHLBI NIH HHS/United States ; R01 DK093595/DK/NIDDK NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome ; *Genome, Human ; Humans ; }, abstract = {Studies of the impact of host genetics on gut microbiome composition have mainly focused on the impact of individual single nucleotide polymorphisms (SNPs) on gut microbiome composition, without considering their collective impact or the specific functions of the microbiome. To assess the aggregate role of human genetics on the gut microbiome composition and function, we apply sparse canonical correlation analysis (sCCA), a flexible, multivariate data integration method. A critical attribute of metagenome data is its sparsity, and here we propose application of a Tweedie distribution to accommodate this. We use the TwinsUK cohort to analyze the gut microbiomes and human variants of 250 individuals. Sparse CCA, or sCCA, identified SNPs in microbiome-associated metabolic traits (BMI, blood pressure) and microbiome-associated disorders (type 2 diabetes, some neurological disorders) and certain cancers. Both common and rare microbial functions such as secretion system proteins or antibiotic resistance were found to be associated with host genetics. sCCA applied to microbial species abundances found known associations such as Bifidobacteria species, as well as novel associations. Despite our small sample size, our method can identify not only previously known associations, but novel ones as well. Overall, we present a new and flexible framework for examining host-microbiome genetic interactions, and we provide a new dimension to the current debate around the role of human genetics on the gut microbiome.}, } @article {pmid35262396, year = {2022}, author = {Kong, G and Lê Cao, KA and Hannan, AJ}, title = {Alterations in the Gut Fungal Community in a Mouse Model of Huntington's Disease.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0219221}, pmid = {35262396}, issn = {2165-0497}, mesh = {Animals ; Bacteria/genetics ; Disease Models, Animal ; *Gastrointestinal Microbiome/genetics ; *Huntington Disease/genetics/microbiology ; Metagenomics ; Mice ; Mice, Transgenic ; *Mycobiome/genetics ; }, abstract = {Huntington's disease (HD) is a neurodegenerative disorder caused by a trinucleotide expansion in the HTT gene, which is expressed throughout the brain and body, including the gut epithelium and enteric nervous system. Afflicted individuals suffer from progressive impairments in motor, psychiatric, and cognitive faculties, as well as peripheral deficits, including the alteration of the gut microbiome. However, studies characterizing the gut microbiome in HD have focused entirely on the bacterial component, while the fungal community (mycobiome) has been overlooked. The gut mycobiome has gained recognition for its role in host homeostasis and maintenance of the gut epithelial barrier. We aimed to characterize the gut mycobiome profile in HD using fecal samples collected from the R6/1 transgenic mouse model (and wild-type littermate controls) from 4 to 12 weeks of age, corresponding to presymptomatic through to early disease stages. Shotgun sequencing was performed on fecal DNA samples, followed by metagenomic analyses. The HD gut mycobiome beta diversity was significantly different from that of wild-type littermates at 12 weeks of age, while no genotype differences were observed at the earlier time points. Similarly, greater alpha diversity was observed in the HD mice by 12 weeks of age. Key taxa, including Malassezia restricta, Yarrowia lipolytica, and Aspergillus species, were identified as having a negative association with HD. Furthermore, integration of the bacterial and fungal data sets at 12 weeks of age identified negative correlations between the HD-associated fungal species and Lactobacillus reuteri. These findings provide new insights into gut microbiome alterations in HD and may help identify novel therapeutic targets. IMPORTANCE Huntington's disease (HD) is a fatal neurodegenerative disorder affecting both the mind and body. We have recently discovered that gut bacteria are disrupted in HD. The present study provides the first evidence of an altered gut fungal community (mycobiome) in HD. The genomes of many thousands of gut microbes were sequenced and used to assess "metagenomics" in particular the different types of fungal species in the HD versus control gut, in a mouse model. At an early disease stage, before the onset of symptoms, the overall gut mycobiome structure (array of fungi) in HD mice was distinct from that of their wild-type littermates. Alterations of multiple key fungi species were identified as being associated with the onset of disease symptoms, some of which showed strong correlations with the gut bacterial community. This study highlights the potential role of gut fungi in HD and may facilitate the development of novel therapeutic approaches.}, } @article {pmid35260444, year = {2022}, author = {Kartal, E and Schmidt, TSB and Molina-Montes, E and Rodríguez-Perales, S and Wirbel, J and Maistrenko, OM and Akanni, WA and Alashkar Alhamwe, B and Alves, RJ and Carrato, A and Erasmus, HP and Estudillo, L and Finkelmeier, F and Fullam, A and Glazek, AM and Gómez-Rubio, P and Hercog, R and Jung, F and Kandels, S and Kersting, S and Langheinrich, M and Márquez, M and Molero, X and Orakov, A and Van Rossum, T and Torres-Ruiz, R and Telzerow, A and Zych, K and , and , and Benes, V and Zeller, G and Trebicka, J and Real, FX and Malats, N and Bork, P}, title = {A faecal microbiota signature with high specificity for pancreatic cancer.}, journal = {Gut}, volume = {71}, number = {7}, pages = {1359-1372}, pmid = {35260444}, issn = {1468-3288}, support = {P30 CA086862/CA/NCI NIH HHS/United States ; }, mesh = {Biomarkers, Tumor ; CA-19-9 Antigen ; *Carcinoma, Pancreatic Ductal/diagnosis/genetics ; Case-Control Studies ; Humans ; *Microbiota ; *Pancreatic Neoplasms/diagnosis/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Recent evidence suggests a role for the microbiome in pancreatic ductal adenocarcinoma (PDAC) aetiology and progression.

OBJECTIVE: To explore the faecal and salivary microbiota as potential diagnostic biomarkers.

METHODS: We applied shotgun metagenomic and 16S rRNA amplicon sequencing to samples from a Spanish case-control study (n=136), including 57 cases, 50 controls, and 29 patients with chronic pancreatitis in the discovery phase, and from a German case-control study (n=76), in the validation phase.

RESULTS: Faecal metagenomic classifiers performed much better than saliva-based classifiers and identified patients with PDAC with an accuracy of up to 0.84 area under the receiver operating characteristic curve (AUROC) based on a set of 27 microbial species, with consistent accuracy across early and late disease stages. Performance further improved to up to 0.94 AUROC when we combined our microbiome-based predictions with serum levels of carbohydrate antigen (CA) 19-9, the only current non-invasive, Food and Drug Administration approved, low specificity PDAC diagnostic biomarker. Furthermore, a microbiota-based classification model confined to PDAC-enriched species was highly disease-specific when validated against 25 publicly available metagenomic study populations for various health conditions (n=5792). Both microbiome-based models had a high prediction accuracy on a German validation population (n=76). Several faecal PDAC marker species were detectable in pancreatic tumour and non-tumour tissue using 16S rRNA sequencing and fluorescence in situ hybridisation.

CONCLUSION: Taken together, our results indicate that non-invasive, robust and specific faecal microbiota-based screening for the early detection of PDAC is feasible.}, } @article {pmid35259379, year = {2022}, author = {Mai, Y and Peng, S and Lai, Z and Wang, X}, title = {Saltwater intrusion affecting NO2[-] accumulation in demersal fishery species by bacterially mediated N-cycling.}, journal = {The Science of the total environment}, volume = {827}, number = {}, pages = {154371}, doi = {10.1016/j.scitotenv.2022.154371}, pmid = {35259379}, issn = {1879-1026}, mesh = {Bacteria/genetics ; *Ecosystem ; Estuaries ; Fisheries ; *Nitrogen Dioxide ; Water ; }, abstract = {To investigate the underlying effects of saltwater intrusion (SWI) on bottom aquatic ecosystems, a set of environmental parameters and the bacterial community were determined and analyzed by sampling bottom water and surface sediments at the Modaomen waterway of the Pearl River Estuary. Biodiversity of fishery species and their relationship with the environment variables were analyzed together. NO3[-] and NO2[-] concentration down-regulation and NH4[+] concentration up-regulation in water and sediment were observed along the resulting salinity gradient, indicating that SWI affected N-cycling. Further investigation via 16 s sequencing revealed that taxonomic and functional composition of the bacterial community in the sediment displayed greater discretization than in water, implying that SWI exerted a greater impact on the sedimentary bacterial community. Metagenomic sequencing showed that the sedimentary bacterial community was associated with NO3[-], NO2[-], and NH4[+] transformation under SWI, and that this was driven by salinity and conductivity. Nitrogen metabolism and denitrification related genes were expressed at higher levels in high salinity than in low salinity, consistent with the increased enzymatic activities of NiR and NR. The NO2[-] concentration in the muscle of six selected fishery species was significantly decreased by 11.15-65.74% (P < 0.05) along the salinity gradient, indicating that SWI reduced NO2[-] accumulation. The results suggest that SWI alleviates NO2[-] accumulation in demersal fishery species via bacterial mediation of N-cycling.}, } @article {pmid35259160, year = {2022}, author = {Kieser, S and Zdobnov, EM and Trajkovski, M}, title = {Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart.}, journal = {PLoS computational biology}, volume = {18}, number = {3}, pages = {e1009947}, pmid = {35259160}, issn = {1553-7358}, mesh = {Animals ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome/genetics ; Metagenomics ; Mice ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Mouse is the most used model for studying the impact of microbiota on its host, but the repertoire of species from the mouse gut microbiome remains largely unknown. Accordingly, the similarity between human and mouse microbiomes at a low taxonomic level is not clear. We construct a comprehensive mouse microbiota genome (CMMG) catalog by assembling all currently available mouse gut metagenomes and combining them with published reference and metagenome-assembled genomes. The 41'798 genomes cluster into 1'573 species, of which 78.1% are uncultured, and we discovered 226 new genera, seven new families, and one new order. CMMG enables an unprecedented coverage of the mouse gut microbiome exceeding 86%, increases the mapping rate over four-fold, and allows functional microbiota analyses of human and mouse linking them to the driver species. Comparing CMMG to microbiota from the unified human gastrointestinal genomes shows an overlap of 62% at the genus but only 10% at the species level, demonstrating that human and mouse gut microbiota are largely distinct. CMMG contains the most comprehensive collection of consistently functionally annotated species of the mouse and human microbiome to date, setting the ground for analysis of new and reanalysis of existing datasets at an unprecedented depth.}, } @article {pmid35258762, year = {2022}, author = {Xu, X and Zhang, W and Guo, M and Xiao, C and Fu, Z and Yu, S and Jiang, L and Wang, S and Ling, Y and Liu, F and Tan, Y and Chen, S}, title = {Integrated analysis of gut microbiome and host immune responses in COVID-19.}, journal = {Frontiers of medicine}, volume = {16}, number = {2}, pages = {263-275}, pmid = {35258762}, issn = {2095-0225}, mesh = {*COVID-19 ; Clostridiales ; *Gastrointestinal Microbiome ; Humans ; Immunity ; Leukocytes, Mononuclear ; SARS-CoV-2 ; }, abstract = {Emerging evidence indicates that the gut microbiome contributes to the host immune response to infectious diseases. Here, to explore the role of the gut microbiome in the host immune responses in COVID-19, we conducted shotgun metagenomic sequencing and immune profiling of 14 severe/critical and 24 mild/moderate COVID-19 cases as well as 31 healthy control samples. We found that the diversity of the gut microbiome was reduced in severe/critical COVID-19 cases compared to mild/moderate ones. We identified the abundance of some gut microbes altered post-SARS-CoV-2 infection and related to disease severity, such as Enterococcus faecium, Coprococcus comes, Roseburia intestinalis, Akkermansia muciniphila, Bacteroides cellulosilyticus and Blautia obeum. We further analyzed the correlation between the abundance of gut microbes and host responses, and obtained a correlation map between clinical features of COVID-19 and 16 severity-related gut microbe, including Coprococcus comes that was positively correlated with CD3[+]/CD4[+]/CD8[+] lymphocyte counts. In addition, an integrative analysis of gut microbiome and the transcriptome of peripheral blood mononuclear cells (PBMCs) showed that genes related to viral transcription and apoptosis were up-regulated in Coprococcus comes low samples. Moreover, a number of metabolic pathways in gut microbes were also found to be differentially enriched in severe/critical or mild/moderate COVID-19 cases, including the superpathways of polyamine biosynthesis II and sulfur oxidation that were suppressed in severe/critical COVID-19. Together, our study highlighted a potential regulatory role of severity related gut microbes in the immune response of host.}, } @article {pmid35258452, year = {2022}, author = {Zhang, X and Zhang, X and Tong, F and Cai, Y and Zhang, Y and Song, H and Tian, X and Yan, C and Han, Y}, title = {Gut microbiota induces high platelet response in patients with ST segment elevation myocardial infarction after ticagrelor treatment.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35258452}, issn = {2050-084X}, mesh = {Animals ; Dysbiosis/drug therapy ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Percutaneous Coronary Intervention ; Platelet Aggregation Inhibitors/pharmacokinetics/therapeutic use ; *ST Elevation Myocardial Infarction/drug therapy ; Ticagrelor/therapeutic use ; Treatment Outcome ; }, abstract = {BACKGROUND: Ticagrelor is a first-line drug for the treatment of acute ST elevation myocardial infarction (STEMI). However, approximately 20% STEMI patients taking ticagrelor exhibited a delayed response and the mechanism was still unclear.

METHODS: To explore the mechanism of the poor response of ticagrelor in post-percutaneous coronary intervention (PCI) patients, we enrolled 65 high platelet reactivity (HPR) patients and 90 controls (normal platelet reactivity [NPR]). Pharmacokinetic assessment result showed that the plasma concentrations of ticagrelor and its metabolism production, AR-C124910XX, were lower in HPR patients than controls. Further single nucloetide polymorphism (SNP) analysis identified that there is no difference in ATP binding cassette subfamily B member 1 (ABCB1) gene expression between the NPR group and the HPR group. Metagenomic and metabolomic analyses of fecal samples showed that HPR patients had higher microbial richness and diversity. Transplantation of the gut microbiota from HPR donors to microbiota-depleted mice obviously decreased plasma concentration of ticagrelor.

RESULTS: Our findings highlight that gut microbiota dysbiosis may be an important mechanism for the ticagrelor of HPR in patients with STEMI and support that modify gut microbiota is a potential therapeutic option for STEMI.

CONCLUSIONS: Our findings highlight that gut microbiota dysbiosis may be an important mechanism for the ticagrelor of HPR in patients with ST elevation myocardial infarction (STEMI) and support that modify gut microbiota is a potential therapeutic option for STEMI.

FUNDING: NSFC 82170297 and 82070300 from the National Natural Science Foundation of China.}, } @article {pmid35258341, year = {2022}, author = {Lewin, GR and Davis, NM and McDonald, BR and Book, AJ and Chevrette, MG and Suh, S and Boll, A and Currie, CR}, title = {Long-Term Cellulose Enrichment Selects for Highly Cellulolytic Consortia and Competition for Public Goods.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0151921}, pmid = {35258341}, issn = {2379-5077}, support = {T32 GM007215/GM/NIGMS NIH HHS/United States ; T32 GM008505/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Cellulose/metabolism ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria ; Polysaccharides/metabolism ; Mammals/genetics ; }, abstract = {The complexity of microbial communities hinders our understanding of how microbial diversity and microbe-microbe interactions impact community functions. Here, using six independent communities originating from the refuse dumps of leaf-cutter ants and enriched using the plant polymer cellulose as the sole source of carbon, we examine how changes in bacterial diversity and interactions impact plant biomass decomposition. Over up to 60 serial transfers (∼8 months) using Whatman cellulose filter paper, cellulolytic ability increased and then stabilized in four enrichment lines and was variable in two lines. Bacterial community characterization using 16S rRNA gene amplicon sequencing showed community succession differed between the highly cellulolytic enrichment lines and those that had slower and more variable cellulose degradation rates. Metagenomic and metatranscriptomic analyses revealed that Cellvibrio and/or Cellulomonas dominated each enrichment line and produced the majority of cellulase enzymes, while diverse taxa were retained within these communities over the duration of transfers. Interestingly, the less cellulolytic communities had a higher diversity of organisms competing for the cellulose breakdown product cellobiose, suggesting that cheating slowed cellulose degradation. In addition, we found competitive exclusion as an important factor shaping all of the communities, with a negative correlation of Cellvibrio and Cellulomonas abundance within individual enrichment lines and the expression of genes associated with the production of secondary metabolites, toxins, and other antagonistic compounds. Our results provide insights into how microbial diversity and competition affect the stability and function of cellulose-degrading communities. IMPORTANCE Microbial communities are a key driver of the carbon cycle through the breakdown of complex polysaccharides in diverse environments including soil, marine systems, and the mammalian gut. However, due to the complexity of these communities, the species-species interactions that impact community structure and ultimately shape the rate of decomposition are difficult to define. Here, we performed serial enrichment on cellulose using communities inoculated from leaf-cutter ant refuse dumps, a cellulose-rich environment. By concurrently tracking cellulolytic ability and community composition and through metagenomic and metatranscriptomic sequencing, we analyzed the ecological dynamics of the enrichment lines. Our data suggest that antagonism is prevalent in these communities and that competition for soluble sugars may slow degradation and lead to community instability. Together, these results help reveal the relationships between competition and polysaccharide decomposition, with implications in diverse areas ranging from microbial community ecology to cellulosic biofuels production.}, } @article {pmid35258340, year = {2022}, author = {Modha, S and Robertson, DL and Hughes, J and Orton, RJ}, title = {Quantifying and Cataloguing Unknown Sequences within Human Microbiomes.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0146821}, pmid = {35258340}, issn = {2379-5077}, support = {MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; MR/S502479/1//UKRI | Medical Research Council (MRC)/ ; MC_UU_1201412//UKRI | Medical Research Council (MRC)/ ; }, mesh = {Animals ; Humans ; *Ursidae/genetics ; *Microbiota/genetics ; Metagenome ; Metagenomics ; Databases, Factual ; }, abstract = {Advances in genome sequencing technologies and lower costs have enabled the exploration of a multitude of known and novel environments and microbiomes. This has led to an exponential growth in the raw sequence data that are deposited in online repositories. Metagenomic and metatranscriptomic data sets are typically analysed with regard to a specific biological question. However, it is widely acknowledged that these data sets are comprised of a proportion of sequences that bear no similarity to any currently known biological sequence, and this so-called "dark matter" is often excluded from downstream analyses. In this study, a systematic framework was developed to assemble, identify, and measure the proportion of unknown sequences present in distinct human microbiomes. This framework was applied to 40 distinct studies, comprising 963 samples, and covering 10 different human microbiomes including fecal, oral, lung, skin, and circulatory system microbiomes. We found that while the human microbiome is one of the most extensively studied, on average 2% of assembled sequences have not yet been taxonomically defined. However, this proportion varied extensively among different microbiomes and was as high as 25% for skin and oral microbiomes that have more interactions with the environment. A rate of taxonomic characterization of 1.64% of unknown sequences being characterized per month was calculated from these taxonomically unknown sequences discovered in this study. A cross-study comparison led to the identification of similar unknown sequences in different samples and/or microbiomes. Both our computational framework and the novel unknown sequences produced are publicly available for future cross-referencing. Our approach led to the discovery of several novel viral genomes that bear no similarity to sequences in the public databases. Some of these are widespread as they have been found in different microbiomes and studies. Hence, our study illustrates how the systematic characterization of unknown sequences can help the discovery of novel microbes, and we call on the research community to systematically collate and share the unknown sequences from metagenomic studies to increase the rate at which the unknown sequence space can be classified.}, } @article {pmid35257467, year = {2022}, author = {Han, Y and Kim, G and Ahn, E and Jung, S and Jung, Y and Kim, Y and Ha, E and Heo, Y and Ryu, DH and Park, H and Hwang, GS}, title = {Integrated metagenomics and metabolomics analysis illustrates the systemic impact of the gut microbiota on host metabolism after bariatric surgery.}, journal = {Diabetes, obesity & metabolism}, volume = {24}, number = {7}, pages = {1224-1234}, pmid = {35257467}, issn = {1463-1326}, mesh = {*Bariatric Surgery ; Bile Acids and Salts ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolome ; Metabolomics/methods ; Metagenomics ; Obesity/surgery ; RNA, Ribosomal, 16S/genetics ; }, abstract = {AIM: To explore how bariatric surgery (BS) modified the obesity-associated gut microbiome, the host metabolome, and their interactions in obese Korean patients.

MATERIALS AND METHODS: Stool and fasting blood samples were obtained before and 1, 3, 6, and 12 months after BS from 52 patients enrolled in the Korean Obesity Surgical Treatment Study. We analysed the gut microbiome by 16S rRNA gene sequencing and the serum metabolome, including bile acids, by nuclear magnetic resonance spectroscopy and ultrahigh-performance liquid chromatography/triple quadrupole mass spectrometry.

RESULTS: Stool metagenomics showed that 27 microbiota were enriched and 14 microbiota were reduced after BS, whereas the abundances and diversity of observed features were increased. The levels of branched-chain amino acids and metabolites of energy metabolism in serum were decreased after surgery, whereas the levels of metabolites related to microbial metabolism, including dimethyl sulphone, glycine, and secondary bile acids, were increased in the serum samples. In addition, we found notable mutual associations among metabolites and gut microbiome changes attributed to BS.

CONCLUSIONS: Changes in the gut microbiome community and systemic levels of amino acids and sugars were directly derived from anatomical changes in the gastrointestinal tract after BS. We hypothesized that the observed increases in microbiome-related serum metabolites were a result of complex and indirect changes derived from BS. Ethnic-specific environmental or genetic factors could affect Korean-specific postmetabolic modification in obese patients who undergo BS.}, } @article {pmid35256725, year = {2022}, author = {Marquet, M and Zöllkau, J and Pastuschek, J and Viehweger, A and Schleußner, E and Makarewicz, O and Pletz, MW and Ehricht, R and Brandt, C}, title = {Evaluation of microbiome enrichment and host DNA depletion in human vaginal samples using Oxford Nanopore's adaptive sequencing.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {4000}, pmid = {35256725}, issn = {2045-2322}, mesh = {DNA ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Infant, Newborn ; *Microbiota/genetics ; *Nanopores ; Pregnancy ; *Premature Birth ; }, abstract = {Metagenomic sequencing is promising for clinical applications to study microbial composition concerning disease or patient outcomes. Alterations of the vaginal microbiome are associated with adverse pregnancy outcomes, like preterm premature rupture of membranes and preterm birth. Methodologically these samples often have to deal with low relative amounts of prokaryotic DNA and high amounts of host DNA (> 90%), decreasing the overall microbial resolution. Nanopore's adaptive sampling method offers selective DNA depletion or target enrichment to directly reject or accept DNA molecules during sequencing without specialized sample preparation. Here, we demonstrate how selective 'human host depletion' resulted in a 1.70 fold (± 0.27 fold) increase in total sequencing depth, providing higher taxonomic profiling sensitivity. At the same time, the microbial composition remains consistent with the control experiments. The complete removal of all human host sequences is not yet possible and should be considered as an ethical approval statement might still be necessary. Adaptive sampling increased microbial sequencing yield in all 15 sequenced clinical routine vaginal samples, making it a valuable tool for clinical surveillance and medical-based research, which can be used in addition to other host depletion methods before sequencing.}, } @article {pmid35255937, year = {2022}, author = {van Dijk, LR and Walker, BJ and Straub, TJ and Worby, CJ and Grote, A and Schreiber, HL and Anyansi, C and Pickering, AJ and Hultgren, SJ and Manson, AL and Abeel, T and Earl, AM}, title = {StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {74}, pmid = {35255937}, issn = {1474-760X}, support = {R01 DK121822/DK/NIDDK NIH HHS/United States ; U01 AI095776/AI/NIAID NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Humans ; Metagenome ; Metagenomics ; *Microbiota/genetics ; }, abstract = {Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamics are underexplored due to the difficulties of studying them. We introduce the Strain Genome Explorer (StrainGE) toolkit, which deconvolves strain mixtures and characterizes component strains at the nucleotide level from short-read metagenomic sequencing with higher sensitivity and resolution than other tools. StrainGE is able to identify strains at 0.1x coverage and detect variants for multiple conspecific strains within a sample from coverages as low as 0.5x.}, } @article {pmid35254122, year = {2022}, author = {Mizutani, T and Ishizaka, A and Koga, M and Ikeuchi, K and Saito, M and Adachi, E and Yamayoshi, S and Iwatsuki-Horimoto, K and Yasuhara, A and Kiyono, H and Matano, T and Suzuki, Y and Tsutsumi, T and Kawaoka, Y and Yotsuyanagi, H}, title = {Correlation Analysis between Gut Microbiota Alterations and the Cytokine Response in Patients with Coronavirus Disease during Hospitalization.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0168921}, pmid = {35254122}, issn = {2165-0497}, mesh = {Bacteria/genetics ; *COVID-19 ; Cytokines ; Dysbiosis/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; Hospitalization ; Humans ; Inflammation ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The role of the intestinal microbiota in coronavirus disease 2019 (COVID-19) is being elucidated. Here, we analyzed the temporal changes in microbiota composition and the correlation between inflammation biomarkers/cytokines and microbiota in hospitalized COVID-19 patients. We obtained stool specimens, blood samples, and patient records from 22 hospitalized COVID-19 patients and performed 16S rRNA metagenomic analysis of stool samples over the course of disease onset compared to 40 healthy individual stool samples. We analyzed the correlation between the changes in the gut microbiota and plasma proinflammatory cytokine levels. Immediately after admission, differences in the gut microbiota were observed between COVID-19 patients and healthy subjects, mainly including enrichment of the classes Bacilli and Coriobacteriia and decrease in abundance of the class Clostridia. The bacterial profile continued to change throughout the hospitalization, with a decrease in short-chain fatty acid-producing bacteria including Faecalibacterium and an increase in the facultatively anaerobic bacteria Escherichia-Shigella. A consistent increase in Eggerthella belonging to the class Coriobacteriia was observed. The abundance of the class Clostridia was inversely correlated with interferon-γ level and that of the phylum Actinobacteria, which was enriched in COVID-19, and was positively correlated with gp130/sIL-6Rb levels. Dysbiosis was continued even after 21 days from onset. The intestines tended to be an aerobic environment in hospitalized COVID-19 patients. Because the composition of the gut microbiota correlates with the levels of proinflammatory cytokines, this finding emphasizes the need to understand how pathology is related to the temporal changes in the specific gut microbiota observed in COVID-19 patients. IMPORTANCE There is growing evidence that the commensal microbiota of the gastrointestinal and respiratory tracts regulates local and systemic inflammation (gut-lung axis). COVID-19 is primarily a respiratory disease, but the involvement of microbiota changes in the pathogenesis of this disease remains unclear. The composition of the gut microbiota of patients with COVID-19 changed over time during hospitalization, and the intestines tended to be an aerobic environment in hospitalized COVID-19 patients. These changes in gut microbiota may induce increased intestinal permeability, called leaky gut, allowing bacteria and toxins to enter the circulatory system and further aggravate the systemic inflammatory response. Since gut microbiota composition correlates with levels of proinflammatory cytokines, this finding highlights the need to understand how pathology relates to the gut environment, including the temporal changes in specific gut microbiota observed in COVID-19 patients.}, } @article {pmid35253207, year = {2022}, author = {Pfenninger, M and Bálint, M}, title = {On the use of population genomic time series for environmental monitoring.}, journal = {American journal of botany}, volume = {109}, number = {4}, pages = {497-499}, doi = {10.1002/ajb2.1836}, pmid = {35253207}, issn = {1537-2197}, mesh = {*Environmental Monitoring ; *Metagenomics ; Time Factors ; }, } @article {pmid35250904, year = {2021}, author = {Song, Y and Hou, J and Kwok, JSL and Weng, H and Tang, MF and Wang, MH and Leung, ASY and Tao, KP and Wong, GWK and Chan, RWY and Tsui, SKW and Leung, TF}, title = {Whole-Genome Shotgun Sequencing for Nasopharyngeal Microbiome in Pre-school Children With Recurrent Wheezing.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {792556}, pmid = {35250904}, issn = {1664-302X}, abstract = {Microbiome mediates early life immune deviation in asthma development. Recurrent wheeze (RW) in pre-school years is a risk factor for asthma diagnosis in school-age children. Dysbiosis exists in asthmatic airways, while its origin in pre-school years and relationship to RW is not clearly defined. This study investigated metagenomics of nasopharyngeal microbiome in pre-school children with RW. We applied whole-genome shotgun sequencing and human rhinovirus (HRV) detection on nasopharyngeal samples collected from three groups of pre-school children: (i) RW group: 16 children at-risk for asthma who were hospitalized for RW, (ii) inpatient control (IC): 18 subjects admitted for upper respiratory infection, and (iii) community control (CC): 36 children without respiratory syndromes. Sequence reads were analyzed by MetaPhlAn2 and HUMAnN2 algorithm for taxonomic and functional identification. Linear discriminant analysis effect size (LEfSe) analysis was used to identify discriminative features. We identified that Moraxella catarrhalis and Dolosigranulum pigrum were predominant species in nasopharynx. RW had lower alpha diversity (Shannon diversity index) than CC (0.48 vs. 1.07; P adj = 0.039), characterized by predominant Proteobacteria. LEfSe analysis revealed D. pigrum was the only discriminative species across groups (LDA = 5.57, P = 0.002), with its relative abundance in RW, IC, and CC being 9.6, 14.2, and 37.3%, respectively (P < 0.05). LEfSe identified five (ribo)nucleotides biosynthesis pathways to be group discriminating. Adjusting for HRV status, pre-school children with RW have lower nasopharyngeal biodiversity, which is associated with Proteobacteria predominance and lower abundance of D. pigrum. Along with discriminative pathways found in RW and CC, these microbial biomarkers help to understand RW pathogenesis.}, } @article {pmid35247565, year = {2022}, author = {Gupta, J and Rathour, R and Dupont, C and Mishra, A and Shekhar Thakur, I}, title = {Biogeochemical profiling and taxonomic characterization of municipal landfill site by metagenomic sequencing.}, journal = {Bioresource technology}, volume = {351}, number = {}, pages = {126936}, doi = {10.1016/j.biortech.2022.126936}, pmid = {35247565}, issn = {1873-2976}, mesh = {Metagenome ; *Metagenomics ; *Microbiota/genetics ; Phylogeny ; Waste Disposal Facilities ; }, abstract = {Most of the discarded waste material paves their way to the utmost common dumping grounds, Landfills. Despite their widespread use, the landfill microbiomes are still not well characterized. Metagenomics approach provides insight into the identification of operational parameters influencing the microbiome composition and their biodegradation competencies. The metagenomic DNA was prepared to explore taxonomical community structure, phylogenetic relationships, and functional profile at the same time. A total of 100,021,052 high-quality filtered reads were acquired with a GC abundance of 62.59%. Taxonomical abundance revealed the dominance of phylum Proteobacteria and genes involved in biomolecules metabolism, aromatic compound degradation, stress tolerance, xenobiotic biodegradation etc. were revealed functionally. The intricate heterogeneous environment of landfill revealed well flourished biogeochemical metabolic profiles including nitrogen metabolism. This is the first study for the generated metagenome of Ghazipur landfill and the obtained results propose that microbial communities in landfill settings are far more intricate than expected. It remain mostly unexplored which demands the usage of multiple platforms for a better understanding.}, } @article {pmid35247173, year = {2022}, author = {Jimoh, AA and Ikhimiukor, OO and Adeleke, R}, title = {Prospects in the bioremediation of petroleum hydrocarbon contaminants from hypersaline environments: A review.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {24}, pages = {35615-35642}, pmid = {35247173}, issn = {1614-7499}, mesh = {Biodegradation, Environmental ; Hydrocarbons ; *Microbiota ; *Petroleum ; *Petroleum Pollution/analysis ; Soil Microbiology ; *Soil Pollutants ; }, abstract = {Hypersaline environments are underappreciated and are frequently exposed to pollution from petroleum hydrocarbons. Unlike other environs, the high salinity conditions present are a deterrent to various remediation techniques. There is also production of hypersaline waters from oil-polluted ecosystems which contain toxic hydrophobic pollutants that are threat to public health, environmental protection, and sustainability. Currently, innovative advances are being proposed for the remediation of oil-contaminated hypersaline regions. Such advancements include the exploration and stimulation of native microbial communities capable of utilizing and degrading petroleum hydrocarbons. However, prevailing salinity in these environments is unfavourable for the growth of non-halophylic microorganisms, thus limiting effective bioremediation options. An in-depth understanding of the potentials of various remediation technologies of hydrocarbon-polluted hypersaline environments is lacking. Thus, we present an overview of petroleum hydrocarbon pollution in hypersaline ecosystems and discuss the challenges and prospects associated with several technologies that may be employed in remediation of hydrocarbon pollution in the presence of delimiting high salinities. The application of biological remediation technologies including the utilization of halophilic and halotolerant microorganisms is also discussed.}, } @article {pmid35246229, year = {2022}, author = {Zhou, H and Beltrán, JF and Brito, IL}, title = {Host-microbiome protein-protein interactions capture disease-relevant pathways.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {72}, pmid = {35246229}, issn = {1474-760X}, support = {DP2 HL141007/HL/NHLBI NIH HHS/United States ; }, mesh = {*Diabetes Mellitus, Type 2 ; *Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases/genetics ; Metagenomics ; *Microbiota ; Obesity ; }, abstract = {BACKGROUND: Host-microbe interactions are crucial for normal physiological and immune system development and are implicated in a variety of diseases, including inflammatory bowel disease (IBD), colorectal cancer (CRC), obesity, and type 2 diabetes (T2D). Despite large-scale case-control studies aimed at identifying microbial taxa or genes involved in pathogeneses, the mechanisms linking them to disease have thus far remained elusive.

RESULTS: To identify potential pathways through which human-associated bacteria impact host health, we leverage publicly-available interspecies protein-protein interaction (PPI) data to find clusters of microbiome-derived proteins with high sequence identity to known human-protein interactors. We observe differential targeting of putative human-interacting bacterial genes in nine independent metagenomic studies, finding evidence that the microbiome broadly targets human proteins involved in immune, oncogenic, apoptotic, and endocrine signaling pathways in relation to IBD, CRC, obesity, and T2D diagnoses.

CONCLUSIONS: This host-centric analysis provides a mechanistic hypothesis-generating platform and extensively adds human functional annotation to commensal bacterial proteins.}, } @article {pmid35243810, year = {2022}, author = {Wang, D and Zhang, T and Lu, Y and Wang, C and Wu, Y and Li, J and Tao, Y and Deng, L and Zhang, X and Ma, J}, title = {Helicobacter pylori infection affects the human gastric microbiome, as revealed by metagenomic sequencing.}, journal = {FEBS open bio}, volume = {12}, number = {6}, pages = {1188-1196}, pmid = {35243810}, issn = {2211-5463}, mesh = {*Gastritis/epidemiology/microbiology/pathology ; *Gastrointestinal Microbiome ; *Helicobacter Infections/genetics ; *Helicobacter pylori/genetics ; Humans ; *Microbiota/genetics ; }, abstract = {Helicobacter pylori infection is a prevalent infectious disease, associated with many gastric diseases, including gastritis, gastric ulcer, and gastric cancer. To reveal the characteristics of the gastric microbiome in patients infected with H. pylori, we performed metagenomic shotgun sequencing of stomach swab samples from 96 patients and then conducted metagenomic association analyses between alterations in the gastric microbiome and H. pylori infection status. The overall composition of the gastric microbiota in H. pylori-infected individuals was distinctly different from the negative controls; H. pylori became the dominant species after colonizing the human stomach and significantly decreased the α-diversity of the gastric community (P < 0.05, Wilcoxon rank-sum test). We also identified 6 HPI-associated microbial species (FDR < 0.05, Wilcoxon rank-sum test): Stenotrophomonas maltophilia, Stenotrophomonas unclassified, Chryseobacterium unclassified, Pedobacter unclassified, Variovorax unclassified, and Pseudomonas stutzeri. Furthermore, 55 gastric microbial pathways were enriched in the H. pylori-positive group, whereas only 2 pathways were more abundant in the H. pylori-negative group: dTDP-L-rhamnose biosynthesis and tetrapyrrole biosynthesis (FDR < 0.05, Wilcoxon rank-sum test). Gastritis was not associated with non-H. pylori species in the stomach (P > 0.05, Wilcoxon rank-sum test). This study revealed alterations in gastric microbial taxa and function associated with HPI in the Chinese population, which provides an insight into gastric microbial interactions and their potential role in the pathological process of gastric diseases.}, } @article {pmid35242946, year = {2022}, author = {Purwoko, D and Safarrida, A and Tajuddin, T and Rupaedah, B and Suyono, A and Wahid, A and Sugianto, M and Suja'i, I}, title = {Metagenomic data of microbial in natural empty fruit bunches degradation.}, journal = {Data in brief}, volume = {41}, number = {}, pages = {107967}, pmid = {35242946}, issn = {2352-3409}, abstract = {Oil palm empty fruit bunches (OPEFB) are the lignocellulosic complex organic waste material from palm oil mills that is cheap, environmentally friendly, and abundant in Indonesia. Slow degradation of OPEFB becomes a problem for oil palm plantations. OPEFB which has decayed naturally for 6 months, 1 year, and 2 years were obtained from the Oil Palm Plantation, PTPN VIII Cikasungka, Bogor, Indonesia. In this study, fungal and bacterial diversity in naturally decaying OPEFB in plantations was identified using Illumina MiSeq sequencing of the ITS2 for fungal, the V3 region of the 16S rRNA gene, and the V4 region of the 18S rRNA gene for bacterial. Bacterial diversity in decaying OPEFB was dominated by the phylum Planctomycetes (40-60%), whereas most of the fungal sequences taken belonged to Ascomycota (60-90%). Biodiversity profile resulting from metagenomic analysis is useful for increasing knowledge about microbial composition in the natural degradation process of OPEFB. The resulting data can be used to compare the diversity of bacteria at different weathering times and depths. In-depth observation of the diversity of lignin-degrading microbes from the natural decomposition of OPEFB has the potential to discover novel enzymes and ligninolytic activities that are useful for the fast degradation of OPEFB, production of biofuels based on enzymatic technology, and the development of high value-added biomass products.}, } @article {pmid35241840, year = {2022}, author = {Ma, Y and Guo, Z and Xia, B and Zhang, Y and Liu, X and Yu, Y and Tang, N and Tong, X and Wang, M and Ye, X and Feng, J and Chen, Y and Wang, J}, title = {Identification of antimicrobial peptides from the human gut microbiome using deep learning.}, journal = {Nature biotechnology}, volume = {40}, number = {6}, pages = {921-931}, pmid = {35241840}, issn = {1546-1696}, mesh = {Adenosine Monophosphate ; Animals ; Anti-Bacterial Agents/chemistry ; Antimicrobial Peptides ; *Deep Learning ; *Gastrointestinal Microbiome ; Humans ; Mice ; Peptides/chemistry/pharmacology ; }, abstract = {The human gut microbiome encodes a large variety of antimicrobial peptides (AMPs), but the short lengths of AMPs pose a challenge for computational prediction. Here we combined multiple natural language processing neural network models, including LSTM, Attention and BERT, to form a unified pipeline for candidate AMP identification from human gut microbiome data. Of 2,349 sequences identified as candidate AMPs, 216 were chemically synthesized, with 181 showing antimicrobial activity (a positive rate of >83%). Most of these peptides have less than 40% sequence homology to AMPs in the training set. Further characterization of the 11 most potent AMPs showed high efficacy against antibiotic-resistant, Gram-negative pathogens and demonstrated significant efficacy in lowering bacterial load by more than tenfold against a mouse model of bacterial lung infection. Our study showcases the potential of machine learning approaches for mining functional peptides from metagenome data and accelerating the discovery of promising AMP candidate molecules for in-depth investigations.}, } @article {pmid35241796, year = {2022}, author = {Bloom, SM and Mafunda, NA and Woolston, BM and Hayward, MR and Frempong, JF and Abai, AB and Xu, J and Mitchell, AJ and Westergaard, X and Hussain, FA and Xulu, N and Dong, M and Dong, KL and Gumbi, T and Ceasar, FX and Rice, JK and Choksi, N and Ismail, N and Ndung'u, T and Ghebremichael, MS and Relman, DA and Balskus, EP and Mitchell, CM and Kwon, DS}, title = {Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation.}, journal = {Nature microbiology}, volume = {7}, number = {3}, pages = {434-450}, pmid = {35241796}, issn = {2058-5276}, support = {P30 AI060354/AI/NIAID NIH HHS/United States ; R01 AI111918/AI/NIAID NIH HHS/United States ; T32 AI007387/AI/NIAID NIH HHS/United States ; }, mesh = {Cysteine/metabolism ; Female ; Humans ; Lactobacillus/genetics/metabolism ; Metronidazole/metabolism/pharmacology/therapeutic use ; *Microbiota ; Vagina/microbiology ; *Vaginosis, Bacterial/drug therapy/microbiology ; }, abstract = {Vaginal microbiota composition affects many facets of reproductive health. Lactobacillus iners-dominated microbial communities are associated with poorer outcomes, including higher risk of bacterial vaginosis (BV), compared with vaginal microbiota rich in L. crispatus. Unfortunately, standard-of-care metronidazole therapy for BV typically results in dominance of L. iners, probably contributing to post-treatment relapse. Here we generate an L. iners isolate collection comprising 34 previously unreported isolates from 14 South African women with and without BV and 4 previously unreported isolates from 3 US women. We also report an associated genome catalogue comprising 1,218 vaginal Lactobacillus isolate genomes and metagenome-assembled genomes from >300 women across 4 continents. We show that, unlike L. crispatus, L. iners growth is dependent on L-cysteine in vitro and we trace this phenotype to the absence of canonical cysteine biosynthesis pathways and a restricted repertoire of cysteine-related transport mechanisms. We further show that cysteine concentrations in cervicovaginal lavage samples correlate with Lactobacillus abundance in vivo and that cystine uptake inhibitors selectively inhibit L. iners growth in vitro. Combining an inhibitor with metronidazole promotes L. crispatus dominance of defined BV-like communities in vitro by suppressing L. iners growth. Our findings enable a better understanding of L. iners biology and suggest candidate treatments to modulate the vaginal microbiota to improve reproductive health for women globally.}, } @article {pmid35241676, year = {2022}, author = {Lapidot, Y and Reshef, L and Maya, M and Cohen, D and Gophna, U and Muhsen, K}, title = {Socioeconomic disparities and household crowding in association with the fecal microbiome of school-age children.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {10}, pmid = {35241676}, issn = {2055-5008}, mesh = {Child ; *Crowding ; Family Characteristics ; Humans ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The development of the gut microbiome occurs mainly during the first years of life; however, little is known on the role of environmental and socioeconomic exposures, particularly within the household, in shaping the microbial ecology through childhood. We characterized differences in the gut microbiome of school-age healthy children, in association with socioeconomic disparities and household crowding. Stool samples were analyzed from 176 Israeli Arab children aged six to nine years from three villages of different socioeconomic status (SES). Sociodemographic data were collected through interviews with the mothers. We used 16 S rRNA gene sequencing to characterize the gut microbiome, including an inferred analysis of metabolic pathways. Differential analysis was performed using the analysis of the composition of microbiomes (ANCOM), with adjustment for covariates. An analysis of inferred metagenome functions was performed implementing PICRUSt2. Gut microbiome composition differed across the villages, with the largest difference attributed to socioeconomic disparities, with household crowding index being a significant explanatory variable. Living in a low SES village and high household crowding were associated with increased bacterial richness and compositional differences, including an over-representation of Prevotella copri and depleted Bifidobacterium. Secondary bile acid synthesis, d-glutamine and d-glutamate metabolism and Biotin metabolism were decreased in the lower SES village. In summary, residential SES is a strong determinant of the gut microbiome in healthy school-age children, mediated by household crowding and characterized by increased bacterial richness and substantial taxonomic and metabolic differences. Further research is necessary to explore possible implications of SES-related microbiome differences on children's health and development.}, } @article {pmid35240353, year = {2022}, author = {Yang, WY and Chou, CH and Wang, C}, title = {The effects of feed supplementing Akkemansia muciniphila on incidence, severity, and gut microbiota of necrotic enteritis in chickens.}, journal = {Poultry science}, volume = {101}, number = {4}, pages = {101751}, pmid = {35240353}, issn = {1525-3171}, mesh = {Animal Feed/analysis ; Animals ; Chickens ; *Clostridium Infections/pathology/prevention & control/veterinary ; Clostridium perfringens ; *Coccidiosis/parasitology/prevention & control/veterinary ; *Eimeria ; *Enteritis/pathology/prevention & control/veterinary ; *Gastrointestinal Microbiome ; Incidence ; Mucins ; *Poultry Diseases/parasitology/prevention & control ; }, abstract = {Akkermansia muciniphila (AM) is a mucin-degrading anaerobe, exerting beneficial effects on gut integrity improvement, inflammatory alleviation, and metabolic regulations in humans. Excess amounts of mucin and mucogenesis in the gut facilitate the development of necrotic enteritis (NE) in chickens. The study aimed to evaluate the effects of oral inoculation of AM on NE prevention and gut modulation in a NE-reproduced model coinfecting with Clostridium perfringens (CP) and Eimeria parasites. A total of 105 commercial 1-day-old broilers were randomly allocated into 5 groups, respectively challenged with Eimeria (Eimeria group), Eimeria and CP (Eimeria+CP group), Eimeria and CP with AM (Eimeria+CP+AM group), Eimeria and AM (Eimeria+AM group), and a placebo (Noninfected group). The treatment of AM exhibited a low degree of amelioration on NE severity. The application neither protected broilers from NE by decreasing NE-positive numbers nor reached a significant reduction in lesion scores in the small intestines. The development of NE reduced species diversity in jejunal microbiota; the pretreatments of AM exacerbated the consequence by losing species richness and promoted the similarity of the jejunal microbial community presented in the Eimeria+CP group. The participation of AM enhanced the increments of genera Clostridium sensu stricto 1 and Escherichia_Shigella and decreased the number of Lactobacillus. The significant variations of genera Clostridium sensu stricto 1 and Lactobacillus in jejunal microbiota were associated with NE development and promotion. In conclusion, oral inoculation of AM promoted the development of NE and modulated the jejunal microbiota favorable for CP overgrowth in broilers. The application of AM as a probiotic in broilers should be cautious on account of the effects to predispose NE.}, } @article {pmid35239511, year = {2022}, author = {Severyn, CJ and Siranosian, BA and Kong, ST and Moreno, A and Li, MM and Chen, N and Duncan, CN and Margossian, SP and Lehmann, LE and Sun, S and Andermann, TM and Birbrayer, O and Silverstein, S and Reynolds, CG and Kim, S and Banaei, N and Ritz, J and Fodor, AA and London, WB and Bhatt, AS and Whangbo, JS}, title = {Microbiota dynamics in a randomized trial of gut decontamination during allogeneic hematopoietic cell transplantation.}, journal = {JCI insight}, volume = {7}, number = {7}, pages = {}, pmid = {35239511}, issn = {2379-3708}, support = {R01 AI148623/AI/NIAID NIH HHS/United States ; P01 CA229092/CA/NCI NIH HHS/United States ; T32 HG002295/HG/NHGRI NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; T32 DK098132/DK/NIDDK NIH HHS/United States ; K23 AI163365/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Child ; Decontamination ; *Graft vs Host Disease/etiology/prevention & control ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Humans ; Mice ; *Microbiota ; Pilot Projects ; }, abstract = {BACKGROUNDGut decontamination (GD) can decrease the incidence and severity of acute graft-versus-host disease (aGVHD) in murine models of allogeneic hematopoietic cell transplantation (HCT). In this pilot study, we examined the impact of GD on gut microbiome composition and the incidence of aGVHD in HCT patients.METHODSWe randomized 20 patients undergoing allogeneic HCT to receive (GD) or not receive (no-GD) oral vancomycin-polymyxin B from day -5 through neutrophil engraftment. We evaluated shotgun metagenomic sequencing of serial stool samples to compare the composition and diversity of the gut microbiome between study arms. We assessed clinical outcomes in the 2 arms and performed strain-specific analyses of pathogens that caused bloodstream infections (BSI).RESULTSThe 2 arms did not differ in the predefined primary outcome of Shannon diversity of the gut microbiome at 2 weeks post-HCT (genus, P = 0.8; species, P = 0.44) or aGVHD incidence (P = 0.58). Immune reconstitution of T cell and B cell subsets was similar between groups. Five patients in the no-GD arm had 8 BSI episodes versus 1 episode in the GD arm (P = 0.09). The BSI-causing pathogens were traceable to the gut in 7 of 8 BSI episodes in the no-GD arm, including Staphylococcus species.CONCLUSIONWhile GD did not differentially affect Shannon diversity or clinical outcomes, our findings suggest that GD may protect against gut-derived BSI in HCT patients by decreasing the prevalence or abundance of gut pathogens.TRIAL REGISTRATIONClinicalTrials.gov NCT02641236.FUNDINGNIH, Damon Runyon Cancer Research Foundation, V Foundation, Sloan Foundation, Emerson Collective, and Stanford Maternal & Child Health Research Institute.}, } @article {pmid35239463, year = {2022}, author = {Fang, Z and Pan, T and Li, L and Wang, H and Zhu, J and Zhang, H and Zhao, J and Chen, W and Lu, W}, title = {Bifidobacterium longum mediated tryptophan metabolism to improve atopic dermatitis via the gut-skin axis.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2044723}, pmid = {35239463}, issn = {1949-0984}, mesh = {Animals ; Bifidobacterium/genetics/metabolism ; *Bifidobacterium longum/genetics/metabolism ; *Dermatitis, Atopic ; *Gastrointestinal Microbiome ; Humans ; Indoles/metabolism ; Receptors, Aryl Hydrocarbon/genetics/metabolism ; Tryptophan/metabolism ; }, abstract = {Gut microbial disturbance affects allergic diseases including asthma, atopic dermatitis (AD) via the aberrant immune response. Some Bifidobacterial species and strains have been reported to improve AD via modulating immune-microbe interactions in patients. However, the effective metabolites and mechanism of alleviating AD in bifidobacteria remain to be elucidated. This study aimed to explore the microbial metabolite and mechanism of Bifidobacterium longum to improve AD. Based on shotgun metagenomic sequencing and UHPLC Q-Exactive-MS targeted metabolic experiments in vitro and in vivo, we focused on tryptophan metabolism and indole derivatives, which are endogenous ligands for aryl hydrocarbon receptor (AHR). Indole-3-carbaldehyde (I3C), a tryptophan metabolite of B. longum CCFM1029 activated AHR-mediated immune signaling pathway to improve AD symptoms in animal and clinical experiments. B. longum CCFM1029 upregulated tryptophan metabolism and increased I3C to suppress aberrant T helper 2 type immune responses, but these benefits were eliminated by AHR antagonist CH223191. Furthermore, B. longum CCFM1029 reshaped gut microbial composition in AD patients, increased fecal and serum I3C, and maintained the abundance of Lachnospiraceae related to tryptophan metabolism of gut microbiota. The results suggested that based on the interactions of the gut-skin axis, B. longum CCFM1029 upregulated tryptophan metabolism and produced I3C to activate AHR-mediated immune response, alleviating AD symptoms. Indole derivates, microbial metabolites of tryptophan, may be the potential metabolites of bifidobacteria to alleviate AD via the AHR signaling pathway.}, } @article {pmid35239207, year = {2022}, author = {de Souza Colombo, G and Viana Mendes, I and de Morais Souto, B and Chaves Barreto, C and Assis Serra, L and Ferreira Noronha, E and Skorupa Parachin, N and Moreira de Almeida, JR and Ferraz Quirino, B}, title = {Identification and functional expression of a new xylose isomerase from the goat rumen microbiome in Saccharomyces cerevisiae.}, journal = {Letters in applied microbiology}, volume = {74}, number = {6}, pages = {941-948}, doi = {10.1111/lam.13689}, pmid = {35239207}, issn = {1472-765X}, support = {//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; //Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; //Fundação de Amparo à Pesquisa do Distrito Federal/ ; }, mesh = {*Aldose-Ketose Isomerases/genetics/metabolism ; Animals ; Fermentation ; *Goats/microbiology ; *Microbiota ; Phylogeny ; *Rumen/enzymology/microbiology ; *Saccharomyces cerevisiae/metabolism ; Xylose/metabolism ; }, abstract = {The current climate crisis demands replacement of fossil energy sources with sustainable alternatives. In this scenario, second-generation bioethanol, a product of lignocellulosic biomass fermentation, represents a more sustainable alternative. However, Saccharomyces cerevisiae cannot metabolize pentoses, such as xylose, present as a major component of lignocellulosic biomass. Xylose isomerase (XI) is an enzyme that allows xylose consumption by yeasts, because it converts xylose into xylulose, which is further converted to ethanol by the pentose-phosphate pathway. Only a few XI were successfully expressed in S. cerevisiae strains. This work presents a new bacterial XI, named GR-XI 1, obtained from a Brazilian goat rumen metagenomic library. Phylogenetic analysis confirmed the bacterial origin of the gene, which is related to Firmicutes XIs. After codon optimization, this enzyme, renamed XySC1, was functionally expressed in S. cerevisiae, allowing growth in media with xylose as sole carbon source. Overexpression of XySC1 in S. cerevisiae allowed the recombinant strain to efficiently consume and metabolize xylose under aerobic conditions.}, } @article {pmid35238677, year = {2022}, author = {Bohl, JA and Lay, S and Chea, S and Ahyong, V and Parker, DM and Gallagher, S and Fintzi, J and Man, S and Ponce, A and Sreng, S and Kong, D and Oliveira, F and Kalantar, K and Tan, M and Fahsbender, L and Sheu, J and Neff, N and Detweiler, AM and Yek, C and Ly, S and Sath, R and Huch, C and Kry, H and Leang, R and Huy, R and Lon, C and Tato, CM and DeRisi, JL and Manning, JE}, title = {Discovering disease-causing pathogens in resource-scarce Southeast Asia using a global metagenomic pathogen monitoring system.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {11}, pages = {e2115285119}, pmid = {35238677}, issn = {1091-6490}, mesh = {Asia, Southeastern/epidemiology ; Cambodia/epidemiology ; *Disease Susceptibility ; Female ; Fever/epidemiology/etiology ; *Health Resources ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metagenome ; Metagenomics/*methods ; *Public Health Surveillance ; Seroepidemiologic Studies ; }, abstract = {SignificanceMetagenomic pathogen sequencing offers an unbiased approach to characterizing febrile illness. In resource-scarce settings with high biodiversity, it is critical to identify disease-causing pathogens in order to understand burden and to prioritize efforts for control. Here, metagenomic next-generation sequencing (mNGS) characterization of the pathogen landscape in Cambodia revealed diverse vector-borne and zoonotic pathogens irrespective of age and gender as risk factors. Identification of key pathogens led to changes in national program surveillance. This study is a "real world" example of the use of mNGS surveillance of febrile individuals, executed in-country, to identify outbreaks of vector-borne, zoonotic, and other emerging pathogens in a resource-scarce setting.}, } @article {pmid35237854, year = {2022}, author = {Sze, C and Pressler, M and Lee, JR and Chughtai, B}, title = {The gut, vaginal, and urine microbiome in overactive bladder: a systematic review.}, journal = {International urogynecology journal}, volume = {33}, number = {5}, pages = {1157-1164}, pmid = {35237854}, issn = {1433-3023}, mesh = {Bacteria ; Child ; Female ; Humans ; *Microbiota ; *Urinary Bladder, Overactive/microbiology ; *Urinary Tract/microbiology ; Vagina ; }, abstract = {INTRODUCTION AND HYPOTHESIS: The objective was to systemically review the current literature on the association of gut, vaginal, and urinary dysbiosis in female patients with overactive bladder (OAB).

METHODS: We performed a comprehensive literature search following the Preferred Reporting Items for Systematic Review and Meta-analysis (PRISMA) protocols for systematic reviews. In the EMBASE, CINAHL, and Medline databases, a search was conducted using key words such as "microbiome," "microbiota," "microflora," "overactive bladder," "urge," "gut," "vaginal." Articles were screened using the online tool www.covidence.org . Two independent reviewers screened studies at each stage and resolved conflicts together. We excluded papers that discussed pediatric patients and animal studies. In total, 13 articles met this criterion, which included 6 abstracts.

RESULTS: After identifying 817 unique references, 13 articles met the criteria for data extraction. Articles were published from 2017 to 2021. No study reported the same microbiota abundance, even in healthy individuals. Overall, there was a loss of bacterial diversity in OAB patients compared with controls. Additionally, the bacterial composition of the controls and OAB patients was not significantly different, especially if the urine was collected midstream. Overall, the composition of the microbiome is dependent on the specimen collection methodology, and the metagenomic sequencing technique utilized. OAB urine microbiome is more predisposed to alteration from the gut or vaginal influences than in controls.

CONCLUSIONS: Current evidence suggested a potential relationship among gut, vaginal, and urinary microbiome in OAB patients, but there are very limited studies.}, } @article {pmid35237276, year = {2022}, author = {Yang, Y and Zheng, X and Wang, Y and Tan, X and Zou, H and Feng, S and Zhang, H and Zhang, Z and He, J and Cui, B and Zhang, X and Wu, Z and Dong, M and Cheng, W and Tao, S and Wei, H}, title = {Human Fecal Microbiota Transplantation Reduces the Susceptibility to Dextran Sulfate Sodium-Induced Germ-Free Mouse Colitis.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {836542}, pmid = {35237276}, issn = {1664-3224}, mesh = {Animals ; Anti-Inflammatory Agents/pharmacology ; Bacteria/metabolism ; *Colitis/drug therapy/therapy ; *Colitis, Ulcerative/drug therapy/therapy ; Dextran Sulfate/toxicity ; Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Humans ; Mice ; }, abstract = {In clinical practice, fecal microbiota transplantation (FMT) has been used to treat inflammatory bowel disease (IBD), and has shown certain effects. However, the selection of FMT donors and the mechanism underlying the effect of FMT intervention in IBD require further exploration. In this study, dextran sodium sulfate (DSS)-induced colitis mice were used to determine the differences in the protection of colitis symptoms, inflammation, and intestinal barrier, by FMT from two donors. Intriguingly, pre-administration of healthy bacterial fluid significantly relieved the symptoms of colitis compared to the ulcerative colitis (UC) bacteria. In addition, healthy donor (HD) bacteria significantly reduced the levels of inflammatory markers Myeloperoxidase (MPO) and Eosinophil peroxidase (EPO), and various pro-inflammatory factors, in colitis mice, and increased the secretion of the anti-inflammatory factor IL-10. Metagenomic sequencing indicated higher species diversity and higher abundance of anti-inflammatory bacteria in the HD intervention group, including Alistipes putredinis, Akkermansia muciniphila, Bifidobacterium adolescentis, short-chain fatty acids (SCFAs)-producing bacterium Christensenella minuta, and secondary bile acids (SBAs)-producing bacterium Clostridium leptum. In the UC intervention group, the SCFA-producing bacterium Bacteroides stercoris, IBD-related bacterium Ruminococcus gnavus, Enterococcus faecalis, and the conditional pathogen Bacteroides caccae, were more abundant. Metabolomics analysis showed that the two types of FMT significantly modulated the metabolism of DSS-induced mice. Moreover, compared with the UC intervention group, indoleacetic acid and unsaturated fatty acids (DHA, DPA, and EPA) with anti-inflammatory effects were significantly enriched in the HD intervention group. In summary, these results indicate that FMT can alleviate the symptoms of colitis, and the effect of HD intervention is better than that of UC intervention. This study offers new insights into the mechanisms of FMT clinical intervention in IBD.}, } @article {pmid35235560, year = {2022}, author = {Tierney, BT and Tan, Y and Yang, Z and Shui, B and Walker, MJ and Kent, BM and Kostic, AD and Patel, CJ}, title = {Systematically assessing microbiome-disease associations identifies drivers of inconsistency in metagenomic research.}, journal = {PLoS biology}, volume = {20}, number = {3}, pages = {e3001556}, pmid = {35235560}, issn = {1545-7885}, support = {R01 AI127250/AI/NIAID NIH HHS/United States ; R01 ES032470/ES/NIEHS NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/classification/*genetics ; Biomedical Research/*methods ; Cardiovascular Diseases/metabolism/microbiology ; Colorectal Neoplasms/metabolism/microbiology ; Diabetes Mellitus, Type 1/metabolism/microbiology ; Diabetes Mellitus, Type 2/metabolism/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Inflammatory Bowel Diseases/metabolism/microbiology ; Liver Cirrhosis/metabolism/microbiology ; Metagenome/*genetics ; Metagenomics/*methods ; Models, Theoretical ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Evaluating the relationship between the human gut microbiome and disease requires computing reliable statistical associations. Here, using millions of different association modeling strategies, we evaluated the consistency-or robustness-of microbiome-based disease indicators for 6 prevalent and well-studied phenotypes (across 15 public cohorts and 2,343 individuals). We were able to discriminate between analytically robust versus nonrobust results. In many cases, different models yielded contradictory associations for the same taxon-disease pairing, some showing positive correlations and others negative. When querying a subset of 581 microbe-disease associations that have been previously reported in the literature, 1 out of 3 taxa demonstrated substantial inconsistency in association sign. Notably, >90% of published findings for type 1 diabetes (T1D) and type 2 diabetes (T2D) were particularly nonrobust in this regard. We additionally quantified how potential confounders-sequencing depth, glucose levels, cholesterol, and body mass index, for example-influenced associations, analyzing how these variables affect the ostensible correlation between Faecalibacterium prausnitzii abundance and a healthy gut. Overall, we propose our approach as a method to maximize confidence when prioritizing findings that emerge from microbiome association studies.}, } @article {pmid35234986, year = {2022}, author = {Kachroo, N and Monga, M and Miller, AW}, title = {Comparative functional analysis of the urinary tract microbiome for individuals with or without calcium oxalate calculi.}, journal = {Urolithiasis}, volume = {50}, number = {3}, pages = {303-317}, pmid = {35234986}, issn = {2194-7236}, support = {R01 DK121689/DK/NIDDK NIH HHS/United States ; 1R01DK121689-01A1/DK/NIDDK NIH HHS/United States ; }, mesh = {Calcium/urine ; Calcium Oxalate/metabolism ; Female ; Humans ; *Kidney Calculi ; Male ; *Microbiota ; *Urinary Calculi/urine ; *Urinary Tract/chemistry/metabolism ; *Urolithiasis/urine ; }, abstract = {Individuals with urinary stone disease (USD) exhibit dysbiosis in the urinary tract and the loss of Lactobacillus that promote urinary tract health. However, the microbial metabolic functions that differentiate individuals with USD from healthy individuals are unknown. The objective of the current study was to determine the microbial functions across prokaryotic, viral, fungal, and protozoan domains that are associated with calcium oxalate (CaOx) stone formers through comparative shotgun metagenomics of midstream, voided urine samples for a small number of patients (n = 5 CaOx stone formers, n = 5 healthy controls). Results revealed that CaOx stone formers had reduced levels of genes associated with oxalate metabolism, as well as transmembrane transport, proteolysis, and oxidation-reduction processes. From 17 draft genomes extracted from the data and > 42,000 full length reference genomes, genes enriched in the Control group mapped overwhelming to Lactobacillus crispatus and those associated with CaOx mapped to Pseudomonas aeruginosa and Burkholderia sp. The microbial functions that differentiated the clinical cohorts are associated with known mechanisms of stone formation. While the prokaryotes most differentiated the CaOx and Control groups, a diverse, trans-domain microbiome was apparent. While our sample numbers were small, results corroborate previous studies and suggest specific microbial metabolic pathways in the urinary tract that modulate stone formation. Future studies that target these metabolic pathways as well as the influence of viruses, fungi, and protozoa on urinary tract physiology is warranted.}, } @article {pmid35234490, year = {2022}, author = {Tourlousse, DM and Narita, K and Miura, T and Ohashi, A and Matsuda, M and Ohyama, Y and Shimamura, M and Furukawa, M and Kasahara, K and Kameyama, K and Saito, S and Goto, M and Shimizu, R and Mishima, R and Nakayama, J and Hosomi, K and Kunisawa, J and Terauchi, J and Sekiguchi, Y and Kawasaki, H}, title = {Characterization and Demonstration of Mock Communities as Control Reagents for Accurate Human Microbiome Community Measurements.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0191521}, pmid = {35234490}, issn = {2165-0497}, mesh = {DNA ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Indicators and Reagents ; Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; }, abstract = {Standardization and quality assurance of microbiome community analysis by high-throughput DNA sequencing require widely accessible and well-characterized reference materials. Here, we report on newly developed DNA and whole-cell mock communities to serve as control reagents for human gut microbiota measurements by shotgun metagenomics and 16S rRNA gene amplicon sequencing. The mock communities were formulated as near-even blends of up to 20 bacterial species prevalent in the human gut, span a wide range of genomic guanine-cytosine (GC) contents, and include multiple strains with Gram-positive type cell walls. Through a collaborative study, we carefully characterized the mock communities by shotgun metagenomics, using previously developed standardized protocols for DNA extraction and sequencing library construction. Further, we validated fitness of the mock communities for revealing technically meaningful differences among protocols for DNA extraction and metagenome/16S rRNA gene amplicon library construction. Finally, we used the mock communities to reveal varying performance of metagenome-based taxonomic profilers and the impact of trimming and filtering of sequencing reads on observed species profiles. The latter showed that aggressive preprocessing of reads may result in substantial GC-dependent bias and should thus be carefully evaluated to minimize unintended effects on species abundances. Taken together, the mock communities are expected to support a myriad of applications that rely on well-characterized control reagents, ranging from evaluation and optimization of methods to assessment of reproducibility in interlaboratory studies and routine quality control. IMPORTANCE Application of high-throughput DNA sequencing has greatly accelerated human microbiome research and its translation into new therapeutic and diagnostic capabilities. Microbiome community analyses results can, however, vary considerably across studies or laboratories, and establishment of measurement standards to improve accuracy and reproducibility has become a priority. The here-developed mock communities, which are available from the NITE Biological Resource Center (NBRC) at the National Institute of Technology and Evaluation (NITE, Japan), provide well-characterized control reagents that allow users to judge the accuracy of their measurement results. Widespread and consistent adoption of the mock communities will improve reproducibility and comparability of microbiome community analyses, thereby supporting and accelerating human microbiome research and development.}, } @article {pmid35232471, year = {2022}, author = {France, MT and Fu, L and Rutt, L and Yang, H and Humphrys, MS and Narina, S and Gajer, PM and Ma, B and Forney, LJ and Ravel, J}, title = {Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {66}, pmid = {35232471}, issn = {1474-760X}, support = {UH2 AI083264/AI/NIAID NIH HHS/United States ; R01 NR015495/NR/NINR NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Female ; Humans ; Lactobacillus/genetics ; *Microbiota/genetics ; Mucins ; RNA, Ribosomal, 16S/genetics ; *Vagina/microbiology ; }, abstract = {BACKGROUND: Vaginal bacterial communities dominated by Lactobacillus species are associated with a reduced risk of various adverse health outcomes. However, somewhat unexpectedly, many healthy women have microbiota that are not dominated by lactobacilli. To determine the factors that drive vaginal community composition we characterized the genetic composition and transcriptional activities of vaginal microbiota in healthy women.

RESULTS: We demonstrate that the abundance of a species is not always indicative of its transcriptional activity and that impending changes in community composition can be predicted from metatranscriptomic data. Functional comparisons highlight differences in the metabolic activities of these communities, notably in their degradation of host produced mucin but not glycogen. Degradation of mucin by communities not dominated by Lactobacillus may play a role in their association with adverse health outcomes. Finally, we show that the transcriptional activities of L. crispatus, L. iners, and Gardnerella vaginalis vary with the taxonomic composition of the communities in which they reside. Notably, L. iners and G. vaginalis both demonstrate lower expression of their cholesterol-dependent cytolysins when co-resident with Lactobacillus spp. and higher expression when co-resident with other facultative and obligate anaerobes. The pathogenic potential of these species may depend on the communities in which they reside and thus could be modulated by interventional strategies.

CONCLUSIONS: Our results provide insight to the functional ecology of the vaginal microbiota, demonstrate the diagnostic potential of metatranscriptomic data, and reveal strategies for the management of these ecosystems.}, } @article {pmid35230155, year = {2022}, author = {Yang, J and Tong, C and Xiao, D and Xie, L and Zhao, R and Huo, Z and Tang, Z and Hao, J and Zeng, Z and Xiong, W}, title = {Metagenomic Insights into Chicken Gut Antibiotic Resistomes and Microbiomes.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0190721}, pmid = {35230155}, issn = {2165-0497}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Chickens ; Genes, Bacterial ; Lactobacillus ; Metagenome ; Metagenomics/methods ; *Microbiota ; }, abstract = {The chicken gut microbiota, as a reservoir of antibiotic resistance genes (ARGs), poses a high risk to humans and animals worldwide. Yet a comprehensive exploration of the chicken gut antibiotic resistomes remains incomplete. In this study, we established the largest chicken gut resistance gene catalogue to date through metagenomic analysis of 629 chicken gut samples. We found significantly higher abundance of ARGs in the Chinese chicken gut than that in the Europe. tetX, mcr, and blaNDM, the genes resistant to antibiotics of last resort for human and animal health, were detected in the Chinese chicken gut. The abundance of ARGs was linearly correlated with that of mobile genetic elements (MGEs). The host-tracking analysis identified Escherichia, Enterococcus, Staphylococcus, Klebsiella, and Lactobacillus as the major ARG hosts. Especially, Lactobacillus, an intestinal probiotic, carried multiple drug resistance genes, and was proportional to ISLhe63, highlighting its potential risk in agricultural production processes. We first established a reference gene catalogue of chicken gut antibiotic resistomes. Our study helps to improve the knowledge and understanding of chicken antibiotic resistomes for knowledge-based sustainable chicken meat production. IMPORTANCE The prevalence of antibiotic resistance genes in the chicken gut environment poses a serious threat to human health; however, we lack a comprehensive exploration of antibiotic resistomes and microbiomes in the chicken gut environment. The results of this study demonstrate the diversity and abundance of antibiotic resistance genes and flora in the chicken gut environment and identify a variety of potential hosts carrying antibiotic resistance genes. Further analysis showed that mobile genetic elements were linearly correlated with antibiotic resistance genes abundance, implying that we should pay attention to the role played by mobile genetic elements in antibiotic resistance genes transmission. We established a reference genome of gut antibiotic resistance genes in chickens, which will help to rationalize the use of drugs in poultry farming.}, } @article {pmid35229726, year = {2022}, author = {Underhill, DM and Braun, J}, title = {Fungal microbiome in inflammatory bowel disease: a critical assessment.}, journal = {The Journal of clinical investigation}, volume = {132}, number = {5}, pages = {}, pmid = {35229726}, issn = {1558-8238}, mesh = {Animals ; Bacteria ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/genetics/microbiology ; Metagenomics ; Mice ; *Microbiota ; *Mycobiome/genetics ; }, abstract = {The gut microbiome is at the center of inflammatory bowel disease (IBD) pathogenesis and disease activity. While this has mainly been studied in the context of the bacterial microbiome, recent advances have provided tools for the study of host genetics and metagenomics of host-fungal interaction. Through these tools, strong evidence has emerged linking certain fungal taxa, such as Candida and Malassezia, with cellular and molecular pathways of IBD disease biology. Mouse models and human fecal microbial transplant also suggest that some disease-participatory bacteria and fungi may act not via the host directly, but via their fungal-bacterial ecologic interactions. We hope that these insights, and the study design and multi-omics strategies used to develop them, will facilitate the inclusion of the fungal community in basic and translational IBD research.}, } @article {pmid35229650, year = {2022}, author = {Pinto, M and Zhao, Z and Klun, K and Libowitzky, E and Herndl, GJ}, title = {Microbial Consortiums of Putative Degraders of Low-Density Polyethylene-Associated Compounds in the Ocean.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0141521}, pmid = {35229650}, issn = {2379-5077}, support = {P 28781/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Polyethylene/chemistry ; *Microbial Consortia ; Bacteria ; Plastics/metabolism ; Oceans and Seas ; }, abstract = {Polyethylene (PE) is one of the most abundant plastics in the ocean. The development of a biofilm on PE in the ocean has been reported, yet whether some of the biofilm-forming organisms can biodegrade this plastic in the environment remains unknown. Via metagenomics analysis, we taxonomically and functionally analyzed three biofilm communities using low-density polyethylene (LDPE) as their sole carbon source for 2 years. Several of the taxa that increased in relative abundance over time were closely related to known degraders of alkane and other hydrocarbons. Alkane degradation has been proposed to be involved in PE degradation, and most of the organisms increasing in relative abundance over time harbored genes encoding proteins essential in alkane degradation, such as the genes alkB and CYP153, encoding an alkane monooxygenase and a cytochrome P450 alkane hydroxylase, respectively. Weight loss of PE sheets when incubated with these communities and chemical and electron microscopic analyses provided evidence for alteration of the PE surface over time. Taken together, these results provide evidence for the utilization of LDPE-associated compounds by the prokaryotic communities. This report identifies a group of genes potentially involved in the degradation of the LDPE polymeric structure and/or associated plastic additives in the ocean and describes a phylogenetically diverse community of plastic biofilm-dwelling microbes with the potential for utilizing LDPE-associated compounds as carbon and energy source. IMPORTANCE Low-density polyethylene (LDPE) is one of the most used plastics worldwide, and a large portion of it ends up in the ocean. Very little is known about its fate in the ocean and whether it can be biodegraded by microorganisms. By combining 2-year incubations with metagenomics, respiration measurements, and LDPE surface analysis, we identified bacteria and associated genes and metabolic pathways potentially involved in LDPE biodegradation. After 2 years of incubation, two of the microbial communities exhibited very similar taxonomic compositions mediating changes to the LDPE pieces they were incubated with. We provide evidence that there are plastic-biofilm dwelling bacteria in the ocean that might have the potential to degrade LDPE-associated compounds and that alkane degradation pathways might be involved.}, } @article {pmid35229641, year = {2022}, author = {Lv, Y and Yang, S and Xiao, X and Zhang, Y}, title = {Stimulated Organic Carbon Cycling and Microbial Community Shift Driven by a Simulated Cold-Seep Eruption.}, journal = {mBio}, volume = {13}, number = {2}, pages = {e0008722}, pmid = {35229641}, issn = {2150-7511}, support = {2016YFC0300709//National Key R&D Program of China/ ; 41776173//NNSF of China/ ; 41921006//NNSF of China/ ; 42122043//NNSF of China/ ; 41476123//NNSF of China/ ; }, mesh = {Carbon Cycle ; Metagenomics ; Methane ; *Methylococcaceae ; *Microbiota ; }, abstract = {Cold seeps are a major methane source in marine systems, and microbe-mediated anaerobic oxidation of methane (AOM) serves as an effective barrier for preventing methane emissions from sediment to water. However, how the periodic eruption of cold seeps drives the microbial community shift and further affects carbon cycling has been largely neglected, mainly due to the technical challenge of analyzing the in situ communities undergoing such geological events. Using a continuously running high-pressure bioreactor to simulate these events, we found that under the condition of simulated eruptions, the abundance of AOM-related species decreased, and some methane was oxidized to methyl compounds to feed heterotrophs. The methanogenic archaeon Methanolobus replaced ANME-2a as the dominant archaeal group; moreover, the levels of methylotrophic bacteria, such as Pseudomonas, Halomonas, and Methylobacter, quickly increased, while those of sulfate-reducing bacteria decreased. According to the genomic analysis, Methylobacter played an important role in incomplete methane oxidation during eruptions; this process was catalyzed by the genes pmoABC under anaerobic conditions when the methane pressure was high, possibly generating organic carbon. Additionally, the findings showed that methyl compounds can also be released to the environment during methanogenesis and AOM under eruption conditions when the methane pressure is high. IMPORTANCE In the ocean, almost all of the emission and consumption of deeply buried methane occurs in cold seeps; therefore, understanding the methane cycling in cold seeps is crucial to estimating the oceanic methane budget. Cold-seep eruptions often lead to the dramatic destruction of microbial ecosystems that drive methane cycling. Because of technical challenges, the direct monitoring of these communities as well as the activity shifts during eruptions has never been achieved. In this study, we took an alternative approach by simulating cold-seep eruptions and using genome-resolved metagenomics to interpret the dynamic changes in the microbial community. The results show that the periodical cold-seep eruptions intensify organic carbon cycling, undermine the direct oxidation of methane to carbon dioxide, and drive microbial community shifts. These results further suggest that a more sophisticated calculation of the methane budget in cold seeps that considers their eruption status is needed.}, } @article {pmid35229389, year = {2022}, author = {Coatsworth, H and Bozic, J and Carrillo, J and Buckner, EA and Rivers, AR and Dinglasan, RR and Mathias, DK}, title = {Intrinsic variation in the vertically transmitted core virome of the mosquito Aedes aegypti.}, journal = {Molecular ecology}, volume = {31}, number = {9}, pages = {2545-2561}, doi = {10.1111/mec.16412}, pmid = {35229389}, issn = {1365-294X}, support = {U01 CK000510/CK/NCEZID CDC HHS/United States ; U01CK000510/CC/CDC HHS/United States ; }, mesh = {*Aedes/genetics ; Animals ; *Insect Viruses/genetics ; Mosquito Vectors/genetics ; Phylogeny ; *RNA Viruses ; Virome/genetics ; *Viruses ; }, abstract = {Virome studies among metazoans have revealed the ubiquity of RNA viruses in animals, contributing to a fundamental rethinking of the relationships between organisms and their microbiota. Mosquito viromes, often scrutinized due to their public health relevance, may also provide insight into broadly applicable concepts, such as a "core virome," a set of viruses consistently associated with a host species or population that may fundamentally impact its basic biology. A subset of mosquito-associated viruses (MAVs) could comprise such a core, and MAVs can be categorized as (i) arboviruses, which alternate between mosquito and vertebrate hosts, (ii) insect-specific viruses, which cannot replicate in vertebrate cells, and (iii) viruses with unknown specificity. MAVs have been widely characterized in the disease vector Aedes aegypti, and the occurrence of a core virome in this species has been proposed but remains unclear. Using a wild population previously surveyed for MAVs and a common laboratory strain, we investigated viromes in reproductive tissue via metagenomic RNA sequencing. Virome composition varied across samples, but four groups comprised >97% of virus sequences: a novel partiti-like virus (Partitiviridae), a toti-like virus (Totiviridae), unclassified Riboviria, and four orthomyxo-like viruses (Orthormyxoviridae). Whole or partial genomes for the partiti-like virus, toti-like virus, and one orthomyxo-like virus were assembled and analysed phylogenetically. Multigenerational maintenance of these MAVs was confirmed by RT-PCR, indicating vertical transmission as a mechanism for persistence. This study provides fundamental information regarding MAV ecology and variability in A. aegypti and the potential for vertically maintained core viromes at the population level.}, } @article {pmid35228751, year = {2022}, author = {Lee, KA and Thomas, AM and Bolte, LA and Björk, JR and de Ruijter, LK and Armanini, F and Asnicar, F and Blanco-Miguez, A and Board, R and Calbet-Llopart, N and Derosa, L and Dhomen, N and Brooks, K and Harland, M and Harries, M and Leeming, ER and Lorigan, P and Manghi, P and Marais, R and Newton-Bishop, J and Nezi, L and Pinto, F and Potrony, M and Puig, S and Serra-Bellver, P and Shaw, HM and Tamburini, S and Valpione, S and Vijay, A and Waldron, L and Zitvogel, L and Zolfo, M and de Vries, EGE and Nathan, P and Fehrmann, RSN and Bataille, V and Hospers, GAP and Spector, TD and Weersma, RK and Segata, N}, title = {Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma.}, journal = {Nature medicine}, volume = {28}, number = {3}, pages = {535-544}, pmid = {35228751}, issn = {1546-170X}, support = {10589/CRUK_/Cancer Research UK/United Kingdom ; 11963/CRUK_/Cancer Research UK/United Kingdom ; A22902/CRUK_/Cancer Research UK/United Kingdom ; A27412/CRUK_/Cancer Research UK/United Kingdom ; 19167/CRUK_/Cancer Research UK/United Kingdom ; MR/M019012/1/MRC_/Medical Research Council/United Kingdom ; R01 CA230551/CA/NCI NIH HHS/United States ; 100282/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; U01 CA230551/CA/NCI NIH HHS/United States ; 22902/CRUK_/Cancer Research UK/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Immune Checkpoint Inhibitors/therapeutic use ; *Melanoma/drug therapy/genetics ; Reproducibility of Results ; *Skin Neoplasms/drug therapy/genetics ; }, abstract = {The composition of the gut microbiome has been associated with clinical responses to immune checkpoint inhibitor (ICI) treatment, but there is limited consensus on the specific microbiome characteristics linked to the clinical benefits of ICIs. We performed shotgun metagenomic sequencing of stool samples collected before ICI initiation from five observational cohorts recruiting ICI-naive patients with advanced cutaneous melanoma (n = 165). Integrating the dataset with 147 metagenomic samples from previously published studies, we found that the gut microbiome has a relevant, but cohort-dependent, association with the response to ICIs. A machine learning analysis confirmed the link between the microbiome and overall response rates (ORRs) and progression-free survival (PFS) with ICIs but also revealed limited reproducibility of microbiome-based signatures across cohorts. Accordingly, a panel of species, including Bifidobacterium pseudocatenulatum, Roseburia spp. and Akkermansia muciniphila, associated with responders was identified, but no single species could be regarded as a fully consistent biomarker across studies. Overall, the role of the human gut microbiome in ICI response appears more complex than previously thought, extending beyond differing microbial species simply present or absent in responders and nonresponders. Future studies should adopt larger sample sizes and take into account the complex interplay of clinical factors with the gut microbiome over the treatment course.}, } @article {pmid35227842, year = {2022}, author = {Du, C and Yang, F and Li, X and Liao, H and Li, Z and Gao, J and Zhang, L}, title = {Metagenomic analysis of microbial community structure and distribution of resistance genes in Daihai Lake, China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {302}, number = {}, pages = {119065}, doi = {10.1016/j.envpol.2022.119065}, pmid = {35227842}, issn = {1873-6424}, mesh = {Animals ; Anti-Bacterial Agents ; China ; Genes, Bacterial ; *Lakes/microbiology ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {The emergence of resistance genes is a global phenomenon that poses a significant threat to both animals and humans. Lakes are important reservoirs of genes that confer resistant to antibiotics and metals. In this study, we investigated the distribution and diversity of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in the sediment of Daihai Lake using high-throughput sequencing and metagenomic analysis. The results indicated that all sampling sites had similar bacterial community structures, with Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes being the most abundant. A total of 16 ARG types containing 111 ARG subtypes were deposited in the sediment. Among the resistance genes to bacitracin, multidrug, macrolide-lincosamide-streptogramin (MLS), tetracycline, beta-lactam, and sulfonamide were the dominant ARG types, accounting for 89.9-94.3% of the total ARGs. Additionally, 15 MRG types consisting of 146 MRG subtypes were identified. In all samples, MRGs of the same type presented resistance to Pb, Ni, Hg, W, Zn, Ag, Cr, Fe, As, Cu, and multimetals. Overall, the distribution and diversity of antibiotic and metal resistance genes showed no significant differences in the samples. Plasmids (91.03-91.82%) were the most dominant mobile genetic elements in the sediments of Daihai Lake. Network analysis indicated that the target ARGs and MRGs were significantly positively correlated with the microorganisms. Potential hosts for various ARGs and MRGs include Proteobacteria, Euryarchaeota, Actinobacteria, Chloroflexi, and Bacteroidetes.}, } @article {pmid35227465, year = {2022}, author = {Chen, K and Wei, X and Kortesniemi, M and Pariyani, R and Zhang, Y and Yang, B}, title = {Effects of acylated and nonacylated anthocyanins extracts on gut metabolites and microbiota in diabetic Zucker rats: A metabolomic and metagenomic study.}, journal = {Food research international (Ottawa, Ont.)}, volume = {153}, number = {}, pages = {110978}, doi = {10.1016/j.foodres.2022.110978}, pmid = {35227465}, issn = {1873-7145}, mesh = {Animals ; Anthocyanins/analysis ; *Diabetes Mellitus, Experimental ; *Gastrointestinal Microbiome ; Metabolomics ; Plant Extracts/chemistry ; Rats ; Rats, Zucker ; }, abstract = {Anthocyanins have been shown to have prebiotic properties. This study investigated the impact of nonacylated anthocyanins and acylated anthocyanins on fecal and cecal metabolites and colonic gut microbiota in diabetic state using [1]H nuclear magnetic resonance (NMR) metabolomics and metagenomic sequencing. Zucker diabetic fatty rats fed with high-fat diet were gavaged with nonacylated anthocyanins extracted from bilberries (NAAB) or acylated anthocyanins extracted from purple potatoes (AAPP) at daily doses of 25 and 50 mg/kg body weight for 8 weeks. Lean Zucker rats fed with normal diet (ND) and high-fat diet (Con) were used as healthy controls groups. Binned NMR spectra and sequenced gene abundance were used for data analysis. Dysbiosis of colonic microbiota and gut metabolites in the diabetic rats were observed compared to the lean Zucker rats. Both anthocyanin extracts increased cecal sugar levels and the abundance of Peptostreptococcaceae sp. and decreased the abundance of Parabacteroides spp. in colon. In addition to the increased fecal short-chain fatty acids, AAPP decreased colonic Ruminococcus torques and Lachnospiraceae bacterium 4_1_37FAA abundances and increased oxidative phosphorylation. The anthocyanin extracts modulated the gut metabolism and microbiota in diabetes, with AAPP showing more regulatory and beneficial effects on diabetes.}, } @article {pmid35227283, year = {2022}, author = {Du, Y and Sun, F}, title = {HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {63}, pmid = {35227283}, issn = {1474-760X}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; R01 GM131407/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Cluster Analysis ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Recovering high-quality metagenome-assembled genomes (MAGs) from complex microbial ecosystems remains challenging. Recently, high-throughput chromosome conformation capture (Hi-C) has been applied to simultaneously study multiple genomes in natural microbial communities. We develop HiCBin, a novel open-source pipeline, to resolve high-quality MAGs utilizing Hi-C contact maps. HiCBin employs the HiCzin normalization method and the Leiden clustering algorithm and includes the spurious contact detection into binning pipelines for the first time. HiCBin is validated on one synthetic and two real metagenomic samples and is shown to outperform the existing Hi-C-based binning methods. HiCBin is available at https://github.com/dyxstat/HiCBin .}, } @article {pmid35223729, year = {2022}, author = {Kettenburg, G and Kistler, A and Ranaivoson, HC and Ahyong, V and Andrianiaina, A and Andry, S and DeRisi, JL and Gentles, A and Raharinosy, V and Randriambolamanantsoa, TH and Ravelomanantsoa, NAF and Tato, CM and Dussart, P and Heraud, JM and Brook, CE}, title = {Full Genome Nobecovirus Sequences From Malagasy Fruit Bats Define a Unique Evolutionary History for This Coronavirus Clade.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {786060}, pmid = {35223729}, issn = {2296-2565}, support = {DP2 AI171120/AI/NIAID NIH HHS/United States ; R01 AI129822/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *COVID-19 ; *Chiroptera ; Humans ; Phylogeny ; *Severe acute respiratory syndrome-related coronavirus ; SARS-CoV-2 ; }, abstract = {Bats are natural reservoirs for both Alpha- and Betacoronaviruses and the hypothesized original hosts of five of seven known zoonotic coronaviruses. To date, the vast majority of bat coronavirus research has been concentrated in Asia, though coronaviruses are globally distributed; indeed, SARS-CoV and SARS-CoV-2-related Betacoronaviruses in the subgenus Sarbecovirus have been identified circulating in Rhinolophid bats in both Africa and Europe, despite the relative dearth of surveillance in these regions. As part of a long-term study examining the dynamics of potentially zoonotic viruses in three species of endemic Madagascar fruit bat (Pteropus rufus, Eidolon dupreanum, Rousettus madagascariensis), we carried out metagenomic Next Generation Sequencing (mNGS) on urine, throat, and fecal samples obtained from wild-caught individuals. We report detection of RNA derived from Betacoronavirus subgenus Nobecovirus in fecal samples from all three species and describe full genome sequences of novel Nobecoviruses in P. rufus and R. madagascariensis. Phylogenetic analysis indicates the existence of five distinct Nobecovirus clades, one of which is defined by the highly divergent ancestral sequence reported here from P. rufus bats. Madagascar Nobecoviruses derived from P. rufus and R. madagascariensis demonstrate, respectively, Asian and African phylogeographic origins, mirroring those of their fruit bat hosts. Bootscan recombination analysis indicates significant selection has taken place in the spike, nucleocapsid, and NS7 accessory protein regions of the genome for viruses derived from both bat hosts. Madagascar offers a unique phylogeographic nexus of bats and viruses with both Asian and African phylogeographic origins, providing opportunities for unprecedented mixing of viral groups and, potentially, recombination. As fruit bats are handled and consumed widely across Madagascar for subsistence, understanding the landscape of potentially zoonotic coronavirus circulation is essential for mitigation of future zoonotic threats.}, } @article {pmid35223559, year = {2022}, author = {Feng, G and Zhang, J and Zhang, Y and Li, C and Zhang, D and Li, Y and Zhou, H and Li, N and Xiao, P}, title = {Metagenomic Analysis of Togaviridae in Mosquito Viromes Isolated From Yunnan Province in China Reveals Genes from Chikungunya and Ross River Viruses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {849662}, pmid = {35223559}, issn = {2235-2988}, mesh = {Animals ; *Chikungunya Fever ; China ; *Culicidae ; Horses ; Humans ; Phylogeny ; Ross River virus/genetics ; Togaviridae ; Virome ; *Viruses/genetics ; }, abstract = {We collected 5,500 mosquitoes belonging to six species in three locations in China. Their viromes were tested using metagenomic sequencing and bioinformatic analysis. The affluent viral sequences that were detected and annotated belong to 22 viral taxonomic families. Then, PCR was performed to confirm the results, followed by phylogenetic analysis. Herein, part of mosquito virome was identified, including chikungunya virus (CHIKV), Getah virus (GETV), and Ross river virus (RRV). After metagenomic analysis, seven CHIKV sequences were verified by PCR amplification, among which CHIKV-China/YN2018-1 had the highest homology with the CHIKV isolated in Senegal, 1983, with a nucleotide (nt) identity of at least 81%, belonging to genotype West Africa viral genes. Five GETV sequences were identified, which had a high homology with the GETV sequences isolated from Equus caballus in Japan, 1978, with a (nt) identity of at least 97%. The newly isolated virus CHIKV-China/YN2018-1 became more infectious after passage of the BHK-21 cell line to the Vero cell line. The newly identified RRV gene had the highest homology with the 2006 RRV isolate from Australia, with a (nt) identity of at least 94%. In addition, numerous known and unknown viruses have also been detected in mosquitoes from Yunnan province, China, and propagation tests will be carried out.}, } @article {pmid35222325, year = {2022}, author = {Ataeian, M and Liu, Y and Kouris, A and Hawley, AK and Strous, M}, title = {Ecological Interactions of Cyanobacteria and Heterotrophs Enhances the Robustness of Cyanobacterial Consortium for Carbon Sequestration.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {780346}, pmid = {35222325}, issn = {1664-302X}, abstract = {Lack of robustness is a major barrier to foster a sustainable cyanobacterial biotechnology. Use of cyanobacterial consortium increases biodiversity, which provides functional redundancy and prevents invading species from disrupting the production ecosystem. Here we characterized a cyanobacterial consortium enriched from microbial mats of alkaline soda lakes in BC, Canada, at high pH and alkalinity. This consortium has been grown in open laboratory culture for 4 years without crashes. Using shotgun metagenomic sequencing, 29 heterotrophic metagenome-assembled-genomes (MAGs) were retrieved and were assigned to Bacteroidota, Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobiota, Patescibacteria, Planctomycetota, and Archaea. In combination with metaproteomics, the overall stability of the consortium was determined under different cultivation conditions. Genome information from each heterotrophic population was investigated for six ecological niches created by cyanobacterial metabolism and one niche for phototrophy. Genome-resolved metaproteomics with stable isotope probing using [13]C-bicarbonate (protein/SIP) showed tight coupling of carbon transfer from cyanobacteria to the heterotrophic populations, specially Wenzhouxiangella. The community structure was compared to a previously described consortium of a closely related cyanobacteria, which indicated that the results may be generalized. Productivity losses associated with heterotrophic metabolism were relatively small compared to other losses during photosynthesis.}, } @article {pmid35221319, year = {2022}, author = {Moreno-Sanz, B and Montes, MT and Manzano, S and Espinosa-Martos, I and Cárdenas, N and Esteban, S and Cruz, M and Jiménez, E and de Pipaón, MS}, title = {Randomized, Double-Blind, Placebo-Controlled Study to Assess the Effect of Two Probiotics on the Preterms' Gut Microbiota.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {74}, number = {6}, pages = {e153-e159}, doi = {10.1097/MPG.0000000000003427}, pmid = {35221319}, issn = {1536-4801}, mesh = {Bifidobacterium ; Double-Blind Method ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Lactobacillus ; *Probiotics/therapeutic use ; }, abstract = {OBJECTIVE: To evaluate the effect of a new probiotic strain combination, Ligilactobacillus salivarius subsp infantis PS11603 and Bifidobacterium longum PS10402, on gut bacterial colonization of preterm infants.

METHODS: A randomized, double-blind, placebo-controlled study was conducted in preterm infants from 28 weeks + 0days to 30 weeks + 6days of gestation. Thirty preterm infants were randomly selected after birth to receive either probiotics or placebo. Stool samples were collected before product intake and then sequentially during the first weeks of their admission. Classical microbiological, metagenomics and multiplex immunological analyses were performed to assess the bacterial and immune profile of the samples.

RESULTS: Twenty-seven infants completed the study (14 vs 13, probiotic and placebo groups). A higher number of participants were colonized by Lactobacilli in the probiotic group than in the placebo group (93% vs 46%; P  = 0.013). Similar results were obtained when analysing bifidobacterial colonization (100% vs 69%; P  = 0.041). Earlier colonization was observed in the probiotics group versus the placebo group, specifically 5 weeks for Lactobacillus and 1 week for Bifidobacterium. Although no effect was observed in the faecal immunological profile, a decreasing trend could be observed in Th17 response during the first week of probiotic treatment. None of the adverse events (AEs) registered were related to product intake.

CONCLUSION: Probiotic supplementation with L salivarius PS11603 and B longum subsp. infantis PS10402 enhanced an earlier colonization of Lactobacillus and Bifidobacterium in preterm infants' guts in 5 and 1 week, respectively. A higher number of infants were colonized by Lactobacilli with the probiotics' intake at the end of the study.}, } @article {pmid35219318, year = {2022}, author = {Gholizadeh, S and Mohammadi, SA and Salekdeh, GH}, title = {Changes in root microbiome during wheat evolution.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {64}, pmid = {35219318}, issn = {1471-2180}, mesh = {*Aegilops/genetics ; Genome, Plant ; Humans ; *Microbiota/genetics ; Phylogeny ; Plant Breeding ; RNA, Ribosomal, 16S/genetics ; Triticum/microbiology ; }, abstract = {BACKGROUND: Although coevolutionary signatures of host-microbe interactions are considered to engineer the healthy microbiome of humans, little is known about the changes in root-microbiome during plant evolution. To understand how the composition of the wheat and its ancestral species microbiome have changed over the evolutionary processes, we performed a 16S rRNA metagenomic analysis on rhizobacterial communities associated with a phylogenetic framework of four Triticum species T. urartu, T. turgidum, T. durum, and T. aestivum along with their ancestral species Aegilops speltoides, and Ae. tauschii during vegetative and reproductive stages.

RESULTS: In this study, we illustrated that the genome contents of wild species Aegilops speltoides and Ae. tauschii can be significant factors determining the composition of root-associated bacterial communities in domesticated bread wheat. Although it was found that domestication and modern breeding practices might have had a significant impact on microbiome-plant interactions especially at the reproductive stage, we observed an extensive and selective control by wheat genotypes on associated rhizobacterial communities at the same time. Our data also showed a strong genotypic variation within species of T. aestivum and Ae. tauschii, suggesting potential breeding targets for plants surveyed.

CONCLUSIONS: This study performed with different genotypes of Triticum and Aegilops species is the first study showing that the genome contents of Ae. speltoides and Ae. tauschii along with domestication-related changes can be significant factors determining the composition of root-associated bacterial communities in bread wheat. It is also indirect evidence that shows a very extensive range of host traits and genes are probably involved in host-microbe interactions. Therefore, understanding the wheat root-associated microbiome needs to take into consideration of its polygenetic mosaic nature.}, } @article {pmid35218819, year = {2022}, author = {Zhou, S and Wang, J and Chen, L and Wang, J and Zhao, F}, title = {Microbial community structure and functional genes drive soil priming effect following afforestation.}, journal = {The Science of the total environment}, volume = {825}, number = {}, pages = {153925}, doi = {10.1016/j.scitotenv.2022.153925}, pmid = {35218819}, issn = {1879-1026}, mesh = {Bacteria ; Carbon/analysis ; China ; *Microbiota ; Nitrogen/analysis ; *Robinia/microbiology ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Afforestation substantially modifies native soil organic carbon (SOC) decomposition via plant carbon inputs (the priming effect), and in turn, triggers vital biogeochemical processes that influence the regulation of soil carbon dynamics. Soil microbes are crucial in regulating the direction and magnitude of the priming effect. In the present study, we performed metagenomic sequencing and [13]C-glucose labeling analyses of microbial communities and priming effects across a Robinia pseudoacacia afforestation chronosequence (14-, 20-, 30-, and 45-year-old stands) in the Loess Plateau in China, with adjacent farmland being selected as a control. Our results revealed that the cumulative priming effect across five sites along the afforestation chronosequence initially increased and approached a peak value in the 20-year-old stand, after which it declined. The priming effect was predominantly driven by the microbial community structure (i.e., the fungal-to-bacterial ratios and relative abundances of Proteobacteria and Actinobacteria), and stable C decomposition genes and C-degrading enzymes. Specifically, among the key functional genes correlated with priming effect, which were identified in orders Rhizobiales and Pseudonocardiales, considerably promoted SOC priming. Overall, our findings indicate that afforestation alters soil microbial community structure and function, particularly with respect to enhancing stable soil C decomposition genes, which may promote SOC priming. The findings of the present study could enhance our understanding of fresh C input-induced changes associated with C mineralization in the context of the revegetation of ecologically fragile areas.}, } @article {pmid35216552, year = {2022}, author = {Mekadim, C and Skalnikova, HK and Cizkova, J and Cizkova, V and Palanova, A and Horak, V and Mrazek, J}, title = {Dysbiosis of skin microbiome and gut microbiome in melanoma progression.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {63}, pmid = {35216552}, issn = {1471-2180}, mesh = {Animals ; Bacteria/genetics ; Dysbiosis/microbiology ; Feces/microbiology ; Fusobacterium ; *Gastrointestinal Microbiome/genetics ; *Melanoma ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Swine ; Tumor Microenvironment ; }, abstract = {BACKGROUND: The microbiome alterations are associated with cancer growth and may influence the immune system and response to therapy. Particularly, the gut microbiome has been recently shown to modulate response to melanoma immunotherapy. However, the role of the skin microbiome has not been well explored in the skin tumour microenvironment and the link between the gut microbiome and skin microbiome has not been investigated in melanoma progression. Therefore, the aim of the present study was to examine associations between dysbiosis in the skin and gut microbiome and the melanoma growth using MeLiM porcine model of melanoma progression and spontaneous regression.

RESULTS: Parallel analysis of cutaneous microbiota and faecal microbiota of the same individuals was performed in 8 to 12 weeks old MeLiM piglets. The bacterial composition of samples was analysed by high throughput sequencing of the V4-V5 region of the 16S rRNA gene. A significant difference in microbiome diversity and richness between melanoma tissue and healthy skin and between the faecal microbiome of MeLiM piglets and control piglets were observed. Both Principal Coordinate Analysis and Non-metric multidimensional scaling revealed dissimilarities between different bacterial communities. Linear discriminant analysis effect size at the genus level determined different potential biomarkers in multiple bacterial communities. Lactobacillus, Clostridium sensu stricto 1 and Corynebacterium 1 were the most discriminately higher genera in the healthy skin microbiome, while Fusobacterium, Trueperella, Staphylococcus, Streptococcus and Bacteroides were discriminately abundant in melanoma tissue microbiome. Bacteroides, Fusobacterium and Escherichia-Shigella were associated with the faecal microbiota of MeLiM piglets. Potential functional pathways analysis based on the KEGG database indicated significant differences in the predicted profile metabolisms between the healthy skin microbiome and melanoma tissue microbiome. The faecal microbiome of MeLiM piglets was enriched by genes related to membrane transports pathways allowing for the increase of intestinal permeability and alteration of the intestinal mucosal barrier.

CONCLUSION: The associations between melanoma progression and dysbiosis in the skin microbiome as well as dysbiosis in the gut microbiome were identified. Results provide promising information for further studies on the local skin and gut microbiome involvement in melanoma progression and may support the development of new therapeutic approaches.}, } @article {pmid35215951, year = {2022}, author = {Du, H and Zhang, L and Zhang, X and Yun, F and Chang, Y and Tuersun, A and Aisaiti, K and Ma, Z}, title = {Metagenome-Assembled Viral Genomes Analysis Reveals Diversity and Infectivity of the RNA Virome of Gerbillinae Species.}, journal = {Viruses}, volume = {14}, number = {2}, pages = {}, pmid = {35215951}, issn = {1999-4915}, mesh = {Animals ; Animals, Wild/virology ; China ; Genetic Variation ; Genome, Viral/*genetics ; Genotype ; Gerbillinae/classification/*virology ; Humans ; Metagenomics ; Phylogeny ; RNA Viruses/classification/*genetics/isolation & purification/pathogenicity ; RNA, Viral/genetics ; Viral Proteins/genetics ; Viral Zoonoses/virology ; Virome/*genetics ; }, abstract = {Rodents are a known reservoir for extensive zoonotic viruses, and also possess a propensity to roost in human habitation. Therefore, it is necessary to identify and catalogue the potentially emerging zoonotic viruses that are carried by rodents. Here, viral metagenomic sequencing was used for zoonotic virus detection and virome characterization on 32 Great gerbils of Rhombomys opimus, Meriones meridianus, and Meiiones Unguiculataus species in Xinjiang, Northwest China. In total, 1848 viral genomes that are potentially pathogenic to rodents and humans, as well as to other wildlife, were identified namely Retro-, Flavi-, Pneumo-, Picobirna-, Nairo-, Arena-, Hepe-, Phenui-, Rhabdo-, Calici-, Reo-, Corona-, Orthomyxo-, Peribunya-, and Picornaviridae families. In addition, a new genotype of rodent Hepacivirus was identified in heart and lung homogenates of seven viscera pools and phylogenetic analysis revealed the closest relationship to rodent Hepacivirus isolate RtMm-HCV/IM2014 that was previously reported to infect rodents from Inner Mongolia, China. Moreover, nine new genotype viral sequences that corresponded to Picobirnaviruses (PBVs), which have a bi-segmented genome and belong to the family Picobirnaviridae, comprising of three segment I and six segment II sequences, were identified in intestines and liver of seven viscera pools. In the two phylogenetic trees that were constructed using ORF1 and ORF2 of segment I, the three segment I sequences were clustered into distinct clades. Additionally, phylogenetic analysis showed that PBV sequences were distributed in the whole tree that was constructed using the RNA-dependent RNA polymerase (RdRp) gene of segment II with high diversity, sharing 68.42-82.67% nucleotide identities with other genogroup I and genogroup II PBV strains based on the partial RdRp gene. By RNA sequencing, we found a high degree of biodiversity of Retro-, Flavi-, Pneumo-, and Picobirnaridae families and other zoonotic viruses in gerbils, indicating that zoonotic viruses are a common presence in gerbils from Xinjiang, China. Therefore, further research is needed to determine the zoonotic potential of these viruses that are carried by other rodent species from different ecosystems and wildlife in general.}, } @article {pmid35215871, year = {2022}, author = {Bai, GH and Lin, SC and Hsu, YH and Chen, SY}, title = {The Human Virome: Viral Metagenomics, Relations with Human Diseases, and Therapeutic Applications.}, journal = {Viruses}, volume = {14}, number = {2}, pages = {}, pmid = {35215871}, issn = {1999-4915}, mesh = {Animals ; COVID-19/therapy ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenome ; Metagenomics/*methods ; Mice ; Obesity/complications ; SARS-CoV-2/genetics ; Virome/*genetics ; Virus Diseases/*drug therapy/therapy ; Viruses/classification/genetics ; }, abstract = {The human body is colonized by a wide range of microorganisms. The field of viromics has expanded since the first reports on the detection of viruses via metagenomic sequencing in 2002. With the continued development of reference materials and databases, viral metagenomic approaches have been used to explore known components of the virome and discover new viruses from various types of samples. The virome has attracted substantial interest since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic. Increasing numbers of studies and review articles have documented the diverse virome in various sites in the human body, as well as interactions between the human host and the virome with regard to health and disease. However, there have been few studies of direct causal relationships. Viral metagenomic analyses often lack standard references and are potentially subject to bias. Moreover, most virome-related review articles have focused on the gut virome and did not investigate the roles of the virome in other sites of the body in human disease. This review presents an overview of viral metagenomics, with updates regarding the relations between alterations in the human virome and the pathogenesis of human diseases, recent findings related to COVID-19, and therapeutic applications related to the human virome.}, } @article {pmid35215838, year = {2022}, author = {Forero-Junco, LM and Alanin, KWS and Djurhuus, AM and Kot, W and Gobbi, A and Hansen, LH}, title = {Bacteriophages Roam the Wheat Phyllosphere.}, journal = {Viruses}, volume = {14}, number = {2}, pages = {}, pmid = {35215838}, issn = {1999-4915}, mesh = {Bacteriophages/classification/genetics/*isolation & purification ; Genome, Viral/genetics ; Metagenome/genetics ; Microbiota ; Plant Leaves/microbiology ; Pseudomonadaceae/classification/genetics/isolation & purification/virology ; Toxins, Biological/genetics ; Triticum/*microbiology ; }, abstract = {The phyllosphere microbiome plays an important role in plant fitness. Recently, bacteriophages have been shown to play a role in shaping the bacterial community composition of the phyllosphere. However, no studies on the diversity and abundance of phyllosphere bacteriophage communities have been carried out until now. In this study, we extracted, sequenced, and characterized the dsDNA and ssDNA viral community from a phyllosphere for the first time. We sampled leaves from winter wheat (Triticum aestivum), where we identified a total of 876 virus operational taxonomic units (vOTUs), mostly predicted to be bacteriophages with a lytic lifestyle. Remarkably, 848 of these vOTUs corresponded to new viral species, and we estimated a minimum of 2.0 × 10[6] viral particles per leaf. These results suggest that the wheat phyllosphere harbors a large and active community of novel bacterial viruses. Phylloviruses have potential applications as biocontrol agents against phytopathogenic bacteria or as microbiome modulators to increase plant growth-promoting bacteria.}, } @article {pmid35213794, year = {2022}, author = {Meng, J and Németh, Z and Peng, M and Fekete, E and Garrigues, S and Lipzen, A and Ng, V and Savage, E and Zhang, Y and Grigoriev, IV and Mäkelä, MR and Karaffa, L and de Vries, RP}, title = {GalR, GalX and AraR co-regulate d-galactose and l-arabinose utilization in Aspergillus nidulans.}, journal = {Microbial biotechnology}, volume = {15}, number = {6}, pages = {1839-1851}, pmid = {35213794}, issn = {1751-7915}, mesh = {Arabinose/metabolism ; *Aspergillus nidulans/genetics/metabolism ; Galactose/metabolism ; Gene Expression Regulation, Fungal ; Polysaccharides/metabolism ; Transcription Factors/metabolism ; }, abstract = {Filamentous fungi produce a wide variety of enzymes in order to efficiently degrade plant cell wall polysaccharides. The production of these enzymes is controlled by transcriptional regulators, which also control the catabolic pathways that convert the released monosaccharides. Two transcriptional regulators, GalX and GalR, control d-galactose utilization in the model filamentous fungus Aspergillus nidulans, while the arabinanolytic regulator AraR regulates l-arabinose catabolism. d-Galactose and l-arabinose are commonly found together in polysaccharides, such as arabinogalactan, xylan and rhamnogalacturonan I. Therefore, the catabolic pathways that convert d-galactose and l-arabinose are often also likely to be active simultaneously. In this study, we investigated the interaction between GalX, GalR and AraR in d-galactose and l-arabinose catabolism. For this, we generated single, double and triple mutants of the three regulators, and analysed their growth and enzyme and gene expression profiles. Our results clearly demonstrated that GalX, GalR and AraR co-regulate d-galactose catabolism in A. nidulans. GalX has a prominent role on the regulation of genes of d-galactose oxido-reductive pathway, while AraR can compensate for the absence of GalR and/or GalX.}, } @article {pmid35212476, year = {2022}, author = {Belouhova, M and Daskalova, E and Yotinov, I and Topalova, Y and Velkova, L and Dolashki, A and Dolashka, P}, title = {Microbial diversity of garden snail mucus.}, journal = {MicrobiologyOpen}, volume = {11}, number = {1}, pages = {e1263}, pmid = {35212476}, issn = {2045-8827}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/classification/genetics/*isolation & purification ; Computational Biology ; In Situ Hybridization, Fluorescence ; Isoelectric Point ; Metagenomics ; Microbiota ; Mucus/chemistry/microbiology ; RNA, Ribosomal, 16S/genetics ; Snails/chemistry/*microbiology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Tandem Mass Spectrometry ; }, abstract = {The search for new natural compounds for application in medicine and cosmetics is a trend in biotechnology. One of the sources of such active compounds is the snail mucus. Snail physiology and the biological activity of their fluids (especially the mucus) are still poorly studied. Only a few previous studies explored the relationship between snails and their microbiome. The present study was focused on the biodiversity of the snail mucus used in the creation of cosmetic products, therapeutics, and nutraceuticals. The commonly used cultivation techniques were applied for the determination of the number of major bacterial groups. Fluorescence in situ hybridization for key taxa was performed. The obtained images were subjected to digital image analysis. Sequencing of the 16S rRNA gene was also done. The results showed that the mucus harbors a rich bacterial community (10.78 × 10[10] CFU/ml). Among the dominant bacteria, some are known for their ability to metabolize complex polysaccharides or are usually found in soil and plants (Rhizobiaceae, Shewanella, Pedobacter, Acinetobacter, Alcaligenes). The obtained data demonstrated that the snail mucus creates a unique environment for the development of the microbial community that differs from other parts of the animal and which resulted from the combined contribution of the microbiomes derived from the soil, plants, and the snails.}, } @article {pmid35211421, year = {2022}, author = {Plauzolles, A and Toumi, E and Bonnet, M and Pénaranda, G and Bidaut, G and Chiche, L and Allardet-Servent, J and Retornaz, F and Goutorbe, B and Halfon, P}, title = {Human Stool Preservation Impacts Taxonomic Profiles in 16S Metagenomics Studies.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {722886}, pmid = {35211421}, issn = {2235-2988}, mesh = {Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Specimen Handling/methods ; }, abstract = {Microbiotas play critical roles in human health, yet in most cases scientists lack standardized and reproducible methods from collection and preservation of samples, as well as the choice of omic analysis, up to the data processing. To date, stool sample preservation remains a source of technological bias in metagenomic sequencing, despite newly developed storage solutions. Here, we conducted a comparative study of 10 storage methods for human stool over a 14-day period of storage at fluctuating temperatures. We first compared the performance of each stabilizer with observed bacterial composition variation within the same specimen. Then, we identified the nature of the observed variations to determine which bacterial populations were more impacted by the stabilizer. We found that DNA stabilizers display various stabilizing efficacies and affect the recovered bacterial profiles thus highlighting that some solutions are more performant in preserving the true gut microbial community. Furthermore, our results showed that the bias associated with the stabilizers can be linked to the phenotypical traits of the bacterial populations present in the studied samples. Although newly developed storage solutions have improved our capacity to stabilize stool microbial content over time, they are nevertheless not devoid of biases hence requiring the implantation of standard operating procedures. Acknowledging the biases and limitations of the implemented method is key to better interpret and support true associated microbiome patterns that will then lead us towards personalized medicine, in which the microbiota profile could constitute a reliable tool for clinical practice.}, } @article {pmid35209934, year = {2022}, author = {Fan, L and Ren, J and Chen, Y and Wang, Y and Guo, Z and Bu, P and Yang, J and Ma, W and Zhu, B and Zhao, Y and Cai, J}, title = {Effect of fecal microbiota transplantation on primary hypertension and the underlying mechanism of gut microbiome restoration: protocol of a randomized, blinded, placebo-controlled study.}, journal = {Trials}, volume = {23}, number = {1}, pages = {178}, pmid = {35209934}, issn = {1745-6215}, support = {81630014//national natural science foundation of china/ ; BJJWZYJH01201910023029//beijing outstanding young scientist program/ ; }, mesh = {Blood Pressure Monitoring, Ambulatory ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Humans ; *Hypertension/therapy ; Multicenter Studies as Topic ; Pulse Wave Analysis ; Randomized Controlled Trials as Topic ; Treatment Outcome ; }, abstract = {BACKGROUND: Hypertension is currently the leading modifiable cause of global morbidity and mortality, leading to substantial health and financial burdens. Although multiple studies of management models and innovative therapeutic strategies for hypertension have been conducted, there are still gaps in the field, with a poor control rate reflecting a lack of novel, effective, clinically translated medication or intervention options. Recent animal and human studies repeatedly confirmed a link between the microbiota and hypertension. Of note is our previous study establishing a cause-and-effect relationship between the gut microbiota and blood pressure elevation. A hypothesis of gut microbiota intervention for treating hypertension is thus postulated, and fecal microbiota transplantation (FMT) from healthy donors was performed.

METHODS: A multicenter, randomized, placebo-controlled, blinded clinical trial will be performed in 120 grade 1 hypertensive patients for 3 months. All recruited patients will be randomly assigned in a 1:1 ratio to take oral FMT capsules or placebo capsules on day 1, day 7, and day 14 and will be followed up on day 30, day 60, and day 90. The primary outcome is the change in office systolic blood pressure from baseline to day 30. The main secondary outcomes are BP indicators, including changes in systolic and diastolic blood pressure from office and 24-h ambulatory blood pressure monitoring; assessments of ankle-branchial index and pulse wave velocity; profiling of fecal microbial composition and function; profiling of fecal and serum metabolome; changes in levels of blood glucose, blood lipids, and body mass index; and assessment of adverse events as a measure of safety.

DISCUSSION: Expanding upon our previous research on the role of the gut microbiota in the pathogenesis of hypertension, this study serves as a clinical translation advancement and explores the potential of fecal microbiota transplantation for treating hypertension. The underlying mechanisms, particularly the roles of specific microorganisms or their postbiotics in blood pressure amelioration, will also be investigated via multiple approaches, such as metagenomic sequencing and metabolomic profiling.

TRIAL REGISTRATION: ClinicalTrials.gov NCT04406129 . Registered on May 28, 2020.}, } @article {pmid35209070, year = {2022}, author = {Liu, W and He, K and Wu, D and Zhou, L and Li, G and Lin, Z and Yang, X and Liu, J and Pui Man Hoi, M}, title = {Natural Dietary Compound Xanthohumol Regulates the Gut Microbiota and Its Metabolic Profile in a Mouse Model of Alzheimer's Disease.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {4}, pages = {}, pmid = {35209070}, issn = {1420-3049}, support = {SZXK069//Shenzhen Key Medical Discipline Construction Fund/ ; SZSM201611090//Sanming Project of Medicine in Shenzhen/ ; File no. 127/2014/A3, 0015/2019/ASC, 0023/2020/AFJ, 0035/2020/AGJ//The Science and Technology Development Fund, Macau SAR/ ; Project no. MYRG2015-0061-ICMS-QRCM, MYRG2017-00150-ICMS//The University of Macau Research Grant/ ; }, mesh = {Alzheimer Disease/drug therapy/etiology/metabolism/pathology ; Amyloid beta-Peptides/metabolism ; Animals ; Biodiversity ; Biological Products/chemistry/*pharmacology ; Cognition/drug effects ; Disease Models, Animal ; Flavonoids/chemistry/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Metabolome/*drug effects ; Metagenome ; Metagenomics/methods ; Mice ; Mice, Transgenic ; Propiophenones/chemistry/*pharmacology ; }, abstract = {Discovering new and effective drugs for the treatment of Alzheimer's disease (AD) is a major clinical challenge. This study focuses on chemical modulation of the gut microbiome in an established murine AD model. We used the 16S rDNA sequencing technique to investigate the effect of xanthohumol (Xn) on the diversity of intestinal microflora in 2-month- and 6-month-old APP/PS1 mice, respectively. APP/PS1 and wild-type mice were treated by gavage with corn oil with or without Xn every other day for 90 days. Prior to and following treatment, animals were tested for spatial learning, cognitive and memory function. We found Xn reduced cognitive dysfunction in APP/PS1 mice and significantly regulated the composition and abundance of gut microbiota both in prevention experiments (with younger mice) and therapeutic experiments (with older mice). Differential microflora Gammaproteobacteria were significantly enriched in APP/PS1 mice treated with Xn. Nodosilineaceae and Rikenellaceae may be the specific microflora modulated by Xn. The penicillin and cephalosporin biosynthesis pathway and the atrazine degradation pathway may be the principal modulation pathways. Taken together, oral treatment with Xn may have a neuroprotective role by regulating the composition of intestinal microflora, a result that contributes to the scientific basis for a novel prophylactic and therapeutic approach to AD.}, } @article {pmid35205333, year = {2022}, author = {Bailén, M and Tabone, M and Bressa, C and Lominchar, MGM and Larrosa, M and González-Soltero, R}, title = {Unraveling Gut Microbiota Signatures Associated with PPARD and PARGC1A Genetic Polymorphisms in a Healthy Population.}, journal = {Genes}, volume = {13}, number = {2}, pages = {}, pmid = {35205333}, issn = {2073-4425}, mesh = {*Diabetes Mellitus, Type 2/genetics ; *Gastrointestinal Microbiome/genetics ; Heat-Shock Proteins/genetics ; Humans ; *PPAR delta/genetics ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/genetics ; Polymorphism, Single Nucleotide/genetics ; Sugars ; Transcription Factors/genetics ; }, abstract = {Recent studies have revealed the importance of the gut microbiota in the regulation of metabolic phenotypes of highly prevalent metabolic diseases such as obesity, type II diabetes mellitus (T2DM) and cardiovascular disease. Peroxisome proliferator-activated receptors (PPARs) are a family of ligand-activated nuclear receptors that interact with PPAR-γ co-activator-1α (PPARGC1A) to regulate lipid and glucose metabolism. Genetic polymorphisms in PPARD (rs 2267668; A/G) and PPARGC1A (rs 8192678; G/A) are linked to T2DM. We studied the association between the single-nucleotide polymorphisms (SNPs) rs 2267668 and rs 8192678 and microbiota signatures and their relation to predicted metagenome functions, with the aim of determining possible microbial markers in a healthy population. Body composition, physical exercise and diet were characterized as potential confounders. Microbiota analysis of subjects with PPARGC1A (rs 8192678) and PPARD (rs 2267668) SNPs revealed certain taxa associated with the development of insulin resistance and T2DM. Kyoto encyclopedia of gene and genomes analysis of metabolic pathways predicted from metagenomes highlighted an overrepresentation of ABC sugar transporters for the PPARGC1A (rs 8192678) SNP. Our findings suggest an association between sugar metabolism and the PPARGC1A rs 8192678 (G/A) genotype and support the notion of specific microbiota signatures as factors related to the onset of T2DM.}, } @article {pmid35202611, year = {2022}, author = {Jia, B and Kim, KH and Ruan, W and Kim, HM and Jeon, CO}, title = {Lantibiotic-encoding Streptococcus in the human microbiome are underlying risk factors for liver diseases.}, journal = {The Journal of infection}, volume = {84}, number = {5}, pages = {e70-e72}, doi = {10.1016/j.jinf.2022.02.020}, pmid = {35202611}, issn = {1532-2742}, mesh = {*Bacteriocins ; Humans ; Liver Cirrhosis ; *Liver Diseases ; *Microbiota ; Risk Factors ; Streptococcus ; }, } @article {pmid35202432, year = {2022}, author = {Zhang, L and Xu, Y and Li, H and Li, B and Duan, G and Zhu, C}, title = {The role of probiotics in children with autism spectrum disorders: A study protocol for a randomised controlled trial.}, journal = {PloS one}, volume = {17}, number = {2}, pages = {e0263109}, pmid = {35202432}, issn = {1932-6203}, mesh = {Autism Spectrum Disorder/*drug therapy/microbiology/pathology ; Bifidobacterium/genetics/pathogenicity ; Child ; Child, Preschool ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Gastrointestinal Tract/drug effects/microbiology ; Humans ; Inflammation/drug therapy/genetics/immunology/microbiology ; Male ; Metagenome/drug effects/*genetics ; Placebos ; Probiotics/*administration & dosage/adverse effects ; }, abstract = {BACKGROUND: Autism spectrum disorder (ASD) is a neurological and developmental condition that begins in infancy or earlier and lasts through the individual's lifetime. The aetiology and mechanisms of ASD are not yet fully understood, and current treatment comprises mainly education and rehabilitation, without significant improvement in the core symptoms. Recent studies suggest that microbiota change in children with ASD after the ingestion of probiotics may improve the balance of microbiota and thus ASD symptoms.

OBJECTIVE: The objectives of this study are to evaluate the efficacy of probiotics on the symptoms of children with ASD and the possible mechanisms involved.

METHODS: This is a prospective controlled trial. A total of 160 children with ASD will be stratified and allocated to placebo and probiotics groups randomised according to the severity of their ASD symptoms. The probiotics group will be given probiotics supplements orally twice a day for 3 months and the control group will be given a placebo at the same amount, in addition to the baseline therapy of education and rehabilitation. All the children will be evaluated systematically by using different scales, questionnaires before, during, and after 3 months' treatment, as well as 3 months after discontinuation. The potential impact of probiotics on immunity and inflammation, metabolism, and metagenome will also be investigated.

DISCUSSION: Our previous study showed that the abundance of intestinal flora was greatly different in children with ASD, and that Bifidobacterium was associated with the severity of ASD. In the present study, we will investigate the impact of probiotics supplementation on the symptoms of Children with ASD, with the purpose of evaluating the possible therapeutic effects of additives on ASD and of providing a reference for clinical treatment. The results will help to disclose as yet unknown relationship between probiotics and ASD.

TRIAL REGISTRATION: This study has been registered with Chinese Clinical Trial Registry (ChiCTR-2000037941).}, } @article {pmid35196818, year = {2022}, author = {Lu, J and Yang, S and Wang, C and Wang, H and Gong, G and Xi, Y and Pan, J and Wang, X and Zeng, J and Zhang, J and Li, P and Shen, Q and Shan, T and Zhang, W}, title = {Gut Virome of the World's Highest-Elevation Lizard Species (Phrynocephalus erythrurus and Phrynocephalus theobaldi) Reveals Versatile Commensal Viruses.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0187221}, pmid = {35196818}, issn = {2165-0497}, mesh = {Animals ; Bacteriophages/genetics ; *Gastrointestinal Microbiome ; Lizards/metabolism/*virology ; Metagenome ; Metagenomics ; Phylogeny ; Symbiosis/*physiology ; Tibet ; *Virome/physiology ; Viruses/classification/genetics ; }, abstract = {The gut virome is a reservoir of diverse symbiotic and pathogenic viruses coevolving with their hosts, and yet limited research has explored the gut viromes of highland-dwelling rare species. Using viral metagenomic analysis, the viral communities of the Phrynocephalus lizards living in the Qinghai-Tibet Plateau were investigated. Phage-encoded functional genes and antibiotic resistance genes (ARGs) were analyzed. The viral communities of different lizard species were all predominated by bacteriophages, especially the Caudovirales order. The virome of Phrynocephalus erythrurus living around the Namtso Lake possessed a unique structure, with the greatest abundance of the Parvoviridae family and the highest number of exclusive viral species. Several vertebrate-infecting viruses were discovered, including caliciviruses, astroviruses, and parvoviruses. Phylogenetic analyses demonstrated that the virus hallmark genes of bacteriophages possessed high genetic diversity. After functional annotation, the majority of phage-associated functional genes were classified in the energy metabolism category. In addition, plenty of ARGs belonging to the multidrug category were discovered, and five ARGs were exclusive to the virome from Phrynocephalus theobaldi. This study provided the first insight into the structure and function of the virome in highland lizards, contributing to the protection of threatened lizard species. Also, our research is of exemplary significance for the gut virome research of lizard species and other cold-blooded and highland-dwelling animals, prompting a better understanding of the interspecific differences and transmission of commensal viruses. IMPORTANCE The Phrynocephalus lizards inhabiting the Qinghai-Tibet Plateau (QTP) are considered to be the highest-altitude lizard species in the world, and they have been added to the IUCN list of threatened species. Living in the QTP with hypoxic, arid, natural conditions, the lizards presented a unique pattern of gut virome, which could provide both positive and negative effects, such as the enrichment of functional genes and the dissemination of antibiotic resistance genes (ARGs). This work provides the foundation for further research on the gut virome in these endangered lizard species and other cold-blooded and highland-dwelling animals, contributing to the maintenance of ecological balance on the plateau.}, } @article {pmid35196800, year = {2022}, author = {Xiao, G and Cai, Z and Guo, Q and Ye, T and Tang, Y and Guan, P and Zhang, J and Ou, M and Fu, X and Ren, L and Yu, M and Wang, Z and Liu, L and Yang, L and Zhang, G}, title = {Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0190121}, pmid = {35196800}, issn = {2165-0497}, mesh = {Adult ; Bronchoalveolar Lavage Fluid ; Drug Resistance, Bacterial ; Female ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Lung/*microbiology ; Male ; *Metagenome ; Metagenomics/*methods ; Microbiota/drug effects/*physiology ; Mycobacterium tuberculosis ; RNA, Ribosomal, 16S/genetics ; Sputum ; Tuberculosis, Pulmonary/drug therapy/*metabolism ; }, abstract = {The microbiota plays an important role in human health and disease development. The lung microbiota profile in pulmonary tuberculosis (TB) patients and the effects of anti-TB treatment on the profile need to be determined thoroughly and comprehensively. This study primarily aimed to determine the lung microbiota profile associated with pulmonary TB and characterize the longitudinal changes during anti-TB treatment. A total of 53 participants, comprising 8 healthy individuals, 12 untreated pulmonary TB patients, 15 treated pulmonary TB patients, 11 cured pulmonary TB patients, and 7 lung cancer patients, were recruited in the present study. Bronchioalveolar lavage fluid (BALF) samples were collected from the above participants, and throat swabs were taken from healthy individuals. Microbiomes in the samples were examined using metagenomic next-generation sequencing (mNGS). Differences in microbiota profiles were determined through a comparison of the indicated groups. Our findings indicated that the BALF samples displayed decreased richness and diversity of the microbiota compared to those of the throat swab samples, and these two kinds of samples exhibited obvious separation on principal-coordinate analysis (PCoA) plots. Untreated pulmonary TB patients displayed a unique lung microbiota signature distinct from that of healthy individuals and lung cancer patients. Our data first demonstrated that anti-TB treatment with first-line drugs increases alpha diversity and significantly affects the beta diversity of the lung microbiota, while it also induces antibiotic resistance genes (ARGs). IMPORTANCE Characterization of the lung microbiota could lead to a better understanding of the pathogenesis of pulmonary TB. Here, we applied the metagenomic shotgun sequencing instead of 16S rRNA sequencing method to characterize the lung microbiota using the BALF samples instead of sputum. We found that alterations in the lung microbiota are associated with TB infection and that anti-TB treatment significantly affects the alpha and beta diversity of the lung microbiota in pulmonary TB patients. These findings could help us better understand TB pathogenesis.}, } @article {pmid35195242, year = {2022}, author = {Díaz-Cruz, GA and Cassone, BJ}, title = {Changes in the phyllosphere and rhizosphere microbial communities of soybean in the presence of pathogens.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {3}, pages = {}, doi = {10.1093/femsec/fiac022}, pmid = {35195242}, issn = {1574-6941}, mesh = {*Microbiota ; *Mycobiome ; Rhizosphere ; Soil Microbiology ; Glycine max ; }, abstract = {Soybean (Glycine max L.) is host to an array of foliar- and root-infecting pathogens that can cause significant yield losses. To provide insights into the roles of microorganisms in disease development, we evaluated the bacterial and fungal communities associated with the soybean rhizosphere and phyllosphere. For this, leaf and soil samples of healthy, Phytophthora sojae-infected and Septoria glycines-infected plants were sampled at three stages during the production cycle, and then subjected to 16S and Internal Transcribed Spacer (ITS) amplicon sequencing. The results indicated that biotic stresses did not have a significant impact on species richness and evenness regardless of growth stage. However, the structure and composition of soybean microbial communities were dramatically altered by biotic stresses, particularly for the fungal phyllosphere. Additionally, we cataloged a variety of microbial genera that were altered by biotic stresses and their associations with other genera, which could serve as biological indicators for disease development. In terms of soybean development, the rhizosphere and phyllosphere had distinct microbial communities, with the fungal phyllosphere most influenced by growth stage. Overall, this study characterized the phyllosphere and rhizosphere microbial communities of soybean, and described the impact of pathogen infection and plant development in shaping these bacterial and fungal communities.}, } @article {pmid35194028, year = {2022}, author = {Tamburini, FB and Maghini, D and Oduaran, OH and Brewster, R and Hulley, MR and Sahibdeen, V and Norris, SA and Tollman, S and Kahn, K and Wagner, RG and Wade, AN and Wafawanaka, F and Gómez-Olivé, FX and Twine, R and Lombard, Z and , and Hazelhurst, S and Bhatt, AS}, title = {Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {926}, pmid = {35194028}, issn = {2041-1723}, support = {K43 TW010698/TW/FIC NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; 085477/Z/08/Z/WT_/Wellcome Trust/United Kingdom ; R25 TW009338/TW/FIC NIH HHS/United States ; U54 HG006938/HG/NHGRI NIH HHS/United States ; 058893/Z/99/A/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 085477/B/08/Z/WT_/Wellcome Trust/United Kingdom ; 069683/Z/02/Z/WT_/Wellcome Trust/United Kingdom ; P30 CA124435/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; *Microbiota ; Rural Population ; South Africa ; }, abstract = {Human gut microbiome research focuses on populations living in high-income countries and to a lesser extent, non-urban agriculturalist and hunter-gatherer societies. The scarcity of research between these extremes limits our understanding of how the gut microbiota relates to health and disease in the majority of the world's population. Here, we evaluate gut microbiome composition in transitioning South African populations using short- and long-read sequencing. We analyze stool from adult females living in rural Bushbuckridge (n = 118) or urban Soweto (n = 51) and find that these microbiomes are taxonomically intermediate between those of individuals living in high-income countries and traditional communities. We demonstrate that reference collections are incomplete for characterizing microbiomes of individuals living outside high-income countries, yielding artificially low beta diversity measurements, and generate complete genomes of undescribed taxa, including Treponema, Lentisphaerae, and Succinatimonas. Our results suggest that the gut microbiome of South Africans does not conform to a simple "western-nonwestern" axis and contains undescribed microbial diversity.}, } @article {pmid35191911, year = {2022}, author = {Dong, S and Xin, Z and He, W and Zhang, Y and Xiong, J and Wang, J and Liao, Z and Wang, L and Zhong, Q and Wei, H and Fang, X}, title = {Correlation between the regulation of intestinal bacteriophages by green tea polyphenols and the flora diversity in SPF mice.}, journal = {Food & function}, volume = {13}, number = {5}, pages = {2952-2965}, doi = {10.1039/d1fo03694g}, pmid = {35191911}, issn = {2042-650X}, mesh = {Animals ; Antioxidants/chemistry/*pharmacology ; Bacteroidetes/drug effects ; Gastrointestinal Microbiome/drug effects ; Male ; Mice ; Mice, Inbred C57BL ; Polyphenols/chemistry/*pharmacology ; Specific Pathogen-Free Organisms ; *Tea ; }, abstract = {Green tea polyphenols (GTP) play an important role in shaping the gut microbiome, comprising a range of densely colonizing microorganisms, including bacteriophages. Previous studies focused on the effect of GTP on the bacteria in the gut microbiota. However, little is known about the role of GTP in the bacteriophage composition of healthy intestines. In this study, SPF male C57BL/6J mice were divided into a polyphenol-free diet group and a tea polyphenol diet group where drinking water was supplemented with 0.1% GTP for 28 days. The ultra-deep metagenomic sequencing of virus-like particle preparations and bacterial 16S rRNA sequencing were performed on mouse stool samples. Changes in the gut bacteriome, bacteriophages, and bacterial-bacteriophage correlations were then compared between the groups. The results revealed an abundance of Firmicutes, a significant decrease in Bacteroidetes, and a significant increase in the ratio of F/B after GTP exposure. The GTP altered the abundance (relative abundance > 1.00%) of Bifidobacterium (regulation rate of 89.78% and the abundance up-regulated by 0.89%) and Akkermansia (regulation rate of 99.70% and the abundance down-regulated by 1.77%). The abundance of Faecalibaculum (regulation rate of 60.17%) increased by 24.38% following GTP treatment. The GTP also altered the abundance of Salmonella phage (regulation rate of 98.64% and the abundance up-regulated by 3.16%) and that of Gordonia_phage_Yakult (regulation rate of 99.99% and the abundance down-regulated by 5.44%). It significantly increased the intestine's lytic phages and reduced the temperate phages by 29.22%. The dominant microorganisms (relative abundance >1.00%) of Bifidobacterium and Dubosiella had a significantly negative relationship with the Faecalibacterium phage and a significantly positive relationship with the Lactobacillus prophage. Exposure to GTP positively promoted changes in the gut bacteriophage community and interaction network in the microbial community of the SPF mice. These findings highlight the importance of "profitable" bacteriophage-bacteria relationships and reveal a potential mechanism of GTP towards the regulation of intestinal flora via intestinal phage communities.}, } @article {pmid35191776, year = {2022}, author = {Gautam, A and Felderhoff, H and Bağci, C and Huson, DH}, title = {Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0140821}, pmid = {35191776}, issn = {2379-5077}, mesh = {*Software ; *Microbiota ; Metagenome ; Sequence Analysis, DNA ; Databases, Genetic ; }, abstract = {In microbiome analysis, one main approach is to align metagenomic sequencing reads against a protein reference database, such as NCBI-nr, and then to perform taxonomic and functional binning based on the alignments. This approach is embodied, for example, in the standard DIAMOND+MEGAN analysis pipeline, which first aligns reads against NCBI-nr using DIAMOND and then performs taxonomic and functional binning using MEGAN. Here, we propose the use of the AnnoTree protein database, rather than NCBI-nr, in such alignment-based analyses to determine the prokaryotic content of metagenomic samples. We demonstrate a 2-fold speedup over the usage of the prokaryotic part of NCBI-nr and increased assignment rates, in particular assigning twice as many reads to KEGG. In addition to binning to the NCBI taxonomy, MEGAN now also bins to the GTDB taxonomy. IMPORTANCE The NCBI-nr database is not explicitly designed for the purpose of microbiome analysis, and its increasing size makes its unwieldy and computationally expensive for this purpose. The AnnoTree protein database is only one-quarter the size of the full NCBI-nr database and is explicitly designed for metagenomic analysis, so it should be supported by alignment-based pipelines.}, } @article {pmid35191646, year = {2022}, author = {Campos, PM and Miska, KB and Kahl, S and Jenkins, MC and Shao, J and Proszkowiec-Weglarz, M}, title = {Effects of Eimeria tenella on Cecal Luminal and Mucosal Microbiota in Broiler Chickens.}, journal = {Avian diseases}, volume = {66}, number = {1}, pages = {39-52}, doi = {10.1637/21-00068}, pmid = {35191646}, issn = {1938-4351}, mesh = {Animals ; Cecum/microbiology ; Chickens/genetics ; *Coccidiosis/parasitology/veterinary ; *Eimeria tenella ; Escherichia coli/genetics ; *Gastrointestinal Microbiome ; *Microbiota ; *Poultry Diseases/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The intestinal disease coccidiosis, caused by parasitic Eimeria species, severely impacts poultry production, leading to an estimated $14 billion in annual losses worldwide. As the poultry industry moves away from antibiotics as a treatment for diseases, a better understanding of the microbiota is required to develop other solutions such as probiotics, prebiotics, and nutritional supplements. This study aimed to investigate the effects of Eimeria tenella infection on luminal (cecal contents [CeC]) and mucosal (cecal epithelial scrapings [CeS]) microbial populations in 288 Ross 708 broiler chickens at multiple time points postinfection (PI). By use of 16S rRNA amplicon sequencing, it was revealed that microbial diversity differed in infected (IF) chickens in comparison to the control (C) in both CeC and CeS microbiota at the peak of infection (7 days PI), when simultaneously IF birds saw reduced body weight gain and a higher feed conversion ratio. Infection resulted in a significant differential abundance of some bacterial taxa, including increases in potential secondary pathogens Escherichia coli, Enterococcus, Clostridium, and Proteus and a decrease in the short chain fatty acid-producing family Lachnospiraceae. Predicted metagenomic pathways associated with E. coli, such as those responsible for amino acid biosynthesis, were differentially expressed in IF birds. In conclusion, our results show that E. tenella infection disturbs luminal and mucosal microbiota balance in chickens. Moreover, the luminal microbiota seems to be more susceptible to prolonged imbalance due to IF, whereas the mucosal microbiota appeared to be affected only in the short term, demonstrating the importance of researching both the luminal and mucosal microbiota of the cecum.}, } @article {pmid35190727, year = {2022}, author = {Metwaly, A and Reitmeier, S and Haller, D}, title = {Microbiome risk profiles as biomarkers for inflammatory and metabolic disorders.}, journal = {Nature reviews. Gastroenterology & hepatology}, volume = {19}, number = {6}, pages = {383-397}, pmid = {35190727}, issn = {1759-5053}, mesh = {Biomarkers ; *Diabetes Mellitus, Type 2/microbiology ; Dysbiosis/microbiology ; Humans ; *Metabolic Diseases ; *Microbiota ; }, abstract = {The intestine harbours a complex array of microorganisms collectively known as the gut microbiota. The past two decades have witnessed increasing interest in studying the gut microbiota in health and disease, largely driven by rapid innovation in high-throughput multi-omics technologies. As a result, microbial dysbiosis has been linked to many human pathologies, including type 2 diabetes mellitus and inflammatory bowel disease. Integrated analyses of multi-omics data, including metagenomics and metabolomics along with measurements of host response and cataloguing of bacterial isolates, have identified many bacteria and bacterial products that are correlated with disease. Nevertheless, insight into the mechanisms through which microbes affect intestinal health requires going beyond correlation to causation. Current understanding of the contribution of the gut microbiota to disease causality remains limited, largely owing to the heterogeneity of microbial community structures, interindividual differences in disease evolution and incomplete understanding of the mechanisms that integrate microbiota-derived signals into host signalling pathways. In this Review, we provide a broad insight into the microbiome signatures linked to inflammatory and metabolic disorders, discuss outstanding challenges in this field and propose applications of multi-omics technologies that could lead to an improved mechanistic understanding of microorganism-host interactions.}, } @article {pmid35189961, year = {2022}, author = {Coker, OO and Liu, C and Wu, WKK and Wong, SH and Jia, W and Sung, JJY and Yu, J}, title = {Altered gut metabolites and microbiota interactions are implicated in colorectal carcinogenesis and can be non-invasive diagnostic biomarkers.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {35}, pmid = {35189961}, issn = {2049-2618}, mesh = {*Adenoma/diagnosis ; Carcinogenesis ; *Colorectal Neoplasms/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Gut microbiota contributes to colorectal cancer (CRC) pathogenesis through microbes and their metabolites. The importance of microbiota-associated metabolites in colorectal carcinogenesis highlights the need to investigate the gut metabolome along the adenoma-carcinoma sequence to determine their mechanistic implications in the pathogenesis of CRC. To date, how and which microbes and metabolites interactively promote early events of CRC development are still largely unclear. We aim to determine gut microbiota-associated metabolites and their linkage to colorectal carcinogenesis.

RESULTS: We performed metabolomics and metagenomics profiling on fecal samples from 386 subjects including 118 CRC patients, 140 colorectal adenomas (CRA) patients and 128 healthy subjects as normal controls (NC). We identified differences in the gut metabolite profiles among NC, CRA and CRC groups by partial least squares-discriminant and principal component analyses. Among the altered metabolites, norvaline and myristic acid showed increasing trends from NC, through CRA, to CRC. CRC-associated metabolites were enriched in branched-chain amino acids, aromatic amino acids and aminoacyl-tRNA biosynthesis pathways. Moreover, metabolites marker signature (twenty metabolites) classified CRC from NC subjects with an area under the curve (AUC) of 0.80, and CRC from CRA with an AUC of 0.79. Integrative analyses of metabolomics and metagenomics profiles demonstrated that the relationships among CRC-associated metabolites and bacteria were altered across CRC stages; certain associations exhibited increasing or decreasing strengths while some were reversed from negative to positive or vice versa. Combinations of gut bacteria with the metabolite markers improved their diagnostic performances; CRC vs NC, AUC: 0.94; CRC vs CRA, AUC 0.92; and CRA vs NC, AUC: 0.86, indicating a potential for early diagnosis of colorectal neoplasia.

CONCLUSIONS: This study underscores potential early-driver metabolites in stages of colorectal tumorigenesis. The Integrated metabolite and microbiome analysis demonstrates that gut metabolites and their association with gut microbiota are perturbed along colorectal carcinogenesis. Fecal metabolites can be utilized, in addition to bacteria, for non-invasive diagnosis of colorectal neoplasia. Video Abstract.}, } @article {pmid35188453, year = {2022}, author = {Forde, TL and Dennis, TPW and Aminu, OR and Harvey, WT and Hassim, A and Kiwelu, I and Medvecky, M and Mshanga, D and Van Heerden, H and Vogel, A and Zadoks, RN and Mmbaga, BT and Lembo, T and Biek, R}, title = {Population genomics of Bacillus anthracis from an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity.}, journal = {Microbial genomics}, volume = {8}, number = {2}, pages = {}, pmid = {35188453}, issn = {2057-5858}, support = {BB/L018926/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; FORDE/BB/R012075/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L018845/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L018845/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L017679/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L018926/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 096400/Z/11/Z/WT_/Wellcome Trust/United Kingdom ; BB/J010367/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Anthrax/epidemiology/microbiology/veterinary ; *Bacillus anthracis/genetics ; Genomics ; Metagenomics ; Phylogeography ; }, abstract = {Genomic sequencing has revolutionized our understanding of bacterial disease epidemiology, but remains underutilized for zoonotic pathogens in remote endemic settings. Anthrax, caused by the spore-forming bacterium Bacillus anthracis, remains a threat to human and animal health and rural livelihoods in low- and middle-income countries. While the global genomic diversity of B. anthracis has been well-characterized, there is limited information on how its populations are genetically structured at the scale at which transmission occurs, critical for understanding the pathogen's evolution and transmission dynamics. Using a uniquely rich dataset, we quantified genome-wide SNPs among 73 B. anthracis isolates derived from 33 livestock carcasses sampled over 1 year throughout the Ngorongoro Conservation Area, Tanzania, a region hyperendemic for anthrax. Genome-wide SNPs distinguished 22 unique B. anthracis genotypes (i.e. SNP profiles) within the study area. However, phylogeographical structure was lacking, as identical SNP profiles were found throughout the study area, likely the result of the long and variable periods of spore dormancy and long-distance livestock movements. Significantly, divergent genotypes were obtained from spatio-temporally linked cases and even individual carcasses. The high number of SNPs distinguishing isolates from the same host is unlikely to have arisen during infection, as supported by our simulation models. This points to an unexpectedly wide transmission bottleneck for B. anthracis, with an inoculum comprising multiple variants being the norm. Our work highlights that inferring transmission patterns of B. anthracis from genomic data will require analytical approaches that account for extended and variable environmental persistence, as well as co-infection.}, } @article {pmid35187178, year = {2022}, author = {Sun, RX and Huang, WJ and Xiao, Y and Wang, DD and Mu, GH and Nan, H and Ni, BR and Huang, XQ and Wang, HC and Liu, YF and Fu, Q and Zhao, JX}, title = {Shenlian (SL) Decoction, a Traditional Chinese Medicine Compound, May Ameliorate Blood Glucose via Mediating the Gut Microbiota in db/db Mice.}, journal = {Journal of diabetes research}, volume = {2022}, number = {}, pages = {7802107}, pmid = {35187178}, issn = {2314-6753}, mesh = {Animals ; Blood Glucose/*drug effects/metabolism ; China ; Coptis/*metabolism ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects/physiology ; Medicine, Chinese Traditional/methods/*standards ; Mice ; Mice, Inbred C57BL/metabolism ; Panax/*metabolism ; }, abstract = {Shenlian (SL) decoction is a herbal formula composed of Coptis and ginseng, of which berberine and ginsenoside are the main constituents. Even though SL decoction is widely used in treating diabetes in China, the mechanism of its antidiabetes function still needs further study. Gut microbiota disorder is one of the important factors that cause diabetes. To explore the effect of SL decoction on intestinal microbiota, gut microbiota of mice was analyzed by sequencing the gut bacterial 16S rRNA V3+V4 region and metagenomics. In this study, results demonstrated that SL decoction had a better hypoglycemic effect and β cell protection effect than either ginseng or Coptis chinensis. Alpha diversity analysis showed that all interventions with ginseng, Coptis, and SL decoction could reverse the increased diversity and richness of gut microbiota in db/db mice. PCoA analysis showed oral SL decoction significantly alters gut microbiota composition in db/db mice. 395 OTUs showed significant differences after SL treatment, of which 37 OTUs enriched by SL decoction showed a significant negative correlation with FBG, and 204 OTUs decreased by SL decoction showed a significant positive correlation with FBG. Results of KEGG analysis and metagenomic sequencing showed that SL decoction could reduce the Prevotellaceae, Rikenellaceae, and Helicobacteraceae, which were related to lipopolysaccharide biosynthesis, riboflavin metabolism, and peroxisome, respectively. It could also upregulate the abundance of Bacteroidaceae, which contributed to the metabolism of starch and sucrose as well as pentose-glucuronate interconversions. In the species level, SL decoction significantly upregulates the relative abundance of Bacteroides_acidifaciens which showed a significant negative correlation with FBG and was reported to be a potential agent for modulating metabolic disorders such as diabetes and obesity. In conclusion, SL decoction was effective in hypoglycemia and its mechanism may be related to regulating gut microbiota via upregulating Bacteroides_acidifaciens.}, } @article {pmid35186803, year = {2022}, author = {Manzanares-Leal, GL and Coronel-Martínez, JA and Rodríguez-Morales, M and Rangel-Cuevas, I and Bustamante-Montes, LP and Sandoval-Trujillo, H and Ramírez-Durán, N}, title = {Preliminary Identification of the Aerobic Cervicovaginal Microbiota in Mexican Women With Cervical Cancer as the First Step Towards Metagenomic Studies.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {838491}, pmid = {35186803}, issn = {2235-2988}, mesh = {Adult ; Aged ; Cross-Sectional Studies ; Female ; Humans ; *Microbiota/genetics ; Middle Aged ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; *Uterine Cervical Neoplasms ; Vagina/microbiology ; Young Adult ; }, abstract = {Cervical cancer (CC) is considered a public health problem. Recent studies have evaluated the possible relationship between the cervicovaginal microbiome and gynecologic cancer but have not studied the relationship between aerobic bacterial communities and neoplasia. The study aimed to identify the cultivable aerobic bacterial microbiota in women with cervical cancer as a preliminary approach to the metagenomic study of the cervicovaginal microbiome associated with cervical cancer in Mexican women. An observational cross-sectional study was conducted, including 120 women aged 21-71 years, divided into two study groups, women with locally advanced CC (n=60) and women without CC (n=60). Sociodemographic, gynecological-obstetric, sexual, and habit data were collected. Cervicovaginal samples were collected by swabbing, from which standard microbiological methods obtained culturable bacteria. The strains were genetically characterized by PCR-RFLP of the 16S rRNA gene and subsequently identified by sequencing the same gene. Variables regularly reported as risk factors for the disease were found in women with CC. Differences were found in the prevalence and number of species isolated in each study group. Bacteria commonly reported in women with aerobic vaginitis were identified. There were 12 species in women with CC, mainly Corynebacterium spp. and Staphylococcus spp.; we found 13 bacterial species in the group without cancer, mainly Enterococcus spp. and Escherichia spp. The advanced stages presented a more significant number of isolates and species. This study provided a preliminary test for cervicovaginal metagenomic analysis, demonstrating the presence of aerobic cervicovaginal dysbiosis in women with CC and the need for more in-depth studies.}, } @article {pmid35185922, year = {2022}, author = {Thomas, JP and Modos, D and Rushbrook, SM and Powell, N and Korcsmaros, T}, title = {The Emerging Role of Bile Acids in the Pathogenesis of Inflammatory Bowel Disease.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {829525}, pmid = {35185922}, issn = {1664-3224}, support = {/DH_/Department of Health/United Kingdom ; BB/CSP1720/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9819/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bile Acids and Salts/metabolism/*physiology ; Dysbiosis/pathology ; Gastrointestinal Microbiome/*physiology ; Humans ; Inflammatory Bowel Diseases/*etiology ; Intestinal Mucosa/pathology ; }, abstract = {Inflammatory bowel disease (IBD) is a chronic immune-mediated inflammatory disorder of the gastrointestinal tract that arises due to complex interactions between host genetic risk factors, environmental factors, and a dysbiotic gut microbiota. Although metagenomic approaches have attempted to characterise the dysbiosis occurring in IBD, the precise mechanistic pathways interlinking the gut microbiota and the intestinal mucosa are still yet to be unravelled. To deconvolute these complex interactions, a more reductionist approach involving microbial metabolites has been suggested. Bile acids have emerged as a key class of microbiota-associated metabolites that are perturbed in IBD patients. In recent years, metabolomics studies have revealed a consistent defect in bile acid metabolism with an increase in primary bile acids and a reduction in secondary bile acids in IBD patients. This review explores the evolving evidence that specific bile acid metabolites interact with intestinal epithelial and immune cells to contribute to the inflammatory milieu seen in IBD. Furthermore, we summarise evidence linking bile acids with intracellular pathways that are known to be relevant in IBD including autophagy, apoptosis, and the inflammasome pathway. Finally, we discuss how novel experimental and bioinformatics approaches could further advance our understanding of the role of bile acids and inform novel therapeutic strategies in IBD.}, } @article {pmid35184470, year = {2022}, author = {Zhang, Z and Bai, HH and Zong, XN and Li, T and Liu, ZH}, title = {[Dynamics of vaginal microbiota in women of reproductive age during the menstrual cycle].}, journal = {Zhonghua fu chan ke za zhi}, volume = {57}, number = {2}, pages = {101-109}, doi = {10.3760/cma.j.cn112141-20211031-00631}, pmid = {35184470}, issn = {0529-567X}, support = {7214230//Beijing Natural Science Foundation/ ; FCYY201916//Special Training Program for Young and Middle-aged Subject Backbone of Beijing Obstetrics and Gynecology Hospital, Capital Medical University/ ; }, mesh = {Female ; Humans ; Luteal Phase ; *Menstrual Cycle ; Menstruation ; *Microbiota ; Pregnancy ; Vagina/microbiology ; }, abstract = {Objective: To investigate the dynamic changes of vaginal microbiota in different phases of menstrual cycle in healthy Chinese women of childbearing age. Methods: A total of 11 healthy women of childbearing age with regular menstruation, who had physical examination in the Gynecology Clinic of Beijing Obstetrics and Gynecology Hospital from September to December 2020 were randomly selected as research subjects. Vaginal secretions were collected during menstrual phase (2nd-3rd day), mid-follicular phase (7th-8th day), and mid-luteal phase (21st-22nd day) for microbiota analysis through metagenomic sequencing. Results: (1) Vaginal microbiota species were the most diverse in menstrual phase and the least in follicular phase, observing dominant vaginal bacteria gradually changing to Lactobacillus from menstrual phase to follicular phase and then to luteal phase. (2) The dynamic evolution of vaginal microbiota from menstrual phase to follicular phase and then to luteal phase was divided into: no change in dominant bacteria, replacement of dominant bacteria, changes in the proportion of dominant bacteria, and recurrence of dominant bacteria (non-Lactobacillus-dominance appeared again in luteal phase after returning to normal Lactobacillus-dominance in follicular phase). (3) Prevotella, especially Prevotella_bivia, was significantly higher during menstrual phase. Conclusions: Healthy vaginal microbiota should be relatively stable, but also have the ability of dynamic change and self-recovery. Prevotella plays a central role among opportunistic pathogens in the vagina, whose function remains to be investigated.}, } @article {pmid35184168, year = {2022}, author = {Darriaut, R and Lailheugue, V and Masneuf-Pomarède, I and Marguerit, E and Martins, G and Compant, S and Ballestra, P and Upton, S and Ollat, N and Lauvergeat, V}, title = {Grapevine rootstock and soil microbiome interactions: Keys for a resilient viticulture.}, journal = {Horticulture research}, volume = {9}, number = {}, pages = {}, pmid = {35184168}, issn = {2662-6810}, abstract = {Soil microbiota has increasingly been shown to play an integral role in viticulture resilience. The emergence of new metagenomic and culturomic technologies has led to significant advances in the study of microbial biodiversity. In the agricultural sector, soil and plant microbiomes have been found to significantly improve resistance to environmental stressors and diseases, as well as influencing crop yields and fruit quality thus improving sustainability under shifting environments. Grapevines are usually cultivated as a scion grafted on rootstocks, which are selected according to pedoclimatic conditions and cultural practices, known as terroir. The rootstock connects the surrounding soil to the vine's aerial part and impacts scion growth and berry quality. Understanding rootstock and soil microbiome dynamics is a relevant and important field of study, which may be critical to improve viticulture sustainability and resilience. This review aims to highlight the relationship between grapevine roots and telluric microbiota diversity and activity. In addition, this review explores the concept of core microbiome regarding potential applications of soil microbiome engineering with the goal of enhancing grapevine adaptation to biotic and abiotic stress.}, } @article {pmid35184054, year = {2022}, author = {Okafuji, H and Iida, N and Kitamura, K and Seishima, J and Wang, Z and Yutani, M and Yoshio, T and Yamashita, T and Sakai, Y and Honda, M and Yamashita, T and Fujinaga, Y and Shinkura, R and Hamaguchi, Y and Mizukoshi, E and Kaneko, S}, title = {Oral Corticosteroids Impair Mucin Production and Alter the Posttransplantation Microbiota in the Gut.}, journal = {Digestion}, volume = {103}, number = {4}, pages = {269-286}, doi = {10.1159/000522039}, pmid = {35184054}, issn = {1421-9867}, mesh = {Adrenal Cortex Hormones ; Animals ; *Colitis, Ulcerative/therapy ; Feces ; Inflammation ; Mice ; *Microbiota ; Mucins ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; }, abstract = {INTRODUCTION: Gut microbiota alterations cause inflammation in patients with ulcerative colitis (UC). Fecal microbiota transplantation (FMT) enables manipulating the microbiota's composition, but the mechanisms underlying colonization of the posttransplantation microbiota are poorly understood.

METHODS: In this open-label, nonrandomized study, the FMT efficacy and changes in the gut microbiota were evaluated in 8 UC patients with mild-to-moderately active endoscopic colonic lesions. Compositional changes in the fecal and mucosal microbiotas between donors and recipients were examined via 16S rRNA-based sequencing. To investigate the effects of oral corticosteroids on microbiota colonization, FMT was performed in germ-free prednisolone (PSL)-administered mice to examine the factors determining colonization.

RESULTS: Four UC patients achieved clinical remission (CR) after FMT, and 3 also achieved endoscopic remission. The fecal microbiotas of the CR patients changed similar to those of the donors after FMT. The mucin-coding gene, MUC2, was less expressed in the colons of the PSL-dependent patients than in the PSL-free patients. In the mice, PSL treatment decreased the fecal mucin production and altered the posttransplantation fecal microbiota composition. Adding either exogenous mucin or the mucin secretagogue, rebamipide, partially alleviated the PSL-induced dysbiosis of the gut microbiota. Administering rebamipide with FMT from healthy donors relieved inflammation in mice with Enterococcus faecium-induced colitis.

CONCLUSION: Colonic mucin controlled the gut microbiota composition, and oral corticosteroid treatment modified the gut microbiota partly by reducing the colonic mucin.}, } @article {pmid35183223, year = {2022}, author = {Yang, M and Liu, Q and Dai, M and Peng, R and Li, X and Zuo, W and Gou, J and Zhou, F and Yu, S and Liu, H and Huang, M}, title = {FOXQ1-mediated SIRT1 upregulation enhances stemness and radio-resistance of colorectal cancer cells and restores intestinal microbiota function by promoting β-catenin nuclear translocation.}, journal = {Journal of experimental & clinical cancer research : CR}, volume = {41}, number = {1}, pages = {70}, pmid = {35183223}, issn = {1756-9966}, mesh = {Animals ; Cell Line, Tumor ; Colorectal Neoplasms/*genetics/pathology ; Female ; Forkhead Transcription Factors/*metabolism ; Gastrointestinal Microbiome ; Humans ; Male ; Mice ; Mice, Nude ; Neoplastic Stem Cells/*metabolism ; Sirtuin 1/*metabolism ; Up-Regulation ; beta Catenin/*metabolism ; }, abstract = {BACKGROUND: Resistance of colorectal cancer (CRC) cells to radiotherapy considerably contributes to poor clinical outcomes of CRC patients. Microarray profiling in this study revealed the differentially expressed forkhead box Q1 (FOXQ1) in CRC, and thus we aimed to illustrate the role of FOXQ1 in CRC by modulating stemness and radio-resistance of CRC cells.

METHODS: CRC and adjacent normal tissues were collected from CRC patients, and the correlation between FOXQ1 expression and CRC prognosis was analyzed. Subsequently, we determined the expression of FOXQ1, sirtuin 1 (SIRT1) and β-catenin in CRC tissues and cell lines. The binding affinity between FOXQ1 and SIRT1 and that between SIRT1 and β-catenin were validated with luciferase reporter gene, Co-IP and ChIP assays. Following a metagenomics analysis of CRC intestinal microbiota, the effects of the FOXQ1/SIRT1/β-catenin axis on CRC stem cell phenotypes and radio-resistance was evaluated in vitro and in vivo through manipulation of gene expression. Besides, mouse feces were collected to examine changes in intestinal microbiota.

RESULTS: FOXQ1 was highly expressed in CRC tissues and cells and positively correlated with poor prognosis of CRC patients. FOXQ1 overexpression contributed to resistance of CRC cells to radiation. Knockdown of FOXQ1 inhibited the stemness of CRC cells and reversed their radio-resistance. FOXQ1 enhanced the transcriptional expression of SIRT1, and SIRT1 enhanced the expression and nuclear translocation of β-catenin. Knockdown of FOXQ1 repressed SIRT1 expression, thus reducing the stemness and radio-resistance of CRC cells. Moreover, FOXQ1 knockdown suppressed CRC xenograft formation in xenograft-bearing nude mice through inhibiting SIRT1 and β-catenin to reduce the content of pathological bacteria that were up-regulated in CRC.

CONCLUSION: FOXQ1-mediated SIRT1 upregulation augments expression and nuclear translocation of β-catenin and benefits CRC-related intestinal pathological bacterial, thereby enhancing the stemness and radio-resistance of CRC cells.}, } @article {pmid35181739, year = {2022}, author = {Liew, KJ and Liang, CH and Lau, YT and Yaakop, AS and Chan, KG and Shahar, S and Shamsir, MS and Goh, KM}, title = {Thermophiles and carbohydrate-active enzymes (CAZymes) in biofilm microbial consortia that decompose lignocellulosic plant litters at high temperatures.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {2850}, pmid = {35181739}, issn = {2045-2322}, mesh = {Archaea/enzymology/genetics ; Bacteria/chemistry/genetics ; Biodiversity ; *Biofilms ; Carbohydrates/*chemistry ; Glycoside Hydrolases/chemistry ; Hot Temperature ; Lignin/*chemistry ; Metagenome/genetics ; Microbial Consortia/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The SKY hot spring is a unique site filled with a thick layer of plant litter. With the advancement of next-generation sequencing, it is now possible to mine many new biocatalyst sequences. In this study, we aimed to (i) identify the metataxonomic of prokaryotes and eukaryotes in microbial mats using 16S and 18S rRNA markers, (ii) and explore carbohydrate degrading enzymes (CAZymes) that have a high potential for future applications. Green microbial mat, predominantly photosynthetic bacteria, was attached to submerged or floating leaves litter. At the spring head, the sediment mixture consisted of plant debris, predominantly brownish-reddish gelatinous microbial mat, pale tan biofilm, and grey-white filament biofilm. The population in the spring head had a higher percentage of archaea and hyperthermophiles than the green mat. Concurrently, we cataloged nearly 10,000 sequences of CAZymes in both green and brown biofilms using the shotgun metagenomic sequencing approach. These sequences include β-glucosidase, cellulase, xylanase, α-N-arabinofuranosidase, α-L-arabinofuranosidase, and other CAZymes. In conclusion, this work elucidated that SKY is a unique hot spring due to its rich lignocellulosic material, often absent in other hot springs. The data collected from this study serves as a repository of new thermostable macromolecules, in particular families of glycoside hydrolases.}, } @article {pmid35181661, year = {2022}, author = {Johansen, J and Plichta, DR and Nissen, JN and Jespersen, ML and Shah, SA and Deng, L and Stokholm, J and Bisgaard, H and Nielsen, DS and Sørensen, SJ and Rasmussen, S}, title = {Genome binning of viral entities from bulk metagenomics data.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {965}, pmid = {35181661}, issn = {2041-1723}, mesh = {Bacteriophages/*classification/genetics ; Gastrointestinal Microbiome/*genetics/physiology ; Gastrointestinal Tract/*virology ; Genome, Viral/genetics ; Humans ; Metagenome/*genetics ; Metagenomics ; Virome/*genetics/physiology ; }, abstract = {Despite the accelerating number of uncultivated virus sequences discovered in metagenomics and their apparent importance for health and disease, the human gut virome and its interactions with bacteria in the gastrointestinal tract are not well understood. This is partly due to a paucity of whole-virome datasets and limitations in current approaches for identifying viral sequences in metagenomics data. Here, combining a deep-learning based metagenomics binning algorithm with paired metagenome and metavirome datasets, we develop Phages from Metagenomics Binning (PHAMB), an approach that allows the binning of thousands of viral genomes directly from bulk metagenomics data, while simultaneously enabling clustering of viral genomes into accurate taxonomic viral populations. When applied on the Human Microbiome Project 2 (HMP2) dataset, PHAMB recovered 6,077 high-quality genomes from 1,024 viral populations, and identified viral-microbial host interactions. PHAMB can be advantageously applied to existing and future metagenomes to illuminate viral ecological dynamics with other microbiome constituents.}, } @article {pmid35181108, year = {2022}, author = {Zhang, J and Liu, S and Sun, H and Jiang, Z and Xu, Y and Mao, J and Qian, B and Wang, L and Mao, J}, title = {Metagenomics-based insights into the microbial community profiling and flavor development potentiality of baijiu Daqu and huangjiu wheat Qu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {152}, number = {}, pages = {110707}, doi = {10.1016/j.foodres.2021.110707}, pmid = {35181108}, issn = {1873-7145}, mesh = {Amylases ; Fermentation ; Metabolic Networks and Pathways ; *Metagenomics ; *Microbiota/genetics ; }, abstract = {Daqu and wheat Qu are saccharification and fermenting agents in Chinese huangjiu and baijiu production. This study aimed to investigate the difference between Daqu and wheat Qu in physicochemical indices, microbial communities, functional genes, and the metabolic network of key microbes responsible for flavor synthesis by whole-metagenome sequencing and metabolite analysis. Herein, physicochemical indices indicated that compared with wheat Qu, Daqu exhibited higher protease and cellulase activity and acidity, and lower glucoamylase and amylase enzyme activity. Metagenomic sequencing reveals that although Daqu and wheat Qu community composition have significant differences at species level, they have similar functional genes. Daqu were enriched in Pediococcus pentosaceus, Weissella paramesenteroides, Rasamsonia emersonii and Byssochlamys spectabilis (22.48% of the total abundance), while wheat Qu harbored greater abundances of Saccharopolyspora (54.78%, Saccharopolyspora rectivirgula, Saccharopolyspora shandongensis, Saccharopolyspora hirsuta, Saccharopolyspora spinose, and Saccharopolyspora erythraea). From a functional perspective, the important functions of Daqu and wheat Qu are both amino acid metabolism and carbohydrate metabolism. Meanwhile, a combined analysis among microbiota, functional genes, and dominant flavors indicated S. shandongensis, S. rectivirgula, and S. spinose might be the main contributor to the synthesis of flavor compounds in wheat Qu, while R. emersonii, W. paramesenteroides, Leuconostoc citreum, Leuconostoc mesenteroides, Weissella cibaria and P. pentosaceus may make the greatest contribution to flavor compounds synthesis in Daqu. This study reveals the microbial and functional dissimilarities of Daqu and wheat Qu, and helps elucidating different metabolic roles of microbes during flavor formation.}, } @article {pmid35181074, year = {2022}, author = {Young Kim, S and Ban, GH and Won Hong, Y and Ji Jang, M and Ae Kim, S}, title = {Microbiome shifts in sprouts (alfalfa, radish, and rapeseed) during production from seed to sprout using 16S rRNA microbiome sequencing.}, journal = {Food research international (Ottawa, Ont.)}, volume = {152}, number = {}, pages = {110896}, doi = {10.1016/j.foodres.2021.110896}, pmid = {35181074}, issn = {1873-7145}, mesh = {*Brassica napus ; Colony Count, Microbial ; Food Microbiology ; Humans ; Medicago sativa ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Raphanus ; Seeds ; }, abstract = {Sprouts harbor high levels of bacteria and have been implicated in massive outbreaks of foodborne illnesses. The elucidation of microbial profiles in sprouts is important; however, little is known about the changes in the microbial composition during production. The present study aimed to define the microbial ecology of sprouts during the stages of production using 16S rRNA metagenome sequencing and culture-dependent methods. Samples of three types of sprouts (alfalfa, radish, and rapeseed) were collected from each stage of production (seed, soaking, germination 1 (Germ 1), germination 2 (Germ 2), sprouting, unwashed, and washed sprouts; n = 105) and subjected to microbiome analyses as well as quantitative and qualitative analyses. Aerobic plate count (APC) and coliforms levels significantly increased within one day (Germ 1) by 3.9-4.4 and 4.2-5.2 log CFU/g, respectively, and levels up to 8.0-9.0 and 6.9-9.0 log CFU/g, respectively, were recorded at the final stage. During production, the microbial communities in alfalfa sprouts simplified into Enterobacteriaceae (80.97-99.29%), whereas the radish and rapeseed sprouts were dominated by microbial communities belonging to two families, the Enterobacteriaceae (radish: 32-43.4%, rapeseed: 24.11-38.39%) and Pseudomonadaceae (radish: 30.53-46.45%, rapeseed: 41.51-57.34%). This suggests that the sprout manufacturing conditions could promote the growth of particular bacterium. Alpha diversity analysis revealed a diverse bacterial community structure in the seeds; however, the diversity sharply declined until Germ 1 and recovered during the production steps thereafter. Beta diversity results suggested that the pattern of microbial composition, and the major shifts in composition, differed by seed type. Significant changes in the bacterial community were observed during the soaking (alfalfa), Germ 1 (radish), and Germ 2 (rapeseed) stages. The present study is the first fundamental report to investigate microbial changes by during the various stages of the sprouting process. The results highlight the potential risk of sprouts regarding foodborne illness and facilitate the determination of effective intervention points during sprout production.}, } @article {pmid35178126, year = {2022}, author = {Chattopadhyay, I and Gundamaraju, R and Jha, NK and Gupta, PK and Dey, A and Mandal, CC and Ford, BM}, title = {Interplay between Dysbiosis of Gut Microbiome, Lipid Metabolism, and Tumorigenesis: Can Gut Dysbiosis Stand as a Prognostic Marker in Cancer?.}, journal = {Disease markers}, volume = {2022}, number = {}, pages = {2941248}, pmid = {35178126}, issn = {1875-8630}, mesh = {*Carcinogenesis ; Dysbiosis/*complications ; *Gastrointestinal Microbiome ; Humans ; *Lipid Metabolism ; Neoplasms/*etiology ; Prognosis ; }, abstract = {The gut bacterial community is involved in the metabolism of bile acids and short-chain fatty acids (SCFAs). Bile acids are involved in the absorption of fat and the regulation of lipid homeostasis through emulsification and are transformed into unconjugated bile acids by the gut microbiota. The gut microbiota is actively involved in the production of bile acid metabolites, such as deoxycholic acid, lithocholic acid, choline, and SCFAs such as acetate, butyrate, and propionate. Metabolites derived from the gut microbiota or modified gut microbiota metabolites contribute significantly to host pathophysiology. Gut bacterial metabolites, such as deoxycholic acid, contribute to the development of hepatocellular carcinoma and colon cancer by factors such as inflammation and oxidative DNA damage. Butyrate, which is derived from gut bacteria such as Megasphaera, Roseburia, Faecalibacterium, and Clostridium, is associated with the activation of Treg cell differentiation in the intestine through histone acetylation. Butyrate averts the action of class I histone deacetylases (HDAC), such as HDAC1 and HDAC3, which are responsible for the transcription of genes such as p21/Cip1, and cyclin D3 through hyperacetylation of histones, which orchestrates G1 cell cycle arrest. It is essential to identify the interaction between the gut microbiota and bile acid and SCFA metabolism to understand their role in gastrointestinal carcinogenesis including colon, gastric, and liver cancer. Metagenomic approaches with bioinformatic analyses are used to identify the bacterial species in the metabolism of bile acids and SCFAs. This review provides an overview of the current knowledge of gut microbiota-derived bile acid metabolism in tumor development and whether it can stand as a marker for carcinogenesis. Additionally, this review assesses the evidence of gut microbiota-derived short-chain fatty acids including butyric acid in antitumor activity. Future research is required to identify the beneficial commensal gut bacteria and their metabolites which will be considered to be therapeutic targets in inflammation-mediated gastrointestinal cancers.}, } @article {pmid35177860, year = {2022}, author = {Fromentin, S and Forslund, SK and Chechi, K and Aron-Wisnewsky, J and Chakaroun, R and Nielsen, T and Tremaroli, V and Ji, B and Prifti, E and Myridakis, A and Chilloux, J and Andrikopoulos, P and Fan, Y and Olanipekun, MT and Alves, R and Adiouch, S and Bar, N and Talmor-Barkan, Y and Belda, E and Caesar, R and Coelho, LP and Falony, G and Fellahi, S and Galan, P and Galleron, N and Helft, G and Hoyles, L and Isnard, R and Le Chatelier, E and Julienne, H and Olsson, L and Pedersen, HK and Pons, N and Quinquis, B and Rouault, C and Roume, H and Salem, JE and Schmidt, TSB and Vieira-Silva, S and Li, P and Zimmermann-Kogadeeva, M and Lewinter, C and Søndertoft, NB and Hansen, TH and Gauguier, D and Gøtze, JP and Køber, L and Kornowski, R and Vestergaard, H and Hansen, T and Zucker, JD and Hercberg, S and Letunic, I and Bäckhed, F and Oppert, JM and Nielsen, J and Raes, J and Bork, P and Stumvoll, M and Segal, E and Clément, K and Dumas, ME and Ehrlich, SD and Pedersen, O}, title = {Microbiome and metabolome features of the cardiometabolic disease spectrum.}, journal = {Nature medicine}, volume = {28}, number = {2}, pages = {303-314}, pmid = {35177860}, issn = {1546-170X}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/L01632X/1/MRC_/Medical Research Council/United Kingdom ; MR/S020039/1/MRC_/Medical Research Council/United Kingdom ; 204834/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; /DH_/Department of Health/United Kingdom ; }, mesh = {*Cardiovascular Diseases ; *Diabetes Mellitus, Type 2 ; Humans ; Longitudinal Studies ; Metabolome ; *Microbiota ; Middle Aged ; }, abstract = {Previous microbiome and metabolome analyses exploring non-communicable diseases have paid scant attention to major confounders of study outcomes, such as common, pre-morbid and co-morbid conditions, or polypharmacy. Here, in the context of ischemic heart disease (IHD), we used a study design that recapitulates disease initiation, escalation and response to treatment over time, mirroring a longitudinal study that would otherwise be difficult to perform given the protracted nature of IHD pathogenesis. We recruited 1,241 middle-aged Europeans, including healthy individuals, individuals with dysmetabolic morbidities (obesity and type 2 diabetes) but lacking overt IHD diagnosis and individuals with IHD at three distinct clinical stages-acute coronary syndrome, chronic IHD and IHD with heart failure-and characterized their phenome, gut metagenome and serum and urine metabolome. We found that about 75% of microbiome and metabolome features that distinguish individuals with IHD from healthy individuals after adjustment for effects of medication and lifestyle are present in individuals exhibiting dysmetabolism, suggesting that major alterations of the gut microbiome and metabolome might begin long before clinical onset of IHD. We further categorized microbiome and metabolome signatures related to prodromal dysmetabolism, specific to IHD in general or to each of its three subtypes or related to escalation or de-escalation of IHD. Discriminant analysis based on specific IHD microbiome and metabolome features could better differentiate individuals with IHD from healthy individuals or metabolically matched individuals as compared to the conventional risk markers, pointing to a pathophysiological relevance of these features.}, } @article {pmid35177633, year = {2022}, author = {Schweitzer, HD and Smith, HJ and Barnhart, EP and McKay, LJ and Gerlach, R and Cunningham, AB and Malmstrom, RR and Goudeau, D and Fields, MW}, title = {Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {7}, pmid = {35177633}, issn = {2055-5008}, mesh = {*Coal ; Metagenomics ; Methane ; *Microbiota ; Sulfates ; }, abstract = {Environmentally relevant metagenomes and BONCAT-FACS derived translationally active metagenomes from Powder River Basin coal seams were investigated to elucidate potential genes and functional groups involved in hydrocarbon degradation to methane in coal seams with high- and low-sulfate levels. An advanced subsurface environmental sampler allowed the establishment of coal-associated microbial communities under in situ conditions for metagenomic analyses from environmental and translationally active populations. Metagenomic sequencing demonstrated that biosurfactants, aerobic dioxygenases, and anaerobic phenol degradation pathways were present in active populations across the sampled coal seams. In particular, results suggested the importance of anaerobic degradation pathways under high-sulfate conditions with an emphasis on fumarate addition. Under low-sulfate conditions, a mixture of both aerobic and anaerobic pathways was observed but with a predominance of aerobic dioxygenases. The putative low-molecular-weight biosurfactant, lichysein, appeared to play a more important role compared to rhamnolipids. The methods used in this study-subsurface environmental samplers in combination with metagenomic sequencing of both total and translationally active metagenomes-offer a deeper and environmentally relevant perspective on community genetic potential from coal seams poised at different redox conditions broadening the understanding of degradation strategies for subsurface carbon.}, } @article {pmid35173154, year = {2022}, author = {Reyman, M and van Houten, MA and Watson, RL and Chu, MLJN and Arp, K and de Waal, WJ and Schiering, I and Plötz, FB and Willems, RJL and van Schaik, W and Sanders, EAM and Bogaert, D}, title = {Effects of early-life antibiotics on the developing infant gut microbiome and resistome: a randomized trial.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {893}, pmid = {35173154}, issn = {2041-1723}, support = {SCAF/16/03/CSO_/Chief Scientist Office/United Kingdom ; }, mesh = {Amoxicillin-Potassium Clavulanate Combination/pharmacology ; Anti-Bacterial Agents/adverse effects/*pharmacology ; Bacteria/*classification/*isolation & purification ; Bifidobacterium/isolation & purification ; Cefotaxime/pharmacology ; Enterococcus/isolation & purification ; Gastrointestinal Microbiome/*drug effects/genetics ; Gentamicins/pharmacology ; Humans ; Infant, Newborn ; Klebsiella/isolation & purification ; Microbial Sensitivity Tests ; Neonatal Sepsis/*drug therapy ; Penicillins/pharmacology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Broad-spectrum antibiotics for suspected early-onset neonatal sepsis (sEONS) may have pronounced effects on gut microbiome development and selection of antimicrobial resistance when administered in the first week of life, during the assembly phase of the neonatal microbiome. Here, 147 infants born at ≥36 weeks of gestational age, requiring broad-spectrum antibiotics for treatment of sEONS in their first week of life were randomized 1:1:1 to receive three commonly prescribed intravenous antibiotic combinations, namely penicillin + gentamicin, co-amoxiclav + gentamicin or amoxicillin + cefotaxime (ZEBRA study, Trial Register NL4882). Average antibiotic treatment duration was 48 hours. A subset of 80 non-antibiotic treated infants from a healthy birth cohort served as controls (MUIS study, Trial Register NL3821). Rectal swabs and/or faeces were collected before and immediately after treatment, and at 1, 4 and 12 months of life. Microbiota were characterized by 16S rRNA-based sequencing and a panel of 31 antimicrobial resistance genes was tested using targeted qPCR. Confirmatory shotgun metagenomic sequencing was executed on a subset of samples. The overall gut microbial community composition and antimicrobial resistance gene profile majorly shift directly following treatment (R[2 ]= 9.5%, adjusted p-value = 0.001 and R[2 ]= 7.5%, adjusted p-value = 0.001, respectively) and normalize over 12 months (R[2] = 1.1%, adjusted p-value = 0.03 and R[2 ]= 0.6%, adjusted p-value = 0.23, respectively). We find a decreased abundance of Bifidobacterium spp. and increased abundance of Klebsiella and Enterococcus spp. in the antibiotic treated infants compared to controls. Amoxicillin + cefotaxime shows the largest effects on both microbial community composition and antimicrobial resistance gene profile, whereas penicillin + gentamicin exhibits the least effects. These data suggest that the choice of empirical antibiotics is relevant for adverse ecological side-effects.}, } @article {pmid35172890, year = {2022}, author = {Zhou, Z and Tran, PQ and Breister, AM and Liu, Y and Kieft, K and Cowley, ES and Karaoz, U and Anantharaman, K}, title = {METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {33}, pmid = {35172890}, issn = {2049-2618}, support = {T15 LM007359/LM/NLM NIH HHS/United States ; T32 GM140935/GM/NIGMS NIH HHS/United States ; }, mesh = {*Genome, Microbial ; Humans ; Lakes ; Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling.

RESULTS: We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric "MW-score" (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut.

CONCLUSION: METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC . Video abstract.}, } @article {pmid35171009, year = {2022}, author = {Dong, B and Lin, X and Jing, X and Hu, T and Zhou, J and Chen, J and Xiao, L and Wang, B and Chen, Z and Liu, J and Hu, Y and Liu, G and Liu, S and Liu, J and Wei, W and Zou, Y}, title = {A Bacterial Genome and Culture Collection of Gut Microbial in Weanling Piglet.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0241721}, pmid = {35171009}, issn = {2165-0497}, support = {201918/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; *Genome, Bacterial ; Male ; Metagenomics ; Phylogeny ; Swine/growth & development/*microbiology ; }, abstract = {The microbiota hosted in the pig gastrointestinal tract are important to health of this biomedical model. However, the individual species and functional repertoires that make up the pig gut microbiome remain largely undefined. Here we comprehensively investigated the genomes and functions of the piglet gut microbiome using culture-based and metagenomics approaches. A collection included 266 cultured genomes and 482 metagenome-assembled genomes (MAGs) that were clustered to 428 species across 10 phyla was established. Among these clustered species, 333 genomes represent potential new species. Less matches between cultured genomes and MAGs revealed a substantial bias for the acquisition of reference genomes by the two strategies. Glycoside hydrolases was the dominant category of carbohydrate-active enzymes. Four-hundred forty-five secondary metabolite biosynthetic genes were predicted from 292 genomes with bacteriocin being the most. Pan genome analysis of Limosilactobacillus reuteri uncover the biosynthesis of reuterin was strain-specific and the production was experimentally determined. This study provides a comprehensive view of the microbiome composition and the function landscape of the gut of weanling piglets and a valuable bacterial resource for further experimentations. IMPORTANCE The microorganism communities resided in mammalian gastrointestinal tract impacted the health and disease of the host. Our study complements metagenomic analysis with culture-based approach to establish a bacteria and genome collection and comprehensively investigate the microbiome composition and function of the gut of weanling piglets. We provide a valuable resource for further study of gut microbiota of weanling piglet and development of probiotics for prevention of disease.}, } @article {pmid35170078, year = {2022}, author = {Zhang, L and Xu, Z and Mak, JWY and Chow, KM and Lui, G and Li, TCM and Wong, CK and Chan, PKS and Ching, JYL and Fujiwara, Y and Chan, FKL and Ng, SC}, title = {Gut microbiota-derived synbiotic formula (SIM01) as a novel adjuvant therapy for COVID-19: An open-label pilot study.}, journal = {Journal of gastroenterology and hepatology}, volume = {37}, number = {5}, pages = {823-831}, pmid = {35170078}, issn = {1440-1746}, support = {//The DH Chen Foundation/ ; }, mesh = {Bacteria ; *COVID-19/therapy ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Immunoglobulin G ; Pilot Projects ; SARS-CoV-2 ; *Synbiotics ; }, abstract = {BACKGROUND AND AIM: Gut dysbiosis is associated with immune dysfunction and severity of COVID-19. Whether targeting dysbiosis will improve outcomes of COVID-19 is unknown. This study aimed to assess the effects of a novel gut microbiota-derived synbiotic formula (SIM01) as an adjuvant therapy on immunological responses and changes in gut microbiota of hospitalized COVID-19 patients.

METHODS: This was an open-label, proof-of-concept study. Consecutive COVID-19 patients admitted to an infectious disease referral center in Hong Kong were given a novel formula of Bifidobacteria strains, galactooligosaccharides, xylooligosaccharide, and resistant dextrin (SIM01). The latter was derived from metagenomic databases of COVID-19 patients and healthy population. COVID-19 patients who were admitted under another independent infectious disease team during the same period without receiving SIM01 acted as controls. All patients received standard treatments for COVID-19 according to the hospital protocol. We assessed antibody response, plasma proinflammatory markers, nasopharyngeal SARS-CoV-2 viral load, and fecal microbiota profile from admission up to week 5.

RESULTS: Twenty-five consecutive COVID-19 patients received SIM01 for 28 days; 30 patients who did not receive the formula acted as controls. Significantly more patients receiving SIM01 than controls developed SARS-CoV-2 IgG antibody (88% vs 63.3%; P = 0.037) by Day 16. One (4%) and 8 patients (26.7%) in the SIM01 and control group, respectively, failed to develop positive IgG antibody upon discharge. At week 5, plasma levels of interleukin (IL)-6, monocyte chemoattractant protein-1 (MCP-1), macrophage colony-stimulating factor (M-CSF), tumor necrosis factor (TNF-α), and IL-1RA reduced significantly in the SIM01 but not in the control group. There was a significant negative correlation of nasopharyngeal SARS-CoV-2 viral load and SIM01 intervention. Metagenomic analysis showed that bacterial species in SIM01 formula were found in greater abundance leading to enrichment of commensal bacteria and suppression of opportunistic pathogens in COVID-19 patients by week 4 and week 5.

CONCLUSIONS: This proof-of-concept study suggested that the use of a novel gut microbiota-derived synbiotic formula, SIM01, hastened antibody formation against SARS-CoV-2, reduced nasopharyngeal viral load, reduced pro-inflammatory immune markers, and restored gut dysbiosis in hospitalised COVID-19 patients.}, } @article {pmid35169130, year = {2022}, author = {Aasmets, O and Krigul, KL and Lüll, K and Metspalu, A and Org, E}, title = {Gut metagenome associations with extensive digital health data in a volunteer-based Estonian microbiome cohort.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {869}, pmid = {35169130}, issn = {2041-1723}, mesh = {Anti-Bacterial Agents/therapeutic use ; *Databases, Factual ; Dysbiosis/chemically induced/microbiology ; Electronic Health Records ; Estonia ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenome/*genetics ; Pharmaceutical Preparations ; Surveys and Questionnaires ; }, abstract = {Microbiome research is starting to move beyond the exploratory phase towards interventional trials and therefore well-characterized cohorts will be instrumental for generating hypotheses and providing new knowledge. As part of the Estonian Biobank, we established the Estonian Microbiome Cohort which includes stool, oral and plasma samples from 2509 participants and is supplemented with multi-omic measurements, questionnaires, and regular linkages to national electronic health records. Here we analyze stool data from deep metagenomic sequencing together with rich phenotyping, including 71 diseases, 136 medications, 21 dietary questions, 5 medical procedures, and 19 other factors. We identify numerous relationships (n = 3262) with different microbiome features. In this study, we extend the understanding of microbiome-host interactions using electronic health data and show that long-term antibiotic usage, independent from recent administration, has a significant impact on the microbiome composition, partly explaining the common associations between diseases.}, } @article {pmid35167588, year = {2022}, author = {Abdill, RJ and Adamowicz, EM and Blekhman, R}, title = {Public human microbiome data are dominated by highly developed countries.}, journal = {PLoS biology}, volume = {20}, number = {2}, pages = {e3001536}, pmid = {35167588}, issn = {1545-7885}, support = {R35 GM128716/GM/NIGMS NIH HHS/United States ; }, mesh = {Asia ; Bangladesh ; Canada ; Developed Countries ; Europe ; Gastrointestinal Microbiome/*genetics ; Genomics/*methods/statistics & numerical data ; Geography ; Humans ; India ; Metagenome/*genetics ; Metagenomics/*methods/statistics & numerical data ; Microbiota/*genetics ; Pakistan ; United States ; }, abstract = {The importance of sampling from globally representative populations has been well established in human genomics. In human microbiome research, however, we lack a full understanding of the global distribution of sampling in research studies. This information is crucial to better understand global patterns of microbiome-associated diseases and to extend the health benefits of this research to all populations. Here, we analyze the country of origin of all 444,829 human microbiome samples that are available from the world's 3 largest genomic data repositories, including the Sequence Read Archive (SRA). The samples are from 2,592 studies of 19 body sites, including 220,017 samples of the gut microbiome. We show that more than 71% of samples with a known origin come from Europe, the United States, and Canada, including 46.8% from the US alone, despite the country representing only 4.3% of the global population. We also find that central and southern Asia is the most underrepresented region: Countries such as India, Pakistan, and Bangladesh account for more than a quarter of the world population but make up only 1.8% of human microbiome samples. These results demonstrate a critical need to ensure more global representation of participants in microbiome studies.}, } @article {pmid35166723, year = {2022}, author = {Pettinelli, P and Arendt, BM and Schwenger, KJP and Sivaraj, S and Bhat, M and Comelli, EM and Lou, W and Allard, JP}, title = {Relationship Between Hepatic Gene Expression, Intestinal Microbiota, and Inferred Functional Metagenomic Analysis in NAFLD.}, journal = {Clinical and translational gastroenterology}, volume = {13}, number = {7}, pages = {e00466}, pmid = {35166723}, issn = {2155-384X}, support = {NMD-86922//CIHR/Canada ; MOP-89705//CIHR/Canada ; }, mesh = {Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Gene Expression ; Humans ; *Insulin Resistance ; *Non-alcoholic Fatty Liver Disease/complications ; }, abstract = {INTRODUCTION: We previously reported a lower fecal abundance of Ruminococcus spp., Faecalibacterium prausnitzii , and Coprococcus spp. in nonalcoholic fatty liver disease (NAFLD). In this article, we assess the associations between hepatic gene expression, the specific taxa, and bacterial pathways.

METHODS: The relationships between hepatic genes that were differentially expressed in patients with NAFLD vs healthy controls (HC) and the abundance of these specific taxa were studied. Inferred functional metagenomic analysis using Piphillin was also performed to investigate associations with bacterial pathways.

RESULTS: Fifteen patients with NAFLD and 6 HC participated. Of 728 hepatic genes examined, 176 correlated with the abundance of Ruminococcus spp., 138 with F. prausnitzii , and 92 with Coprococcus spp. For Ruminococcus spp., genes were enriched in gene ontology (GO) terms related to apoptotic process, response to external and cytokine stimuli, and regulation of signaling. Several genes related to the Kyoto Encyclopedia of Genes and Genomes pathway insulin resistance were correlated with F. prausnitzii . The hepatic genes associated with F. prausnitzii were enriched in GO terms related to cellular response to different stimuli, apoptotic process, and regulation of metabolic pathways. For Coprococcus spp., only the GO term response to external stimulus was enriched. There was a distinct pattern of associations between hepatic genes and bacterial taxa in NAFLD vs HC. For bacterial pathways, 65 and 18 hepatic genes correlated with bacterial metabolic functions in NAFLD and HC, respectively.

DISCUSSION: Hepatic gene expression related to insulin resistance, inflammation, external stimuli, and apoptosis correlated with bacterial taxa. Patients with NAFLD showed a higher presence of bacterial pathways associated with lipid metabolism.}, } @article {pmid35166562, year = {2022}, author = {Ruhl, IA and Sheremet, A and Smirnova, AV and Sharp, CE and Grasby, SE and Strous, M and Dunfield, PF}, title = {Microbial Functional Diversity Correlates with Species Diversity along a Temperature Gradient.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0099121}, pmid = {35166562}, issn = {2379-5077}, mesh = {Temperature ; RNA, Ribosomal, 16S/genetics ; *Bacteria ; Archaea ; *Microbiota ; }, abstract = {Microbial community diversity is often correlated with physical environmental stresses like acidity, salinity, and temperature. For example, species diversity usually declines with increasing temperature above 20°C. However, few studies have examined whether the genetic functional diversity of community metagenomes varies in a similar way as species diversity along stress gradients. Here, we investigated bacterial communities in thermal spring sediments ranging from 21 to 88°C, representing communities of 330 to 3,800 bacterial and archaeal species based on 16S rRNA gene amplicon analysis. Metagenomes were sequenced, and Pfam abundances were used as a proxy for metagenomic functional diversity. Significant decreases in both species diversity and Pfam diversity were observed with increasing temperatures. The relationship between Pfam diversity and species diversity followed a power function with the steepest slopes in the high-temperature, low-diversity region of the gradient. Species additions to simple thermophilic communities added many new Pfams, while species additions to complex mesophilic communities added relatively fewer new Pfams, indicating that species diversity does not approach saturation as rapidly as Pfam diversity does. Many Pfams appeared to have distinct temperature ceilings of 60 to 80°C. This study suggests that temperature stress limits both taxonomic and functional diversity of microbial communities, but in a quantitatively different manner. Lower functional diversity at higher temperatures is probably due to two factors, including (i) the absence of many enzymes not adapted to thermophilic conditions, and (ii) the fact that high-temperature communities are comprised of fewer species with smaller average genomes and, therefore, contain fewer rare functions. IMPORTANCE Only recently have microbial ecologists begun to assess quantitatively how microbial species diversity correlates with environmental factors like pH, temperature, and salinity. However, still, very few studies have examined how the number of distinct biochemical functions of microbial communities, termed functional diversity, varies with the same environmental factors. Our study examined 18 microbial communities sampled across a wide temperature gradient and found that increasing temperature reduced both species and functional diversity, but in different ways. Initially, functional diversity increased sharply with increasing species diversity but eventually plateaued, following a power function. This pattern has been previously predicted in theoretical models, but our study validates this predicted power function with field metagenomic data. This study also presents a unique overview of the distribution of metabolic functions along a temperature gradient, demonstrating that many functions have temperature "ceilings" above which they are no longer found.}, } @article {pmid35165305, year = {2022}, author = {Xu, B and Li, F and Cai, L and Zhang, R and Fan, L and Zhang, C}, title = {A holistic genome dataset of bacteria, archaea and viruses of the Pearl River estuary.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {49}, pmid = {35165305}, issn = {2052-4463}, support = {91951120//National Natural Science Foundation of China (National Science Foundation of China)/ ; 91851210//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Estuaries ; Genome ; *Microbiota/genetics ; Rivers ; *Viruses/genetics ; }, abstract = {Estuaries are one of the most important coastal ecosystems. While microbiomes and viromes have been separately investigated in some estuaries, few studies holistically deciphered the genomes and connections of viruses and their microbial hosts along an estuarine salinity gradient. Here we applied deep metagenomic sequencing on microbial and viral communities in surface waters of the Pearl River estuary, one of China's largest estuaries with strong anthropogenic impacts. Overall, 1,205 non-redundant prokaryotic genomes with ≥50% completeness and ≤10% contamination, and 78,502 non-redundant viral-like genomes were generated from samples of three size fractions and five salinity levels. Phylogenomic analysis and taxonomy classification show that majority of these estuarine prokaryotic and viral genomes are novel at species level according to public databases. Potential connections between the microbial and viral populations were further investigated by host-virus matching. These combined microbial and viral genomes provide an important complement of global marine genome datasets and should greatly facilitate our understanding of microbe-virus interactions, evolution and their implications in estuarine ecosystems.}, } @article {pmid35162506, year = {2022}, author = {Zambrano-Romero, A and Ramirez-Villacis, DX and Trueba, G and Sierra-Alvarez, R and Leon-Reyes, A and Cardenas, P and Ochoa-Herrera, V}, title = {Dynamics of Microbial Communities during the Removal of Copper and Zinc in a Sulfate-Reducing Bioreactor with a Limestone Pre-Column System.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {3}, pages = {}, pmid = {35162506}, issn = {1660-4601}, mesh = {Bioreactors/microbiology ; Calcium Carbonate ; Copper ; *Microbiota ; *Sulfates/chemistry ; Zinc ; }, abstract = {Biological treatment using sulfate-reducing bacteria (SRB) is a promising approach to remediate acid rock drainage (ARD). Our purpose was to assess the performance of a sequential system consisting of a limestone bed filter followed by a sulfate-reducing bioreactor treating synthetic ARD for 375 days and to evaluate changes in microbial composition. The treatment system was effective in increasing the pH of the ARD from 2.7 to 7.5 and removed total Cu(II) and Zn(II) concentrations by up to 99.8% and 99.9%, respectively. The presence of sulfate in ARD promoted sulfidogenesis and changed the diversity and structure of the microbial communities. Methansarcina spp. was the most abundant amplicon sequence variant (ASV); however, methane production was not detected. Biodiversity indexes decreased over time with the bioreactor operation, whereas SRB abundance remained stable. Desulfobacteraceae, Desulfocurvus, Desulfobulbaceae and Desulfovibrio became more abundant, while Desulfuromonadales, Desulfotomaculum and Desulfobacca decreased. Geobacter and Syntrophobacter were enriched with bioreactor operation time. At the beginning, ASVs with relative abundance <2% represented 65% of the microbial community and 21% at the end of the study period. Thus, the results show that the microbial community gradually lost diversity while the treatment system was highly efficient in remediating ARD.}, } @article {pmid35158407, year = {2022}, author = {Besaury, L and Rémond, C}, title = {Culturable and metagenomic approaches of wheat bran and wheat straw phyllosphere's highlight new lignocellulolytic microorganisms.}, journal = {Letters in applied microbiology}, volume = {74}, number = {6}, pages = {840-850}, doi = {10.1111/lam.13676}, pmid = {35158407}, issn = {1472-765X}, support = {//French Region Grand Est, Grand Reims and the European Regional Development Fund./ ; }, mesh = {Bacteria ; *Dietary Fiber/metabolism ; Ecosystem ; *Metagenome ; Metagenomics ; Microbial Consortia/genetics ; }, abstract = {The phyllosphere, defined as the aerial parts of plants, is one of the most prevalent microbial habitats on earth. The microorganisms present on the phyllosphere can have several interactions with the plant. The phyllosphere represents then a unique niche where microorganisms have evolved through time in that stressful environment and may have acquired the ability to degrade lignocellulosic plant cell walls in order to survive to oligotrophic conditions. The dynamic lignocellulolytic potential of two phyllospheric microbial consortia (wheat straw and wheat bran) has been studied. The microbial diversity rapidly changed between the native phyllospheres and the final degrading microbial consortia after 48 h of culture. Indeed, the initial microbial consortia was dominated by the Ralstonia (35·8%) and Micrococcus (75·2%) genera for the wheat bran and wheat straw whereas they were dominated by Candidatus phytoplasma (59%) and Acinetobacter (31·8%) in the final degrading microbial consortia respectively. Culturable experiments leading to the isolation of several new lignocellulolytic isolates (belonging to Moraxella and Atlantibacter genera) and metagenomic reconstruction of the microbial consortia highlighted the existence of an unpredicted microbial diversity involved in lignocellulose fractionation but also the existence of new pathways in known genera (presence of CE2 for Acinetobacter, several AAs for Pseudomonas and several GHs for Bacillus in different metagenomes-assembled genomes). The phyllosphere from agricultural co-products represents then a new niche as a lignocellulolytic degrading ecosystem.}, } @article {pmid35157108, year = {2023}, author = {Mo, S and He, S and Sang, Y and Li, J and Kashif, M and Zhang, Z and Su, G and Jiang, C}, title = {Integration of Microbial Transformation Mechanism of Polyphosphate Accumulation and Sulfur Cycle in Subtropical Marine Mangrove Ecosystems with Spartina alterniflora Invasion.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {478-494}, pmid = {35157108}, issn = {1432-184X}, support = {31760437//National Natural Science Foundation of China/ ; GUIKEZY21195021//Funding Project of Chinese Central Government Guiding to the Guangxi Local Science and Technology Development/ ; 2019GXNSFFA245011//Natural Science Fund for Distinguished Young Scholars of Guangxi Zhuang Autonomous Region of China/ ; AD20297142//China-ASEAN International Innovative Center for Health Industry of Traditional Chinese Medicine/ ; 2022KA02//Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University/ ; YCBZ2021012//Innovation Project of Guangxi Graduate Education/ ; YCSW2021064//Innovation Project of Guangxi Graduate Education/ ; }, mesh = {*Wetlands ; Polyphosphates/analysis/metabolism ; Phylogeny ; Introduced Species ; Nitrogen/metabolism ; Phosphorus/metabolism ; Poaceae ; *Microbiota ; Sulfur/metabolism ; Sulfates/metabolism ; China ; }, abstract = {Excessive phosphorus can lead to eutrophication in marine and coastal ecosystems. Sulfur metabolism-associated microorganisms stimulate biological phosphorous removal. However, the integrating co-biotransformation mechanism of phosphorus and sulfur in subtropical marine mangrove ecosystems with Spartina alterniflora invasion is poorly understood. In this study, an ecological model of the coupling biotransformation of sulfur and phosphorus is constructed using metagenomic analysis and quantitative polymerase chain reaction strategies. Phylogenetic analysis profiling, a distinctive microbiome with high frequencies of Gammaproteobacteria and Deltaproteobacteria, appears to be an adaptive characteristic of microbial structures in subtropical mangrove ecosystems. Functional analysis reveals that the levels of sulfate reduction, sulfur oxidation, and poly-phosphate (Poly-P) aggregation decrease with increasing depth. However, at depths of 25-50 cm in the mangrove ecosystems with S. alterniflora invasion, the abundance of sulfate reduction genes, sulfur oxidation genes, and polyphosphate kinase (ppk) significantly increased. A strong positive correlation was found among ppk, sulfate reduction, sulfur oxidation, and sulfur metabolizing microorganisms, and the content of sulfide was significantly and positively correlated with the abundance of ppk. Further microbial identification suggested that Desulfobacterales, Anaerolineales, and Chromatiales potentially drove the coupling biotransformation of phosphorus and sulfur cycling. In particular, Desulfobacterales exhibited dominance in the microbial community structure. Our findings provided insights into the simultaneous co-biotransformation of phosphorus and sulfur bioconversions in subtropical marine mangrove ecosystems with S. alterniflora invasion.}, } @article {pmid35156268, year = {2022}, author = {Wang, H and Li, J and Liang, X and Tao, S and Wu, Z and Wei, G}, title = {Taxonomic and functional diversity of Dendrobium officinale microbiome in Danxia habitat.}, journal = {Journal of applied microbiology}, volume = {132}, number = {5}, pages = {3758-3770}, doi = {10.1111/jam.15488}, pmid = {35156268}, issn = {1365-2672}, mesh = {*Basidiomycota/genetics ; *Dendrobium/genetics/microbiology ; Humans ; Metagenomics ; *Microbiota/genetics ; Plant Roots/microbiology ; Plants ; Rhizosphere ; Soil Microbiology ; }, abstract = {AIMS: Microbial communities that inhabit plants are crucial for plant survival and well-being including growth in stressful environments. The medicinal plant, Dendrobium officinale grows in the barren soils of the Danxia Habitat. However, the microbiome composition and functional potential for growth of this plant in this environment are still unexplored.

METHODS AND RESULTS: In this study, we analysed the taxonomic and functional diversity of the D. officinale Microbiome by metagenomic sequencing of both rhizosphere and endosphere samples. A total of 155 phyla, 122 classes, 271 orders, 620 families and 2194 genera were identified from all samples. The rhizospheric microbes (DXRh) were mainly composed of Proteobacteria and Acidobacteria, while Basidiomycota and Ascomycota were the most dominant phyla in root endosphere (DXRo) and stem endosphere (DXS), respectively. Most of the dominant microbial communities had been reported to have diverse functional potentials that can help plant growth and development in stressful and nutrient-deprived ecological environmental. These include plant growth promoting rhizobacteria (PGPR) such as Massilia, Pseudomonas, Bradyrhizobium, Klebsiella, Streptomyces, Leclercia, Paenibacillus, Frankia and Enterobacter in the DXRh, Tulasnella and Serendipita in the DXRo, Colletotrichum and Burkholderia in the DXS and Paraburkholderia, Rhizophagus and Acetobacter in endosphere. Analysis using the KEGG, eggNOG and CAZy databases showed that metabolic pathways such as carbohydrate metabolism, amino acid metabolism, energy metabolism, genetic information processing and environmental information processing are significantly abundant, which may be related to the survival, growth and development of D. officinale in a stressful environment.

CONCLUSIONS: We speculated that the microbial community with diverse taxonomic structures and metabolic functions inhabiting in different niches of plants supports the survival and growth of D. officinale in the stressful environment of Danxia Habitat.

This study provided an important data resource for microbes associated with D. officinale and theoretical foundation for further studies.}, } @article {pmid36212901, year = {2021}, author = {Shifera, AS and Pockrandt, C and Rincon, N and Ge, Y and Lu, J and Varabyou, A and Jedlicka, AE and Sun, K and Scott, AL and Eberhart, C and Thorne, JE and Salzberg, SL}, title = {Identification of microbial agents in tissue specimens of ocular and periocular sarcoidosis using a metagenomics approach.}, journal = {F1000Research}, volume = {10}, number = {}, pages = {820}, pmid = {36212901}, issn = {2046-1402}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; *Sarcoidosis/diagnosis/genetics ; }, abstract = {Background: Metagenomic sequencing has the potential to identify a wide range of pathogens in human tissue samples. Sarcoidosis is a complex disorder whose etiology remains unknown and for which a variety of infectious causes have been hypothesized. We sought to conduct metagenomic sequencing on cases of ocular and periocular sarcoidosis, none of them with previously identified infectious causes. Methods: Archival tissue specimens of 16 subjects with biopsies of ocular and periocular tissues that were positive for non-caseating granulomas were used as cases. Four archival tissue specimens that did not demonstrate non-caseating granulomas were also included as controls. Genomic DNA was extracted from tissue sections. DNA libraries were generated from the extracted genomic DNA and the libraries underwent next-generation sequencing. Results: We generated between 4.8 and 20.7 million reads for each of the 16 cases plus four control samples. For eight of the cases, we identified microbial pathogens that were present well above the background, with one potential pathogen identified for seven of the cases and two possible pathogens for one of the cases. Five of the eight cases were associated with bacteria (Campylobacter concisus, Neisseria elongata, Streptococcus salivarius, Pseudopropionibacterium propionicum, and Paracoccus yeei), two cases with fungi (Exophiala oligosperma, Lomentospora prolificans and Aspergillus versicolor) and one case with a virus (Mupapillomavirus 1). Interestingly, four of the five bacterial species are also part of the human oral microbiome. Conclusions: Using a metagenomic sequencing we identified possible infectious causes in half of the ocular and periocular sarcoidosis cases analyzed. Our findings support the proposition that sarcoidosis could be an etiologically heterogenous disease. Because these are previously banked samples, direct follow-up in the respective patients is impossible, but these results suggest that sequencing may be a valuable tool in better understanding the etiopathogenesis of sarcoidosis and in diagnosing and treating this disease.}, } @article {pmid35154087, year = {2021}, author = {Song, L and Huang, Y and Liu, G and Li, X and Xiao, Y and Liu, C and Zhang, Y and Li, J and Xu, J and Lu, S and Ren, Z}, title = {A Novel Immunobiotics Bacteroides dorei Ameliorates Influenza Virus Infection in Mice.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {828887}, pmid = {35154087}, issn = {1664-3224}, mesh = {Animals ; Bacteroides/*immunology ; Biomarkers ; Brain-Gut Axis/immunology ; Cytokines/blood/metabolism ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/immunology ; Host-Pathogen Interactions/*immunology ; Immunomodulation ; Influenza A virus/*physiology ; Interferons/metabolism ; Metagenome ; Metagenomics/methods ; Mice ; Microbial Interactions/*immunology ; Orthomyxoviridae Infections/*immunology/metabolism/pathology/*virology ; Probiotics ; Quercetin/metabolism ; Viral Load ; }, abstract = {OBJECTIVE: Probiotics can modulate immune responses to resist influenza infection. This study aims to evaluate the anti-viral efficacy of B. dorei.

METHODS: C57BL/6J mice were infected with influenza virus together with treatment of PBS vehicle, B. dorei, or oseltamivir respectively. Anti-influenza potency of B. dorei and the underlying mechanism were determined by measuring survival rate, lung viral load and pathology, gene expression and production of cytokines and chemokines, and analysis of gut microbiota.

RESULTS: Administration of B. dorei increased (by 30%) the survival of influenza-infected mice, and improved their weight loss, lung pathology, lung index, and colon length compared to the vehicle control group. B. dorei treatment reduced (by 61%) the viral load of lung tissue and increased expression of type 1 interferon more rapidly at day 3 postinfection. At day 7 postinfection, B. dorei-treated mice showed lower local (lung) and systemic (serum) levels of interferon and several proinflammatory cytokines or chemokines (IL-1β, IL-6, TNF-α, IL-10, MCP-1 and IP-10) with a efficacy comparable to oseltamivi treatment. B. dorei treatment also altered gut microbiota as indicated by increased levels of Bacteroides, Prevotella, and Lactobacillus and decreased levels of Escherichia, Shigella, and Parabacteroides.

CONCLUSION: B. dorei has anti-influenza effect. Its working mechanisms involve promoting earlier interferon expression and down-regulating both local and systemic inflammatory response. B. dorei changes the composition of gut microbiota, which may also contribute to its beneficial effects.}, } @article {pmid35152539, year = {2022}, author = {Klein, F and Wellhöner, F and Plumeier, I and Kahl, S and Chhatwal, P and Vital, M and Voigtländer, T and Pieper, DH and Manns, MP and Lenzen, H and Solbach, P and Heidrich, B}, title = {The biliary microbiome in ischaemic-type biliary lesions can be shaped by stenting but is resilient to antibiotic treatment.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {42}, number = {5}, pages = {1070-1083}, doi = {10.1111/liv.15194}, pmid = {35152539}, issn = {1478-3231}, mesh = {Anti-Bacterial Agents/therapeutic use ; *Biliary Tract ; Humans ; Ischemia ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {This study aims to characterize the biliary microbiome as neglected factor in patients with ischaemic-type biliary lesions (ITBL) after liver transplantation. Therefore, the V1-V2 region of the 16S rRNA gene was sequenced in 175 bile samples. Samples from patients with anastomotic strictures (AS) served as controls. Multivariate analysis and in silico metagenomics were applied cross-sectionally and longitudinally. The microbial community differed significantly between ITBL and AS in terms of alpha and beta diversity. Both, antibiotic treatment and stenting were associated independently with differences in the microbial community structure. In contrast to AS, in ITBL stenting was associated with pronounced differences in the biliary microbiome, whereas no differences associated with antibiotic treatment could be observed in ITBL contrasting the pronounced differences found in AS. Bacterial pathways involved in the production of antibacterial metabolites were increased in ITBL with antibiotic treatment. After liver transplantation, the biliary tract harbours a complex microbial community with significant differences between ITBL and AS. Fundamental changes in the microbial community in ITBL can be achieved with biliary stenting. However, the effect of antibiotic treatment in ITBL was minimal. Therefore, antibiotics should be administered wisely in order to reduce emerging resistance of the biliary microbiome towards external antibiotics.}, } @article {pmid35151268, year = {2022}, author = {Da Silva, K and Guilly, S and Thirion, F and Le Chatelier, E and Pons, N and Roume, H and Quinquis, B and Ehrlich, SD and Bekkat, N and Mathiex-Fortunet, H and Sokol, H and Doré, J}, title = {Long-term diosmectite use does not alter the gut microbiota in adults with chronic diarrhea.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {54}, pmid = {35151268}, issn = {1471-2180}, mesh = {Adolescent ; Adult ; Bacteria/classification/genetics ; Chronic Disease/therapy ; Diarrhea/*drug therapy ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/*genetics ; Humans ; Male ; *Metagenome ; Middle Aged ; Silicates/*therapeutic use ; Young Adult ; }, abstract = {BACKGROUND: Diosmectite, a natural colloidal clay, has been used worldwide for a number of approved indications, including the treatment of chronic functional diarrhea. Here, we used high-resolution whole metagenome shotgun sequencing to assess the impact of a 5 weeks administration of diosmectite (3 g/sachet, 3 sachets/day) on the fecal microbiota of 35 adults with functional chronic diarrhea.

RESULTS: Gut microbiota was not impacted by diosmectite administration. In particular, richness remained stable and no microbial species displayed a significant evolution. Segregating patients either by diosmectite response (non responder, early responder, late responder) or by nationality (Great-Britain or Netherlands) yielded the same results.

CONCLUSION: We concluded that no microbiota-related physiological alterations are expected upon long-term treatment with diosmectite.

TRIAL REGISTRATION: Clinicaltrials.gov NCT03045926.}, } @article {pmid35151255, year = {2022}, author = {Qi, Q and Liu, YN and Lv, SY and Wu, HG and Zhang, LS and Cao, Z and Liu, HR and Wang, XM and Wu, LY}, title = {Gut microbiome alterations in colitis rats after moxibustion at bilateral Tianshu acupoints.}, journal = {BMC gastroenterology}, volume = {22}, number = {1}, pages = {62}, pmid = {35151255}, issn = {1471-230X}, support = {2015CB554501//National Basic Research Program of China (973 program)/ ; 20ZR1453100//Natural Science Foundation of Shanghai/ ; 81473758//National Natural Science Foundation of China/ ; 81674074//National Natural Science Foundation of China/ ; ZY(2018-2020)-CCCX-2004-01//Three-year Action Plan Project of Shanghai Traditional Chinese Medicine Development/ ; }, mesh = {Acupuncture Points ; Animals ; *Colitis/chemically induced/therapy ; *Colitis, Ulcerative/therapy ; Dextran Sulfate ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Male ; *Moxibustion ; Rats ; }, abstract = {BACKGROUND: The pathogenesis of ulcerative colitis (UC) is closely related to the gut microbiota. Moxibustion has been used to improve the inflammation and gastrointestinal dysfunctions in gastrointestinal disorders such as UC. In this study, we investigated whether moxibustion could improve the gut microbial dysbiosis induced by dextran sulphate sodium.

METHODS: Twenty-five male rats were randomly assigned into five groups. The UC rat model was established by administering DSS solution. The rats in the moxibustion and normal rats with moxibustion groups were treated with moxibustion at Tianshu (bilateral, ST25) points, and the mesalazine group rats were treated with mesalazine once daily for 7 consecutive days. Disease activity index (DAI) and haematoxylin and eosin staining were used to evaluate the effect of moxibustion. Gut microbiota profiling was conducted by metagenomic high throughput sequencing technology. The gut microbiota composition, diversity and function were analyzed and compared using metagenomics methodologies.

RESULTS: The DAI scores and histopathology scores in the moxibustion and mesalazine groups were significantly decreased compared with the UC group (P < 0.01). Moxibustion treatment increased abundance levels of Bacteroidetes, Actinobacteria, Ascomycota, Synergistetes and decreased abundance of Firmicutes, Proteobacteria. At the genus level, the abundance of Bacteroides, Bacteroides_bacterium_M7, Prevotella, Bacteroidales_bacterium_H2, were increased and Bacteroides_bacterium_H3, Parabacteroides, Porphyromonas, Alistipes, Parasutterella were decreased in the UC group in comparsion with those in the NG group. Moxibustion increased the abundance of Bacteroides and Bacteroides_bacterium_H3 and decreased Bacteroides_bacterium_M7, Prevotella, Bacteroidales_bacterium_H2. In UC group, the specie Bacteroides_massiliensis was negatively (P < 0.05) correlated with IL-23, Bacteroides_eggerthii_CAG109 and Bacteroides_eggerthii were negatively (P < 0.05) correlated with TGF-β. And the species Prevotella_sp_CAG1031 and Bacteroides_bacterium_H2 were significant positively (P < 0.05) correlated with IL-23. In addition, compare with the normal group, genes involved in certain metabolic pathways, such as energy production and conversion, amino acid transport and metabolism, carbohydrate transport and metabolism, were under-represented in the UC group, and these changes in the metabolic pathways could be reversed by moxibustion treatment and mesalazine treatment.

CONCLUSIONS: Our findings suggest that moxibustion treatment may protect the host from mucosal inflammation by modulating the intestinal microbiota community.}, } @article {pmid35148177, year = {2022}, author = {He, J and Chu, Y and Li, J and Meng, Q and Liu, Y and Jin, J and Wang, Y and Wang, J and Huang, B and Shi, L and Shi, X and Tian, J and Zhufeng, Y and Feng, R and Xiao, W and Gan, Y and Guo, J and Shao, C and Su, Y and Hu, F and Sun, X and Yu, J and Kang, Y and Li, Z}, title = {Intestinal butyrate-metabolizing species contribute to autoantibody production and bone erosion in rheumatoid arthritis.}, journal = {Science advances}, volume = {8}, number = {6}, pages = {eabm1511}, pmid = {35148177}, issn = {2375-2548}, mesh = {Animals ; Anti-Inflammatory Agents/therapeutic use ; *Arthritis, Rheumatoid/drug therapy ; Butyrates/therapeutic use ; *Gastrointestinal Microbiome ; Humans ; Mice ; T-Lymphocytes, Regulatory/metabolism ; }, abstract = {The imbalance between pathogenic and beneficial species of the intestinal microbiome and metabolism in rheumatoid arthritis (RA) remains unclarified. Here, using shotgun-based metagenome sequencing for a treatment-naïve patient cohort and a "quasi-paired cohort" method, we observed a deficiency of butyrate-producing species and an overwhelming number of butyrate consumers in RA patients. These outcomes mainly occurred in patients with positive ACPA, with a mean AUC of 0.94. This panel was also validated in established RA with an AUC of 0.986 in those with joint deformity. In addition, we showed that butyrate promoted Tregs, while suppressing Tconvs and osteoclasts, due to potentiation of the reduction in HDAC expression and down-regulation of proinflammatory cytokine genes. Dietary butyrate supplementation conferred anti-inflammatory benefits in a mouse model by rebalancing TFH cells and Tregs, as well as reducing antibody production. These findings reveal the critical role of butyrate-metabolizing species and suggest the potential of butyrate-based therapies for RA patients.}, } @article {pmid35147634, year = {2022}, author = {Song, Y and Sun, L and Ma, P and Xu, L and Xiao, P}, title = {Dihydromyricetin prevents obesity via regulating bile acid metabolism associated with the farnesoid X receptor in ob/ob mice.}, journal = {Food & function}, volume = {13}, number = {5}, pages = {2491-2503}, doi = {10.1039/d1fo03971g}, pmid = {35147634}, issn = {2042-650X}, mesh = {Animals ; Disease Models, Animal ; Flavones/*pharmacology/therapeutic use ; Flavonols/*pharmacology/therapeutic use ; Gastrointestinal Microbiome/drug effects ; Lipid Metabolism/drug effects ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Obese ; Obesity/*prevention & control ; Receptors, Cytoplasmic and Nuclear/metabolism ; }, abstract = {With the high incidence of obesity around the globe, the potential role of bile acid metabolism and gut microbiota in modulating obesity aroused great enthusiasm. Here we studied the anti-obesity effect of dihydromyricetin (DHM), the main biologically active component in Ampelopsis grossedentata, which was applied for thousands of years in the form of tea beverages. A 12-week treatment of DHM significantly reduced body weight gain of the ob/ob mice. Meanwhile, serum parameters that are closely associated with obesity, including levels of total cholesterol, triglyceride, low density lipoprotein, nonestesterified fatty acid, and activity of alanine amino transferase and aspartate aminotransferase were all lower than the non-treated ob/ob mice. Using LC-MS/MS technology, we determined that DHM could enhance the bile acid (BA) conjugation, BA transport in the liver and inhibit the reabsorption of BAs in the ileum mediated by farnesoid X receptor (FXR)-related signalling pathways. Key genes in regulating enterohepatic circulation of BAs were verified by qPCR, and regulators related to FXR pathway were verified by western-blot. We also found that DHM could effectively inhibit the de novo lipogenesis through FXR-SREBP-1C pathway in the liver. In addition, metagenome analysis of the microbiota showed that DHM may affect the activity of bile salt hydrolase by inhibiting the level of Lactobacillus. In summary, the anti-obesity effect of DHM may be attributed to its positive effects on BA metabolism associated with FXR activation.}, } @article {pmid35145519, year = {2022}, author = {Huang, Y and Zhu, N and Zheng, X and Liu, Y and Lu, H and Yin, X and Hao, H and Tan, Y and Wang, D and Hu, H and Liang, Y and Li, X and Hu, Z and Yin, Y}, title = {Intratumor Microbiome Analysis Identifies Positive Association Between Megasphaera and Survival of Chinese Patients With Pancreatic Ductal Adenocarcinomas.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {785422}, pmid = {35145519}, issn = {1664-3224}, mesh = {Aged ; Aged, 80 and over ; Animals ; Biomarkers ; Carcinoma, Pancreatic Ductal/*mortality/*pathology/therapy ; China ; Cytokines/metabolism ; Disease Models, Animal ; Dysbiosis ; Female ; Humans ; Immunohistochemistry ; Male ; *Megasphaera/classification/genetics ; Metabolic Networks and Pathways ; Metagenome ; Metagenomics/methods ; Mice ; *Microbiota ; Middle Aged ; Molecular Targeted Therapy ; Neoplasm Staging ; Pancreatic Neoplasms/*mortality/*pathology/therapy ; Prognosis ; Treatment Outcome ; *Tumor Microenvironment ; }, abstract = {Human tumors harbor a plethora of microbiota. It has been shown that the composition and diversity of intratumor microbiome are significantly associated with the survival of patients with pancreatic ductal adenocarcinoma (PDAC). However, the association in Chinese patients as well as the effect of different microorganisms on inhibiting tumor growth are unclear. In this study, we collected tumor samples resected from long-term and short-term PDAC survivors and performed 16S rRNA amplicon sequencing. We found that the microbiome in samples with different survival time were significantly different, and the differential bacterial composition was associated with the metabolic pathways in the tumor microenvironment. Furthermore, administration of Megasphaera, one of the differential bacteria, induced a better tumor growth inhibition effect when combined with the immune checkpoint inhibitor anti-programmed cell death-1 (anti-PD-1) treatment in mice bearing 4T1 tumor. These results indicate that specific intratumor microbiome can enhance the anti-tumor effect in the host, laying a foundation for further clarifying the underlying detailed mechanism.}, } @article {pmid35145088, year = {2022}, author = {Tong, F and Wang, T and Gao, NL and Liu, Z and Cui, K and Duan, Y and Wu, S and Luo, Y and Li, Z and Yang, C and Xu, Y and Lin, B and Yang, L and Pauciullo, A and Shi, D and Hua, G and Chen, WH and Liu, Q}, title = {The microbiome of the buffalo digestive tract.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {823}, pmid = {35145088}, issn = {2041-1723}, mesh = {Animals ; Bacteria/genetics ; Cattle ; DNA, Bacterial ; Dietary Fiber/metabolism ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics/*physiology ; Gastrointestinal Tract/*microbiology ; Genome, Microbial ; High-Throughput Nucleotide Sequencing ; Male ; *Metagenome ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rumen/microbiology ; }, abstract = {Buffalo is an important livestock species. Here, we present a comprehensive metagenomic survey of the microbial communities along the buffalo digestive tract. We analysed 695 samples covering eight different sites in three compartments (four-chambered stomach, intestine, and rectum). We mapped ~85% of the raw sequence reads to 4,960 strain-level metagenome-assembled genomes (MAGs) and 3,255 species-level MAGs, 90% of which appear to correspond to new species. In addition, we annotated over 5.8 million nonredundant proteins from the MAGs. In comparison with the rumen microbiome of cattle, the buffalo microbiota seems to present greater potential for fibre degradation and less potential for methane production. Our catalogue of microbial genomes and the encoded proteins provides insights into microbial functions and interactions at distinct sites along the buffalo digestive tract.}, } @article {pmid35143795, year = {2022}, author = {Yang, P and Hao, S and Han, M and Xu, J and Yu, S and Chen, C and Zhang, H and Ning, K}, title = {Analysis of antibiotic resistance genes reveals their important roles in influencing the community structure of ocean microbiome.}, journal = {The Science of the total environment}, volume = {823}, number = {}, pages = {153731}, doi = {10.1016/j.scitotenv.2022.153731}, pmid = {35143795}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microbiota ; Oceans and Seas ; }, abstract = {Antibiotic resistance gene (ARG) content is a well-established driver of microbial abundance and diversity in an environment. By reanalyzing 132 metagenomic datasets from the Tara Oceans project, we aim to unveil the associations between environmental factors, the ocean microbial community structure and ARG contents. We first investigated the structural patterns of microbial communities including both prokaryotes such as bacteria and eukaryotes such as protists. Additionally, several ARG-dominant horizontal gene transfer events between Protist and Prokaryote have been identified, indicating the potential roles of ARG in shaping the ocean microbial communities. For a deeper insight into the role of ARGs in ocean microbial communities on a global scale, we identified 1926 unique types of ARGs and discovered that the ARGs are more abundant and diverse in the mesopelagic zone than other water layers, potentially caused by limited resources. Finally, we found that ARG-enriched genera were often more abundant compared to their ARG-less neighbors in the same environment (e.g. coastal oceans). A deeper understanding of the ARG-microbiome relationships could help in the conservation of the oceanic ecosystem.}, } @article {pmid35140064, year = {2022}, author = {Ng, SC and Peng, Y and Zhang, L and Mok, CK and Zhao, S and Li, A and Ching, JY and Liu, Y and Yan, S and Chan, DLS and Zhu, J and Chen, C and Fung, AC and Wong, KK and Hui, DS and Chan, FK and Tun, HM}, title = {Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events.}, journal = {Gut}, volume = {71}, number = {6}, pages = {1106-1116}, pmid = {35140064}, issn = {1468-3288}, mesh = {Adult ; Antibodies, Neutralizing ; Antibodies, Viral ; BNT162 Vaccine ; *COVID-19/prevention & control ; COVID-19 Vaccines/adverse effects ; *Gastrointestinal Microbiome ; Humans ; Immunogenicity, Vaccine ; Prospective Studies ; SARS-CoV-2 ; Vaccines, Synthetic ; mRNA Vaccines ; }, abstract = {OBJECTIVE: The gut microbiota plays a key role in modulating host immune response. We conducted a prospective, observational study to examine gut microbiota composition in association with immune responses and adverse events in adults who have received the inactivated vaccine (CoronaVac; Sinovac) or the mRNA vaccine (BNT162b2; BioNTech; Comirnaty).

DESIGN: We performed shotgun metagenomic sequencing in stool samples of 138 COVID-19 vaccinees (37 CoronaVac and 101 BNT162b2 vaccinees) collected at baseline and 1 month after second dose of vaccination. Immune markers were measured by SARS-CoV-2 surrogate virus neutralisation test and spike receptor-binding domain IgG ELISA.

RESULTS: We found a significantly lower immune response in recipients of CoronaVac than BNT162b2 vaccines (p<0.05). Bifidobacterium adolescentis was persistently higher in subjects with high neutralising antibodies to CoronaVac vaccine (p=0.023) and their baseline gut microbiome was enriched in pathways related to carbohydrate metabolism (linear discriminant analysis (LDA) scores >2 and p<0.05). Neutralising antibodies in BNT162b2 vaccinees showed a positive correlation with the total abundance of bacteria with flagella and fimbriae including Roseburia faecis (p=0.028). The abundance of Prevotella copri and two Megamonas species were enriched in individuals with fewer adverse events following either of the vaccines indicating that these bacteria may play an anti-inflammatory role in host immune response (LDA scores>3 and p<0.05).

CONCLUSION: Our study has identified specific gut microbiota markers in association with improved immune response and reduced adverse events following COVID-19 vaccines. Microbiota-targeted interventions have the potential to complement effectiveness of COVID-19 vaccines.}, } @article {pmid35139923, year = {2022}, author = {Yang, S and Liu, Y and Yang, N and Lan, Y and Lan, W and Feng, J and Yue, B and He, M and Zhang, L and Zhang, A and Price, M and Li, J and Fan, Z}, title = {The gut microbiome and antibiotic resistome of chronic diarrhea rhesus macaques (Macaca mulatta) and its similarity to the human gut microbiome.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {29}, pmid = {35139923}, issn = {2049-2618}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Diarrhea/drug therapy/microbiology/veterinary ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Macaca mulatta ; *Microbiota ; }, abstract = {BACKGROUND: Chronic diarrhea is a common disease causing morbidity and mortality of captive rhesus macaques (RMs, Macaca mulatta). Chronic diarrhea in RMs is typically characterized by long-term diarrhea and a weak response to antibiotic treatment. Diarrhea is also a common disease in humans and can cause death. However, the etiology of about half of diarrheal cases of humans is still unclear. Therefore, we performed shotgun metagenomic sequencing to characterize the differences in the gut microbiome and resistome of chronic diarrhea RMs and asymptomatic individuals.

RESULTS: Our results showed Lactobacillus spp. (mainly L. johnsonii, L. reuteri and L. amylovorus) were significantly depleted in chronic diarrhea RM guts compared to asymptomatic individuals (5.2 vs 42.4%). Functional annotation of genes suggested these Lactobacillus spp. carried genes involved in the adhesion of intestinal epithelial cells and production of bacteriocin. Chronic diarrhea RM guts also had a significantly greater abundance of many other gut bacteria, including mucin-degrading bacteria and opportunistic pathogens. The metabolic pathways of chronic diarrhea RM gut microbiome were enriched in aerobactin biosynthesis, while the metabolic pathways of asymptomatic RM gut microbiome were enriched in the production of short-chain fatty acids (SCFAs). Chronic diarrhea RM guts had a significantly greater abundance of antibiotic resistance genes (ARGs), such as ermF, aph(3')-IIIa, ermB, and floR. The strains isolated from feces and tissue fluid of chronic diarrhea RMs had higher resistance rates to the majority of tested antibiotics, but not cephamycin and carbapenem antibiotics. Gut microbial composition comparisons showed that several captive nonhuman primate (NHP) guts were more similar to the guts of humans with a non-westernized diet than humans with a westernized diet. Chronic diarrhea RM gut microbiome was strikingly similar to rural-living humans with diarrhea and humans with a non-westernized diet than asymptomatic RMs.

CONCLUSIONS: Our results suggested chronic diarrhea significantly altered the composition and metabolic pathways of the RM gut microbiome. The frequent use of antibiotics caused antibiotic resistance in chronic diarrhea RM gut microbiome with serious consequences for individual treatment and survival. The findings of this study will help us to improve the effective prevention and treatment of diarrhea in RMs. Video Abstract.}, } @article {pmid35139420, year = {2022}, author = {Sudagidan, M and Ozalp, VC and Can, Ö and Eligül, H and Yurt, MNZ and Tasbasi, BB and Acar, EE and Kavruk, M and Koçak, O}, title = {Surface microbiota and associated staphylococci of houseflies (Musca domestica) collected from different environmental sources.}, journal = {Microbial pathogenesis}, volume = {164}, number = {}, pages = {105439}, doi = {10.1016/j.micpath.2022.105439}, pmid = {35139420}, issn = {1096-1208}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Female ; *Houseflies ; Male ; *Microbiota ; Oxacillin ; Staphylococcus ; Staphylococcus epidermidis/genetics ; }, abstract = {Houseflies (Musca domestica) are important mechanical vectors for the transmission of pathogenic microorganisms. In this study, 129 houseflies (69 males and 60 females) were collected from 10 different environmental sources and a laboratory population was used. The surface microbiota of houseflies was identified by Next-Generation Sequencing. Staphylococci from the surfaces of houseflies were selectively isolated and their virulence genes, antibiotic susceptibilities, biofilm formation, and clonal relatedness were determined. Metagenomic analysis results demonstrated that Staphylococcus, Bacillus, and Enterococcus were mostly present on the surface of houseflies at the genus level. Additionally, the isolated 32 staphylococcal strains were identified as Staphylococcus sciuri (n = 11), S. saprophyticus (n = 9), S. arlettae (n = 6), S. xylosus (n = 4), S. epidermidis (n = 1) and S. gallinarum (n = 1). tetK, tetM, tetL, ermC, msrAB, and aad6 genes were found to carry by some of the staphylococcal strains. The strains were mostly resistant to oxacillin, penicillin, and erythromycin and three strains were multi-drug resistant. There was a statistical difference between housefly collection places and antibiotic resistance of isolated staphylococci to penicillin G, gentamicin, and erythromycin (p < 0.05). Biofilm test showed that 17 strains were strong biofilm formers, and it plays important role in the transmission of these bacteria on the surface of houseflies. Staphylococcal strains showed extracellular proteolytic and lipolytic activity in 31 and 12 strains, respectively. Closely related species were found in PFGE analysis from different environmental sources. By this study, surface microbiota and carriage of pathogenic staphylococci on the surfaces of houseflies and their virulence properties were elucidated.}, } @article {pmid35137064, year = {2022}, author = {Šantl-Temkiv, T and Amato, P and Casamayor, EO and Lee, PKH and Pointing, SB}, title = {Microbial ecology of the atmosphere.}, journal = {FEMS microbiology reviews}, volume = {46}, number = {4}, pages = {}, pmid = {35137064}, issn = {1574-6976}, mesh = {*Atmosphere/chemistry ; Metagenomics ; *Microbiota ; }, abstract = {The atmosphere connects habitats across multiple spatial scales via airborne dispersal of microbial cells, propagules and biomolecules. Atmospheric microorganisms have been implicated in a variety of biochemical and biophysical transformations. Here, we review ecological aspects of airborne microorganisms with respect to their dispersal, activity and contribution to climatic processes. Latest studies utilizing metagenomic approaches demonstrate that airborne microbial communities exhibit pronounced biogeography, driven by a combination of biotic and abiotic factors. We quantify distributions and fluxes of microbial cells between surface habitats and the atmosphere and place special emphasis on long-range pathogen dispersal. Recent advances have established that these processes may be relevant for macroecological outcomes in terrestrial and marine habitats. We evaluate the potential biological transformation of atmospheric volatile organic compounds and other substrates by airborne microorganisms and discuss clouds as hotspots of microbial metabolic activity in the atmosphere. Furthermore, we emphasize the role of microorganisms as ice nucleating particles and their relevance for the water cycle via formation of clouds and precipitation. Finally, potential impacts of anthropogenic forcing on the natural atmospheric microbiota via emission of particulate matter, greenhouse gases and microorganisms are discussed.}, } @article {pmid35136954, year = {2022}, author = {Ventolero, MF and Wang, S and Hu, H and Li, X}, title = {Computational analyses of bacterial strains from shotgun reads.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {2}, pages = {}, doi = {10.1093/bib/bbac013}, pmid = {35136954}, issn = {1477-4054}, mesh = {Bacteria/genetics ; Genome, Bacterial ; Metagenome ; *Metagenomics/methods ; *Microbiota ; Sequence Analysis, DNA/methods ; }, abstract = {Shotgun sequencing is routinely employed to study bacteria in microbial communities. With the vast amount of shotgun sequencing reads generated in a metagenomic project, it is crucial to determine the microbial composition at the strain level. This study investigated 20 computational tools that attempt to infer bacterial strain genomes from shotgun reads. For the first time, we discussed the methodology behind these tools. We also systematically evaluated six novel-strain-targeting tools on the same datasets and found that BHap, mixtureS and StrainFinder performed better than other tools. Because the performance of the best tools is still suboptimal, we discussed future directions that may address the limitations.}, } @article {pmid35136548, year = {2022}, author = {Li, F and Yang, S and Zhang, L and Qiao, L and Wang, L and He, S and Li, J and Yang, N and Yue, B and Zhou, C}, title = {Comparative metagenomics analysis reveals how the diet shapes the gut microbiota in several small mammals.}, journal = {Ecology and evolution}, volume = {12}, number = {1}, pages = {e8470}, pmid = {35136548}, issn = {2045-7758}, abstract = {The gut microbiomes of the host are large and complex communities, which helps to maintain homeostasis, improves digestive efficiency, and promotes the development of the immune system. The small mammals distributed in Sichuan Province are the most popular species for biodiversity research in Southwest China. However, the effects of different diets on the structure and function of the gut microbial community of these small mammals are poorly understood. In this study, whole-metagenome shotgun sequencing has been used to analyze the composition and functional structures of the gut microbiota of seven small mammals in Laojunshan National Nature Reserve, Sichuan Province, China. Taxonomic classification revealed that the most abundant phyla in the gut of seven small mammals were Bacteroides, Proteobacteria, and Firmicutes. Moreover, Hafnia, Lactobacillus, and Yersinia were the most abundant genus in the gut microbiomes of these seven species. At the functional level, we annotated a series of KEGG functional pathways, six Cazy categories, and 46,163 AROs in the gut microbiomes of the seven species. Comparative analysis found that the difference in the gut microbiomes between the Soricidea and Muridae concentrated on the increase in the F/B (Firmicutes/Bacteroides) ratio in the Soricidea group, probably driven by the high-fat and -calorie digestive requirements due to their insectivorous diet. The comparative functional profiling revealed that functions related to metabolism and carbohydrates were significantly more abundant in Muridae group, which may be attributed to their high carbohydrate digestion requirements caused by their herbivorous diet. These data suggested that different diets in the host may play an important role in shaping the gut microbiota, and lay the foundation for teasing apart the influences of heritable and environmental factors on the evolution of gut microbial communities.}, } @article {pmid35135613, year = {2022}, author = {Zhang, XL and Deng, YP and Yang, T and Li, LY and Cheng, TY and Liu, GH and Duan, DY}, title = {Metagenomics of the midgut microbiome of Rhipicephalus microplus from China.}, journal = {Parasites & vectors}, volume = {15}, number = {1}, pages = {48}, pmid = {35135613}, issn = {1756-3305}, support = {31902294//the National Science Foundation of China/ ; 2018RS3085//the Planned Programme of Hunan Province Science and Technology Innovation/ ; KH2002001//the Training Programme for Excellent Young Innovators of Changsha/ ; 2020JJ5230//the Natural Science Foundation of Hunan Province, China/ ; 19A235//the Research Foundation of Education Bureau of Hunan Province, China/ ; }, mesh = {*Anaplasmosis ; Animals ; Cattle ; *Cattle Diseases ; Female ; Metagenomics ; *Microbiota/genetics ; *Rhipicephalus/genetics ; *Tick Infestations/veterinary ; *Tick-Borne Diseases ; }, abstract = {BACKGROUND: Ticks, which are ectoparasites of animals, may carry multiple pathogens. The cattle tick Rhipicephalus microplus is an important bovine parasite in China. However, the midgut microbiome of R. microplus from China has not been characterized via metagenomic methods.

METHODS: Rhipicephalus microplus were collected from cattle in the city of Changsha in Hunan province, China. The DNA of the midgut contents was extracted from fully engorged adult female R. microplus. A DNA library was constructed and sequenced using an Illumina HiSeq sequencing platform. SOAPdenovo software was used to assemble and analyze the clean data. The latent class analysis algorithm applied to system classification by MEGAN software was used to annotate the information on the species' sequences. DIAMOND software was used to compare unigenes with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and functional annotation was carried out based on the results of the comparison.

RESULTS: The dominant phyla in the five samples were Firmicutes, Proteobacteria, and Actinobacteria. Streptococcus, Mycobacterium, Anaplasma, Enterococcus, Shigella, Lactobacillus, Brachyspira, Pseudomonas, Enterobacter, Bacillus, and Lactococcus were the dominant genera in the five samples. The endosymbiotic bacterium Wolbachia was also detected in all of the samples. Mycobacterium malmesburyense, Streptococcus pneumoniae, Anaplasma phagocytophilum, Enterococcus faecium, Shigella sonnei, Enterococcus faecalis, Lactobacillus casei, Brachyspira hampsonii, Pseudomonas syringae, Enterobacter cloacae, and Lactococcus garvieae were the dominant species in the five samples. In addition to these bacterial species, we also detected some eukaryotes, such as Rhizophagus irregularis, Enterospora canceri, Smittium culicis, Zancudomyces culisetae, Trachipleistophora hominis, and viruses such as orf virus, human endogenous retrovirus type W, enzootic nasal tumor virus of goats, bovine retrovirus CH15, and galidia endogenous retrovirus in all of the samples at the species level. The results of the annotated KEGG pathway predictions for the gene functions of the midgut microflora of R. microplus indicated genes involved in lipid and amino acid metabolism, infectious diseases (e.g., Streptococcus pneumonia infection, human granulocytic anaplasmosis, Shigella sonnei infection, Salmonella enterica infection, and pathogenic Escherichia coli infection), and cancer.

CONCLUSIONS: Our study revealed that the midgut microbiome of R. microplus is not only composed of a large number of bacteria, but that a portion also comprises eukaryotes and viruses. The data presented here enhance our understanding of this tick's midgut microbiome and provide fundamental information for the control of ticks and tick-borne diseases.}, } @article {pmid35134527, year = {2022}, author = {He, Y and Song, Z and Dong, X and Zheng, Q and Peng, X and Jia, X}, title = {Candida tropicalis prompted effectively simultaneous removal of carbon, nitrogen and phosphorus in activated sludge reactor: Microbial community succession and functional characteristics.}, journal = {Bioresource technology}, volume = {348}, number = {}, pages = {126820}, doi = {10.1016/j.biortech.2022.126820}, pmid = {35134527}, issn = {1873-2976}, mesh = {Bioreactors ; Candida tropicalis/metabolism ; Carbon ; *Microbiota ; Nitrogen/metabolism ; Phosphorus/metabolism ; *Sewage/microbiology ; Waste Disposal, Fluid/methods ; }, abstract = {A new Candida tropicalis that simultaneously remove nitrogen and phosphorus, and degrade organic matters was isolated. Three continuous stirred tank reactors inoculated with C. tropicalis, activated sludge, and their co-existing system in aerobic condition were operated for 150 days. Results demonstrated that the inoculation of C. tropicalis in the co-existing system remarkably improved the carbon, nitrogen, and phosphorus removal efficiencies. The co-existing system had increased carbon, nitrogen, and phosphorus removal efficiencies (92%, 73%, and 63%, respectively); decreased biomass (reduced from 1200 mg/L to 500 mg/L); and C. tropicalis as the dominant strain. The relative abundance of traditional nitrogen- and phosphorus-removing microorganisms, such as Mycobacterium, Flavonifactor, and Devsia, increased in the co-existing system. Metagenomic analysis showed that the presence of the PCYT2, EPT1, and phnPP genes and more complexed metabolism pathways in the co-existing system might be responsible for the more activated metabolism process.}, } @article {pmid35130266, year = {2022}, author = {Briscoe, L and Balliu, B and Sankararaman, S and Halperin, E and Garud, NR}, title = {Evaluating supervised and unsupervised background noise correction in human gut microbiome data.}, journal = {PLoS computational biology}, volume = {18}, number = {2}, pages = {e1009838}, pmid = {35130266}, issn = {1553-7358}, support = {R01 HG010505/HG/NHGRI NIH HHS/United States ; R35 GM125055/GM/NIGMS NIH HHS/United States ; U01 HG012079/HG/NHGRI NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; }, abstract = {The ability to predict human phenotypes and identify biomarkers of disease from metagenomic data is crucial for the development of therapeutics for microbiome-associated diseases. However, metagenomic data is commonly affected by technical variables unrelated to the phenotype of interest, such as sequencing protocol, which can make it difficult to predict phenotype and find biomarkers of disease. Supervised methods to correct for background noise, originally designed for gene expression and RNA-seq data, are commonly applied to microbiome data but may be limited because they cannot account for unmeasured sources of variation. Unsupervised approaches address this issue, but current methods are limited because they are ill-equipped to deal with the unique aspects of microbiome data, which is compositional, highly skewed, and sparse. We perform a comparative analysis of the ability of different denoising transformations in combination with supervised correction methods as well as an unsupervised principal component correction approach that is presently used in other domains but has not been applied to microbiome data to date. We find that the unsupervised principal component correction approach has comparable ability in reducing false discovery of biomarkers as the supervised approaches, with the added benefit of not needing to know the sources of variation apriori. However, in prediction tasks, it appears to only improve prediction when technical variables contribute to the majority of variance in the data. As new and larger metagenomic datasets become increasingly available, background noise correction will become essential for generating reproducible microbiome analyses.}, } @article {pmid35130125, year = {2022}, author = {Lawrence, D and Campbell, DE and Schriefer, LA and Rodgers, R and Walker, FC and Turkin, M and Droit, L and Parkes, M and Handley, SA and Baldridge, MT}, title = {Single-cell genomics for resolution of conserved bacterial genes and mobile genetic elements of the human intestinal microbiota using flow cytometry.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2029673}, pmid = {35130125}, issn = {1949-0984}, support = {R01 OD024917/OD/NIH HHS/United States ; RC2 DK116713/DK/NIDDK NIH HHS/United States ; T32 DK077653/DK/NIDDK NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteria/classification/*cytology/*genetics/isolation & purification ; Feces/microbiology ; Flow Cytometry/*methods ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; Interspersed Repetitive Sequences ; Phylogeny ; Single-Cell Analysis ; }, abstract = {As our understanding of the importance of the human microbiota in health and disease grows, so does our need to carefully resolve and delineate its genomic content. 16S rRNA gene-based analyses yield important insights into taxonomic composition, and metagenomics-based approaches reveal the functional potential of microbial communities. However, these methods generally fail to directly link genetic features, including bacterial genes and mobile genetic elements, to each other and to their source bacterial genomes. Further, they are inadequate to capture the microdiversity present within a genus, species, or strain of bacteria within these complex communities. Here, we present a method utilizing fluorescence-activated cell sorting for isolation of single bacterial cells, amplifying their genomes, screening them by 16S rRNA gene analysis, and selecting cells for genomic sequencing. We apply this method to both a cultured laboratory strain of Escherichia coli and human stool samples. Our analyses reveal the capacity of this method to provide nearly complete coverage of bacterial genomes when applied to isolates and partial genomes of bacterial species recovered from complex communities. Additionally, this method permits exploration and comparison of conserved and variable genomic features between individual cells. We generate assemblies of novel genomes within the Ruminococcaceae family and the Holdemanella genus by combining several 16S rRNA gene-matched single cells, and report novel prophages and conjugative transposons for both Bifidobacterium and Ruminococcaceae. Thus, we demonstrate an approach for flow cytometric separation and sequencing of single bacterial cells from the human microbiota, which yields a variety of critical insights into both the functional potential of individual microbes and the variation among those microbes. This method definitively links a variety of conserved and mobile genomic features, and can be extended to further resolve diverse elements present in the human microbiota.}, } @article {pmid35129656, year = {2022}, author = {Yang, L and Wan, Y and Li, W and Liu, C and Li, HF and Dong, Z and Zhu, K and Jiang, S and Shang, E and Qian, D and Duan, J}, title = {Targeting intestinal flora and its metabolism to explore the laxative effects of rhubarb.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {4}, pages = {1615-1631}, pmid = {35129656}, issn = {1432-0614}, support = {ZDXM-1-10//Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization/ ; No.82074126//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Feces/microbiology ; *Gastrointestinal Microbiome ; Laxatives/analysis/pharmacology/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Rats ; *Rheum/chemistry ; }, abstract = {Rhubarb, a traditional herb, has been used in clinical practice for hundreds of years to cure constipation, but its mechanism is still not clear enough. Currently, growing evidence suggests that intestinal flora might be a potential target for the treatment of constipation. Thus, the aim of this study was to clarify the laxative effect of rhubarb via systematically analyzing the metagenome and metabolome of the gut microbiota. In this study, the laxative effects of rhubarb were investigated by loperamide-induced constipation in rats. The gut microbiota was determined by high-throughput sequencing of 16S rRNA gene. Ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry was used for fecal metabolomics analysis. The data showed that rhubarb could significantly shorten gastrointestinal transit time, increase fecal water content and defecation frequency, improve gastrointestinal hormone disruption, and protect the colon mucus layer. Analysis of 16S rRNA gene sequencing indicated that rhubarb could improve the disorder of intestinal microbiota in constipated rats. For example, beneficial bacteria such as Ligilactobacillus, Limosilalactobacillus, and Prevotellaceae UCG-001 were remarkably increased, and pathogens such as Escherichia-Shigella were significantly decreased after rhubarb treatment. Additionally, the fecal metabolic profiles of constipated rats were improved by rhubarb. After rhubarb treatment, metabolites such as chenodeoxycholic acid, cholic acid, prostaglandin F2α, and α-linolenic acid were markedly increased in constipation rats; in contrast, the metabolites such as lithocholic acid, calcidiol, and 10-hydroxystearic acid were notably reduced in constipation rats. Moreover, correlation analysis indicated a close relationship between intestinal flora, fecal metabolites, and biochemical indices associated with constipation. In conclusion, the amelioration of rhubarb in constipation might modulate the intestinal microflora and its metabolism. Moreover, the application of fecal metabolomics could provide a new strategy to uncover the mechanism of herbal medicines.Key points• Rhubarb could significantly improve gut microbiota disorder in constipation rats.• Rhubarb could markedly modulate the fecal metabolite profile of constipated rats.}, } @article {pmid35129649, year = {2023}, author = {Doane, MP and Johnson, CJ and Johri, S and Kerr, EN and Morris, MM and Desantiago, R and Turnlund, AC and Goodman, A and Mora, M and Lima, LFO and Nosal, AP and Dinsdale, EA}, title = {The Epidermal Microbiome Within an Aggregation of Leopard Sharks (Triakis semifasciata) Has Taxonomic Flexibility with Gene Functional Stability Across Three Time-points.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {747-764}, pmid = {35129649}, issn = {1432-184X}, support = {1330800//National Science Foundation/ ; 1323809//National Science Foundation/ ; }, mesh = {Animals ; *Sharks ; Epidermis ; *Microbiota ; }, abstract = {The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein-rich mucus that collectively, influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiome of the Triakis semifasciata (leopard shark) at three time-points collected across 4 years to identify links between microbial groups and host metabolism. Our aims include (1) describing the variation of microbiome taxa over time and identifying recurrent microbiome members (present across all time-points); (2) investigating the relationship between the recurrent and flexible taxa (those which are not found consistently across time-points); (3) describing the functional compositions of the microbiome which may suggest links with the host metabolism; and (4) identifying whether metabolic processes are shared across microbial genera or are unique to specific taxa. Microbial members of the microbiome showed high similarity between all individuals (Bray-Curtis similarity index = 82.7, where 0 = no overlap, 100 = total overlap) with the relative abundance of those members varying across sampling time-points, suggesting flexibility of taxa in the microbiome. One hundred and eighty-eight genera were identified as recurrent, including Pseudomonas, Erythrobacter, Alcanivorax, Marinobacter, and Sphingopxis being consistently abundant across time-points, while Limnobacter and Xyella exhibited switching patterns with high relative abundance in 2013, Sphingobium and Sphingomona in 2015, and Altermonas, Leeuwenhoekiella, Gramella, and Maribacter in 2017. Of the 188 genera identified as recurrent, the top 19 relatively abundant genera formed three recurrent groups. The microbiome also displayed high functional similarity between individuals (Bray-Curtis similarity index = 97.6) with gene function composition remaining consistent across all time-points. These results show that while the presence of microbial genera exhibits consistency across time-points, their abundances do fluctuate. Microbial functions however remain stable across time-points; thus, we suggest the leopard shark microbiomes exhibit functional redundancy. We show coexistence of microbes hosted in elasmobranch microbiomes that encode genes involved in utilizing nitrogen, but not fixing nitrogen, degrading urea, and resistant to heavy metal.}, } @article {pmid35128832, year = {2022}, author = {Zeybel, M and Arif, M and Li, X and Altay, O and Yang, H and Shi, M and Akyildiz, M and Saglam, B and Gonenli, MG and Yigit, B and Ulukan, B and Ural, D and Shoaie, S and Turkez, H and Nielsen, J and Zhang, C and Uhlén, M and Borén, J and Mardinoglu, A}, title = {Multiomics Analysis Reveals the Impact of Microbiota on Host Metabolism in Hepatic Steatosis.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {9}, number = {11}, pages = {e2104373}, pmid = {35128832}, issn = {2198-3844}, support = {//Knut and Alice Wallenberg Foundation/ ; //ScandiBio Therapeutics AB, Sweden/ ; //PoLiMeR Innovative Training Network/ ; 812616//Marie Skłodowska-Curie/ ; //European Union's Horizon 2020/ ; sens2019031//Uppsala Multidisciplinary Center for Advanced Computational Science/ ; }, mesh = {Dysbiosis/genetics ; *Fatty Liver/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; *Microbiota/genetics ; }, abstract = {Metabolic dysfunction-associated fatty liver disease (MAFLD) is a complex disease involving alterations in multiple biological processes regulated by the interactions between obesity, genetic background, and environmental factors including the microbiome. To decipher hepatic steatosis (HS) pathogenesis by excluding critical confounding factors including genetic variants and diabetes, 56 heterogenous MAFLD patients are characterized by generating multiomics data including oral and gut metagenomics as well as plasma metabolomics and inflammatory proteomics data. The dysbiosis in the oral and gut microbiome is explored and the host-microbiome interactions based on global metabolic and inflammatory processes are revealed. These multiomics data are integrated using the biological network and HS's key features are identified using multiomics data. HS is finally predicted using these key features and findings are validated in a follow-up cohort, where 22 subjects with varying degree of HS are characterized.}, } @article {pmid35127566, year = {2021}, author = {Yan, H and Qin, Q and Chen, J and Yan, S and Li, T and Gao, X and Yang, Y and Li, A and Ding, S}, title = {Gut Microbiome Alterations in Patients With Visceral Obesity Based on Quantitative Computed Tomography.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {823262}, pmid = {35127566}, issn = {2235-2988}, mesh = {*Gastrointestinal Microbiome ; Humans ; Obesity, Abdominal ; Risk Factors ; Tomography, X-Ray Computed ; Uric Acid ; }, abstract = {The gut microbiota is crucial in the pathogenesis of obesity. Abdominal obesity is known to significantly increase the risk of metabolic syndrome and cardiovascular disease, so further study is needed to investigate the changes of intestinal microorganisms in patients with excessive visceral fat. In our study, 41 people (n = 41) with normal body mass index (BMI) (18.5 ≤ BMI < 23.9) were included and divided into the low visceral fat area (L-VFA) group (n = 23, VFA < 100 cm[2]) and the high visceral fat area (H-VFA) group (n = 18, VFA ≥ 100 cm[2]). Several clinical indicators of the H-VFA group were significantly higher than those of the L-VFA group, including the waist circumference (WC), the fasting blood glucose (FBG), the triglyceride (TG), the total cholesterol (TC), the low-density lipoprotein cholesterol (LDL), the serum uric acid (SUA), the white blood cell count (WBC), the blood neutrophil count (NEC), and the blood lymphocyte count (LYC). Using whole-genome shotgun sequencing, we found that the types of the intestinal microbiota of H-VFA patients were different from those of the L-VFA patients, with 18 bacteria enriched in the H-VFA group and nine bacteria in the L-VFA group. A total of 16 species of gut microbes showed a strong correlation with VFA, and Escherichia coli has the strongest correlation, followed by Mitsuokella unclassified, Bifidobacterium longum, Escherichia unclassified, Ruminococcus torques, Dialister succinatiphilus, Eubacterium hallii, and Ruminococcus gnavus. Compared to the VFA, only two species show a strong correlation with BMI and WC. Further functional genetic studies suggested that the degradation of short-chain fatty acids (SCFAs) and the generation of lipopolysaccharide (LPS) might be related to visceral fat accumulation. Together, visceral fat was more closely correlated with the gut microbiome compared with BMI and WC. It suggested an intrinsic connection between the gut microbiome and visceral fat and its related metabolic disorders. Specific microbial species and pathways associated with visceral fat accumulation might contribute to new targeted therapies for visceral fat and its metabolic disorders.}, } @article {pmid35124050, year = {2022}, author = {Ercole, E and Adamo, M and Lumini, E and Fusconi, A and Mucciarelli, M}, title = {Alpine constructed wetlands: A metagenomic analysis reveals microbial complementary structure.}, journal = {The Science of the total environment}, volume = {822}, number = {}, pages = {153640}, doi = {10.1016/j.scitotenv.2022.153640}, pmid = {35124050}, issn = {1879-1026}, mesh = {Bacteria/genetics ; *Carex Plant ; *Microbiota ; Waste Disposal, Fluid/methods ; Wastewater ; *Water Purification ; Wetlands ; }, abstract = {Constructed wetlands (CWs) are used to water treatment worldwide, however their application at high-altitude is poorly studied. In order to survive mountain winters, CWs rely on native flora and associated microbial communities. However, the choice of plant-microbes pairs more suitable for water treatment is challenging in alpine environments. Using a metagenomic approach, we investigated the composition of prokaryotes and fungal communities, through extensive sampling inside a constructed wetland in the SW-Alps. Best performing plant species were searched among those hosting the most diverse and resilient microbial communities and to this goal, we analysed them in the natural environment also. Our results showed that microbial communities were less diverse in the CW than at natural conditions, and they differed from plant to plant, revealing a clear variation in taxonomic composition between forbs and gramineous plants. Carex rostrata, Deschampsia caespitosa and Rumex alpinus hosted bacteria very active in N-cycles. Moreover, fungal and prokaryotic communities associated to R. alpinus (Polygonaceae) turned to be the richest and stable among the studied species. In our opinion, this species should be prioritized in CWs at high elevations, also in consideration of its low maintenance requirements.}, } @article {pmid35123235, year = {2022}, author = {Özel Duygan, BD and van der Meer, JR}, title = {Recent advances in microbial community analysis from machine learning of multiparametric flow cytometry data.}, journal = {Current opinion in biotechnology}, volume = {75}, number = {}, pages = {102688}, doi = {10.1016/j.copbio.2022.102688}, pmid = {35123235}, issn = {1879-0429}, mesh = {Flow Cytometry/methods ; Machine Learning ; *Microbiota ; }, abstract = {Dynamic analysis of microbial composition is crucial for understanding community functioning and detecting dysbiosis. Compositional information is mostly obtained through sequencing of taxonomic markers or whole meta-genomes, which may be productively complemented by real-time quantitative community multiparametric flow cytometry data (FCM). Patterns and clusters in FCM community data can be distinguished and compared by unsupervised machine learning. Alternatively, FCM data from preselected individual strain phenotypes can be used for supervised machine-training in order to differentiate similar cell types within communities. Both types of machine learning can quantitatively deconvolute community FCM data sets and rapidly analyse global changes in response to treatment. Procedures may further be optimized for recurrent microbiome samples to simultaneously quantify physiological and compositional states.}, } @article {pmid35123073, year = {2022}, author = {Li, H and Meier-Kolthoff, JP and Hu, C and Wang, Z and Zhu, J and Zheng, W and Tian, Y and Guo, F}, title = {Panoramic Insights into Microevolution and Macroevolution of A Prevotella copri-containing Lineage in Primate Guts.}, journal = {Genomics, proteomics & bioinformatics}, volume = {20}, number = {2}, pages = {334-349}, pmid = {35123073}, issn = {2210-3244}, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; Prevotella/genetics ; Primates/genetics ; Mammals ; }, abstract = {Prevotella copri and its related taxa are widely detected in mammalian gut microbiomes and have been linked with an enterotype in humans. However, their microevolution and macroevolution among hosts are poorly characterized. In this study, extensively collected marker genes and genomes were analyzed to trace their evolutionary history, host specificity, and biogeographic distribution. Investigations based on marker genes and genomes suggest that a P. copri-containing lineage (PCL) harbors diverse species in higher primates. Firstly, P. copri in the human gut consisted of multiple groups exhibiting high genomic divergence and conspicuous but non-strict biogeographic patterns. Most African strains with high genomic divergence from other strains were phylogenetically located at the root of the species, indicating the co-evolutionary history of P. copri and Homo sapiens. Secondly, although long-term co-evolution between PCL and higher primates was revealed, sporadic signals of co-speciation and extensive host jumping of PCL members were suggested among higher primates. Metagenomic and phylogenetic analyses indicated that P. copri and other PCL species found in domesticated mammals had been recently transmitted from humans. Thirdly, strong evidence was found on the extensively horizontal transfer of genes (e.g., genes encoding carbohydrate-active enzymes) among sympatric P. copri groups and PCL species in the same primate host. Our study provides panoramic insights into the combined effects of vertical and horizontal transmission, as well as potential niche adaptation, on the microevolutionary and macroevolutionary history for an enterotype-representative lineage.}, } @article {pmid35120121, year = {2022}, author = {Hernandez-Castro, LE and Villacís, AG and Jacobs, A and Cheaib, B and Day, CC and Ocaña-Mayorga, S and Yumiseva, CA and Bacigalupo, A and Andersson, B and Matthews, L and Landguth, EL and Costales, JA and Llewellyn, MS and Grijalva, MJ}, title = {Population genomics and geographic dispersal in Chagas disease vectors: Landscape drivers and evidence of possible adaptation to the domestic setting.}, journal = {PLoS genetics}, volume = {18}, number = {2}, pages = {e1010019}, pmid = {35120121}, issn = {1553-7404}, support = {P20 GM130418/GM/NIGMS NIH HHS/United States ; R15 AI105749/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptation, Biological/genetics ; Animals ; Chagas Disease/*epidemiology/*genetics ; Disease Vectors ; Ecosystem ; Ecuador/epidemiology ; Gene Expression/genetics ; Gene Expression Profiling/methods ; Gene Flow ; Insect Vectors/genetics ; Metagenomics/methods ; Polymorphism, Single Nucleotide/genetics ; Population Density ; Rhodnius/*genetics/pathogenicity ; Transcriptome/genetics ; Trypanosoma cruzi/genetics ; }, abstract = {Accurate prediction of vectors dispersal, as well as identification of adaptations that allow blood-feeding vectors to thrive in built environments, are a basis for effective disease control. Here we adopted a landscape genomics approach to assay gene flow, possible local adaptation, and drivers of population structure in Rhodnius ecuadoriensis, an important vector of Chagas disease. We used a reduced-representation sequencing technique (2b-RADseq) to obtain 2,552 SNP markers across 272 R. ecuadoriensis samples from 25 collection sites in southern Ecuador. Evidence of high and directional gene flow between seven wild and domestic population pairs across our study site indicates insecticide-based control will be hindered by repeated re-infestation of houses from the forest. Preliminary genome scans across multiple population pairs revealed shared outlier loci potentially consistent with local adaptation to the domestic setting, which we mapped to genes involved with embryogenesis and saliva production. Landscape genomic models showed elevation is a key barrier to R. ecuadoriensis dispersal. Together our results shed early light on the genomic adaptation in triatomine vectors and facilitate vector control by predicting that spatially-targeted, proactive interventions would be more efficacious than current, reactive approaches.}, } @article {pmid35119363, year = {2022}, author = {Goyal, A and Bittleston, LS and Leventhal, GE and Lu, L and Cordero, OX}, title = {Interactions between strains govern the eco-evolutionary dynamics of microbial communities.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35119363}, issn = {2050-084X}, mesh = {Biodiversity ; Biological Evolution ; Metagenome ; *Microbiota/genetics ; *Sarraceniaceae/genetics ; }, abstract = {Genomic data has revealed that genotypic variants of the same species, that is, strains, coexist and are abundant in natural microbial communities. However, it is not clear if strains are ecologically equivalent, and at what characteristic genetic distance they might exhibit distinct interactions and dynamics. Here, we address this problem by tracking 10 taxonomically diverse microbial communities from the pitcher plant Sarracenia purpurea in the laboratory for more than 300 generations. Using metagenomic sequencing, we reconstruct their dynamics over time and across scales, from distant phyla to closely related genotypes. We find that most strains are not ecologically equivalent and exhibit distinct dynamical patterns, often being significantly more correlated with strains from another species than their own. Although even a single mutation can affect laboratory strains, on average, natural strains typically decouple in their dynamics beyond a genetic distance of 100 base pairs. Using mathematical consumer-resource models, we show that these taxonomic patterns emerge naturally from ecological interactions between community members, but only if the interactions are coarse-grained at the level of strains, not species. Finally, by analyzing genomic differences between strains, we identify major functional hubs such as transporters, regulators, and carbohydrate-catabolizing enzymes, which might be the basis for strain-specific interactions. Our work suggests that fine-scale genetic differences in natural communities could be created and stabilized via the rapid diversification of ecological interactions between strains.}, } @article {pmid35118437, year = {2022}, author = {Pryszlak, A and Wenzel, T and Seitz, KW and Hildebrand, F and Kartal, E and Cosenza, MR and Benes, V and Bork, P and Merten, CA}, title = {Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics.}, journal = {Cell reports methods}, volume = {2}, number = {1}, pages = {None}, pmid = {35118437}, issn = {2667-2375}, support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Microfluidics/methods ; Genomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; }, abstract = {We report a droplet microfluidic method to target and sort individual cells directly from complex microbiome samples and to prepare these cells for bulk whole-genome sequencing without cultivation. We characterize this approach by recovering bacteria spiked into human stool samples at a ratio as low as 1:250 and by successfully enriching endogenous Bacteroides vulgatus to the level required for de novo assembly of high-quality genomes. Although microbiome strains are increasingly demanded for biomedical applications, a vast majority of species and strains are uncultivated and without reference genomes. We address this shortcoming by encapsulating complex microbiome samples directly into microfluidic droplets and amplifying a target-specific genomic fragment using a custom molecular TaqMan probe. We separate those positive droplets by droplet sorting, selectively enriching single target strain cells. Finally, we present a protocol to purify the genomic DNA while specifically removing amplicons and cell debris for high-quality genome sequencing.}, } @article {pmid35118004, year = {2021}, author = {Yu, X and Jin, Y and Zhou, W and Xiao, T and Wu, Z and Su, J and Gao, H and Shen, P and Zheng, B and Luo, Q and Li, L and Xiao, Y}, title = {Rifaximin Modulates the Gut Microbiota to Prevent Hepatic Encephalopathy in Liver Cirrhosis Without Impacting the Resistome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {761192}, pmid = {35118004}, issn = {2235-2988}, mesh = {Escherichia coli ; *Gastrointestinal Microbiome/physiology ; *Hepatic Encephalopathy/drug therapy/etiology/prevention & control ; Humans ; Liver Cirrhosis/complications/microbiology ; Prospective Studies ; Rifaximin/therapeutic use ; }, abstract = {The gut microbiota has an important role in the pathogenesis of hepatic encephalopathy(HE). Rifaximin, an intestinal non-absorbable antibacterial agent, is effective in the treatment of HE. However, whether long-term prophylactic use induces antibacterial resistance and its mechanism for treating HE remains unclear. This prospective study assessed the impact of 12 weeks rifaximin administration on the gut microbiota and resistome in cirrhotic patients. Fecal sampling was conducted 1 day before the first rifaximin administration and at Weeks 1, 2, 4, 6, 8, 10, 12 of the study. Thirty cirrhotic patients who were in remission from recurrent HE was enrolled to receive rifaximin (400mg TID for 12 weeks). Rifaximin improved hyperammonemia and cognitive function in the 21 patients who completed rifaximin treatment. The dynamic observations showed the gut microbiota diversity, composition and the number of resistance genes, plasmids, insertion sequences did not change significantly during the period(P>0.05). Metabolic pathways such as aromatic amino acids, tryptophan synthesis, urea cycle, and LPS synthesis reduced. No new antimicrobial resistance genes was emergenced. However, the number of aminoglycosides, rifamycin and phenolic resistance genes increased, whereas tetracycline, fosfomycin and cephamycin decreased (P<0.05). Changes in the abundance of E. coli, K. pneumoniae, and B. longum strains correlated with changes of resistance genes. Prophylactic use of rifaximin for 12 weeks improved hyperammonemia and neurophysiological function, maintained gut microbiota diversity, composition and did not change the overall resistome. Rifaximin altered expression of HE-related metabolic pathways. All of these effects could play a key role in preventing HE. Clinical Trial Registration: ChiCTR1900022234 (registered at the Chinese Clinical Trial Registry).}, } @article {pmid35115690, year = {2022}, author = {Lopera-Maya, EA and Kurilshikov, A and van der Graaf, A and Hu, S and Andreu-Sánchez, S and Chen, L and Vila, AV and Gacesa, R and Sinha, T and Collij, V and Klaassen, MAY and Bolte, LA and Gois, MFB and Neerincx, PBT and Swertz, MA and , and Harmsen, HJM and Wijmenga, C and Fu, J and Weersma, RK and Zhernakova, A and Sanna, S}, title = {Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project.}, journal = {Nature genetics}, volume = {54}, number = {2}, pages = {143-151}, pmid = {35115690}, issn = {1546-1718}, mesh = {ABO Blood-Group System/*genetics ; *Bacterial Physiological Phenomena ; Bifidobacterium/physiology ; Diet ; Fucosyltransferases/genetics ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; *Genetic Variation ; Genome, Human ; Genome-Wide Association Study ; *Host Microbial Interactions ; Humans ; Lactase/*genetics ; Metabolic Networks and Pathways ; Metagenome ; Multifactorial Inheritance ; Netherlands ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Sodium Chloride, Dietary ; Triglycerides/blood ; Galactoside 2-alpha-L-fucosyltransferase ; }, abstract = {Host genetics are known to influence the gut microbiome, yet their role remains poorly understood. To robustly characterize these effects, we performed a genome-wide association study of 207 taxa and 205 pathways representing microbial composition and function in 7,738 participants of the Dutch Microbiome Project. Two robust, study-wide significant (P < 1.89 × 10[-10]) signals near the LCT and ABO genes were found to be associated with multiple microbial taxa and pathways and were replicated in two independent cohorts. The LCT locus associations seemed modulated by lactose intake, whereas those at ABO could be explained by participant secretor status determined by their FUT2 genotype. Twenty-two other loci showed suggestive evidence (P < 5 × 10[-8]) of association with microbial taxa and pathways. At a more lenient threshold, the number of loci we identified strongly correlated with trait heritability, suggesting that much larger sample sizes are needed to elucidate the remaining effects of host genetics on the gut microbiome.}, } @article {pmid35115689, year = {2022}, author = {Qin, Y and Havulinna, AS and Liu, Y and Jousilahti, P and Ritchie, SC and Tokolyi, A and Sanders, JG and Valsta, L and Brożyńska, M and Zhu, Q and Tripathi, A and Vázquez-Baeza, Y and Loomba, R and Cheng, S and Jain, M and Niiranen, T and Lahti, L and Knight, R and Salomaa, V and Inouye, M and Méric, G}, title = {Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort.}, journal = {Nature genetics}, volume = {54}, number = {2}, pages = {134-142}, pmid = {35115689}, issn = {1546-1718}, support = {MR/L003120/1/MRC_/Medical Research Council/United Kingdom ; UL1 TR001442/TR/NCATS NIH HHS/United States ; P42 ES010337/ES/NIEHS NIH HHS/United States ; RG/18/13/33946/BHF_/British Heart Foundation/United Kingdom ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 DK124318/DK/NIDDK NIH HHS/United States ; U01 DK061734/DK/NIDDK NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R01 DK121378/DK/NIDDK NIH HHS/United States ; /CSO_/Chief Scientist Office/United Kingdom ; RG/13/13/30194/BHF_/British Heart Foundation/United Kingdom ; R01 DK106419/DK/NIDDK NIH HHS/United States ; }, mesh = {ABO Blood-Group System/genetics ; Bifidobacterium/physiology ; Clostridiales/physiology ; Cohort Studies ; Colorectal Neoplasms/genetics/microbiology ; Depressive Disorder, Major/genetics/microbiology ; *Diet ; Dietary Fiber ; Enterococcus faecalis/physiology ; *Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/*microbiology ; *Genetic Variation ; Genome-Wide Association Study ; *Host Microbial Interactions ; Humans ; Lactase/genetics ; Mediator Complex/genetics ; Mendelian Randomization Analysis ; Metagenome ; Morganella/physiology ; *Polymorphism, Single Nucleotide ; }, abstract = {Human genetic variation affects the gut microbiota through a complex combination of environmental and host factors. Here we characterize genetic variations associated with microbial abundances in a single large-scale population-based cohort of 5,959 genotyped individuals with matched gut microbial metagenomes, and dietary and health records (prevalent and follow-up). We identified 567 independent SNP-taxon associations. Variants at the LCT locus associated with Bifidobacterium and other taxa, but they differed according to dairy intake. Furthermore, levels of Faecalicatena lactaris associated with ABO, and suggested preferential utilization of secreted blood antigens as energy source in the gut. Enterococcus faecalis levels associated with variants in the MED13L locus, which has been linked to colorectal cancer. Mendelian randomization analysis indicated a potential causal effect of Morganella on major depressive disorder, consistent with observational incident disease analysis. Overall, we identify and characterize the intricate nature of host-microbiota interactions and their association with disease.}, } @article {pmid35115615, year = {2022}, author = {Lee, CZ and Zoqratt, MZHM and Phipps, ME and Barr, JJ and Lal, SK and Ayub, Q and Rahman, S}, title = {The gut virome in two indigenous populations from Malaysia.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {1824}, pmid = {35115615}, issn = {2045-2322}, mesh = {Feces/virology ; Female ; Gastrointestinal Microbiome/*genetics ; *Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; *Indigenous Peoples ; Malaysia ; Metagenomics/methods ; Phylogeny ; Virome/genetics ; Viruses/classification/*genetics ; }, abstract = {The human gut contains a complex microbiota dominated by bacteriophages but also containing other viruses and bacteria and fungi. There are a growing number of techniques for the extraction, sequencing, and analysis of the virome but currently no standardized protocols. This study established an effective workflow for virome analysis to investigate the virome of stool samples from two understudied ethnic groups from Malaysia: the Jakun and Jehai Orang Asli. By using the virome extraction and analysis workflow with the Oxford Nanopore Technology, long-read sequencing successfully captured close to full-length viral genomes. The virome composition of the two indigenous Malaysian communities were remarkably different from those found in other parts of the world. Additionally, plant viruses found in the viromes of these individuals were attributed to traditional food-seeking methods. This study establishes a human gut virome workflow and extends insights into the healthy human gut virome, laying the groundwork for comparative studies.}, } @article {pmid35115599, year = {2022}, author = {Stege, PB and Hordijk, J and Shetty, SA and Visser, M and Viveen, MC and Rogers, MRC and Gijsbers, E and Dierikx, CM and van der Plaats, RQJ and van Duijkeren, E and Franz, E and Willems, RJL and Fuentes, S and Paganelli, FL}, title = {Impact of long-term dietary habits on the human gut resistome in the Dutch population.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {1892}, pmid = {35115599}, issn = {2045-2322}, mesh = {Adult ; Bacteria/drug effects/*genetics/growth & development ; *Diet ; Diet, Vegan ; Diet, Vegetarian ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; *Feeding Behavior ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; Meat ; Metagenome ; Metagenomics ; Middle Aged ; Netherlands ; Nutritive Value ; Seafood ; Time Factors ; Vegetables ; }, abstract = {The human gut microbiome plays a central role in health and disease. Environmental factors, such as lifestyle and diet, are known to shape the gut microbiome as well as the reservoir of resistance genes that these microbes harbour; the resistome. In this study we assessed whether long-term dietary habits within a single geographical region (the Netherlands) impact the human gut resistome. Faecal samples from Dutch omnivores, pescatarians, vegetarians and vegans were analysed by metagenomic shotgun sequencing (MSS) (n = 149) and resistome capture sequencing approach (ResCap) (n = 64). Among all diet groups, 119 and 145 unique antibiotic resistance genes (ARGs) were detected by MSS or ResCap, respectively. Five or fifteen ARGs were shared between all diet groups, based on MSS and ResCap, respectively. The total number of detected ARGs by MSS or ResCap was not significantly different between the groups. MSS also revealed that vegans have a distinct microbiome composition, compared to other diet groups. Vegans had a lower abundance of Streptococcus thermophilus and Lactococcus lactis compared to pescatarians and a lower abundance of S. thermophilus when compared to omnivores. In summary, our study showed that long-term dietary habits are not associated with a specific resistome signature.}, } @article {pmid35114943, year = {2022}, author = {Le Roy, CI and Kurilshikov, A and Leeming, ER and Visconti, A and Bowyer, RCE and Menni, C and Falchi, M and Koutnikova, H and Veiga, P and Zhernakova, A and Derrien, M and Spector, TD}, title = {Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {39}, pmid = {35114943}, issn = {1471-2180}, support = {MR/N01183X/1/MRC_/Medical Research Council/United Kingdom ; MR/N030125/1/MRC_/Medical Research Council/United Kingdom ; DP2 OD007444/CD/ODCDC CDC HHS/United States ; DP2 OD007444/OD/NIH HHS/United States ; R01 DK093595/DK/NIDDK NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; RO1 DK093595/NH/NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Bacteria/classification/*genetics/isolation & purification ; Cohort Studies ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; *Metabolome ; Metabolomics/methods ; *Metagenome ; Metagenomics/methods ; Microbiota/genetics ; Middle Aged ; Probiotics/*administration & dosage ; RNA, Ribosomal, 16S/genetics ; Surveys and Questionnaires ; United Kingdom ; Yogurt/*microbiology ; }, abstract = {BACKGROUND: Yoghurt contains live bacteria that could contribute via modulation of the gut microbiota to its reported beneficial effects such as reduced body weight gain and lower incidence of type 2 diabetes. To date, the association between yoghurt consumption and the composition of the gut microbiota is underexplored. Here we used clinical variables, metabolomics, 16S rRNA and shotgun metagenomic sequencing data collected on over 1000 predominantly female UK twins to define the link between the gut microbiota and yoghurt-associated health benefits.

RESULTS: According to food frequency questionnaires (FFQ), 73% of subjects consumed yoghurt. Consumers presented a healthier diet pattern (healthy eating index: beta = 2.17 ± 0.34; P = 2.72x10[-10]) and improved metabolic health characterised by reduced visceral fat (beta = -28.18 ± 11.71 g; P = 0.01). According to 16S rRNA gene analyses and whole shotgun metagenomic sequencing approach consistent taxonomic variations were observed with yoghurt consumption. More specifically, we identified higher abundance of species used as yoghurt starters Streptococcus thermophilus (beta = 0.41 ± 0.051; P = 6.14x10[-12]) and sometimes added Bifidobacterium animalis subsp. lactis (beta = 0.30 ± 0.052; P = 1.49x10[-8]) in the gut of yoghurt consumers. Replication in 1103 volunteers from the LifeLines-DEEP cohort confirmed the increase of S. thermophilus among yoghurt consumers. Using food records collected the day prior to faecal sampling we showed than an increase in these two yoghurt bacteria could be transient. Metabolomics analysis revealed that B. animalis subsp. lactis was associated with 13 faecal metabolites including a 3-hydroxyoctanoic acid, known to be involved in the regulation of gut inflammation.

CONCLUSIONS: Yoghurt consumption is associated with reduced visceral fat mass and changes in gut microbiome including transient increase of yoghurt-contained species (i.e. S. thermophilus and B. lactis).}, } @article {pmid35113183, year = {2023}, author = {Dong, X and Lan, H and Huang, L and Zhang, H and Lin, X and Weng, S and Peng, Y and Lin, J and Wang, JH and Peng, J and Yang, Y}, title = {Metagenomic Views of Microbial Communities in Sand Sediments Associated with Coral Reefs.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {465-477}, pmid = {35113183}, issn = {1432-184X}, mesh = {Animals ; Coral Reefs ; Ecosystem ; Sand ; Metagenomics ; Bacteria/genetics ; *Microbiota ; Proteobacteria ; *Anthozoa/microbiology ; }, abstract = {Reef sediments, the home for microbes with high abundances, provide an important source of carbonates and nutrients for the growth and maintenance of coral reefs. However, there is a lack of systematic research on the composition of microbial community in sediments of different geographic sites and their potential effect on nutrient recycling and health of the coral reef ecosystem. In combination of biogeochemical measurements with gene- and genome-centric metagenomics, we assessed microbial community compositions and functional diversity, as well as profiles of antibiotic resistance genes in surface sediments of 16 coral reef sites at different depths from the Xisha islands in the South China Sea. Reef sediment microbiomes are diverse and novel at lower taxonomic ranks, dominated by Proteobacteria and Planctomycetota. Most reef sediment bacteria potentially participate in biogeochemical cycling via oxidizing various organic and inorganic compounds as energy sources. High abundances of Proteobacteria (mostly Rhizobiales and Woeseiales) are metabolically flexible and contain rhodopsin genes. Various classes of antibiotic resistance genes, hosted by diverse bacterial lineages, were identified to confer resistance to multidrug, aminoglycoside, and other antibiotics. Overall, our findings expanded the understanding of reef sediment microbial ecology and provided insights for their link to the coral reef ecosystem health.}, } @article {pmid35112152, year = {2023}, author = {LeBlanc, N}, title = {Green Manures Alter Taxonomic and Functional Characteristics of Soil Bacterial Communities.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {684-697}, pmid = {35112152}, issn = {1432-184X}, support = {2038-22000-016-000-D//USDA-ARS/ ; 2038-22430-003-000-D//USDA-ARS/ ; }, mesh = {*Soil ; Manure ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria ; Plants ; Soil Microbiology ; }, abstract = {Incorporation of plant biomass into soil as green manures can reduce soilborne diseases and improve crop and soil health in agricultural ecosystems. Soil microbial communities can mediate beneficial effects of these amendments, but their response to different types of green manures is poorly understood. This study tested the effect of green manures from broccoli, marigold, and sudangrass on taxonomic and functional characteristics of soil bacterial communities. Green manures were amended to field soil and maintained in microcosms artificially infested with the soilborne plant pathogen Verticillium dahliae. Lettuce seedlings were transplanted into green manure amended and fallow soil and maintained under growth chamber conditions for 12 weeks. Bacterial communities in bulk and rhizosphere soils were characterized using nanopore sequencing of 16S rRNA and shotgun metagenome libraries. Under microcosm conditions, all green manures reduced the abundance of the soilborne plant pathogen V. dahliae and altered the taxonomic composition of bacterial communities. Twelve weeks following amendment, green manures had differential effects on lettuce yield as well as the taxonomic diversity and composition of soil bacterial communities. In addition, multiple green manures increased the abundance of bacterial functional traits in rhizosphere soil related to iron and polysaccharide acquisition and decreased the abundance of functional traits related to bacterial protein secretion systems. This study demonstrates green manures alter the taxonomic composition and functional traits in soil bacterial communities suggesting these changes may impact beneficial effects of green manures on plant and soil health.}, } @article {pmid35112151, year = {2023}, author = {Mishra, A and Singh, L and Singh, D}, title = {Unboxing the black box-one step forward to understand the soil microbiome: A systematic review.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {669-683}, pmid = {35112151}, issn = {1432-184X}, mesh = {*Ecosystem ; Soil/chemistry ; Soil Microbiology ; Biodiversity ; *Microbiota ; Climate Change ; }, abstract = {Soil is one of the most important assets of the planet Earth, responsible for maintaining the biodiversity and managing the ecosystem services for both managed and natural ecosystems. It encompasses large proportion of microscopic biodiversity, including prokaryotes and the microscopic eukaryotes. Soil microbiome is critical in managing the soil functions, but their activities have diminutive recognition in few systems like desert land and forest ecosystems. Soil microbiome is highly dependent on abiotic and biotic factors like pH, carbon content, soil structure, texture, and vegetation, but it can notably vary with ecosystems and the respective inhabitants. Thus, unboxing this black box is essential to comprehend the basic components adding to the soil systems and supported ecosystem services. Recent advancements in the field of molecular microbial ecology have delivered commanding tools to examine this genetic trove of soil biodiversity. Objective of this review is to provide a critical evaluation of the work on the soil microbiome, especially since the advent of the NGS techniques. The review also focuses on advances in our understanding of soil communities, their interactions, and functional capabilities along with understanding their role in maneuvering the biogeochemical cycle while underlining and tapping the unprecedented metagenomics data to infer the ecological attributes of yet undiscovered soil microbiome. This review focuses key research directions that could shape the future of basic and applied research into the soil microbiome. This review has led us to understand that it is difficult to generalize that soil microbiome plays a substantiated role in shaping the soil networks and it is indeed a vital resource for sustaining the ecosystem functioning. Exploring soil microbiome will help in unlocking their roles in various soil network. It could be resourceful in exploring and forecasting its impacts on soil systems and for dealing with alleviating problems like rapid climate change.}, } @article {pmid35110685, year = {2022}, author = {Miyauchi, E and Taida, T and Kawasumi, M and Ohkusa, T and Sato, N and Ohno, H}, title = {Analysis of colonic mucosa-associated microbiota using endoscopically collected lavage.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {1758}, pmid = {35110685}, issn = {2045-2322}, mesh = {Bacteria/genetics/isolation & purification ; Cigarette Smoking ; Colon/*microbiology ; DNA, Bacterial ; *Endoscopy ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Intestinal Mucosa/microbiology ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The bacterial composition of the gut lumen and mucosa is distinct and the mucosa-associated bacteria are thought to play a more critical role in interactions with the host immune system. However, limited studies of the gut mucosal microbiota in humans have been available due to methodological challenges. Here, we evaluated the potential use of colonic lavage samples for mucosal microbiota analysis in humans. Among the different types of colonic mucosal samples collected from healthy volunteers, the lavage samples contained a higher amount of bacterial DNA and were less contaminated with host DNA compared to mucosal brushing (brush) and biopsy. Although 16S gene amplicon sequencing showed that the bacterial composition of the lavage was intermediate between that of feces and biopsy, mucosal bacteria abundant in the biopsy were also enriched in lavage samples. Furthermore, differences in mucosal microbes between non-smokers and smokers were detectable in lavage samples. Our data emphasize that colonic lavage is suitable for analysis of the mucosal microbiota. Given its minimal invasiveness and high bacterial DNA content, the colonic lavage will promote research on the human mucosal microbiota, especially in gastrointestinal disorders.}, } @article {pmid35110663, year = {2022}, author = {Ni, J and Yang, H and Chen, L and Xu, J and Zheng, L and Xie, G and Shen, C and Li, W and Liu, Q}, title = {Metagenomic analysis of microbial community structure and function in a improved biofilter with odorous gases.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {1731}, pmid = {35110663}, issn = {2045-2322}, mesh = {Ammonia/analysis ; Biodegradation, Environmental ; Biosolids/*microbiology ; Filtration ; Gases/*analysis ; Hydrogen Sulfide/analysis ; Industrial Waste/*analysis ; *Metagenome ; *Metagenomics ; *Microbiota ; Odorants/*analysis ; Phylogeny ; Sewage/*microbiology ; }, abstract = {Biofilters have been broadly applied to degrade the odorous gases from industrial emissions. A industrial scale biofilter was set up to treat the odorous gases. To explore biofilter potentials, the microbial community structure and function must be well defined. Using of improved biofilter, the differences in microbial community structures and functions in biofilters before and after treatment were investigated by metagenomic analysis. Odorous gases have the potential to alter the microbial community structure in the sludge of biofilter. A total of 90,016 genes assigned into various functional metabolic pathways were identified. In the improved biofilter, the dominant phyla were Proteobacteria, Planctomycetes, and Chloroflexi, and the dominant genera were Thioalkalivibrio, Thauera, and Pseudomonas. Several xenobiotic biodegradation-related pathways showed significant changes during the treatment process. Compared with the original biofilter, Thermotogae and Crenarchaeota phyla were significantly enriched in the improved biofilter, suggesting their important role in nitrogen-fixing. Furthermore, several nitrogen metabolic pathway-related genes, such as nirA and nifA, and sulfur metabolic pathway-related genes, such as fccB and phsA, were considered to be efficient genes that were involved in removing odorous gases. Our findings can be used for improving the efficiency of biofilter and helping the industrial enterprises to reduce the emission of waste gases.}, } @article {pmid35108565, year = {2022}, author = {Mondal, HK and Maji, UJ and Mohanty, S and Sahoo, PK and Maiti, NK}, title = {Alteration of gut microbiota composition and function of Indian major carp, rohu (Labeo rohita) infected with Argulus siamensis.}, journal = {Microbial pathogenesis}, volume = {164}, number = {}, pages = {105420}, doi = {10.1016/j.micpath.2022.105420}, pmid = {35108565}, issn = {1096-1208}, mesh = {Animals ; *Arguloida ; *Carps ; *Fish Diseases/parasitology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Gut microbiome homeostasis is critical in preventing diseases. However, the effect of disease on gut microbiota assembly remains unclear. At present, there are no reports on the composition and functional analysis of intestinal microbiota of Indian major carp, rohu (L. rohita) infected with ectoparasite, Argulus. In this study, we analysed and compared the intestinal microbiota of healthy and Argulus-infected rohu by 16S rRNA amplicon sequencing. Argulus infection could significantly influence the diversity and richness of the gut microbiota. However, abundance of Actinobacteria and Patescibacteria were enriched significantly in Argulus-infected fish. Venn diagram revealed that there were many more unique genera in the infected group as compared to control fish. The genera, Stenotrophomonas and Pirellula were significantly increased in infected fish while the abundance of Reyranella was decreased. LEfSe analysis showed a significant enrichment in abundances of 11 taxa in healthy group and 17 taxa in infected group. Furthermore, genera Rubellimicrobium, Dielma, Hyphomicrobium, Reyranella, Streptomyces and Cloacibacterium performed the best in differentiating between both the groups. Predicted microbiota function by PICRUSt revealed that the gut microbiota of infected fish was mainly associated with enriched synthesis of chitinases, chitin binding proteins, osmoprotectant proteins and sulfatases enzymes. There was a positive association between the structural and functional composition of the gut microbiota. The results indicated that the Argulus infection could affect the intestinal microbiota composition and function of rohu.}, } @article {pmid35108450, year = {2022}, author = {Avirineni, BS and Singh, A and Zapata, RC and Stevens, RD and Phillips, CD and Chelikani, PK}, title = {Diets Containing Egg or Whey Protein and Inulin Fiber Improve Energy Balance and Modulate Gut Microbiota in Exercising Obese Rats.}, journal = {Molecular nutrition & food research}, volume = {66}, number = {7}, pages = {e2100653}, doi = {10.1002/mnfr.202100653}, pmid = {35108450}, issn = {1613-4133}, support = {#G-18-0022205//Heart and Stroke foundation of Canada/ ; NSERC #355993//Natural Sciences and Engineering Research Council of Canada/ ; //Texas Tech University School of Veterinary Medicine/ ; }, mesh = {Animals ; Diet, High-Fat/adverse effects ; Energy Metabolism ; *Gastrointestinal Microbiome ; *Inulin/metabolism/pharmacology ; Male ; Obesity/metabolism ; Rats ; Whey Proteins/pharmacology ; }, abstract = {SCOPE: Dietary protein, prebiotic fiber, and exercise individually have been shown to aid in weight loss; however less is known of their combined effects on energy balance. The effects of diets high in protein and fiber, with exercise, on energy balance, hormones, and gut microbiota, were determined.

METHODS AND RESULTS: Obese male rats were fed high-fat diets with high protein and fiber contents from egg protein and cellulose, egg protein and inulin, whey protein and cellulose, or whey protein and inulin, together with treadmill exercise. We found that inulin enriched diets decreased energy intake and respiratory quotient (RQ), increased energy expenditure (EE), and upregulated transcripts for cholecystokinin (CCK), peptide YY, and proglucagon in distal gut. Notably, CCK1-receptor blockade attenuated the hypophagic effects of diets and in particular whey-inulin diet, and β-adrenergic blockade reduced EE across all diets. Egg-cellulose, egg-inulin, and whey-inulin diets decreased weight gain, adiposity, and hepatic lipidosis; decreased lipogenic transcripts, improved glycemic control, and upregulated hepatic glucose metabolism transcripts; and decreased plasma insulin and leptin. Importantly, diet was linked to altered gut microbial composition and plasma metabolomics, and a subset of predicted metagenome pathways and plasma metabolites significantly correlated, with plasma butyric acid the most strongly associated to metagenome function.

CONCLUSION: Combination of dietary egg or whey protein with inulin and exercise improved energy balance, glucose metabolism, upregulated anorectic hormones, and selectively modulated gut microbiota and plasma metabolites.}, } @article {pmid35108096, year = {2022}, author = {Scales, NC and Chase, AB and Finks, SS and Malik, AA and Weihe, C and Allison, SD and Martiny, AC and Martiny, JBH}, title = {Differential Response of Bacterial Microdiversity to Simulated Global Change.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {6}, pages = {e0242921}, pmid = {35108096}, issn = {1098-5336}, mesh = {Bacteria/genetics ; *Ecosystem ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Soil ; Soil Microbiology ; }, abstract = {Global change experiments often observe shifts in bacterial community composition based on 16S rRNA gene sequences. However, this genetic region can mask a large amount of genetic and phenotypic variation among bacterial strains sharing even identical 16S regions. As such, it remains largely unknown whether variation at the sub-16S level, sometimes termed microdiversity, responds to environmental perturbations and whether such changes are relevant to ecosystem processes. Here, we investigated microdiversity within Curtobacterium, the dominant bacterium found in the leaf litter layer of soil, to simulated drought and nitrogen addition in a field experiment. We first developed and validated Curtobacterium-specific primers of the groEL gene to assess microdiversity within this lineage. We then tracked the response of this microdiversity to simulated global change in two adjacent plant communities, grassland and coastal sage scrub (CSS). Curtobacterium microdiversity responded to drought but not nitrogen addition, indicating variation within the genus of drought tolerance but not nitrogen response. Further, the response of microdiversity to drought depended on the ecosystem, suggesting that litter substrate selects for a distinct composition of microdiversity that is constrained in its response, perhaps related to tradeoffs in resource acquisition traits. Supporting this interpretation, a metagenomic analysis revealed that the composition of Curtobacterium-encoded carbohydrate-active enzymes (CAZymes) varied distinctly across the two ecosystems. Identifying the degree to which relevant traits are phylogenetically conserved may help to predict when the aggregated response of a 16S-defined taxon masks differential responses of finer-scale bacterial diversity to global change. IMPORTANCE Microbial communities play an integral role in global biogeochemical cycling, but our understanding of how global change will affect microbial community structure and functioning remains limited. Microbiome analyses typically aggregate large amounts of genetic diversity which may obscure finer variation in traits. This study found that fine-scale diversity (or microdiversity) within the bacterial genus Curtobacterium was affected by simulated global changes. However, the degree to which this was true depended on the type of global change, as the composition of Curtobacterium microdiversity was affected by drought, but not by nitrogen addition. Further, these changes were associated with variation in carbon degradation traits. Future work might improve predictions of microbial community responses to global change by considering microdiversity.}, } @article {pmid35107340, year = {2022}, author = {Baumann, KBL and Thoma, R and Callbeck, CM and Niederdorfer, R and Schubert, CJ and Müller, B and Lever, MA and Bürgmann, H}, title = {Microbial Nitrogen Transformation Potential in Sediments of Two Contrasting Lakes Is Spatially Structured but Seasonally Stable.}, journal = {mSphere}, volume = {7}, number = {1}, pages = {e0101321}, pmid = {35107340}, issn = {2379-5042}, mesh = {Eutrophication ; *Lakes/microbiology ; *Microbiota ; Nitrates/analysis ; Nitrogen ; }, abstract = {The nitrogen (N) cycle is of global importance, as N is an essential element and a limiting nutrient in terrestrial and aquatic ecosystems. Excessive anthropogenic N fertilizer usage threatens sensitive downstream aquatic ecosystems. Although freshwater lake sediments remove N through various microbially mediated processes, few studies have investigated the microbial communities involved. In an integrated biogeochemical and microbiological study on a eutrophic and oligotrophic lake, we estimated N removal rates from pore water concentration gradients in sediments. Simultaneously, the abundance of different microbial N transformation genes was investigated using metagenomics on a seasonal and spatial scale. We observed that contrasting nutrient concentrations in sediments were associated with distinct microbial community compositions and significant differences in abundances of various N transformation genes. For both characteristics, we observed a more pronounced spatial than seasonal variability within each lake. The eutrophic Lake Baldegg showed a higher denitrification potential with higher nosZ gene (N2O reductase) abundances and higher nirS:nirK (nitrite reductase) ratios, indicating a greater capacity for complete denitrification. Correspondingly, this lake had a higher N removal efficiency. The oligotrophic Lake Sarnen, in contrast, had a higher potential for nitrification. Specifically, it harbored a high abundance of Nitrospira, including some with the potential for comammox. Our results demonstrate that knowledge of the genomic N transformation potential is important for interpreting N process rates and understanding how the lacustrine sedimentary N cycle responds to variations in trophic conditions. IMPORTANCE Anthropogenic nitrogen (N) inputs can lead to eutrophication in surface waters, especially in N-limited coastal ecosystems. Lakes effectively remove reactive N by transforming it to N2 through microbial denitrification or anammox. The rates and distributions of these microbial processes are affected by factors such as the amount and quality of settling organic material and nitrate concentrations. However, the microbial communities mediating these N transformation processes in freshwater lake sediments remain largely unknown. We provide the first seasonally and spatially resolved metagenomic analysis of the N cycle in sediments of two lakes with different trophic states. We show that lakes with different trophic states select for distinct communities of N-cycling microorganisms with contrasting functional potentials for N transformation.}, } @article {pmid35107058, year = {2023}, author = {Torquati, L and Gajanand, T and Cox, ER and Willis, CRG and Zaugg, J and Keating, SE and Coombes, JS}, title = {Effects of exercise intensity on gut microbiome composition and function in people with type 2 diabetes.}, journal = {European journal of sport science}, volume = {23}, number = {4}, pages = {530-541}, doi = {10.1080/17461391.2022.2035436}, pmid = {35107058}, issn = {1536-7290}, mesh = {Humans ; *Diabetes Mellitus, Type 2 ; *Gastrointestinal Microbiome ; Prospective Studies ; Exercise ; Butyrates ; }, abstract = {Exercise is positively associated with higher microbial diversity, but there is limited information on exercise intensity's effect on gut microbiome composition and function in clinical populations. This study examines whether different intensities of exercise exert differential effects on gut microbiome composition and function in low active people with type 2 diabetes. This is a sub-study of the Exercise for Type 2 Diabetes Study, a single centre, prospective, randomised controlled trial. Participants (n = 12) completed 8-weeks of combined aerobic and resistance moderate intensity continuous training (C-MICT) or combined aerobic and resistance high-intensity interval training (C-HIIT). Faecal samples were collected before and after intervention to measure gut microbiome composition and metabolic pathways (metagenome shotgun sequencing) and short-chain fatty acids. Post-exercise α-diversity was different between groups as was the relative abundance of specific taxa was (p < .05). Post-exercise relative abundance of Bifidobacterium, A. municiphila, and butyrate-producers Lachnospira eligens, Enterococcus spp., and Clostridium Cluster IV were higher at lower exercise intensity. Other butyrate-producers (from Eryspelothrichales and Oscillospirales), and methane producer Methanobrevibacter smithii were higher at higher exercise intensity. Pyruvate metabolism (ko00620),COG "Cell wall membrane envelope biogenesis" and "Unknown function" pathways were significantly different between groups and higher in C-MICT post-exercise. Differential abundance analysis on KO showed higher expression of Two-component system in C-HIIT. Transcription factors and "unknown metabolism" related pathways decreased in both groups. There were no significant between group changes in faecal short chain fatty acids. Exercise intensity had a distinct effect on gut microbiome abundance and metabolic function, without impacting short-chain fatty acid output.HighlightsEvidence of exercise effect on gut microbiome outcomes is limited to healthy and athletic populationsIn low active people with type 2 diabetes, different exercise intensities increased specific health promoting and butyrate producers species, and showed differentially abundant gut microbiome metabolic pathways.Further investigation is warranted, and if this supports the present findings, then specific exercise intensities may be promoted to target specific species and optimise gut health.}, } @article {pmid35105664, year = {2022}, author = {de Vos, WM and Tilg, H and Van Hul, M and Cani, PD}, title = {Gut microbiome and health: mechanistic insights.}, journal = {Gut}, volume = {71}, number = {5}, pages = {1020-1032}, pmid = {35105664}, issn = {1468-3288}, mesh = {Bacteria/metabolism ; Bile Acids and Salts/metabolism ; *Diabetes Mellitus, Type 2 ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Humans ; Receptors, G-Protein-Coupled/metabolism ; }, abstract = {The gut microbiota is now considered as one of the key elements contributing to the regulation of host health. Virtually all our body sites are colonised by microbes suggesting different types of crosstalk with our organs. Because of the development of molecular tools and techniques (ie, metagenomic, metabolomic, lipidomic, metatranscriptomic), the complex interactions occurring between the host and the different microorganisms are progressively being deciphered. Nowadays, gut microbiota deviations are linked with many diseases including obesity, type 2 diabetes, hepatic steatosis, intestinal bowel diseases (IBDs) and several types of cancer. Thus, suggesting that various pathways involved in immunity, energy, lipid and glucose metabolism are affected.In this review, specific attention is given to provide a critical evaluation of the current understanding in this field. Numerous molecular mechanisms explaining how gut bacteria might be causally linked with the protection or the onset of diseases are discussed. We examine well-established metabolites (ie, short-chain fatty acids, bile acids, trimethylamine N-oxide) and extend this to more recently identified molecular actors (ie, endocannabinoids, bioactive lipids, phenolic-derived compounds, advanced glycation end products and enterosynes) and their specific receptors such as peroxisome proliferator-activated receptor alpha (PPARα) and gamma (PPARγ), aryl hydrocarbon receptor (AhR), and G protein-coupled receptors (ie, GPR41, GPR43, GPR119, Takeda G protein-coupled receptor 5).Altogether, understanding the complexity and the molecular aspects linking gut microbes to health will help to set the basis for novel therapies that are already being developed.}, } @article {pmid35103487, year = {2022}, author = {No, JH and Nishu, SD and Hong, JK and Lyou, ES and Kim, MS and Wee, GN and Lee, TK}, title = {Raman-Deuterium Isotope Probing and Metagenomics Reveal the Drought Tolerance of the Soil Microbiome and Its Promotion of Plant Growth.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0124921}, pmid = {35103487}, issn = {2379-5077}, mesh = {*Soil/chemistry ; Drought Resistance ; Plant Growth Regulators ; Deuterium ; Metagenomics ; *Microbiota ; Plants/microbiology ; }, abstract = {Drought has become a major agricultural threat leading crop yield loss. Although a few species of rhizobacteria have the ability to promote plant growth under drought, the drought tolerance of the soil microbiome and its relationship with the promotion of plant growth under drought are scarcely studied. This study aimed to develop a novel approach for assessing drought tolerance in agricultural land by quantitatively measuring microbial phenotypes using stable isotopes and Raman spectroscopy. Raman spectroscopy with deuterium isotope probing was used to identify the Raman signatures of drought effects from drought-tolerant bacteria. Counting drought-tolerant cells by applying these phenotypic properties to agricultural samples revealed that 0% to 52.2% of all measured single cells had drought-tolerant properties, depending on the soil sample. The proportions of drought-tolerant cells in each soil type showed similar tendencies to the numbers of revived pea plants cultivated under drought. The phenotype of the soil microbiome and plant behavior under drought conditions therefore appeared to be highly related. Studying metagenomics suggested that there was a reliable link between the phenotype and genotype of the soil microbiome that could explain mechanisms that promote plant growth in drought. In particular, the proportion of drought-tolerant cells was highly correlated with genes encoding phytohormone production, including tryptophan synthase and isopentenyl-diphosphate delta-isomerase; these enzymes are known to alleviate drought stress. Raman spectroscopy with deuterium isotope probing shows high potential as an alternative technology for quantitatively assessing drought tolerance through phenotypic analysis of the soil microbiome. IMPORTANCE Soil microbiome has played a critical role in the plant survival during drought. However, the drought tolerance of soil microbiome and its ability to promote plant growth under drought is still scarcely studied. In this study, we identified the Raman signature (i.e., phenotype) of drought effects from drought-tolerant bacteria in agricultural soil samples using Raman-deuterium isotope probing (Raman-DIP). Moreover, the number of drought-tolerant cells measured by Raman-DIP was highly related to the survival rate of plant cultivation under drought and the abundance of genes encoding phytohormone production alleviating drought stress in plant. These results suggest Raman-DIP is a promising technology for measuring drought tolerance of soil microbiome. This result give us important insight into further studies of a reliable link between phenotype and genotype of soil microbiome for future plant-bacteria interaction research.}, } @article {pmid35103093, year = {2022}, author = {Zhao, G and Xiang, Y and Wang, X and Dai, B and Zhang, X and Ma, L and Yang, H and Lyu, W}, title = {Exploring the Possible Link between the Gut Microbiome and Fat Deposition in Pigs.}, journal = {Oxidative medicine and cellular longevity}, volume = {2022}, number = {}, pages = {1098892}, pmid = {35103093}, issn = {1942-0994}, mesh = {Abdominal Fat/*metabolism/pathology ; Acetyl-CoA Carboxylase/genetics/metabolism ; Animals ; Archaea/genetics/isolation & purification/metabolism ; Bacteria/genetics/isolation & purification/metabolism ; Colon/metabolism/microbiology ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Glutathione Peroxidase/blood ; Liver/metabolism ; Malondialdehyde/blood ; Metagenomics ; Muscle, Skeletal/pathology/physiology ; Oxidative Stress/genetics ; PPAR gamma/genetics/metabolism ; Swine ; }, abstract = {Excessive lipid accumulation and high oxidative stress have become a serious health and economic problem in the pig industry. Fatness characteristics are crucial in pig production since they are closely related to meat quality. The gut microbiome is well acknowledged as a key element in fat deposition. But the link between gut microbiota and fat accumulation in pigs remains elusive. To examine whether there is a link between pigs' gut microbiome, lipogenic properties, and oxidative stress, we selected 5 high-fat pigs and 5 low-fat pigs from 60 250-day-old Jinhua pigs in the present study and collected the colon content, serum sample, and liver and abdominal fat segments from each pig for metagenomic analysis, the oxidative stress assay, and RT-qPCR analysis, respectively. The backfat thickness and fat content of the longissimus dorsi muscle were considerably higher in the high-fat pigs than in the low-fat pigs (P < 0.05). An obvious difference in GSH-Px and MDA in the serum between the high- and low-fat pigs was observed. After RT-qPCR analysis, we found the gene expression of ACC1 and SREBP1 in the liver and FAS, PPARγ, and LPL in the abdominal fat were significantly higher in high-fat pigs than in low-fat pigs (P < 0.05). Additionally, metagenomic sequencing revealed that high-fat pigs had a higher abundance of Archaeal species with methanogenesis functions, leading to more-efficient fat deposition, while low-fat pigs had higher abundances of butyrate-producing bacteria species that improved the formation of SCFAs, especially butyrate, thus alleviating fat deposition in pigs. Furthermore, a total of 17 CAZyme families were identified to give significant enrichments in different fat phenotypes of pigs. This study would provide a detailed understanding of how the gut microbiome influences fat deposition in pigs, as well as a hint for improving growth performance and fatness traits by manipulating the gut microbiome.}, } @article {pmid35102501, year = {2022}, author = {Gurbanov, R and Kabaoğlu, U and Yağcı, T}, title = {Metagenomic analysis of intestinal microbiota in wild rats living in urban and rural habitats.}, journal = {Folia microbiologica}, volume = {67}, number = {3}, pages = {469-477}, pmid = {35102501}, issn = {1874-9356}, support = {2019-01. BŞEÜ.01-01//Scientific Research Project fund of Bilecik Şeyh Edebali University/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mammals/genetics ; Metagenome ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Rats ; }, abstract = {Mammals have a symbiotic relationship with various microorganisms called microbiota throughout their lives. These microorganisms are known to affect the host's physiology, health, and even mental balance. The development of the gut microbiota is regulated by a complex interaction between host and environmental factors, including diet and lifestyle. Herein, it is aimed to elucidate the differences in the gut microbiota of rats living in urban and rural habitats. The taxonomic changes in the gut microbiota of wild rats belonging to Rattus rattus species caught from urban and rural areas of Western Anatolian (Bilecik province) were examined comparatively by 16S rRNA next-generation sequencing technique. Laboratory rats were used as reference animals. The alpha diversities were found lower in the rural rats with respect to the urban rats, whereas the highest alpha diversity was calculated for laboratory rats. The lower Firmicutes to Bacteroidetes ratios (F/B ratio) were accounted for both rural and laboratory rats compared with urban rats. The Proteobacteria to Actinobacteria ratio (P/A ratio) was lower for rural rats, but higher for laboratory rats, compared with urban rats. The heatmap analyses of taxonomic units in the microbiota of each group demonstrated distinct patterns at the species and genus levels. The study provided metagenomic data on the gut microbiota of rats residing in urban and rural habitats, offering a different perspective on future environmental biomonitoring studies.}, } @article {pmid35102136, year = {2022}, author = {Siranosian, BA and Brooks, EF and Andermann, T and Rezvani, AR and Banaei, N and Tang, H and Bhatt, AS}, title = {Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {586}, pmid = {35102136}, issn = {2041-1723}, support = {P01 CA049605/CA/NCI NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; /CC/CDC HHS/United States ; }, mesh = {Adult ; Aged ; Anti-Bacterial Agents/pharmacology ; Bacteria/*metabolism ; Bacterial Infections/*transmission ; Cross Infection/microbiology/transmission ; Drug Resistance, Microbial/drug effects/genetics ; Enterococcus faecium/drug effects/isolation & purification ; Escherichia coli/drug effects/isolation & purification ; Female ; *Gastrointestinal Microbiome/drug effects ; Hematopoietic Stem Cell Transplantation ; *Hospitalization ; Hospitals ; Humans ; Length of Stay ; Male ; Metagenome/genetics ; Metagenomics ; Middle Aged ; Phylogeny ; Probiotics ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Bacterial bloodstream infections are a major cause of morbidity and mortality among patients undergoing hematopoietic cell transplantation (HCT). Although previous research has demonstrated that pathogens may translocate from the gut microbiome into the bloodstream to cause infections, the mechanisms by which HCT patients acquire pathogens in their microbiome have not yet been described. Here, we use linked-read and short-read metagenomic sequencing to analyze 401 stool samples collected from 149 adults undergoing HCT and hospitalized in the same unit over three years, many of whom were roommates. We use metagenomic assembly and strain-specific comparison methods to search for high-identity bacterial strains, which may indicate transmission between the gut microbiomes of patients. Overall, the microbiomes of patients who share time and space in the hospital do not converge in taxonomic composition. However, we do observe six pairs of patients who harbor identical or nearly identical strains of the pathogen Enterococcus faecium, or the gut commensals Akkermansia muciniphila and Hungatella hathewayi. These shared strains may result from direct transmission between patients who shared a room and bathroom, acquisition from a common hospital source, or transmission from an unsampled intermediate. We also identify multiple patients with identical strains of species commonly found in commercial probiotics, including Lactobacillus rhamnosus and Streptococcus thermophilus. In summary, our findings indicate that sharing of identical pathogens between the gut microbiomes of multiple patients is a rare phenomenon. Furthermore, the observed potential transmission of commensal, immunomodulatory microbes suggests that exposure to other humans may contribute to microbiome reassembly post-HCT.}, } @article {pmid35100347, year = {2022}, author = {Ruuskanen, MO and Erawijantari, PP and Havulinna, AS and Liu, Y and Méric, G and Tuomilehto, J and Inouye, M and Jousilahti, P and Salomaa, V and Jain, M and Knight, R and Lahti, L and Niiranen, TJ}, title = {Gut Microbiome Composition Is Predictive of Incident Type 2 Diabetes in a Population Cohort of 5,572 Finnish Adults.}, journal = {Diabetes care}, volume = {45}, number = {4}, pages = {811-818}, pmid = {35100347}, issn = {1935-5548}, support = {CH/12/2/29428/BHF_/British Heart Foundation/United Kingdom ; RG/13/13/30194/BHF_/British Heart Foundation/United Kingdom ; RG/18/13/33946/BHF_/British Heart Foundation/United Kingdom ; }, mesh = {Adult ; Cohort Studies ; Cross-Sectional Studies ; *Diabetes Mellitus, Type 2/epidemiology ; Female ; Finland/epidemiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Middle Aged ; }, abstract = {OBJECTIVE: To examine the previously unknown long-term association between gut microbiome composition and incident type 2 diabetes in a representative population cohort.

RESEARCH DESIGN AND METHODS: We collected fecal samples from 5,572 Finns (mean age 48.7 years; 54.1% women) in 2002 who were followed up for incident type 2 diabetes until 31 December 2017. The samples were sequenced using shotgun metagenomics. We examined associations between gut microbiome composition and incident diabetes using multivariable-adjusted Cox regression models. We first used the eastern Finland subpopulation to obtain initial findings and validated these in the western Finland subpopulation.

RESULTS: Altogether, 432 cases of incident diabetes occurred over the median follow-up of 15.8 years. We detected four species and two clusters consistently associated with incident diabetes in the validation models. These four species were Clostridium citroniae (hazard ratio [HR] 1.21; 95% CI 1.04-1.42), C. bolteae (HR 1.20; 95% CI 1.04-1.39), Tyzzerella nexilis (HR 1.17; 95% CI 1.01-1.36), and Ruminococcus gnavus (HR 1.17; 95% CI 1.01-1.36). The positively associated clusters, cluster 1 (HR 1.18; 95% CI 1.02-1.38) and cluster 5 (HR 1.18; 95% CI 1.02-1.36), mostly consisted of these same species.

CONCLUSIONS: We observed robust species-level taxonomic features predictive of incident type 2 diabetes over long-term follow-up. These findings build on and extend previous mainly cross-sectional evidence and further support links between dietary habits, metabolic diseases, and type 2 diabetes that are modulated by the gut microbiome. The gut microbiome can potentially be used to improve disease prediction and uncover novel therapeutic targets for diabetes.}, } @article {pmid35100064, year = {2022}, author = {Vuong, P and Wise, MJ and Whiteley, AS and Kaur, P}, title = {Small investments with big returns: environmental genomic bioprospecting of microbial life.}, journal = {Critical reviews in microbiology}, volume = {48}, number = {5}, pages = {641-655}, doi = {10.1080/1040841X.2021.2011833}, pmid = {35100064}, issn = {1549-7828}, mesh = {Biodegradation, Environmental ; Bioprospecting ; Metagenome ; *Metagenomics/methods ; *Microbiota/physiology ; }, abstract = {Microorganisms and their natural products are major drivers of ecological processes and industrial applications. Microbial bioprospecting has been critical for the advancement in various fields such as pharmaceuticals, sustainable industries, food security and bioremediation. Next generation sequencing has been paramount in the exploration of diverse environmental microbiomes. It presents a culture-independent approach to investigating hitherto uncultured taxa, resulting in the creation of massive sequence databases, which are available in the public domain. Genome mining searches available (meta)genomic data for target biosynthetic genes, and combined with the large-scale public data, this in-silico bioprospecting method presents an efficient and extensive way to uncover microbial bioproducts. Bioinformatic tools have progressed to a stage where we can recover genomes from the environment; these metagenome-assembled genomes present a way to understand the metabolic capacity of microorganisms in a physiological and ecological context. Environmental sampling been extensive across various ecological settings, including microbiomes with unique physicochemical properties that could influence the discovery of novel functions and metabolic pathways. Although in-silico methods cannot completely substitute in-vitro studies, the contextual information it provides is invaluable for understanding the ecological and taxonomic distribution of microbial genotypes and to form effective strategies for future microbial bioprospecting efforts.}, } @article {pmid35095912, year = {2021}, author = {Yang, K and Deng, X and Jian, S and Zhang, M and Wen, C and Xin, Z and Zhang, L and Tong, A and Ye, S and Liao, P and Xiao, Z and He, S and Zhang, F and Deng, J and Zhang, L and Deng, B}, title = {Gallic Acid Alleviates Gut Dysfunction and Boosts Immune and Antioxidant Activities in Puppies Under Environmental Stress Based on Microbiome-Metabolomics Analysis.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {813890}, pmid = {35095912}, issn = {1664-3224}, mesh = {Age Factors ; Animal Feed ; Animals ; Antioxidants/*pharmacology ; Biomarkers ; Dogs ; Environment ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Gallic Acid/*pharmacology ; Gas Chromatography-Mass Spectrometry ; Gastrointestinal Microbiome/*drug effects ; Immunologic Factors/*pharmacology ; Lipid Metabolism/drug effects ; Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Microbiota/*drug effects ; RNA, Ribosomal, 16S ; Stress, Physiological/*drug effects ; }, abstract = {Early-life exposure to environmental stress disrupts the gut barrier and leads to inflammatory responses and changes in gut microbiota composition. Gallic acid (GA), a natural plant polyphenol, has received significant interest for its antioxidant, anti-inflammatory, and antimicrobial properties that support the maintenance of intestinal health. To assess whether dietary supplementation of GA alleviates environmental stress, a total of 19 puppies were randomly allocated to the following three dietary treatments for 2 weeks: 1) basal diet (control (CON)); 2) basal diet + transportation (TS); and 3) basal diet with the addition of 500 mg/kg of GA + transportation (TS+GA). After a 1-week supplementation period, puppies in the TS and TS+GA groups were transported from a stressful environment to another livable location, and puppies in the CON group were then left in the stressful environment. Results indicated that GA markedly reduced the diarrhea rate in puppies throughout the trial period and caused a moderate decline of serum cortisol and HSP-70 levels after transportation. Also, GA alleviated the oxidative stress and inflammatory response caused by multiple environmental stressors. Meanwhile, puppies fed GA had a higher abundance of fecal Firmicutes and Lactobacillus and lower Proteobacteria, Escherichia-Shigella, and Clostridium_sensu_stricto_1 after transportation. As a result, the TS+GA group had the highest total short-chain fatty acids and acetic acid. Also, the fecal and serum metabolomics analyses revealed that GA markedly reversed the abnormalities of amino acid metabolism, lipid metabolism, carbohydrate metabolism, and nucleotide metabolism caused by stresses. Finally, Spearman's correlation analysis was carried out to explore the comprehensive microbiota and metabolite relationships. Overall, dietary supplementation of GA alleviates oxidative stress and inflammatory response in stressed puppies by causing beneficial shifts on gut microbiota and metabolites that may support gut and host health.}, } @article {pmid35095808, year = {2021}, author = {Wang, N and Li, H and Wang, B and Ding, J and Liu, Y and Wei, Y and Li, J and Ding, GC}, title = {Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and Compost.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {798476}, pmid = {35095808}, issn = {1664-302X}, abstract = {Compost is frequently served as the first reservoir for plants to recruit rhizosphere microbiome when used as growing substrate in the seedling nursery. In the present study, recruitment of rhizosphere microbiome from two composts by tomato, pepper, or maize was addressed by shotgun metagenomics and 16S rRNA amplicon sequencing. The 16S rRNA amplicon sequencing analysis showed that 41% of variation in the rhizosphere bacterial community was explained by compost, in contrast to 23% by plant species. Proteobacterial genera were commonly recruited by all three plant species with specific selections for Ralstonia by tomato and Enterobacteria by maize. These findings were confirmed by analysis of 16S rRNA retrieved from the shotgun metagenomics library. Approximately 70% of functional gene clusters differed more than sevenfold in abundance between rhizosphere and compost. Functional groups associated with the sensing and up-taking of C3 and C4 carboxylic acids, amino acids, monosaccharide, production of antimicrobial substances, and antibiotic resistance were over-represented in the rhizosphere. In summary, compost and plant species synergistically shaped the composition of the rhizosphere microbiome and selected for functional traits associated with the competition on root exudates.}, } @article {pmid35094961, year = {2022}, author = {Cantoni, C and Lin, Q and Dorsett, Y and Ghezzi, L and Liu, Z and Pan, Y and Chen, K and Han, Y and Li, Z and Xiao, H and Gormley, M and Liu, Y and Bokoliya, S and Panier, H and Suther, C and Evans, E and Deng, L and Locca, A and Mikesell, R and Obert, K and Newland, P and Wu, Y and Salter, A and Cross, AH and Tarr, PI and Lovett-Racke, A and Piccio, L and Zhou, Y}, title = {Alterations of host-gut microbiome interactions in multiple sclerosis.}, journal = {EBioMedicine}, volume = {76}, number = {}, pages = {103798}, pmid = {35094961}, issn = {2352-3964}, support = {P30 DK052574/DK/NIDDK NIH HHS/United States ; R01 NS102633/NS/NINDS NIH HHS/United States ; UL1 TR000448/TR/NCATS NIH HHS/United States ; UL1 TR002345/TR/NCATS NIH HHS/United States ; }, mesh = {Chromatography, Liquid ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolome ; Metagenomics ; *Multiple Sclerosis/etiology ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: Multiple sclerosis (MS) has a complex genetic, immune and metabolic pathophysiology. Recent studies implicated the gut microbiome in MS pathogenesis. However, interactions between the microbiome and host immune system, metabolism and diet have not been studied over time in this disorder.

METHODS: We performed a six-month longitudinal multi-omics study of 49 participants (24 untreated relapse remitting MS patients and 25 age, sex, race matched healthy control individuals. Gut microbiome composition and function were characterized using 16S and metagenomic shotgun sequencing. Flow cytometry was used to characterize blood immune cell populations and cytokine profiles. Circulating metabolites were profiled by untargeted UPLC-MS. A four-day food diary was recorded to capture the habitual dietary pattern of study participants.

FINDINGS: Together with changes in blood immune cells, metagenomic analysis identified a number of gut microbiota decreased in MS patients compared to healthy controls, and microbiota positively or negatively correlated with degree of disability in MS patients. MS patients demonstrated perturbations of their blood metabolome, such as linoleate metabolic pathway, fatty acid biosynthesis, chalcone, dihydrochalcone, 4-nitrocatechol and methionine. Global correlations between multi-omics demonstrated a disrupted immune-microbiome relationship and a positive blood metabolome-microbiome correlation in MS. Specific feature association analysis identified a potential correlation network linking meat servings with decreased gut microbe B. thetaiotaomicron, increased Th17 cell and greater abundance of meat-associated blood metabolites. The microbiome and metabolome profiles remained stable over six months in MS and control individuals.

INTERPRETATION: Our study identified multi-system alterations in gut microbiota, immune and blood metabolome of MS patients at global and individual feature level. Multi-OMICS data integration deciphered a potential important biological network that links meat intakes with increased meat-associated blood metabolite, decreased polysaccharides digesting bacteria, and increased circulating proinflammatory marker.

FUNDING: This work was supported by the Washington University in St. Louis Institute of Clinical and Translational Sciences, funded, in part, by Grant Number # UL1 TR000448 from the National Institutes of Health, National Center for Advancing Translational Sciences, Clinical and Translational Sciences Award (Zhou Y, Piccio, L, Lovett-Racke A and Tarr PI); R01 NS10263304 (Zhou Y, Piccio L); the Leon and Harriet Felman Fund for Human MS Research (Piccio L and Cross AH). Cantoni C. was supported by the National MS Society Career Transition Fellowship (TA-180531003) and by donations from Whitelaw Terry, Jr. / Valerie Terry Fund. Ghezzi L. was supported by the Italian Multiple Sclerosis Society research fellowship (FISM 2018/B/1) and the National Multiple Sclerosis Society Post-Doctoral Fellowship (FG-190734474). Anne Cross was supported by The Manny & Rosalyn Rosenthal-Dr. John L. Trotter MS Center Chair in Neuroimmunology of the Barnes-Jewish Hospital Foundation. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.}, } @article {pmid35093600, year = {2022}, author = {Shu, W and Shanjian, C and Jinpiao, L and Qishui, O}, title = {Gut microbiota dysbiosis in patients with hepatitis B virus-related cirrhosis.}, journal = {Annals of hepatology}, volume = {27}, number = {2}, pages = {100676}, doi = {10.1016/j.aohep.2022.100676}, pmid = {35093600}, issn = {1665-2681}, mesh = {Dysbiosis/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Hepatitis B virus/genetics ; Humans ; Liver Cirrhosis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {INTRODUCTION AND AIM: Chronic hepatitis B (CHB) is a global epidemic disease that results from hepatitis B virus (HBV) infection and may progress to liver cirrhosis. The relationship between hepatitis B virus-related cirrhosis (HBV-RC) and gut microbiota dysbiosis is still unclear. The aim of this study is to elucidate the compositional and functional characteristics of the gut microbiota in the patients with liver cirrhosis and healthy individuals.

MATERIALS AND METHODS: We analyzed the gut microbiome in patients with HBV-RC and healthy individuals by 16S rRNA sequencing and metagenomic sequencing of fecal samples. A total of 113 genera, 85 families, 57 orders, 44 classes and 21 phyla were performed.

RESULTS: Our results suggests that the composition of the gut microbiota had changed in the early stages of cirrhosis. We further identified more than 17 genera with different richness in compensated and decompensated cirrhosis groups. PICRUSt analysis showed that changes in bacterial composition can lead to significant changes in gene function, which may be one of the causes of liver cirrhosis.

CONCLUSION: Our study demonstrated that the composition of gut microbiota changed at different phases of HBV-RC. Gut microbiome transformation may be a biological factor in the progression of cirrhosis.}, } @article {pmid35093028, year = {2022}, author = {Cazals, A and Estellé, J and Bruneau, N and Coville, JL and Menanteau, P and Rossignol, MN and Jardet, D and Bevilacqua, C and Rau, A and Bed'Hom, B and Velge, P and Calenge, F}, title = {Differences in caecal microbiota composition and Salmonella carriage between experimentally infected inbred lines of chickens.}, journal = {Genetics, selection, evolution : GSE}, volume = {54}, number = {1}, pages = {7}, pmid = {35093028}, issn = {1297-9686}, mesh = {Animals ; Chickens/genetics ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Salmonella Infections, Animal/genetics ; Salmonella enteritidis/genetics ; }, abstract = {BACKGROUND: Salmonella Enteritidis (SE) is one of the major causes of human foodborne intoxication resulting from consumption of contaminated poultry products. Genetic selection of animals that are more resistant to Salmonella carriage and modulation of the gut microbiota are two promising ways to decrease individual Salmonella carriage. The aims of this study were to identify the main genetic and microbial factors that control the level of Salmonella carriage in chickens (Gallus gallus) under controlled experimental conditions. Two-hundred and forty animals from the White Leghorn inbred lines N and 61 were infected by SE at 7 days of age. After infection, animals were kept in isolators to reduce recontamination of birds by Salmonella. Caecal contents were sampled at 12 days post-infection and used for DNA extraction. Microbiota DNA was used to measure individual counts of SE by digital PCR and to determine the bacterial taxonomic composition, using a 16S rRNA gene high-throughput sequencing approach.

RESULTS: Our results confirmed that the N line is more resistant to Salmonella carriage than the 61 line, and that intra-line variability is higher for the 61 line. Furthermore, the 16S analysis showed strong significant differences in microbiota taxonomic composition between the two lines. Among the 617 operational taxonomic units (OTU) observed, more than 390 were differentially abundant between the two lines. Furthermore, within the 61 line, we found a difference in the microbiota taxonomic composition between the high and low Salmonella carriers, with 39 differentially abundant OTU. Using metagenome functional prediction based on 16S data, several metabolic pathways that are potentially associated to microbiota taxonomic differences (e.g. short chain fatty acids pathways) were identified between high and low carriers.

CONCLUSIONS: Overall, our findings demonstrate that the caecal microbiota composition differs between genetic lines of chickens. This could be one of the reasons why the investigated lines differed in Salmonella carriage levels under experimental infection conditions.}, } @article {pmid35090847, year = {2022}, author = {Zhang, M and Zhou, Z and Zhang, J and Yu, Y and Sun, L and Lu, T and Qian, H}, title = {Metagenomic ecotoxicity assessment of trace difenoconazole on freshwater microbial community.}, journal = {Chemosphere}, volume = {294}, number = {}, pages = {133742}, doi = {10.1016/j.chemosphere.2022.133742}, pmid = {35090847}, issn = {1879-1298}, mesh = {*Dioxolanes/toxicity ; Fresh Water ; *Fungicides, Industrial/metabolism ; *Microbiota ; Triazoles/chemistry ; }, abstract = {Difenoconazole, a typical triazole fungicide, inhibits the activity of cytochrome P450 enzyme in fungi, and is extensively used in protecting fruits, vegetables, and cereal crops. However, reports elucidating the effects of difenoconazole on aquatic microbial communities are limited. Our study showed that difenoconazole promoted microalgae growth at concentrations ranging from 0.1 to 5 μg/L, which was similar with its environmental residual concentrations. Metagenomic analysis revealed that the aquatic microbial structure could self-regulate to cope with difenoconazole-induced stress by accumulating bacteria exhibiting pollutant degrading abilities. In the short-term, several functional pathways related to xenobiotic biodegradation and analysis were upregulated to provide ability for aquatic microbial community to process xenobiotic stress. Moreover, most disturbed ecological functions were recovered due to the redundancy of microbial communities after prolonged exposure. Furthermore, the risks associated with the dissemination of antibiotic resistance genes were enhanced by difenoconazole in the short-term. Overall, our study contributes to a comprehensive understanding of the difenoconazole-induced ecological impacts and the behavior of aquatic microbial communities that are coping with xenobiotic stress.}, } @article {pmid35089099, year = {2022}, author = {Xia, R and Shi, Y and Wang, X and Wu, Y and Sun, M and Hu, F}, title = {Metagenomic Sequencing Reveals that the Assembly of Functional Genes and Taxa Varied Highly and Lacked Redundancy in the Earthworm Gut Compared with Soil under Vanadium Stress.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0125321}, pmid = {35089099}, issn = {2379-5077}, mesh = {Animals ; Soil ; Vanadium ; *Oligochaeta/microbiology ; *Gastrointestinal Microbiome ; *Microbiota ; Bacteria ; }, abstract = {Exploring the ecological mechanism of microbial community assembly in soil and the earthworm gut in a vanadium polluted environment could help us understand the effects of vanadium stress on microbial diversity maintenance and function, as well as the mechanism of microbial mitigation of vanadium stress. Combining metagenomic sequencing and abundance distribution models, we explored the assembly of earthworm intestinal bacteria and native soil bacteria after 21 days of earthworm exposure to a gradient level of vanadate (0 to 300 mg kg[-1]) in soil. Stochastic processes dominated the assembly of both genes and taxa in earthworm gut and soil. Both the composition of taxa and functional genes in earthworm gut varied highly with the vanadium concentration, while in soil, only the taxa changed significantly, whereas the functional genes were relatively stable. The functional redundancy in soil, but not in the earthworm gut, was confirmed by a Mantel test and analysis of similarities (ANOSIM) test. In addition, vanadium detoxifying gene (VDG)-carrying taxa were more diverse but less abundant in soil than in the worm gut; and VDGs were more abundant in soil than in the worm gut. Their wider niche breadth indicated that VDG-carrying taxa were generalists in soil, in contrast to their role in the worm gut. These results suggested that earthworm intestinal and soil microbes adopted different strategies to counteract vanadium stress. The results provide new insights into the effects of soil vanadium stress on the assembly of earthworm gut and soil microbiota from both bacterial taxa and genetic function perspectives. IMPORTANCE Metagenomic sequencing revealed the variation of functional genes in the microbial community in soil and earthworm gut with increasing vanadium concentrations, which provided a new insight to explore the effect of vanadium stress on microbial community assembly from the perspective of functional genes. Our results reinforced the view that functional genes and taxa do not appear to have a simple corresponding relationship. Taxa are more sensitive compared with functional genes, suggesting the existence of bacterial functional redundancy in soil, but not in the earthworm gut. These observations indicate different assembly patterns of earthworm intestinal and soil bacteria under vanadium stress. Thus, it is important and necessary to include genetic functions to comprehensively understand microbial community assembly.}, } @article {pmid35089052, year = {2022}, author = {Casey, E and McDonnell, B and White, K and Stamou, P and Crowley, T and O'Neill, I and Lavelle, K and Hayes, S and Lugli, GA and Arboleya, S and James, K and Ventura, M and Martinez, I and Gueimonde, M and Dal Bello, F and Nally, K and Mahony, J and van Sinderen, D}, title = {Needle in a Whey-Stack: PhRACS as a Discovery Tool for Unknown Phage-Host Combinations.}, journal = {mBio}, volume = {13}, number = {1}, pages = {e0333421}, pmid = {35089052}, issn = {2150-7511}, mesh = {Humans ; *Bacteriophages/genetics ; Whey ; Bacteriophage Receptors ; *Microbiota ; Bacteria/genetics ; Metagenomics/methods ; }, abstract = {The field of metagenomics has rapidly expanded to become the go-to method for complex microbial community analyses. However, there is currently no straightforward route from metagenomics to traditional culture-based methods of strain isolation, particularly in (bacterio)phage biology, leading to an investigative bottleneck. Here, we describe a method that exploits specific phage receptor binding protein (RBP)-host cell surface receptor interaction enabling isolation of phage-host combinations from an environmental sample. The method was successfully applied to two complex sample types-a dairy-derived whey sample and an infant fecal sample, enabling retrieval of specific and culturable phage hosts. IMPORTANCE PhRACS aims to bridge the current divide between in silico genetic analyses (i.e., phageomic studies) and traditional culture-based methodology. Through the labeling of specific bacterial hosts with fluorescently tagged recombinant phage receptor binding proteins and the isolation of tagged cells using flow cytometry, PhRACS allows the full potential of phageomic data to be realized in the wet laboratory.}, } @article {pmid35088527, year = {2022}, author = {Li, XL and Cui, JJ and Zheng, WS and Zhang, JL and Li, R and Ma, XL and Lin, M and Guo, HH and Li, C and Yu, XY and Du, P and Zhao, LM and He, S and Lan, P and Jiang, JD and Che, Y and Wang, LL}, title = {Bicyclol Alleviates Atherosclerosis by Manipulating Gut Microbiota.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {18}, number = {9}, pages = {e2105021}, doi = {10.1002/smll.202105021}, pmid = {35088527}, issn = {1613-6829}, mesh = {Animals ; *Atherosclerosis/drug therapy ; Biphenyl Compounds/pharmacology/therapeutic use ; Dysbiosis ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred C57BL ; }, abstract = {Atherosclerosis (AS) is associated with high morbidity and mortality, thus imposing a growing burden on modern society. Herb-derived bicyclol (BIC) is a versatile bioactive compound that can be used to treat AS. However, its efficacy in AS is not yet described. Here, it is shown that BIC normalizes gut microflora dysbiosis induced by a high fat diet in Apoe[(-/-)] mice. Metagenome-wide association study analysis verifies that the modulation on carbohydrate-active enzymes and short-chain fatty acid generating genes in gut flora is among the mechanisms. The gut healthiness, especially the gut immunity and integrity, is restored by BIC intervention, leading to improved systemic immune cell dynamic and liver functions. Accordingly, the endothelial activation, macrophage infiltration, and cholesterol ester accumulation in the aortic arch are alleviated by BIC to lessen the plaque onset. Moreover, it is proved that the therapeutic effect of BIC on AS is transmissible by fecal microbiota transplantation. The current study, for the first time, demonstrates the antiatherosclerotic effects of BIC and shows that its therapeutic value can at least partially be attributed to its manipulation of gut microbiota.}, } @article {pmid35087906, year = {2022}, author = {Liu, J and Gu, X and Li, H}, title = {Assembly of 97 Novel Bacterial Genomes in the Microbial Community Affiliated with Polyvinyl Alcohol in Soil of Northern China.}, journal = {BioMed research international}, volume = {2022}, number = {}, pages = {2229147}, pmid = {35087906}, issn = {2314-6141}, mesh = {Bacteria ; China ; Genome, Bacterial/genetics ; *Microbiota/genetics ; Oxidoreductases/metabolism ; Phylogeny ; Polyvinyl Alcohol ; RNA, Ribosomal, 16S/genetics ; *Soil ; Soil Microbiology ; }, abstract = {BACKGROUND: Undeveloped ecosystems belong to rich source of microbial population, of which resources remain unearthed. A kind of polymeric compound system with high polyvinyl alcohol (PVA) content has been reported and named Taisui. Marker gene amplification showed that Taisui harbored little-explored microbial communities.

AIM: To address this issue, our study attempted to recover draft genomes and functional potential from microbial communities in Taisui using the metagenomic approach. Material and Methods. Taisui communities provided 97 novel bacterial genomes from 13 bacterial phyla, including bacteria candidate phylum. Two novel genus-level lineages were recovered from Planctomycetes and Chloroflexi. Based on the draft genomes, we expanded the number of taxa with potential productions of PKS and NRPS in phyla including Candidatus Dadabacteria, Chloroflexi, and Planctomycetes.

RESULTS: A rich diversity of PVA dehydrogenase genes from 4 phyla, involving Proteobacteria, Acidobacteria, Acitinobacteria, and Planctomycetes, were identified. The phylogenetic tree of PVA dehydrogenase showed the possibility of horizontal gene transfer between microbes.

CONCLUSION: Our study underscores the substantial microbial diversity and PVA degradation potential in the previously unexplored Taisui system.}, } @article {pmid35087228, year = {2022}, author = {Mills, RH and Dulai, PS and Vázquez-Baeza, Y and Sauceda, C and Daniel, N and Gerner, RR and Batachari, LE and Malfavon, M and Zhu, Q and Weldon, K and Humphrey, G and Carrillo-Terrazas, M and Goldasich, LD and Bryant, M and Raffatellu, M and Quinn, RA and Gewirtz, AT and Chassaing, B and Chu, H and Sandborn, WJ and Dorrestein, PC and Knight, R and Gonzalez, DJ}, title = {Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity.}, journal = {Nature microbiology}, volume = {7}, number = {2}, pages = {262-276}, pmid = {35087228}, issn = {2058-5276}, support = {P30 DK120515/DK/NIDDK NIH HHS/United States ; P30 NS047101/NS/NINDS NIH HHS/United States ; T32 DK007202/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Animals ; Bacterial Proteins/classification/genetics ; Bacteroides/enzymology/*pathogenicity ; Cohort Studies ; Colitis, Ulcerative/*microbiology/*physiopathology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Longitudinal Studies ; Male ; Metagenome ; Metagenomics/*methods ; Mice ; Middle Aged ; Peptide Hydrolases/classification/*genetics ; Proteomics/*methods ; Severity of Illness Index ; }, abstract = {Ulcerative colitis (UC) is driven by disruptions in host-microbiota homoeostasis, but current treatments exclusively target host inflammatory pathways. To understand how host-microbiota interactions become disrupted in UC, we collected and analysed six faecal- or serum-based omic datasets (metaproteomic, metabolomic, metagenomic, metapeptidomic and amplicon sequencing profiles of faecal samples and proteomic profiles of serum samples) from 40 UC patients at a single inflammatory bowel disease centre, as well as various clinical, endoscopic and histologic measures of disease activity. A validation cohort of 210 samples (73 UC, 117 Crohn's disease, 20 healthy controls) was collected and analysed separately and independently. Data integration across both cohorts showed that a subset of the clinically active UC patients had an overabundance of proteases that originated from the bacterium Bacteroides vulgatus. To test whether B. vulgatus proteases contribute to UC disease activity, we first profiled B. vulgatus proteases found in patients and bacterial cultures. Use of a broad-spectrum protease inhibitor improved B. vulgatus-induced barrier dysfunction in vitro, and prevented colitis in B. vulgatus monocolonized, IL10-deficient mice. Furthermore, transplantation of faeces from UC patients with a high abundance of B. vulgatus proteases into germfree mice induced colitis dependent on protease activity. These results, stemming from a multi-omics approach, improve understanding of functional microbiota alterations that drive UC and provide a resource for identifying other pathways that could be inhibited as a strategy to treat this disease.}, } @article {pmid35087227, year = {2022}, author = {Liu, NN and Jiao, N and Tan, JC and Wang, Z and Wu, D and Wang, AJ and Chen, J and Tao, L and Zhou, C and Fang, W and Cheong, IH and Pan, W and Liao, W and Kozlakidis, Z and Heeschen, C and Moore, GG and Zhu, L and Chen, X and Zhang, G and Zhu, R and Wang, H}, title = {Multi-kingdom microbiota analyses identify bacterial-fungal interactions and biomarkers of colorectal cancer across cohorts.}, journal = {Nature microbiology}, volume = {7}, number = {2}, pages = {238-250}, pmid = {35087227}, issn = {2058-5276}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Adult ; Aged ; Bacteria/classification/*genetics/metabolism ; Biomarkers/analysis ; Cohort Studies ; Colorectal Neoplasms/classification/*diagnosis ; Dysbiosis/microbiology ; Feces/microbiology ; Female ; Fungi/classification/*genetics/metabolism ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Microbial Interactions/*genetics ; Middle Aged ; Sequence Analysis, DNA ; Viruses/classification/genetics ; }, abstract = {Despite recent progress in our understanding of the association between the gut microbiome and colorectal cancer (CRC), multi-kingdom gut microbiome dysbiosis in CRC across cohorts is unexplored. We investigated four-kingdom microbiota alterations using CRC metagenomic datasets of 1,368 samples from 8 distinct geographical cohorts. Integrated analysis identified 20 archaeal, 27 bacterial, 20 fungal and 21 viral species for each single-kingdom diagnostic model. However, our data revealed superior diagnostic accuracy for models constructed with multi-kingdom markers, in particular the addition of fungal species. Specifically, 16 multi-kingdom markers including 11 bacterial, 4 fungal and 1 archaeal feature, achieved good performance in diagnosing patients with CRC (area under the receiver operating characteristic curve (AUROC) = 0.83) and maintained accuracy across 3 independent cohorts. Coabundance analysis of the ecological network revealed associations between bacterial and fungal species, such as Talaromyces islandicus and Clostridium saccharobutylicum. Using metagenome shotgun sequencing data, the predictive power of the microbial functional potential was explored and elevated D-amino acid metabolism and butanoate metabolism were observed in CRC. Interestingly, the diagnostic model based on functional EggNOG genes achieved high accuracy (AUROC = 0.86). Collectively, our findings uncovered CRC-associated microbiota common across cohorts and demonstrate the applicability of multi-kingdom and functional markers as CRC diagnostic tools and, potentially, as therapeutic targets for the treatment of CRC.}, } @article {pmid35087123, year = {2022}, author = {Domènech, L and Willis, J and Alemany-Navarro, M and Morell, M and Real, E and Escaramís, G and Bertolín, S and Sánchez Chinchilla, D and Balcells, S and Segalàs, C and Estivill, X and Menchón, JM and Gabaldón, T and Alonso, P and Rabionet, R}, title = {Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {1448}, pmid = {35087123}, issn = {2045-2322}, mesh = {Adult ; Brain-Gut Axis/*immunology ; Case-Control Studies ; DNA, Bacterial/isolation & purification ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/*immunology ; Healthy Volunteers ; Humans ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Obsessive-Compulsive Disorder/immunology/*microbiology ; Oropharynx/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Although the etiology of obsessive-compulsive disorder (OCD) is largely unknown, it is accepted that OCD is a complex disorder. There is a known bi-directional interaction between the gut microbiome and brain activity. Several authors have reported associations between changes in gut microbiota and neuropsychiatric disorders, including depression or autism. Furthermore, a pediatric-onset neuropsychiatric OCD-related syndrome occurs after streptococcal infection, which might indicate that exposure to certain microbes could be involved in OCD susceptibility. However, only one study has investigated the microbiome of OCD patients to date. We performed 16S ribosomal RNA gene-based metagenomic sequencing to analyze the stool and oropharyngeal microbiome composition of 32 OCD cases and 32 age and gender matched controls. We estimated different α- and β-diversity measures and performed LEfSe and Wilcoxon tests to assess differences in bacterial distribution. OCD stool samples showed a trend towards lower bacterial α-diversity, as well as an increase of the relative abundance of Rikenellaceae, particularly of the genus Alistipes, and lower relative abundance of Prevotellaceae, and two genera within the Lachnospiraceae: Agathobacer and Coprococcus. However, we did not observe a different Bacteroidetes to Firmicutes ratio between OCD cases and controls. Analysis of the oropharyngeal microbiome composition showed a lower Fusobacteria to Actinobacteria ratio in OCD cases. In conclusion, we observed an imbalance in the gut and oropharyngeal microbiomes of OCD cases, including, in stool, an increase of bacteria from the Rikenellaceae family, associated with gut inflammation, and a decrease of bacteria from the Coprococcus genus, associated with DOPAC synthesis.}, } @article {pmid35086715, year = {2022}, author = {He, Q and Yang, C and Kang, X and Chen, Y and Zhang, T and Zhang, H and Kwok, LY}, title = {Intake of Bifidobacterium lactis Probio-M8 fermented milk protects against alcoholic liver disease.}, journal = {Journal of dairy science}, volume = {105}, number = {4}, pages = {2908-2921}, doi = {10.3168/jds.2021-21265}, pmid = {35086715}, issn = {1525-3198}, mesh = {Animals ; *Bifidobacterium animalis/metabolism ; *Gastrointestinal Microbiome ; *Liver Diseases, Alcoholic/prevention & control/veterinary ; Milk ; *Probiotics ; Rats ; }, abstract = {Alcoholic liver disease (ALD) is a liver disease caused by long-term heavy drinking, which is characterized by increased inflammation and oxidative stress in the liver and gut dysbiosis. The purpose of this study was to investigate the protective effect of administering ordinary and probiotic- (containing the Bifidobacterium animalis ssp. lactis Probio-M8 strain; M8) fermented milk to rats. Several biochemical parameters and the fecal metagenomes were monitored before (d 0) and after (d 42) the intervention. Our results confirmed that alcohol could cause significant changes in the liver levels of the proinflammatory cytokine IL-1β, antioxidation indicators, and liver function-related indicators; meanwhile, the gut bacterial and viral microbiota were disrupted with significant reduction in microbial diversity and richness. Feeding the rats with Probio-M8-fermented milk effectively maintained the gut microbiota stability, reduced liver inflammation and oxidative stress, and mitigated liver damages in ALD. Moreover, the Probio-M8-fermented milk reversed alcohol-induced dysbiosis by restoring the gut microbiota diversity, richness, and composition. Four predicted fecal metabolites (inositol, tryptophan, cortisol, and vitamin K2) increased after the intervention, which might help regulate liver metabolism and alleviate ALD-related symptoms. In short, our data supported that consuming Probio-M8-fermented milk effectively mitigated ALD. The protective effect against ALD could be related to changes in the gut microbiome after probiotic-fermented milk consumption. However, such observation and the causal relationship among probiotic milk consumption, changes in gut microbiome, and disease alleviation would still need to be further confirmed. Nevertheless, this study has shown in a rat model that consuming probiotic-fermented milk could protect against ALD.}, } @article {pmid35086016, year = {2022}, author = {Rocchetti, G and Luisa Callegari, M and Senizza, A and Giuberti, G and Ruzzolini, J and Romani, A and Urciuoli, S and Nediani, C and Lucini, L}, title = {Oleuropein from olive leaf extracts and extra-virgin olive oil provides distinctive phenolic profiles and modulation of microbiota in the large intestine.}, journal = {Food chemistry}, volume = {380}, number = {}, pages = {132187}, doi = {10.1016/j.foodchem.2022.132187}, pmid = {35086016}, issn = {1873-7072}, mesh = {Intestine, Large ; Iridoid Glucosides ; *Microbiota ; Olea ; Olive Oil ; Plant Extracts ; *Plant Oils ; }, abstract = {The interest in the modulation of gut microbiota by polyphenols from olives and derived products is increasing. In this work, phenolic leaf extracts (PLE) were in vitro faecal fermented to evaluate the changes in phenolic profiles and the impact on microbiota, using a commercial extra-virgin olive oil (EVOO) as reference. The in vitro fermentation decreased oleuropein content in PLE, determining an increase of hydroxytyrosol and other phenolic metabolites. An increase (p < 0.05) of hydroxytyrosol (LogFC = 6.02; VIP score = 1.05) was also observed in fermented EVOO. Besides, PLE significantly (p < 0.05) changed amino acids (LogFC = 6.1) and fatty acids (LogFC = 5.9) profile of the faeces. Metagenomic sequencing revealed that Coriobacteriaceae at the family level, and Collinsella at the genus level, were the most affected by PLE fermentation. These findings support the modulation of the gut microbiota exerted by phenolics from PLE and EVOO.}, } @article {pmid35085655, year = {2022}, author = {Malla, MA and Dubey, A and Raj, A and Kumar, A and Upadhyay, N and Yadav, S}, title = {Emerging frontiers in microbe-mediated pesticide remediation: Unveiling role of omics and In silico approaches in engineered environment.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {299}, number = {}, pages = {118851}, doi = {10.1016/j.envpol.2022.118851}, pmid = {35085655}, issn = {1873-6424}, mesh = {Agriculture ; Humans ; *Microbiota ; *Pesticides/analysis ; Soil ; Soil Microbiology ; }, abstract = {The overuse of pesticides for augmenting agriculture productivity always comes at the cost of environment, biodiversity, and human health and has put the land, water, and environmental footprints under severe threat throughout the globe. Underpinning and maximizing the microbiome functions in pesticide-contaminated environments has become a prerequisite for a sustainable environment and resilient agriculture. It is imperative to elucidate the metabolic network of the microbial communities and environmental variables at the contaminated site to predict the best strategy for remediation and soil microbe-pesticide interactions. High throughput next-generation sequencing and in silico analysis allow us to identify and discern the members and characteristics of core microbiomes at the contaminated site. Integration of modern high throughput multi-omics investigations and informatics pipelines provide novel approaches and pathways to capitalize on the core microbiomes for enhancing environmental functioning and mitigation. The role of eco-genomics tools in visualising the microbial network, taxonomy, functional potential, and environmental variables in contaminated habitats is discussed in this review. The integrated role of the potential microbe identification as individual or consortia, mechanistic approach for pesticide degradation, identification of responsible enzymes/genes, and in silico approach is emphasized for the prospects of the area.}, } @article {pmid35085485, year = {2022}, author = {Gowda, K and Ping, D and Mani, M and Kuehn, S}, title = {Genomic structure predicts metabolite dynamics in microbial communities.}, journal = {Cell}, volume = {185}, number = {3}, pages = {530-546.e25}, doi = {10.1016/j.cell.2021.12.036}, pmid = {35085485}, issn = {1097-4172}, mesh = {Biomass ; Denitrification ; Genome ; *Genomics ; *Metabolomics ; Microbiota/*genetics ; Models, Biological ; Nitrates/metabolism ; Nitrites/metabolism ; Phenotype ; Regression Analysis ; Reproducibility of Results ; }, abstract = {The metabolic activities of microbial communities play a defining role in the evolution and persistence of life on Earth, driving redox reactions that give rise to global biogeochemical cycles. Community metabolism emerges from a hierarchy of processes, including gene expression, ecological interactions, and environmental factors. In wild communities, gene content is correlated with environmental context, but predicting metabolite dynamics from genomes remains elusive. Here, we show, for the process of denitrification, that metabolite dynamics of a community are predictable from the genes each member of the community possesses. A simple linear regression reveals a sparse and generalizable mapping from gene content to metabolite dynamics for genomically diverse bacteria. A consumer-resource model correctly predicts community metabolite dynamics from single-strain phenotypes. Our results demonstrate that the conserved impacts of metabolic genes can predict community metabolite dynamics, enabling the prediction of metabolite dynamics from metagenomes, designing denitrifying communities, and discovering how genome evolution impacts metabolism.}, } @article {pmid35085328, year = {2022}, author = {Fukuchi, M and Sugita, M and Banjo, M and Yonekura, K and Sasuga, Y}, title = {The impact of a competitive event and the efficacy of a lactic acid bacteria-fermented soymilk extract on the gut microbiota and urinary metabolites of endurance athletes: An open-label pilot study.}, journal = {PloS one}, volume = {17}, number = {1}, pages = {e0262906}, pmid = {35085328}, issn = {1932-6203}, mesh = {Adult ; *Athletes ; Biomarkers/urine ; Complex Mixtures/*administration & dosage ; Female ; *Fermented Beverages ; *Gastrointestinal Microbiome ; Humans ; *Lactobacillales ; Male ; Physical Endurance/*drug effects ; Pilot Projects ; *Glycine max ; }, abstract = {Diet and exercise can alter the gut microbiota, but recent studies have assessed the impact of athletic competition on gut microbiota and host metabolites. We designed an open-label pilot study to investigate the effects of both official competition and a multi-strain lactic acid bacteria-fermented soymilk extract (LEX) on the gut microbiota in Japanese college endurance athletes. The analysis of fecal 16S rRNA metagenome and urinary metabolites was used to identify changes in gut microbiota composition and host metabolism. When the fecal microbiota were investigated before and after a race without using of a supplement (pre-observation period), there was an increase in the phylum Firmicutes and decrease in Bacteroidetes. However, no changes in these phyla were seen before and after a race in those who consumed LEX. Before and after LEX ingestion, changes in urinary metabolites included a significant reduction in yeast and fungal markers, neurotransmitters, and mitochondrial metabolites including the TCA cycle. There were several correlations between urinary metabolites and the composition of fecal microbiota. For example, the level of tricarballylic acid was positively correlated with the composition ratio of phylum Firmicutes (Pearson's r = 0.66; p < 0.01). The bacterial species Parabacteroides distasonis was also found to correlate moderately with several urinary metabolites. These findings suggest two possibilities. First, endurance athletes experience significant fluctuations in gut microbiota after a single competition. Second, LEX ingestion may improve yeast and fungal overgrowth in the gastrointestinal tract and enhancing mitochondrial metabolic function.}, } @article {pmid35084011, year = {2022}, author = {Kang, S and You, HJ and Ju, Y and Kim, HJ and Jeong, YJ and Johnston, TV and Ji, GE and Ku, S and Park, MS}, title = {Butyl-fructooligosaccharides modulate gut microbiota in healthy mice and ameliorate ulcerative colitis in a DSS-induced model.}, journal = {Food & function}, volume = {13}, number = {4}, pages = {1834-1845}, doi = {10.1039/d1fo03337a}, pmid = {35084011}, issn = {2042-650X}, mesh = {Animals ; Colitis, Ulcerative/chemically induced/*metabolism ; Dextran Sulfate/adverse effects ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; Mice ; Oligosaccharides/*pharmacology ; }, abstract = {Butyl-fructooligosaccharides (B-FOSs) are newly synthesized prebiotics composed of short-chain FOS (GF2, 1-kestose; GF3, nystose; GF4, fructofuranosyl-nystose; GF5, 1-F-(1-b-D-fructofuranosyl)-2-nystose) bound with one or two butyric groups by ester bonds. Previous in vitro studies have shown that B-FOS treatment increases butyrate production and protects the growth of butyrate-producing bacteria during fermentation. The aim of this study was to further test B-FOS as a novel prebiotic compound by evaluating the effect of B-FOS on gut microbiota via 16S rRNA metagenomic analysis in an Institute of Cancer Research (ICR) mouse model and examining its anti-inflammatory efficacy in a mouse model of colitis induced by dextran sodium sulphate (DSS). In the healthy ICR mouse study, linear discriminant analysis effect size results revealed that Bifidobacterium was the representative phylotype in the B-FOS treatment compared to the control group. Furthermore, the cecal butyrate concentration of the B-FOS group was significantly higher than that of the control (P < 0.05). The high concentration of butyrate in the B-FOS treatment was probably associated with the high relative abundance of clusters of orthologous group (COG) 4770 (acetyl/propionyl-CoA carboxylase). In the DSS-induced infection study, B-FOS significantly ameliorated the symptoms of DSS-induced colitis, increased the mRNA expression of occludin, decreased tumor necrosis factor-α (TNF-α), interferon-γ (IFN-γ) and interleukin (IL-8) in the colon tissues, and significantly increased cecal butyrate concentrations. These findings suggest that B-FOS ameliorated DSS-induced colitis by maintaining the epithelial barrier and reducing the secretion of inflammation related cytokines.}, } @article {pmid35083969, year = {2022}, author = {Fishbein, SR and Robinson, JI and Hink, T and Reske, KA and Newcomer, EP and Burnham, CD and Henderson, JP and Dubberke, ER and Dantas, G}, title = {Multi-omics investigation of Clostridioides difficile-colonized patients reveals pathogen and commensal correlates of C. difficile pathogenesis.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35083969}, issn = {2050-084X}, support = {R01 DK111930/DK/NIDDK NIH HHS/United States ; T32 DK077653/DK/NIDDK NIH HHS/United States ; R01 AT009741/AT/NCCIH NIH HHS/United States ; R01 OH011578/OH/NIOSH CDC HHS/United States ; }, mesh = {Clostridioides difficile/*genetics/*growth & development ; Clostridium Infections/*microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metabolomics ; Metagenomics ; Ribotyping ; Symbiosis ; }, abstract = {Clostridioides difficile infection (CDI) imposes a substantial burden on the health care system in the United States. Understanding the biological basis for the spectrum of C. difficile-related disease manifestations is imperative to improving treatment and prevention of CDI. Here, we investigate the correlates of asymptomatic C. difficile colonization using a multi-omics approach. We compared the fecal microbiome and metabolome profiles of patients with CDI versus asymptomatically colonized patients, integrating clinical and pathogen factors into our analysis. We found that CDI patients were more likely to be colonized by strains with the binary toxin (CDT) locus or strains of ribotype 027, which are often hypervirulent. We find that microbiomes of asymptomatically colonized patients are significantly enriched for species in the class Clostridia relative to those of symptomatic patients. Relative to CDI microbiomes, asymptomatically colonized patient microbiomes were enriched with sucrose degradation pathways encoded by commensal Clostridia, in addition to glycoside hydrolases putatively involved in starch and sucrose degradation. Fecal metabolomics corroborates the carbohydrate degradation signature: we identify carbohydrate compounds enriched in asymptomatically colonized patients relative to CDI patients. Further, we reveal that across C. difficile isolates, the carbohydrates sucrose, rhamnose, and lactulose do not serve as robust growth substrates in vitro, consistent with their enriched detection in our metagenomic and metabolite profiling of asymptomatically colonized individuals. We conclude that pathogen genetic variation may be strongly related to disease outcome. More interestingly, we hypothesize that in asymptomatically colonized individuals, carbohydrate metabolism by other commensal Clostridia may prevent CDI by inhibiting C. difficile proliferation. These insights into C. difficile colonization and putative commensal competition suggest novel avenues to develop probiotic or prebiotic therapeutics against CDI.}, } @article {pmid35082799, year = {2021}, author = {Han, Z and Cen, C and Ou, Q and Pan, Y and Zhang, J and Huo, D and Chen, K}, title = {The Potential Prebiotic Berberine Combined With Methimazole Improved the Therapeutic Effect of Graves' Disease Patients Through Regulating the Intestinal Microbiome.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {826067}, pmid = {35082799}, issn = {1664-3224}, mesh = {Berberine/administration & dosage/*therapeutic use ; Biomarkers ; Disease Management ; Drug Therapy, Combination ; Dysbiosis ; Gastrointestinal Microbiome/*drug effects ; Graves Disease/diagnosis/etiology/*therapy ; Humans ; Metabolic Networks and Pathways ; Metagenome ; Metagenomics/methods ; Methimazole/administration & dosage/*therapeutic use ; Models, Biological ; Prebiotics/*administration & dosage ; Thyroid Function Tests ; Treatment Outcome ; }, abstract = {Graves' disease, a typical metabolism disorder, causes diffuse goiter accompanied by ocular abnormalities and ocular dysfunction. Although methimazole (MI) is a commonly used drug for the treatment of GD, the efficacy of methimazole is only limited to the control of clinical indicators, and the side effects of MI should be seriously considered. Here, we designed a 6-month clinical trial that divided the patients into two groups: a methimazole group (n=8) and a methimazole combined with potential prebiotic berberine group (n=10). The effects of both treatments on thyroid function and treatment outcomes in patients with GD were assessed by thyroid index measurements and gut microbiota metagenomic sequencing. The results showed that the addition of berberine restored the patients' TSH and FT3 indices to normal levels, whereas MI alone restored only FT3. In addition, TRAb was closer to the healthy threshold at the end of treatment with the drug combination. MI alone failed to modulate the gut microbiota of the patients. However, the combination of berberine with methimazole significantly altered the microbiota structure of the patients, increasing the abundance of the beneficial bacteria Lactococcus lactis while decreasing the abundance of the pathogenic bacteria Enterobacter hormaechei and Chryseobacterium indologenes. Furthermore, further mechanistic exploration showed that the addition of berberine resulted in a significant upregulation of the synthesis of enterobactin, which may have increased iron functioning and thus restored thyroid function. In conclusion, methimazole combined with berberine has better efficacy in patients with GD, suggesting the potential benefit of berberine combined with methimazole in modulating the composition of intestinal microbes in the treatment of GD, providing new strong evidence for the effectiveness of combining Chinese and Western drugs from the perspective of modulating the intestinal microbiota.}, } @article {pmid35082293, year = {2022}, author = {Fetters, AM and Cantalupo, PG and Wei, N and Robles, MTS and Stanley, AM and Stephens, JD and Pipas, JM and Ashman, TL}, title = {The pollen virome of wild plants and its association with variation in floral traits and land use.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {523}, pmid = {35082293}, issn = {2041-1723}, mesh = {Amino Acid Sequence ; Animals ; Ecology ; Flowers ; Genome, Viral ; *Phenotype ; Phylogeny ; Plants/*virology ; Pollen/*virology ; Pollination ; Seeds ; *Virome/genetics ; Viruses/classification/genetics ; }, abstract = {Pollen is a unique vehicle for viral spread. Pollen-associated viruses hitchhike on or within pollen grains and are transported to other plants by pollinators. They are deposited on flowers and have a direct pathway into the plant and next generation via seeds. To discover the diversity of pollen-associated viruses and identify contributing landscape and floral features, we perform a species-level metagenomic survey of pollen from wild, visually asymptomatic plants, located in one of four regions in the United States of America varying in land use. We identify many known and novel pollen-associated viruses, half belonging to the Bromoviridae, Partitiviridae, and Secoviridae viral families, but many families are represented. Across the regions, species harbor more viruses when surrounded by less natural and more human-modified environments than the reverse, but we note that other region-level differences may also covary with this. When examining the novel connection between virus richness and floral traits, we find that species with multiple, bilaterally symmetric flowers and smaller, spikier pollen harbored more viruses than those with opposite traits. The association of viral diversity with floral traits highlights the need to incorporate plant-pollinator interactions as a driver of pollen-associated virus transport into the study of plant-viral interactions.}, } @article {pmid35082169, year = {2022}, author = {Liu, Q and Mak, JWY and Su, Q and Yeoh, YK and Lui, GC and Ng, SSS and Zhang, F and Li, AYL and Lu, W and Hui, DS and Chan, PK and Chan, FKL and Ng, SC}, title = {Gut microbiota dynamics in a prospective cohort of patients with post-acute COVID-19 syndrome.}, journal = {Gut}, volume = {71}, number = {3}, pages = {544-552}, doi = {10.1136/gutjnl-2021-325989}, pmid = {35082169}, issn = {1468-3288}, mesh = {COVID-19/*complications/diagnosis/microbiology ; Follow-Up Studies ; Gastrointestinal Microbiome/*physiology ; Humans ; Metagenomics/*methods ; Prospective Studies ; *SARS-CoV-2 ; Severity of Illness Index ; Post-Acute COVID-19 Syndrome ; }, abstract = {BACKGROUND: Long-term complications after COVID-19 are common, but the potential cause for persistent symptoms after viral clearance remains unclear.

OBJECTIVE: To investigate whether gut microbiome composition is linked to post-acute COVID-19 syndrome (PACS), defined as at least one persistent symptom 4 weeks after clearance of the SARS-CoV-2 virus.

METHODS: We conducted a prospective study of 106 patients with a spectrum of COVID-19 severity followed up from admission to 6 months and 68 non-COVID-19 controls. We analysed serial faecal microbiome of 258 samples using shotgun metagenomic sequencing, and correlated the results with persistent symptoms at 6 months.

RESULTS: At 6 months, 76% of patients had PACS and the most common symptoms were fatigue, poor memory and hair loss. Gut microbiota composition at admission was associated with occurrence of PACS. Patients without PACS showed recovered gut microbiome profile at 6 months comparable to that of non-COVID-19 controls. Gut microbiome of patients with PACS were characterised by higher levels of Ruminococcus gnavus, Bacteroides vulgatus and lower levels of Faecalibacterium prausnitzii. Persistent respiratory symptoms were correlated with opportunistic gut pathogens, and neuropsychiatric symptoms and fatigue were correlated with nosocomial gut pathogens, including Clostridium innocuum and Actinomyces naeslundii (all p<0.05). Butyrate-producing bacteria, including Bifidobacterium pseudocatenulatum and Faecalibacterium prausnitzii showed the largest inverse correlations with PACS at 6 months.

CONCLUSION: These findings provided observational evidence of compositional alterations of gut microbiome in patients with long-term complications of COVID-19. Further studies should investigate whether microbiota modulation can facilitate timely recovery from post-acute COVID-19 syndrome.}, } @article {pmid35080120, year = {2022}, author = {Qian, L and Yu, X and Zhou, J and Gu, H and Ding, J and Peng, Y and He, Q and Tian, Y and Liu, J and Wang, S and Wang, C and Shu, L and Yan, Q and He, J and Liu, G and Tu, Q and He, Z}, title = {MCycDB: A curated database for comprehensively profiling methane cycling processes of environmental microbiomes.}, journal = {Molecular ecology resources}, volume = {22}, number = {5}, pages = {1803-1823}, doi = {10.1111/1755-0998.13589}, pmid = {35080120}, issn = {1755-0998}, support = {311020005//Innovation Group Projects of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 311021006//Innovation Group Projects of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; ZR2020YQ21//Natural Science Foundations of Shandong Province/ ; 312020004//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 2017YFA0604300//National Key Research and Development Program of China/ ; 2019YFA0606700//National Key Research and Development Program of China/ ; 2020YFA0607600//National Key Research and Development Program of China/ ; 31770539//National Natural Science Foundation of China/ ; 31870469//National Natural Science Foundation of China/ ; 31971446//National Natural Science Foundation of China/ ; 41676105//National Natural Science Foundation of China/ ; 41771095//National Natural Science Foundation of China/ ; 62170346//National Natural Science Foundation of China/ ; 91951207//National Natural Science Foundation of China/ ; 92051110//National Natural Science Foundation of China/ ; }, mesh = {Archaea/genetics ; Bacteria ; Metagenome ; *Methane/metabolism ; *Microbiota/genetics ; }, abstract = {Methane is a critical greenhouse gas with significant impacts on environmental and global change. However, CH4 cycling processes and coupling mechanisms with the biogeochemical cycling of carbon, nitrogen, sulfur and metals in the environment remain elusive. To fill such knowledge gaps, we constructed a manually curated methane cycling database (MCycDB) for comprehensive and accurate analysis of methane cycling microbial communities. MCycDB contains 298 methane cycling gene families covering 10 methane metabolism pathways with 610,208 representative sequences, and associated reference sequences from the NCBI RefSeq database with 48 phyla and 2,197 genera, and five phyla and 100 genera for bacteria and archaea, respectively. Also, homologous groups from public orthology databases were identified and included in MCycDB to reduce false positive assignments. We applied MCycDB to profile methane cycling gene families and associated taxonomic groups from various environments. Gene families involved in methanogenesis were abundant in hot spring sediment and less abundant in freshwater, whereas the ones involved in aerobic oxidation of methane were abundant in permafrost and peatland. This study demonstrates that MCycDB is a useful tool for studying microbially-driven methane cycling processes with high specificity, coverage and accuracy.}, } @article {pmid35078690, year = {2022}, author = {Kutsuwada, Y and Yokota, K and Yoshida, K and Tsuda, H and Watanabe, K and Matsumoto, A and Iwamoto, S}, title = {Association of HLA-DPB1, NLRP10, OVOL1, and ABCC11 with the axillary microbiome in a Japanese population.}, journal = {Journal of dermatological science}, volume = {105}, number = {2}, pages = {98-104}, doi = {10.1016/j.jdermsci.2022.01.003}, pmid = {35078690}, issn = {1873-569X}, mesh = {*ATP-Binding Cassette Transporters/genetics ; *Adaptor Proteins, Signal Transducing/genetics ; Alleles ; Apoptosis Regulatory Proteins/genetics ; DNA-Binding Proteins/genetics ; Gene Frequency ; *HLA-DP beta-Chains/genetics ; Humans ; Japan ; Male ; *Microbiota/genetics ; Skin/*microbiology ; *Transcription Factors/genetics ; }, abstract = {BACKGROUND: The distinct diversity of the human skin microbiome depends not only on the body site but also the individual. Host-commensal interactions have been described for the gut microbiome, but little is known about the epidermal microbiome.

OBJECTIVE: The present study investigated whether genetic variants associated with skin traits affect the axillary microbiome.

METHODS: Eight skin trait-related single nucleotide polymorphisms and HLA-A, -B, -C, and -DPB1 were genotyped in 186 Japanese males. From axillary swabs, the intensity of a representative axillary odor, trans (E) isomer of 3-methyl-2-hexenoic acid (E3M2H), was quantified with gas chromatography-tandem mass spectrometry analysis, the diversity of the axillary microbiome was evaluated with a 16 s rRNA metagenomic approach, and the association of these characteristics was assessed statistically.

RESULTS: A risk allele for atopic dermatitis of rs878860 in NLRP10 and the allele for wet earwax of rs17822931 in ABCC11 decreased the relative abundance of Corynebacterium. Conversely, these alleles increased the relative abundance of Staphylococcus. Metagenomic analysis revealed that β-diversity showed significant dissimilarity at the weighted Unifrac distance between minor allele carrier and non-carrier groups in HLA-DPB1*05:01, rs17822931, and rs878860. HLA-DPB1*04:01, HLA-DPB1*05:01, and rs17822931 were associated with E3M2H.

CONCLUSIONS: We identified novel candidate loci associated with the axillary microbiome and malodor.}, } @article {pmid35078506, year = {2022}, author = {Sun, Z and Huang, S and Zhu, P and Tzehau, L and Zhao, H and Lv, J and Zhang, R and Zhou, L and Niu, Q and Wang, X and Zhang, M and Jing, G and Bao, Z and Liu, J and Wang, S and Xu, J}, title = {Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {36}, pmid = {35078506}, issn = {1474-760X}, mesh = {Bacteria/genetics ; Biomass ; High-Throughput Nucleotide Sequencing ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Microbiome samples with low microbial biomass or severe DNA degradation remain challenging for amplicon-based or whole-metagenome sequencing approaches. Here, we introduce 2bRAD-M, a highly reduced and cost-effective strategy which only sequences ~ 1% of metagenome and can simultaneously produce species-level bacterial, archaeal, and fungal profiles. 2bRAD-M can accurately generate species-level taxonomic profiles for otherwise hard-to-sequence samples with merely 1 pg of total DNA, high host DNA contamination, or severely fragmented DNA from degraded samples. Tests of 2bRAD-M on various stool, skin, environmental, and clinical FFPE samples suggest a successful reconstruction of comprehensive, high-resolution microbial profiles.}, } @article {pmid35077538, year = {2022}, author = {Agostinetto, G and Brusati, A and Sandionigi, A and Chahed, A and Parladori, E and Balech, B and Bruno, A and Pescini, D and Casiraghi, M}, title = {ExTaxsI: an exploration tool of biodiversity molecular data.}, journal = {GigaScience}, volume = {11}, number = {}, pages = {}, pmid = {35077538}, issn = {2047-217X}, mesh = {*Biodiversity ; Genomics ; *Metadata ; Metagenomics ; }, abstract = {BACKGROUND: The increasing availability of multi-omics data is leading to regularly revised estimates of existing biodiversity data. In particular, the molecular data enable novel species to be characterized and the information linked to those already observed to be increased with new genomics data. For this reason, the management and visualization of existing molecular data, and their related metadata, through the implementation of easy-to-use IT tools have become a key point to design future research. The more users are able to access biodiversity-related information, the greater the ability of the scientific community to expand its knowledge in this area.

RESULTS: In this article we focus on the development of ExTaxsI (Exploring Taxonomy Information), an IT tool that can retrieve biodiversity data stored in NCBI databases and provide a simple and explorable visualization. We use 3 case studies to show how an efficient organization of the available data can lead to obtaining new information that is fundamental as a starting point for new research. Using this approach highlights the limits in the distribution of data availability, a key factor to consider in the experimental design phase of broad-spectrum studies such as metagenomics.

CONCLUSIONS: ExTaxsI can easily retrieve molecular data and its metadata with an explorable visualization, with the aim of helping researchers to improve experimental designs and highlight the main gaps in the coverage of available data.}, } @article {pmid35076278, year = {2022}, author = {Lozada-Fernández, VV and deLeon, O and Kellogg, SL and Saravia, FL and Hadiono, MA and Atkinson, SN and Grobe, JL and Kirby, JR}, title = {Nicotinamide Riboside-Conditioned Microbiota Deflects High-Fat Diet-Induced Weight Gain in Mice.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0023021}, pmid = {35076278}, issn = {2379-5077}, support = {R01 HL134850/HL/NHLBI NIH HHS/United States ; P01 HL084207/HL/NHLBI NIH HHS/United States ; R01 AI108255/AI/NIAID NIH HHS/United States ; T32 GM080202/GM/NIGMS NIH HHS/United States ; }, mesh = {Male ; Humans ; Animals ; Mice ; Diet, High-Fat ; NAD/adverse effects ; *Diabetes Mellitus, Type 2 ; Mice, Inbred C57BL ; Weight Gain ; Obesity/chemically induced ; *Gastrointestinal Microbiome ; Vitamins/adverse effects ; }, abstract = {The gut microbiome plays an essential role in host energy homeostasis and influences the development of obesity and related conditions. Studies demonstrate that nicotinamide riboside (NR) supplementation for diet-induced obesity (DIO) reduces weight gain and increases energy expenditure in mice. NR is a vitamin B3 derivative and an NAD[+] precursor with potential for treating human diseases arising from mitochondrial degeneration, including obesity and type 2 diabetes. Gut bacteria produce vitamin B3 in the colon and are capable of salvaging and metabolizing vitamin B3 and its derivatives. However, it is unknown how dietary supplementation of NR alters the microbiome and if those alterations contribute to deflection of weight gain. In this study, we fed C57BL/6J male mice a high-fat diet (HFD) supplemented with or without NR and performed a fecal material transfer (FMT) to establish a link between NR-conditioned microbiota and NR-induced deflection of weight gain. FMT from NR-treated donors to naive mice fed a HFD was sufficient to deflect weight gain by increasing energy expenditure. We also investigated the effects of NR on the microbiome by using metagenomics sequencing. We found that NR-treated mice displayed an altered gut microbial composition relative to controls and that fecal transplant resulted in a distinct functional metabolic profile characterized by enrichment of butyrate-producing Firmicutes. NR-treated donors and subsequent FMT recipients share a similar enrichment of metagenomic biomarkers relative to controls. These findings suggest that microbial factors contribute to the beneficial effects of dietary NR supplementation, which may be useful to enhance the therapeutic effects of NR. IMPORTANCE With obesity and type 2 diabetes (T2D) at epidemic levels, we need to understand the complex nature of these diseases to design better therapeutics. The underlying causes of both obesity and T2D are complex, but both are thought to develop, in part, based on contributions from the gut microbiota. Nicotinamide riboside is a gut-derived vitamin B3 derivative and NAD[+] precursor which has the potential to treat and prevent metabolic disorders by ameliorating mitochondrial dysfunction. Understanding how NR affects the gut microbiome and whether NR-conditioned microbiota contributes to weight loss in the host would (i) improve diagnosis and treatments for obesity and other metabolic pathologies, (ii) tailor treatments to satisfy the needs of each individual moving toward the future of precision medicine, and (iii) benefit other scientific fields that currently investigate the effects of NR in other disease pathologies.}, } @article {pmid35076024, year = {2022}, author = {Miki, Y and Taketomi, Y and Kidoguchi, Y and Yamamoto, K and Muramatsu, K and Nishito, Y and Park, J and Hosomi, K and Mizuguchi, K and Kunisawa, J and Soga, T and Boilard, E and B Gowda, SG and Ikeda, K and Arita, M and Murakami, M}, title = {Group IIA secreted phospholipase A2 controls skin carcinogenesis and psoriasis by shaping the gut microbiota.}, journal = {JCI insight}, volume = {7}, number = {2}, pages = {}, pmid = {35076024}, issn = {2379-3708}, mesh = {Animals ; Carcinogenesis/immunology ; Disease Models, Animal ; Gastrointestinal Microbiome/*immunology ; Gene Expression Profiling ; Gene Expression Regulation/immunology ; Group II Phospholipases A2/*metabolism ; Inflammation/microbiology ; Mice ; Mice, Inbred BALB C ; Pathology, Molecular/methods ; *Psoriasis/immunology/microbiology ; *Skin Neoplasms/immunology/microbiology ; }, abstract = {Besides promoting inflammation by mobilizing lipid mediators, group IIA secreted phospholipase A2 (sPLA2-IIA) prevents bacterial infection by degrading bacterial membranes. Here, we show that, despite the restricted intestinal expression of sPLA2-IIA in BALB/c mice, its genetic deletion leads to amelioration of cancer and exacerbation of psoriasis in distal skin. Intestinal expression of sPLA2-IIA is reduced after treatment with antibiotics or under germ-free conditions, suggesting its upregulation by gut microbiota. Metagenome, transcriptome, and metabolome analyses have revealed that sPLA2-IIA deficiency alters the gut microbiota, accompanied by notable changes in the intestinal expression of genes related to immunity and metabolism, as well as in the levels of various blood metabolites and fecal bacterial lipids, suggesting that sPLA2-IIA contributes to shaping of the gut microbiota. The skin phenotypes in Pla2g2a-/- mice are lost (a) when they are cohoused with littermate WT mice, resulting in the mixing of the microbiota between the genotypes, or (b) when they are housed in a more stringent pathogen-free facility, where Pla2g2a expression in WT mice is low and the gut microbial compositions in both genotypes are nearly identical. Thus, our results highlight a potentially new aspect of sPLA2-IIA as a modulator of gut microbiota, perturbation of which affects distal skin responses.}, } @article {pmid35075183, year = {2022}, author = {Vatanen, T and Sakwinska, O and Wilson, B and Combremont, S and Cutfield, WS and Chan, SY and Godfrey, KM and , and O'Sullivan, JM}, title = {Transcription shifts in gut bacteria shared between mothers and their infants.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {1276}, pmid = {35075183}, issn = {2045-2322}, support = {MC_UP_A620_1015/MRC_/Medical Research Council/United Kingdom ; MC_UU_12011/1/MRC_/Medical Research Council/United Kingdom ; MC_UP_A620_1014/MRC_/Medical Research Council/United Kingdom ; MC_PC_21003/MRC_/Medical Research Council/United Kingdom ; G0400491/MRC_/Medical Research Council/United Kingdom ; MC_PC_21000/MRC_/Medical Research Council/United Kingdom ; MC_U147585827/MRC_/Medical Research Council/United Kingdom ; MC_U147585824/MRC_/Medical Research Council/United Kingdom ; MC_PC_21001/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Female ; *Gastrointestinal Microbiome ; Humans ; *Infant ; *Metagenome ; *Mothers ; Pilot Projects ; *Transcriptome ; }, abstract = {The infant gut microbiome contains a portion of bacteria that originate from the maternal gut. In the infant gut these bacteria encounter a new metabolic environment that differs from the adult gut, consequently requiring adjustments in their activities. We used pilot community RNA sequencing data (metatranscriptomes) from ten mother-infant dyads participating in the NiPPeR Study to characterize bacterial gene expression shifts following mother-to-infant transmission. Maternally-derived bacterial strains exhibited large scale gene expression shifts following the transmission to the infant gut, with 12,564 activated and 14,844 deactivated gene families. The implicated genes were most numerous and the magnitude shifts greatest in Bacteroides spp. This pilot study demonstrates environment-dependent, strain-specific shifts in gut bacteria function and underscores the importance of metatranscriptomic analysis in microbiome studies.}, } @article {pmid35067915, year = {2022}, author = {Shahraki, MF and Atanaki, FF and Ariaeenejad, S and Ghaffari, MR and Norouzi-Beirami, MH and Maleki, M and Salekdeh, GH and Kavousi, K}, title = {A computational learning paradigm to targeted discovery of biocatalysts from metagenomic data: A case study of lipase identification.}, journal = {Biotechnology and bioengineering}, volume = {119}, number = {4}, pages = {1115-1128}, doi = {10.1002/bit.28037}, pmid = {35067915}, issn = {1097-0290}, mesh = {High-Throughput Nucleotide Sequencing/methods ; Lipase/chemistry/genetics ; *Metagenome ; *Metagenomics/methods ; Temperature ; }, abstract = {The growing adoption of enzymes as biocatalysts in various industries has accentuated the demand for acquiring access to the great natural diversity and, in the meantime, the advent and advancements of metagenomics and high-throughput sequencing technologies have offered an unprecedented opportunity to explore this extensive resource. Lipases, enzymes responsible for the biological turnover of lipids, are among the most commercialized biocatalysts with numerous applications in different domains and therefore are of high industrial value. The relatively costly and time-consuming wet-lab experimental pipelines commonly used for novel enzyme discovery, highlight the necessity of agile in silico approaches to keep pace with the exponential growth of available sequencing data. In the present study, an in-depth analysis of a tannery wastewater metagenome, including taxonomic and enzymatic profiling, was performed. Using sequence homology-based screening methods and supervised machine learning-based regression models aimed at prediction of lipases' pH and temperature optima, the metagenomic data set was screened for lipolytic enzymes, which led to the isolation of alkaline and highly thermophilic novel lipase. Moreover, MeTarEnz (metagenomic targeted enzyme miner) software was developed and made freely accessible (at https://cbb.ut.ac.ir/MeTarEnz) as a part of this study. MeTarEnz offers several functions to automate the process of targeted enzyme mining from high-throughput sequencing data. This study highlights the competence of computational approaches in exploring vast biodiversity within environmental niches, while providing a set of practical in silico tools as well as a generalized methodology to facilitate the sequence-based mining of biocatalysts.}, } @article {pmid35067170, year = {2022}, author = {Jin, H and You, L and Zhao, F and Li, S and Ma, T and Kwok, LY and Xu, H and Sun, Z}, title = {Hybrid, ultra-deep metagenomic sequencing enables genomic and functional characterization of low-abundance species in the human gut microbiome.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2021790}, pmid = {35067170}, issn = {1949-0984}, mesh = {Bacteria/classification/*genetics/*isolation & purification ; Bacteriophages/classification/genetics/isolation & purification ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genomics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota ; Phylogeny ; }, abstract = {A large number of microbial genomes have already been identified from the human gut microbiome, but the understanding of the role of the low-abundance species at the individual level remains challenging, largely due to the relatively shallow sequencing depth used in most studies. To improve genome assembling performance, a HiSeq-PacBio hybrid, ultra-deep metagenomic sequencing approach was used to reconstruct metagenomic-assembled genomes (MAGs) from 12 fecal samples. Such approach combined third-generation sequencing with ultra-deep second-generation sequencing to improve the sequencing coverage of the low-abundance subpopulation in the gut microbiome. Our study generated a total of 44 megabase-scale scaffolds, achieving four single-scaffolds of complete (circularized, no gaps) MAGs (CMAGs) that were the first circular genomes of their species. Moreover, 475 high-quality MAGs were assembled across all samples. Among them, 234 MAGs were currently uncultured, including 24 MAGs that were not found in any public genome database. Additionally, 287 and 77 MAGs were classified as low-abundance (0.1-1%) and extra-low-abundance (<0.1%) gut species in each individual, respectively. Our results also revealed individual-specific genomic features in the MAG profiles, including microbial genome growth rate, selective pressure, and frequency of chromosomal mobile genetic elements. Finally, thousands of extrachromosomal mobile genetic elements were identified from the metagenomic data, including 5097 bacteriophages and 79 novel plasmid genomes. Overall, our strategy represents an important step toward comprehensive genomic and functional characterization of the human gut microbiome at an individual level.}, } @article {pmid35066694, year = {2022}, author = {Liu, J and Luo, W and Chen, Q and Chen, X and Zhou, G and Sun, H}, title = {Curcumin sensitizes response to cytarabine in acute myeloid leukemia by regulating intestinal microbiota.}, journal = {Cancer chemotherapy and pharmacology}, volume = {89}, number = {2}, pages = {243-253}, pmid = {35066694}, issn = {1432-0843}, mesh = {Animals ; Antineoplastic Combined Chemotherapy Protocols/administration & dosage/*pharmacology ; Cholesterol/biosynthesis ; Curcumin/administration & dosage ; Cytarabine/administration & dosage ; Drug Resistance, Neoplasm ; Drug Synergism ; Gastrointestinal Microbiome/*drug effects ; HL-60 Cells ; Humans ; Leukemia, Myeloid, Acute/*drug therapy/microbiology ; Male ; Metabolomics ; Metagenomics ; Mice ; Xenograft Model Antitumor Assays ; }, abstract = {PURPOSE: To address whether Curcumin has synergistic effect with cytarabine (Ara-C) in treating acute myeloid leukemia (AML).

METHODS: A xenograft AML mouse model was established by injecting HL-60 cells into tail vein of mice to assess the function of Curcumin. Mononuclear cells (MNCs) isolated from AML mice and AML cell lines were used to examine the effect of Curcumin. Metagenomics and metabolomics were used to evaluate the alteration of intestinal microbiota and the change of metabolites in MNCs.

RESULTS: Curcumin treatment sensitized response to Ara-C in MNCs of AML mice, but had no direct effect on AML cell lines. Metagenomics revealed an alteration of intestinal microbiota with Curcumin treatment, which contributes to sensitized response to Ara-C. Curcumin treatment led to enhanced intestinal intact to sensitize response to Ara-C in AML mice, through reducing mucus degrading bacteria. Metabolomics demonstrated that Curcumin treatment led to decreased cholesterol in MNCs of AML mice. Further study proved that Curcumin treatment resulted in inhibition of SQLE, a key enzyme of cholesterol biosynthesis, to increase sensitivity to Ara-C.

CONCLUSION: Curcumin sensitizes response to Ara-C through regulating microbiota, highlighting the importance of intestinal intact strengthening in chemoresistant therapy. Moreover, aiming at cholesterol synthesis is promising in AML treatment.}, } @article {pmid35066408, year = {2022}, author = {Graham, EH and Clarke, JL and Fernando, SC and Herr, JR and Adamowicz, MS}, title = {The application of the skin virome for human identification.}, journal = {Forensic science international. Genetics}, volume = {57}, number = {}, pages = {102662}, doi = {10.1016/j.fsigen.2022.102662}, pmid = {35066408}, issn = {1878-0326}, mesh = {DNA ; *Forensic Anthropology ; Genome, Viral ; Humans ; Metagenome ; Metagenomics ; *Virome ; }, abstract = {The use of skin virome offers a unique approach for human identification purposes in instances where a viable and statistically relevant human DNA profile is unavailable. The skin virome may act as an alternative DNA profile and/or an additional form of probative genetic material. To date, no study has attempted to investigate the human virome over a time series across various physical locations of the body to identify its diagnostic potential as a tool for human identification. For this study, we set out to evaluate the stability, diversity, and individualization of the human skin virome. An additional goal was to identify putative viral signatures that can be used in conjunction with traditional forensic STR loci. In order to accomplish this, human viral metagenomes were collected and sequenced from 42 individuals at three anatomical locations (left hand, right hand, and scalp) across multiple collection periods over a 6-month window of time. Assembly dependent and independent bioinformatic approaches, along with a database centered assessment of viral identification, resulted in three sets of stable putative viral markers. In total, with the three sets combined, we identified 59 viral biomarker regions, consisting of viral species and uncharacterized viral genome assemblies, that were stable over the sampling period. Additionally, we found the abundance profiles of these 59 viral biomarkers, based on presence or absence, to be significantly different across subjects (P < 0.001). Here we demonstrate that not only is the human virome applicable to be used for human identification, but we have identified many viral signatures that can putatively be used for forensic applications, thus providing a foundation to the novel field of forensic virology.}, } @article {pmid35065652, year = {2022}, author = {Salachan, PV and Sørensen, KD}, title = {Dysbiotic microbes and how to find them: a review of microbiome profiling in prostate cancer.}, journal = {Journal of experimental & clinical cancer research : CR}, volume = {41}, number = {1}, pages = {31}, pmid = {35065652}, issn = {1756-9966}, mesh = {Dysbiosis/*physiopathology ; Humans ; Male ; Microbiota/*physiology ; Prostatic Neoplasms/*physiopathology ; }, abstract = {The role of the microbiota in human health and disease is well established, including its effects on several cancer types. However, the role of microbial dysbiosis in prostate cancer development, progression, and response to treatment is less well understood. This knowledge gap could perhaps be implicated in the lack of better risk stratification and prognostic tools that incorporate risk factors such as bacterial infections and inflammatory signatures. With over a decade's research investigating associations between microbiome and prostate carcinogenesis, we are ever closer to finding the crucial biological link between the two. Yet, definitive answers remain elusive, calling for continued research into this field. In this review, we outline the three frequently used NGS based analysis methodologies that are used for microbiome profiling, thereby serving as a quick guide for future microbiome research. We next provide a detailed overview of the current knowledge of the role of the human microbiome in prostate cancer development, progression, and treatment response. Finally, we describe proposed mechanisms of host-microbe interactions that could lead to prostate cancer development, progression or treatment response.}, } @article {pmid35064149, year = {2022}, author = {Altshuler, I and Raymond-Bouchard, I and Magnuson, E and Tremblay, J and Greer, CW and Whyte, LG}, title = {Unique high Arctic methane metabolizing community revealed through in situ [13]CH4-DNA-SIP enrichment in concert with genome binning.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {1160}, pmid = {35064149}, issn = {2045-2322}, mesh = {Arctic Regions ; *Carbon Cycle ; Carbon Isotopes ; Genome, Bacterial ; Greenhouse Gases/*metabolism ; Methane/chemistry/isolation & purification/*metabolism ; Microbiota/*genetics ; Permafrost/*microbiology ; }, abstract = {Greenhouse gas (GHG) emissions from Arctic permafrost soils create a positive feedback loop of climate warming and further GHG emissions. Active methane uptake in these soils can reduce the impact of GHG on future Arctic warming potential. Aerobic methane oxidizers are thought to be responsible for this apparent methane sink, though Arctic representatives of these organisms have resisted culturing efforts. Here, we first used in situ gas flux measurements and qPCR to identify relative methane sink hotspots at a high Arctic cytosol site, we then labeled the active microbiome in situ using DNA Stable Isotope Probing (SIP) with heavy [13]CH4 (at 100 ppm and 1000 ppm). This was followed by amplicon and metagenome sequencing to identify active organisms involved in CH4 metabolism in these high Arctic cryosols. Sequencing of [13]C-labeled pmoA genes demonstrated that type II methanotrophs (Methylocapsa) were overall the dominant active methane oxidizers in these mineral cryosols, while type I methanotrophs (Methylomarinovum) were only detected in the 100 ppm SIP treatment. From the SIP-[13]C-labeled DNA, we retrieved nine high to intermediate quality metagenome-assembled genomes (MAGs) belonging to the Proteobacteria, Gemmatimonadetes, and Chloroflexi, with three of these MAGs containing genes associated with methanotrophy. A novel Chloroflexi MAG contained a mmoX gene along with other methane oxidation pathway genes, identifying it as a potential uncultured methane oxidizer. This MAG also contained genes for copper import, synthesis of biopolymers, mercury detoxification, and ammonia uptake, indicating that this bacterium is strongly adapted to conditions in active layer permafrost and providing new insights into methane biogeochemical cycling. In addition, Betaproteobacterial MAGs were also identified as potential cross-feeders with methanotrophs in these Arctic cryosols. Overall, in situ SIP labeling combined with metagenomics and genome binning demonstrated to be a useful tool for discovering and characterizing novel organisms related to specific microbial functions or biogeochemical cycles of interest. Our findings reveal a unique and active Arctic cryosol microbial community potentially involved in CH4 cycling.}, } @article {pmid35063245, year = {2022}, author = {Singh, G and Haileselassie, Y and Briscoe, L and Bai, L and Patel, A and Sanjines, E and Hendler, S and Singh, PK and Garud, NR and Limketkai, BN and Habtezion, A}, title = {The effect of gastric acid suppression on probiotic colonization in a double blinded randomized clinical trial.}, journal = {Clinical nutrition ESPEN}, volume = {47}, number = {}, pages = {70-77}, doi = {10.1016/j.clnesp.2021.11.005}, pmid = {35063245}, issn = {2405-4577}, mesh = {Adolescent ; Adult ; Female ; Gastric Acid ; *Gastroesophageal Reflux/drug therapy ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; *Probiotics ; Proton Pump Inhibitors/adverse effects ; Young Adult ; }, abstract = {BACKGROUND & AIMS: Probiotics contain living microorganisms consumed for their putative benefits on the intestinal microbiota and general health and a concept is emerging to use probiotic as a therapeutic intervention to reduce proton pump inhibitors (PPIs) negative effects, but data is lacking. The use of PPIs can result in disordered gut microbiota, leading to a risk of enteric infections. PPIs are frequently prescribed in the general practice setting for gastroesophageal reflux disease (GERD), peptic ulcer disease, and related conditions. Despite the availability and widespread use of probiotics and acid-suppressing medications, the effect of PPIs-induced gastric acid suppression on the survival and colonization of probiotics bacterial species is currently unclear. We hypothesized that gastric acid suppression may improve intestinal colonization of probiotics bacterial species and probiotic intervention may have a potential role in mitigating untoward effects of PPI.

METHODS: In a randomized, double-blind, placebo-controlled study, healthy subjects were given either proton pump inhibitor (PPI, n = 15) or placebo (n = 15) over 6 weeks. All subjects then consumed multi-strain probiotics from weeks 2-6. Thirty participants (10 males, 20 females, age range: 18-56 years) were enrolled in the study. Shotgun metagenomic sequencing and untargeted metabolomics analyses were performed on stool samples collected at week 0, 2, and 6.

RESULTS: Short term PPI treatment increased the microbial abundance of Streptococcaceae (p = 0.004), Leuconostacaceae (p = 0.001), and Pasteurellaceae (p = 0.020) at family level and corresponding genus levels. The metabolomic analysis of the stools revealed a change in 10 metabolites where Gly Arg Val and phenylacetic acid were consistently increased compared to the baseline. Probiotic intervention inhibited PPI-induced microbial changes such as a decrease in Leuconostacaceae family (p = 0.01) and led to an increase in metabolite 1H-Indole-4-carbaldehyde. Notably, PPI enhanced the colonization of certain probiotic bacterial species like Streptococcus thermophilus (p < 0.05) along with other species present in the multi-strain probiotic.

CONCLUSION: Acid suppression enhanced certain probiotic associated bacterial colonization and probiotics in turn suppressed PPI-mediated intestinal microbial alterations. Thus, probiotics in combination with PPI might be a beneficial strategy that allows probiotic colonization and suppress PPI-induced microbial perturbations. CLINICAL TRIALS.

GOV, NUMBER: NCT03327051.}, } @article {pmid35059329, year = {2021}, author = {Zuppi, M and Hendrickson, HL and O'Sullivan, JM and Vatanen, T}, title = {Phages in the Gut Ecosystem.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {822562}, pmid = {35059329}, issn = {2235-2988}, mesh = {Bacteria ; *Bacteriophages ; Ecosystem ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; *Viruses ; }, abstract = {Phages, short for bacteriophages, are viruses that specifically infect bacteria and are the most abundant biological entities on earth found in every explored environment, from the deep sea to the Sahara Desert. Phages are abundant within the human biome and are gaining increasing recognition as potential modulators of the gut ecosystem. For example, they have been connected to gastrointestinal diseases and the treatment efficacy of Fecal Microbiota Transplant. The ability of phages to modulate the human gut microbiome has been attributed to the predation of bacteria or the promotion of bacterial survival by the transfer of genes that enhance bacterial fitness upon infection. In addition, phages have been shown to interact with the human immune system with variable outcomes. Despite the increasing evidence supporting the importance of phages in the gut ecosystem, the extent of their influence on the shape of the gut ecosystem is yet to be fully understood. Here, we discuss evidence for phage modulation of the gut microbiome, postulating that phages are pivotal contributors to the gut ecosystem dynamics. We therefore propose novel research questions to further elucidate the role(s) that they have within the human ecosystem and its impact on our health and well-being.}, } @article {pmid35055056, year = {2022}, author = {Kawalec, A and Zwolińska, D}, title = {Emerging Role of Microbiome in the Prevention of Urinary Tract Infections in Children.}, journal = {International journal of molecular sciences}, volume = {23}, number = {2}, pages = {}, pmid = {35055056}, issn = {1422-0067}, mesh = {Age Factors ; Child ; Child, Preschool ; Diet ; Disease Management ; Disease Susceptibility ; Humans ; Immunologic Factors/therapeutic use ; Metagenome ; Metagenomics/methods ; *Microbiota ; Molecular Diagnostic Techniques ; Probiotics/administration & dosage ; Urinary Tract Infections/diagnosis/epidemiology/*etiology/*prevention & control ; Vaccines/therapeutic use ; }, abstract = {The microbiome of the urinary tract plays a significant role in maintaining health through the impact on bladder homeostasis. Urobiome is of great importance in maintaining the urothelial integrity and preventing urinary tract infection (UTI), as well as promoting local immune function. Dysbiosis in this area has been linked to an increased risk of UTIs, nephrolithiasis, and dysfunction of the lower urinary tract. However, the number of studies in the pediatric population is limited, thus the characteristic of the urobiome in children, its role in a child's health, and pediatric urologic diseases are not completely understood. This review aims to characterize the healthy urobiome in children, the role of dysbiosis in urinary tract infection, and to summarize the strategies to modification and reshape disease-prone microbiomes in pediatric patients with recurrent urinary tract infections.}, } @article {pmid35055048, year = {2022}, author = {Costa, A and Rani, B and Bastiaanssen, TFS and Bonfiglio, F and Gunnigle, E and Provensi, G and Rossitto, M and Boehme, M and Strain, C and Martínez, CS and Blandina, P and Cryan, JF and Layé, S and Corradetti, R and Passani, MB}, title = {Diet Prevents Social Stress-Induced Maladaptive Neurobehavioural and Gut Microbiota Changes in a Histamine-Dependent Manner.}, journal = {International journal of molecular sciences}, volume = {23}, number = {2}, pages = {}, pmid = {35055048}, issn = {1422-0067}, support = {AMBROSIAC//JPI-Healthy Diet for Healthy Life Project/ ; FRM PRINSS DEQ20170336724//Fondation pour la Recherche Médicale/ ; }, mesh = {Animals ; Behavior, Animal ; Biomarkers ; Body Weight ; Cytokines/metabolism ; *Diet ; *Dysbiosis ; Fatty Acids/metabolism ; *Gastrointestinal Microbiome ; Gene Expression ; Hippocampus/metabolism/physiopathology ; Histamine/*metabolism ; Locomotion ; Male ; Metagenome ; Metagenomics ; Mice ; Mice, Knockout ; Models, Animal ; *Social Behavior ; *Stress, Psychological ; }, abstract = {Exposure to repeated social stress may cause maladaptive emotional reactions that can be reduced by healthy nutritional supplementation. Histaminergic neurotransmission has a central role in orchestrating specific behavioural responses depending on the homeostatic state of a subject, but it remains to be established if it participates in the protective effects against the insults of chronic stress afforded by a healthy diet. By using C57BL/6J male mice that do not synthesize histamine (Hdc[-/-]) and their wild type (Hdc[+/+]) congeners we evaluated if the histaminergic system participates in the protective action of a diet enriched with polyunsaturated fatty acids and vitamin A on the deleterious effect of chronic stress. Behavioural tests across domains relevant to cognition and anxiety were performed. Hippocampal synaptic plasticity, cytokine expression, hippocampal fatty acids, oxylipins and microbiota composition were also assessed. Chronic stress induced social avoidance, poor recognition memory, affected hippocampal long-term potentiation, changed the microbiota profile, brain cytokines, fatty acid and oxylipins composition of both Hdc[-/-] and Hdc[+/+] mice. Dietary enrichment counteracted stress-induced deficits only in Hdc[+/+] mice as histamine deficiency prevented almost all the diet-related beneficial effects. Interpretation: Our results reveal a previously unexplored and novel role for brain histamine as a mediator of many favorable effects of the enriched diet. These data present long-reaching perspectives in the field of nutritional neuropsychopharmacology.}, } @article {pmid35055031, year = {2022}, author = {Martin, S and Foulon, A and El Hage, W and Dufour-Rainfray, D and Denis, F}, title = {Is There a Link between Oropharyngeal Microbiome and Schizophrenia? A Narrative Review.}, journal = {International journal of molecular sciences}, volume = {23}, number = {2}, pages = {}, pmid = {35055031}, issn = {1422-0067}, mesh = {Animals ; Antipsychotic Agents/administration & dosage/adverse effects/therapeutic use ; *Disease Susceptibility ; Dysbiosis ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota/drug effects ; Neuroinflammatory Diseases/etiology/metabolism ; Oropharynx/*microbiology ; Periodontal Diseases/complications/etiology ; Saliva/microbiology ; Schizophrenia/drug therapy/*etiology/metabolism ; }, abstract = {The study aimed to examine the impact of the oropharyngeal microbiome in the pathophysiology of schizophrenia and to clarify whether there might be a bidirectional link between the oral microbiota and the brain in a context of dysbiosis-related neuroinflammation. We selected nine articles including three systemic reviews with several articles from the same research team. Different themes emerged, which we grouped into 5 distinct parts concerning the oropharyngeal phageome, the oropharyngeal microbiome, the salivary microbiome and periodontal disease potentially associated with schizophrenia, and the impact of drugs on the microbiome and schizophrenia. We pointed out the presence of phageoma in patients suffering from schizophrenia and that periodontal disease reinforces the role of inflammation in the pathophysiology of schizophrenia. Moreover, saliva could be an interesting substrate to characterize the different stages of schizophrenia. However, the few studies we have on the subject are limited in scope, and some of them are the work of a single team. At this stage of knowledge, it is difficult to conclude on the existence of a bidirectional link between the brain and the oral microbiome. Future studies on the subject will clarify these questions that for the moment remain unresolved.}, } @article {pmid35055002, year = {2022}, author = {Zhang, X and Xiong, Z and Li, M and Zheng, N and Zhao, S and Wang, J}, title = {Activity- and Enrichment-Based Metaproteomics Insights into Active Urease from the Rumen Microbiota of Cattle.}, journal = {International journal of molecular sciences}, volume = {23}, number = {2}, pages = {}, pmid = {35055002}, issn = {1422-0067}, support = {CAAS-ZDXT2019004//Scientific Research Project for Major Achievements of the Agricultural Science and Technology Innovation Program/ ; 2004DA125184G2108//State Key Laboratory of Animal Nutrition/ ; }, mesh = {Amino Acid Sequence ; Animals ; Cattle ; Enzyme Activation ; *Metagenomics/methods ; *Microbiota ; Models, Molecular ; Protein Conformation ; *Proteomics/methods ; Rumen/*microbiology ; Structure-Activity Relationship ; Urease/chemistry/*metabolism ; }, abstract = {Regulation of microbial urease activity plays a crucial role in improving the utilization efficiency of urea and reducing nitrogen emissions to the environment for ruminant animals. Dealing with the diversity of microbial urease and identifying highly active urease as the target is the key for future regulation. However, the identification of active urease in the rumen is currently limited due to large numbers of uncultured microorganisms. In the present study, we describe an activity- and enrichment-based metaproteomic analysis as an approach for the discovery of highly active urease from the rumen microbiota of cattle. We conducted an optimization method of protein extraction and purification to obtain higher urease activity protein. Cryomilling was the best choice among the six applied protein extraction methods (ultrasonication, bead beating, cryomilling, high-pressure press, freeze-thawing, and protein extraction kit) for obtaining protein with high urease activity. The extracted protein by cryomilling was further enriched through gel filtration chromatography to obtain the fraction with the highest urease activity. Then, by using SDS-PAGE, the gel band including urease was excised and analyzed using LC-MS/MS, searching against a metagenome-derived protein database. Finally, we identified six microbial active ureases from 2225 rumen proteins, and the identified ureases were homologous to those of Fibrobacter and Treponema. Moreover, by comparing the 3D protein structures of the identified ureases and known ureases, we found that the residues in the β-turn of flap regions were nonconserved, which might be crucial in influencing the flexibility of flap regions and urease activity. In conclusion, the active urease from rumen microbes was identified by the approach of activity- and enrichment-based metaproteomics, which provides the target for designing a novel efficient urease inhibitor to regulate rumen microbial urease activity.}, } @article {pmid35053147, year = {2022}, author = {Yongsawas, R and Inta, A and Kampuansai, J and Pandith, H and Suwannarach, N and Lamyong, S and Chantawannakul, P and Chitov, T and Disayathanoowat, T}, title = {Bacterial Communities in Lanna Phak-Gard-Dong (Pickled Mustard Green) from Three Different Ethnolinguistic Groups in Northern Thailand.}, journal = {Biology}, volume = {11}, number = {1}, pages = {}, pmid = {35053147}, issn = {2079-7737}, support = {grant number BDC-PG3-163006//The Center of Excellence on Biodiversity (BDC), Office of Higher Education Commission, Thailand/ ; }, abstract = {The Lanna region, the main part of northern Thailand, is a place of ethnic diversity. In this study, we investigated phak-gard-dong (PGD), or pickled mustard green (Brassica juncea L. Czern.), for its beneficial bacteria content and to analyse the variations in bacterial compositions among the PGD of three different ethnolinguistic groups, the Karen, Lawa, and Shan. DNA was extracted from the PGD pickled brine, and 16S rRNA gene Illumina sequencing was performed. Metagenomic data were analysed and the results demonstrated that the dominant bacterial species were Weissella (54.2%, 65.0%, and 10.0%) and Lactobacillus (17.5%, 5.6%, and 79.1%) in the PGD of the Karen, Lawa, and Shan, respectively. Pediococcus was found only in the PGD of the Karen and Shan. Bacterial communities in PGD of the Lawa were distinctive from the other ethnic groups, both in the alpha and beta diversity, as well as the predicted functions of the bacterial communities. In addition, overall network analysis results were correlated to bacterial proportions in every ethnic PGD. We suggest that all ethnic PGDs have the potential to be a good source of beneficial bacteria, warranting its conservation and further development into health food products.}, } @article {pmid35051998, year = {2022}, author = {Hiraoka, S and Sumida, T and Hirai, M and Toyoda, A and Kawagucci, S and Yokokawa, T and Nunoura, T}, title = {Diverse DNA modification in marine prokaryotic and viral communities.}, journal = {Nucleic acids research}, volume = {50}, number = {3}, pages = {1531-1550}, pmid = {35051998}, issn = {1362-4962}, mesh = {DNA/genetics ; DNA Methylation/genetics ; *DNA Modification Methylases/genetics ; *Epigenomics ; Methyltransferases/genetics ; Prokaryotic Cells/metabolism ; }, abstract = {DNA chemical modifications, including methylation, are widespread and play important roles in prokaryotes and viruses. However, current knowledge of these modification systems is severely biased towards a limited number of culturable prokaryotes, despite the fact that a vast majority of microorganisms have not yet been cultured. Here, using single-molecule real-time sequencing, we conducted culture-independent 'metaepigenomic' analyses (an integrated analysis of metagenomics and epigenomics) of marine microbial communities. A total of 233 and 163 metagenomic-assembled genomes (MAGs) were constructed from diverse prokaryotes and viruses, respectively, and 220 modified motifs and 276 DNA methyltransferases (MTases) were identified. Most of the MTase genes were not genetically linked with the endonuclease genes predicted to be involved in defense mechanisms against extracellular DNA. The MTase-motif correspondence found in the MAGs revealed 10 novel pairs, 5 of which showed novel specificities and experimentally confirmed the catalytic specificities of the MTases. We revealed novel alternative specificities in MTases that are highly conserved in Alphaproteobacteria, which may enhance our understanding of the co-evolutionary history of the methylation systems and the genomes. Our findings highlight diverse unexplored DNA modifications that potentially affect the ecology and evolution of prokaryotes and viruses in nature.}, } @article {pmid35051422, year = {2022}, author = {Volodina, DE and Gureev, AP and Shaforostova, EA and Gryaznova, MV and Ignatyeva, DA and Popov, VN}, title = {Effect of l-carnitine and mildronate on the mitochondrial metabolism of heart and bacterial composition of the gut microbiome in ageing mice.}, journal = {Life sciences}, volume = {293}, number = {}, pages = {120333}, doi = {10.1016/j.lfs.2022.120333}, pmid = {35051422}, issn = {1879-0631}, mesh = {Aging/drug effects/*metabolism ; Animals ; Bifidobacterium/metabolism ; Cardiovascular Agents/*pharmacology ; Carnitine/*pharmacology ; DNA, Mitochondrial/metabolism ; Female ; Gastrointestinal Microbiome/drug effects/*physiology ; Male ; Methylhydrazines/*pharmacology ; Mice ; Mice, Inbred C57BL ; Mitochondria, Heart/drug effects/*metabolism ; }, abstract = {Ageing is the most significant risk factor for cardiovascular diseases. l-Carnitine has a potent cardioprotective effect and its synthesis decreases during ageing. At the same time, there are pharmaceuticals, such as mildronate which, on the contrary, are aimed at reducing the concentration of l-carnitine in the heart and lead to slows down the oxidation of fatty acids in mitochondria. Despite this, both l-carnitine and mildronate are positioned as cardio protectors. We showed that l-carnitine supplementation to the diet of 15-month-old mice increased expression of the PGC-1α gene, which is responsible for the regulation of fatty acid oxidation, and the Nrf2 gene, which is responsible for protecting mitochondria by regulating the expression of antioxidants and mitophagy, in the heart. Mildronate activated the expression of genes that regulate glucose metabolism. Probably, this metabolic shift may protect the mitochondria of the heart from the accumulation of acyl-carnitine, which occurs during the oxidation of fatty acids under oxygen deficiency. Both pharmaceuticals impacted the gut microbiome bacterial composition. l-Carnitine increased the level of Lachnoanaerobaculum and [Eubacterium] hallii group, mildronate increased the level of Bifidobacterium, Rikinella, Christensenellaceae. Considered, that these bacteria for protection the organism from various pathogens and chronic inflammation. Thus, we suggested that the positive effects of both drugs on the mitochondria metabolism and gut microbiome bacterial composition may contribute to the protection of the heart during ageing.}, } @article {pmid35051369, year = {2022}, author = {Jin, WB and Li, TT and Huo, D and Qu, S and Li, XV and Arifuzzaman, M and Lima, SF and Shi, HQ and Wang, A and Putzel, GG and Longman, RS and Artis, D and Guo, CJ}, title = {Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome.}, journal = {Cell}, volume = {185}, number = {3}, pages = {547-562.e22}, pmid = {35051369}, issn = {1097-4172}, support = {R21 AI142213/AI/NIAID NIH HHS/United States ; R01 AI095466/AI/NIAID NIH HHS/United States ; DP2 HD101401/HD/NICHD NIH HHS/United States ; R01 DK126871/DK/NIDDK NIH HHS/United States ; R01 AI151599/AI/NIAID NIH HHS/United States ; R01 DK128257/DK/NIDDK NIH HHS/United States ; U01 AI095608/AI/NIAID NIH HHS/United States ; R01 DK114252/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bile Acids and Salts/metabolism ; CRISPR-Cas Systems/genetics ; Clostridium/genetics ; Colitis/chemically induced/microbiology/pathology ; Dextran Sulfate ; Drug Resistance, Microbial/genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer Techniques ; *Genes, Bacterial ; Germ-Free Life ; Inflammation/pathology ; Intestines/pathology ; Male ; Metabolome/genetics ; Metagenomics ; Mice, Inbred C57BL ; Mice, Knockout ; Mutagenesis, Insertional/genetics ; Mutation/genetics ; RNA, Ribosomal, 16S/genetics ; Transcription, Genetic ; Mice ; }, abstract = {Hundreds of microbiota genes are associated with host biology/disease. Unraveling the causal contribution of a microbiota gene to host biology remains difficult because many are encoded by nonmodel gut commensals and not genetically targetable. A general approach to identify their gene transfer methodology and build their gene manipulation tools would enable mechanistic dissections of their impact on host physiology. We developed a pipeline that identifies the gene transfer methods for multiple nonmodel microbes spanning five phyla, and we demonstrated the utility of their genetic tools by modulating microbiome-derived short-chain fatty acids and bile acids in vitro and in the host. In a proof-of-principle study, by deleting a commensal gene for bile acid synthesis in a complex microbiome, we discovered an intriguing role of this gene in regulating colon inflammation. This technology will enable genetically engineering the nonmodel gut microbiome and facilitate mechanistic dissection of microbiota-host interactions.}, } @article {pmid35051309, year = {2022}, author = {Fan, C and Zhang, L and Jia, S and Tang, X and Fu, H and Li, W and Liu, C and Zhang, H and Cheng, Q and Zhang, Y}, title = {Seasonal variations in the composition and functional profiles of gut microbiota reflect dietary changes in plateau pikas.}, journal = {Integrative zoology}, volume = {17}, number = {3}, pages = {379-395}, pmid = {35051309}, issn = {1749-4877}, support = {152111KYSB20160089//Hefei Science Center, Chinese Academy of Sciences/ ; 2021-ZJ-Y01//Qinghai innovation platform construction project by Chinese Academy of Sciences/ ; //The project of western light for interdisciplinary team/ ; //Sanjiangyaun National Park Animal Genome Program/ ; 2019-ZJ-7024//Natural Science Foundation of Qinghai Province/ ; }, mesh = {Animals ; Carbohydrates ; *Gastrointestinal Microbiome ; *Lagomorpha/genetics ; RNA, Ribosomal, 16S/genetics ; Seasons ; }, abstract = {Seasonal variations in gut microbiota of small mammals and how they are influenced by environmental variables are relatively poorly understood. We sampled 162 wild plateau pikas (Ochotona curzoniae) in 4 seasons over 2 and a half years and recorded the air temperature, precipitation, and nutrient content in edible vegetation at the sampling site. After conducting 16S rRNA and shotgun metagenomic sequencing, we found that the highest alpha diversity, the relative abundance of Firmicutes, and the simplest co-occurrence network occurred in winter, whereas the highest relative abundance of Proteobacteria and the most complex network structure were observed in spring. The highest relative abundance of Verrucomicrobiota and Spirochaetota was seen in summer and autumn, respectively. Air temperature, precipitation, and the contents of crude protein, crude fiber, and polysaccharide in vegetation had significant effects on the seasonal changes in gut microbiota. Diet contributed more to microbial variation than climatic factors. Metagenomic analysis revealed that the amino acid metabolism pathway and axillary activity enzymes were most abundant in summer, while abundance of carbohydrate-binding modules and carbohydrate esterases was highest in spring. These microbial variations were related to the changes in dietary nutrition, indicating that gut microbiota of plateau pika contribute to the efficient use of food resources. This study provides new evidence of how external environmental factors affect the intestinal environment of small mammals.}, } @article {pmid35049196, year = {2021}, author = {Wang, G and Cong, D and Ju, H and Sun, J and Li, C and Zhang, Z and Chu, Y and Wu, X}, title = {Community intervention study of viscera massage in overweight/obese type 2 diabetes high-risk population.}, journal = {Medicine}, volume = {100}, number = {48}, pages = {e27932}, pmid = {35049196}, issn = {1536-5964}, support = {[2020]498//Department of Finance of Jilin Province/ ; 2019YFC1709904//National Basic Research Program of China (973 Program)/ ; JJKH20210959KJ//Education Department of Jilin Province/ ; 20200403124SF//Jilin Scientific and Technological Development Program/ ; 2020J065//Jilin Provincial Health and Family Planning Commission/ ; }, mesh = {Abdomen ; *Gastrointestinal Microbiome ; Humans ; Massage/*methods ; Obesity/*complications/therapy ; Overweight ; Prediabetic State/complications/*therapy ; Viscera ; }, abstract = {BACKGROUND: Prediabetes is an intermediate metabolic state between normoglycemia and diabetes. Without intervention, prediabetes often progresses to diabetes and prediabetes is associated with increased risk of cardiovascular disease, cancer, renal disease, and dementia. Lifestyle modification play a major role in controlling prediabetes. But lifestyle interventions are often with poor compliance and side effects of drugs are often be dislike by people. As a non-invasive therapy with no side effects, abdominal massage (AM), also called viscera massage in China, has been used to treat prediabetes and obesity-associated diseases. The gut microbiota has been recognized as an important factor in the development of metabolic diseases. Individuals with prediabetes have aberrant intestinal microbiota character. Colonic transport time and stool consistency are strongly associated with gut microbiota. Viscera massage can ease constipation by reducing colonic transport time and promoting intestinal motility. We can infer that viscera massage can modulate composition of gut microbiota affects human metabolism. So, in this trial, we will explore the mechanism of viscera massage on prediabetes from the perspective of intestinal microbiota.

METHODS AND DESIGN: Eighty prediabetes individuals will be recruited for this study. Eighty prediabetes individuals will be divided into lifestyle intervention group and viscera massage + lifestyle intervention group by a simple random method. Each group will have 40 individuals. The manipulation of the viscera massage + lifestyle intervention group will be mainly carried out through rubbing the abdomen, kneading abdomen, vibrating abdomen, and pressing the abdomen, 30 minutes per time, once a day, with 2 days off every 5 days. Lifestyle interventions will be performed by combining pushing healthy lifestyle guidance information through Wechat application and giving face-to-face advice together daily. The lifestyle intervention group will receive healthy lifestyle intervention only. All the intervention will be conducted for 4 weeks. Weight, body mass index (BMI), waist circumference, waist-to-hip ratio, and waist-to-height ratio will be measured at the last day of every week. Triglycerides, total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, fasting blood-glucose, 2-hour post-meal blood glucose (2hPG) and glycosylated hemoglobin, fasting insulin and insulin resistance index will be tested at the first day and last day of the intervention course. The fecal samples of subjects will be gathered at the first day and last day of the intervention course and will be performed 16S rRNA gene sequencing and metagenomic detection. Finally, the effect and potential mechanism of viscera massage on prediabetes will be discussed in combination with all the results.

DISCUSSION: The results of this study will be used to verify the effect of AM on prediabetes and explore the mechanism of AM on prediabetes from the perspective of gut microbiota.}, } @article {pmid35049120, year = {2022}, author = {Youngblut, ND and de la Cuesta-Zuluaga, J and Ley, RE}, title = {Incorporating genome-based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes.}, journal = {Environmental microbiology}, volume = {24}, number = {9}, pages = {3966-3984}, doi = {10.1111/1462-2920.15910}, pmid = {35049120}, issn = {1462-2920}, mesh = {Humans ; *Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Tree-based diversity measures incorporate phylogenetic or functional relatedness into comparisons of microbial communities. This can improve the identification of explanatory factors compared to tree-agnostic diversity measures. However, applying tree-based diversity measures to metagenome data is more challenging than for single-locus sequencing (e.g. 16S rRNA gene). Utilizing the Genome Taxonomy Database for species-level metagenome profiling allows for functional diversity measures based on genomic content or traits inferred from it. Still, it is unclear how metagenome-based assessments of microbiome diversity benefit from incorporating phylogeny or function into measures of diversity. We assessed this by measuring phylogeny-based, function-based and tree-agnostic diversity measures from a large, global collection of human gut metagenomes composed of 30 studies and 2943 samples. We found tree-based measures to explain phenotypic variation (e.g. westernization, disease status and gender) better or equivalent to tree-agnostic measures. Ecophylogenetic and functional diversity measures provided unique insight into how microbiome diversity was partitioned by phenotype. Tree-based measures greatly improved machine learning model performance for predicting westernization, disease status and gender, relative to models trained solely on tree-agnostic measures. Our findings illustrate the usefulness of tree- and function-based measures for metagenomic assessments of microbial diversity, which is a fundamental component of microbiome science.}, } @article {pmid35049092, year = {2022}, author = {Furuhashi, H and Takayasu, L and Isshi, K and Hara, Y and Ono, S and Kato, M and Sumiyama, K and Suda, W}, title = {Effect of storage temperature and flash-freezing on salivary microbiota profiles based on 16S rRNA-targeted sequencing.}, journal = {European journal of oral sciences}, volume = {130}, number = {2}, pages = {e12852}, doi = {10.1111/eos.12852}, pmid = {35049092}, issn = {1600-0722}, mesh = {DNA, Bacterial ; Feces ; Freezing ; *Gastrointestinal Microbiome/genetics ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Temperature ; }, abstract = {The sample storage environment affects gut microbial profiles as assessed using 16S rRNA sequencing. However, the influence of storage condition on human salivary microbial profiles has not been well characterized. Here, we performed an observational study to assess the robustness of microbiota profiles in three different storage environments (-80°C after flash-freezing, -80°C, and -15°C; all for 14 days) compared to immediate DNA extraction using the MiSeq Illumina platform. Notably, the 16S rRNA V1-V2 region amplicon sequencing revealed no difference in microbiota profiles between the immediate extraction and each of three storage conditions. An almost perfect correlation was shown between the immediate extraction and the -15°C storage group for relative abundance at the genus and operational taxonomic unit levels. The intraindividual UniFrac distances among storage methods were significantly shorter than those of interindividual distances. None of the amount of extracted DNA, the α-diversity indices, or the relative abundance at the phylum/genus/operational taxonomic unit level differed among storage methods. These findings indicate that a storage temperature of -15°C without flash-freezing may be optimal in terms of cost advantage and simplicity in 16S rRNA sequencing-based salivary microbial research.}, } @article {pmid35048279, year = {2022}, author = {Serag, AM and Abdel-Sabour, MS and El-Hadidi, M and Maged, M and Magdy, M and Ramadan, MF and Refaat, MH}, title = {Comparative 16S Metabarcoding of Nile Tilapia Gut Microbiota from the Northern Lakes of Egypt.}, journal = {Applied biochemistry and biotechnology}, volume = {194}, number = {5}, pages = {2168-2182}, pmid = {35048279}, issn = {1559-0291}, mesh = {Animals ; Bacteria/genetics ; *Cichlids/genetics/microbiology ; Egypt ; *Gastrointestinal Microbiome/genetics ; Lakes ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Nile tilapia, Oreochromis niloticus, is the principal fish bred in Egypt. A pilot study was designed to analyze the bacterial composition of the Nile tilapia fish guts from two saltwater lakes in Northern Egypt. Fish samples were obtained from two Delta lakes: Manzala (ML) and Borollus (BL). DNA was extracted, and the bacterial communities in the stomach content were classified (down to the species level) using the 16S rRNA-based analysis. From the two metagenomics libraries in this study, 1,426,740 reads of the amplicon sequence corresponding to 508 total taxonomic operational units were recorded. The most prevalent bacterial phyla were Proteobacteria, Firmicutes, Actinobacteria, and Synergistetes in all samples. Some of the strains identified belong to classes of pathogenic zoonotic bacteria. A notable difference was observed between gut bacteria of Nile tilapia fish obtained from BL and ML. There is a remarkable indication that Nile tilapia fish living in BL is heavily burdened with pathogenic microbes most remarkably those involved with methylation of mercury and its accumulation in fish organs. These pathogenic microbes could have clinical implications and correlated with many diseases. This result was also consistent with the metagenomic data's functional prediction that indicated that Nile tilapia species harboring these two Egyptian northern lakes may be exposed to numerous anthropogenic pollutants. The findings show that the host environment has a significant impact on the composition of its microbiota. The first step towards exploring the better management of this profit-making fish is recognizing the structure of the microbiome.}, } @article {pmid35045876, year = {2022}, author = {Pan, J and Xu, W and Zhou, Z and Shao, Z and Dong, C and Liu, L and Luo, Z and Li, M}, title = {Genome-resolved evidence for functionally redundant communities and novel nitrogen fixers in the deyin-1 hydrothermal field, Mid-Atlantic Ridge.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {8}, pmid = {35045876}, issn = {2049-2618}, mesh = {*Hydrothermal Vents/microbiology ; *Microbiota/genetics ; Nitrogen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Deep-sea hydrothermal vents represent unique ecosystems that redefine our understanding of the limits of life. They are widely distributed in deep oceans and typically form along mid-ocean ridges. To date, the hydrothermal systems in the Mid-Atlantic Ridge south of 14°S remain barely explored, limiting our understanding of the microbial community in this distinct ecosystem. The Deyin-1 is a newly discovered hydrothermal field in this area. By applying the metagenomic analysis, we aim at gaining much knowledge of the biodiversity and functional capability of microbial community inhabiting this field.

RESULTS: In the current study, 219 metagenomic assembled genomes (MAGs) were reconstructed, unveiling a diverse and variable community dominated by Bacteroidetes, Nitrospirae, Alpha-, Delta-, and Gammaproteobacteria in the active and inactive chimney samples as well as hydrothermal oxide samples. Most of these major taxa were potentially capable of using reduced sulfur and hydrogen as primary energy sources. Many members within the major taxa exhibited potentials of metabolic plasticity by possessing multiple energy metabolic pathways. Among these samples, different bacteria were found to be the major players of the same metabolic pathways, further supporting the variable and functionally redundant community in situ. In addition, a high proportion of MAGs harbored the genes of carbon fixation and extracellular carbohydrate-active enzymes, suggesting that both heterotrophic and autotrophic strategies could be essential for their survival. Notably, for the first time, the genus Candidatus Magnetobacterium was shown to potentially fix nitrogen, indicating its important role in the nitrogen cycle of inactive chimneys. Moreover, the metabolic plasticity of microbes, diverse and variable community composition, and functional redundancy of microbial communities may represent the adaptation strategies to the geochemically complex and fluctuating environmental conditions in deep-sea hydrothermal fields.

CONCLUSIONS: This represents the first assembled-genome-based investigation into the microbial community and metabolism of a hydrothermal field in the Mid-Atlantic Ridge south of 14°S. The findings revealed that a high proportion of microbes could benefit from simultaneous use of heterotrophic and autotrophic strategies in situ. It also presented novel members of potential diazotrophs and highlighted the metabolic plasticity and functional redundancy across deep-sea hydrothermal systems. Video abstract.}, } @article {pmid35045853, year = {2022}, author = {Sun, Z and Song, ZG and Liu, C and Tan, S and Lin, S and Zhu, J and Dai, FH and Gao, J and She, JL and Mei, Z and Lou, T and Zheng, JJ and Liu, Y and He, J and Zheng, Y and Ding, C and Qian, F and Zheng, Y and Chen, YM}, title = {Gut microbiome alterations and gut barrier dysfunction are associated with host immune homeostasis in COVID-19 patients.}, journal = {BMC medicine}, volume = {20}, number = {1}, pages = {24}, pmid = {35045853}, issn = {1741-7015}, support = {2017SHZDZX01//Science and Technology Commission of Shanghai Municipality/ ; 20490780100//Science and Technology Commission of Shanghai Municipality for International Partnership Project/ ; 31741072//National Natural Science Foundation of China/ ; 81973032//National Natural Science Foundation of China/ ; 32041004//National Natural Science Foundation of China/ ; 31930001//National Natural Science Foundation of China/ ; 3213000167//National Natural Science Foundation of China/ ; }, mesh = {*COVID-19 ; Dysbiosis ; *Gastrointestinal Microbiome ; Homeostasis ; Humans ; SARS-CoV-2 ; }, abstract = {BACKGROUND: COVID-19 is an infectious disease characterized by multiple respiratory and extrapulmonary manifestations, including gastrointestinal symptoms. Although recent studies have linked gut microbiota to infectious diseases such as influenza, little is known about the role of the gut microbiota in COVID-19 pathophysiology.

METHODS: To better understand the host-gut microbiota interactions in COVID-19, we characterized the gut microbial community and gut barrier function using metagenomic and metaproteomic approaches in 63 COVID-19 patients and 8 non-infected controls. Both immunohematological parameters and transcriptional profiles were measured to reflect the immune response in COVID-19 patients.

RESULTS: Altered gut microbial composition was observed in COVID-19 patients, which was characterized by decreased commensal species and increased opportunistic pathogenic species. Severe illness was associated with higher abundance of four microbial species (i.e., Burkholderia contaminans, Bacteroides nordii, Bifidobacterium longum, and Blautia sp. CAG 257), six microbial pathways (e.g., glycolysis and fermentation), and 10 virulence genes. These severity-related microbial features were further associated with host immune response. For example, the abundance of Bu. contaminans was associated with higher levels of inflammation biomarkers and lower levels of immune cells. Furthermore, human-origin proteins identified from both blood and fecal samples suggested gut barrier dysfunction in COVID-19 patients. The circulating levels of lipopolysaccharide-binding protein increased in patients with severe illness and were associated with circulating inflammation biomarkers and immune cells. Besides, proteins of disease-related bacteria (e.g., B. longum) were detectable in blood samples from patients.

CONCLUSIONS: Our results suggest that the dysbiosis of the gut microbiome and the dysfunction of the gut barrier might play a role in the pathophysiology of COVID-19 by affecting host immune homeostasis.}, } @article {pmid35045174, year = {2022}, author = {Shilo, S and Godneva, A and Rachmiel, M and Korem, T and Bussi, Y and Kolobkov, D and Karady, T and Bar, N and Wolf, BC and Glantz-Gashai, Y and Cohen, M and Zuckerman-Levin, N and Shehadeh, N and Gruber, N and Levran, N and Koren, S and Weinberger, A and Pinhas-Hamiel, O and Segal, E}, title = {The Gut Microbiome of Adults With Type 1 Diabetes and Its Association With the Host Glycemic Control.}, journal = {Diabetes care}, volume = {45}, number = {3}, pages = {555-563}, doi = {10.2337/dc21-1656}, pmid = {35045174}, issn = {1935-5548}, mesh = {Adult ; Blood Glucose ; Blood Glucose Self-Monitoring ; *Diabetes Mellitus, Type 1/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Glycemic Control ; Humans ; }, abstract = {OBJECTIVE: Previous studies have demonstrated an association between gut microbiota composition and type 1 diabetes (T1D) pathogenesis. However, little is known about the composition and function of the gut microbiome in adults with longstanding T1D or its association with host glycemic control.

RESEARCH DESIGN AND METHODS: We performed a metagenomic analysis of the gut microbiome obtained from fecal samples of 74 adults with T1D, 14.6 ± 9.6 years following diagnosis, and compared their microbial composition and function to 296 age-matched healthy control subjects (1:4 ratio). We further analyzed the association between microbial taxa and indices of glycemic control derived from continuous glucose monitoring measurements and blood tests and constructed a prediction model that solely takes microbiome features as input to evaluate the discriminative power of microbial composition for distinguishing individuals with T1D from control subjects.

RESULTS: Adults with T1D had a distinct microbial signature that separated them from control subjects when using prediction algorithms on held-out subjects (area under the receiver operating characteristic curve = 0.89 ± 0.03). Linear discriminant analysis showed several bacterial species with significantly higher scores in T1D, including Prevotella copri and Eubacterium siraeum, and species with higher scores in control subjects, including Firmicutes bacterium and Faecalibacterium prausnitzii (P < 0.05, false discovery rate corrected for all). On the functional level, several metabolic pathways were significantly lower in adults with T1D. Several bacterial taxa and metabolic pathways were associated with the host's glycemic control.

CONCLUSIONS: We identified a distinct gut microbial signature in adults with longstanding T1D and associations between microbial taxa, metabolic pathways, and glycemic control indices. Additional mechanistic studies are needed to identify the role of these bacteria for potential therapeutic strategies.}, } @article {pmid35044669, year = {2022}, author = {Kumar, RS and Mishra, N and Kumar, A}, title = {Characterization of Tobacco Microbiome by Metagenomics Approach.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2413}, number = {}, pages = {229-244}, pmid = {35044669}, issn = {1940-6029}, mesh = {Humans ; Metagenomics ; *Microbiota/genetics ; *Mouth Neoplasms/etiology ; RNA, Ribosomal, 16S/genetics ; *Tobacco Products ; Tobacco Use ; }, abstract = {Chronic consumption of tobacco in all forms, either smoked/smokeless forms, causes major health hazards to humans that include cancer, cardiovascular, lung diseases, diabetes, fertility issues, etc. Among tobacco-mediated cancers, the prominent one being the oral cancers are caused due to chronic tobacco chewing. The biochemicals present in tobacco are involved in carcinogenesis, and their presence is partly mediated by the existence of microbes in tobacco products. The microbial characterization has been evolved from classical microscopical observation to the recent development of 16S rRNA sequencing by next-generation sequencing methods. The metagenomics approach using 16S rRNA-based next-generation sequencing methods enables the detection and characterization of the complete microbial community of tobacco, including both cultivable and non-cultivable microorganisms. Identification of microbes will help in devising strategies to limit the carcinogenic compounds present in tobacco.}, } @article {pmid35041771, year = {2022}, author = {Ahearn-Ford, S and Berrington, JE and Stewart, CJ}, title = {Development of the gut microbiome in early life.}, journal = {Experimental physiology}, volume = {107}, number = {5}, pages = {415-421}, pmid = {35041771}, issn = {1469-445X}, support = {/WT_/Wellcome Trust/United Kingdom ; 221745/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Enterocolitis, Necrotizing ; Feces ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Infant, Premature ; RNA, Ribosomal, 16S/genetics ; }, abstract = {NEW FINDINGS: What is the topic of this review? The importance of the early life gut microbiome, with a focus on preterm infants and microbially related diseases. Current techniques to study the preterm gut microbiome are appraised, and the potential of recent methodological advancements is discussed. What advances does it highlight? Recent findings in the field achieved by the application of advanced technologies, the applicability of intestinally derived organoid models to study host-microbiome interactions in the preterm gut, and recent developments in enhancing the physiological relevance of such models. Preterm intestinally derived organoids may provide novel insights into the mechanisms underlying preterm disease, as well as diagnosis and treatment opportunities. These models have huge translational potential, offering a step towards precision medicine.

ABSTRACT: Accumulating evidence affirms the importance of the gut microbiome in both health and disease. In early life, there exists a critical period in which the composition of gut microbes is particularly malleable and subject to a wide range of influencing factors. Disturbances to microbial communities during this time may be beneficial or detrimental to short and long-term health outcomes. For infants born prematurely, naïve immune systems, immature gastrointestinal tracts and additional clinical needs put this population at high risk of abnormal microbial colonisation, resulting in increased susceptibility to diseases including necrotising enterocolitis (NEC) and late-onset sepsis (LOS). Traditional cell culture methods, gnotobiotic animals, molecular sequencing techniques (16S rRNA gene sequencing and metagenomics) and advanced 'omics' technologies (transcriptomics, proteomics and metabolomics) have been fundamental in exploring the associations between diet, gut microbes, microbial functions and disease. Despite significant investment and ongoing research efforts, prevention and treatment strategies in NEC and LOS remain limited. Recent endeavours have focused on searching for new, more physiologically relevant models to simulate the preterm intestine. Preterm intestinally derived organoids represent a promising in vitro approach in the study of host-microbiome interactions in the preterm infant gut, offering new and exciting possibilities in this field.}, } @article {pmid35040752, year = {2022}, author = {Chen, Y and Wang, H and Lu, W and Wu, T and Yuan, W and Zhu, J and Lee, YK and Zhao, J and Zhang, H and Chen, W}, title = {Human gut microbiome aging clocks based on taxonomic and functional signatures through multi-view learning.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2025016}, pmid = {35040752}, issn = {1949-0984}, mesh = {*Aging ; Bacteria/*classification/genetics/isolation & purification ; Biomarkers/analysis ; Cohort Studies ; *Gastrointestinal Microbiome ; Humans ; *Machine Learning ; Metagenomics ; }, abstract = {The human gut microbiome is a complex ecosystem that is closely related to the aging process. However, there is currently no reliable method to make full use of the metagenomics data of the gut microbiome to determine the age of the host. In this study, we considered the influence of geographical factors on the gut microbiome, and a total of 2604 filtered metagenomics data from the gut microbiome were used to construct an age prediction model. Then, we developed an ensemble model with multiple heterogeneous algorithms and combined species and pathway profiles for multi-view learning. By integrating gut microbiome metagenomics data and adjusting host confounding factors, the model showed high accuracy (R[2] = 0.599, mean absolute error = 8.33 years). Besides, we further interpreted the model and identify potential biomarkers for the aging process. Among these identified biomarkers, we found that Finegoldia magna, Bifidobacterium dentium, and Clostridium clostridioforme had increased abundance in the elderly. Moreover, the utilization of amino acids by the gut microbiome undergoes substantial changes with increasing age which have been reported as the risk factors for age-associated malnutrition and inflammation. This model will be helpful for the comprehensive utilization of multiple omics data, and will allow greater understanding of the interaction between microorganisms and age to realize the targeted intervention of aging.}, } @article {pmid35040702, year = {2022}, author = {Dragone, NB and Henley, JB and Holland-Moritz, H and Diaz, M and Hogg, ID and Lyons, WB and Wall, DH and Adams, BJ and Fierer, N}, title = {Elevational Constraints on the Composition and Genomic Attributes of Microbial Communities in Antarctic Soils.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0133021}, pmid = {35040702}, issn = {2379-5077}, mesh = {*Soil/chemistry ; Antarctic Regions ; Soil Microbiology ; Bacteria ; Archaea ; *Microbiota ; Metagenomics/methods ; }, abstract = {The inland soils found on the Antarctic continent represent one of the more challenging environments for microbial life on Earth. Nevertheless, Antarctic soils harbor unique bacterial and archaeal (prokaryotic) communities able to cope with extremely cold and dry conditions. These communities are not homogeneous, and the taxonomic composition and functional capabilities (genomic attributes) of these communities across environmental gradients remain largely undetermined. We analyzed the prokaryotic communities in soil samples collected from across the Shackleton Glacier region of Antarctica by coupling quantitative PCR, marker gene amplicon sequencing, and shotgun metagenomic sequencing. We found that elevation was the dominant factor explaining differences in the structures of the soil prokaryotic communities, with the drier and saltier soils found at higher elevations harboring less diverse communities and unique assemblages of cooccurring taxa. The higher-elevation soil communities also had lower maximum potential growth rates (as inferred from metagenome-based estimates of codon usage bias) and an overrepresentation of genes associated with trace gas metabolism. Together, these results highlight the utility of assessing community shifts across pronounced environmental gradients to improve our understanding of the microbial diversity found in Antarctic soils and the strategies used by soil microbes to persist at the limits of habitability. IMPORTANCE Antarctic soils represent an ideal system to study how environmental properties shape the taxonomic and functional diversity of microbial communities given the relatively low diversity of Antarctic soil microbial communities and the pronounced environmental gradients that occur across soils located in reasonable proximity to one another. Moreover, the challenging environmental conditions typical of most Antarctic soils present an opportunity to investigate the traits that allow soil microbes to persist in some of the most inhospitable habitats on Earth. We used cultivation-independent methods to study the bacterial and archaeal communities found in soil samples collected from across the Shackleton Glacier region of the Transantarctic Mountains. We show that those environmental characteristics associated with elevation have the greatest impact on the structure of these microbial communities, with the colder, drier, and saltier soils found at higher elevations sustaining less diverse communities that were distinct from those in more hospitable soils with respect to their composition, genomic attributes, and overall life-history strategies. Notably, the harsher conditions found in higher-elevation soils likely select for taxa with lower maximum potential growth rates and an increased reliance on trace gas metabolism to support growth.}, } @article {pmid35039616, year = {2022}, author = {Zheng, X and Jahn, MT and Sun, M and Friman, VP and Balcazar, JL and Wang, J and Shi, Y and Gong, X and Hu, F and Zhu, YG}, title = {Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes.}, journal = {The ISME journal}, volume = {16}, number = {5}, pages = {1397-1408}, pmid = {35039616}, issn = {1751-7370}, support = {RSG\R1\180213//Royal Society/ ; }, mesh = {Bacteria/genetics ; Biodegradation, Environmental ; DNA Viruses ; Metagenomics ; *Microbiota/genetics ; *Pesticides/analysis ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; *Viruses/genetics ; }, abstract = {Viruses significantly influence local and global biogeochemical cycles and help bacteria to survive in different environments by encoding various auxiliary metabolic genes (AMGs) associated with energy acquisition, stress tolerance and degradation of xenobiotics. Here we studied whether bacterial (dsDNA) virus encoded AMGs are enriched in organochlorine pesticide (OCP) contaminated soil in China and if viral AMGs include genes linked to OCP biodegradation. Using metagenomics, we found that OCP-contaminated soils displayed a lower bacterial, but higher diversity of viruses that harbored a higher relative abundance of AMGs linked to pesticide degradation and metabolism. Furthermore, the diversity and relative abundance of AMGs significantly increased along with the severity of pesticide contamination, and several biodegradation genes were identified bioinformatically in viral metagenomes. Functional assays were conducted to experimentally demonstrate that virus-encoded L-2-haloacid dehalogenase gene (L-DEX) is responsible for the degradation of L-2-haloacid pesticide precursors, improving bacterial growth at sub-inhibitory pesticide concentrations. Taken together, these results demonstrate that virus-encoded AMGs are linked to bacterial metabolism and biodegradation, being more abundant and diverse in soils contaminated with pesticides. Moreover, our findings highlight the importance of virus-encoded accessory genes for bacterial ecology in stressful environments, providing a novel avenue for using viruses in the bioremediation of contaminated soils.}, } @article {pmid35039534, year = {2022}, author = {Lee, SJ and Rho, M}, title = {Multimodal deep learning applied to classify healthy and disease states of human microbiome.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {824}, pmid = {35039534}, issn = {2045-2322}, support = {2017M3A9F3041232//National Research Foundation of Korea/ ; 2020-0-01373//Institute of Information & Communications Technology Planning & Evaluation (IITP)/ ; }, mesh = {Colorectal Neoplasms/diagnosis/*microbiology ; *Deep Learning ; Diabetes Mellitus, Type 2/diagnosis/*microbiology ; Genome, Microbial/*genetics ; *Healthy Volunteers ; Humans ; Inflammatory Bowel Diseases/diagnosis/*microbiology ; Liver Cirrhosis/diagnosis/*microbiology ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {Metagenomic sequencing methods provide considerable genomic information regarding human microbiomes, enabling us to discover and understand microbial diseases. Compositional differences have been reported between patients and healthy people, which could be used in the diagnosis of patients. Despite significant progress in this regard, the accuracy of these tools needs to be improved for applications in diagnostics and therapeutics. MDL4Microbiome, the method developed herein, demonstrated high accuracy in predicting disease status by using various features from metagenome sequences and a multimodal deep learning model. We propose combining three different features, i.e., conventional taxonomic profiles, genome-level relative abundance, and metabolic functional characteristics, to enhance classification accuracy. This deep learning model enabled the construction of a classifier that combines these various modalities encoded in the human microbiome. We achieved accuracies of 0.98, 0.76, 0.84, and 0.97 for predicting patients with inflammatory bowel disease, type 2 diabetes, liver cirrhosis, and colorectal cancer, respectively; these are comparable or higher than classical machine learning methods. A deeper analysis was also performed on the resulting sets of selected features to understand the contribution of their different characteristics. MDL4Microbiome is a classifier with higher or comparable accuracy compared with other machine learning methods, which offers perspectives on feature generation with metagenome sequences in deep learning models and their advantages in the classification of host disease status.}, } @article {pmid35039079, year = {2022}, author = {Adu-Oppong, B and Thänert, R and Wallace, MA and Burnham, CD and Dantas, G}, title = {Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {6}, pmid = {35039079}, issn = {2049-2618}, support = {UL1 TR002345/TR/NCATS NIH HHS/United States ; }, mesh = {Dysbiosis ; Humans ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Urinary Tract Infections/diagnosis/microbiology ; }, abstract = {BACKGROUND: The lack of a definition of urinary microbiome health convolutes diagnosis of urinary tract infections (UTIs), especially when non-traditional uropathogens or paucity of bacteria are recovered from symptomatic patients in routine standard-of-care urine tests. Here, we used shotgun metagenomic sequencing to characterize the microbial composition of asymptomatic volunteers in a set of 30 longitudinally collected urine specimens. Using permutation tests, we established a range of asymptomatic microbiota states, and use these to contextualize the microbiota of 122 urine specimens collected from patients with suspected UTIs diagnostically categorized by standard-of-care urinalysis within that range. Finally, we used a standard-of-care culture protocol to evaluate the efficiency of culture-based recovery of the urinary microbiota.

RESULTS: The majority of genitourinary microbiota in individals suspected to have UTI overlapped with the spectrum of asymptomatic microbiota states. Longitudinal characterization of the genitourinary microbiome in urine specimens collected from asymptomatic volunteers revealed fluctuations of microbial functions and taxonomy over time. White blood cell counts from urinalysis suggested that urine specimens categorized as 'insignificant', 'contaminated', or 'no-growth' by conventional culture methods frequently showed signs of urinary tract inflammation, but this inflammation is not associated with genitourinary microbiota dysbiosis. Comparison of directly sequenced urine specimens with standard-of-care culturing confirmed that culture-based diagnosis biases genitourinary microbiota recovery towards the traditional uropathogens Escherichia coli and Klebsiella pneumoniae.

CONCLUSION: Here, we utilize shotgun metagenomic sequencing to establish a baseline of asymptomatic genitourinary microbiota states. Using this baseline we establish substantial overlap between symptomatic and asymptomatic genitourinary microbiota states. Our results establish that bacterial presence alone does not explain the onset of clinical symptoms. Video Abstract.}, } @article {pmid35038012, year = {2022}, author = {Zhou, SP and Zhou, HY and Sun, JC and Liu, C and Ke, X and Zou, SP and Xue, YP and Zheng, YG}, title = {Bacterial dynamics and functions driven by bulking agents to enhance organic degradation in food waste in-situ rapid biological reduction (IRBR).}, journal = {Bioprocess and biosystems engineering}, volume = {45}, number = {4}, pages = {689-700}, pmid = {35038012}, issn = {1615-7605}, mesh = {Bacteria ; Food ; *Microbiota ; *Refuse Disposal/methods ; Triticum ; }, abstract = {This study investigated the effects of different bulking agents (i.e., sawdust, wheat straw, rice straw, and corncob) on bacterial structure and functions for organic degradation during food waste in-situ rapid biological reduction (IRBR) inoculated with microbial agent. Results showed that the highest organic degradation (409.5 g/kg total solid) and volatile solids removal efficiency (41.0%) were achieved when wheat straw was used, largely because the degradation of readily degradable substrates and cellulose was promoted by this bulking agent. Compared with other three bulking agents, the utilization of wheat straw was conducive to construct a more suitable environmental condition (moisture content of 18.0-28.2%, pH of 4.91-5.87) for organic degradation during IRBR process, by virtue of its excellent structural and physiochemical properties. Microbial community analysis suggested that the high-moisture environment in rice straw treatment promoted the growth of Staphylococcus and inhibited the activity of the inoculum. By contrast, lowest bacterial richness was observed in corncob treatment due to the faster water loss. Compared with these two bulking agents, sawdust and wheat straw treatment led to a more stable bacterial community structure, and the inoculated Bacillus gradually became the dominant genus (36.6-57.8%) in wheat straw treatment. Predicted metagenomics analysis showed that wheat straw treatment exhibited the highest carbohydrate metabolism activity which improved the pyruvate, amino sugar and nucleotide sugar metabolism, and thereby promoted the organic degradation and humic substrate production. These results indicated that wheat straw was a more desirable bulking agent, and revealed the potential microbial organics degradation mechanism in IRBR process.}, } @article {pmid35037767, year = {2022}, author = {Shen, Y and Laue, HE and Shrubsole, MJ and Wu, H and Bloomquist, TR and Larouche, A and Zhao, K and Gao, F and Boivin, A and Prada, D and Hunting, DJ and Gillet, V and Takser, L and Baccarelli, AA}, title = {Associations of Childhood and Perinatal Blood Metals with Children's Gut Microbiomes in a Canadian Gestation Cohort.}, journal = {Environmental health perspectives}, volume = {130}, number = {1}, pages = {17007}, pmid = {35037767}, issn = {1552-9924}, support = {P30 ES009089/ES/NIEHS NIH HHS/United States ; R01 ES027845/ES/NIEHS NIH HHS/United States ; R21 ES024841/ES/NIEHS NIH HHS/United States ; T32 CA134286/CA/NCI NIH HHS/United States ; }, mesh = {Canada/epidemiology ; Child ; Cohort Studies ; Female ; *Gastrointestinal Microbiome ; Humans ; Metals ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The gut microbiome is important in modulating health in childhood. Metal exposures affect multiple health outcomes, but their ability to modify bacterial communities in children is poorly understood.

OBJECTIVES: We assessed the associations of childhood and perinatal blood metal levels with childhood gut microbiome diversity, structure, species, gene family-inferred species, and potential pathway alterations.

METHODS: We assessed the gut microbiome using 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing in stools collected from 6- to 7-year-old children participating in the GESTation and Environment (GESTE) cohort study. We assessed blood metal concentrations [cadmium (Cd), manganese (Mn), mercury (Hg), lead (Pb), selenium (Se)] at two time points, namely, perinatal exposures at delivery (N=70) and childhood exposures at the 6- to 7-y follow-up (N=68). We used multiple covariate-adjusted statistical models to determine microbiome associations with continuous blood metal levels, including linear regression (Shannon and Pielou alpha diversity indexes), permutational multivariate analysis of variance (adonis; beta diversity distance matrices), and multivariable association model (MaAsLin2; phylum, family, species, gene family-inferred species, and pathways).

RESULTS: Children's blood Mn and Se significantly associated with microbiome phylum [e.g., Verrucomicrobiota (coef=-0.305, q=0.031; coef=0.262, q=0.084, respectively)] and children's blood Mn significantly associated with family [e.g., Eggerthellaceae (coef=-0.228, q=0.052)]-level differences. Higher relative abundance of potential pathogens (e.g., Flavonifractor plautii), beneficial species (e.g., Bifidobacterium longum, Faecalibacterium prausnitzii), and both potentially pathogenic and beneficial species (e.g., Bacteriodes vulgatus, Eubacterium rectale) inferred from gene families were associated with higher childhood or perinatal blood Cd, Hg, and Pb (q<0.1). We found significant negative associations between childhood blood Pb and acetylene degradation pathway abundance (q<0.1). Finally, neither perinatal nor childhood metal concentrations were associated with children's gut microbial inter- and intrasubject diversity.

DISCUSSION: Our findings suggest both long- and short-term associations between metal exposure and the childhood gut microbiome, with stronger associations observed with more recent exposure. Future epidemiologic analyses may elucidate whether the observed changes in the microbiome relate to children's health. https://doi.org/10.1289/EHP9674.}, } @article {pmid35036494, year = {2022}, author = {Tran, DM and Huynh, TU and Nguyen, TH and Do, TO and Tran, TPH and Nguyen, QV and Nguyen, AD}, title = {Soil microbiome dataset from Yok Don national park in the Central Highlands region of Vietnam.}, journal = {Data in brief}, volume = {40}, number = {}, pages = {107798}, pmid = {35036494}, issn = {2352-3409}, abstract = {The Central Highlands region contains most of the national parks in Vietnam with different ecosystems, including the national parks of Kon Ka Kinh, Chu Mon Ray, Chu Yang Sin, Yok Don, Bidoup-Nui Ba, and Ta Dung. Thus, this region is considered a center with the highest biodiversity in Vietnam [1]. Among the national parks, Yok Don is unique in its conservation of the dry deciduous dipterocarp forest. Furthermore, Yok Don is the second-largest park in Vietnam; it has the most different ecosystem compared with other national parks in this region [2]. Although some studies have investigated biodiversity preservation in the region, some other studies have only dealt with medicinal plants, lichens, and the rhizospheric bacteria of cultivated black pepper [1,[3], [4], [5]. To the best of our knowledge, no research on the microbial communities in Yok Don national park and in the Central Highlands has been reported. At present, global warming and a decrease in the forest area in the Central Highlands have led to the ongoing reduction in biodiversity and microbial resources. The current study reports the microbiome dataset from the soil sample collected in Yok Don national park. Metagenomic next-generation sequencing was used to characterize the microbial communities in the sample. The metagenome dataset generated provides information on microbial diversity and its functionality and can be useful for further studies on the conservation and use of microbial genetic resources in this region.}, } @article {pmid35034639, year = {2022}, author = {Amundson, KK and Borton, MA and Daly, RA and Hoyt, DW and Wong, A and Eder, E and Moore, J and Wunch, K and Wrighton, KC and Wilkins, MJ}, title = {Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {5}, pmid = {35034639}, issn = {2049-2618}, support = {P30 CA046934/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; Canada ; *Hydraulic Fracking ; *Microbiota/genetics ; Predatory Behavior ; }, abstract = {BACKGROUND: Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface ecosystems. Shale formations underly much of the continental USA and display geographically distinct gradients in temperature and salinity. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation.

RESULTS: We collected materials used during the hydraulic fracturing process (i.e., chemicals, drill muds) paired with temporal sampling of water produced from three different hydraulically fractured wells in the STACK (Sooner Trend Anadarko Basin, Canadian and Kingfisher) shale play in OK, USA. Relative to other shale formations, our metagenomic and metabolomic analyses revealed an expanded taxonomic and metabolic diversity of microorganisms that colonize and persist in fractured shales. Importantly, temporal sampling across all three hydraulic fracturing wells traced the degradation of complex polymers from the hydraulic fracturing process to the production and consumption of organic acids that support sulfate- and thiosulfate-reducing bacteria. Furthermore, we identified 5587 viral genomes and linked many of these to the dominant, colonizing microorganisms, demonstrating the key role that viral predation plays in community dynamics within this closed, engineered system. Lastly, top-side audit sampling of different source materials enabled genome-resolved source tracking, revealing the likely sources of many key colonizing and persisting taxa in these ecosystems.

CONCLUSIONS: These findings highlight the importance of resource utilization and resistance to viral predation as key traits that enable specific microbial taxa to persist across fractured shale ecosystems. We also demonstrate the importance of materials used in the hydraulic fracturing process as both a source of persisting shale microorganisms and organic substrates that likely aid in sustaining the microbial community. Moreover, we showed that different physicochemical conditions (i.e., salinity, temperature) can influence the composition and functional potential of persisting microbial communities in shale ecosystems. Together, these results expand our knowledge of microbial life in deep subsurface shales and have important ramifications for management and treatment of microbial biomass in hydraulically fractured wells. Video Abstract.}, } @article {pmid35034142, year = {2023}, author = {Tran, HT and Nguyen, HM and Nguyen, TM and Chang, C and Huang, WL and Huang, CL and Chiang, TY}, title = {Microbial Communities Along 2,3,7,8-tetrachlorodibenzodioxin Concentration Gradient in Soils Polluted with Agent Orange Based on Metagenomic Analyses.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {197-208}, pmid = {35034142}, issn = {1432-184X}, support = {105-2622-B-006 -008 -CC2//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Agent Orange ; Soil ; *Polychlorinated Dibenzodioxins/analysis ; *Dioxins ; Bacteria/genetics ; *Microbiota ; Acidobacteria/genetics ; Firmicutes ; Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The 2,3,7,8-tetrachlorodibenzodioxin (TCDD), a contaminant in Agent Orange released during the US-Vietnam War, led to a severe environmental crisis. Approximately, 50 years have passed since the end of this war, and vegetation has gradually recovered from the pollution. Soil bacterial communities were investigated by 16S metagenomics in habitats with different vegetation physiognomies in Central Vietnam, namely, forests (S0), barren land (S1), grassland (S2), and developing woods (S3). Vegetation complexity was negatively associated with TCDD concentrations, revealing the reasoning behind the utilization of vegetation physiognomy as an indicator for ecological succession along the gradient of pollutants. Stark changes in bacterial composition were detected between S0 and S1, with an increase in Firmicutes and a decrease in Acidobacteria and Bacteroidetes. Notably, dioxin digesters Arthrobacter, Rhodococcus, Comamonadaceae, and Bacialles were detected in highly contaminated soil (S1). Along the TCDD gradients, following the dioxin decay from S1 to S2, the abundance of Firmicutes and Actinobacteria decreased, while that of Acidobacteria increased; slight changes occurred at the phylum level from S2 to S3. Although metagenomics analyses disclosed a trend toward bacterial communities before contamination with vegetation recovery, non-metric multidimensional scaling analysis unveiled a new trajectory deviating from the native state. Recovery of the bacterial community may have been hindered, as indicated by lower bacterial diversity in S3 compared to S0 due to a significant loss of bacterial taxa and recruitment of fewer colonizers. The results indicate that dioxins significantly altered the soil microbiomes into a state of disorder with a deviating trajectory in restoration.}, } @article {pmid35032344, year = {2022}, author = {Rasmussen, JA and Villumsen, KR and von Gersdorff Jørgensen, L and Forberg, T and Zuo, S and Kania, PW and Buchmann, K and Kristiansen, K and Bojesen, AM and Limborg, MT}, title = {Integrative analyses of probiotics, pathogenic infections and host immune response highlight the importance of gut microbiota in understanding disease recovery in rainbow trout (Oncorhynchus mykiss).}, journal = {Journal of applied microbiology}, volume = {132}, number = {4}, pages = {3201-3216}, doi = {10.1111/jam.15433}, pmid = {35032344}, issn = {1365-2672}, support = {DNRF143//Danmarks Grundforskningsfond/ ; 34009-17-1218//Miljøstyrelsen/ ; 8022-00005B//Det Frie Forskningsråd/ ; }, mesh = {Animals ; *Fish Diseases/microbiology ; *Gastrointestinal Microbiome ; Immunity ; *Oncorhynchus mykiss/microbiology ; *Probiotics ; *Yersinia Infections/microbiology/veterinary ; Yersinia ruckeri ; }, abstract = {AIMS: Given the pivotal role played by the gut microbiota in regulating the host immune system, great interest has arisen in the possibility of controlling fish health by modulating the gut microbiota. Hence, there is a need to better understand of the host-microbiota interactions after disease responses to optimize the use of probiotics to strengthen disease resilience and recovery.

METHODS AND RESULTS: We tested the effects of a probiotic feed additive in rainbow trout and challenged the fish with the causative agent for enteric red mouth disease, Yersinia ruckeri. We evaluated the survival, host immune gene expression and the gut microbiota composition. Results revealed that provision of probiotics and exposure to Y. ruckeri induced immune gene expression in the host, which were associated with changes in the gut microbiota. Subsequently, infection with Y. ruckeri had very little effect on microbiota composition when probiotics were applied, indicating that probiotics increased stabilisation of the microbiota. Our analysis revealed potential biomarkers for monitoring infection status and fish health. Finally, we used modelling approaches to decipher interactions between gut bacteria and the host immune gene responses, indicating removal of endogenous bacteria elicited by non-specific immune responses.

CONCLUSIONS: We discuss the relevance of these results emphasizing the importance of host-microbiota interactions, including the protective potential of the gut microbiota in disease responses.

Our results highlight the functional consequences of probiotic-induced changes in the gut microbiota post infection and the resulting host immune response.}, } @article {pmid35030982, year = {2022}, author = {Tan, R and Jin, M and Shao, Y and Yin, J and Li, H and Chen, T and Shi, D and Zhou, S and Li, J and Yang, D}, title = {High-sugar, high-fat, and high-protein diets promote antibiotic resistance gene spreading in the mouse intestinal microbiota.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2022442}, pmid = {35030982}, issn = {1949-0984}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/*genetics/metabolism ; Bacterial Proteins/metabolism ; Dietary Fats/adverse effects/analysis/*metabolism ; Dietary Proteins/adverse effects/analysis/*metabolism ; Dietary Sugars/adverse effects/analysis/*metabolism ; *Drug Resistance, Bacterial ; *Gastrointestinal Microbiome ; Gene Amplification ; Gene Transfer, Horizontal ; Humans ; Male ; Mice ; Mice, Inbred BALB C ; }, abstract = {Diet can not only provide nutrition for intestinal microbiota, it can also remodel them. However, is unclear whether and how diet affects the spread of antibiotic resistance genes (ARGs) in the intestinal microbiota. Therefore, we employed selected high-sugar, high-fat, high-protein, and normal diets to explore the effect. The results showed that high-sugar, high-fat, and high-protein diets promoted the amplification and transfer of exogenous ARGs among intestinal microbiota, and up-regulated the expression of trfAp and trbBp while significantly altered the intestinal microbiota and its metabolites. Inflammation-related products were strongly correlated with the spread of ARGs, suggesting the intestinal microenvironment after diet remodeling might be conducive to the spreading of ARGs. This may be attributed to changes in bacterial membrane permeability, the SOS response, and bacterial composition and diversity caused by diet-induced inflammation. In addition, acceptor bacteria (zygotes) screened by flow cytometry were mostly Proteobacteria, Firmicutes and Actinobacteria, and most were derived from dominant intestinal bacteria remodeled by diet, indicating that the transfer of ARGs was closely linked to diet, and had some selectivity. Metagenomic results showed that the gut resistance genome could be affected not only by diet, but by exogenous antibiotic resistant bacteria (ARB). Many ARG markers coincided with bacterial markers in diet groups. Therefore, dominant bacteria in different diets are important hosts of ARGs in specific dietary environments, but the many pathogenic bacteria present may cause serious harm to human health.}, } @article {pmid35027090, year = {2022}, author = {Rajala, P and Cheng, DQ and Rice, SA and Lauro, FM}, title = {Sulfate-dependant microbially induced corrosion of mild steel in the deep sea: a 10-year microbiome study.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {4}, pmid = {35027090}, issn = {2049-2618}, mesh = {Bacteria/genetics/metabolism ; Biofilms ; Corrosion ; *Microbiota ; *Steel/chemistry ; Sulfates/metabolism ; }, abstract = {BACKGROUND: Metal corrosion in seawater has been extensively studied in surface and shallow waters. However, infrastructure is increasingly being installed in deep-sea environments, where extremes of temperature, salinity, and high hydrostatic pressure increase the costs and logistical challenges associated with monitoring corrosion. Moreover, there is currently only a rudimentary understanding of the role of microbially induced corrosion, which has rarely been studied in the deep-sea. We report here an integrative study of the biofilms growing on the surface of corroding mooring chain links that had been deployed for 10 years at ~2 km depth and developed a model of microbially induced corrosion based on flux-balance analysis.

METHODS: We used optical emission spectrometry to analyze the chemical composition of the mooring chain and energy-dispersive X-ray spectrometry coupled with scanning electron microscopy to identify corrosion products and ultrastructural features. The taxonomic structure of the microbiome was determined using shotgun metagenomics and was confirmed by 16S amplicon analysis and quantitative PCR of the dsrB gene. The functional capacity was further analyzed by generating binned, genomic assemblies and performing flux-balance analysis on the metabolism of the dominant taxa.

RESULTS: The surface of the chain links showed intensive and localized corrosion with structural features typical of microbially induced corrosion. The microbiome on the links differed considerably from that of the surrounding sediment, suggesting selection for specific metal-corroding biofilms dominated by sulfur-cycling bacteria. The core metabolism of the microbiome was reconstructed to generate a mechanistic model that combines biotic and abiotic corrosion. Based on this metabolic model, we propose that sulfate reduction and sulfur disproportionation might play key roles in deep-sea corrosion.

CONCLUSIONS: The corrosion rate observed was higher than what could be expected from abiotic corrosion mechanisms under these environmental conditions. High corrosion rate and the form of corrosion (deep pitting) suggest that the corrosion of the chain links was driven by both abiotic and biotic processes. We posit that the corrosion is driven by deep-sea sulfur-cycling microorganisms which may gain energy by accelerating the reaction between metallic iron and elemental sulfur. The results of this field study provide important new insights on the ecophysiology of the corrosion process in the deep sea.}, } @article {pmid35026256, year = {2022}, author = {Wang, J and Zhang, Y and Ding, Y and Song, H and Liu, T}, title = {Analysis of microbial community resistance mechanisms in groundwater contaminated with SAs and high NH4[+]-Fe-Mn.}, journal = {The Science of the total environment}, volume = {817}, number = {}, pages = {153036}, doi = {10.1016/j.scitotenv.2022.153036}, pmid = {35026256}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; *Groundwater/chemistry ; *Microbiota ; Rivers ; Sulfonamides ; }, abstract = {The resistance mechanism of microbial communities in contaminated groundwater under the combined stress of sulfonamide antibiotics (SAs), NH4[+], and Fe-Mn exceeding the standard levels was studied in an agricultural area along the Songhua River in Northeast China with developed livestock and poultry breeding. Representative points were selected in the study area to explore the response of environmental parameters and microbial communities, and microscopic experiments with different SA concentrations were conducted with background groundwater. The results showed a complex relationship between microbial communities and environmental factors. The environmental factors SM, SM2, SMX, DOC, NO3[-], Fe, Mn, and HCO3[-] significantly affected the microbial community, with SMX, DOC, and Mn having the greatest effect. Three types of antibiotics with similar properties had different effects on the microbial community, and these effects were not simply additive or superimposed. After adding SAs, Proteobacteria with multi-resistance (99.85%) became the dominant phylum, and Acinetobacter (98.68%) became the dominant genus with SA resistance. SAs have a significant influence on bacterial chemotaxis, transporters, substance transport, and metabolism. Microorganisms resist the influence of SAs via a series of resistance mechanisms, such as enhancing the synthesis of relevant enzymes, generating new biochemical reactions, and reducing the transport of harmful substances through cell membranes. We also found that the proportion of exogenous compound degradation and metabolism-related functional genes in the presence of high SA concentrations increased significantly, which may be related to the degradation of SAs by microorganisms.}, } @article {pmid35023810, year = {2022}, author = {Udayan, S and Stamou, P and Crispie, F and Hickey, A and Floyd, AN and Hsieh, CS and Cotter, PD and O'Sullivan, O and Melgar, S and O'Toole, PW and Newberry, RD and Rossini, V and Nally, K}, title = {Identification of Gut Bacteria such as Lactobacillus johnsonii that Disseminate to Systemic Tissues of Wild Type and MyD88-/- Mice.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2007743}, pmid = {35023810}, issn = {1949-0984}, support = {U01 AI163073/AI/NIAID NIH HHS/United States ; R01 DK097317/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification ; Bacterial Physiological Phenomena ; Dendritic Cells/microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Lactobacillus johnsonii/genetics/*physiology ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Myeloid Differentiation Factor 88/*deficiency/genetics ; }, abstract = {In healthy hosts the gut microbiota is restricted to gut tissues by several barriers some of which require MyD88-dependent innate immune sensor pathways. Nevertheless, some gut taxa have been reported to disseminate to systemic tissues. However, the extent to which this normally occurs during homeostasis in healthy organisms is still unknown. In this study, we recovered viable gut bacteria from systemic tissues of healthy wild type (WT) and MyD88[-/-] mice. Shotgun metagenomic-sequencing revealed a marked increase in the relative abundance of L. johnsonii in intestinal tissues of MyD88[-/-] mice compared to WT mice. Lactobacillus johnsonii was detected most frequently from multiple systemic tissues and at higher levels in MyD88[-/-] mice compared to WT mice. Viable L. johnsonii strains were recovered from different cell types sorted from intestinal and systemic tissues of WT and MyD88[-/-] mice. L. johnsonii could persist in dendritic cells and may represent murine immunomodulatory endosymbionts.}, } @article {pmid35021874, year = {2022}, author = {Wang, Y and Tian, S and Wu, N and Liu, W and Li, L and Wang, X}, title = {Differential Microbial Communities in Paddy Soils Between Guiyang Plateaus and Chengdu Basins Drive the Incidence of Rice Bacterial Diseases.}, journal = {Plant disease}, volume = {106}, number = {7}, pages = {1882-1889}, doi = {10.1094/PDIS-09-21-1974-RE}, pmid = {35021874}, issn = {0191-2917}, mesh = {Bacteria/genetics ; *Bacterial Infections ; China ; Incidence ; *Microbiota ; *Oryza/microbiology ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Southwest China has the most complex rice-growing regions in China. With great differences in topography, consisting mainly of basins and plateaus, ecological factors differ greatly between regions. In this study, bulk paddy soils collected from long-term rice fields in Chengdu (basins) and Guiyang (plateaus) were used to study the correlation between microbial diversity and the incidence of rice bacterial diseases. Results showed that the microbial community composition in paddy soils and the microbial functional categories differed significantly between basins and plateaus. They shared >70% of the dominant genera (abundance >1%), but the abundance of the dominant genera differed significantly. Functional analysis found that bulk paddy soils from Chengdu were significantly enriched in virulence factor-related genes; soils from Guiyang were enriched in biosynthesis of secondary metabolites, especially antibiotics. Correspondingly, Chengdu was significantly enriched in leaf bacterial pathogens Acidovorax, Xanthomonas, and Pseudomonas. Greenhouse experiments and correlation analysis showed that soil chemical properties had a greater effect on microbial community composition and positively correlated with the higher incidence of rice bacterial foot rot in Guiyang, whereas temperature had a greater effect on soil microbial functions and positively correlated with the higher severity index of leaf bacterial diseases in Chengdu. Our results provide a new perspective on how differences in microbial communities in paddy soils can influence the incidence of rice bacterial diseases in areas with different topographies.}, } @article {pmid35021085, year = {2022}, author = {Gulyaeva, A and Garmaeva, S and Ruigrok, RAAA and Wang, D and Riksen, NP and Netea, MG and Wijmenga, C and Weersma, RK and Fu, J and Vila, AV and Kurilshikov, A and Zhernakova, A}, title = {Discovery, diversity, and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts.}, journal = {Cell reports}, volume = {38}, number = {2}, pages = {110204}, doi = {10.1016/j.celrep.2021.110204}, pmid = {35021085}, issn = {2211-1247}, mesh = {Adult ; Aged ; Bacteria/genetics/virology ; Bacteriophages/*genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Genome, Viral ; Humans ; Inflammatory Bowel Diseases/virology ; Male ; Metagenome/*genetics ; Metagenomics/methods ; Middle Aged ; Netherlands ; Obesity/virology ; Phylogeny ; }, abstract = {The crAss-like phages are a diverse group of related viruses that includes some of the most abundant viruses of the human gut. To explore their diversity and functional role in human population and clinical cohorts, we analyze gut metagenomic data collected from 1,950 individuals from the Netherlands. We identify 1,556 crAss-like phage genomes, including 125 species-level and 32 genus-level clusters absent from the reference databases used. Analysis of their genomic features shows that closely related crAss-like phages can possess strikingly divergent regions responsible for transcription, presumably acquired through recombination. Prediction of crAss-like phage hosts points primarily to bacteria of the phylum Bacteroidetes, consistent with previous reports. Finally, we explore the temporal stability of crAss-like phages over a 4-year period and identify associations between the abundance of crAss-like phages and several human phenotypes, including depletion of crAss-like phages in inflammatory bowel disease patients.}, } @article {pmid35021078, year = {2022}, author = {Hu, D and Fuller, NR and Caterson, ID and Holmes, AJ and Reeves, PR}, title = {Single-gene long-read sequencing illuminates Escherichia coli strain dynamics in the human intestinal microbiome.}, journal = {Cell reports}, volume = {38}, number = {2}, pages = {110239}, doi = {10.1016/j.celrep.2021.110239}, pmid = {35021078}, issn = {2211-1247}, mesh = {Adult ; DNA, Bacterial/genetics ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/metabolism ; Feces/microbiology ; Female ; Flagellin/genetics/metabolism ; Gastrointestinal Microbiome/*genetics/physiology ; Gene Expression/genetics ; Genetic Variation/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Intestines ; Male ; Microbiota/genetics ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Transcriptome/*genetics ; }, abstract = {Gut microbiome is of major interest due to its close relationship to health and disease. Bacteria usually vary in gene content, leading to functional variations within species, so resolution higher than species-level methods is needed for ecological and clinical relevance. We design a protocol to identify strains in selected species with high discrimination and in high numbers by amplicon sequencing of the flagellin gene. We apply the protocol to fecal samples from a human diet trial, targeting Escherichia coli. Across the 119 samples from 16 individuals, there are 1,532 amplicon sequence variants (ASVs), but only 32 ASVs are dominant in one or more fecal samples, despite frequent dominant strain turnover. Major strains in an intestine are found to be commonly accompanied by a large number of satellite cells, and many are identified as potential extraintestinal pathogens. The protocol could be used to track epidemics or investigate the intra- or inter-host diversity of pathogens.}, } @article {pmid35020412, year = {2022}, author = {Du, Y and Laperriere, SM and Fuhrman, J and Sun, F}, title = {Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {29}, number = {2}, pages = {106-120}, pmid = {35020412}, issn = {1557-8666}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; R01 GM131407/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Bias ; Chromosomes/genetics ; Computational Biology ; High-Throughput Nucleotide Sequencing/statistics & numerical data ; Linear Models ; Logistic Models ; Metagenome ; Metagenomics/*statistics & numerical data ; Microbiota/genetics ; Regression Analysis ; Software ; Yeasts/genetics ; }, abstract = {High-throughput chromosome conformation capture (Hi-C) has recently been applied to natural microbial communities and revealed great potential to study multiple genomes simultaneously. Several extraneous factors may influence chromosomal contacts rendering the normalization of Hi-C contact maps essential for downstream analyses. However, the current paucity of metagenomic Hi-C normalization methods and the ignorance for spurious interspecies contacts weaken the interpretability of the data. Here, we report on two types of biases in metagenomic Hi-C experiments: explicit biases and implicit biases, and introduce HiCzin, a parametric model to correct both types of biases and remove spurious interspecies contacts. We demonstrate that the normalized metagenomic Hi-C contact maps by HiCzin result in lower biases, higher capability to detect spurious contacts, and better performance in metagenomic contig clustering.}, } @article {pmid35019699, year = {2022}, author = {Jeon, S and Kim, H and Kim, J and Seol, D and Jo, J and Choi, Y and Cho, S and Kim, H}, title = {Positive Effect of Lactobacillus acidophilus EG004 on Cognitive Ability of Healthy Mice by Fecal Microbiome Analysis Using Full-Length 16S-23S rRNA Metagenome Sequencing.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0181521}, pmid = {35019699}, issn = {2165-0497}, mesh = {Animals ; Biodiversity ; Brain-Gut Axis ; *Cognition ; Disease Models, Animal ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics/*physiology ; Lactobacillus/genetics/physiology ; Lactobacillus acidophilus/*genetics/*physiology ; Male ; *Metagenome ; Mice ; Mice, Inbred C57BL ; Neurodegenerative Diseases ; Probiotics/pharmacology/therapeutic use ; RNA, Ribosomal, 23S/*genetics ; }, abstract = {Evidence for the concept of the "gut-brain axis" (GBA) has risen. Many types of research demonstrated the mechanism of the GBA and the effect of probiotic intake. Although many studies have been reported, most were focused on neurodegenerative disease and, it is still not clear what type of bacterial strains have positive effects. We designed an experiment to discover a strain that positively affects brain function, which can be recognized through changes in cognitive processes using healthy mice. The experimental group consisted of a control group and three probiotic consumption groups, namely, Lactobacillus acidophilus, Lacticaseibacillus paracasei, and Lacticaseibacillus rhamnosus. Three experimental groups fed probiotics showed an improved cognitive ability by cognitive-behavioral tests, and the group fed on L. acidophilus showed the highest score. To provide an understanding of the altered microbial composition effect on the brain, we performed full 16S-23S rRNA sequencing using Nanopore, and operational taxonomic units (OTUs) were identified at species level. In the group fed on L. acidophilus, the intestinal bacterial ratio of Firmicutes and Proteobacteria phyla increased, and the bacterial proportions of 16 species were significantly different from those of the control group. We estimated that the positive results on the cognitive behavioral tests were due to the increased proportion of the L. acidophilus EG004 strain in the subjects' intestines since the strain can produce butyrate and therefore modulate neurotransmitters and neurotrophic factors. We expect that this strain expands the industrial field of L. acidophilus and helps understand the mechanism of the gut-brain axis. IMPORTANCE Recently, the concept of the "gut-brain axis" has risen and suggested that microbes in the GI tract affect the brain by modulating signal molecules. Although many pieces of research were reported in a short period, a signaling mechanism and the effects of a specific bacterial strain are still unclear. Besides, since most of the research was focused on neurodegenerative disease, the study with a healthy animal model is still insufficient. In this study, we show using a healthy animal model that a bacterial strain (Lactobacillus acidophilus EG004) has a positive effect on mouse cognitive ability. We experimentally verified an improved cognitive ability by cognitive behavioral tests. We performed full 16S-23S rRNA sequencing using a Nanopore MinION instrument and provided the gut microbiome composition at the species level. This microbiome composition consisted of candidate microbial groups as a biomarker that shows positive effects on cognitive ability. Therefore, our study suggests a new perspective for probiotic strain use applicable for various industrialization processes.}, } @article {pmid35019688, year = {2022}, author = {Lin, B and Wang, M and Gao, R and Ye, Z and Yu, Y and He, W and Qiao, N and Ma, Z and Ji, C and Shi, C and Zhou, X and Wang, Y and Zeng, F and Zhang, L and Gong, W and Cao, Z and Zhou, P and Melnikov, V and Ye, H and Li, Y and Zhang, Z and He, M and Qin, H and Zhang, Y}, title = {Characteristics of Gut Microbiota in Patients with GH-Secreting Pituitary Adenoma.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0042521}, pmid = {35019688}, issn = {2165-0497}, mesh = {Adult ; Bacteria/classification/genetics/*isolation & purification ; Case-Control Studies ; DNA, Bacterial/genetics ; Dysbiosis/microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Growth Hormone/metabolism ; Growth Hormone-Secreting Pituitary Adenoma/metabolism/*microbiology ; Humans ; Insulin-Like Growth Factor I/metabolism ; Male ; Metagenomics ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Prior study has demonstrated that gut microbiota at the genus level is significantly altered in patients with growth hormone (GH)-secreting pituitary adenoma (GHPA). Yet, no studies exist describing the state of gut microbiota at species level in GHPA. We performed a study using 16S rRNA amplicon sequencing in a cohort of patients with GH-secreting pituitary adenoma (GHPA, n = 28) and healthy controls (n = 67). Among them, 9 patients and 10 healthy controls were randomly chosen and enrolled in metagenomics shotgun sequencing, generating 280,426,512 reads after aligning to NCBI GenBank DataBase to acquire taxa information at the species level. Weighted UniFrac analysis revealed that microbial diversity was notably decreased in patients with GHPA, consistent with a previous study. With 16S rRNA sequencing, after correction for false-discovery rate (FDR), rank-sum test at the genus level revealed that the relative abundance of Oscillibacter and Enterobacter was remarkably increased in patients and Blautia and Romboutsia genera predominated in the controls, augmented by additional LEfSe (linear discriminant analysis effect size) analysis. As for further comparison at the species level with metagenomics sequencing, rank-sum test together with LEfSe analysis confirmed the enrichment of Alistipes shahii and Odoribacter splanchnicus in the patient group. Notably, LEfSe analysis with metagenomics also demonstrated that Enterobacter sp. DC1 and Enterobacter sp. 940 PEND, derived from Enterobacter, were both significantly enriched in patients. Functional analysis showed that amino acid metabolism pathway was remarkably enriched in GHPA, while carbohydrate metabolism pathway was notably enriched in controls. Further, significant positive correlations were observed between Enterobacter and baseline insulin-like growth factor 1 (IGF-1), indicating that Enterobacter may be strongly associated with GH/IGF-1 axis in GHPA. Our data extend our insight into the GHPA microbiome, which may shed further light on GHPA pathogenesis and facilitate the exploration of novel therapeutic targets based on microbiota manipulation. IMPORTANCE Dysbiosis of gut microbiota is associated not only with intestinal disorders but also with numerous extraintestinal diseases. Growth hormone-secreting pituitary adenoma (GHPA) is an insidious disease with persistent hypersecretion of GH and IGF-1, causing increased morbidity and mortality. Researches have reported that the GH/IGF-1 axis exerts its own influence on the intestinal microflora. Here, the results showed that compared with healthy controls, GHPA patients not only decreased the alpha diversity of the intestinal flora but also significantly changed their beta diversity. Further, metagenomics shotgun sequencing in the present study exhibited that Enterobacter sp. DC1 and Enterobacter sp. 940 PEND were enriched in patients. Also, we were pleasantly surprised to find that the Enterobacter genus was strongly positively correlated with baseline IGF-1 levels. Collectively, our work provides the first glimpse of the dysbiosis of the gut microbiota at species level, providing a better understanding of the pathophysiological process of GHPA.}, } @article {pmid35019672, year = {2022}, author = {Sun, Z and Zhang, M and Li, M and Bhaskar, Y and Zhao, J and Ji, Y and Cui, H and Zhang, H and Sun, Z}, title = {Interactions between Human Gut Microbiome Dynamics and Sub-Optimal Health Symptoms during Seafaring Expeditions.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0092521}, pmid = {35019672}, issn = {2165-0497}, mesh = {Adult ; Bacteria/classification/genetics/*isolation & purification ; Cohort Studies ; Diet ; *Expeditions/psychology ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Health Status ; Humans ; Male ; Metagenomics ; Microbiota ; Military Personnel/psychology ; Young Adult ; }, abstract = {During long ocean voyages, crew members are subject to complex pressures from their living and working environment, which lead to chronic diseases-like sub-optimal health status. Although the association between dysbiotic gut microbiome and chronic diseases has been broadly reported, the correlation between the sub-optimal health status and gut microbiome remains elusive. Here, the health status of 77 crew members (20-35 years old Chinese, male) during a 135-day sea expedition was evaluated using the shotgun metagenomics of stool samples and health questionnaires taken before and after the voyage. We found five core symptoms (e.g., abnormal defecation frequency, insomnia, poor sleep quality, nausea, and overeating) in 55 out of 77 crew members suffering from sub-optimal health status, and this was termed "seafaring syndrome" (SS) in this study. Significant correlation was found between the gut microbiome and SS rather than any single symptom. For example, SS was proven to be associated with individual perturbation in the gut microbiome, and the microbial dynamics between SS and non-SS samples were different during the voyage. Moreover, the microbial signature for SS was identified using the variation of 19 bacterial species and 26 gene families. Furthermore, using a Random Forest model, SS was predicted with high accuracy (84.4%, area under the concentration-time curve = 0.91) based on 28 biomarkers from pre-voyage samples, and the prediction model was further validated by another 30-day voyage cohort (accuracy = 83.3%). The findings in this study provide insights to help us discover potential predictors or even therapeutic targets for dysbiosis-related diseases. IMPORTANCE Systemic and chronic diseases are important health problems today and have been proven to be strongly associated with dysbiotic gut microbiome. Studying the association between the gut microbiome and sub-optimal health status of humans in extreme environments (such as ocean voyages) will give us a better understanding of the interactions between observable health signs and a stable versus dysbiotic gut microbiome states. In this paper, we illustrated that ocean voyages could trigger different symptoms for different crew member cohorts due to individual differences; however, the co-occurrence of high prevalence symptoms indicated widespread perturbation of the gut microbiome. By investigating the microbial signature and gut microbiome dynamics, we demonstrated that such sub-optimal health status can be predicted even before the voyage. We termed this phenomenon as "seafaring syndrome." This study not only provides the potential strategy for health management in extreme environments but also can assist the prediction of other dysbiosis-related diseases.}, } @article {pmid35017197, year = {2022}, author = {Belda, E and Voland, L and Tremaroli, V and Falony, G and Adriouch, S and Assmann, KE and Prifti, E and Aron-Wisnewsky, J and Debédat, J and Le Roy, T and Nielsen, T and Amouyal, C and André, S and Andreelli, F and Blüher, M and Chakaroun, R and Chilloux, J and Coelho, LP and Dao, MC and Das, P and Fellahi, S and Forslund, S and Galleron, N and Hansen, TH and Holmes, B and Ji, B and Krogh Pedersen, H and Le, P and Le Chatelier, E and Lewinter, C and Mannerås-Holm, L and Marquet, F and Myridakis, A and Pelloux, V and Pons, N and Quinquis, B and Rouault, C and Roume, H and Salem, JE and Sokolovska, N and Søndertoft, NB and Touch, S and Vieira-Silva, S and , and Galan, P and Holst, J and Gøtze, JP and Køber, L and Vestergaard, H and Hansen, T and Hercberg, S and Oppert, JM and Nielsen, J and Letunic, I and Dumas, ME and Stumvoll, M and Pedersen, OB and Bork, P and Ehrlich, SD and Zucker, JD and Bäckhed, F and Raes, J and Clément, K}, title = {Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism.}, journal = {Gut}, volume = {71}, number = {12}, pages = {2463-2480}, pmid = {35017197}, issn = {1468-3288}, support = {MR/L01632X/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; Mice ; Animals ; Prebiotics ; *Gastrointestinal Microbiome ; *Obesity, Morbid/surgery ; Biotin/pharmacology ; *Diabetes Mellitus, Type 2 ; *Vitamin B Complex/pharmacology ; Mice, Inbred C57BL ; Obesity/metabolism ; Inflammation ; }, abstract = {OBJECTIVES: Gut microbiota is a key component in obesity and type 2 diabetes, yet mechanisms and metabolites central to this interaction remain unclear. We examined the human gut microbiome's functional composition in healthy metabolic state and the most severe states of obesity and type 2 diabetes within the MetaCardis cohort. We focused on the role of B vitamins and B7/B8 biotin for regulation of host metabolic state, as these vitamins influence both microbial function and host metabolism and inflammation.

DESIGN: We performed metagenomic analyses in 1545 subjects from the MetaCardis cohorts and different murine experiments, including germ-free and antibiotic treated animals, faecal microbiota transfer, bariatric surgery and supplementation with biotin and prebiotics in mice.

RESULTS: Severe obesity is associated with an absolute deficiency in bacterial biotin producers and transporters, whose abundances correlate with host metabolic and inflammatory phenotypes. We found suboptimal circulating biotin levels in severe obesity and altered expression of biotin-associated genes in human adipose tissue. In mice, the absence or depletion of gut microbiota by antibiotics confirmed the microbial contribution to host biotin levels. Bariatric surgery, which improves metabolism and inflammation, associates with increased bacterial biotin producers and improved host systemic biotin in humans and mice. Finally, supplementing high-fat diet-fed mice with fructo-oligosaccharides and biotin improves not only the microbiome diversity, but also the potential of bacterial production of biotin and B vitamins, while limiting weight gain and glycaemic deterioration.

CONCLUSION: Strategies combining biotin and prebiotic supplementation could help prevent the deterioration of metabolic states in severe obesity.

TRIAL REGISTRATION NUMBER: NCT02059538.}, } @article {pmid35017031, year = {2022}, author = {Boeri, L and Donnaloja, F and Campanile, M and Sardelli, L and Tunesi, M and Fusco, F and Giordano, C and Albani, D}, title = {Using integrated meta-omics to appreciate the role of the gut microbiota in epilepsy.}, journal = {Neurobiology of disease}, volume = {164}, number = {}, pages = {105614}, doi = {10.1016/j.nbd.2022.105614}, pmid = {35017031}, issn = {1095-953X}, mesh = {Epilepsy/*microbiology ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; Metagenomics ; }, abstract = {The way the human microbiota may modulate neurological pathologies is a fascinating matter of research. Epilepsy is a common neurological disorder, which has been largely investigated in correlation with microbiota health and function. However, the mechanisms that regulate this apparent connection are scarcely defined, and extensive effort has been conducted to understand the role of microbiota in preventing and reducing epileptic seizures. Intestinal bacteria seem to modulate the seizure frequency mainly by releasing neurotransmitters and inflammatory mediators. In order to elucidate the complex microbial contribution to epilepsy pathophysiology, integrated meta-omics could be pivotal. In fact, the combination of two or more meta-omics approaches allows a multifactorial study of microbial activity within the frame of disease or drug treatments. In this review, we provide information depicting and supporting the use of multi-omics to study the microbiota-epilepsy connection. We described different meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics), focusing on current technical challenges in stool collection procedures, sample extraction methods and data processing. We further discussed the current advantages and limitations of using the integrative approach of multi-omics in epilepsy investigations.}, } @article {pmid35016998, year = {2022}, author = {Franck, M and de Toro-Martín, J and Varin, TV and Garneau, V and Pilon, G and Roy, D and Couture, P and Couillard, C and Marette, A and Vohl, MC}, title = {Raspberry consumption: identification of distinct immune-metabolic response profiles by whole blood transcriptome profiling.}, journal = {The Journal of nutritional biochemistry}, volume = {101}, number = {}, pages = {108946}, doi = {10.1016/j.jnutbio.2022.108946}, pmid = {35016998}, issn = {1873-4847}, mesh = {Adult ; Biological Variation, Population ; C-Reactive Protein/analysis ; Cytokines/biosynthesis ; *Diet ; Feces ; Female ; Fruit ; Gastrointestinal Microbiome ; Gene Expression Profiling ; Humans ; Immunity/*genetics ; Lipidomics ; Lipids/*blood ; Lymphocyte Activation ; Male ; *Metabolome ; *Rubus ; *Transcriptome ; }, abstract = {Numerous studies have reported that diets rich in phenolic compounds are beneficial to immune-metabolic health, yet these effects are heterogeneous and the underlying mechanisms are poorly understood. To investigate the inter-individual variability of the immune-metabolic response to raspberry consumption, whole-blood RNAseq data from 24 participants receiving 280 g/d of raspberries for 8 weeks were used for the identification of responsiveness subgroups by using partial least squares-discriminant analysis (PLSDA) and hierarchical clustering. Transcriptomic-based clustering regrouped participants into two distinct subgroups of 13 and 11 participants, so-called responders and non-responders, respectively. Following raspberry consumption, a significant decrease in triglycerides, cholesterol and C-reactive protein levels were found in responders, as compared to non-responders. Two major gene expression components of 100 and 220 genes were identified by sparse PLSDA as those better discriminating responders from non-responders, and functional analysis identified pathways related to cytokine production, leukocyte activation and immune response as significantly enriched with most discriminant genes. As compared to non-responders, the plasma lipidomic profile of responders was characterized by a significant decrease in triglycerides and an increase in phosphatidylcholines following raspberry consumption. Prior to the intervention, a distinct metagenomic profile was identified by PLSDA between responsiveness subgroups, and the Firmicutes-to-Bacteroidota ratio was found significantly lower in responders, as compared to non-responders. Findings point to this transcriptomic-based clustering approach as a suitable tool to identify distinct responsiveness subgroups to raspberry consumption. This approach represents a promising framework to tackle the issue of inter-individual variability in the understanding of the impact of foods on immune-metabolic health.}, } @article {pmid35016706, year = {2022}, author = {Bolte, EE and Moorshead, D and Aagaard, KM}, title = {Maternal and early life exposures and their potential to influence development of the microbiome.}, journal = {Genome medicine}, volume = {14}, number = {1}, pages = {4}, pmid = {35016706}, issn = {1756-994X}, support = {F30 HD104278/HD/NICHD NIH HHS/United States ; R01 DK089201/DK/NIDDK NIH HHS/United States ; R01 HD091731/HD/NICHD NIH HHS/United States ; R21 ES029462/ES/NIEHS NIH HHS/United States ; }, mesh = {Adult ; Animals ; Child ; Female ; Humans ; Maternal Exposure/adverse effects ; *Microbiota ; Mothers ; Obesity ; Pregnancy ; }, abstract = {At the dawn of the twentieth century, the medical care of mothers and children was largely relegated to family members and informally trained birth attendants. As the industrial era progressed, early and key public health observations among women and children linked the persistence of adverse health outcomes to poverty and poor nutrition. In the time hence, numerous studies connecting genetics ("nature") to public health and epidemiologic data on the role of the environment ("nurture") have yielded insights into the importance of early life exposures in relation to the occurrence of common diseases, such as diabetes, allergic and atopic disease, cardiovascular disease, and obesity. As a result of these parallel efforts in science, medicine, and public health, the developing brain, immune system, and metabolic physiology are now recognized as being particularly vulnerable to poor nutrition and stressful environments from the start of pregnancy to 3 years of age. In particular, compelling evidence arising from a diverse array of studies across mammalian lineages suggest that modifications to our metagenome and/or microbiome occur following certain environmental exposures during pregnancy and lactation, which in turn render risk of childhood and adult diseases. In this review, we will consider the evidence suggesting that development of the offspring microbiome may be vulnerable to maternal exposures, including an analysis of the data regarding the presence or absence of a low-biomass intrauterine microbiome.}, } @article {pmid35014874, year = {2022}, author = {Palomo, A and Dechesne, A and Cordero, OX and Smets, BF}, title = {Evolutionary Ecology of Natural Comammox Nitrospira Populations.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0113921}, pmid = {35014874}, issn = {2379-5077}, mesh = {*Ammonia/metabolism ; Nitrites/metabolism ; Oxidation-Reduction ; Bacteria/genetics ; *Microbiota ; }, abstract = {Microbes commonly exist in diverse and complex communities where species interact, and their genomic repertoires evolve over time. Our understanding of species interaction and evolution has increased during the last decades, but most studies of evolutionary dynamics are based on single species in isolation or in experimental systems composed of few interacting species. Here, we use the microbial ecosystem found in groundwater-fed sand filter as a model to avoid this limitation. In these open systems, diverse microbial communities experience relatively stable conditions, and the coupling between chemical and biological processes is generally well defined. Metagenomic analysis of 12 sand filters communities revealed systematic co-occurrence of at least five comammox Nitrospira species, likely promoted by low ammonium concentrations. These Nitrospira species showed intrapopulation sequence diversity, although possible clonal expansion was detected in a few abundant local comammox populations. Nitrospira species showed low homologous recombination and strong purifying selection, the latter process being especially strong in genes essential in energy metabolism. Positive selection was detected for genes related to resistance to foreign DNA and phages. We found that, compared to other habitats, groundwater-fed sand filters impose strong purifying selection and low recombination on comammox Nitrospira populations. These results suggest that evolutionary processes are more affected by habitat type than by species identity. Together, this study improves our understanding of species interaction and evolution in complex microbial communities and sheds light on the environmental dependency of evolutionary processes. IMPORTANCE Microbial species interact with each other and their environment (ecological processes) and undergo changes in their genomic repertoire over time (evolutionary processes). How these two classes of processes interact is largely unknown, especially for complex communities, as most studies of microbial evolutionary dynamics consider single species in isolation or a few interacting species in simplified experimental systems. In this study, these limitations are circumvented by examining the microbial communities found in stable and well-described groundwater-fed sand filters. Combining metagenomics and strain-level analyses, we identified the microbial interactions and evolutionary processes affecting comammox Nitrospira, a recently discovered bacterial type capable of performing the whole nitrification process. We found that abundant and co-occurrent Nitrospira populations in groundwater-fed sand filters are characterized by low recombination and strong purifying selection. In addition, by comparing these observations with those obtained from Nitrospira species inhabiting other environments, we revealed that evolutionary processes are more affected by habitat type than by species identity.}, } @article {pmid35014868, year = {2022}, author = {Wu, X and Rensing, C and Han, D and Xiao, KQ and Dai, Y and Tang, Z and Liesack, W and Peng, J and Cui, Z and Zhang, F}, title = {Genome-Resolved Metagenomics Reveals Distinct Phosphorus Acquisition Strategies between Soil Microbiomes.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0110721}, pmid = {35014868}, issn = {2379-5077}, mesh = {*Phosphorus/metabolism ; Soil ; Soil Microbiology ; Bacteria ; *Microbiota ; Phosphates/metabolism ; }, abstract = {Enhancing soil phosphate solubilization is a promising strategy for agricultural sustainability, while little is known about the mechanisms of how microorganisms cope with differing phosphorus availability. Using a combination of genome-resolved metagenomics and amplicon sequencing, we investigated the microbial mechanisms involved in phosphorus cycling under three agricultural treatments in a wheat-maize rotation system and two natural reforestation treatments. Available soil phosphorus was the key factor shaping bacterial and fungal community composition and function across our agricultural and reforestation sites. Membrane-bound quinoprotein glucose dehydrogenase (PQQGDH) and exopolyphosphatases (PPX) governed microbial phosphate solubilization in agroecosystems. In contrast, genes encoding glycerol-3-phosphate transporters (ugpB, ugpC, and ugpQ) displayed a significantly greater abundance in the reforestation soils. The gcd gene encoding PQQGDH was found to be the best determinant for bioavailable soil phosphorus. Metagenome-assembled genomes (MAGs) affiliated with Cyclobacteriaceae and Vicinamibacterales were obtained from agricultural soils. Their MAGs harbored not only gcd but also the pit gene encoding low-affinity phosphate transporters. MAGs obtained from reforestation soils were affiliated with Microtrichales and Burkholderiales. These contain ugp genes but no gcd, and thereby are indicative of a phosphate transporter strategy. Our study demonstrates that knowledge of distinct microbial phosphorus acquisition strategies between agricultural and reforestation soils could help in linking microbial processes with phosphorus cycling. IMPORTANCE The soil microbiome is the key player regulating phosphorus cycling processes. Identifying phosphate-solubilizing bacteria and utilizing them for release of recalcitrant phosphate that is bound to rocks or minerals have implications for improving crop nutrient acquisition and crop productivity. In this study, we combined functional metagenomics and amplicon sequencing to analyze microbial phosphorus cycling processes in natural reforestation and agricultural soils. We found that the phosphorus acquisition strategies significantly differed between these two ecosystems. A microbial phosphorus solubilization strategy dominated in the agricultural soils, while a microbial phosphate transporter strategy was observed in the reforestation soils. We further identified microbial taxa that contributed to enhanced phosphate solubilization in the agroecosystem. These microbes are predicted to be beneficial for the increase in phosphate bioavailability through agricultural practices.}, } @article {pmid35013454, year = {2022}, author = {Casimiro-Soriguer, CS and Loucera, C and Peña-Chilet, M and Dopazo, J}, title = {Towards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {450}, pmid = {35013454}, issn = {2045-2322}, support = {PAIDI2020- DOC_00350//Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía/ ; PID2020-117979RB-I00//Ministerio de Ciencia e Innovación/ ; IMP/0019//Instituto de Salud Carlos III/ ; 813533//H2020 Marie Skłodowska-Curie Actions/ ; 676559//H2020 Research Infrastructures/ ; }, mesh = {Adenoma/*microbiology ; Colorectal Neoplasms/*microbiology ; *Gastrointestinal Microbiome ; Humans ; *Machine Learning ; Metagenomics/*methods ; }, abstract = {Gut microbiome is gaining interest because of its links with several diseases, including colorectal cancer (CRC), as well as the possibility of being used to obtain non-intrusive predictive disease biomarkers. Here we performed a meta-analysis of 1042 fecal metagenomic samples from seven publicly available studies. We used an interpretable machine learning approach based on functional profiles, instead of the conventional taxonomic profiles, to produce a highly accurate predictor of CRC with better precision than those of previous proposals. Moreover, this approach is also able to discriminate samples with adenoma, which makes this approach very promising for CRC prevention by detecting early stages in which intervention is easier and more effective. In addition, interpretable machine learning methods allow extracting features relevant for the classification, which reveals basic molecular mechanisms accounting for the changes undergone by the microbiome functional landscape in the transition from healthy gut to adenoma and CRC conditions. Functional profiles have demonstrated superior accuracy in predicting CRC and adenoma conditions than taxonomic profiles and additionally, in a context of explainable machine learning, provide useful hints on the molecular mechanisms operating in the microbiota behind these conditions.}, } @article {pmid35013297, year = {2022}, author = {Yan, W and Hall, AB and Jiang, X}, title = {Bacteroidales species in the human gut are a reservoir of antibiotic resistance genes regulated by invertible promoters.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {1}, pmid = {35013297}, issn = {2055-5008}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; Phase Variation ; }, abstract = {Antibiotic-resistance genes (ARGs) regulated by invertible promoters can mitigate the fitness cost of maintaining ARGs in the absence of antibiotics and could potentially prolong the persistence of ARGs in bacterial populations. However, the origin, prevalence, and distribution of these ARGs regulated by invertible promoters remains poorly understood. Here, we sought to assess the threat posed by ARGs regulated by invertible promoters by systematically searching for ARGs regulated by invertible promoters in the human gut microbiome and examining their origin, prevalence, and distribution. Through metagenomic assembly of 2227 human gut metagenomes and genomic analysis of the Unified Human Gastrointestinal Genome (UHGG) collection, we identified ARGs regulated by invertible promoters and categorized them into three classes based on the invertase-regulating phase variation. In the human gut microbiome, ARGs regulated by invertible promoters are exclusively found in Bacteroidales species. Through genomic analysis, we observed that ARGs regulated by invertible promoters have convergently originated from ARG insertions into glycan-synthesis loci that were regulated by invertible promoters at least three times. Moreover, all three classes of invertible promoters regulating ARGs are located within integrative conjugative elements (ICEs). Therefore, horizontal transfer via ICEs could explain the wide taxonomic distribution of ARGs regulated by invertible promoters. Overall, these findings reveal that glycan-synthesis loci regulated by invertible promoters in Bacteroidales species are an important hotspot for the emergence of clinically-relevant ARGs regulated by invertible promoters.}, } @article {pmid35013099, year = {2022}, author = {Zhao, H and Jin, K and Jiang, C and Pan, F and Wu, J and Luan, H and Zhao, Z and Chen, J and Mou, T and Wang, Z and Lu, J and Lu, S and Hu, S and Xu, Y and Huang, M}, title = {A pilot exploration of multi-omics research of gut microbiome in major depressive disorders.}, journal = {Translational psychiatry}, volume = {12}, number = {1}, pages = {8}, pmid = {35013099}, issn = {2158-3188}, mesh = {Brain ; *Depressive Disorder, Major ; *Gastrointestinal Microbiome ; Gray Matter ; Humans ; *Microbiota ; }, abstract = {The pathophysiology of major depressive disorder (MDD) remains obscure. Recently, the microbiota-gut-brain (MGB) axis's role in MDD has an increasing attention. However, the specific mechanism of the multi-level effects of gut microbiota on host metabolism, immunity, and brain structure is unclear. Multi-omics approaches based on the analysis of different body fluids and tissues using a variety of analytical platforms have the potential to provide a deeper understanding of MGB axis disorders. Therefore, the data of metagenomics, metabolomic, inflammatory factors, and MRI scanning are collected from the two groups including 24 drug-naïve MDD patients and 26 healthy controls (HCs). Then, the correlation analysis is performed in all omics. The results confirmed that there are many markedly altered differences, such as elevated Actinobacteria abundance, plasma IL-1β concentration, lipid, vitamin, and carbohydrate metabolism disorder, and diminished grey matter volume (GMV) of inferior frontal gyrus (IFG) in the MDD patients. Notably, three kinds of discriminative bacteria, Ruminococcus bromii, Lactococcus chungangensis, and Streptococcus gallolyticus have an extensive correlation with metabolome, immunology, GMV, and clinical symptoms. All three microbiota are closely related to IL-1β and lipids (as an example, phosphoethanolamine (PEA)). Besides, Lactococcus chungangensis is negatively related to the GMV of left IFG. Overall, this study demonstrate that the effects of gut microbiome exert in MDD is multifactorial.}, } @article {pmid35011106, year = {2022}, author = {Pivari, F and Mingione, A and Piazzini, G and Ceccarani, C and Ottaviano, E and Brasacchio, C and Dei Cas, M and Vischi, M and Cozzolino, MG and Fogagnolo, P and Riva, A and Petrangolini, G and Barrea, L and Di Renzo, L and Borghi, E and Signorelli, P and Paroni, R and Soldati, L}, title = {Curcumin Supplementation (Meriva[®]) Modulates Inflammation, Lipid Peroxidation and Gut Microbiota Composition in Chronic Kidney Disease.}, journal = {Nutrients}, volume = {14}, number = {1}, pages = {}, pmid = {35011106}, issn = {2072-6643}, mesh = {Aged ; Case-Control Studies ; Curcumin/*administration & dosage ; *Dietary Supplements ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Inflammation ; Lipid Peroxidation/*drug effects ; Male ; Pilot Projects ; Renal Insufficiency, Chronic/*therapy/urine ; Treatment Outcome ; Uremic Toxins/urine ; }, abstract = {Chronic kidney disease (CKD) subjects suffer from high risk of cardiovascular mortality, and any intervention preventing the progression of CKD may have an enormous impact on public health. In the last decade, there has been growing awareness that the gut microbiota (GM) can play a pivotal role in controlling the pathogenesis of systemic inflammatory state and CKD progression. To ameliorate the quality of life in CKD subjects, the use of dietary supplements has increased over time. Among those, curcumin has demonstrated significant in vitro anti-inflammatory properties. In this pilot study, 24 CKD patients and 20 healthy volunteers were recruited. CKD patients followed nutritional counselling and were supplemented with curcumin (Meriva[®]) for six months. Different parameters were evaluated at baseline and after 3-6 months: uremic toxins, metagenomic of GM, and nutritional, inflammatory, and oxidative status. Curcumin significantly reduced plasma pro-inflammatory mediators (CCL-2, IFN-γ, and IL-4) and lipid peroxidation. Regarding GM, after 6 months of curcumin supplementation, Escherichia-Shigella was significantly lower, while Lachnoclostridium was significant higher. Notably, at family level, Lactobacillaceae spp. were found significantly higher in the last 3 months of supplementation. No adverse events were observed in the supplemented group, confirming the good safety profile of curcumin phytosome after long-term administration.}, } @article {pmid35010887, year = {2021}, author = {Pinart, M and Dötsch, A and Schlicht, K and Laudes, M and Bouwman, J and Forslund, SK and Pischon, T and Nimptsch, K}, title = {Gut Microbiome Composition in Obese and Non-Obese Persons: A Systematic Review and Meta-Analysis.}, journal = {Nutrients}, volume = {14}, number = {1}, pages = {}, pmid = {35010887}, issn = {2072-6643}, support = {01EA1906B//Federal Ministry of Food and Agriculture/ ; }, mesh = {Bacteria/*classification/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Obesity/*microbiology ; }, abstract = {Whether the gut microbiome in obesity is characterized by lower diversity and altered composition at the phylum or genus level may be more accurately investigated using high-throughput sequencing technologies. We conducted a systematic review in PubMed and Embase including 32 cross-sectional studies assessing the gut microbiome composition by high-throughput sequencing in obese and non-obese adults. A significantly lower alpha diversity (Shannon index) in obese versus non-obese adults was observed in nine out of 22 studies, and meta-analysis of seven studies revealed a non-significant mean difference (-0.06, 95% CI -0.24, 0.12, I[2] = 81%). At the phylum level, significantly more Firmicutes and fewer Bacteroidetes in obese versus non-obese adults were observed in six out of seventeen, and in four out of eighteen studies, respectively. Meta-analyses of six studies revealed significantly higher Firmicutes (5.50, 95% 0.27, 10.73, I[2] = 81%) and non-significantly lower Bacteroidetes (-4.79, 95% CI -10.77, 1.20, I[2] = 86%). At the genus level, lower relative proportions of Bifidobacterium and Eggerthella and higher Acidaminococcus, Anaerococcus, Catenibacterium, Dialister, Dorea, Escherichia-Shigella, Eubacterium, Fusobacterium, Megasphera, Prevotella, Roseburia, Streptococcus, and Sutterella were found in obese versus non-obese adults. Although a proportion of studies found lower diversity and differences in gut microbiome composition in obese versus non-obese adults, the observed heterogeneity across studies precludes clear answers.}, } @article {pmid35007432, year = {2021}, author = {Ibrahim, A and Maatouk, M and Rajaonison, A and Zgheib, R and Haddad, G and Bou Khalil, J and Raoult, D and Bittar, F}, title = {Adapted Protocol for Saccharibacteria Cocultivation: Two New Members Join the Club of Candidate Phyla Radiation.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0106921}, pmid = {35007432}, issn = {2165-0497}, mesh = {Actinomycetaceae/classification/genetics/*growth & development/metabolism ; Bacteria/classification/genetics/*growth & development/metabolism ; Coculture Techniques/instrumentation/*methods ; Culture Media/metabolism ; Humans ; Microbiota ; Polymerase Chain Reaction ; }, abstract = {The growing application of metagenomics to different ecological and microbiome niches in recent years has enhanced our knowledge of global microbial biodiversity. Among these abundant and widespread microbes, the candidate phyla radiation (CPR) group has been recognized as representing a large proportion of the microbial kingdom (>26%). CPR are characterized by their obligate symbiotic or exoparasitic activity with other microbial hosts, mainly bacteria. Currently, isolating CPR is still considered challenging for microbiologists. The idea of this study was to develop an adapted protocol for the coculture of CPR with a suitable bacterial host. Based on various sputum samples, we tried to enrich CPR (Saccharibacteria members) and to cocultivate them with pure hosts (Schaalia odontolytica). This protocol was monitored by TaqMan real-time quantitative PCR (qPCR) using a system specific for Saccharibacteria designed in this study, as well as by electron microscopy and sequencing. We succeeded in coculturing and sequencing the complete genomes of two new Saccharibacteria species, "Candidatus Minimicrobia naudis" and "Candidatus Minimicrobia vallesae." In addition, we noticed a decrease in the CT values of Saccharibacteria and a significant multiplication through their physical association with Schaalia odontolytica strains in the enriched medium that we developed. This work may help bridge gaps in the genomic database by providing new CPR members, and in the future, their currently unknown characteristics may be revealed. IMPORTANCE In this study, the first TaqMan real-time quantitative PCR (qPCR) system, targeting Saccharibacteria phylum, has been developed. This technique can specifically quantify Saccharibacteria members in any sample of interest in order to investigate their prevalence. In addition, another easy, specific, and sensitive protocol has been developed to maintain the viability of Saccharibacteria cells in an enriched medium with their bacterial host. The use of this protocol facilitates subsequent studies of the phenotypic characteristics of CPR and their physical interactions with bacterial species, as well as the sequencing of new genomes to improve the current database.}, } @article {pmid35007400, year = {2022}, author = {Zhang, J and Zhang, F and Tay, WT and Robin, C and Shi, Y and Guan, F and Yang, Y and Wu, Y}, title = {Population genomics provides insights into lineage divergence and local adaptation within the cotton bollworm.}, journal = {Molecular ecology resources}, volume = {22}, number = {5}, pages = {1875-1891}, doi = {10.1111/1755-0998.13581}, pmid = {35007400}, issn = {1755-0998}, support = {31930093//National Natural Science Foundation of China/ ; BP0719029//The SAFEA of China/ ; }, mesh = {Animals ; Biodiversity ; Gossypium ; *Insecticides ; Larva/genetics ; Metagenomics ; *Moths/genetics ; Temperature ; }, abstract = {The cotton bollworm Helicoverpa armigera is a cosmopolitan pest and its diverse habitats plausibly contribute to the formation of diverse lineages. Despite the significant threat it poses to economic crops worldwide, its evolutionary history and genetic basis of local adaptation are poorly understood. In this study, we de novo assembled a high-quality chromosome-level reference genome of H. a. armigera (contig N50 = 7.34 Mb), with 99.13% of the HaSCD2 assembly assigned to 31 chromosomes (Z-chromosome + 30 autosomes). We constructed an ultradense variation map across 14 cotton bollworm populations and identified a novel lineage in northwestern China. Historical inference showed that effective population size changes coincided with global temperature fluctuation. We identified nine differentiated genes in the three H. armigera lineages (H. a. armigera, H. a. conferta and the new northwestern Chinese lineage), of which per and clk genes are involved in circadian rhythm. Selective sweep analyses identified a series of Gene Ontology categories related to climate adaptation, feeding behaviour and insecticide tolerance. Our findings reveal fundamental knowledge of the local adaptation of different cotton bollworm lineages and will guide the formulation of cotton bollworm management measures at different scales.}, } @article {pmid35004342, year = {2021}, author = {Wirth, R and Pap, B and Maróti, G and Vályi, P and Komlósi, L and Barta, N and Strang, O and Minárovits, J and Kovács, KL}, title = {Toward Personalized Oral Diagnosis: Distinct Microbiome Clusters in Periodontitis Biofilms.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {747814}, pmid = {35004342}, issn = {2235-2988}, mesh = {Biofilms ; Dysbiosis ; Gingiva ; Humans ; *Microbiota ; *Periodontitis/diagnosis ; }, abstract = {Periodontitis is caused by pathogenic subgingival microbial biofilm development and dysbiotic interactions between host and hosted microbes. A thorough characterization of the subgingival biofilms by deep amplicon sequencing of 121 individual periodontitis pockets of nine patients and whole metagenomic analysis of the saliva microbial community of the same subjects were carried out. Two biofilm sampling methods yielded similar microbial compositions. Taxonomic mapping of all biofilms revealed three distinct microbial clusters. Two clinical diagnostic parameters, probing pocket depth (PPD) and clinical attachment level (CAL), correlated with the cluster mapping. The dysbiotic microbiomes were less diverse than the apparently healthy ones of the same subjects. The most abundant periodontal pathogens were also present in the saliva, although in different representations. The single abundant species Tannerella forsythia was found in the diseased pockets in about 16-17-fold in excess relative to the clinically healthy sulcus, making it suitable as an indicator of periodontitis biofilms. The discrete microbial communities indicate strong selection by the host immune system and allow the design of targeted antibiotic treatment selective against the main periodontal pathogen(s) in the individual patients.}, } @article {pmid34999397, year = {2022}, author = {Chang, HM and Chen, SS and Hsiao, SS and Chang, WS and Chien, IC and Duong, CC and Nguyen, TXQ}, title = {Water reclamation and microbial community investigation: Treatment of tetramethylammonium hydroxide wastewater through an anaerobic osmotic membrane bioreactor hybrid system.}, journal = {Journal of hazardous materials}, volume = {427}, number = {}, pages = {128200}, doi = {10.1016/j.jhazmat.2021.128200}, pmid = {34999397}, issn = {1873-3336}, mesh = {Anaerobiosis ; Bioreactors ; Membranes, Artificial ; *Microbiota ; Osmosis ; Quaternary Ammonium Compounds ; RNA, Ribosomal, 16S/genetics ; Wastewater ; Water ; *Water Purification ; }, abstract = {Tetramethylammonium hydroxide (TMAH) is a toxic photoresist developer used in the photolithography process in thin-film transistor liquid crystal display (TFT-LCD) production, and it can be removed through anaerobic treatment. TMAH cannot be released into the environment because of its higher toxicity. A tight membrane, such as a forward osmosis (FO) membrane, together with an anaerobic biological process can ensure that no TMAH is released into the environment. Thus, for the first time, an anaerobic osmotic membrane bioreactor (AnOMBR) hybrid system was developed in this study to treat a low-strength TMAH wastewater and to simultaneously investigate its microbial community. Microfiltration extraction was used to mitigate the salinity accumulation, and a periodically physical water cleaning was utilized to mitigate the FO membrane fouling. The diluted draw solute (MgSO4) was reconcentrated and reused by a membrane distillation (MD) process in the AnOMBR to achieve 99.99% TMAH removal in this AnOMBR-MD hybrid system, thereby ensuring that no TMAH is released into the natural environment. Moreover, the membrane fouling in the feed and draw sides were analyzed through the fluorescence excitation-emission matrix (FEEM) spectrophotometry to confirm that the humic acid-like materials were the primary membrane fouling components in this AnOMBR. Additionally, 16S rRNA metagenomics analysis indicated that Methanosaeta was the predominant contributor to methanogenesis and proliferated during the long-term operation. The methane yield was increased from 0.2 to 0.26 L CH4/g COD when the methanogen species acclimatized to the saline system.}, } @article {pmid34998910, year = {2022}, author = {Liew, WP and Sabran, MR and Than, LT and Abd-Ghani, F}, title = {Metagenomic and proteomic approaches in elucidating aflatoxin B1 detoxification mechanisms of probiotic Lactobacillus casei Shirota towards intestine.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {160}, number = {}, pages = {112808}, doi = {10.1016/j.fct.2022.112808}, pmid = {34998910}, issn = {1873-6351}, mesh = {Aflatoxin B1/*toxicity ; Animals ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Inflammation/*drug therapy/etiology/genetics/microbiology ; Intestines/drug effects/metabolism/microbiology ; Lacticaseibacillus casei/*physiology ; Male ; Metagenomics ; Probiotics/*administration & dosage ; Proteomics ; Rats ; Rats, Sprague-Dawley ; }, abstract = {The modulation of gut microbiota and proteome due to aflatoxin B1 (AFB1) by probiotics remains unclear. This study investigated the alterations of gut microbiota and proteome in AFB1-exposed rats treated with probiotic Lactobacillus casei Shirota (Lcs). Forty male Sprague Dawley rats were randomly divided into five groups (n = 8) comprised control, AFB1, AFB1+activated charcoal, AFB1+Lcs, and Lcs groups. The rats were subjected to different treatments via oral gavage for four weeks. Urine and serum were collected for the measurement of AFB1 biomarkers and organs were harvested for histological analysis. Metagenomic sequencing was performed on fecal samples to profile gut microbiota. Besides, AFB1 most affected organ i.e. jejunum was subjected to proteomic analysis. The results indicated that Lcs intervention significantly reduced AFB1 biomarkers. H&E-stained intestine showed Lcs alleviated AFB1-induced inflammation and abnormal cell growth, particularly at the jejunum. Although AFB1 increased potentially pathogenic bacteria and reduced beneficial bacteria abundance in feces, the microbiota composition was normalized with Lcs treatment. The gut proteome analysis of the jejunum sample showed several pathways of AFB1 toxicity, wherein Lcs treatment demonstrated its protective effect. It is concluded that metagenomic and proteomic approaches are useful tools to understand AFB1-Lcs interaction and detoxification mechanism in the gut.}, } @article {pmid34998802, year = {2022}, author = {Pratt, M and Forbes, JD and Knox, NC and Van Domselaar, G and Bernstein, CN}, title = {Colorectal Cancer Screening in Inflammatory Bowel Diseases-Can Characterization of GI Microbiome Signatures Enhance Neoplasia Detection?.}, journal = {Gastroenterology}, volume = {162}, number = {5}, pages = {1409-1423.e1}, doi = {10.1053/j.gastro.2021.12.287}, pmid = {34998802}, issn = {1528-0012}, mesh = {Colonoscopy ; *Colorectal Neoplasms/diagnosis/epidemiology ; Early Detection of Cancer/methods ; Humans ; *Inflammatory Bowel Diseases/diagnosis ; *Microbiota ; }, abstract = {Current noninvasive methods for colorectal cancer (CRC) screening are not optimized for persons with inflammatory bowel diseases (IBDs), requiring patients to undergo frequent interval screening via colonoscopy. Although colonoscopy-based screening reduces CRC incidence in IBD patients, rates of interval CRC remain relatively high, highlighting the need for more targeted approaches. In recent years, the discovery of disease-specific microbiome signatures for both IBD and CRC has begun to emerge, suggesting that stool-based biomarker detection using metagenomics and other culture-independent technologies may be useful for personalized, early, noninvasive CRC screening in IBD patients. Here we discuss the utility of the stool microbiome as a noninvasive CRC screening tool. Comparing the performance of multiple microbiome-based CRC classifiers, including several multi-cohort meta-analyses, we find that noninvasive detection of colorectal adenomas and carcinomas from microbial biomarkers is an active area of study with promising early results.}, } @article {pmid34996879, year = {2022}, author = {Chen, SJ and Chen, CC and Liao, HY and Lin, YT and Wu, YW and Liou, JM and Wu, MS and Kuo, CH and Lin, CH}, title = {Association of Fecal and Plasma Levels of Short-Chain Fatty Acids With Gut Microbiota and Clinical Severity in Patients With Parkinson Disease.}, journal = {Neurology}, volume = {98}, number = {8}, pages = {e848-e858}, pmid = {34996879}, issn = {1526-632X}, mesh = {Cohort Studies ; Fatty Acids, Volatile/analysis/metabolism ; Feces/chemistry ; *Gastrointestinal Microbiome ; Humans ; *Parkinson Disease/drug therapy/metabolism ; }, abstract = {BACKGROUND AND OBJECTIVES: Short-chain fatty acids (SCFAs) are gut microbial metabolites that promote the disease process in a rodent model of Parkinson disease (PD), but fecal levels of SCFAs in patients with PD are reduced. Simultaneous assessments of fecal and plasma SCFA levels, and their interrelationships with the PD disease process, are scarce. We aimed to compare fecal and plasma levels of different SCFA subtypes in patients with PD and healthy controls to delineate their interrelations and link to gut microbiota changes and clinical severity of PD.

METHODS: A cohort of 96 patients with PD and 85 controls were recruited from National Taiwan University Hospital. Fecal and plasma concentrations of SCFAs were measured using chromatography and mass spectrometry. Gut microbiota was analyzed using metagenomic shotgun sequencing. Body mass index and medical comorbidities were evaluated and dietary information was obtained using a food frequency questionnaire. To assess motor and cognitive impairment, we used the Movement Disorder Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) and the Mini-Mental Status Examination (MMSE).

RESULTS: Compared with controls, patients with PD had lower fecal but higher plasma concentrations of acetate, propionate, and butyrate. After adjustment for age, sex, disease duration, and anti-PD medication dosage, MDS-UPDRS part III motor scores correlated with reduced fecal levels of acetate (ρ = -0.37, p = 0.012), propionate (ρ = -0.32, p = 0.036), and butyrate (ρ = -0.40, p = 0.004) and with increased plasma propionate concentrations (ρ = 0.26, p = 0.042) in patients with PD. MMSE scores negatively correlated with plasma levels of butyrate (ρ = -0.09, p = 0.027) and valerate (ρ = -0.032, p = 0.033) after adjustment for confounders. SCFAs-producing gut bacteria correlated positively with fecal levels of SCFAs in healthy controls but revealed no association in patients with PD. In the PD patient group, the abundance of proinflammatory microbes, such as Clostridiales bacterium NK3B98 and Ruminococcus sp AM07-15, significantly correlated with decreased fecal levels and increased plasma levels of SCFAs, especially propionic acid.

DISCUSSION: Reductions in fecal SCFAs but increased plasma SCFAs were observed in patients with PD and corelated to specific gut microbiota changes and the clinical severity of PD.

CLASSIFICATION OF EVIDENCE: This study provides Class III evidence that gut metabolite SCFAs distinguish between patients with PD and controls and are associated with disease severity in patients with PD.}, } @article {pmid34996363, year = {2022}, author = {Jia, B and Chang, X and Fu, Y and Heng, W and Ye, Z and Liu, P and Liu, L and Al Shoffe, Y and Watkins, CB and Zhu, L}, title = {Metagenomic analysis of rhizosphere microbiome provides insights into occurrence of iron deficiency chlorosis in field of Asian pears.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {18}, pmid = {34996363}, issn = {1471-2180}, mesh = {Bacteria/classification/genetics/isolation & purification/metabolism ; Fungi/classification/genetics/isolation & purification/metabolism ; Gene Ontology ; Iron/analysis/metabolism ; Metagenomics ; *Microbiota ; Minerals/analysis/metabolism ; Plant Leaves/metabolism/microbiology/ultrastructure ; Plant Necrosis and Chlorosis/*microbiology ; Plant Roots/growth & development/microbiology ; Pyrus/metabolism/*microbiology/ultrastructure ; *Rhizosphere ; Soil/chemistry ; Soil Microbiology ; Water/analysis ; }, abstract = {BACKGROUND: Fe-deficiency chlorosis (FDC) of Asian pear plants is widespread, but little is known about the association between the microbial communities in the rhizosphere soil and leaf chlorosis. The leaf mineral concentration, leaf subcellular structure, soil physiochemical properties, and bacterial species community and distribution had been analysed to gain insights into the FDC in Asian pear plant.

RESULTS: The total Fe in leaves with Fe-deficiency was positively correlated with total K, Mg, S, Cu, Zn, Mo and Cl contents, but no differences of available Fe (AFe) were detected between the rhizosphere soil of chlorotic and normal plants. Degraded ribosomes and degraded thylakloid stacks in chloroplast were observed in chlorotic leaves. The annotated microbiome indicated that there were 5 kingdoms, 52 phyla, 94 classes, 206 orders, 404 families, 1,161 genera, and 3,043 species in the rhizosphere soil of chlorotic plants; it was one phylum less and one order, 11 families, 59 genera, and 313 species more than in that of normal plant. Bacterial community and distribution patterns in the rhizosphere soil of chlorotic plants were distinct from those of normal plants and the relative abundance and microbiome diversity were more stable in the rhizosphere soils of normal than in chlorotic plants. Three (Nitrospira defluvii, Gemmatirosa kalamazoonesis, and Sulfuricella denitrificans) of the top five species (N. defluvii, G. kalamazoonesis, S. denitrificans, Candidatus Nitrosoarchaeum koreensis, and Candidatus Koribacter versatilis). were the identical and aerobic in both rhizosphere soils, but their relative abundance decreased by 48, 37, and 22%, respectively, and two of them (G. aurantiaca and Ca. S. usitatus) were substituted by an ammonia-oxidizing soil archaeon, Ca. N. koreensis and a nitrite and nitrate reduction related species, Ca. K. versatilis in that of chlorotic plants, which indicated the adverse soil aeration in the rhizosphere soil of chlorotic plants. A water-impermeable tables was found to reduce the soil aeration, inhibit root growth, and cause some absorption root death from infection by Fusarium solani.

CONCLUSIONS: It was waterlogging or/and poor drainage of the soil may inhibit Fe uptake not the amounts of AFe in the rhizosphere soil of chlorotic plants that caused FDC in this study.}, } @article {pmid34995620, year = {2022}, author = {Liu, J and Liu, Y and Dong, W and Li, J and Yu, S and Wang, J and Zuo, R}, title = {Shifts in microbial community structure and function in polycyclic aromatic hydrocarbon contaminated soils at petrochemical landfill sites revealed by metagenomics.}, journal = {Chemosphere}, volume = {293}, number = {}, pages = {133509}, doi = {10.1016/j.chemosphere.2021.133509}, pmid = {34995620}, issn = {1879-1298}, mesh = {Metagenomics ; *Microbiota ; *Polycyclic Aromatic Hydrocarbons/analysis ; Soil ; *Soil Pollutants/analysis ; Waste Disposal Facilities ; }, abstract = {Investigations of the microbial community structures, potential functions and polycyclic aromatic hydrocarbon (PAH) degradation-related genes in PAH-polluted soils are useful for risk assessments, microbial monitoring, and the potential bioremediation of soils polluted by PAHs. In this study, five soil sampling sites were selected at a petrochemical landfill in Beijing, China, to analyze the contamination characteristics of PAHs and their impact on microorganisms. The concentrations of 16 PAHs were detected by gas chromatography-mass spectrometry. The total concentrations of the PAHs ranged from ND to 3166.52 μg/kg, while phenanthrene, pyrene, fluoranthene and benzo [ghi]perylene were the main components in the soil samples. According to the specific PAH ratios, the PAHs mostly originated from petrochemical wastes in the landfill. The levels of the total toxic benzo [a]pyrene equivalent (1.63-107.73 μg/kg) suggested that PAHs might result in adverse effects on soil ecosystems. The metagenomic analysis showed that the most abundant phyla in the soils were Proteobacteria and Actinobacteria, and Solirubrobacter was the most important genus. At the genus level, Bradyrhizobium, Mycobacterium and Anaeromyxobacter significantly increased under PAH stress. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, the most abundant category of functions that are involved in adapting to contaminant pressures was identified. Ten PAH degradation-related genes were significantly influenced by PAH pressure and showed correlations with PAH concentrations. All of the results suggested that the PAHs from the petrochemical landfill could be harmful to soil environments and impact the soil microbial community structures, while microorganisms would change their physiological functions to resist pollutant stress.}, } @article {pmid34995388, year = {2023}, author = {Nappi, J and Goncalves, P and Khan, T and Majzoub, ME and Grobler, AS and Marzinelli, EM and Thomas, T and Egan, S}, title = {Differential priority effects impact taxonomy and functionality of host-associated microbiomes.}, journal = {Molecular ecology}, volume = {32}, number = {23}, pages = {6278-6293}, doi = {10.1111/mec.16336}, pmid = {34995388}, issn = {1365-294X}, support = {DP180104041//Australian Research Council/ ; FT130100828//Australian Research Council/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenome ; *Ulva/genetics ; *Rhodobacteraceae/genetics ; }, abstract = {Most multicellular eukaryotes host complex communities of microorganisms, but the factors that govern their assembly are poorly understood. The settlement of specific microorganisms may have a lasting impact on community composition, a phenomenon known as the priority effect. Priority effects of individual bacterial strains on a host's microbiome are, however, rarely studied and their impact on microbiome functionality remains unknown. We experimentally tested the effect of two bacterial strains (Pseudoalteromonas tunicata D2 and Pseudovibrio sp. D323) on the assembly and succession of the microbial communities associated with the green macroalga Ulva australis. Using 16S rRNA gene sequencing and qPCR, we found that both strains exert a priority effect, with strain D2 causing initially strong but temporary taxonomic changes and strain D323 causing weaker but consistent changes. Consistent changes were predominately facilitatory and included taxa that may benefit the algal host. Metagenome analyses revealed that the strains elicited both shared (e.g., depletion of type III secretion system genes) and unique (e.g., enrichment of antibiotic resistance genes) effects on the predicted microbiome functionality. These findings indicate strong idiosyncratic effects of colonizing bacteria on the structure and function of host-associated microbial communities. Understanding the idiosyncrasies in priority effects is key for the development of novel probiotics to improve host condition.}, } @article {pmid34989986, year = {2022}, author = {Philips, CA and Augustine, P and Ganesan, K and Ranade, S and Chopra, V and Patil, K and Shende, S and Ahamed, R and Kumbar, S and Rajesh, S and George, T and Mohanan, M and Mohan, N and Phadke, N and Rani, M and Narayanan, A and Jagan, SM}, title = {The role of gut microbiota in clinical complications, disease severity, and treatment response in severe alcoholic hepatitis.}, journal = {Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology}, volume = {41}, number = {1}, pages = {37-51}, pmid = {34989986}, issn = {0975-0711}, mesh = {*Acute Kidney Injury ; *End Stage Liver Disease ; *Gastrointestinal Microbiome ; Granulocyte Colony-Stimulating Factor/therapeutic use ; *Hepatitis, Alcoholic/microbiology ; Humans ; Male ; Severity of Illness Index ; }, abstract = {BACKGROUND: Dysbiotic gut bacteria engage in the development and progression of severe alcoholic hepatitis (SAH). We aimed to characterize bacterial communities associated with clinical events (CE), identify significant bacteria linked to CE, and define bacterial relationships associated with specific CE and outcomes at baseline and after treatment in SAH.

METHODS: We performed 16-s rRNA sequencing on stool samples (n=38) collected at admission and the last follow-up within 90 days in SAH patients (n=26; 12 corticosteroids; 14 granulocyte colony-stimulating factor, [G-CSF]). Validated pipelines were used to plot bacterial communities, profile functional metabolism, and identify significant taxa and functional metabolites. Conet/NetworkX® was utilized to identify significant non-random patterns of bacterial co-presence and mutual exclusion for clinical events.

RESULTS: All the patients were males with median discriminant function (DF) 64, Child-Turcotte-Pugh (CTP) 12, and model for end-stage liver disease (MELD) score 25.5. At admission, 27%, 42%, and 58% had acute kidney injury (AKI), hepatic encephalopathy (HE), and infections respectively; 38.5% died at end of follow-up. Specific bacterial families were associated with HE, sepsis, disease severity, and death. Lachnobacterium and Catenibacterium were associated with HE, and Pediococcus with death after steroid treatment. Change from Enterococcus (promotes AH) to Barnesiella (inhibits E. faecium) was significant after G-CSF. Phenylpropanoid-biosynthesis (innate-immunity) and glycerophospholipid-metabolism (cellular-integrity) pathways in those without infections and the death, respectively, were upregulated. Mutual interactions between Enterococcus cecorum, Acinetobacter schindleri, and Mitsuokella correlated with admission AKI.

CONCLUSIONS: Specific gut microbiota, their interactions, and metabolites are associated with complications of SAH and treatment outcomes. Microbiota-based precision medicine as adjuvant treatment may be a new therapeutic area.}, } @article {pmid34989406, year = {2022}, author = {Ferravante, C and Sanna, G and Melone, V and Fromentier, A and Rocco, T and D'Agostino, Y and Lamberti, J and Alexandrova, E and Pecoraro, G and Pagliano, P and Astorri, R and Manzin, A and Weisz, A and Giurato, G and Galdiero, M and Rizzo, F and Franci, G}, title = {Nasopharyngeal virome analysis of COVID-19 patients during three different waves in Campania region of Italy.}, journal = {Journal of medical virology}, volume = {94}, number = {5}, pages = {2275-2283}, pmid = {34989406}, issn = {1096-9071}, support = {//PRIN 2017 "Natural and pharmacological inhibition of the early phase of viral replication (VirSudNet)" N° 2017M8R7N9/ ; //Ministero dell'Istruzione, Università e Ricerca, progr. POC R&I 2014-2020 and PON R&I 2014-2020 'Dottorati innovativi con caratterizzazione industriale' XXXV Ciclo (Fellowships DOT1328517, CUP D52G19000580006 to V.M. and DOT1318705, CUP: E66C18000940007 to C.F.). TR and YD'A are fellows of Rete Oncologica Campana and EA is a fellow of Fondazione U. Veronesi./ ; //CF, JL, VM are PhD student of the Research Doctorate in Veterinary Sciences of the University of Napoli 'Federico II', in 'Molecular and Translational Oncology and Innovative Medical-Surgical Technologies', University of Catanzaro "Magna Graecia" and in 'Translational Medicine for Development and Active Ageing' of the University of Salerno./ ; //Regione Campania (grants 'GENOMAeSALUTE', POR Campania FESR 2014/2020, azione 1.5; CUP: B41C17000080007 and 'Monitoring the spread and genomic variability of the Covid 19 virus in Campania using NGS technology,' POR Campania FESR 2014/2020, CUP: B14I20001980006)/ ; }, mesh = {*COVID-19/epidemiology/therapy/virology ; Humans ; Italy/epidemiology ; *Nasopharynx/virology ; Pandemics ; SARS-CoV-2 ; Virome ; }, abstract = {From December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has spread rapidly, leading to a global pandemic. Little is known about possible relationships between SARS-CoV-2 and other viruses in the respiratory system affecting patient prognosis and outcomes. This study aims to characterize respiratory virome profiles in association with SARS-CoV-2 infection and disease severity, through the analysis in 89 nasopharyngeal swabs collected in a patient's cohort from the Campania region (Southern Italy). Results show coinfections with viral species belonging to Coronaviridae, Retroviridae, Herpesviridae, Poxviridae, Pneumoviridae, Pandoraviridae, and Anelloviridae families and only 2% of the cases (2/89) identified respiratory viruses.}, } @article {pmid34987633, year = {2022}, author = {Png, CW and Lee, WJJ and Chua, SJ and Zhu, F and , and Yeoh, KG and Zhang, Y}, title = {Mucosal microbiome associates with progression to gastric cancer.}, journal = {Theranostics}, volume = {12}, number = {1}, pages = {48-58}, pmid = {34987633}, issn = {1838-7640}, mesh = {Dysbiosis/*microbiology ; Gastric Mucosa/*microbiology ; *Gastrointestinal Microbiome ; Helicobacter pylori ; Humans ; Longitudinal Studies ; Prospective Studies ; Stomach Neoplasms/*microbiology ; }, abstract = {Background & Aims: Dysbiosis is associated with gastric cancer (GC) development. However, no longitudinal study was carried out to identify key bacteria that could predict for GC progression. Here, we aimed to investigate changes in bacterial metagenome prior to GC and develop a microbiome-based predictive model to accurately classify patients at risk of GC. Methods: Bacterial 16S rDNA was sequenced from 89 gastric antral biopsies obtained from 43 participants. This study was nested in a prospective, longitudinal study, whereby study participants underwent screening gastroscopy, with further 1-2 yearly surveillance gastroscopies for at least 5 years. Putative bacterial taxonomic and functional features associated with GC carcinogenesis were identified by comparing between controls, patients with gastric intestinal metaplasia (IM) and patients with early gastric neoplasia (EGN). Results: Patients with EGN had enrichment of Proteobacteria (in particular Proteus genus) and depletion of Bacteroidetes (in particular S24-7 family) in their gastric mucosa. Sequencing identified more patients with Helicobacter pylori compared to histopathological assessment, while H. pylori was also significantly enriched in EGN. Furthermore, a total of 261 functional features, attributing to 97 KEGG pathways were differentially abundant at baseline between patients who subsequent developed EGN (n = 13/39) and those who did not. At the same time, a constellation of six microbial taxonomic features present at baseline, provided the highest classifying power for subsequent EGN (AUC = 0.82). Conclusion: Our study highlights early microbial changes associated with GC carcinogenesis, suggesting a potential role for prospective microbiome surveillance for GC.}, } @article {pmid34987055, year = {2022}, author = {Joseph, TA and Chlenski, P and Litman, A and Korem, T and Pe'er, I}, title = {Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates.}, journal = {Genome research}, volume = {32}, number = {3}, pages = {558-568}, pmid = {34987055}, issn = {1549-5469}, support = {U01 CA217858/CA/NCI NIH HHS/United States ; U54 CA209997/CA/NCI NIH HHS/United States ; }, mesh = {Case-Control Studies ; Genome, Bacterial ; Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; }, abstract = {Patterns of sequencing coverage along a bacterial genome-summarized by a peak-to-trough ratio (PTR)-have been shown to accurately reflect microbial growth rates, revealing a new facet of microbial dynamics and host-microbe interactions. Here, we introduce Compute PTR (CoPTR): a tool for computing PTRs from complete reference genomes and assemblies. Using simulations and data from growth experiments in simple and complex communities, we show that CoPTR is more accurate than the current state of the art while also providing more PTR estimates overall. We further develop a theory formalizing a biological interpretation for PTRs. Using a reference database of 2935 species, we applied CoPTR to a case-control study of 1304 metagenomic samples from 106 individuals with inflammatory bowel disease. We show that growth rates are personalized, are only loosely correlated with relative abundances, and are associated with disease status. We conclude by showing how PTRs can be combined with relative abundances and metabolomics to investigate their effect on the microbiome.}, } @article {pmid34986419, year = {2022}, author = {Ariaeenejad, S and Kavousi, K and Mamaghani, ASA and Ghasemitabesh, R and Hosseini Salekdeh, G}, title = {Simultaneous hydrolysis of various protein-rich industrial wastes by a naturally evolved protease from tannery wastewater microbiota.}, journal = {The Science of the total environment}, volume = {815}, number = {}, pages = {152796}, doi = {10.1016/j.scitotenv.2021.152796}, pmid = {34986419}, issn = {1879-1026}, mesh = {Animals ; Hydrolysis ; Industrial Waste/analysis ; *Microbiota ; Peptide Hydrolases ; *Wastewater ; }, abstract = {Elimination of protein-rich waste materials is one of the vital environmental protection requirements. Using of non-naturally occurring chemicals for their remediation properties can potentially induce new pollutants. Therefore, enzymes encoded in the genomes of microorganisms evolved in the same environment can be considered suitable alternatives to chemicals. Identification of efficient proteases that can hydrolyze recalcitrant, protein-rich wastes produced by various industrial processes has been widely welcomed as an eco-friendly waste management strategy. In this direction, we attempted to screen a thermo-halo-alkali-stable metagenome-derived protease (PersiProtease1) from tannery wastewater. The PersiProtease1 exhibited high pH stability over a wide range and at 1 h in pH 11.0 maintained 87.59% activity. The enzyme possessed high thermal stability while retaining 76.64% activity after 1 h at 90 °C. Moreover, 65.34% of the initial activity of the enzyme remained in the presence of 6 M NaCl, showing tolerance against high salinity. The presence of various metal ions, inhibitors, and organic solvents did not remarkably inhibit the activity of the discovered protease. The PersiProtease1 was extracted from the tannery wastewater microbiota and efficiently applied for biodegradation of real sample tannery wastewater protein, chicken feathers, whey protein, dehairing sheepskins, and waste X-ray films. PersiProtease1 proved its enormous potential in simultaneous biodegradation of solid and liquid protein-rich industrial wastes based on the results.}, } @article {pmid34986315, year = {2022}, author = {Mejia, ME and Ottinger, S and Vrbanac, A and Babu, P and Zulk, JJ and Moorshead, D and Bode, L and Nizet, V and Patras, KA}, title = {Human Milk Oligosaccharides Reduce Murine Group B Streptococcus Vaginal Colonization with Minimal Impact on the Vaginal Microbiota.}, journal = {mSphere}, volume = {7}, number = {1}, pages = {e0088521}, pmid = {34986315}, issn = {2379-5042}, support = {T32 GM136554/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/genetics ; Female ; Humans ; Infant, Newborn ; Mice ; *Microbiota ; Milk, Human ; Oligosaccharides/therapeutic use ; Pregnancy ; *Premature Birth ; RNA, Ribosomal, 16S ; Streptococcus agalactiae ; }, abstract = {Group B Streptococcus (GBS) colonizes the vaginal mucosa of a significant percentage of healthy women and is a leading cause of neonatal bacterial infections. Currently, pregnant women are screened in the last month of pregnancy, and GBS-positive women are given antibiotics during parturition to prevent bacterial transmission to the neonate. Recently, human milk oligosaccharides (HMOs) isolated from breastmilk were found to inhibit GBS growth and biofilm formation in vitro, and women that make certain HMOs are less likely to be vaginally colonized with GBS. Using in vitro human vaginal epithelial cells and a murine vaginal colonization model, we tested the impact of HMO treatment on GBS burdens and the composition of the endogenous microbiota by 16S rRNA amplicon sequencing. HMO treatment reduced GBS vaginal burdens in vivo with minimal alterations to the vaginal microbiota. HMOs displayed potent inhibitory activity against GBS in vitro, but HMO pretreatment did not alter adherence of GBS or the probiotic Lactobacillus rhamnosus to human vaginal epithelial cells. In addition, disruption of a putative GBS glycosyltransferase (Δsan_0913) rendered the bacterium largely resistant to HMO inhibition in vitro and in vivo but did not compromise its adherence, colonization, or biofilm formation in the absence of HMOs. We conclude that HMOs are a promising therapeutic bioactive to limit GBS vaginal colonization with minimal impacts on the vaginal microenvironment. IMPORTANCE During pregnancy, GBS ascension into the uterus can cause fetal infection or preterm birth. In addition, GBS exposure during labor creates a risk of serious disease in the vulnerable newborn and mother postpartum. Current recommended prophylaxis consists of administering broad-spectrum antibiotics to GBS-positive mothers during labor. Although antibiotics have significantly reduced GBS neonatal disease, there are several unintended consequences, including altered neonatal gut bacteria and increased risk for other types of infection. Innovative preventions displaying more targeted antimicrobial activity, while leaving the maternal microbiota intact, are thus appealing. Using a mouse model, we found that human milk oligosaccharides (HMOs) reduce GBS burdens without perturbing the vaginal microbiota. We conclude that HMOs are a promising alternative to antibiotics to reduce GBS neonatal disease.}, } @article {pmid34984487, year = {2022}, author = {He, Q and Zhang, Y and Ma, D and Zhang, W and Zhang, H}, title = {Lactobacillus casei Zhang exerts anti-obesity effect to obese glut1 and gut-specific-glut1 knockout mice via gut microbiota modulation mediated different metagenomic pathways.}, journal = {European journal of nutrition}, volume = {61}, number = {4}, pages = {2003-2014}, pmid = {34984487}, issn = {1436-6215}, support = {31720103911//national natural science foundation of china/ ; 31972083//national natural science foundation of china/ ; 32001711//national natural science foundation of china/ ; }, mesh = {Animals ; Body Weight ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Glucose ; Glucose Transporter Type 1/genetics ; *Lacticaseibacillus casei ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Mice, Obese ; Obesity/etiology ; }, abstract = {PURPOSE: Obesity is a major risk factor for various metabolic diseases, including metabolic syndrome and type-2 diabetes. Glucose transporter 1 (GLUT1) impairment has been proposed as a mechanism of fat accumulation and glucose tolerance. Our aims were to determine the role of intestinal epithelial glut1 activity in obesity and the mechanism of anti-obesity effect of Lactobacillus casei Zhang (LCZ) intervention in the absence of gut villi-specific glut1 expression.

METHODS: This study compared the body weight, intestinal microbiota perturbations, fat mass accumulation, and glucose tolerance (by oral glucose tolerance test) between high-fat diet fed villi-specific glut1 knockout (KO) mice and control mice (glut1 flox/flox) with/without LCZ intervention. The intestinal microbiota was evaluated by metagenomic sequencing.

RESULTS: Our results showed that villi-specific glut1 KO mice had more fat deposition at the premetaphase stage, impaired glucose tolerance, and obvious alterations in gut microbiota compared to control mice. Probiotic administration significantly lowered the body weight, the weights of mesenteric and perirenal white adipose tissues (WAT), and mediated gut microbiota modulation in both types of KO and control mice. The species Barnesiella intestinihominis and Faecalibaculum rodentium might contribute to fasting fat mass accumulation associated with gut-specific glut1 inactivation, while the probiotic-mediated anti-obesity effect was linked to members of the Bacteroides genera, Odoribacter genera and Alistipes finegoldii.

CONCLUSION: Our study demonstrated that abrogating gut epithelial GLUT1 activity affected the gut microbiota, fat mass accumulation, and glucose tolerance; and LCZ administration reduced fat mass accumulation and central obesity.}, } @article {pmid34983966, year = {2022}, author = {Harvey, E and Holmes, EC}, title = {Diversity and evolution of the animal virome.}, journal = {Nature reviews. Microbiology}, volume = {20}, number = {6}, pages = {321-334}, pmid = {34983966}, issn = {1740-1534}, mesh = {Animals ; *COVID-19 ; Genome, Viral ; Humans ; Pandemics ; Phylogeny ; Virome/genetics ; *Viruses/genetics ; }, abstract = {The COVID-19 pandemic has given the study of virus evolution and ecology new relevance. Although viruses were first identified more than a century ago, we likely know less about their diversity than that of any other biological entity. Most documented animal viruses have been sampled from just two phyla - the Chordata and the Arthropoda - with a strong bias towards viruses that infect humans or animals of economic and social importance, often in association with strong disease phenotypes. Fortunately, the recent development of unbiased metagenomic next-generation sequencing is providing a richer view of the animal virome and shedding new light on virus evolution. In this Review, we explore our changing understanding of the diversity, composition and evolution of the animal virome. We outline the factors that determine the phylogenetic diversity and genomic structure of animal viruses on evolutionary timescales and show how this impacts assessment of the risk of disease emergence in the short term. We also describe the ongoing challenges in metagenomic analysis and outline key themes for future research. A central question is how major events in the evolutionary history of animals, such as the origin of the vertebrates and periodic mass extinction events, have shaped the diversity and evolution of the viruses they carry.}, } @article {pmid34980918, year = {2022}, author = {Liu, X and Tong, X and Zou, Y and Lin, X and Zhao, H and Tian, L and Jie, Z and Wang, Q and Zhang, Z and Lu, H and Xiao, L and Qiu, X and Zi, J and Wang, R and Xu, X and Yang, H and Wang, J and Zong, Y and Liu, W and Hou, Y and Zhu, S and Jia, H and Zhang, T}, title = {Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome.}, journal = {Nature genetics}, volume = {54}, number = {1}, pages = {52-61}, pmid = {34980918}, issn = {1546-1718}, mesh = {Blood/*metabolism ; Cohort Studies ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Genome-Wide Association Study ; Glutamic Acid/blood ; Humans ; Mendelian Randomization Analysis ; Metagenome ; Triglycerides/blood ; }, abstract = {The gut microbiome has been implicated in a variety of physiological states, but controversy over causality remains unresolved. Here, we performed bidirectional Mendelian randomization analyses on 3,432 Chinese individuals with whole-genome, whole-metagenome, anthropometric and blood metabolic trait data. We identified 58 causal relationships between the gut microbiome and blood metabolites, and replicated 43 of them. Increased relative abundances of fecal Oscillibacter and Alistipes were causally linked to decreased triglyceride concentration. Conversely, blood metabolites such as glutamic acid appeared to decrease fecal Oxalobacter, and members of Proteobacteria were influenced by metabolites such as 5-methyltetrahydrofolic acid, alanine, glutamate and selenium. Two-sample Mendelian randomization with data from Biobank Japan partly corroborated results with triglyceride and with uric acid, and also provided causal support for published fecal bacterial markers for cancer and cardiovascular diseases. This study illustrates the value of human genetic information to help prioritize gut microbial features for mechanistic and clinical studies.}, } @article {pmid34980911, year = {2022}, author = {Bickhart, DM and Kolmogorov, M and Tseng, E and Portik, DM and Korobeynikov, A and Tolstoganov, I and Uritskiy, G and Liachko, I and Sullivan, ST and Shin, SB and Zorea, A and Andreu, VP and Panke-Buisse, K and Medema, MH and Mizrahi, I and Pevzner, PA and Smith, TPL}, title = {Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities.}, journal = {Nature biotechnology}, volume = {40}, number = {5}, pages = {711-719}, pmid = {34980911}, issn = {1546-1696}, support = {R44 AI150008/AI/NIAID NIH HHS/United States ; R44 AI162570/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Feces ; *Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; Sheep ; }, abstract = {Microbial communities might include distinct lineages of closely related organisms that complicate metagenomic assembly and prevent the generation of complete metagenome-assembled genomes (MAGs). Here we show that deep sequencing using long (HiFi) reads combined with Hi-C binning can address this challenge even for complex microbial communities. Using existing methods, we sequenced the sheep fecal metagenome and identified 428 MAGs with more than 90% completeness, including 44 MAGs in single circular contigs. To resolve closely related strains (lineages), we developed MAGPhase, which separates lineages of related organisms by discriminating variant haplotypes across hundreds of kilobases of genomic sequence. MAGPhase identified 220 lineage-resolved MAGs in our dataset. The ability to resolve closely related microbes in complex microbial communities improves the identification of biosynthetic gene clusters and the precision of assigning mobile genetic elements to host genomes. We identified 1,400 complete and 350 partial biosynthetic gene clusters, most of which are novel, as well as 424 (298) potential host-viral (host-plasmid) associations using Hi-C data.}, } @article {pmid34980289, year = {2022}, author = {Yang, Y and Sun, J and Chen, C and Zhou, Y and Van Dover, CL and Wang, C and Qiu, JW and Qian, PY}, title = {Metagenomic and metatranscriptomic analyses reveal minor-yet-crucial roles of gut microbiome in deep-sea hydrothermal vent snail.}, journal = {Animal microbiome}, volume = {4}, number = {1}, pages = {3}, pmid = {34980289}, issn = {2524-4671}, support = {DY135-E2-1-03//China Ocean Mineral Resources Research and Development Association/ ; GML2019ZD0409//the Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 2019B030302004-04//the Major Basic and Applied Basic Research Projects of Guangdong Province/ ; SMSEGL20SC01//the Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 91951201//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Marine animals often exhibit complex symbiotic relationship with gut microbes to attain better use of the available resources. Many animals endemic to deep-sea chemosynthetic ecosystems host chemoautotrophic bacteria endocellularly, and they are thought to rely entirely on these symbionts for energy and nutrition. Numerous investigations have been conducted on the interdependence between these animal hosts and their chemoautotrophic symbionts. The provannid snail Alviniconcha marisindica from the Indian Ocean hydrothermal vent fields hosts a Campylobacterial endosymbiont in its gill. Unlike many other chemosymbiotic animals, the gut of A. marisindica is reduced but remains functional; yet the contribution of gut microbiomes and their interactions with the host remain poorly characterised.

RESULTS: Metagenomic and metatranscriptomic analyses showed that the gut microbiome of A. marisindica plays key nutritional and metabolic roles. The composition and relative abundance of gut microbiota of A. marisindica were different from those of snails that do not depend on endosymbiosis. The relative abundance of microbial taxa was similar amongst three individuals of A. marisindica with significant inter-taxa correlations. These correlations suggest the potential for interactions between taxa that may influence community assembly and stability. Functional profiles of the gut microbiome revealed thousands of additional genes that assist in the use of vent-supplied inorganic compounds (autotrophic energy source), digest host-ingested organics (carbon source), and recycle the metabolic waste of the host. In addition, members of five taxonomic classes have the potential to form slime capsules to protect themselves from the host immune system, thereby contributing to homeostasis. Gut microbial ecology and its interplay with the host thus contribute to the nutritional and metabolic demands of A. marisindica.

CONCLUSIONS: The findings advance the understanding of how deep-sea chemosymbiotic animals use available resources through contributions from gut microbiota. Gut microbiota may be critical in the survival of invertebrate hosts with autotrophic endosymbionts in extreme environments.}, } @article {pmid34975886, year = {2021}, author = {Yan, H and Su, R and Xue, H and Gao, C and Li, X and Wang, C}, title = {Pharmacomicrobiology of Methotrexate in Rheumatoid Arthritis: Gut Microbiome as Predictor of Therapeutic Response.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {789334}, pmid = {34975886}, issn = {1664-3224}, mesh = {Antirheumatic Agents/*pharmacology/therapeutic use ; Arthritis, Rheumatoid/*drug therapy/immunology/microbiology ; Dose-Response Relationship, Drug ; Gastrointestinal Microbiome/*drug effects/immunology ; Humans ; Methotrexate/*pharmacology/therapeutic use ; Treatment Outcome ; }, abstract = {Rheumatoid arthritis (RA) is a disabling autoimmune disease with invasive arthritis as the main manifestation and synovitis as the basic pathological change, which can cause progressive destruction of articular cartilage and bone, ultimately leading to joint deformity and loss of function. Since its introduction in the 1980s and its widespread use in the treatment of RA, low-dose methotrexate (MTX) therapy has dramatically changed the course and outcome of RA treatment. The clinical use of this drug will be more rational with a better understanding of the pharmacology, anti-inflammatory mechanisms of action and adverse reaction about it. At present, the current clinical status of newly diagnosed RA is that MTX is initiated first regardless of the patients' suitability. But up to 50% of patients could not reach adequate clinical efficacy or have severe adverse events. Prior to drug initiation, a prognostic tool for treatment response is lacking, which is thought to be the most important cause of the situation. A growing body of studies have shown that differences in microbial metagenomes (including bacterial strains, genes, enzymes, proteins and/or metabolites) in the gastrointestinal tract of RA patients may at least partially determine their bioavailability and/or subsequent response to MTX. Based on this, some researchers established a random forest model to predict whether different RA patients (with different gut microbiome) would respond to MTX. Of course, MTX, in turn, alters the gut microbiome in a dose-dependent manner. The interaction between drugs and microorganisms is called pharmacomicrobiology. Then, the concept of precision medicine has been raised. In this view, we summarize the characteristics and anti-inflammatory mechanisms of MTX and highlight the interaction between gut microbiome and MTX aiming to find the optimal treatment for patients according to individual differences and discuss the application and prospect of precision medicine.}, } @article {pmid34974193, year = {2022}, author = {Liu, C and Sun, Z and Shali, S and Mei, Z and Chang, S and Mo, H and Xu, L and Pu, Y and Guan, H and Chen, GC and Qi, Q and Quan, Z and Qi, J and Yao, K and Dai, Y and Zheng, Y and Ge, J}, title = {The gut microbiome and microbial metabolites in acute myocardial infarction.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {49}, number = {6}, pages = {569-578}, doi = {10.1016/j.jgg.2021.12.007}, pmid = {34974193}, issn = {1673-8527}, mesh = {Choline ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; *Myocardial Infarction/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Emerging evidence has highlighted the role of gut microbiome in human health. However, the integrative role of gut microbiome and microbial metabolites in acute myocardial infarction (AMI) remains unclear. The current study profiles the microbial community through 16S rRNA gene sequencing and shotgun metagenomic sequencing and measures fecal short-chain fatty acids and circulating choline pathway metabolites among 117 new-onset AMI cases and 78 controls. Significant microbial alternations are observed in AMI patients compared with controls (P = 0.001). The abundances of nine species (e.g., Streptococcus salivarius and Klebsiella pneumoniae) are positively associated, and one species (Roseburia hominis) is inversely associated with AMI status and severity. A gut microbial score at disease onset is associated with the risk of major adverse cardiovascular events in 3.2 years (hazard ratio [95% CI]: 2.01 [1.04-4.24]) in AMI patients. The molar proportions of fecal acetate and butyrate are higher, and the circulating levels of choline and carnitine are lower in AMI patients than in controls. In addition, disease classifiers show that AMI cases and controls have a more distinct pattern in taxonomical composition than in pathways or metabolites. Our findings suggest that microbial composition and functional potentials are associated with AMI status and severity.}, } @article {pmid34974121, year = {2022}, author = {de Lima, AMDL and de Lima Rosa, G and Müller Guzzo, EF and Padilha, RB and Costa da Silva, R and Silveira, AK and de Lima Morales, D and Conci de Araujo, M and Fonseca Moreira, JC and Barth, AL and Coitinho, AS and Van Der Sand, ST}, title = {Gut microbiota modulation by prednisolone in a rat kindling model of pentylenetetrazol (PTZ)-induced seizure.}, journal = {Microbial pathogenesis}, volume = {163}, number = {}, pages = {105376}, doi = {10.1016/j.micpath.2021.105376}, pmid = {34974121}, issn = {1096-1208}, mesh = {Animals ; *Gastrointestinal Microbiome ; Male ; *Pentylenetetrazole ; Prednisolone ; Rats ; Rats, Wistar ; Seizures/chemically induced ; }, abstract = {The gut microbiota is a complex community composed by several microorganisms that interact in the maintenance of homeostasis and contribute to physiological processes, including brain function. The relationship of the taxonomic composition of the gut microbiota with neurological diseases such as autism, Parkinson's, Alzheimer's, anxiety, and depression is widely recognized. The immune system is an important intermediary between the gut microbiota and the central nervous system, being one of the communication routes of the gut-brain axis. Although the complexity of the relationship between inflammation and epilepsy has not yet been elucidated, inflammatory processes are similar in many ways to the consequences of dysbiosis and contribute to disease progression. This study aimed to analyze the taxonomic composition of the gut microbiota of rats treated with prednisolone in a kindling model of epilepsy. Male Wistar rats (90 days, n = 24) divided into four experimental groups: sodium chloride solution 0.9 g%, diazepam 2 mg/kg, prednisolone 1 mg/kg, and prednisolone 5 mg/kg administered intraperitoneally (i.p.) for 14 days. The kindling model was induced by pentylenetetrazole (PTZ) 25 mg/kg i.p. on alternate days. The taxonomic profile was established by applying metagenomic DNA sequencing. There was no change in alpha diversity, and the composition of the gut microbiota between prednisolone and diazepam was similar. The significant increase in Verrucomicrobia, Saccharibacteria, and Actinobacteria may be related to the protective activity against seizures and inflammatory processes that cause some cases of epilepsy. Further studies are needed to investigate the functional influence that these species have on epilepsy and the inflammatory processes that trigger it.}, } @article {pmid34973527, year = {2022}, author = {Kamel, HL and Hanora, A and Solyman, SM}, title = {Metataxanomic, bioactivity and microbiome analysis of Red Sea marine sponges from Egypt.}, journal = {Marine genomics}, volume = {61}, number = {}, pages = {100920}, doi = {10.1016/j.margen.2021.100920}, pmid = {34973527}, issn = {1876-7478}, mesh = {Animals ; Egypt ; Indian Ocean ; *Microbiota ; *Porifera ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Red Sea marine sponges (phylum Porifera) and associated microorganisms harbor a wide range of microorganisms, which are considered an essential source of bioactive products. In this study, we screened both the crude extracts of Red Sea marine sponges and their associated bacterial extract for antimicrobial activity and antiviral activity. Molecular characterization of bioactive producers was performed using16S rRNA sequencing, in addition to metagenomic analysis of three representative sponges utilizing the 16S rRNA gene V3-V4 region sequencing in two different seasons. Twelve samples were collected from five different sponge species by scuba diving, and all the crude extracts of sponges showed antimicrobial activity except Negombata corticata. Moreover, 84 out of 110 bacterial isolates extracts demonstrated antimicrobial activity against at least one tested microorganism. These results revealed the bioactivity and biodiversity of the Red Sea marine invertebrates-associated bacteria. It was found that the bioactive isolates belong to several bacterial groups. The bacterial communities of Negombata magnifica, Negombata corticata, and Siphonochalina siphonella were shown with great diversity and differences in the bacterial percentage, diversity, and unique community composition at different seasons in each sponge species. Unique microenvironment for each sponge species may be linked to the production of specific bioactive product.}, } @article {pmid34972143, year = {2021}, author = {Tongununui, P and Kuriya, Y and Murata, M and Sawada, H and Araki, M and Nomura, M and Morioka, K and Ichie, T and Ikejima, K and Adachi, K}, title = {Mangrove crab intestine and habitat sediment microbiomes cooperatively work on carbon and nitrogen cycling.}, journal = {PloS one}, volume = {16}, number = {12}, pages = {e0261654}, pmid = {34972143}, issn = {1932-6203}, mesh = {Acetylene/chemistry ; Animals ; Brachyura/*metabolism ; Carbon/metabolism ; *Carbon Cycle ; Cellulase/metabolism ; Cellulose/chemistry ; *Ecosystem ; Forests ; *Gastrointestinal Microbiome ; *Geologic Sediments ; Intestines/*metabolism ; Metagenome ; Microbiota ; Nitrogen/metabolism ; *Nitrogen Cycle ; Nitrogenase/metabolism ; Phenotype ; RNA, Ribosomal, 16S/metabolism ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; Species Specificity ; Thailand ; }, abstract = {Mangrove ecosystems, where litter and organic components are degraded and converted into detrital materials, support rich coastal fisheries resources. Sesarmid (Grapsidae) crabs, which feed on mangrove litter, play a crucial role in material flow in carbon-rich and nitrogen-limited mangrove ecosystems; however, the process of assimilation and conversion into detritus has not been well studied. In this study, we performed microbiome analyses of intestinal bacteria from three species of mangrove crab and five sediment positions in the mud lobster mounds, including the crab burrow wall, to study the interactive roles of crabs and sediment in metabolism. Metagenome analysis revealed species-dependent intestinal profiles, especially in Neosarmatium smithi, while the sediment microbiome was similar in all positions, albeit with some regional dependency. The microbiome profiles of crab intestines and sediments were significantly different in the MDS analysis based on OTU similarity; however, 579 OTUs (about 70% of reads in the crab intestinal microbiome) were identical between the intestinal and sediment bacteria. In the phenotype prediction, cellulose degradation was observed in the crab intestine. Cellulase activity was detected in both crab intestine and sediment. This could be mainly ascribed to Demequinaceae, which was predominantly found in the crab intestines and burrow walls. Nitrogen fixation was also enriched in both the crab intestines and sediments, and was supported by the nitrogenase assay. Similar to earlier reports, sulfur-related families were highly enriched in the sediment, presumably degrading organic compounds as terminal electron acceptors under anaerobic conditions. These results suggest that mangrove crabs and habitat sediment both contribute to carbon and nitrogen cycling in the mangrove ecosystem via these two key reactions.}, } @article {pmid34971956, year = {2022}, author = {Zeng, H and Hu, W and Liu, G and Xu, H and Wei, Y and Zhang, J and Shi, H}, title = {Microbiome-wide association studies between phyllosphere microbiota and ionome highlight the beneficial symbiosis of Lactococcus lactis in alleviating aluminium in cassava.}, journal = {Plant physiology and biochemistry : PPB}, volume = {171}, number = {}, pages = {66-74}, doi = {10.1016/j.plaphy.2021.12.029}, pmid = {34971956}, issn = {1873-2690}, mesh = {Aluminum ; *Lactococcus lactis ; *Manihot/genetics ; *Microbiota ; Symbiosis ; }, abstract = {The phyllosphere is one of the most abundant habitats for global microbiota. The ionome is the composition of mineral elements in plants. The correlation between phyllosphere microbiota and the ionome remains elusive in plants, especially in the most important tropical crop cassava. In this study, microbiome-wide association studies (MWASs) of thirty varieties were performed to reveal the association between phyllosphere microbiota and ionomic variations in cassava. Annotation of metagenomic species identified some species that were significantly correlated with ionomic variations in cassava. Among them, Lactococcus lactis abundance was negatively associated with leaf aluminium (Al) levels but positively related to leaf potassium (K) levels. Notably, both the reference and isolated L. lactis showed strong binding capacity to Al. Further bacterial transplantation of isolated L. lactis could significantly decrease endogenous Al levels but increase K levels in cassava, and it can also lead to increased citric acid and lactic acid levels as well as higher transcript levels of K uptake-related genes. Taken together, this study reveals the involvement of phyllosphere microbiota in ionomic variation in cassava, and the correlation between L. lactis abundance and Al and K levels provides novel insights into alleviating Al accumulation and promoting K uptake simultaneously.}, } @article {pmid34971560, year = {2022}, author = {Beresford-Jones, BS and Forster, SC and Stares, MD and Notley, G and Viciani, E and Browne, HP and Boehmler, DJ and Soderholm, AT and Kumar, N and Vervier, K and Cross, JR and Almeida, A and Lawley, TD and Pedicord, VA}, title = {The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping.}, journal = {Cell host & microbe}, volume = {30}, number = {1}, pages = {124-138.e8}, pmid = {34971560}, issn = {1934-6069}, support = {/WT_/Wellcome Trust/United Kingdom ; P30 CA008748/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification/genetics/*isolation & purification/metabolism ; Butyrates/metabolism ; Gastrointestinal Microbiome/*physiology ; Genome, Bacterial ; Humans ; Metagenome/genetics ; Mice ; Models, Animal ; }, abstract = {Human health and disease have increasingly been shown to be impacted by the gut microbiota, and mouse models are essential for investigating these effects. However, the compositions of human and mouse gut microbiotas are distinct, limiting translation of microbiota research between these hosts. To address this, we constructed the Mouse Gastrointestinal Bacteria Catalogue (MGBC), a repository of 26,640 high-quality mouse microbiota-derived bacterial genomes. This catalog enables species-level analyses for mapping functions of interest and identifying functionally equivalent taxa between the microbiotas of humans and mice. We have complemented this with a publicly deposited collection of 223 bacterial isolates, including 62 previously uncultured species, to facilitate experimental investigation of individual commensal bacteria functions in vitro and in vivo. Together, these resources provide the ability to identify and test functionally equivalent members of the host-specific gut microbiotas of humans and mice and support the informed use of mouse models in human microbiota research.}, } @article {pmid34970896, year = {2021}, author = {Peng, X and Zhao, Y and Lin, T and Shu, X and Hou, L and Gao, L and Wang, H and Ge, N and Yue, J}, title = {[Research of relationship between frailty and gut microbiota on middle-aged and the aged patients with diabetes].}, journal = {Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi}, volume = {38}, number = {6}, pages = {1126-1133}, pmid = {34970896}, issn = {1001-5515}, mesh = {Aged ; *Diabetes Mellitus ; *Epstein-Barr Virus Infections ; *Frailty ; *Gastrointestinal Microbiome ; Herpesvirus 4, Human ; Humans ; Middle Aged ; }, abstract = {Gut microbiota plays an important role in development of diabetes with frailty. Therefore, it is of great significance to study the structural and functional characteristics of gut microbiota in Chinese with frailty. Totally 30 middle-aged and the aged participants in communities with diabetes were enrolled in this study, and their feces were collected. At the same time, we developed a metagenome analysis to explore the different of the structural and functional characteristics between diabetes with frailty and diabetes without frailty. The results showed the alpha diversity of intestinal microbiota in diabetes with frailty was lower. Collinsella and Butyricimonas were more abundant in diabetes with frailty. The functional characteristics showed that histidine metabolism, Epstein-Barr virus infection, sulfur metabolism, and biosynthesis of type Ⅱ polyketide products were upregulated in diabetes with frailty. Otherwise, butanoate metabolism and phenylalanine metabolism were down-regulated in diabetes with frailty. This research provides theoretical basic for exploring the mechanism of the gut microbiota on the occurrence and development of diabetes with frailty, and provides a basic for prevention and intervention of it.}, } @article {pmid34970508, year = {2021}, author = {Jiang, Q and Liu, X and Yang, Q and Chen, L and Yang, D}, title = {Salivary Microbiome in Adenoid Cystic Carcinoma Detected by 16S rRNA Sequencing and Shotgun Metagenomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {774453}, pmid = {34970508}, issn = {2235-2988}, mesh = {*Carcinoma, Adenoid Cystic ; Humans ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Salivary Gland Neoplasms ; }, abstract = {Microorganisms are confirmed to be closely related to the occurrence and development of cancers in human beings. However, there has been no published report detailing relationships between the oral microbiota and salivary adenoid cystic carcinoma (SACC). In this study, unstimulated saliva was collected from 13 SACC patients and 10 healthy controls. The microbial diversities, compositions and functions were comprehensively analyzed after 16S rRNA sequencing and whole-genome shotgun metagenomic sequencing. The alpha diversity showed no significant difference between SACC patients and healthy controls, while beta diversity showed a separation trend. The SACC patients showed higher abundances of Streptococcus and Rothia, while Prevotella and Alloprevotella were more abundant in healthy controls. The prevalent KEGG pathways, carbohydrate-active enzymes, antibiotic resistances and virulence factors as well as the biomarkers in SACC were determined by functional gene analysis. Our study preliminarily investigated the salivary microbiome of SACC patients compared with healthy controls and might be the basis for further studies on novel diagnostic and treatment strategies.}, } @article {pmid34970262, year = {2021}, author = {Gao, G and Ma, T and Zhang, T and Jin, H and Li, Y and Kwok, LY and Zhang, H and Sun, Z}, title = {Adjunctive Probiotic Lactobacillus rhamnosus Probio-M9 Administration Enhances the Effect of Anti-PD-1 Antitumor Therapy via Restoring Antibiotic-Disrupted Gut Microbiota.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {772532}, pmid = {34970262}, issn = {1664-3224}, mesh = {Animals ; Anti-Bacterial Agents/*adverse effects ; Bacteroides/drug effects/growth & development ; Bifidobacterium/drug effects/growth & development ; Cell Line, Tumor ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Immune Checkpoint Inhibitors/*administration & dosage ; *Lacticaseibacillus rhamnosus ; Mice, Inbred BALB C ; Neoplasms/microbiology/*therapy ; Probiotics/*therapeutic use ; Programmed Cell Death 1 Receptor/*antagonists & inhibitors ; Mice ; }, abstract = {Emerging evidence supports that the efficacy of immune checkpoint blockade (ICB) therapy is associated with the host's gut microbiota, as prior antibiotic intake often leads to poor outcome and low responsiveness toward ICB treatment. Therefore, we hypothesized that the efficacy of ICB therapy like anti-programmed cell death protein-1 (PD-1) treatment required an intact host gut microbiota, and it was established that probiotics could enhance the recovery of gut microbiota disruption by external stimuli. Thus, the present study aimed to evaluate the effect of the probiotics, Lactobacillus rhamnosus Probio-M9, on recovering antibiotic-disrupted gut microbiota and its impact on the outcome of ICB therapy in tumor-bearing mice. We first disrupted the mouse microbiota by antibiotics and then remediated the gut microbiota by probiotics or naturally. Tumor transplantation was then performed, followed by anti-PD-1-based antitumor therapy. Changes in the fecal metagenomes and the tumor suppression effect were monitored during different stages of the experiment. Our results showed that Probio-M9 synergized with ICB therapy, significantly improving tumor inhibition compared with groups not receiving the probiotic treatment (P < 0.05 at most time points). The synergistic effect was accompanied by effective restoration of antibiotic-disrupted fecal microbiome that was characterized by a drastically reduced Shannon diversity value and shifted composition of dominating taxa. Moreover, probiotic administration significantly increased the relative abundance of beneficial bacteria (e.g., Bifidobacterium pseudolongum, Parabacteroides distasonis, and some Bacteroides species; 0.0001 < P < 0.05). The gut microbiome changes were accompanied by mild reshaping of the functional metagenomes characterized by enrichment in sugar degradation and vitamin and amino acid synthesis pathways. Collectively, this study supported that probiotic administration could enhance the efficacy and responsiveness of anti-PD-1-based immunotherapy, and Probio-M9 could be a potential candidate of microbe-based synergistic tumor therapeutics. The preclinical data obtained here would support the design of future human clinical trials for further consolidating the current findings and for safety assessment of probiotic adjunctive treatment in ICB therapy.}, } @article {pmid34969979, year = {2022}, author = {Valles-Colomer, M and Bacigalupe, R and Vieira-Silva, S and Suzuki, S and Darzi, Y and Tito, RY and Yamada, T and Segata, N and Raes, J and Falony, G}, title = {Variation and transmission of the human gut microbiota across multiple familial generations.}, journal = {Nature microbiology}, volume = {7}, number = {1}, pages = {87-96}, pmid = {34969979}, issn = {2058-5276}, support = {R01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/*genetics ; Bacterial Physiological Phenomena/genetics ; Child ; Child, Preschool ; Cohort Studies ; *Family ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics/physiology ; Humans ; *Metagenome ; Metagenomics/methods ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Although the composition and functional potential of the human gut microbiota evolve over the lifespan, kinship has been identified as a key covariate of microbial community diversification. However, to date, sharing of microbiota features within families has mostly been assessed between parents and their direct offspring. Here we investigate the potential transmission and persistence of familial microbiome patterns and microbial genotypes in a family cohort (n = 102) spanning 3 to 5 generations over the same female bloodline. We observe microbiome community composition associated with kinship, with seven low abundant genera displaying familial distribution patterns. While kinship and current cohabitation emerge as closely entangled variables, our explorative analyses of microbial genotype distribution and transmission estimates point at the latter as a key covariate of strain dissemination. Highest potential transmission rates are estimated between sisters and mother-daughter pairs, decreasing with increasing daughter's age and being higher among cohabiting pairs than those living apart. Although rare, we detect potential transmission events spanning three and four generations, primarily involving species of the genera Alistipes and Bacteroides. Overall, while our analyses confirm the existence of family-bound microbiome community profiles, transmission or co-acquisition of bacterial strains appears to be strongly linked to cohabitation.}, } @article {pmid34969477, year = {2022}, author = {Guo, M and Jiang, Y and Xie, J and Cao, Q and Zhang, Q and Mabruk, A and Chen, C}, title = {Bamboo charcoal addition enhanced the nitrogen removal of anammox granular sludge with COD: Performance, physicochemical characteristics and microbial community.}, journal = {Journal of environmental sciences (China)}, volume = {115}, number = {}, pages = {55-64}, doi = {10.1016/j.jes.2021.07.010}, pmid = {34969477}, issn = {1001-0742}, mesh = {Anaerobic Ammonia Oxidation ; Anaerobiosis ; Biological Oxygen Demand Analysis ; Bioreactors ; Charcoal ; Denitrification ; *Microbiota ; Nitrogen ; Oxidation-Reduction ; Planctomycetes ; *Sewage ; }, abstract = {The effects of different chemical oxygen demand (COD) concentrations on the anammox granular sludge with Bamboo Charcoal (BC) addition were evaluated in UASB reactor. The results showed that the average total nitrogen (TN) removal efficiency was reduced from 85.9% to 81.4% when COD concentration was increased from 50 to 150 mg/L. However, the TN removal efficiency of BC addition reactors was dramatically 3.1%-6.4% higher than that without BC under different COD concentrations. The average diameter of granular sludge was 0.13 mm higher than that without BC. The settling velocity was increased by elevated COD concentration, while the EPS and VSS/SS were increased with BC addition. The high-throughput Miseq sequencing analyses revealed that the bacterial diversity and richness were decreased under COD addition, and the Planctomycetes related to anammox bacteria were Candidatus Brocadia and Candidatus Kuenenia. The Metagenomic sequencing indicated that the abundance of denitrification related functional genes all increased with elevated COD, while the abundance of anammox related functional genes of decreased. The functional genes related to anammox was hydrazine synthase encoding genes (hzsA, hzsB and hzsB). The average relative abundance of hzs genes in the reactor with BC addition was higher than the control at COD concentrations of 50 mg/L and 150 mg/L. The functional genes of denitrification mediated by BC were higher than those without BC throughout the operation phase. It is interesting to note that BC addition greatly enriched the related functional genes of denitrification and anammox.}, } @article {pmid34969161, year = {2022}, author = {Wang, L and Yao, H and Tong, T and Lau, K and Leung, SY and Ho, JWK and Leung, WK}, title = {Dynamic changes in antibiotic resistance genes and gut microbiota after Helicobacter pylori eradication therapies.}, journal = {Helicobacter}, volume = {27}, number = {2}, pages = {e12871}, doi = {10.1111/hel.12871}, pmid = {34969161}, issn = {1523-5378}, support = {//Hong Kong Jockey Club/ ; }, mesh = {Amoxicillin/therapeutic use ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Clarithromycin/pharmacology/therapeutic use ; Drug Resistance, Microbial ; Drug Therapy, Combination ; *Gastrointestinal Microbiome/genetics ; *Helicobacter Infections/microbiology ; *Helicobacter pylori/genetics ; Humans ; }, abstract = {BACKGROUND: Short-term antibiotics exposure is associated with alterations in microbiota and antibiotic resistance genes (ARGs) in the human gut. While antibiotics are critical in the successful eradication of Helicobacter pylori, the short-term and long-term impacts on the composition and quantity of antibiotics resistance genes after H. pylori eradication are unclear. This study used whole-genome shotgun metagenomic of stool samples to characterize the gut microbiota and ARGs, before and after H. pylori eradication therapy.

RESULTS: Forty-four H. pylori-infected patients were recruited, including 21 treatment naïve patients who received clarithromycin-based triple therapy (CLA group) and 23 patients who failed previous therapies, in which 10 received levofloxacin-based quadruple therapy (LEVO group) and 13 received other combinations (OTHER group). Stool samples were collected at baseline (before current treatment), 6 week and 6 month after eradication therapy. At baseline, there was only a slight difference among the three groups on ARGs and gut microbiota. After eradication therapy, there was a transient but significant increase in gut ARGs 6 week post-therapy, among which the LEVO group had the most significant ARGs alteration compared to other two groups. For treatment naïve patients, those with higher ErmF abundance were prone to fail CLA eradication and gain more ARGs after treatment. For gut microbiota, the bacteria richness decreased at 6 week and there was a significant difference in microbiota community among the three groups at 6 week.

CONCLUSIONS: Our findings demonstrated the dynamic alterations in gut microbiota and ARGs induced by different eradication therapies, which could influence the choices of antibiotics in eradication therapy.}, } @article {pmid34968606, year = {2022}, author = {Varghese, VK and Poddar, BJ and Shah, MP and Purohit, HJ and Khardenavis, AA}, title = {A comprehensive review on current status and future perspectives of microbial volatile fatty acids production as platform chemicals.}, journal = {The Science of the total environment}, volume = {815}, number = {}, pages = {152500}, doi = {10.1016/j.scitotenv.2021.152500}, pmid = {34968606}, issn = {1879-1026}, mesh = {Bioreactors ; *Fatty Acids, Volatile ; Fermentation ; Hydrogen-Ion Concentration ; Metabolic Engineering ; *Microbiota ; Sewage ; }, abstract = {Volatile fatty acids (VFA), the secondary metabolite of microbial fermentation, are used in a wide range of industries for production of commercially valuable chemicals. In this review, the fermentative production of VFAs by both pure as well mixed microbial cultures is highlighted along with the strategies for enhancing the VFA production through innovations in existing approaches. Role of conventionally applied tools for the optimization of operational parameters such as pH, temperature, retention time, organic loading rate, and headspace pressure has been discussed. Furthermore, a comparative assessment of above strategies on VFA production has been done with alternate developments such as co-fermentation, substrate pre-treatment, and in situ removal from fermented broth. The review also highlights the applications of different bioreactor geometries in the optimum production of VFAs and how metagenomic tools could provide a detailed insight into the microbial communities and their functional attributes that could be subjected to metabolic engineering for the efficient production of VFAs.}, } @article {pmid34966824, year = {2021}, author = {Gao, B and Zhao, X and Liu, X and Yang, X and Zhang, A and Huang, H and Liou, YL and Xu, D}, title = {Imbalance of the Gut Microbiota May Be Associated with Missed Abortions: A Perspective Study from a General Hospital of Hunan Province.}, journal = {Journal of immunology research}, volume = {2021}, number = {}, pages = {5571894}, pmid = {34966824}, issn = {2314-7156}, mesh = {Abortion, Missed/*etiology ; Adult ; Biodiversity ; China ; Computational Biology/methods ; Disease Susceptibility ; Dysbiosis/*complications/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/methods ; Mycoplasma ; Pregnancy ; Risk Factors ; }, abstract = {OBJECTIVE: To conduct a preliminary investigation that shows the possible correlation between the change of gut microbiota and missed abortions (MAs), which further provides a new potential insight for the prevention and therapy of MAs.

METHOD: One hundred women, including 50 patients with MAs (case group) and 50 normal pregnant women (control group), were enrolled in the study. Fecal specimens were collected in the first trimester. Bacterial DNA was extracted, hybridized with primers of specific genes, and then detected by bacterial chip. The composition and the relative abundance of the gut microbiota were compared and analyzed. Furthermore, Kyoto Encyclopedia of Genes and Genomes enrichment analysis was used to explore the relative pathways.

RESULTS: (1) The α-diversity and β-diversity of the gut microbiota in patients with MAs were significantly lower than that those in normal pregnant women (P < 0.05). At the phylum level, Firmicutes, Proteobacteria, Actinomycetes, and Bacteroidetes accounted for the main proportion of intestinal flora in the 2 groups. Only Actinobacteria was high in the case group. Significant differences were found between the two groups at the phylum level (P < 0.05). Prevotella, Lactobacillus, and Paracoccus were significantly more abundant in the control group than in the case group at the genus level (P < 0.05). (2) KEGG pathway enrichment analysis found significant differences in 27 signaling pathways and metabolic pathways between the two groups of differentially expressed genes (all adjusted P < 0.05). (3) The positive rate of M. hominins (MH) detection in the control group was significantly higher in the MA group (χ [2] = 7.853, P = 0.004).

CONCLUSION: The high abundance of Actinobacteria in the MA group was the first time found and reported in the study. The dysbiosis of the gut microbiota correlates with MAs. This study provided insights into the potential change of gut microbiota of MAs and the potential underlying mechanisms through certain impaired lipid metabolism and aroused inflammation pathways. Comprehensive insights regarding gut microbiota may facilitate improved understanding and the development of novel therapeutic and preventive strategies for MAs.}, } @article {pmid34965016, year = {2021}, author = {Yu, JS and Youn, GS and Choi, J and Kim, CH and Kim, BY and Yang, SJ and Lee, JH and Park, TS and Kim, BK and Kim, YB and Roh, SW and Min, BH and Park, HJ and Yoon, SJ and Lee, NY and Choi, YR and Kim, HS and Gupta, H and Sung, H and Han, SH and Suk, KT and Lee, DY}, title = {Lactobacillus lactis and Pediococcus pentosaceus-driven reprogramming of gut microbiome and metabolome ameliorates the progression of non-alcoholic fatty liver disease.}, journal = {Clinical and translational medicine}, volume = {11}, number = {12}, pages = {e634}, pmid = {34965016}, issn = {2001-1326}, mesh = {Animals ; Benzofurans/metabolism ; Cellular Reprogramming/*immunology/physiology ; Diet, Western/adverse effects ; Disease Models, Animal ; Feces/microbiology ; Gastrointestinal Microbiome/*immunology/physiology ; Lactobacillus/*metabolism/pathogenicity ; Metabolome/*immunology/physiology ; Mice ; Non-alcoholic Fatty Liver Disease/*drug therapy/physiopathology ; Pediococcus pentosaceus/*metabolism/pathogenicity ; Quinolines/metabolism ; }, abstract = {BACKGROUND: Although microbioa-based therapies have shown putative effects on the treatment of non-alcoholic fatty liver disease (NAFLD), it is not clear how microbiota-derived metabolites contribute to the prevention of NAFLD. We explored the metabolomic signature of Lactobacillus lactis and Pediococcus pentosaceus in NAFLD mice and its association in NAFLD patients.

METHODS: We used Western diet-induced NAFLD mice, and L. lactis and P. pentosaceus were administered to animals in the drinking water at a concentration of 10[9] CFU/g for 8 weeks. NAFLD severity was determined based on liver/body weight, pathology and biochemistry markers. Caecal samples were collected for the metagenomics by 16S rRNA sequencing. Metabolite profiles were obtained from caecum, liver and serum. Human stool samples (healthy control [n = 22] and NAFLD patients [n = 23]) were collected to investigate clinical reproducibility for microbiota-derived metabolites signature and metabolomics biomarker.

RESULTS: L. lactis and P. pentosaceus supplementation effectively normalized weight ratio, NAFLD activity score, biochemical markers, cytokines and gut-tight junction. While faecal microbiota varied according to the different treatments, key metabolic features including short chain fatty acids (SCFAs), bile acids (BAs) and tryptophan metabolites were analogously restored by both probiotic supplementations. The protective effects of indole compounds were validated with in vitro and in vivo models, including anti-inflammatory effects. The metabolomic signatures were replicated in NAFLD patients, accompanied by the comparable levels of Firmicutes/Bacteroidetes ratio, which was significantly higher (4.3) compared with control (0.6). Besides, the consequent biomarker panel with six stool metabolites (indole, BAs, and SCFAs) showed 0.922 (area under the curve) in the diagnosis of NAFLD.

CONCLUSIONS: NAFLD progression was robustly associated with metabolic dys-regulations in the SCFAs, bile acid and indole compounds, and NAFLD can be accurately diagnosed using the metabolites. L. lactis and P. pentosaceus ameliorate NAFLD progression by modulating gut metagenomic and metabolic environment, particularly tryptophan pathway, of the gut-liver axis.}, } @article {pmid34964297, year = {2021}, author = {Becsei, Á and Solymosi, N and Csabai, I and Magyar, D}, title = {Detection of antimicrobial resistance genes in urban air.}, journal = {MicrobiologyOpen}, volume = {10}, number = {6}, pages = {e1248}, pmid = {34964297}, issn = {2045-8827}, mesh = {*Air Microbiology ; Bacteria/*genetics ; Cities ; Drug Resistance, Bacterial/*genetics ; *Genes, Bacterial ; Metagenome ; *Microbiota ; Sensitivity and Specificity ; }, abstract = {To understand antibiotic resistance in pathogenic bacteria, we need to monitor environmental microbes as reservoirs of antimicrobial resistance genes (ARGs). These bacteria are present in the air and can be investigated with the whole metagenome shotgun sequencing approach. This study aimed to investigate the feasibility of a method for metagenomic analysis of microbial composition and ARGs in the outdoor air. Air samples were collected with a Harvard impactor in the PM10 range at 50 m from a hospital in Budapest. From the DNA yielded from samples of PM10 fraction single-end reads were generated with an Ion Torrent sequencer. During the metagenomic analysis, reads were classified taxonomically. The core bacteriome was defined. Reads were assembled to contigs and the ARG content was analyzed. The dominant genera in the core bacteriome were Bacillus, Acinetobacter, Leclercia and Paenibacillus. Among the identified ARGs best hits were vanRA, Bla1, mphL, Escherichia coli EF-Tu mutants conferring resistance to pulvomycin; BcI, FosB, and mphM. Despite the low DNA content of the samples of PM10 fraction, the number of detected airborne ARGs was surprisingly high.}, } @article {pmid34964273, year = {2022}, author = {Takizawa, S and Asano, R and Fukuda, Y and Baba, Y and Tada, C and Nakai, Y}, title = {Shifts in xylanases and the microbial community associated with xylan biodegradation during treatment with rumen fluid.}, journal = {Microbial biotechnology}, volume = {15}, number = {6}, pages = {1729-1743}, pmid = {34964273}, issn = {1751-7915}, mesh = {Animals ; Bacteria/genetics/metabolism ; Cattle ; *Ciliophora/metabolism ; Fatty Acids, Volatile/metabolism ; Gases/metabolism ; Methane/metabolism ; *Microbiota ; Rumen/microbiology ; Xylans/metabolism ; }, abstract = {Treatment with rumen fluid improves methane production from non-degradable lignocellulosic biomass during subsequent methane fermentation; however, the kinetics of xylanases during treatment with rumen fluid remain unclear. This study aimed to identify key xylanases contributing to xylan degradation and their individual activities during xylan treatment with bovine rumen microorganisms. Xylan was treated with bovine rumen fluid at 37°C for 48 h under anaerobic conditions. Total solids were degraded into volatile fatty acids and gases during the first 24 h. Zymography showed that xylanases of 24, 34, 85, 180, and 200 kDa were highly active during the first 24 h. Therefore, these xylanases are considered to be crucial for xylan degradation during treatment with rumen fluid. Metagenomic analysis revealed that the rumen microbial community's structure and metabolic function temporally shifted during xylan biodegradation. Although statistical analyses did not reveal significantly positive correlations between xylanase activities and known xylanolytic bacterial genera, they positively correlated with protozoal (e.g., Entodinium, Diploplastron, and Eudiplodinium) and fungal (e.g., Neocallimastix, Orpinomyces, and Olpidium) genera and unclassified bacteria. Our findings suggest that rumen protozoa, fungi, and unclassified bacteria are associated with key xylanase activities, accelerating xylan biodegradation into volatile fatty acids and gases, during treatment of lignocellulosic biomass with rumen fluid.}, } @article {pmid34963581, year = {2022}, author = {Caravaca, F and Torres, P and Díaz, G and Roldán, A}, title = {Elevated functional versatility of the soil microbial community associated with the invader Carpobrotus edulis across a broad geographical scale.}, journal = {The Science of the total environment}, volume = {813}, number = {}, pages = {152627}, doi = {10.1016/j.scitotenv.2021.152627}, pmid = {34963581}, issn = {1879-1026}, mesh = {Introduced Species ; *Microbiota ; Rhizosphere ; *Soil ; Soil Microbiology ; }, abstract = {Exotic invasive plants may shape their own rhizosphere microbial community during global invasions. Nevertheless, the impacts of such plant invasions on the functional capacities of soil microbial communities remain poorly explored. We used an approach at a broad geographical scale to estimate the composition and abundance of the fungal functional groups, as well as the bacterial metabolic functions, associated with the rhizospheres of Carpobrotus edulis (L.) L. Bolus and the predominant native plants in coastal ecosystems located in different geographical regions. We used the ASV method to infer the potential functions of the soil microbial community with the PICRUSt2 and FUNGuild tools. The predictive functional profiling of the bacterial communities differed between the rhizospheres of the invasive and native plants, regardless of the biogeographic location of the invaded soil. Some predicted pathways related to the biosynthesis of nucleotides such as ppGpp and pppGpp, lipids, carbohydrates and secondary metabolites and the degradation of organic matter were enriched in the C. edulis rhizosphere. Moreover, the invasive microbiota was characterised by a greater richness and diversity of catabolic enzymes involved in nutrients cycling and higher relative abundances of saprotrophs and pathotrophs. Invasion by C. edulis promoted a shift in the potential functional versatility of the soil microbial communities, which can cope with nutrient limitations and biotic stress, and can favour the establishment of the invasive plant, but also alter the functioning and stability of the invaded ecosystems.}, } @article {pmid34963452, year = {2021}, author = {Lin, H and Guo, Q and Wen, Z and Tan, S and Chen, J and Lin, L and Chen, P and He, J and Wen, J and Chen, Y}, title = {The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors.}, journal = {Microbial cell factories}, volume = {20}, number = {1}, pages = {233}, pmid = {34963452}, issn = {1475-2859}, support = {No. 81770529//National Natural Science Foundation of China/ ; No. 82070543//National Natural Science Foundation of China/ ; }, mesh = {Adult ; Aged ; Anxiety/*microbiology/*therapy ; Depression/*microbiology/*therapy ; Diarrhea/microbiology/therapy ; Escherichia/classification ; Eubacterium/classification ; Faecalibacterium/classification ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Hemiterpenes/metabolism ; High-Throughput Nucleotide Sequencing ; Humans ; Irritable Bowel Syndrome/complications/*microbiology/therapy ; Male ; *Metagenome ; Middle Aged ; Pentanoic Acids/metabolism ; Quality of Life ; }, abstract = {BACKGROUND: Anxiety and depression are complications in Irritable bowel syndrome (IBS) patients. In this study, we recruited 18 IBS patients with mild-modest anxiety and depression behaviors, and after the screening, we defined the FMT treatment group (n = 9) and the control group (n = 9). The IBS symptom severity scale (IBS-SSS), Hamilton Anxiety Rating Scale (HAM-A), Hamilton Depression Rating Scale (HAM-D), Irritable Bowel Syndrome Quality of Life (IBS-QOL) and Bristol stool scale (BSS) were evaluated one week before FMT (baseline), one-week-, one-month-, two-month-, and three-month-following FMT. Meanwhile, we determined the SCFAs in the patient's feces and serum and continued the metagenomic analysis of the microorganisms in the patient's feces.

RESULTS: The results showed that the patient's anxiety and depression behavior gradually improved with FMT treatment. Moreover, the illness and quality of life had also been relieved significantly. The content of isovaleric acid and valeric acid was significantly reduced in the FMT group compared to the Col group. Metagenomic analysis showed that FMT treatment decreased the abundance of Faecalibacterium, Eubacterium and Escherichia. From KEGG functional analysis, we confirmed that the top five abundant pathways were "bacterial chemotaxis, "flagellar assembly", "glycine, serine and threonine metabolism", "apoptosis", and "bacterial invasion of epithelial cells".

CONCLUSIONS: FMT treatment can effectively alleviate the anxiety and depression behaviors of IBS-D patients and reduce the IBS-SSS score, indicating that FMT can improve patients' symptoms. The high throughput sequencing results show that Bifidobacterium and Escherichia play the most critical role in the formation and recovery of IBS-D patients. The GC/MS data indicated that faeces isovaleric acid and valeric acid might be more suitable as a metabolic indicator of IBS-D remission. Trial registration ChiCTR, ChiCTR1900024924, Registered 3 August 2019, https://www.chictr.org.cn/showproj.aspx?proj=41676 .}, } @article {pmid34962589, year = {2021}, author = {Kalu, CM and Ogola, HJO and Selvarajan, R and Tekere, M and Ntushelo, K}, title = {Correlations Between Root Metabolomics and Bacterial Community Structures in the Phragmites australis Under Acid Mine Drainage-Polluted Wetland Ecosystem.}, journal = {Current microbiology}, volume = {79}, number = {1}, pages = {34}, pmid = {34962589}, issn = {1432-0991}, support = {129095//national research foundation/ ; }, mesh = {Bacteria/genetics ; Biodegradation, Environmental ; Ecosystem ; Metabolomics ; *Metals, Heavy/analysis/toxicity ; *Microbiota ; Rhizosphere ; Wetlands ; }, abstract = {Despite root microecology playing critical role in plant growth and fidelity, relatively few studies have focused on the link between the microbial communities and root metabolome in the aquatic macrophytes under heavy metal (HM) pollution. Using high-throughput metagenomic sequencing, targeted metabolomics and community-level physiological profile analyses, we investigated the symbiotic associations between Phragmites australis with rhizospheric bacterial communities under differing acid mine drainage (AMD) pollution. Results indicated that AMD pollution and root localization significantly affected root metabolome profiles. Higher accumulation of adenosine monophosphate, inosine, methionine, carnitine and dimethylglycine were observed in the rhizosphere under AMD than non-AMD habitat. Overall, the bacterial diversity and richness, and functional (metabolic) diversity were lower under high-AMD pollution. While non-AMD site was enriched with members of phylum Firmicutes, Proteobacteria were the most abundant taxa in the rhizosphere and endosphere under AMD-polluted sites. Further, plant growth promoting rhizobacteria (Rhizobium, Delftia, Bradyrhizobium, and Mesorhizobium) and metal-tolerant bacteria (Bacillus, Arthrobacter, Massilia and Methylocystis) were most abundant in AMD-polluted than non-AMD habitat. Finally, pH, TDS (total dissolved solids), Cu, Cr, Fe, and Zn content were the key environmental factors that strongly contributed to the spatial perturbation of rhizospheric metabolites, proteobacterial and acidobacterial taxa. Overall, the study linked the differential endospheric and rhizospheric bacterial community and metabolite profiles in P. australis under AMD environment and provided insights into HM adaptability and phytoremediation potential.}, } @article {pmid34961896, year = {2021}, author = {Johny, TK and Puthusseri, RM and Bhat, SG}, title = {Metagenomic landscape of taxonomy, metabolic potential and resistome of Sardinella longiceps gut microbiome.}, journal = {Archives of microbiology}, volume = {204}, number = {1}, pages = {87}, pmid = {34961896}, issn = {1432-072X}, support = {MOES/10-MLR/2/2007//centre for marine living resources & ecology- ministry of earth sciences, government of india/ ; MOES/10-MLRTD/03/2013//centre for marine living resources & ecology- ministry of earth sciences, government of india/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Fishes ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Fish gut microbiota, encompassing a colossal reserve of microbes represents a dynamic ecosystem, influenced by a myriad of environmental and host factors. The current study presents a comprehensive insight into Sardinella longiceps gut microbiome using whole metagenome shotgun sequencing. Taxonomic profiling identified the predominance of phylum Proteobacteria, comprising of Photobacterium, Vibrio and Shewanella sp. Functional annotation revealed the dominance of Clustering based subsystems, Carbohydrate, and Amino acids and derivatives. Analysis of Virulence, disease and defense subsystem identified genes conferring resistance to antibiotics and toxic compounds, like multidrug resistance efflux pumps and resistance genes for fluoroquinolones and heavy metals like cobalt, zinc, cadmium and copper. The presence of overlapping genetic mechanisms of resistance to antibiotics and heavy metals, like the efflux pumps is a serious cause of concern as it is likely to aggravate co-selection pressure, leading to an increased dissemination of these resistance genes to fish and humans.}, } @article {pmid34960807, year = {2021}, author = {Folgueiras-González, A and van den Braak, R and Deijs, M and Kuller, W and Sietsma, S and Thuring, V and van der Hoek, L and de Groof, A}, title = {Dynamics of the Enteric Virome in a Swine Herd Affected by Non-PCV2/PRRSV Postweaning Wasting Syndrome.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, pmid = {34960807}, issn = {1999-4915}, mesh = {Animals ; Astroviridae/isolation & purification ; Enteroviruses, Porcine/*isolation & purification ; Female ; Intestines/*virology ; Male ; Metagenomics ; Rotavirus/*isolation & purification ; Sapovirus/*isolation & purification ; Swine ; Swine Diseases/*virology ; Virome/*physiology ; Wasting Syndrome/*veterinary/virology ; Weaning ; }, abstract = {A commercial pig farm with no history of porcine circovirus 2 (PCV2) or porcine reproductive and respiratory syndrome virus (PRRSV) repeatedly reported a significant reduction in body weight gain and wasting symptoms in approximately 20-30% of the pigs in the period between three and six weeks after weaning. As standard clinical interventions failed to tackle symptomatology, viral metagenomics were used to describe and monitor the enteric virome at birth, 3 weeks, 4 weeks, 6 weeks, and 9 weeks of age. The latter four sampling points were 7 days, 3 weeks, and 6 weeks post weaning, respectively. Fourteen distinct enteric viruses were identified within the herd, which all have previously been linked to enteric diseases. Here we show that wasting is associated with alterations in the enteric virome of the pigs, characterized by: (1) the presence of enterovirus G at 3 weeks of age, followed by a higher prevalence of the virus in wasting pigs at 6 weeks after weaning; (2) rotaviruses at 3 weeks of age; and (3) porcine sapovirus one week after weaning. However, the data do not provide a causal link between specific viral infections and the postweaning clinical problems on the farm. Together, our results offer evidence that disturbances in the enteric virome at the preweaning stage and early after weaning have a determining role in the development of intestinal barrier dysfunctions and nutrient uptake in the postweaning growth phase. Moreover, we show that the enteric viral load sharply increases in the week after weaning in both healthy and wasting pigs. This study is also the first to report the dynamics and co-infection of porcine rotavirus species and porcine astrovirus genetic lineages during the first 9 weeks of the life of domestic pigs.}, } @article {pmid34960726, year = {2021}, author = {Redila, CD and Prakash, V and Nouri, S}, title = {Metagenomics Analysis of the Wheat Virome Identifies Novel Plant and Fungal-Associated Viral Sequences.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, pmid = {34960726}, issn = {1999-4915}, mesh = {Base Sequence ; Fungal Viruses/classification/*genetics/*isolation & purification ; Fungi/virology ; Genome, Viral ; Metagenomics ; Phylogeny ; Plant Diseases/*virology ; Triticum/microbiology ; *Virome ; Viruses/classification/*genetics/*isolation & purification ; }, abstract = {Wheat viruses including wheat streak mosaic virus, Triticum mosaic virus, and barley yellow dwarf virus cost substantial losses in crop yields every year. Although there have been extensive studies conducted on these known wheat viruses, currently, there is limited knowledge about all components of the wheat (Triticum aestivum L.) virome. Here, we determined the composition of the wheat virome through total RNA deep sequencing of field-collected leaf samples. Sequences were de novo assembled after removing the host reads, and BLASTx searches were conducted. In addition to the documented wheat viruses, novel plant and fungal-associated viral sequences were identified. We obtained the full genome sequence of the first umbra-like associated RNA virus tentatively named wheat umbra-like virus in cereals. Moreover, a novel bi-segmented putative virus tentatively named wheat-associated vipovirus sharing low but significant similarity with both plant and fungal-associated viruses was identified. Additionally, a new putative fungal-associated tobamo-like virus and novel putative Mitovirus were discovered in wheat samples. The discovery and characterization of novel viral sequences associated with wheat is important to determine if these putative viruses may pose a threat to the wheat industry or have the potential to be used as new biological control agents for wheat pathogens either as wild-type or recombinant viruses.}, } @article {pmid34960693, year = {2021}, author = {Paim, WP and Maggioli, MF and Falkenberg, SM and Ramachandran, A and Weber, MN and Canal, CW and Bauermann, FV}, title = {Virome Characterization in Commercial Bovine Serum Batches-A Potentially Needed Testing Strategy for Biological Products.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, pmid = {34960693}, issn = {1999-4915}, mesh = {Animals ; Bacteriophages/genetics/*isolation & purification ; *Biological Products ; Cattle/*blood ; DNA Viruses/genetics/*isolation & purification ; Drug Contamination ; High-Throughput Nucleotide Sequencing ; Phylogeny ; RNA Viruses/genetics/*isolation & purification ; Serum/*virology ; *Virome ; }, abstract = {Bovine serum has been widely used as a universal supplement in culture media and other applications, including the manufacture of biological products and the production of synthetic meat. Currently, commercial bovine serum is tested for possible viral contaminants following regional guidelines. Regulatory agencies' established tests focused on detecting selected animal origin viruses and are based on virus isolation, immunofluorescence, and hemadsorption assays. However, these tests may fail to detect new or emerging viruses in biological products. High-throughput sequencing is a powerful option since no prior knowledge of the viral targets is required. In the present study, we evaluate the virome of seven commercial batches of bovine serum from Mexico (one batch), New Zealand (two batches), and the United States (four batches) using a specific preparation and enrichment method for pooled samples and sequencing using an Illumina platform. A variety of circular replicase-encoding single-stranded (CRESS) DNA families (Genomoviridae, Circoviridae, and Smacoviridae) was identified. Additionally, CrAssphage, a recently discovered group of bacteriophage correlated with fecal contamination, was identified in 85% of the tested batches. Furthermore, sequences representing viral families with single-stranded DNA (Parvoviridae), double-stranded DNA (Polyomaviridae and Adenoviridae), single-stranded RNA (Flaviviridae, Picornaviridae, and Retroviridae), and double-stranded RNA (Reoviridae) were identified. These results support that high-throughput sequencing associated with viral enrichment is a robust tool and should be considered an additional layer of safety when testing pooled biologicals to detect viral contaminants overlooked by the current testing protocols.}, } @article {pmid34960644, year = {2021}, author = {Litov, AG and Belova, OA and Kholodilov, IS and Gadzhikurbanov, MN and Gmyl, LV and Oorzhak, ND and Saryglar, AA and Ishmukhametov, AA and Karganova, GG}, title = {Possible Arbovirus Found in Virome of Melophagus ovinus.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, pmid = {34960644}, issn = {1999-4915}, mesh = {Animals ; Arboviruses/*genetics/isolation & purification ; Cell Line ; Diptera/*virology ; Ectoparasitic Infestations/*virology ; Phylogeny ; Reoviridae ; Rhabdoviridae ; Russia ; Sheep ; Sheep Diseases/*parasitology ; *Virome ; }, abstract = {Members of the Lipopteninae subfamily are blood-sucking ectoparasites of mammals. The sheep ked (Melophagus ovinus) is a widely distributed ectoparasite of sheep. It can be found in most sheep-rearing areas and can cause skin irritation, restlessness, anemia, weight loss and skin injuries. Various bacteria and some viruses have been detected in M. ovinus; however, the virome of this ked has never been studied using modern approaches. Here, we study the virome of M. ovinus collected in the Republic of Tuva, Russia. In our research, we were able to assemble full genomes for five novel viruses, related to the Rhabdoviridae (Sigmavirus), Iflaviridae, Reoviridae and Solemoviridae families. Four viruses were found in all five of the studied pools, while one virus was found in two pools. Phylogenetically, all of the novel viruses clustered together with various recently described arthropod viruses. All the discovered viruses were tested on their ability to replicate in the mammalian porcine embryo kidney (PEK) cell line. Aksy-Durug Melophagus sigmavirus RNA was detected in the PEK cell line cultural supernate after the first, second and third passages. Such data imply that this virus might be able to replicate in mammalian cells, and thus, can be considered as a possible arbovirus.}, } @article {pmid34960634, year = {2021}, author = {do Socorro Fôro Ramos, E and de Oliveira Ribeiro, G and Villanova, F and de Padua Milagres, FA and Brustulin, R and Araújo, ELL and Pandey, RP and Raj, VS and Deng, X and Delwart, E and Luchs, A and da Costa, AC and Leal, É}, title = {Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, pmid = {34960634}, issn = {1999-4915}, mesh = {Acute Disease ; Adenoviridae/genetics ; Adolescent ; Adult ; Aged ; Bacteriophages/genetics ; Brazil/epidemiology ; Child ; Child, Preschool ; Feces/virology ; Female ; Gastroenteritis/epidemiology/*virology ; Humans ; Male ; *Metagenomics ; Middle Aged ; Norovirus/genetics ; Rotavirus/genetics ; Virome/*genetics ; Viruses/classification/*genetics/isolation & purification ; Young Adult ; }, abstract = {Metagenomics based on the next-generation sequencing (NGS) technique is a target-independent assay that enables the simultaneous detection and genomic characterization of all viruses present in a sample. There is a limited amount of data about the virome of individuals with gastroenteritis (GI). In this study, the enteric virome of 250 individuals (92% were children under 5 years old) with GI living in the northeastern and northern regions of Brazil was characterized. Fecal samples were subjected to NGS, and the metagenomic analysis of virus-like particles (VLPs) identified 11 viral DNA families and 12 viral RNA families. As expected, the highest percentage of viral sequences detected were those commonly associated with GI, including rotavirus, adenovirus, norovirus (94.8%, 82% and 71.2%, respectively). The most common co-occurrences, in a single individual, were the combinations of rotavirus-adenovirus, rotavirus-norovirus, and norovirus-adenovirus (78%, 69%, and 62%, respectively). In the same way, common fecal-emerging human viruses were also detected, such as parechovirus, bocaporvirus, cosavirus, picobirnavirus, cardiovirus, salivirus, and Aichivirus. In addition, viruses that infect plants, nematodes, fungi, protists, animals, and arthropods could be identified. A large number of unclassified viral contigs were also identified. We show that the metagenomics approach is a powerful and promising tool for the detection and characterization of different viruses in clinical GI samples.}, } @article {pmid34960611, year = {2021}, author = {Happel, AU and Balle, C and Maust, BS and Konstantinus, IN and Gill, K and Bekker, LG and Froissart, R and Passmore, JA and Karaoz, U and Varsani, A and Jaspan, H}, title = {Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, pmid = {34960611}, issn = {1999-4915}, support = {T32 HD007233/HD/NICHD NIH HHS/United States ; R01 AI094586/NH/NIH HHS/United States ; R01 HD083040/NH/NIH HHS/United States ; }, mesh = {Adolescent ; Bacteriophages/*isolation & purification ; Cohort Studies ; Female ; Humans ; *Metagenome ; *Microbiota ; South Africa/epidemiology ; *Vagina/microbiology/virology ; }, abstract = {The interaction between gut bacterial and viral microbiota is thought to be important in human health. While fluctuations in female genital tract (FGT) bacterial microbiota similarly determine sexual health, little is known about the presence, persistence, and function of vaginal bacteriophages. We conducted shotgun metagenome sequencing of cervicovaginal samples from South African adolescents collected longitudinally, who received no antibiotics. We annotated viral reads and circular bacteriophages, identified CRISPR loci and putative prophages, and assessed their diversity, persistence, and associations with bacterial microbiota composition. Siphoviridae was the most prevalent bacteriophage family, followed by Myoviridae, Podoviridae, Herelleviridae, and Inoviridae. Full-length siphoviruses targeting bacterial vaginosis (BV)-associated bacteria were identified, suggesting their presence in vivo. CRISPR loci and prophage-like elements were common, and genomic analysis suggested higher diversity among Gardnerella than Lactobacillus prophages. We found that some prophages were highly persistent within participants, and identical prophages were present in cervicovaginal secretions of multiple participants, suggesting that prophages, and thus bacterial strains, are shared between adolescents. The number of CRISPR loci and prophages were associated with vaginal microbiota stability and absence of BV. Our analysis suggests that (pro)phages are common in the FGT and vaginal bacteria and (pro)phages may interact.}, } @article {pmid34960001, year = {2021}, author = {Kaashyap, M and Cohen, M and Mantri, N}, title = {Microbial Diversity and Characteristics of Kombucha as Revealed by Metagenomic and Physicochemical Analysis.}, journal = {Nutrients}, volume = {13}, number = {12}, pages = {}, pmid = {34960001}, issn = {2072-6643}, mesh = {Acetobacter/isolation & purification ; Bacteria/classification ; Chemical Phenomena ; Fermentation ; Humans ; Kombucha Tea/*analysis/*microbiology ; Metagenomics/*methods ; *Microbiota ; Phenols/analysis ; Probiotics/analysis ; Proteins/analysis ; RNA, Ribosomal, 16S/genetics ; Tea/chemistry ; Yeasts/classification ; }, abstract = {Kombucha is a fermented tea made from a Symbiotic Culture of Bacteria and Yeast (SCOBY) with a long history of use as a health tonic. It is likely that most health benefits come from the tea and fermentation metabolites from specific microbial communities. Despite its growing importance as a functional health drink, the microbial ecosystem present in kombucha has not been fully documented. To characterize the microbial composition and biochemical properties of 'The Good Brew' original base kombucha, we used metagenomics amplicon (16S rRNA and ITS) sequencing to identify the microbial communities at the taxonomic level. We identified 34 genera with 200 microbial species yet described in kombucha. The dominance of organic acid producing microorganisms Acetobacter, Komagataeibacter and Starmerella are healthy for the human gut and their glucose metabolising activities have a putative role in preventing conditions such as diabetes and obesity. Kombucha contains high protein (3.31 µg/mL), high phenolic content (290.4 mg/100 mL) and low sugars (glucose: 1.87 g/L; sucrose 1.11 g/L; fructose: 0.05 g/L) as compared to green tea. The broad microbial diversity with proven health benefits for the human gut suggests kombucha is a powerful probiotic. These findings are important to improve the commercial value of kombucha and uncover the immense prospects for health benefits.}, } @article {pmid34956932, year = {2021}, author = {Li, Z and Chen, G and Wang, P and Sun, M and Zhao, J and Li, A and Sun, Q}, title = {Alterations of the Oral Microbiota Profiles in Chinese Patient With Oral Cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {780067}, pmid = {34956932}, issn = {2235-2988}, mesh = {*Carcinoma, Squamous Cell ; China ; Humans ; *Microbiota ; *Mouth Neoplasms ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Oral cancer is the most common malignant tumor in the oral and maxillofacial region, of which more than 90% is squamous cell carcinoma. The incidence of oral cancer is on the rise worldwide. An imbalance between the microorganism composition and its host may lead to the occurrence of oral malignant tumors. Accumulating evidence suggests that the oral microbiota plays an important role in oral cancer; however, the association between oral microbiota and oral cancer has not yet been comprehensively studied. In this study, metagenomic sequencing was used to compare the microbial composition of three groups of samples from Chinese patients with oral cancer, patients with precancerous lesion, and normal individuals. In terms of microbiota richness, the oral microbiota of patients with precancerous lesions was richer than that of oral cancer patients and healthy controls, whereas in terms of microbiota diversity, there was little difference between the three groups. The three groups of samples exhibited statistically significant differences in microbiota composition and metabolic function at the family, genus, and species levels (P < 0.05). The differentially enriched phylum in oral cancer samples was Bacteroidetes (P < 0.05). At the genus level, the main differentially enriched taxa were Prevotella, Peptostreptococcus, Carnobacterium, and Diastella (P < 0.05). The species level was differentially enriched in Prevotella intermedia and Peptostreptococcus stomatis (p < 0.05). The prediction of microbiota function shows that oral cancer is mainly associated with coenzyme A biosynthesis, phosphopantothenic acid biosynthesis, inosine 5'-phosphate degradation, and riboflavin biosynthesis. Furthermore, the increase in C-reactive protein level in oral cancer patients was found to be closely related to P. intermedia. Overall, oral bacterial profiles showed significant differences between the oral cancer group and normal group. Hence, microbes can be employed as diagnostic markers and treatment targets for oral cancer.}, } @article {pmid34954826, year = {2022}, author = {Speruda, M and Piecuch, A and Borzęcka, J and Kadej, M and Ogórek, R}, title = {Microbial traces and their role in forensic science.}, journal = {Journal of applied microbiology}, volume = {132}, number = {4}, pages = {2547-2557}, doi = {10.1111/jam.15426}, pmid = {34954826}, issn = {1365-2672}, mesh = {Cadaver ; Forensic Sciences ; Humans ; *Microbiota/genetics ; *Postmortem Changes ; RNA, Ribosomal, 16S ; }, abstract = {Forensic microbiology, also known as the microbiology of death, is an emerging branch of science that is still underused in criminal investigations. Some of the cases might be difficult to solve with commonly used forensic methods, and then they become an operational field for microbiological and mycological analyses. The aim of our review is to present significant achievements of selected studies on the thanatomicrobiome (micro-organisms found in the body, organs and fluids after death) and epinecrotic community (micro-organisms found on decaying corpses) that can be used in forensic sciences. Research carried out as a part of the forensic microbiology deals with the thanatomicrobiome and the necrobiome-communities of micro-organisms that live inside and outside of a putrefying corpse. Change of species composition observed in each community is a valuable feature that gives a lot of information related to the crime. It is mainly used in the estimation of post-mortem interval (PMI). In some criminal investigations, such noticeable changes in the microbiome and mycobiome can determine the cause or the actual place of death. The microbial traces found at the crime scene can also provide clear evidence of guilt. Nowadays, identification of micro-organisms isolated from the body or environment is based on metagenome analysis and 16S rRNA gene amplicon-based sequencing for bacteria and ITS rRNA gene amplicon-based sequencing for fungi. Cultivation methods are still in use and seem to be more accurate; however, they require much more time to achieve a final result, which is an unwanted feature in any criminal investigation.}, } @article {pmid34954661, year = {2022}, author = {Van Brussel, K and Holmes, EC}, title = {Zoonotic disease and virome diversity in bats.}, journal = {Current opinion in virology}, volume = {52}, number = {}, pages = {192-202}, pmid = {34954661}, issn = {1879-6265}, mesh = {Animals ; *Chiroptera ; Disease Reservoirs ; Ecosystem ; Humans ; *Middle East Respiratory Syndrome Coronavirus ; Phylogeny ; Virome ; Zoonoses ; }, abstract = {The emergence of zoonotic viral diseases in humans commonly reflects exposure to mammalian wildlife. Bats (order Chiroptera) are arguably the most important mammalian reservoir for zoonotic viruses, with notable examples including Severe Acute Respiratory Syndrome coronaviruses 1 and 2, Middle East Respiratory Syndrome coronavirus, henipaviruses and lyssaviruses. Herein, we outline our current knowledge on the diversity of bat viromes, particularly through the lens of metagenomic next-generation sequencing and in the context of disease emergence. A key conclusion is that although bats harbour abundant virus diversity, the vast majority of bat viruses have not emerged to cause disease in new hosts such that bats are better regarded as critical but endangered components of global ecosystems.}, } @article {pmid34954158, year = {2022}, author = {Zhao, X and Liu, M and Yang, S and Gong, H and Ma, J and Li, C and Wang, K}, title = {Performance and microbial community evaluation of full-scale two-phase anaerobic digestion of waste activated sludge.}, journal = {The Science of the total environment}, volume = {814}, number = {}, pages = {152525}, doi = {10.1016/j.scitotenv.2021.152525}, pmid = {34954158}, issn = {1879-1026}, mesh = {Anaerobiosis ; Bioreactors ; Methane ; *Microbiota ; *Sewage ; }, abstract = {"Temperature Staging and Biological Phasing" (TSBP) is an improved two-phase anaerobic digestion (AD) technology. This technology hydrolyzes waste activated sludge (WAS) at 45 °C and converts methane at mesophilic temperature (35-38 °C), with hydraulic retention times of 3-5 d and 14-17 d, respectively. In this study, the performance and microbial community dynamics of full-scale TSBP-based sludge anaerobic digestion system were studied, and the technology was evaluated by energy balance and ecological benefit analysis. The stable operation for 390 d showed that the cumulative biogas yield was about 349,041 m[3], the maximum biogas yield rate was 563.68 L/kg VS, and the VS degradation rate of organic matters in the sludge was 47.19%. Proteobacteria and Firmicutes were found to be the dominant bacteria in both thermophilic and mesophilic reactors. Methanobacterium and Methanosarcina were the two most abundant methanogenic genera in the AD samples. The aceticlastic methanogenesis was likely the predominant production pathway of methane in AD processes based on metagenomics. The TSBP system operated stably, and the recovered energy could achieve energy self-sufficiency, which provided technical reference for the anaerobic treatment of sludge.}, } @article {pmid34953835, year = {2022}, author = {Mercado, JV and Koyama, M and Nakasaki, K}, title = {Short-term changes in the anaerobic digestion microbiome and biochemical pathways with changes in organic load.}, journal = {The Science of the total environment}, volume = {813}, number = {}, pages = {152585}, doi = {10.1016/j.scitotenv.2021.152585}, pmid = {34953835}, issn = {1879-1026}, mesh = {Anaerobiosis ; *Bioreactors ; Methane ; *Microbiota ; Sewage ; }, abstract = {Fluctuations in organic loading rate are frequently experienced in practical-scale anaerobic digestion systems. These impose shocks to the microbiome leading to process instability and failure. This study elucidated the short-term changes in biochemical pathways and the contributions of microbial groups involved in anaerobic digestion with varying organic load shocks. A mixture of starch and hipolypeptone corresponding to a carbon-to‑nitrogen ratio of 25 was used as substrate. Batch vial reactors were run using acclimatized sludge fed with organic load varying from 0 to 5 g VS/L. Methane yield decreased with increasing organic load. The microbiome alpha diversity represented as the number of operational taxonomic units (OTUs) and the Shannon index both decreased with organic load indicating microbiome specialization. The biochemical pathways predicted using PICRUSt2 were analyzed along with the corresponding contributions of microbial groups leading to a proposed pathway of substrate utilization. Genus Trichococcus (order Lactobacillales) increased in contribution to starch degradation pathways with increase in organic load while genus Macellibacteroides (order Bacteroidales) was prominent in contribution to bacterial anaerobic digestion pathways. Strictly acetoclastic Methanosaeta increased in prominence over hydrogenotrophic Methanolinea with increase in organic load. Results from this study provide better understanding of how anaerobic digesters respond to organic load shocks.}, } @article {pmid34952941, year = {2022}, author = {Saheb Kashaf, S and Proctor, DM and Deming, C and Saary, P and Hölzer, M and , and Taylor, ME and Kong, HH and Segre, JA and Almeida, A and Finn, RD}, title = {Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions.}, journal = {Nature microbiology}, volume = {7}, number = {1}, pages = {169-179}, pmid = {34952941}, issn = {2058-5276}, support = {ZIA HG000180/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Bacteria/classification/genetics/growth & development/*isolation & purification ; Child ; Child, Preschool ; Colony Count, Microbial/methods ; Female ; *Genome, Microbial ; Humans ; Infant ; Infant, Newborn ; Male ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Middle Aged ; Phylogeny ; Skin/*microbiology ; Symbiosis ; Young Adult ; }, abstract = {Human skin functions as a physical barrier to foreign pathogen invasion and houses numerous commensals. Shifts in the human skin microbiome have been associated with conditions ranging from acne to atopic dermatitis. Previous metagenomic investigations into the role of the skin microbiome in health or disease have found that much of the sequenced data do not match reference genomes, making it difficult to interpret metagenomic datasets. We combined bacterial cultivation and metagenomic sequencing to assemble the Skin Microbial Genome Collection (SMGC), which comprises 622 prokaryotic species derived from 7,535 metagenome-assembled genomes and 251 isolate genomes. The metagenomic datasets that we generated were combined with publicly available skin metagenomic datasets to identify members and functions of the human skin microbiome. The SMGC collection includes 174 newly identified bacterial species and 12 newly identified bacterial genera, including the abundant genus 'Candidatus Pellibacterium', which has been newly associated with the skin. The SMGC increases the characterized set of known skin bacteria by 26%. We validated the SMGC metagenome-assembled genomes by comparing them with sequenced isolates obtained from the same samples. We also recovered 12 eukaryotic species and assembled thousands of viral sequences, including newly identified clades of jumbo phages. The SMGC enables classification of a median of 85% of skin metagenomic sequences and provides a comprehensive view of skin microbiome diversity, derived primarily from samples obtained in North America.}, } @article {pmid34951957, year = {2022}, author = {Bell, HN and Rebernick, RJ and Goyert, J and Singhal, R and Kuljanin, M and Kerk, SA and Huang, W and Das, NK and Andren, A and Solanki, S and Miller, SL and Todd, PK and Fearon, ER and Lyssiotis, CA and Gygi, SP and Mancias, JD and Shah, YM}, title = {Reuterin in the healthy gut microbiome suppresses colorectal cancer growth through altering redox balance.}, journal = {Cancer cell}, volume = {40}, number = {2}, pages = {185-200.e6}, pmid = {34951957}, issn = {1878-3686}, support = {R01 CA148828/CA/NCI NIH HHS/United States ; R01 DK095201/DK/NIDDK NIH HHS/United States ; P30 CA046592/CA/NCI NIH HHS/United States ; R01 CA245546/CA/NCI NIH HHS/United States ; R01 CA248160/CA/NCI NIH HHS/United States ; T32 GM007863/GM/NIGMS NIH HHS/United States ; I01 BX004842/BX/BLRD VA/United States ; R37 CA237421/CA/NCI NIH HHS/United States ; R01 NS099280/NS/NINDS NIH HHS/United States ; F30 CA257292/CA/NCI NIH HHS/United States ; P50 HD104463/HD/NICHD NIH HHS/United States ; P30 DK089503/DK/NIDDK NIH HHS/United States ; P50 CA130810/CA/NCI NIH HHS/United States ; R01 CA244931/CA/NCI NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; F31 NS127371/NS/NINDS NIH HHS/United States ; F99 CA264414/CA/NCI NIH HHS/United States ; F31 CA247457/CA/NCI NIH HHS/United States ; U24 DK097153/DK/NIDDK NIH HHS/United States ; T32 GM007315/GM/NIGMS NIH HHS/United States ; R01 CA215607/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Biomarkers ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Colorectal Neoplasms/*metabolism/*pathology ; Disease Models, Animal ; Energy Metabolism ; *Gastrointestinal Microbiome ; Glutathione/metabolism ; Glyceraldehyde/*analogs & derivatives/metabolism/pharmacology ; Host Microbial Interactions ; Humans ; Intestinal Mucosa/metabolism/microbiology/pathology ; Metabolomics/methods ; Metagenomics/methods ; Mice ; Models, Biological ; *Oxidation-Reduction/drug effects ; Oxidative Stress ; Propane/*metabolism/pharmacology ; Signal Transduction ; Xenograft Model Antitumor Assays ; }, abstract = {Microbial dysbiosis is a colorectal cancer (CRC) hallmark and contributes to inflammation, tumor growth, and therapy response. Gut microbes signal via metabolites, but how the metabolites impact CRC is largely unknown. We interrogated fecal metabolites associated with mouse models of colon tumorigenesis with varying mutational load. We find that microbial metabolites from healthy mice or humans are growth-repressive, and this response is attenuated in mice and patients with CRC. Microbial profiling reveals that Lactobacillus reuteri and its metabolite, reuterin, are downregulated in mouse and human CRC. Reuterin alters redox balance, and reduces proliferation and survival in colon cancer cells. Reuterin induces selective protein oxidation and inhibits ribosomal biogenesis and protein translation. Exogenous Lactobacillus reuteri restricts colon tumor growth, increases tumor reactive oxygen species, and decreases protein translation in vivo. Our findings indicate that a healthy microbiome and specifically, Lactobacillus reuteri, is protective against CRC through microbial metabolite exchange.}, } @article {pmid34949778, year = {2022}, author = {Shi, ZJ and Dimitrov, B and Zhao, C and Nayfach, S and Pollard, KS}, title = {Fast and accurate metagenotyping of the human gut microbiome with GT-Pro.}, journal = {Nature biotechnology}, volume = {40}, number = {4}, pages = {507-516}, pmid = {34949778}, issn = {1546-1696}, mesh = {*Gastrointestinal Microbiome/genetics ; Genotype ; Humans ; Metagenome/genetics ; Metagenomics/methods ; *Microbiota/genetics ; Software ; }, abstract = {Single nucleotide polymorphisms (SNPs) in metagenomics are used to quantify population structure, track strains and identify genetic determinants of microbial phenotypes. However, existing alignment-based approaches for metagenomic SNP detection require high-performance computing and enough read coverage to distinguish SNPs from sequencing errors. To address these issues, we developed the GenoTyper for Prokaryotes (GT-Pro), a suite of methods to catalog SNPs from genomes and use unique k-mers to rapidly genotype these SNPs from metagenomes. Compared to methods that use read alignment, GT-Pro is more accurate and two orders of magnitude faster. Using high-quality genomes, we constructed a catalog of 104 million SNPs in 909 human gut species and used unique k-mers targeting this catalog to characterize the global population structure of gut microbes from 7,459 samples. GT-Pro enables fast and memory-efficient metagenotyping of millions of SNPs on a personal computer.}, } @article {pmid34946200, year = {2021}, author = {Bordugo, A and Salvetti, E and Rodella, G and Piazza, M and Dianin, A and Amoruso, A and Piacentini, G and Pane, M and Torriani, S and Vitulo, N and Felis, GE}, title = {Assessing Gut Microbiota in an Infant with Congenital Propionic Acidemia before and after Probiotic Supplementation.}, journal = {Microorganisms}, volume = {9}, number = {12}, pages = {}, pmid = {34946200}, issn = {2076-2607}, abstract = {Propionic Acidemia (PA) is a rare inherited metabolic disorder caused by the enzymatic block of propionyl-CoA carboxylase with the consequent accumulation of propionic acid, which is toxic for the brain and cardiac cells. Since a considerable amount of propionate is produced by intestinal bacteria, interest arose in the attempt to reduce propionate-producing bacteria through a monthly antibiotic treatment of metronidazole. In the present study, we investigated the gut microbiota structure of an infant diagnosed at 4 days of life through Expanded Newborn Screening (NBS) and treated the child following international guidelines with a special low-protein diet, specific medications and strict biochemical monitoring. Microbiota composition was assessed during the first month of life, and the presence of Bacteroides fragilis, known to be associated with propionate production, was effectively decreased by metronidazole treatment. After five antibiotic therapy cycles, at 4 months of age, the infant was supplemented with a daily mixture of three bifidobacterial strains, known not to be propionate producers. The supplementation increased the population of bifidobacteria, with Bifidobacterium breve as the dominating species; Ruminococcus gnavus, an acetate and formate producer, was also identified. Metabarcoding analysis, compared with low coverage whole metagenome sequencing, proved to capture all the microbial biodiversity and could be the elected tool for fast and cost-effective monitoring protocols to be implemented in the follow up of rare metabolic disorders such as PA. Data obtained could be a possible starting point to set up tailored microbiota modification treatment studies in the attempt to improve the quality of life of people affected by propionic acidemia.}, } @article {pmid34941731, year = {2021}, author = {Hu, D and Giesy, JP and Guo, M and Ung, WK and Kong, Y and Mok, KM and Lee, SM}, title = {Temporal Patterns of Bacterial and Viral Communities during Algae Blooms of a Reservoir in Macau.}, journal = {Toxins}, volume = {13}, number = {12}, pages = {}, pmid = {34941731}, issn = {2072-6651}, mesh = {Bacteria/*growth & development ; Biodiversity ; Environmental Monitoring ; *Eutrophication ; Macau ; RNA, Ribosomal, 16S ; Viruses/*growth & development ; *Water Microbiology ; }, abstract = {Compositions of microbial communities associated with blooms of algae in a storage reservoir in Macau, China were investigated between 2013 and 2016. Algae were enumerated by visible light microscopy. Profiles of organisms in water were examined by 16S rRNA sequences and viral metagenomics, based on next generation sequencing. Results of 16S rRNA sequencing indicated that majority of the identified organisms were bacteria closely related to Proteobacteria, Cyanobacteria, Verrucomicrobia, Bacteroidetes, and Actinobacteria. Metagenomics sequences demonstrated that the dominant virus was Phycodnavirus, accounting for 70% of the total population. Patterns of relative numbers of bacteria in the microbial community and their temporal changes were determined through alpha diversity indices, principal coordinates analysis (PCoA), relative abundance, and visualized by Venn diagrams. Ways in which the bacterial and viral communities are influenced by various water-related variables were elucidated based on redundancy analysis (RDA). Relationships of the relative numbers of bacteria with trophic status in a reservoir used for drinking water in Macau, provided insight into associations of Phycodnavirus and Proteobacteria with changes in blooms of algae.}, } @article {pmid34940122, year = {2021}, author = {Ghannoum, MA and McCormick, TS and Retuerto, M and Bebek, G and Cousineau, S and Hartman, L and Barth, C and Schrom, K}, title = {Evaluation of Microbiome Alterations Following Consumption of BIOHM, a Novel Probiotic.}, journal = {Current issues in molecular biology}, volume = {43}, number = {3}, pages = {2135-2146}, pmid = {34940122}, issn = {1467-3045}, support = {R01 AI145289/AI/NIAID NIH HHS/United States ; AI145289//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Candida albicans ; Dysbiosis/*microbiology ; Healthy Volunteers ; Humans ; Metagenomics/methods ; Microbial Interactions ; *Microbiota ; Mycobiome ; Probiotics/*administration & dosage ; RNA, Ribosomal, 16S ; }, abstract = {Gastrointestinal microbiome dysbiosis may result in harmful effects on the host, including those caused by inflammatory bowel diseases (IBD). The novel probiotic BIOHM, consisting of Bifidobacterium breve, Saccharomyces boulardii, Lactobacillus acidophilus, L. rhamnosus, and amylase, was developed to rebalance the bacterial-fungal gut microbiome, with the goal of reducing inflammation and maintaining a healthy gut population. To test the effect of BIOHM on human subjects, we enrolled a cohort of 49 volunteers in collaboration with the Fermentation Festival group (Santa Barbara, CA, USA). The profiles of gut bacterial and fungal communities were assessed via stool samples collected at baseline and following 4 weeks of once-a-day BIOHM consumption. Mycobiome analysis following probiotic consumption revealed an increase in Ascomycota levels in enrolled individuals and a reduction in Zygomycota levels (p value < 0.01). No statistically significant difference in Basidiomycota was detected between pre- and post-BIOHM samples and control abundance profiles (p > 0.05). BIOHM consumption led to a significant reduction in the abundance of Candida genus in tested subjects (p value < 0.013), while the abundance of C. albicans also trended lower than before BIOHM use, albeit not reaching statistical significance. A reduction in the abundance of Firmicutes at the phylum level was observed following BIOHM use, which approached levels reported for control individuals reported in the Human Microbiome Project data. The preliminary results from this clinical study suggest that BIOHM is capable of significantly rebalancing the bacteriome and mycobiome in the gut of healthy individuals, suggesting that further trials examining the utility of the BIOHM probiotic in individuals with gastrointestinal symptoms, where dysbiosis is considered a source driving pathogenesis, are warranted.}, } @article {pmid34939673, year = {2022}, author = {Rahaman, MM and Sarkar, MMH and Rahman, MS and Islam, MR and Islam, I and Saha, O and Akter, S and Banu, TA and Jahan, I and Habib, MA and Goswami, B and Bari, L and Malek, MA and Khan, MS}, title = {Genomic characterization of the dominating Beta, V2 variant carrying vaccinated (Oxford-AstraZeneca) and nonvaccinated COVID-19 patient samples in Bangladesh: A metagenomics and whole-genome approach.}, journal = {Journal of medical virology}, volume = {94}, number = {4}, pages = {1670-1688}, doi = {10.1002/jmv.27537}, pmid = {34939673}, issn = {1096-9071}, mesh = {Adolescent ; Adult ; Aged ; Bacteria/classification/genetics ; Bacterial Infections/epidemiology/microbiology/virology ; Bangladesh/epidemiology ; COVID-19/epidemiology/microbiology/prevention & control/*virology ; ChAdOx1 nCoV-19/*administration & dosage ; Coinfection/epidemiology/microbiology/virology ; Drug Resistance, Bacterial/genetics ; Female ; Genome, Bacterial/genetics ; Genome, Viral/genetics ; Humans ; Male ; *Metagenomics ; Microbiota/genetics ; Middle Aged ; Mutation ; Phylogeny ; SARS-CoV-2/classification/*genetics/isolation & purification ; Selection, Genetic ; Vaccination ; Viral Proteins/genetics ; Young Adult ; }, abstract = {Bangladesh is experiencing a second wave of COVID-19 since March 2021, despite the nationwide vaccination drive with ChAdOx1 (Oxford-AstraZeneca) vaccine from early February 2021. Here, we characterized 19 nasopharyngeal swab (NPS) samples from COVID-19 suspect patients using genomic and metagenomic approaches. Screening for SARS-CoV-2 by reverse transcriptase polymerase chain reaction and metagenomic sequencing revealed 17 samples of COVID-19 positive (vaccinated = 10, nonvaccinated = 7) and 2 samples of COVID-19 negative. We did not find any significant correlation between associated factors including vaccination status, age or sex of the patients, diversity or abundance of the coinfected organisms/pathogens, and the abundance of SARS-CoV-2. Though the first wave of the pandemic was dominated by clade 20B, Beta, V2 (South African variant) dominated the second wave (January 2021 to May 2021), while the third wave (May 2021 to September 2021) was responsible for Delta variants of the epidemic in Bangladesh including both vaccinated and unvaccinated infections. Noteworthily, the receptor binding domain (RBD) region of S protein of all the isolates harbored similar substitutions including K417N, E484K, and N501Y that signify the Beta, while D614G, D215G, D80A, A67V, L18F, and A701V substitutions were commonly found in the non-RBD region of Spike proteins. ORF7b and ORF3a genes underwent a positive selection (dN/dS ratio 1.77 and 1.24, respectively), while the overall S protein of the Bangladeshi SARS-CoV-2 isolates underwent negative selection pressure (dN/dS = 0.621). Furthermore, we found different bacterial coinfections like Streptococcus agalactiae, Neisseria meningitidis, Elizabethkingia anophelis, Stenotrophomonas maltophilia, Klebsiella pneumoniae, and Pseudomonas plecoglossicida, expressing a number of antibiotic resistance genes such as tetA and tetM. Overall, this approach provides valuable insights on the SARS-CoV-2 genomes and microbiome composition from both vaccinated and nonvaccinated patients in Bangladesh.}, } @article {pmid34939130, year = {2023}, author = {Trzebny, A and Slodkowicz-Kowalska, A and Björkroth, J and Dabert, M}, title = {Microsporidian Infection in Mosquitoes (Culicidae) Is Associated with Gut Microbiome Composition and Predicted Gut Microbiome Functional Content.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {247-263}, pmid = {34939130}, issn = {1432-184X}, support = {2020/37/N/NZ8/01735//Narodowe Centrum Nauki/ ; 05/IDUB/2019/94//Initiative of Excellence - Research University at Adam Mickiewicz University, Poznan, Poland/ ; }, mesh = {Animals ; Female ; *Culicidae/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria/genetics ; *Microsporidia/genetics ; }, abstract = {The animal gut microbiota consist of many different microorganisms, mainly bacteria, but archaea, fungi, protozoans, and viruses may also be present. This complex and dynamic community of microorganisms may change during parasitic infection. In the present study, we investigated the effect of the presence of microsporidians on the composition of the mosquito gut microbiota and linked some microbiome taxa and functionalities to infections caused by these parasites. We characterised bacterial communities of 188 mosquito females, of which 108 were positive for microsporidian DNA. To assess how bacterial communities change during microsporidian infection, microbiome structures were identified using 16S rRNA microbial profiling. In total, we identified 46 families and four higher taxa, of which Comamonadaceae, Enterobacteriaceae, Flavobacteriaceae and Pseudomonadaceae were the most abundant mosquito-associated bacterial families. Our data suggest that the mosquito gut microbial composition varies among host species. In addition, we found a correlation between the microbiome composition and the presence of microsporidians. The prediction of metagenome functional content from the 16S rRNA gene sequencing suggests that microsporidian infection is characterised by some bacterial species capable of specific metabolic functions, especially the biosynthesis of ansamycins and vancomycin antibiotics and the pentose phosphate pathway. Moreover, we detected a positive correlation between the presence of microsporidian DNA and bacteria belonging to Spiroplasmataceae and Leuconostocaceae, each represented by a single species, Spiroplasma sp. PL03 and Weissella cf. viridescens, respectively. Additionally, W. cf. viridescens was observed only in microsporidian-infected mosquitoes. More extensive research, including intensive and varied host sampling, as well as determination of metabolic activities based on quantitative methods, should be carried out to confirm our results.}, } @article {pmid34938813, year = {2021}, author = {Wang, S and Chen, H and Wen, X and Mu, J and Sun, M and Song, X and Liu, B and Chen, J and Fan, X}, title = {The Efficacy of Fecal Microbiota Transplantation in Experimental Autoimmune Encephalomyelitis: Transcriptome and Gut Microbiota Profiling.}, journal = {Journal of immunology research}, volume = {2021}, number = {}, pages = {4400428}, pmid = {34938813}, issn = {2314-7156}, mesh = {Animals ; Biomarkers ; Disease Management ; Disease Models, Animal ; Disease Susceptibility/immunology ; Encephalomyelitis, Autoimmune, Experimental/diagnosis/*etiology/*therapy ; *Fecal Microbiota Transplantation ; Female ; *Gastrointestinal Microbiome ; Intestinal Mucosa/metabolism/pathology ; Metagenomics/methods ; Mice ; Phylogeny ; RNA, Ribosomal, 16S ; Severity of Illness Index ; Spinal Cord/immunology/metabolism/pathology ; *Transcriptome ; Treatment Outcome ; }, abstract = {OBJECTIVE: To study the protective effect of fecal microbiota transplantation (FMT) on experimental autoimmune encephalomyelitis (EAE) and reveal its potential intestinal microflora-dependent mechanism through analyses of the intestinal microbiota and spinal cord transcriptome in mice.

METHOD: We measured the severity of disease by clinical EAE scores and H&E staining. Gut microbiota alteration in the gut and differentially expressed genes (DEGs) in the spinal cord were analyzed through 16S rRNA and transcriptome sequencing. Finally, we analyzed associations between the relative abundance of intestinal microbiota constituents and DEGs.

RESULTS: We observed that clinical EAE scores were lower in the EAE+FMT group than in the EAE group. Meanwhile, mice in the EAE+FMT group also had a lower number of infiltrating cells. The results of 16S rRNA sequence analysis showed that FMT increased the relative abundance of Firmicutes and Proteobacteria and reduced the abundance of Bacteroides and Actinobacteria. Meanwhile, FMT could modulate gut microbiota balance, especially via increasing the relative abundance of g_Adlercreutzia, g_Sutterella, g_Prevotella_9, and g_Tyzzerella_3 and decreasing the relative abundance of g_Turicibacter. Next, we analyzed the transcriptome of mouse spinal cord tissue and found that 1476 genes were differentially expressed between the EAE and FMT groups. The analysis of these genes showed that FMT mainly participated in the inflammatory response. Correlation analysis between gut microbes and transcriptome revealed that the relative abundance of Adlercreutzia was correlated with the expression of inflammation-related genes negatively, including Casp6, IL1RL2 (IL-36R), IL-17RA, TNF, CCL3, CCR5, and CCL8, and correlated with the expression of neuroprotection-related genes positively, including Snap25, Edil3, Nrn1, Cpeb3, and Gpr37.

CONCLUSION: Altogether, FMT may selectively regulate gene expression to improve inflammation and maintain the stability of the intestinal environment in a gut microbiota-dependent manner.}, } @article {pmid34937787, year = {2022}, author = {Mirza, AI and Zhu, F and Knox, N and Forbes, JD and Van Domselaar, G and Bernstein, CN and Graham, M and Marrie, RA and Hart, J and Yeh, EA and Arnold, DL and Bar-Or, A and O'Mahony, J and Zhao, Y and Hsiao, W and Banwell, B and Waubant, E and Tremlett, H}, title = {Metagenomic Analysis of the Pediatric-Onset Multiple Sclerosis Gut Microbiome.}, journal = {Neurology}, volume = {98}, number = {10}, pages = {e1050-e1063}, pmid = {34937787}, issn = {1526-632X}, mesh = {Adolescent ; Adult ; Canada ; Child ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; *Multiple Sclerosis ; Young Adult ; }, abstract = {BACKGROUND AND OBJECTIVES: Little is known of the functional potential of the gut microbiome in pediatric-onset multiple sclerosis (MS). We performed metagenomic analyses using stool samples from individuals with pediatric-onset MS and unaffected controls.

METHODS: Persons ≤21 years old enrolled in the Canadian Pediatric Demyelinating Disease Network providing a stool sample were eligible. Twenty patients with MS (McDonald criteria) with symptom onset <18 years were matched to 20 controls by sex, age (±3 years), stool consistency, and race. Microbial taxonomy and functional potentials were estimated from stool sample-derived metagenomic reads and compared by disease status (MS vs controls) and disease-modifying drug (DMD) exposure using alpha diversity, relative abundance, and prevalence using Wilcoxon rank sum, ALDEx2, and Fisher exact tests, respectively.

RESULTS: Individuals with MS were aged 13.6 years (mean) at symptom onset and 8 were DMD-naive. Mean ages at stool sample were 16.1 and 15.4 years for MS and control participants, respectively; 80% were girls. Alpha diversity of enzymes and proteins did not differ by disease or DMD status (p > 0.20), but metabolic pathways, gene annotations, and microbial taxonomy did. Individuals with MS (vs controls) exhibited higher methanogenesis prevalence (odds ratio 10, p = 0.044) and Methanobrevibacter abundance (log2 fold change [LFC] 1.7, p = 0.0014), but lower homolactic fermentation abundance (LFC -0.48, p = 0.039). Differences by DMD status included lower phosphate butyryl transferase for DMD-naive vs exposed patients with MS (LFC -1.0, p = 0.033).

DISCUSSION: The gut microbiome's functional potential and taxonomy differed between individuals with pediatric-onset MS vs controls, including higher prevalence of a methane-producing pathway from Archaea and depletion of the lactate fermentation pathway. DMD exposure was associated with butyrate-producing enzyme enrichment. Together these findings indicate that the gut microbiome of individuals with MS may have a disturbed functional potential.}, } @article {pmid34936382, year = {2021}, author = {Jo, JH and Harkins, CP and Schwardt, NH and Portillo, JA and , and Zimmerman, MD and Carter, CL and Hossen, MA and Peer, CJ and Polley, EC and Dartois, V and Figg, WD and Moutsopoulos, NM and Segre, JA and Kong, HH}, title = {Alterations of human skin microbiome and expansion of antimicrobial resistance after systemic antibiotics.}, journal = {Science translational medicine}, volume = {13}, number = {625}, pages = {eabd8077}, pmid = {34936382}, issn = {1946-6242}, support = {S10 OD023524/OD/NIH HHS/United States ; Z99 AR999999/ImNIH/Intramural NIH HHS/United States ; ZIA BC010938/ImNIH/Intramural NIH HHS/United States ; ZIA BC011558/ImNIH/Intramural NIH HHS/United States ; }, mesh = {*Anti-Bacterial Agents/therapeutic use ; Drug Resistance, Bacterial/genetics ; Humans ; *Microbiota ; Prospective Studies ; Trimethoprim, Sulfamethoxazole Drug Combination ; }, abstract = {Although systemic antibiotics are critical in controlling infections and reducing morbidity and mortality, overuse of antibiotics is presumed to contribute to negative repercussions such as selection of antimicrobial-resistant organisms and collateral damage to commensal microbes. In a prospective, randomized study of four clinically relevant antibiotic regimens [doxycycline (20 mg or 100 mg), cephalexin, or trimethoprim/sulfamethoxazole], we investigated microbial alterations on skin after administration of systemic antibiotics to healthy human volunteers. Samples from different skin and oral sites, as well as stool, were collected before, during, and up to 1 year after antibiotic use, and shotgun metagenomic sequencing was performed. Taxonomic analysis showed that subjects receiving doxycycline 100 mg and trimethoprim/sulfamethoxazole (TMP/SMX) exhibited greater changes to their skin microbial communities, as compared to those receiving other regimens or untreated controls. Oral and stool microbiota also demonstrated fluctuations after antibiotics. Bacterial culturing in combination with whole-genome sequencing revealed specific emergence, expansion, and persistence of antibiotic-resistant staphylococci harboring tetK or tetL and dfrC or dfrG genes in all subjects who received doxycycline 100 mg or TMP/SMX, respectively. Last, analysis of metagenomic data revealed an increase of genes involved in gene mobilization, indicating stress responses of microbes to antibiotics. Collectively, these findings demonstrate direct, long-lasting effects of antibiotics on skin microbial communities, highlighting the skin microbiome as a site for the development and persistence of antibiotic resistance and the risks of overprescribing.}, } @article {pmid34935421, year = {2021}, author = {Shen, S and Huo, D and Ma, C and Jiang, S and Zhang, J}, title = {Expanding the Colorectal Cancer Biomarkers Based on the Human Gut Phageome.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0009021}, pmid = {34935421}, issn = {2165-0497}, mesh = {Austria ; Bacteriophages/classification/genetics/*isolation & purification ; Biomarkers, Tumor ; China ; Cohort Studies ; Colitis, Ulcerative/virology ; Colorectal Neoplasms/*virology ; Crohn Disease/virology ; Feces/virology ; Gastrointestinal Tract/virology ; Humans ; Japan ; Metagenome ; *Virome ; }, abstract = {With the increasing prevalence of colorectal cancer (CRC), extending the present biomarkers for the diagnosis of colorectal cancer is crucial. Previous studies have highlighted the importance of bacteriophages in gastrointestinal diseases, suggesting the potential value of gut phageome in early CRC diagnostic. Here, based on 317 metagenomic samples of three discovery cohorts collected from China (Hong Kong), Austria, and Japan, five intestinal bacteriophages, including Fusobacterium nucleatum, Peptacetobacter hiranonis, and Parvimonas micra phages were identified as potential CRC biomarkers. The five CRC enriched bacteriophagic markers classified patients from controls with an area under the receiver-operating characteristics curve (AUC) of 0.8616 across different populations. Subsequently, we used a total of 80 samples from China (Hainan) and Italy for validation. The AUC of the validation cohort is 0.8197. Moreover, to further explore the specificity of the five intestinal bacteriophage biomarkers in a broader background, we performed a confirmatory meta-analysis using two inflammatory bowel disease cohorts, ulcerative colitis (UC) and Crohn's disease (CD). Excitingly, we observed that the five CRC-enriched phage markers also exhibited high discrimination in UC (AUC = 78.02%). Unfortunately, the five CRC-rich phage markers did not show high resolution in CD (AUC = 48.00%). The present research expands the potential of microbial biomarkers in CRC diagnosis by building a more accurate classification model based on the human gut phageome, providing a new perspective for CRC gut phagotherapy. IMPORTANCE Worldwide, by 2020, colorectal cancer has become the third most common cancer after lung and breast cancer. Phages are strictly host-specific, and this specificity makes them more accurate as biomarkers, but phage biomarkers for colorectal cancer have not been thoroughly explored. Therefore, it is crucial to extend the existing phage biomarkers for the diagnosis of colorectal cancer. Here, we innovatively constructed a relatively accurate prediction model, including: three discovery cohorts, two additional validation cohorts and two cross-disease cohorts. A total of five possible biomarkers of intestinal bacteriophages were obtained. They are Peptacetobacter hiranonis Phage, Fusobacterium nucleatum animalis 7_1 Phage, Fusobacterium nucleatum polymorphum Phage, Fusobacterium nucleatum animalis 4_8 Phage, and Parvimonas micra Phage. This study aims at identifying fine-scale species-strain level phage biomarkers for colorectal cancer diseases, so as to expand the existing CRC biomarkers and provide a new perspective for intestinal phagocytosis therapy of colorectal cancer.}, } @article {pmid34932985, year = {2022}, author = {Kim, AH and Armah, G and Dennis, F and Wang, L and Rodgers, R and Droit, L and Baldridge, MT and Handley, SA and Harris, VC}, title = {Enteric virome negatively affects seroconversion following oral rotavirus vaccination in a longitudinally sampled cohort of Ghanaian infants.}, journal = {Cell host & microbe}, volume = {30}, number = {1}, pages = {110-123.e5}, pmid = {34932985}, issn = {1934-6069}, support = {R01 AI139314/AI/NIAID NIH HHS/United States ; R01 OD024917/OD/NIH HHS/United States ; RC2 DK116713/DK/NIDDK NIH HHS/United States ; T32 AI007163/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/classification ; Bacteriophages ; Cohort Studies ; Coinfection ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Ghana ; Humans ; Immunization ; Infant ; Intestine, Small/*virology ; Male ; Metagenome ; Rotavirus/*physiology ; Rotavirus Infections/*immunology/virology ; Rotavirus Vaccines ; Seroconversion ; Vaccination ; Vaccines, Attenuated ; Virome/*physiology ; }, abstract = {Rotavirus vaccines (RVVs) have substantially diminished mortality from severe rotavirus (RV) gastroenteritis but are significantly less effective in low- and middle-income countries (LMICs), limiting their life-saving potential. The etiology of RVV's diminished effectiveness remains incompletely understood, but the enteric microbiota has been implicated in modulating immunity to RVVs. Here, we analyze the enteric microbiota in a longitudinal cohort of 122 Ghanaian infants, evaluated over the course of 3 Rotarix vaccinations between 6 and 15 weeks of age, to assess whether bacterial and viral populations are distinct between non-seroconverted and seroconverted infants. We identify bacterial taxa including Streptococcus and a poorly classified taxon in Enterobacteriaceae as positively correlating with seroconversion. In contrast, both bacteriophage diversity and detection of Enterovirus B and multiple novel cosaviruses are negatively associated with RVV seroconversion. These findings suggest that virome-RVV interference is an underappreciated cause of poor vaccine performance in LMICs.}, } @article {pmid34931478, year = {2022}, author = {Mashiah, J and Karady, T and Fliss-Isakov, N and Sprecher, E and Slodownik, D and Artzi, O and Samuelov, L and Ellenbogen, E and Godneva, A and Segal, E and Maharshak, N}, title = {Clinical efficacy of fecal microbial transplantation treatment in adults with moderate-to-severe atopic dermatitis.}, journal = {Immunity, inflammation and disease}, volume = {10}, number = {3}, pages = {e570}, pmid = {34931478}, issn = {2050-4527}, mesh = {Adult ; *Dermatitis, Atopic/drug therapy ; Fecal Microbiota Transplantation/adverse effects/methods ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Treatment Outcome ; }, abstract = {BACKGROUND: Atopic dermatitis (AD) is a remitting relapsing chronic eczematous pruritic disease. Several studies suggest that gut microbiota may influence AD by immune system regulation.

METHODS: We performed the first in-human efficacy and safety assessment of fecal microbiota transplantation (FMT) for AD adult patients. All patients received 2 placebo transplantations followed by 4 FMTs each 2 weeks apart. AD severity and fecal microbiome profile were evaluated by the Scoring Atopic Dermatitis Score (SCORAD), the weekly frequency of topical corticosteroids usage, and gut microbiota metagenomic analysis, at the study beginning, before every FMT, and 1-8 months after the last FMT.

RESULTS: Nine patients completed the study protocol. There was no significant change in the SCORAD score following the two placebo transplants. The average SCORAD score significantly decreased from baseline at Weeks 4-12 (before and 2 weeks after 4 times of FMT) (59.2 ± 34.9%, Wilcoxon p = .011), 50% and 75% decrease was achieved by 7 (77%) and 4 (44%) patients, respectively. At Week 18 (8 weeks after the last FMT) the average SCORAD score decreased from baseline at Week 4 (85.5 ± 8.4%, Wilcoxon p = .018), 50% and 75% decrease was achieved by 7 (77%) and 6 (66.7%) patients respectively. Weekly topical corticosteroids usage was diminished during the study and follow-up period as well. Two patients had a quick relapse and were switched to a different treatment. Two patients developed exacerbations alleviated after an additional fifth FMT. Metagenomic analysis of the fecal microbiota of patients and donors showed bacterial strains transmission from donors to patients. No adverse events were recorded during the study and follow-up period.

CONCLUSIONS: FMT may be a safe and effective therapeutic intervention for AD patients, associated with transfer of specific microbial species from the donors to the patients. Further studies are required to reconfirm these results.}, } @article {pmid34930242, year = {2021}, author = {Olekhnovich, EI and Batotsyrenova, EG and Yunes, RA and Kashuro, VA and Poluektova, EU and Veselovsky, VA and Ilina, EN and Danilenko, VN and Klimina, KM}, title = {The effects of Levilactobacillus brevis on the physiological parameters and gut microbiota composition of rats subjected to desynchronosis.}, journal = {Microbial cell factories}, volume = {20}, number = {1}, pages = {226}, pmid = {34930242}, issn = {1475-2859}, support = {075-15-2019-1669//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {Animals ; Circadian Rhythm/*physiology ; *Darkness ; Gastrointestinal Microbiome/genetics/*physiology ; Levilactobacillus brevis/*physiology ; *Light ; Male ; Probiotics/administration & dosage ; Rats ; }, abstract = {BACKGROUND: All living organisms have developed during evolution complex time-keeping biological clocks that allowed them to stay attuned to their environments. Circadian rhythms cycle on a near 24 h clock. These encompass a variety of changes in the body ranging from blood hormone levels to metabolism, to the gut microbiota composition and others. The gut microbiota, in return, influences the host stress response and the physiological changes associated with it, which makes it an important determinant of health. Lactobacilli are traditionally consumed for their prophylactic and therapeutic benefits against various diseases, namely, the inflammatory bowel syndrome, and even emerged recently as promising psychobiotics. However, the potential role of lactobacilli in the normalization of circadian rhythms has not been addressed.

RESULTS: Two-month-old male rats were randomly divided into three groups and housed under three different light/dark cycles for three months: natural light, constant light and constant darkness. The strain Levilactobacillus brevis 47f was administered to rats at a dose of 0.5 ml per rat for one month and The rats were observed for the following two months. As a result, we identified the biomarkers associated with intake of L. brevis 47f. Changing the light regime for three months depleted the reserves of the main buffer in the cell-reduced glutathione. Intake of L. brevis 47f for 30 days restored cellular reserves of reduced glutathione and promoted redox balance. Our results indicate that the levels of urinary catecholamines correlated with light/dark cycles and were influenced by intake of L. brevis 47f. The gut microbiota of rats was also influenced by these factors. L. brevis 47f intake was associated with an increase in the relative abundance of Faecalibacterium and Roseburia and a decrease in the relative abundance of Prevotella and Bacteroides.

CONCLUSIONS: The results of this study show that oral administration of L. brevis 47f, for one month, to rats housed under abnormal lightning conditions (constant light or constant darkness) normalized their physiological parameters and promoted the gut microbiome's balance.}, } @article {pmid34928868, year = {2021}, author = {Nobel, YR and Rozenberg, F and Park, H and Freedberg, DE and Blaser, MJ and Green, PHR and Uhlemann, AC and Lebwohl, B}, title = {Lack of Effect of Gluten Challenge on Fecal Microbiome in Patients With Celiac Disease and Non-Celiac Gluten Sensitivity.}, journal = {Clinical and translational gastroenterology}, volume = {12}, number = {12}, pages = {e00441}, pmid = {34928868}, issn = {2155-384X}, support = {R01 AI116939/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; *Celiac Disease ; *Gastrointestinal Microbiome/physiology ; Glutens/adverse effects ; Humans ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; }, abstract = {INTRODUCTION: Celiac disease (CD) may be associated with gut microbial dysbiosis. Whether discrete gluten exposure in subjects with well-controlled disease on a gluten-free diet impacts the gut microbiome is unknown and may have implications for understanding disease activity and symptoms. We conducted a prospective study to evaluate the impact of gluten exposure on the gut microbiome in patients with CD and nonceliac gluten sensitivity (NCGS).

METHODS: Subjects with CD (n = 9) and NCGS (n = 8) previously on a gluten-free diet were administered a 14-day gluten challenge (5 g of gluten per day) and compared with controls (n = 8) on a usual gluten-containing diet. Stool was collected for fecal microbiome analysis using 16S rRNA gene and metagenomic sequencing before, during, and after the gluten challenge. Symptoms were assessed using 2 validated clinical scales.

RESULTS: Among subjects with CD and NCGS, there were no significant fecal microbial changes in response to gluten challenge. Gut microbiome composition differed among controls, subjects with CD, and subjects with NCGS at baseline, and these differences persisted despite gluten exposure. Gastrointestinal and general health symptoms reported by subjects with CD and NCGS were worst in the middle of gluten challenge and lessened by its end, with no consistent associations with gut microbiome composition.

DISCUSSION: Pre-existing fecal microbiome diversity was unaffected by gluten challenge in adult subjects with CD and NCGS. These findings suggest that current microbiome status is unrelated to current disease activity and disease severity.}, } @article {pmid34925329, year = {2021}, author = {Guo, Y and Huang, X and Sun, X and Yu, Y and Wang, Y and Zhang, B and Cao, J and Wen, S and Li, Y and Wang, X and Cai, S and Xia, W and Wei, F and Duan, J and Dong, H and Guo, S and Zhang, F and Zheng, D and Sun, Z}, title = {The Underrated Salivary Virome of Men Who Have Sex With Men Infected With HIV.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {759253}, pmid = {34925329}, issn = {1664-3224}, mesh = {Adult ; Cross-Sectional Studies ; HIV Infections/*virology ; Homosexuality, Male ; Humans ; Male ; Metagenomics ; Saliva/*virology ; *Sexual and Gender Minorities ; Virome ; }, abstract = {Salivary virome is important for oral ecosystem, but there are few reports on people living with HIV. We performed metagenomic sequencing to compare composition and functional genes of salivary virobiota between one HIV-negative and four HIV-positive groups in which participants were all men who have sex with men (MSM) with different immunosuppression statuses (five samples per group) to find the evidence that salivary virobiota plays a role in the pathogenesis of oral disease. Acute-stage subjects achieved a positive result of HIV RNA, but HIV antibody negative or indeterminate, whereas individuals with mild, moderate, and severe immunosuppression exhibited CD4[+] T-lymphocyte counts of at least 500, 200-499, and less than 200 cells/μL or opportunistic infection, respectively. The results showed the composition of salivary virus genera in subjects with mild immunosuppression was the most similar to that in healthy people, followed by that in the acute stage; under severe immunosuppression, virus genera were suppressed and more similar to that under moderate immunosuppression. Furthermore, abnormally high abundance of Lymphocryptovirus was particularly obvious in MSM with HIV infection. Analysis of KEGG Pathway revealed that Caulobacter cell cycle, which affects cell duplication, became shorter in HIV-positive subjects. It is worth noting that in acute-stage participants, protein digestion and absorption related to the anti-HIV-1 activity of secretory leukocyte protease inhibitor was increased. Moreover, in the severely immunosuppressed subjects, glutathione metabolism, which is associated with the activation of lymphocytes, was enhanced. Nevertheless, the ecological dysbiosis in HIV-positive salivary virobiota possibly depended on the changes in blood viral load, and salivary dysfunction of MSM infected with HIV may be related to CD4 counts. Ribonucleoside diphosphate reductase subunit M1 in purine metabolism was negatively correlated, though weakly, to CD4 counts, which may be related to the promotion of HIV-1 DNA synthesis in peripheral blood lymphocytes. 7-Cyano-7-deazaguanine synthase in folate biosynthesis was weakly positively correlated with HIV viral load, suggesting that this compound was produced excessively to correct oral dysfunction for maintaining normal cell development. Despite the limited number of samples, the present study provided insight into the potential role of salivary virome in the oral function of HIV infected MSM.}, } @article {pmid34923897, year = {2022}, author = {Bihl, S and de Goffau, M and Podlesny, D and Segata, N and Shanahan, F and Walter, J and Fricke, WF}, title = {When to suspect contamination rather than colonization - lessons from a putative fetal sheep microbiome.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2005751}, pmid = {34923897}, issn = {1949-0984}, mesh = {Animals ; Bacteria/classification/genetics/growth & development/*isolation & purification ; DNA Contamination ; Female ; Fetus/*microbiology ; *Gastrointestinal Microbiome ; Pregnancy ; Sheep/*microbiology ; }, abstract = {There is an ongoing controversy around the existence of a prenatal, fetal microbiome in humans, livestock, and other animals. The 'in utero microbial colonization' hypothesis challenges the clinical paradigm of the 'sterile womb' but has been criticized for its reliance on DNA-based evidence to detect microbiomes and the failure to conciliate the routine experimental derivation of germ-free animals from surgically resected embryos with a thriving fetal microbiome. In order to avoid the propagation of misinformation in the scientific literature, a critical assessment and careful review of newly published studies, particularly those that challenge the convincing current clinical dogma of the sterile womb, is of critical importance.We read with interest a recent publication that postulated the presence of a fetal microbiome in sheep, but questioned the plausibility of the reported findings and their meaningfulness to prove "microbial colonisation of the fetal gut […] in utero". We reanalyzed the published metagenomic and metatranscriptomic sequence data from the original publication and identified evidence for different types of contamination that affected all samples alike and could explain the reported findings without requiring the existence of a fetal microbiome.Our reanalysis challenges the reported findings as supportive of a prenatal fetal lamb microbiome. The shortcomings of the original analysis and data interpretation highlight common problems of low-biomass microbiome projects. We propose genomic independence of separate biological samples, i.e. distinctive profiles at the microbial strain level, as a potential new microbiome marker to increase confidence in metagenomics analyses of controversial low-biomass microbiomes.}, } @article {pmid34923019, year = {2022}, author = {Chen, X and Wang, J and Pan, C and Feng, L and Guo, Q and Chen, S and Xie, S}, title = {Metagenomic analysis reveals the response of microbial community in river sediment to accidental antimony contamination.}, journal = {The Science of the total environment}, volume = {813}, number = {}, pages = {152484}, doi = {10.1016/j.scitotenv.2021.152484}, pmid = {34923019}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Antimony/analysis/toxicity ; Genes, Bacterial ; Humans ; Metagenomics ; *Metals, Heavy ; *Microbiota ; Rivers ; }, abstract = {The mining of deposits containing metals like antimony (Sb) causes serious environmental issues that threaten human health and ecological systems. However, information on the effect of Sb on freshwater sediment microorganisms and the mechanism of microbial Sb resistance is still very limited. This was the first attempt to explore microbial communities in river sediments impacted by accidental Sb spill. Metagenomic analysis revealed the high relative abundance of Proteobacteria and Actinobacteria in all the studied river sediments, showing their advantage in resistance to Sb pollution. Under Sb stress, microbial functions related to DNA repair and ion transport were enhanced. Increase in heavy metal resistance genes (HMRGs), particularly Sb transport-related arsB gene, was observed at Sb spill-impacted sites. HMRGs were significantly correlated with ARGs and MGEs, and the abundant MGEs at Sb spill-impacted sites might contribute to the increase in HMRGs and ARGs via horizontal gene transfer. Deinococcus, Sphingopyxis and Paracoccus were identified as potential tolerant genera under Sb pressure and might be related to the transmission of HMRGs and ARGs. This study can add new insights towards the effect of accidental metal spill on sediment microbial community.}, } @article {pmid34922301, year = {2022}, author = {Gabashvili, E and Kobakhidze, S and Chkhikvishvili, T and Tabatadze, L and Tsiklauri, R and Dadiani, K and Koulouris, S and Kotetishvili, M}, title = {Metagenomic and Recombination Analyses of Antimicrobial Resistance Genes from Recreational Waters of Black Sea Coastal Areas and Other Marine Environments Unveil Extensive Evidence for Their both Intrageneric and Intergeneric Transmission across Genetically Very Diverse Microbial Communities.}, journal = {Marine genomics}, volume = {61}, number = {}, pages = {100916}, doi = {10.1016/j.margen.2021.100916}, pmid = {34922301}, issn = {1876-7478}, mesh = {Anti-Bacterial Agents/pharmacology ; Black Sea ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Humans ; *Metagenomics ; *Microbiota ; Recombination, Genetic ; }, abstract = {Microbial communities of marine coastal recreation waters have become large reservoirs of AMR genes (ARGs), contributing to the emergence and transmission of various zoonotic, foodborne and other infections that exhibit resistance to various antibiotics. Thus, it is highly imperative to determine ARGs assemblages as well as mechanisms and trajectories of their transmission across these microbial communities for our better understanding of the evolutionary trends of AMR (AMR). In this study, using metagenomics approaches, we screened for ARGs in recreation waters of the Black Sea coastal areas of the Batumi City (Georgia). Also, a large array of the recombination detection algorithms of the SplitsTree, RDP4, and GARD was applied to elucidate genetic recombination of ARGs and trajectories of their transmission across various marine microbial communities. The metagenomics analyses of sea water samples, obtained from across the above marine sites, could identify putative ARGs encoding for multidrug resistance efflux transporters mainly from the Major Facilitator and Resistance Nodulation Division superfamilies. The data, generated by SplitsTree (fit ≥95.619; bootstrap values ≥ 95; Phi p ≤ 0.0494), RDP4 (p ≤ 0.0490), and GARD, provided strong statistical evidence not only for intrageneric recombination of these ARGs, but also for their intergeneric recombination across fairly large and diverse microbial communities of marine environment. These bacteria included both human pathogenic and nonpathogenic species, exhibiting collectively the genera of Vibrio, Aeromonas, Synechococcus, Citromicrobium, Rhodobacteraceae, Pseudoalteromonas, Altererythrobacter, Erythrobacter, Altererythrobacter, Marivivens, Xuhuaishuia, and Loktanella. The above nonpathogenic bacteria are strongly suggested to contribute to ARGs transmission in marine ecosystems.}, } @article {pmid34920070, year = {2022}, author = {Zhang, L and Wang, Y and Wu, F and Wang, X and Feng, Y and Wang, Y}, title = {MDG, an Ophiopogon japonicus polysaccharide, inhibits non-alcoholic fatty liver disease by regulating the abundance of Akkermansia muciniphila.}, journal = {International journal of biological macromolecules}, volume = {196}, number = {}, pages = {23-34}, doi = {10.1016/j.ijbiomac.2021.12.036}, pmid = {34920070}, issn = {1879-0003}, mesh = {Akkermansia/drug effects ; Animals ; Diet, High-Fat ; Disease Models, Animal ; Drugs, Chinese Herbal ; Gastrointestinal Microbiome/*drug effects ; Lipid Metabolism/drug effects ; Liver/drug effects/metabolism/pathology ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Non-alcoholic Fatty Liver Disease/*drug therapy/etiology/metabolism ; Ophiopogon/*chemistry ; Polysaccharides/chemistry/*pharmacology ; }, abstract = {MDG, a polysaccharide derived from Ophiopogon japonicus, displays a protective effect against obesity and non-alcoholic fatty liver disease (NAFLD). However, there is no definitive evidence proving the specific mechanism of MDG against NAFLD. The results showed MDG supplementation ameliorated lipid accumulation, liver steatosis, and chronic inflammation in high-fat diet-induced NAFLD mice. Besides, MDG increased the abundance and diversity of microbial communities in the gut. These effects were mediated by the colonization of fecal microbiota. Further investigation revealed that Akkermansia muciniphila levels correlated negatively with NAFLD development, and lipid metabolism-related signaling might be the key regulator. Our study suggested that MDG treatment could inhibit obesity and the NAFLD process by modulating lipid-related pathways via altering the structure and diversity of gut microbiota. In addition, Akkermansia miniciphila might be a promising candidate in future research into NAFLD.}, } @article {pmid34915097, year = {2022}, author = {Delacuvellerie, A and Géron, A and Gobert, S and Wattiez, R}, title = {New insights into the functioning and structure of the PE and PP plastispheres from the Mediterranean Sea.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {295}, number = {}, pages = {118678}, doi = {10.1016/j.envpol.2021.118678}, pmid = {34915097}, issn = {1873-6424}, mesh = {Bacteria/genetics ; Mediterranean Sea ; *Microbiota ; Plastics ; *Seawater ; }, abstract = {Plastic debris are accumulating in the marine environment and aggregate microorganisms that form a new ecosystem called the plastisphere. Better understanding the plastisphere is crucial as it has self-sufficient organization and carries pathogens or organisms that may be involved in the pollutant adsorption and/or plastic degradation. To date, the plastisphere is mainly described at the taxonomic level and the functioning of its microbial communities still remains poorly documented. In this work, metagenomic and metaproteomic analyzes were performed on the plastisphere of polypropylene and polyethylene plastic debris sampled on a pebble beach from the Mediterranean Sea. Our results confirmed that the plastisphere was organized as self-sufficient ecosystems containing highly active primary producers, heterotrophs and predators such as nematode. Interestingly, the chemical composition of the polymer did not impact the structure of the microbial communities but rather influenced the functions expressed. Despite the fact that the presence of hydrocarbon-degrading bacteria was observed in the metagenomes, polymer degradation metabolisms were not detected at the protein level. Finally, hydrocarbon degrader (i.e., Alcanivorax) and pathogenic bacteria (i.e., Vibrionaceae) were observed in the plastispheres but were not very active as no proteins involved in polymer degradation or pathogeny were detected. This work brings new insights into the functioning of the microbial plastisphere developed on plastic marine debris.}, } @article {pmid34911987, year = {2021}, author = {Soto-Giron, MJ and Kim, JN and Schott, E and Tahmin, C and Ishoey, T and Mincer, TJ and DeWalt, J and Toledo, G}, title = {The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {24017}, pmid = {34911987}, issn = {2045-2322}, mesh = {*Biodiversity ; Computational Biology/methods ; Food Microbiology ; Genetic Variation ; *Host Microbial Interactions ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Molecular Sequence Annotation ; Phylogeny ; Plants, Edible/*microbiology ; }, abstract = {Plant microbiomes have been extensively studied for their agricultural relevance on growth promotion and pathogenesis, but little is known about their role as part of the diet when fresh fruits and vegetables are consumed raw. Most studies describing these communities are based on 16S rRNA gene amplicon surveys, limiting our understanding of the taxonomic resolution at the species level and functional capabilities. In this study, we characterized microbes colonizing tomatoes, spinach, brined olives, and dried figs using shotgun metagenomics. We recovered metagenome-assembled genomes of novel lactic acid bacteria from green olives and identified high intra- and inter-specific diversity of Pseudomonas in tomatoes. All samples were colonized by Pseudomonas, consistent with other reports with distinct community structure. Functional characterization showed the presence of enzymes involved in vitamin and short chain fatty acid metabolism and degradation of diverse carbohydrate substrates including plant fibers. The dominant bacterial members were isolated, sequenced, and mapped to its metagenome confirming their identity and indicating the microbiota is culturable. Our results reveal high genetic diversity, previously uncultured genera, and specific functions reflecting a likely plant host association. This study highlights the potential that plant microbes can play when consumed as part of our diet and proposes these as transient contributors to the gut microbiome.}, } @article {pmid34911583, year = {2021}, author = {Allali, I and Abotsi, RE and Tow, LA and Thabane, L and Zar, HJ and Mulder, NM and Nicol, MP}, title = {Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {241}, pmid = {34911583}, issn = {2049-2618}, support = {U54 HG009824/HG/NHGRI NIH HHS/United States ; U41 HG006941/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; Mass Screening ; *Microbiota ; Public Health ; South Africa ; Uganda ; }, abstract = {BACKGROUND: The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies.

METHODOLOGY: We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction.

RESULTS: We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168).

CONCLUSIONS: There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.}, } @article {pmid34910917, year = {2021}, author = {Wurster, JI and Peterson, RL and Brown, CE and Penumutchu, S and Guzior, DV and Neugebauer, K and Sano, WH and Sebastian, MM and Quinn, RA and Belenky, P}, title = {Streptozotocin-induced hyperglycemia alters the cecal metabolome and exacerbates antibiotic-induced dysbiosis.}, journal = {Cell reports}, volume = {37}, number = {11}, pages = {110113}, pmid = {34910917}, issn = {2211-1247}, support = {R21 AT010366/AT/NCCIH NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; P20 GM121344/GM/NIGMS NIH HHS/United States ; R01 DK125382/DK/NIDDK NIH HHS/United States ; P30 CA016672/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Cecum/*metabolism/microbiology ; Diabetes Mellitus, Experimental/complications ; *Drug Resistance, Bacterial ; Dysbiosis/drug therapy/etiology/metabolism/*pathology ; Female ; Gastrointestinal Microbiome ; Hyperglycemia/drug therapy/etiology/metabolism/*pathology ; Male ; *Metabolome ; Metagenome ; Mice ; Mice, Inbred C57BL ; Microbiota ; Salmonella Infections, Animal/drug therapy/metabolism/microbiology/*pathology ; Salmonella enterica ; Transcriptome ; }, abstract = {It is well established in the microbiome field that antibiotic (ATB) use and metabolic disease both impact the structure and function of the gut microbiome. But how host and microbial metabolism interacts with ATB susceptibility to affect the resulting dysbiosis remains poorly understood. In a streptozotocin-induced model of hyperglycemia (HG), we use a combined metagenomic, metatranscriptomic, and metabolomic approach to profile changes in microbiome taxonomic composition, transcriptional activity, and metabolite abundance both pre- and post-ATB challenge. We find that HG impacts both microbiome structure and metabolism, ultimately increasing susceptibility to amoxicillin. HG exacerbates drug-induced dysbiosis and increases both phosphotransferase system activity and energy catabolism compared to controls. Finally, HG and ATB co-treatment increases pathogen susceptibility and reduces survival in a Salmonella enterica infection model. Our data demonstrate that induced HG is sufficient to modify the cecal metabolite pool, worsen the severity of ATB dysbiosis, and decrease colonization resistance.}, } @article {pmid34910161, year = {2022}, author = {Williams, CJ and Torquati, L and Li, Z and Lea, RA and Croci, I and Keating, E and Little, JP and Eynon, N and Coombes, JS}, title = {Oligofructose-Enriched Inulin Intake, Gut Microbiome Characteristics, and the V̇O2 Peak Response to High-Intensity Interval Training in Healthy Inactive Adults.}, journal = {The Journal of nutrition}, volume = {152}, number = {3}, pages = {680-689}, doi = {10.1093/jn/nxab426}, pmid = {34910161}, issn = {1541-6100}, mesh = {Adult ; Female ; *Gastrointestinal Microbiome ; *High-Intensity Interval Training/methods ; Humans ; Inulin/pharmacology ; Lactic Acid ; Male ; Oligosaccharides ; Oxygen Consumption/physiology ; }, abstract = {BACKGROUND: The gut microbiome has been associated with cardiorespiratory fitness.

OBJECTIVES: To assess the effects of oligofructose (FOS)-enriched inulin supplementation on the gut microbiome and the peak oxygen uptake (V̇O2peak) response to high-intensity interval training (HIIT).

METHODS: The study was a randomized controlled trial. Forty sedentary and apparently healthy adults [n = 31 women; aged 31.8 ± 9.8 y, BMI (in kg⋅m-2) 25.9 ± 4.3] were randomly allocated to 1) 6 wk of supervised HIIT (4 × 4-min bouts at 85-95% peak heart rate, interspersed with 3 min of active recovery, 3·wk-1) + 12 g·d-1 of FOS-enriched inulin (HIIT-I) or 2) 6 wk of supervised HIIT (3·wk-1, 4 × 4-min bouts) + 12 g·d-1 of maltodextrin/placebo (HIIT-P). Each participant completed an incremental treadmill test to assess V̇O2peak and ventilatory thresholds (VTs), provided a stool and blood sample, and completed a 24-h diet recall questionnaire and FFQ before and after the intervention. Gut microbiome analyses were performed using metagenomic sequencing. Fecal short-chain fatty acids were measured by mass spectrometry.

RESULTS: There were no differences in the mean change in V̇O2peak response between groups (P = 0.58). HIIT-I had a greater improvement in VTs than HIIT-P [VT1 (lactate accumulation): mean difference + 4.3% and VT2 (lactate threshold): +4.2%, P < 0.05]. HIIT-I had a greater increase in the abundance of Bifidobacterium taxa [false discovery rate (FDR) < 0.05] and several metabolic processes related to exercise capacity (FDR < 0.05). Exploratory analysis of merged data found participants with a greater response to HIIT (V̇O2peak ≥3.5 mL⋅kg-1⋅min-1) had a 2.2-fold greater mean abundance of gellan degradation pathways (FDR < 0.05) and a greater, but not significant, abundance of Bifidobacterium uniformis species (P < 0.00023, FDR = 0.08).

CONCLUSIONS: FOS-enriched inulin supplementation did not potentiate HIIT-induced improvements in V̇O2peak but led to gut microbiome changes possibly associated with greater ventilatory threshold improvements in healthy inactive adults. Gellan degradation pathways and B. uniformis spp. were associated with greater V̇O2peak responses to HIIT.}, } @article {pmid34908504, year = {2021}, author = {Kang, Y and Ji, X and Guo, L and Xia, H and Yang, X and Xie, Z and Shi, X and Wu, R and Feng, D and Wang, C and Chen, M and Zhang, W and Wei, H and Guan, Y and Ye, K and Zhao, G}, title = {Cerebrospinal Fluid from Healthy Pregnant Women Does Not Harbor a Detectable Microbial Community.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0076921}, pmid = {34908504}, issn = {2165-0497}, mesh = {Adult ; Bacteria/classification/genetics/*isolation & purification ; Bacteriophages/*isolation & purification ; Blood-Brain Barrier/microbiology ; Cerebrospinal Fluid/*microbiology ; DNA, Bacterial/cerebrospinal fluid ; DNA, Viral/cerebrospinal fluid ; Female ; Healthy Volunteers ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/genetics ; Metagenomics ; Microbiota ; Pregnancy ; }, abstract = {Cerebrospinal fluid (CSF) circulating in the human central nervous system has long been considered aseptic in healthy individuals, because normally, the blood-brain barrier can protect against microbial invasions. However, this dogma has been called into question by several reports that microbes were identified in human brains, raising the question of whether there is a microbial community in the CSF of healthy individuals without neurological diseases. Here, we collected CSF samples and other samples, including one-to-one matched oral and skin swab samples (positive controls), from 23 pregnant women aged between 23 and 40 years. Normal saline samples (negative controls), sterile swabs, and extraction buffer samples (contamination controls) were also collected. Twelve of the CSF specimens were also used to evaluate the physiological activities of detected microbes. Metagenomic and metatranscriptomic sequencing was performed in these 116 specimens. A total of 620 nonredundant microbes were detected, which were dominated by bacteria (74.6%) and viruses (24.2%), while in CSF samples, metagenomic sequencing found only 26 nonredundant microbes, including one eukaryote, four bacteria, and 21 viruses (mostly bacteriophages). The beta diversity of microbes compared between CSF metagenomic samples and other types of samples (except negative controls) was significantly different from that of the CSF self-comparison. In addition, there was no active or viable microbe in the matched metagenomic and metatranscriptomic sequencing of CSF specimens after subtracting those also found in normal saline, DNA extraction buffer, and skin swab specimens. In conclusion, our results showed no strong evidence of a colonized microbial community present in the CSF of healthy individuals. IMPORTANCE The microbiome is prevalent throughout human bodies, with profound health implications. However, it remains unclear whether it is present and active in human CSF, which has been long considered aseptic due to the blood-brain barrier. Here, we applied unbiased metagenomic and metatranscriptomic sequencing to detect the presence of a microbiome in CSF collected from 23 pregnant women with matched controls. Analysis of 116 specimens found no strong evidence to support the presence of a colonized microbiome in CSF. Our findings will strengthen our understanding of the internal environment of the CSF in healthy people, which has strong implications for human health, especially for neurological infections and disorders, and will help further disease diagnostics, prevention, and therapeutics in clinical settings.}, } @article {pmid34908121, year = {2022}, author = {Miao, Y and Liu, F and Hou, T and Liu, Y}, title = {Virtifier: a deep learning-based identifier for viral sequences from metagenomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {5}, pages = {1216-1222}, doi = {10.1093/bioinformatics/btab845}, pmid = {34908121}, issn = {1367-4811}, support = {QT202109//Youth Science and Technology Talent Support Project of Jilin Province/ ; 2019M651204//China Postdoctoral Science Foundation/ ; }, mesh = {Humans ; Metagenome ; *Deep Learning ; Software ; Neural Networks, Computer ; *Microbiota ; }, abstract = {MOTIVATION: Viruses, the most abundant biological entities on earth, are important components of microbial communities, and as major human pathogens, they are responsible for human mortality and morbidity. The identification of viral sequences from metagenomes is critical for viral analysis. As massive quantities of short sequences are generated by next-generation sequencing, most methods utilize discrete and sparse one-hot vectors to encode nucleotide sequences, which are usually ineffective in viral identification.

RESULTS: In this article, Virtifier, a deep learning-based viral identifier for sequences from metagenomic data is proposed. It includes a meaningful nucleotide sequence encoding method named Seq2Vec and a variant viral sequence predictor with an attention-based long short-term memory (LSTM) network. By utilizing a fully trained embedding matrix to encode codons, Seq2Vec can efficiently extract the relationships among those codons in a nucleotide sequence. Combined with an attention layer, the LSTM neural network can further analyze the codon relationships and sift the parts that contribute to the final features. Experimental results of three datasets have shown that Virtifier can accurately identify short viral sequences (<500 bp) from metagenomes, surpassing three widely used methods, VirFinder, DeepVirFinder and PPR-Meta. Meanwhile, a comparable performance was achieved by Virtifier at longer lengths (>5000 bp).

A Python implementation of Virtifier and the Python code developed for this study have been provided on Github https://github.com/crazyinter/Seq2Vec. The RefSeq genomes in this article are available in VirFinder at https://dx.doi.org/10.1186/s40168-017-0283-5. The CAMI Challenge Dataset 3 CAMI_high dataset in this article is available in CAMI at https://data.cami-challenge.org/participate. The real human gut metagenomes in this article are available at https://dx.doi.org/10.1101/gr.142315.112.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid34907334, year = {2021}, author = {Tamashiro, R and Strange, L and Schnackenberg, K and Santos, J and Gadalla, H and Zhao, L and Li, EC and Hill, E and Hill, B and Sidhu, G and Kirst, M and Walker, C and Wang, GP}, title = {Stability of healthy subgingival microbiome across space and time.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {23987}, pmid = {34907334}, issn = {2045-2322}, support = {R56 DE021556/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Female ; Gingiva/*microbiology ; Humans ; Male ; *Metagenome ; Microbiota/*genetics ; }, abstract = {The subgingival microbiome is one of the most stable microbial ecosystems in the human body. Alterations in the subgingival microbiome have been associated with periodontal disease, but their variations over time and between different subgingival sites in periodontally healthy individuals have not been well described. We performed extensive, longitudinal sampling of the subgingival microbiome from five periodontally healthy individuals to define baseline spatial and temporal variations. A total of 251 subgingival samples from 5 subjects were collected over 6-12 months and deep sequenced. The overall microbial diversity and composition differed significantly between individuals. Within each individual, we observed considerable differences in microbiome composition between different subgingival sites. However, for a given site, the microbiome was remarkably stable over time, and this stability was associated with increased microbial diversity but was inversely correlated with the enrichment of putative periodontal pathogens. In contrast to microbiome composition, the predicted functional metagenome was similar across space and time, suggesting that periodontal health is associated with shared gene functions encoded by different microbiome consortia that are individualized. To our knowledge, this is one of the most detailed longitudinal analysis of the healthy subgingival microbiome to date that examined the longitudinal variability of different subgingival sites within individuals. These results suggest that a single measurement of the healthy subgingival microbiome at a given site can provide long term information of the microbial composition and functional potential, but sampling of each site is necessary to define the composition and community structure at individual subgingival sites.}, } @article {pmid34906246, year = {2021}, author = {Chaudhari, NM and Overholt, WA and Figueroa-Gonzalez, PA and Taubert, M and Bornemann, TLV and Probst, AJ and Hölzer, M and Marz, M and Küsel, K}, title = {The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers.}, journal = {Environmental microbiome}, volume = {16}, number = {1}, pages = {24}, pmid = {34906246}, issn = {2524-6372}, support = {SFB 1076 -Project Number 218627073//deutsche forschungsgemeinschaft/ ; FZT 118 - 202548816//deutsche forschungsgemeinschaft/ ; Germany's Excellence Strategy - EXC 2051 - Project-ID 390713860//deutsche forschungsgemeinschaft/ ; Nachwuchsgruppe Dr. Alexander Probst//ministerium für kultur und wissenschaft des landes nordrhein-westfalen/ ; }, abstract = {BACKGROUND: The highly diverse Cand. Patescibacteria are predicted to have minimal biosynthetic and metabolic pathways, which hinders understanding of how their populations differentiate in response to environmental drivers or host organisms. Their mechanisms employed to cope with oxidative stress are largely unknown. Here, we utilized genome-resolved metagenomics to investigate the adaptive genome repertoire of Patescibacteria in oxic and anoxic groundwaters, and to infer putative host ranges.

RESULTS: Within six groundwater wells, Cand. Patescibacteria was the most dominant (up to 79%) super-phylum across 32 metagenomes sequenced from DNA retained on 0.2 and 0.1 µm filters after sequential filtration. Of the reconstructed 1275 metagenome-assembled genomes (MAGs), 291 high-quality MAGs were classified as Cand. Patescibacteria. Cand. Paceibacteria and Cand. Microgenomates were enriched exclusively in the 0.1 µm fractions, whereas candidate division ABY1 and Cand. Gracilibacteria were enriched in the 0.2 µm fractions. On average, Patescibacteria enriched in the smaller 0.1 µm filter fractions had 22% smaller genomes, 13.4% lower replication measures, higher proportion of rod-shape determining proteins, and of genomic features suggesting type IV pili mediated cell-cell attachments. Near-surface wells harbored Patescibacteria with higher replication rates than anoxic downstream wells characterized by longer water residence time. Except prevalence of superoxide dismutase genes in Patescibacteria MAGs enriched in oxic groundwaters (83%), no major metabolic or phylogenetic differences were observed. The most abundant Patescibacteria MAG in oxic groundwater encoded a nitrate transporter, nitrite reductase, and F-type ATPase, suggesting an alternative energy conservation mechanism. Patescibacteria consistently co-occurred with one another or with members of phyla Nanoarchaeota, Bacteroidota, Nitrospirota, and Omnitrophota. Among the MAGs enriched in 0.2 µm fractions,, only 8% Patescibacteria showed highly significant one-to-one correlation, mostly with Omnitrophota. Motility and transport related genes in certain Patescibacteria were highly similar to genes from other phyla (Omnitrophota, Proteobacteria and Nanoarchaeota).

CONCLUSION: Other than genes to cope with oxidative stress, we found little genomic evidence for niche adaptation of Patescibacteria to oxic or anoxic groundwaters. Given that we could detect specific host preference only for a few MAGs, we speculate that the majority of Patescibacteria is able to attach multiple hosts just long enough to loot or exchange supplies.}, } @article {pmid34906228, year = {2021}, author = {Shin, J and Noh, JR and Choe, D and Lee, N and Song, Y and Cho, S and Kang, EJ and Go, MJ and Ha, SK and Chang, DH and Kim, JH and Kim, YH and Kim, KS and Jung, H and Kim, MH and Sung, BH and Lee, SG and Lee, DH and Kim, BC and Lee, CH and Cho, BK}, title = {Ageing and rejuvenation models reveal changes in key microbial communities associated with healthy ageing.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {240}, pmid = {34906228}, issn = {2049-2618}, mesh = {Aging ; Animals ; *Gastrointestinal Microbiome/genetics ; *Healthy Aging ; Mice ; *Microbiota ; Rejuvenation ; }, abstract = {BACKGROUND: The gut microbiota is associated with diverse age-related disorders. Several rejuvenation methods, such as probiotic administration and faecal microbiota transplantation, have been applied to alter the gut microbiome and promote healthy ageing. Nevertheless, prolongation of the health span of aged mice by remodelling the gut microbiome remains challenging.

RESULTS: Here, we report the changes in gut microbial communities and their functions in mouse models during ageing and three rejuvenation procedures including co-housing, serum-injection and parabiosis. Our results showed that the compositional structure and gene abundance of the intestinal microbiota changed dynamically during the ageing process. Through the three rejuvenation procedures, we observed that the microbial community and intestinal immunity of aged mice were comparable to those of young mice. The results of metagenomic data analysis underscore the importance of the high abundance of Akkermansia and the butyrate biosynthesis pathway in the rejuvenated mouse group. Furthermore, oral administration of Akkermansia sufficiently ameliorated the senescence-related phenotype in the intestinal systems in aged mice and extended the health span, as evidenced by the frailty index and restoration of muscle atrophy.

CONCLUSIONS: In conclusion, the changes in key microbial communities and their functions during ageing and three rejuvenation procedures, and the increase in the healthy lifespan of aged mice by oral administration of Akkermansia. Our results provide a rationale for developing therapeutic strategies to achieve healthy active ageing. Video abstract.}, } @article {pmid34905206, year = {2022}, author = {Raza, A and Wu, Q}, title = {Diagnosis of Viral Diseases Using Deep Sequencing and Metagenomics Analyses.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2400}, number = {}, pages = {225-243}, pmid = {34905206}, issn = {1940-6029}, mesh = {Computational Biology ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Plants ; RNA ; *Virus Diseases/diagnosis/genetics ; }, abstract = {Viruses are ubiquitous in nature and exist in a variety of habitats. The advancement in sequencing technologies has revolutionized the understanding of viral biodiversity associated with plant diseases. Deep sequencing combined with metagenomics is a powerful approach that has proven to be revolutionary in the last decade and involves the direct analysis of viral genomes present in a diseased tissue sample. This protocol describes the details of RNA extraction and purification from wild rice plant and their yield, RNA purity, and integrity assessment. As a final step, bioinformatics data analysis including demultiplexing, quality control, de novo transcriptome assembly, taxonomic allocation and read mapping following Illumina HiSeq small and total RNA sequencing are described. Furthermore, the total RNAs extraction protocol and an additional ribosomal rRNAs depletion step which are significantly important for viral genomes construction are provided.}, } @article {pmid34904950, year = {2021}, author = {Ankersen, DV and Weimers, P and Bennedsen, M and Haaber, AB and Fjordside, EL and Beber, ME and Lieven, C and Saboori, S and Vad, N and Rannem, T and Marker, D and Paridaens, K and Frahm, S and Jensen, L and Rosager Hansen, M and Burisch, J and Munkholm, P}, title = {Long-Term Effects of a Web-Based Low-FODMAP Diet Versus Probiotic Treatment for Irritable Bowel Syndrome, Including Shotgun Analyses of Microbiota: Randomized, Double-Crossover Clinical Trial.}, journal = {Journal of medical Internet research}, volume = {23}, number = {12}, pages = {e30291}, pmid = {34904950}, issn = {1438-8871}, mesh = {Cross-Over Studies ; Diet ; Humans ; Internet ; *Irritable Bowel Syndrome/therapy ; *Microbiota ; *Probiotics/therapeutic use ; }, abstract = {BACKGROUND: The long-term management of irritable bowel syndrome (IBS) poses many challenges. In short-term studies, eHealth interventions have been demonstrated to be safe and practical for at-home monitoring of the effects of probiotic treatments and a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs). IBS has been linked to alterations in the microbiota.

OBJECTIVE: The aim of this study was to determine whether a web-based low-FODMAP diet (LFD) intervention and probiotic treatment were equally good at reducing IBS symptoms, and whether the response to treatments could be explained by patients' microbiota.

METHODS: Adult IBS patients were enrolled in an open-label, randomized crossover trial (for nonresponders) with 1 year of follow-up using the web application IBS Constant Care (IBS CC). Patients were recruited from the outpatient clinic at the Department of Gastroenterology, North Zealand University Hospital, Denmark. Patients received either VSL#3 for 4 weeks (2 × 450 billion colony-forming units per day) or were placed on an LFD for 4 weeks. Patients responding to the LFD were reintroduced to foods high in FODMAPs, and probiotic responders received treatments whenever they experienced a flare-up of symptoms. Treatment response and symptom flare-ups were defined as a reduction or increase, respectively, of at least 50 points on the IBS Severity Scoring System (IBS-SSS). Web-based ward rounds were performed daily by the study investigator. Fecal microbiota were analyzed by shotgun metagenomic sequencing (at least 10 million 2 × 100 bp paired-end sequencing reads per sample).

RESULTS: A total of 34 IBS patients without comorbidities and 6 healthy controls were enrolled in the study. Taken from participating subjects, 180 fecal samples were analyzed for their microbiota composition. Out of 21 IBS patients, 12 (57%) responded to the LFD and 8 (38%) completed the reintroduction of FODMAPs. Out of 21 patients, 13 (62%) responded to their first treatment of VSL#3 and 7 (33%) responded to multiple VSL#3 treatments. A median of 3 (IQR 2.25-3.75) probiotic treatments were needed for sustained symptom control. LFD responders were reintroduced to a median of 14.50 (IQR 7.25-21.75) high-FODMAP items. No significant difference in the median reduction of IBS-SSS for LFD versus probiotic responders was observed, where for LFD it was -126.50 (IQR -196.75 to -76.75) and for VSL#3 it was -130.00 (IQR -211.00 to -70.50; P>.99). Responses to either of the two treatments were not able to be predicted using patients' microbiota.

CONCLUSIONS: The web-based LFD intervention and probiotic treatment were equally efficacious in managing IBS symptoms. The response to treatments could not be explained by the composition of the microbiota. The IBS CC web application was shown to be practical, safe, and useful for clinical decision making in the long-term management of IBS. Although this study was underpowered, findings from this study warrant further research in a larger sample of patients with IBS to confirm these long-term outcomes.

TRIAL REGISTRATION: ClinicalTrials.gov NCT03586622; https://clinicaltrials.gov/ct2/show/NCT03586622.}, } @article {pmid34904945, year = {2021}, author = {Rego, A and Fernandez-Guerra, A and Duarte, P and Assmy, P and Leão, PN and Magalhães, C}, title = {Secondary metabolite biosynthetic diversity in Arctic Ocean metagenomes.}, journal = {Microbial genomics}, volume = {7}, number = {12}, pages = {}, pmid = {34904945}, issn = {2057-5858}, mesh = {Arctic Regions ; Bacteria/*classification/genetics/isolation & purification/metabolism ; Bacterial Proteins/genetics ; *Biosynthetic Pathways ; High-Throughput Nucleotide Sequencing ; Humans ; Microbiota ; Multigene Family ; Oceans and Seas ; Phylogeny ; Secondary Metabolism ; Sequence Analysis, DNA/*methods ; Water Microbiology ; }, abstract = {Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are mega enzymes responsible for the biosynthesis of a large fraction of natural products (NPs). Molecular markers for biosynthetic genes, such as the ketosynthase (KS) domain of PKSs, have been used to assess the diversity and distribution of biosynthetic genes in complex microbial communities. More recently, metagenomic studies have complemented and enhanced this approach by allowing the recovery of complete biosynthetic gene clusters (BGCs) from environmental DNA. In this study, the distribution and diversity of biosynthetic genes and clusters from Arctic Ocean samples (NICE-2015 expedition), was assessed using PCR-based strategies coupled with high-throughput sequencing and metagenomic analysis. In total, 149 KS domain OTU sequences were recovered, 36 % of which could not be assigned to any known BGC. In addition, 74 bacterial metagenome-assembled genomes were recovered, from which 179 BGCs were extracted. A network analysis identified potential new NP families, including non-ribosomal peptides and polyketides. Complete or near-complete BGCs were recovered, which will enable future heterologous expression efforts to uncover the respective NPs. Our study represents the first report of biosynthetic diversity assessed for Arctic Ocean metagenomes and highlights the potential of Arctic Ocean planktonic microbiomes for the discovery of novel secondary metabolites. The strategy employed in this study will enable future bioprospection, by identifying promising samples for bacterial isolation efforts, while providing also full-length BGCs for heterologous expression.}, } @article {pmid34903850, year = {2022}, author = {Gregor, R and Probst, M and Eyal, S and Aksenov, A and Sasson, G and Horovitz, I and Dorrestein, PC and Meijler, MM and Mizrahi, I}, title = {Mammalian gut metabolomes mirror microbiome composition and host phylogeny.}, journal = {The ISME journal}, volume = {16}, number = {5}, pages = {1262-1274}, pmid = {34903850}, issn = {1751-7370}, support = {P41 GM103484/GM/NIGMS NIH HHS/United States ; S10 RR029121/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Mammals ; Metabolome ; *Microbiota ; Phylogeny ; }, abstract = {In the past decade, studies on the mammalian gut microbiome have revealed that different animal species have distinct gut microbial compositions. The functional ramifications of this variation in microbial composition remain unclear: do these taxonomic differences indicate microbial adaptations to host-specific functionality, or are these diverse microbial communities essentially functionally redundant, as has been indicated by previous metagenomics studies? Here, we examine the metabolic content of mammalian gut microbiomes as a direct window into ecosystem function, using an untargeted metabolomics platform to analyze 101 fecal samples from a range of 25 exotic mammalian species in collaboration with a zoological center. We find that mammalian metabolomes are chemically diverse and strongly linked to microbiome composition, and that metabolome composition is further correlated to the phylogeny of the mammalian host. Specific metabolites enriched in different animal species included modified and degraded host and dietary compounds such as bile acids and triterpenoids, as well as fermentation products such as lactate and short-chain fatty acids. Our results suggest that differences in microbial taxonomic composition are indeed translated to host-specific metabolism, indicating that taxonomically distant microbiomes are more functionally diverse than redundant.}, } @article {pmid34903050, year = {2021}, author = {Beller, L and Deboutte, W and Falony, G and Vieira-Silva, S and Tito, RY and Valles-Colomer, M and Rymenans, L and Jansen, D and Van Espen, L and Papadaki, MI and Shi, C and Yinda, CK and Zeller, M and Faust, K and Van Ranst, M and Raes, J and Matthijnssens, J}, title = {Successional Stages in Infant Gut Microbiota Maturation.}, journal = {mBio}, volume = {12}, number = {6}, pages = {e0185721}, pmid = {34903050}, issn = {2150-7511}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Cohort Studies ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Humans ; Infant ; Infant, Newborn/*growth & development ; Male ; }, abstract = {Disturbances in the primary colonization of the infant gut can result in lifelong consequences and have been associated with a range of host conditions. Although early-life factors have been shown to affect infant gut microbiota development, our current understanding of human gut colonization in early life remains limited. To gain more insights into the unique dynamics of this rapidly evolving ecosystem, we investigated the microbiota over the first year of life in eight densely sampled infants (n = 303 total samples). To evaluate the gut microbiota maturation transition toward an adult configuration, we compared the microbiome composition of the infants to that of the Flemish Gut Flora Project (FGFP) population (n = 1,106). We observed the infant gut microbiota to mature through three distinct, conserved stages of ecosystem development. Across these successional gut microbiota maturation stages, the genus predominance was observed to shift from Escherichia over Bifidobacterium to Bacteroides. Both disease and antibiotic treatment were observed to be associated occasionally with gut microbiota maturation stage regression, a transient setback in microbiota maturation dynamics. Although the studied microbiota trajectories evolved to more adult-like constellations, microbiome community typing against the background of the FGFP cohort clustered all infant samples within the (in adults) potentially dysbiotic Bacteroides 2 (Bact2) enterotype. We confirmed the similarities between infant gut microbial colonization and adult dysbiosis. Profound knowledge about the primary gut colonization process in infants might provide crucial insights into how the secondary colonization of a dysbiotic adult gut can be redirected. IMPORTANCE After birth, microbial colonization of the infant intestinal tract is important for health later in life. However, this initial process is highly dynamic and influenced by many factors. Studying this process in detail requires a dense longitudinal sampling effort. In the current study, the bacterial microbiota of >300 stool samples was analyzed from 8 healthy infants, suggesting that the infant gut microbial population matures along a path involving distinct microbial constellations and that the timing of these transitions is infant specific and can temporarily retrace upon external events. We also showed that the infant microbial populations show similarities to suboptimal bacterial populations in the guts of adults. These insights are crucial for a better understanding of the dynamics and characteristics of a "healthy gut microbial population" in both infants and adults and might allow the identification of intervention targets in cases of microbial disturbances or disease.}, } @article {pmid34897962, year = {2022}, author = {Sahu, RP and Kazy, SK and Bose, H and Mandal, S and Dutta, A and Saha, A and Roy, S and Dutta Gupta, S and Mukherjee, A and Sar, P}, title = {Microbial diversity and function in crystalline basement beneath the Deccan Traps explored in a 3 km borehole at Koyna, western India.}, journal = {Environmental microbiology}, volume = {24}, number = {6}, pages = {2837-2853}, doi = {10.1111/1462-2920.15867}, pmid = {34897962}, issn = {1462-2920}, mesh = {Bacteria ; Carbon Cycle ; India ; *Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {Deep terrestrial subsurface represents a huge repository of global prokaryotic biomass. Given its vastness and importance, microbial life within the deep subsurface continental crust remains under-represented in global studies. We characterize the microbial communities of deep, extreme and oligotrophic realm hosted by crystalline Archaean granitic rocks underneath the Deccan Traps, through sampling via 3000 m deep scientific borehole at Koyna, India through metagenomics, amplicon sequencing and cultivation-based analyses. Gene sequences 16S rRNA (7.37 × 10[6]) show considerable bacterial diversity and the existence of a core microbiome (5724 operational taxonomic units conserved out of a total 118,064 OTUs) across the depths. Relative abundance of different taxa of core microbiome varies with depth in response to prevailing lithology and geochemistry. Co-occurrence network analysis and cultivation attempt to elucidate close interactions among autotrophic and organotrophic bacteria. Shotgun metagenomics reveals a major role of autotrophic carbon fixation via the Wood-Ljungdahl pathway and genes responsible for energy and carbon metabolism. Deeper analysis suggests the existence of an 'acetate switch', coordinating biosynthesis and cellular homeostasis. We conclude that the microbial life in the nutrient- and energy-limited deep granitic crust is constrained by the depth and managed by a few core members via a close interplay between autotrophy and organotrophy.}, } @article {pmid34896845, year = {2022}, author = {Lai, J and Li, A and Jiang, J and Yuan, X and Zhang, P and Xi, C and Wu, L and Wang, Z and Chen, J and Lu, J and Lu, S and Mou, T and Zhou, H and Wang, D and Huang, M and Dong, F and Li, MD and Xu, Y and Song, X and Hu, S}, title = {Metagenomic analysis reveals gut bacterial signatures for diagnosis and treatment outcome prediction in bipolar depression.}, journal = {Psychiatry research}, volume = {307}, number = {}, pages = {114326}, doi = {10.1016/j.psychres.2021.114326}, pmid = {34896845}, issn = {1872-7123}, mesh = {*Bipolar Disorder/diagnosis/drug therapy ; Dysbiosis ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; Treatment Outcome ; }, abstract = {BACKGROUND: We aimed to characterize gut microbial alterations in depressed patients with bipolar disorder (BD) following quetiapine monotherapy and explored its potential for disease diagnosis and outcome prediction.

METHODS: Fecal samples were obtained from 60 healthy individuals and 62 patients in acute depressive episodes. All patients received one-month quetiapine treatment after enrollment. The structure of gut microbiota was measured with metagenomic sequencing, and its correlation with clinical profiles and brain function as indicated by resting-state functional magnetic resonance imaging was analyzed. Random forest models based on bacterial species were constructed to distinguish patients from controls, and responders from non-responders, respectively.

RESULTS: BD patients displayed specific alterations in gut microbial diversity and composition. Quetiapine treatment increased the diversity of microbial communities and changed the composition. The abundance of Clostridium bartlettii was negatively associated with age, baseline depression severity, while positively associated with spontaneous neural oscillation in the hippocampus. Tree-based classification models for (1) patients and controls and (2) responders and non-responders showed an area under the curve of 0.733 and 0.800, respectively.

CONCLUSION: Our findings add new evidence to the existing literature regarding gut dysbiosis in BD and reveal the potential of microbe-based biomarkers for disease diagnosis and treatment outcome prediction.}, } @article {pmid34896510, year = {2022}, author = {Zhou, L and Xu, P and Gong, J and Huang, S and Chen, W and Fu, B and Zhao, Z and Huang, X}, title = {Metagenomic profiles of the resistome in subtropical estuaries: Co-occurrence patterns, indicative genes, and driving factors.}, journal = {The Science of the total environment}, volume = {810}, number = {}, pages = {152263}, doi = {10.1016/j.scitotenv.2021.152263}, pmid = {34896510}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Ecosystem ; *Estuaries ; Genes, Bacterial ; *Metagenomics ; }, abstract = {Estuaries are resistome hotspots owing to resistome accumulation and propagation at these locations from surrounding rivers, yet the large-scale biogeographic pattern of resistome, especially biocide and metal resistance genes (BMRGs) and its driving mechanisms in estuarine waters remains to be elucidated. Here, a metagenomics-based approach was firstly used to investigate resistome and mobilome profiles in waters from 30 subtropical estuaries, South China. The Pearl River estuaries had a higher diversity and abundance of antibiotic resistance genes (ARGs), BMRGs, and mobile genetic elements (MGEs) when compared with estuaries from east and west regions. Genes resistant to multiple antibiotics, metals, and biocides were the most abundant gene types in the resistome. The abundance of MGEs (e.g., intI1, IS91, and tnpA) was highly associated with the total abundance of resistance genes, suggesting their utility as potential indicators for quantitative estimations of the resistome contamination. Further, MGEs contributed more than bacterial communities in shaping the resistome in subtropical estuaries. Physicochemical factors (e.g., pH) regulated MGE composition and stochastic assembly, which mediated the co-selection of ARGs and BMRGs via horizontal gene transfer. Our findings have important implications and provide a reference on the management of ARGs and BMRGs in subtropical estuarine ecosystems.}, } @article {pmid34896404, year = {2022}, author = {Demir, M and Lang, S and Hartmann, P and Duan, Y and Martin, A and Miyamoto, Y and Bondareva, M and Zhang, X and Wang, Y and Kasper, P and Bang, C and Roderburg, C and Tacke, F and Steffen, HM and Goeser, T and Kruglov, A and Eckmann, L and Stärkel, P and Fouts, DE and Schnabl, B}, title = {The fecal mycobiome in non-alcoholic fatty liver disease.}, journal = {Journal of hepatology}, volume = {76}, number = {4}, pages = {788-799}, pmid = {34896404}, issn = {1600-0641}, support = {R01 AA020703/AA/NIAAA NIH HHS/United States ; I01 BX004594/BX/BLRD VA/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 AA026939/AA/NIAAA NIH HHS/United States ; }, mesh = {Animals ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Liver ; Mice ; *Mycobiome ; *Non-alcoholic Fatty Liver Disease/etiology ; Saccharomyces cerevisiae ; }, abstract = {BACKGROUND & AIMS: Studies investigating the gut-liver axis have largely focused on bacteria, whereas little is known about commensal fungi. We characterized fecal fungi in patients with non-alcoholic fatty liver disease (NAFLD) and investigated their role in a fecal microbiome-humanized mouse model of Western diet-induced steatohepatitis.

METHODS: We performed fungal internal transcribed spacer 2 sequencing using fecal samples from 78 patients with NAFLD, 16 controls and 73 patients with alcohol use disorder. Anti-Candida albicans (C. albicans) IgG was measured in blood samples from 17 controls and 79 patients with NAFLD. Songbird, a novel multinominal regression tool, was used to investigate mycobiome changes. Germ-free mice were colonized with feces from patients with non-alcoholic steatohepatitis (NASH), fed a Western diet for 20 weeks and treated with the antifungal amphotericin B.

RESULTS: The presence of non-obese NASH or F2-F4 fibrosis was associated with a distinct fecal mycobiome signature. Changes were characterized by an increased log-ratio for Mucor sp./Saccharomyces cerevisiae (S. cerevisiae) in patients with NASH and F2-F4 fibrosis. The C. albicans/S. cerevisiae log-ratio was significantly higher in non-obese patients with NASH when compared with non-obese patients with NAFL or controls. We observed a different fecal mycobiome composition in patients with NAFLD and advanced fibrosis compared to those with alcohol use disorder and advanced fibrosis. Plasma anti-C. albicans IgG was increased in patients with NAFLD and advanced fibrosis. Gnotobiotic mice, colonized with human NASH feces and treated with amphotericin B were protected from Western diet-induced steatohepatitis.

CONCLUSIONS: Non-obese patients with NAFLD and more advanced disease have a different fecal mycobiome composition to those with mild disease. Antifungal treatment ameliorates diet-induced steatohepatitis in mice. Intestinal fungi could be an attractive target to attenuate NASH.

LAY SUMMARY: Non-alcoholic fatty liver disease is one of the most common chronic liver diseases and is associated with changes in the fecal bacterial microbiome. We show that patients with non-alcoholic fatty liver disease and more severe disease stages have a specific composition of fecal fungi and an increased systemic immune response to Candida albicans. In a fecal microbiome-humanized mouse model of Western diet-induced steatohepatitis, we show that treatment with antifungals reduces liver damage.}, } @article {pmid34894514, year = {2022}, author = {Zhu, W and Yang, D and Chang, L and Zhang, M and Zhu, L and Jiang, J}, title = {Animal gut microbiome mediates the effects of antibiotic pollution on an artificial freshwater system.}, journal = {Journal of hazardous materials}, volume = {425}, number = {}, pages = {127968}, doi = {10.1016/j.jhazmat.2021.127968}, pmid = {34894514}, issn = {1873-3336}, mesh = {Animals ; Anti-Bacterial Agents/toxicity ; Bacteria/genetics ; Fresh Water ; *Gastrointestinal Microbiome ; *Microbiota ; }, abstract = {The antibiotic pollution has become an emerging environmental problem worldwide, but the ecological outcomes remain to be elucidated, especially very little is known about the interactions between antibiotics and different ecological elements. In this study, the long-term influences of three representative antibiotics, i.e., tetracycline, erythromycin, and sulfamethoxazole, were investigated focusing on a simplified artificial freshwater system composed of amphibian tadpoles, gut and environmental bacterial and fungi communities, and water parameters. Results demonstrated that antibiotic exposure reduced tadpole's fitness with increased mortality and physiological abnormality, and altered the water quality, particularly the nitrogen homeostasis. Sequential analyses at organism, symbiont, and systematic levels revealed that antibiotics disrupted tadpole metabolome (e.g., tetrahydrobiopterin metabolism) directly by off-target effects. Antibiotics also reshaped the tadpole gut bacterial and fungi diversity and composition, which partly accounted for the tadpole's health condition. Moreover, changes of tadpole gut microbiome (i.e., Cyanobacteria and Basidiomycota OTUs) partly explained the variations of water parameters. In contrast, environmental microbiota and metagenome stayed relatively stable, and didn't contribute to the environmental variations. These results highlighted the pivotal role of gut microbiome in mediating the effects of antibiotics on the host and the environment, which would extend our understanding on the ecological outcomes caused by antibiotic pollution.}, } @article {pmid34893656, year = {2021}, author = {Cholewińska, P and Wołoszyńska, M and Michalak, M and Czyż, K and Rant, W and Smoliński, J and Wyrostek, A and Wojnarowski, K}, title = {Influence of selected factors on the Firmicutes, Bacteroidetes phyla and the Lactobacillaceae family in the digestive tract of sheep.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {23801}, pmid = {34893656}, issn = {2045-2322}, mesh = {Age Factors ; Animals ; Biodiversity ; Body Weight ; Feces/microbiology ; Firmicutes/*physiology ; *Gastrointestinal Microbiome ; *Host Microbial Interactions ; Lactobacillaceae/*physiology ; Metagenome ; Metagenomics/methods ; Milk ; Sheep ; }, abstract = {In this study, we used 10 healthy sheep, which gave birth to healthy twins. Stool samples were collected from mothers and their offspring 3 times during the study (0, 28 and 56 day postpartum). Milk samples were taken from the mothers at the same time. RT PCR analysis of faeces and milk was performed in order to assess the level of bacteria from the Firmicutes and Bacteroidetes phyla including the family Lactobacillaceae (phylum Firmicutes). The composition of mother's milk was also analyzed and their BCS. The data were compiled statistically. The obtained results showed that the level of the studied groups of bacteria may change due to the change of diet. Additionally, there were significant differences between lambs and mothers in the levels of the studied groups of bacteria. Analysis also shown that in the digestive system of mothers was a smaller disproportion in the level of the studied bacterial phyla than in lambs. The results also indicated the occurrence of differences in the bacterial composition at the individual level, both in ewes and their offspring. Additionally, in the conducted experiment, there were differences in the level of Firmicutes and Bacteroidetes groups depending on the sex.}, } @article {pmid34893089, year = {2021}, author = {Wang, Z and Usyk, M and Vázquez-Baeza, Y and Chen, GC and Isasi, CR and Williams-Nguyen, JS and Hua, S and McDonald, D and Thyagarajan, B and Daviglus, ML and Cai, J and North, KE and Wang, T and Knight, R and Burk, RD and Kaplan, RC and Qi, Q}, title = {Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {336}, pmid = {34893089}, issn = {1474-760X}, support = {HHSN268201000031C/HL/NHLBI NIH HHS/United States ; N01HC65236/HL/NHLBI NIH HHS/United States ; R01 DK120870/DK/NIDDK NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; R01 DK119268/DK/NIDDK NIH HHS/United States ; N01HC65235/HL/NHLBI NIH HHS/United States ; N01HC65233/HL/NHLBI NIH HHS/United States ; R01 HL060712/HL/NHLBI NIH HHS/United States ; HHSN261201300005I/CA/NCI NIH HHS/United States ; R01 HL136266/HL/NHLBI NIH HHS/United States ; HHSN268201000001I/HL/NHLBI NIH HHS/United States ; N01HC65237/HL/NHLBI NIH HHS/United States ; N01HC65234/HL/NHLBI NIH HHS/United States ; HHSN261201300004I/CA/NCI NIH HHS/United States ; HHSN268201000021C/HL/NHLBI NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; P30 DK020541/DK/NIDDK NIH HHS/United States ; P30 DK111022/DK/NIDDK NIH HHS/United States ; }, mesh = {Acculturation ; Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/genetics ; Cohort Studies ; Diet ; *Eating ; Emigrants and Immigrants ; *Emigration and Immigration ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Hispanic or Latino ; Humans ; Male ; Metagenomics ; Middle Aged ; Obesity/*microbiology ; RNA, Ribosomal, 16S ; United States ; }, abstract = {BACKGROUND: Obesity and related comorbidities are major health concerns among many US immigrant populations. Emerging evidence suggests a potential involvement of the gut microbiome. Here, we evaluated gut microbiome features and their associations with immigration, dietary intake, and obesity in 2640 individuals from a population-based study of US Hispanics/Latinos.

RESULTS: The fecal shotgun metagenomics data indicate that greater US exposure is associated with reduced ɑ-diversity, reduced functions of fiber degradation, and alterations in individual taxa, potentially related to a westernized diet. However, a majority of gut bacterial genera show paradoxical associations, being reduced with US exposure and increased with fiber intake, but increased with obesity. The observed paradoxical associations are not explained by host characteristics or variation in bacterial species but might be related to potential microbial co-occurrence, as seen by positive correlations among Roseburia, Prevotella, Dorea, and Coprococcus. In the conditional analysis with mutual adjustment, including all genera associated with both obesity and US exposure in the same model, the positive associations of Roseburia and Prevotella with obesity did not persist, suggesting that their positive associations with obesity might be due to their co-occurrence and correlations with obesity-related taxa, such as Dorea and Coprococcus.

CONCLUSIONS: Among US Hispanics/Latinos, US exposure is associated with unfavorable gut microbiome profiles for obesity risk, potentially related to westernized diet during acculturation. Microbial co-occurrence could be an important factor to consider in future studies relating individual gut microbiome taxa to environmental factors and host health and disease.}, } @article {pmid34890626, year = {2022}, author = {Howard, B and Bascom, CC and Hu, P and Binder, RL and Fadayel, G and Huggins, TG and Jarrold, BB and Osborne, R and Rocchetta, HL and Swift, D and Tiesman, JP and Song, Y and Wang, Y and Wehmeyer, K and Kimball, AB and Isfort, RJ}, title = {Aging-Associated Changes in the Adult Human Skin Microbiome and the Host Factors that Affect Skin Microbiome Composition.}, journal = {The Journal of investigative dermatology}, volume = {142}, number = {7}, pages = {1934-1946.e21}, doi = {10.1016/j.jid.2021.11.029}, pmid = {34890626}, issn = {1523-1747}, mesh = {Adult ; Aging ; Bacteria/genetics ; Female ; Humans ; Lipids ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Skin/microbiology ; }, abstract = {Understanding the changes in the skin microbiome and their relationship to host skin factors during aging remains largely unknown. To better understand this phenomenon, we collected samples for metagenomic and host skin factor analyses from the forearm, buttock, and facial skin from 158 Caucasian females aged 20‒24, 30‒34, 40‒44, 50‒54, 60‒64, and 70‒74 years. Metagenomics analysis was performed using 16S ribosomal RNA gene sequencing, whereas host sebocyte gland area, skin lipids, natural moisturizing factors, and antimicrobial peptides measurements were also performed. These analyses showed that skin bacterial diversity increased at all the skin sites with increasing age. Of the bacterial genera with an average relative abundance >1%, only Lactobacillus and Cutibacterium demonstrated a significant change (decrease) in abundance at all sampled skin sites with increasing age. Additional bacterial genera demonstrated significant age- and site-specific changes in abundance. Analysis of sebocyte area, natural moisturizing factors, lipids, and antimicrobial peptides showed an age-related decrease in sebocyte area and increases in natural moisturizing factors/antimicrobial peptides/skin lipids, all of which correlated with changes in specific bacterial genera. In conclusion, the human skin microbiome undergoes age-associated alterations that may reflect underlying age-related changes in cutaneous biology.}, } @article {pmid34890483, year = {2022}, author = {Shen, Z and Wang, F and Liang, Y and Li, Y and Liu, Q and Liu, F}, title = {Diversity and functions of microbes in surface sediments under heavy metal pollution of western Chaohu Lake.}, journal = {Letters in applied microbiology}, volume = {75}, number = {5}, pages = {1093-1102}, doi = {10.1111/lam.13627}, pmid = {34890483}, issn = {1472-765X}, support = {41371444//the National Science Foundation of China/ ; KJ2017ZD55//the Innovation Team of Scientific Research Platform of Anhui Province, China/ ; }, mesh = {Lakes/analysis ; Geologic Sediments/chemistry ; Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; *Metals, Heavy/analysis ; *Nucleic Acids ; China ; }, abstract = {Heavy metal pollution is a global concern. Targeting at the surface sediments in western Chaohu Lake and using metagenome sequencing, we probed into the mechanism of how microbes adapted to heavy metal-polluted sediments under natural conditions. It was found the heavy metal pollution intensity of the three typical sampling places ranked as estuary of Nanfeihe River (NFH) > Zhongmiao Town (HZ) > Hongshizui (HSZ). Totally 129 phyla, 2631 genera and 12 989 species were detected in the sediment samples, and HSZ, HZ and NFH had 35, 51 and 67 exclusive genera, respectively. The bacterial biomass and virus quantity from NFH accounted for 22·84 and 70·69% of total quantities, respectively, and the microbial community compositions in NFH were also different from those in HSZ and HZ. Metagenomics sequencing and functional gene annotation showed NFH contained many functional genes related to nucleic acid transport and metabolism, ribosome structures and biological origin, replication recombining and repair and inorganic ion transport and metabolism. Kyoto Encyclopedia of Genes and Genomes analysis suggested the sediments from NFH were rich in enzymes correlated with heavy metal transport and reduction. Our findings offer some scientific basis for Chaohu Lake control and microbe resource utilization.}, } @article {pmid34888258, year = {2021}, author = {Zhang, T and Zhang, S and Jin, C and Lin, Z and Deng, T and Xie, X and Deng, L and Li, X and Ma, J and Ding, X and Liu, Y and Shan, Y and Yu, Z and Wang, Y and Chen, G and Li, J}, title = {A Predictive Model Based on the Gut Microbiota Improves the Diagnostic Effect in Patients With Cholangiocarcinoma.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {751795}, pmid = {34888258}, issn = {2235-2988}, mesh = {*Bile Duct Neoplasms/diagnosis ; Bile Ducts, Intrahepatic ; Case-Control Studies ; *Cholangiocarcinoma/diagnosis ; Early Detection of Cancer ; Feces ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cholangiocarcinoma (CCA) is a malignant hepatic tumor with a poor prognosis, which needs early diagnosis urgently. The gut microbiota has been shown to play a crucial role in the progression of liver cancer. Here, we explored a gut microbiota model covering genera Burkholderia-Caballeronia-Paraburkholderia, Faecalibacterium, and Ruminococcus_1 (B-F-R) for CCA early diagnosis. A case-control study was conducted to enroll 53 CCA patients, 47 cholelithiasis patients, and 40 healthy controls. The feces samples and clinical information of participants were collected in the same period. The gut microbiota and its diversity of individuals were accessed with 16S rDNA sequencing, and the gut microbiota profile was evaluated according to microbiota diversity. Finally, four enriched genera in the CCA group (genera Bacteroides, Muribaculaceae_unclassified, Muribaculum, and Alistipes) and eight enriched genera in the cholelithiasis group (genera Bifidobacterium, Streptococcus, Agathobacter, Ruminococcus_gnavus_group, Faecalibacterium, Subdoligranulum, Collinsella, Escherichia-Shigella) constitute an overall different microbial community composition (P = 0.001). The B-F-R genera model with better diagnostic value than carbohydrate antigen 19-9 (CA19-9) was identified by random forest and Statistical Analysis of Metagenomic Profiles (STAMP) to distinguish CCA patients from healthy controls [area under the curve (AUC) = 0.973, 95% CI = 0.932-1.0]. Moreover, the correlative analysis found that genera Burkholderia-Caballeronia-Paraburkholderia were positively correlated with body mass index (BMI). The significantly different microbiomes between cholelithiasis and CCA were found via principal coordinates analysis (PCoA) and linear discriminant analysis effect size (LEfSe), and Venn diagram and LEfSe were utilized to identify four genera by comparing microbial compositions among patients with malignant obstructive jaundice (MOJ-Y) or not (MOJ-N). In brief, our findings suggest that gut microbiota vary from benign and malignant hepatobiliary diseases to healthy people and provide evidence supporting gut microbiota to be a non-invasive biomarker for the early diagnosis of CCA.}, } @article {pmid34887548, year = {2022}, author = {Conrad, RE and Viver, T and Gago, JF and Hatt, JK and Venter, SN and Rossello-Mora, R and Konstantinidis, KT}, title = {Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations.}, journal = {The ISME journal}, volume = {16}, number = {5}, pages = {1222-1234}, pmid = {34887548}, issn = {1751-7370}, support = {1831582//National Science Foundation (NSF)/ ; 1759831//National Science Foundation (NSF)/ ; }, mesh = {Bacteria/genetics ; *Genome, Bacterial ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Metagenomic surveys have revealed that natural microbial communities are predominantly composed of sequence-discrete, species-like populations but the genetic and/or ecological processes that maintain such populations remain speculative, limiting our understanding of population speciation and adaptation to perturbations. To address this knowledge gap, we sequenced 112 Salinibacter ruber isolates and 12 companion metagenomes from four adjacent saltern ponds in Mallorca, Spain that were experimentally manipulated to dramatically alter salinity and light intensity, the two major drivers of this ecosystem. Our analyses showed that the pangenome of the local Sal. ruber population is open and similar in size (~15,000 genes) to that of randomly sampled Escherichia coli genomes. While most of the accessory (noncore) genes were isolate-specific and showed low in situ abundances based on the metagenomes compared to the core genes, indicating that they were functionally unimportant and/or transient, 3.5% of them became abundant when salinity (but not light) conditions changed and encoded for functions related to osmoregulation. Nonetheless, the ecological advantage of these genes, while significant, was apparently not strong enough to purge diversity within the population. Collectively, our results provide an explanation for how this immense intrapopulation gene diversity is maintained, which has implications for the prokaryotic species concept.}, } @article {pmid34887510, year = {2021}, author = {Hrbacek, J and Morais, D and Cermak, P and Hanacek, V and Zachoval, R}, title = {Alpha-diversity and microbial community structure of the male urinary microbiota depend on urine sampling method.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {23758}, pmid = {34887510}, issn = {2045-2322}, mesh = {Aged ; *Biodiversity ; Comorbidity ; Humans ; Male ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Urinalysis ; Urinary Tract/*microbiology ; }, abstract = {Considerable variation exists in the methodology of urinary microbiota studies published so far including the cornerstone of any biomedical analysis: sample collection. The aim of this study was to compare the urinary microbiota of first-catch voided urine (FCU), mid-stream voided urine (MSU) and aseptically catheterised urine in men and define the most suitable urine sampling method. Forty-nine men (mean age 71.3 years) undergoing endoscopic urological procedures were enrolled in the study. Each of them contributed three samples: first-catch urine (FCU), mid-stream urine (MSU) and a catheterised urine sample. The samples were subjected to next-generation sequencing (NGS, n = 35) and expanded quantitative urine culture (EQUC, n = 31). Using NGS, Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant phyla in our population. The most abundant genera (in order of relative abundance) included: Prevotella, Veillonella, Streptococcus, Porphyromonas, Campylobacter, Pseudomonas, Staphylococcus, Ezakiella, Escherichia and Dialister. Eighty-two of 105 samples were dominated by a single genus. FCU, MSU and catheterised urine samples differed significantly in three of five alpha-diversity measures (ANOVA, p < 0.05): estimated number of operational taxonomic units, Chao1 and abundance-based coverage estimators. Beta-diversity comparisons using the PIME method (Prevalence Interval for Microbiome Evaluation) resulted in clustering of urine samples according to the mode of sampling. EQUC detected cultivable bacteria in 30/31 (97%) FCU and 27/31 (87%) MSU samples. Only 4/31 (13%) of catheterised urine samples showed bacterial growth. Urine samples obtained by transurethral catheterisation under aseptic conditions seem to differ from spontaneously voided urine samples. Whether the added value of a more exact reflection of the bladder microbiota free from urethral contamination outweighs the invasiveness of urethral catheterisation remains to be determined.}, } @article {pmid34887434, year = {2021}, author = {Goswami, K and Shope, AJ and Tokarev, V and Wright, JR and Unverdorben, LV and Ly, T and Chen See, J and McLimans, CJ and Wong, HT and Lock, L and Clarkson, S and Parvizi, J and Lamendella, R}, title = {Comparative meta-omics for identifying pathogens associated with prosthetic joint infection.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {23749}, pmid = {34887434}, issn = {2045-2322}, mesh = {Aged ; Aged, 80 and over ; Arthritis, Infectious/diagnosis/*etiology ; Biodiversity ; Computational Biology/methods ; Female ; Gene Expression Profiling ; Humans ; Male ; Metagenome ; Metagenomics/*methods ; Middle Aged ; Prosthesis-Related Infections/diagnosis/*etiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Prosthetic joint infections (PJI) are economically and personally costly, and their incidence has been increasing in the United States. Herein, we compared 16S rRNA amplicon sequencing (16S), shotgun metagenomics (MG) and metatranscriptomics (MT) in identifying pathogens causing PJI. Samples were collected from 30 patients, including 10 patients undergoing revision arthroplasty for infection, 10 patients receiving revision for aseptic failure, and 10 patients undergoing primary total joint arthroplasty. Synovial fluid and peripheral blood samples from the patients were obtained at time of surgery. Analysis revealed distinct microbial communities between primary, aseptic, and infected samples using MG, MT, (PERMANOVA p = 0.001), and 16S sequencing (PERMANOVA p < 0.01). MG and MT had higher concordance with culture (83%) compared to 0% concordance of 16S results. Supervised learning methods revealed MT datasets most clearly differentiated infected, primary, and aseptic sample groups. MT data also revealed more antibiotic resistance genes, with improved concordance results compared to MG. These data suggest that a differential and underlying microbial ecology exists within uninfected and infected joints. This study represents the first application of RNA-based sequencing (MT). Further work on larger cohorts will provide opportunities to employ deep learning approaches to improve accuracy, predictive power, and clinical utility.}, } @article {pmid34885912, year = {2021}, author = {Marfil-Santana, MD and Martínez-Cárdenas, A and Ruíz-Hernández, A and Vidal-Torres, M and Márquez-Velázquez, NA and Figueroa, M and Prieto-Davó, A}, title = {A Meta-Omics Analysis Unveils the Shift in Microbial Community Structures and Metabolomics Profiles in Mangrove Sediments Treated with a Selective Actinobacterial Isolation Procedure.}, journal = {Molecules (Basel, Switzerland)}, volume = {26}, number = {23}, pages = {}, pmid = {34885912}, issn = {1420-3049}, support = {UNAM-DGAPA-PAPIIT TA200415//National Autonomous University of Mexico/ ; UNAM-DGAPA-PAPIIT IN222220//National Autonomous University of Mexico/ ; Proyecto Semilla FQ//National Autonomous University of Mexico/ ; }, mesh = {Actinobacteria/genetics/*isolation & purification/metabolism ; Geologic Sediments/*microbiology ; Metabolome ; Metabolomics ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Mangrove sediment ecosystems in the coastal areas of the Yucatan peninsula are unique environments, influenced by their karstic origin and connection with the world's largest underground river. The microbial communities residing in these sediments are influenced by the presence of mangrove roots and the trading chemistry for communication between sediment bacteria and plant roots can be targeted for secondary metabolite research. To explore the secondary metabolite production potential of microbial community members in mangrove sediments at the "El Palmar" natural reserve in Sisal, Yucatan, a combined meta-omics approach was applied. The effects of a cultivation medium reported to select for actinomycetes within mangrove sediments' microbial communities was also analyzed. The metabolome of the microbial communities was analyzed by high-resolution liquid chromatography-tandem mass spectrometry, and molecular networking analysis was used to investigate if known natural products and their variants were present. Metagenomic results suggest that the sediments from "El Palmar" harbor a stable bacterial community independently of their distance from mangrove tree roots. An unexpected decrease in the observed abundance of actinomycetes present in the communities occurred when an antibiotic-amended medium considered to be actinomycete-selective was applied for a 30-day period. However, the use of this antibiotic-amended medium also enhanced production of secondary metabolites within the microbial community present relative to the water control, suggesting the treatment selected for antibiotic-resistant bacteria capable of producing a higher number of secondary metabolites. Secondary metabolite mining of "El Palmar" microbial community metagenomes identified polyketide synthase and non-ribosomal peptide synthetases' biosynthetic genes in all analyzed metagenomes. The presence of these genes correlated with the annotation of several secondary metabolites from the Global Natural Product Social Molecular Networking database. These results highlight the biotechnological potential of the microbial communities from "El Palmar", and show the impact selective media had on the composition of communities of actinobacteria.}, } @article {pmid34884735, year = {2021}, author = {Hernandez-Baixauli, J and Puigbò, P and Abasolo, N and Palacios-Jordan, H and Foguet-Romero, E and Suñol, D and Galofré, M and Caimari, A and Baselga-Escudero, L and Bas, JMD and Mulero, M}, title = {Alterations in Metabolome and Microbiome Associated with an Early Stress Stage in Male Wistar Rats: A Multi-Omics Approach.}, journal = {International journal of molecular sciences}, volume = {22}, number = {23}, pages = {}, pmid = {34884735}, issn = {1422-0067}, mesh = {Animals ; Biomarkers/blood/urine ; Male ; *Metabolome ; *Microbiota ; Rats, Wistar ; Stress, Psychological/*metabolism/microbiology ; Rats ; }, abstract = {Stress disorders have dramatically increased in recent decades becoming the most prevalent psychiatric disorder in the United States and Europe. However, the diagnosis of stress disorders is currently based on symptom checklist and psychological questionnaires, thus making the identification of candidate biomarkers necessary to gain better insights into this pathology and its related metabolic alterations. Regarding the identification of potential biomarkers, omic profiling and metabolic footprint arise as promising approaches to recognize early biochemical changes in such disease and provide opportunities for the development of integrative candidate biomarkers. Here, we studied plasma and urine metabolites together with metagenomics in a 3 days Chronic Unpredictable Mild Stress (3d CUMS) animal approach that aims to focus on the early stress period of a well-established depression model. The multi-omics integration showed a profile composed by a signature of eight plasma metabolites, six urine metabolites and five microbes. Specifically, threonic acid, malic acid, alpha-ketoglutarate, succinic acid and cholesterol were proposed as key metabolites that could serve as key potential biomarkers in plasma metabolome of early stages of stress. Such findings targeted the threonic acid metabolism and the tricarboxylic acid (TCA) cycle as important pathways in early stress. Additionally, an increase in opportunistic microbes as virus of the Herpesvirales was observed in the microbiota as an effect of the primary stress stages. Our results provide an experimental biochemical characterization of the early stage of CUMS accompanied by a subsequent omic profiling and a metabolic footprinting that provide potential candidate biomarkers.}, } @article {pmid34883258, year = {2022}, author = {Liu, X and Shen, M and Yan, H and Long, P and Jiang, H and Zhang, Y and Zhou, L and Yu, K and Qiu, G and Yang, H and Li, X and Min, X and He, M and Zhang, X and Choi, H and Wang, C and Wu, T}, title = {Alternations in the gut microbiota and metabolome with newly diagnosed unstable angina.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {49}, number = {3}, pages = {240-248}, doi = {10.1016/j.jgg.2021.11.009}, pmid = {34883258}, issn = {1673-8527}, mesh = {Angina, Unstable/diagnosis/genetics ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolome ; }, abstract = {Gut microbiota plays an important role in coronary heart disease, but its compositional and functional changes in unstable angina (UA) remain unexplored. We performed metagenomic sequencing of 133 newly diagnosed UA patients and 133 sex- and age-matched controls, and profiled the fecal and plasma metabolomes in 30 case-control pairs. The alpha diversity of gut microbiota was increased in UA patients: the adjusted odds ratios (ORs) per standard deviation increase in Shannon and Simpson indices were 1.30 (95% confidence interval, 1.01-1.70) and 1.36 (1.05-1.81), respectively. Two common species (depleted Klebsiella pneumoniae and enriched Streptococcus parasanguinis; P ≤ 0.002) and three rare species (depleted Weissella confusa, enriched Granulicatella adiacens and Erysipelotrichaceae bacterium 6_1_45; P ≤ 0.005) were associated with UA. The UA-associated gut microbiota was depleted in the pathway of L-phenylalanine degradation (P = 0.001), primarily contributed by Klebsiella pneumoniae. Consistently, we found increased circulating phenylalanine in UA patients (OR = 2.76 [1.17-8.16]). Moreover, Streptococcusparasanguinis was negatively correlated with fecal citrulline (Spearman's rs = -0.470, P = 0.009), a metabolite depleted in UA patients (OR = 0.26 [0.08-0.63]). These findings are informative to help understand the metabolic connection between gut microbiota and UA.}, } @article {pmid34882353, year = {2021}, author = {Balmasova, IP and Tsarev, VN and Unanyan, KG and Ippolitov, EV and Tsareva, TV and Kharakh, YN and Akhmedov, GD and Stepanova, SY and Katkov, II and Arutyunov, SD}, title = {Diagnostic value of microbiome biomarkers of the periodonite microbiome in patients with the association of chronic periodontitis and diabetes mellitus type 2.}, journal = {Klinicheskaia laboratornaia diagnostika}, volume = {66}, number = {11}, pages = {678-683}, doi = {10.51620/0869-2084-2021-66-11-678-683}, pmid = {34882353}, issn = {0869-2084}, mesh = {Biomarkers ; *Chronic Periodontitis/diagnosis ; *Diabetes Mellitus, Type 2/complications ; Humans ; Laboratories, Clinical ; *Microbiota ; }, abstract = {The place of high-tech methods of molecular biology in clinical laboratory diagnostics of various diseases and the development of a system of biomarkers as an important component of diagnostic research is currently attracting the closest attention of the scientific community. In this paper, an attempt is made to use high-tech metagenomic analysis to solve problems that arise due to the high frequency of association of periodontal diseases with systemic pathology, in particular, with type 2 diabetes mellitus. The aim of the study was to determine the taxonomic and metabolic features of the microbiome of periodontal tissues in periodontal diseases associated with type 2 diabetes mellitus, as a model of the ratio of local and systemic effects of periodontal pathogenic bacteria. The study included 16S shotgun sequencing of bacterial DNA as part of biological material from periodontal pockets/dentoalveolar furrows of 46 people - 15 patients with chronic periodontitis associated with type 2 diabetes mellitus, 15 patients with chronic periodontitis unrelated to systemic pathology, as well as 16 healthy people in the control group, followed by bioinformatic processing of the data obtained. The obtained data allowed us to establish the taxonomic features of the periodontal microbiome in the association of chronic periodontitis with type 2 diabetes mellitus, which included the predominance of representatives of the families Prevotellaceae and Spirochaetaceae in its composition. The features of metabolic processes in periodontal tissues with the participation of the microbiome were also revealed, which consisted in an increase in the exchange of cysteine and methionine against the background of a decrease in the metabolism of pyrimidine, methane, sphingolipids, and the synthesis of fatty acids, which are of diagnostic value in assessing the condition of patients with type 2 diabetes mellitus.}, } @article {pmid34881191, year = {2021}, author = {Afolayan, AO and Biagi, E and Rampelli, S and Candela, M and Brigidi, P and Turroni, S and Ayeni, FA}, title = {The Gut Microbiota of an Individual Varies With Intercontinental Four-Month Stay Between Italy and Nigeria: A Pilot Study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {725769}, pmid = {34881191}, issn = {2235-2988}, mesh = {Feces ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; Nigeria ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Despite well-established knowledge of the role of diet and the geographic effect on the gut microbiota of human populations, the temporal dynamics of the individual microbiota profile across changes associated with intercontinental short residence are still far from being understood. This pilot study sought to provide insights into the trajectory of the gut microbiota of an individual during a two-month stay in Italy and a subsequent two-month stay in Nigeria, by 16S rRNA gene sequencing and inferred metagenomics. The gut microbiota underwent massive but temporary changes, both taxonomically and based on predicted functionality. The faecal microbiota associated with the short stay in Italy progressively lost diversity and showed a dominance of Firmicutes, while after returning to Nigeria, the microbial community quickly regained the typical profile, in terms of biodiversity and bacterial signatures of traditional lifestyle, i.e., Prevotella and Treponema. Predicted pathways involved in glycolysis, fermentation and N-acetylneuraminate degradation were enriched during the subsequent two-month stay in Nigeria, whereas pathways associated with amino acid and peptidoglycan synthesis and maturation became over-represented during short stay in Italy. Our findings stress the plasticity of the individual gut microbiota even during a short-term travel, with loss/gain of taxonomic and functional features that mirror those of the gut microbiota of indigenous people dwelling therein.}, } @article {pmid34880054, year = {2022}, author = {Tomofuji, Y and Kishikawa, T and Maeda, Y and Ogawa, K and Nii, T and Okuno, T and Oguro-Igashira, E and Kinoshita, M and Yamamoto, K and Sonehara, K and Yagita, M and Hosokawa, A and Motooka, D and Matsumoto, Y and Matsuoka, H and Yoshimura, M and Ohshima, S and Nakamura, S and Inohara, H and Mochizuki, H and Takeda, K and Kumanogoh, A and Okada, Y}, title = {Whole gut virome analysis of 476 Japanese revealed a link between phage and autoimmune disease.}, journal = {Annals of the rheumatic diseases}, volume = {81}, number = {2}, pages = {278-288}, pmid = {34880054}, issn = {1468-2060}, mesh = {Asian People ; Autoimmune Diseases/*virology ; *Bacteriophages ; Case-Control Studies ; *Gastrointestinal Microbiome ; Humans ; *Virome ; }, abstract = {OBJECTIVE: The relationship between autoimmune diseases and the gut microbiome has been intensively studied, and several autoimmunity-associated bacterial taxa have been identified. However, much less is known about the roles of the gut virome in autoimmune diseases.

METHODS: Here, we performed a whole gut virome analysis based on the shotgun sequencing of 476 Japanese which included patients with rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), multiple sclerosis and healthy control subjects.

RESULTS: Our case-control comparison of the viral abundance revealed that crAss-like phages, which are one of the main components of a healthy gut virome, significantly decreased in the gut of the patients with autoimmune disease, specifically the patients with RA and SLE. In addition, Podoviridae significantly decreased in the gut of the patients with SLE. To understand how these viruses affected the bacteriome, we performed a quantitative virus-bacterium association analysis and clustered regularly interspaced short palindromic repeat-based virus-bacterium interaction analysis. We identified a symbiosis between Podoviridae and Faecalibacterium. In addition, multiple bacterial targets of crAss-like phages were identified (eg, Ruminococcus spp).

CONCLUSION: Our data suggest that the gut virome can affect our body either directly or via bacteria. Our analyses have elucidated a previously missing part of the autoimmunity-associated gut microbiome and presented new candidates that contribute to the development of autoimmune diseases.}, } @article {pmid34878610, year = {2021}, author = {Kumar, V and Kumar, S and Singh, D}, title = {Metagenomic insights into Himalayan glacial and kettle lake sediments revealed microbial community structure, function, and stress adaptation strategies.}, journal = {Extremophiles : life under extreme conditions}, volume = {26}, number = {1}, pages = {3}, pmid = {34878610}, issn = {1433-4909}, support = {MLP0143//CSIR-Institute of Himalayan Bioresource Technology/ ; }, mesh = {Geologic Sediments ; *Lakes ; Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Glacial and kettle lakes in the high-altitude Himalayas are unique habitats with significant scope for microbial ecology. The present study provides insights into bacterial community structure and function of the sediments of two high-altitude lakes using 16S amplicon and whole-genome shotgun (WGS) metagenomics. Microbial communities in the sediments of Parvati kund (glacial lake) and Bhoot ground (kettle lake) majorly consist of bacteria and a small fraction of archaea and eukaryota. The bacterial population has an abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Firmicutes, and Verrucomicrobia. Despite the common phyla, the sediments from each lake have a distinct distribution of bacterial and archaeal taxa. The analysis of the WGS metagenomes at the functional level provides a broad picture of microbial community metabolism of key elements and suggested chemotrophs as the major primary producers. In addition, the findings also revealed that polyhydroxyalkanoates (PHA) are a crucial stress adaptation molecule. The abundance of PHA metabolism in Alpha- and Betaproteobacteria and less representation in other bacterial and archaeal classes in both metagenomes was disclosed. The metagenomic insights provided an incisive view of the microbiome from Himalayan lake's sediments. It has also opened the scope for further bioprospection from virgin Himalayan niches.}, } @article {pmid34876793, year = {2021}, author = {Chung, MW and Kim, MJ and Won, EJ and Lee, YJ and Yun, YW and Cho, SB and Joo, YE and Hwang, JE and Bae, WK and Chung, IJ and Shin, MG and Shin, JH}, title = {Gut microbiome composition can predict the response to nivolumab in advanced hepatocellular carcinoma patients.}, journal = {World journal of gastroenterology}, volume = {27}, number = {42}, pages = {7340-7349}, pmid = {34876793}, issn = {2219-2840}, mesh = {*Carcinoma, Hepatocellular/drug therapy ; Feces ; *Gastrointestinal Microbiome ; Humans ; *Liver Neoplasms/drug therapy ; Male ; Nivolumab/therapeutic use ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Immunotherapy has revolutionized the clinical outcomes of intractable cancer patients. Little is known about the intestinal nonpathogenic bacterial composition of hepatocellular carcinoma (HCC) patients treated by immunotherapy.

AIM: To determine whether there is a correlation between gut bacterial composition and prognosis in HCC patients.

METHODS: From September 2019 to March 2020, we prospectively collected fecal samples and examined the gut microbiome of 8 advanced HCC patients treated with nivolumab as a second- or third-line systemic treatment. Fecal samples were collected before the start of immunotherapy. Fecal samples of patients with progression during treatment were collected at the time of progression, and fecal samples of patients who showed good response to nivolumab were collected after 5-7 mo as follow-up. Metagenomic data from 16S ribosomal RNA sequencing were analyzed using CLC Genomics Workbench. Microbiome data were analyzed according to therapeutic response.

RESULTS: All 8 patients were male, of which 6 had underlying chronic hepatitis B. A higher Shannon index was found in the responders than in the non-responders after nivolumab therapy (P = 0.036). The unweighted beta diversity analysis also showed that the overall bacterial community structure and phylogenetic diversity were clearly distinguished according to therapeutic response. There was no significant difference in the diversity or composition of the patient gut microbiome according to the immunotherapy used. Several taxa specific to therapeutic response were designated as follows: Dialister pneumosintes, Escherichia coli, Lactobacillus reteri, Streptococcus mutans, Enterococcus faecium, Streptococcus gordonii, Veillonella atypica, Granulicatella sp., and Trchuris trichiura for the non-responders; Citrobacter freundii, Azospirillum sp. and Enterococcus durans for the responders. Of note, a skewed Firmicutes/Bacteroidetes ratio and a low Prevotella/Bacteroides ratio can serve as predictive markers of non-response, whereas the presence of Akkermansia species predicts a good response.

CONCLUSION: The current presumptive study suggests a potential role for the gut microbiome as a prognostic marker for the response to nivolumab in treatment of HCC patients.}, } @article {pmid34876683, year = {2022}, author = {Taubert, M and Overholt, WA and Heinze, BM and Matanfack, GA and Houhou, R and Jehmlich, N and von Bergen, M and Rösch, P and Popp, J and Küsel, K}, title = {Bolstering fitness via CO2 fixation and organic carbon uptake: mixotrophs in modern groundwater.}, journal = {The ISME journal}, volume = {16}, number = {4}, pages = {1153-1162}, pmid = {34876683}, issn = {1751-7370}, support = {218627073//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; MetaPro//Helmholtz-Zentrum für Umweltforschung (Helmholtz Centre for Environmental Research)/ ; }, mesh = {Carbon ; Carbon Dioxide ; *Groundwater ; *Microbiota ; }, abstract = {Current understanding of organic carbon inputs into ecosystems lacking photosynthetic primary production is predicated on data and inferences derived almost entirely from metagenomic analyses. The elevated abundances of putative chemolithoautotrophs in groundwaters suggest that dark CO2 fixation is an integral component of subsurface trophic webs. To understand the impact of autotrophically fixed carbon, the flux of CO2-derived carbon through various populations of subsurface microbiota must first be resolved, both quantitatively and temporally. Here we implement novel Stable Isotope Cluster Analysis to render a time-resolved and quantitative evaluation of [13]CO2-derived carbon flow through a groundwater community in microcosms stimulated with reduced sulfur compounds. We demonstrate that mixotrophs, not strict autotrophs, were the most abundant active organisms in groundwater microcosms. Species of Hydrogenophaga, Polaromonas, Dechloromonas, and other metabolically versatile mixotrophs drove the production and remineralization of organic carbon. Their activity facilitated the replacement of 43% and 80% of total microbial carbon stores in the groundwater microcosms with [13]C in just 21 and 70 days, respectively. The mixotrophs employed different strategies for satisfying their carbon requirements by balancing CO2 fixation and uptake of available organic compounds. These different strategies might provide fitness under nutrient-limited conditions, explaining the great abundances of mixotrophs in other oligotrophic habitats, such as the upper ocean and boreal lakes.}, } @article {pmid34876615, year = {2021}, author = {Gao, B and Jose, A and Alonzo-Palma, N and Malik, T and Shankaranarayanan, D and Regunathan-Shenk, R and Raj, DS}, title = {Butyrate producing microbiota are reduced in chronic kidney diseases.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {23530}, pmid = {34876615}, issn = {2045-2322}, mesh = {Adolescent ; Bacteria/genetics/metabolism ; Butyrates/*metabolism ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Male ; Metagenomics/methods ; Renal Insufficiency, Chronic/*microbiology ; Severity of Illness Index ; }, abstract = {Chronic kidney disease is a major public health concern that affects millions of people globally. Alterations in gut microbiota composition have been observed in patients with chronic kidney disease. Nevertheless, the correlation between the gut microbiota and disease severity has not been investigated. In this study, we performed shot-gun metagenomics sequencing and identified several taxonomic and functional signatures associated with disease severity in patients with chronic kidney disease. We noted that 19 microbial genera were significantly associated with the severity of chronic kidney disease. The butyrate-producing bacteria were reduced in patients with advanced stages of chronic kidney diseases. In addition, functional metagenomics showed that two-component systems, metabolic activity and regulation of co-factor were significantly associated with the disease severity. Our study provides valuable information for the development of microbiota-oriented therapeutic strategies for chronic kidney disease.}, } @article {pmid34875513, year = {2022}, author = {Iasakov, TR and Kanapatskiy, TA and Toshchakov, SV and Korzhenkov, AA and Ulyanova, MO and Pimenov, NV}, title = {The Baltic Sea methane pockmark microbiome: The new insights into the patterns of relative abundance and ANME niche separation.}, journal = {Marine environmental research}, volume = {173}, number = {}, pages = {105533}, doi = {10.1016/j.marenvres.2021.105533}, pmid = {34875513}, issn = {1879-0291}, mesh = {Anaerobiosis ; Archaea/genetics ; Geologic Sediments ; *Methane ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; Planctomycetes ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Pockmarks are important "pumps", which are believed to play a significant role in the global methane cycling and harboring a unique assemblage of very diverse prokaryotes. This study reports the results of massive sequencing of the 16S rRNA gene V4 hypervariable regions for the samples from thirteen pockmark horizons (the Baltic Sea) collected at depths from 0 to 280 cm below seafloor (cmbsf) and the rates of microbially mediated anaerobic oxidation of methane (AOM) and sulfate reduction (SR). Altogether, 76 bacterial and 12 archaeal phyla were identified, 23 of which were candidate divisions. Of the total obtained in the pockmark sequences, 84.3% of them were classified as Bacteria and 12.4% as Archaea; 3.3% of the sequences were assigned to unknown operational taxonomic units (OTUs). Members of the phyla Planctomycetota, Chloroflexota, Desulfobacterota, Caldatribacteriota, Acidobacteriota and Proteobacteria predominated across all horizons, comprising 58.5% of the total prokaryotic community. These phyla showed different types of patterns of relative abundance. Analysis of AOM-SR-mediated prokaryotes abundance and biogeochemical measurements revealed that ANME-2a-2b subcluster was predominant in sulfate-rich upper horizons (including sulfate-methane transition zone (SMTZ)) and together with sulfate-reducing bacterial group SEEP-SRB1 had a primary role in AOM coupled to SR. At deeper sulfate-depleted horizons ANME-2a-2b shifted to ANME-1a and ANME-1b which alone mediated AOM or switch to methanogenic metabolism. Shifting of the ANME subclusters depending on depth reflect a tendency for niche separation in these groups. It was shown that the abundance of Caldatribacteriota and organohalide-respiring Dehalococcoidia (Chloroflexota) exhibited a strong correlation with AOM rates. This is the first detailed study of depth profiles of prokaryotic diversity, patterns of relative abundance, and ANME niche separation in the Baltic Sea pockmark microbiomes sheds light on assembly of prokaryotes in a pockmark.}, } @article {pmid34873691, year = {2022}, author = {Liu, Y and Zhang, F}, title = {Comparison of whole goat milk and its major fractions regarding the modulation of gut microbiota.}, journal = {Journal of the science of food and agriculture}, volume = {102}, number = {9}, pages = {3618-3627}, doi = {10.1002/jsfa.11708}, pmid = {34873691}, issn = {1097-0010}, support = {2021TD-31//Key Industry Innovation Chain of Shaanxi/ ; 31801566//National Natural Science Foundation of China/ ; 2020ZDLNY02-08//Shaanxi Provincial Science and Technology Department/ ; }, mesh = {Animals ; Bacteria/genetics ; Caseins ; *Gastrointestinal Microbiome ; Goats ; Lactobacillus ; Mice ; Milk/microbiology ; Whey Proteins ; }, abstract = {BACKGROUND: Goat milk can be important for human nutrition because of its nutritional value, which may be attributed to its richness in protein, lactose, fat, and other bioactive components. This study compared the diversity and composition of gut microbiota in response to whole goat milk and its major fractions (milk fat, casein, milk whey, whey protein, and whey supernatant). Goat milk, its major fractions, and sterile distilled water (for the control group) were administered to mice intragastrically, and gut microbiota were compared in these groups using metagenomic analysis.

RESULTS: We observed distinct patterns of gut microbiota from different diet groups. The sample distance heatmap showed that, compared with other goat milk fractions, gut microbiota in the casein group was more similar to that in the whole goat-milk group. The relative abundance of the genus Lactobacillus increased significantly after whole goat-milk treatment; the milk whey fraction increased the abundance of Blautia; milk fat and milk whey related fractions treatment promoted the population of Bacteroides. The network analysis showed that genera Lactobacillus and Lactococcus were negatively associated with Helicobacter and Acinetobacter, respectively.

CONCLUSION: Fractions of goat milk could contain different gut microbiota from whole goat milk. Consumption of certain goat milk fractions could increase the ingestion of beneficial bacteria and inhibit the growth of some pathogenic bacteria. Our results could provide the basis for the research into and development of goat-milk based functional foods. © 2021 Society of Chemical Industry.}, } @article {pmid34873061, year = {2021}, author = {Yang, P and Zheng, W and Ning, K and Zhang, Y}, title = {Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {49}, pages = {}, pmid = {34873061}, issn = {1091-6490}, support = {R01 AI134678/AI/NIAID NIH HHS/United States ; R35 GM136422/GM/NIGMS NIH HHS/United States ; S10 OD026825/OD/NIH HHS/United States ; }, mesh = {Algorithms ; Computational Biology/methods ; Databases, Protein ; Deep Learning ; Ecosystem ; Evolution, Molecular ; Humans ; Metagenome/genetics ; Microbiota/*genetics ; Neural Networks, Computer ; Protein Conformation ; Protein Folding ; Proteins/chemistry ; Sequence Alignment/*methods ; Sequence Analysis, Protein/*methods ; Sequence Homology ; }, abstract = {Information derived from metagenome sequences through deep-learning techniques has significantly improved the accuracy of template free protein structure modeling. However, most of the deep learning-based modeling studies are based on blind sequence database searches and suffer from low efficiency in computational resource utilization and model construction, especially when the sequence library becomes prohibitively large. We proposed a MetaSource model built on 4.25 billion microbiome sequences from four major biomes (Gut, Lake, Soil, and Fermentor) to decode the inherent linkage of microbial niches with protein homologous families. Large-scale protein family folding experiments on 8,700 unknown Pfam families showed that a microbiome targeted approach with multiple sequence alignment constructed from individual MetaSource biomes requires more than threefold less computer memory and CPU (central processing unit) time but generates contact-map and three-dimensional structure models with a significantly higher accuracy, compared with that using combined metagenome datasets. These results demonstrate an avenue to bridge the gap between the rapidly increasing metagenome databases and the limited computing resources for efficient genome-wide database mining, which provides a useful bluebook to guide future microbiome sequence database and modeling development for high-accuracy protein structure and function prediction.}, } @article {pmid34873013, year = {2021}, author = {Mao, J and Wang, D and Long, J and Yang, X and Lin, J and Song, Y and Xie, F and Xun, Z and Wang, Y and Wang, Y and Li, Y and Sun, H and Xue, J and Song, Y and Zuo, B and Zhang, J and Bian, J and Zhang, T and Yang, X and Zhang, L and Sang, X and Zhao, H}, title = {Gut microbiome is associated with the clinical response to anti-PD-1 based immunotherapy in hepatobiliary cancers.}, journal = {Journal for immunotherapy of cancer}, volume = {9}, number = {12}, pages = {}, pmid = {34873013}, issn = {2051-1426}, mesh = {Biliary Tract Neoplasms/*drug therapy/immunology/microbiology/pathology ; Carcinoma, Hepatocellular/*drug therapy/immunology/microbiology/pathology ; DNA, Bacterial/analysis/*genetics ; Female ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Humans ; Immune Checkpoint Inhibitors/*therapeutic use ; Liver Neoplasms/*drug therapy/immunology/microbiology/pathology ; Male ; Metagenomics ; Middle Aged ; Prognosis ; Programmed Cell Death 1 Receptor/*antagonists & inhibitors ; Survival Rate ; }, abstract = {BACKGROUND: The gut microbiome is associated with the response to immunotherapy for different cancers. However, the impact of the gut microbiome on hepatobiliary cancers receiving immunotherapy remains unknown. This study aims to investigate the relationship between the gut microbiome and the clinical response to anti-programmed cell death protein 1 (PD-1) immunotherapy in patients with advanced hepatobiliary cancers.

METHODS: Patients with unresectable hepatocellular carcinoma or advanced biliary tract cancers who have progressed from first-line chemotherapy (gemcitabine plus cisplatin) were enrolled. Fresh stool samples were collected before and during anti-PD-1 treatment and analyzed with metagenomic sequencing. Significantly differentially enriched taxa and prognosis associated taxa were identified. The Kyoto Encyclopedia of Genes and Genomes database and MetaCyc database were further applied to annotate the differentially enriched taxa to explore the potential mechanism of the gut microbiome influencing cancer immunotherapy.

RESULTS: In total, 65 patients with advanced hepatobiliary cancers receiving anti-PD-1 treatment were included in this study. Seventy-four taxa were significantly enriched in the clinical benefit response (CBR) group and 40 taxa were significantly enriched in the non-clinical benefit (NCB) group. Among these taxa, patients with higher abundance of Lachnospiraceae bacterium-GAM79 and Alistipes sp Marseille-P5997, which were significantly enriched in the CBR group, achieved longer progression-free survival (PFS) and overall survival (OS) than patients with lower abundance. Higher abundance of Ruminococcus calidus and Erysipelotichaceae bacterium-GAM147 enriched in the CBR group was also observed in patients with better PFS. In contrast, worse PFS and OS were found in patients with higher abundance of Veillonellaceae, which was significantly enriched in the NCB group. Functional annotation indicated that the taxa enriched in the CBR group were associated with energy metabolism while the taxa enriched in the NCB group were associated with amino acid metabolism, which may modulate the clinical response to immunotherapy in hepatobiliary cancers. In addition, immunotherapy-related adverse events were affected by the gut microbiome diversity and relative abundance.

CONCLUSIONS: We demonstrate that the gut microbiome is associated with the clinical response to anti-PD-1 immunotherapy in patients with hepatobiliary cancers. Taxonomic signatures enriched in responders are effective biomarkers to predict the clinical response and survival benefit of immunotherapy, which might provide a new therapeutic target to modulate the response to cancer immunotherapy.}, } @article {pmid34872176, year = {2022}, author = {Chen, X and Hu, X and Lu, Q and Yang, Y and Linghu, S and Zhang, X}, title = {Study on the differences in sludge toxicity and microbial community structure caused by catechol, resorcinol and hydroquinone with metagenomic analysis.}, journal = {Journal of environmental management}, volume = {302}, number = {Pt A}, pages = {114027}, doi = {10.1016/j.jenvman.2021.114027}, pmid = {34872176}, issn = {1095-8630}, mesh = {Bioreactors ; Catechols/toxicity ; Hydroquinones/toxicity ; *Microbiota ; Resorcinols/toxicity ; *Sewage ; }, abstract = {The aerobic biodegradation rate, organic toxicity and microbial community structure of activated sludge acclimated by catechol, resorcinol and hydroquinone were investigated, to study the relationship between microbial structure and sludge organic toxicity caused by phenolic compounds. At the stable operation stage, the degradation rates of the dihydroxy benzenes in a single sequencing batch reactor (SBR) cycle were followed the order: resorcinol (89.71%) > hydroquinone (85.64%) > catechol (59.62%). Sludge toxicity bioassay indicated that the toxicity of sludge was catechol (45.63%) > hydroquinone (40.28%) > resorcinol (38.15%). The accumulation of secondary metabolites such as 5-10 kDa tryptophan and tyrosine protein substances caused the differential sludge toxicity. Microbial metagenomic analysis showed that the toxicity of sludge was significantly related to the microbial community structure. Thauera, Azoarcus, Pseudomonas and other Proteobacteria formed in the sludge during acclimation. Catechol group had the least dominant bacteria and loop ring opening enzyme genes (catA, dmpB, dxnF, hapD) numbers. Therefore, the degradation of catechol was the most difficult than resorcinol and hydroquinone, resulting the highest sludge toxicity.}, } @article {pmid34867834, year = {2021}, author = {Thomas, P and Sahu, PK}, title = {Vertical Transmission of Diverse Cultivation-Recalcitrant Endophytic Bacteria Elucidated Using Watermelon Seed Embryos.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {635810}, pmid = {34867834}, issn = {1664-302X}, abstract = {Seed transmission of endophytic microorganisms is a growing research area in plant biology and microbiology. We employed cultivation versus cultivation-independent approaches on excised embryos from watermelon seeds (6-12 months in storage) and on embryo-derived in vitro seedlings (EIVS) to assess the vertical transmission of endophytic bacteria. Surface-disinfected watermelon seeds bore abundant residual bacteria in the testa and perisperm tissues, predominantly Bacillus spp. propounding the essentiality of excluding all non-embryonic tissues for vertical transmission studies. Tissue homogenates from re-disinfected seed embryos displayed no cultivable bacteria during the 1-week monitoring. Bright-field live microscopy revealed abundant bacteria in tissue homogenates and in embryo sections as intracellular motile particles. Confocal imaging on embryo sections after SYTO-9 staining and eubacterial fluorescent in situ hybridization (FISH) endorsed enormous bacterial colonization. Quantitative Insights Into Microbial Ecology (QIIME)-based 16S rRNA V3-V4 taxonomic profiling excluding the preponderant chloroplast and mitochondrial sequences revealed a high bacterial diversity in watermelon seed embryos mainly Firmicutes barring spore formers followed by Proteobacteria, Bacteroidetes, and Actinobacteria, and other minor phyla. Embryo-base (comprising the radicle plus plumule parts) and embryo-cotyledon parts differed in bacterial profiles with the abundance of Firmicutes in the former and Proteobacteria dominance in the latter. EIVS displayed a higher bacterial diversity over seed embryos indicating the activation from the dormant stage of more organisms in seedlings or their better amenability to DNA techniques. It also indicated embryo-to-seedling bacterial transmission, varying taxonomic abundances for seed embryos and seedlings, and differing phylogenic profiles for root, hypocotyl, and cotyledon/shoot-tip tissues. Investigations on different watermelon cultivars confirmed the embryo transmission of diverse cultivation recalcitrant endophytic bacteria. Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes formed the core phyla across different cultivars with 80-90% similarity at genus to phylum levels. Conversely, freshly harvested seeds displayed a dominance of Proteobacteria. The findings revealed that dicot seeds such as in different watermelon cultivars come packaged with abundant and diverse vertical and seedling-transmissible cultivation recalcitrant endophytic bacteria with significant implications for plant biology.}, } @article {pmid34865900, year = {2022}, author = {Zhu, F and Yan, Y and Doyle, E and Zhu, C and Jin, X and Chen, Z and Wang, C and He, H and Zhou, D and Gu, C}, title = {Microplastics altered soil microbiome and nitrogen cycling: The role of phthalate plasticizer.}, journal = {Journal of hazardous materials}, volume = {427}, number = {}, pages = {127944}, doi = {10.1016/j.jhazmat.2021.127944}, pmid = {34865900}, issn = {1873-3336}, mesh = {*Microbiota ; *Microplastics ; Nitrogen ; Phthalic Acids ; Plasticizers ; Plastics ; Soil ; Soil Microbiology ; }, abstract = {Microplastics are emerging contaminants that are increasingly detected in soil environment, but their impact on soil microbiota and related biogeochemical processes remains poorly understood. In particular, the mechanisms involved (e.g., the role of chemical additives) are still elusive. In this study, we found that plasticizer-containing polyvinyl chloride (PVC) microplastics at 0.5% (w/w) significantly increased soil NH4[+]-N content and decreased NO3[-]-N content by up to 91%, and shaped soil microbiota into a microbial system with more nitrogen-fixing microorganisms (as indicated by nifDHK gene abundance), urea decomposers (ureABC genes and urease activity) and nitrate reducers (nasA, NR, NIT-6 and napAB genes), and less nitrifiers (amoC gene and potential nitrification rate). Exposure to plasticizer alone had a similar effect on soil nitrogen parameters but microplastics of pure PVC polymer (either granule or film) had little effect over 60 days, indicating that phthalate plasticizer released from microplastics was the main driver of effects observed. Furthermore, a direct link between phthalate plasticizer, microbial taxonomic changes and altered nitrogen metabolism was established by the isolation of phthalate-degrading bacteria involved in nitrogen cycling. This study highlights the importance of chemical additives in determining the interplay of microplastics with microbes and nutrient cycling, which needs to be considered in future studies.}, } @article {pmid34865800, year = {2021}, author = {Zhang, Z and Han, Z and Wu, Y and Jiang, S and Ma, C and Zhang, Y and Zhang, J}, title = {Metagenomics assembled genome scale analysis revealed the microbial diversity and genetic polymorphism of Lactiplantibacillus plantarum in traditional fermented foods of Hainan, China.}, journal = {Food research international (Ottawa, Ont.)}, volume = {150}, number = {Pt A}, pages = {110785}, doi = {10.1016/j.foodres.2021.110785}, pmid = {34865800}, issn = {1873-7145}, mesh = {*Fermented Foods ; Food Microbiology ; Humans ; Metagenomics ; *Microbiota ; Polymorphism, Genetic ; }, abstract = {Exploring the microbiome in fermented foods and their effects on food quality and sustainability is beneficial to provide data support for understanding how they affects human physiology. Here, metagenomic sequencing and metagenomic assembled genomes (MAGs) were applied to appraise the microbial diversity of fermented Yucha (FYC) and fermented vegetables (FVE). The antibiotic resistance genes (ARGs) enrichment and genetic polymorphism of Lactiplantibacillus plantarum in fermented foods of different regions were compared. The results showed that Lactiplantibacillus plantarum was the dominant species in FYC, while Lactiplantibacillus fermentum in FVE occupied the dominant position. From 32 high-quality MAGs, the central differential Lactic acid bacteria were higher in FVE. By comparing the Lactiplantibacillus plantarum MAGs in Hainan and Other regions, we found that the total Single Nucleotide Polymorphisms of Lactiplantibacillus plantarum in Hainan were significantly higher than other areas. Six non-synonymous mutations were included in the primary differential mutation, especially TrkA family potassium uptake protein and MerR family transcriptional regulator, which may be related to the hypersaline environment and highest ARGs enrichment in Hainan. This research provides valuable insight into our understanding of the microbiome of fermented food. Meanwhile, the analysis of Lactiplantibacillus plantarum genetic polymorphism based on MAGs helps us understand this strain's evolutionary history.}, } @article {pmid34864967, year = {2021}, author = {Sato, Y and Takebe, H and Tominaga, K and Oishi, K and Kumagai, H and Yoshida, T and Hirooka, H}, title = {Taxonomic and functional characterization of the rumen microbiome of Japanese Black cattle revealed by 16S rRNA gene amplicon and metagenome shotgun sequencing.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {12}, pages = {}, doi = {10.1093/femsec/fiab152}, pmid = {34864967}, issn = {1574-6941}, mesh = {Animals ; Cattle ; Diet ; Genes, rRNA ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Rumen ; }, abstract = {This study aimed to determine the taxonomic and functional characteristics of the Japanese Black (JB) steer rumen microbiome. The rumen microbiomes of six JB steers (age 14.7 ± 1.44 months) and six JB sires × Holstein dams crossbred (F1) steers (age 11.1 ± 0.39 months), fed the same diet, were evaluated. Based on 16S rRNA gene sequencing, the beta diversity revealed differences in microbial community structures between the JB and F1 rumen. Shotgun sequencing showed that Fibrobacter succinogenes and two Ruminococcus spp., which are related to cellulose degradation were relatively more abundant in the JB steer rumen than in the F1 rumen. Furthermore, the 16S rRNA gene copy number of F. succinogenes was significantly higher in the JB steer rumen than in the F1 rumen according to quantitative real-time polymerase chain reaction analysis. Genes encoding the enzymes that accelerate cellulose degradation and those associated with hemicellulose degradation were enriched in the JB steer rumen. Although Prevotella spp. were predominant both in the JB and F1 rumen, the genes encoding carbohydrate-active enzymes of Prevotella spp. may differ between JB and F1.}, } @article {pmid34864203, year = {2022}, author = {Maran, MIJ and Davis G, DJ}, title = {Benefits of merging paired-end reads before pre-processing environmental metagenomics data.}, journal = {Marine genomics}, volume = {61}, number = {}, pages = {100914}, doi = {10.1016/j.margen.2021.100914}, pmid = {34864203}, issn = {1876-7478}, mesh = {Biodiversity ; *High-Throughput Nucleotide Sequencing ; *Metagenomics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: High throughput sequencing of environmental DNA has applications in biodiversity monitoring, taxa abundance estimation, understanding the dynamics of community ecology, and marine species studies and conservation. Environmental DNA, especially, marine eDNA, has a fast degradation rate. Aside from the good quality reads, the data could have a significant number of reads that fall slightly below the default PHRED quality threshold of 30 on sequencing. For quality control, trimming methods are employed, which generally precede the merging of the read pairs. However, in the case of eDNA, a significant percentage of reads within the acceptable quality score range are also dropped.

METHODS: To infer the ideal merge tool that is sensitive to eDNA, two Hiseq paired-end eDNA datasets were utilized to study the merging by the tools - FLASH (Fast Length Adjustment of SHort reads), PANDAseq, COPE, BBMerge, and VSEARCH without preprocessing. We assessed these tools on the following parameters: Time taken to process, the quality, and the number of merged reads. Trimmomatic, a widely-used preprocessing tool, was also assessed by preprocessing the datasets at different parameters for the two approaches of preprocessing: Sliding Window and Maximum Information. The preprocessed read pairs were then merged using the ideal merge tool identified earlier.

RESULTS: FLASH is the most efficient merge tool balancing data conservation, quality of reads, and processing time. We compared Trimmomatic's two quality trimming options with increasing strictness with FLASH's direct merge. The raw reads processed with Trimmomatic then merged, yielded a significant drop in reads compared to the direct merge. An average of 29% of reads was dropped when directly merged with FLASH. Maximum Information option resulted in 30.7% to 68.05% read loss with lowest and highest stringency parameters, respectively. The Sliding Window approach conserves approximately 10% more reads at a PHRED score of 25 set as the threshold for a window of size 4. The lowered PHRED cut off conserves about 50% of the reads that could potentially be informative. We noted no significant reduction of data while optimizing the number of reads read in a window with the ideal quality (Q) score.

CONCLUSIONS: Losing reads can negatively impact the downstream processing of the environmental data, especially for sequence alignment studies. The quality trim-first-merge-later approach can significantly decrease the number of reads conserved. However, direct merging of pair-end reads using FLASH conserved more than 60% of the reads. Therefore, direct merging of the paired-end reads can prevent potential removal of informative reads that do not comply by the trimming tool's strict checks. FLASH to be an efficient tool in conserving reads while carrying out quality trimming in moderation. Overall, our results show that merging paired-end reads of eDNA data before trimming can conserve more reads.}, } @article {pmid34864063, year = {2022}, author = {Pradhan, S and Ray, P and Aich, P}, title = {Microbiota transplantation from younger to older mice could restore lost immunity to effectively clear salmonella infection in Th2-biased BALB/c mice.}, journal = {Life sciences}, volume = {288}, number = {}, pages = {120201}, doi = {10.1016/j.lfs.2021.120201}, pmid = {34864063}, issn = {1879-0631}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*growth & development ; Cecum/*transplantation ; Fecal Microbiota Transplantation/*methods ; Gastrointestinal Microbiome ; Homeostasis ; Immunity, Innate ; Male ; Metabolome ; Metagenomics ; Mice ; Mice, Inbred BALB C ; Salmonella/drug effects/genetics/*immunology/metabolism ; Salmonella Infections/immunology/metabolism/microbiology/*therapy ; Th2 Cells/*immunology ; }, abstract = {AIMS: The composition, overtly abundance, and diversity of gut microbiota, play a significant role in maintaining physiological homeostasis with age. Reports revealed that the gut microbial profile might be correlated with immunity and metabolism. It is, therefore, tantamount to know if an older individual can achieve the immunity and metabolic profile of a younger individual by receiving the gut microbiome of a younger individual. In the current report, we have studied the effects of cecal microbiota transplantation (CMT) from younger to older mice.

MATERIALS AND METHODS: In this study, older BALB/c mice (23 weeks) received CMT from younger BALB/c mice (3 weeks).

KEY FINDINGS: CMT recipient mice showed altered expressions of immune and tight junction protein genes in the colon of mice, while the non-CMT recipient mice did not. Older mice were treated with AVNM to make them compatible with CMT. Further data from metabolite studies revealed that AVNM treatment mainly affected the aromatic amino acid biosynthesis pathway while CMT mostly affected the metabolism of different carbohydrates. We repeated the analysis in C57BL/6 mice without any significant effects of CMT.

SIGNIFICANCE: Results revealed that mice who received CMT showed more efficient restoration of gut microbiota than non-CMT recipient mice. CMT caused the alleviation of Salmonella infection and efficient recovery of the cecal index in the mice following antibiotics treatment.}, } @article {pmid34862696, year = {2022}, author = {Jiao, S and Chen, W and Wei, G}, title = {Core microbiota drive functional stability of soil microbiome in reforestation ecosystems.}, journal = {Global change biology}, volume = {28}, number = {3}, pages = {1038-1047}, doi = {10.1111/gcb.16024}, pmid = {34862696}, issn = {1365-2486}, mesh = {Metagenomics ; *Microbiota ; *Soil ; Soil Microbiology ; }, abstract = {Revealing the ecological roles of core microbiota in the maintenance of the functional stability of soil microbiomes is crucial for sustainable ecosystem functioning; however, there is a dearth of whole-soil profile studies on the fundamental topic in microbial ecology, especially in the context of ecological restoration. Here, we explored whether core microbiota influence the temporal changes in the functional stability of soil microbiomes throughout the soil profile (i.e., soil depths of 0-300 cm) during natural succession in restored ex-arable ecosystems, via high-throughput amplicon and metagenomic sequencing. We revealed that core microbiota were essential for the maintenance of the functional stability of soil microbiomes in reforestation ecosystems. Specifically, the core taxa within one cluster of soil network, which had similar ecological preferences, had major contributions to functional stability. Reforestation significantly decreased the functional stability of soil microbiomes, which exhibited significant variations along the vertical soil profile in the reforested soils. Overall, the findings enhance our understanding of the factors driving functional stability in soil microbiomes, and suggests that core microbiota should be considered a key factor and integrated in policy and management activities targeting the enhancement and maintenance of functional stability and ecosystem sustainability in ecological restoration programs.}, } @article {pmid34862599, year = {2022}, author = {Li, Y and Zhao, D and Qian, M and Liu, J and Pan, C and Zhang, X and Duan, X and Zhang, Y and Jia, W and Wang, L}, title = {Amlodipine, an anti-hypertensive drug, alleviates non-alcoholic fatty liver disease by modulating gut microbiota.}, journal = {British journal of pharmacology}, volume = {179}, number = {9}, pages = {2054-2077}, doi = {10.1111/bph.15768}, pmid = {34862599}, issn = {1476-5381}, mesh = {Amlodipine/pharmacology/therapeutic use ; Animals ; Antihypertensive Agents/pharmacology/therapeutic use ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Mice ; *Non-alcoholic Fatty Liver Disease/drug therapy/metabolism ; }, abstract = {BACKGROUND AND PURPOSE: Non-alcoholic fatty liver disease (NAFLD) represents a severe public health problem. It often coexists with hypertension in the context of metabolic syndrome. We investigated the effects of amlodipine on NAFLD combined with hypertension and investigated the underlying mechanism/s.

EXPERIMENTAL APPROACH: Mice were fed with high-fat diet (HFD) and 0.05% N-nitro-L-arginine methylester sterile water to induce NAFLD with hypertension. Gut microbiota composition and function were assessed by 16S ribosomal DNA and metagenomic sequencing. Untargeted metabolome profiles were applied to identify differential metabolites in mice caecum.

KEY RESULTS: Amlodipine besylate and amlodipine aspartate significantly decreased liver injury and hepatic steatosis, and improved lipid metabolism with a concomitant reduction in the expression of lipogenic genes in mice with NAFLD and hypertension. Mechanistically, amlodipine besylate and amlodipine aspartate have potential to restore intestinal barrier integrity and improve antimicrobial defence, along with the elevated abundances of Akkermansia, Bacteroides and Lactobacillus. Noteworthily, the gut microbiota in amlodipine besylate- and amlodipine aspartate-treated mice had higher abundance of functional genes involved in taurine and hypotaurine metabolism. Consistently, the strengthened taurine and hypotaurine metabolism was confirmed by untargeted metabolome analysis. Based on the correlation and causal analysis, the altered gut microbiota composition and the enhancement of taurine and hypotaurine metabolism may synergistically decreased alanine aminotransferase, liver triglycerides, lipogenic genes and plasma cholesterol in HFD-fed hypertensive mice.

CONCLUSION AND IMPLICATIONS: Amlodipine besylate and amlodipine aspartate exert multifactorial improvements in NAFLD and hypertension by modulating gut microbiota. They may serve as promising therapeutic agents for treating these diseases.}, } @article {pmid34862421, year = {2021}, author = {Palomba, A and Tanca, A and Abbondio, M and Sau, R and Serra, M and Marongiu, F and Fraumene, C and Pagnozzi, D and Laconi, E and Uzzau, S}, title = {Time-restricted feeding induces Lactobacillus- and Akkermansia-specific functional changes in the rat fecal microbiota.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {85}, pmid = {34862421}, issn = {2055-5008}, support = {FAR 2019/2020//Università degli Studi di Sassari (University of Sassari)/ ; }, mesh = {Akkermansia ; Animals ; *Gastrointestinal Microbiome ; Lactobacillus ; *Microbiota ; Rats ; Verrucomicrobia ; }, abstract = {Diet is a key factor influencing gut microbiota (GM) composition and functions, which in turn affect host health. Among dietary regimens, time-restricted (TR) feeding has been associated to numerous health benefits. The impact of TR feeding on the GM composition has been mostly explored by means of metagenomic sequencing. To date, however, little is known about the modulation of GM functions by this dietary regimen. Here, we analyzed the effects of TR feeding on GM functions by evaluating protein expression changes in a rat model through a metaproteomic approach. We observed that TR feeding has a relevant impact on GM functions, specifically leading to an increased abundance of several enzymes involved in carbohydrate and protein metabolism and expressed by Lactobacillus spp. and Akkermansia muciniphila. Taken together, these results contribute to deepening our knowledge about the key relationship between diet, GM, and health.}, } @article {pmid34862253, year = {2022}, author = {Dutta, M and Lim, JJ and Cui, JY}, title = {Pregnane X Receptor and the Gut-Liver Axis: A Recent Update.}, journal = {Drug metabolism and disposition: the biological fate of chemicals}, volume = {50}, number = {4}, pages = {478-491}, pmid = {34862253}, issn = {1521-009X}, support = {P30 ES005605/ES/NIEHS NIH HHS/United States ; R01 ES031098/ES/NIEHS NIH HHS/United States ; R01 ES030197/ES/NIEHS NIH HHS/United States ; T32 ES007032/ES/NIEHS NIH HHS/United States ; R01 GM111381/GM/NIGMS NIH HHS/United States ; P30 ES007033/ES/NIEHS NIH HHS/United States ; R01 ES025708/ES/NIEHS NIH HHS/United States ; }, mesh = {Female ; *Gastrointestinal Microbiome/physiology ; Humans ; *Liver/metabolism/physiology ; Male ; *Pregnane X Receptor/metabolism ; Receptors, Cytoplasmic and Nuclear/metabolism ; Receptors, Steroid/metabolism ; *Xenobiotics/metabolism ; }, abstract = {It is well-known that the pregnane X receptor (PXR)/Nr1i2 is a critical xenobiotic-sensing nuclear receptor enriched in liver and intestine and is responsible for drug-drug interactions, due to its versatile ligand binding domain (LBD) and target genes involved in xenobiotic biotransformation. PXR can be modulated by various xenobiotics including pharmaceuticals, nutraceuticals, dietary factors, and environmental chemicals. Microbial metabolites such as certain secondary bile acids (BAs) and the tryptophan metabolite indole-3-propionic acid (IPA) are endogenous PXR activators. Gut microbiome is increasingly recognized as an important regulator for host xenobiotic biotransformation and intermediary metabolism. PXR regulates and is regulated by the gut-liver axis. This review summarizes recent research advancements leveraging pharmaco- and toxico-metagenomic approaches that have redefined the previous understanding of PXR. Key topics covered in this review include: (1) genome-wide investigations on novel PXR-target genes, novel PXR-DNA interaction patterns, and novel PXR-targeted intestinal bacteria; (2) key PXR-modulating activators and suppressors of exogenous and endogenous sources; (3) novel bidirectional interactions between PXR and gut microbiome under physiologic, pathophysiological, pharmacological, and toxicological conditions; and (4) modifying factors of PXR-signaling including species and sex differences and time (age, critical windows of exposure, and circadian rhythm). The review also discusses critical knowledge gaps and important future research topics centering around PXR. SIGNIFICANCE STATEMENT: This review summarizes recent research advancements leveraging O'mics approaches that have redefined the previous understanding of the xenobiotic-sensing nuclear receptor pregnane X receptor (PXR). Key topics include: (1) genome-wide investigations on novel PXR-targeted host genes and intestinal bacteria as well as novel PXR-DNA interaction patterns; (2) key PXR modulators including microbial metabolites under physiological, pathophysiological, pharmacological, and toxicological conditions; and (3) modifying factors including species, sex, and time.}, } @article {pmid34861636, year = {2022}, author = {Wang, XH and Yang, YN and Liang, Y and Lang, R and Zeng, Q and Yan, L and Yu, RH and Wu, CM}, title = {Structural modulation of gut microbiota during alleviation of experimental passive Heymann nephritis in rats by a traditional Chinese herbal formula.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {145}, number = {}, pages = {112475}, doi = {10.1016/j.biopha.2021.112475}, pmid = {34861636}, issn = {1950-6007}, mesh = {Animals ; Antioxidants/pharmacology ; Apoptosis/drug effects ; Dose-Response Relationship, Drug ; Drug Monitoring ; Drugs, Chinese Herbal/analysis/*pharmacology ; *Gastrointestinal Microbiome/drug effects/physiology ; *Glomerulonephritis, Membranous/drug therapy/metabolism/microbiology ; Oxidative Stress/drug effects ; *Podocytes/drug effects/metabolism ; Rats ; Treatment Outcome ; }, abstract = {BACKGROUND: Jianpi-Qushi-Heluo formula (JQHF) has been used to treat idiopathic membranous nephropathy (IMN) in hospitals for many years.

PURPOSE: Elucidating the protective effect and exploring the potential mechanism of JQHF against IMN.

METHODS: Passive Heymann nephritis (PHN) was induced in rats by a single tail vein injection of anti-Fx1A antiserum. Then, the animals were treated with JQHF at 16.2 g/kg or 32.4 g/kg, with benzepril (10 mg/kg) as a positive control. Renal function was evaluated by biochemical measurements and pathological testing. Fecal samples were collected before and after treatment to analyze the gut microbiota composition by shotgun whole metagenome sequencing.

RESULTS: JQHF exhibited potent efficacy in ameliorating PHN at both doses, as revealed by decreasing the deposition of IgG and C5b-9, relieving podocyte injury, and reducing glomerular and tubular cell apoptosis. The lower dose was corresponding to the clinical dosage and showed better therapeutic effects than the higher dose. Metagenomic analysis showed that gavage with 16.2 g/kg of JQHF shifted the structure of the gut microbiota in PHN rats and significantly increased the relative abundances of Prevotella copri, Lactobacillus vaginalis and Subdoligranulum variabile. Particularly, S. variabile was strongly negatively correlated with serum levels of TC and TG, the deposition of IgG and C5b-9, and apoptosis of glomerular cells.

CONCLUSIONS: The JQHF is an effective agent for the treatment of experimental PHN. The PHN-allevating effect of JQHF is associated with specific alternation of gut microbiota.}, } @article {pmid34861073, year = {2022}, author = {Chellappa, SL and Engen, PA and Naqib, A and Qian, J and Vujovic, N and Rahman, N and Green, SJ and Garaulet, M and Keshavarzian, A and Scheer, FAJL}, title = {Proof-of-principle demonstration of endogenous circadian system and circadian misalignment effects on human oral microbiota.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {36}, number = {1}, pages = {e22043}, pmid = {34861073}, issn = {1530-6860}, support = {R01 DK099512/DK/NIDDK NIH HHS/United States ; R01 HL118601/HL/NHLBI NIH HHS/United States ; R24 AA026801/AA/NIAAA NIH HHS/United States ; R01 DK102696/DK/NIDDK NIH HHS/United States ; R01 HL140574/HL/NHLBI NIH HHS/United States ; UL1 TR001102/TR/NCATS NIH HHS/United States ; K99 HL148500/HL/NHLBI NIH HHS/United States ; R01 DK105072/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; *Circadian Rhythm ; Female ; Humans ; Male ; *Microbiota ; Mouth/*microbiology ; Proof of Concept Study ; Saliva/*microbiology ; *Shift Work Schedule ; }, abstract = {Circadian misalignment-the misalignment between the central circadian "clock" and behavioral and environmental cycles (including sleep/wake, fasting/eating, dark/light)-results in adverse cardiovascular and metabolic effects. Potential underlying mechanisms for these adverse effects include alterations in the orogastrointestinal microbiota. However, it remains unknown whether human oral microbiota has endogenous circadian rhythms (i.e., independent of sleep/wake, fasting/eating, and dark/light cycles) and whether circadian misalignment influences oral microbiota community composition. Healthy young individuals [27.3 ± 2.3 years (18-35 years), 4 men and 2 women, body-mass index range: 18-28 kg/m[2] ] were enrolled in a stringently controlled 14-day circadian laboratory protocol. This included a 32-h constant routine (CR) protocol (endogenous circadian baseline assessment), a forced desynchrony protocol with four 28-h "days" under ~3 lx to induce circadian misalignment, and a post-misalignment 40-h CR protocol. Microbiota assessments were performed on saliva samples collected every 4 h throughout both CR protocols. Total DNA was extracted and processed using high-throughput 16S ribosomal RNA gene amplicon sequencing. The relative abundance of specific oral microbiota populations, i.e., one of the five dominant phyla, and three of the fourteen dominant genera, exhibited significant endogenous circadian rhythms. Importantly, circadian misalignment dramatically altered the oral microbiota landscape, such that four of the five dominant phyla and eight of the fourteen dominant genera exhibited significant circadian misalignment effects. Moreover, circadian misalignment significantly affected the metagenome functional content of oral microbiota (inferred gene content analysis), as indicated by changes in specific functional pathways associated with metabolic control and immunity. Collectively, our proof-of-concept study provides evidence for endogenous circadian rhythms in human oral microbiota and show that even relatively short-term experimental circadian misalignment can dramatically affect microbiota community composition and functional pathways involved in metabolism and immune function. These proof-of-principle findings have translational relevance to individuals typically exposed to circadian misalignment, including night shift workers and frequent flyers.}, } @article {pmid34857933, year = {2022}, author = {Weiss, AS and Burrichter, AG and Durai Raj, AC and von Strempel, A and Meng, C and Kleigrewe, K and Münch, PC and Rössler, L and Huber, C and Eisenreich, W and Jochum, LM and Göing, S and Jung, K and Lincetto, C and Hübner, J and Marinos, G and Zimmermann, J and Kaleta, C and Sanchez, A and Stecher, B}, title = {In vitro interaction network of a synthetic gut bacterial community.}, journal = {The ISME journal}, volume = {16}, number = {4}, pages = {1095-1109}, pmid = {34857933}, issn = {1751-7370}, support = {395357507//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 315980449//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; CRC 1182//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Cluster of Excellence 2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 865615//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; }, mesh = {Animals ; Bacteria/genetics/metabolism ; *Gastrointestinal Microbiome ; Metabolic Networks and Pathways ; Mice ; *Microbiota ; Nutrients ; }, abstract = {A key challenge in microbiome research is to predict the functionality of microbial communities based on community membership and (meta)-genomic data. As central microbiota functions are determined by bacterial community networks, it is important to gain insight into the principles that govern bacteria-bacteria interactions. Here, we focused on the growth and metabolic interactions of the Oligo-Mouse-Microbiota (OMM[12]) synthetic bacterial community, which is increasingly used as a model system in gut microbiome research. Using a bottom-up approach, we uncovered the directionality of strain-strain interactions in mono- and pairwise co-culture experiments as well as in community batch culture. Metabolic network reconstruction in combination with metabolomics analysis of bacterial culture supernatants provided insights into the metabolic potential and activity of the individual community members. Thereby, we could show that the OMM[12] interaction network is shaped by both exploitative and interference competition in vitro in nutrient-rich culture media and demonstrate how community structure can be shifted by changing the nutritional environment. In particular, Enterococcus faecalis KB1 was identified as an important driver of community composition by affecting the abundance of several other consortium members in vitro. As a result, this study gives fundamental insight into key drivers and mechanistic basis of the OMM[12] interaction network in vitro, which serves as a knowledge base for future mechanistic in vivo studies.}, } @article {pmid34856363, year = {2022}, author = {Morikawa, A and Kawabata, A and Shirahige, K and Akiyama, T and Okamoto, A and Sutani, T}, title = {Altered cervicovaginal microbiota in premenopausal ovarian cancer patients.}, journal = {Gene}, volume = {811}, number = {}, pages = {146083}, doi = {10.1016/j.gene.2021.146083}, pmid = {34856363}, issn = {1879-0038}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacterial Typing Techniques/methods ; Biomarkers ; Carcinoma, Ovarian Epithelial/*microbiology ; Case-Control Studies ; Cervix Uteri/*microbiology ; DNA, Bacterial ; Female ; Humans ; Japan ; Lactobacillus/classification/genetics ; Metagenome ; *Microbiota ; Middle Aged ; Ovarian Neoplasms/*microbiology ; Postmenopause ; Premenopause ; RNA, Ribosomal, 16S ; Vagina/*microbiology ; Young Adult ; }, abstract = {Nearly three hundred thousand female patients are diagnosed with ovarian cancer in the world annually, and this number shows an increasing trend. However, characteristic symptoms caused by ovarian cancer are so few that early diagnosis remains challenging, and an effective screening method has not yet been established. Here, we conducted a case-control study in Japan to analyze the association between cervicovaginal microbiome and ovarian cancer, using 16S rRNA amplicon sequencing. Analysis of DNA extracted from cervical smear samples revealed Lactobacillus-dominant and Lactobacillus-deficient, highly-diversified bacterial communities in premenopausal and postmenopausal healthy controls, respectively, as reported for vaginal microbiota previously. We found that cervicovaginal microbiota in ovarian cancer patients, regardless of their menopausal status, were frequently a diversified community and similar to those in healthy subjects at postmenopausal ages. The diverse microbiota was associated with the major histotypes of epithelial ovarian cancer, including serous ovarian cancer and ovarian clear cell cancer. The present study implies the potential of a cervicovaginal microbiome biomarker in screening ovarian cancer in premenopausal women.}, } @article {pmid34856283, year = {2022}, author = {Marcoleta, AE and Arros, P and Varas, MA and Costa, J and Rojas-Salgado, J and Berríos-Pastén, C and Tapia-Fuentes, S and Silva, D and Fierro, J and Canales, N and Chávez, FP and Gaete, A and González, M and Allende, ML and Lagos, R}, title = {The highly diverse Antarctic Peninsula soil microbiota as a source of novel resistance genes.}, journal = {The Science of the total environment}, volume = {810}, number = {}, pages = {152003}, doi = {10.1016/j.scitotenv.2021.152003}, pmid = {34856283}, issn = {1879-1026}, mesh = {Antarctic Regions ; Anti-Bacterial Agents ; Genes, Bacterial ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Soil ; }, abstract = {The rise of multiresistant bacterial pathogens is currently one of the most critical threats to global health, encouraging a better understanding of the evolution and spread of antimicrobial resistance. In this regard, the role of the environment as a source of resistance mechanisms remains poorly understood. Moreover, we still know a minimal part of the microbial diversity and resistome present in remote and extreme environments, hosting microbes that evolved to resist harsh conditions and thus a potentially rich source of novel resistance genes. This work demonstrated that the Antarctic Peninsula soils host a remarkable microbial diversity and a widespread presence of autochthonous antibiotic-resistant bacteria and resistance genes. We observed resistance to a wide array of antibiotics among isolates, including Pseudomonas resisting ten or more different compounds, with an overall increased resistance in bacteria from non-intervened areas. In addition, genome analysis of selected isolates showed several genes encoding efflux pumps, as well as a lack of known resistance genes for some of the resisted antibiotics, including colistin, suggesting novel uncharacterized mechanisms. By combining metagenomic approaches based on analyzing raw reads, assembled contigs, and metagenome-assembled genomes, we found hundreds of widely distributed genes potentially conferring resistance to different antibiotics (including an outstanding variety of inactivation enzymes), metals, and biocides, hosted mainly by Polaromonas, Pseudomonas, Streptomyces, Variovorax, and Burkholderia. Furthermore, a proportion of these genes were found inside predicted plasmids and other mobile elements, including a putative OXA-like carbapenemase from Polaromonas harboring conserved key residues and predicted structural features. All this evidence indicates that the Antarctic Peninsula soil microbiota has a broad natural resistome, part of which could be transferred horizontally to pathogenic bacteria, acting as a potential source of novel resistance genes.}, } @article {pmid34855234, year = {2022}, author = {Zarei, A and Javid, H and Sanjarian, S and Senemar, S and Zarei, H}, title = {Metagenomics studies for the diagnosis and treatment of prostate cancer.}, journal = {The Prostate}, volume = {82}, number = {3}, pages = {289-297}, doi = {10.1002/pros.24276}, pmid = {34855234}, issn = {1097-0045}, mesh = {Genitalia, Male/*microbiology ; Humans ; Male ; Metagenomics/*methods ; Microbiota/*genetics ; Precision Medicine ; *Prostatic Neoplasms/genetics/metabolism/therapy ; }, abstract = {AIM: Mutation occurs in the prostate cell genes, leading to abnormal prostate proliferation and ultimately cancer. Prostate cancer (PC) is one of the most common cancers amongst men, and its prevalence worldwide increases relative to men's age. About 16% of the world's cancers are the result of microbes in the human body. Impaired population balance of symbiosis microbes in the human reproductive system is linked to PC development.

DISCUSSION: With the advent of metagenomics science, the genome sequence of the microbiota of the human body has been unveiled. Therefore, it is now possible to identify a higher range of microbiome changes in PC tissue via the Next Generation Technique, which will have positive consequences in personalized medicine. In this review, we intend to question the role of metagenomics studies in the diagnosis and treatment of PC.

CONCLUSION: The microbial imbalance in the men's genital tract might have an effect on prostate health. Based on next-generation sequencing-generated data, Proteobacteria, Firmicutes, Actinobacteria, and Bacteriodetes are the nine frequent phyla detected in a PC sample, which might be involved in inducing mutation in the prostate cells that cause cancer.}, } @article {pmid34852439, year = {2021}, author = {Xie, J and Zou, X and Chang, Y and Chen, C and Ma, J and Liu, H and Cui, MH and Zhang, TC}, title = {Bioelectrochemical systems with a cathode of stainless-steel electrode for treatment of refractory wastewater: Influence of electrode material on system performance and microbial community.}, journal = {Bioresource technology}, volume = {342}, number = {}, pages = {125959}, doi = {10.1016/j.biortech.2021.125959}, pmid = {34852439}, issn = {1873-2976}, mesh = {*Bioelectric Energy Sources ; Electrodes ; *Microbiota ; Stainless Steel ; Wastewater ; }, abstract = {The large-scale application of the bioelectrochemical system (BES) is limited by the cost-effective electrode materials. In this study, five kinds of stainless-steel materials were used as the cathode of the BES coupled with anaerobic digestion (BES-AD) for the treatment of diluted N, N-dimethylacetamide (DMAC) wastewater. Compared with a carbon-cloth cathode, BES-AD with a stainless-steel cathode had more engineering due to its low cost, although the operating efficiencies were slightly inferior. Stainless-steel mesh with a 100 µm aperture (SSM-100 μm) was the most cost-effective electrode and the implanted BES exhibited better COD removal efficiency, electrochemical performance and biodegradability. Analysis of microbial community revealed the synergetic effect between exoelectrogen and fermentative bacteria had been strengthened in the SSM-100 μm cathode biofilm. Function analysis of the microbial community based on PICRUSt predicted metagenomes revealed that the metabolic pathways of xenobiotics biodegradation and metabolism in the SSM-100 μm cathode were stimulated.}, } @article {pmid34851722, year = {2022}, author = {Zheng, B and He, Y and Zhang, P and Huo, YX and Yin, Y}, title = {Polyphenol Utilization Proteins in the Human Gut Microbiome.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {3}, pages = {e0185121}, pmid = {34851722}, issn = {1098-5336}, support = {R01 GM140370/GM/NIGMS NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome ; Gastrointestinal Tract/metabolism ; Humans ; Metagenome ; *Microbiota ; Polyphenols/metabolism ; }, abstract = {Dietary polyphenols can significantly benefit human health, but their bioavailability is metabolically controlled by human gut microbiota. To facilitate the study of polyphenol metabolism for human gut health, we have manually curated experimentally characterized polyphenol utilization proteins (PUPs) from published literature. This resulted in 60 experimentally characterized PUPs (named seeds) with various metadata, such as species and substrate. Further database search found 107,851 homologs of the seeds from UniProt and UHGP (unified human gastrointestinal protein) databases. All PUP seeds and homologs were classified into protein classes, families, and subfamilies based on Enzyme Commission (EC) numbers, Pfam (protein family) domains, and sequence similarity networks. By locating PUP homologs in the genomes of UHGP, we have identified 1,074 physically linked PUP gene clusters (PGCs), which are potentially involved in polyphenol metabolism in the human gut. The gut microbiome of Africans was consistently ranked the top in terms of the abundance and prevalence of PUP homologs and PGCs among all geographical continents. This reflects the fact that dietary polyphenols are consumed by the African population more commonly than by other populations, such as Europeans and North Americans. A case study of the Hadza hunter-gatherer microbiome verified the feasibility of using dbPUP to profile metagenomic data for biologically meaningful discovery, suggesting an association between diet and PUP abundance. A Pfam domain enrichment analysis of PGCs identified a number of putatively novel PUP families. Lastly, a user-friendly web interface (https://bcb.unl.edu/dbpup/) provides all the data online to facilitate the research of polyphenol metabolism for improved human health. IMPORTANCE Long-term consumption of polyphenol-rich foods has been shown to lower the risk of various human diseases, such as cardiovascular diseases, cancers, and metabolic diseases. Raw polyphenols are often enzymatically processed by gut microbiome, which contains various polyphenol utilization proteins (PUPs) to produce metabolites with much higher bioaccessibility to gastrointestinal cells. This study delivered dbPUP as an online database for experimentally characterized PUPs and their homologs in human gut microbiome. This work also performed a systematic classification of PUPs into enzyme classes, families, and subfamilies. The signature Pfam domains were identified for PUP families, enabling conserved domain-based PUP annotation. This standardized sequence similarity-based PUP classification system offered a guideline for the future inclusion of new experimentally characterized PUPs and the creation of new PUP families. An in-depth data analysis was further conducted on PUP homologs and physically linked PUP gene clusters (PGCs) in gut microbiomes of different human populations.}, } @article {pmid34851441, year = {2022}, author = {Oh, HN and Myeong, NR and Kim, T and Min, GS and Kim, S and Sul, WJ}, title = {Changes in Fecal Pellet Microbiome of the Cold-Adapted Antarctic Copepod Tigriopus kingsejongensis at Different Temperatures and Developmental Stages.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1029-1041}, pmid = {34851441}, issn = {1432-184X}, support = {Graduate Research Scholarship in 2016//Chung-Ang University/ ; NRF-2019R1A2C1090861//National Research Foundation of Korea/ ; PE21140//Korea Polar Research Institute/ ; }, mesh = {Animals ; *Copepoda ; Temperature ; Antarctic Regions ; Cold Temperature ; *Microbiota ; }, abstract = {Tigriopus kingsejongensis, a copepod species reported from the King Sejong Station, Antarctica, serves as a valuable food resource in ecosystems. We cultured T. kingsejongensis at three different temperatures (2 °C, 8 °C, and 15 °C) in a laboratory to observe the changes in its fecal pellet microbiome depending on the cultivation temperatures and developmental stages. We observed that the fecal pellet microbiome of the copepod changed with temperature: a lower microbial diversity, higher abundance of the aquatic bacterium Vibrio, and lower abundance of the psychrophilic bacterium Colwellia were noted at higher temperatures. In addition, the fecal pellet microbiome of the copepod changed according to the developmental stage: a lower microbial diversity was noted in egg-attached copepods than in nauplii at 8 °C. We further analyzed three shotgun metagenomes from the fecal pellet samples of T. kingsejongensis at different temperatures and obtained 44 metagenome-assembled genomes (MAGs). We noted that MAGs of V. splendidus D contained glycosyl hydrolases (GHs) encoding chitinases and virulence factors at a higher relative abundance at 15 °C than at lower temperatures. These results indicate that increasing temperature affects the fecal pellet microbiome and the development of copepods. The findings are helpful to understand the changes in cold-adapted copepods and the effect of temperature on their growth.}, } @article {pmid34851181, year = {2021}, author = {Wu, K and Xu, Y and Zhang, W and Mao, H and Chen, B and Zheng, Y and Hu, X}, title = {Differences in Fecal Microbiome and Antimicrobial Resistance between Captive and Free-Range Sika Deer under the Same Exposure of Antibiotic Anthelmintics.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0191821}, pmid = {34851181}, issn = {2165-0497}, mesh = {Animal Husbandry/*methods ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics/isolation & purification ; Deer/*microbiology/physiology ; *Drug Resistance, Bacterial ; Ecosystem ; Feces/*microbiology ; *Gastrointestinal Microbiome ; }, abstract = {This study aimed to compare the fecal microbiome and antimicrobial resistance between captive and free-range sika deer with the same exposure to antibiotic anthelmintics. The taxonomic differences mainly involved significant changes in the dominant phyla, genera, and species. Linear discriminant analysis effect size (LEfSe) analysis revealed that 22 taxa were significantly different between the two groups. The KEGG analysis showed that the fecal microbiome metabolic function, and all level 2 categories in metabolism had higher abundance in the free-range deer. Based on the carbohydrate-active enzyme (CAZy) database analysis, glycoside hydrolases and carbohydrate-binding modules showed remarkable differences between the two groups. Regarding antibiotic resistance, tetQ and lnuC dominated the antibiotic resistance ontology (ARO) terms, and tetracycline and lincosamide resistance dominated the antimicrobial resistance patterns. Furthermore, the lnuC, ErmF, and tetW/N/W AROs and lincosamide resistance showed higher abundance in the captive deer, suggesting that captivity may yield more serious resistance issues because of the differences in greenfeed diet, breeding density, and/or housing environment. The results also revealed important associations between the phylum Proteobacteria, genus Prevotella, and major antibiotic resistance genes. Although the present study was a pilot study with a limited sample size that was insufficient control for some potential factors, it serves as the metagenomic study on the microbial communities and antimicrobial resistance in sika deer. IMPORTANCE We used a metagenomic approach to investigate whether and how captive and free-range impact the microbial communities and antimicrobial resistance in sika deer. The results provide solid evidence of the significant impacts on the microbial composition and function in captive and free-range sika deer. Interestingly, although the sika deer had the same exposure to antibiotic anthelmintics, the antimicrobial resistances were affected by the breeding environment.}, } @article {pmid34851167, year = {2021}, author = {Smith, BJ and Miller, RA and Schmidt, TM}, title = {Muribaculaceae Genomes Assembled from Metagenomes Suggest Genetic Drivers of Differential Response to Acarbose Treatment in Mice.}, journal = {mSphere}, volume = {6}, number = {6}, pages = {e0085121}, pmid = {34851167}, issn = {2379-5042}, support = {P30 AG024824/AG/NIA NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; }, mesh = {Acarbose/*pharmacology ; Animals ; Bacteria/*classification/drug effects/isolation & purification ; Fatty Acids, Volatile/metabolism ; Feces/chemistry/microbiology ; Female ; Fermentation/*drug effects ; Gastrointestinal Microbiome/*drug effects ; Longevity/*drug effects ; Male ; Metagenome ; Mice ; }, abstract = {The drug acarbose is used to treat diabetes and, by inhibiting α-amylase in the small intestine, increases the amount of starch entering the lower digestive tract. This results in changes to the composition of the microbiota and their fermentation products. Acarbose also increases longevity in mice, an effect that has been correlated with increased production of the short-chain fatty acids propionate and butyrate. In experiments replicated across three study sites, two distantly related species in the bacterial family Muribaculaceae were dramatically more abundant in acarbose-treated mice, distinguishing these responders from other members of the family. Bacteria in the family Muribaculaceae are predicted to produce propionate as a fermentation end product and are abundant and diverse in the guts of mice, although few isolates are available. We reconstructed genomes from metagenomes (MAGs) for nine populations of Muribaculaceae to examine factors that distinguish species that respond positively to acarbose. We found two closely related MAGs (B1A and B1B) from one responsive species that both contain a polysaccharide utilization locus with a predicted extracellular α-amylase. These genomes also shared a periplasmic neopullulanase with another, distantly related MAG (B2) representative of the only other responsive species. This gene differentiated these three MAGs from MAGs representative of nonresponding species. Differential gene content in B1A and B1B may be associated with the inconsistent response of this species to acarbose across study sites. This work demonstrates the utility of culture-free genomics for inferring the ecological roles of gut bacteria, including their response to pharmaceutical perturbations. IMPORTANCE The drug acarbose is used to treat diabetes by preventing the breakdown of starch in the small intestine, resulting in dramatic changes in the abundance of some members of the gut microbiome and its fermentation products. In mice, several of the bacteria that respond most positively are classified in the family Muribaculaceae, members of which produce propionate as a primary fermentation product. Propionate has been associated with gut health and increased longevity in mice. We found that genomes of the most responsive Muribaculaceae showed signs of specialization for starch fermentation, presumably providing them a competitive advantage in the large intestine of animals consuming acarbose. Comparisons among genomes enhance existing models for the ecological niches occupied by members of this family. In addition, genes encoding one type of enzyme known to participate in starch breakdown were found in all three genomes from responding species but none of the other genomes.}, } @article {pmid34851164, year = {2021}, author = {Murray, AE and Lo, CC and Daligault, HE and Avalon, NE and Read, RW and Davenport, KW and Higham, ML and Kunde, Y and Dichosa, AEK and Baker, BJ and Chain, PSG}, title = {Discovery of an Antarctic Ascidian-Associated Uncultivated Verrucomicrobia with Antimelanoma Palmerolide Biosynthetic Potential.}, journal = {mSphere}, volume = {6}, number = {6}, pages = {e0075921}, pmid = {34851164}, issn = {2379-5042}, support = {R21 CA205932/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Antarctic Regions ; Macrolides/*analysis ; *Microbiota ; Multigene Family ; Phylogeny ; RNA, Ribosomal, 16S ; Urochordata/*microbiology ; Verrucomicrobia/*genetics ; }, abstract = {The Antarctic marine ecosystem harbors a wealth of biological and chemical innovation that has risen in concert over millennia since the isolation of the continent and formation of the Antarctic circumpolar current. Scientific inquiry into the novelty of marine natural products produced by Antarctic benthic invertebrates led to the discovery of a bioactive macrolide, palmerolide A, that has specific activity against melanoma and holds considerable promise as an anticancer therapeutic. While this compound was isolated from the Antarctic ascidian Synoicum adareanum, its biosynthesis has since been hypothesized to be microbially mediated, given structural similarities to microbially produced hybrid nonribosomal peptide-polyketide macrolides. Here, we describe a metagenome-enabled investigation aimed at identifying the biosynthetic gene cluster (BGC) and palmerolide A-producing organism. A 74-kbp candidate BGC encoding the multimodular enzymatic machinery (hybrid type I-trans-AT polyketide synthase-nonribosomal peptide synthetase and tailoring functional domains) was identified and found to harbor key features predicted as necessary for palmerolide A biosynthesis. Surveys of ascidian microbiome samples targeting the candidate BGC revealed a high correlation between palmerolide gene targets and a single 16S rRNA gene variant (R = 0.83 to 0.99). Through repeated rounds of metagenome sequencing followed by binning contigs into metagenome-assembled genomes, we were able to retrieve a nearly complete genome (10 contigs) of the BGC-producing organism, a novel verrucomicrobium within the Opitutaceae family that we propose here as "Candidatus Synoicihabitans palmerolidicus." The refined genome assembly harbors five highly similar BGC copies, along with structural and functional features that shed light on the host-associated nature of this unique bacterium. IMPORTANCE Palmerolide A has potential as a chemotherapeutic agent to target melanoma. We interrogated the microbiome of the Antarctic ascidian, Synoicum adareanum, using a cultivation-independent high-throughput sequencing and bioinformatic strategy. The metagenome-encoded biosynthetic machinery predicted to produce palmerolide A was found to be associated with the genome of a member of the S. adareanum core microbiome. Phylogenomic analysis suggests the organism represents a new deeply branching genus, "Candidatus Synoicihabitans palmerolidicus," in the Opitutaceae family of the Verrucomicrobia phylum. The Ca. Synoicihabitans palmerolidicus 4.29-Mb genome encodes a repertoire of carbohydrate-utilizing and transport pathways, a chemotaxis system, flagellar biosynthetic capacity, and other regulatory elements enabling its ascidian-associated lifestyle. The palmerolide producer's genome also contains five distinct copies of the large palmerolide biosynthetic gene cluster that may provide structural complexity of palmerolide variants.}, } @article {pmid34847370, year = {2021}, author = {Wang, D and Doestzada, M and Chen, L and Andreu-Sánchez, S and van den Munckhof, ICL and Augustijn, HE and Koehorst, M and Ruiz-Moreno, AJ and Bloks, VW and Riksen, NP and Rutten, JHW and Joosten, LAB and Netea, MG and Wijmenga, C and Zhernakova, A and Kuipers, F and Fu, J}, title = {Characterization of gut microbial structural variations as determinants of human bile acid metabolism.}, journal = {Cell host & microbe}, volume = {29}, number = {12}, pages = {1802-1814.e5}, doi = {10.1016/j.chom.2021.11.003}, pmid = {34847370}, issn = {1934-6069}, mesh = {Bacteria/genetics ; Bile Acids and Salts/*metabolism ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Life Style ; Lipid Metabolism ; Metagenome ; *Microbiota ; Obesity ; Signal Transduction ; }, abstract = {Bile acids (BAs) facilitate intestinal fat absorption and act as important signaling molecules in host-gut microbiota crosstalk. BA-metabolizing pathways in the microbial community have been identified, but it remains largely unknown how the highly variable genomes of gut bacteria interact with host BA metabolism. We characterized 8,282 structural variants (SVs) of 55 bacterial species in the gut microbiomes of 1,437 individuals from two cohorts and performed a systematic association study with 39 plasma BA parameters. Both variations in SV-based continuous genetic makeup and discrete clusters showed correlations with BA metabolism. Metagenome-wide association analysis identified 809 replicable associations between bacterial SVs and BAs and SV regulators that mediate the effects of lifestyle factors on BA metabolism. This is the largest microbial genetic association analysis to demonstrate the impact of bacterial SVs on human BA composition, and it highlights the potential of targeting gut microbiota to regulate BA metabolism through lifestyle intervention.}, } @article {pmid34847216, year = {2021}, author = {Sirven, MA and Venancio, VP and Shankar, S and Klemashevich, C and Castellón-Chicas, MJ and Fang, C and Mertens-Talcott, SU and Talcott, ST}, title = {Ulcerative colitis results in differential metabolism of cranberry polyphenols by the colon microbiome in vitro.}, journal = {Food & function}, volume = {12}, number = {24}, pages = {12751-12764}, doi = {10.1039/d1fo03047g}, pmid = {34847216}, issn = {2042-650X}, mesh = {Adolescent ; Adult ; Aged ; Colitis, Ulcerative/*metabolism ; Colon/metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; In Vitro Techniques ; Male ; Middle Aged ; Plant Extracts/metabolism ; Polyphenols/*metabolism ; Vaccinium macrocarpon/*metabolism ; Young Adult ; }, abstract = {The microbiome plays a major role in polyphenol metabolism, producing metabolites that are bioavailable and potentially more bioactive than the compounds from which they are derived. However, the microbiome can vary among individuals, and especially for those with co-morbidities, such as ulcerative colitis. In subjects with ulcerative colitis, the consequence of a 'dysbiotic' microbiome is characterized by decreased diversity of microbiota that may impact their capability to metabolize polyphenols into bioavailable metabolites. On this premise, the microbiome metabolism of cranberry polyphenols between healthy individuals and those with ulcerative colitis was compared in vitro. Fecal samples from volunteers, with or without diagnosed ulcerative colitis, were cultured anaerobically in the presence of cranberry polyphenols. The resulting metabolites were then quantified via LC-ESI-MS/MS. 16S rRNA metagenomics analysis was also utilized to assess differences in microbiota composition between healthy and ulcerative colitis microbiomes and the modulatory effects of cranberry polyphenols on microbiota composition. Healthy microbiomes produced higher (p < 0.05) concentrations of 5-(3',4'-dihydroxyphenyl)-gamma-valerolactone and 3-hydroxyphenylacetic acid in comparison to ulcerative colitis microbiomes. Additionally, healthy microbiomes contained a higher (p < 0.05) abundance of Ruminococcaceae, which could explain their ability to produce higher concentrations of cranberry polyphenol metabolites. Health status and the presence of cranberry polyphenols also significantly impacted the production of several short-chain and branched-chain fatty acids. These results suggest that efficiency of polyphenol metabolism is dependent on microbiota composition and future works should include metabolite data to account for inter-individual differences in polyphenol metabolism.}, } @article {pmid34844317, year = {2022}, author = {Chen, S and Holyoak, M and Liu, H and Bao, H and Ma, Y and Dou, H and Jiang, G}, title = {Effects of spatially heterogeneous warming on gut microbiota, nutrition and gene flow of a heat-sensitive ungulate population.}, journal = {The Science of the total environment}, volume = {806}, number = {Pt 1}, pages = {150537}, doi = {10.1016/j.scitotenv.2021.150537}, pmid = {34844317}, issn = {1879-1026}, mesh = {Animals ; *Deer ; Ecosystem ; *Gastrointestinal Microbiome ; Gene Flow ; Hot Temperature ; }, abstract = {Effects of climate warming on trophic cascades are increasingly reported for large herbivores occupying northern latitudes. During the last 40 years, moose (Alces alces) in northeast China have lost nearly half of their historical distribution through their habitat shifting northwards. There are many possible causes of bottom-up and top-down effects of temperature and for moose in northeast China they are poorly understood. Of particular relevance are the effects of extrinsic environmental factors on gene flow, nutritional adaptions, and gut microbiota that occur as moose populations retreat northwards. We combined molecular biology, nutritional ecology and metagenomics to gain deeper mechanistic insights into the effects of temperature on moose populations. In this study, we revealed that the direction and intensity of gene flow is consistent with global warming driving retreats of moose populations. We interpret this as evidence for the northward movement of moose populations, with cooler northern populations receiving more immigrants and warmer southern populations supplying emigrants. Comparison across latitudes showed that warmer late spring temperatures were associated with plant community composition and facilitated related changes in moose protein and carbohydrate intake through altering forage availability, forage quality and diet composition. Furthermore, these nutrient shifts were accompanied by changes in gut microbial composition and functional pathways related to nutrient metabolism. This study provided insights into mechanisms driving effects of spatial heterogeneous warming on genetic, nutritional and physiological adaptions related to key demographic rates and patterns of survival of heat-sensitive ungulates along a latitude gradient. Understanding such changes helps to identify key habitat areas and plant species to ensure accurate assessment of population status and targeted management of moose populations.}, } @article {pmid34844052, year = {2022}, author = {Chen, WY and Wu, JH}, title = {Microbiome composition resulting from different substrates influences trichloroethene dechlorination performance.}, journal = {Journal of environmental management}, volume = {303}, number = {}, pages = {114145}, doi = {10.1016/j.jenvman.2021.114145}, pmid = {34844052}, issn = {1095-8630}, mesh = {Biodegradation, Environmental ; *Chloroflexi/genetics ; Fermentation ; *Microbiota ; *Trichloroethylene ; }, abstract = {Hydrogen-releasing substrates can stimulate the reductive dechlorination of trichloroethene (TCE) mediated by organohalide-respiring bacteria (OHRB) at contaminated sites. However, how the substrate affects microbiome assembly and the accompanying influences on the growth of OHRB and reductive TCE dechlorination remains unclear. We evaluated the effects of microbial community structures and potential functions on the reductive dechlorination of TCE in three anaerobic reactors with acetate, soybean oil, or molasses as the substrate and no cobalamin or amino acid supplementation. The molasses-fed reactor exhibited superior performance and dechlorination of TCE loadings to ethene, and the oil-fed reactor exhibited a high growth rate of the key OHRB, Dehalococcoides. This finding suggests an effect of the substrate on reductive dechlorination and the growth of Dehalococcoides. The three reactors developed distinct microbial community structures and the predicted metagenomes were distinguished on the basis of vitamin and amino acid metabolisms as well as fermentation pathways. In addition to the diversified hydrogen-producing pathways, the molasses-induced microbiome exhibited high potential to synthesize the cobalamin, which may account for its high Dehalococcoides activity and thus effective dechlorination performance. The substrate dependence of microbiomes may provide insight into strategies of exogenous amino acid supplementation to benefit Dehalococcoides growth. This study adds novel insight into the interplay of hydrogen-releasing substrates and OHRB. The results may contribute to the development of tailored and cost-effective management for the reductive dechlorination of chlorinated solvents in bioremediation.}, } @article {pmid34843867, year = {2021}, author = {Novak, B and Lopes Hasuda, A and Ghanbari, M and Mayumi Maruo, V and Bracarense, APFRL and Neves, M and Emsenhuber, C and Wein, S and Oswald, IP and Pinton, P and Schatzmayr, D}, title = {Effects of Fusarium metabolites beauvericin and enniatins alone or in mixture with deoxynivalenol on weaning piglets.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {158}, number = {}, pages = {112719}, doi = {10.1016/j.fct.2021.112719}, pmid = {34843867}, issn = {1873-6351}, mesh = {Animals ; Depsipeptides/*toxicity ; Eating/drug effects ; Fusarium/metabolism ; Gastrointestinal Microbiome/drug effects/*genetics ; Intestines/drug effects/pathology ; Liver/drug effects/enzymology/pathology ; Swine ; Trichothecenes/*toxicity ; Weaning ; Weight Gain/*drug effects ; }, abstract = {The impact of the Fusarium-derived metabolites beauvericin, enniatin B and B1 (EB) alone or in combination with deoxynivalenol (DON) was investigated in 28-29 days old weaning piglets over a time period of 14 days. The co-application of EB and DON (EB + DON) led to a significant decrease in the weight gain of the animals. Liver enzyme activities in plasma were significantly decreased at day 14 in piglets receiving the EB + DON-containing diet compared to piglets receiving the control diet. All mycotoxin-contaminated diets led to moderate to severe histological lesions in the jejunum, the liver and lymph nodes. Shotgun metagenomics revealed a significant effect of EB-application on the gut microbiota. Our results provide novel insights into the harmful impact of emerging mycotoxins alone or with DON on the performance, gut health and immunological parameters in pigs.}, } @article {pmid34841779, year = {2021}, author = {Yin, Y and Yu, R and Chen, H}, title = {[Shotgun metagenome sequencing of Chinese gut microbiota: a review].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {37}, number = {11}, pages = {3717-3733}, doi = {10.13345/j.cjb.210556}, pmid = {34841779}, issn = {1872-2075}, mesh = {China ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; United States ; }, abstract = {The research on the relationship between gut microbiota and human health continues to be a hot topic in the field of life science. Culture independent 16S rRNA gene high-throughput sequencing is the current main research method. However, with the reduction of sequencing cost and the maturity of data analysis methods, shotgun metagenome sequencing is gradually becoming an important method for the study of gut microbiome due to its advantages of obtaining more information. With the support from the human microbiome project, 30 805 metagenome samples were sequenced in the United States. By searching NCBI PubMed and SRA databases, it was found that 72 studies collecting about 10 000 Chinese intestinal samples were used for metagenome sequencing. To date, only 56 studies were published, including 16 related to metabolic diseases, 16 related to infectious and immune diseases, and 12 related to cardiovascular and cerebrovascular diseases. The samples were mainly collected in Beijing, Guangzhou, Shanghai and other cosmopolitan cities, where great differences exist in sequencing platforms and methods. The outcome of most studies are based on correlation analysis, which has little practical value in guiding the diagnosis and treatment of clinical diseases. Standardizing sampling methods, sequencing platform and data analysis process, and carrying out multi center parallel research will contribute to data integration and comparative analysis. Moreover, insights into the functional verification and molecular mechanism by using the combination of transcriptomics, proteomics and culturomics will enable the gut microbiota research to better serve the clinical diagnosis and treatment.}, } @article {pmid34839011, year = {2022}, author = {Becker, A and Schmartz, GP and Gröger, L and Grammes, N and Galata, V and Philippeit, H and Weiland, J and Ludwig, N and Meese, E and Tierling, S and Walter, J and Schwiertz, A and Spiegel, J and Wagenpfeil, G and Faßbender, K and Keller, A and Unger, MM}, title = {Effects of Resistant Starch on Symptoms, Fecal Markers, and Gut Microbiota in Parkinson's Disease - The RESISTA-PD Trial.}, journal = {Genomics, proteomics & bioinformatics}, volume = {20}, number = {2}, pages = {274-287}, pmid = {34839011}, issn = {2210-3244}, mesh = {Humans ; Bacteria/genetics ; Biomarkers ; Butyrates/pharmacology ; Fatty Acids, Volatile/pharmacology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Leukocyte L1 Antigen Complex/pharmacology ; *Parkinson Disease/drug therapy ; Prebiotics ; Resistant Starch ; }, abstract = {The composition of the gut microbiota is linked to multiple diseases, including Parkinson's disease (PD). Abundance of bacteria producing short-chain fatty acids (SCFAs) and fecal SCFA concentrations are reduced in PD. SCFAs exert various beneficial functions in humans. In the interventional, monocentric, open-label clinical trial "Effects of Resistant Starch on Bowel Habits, Short Chain Fatty Acids and Gut Microbiota in Parkinson'sDisease" (RESISTA-PD; ID: NCT02784145), we aimed at altering fecal SCFAs by an 8-week prebiotic intervention with resistant starch (RS). We enrolled 87 subjects in three study-arms: 32 PD patients received RS (PD + RS), 30 control subjects received RS, and 25 PD patients received solely dietary instructions. We performed paired-end 100 bp length metagenomic sequencing of fecal samples using the BGISEQ platform at an average of 9.9 GB. RS was well-tolerated. In the PD + RS group, fecal butyrate concentrations increased significantly, and fecal calprotectin concentrations dropped significantly after 8 weeks of RS intervention. Clinically, we observed a reduction in non-motor symptom load in the PD + RS group. The reference-based analysis of metagenomes highlighted stable alpha-diversity and beta-diversity across the three groups, including bacteria producing SCFAs. Reference-free analysis suggested punctual, yet pronounced differences in the metagenomic signature in the PD + RS group. RESISTA-PD highlights that a prebiotic treatment with RS is safe and well-tolerated in PD. The stable alpha-diversity and beta-diversity alongside altered fecal butyrate and calprotectin concentrations call for long-term studies, also investigating whether RS is able to modify the clinical course of PD.}, } @article {pmid34838907, year = {2022}, author = {Zhang, T and Li, J and Wang, N and Wang, H and Yu, L}, title = {Metagenomic analysis reveals microbiome and resistome in the seawater and sediments of Kongsfjorden (Svalbard, High Arctic).}, journal = {The Science of the total environment}, volume = {809}, number = {}, pages = {151937}, doi = {10.1016/j.scitotenv.2021.151937}, pmid = {34838907}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Genes, Bacterial ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; Seawater ; Svalbard ; }, abstract = {Kongsfjorden in the high Arctic, a typical Arctic fjord, experienced long-time input of nutrients and pollutants from the remote and local resources, providing a platform for characterizing the diversity and distribution of antibiotic resistance genes (ARGs). However, the microbiome and antibiotic resistome in this pristine marine system have not been well documented. The present study aimed to characterize the diversity and distribution of bacterial communities and associated ARGs in seawater (12 samples) and sediments (13 samples) of Kongsfjorden via metagenomic analysis. In terms of both bacterial community compositions and ARG profiles, the seawater was significantly distinct from sediment. Only 29 ARG subtypes were detected in the Arctic seawater and sediments. Furthermore, three geochemical factors (i.e., longitude, depth, and PO4[3-]) greatly influenced the bacterial communities in sediment samples, while longitude, depth, and latitude were crucial geochemical factors influencing the ARG profiles in sediment samples. Procrustes analysis revealed a significant correlation between bacterial community compositions and ARG profiles in seawater and sediment samples. Further analysis revealed the metagenome-assembled genomes (MAGs) with ARG subtypes. Overall, our study provides insights into the microbiome and resistome in a pristine Arctic fjord, thereby providing vital information for environmental management.}, } @article {pmid34838398, year = {2022}, author = {Yang, P and Zhong, G and Yang, J and Zhao, L and Sun, D and Tian, Y and Li, R and Rong, L}, title = {Metagenomic and metabolomic profiling reveals the correlation between the microbiota and flavor compounds and nutrients in fermented sausages.}, journal = {Food chemistry}, volume = {375}, number = {}, pages = {131645}, doi = {10.1016/j.foodchem.2021.131645}, pmid = {34838398}, issn = {1873-7072}, mesh = {Fermentation ; Food Microbiology ; *Meat Products/analysis ; *Microbiota ; Nutrients ; }, abstract = {Understanding the interrelationships between the differentially abundant microorganisms and metabolites of traditional "Fuet" fermented sausages (FSs) and inoculated fermented sausages (IFSs) can help us identify key species that are missing from commercial starter cultures to reproduce the flavor compounds and nutrients of traditional Fuet FSs. IFSs, inoculated with P. pentosaceus, P. acidilactici, S. xylosus, S. carnosus (SBM-52) or P. pentosaceus, and S. xylosus (THM-17), were deficient in reproducing the volatilome profile (in particular esters, methyl aldehydes, and methyl ketones) of traditional Fuet FSs because of the lack of diverse Staphylococci (S. carnosus, S. xylosus, S. equorum, and S. saprophyticus). Moreover, the combination of Pediococcus and Staphylococcus were positively associated with amino acid, fatty acid, l-anserine, and l-carnosine levels. Pyridoxal and indolelactic acid levels were significantly increased in IFSs with the addition of P. acidilactici and S. carnosus, which were positively associated with vitamin B6 and tryptophan metabolic pathways.}, } @article {pmid34838108, year = {2021}, author = {Lin, D and Zheng, X and Sanogo, B and Ding, T and Sun, X and Wu, Z}, title = {Bacterial composition of midgut and entire body of laboratory colonies of Aedes aegypti and Aedes albopictus from Southern China.}, journal = {Parasites & vectors}, volume = {14}, number = {1}, pages = {586}, pmid = {34838108}, issn = {1756-3305}, support = {2020YFC1200100//the National Key R&D Program of China/ ; 2016YFC1200500//the National Key R&D Program of China/ ; 2019A1515012068//Natural Science Foundation of Guangdong Province/ ; 2020A1515010896//Natural Science Foundation of Guangdong Province/ ; 2021A1515010976//Natural Science Foundation of Guangdong Province/ ; 82072308//the National Natural Science Foundation of China/ ; 82002168//the National Natural Science Foundation of China/ ; 20201192//the 6th Nuclear Energy R&D Project/ ; B12003//The 111 Project/ ; }, mesh = {Aedes/*microbiology ; Animals ; *Bacteria/classification/genetics/isolation & purification ; China ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Laboratories ; Metagenomics ; Mosquito Vectors/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Aedes aegypti and Aedes albopictus are invasive mosquito species and significantly impact human health in southern China. Microbiota are confirmed to affect the development and immunity of mosquitoes. However, scientists have focused more on midgut microbiota of female mosquitoes and bacterial differences between female and male Aedes mosquitoes. The relationship between the midgut and entire body microbiota of Aedes is unclear. In this study, we collected mosquito samples reared under the same laboratory conditions and compared the microbial composition of midgut and entire bodies of Aedes aegypti and Aedes albopictus using 16S rRNA gene sequencing.

METHODS: In this study, we collected mosquito samples reared under the same laboratory conditions and compared the microbial composition of midgut and entire bodies of Aedes aegypti and Aedes albopictus using 16S rRNA gene sequencing.

RESULTS: A total of 341 OTUs were identified, showing that Proteobacteria was the dominant phylum and Methylobacterium the dominant genus in both Aedes aegypti and Aedes albopictus. The bacterial diversity and community structures of the entire bodies were similar between males and females in both Aedes aegypti and Aedes albopictus. Conversely, the bacterial compositions of male and female Aedes aegypti and Aedes albopictus were significantly different. NMDS analysis, UPGMA analysis, diversity indices and OTU distribution demonstrated that compositions and structures in midgut microbiota were similar but significantly different in the entire bodies of Aedes aegypti and Aedes albopictus. Functional prediction analysis showed that metabolism and environmental information processing were the dominant KEGG pathways at level 1. Our study showed that there were significantly different level 2 and 3 KEGG pathways in the midgut microbiota (16 level 2 and 24 level 3) and the entire bodies (33 level 2 and 248 level 3) between female Aedes albopictus and Aedes Aegypti.

CONCLUSIONS: Our findings that Aedes aegypti and Aedes albopictus reared in the same laboratory harbor a similar gut bacterial microbiome but different entire body microbiota imply that the gut microbiota of adult mosquitoes is environmentally determined regardless of the host genotype, but the entire body microbiota is more genetically determined. Our findings improved the understanding of the microbiota in the entire and partial tissues of Aedes mosquitoes.}, } @article {pmid34838016, year = {2021}, author = {He, J and He, X and Ma, Y and Yang, L and Fang, H and Shang, S and Xia, H and Lian, G and Tang, H and Wang, Q and Wang, J and Lin, Z and Wen, J and Liu, Y and Zhai, C and Wang, W and Jiang, X and Xuan, J and Liu, M and Lu, S and Li, X and Wang, H and Ouyang, C and Cao, M and Lin, A and Zhang, B and Wu, D and Chen, Y and Xiao, C}, title = {A comprehensive approach to stool donor screening for faecal microbiota transplantation in China.}, journal = {Microbial cell factories}, volume = {20}, number = {1}, pages = {216}, pmid = {34838016}, issn = {1475-2859}, support = {81730003//national natural science foundation of china/ ; 82004433//national natural science foundation of china/ ; 2017ZX09304021//national major science and technology projects of china/ ; 16CZX064//national office for philosophy and social sciences/ ; }, mesh = {Adolescent ; Adult ; China ; Clostridium Infections/therapy ; Computational Biology/methods ; Donor Selection/*methods ; Fecal Microbiota Transplantation/*methods ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metagenomics/*methods ; Retrospective Studies ; *Tissue Donors ; Young Adult ; }, abstract = {BACKGROUND: Faecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridium difficile infections and chronic gastrointestional infections. However, the risks of FMT and the selection process of suitable donors remain insufficiently characterized. The eligibility rate for screening, underlying microbial basis, and core ethical issues of stool donors for FMT are yet to be elucidated in China.

RESULTS: The potential stool donors were screened from December 2017 to December 2019 with the help of an online survey, clinical assessments, and stool and blood testing. Bioinformatics analyses were performed, and the composition and stability of gut microbiota in stool obtained from eligible donors were dynamically observed using metagenomics. Meanwhile, we build a donor microbial evaluation index (DoMEI) for stool donor screening. In the screening process, we also focused on ethical principles and requirements. Of the 2071 participants, 66 donors were selected via the screening process (3.19% success rate). Although there were significant differences in gut microbiota among donors, we found that the changes in the gut microbiota of the same donor were typically more stable than those between donors over time.

CONCLUSIONS: DoMEI provides a potential reference index for regular stool donor re-evaluation. In this retrospective study, we summarised the donor recruitment and screening procedure ensuring the safety and tolerability for FMT in China. Based on the latest advances in this field, we carried out rigorous recommendation and method which can assist stool bank and clinicians to screen eligible stool donor for FMT.}, } @article {pmid34837955, year = {2021}, author = {Yan, Y and Yi, X and Duan, Y and Jiang, B and Huang, T and Inglis, BM and Zheng, B and Si, W}, title = {Alteration of the gut microbiota in rhesus monkey with spontaneous osteoarthritis.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {328}, pmid = {34837955}, issn = {1471-2180}, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification ; Biomarkers ; Disease Models, Animal ; Female ; *Gastrointestinal Microbiome ; Humans ; Knee Joint/pathology ; Macaca mulatta ; Osteoarthritis/*microbiology/pathology ; }, abstract = {BACKGROUND: The spontaneous osteoarthritis (OA) in rhesus macaque is similar to OA in human, which maintains an upright body posture and shows very similar biomechanical properties of bones to humans. At present, there is no good treatment for OA. This study aims to explore relationship between OA and intestinal microbiota, and provide a reference for the treatment of clinical OA.

RESULTS: We collected colonic contents of the 20 rhesus macaque (6-15 years old, female) for intestinal microbiota analysis by metagenomics sequencing, of which 10 were spontaneous OA monkeys and 10 were normal monkeys. Our results showed the diversity of gut microbiota in monkeys with OA was decreased compared to the normal monkeys (p = 0.16). Mollicutes, Tenericutes, Coprobacillus and Faecalitalea may be biomarkers for the monkeys of OA. Lactobacillus found significantly increased in OA monkeys. Prevotella and Ruminococcus were higher in the normal group than OA group. Zinc/manganese transport system permease protein (p = 0.0011) and Cyclopropane-fatty-acyl-phospholipid synthase (p = 0.0012) are a microbiota metabolic pathway related to cartilage production.

CONCLUSIONS: Our results indicate that the diversity and composition of intestinal microbiota in monkeys with OA are different compared to the normal monkeys. we have found microbes that may be a biomarker for the diagnosis of osteoarthritis. Functional analysis of the microbiota also predicts cartilage damage in the monkeys with osteoarthritis. Non-human primates are closely related to humans, so this study can provide a reference for the development of drugs for the treatment of OA.}, } @article {pmid34836555, year = {2021}, author = {Hwang, Y and Schulze-Makuch, D and Arens, FL and Saenz, JS and Adam, PS and Sager, C and Bornemann, TLV and Zhao, W and Zhang, Y and Airo, A and Schloter, M and Probst, AJ}, title = {Leave no stone unturned: individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {234}, pmid = {34836555}, issn = {2049-2618}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Desert Climate ; *Microbiota ; Soil Microbiology ; }, abstract = {BACKGROUND: The hyperarid core of the Atacama Desert is an extremely harsh environment thought to be colonized by only a few heterotrophic bacterial species. Current concepts for understanding this extreme ecosystem are mainly based on the diversity of these few species, yet a substantial area of the Atacama Desert hyperarid topsoil is covered by expansive boulder accumulations, whose underlying microbiomes have not been investigated so far. With the hypothesis that these sheltered soils harbor uniquely adapted microbiomes, we compared metagenomes and geochemistry between soils below and beside boulders across three distantly located boulder accumulations in the Atacama Desert hyperarid core.

RESULTS: Genome-resolved metagenomics of eleven samples revealed substantially different microbial communities in soils below and beside boulders, despite the presence of shared species. Archaea were found in significantly higher relative abundance below the boulders across all samples within distances of up to 205 km. These key taxa belong to a novel genus of ammonia-oxidizing Thaumarchaeota, Candidatus Nitrosodeserticola. We resolved eight mid-to-high quality genomes of this genus and used comparative genomics to analyze its pangenome and site-specific adaptations. Ca. Nitrosodeserticola genomes contain genes for ammonia oxidation, the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway, and acetate utilization indicating a chemolithoautotrophic and mixotrophic lifestyle. They also possess the capacity for tolerating extreme environmental conditions as highlighted by the presence of genes against oxidative stress and DNA damage. Site-specific adaptations of the genomes included the presence of additional genes for heavy metal transporters, multiple types of ATP synthases, and divergent genes for aquaporins.

CONCLUSION: We provide the first genomic characterization of hyperarid soil microbiomes below the boulders in the Atacama Desert, and report abundant and highly adapted Thaumarchaeaota with ammonia oxidation and carbon fixation potential. Ca. Nitrosodeserticola genomes provide the first metabolic and physiological insight into a thaumarchaeal lineage found in globally distributed terrestrial habitats characterized by various environmental stresses. We consequently expand not only the known genetic repertoire of Thaumarchaeota but also the diversity and microbiome functioning in hyperarid ecosystems. Video Abstract.}, } @article {pmid34836550, year = {2021}, author = {Ter Horst, AM and Santos-Medellín, C and Sorensen, JW and Zinke, LA and Wilson, RM and Johnston, ER and Trubl, G and Pett-Ridge, J and Blazewicz, SJ and Hanson, PJ and Chanton, JP and Schadt, CW and Kostka, JE and Emerson, JB}, title = {Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {233}, pmid = {34836550}, issn = {2049-2618}, mesh = {*Ecosystem ; Minnesota ; *Soil/chemistry ; Soil Microbiology ; Virome ; }, abstract = {BACKGROUND: Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems.

RESULTS: Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH4 and CO2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes.

CONCLUSIONS: Results suggest strong viral "species" boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics. Video abstract The importance of Minnesota peat viromes in revealing terrestrial and aquatic niche partitioning for viral populations.}, } @article {pmid34836316, year = {2021}, author = {Enaud, R and Cambos, S and Viaud, E and Guichoux, E and Chancerel, E and Marighetto, A and Etchamendy, N and Clark, S and Mohammedi, K and Cota, D and Delhaes, L and Gatta-Cherifi, B}, title = {Gut Microbiota and Mycobiota Evolution Is Linked to Memory Improvement after Bariatric Surgery in Obese Patients: A Pilot Study.}, journal = {Nutrients}, volume = {13}, number = {11}, pages = {}, pmid = {34836316}, issn = {2072-6643}, mesh = {Adolescent ; Adult ; Aged ; Bacteria/classification/growth & development ; *Bariatric Surgery ; Feces/microbiology ; Female ; Fungi/growth & development ; *Gastrointestinal Microbiome ; Humans ; Male ; *Memory ; Middle Aged ; *Mycobiome ; Obesity, Morbid/microbiology/psychology/*surgery ; Pilot Projects ; Prospective Studies ; Young Adult ; }, abstract = {Patients with obesity are known to exhibit gut microbiota dysbiosis and memory deficits. Bariatric surgery (BS) is currently the most efficient anti-obesity treatment and may improve both gut dysbiosis and cognition. However, no study has investigated association between changes of gut microbiota and cognitive function after BS. We prospectively evaluated 13 obese patients on anthropometric data, memory functions, and gut microbiota-mycobiota before and six months after BS. The Rey Auditory Verbal Learning Test (AVLT) and the symbol span (SS) of the Weschler Memory Scale were used to assess verbal and working memory, respectively. Fecal microbiota and mycobiota were longitudinally analyzed by 16S and ITS2 rRNA sequencing respectively. AVLT and SS scores were significantly improved after BS (AVLT scores: 9.7 ± 1.7 vs. 11.2 ± 1.9, p = 0.02, and SS scores: 9.7 ± 23.0 vs. 11.6 ± 2.9, p = 0.05). An increase in bacterial alpha-diversity, and Ruminococcaceae, Prevotella, Agaricus, Rhodotorula, Dipodascus, Malassezia, and Mucor were significantly associated with AVLT score improvement after BS, while an increase in Prevotella and a decrease in Clostridium, Akkermansia,&nbsp;Dipodascus and Candida were linked to SS scores improvement. We identified several changes in the microbial communities that differ according to the improvement of either the verbal or working memories, suggesting a complex gut-brain-axis that evolves after BS.}, } @article {pmid34836246, year = {2021}, author = {Lutsiv, T and Weir, TL and McGinley, JN and Neil, ES and Wei, Y and Thompson, HJ}, title = {Compositional Changes of the High-Fat Diet-Induced Gut Microbiota upon Consumption of Common Pulses.}, journal = {Nutrients}, volume = {13}, number = {11}, pages = {}, pmid = {34836246}, issn = {2072-6643}, support = {3060-21650-001-08S//Agricultural Research Service/ ; }, mesh = {Animals ; Biodiversity ; Cecum/microbiology ; Diet ; *Diet, High-Fat ; Discriminant Analysis ; *Feeding Behavior ; *Gastrointestinal Microbiome ; *Lens Plant ; Male ; Mice, Inbred C57BL ; Phylogeny ; Mice ; }, abstract = {The gut microbiome is involved in the host's metabolism, development, and immunity, which translates to measurable impacts on disease risk and overall health. Emerging evidence supports pulses, i.e., grain legumes, as underutilized nutrient-dense, culinarily versatile, and sustainable staple foods that promote health benefits through modulating the gut microbiota. Herein, the effects of pulse consumption on microbial composition in the cecal content of mice were assessed. Male mice were fed an obesogenic diet formulation with or without 35% of the protein component comprised by each of four commonly consumed pulses-lentil (Lens culinaris L.), chickpea (Cicer arietinum L.), common bean (Phaseolus vulgaris L.), or dry pea (Pisum sativum L.). Mice consuming pulses had distinct microbial communities from animals on the pulse-free diet, as evidenced by β-diversity ordinations. At the phylum level, animals consuming pulses showed an increase in Bacteroidetes and decreases in Proteobacteria and Firmicutes. Furthermore, α-diversity was significantly higher in pulse-fed animals. An ecosystem of the common bacteria that were enhanced, suppressed, or unaffected by most of the pulses was identified. These compositional changes are accompanied by shifts in predicted metagenome functions and are concurrent with previously reported anti-obesogenic physiologic outcomes, suggestive of microbiota-associated benefits of pulse consumption.}, } @article {pmid34836186, year = {2021}, author = {Liu, AT and Chen, S and Jena, PK and Sheng, L and Hu, Y and Wan, YY}, title = {Probiotics Improve Gastrointestinal Function and Life Quality in Pregnancy.}, journal = {Nutrients}, volume = {13}, number = {11}, pages = {}, pmid = {34836186}, issn = {2072-6643}, support = {Department of Obstetrics and Gynecology at UC Davis//University of California, Davis/ ; Start Up//University of California, Davis/ ; 1S10OD010786-01//National Institute of Health/ ; }, mesh = {Adult ; Akkermansia ; Amidohydrolases/metabolism ; Bile Acids and Salts/metabolism ; Dysbiosis/*drug therapy ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Gastrointestinal Tract/*metabolism/microbiology ; Humans ; Lactobacillus ; Metabolomics/methods ; Nausea/drug therapy ; Pregnancy ; Pregnancy Complications/*drug therapy ; Probiotics/*administration & dosage ; *Quality of Life ; Vomiting/drug therapy ; }, abstract = {We studied whether probiotics were beneficial for hormonal change-associated dysbiosis, which may influence the enteric nervous system and GI function during early pregnancy. The study was 16 days consisting of two cycles of six daily probiotics mainly Lactobacillus and 2 days without probiotics. Daily surveys were conducted to monitor GI function and life quality. A subset of the participants who contributed fecal specimens was used for microbiota metagenomic sequencing, metabolomics, and quantification of bacterial genes to understand potential underlying mechanisms. Statistical analyses were done by generalized linear mixed-effects models. Thirty-two obstetric patients and 535 daily observations were included. The data revealed that probiotic supplementation significantly reduced the severity of nausea, vomiting, constipation, and improved life quality. Moreover, a low copy number of fecal bsh (bile salt hydrolase), which generates free bile acids, was associated with high vomiting scores and probiotic intake increased fecal bsh. In exploratory analysis without adjusting for multiplicity, a low fecal α-tocopherol, as well as a high abundance of Akkemansia muciniphila, was associated with high vomiting scores and times, respectively. The potential implications of these biomarkers in pregnancy and GI function are discussed. Probiotics likely produce free bile acids to facilitate intestinal mobility and metabolism.}, } @article {pmid34836145, year = {2021}, author = {Al Khalaf, AK and Abdulrahman, AO and Kaleem, M and Nur, SM and Asseri, AH and Choudhry, H and Khan, MI}, title = {Comparative Analysis of the Impact of Urolithins on the Composition of the Gut Microbiota in Normal-Diet Fed Rats.}, journal = {Nutrients}, volume = {13}, number = {11}, pages = {}, pmid = {34836145}, issn = {2072-6643}, mesh = {Animals ; Coumarins/*pharmacology ; Food Ingredients ; Functional Food ; Gastrointestinal Microbiome/*drug effects ; Male ; Metagenome/*drug effects ; Rats ; Rats, Wistar ; }, abstract = {The gut microbiota consists of a community of microorganisms that inhabit the large intestine. These microbes play important roles in maintaining gut barrier integrity, inflammation, lipid and carbohydrate metabolism, immunity, and protection against pathogens. However, recent studies have shown that dysfunction in the gut microbiota composition can lead to the development of several diseases. Urolithin A has recently been approved as a functional food ingredient. In this study, we examined the potentials of urolithin A (Uro-A) and B (Uro-B) in improving metabolic functions and their impact on gut microbiota composition under a metabolically unchallenged state in normal rats. Male Wistar rats (n = 18) were randomly segregated into three groups, with Group 1 serving as the control group. Groups 2 and 3 were administered with 2.5 mg/kg Uro-A and Uro-B, respectively, for four weeks. Our results showed that both Uro-A and B improved liver and kidney functions without affecting body weight. Metagenomic analysis revealed that both Uro-A and B induced the growth of Akkermansia. However, Uro-A decreased species diversity and microbial richness and negatively impacted the composition of pathogenic microbes in normal rats. Taken together, this study showed the differential impacts of Uro-A and B on the gut microbiota composition in normal rats and would thus serve as a guide in the choice of these metabolites as a functional food ingredient or prebiotic.}, } @article {pmid34836140, year = {2021}, author = {Wilson, ML and Davies, IG and Waraksa, W and Khayyatzadeh, SS and Al-Asmakh, M and Mazidi, M}, title = {The Impact of Microbial Composition on Postprandial Glycaemia and Lipidaemia: A Systematic Review of Current Evidence.}, journal = {Nutrients}, volume = {13}, number = {11}, pages = {}, pmid = {34836140}, issn = {2072-6643}, mesh = {Gastrointestinal Microbiome/*physiology ; Humans ; Hyperglycemia/*microbiology ; Hyperlipidemias/*microbiology ; Nutritional Physiological Phenomena/*physiology ; Postprandial Period/*physiology ; }, abstract = {Postprandial hyperglycaemia is associated with increased risk of cardiovascular disease. Recent studies highlight the role of the gut microbiome in influencing postprandial glycaemic (PPG) and lipidaemic (PPL) responses. The authors of this review sought to address the question: "To what extent does individual gut microbiome diversity and composition contribute to PPG and PPL responses?". CINAHL Plus, PubMed, Web of Science, and the Cochrane Central Register of Controlled Trials (CENTRAL) databases were searched from January 2010 to June 2020. Following screening, 22 studies were eligible to be included in the current review. All trials reported analysis of gut microbiome diversity and composition and PPG and/or PPL. Results were reported according to the 'Preferred Reporting Items for Systematic Reviews and Meta-Analysis' (PRISMA) statement. Individual microbiota structure was found to play a key role in determining postprandial metabolic responses in adults and is attributed to a complex interplay of diet, microbiota composition, and metagenomic activity, which may be predicted by metagenomic analysis. Alterations of gut microbiota, namely relative abundance of bacterial phylum Actinobacteria and Proteobacteria, along with Enterobacteriaceae, were associated with individual variation in postprandial glycaemic response in adults. The findings of the current review present new evidence to support a personalised approach to nutritional recommendations and guidance for optimal health, management, and treatment of common metabolic disorders. In conclusion, personalised nutrition approaches based on individual microbial composition may improve postprandial regulation of glucose and lipids, providing a potential strategy to ameliorate cardiometabolic health outcomes.}, } @article {pmid34836120, year = {2021}, author = {Jollet, M and Nay, K and Chopard, A and Bareille, MP and Beck, A and Ollendorff, V and Vernus, B and Bonnieu, A and Mariadassou, M and Rué, O and Derbré, F and Goustard, B and Koechlin-Ramonatxo, C}, title = {Does Physical Inactivity Induce Significant Changes in Human Gut Microbiota? New Answers Using the Dry Immersion Hypoactivity Model.}, journal = {Nutrients}, volume = {13}, number = {11}, pages = {}, pmid = {34836120}, issn = {2072-6643}, support = {4800000997 and 4800001079//Centre National d'Études Spatiales/ ; }, mesh = {Adult ; Feces/chemistry/microbiology ; Gastrointestinal Microbiome/*physiology ; Healthy Volunteers ; Humans ; Immersion/physiopathology ; Male ; Propionates/metabolism ; Rest/*physiology ; *Sedentary Behavior ; Weightlessness Simulation ; }, abstract = {Gut microbiota, a major contributor to human health, is influenced by physical activity and diet, and displays a functional cross-talk with skeletal muscle. Conversely, few data are available on the impact of hypoactivity, although sedentary lifestyles are widespread and associated with negative health and socio-economic impacts. The study aim was to determine the effect of Dry Immersion (DI), a severe hypoactivity model, on the human gut microbiota composition. Stool samples were collected from 14 healthy men before and after 5 days of DI to determine the gut microbiota taxonomic profiles by 16S metagenomic sequencing in strictly controlled dietary conditions. The α and β diversities indices were unchanged. However, the operational taxonomic units associated with the Clostridiales order and the Lachnospiraceae family, belonging to the Firmicutes phylum, were significantly increased after DI. Propionate, a short-chain fatty acid metabolized by skeletal muscle, was significantly reduced in post-DI stool samples. The finding that intestine bacteria are sensitive to hypoactivity raises questions about their impact and role in chronic sedentary lifestyles.}, } @article {pmid34835502, year = {2021}, author = {Papadakis, P and Konteles, S and Batrinou, A and Ouzounis, S and Tsironi, T and Halvatsiotis, P and Tsakali, E and Van Impe, JFM and Vougiouklaki, D and Strati, IF and Houhoula, D}, title = {Characterization of Bacterial Microbiota of P.D.O. Feta Cheese by 16S Metagenomic Analysis.}, journal = {Microorganisms}, volume = {9}, number = {11}, pages = {}, pmid = {34835502}, issn = {2076-2607}, support = {956126//European Union Horizon 2020 Research and Innovation program under the Marie Skłodowska-Curie Grant Agreement/ ; }, abstract = {BACKGROUND: The identification of bacterial species in fermented PDO (protected designation of origin) cheese is important since they contribute significantly to the final organoleptic properties, the ripening process, the shelf life, the safety and the overall quality of cheese.

METHODS: Ten commercial PDO feta cheeses from two geographic regions of Greece, Epirus and Thessaly, were analyzed by 16S metagenomic analysis.

RESULTS: The biodiversity of all the tested feta cheese samples consisted of five phyla, 17 families, 38 genera and 59 bacterial species. The dominant phylum identified was Firmicutes (49% of the species), followed by Proteobacteria (39% of the species), Bacteroidetes (7% of the species), Actinobacteria (4% of the species) and Tenericutes (1% of the species). Streptococcaceae and Lactobacillaceae were the most abundant families, in which starter cultures of lactic acid bacteria (LAB) belonged, but also 21 nonstarter lactic acid bacteria (NSLAB) were identified. Both geographical areas showed a distinctive microbiota fingerprint, which was ultimately overlapped by the application of starter cultures. In the rare biosphere of the feta cheese, Zobellella taiwanensis and Vibrio diazotrophicus, two Gram-negative bacteria which were not previously reported in dairy samples, were identified.

CONCLUSIONS: The application of high-throughput DNA sequencing may provide a detailed microbial profile of commercial feta cheese produced with pasteurized milk.}, } @article {pmid34835128, year = {2021}, author = {Cebriá-Mendoza, M and Bracho, MA and Arbona, C and Larrea, L and Díaz, W and Sanjuán, R and Cuevas, JM}, title = {Exploring the Diversity of the Human Blood Virome.}, journal = {Viruses}, volume = {13}, number = {11}, pages = {}, pmid = {34835128}, issn = {1999-4915}, mesh = {*Genome, Viral ; Healthy Volunteers ; Humans ; Spain ; *Virome ; Viruses/*isolation & purification ; }, abstract = {Metagenomics is greatly improving our ability to discover new viruses, as well as their possible associations with disease. However, metagenomics has also changed our understanding of viruses in general. The vast expansion of currently known viral diversity has revealed a large fraction of non-pathogenic viruses, and offers a new perspective in which viruses function as important components of many ecosystems. In this vein, studies of the human blood virome are often motivated by the search for new viral diseases, especially those associated with blood transfusions. However, these studies have revealed the common presence of apparently non-pathogenic viruses in blood, particularly human anelloviruses and, to a lower extent, human pegiviruses (HPgV). To shed light on the diversity of the human blood virome, we subjected pooled plasma samples from 587 healthy donors in Spain to a viral enrichment protocol, followed by massive parallel sequencing. This showed that anelloviruses were clearly the major component of the blood virome and showed remarkable diversity. In total, we assembled 332 complete or near-complete anellovirus genomes, 50 of which could be considered new species. HPgV was much less frequent, but we, nevertheless, recovered 17 different isolates that we subsequently used for characterizing the diversity of this virus. In-depth investigation of the human blood virome should help to elucidate the ecology of these viruses, and to unveil potentially associated diseases.}, } @article {pmid34834969, year = {2021}, author = {Chase, EE and Monteil-Bouchard, S and Gobet, A and Andrianjakarivony, FH and Desnues, C and Blanc, G}, title = {A High Rate Algal Pond Hosting a Dynamic Community of RNA Viruses.}, journal = {Viruses}, volume = {13}, number = {11}, pages = {}, pmid = {34834969}, issn = {1999-4915}, mesh = {Animals ; Biodiversity ; Biomass ; Metagenome ; Microalgae/*virology ; *Phylogeny ; Pilot Projects ; *Ponds ; RNA Viruses/*classification/genetics ; Rotifera/virology ; Seasons ; Water ; *Water Microbiology ; }, abstract = {Despite a surge of RNA virome sequencing in recent years, there are still many RNA viruses to uncover-as indicated by the relevance of viral dark matter to RNA virome studies (i.e., putative viruses that do not match to taxonomically identified viruses). This study explores a unique site, a high-rate algal pond (HRAP), for culturing industrially microalgae, to elucidate new RNA viruses. The importance of viral-host interactions in aquatic systems are well documented, and the ever-expanding microalgae industry is no exception. As the industry becomes a more important source of sustainable plastic manufacturing, a producer of cosmetic pigments and alternative protein sources, and a means of CO2 remediation in the face of climate change, studying microalgal viruses becomes a vital practice for proactive management of microalgae cultures at the industrial level. This study provides evidence of RNA microalgal viruses persisting in a CO2 remediation pilot project HRAP and uncovers the diversity of the RNA virosphere contained within it. Evidence shows that family Marnaviridae is cultured in the basin, alongside other potential microalgal infecting viruses (e.g., family Narnaviridae, family Totitiviridae, and family Yueviridae). Finally, we demonstrate that the RNA viral diversity of the HRAP is temporally dynamic across two successive culturing seasons.}, } @article {pmid34834933, year = {2021}, author = {Turzynski, V and Monsees, I and Moraru, C and Probst, AJ}, title = {Imaging Techniques for Detecting Prokaryotic Viruses in Environmental Samples.}, journal = {Viruses}, volume = {13}, number = {11}, pages = {}, pmid = {34834933}, issn = {1999-4915}, mesh = {Genome, Viral ; Metagenomics ; Microscopy/*methods ; Microscopy, Electron/*methods ; Virome ; Viruses/classification/*genetics/isolation & purification/ultrastructure ; }, abstract = {Viruses are the most abundant biological entities on Earth with an estimate of 10[31] viral particles across all ecosystems. Prokaryotic viruses-bacteriophages and archaeal viruses-influence global biogeochemical cycles by shaping microbial communities through predation, through the effect of horizontal gene transfer on the host genome evolution, and through manipulating the host cellular metabolism. Imaging techniques have played an important role in understanding the biology and lifestyle of prokaryotic viruses. Specifically, structure-resolving microscopy methods, for example, transmission electron microscopy, are commonly used for understanding viral morphology, ultrastructure, and host interaction. These methods have been applied mostly to cultivated phage-host pairs. However, recent advances in environmental genomics have demonstrated that the majority of viruses remain uncultivated, and thus microscopically uncharacterized. Although light- and structure-resolving microscopy of viruses from environmental samples is possible, quite often the link between the visualization and the genomic information of uncultivated prokaryotic viruses is missing. In this minireview, we summarize the current state of the art of imaging techniques available for characterizing viruses in environmental samples and discuss potential links between viral imaging and environmental genomics for shedding light on the morphology of uncultivated viruses and their lifestyles in Earth's ecosystems.}, } @article {pmid34831411, year = {2021}, author = {Schierova, D and Roubalova, R and Kolar, M and Stehlikova, Z and Rob, F and Jackova, Z and Coufal, S and Thon, T and Mihula, M and Modrak, M and Kverka, M and Bajer, L and Kostovcikova, K and Drastich, P and Hercogova, J and Novakova, M and Vasatko, M and Lukas, M and Tlaskalova-Hogenova, H and Jiraskova Zakostelska, Z}, title = {Fecal Microbiome Changes and Specific Anti-Bacterial Response in Patients with IBD during Anti-TNF Therapy.}, journal = {Cells}, volume = {10}, number = {11}, pages = {}, pmid = {34831411}, issn = {2073-4409}, support = {grant number NV18-09-00493.//Ministry of Health of the Czech Republic/ ; }, mesh = {Adult ; Antibodies/blood ; Biodiversity ; Case-Control Studies ; Feces/*microbiology ; Female ; Fungi/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Inflammatory Bowel Diseases/blood/*drug therapy/*microbiology/surgery ; Interleukin-17/metabolism ; Leukocytes, Mononuclear/metabolism ; Male ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Tumor Necrosis Factor Inhibitors/*therapeutic use ; }, abstract = {Inflammatory bowel diseases (IBD) are chronic disorders of the gastrointestinal tract that have been linked to microbiome dysbiosis and immune system dysregulation. We investigated the longitudinal effect of anti-TNF therapy on gut microbiota composition and specific immune response to commensals in IBD patients. The study included 52 patients tracked over 38 weeks of therapy and 37 healthy controls (HC). To characterize the diversity and composition of the gut microbiota, we used amplicon sequencing of the V3V4 region of 16S rRNA for the bacterial community and of the ITS1 region for the fungal community. We measured total antibody levels as well as specific antibodies against assorted gut commensals by ELISA. We found diversity differences between HC, Crohn's disease, and ulcerative colitis patients. The bacterial community of patients with IBD was more similar to HC at the study endpoint, suggesting a beneficial shift in the microbiome in response to treatment. We identified factors such as disease severity, localization, and surgical intervention that significantly contribute to the observed changes in the gut bacteriome. Furthermore, we revealed increased IgM levels against specific gut commensals after anti-TNF treatment. In summary, this study, with its longitudinal design, brings insights into the course of anti-TNF therapy in patients with IBD and correlates the bacterial diversity with disease severity in patients with ulcerative colitis (UC).}, } @article {pmid34830313, year = {2021}, author = {Fling, RR and Zacharewski, TR}, title = {Aryl Hydrocarbon Receptor (AhR) Activation by 2,3,7,8-Tetrachlorodibenzo-p-Dioxin (TCDD) Dose-Dependently Shifts the Gut Microbiome Consistent with the Progression of Non-Alcoholic Fatty Liver Disease.}, journal = {International journal of molecular sciences}, volume = {22}, number = {22}, pages = {}, pmid = {34830313}, issn = {1422-0067}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; P42ES004911/ES/NIEHS NIH HHS/United States ; R01 ES029541/ES/NIEHS NIH HHS/United States ; T32 ES007255/ES/NIEHS NIH HHS/United States ; R01ES029541/ES/NIEHS NIH HHS/United States ; MICL02603//The AgBioResearch at Michigan State University/ ; T32ES00725/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Bacteroidetes/genetics/growth & development/isolation & purification ; Basic Helix-Loop-Helix Transcription Factors/agonists/*genetics/metabolism ; Dysbiosis/chemically induced/*genetics/metabolism/pathology ; Gastrointestinal Microbiome/*drug effects/genetics ; Gene Expression Regulation ; Humans ; Lactobacillus/classification/genetics/growth & development/isolation & purification ; Liver/drug effects/metabolism/pathology ; Liver Cirrhosis/genetics/metabolism/pathology ; Male ; Metabolic Networks and Pathways/genetics ; Mice ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/chemically induced/*genetics/metabolism/pathology ; Polychlorinated Dibenzodioxins/*pharmacology ; Receptors, Aryl Hydrocarbon/agonists/*genetics/metabolism ; }, abstract = {Gut dysbiosis with disrupted enterohepatic bile acid metabolism is commonly associated with non-alcoholic fatty liver disease (NAFLD) and recapitulated in a NAFLD-phenotype elicited by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in mice. TCDD induces hepatic fat accumulation and increases levels of secondary bile acids, including taurolithocholic acid and deoxycholic acid (microbial modified bile acids involved in host bile acid regulation signaling pathways). To investigate the effects of TCDD on the gut microbiota, the cecum contents of male C57BL/6 mice orally gavaged with sesame oil vehicle or 0.3, 3, or 30 µg/kg TCDD were examined using shotgun metagenomic sequencing. Taxonomic analysis identified dose-dependent increases in Lactobacillus species (i.e., Lactobacillus reuteri). Increased species were also associated with dose-dependent increases in bile salt hydrolase sequences, responsible for deconjugation reactions in secondary bile acid metabolism. Increased L. reuteri levels were further associated with mevalonate-dependent isopentenyl diphosphate (IPP) biosynthesis and o-succinylbenzoate synthase, a menaquinone biosynthesis associated gene. Analysis of the gut microbiomes from cirrhosis patients identified an increased abundance of genes from the mevalonate-dependent IPP biosynthesis as well as several other menaquinone biosynthesis genes, including o-succinylbenzoate synthase. These results extend the association of lactobacilli with the AhR/intestinal axis in NAFLD progression and highlight the similarities between TCDD-elicited phenotypes in mice to human NAFLD.}, } @article {pmid34829197, year = {2021}, author = {Rayko, M and Sokornova, S and Lapidus, A}, title = {Fungal Metagenome of Chernevaya Taiga Soils: Taxonomic Composition, Differential Abundance and Factors Related to Plant Gigantism.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {7}, number = {11}, pages = {}, pmid = {34829197}, issn = {2309-608X}, support = {19-16-00049//Russian Science Foundation/ ; }, abstract = {The Chernevaya taiga of Western Siberia is a unique and complex ecosystem, distinguished by the unusually large sizes of herbaceous plants, the reasons for which are poorly understood. Here, we explored the fungal diversity of the Chernevaya taiga soils in the Tomsk regions of Western Siberia in comparison with other soil types. The soil biomes of Chernevaya taiga and the control regions were investigated using Illumina ITS rRNA sequencing, and taxonomic analysis revealed a predominance of fungal phyla in the different soils. These results demonstrate that the fungi of the Chernevaya taiga regions have a higher species diversity (Faith's PD) vs. the control soils, and the diversity is due more to the sampling sites rather than to the seasons (Bray-Curtis distance). We studied most of the differentially abundant taxa among the soil types, and we annotated the taxa with their ecological guilds and trophic types. Some of the abundant fungal taxa in the summer- and fall-Chernevaya taiga samples belong to the phylum Glomeromycota-arbuscular mycorrhizal symbiotrophs, which are known to establish symbiotic relationships and enhance plant growth. Additionally, several OTUs were assigned to novel genera in the Glomeraceae and Claroideoglomeraceae families. Our findings add a potential explanation of the high productivity and plant gigantism in Chernevaya taiga and expand our knowledge of fungal biodiversity.}, } @article {pmid34828970, year = {2021}, author = {Barbieri, F and Tabanelli, G and Montanari, C and Dall'Osso, N and Šimat, V and Smole Možina, S and Baños, A and Özogul, F and Bassi, D and Fontana, C and Gardini, F}, title = {Mediterranean Spontaneously Fermented Sausages: Spotlight on Microbiological and Quality Features to Exploit Their Bacterial Biodiversity.}, journal = {Foods (Basel, Switzerland)}, volume = {10}, number = {11}, pages = {}, pmid = {34828970}, issn = {2304-8158}, support = {Project ID 1467//PRIMA programme (supported by the European Union H2020 programme)/ ; }, abstract = {The wide array of spontaneously fermented sausages of the Mediterranean area can represent a reservoir of microbial biodiversity and can be an important source of new technological and functional strains able to preserve product properties, counteracting the impoverishment of their organoleptic typical features due to the introduction of commercial starter cultures. We analysed 15 artisanal salamis from Italy, Spain, Croatia and Slovenia to evaluate the microbiota composition, through culture-dependent and culture-independent techniques (i.e., metagenomic analysis), chemical-physical features, biogenic amines and aroma profile. The final pH varied according to origin and procedures (e.g., higher pH in Italian samples due to long ripening and mold growth). Lactic acid bacteria (LAB) and coagulase-negative cocci (CNC) were the dominant population, with highest LAB counts in Croatian and Italian samples. Metagenomic analysis showed high variability in qualitative and quantitative microbial composition: among LAB, Latilactobacillus sakei was the dominant species, but Companilactobacillus spp. was present in high amounts (45-55% of the total ASVs) in some Spanish sausages. Among staphylococci, S. epidermidis, S. equorum, S. saprophyticus, S. succinus and S. xylosus were detected. As far as biogenic amines, tyramine was always present, while histamine was found only in two Spanish samples. These results can valorize the bacterial genetic heritage present in Mediterranean products, to find new candidates of autochthonous starter cultures or bioprotective agents.}, } @article {pmid34828362, year = {2021}, author = {Lach, J and Jęcz, P and Strapagiel, D and Matera-Witkiewicz, A and Stączek, P}, title = {The Methods of Digging for "Gold" within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools.}, journal = {Genes}, volume = {12}, number = {11}, pages = {}, pmid = {34828362}, issn = {2073-4425}, mesh = {Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; Biological Products/*analysis ; Computational Biology ; Data Mining ; Genome, Archaeal ; Genome, Bacterial ; Salt Tolerance ; Sequence Analysis, DNA/*methods ; }, abstract = {Halophiles, the salt-loving organisms, have been investigated for at least a hundred years. They are found in all three domains of life, namely Archaea, Bacteria, and Eukarya, and occur in saline and hypersaline environments worldwide. They are already a valuable source of various biomolecules for biotechnological, pharmaceutical, cosmetological and industrial applications. In the present era of multidrug-resistant bacteria, cancer expansion, and extreme environmental pollution, the demand for new, effective compounds is higher and more urgent than ever before. Thus, the unique metabolism of halophilic microorganisms, their low nutritional requirements and their ability to adapt to harsh conditions (high salinity, high pressure and UV radiation, low oxygen concentration, hydrophobic conditions, extreme temperatures and pH, toxic compounds and heavy metals) make them promising candidates as a fruitful source of bioactive compounds. The main aim of this review is to highlight the nucleic acid sequencing experimental strategies used in halophile studies in concert with the presentation of recent examples of bioproducts and functions discovered in silico in the halophile's genomes. We point out methodological gaps and solutions based on in silico methods that are helpful in the identification of valuable bioproducts synthesized by halophiles. We also show the potential of an increasing number of publicly available genomic and metagenomic data for halophilic organisms that can be analysed to identify such new bioproducts and their producers.}, } @article {pmid34827957, year = {2021}, author = {Benmazouz, I and Jokimäki, J and Lengyel, S and Juhász, L and Kaisanlahti-Jokimäki, ML and Kardos, G and Paládi, P and Kövér, L}, title = {Corvids in Urban Environments: A Systematic Global Literature Review.}, journal = {Animals : an open access journal from MDPI}, volume = {11}, number = {11}, pages = {}, pmid = {34827957}, issn = {2076-2615}, support = {SH-00355-004/2019//Stipendium Hungaricum program/ ; NKFIH-OTKA K134391//National Research, Development, and Innovation Office of Hungary/ ; }, abstract = {Urbanization is one of the most prevalent drivers of biodiversity loss, yet few taxonomic groups are remarkably successful at adapting to urban environments. We systematically surveyed the global literature on the effects of urbanization on species of family Corvidae (crows, choughs, jackdaws, jays, magpies, nutcrackers, ravens, rooks, treepies) to assess the occurrence of corvids in urban environments and the factors affecting their success. We found a total of 424 primary research articles, and the number of articles has increased exponentially since the 1970s. Most studies were carried out in cities of Europe and North America (45.5% and 31.4%, respectively) and were directed on a single species (75.2). We found that 30 corvid species (23% of 133 total) regularly occur in urban environments. The majority (72%) of the studies reported positive effects of urbanization on corvids, with 85% of studies detecting population increases and 64% of studies detecting higher breeding success with urbanization. Of the factors proposed to explain corvids' success (availability of nesting sites and food sources, low predation and persecution), food availability coupled with diet shifts emerged as the most important factors promoting Corvidae to live in urban settings. The breeding of corvids in urban environments was further associated with earlier nesting, similar or larger clutches, lower hatching but higher fledging success, reduced home range size and limited territoriality, increased tolerance towards humans and increasing frequency of conflicts with humans. Despite geographic and taxonomic biases in our literature sample, our review indicates that corvids show both flexibility in resource use and behavioral plasticity that enable them to exploit novel resources for nesting and feeding. Corvids can thus be urban exploiters of the large-scale modifications of ecosystems caused by urbanization.}, } @article {pmid34826491, year = {2022}, author = {Nóbrega, MS and Silva, BS and Tschoeke, DA and Appolinario, LR and Calegario, G and Venas, TM and Macedo, L and Asp, N and Cherene, B and Marques, JSJ and Seidel, M and Dittmar, T and Santos, IR and de Rezende, CE and Thompson, CC and Thompson, FL}, title = {Mangrove microbiome reveals importance of sulfur metabolism in tropical coastal waters.}, journal = {The Science of the total environment}, volume = {813}, number = {}, pages = {151889}, doi = {10.1016/j.scitotenv.2021.151889}, pmid = {34826491}, issn = {1879-1026}, mesh = {Carbon ; Estuaries ; *Microbiota ; Nitrogen ; Sulfur ; Wetlands ; }, abstract = {Mangroves under macro-tidal regimes are global carbon sequestration hotspots but the microbial drivers of biogeochemical cycles remain poorly understood. Here, we investigate the drivers of mangrove microbial community composition across a porewater-creek-estuary-ocean continuum. Observations were performed on the Amazon region in one of the largest mangrove systems worldwide with effective sequestration of organic carbon buried in soils and dissolved carbon via outwelling to the ocean. The potential export to the adjacent oceanic region ranged from 57 to 380 kg of dissolved and particulate organic carbon per second (up to 33 thousand tons C per day). Macro tides modulated microbial communities and their metabolic processes, e.g., anoxygenic phototrophy, sulfur, and nitrogen cycling. Respiration, sulfur metabolism and dissolved organic carbon (DOC) levels were linked to functional groups and microbial cell counts. Total microbial counts decreased and cyanobacteria counts peaked in the spring tide. The microbial groups driving carbon, nitrogen, sulfur and methane cycles were consistent across all spatial scales. Taxonomic groups engaged in sulfur cycling (Allochromatium, Desulfovibrio, and Thibacillus) within mangroves were abundant at all scales. Tidally-driven porewater exchange within mangroves drove a progressive increase of sulfur cycle taxonomic groups and their functional genes both temporally (tidal cycles) and spatially (from mangrove porewater to continental shelf). Overall, we revealed a unified and consistent response of microbiomes at different spatial and temporal scales to tidally-driven mangrove porewater exchange.}, } @article {pmid34826164, year = {2022}, author = {Ma, Y and Liu, D and Wariss, HM and Zhang, R and Tao, L and Milne, RI and Sun, W}, title = {Demographic history and identification of threats revealed by population genomic analysis provide insights into conservation for an endangered maple.}, journal = {Molecular ecology}, volume = {31}, number = {3}, pages = {767-779}, doi = {10.1111/mec.16289}, pmid = {34826164}, issn = {1365-294X}, support = {2017FY100100//Survey and Germplasm Conservation of Plant Species with Extremely Small Populations in Southwest China/ ; 2019QZKK0502//Second Tibetan Plateau Scientific Expedition and Research Program/ ; U1302262//NSFC (National Natural Science Foundation of China) Yunnan Joint Fund/ ; 2019HC015//Yunnan Science and Technology Innovation Team Program for PSESP Conservation and Utilization/ ; }, mesh = {*Acer/genetics ; Animals ; Anthropogenic Effects ; China ; Endangered Species ; Genetic Variation ; Genomics ; Humans ; Metagenomics ; Population Density ; }, abstract = {Recent advancements in whole genome sequencing techniques capable of covering nearly all the nucleotide variations of a genome would make it possible to set up a conservation framework for threatened plants at the genomic level. Here we applied a whole genome resequencing approach to obtain genome-wide data from 105 individuals sampled from the 10 currently known extant populations of Acer yangbiense, an endangered species with fragmented habitats and restricted distribution in Yunnan, China. To inform meaningful conservation action, we investigated what factors might have contributed to the formation of its extremely small population sizes and what threats it currently suffers at a genomic level. Our results revealed that A. yangbiense has low genetic diversity and comprises different numbers of genetic groups based on neutral (seven) and selected loci (13), with frequent gene flow between populations. Repeated bottleneck events, particularly the most recent one occurring within ~10,000 years before present, which decreased its effective population size (Ne) < 200, and severe habitat fragmentation resulting from anthropogenic activities as well as a biased gender ratio of mature individuals in its natural habitat, might have together contributed to the currently fragmented and endangered status of A. yangbiense. The species has suffered from inbreeding and deleterious mutation load, both of which varied among populations but had similar patterns; that is, populations with higher FROH (frequency of runs of homozygosity) always carried a larger number of deleterious mutations in the homozygous state than in populations with lower FROH. In addition, based on our genetic differentiation results, and the distribution patterns of homozygous deleterious mutations in individuals, we recommend certain conservation actions regarding the genetic rescue of A. yangbiense. Overall, our study provides meaningful insights into the conservation genetics and a framework for the further conservation for the endangered A. yangbiense.}, } @article {pmid34825657, year = {2021}, author = {Kakati, P and Paine, SK and Bhattacharjee, CK and Bhattacharyya, C and Sharma, A and Phukan, D and Barman, NN and Basu, A}, title = {Gut microbiome architecture of wild greater one-horned rhinoceros:a vulnerable species from Kaziranga National Park, India.}, journal = {Journal of genetics}, volume = {100}, number = {}, pages = {}, pmid = {34825657}, issn = {0973-7731}, mesh = {Animals ; Animals, Wild/microbiology ; Bacteria/classification/isolation & purification ; Feces/microbiology ; Fungi/classification/isolation & purification ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/veterinary ; India ; Perissodactyla/*microbiology ; }, abstract = {Rhinoceros unicornis, also known as the greater one-horned rhinoceros (GoHR), is a vulnerable wildlife species found in the Indian subcontinent with an estimated global population of 3582, of which an estimated 2995 resides in India. The Kaziranga National Park of Assam is the home to ~80.56% of the GoH population in India. Recent advances in genetics and microbial studies underscored the importance of gut microbial symbiosis as a crucial factor for host metabolic health and environmental interaction, particularly for higher mammals. Alteration of the normal microbiome can also be an indicator of chronic disease and infection. Freshly voided dung samples from nine dung heaps of free ranging or wild GoH rhinoceros were collected from Kaziranga National Park for mapping the gut microbial architecture through 16S-metagenomic approach. In our sample, the GoH gut harbours 168.8±12.55 (SE) bacteria-specific OTUs belonging to 21 phyla of which the gram-negative Proteobacteria is the most abundant phyla. Other abundant phylas found in the GoH gut are Firmicutes and Bacteroidetes. Although the GoH rhinoceros gut can utilize fibrous plant by microbial fermentation, the aerobic, nonfermenting Acinetobacter (20.7%), Stenotrophomonas (17.8%) and Brevundimonas (9.1%) constitute about 50% of all identified genus. Functional prediction of the GoH microbiome reveals that>50% of the bacteria present are involved in metabolism followed by cellular processes and information processing. A significant proportion (>1%) are associated with different diseases. In summary, our study characterized bacterial communities of nine wild GoH to identify some unique features and its implication in disease and survival of GoH.}, } @article {pmid34825005, year = {2021}, author = {Yang, X and Xiao, H and Zeng, Y and Huang, L and Ji, K and Deng, D and Yang, W and Liu, L}, title = {Tianwang Buxin Granules Influence the Intestinal Flora in Perimenopausal Insomnia.}, journal = {BioMed research international}, volume = {2021}, number = {}, pages = {9979511}, pmid = {34825005}, issn = {2314-6141}, mesh = {Adult ; Case-Control Studies ; Drugs, Chinese Herbal/administration & dosage/*therapeutic use ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Hot Flashes/drug therapy/etiology/microbiology ; Humans ; Male ; Middle Aged ; *Perimenopause ; Phytotherapy ; Sleep Initiation and Maintenance Disorders/*drug therapy/etiology/*microbiology ; }, abstract = {METHODS: The subjects included 13 PI patients from the Hubei Provincial Hospital of TCM, Hubei University of TCM, and Wuhan Traditional Chinese Medicine Hospital, and the corresponding noninsomniac spouses of the patients were selected as controls. TWBXG was continuously administered for 4 weeks. The feces of PI patients and their noninsomniac spouses before and after treatment with TWBXG were collected. The intestinal flora composition of each group was detected by metagenomic sequencing, and the efficacy of TWBXG was evaluated by the PSQI scale.

RESULTS: Compared with the control group, the model group showed an increase in the abundance of Roseburia faecis, Ruminococcus, Prevotella copri, Fusicatenibacter saccharivorans, and Blautia obeum, while those of Bacteroides, fecal Bacteroidetes, and Faecalibacterium prausnitzii were decreased. Compared with pretreatment, the PSQI score was significantly reduced (P < 0.05), the abundance of Bacteroides, fecal Bacteroidetes, and Faecalibacterium prausnitzii increased, and that of Roseburia faecis, Ruminococcus, Prevotella copri, Fusicatenibacter saccharivorans, and Blautia obeum decreased after treatment. However, there was still a certain gap in the abundance of related flora in the treatment group compared with the control.

CONCLUSION: PI is associated with disturbances in the intestinal flora and is mainly related to the disorders of Roseburia faecis, Ruminococcus, Prevotella copri, Fusicatenibacter saccharivorans, Blautia obeum, Bacteroides, fecal Bacteroidetes, and Faecalibacterium prausnitzii. TWBXG can effectively treat PI, and its effect may be achieved by regulating the disordered intestinal flora. Clinical Trials. The study was registered in the Chinese clinical trial registry and approved by the World Health Organization clinical trial registration platform (Effects of the modified Tianwang Buxin granule and modified Tianwang Buxin decoction pieces on insomnia: a randomized, controlled trial, ChiCTR-IPR-17011549).}, } @article {pmid34824318, year = {2021}, author = {Chen, YF and Hsieh, AH and Wang, LC and Huang, YJ and Yun-Chen Tsai, and Tseng, WY and Kuo, YL and Luo, SF and Yu, KH and Kuo, CF}, title = {Fecal microbiota changes in NZB/W F1 mice after induction of lupus disease.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {22953}, pmid = {34824318}, issn = {2045-2322}, support = {108-2314-B-182A-064//Ministry of Science and Technology, Taiwan/ ; CMRPG3G0851//Chang Gung Memorial Hospital, Linkou/ ; CMRPG3F1703//Chang Gung Memorial Hospital, Linkou/ ; CMRPG3H1393//Chang Gung Memorial Hospital, Linkou/ ; }, mesh = {Animals ; *Bacteria/classification/genetics/isolation & purification ; DNA, Bacterial ; Disease Models, Animal ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Lupus Erythematosus, Systemic/*microbiology ; Metagenomics ; Mice ; Mice, Inbred NZB ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The association between the gut microbiota and the development of lupus is unclear. We investigated alterations in the gut microbiota after induction of lupus in a murine model using viral peptide of human cytomegalovirus (HCMV). Three treatment arms for the animals were prepared: intraperitoneal injection of HCMVpp65 peptide, adjuvant alone, and PBS injection. Feces were collected before and after lupus induction biweekly for 16S rRNA sequencing. HCMVpp65 peptide immunization induced lupus-like effects, with higher levels of anti-dsDNA antibodies, creatinine, proteinuria, and glomerular damage, compared with mice treated with nothing or adjuvant only. The Simpson diversity value was higher in mice injected with HCMVpp65 peptide, but there was no difference in ACE or Chao1 among the three groups. Statistical analysis of metagenomic profiles showed a higher abundance of various families (Saccharimonadaceae, Marinifiaceae, and Desulfovibrionaceae) and genera (Candidatus Saccharimonas, Roseburia, Odoribacter, and Desulfovibrio) in HCMVpp65 peptide-treated mice. Significant correlations between increased abundances of related genera (Candidatus Saccharimonas, Roseburia, Odoribacter, and Desulfovibrio) and HCMVpp65 peptide immunization-induced lupus-like effects were observed. This study provides insight into the changes in the gut microbiota after lupus onset in a murine model.}, } @article {pmid34824209, year = {2021}, author = {Kandathil, AJ and Cox, AL and Page, K and Mohr, D and Razaghi, R and Ghanem, KG and Tuddenham, SA and Hsieh, YH and Evans, JL and Coller, KE and Timp, W and Celentano, DD and Ray, SC and Thomas, DL}, title = {Plasma virome and the risk of blood-borne infection in persons with substance use disorder.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6909}, pmid = {34824209}, issn = {2041-1723}, support = {R37 DA013806/DA/NIDA NIH HHS/United States ; U19 AI159822/AI/NIAID NIH HHS/United States ; R01 DA016017/DA/NIDA NIH HHS/United States ; R21 DA053145/DA/NIDA NIH HHS/United States ; R01 DA013806/DA/NIDA NIH HHS/United States ; }, mesh = {Adult ; Amino Acid Sequence ; Anelloviridae ; *Blood-Borne Infections ; Blood-Borne Pathogens ; Female ; Hepatitis C/epidemiology ; Humans ; Knowledge ; Male ; Metagenomics ; Phylogeny ; *Plasma ; Public Health ; *Substance-Related Disorders ; *Virome ; Young Adult ; }, abstract = {There is an urgent need for innovative methods to reduce transmission of bloodborne pathogens like HIV and HCV among people who inject drugs (PWID). We investigate if PWID who acquire non-pathogenic bloodborne viruses like anelloviruses and pegiviruses might be at greater risk of acquiring a bloodborne pathogen. PWID who later acquire HCV accumulate more non-pathogenic viruses in plasma than matched controls who do not acquire HCV infection. Additionally, phylogenetic analysis of those non-pathogenic virus sequences reveals drug use networks. Here we find first in Baltimore and confirm in San Francisco that the accumulation of non-pathogenic viruses in PWID is a harbinger for subsequent acquisition of pathogenic viruses, knowledge that may guide the prioritization of the public health resources to combat HIV and HCV.}, } @article {pmid34824201, year = {2021}, author = {Li, L and Solvi, C and Zhang, F and Qi, Z and Chittka, L and Zhao, W}, title = {Gut microbiome drives individual memory variation in bumblebees.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6588}, pmid = {34824201}, issn = {2041-1723}, mesh = {Animals ; Bacteria/genetics/metabolism ; Bees/*microbiology/*physiology ; Gastrointestinal Microbiome/genetics/*physiology ; Glycerophospholipids/metabolism ; Individuality ; Lactobacillus/genetics/metabolism ; Memory, Long-Term/*physiology ; Metabolomics ; Metagenome ; *Metagenomics ; }, abstract = {The potential of the gut microbiome as a driver of individual cognitive differences in natural populations of animals remains unexplored. Here, using metagenomic sequencing of individual bumblebee hindguts, we find a positive correlation between the abundance of Lactobacillus Firm-5 cluster and memory retention on a visual discrimination task. Supplementation with the Firm-5 species Lactobacillus apis, but not other non-Firm-5 bacterial species, enhances bees' memory. Untargeted metabolomics after L. apis supplementation show increased LPA (14:0) glycerophospholipid in the haemolymph. Oral administration of the LPA increases long-term memory significantly. Based on our findings and metagenomic/metabolomic analyses, we propose a molecular pathway for this gut-brain interaction. Our results provide insights into proximate and ultimate causes of cognitive differences in natural bumblebee populations.}, } @article {pmid34823595, year = {2021}, author = {Panwar, P and Allen, MA and Williams, TJ and Haque, S and Brazendale, S and Hancock, AM and Paez-Espino, D and Cavicchioli, R}, title = {Remarkably coherent population structure for a dominant Antarctic Chlorobium species.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {231}, pmid = {34823595}, issn = {2049-2618}, mesh = {Antarctic Regions ; *Chlorobium/genetics ; Ecosystem ; Lakes/microbiology ; Metagenome ; *Microbiota ; }, abstract = {BACKGROUND: In Antarctica, summer sunlight enables phototrophic microorganisms to drive primary production, thereby "feeding" ecosystems to enable their persistence through the long, dark winter months. In Ace Lake, a stratified marine-derived system in the Vestfold Hills of East Antarctica, a Chlorobium species of green sulphur bacteria (GSB) is the dominant phototroph, although its seasonal abundance changes more than 100-fold. Here, we analysed 413 Gb of Antarctic metagenome data including 59 Chlorobium metagenome-assembled genomes (MAGs) from Ace Lake and nearby stratified marine basins to determine how genome variation and population structure across a 7-year period impacted ecosystem function.

RESULTS: A single species, Candidatus Chlorobium antarcticum (most similar to Chlorobium phaeovibrioides DSM265) prevails in all three aquatic systems and harbours very little genomic variation (≥ 99% average nucleotide identity). A notable feature of variation that did exist related to the genomic capacity to biosynthesize cobalamin. The abundance of phylotypes with this capacity changed seasonally ~ 2-fold, consistent with the population balancing the value of a bolstered photosynthetic capacity in summer against an energetic cost in winter. The very high GSB concentration (> 10[8] cells ml[-1] in Ace Lake) and seasonal cycle of cell lysis likely make Ca. Chlorobium antarcticum a major provider of cobalamin to the food web. Analysis of Ca. Chlorobium antarcticum viruses revealed the species to be infected by generalist (rather than specialist) viruses with a broad host range (e.g., infecting Gammaproteobacteria) that were present in diverse Antarctic lakes. The marked seasonal decrease in Ca. Chlorobium antarcticum abundance may restrict specialist viruses from establishing effective lifecycles, whereas generalist viruses may augment their proliferation using other hosts.

CONCLUSION: The factors shaping Antarctic microbial communities are gradually being defined. In addition to the cold, the annual variation in sunlight hours dictates which phototrophic species can grow and the extent to which they contribute to ecosystem processes. The Chlorobium population studied was inferred to provide cobalamin, in addition to carbon, nitrogen, hydrogen, and sulphur cycling, as critical ecosystem services. The specific Antarctic environmental factors and major ecosystem benefits afforded by this GSB likely explain why such a coherent population structure has developed in this Chlorobium species. Video abstract.}, } @article {pmid34821475, year = {2021}, author = {Kopprio, GA and Luyen, ND and Cuong, LH and Duc, TM and Fricke, A and Kunzmann, A and Huong, LM and Gärdes, A}, title = {Insights into the bacterial community composition of farmed Caulerpa lentillifera: A comparison between contrasting health states.}, journal = {MicrobiologyOpen}, volume = {10}, number = {6}, pages = {e1253}, pmid = {34821475}, issn = {2045-8827}, mesh = {Bacteria/classification ; *Bacterial Physiological Phenomena ; Caulerpa/*microbiology/physiology ; Host Microbial Interactions ; *Microbiota ; Plant Diseases/*microbiology ; }, abstract = {The bacterial communities of Caulerpa lentillifera were studied during an outbreak of an unknown disease in a sea grape farm from Vietnam. Clear differences between healthy and diseased cases were observed at the order, genus, and Operational Taxonomic Unit (OTU) level. A richer diversity was detected in the diseased thalli of C. lentillifera, as well as the dominance of the orders Flavobacteriales (phylum Bacteroidetes) and Phycisphaerales (Planctomycetes). Aquibacter, Winogradskyella, and other OTUs of the family Flavobacteriaceae were hypothesized as detrimental bacteria, this family comprises some well-known seaweed pathogens. Phycisphaera together with other Planctomycetes and Woeseia were probably saprophytes of C. lentillifera. The Rhodobacteraceae and Rhodovulum dominated the bacterial community composition of healthy C. lentillifera. The likely beneficial role of Bradyrhizobium, Paracoccus, and Brevundimonas strains on nutrient cycling and phytohormone production was discussed. The bleaching of diseased C. lentillifera might not only be associated with pathogens but also with an oxidative response. This study offers pioneering insights on the co-occurrence of C. lentillifera-attached bacteria, potential detrimental or beneficial microbes, and a baseline for understanding the C. lentillifera holobiont. Further applied and basic research is urgently needed on C. lentillifera microbiome, shotgun metagenomic, metatranscriptomic, and metabolomic studies as well as bioactivity assays are recommended.}, } @article {pmid34821239, year = {2021}, author = {Jin, Z and Fang, Z and Pei, Z and Wang, H and Zhu, J and Lee, YK and Zhang, H and Zhao, J and Lu, W and Chen, W}, title = {A low molecular weight brown algae Laminaria japonica glycan modulation of gut microbiota and body weight in mice.}, journal = {Food & function}, volume = {12}, number = {24}, pages = {12606-12620}, doi = {10.1039/d1fo03024h}, pmid = {34821239}, issn = {2042-650X}, mesh = {Animals ; Body Weight/*drug effects ; Gastrointestinal Microbiome/*drug effects ; Laminaria/*metabolism ; Male ; Mice ; Mice, Inbred BALB C ; Models, Animal ; Polysaccharides/*metabolism ; }, abstract = {Brown algae glycan from Laminaria japonica (LJNP) is a heterogeneous glycan with two apparent molecular weights of 1.1 and 37.3 kDa, and is mainly composed of α β-glucan and a few fucosyl residues. To explore the regulation of gut microbiota and the host, LJNP and 2'-fucosyllactose (2'FL) were compared to investigate their effect on mice via oral administration. Using metagenomic and metabolomic analyses, we found that 2'FL mainly relied on Adlercreutzia equolifaciens and Akkermansia muciniphila to improve gut amino acid and bile acid metabolism, whereas LJNP mainly drove Bacteroides vulgatus and Bacteroides uniformis to regulate gut amino acid metabolism and glycometabolism. Moreover, LJNP showed a weight loss effect and better protection of the intestinal barrier than 2'FL. We further employed LJNP and 2'FL on a germ-free mice model. Interestingly, the body weight management was not microbiome mediated. This study showed that LJNP can ameliorate the intestinal barrier through modulation of the gut microbiota, maintain the blood glucose level, and regulate body weight and the antioxidant function. Although the benefits of LJNP on host health were partly revealed, mechanisms such as the weight loss effect require further study.}, } @article {pmid34821235, year = {2021}, author = {Robinson, SL and Piel, J and Sunagawa, S}, title = {A roadmap for metagenomic enzyme discovery.}, journal = {Natural product reports}, volume = {38}, number = {11}, pages = {1994-2023}, pmid = {34821235}, issn = {1460-4752}, mesh = {Amino Acid Sequence ; Biological Products/metabolism ; Catalytic Domain ; Cytochrome P-450 Enzyme System/chemistry/physiology ; Enzymes/chemistry/*isolation & purification ; Machine Learning ; Metagenomics/*methods ; Microbiota ; Phylogeny ; }, abstract = {Covering: up to 2021Metagenomics has yielded massive amounts of sequencing data offering a glimpse into the biosynthetic potential of the uncultivated microbial majority. While genome-resolved information about microbial communities from nearly every environment on earth is now available, the ability to accurately predict biocatalytic functions directly from sequencing data remains challenging. Compared to primary metabolic pathways, enzymes involved in secondary metabolism often catalyze specialized reactions with diverse substrates, making these pathways rich resources for the discovery of new enzymology. To date, functional insights gained from studies on environmental DNA (eDNA) have largely relied on PCR- or activity-based screening of eDNA fragments cloned in fosmid or cosmid libraries. As an alternative, shotgun metagenomics holds underexplored potential for the discovery of new enzymes directly from eDNA by avoiding common biases introduced through PCR- or activity-guided functional metagenomics workflows. However, inferring new enzyme functions directly from eDNA is similar to searching for a 'needle in a haystack' without direct links between genotype and phenotype. The goal of this review is to provide a roadmap to navigate shotgun metagenomic sequencing data and identify new candidate biosynthetic enzymes. We cover both computational and experimental strategies to mine metagenomes and explore protein sequence space with a spotlight on natural product biosynthesis. Specifically, we compare in silico methods for enzyme discovery including phylogenetics, sequence similarity networks, genomic context, 3D structure-based approaches, and machine learning techniques. We also discuss various experimental strategies to test computational predictions including heterologous expression and screening. Finally, we provide an outlook for future directions in the field with an emphasis on meta-omics, single-cell genomics, cell-free expression systems, and sequence-independent methods.}, } @article {pmid34819672, year = {2021}, author = {Balaich, J and Estrella, M and Wu, G and Jeffrey, PD and Biswas, A and Zhao, L and Korennykh, A and Donia, MS}, title = {The human microbiome encodes resistance to the antidiabetic drug acarbose.}, journal = {Nature}, volume = {600}, number = {7887}, pages = {110-115}, pmid = {34819672}, issn = {1476-4687}, support = {R01 GM110161/GM/NIGMS NIH HHS/United States ; DP2 AI124441/AI/NIAID NIH HHS/United States ; T32 GM007388/GM/NIGMS NIH HHS/United States ; P41 GM111244/GM/NIGMS NIH HHS/United States ; 1013579/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Acarbose/metabolism/*pharmacology ; Amylases/metabolism ; Animals ; Drug Resistance, Bacterial/*drug effects ; Gastrointestinal Microbiome/*drug effects ; Humans ; Hypoglycemic Agents/metabolism/*pharmacology ; *Inactivation, Metabolic ; Metagenome/drug effects/*genetics ; Models, Molecular ; Mouth/drug effects/*microbiology ; Phosphotransferases (Alcohol Group Acceptor)/chemistry/*genetics/metabolism ; }, abstract = {The human microbiome encodes a large repertoire of biochemical enzymes and pathways, most of which remain uncharacterized. Here, using a metagenomics-based search strategy, we discovered that bacterial members of the human gut and oral microbiome encode enzymes that selectively phosphorylate a clinically used antidiabetic drug, acarbose[1,2], resulting in its inactivation. Acarbose is an inhibitor of both human and bacterial α-glucosidases[3], limiting the ability of the target organism to metabolize complex carbohydrates. Using biochemical assays, X-ray crystallography and metagenomic analyses, we show that microbiome-derived acarbose kinases are specific for acarbose, provide their harbouring organism with a protective advantage against the activity of acarbose, and are widespread in the microbiomes of western and non-western human populations. These results provide an example of widespread microbiome resistance to a non-antibiotic drug, and suggest that acarbose resistance has disseminated in the human microbiome as a defensive strategy against a potential endogenous producer of a closely related molecule.}, } @article {pmid34819600, year = {2021}, author = {Tozzi, AE and Del Chierico, F and Pandolfi, E and Reddel, S and Gesualdo, F and Gardini, S and Guarrasi, V and Russo, L and Croci, I and Campagna, I and Linardos, G and Concato, C and Villani, A and Putignani, L}, title = {Nasopharyngeal microbiota in hospitalized children with Bordetella pertussis and Rhinovirus infection.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {22858}, pmid = {34819600}, issn = {2045-2322}, mesh = {Bordetella Infections/diagnosis/*microbiology ; Bordetella pertussis/*isolation & purification ; *Coinfection ; Dysbiosis ; Female ; *Hospitalization ; Host-Pathogen Interactions ; Humans ; Infant ; Male ; Metagenome ; Metagenomics ; Microbiota ; Nasopharynx/*microbiology/*virology ; Picornaviridae Infections/diagnosis/*virology ; Rhinovirus/*isolation & purification ; Ribotyping ; }, abstract = {Despite great advances in describing Bordetella pertussis infection, the role of the host microbiota in pertussis pathogenesis remains unexplored. Indeed, the microbiota plays important role in defending against bacterial and viral respiratory infections. We investigated the nasopharyngeal microbiota in infants infected by B. pertussis (Bp), Rhinovirus (Rv) and simultaneously by both infectious agents (Bp + Rv). We demonstrated a specific nasopharyngeal microbiome profiles for Bp group, compared to Rv and Bp + Rv groups, and a reduction of microbial richness during coinfection compared to the single infections. The comparison amongst the three groups showed the increase of Alcaligenaceae and Achromobacter in Bp and Moraxellaceae and Moraxella in Rv group. Furthermore, correlation analysis between patients' features and nasopharyngeal microbiota profile highlighted a link between delivery and feeding modality, antibiotic administration and B. pertussis infection. A model classification demonstrated a microbiota fingerprinting specific of Bp and Rv infections. In conclusion, external factors since the first moments of life contribute to the alteration of nasopharyngeal microbiota, indeed increasing the susceptibility of the host to the pathogens' infections. When the infection is triggered, the presence of infectious agents modifies the microbiota favoring the overgrowth of commensal bacteria that turn in pathobionts, hence contributing to the disease severity.}, } @article {pmid34819495, year = {2021}, author = {Hafner, L and Pichon, M and Burucoa, C and Nusser, SHA and Moura, A and Garcia-Garcera, M and Lecuit, M}, title = {Listeria monocytogenes faecal carriage is common and depends on the gut microbiota.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6826}, pmid = {34819495}, issn = {2041-1723}, mesh = {Animals ; Carrier State/diagnosis/*epidemiology/microbiology ; DNA, Bacterial/isolation & purification ; Datasets as Topic ; Disease Models, Animal ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Listeria monocytogenes/genetics/*isolation & purification/pathogenicity ; Male ; Metagenomics/statistics & numerical data ; Mice ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Virulence ; }, abstract = {Listeria genus comprises two pathogenic species, L. monocytogenes (Lm) and L. ivanovii, and non-pathogenic species. All can thrive as saprophytes, whereas only pathogenic species cause systemic infections. Identifying Listeria species' respective biotopes is critical to understand the ecological contribution of Listeria virulence. In order to investigate the prevalence and abundance of Listeria species in various sources, we retrieved and analyzed 16S rRNA datasets from MG-RAST metagenomic database. 26% of datasets contain Listeria sensu stricto sequences, and Lm is the most prevalent species, most abundant in soil and host-associated environments, including 5% of human stools. Lm is also detected in 10% of human stool samples from an independent cohort of 900 healthy asymptomatic donors. A specific microbiota signature is associated with Lm faecal carriage, both in humans and experimentally inoculated mice, in which it precedes Lm faecal carriage. These results indicate that Lm faecal carriage is common and depends on the gut microbiota, and suggest that Lm faecal carriage is a crucial yet overlooked consequence of its virulence.}, } @article {pmid34818799, year = {2022}, author = {Hernández-Álvarez, C and García-Oliva, F and Cruz-Ortega, R and Romero, MF and Barajas, HR and Piñero, D and Alcaraz, LD}, title = {Squash root microbiome transplants and metagenomic inspection for in situ arid adaptations.}, journal = {The Science of the total environment}, volume = {805}, number = {}, pages = {150136}, doi = {10.1016/j.scitotenv.2021.150136}, pmid = {34818799}, issn = {1879-1026}, mesh = {*Cucurbita ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Plant Roots ; RNA, Ribosomal, 16S ; *Rhizobiaceae ; Rhizosphere ; Soil Microbiology ; Streptomyces ; }, abstract = {Arid zones contain a diverse set of microbes capable of survival under dry conditions, some of which can form relationships with plants under drought stress conditions to improve plant health. We studied squash (Cucurbita pepo L.) root microbiome under historically arid and humid sites, both in situ and performing a common garden experiment. Plants were grown in soils from sites with different drought levels, using in situ collected soils as the microbial source. We described and analyzed bacterial diversity by 16S rRNA gene sequencing (N = 48) from the soil, rhizosphere, and endosphere. Proteobacteria were the most abundant phylum present in humid and arid samples, while Actinobacteriota abundance was higher in arid ones. The β-diversity analyses showed split microbiomes between arid and humid microbiomes, and aridity and soil pH levels could explain it. These differences between humid and arid microbiomes were maintained in the common garden experiment, showing that it is possible to transplant in situ diversity to the greenhouse. We detected a total of 1009 bacterial genera; 199 exclusively associated with roots under arid conditions. By 16S and shotgun metagenomics, we identified dry-associated taxa such as Cellvibrio, Ensifer adhaerens, and Streptomyces flavovariabilis. With shotgun metagenomic sequencing of rhizospheres (N = 6), we identified 2969 protein families in the squash core metagenome and found an increased number of exclusively protein families from arid (924) than humid samples (158). We found arid conditions enriched genes involved in protein degradation and folding, oxidative stress, compatible solute synthesis, and ion pumps associated with osmotic regulation. Plant phenotyping allowed us to correlate bacterial communities with plant growth. Our study revealed that it is possible to evaluate microbiome diversity ex-situ and identify critical species and genes involved in plant-microbe interactions in historically arid locations.}, } @article {pmid34818790, year = {2022}, author = {Soto, DF and Franzetti, A and Gómez, I and Huovinen, P}, title = {Functional filtering and random processes affect the assembly of microbial communities of snow algae blooms at Maritime Antarctic.}, journal = {The Science of the total environment}, volume = {805}, number = {}, pages = {150305}, doi = {10.1016/j.scitotenv.2021.150305}, pmid = {34818790}, issn = {1879-1026}, mesh = {Antarctic Regions ; Bacteria/genetics ; Eutrophication ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The increasing temperatures at the West Antarctic Peninsula (Maritime Antarctic) could lead to a higher occurrence of snow algal blooms which are ubiquitous events that change the snow coloration, reducing albedo and in turn exacerbating melting. However, there is a limited understanding of snow algae blooms biodiversity, composition, and their functional profiles, especially in one of the world's areas most affected by climate change. In this study we used 16S rRNA and 18S rRNA metabarcoding, and shotgun metagenomics to assess the diversity, composition, and functional potential of the snow algae blooms bacterial and eukaryotic communities at three different sites of Maritime Antarctic, between different colors of the algae blooms and between seasonal and semi-permanent snowfields. We tested the hypothesis that the functional potential of snow algae blooms is conserved despite a changing taxonomic composition. Furthermore, we determined taxonomic co-occurrence patterns of bacteria and eukaryotes and assessed the potential for the exchange of metabolites among bacterial taxa. Here, we tested the prediction that there are co-occurring taxa within snow algae whose biotic interactions are marked by the exchange of metabolites. Our results show that the composition of snow algae blooms vary significantly among sites. For instance, a higher abundance of fungi and protists were detected in Fildes Peninsula compared with Doumer Island and O'Higgins. Likewise, the composition varied between snow colors and snow types. However, the functional potential varied only among sampling sites with a higher abundance of genes involved in tolerance to environmental stress at O'Higgins. Co-occurrence patterns of dominant bacterial genera such as Pedobacter, Polaromonas, Flavobacterium and Hymenobacter were recorded, contrasting the absence of co-occurring patterns displayed by Chlamydomonadales algae with other eukaryotes. Finally, genome-scale metabolic models revealed that bacteria within snow algae blooms likely compete for resources instead of forming cooperative communities.}, } @article {pmid34818768, year = {2022}, author = {He, J and Zhang, N and Muhammad, A and Shen, X and Sun, C and Li, Q and Hu, Y and Shao, Y}, title = {From surviving to thriving, the assembly processes of microbial communities in stone biodeterioration: A case study of the West Lake UNESCO World Heritage area in China.}, journal = {The Science of the total environment}, volume = {805}, number = {}, pages = {150395}, doi = {10.1016/j.scitotenv.2021.150395}, pmid = {34818768}, issn = {1879-1026}, mesh = {Archaea ; Biodiversity ; China ; *Lakes ; *Microbiota ; UNESCO ; }, abstract = {Serious concerns regarding stone biodeterioration have been raised due to the loss of aesthetic value and hidden dangers in stone cultural heritages and buildings. Stone biodeterioration involves a complex ecological interplay among organisms, however, the ecological mechanisms (deterministic or stochastic processes) that determine the microbial community on stone remain poorly understood. Here, using both amplicon and shotgun metagenomic sequencing approaches, we comprehensively investigated the biodiversity, assembly, and function of communities (including prokaryotes, fungi, microfauna, and plants) on various types of deteriorating limestone across different habitats in Feilaifeng. By generalizing classic ecological models to stone habitats, we further uncovered and quantified the mechanisms underlying microbial community assembly processes and microbial interactions within the biodeteriorated limestone. Community profiling revealed stable ecosystem functional potential despite high taxonomic variation across different biodeterioration types, suggesting non-random community assembly. Increased niche differentiation occurred in prokaryotes and fungi but not in microfauna and plant during biodeterioration. Certain microbial groups such as nitrifying archaea and bacteria showed wider niche breadth and likely contributing to the initiation, succession and expansion of stone biodeterioration. Consistently, prokaryotes were more strongly structured by selection-based deterministic processes, while micro-eukaryotes were more influenced by dispersal and drift-based stochastic processes. Importantly, microbial coexistence maintains network robustness within stone microbiotas, highlighting mutual cooperation among functional microorganisms. These results provide new insights into microbial community assembly mechanisms in stone ecosystems and may aid in the sustainable conservation of stone materials of interest.}, } @article {pmid34818103, year = {2022}, author = {Huang, T and Lu, ZM and Peng, MY and Chai, LJ and Zhang, XJ and Shi, JS and Li, Q and Xu, ZH}, title = {Constructing a Defined Starter for Multispecies Vinegar Fermentation via Evaluation of the Vitality and Dominance of Functional Microbes in an Autochthonous Starter.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {3}, pages = {e0217521}, pmid = {34818103}, issn = {1098-5336}, mesh = {*Acetic Acid/metabolism ; Fermentation ; Food Microbiology ; Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {Mature vinegar culture has usually been used as a type of autochthonous starter to rapidly initiate the next batch of acetic acid fermentation (AAF) and maintain the batch-to-batch uniformity of AAF in the production of traditional cereal vinegar. However, the vitality and dominance of functional microbes in autochthonous starters remain unclear, which hinders further improvement of fermentation yield and production. Here, based on metagenomic (MG), metatranscriptomic (MT), and 16S rRNA gene sequencings, 11 bacterial operational taxonomic units (OTUs) with significant metabolic activity (MT/MG ratio >1) and dominance (relative abundance >1%) were targeted in the autochthonous vinegar starter, all of which were assigned to 4 species (Acetobacter pasteurianus, Lactobacillus acetotolerans, L. helveticus, Acetilactobacillus jinshanensis). Then, we evaluated the successions and interactions of these 11 bacterial OTUs at different AAF stages. Last, a defined starter was constructed with 4 core species isolated from the autochthonous starter (A. pasteurianus, L. acetotolerans, L. helveticus, Ac. jinshanensis). The defined starter culture could rapidly initiate the AAF in a sterile or unsterilized environment, and similar dynamics of metabolites (ethanol, titratable acidity, acetic acid, lactic acid, and volatile compounds) and environmental indexes (temperature, pH) of fermentation were observed as compared with that of autochthonous starter (P > 0.05). This work provides a method to construct a defined microbiota from a complex system while preserving its metabolic function. IMPORTANCE Complex microorganisms are beneficial to the flavor formation in natural food fermentation, but they also pose challenges to the mass production of standardized products. It is attractive to construct a defined starter to rapidly initiate fermentation process and significantly improve fermentation yield. This study provides a comprehensive understanding of vital and dominant species in the autochthonous vinegar starter via multi-omics, and designs a defined microbial community for the efficient fermentation of cereal vinegar.}, } @article {pmid34817640, year = {2022}, author = {Wu-Chuang, A and Obregon, D and Estrada-Peña, A and Cabezas-Cruz, A}, title = {Thermostable Keystone Bacteria Maintain the Functional Diversity of the Ixodes scapularis Microbiome Under Heat Stress.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1224-1235}, pmid = {34817640}, issn = {1432-184X}, mesh = {Male ; Animals ; *Ixodes/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Heat-Shock Response ; }, abstract = {Variations in the composition and diversity of tick microbiome due to high temperatures may influence the hierarchy of community members as a response to environmental change. Modifications in the community structure are hypothesized to drive alterations in the presence and/or abundance of functional pathways in the bacterial metagenome. In this study, this hypothesis was tested by using published 16S rRNA datasets of Ixodes scapularis males incubated at different temperatures (i.e., 4, 20, 30, and 37 °C) in a laboratory setting. Changes in community structure and functional profiles in response to temperature shifts were measured using co-occurrence networks and metagenome inference. Results from laboratory-reared ticks were then compared with those of field-collected ticks. The results from laboratory-reared ticks showed that high temperature altered the structure of the microbial community and decreased the number of keystone taxa. Notably, four taxa were identified as keystone in all the temperatures, and the functional diversity of the tick microbiome was contained in the four thermostable keystone their associated bacterial taxa. Three of the thermostable keystone taxa were also found in free-living ticks collected in Massachusetts. Moreover, the comparison of functional profiles of laboratory-reared and field-collected ticks revealed the existence of an important set of metabolic pathways that were common among the different datasets. Similar to the laboratory-reared ticks, the keystone taxa identified in field-collected ticks alongside their consortia (co-occurring taxa) were sufficient to retain the majority of the metabolic pathways in the functional profile. These results suggest that keystone taxa are essential in the stability and the functional resiliency of the tick microbiome under heat stress.}, } @article {pmid34817234, year = {2021}, author = {Garber, AI and Zehnpfennig, JR and Sheik, CS and Henson, MW and Ramírez, GA and Mahon, AR and Halanych, KM and Learman, DR}, title = {Metagenomics of Antarctic Marine Sediment Reveals Potential for Diverse Chemolithoautotrophy.}, journal = {mSphere}, volume = {6}, number = {6}, pages = {e0077021}, pmid = {34817234}, issn = {2379-5042}, mesh = {Antarctic Regions ; Carbon/metabolism ; Carbon Cycle ; Chemoautotrophic Growth/*physiology ; Climate Change ; Geologic Sediments/*microbiology ; Metagenome/physiology ; *Metagenomics ; Microbiota/*physiology ; Nitrogen/metabolism ; Phylogeny ; Sulfur/metabolism ; }, abstract = {The microbial biogeochemical processes occurring in marine sediment in Antarctica remain underexplored due to limited access. Further, these polar habitats are unique, as they are being exposed to significant changes in their climate. To explore how microbes drive biogeochemistry in these sediments, we performed a shotgun metagenomic survey of marine surficial sediment (0 to 3 cm of the seafloor) collected from 13 locations in western Antarctica and assembled 16 high-quality metagenome assembled genomes for focused interrogation of the lifestyles of some abundant lineages. We observe an abundance of genes from pathways for the utilization of reduced carbon, sulfur, and nitrogen sources. Although organotrophy is pervasive, nitrification and sulfide oxidation are the dominant lithotrophic pathways and likely fuel carbon fixation via the reverse tricarboxylic acid and Calvin cycles. Oxygen-dependent terminal oxidases are common, and genes for reduction of oxidized nitrogen are sporadically present in our samples. Our results suggest that the underlying benthic communities are well primed for the utilization of settling organic matter, which is consistent with findings from highly productive surface water. Despite the genetic potential for nitrate reduction, the net catabolic pathway in our samples remains aerobic respiration, likely coupled to the oxidation of sulfur and nitrogen imported from the highly productive Antarctic water column above. IMPORTANCE The impacts of climate change in polar regions, like Antarctica, have the potential to alter numerous ecosystems and biogeochemical cycles. Increasing temperature and freshwater runoff from melting ice can have profound impacts on the cycling of organic and inorganic nutrients between the pelagic and benthic ecosystems. Within the benthos, sediment microbial communities play a critical role in carbon mineralization and the cycles of essential nutrients like nitrogen and sulfur. Metagenomic data collected from sediment samples from the continental shelf of western Antarctica help to examine this unique system and document the metagenomic potential for lithotrophic metabolisms and the cycles of both nitrogen and sulfur, which support not only benthic microbes but also life in the pelagic zone.}, } @article {pmid34816752, year = {2022}, author = {Ali, MJ}, title = {Functional metagenomic profile of the lacrimal sac microbial communities in primary acquired nasolacrimal duct obstruction: The Lacriome paper 2.}, journal = {European journal of ophthalmology}, volume = {32}, number = {4}, pages = {2059-2066}, doi = {10.1177/11206721211064015}, pmid = {34816752}, issn = {1724-6016}, mesh = {*Dacryocystorhinostomy ; Humans ; *Lacrimal Duct Obstruction/genetics ; Metagenome ; *Microbiota/genetics ; *Nasolacrimal Duct/surgery ; Prospective Studies ; }, abstract = {PURPOSE: To study the functional metagenomic profile of the microbes isolated from the lacrimal sac of patients with primary acquired nasolacrimal duct obstruction.

METHODS: A prospective study was performed on 10 consecutive lacrimal sac samples obtained for the metagenomic analysis from patients with primary acquired nasolacrimal duct obstruction (who underwent endoscopic dacryocystorhinostomy at a tertiary care Dacryology service. The samples were collected intraoperatively soon after a full-length lacrimal sac marsupialization and immediately transported on ice to the laboratory. Following DNA extraction and library preparation, a whole shotgun metagenome sequencing was performed on the Illumina NOVASEQ 6000[TM] platform. The downstream processing and bioinformatics of the samples were performed using multiple software packaged in SqueezeMeta[TM] pipeline and functional analysis using the MG-RAST[TM] pipeline.

RESULTS: The microbial gene mapping and protein prediction demonstrated proteins with known functions to range from 66.41% to 84.03% across the samples. The functional category distribution of Kyoto Encyclopedia of Genes and Genomes ortholog (level 1 data) showed metabolism to be the most commonly involved function followed by environmental information processes, genetic information processes and cellular processes. The functional subsystem profiling demonstrated genes associated with carbohydrate, protein and RNA metabolism, Amino acids and their derivatives, cofactors and prosthetic groups and factors involved in cell structure regulation and cell cycle control.

CONCLUSION: This is the first functional metagenomic profile of the lacrimal sac microbiota from patients with primary acquired nasolacrimal duct obstruction. Functional analysis has provided newer insights into the ecosystem dynamics and strategies of microbial communities inhabiting the lacrimal sac. Further Lacriome studies may provide clues for better understanding of the disease etiopathogenesis.}, } @article {pmid34814938, year = {2021}, author = {Neves, ALA and Yu, J and Suzuki, Y and Baez-Magana, M and Arutyunova, E and O'Hara, E and McAllister, T and Ominski, KH and Lemieux, MJ and Guan, LL}, title = {Accelerated discovery of novel glycoside hydrolases using targeted functional profiling and selective pressure on the rumen microbiome.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {229}, pmid = {34814938}, issn = {2049-2618}, mesh = {Animals ; Cattle ; Glycoside Hydrolases/genetics/metabolism ; Metagenome ; Metagenomics ; *Microbiota ; *Rumen/microbiology ; }, abstract = {BACKGROUND: Carbohydrate-active enzymes (CAZymes) form the most widespread and structurally diverse set of enzymes involved in the breakdown, biosynthesis, or modification of lignocellulose that can be found in living organisms. However, the structural diversity of CAZymes has rendered the targeted discovery of novel enzymes extremely challenging, as these proteins catalyze many different chemical reactions and are sourced by a vast array of microbes. Consequently, many uncharacterized members of CAZyme families of interest have been overlooked by current methodologies (e.g., metagenomic screening) used to discover lignocellulolytic enzymes.

RESULTS: In the present study, we combined phenotype-based selective pressure on the rumen microbiota with targeted functional profiling to guide the discovery of unknown CAZymes. In this study, we found 61 families of glycoside hydrolases (GH) (out of 182 CAZymes) from protein sequences deposited in the CAZy database-currently associated with more than 20,324 microbial genomes. Phenotype-based selective pressure on the rumen microbiome showed that lignocellulolytic bacteria (e.g., Fibrobacter succinogenes, Butyrivibrio proteoclasticus) and three GH families (e.g., GH11, GH13, GH45) exhibited an increased relative abundance in the rumen of feed efficient cattle when compared to their inefficient counterparts. These results paved the way for the application of targeted functional profiling to screen members of the GH11 and GH45 families against a de novo protein reference database comprised of 1184 uncharacterized enzymes, which led to the identification of 18 putative xylanases (GH11) and three putative endoglucanases (GH45). The biochemical proof of the xylanolytic activity of the newly discovered enzyme validated the computational simulations and demonstrated the stability of the most abundant xylanase.

CONCLUSIONS: These findings contribute to the discovery of novel enzymes for the breakdown, biosynthesis, or modification of lignocellulose and demonstrate that the rumen microbiome is a source of promising enzyme candidates for the biotechnology industry. The combined approaches conceptualized in this study can be adapted to any microbial environment, provided that the targeted microbiome is easy to manipulate and facilitates enrichment for the microbes of interest. Video Abstract.}, } @article {pmid34812271, year = {2021}, author = {Wang, Y and Sun, M and Duan, Y}, title = {Metagenomic Sequencing Analysis for Acne Using Machine Learning Methods Adapted to Single or Multiple Data.}, journal = {Computational and mathematical methods in medicine}, volume = {2021}, number = {}, pages = {8008731}, pmid = {34812271}, issn = {1748-6718}, mesh = {Acne Vulgaris/*genetics/metabolism/*microbiology ; Canonical Correlation Analysis ; Case-Control Studies ; Computational Biology ; Face/microbiology ; Humans ; Lipids/analysis/genetics ; *Machine Learning ; *Metagenome ; Metagenomics/statistics & numerical data ; Microbiota/genetics ; Principal Component Analysis ; Skin/chemistry/microbiology ; }, abstract = {The human health status can be assessed by the means of research and analysis of the human microbiome. Acne is a common skin disease whose morbidity increases year by year. The lipids which influence acne to a large extent are studied by metagenomic methods in recent years. In this paper, machine learning methods are used to analyze metagenomic sequencing data of acne, i.e., all kinds of lipids in the face skin. Firstly, lipids data of the diseased skin (DS) samples and the healthy skin (HS) samples of acne patients and the normal control (NC) samples of healthy person are, respectively, analyzed by using principal component analysis (PCA) and kernel principal component analysis (KPCA). Then, the lipids which have main influence on each kind of sample are obtained. In addition, a multiset canonical correlation analysis (MCCA) is utilized to get lipids which can differentiate the face skins of the above three samples. The experimental results show the machine learning methods can effectively analyze metagenomic sequencing data of acne. According to the results, lipids which only influence one of the three samples or the lipids which simultaneously have different degree of influence on these three samples can be used as indicators to judge skin statuses.}, } @article {pmid34810234, year = {2022}, author = {Vervier, K and Moss, S and Kumar, N and Adoum, A and Barne, M and Browne, H and Kaser, A and Kiely, CJ and Neville, BA and Powell, N and Raine, T and Stares, MD and Zhu, A and De La Revilla Negro, J and Lawley, TD and Parkes, M}, title = {Two microbiota subtypes identified in irritable bowel syndrome with distinct responses to the low FODMAP diet.}, journal = {Gut}, volume = {71}, number = {9}, pages = {1821-1830}, pmid = {34810234}, issn = {1468-3288}, support = {/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Diet ; Diet, Carbohydrate-Restricted ; Disaccharides/metabolism ; Fermentation ; *Gastrointestinal Microbiome ; Humans ; *Irritable Bowel Syndrome ; Monosaccharides ; Oligosaccharides ; }, abstract = {OBJECTIVE: Reducing FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides and polyols) can be clinically beneficial in IBS but the mechanism is incompletely understood. We aimed to detect microbial signatures that might predict response to the low FODMAP diet and assess whether microbiota compositional and functional shifts could provide insights into its mode of action.

DESIGN: We used metagenomics to determine high-resolution taxonomic and functional profiles of the stool microbiota from IBS cases and household controls (n=56 pairs) on their usual diet. Clinical response and microbiota changes were studied in 41 pairs after 4 weeks on a low FODMAP diet.

RESULTS: Unsupervised analysis of baseline IBS cases pre-diet identified two distinct microbiota profiles, which we refer to as IBS[P] (pathogenic-like) and IBS[H] (health-like) subtypes. IBS[P] microbiomes were enriched in Firmicutes and genes for amino acid and carbohydrate metabolism, but depleted in Bacteroidetes species. IBS[H] microbiomes were similar to controls. On the low FODMAP diet, IBS[H] and control microbiota were unaffected, but the IBS[P] signature shifted towards a health-associated microbiome with an increase in Bacteroidetes (p=0.009), a decrease in Firmicutes species (p=0.004) and normalisation of primary metabolic genes. The clinical response to the low FODMAP diet was greater in IBS[P] subjects compared with IBS[H] (p=0.02).

CONCLUSION: 50% of IBS cases manifested a 'pathogenic' gut microbial signature. This shifted towards the healthy profile on the low FODMAP diet; and IBS[P] cases showed an enhanced clinical responsiveness to the dietary therapy. The effectiveness of FODMAP reduction in IBS[P] may result from the alterations in gut microbiota and metabolites produced. Microbiota signatures could be useful as biomarkers to guide IBS treatment; and investigating IBS[P] species and metabolic pathways might yield insights regarding IBS pathogenic mechanisms.}, } @article {pmid34807727, year = {2022}, author = {Wang, Y and Wu, M and Wang, Y and Wang, X and Yu, M and Liu, G and Tang, H}, title = {Diversity and function of microbial communities in the sand sheath of Agropyron cristatum by metagenomic analysis.}, journal = {Canadian journal of microbiology}, volume = {68}, number = {3}, pages = {177-189}, doi = {10.1139/cjm-2021-0129}, pmid = {34807727}, issn = {1480-3275}, mesh = {*Agropyron/genetics ; Metagenomics ; *Microbiota/genetics ; Sand ; Soil ; Soil Microbiology ; }, abstract = {The roots of most gramineous plants are surrounded by a variety of microorganisms; however, few studies have focused on the rhizosheath of psammophytes. Therefore, in this study, we used Illumina HiSeq high-throughput sequencing technology to analyse the composition and functional diversity of microbial communities in the rhizosheath of sand-grown Agropyron cristatum (L.) Gaertn. We found that the number of species and functions of microbial communities gradually decreased from the rhizosheath to the bulk soil. Thus, the microbial composition of the rhizosheath was richer and more diverse, and the abundance of bacteria, including Sphingosinicella, Rhizorhabdus, Friedmanniella, Geodermatophilus, Blastococcus, and Oscillatoria, was higher, and the abundance of fungi, such as Mycothermus, was higher. The abundance of CO2 fixation-related genes (acsA, Pcc, and cbbL) in the carbon cycle; NO3[-], NO2[-], NH2OH, and N2 transformation genes (nrtP, nirS, hao, and nifK) in the nitrogen cycle; soxB/A/C, Sat, and dsrB genes in the sulphur cycle; and 1-phosphate mannitol dehydrogenase (MtlD) gene and polyketide synthase gene (pks) were higher in the rhizosheath than in the bulk soil, as well as genes related to phosphorus uptake in the phosphorus cycle. Our findings showed that the rhizosheath may host the predominant microbial species related to the formation of a rhizosheath.}, } @article {pmid34802820, year = {2022}, author = {Zhang, P and Lu, G and Sun, Y and Yan, Z and Dang, T and Liu, J}, title = {Metagenomic analysis explores the interaction of aged microplastics and roxithromycin on gut microbiota and antibiotic resistance genes of Carassius auratus.}, journal = {Journal of hazardous materials}, volume = {425}, number = {}, pages = {127773}, doi = {10.1016/j.jhazmat.2021.127773}, pmid = {34802820}, issn = {1873-3336}, mesh = {Animals ; Anti-Bacterial Agents/toxicity ; Drug Resistance, Microbial/genetics ; *Gastrointestinal Microbiome ; Goldfish/genetics ; Microplastics ; Plastics ; *Roxithromycin ; *Water Pollutants, Chemical/analysis/toxicity ; }, abstract = {The aging process changes the physicochemical structure of microplastics and affects environmental behaviors and toxicological effects of coexisting pollutants, thereby posing ecological risks. In this study, the effects of aged polystyrene microplastics alone or in combination with the 100 μg/L roxithromycin (ROX) on intestines of Carassius auratus were investigated. The carrier effect of microplastics was enhanced by aging due to changes in functional groups and surface area, which led to an increase in the bioaccumulation of ROX. The combined exposure of aged microplastics (APS) and ROX caused more inflammatory cell infiltration and cilia defects, and significantly inhibited the activity of amylase and lipase. Metagenomic sequencing revealed that the combined exposure of microplastics and ROX increased the abundance of Gemmobacter, Bosea, Rhizobium, and Shinella and decreased the abundance of Cetobacterium and Akkermansia (p < 0.05). The presence of APS enhanced the selective enrichment of antibiotic resistance genes. What's more, the influence of microplastics and antibiotics on gut microbiota was closely related to carbohydrate metabolism and amino acid metabolism activities, as well as the abundance of baca and sul1 resistance genes. These results expand our understanding of the interaction mechanism between APS and antibiotics in real aquatic environment.}, } @article {pmid34799562, year = {2021}, author = {Yang, Y and Du, L and Shi, D and Kong, C and Liu, J and Liu, G and Li, X and Ma, Y}, title = {Dysbiosis of human gut microbiome in young-onset colorectal cancer.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6757}, pmid = {34799562}, issn = {2041-1723}, mesh = {Adult ; Age of Onset ; Aged ; Case-Control Studies ; Clostridiales/isolation & purification ; Colorectal Neoplasms/diagnosis/*microbiology ; Dysbiosis/*complications/diagnosis/microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Male ; Middle Aged ; Streptococcus/isolation & purification ; }, abstract = {The incidence of sporadic young-onset colorectal cancer (yCRC) is increasing. A significant knowledge gap exists in the gut microbiota and its diagnostic value for yCRC patients. Through 16S rRNA gene sequencing, 728 samples are collected to identify microbial markers, and an independent cohort of 310 samples is used to validate the results. Furthermore, species-level and functional analysis are performed by metagenome sequencing using 200 samples. Gut microbial diversity is increased in yCRC. Flavonifractor plautii is an important bacterial species in yCRC, while genus Streptococcus contains the key phylotype in the old-onset colorectal cancer. Functional analysis reveals that yCRC has unique characteristics of bacterial metabolism characterized by the dominance of DNA binding and RNA-dependent DNA biosynthetic process. The random forest classifier model achieves a powerful classification potential. This study highlights the potential of the gut microbiota biomarkers as a promising non-invasive tool for the accurate detection and distinction of individuals with yCRC.}, } @article {pmid34798540, year = {2022}, author = {Sazykina, MA and Minkina, TM and Konstantinova, EY and Khmelevtsova, LE and Azhogina, TN and Antonenko, EM and Karchava, SK and Klimova, MV and Sushkova, SN and Polienko, EA and Birukova, OA and Mandzhieva, SS and Kudeevskaya, EM and Khammami, MI and Rakin, AV and Sazykin, IS}, title = {Pollution impact on microbial communities composition in natural and anthropogenically modified soils of Southern Russia.}, journal = {Microbiological research}, volume = {254}, number = {}, pages = {126913}, doi = {10.1016/j.micres.2021.126913}, pmid = {34798540}, issn = {1618-0623}, mesh = {Anthropogenic Effects ; Bacteria/*drug effects ; *Biodiversity ; *Environmental Pollutants/pharmacology ; *Microbiota/drug effects ; Polycyclic Aromatic Hydrocarbons/pharmacology ; *Soil Microbiology ; }, abstract = {Metagenomic studies of soil microbocenoses are extremely relevant nowadays. The study of pollution impact on soil microbiomes is of particular interest. The structure of microbial communities in soils with different levels of pollution by polycyclic aromatic hydrocarbons (PAHs) and potentially toxic elements (PTEs) was studied. High bacterial biodiversity was found in all the studied soil samples, but its lowest values are found in soil samples taken on the territory of technogenically polluted Lake Atamanskoye. Assessment of soil pollution showed the highest content of polycyclic aromatic hydrocarbons (PAHs) and potentially toxic elements (PTEs) for the soils Lake Atamanskoye. The high content of pollutants negatively affects the abundance of representatives of the phyla Actinobacteria, Planctomycetes, Verrucomicrobia, and Nitrospirae. Such phyla as Proteobacteria, Candidate Divisions TM7, OD1, WPS-2, Chlamydiae, Cyanobacteria are characterized by positive direct correlation with the content of pollutants, especially with PAHs. A cooperative effect of decrease in the number of Actinobacteria and Proteobacteria with an increase in Armatimonadetes probably corresponds to PTEs contamination. The proportion of Candidate Division OD1, Chlamydiae, Cyanobacteria, and Candidate Division WPS-2 was increased in the soil microbiome under the influence of severe combined pollution. Pollutants negatively affect the abundance of dominant unclassified_o__Gaiellales and unclassified_o__WD2101 genera. Iamia, Salinibacterium, Arthrobacter, Kaistobacter, Thiobacillus genera are characterized by a low abundance, but they are presumably the most resistant to soil pollution. It was revealed that the level of soil pollution largely determines the composition and diversity of bacterial communities in the soils of the studied territories. Operating taxonomic units have been established that have prognostic value for assessing the state, level of soil pollution, and their biological safety.}, } @article {pmid34795385, year = {2021}, author = {Feng, Y and Wang, Y and Zhu, B and Gao, GF and Guo, Y and Hu, Y}, title = {Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {1305}, pmid = {34795385}, issn = {2399-3642}, mesh = {Animals ; Archaea/genetics ; Bacteria/*genetics ; Bacterial Proteins/analysis ; Chickens/*microbiology ; *Drug Resistance, Bacterial ; Drug Resistance, Microbial ; Gastrointestinal Microbiome/*genetics ; *Genome, Bacterial ; Glycoside Hydrolases/analysis ; Lactobacillus/isolation & purification ; *Metagenome ; }, abstract = {Gut microbial reference genomes and gene catalogs are necessary for understanding the chicken gut microbiome. Here, we assembled 12,339 microbial genomes and constructed a gene catalog consisting of ~16.6 million genes by integrating 799 public chicken gut microbiome samples from ten countries. We found that 893 and 38 metagenome-assembled genomes (MAGs) in our dataset were putative novel species and genera, respectively. In the chicken gut, Lactobacillus aviarius and Lactobacillus crispatus were the most common lactic acid bacteria, and glycoside hydrolases were the most abundant carbohydrate-active enzymes (CAZymes). Antibiotic resistome profiling results indicated that Chinese chicken samples harbored a higher relative abundance but less diversity of antimicrobial resistance genes (ARGs) than European samples. We also proposed the effects of geography and host species on the gut resistome. Our study provides the largest integrated metagenomic dataset from the chicken gut to date and demonstrates its value in exploring chicken gut microbial genes.}, } @article {pmid34795375, year = {2021}, author = {Van Goethem, MW and Osborn, AR and Bowen, BP and Andeer, PF and Swenson, TL and Clum, A and Riley, R and He, G and Koriabine, M and Sandor, L and Yan, M and Daum, CG and Yoshinaga, Y and Makhalanyane, TP and Garcia-Pichel, F and Visel, A and Pennacchio, LA and O'Malley, RC and Northen, TR}, title = {Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {1302}, pmid = {34795375}, issn = {2399-3642}, support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; }, mesh = {Bacteria/genetics/*metabolism ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Multigene Family ; *Secondary Metabolism ; *Soil Microbiology ; Utah ; }, abstract = {Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 712 full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night primarily in cyanobacteria, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.}, } @article {pmid34795298, year = {2021}, author = {Armstrong, AJS and Parmar, V and Blaser, MJ}, title = {Assessing saliva microbiome collection and processing methods.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {81}, pmid = {34795298}, issn = {2055-5008}, support = {R01 AI158911/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Bacteria/genetics ; COVID-19/genetics ; DNA/genetics ; DNA, Bacterial/genetics ; Female ; Humans ; Male ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/*genetics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; SARS-CoV-2/pathogenicity ; Saliva/*microbiology ; Sequence Analysis, DNA/methods ; }, abstract = {The oral microbiome has been connected with lung health and may be of significance in the progression of SARS-CoV-2 infection. Saliva-based SARS-CoV-2 tests provide the opportunity to leverage stored samples for assessing the oral microbiome. However, these collection kits have not been tested for their accuracy in measuring the oral microbiome. Saliva is highly enriched with human DNA and reducing it prior to shotgun sequencing may increase the depth of bacterial reads. We examined both the effect of saliva collection method and sequence processing on measurement of microbiome depth and diversity by 16S rRNA gene amplicon and shotgun metagenomics. We collected 56 samples from 22 subjects. Each subject provided saliva samples with and without preservative, and a subset provided a second set of samples the following day. 16S rRNA gene (V4) sequencing was performed on all samples, and shotgun metagenomics was performed on a subset of samples collected with preservative with and without human DNA depletion before sequencing. We observed that the beta diversity distances within subjects over time was smaller than between unrelated subjects, and distances within subjects were smaller in samples collected with preservative. Samples collected with preservative had higher alpha diversity measuring both richness and evenness. Human DNA depletion before extraction and shotgun sequencing yielded higher total and relative reads mapping to bacterial sequences. We conclude that collecting saliva with preservative may provide more consistent measures of the oral microbiome and depleting human DNA increases yield of bacterial sequences.}, } @article {pmid34795236, year = {2021}, author = {Darnaud, M and De Vadder, F and Bogeat, P and Boucinha, L and Bulteau, AL and Bunescu, A and Couturier, C and Delgado, A and Dugua, H and Elie, C and Mathieu, A and Novotná, T and Ouattara, DA and Planel, S and Saliou, A and Šrůtková, D and Yansouni, J and Stecher, B and Schwarzer, M and Leulier, F and Tamellini, A}, title = {A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6686}, pmid = {34795236}, issn = {2041-1723}, support = {U2C DK119886/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics ; Body Weight/genetics/physiology ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; *Germ-Free Life ; Male ; Metagenomics/methods ; Mice, Inbred C57BL ; Phenotype ; Species Specificity ; *Specific Pathogen-Free Organisms ; Whole Genome Sequencing/*methods ; Mice ; }, abstract = {Mus musculus is the classic mammalian model for biomedical research. Despite global efforts to standardize breeding and experimental procedures, the undefined composition and interindividual diversity of the microbiota of laboratory mice remains a limitation. In an attempt to standardize the gut microbiome in preclinical mouse studies, here we report the development of a simplified mouse microbiota composed of 15 strains from 7 of the 20 most prevalent bacterial families representative of the fecal microbiota of C57BL/6J Specific (and Opportunistic) Pathogen-Free (SPF/SOPF) animals and the derivation of a standardized gnotobiotic mouse model called GM15. GM15 recapitulates extensively the functionalities found in the C57BL/6J SOPF microbiota metagenome, and GM15 animals are phenotypically similar to SOPF or SPF animals in two different facilities. They are also less sensitive to the deleterious effects of post-weaning malnutrition. In this work, we show that the GM15 model provides increased reproducibility and robustness of preclinical studies by limiting the confounding effect of fluctuation in microbiota composition, and offers opportunities for research focused on how the microbiota shapes host physiology in health and disease.}, } @article {pmid34793492, year = {2021}, author = {Marfil-Sánchez, A and Seelbinder, B and Ni, Y and Varga, J and Berta, J and Hollosi, V and Dome, B and Megyesfalvi, Z and Dulka, E and Galffy, G and Weiss, GJ and Panagiotou, G and Lohinai, Z}, title = {Gut microbiome functionality might be associated with exercise tolerance and recurrence of resected early-stage lung cancer patients.}, journal = {PloS one}, volume = {16}, number = {11}, pages = {e0259898}, pmid = {34793492}, issn = {1932-6203}, mesh = {Bacteria/classification ; Bacterial Physiological Phenomena ; Exercise Test ; *Exercise Tolerance ; Fungi/classification/physiology ; *Gastrointestinal Microbiome ; Humans ; Lung Neoplasms/*microbiology/*physiopathology/surgery ; Neoplasm Recurrence, Local ; Respiratory Function Tests ; }, abstract = {Impaired exercise tolerance and lung function is a marker for increased mortality in lung cancer patients undergoing lung resection surgery. Recent data suggest that the gut-lung axis regulates systemic metabolic and immune functions, and microbiota might alter exercise tolerance. Here, we aimed to evaluate the associations between gut microbiota and outcomes in lung cancer patients who underwent lung resection surgery. We analysed stool samples, from 15 early-stage lung cancer patients, collected before and after surgical resection using shotgun metagenomic and Internal Transcribed Spacer (ITS) sequencing. We analysed microbiome and mycobiome associations with post-surgery lung function and cardiopulmonary exercise testing (CPET) to assess the maximum level of work achieved. There was a significant difference, between pre- and post-surgical resection samples, in microbial community functional profiles and several species from Alistipes and Bacteroides genus, associated with the production of SCFAs, increased significantly in abundance. Interestingly, an increase in VO2 coincides with an increase in certain species and the "GABA shunt" pathway, suggesting that treatment outcome might improve by enriching butyrate-producing species. Here, we revealed associations between specific gut bacteria, fungi, and their metabolic pathways with the recovery of lung function and exercise capacity.}, } @article {pmid34793277, year = {2021}, author = {Marfil-Sánchez, A and Zhang, L and Alonso-Pernas, P and Mirhakkak, M and Mueller, M and Seelbinder, B and Ni, Y and Santhanam, R and Busch, A and Beemelmanns, C and Ermolaeva, M and Bauer, M and Panagiotou, G}, title = {An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1993598}, pmid = {34793277}, issn = {1949-0984}, mesh = {Animals ; Anti-Bacterial Agents/*adverse effects ; Bacteria/classification/drug effects/metabolism/pathogenicity ; Bile Acids and Salts/metabolism ; Candida/classification/drug effects/metabolism/pathogenicity ; *Critical Illness ; Drug Resistance, Fungal/drug effects ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infections/microbiology ; Intensive Care Units ; Metabolome/*drug effects ; Moths ; }, abstract = {Antibiotics are commonly used in the Intensive Care Unit (ICU); however, several studies showed that the impact of antibiotics to prevent infection, multi-organ failure, and death in the ICU is less clear than their benefit on course of infection in the absence of organ dysfunction. We characterized here the compositional and metabolic changes of the gut microbiome induced by critical illness and antibiotics in a cohort of 75 individuals in conjunction with 2,180 gut microbiome samples representing 16 different diseases. We revealed an "infection-vulnerable" gut microbiome environment present only in critically ill treated with antibiotics (ICU[+]). Feeding of Caenorhabditis elegans with Bifidobacterium animalis and Lactobacillus crispatus, species that expanded in ICU[+] patients, revealed a significant negative impact of these microbes on host viability and developmental homeostasis. These results suggest that antibiotic administration can dramatically impact essential functional activities in the gut related to immune responses more than critical illness itself, which might explain in part untoward effects of antibiotics in the critically ill.}, } @article {pmid34793112, year = {2021}, author = {Mitchell, AB and Li, CX and Oliver, BGG and Holmes, EC and Glanville, AR}, title = {High-resolution Metatranscriptomic Characterization of the Pulmonary RNA Virome After Lung Transplantation.}, journal = {Transplantation}, volume = {105}, number = {12}, pages = {2546-2553}, doi = {10.1097/TP.0000000000003713}, pmid = {34793112}, issn = {1534-6080}, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Longitudinal Studies ; Lung ; *Lung Transplantation/adverse effects ; *RNA ; Virome/genetics ; }, abstract = {BACKGROUND: Lung transplantation provides a unique opportunity to investigate the constituents and temporal dynamics of the human pulmonary microbiome after lung transplantation. For methodological reasons, prior studies using metagenomics have detected DNA viruses but not demonstrated the presence of RNA viruses, including those that are common community acquired. In this proof-of-concept study, we aimed to further characterize the pulmonary microbiome after lung transplantation by using metagenomic next-generation sequencing (mNGS), with a particular focus on the RNA virome.

METHODS: We performed a single-center longitudinal study of lower respiratory tract RNA viruses and bacteria using bronchoalveolar lavage at postoperative day 1 and week 6 analyzed with total RNA sequencing (metatranscriptomics). Five primary and 5 repeat transplant recipients were recruited.

RESULTS: mNGS identified 5 RNA viruses (nil in the normal saline control), including 4 species of human rhinovirus not previously reported in Australia: A7 (HRV-A7), C22 (HRV-C22), B52 (HRV-B52), and B72 (HRV-B72). Overall, 12/20 specimens were virus positive in 7/10 cases. Human parainfluenza virus 3 was the most frequent virus in 7/20 specimens in 5/10 cases. In this small study, we did not detect a significant difference in abundance and diversity of RNA viruses and bacteria at postoperative day 1 and 6 wk, nor differences between retransplant recipients and primary lung transplant recipients.

CONCLUSIONS: Our study demonstrates how mNGS can also identify RNA viruses within the human pulmonary virome, including novel RNA viruses, and paves the way for a greater understanding of the complex relationships among the constituents of the pulmonary infectome.}, } @article {pmid34792274, year = {2021}, author = {Jauregi, L and Epelde, L and González, A and Lavín, JL and Garbisu, C}, title = {Reduction of the resistome risk from cow slurry and manure microbiomes to soil and vegetable microbiomes.}, journal = {Environmental microbiology}, volume = {23}, number = {12}, pages = {7643-7660}, doi = {10.1111/1462-2920.15842}, pmid = {34792274}, issn = {1462-2920}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; Female ; Genes, Bacterial/genetics ; Livestock ; *Manure ; *Microbiota/genetics ; Soil ; Soil Microbiology ; Vegetables ; }, abstract = {In cow farms, the interaction between animal and environmental microbiomes creates hotspots for antibiotic resistance dissemination. A shotgun metagenomic approach was used to survey the resistome risk in five dairy cow farms. To this purpose, 10 environmental compartments were sampled: 3 of them linked to productive cows (fresh slurry, stored slurry, slurry-amended pasture soil); 6 of them to non-productive heifers and dry cows (faeces, fresh manure, aged manure, aged manure-amended orchard soil, vegetables-lettuces and grazed soil); and, finally, unamended control soil. The resistome risk was assessed using MetaCompare, a computational pipeline which scores the resistome risk according to possible links between antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and human pathogens. The resistome risk decreased from slurry and manure microbiomes to soil and vegetable microbiomes. In total (sum of all the compartments), 18,157 ARGs were detected: 24% related to ansamycins, 21% to multidrugs, 14% to aminoglycosides, 12% to tetracyclines, 9% to β-lactams, and 9% to macrolide-lincosamide-streptogramin B. All but two of the MGE-associated ARGs were only found in the animal dejections (not in soil or vegetable samples). Several ARGs with potential as resistome risk markers (based on their presence in hubs of co-occurrence networks and high dissemination potential) were identified. As a precautionary principle, improved management of livestock dejections is necessary to minimize the risk of antibiotic resistance.}, } @article {pmid34792102, year = {2021}, author = {He, Q and Huang, J and Zheng, T and Lin, D and Zhang, H and Li, J and Sun, Z}, title = {Treatment with mixed probiotics induced, enhanced and diversified modulation of the gut microbiome of healthy rats.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {12}, pages = {}, doi = {10.1093/femsec/fiab151}, pmid = {34792102}, issn = {1574-6941}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Microbiota ; *Probiotics ; Rats ; Rats, Wistar ; }, abstract = {Previous studies demonstrated that multi-strain probitics could more strongly regulate intestinal cytokines and the mucosal barrier than the individual ingredient strains. Nevertheless, the potentially different gut microbiome modulation effects between multi-strain and single-strain probiotics treatments remain unexplored. Here, we administered three different Lactiplantibacillus plantarum strains or their mixture to healthy Wistar rats and compared the shift of gut microbiome among the treatment groups. A 4-week intervention with mixed probiotics induced more drastic and diversified gut microbiome modulation than single-strain probiotics administration (alpha diversity increased 8% and beta diversity increased 18.7%). The three single-strain probiotics treatments all converged the gut microbiota, decreasing between-individual beta diversity by 12.7% on average after the treatment, while multi-strain probiotics treatment diversified the gut microbiome and increased between-individual beta diversity by 37.2% on average. Covariation analysis of the gut microbes suggests that multi-strain probiotics could exert synergistic, modified and enhanced modulation effects on the gut microbiome based on strain-specific modulation effects of probiotics. The more heterogeneous responses to the multi-strain probiotics treatment suggest that future precision microbiome modulation should consider the potential interactions of the probiotic strains, and personalized response to probiotic formulas due to heterogenous gut microbial compositions.}, } @article {pmid34791031, year = {2022}, author = {Van Rossum, T and Costea, PI and Paoli, L and Alves, R and Thielemann, R and Sunagawa, S and Bork, P}, title = {metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {4}, pages = {1162-1164}, pmid = {34791031}, issn = {1367-4811}, support = {ERC-AdG-669830//European Union's Horizon 2020 Research and Innovation Programme/ ; 01GL1746B//Bundesministerium für Bildung und Forschung/ ; 205321_184955//Swiss National Science Foundation (SNSF)/ ; //Eidgenössische Technische Hochschule (ETH) Zürich/ ; //European Molecular Biology Laboratory (EMBL)/ ; }, mesh = {Humans ; Metagenome ; Software ; *Microbiota ; *Gastrointestinal Microbiome ; Phenotype ; }, abstract = {SUMMARY: Taxonomic analysis of microbial communities is well supported at the level of species and strains. However, species can contain significant phenotypic diversity and strains are rarely widely shared across global populations. Stratifying the diversity between species and strains can identify 'subspecies', which are a useful intermediary. High-throughput identification and profiling of subspecies is not yet supported in the microbiome field. Here, we use an operational definition of subspecies based on single nucleotide variant (SNV) patterns within species to identify and profile subspecies in metagenomes, along with their distinctive SNVs and genes. We incorporate this method into metaSNV v2, which extends existing SNV-calling software to support further SNV interpretation for population genetics. These new features support microbiome analyses to link SNV profiles with host phenotype or environment and niche-specificity. We demonstrate subspecies identification in marine and fecal metagenomes. In the latter, we analyze 70 species in 7524 adult and infant subjects, supporting a common subspecies population structure in the human gut microbiome and illustrating some limits in subspecies calling.

Source code, documentation, tutorials and test data are available at https://github.com/metasnv-tool/metaSNV and https://metasnv.embl.de.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid34788940, year = {2022}, author = {Tian, L and Chang, J and Shi, S and Ji, L and Zhang, J and Sun, Y and Li, X and Li, X and Xie, H and Cai, Y and Chen, D and Wang, J and van Veen, JA and Kuramae, EE and Tran, LP and Tian, C}, title = {Comparison of methane metabolism in the rhizomicrobiomes of wild and related cultivated rice accessions reveals a strong impact of crop domestication.}, journal = {The Science of the total environment}, volume = {803}, number = {}, pages = {150131}, doi = {10.1016/j.scitotenv.2021.150131}, pmid = {34788940}, issn = {1879-1026}, mesh = {Domestication ; Methane ; *Oryza/genetics ; Plant Breeding ; Rhizosphere ; }, abstract = {Microbial communities from rhizosphere (rhizomicrobiomes) have been significantly impacted by domestication as evidenced by a comparison of the rhizomicrobiomes of wild and related cultivated rice accessions. While there have been many published studies focusing on the structure of the rhizomicrobiome, studies comparing the functional traits of the microbial communities in the rhizospheres of wild rice and cultivated rice accessions are not yet available. In this study, we used metagenomic data from experimental rice plots to analyze the potential functional traits of the microbial communities in the rhizospheres of wild rice accessions originated from Africa and Asia in comparison with their related cultivated rice accessions. The functional potential of rhizosphere microbial communities involved in alanine, aspartate and glutamate metabolism, methane metabolism, carbon fixation pathways, citrate cycle (TCA cycle), pyruvate metabolism and lipopolysaccharide biosynthesis pathways were found to be enriched in the rhizomicrobiomes of wild rice accessions. Notably, methane metabolism in the rhizomicrobiomes of wild and cultivated rice accessions clearly differed. Key enzymes involved in methane production and utilization were overrepresented in the rhizomicrobiome samples obtained from wild rice accessions, suggesting that the rhizomicrobiomes of wild rice maintain a different ecological balance for methane production and utilization compared with those of the related cultivated rice accessions. A novel assessment of the impact of rice domestication on the primary metabolic pathways associated with microbial taxa in the rhizomicrobiomes was performed. Results indicated a strong impact of rice domestication on methane metabolism; a process that represents a critical function of the rhizosphere microbial community of rice. The findings of this study provide important information for future breeding of rice varieties with reduced methane emission during cultivation for sustainable agriculture.}, } @article {pmid34788838, year = {2022}, author = {Dai, D and Zhu, J and Sun, C and Li, M and Liu, J and Wu, S and Ning, K and He, LJ and Zhao, XM and Chen, WH}, title = {GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison.}, journal = {Nucleic acids research}, volume = {50}, number = {D1}, pages = {D777-D784}, pmid = {34788838}, issn = {1362-4962}, mesh = {Biomarkers/blood ; *Databases, Genetic ; Datasets as Topic ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Internet ; Intestinal Neoplasms/blood/genetics/*microbiology/pathology ; *Metagenome ; *Microbiota ; Molecular Sequence Annotation ; Phenotype ; RNA, Ribosomal, 16S ; Software ; }, abstract = {GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purposes are to increase the reusability and accessibility of human gut metagenomic data, and enable cross-project and phenotype comparisons. To achieve these goals, we performed manual curation on the meta-data and organized the datasets in a phenotype-centric manner. GMrepo v2 contains 353 projects and 71,642 runs/samples, which are significantly increased from the previous version. Among these runs/samples, 45,111 and 26,531 were obtained by 16S rRNA amplicon and whole-genome metagenomics sequencing, respectively. We also increased the number of phenotypes from 92 to 133. In addition, we introduced disease-marker identification and cross-project/phenotype comparison. We first identified disease markers between two phenotypes (e.g. health versus diseases) on a per-project basis for selected projects. We then compared the identified markers for each phenotype pair across datasets to facilitate the identification of consistent microbial markers across datasets. Finally, we provided a marker-centric view to allow users to check if a marker has different trends in different diseases. So far, GMrepo includes 592 marker taxa (350 species and 242 genera) for 47 phenotype pairs, identified from 83 selected projects. GMrepo v2 is freely available at: https://gmrepo.humangut.info.}, } @article {pmid34788687, year = {2021}, author = {Gago, JF and Viver, T and Urdiain, M and Pastor, S and Kämpfer, P and Robledo, PA and Ferreira, E and Rosselló-Móra, R}, title = {Comparative genome analysis of the genus Hydrotalea and proposal of the novel species Hydrotalea lipotrueae sp. nov., isolated from a groundwater aquifer in the south of Mallorca Island, Spain.}, journal = {Systematic and applied microbiology}, volume = {44}, number = {6}, pages = {126277}, doi = {10.1016/j.syapm.2021.126277}, pmid = {34788687}, issn = {1618-0984}, mesh = {Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; *Genomics ; *Groundwater ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spain ; }, abstract = {From a collection of > 140 strains isolated from groundwater with thermal anomalies for the purpose of obtaining good candidates with applications in the cosmetic industry, two strains were selected because of their taxonomic novelty. Among the isolates, strains TMF_100[T] and TFM_099 stood out for their potential biotechnological relevance, and a comparative analysis of 16S rRNA gene sequences indicated that these strains represented a new species of the genus Hydrotalea. In addition, from the public genomic databases, metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) could be retrieved that affiliated with this genus. These MAGs and SAGs had been obtained from different environmental samples, such as acid mine drainage or marine sediments. In addition to the description of the new species, the ecological relevance of the members of this genus was demonstrated by means of denitrification, CRISPR-Cas system diversity and heavy metal resistance, as well as their wide geographical distribution and environmental versatility. Supported by the taxonomic study, together with physiological and morphological differences and ecological features, we concluded that strain TMF_100[T] represented a novel species within the genus Hydrotalea, for which we propose the name Hydrotalea lipotrueae sp. nov.}, } @article {pmid34788443, year = {2022}, author = {Carneiro, PAM and Pasquatti, TN and Lima, DAR and Rodrigues, RA and Takatani, H and Silva, CBDG and Jardim, R and Abramovitch, RB and Wilkins, MJ and Davila, AMR and Araujo, FR and Kaneene, JB}, title = {Milk Contamination by Mycobacterium tuberculosis Complex, Implications for Public Health in Amazonas, Brazil.}, journal = {Journal of food protection}, volume = {85}, number = {11}, pages = {1667-1673}, doi = {10.4315/JFP-21-303}, pmid = {34788443}, issn = {1944-9097}, mesh = {Animals ; Humans ; Female ; Cattle ; Milk/microbiology ; Brazil ; *Mycobacterium tuberculosis ; Buffaloes ; Public Health ; *Tuberculosis ; *Tuberculosis, Bovine/epidemiology ; }, abstract = {ABSTRACT: In Brazil, contamination of raw milk with Mycobacterium tuberculosis complex (MTC) has been reported in several states. The highest rate of consumption of raw milk and its derivatives in Brazil occurs in Amazonas. This state also has the highest prevalence of tuberculosis in both humans and livestock. We assessed the contamination of cow's milk and buffalo's milk with MTC in Amazonas, focusing on Mycobacterium bovis, the species most commonly found in cattle and buffalo. In 2019, 250 samples of raw milk (91 from cattle, 159 from buffalo) were collected before processing from three milk plants in the state of Amazonas. The samples were placed into 21 pools and analyzed using shotgun metagenomic sequencing and taxonomic classification with Kraken 2 and MegaBLAST. To confirm the identity of mycobacterial species found, BLASTN was used to identify specific genomic positions in the TbD1 and RD1 regions and flanking RD4 region. MTC genetic material was identified in all pools of raw milk. Genetic material consistent with M. bovis was identified in seven pools of raw milk (1 from cattle, 6 from buffalo). Buffalo's milk had significantly higher MTC reads than did cow's milk. The common practice of consumption of raw milk and its derivatives in Amazonas presents a risk to public health. Urgent measures to prevent transmission of foodborne tuberculosis are needed in the Amazon region. Greater efforts and resources also should be directed toward elimination of bovine tuberculosis in cattle and buffalo herds in Amazonas and the rest of Brazil.}, } @article {pmid34787462, year = {2021}, author = {Lu, H and Gao, NL and Tong, F and Wang, J and Li, H and Zhang, R and Ma, H and Yang, N and Zhang, Y and Wang, Y and Liang, Z and Zeng, H and Chen, WH and Dong, X}, title = {Alterations of the Human Lung and Gut Microbiomes in Non-Small Cell Lung Carcinomas and Distant Metastasis.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0080221}, pmid = {34787462}, issn = {2165-0497}, mesh = {Actinobacteria/isolation & purification ; Bacteria/*classification/isolation & purification ; Bacteroidetes/isolation & purification ; Biomarkers ; Carcinoma, Non-Small-Cell Lung/*pathology ; Dysbiosis/*microbiology ; Feces/microbiology ; Female ; Firmicutes/isolation & purification ; Fusobacteria/isolation & purification ; Gastrointestinal Microbiome/*physiology ; Humans ; Lung/*microbiology ; Lung Neoplasms/*pathology ; Male ; Middle Aged ; Neoplasm Metastasis/diagnosis/pathology ; Proteobacteria/isolation & purification ; Sputum/microbiology ; }, abstract = {Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related deaths worldwide. Although dysbiosis of the lung and gut microbiota have been associated with NSCLC, their relative contributions are unclear; in addition, their roles in distant metastasis (DM) are still illusive. We recruited in total 121 participants, including 87 newly diagnosed treatment-naive NSCLC patients of various stages and 34 healthy volunteers, and surveyed their fecal and sputum microbiota. We compared the microbial profiles between groups, identified microbial biomarkers, and generated machine learning models for distinguishing healthy individuals from patients with NSCLC and patients of various stages. We found significant perturbations of gut and sputum microbiota in patients with NSCLC and DM. A machine learning model combining both microbiota (combined model) performed better than an individual data set in patient stratification, with the highest area under the curve (AUC) value of 0.896. Sputum and gut microbiota both contributed to the combined model; in most cases, sputum-only models performed similar to the combined models. Several microbial biomarkers were shared by both microbiotas, indicating their similar roles at distinct body sites. Microbial biomarkers of distinct disease stages were mostly shared, suggesting biomarkers for DM could be acquired early. Furthermore, Pseudomonas aeruginosa, a species previously associated with wound infections, was significantly more abundant in brain metastasis, indicating that distinct types of DMs could have different microbes. Our results indicate that alterations of the sputum microbiota have stronger relationships with NSCLC and DM than the gut and strongly support the feasibility of metagenome-based noninvasive disease diagnosis and risk evaluation. (This study has been registered at ClinicalTrials.gov under registration no. NCT03454685). IMPORTANCE Our survey on gut and sputum microbiota revealed that both were significantly disturbed in non-small cell lung cancer (NSCLC) and associated with distant metastasis (DM) while only the sputum microbiota was associated with non-DM NSCLC. The lung microbiota could therefore have a stronger association with (and thus may contribute more to) disease development than the gut microbiota. Mathematic models using both microbiotas performed better in patient stratification than using individual microbiota. Sputum models, however, performed similar to the combined models, suggesting a convenient, noninvasive diagnostic for NSCLC. Microbial biomarkers of distinct disease stages were mostly shared, suggesting that the same set of microbes were underlying disease progression, and the signals for distant metastasis could be acquired at early stages of the disease. Our results strongly support the feasibility of noninvasive diagnosis of NSCLC, including distant metastasis, are of clinical importance, and should warrant further research on the underlying molecular mechanisms.}, } @article {pmid34787447, year = {2021}, author = {Mise, K and Masuda, Y and Senoo, K and Itoh, H}, title = {Undervalued Pseudo-nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers.}, journal = {mSphere}, volume = {6}, number = {6}, pages = {e0078521}, pmid = {34787447}, issn = {2379-5042}, mesh = {Ecosystem ; Metagenome ; *Metagenomics ; Microbiota/*genetics/physiology ; Nitrogen/metabolism ; *Nitrogen Fixation ; Oxidoreductases/*genetics ; Phylogeny ; }, abstract = {Nitrogen fixation, a distinct process incorporating the inactive atmospheric nitrogen into the active biological processes, has been a major topic in biological and geochemical studies. Currently, insights into diversity and distribution of nitrogen-fixing microbes are dependent upon homology-based analyses of nitrogenase genes, especially the nifH gene, which are broadly conserved in nitrogen-fixing microbes. Here, we report the pitfall of using nifH as a marker of microbial nitrogen fixation. We exhaustively analyzed genomes in RefSeq (231,908 genomes) and KEGG (6,509 genomes) and cooccurrence and gene order patterns of nitrogenase genes (including nifH) therein. Up to 20% of nifH-harboring genomes lacked nifD and nifK, which encode essential subunits of nitrogenase, within 10 coding sequences upstream or downstream of nifH or on the same genome. According to a phenotypic database of prokaryotes, no species and strains harboring only nifH possess nitrogen-fixing activities, which shows that these nifH genes are "pseudo"-nifH genes. Pseudo-nifH sequences mainly belong to anaerobic microbes, including members of the class Clostridia and methanogens. We also detected many pseudo-nifH reads from metagenomic sequences of anaerobic environments such as animal guts, wastewater, paddy soils, and sediments. In some samples, pseudo-nifH overwhelmed the number of "true" nifH reads by 50% or 10 times. Because of the high sequence similarity between pseudo- and true-nifH, pronounced amounts of nifH-like reads were not confidently classified. Overall, our results encourage reconsideration of the conventional use of nifH for detecting nitrogen-fixing microbes, while suggesting that nifD or nifK would be a more reliable marker. IMPORTANCE Nitrogen-fixing microbes affect biogeochemical cycling, agricultural productivity, and microbial ecosystems, and their distributions have been investigated intensively using genomic and metagenomic sequencing. Currently, insights into nitrogen fixers in the environment have been acquired by homology searches against nitrogenase genes, particularly the nifH gene, in public databases. Here, we report that public databases include a significant amount of incorrectly annotated nifH sequences (pseudo-nifH). We exhaustively investigated the genomic structures of nifH-harboring genomes and found hundreds of pseudo-nifH sequences in RefSeq and KEGG. Over half of these pseudo-nifH sequences belonged to members of the class Clostridia, which is supposed to be a prominent nitrogen-fixing clade. We also found that the abundance of nitrogen fixers in metagenomes could be overestimated by 1.5 to >10 times due to pseudo-nifH recorded in public databases. Our results encourage reconsideration of the prevalent use of nifH as a marker of nitrogen-fixing microbes.}, } @article {pmid34787442, year = {2021}, author = {Guajardo-Leiva, S and Santos, F and Salgado, O and Regeard, C and Quillet, L and Díez, B}, title = {Unveiling Ecological and Genetic Novelty within Lytic and Lysogenic Viral Communities of Hot Spring Phototrophic Microbial Mats.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0069421}, pmid = {34787442}, issn = {2165-0497}, mesh = {Bacteria/classification/genetics/radiation effects/*virology ; Biodiversity ; Genetic Variation ; Hot Springs/*virology ; *Lysogeny ; Metagenome ; Phototrophic Processes ; Phylogeny ; Virus Physiological Phenomena ; Viruses/classification/*genetics/isolation & purification ; }, abstract = {Viruses exert diverse ecosystem impacts by controlling their host community through lytic predator-prey dynamics. However, the mechanisms by which lysogenic viruses influence their host-microbial community are less clear. In hot springs, lysogeny is considered an active lifestyle, yet it has not been systematically studied in all habitats, with phototrophic microbial mats (PMMs) being particularly not studied. We carried out viral metagenomics following in situ mitomycin C induction experiments in PMMs from Porcelana hot spring (Northern Patagonia, Chile). The compositional changes of viral communities at two different sites were analyzed at the genomic and gene levels. Furthermore, the presence of integrated prophage sequences in environmental metagenome-assembled genomes from published Porcelana PMM metagenomes was analyzed. Our results suggest that virus-specific replicative cycles (lytic and lysogenic) were associated with specific host taxa with different metabolic capacities. One of the most abundant lytic viral groups corresponded to cyanophages, which would infect the cyanobacteria Fischerella, the most active and dominant primary producer in thermophilic PMMs. Likewise, lysogenic viruses were related exclusively to chemoheterotrophic bacteria from the phyla Proteobacteria, Firmicutes, and Actinobacteria. These temperate viruses possess accessory genes to sense or control stress-related processes in their hosts, such as sporulation and biofilm formation. Taken together, these observations suggest a nexus between the ecological role of the host (metabolism) and the type of viral lifestyle in thermophilic PMMs. This has direct implications in viral ecology, where the lysogenic-lytic switch is determined by nutrient abundance and microbial density but also by the metabolism type that prevails in the host community. IMPORTANCE Hot springs harbor microbial communities dominated by a limited variety of microorganisms and, as such, have become a model for studying community ecology and understanding how biotic and abiotic interactions shape their structure. Viruses in hot springs are shown to be ubiquitous, numerous, and active components of these communities. However, lytic and lysogenic viral communities of thermophilic phototrophic microbial mats (PMMs) remain largely unexplored. In this work, we use the power of viral metagenomics to reveal changes in the viral community following a mitomycin C induction experiment in PMMs. The importance of our research is that it will improve our understanding of viral lifestyles in PMMs via exploring the differences in the composition of natural and induced viral communities at the genome and gene levels. This novel information will contribute to deciphering which biotic and abiotic factors may control the transitions between lytic and lysogenic cycles in these extreme environments.}, } @article {pmid34786660, year = {2022}, author = {Komuroglu, AU and Seckin, H and Ertaş, M and Meydan, I}, title = {Metagenomic Analysis of Intestinal Microbiota in Florated Rats.}, journal = {Biological trace element research}, volume = {200}, number = {7}, pages = {3275-3283}, pmid = {34786660}, issn = {1559-0720}, mesh = {Animals ; Fluorine ; *Gastrointestinal Microbiome ; Lipid Peroxidation ; Male ; Mice ; RNA, Ribosomal, 16S ; Rats ; Rats, Wistar ; }, abstract = {Changes in gut microbiota have shown that it plays an important role in animal health and metabolic diseases. The intestinal microbiota is a complex structure that functions as an organ system with the presence of trillions of microorganisms. In this study, changes in the intestinal microbiota of Wistar rats with high fluorine were evaluated. Water containing 100 ppm NaF was given to 14 male Wistar albino rats as drinking water for 12 weeks. Fluorine is known to be an inducer of protein oxidation, lipid peroxidation, modulation of intracellular redox homeostasis, and oxidative stress. In this study, it was determined that the level of MDA (molandialdehyde), one of the oxidative stress parameters, increased significantly in the intestinal tissue after fluorine intoxication. The decrease in CAT (catalase) and SOD (superoxide dismutase) enzyme activities was found to be statistically significant. Intestinal tissues were taken under aseptic conditions and microorganisms found in flora were replicated by V3-V4 16S rRNA gene-specific primers. As a result of the sequence analysis, a statistical comparison of the control group and the fluorine applied group was made. The study we have done showed that there was a significant difference in species diversity in the intestinal microbiota of mice treated with fluorine. As a result, the composition of the intestinal microflora, especially Lactobacillus species, was significantly changed in rats with high fluorine.}, } @article {pmid34784973, year = {2021}, author = {Wu, J and Lang, H and Mu, X and Zhang, Z and Su, Q and Hu, X and Zheng, H}, title = {Honey bee genetics shape the strain-level structure of gut microbiota in social transmission.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {225}, pmid = {34784973}, issn = {2049-2618}, mesh = {Animals ; Bacteria/genetics ; Bees ; Bifidobacterium/genetics ; *Gastrointestinal Microbiome/genetics ; Genome-Wide Association Study ; *Microbiota ; }, abstract = {BACKGROUND: Honey bee gut microbiota transmitted via social interactions are beneficial to the host health. Although the microbial community is relatively stable, individual variations and high strain-level diversity have been detected across honey bees. Although the bee gut microbiota structure is influenced by environmental factors, the heritability of the gut members and the contribution of the host genetics remains elusive. Considering bees within a colony are not readily genetically identical due to the polyandry of the queen, we hypothesize that the microbiota structure can be shaped by host genetics.

RESULTS: We used shotgun metagenomics to simultaneously profile the microbiota and host genotypes of bees from hives of four different subspecies. Gut composition is more distant between genetically different bees at both phylotype- and "sequence-discrete population" levels. We then performed a successive passaging experiment within colonies of hybrid bees generated by artificial insemination, which revealed that the microbial composition dramatically shifts across batches of bees during the social transmission. Specifically, different strains from the phylotype of Snodgrassella alvi are preferentially selected by genetically varied hosts, and strains from different hosts show a remarkably biased distribution of single-nucleotide polymorphism in the Type IV pili loci. Genome-wide association analysis identified that the relative abundance of a cluster of Bifidobacterium strains is associated with the host glutamate receptor gene specifically expressed in the bee brain. Finally, mono-colonization of Bifidobacterium with a specific polysaccharide utilization locus impacts the alternative splicing of the gluR-B gene, which is associated with an increased GABA level in the brain.

CONCLUSIONS: Our results indicated that host genetics influence the bee gut composition and suggest a gut-brain connection implicated in the gut bacterial strain preference. Honey bees have been used extensively as a model organism for social behaviors, genetics, and the gut microbiome. Further identification of host genetic function as a shaping force of microbial structure will advance our understanding of the host-microbe interactions. Video abstract.}, } @article {pmid34784754, year = {2022}, author = {Mahlanza, T and Makwarela, L and Roberts, R and van der Merwe, M}, title = {Occurrence of the Iflavirus-like Tomato Matilda Virus in Solanum Species in South Africa.}, journal = {Plant disease}, volume = {}, number = {}, pages = {PDIS03210613PDN}, doi = {10.1094/PDIS-03-21-0613-PDN}, pmid = {34784754}, issn = {0191-2917}, } @article {pmid34782034, year = {2021}, author = {Thurman, CE and Klores, MM and Wolfe, AE and Poueymirou, WT and Levee, EM and Ericsson, AC and Franklin, CL and Reddyjarugu, B}, title = {Effect of Housing Condition and Diet on the Gut Microbiota of Weanling Immunocompromised Mice.}, journal = {Comparative medicine}, volume = {71}, number = {6}, pages = {485-491}, pmid = {34782034}, issn = {2769-819X}, support = {U42 OD010918/OD/NIH HHS/United States ; U42 RR014821/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Diet ; *Gastrointestinal Microbiome ; Housing Quality ; Mice ; *Microbiota ; }, abstract = {Gastrointestinal microbiota are affected by a wide variety of extrinsic and intrinsic factors. In the husbandry of laboratory mice and design of experiments, controlling these factors where possible provides more reproducible results. However, the microbiome is dynamic, particularly in the weeks immediately after weaning. In this study, we characterized the baseline gastrointestinal microbiota of immunocompromised mice housed under standard conditions for our facility for 6 weeks after weaning, with housing either in an isolator or in individually ventilated cages and a common antibiotic diet (trimethoprim sulfamethoxazole). We compared these conditions to a group fed a standard diet and a group that was weaned to a standard diet then switched to antibiotic diet after 2 weeks. We found no clear effect of diet on richness and α diversity of the gastrointestinal microbiota. However, diet did affect which taxa were enriched at the end of the experiment. The change to antibiotic diet during the experiment did not convert the gastrointestinal microbiome to a state similar to mice consistently fed antibiotic diet, which may highlight the importance of the initial post-weaning period in the establishment of the gastrointestinal microbiome. We also observed a strong effect of housing type (isolator compared with individually ventilated cage) on the richness, α diversity, β diversity, and taxa enriched over the course of the experiment. Investigating whether the diet or microbiome affects a certain strain's phenotype is warranted in some cases. However, our findings do not suggest that maintaining immunocompromised mice on antibiotic feed has a clinical benefit when potential pathogens are operationally excluded, nor does it result in a more consistent or controlled microbiome in the post-weaning period.}, } @article {pmid34782020, year = {2021}, author = {Ellison, AR and Wilcockson, D and Cable, J}, title = {Circadian dynamics of the teleost skin immune-microbiome interface.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {222}, pmid = {34782020}, issn = {2049-2618}, support = {BB/R010609/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Circadian Rhythm ; *Microbiota/genetics ; *Oncorhynchus mykiss/genetics/metabolism ; Photoperiod ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {BACKGROUND: Circadian rhythms of host immune activity and their microbiomes are likely pivotal to health and disease resistance. The integration of chronotherapeutic approaches to disease mitigation in managed animals, however, is yet to be realised. In aquaculture, light manipulation is commonly used to enhance growth and control reproduction but may have unknown negative consequences for animal health. Infectious diseases are a major barrier to sustainable aquaculture and understanding the circadian dynamics of fish immunity and crosstalk with the microbiome is urgently needed.

RESULTS: Here, using rainbow trout (Oncorhynchus mykiss) as a model, we combine 16S rRNA metabarcoding, metagenomic sequencing and direct mRNA quantification methods to simultaneously characterise the circadian dynamics of skin clock and immune gene expression, and daily changes of skin microbiota. We demonstrate daily rhythms in fish skin immune expression and microbiomes, which are modulated by photoperiod and parasitic lice infection. We identify putative associations of host clock and immune gene profiles with microbial composition. Our results suggest circadian perturbation, that shifts the magnitude and timing of immune and microbiota activity, is detrimental to fish health.

CONCLUSIONS: The substantial circadian dynamics and fish host expression-microbiome relationships we find represent a valuable foundation for investigating the utility of chronotherapies in aquaculture, and more broadly contributes to our understanding of the role of microbiomes in circadian health of vertebrates. Video Abstract.}, } @article {pmid34781411, year = {2022}, author = {Sivaraj, S and Copeland, JK and Malik, A and Pasini, E and Angeli, M and Azhie, A and Husain, S and Kumar, D and Allard, J and Guttman, DS and Humar, A and Bhat, M}, title = {Characterization and predictive functional profiles on metagenomic 16S rRNA data of liver transplant recipients: A longitudinal study.}, journal = {Clinical transplantation}, volume = {36}, number = {2}, pages = {e14534}, doi = {10.1111/ctr.14534}, pmid = {34781411}, issn = {1399-0012}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Humans ; *Liver Transplantation ; Longitudinal Studies ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Long-term survival after Liver Transplantation (LT) is often compromised by infectious and metabolic complications. We aimed to delineate alterations in intestinal microbiome (IM) over time that could contribute to medical complications compromising long-term survival following LT. Fecal samples from LT recipients were collected at 3 months (3 M) and 6 months (6 M) post-LT. The bacterial DNA was extracted using E.Z.N.A. Stool DNA Kit and 16S rRNA gene sequencing at V4 hypervariable region was performed. DADA2 and Phyloseq was implemented to analyze the taxonomic composition. Differentially abundant taxa were identified by metagenomeSeq and LEfSe. Piphillin, an Inferred functional metagenomic analysis tool was used to study the bacterial functional content. For comparison, healthy samples were extracted from NCBI and analyzed similarly. The taxonomic & functional profiles of LT recipients were validated with metagenomic sequencing data from animals exposed to immunosuppressants using Venny. Our findings provide a new perspective on longitudinal increase in specific IM communities post-LT along with an increase in bacterial genes associated with metabolic and infectious disease.}, } @article {pmid34780902, year = {2022}, author = {Innard, N and Chong, JPJ}, title = {The challenges of monitoring and manipulating anaerobic microbial communities.}, journal = {Bioresource technology}, volume = {344}, number = {Pt B}, pages = {126326}, doi = {10.1016/j.biortech.2021.126326}, pmid = {34780902}, issn = {1873-2976}, mesh = {Anaerobiosis ; Animals ; Biomass ; *Bioreactors ; *Microbiota ; }, abstract = {Mixed anaerobic microbial communities are a key component in valorization of waste biomass via anaerobic digestion. Similar microbial communities are important as soil and animal microbiomes and have played a critical role in shaping the planet as it is today. Understanding how individual species within communities interact with others and their environment is important for improving performance and potential applications of an inherently green technology. Here, the challenges associated with making measurements critical to assessing the status of anaerobic microbial communities are considered. How these measurements could be incorporated into control philosophies and augment the potential of anaerobic microbial communities to produce different and higher value products from waste materials are discussed. The benefits and pitfalls of current genetic and molecular approaches to measuring and manipulating anaerobic microbial communities and the challenges which should be addressed to realise the potential of this exciting technology are explored.}, } @article {pmid34779841, year = {2021}, author = {Curry, KD and Nute, MG and Treangen, TJ}, title = {It takes guts to learn: machine learning techniques for disease detection from the gut microbiome.}, journal = {Emerging topics in life sciences}, volume = {5}, number = {6}, pages = {815-827}, pmid = {34779841}, issn = {2397-8554}, support = {T15 LM007093/LM/NLM NIH HHS/United States ; P01 AI152999/AI/NIAID NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Machine Learning ; Metagenome ; Metagenomics/methods ; *Microbiota ; }, abstract = {Associations between the human gut microbiome and expression of host illness have been noted in a variety of conditions ranging from gastrointestinal dysfunctions to neurological deficits. Machine learning (ML) methods have generated promising results for disease prediction from gut metagenomic information for diseases including liver cirrhosis and irritable bowel disease, but have lacked efficacy when predicting other illnesses. Here, we review current ML methods designed for disease classification from microbiome data. We highlight the computational challenges these methods have effectively overcome and discuss the biological components that have been overlooked to offer perspectives on future work in this area.}, } @article {pmid34778105, year = {2021}, author = {Pang, L and Wang, Y and Ye, Y and Zhou, Y and Zhi, Q and Lin, H}, title = {Metagenomic Analysis of Dental Plaque on Pit and Fissure Sites With and Without Caries Among Adolescents.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {740981}, pmid = {34778105}, issn = {2235-2988}, mesh = {Adolescent ; Biofilms ; *Dental Caries ; Dental Caries Susceptibility ; *Dental Plaque ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {Caries is one of the most prevalent infectious diseases worldwide and is driven by the dysbiosis of dental biofilms adhering to tooth surfaces. The pits and fissured surfaces are the most susceptible sites of caries. However, information on the taxonomic composition and functional characteristics of the plaque microbiota in the pit and fissure sites is very limited. This study aimed to use metagenomic sequencing analyses to investigate the relationship between the plaque microbiome in the pit and fissure site and caries in adolescents. A total of 20 adolescents with active pit and fissure surface caries were involved as well as 20 age-matched, caries-free teenagers for control tests. Plaque samples were collected from the pit and fissure site and were subjected to metagenomic analyses, in which the microbial communities were investigated. Our results showed that the microbiota diversity was similar between those two groups. At the species level, the relative abundances of A. gerencseriae, P. acidifaciens, P. multisaccharivorax, S. oralis, S. mutans, and P. denticolens were higher in the caries-active group. N. elongata, C. hominis, and A. johnsonii were relatively more abundant in the caries-free groups. Functional analysis suggested that the metabolic pathway was the most abundant pathway, and the functional traits of the level 2 pathways included amino acid metabolism, metabolism of cofactors, and vitamins and carbohydrate metabolism. Our results also revealed that the caries group displayed several alterations in metabolic pathways, including enriched functions in carbohydrate digestion and absorption. This study suggested that in addition to the specific anatomical structures of the pit and fissured surfaces, the fundamental differences in the plaque microbiome may also be related to the susceptibility of pit and fissure caries.}, } @article {pmid34776340, year = {2022}, author = {McFarlane, C and Krishnasamy, R and Stanton, T and Savill, E and Snelson, M and Mihala, G and Morrison, M and Johnson, DW and Campbell, KL}, title = {Diet Quality and Protein-Bound Uraemic Toxins: Investigation of Novel Risk Factors and the Role of Microbiome in Chronic Kidney Disease.}, journal = {Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation}, volume = {32}, number = {5}, pages = {542-551}, doi = {10.1053/j.jrn.2021.10.003}, pmid = {34776340}, issn = {1532-8503}, mesh = {Animals ; Cresols ; Cross-Sectional Studies ; Diet ; Dietary Fiber ; Humans ; Indican ; *Microbiota ; *Renal Insufficiency, Chronic ; Risk Factors ; Sulfates ; Uremic Toxins ; }, abstract = {OBJECTIVE: This study aims to explore the associations between diet quality, uraemic toxins, and gastrointestinal microbiota in the chronic kidney disease (CKD) population.

METHODS: This is a baseline cross-sectional study of adults with CKD participating in a randomized controlled trial of prebiotic and probiotic supplementation. Dietary intake was measured using a seven-day diet history method, administered by a specialist dietitian. Diet quality was assessed using plant-based diet index (PDI) (overall PDI, healthy PDI, and unhealthy PDI), food group analysis, protein intake, fiber intake, and dietary protein-to-fiber ratio. Serum uraemic toxins (free and total; indoxyl sulfate and p-cresyl sulfate) were determined by ultraperformance liquid chromatography. Gastrointestinal microbiota richness, diversity, composition, and functional capacity were analyzed via metagenomic sequencing.

RESULTS: Sixty-eight adults [median age: 70 (interquartile range: 58-75) years, 66% male] with an estimated glomerular filtration rate of 34 ± 11 mL/min/1.73 m[2] were included, with 40 participants completing the optional fecal substudy. Dietary fiber intake was associated with lower levels of total indoxyl sulfate, whereas the healthy plant-based diet index was associated with lower levels of free p-cresyl sulfate. A higher protein-to-fiber ratio was associated with an increased relative abundance of unclassified members of order Oscillospirales. Intake of vegetables and whole grains was correlated with Subdoligranulum formicile, whereas an unclassified Prevotella species was correlated with potatoes and food items considered discretionary, including sweet drinks, sweet desserts, and animal fats.

CONCLUSIONS: Diet quality may influence uraemic toxin generation and gut microbiota diversity, composition, and function in adults with CKD. Well-designed dietary intervention studies targeting the production of uraemic toxins and exploring the impact on gut microbiome are warranted in the CKD population.}, } @article {pmid34774959, year = {2022}, author = {Deng, C and Zhao, R and Qiu, Z and Li, B and Zhang, T and Guo, F and Mu, R and Wu, Y and Qiao, X and Zhang, L and Cheng, JJ and Ni, J and Yu, K}, title = {Genome-centric metagenomics provides new insights into the microbial community and metabolic potential of landfill leachate microbiota.}, journal = {The Science of the total environment}, volume = {816}, number = {}, pages = {151635}, doi = {10.1016/j.scitotenv.2021.151635}, pmid = {34774959}, issn = {1879-1026}, mesh = {Humans ; Metagenome ; Metagenomics ; *Microbiota ; Waste Disposal Facilities ; *Water Pollutants, Chemical/analysis ; }, abstract = {Landfills are important sources of microorganisms associated with anaerobic digestion. However, the knowledge on microbiota along with their functional potential in this special habitat are still lacking. In this study, we recovered 1168 non-redundant metagenome-assembled genomes (MAGs) from nine landfill leachate samples collected from eight cities across China, spanning 42 phyla, 73 classes, 114 orders, 189 families, and 267 genera. Totally, 74.1% of 1168 MAGs could not be classified to any known species and 5.9% of these MAGs belonged to microbial dark matter phyla. Two putative novel classes were discovered from landfill leachate samples. The identification of thousands of novel carbohydrate-active enzymes showed similar richness level compared to the cow rumen microbiota. The methylotrophic methanogenic pathway was speculated to contribute significantly to methane production in the landfill leachate because of its co-occurrence with the acetoclastic and hydrogenotrophic methanogenic pathways. The genetic potential of dissimilatory nitrate reduction to ammonium (DNRA) was observed, implying DNRA may play a role in ammonium generation in landfill leachate. These findings implied that landfill leachate might be a valuable microbial resource repository and filled the previous understanding gaps for both methanogenesis and nitrogen cycling in landfill leachate microbiota. Our study provides a comprehensive genomic catalog and substantially provides unprecedented taxonomic and functional profiles of the landfill leachate microbiota.}, } @article {pmid34774941, year = {2022}, author = {Su, Z and Wen, D}, title = {Characterization of antibiotic resistance across Earth's microbial genomes.}, journal = {The Science of the total environment}, volume = {816}, number = {}, pages = {151613}, doi = {10.1016/j.scitotenv.2021.151613}, pmid = {34774941}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Genome, Microbial ; Humans ; Metagenome ; *Microbiota ; }, abstract = {Widespread antibiotic resistance across Earth's habitats has become a critical health concern. However, large-scale investigation on the distribution of antibiotic resistance genes (ARGs) in the microbiomes from most types of ecosystem is still lacking. In this study, we provide a comprehensive characterization of ARGs for 52,515 microbial genomes covering various Earth's ecosystems, and conduct the risk assessment for ARG-carrying species based on further identification of mobile genetic elements (MGEs) and virulence factor genes (VFGs). We identify a total of 6159 ARG-carrying metagenome-assembled genomes (ACMs), and most of them are recovered from human gut and city subway. Our results show that efflux pump is the most common mechanism for bacteria to acquire multidrug resistance genes in Earth's microbiomes. Enterobacteriaceae species are the largest hosts of ARGs, accounting for 14% of total ACMs with 64% of the total ARG hits. Most of ARG-carrying species are unique in the different ecosystem categories, while 33 potential background ARGs are commonly shared by all ecosystem categories. We then detect 36 high-risk ARGs that likely threat public health in all ACMs. Based on ranking the importance of ARG-carrying species in the different ecosystem categories, several bacterial taxa such as Escherichia coli, Enterococcus faecalis, and Pseudomonas_A stutzeri are recognized as priority species for surveillance and control. Overall, our study gives a broad view of ARG-host associations in the environments.}, } @article {pmid34773153, year = {2021}, author = {Kwon, YJ and Kwak, HJ and Lee, HK and Lim, HC and Jung, DH}, title = {Comparison of bacterial community profiles from large intestine specimens, rectal swabs, and stool samples.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {24}, pages = {9273-9284}, pmid = {34773153}, issn = {1432-0614}, mesh = {Bacteria/genetics ; Feces ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Rectum ; }, abstract = {The human gastrointestinal tract contains a complex and dynamic population of microorganisms, known as the gut microbiota. Although interest in the role of the gut microbiota in human health has increased in recent years, there remains no standard sampling protocol for analyzing these organisms. Here, we aimed to characterize the microbial composition of distinct segments of the large intestine and to determine whether rectal swabs are suitable for identifying colon microbiota. A total of 100 participants who underwent screening colonoscopy from October 2019 to October 2020 were included in this study. Large intestinal samples (ascending colon, descending colon, sigmoid colon, and rectum) were aspirated by colonoscopy. Rectal swabs were collected before colonoscopy, and stool samples were collected before patients began colonoscopy preparation. All samples were subjected to 16S ribosomal RNA gene sequencing. We identified differences in the number of phylum-level operational taxonomic units among large intestinal samples, rectal swabs, and stool. Five major phyla were detected in all samples (Firmicutes, Bacteroides, Proteobacteria, Actinobacteria, Fusobacteria), although their relative abundances varied. Notably, we found that the microbial compositions of rectal swabs were most similar to those of the sigmoid colon and rectum, whereas the microbiota in stool were relatively different than those from the large intestine and rectal swabs. Our results reveal the existence of microbial heterogeneity within different large intestinal compartments and further suggest that rectal swabs are an acceptable and practical tool for gut microbiota analysis. KEY POINTS: • Our findings highlight local microbiome variations within different regions of the large intestine. • Stool samples do not appear to fully recapitulate the gut microbiome. • Our data from a large population-based cohort indicate that rectal swabs can be used to study the gut microbiome.}, } @article {pmid34772759, year = {2021}, author = {Kardos, M and Armstrong, EE and Fitzpatrick, SW and Hauser, S and Hedrick, PW and Miller, JM and Tallmon, DA and Funk, WC}, title = {The crucial role of genome-wide genetic variation in conservation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {48}, pages = {}, pmid = {34772759}, issn = {1091-6490}, support = {RL5 GM118990/GM/NIGMS NIH HHS/United States ; UL1 GM118991/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biodiversity ; Conservation of Natural Resources ; Ecosystem ; Genetic Fitness/genetics ; Genetic Variation/*genetics ; Genetics ; Genetics, Population/methods ; Genome/*genetics ; Genomics ; Inbreeding ; Metagenomics/methods ; Population Dynamics/*trends ; }, abstract = {The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations toward extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide genetic variation on long-term population viability will only worsen the biodiversity crisis.}, } @article {pmid34769481, year = {2021}, author = {Silveira, CB and Cobián-Güemes, AG and Uranga, C and Baker, JL and Edlund, A and Rohwer, F and Conrad, D}, title = {Multi-Omics Study of Keystone Species in a Cystic Fibrosis Microbiome.}, journal = {International journal of molecular sciences}, volume = {22}, number = {21}, pages = {}, pmid = {34769481}, issn = {1422-0067}, support = {S00022215 to CS//Cystic Fibrosis Research Inc./ ; S00023377 to FLR//Cystic Fibrosis Research Inc./ ; to FLR//Spruance Foundation/ ; }, mesh = {Adult ; Anti-Bacterial Agents/therapeutic use ; Cystic Fibrosis/complications/*microbiology/therapy ; Genomics/methods ; Humans ; Lung/microbiology ; Male ; Metabolomics/methods ; Metagenomics/*methods ; *Microbiota/genetics ; Respiratory Function Tests ; Respiratory Insufficiency/genetics/metabolism/microbiology/therapy ; Sputum/microbiology ; }, abstract = {Ecological networking and in vitro studies predict that anaerobic, mucus-degrading bacteria are keystone species in cystic fibrosis (CF) microbiomes. The metabolic byproducts from these bacteria facilitate the colonization and growth of CF pathogens like Pseudomonas aeruginosa. Here, a multi-omics study informed the control of putative anaerobic keystone species during a transition in antibiotic therapy of a CF patient. A quantitative metagenomics approach combining sequence data with epifluorescence microscopy showed that during periods of rapid lung function loss, the patient's lung microbiome was dominated by the anaerobic, mucus-degrading bacteria belonging to Streptococcus, Veillonella, and Prevotella genera. Untargeted metabolomics and community cultures identified high rates of fermentation in these sputa, with the accumulation of lactic acid, citric acid, and acetic acid. P. aeruginosa utilized these fermentation products for growth, as indicated by quantitative transcriptomics data. Transcription levels of P. aeruginosa genes for the utilization of fermentation products were proportional to the abundance of anaerobic bacteria. Clindamycin therapy targeting Gram-positive anaerobes rapidly suppressed anaerobic bacteria and the accumulation of fermentation products. Clindamycin also lowered the abundance and transcription of P. aeruginosa, even though this patient's strain was resistant to this antibiotic. The treatment stabilized the patient's lung function and improved respiratory health for two months, lengthening by a factor of four the between-hospitalization time for this patient. Killing anaerobes indirectly limited the growth of P. aeruginosa by disrupting the cross-feeding of fermentation products. This case study supports the hypothesis that facultative anaerobes operated as keystone species in this CF microbiome. Personalized multi-omics may become a viable approach for routine clinical diagnostics in the future, providing critical information to inform treatment decisions.}, } @article {pmid34769377, year = {2021}, author = {Usyskin-Tonne, A and Hadar, Y and Minz, D}, title = {Spike Formation Is a Turning Point Determining Wheat Root Microbiome Abundance, Structures and Functions.}, journal = {International journal of molecular sciences}, volume = {22}, number = {21}, pages = {}, pmid = {34769377}, issn = {1422-0067}, support = {1281/13//Israel Science Foundation/ ; }, mesh = {Bacteria/classification/genetics/*growth & development ; *Metagenome ; *Microbiota ; Phylogeny ; Plant Roots/genetics/*growth & development/microbiology ; Triticum/genetics/*growth & development/microbiology ; }, abstract = {Root selection of their associated microbiome composition and activities is determined by the plant's developmental stage and distance from the root. Total gene abundance, structure and functions of root-associated and rhizospheric microbiomes were studied throughout wheat growth season under field conditions. On the root surface, abundance of the well-known wheat colonizers Proteobacteria and Actinobacteria decreased and increased, respectively, during spike formation, whereas abundance of Bacteroidetes was independent of spike formation. Metagenomic analysis combined with functional co-occurrence networks revealed a significant impact of plant developmental stage on its microbiome during the transition from vegetative growth to spike formation. For example, gene functions related to biofilm and sensorial movement, antibiotic production and resistance and carbons and amino acids and their transporters. Genes associated with these functions were also in higher abundance in root vs. the rhizosphere microbiome. We propose that abundance of transporter-encoding genes related to carbon and amino acid, may mirror the availability and utilization of root exudates. Genes related to antibiotic resistance mechanisms were abundant during vegetative growth, while after spike formation, genes related to the biosynthesis of various antibiotics were enriched. This observation suggests that during root colonization and biofilm formation, bacteria cope with competitor's antibiotics, whereas in the mature biofilm stage, they invest in inhibiting new colonizers. Additionally, there is higher abundance of genes related to denitrification in rhizosphere compared to root-associated microbiome during wheat growth, possibly due to competition with the plant over nitrogen in the root vicinity. We demonstrated functional and phylogenetic division in wheat root zone microbiome in both time and space: pre- and post-spike formation, and root-associated vs. rhizospheric niches. These findings shed light on the dynamics of plant-microbe and microbe-microbe interactions in the developing root zone.}, } @article {pmid34767757, year = {2021}, author = {Yap, CX and Henders, AK and Alvares, GA and Wood, DLA and Krause, L and Tyson, GW and Restuadi, R and Wallace, L and McLaren, T and Hansell, NK and Cleary, D and Grove, R and Hafekost, C and Harun, A and Holdsworth, H and Jellett, R and Khan, F and Lawson, LP and Leslie, J and Frenk, ML and Masi, A and Mathew, NE and Muniandy, M and Nothard, M and Miller, JL and Nunn, L and Holtmann, G and Strike, LT and de Zubicaray, GI and Thompson, PM and McMahon, KL and Wright, MJ and Visscher, PM and Dawson, PA and Dissanayake, C and Eapen, V and Heussler, HS and McRae, AF and Whitehouse, AJO and Wray, NR and Gratten, J}, title = {Autism-related dietary preferences mediate autism-gut microbiome associations.}, journal = {Cell}, volume = {184}, number = {24}, pages = {5916-5931.e17}, doi = {10.1016/j.cell.2021.10.015}, pmid = {34767757}, issn = {1097-4172}, mesh = {Adolescent ; Age Factors ; Autistic Disorder/diagnosis/*microbiology ; Behavior ; Child ; Child, Preschool ; Feces/microbiology ; *Feeding Behavior ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Phenotype ; Phylogeny ; Species Specificity ; }, abstract = {There is increasing interest in the potential contribution of the gut microbiome to autism spectrum disorder (ASD). However, previous studies have been underpowered and have not been designed to address potential confounding factors in a comprehensive way. We performed a large autism stool metagenomics study (n = 247) based on participants from the Australian Autism Biobank and the Queensland Twin Adolescent Brain project. We found negligible direct associations between ASD diagnosis and the gut microbiome. Instead, our data support a model whereby ASD-related restricted interests are associated with less-diverse diet, and in turn reduced microbial taxonomic diversity and looser stool consistency. In contrast to ASD diagnosis, our dataset was well powered to detect microbiome associations with traits such as age, dietary intake, and stool consistency. Overall, microbiome differences in ASD may reflect dietary preferences that relate to diagnostic features, and we caution against claims that the microbiome has a driving role in ASD.}, } @article {pmid34767249, year = {2021}, author = {Schielzeth, H and Wolf, JBW}, title = {Community genomics: a community-wide perspective on within-species genetic diversity.}, journal = {American journal of botany}, volume = {108}, number = {11}, pages = {2108-2111}, doi = {10.1002/ajb2.1796}, pmid = {34767249}, issn = {1537-2197}, mesh = {*Biodiversity ; Ecosystem ; Genetic Variation ; *Metagenomics ; }, } @article {pmid34766210, year = {2022}, author = {Sanseverino, I and Pretto, P and António, DC and Lahm, A and Facca, C and Loos, R and Skejo, H and Beghi, A and Pandolfi, F and Genoni, P and Lettieri, T}, title = {Metagenomics Analysis to Investigate the Microbial Communities and Their Functional Profile During Cyanobacterial Blooms in Lake Varese.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {850-868}, pmid = {34766210}, issn = {1432-184X}, mesh = {*Cyanobacteria/genetics ; Eutrophication ; Humans ; Lakes/microbiology ; Metagenomics ; *Microbiota/genetics ; Water/analysis ; }, abstract = {Toxic cyanobacterial blooms represent a natural phenomenon caused by a mass proliferation of photosynthetic prokaryotic microorganisms in water environments. Bloom events have been increasingly reported worldwide and their occurrence can pose serious threats to aquatic organisms and human health. In this study, we assessed the microbial composition, with a focus on Cyanobacteria, in Lake Varese, a eutrophic lake located in northern Italy. Water samples were collected and used for obtaining a 16S-based taxonomic profile and performing a shotgun sequencing analysis. The phyla found to exhibit the greatest relative abundance in the lake included Proteobacteria, Cyanobacteria, Actinobacteriota and Bacteroidota. In the epilimnion and at 2.5 × Secchi depth, Cyanobacteria were found to be more abundant compared to the low levels detected at greater depths. The blooms appear to be dominated mainly by the species Lyngbya robusta, and a specific functional profile was identified, suggesting that distinct metabolic processes characterized the bacterial population along the water column. Finally, analysis of the shotgun data also indicated the presence of a large and diverse phage population.}, } @article {pmid34763917, year = {2022}, author = {Vasquez, A and Nydam, D and Foditsch, C and Warnick, L and Wolfe, C and Doster, E and Morley, PS}, title = {Characterization and comparison of the microbiomes and resistomes of colostrum from selectively treated dry cows.}, journal = {Journal of dairy science}, volume = {105}, number = {1}, pages = {637-653}, doi = {10.3168/jds.2021-20675}, pmid = {34763917}, issn = {1525-3198}, mesh = {Animals ; Anti-Bacterial Agents/therapeutic use ; Cattle ; *Cattle Diseases/drug therapy ; Colostrum ; Female ; Lactation ; Mammary Glands, Animal ; *Mastitis, Bovine/drug therapy ; *Microbiota ; Milk ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Professionals in animal agriculture promote prudent use of antimicrobials to address public and animal health concerns, such as reduction of antimicrobial residues and antimicrobial resistance (AMR) in products. Few studies evaluate the effect of selective dry-cow therapy on preservation of the milk microbiome or the profile of AMR genes (the resistome) present at freshening. Our objectives were to characterize and compare the microbiomes and resistomes in the colostrum of cows with low somatic cell count that were treated or not treated with intramammary cephapirin benzathine at dry-off. From a larger parent study, cows on a New York dairy farm eligible for dry-off and with histories of somatic cell counts ≤200,000 cells/mL were enrolled to this study (n = 307). Cows were randomly assigned to receive an intramammary antimicrobial and external teat sealant (ABXTS) or sealant only (TS) at dry-off. Composite colostrum samples taken within 4 h of freshening, and quarter milk samples taken at 1 to 7 d in milk were subjected to aerobic culture. The DNA extraction was performed on colostrum from cows with culture-negative samples (ABXTS = 43; TS = 33). The DNA from cows of the same treatment group and parity were pooled (26 pools; ABXTS = 12; TS = 14) for 16S rRNA metagenomic sequencing. Separately, the resistome was captured using a custom RNA bait library for target-enriched sequencing. Sequencing reads were aligned to taxonomic and AMR databases to characterize the microbiome and resistome, respectively. The R statistical program was used to tabulate abundances and to analyze differences in diversity measures and in composition between treatment groups. In the microbiome, the most abundant phyla were Firmicutes (68%), Proteobacteria (23%), Actinobacteria (4%), and Bacteroidetes (3%). Shannon and richness diversity means were 0.93 and 14.7 for ABXTS and 0.94 and 13.1 for TS, respectively. Using analysis of similarities (ANOSIM), overall microbiome composition was found to be similar between treatment groups at the phylum (ANOSIM R = 0.005), class (ANOSIM R = 0.04), and order (ANOSIM R = -0.04) levels. In the resistome, we identified AMR gene accessions associated with 14 unique mechanisms of resistance across 9 different drug classes in 14 samples (TS = 9, ABXTS = 5). The majority of reads aligned to gene accessions that confer resistance to aminoglycoside (TS = ABXTS each 35% abundance), tetracycline (TS = 22%, ABXTS = 54%), and β-lactam classes (TS = 15%, ABXTS = 12%). Shannon diversity means for AMR class and mechanism, respectively, were 0.66 and 0.69 for TS and 0.19 and 0.19 for ABXTS. Resistome richness diversity means for class and mechanism were 3.1 and 3.4 for TS and 1.4 and 1.4 for ABXTS. Finally, resistome composition was similar between groups at the class (ANOSIM R = -0.20) and mechanism levels (ANOSIM R = 0.01). Although no critical differences were found between treatment groups regarding their microbiome or resistome composition in this study, a larger sample size, deeper sequencing, and additional methodology is needed to identify more subtle differences, such as between lower-abundance features.}, } @article {pmid34763672, year = {2021}, author = {Najafi, S and Abedini, F and Azimzadeh Jamalkandi, S and Shariati, P and Ahmadi, A and Gholami Fesharaki, M}, title = {The composition of lung microbiome in lung cancer: a systematic review and meta-analysis.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {315}, pmid = {34763672}, issn = {1471-2180}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/genetics/growth & development/*isolation & purification ; DNA, Bacterial/genetics ; Female ; Humans ; Lung/*microbiology ; Lung Neoplasms/*microbiology ; Male ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Although recent studies have indicated that imbalance in the respiratory microbiome composition is linked to several chronic respiratory diseases, the association between the lung microbiome and lung cancer has not been extensively studied. Conflicting reports of individual studies on respiratory microbiome alterations in lung cancer complicate the matter for specifying how the lung microbiome is linked to lung cancer. Consequently, as the first meta-analysis on this topic, we integrate publicly available 16S rRNA gene sequence data on lung tissue samples of lung cancer patients to identify bacterial taxa which differ consistently between case and control groups.

RESULTS: The findings of the current study suggest that the relative abundance of several bacterial taxa including Actinobacteria phylum, Corynebacteriaceae and Halomonadaceae families, and Corynebacterium, Lachnoanaerobaculum, and Halomonas genera is significantly decreased (p < 0.05) in lung tumor tissues of lung cancer patients in comparison with tumor-adjacent normal tissues.

CONCLUSIONS: Despite the underlying need for scrutinizing the findings further, the present study lays the groundwork for future research and adds to our limited understanding of the key role of the lung microbiome and its complex interaction with lung cancer. More data on demographic factors and tumor tissue types would help establish a greater degree of accuracy in characterizing the lung microbial community which accords with subtypes and stages of the disease and fully capturing the changes of the lung microbiome in lung cancer.}, } @article {pmid34763597, year = {2021}, author = {Nalpas, N and Hoyles, L and Anselm, V and Ganief, T and Martinez-Gili, L and Grau, C and Droste-Borel, I and Davidovic, L and Altafaj, X and Dumas, ME and Macek, B}, title = {An integrated workflow for enhanced taxonomic and functional coverage of the mouse fecal metaproteome.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1994836}, pmid = {34763597}, issn = {1949-0984}, support = {MR/L01632X/1/MRC_/Medical Research Council/United Kingdom ; MR/M501797/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Bacterial Proteins/*chemistry/genetics/metabolism ; Cohort Studies ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Male ; Mass Spectrometry ; Metagenome ; Mice ; Proteomics ; Workflow ; }, abstract = {Intestinal microbiota plays a key role in shaping host homeostasis by regulating metabolism, immune responses and behavior. Its dysregulation has been associated with metabolic, immune and neuropsychiatric disorders and is accompanied by changes in bacterial metabolic regulation. Although proteomics is well suited for analysis of individual microbes, metaproteomics of fecal samples is challenging due to the physical structure of the sample, presence of contaminating host proteins and coexistence of hundreds of taxa. Furthermore, there is a lack of consensus regarding preparation of fecal samples, as well as downstream bioinformatic analyses following metaproteomics data acquisition. Here we assess sample preparation and data analysis strategies applied to mouse feces in a typical mass spectrometry-based metaproteomic experiment. We show that subtle changes in sample preparation protocols may influence interpretation of biological findings. Two-step database search strategies led to significant underestimation of false positive protein identifications. Unipept software provided the highest sensitivity and specificity in taxonomic annotation of the identified peptides of unknown origin. Comparison of matching metaproteome and metagenome data revealed a positive correlation between protein and gene abundances. Notably, nearly all functional categories of detected protein groups were differentially abundant in the metaproteome compared to what would be expected from the metagenome, highlighting the need to perform metaproteomics when studying complex microbiome samples.}, } @article {pmid34763361, year = {2021}, author = {Deka, N and Hassan, S and Seghal Kiran, G and Selvin, J}, title = {Insights into the role of vaginal microbiome in women's health.}, journal = {Journal of basic microbiology}, volume = {61}, number = {12}, pages = {1071-1084}, doi = {10.1002/jobm.202100421}, pmid = {34763361}, issn = {1521-4028}, mesh = {Dysbiosis ; Female ; Humans ; *Microbiota ; Vagina ; *Vaginosis, Bacterial ; Women's Health ; }, abstract = {The vaginal microbiome is a complex and dynamic microecosystem that fluctuates continually throughout a woman's life. Lactobacillus, a bacterium that possesses antibacterial properties dominates a healthy vaginal microbiome. Bacterial vaginosis is the most common vaginal disorder that has been linked with the dysbiosis of normal vaginal microbiota. Despite the importance of vaginal microbiome, little is known about functions it performs especially, how it helps in protecting the female reproductive tract. This knowledge gap is a significant impediment to the development of effective and feasible clinical treatments that might be required to improve women's health. Thus, a deeper understanding of the functional aspects and not just the composition of vaginal microbiome may aid in improving the diagnostics and treatment strategies. Recent advancement in molecular methods and computational biology have allowed researchers to acquire more knowledge about the vaginal microbiome. The use of metagenomics (culture-independent high-throughput technology) and bioinformatics tools have improved our understanding of the vaginal microbiome. In this review, we have attempted to explore the factors that may alter normal vaginal microbiota homeostasis such as age, sexual behavior, ethnicity, and hygiene, and so forth. We also discuss the role of probiotics in restoring healthy vaginal microbiome.}, } @article {pmid34763180, year = {2021}, author = {Liang, G and Cobián-Güemes, AG and Albenberg, L and Bushman, F}, title = {The gut virome in inflammatory bowel diseases.}, journal = {Current opinion in virology}, volume = {51}, number = {}, pages = {190-198}, doi = {10.1016/j.coviro.2021.10.005}, pmid = {34763180}, issn = {1879-6265}, support = {R61 HL137063/HL/NHLBI NIH HHS/United States ; R01 HL113252/HL/NHLBI NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Humans ; Inflammatory Bowel Diseases/*virology ; *Metagenomics ; Virome/*genetics ; Viruses/*genetics/*isolation & purification ; }, abstract = {Dysbiosis of the microbiome has been extensively studied in inflammatory bowel diseases (IBD). The roles of bacteria and fungi have been studied in detail, but viral communities, an important component of the microbiome, have been less thoroughly investigated. Metagenomics provided a way to fill this gap by using DNA sequencing to enumerate all viruses in a sample, termed the 'virome'. Such methods have now been employed in several studies to assess associations between viral communities and IBD, yielding several commonly seen properties, including an increase in tailed bacteriophage (Caudovirales) and a decrease in the spherical Microviridae. Numerous studies of single human viruses have been carried out, but no one virus has emerged as tightly associated, focusing attention on whole virome communities and further factors. This review provides an overview of research on the human virome in IBD, with emphasis on (1) dynamics of the gut virome, (2) candidate mechanisms of virome alterations with disease, (3) methods for studying the virome, and (4) potentially actionable implications of virome data.}, } @article {pmid34763095, year = {2022}, author = {Levi Mortera, S and Vernocchi, P and Basadonne, I and Zandonà, A and Chierici, M and Durighello, M and Marzano, V and Gardini, S and Gasbarrini, A and Urbani, A and Vicari, S and Roncada, P and Furlanello, C and Venuti, P and Putignani, L}, title = {A metaproteomic-based gut microbiota profiling in children affected by autism spectrum disorders.}, journal = {Journal of proteomics}, volume = {251}, number = {}, pages = {104407}, doi = {10.1016/j.jprot.2021.104407}, pmid = {34763095}, issn = {1876-7737}, mesh = {Aged ; *Autism Spectrum Disorder/complications/metabolism ; Child ; Chromatography, Liquid ; *Gastrointestinal Microbiome/physiology ; Humans ; RNA, Ribosomal, 16S/genetics ; Tandem Mass Spectrometry ; }, abstract = {During the last decade, the evidences on the relationship between neurodevelopmental disorders and the microbial communities of the intestinal tract have considerably grown. Particularly, the role of gut microbiota (GM) ecology and predicted functions in Autism Spectrum Disorders (ASD) has been especially investigated by 16S rRNA targeted and shotgun metagenomics, trying to assess disease signature and their correlation with cognitive impairment or gastrointestinal (GI) manifestations of the disease. Herein we present a metaproteomic approach to point out the microbial gene expression profiles, their functional annotations, and the taxonomic distribution of gut microbial communities in ASD children. We pursued a LC-MS/MS based investigation, to compare the GM profiles of patients with those of their respective relatives and aged-matched controls, providing a quantitative evaluation of bacterial metaproteins by SWATH analysis. All data were managed by a multiple step bioinformatic pipeline, including network analysis. In particular, comparing ASD subjects with CTRLs, up-regulation was found for some metaproteins associated with Clostridia and with carbohydrate metabolism (glyceraldehyde-3-phosphate and glutamate dehydrogenases), while down-regulation was observed for others associated with Bacteroidia (SusC and SusD family together with the TonB dependent receptor). Moreover, network analysis highlighted specific microbial correlations among ASD subgroups characterized by different functioning levels and GI symptoms. SIGNIFICANCE: To the best of our knowledge, this study represents the first metaproteomic investigation on the gut microbiota of ASD children compared with relatives and age-matched CTRLs. Remarkably, the applied SWATH methodology allowed the attribution of differentially regulated functions to specific microbial taxa, offering a novel and complementary point of view with respect to previous studies.}, } @article {pmid34760716, year = {2021}, author = {Xie, J and Cho, H and Lin, BM and Pillai, M and Heimisdottir, LH and Bandyopadhyay, D and Zou, F and Roach, J and Divaris, K and Wu, D}, title = {Improved Metabolite Prediction Using Microbiome Data-Based Elastic Net Models.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {734416}, pmid = {34760716}, issn = {2235-2988}, support = {R03 DE028983/DE/NIDCR NIH HHS/United States ; T15 LM012500/LM/NLM NIH HHS/United States ; P30 CA016059/CA/NCI NIH HHS/United States ; U01 DE025046/DE/NIDCR NIH HHS/United States ; }, mesh = {Child ; Child, Preschool ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolome ; Metabolomics ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Microbiome data are becoming increasingly available in large health cohorts, yet metabolomics data are still scant. While many studies generate microbiome data, they lack matched metabolomics data or have considerable missing proportions of metabolites. Since metabolomics is key to understanding microbial and general biological activities, the possibility of imputing individual metabolites or inferring metabolomics pathways from microbial taxonomy or metagenomics is intriguing. Importantly, current metabolomics profiling methods such as the HMP Unified Metabolic Analysis Network (HUMAnN) have unknown accuracy and are limited in their ability to predict individual metabolites. To address this gap, we developed a novel metabolite prediction method, and we present its application and evaluation in an oral microbiome study. The new method for predicting metabolites using microbiome data (ENVIM) is based on the elastic net model (ENM). ENVIM introduces an extra step to ENM to consider variable importance (VI) scores, and thus, achieves better prediction power. We investigate the metabolite prediction performance of ENVIM using metagenomic and metatranscriptomic data in a supragingival biofilm multi-omics dataset of 289 children ages 3-5 who were participants of a community-based study of early childhood oral health (ZOE 2.0) in North Carolina, United States. We further validate ENVIM in two additional publicly available multi-omics datasets generated from studies of gut health. We select gene family sets based on variable importance scores and modify the existing ENM strategy used in the MelonnPan prediction software to accommodate the unique features of microbiome and metabolome data. We evaluate metagenomic and metatranscriptomic predictors and compare the prediction performance of ENVIM to the standard ENM employed in MelonnPan. The newly developed ENVIM method showed superior metabolite predictive accuracy than MelonnPan when trained with metatranscriptomics data only, metagenomics data only, or both. Better metabolite prediction is achieved in the gut microbiome compared with the oral microbiome setting. We report the best-predictable compounds in all these three datasets from two different body sites. For example, the metabolites trehalose, maltose, stachyose, and ribose are all well predicted by the supragingival microbiome.}, } @article {pmid34759297, year = {2021}, author = {Latorre-Pérez, A and Hernández, M and Iglesias, JR and Morán, J and Pascual, J and Porcar, M and Vilanova, C and Collado, L}, title = {The Spanish gut microbiome reveals links between microorganisms and Mediterranean diet.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {21602}, pmid = {34759297}, issn = {2045-2322}, support = {DI-17-09613//Spanish Ministerio de Ciencia, Innovación y Universidades/ ; }, mesh = {Adolescent ; Adult ; Aged ; Bacteria/genetics ; Child ; Diet ; *Diet, Mediterranean ; Ecosystem ; Feces/microbiology ; Feeding Behavior ; Female ; *Gastrointestinal Microbiome ; Genomics ; Geography ; Healthy Volunteers ; Humans ; Life Style ; Male ; Middle Aged ; RNA, Ribosomal, 16S/*metabolism ; Spain ; Young Adult ; }, abstract = {Despite the increasing evidence of links between human gut and health, the number of gut microbiomes that have been studied to date at a country level are surprisingly low. Mediterranean countries, including some of the most long-lived and healthy countries in the world, have not been considered so far in those studies at a large scale. The main objective of this work is to characterize the gut microbiome of a healthy adult population of a Mediterranean, paradigmatically healthy country: Spain. Stool samples from 530 healthy volunteers were collected, total metagenomic DNA extracted, and the microbial profiles determined through 16S rRNA metataxonomic sequencing. Our results confirm the associations between several microbial markers and different variables, including sex, age, BMI and diet choices, and bring new insights into the relationship between microbiome and diet in the Spanish population. Remarkably, some of the associations found, such as the decrease of Faecalibacterium with age or the link of Flavonifractor with less healthy dietary habits, have been barely noticed in other large-scale cohorts. On the other hand, a range of links between microorganisms, diet, and lifestyle coincide with those reported in other populations, thus increasing the robustness of such associations and confirming the importance of these microbial markers across different countries. Overall, this study describes the Spanish "normal" microbiome, providing a solid baseline for future studies investigating the effects of gut microbiome composition and deviations in the adherence to the Mediterranean diet.}, } @article {pmid34758191, year = {2022}, author = {Briscoe, AG and Nichols, S and Hartikainen, H and Knipe, H and Foster, R and Green, AJ and Okamura, B and Bass, D}, title = {High-throughput sequencing of faeces provides evidence for dispersal of parasites and pathogens by migratory waterbirds.}, journal = {Molecular ecology resources}, volume = {22}, number = {4}, pages = {1303-1318}, doi = {10.1111/1755-0998.13548}, pmid = {34758191}, issn = {1755-0998}, support = {//NHM Disease Initiative/ ; CGL2016-76067-P//Spanish National Plan project/ ; //NHM Life Sciences Departmental Investment Fund/ ; FC1215//Department for Environment, Food and Rural Affairs/ ; }, mesh = {Animals ; Feces/parasitology ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; *Parasites/genetics ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Examination of faecal material has demonstrated how a broad range of organisms are distributed by bird movements. Such research has largely focused on dispersal of plant seeds by frugivores and of freshwater organisms by waterbirds. However, with few exceptions (e.g. avian influenza, Ebola virus), there is a dearth of evidence for transport of parasites and pathogens. High-throughput sequencing methods now provide a powerful means of addressing this knowledge gap by elucidating faecal contents in unprecedented detail. We collected faeces excreted by a range of migratory waterbirds in south-west Spain and pooled faecal DNA to create libraries reflective of feeding behavior. We created sets of libraries using high-throughput metagenomic and amplicon sequencing. For the latter we employed two sets of primers to broadly target the V4 region of the 18S rRNA gene (one set amplifying the region across all eukaryotes, the other excluding amplification of metazoans). Libraries revealed a wide diversity of eukaryotes, including parasites of the faecal producers themselves, parasites of food items, or those incidentally ingested. We also detected novel microbial eukaryotic taxa and found that parasite assemblage profiles were relatively distinct. Comparing the performance of the methods used supports their joint use for future studies of diversity and abundance. Because viable stages of many parasites are likely to be present in faeces, our results suggest significant levels of bird-mediated dispersal of parasites (both from avian and other hosts). Our methods revealed much hidden biodiversity, and allowed identification of the individuals who produced the faecal samples to species level, facilitating the study of interaction networks.}, } @article {pmid34758050, year = {2021}, author = {Alkema, W and Boekhorst, J and Eijlander, RT and Schnittger, S and De Gruyter, F and Lukovac, S and Schilling, K and Kortman, GAM}, title = {Charting host-microbe co-metabolism in skin aging and application to metagenomics data.}, journal = {PloS one}, volume = {16}, number = {11}, pages = {e0258960}, pmid = {34758050}, issn = {1932-6203}, mesh = {Adult ; Aged ; Bacteria/genetics/metabolism ; Ceramides/metabolism ; Fatty Acids/metabolism ; Female ; Genes, Bacterial ; Healthy Volunteers ; Host Microbial Interactions/genetics ; Humans ; Markov Chains ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Signal Transduction/genetics ; Skin/metabolism/*microbiology ; Skin Aging/*genetics ; Skin Pigmentation/genetics ; }, abstract = {During aging of human skin, a number of intrinsic and extrinsic factors cause the alteration of the skin's structure, function and cutaneous physiology. Many studies have investigated the influence of the skin microbiome on these alterations, but the molecular mechanisms that dictate the interplay between these factors and the skin microbiome are still not fully understood. To obtain more insight into the connection between the skin microbiome and the human physiological processes involved in skin aging, we performed a systematic study on interconnected pathways of human and bacterial metabolic processes that are known to play a role in skin aging. The bacterial genes in these pathways were subsequently used to create Hidden Markov Models (HMMs), which were applied to screen for presence of defined functionalities in both genomic and metagenomic datasets of skin-associated bacteria. These models were further applied on 16S rRNA gene sequencing data from skin microbiota samples derived from female volunteers of two different age groups (25-28 years ('young') and 59-68 years ('old')). The results show that the main bacterial pathways associated with aging skin are those involved in the production of pigmentation intermediates, fatty acids and ceramides. This study furthermore provides evidence for a relation between skin aging and bacterial enzymes involved in protein glycation. Taken together, the results and insights described in this paper provide new leads for intervening with bacterial processes that are associated with aging of human skin.}, } @article {pmid34756979, year = {2022}, author = {Liu, L and Wang, F and Xu, S and Yan, Z and Ji, M}, title = {Long-term effect of fulvic acid amendment on the anammox biofilm system at 15 ℃: performance, microbial community and metagenomics analysis.}, journal = {Bioresource technology}, volume = {344}, number = {Pt B}, pages = {126234}, doi = {10.1016/j.biortech.2021.126234}, pmid = {34756979}, issn = {1873-2976}, mesh = {Anaerobic Ammonia Oxidation ; Anaerobiosis ; Benzopyrans ; Biofilms ; Bioreactors ; *Metagenomics ; *Microbiota ; Nitrogen ; Oxidation-Reduction ; }, abstract = {The role of fulvic acid (FA) on the anammox system at 15 ℃ was investigated. After operation for 113 days, total inorganic nitrogen removal efficiency in FA amendment reactor achieved to 58.6% on average, higher than that of control group (42.1%). Anammox-related functional genes, i.e., hzo and hzs, also demonstrated higher expression level after introduction of FA. It was observed that Candidatus Kuenenia became more competitive than Candidatus Brocadia with the existence of FA at 15 ℃. Also, co-occurrence analysis showed that FA stimulated the complexity and interactive relationship of microbial communities in the anammox system. Metagenomics analysis revealed that FA introduction stimulated relative abundances of genes in central pathway of tricarboxylic acid cycle such as ACO, IDH, OGDH, SCS, FUM, and MDH. Meanwhile, metabolomics analysis revealed that metabolites related to amino sugar metabolic pathways (glucose 1-phosphate, UDP-D-glucuronate, UDP) and redox reactions (NAD[+] and NADH) improved in the FA amendment reactor.}, } @article {pmid34756812, year = {2021}, author = {Uddin, TM and Chakraborty, AJ and Khusro, A and Zidan, BRM and Mitra, S and Emran, TB and Dhama, K and Ripon, MKH and Gajdács, M and Sahibzada, MUK and Hossain, MJ and Koirala, N}, title = {Antibiotic resistance in microbes: History, mechanisms, therapeutic strategies and future prospects.}, journal = {Journal of infection and public health}, volume = {14}, number = {12}, pages = {1750-1766}, doi = {10.1016/j.jiph.2021.10.020}, pmid = {34756812}, issn = {1876-035X}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria ; *Bacterial Infections/drug therapy ; Biofilms ; *Drug Resistance, Multiple, Bacterial ; Humans ; }, abstract = {Antibiotics have been used to cure bacterial infections for more than 70 years, and these low-molecular-weight bioactive agents have also been used for a variety of other medicinal applications. In the battle against microbes, antibiotics have certainly been a blessing to human civilization by saving millions of lives. Globally, infections caused by multidrug-resistant (MDR) bacteria are on the rise. Antibiotics are being used to combat diversified bacterial infections. Synthetic biology techniques, in combination with molecular, functional genomic, and metagenomic studies of bacteria, plants, and even marine invertebrates are aimed at unlocking the world's natural products faster than previous methods of antibiotic discovery. There are currently only few viable remedies, potential preventive techniques, and a limited number of antibiotics, thereby necessitating the discovery of innovative medicinal approaches and antimicrobial therapies. MDR is also facilitated by biofilms, which makes infection control more complex. In this review, we have spotlighted comprehensively various aspects of antibiotics viz. overview of antibiotics era, mode of actions of antibiotics, development and mechanisms of antibiotic resistance in bacteria, and future strategies to fight the emerging antimicrobial resistant threat.}, } @article {pmid34756056, year = {2021}, author = {Binia, A and Siegwald, L and Sultana, S and Shevlyakova, M and Lefebvre, G and Foata, F and Combremont, S and Charpagne, A and Vidal, K and Sprenger, N and Rahman, M and Palleja, A and Eklund, AC and Nielsen, HB and Brüssow, H and Sarker, SA and Sakwinska, O}, title = {The Influence of FUT2 and FUT3 Polymorphisms and Nasopharyngeal Microbiome on Respiratory Infections in Breastfed Bangladeshi Infants from the Microbiota and Health Study.}, journal = {mSphere}, volume = {6}, number = {6}, pages = {e0068621}, pmid = {34756056}, issn = {2379-5042}, mesh = {Bacteria/*classification/growth & development ; Bangladesh ; *Breast Feeding ; Female ; Fucosyltransferases/*metabolism ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Milk, Human/*metabolism ; Mothers ; Respiratory Tract Infections/microbiology ; Galactoside 2-alpha-L-fucosyltransferase ; }, abstract = {Acute respiratory infections (ARIs) are one of the most common causes of morbidity and mortality in young children. The aim of our study was to examine whether variation in maternal FUT2 (α1,2-fucosyltransferase 2) and FUT3 (α1,3/4-fucosyltransferase 3) genes, which shape fucosylated human milk oligosaccharides (HMOs) in breast milk, are associated with the occurrence of ARIs in breastfed infants as well as the influence of the nasopharyngeal microbiome on ARI risk. Occurrences of ARIs were prospectively recorded in a cohort of 240 breastfed Bangladeshi infants from birth to 2 years. Secretor and Lewis status was established by sequencing of FUT2/3 genes. The nasopharyngeal microbiome was characterized by shotgun metagenomics, complemented by specific detection of respiratory pathogens; 88.6% of mothers and 91% of infants were identified as secretors. Maternal secretor status was associated with reduced ARI incidence among these infants in the period from birth to 6 months (incidence rate ratio [IRR], 0.66; 95% confidence interval [CI], 0.47 to 0.94; P = 0.020), but not at later time periods. The nasopharyngeal microbiome, despite precise characterization to the species level, was not predictive of subsequent ARIs. The observed risk reduction of ARIs among infants of secretor mothers during the predominant breastfeeding period is consistent with the hypothesis that fucosylated oligosaccharides in human milk contribute to protection against respiratory infections. However, we found no evidence that modulation of the nasopharyngeal microbiome influenced ARI risk. IMPORTANCE The observed risk reduction of acute respiratory infections (ARIs) among infants of secretor mothers during the predominant breastfeeding period is consistent with the hypothesis that fucosylated oligosaccharides in human milk contribute to protection against respiratory infections. Respiratory pathogens were only weak modulators of risk, and the nasopharyngeal microbiome did not influence ARI risk, suggesting that the associated protective effects of human milk oligosaccharides (HMOs) are not conveyed via changes in the nasopharyngeal microbiome. Our observations add to the evidence for a role of fucosylated HMOs in protection against respiratory infections in exclusively or predominantly breastfed infants in low-resource settings. There is no indication that the nasopharyngeal microbiome substantially modulates the risk of subsequent mild ARIs. Larger studies are needed to provide mechanistic insights on links between secretor status, HMOs, and risk of respiratory infections.}, } @article {pmid34752719, year = {2022}, author = {Scherz, V and Greub, G and Bertelli, C}, title = {Building up a clinical microbiota profiling: a quality framework proposal.}, journal = {Critical reviews in microbiology}, volume = {48}, number = {3}, pages = {356-375}, doi = {10.1080/1040841X.2021.1975642}, pmid = {34752719}, issn = {1549-7828}, mesh = {Humans ; *Metagenomics/methods ; *Microbiota ; Reproducibility of Results ; }, abstract = {Extensive characterization of the human microbiota has revealed promising relationships between microbial composition and health or disease, generating interest in biomarkers derived from microbiota profiling. However, microbiota complexity and technical challenges strongly influencing the results limit the generalization of microbiota profiling and question its clinical utility. In addition, no quality management scheme has been adapted to the specificities of microbiota profiling, notably due to the heterogeneity in methods and results. In this review, we discuss possible adaptation of classical quality management tools routinely used in diagnostic laboratories to microbiota profiling and propose a specific framework. Multiple quality controls are needed to cover all steps, from sampling to data processing. Standard operating procedures, primarily developed for wet lab analyses, must be adapted to the use of bioinformatic tools. Finally, requirements for test validation and proficiency testing must take into account expected discrepancies in results due to the heterogeneity of the processes. The proposed quality management framework should support the implementation of routine microbiota profiling by clinical laboratories to support patient care. Furthermore, its use in research laboratories would improve publication reproducibility as well as transferability of methods and results to routine practice.}, } @article {pmid34750528, year = {2022}, author = {Han, L and Zhao, L and Zhou, Y and Yang, C and Xiong, T and Lu, L and Deng, Y and Luo, W and Chen, Y and Qiu, Q and Shang, X and Huang, L and Mo, Z and Huang, S and Huang, S and Liu, Z and Yang, W and Zhai, L and Ning, Z and Lin, C and Huang, T and Cheng, C and Zhong, LLD and Li, S and Bian, Z and Fang, X}, title = {Altered metabolome and microbiome features provide clues in understanding irritable bowel syndrome and depression comorbidity.}, journal = {The ISME journal}, volume = {16}, number = {4}, pages = {983-996}, pmid = {34750528}, issn = {1751-7370}, mesh = {Comorbidity ; Depression ; Feces/microbiology ; Humans ; *Irritable Bowel Syndrome/complications/diagnosis/metabolism ; Metabolome ; *Microbiota ; Tryptophan/metabolism ; }, abstract = {Irritable bowel syndrome (IBS) is one of the functional gastrointestinal disorders characterized by chronic and/or recurrent symptoms of abdominal pain and irregular defecation. Changed gut microbiota has been proposed to mediate IBS; however, contradictory results exist, and IBS-specific microbiota, metabolites, and their interactions remain poorly understood. To address this issue, we performed metabolomic and metagenomic profiling of stool and serum samples based on discovery (n = 330) and validation (n = 101) cohorts. Fecal metagenomic data showed moderate dysbiosis compared with other diseases, in contrast, serum metabolites showed significant differences with greater power to distinguish IBS patients from healthy controls. Specifically, 726 differentially abundant serum metabolites were identified, including a cluster of fatty acyl-CoAs enriched in IBS. We further identified 522 robust associations between differentially abundant gut bacteria and fecal metabolites, of which three species including Odoribacter splanchnicus, Escherichia coli, and Ruminococcus gnavus were strongly associated with the low abundance of dihydropteroic acid. Moreover, dysregulated tryptophan/serotonin metabolism was found to be correlated with the severity of IBS depression in both fecal and serum metabolomes, characterized by a shift in tryptophan metabolism towards kynurenine production. Collectively, our study revealed serum/fecal metabolome alterations and their relationship with gut microbiome, highlighted the massive alterations of serum metabolites, which empower to recognize IBS patients, suggested potential roles of metabolic dysregulation in IBS pathogenesis, and offered new clues to understand IBS depression comorbidity. Our study provided a valuable resource for future studies, and would facilitate potential clinical applications of IBS featured microbiota and/or metabolites.}, } @article {pmid34748542, year = {2021}, author = {Robeson, MS and O'Rourke, DR and Kaehler, BD and Ziemski, M and Dillon, MR and Foster, JT and Bokulich, NA}, title = {RESCRIPt: Reproducible sequence taxonomy reference database management.}, journal = {PLoS computational biology}, volume = {17}, number = {11}, pages = {e1009581}, pmid = {34748542}, issn = {1553-7358}, mesh = {Animals ; Classification ; Computational Biology ; DNA Barcoding, Taxonomic ; *Database Management Systems ; Databases, Genetic/*statistics & numerical data ; Databases, Nucleic Acid ; Genomics ; Humans ; Metagenome ; Metagenomics ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis ; *Software ; }, abstract = {Nucleotide sequence and taxonomy reference databases are critical resources for widespread applications including marker-gene and metagenome sequencing for microbiome analysis, diet metabarcoding, and environmental DNA (eDNA) surveys. Reproducibly generating, managing, using, and evaluating nucleotide sequence and taxonomy reference databases creates a significant bottleneck for researchers aiming to generate custom sequence databases. Furthermore, database composition drastically influences results, and lack of standardization limits cross-study comparisons. To address these challenges, we developed RESCRIPt, a Python 3 software package and QIIME 2 plugin for reproducible generation and management of reference sequence taxonomy databases, including dedicated functions that streamline creating databases from popular sources, and functions for evaluating, comparing, and interactively exploring qualitative and quantitative characteristics across reference databases. To highlight the breadth and capabilities of RESCRIPt, we provide several examples for working with popular databases for microbiome profiling (SILVA, Greengenes, NCBI-RefSeq, GTDB), eDNA and diet metabarcoding surveys (BOLD, GenBank), as well as for genome comparison. We show that bigger is not always better, and reference databases with standardized taxonomies and those that focus on type strains have quantitative advantages, though may not be appropriate for all use cases. Most databases appear to benefit from some curation (quality filtering), though sequence clustering appears detrimental to database quality. Finally, we demonstrate the breadth and extensibility of RESCRIPt for reproducible workflows with a comparison of global hepatitis genomes. RESCRIPt provides tools to democratize the process of reference database acquisition and management, enabling researchers to reproducibly and transparently create reference materials for diverse research applications. RESCRIPt is released under a permissive BSD-3 license at https://github.com/bokulich-lab/RESCRIPt.}, } @article {pmid34747693, year = {2021}, author = {Yang, W and Lin, YC and Johnson, W and Dai, N and Vaisvila, R and Weigele, P and Lee, YJ and Corrêa, IR and Schildkraut, I and Ettwiller, L}, title = {A genome-phenome association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34747693}, issn = {2050-084X}, mesh = {Cytosine/*metabolism ; DNA, Bacterial/*metabolism ; Escherichia coli K12/*genetics ; *Genome, Bacterial ; Microbiota/*genetics ; RNA, Bacterial/*metabolism ; }, abstract = {Shotgun metagenomic sequencing is a powerful approach to study microbiomes in an unbiased manner and of increasing relevance for identifying novel enzymatic functions. However, the potential of metagenomics to relate from microbiome composition to function has thus far been underutilized. Here, we introduce the Metagenomics Genome-Phenome Association (MetaGPA) study framework, which allows linking genetic information in metagenomes with a dedicated functional phenotype. We applied MetaGPA to identify enzymes associated with cytosine modifications in environmental samples. From the 2365 genes that met our significance criteria, we confirm known pathways for cytosine modifications and proposed novel cytosine-modifying mechanisms. Specifically, we characterized and identified a novel nucleic acid-modifying enzyme, 5-hydroxymethylcytosine carbamoyltransferase, that catalyzes the formation of a previously unknown cytosine modification, 5-carbamoyloxymethylcytosine, in DNA and RNA. Our work introduces MetaGPA as a novel and versatile tool for advancing functional metagenomics.}, } @article {pmid34747331, year = {2021}, author = {Shen, TD and Daniel, SG and Patel, S and Kaplan, E and Phung, L and Lemelle-Thomas, K and Chau, L and Herman, L and Trisolini, C and Stonelake, A and Toal, E and Khungar, V and Bittinger, K and Reddy, KR and Wu, GD}, title = {The Mucosally-Adherent Rectal Microbiota Contains Features Unique to Alcohol-Related Cirrhosis.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1987781}, pmid = {34747331}, issn = {1949-0984}, support = {K08 DK106457/DK/NIDDK NIH HHS/United States ; P30 DK050306/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/genetics/*isolation & purification ; *Bacterial Adhesion ; Bacterial Physiological Phenomena ; Cross-Sectional Studies ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/microbiology ; Liver Cirrhosis, Alcoholic/*microbiology ; Male ; Middle Aged ; Rectum/*microbiology ; Young Adult ; }, abstract = {Most studies examining correlations between the gut microbiota and disease states focus on fecal samples due to ease of collection, yet there are distinct differences when compared to samples collected from the colonic mucosa. Although fecal microbiota has been reported to be altered in cirrhosis, correlation with mucosal microbiota characterized via rectal swab has not been previously described in this patient population. We conducted a cross-sectional analysis using 39 stool and 39 rectal swabs from adult patients with cirrhosis of different etiologies and performed shotgun metagenomic sequencing. Bacterial growth studies were performed with Escherichia coli. Two asaccharolytic bacterial taxa, Finegoldia magna and Porphyromonas asaccharolytica, were increased in rectal swabs relative to stool (FDR < 0.01). Genomic analysis of the microbiome revealed 58 genes and 16 pathways that differed between stool and rectal swabs (FDR < 0.05), where rectal swabs were enriched for pathways associated with protein synthesis and cellular proliferation but decreased in carbohydrate metabolism. Although no features in the fecal microbiome differentiated cirrhosis etiologies, the mucosal microbiome revealed decreased abundances of E. coli and Enterobacteriaceae in alcohol-related cirrhosis relative to non-alcohol related cirrhosis (FDR < 0.05). In vitro bacterial culture studies showed that physiological concentrations of ethanol and its oxidative metabolites inhibited E. coli growth in a pH- and concentration-dependent manner. Characterization of the mucosally associated gut microbiome via rectal swab revealed findings consistent with amino acid/nitrogen abundance versus carbohydrate limitation in the mucosal microenvironment as well as unique features of alcohol-related cirrhosis possibly consistent with the influence of host-derived metabolites on the composition of mucosally adherent microbiota.}, } @article {pmid34745150, year = {2021}, author = {Zhu, L and Wu, Y and Lin, C and Tang, L and Yu, B and Wan, W and Xuan, J and Du, Y and Chen, Z and Liang, W}, title = {Dynamic Microbial Shifts and Signatures of Long-Term Remission in Allergic Rhinitis After an Herbal Formula Treatment.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {774966}, pmid = {34745150}, issn = {1664-3224}, mesh = {Adolescent ; Adult ; Biomarkers ; Disease Management ; Disease Susceptibility ; Drugs, Chinese Herbal/*adverse effects/therapeutic use ; Dysbiosis/*diagnosis/*etiology ; Female ; Follow-Up Studies ; Gastrointestinal Microbiome/drug effects ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; RNA, Ribosomal, 16S ; Rhinitis, Allergic/*complications/drug therapy ; Young Adult ; }, abstract = {A mixed Chinese herbal formula, Xiao-Qing-Long-Decoction (XQLD), may contribute to sustained remission in allergic rhinitis (AR), but it is unknown which factors determine such long-term effect. Here, we aimed to identify bacterial signatures associated with sustained remission. To this end, samples from AR patients at four different times were analyzed to compare the dynamic bacterial community and structure shifts. Diversity indices Chao1 showed significant difference across different time (p<0.05), and the Kruskal-Wallis test identified that Dialister (OTU_31), Roseburia (OTU_36), Bacteroides (OTU_22), Bacteroides (OTU_2040), and Prevotella_9 (OTU_5) were the significant differential bacterial taxa (p<0.05). These distinctive genera were significantly associated with the change of AR clinical indices and the predicted functional pathways such as PPAR signaling pathway, peroxisome, and citrate cycle (TCA cycle) (p<0.05), indicating that they may be important bacterial signatures involving in the sustained remission in AR (p<0.05). Besides, lower Firmicutes/Bacteroidetes (F/B) ratio at 6 months follow-up may also contribute to the long-term remission of AR. No seriously adverse events and safety concerns were observed in this study. In conclusion, XQLD is a meaningful, long-term efficient and safe medication for AR treatment. The underlying mechanisms of sustained remission in AR after XQLD treatment may be associated with the dynamic alteration of featured gut bacteria taxa.}, } @article {pmid34745012, year = {2021}, author = {Jia, R and Huang, M and Qian, L and Yan, X and Lv, Q and Ye, H and Ye, L and Wu, X and Chen, W and Chen, Y and Jia, Y and Huang, Y and Wu, H}, title = {The Depletion of Carbohydrate Metabolic Genes in the Gut Microbiome Contributes to the Transition From Central Obesity to Type 2 Diabetes.}, journal = {Frontiers in endocrinology}, volume = {12}, number = {}, pages = {747646}, pmid = {34745012}, issn = {1664-2392}, mesh = {Adult ; Biomarkers/metabolism ; Carbohydrate Metabolism/*genetics ; Case-Control Studies ; China ; Diabetes Mellitus, Type 2/*etiology/genetics/metabolism/microbiology ; Disease Progression ; Disease Susceptibility ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metagenome/physiology ; Obesity, Abdominal/genetics/metabolism/*microbiology/pathology ; RNA, Ribosomal, 16S/analysis/genetics ; Risk Factors ; Transcriptome ; }, abstract = {Obesity, especially central obesity, is a strong risk factor for developing type 2 diabetes (T2D). However, the mechanism underlying the progression from central obesity to T2D remains unknown. Therefore, we analyzed the gut microbial profiles of central obese individuals with or without T2D from a Chinese population. Here we reported both the microbial compositional and gene functional alterations during the progression from central obesity to T2D. Several opportunistic pathogens were enriched in obese T2D patients. We also characterized thousands of genes involved in sugar and amino acid metabolism whose abundance were significantly depleted in obese T2D group. Moreover, the abundance of those genes was negatively associated with plasma glycemia level and percentage of individuals with impaired plasma glucose status. Therefore, our study indicates that the abundance of those depleted genes can be used as a potential biomarker to identify central obese individuals with high risks of developing T2D.}, } @article {pmid34743650, year = {2021}, author = {Bajaj, JS and Shamsaddini, A and Acharya, C and Fagan, A and Sikaroodi, M and Gavis, E and McGeorge, S and Khoruts, A and Fuchs, M and Sterling, RK and Lee, H and Gillevet, PM}, title = {Multiple bacterial virulence factors focused on adherence and biofilm formation associate with outcomes in cirrhosis.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1993584}, pmid = {34743650}, issn = {1949-0984}, support = {I01 CX001076/CX/CSRD VA/United States ; R01 HS025412/HS/AHRQ HHS/United States ; R21 TR003095/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Aged ; Bacteria/genetics ; *Bacterial Adhesion ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/*metabolism ; *Biofilms ; Cohort Studies ; Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Liver Cirrhosis/*microbiology/therapy ; Male ; Middle Aged ; Virulence Factors/genetics/*metabolism ; Young Adult ; }, abstract = {BACKGROUND & AIMS: Altered gut microbiota is associated with poor outcomes in cirrhosis, including infections and hepatic encephalopathy (HE). However, the role of bacterial virulence factors (VFs) is unclear. Aim: Define association of VFs with cirrhosis severity and infections, their linkage with outcomes, and impact of fecal microbiota transplant (FMT).

METHODS: VF abundances were determined using metagenomic analysis in stools from controls and cirrhosis patients (compensated, HE-only, ascites-only, both and infected). Patients were followed for 90-day hospitalizations and 1-year death. Stool samples collected before/after a placebo-controlled FMT trial were also analyzed. Bacterial species and VFs for all species and selected pathogens (Escherichia, Klebsiella, Pseudomonas, Staphylococcus, Streptococcus, and Enterococcus spp) were compared between groups. Multi-variable analyses were performed for clinical biomarkers and VFs for outcome prediction. Changes in VFs pre/post-FMT and post-FMT/placebo were analyzed. Results: We included 233 subjects (40 controls, 43 compensated, 30 HE-only, 20 ascites-only, 70 both, and 30 infected). Decompensated patients, especially those with infections, had higher VFs coding for siderophores, biofilms, and adhesion factors versus the rest. Biofilm and adhesion VFs from Enterobacteriaceae and Enterococcus spp associated with death and hospitalizations independent of clinical factors regardless of when all VFs or selected pathogens were analyzed. FMT was associated with reduced VF post-FMT versus pre-FMT and post-placebo groups.

CONCLUSIONS: Virulence factors from multiple species focused on adhesion and biofilms increased with decompensation and infections, associated with death and hospitalizations independent of clinical factors, and were attenuated with FMT. Strategies focused on targeting multiple virulence factors could potentially impact outcomes in cirrhosis.

PRESENTATIONS: Portions of this manuscript were an oral presentation in the virtual International Liver Congress 2021.

ABBREVIATIONS: VF: virulence factors, HE: hepatic encephalopathy, FMT: Fecal microbiota transplant, PPI: proton pump inhibitors, LPS: lipopolysaccharides, VFDB: Virulence factor database, OTU: operational taxonomic units, SBP: spontaneous bacterial peritonitis, UTI: urinary tract infections, MRSA: methicillin resistant Staphylococcus aureus, VRE: vancomycin-resistant Enterococcus, MAAsLin2: Microbiome Multivariable Associations with Linear Models, LPS: lipopolysaccharides, AKI: acute kidney injury.}, } @article {pmid34743175, year = {2022}, author = {Jurgensen, SK and Roux, S and Schwenck, SM and Stewart, FJ and Sullivan, MB and Brum, JR}, title = {Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state.}, journal = {The ISME journal}, volume = {16}, number = {4}, pages = {972-982}, pmid = {34743175}, issn = {1751-7370}, support = {OCE #1658040//National Science Foundation (NSF)/ ; 1746902//National Science Foundation (NSF)/ ; 1151698//National Science Foundation (NSF)/ ; RC944//Alfred P. Sloan Foundation/ ; 346253//Simons Foundation/ ; GBMF #3790//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; }, mesh = {*Microbiota ; Oxygen/metabolism ; Seawater/chemistry ; *Viruses/genetics/metabolism ; Water ; }, abstract = {Microbial communities in oxygen minimum zones (OMZs) are known to have significant impacts on global biogeochemical cycles, but viral influence on microbial processes in these regions are much less studied. Here we provide baseline ecological patterns using microscopy and viral metagenomics from the Eastern Tropical North Pacific (ETNP) OMZ region that enhance our understanding of viruses in these climate-critical systems. While extracellular viral abundance decreased below the oxycline, viral diversity and lytic infection frequency remained high within the OMZ, demonstrating that viral influences on microbial communities were still substantial without the detectable presence of oxygen. Viral community composition was strongly related to oxygen concentration, with viral populations in low-oxygen portions of the water column being distinct from their surface layer counterparts. However, this divergence was not accompanied by the expected differences in viral-encoded auxiliary metabolic genes (AMGs) relating to nitrogen and sulfur metabolisms that are known to be performed by microbial communities in these low-oxygen and anoxic regions. Instead, several abundant AMGs were identified in the oxycline and OMZ that may modulate host responses to low-oxygen stress. We hypothesize that this is due to selection for viral-encoded genes that influence host survivability rather than modulating host metabolic reactions within the ETNP OMZ. Together, this study shows that viruses are not only diverse throughout the water column in the ETNP, including the OMZ, but their infection of microorganisms has the potential to alter host physiological state within these biogeochemically important regions of the ocean.}, } @article {pmid34743174, year = {2022}, author = {Sakoula, D and Smith, GJ and Frank, J and Mesman, RJ and Kop, LFM and Blom, P and Jetten, MSM and van Kessel, MAHJ and Lücker, S}, title = {Universal activity-based labeling method for ammonia- and alkane-oxidizing bacteria.}, journal = {The ISME journal}, volume = {16}, number = {4}, pages = {958-971}, pmid = {34743174}, issn = {1751-7370}, support = {339880//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 016.Vidi.189.050//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; SIAM 024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 016.Veni.192.062//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 339880//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Euratom (H2020 Euratom Research and Training Programme 2014-2018)/ ; }, mesh = {*Alkanes/metabolism ; *Ammonia/metabolism ; Archaea/genetics ; Bacteria ; In Situ Hybridization, Fluorescence ; Mixed Function Oxygenases/metabolism ; Oxidation-Reduction ; Phylogeny ; }, abstract = {The advance of metagenomics in combination with intricate cultivation approaches has facilitated the discovery of novel ammonia-, methane-, and other short-chain alkane-oxidizing microorganisms, indicating that our understanding of the microbial biodiversity within the biogeochemical nitrogen and carbon cycles still is incomplete. The in situ detection and phylogenetic identification of novel ammonia- and alkane-oxidizing bacteria remain challenging due to their naturally low abundances and difficulties in obtaining new isolates from complex samples. Here, we describe an activity-based protein profiling protocol allowing cultivation-independent unveiling of ammonia- and alkane-oxidizing bacteria. In this protocol, 1,7-octadiyne is used as a bifunctional enzyme probe that, in combination with a highly specific alkyne-azide cycloaddition reaction, enables the fluorescent or biotin labeling of cells harboring active ammonia and alkane monooxygenases. Biotinylation of these enzymes in combination with immunogold labeling revealed the subcellular localization of the tagged proteins, which corroborated expected enzyme targets in model strains. In addition, fluorescent labeling of cells harboring active ammonia or alkane monooxygenases provided a direct link of these functional lifestyles to phylogenetic identification when combined with fluorescence in situ hybridization. Furthermore, we show that this activity-based labeling protocol can be successfully coupled with fluorescence-activated cell sorting for the enrichment of nitrifiers and alkane-oxidizing bacteria from complex environmental samples, enabling the recovery of high-quality metagenome-assembled genomes. In conclusion, this study demonstrates a novel, functional tagging technique for the reliable detection, identification, and enrichment of ammonia- and alkane-oxidizing bacteria present in complex microbial communities.}, } @article {pmid34742104, year = {2022}, author = {Yan, Y and Li, H and Fayyaz, A and Gai, Y}, title = {Metagenomic and network analysis revealed wide distribution of antibiotic resistance genes in monkey gut microbiota.}, journal = {Microbiological research}, volume = {254}, number = {}, pages = {126895}, doi = {10.1016/j.micres.2021.126895}, pmid = {34742104}, issn = {1618-0623}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Gastrointestinal Microbiome/drug effects/genetics ; *Haplorhini/microbiology ; Metagenomics ; }, abstract = {The emergence and spread of drug-resistant microorganisms that have acquired new resistance mechanisms, leading to antibiotic resistance, continue to threaten the health of humans and animals worldwide. Non-human primates (NHPs), as close living relatives of human beings in the world, have a high degree of genetic and physiological similarity to humans. However, despite its importance, we lack a comprehensive characterization or understanding of the similarities and differences of the antibiotic resistance genes of the gut microbiome carried by non-human primates and humans. In the present study, the diversity and abundance of antibiotic resistance genes carried by the gut microbiota of cynomolgus monkeys (Macaca fascicularis) were investigated by metagenomic analysis. In total, 60 resistance types conferring resistance to 11 categories of antibiotics were identified in the gut microbiome of cynomolgus monkeys. Interestingly, the composition and abundance of ARGs carried by the gut microbiota of cynomolgus monkeys can be significantly affected by dietary changes. Moreover, we found that all ARG types carried by humans are also present in cynomolgus monkeys. The tetracycline resistance gene tet(37) is evolutionarily conserved and highly homologous. Taken together, our study provides a comprehensive overview of the diversity and richness of ARGs in the gut microbiota of cynomolgus monkeys and underlines the potentially crucial role of diet in the gut health of monkeys and humans.}, } @article {pmid34742036, year = {2021}, author = {Stockdale, SR and Hill, C}, title = {Progress and prospects of the healthy human gut virome.}, journal = {Current opinion in virology}, volume = {51}, number = {}, pages = {164-171}, doi = {10.1016/j.coviro.2021.10.001}, pmid = {34742036}, issn = {1879-6265}, mesh = {*Health ; Humans ; Intestines/*virology ; Metagenomics ; *Virome/genetics ; Viruses/genetics/*isolation & purification ; }, abstract = {Not all viruses associated with humans cause disease. Non-pathogenic human-infecting viruses are predicted as important for immune system induction and preparation. Phages that infect bacteria are the most abundant predators of the human microbial ecosystem, promoting and maintaining bacterial diversity. Metagenomic analyses of the human gut virome and microbiome are unravelling the intricate predator-prey dynamics of phage-bacteria co-existence, co-evolution, and their interplay with the human host. While most adults harbour a distinctly individualistic and persistent community of virulent phages, new-borns are dominated by temperate phages heavily influenced by environmental exposures. The future development of microbiome-based interventions, therapeutics, and manipulation, will require a greater understanding of the human microbiome and the virome.}, } @article {pmid34741944, year = {2022}, author = {Ding, X and Lan, W and Yan, A and Li, Y and Katayama, Y and Gu, JD}, title = {Microbiome characteristics and the key biochemical reactions identified on stone world cultural heritage under different climate conditions.}, journal = {Journal of environmental management}, volume = {302}, number = {Pt A}, pages = {114041}, doi = {10.1016/j.jenvman.2021.114041}, pmid = {34741944}, issn = {1095-8630}, mesh = {*Microbiota/genetics ; Nitrogen ; Sulfur ; }, abstract = {The surfaces of historical stone monuments are visibly covered with a layer of colonizing microorganisms and their degradation products. In this study, a metadata analysis was conducted using the microbial sequencing data available from NCBI database to determine the diversity, biodeterioration potential and functionality of the stone microbiome on important world cultural heritage sites under four different climatic conditions. The retrieved stone microbial community composition in these metagenomes shows a clear association between climate types of the historical monuments and the diversity and taxonomic composition of the stone microbiomes. Shannon diversity values showed that microbial communities on stone monuments exposed to dry climate were more diverse than those under humid ones. In particular, functions associated with photosynthesis and UV resistance were identified from geographical locations under different climate types. The distribution of key microbial determinants responsible for stone deterioration was linked to survival under extreme environmental conditions and biochemical capabilities and reactions. Among them, biochemical reactions of the microbial nitrogen and sulfur cycles were most predominant. These stone-dwelling microbiomes on historical stone monuments were highly diverse and self-sustaining driven by energy metabolism and biomass accumulation. And metabolic products of the internal geomicrobiological nitrogen cycling on these ancient monuments play a unique role in the biodeterioration of stone monuments. These results highlight the significance of identifying the essential microbial biochemical reactions to advance the understanding of stone biodeterioration for protection management.}, } @article {pmid34741331, year = {2021}, author = {Han, W and Hou, J}, title = {Letter: cross-linkage between bacterial taxonomy and gene functions-a study of metagenome-assembled genomes of gut microbiota in adult non-alcoholic fatty liver disease.}, journal = {Alimentary pharmacology & therapeutics}, volume = {54}, number = {11-12}, pages = {1505-1507}, doi = {10.1111/apt.16628}, pmid = {34741331}, issn = {1365-2036}, mesh = {Adult ; Biomarkers ; *Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract ; Humans ; Metagenome ; *Non-alcoholic Fatty Liver Disease/genetics ; }, } @article {pmid34741032, year = {2021}, author = {Li, Y and Kreuzer, M and Clayssen, Q and Ebert, MO and Ruscheweyh, HJ and Sunagawa, S and Kunz, C and Attwood, G and Amelchanka, S and Terranova, M}, title = {The rumen microbiome inhibits methane formation through dietary choline supplementation.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {21761}, pmid = {34741032}, issn = {2045-2322}, mesh = {Animals ; Cattle ; Choline/*administration & dosage ; Dietary Supplements ; *Gastrointestinal Microbiome ; Lipotropic Agents/*administration & dosage ; Methane/*biosynthesis ; Rumen/*microbiology ; }, abstract = {Enteric fermentation from ruminants is a primary source of anthropogenic methane emission. This study aims to add another approach for methane mitigation by manipulation of the rumen microbiome. Effects of choline supplementation on methane formation were quantified in vitro using the Rumen Simulation Technique. Supplementing 200 mM of choline chloride or choline bicarbonate reduced methane emissions by 97-100% after 15 days. Associated with the reduction of methane formation, metabolomics analysis revealed high post-treatment concentrations of ethanol, which likely served as a major hydrogen sink. Metagenome sequencing showed that the methanogen community was almost entirely lost, and choline-utilizing bacteria that can produce either lactate, ethanol or formate as hydrogen sinks were enriched. The taxa most strongly associated with methane mitigation were Megasphaera elsdenii and Denitrobacterium detoxificans, both capable of consuming lactate, which is an intermediate product and hydrogen sink. Accordingly, choline metabolism promoted the capability of bacteria to utilize alternative hydrogen sinks leading to a decline of hydrogen as a substrate for methane formation. However, fermentation of fibre and total organic matter could not be fully maintained with choline supplementation, while amino acid deamination and ethanolamine catabolism produced excessive ammonia, which would reduce feed efficiency and adversely affect live animal performance.}, } @article {pmid34740703, year = {2022}, author = {Zhou, G and Tao, HB and Wen, X and Wang, YS and Peng, H and Liu, HZ and Yang, XJ and Huang, XM and Shi, QS and Xie, XB}, title = {Metagenomic analysis of microbial communities and antibiotic resistance genes in spoiled household chemicals.}, journal = {Chemosphere}, volume = {291}, number = {Pt 1}, pages = {132766}, doi = {10.1016/j.chemosphere.2021.132766}, pmid = {34740703}, issn = {1879-1298}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Numerous attempts have been utilized to unveil the occurrences of antibiotic resistance genes (ARGs) in human-associated and non-human-associated samples. However, spoiled household chemicals, which are usually neglected by the public, may be also a reservoir of ARGs because of the excessive and inappropriate uses of industrial drugs. Based upon the Comprehensive Antibiotic Research Database, a metagenomic sequencing method was utilized to detect and quantify Antibiotic Resistance Ontology (AROs) in six spoiled household chemicals, including hair conditioner, dishwashing detergent, bath shampoo, hand sanitizer, and laundry detergent. Proteobacteria was found to be the dominant phylum in all the samples. Functional annotation of the unigenes obtained against the KEGG pathway, eggNOG and CAZy databases demonstrated a diversity of their functions. Moreover, 186 types of AROs that were members of 72 drug classes were identified. Multidrug resistance genes were the most dominant types, and there were 17 AROs whose resistance mechanisms were categorized into the resistance-nodulation-cell division antibiotic efflux pump among the top 20 AROs. Moreover, Proteobacteria was the dominant carrier of AROs with the primary resistance mechanism of antibiotic efflux. The maximum temperature of the months of collection significantly affected the distributions of AROs. Additionally, the isolated individual bacterium from spoiled household chemicals and artificial mixed communities of isolated bacteria demonstrated diverse resistant abilities to different biocides. This study demonstrated that there are abundant microorganisms and a broad spectrum profile of AROs in spoiled household chemicals that might induce a severe threat to public healthy securities and merit particular attention.}, } @article {pmid34740587, year = {2021}, author = {Corrêa, PS and Mendes, LW and Lemos, LN and Sampaio, ACK and Issakowicz, J and McManus, CM and Tsai, SM and Faciola, AP and Abdalla, AL and Louvandini, H}, title = {The effect of Haemonchus contortus and Trichostrongylus colubriforms infection on the ruminal microbiome of lambs.}, journal = {Experimental parasitology}, volume = {231}, number = {}, pages = {108175}, doi = {10.1016/j.exppara.2021.108175}, pmid = {34740587}, issn = {1090-2449}, mesh = {Animals ; Chromatography, Gas/methods/veterinary ; DNA/chemistry/isolation & purification ; Flame Ionization/veterinary ; *Gastrointestinal Microbiome ; Haemonchiasis/complications/microbiology/*veterinary ; Metagenomics ; Methane/analysis/metabolism ; Purines/urine ; Real-Time Polymerase Chain Reaction/veterinary ; Rumen/*microbiology ; Sequence Analysis, DNA/veterinary ; Sheep ; Sheep Diseases/*microbiology/*parasitology ; Trichostrongyloidiasis/complications/microbiology/*veterinary ; }, abstract = {We evaluated Haemonchus contortus (HC) and Trichostrongylus colubriformis (TC) infection on the ruminal microbial community of Santa Ines lambs to better understand the pathophysiology of parasite infections and the interactions among gastrointestinal nematodes and gut resident microbiota. In this study, 18 six months of age lambs were maintained for 34 days in individual pens divided into three treatments that included animals infected with HC and TC, and control (infection-free). Haematological, ruminal parameter and microbial nitrogen absorbed by pune derivatives, as well as enteric methane emission (CH4), were analysed, and the rumen microbial taxonomic and functional profile assessed by shotgun metagenomics. The analysis showed that total protein, albumin, urea, and butyrate level were lower in animals infected by both parasites, while HC infection also decreased the haemoglobin level. Both infected groups (TC and HC) increased the enteric methane emission (CH4). TC and HC infections increased the diversity and richness of functional microbial genes. Most alterations in the rumen microbiome composition of infected groups are associated with the suppression of microbes involved in microbial homeostasis maintenance and expansion of the archaeal community in the infected animals. Infection led to an increased abundance of nitrogen, amino acid, protein, and energy metabolism genes. Overall, TC and HC infection increased the enteric methane emission, negatively affected taxon's responsible for maintenance de rumen homeostasis and modulated some important genes related to protein and energy metabolism.}, } @article {pmid34738400, year = {2021}, author = {Chen, LY and Chen, YZ and Mi, YG and Sun, YL and Zheng, HY and Ding, CJ and Wang, WM}, title = {[Comparative study on anti-depressant effect of Zhizichi Decoction and its solid fermentation product on CUMS rats].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {46}, number = {19}, pages = {5044-5051}, doi = {10.19540/j.cnki.cjcmm.20210713.406}, pmid = {34738400}, issn = {1001-5302}, mesh = {Animals ; Depression/drug therapy ; Disease Models, Animal ; Fermentation ; *Gastrointestinal Microbiome ; *Hippocampus ; Rats ; Stress, Psychological ; }, abstract = {Chronic unpredicted mild stress(CUMS) combined with isolated feeding was used to induce depressed rat model. The anti-depressant effects of Zhizichi Decoction(ZZCD) and its solid fermented product(ZZC) were analyzed by behavioral test and comparison of pathological tissues of hippocampus and liver, metabolic characteristics of intestinal flora, and relative abundance of species. The results showed that ZZC could increase sucrose preference, shorten the immobility time in the forced swim test and tail suspension test(P<0.05), and repair damaged hippocampus and liver tissues, and the effect was superior to that of ZZCD. The results of Biolog ECO plates showed that the average well color development(AWCD) of intestinal flora in the model group significantly decreased and the metabolic levels of sugar and amino acids were reduced, while the AWCD of the treatment groups increased. The metabolic levels of the two carbon sources were improved in the ZZC group, while only sugar metabolic level was elevated in the ZZCD group. Metagenomic analysis of intestinal flora showed that the ratio of Firmicutes/Bacteroidetes was 3.87 in the control group, 21.77 in the model group, 5.91 in the ZZC group, and 18.48 in the ZZCD group. Lactobacillus increased by 3.28 times, and Prevotella and Bacteroidetes decreased by 75.59% and 76.39%, respectively in the model group as compared with that in the control group. Lactobacillus decreased by 31.13%, and Prevotella and Bacteroidetes increased by more than three times in the ZZC group as compared with that in the model group, while the corresponding changes in the ZZCD group were not significant. ZZC could improve depression-like beha-viors by regulating the structure of intestinal flora and metabolic functions and repairing damaged hippocampus and liver tissues in depressed rats, showing an anti-depressant effect superior to that of ZZCD. This study is expected to provide a basis for the development of new anti-depressant food products.}, } @article {pmid34738169, year = {2021}, author = {Zada, S and Xie, J and Yang, M and Yang, X and Sajjad, W and Rafiq, M and Hasan, F and Hu, Z and Wang, H}, title = {Composition and functional profiles of microbial communities in two geochemically and mineralogically different caves.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {23}, pages = {8921-8936}, pmid = {34738169}, issn = {1432-0614}, support = {32070113//national natural science foundation of china/ ; 2019ST023//guangdong science and technology department/ ; 2019A1515011139//guangdong science and technology department/ ; }, mesh = {Archaea/genetics ; Bacteria/genetics ; *Caves ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbial communities in cave ecosystems have specific survival strategies, which is far from being well explicated. Here, we reported the genetic and functional diversity of bacteria and archaea in typical limestone (Kashmir Cave) and silicate-containing (Tiser Cave) caves. X-ray diffraction (XRD) and Fourier transform infrared spectroscopic (FTIR) analyses revealed the different geochemical and mineral compositions of the two caves. Amplicon barcode sequencing revealed the dominancy of Actinobacteria and Proteobacteria in Kashmir and Tiser Caves. Bacteroidetes and Firmicutes were the dominant phyla in Tiser Cave, and the abundance is relatively small in Kashmir Cave. Archaea was also abundant prokaryotes in Kashmir Cave, but it only accounted for 0.723% of the total prokaryote sequences in Tiser Cave. Functional analysis based on metagenomic sequencing data revealed that a large number of functional potential genes involved in nutrient metabolism and biosynthesis of bioactive compounds in Tiser and Kashmir Cave samples could significantly influence the biogeochemical cycle and secondary metabolite production in cave habitats. In addition, the two caves were also found to be rich in biosynthetic genes, encoding bioactive compounds, such as monobactam and prodigiosin, indicating that these caves could be potential habitats for the isolation of antibiotics. This study provides a comprehensive insight into the diversity of bacteria and archaea in cave ecosystems and helps to better understand the special survival strategies of microorganisms in cave ecosystems.Key points• Geochemically distinct caves possess unique microbial community structure.• Cavernicoles could be important candidates for antibiotic production.• Cavernicoles are important for biogeochemical cycling.}, } @article {pmid34737748, year = {2021}, author = {Pallikkuth, S and Mendez, R and Russell, K and Sirupangi, T and Kvistad, D and Pahwa, R and Villinger, F and Banerjee, S and Pahwa, S}, title = {Age Associated Microbiome and Microbial Metabolites Modulation and Its Association With Systemic Inflammation in a Rhesus Macaque Model.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {748397}, pmid = {34737748}, issn = {1664-3224}, support = {R01 AI123048/AI/NIAID NIH HHS/United States ; R01 AG068110/AG/NIA NIH HHS/United States ; P30 AI073961/AI/NIAID NIH HHS/United States ; }, mesh = {Aging/*immunology ; Animals ; Bacteria/metabolism ; C-Reactive Protein/analysis ; Cytokines/blood ; Disease Models, Animal ; Dysbiosis/immunology/metabolism/*microbiology ; Feces/chemistry/microbiology ; Female ; *Gastrointestinal Microbiome/physiology ; Inflammation/immunology/metabolism/*microbiology ; Macaca mulatta ; Male ; Symbiosis ; Tandem Mass Spectrometry ; Tumor Necrosis Factor-alpha/blood ; }, abstract = {Aging is associated with declining immunity and inflammation as well as alterations in the gut microbiome with a decrease of beneficial microbes and increase in pathogenic ones. The aim of this study was to investigate the age associated gut microbiome in relation to immunologic and metabolic profile in a non-human primate (NHP) model. 12 geriatric (age 19-24 years) and 4 young adult (age 3-4 years) Rhesus macaques were included in this study. Immune cell subsets were characterized in peripheral blood mononuclear cells (PBMC) by flow cytometry and plasma cytokines levels were determined by bead based multiplex cytokine analysis. Stool samples were collected by ileal loop and investigated for microbiome analysis by shotgun metagenomics. Serum, gut microbial lysate, and microbe-free fecal extract were subjected to metabolomic analysis by mass-spectrometry. Our results showed that the gut microbiome in geriatric animals had higher abundance of Archaeal and Proteobacterial species and lower Firmicutes than the young adults. Highly abundant microbes in the geriatric animals showed a direct association with plasma biomarkers of inflammation and immune activation such as neopterin, CRP, TNF, IL-2, IL-6, IL-8 and IFN-γ. Significant enrichment of metabolites that contribute to inflammatory and cytotoxic pathways was observed in serum and feces of geriatric animals compared to the young adults. We conclude that aging NHP undergo immunosenescence and age associated alterations in the gut microbiome that has a distinct metabolic profile. Aging NHP can serve as a model for investigating the relationship of the gut microbiome to particular age-associated comorbidities and for strategies aimed at modulating the microbiome.}, } @article {pmid34737725, year = {2021}, author = {Arora, T and Tremaroli, V}, title = {Therapeutic Potential of Butyrate for Treatment of Type 2 Diabetes.}, journal = {Frontiers in endocrinology}, volume = {12}, number = {}, pages = {761834}, pmid = {34737725}, issn = {1664-2392}, mesh = {Animals ; Bacteria/metabolism ; Butyrates/*pharmacology ; Diabetes Mellitus, Type 2/*drug therapy ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects ; Humans ; }, abstract = {Metagenomics studies have shown that type 2 diabetes (T2D) is associated with an altered gut microbiota. Whereas different microbiota patterns have been observed in independent human cohorts, reduction of butyrate-producing bacteria has consistently been found in individuals with T2D, as well as in those with prediabetes. Butyrate is produced in the large intestine by microbial fermentations, particularly of dietary fiber, and serves as primary fuel for colonocytes. It also acts as histone deacetylase inhibitor and ligand to G-protein coupled receptors, affecting cellular signaling in target cells, such as enteroendocrine cells. Therefore, butyrate has become an attractive drug target for T2D, and treatment strategies have been devised to increase its intestinal levels, for example by supplementation of butyrate-producing bacteria and dietary fiber, or through fecal microbiota transplant (FMT). In this review, we provide an overview of current literature indicating that these strategies have yielded encouraging results and short-term benefits in humans, but long-term improvements of glycemic control have not been reported so far. Further studies are required to find effective approaches to restore butyrate-producing bacteria and butyrate levels in the human gut, and to investigate their impact on glucose regulation in T2D.}, } @article {pmid34736984, year = {2021}, author = {Ladaycia, A and Passirani, C and Lepeltier, E}, title = {Microbiota and nanoparticles: Description and interactions.}, journal = {European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V}, volume = {169}, number = {}, pages = {220-240}, doi = {10.1016/j.ejpb.2021.10.015}, pmid = {34736984}, issn = {1873-3441}, mesh = {Dysbiosis/etiology/physiopathology/prevention & control ; Health ; Humans ; Metagenome ; *Microbiota/drug effects/physiology ; *Nanoparticles/adverse effects/metabolism/therapeutic use ; }, abstract = {The healthy human body is inhabited with a large number of bacteria, forming natural flora. It is even estimated that for a human body, its amount of DNA is less important that its bacterial genetic material. This flora plays major roles in the sickness and health of the human body and any change in its composition may lead to different diseases. Nanoparticles are widely used in numerous fields: cosmetics, food, industry, and as drug delivery carrier in the medical field. Being included in these various applications, nanoparticles may interact with the human body at various levels and with different mechanisms. These interactions differ depending on the nanoparticle nature, its structure, its concentration and manifest in different ways on the microbiota, leading to its destabilization, its restoring or showing no toxic effect. Nanoparticles may also be used as a vehicle to regulate the microbiota or to treat some of its diseases.}, } @article {pmid34736047, year = {2021}, author = {Karadayı, S}, title = {Assessment of the link between evidence and crime scene through soil bacterial and fungal microbiome: A mock case in forensic study.}, journal = {Forensic science international}, volume = {329}, number = {}, pages = {111060}, doi = {10.1016/j.forsciint.2021.111060}, pmid = {34736047}, issn = {1872-6283}, mesh = {Bacteria/genetics ; Crime ; Homicide ; *Microbiota ; Mycobiome ; Soil ; *Soil Microbiology ; }, abstract = {In forensic studies, soil traces can be used to find clues to the origin of an unknown sample or the relationship between a crime scene and a suspect and can provide invaluable evidence as they frequently adhere to objects, with high persistence. In this study, it was aimed to investigate the potential of the bacterial and fungal microbiome diversity of the soil to be used as legitimate evidence in the resolution of homicide cases. Within the scope of a mock homicide case scenario, a total of 12 soil samples were collected, including two evidence samples, three crime scene samples and seven non-crime scene related control samples. Both bacterial and fungal microbiome profiles of these samples were analysed using Illumina NovaSeq platform. The resulting sequences were analysed using QIIME 2 microbiome bioinformatics platform. Beta diversity analysis was performed to determine the difference between samples. In bacterial community analyses, it has been observed that it is difficult to distinguish evidence samples and crime scene samples from control samples at phylum and class level, whereas differentiation could be made at genus and species level. Fungal community analyses allowed to distinguish evidence samples and crime scene samples from control samples at both phylum and class and genus and species level. Principal coordinate analysis (PCoA) results showed that distance between evidence samples and crime scene reference samples was closer to each other than non-crime scene related control samples. The results of this study showed that bacterial and especially fungal DNA in soil has the potential to contribute effectively to the resolution of forensic cases. Thus, it has been understood that it is possible to establish a relationship between the case and the crime scene with the help of microbiome analyses on soil samples obtained in homicide cases.}, } @article {pmid34734869, year = {2021}, author = {Mihajlović, A and Mladenović, K and Lončar-Turukalo, T and Brdar, S}, title = {Machine Learning Based Metagenomic Prediction of Inflammatory Bowel Disease.}, journal = {Studies in health technology and informatics}, volume = {285}, number = {}, pages = {165-170}, doi = {10.3233/SHTI210591}, pmid = {34734869}, issn = {1879-8365}, mesh = {Actinobacteria ; Bacteroidetes ; *Colitis, Ulcerative/diagnosis/microbiology ; *Crohn Disease/diagnosis/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases/diagnosis/microbiology ; Machine Learning ; Porphyromonas endodontalis ; Staphylococcus hominis ; }, abstract = {In this study, we investigate faecal microbiota composition, in an attempt to evaluate performance of classification algorithms in identifying Inflammatory Bowel Disease (IBD) and its two types: Crohn's disease (CD) and ulcerative colitis (UC). From many investigated algorithms, a random forest (RF) classifier was selected for detailed evaluation in three-class (CD versus UC versus nonIBD) classification task and two binary (nonIBD versus IBD and CD versus UC) classification tasks. We dealt with class imbalance, performed extensive parameter search, dimensionality reduction and two-level classification. In three-class classification, our best model reaches F1 score of 91% in average, which confirms the strong connection of IBD and gastrointestinal microbiome. Among most important features in three-class classification are species Staphylococcus hominis, Porphyromonas endodontalis, Slackia piriformis and genus Bacteroidetes.}, } @article {pmid34734352, year = {2021}, author = {Lee, H and Jeong, J and Oh, Y and Lee, CJ and Mun, S and Lee, DG and Jo, H and Heo, YM and Baek, C and Heo, CY and Kang, SM and Han, K}, title = {Comparative analysis of human facial skin microbiome between topical sites compared to entire face.}, journal = {Genes & genomics}, volume = {43}, number = {12}, pages = {1483-1495}, pmid = {34734352}, issn = {2092-9293}, mesh = {Adult ; Face/*microbiology ; Humans ; Male ; *Microbiota ; Organ Specificity ; Skin/*microbiology ; }, abstract = {BACKGROUND: Skin is an essential outer barrier and supports the growth of commensal microorganisms that protects a host from the offense of foreign toxic organisms. With the rapid development of next-generation sequencing (NGS)-based applications, skin microbiome research for facial health care has reached industry growth, such as therapy and cosmetic product development. Despite the acceleration of skin microbiome research, experimental standardization protocol has not yet been established in the facial site and method of sampling.

OBJECTIVE: Thus, we aimed to investigate the differences in microbial composition at each facial site (cheek, mouth, forehead, and entire face) using comprehensive microbiome analysis.

METHODS: Twelve specimens from three men (four specimens per one person) were collected. The hypervariable regions (V3-V4) of the bacterial 16S rRNA gene were targeted for 16S amplicon library construction and classification of bacterial taxonomy. Skin microbial composition for all specimens was investigated, and the differences site-by-site in skin microbial composition were analyzed and evaluated by the various statistical tests.

RESULTS: We were able to validate the independent correlation between the skin microbiome composition and the facial sites. The cheek site showed the highest alpha-diversity in richness and evenness scores compared to the forehead and mouth. The cheek and mouth sites showed a positive correlation (R[2] value > 0.93) with the entire face, while the forehead sites were negatively correlated (R[2] value < 0.2). Given the relative abundance based on statistical correlation analysis, we estimated that the cheek site could be considered an optimal topical site to replace the entire face.

CONCLUSION: Our study suggests that skin microbiome profiling of four facial sites confirms that the cheek shows the most similar skin flora with the entire face. This study would be informative for preventing bias caused by sampling methods before researching and understanding skin cosmetics development or skin diseases.}, } @article {pmid34734313, year = {2021}, author = {Zhang, M and Niu, Y and Wang, W and Bai, SH and Luo, H and Tang, L and Chen, F and Xu, Z and Guo, X}, title = {Responses of microbial function, biomass and heterotrophic respiration, and organic carbon in fir plantation soil to successive nitrogen and phosphorus fertilization.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {23}, pages = {8907-8920}, pmid = {34734313}, issn = {1432-0614}, support = {31560204//national natural science foundation of china/ ; 41907085//National Natural Science Foundation of China/ ; }, mesh = {Biomass ; Fertilization ; *Microbiota ; Nitrogen/analysis ; Phosphorus ; Respiration ; *Soil ; Soil Microbiology ; }, abstract = {Carbon dioxide (CO2) emissions from forest ecosystems originate largely from soil respiration, and microbial heterotrophic respiration plays a critical role in determining organic carbon (C) stock. This study investigated the impacts of successive nitrogen (N) and phosphorus (P) fertilization after 9 years on soil organic C stock; CO2 emission; and microbial biomass, community, and function in a Chinese fir plantation. The annual fertilization rates were (1) CK, control without N or P fertilization; (2) N50, 50 kg N ha[-1]; (3) N100, 100 kg N ha[-1]; (4) P50, 50 kg P ha[-1]; (5) N50P50, 50 kg N ha[-1] + 50 kg P ha[-1]; and (6) N100P50, 100 kg N ha[-1] + 50 kg P ha[-1]. The N100P50 treatment had the highest cumulative soil CO2 emissions, but the CK treatment had the lowest cumulative soil CO2 emissions among all treatments. The declines of soil organic C (SOC) after successive 9-year fertilization were in the order of 100 kg N ha[-1] year[-1] > 50 kg N ha[-1] year[-1] > CK. Compared to the CK treatment, successive N fertilization significantly changed soil microbial communities at different application rates and increased the relative gene abundances of glycoside hydrolases, glycosyl transferases, carbohydrate-binding modules, and polysaccharide lyases at 100 kg N ha[-1] year[-1]. Relative to P fertilization alone (50 kg P ha[-1] year[-1]), combined N and P fertilization significantly altered the soil microbial community structure and favored more active soil microbial metabolism. Microbial community and metabolism changes caused by N fertilization could have enhanced CO2 emission from heterotrophic respiration and eventually led to the decrease in organic C stock in the forest plantation soil. KEY POINTS: • N fertilization, alone or with P, favored more active microbial metabolism genes. • 100 kg N ha[-1] fertilization significantly changed microbial community and function. • N fertilization led to a "domino effect" on the decrease of soil C stock.}, } @article {pmid34732816, year = {2022}, author = {Laue, HE and Karagas, MR and Coker, MO and Bellinger, DC and Baker, ER and Korrick, SA and Madan, JC}, title = {Sex-specific relationships of the infant microbiome and early-childhood behavioral outcomes.}, journal = {Pediatric research}, volume = {92}, number = {2}, pages = {580-591}, pmid = {34732816}, issn = {1530-0447}, support = {UH3 OD023275/OD/NIH HHS/United States ; P42 ES007373/ES/NIEHS NIH HHS/United States ; T32 CA134286/CA/NCI NIH HHS/United States ; P20 ES018175/ES/NIEHS NIH HHS/United States ; P01 ES022832/ES/NIEHS NIH HHS/United States ; P20 GM104416/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Child ; Child, Preschool ; Cross-Sectional Studies ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Vitamin B 6 ; }, abstract = {BACKGROUND: A link between the gut microbiome and behavior is hypothesized, but most previous studies are cross-sectional or in animal models. The modifying role of host sex is poorly characterized. We aimed to identify sex-specific prospective associations between the early-life gut microbiome and preschool-age neurobehavior.

METHODS: In a prospective cohort, gut microbiome diversity and taxa were estimated with 16S rRNA sequencing at 6 weeks, 1 year, and 2 years. Species and gene pathways were inferred from metagenomic sequencing at 6 weeks and 1 year. When subjects were 3 years old, parents completed the Behavioral Assessment System for Children, second edition (BASC-2). A total of 260 children contributed 523 16S rRNA and 234 metagenomics samples to analysis. Models adjusted for sociodemographic characteristics.

RESULTS: Higher diversity at 6 weeks was associated with better internalizing problems among boys, but not girls [βBoys = -1.86 points/SD Shannon diversity; 95% CI (-3.29, -0.42), pBoys = 0.01, βGirls = 0.22 (-1.43, 1.87), pGirls = 0.8, pinteraction = 0.06]. Among other taxa-specific associations, Bifidobacterium at 6 weeks was associated with Adaptive Skills scores in a sex-specific manner. We observed relationships between functional features and BASC-2 scores, including vitamin B6 biosynthesis pathways and better Depression scores.

CONCLUSIONS: This study advances our understanding of microbe-host interactions with implications for childhood behavioral health.

IMPACT: This is one of the first studies to examine the early-life microbiome and neurobehavior, and the first to examine prospective sex-specific associations. Infant and early-childhood microbiomes relate to neurobehavior including anxiety, depression, hyperactivity, and social behaviors in a time- and sex-specific manner. Our findings suggest future studies should evaluate whether host sex impacts the relationship between the gut microbiome and behavioral health outcomes.}, } @article {pmid34732568, year = {2021}, author = {Ortiz, M and Leung, PM and Shelley, G and Jirapanjawat, T and Nauer, PA and Van Goethem, MW and Bay, SK and Islam, ZF and Jordaan, K and Vikram, S and Chown, SL and Hogg, ID and Makhalanyane, TP and Grinter, R and Cowan, DA and Greening, C}, title = {Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {45}, pages = {}, pmid = {34732568}, issn = {1091-6490}, mesh = {Antarctic Regions ; Autotrophic Processes ; Biodiversity ; *Desert Climate ; Gases/*metabolism ; Hydrogenase/metabolism ; Ice Cover/*microbiology ; Metagenome ; *Microbiota ; Oxidation-Reduction ; Phototrophic Processes ; *Soil Microbiology ; }, abstract = {Numerous diverse microorganisms reside in the cold desert soils of continental Antarctica, though we lack a holistic understanding of the metabolic processes that sustain them. Here, we profile the composition, capabilities, and activities of the microbial communities in 16 physicochemically diverse mountainous and glacial soils. We assembled 451 metagenome-assembled genomes from 18 microbial phyla and inferred through Bayesian divergence analysis that the dominant lineages present are likely native to Antarctica. In support of earlier findings, metagenomic analysis revealed that the most abundant and prevalent microorganisms are metabolically versatile aerobes that use atmospheric hydrogen to support aerobic respiration and sometimes carbon fixation. Surprisingly, however, hydrogen oxidation in this region was catalyzed primarily by a phylogenetically and structurally distinct enzyme, the group 1l [NiFe]-hydrogenase, encoded by nine bacterial phyla. Through gas chromatography, we provide evidence that both Antarctic soil communities and an axenic Bacteroidota isolate (Hymenobacter roseosalivarius) oxidize atmospheric hydrogen using this enzyme. Based on ex situ rates at environmentally representative temperatures, hydrogen oxidation is theoretically sufficient for soil communities to meet energy requirements and, through metabolic water production, sustain hydration. Diverse carbon monoxide oxidizers and abundant methanotrophs were also active in the soils. We also recovered genomes of microorganisms capable of oxidizing edaphic inorganic nitrogen, sulfur, and iron compounds and harvesting solar energy via microbial rhodopsins and conventional photosystems. Obligately symbiotic bacteria, including Patescibacteria, Chlamydiae, and predatory Bdellovibrionota, were also present. We conclude that microbial diversity in Antarctic soils reflects the coexistence of metabolically flexible mixotrophs with metabolically constrained specialists.}, } @article {pmid34732245, year = {2021}, author = {Su, Q and Wang, Q and Mu, X and Chen, H and Meng, Y and Zhang, X and Zheng, L and Hu, X and Zhai, Y and Zheng, H}, title = {Strain-level analysis reveals the vertical microbial transmission during the life cycle of bumblebee.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {216}, pmid = {34732245}, issn = {2049-2618}, mesh = {Animals ; Bacteria/genetics ; Bees ; *Gastrointestinal Microbiome/genetics ; Life Cycle Stages ; *Metagenome ; Metagenomics ; }, abstract = {BACKGROUND: Microbial acquisition and development of the gut microbiota impact the establishment of a healthy host-microbes symbiosis. Compared with other animals, the eusocial bumblebees and honeybees possess a simple, recurring, and similar set of gut microbiota. However, all bee gut phylotypes have high strain-level diversity. Gut communities of different bee species are composed of host-specific groups of strains. The variable genomic regions among strains of the same species often confer critical functional differences, such as carbon source utilization, essential for the natural selection of specific strains. The annual bumblebee colony founded by solitary queens enables tracking the transmission routes of gut bacteria during development stages.

RESULTS: Here, we first showed the changes in the microbiome of individual bumblebees across their holometabolous life cycle. Some core gut bacteria persist throughout different stages of development. Gut microbiota of newly emerged workers always resembles those of their queens, suggesting a vertical transmission of strains from queens to the newborn workers. We then follow the dynamic changes in the gut community by comparing strain-level metagenomic profiles of queen-worker pairs longitudinally collected across different stages of the nest development. Species composition of both queen and worker shifts with the colony's growth, and the queen-to-worker vertical inheritance of specific strains was identified. Finally, comparative metagenome analysis showed clear host-specificity for microbes across different bee hosts. Species from honeybees often possess a higher level of strain variation, and they also exhibited more complex gene repertoires linked to polysaccharide digestion. Our results demonstrate bacterial transmission events in bumblebee, highlighting the role of social interactions in driving the microbiota composition.

CONCLUSIONS: By the community-wide metagenomic analysis based on the custom genomic database of bee gut bacteria, we reveal strain transmission events at high resolution and the dynamic changes in community structure along with the colony development. The social annual life cycle of bumblebees is key for the acquisition and development of the gut microbiota. Further studies using the bumblebee model will advance our understanding of the microbiome transmission and the underlying mechanisms, such as strain competition and niche selection. Video Abstract.}, } @article {pmid34730411, year = {2021}, author = {Vosloo, S and Huo, L and Anderson, CL and Dai, Z and Sevillano, M and Pinto, A}, title = {Evaluating de Novo Assembly and Binning Strategies for Time Series Drinking Water Metagenomes.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0143421}, pmid = {34730411}, issn = {2165-0497}, mesh = {Algorithms ; Archaea/*genetics ; Bacteria/*genetics ; Drinking Water/chemistry/*microbiology ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/genetics ; Time Factors ; Water Microbiology ; Water Quality ; }, abstract = {Reconstructing microbial genomes from metagenomic short-read data can be challenging due to the unknown and uneven complexity of microbial communities. This complexity encompasses highly diverse populations, which often includes strain variants. Reconstructing high-quality genomes is a crucial part of the metagenomic workflow, as subsequent ecological and metabolic inferences depend on their accuracy, quality, and completeness. In contrast to microbial communities in other ecosystems, there has been no systematic assessment of genome-centric metagenomic workflows for drinking water microbiomes. In this study, we assessed the performance of a combination of assembly and binning strategies for time series drinking water metagenomes that were collected over 6 months. The goal of this study was to identify the combination of assembly and binning approaches that result in high-quality and -quantity metagenome-assembled genomes (MAGs), representing most of the sequenced metagenome. Our findings suggest that the metaSPAdes coassembly strategies had the best performance, as they resulted in larger and less fragmented assemblies, with at least 85% of the sequence data mapping to contigs greater than 1 kbp. Furthermore, a combination of metaSPAdes coassembly strategies and MetaBAT2 produced the highest number of medium-quality MAGs while capturing at least 70% of the metagenomes based on read recruitment. Utilizing different assembly/binning approaches also assists in the reconstruction of unique MAGs from closely related species that would have otherwise collapsed into a single MAG using a single workflow. Overall, our study suggests that leveraging multiple binning approaches with different metaSPAdes coassembly strategies may be required to maximize the recovery of good-quality MAGs. IMPORTANCE Drinking water contains phylogenetic diverse groups of bacteria, archaea, and eukarya that affect the esthetic quality of water, water infrastructure, and public health. Taxonomic, metabolic, and ecological inferences of the drinking water microbiome depend on the accuracy, quality, and completeness of genomes that are reconstructed through the application of genome-resolved metagenomics. Using time series metagenomic data, we present reproducible genome-centric metagenomic workflows that result in high-quality and -quantity genomes, which more accurately signifies the sequenced drinking water microbiome. These genome-centric metagenomic workflows will allow for improved taxonomic and functional potential analysis that offers enhanced insights into the stability and dynamics of drinking water microbial communities.}, } @article {pmid34729961, year = {2021}, author = {Shoemaker, R and Kim, J}, title = {Urobiome: An outlook on the metagenome of urological diseases.}, journal = {Investigative and clinical urology}, volume = {62}, number = {6}, pages = {611-622}, pmid = {34729961}, issn = {2466-054X}, support = {1U01DK103260/NH/NIH HHS/United States ; UL1 TR000124/TR/NCATS NIH HHS/United States ; 1R01DK100974/NH/NIH HHS/United States ; R01 DK100974/DK/NIDDK NIH HHS/United States ; U01 DK103260/DK/NIDDK NIH HHS/United States ; UL1 TR001881/TR/NCATS NIH HHS/United States ; U24 DK097154/NH/NIH HHS/United States ; U01DP006079/ACL/ACL HHS/United States ; U24 DK097154/DK/NIDDK NIH HHS/United States ; 1U01DP006079/CC/CDC HHS/United States ; }, mesh = {Causality ; Humans ; *Metagenome ; Microbiota/*physiology ; Urinary Tract/*microbiology ; *Urologic Diseases/epidemiology/microbiology/therapy ; }, abstract = {The urinary tract likely plays a role in the development of various urinary diseases due to the recently recognized notion that urine is not sterile. In this mini review, we summarize the current literature regarding the urinary microbiome and mycobiome and its relationship to various urinary diseases. It has been recently discovered that the healthy urinary tract contains a host of microorganisms, creating a urinary microbiome. The relative abundance and type of bacteria varies, but generally, deviations in the standard microbiome are observed in individuals with urologic diseases, such as bladder cancer, benign prostatic hyperplasia, urgency urinary incontinence, overactive bladder syndrome, interstitial cystitis, bladder pain syndrome, and urinary tract infections. However, whether this change is causative, or correlative has yet to be determined. In summary, the urinary tract hosts a complex microbiome. Changes in this microbiome may be indicative of urologic diseases and can be tracked to predict, prevent, and treat them in individuals. However, current analytical and sampling collection methods may present limitations to the development in the understanding of the urinary microbiome and its relationship with various urinary diseases. Further research on the differences between healthy and diseased microbiomes, the long-term effects of antibiotic treatments on the urobiome, and the effect of the urinary mycobiome on general health will be important in developing a comprehensive understanding of the urinary microbiome and its relationship to the human body.}, } @article {pmid34727738, year = {2022}, author = {Kawabata, S and Takagaki, M and Nakamura, H and Oki, H and Motooka, D and Nakamura, S and Nishida, T and Terada, E and Izutsu, N and Takenaka, T and Matsui, Y and Yamada, S and Asai, K and Tateishi, A and Umehara, T and Yano, Y and Bamba, Y and Matsumoto, K and Kishikawa, T and Okada, Y and Iida, T and Kishima, H}, title = {Dysbiosis of Gut Microbiome Is Associated With Rupture of Cerebral Aneurysms.}, journal = {Stroke}, volume = {53}, number = {3}, pages = {895-903}, doi = {10.1161/STROKEAHA.121.034792}, pmid = {34727738}, issn = {1524-4628}, mesh = {Aged ; Aneurysm, Ruptured/*microbiology ; *Campylobacter/classification/growth & development/isolation & purification ; Dysbiosis/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intracranial Aneurysm/*microbiology ; Male ; Middle Aged ; }, abstract = {BACKGROUND AND PURPOSE: Environmental factors are important with respect to the rupture of cerebral aneurysms. However, the relationship between the gut microbiome, an environmental factor, and aneurysm rupture is unclear. Therefore, we compared the gut microbiome in patients with unruptured intracranial aneurysms (UIAs) and ruptured aneurysms (RAs) to identify the specific bacteria causing the rupture of cerebral aneurysms.

METHODS: A multicenter, prospective case-control study was conducted over one year from 2019 to 2020. The fecal samples of patients with stable UIAs and RAs immediately after onset were collected. Their gut microbiomes were analyzed using 16S rRNA sequencing. Subsequently, a phylogenetic tree was constructed, and polymerase chain reaction was performed to identify the specific species.

RESULTS: A total of 28 RAs and 33 UIAs were included in this study. There was no difference in patient characteristics between RAs and UIAs: age, sex, hypertension, dyslipidemia, diabetes status, body mass index, and smoking. No difference was observed in alpha diversity; however, beta diversity was significantly different in the unweighted UniFrac distances. At the phylum level, the relative abundance of Campylobacter in the RA group was larger than that in the UIA group. Furthermore, the gut microbiome in the RA and UIA groups exhibited significantly different taxonomies. However, Campylobacter was focused on because it is widely known as pathogenic among these bacteria. Then, a phylogenetic tree of operational taxonomic units related to Campylobacter was constructed and 4 species were identified. Polymerase chain reaction for these species identified that the abundance of the genus Campylobacter and Campylobacter ureolyticus was significantly higher in the RA group.

CONCLUSIONS: The gut microbiome profile of patients with stable UIAs and RAs were significantly different. The genus Campylobacter and Campylobacter ureolyticus may be associated with the rupture of cerebral aneurysms.}, } @article {pmid34727151, year = {2021}, author = {Wang, L and Zhang, J and Zhou, M and Chen, Q and Yang, X and Hou, Y and Huang, M and Man, C and Jiang, Y}, title = {Evaluation of the effect of antibiotics on gut microbiota in early life based on culturomics, SMRT sequencing and metagenomics sequencing methods.}, journal = {Analytical methods : advancing methods and applications}, volume = {13}, number = {43}, pages = {5144-5156}, doi = {10.1039/d1ay01106e}, pmid = {34727151}, issn = {1759-9679}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Metagenomics/methods ; *Neurodegenerative Diseases ; Sequence Analysis, DNA ; }, abstract = {Symbiotic gut microbiota in early life plays a vital role in human health, and changes in its communication and function are associated with various complex disorders. In this study, we analyzed the gut flora communication of 6 infants at 4 months of age and determined the disturbances related to antibiotic treatment. By the culturomics and Single Molecule Real-time sequencing methods, a total of 6234 strains were divided into 16 genera and 45 species. The alpha diversity of culturable microorganisms in amoxicillin-treated infants was significantly less than that in healthy infants (p <0.05), as indicated by Chao 1, observed species and Faith's PD index. According to metagenomics, the dominant genus and species were Bifidobacterium and B. longum in the healthy group. After treatment with amoxicillin, the dominant genus and species shifted to Enterococcus and E. faecium. Based on the functional annotation of metagenomics, amoxicillin affected the metabolic function of the gut microbiome by activating carbohydrate and lipid metabolism and inhibiting amino acid metabolism. Besides, the intake of antibiotics in early life increased the risk of neurodegenerative disease, virus infectious disease and antimicrobial resistance. The Antibiotic Resistance Genes Database annotation result indicated that the abundance of drug-resistance genes in the antibiotic group was higher than that in the healthy group. These genes were associated with resistance to bacitracin, most of which were associated with K. pneumonia. These findings can provide guidance in the clinic on the proper usage of antibiotics.}, } @article {pmid34725503, year = {2022}, author = {Gaurav, K and Arora, S and Silva, P and Sánchez-Martín, J and Horsnell, R and Gao, L and Brar, GS and Widrig, V and John Raupp, W and Singh, N and Wu, S and Kale, SM and Chinoy, C and Nicholson, P and Quiroz-Chávez, J and Simmonds, J and Hayta, S and Smedley, MA and Harwood, W and Pearce, S and Gilbert, D and Kangara, N and Gardener, C and Forner-Martínez, M and Liu, J and Yu, G and Boden, SA and Pascucci, A and Ghosh, S and Hafeez, AN and O'Hara, T and Waites, J and Cheema, J and Steuernagel, B and Patpour, M and Justesen, AF and Liu, S and Rudd, JC and Avni, R and Sharon, A and Steiner, B and Kirana, RP and Buerstmayr, H and Mehrabi, AA and Nasyrova, FY and Chayut, N and Matny, O and Steffenson, BJ and Sandhu, N and Chhuneja, P and Lagudah, E and Elkot, AF and Tyrrell, S and Bian, X and Davey, RP and Simonsen, M and Schauser, L and Tiwari, VK and Randy Kutcher, H and Hucl, P and Li, A and Liu, DC and Mao, L and Xu, S and Brown-Guedira, G and Faris, J and Dvorak, J and Luo, MC and Krasileva, K and Lux, T and Artmeier, S and Mayer, KFX and Uauy, C and Mascher, M and Bentley, AR and Keller, B and Poland, J and Wulff, BBH}, title = {Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement.}, journal = {Nature biotechnology}, volume = {40}, number = {3}, pages = {422-431}, pmid = {34725503}, issn = {1546-1696}, support = {BB/P016855/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N019113/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/J/000PR8000/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9814/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/I002561/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/PPR1740/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M011216/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Aegilops/genetics ; Bread ; Genomics ; Metagenomics ; Plant Breeding ; Triticum/genetics ; }, abstract = {Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.}, } @article {pmid34724986, year = {2021}, author = {Tong, X and Leung, MHY and Shen, Z and Lee, JYY and Mason, CE and Lee, PKH}, title = {Metagenomic insights into the microbial communities of inert and oligotrophic outdoor pier surfaces of a coastal city.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {213}, pmid = {34724986}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Metagenome ; Metagenomics ; *Microbiota/genetics ; Proteobacteria/genetics ; }, abstract = {BACKGROUND: Studies of the microbiomes on surfaces in built environment have largely focused on indoor spaces, while outdoor spaces have received far less attention. Piers are engineered infrastructures commonly found in coastal areas, and due to their unique locations at the interface between terrestrial and aquatic ecosystems, pier surfaces are likely to harbor interesting microbiology. In this study, the microbiomes on the metal and concrete surfaces at nine piers located along the coastline of Hong Kong were investigated by metagenomic sequencing. The roles played by different physical attributes and environmental factors in shaping the taxonomic composition and functional traits of the pier surface microbiomes were determined. Metagenome-assembled genomes were reconstructed and their putative biosynthetic gene clusters were characterized in detail.

RESULTS: Surface material was found to be the strongest factor in structuring the taxonomic and functional compositions of the pier surface microbiomes. Corrosion-related bacteria were significantly enriched on metal surfaces, consistent with the pitting corrosion observed. The differential enrichment of taxa mediating biodegradation suggests differences between the metal and concrete surfaces in terms of specific xenobiotics being potentially degraded. Genome-centric analysis detected the presence of many novel species, with the majority of them belonging to the phylum Proteobacteria. Genomic characterization showed that the potential metabolic functions and secondary biosynthetic capacity were largely correlated with taxonomy, rather than surface attributes and geography.

CONCLUSIONS: Pier surfaces are a rich reservoir of abundant novel bacterial species. Members of the surface microbial communities use different mechanisms to counter the stresses under oligotrophic conditions. A better understanding of the outdoor surface microbiomes located in different environments should enhance the ability to maintain outdoor surfaces of infrastructures. Video Abstract.}, } @article {pmid34721409, year = {2021}, author = {Castejón, P and Cabas, I and Gómez, V and Chaves-Pozo, E and Cerezo-Ortega, I and Moriñigo, MÁ and Martínez-Manzanares, E and Galindo-Villegas, J and García-Ayala, A}, title = {Vaccination of Gilthead Seabream After Continuous Xenoestrogen Oral Exposure Enhances the Gut Endobolome and Immune Status via GPER1.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {742827}, pmid = {34721409}, issn = {1664-3224}, mesh = {Adjuvants, Immunologic/pharmacology ; Animals ; Endocrine Disruptors/toxicity ; Ethinyl Estradiol/*toxicity ; Fish Proteins/immunology/metabolism ; Gastrointestinal Microbiome/*immunology ; Hemocyanins/immunology ; Receptors, Estrogen/*immunology/metabolism ; Receptors, G-Protein-Coupled/*immunology/metabolism ; Sea Bream/*immunology/metabolism ; Vaccination ; }, abstract = {In fish culture settings, the exogenous input of steroids is a matter of concern. Recently, we unveiled that in the gilthead seabream (Sparus aurata), the G protein-coupled estrogen receptor agonist G-1 (G1) and the endocrine disruptor 17α-ethinylestradiol (EE2) are potent modulators in polyreactive antibody production. However, the integral role of the microbiota upon immunity and antibody processing in response to the effect of EE2 remains largely unexplored. Here, juvenile seabreams continuously exposed for 84 days to oral G1 or EE2 mixed in the fish food were intraperitoneally (i.p.) immune primed on day 42 with the model antigen keyhole limpet hemocyanin (KLH). A critical panel of systemic and mucosal immune markers, serum VTG, and humoral, enzymatic, and bacteriolytic activities were recorded and correlated with gut bacterial metagenomic analysis 1 day post-priming (dpp). Besides, at 15 dpp, animals received a boost to investigate the possible generation of specific anti-KLH antibodies at the systemic and mucosal interphases by the end of the trial. On day 43, EE2 but not G1 induced a significant shift in the serum VTG level of naive fish. Simultaneously, significant changes in some immune enzymatic activities in the serum and gut mucus of the EE2-treated group were recorded. In comparison, the vaccine priming immunization resulted in an attenuated profile of most enzymatic activities in the same group. The gut genes qPCR analysis exhibited a related pattern, only emphasized by a significant shift in the EE2 group's il1b expression. The gut bacterial microbiome status underwent 16S rRNA dynamic changes in alpha diversity indices, only with the exposure to oral G1, supporting functional alterations on cellular processes, signaling, and lipid metabolism in the microbiota. By the same token, the immunization elevated the relative abundance of Fusobacteria only in the control group, while this phylum was depleted in both the treated groups. Remarkably, the immunization also promoted changes in the bacterial class Betaproteobacteria and the estrogen-associated genus Novosphingobium. Furthermore, systemic and mucosal KLH-specific immunoglobulin (Ig)M and IgT levels in the fully vaccinated fish showed only slight changes 84 days post-estrogenic oral administration. In summary, our results highlight the intrinsic relationship among estrogens, their associated receptors, and immunization in the ubiquitous fish immune regulation and the subtle but significant crosstalk with the gut endobolome.}, } @article {pmid34719741, year = {2021}, author = {Huergo, LF and Conzentino, M and Gonçalves, MV and Gernet, MV and Reis, RA and Pedrosa, FO and Baura, VA and Pires, A and Gerhardt, ECM and Tuleski, TR and Balsanelli, E and Guizelini, D and Souza, EM and Chandra, G and Cruz, LM}, title = {The microbiome of a shell mound: ancient anthropogenic waste as a source of Streptomyces degrading recalcitrant polysaccharides.}, journal = {World journal of microbiology & biotechnology}, volume = {37}, number = {12}, pages = {210}, pmid = {34719741}, issn = {1573-0972}, mesh = {Archaea ; Bacteria/genetics/isolation & purification/metabolism ; Biodiversity ; Biotechnology ; Brazil ; Carbon/metabolism ; Carboxymethylcellulose Sodium ; Cellulose ; Chitin ; DNA, Ribosomal ; Hydrolases ; Metagenome ; *Microbiota ; Polysaccharides/*metabolism ; Proteobacteria ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; Streptomyces/genetics/isolation & purification/*metabolism ; Xylans/metabolism ; }, abstract = {Metagenome amplicon DNA sequencing and traditional cell culture techniques are helping to uncover the diversity and the biotechnological potential of prokaryotes in different habitats around the world. It has also had a profound impact on microbial taxonomy in the last decades. Here we used metagenome 16S rDNA amplicon sequencing to reveal the microbiome composition of different layers of an anthropogenic soil collected at a shell mound Sambaqui archeological site. The Samabaqui soil microbiome is mainly composed by phyla Acidobacteria, Rokubacteria, Proteobacteria and Thaumarchaeota. Using culture-dependent analysis we obtained few Streptomyces isolates from the Sambaqui soil. One of the isolates, named Streptomyces sp. S3, was able to grow in minimal medium containing recalcitrant polysaccharides including chitin, xylan, carboxymethylcellulose or microcrystalline cellulose as sole carbon sources. The activities of enzymes degrading these compounds were confirmed in cell free supernatants. The genome sequence revealed not only an arsenal of genes related to polysaccharides degradation but also biosynthetic gene clusters which may be involved in the production of biotechnologically interesting secondary metabolites.}, } @article {pmid34719313, year = {2021}, author = {Hong, L and Chen, Y and Ye, L}, title = {Characteristics of the lung microbiota in lower respiratory tract infections with and without history of pneumonia.}, journal = {Bioengineered}, volume = {12}, number = {2}, pages = {10480-10490}, pmid = {34719313}, issn = {2165-5987}, mesh = {Adult ; Aged ; Algorithms ; Bronchoalveolar Lavage Fluid/microbiology ; Community-Acquired Infections/microbiology/pathology ; Discriminant Analysis ; Female ; Humans ; Lung/*microbiology/*pathology ; Male ; *Microbiota ; Middle Aged ; Models, Biological ; Phylogeny ; Pneumonia/*microbiology/*pathology ; }, abstract = {Lung microbiota plays an important role in many diseases including lower respiratory tract infections (LRTI) and pneumonia. This study aimed to explore the effects of community-acquired pneumonia (CAP) on microbial diversity and identify potential biomarkers of respiratory tract in CAP LRTI patients. In the current study, a comprehensive bioinformatics analysis was performed based on metagenomic next-generation sequencing technology, followed by alpha and beta diversity, LEfSe, and co-occurrence network analysis, and random forest model construction. Our results showed that CAP dramatically influenced taxon abundance, and the significant differences in microbiota including Proteobacteria, Bacteroidetes, Euryarchaeota, Firmicutes and Spirochetes were observed at the phylum level. Co-occurrence network selected out novel modules involved in microbial proliferation-associated pathways. A random forest model screened Klebsiella pneumoniae and Bacillus cereus as potential diagnostic biomarkers with high AUC values. The microbial composition was different between CAP LRTI patients and non-CAP LRTI patients. Klebsiella pneumoniae and Bacillus cereus were strongly associated with increased severity of LRTI with a pneumonia history. Our findings provided an insight for a better understanding of community and structure of lung microbiota for future diagnosis and treatment in LRTI patients with a history of pneumonia. Moreover, these microbes were considered as potential biomarkers for predicting the risks for the treatment strategies of LRTI.}, } @article {pmid34718713, year = {2022}, author = {Jin, H and Hu, G and Sun, C and Duan, Y and Zhang, Z and Liu, Z and Zhao, XM and Chen, WH}, title = {mBodyMap: a curated database for microbes across human body and their associations with health and diseases.}, journal = {Nucleic acids research}, volume = {50}, number = {D1}, pages = {D808-D816}, pmid = {34718713}, issn = {1362-4962}, mesh = {Asthma/microbiology/pathology ; Bacteria/classification/*genetics/metabolism ; Body Mass Index ; Crohn Disease/microbiology/pathology ; Cystic Fibrosis/microbiology/pathology ; DNA, Bacterial/genetics ; *Databases, Factual ; Endometrial Neoplasms/microbiology/pathology ; Enterocolitis, Necrotizing/microbiology/pathology ; Female ; High-Throughput Nucleotide Sequencing ; Human Body ; Humans ; Internet ; Metadata ; *Metagenome ; Microbiota/*genetics ; Phylogeny ; Pulmonary Disease, Chronic Obstructive/microbiology/pathology ; Respiratory Tract Infections/microbiology/pathology ; *Software ; Vaginosis, Bacterial/microbiology/pathology ; }, abstract = {mBodyMap is a curated database for microbes across the human body and their associations with health and diseases. Its primary aim is to promote the reusability of human-associated metagenomic data and assist with the identification of disease-associated microbes by consistently annotating the microbial contents of collected samples using state-of-the-art toolsets and manually curating the meta-data of corresponding human hosts. mBodyMap organizes collected samples based on their association with human diseases and body sites to enable cross-dataset integration and comparison. To help users find microbes of interest and visualize and compare their distributions and abundances/prevalence within different body sites and various diseases, the mBodyMap database is equipped with an intuitive interface and extensive graphical representations of the collected data. So far, it contains a total of 63 148 runs, including 14 401 metagenomes and 48 747 amplicons related to health and 56 human diseases, from within 22 human body sites across 136 projects. Also available in the database are pre-computed abundances and prevalence of 6247 species (belonging to 1645 genera) stratified by body sites and diseases. mBodyMap can be accessed at: https://mbodymap.microbiome.cloud.}, } @article {pmid34718699, year = {2022}, author = {Yang, W and Feiner, N and Salvi, D and Laakkonen, H and Jablonski, D and Pinho, C and Carretero, MA and Sacchi, R and Zuffi, MAL and Scali, S and Plavos, K and Pafilis, P and Poulakakis, N and Lymberakis, P and Jandzik, D and Schulte, U and Aubret, F and Badiane, A and Perez I de Lanuza, G and Abalos, J and While, GM and Uller, T}, title = {Population Genomics of Wall Lizards Reflects the Dynamic History of the Mediterranean Basin.}, journal = {Molecular biology and evolution}, volume = {39}, number = {1}, pages = {}, pmid = {34718699}, issn = {1537-1719}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Genetic Variation ; *Lizards/genetics ; *Metagenomics ; Phylogeny ; Phylogeography ; }, abstract = {The Mediterranean Basin has experienced extensive change in geology and climate over the past six million years. Yet, the relative importance of key geological events for the distribution and genetic structure of the Mediterranean fauna remains poorly understood. Here, we use population genomic and phylogenomic analyses to establish the evolutionary history and genetic structure of common wall lizards (Podarcis muralis). This species is particularly informative because, in contrast to other Mediterranean lizards, it is widespread across the Iberian, Italian, and Balkan Peninsulas, and in extra-Mediterranean regions. We found strong support for six major lineages within P. muralis, which were largely discordant with the phylogenetic relationship of mitochondrial DNA. The most recent common ancestor of extant P. muralis was likely distributed in the Italian Peninsula, and experienced an "Out-of-Italy" expansion following the Messinian salinity crisis (∼5 Mya), resulting in the differentiation into the extant lineages on the Iberian, Italian, and Balkan Peninsulas. Introgression analysis revealed that both inter- and intraspecific gene flows have been pervasive throughout the evolutionary history of P. muralis. For example, the Southern Italy lineage has a hybrid origin, formed through admixture between the Central Italy lineage and an ancient lineage that was the sister to all other P. muralis. More recent genetic differentiation is associated with the onset of the Quaternary glaciations, which influenced population dynamics and genetic diversity of contemporary lineages. These results demonstrate the pervasive role of Mediterranean geology and climate for the evolutionary history and population genetic structure of extant species.}, } @article {pmid34718358, year = {2022}, author = {Petrick, JL and Wilkinson, JE and Michaud, DS and Cai, Q and Gerlovin, H and Signorello, LB and Wolpin, BM and Ruiz-Narváez, EA and Long, J and Yang, Y and Johnson, WE and Shu, XO and Huttenhower, C and Palmer, JR}, title = {The oral microbiome in relation to pancreatic cancer risk in African Americans.}, journal = {British journal of cancer}, volume = {126}, number = {2}, pages = {287-296}, pmid = {34718358}, issn = {1532-1827}, support = {R01 CA058420/CA/NCI NIH HHS/United States ; U01 CA164974/CA/NCI NIH HHS/United States ; U01 CA187508/CA/NCI NIH HHS/United States ; }, mesh = {Black People/*genetics ; Case-Control Studies ; Female ; Humans ; Male ; *Microbiota ; Middle Aged ; Mouth/*microbiology ; Pancreatic Neoplasms/epidemiology/microbiology/*pathology ; Prospective Studies ; Risk Factors ; United States/epidemiology ; Black or African American ; }, abstract = {BACKGROUND: African Americans have the highest pancreatic cancer incidence of any racial/ethnic group in the United States. The oral microbiome was associated with pancreatic cancer risk in a recent study, but no such studies have been conducted in African Americans. Poor oral health, which can be a cause or effect of microbial populations, was associated with an increased risk of pancreatic cancer in a single study of African Americans.

METHODS: We prospectively investigated the oral microbiome in relation to pancreatic cancer risk among 122 African-American pancreatic cancer cases and 354 controls. DNA was extracted from oral wash samples for metagenomic shotgun sequencing. Alpha and beta diversity of the microbial profiles were calculated. Multivariable conditional logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for associations between microbes and pancreatic cancer risk.

RESULTS: No associations were observed with alpha or beta diversity, and no individual microbial taxa were differentially abundant between cases and control, after accounting for multiple comparisons. Among never smokers, there were elevated ORs for known oral pathogens: Porphyromonas gingivalis (OR = 1.69, 95% CI: 0.80-3.56), Prevotella intermedia (OR = 1.40, 95% CI: 0.69-2.85), and Tannerella forsythia (OR = 1.36, 95% CI: 0.66-2.77).

CONCLUSIONS: Previously reported associations between oral taxa and pancreatic cancer were not present in this African-American population overall.}, } @article {pmid34715437, year = {2021}, author = {Lugli, GA and Calvete-Torre, I and Alessandri, G and Milani, C and Turroni, F and Laiolo, P and Ossiprandi, MC and Margolles, A and Ruiz, L and Ventura, M}, title = {Phylogenetic classification of ten novel species belonging to the genus Bifidobacterium comprising B. phasiani sp. nov., B. pongonis sp. nov., B. saguinibicoloris sp. nov., B. colobi sp. nov., B. simiiventris sp. nov., B. santillanense sp. nov., B. miconis sp. nov., B. amazonense sp. nov., B. pluvialisilvae sp. nov., and B. miconisargentati sp. nov.}, journal = {Systematic and applied microbiology}, volume = {44}, number = {6}, pages = {126273}, doi = {10.1016/j.syapm.2021.126273}, pmid = {34715437}, issn = {1618-0984}, mesh = {Animals ; Bacterial Typing Techniques ; Base Composition ; *Bifidobacterium/genetics ; DNA, Bacterial/genetics ; *Fatty Acids ; Feces ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Ten Bifidobacterium strains, i.e., 6T3, 64T4, 79T10, 80T4, 81T8, 82T1, 82T10, 82T18, 82T24, and 82T25, were isolated from mantled guereza (Colobus guereza), Sumatran orangutan (Pongo abeli), silvery marmoset (Mico argentatus), golden lion tamarin (Leontopithecus rosalia), pied tamarin (Saguinus bicolor), and common pheasant (Phaisanus colchinus). Cells are Gram-positive, non-motile, non-sporulating, facultative anaerobic, and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on the core genome sequences revealed that isolated strains exhibit close phylogenetic relatedness with Bifidobacterium genus members belonging to the Bifidobacterium bifidum, Bifidobacterium longum, Bifidobacterium pullorum, and Bifidobacterium tissieri phylogenetic groups. Phenotypic characterization and genotyping based on the genome sequences clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, B. phasiani sp. nov. (6T3 = LMG 32224[T] = DSM 112544[T]), B. pongonis sp. nov. (64T4 = LMG 32281[T] = DSM 112547[T]), B. saguinibicoloris sp. nov. (79T10 = LMG 32232[T] = DSM 112543[T]), B. colobi sp. nov. (80T4 = LMG 32225[T] = DSM 112552[T]), B. simiiventris sp. nov. (81T8 = LMG 32226[T] = DSM 112549[T]), B. santillanense sp. nov. (82T1 = LMG 32284[T] = DSM 112550[T]), B. miconis sp. nov. (82T10 = LMG 32282[T] = DSM 112551[T]), B. amazonense sp. nov. (82T18 = LMG 32297[T] = DSM 112548[T]), pluvialisilvae sp. nov. (82T24 = LMG 32229[T] = DSM 112545[T]), and B. miconisargentati sp. nov. (82T25 = LMG 32283[T] = DSM 112546[T]) are proposed as novel Bifidobacterium species.}, } @article {pmid34714788, year = {2021}, author = {Mongodin, EF and Saxena, V and Iyyathurai, J and Lakhan, R and Ma, B and Silverman, E and Lee, ZL and Bromberg, JS}, title = {Chronic rejection as a persisting phantom menace in organ transplantation: a new hope in the microbiota?.}, journal = {Current opinion in organ transplantation}, volume = {26}, number = {6}, pages = {567-581}, pmid = {34714788}, issn = {1531-7013}, support = {P01 AI153003/AI/NIAID NIH HHS/United States ; R01 AI114496/AI/NIAID NIH HHS/United States ; R01 HL148672/HL/NHLBI NIH HHS/United States ; R37 AI062765/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Intestines ; *Microbiota ; *Organ Transplantation/adverse effects ; }, abstract = {PURPOSE OF REVIEW: The microbiota plays an important role in health and disease. During organ transplantation, perturbations in microbiota influence transplant outcome. We review recent advances in characterizing microbiota and studies on regulation of intestinal epithelial barrier function and mucosal and systemic immunity by microbiota and their metabolites. We discuss implications of these interactions on transplant outcomes.

RECENT FINDINGS: Metagenomic approaches have helped the research community identify beneficial and harmful organisms. Microbiota regulates intestinal epithelial functions. Signals released by epithelial cells or microbiota trigger pro-inflammatory or anti-inflammatory effects on innate and adaptive immune cells, influencing the structure and function of the immune system. Assessment and manipulation of microbiota can be used for biomarkers for diagnosis, prognosis, and therapy.

SUMMARY: The bidirectional dialogue between the microbiota and immune system is a major influence on immunity. It can be targeted for biomarkers or therapy. Recent studies highlight a close association of transplant outcomes with microbiota, suggesting exciting potential avenues for management of host physiology and organ transplantation.}, } @article {pmid34714225, year = {2021}, author = {Lu, X and Hua, X and Wang, Y and Zhang, D and Jiang, S and Yang, S and Wang, X and Shen, Q and Zhou, T and Lin, Z and Zhang, W and Cui, L}, title = {Comparison of gut viral communities in diarrhoea and healthy dairy calves.}, journal = {The Journal of general virology}, volume = {102}, number = {10}, pages = {}, doi = {10.1099/jgv.0.001663}, pmid = {34714225}, issn = {1465-2099}, mesh = {Animals ; Caliciviridae/classification/genetics/isolation & purification ; Cattle/*virology ; Cattle Diseases/*virology ; DNA Viruses/classification/genetics/isolation & purification ; Dairying ; Diarrhea/*veterinary/virology ; Feces/virology ; Genome, Viral ; Intestines/*virology ; Mamastrovirus/classification/genetics/isolation & purification ; Metagenomics ; Phylogeny ; *Virome ; }, abstract = {Calf diarrhoea has been a major cause of economic losses in the global dairy industry. Many factors, including multiple pathogen infections, can directly or indirectly cause calf diarrhoea. This study compared the faecal virome between 15 healthy calves and 15 calves with diarrhoea. Significantly lower diversity of viruses was found in samples from animals with diarrhoea than those in the healthy ones, and this feature may also be related to the age of the calves. Viruses belonging to the families Astroviridae and Caliciviridae that may cause diarrhoea in dairy calves have been characterized, which revealed that reads of caliciviruses and astroviruses in diarrhoea calves were much higher than those in healthy calves. Five complete genomic sequences closely related to Smacoviridae have been identified, which may participate in the regulation of the gut virus community ecology of healthy hosts together with bacteriophages. This research provides a theoretical basis for further understanding of known or potential enteric pathogens related to calf diarrhoea.}, } @article {pmid34713713, year = {2021}, author = {Ferrell, M and Bazeley, P and Wang, Z and Levison, BS and Li, XS and Jia, X and Krauss, RM and Knight, R and Lusis, AJ and Garcia-Garcia, JC and Hazen, SL and Tang, WHW}, title = {Fecal Microbiome Composition Does Not Predict Diet-Induced TMAO Production in Healthy Adults.}, journal = {Journal of the American Heart Association}, volume = {10}, number = {21}, pages = {e021934}, pmid = {34713713}, issn = {2047-9980}, support = {R01 HL130819/HL/NHLBI NIH HHS/United States ; R01 HL144651/HL/NHLBI NIH HHS/United States ; R01 DK106000/DK/NIDDK NIH HHS/United States ; R01 HL103866/HL/NHLBI NIH HHS/United States ; R01 HL147883/HL/NHLBI NIH HHS/United States ; R01 HL126827/HL/NHLBI NIH HHS/United States ; T32 GM007250/GM/NIGMS NIH HHS/United States ; T32 HL134622/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Bacteria/metabolism ; Choline/metabolism ; Cross-Over Studies ; Diet ; Feces ; Gastrointestinal Microbiome ; Humans ; Lyases/metabolism ; Methylamines/blood ; *Microbiota ; }, abstract = {Background Trimethylamine-N-oxide (TMAO) is a small molecule derived from the metabolism of dietary nutrients by gut microbes and contributes to cardiovascular disease. Plasma TMAO increases following consumption of red meat. This metabolic change is thought to be partly because of the expansion of gut microbes able to use nutrients abundant in red meat. Methods and Results We used data from a randomized crossover study to estimate the degree to which TMAO can be estimated from fecal microbial composition. Healthy participants received a series of 3 diets that differed in protein source (red meat, white meat, and non-meat), and fecal, plasma, and urine samples were collected following 4 weeks of exposure to each diet. TMAO was quantitated in plasma and urine, while shotgun metagenomic sequencing was performed on fecal DNA. While the cai gene cluster was weakly correlated with plasma TMAO (rho=0.17, P=0.0007), elastic net models of TMAO were not improved by abundances of bacterial genes known to contribute to TMAO synthesis. A global analysis of all taxonomic groups, genes, and gene families found no meaningful predictors of TMAO. We postulated that abundances of known genes related to TMAO production do not predict bacterial metabolism, and we measured choline- and carnitine-trimethylamine lyase activity during fecal culture. Trimethylamine lyase genes were only weakly correlated with the activity of the enzymes they encode. Conclusions Fecal microbiome composition does not predict systemic TMAO because, in this case, gene copy number does not predict bacterial metabolic activity. Registration URL: https://www.clinicaltrials.gov; Unique identifier: NCT01427855.}, } @article {pmid34711812, year = {2021}, author = {Wang, X and Ning, Y and Li, C and Gong, Y and Huang, R and Hu, M and Poulet, B and Xu, K and Zhao, G and Zhou, R and Lammi, MJ and Guo, X}, title = {Alterations in the gut microbiota and metabolite profiles of patients with Kashin-Beck disease, an endemic osteoarthritis in China.}, journal = {Cell death & disease}, volume = {12}, number = {11}, pages = {1015}, pmid = {34711812}, issn = {2041-4889}, support = {81803179//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81803178//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81620108026//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Biodiversity ; Case-Control Studies ; China/epidemiology ; Discriminant Analysis ; *Endemic Diseases ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Gene Expression Profiling ; Humans ; Kashin-Beck Disease/epidemiology/*metabolism/*microbiology ; Least-Squares Analysis ; *Metabolomics ; Metagenomics ; Osteoarthritis/epidemiology/*metabolism/*microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; Risk Assessment ; }, abstract = {Kashin-Beck disease (KBD) is a severe osteochondral disorder that may be driven by the interaction between genetic and environmental factors. We aimed to improve our understanding of the gut microbiota structure in KBD patients of different grades and the relationship between the gut microbiota and serum metabolites. Fecal and serum samples collected from KBD patients and normal controls (NCs) were used to characterize the gut microbiota using 16S rDNA gene and metabolomic sequencing via liquid chromatography-mass spectrometry (LC/MS). To identify whether gut microbial changes at the species level are associated with the genes or functions of the gut bacteria in the KBD patients, metagenomic sequencing of fecal samples from grade I KBD, grade II KBD and NC subjects was performed. The KBD group was characterized by elevated levels of Fusobacteria and Bacteroidetes. A total of 56 genera were identified to be significantly differentially abundant between the two groups. The genera Alloprevotella, Robinsoniella, Megamonas, and Escherichia_Shigella were more abundant in the KBD group. Consistent with the 16S rDNA analysis at the genus level, most of the differentially abundant species in KBD subjects belonged to the genus Prevotella according to metagenomic sequencing. Serum metabolomic analysis identified some differentially abundant metabolites among the grade I and II KBD and NC groups that were involved in lipid metabolism metabolic networks, such as that for unsaturated fatty acids and glycerophospholipids. Furthermore, we found that these differences in metabolite levels were associated with altered abundances of specific species. Our study provides a comprehensive landscape of the gut microbiota and metabolites in KBD patients and provides substantial evidence of a novel interplay between the gut microbiome and metabolome in KBD pathogenesis.}, } @article {pmid34710620, year = {2022}, author = {Ding, X and Zhou, J and Chai, Y and Yan, Z and Liu, X and Dong, Y and Mei, X and Jiang, Y and Lei, H}, title = {A metagenomic study of the gut microbiome in PTB'S disease.}, journal = {Microbes and infection}, volume = {24}, number = {2}, pages = {104893}, doi = {10.1016/j.micinf.2021.104893}, pmid = {34710620}, issn = {1769-714X}, mesh = {Bacteria ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: There is an abundant link between the gut microbiota and human health and it plays a critical role in the clinic. It is recognized that microbial dysregulation contributes to the pathogenesis of tuberculosis (TB) but the underlying mechanisms remain unclear. In this study, we investigated the association of gut microbiome composition with TB as well as its possible roles in the development of this disease.

METHODS: Fecal samples were collected from 10 TB patients and 20 healthy control samples. DNA extracted from fecal samples was subjected to 16S rDNA gene sequencing analysis on the Illumina MiSeq platform.

RESULTS: Compared with healthy control samples, the gut microbiome of patients with TB was characterized by the decreased Alpha diversity. Perhaps, the decrease of microbial diversity which results in microbial dysregulation is the reason for clinical patients with more symptoms. The PTB group showed the most unique microbiota by higher abundance of Bifidobacteriaceae, Bifidobacteriales, Coriobacteriaceae, Coriobacteriales, Actinobacteria, Caulobacteraceae, Phyllobacteriaceae, Rhizobiales, Burkholderiaceae, Burkholderiaceae. Inflammatory status in PTB patients may be associated with the increased abundance of Clostridia and decreased abundance of Prevotella. We found that the abundance of Solobacterium and Actinobacteria was higher in the patients. There were 4 significant differences (p < 0.05) in the two groups which belonged to four metabolic categories, including endocytosis, phosphotransferase system (PTS), toluene degradation, and amoebiasis.

CONCLUSION: We applied the approach of metagenomic sequencing to characterize the features of gut microbiota in PTB patients. The present study provided a detailed analysis of the characterization of the gut microbiota in patients based on the clinic. According to the metagenome analysis, our results indicated that the gut microbiota in PTB patients was significantly different from healthy control samples as characterized by the bacteria and metabolic pathway. The richness of the gut microbiota in patients was revealed. It was hypothesized that the above-mentioned changes of the gut microbiota could exert an impact on the development of PTB through the downstream regulation of the immune status of the host by way of the gut-lung axis.}, } @article {pmid34710599, year = {2022}, author = {Kim, H and Kang, S and Sang, BI}, title = {Metabolic cascade of complex organic wastes to medium-chain carboxylic acids: A review on the state-of-the-art multi-omics analysis for anaerobic chain elongation pathways.}, journal = {Bioresource technology}, volume = {344}, number = {Pt A}, pages = {126211}, doi = {10.1016/j.biortech.2021.126211}, pmid = {34710599}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Bioreactors ; Carboxylic Acids ; Fermentation ; *Microbiota ; }, abstract = {Medium-chain carboxylic acid (MCCA) production from organic wastes has attracted much attention because of their higher energy contents and diverse applications. Anaerobic reactor microbiomes are stable and resilient and have resulted in efficient performance during many years of operation for thousands of full-scale anaerobic digesters worldwide. The method underlying how the relevant microbial pathways contribute to elongate carbon chains in reactor microbiomes is important. In particular, the reverse β-oxidation pathway genes are critical to upgrading short-chain fermentation products to MCCAs via a chain elongation (CE) process. Diverse genomics and metagenomics studies have been conducted in various fields, ranging from intracellular metabolic pathways to metabolic cascades between different strains. This review covers taxonomic approach to culture processes depending on types of organic wastes and the deeper understanding of genome and metagenome-scale CE pathway construction, and the co-culture and multi-omics technology that should be addressed in future research.}, } @article {pmid34710519, year = {2022}, author = {Dias, D and Fonseca, C and Mendo, S and Caetano, T}, title = {A closer look on the variety and abundance of the faecal resistome of wild boar.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {292}, number = {Pt B}, pages = {118406}, doi = {10.1016/j.envpol.2021.118406}, pmid = {34710519}, issn = {1873-6424}, mesh = {Animals ; Anti-Bacterial Agents ; Escherichia coli ; Feces ; Genes, Bacterial ; Humans ; *Microbiota ; *Sus scrofa ; Swine ; }, abstract = {Antimicrobial resistance (AMR) is a serious problem for public and animal health, and also for the environment. Monitoring and reporting the occurrence of AMR determinants and bacteria with the potential to disseminate is a priority for health surveillance programs around the world and critical to the One Health concept. Wildlife is a reservoir of AMR, and human activities can strongly influence their resistome. The main goal of this work was to study the resistome of wild boar faecal microbiome, one of the most important game species in Europe using metagenomic and culturing approaches. The most abundant genes identified by the high-throughput qPCR array encode mobile genetic elements, including integrons, which can promote the dissemination of AMR determinants. A diverse set of genes (n = 62) conferring resistance to several classes of antibiotics (ARGs), some of them included in the WHO list of critically important antimicrobials were also detected. The most abundant ARGs confer resistance to tetracyclines and aminoglycosides. The phenotypic resistance of E. coli and Enterococcus spp. were also investigated, and together supported the metagenomic results. As the wild boar is an omnivorous animal, it can be a disseminator of AMR bacteria and ARGs to livestock, humans, and the environment. This study supports that wild boar can be a key sentinel species in ecosystems surveillance and should be included in National Action Plans to fight AMR, adopting a One Health approach.}, } @article {pmid34710422, year = {2022}, author = {DeBofsky, A and Xie, Y and Challis, JK and Ankley, PJ and Brinkmann, M and Jones, PD and Giesy, JP}, title = {16S rRNA metabarcoding unearths responses of rare gut microbiome of fathead minnows exposed to benzo[a]pyrene.}, journal = {The Science of the total environment}, volume = {807}, number = {Pt 3}, pages = {151060}, doi = {10.1016/j.scitotenv.2021.151060}, pmid = {34710422}, issn = {1879-1026}, mesh = {Animals ; Benzo(a)pyrene/toxicity ; *Cyprinidae ; *Gastrointestinal Microbiome ; Genomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Activities of gut microbiomes are often overlooked in assessments of ecotoxicological effects of environmental contaminants. Effects of the polycyclic aromatic hydrocarbon, benzo[a]pyrene (BaP) on active gut microbiomes of juvenile fathead minnows (Pimephales promelas) were investigated. Fish were exposed for two weeks, to concentrations of 0, 1, 10, 100, or 1000 μg BaP g[-1] in the diet. The active gut microbiome was characterized using 16S rRNA metabarcoding to determine its response to dietary exposure of BaP. BaP reduced alpha-diversity at the greatest exposure concentrations. Additionally, exposure to BaP altered community composition of active microbiome and resulted in differential proportion of taxa associated with hydrocarbon degradation and fish health. Neighborhood selection networks of active microbiomes were not reduced with greater concentrations of BaP, which suggests ecological resistance and/or resilience of gut microbiota. The active gut microbiome had a similar overall biodiversity as that of the genomic gut microbiota, but had a distinct composition from that of the 16S rDNA profile. Responses of alpha- and beta-diversities of the active microbiome to BaP exposure were consistent with that of genomic microbiomes. Normalized activity of microbiome via the ratio of rRNA to rDNA abundance revealed rare taxa that became active or dormant due to exposure to BaP. These differences highlight the need to assess both 16S rDNA and rRNA metabarcoding to fully derive bacterial compositional changes resulting from exposure to contaminants.}, } @article {pmid34709713, year = {2022}, author = {Elgarten, CW and Tanes, C and Lee, JJ and Danziger-Isakov, LA and Grimley, MS and Green, M and Michaels, MG and Barnum, JL and Ardura, MI and Auletta, JJ and Blumenstock, J and Seif, AE and Bittinger, KL and Fisher, BT}, title = {Early stool microbiome and metabolome signatures in pediatric patients undergoing allogeneic hematopoietic cell transplantation.}, journal = {Pediatric blood & cancer}, volume = {69}, number = {1}, pages = {e29384}, pmid = {34709713}, issn = {1545-5017}, support = {HHSN272201600014C/AI/NIAID NIH HHS/United States ; }, mesh = {Child ; Feces ; *Gastrointestinal Microbiome ; *Hematopoietic Stem Cell Transplantation ; Humans ; Metabolome ; *Microbiota ; }, abstract = {BACKGROUND: The contribution of the gastrointestinal tract microbiome to outcomes after allogeneic hematopoietic cell transplantation (HCT) is increasingly recognized. Investigations of larger pediatric cohorts aimed at defining the microbiome state and associated metabolic patterns pretransplant are needed.

METHODS: We sought to describe the pretransplant stool microbiome in pediatric allogenic HCT patients at four centers. We performed shotgun metagenomic sequencing and untargeted metabolic profiling on pretransplant stool samples. Samples were compared with normal age-matched controls and by clinical characteristics. We then explored associations between stool microbiome measurements and metabolite concentrations.

RESULTS: We profiled stool samples from 88 pediatric allogeneic HCT patients, a median of 4 days before transplant. Pretransplant stool samples differed from healthy controls based on indices of alpha diversity and in the proportional abundance of specific taxa and bacterial genes. Relative to stool from healthy patients, samples from HCT patients had decreased proportion of Bacteroides, Ruminococcaeae, and genes involved in butyrate production, but were enriched for gammaproteobacterial species. No systematic differences in stool microbiome or metabolomic profiles by age, transplant indication, or hospital were noted. Stool metabolites demonstrated strong correlations with microbiome composition.

DISCUSSION: Stool samples from pediatric allogeneic HCT patients demonstrate substantial dysbiosis early in the transplant course. As microbiome disruptions associate with adverse transplant outcomes, pediatric-specific analyses examining longitudinal microbiome and metabolome changes are imperative to identify causal associations and to inform rational design of interventions.}, } @article {pmid34708327, year = {2021}, author = {de Medeiros Azevedo, T and Aburjaile, FF and Ferreira-Neto, JRC and Pandolfi, V and Benko-Iseppon, AM}, title = {The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications.}, journal = {World journal of microbiology & biotechnology}, volume = {37}, number = {12}, pages = {206}, pmid = {34708327}, issn = {1573-0972}, mesh = {Agricultural Inoculants ; Agriculture ; Biotechnology/*methods ; Computational Biology ; *Endophytes ; Humans ; Metagenomics/methods ; *Microbiota ; Plant Roots/microbiology ; Plants/*microbiology ; Soil ; Soil Microbiology ; }, abstract = {Similar to other organisms, plants establish interactions with a variety of microorganisms in their natural environment. The plant microbiome occupies the host plant's tissues, either internally or on its surfaces, showing interactions that can assist in its growth, development, and adaptation to face environmental stresses. The advance of metagenomics and metatranscriptomics approaches has strongly driven the study and recognition of plant microbiome impacts. Research in this regard provides comprehensive information about the taxonomic and functional aspects of microbial plant communities, contributing to a better understanding of their dynamics. Evidence of the plant microbiome's functional potential has boosted its exploitation to develop more ecological and sustainable agricultural practices that impact human health. Although microbial inoculants' development and use are promising to revolutionize crop production, interdisciplinary studies are needed to identify new candidates and promote effective practical applications. On the other hand, there are challenges in understanding and analyzing complex data generated within a plant microbiome project's scope. This review presents aspects about the complex structuring and assembly of the microbiome in the host plant's tissues, metagenomics, and metatranscriptomics approaches for its understanding, covering descriptions of recent studies concerning metagenomics to characterize the microbiome of non-model plants under different aspects. Studies involving bio-inoculants, isolated from plant microbial communities, capable of assisting in crops' productivity, are also reviewed.}, } @article {pmid34707622, year = {2021}, author = {Yamazaki, K and Kato, T and Tsuboi, Y and Miyauchi, E and Suda, W and Sato, K and Nakajima, M and Yokoji-Takeuchi, M and Yamada-Hara, M and Tsuzuno, T and Matsugishi, A and Takahashi, N and Tabeta, K and Miura, N and Okuda, S and Kikuchi, J and Ohno, H and Yamazaki, K}, title = {Oral Pathobiont-Induced Changes in Gut Microbiota Aggravate the Pathology of Nonalcoholic Fatty Liver Disease in Mice.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {766170}, pmid = {34707622}, issn = {1664-3224}, mesh = {Administration, Oral ; Animals ; Choline Deficiency ; Diet, High-Fat ; Feces/microbiology ; *Gastrointestinal Microbiome ; Hep G2 Cells ; Humans ; Liver/pathology ; Male ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/*microbiology/pathology ; *Porphyromonas gingivalis ; *Prevotella intermedia ; RNA, Ribosomal, 16S ; Mice ; }, abstract = {BACKGROUND & AIMS: Periodontitis increases the risk of nonalcoholic fatty liver disease (NAFLD); however, the underlying mechanisms are unclear. Here, we show that gut dysbiosis induced by oral administration of Porphyromonas gingivalis, a representative periodontopathic bacterium, is involved in the aggravation of NAFLD pathology.

METHODS: C57BL/6N mice were administered either vehicle, P. gingivalis, or Prevotella intermedia, another periodontopathic bacterium with weaker periodontal pathogenicity, followed by feeding on a choline-deficient, l-amino acid-defined, high-fat diet with 60 kcal% fat and 0.1% methionine (CDAHFD60). The gut microbial communities were analyzed by pyrosequencing the 16S ribosomal RNA genes. Metagenomic analysis was used to determine the relative abundance of the Kyoto Encyclopedia of Genes and Genomes pathways encoded in the gut microbiota. Serum metabolites were analyzed using nuclear magnetic resonance-based metabolomics coupled with multivariate statistical analyses. Hepatic gene expression profiles were analyzed via DNA microarray and quantitative polymerase chain reaction.

RESULTS: CDAHFD60 feeding induced hepatic steatosis, and in combination with bacterial administration, it further aggravated NAFLD pathology, thereby increasing fibrosis. Gene expression analysis of liver samples revealed that genes involved in NAFLD pathology were perturbed, and the two bacteria induced distinct expression profiles. This might be due to quantitative and qualitative differences in the influx of bacterial products in the gut because the serum endotoxin levels, compositions of the gut microbiota, and serum metabolite profiles induced by the ingested P. intermedia and P. gingivalis were different.

CONCLUSIONS: Swallowed periodontopathic bacteria aggravate NAFLD pathology, likely due to dysregulation of gene expression by inducing gut dysbiosis and subsequent influx of gut bacteria and/or bacterial products.}, } @article {pmid34707567, year = {2021}, author = {Zhai, Z and Liu, J and Niu, KM and Lin, C and Tu, Y and Liu, Y and Cai, L and Liu, H and Ouyang, K}, title = {Integrated Metagenomics and Metabolomics to Reveal the Effects of Policosanol on Modulating the Gut Microbiota and Lipid Metabolism in Hyperlipidemic C57BL/6 Mice.}, journal = {Frontiers in endocrinology}, volume = {12}, number = {}, pages = {722055}, pmid = {34707567}, issn = {1664-2392}, mesh = {Animals ; Diet, High-Fat ; Fatty Alcohols/*pharmacology ; Gastrointestinal Microbiome/*drug effects/genetics ; *Hyperlipidemias/genetics/metabolism/microbiology/pathology ; Lipid Metabolism/*drug effects/genetics ; Male ; Metabolomics/methods ; Metagenomics/methods ; Mice ; Mice, Inbred C57BL ; Mice, Obese ; Obesity/genetics/metabolism/microbiology/pathology ; Systems Integration ; Thermogenesis/drug effects/genetics ; }, abstract = {The aim of the study was to investigate the regulatory effects of policosanol on hyperlipidemia, gut microbiota and metabolic status in a C57BL/6 mouse model. A total of 35 C57BL/6 mice were assigned to 3 groups, chow (n=12), high fat diet (HFD, n=12) and HFD+policosanol (n=11), then treated for 18 weeks. Policosanol supplementation significantly reduced serum triglycerides and total cholesterol, as well as the weight of brown adipose tissue (BAT) (p<0.05), without affecting body weight in HFD-fed mice (p>0.05). Combined 16S rRNA gene sequencing and untargeted metabolomic analysis demonstrated that policosanol had regulatory effects on gut microbiota and serum metabolism in mice. In obese mice, policosanol increased the proportion of Bacteroides, decreased the proportion of Firmicutes, and increased the ratio of Bacteroides to Firmicutes (p<0.05). Policosanol promoted lipolysis and thermogenesis process, including tricarboxylic acid (TCA) cycle and pyruvate cycle, correlated with the increasing level of Bacteroides, Parasutterella, and decreasing level of Lactobacillus and Candidatus_Saccharimonas. Moreover, policosanol decreased fatty acid synthase (FAS) in the iWAT of obese mice. Policosanol also increased peroxisome proliferators-activated receptor-γ (PPARγ), uncoupling Protein-1 (UCP-1), peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α) and PR domain containing 16 (PRDM16) in brown adipose tissue (BAT) obese mice (p<0.05). This study presents the new insight that policosanol may inhibit the synthesis of fatty acids, and promote lipolysis, thermogenesis related gene expression and regulate gut microbiota constituents, which provides potential for policosanol as an antihyperlipidemia functional food additive and provide new evidence for whole grain food to replace refined food.}, } @article {pmid34704805, year = {2021}, author = {Tarracchini, C and Milani, C and Longhi, G and Fontana, F and Mancabelli, L and Pintus, R and Lugli, GA and Alessandri, G and Anzalone, R and Viappiani, A and Turroni, F and Mussap, M and Dessì, A and Cesare Marincola, F and Noto, A and De Magistris, A and Vincent, M and Bernasconi, S and Picaud, JC and Fanos, V and Ventura, M}, title = {Unraveling the Microbiome of Necrotizing Enterocolitis: Insights in Novel Microbial and Metabolomic Biomarkers.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0117621}, pmid = {34704805}, issn = {2165-0497}, mesh = {Biomarkers/analysis ; Clostridium/genetics/*isolation & purification ; Clostridium perfringens/genetics/*isolation & purification ; Dysbiosis/*microbiology ; Enterocolitis, Necrotizing/*microbiology/pathology ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Infant, Low Birth Weight/metabolism ; Infant, Newborn ; Infant, Premature ; Infant, Premature, Diseases/*microbiology ; Intestines/microbiology ; Lactic Acid/analysis ; Metagenome/genetics ; }, abstract = {Necrotizing enterocolitis (NEC) is among the most relevant gastrointestinal diseases affecting mostly prematurely born infants with low birth weight. While intestinal dysbiosis has been proposed as one of the possible factors involved in NEC pathogenesis, the role of the gut microbiota remains poorly understood. In this study, the gut microbiota of preterm infants was explored to highlight differences in the composition between infants affected by NEC and infants prior to NEC development. A large-scale gut microbiome analysis was performed, including 47 shotgun sequencing data sets generated in the framework of this study, along with 124 retrieved from publicly available repositories. Meta-analysis led to the identification of preterm community state types (PT-CSTs), which recur in healthy controls and NEC infants. Such analyses revealed an overgrowth of a range of opportunistic microbial species accompanying the loss of gut microbial biodiversity in NEC subjects. Moreover, longitudinal insights into preterm infants prior to NEC development indicated Clostridium neonatale and Clostridium perfringens species as potential biomarkers for predictive early diagnosis of this disease. Furthermore, functional investigation of the enzymatic reaction profiles associated with pre-NEC condition suggested DL-lactate as a putative metabolic biomarker for early detection of NEC onset. IMPORTANCE Necrotizing enterocolitis (NEC) is a severe gastrointestinal disease occurring predominantly in premature infants whose etiology is still not fully understood. In this study, the analysis of infant fecal samples through shotgun metagenomics approaches revealed a marked reduction of the intestinal (bio)diversity and an overgrowth of (opportunistic) pathogens associated with the NEC development. In particular, dissection of the infant's gut microbiome before NEC diagnosis highlighted the potential involvement of Clostridium genus members in the progression of NEC. Remarkably, our analyses highlighted a gastrointestinal DL-lactate accumulation among NEC patients that might represent a novel potential functional biomarker for the early diagnosis of NEC.}, } @article {pmid34704793, year = {2021}, author = {Zheng, Y and Xu, Z and Liu, H and Liu, Y and Zhou, Y and Meng, C and Ma, S and Xie, Z and Li, Y and Zhang, CS}, title = {Patterns in the Microbial Community of Salt-Tolerant Plants and the Functional Genes Associated with Salt Stress Alleviation.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0076721}, pmid = {34704793}, issn = {2165-0497}, mesh = {Agriculture ; Bacteria/classification/genetics ; Biodiversity ; Metagenomics ; Microbiota/genetics/*physiology ; Nitrogen ; RNA, Ribosomal, 16S/genetics ; *Salt Stress ; Salt-Tolerant Plants/*microbiology/*physiology ; Soil ; Soil Microbiology ; }, abstract = {Salinity is an important abiotic stress affecting plant growth. We have known that plants can recruit beneficial microbes from the surrounding soil. However, the ecological functions of the core microbiome in salt-tolerant plants, together with their driving factors, remain largely unexplored. Here, we employed both amplicon and shotgun metagenomic sequencing to investigate the microbiome and function signatures of bulk soil and rhizocompartment samples from three salt-tolerant plants (legumes Glycine soja and Sesbania cannabina and nonlegume Sorghum bicolor). Strong filtration effects for microbes and functional genes were found in the rhizocompartments following a spatial gradient. The dominant bacteria belonged to Ensifer for legumes and Bacillus for S. bicolor. Although different salt-tolerant plants harbored distinct bacterial communities, they all enriched genes involved in cell motility, Na[+] transport, and plant growth-promoting function (e.g., nitrogen fixation and phosphate solubilization) in rhizoplane soils, implying that the microbiome assembly of salt-tolerant plants might depend on the ecological functions of microbes rather than microbial taxa. Moreover, three metagenome-assembled genomes affiliated to Ensifer were obtained, and their genetic basis for salt stress alleviation were predicted. Soil pH, electrical conductivity, and total nitrogen were the most important driving factors for explaining the above microbial and functional gene selection. Correspondingly, the growth of an endophyte, Ensifer meliloti CL09, was enhanced by providing root exudates, suggesting that root exudates might be one of factors in the selection of rhizosphere and endosphere microbiota. Overall, this study reveals the ecological functions of the populations inhabiting the root of salt-tolerant plants. IMPORTANCE Salinity is an important but little-studied abiotic stressor affecting plant growth. Although several previous reports have examined salt-tolerant plant microbial communities, we still lack a comprehensive understanding about the functional characteristics and genomic information of this population. The results of this study revealed the root-enriched and -depleted bacterial groups, and found three salt-tolerant plants harbored different bacterial populations. The prediction of three metagenome-assembled genomes confirmed the critical role of root dominant species in helping plants tolerate salt stress. Further analysis indicated that plants enriched microbiome from soil according to their ecological functions but not microbial taxa. This highlights the importance of microbial function in enhancing plant adaptability to saline soil and implies that we should pay more attention to microbial function and not only to taxonomic information. Ultimately, these results provide insight for future agriculture using the various functions of microorganisms on the saline soil.}, } @article {pmid34704787, year = {2021}, author = {Stubbendieck, RM and Zelasko, SE and Safdar, N and Currie, CR}, title = {Biogeography of Bacterial Communities and Specialized Metabolism in Human Aerodigestive Tract Microbiomes.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0166921}, pmid = {34704787}, issn = {2165-0497}, support = {TL1 TR002375/TR/NCATS NIH HHS/United States ; T15 LM007359/LM/NLM NIH HHS/United States ; T32 GM140935/GM/NIGMS NIH HHS/United States ; U01 AI125053/AI/NIAID NIH HHS/United States ; U19 AI142720/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/*isolation & purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biosynthetic Pathways ; Cheek/microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Genome, Bacterial ; Humans ; Microbiota ; Mouth/microbiology ; Nasal Cavity/microbiology ; Phylogeny ; }, abstract = {The aerodigestive tract (ADT) is the primary portal through which pathogens and other invading microbes enter the body. As the direct interface with the environment, we hypothesize that the ADT microbiota possess biosynthetic gene clusters (BGCs) for antibiotics and other specialized metabolites to compete with both endogenous and exogenous microbes. From 1,214 bacterial genomes, representing 136 genera and 387 species that colonize the ADT, we identified 3,895 BGCs. To determine the distribution of BGCs and bacteria in different ADT sites, we aligned 1,424 metagenomes, from nine different ADT sites, onto the predicted BGCs. We show that alpha diversity varies across the ADT and that each site is associated with distinct bacterial communities and BGCs. We identify specific BGC families enriched in the buccal mucosa, external naris, gingiva, and tongue dorsum despite these sites harboring closely related bacteria. We reveal BGC enrichment patterns indicative of the ecology at each site. For instance, aryl polyene and resorcinol BGCs are enriched in the gingiva and tongue, which are colonized by many anaerobes. In addition, we find that streptococci colonizing the tongue and cheek possess different ribosomally synthesized and posttranslationally modified peptide BGCs. Finally, we highlight bacterial genera with BGCs but are underexplored for specialized metabolism and demonstrate the bioactivity of Actinomyces against other bacteria, including human pathogens. Together, our results demonstrate that specialized metabolism in the ADT is extensive and that by exploring these microbiomes further, we will better understand the ecology and biogeography of this system and identify new bioactive natural products. IMPORTANCE Bacteria produce specialized metabolites to compete with other microbes. Though the biological activities of many specialized metabolites have been determined, our understanding of their ecology is limited, particularly within the human microbiome. As the aerodigestive tract (ADT) faces the external environment, bacteria colonizing this tract must compete both among themselves and with invading microbes, including human pathogens. We analyzed the genomes of ADT bacteria to identify biosynthetic gene clusters (BGCs) for specialized metabolites. We found that the majority of ADT BGCs are uncharacterized and the metabolites they encode are unknown. We mapped the distribution of BGCs across the ADT and determined that each site is associated with its own distinct bacterial community and BGCs. By further characterizing these BGCs, we will inform our understanding of ecology and biogeography across the ADT, and we may uncover new specialized metabolites, including antibiotics.}, } @article {pmid34702904, year = {2021}, author = {Qi, F and Jia, Y and Mu, R and Ma, G and Guo, Q and Meng, Q and Yu, G and Xie, J}, title = {Convergent community structure of algal-bacterial consortia and its effects on advanced wastewater treatment and biomass production.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {21118}, pmid = {34702904}, issn = {2045-2322}, mesh = {Bacteria/*growth & development ; *Biomass ; Microalgae/*growth & development ; *Microbial Consortia ; *Photobioreactors ; *Water Purification ; }, abstract = {Microalgal-bacterial consortium is an effective way to meet increasingly stringent standards in wastewater treatment. However, the mechanism of wastewater removal effect has not been properly explained in community structure by phycosphere. And little is known about that the concept of macroecology was introduced into phycosphere to explain the phenomenon. In the study, the algal-bacterial consortia with different ratios of algae and sludge were cultured in same aerobic wastewater within 48 h in photobioreactors (PSBRs). Community structure at start and end was texted by metagenomic analysis. Bray-Curtis similarities analysis based on microbial community showed that there was obvious convergent succession in all consortia, which is well known as "convergence" in macroecology. The result showed that Bray-Curtis similarities at End (overall above 0.88) were higher than these at Start (almost less than 0.66). In terms of community structure, the consortium with 5:1 ratio at Start are the more similar with the consortia at End by which the maximum removal of total dissolved nitrogen (TDN, 73.69%), total dissolved phosphorus (TDP, 94.40%) and NH3-N (93.26%) in wastewater treatment process and biomass production (98.2%) higher than other consortia, according with climax community in macroecology with the highest resource utilization than other communities. Therefore, the macroecology can be introduced into phycosphere to explain the consortium for advanced wastewater treatment and optimization community structure. And the study revealed a novel insight into treatment effect and community structure of algal-bacterial consortia for advanced wastewater treatment, a new idea for to shortening the culture time of consortium and optimize predicting their ecological community structure and predicting ecological community.}, } @article {pmid34702846, year = {2021}, author = {Maggiori, C and Raymond-Bouchard, I and Brennan, L and Touchette, D and Whyte, L}, title = {MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {21041}, pmid = {34702846}, issn = {2045-2322}, mesh = {Ice Cover/*microbiology ; *Metagenome ; *Metagenomics ; Microbiota/*genetics ; }, abstract = {Genome reconstruction from metagenomes enables detailed study of individual community members, their metabolisms, and their survival strategies. Obtaining high quality metagenome-assembled genomes (MAGs) is particularly valuable in extreme environments like sea ice cryoconites, where the native consortia are recalcitrant to culture and strong astrobiology analogues. We evaluated three separate approaches for MAG generation from Allen Bay, Nunavut sea ice cryoconites-HiSeq-only, MinION-only, and hybrid (HiSeq + MinION)-where field MinION sequencing yielded a reliable metagenome. The hybrid assembly produced longer contigs, more coding sequences, and more total MAGs, revealing a microbial community dominated by Bacteroidetes. The hybrid MAGs also had the highest completeness, lowest contamination, and highest N50. A putatively novel species of Octadecabacter is among the hybrid MAGs produced, containing the genus's only known instances of genomic potential for nitrate reduction, denitrification, sulfate reduction, and fermentation. This study shows that the inclusion of MinION reads in traditional short read datasets leads to higher quality metagenomes and MAGs for more accurate descriptions of novel microorganisms in this extreme, transient habitat and has produced the first hybrid MAGs from an extreme environment.}, } @article {pmid34700384, year = {2021}, author = {Zrimec, J and Kokina, M and Jonasson, S and Zorrilla, F and Zelezniak, A}, title = {Plastic-Degrading Potential across the Global Microbiome Correlates with Recent Pollution Trends.}, journal = {mBio}, volume = {12}, number = {5}, pages = {e0215521}, pmid = {34700384}, issn = {2150-7511}, mesh = {Bacteria/classification/enzymology/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Environmental Pollutants/metabolism ; *Microbiota ; Plastics/*metabolism ; Seawater/microbiology ; Soil Microbiology ; }, abstract = {Biodegradation is a plausible route toward sustainable management of the millions of tons of plastic waste that have accumulated in terrestrial and marine environments. However, the global diversity of plastic-degrading enzymes remains poorly understood. Taking advantage of global environmental DNA sampling projects, here we constructed hidden Markov models from experimentally verified enzymes and mined ocean and soil metagenomes to assess the global potential of microorganisms to degrade plastics. By controlling for false positives using gut microbiome data, we compiled a catalogue of over 30,000 nonredundant enzyme homologues with the potential to degrade 10 different plastic types. While differences between the ocean and soil microbiomes likely reflect the base compositions of these environments, we find that ocean enzyme abundance increases with depth as a response to plastic pollution and not merely taxonomic composition. By obtaining further pollution measurements, we observed that the abundance of the uncovered enzymes in both ocean and soil habitats significantly correlates with marine and country-specific plastic pollution trends. Our study thus uncovers the earth microbiome's potential to degrade plastics, providing evidence of a measurable effect of plastic pollution on the global microbial ecology as well as a useful resource for further applied research. IMPORTANCE Utilization of synthetic biology approaches to enhance current plastic degradation processes is of crucial importance, as natural plastic degradation processes are very slow. For instance, the predicted lifetime of a polyethylene terephthalate (PET) bottle under ambient conditions ranges from 16 to 48 years. Moreover, although there is still unexplored diversity in microbial communities, synergistic degradation of plastics by microorganisms holds great potential to revolutionize the management of global plastic waste. To this end, the methods and data on novel plastic-degrading enzymes presented here can help researchers by (i) providing further information about the taxonomic diversity of such enzymes as well as understanding of the mechanisms and steps involved in the biological breakdown of plastics, (ii) pointing toward the areas with increased availability of novel enzymes, and (iii) giving a basis for further application in industrial plastic waste biodegradation. Importantly, our findings provide evidence of a measurable effect of plastic pollution on the global microbial ecology.}, } @article {pmid34699120, year = {2022}, author = {Yalcin, SS and Aksu, T and Kuskonmaz, B and Ozbek, NY and Pérez-Brocal, V and Celik, M and Uckan Cetinkaya, D and Moya, A and Dinleyici, EC}, title = {Intestinal mycobiota composition and changes in children with thalassemia who underwent allogeneic hematopoietic stem cell transplantation.}, journal = {Pediatric blood & cancer}, volume = {69}, number = {1}, pages = {e29411}, doi = {10.1002/pbc.29411}, pmid = {34699120}, issn = {1545-5017}, mesh = {Child, Preschool ; *Gastrointestinal Microbiome ; *Graft vs Host Disease ; *Hematopoietic Stem Cell Transplantation ; Humans ; Male ; *Thalassemia ; Transplantation, Homologous ; }, abstract = {BACKGROUND: Allogeneic hematopoietic stem cell transplantation (HSCT) alters the diversity of the intestinal bacterial microbiota. This study aimed to evaluate human mycobiota composition pre-HSCT and post-HSCT in children with thalassemia.

METHOD: Ten children with thalassemia undergoing allogeneic HSCT were enrolled. The stool samples were collected before the transplantation regimen, before the transplant day, and +15, +30 days, and three months after transplantation. Stool samples were also collected from the donor and the patient's caregivers. Gut mycobiota composition was evaluated with metagenomic analysis.

RESULTS: Pretransplant mycobiota of children with thalassemia (the predominant genus was Saccharomyces, 64.1%) has been shown to approximate the diverse mycobiota compositions of healthy adult donors but becomes altered (lower diversity) following transplant procedures. Three months after HSCT, phyla Ascomycota and Basidiomycota were 83.4% and 15.6%, respectively. The predominant species were Saccaharomyces_uc and Saccharomyces cerevisiae (phylum Ascomycota); we also observed Malassezia restricta and Malassezia globosa (phylum Basidiomycota) (∼13%). On day 90 after HSCT, we observed 65.3% M. restricta and 18.4% M. globosa predominance at the species level in a four-year-old boy with acute graft-versus-host disease (GVHD) (skin and gut involvement) 19 days after transplantation included.

CONCLUSION: The mycobiota composition of children with thalassemia altered after HSCT. We observed Malassezia predominance in a child with GVHD. Further studies in children with GVHD will identify this situation.}, } @article {pmid34697892, year = {2021}, author = {Merges, D and Dal Grande, F and Greve, C and Otte, J and Schmitt, I}, title = {Virus diversity in metagenomes of a lichen symbiosis (Umbilicaria phaea): complete viral genomes, putative hosts and elevational distributions.}, journal = {Environmental microbiology}, volume = {23}, number = {11}, pages = {6637-6650}, doi = {10.1111/1462-2920.15802}, pmid = {34697892}, issn = {1462-2920}, mesh = {*Ascomycota/genetics ; *Bacteriophages/genetics ; Genome, Viral/genetics ; *Lichens/genetics/microbiology ; Metagenome ; Phylogeny ; Symbiosis ; }, abstract = {Viruses can play critical roles in symbioses by initiating horizontal gene transfer, affecting host phenotypes, or expanding their host's ecological niche. However, knowledge of viral diversity and distribution in symbiotic organisms remains elusive. Here we use deep-sequenced metagenomic DNA (PacBio Sequel II; two individuals), paired with a population genomics approach (Pool-seq; 11 populations, 550 individuals) to understand viral distributions in the lichen Umbilicaria phaea. We assess (i) viral diversity in lichen thalli, (ii) putative viral hosts (fungi, algae, bacteria) and (iii) viral distributions along two replicated elevation gradients. We identified five novel viruses, showing 28%-40% amino acid identity to known viruses. They tentatively belong to the families Caulimoviridae, Myoviridae, Podoviridae and Siphoviridae. Our analysis suggests that the Caulimovirus is associated with green algal photobionts (Trebouxia) of the lichen, and the remaining viruses with bacterial hosts. We did not detect viral sequences in the mycobiont. Caulimovirus abundance decreased with increasing elevation, a pattern reflected by a specific algal lineage hosting this virus. Bacteriophages showed population-specific patterns. Our work provides the first comprehensive insights into viruses associated with a lichen holobiont and suggests an interplay of viral hosts and environment in structuring viral distributions.}, } @article {pmid34696523, year = {2021}, author = {Hsieh, SY and Tariq, MA and Telatin, A and Ansorge, R and Adriaenssens, EM and Savva, GM and Booth, C and Wileman, T and Hoyles, L and Carding, SR}, title = {Comparison of PCR versus PCR-Free DNA Library Preparation for Characterising the Human Faecal Virome.}, journal = {Viruses}, volume = {13}, number = {10}, pages = {}, pmid = {34696523}, issn = {1999-4915}, support = {BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356 410/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteriophages/genetics ; Cloning, Molecular/*methods ; Feces/virology ; Gastrointestinal Microbiome/*genetics ; Gene Library ; Genome, Viral/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome/genetics ; Metagenomics/methods ; Nucleic Acid Amplification Techniques/methods ; Sequence Analysis, DNA/methods ; Virome/*genetics ; Viruses/genetics ; }, abstract = {The human intestinal microbiota is abundant in viruses, comprising mainly bacteriophages, occasionally outnumbering bacteria 10:1 and is termed the virome. Due to their high genetic diversity and the lack of suitable tools and reference databases, the virome remains poorly characterised and is often referred to as "viral dark matter". However, the choice of sequencing platforms, read lengths and library preparation make study design challenging with respect to the virome. Here we have compared the use of PCR and PCR-free methods for sequence-library construction on the Illumina sequencing platform for characterising the human faecal virome. Viral DNA was extracted from faecal samples of three healthy donors and sequenced. Our analysis shows that most variation was reflecting the individually specific faecal virome. However, we observed differences between PCR and PCR-free library preparation that affected the recovery of low-abundance viral genomes. Using three faecal samples in this study, the PCR library preparation samples led to a loss of lower-abundance vOTUs evident in their PCR-free pairs (vOTUs 128, 6202 and 8364) and decreased the alpha-diversity indices (Chao1 p-value = 0.045 and Simpson p-value = 0.044). Thus, differences between PCR and PCR-free methods are important to consider when investigating "rare" members of the gut virome, with these biases likely negligible when investigating moderately and highly abundant viruses.}, } @article {pmid34696369, year = {2021}, author = {Hasiów-Jaroszewska, B and Boezen, D and Zwart, MP}, title = {Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities.}, journal = {Viruses}, volume = {13}, number = {10}, pages = {}, pmid = {34696369}, issn = {1999-4915}, mesh = {Biodiversity ; Computational Biology/methods ; DNA Viruses/genetics ; Genome, Viral/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenome/genetics ; Metagenomics/*methods ; Plant Weeds/*genetics/*virology ; Plants/genetics/virology ; Viruses/classification/genetics ; Viruses, Unclassified/genetics ; }, abstract = {High throughput sequencing (HTS) has revolutionised virus detection and discovery, allowing for the untargeted characterisation of whole viromes. Viral metagenomics studies have demonstrated the ubiquity of virus infection - often in the absence of disease symptoms - and tend to discover many novel viruses, highlighting the small fraction of virus biodiversity described to date. The majority of the studies using high-throughput sequencing to characterise plant viromes have focused on economically important crops, and only a small number of studies have considered weeds and wild plants. Characterising the viromes of wild plants is highly relevant, as these plants can affect disease dynamics in crops, often by acting as viral reservoirs. Moreover, the viruses in unmanaged systems may also have important effects on wild plant populations and communities. Here, we review metagenomic studies on weeds and wild plants to show the benefits and limitations of this approach and identify knowledge gaps. We consider key genomics developments that are likely to benefit the field in the near future. Although only a small number of HTS studies have been performed on weeds and wild plants, these studies have already discovered many novel viruses, demonstrated unexpected trends in virus distributions, and highlighted the potential of metagenomics as an approach.}, } @article {pmid34695658, year = {2021}, author = {Nabwera, HM and Espinoza, JL and Worwui, A and Betts, M and Okoi, C and Sesay, AK and Bancroft, R and Agbla, SC and Jarju, S and Bradbury, RS and Colley, M and Jallow, AT and Liu, J and Houpt, ER and Prentice, AM and Antonio, M and Bernstein, RM and Dupont, CL and Kwambana-Adams, BA}, title = {Interactions between fecal gut microbiome, enteric pathogens, and energy regulating hormones among acutely malnourished rural Gambian children.}, journal = {EBioMedicine}, volume = {73}, number = {}, pages = {103644}, pmid = {34695658}, issn = {2352-3964}, support = {MC_PC_MR/R020183/1/MRC_/Medical Research Council/United Kingdom ; MC_U123292701/MRC_/Medical Research Council/United Kingdom ; MC_UU_00026/3/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Biodiversity ; Cross-Sectional Studies ; Disease Susceptibility ; *Energy Metabolism ; Enterobacteriaceae/pathogenicity ; Feces/microbiology ; Gambia/epidemiology ; *Gastrointestinal Microbiome ; Hormones/*metabolism ; *Host-Pathogen Interactions ; Humans ; Metagenome ; Metagenomics/methods ; Phenotype ; Rural Population ; Severe Acute Malnutrition/diagnosis/epidemiology/*etiology/*metabolism ; Virulence Factors ; }, abstract = {BACKGROUND: The specific roles that gut microbiota, known pathogens, and host energy-regulating hormones play in the pathogenesis of non-edematous severe acute malnutrition (marasmus SAM) and moderate acute malnutrition (MAM) during outpatient nutritional rehabilitation are yet to be explored.

METHODS: We applied an ensemble of sample-specific (intra- and inter-modality) association networks to gain deeper insights into the pathogenesis of acute malnutrition and its severity among children under 5 years of age in rural Gambia, where marasmus SAM is most prevalent.

FINDINGS: Children with marasmus SAM have distinct microbiome characteristics and biologically-relevant multimodal biomarkers not observed among children with moderate acute malnutrition. Marasmus SAM was characterized by lower microbial richness and biomass, significant enrichments in Enterobacteriaceae, altered interactions between specific Enterobacteriaceae and key energy regulating hormones and their receptors.

INTERPRETATION: Our findings suggest that marasmus SAM is characterized by the collapse of a complex system with nested interactions and key associations between the gut microbiome, enteric pathogens, and energy regulating hormones.  Further exploration of these systems will help inform innovative preventive and therapeutic interventions.

FUNDING: The work was supported by the UK Medical Research Council (MRC; MC-A760-5QX00) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement; Bill and Melinda Gates Foundation (OPP 1066932) and the National Institute of Medical Research (NIMR), UK. This network analysis was supported by NIH U54GH009824 [CLD] and NSF OCE-1558453 [CLD].}, } @article {pmid34695305, year = {2021}, author = {Carasso, S and Fishman, B and Lask, LS and Shochat, T and Geva-Zatorsky, N and Tauber, E}, title = {Metagenomic analysis reveals the signature of gut microbiota associated with human chronotypes.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {35}, number = {11}, pages = {e22011}, doi = {10.1096/fj.202100857RR}, pmid = {34695305}, issn = {1530-6860}, mesh = {Adult ; *Circadian Rhythm ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Surveys and Questionnaires ; Young Adult ; }, abstract = {Patterns of diurnal activity differ substantially between individuals, with early risers and late sleepers being examples of opposite chronotypes. Growing evidence suggests that the late chronotype significantly impacts the risk of developing mood disorders, obesity, diabetes, and other chronic diseases. Despite the vast potential of utilizing chronotype information for precision medicine, those factors that shape chronotypes remain poorly understood. Here, we assessed whether the various chronotypes are associated with different gut microbiome compositions. Using metagenomic sequencing analysis, we established a distinct signature associated with chronotype based on two bacterial genera, Alistipes (elevated in "larks") and Lachnospira (elevated in "owls"). We identified three metabolic pathways associated with the early chronotype, and linked distinct dietary patterns with different chronotypes. Our work demonstrates an association between the gut microbiome and chronotype and may represent the first step towards developing dietary interventions aimed at ameliorating the deleterious health correlates of the late chronotype.}, } @article {pmid34694925, year = {2022}, author = {Bendia, AG and Callefo, F and Araújo, MN and Sanchez, E and Teixeira, VC and Vasconcelos, A and Battilani, G and Pellizari, VH and Rodrigues, F and Galante, D}, title = {Metagenome-Assembled Genomes from Monte Cristo Cave (Diamantina, Brazil) Reveal Prokaryotic Lineages As Functional Models for Life on Mars.}, journal = {Astrobiology}, volume = {22}, number = {3}, pages = {293-312}, doi = {10.1089/ast.2021.0016}, pmid = {34694925}, issn = {1557-8070}, mesh = {Brazil ; Caves/microbiology ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Microbial communities have been explored in various terrestrial subsurface ecosystems, showing metabolic potentials that could generate noteworthy morphological and molecular biosignatures. Recent advancements in bioinformatic tools have allowed for descriptions of novel and yet-to-be cultivated microbial lineages in different ecosystems due to the genome reconstruction approach from metagenomic data. Using shotgun metagenomic data, we obtained metagenome-assembled genomes related to cultivated and yet-to-be cultivated prokaryotic lineages from a silica and iron-rich cave (Monte Cristo) in Minas Gerais State, Brazil. The Monte Cristo Cave has been shown to possess a high diversity of genes involved with different biogeochemical cycles, including reductive and oxidative pathways related to carbon, sulfur, nitrogen, and iron. Three genomes were selected for pangenomic analysis, assigned as Truepera sp., Ca. Methylomirabilis sp., and Ca. Koribacter sp. based on their lifestyles (radiation resistance, anaerobic methane oxidation, and potential iron oxidation). These bacteria exhibit genes involved with multiple DNA repair strategies, starvation, and stress response. Because these groups have few reference genomes deposited in databases, our study adds important genomic information about these lineages. The combination of techniques applied in this study allowed us to unveil the potential relationships between microbial genomes and their ecological processes with the cave mineralogy and highlight the lineages involved with anaerobic methane oxidation, iron oxidation, and radiation resistance as functional models for the search for extant life-forms outside our planet in silica- and iron-rich environments and potentially on Mars.}, } @article {pmid34694375, year = {2022}, author = {de Castilhos, J and Zamir, E and Hippchen, T and Rohrbach, R and Schmidt, S and Hengler, S and Schumacher, H and Neubauer, M and Kunz, S and Müller-Esch, T and Hiergeist, A and Gessner, A and Khalid, D and Gaiser, R and Cullin, N and Papagiannarou, SM and Beuthien-Baumann, B and Krämer, A and Bartenschlager, R and Jäger, D and Müller, M and Herth, F and Duerschmied, D and Schneider, J and Schmid, RM and Eberhardt, JF and Khodamoradi, Y and Vehreschild, MJGT and Teufel, A and Ebert, MP and Hau, P and Salzberger, B and Schnitzler, P and Poeck, H and Elinav, E and Merle, U and Stein-Thoeringer, CK}, title = {Severe Dysbiosis and Specific Haemophilus and Neisseria Signatures as Hallmarks of the Oropharyngeal Microbiome in Critically Ill Coronavirus Disease 2019 (COVID-19) Patients.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {75}, number = {1}, pages = {e1063-e1071}, doi = {10.1093/cid/ciab902}, pmid = {34694375}, issn = {1537-6591}, mesh = {Adult ; *COVID-19 ; Critical Illness ; Cross-Sectional Studies ; Dysbiosis ; Haemophilus ; Humans ; *Microbiota ; Neisseria ; SARS-CoV-2 ; }, abstract = {BACKGROUND: At the entry site of respiratory virus infections, the oropharyngeal microbiome has been proposed as a major hub integrating viral and host immune signals. Early studies suggested that infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are associated with changes of the upper and lower airway microbiome, and that specific microbial signatures may predict coronavirus disease 2019 (COVID-19) illness. However, the results are not conclusive, as critical illness can drastically alter a patient's microbiome through multiple confounders.

METHODS: To study oropharyngeal microbiome profiles in SARS-CoV-2 infection, clinical confounders, and prediction models in COVID-19, we performed a multicenter, cross-sectional clinical study analyzing oropharyngeal microbial metagenomes in healthy adults, patients with non-SARS-CoV-2 infections, or with mild, moderate, and severe COVID-19 (n = 322 participants).

RESULTS: In contrast to mild infections, patients admitted to a hospital with moderate or severe COVID-19 showed dysbiotic microbial configurations, which were significantly pronounced in patients treated with broad-spectrum antibiotics, receiving invasive mechanical ventilation, or when sampling was performed during prolonged hospitalization. In contrast, specimens collected early after admission allowed us to segregate microbiome features predictive of hospital COVID-19 mortality utilizing machine learning models. Taxonomic signatures were found to perform better than models utilizing clinical variables with Neisseria and Haemophilus species abundances as most important features.

CONCLUSIONS: In addition to the infection per se, several factors shape the oropharyngeal microbiome of severely affected COVID-19 patients and deserve consideration in the interpretation of the role of the microbiome in severe COVID-19. Nevertheless, we were able to extract microbial features that can help to predict clinical outcomes.}, } @article {pmid34693651, year = {2021}, author = {Zhang, M and Liu, D and Zhou, H and Liu, X and Li, X and Cheng, Y and Gao, B and Chen, J}, title = {Intestinal flora characteristics of advanced non-small cell lung cancer in China and their role in chemotherapy based on metagenomics: A prospective exploratory cohort study.}, journal = {Thoracic cancer}, volume = {12}, number = {24}, pages = {3293-3303}, pmid = {34693651}, issn = {1759-7714}, mesh = {Aged ; Antineoplastic Combined Chemotherapy Protocols/*therapeutic use ; Carcinoma, Non-Small-Cell Lung/*drug therapy/*microbiology ; China ; Cohort Studies ; Female ; Gastrointestinal Microbiome/*drug effects/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Lung Neoplasms/*drug therapy/*microbiology ; Male ; Metagenomics ; Middle Aged ; Platinum/therapeutic use ; Prospective Studies ; }, abstract = {BACKGROUND: Lung cancer has the highest mortality rate among malignant tumors, with non-small cell lung cancer (NSCLC) being the most common type. As the main component of the human microflora, the intestinal flora interacts with the human body to affect immunity, metabolism, and the formation of diseases.

METHODS: Forty-five patients with advanced NSCLC who received platinum-containing dual-drug chemotherapy were enrolled in a prospective exploratory cohort study. The intestinal flora was dynamically collected at baseline and after two chemotherapy cycles. Next-generation sequencing and metagenomics were then used to analyze the species and function of the intestinal flora at all levels.

RESULTS: Significant differences in the intestinal flora of patients with NSCLC were found according to sex and age. At the family level, the abundances of Streptococcaceae, Lactobacillaceae, and Leuconostocaceae after platinum-containing dual-drug chemotherapy were significantly higher compared to those before chemotherapy. At the family level, patients with chemotherapy-induced gastrointestinal reactions had a significantly higher abundance of Leuconostocaceae than those without gastrointestinal responses. Meanwhile, patients with gastrointestinal reactions had higher metabolism, human diseases, cellular processes, and environmental information processing than those who did not. At the genus level, responders had higher abundances of Bacteroides compared to nonresponders. Moreover, nonresponders had higher levels of the six major metabolic pathways compared to responders.

CONCLUSIONS: The intestinal flora of Chinese patients with advanced NSCLC differed according to sex and age. Moreover, significant differences in the intestinal flora were noted after chemotherapy, which could be associated with chemotherapy-induced gastrointestinal reactions and the efficacy of chemotherapy.}, } @article {pmid34693622, year = {2021}, author = {Sun, H and Liu, J and Tan, S and Zheng, Y and Wang, X and Liang, J and Todd, JD and Zhang, XH}, title = {Spatiotemporal distribution of bacterial dimethylsulfoniopropionate producing and catabolic genes in the Changjiang Estuary.}, journal = {Environmental microbiology}, volume = {23}, number = {11}, pages = {7073-7092}, doi = {10.1111/1462-2920.15813}, pmid = {34693622}, issn = {1462-2920}, mesh = {*Estuaries ; Phylogeny ; Seawater/microbiology ; *Sulfonium Compounds/metabolism ; }, abstract = {The osmolyte dimethylsulfoniopropionate (DMSP) is produced in petagram amounts by marine microorganisms. Estuaries provide natural gradients in salinity and nutrients, factors known to regulate DMSP production; yet there have been no molecular studies of DMSP production and cycling across these gradients. Here, we study the abundance, distribution and transcription of key DMSP synthesis (e.g. dsyB and mmtN) and catabolic (e.g. dddP and dmdA) genes along the salinity gradient of the Changjiang Estuary. DMSP levels did not correlate with Chl a across the salinity gradient. In contrast, DMSP concentration, abundance of bacterial DMSP producers and their dsyB and mmtN transcripts were lowest in the freshwater samples and increased abruptly with salinity in the transitional and seawater samples. Metagenomics analysis suggests bacterial DMSP-producers were more abundant than their algal equivalents and were more prominent in summer than winter samples. Bacterial DMSP catabolic genes and their transcripts followed the same trend of being greatly enhanced in transitional and seawater samples with higher DMSP levels than freshwater samples. DMSP cleavage was likely the dominant catabolic pathway, with DMSP lyase genes being ~4.3-fold more abundant than the demethylase gene dmdA. This is an exemplar study for future research on microbial DMSP cycling in estuary environments.}, } @article {pmid34693512, year = {2021}, author = {G Giske, C and Allander, T and Fröding, I and Ininbergs, K and Mölling, P and Engstrand, L and Albert, J}, title = {[Precision diagnostics in clinical microbiology].}, journal = {Lakartidningen}, volume = {118}, number = {}, pages = {}, pmid = {34693512}, issn = {1652-7518}, mesh = {Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; }, abstract = {Genomic methods have had a major impact in clinical microbiology in the last decades. Microbial genomes are relatively small and therefore easier to characterise than human genomes. In both bacteriology and in virology, genomic methods have largely been used for molecular epidemiology, but also for molecular resistance testing of microorganisms. Targeted sequencing of predefined or isolated microorganisms was initially a dominant method but has gradually been supplemented with metagenomic diagnostics. Metagenomics aims at mapping all microorganisms - pathogenic as well as apathogenic - in a sample without determining in advance which agent(s) the analysis is targeting. Finally, there is also an increasing interest in mapping the significance of the microbiome, i.e. normal flora, both in health and disease.}, } @article {pmid34693062, year = {2021}, author = {Lahlali, R and Ibrahim, DSS and Belabess, Z and Kadir Roni, MZ and Radouane, N and Vicente, CSL and Menéndez, E and Mokrini, F and Barka, EA and Galvão de Melo E Mota, M and Peng, G}, title = {High-throughput molecular technologies for unraveling the mystery of soil microbial community: challenges and future prospects.}, journal = {Heliyon}, volume = {7}, number = {10}, pages = {e08142}, pmid = {34693062}, issn = {2405-8440}, abstract = {Soil microbial communities play a crucial role in soil fertility, sustainability, and plant health. However, intensive agriculture with increasing chemical inputs and changing environments have influenced native soil microbial communities. Approaches have been developed to study the structure, diversity, and activity of soil microbes to better understand the biology and plant-microbe interactions in soils. Unfortunately, a good understanding of soil microbial community remains a challenge due to the complexity of community composition, interactions of the soil environment, and limitations of technologies, especially related to the functionality of some taxa rarely detected using conventional techniques. Culture-based methods have been shown unable and sometimes are biased for assessing soil microbial communities. To gain further knowledge, culture-independent methods relying on direct analysis of nucleic acids, proteins, and lipids are worth exploring. In recent years, metagenomics, metaproteomics, metatranscriptomics, and proteogenomics have been increasingly used in studying microbial ecology. In this review, we examined the importance of microbial community to soil quality, the mystery of rhizosphere and plant-microbe interactions, and the biodiversity and multi-trophic interactions that influence the soil structure and functionality. The impact of the cropping system and climate change on the soil microbial community was also explored. Importantly, progresses in molecular biology, especially in the development of high-throughput biotechnological tools, were extensively assessed for potential uses to decipher the diversity and dynamics of soil microbial communities, with the highlighted advantages/limitations.}, } @article {pmid34690962, year = {2021}, author = {Chen, H and Ma, K and Huang, Y and Yao, Z and Chu, C}, title = {Stable Soil Microbial Functional Structure Responding to Biodiversity Loss Based on Metagenomic Evidences.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {716764}, pmid = {34690962}, issn = {1664-302X}, abstract = {Anthropogenic disturbances and global climate change are causing large-scale biodiversity loss and threatening ecosystem functions. However, due to the lack of knowledge on microbial species loss, our understanding on how functional profiles of soil microbes respond to diversity decline is still limited. Here, we evaluated the biotic homogenization of global soil metagenomic data to examine whether microbial functional structure is resilient to significant diversity reduction. Our results showed that although biodiversity loss caused a decrease in taxonomic species by 72%, the changes in the relative abundance of diverse functional categories were limited. The stability of functional structures associated with microbial species richness decline in terrestrial systems suggests a decoupling of taxonomy and function. The changes in functional profile with biodiversity loss were function-specific, with broad-scale metabolism functions decreasing and typical nutrient-cycling functions increasing. Our results imply high levels of microbial physiological versatility in the face of significant biodiversity decline, which, however, does not necessarily mean that a loss in total functional abundance, such as microbial activity, can be overlooked in the background of unprecedented species extinction.}, } @article {pmid34687739, year = {2022}, author = {Zhang, F and Wan, Y and Zuo, T and Yeoh, YK and Liu, Q and Zhang, L and Zhan, H and Lu, W and Xu, W and Lui, GCY and Li, AYL and Cheung, CP and Wong, CK and Chan, PKS and Chan, FKL and Ng, SC}, title = {Prolonged Impairment of Short-Chain Fatty Acid and L-Isoleucine Biosynthesis in Gut Microbiome in Patients With COVID-19.}, journal = {Gastroenterology}, volume = {162}, number = {2}, pages = {548-561.e4}, pmid = {34687739}, issn = {1528-0012}, mesh = {Adult ; Biomarkers/blood ; COVID-19/*microbiology ; Case-Control Studies ; Fatty Acids, Volatile/*biosynthesis ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Immunity/*physiology ; Isoleucine/*biosynthesis ; Male ; Metagenomics ; Middle Aged ; Phylogeny ; SARS-CoV-2 ; Severity of Illness Index ; }, abstract = {BACKGROUND AND AIMS: Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is associated with altered gut microbiota composition. Phylogenetic groups of gut bacteria involved in the metabolism of short chain fatty acids (SCFAs) were depleted in SARS-CoV-2-infected patients. We aimed to characterize a functional profile of the gut microbiome in patients with COVID-19 before and after disease resolution.

METHODS: We performed shotgun metagenomic sequencing on fecal samples from 66 antibiotics-naïve patients with COVID-19 and 70 non-COVID-19 controls. Serial fecal samples were collected (at up to 6 times points) during hospitalization and beyond 1 month after discharge. We assessed gut microbial pathways in association with disease severity and blood inflammatory markers. We also determined changes of microbial functions in fecal samples before and after disease resolution and validated these functions using targeted analysis of fecal metabolites.

RESULTS: Compared with non-COVID-19 controls, patients with COVID-19 with severe/critical illness showed significant alterations in gut microbiome functionality (P < .001), characterized by impaired capacity of gut microbiome for SCFA and L-isoleucine biosynthesis and enhanced capacity for urea production. Impaired SCFA and L-isoleucine biosynthesis in gut microbiome persisted beyond 30 days after recovery in patients with COVID-19. Targeted analysis of fecal metabolites showed significantly lower fecal concentrations of SCFAs and L-isoleucine in patients with COVID-19 before and after disease resolution. Lack of SCFA and L-isoleucine biosynthesis significantly correlated with disease severity and increased plasma concentrations of CXCL-10, NT- proB-type natriuretic peptide, and C-reactive protein (all P < .05).

CONCLUSIONS: Gut microbiome of patients with COVID-19 displayed impaired capacity for SCFA and L-isoleucine biosynthesis that persisted even after disease resolution. These 2 microbial functions correlated with host immune response underscoring the importance of gut microbial functions in SARS-CoV-2 infection pathogenesis and outcome.}, } @article {pmid34686940, year = {2021}, author = {Sabater, C and Cobo-Díaz, JF and Álvarez-Ordóñez, A and Ruas-Madiedo, P and Ruiz, L and Margolles, A}, title = {Novel methods of microbiome analysis in the food industry.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {24}, number = {4}, pages = {593-605}, pmid = {34686940}, issn = {1618-1905}, support = {818368//h2020 food/ ; RTI2018-095021-J-I00//agencia estatal de investigación/ ; AGL2016-78085-P//agencia estatal de investigación/ ; AGL2016-78311-R//agencia estatal de investigación/ ; FJC2019-042125-I//agencia estatal de investigación/ ; }, mesh = {Drug Resistance, Microbial ; Food Industry ; Metagenome ; *Metagenomics ; *Microbiota ; }, abstract = {The study of the food microbiome has gained considerable interest in recent years, mainly due to the wide range of applications that can be derived from the analysis of metagenomes. Among these applications, it is worth mentioning the possibility of using metagenomic analyses to determine food authenticity, to assess the microbiological safety of foods thanks to the detection and tracking of pathogens, antibiotic resistance genes and other undesirable traits, as well to identify the microorganisms responsible for food processing defects. Metataxonomics and metagenomics are currently the gold standard methodologies to explore the full potential of metagenomes in the food industry. However, there are still a number of challenges that must be solved in order to implement these methods routinely in food chain monitoring, and for the regulatory agencies to take them into account in their opinions. These challenges include the difficulties of analysing foods and food-related environments with a low microbial load, the lack of validated bioinformatics pipelines adapted to food microbiomes and the difficulty of assessing the viability of the detected microorganisms. This review summarizes the methods of microbiome analysis that have been used, so far, in foods and food-related environments, with a specific focus on those involving Next-Generation Sequencing technologies.}, } @article {pmid34686748, year = {2021}, author = {Sarker, S}, title = {Metagenomic detection and characterisation of multiple viruses in apparently healthy Australian Neophema birds.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {20915}, pmid = {34686748}, issn = {2045-2322}, mesh = {Animals ; Australia ; Biological Evolution ; Bird Diseases/virology ; Endangered Species ; Humans ; Metagenome/*genetics ; Metagenomics/methods ; Parrots/*virology ; Phylogeny ; Virus Diseases/virology ; Viruses/*genetics ; }, abstract = {Emerging viral pathogens are a significant concern, with potential consequences for human, animal and environmental health. Over the past several decades, many novel viruses have been found in animals, including birds, and often pose a significant threat to vulnerable species. However, despite enormous interest in virus research, little is known about virus communities (viromes) in Australian Neophema birds. Therefore, this study was designed to characterise the viromes of Neophema birds and track the evolutionary relationships of recently emerging psittacine siadenovirus F (PsSiAdV-F) circulating in the critically endangered, orange-bellied parrot (OBP, Neophema chrysogaster), using a viral metagenomic approach. This study identified 16 viruses belonging to the families Adenoviridae, Circoviridae, Endornaviridae, Picobirnaviridae and Picornaviridae. In addition, this study demonstrated a potential evolutionary relationship of a PsSiAdV-F sequenced previously from the critically endangered OBP. Strikingly, five adenoviral contigs identified in this study show the highest identities with human adenovirus 2 and human mastadenovirus C. This highlights an important and unexpected aspects of the avian virome and warrants further studies dedicated to this subject. Finally, the findings of this study emphasise the importance of testing birds used for trade or in experimental settings for potential pathogens to prevent the spread of infections.}, } @article {pmid34685776, year = {2021}, author = {Kameli, N and Becker, HEF and Welbers, T and Jonkers, DMAE and Penders, J and Savelkoul, P and Stassen, FR}, title = {Metagenomic Profiling of Fecal-Derived Bacterial Membrane Vesicles in Crohn's Disease Patients.}, journal = {Cells}, volume = {10}, number = {10}, pages = {}, pmid = {34685776}, issn = {2073-4409}, mesh = {Bacteria/*metabolism ; Biodiversity ; Cell Membrane/*metabolism ; Crohn Disease/*microbiology ; DNA, Bacterial/genetics ; Feces/*microbiology ; Humans ; *Metagenomics ; }, abstract = {BACKGROUND: In the past, many studies suggested a crucial role for dysbiosis of the gut microbiota in the etiology of Crohn's disease (CD). However, despite being important players in host-bacteria interaction, the role of bacterial membrane vesicles (MV) has been largely overlooked in the pathogenesis of CD. In this study, we addressed the composition of the bacterial and MV composition in fecal samples of CD patients and compared this to the composition in healthy individuals.

METHODS: Fecal samples from six healthy subjects (HC) in addition to twelve CD patients (six active, six remission) were analyzed in this study. Fecal bacterial membrane vesicles (fMVs) were isolated by a combination of ultrafiltration and size exclusion chromatography. DNA was obtained from the fMV fraction, the pellet of dissolved feces as bacterial DNA (bDNA), or directly from feces as fecal DNA (fDNA). The fMVs were characterized by nanoparticle tracking analysis and cryo-electron microscopy. Amplicon sequencing of 16s rRNA V4 hypervariable gene regions was conducted to assess microbial composition of all fractions.

RESULTS: Beta-diversity analysis showed that the microbial community structure of the fMVs was significantly different from the microbial profiles of the fDNA and bDNA. However, no differences were observed in microbial composition between fDNA and bDNA. The microbial richness of fMVs was significantly decreased in CD patients compared to HC, and even lower in active patients. Profiling of fDNA and bDNA demonstrated that Firmicutes was the most dominant phylum in these fractions, while in fMVs Bacteroidetes was dominant. In fMV, several families and genera belonging to Firmicutes and Proteobacteria were significantly altered in CD patients when compared to HC.

CONCLUSION: The microbial alterations of MVs in CD patients particularly in Firmicutes and Proteobacteria suggest a possible role of MVs in host-microbe symbiosis and induction or progression of inflammation in CD pathogenesis. Yet, the exact role for these fMV in the pathogenesis of the disease needs to be elucidated in future studies.}, } @article {pmid34684657, year = {2021}, author = {Hossain, F and Majumder, S and David, J and Bunnell, BA and Miele, L}, title = {Obesity Modulates the Gut Microbiome in Triple-Negative Breast Cancer.}, journal = {Nutrients}, volume = {13}, number = {10}, pages = {}, pmid = {34684657}, issn = {2072-6643}, support = {U54 GM104940/GM/NIGMS NIH HHS/United States ; }, mesh = {Analysis of Variance ; Animals ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Mice ; Obesity/*complications/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; Triple Negative Breast Neoplasms/*complications/*microbiology ; }, abstract = {Triple-negative breast cancer (TNBC) is an aggressive, molecularly heterogeneous subtype of breast cancer. Obesity is associated with increased incidence and worse prognosis in TNBC through various potential mechanisms. Recent evidence suggests that the gut microbiome plays a central role in the progression of cancer, and that imbalances or dysbiosis in the population of commensal microbiota can lead to inflammation and contribute to tumor progression. Obesity is characterized by low-grade inflammation, and gut dysbiosis is associated with obesity, chronic inflammation, and failure of cancer immunotherapy. However, the debate on what constitutes a "healthy" gut microbiome is ongoing, and the connection among the gut microbiome, obesity, and TNBC has not yet been addressed. This study aims to characterize the role of obesity in modulating the gut microbiome in a syngeneic mouse model of TNBC. 16S rRNA sequencing and metagenomic analyses were performed to analyze and annotate genus and taxonomic profiles. Our results suggest that obesity decreases alpha diversity in the gut microbiome. Metagenomic analysis revealed that obesity was the only significant factor explaining the similarity of the bacterial communities according to their taxonomic profiles. In contrast to the analysis of taxonomic profiles, the analysis of variation of functional profiles suggested that obesity status, tumor presence, and the obesity-tumor interaction were significant in explaining the variation of profiles, with obesity having the strongest correlation. The presence of tumor modified the profiles to a greater extent in obese than in lean animals. Further research is warranted to understand the impact of the gut microbiome on TNBC progression and immunotherapy.}, } @article {pmid34684567, year = {2021}, author = {Rousta, E and Oka, A and Liu, B and Herzog, J and Bhatt, AP and Wang, J and Habibi Najafi, MB and Sartor, RB}, title = {The Emulsifier Carboxymethylcellulose Induces More Aggressive Colitis in Humanized Mice with Inflammatory Bowel Disease Microbiota Than Polysorbate-80.}, journal = {Nutrients}, volume = {13}, number = {10}, pages = {}, pmid = {34684567}, issn = {2072-6643}, support = {P01 DK094779/DK/NIDDK NIH HHS/United States ; P40 OD010995/OD/NIH HHS/United States ; P01DK094779, P40OD010995, P30DK034987, K01DK119582//the US Public Health Service National Institutes of Health (NIH)/ ; #2434 and 708151//the Crohn's & Colitis Foundation/ ; }, mesh = {Animals ; Biomarkers/metabolism ; Body Weight/drug effects ; Carboxymethylcellulose Sodium/*adverse effects ; Colitis/*chemically induced/*microbiology/pathology ; Colon/metabolism/pathology ; Emulsifying Agents/*adverse effects ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gene Expression Regulation/drug effects ; Humans ; Inflammation/pathology ; Inflammatory Bowel Diseases/*microbiology ; Male ; Metabolic Networks and Pathways/drug effects ; Mice, Inbred C57BL ; Polysorbates/*adverse effects ; RNA, Messenger/genetics/metabolism ; Mice ; }, abstract = {Commonly used synthetic dietary emulsifiers, including carboxymethylcellulose (CMC) and polysorbate-80 (P80), promote intestinal inflammation. We compared abilities of CMC vs. P80 to potentiate colitis and impact human microbiota in an inflammatory environment using a novel colitis model of ex-germ-free (GF) IL10[-/-] mice colonized by pooled fecal transplant from three patients with active inflammatory bowel diseases. After three days, mice received 1% CMC or P80 in drinking water or water alone for four weeks. Inflammation was quantified by serial fecal lipocalin 2 (Lcn-2) and after four weeks by blinded colonic histologic scores and colonic inflammatory cytokine gene expression. Microbiota profiles in cecal contents were determined by shotgun metagenomic sequencing. CMC treatment significantly increased fecal Lcn-2 levels compared to P80 and water treatment by one week and throughout the experiment. Likewise, CMC treatment increased histologic inflammatory scores and colonic inflammatory cytokine gene expression compared with P80 and water controls. The two emulsifiers differentially affected specific intestinal microbiota. CMC did not impact bacterial composition but significantly decreased Caudoviricetes (bacteriophages), while P80 exposure non-significantly increased the abundance of both Actinobacteria and Proteobacteria. Commonly used dietary emulsifiers have different abilities to induce colitis in humanized mice. CMC promotes more aggressive inflammation without changing bacterial composition.}, } @article {pmid34684459, year = {2021}, author = {Ahrens, AP and Culpepper, T and Saldivar, B and Anton, S and Stoll, S and Handberg, EM and Xu, K and Pepine, C and Triplett, EW and Aggarwal, M}, title = {A Six-Day, Lifestyle-Based Immersion Program Mitigates Cardiovascular Risk Factors and Induces Shifts in Gut Microbiota, Specifically Lachnospiraceae, Ruminococcaceae, Faecalibacterium prausnitzii: A Pilot Study.}, journal = {Nutrients}, volume = {13}, number = {10}, pages = {}, pmid = {34684459}, issn = {2072-6643}, support = {N/A//Whole Foods, Inc./ ; }, mesh = {Adult ; Biodiversity ; Biomarkers ; Body Weights and Measures ; *Diet ; Disease Susceptibility ; Faecalibacterium prausnitzii ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; *Heart Disease Risk Factors ; Humans ; *Life Style ; Male ; Metagenomics/methods ; Middle Aged ; Pilot Projects ; Ruminococcus ; }, abstract = {Cardiovascular disease (CVD) prevalence remains elevated globally. We have previously shown that a one-week lifestyle "immersion program" leads to clinical improvements and sustained improvements in quality of life in moderate to high atherosclerotic CVD (ASCVD) risk individuals. In a subsequent year of this similarly modeled immersion program, we again collected markers of cardiovascular health and, additionally, evaluated intestinal microbiome composition. ASCVD risk volunteers (n = 73) completed the one-week "immersion program" involving nutrition (100% plant-based foods), stress management education, and exercise. Anthropometric measurements and CVD risk factors were compared at baseline and post intervention. A subgroup (n = 22) provided stool, which we analyzed with 16S rRNA sequencing. We assessed abundance changes within-person, correlated the abundance shifts with clinical changes, and inferred functional pathways using PICRUSt. Reductions in blood pressure, total cholesterol, and triglycerides, were observed without reduction in weight. Significant increases in butyrate producers were detected, including Lachnospiraceae and Oscillospirales. Within-person, significant shifts in relative abundance (RA) occurred, e.g., increased Lachnospiraceae (+58.8% RA, p = 0.0002), Ruminococcaceae (+82.1%, p = 0.0003), Faecalibacterium prausnitzii (+54.5%, p = 0.002), and diversification and richness. Microbiota changes significantly correlated with body mass index (BMI), blood pressure (BP), cholesterol, high-sensitivity C-reactive protein (hsCRP), glucose, and trimethylamine N-oxide (TMAO) changes. Pairwise decreases were inferred in microbial genes corresponding to cancer, metabolic disease, and amino acid metabolism. This brief lifestyle-based intervention improved lipids and BP and enhanced known butyrate producers, without significant weight loss. These results demonstrate a promising non-pharmacological preventative strategy for improving cardiovascular health.}, } @article {pmid34681921, year = {2021}, author = {Lacroix, V and Cassard, A and Mas, E and Barreau, F}, title = {Multi-Omics Analysis of Gut Microbiota in Inflammatory Bowel Diseases: What Benefits for Diagnostic, Prognostic and Therapeutic Tools?.}, journal = {International journal of molecular sciences}, volume = {22}, number = {20}, pages = {}, pmid = {34681921}, issn = {1422-0067}, mesh = {Bacteria/*classification/isolation & purification ; Disease Progression ; Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Metagenomics/*methods ; Phylogeny ; Precision Medicine ; }, abstract = {Inflammatory bowel diseases (IBDs), which include Crohn's disease and ulcerative colitis, are multifactorial diseases that involve in particular a modification of the gut microbiota, known as dysbiosis. The initial sets of metataxonomic and metagenomic data first made it possible to approximate the microbiota profile in IBD. In addition, today the new 'omics' techniques have enabled us to draw up a functional and integrative map of the microbiota. The key concern in IBD is to develop biomarkers that allow us to assess the activity of the disease and predict the complications and progression, while also guiding the therapeutic care so as to develop personalized medicine. In this review, we present all of the latest discoveries on the microbiota provided by "omics" and we outline the benefits of these techniques in developing new diagnostic, prognostic and therapeutic tools.}, } @article {pmid34680891, year = {2021}, author = {Alili, R and Belda, E and Le, P and Wirth, T and Zucker, JD and Prifti, E and Clément, K}, title = {Exploring Semi-Quantitative Metagenomic Studies Using Oxford Nanopore Sequencing: A Computational and Experimental Protocol.}, journal = {Genes}, volume = {12}, number = {10}, pages = {}, pmid = {34680891}, issn = {2073-4425}, mesh = {Computational Biology/methods ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenomics ; Nanopore Sequencing/*methods ; }, abstract = {The gut microbiome plays a major role in chronic diseases, of which several are characterized by an altered composition and diversity of bacterial communities. Large-scale sequencing projects allowed for characterizing the perturbations of these communities. However, translating these discoveries into clinical applications remains a challenge. To facilitate routine implementation of microbiome profiling in clinical settings, portable, real-time, and low-cost sequencing technologies are needed. Here, we propose a computational and experimental protocol for whole-genome semi-quantitative metagenomic studies of human gut microbiome with Oxford Nanopore sequencing technology (ONT) that could be applied to other microbial ecosystems. We developed a bioinformatics protocol to analyze ONT sequences taxonomically and functionally and optimized preanalytic protocols, including stool collection and DNA extraction methods to maximize read length. This is a critical parameter for the sequence alignment and classification. Our protocol was evaluated using simulations of metagenomic communities, which reflect naturally occurring compositional variations. Next, we validated both protocols using stool samples from a bariatric surgery cohort, sequenced with ONT, Illumina, and SOLiD technologies. Results revealed similar diversity and microbial composition profiles. This protocol can be implemented in a clinical or research setting, bringing rapid personalized whole-genome profiling of target microbiome species.}, } @article {pmid34678464, year = {2022}, author = {Liu, W and Fang, X and Zhou, Y and Dou, L and Dou, T}, title = {Machine learning-based investigation of the relationship between gut microbiome and obesity status.}, journal = {Microbes and infection}, volume = {24}, number = {2}, pages = {104892}, doi = {10.1016/j.micinf.2021.104892}, pmid = {34678464}, issn = {1769-714X}, mesh = {Body Mass Index ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; Machine Learning ; Obesity ; }, abstract = {Gut microbiota is believed to play a crucial role in obesity. However, the consistent findings among published studies regarding microbiome-obesity interaction are relatively rare, and one of the underlying causes could be the limited sample size of cohort studies. In order to identify gut microbiota changes between normal-weight individuals and obese individuals, fecal samples along with phenotype information from 2262 Chinese individuals were collected and analyzed. Compared with normal-weight individuals, the obese individuals exhibit lower diversity of species and higher diversity of metabolic pathways. In addition, various machine learning models were employed to quantify the relationship between obesity status and Body mass index (BMI) values, of which support vector machine model achieves best performance with 0.716 classification accuracy and 0.485 R[2] score. In addition to two well-established obesity-associated species, three species that have potential to be obesity-related biomarkers, including Bacteroides caccae, Odoribacter splanchnicus and Roseburia hominis were identified. Further analyses of functional pathways also reveal some enriched pathways in obese individuals. Collectively, our data demonstrates tight relationship between obesity and gut microbiota in a large-scale Chinese population. These findings may provide potential targets for the prevention and treatment of obesity.}, } @article {pmid34677676, year = {2022}, author = {Biassoni, R and Di Marco, E and Squillario, M and Ugolotti, E and Mosconi, M and Faticato, MG and Mattioli, G and Avanzini, S and Pini Prato, A}, title = {Pathways and microbiome modifications related to surgery and enterocolitis in Hirschsprung disease.}, journal = {Pediatric surgery international}, volume = {38}, number = {1}, pages = {83-98}, pmid = {34677676}, issn = {1437-9813}, support = {GR-2011-02347381//ministero della salute/ ; }, mesh = {*Enteric Nervous System ; *Enterocolitis ; Feces ; *Hirschsprung Disease/surgery ; Humans ; *Microbiota ; }, abstract = {BACKGROUND: Hirschsprung disease (HSCR) is a congenital anomaly of the enteric nervous system. Abnormal microbiome composition was reported in HSCR patients. In this study, we addressed and analyzed microbiome modifications with relation tosurgery and HSCR associated enterocolitis (HAEC).

METHODS: The faecal microbiome of 31 HSCR patients (overall 64 samples) was analyzed. HAEC was diagnosed and classified according to a combination of Pastor's and Elhalabi's criteria. Stool samples were analyzed by 16S sequencing (7 out of 9 polymorphic regions). Compositional and relative abundance profiles, as well as the functional potentials of the microbial community, were analyzed with the marker gene sequencing profiles using PICRUSt.

RESULTS: The relative abundance of Bacteroidetes showed a severe decrease with slow recovery after surgery. Conversely, Proteobacteria transiently increased their abundance. Noteworthy, a strong linkage has been found between Proteobacteria descendants and HAEC occurrences. The inferred functional analysis indicated that virulence factors and fimbriae or pili might be associated with HAEC.

CONCLUSIONS: Our study, addressing microbiome dynamics, demonstrated relevant changes after surgical manipulation. Alpha-diversity analyses indicated that surgery deeply affects microbiome composition. Proteobacteria and Enterobacteriaceae seem to play a pivotal role in HAEC occurrences. Several virulence factors, such as fimbriae or pili, might explain the HAEC-predisposing potential of selected microbiomes. These results suggest some innovative therapeutic approaches that deserve to be tested in appropriate clinical trials.}, } @article {pmid34677583, year = {2022}, author = {Pärnänen, KMM and Hultman, J and Markkanen, M and Satokari, R and Rautava, S and Lamendella, R and Wright, J and McLimans, CJ and Kelleher, SL and Virta, MP}, title = {Early-life formula feeding is associated with infant gut microbiota alterations and an increased antibiotic resistance load.}, journal = {The American journal of clinical nutrition}, volume = {115}, number = {2}, pages = {407-421}, pmid = {34677583}, issn = {1938-3207}, mesh = {Bacterial Proteins/*metabolism ; Cross-Sectional Studies ; Drug Resistance, Microbial/*genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Infant Formula/*microbiology ; *Infant Nutritional Physiological Phenomena ; Infant, Newborn ; Infant, Premature ; Linear Models ; Male ; }, abstract = {BACKGROUND: Infants are at a high risk of acquiring fatal infections, and their treatment relies on functioning antibiotics. Antibiotic resistance genes (ARGs) are present in high numbers in antibiotic-naive infants' gut microbiomes, and infant mortality caused by resistant infections is high. The role of antibiotics in shaping the infant resistome has been studied, but there is limited knowledge on other factors that affect the antibiotic resistance burden of the infant gut.

OBJECTIVES: Our objectives were to determine the impact of early exposure to formula on the ARG load in neonates and infants born either preterm or full term. Our hypotheses were that diet causes a selective pressure that influences the microbial community of the infant gut, and formula exposure would increase the abundance of taxa that carry ARGs.

METHODS: Cross-sectionally sampled gut metagenomes of 46 neonates were used to build a generalized linear model to determine the impact of diet on ARG loads in neonates. The model was cross-validated using neonate metagenomes gathered from public databases using our custom statistical pipeline for cross-validation.

RESULTS: Formula-fed neonates had higher relative abundances of opportunistic pathogens such as Staphylococcus aureus, Staphylococcus epidermidis, Klebsiella pneumoniae, Klebsiella oxytoca, and Clostridioides difficile. The relative abundance of ARGs carried by gut bacteria was 69% higher in the formula-receiving group (fold change, 1.69; 95% CI: 1.12-2.55; P = 0.013; n = 180) compared to exclusively human milk-fed infants. The formula-fed infants also had significantly less typical infant bacteria, such as Bifidobacteria, that have potential health benefits.

CONCLUSIONS: The novel finding that formula exposure is correlated with a higher neonatal ARG burden lays the foundation that clinicians should consider feeding mode in addition to antibiotic use during the first months of life to minimize the proliferation of antibiotic-resistant gut bacteria in infants.}, } @article {pmid34676935, year = {2022}, author = {Petrelli, S and Buglione, M and Maselli, V and Troiano, C and Larson, G and Frantz, L and Manin, A and Ricca, E and Baccigalupi, L and Wright, D and Pietri, C and Fulgione, D}, title = {Population genomic, olfactory, dietary, and gut microbiota analyses demonstrate the unique evolutionary trajectory of feral pigs.}, journal = {Molecular ecology}, volume = {31}, number = {1}, pages = {220-237}, pmid = {34676935}, issn = {1365-294X}, support = {NE/S00078X/1//Natural Environment Research Council/ ; NE/K005243/1//Natural Environmental Research Council/ ; NE/K003259/1//Natural Environmental Research Council/ ; NE/S007067/1//Natural Environmental Research Council/ ; ERC-2013-StG-337574-UNDEAD/ERC_/European Research Council/International ; ERC-2019-StG-853272-PALAEOFARM/ERC_/European Research Council/International ; }, mesh = {Animals ; Breeding ; Diet/veterinary ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Sus scrofa/genetics ; Swine/genetics ; }, abstract = {Domestication is an intriguing evolutionary process. Many domestic populations are subjected to strong human-mediated selection, and when some individuals return to the wild, they are again subjected to selective forces associated with new environments. Generally, these feral populations evolve into something different from their wild predecessors and their members typically possess a combination of both wild and human selected traits. Feralisation can manifest in different forms on a spectrum from a wild to a domestic phenotype. This depends on how the rewilded domesticated populations can readapt to natural environments based on how much potential and flexibility the ancestral genome retains after its domestication signature. Whether feralisation leads to the evolution of new traits that do not exist in the wild or to convergence with wild forms, however, remains unclear. To address this question, we performed population genomic, olfactory, dietary, and gut microbiota analyses on different populations of Sus scrofa (wild boar, hybrid, feral and several domestic pig breeds). Porcine single nucleotide polymorphisms (SNPs) analysis shows that the feral population represents a cluster distinctly separate from all others. Its members display signatures of past artificial selection, as demonstrated by values of FST in specific regions of the genome and bottleneck signature, such as the number and length of runs of homozygosity. Generalised FST values, reacquired olfactory abilities, diet, and gut microbiota variation show current responses to natural selection. Our results suggest that feral pigs are an independent evolutionary unit which can persist so long as levels of human intervention remain unchanged.}, } @article {pmid34675137, year = {2021}, author = {Kim, H and Cho, JH and Song, M and Cho, JH and Kim, S and Kim, ES and Keum, GB and Kim, HB and Lee, JH}, title = {Evaluating the Prevalence of Foodborne Pathogens in Livestock Using Metagenomics Approach.}, journal = {Journal of microbiology and biotechnology}, volume = {31}, number = {12}, pages = {1701-1708}, pmid = {34675137}, issn = {1738-8872}, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification ; Cattle ; Chickens ; Feces/microbiology ; Food Safety ; Foodborne Diseases/*microbiology ; Livestock/*microbiology ; *Metagenomics ; Microbiota ; Prevalence ; Swine ; }, abstract = {Food safety is the most important global health issue due to foodborne pathogens after consumption of contaminated food. Foodborne bacteria such as Escherichia coli, Salmonella enterica, Staphylococcus aureus, Campylobacter spp., Bacillus cereus, Vibrio spp., Yersinia enterocolitica and Clostridium perfringens are leading causes of the majority of foodborne illnesses and deaths. These foodborne pathogens often come from the livestock feces, thus, we analyzed fecal microbial communities of three different livestock species to investigate the prevalence of foodborne pathogens in livestock feces using metagenomics analysis. Our data showed that alpha diversities of microbial communities were different according to livestock species. The microbial diversity of cattle feces was higher than that of chicken or pig feces. Moreover, microbial communities were significantly different among these three livestock species (cattle, chicken, and pig). At the genus level, Staphylococcus and Clostridium were found in all livestock feces, with chicken feces having higher relative abundances of Staphylococcus and Clostridium than cattle and pig feces. Genera Bacillus, Campylobacter, and Vibrio were detected in cattle feces. Chicken samples contained Bacillus, Listeria, and Salmonella with low relative abundance. Other genera such as Corynebacterium, Streptococcus, Neisseria, Helicobacter, Enterobacter, Klebsiella, and Pseudomonas known to be opportunistic pathogens were also detected in cattle, chicken, and pig feces. Results of this study might be useful for controlling the spread of foodborne pathogens in farm environments known to provide natural sources of these microorganisms.}, } @article {pmid34673779, year = {2021}, author = {Sugimoto, R and Nishimura, L and Nguyen, PT and Ito, J and Parrish, NF and Mori, H and Kurokawa, K and Nakaoka, H and Inoue, I}, title = {Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: Viruses, plasmids, and more.}, journal = {PLoS computational biology}, volume = {17}, number = {10}, pages = {e1009428}, pmid = {34673779}, issn = {1553-7358}, mesh = {Archaea/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenome/*genetics ; Metagenomics ; Plasmids/*genetics ; Sequence Analysis, DNA ; Viruses/*genetics ; }, abstract = {Viruses are the most numerous biological entity, existing in all environments and infecting all cellular organisms. Compared with cellular life, the evolution and origin of viruses are poorly understood; viruses are enormously diverse, and most lack sequence similarity to cellular genes. To uncover viral sequences without relying on either reference viral sequences from databases or marker genes that characterize specific viral taxa, we developed an analysis pipeline for virus inference based on clustered regularly interspaced short palindromic repeats (CRISPR). CRISPR is a prokaryotic nucleic acid restriction system that stores the memory of previous exposure. Our protocol can infer CRISPR-targeted sequences, including viruses, plasmids, and previously uncharacterized elements, and predict their hosts using unassembled short-read metagenomic sequencing data. By analyzing human gut metagenomic data, we extracted 11,391 terminally redundant CRISPR-targeted sequences, which are likely complete circular genomes. The sequences included 2,154 tailed-phage genomes, together with 257 complete crAssphage genomes, 11 genomes larger than 200 kilobases, 766 genomes of Microviridae species, 56 genomes of Inoviridae species, and 95 previously uncharacterized circular small genomes that have no reliably predicted protein-coding gene. We predicted the host(s) of approximately 70% of the discovered genomes at the taxonomic level of phylum by linking protospacers to taxonomically assigned CRISPR direct repeats. These results demonstrate that our protocol is efficient for de novo inference of CRISPR-targeted sequences and their host prediction.}, } @article {pmid34673641, year = {2022}, author = {Torre, E and Sola, D and Caramaschi, A and Mignone, F and Bona, E and Fallarini, S}, title = {A Pilot Study on Clinical Scores, Immune Cell Modulation, and Microbiota Composition in Allergic Patients with Rhinitis and Asthma Treated with a Probiotic Preparation.}, journal = {International archives of allergy and immunology}, volume = {183}, number = {2}, pages = {186-200}, doi = {10.1159/000518952}, pmid = {34673641}, issn = {1423-0097}, mesh = {Adult ; Asthma/*diagnosis/*etiology/*therapy ; Biomarkers ; Cytokines/metabolism ; Disease Management ; Disease Susceptibility ; Female ; Humans ; Immunity ; Immunophenotyping ; Leukocyte Count ; Male ; Metagenomics/methods ; Microbiota ; Middle Aged ; Pilot Projects ; Probiotics/therapeutic use ; Prognosis ; Rhinitis/*diagnosis/*etiology/*therapy ; Treatment Outcome ; Young Adult ; }, abstract = {BACKGROUND: Specific drugs and/or immunotherapies are widely used to treat allergies, but drug-induced adverse effects recently led to explore new additional strategies. We studied whether a probiotic preparation (iPROB®; Anallergo SpA, Florence, Italy) is effective in allergic patients and the mechanisms underlying clinical outcomes.

METHODS: Eligible patients (n = 28), all suffering from allergic rhinitis with/without bronchial asthma, were consecutively recruited at the Allergology Medical Unit (Novara, Italy) and treated with this probiotic. From each patient, we collected blood and stool samples at the baseline, after 60 days of probiotic supplementation, and after 60 days from probiotic discontinuation. In each blood sample, the percentage of hematopoietic stem cells, eosinophils, and basophils was measured by FACS. To analyze stool microbiota composition, genomic DNA was extracted, bacterial 16S DNA libraries sequenced by Illumina platform (Miseq), and raw sequences processed. Generated data were statistically analyzed.

RESULTS: Probiotic-treated patients showed a significant decrease in Average Rhinitis Total Symptom Score (d = -10.5714), and Visual Analog Scale (d = -2.00) clinical indices, as well as important improvements in quality of life. In whole blood, a significant reduction in the percentage of activated eosinophils and basophils was determined, and this effect persisted after specific cell stimulation. Consistently, the serum levels of IL-4 and IL-5 decreased after probiotic treatment, suggesting a reduction in the Th2 cytokine profile. In addition, microbiome genomic analysis (n = 6) showed an increase in microbiome biodiversity, which positively correlates with clinical and cellular data.

CONCLUSION: Present study suggests that iPROB® preparation has clinical/biological properties to be a valid add-on supplementation in allergic patients with asthma and rhinitis.}, } @article {pmid34671161, year = {2021}, author = {Wang, Y and Pedersen, MW and Alsos, IG and De Sanctis, B and Racimo, F and Prohaska, A and Coissac, E and Owens, HL and Merkel, MKF and Fernandez-Guerra, A and Rouillard, A and Lammers, Y and Alberti, A and Denoeud, F and Money, D and Ruter, AH and McColl, H and Larsen, NK and Cherezova, AA and Edwards, ME and Fedorov, GB and Haile, J and Orlando, L and Vinner, L and Korneliussen, TS and Beilman, DW and Bjørk, AA and Cao, J and Dockter, C and Esdale, J and Gusarova, G and Kjeldsen, KK and Mangerud, J and Rasic, JT and Skadhauge, B and Svendsen, JI and Tikhonov, A and Wincker, P and Xing, Y and Zhang, Y and Froese, DG and Rahbek, C and Bravo, DN and Holden, PB and Edwards, NR and Durbin, R and Meltzer, DJ and Kjær, KH and Möller, P and Willerslev, E}, title = {Late Quaternary dynamics of Arctic biota from ancient environmental genomics.}, journal = {Nature}, volume = {600}, number = {7887}, pages = {86-92}, pmid = {34671161}, issn = {1476-4687}, support = {207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; /ERC_/European Research Council/International ; 207492/WT_/Wellcome Trust/United Kingdom ; WT220023/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 069906/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Arctic Regions ; *Biota ; Climate Change/history ; DNA, Ancient/*analysis ; DNA, Environmental/*analysis ; Databases, Genetic ; Datasets as Topic ; Extinction, Biological ; Geologic Sediments ; Grassland ; Greenland ; Haplotypes/genetics ; Herbivory/genetics ; History, Ancient ; Humans ; Lakes ; Mammoths ; *Metagenomics ; Mitochondria/genetics ; Perissodactyla ; Permafrost ; Phylogeny ; Plants/genetics ; Population Dynamics ; Rain ; Siberia ; Spatio-Temporal Analysis ; Wetlands ; }, abstract = {During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood[1-8]. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe-tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.}, } @article {pmid34669745, year = {2021}, author = {Essigmann, HT and Hoffman, KL and Petrosino, JF and Jun, G and Aguilar, D and Hanis, CL and DuPont, HL and Brown, EL}, title = {The impact of the Th17:Treg axis on the IgA-Biome across the glycemic spectrum.}, journal = {PloS one}, volume = {16}, number = {10}, pages = {e0258812}, pmid = {34669745}, issn = {1932-6203}, support = {R01 DK116378/DK/NIDDK NIH HHS/United States ; R01 DK118631/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Bacteria/*classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Diabetes Mellitus, Type 2/*immunology/microbiology ; Epigenesis, Genetic ; Female ; Gastrointestinal Microbiome ; Humans ; Immunoglobulin A, Secretory/*metabolism ; Male ; Mexican Americans ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; T-Lymphocytes, Regulatory/*immunology ; Th17 Cells/*immunology ; }, abstract = {Secretory IgA (SIgA) is released into mucosal surfaces where its function extends beyond that of host defense to include the shaping of resident microbial communities by mediating exclusion/inclusion of respective microbes and regulating bacterial gene expression. In this capacity, SIgA acts as the fulcrum on which host immunity and the health of the microbiota are balanced. We recently completed an analysis of the gut and salivary IgA-Biomes (16S rDNA sequencing of SIgA-coated/uncoated bacteria) in Mexican-American adults that identified IgA-Biome differences across the glycemic spectrum. As Th17:Treg ratio imbalances are associated with gut microbiome dysbiosis and chronic inflammatory conditions such as type 2 diabetes, the present study extends our prior work by examining the impact of Th17:Treg ratios (pro-inflammatory:anti-inflammatory T-cell ratios) and the SIgA response (Th17:Treg-SIgA axis) in shaping microbial communities. Examining the impact of Th17:Treg ratios (determined by epigenetic qPCR lymphocyte subset quantification) on the IgA-Biome across diabetes phenotypes identified a proportional relationship between Th17:Treg ratios and alpha diversity in the stool IgA-Biome of those with dysglycemia, significant changes in community composition of the stool and salivary microbiomes across glycemic profiles, and genera preferentially abundant by T-cell inflammatory phenotype. This is the first study to associate epigenetically quantified Th17:Treg ratios with both the larger and SIgA-fractionated microbiome, assess these associations in the context of a chronic inflammatory disease, and offers a novel frame through which to evaluate mucosal microbiomes in the context of host responses and inflammation.}, } @article {pmid34668749, year = {2021}, author = {Zhai, Z and Zhang, Z and Zhao, G and Liu, X and Qin, F and Zhao, Y}, title = {Genomic Characterization of Two Novel RCA Phages Reveals New Insights into the Diversity and Evolution of Marine Viruses.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0123921}, pmid = {34668749}, issn = {2165-0497}, mesh = {Bacteriophages/classification/*genetics/*isolation & purification ; Biodiversity ; Evolution, Molecular ; Genome, Viral ; Genomics ; Phylogeny ; Roseobacter/virology ; Seawater/*virology ; *Virome ; }, abstract = {Viruses are the most abundant living entities in marine ecosystems, playing critical roles in altering the structure and function of microbial communities and driving ocean biogeochemistry. Phages that infect Roseobacter clade-affiliated (RCA) cluster strains are an important component of marine viral communities. Here, we characterize the genome sequences of two new RCA phages, CRP-9 and CRP-13, which infect RCA strain FZCC0023. Genomic analysis reveals that CRP-9 and CRP-13 represent a novel evolutionary lineage of marine phages. They both have a DNA replication module most similar to those in Cobavirus group phages. In contrast, their morphogenesis and packaging modules are distinct from those in cobaviruses but homologous to those in HMO-2011-type phages. The genomic architecture of CRP-9 and CRP-13 suggests a genomic recombination event between distinct phage groups. Metagenomic data sets were examined for metagenome-assembled viral genomes (MAVGs) with similar recombinant genome architectures. Fifteen CRP-9-type MAVGs were identified from marine viromes. Additionally, 158 MAVGs were identified containing HMO-2011-type morphogenesis and packaging modules with other types of DNA replication genes, providing more evidence that recombination between different phage groups is a major driver of phage evolution. Altogether, this study significantly expands the understanding of diversity and evolution of marine roseophages. Meanwhile, the analysis of these novel RCA phages and MAVGs highlights the critical role of recombination in shaping phage diversity. These phage sequences are valuable resources for inferring the evolutionary connection of distinct phage groups. IMPORTANCE Diversity and evolution of phages that infect the relatively slow-growing but dominant Roseobacter lineages are largely unknown. In this study, RCA phages CRP-9 and CRP-13 have been isolated on a Roseobacter RCA strain and shown to have a unique genomic architecture, which appears to be the result of a recombination event. CRP-9 and CRP-13 have a DNA replication module most similar to those in Cobavirus group phages and morphogenesis and packaging modules most similar to those in HMO-2011-type phages. HMO-2011-type morphogenesis and packaging modules are found in combination with distinct types of DNA replication genes, suggesting compatibility with various DNA replication modules. Altogether, this study contributes toward a better understanding of marine viral diversity and evolution.}, } @article {pmid34668733, year = {2021}, author = {Youseif, SH and Abd El-Megeed, FH and Humm, EA and Maymon, M and Mohamed, AH and Saleh, SA and Hirsch, AM}, title = {Comparative Analysis of the Cultured and Total Bacterial Community in the Wheat Rhizosphere Microbiome Using Culture-Dependent and Culture-Independent Approaches.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0067821}, pmid = {34668733}, issn = {2165-0497}, mesh = {Agriculture ; Bacteria/*classification/genetics ; Biodiversity ; Metagenome ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S ; *Rhizosphere ; Soil ; *Soil Microbiology ; Triticum/*microbiology ; }, abstract = {Rhizosphere and root-associated bacteria are key components of crop production and sustainable agriculture. However, utilization of these beneficial bacteria is often limited by conventional culture techniques because a majority of soil microorganisms cannot be cultured using standard laboratory media. Therefore, the purpose of this study was to improve culturability and investigate the diversity of the bacterial communities from the wheat rhizosphere microbiome collected from three locations in Egypt with contrasting soil characteristics by using metagenomic analysis and improved culture-based methods. The improved strategies of the culture-dependent approach included replacing the agar in the medium with gellan gums and modifying its preparation by autoclaving the phosphate and gelling agents separately. Compared to the total operational taxonomic units (OTUs) observed from the metagenomic data sets derived from the three analyzed soils, 1.86 to 2.52% of the bacteria were recovered using the modified cultivation strategies, whereas less than 1% were obtained employing the standard cultivation protocols. Twenty-one percent of the cultivable isolates exhibited multiple plant growth-promoting (PGP) properties, including P solubilization activity and siderophore production. From the metagenomic analysis, the most abundant phyla were Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, and Firmicutes. Moreover, the relative abundance of the specific bacterial taxa was correlated with the soil characteristics, demonstrating the effect of the soil in modulating the plant rhizosphere microbiome. IMPORTANCE Bacteria colonizing the rhizosphere, a narrow zone of soil surrounding the root system, are known to have beneficial effects in improving the growth and stress tolerance of plants. However, most bacteria in natural environments, especially those in rhizosphere soils, are recalcitrant to cultivation using traditional techniques, and thus their roles in soil health and plant growth remain unexplored. Hence, investigating new culture media and culture conditions to bring "not-yet-cultured" species into cultivation and to identify new functions is still an important task for all microbiologists. To this end, we describe improved cultivation protocols that increase the number and diversity of cultured bacteria from the rhizosphere of wheat plants. Using such approaches will lead to new insights into culturing more beneficial bacteria that live in the plant rhizosphere, in so doing creating greater opportunities not only for field application but also for promoting sustainability.}, } @article {pmid34668097, year = {2021}, author = {González-Castillo, A and Carballo, JL and Bautista-Guerrero, E}, title = {Genomics and phylogeny of the proposed phylum 'Candidatus Poribacteria' associated with the excavating sponge Thoosa mismalolli.}, journal = {Antonie van Leeuwenhoek}, volume = {114}, number = {12}, pages = {2163-2174}, pmid = {34668097}, issn = {1572-9699}, support = {254806//CONACYT-SEP/ ; }, mesh = {Animals ; *Bacteria/genetics ; Genomics ; Metagenome ; *Microbiota ; Phylogeny ; }, abstract = {Members of the proposed phylum 'Candidatus Poribacteria' are among the most abundant microorganisms in the highly diverse microbiome of the sponge mesohyl. Genomic and phylogenetic characteristics of this proposed phylum are barely known. In this study, we analyzed metagenome-assembled genomes (MAGs) obtained from the coral reef excavating sponge Thoosa mismalolli from the Mexican Pacific Ocean. Two MAGs were extracted and analyzed together with 32 MAGs and single-amplified genomes (SAGs) obtained from NCBI. The phylogenetic tree based on the sequences of 139 single-copy genes (SCG) showed two clades. Clade A (23 genomes) represented 67.7% of the total of the genomes, while clade B (11 genomes) comprised 32.3% of the genomes. The Average Nucleotide Identity (ANI) showed values between 66 and 99% for the genomes of the proposed phylum, and the pangenome of genomes revealed a total of 37,234 genes that included 1722 core gene. The number of genes used in the phylogenetic analysis increased from 28 (previous studies) to 139 (this study), which allowed a better resolution of the phylogeny of the proposed phylum. The results supported the two previously described classes, 'Candidatus Entoporibacteria' and 'Candidatus Pelagiporibacteria', and the genomes SB0101 and SB0202 obtained in this study belong to two new species of the class 'Candidatus Entoporibacteria'. This is the first comparative study that includes MAGs from a non-sponge host (Porites lutea) to elucidate the taxonomy of the poorly known Candidatus phylum in a polyphasic approach. Finally, our study also contributes to the sponge microbiome project by reporting the first MAGs of the proposed phylum 'Candidatus Poribacteria' isolated from the excavating sponge T. mismalolli.}, } @article {pmid34665113, year = {2021}, author = {Cassir, N and Belkacemi, S and Ballouche, M and Khelaifia, S and La Scola, B}, title = {Evaluation of Culture Top transport systems for assessing the bacterial diversity of microbiota by culturomics as compared to a routine transport system.}, journal = {Journal of medical microbiology}, volume = {70}, number = {10}, pages = {}, doi = {10.1099/jmm.0.001411}, pmid = {34665113}, issn = {1473-5644}, mesh = {Bacteria/*isolation & purification ; *Culture Media ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/methods ; Specimen Handling/*methods ; }, abstract = {In recent years, metagenomics and then culturomics, which consists of the multiplication of media and culture conditions and the rapid identification of all bacterial colonies, have generated renewed interest in the human microbiota, and diseases associated with modifications in its composition in particular. The sample transport media included in diverse swab transport systems and the storage conditions are among the factors that influence the results of the culturomics. In this study, we compared the results of culturomics from paired skin, oral and rectal swabs from intensive care unit (ICU) patients using Culture Top sample transport medium as compared to our routine one. From 152 clinical samples, we were able to isolate and identify 45 600 colonies, belonging to 338 different bacterial species. The transport system Culture Top identified 282 different bacterial species, while 244 were identified by our routine system. Of these, 188 different bacterial species were commonly identified using both transport systems, while 94 (27.8 %) and 56 (16.5 %) were only identified using Culture Top and our routine system, respectively (P<0.001), but there was no significant difference in bacterial diversity at the genus or phylum level, or in terms of their type of respiration and cell wall. In conclusion, the Culture Top transport system appears to be complementary to our routine system, although it seems slightly superior in terms of isolated bacterial species.}, } @article {pmid34664721, year = {2022}, author = {Wu, F and Yang, L and Hao, Y and Zhou, B and Hu, J and Yang, Y and Bedi, S and Sanichar, NG and Cheng, C and Perez-Perez, G and Tseng, W and Tseng, W and Tseng, M and Francois, F and Khan, AR and Li, Y and Blaser, MJ and Shu, XO and Long, J and Li, H and Pei, Z and Chen, Y}, title = {Oral and gastric microbiome in relation to gastric intestinal metaplasia.}, journal = {International journal of cancer}, volume = {150}, number = {6}, pages = {928-940}, pmid = {34664721}, issn = {1097-0215}, support = {R01 DK110014/DK/NIDDK NIH HHS/United States ; P30 ES000260/ES/NIEHS NIH HHS/United States ; P42 ES010349/ES/NIEHS NIH HHS/United States ; R01 CA204113/CA/NCI NIH HHS/United States ; P30 ES009089/ES/NIEHS NIH HHS/United States ; }, mesh = {Aged ; Case-Control Studies ; Female ; Gastric Mucosa/*pathology ; Gastrointestinal Microbiome/*physiology ; Helicobacter pylori/isolation & purification ; Humans ; Male ; Metagenomics ; Metaplasia ; Middle Aged ; Mouth Mucosa/*microbiology ; Precancerous Conditions/*etiology ; Stomach Neoplasms/*etiology ; }, abstract = {Evidence suggests that Helicobacter pylori plays a role in gastric cancer (GC) initiation. However, epidemiologic studies on the specific role of other bacteria in the development of GC are lacking. We conducted a case-control study of 89 cases with gastric intestinal metaplasia (IM) and 89 matched controls who underwent upper gastrointestinal endoscopy at three sites affiliated with NYU Langone Health. We performed shotgun metagenomic sequencing using oral wash samples from 89 case-control pairs and antral mucosal brushing samples from 55 case-control pairs. We examined the associations of relative abundances of bacterial taxa and functional pathways with IM using conditional logistic regression with and without elastic-net penalty. Compared with controls, oral species Peptostreptococcus stomatis, Johnsonella ignava, Neisseria elongata and Neisseria flavescens were enriched in cases (odds ratios [ORs] = 1.29-1.50, P = .004-.01) while Lactobacillus gasseri, Streptococcus mutans, S parasanguinis and S sanguinis were under-represented (ORs = 0.66-0.76, P = .006-.042) in cases. Species J ignava and Filifactor alocis in the gastric microbiota were enriched (ORs = 3.27 and 1.43, P = .005 and .035, respectively), while S mutans, S parasanguinis and S sanguinis were under-represented (ORs = 0.61-0.75, P = .024-.046), in cases compared with controls. The lipopolysaccharide and ubiquinol biosynthesis pathways were more abundant in IM, while the sugar degradation pathways were under-represented in IM. The findings suggest potential roles of certain oral and gastric microbiota, which are correlated with regulation of pathways associated with inflammation, in the development of gastric precancerous lesions.}, } @article {pmid34664588, year = {2021}, author = {Li, Q and Wu, T and Zhang, M and Chen, H and Liu, R}, title = {Induction of the glycolysis product methylglyoxal on trimethylamine lyase synthesis in the intestinal microbiota from mice fed with choline and dietary fiber.}, journal = {Food & function}, volume = {12}, number = {20}, pages = {9880-9893}, doi = {10.1039/d1fo01481a}, pmid = {34664588}, issn = {2042-650X}, mesh = {Animals ; Choline/*pharmacology ; Diet/methods ; Dietary Fiber/*pharmacology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Glycine/metabolism ; Glycolysis ; Lyases/genetics/*metabolism ; Metabolomics/methods ; Metagenomics/methods ; Methylamines/*metabolism ; Mice ; Mice, Inbred C57BL ; Pyruvaldehyde/*metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The present study investigated the induction of the glycolysis product methylglyoxal by trimethylamine (TMA) lyase synthesis in the intestinal microbiota and investigated the intervention mechanism of the effects of dietary fiber on methylglyoxal formation. Intestinal digesta samples, collected from the ceca of mice fed with choline-rich and fiber-supplemented diets, were incubated in an anaerobic environment at 37 °C and pH 7.0 with choline, glycine, and methylglyoxal as inductive factors. The differences between the gut microbiota and its metagenomic and metabonomics profiles were determined using 16S rRNA gene sequencing analysis. The results elucidated that the different dietary interventions could induce differences in the composition of the microbiota, gene expression profiles associated with glycine metabolism, and glycolysis. As compared to the gut microbiota of choline-diet fed mice, fiber supplementation effectively altered the composition of the microbiota and inhibited the genes involved in choline metabolism, glycine and methylglyoxal accumulation, and TMA lyase expression, and improved the methylglyoxal utilization by regulating the pathway related to pyruvate production. However, the intervention of exogenous methylglyoxal significantly decreased these effects. These findings successfully revealed the correlations between the TMA lyase expression and glycine level, as well as the inhibitory effects of dietary fiber on the glycine level, thereby highlighting the role of common glycolytic metabolites as a potential target for TMA production.}, } @article {pmid34664266, year = {2022}, author = {Yang, Y and Long, J and Wang, C and Blot, WJ and Pei, Z and Shu, X and Wu, F and Rothman, N and Wu, J and Lan, Q and Cai, Q and Zheng, W and Chen, Y and Shu, XO}, title = {Prospective study of oral microbiome and gastric cancer risk among Asian, African American and European American populations.}, journal = {International journal of cancer}, volume = {150}, number = {6}, pages = {916-927}, pmid = {34664266}, issn = {1097-0215}, support = {U01CA202979/CA/NCI NIH HHS/United States ; R00 CA230205/CA/NCI NIH HHS/United States ; UM1 CA173640/CA/NCI NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; U01 CA202979/CA/NCI NIH HHS/United States ; UM1CA173640/CA/NCI NIH HHS/United States ; K99 CA230205/CA/NCI NIH HHS/United States ; UM1CA182910/CA/NCI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; R01 CA207466/CA/NCI NIH HHS/United States ; UM1 CA182910/CA/NCI NIH HHS/United States ; P30 CA68485//Vanderbilt-Ingram Cancer Center/ ; R01 CA204113/CA/NCI NIH HHS/United States ; R01CA204113/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Black or African American ; Aged ; Asian People ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Metabolic Networks and Pathways ; Middle Aged ; Mouth/*microbiology ; Prospective Studies ; Risk ; Stomach Neoplasms/ethnology/*etiology/metabolism/microbiology ; White People ; }, abstract = {Colonization of specific bacteria in the human mouth was reported to be associated with gastric cancer risk. However, previous studies were limited by retrospective study designs and low taxonomic resolutions. We performed a prospective case-control study nested within three cohorts to investigate the relationship between oral microbiome and gastric cancer risk. Shotgun metagenomic sequencing was employed to characterize the microbiome in prediagnostic buccal samples from 165 cases and 323 matched controls. Associations of overall microbial richness and abundance of microbial taxa, gene families and metabolic pathways with gastric cancer risk were evaluated via conditional logistic regression. Analyses were performed within each cohort, and results were combined by meta-analyses. We found that overall microbial richness was associated with decreased gastric cancer risk, with an odds ratio (OR) per standard deviation (SD) increase in Simpson's reciprocal index of 0.77 (95% confidence interval [CI] = 0.61-0.99). Nine taxa, 38 gene families and six pathways also showed associations with gastric cancer risk at P < .05. Neisseria mucosa and Prevotella pleuritidis were enriched, while Mycoplasma orale and Eubacterium yurii were depleted among cases with ORs and 95% CIs per SD increase in centered log-ratio transformed taxa abundance of 1.31 (1.03-1.67), 1.26 (1.00-1.57), 0.74 (0.59-0.94) and 0.80 (0.65-0.98), respectively. The top two gene families (P = 3.75 × 10[-4] and 3.91 × 10[-4]) and pathways (P = 1.75 × 10[-3] and 1.53 × 10[-3]) associated with gastric cancer were related to the decreased risk and are involved in hexitol metabolism. Our study supports the hypothesis that oral microbiota may play a role in gastric cancer etiology.}, } @article {pmid34663463, year = {2021}, author = {Trubl, G and Kimbrel, JA and Liquet-Gonzalez, J and Nuccio, EE and Weber, PK and Pett-Ridge, J and Jansson, JK and Waldrop, MP and Blazewicz, SJ}, title = {Active virus-host interactions at sub-freezing temperatures in Arctic peat soil.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {208}, pmid = {34663463}, issn = {2049-2618}, mesh = {Freezing ; *Microbiota ; *Soil ; Soil Microbiology ; Temperature ; }, abstract = {BACKGROUND: Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures).

RESULTS: We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H2[18]O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO2) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up [18]O in soil and respired CO2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients.

CONCLUSIONS: Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks. Video abstract.}, } @article {pmid34662347, year = {2021}, author = {Herzog, EL and Wäfler, M and Keller, I and Wolf, S and Zinkernagel, MS and Zysset-Burri, DC}, title = {The importance of age in compositional and functional profiling of the human intestinal microbiome.}, journal = {PloS one}, volume = {16}, number = {10}, pages = {e0258505}, pmid = {34662347}, issn = {1932-6203}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Aged ; Middle Aged ; Male ; Female ; Adult ; *Feces/microbiology ; Machine Learning ; Age Factors ; Metagenome ; Aged, 80 and over ; Aging ; Metagenomics/methods ; Young Adult ; }, abstract = {The intestinal microbiome plays a central role in human health and disease. While its composition is relatively stable throughout adulthood, the microbial balance starts to decrease in later life stages. Thus, in order to maintain a good quality of life, including the prevention of age-associated diseases in the elderly, it is important to understand the dynamics of the intestinal microbiome. In this study, stool samples of 278 participants were sequenced by whole metagenome shotgun sequencing and their taxonomic and functional profiles characterized. The two age groups, below65 and above65, could be separated based on taxonomic and associated functional features using Multivariate Association of Linear Models. In a second approach, through machine learning, biomarkers connecting the intestinal microbiome with age were identified. These results reflect the importance to select age-matched study groups for unbiased metagenomic data analysis and the possibility to generate robust data by applying independent algorithms for data analysis. Furthermore, since the intestinal microbiome can be modulated by antibiotics and probiotics, the data of this study may have implications on preventive strategies of age-associated degradation processes and diseases by microbiome-altering interventions.}, } @article {pmid34661515, year = {2021}, author = {Barraza, A and Montes-Sánchez, JJ and Caamal-Chan, MG and Loera-Muro, A}, title = {Characterization of microbial communities from rumen and large intestine of lactating creole goats grazing in arid plant communities.}, journal = {Microbiology (Reading, England)}, volume = {167}, number = {10}, pages = {}, doi = {10.1099/mic.0.001092}, pmid = {34661515}, issn = {1465-2080}, mesh = {Animals ; Archaea/classification/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; DNA, Ribosomal/genetics ; Desert Climate ; Diet/veterinary ; Feces/chemistry/microbiology ; Female ; Fungi/classification/genetics/isolation & purification ; Gastrointestinal Contents/chemistry ; *Gastrointestinal Microbiome ; Goats/*microbiology ; Intestine, Large/chemistry/*microbiology ; Lactation ; Rumen/chemistry/*microbiology ; Seasons ; }, abstract = {Arid plant communities provide variable diets that can affect digestive microbial communities of free-foraging ruminants. Thus, we used next-generation sequencing of 16S and 18S rDNA to characterize microbial communities in the rumen (regurgitated digesta) and large intestine (faeces) and diet composition of lactating creole goats from five flocks grazing in native plant communities in the Sonoran Desert in the rainy season. The bacterial communities in the rumen and large intestine of the five flocks had similar alpha diversity (Chao1, Shannon, and Simpson indices). However, bacterial community compositions were different: a bacterial community dominated by Proteobacteria in the rumen transitioned to a community dominated by Firmicutes in the large intestine. Bacterial communities of rumen were similar across flocks; similarly occurred with large-intestine communities. Archaea had a minimum presence in the goat digestive tract. We detected phylum Basidiomycota, Ascomycota, and Apicomplexa as the main fungi and protozoa. Analyses suggested different diet compositions; forbs and grasses composed the bulk of plants in the rumen and forbs and shrubs in faeces. Therefore, lactating goats consuming different diets in the Sonoran Desert in the rainy season share a similar core bacterial community in the rumen and another in the large intestine and present low archaeal communities.}, } @article {pmid34661428, year = {2021}, author = {Rykachevsky, A and Stepakov, A and Muzyukina, P and Medvedeva, S and Dobrovolski, M and Burnaev, E and Severinov, K and Savitskaya, E}, title = {SCRAMBLER: A Tool for De Novo CRISPR Array Reconstruction and Its Application for Analysis of the Structure of Prokaryotic Populations.}, journal = {The CRISPR journal}, volume = {4}, number = {5}, pages = {673-685}, doi = {10.1089/crispr.2021.0012}, pmid = {34661428}, issn = {2573-1602}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; Metagenomics/methods ; *Microbiota ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {CRISPR arrays are prokaryotic genomic loci consisting of repeat sequences alternating with unique spacers acquired from foreign nucleic acids. As one of the fastest-evolving parts of the genome, CRISPR arrays can be used to differentiate closely related prokaryotic lineages and track individual strains in prokaryotic communities. However, the assembly of full-length CRISPR arrays sequences remains a problem. Here, we developed SCRAMBLER, a tool that includes several pipelines for assembling CRISPR arrays from high-throughput short-read sequencing data. We assessed its performance with model data sets (Escherichia coli strains containing different CRISPR arrays and imitating prokaryotic communities of different complexities) and intestinal microbiomes of extant and extinct pachyderms. Evaluation of SCRAMBLER's performance using model data sets demonstrated its ability to assemble CRISPR arrays correctly from reads containing pairs of spacers, yielding a precision rate of >80% and a recall rate of 60-85% when checked against ground-truth data. Likewise, SCRAMBLER successfully assembled CRISPR arrays from the environmental samples, as attested by their matching with database entries. SCRAMBLER, an open-source software (github.com/biolab-tools/SCRAMBLER), can facilitate analysis of the composition and dynamics of CRISPR arrays in complex communities.}, } @article {pmid34656848, year = {2021}, author = {Tan-Torres, AL and Brooks, JP and Singh, B and Seashols-Williams, S}, title = {Machine learning clustering and classification of human microbiome source body sites.}, journal = {Forensic science international}, volume = {328}, number = {}, pages = {111008}, doi = {10.1016/j.forsciint.2021.111008}, pmid = {34656848}, issn = {1872-6283}, mesh = {Algorithms ; Cluster Analysis ; Humans ; Machine Learning ; Metagenomics ; *Microbiota ; }, abstract = {Distinct microbial signatures associated with specific human body sites can play a role in the identification of biological materials recovered from the crime scene, but at present, methods that have capability to predict origin of biological materials based on such signatures are limited. Metagenomic sequencing and machine learning (ML) offer a promising enhancement to current identification protocols. We use ML for forensic source body site identification using shotgun metagenomic sequenced data to verify the presence of microbiomic signatures capable of discriminating between source body sites and then show that accurate prediction is possible. The consistency between cluster membership and actual source body site (purity) exceeded 99% at the genus taxonomy using off-the-shelf ML clustering algorithms. Similar results were obtained at the family level. Accurate predictions were observed for genus, family, and order taxonomies, as well as with a core set of 51 genera. The accurate outcomes from our replicable process should encourage forensic scientists to seriously consider integrating ML predictors into their source body site identification protocols.}, } @article {pmid34656033, year = {2021}, author = {Ma, Y and Sun, Y and Sun, L and Liu, X and Zeng, R and Lin, X and Li, Y}, title = {Effects of gut microbiota and fatty acid metabolism on dyslipidemia following weight-loss diets in women: Results from a randomized controlled trial.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {40}, number = {11}, pages = {5511-5520}, doi = {10.1016/j.clnu.2021.09.021}, pmid = {34656033}, issn = {1532-1983}, mesh = {Adult ; Caloric Restriction ; Carnitine/analogs & derivatives/blood ; Diet, Carbohydrate-Restricted ; Diet, Reducing ; Dyslipidemias/*blood/etiology/*microbiology ; Erythrocytes/metabolism ; Fatty Acids/*blood ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Lipid Metabolism ; Middle Aged ; Obesity/complications ; Overweight/complications/*diet therapy ; Treatment Outcome ; Weight Loss ; }, abstract = {BACKGROUND & AIMS: In our early feeding trial among overweight and obese Chinese women, both low-carbohydrate (LC) and calorie-restricted (CR) diets reduced weight and fat mass, but only the LC diet significantly improved dyslipidemia. We aimed to investigate the impacts of altered gut microbiota, fatty acid (FAs), and acylcarnitines, markers of mitochondrial function on blood lipids.

METHODS: Fecal and blood samples from 48 participants at baseline and the end of a 12-week trial were used to perform metagenomics and targeted-metabolomics including erythrocyte FAs and plasma acylcarnitines, respectively.

RESULTS: The two diets altered microbial structure and co-abundance gene clusters (CAGs) at different magnitudes. After a 12-week intervention, the Bacteroidetes/Firmicutes ratio increased significantly in the LC diet (P = 0.015) but not in the CR diet, which only showed an increased trend (P = 0.28). At the microbial function level, the LC group showed lower branched-chain amino acid biosynthesis and higher serine biosynthesis than the CR group. Moreover, the LC diet reduced levels of 14:0 and 16:1n-7 FAs in the de novo lipogenesis pathway, but increased 20:5n-3 compared with the CR diet. Both groups had increased plasma acylcarnitines except that the LC group had larger elevated short-chain acylcarnitines. After backward stepwise selection, a cluster of changed CAGs, FAs and acylcarnitines were found to be associated with improved lipid profile. However, changed CAGs showed higher contribution rates in elevating HDL-cholesterol (81.6%) and reducing triglycerides (89.3%) than changed FAs and acylcarnitines.

CONCLUSIONS: The two weight-loss diets induced different changes of gut microbiota, plasma acylcarnitines, and erythrocyte FAs. Changes in gut microbiota rather than FA or acylcarnitine profiles showed greater contribution to improved lipid profile in these overweight and obese Chinese women.

TRIAL REGISTRATION: The trial was registered at http://clinicaltrials.gov/show/NCT01358890.}, } @article {pmid34654819, year = {2021}, author = {Kumar, G and Suman, A and Lal, S and Ram, RA and Bhatt, P and Pandey, G and Chaudhary, P and Rajan, S}, title = {Bacterial structure and dynamics in mango (Mangifera indica) orchards after long term organic and conventional treatments under subtropical ecosystem.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {20554}, pmid = {34654819}, issn = {2045-2322}, mesh = {Biodiversity ; Mangifera/*microbiology ; Metagenomics ; *Microbiota ; *Organic Agriculture ; Plant Development ; Plant Roots/*microbiology ; *Rhizosphere ; }, abstract = {This study explores the comparative effect of conventional and organic treatments on the rhizosphere microbiome of Mangifera indica cv. Dashehari. The long-term exposures (about 20 years) were monitored under a subtropical ecosystem. Based on plant growth properties and acetylene reduction assay, 12 bacterial isolates (7 from G1-organic and 5 from G2-conventional systems) were identified as Pseudomonas and Bacillus spp. In the conventional system, dehydrogenase activity significantly decreased (0.053 µg TPF formed g[-1] of soil h[-1]) and adversely affected the bacterial diversity composition. In comparison, organic treatments had a good impact on dehydrogenase activity (0.784 µg TPF formed g[-1] of soil h[-1]), alkaline phosphatase (139.25 µg PNP g[-1] soil h[-1]), and bacterial community composition. The Metagenomics approach targeted the V3 and V4 regions to see the impact in the phylum, order, family, genus, and species for both the treatments. Results showed that phylum Acidobacteria (13.6%), Firmicutes (4.84%), and Chloroflexi (2.56%) were dominating in the G2 system whereas phylum Bacteroides (14.55%), Actinobacteria (7.45%), and Proteobacteria (10.82%) were abundantly dominated in the G1 system. Metagenome sequences are at the NCBI-GenBank sequence read archive with SRX8289747 (G1) and SRX8289748 (G2) in the study PRJNA631113. Results indicated that conventional and organic conditions affect rhizosphere microbiome and their environment.}, } @article {pmid34653795, year = {2021}, author = {Wang, A and Shi, K and Ning, D and Cheng, H and Wang, H and Liu, W and Gao, S and Li, Z and Han, J and Liang, B and Zhou, J}, title = {Electrical selection for planktonic sludge microbial community function and assembly.}, journal = {Water research}, volume = {206}, number = {}, pages = {117744}, doi = {10.1016/j.watres.2021.117744}, pmid = {34653795}, issn = {1879-2448}, mesh = {Bioreactors ; *Microbiota ; Plankton ; RNA, Ribosomal, 16S/genetics ; *Sewage ; Wastewater ; }, abstract = {Electrostimulated hydrolysis acidification (eHA) has been used as an efficient biological pre-treatment of refractory industrial wastewater. However, the effects of electrostimulation on the function and assembly of planktonic anaerobic sludge microbial communities are poorly understood. Using 16S rRNA gene and metagenomic sequencing, we investigated planktonic sludge microbial community structure, composition, function, assembly, and microbial interactions in response to electrostimulation. Compared with a conventional hydrolysis acidification (HA) reactor, the planktonic sludge microbial communities selected by electrostimulation promoted biotransformation of the azo dye Alizarin Yellow R. The taxonomic and functional structure and composition were significantly shifted upon electrostimulation with azo dyes degraders (e.g. Acinetobacter and Dechloromonas) and electroactive bacteria (e.g. Pseudomonas) being enriched. More microbial interactions between fermenters and decolorizing and electroactive bacteria, as well as fewer interactions between different fermenters evolved in the eHA microbial communities. Moreover, the decolorizing bacteria were linked to the higher abundance of genes encoding for azo- and nitro-reductases and redox mediator (e.g. ubiquinone) biosynthesis involved in the transformation of azo dye. Microbial community assembly was more driven by deterministic processes upon electrostimulation. This study offers new insights into the effects of electrostimulation on planktonic sludge microbial community function and assembly, and provides a promising strategy for the manipulation of anaerobic sludge microbiomes in HA engineering systems.}, } @article {pmid34653444, year = {2021}, author = {Chimetto Tonon, LA and Rua, C and Crnkovic, CM and Bernardi, DI and Pires Junior, OR and Haddad, CFB and Pedrosa, CSG and Souza, LRQ and Rehen, SK and de Azevedo, GPR and Thompson, CC and Thompson, FL and Berlinck, RGS}, title = {Microbiome associated with the tetrodotoxin-bearing anuran Brachycephalus pitanga.}, journal = {Toxicon : official journal of the International Society on Toxinology}, volume = {203}, number = {}, pages = {139-146}, doi = {10.1016/j.toxicon.2021.10.002}, pmid = {34653444}, issn = {1879-3150}, mesh = {Animals ; Anura ; Bacteria ; *Eugenia ; *Microbiota ; Tetrodotoxin/toxicity ; }, abstract = {The genus Brachycephalus includes small species of aposematic anurans known as microendemic, occurring in the mountains of the Atlantic Forest. Brachycephalus ephippium, B. nodoterga and B. pernix have been reported to contain the neurotoxin tetrodotoxin in skin and viscera. The biological conservation of several Brachycephalus species is currently threatened by climate change, deforestation, and the pandemic caused by the fungus Batrachochytrium dendrobatidis (Bd). Despite the well-known importance of amphibians' associated bacteria in the defensive role against pathogens, there is still a poor understanding of amphibian microbiome composition. The present study investigated the composition of B. pitanga microbial community and the presence of TTX in the host and in cultures of bacterial isolates, using a combination of metagenomics, bacterial culture isolation, mass spectrometry and metabolomic analyses. Results of culture-dependent and -independent analyses characterized the microbial communities associated with the skin and viscera of B. pitanga. Mass spectrometry analysis indicated the presence of TTX in host tissues, while bacterial production of TTX was not observed under the experimental conditions used in this investigation. This is the first report confirming the occurrence of TTX in B. pitanga.}, } @article {pmid34650527, year = {2021}, author = {Hagström, Å and Zweifel, UL and Sundh, J and Osbeck, CMG and Bunse, C and Sjöstedt, J and Müller-Karulis, B and Pinhassi, J}, title = {Composition and Seasonality of Membrane Transporters in Marine Picoplankton.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {714732}, pmid = {34650527}, issn = {1664-302X}, abstract = {In this study, we examined transporter genes in metagenomic and metatranscriptomic data from a time-series survey in the temperate marine environment of the Baltic Sea. We analyzed the abundance and taxonomic distribution of transporters in the 3μm-0.2μm size fraction comprising prokaryotes and some picoeukaryotes. The presence of specific transporter traits was shown to be guiding the succession of these microorganisms. A limited number of taxa were associated with the dominant transporter proteins that were identified for the nine key substrate categories for microbial growth. Throughout the year, the microbial taxa at the level of order showed highly similar patterns in terms of transporter traits. The distribution of transporters stayed the same, irrespective of the abundance of each taxon. This would suggest that the distribution pattern of transporters depends on the bacterial groups being dominant at a given time of the year. Also, we find notable numbers of secretion proteins that may allow marine bacteria to infect and kill prey organisms thus releasing nutrients. Finally, we demonstrate that transporter proteins may provide clues to the relative importance of biogeochemical processes, and we suggest that virtual transporter functionalities may become important components in future population dynamics models.}, } @article {pmid34650231, year = {2022}, author = {McKay, LJ and Nigro, OD and Dlakić, M and Luttrell, KM and Rusch, DB and Fields, MW and Inskeep, WP}, title = {Sulfur cycling and host-virus interactions in Aquificales-dominated biofilms from Yellowstone's hottest ecosystems.}, journal = {The ISME journal}, volume = {16}, number = {3}, pages = {842-855}, pmid = {34650231}, issn = {1751-7370}, support = {P30 GM110732/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria ; Biofilms ; *Host Microbial Interactions ; *Microbiota ; Phylogeny ; Sulfur/metabolism ; }, abstract = {Modern linkages among magmatic, geochemical, and geobiological processes provide clues about the importance of thermophiles in the origin of biogeochemical cycles. The aim of this study was to identify the primary chemoautotrophs and host-virus interactions involved in microbial colonization and biogeochemical cycling at sublacustrine, vapor-dominated vents that represent the hottest measured ecosystems in Yellowstone National Park (~140 °C). Filamentous microbial communities exposed to extreme thermal and geochemical gradients were sampled using a remotely operated vehicle and subjected to random metagenome sequencing and microscopic analyses. Sulfurihydrogenibium (phylum Aquificae) was the predominant lineage (up to 84% relative abundance) detected at vents that discharged high levels of dissolved H2, H2S, and CO2. Metabolic analyses indicated carbon fixation by Sulfurihydrogenibium spp. was powered by the oxidation of reduced sulfur and H2, which provides organic carbon for heterotrophic community members. Highly variable Sulfurihydrogenibium genomes suggested the importance of intra-population diversity under extreme environmental and viral pressures. Numerous lytic viruses (primarily unclassified taxa) were associated with diverse archaea and bacteria in the vent community. Five circular dsDNA uncultivated virus genomes (UViGs) of ~40 kbp length were linked to the Sulfurihydrogenibium metagenome-assembled genome (MAG) by CRISPR spacer matches. Four UViGs contained consistent genome architecture and formed a monophyletic cluster with the recently proposed Pyrovirus genus within the Caudovirales. Sulfurihydrogenibium spp. also contained CRISPR arrays linked to plasmid DNA with genes for a novel type IV filament system and a highly expressed β-barrel porin. A diverse suite of transcribed secretion systems was consistent with direct microscopic analyses, which revealed an extensive extracellular matrix likely critical to community structure and function. We hypothesize these attributes are fundamental to the establishment and survival of microbial communities in highly turbulent, extreme-gradient environments.}, } @article {pmid34649602, year = {2021}, author = {Liu, L and Wang, Y and Yang, Y and Wang, D and Cheng, SH and Zheng, C and Zhang, T}, title = {Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {205}, pmid = {34649602}, issn = {2049-2618}, mesh = {Genome, Bacterial/genetics ; Humans ; Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; *Sewage ; }, abstract = {BACKGROUND: Long-read sequencing has shown its tremendous potential to address genome assembly challenges, e.g., achieving the first telomere-to-telomere assembly of a gapless human chromosome. However, many issues remain unresolved when leveraging error-prone long reads to characterize high-complexity metagenomes, for instance, complete/high-quality genome reconstruction from highly complex systems.

RESULTS: Here, we developed an iterative haplotype-resolved hierarchical clustering-based hybrid assembly (HCBHA) approach that capitalizes on a hybrid (error-prone long reads and high-accuracy short reads) sequencing strategy to reconstruct (near-) complete genomes from highly complex metagenomes. Using the HCBHA approach, we first phase short and long reads from the highly complex metagenomic dataset into different candidate bacterial haplotypes, then perform hybrid assembly of each bacterial genome individually. We reconstructed 557 metagenome-assembled genomes (MAGs) with an average N50 of 574 Kb from a deeply sequenced, highly complex activated sludge (AS) metagenome. These high-contiguity MAGs contained 14 closed genomes and 111 high-quality (HQ) MAGs including full-length rRNA operons, which accounted for 61.1% of the microbial community. Leveraging the near-complete genomes, we also profiled the metabolic potential of the AS microbiome and identified 2153 biosynthetic gene clusters (BGCs) encoded within the recovered AS MAGs.

CONCLUSION: Our results established the feasibility of an iterative haplotype-resolved HCBHA approach to reconstruct (near-) complete genomes from highly complex ecosystems, providing new insights into "complete metagenomics". The retrieved high-contiguity MAGs illustrated that various biosynthetic gene clusters (BGCs) were harbored in the AS microbiome. The high diversity of BGCs highlights the potential to discover new natural products biosynthesized by the AS microbial community, aside from the traditional function (e.g., organic carbon and nitrogen removal) in wastewater treatment. Video Abstract.}, } @article {pmid34649516, year = {2021}, author = {Fleming, E and Pabst, V and Scholar, Z and Xiong, R and Voigt, AY and Zhou, W and Hoyt, A and Hardy, R and Peterson, A and Beach, R and Ondouah-Nzutchi, Y and Dong, J and Bateman, L and Vernon, SD and Oh, J}, title = {Cultivation of common bacterial species and strains from human skin, oral, and gut microbiota.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {278}, pmid = {34649516}, issn = {1471-2180}, support = {R01 AR078634/AR/NIAMS NIH HHS/United States ; U19 AI142733/AI/NIAID NIH HHS/United States ; P30 CA034196/CA/NCI NIH HHS/United States ; R56 AG060746/AG/NIA NIH HHS/United States ; K22 AI119231/AI/NIAID NIH HHS/United States ; R21 AR075174/AR/NIAMS NIH HHS/United States ; DP2 GM126893/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics/*growth & development/isolation & purification ; Bacteriological Techniques/*methods ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/genetics ; Humans ; Mouth/*microbiology ; Skin/*microbiology ; }, abstract = {BACKGROUND: Genomics-driven discoveries of microbial species have provided extraordinary insights into the biodiversity of human microbiota. In addition, a significant portion of genetic variation between microbiota exists at the subspecies, or strain, level. High-resolution genomics to investigate species- and strain-level diversity and mechanistic studies, however, rely on the availability of individual microbes from a complex microbial consortia. High-throughput approaches are needed to acquire and identify the significant species- and strain-level diversity present in the oral, skin, and gut microbiome. Here, we describe and validate a streamlined workflow for cultivating dominant bacterial species and strains from the skin, oral, and gut microbiota, informed by metagenomic sequencing, mass spectrometry, and strain profiling.

RESULTS: Of total genera discovered by either metagenomic sequencing or culturomics, our cultivation pipeline recovered between 18.1-44.4% of total genera identified. These represented a high proportion of the community composition reconstructed with metagenomic sequencing, ranging from 66.2-95.8% of the relative abundance of the overall community. Fourier-Transform Infrared spectroscopy (FT-IR) was effective in differentiating genetically distinct strains compared with whole-genome sequencing, but was less effective as a proxy for genetic distance.

CONCLUSIONS: Use of a streamlined set of conditions selected for cultivation of skin, oral, and gut microbiota facilitates recovery of dominant microbes and their strain variants from a relatively large sample set. FT-IR spectroscopy allows rapid differentiation of strain variants, but these differences are limited in recapitulating genetic distance. Our data highlights the strength of our cultivation and characterization pipeline, which is in throughput, comparisons with high-resolution genomic data, and rapid identification of strain variation.}, } @article {pmid34648730, year = {2021}, author = {Maixner, F and Sarhan, MS and Huang, KD and Tett, A and Schoenafinger, A and Zingale, S and Blanco-Míguez, A and Manghi, P and Cemper-Kiesslich, J and Rosendahl, W and Kusebauch, U and Morrone, SR and Hoopmann, MR and Rota-Stabelli, O and Rattei, T and Moritz, RL and Oeggl, K and Segata, N and Zink, A and Reschreiter, H and Kowarik, K}, title = {Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period.}, journal = {Current biology : CB}, volume = {31}, number = {23}, pages = {5149-5162.e6}, pmid = {34648730}, issn = {1879-0445}, support = {R01 CA230551/CA/NCI NIH HHS/United States ; R01 GM087221/GM/NIGMS NIH HHS/United States ; S10 OD026936/OD/NIH HHS/United States ; }, mesh = {Animals ; Beer ; *Cheese ; Diet ; Fungi ; *Gastrointestinal Microbiome ; Proteomics ; }, abstract = {We subjected human paleofeces dating from the Bronze Age to the Baroque period (18[th] century AD) to in-depth microscopic, metagenomic, and proteomic analyses. The paleofeces were preserved in the underground salt mines of the UNESCO World Heritage site of Hallstatt in Austria. This allowed us to reconstruct the diet of the former population and gain insights into their ancient gut microbiome composition. Our dietary survey identified bran and glumes of different cereals as some of the most prevalent plant fragments. This highly fibrous, carbohydrate-rich diet was supplemented with proteins from broad beans and occasionally with fruits, nuts, or animal food products. Due to these traditional dietary habits, all ancient miners up to the Baroque period have gut microbiome structures akin to modern non-Westernized individuals whose diets are also mainly composed of unprocessed foods and fresh fruits and vegetables. This may indicate a shift in the gut community composition of modern Westernized populations due to quite recent dietary and lifestyle changes. When we extended our microbial survey to fungi present in the paleofeces, in one of the Iron Age samples, we observed a high abundance of Penicillium roqueforti and Saccharomyces cerevisiae DNA. Genome-wide analysis indicates that both fungi were involved in food fermentation and provides the first molecular evidence for blue cheese and beer consumption in Iron Age Europe.}, } @article {pmid34648062, year = {2021}, author = {Lee, K and Oh, HJ and Kang, MS and Kim, S and Ahn, S and Kim, MJ and Kim, SW and Chang, S}, title = {Metagenomic analysis of gut microbiome reveals a dynamic change in Alistipes onderdonkii in the preclinical model of pancreatic cancer, suppressing its proliferation.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {21-22}, pages = {8343-8358}, pmid = {34648062}, issn = {1432-0614}, mesh = {Bacteroidetes ; Cell Line, Tumor ; Cell Proliferation ; Clostridiales ; *Gastrointestinal Microbiome ; Gene Expression Regulation, Neoplastic ; Humans ; Metagenome ; *Pancreatic Neoplasms/genetics ; }, abstract = {Pancreatic cancer is a lethal cancer with aggressive and invasive characteristics. By the time it is diagnosed, patients already have tumors extended to other organs and show extremely low survival rates. The gut microbiome is known to be associated with many diseases and its imbalance affects the pathogenesis of pancreatic cancer. In this study, we established an orthotopic, patient-derived xenograft model to identify how the gut microbiome is linked to pancreatic ductal adenocarcinoma (PDAC). Using the 16S rDNA metagenomic sequencing, we revealed that the levels of Alistipes onderdonkii and Roseburia hominis decreased in the gut microbiome of the PDAC model. To explore the crosstalk between the two bacteria and PDAC cells, we collected the supernatant of the bacteria or cancer cell culture medium and treated it in a cross manner. While the cancer cell medium did not affect bacterial growth, we observed that the A. onderdonkii medium suppressed the growth of the pancreatic primary cancer cells. Using the bromodeoxyuridine/7-amino-actinomycin D (BrdU/7-AAD) staining assay, we confirmed that the A. onderdonkii medium inhibited the proliferation of the pancreatic primary cancer cells. Furthermore, RNA-seq analysis revealed that the A. onderdonkii medium induced unique transcriptomic alterations in the PDAC cells, compared to the normal pancreatic cells. Altogether, our data suggest that the reduction in the A. onderdonkii in the gut microbiome provides a proliferation advantage to the pancreatic cancer cells. KEY POINTS: • Metagenome analysis of pancreatic cancer model reveals A. onderdonkii downregulation. • A. onderdonkii culture supernatant suppressed the proliferation of pancreatic cancer cells. • RNA seq data reveals typical gene expression changes induced by A. onderdonkii.}, } @article {pmid34646784, year = {2021}, author = {Sun, B and Liu, B and Gao, X and Xing, K and Xie, L and Guo, T}, title = {Metagenomic Analysis of Saliva Reveals Disease-Associated Microbiotas in Patients With Periodontitis and Crohn's Disease-Associated Periodontitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {719411}, pmid = {34646784}, issn = {2235-2988}, mesh = {Corynebacterium ; *Crohn Disease/complications ; *Dental Caries ; Humans ; *Microbiota ; *Periodontitis ; Prevotella ; RNA, Ribosomal, 16S/genetics ; Saliva ; }, abstract = {Patients with Crohn's disease frequently develop oral health problems and show a higher prevalence of oral manifestations, such as dental caries and periodontitis, than healthy individuals do. In this study, a metagenomic analysis was carried out to characterize the salivary microbiota in patients with either periodontitis or Crohn's disease-associated periodontitis. Saliva samples were collected from six patients with both Crohn's disease and periodontitis (Cm group), six patients with periodontitis alone (Pm group), and six healthy individuals (Hm group). Genomic DNA was collected from these samples for high-throughput Illumina HiSeq metagenomic sequencing. The composition of the bacterial communities and their metabolic pathways and gene functions were characterized and compared among the three study groups. The salivary microbial communities were significantly different among the three groups, with Firmicutes, Actinobacteria, and Bacteroidetes showing the most significant differences. The Cm and Pm groups had higher abundances of Bacteroides fragilis, Prevotella baroniae, Prevotella enoeca, and Prevotella dentasini than the Hm group. The Cm and Pm groups also showed differences in their salivary microbial communities, in that the Cm group had relatively high abundances of Firmicutes and Proteobacteria, whereas the Pm group had relatively high abundances of Actinobacteria, Bacteroidetes, and Fusobacteria. In total, 34 Pm-associated (e.g., Fusobacteria and Corynebacterium matruchotii), 18 Cm-associated (e.g., Capnocytophaga and Streptococcus oralis), and 18 Hm-associated (e.g., Streptococcus and Bacillales) predominant microbial species were identified. Most genes were involved in carbohydrate and amino acid metabolism, with those of the Cm and Pm groups showing more similarity to one another but significant differences from those of the Hm group. Most of the antibiotic resistance genes were found in the Pm group. In conclusion, the salivary microbial community structure and abundance were distinct among patients with Crohn's disease-associated periodontitis, patients with periodontitis, and healthy individuals. Further studies are needed to evaluate the potential value of these microbiota and microbiome differences in the clinical diagnosis and treatment of oral diseases.}, } @article {pmid34645820, year = {2021}, author = {De Filippis, F and Paparo, L and Nocerino, R and Della Gatta, G and Carucci, L and Russo, R and Pasolli, E and Ercolini, D and Berni Canani, R}, title = {Specific gut microbiome signatures and the associated pro-inflamatory functions are linked to pediatric allergy and acquisition of immune tolerance.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {5958}, pmid = {34645820}, issn = {2041-1723}, mesh = {Allergens/adverse effects/*immunology ; Animals ; Bacteroides/isolation & purification/metabolism ; Bifidobacterium longum/isolation & purification/metabolism ; Case-Control Studies ; Child ; Child, Preschool ; Clostridiales/isolation & purification/metabolism ; Dander/adverse effects/immunology ; Eggs/adverse effects ; Faecalibacterium prausnitzii/isolation & purification/metabolism ; Female ; Food Hypersensitivity/etiology/immunology/*microbiology ; Gastrointestinal Microbiome/*immunology ; Humans ; *Immune Tolerance ; Lipopolysaccharides/biosynthesis ; Male ; Milk/adverse effects/immunology ; Nuts/adverse effects/immunology ; Pollen/chemistry/immunology ; Prunus persica/chemistry/immunology ; Pyroglyphidae/chemistry/immunology ; Respiratory Hypersensitivity/etiology/immunology/*microbiology ; Urease/biosynthesis ; }, abstract = {Understanding the functional potential of the gut microbiome is of primary importance for the design of innovative strategies for allergy treatment and prevention. Here we report the gut microbiome features of 90 children affected by food (FA) or respiratory (RA) allergies and 30 age-matched, healthy controls (CT). We identify specific microbial signatures in the gut microbiome of allergic children, such as higher abundance of Ruminococcus gnavus and Faecalibacterium prausnitzii, and a depletion of Bifidobacterium longum, Bacteroides dorei, B. vulgatus and fiber-degrading taxa. The metagenome of allergic children shows a pro-inflammatory potential, with an enrichment of genes involved in the production of bacterial lipo-polysaccharides and urease. We demonstrate that specific gut microbiome signatures at baseline can be predictable of immune tolerance acquisition. Finally, a strain-level selection occurring in the gut microbiome of allergic subjects is identified. R. gnavus strains enriched in FA and RA showed lower ability to degrade fiber, and genes involved in the production of a pro-inflammatory polysaccharide. We demonstrate that a gut microbiome dysbiosis occurs in allergic children, with R. gnavus emerging as a main player in pediatric allergy. These findings may open new strategies in the development of innovative preventive and therapeutic approaches. Trial: NCT04750980.}, } @article {pmid34644375, year = {2022}, author = {Eshel, A and Sharon, I and Nagler, A and Bomze, D and Danylesko, I and Fein, JA and Geva, M and Henig, I and Shimoni, A and Zuckerman, T and Youngster, I and Koren, O and Shouval, R}, title = {Origins of bloodstream infections following fecal microbiota transplantation: a strain-level analysis.}, journal = {Blood advances}, volume = {6}, number = {2}, pages = {568-573}, pmid = {34644375}, issn = {2473-9537}, support = {P30 CA008748/CA/NCI NIH HHS/United States ; }, mesh = {*Bacteremia/etiology ; Fecal Microbiota Transplantation ; *Graft vs Host Disease ; Humans ; Immunocompromised Host ; *Microbiota ; }, abstract = {We observed high rates of bloodstream infections (BSIs) following fecal microbiota transplantation (FMT) for graft-versus-host-disease (33 events in 22 patients). To trace the BSIs' origin, we applied a metagenomic bioinformatic pipeline screening donor and recipient stool samples for bacteremia-causing strains in 13 cases. Offending strains were not detected in FMT donations. Enterococcus faecium, Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii could be detected in stool samples before emerging in the blood. In this largest report of BSIs post-FMT, we present an approach that may be applicable for evaluating BSI origin following microbiota-based interventions. Our findings support FMT safety in immunocompromised patients but do not rule out FMT as an inducer of bacterial translocation.}, } @article {pmid34643440, year = {2021}, author = {Wang, Z and Zhang, F and Liang, Y and Zheng, K and Gu, C and Zhang, W and Liu, Y and Zhang, X and Shao, H and Jiang, Y and Guo, C and He, H and Wang, H and Sung, YY and Mok, WJ and Wong, LL and He, J and McMinn, A and Wang, M}, title = {Genome and Ecology of a Novel Alteromonas Podovirus, ZP6, Representing a New Viral Genus, Mareflavirus.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0046321}, pmid = {34643440}, issn = {2165-0497}, mesh = {Alteromonas/*virology ; Bacteriophages/classification/*genetics/growth & development/*isolation & purification ; China ; *Genome, Viral ; Myoviridae/classification/*genetics/*isolation & purification ; Open Reading Frames ; Phylogeny ; Seawater/virology ; }, abstract = {Alteromonas is a ubiquitous, abundant, copiotrophic and phytoplankton-associated marine member of the Gammaproteobacteria with a range extending from tropical waters to polar regions and including hadal zones. Here, we describe a novel Alteromonas phage, ZP6, that was isolated from surface coastal waters of Qingdao, China. ZP6 contains a linear, double-stranded, 38,080-bp DNA molecule with 50.1% G+C content and 47 putative open reading frames (ORFs). Three auxiliary metabolic genes were identified, encoding metal-dependent phosphohydrolase, diaminopurine synthetase, and nucleotide pyrophosphohydrolase. The first two ORFs facilitate the replacement of adenine (A) by diaminopurine (Z) in phage genomes and help phages to evade attack from host restriction enzymes. The nucleotide pyrophosphohydrolase enables the host cells to stop programmed cell death and improves the survival rate of the host in a nutrient-depleted environment. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analysis revealed that ZP6 is most closely related to Enhodamvirus but with low similarity (shared genes, <30%, and average nucleotide sequence identity, <65%); it is distinct from other bacteriophages. Together, these results suggest that ZP6 could represent a novel viral genus, here named Mareflavirus. Combining its ability to infect Alteromonas, its harboring of a diaminopurine genome-biosynthetic system, and its representativeness of an understudied viral group, ZP6 could be an important and novel model system for marine virus research. IMPORTANCEAlteromonas is an important symbiotic bacterium of phytoplankton, but research on its bacteriophages is still at an elementary level. Our isolation and genome characterization of a novel Alteromonas podovirus, ZP6, identified a new viral genus of podovirus, namely, Mareflavirus. The ZP6 genome, with a diaminopurine genome-biosynthetic system, is different from those of other isolated Alteromonas phages and will bring new impetus to the development of virus classification and provide important insights into novel viral sequences from metagenomic data sets.}, } @article {pmid34641974, year = {2021}, author = {Muller, E and Algavi, YM and Borenstein, E}, title = {A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {203}, pmid = {34641974}, issn = {2049-2618}, support = {U19 AG057377/AG/NIA NIH HHS/United States ; U19AG057377/NH/NIH HHS/United States ; R01DK095869/NH/NIH HHS/United States ; }, mesh = {Bile Acids and Salts ; Dysbiosis ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolome ; Metabolomics ; *Microbiota ; }, abstract = {BACKGROUND: Microbiome-metabolome studies of the human gut have been gaining popularity in recent years, mostly due to accumulating evidence of the interplay between gut microbes, metabolites, and host health. Statistical and machine learning-based methods have been widely applied to analyze such paired microbiome-metabolome data, in the hope of identifying metabolites that are governed by the composition of the microbiome. Such metabolites can be likely modulated by microbiome-based interventions, offering a route for promoting gut metabolic health. Yet, to date, it remains unclear whether findings of microbially associated metabolites in any single study carry over to other studies or cohorts, and how robust and universal are microbiome-metabolites links.

RESULTS: In this study, we addressed this challenge by performing a comprehensive meta-analysis to identify human gut metabolites that can be predicted based on the composition of the gut microbiome across multiple studies. We term such metabolites "robustly well-predicted". To this end, we processed data from 1733 samples from 10 independent human gut microbiome-metabolome studies, focusing initially on healthy subjects, and implemented a machine learning pipeline to predict metabolite levels in each dataset based on the composition of the microbiome. Comparing the predictability of each metabolite across datasets, we found 97 robustly well-predicted metabolites. These include metabolites involved in important microbial pathways such as bile acid transformations and polyamines metabolism. Importantly, however, other metabolites exhibited large variation in predictability across datasets, suggesting a cohort- or study-specific relationship between the microbiome and the metabolite. Comparing taxonomic contributors to different models, we found that some robustly well-predicted metabolites were predicted by markedly different sets of taxa across datasets, suggesting that some microbially associated metabolites may be governed by different members of the microbiome in different cohorts. We finally examined whether models trained on a control group of a given study successfully predicted the metabolite's level in the disease group of the same study, identifying several metabolites where the model was not transferable, indicating a shift in microbial metabolism in disease-associated dysbiosis.

CONCLUSIONS: Combined, our findings provide a better understanding of the link between the microbiome and metabolites and allow researchers to put identified microbially associated metabolites within the context of other studies. Video abstract.}, } @article {pmid34641962, year = {2021}, author = {Usyk, M and Pandey, A and Hayes, RB and Moran, U and Pavlick, A and Osman, I and Weber, JS and Ahn, J}, title = {Bacteroides vulgatus and Bacteroides dorei predict immune-related adverse events in immune checkpoint blockade treatment of metastatic melanoma.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {160}, pmid = {34641962}, issn = {1756-994X}, support = {R01 CA159036/CA/NCI NIH HHS/United States ; P20 CA252728/NH/NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; U01 CA250186/CA/NCI NIH HHS/United States ; P50 CA225450/CA/NCI NIH HHS/United States ; P20 CA252728/CA/NCI NIH HHS/United States ; R01 CA231295/CA/NCI NIH HHS/United States ; R01 CA164964/CA/NCI NIH HHS/United States ; }, mesh = {Algorithms ; Bacteroides/genetics/*physiology ; Biomarkers, Tumor ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; *Immune Checkpoint Inhibitors ; Melanoma/*immunology/*therapy ; Metagenome ; Metagenomics ; Prospective Studies ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Immune checkpoint blockade (ICB) shows lasting benefits in advanced melanoma; however, not all patients respond to this treatment and many develop potentially life-threatening immune-related adverse events (irAEs). Identifying individuals who will develop irAEs is critical in order to improve the quality of care. Here, we prospectively demonstrate that the gut microbiome predicts irAEs in melanoma patients undergoing ICB.

METHODS: Pre-, during, and post-treatment stool samples were collected from 27 patients with advanced stage melanoma treated with IPI (anti-CTLA-4) and NIVO (anti-PD1) ICB inhibitors at NYU Langone Health. We completed 16S rRNA gene amplicon sequencing, DNA deep shotgun metagenomic, and RNA-seq metatranscriptomic sequencing. The divisive amplicon denoising algorithm (DADA2) was used to process 16S data. Taxonomy for shotgun sequencing data was assigned using MetaPhlAn2, and gene pathways were assigned using HUMAnN 2.0. Compositionally aware differential expression analysis was performed using ANCOM. The Cox-proportional hazard model was used to assess the prospective role of the gut microbiome (GMB) in irAES, with adjustment for age, sex, BMI, immune ICB treatment type, and sequencing batch.

RESULTS: Two natural GMB clusters with distinct community compositions were identified from the analysis of 16S rRNA data (R[2] = 0.16, p < 0.001). In Cox-proportional hazard modeling, these two clusters showed a near 7-fold differential risk for developing irAEs within 1 year of initiating treatment (HR = 6.89 [95% CI: 1.33-35.58]). Using shotgun metagenomics, we further identified 37 bacterial strains differentially expressed between the risk groups, with specific dominance of Bacteroides dorei within the high-risk GMB cluster and Bacteroides vulgatus in the low-risk cluster. The high-risk cluster also appeared to have elevated expression of several functional pathways, including those associated with adenosine metabolism (all FDR < 0.05). A sub-analysis of samples (n = 10 participants) at baseline and 6 and 12 weeks after the start of treatment revealed that the microbiome remained stable over the course of treatment (R[2] = 0.88, p < 0.001).

CONCLUSIONS: We identified two distinct fecal bacterial community clusters which are associated differentially with irAEs in ICB-treated advanced melanoma patients.}, } @article {pmid34641955, year = {2021}, author = {Arikawa, K and Ide, K and Kogawa, M and Saeki, T and Yoda, T and Endoh, T and Matsuhashi, A and Takeyama, H and Hosokawa, M}, title = {Recovery of strain-resolved genomes from human microbiome through an integration framework of single-cell genomics and metagenomics.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {202}, pmid = {34641955}, issn = {2049-2618}, mesh = {Genome, Microbial ; Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Phylogeny ; }, abstract = {BACKGROUND: Obtaining high-quality (HQ) reference genomes from microbial communities is crucial for understanding the phylogeny and function of uncultured microbes in complex microbial ecosystems. Despite improvements in bioinformatic approaches to generate curated metagenome-assembled genomes (MAGs), existing metagenome binners obtain population consensus genomes but they are nowhere comparable to genomes sequenced from isolates in terms of strain level resolution. Here, we present a framework for the integration of single-cell genomics and metagenomics, referred to as single-cell (sc) metagenomics, to reconstruct strain-resolved genomes from microbial communities at once.

RESULTS: Our sc-metagenomics integration framework, termed SMAGLinker, uses single-cell amplified genomes (SAGs) generated using microfluidic technology as binning guides and integrates them with metagenome-assembled genomes (MAGs) to recover improved draft genomes. We compared sc-metagenomics with the metagenomics-alone approach using conventional metagenome binners. The sc-metagenomics approach showed precise contig binning and higher recovery rates (>97%) of rRNA and plasmids than conventional metagenomics in genome reconstruction from the cell mock community. In human microbiota samples, sc-metagenomics recovered the largest number of genomes with a total of 103 gut microbial genomes (21 HQ, with 65 showing >90% completeness) and 45 skin microbial genomes (10 HQ, with 40 showing >90% completeness), respectively. Conventional metagenomics recovered one Staphylococcus hominis genome, whereas sc-metagenomics recovered two S. hominis genomes from identical skin microbiota sample. Single-cell sequencing revealed that these S. hominis genomes were derived from two distinct strains harboring specifically different plasmids. We found that all conventional S. hominis MAGs had a substantial lack or excess of genome sequences and contamination from other Staphylococcus species (S. epidermidis).

CONCLUSIONS: SMAGLinker enabled us to obtain strain-resolved genomes in the mock community and human microbiota samples by assigning metagenomic sequences correctly and covering both highly conserved genes such as rRNA genes and unique extrachromosomal elements, including plasmids. SMAGLinker will provide HQ genomes that are difficult to obtain using metagenomics alone and will facilitate the understanding of microbial ecosystems by elucidating detailed metabolic pathways and horizontal gene transfer networks. SMAGLinker is available at https://github.com/kojiari/smaglinker . Video abstract.}, } @article {pmid34639598, year = {2021}, author = {Kim, PS and Lee, YR and Kwon, YS and Bae, JW and Lee, SJ and Park, YS}, title = {Differences of Gut Microbiota in the Freshwater Blackworm (Lumbriculus variegatus: Oligochaeta) in Two Different Habitat Conditions.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {19}, pages = {}, pmid = {34639598}, issn = {1660-4601}, mesh = {Animals ; *Cyanobacteria ; Fresh Water ; *Gastrointestinal Microbiome/genetics ; *Oligochaeta ; Proteobacteria/genetics ; RNA, Ribosomal, 16S ; }, abstract = {The distribution of organisms is governed by their habitat condition. We analyzed bacterial communities in the gut of the blackworm Lumbriculus variegatus by pyrosequencing of the extracted intestinal metagenomic DNA. Blackworms were collected from two sampling sites with differences in irradiance and riparian vegetation, where site GP7 was covered by riparian vegetation and site GP8 was exposed to sunlight. We obtained the filtered 6414 reads from three samples of each site. At GP7, 271 OTUs were identified, including 32 OTUs unique to the site, whereas at GP8, 238 OTUs were identified, including 22 unique OTUs. Among them, 18 OTUs were shared between both sites. The phylum Proteobacteria was a major component contributing 67.84% and 64.05% of sequences at sites GP7 and GP8, respectively, while each remaining phylum contributed less than 10% at both sites. The two sites differed in microbial community composition and KEGG-indicated biochemical pathways. Community indices such as species richness and Shannon diversity were higher at site GP7 than at GP8. Meanwhile, the abundance of Cyanobacteria was significantly higher at site GP8, while site GP7 showed a greater proportion of genes for membrane transport and carbohydrate metabolism, reflecting differences in food resources.}, } @article {pmid34639125, year = {2021}, author = {Toranzos, GA and Santiago-Rodriguez, TM}, title = {Multiomics and Health: A Holistic Approach to Better Understand the Role of the Microbiome.}, journal = {International journal of molecular sciences}, volume = {22}, number = {19}, pages = {}, doi = {10.3390/ijms221910786}, pmid = {34639125}, issn = {1422-0067}, mesh = {Bacteria/classification/genetics/*growth & development/isolation & purification ; Holistic Health/*standards ; Humans ; *Metabolome ; *Metagenome ; *Microbiota ; *Proteome ; Public Health/*standards ; }, abstract = {The present Special Issue focuses on the latest approaches to health and public health microbiology using multiomics [...].}, } @article {pmid34638954, year = {2021}, author = {Khalyfa, A and Qiao, Z and Raju, M and Shyu, CR and Coghill, L and Ericsson, A and Gozal, D}, title = {Monocarboxylate Transporter-2 Expression Restricts Tumor Growth in a Murine Model of Lung Cancer: A Multi-Omic Analysis.}, journal = {International journal of molecular sciences}, volume = {22}, number = {19}, pages = {}, pmid = {34638954}, issn = {1422-0067}, mesh = {Animals ; Antineoplastic Agents, Hormonal/therapeutic use ; Carcinogenesis/genetics/*metabolism ; Disease Models, Animal ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics ; Gene Expression Regulation, Neoplastic ; Gene Knockout Techniques ; Gene Regulatory Networks ; Lung Neoplasms/drug therapy/genetics/*metabolism/*pathology ; Male ; Metabolome/genetics ; Metabolomics/methods ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Monocarboxylic Acid Transporters/genetics/*metabolism ; Neoplasm Invasiveness/genetics ; RNA, Ribosomal, 16S ; RNA-Seq ; Tamoxifen/therapeutic use ; Treatment Outcome ; Tumor Burden/drug effects/*genetics ; Tumor-Associated Macrophages/immunology/metabolism ; }, abstract = {Monocarboxylate transporter 2 (MCT2) is a major high-affinity pyruvate transporter encoded by the SLC16A7 gene, and is associated with glucose metabolism and cancer. Changes in the gut microbiota and host immune system are associated with many diseases, including cancer. Using conditionally expressed MCT2 in mice and the TC1 lung carcinoma model, we examined the effects of MCT2 on lung cancer tumor growth and local invasion, while also evaluating potential effects on fecal microbiome, plasma metabolome, and bulk RNA-sequencing of tumor macrophages. Conditional MCT2 mice were generated in our laboratory using MCT2[loxP] mouse intercrossed with mCre-Tg mouse to generate MCT2[loxP/loxP]; Cre[+] mouse (MCT2 KO). Male MCT2 KO mice (8 weeks old) were treated with tamoxifen (0.18 mg/g BW) KO or vehicle (CO), and then injected with mouse lung carcinoma TC1 cells (10 × 10[5]/mouse) in the left flank. Body weight, tumor size and weight, and local tumor invasion were assessed. Fecal DNA samples were extracted using PowerFecal kits and bacterial 16S rRNA amplicons were also performed. Fecal and plasma samples were used for GC-MS Polar, as well as non-targeted UHPLC-MS/MS, and tumor-associated macrophages (TAMs) were subjected to bulk RNAseq. Tamoxifen-treated MCT2 KO mice showed significantly higher tumor weight and size, as well as evidence of local invasion beyond the capsule compared with the controls. PCoA and hierarchical clustering analyses of the fecal and plasma metabolomics, as well as microbiota, revealed a distinct separation between the two groups. KO TAMs showed distinct metabolic pathways including the Acetyl-coA metabolic process, activation of immune response, b-cell activation and differentiation, cAMP-mediated signaling, glucose and glutamate processes, and T-cell differentiation and response to oxidative stress. Multi-Omic approaches reveal a substantial role for MCT2 in the host response to TC1 lung carcinoma that may involve alterations in the gut and systemic metabolome, along with TAM-related metabolic pathway. These findings provide initial opportunities for potential delineation of oncometabolic immunomodulatory therapeutic approaches.}, } @article {pmid34637930, year = {2021}, author = {Ali, Z and Shahzadi, I and Majeed, A and Malik, HMT and Waseem, S and Ahmed, I and Anis, RA and Saeed, S and Anees, M}, title = {Comparative analysis of the serum microbiome of HIV infected individuals.}, journal = {Genomics}, volume = {113}, number = {6}, pages = {4015-4021}, doi = {10.1016/j.ygeno.2021.10.005}, pmid = {34637930}, issn = {1089-8646}, mesh = {*HIV Infections/genetics ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {HIV infects the CD4 cells which marks the suppression of our immune system. DNA from serum of healthy, treated and untreated HIV infected individuals was extracted. The DNA was subjected to 16S metagenomic sequencing and analyzed using QIIME2 pipeline. 16S sequencing analysis showed serum microbiome was dominated by Firmicutes, Proteobacteria, Bacteroidota and Actinobacteria. Treated HIV infection showed highest abundance of Firmicutes (66.40%) significantly higher than untreated HIV infection (35.88%) and control (41.89%). Bacilli was most abundant class in treated (63.59%) and second most abundant in untreated (34.53%) while control group showed highest abundance of class Gamma-proteobacteria (45.86%). Untreated HIV infection group showed Enterococcus (10.72%) and Streptococcus (6.599%) as the most abundant species. Untreated HIV infection showed significantly higher (p = 0.0039) species richness than treated and control groups. An altered serum microbiome of treated HIV infection and higher microbial abundance in serum of untreated HIV infection was observed.}, } @article {pmid34637759, year = {2022}, author = {Wu, J and Danko, D and Afshinnekoo, E and Bezdan, D and Bhattacharyya, M and Castro-Nallar, E and Chmielarczyk, A and Hazrin-Chong, NH and Deng, Y and Dias-Neto, E and Frolova, A and Mason-Buck, G and Iraola, G and Jang, S and Łabaj, P and Lee, PKH and Nieto-Caballero, M and Osuolale, OO and Ouzounis, CA and Perlin, MH and Prithiviraj, B and Rascovan, N and Różańska, A and Schriml, LM and Semmler, T and Suzuki, H and Ugalde, JA and Young, B and Werner, J and Zambrano, MM and Zhao, Y and Mason, C and Shi, T and , }, title = {Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association.}, journal = {Environmental research}, volume = {207}, number = {}, pages = {112183}, doi = {10.1016/j.envres.2021.112183}, pmid = {34637759}, issn = {1096-0953}, support = {R01 AI151059/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Humans ; *Metagenome ; Metagenomics ; Microbial Interactions ; *Microbiota/genetics ; }, abstract = {In urban ecosystems, microbes play a key role in maintaining major ecological functions that directly support human health and city life. However, the knowledge about the species composition and functions involved in urban environments is still limited, which is largely due to the lack of reference genomes in metagenomic studies comprises more than half of unclassified reads. Here we uncovered 732 novel bacterial species from 4728 samples collected from various common surface with the matching materials in the mass transit system across 60 cities by the MetaSUB Consortium. The number of novel species is significantly and positively correlated with the city population, and more novel species can be identified in the skin-associated samples. The in-depth analysis of the new gene catalog showed that the functional terms have a significant geographical distinguishability. Moreover, we revealed that more biosynthetic gene clusters (BGCs) can be found in novel species. The co-occurrence relationship between BGCs and genera and the geographical specificity of BGCs can also provide us more information for the synthesis pathways of natural products. Expanded the known urban microbiome diversity and suggested additional mechanisms for taxonomic and functional characterization of the urban microbiome. Considering the great impact of urban microbiomes on human life, our study can also facilitate the microbial interaction analysis between human and urban environment.}, } @article {pmid34637602, year = {2022}, author = {Ponnusamy, A and Ajis, AH and Tan, YS and Chai, LC}, title = {Dynamics of fungal and bacterial microbiome associated with green-mould contaminated sawdust substrate of Pleurotus pulmonarius (grey oyster mushroom).}, journal = {Journal of applied microbiology}, volume = {132}, number = {3}, pages = {2131-2143}, doi = {10.1111/jam.15327}, pmid = {34637602}, issn = {1365-2672}, support = {RP028-15AFR//Universiti Malaya/ ; }, mesh = {*Agaricales ; Bacteria/genetics ; *Microbiota ; *Pleurotus ; }, abstract = {AIMS: Green-mould contamination is identified as one of the challenges faced by mushroom cultivation industry globally which believed to be caused by Trichoderma spp.

METHODS AND RESULTS: To explore the dynamics of microbial population in mushroom substrate during commercial mushroom cultivation and how microbiota might play a role in green-mould contamination, we applied both culturing and targeted metagenomics approaches to identify microbiota in noncomposted sawdust substrates at different cultivation stages. The microbiological analysis showed that the green-mould contaminated substrates harboured higher total mesophilic bacteria count. The green-moulds isolated from the contaminated mushroom substrates were identified as Trichoderma pleurotum (n = 15; 93.8%) and Graphium penicillioides (n = 1; 6.3%). To our surprise, the targeted metagenomic analysis revealed that Graphium comprised 56.3% while Trichoderma consisted of only 36.1% of the total fungi population, suggesting that green-mould contamination might not be caused by Trichoderma alone, but also Graphium that grows very slowly in the laboratory.

CONCLUSION: It is worthwhile to note that G. penicillioides was also isolated in the early stages of mushroom cultivation, but not T. pleurotum. The results indicated that the structure and composition of the bacterial population in the mushroom substrate varied and the bacterial population shifted along the cultivation process.

This study revealed a possibility of G. penicillioides as an overlooked fungi causing green-mould contamination.}, } @article {pmid34637433, year = {2021}, author = {Matsumoto, K and Sakami, T and Watanabe, T and Taniuchi, Y and Kuwata, A and Kakehi, S and Engkong, T and Igarashi, Y and Kinoshita, S and Asakawa, S and Hattori, M and Watabe, S and Ishino, Y and Kobayashi, T and Gojobori, T and Ikeo, K}, title = {Metagenomic analysis provides functional insights into seasonal change of a non-cyanobacterial prokaryotic community in temperate coastal waters.}, journal = {PloS one}, volume = {16}, number = {10}, pages = {e0257862}, pmid = {34637433}, issn = {1932-6203}, mesh = {Bays/microbiology ; Chlorophyll A/metabolism ; Cyanobacteria/*genetics ; Japan ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Phylogeny ; Phytoplankton/*genetics ; RNA, Ribosomal, 16S/genetics ; Salinity ; *Seasons ; Seawater/chemistry/*microbiology ; Temperature ; }, abstract = {The taxonomic compositions of marine prokaryotic communities are known to follow seasonal cycles, but functional metagenomic insights into this seasonality is still limited. We analyzed a total of 22 metagenomes collected at 11 time points over a 14-month period from two sites in Sendai Bay, Japan to obtain seasonal snapshots of predicted functional profiles of the non-cyanobacterial prokaryotic community. Along with taxonomic composition, functional gene composition varied seasonally and was related to chlorophyll a concentration, water temperature, and salinity. Spring phytoplankton bloom stimulated increased abundances of putative genes that encode enzymes in amino acid metabolism pathways. Several groups of functional genes, including those related to signal transduction and cellular communication, increased in abundance during the mid- to post-bloom period, which seemed to be associated with a particle-attached lifestyle. Alternatively, genes in carbon metabolism pathways were generally more abundant in the low chlorophyll a period than the bloom period. These results indicate that changes in trophic condition associated with seasonal phytoplankton succession altered the community function of prokaryotes. Our findings on seasonal changes of predicted function provide fundamental information for future research on the mechanisms that shape marine microbial communities.}, } @article {pmid34636654, year = {2021}, author = {Echeverría-Beirute, F and Varela-Benavides, I and P Jiménez-Madrigal, J and Carvajal-Chacon, M and Guzmán-Hernández, T}, title = {eDNA extraction protocol for metagenomic studies in tropical soils.}, journal = {BioTechniques}, volume = {71}, number = {6}, pages = {580-586}, doi = {10.2144/btn-2021-0057}, pmid = {34636654}, issn = {1940-9818}, mesh = {Biodiversity ; *DNA, Environmental ; Metagenomics/methods ; *Soil ; Soil Microbiology ; }, abstract = {The lack of knowledge about biological communities residing in soils, especially those in tropical regions, represents a constraint to management practices to take advantage of the ecological services provided by soil microbiota to agroecosystems. One of the complexities derived from describing biological diversity in such tropical conditions comes from the methods used to isolate microorganisms without altering the composition of the sample. The goal of this study was to establish a protocol for adequate soil sampling and environmental DNA extraction from a tropical region in Costa Rica. We present an up-to-date protocol optimized for tropical soils which improves sevenfold the amount of DNA extracted without significantly affecting the 260/280 and 260/230 ratios compared with commercially available kits and standard protocols.}, } @article {pmid34635053, year = {2021}, author = {Bao, L and Zhang, C and Lyu, J and Yan, C and Cao, R and Pan, M and Li, Y}, title = {Beware of pharyngeal Fusobacterium nucleatum in COVID-19.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {277}, pmid = {34635053}, issn = {1471-2180}, mesh = {Adult ; Biomarkers/analysis ; COVID-19/*microbiology/virology ; Carrier State/microbiology ; Coinfection/microbiology/virology ; Dysbiosis ; Feces/*microbiology ; Female ; Fusobacterium Infections/*microbiology/virology ; Fusobacterium nucleatum/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; Microbiota ; Middle Aged ; Pharynx/*microbiology/virology ; Sex Factors ; }, abstract = {BACKGROUND: Fusobacterium nucleatum (F. n) is an important opportunistic pathogen causing oral and gastrointestinal disease. Faecalibacterium prausnitzii (F. p) is a next-generation probiotic and could serve as a biomarker of gut eubiosis/dysbiosis to some extent. Alterations in the human oral and gut microbiomes are associated with viral respiratory infection. The aim of this study was to characterise the oral and fecal bacterial biomarker (i.e., F. n and F. p) in COVID-19 patients by qPCR and investigate the pharyngeal microbiome of COVID-19 patients through metagenomic next-generation sequencing (mNGS).

RESULTS: Pharyngeal F. n was significantly increased in COVID-19 patients, and it was higher in male than female patients. Increased abundance of pharyngeal F. n was associated with a higher risk of a positive SARS-CoV-2 test (adjusted OR = 1.32, 95% CI = 1.06 ~ 1.65, P < 0.05). A classifier to distinguish COVID-19 patients from the healthy controls based on the pharyngeal F. n was constructed and achieved an area under the curve (AUC) of 0.843 (95% CI = 0.688 ~ 0.940, P < 0.001). However, the level of fecal F. n and fecal F. p remained unaltered between groups. Besides, mNGS showed that the pharyngeal swabs of COVID-19 patients were dominated by opportunistic pathogens.

CONCLUSIONS: Pharyngeal but not fecal F. n was significantly increased in COVID-19 patients, clinicians should pay careful attention to potential coinfection. Pharyngeal F. n may serve as a promising candidate indicator for COVID-19.}, } @article {pmid34634462, year = {2022}, author = {Orellana, E and Guerrero, LD and Davies-Sala, C and Altina, M and Pontiggia, RM and Erijman, L}, title = {Extracellular hydrolytic potential drives microbiome shifts during anaerobic co-digestion of sewage sludge and food waste.}, journal = {Bioresource technology}, volume = {343}, number = {}, pages = {126102}, doi = {10.1016/j.biortech.2021.126102}, pmid = {34634462}, issn = {1873-2976}, mesh = {Anaerobiosis ; Bioreactors ; Digestion ; Food ; Methane ; *Microbiota ; *Refuse Disposal ; Sewage ; }, abstract = {Bacterial community structure and dynamics in anaerobic digesters are primarily influenced by feedstock composition. It is therefore important to unveil microbial traits that explain microbiome variations in response to substrate changes. Here, gene and genome-centric metagenomics were used to examine microbiome dynamics in four laboratory-scale reactors, in which sewage sludge was co-digested with increasing amounts of food waste. A co-occurrence network revealed microbiome shifts in response to changes in substrate composition and concentration. Food waste concentration correlated with extracellular enzymes and metagenome-assembled genomes (MAGs) involved in the degradation of complex carbohydrates commonly found in fruits and plant cell walls as well as with the abundance of hydrolytic MAGs. A key role was attributed to Proteiniphillum for being the only bacteria that encoded the complete pectin degradation pathway. These results suggest that changes of feedstock composition establish new microbial niches for bacteria with the capacity to degrade newly added substrates.}, } @article {pmid34634272, year = {2022}, author = {Hu, Y and Liu, T and Chen, N and Feng, C}, title = {Changes in microbial community diversity, composition, and functions upon nitrate and Cr(VI) contaminated groundwater.}, journal = {Chemosphere}, volume = {288}, number = {Pt 2}, pages = {132476}, doi = {10.1016/j.chemosphere.2021.132476}, pmid = {34634272}, issn = {1879-1298}, mesh = {Chromium ; *Groundwater ; Metagenomics ; *Microbiota ; Nitrates ; }, abstract = {With the increasing occurrences of nitrate and Cr(VI) pollution globally, microbially driven pollutant reduction and its interaction effects were of growing interest. Despite the increasing number of experimental reports on the simultaneous reduction of nitrate and Cr(VI), a broad picture of the keystone species and metabolic differences in this process remained elusive. This study explored the changing of microorganisms with the introduction of Cr(VI)/NO3[-] through analyzing 242 samples from the NCBI database. The correlation between microbial abundance and environmental factors showed that, the types of energy substances and pollutants species in the environment had an impact on the diversity of microorganisms and community structure. The genus of Zoogloea, Candidatus Accumulibacter, and Candidatus Kapabacteria sp. 59-99 had the ability of denitrification, while genus of Alcaligenes, Kerstersia, Petrimonas, and Leucobacter showed effectively Cr(VI) resistance and reducing ability. Azoarcus, Pseudomonas, and Thauera were recognized as important candidates in the simultaneous reduction of nitrate and Cr(VI). Metagenomic predictions of these microorganisms using PICRUSt2 further highlighted the enrichment of Cr(VI)and nitrate reduction-related genes (such as chrA and norC). Special attention should therefore be paid to these bacteria in subsequent studies to evaluate their performance and mechanisms involved in simultaneous denitrification and chromium removal. The microbial co-occurrence network analysis conducted on this basis emphasized a strong association between community collaboration and pollution removal. Collectively, either site surveys or laboratory experiments, subsequent studies should focus on these microbial populations and the interspecific collaborations as they strongly influence the occurrence of simultaneous nitrate and Cr(VI) reduction.}, } @article {pmid34633706, year = {2022}, author = {Kwan, SY and Jiao, J and Joon, A and Wei, P and Petty, LE and Below, JE and Daniel, CR and Wu, X and Zhang, J and Jenq, RR and Futreal, PA and Hawk, ET and McCormick, JB and Fisher-Hoch, SP and Beretta, L}, title = {Gut microbiome features associated with liver fibrosis in Hispanics, a population at high risk for fatty liver disease.}, journal = {Hepatology (Baltimore, Md.)}, volume = {75}, number = {4}, pages = {955-967}, pmid = {34633706}, issn = {1527-3350}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; P50 CA217674/CA/NCI NIH HHS/United States ; R01 HL142302/HL/NHLBI NIH HHS/United States ; UL1 TR003167/TR/NCATS NIH HHS/United States ; UL1 TR000371/TR/NCATS NIH HHS/United States ; }, mesh = {Bacteroidetes ; *Carcinoma, Hepatocellular/complications ; *Gastrointestinal Microbiome/genetics ; Hispanic or Latino/genetics ; Humans ; Liver Cirrhosis/complications ; *Liver Neoplasms/complications ; *Non-alcoholic Fatty Liver Disease/complications ; }, abstract = {BACKGROUND AND AIMS: Hispanics are disproportionately affected by NAFLD, liver fibrosis, cirrhosis, and HCC. Preventive strategies and noninvasive means to identify those in this population at high risk for liver fibrosis, are urgently needed. We aimed to characterize the gut microbiome signatures and related biological functions associated with liver fibrosis in Hispanics and identify environmental and genetic factors affecting them.

APPROACH AND RESULTS: Subjects of the population-based Cameron County Hispanic Cohort (CCHC; n = 217) were screened by vibration-controlled transient elastography (FibroScan). Among them, 144 (66.7%) had steatosis and 28 (13.0%) had liver fibrosis. The gut microbiome of subjects with liver fibrosis was enriched with immunogenic commensals (e.g., Prevotella copri, Holdemanella, Clostridiaceae 1) and depleted of Bacteroides caccae, Parabacteroides distasonis, Enterobacter, and Marinifilaceae. The liver fibrosis-associated metagenome was characterized by changes in the urea cycle, L-citrulline biosynthesis and creatinine degradation pathways, and altered synthesis of B vitamins and lipoic acid. These metagenomic changes strongly correlated with the depletion of Parabacteroides distasonis and enrichment of Prevotella and Holdemanella. Liver fibrosis was also associated with depletion of bacterial pathways related to L-fucose biosynthesis. Alcohol consumption, even moderate, was associated with high Prevotella abundance. The single-nucleotide polymorphisms rs3769502 and rs7573751 in the NCK adaptor protein 2 (NCK2) gene positively associated with high Prevotella abundance.

CONCLUSION: Hispanics with liver fibrosis display microbiome profiles and associated functional changes that may promote oxidative stress and a proinflammatory environment. These microbiome signatures, together with NCK2 polymorphisms, may have utility in risk modeling and disease prevention in this high-risk population.}, } @article {pmid34632902, year = {2021}, author = {Naseri, M and Houri, H and Yadegar, A and Asadzadeh Aghdaei, H and Zahiri, J}, title = {Investigation of etiology-specific alterations in the gut microbiota in liver cirrhosis.}, journal = {Expert review of gastroenterology & hepatology}, volume = {15}, number = {12}, pages = {1435-1441}, doi = {10.1080/17474124.2021.1991312}, pmid = {34632902}, issn = {1747-4132}, mesh = {Datasets as Topic ; *Gastrointestinal Microbiome ; Humans ; Liver Cirrhosis/*microbiology ; Metagenomics ; }, abstract = {BACKGROUND: Liver cirrhosis can develop as a consequence of many chronic liver diseases, such as viral hepatitis, fatty liver, or alcohol abuse. There are insufficient data on whether the different etiologies of liver cirrhosis could be related to the specific gut microbial alterations. This study aimed to compare the diversity and composition of the gut microbiota in different etiologies of liver cirrhosis.

METHODS: In the current study, the authors used three previously reported metagenomic datasets to investigate the fecal microbiota in cirrhotic patients with distinct etiologies. Microbial diversity and bacterial taxonomic composition were investigated bioinformatically in cirrhotic patients with different etiologies.

RESULTS: The analysis revealed no evidence of a significant difference in microbial diversity between cirrhotic patients with different etiologies. At the family level, cirrhotic patients with nonalcoholic fatty liver disease (NAFLD) showed a significantly higher abundance of the Enterobacteriaceae family and the related genera.

CONCLUSION: No robust microbial signal was found to differentiate between various underlying etiologies in cirrhotic patients. The data indicate that the geographical origin of cirrhotic patients could affect the composition of the gut microbiome, the effect of which obscures the impact of the etiology of cirrhosis.}, } @article {pmid34630388, year = {2021}, author = {Kong, L and Wang, Z and Xiao, C and Zhu, Q and Song, Z}, title = {Glycerol Monolaurate Ameliorated Intestinal Barrier and Immunity in Broilers by Regulating Intestinal Inflammation, Antioxidant Balance, and Intestinal Microbiota.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {713485}, pmid = {34630388}, issn = {1664-3224}, mesh = {Animals ; Antioxidants/*metabolism ; Chickens ; Cytokines/biosynthesis ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Regulation/drug effects ; Immunity, Mucosal/*drug effects ; Immunoglobulin G/blood/immunology ; Intestinal Mucosa/*immunology/*metabolism/pathology ; Laurates/*pharmacology ; Metagenome ; Metagenomics/methods ; Monoglycerides/*pharmacology ; Mucins/genetics/metabolism ; }, abstract = {This study was conducted to investigate the impact of glycerol monolaurate (GML) on performance, immunity, intestinal barrier, and cecal microbiota in broiler chicks. A total of 360 one-day-old broilers (Arbor Acres) with an average weight of 45.7 g were randomly allocated to five dietary groups as follows: basal diet and basal diets complemented with 300, 600, 900, or 1200 mg/kg GML. Samples were collected at 7 and 14 days of age. Results revealed that feed intake increased (P < 0.05) after 900 and 1200 mg/kg GML were administered during the entire 14-day experiment period. Dietary GML decreased (P < 0.05) crypt depth and increased the villus height-to-crypt depth ratio of the jejunum. In the serum and jejunum, supplementation with more than 600 mg/kg GML reduced (P < 0.05) interleukin-1β, tumor necrosis factor-α, and malondialdehyde levels and increased (P < 0.05) the levels of immunoglobulin G, jejunal mucin 2, total antioxidant capacity, and total superoxide dismutase. GML down-regulate (P < 0.05) jejunal interleukin-1β and interferon-γ expression and increased (P < 0.05) the mRNA level of zonula occludens 1 and occludin. A reduced (P < 0.05) expression of toll-like receptor 4 and nuclear factor kappa-B was shown in GML-treated groups. In addition, GML modulated the composition of the cecal microbiota of the broilers, improved (P < 0.05) microbial diversity, and increased (P < 0.05) the abundance of butyrate-producing bacteria. Spearman's correlation analysis revealed that the genera Barnesiella, Coprobacter, Lachnospiraceae, Faecalibacterium, Bacteroides, Odoriacter, and Parabacteroides were related to inflammation and intestinal integrity. In conclusion, GML ameliorated intestinal morphology and barrier function in broiler chicks probably by regulating intestinal immune and antioxidant balance, as well as intestinal microbiota.}, } @article {pmid34630385, year = {2021}, author = {Song, W and Sun, LY and Zhu, ZJ and Wei, L and Qu, W and Zeng, ZG and Liu, Y and Zhang, HM and Guo, W}, title = {Association of Gut Microbiota and Metabolites With Disease Progression in Children With Biliary Atresia.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {698900}, pmid = {34630385}, issn = {1664-3224}, mesh = {Bile Acids and Salts/metabolism ; Biliary Atresia/*metabolism/*microbiology ; Disease Progression ; Dysbiosis/*metabolism ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Infant ; Infant, Newborn ; Male ; Tryptophan/metabolism ; }, abstract = {BACKGROUND AND AIMS: Biliary atresia is the most common cause of liver disease and liver transplantation in children. The accumulation of bile acids in hepatocytes and the stimulation of the intestinal microbiome can aggravate the disease progression. This study investigated changes in the composition of the gut microbiota and its metabolites in biliary atresia and the possible effects of these changes on disease progression.

METHODS: Stool samples of biliary atresia at different disease stages and matched control individuals were collected (early stage: 16 patients, 16 controls; later stage: 16 patients, 10 controls). Metagenomic sequencing was performed to evaluate the gut microbiota structure. Untargeted metabolomics was performed to detect and analyze the metabolites and bile acid composition.

RESULTS: A disturbed gut microbiota structure occurred in the early and later stages of biliary atresia. Klebsiella, Streptococcus, Veillonella, and Enterococcus have always been dominant. The abundance of V. atypica displayed significant changes between the early and later stages of biliary atresia. Combined with clinical indicators, Spearman's analysis showed that Klebsiella and Veillonella atypica strongly correlated with liver enzymes. Enterococcus faecium had an enormously positive relationship with lithocholic acid derivatives. Metabolites involved in tryptophan metabolism were changed in the patients with biliary atresia, which had a significant association with stool V. atypica and blood total bilirubin (p < 0.05).

CONCLUSIONS: The liver damage of biliary atresia was directly or indirectly exacerbated by the interaction of enriched Klebsiella (K. pneumoniae), Veillonella (V. atypica), and Enterococcus (E. faecium) with dysmetabolism of tryptophan and bile acid.}, } @article {pmid34626348, year = {2021}, author = {Van Borm, S and Steensels, M and Mathijs, E and Vandenbussche, F and van den Berg, T and Lambrecht, B}, title = {Metagenomic sequencing determines complete infectious bronchitis virus (avian Gammacoronavirus) vaccine strain genomes and associated viromes in chicken clinical samples.}, journal = {Virus genes}, volume = {57}, number = {6}, pages = {529-540}, pmid = {34626348}, issn = {1572-994X}, support = {773830//horizon 2020 framework programme/ ; }, mesh = {Animals ; Chickens/*virology ; *Genomics ; Infectious bronchitis virus/*classification/*genetics/pathogenicity ; Poultry Diseases/virology ; Virome/*genetics ; }, abstract = {Infectious bronchitis virus (IBV, genus Gammacoronavirus) causes an economically important and highly contagious disease in chicken. Random primed RNA sequencing was applied to two IBV positive clinical samples and one in ovo-passaged virus. The virome of a cloacal swab pool was dominated by IBV (82% of viral reads) allowing de novo assembly of a GI-13 lineage complete genome with 99.95% nucleotide identity to vaccine strain 793B. In addition, substantial read counts (16% of viral reads) allowed the assembly of a near-complete chicken astrovirus genome, while lower read counts identified the presence of chicken calicivirus and avian leucosis virus. Viral reads in a respiratory/intestinal tissue pool were distributed between IBV (22.53%), Sicinivirus (Picornaviridae, 24%), and avian leucosis virus (37.04%). A complete IBV genome with 99.95% nucleotide identity to vaccine strain H120 (lineage GI-1), as well as a near-complete avian leucosis virus genome and a partial Sicinivirus genome were assembled from the tissue sample data. Lower read counts identified chicken calicivirus, Avibirnavirus (infectious bursal disease virus, assembling to 98.85% of segment A and 69.66% of segment B closely related to D3976/1 from Germany, 2017) and avian orthoreovirus, while three avian orthoavulavirus 1 reads confirmed prior real-time RT-PCR result. IBV sequence variation analysis identified both fixed and minor frequency variations in the tissue sample compared to its in ovo-passaged virus. Metagenomic methods allow the determination of complete coronavirus genomes from clinical chicken samples while providing additional insights in RNA virus sequence diversity and coinfecting viruses potentially contributing to pathogenicity.}, } @article {pmid34622635, year = {2021}, author = {Xu, Z and Chen, X and Wei, Y and Zhang, Q and Ji, X}, title = {[Metagenomic analysis of the diversity of microbes in the Napahai plateau wetland and their carbon and nitrogen metabolisms].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {37}, number = {9}, pages = {3276-3292}, doi = {10.13345/j.cjb.200658}, pmid = {34622635}, issn = {1872-2075}, mesh = {*Carbon ; Ecosystem ; Metagenomics ; Nitrogen ; Soil Microbiology ; *Wetlands ; }, abstract = {Due to the special geographical location and the complex ecosystem types, plateau wetlands play important ecological roles in water supply, greenhouse gas regulation and biodiversity preservation. Napahai plateau wetland is a special wetland type with low latitude and high altitude, and its microbial diversity was rarely studied. The diversity of microbial communities in the Napahai plateau wetland was analyzed using metagenomics method. Among the microbes detected, 184 phyla, 3 262 genera and 24 260 species belong to the bacterial domain, 13 phyla and 32 genera belong to the archaeal domain, and 13 phyla and 47 genera belong to the fungal domain. Significant differences in species diversity between soil and water were observed. Acidobacteria, Proteobacteria and Actinobacteria were dominant phyla in soil, while Proteobacteria and Bacteroides were dominant phyla in water. Since the carbon and nitrogen metabolism genes were abundant, the pathways of carbon fixation and nitrogen metabolism were analyzed. Calvin cycle, reductive tricarboxylic acid cycle and 3-hydroxypropionic acid cycle were the main carbon fixation pathways, while Proteobacteria, Chloroflexi, and Crenarchaeota were the main carbon-fixing bacteria group. As for the nitrogen cycle, nitrogen fixation and dissimilatory nitrate reduction were dominant in water, while nitrification and denitrification were dominant in soil. Proteobacteria, Nitrospirae, Verrucomicrobia, Actinobacteria, Thaumarchaeota and Euryarchaeota contributed to the nitrogen cycle. The study on microbial diversity of Napahai plateau wetlands provides new knowledge for the comprehensive management and protection of wetland environment in China.}, } @article {pmid34622235, year = {2021}, author = {Ueda, A and Shinkai, S and Shiroma, H and Taniguchi, Y and Tsuchida, S and Kariya, T and Kawahara, T and Kobayashi, Y and Kohda, N and Ushida, K and Kitamura, A and Yamada, T}, title = {Identification of Faecalibacterium prausnitzii strains for gut microbiome-based intervention in Alzheimer's-type dementia.}, journal = {Cell reports. Medicine}, volume = {2}, number = {9}, pages = {100398}, pmid = {34622235}, issn = {2666-3791}, mesh = {Aged ; Alzheimer Disease/*microbiology ; Amyloid beta-Peptides/metabolism ; Brain/microbiology/pathology ; Cognition ; Cognitive Dysfunction/microbiology ; Dementia/*microbiology ; Faecalibacterium prausnitzii/genetics/isolation & purification/*physiology ; Female ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Male ; Metabolome/genetics ; Metagenome ; Pasteurization ; Principal Component Analysis ; RNA-Seq ; }, abstract = {Evidence linking the gut-brain axis to Alzheimer's disease (AD) is accumulating, but the characteristics of causally important microbes are poorly understood. We perform a fecal microbiome analysis in healthy subjects and those with mild cognitive impairment (MCI) and AD. We find that Faecalibacterium prausnitzii (F. prausnitzii) correlates with cognitive scores and decreases in the MCI group compared with the healthy group. Two isolated strains from the healthy group, live Fp360 and pasteurized Fp14, improve cognitive impairment in an AD mouse model. Whole-genome comparison of isolated strains reveals specific orthologs that are found only in the effective strains and are more abundant in the healthy group compared with the MCI group. Metabolome and RNA sequencing analyses of mouse brains provides mechanistic insights into the relationship between the efficacy of pasteurized Fp14, oxidative stress, and mitochondrial function. We conclude that F. prausnitzii strains with these specific orthologs are candidates for gut microbiome-based intervention in Alzheimer's-type dementia.}, } @article {pmid34622234, year = {2021}, author = {Ahmed, BA and Ong, FJ and Barra, NG and Blondin, DP and Gunn, E and Oreskovich, SM and Szamosi, JC and Syed, SA and Hutchings, EK and Konyer, NB and Singh, NP and Yabut, JM and Desjardins, EM and Anhê, FF and Foley, KP and Holloway, AC and Noseworthy, MD and Haman, F and Carpentier, AC and Surette, MG and Schertzer, JD and Punthakee, Z and Steinberg, GR and Morrison, KM}, title = {Lower brown adipose tissue activity is associated with non-alcoholic fatty liver disease but not changes in the gut microbiota.}, journal = {Cell reports. Medicine}, volume = {2}, number = {9}, pages = {100397}, pmid = {34622234}, issn = {2666-3791}, support = {FDN-154295//CIHR/Canada ; 201709FDN-CEBA-116200//CIHR/Canada ; }, mesh = {Adipose Tissue, Brown/*pathology ; Adiposity ; Adolescent ; Adult ; Animals ; Cold Temperature ; Female ; *Gastrointestinal Microbiome ; Homeostasis ; Humans ; Male ; Mice, Inbred C57BL ; Middle Aged ; Multivariate Analysis ; Non-alcoholic Fatty Liver Disease/*microbiology/*pathology ; Young Adult ; Mice ; }, abstract = {In rodents, lower brown adipose tissue (BAT) activity is associated with greater liver steatosis and changes in the gut microbiome. However, little is known about these relationships in humans. In adults (n = 60), we assessed hepatic fat and cold-stimulated BAT activity using magnetic resonance imaging and the gut microbiota with 16S sequencing. We transplanted gnotobiotic mice with feces from humans to assess the transferability of BAT activity through the microbiota. Individuals with NAFLD (n = 29) have lower BAT activity than those without, and BAT activity is inversely related to hepatic fat content. BAT activity is not related to the characteristics of the fecal microbiota and is not transmissible through fecal transplantation to mice. Thus, low BAT activity is associated with higher hepatic fat accumulation in human adults, but this does not appear to have been mediated through the gut microbiota.}, } @article {pmid34622230, year = {2021}, author = {Lou, YC and Olm, MR and Diamond, S and Crits-Christoph, A and Firek, BA and Baker, R and Morowitz, MJ and Banfield, JF}, title = {Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition.}, journal = {Cell reports. Medicine}, volume = {2}, number = {9}, pages = {100393}, pmid = {34622230}, issn = {2666-3791}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/genetics ; *Bacterial Adhesion ; Carbohydrate Metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genome, Human ; Humans ; Infant ; Infant, Newborn ; Infant, Premature/physiology ; Iron/*metabolism ; Metagenomics ; *Phylogeny ; Siblings ; }, abstract = {Gut microbiome succession affects infant development. However, it remains unclear what factors promote persistence of initial bacterial colonizers in the developing gut. Here, we perform strain-resolved analyses to compare gut colonization of preterm and full-term infants throughout the first year of life and evaluate associations between strain persistence and strain origin as well as genetic potential. Analysis of fecal metagenomes collected from 13 full-term and 9 preterm infants reveals that infants' initially distinct microbiomes converge by age 1 year. Approximately 11% of early colonizers, primarily Bacteroides and Bifidobacterium, persist during the first year of life, and those are more prevalent in full-term, compared with preterm infants. Examination of 17 mother-infant pairs reveals maternal gut strains are significantly more likely to persist in the infant gut than other strains. Enrichment in genes for surface adhesion, iron acquisition, and carbohydrate degradation may explain persistence of some strains through the first year of life.}, } @article {pmid34621696, year = {2021}, author = {Belstrøm, D and Constancias, F and Markvart, M and Sikora, M and Sørensen, CE and Givskov, M}, title = {Transcriptional Activity of Predominant Streptococcus Species at Multiple Oral Sites Associate With Periodontal Status.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {752664}, pmid = {34621696}, issn = {2235-2988}, mesh = {Humans ; Metagenome ; Metagenomics ; *Microbiota ; Saliva ; Streptococcus/genetics ; }, abstract = {BACKGROUND: Streptococcus species are predominant members of the oral microbiota in both health and diseased conditions. The purpose of the present study was to explore if different ecological characteristics, such as oxygen availability and presence of periodontitis, associates with transcriptional activity of predominant members of genus Streptococcus. We tested the hypothesis that genetically closely related Streptococcus species express different transcriptional activities in samples collected from environments with critically different ecological conditions determined by site and inflammatory status.

METHODS: Metagenomic and metatranscriptomic data was retrieved from 66 oral samples, subgingival plaque (n=22), tongue scrapings (n=22) and stimulated saliva (n=22) collected from patients with periodontitis (n=11) and orally healthy individuals (n=11). Species-specific transcriptional activity was computed as Log2(RNA/DNA), and transcriptional activity of predominant Streptococcus species was compared between multiple samples collected from different sites in the same individual, and between individuals with different oral health status.

RESULTS: The predominant Streptococcus species were identified with a site-specific colonization pattern of the tongue and the subgingival plaque. A total of 11, 4 and 2 pathways expressed by S. parasanguinis, S. infantis and S. salivarius, respectively, were recorded with significantly higher transcriptional activity in saliva than in tongue biofilm in healthy individuals. In addition, 18 pathways, including pathways involved in synthesis of peptidoglycan, amino acid biosynthesis, glycolysis and purine nucleotide biosynthesis expressed by S. parasanguinis and 3 pathways expressed by S. salivarius were identified with significantly less transcriptional activity in patients with periodontitis.

CONCLUSION: Data from the present study significantly demonstrates the association of site-specific ecological conditions and presence of periodontitis with transcriptional activity of the predominant Streptococcus species of the oral microbiota. In particular, pathways expressed by S. parasanguinis being involved in peptidoglycan, amino acid biosynthesis, glycolysis, and purine nucleotide biosynthesis were identified to be significantly associated with oral site and/or inflammation status.}, } @article {pmid34619218, year = {2022}, author = {Prado, T and Shubo, T and Freitas, L and Leomil, L and Maranhão, AG and Miagostovich, MP}, title = {Virome in roof-harvested rainwater of a densely urbanized low-income region.}, journal = {The Science of the total environment}, volume = {807}, number = {Pt 2}, pages = {150778}, doi = {10.1016/j.scitotenv.2021.150778}, pmid = {34619218}, issn = {1879-1026}, mesh = {Brazil ; Cities ; Metagenomics ; *Poverty ; Rain/*virology ; *Virome ; }, abstract = {Rainwater harvesting has been considered an affordable practice to supplement the conventional sources of water supply for potable and non-potable uses worldwide. This study characterizes the viral community found in roof-harvested rainwater (RHRW) samples obtained under different rain volumes in a densely urbanized low-income region in Rio de Janeiro, Brazil. Three pilot-scale standardized metal-sheet roofs (same catchment area, material age, and slope - 3%) were installed in the study area aiming at obtaining more reliable and representative samples. Fifty-four samples were collected from six rainfall events from January to April 2019 and concentrated by the skimmed-milk flocculation method. Pools of different rainfall volumes were submitted to high throughput sequencing using the shotgun metagenomic approach. Sequencing was performed on NextSeq platform. Genomic analysis of the virus community revealed that most are RNA non-human viruses, including two main families: Dicistroviridae and Iflaviridae, recognized for infecting arthropods. Bacteriophages were also relatively abundant, with a predominance of DNA phages belonging to Microviridae and Siphoviridae families, showing percentages from 5.3 and 3.7% of the total viral hits present in these samples, respectively. Viral genomic RNA viruses (77%) predominated over DNA viruses (23%). Concerning number of viral species identified, a higher percentage was observed for plant viruses (12 families, 58%). Hepatitis A virus and human klassevirus 1 were detected among the established human pathogens, suggesting the need for RHRW treatment before it is considered for human consumption. Australian bat lyssavirus was also detected, emphasizing the importance of environmental monitoring facing emerging viruses. The results corroborate the influence of the surrounding area on the rainwater quality.}, } @article {pmid34617511, year = {2021}, author = {Ang, QY and Alba, DL and Upadhyay, V and Bisanz, JE and Cai, J and Lee, HL and Barajas, E and Wei, G and Noecker, C and Patterson, AD and Koliwad, SK and Turnbaugh, PJ}, title = {The East Asian gut microbiome is distinct from colocalized White subjects and connected to metabolic health.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34617511}, issn = {2050-084X}, support = {T32 AI060537/AI/NIAID NIH HHS/United States ; R01 DK114034/DK/NIDDK NIH HHS/United States ; T32 HL007185/HL/NHLBI NIH HHS/United States ; R01DK11230403S1/NH/NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; R01 AR074500/AR/NIAMS NIH HHS/United States ; R01DK11230401/DK/NIDDK NIH HHS/United States ; P30 DK098722/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/classification/*isolation & purification ; Bacterial Physiological Phenomena ; California ; Asia, Eastern/ethnology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Metabolism ; *Metagenome ; Metagenomics ; San Francisco ; }, abstract = {East Asians (EAs) experience worse metabolic health outcomes compared to other ethnic groups at lower body mass indices; however, the potential role of the gut microbiota in contributing to these health disparities remains unknown. We conducted a multi-omic study of 46 lean and obese East Asian and White participants living in the San Francisco Bay Area, revealing marked differences between ethnic groups in bacterial richness and community structure. White individuals were enriched for the mucin-degrading Akkermansia muciniphila. East Asian subjects had increased levels of multiple bacterial phyla, fermentative pathways detected by metagenomics, and the short-chain fatty acid end-products acetate, propionate, and isobutyrate. Differences in the gut microbiota between the East Asian and White subjects could not be explained by dietary intake, were more pronounced in lean individuals, and were associated with current geographical location. Microbiome transplantations into germ-free mice demonstrated stable diet- and host genotype-independent differences between the gut microbiotas of East Asian and White individuals that differentially impact host body composition. Taken together, our findings add to the growing body of literature describing microbiome variations between ethnicities and provide a starting point for defining the mechanisms through which the microbiome may shape disparate health outcomes in East Asians.}, } @article {pmid34617072, year = {2021}, author = {Pace, RM and Chu, DM and Prince, AL and Ma, J and Seferovic, MD and Aagaard, KM}, title = {Complex species and strain ecology of the vaginal microbiome from pregnancy to postpartum and association with preterm birth.}, journal = {Med (New York, N.Y.)}, volume = {2}, number = {9}, pages = {1027-1049}, pmid = {34617072}, issn = {2666-6340}, support = {U54 HG004973/HG/NHGRI NIH HHS/United States ; K12 GM084897/GM/NIGMS NIH HHS/United States ; R01 HD091731/HD/NICHD NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; R21 ES029462/ES/NIEHS NIH HHS/United States ; R01 DK089201/DK/NIDDK NIH HHS/United States ; T32 GM007330/GM/NIGMS NIH HHS/United States ; R01 NR014792/NR/NINR NIH HHS/United States ; T32 GM088129/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria ; Child ; Female ; Humans ; Infant, Newborn ; Lactobacillus/genetics ; *Microbiota/genetics ; Postpartum Period ; Pregnancy ; *Premature Birth/microbiology ; RNA, Ribosomal, 16S/genetics ; Vagina/chemistry ; }, abstract = {BACKGROUND: Lactobacillus was described as a keystone bacterial taxon in the human vagina over 100 years ago. Using metagenomics, we and others have characterized lactobacilli and other vaginal taxa across health and disease states, including pregnancy. While shifts in community membership have been resolved at the genus/species level, strain dynamics remain poorly characterized.

METHODS: We performed a metagenomic analysis of the complex ecology of the vaginal econiche during and after pregnancy in a large U.S. based longitudinal cohort of women who were initially sampled in the third trimester of pregnancy, then validated key findings in a second cohort of women initially sampled in the second trimester of pregnancy.

FINDINGS: First, we resolved microbial species and strains, interrogated their co-occurrence patterns, and probed the relationship between keystone species and preterm birth outcomes. Second, to determine the role of human heredity in shaping vaginal microbial ecology in relation to preterm birth, we performed a mtDNA-bacterial species association analysis. Finally, we explored the clinical utility of metagenomics in detection and co-occurrence patterns for the pathobiont Group B Streptococcus (causative bacterium of invasive neonatal sepsis).

CONCLUSIONS: Our highly refined resolutions of the vaginal ecology during and post-pregnancy provide insights into not only structural and functional community dynamics, but highlight the capacity of metagenomics to reveal finer aspects of the vaginal microbial ecologic framework.

FUNDING: NIH-NINR R01NR014792, NIH-NICHD R01HD091731, NIH National Children's Study Formative Research, Burroughs Wellcome Fund Preterm Birth Initiative, March of Dimes Preterm Birth Research Initiative, NIH-NIGMS (K12GM084897, T32GM007330, T32GM088129).}, } @article {pmid34615557, year = {2021}, author = {Wang, Y and Ye, J and Ju, F and Liu, L and Boyd, JA and Deng, Y and Parks, DH and Jiang, X and Yin, X and Woodcroft, BJ and Tyson, GW and Hugenholtz, P and Polz, MF and Zhang, T}, title = {Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {199}, pmid = {34615557}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Bioreactors ; Metagenome ; *Microbiota/genetics ; *Sewage ; }, abstract = {BACKGROUND: Microbial communities in both natural and applied settings reliably carry out myriads of functions, yet how stable these taxonomically diverse assemblages can be and what causes them to transition between states remains poorly understood. We studied monthly activated sludge (AS) samples collected over 9 years from a full-scale wastewater treatment plant to answer how complex AS communities evolve in the long term and how the community functions change when there is a disturbance in operational parameters.

RESULTS: Here, we show that a microbial community in activated sludge (AS) system fluctuated around a stable average for 3 years but was then abruptly pushed into an alternative stable state by a simple transient disturbance (bleaching). While the taxonomic composition rapidly turned into a new state following the disturbance, the metabolic profile of the community and system performance remained remarkably stable. A total of 920 metagenome-assembled genomes (MAGs), representing approximately 70% of the community in the studied AS ecosystem, were recovered from the 97 monthly AS metagenomes. Comparative genomic analysis revealed an increased ability to aggregate in the cohorts of MAGs with correlated dynamics that are dominant after the bleaching event. Fine-scale analysis of dynamics also revealed cohorts that dominated during different periods and showed successional dynamics on seasonal and longer time scales due to temperature fluctuation and gradual changes in mean residence time in the reactor, respectively.

CONCLUSIONS: Our work highlights that communities can assume different stable states under highly similar environmental conditions and that a specific disturbance threshold may lead to a rapid shift in community composition. Video Abstract.}, } @article {pmid34614189, year = {2021}, author = {Zorrilla, F and Buric, F and Patil, KR and Zelezniak, A}, title = {metaGEM: reconstruction of genome scale metabolic models directly from metagenomes.}, journal = {Nucleic acids research}, volume = {49}, number = {21}, pages = {e126}, pmid = {34614189}, issn = {1362-4962}, support = {MC_UU_00025/11/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Databases, Genetic ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenome ; Plants/*genetics ; Soil Microbiology ; }, abstract = {Metagenomic analyses of microbial communities have revealed a large degree of interspecies and intraspecies genetic diversity through the reconstruction of metagenome assembled genomes (MAGs). Yet, metabolic modeling efforts mainly rely on reference genomes as the starting point for reconstruction and simulation of genome scale metabolic models (GEMs), neglecting the immense intra- and inter-species diversity present in microbial communities. Here, we present metaGEM (https://github.com/franciscozorrilla/metaGEM), an end-to-end pipeline enabling metabolic modeling of multi-species communities directly from metagenomes. The pipeline automates all steps from the extraction of context-specific prokaryotic GEMs from MAGs to community level flux balance analysis (FBA) simulations. To demonstrate the capabilities of metaGEM, we analyzed 483 samples spanning lab culture, human gut, plant-associated, soil, and ocean metagenomes, reconstructing over 14,000 GEMs. We show that GEMs reconstructed from metagenomes have fully represented metabolism comparable to isolated genomes. We demonstrate that metagenomic GEMs capture intraspecies metabolic diversity and identify potential differences in the progression of type 2 diabetes at the level of gut bacterial metabolic exchanges. Overall, metaGEM enables FBA-ready metabolic model reconstruction directly from metagenomes, provides a resource of metabolic models, and showcases community-level modeling of microbiomes associated with disease conditions allowing generation of mechanistic hypotheses.}, } @article {pmid34614175, year = {2021}, author = {Jarvis, KG and Hsu, CK and Pettengill, JB and Ihrie, J and Karathia, H and Hasan, NA and Grim, CJ}, title = {Microbiome Population Dynamics of Cold-Smoked Sockeye Salmon during Refrigerated Storage and after Culture Enrichment.}, journal = {Journal of food protection}, volume = {85}, number = {2}, pages = {238-253}, doi = {10.4315/JFP-21-228}, pmid = {34614175}, issn = {1944-9097}, mesh = {Animals ; Cold Temperature ; Colony Count, Microbial ; Food Microbiology ; Food Preservation ; *Listeria monocytogenes ; *Microbiota ; Population Dynamics ; RNA, Ribosomal, 16S ; Salmon/microbiology ; Seafood/microbiology ; Smoke ; }, abstract = {ABSTRACT: Cold-smoked salmon is a ready-to-eat seafood product of high commercial importance. The processing and storage steps facilitate the introduction, growth, and persistence of foodborne pathogens and spoilage bacteria. The growth of commensal bacteria during storage and once the product is opened also influence the quality and safety of cold-smoked salmon. Here we investigated the microbial community through targeted 16S rRNA gene and shotgun metagenomic sequencing as means to better understand the interactions among bacteria in cold-smoked salmon. Cold-smoked salmon samples were tested over 30 days of aerobic storage at 4°C and cultured at each time point in a buffered Listeria enrichment broth (BLEB) commonly used to detect Listeria in foods. The microbiomes were composed of Firmicutes and Proteobacteria, namely, Carnobacterium, Brochothrix, Pseudomonas, Serratia, and Psychrobacter. Pseudomonas species were the most diverse species, with 181 taxa identified. In addition, we identified potential homologs to 10 classes of bacteriocins in microbiomes of cold-smoked salmon stored at 4°C and corresponding BLEB culture enrichments. The findings presented here contribute to our understanding of microbiome population dynamics in cold-smoked salmon, including changes in bacterial taxa during aerobic cold storage and after culture enrichment. This may facilitate improvements to pathogen detection and quality preservation of this food.}, } @article {pmid34613762, year = {2021}, author = {Wagner, E and Fagerlund, A and Langsrud, S and Møretrø, T and Jensen, MR and Moen, B}, title = {Surveillance of Listeria monocytogenes: Early Detection, Population Dynamics, and Quasimetagenomic Sequencing during Selective Enrichment.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {24}, pages = {e0177421}, pmid = {34613762}, issn = {1098-5336}, support = {294910//Norges Forskningsråd (Forskningsrådet)/ ; 314743//Foundation for Research Levy on Agricultural Products (FFL)/ ; }, mesh = {*Food Microbiology ; Genes, Bacterial ; *Listeria monocytogenes/genetics/isolation & purification ; Metagenomics ; *Microbiota ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In this study, we addressed different aspects regarding the implementation of quasimetagenomic sequencing as a hybrid surveillance method in combination with enrichment for early detection of Listeria monocytogenes in the food industry. Different experimental enrichment cultures were used, comprising seven L. monocytogenes strains of different sequence types (STs), with and without a background microbiota community. To assess whether the proportions of the different STs changed over time during enrichment, the growth and population dynamics were assessed using dapE colony sequencing and dapE and 16S rRNA amplicon sequencing. There was a tendency of some STs to have a higher relative abundance during the late stage of enrichment when L. monocytogenes was enriched without background microbiota. When coenriched with background microbiota, the population dynamics of the different STs was more consistent over time. To evaluate the earliest possible time point during enrichment that allows the detection of L. monocytogenes and at the same time the generation of genetic information that enables an estimation regarding the strain diversity in a sample, quasimetagenomic sequencing was performed early during enrichment in the presence of the background microbiota using Oxford Nanopore Technologies Flongle and Illumina MiSeq sequencing. The application of multiple displacement amplification (MDA) enabled detection of L. monocytogenes (and the background microbiota) after only 4 h of enrichment using both applied sequencing approaches. The MiSeq sequencing data additionally enabled the prediction of cooccurring L. monocytogenes strains in the samples. IMPORTANCE We showed that a combination of a short primary enrichment combined with MDA and Nanopore sequencing can accelerate the traditional process of cultivation and identification of L. monocytogenes. The use of Illumina MiSeq sequencing additionally allowed us to predict the presence of cooccurring L. monocytogenes strains. Our results suggest quasimetagenomic sequencing is a valuable and promising hybrid surveillance tool for the food industry that enables faster identification of L. monocytogenes during early enrichment. Routine application of this approach could lead to more efficient and proactive actions in the food industry that prevent contamination and subsequent product recalls and food destruction, economic and reputational losses, and human listeriosis cases.}, } @article {pmid34613754, year = {2021}, author = {Mickol, RL and Eddie, BJ and Malanoski, AP and Yates, MD and Tender, LM and Glaven, SM}, title = {Metagenomic and Metatranscriptomic Characterization of a Microbial Community That Catalyzes Both Energy-Generating and Energy-Storing Electrode Reactions.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {24}, pages = {e0167621}, pmid = {34613754}, issn = {1098-5336}, support = {//DOD | USN | U.S. Naval Research Laboratory (NRL)/ ; }, mesh = {*Deltaproteobacteria/genetics/metabolism ; *Electrodes ; *Metagenomics ; *Microbiota ; *Transcriptome ; }, abstract = {Electroactive bacteria are living catalysts, mediating energy-generating reactions at anodes or energy storage reactions at cathodes via extracellular electron transfer (EET). The Cathode-ANode (CANode) biofilm community was recently shown to facilitate both reactions; however, the identities of the primary constituents and underlying molecular mechanisms remain unknown. Here, we used metagenomics and metatranscriptomics to characterize the CANode biofilm. We show that a previously uncharacterized member of the family Desulfobulbaceae, Desulfobulbaceae-2, which had <1% relative abundance, had the highest relative gene expression and accounted for over 60% of all differentially expressed genes. At the anode potential, differential expression of genes for a conserved flavin oxidoreductase (Flx) and heterodisulfide reductase (Hdr) known to be involved in ethanol oxidation suggests a source of electrons for the energy-generating reaction. Genes for sulfate and carbon dioxide reduction pathways were expressed by Desulfobulbaceae-2 at both potentials and are the proposed energy storage reactions. Reduction reactions may be mediated by direct electron uptake from the electrode or from hydrogen generated at the cathode potential. The Desulfobulbaceae-2 genome is predicted to encode at least 85 multiheme (≥3 hemes) c-type cytochromes, some with as many as 26 heme-binding domains, that could facilitate reversible electron transfer with the electrode. Gene expression in other CANode biofilm species was also affected by the electrode potential, although to a lesser extent, and we cannot rule out their contribution to observed current. Results provide evidence of gene expression linked to energy storage and energy-generating reactions and will enable development of the CANode biofilm as a microbially driven rechargeable battery. IMPORTANCE Microbial electrochemical technologies (METs) rely on electroactive bacteria to catalyze energy-generating and energy storage reactions at electrodes. Known electroactive bacteria are not equally capable of both reactions, and METs are typically configured to be unidirectional. Here, we report on genomic and transcriptomic characterization of a recently described microbial electrode community called the Cathode-ANode (CANode). The CANode community is able to generate or store electrical current based on the electrode potential. During periods where energy is not needed, electrons generated from a renewable source, such as solar power, could be converted into energy storage compounds to later be reversibly oxidized by the same microbial catalyst. Thus, the CANode system can be thought of as a living "rechargeable battery." Results show that a single organism may be responsible for both reactions demonstrating a new paradigm for electroactive bacteria.}, } @article {pmid34612701, year = {2021}, author = {Poulsen, CS and Kaas, RS and Aarestrup, FM and Pamp, SJ}, title = {Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0138721}, pmid = {34612701}, issn = {2165-0497}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics/isolation & purification ; Drug Resistance, Bacterial ; Feces/chemistry/microbiology ; Humans ; *Microbiota ; Preservation, Biological/instrumentation/*methods ; Sewage/chemistry/microbiology ; Specimen Handling/instrumentation/*methods ; Swine ; Temperature ; Time Factors ; }, abstract = {Storage of biological specimens is crucial in the life and medical sciences. Storage conditions for samples can be different for a number of reasons, and it is unclear what effect this can have on the inferred microbiome composition in metagenomics analyses. Here, we assess the effect of common storage temperatures (deep freezer, -80°C; freezer, -20°C; refrigerator, 5°C; room temperature, 22°C) and storage times (immediate sample processing, 0 h; next day, 16 h; over weekend, 64 h; longer term, 4, 8, and 12 months) as well as repeated sample freezing and thawing (2 to 4 freeze-thaw cycles). We examined two different pig feces and sewage samples, unspiked and spiked with a mock community, in triplicate, respectively, amounting to a total of 438 samples (777 Gbp; 5.1 billion reads). Storage conditions had a significant and systematic effect on the taxonomic and functional composition of microbiomes. Distinct microbial taxa and antimicrobial resistance classes were, in some situations, similarly affected across samples, while others were not, suggesting an impact of individual inherent sample characteristics. With an increasing number of freeze-thaw cycles, an increasing abundance of Firmicutes, Actinobacteria, and eukaryotic microorganisms was observed. We provide recommendations for sample storage and strongly suggest including more detailed information in the metadata together with the DNA sequencing data in public repositories to better facilitate meta-analyses and reproducibility of findings. IMPORTANCE Previous research has reported effects of DNA isolation, library preparation, and sequencing technology on metagenomics-based microbiome composition; however, the effect of biospecimen storage conditions has not been thoroughly assessed. We examined the effect of common sample storage conditions on metagenomics-based microbiome composition and found significant and, in part, systematic effects. Repeated freeze-thaw cycles could be used to improve the detection of microorganisms with more rigid cell walls, including parasites. We provide a data set that could also be used for benchmarking algorithms to identify and correct for unwanted batch effects. Overall, the findings suggest that all samples of a microbiome study should be stored in the same way. Furthermore, there is a need to mandate more detailed information about sample storage and processing be published together with DNA sequencing data at the International Nucleotide Sequence Database Collaboration (ENA/EBI, NCBI, DDBJ) or other repositories.}, } @article {pmid34611253, year = {2021}, author = {Kačírová, J and Maďari, A and Mucha, R and Fecskeová, LK and Mujakic, I and Koblížek, M and Nemcová, R and Maďar, M}, title = {Study of microbiocenosis of canine dental biofilms.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {19776}, pmid = {34611253}, issn = {2045-2322}, mesh = {Animals ; Bacteria/classification/genetics ; *Biofilms ; Dogs ; Metagenome ; Metagenomics/methods ; *Microbiota ; Periodontium/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Tooth/*microbiology ; }, abstract = {Dental biofilm is a complex microbial community influenced by many exogenous and endogenous factors. Despite long-term studies, its bacterial composition is still not clearly understood. While most of the research on dental biofilms was conducted in humans, much less information is available from companion animals. In this study, we analyzed the composition of canine dental biofilms using both standard cultivation on solid media and amplicon sequencing, and compared the two approaches. The 16S rRNA gene sequences were used to define the bacterial community of canine dental biofilm with both, culture-dependent and culture-independent methods. After DNA extraction from each sample, the V3-V4 region of the 16S rRNA gene was amplified and sequenced via Illumina MiSeq platform. Isolated bacteria were identified using universal primers and Sanger sequencing. Representatives of 18 bacterial genera belonging to 5 phyla were isolated from solid media. Amplicon sequencing largely expanded this information identifying in total 284 operational taxonomic units belonging to 10 bacterial phyla. Amplicon sequencing revealed much higher diversity of bacteria in the canine dental biofilms, when compared to standard cultivation approach. In contrast, cultured representatives of several bacterial families were not identified by amplicon sequencing.}, } @article {pmid34611238, year = {2021}, author = {Rahman, MS and Hoque, MN and Puspo, JA and Islam, MR and Das, N and Siddique, MA and Hossain, MA and Sultana, M}, title = {Microbiome signature and diversity regulates the level of energy production under anaerobic condition.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {19777}, pmid = {34611238}, issn = {2045-2322}, mesh = {*Anaerobiosis ; *Biodiversity ; Chemical Phenomena ; Computational Biology/methods ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; *Renewable Energy ; }, abstract = {The microbiome of the anaerobic digester (AD) regulates the level of energy production. To assess the microbiome diversity and composition in different stages of anaerobic digestion, we collected 16 samples from the AD of cow dung (CD) origin. The samples were categorized into four groups (Group-I, Group-II, Group-III and Group-IV) based on the level of energy production (CH4%), and sequenced through whole metagenome sequencing (WMS). Group-I (n = 2) belonged to initial time of energy production whereas Group-II (n = 5), Group-III (n = 5), and Group-IV (n = 4) had 21-34%, 47-58% and 71-74% of CH4, respectively. The physicochemical analysis revealed that level of energy production (CH4%) had significant positive correlation with digester pH (r = 0.92, p < 0.001), O2 level (%) (r = 0.54, p < 0.05), and environmental temperature (°C) (r = 0.57, p < 0.05). The WMS data mapped to 2800 distinct bacterial, archaeal and viral genomes through PathoScope (PS) and MG-RAST (MR) analyses. We detected 768, 1421, 1819 and 1774 bacterial strains in Group-I, Group-II, Group-III and Group-IV, respectively through PS analysis which were represented by Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes and Fibrobacteres phyla (> 93.0% of the total abundances). Simultaneously, 343 archaeal strains were detected, of which 95.90% strains shared across four metagenomes. We identified 43 dominant species including 31 bacterial and 12 archaeal species in AD microbiomes, of which only archaea showed positive correlation with digester pH, CH4 concentration, pressure and temperature (Spearman correlation; r > 0.6, p < 0.01). The indicator species analysis showed that the species Methanosarcina vacuolate, Dehalococcoides mccartyi, Methanosarcina sp. Kolksee and Methanosarcina barkeri were highly specific for energy production. The correlation network analysis showed that different strains of Euryarcheota and Firmicutes phyla exhibited significant correlation (p = 0.021, Kruskal-Wallis test; with a cutoff of 1.0) with the highest level (74.1%) of energy production (Group-IV). In addition, top CH4 producing microbiomes showed increased genomic functional activities related to one carbon and biotin metabolism, oxidative stress, proteolytic pathways, membrane-type-1-matrix-metalloproteinase (MT1-MMP) pericellular network, acetyl-CoA production, motility and chemotaxis. Importantly, the physicochemical properties of the AD including pH, CH4 concentration (%), pressure, temperature and environmental temperature were found to be positively correlated with these genomic functional potentials and distribution of ARGs and metal resistance pathways (Spearman correlation; r > 0.5, p < 0.01). This study reveals distinct changes in composition and diversity of the AD microbiomes including different indicator species, and their genomic features that are highly specific for energy production.}, } @article {pmid34611216, year = {2021}, author = {Goolam Mahomed, T and Peters, RPH and Allam, M and Ismail, A and Mtshali, S and Goolam Mahomed, A and Ueckermann, V and Kock, MM and Ehlers, MM}, title = {Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {19758}, pmid = {34611216}, issn = {2045-2322}, mesh = {Aged ; Biodiversity ; Disease Progression ; Female ; Humans ; Lung/*microbiology ; Male ; Metagenome ; Metagenomics ; *Microbiota ; Middle Aged ; Pulmonary Disease, Chronic Obstructive/*diagnosis/*etiology ; Risk Factors ; South Africa/epidemiology ; Sputum/microbiology ; }, abstract = {Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.}, } @article {pmid34608480, year = {2021}, author = {Wang, Y and Li, J and Ma, C and Jiang, S and Li, C and Zhang, L and Zhang, J}, title = {Lactiplantibacillus plantarum HNU082 inhibited the growth of Fusobacterium nucleatum and alleviated the inflammatory response introduced by F. nucleatum invasion.}, journal = {Food & function}, volume = {12}, number = {21}, pages = {10728-10740}, doi = {10.1039/d1fo01388b}, pmid = {34608480}, issn = {2042-650X}, mesh = {Animals ; Biomarkers, Tumor ; Fusobacterium nucleatum/pathogenicity/*physiology ; Gastrointestinal Microbiome ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Inflammation ; *Lactobacillaceae ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Probiotics/*pharmacology ; Transcriptome ; }, abstract = {As a potential biomarker, there is increasing evidence showing that Fusobacterium nucleatum is positively correlated with the occurrence and development of colorectal cancer. Although antibiotics were expected to eliminate F. nucleatum, the side effects associated with gut microbiotal disorders have to be considered. Here, by performing shotgun metagenomic and transcriptome sequencing, we systematically evaluated the antagonistic effects of probiotic Lactiplantibacillus plantarum HNU082 (Lp082) on F. nucleatum in vivo and in vitro. The results showed that the F. nucleatum invasion significantly altered the host intestinal microbiome including the microbial composition, specific species, metabolic pathways and metabolites, as well as impacted the transcriptome of the intestinal epithelial cells. Moreover, the F. nucleatum invasion triggered inflammatory cytokines and inflammatory responses in the intestine but did not develop into colorectal cancer. Excitingly, the Lp082 intervention inhibited the growth of F. nucleatum both in vivo and in vitro and alleviated the inflammatory response introduced by F. nucleatum invasion. Further network-based mechanism exploration demonstrated that Lp082, which negatively correlated to F. nucleatum, maintained the intestinal microbiome homeostasis and prompted the production of beneficial metabolites in the intestine which decreased the expression of inflammatory cytokines in a mouse model. The present research suggested a feasible probiotic intervention strategy for F. nucleatum antagonism in vivo, which may prevent colorectal cancer at the early stage.}, } @article {pmid34608200, year = {2021}, author = {Ito, T and Totoki, T and Takada, S and Otsuka, S and Maruyama, I}, title = {Potential roles of 1,5-anhydro-D-fructose in modulating gut microbiome in mice.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {19648}, pmid = {34608200}, issn = {2045-2322}, mesh = {Animals ; Diet ; Dietary Supplements ; Fructose/*analogs & derivatives/metabolism/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Metagenome ; Metagenomics/methods ; Mice ; NAD/biosynthesis ; Nutrients/biosynthesis ; Vitamins/biosynthesis ; }, abstract = {The gut microbiota has tremendous potential to affect the host's health, in part by synthesizing vitamins and generating nutrients from food that is otherwise indigestible by the host. 1,5-Anhydro-D-fructose (1,5-AF) is a monosaccharide with a wide range of bioactive potentials, including anti-oxidant, anti-inflammatory, and anti-microbial effects. Based on its potential benefits and minimal toxicity, it is anticipated that 1,5-AF will be used as a dietary supplement to support general health. However, the effects of 1,5-AF on the gut microbiota are yet to be clarified. Here, using an unbiased metagenomic approach, we profiled the bacterial taxa and functional genes in the caecal microbiota of mice fed a diet containing either 2% 1,5-AF or a reference sweetener. Supplementation with 1,5-AF altered the composition of the gut microbiota, enriching the proportion of Faecalibacterium prausnitzii. 1,5-AF also altered the metabolomic profile of the gut microbiota, enriching genes associated with nicotinamide adenine dinucleotide biosynthesis. These findings support the potential benefits of 1,5-AF, but further studies are required to clarify the impact of 1,5-AF on health and disease.}, } @article {pmid34607029, year = {2022}, author = {Sun, Y and Duan, C and Cao, N and Ding, C and Huang, Y and Wang, J}, title = {Biodegradable and conventional microplastics exhibit distinct microbiome, functionality, and metabolome changes in soil.}, journal = {Journal of hazardous materials}, volume = {424}, number = {Pt A}, pages = {127282}, doi = {10.1016/j.jhazmat.2021.127282}, pmid = {34607029}, issn = {1873-3336}, mesh = {Metabolome ; *Microbiota ; *Microplastics ; Plastics ; RNA, Ribosomal, 16S/genetics ; Soil ; }, abstract = {Environmental concerns with liberal petroleum-based plastic use have led to demand for sustainable biodegradable alternatives. However, the inadequate end-of-life treatment of plastics may emit microplastics, either conventional or biodegradable, to the terrestrial environment. It is essential to evaluate the possible effects of conventional and biodegradable microplastics on the composition and function of soil microbial communities. Therefore, we conducted a soil microcosm experiment with polyethylene (PE), polystyrene (PS), polylactide (PLA), or polybutylene succinate (PBS) microplastics. The soil microbiome and metabolome were evaluated via 16S rRNA gene sequencing, metagenomics, and untargeted metabolomics. We reported that the presence of conventional or biodegradable microplastics can significantly alter soil microbial community composition. Compared to the control soils, the microbiome in PBS and PLA amended soils exhibited higher potential for uptake of exogenous carbohydrates and amino acids, but a reduced capacity for related metabolic function, potentially due to catabolite repression. No differences in soil metabolome can be observed between conventional microplastic treatments and the control. The potential reason may be that the functional diversity was unaffected by PE and PS microplastics, while the biodegradable particles promoted the soil microbial multifunctionality. Our findings systematically shed light on the influence of conventional and biodegradable microplastics on soil microorganisms, facilitating microplastic regulation.}, } @article {pmid34606860, year = {2022}, author = {Chen, G and Bai, R and Zhang, Y and Zhao, B and Xiao, Y}, title = {Application of metagenomics to biological wastewater treatment.}, journal = {The Science of the total environment}, volume = {807}, number = {Pt 1}, pages = {150737}, doi = {10.1016/j.scitotenv.2021.150737}, pmid = {34606860}, issn = {1879-1026}, mesh = {Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Metagenomics ; *Microbiota ; *Water Purification ; }, abstract = {Biological wastewater treatment is a process in which the microbial metabolism of complex communities transforms pollutants into low- or non-toxic products. Due to the absence of an in-depth understanding of the diversity and complexity of microbial communities, it is very likely to ignore the potential mechanisms of microbial community in wastewater treatment. Metagenomics is a technology based on molecular biology, in which massive gene sequences are obtained from environmental samples and analyzed by bioinformatics to determine the composition and function of a microbial community. Metagenomics can identify the state of microbes in their native environments more effectively than traditional molecular methods. This review summarizes the application of metagenomics to assess microbial communities in biological wastewater treatment, such as the biological removal of phosphorus and nitrogen by bacteria, the study of antibiotic resistance genes (ARGs), and the reduction of heavy metals by microbial communities, with an emphasis on the contribution of microbial diversity and metabolic diversity. Technical bottlenecks in the application of metagenomics to biological wastewater treatment are elucidated, and future research directions for metagenomics are proposed, among which the application of multi-omics will be an important research method for future biological wastewater treatment.}, } @article {pmid34606847, year = {2022}, author = {Lima, SF and Gogokhia, L and Viladomiu, M and Chou, L and Putzel, G and Jin, WB and Pires, S and Guo, CJ and Gerardin, Y and Crawford, CV and Jacob, V and Scherl, E and Brown, SE and Hambor, J and Longman, RS}, title = {Transferable Immunoglobulin A-Coated Odoribacter splanchnicus in Responders to Fecal Microbiota Transplantation for Ulcerative Colitis Limits Colonic Inflammation.}, journal = {Gastroenterology}, volume = {162}, number = {1}, pages = {166-178}, pmid = {34606847}, issn = {1528-0012}, support = {R01 DK114252/DK/NIDDK NIH HHS/United States ; R01 DK120985/DK/NIDDK NIH HHS/United States ; R01 DK128257/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteroidetes/genetics/*immunology/metabolism ; Clinical Trials as Topic ; Colitis/immunology/metabolism/microbiology/*therapy ; Colitis, Ulcerative/diagnosis/immunology/metabolism/microbiology ; Colon/immunology/metabolism/*microbiology ; Disease Models, Animal ; *Fecal Microbiota Transplantation ; Forkhead Transcription Factors/metabolism ; *Gastrointestinal Microbiome/genetics/immunology ; Germ-Free Life ; Humans ; Immunity, Mucosal ; Immunoglobulin A/genetics/*immunology/metabolism ; Intestinal Mucosa/immunology/metabolism/*microbiology ; Intraepithelial Lymphocytes/immunology/metabolism/microbiology ; Metagenome ; Metagenomics ; Mice, Inbred C57BL ; Mice, Knockout ; Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism ; T-Lymphocytes, Regulatory/immunology/metabolism/microbiology ; Treatment Outcome ; Mice ; }, abstract = {BACKGROUND & AIMS: Fecal microbiota transplantation (FMT) is an emerging treatment modality for ulcerative colitis (UC). Several randomized controlled trials have shown efficacy for FMT in the treatment of UC, but a better understanding of the transferable microbiota and their immune impact is needed to develop more efficient microbiome-based therapies for UC.

METHODS: Metagenomic analysis and strain tracking was performed on 60 donor and recipient samples receiving FMT for active UC. Sorting and sequencing of immunoglobulin (Ig) A-coated microbiota (called IgA-seq) was used to define immune-reactive microbiota. Colonization of germ-free or genetically engineered mice with patient-derived strains was performed to determine the mechanism of microbial impact on intestinal immunity.

RESULTS: Metagenomic analysis defined a core set of donor-derived transferable bacterial strains in UC subjects achieving clinical response, which predicted response in an independent trial of FMT for UC. IgA-seq of FMT recipient samples and gnotobiotic mice colonized with donor microbiota identified Odoribacter splanchnicus as a transferable strain shaping mucosal immunity, which correlated with clinical response and the induction of mucosal regulatory T cells. Colonization of mice with O splanchnicus led to an increase in Foxp3[+]/RORγt[+] regulatory T cells, induction of interleukin (IL) 10, and production of short chain fatty acids, all of which were required for O splanchnicus to limit colitis in mouse models.

CONCLUSIONS: This work provides the first evidence of transferable, donor-derived strains that correlate with clinical response to FMT in UC and reveals O splanchnicus as a key component promoting both metabolic and immune cell protection from colitis. These mechanistic features will help enable strategies to enhance the efficacy of microbial therapy for UC. Clinicaltrials.gov ID NCT02516384.}, } @article {pmid34601036, year = {2022}, author = {Tripathi, S and Purchase, D and Al-Rashed, S and Chandra, R}, title = {Microbial community dynamics and their relationships with organic and metal pollutants of sugarcane molasses-based distillery wastewater sludge.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {292}, number = {Pt A}, pages = {118267}, doi = {10.1016/j.envpol.2021.118267}, pmid = {34601036}, issn = {1873-6424}, mesh = {*Environmental Pollutants ; *Microbiota ; Molasses ; *Saccharum ; Sewage ; Waste Disposal, Fluid ; Wastewater ; }, abstract = {Distillery sludge is a major source of aquatic pollution, but little is known about their microbial community and their association with the organic and metal pollutants. Sugarcane molasses-based distillery is an important industry in India, although the waste is usually treated prior to disposal, the treatment is often inadequate. The adverse effects of the organic and metal pollutants in sugarcane molasses-based distillery sludge on the microbial biodiversity and abundance in the disposal site have not been elucidated. This study aims to address this gap of knowledge. Samples were collected from the discharge point, 1 and 2 km downstream (D1, D2, and D3, respectively) of a sugarcane distillery in Uttar Pradesh, India, and their physico-chemical properties characterised. Using QIIME, taxonomic assignment for the V3 and V4 hypervariable regions of 16 S rRNA was performed. The phyla Proteobacteria (28-39%), Firmicutes (20-28%), Bacteriodetes (9-10%), Actinobacteria (5-10%), Tenericutes (1-9%) and Patescibacteria (2%) were the predominant bacteria in all three sites. Euryechaeota, were detected in sites D1 and D2 (1-2%) but absent in D3. Spirochaetes (5%), Sinergistetes (2%) and Cloacimonetes (1%) were only detected in samples from site D1. Shannon, Simpson, Chao1, and Observed-species indices indicated that site D1 (10.18, 0.0013, 36706.55 and 45653.84, respectively) has higher bacterial diversity and richness than D2 (6.66, 0.0001, 25987.71 and 49655.89, respectively) and D3 (8.31, 0.002, 30345.53 and 30654.88, respectively), suggesting the organic and metal pollutants provided the stressors to favour the survival of microbial community that can biodegrade and detoxify them in the distillery sludge. This study confirmed that the treatment of the distillery waste was not sufficiently effective and provided new metagenomic information on its impact on the surrounding microbial community. It also offered new insights into potential bioremediation candidates.}, } @article {pmid34600010, year = {2022}, author = {Su, H and Yuan, P and Lei, H and Zhang, L and Deng, D and Zhang, L and Chen, X}, title = {Long-term chronic exposure to di-(2-ethylhexyl)-phthalate induces obesity via disruption of host lipid metabolism and gut microbiota in mice.}, journal = {Chemosphere}, volume = {287}, number = {Pt 4}, pages = {132414}, doi = {10.1016/j.chemosphere.2021.132414}, pmid = {34600010}, issn = {1879-1298}, mesh = {Animals ; *Diethylhexyl Phthalate/toxicity ; *Gastrointestinal Microbiome ; Lipid Metabolism ; Mice ; Obesity/chemically induced ; Phthalic Acids ; RNA, Ribosomal, 16S/metabolism ; }, abstract = {BACKGROUND: Numerous epidemiological findings have shown that di-(2-ethylhexyl)-phthalate (DEHP), one of industrial plasticizers with endocrine-disrupting properties, positively contributes to high incidence of obesity. However, potential pathogenesis of dietary DEHP exposure-induced obesity remains largely unknown.

METHODS: Chronic DEHP exposure at different doses (0.05 and 5 mg/kg body weight) to mice had been continuously lasted for 14 weeks through the diet. A combination of targeted quantitative metabolomics (LC/GC-MS) with global [1]H NMR-based metabolic profiling to explore the effects of dietary DEHP exposure with different doses on host lipid metabolism of mice. Metagenomics (16S rRNA gene sequencing) was also employed to examine the alterations of gut microbiota composition in the cecal contents of mice after dietary DEHP exposure.

RESULTS: Dietary exposure to DEHP at both doses induced weight gain and hepatic lipogenesis of mice by promoting the uptake of fatty acids and disrupting phospholipids and choline metabolism. Dietary DEHP exposure altered the gut microbiota community with disruption of intestinal morphology and reduction of Firmicutes to Bacteroidetes ratio in the cecal contents of mice. Furthermore, DEHP exposure activated gut microbiota fermentation process producing excess short chain fatty acids of mice.

CONCLUSION: These findings provide systematic evidence that long-term chronic DEHP exposure induces obesity through disruption of host lipid metabolism and gut microbiota in mice, which not only confirm the epidemiological results, but also expand our understanding of metabolic diseases caused by environmental pollutants exposure.}, } @article {pmid34599245, year = {2021}, author = {Ikegami, H and Noguchi, S and Fukuda, K and Akata, K and Yamasaki, K and Kawanami, T and Mukae, H and Yatera, K}, title = {Refinement of microbiota analysis of specimens from patients with respiratory infections using next-generation sequencing.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {19534}, pmid = {34599245}, issn = {2045-2322}, mesh = {Aged ; Aged, 80 and over ; Disease Susceptibility ; Female ; Gene Library ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Respiratory Mucosa/*microbiology ; Respiratory Tract Infections/diagnosis/*etiology ; Retrospective Studies ; }, abstract = {Next-generation sequencing (NGS) technologies have been applied in bacterial flora analysis. However, there is no standardized protocol, and the optimal clustering threshold for estimating bacterial species in respiratory infection specimens is unknown. This study was conducted to investigate the optimal threshold for clustering 16S ribosomal RNA gene sequences into operational taxonomic units (OTUs) by comparing the results of NGS technology with those of the Sanger method, which has a higher accuracy of sequence per single read than NGS technology. This study included 45 patients with pneumonia with aspiration risks and 35 patients with lung abscess. Compared to Sanger method, the concordance rates of NGS technology (clustered at 100%, 99%, and 97% homology) with the predominant phylotype were 78.8%, 71.3%, and 65.0%, respectively. With respect to the specimens dominated by the Streptococcus mitis group, containing several important causative agents of pneumonia, Bray Curtis dissimilarity revealed that the OTUs obtained at 100% clustering threshold (versus those obtained at 99% and 97% thresholds; medians of 0.35, 0.69, and 0.71, respectively) were more similar to those obtained by the Sanger method, with statistical significance (p < 0.05). Clustering with 100% sequence identity is necessary when analyzing the microbiota of respiratory infections using NGS technology.}, } @article {pmid34593634, year = {2021}, author = {López-Pérez, M and Jayakumar, JM and Grant, TA and Zaragoza-Solas, A and Cabello-Yeves, PJ and Almagro-Moreno, S}, title = {Ecological diversification reveals routes of pathogen emergence in endemic Vibrio vulnificus populations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {40}, pages = {}, pmid = {34593634}, issn = {1091-6490}, mesh = {Animals ; Biodiversity ; Ecosystem ; Endemic Diseases ; Florida ; Genetic Markers/genetics ; Humans ; Ostreidae/microbiology ; Phenotype ; Phylogeny ; Vibrio Infections/*microbiology ; Vibrio vulnificus/*genetics/*pathogenicity ; Virulence/genetics ; }, abstract = {Pathogen emergence is a complex phenomenon that, despite its public health relevance, remains poorly understood. Vibrio vulnificus, an emergent human pathogen, can cause a deadly septicaemia with over 50% mortality rate. To date, the ecological drivers that lead to the emergence of clinical strains and the unique genetic traits that allow these clones to colonize the human host remain mostly unknown. We recently surveyed a large estuary in eastern Florida, where outbreaks of the disease frequently occur, and found endemic populations of the bacterium. We established two sampling sites and observed strong correlations between location and pathogenic potential. One site is significantly enriched with strains that belong to one phylogenomic cluster (C1) in which the majority of clinical strains belong. Interestingly, strains isolated from this site exhibit phenotypic traits associated with clinical outcomes, whereas strains from the second site belong to a cluster that rarely causes disease in humans (C2). Analyses of C1 genomes indicate unique genetic markers in the form of clinical-associated alleles with a potential role in virulence. Finally, metagenomic and physicochemical analyses of the sampling sites indicate that this marked cluster distribution and genetic traits are strongly associated with distinct biotic and abiotic factors (e.g., salinity, nutrients, or biodiversity), revealing how ecosystems generate selective pressures that facilitate the emergence of specific strains with pathogenic potential in a population. This knowledge can be applied to assess the risk of pathogen emergence from environmental sources and integrated toward the development of novel strategies for the prevention of future outbreaks.}, } @article {pmid34593230, year = {2021}, author = {Biçer, Y and Telli, AE and Sönmez, G and Telli, N and Uçar, G}, title = {Comparison of microbiota and volatile organic compounds in milk from different sheep breeds.}, journal = {Journal of dairy science}, volume = {104}, number = {12}, pages = {12303-12311}, doi = {10.3168/jds.2021-20911}, pmid = {34593230}, issn = {1525-3198}, mesh = {Animals ; *Microbiota ; Milk/chemistry ; RNA, Ribosomal, 16S/genetics ; Sheep ; Sheep, Domestic ; *Volatile Organic Compounds/analysis ; }, abstract = {In this study, we compared the microbiota and volatile organic compounds (VOC) present in the milk obtained from 3 different sheep breeds, namely Merino, Lacaune, and Assaf. Udder milk was collected from 21 animals, 7 from each breed. Bacterial microflora was determined metagenomically by extracting the DNA from the milk and analyzing the V3-V4 region of the 16S rRNA gene. Headspace solid-phase microextraction gas chromatography-mass spectrometry method was used to analyze VOC. The metagenomic analysis revealed (for Merino, Lacaune, and Assaf milk, respectively) Firmicutes (66.32, 69.36, and 57.08%), Actinobacteria (19.09, 7.67, and 19.40%), Proteobacteria (13.76, 21.06, and 22.19%), and Bacteroidetes (0.84, 1.91, and 1.33%) phyla in the milk samples. Lactobacillus was highly abundant in the milk of 3 breeds (29.64, 43.50, and 18.70%). The genera constituting more than 2% of all bacteria in all groups were Jeotgalicoccus (7.19, 5.34, and 10.77%), Enterococcus (5.18, 9.78, and 3.64%), and Corynebacterium (4.08, 3.00, and 13.44%). A total of 32 different VOC were identified by headspace solid-phase microextration analysis with 9, 30, and 24 different compounds from Merino, Lacaune, and Assaf breeds, respectively. Although ketone was the most abundant compound in Merino milk (71.84%), hydrocarbons were the most detected in Lacaune and Assaf milk (37.18% and 55.42%, respectively). A positive correlation was found between acetone, which was detected at the highest level in all groups, with Salinicoccus, Alloiococcus, Psychrobacter, and Dietzia. In addition, a negative correlation was found between the Lactobacillus genus, detected at the highest level in all groups, with methyl cyclopentane, 3-methylheptane, octane, decane, 3,3-dimethyloctane, and dodecane. Thus, differences were observed in the bacterial microflora and VOC in the sheep milk from different breeds under different feeding and breeding conditions.}, } @article {pmid34592929, year = {2021}, author = {Shao, L and Liao, J and Qian, J and Chen, W and Fan, X}, title = {MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {263}, pmid = {34592929}, issn = {1471-2180}, mesh = {*Databases, Genetic ; Feces/*microbiology ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*instrumentation ; }, abstract = {BACKGROUND: Microbiome big data from population-scale cohorts holds the key to unleash the power of microbiomes to overcome critical challenges in disease control, treatment and precision medicine. However, variations introduced during data generation and processing limit the comparisons among independent studies in respect of interpretability. Although multiple databases have been constructed as platforms for data reuse, they are of limited value since only raw sequencing files are considered.

DESCRIPTION: Here, we present MetaGeneBank, a standardized database that provides details on sample collection and sequencing, and abundances of genes, microbiota and molecular functions for 4470 raw sequencing files (over 12 TB) collected from 16 studies covering over 10 types of diseases and 14 countries using a unified data-processing pipeline. The incorporation of tools that enable browsing and searching with descriptive attributes, gene sequences, microbiota and functions makes the database user-friendly. We found that the source of specimen contributes more than sequencing centers or platforms to the variations of microbiota. Special attention should be paid when re-analyzing sequencing files from different countries.

CONCLUSIONS: Collectively, MetaGeneBank provides a gateway to utilize the untapped potential of gut metagenomic data in helping fighting against human diseases. With the continuous updating of the database in terms of data volume, data types and sample types, MetaGeneBank would undoubtedly be the benchmarking database in the future in respect of data reuse, and would be valuable in translational science.}, } @article {pmid34592621, year = {2021}, author = {Luo, J and Zhang, L and Du, W and Cheng, X and Fang, F and Cao, J and Wu, Y and Su, Y}, title = {Metagenomic approach reveals the fates and mechanisms of antibiotic resistance genes exposed to allicins during waste activated sludge fermentation: Insight of the microbial community, cellular status and gene regulation.}, journal = {Bioresource technology}, volume = {342}, number = {}, pages = {125998}, doi = {10.1016/j.biortech.2021.125998}, pmid = {34592621}, issn = {1873-2976}, mesh = {Anti-Bacterial Agents/pharmacology ; Disulfides ; Drug Resistance, Bacterial ; Fermentation ; Genes, Bacterial/genetics ; *Microbiota ; *Sewage ; Sulfinic Acids ; Wastewater ; }, abstract = {This work revealed the impacts of exogeneous allicins on the antibiotic resistance genes (ARGs) variations during waste activated sludge (WAS) fermentation process. The overall abundance of ARGs was respectively reduced by 4.84 and 9.42% in presence of 0.01 and 0.05 g allicin/g TSS. Allicins disrupted the EPS structure and increased the permeability of cell membranes, which resulted in the release of ARGs for subsequent removal. Allicins also reduced intracellular ATP levels, which was disadvantageous to ARGs dissemination. Besides, allicins affected the microbial community and decreased the abundance of potential hosts based on bacterial taxa-ARGs network analysis. Moreover, the metabolic pathways and genetic expressions (i.e., two-component system, quorum sensing, and SOS response) involved in ARGs propagation were down-regulated, which caused the ARGs alleviation in allicins-stressed reactors. Overall, the simultaneous responses of cellular status, bacterial host, and genetic regulation accounted for the effective ARGs reduction induced by allicins during WAS fermentation.}, } @article {pmid34589441, year = {2021}, author = {Ding, L and Liu, Y and Wu, X and Wu, M and Luo, X and Ouyang, H and Xia, J and Liu, X and Ding, T}, title = {Pathogen Metagenomics Reveals Distinct Lung Microbiota Signatures Between Bacteriologically Confirmed and Negative Tuberculosis Patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {708827}, pmid = {34589441}, issn = {2235-2988}, mesh = {Ascomycota ; Bronchoalveolar Lavage Fluid ; Haemophilus parainfluenzae ; Humans ; Kluyveromyces ; Lung ; Metagenomics ; *Microbiota ; *Mycobacterium tuberculosis/genetics ; Staphylococcus aureus ; *Tuberculosis/microbiology ; }, abstract = {Understanding the dynamics of lung microbiota in tuberculosis patients, especially those who cannot be confirmed bacteriologically in clinical practice, is imperative for accurate diagnosis and effective treatment. This study aims to characterize the distinct lung microbial features between bacteriologically confirmed and negative tuberculosis patients to understand the influence of microbiota on tuberculosis patients. We collected specimens of bronchoalveolar lavage fluid from 123 tuberculosis patients. Samples were subjected to metagenomic next-generation sequencing to reveal the lung microbial signatures. By combining conventional bacterial detection and metagenomic sequencing, 101/123 (82%) tuberculosis patients were bacteriologically confirmed. In addition to Mycobacterium tuberculosis, Staphylococcus aureus, Kluyveromyces lactis, and Pyricularia pennisetigena were also enriched in the bacteriological confirmation group. In contrast, Haemophilus parainfluenzae was enriched in the bacteriologically negative group. Besides, microbial interaction exhibits a different state between bacteriologically confirmed and negative tuberculosis patients. Mycobacterium tuberculosis was confirmed correlated with clinical characteristics such as albumin and chest cavities. Our study comprehensively demonstrates the correlation between unique features of lung microbial dynamics and the clinical characteristics of tuberculosis patients, suggesting the importance of studying the pulmonary microbiome in tuberculosis disease and providing new insights for future precision diagnosis and treatment.}, } @article {pmid34586901, year = {2021}, author = {Fernandes-Martins, MC and Keller, LM and Munro-Ehrlich, M and Zimlich, KR and Mettler, MK and England, AM and Clare, R and Surya, K and Shock, EL and Colman, DR and Boyd, ES}, title = {Ecological Dichotomies Arise in Microbial Communities Due to Mixing of Deep Hydrothermal Waters and Atmospheric Gas in a Circumneutral Hot Spring.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {23}, pages = {e0159821}, pmid = {34586901}, issn = {1098-5336}, support = {CSP 504081//Department of Energy/ ; EAR-1820658//National Science Foundation (NSF)/ ; }, mesh = {*Atmosphere ; Carbon ; *Hot Springs/microbiology ; Metagenomics ; *Microbiota ; Oxygen ; Wyoming ; }, abstract = {Little is known of how the confluence of subsurface and surface processes influences the assembly and habitability of hydrothermal ecosystems. To address this knowledge gap, the geochemical and microbial composition of a high-temperature, circumneutral hot spring in Yellowstone National Park was examined to identify the sources of solutes and their effect on the ecology of microbial inhabitants. Metagenomic analysis showed that populations comprising planktonic and sediment communities are archaeal dominated, are dependent on chemical energy (chemosynthetic), share little overlap in their taxonomic composition, and are differentiated by their inferred use of/tolerance to oxygen and mode of carbon metabolism. The planktonic community is dominated by putative aerobic/aerotolerant autotrophs, while the taxonomic composition of the sediment community is more evenly distributed and comprised of anaerobic heterotrophs. These observations are interpreted to reflect sourcing of the spring by anoxic, organic carbon-limited subsurface hydrothermal fluids and ingassing of atmospheric oxygen that selects for aerobic/aerotolerant organisms that have autotrophic capabilities in the water column. Autotrophy and consumption of oxygen by the planktonic community may influence the assembly of the anaerobic and heterotrophic sediment community. Support for this inference comes from higher estimated rates of genome replication in planktonic populations than sediment populations, indicating faster growth in planktonic populations. Collectively, these observations provide new insight into how mixing of subsurface waters and atmospheric oxygen create dichotomy in the ecology of hot spring communities and suggest that planktonic and sediment communities may have been less differentiated taxonomically and functionally prior to the rise of oxygen at ∼2.4 billion years ago (Gya). IMPORTANCE Understanding the source and availability of energy capable of supporting life in hydrothermal environments is central to predicting the ecology of microbial life on early Earth when volcanic activity was more widespread. Little is known of the substrates supporting microbial life in circumneutral to alkaline springs, despite their relevance to early Earth habitats. Using metagenomic and informatics approaches, water column and sediment habitats in a representative circumneutral hot spring in Yellowstone were shown to be dichotomous, with the former largely hosting aerobic/aerotolerant autotrophs and the latter primarily hosting anaerobic heterotrophs. This dichotomy is attributed to influx of atmospheric oxygen into anoxic deep hydrothermal spring waters. These results indicate that the ecology of microorganisms in circumneutral alkaline springs sourced by deep hydrothermal fluids was different prior to the rise of atmospheric oxygen ∼2.4 Gya, with planktonic and sediment communities likely to be less differentiated than contemporary circumneutral hot springs.}, } @article {pmid34586473, year = {2022}, author = {Méndez-Salazar, EO and Martínez-Nava, GA}, title = {Uric acid extrarenal excretion: the gut microbiome as an evident yet understated factor in gout development.}, journal = {Rheumatology international}, volume = {42}, number = {3}, pages = {403-412}, pmid = {34586473}, issn = {1437-160X}, mesh = {*Gastrointestinal Microbiome ; Gout/etiology/*metabolism ; Humans ; Risk Factors ; Uric Acid/*metabolism ; }, abstract = {Humans do not produce uricase, an enzyme responsible for degrading uric acid. However, some bacteria residing in the gut can degrade one-third of the dietary and endogenous uric acid generated daily. New insights based on metagenomic and metabolomic approaches provide a new interest in exploring the involvement of gut microbiota in gout. Nevertheless, the exact mechanisms underlying this association are complex and have not been widely discussed. In this study, we aimed to review the evidence that suggests uric acid extrarenal excretion and gut microbiome are potential risk factors for developing gout. A literature search was performed in PubMed, Web of Science, and Google Scholar using several keywords, including "gut microbiome AND gout". A remarkable intestinal dysbiosis and shifts in abundance of certain bacterial taxa in gout patients have been consistently reported among different studies. Under this condition, bacteria might have developed adaptive mechanisms for de novo biosynthesis and salvage of purines, and thus, a concomitant alteration in uric acid metabolism. Moreover, gut microbiota can produce substrates that might cross the portal vein so the liver can generate de novo purinogenic amino acids, as well as uric acid. Therefore, the extrarenal excretion of uric acid needs to be considered as a factor in gout development. Nevertheless, further studies are needed to fully understand the role of gut microbiome in uric acid production and its extrarenal excretion, and to point out possible bacteria or bacterial enzymes that could be used as probiotic coadjutant treatment in gout patients.}, } @article {pmid34586399, year = {2021}, author = {Kiguchi, Y and Nishijima, S and Kumar, N and Hattori, M and Suda, W}, title = {Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {28}, number = {6}, pages = {}, pmid = {34586399}, issn = {1756-1663}, support = {19gm0010003h0204//Leading Advanced Projects for Medical Innovation (LEAP)/ ; }, mesh = {Algorithms ; Biomass ; Chimera ; DNA ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; Sequence Analysis, DNA ; *Virome ; }, abstract = {The human gut bacteriophage community (phageome) plays an important role in the host's health and disease; however, the entire structure is poorly understood, partly owing to the generation of many incomplete genomes in conventional short-read metagenomics. Here, we show long-read metagenomics of amplified DNA of low-biomass phageomes with multiple displacement amplification (MDA), involving the development of a novel bioinformatics tool, split amplified chimeric read algorithm (SACRA), that efficiently pre-processed numerous chimeric reads generated through MDA. Using five samples, SACRA markedly reduced the average chimera ratio from 72% to 1.5% in PacBio reads with an average length of 1.8 kb. De novo assembly of chimera-less PacBio long reads reconstructed contigs of ≥5 kb with an average proportion of 27%, which was 1% in contigs from MiSeq short reads, thereby dramatically improving contig length and genome completeness. Comparison of PacBio and MiSeq contigs found MiSeq contig fragmentations frequently near local repeats and hypervariable regions in the phage genomes, and those caused by multiple homologous phage genomes coexisting in the community. We also developed a reference-independent method to assess the completeness of the linear phage genomes. Overall, we established a SACRA-coupled long-read metagenomics robust to highly diverse gut phageomes, identifying high-quality circular and linear phage genomes with adequate sequence quantity.}, } @article {pmid34585986, year = {2021}, author = {Matthews, MK and Malcolm, J and Chaston, JM}, title = {Microbiota Influences Fitness and Timing of Reproduction in the Fruit Fly Drosophila melanogaster.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0003421}, pmid = {34585986}, issn = {2165-0497}, support = {R15 GM140388/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification/genetics ; Drosophila melanogaster/*growth & development/*microbiology ; Fertility/physiology ; Genetic Fitness/*physiology ; Longevity/physiology ; Metagenome/genetics ; Microbiota/*genetics ; Reproduction/physiology ; }, abstract = {Associated microorganisms ("microbiota") play a central role in determining many animals' survival and reproduction characteristics. The impact of these microbial influences on an animal's fitness, or population growth, in a given environment has not been defined as clearly. We focused on microbiota-dependent host fitness by measuring life span and fecundity in Drosophila melanogaster fruit flies reared individually with 14 different bacterial species. Consistent with previous observations, the different bacteria significantly influenced the timing of fly life span and fecundity. Using Leslie matrices, we show that fly fitness was lowest when the microbes caused the flies to invest in life span over fecundity. Computational permutations showed that the positive fitness effect of investing in reproduction was reversed if fly survival over time was low, indicating that the observed fitness influences of the microbes could be context dependent. Finally, we showed that fly fitness is not influenced by bacterial genes that shape fly life span or fly triglyceride content, a trait that is related to fly survival and reproduction. Also, metagenome-wide association did not identify any microbial genes that were associated with variation in fly fitness. Therefore, the bacterial genetic basis for influencing fly fitness remains unknown. We conclude that bacteria influence a fly's reproductive timing more than total reproductive output and that (e.g., environmental) conditions that influence fly survival likely determine which bacteria benefit fly fitness. IMPORTANCE The ability of associated microorganisms ("microbiota") to influence animal life history traits has been recognized and investigated, especially in the past 2 decades. For many microbial communities, there is not always a clear definition of whether the microbiota or its members are beneficial, pathogenic, or relatively neutral to their hosts' fitness. In this study, we report the influence of individual members of the microbiota on Drosophila melanogaster fitness using Leslie matrices that combine the microbial influences on fly survival and reproduction into a single fitness measure. Our results are consistent with a previous report that, in the laboratory, acetic acid bacteria are more beneficial to the flies than many strains of lactic acid bacteria. We add to the previous finding by showing that this benefit depends on fly survival rate. Together, our work helps to show how the microbiota of a fly influences its laboratory fitness and how these effects may translate to a wild setting.}, } @article {pmid34585290, year = {2022}, author = {Kaushal, M and Kolombia, Y and Alakonya, AE and Kuate, AF and Ortega-Beltran, A and Amah, D and Masso, C}, title = {Subterranean Microbiome Affiliations of Plantain (Musa spp.) Under Diverse Agroecologies of Western and Central Africa.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {580-593}, pmid = {34585290}, issn = {1432-184X}, support = {HRST/ST/AURG-II/CALL2/2018//African Union/ ; }, mesh = {Africa, Central ; *Ascomycota/genetics ; Bacteria/genetics ; *Microbiota/physiology ; *Musa/microbiology ; Plant Roots/microbiology ; *Plantago ; Rhizosphere ; Soil Microbiology ; }, abstract = {Plantain (Musa spp.) is a staple food crop and an important source of income for millions of smallholder farmers in sub-Saharan Africa (SSA). However, there is a paucity of knowledge on soil microbial diversity in agroecologies where plantains are grown. Microbial diversity that increases plant performance with multi-trophic interactions involving resiliency to environmental constraints is greatly needed. For this purpose, the bacterial and fungal communities of plantain fields in high rainfall forests (HR) and derived savannas (SV) were studied using Illumina MiSeq for 16S rDNA and ITS amplicon deep sequencing. Microbial richness (α- and β-diversity), operational taxonomic units, and Simpson and Shannon-Wiener indexes (observed species (Sobs), Chao, ACE; P < 0.05) suggested that there were significant differences between HR and SV agroecologies among the most abundant bacterial communities, and some specific dynamic response observed from fungal communities. Proteobacteria formed the predominant bacterial phylum (43.7%) succeeded by Firmicutes (24.7%), and Bacteroidetes (17.6%). Ascomycota, Basidiomycota, and Zygomycota were the three most dominant fungal phyla in both agroecologies. The results also revealed an immense array of beneficial microbes in the roots and rhizosphere of plantain, including Acinetobacter, Bacillus, and Pseudomonas spp. COG and KEGG Orthology database depicted significant variations in the functional attributes of microbes found in the rhizosphere to roots. This result indicates that the different agroecologies and host habitats differentially support the dynamic microbial profile and that helps in altering the structure in the rhizosphere zone for the sake of promoting synergistic host-microbe interactions particularly under resource-poor conditions of SSA.}, } @article {pmid34584255, year = {2021}, author = {Hindson, J}, title = {Mapping the human gut.}, journal = {Nature reviews. Gastroenterology & hepatology}, volume = {18}, number = {11}, pages = {747}, pmid = {34584255}, issn = {1759-5053}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Metagenome ; }, } @article {pmid34584214, year = {2022}, author = {Chen, YJ and Leung, PM and Cook, PLM and Wong, WW and Hutchinson, T and Eate, V and Kessler, AJ and Greening, C}, title = {Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments.}, journal = {The ISME journal}, volume = {16}, number = {3}, pages = {750-763}, pmid = {34584214}, issn = {1751-7370}, mesh = {*Archaea/classification/genetics/isolation & purification/physiology ; *Bacteria/classification/genetics/isolation & purification ; Bacterial Physiological Phenomena ; *Geologic Sediments/microbiology ; Hydrodynamics ; *Microbiota ; }, abstract = {The microbial community composition and biogeochemical dynamics of coastal permeable (sand) sediments differs from cohesive (mud) sediments. Tide- and wave-driven hydrodynamic disturbance causes spatiotemporal variations in oxygen levels, which select for microbial generalists and disrupt redox cascades. In this work, we profiled microbial communities and biogeochemical dynamics in sediment profiles from three sites varying in their exposure to hydrodynamic disturbance. Strong variations in sediment geochemistry, biogeochemical activities, and microbial abundance, composition, and capabilities were observed between the sites. Most of these variations, except for microbial abundance and diversity, significantly correlated with the relative disturbance level of each sample. In line with previous findings, metabolically flexible habitat generalists (e.g., Flavobacteriaceae, Woeseaiceae, Rhodobacteraceae) dominated in all samples. However, we present evidence that aerobic specialists such as ammonia-oxidizing archaea (Nitrosopumilaceae) were more abundant and active in more disturbed samples, whereas bacteria capable of sulfate reduction (e.g., uncultured Desulfobacterales), dissimilatory nitrate reduction to ammonium (DNRA; e.g., Ignavibacteriaceae), and sulfide-dependent chemolithoautotrophy (e.g., Sulfurovaceae) were enriched and active in less disturbed samples. These findings are supported by insights from nine deeply sequenced metagenomes and 169 derived metagenome-assembled genomes. Altogether, these findings suggest that hydrodynamic disturbance is a critical factor controlling microbial community assembly and biogeochemical processes in coastal sediments. Moreover, they strengthen our understanding of the relationships between microbial composition and biogeochemical processes in these unique environments.}, } @article {pmid34584040, year = {2021}, author = {Yoon, Y and Seo, H and Kim, S and Lee, Y and Rahim, MA and Lee, S and Song, HY}, title = {Anti-Tuberculosis Activity of Pediococcus acidilactici Isolated from Young Radish Kimchi against Mycobacterium tuberculosis.}, journal = {Journal of microbiology and biotechnology}, volume = {31}, number = {12}, pages = {1632-1642}, pmid = {34584040}, issn = {1738-8872}, mesh = {Animals ; Antitubercular Agents/administration & dosage/pharmacology ; Culture Media, Conditioned/pharmacology ; Drug Resistance, Multiple/drug effects ; Fermented Foods/*microbiology ; Macrophages/metabolism/microbiology ; Mice ; Microbiota ; Mycobacterium tuberculosis/*drug effects/growth & development ; Nitric Oxide/metabolism ; Pediococcus acidilactici/isolation & purification/*physiology ; Probiotics/administration & dosage/pharmacology ; RAW 264.7 Cells ; RNA, Ribosomal, 16S/genetics ; Raphanus/*microbiology ; }, abstract = {Tuberculosis is a highly contagious disease caused by Mycobacterium tuberculosis. It affects about 10 million people each year and is still one of the leading causes of death worldwide. About 2 to 3 billion people (equivalent to 1 in 3 people in the world) are infected with latent tuberculosis. Moreover, as the number of multidrug-resistant, extensively drug-resistant, and totally drug-resistant strains of M. tuberculosis continues to increase, there is an urgent need to develop new anti-tuberculosis drugs that are different from existing drugs to combat antibiotic-resistant M. tuberculosis. Against this background, we aimed to develop new anti-tuberculosis drugs using probiotics. Here, we report the anti-tuberculosis effect of Pediococcus acidilactici PMC202 isolated from young radish kimchi, a traditional Korean fermented food. Under coculture conditions, PMC202 inhibited the growth of M. tuberculosis. In addition, PMC202 inhibited the growth of drug-sensitive and -resistant M. tuberculosis- infected macrophages at a concentration that did not show cytotoxicity and showed a synergistic effect with isoniazid. In a 2-week, repeated oral administration toxicity study using mice, PMC202 did not cause weight change or specific clinical symptoms. Furthermore, the results of 16S rRNA-based metagenomics analysis confirmed that dysbiosis was not induced in bronchoalveolar lavage fluid after oral administration of PMC202. The anti-tuberculosis effect of PMC202 was found to be related to the reduction of nitric oxide. Our findings indicate that PMC202 could be used as an anti-tuberculosis drug candidate with the potential to replace current chemicalbased drugs. However, more extensive toxicity, mechanism of action, and animal efficacy studies with clinical trials are needed.}, } @article {pmid34583815, year = {2021}, author = {Vad, J and Barnhill, KA and Kazanidis, G and Roberts, JM}, title = {Human impacts on deep-sea sponge grounds: Applying environmental omics to monitoring.}, journal = {Advances in marine biology}, volume = {89}, number = {}, pages = {53-78}, doi = {10.1016/bs.amb.2021.08.004}, pmid = {34583815}, issn = {2162-5875}, mesh = {Animals ; Biodiversity ; *Ecosystem ; Environmental Monitoring ; Human Activities ; Humans ; *Porifera ; Seawater ; }, abstract = {Sponges (Phylum Porifera) are the oldest extant Metazoans. In the deep sea, sponges can occur at high densities forming habitats known as sponge grounds. Sponge grounds can extend over large areas of up to hundreds of km[2] and are biodiversity hotspots. However, as human activities, including deep-water hydrocarbon extraction, continue to expand into areas harbouring sponge grounds, understanding how anthropogenic impacts affect sponges and the ecosystem services they provide at multiple biological scales (community, individual and (sub)cellular levels) is key for achieving sustainable management. This chapter (1) provides an update to the chapter of Advances in Marine Biology Volume 79 entitled "Potential Impacts of Offshore Oil and Gas Activities on Deep-Sea Sponges and the Habitats They Form" and (2) discusses the use of omics as a future tool for deep-sea ecosystem monitoring. While metagenomics and (meta)transcriptomics studies have contributed to improve our understanding of sponge biology in recent years, metabolomics analysis has mostly been used to identify natural products. The sponge metabolome, therefore, remains vastly unknown despite the fact that the metabolome is a key link between the genotype and phenotype, giving us a unique new insight to how key components of an ecosystem are functioning. As the fraction of the metabolome released into the seawater, the sponge exometabolome has only just started to be characterised in comparative environmental metabolomic studies. Yet, the sponge exometabolome constitute a unique opportunity for the identification of biomarkers of sponge health as compounds can be measured in seawater, bypassing the need for physical samples which can still be difficult to collect in the deep sea. Within sponge grounds, the characterisation of a shared sponge exometabolome could lead to the identification of biomarkers of ecosystem functioning and overall health. Challenges remain in establishing omics approaches in environmental monitoring but constant technological advances and reduction in costs means these techniques will become widely available in the future.}, } @article {pmid34582967, year = {2022}, author = {Ferrier, L and Eutamène, H and Siegwald, L and Marquard, AM and Tondereau, V and Chevalier, J and Jacot, GE and Favre, L and Theodorou, V and Vicario, M and Rytz, A and Bergonzelli, G and Garcia-Rodenas, CL}, title = {Human milk oligosaccharides alleviate stress-induced visceral hypersensitivity and associated microbiota dysbiosis.}, journal = {The Journal of nutritional biochemistry}, volume = {99}, number = {}, pages = {108865}, doi = {10.1016/j.jnutbio.2021.108865}, pmid = {34582967}, issn = {1873-4847}, mesh = {Abdominal Pain/*diet therapy/metabolism/microbiology/psychology ; Animals ; Bacteria/classification/genetics/isolation & purification/metabolism ; Dysbiosis/*diet therapy/metabolism/microbiology/psychology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Milk, Human/*metabolism ; Oligosaccharides/analysis/*metabolism ; Stress, Psychological ; }, abstract = {Pain-related functional gastrointestinal disorders (FGIDs) are characterized by visceral hypersensitivity (VHS) associated with alterations in the microbiota-gut-brain axis. Since human milk oligosaccharides (HMOs) modulate microbiota, gut and brain, we investigated whether HMOs impact VHS, and explored the role of gut microbiota. To induce VHS, C57BL/6JRj mice received hourly water avoidance stress (WAS) sessions for 10 d, or antibiotics (ATB) for 12 d. Challenged and unchallenged (Sham) animals were fed AIN93M diet (Cont) or AIN93M containing 1% of a 6-HMO mix (HMO6). VHS was assessed by monitoring the visceromotor response to colorectal distension. Fecal microbiome was analyzed by shotgun metagenomics. The effect of HMO6 sub-blends on VHS and nociceptive pathways was further tested using the WAS model. In mice fed Cont, WAS and ATB increased the visceromotor response to distension. HMO6 decreased WAS-mediated electromyographic rise at most distension volumes and overall Area Under Curve (AUC=6.12±0.50 in WAS/HMO6 vs. 9.46±0.50 in WAS/Cont; P<.0001). In contrast, VHS in ATB animals was not improved by HMO6. In WAS, HMO6 promoted most microbiota taxa and several functional pathways associated with low VHS and decreased those associated with high VHS. Among the sub-blends, 2'FL+DFL and LNT+6'SL reduced visceromotor response close to Sham/Cont values and modulated serotoninergic and CGRPα-related pathways. This research further substantiates the capacity of HMOs to modulate the microbiota-gut-brain communication and identifies mitigation of abdominal pain as a new HMO benefit. Ultimately, our findings suggest the value of specific HMO blends to alleviate pain associated FGIDs such as infantile colic or Irritable Bowel Syndrome.}, } @article {pmid34581614, year = {2023}, author = {Dutta, S and Das, B and Ghosh, TS and Kumar, S and Kaushal, RK and Ray, P and Suri, V and Nair, GB}, title = {Human Milk Microbiome of Healthy Indian Mothers is Dominated by Genus Pseudomonas.}, journal = {Journal of human lactation : official journal of International Lactation Consultant Association}, volume = {39}, number = {2}, pages = {343-352}, doi = {10.1177/08903344211048415}, pmid = {34581614}, issn = {1552-5732}, mesh = {Infant ; Infant, Newborn ; Female ; Humans ; Adult ; *Milk, Human/microbiology ; Lactation ; Breast Feeding ; Mothers ; *Microbiota ; }, abstract = {BACKGROUND: The composition of the human milk microbiome is highly variable and multifactorial. Milk microbiota from various countries show striking differences. There is a paucity of data from healthy lactating Indian mothers.

RESEARCH AIM: To describe the milk microbiota of healthy North Indian women, using a culture-independent, targeted metagenomic approach.

METHODS: We recruited exclusively breastfeeding mothers (N = 22) who had vaginally delivered full-term singleton infants in a tertiary care hospital less than 1 week previously and had not recently consumed systemic antibiotics. Milk samples (5 ml) were collected aseptically, and microbial deoxyribonucleic acid was extracted. Microbial composition and diversity were determined using a 454-pyrosequencing platform. Core genera were identified, and their relative abundances ranked. Heatmaps showing the variation of the ranked abundances and Shannon index were obtained using R.

RESULTS: Participants (all exclusively vegetarian) had a mean (SD) age of 27.2 (3.4) years, postnatal age of 3.9 (1.6) days and gestation 38 (1.2) weeks. The dominant phylum was Proteobacterium (relative abundance 84%) and dominant genus Pseudomonas (relative abundance 61.78%). Eleven species of Pseudomonas were identified, all generally considered nonpathogenic. Based on abundance patterns of the core genera, the milk samples could be grouped: (a) dominated by Pseudomonas with low diversity; (b) less Pseudomonas and high diversity; and (c) dominated by Pseudomonas but high diversity. All neonates were healthy and gaining weight well at 1 month of age.

CONCLUSIONS: Healthy, lactating, vegetarian, North Indian women who deliver at term gestation and have no recent exposure to antibiotics, have a unique milk microbiome dominated by Pseudomonas.}, } @article {pmid34581139, year = {2021}, author = {Lü, XL and Zhao, YP and Lin, QH and Peng, XL and Yin, YF and Jiang, XJ}, title = {[Analysis of the Traits of Nitrogen Metabolism Pathways for Several Forest Soils in Eastern China].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {42}, number = {10}, pages = {4951-4958}, doi = {10.13227/j.hjkx.202101250}, pmid = {34581139}, issn = {0250-3301}, mesh = {Archaea ; China ; Forests ; *Microbiota/genetics ; Nitrification ; Nitrogen ; Oxidation-Reduction ; *Soil ; Soil Microbiology ; }, abstract = {Nitrogen metabolism pathways mediated by microorganisms play an important role in maintaining the structure and functional stability of soil ecosystems. Clarifying the relationships between microbial communities and nitrogen metabolism pathways can expand our understanding of nitrogen metabolism pathways at a microscopic level. However, the horizontal gene transfer of microorganisms means that taxonomy-based methods cannot be easily applied. A growing number of studies have shown that functional traits affect community construction and ecosystem functions. Using methods based on functional traits to study soil microbial communities can, therefore, better characterize nitrogen metabolism pathways. Here, five typical forest soils in China, namely black soil(Harbin, Heilongjiang), dark-brown earth(Changbaishan, Jilin), yellow-brown earth(Wuhan, Hubei), red earth(Fuzhou, Fujian), and humid-thermo ferralitic soil(Ledong, Hainan), were selected to study the traits of nitrogen metabolism pathways using metagenomic technology combined with the trait-based methods. The studied nitrogen metabolism pathways were ammonia assimilation, nitrate dissimilatory reduction, nitrate assimilatory reduction, denitrification, nitrification, nitrogen fixation, and anaerobic ammonia oxidation. The results showed that bacteria dominated the metagenomic library, accounting for 98.02% of all the sequences. Across all domains, the most common pathway was ammonia assimilation. For example, an average of 2830 ammonia assimilation pathway genes were detected for every million annotated bacterial sequences. In comparison, nitrogen fixation and anaerobic ammonia oxidation were the least detected pathways, accounting for 28.3 and 10.7 per million sequences, respectively. Different microorganisms can participate in a same nitrogen metabolism pathway, and the community structure of different soils was variable. The five typical forest soils in China show the same microbial nitrogen metabolism pathway traits; however, the community structure of the microorganisms mediating these processes was found to vary.}, } @article {pmid34580777, year = {2021}, author = {Kunda, P and Mukherjee, A and Dhal, PK}, title = {Insights into endophytic bacterial diversity of rice grown across the different agro-ecological regions of West Bengal, India.}, journal = {World journal of microbiology & biotechnology}, volume = {37}, number = {11}, pages = {184}, pmid = {34580777}, issn = {1573-0972}, mesh = {Bacteria/*classification/genetics/*isolation & purification ; Biodiversity ; Endophytes/*classification/genetics/*isolation & purification ; India ; Metagenomics ; Microbiota ; Oryza/*microbiology ; *Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; Soil ; }, abstract = {Endophytes have recently garnered importance worldwide and multiple studies are being conducted to understand their important role and mechanism of interaction inside plants. But before we indulge in their functions it is necessary to dig into the microbiome. This will help to get a complete picture of the microbes intrinsic to their host and understand changes in community composition with respect to their habitats. To fulfil this requirement in our study we have attempted to dissect the endophytic diversity in roots of rice plant grown across the various agro-ecological zones of West Bengal by undergoing amplicon analysis of their 16S rRNA gene. Based on the measured environmental parameters agro-ecological zones can be divided into two groups: nutrient dense groups, representing zones like Gangetic, Northern hill and Terai-Teesta zone characterised by soil with higher levels of nitrogen (N) and total organic carbon and nutrient low groups representing Coastal saline, Red-laterite and Vindhyan zone mainly characterised by high electroconductivity and pH. Gammaproteobacteria, Alphaproteobacteria, Bacilli and Bacteroidetes were mostly abundant in nutrient dense sites whereas Clostridia and Planctomycetes were concentrated in nutrient low sites. Few genera (Aeromonas, Sulfurospirillum, Uliginosibacterium and Acidaminococcus) are present in samples cultivated in all the zones representing the core microbiome of rice in West Bengal, while some other genera like Lactococcus, Dickeya, Azonexus and Pectobacterium are unique to specific zone. Hence it can be concluded that this study has provided some insight in to the endophytic status of rice grown across the state of West Bengal.}, } @article {pmid34580445, year = {2021}, author = {Aggarwala, V and Mogno, I and Li, Z and Yang, C and Britton, GJ and Chen-Liaw, A and Mitcham, J and Bongers, G and Gevers, D and Clemente, JC and Colombel, JF and Grinspan, A and Faith, J}, title = {Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes.}, journal = {Nature microbiology}, volume = {6}, number = {10}, pages = {1309-1318}, pmid = {34580445}, issn = {2058-5276}, support = {R01 DK123749/DK/NIDDK NIH HHS/United States ; U24 CA224319/CA/NCI NIH HHS/United States ; U01 DK124165/DK/NIDDK NIH HHS/United States ; R01 DK112978/DK/NIDDK NIH HHS/United States ; R01 DK124133/DK/NIDDK NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/classification/genetics/*isolation & purification ; Benchmarking ; Clostridioides difficile/physiology ; Clostridium Infections/microbiology/therapy ; *Fecal Microbiota Transplantation/methods ; Feces/microbiology ; Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; Metagenome/genetics ; Recurrence ; Tissue Donors ; Treatment Outcome ; }, abstract = {Fecal microbiota transplantation (FMT) has been successfully applied to treat recurrent Clostridium difficile infection in humans, but a precise method to measure which bacterial strains stably engraft in recipients and evaluate their association with clinical outcomes is lacking. We assembled a collection of >1,000 different bacterial strains that were cultured from the fecal samples of 22 FMT donors and recipients. Using our strain collection combined with metagenomic sequencing data from the same samples, we developed a statistical approach named Strainer for the detection and tracking of bacterial strains from metagenomic sequencing data. We applied Strainer to evaluate a cohort of 13 FMT longitudinal clinical interventions and detected stable engraftment of 71% of donor microbiota strains in recipients up to 5 years post-FMT. We found that 80% of recipient gut bacterial strains pre-FMT were eliminated by FMT and that post-FMT the strains present persisted up to 5 years later, together with environmentally acquired strains. Quantification of donor bacterial strain engraftment in recipients independently explained (precision 100%, recall 95%) the clinical outcomes (relapse or success) after initial and repeat FMT. We report a compendium of bacterial species and strains that consistently engraft in recipients over time that could be used in defined live biotherapeutic products as an alternative to FMT. Our analytical framework and Strainer can be applied to systematically evaluate either FMT or defined live bacterial therapeutic studies by quantification of strain engraftment in recipients.}, } @article {pmid34579777, year = {2021}, author = {Pérez-Carrascal, OM and Tromas, N and Terrat, Y and Moreno, E and Giani, A and Corrêa Braga Marques, L and Fortin, N and Shapiro, BJ}, title = {Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {194}, pmid = {34579777}, issn = {2049-2618}, mesh = {*Cyanobacteria ; Lakes ; *Microbiota/genetics ; *Microcystis/genetics ; Phylogeny ; }, abstract = {BACKGROUND: Cyanobacteria from the genus Microcystis can form large mucilaginous colonies with attached heterotrophic bacteria-their microbiome. However, the nature of the relationship between Microcystis and its microbiome remains unclear. Is it a long-term, evolutionarily stable association? Which partners benefit? Here we report the genomic diversity of 109 individual Microcystis colonies-including cyanobacteria and associated bacterial genomes-isolated in situ and without culture from Lake Champlain, Canada and Pampulha Reservoir, Brazil.

RESULTS: We identified 14 distinct Microcystis genotypes from Canada, of which only two have been previously reported, and four genotypes specific to Brazil. Microcystis genetic diversity was much greater between than within colonies, consistent with colony growth by clonal expansion rather than aggregation of Microcystis cells. We also identified 72 bacterial species in the microbiome. Each Microcystis genotype had a distinct microbiome composition, and more closely related genotypes had more similar microbiomes. This pattern of phylosymbiosis could be explained by co-phylogeny in only two out of the nine most prevalent associated bacterial genera, Roseomonas and Rhodobacter. These phylogenetically associated genera could enrich the metabolic repertoire of Microcystis, for example by encoding the biosynthesis of complementary carotenoid molecules. In contrast, other colony-associated bacteria showed weaker signals of co-phylogeny, but stronger evidence of horizontal gene transfer with Microcystis. These observations suggest that acquired genes are more likely to be retained in both partners (Microcystis and members of its microbiome) when they are loosely associated, whereas one gene copy is sufficient when the association is physically tight and evolutionarily long-lasting.

CONCLUSIONS: We have introduced a method for culture-free isolation of single colonies from nature followed by metagenomic sequencing, which could be applied to other types of microbes. Together, our results expand the known genetic diversity of both Microcystis and its microbiome in natural settings, and support their long-term, specific, and potentially beneficial associations. Video Abstract.}, } @article {pmid34579474, year = {2021}, author = {Smulders, L and Benítez, E and Moreno, B and López-García, Á and Pozo, MJ and Ferrero, V and de la Peña, E and Alcalá Herrera, R}, title = {Tomato Domestication Affects Potential Functional Molecular Pathways of Root-Associated Soil Bacteria.}, journal = {Plants (Basel, Switzerland)}, volume = {10}, number = {9}, pages = {}, pmid = {34579474}, issn = {2223-7747}, support = {765290//Horizon 2020 Framework Programme/ ; }, abstract = {While it has been well evidenced that plant domestication affects the structure of the root-associated microbiome, there is a poor understanding of how domestication-mediated differences between rhizosphere microorganisms functionally affect microbial ecosystem services. In this study, we explore how domestication influenced functional assembly patterns of bacterial communities in the root-associated soil of 27 tomato accessions through a transect of evolution, from plant ancestors to landraces to modern cultivars. Based on molecular analysis, functional profiles were predicted and co-occurrence networks were constructed based on the identification of co-presences of functional units in the tomato root-associated microbiome. The results revealed differences in eight metabolic pathway categories and highlighted the influence of the host genotype on the potential functions of soil bacterial communities. In general, wild tomatoes differed from modern cultivars and tomato landraces which showed similar values, although all ancestral functional characteristics have been conserved across time. We also found that certain functional groups tended to be more evolutionarily conserved in bacterial communities associated with tomato landraces than those of modern varieties. We hypothesize that the capacity of soil bacteria to provide ecosystem services is affected by agronomic practices linked to the domestication process, particularly those related to the preservation of soil organic matter.}, } @article {pmid34579036, year = {2021}, author = {Chiou, WC and Chang, BH and Tien, HH and Cai, YL and Fan, YC and Chen, WJ and Chu, HF and Chen, YH and Huang, C}, title = {Synbiotic Intervention with an Adlay-Based Prebiotic and Probiotics Improved Diet-Induced Metabolic Disturbance in Mice by Modulation of the Gut Microbiota.}, journal = {Nutrients}, volume = {13}, number = {9}, pages = {}, pmid = {34579036}, issn = {2072-6643}, support = {MOST 110-2628-B-A49A-501 -//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Adipose Tissue ; Animal Feed/analysis ; Animals ; Bacteria/classification/genetics ; Body Weight ; Diet, High-Fat/*adverse effects ; Dysbiosis/*chemically induced ; Dyslipidemias ; Gastrointestinal Microbiome/*drug effects ; Insulin Resistance ; Male ; Mice ; Obesity/chemically induced ; *Prebiotics ; *Probiotics ; *Synbiotics ; }, abstract = {Metabolic syndrome and its associated conditions, such as obesity and type 2 diabetes mellitus (T2DM), are a major public health issue in modern societies. Dietary interventions, including microbiota-directed foods which effectively modulate the gut microbiome, may influence the regulation of obesity and associated comorbidities. Although research on probiotics and prebiotics has been conducted extensively in recent years, diets with the use of synbiotics remain relatively unexplored. Here, we investigated the effects of a novel synbiotic intervention, consisting of an adlay seed extrusion cooked (ASEC)-based prebiotic and probiotic (Lactobacillus paracasei and Bacillus coagulans) on metabolic disorders and microbial dysbiosis in high-fat diet (HFD)-induced obese mice. The ASEC-based synbiotic intervention helped improve HFD-induced body weight gain, hyperlipidemia, impaired glucose tolerance, insulin resistance, and inflammation of the adipose and liver tissues. In addition, data from fecal metagenomics indicated that the ASEC-based synbiotic intervention fostered reconstitution of gut bacterial diversity and composition in HFD-induced obese mice. In particular, the ASEC-based synbiotic intervention increased the relative abundance of families Ruminococcaceae and Muribaculaceae and order Bacteroidales and reduced that of families Lactobacillaceae, Erysipelotrichaceae, and Streptococcaceae in HFD-induced obese mice. Collectively, our results suggest that delayed dietary intervention with the novel ASEC-based synbiotic ameliorates HFD-induced obesity, metabolic disorders, and dysbiosis.}, } @article {pmid34576010, year = {2021}, author = {Pistone, D and Meroni, G and Panelli, S and D'Auria, E and Acunzo, M and Pasala, AR and Zuccotti, GV and Bandi, C and Drago, L}, title = {A Journey on the Skin Microbiome: Pitfalls and Opportunities.}, journal = {International journal of molecular sciences}, volume = {22}, number = {18}, pages = {}, pmid = {34576010}, issn = {1422-0067}, mesh = {Dysbiosis/*microbiology/therapy ; Humans ; Metagenomics/methods ; *Microbiota ; Probiotics/therapeutic use ; Skin/*microbiology ; Skin Diseases/*microbiology/therapy ; }, abstract = {The human skin microbiota is essential for maintaining homeostasis and ensuring barrier functions. Over the years, the characterization of its composition and taxonomic diversity has reached outstanding goals, with more than 10 million bacterial genes collected and cataloged. Nevertheless, the study of the skin microbiota presents specific challenges that need to be addressed in study design. Benchmarking procedures and reproducible and robust analysis workflows for increasing comparability among studies are required. For various reasons and because of specific technical problems, these issues have been investigated in gut microbiota studies, but they have been largely overlooked for skin microbiota. After a short description of the skin microbiota, the review tackles methodological aspects and their pitfalls, covering NGS approaches and high throughput culture-based techniques. Recent insights into the "core" and "transient" types of skin microbiota and how the manipulation of these communities can prevent or combat skin diseases are also covered. Finally, this review includes an overview of the main dermatological diseases, the changes in the microbiota composition associated with them, and the recommended skin sampling procedures. The last section focuses on topical and oral probiotics to improve and maintain skin health, considering their possible applications for skin diseases.}, } @article {pmid34573413, year = {2021}, author = {Chukwuneme, CF and Ayangbenro, AS and Babalola, OO}, title = {Metagenomic Analyses of Plant Growth-Promoting and Carbon-Cycling Genes in Maize Rhizosphere Soils with Distinct Land-Use and Management Histories.}, journal = {Genes}, volume = {12}, number = {9}, pages = {}, pmid = {34573413}, issn = {2073-4425}, mesh = {Agriculture/methods/organization & administration ; Carbon/*metabolism ; Ecosystem ; Humans ; Metabolic Networks and Pathways/genetics ; Metagenome/genetics ; Metagenomics ; Microbiota/*genetics ; Plant Development/*genetics ; *Rhizosphere ; Soil ; Soil Microbiology ; South Africa ; *Zea mays/growth & development/metabolism ; }, abstract = {Many studies have shown that the maize rhizosphere comprises several plant growth-promoting microbes, but there is little or no study on the effects of land-use and management histories on microbial functional gene diversity in the maize rhizosphere soils in Africa. Analyzing microbial genes in the rhizosphere of plants, especially those associated with plant growth promotion and carbon cycling, is important for improving soil fertility and crop productivity. Here, we provide a comparative analysis of microbial genes present in the rhizosphere samples of two maize fields with different agricultural histories using shotgun metagenomics. Genes involved in the nutrient mobilization, including nifA, fixJ, norB, pstA, kefA and B, and ktrB were significantly more abundant (α = 0.05) in former grassland (F1) rhizosphere soils. Among the carbon-cycling genes, the abundance of 12 genes, including all those involved in the degradation of methane were more significant (α = 0.05) in the F1 soils, whereas only five genes were significantly more abundant in the F2 soils. α-diversity indices were different across the samples and significant differences were observed in the β diversity of plant growth-promoting and carbon-cycling genes between the fields (ANOSIM, p = 0.01 and R = 0.52). Nitrate-nitrogen (N-NO3) was the most influential physicochemical parameter (p = 0.05 and contribution = 31.3%) that affected the distribution of the functional genes across the samples. The results indicate that land-use and management histories impact the composition and diversity of plant growth-promoting and carbon-cycling genes in the plant rhizosphere. The study widens our understanding of the effects of anthropogenic activities on plant health and major biogeochemical processes in soils.}, } @article {pmid34571998, year = {2021}, author = {Chang, CJ and Zhang, J and Tsai, YL and Chen, CB and Lu, CW and Huo, YP and Liou, HM and Ji, C and Chung, WH}, title = {Compositional Features of Distinct Microbiota Base on Serum Extracellular Vesicle Metagenomics Analysis in Moderate to Severe Psoriasis Patients.}, journal = {Cells}, volume = {10}, number = {9}, pages = {}, pmid = {34571998}, issn = {2073-4409}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/genetics ; Dysbiosis/microbiology ; Extracellular Vesicles/*microbiology ; Female ; Humans ; Male ; Metagenomics/methods ; Microbiota/*genetics ; Middle Aged ; Psoriasis/*microbiology ; Skin/microbiology ; Young Adult ; }, abstract = {The bacterial microbiota in the skin and intestine of patients with psoriasis were different compared with that of healthy individuals. However, the presence of a distinct blood microbiome in patients with psoriasis is yet to be investigated. In this study, we investigated the differences in bacterial communities in plasma-derived extracellular vesicles (EVs) between patients with moderate to severe psoriasis (PSOs) and healthy controls (HCs). The plasma EVs from the PSO (PASI > 10) (n = 20) and HC (n = 8) groups were obtained via a series of centrifugations, and patterns were examined and confirmed using transmission electron microscopy (TEM) and EV-specific markers. The taxonomic composition of the microbiota was determined by using full-length 16S ribosomal RNA gene sequencing. The PSO group had lower bacterial diversity and richness compared with HC group. Principal coordinate analysis (PCoA)-based clustering was used to assess diversity and validated dysbiosis for both groups. Differences at the level of amplicon sequence variant (ASV) were observed, suggesting alterations in specific ASVs according to health conditions. The HC group had higher levels of the phylum Firmicutes and Fusobacteria than in the PSO group. The order Lactobacillales, family Brucellaceae, genera Streptococcus, and species Kingella oralis and Aquabacterium parvum were highly abundant in the HC group compared with the PSO group. Conversely, the order Bacillales and the genera Staphylococcus and Sphihgomonas, as well as Ralstonia insidiosa, were more abundant in the PSO group. We further predicted the microbiota functional capacities, which revealed significant differences between the PSO and HC groups. In addition to previous studies on microbiome changes in the skin and gut, we demonstrated compositional differences in the microbe-derived EVs in the plasma of PSO patients. Plasma EVs could be an indicator for assessing the composition of the microbiome of PSO patients.}, } @article {pmid34571091, year = {2021}, author = {Rui, M and Zhang, X and Huang, J and Wei, D and Li, Z and Shao, Z and Ju, H and Ren, G}, title = {The baseline oral microbiota predicts the response of locally advanced oral squamous cell carcinoma patients to induction chemotherapy: A prospective longitudinal study.}, journal = {Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology}, volume = {164}, number = {}, pages = {83-91}, doi = {10.1016/j.radonc.2021.09.013}, pmid = {34571091}, issn = {1879-0887}, mesh = {Antineoplastic Combined Chemotherapy Protocols ; *Carcinoma, Squamous Cell/drug therapy ; Cisplatin/therapeutic use ; Fluorouracil ; *Head and Neck Neoplasms ; Humans ; Induction Chemotherapy ; Longitudinal Studies ; *Microbiota ; *Mouth Neoplasms/drug therapy ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Squamous Cell Carcinoma of Head and Neck ; Taxoids ; }, abstract = {PURPOSE: Among oral squamous cell carcinoma (OSCC) patients who receive docetaxel, cisplatin, and 5-fluorouracil (TPF) induction chemotherapy, those with a favorable pathological response tend to obtain satisfactory clinical outcomes, while the total population exhibit no survival benefit. Thus, there is an urgent need to improve the therapeutic effect of TPF by applying personalized treatment according to distinct biomarkers.

METHODS AND MATERIALS: In the present study, we collected oral rinse samples from 44 OSCC patients enrolled in our prospective multicenter random phase II trial before TPF induction chemotherapy to conduct 16S rRNA gene sequencing and metagenomic analysis. Patients were administrated with two cycles of TPF induction chemotherapy (75 mg/m[2] cisplatin and 75 mg/m[2] docetaxel on day 1 and 750 mg/m[2] fluorouracil from the first to the fifth day), and then divided into responsive and nonresponsive groups according to the Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1.

RESULTS: In the 16S rRNA gene sequence analysis, Fusobacterium and Mycoplasma were more enriched in the nonresponsive group, while Slackia was more enriched in the responder group at the genus level. In the metagenomic shotgun sequencing analysis, Fusobacterium nucleatum was more enriched in the nonresponsive group. Functional analysis showed that the platinum drug resistance pathway and microRNAs in cancer and RNA degradation pathways were remarkably associated with patient sensitivity to induction chemotherapy.

CONCLUSIONS: Our data suggest that the oral microbiome may play an important role in the OSCC patient sensitivity to TPF induction chemotherapy and offer novel potential biomarkers for predicting the response to TPF induction chemotherapy.}, } @article {pmid34570681, year = {2021}, author = {Zhang, Y and Hu, B and Agwanda, B and Fang, Y and Wang, J and Kuria, S and Yang, J and Masika, M and Tang, S and Lichoti, J and Fan, Z and Shi, Z and Ommeh, S and Wang, H and Deng, F and Shen, S}, title = {Viromes and surveys of RNA viruses in camel-derived ticks revealing transmission patterns of novel tick-borne viral pathogens in Kenya.}, journal = {Emerging microbes & infections}, volume = {10}, number = {1}, pages = {1975-1987}, pmid = {34570681}, issn = {2222-1751}, mesh = {Animals ; Camelus/*virology ; Genome, Viral/genetics ; Humans ; Kenya/epidemiology ; RNA Virus Infections/*transmission/*veterinary ; RNA Viruses/*genetics ; RNA, Viral/genetics ; Tick Infestations/epidemiology ; Tick-Borne Diseases/epidemiology/*virology ; Ticks/classification/*virology ; Virome/genetics ; }, abstract = {ABSTRACTTick-borne viruses (TBVs) capable of transmitting between ticks and hosts have been increasingly recognized as a global public health concern. In this study, Hyalomma ticks and serum samples from camels were collected using recorded sampling correlations in eastern Kenya. Viromes of pooled ticks were profiled by metagenomic sequencing, revealing a diverse community of viruses related to at least 11 families. Five highly abundant viruses, including three novel viruses (Iftin tick virus, Mbalambala tick virus [MATV], and Bangali torovirus [BanToV]) and new strains of previously identified viruses (Bole tick virus 4 [BLTV4] and Liman tick virus [LMTV]), were characterized in terms of genome sequences, organizations, and phylogeny, and their molecular prevalence was investigated in individual ticks. Moreover, viremia and antibody responses to these viruses have been investigated in camels. MATV, BLTV4, LMTV, and BanToV were identified as viral pathogens that can potentially cause zoonotic diseases. The transmission patterns of these viruses were summarized, suggesting three different types according to the sampling relationships between viral RNA-positive ticks and camels positive for viral RNA and/or antibodies. They also revealed the frequent transmission of BanToV and limited but effective transmission of other viruses between ticks and camels. Furthermore, follow-up surveys on TBVs from tick, animal, and human samples with definite sampling relationships are suggested. The findings revealed substantial threats from the emerging TBVs and may guide the prevention and control of TBV-related zoonotic diseases in Kenya and in other African countries.}, } @article {pmid34568090, year = {2021}, author = {Yu, J and Zhang, H and Chen, L and Ruan, Y and Chen, Y and Liu, Q}, title = {Disease-Associated Gut Microbiota Reduces the Profile of Secondary Bile Acids in Pediatric Nonalcoholic Fatty Liver Disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {698852}, pmid = {34568090}, issn = {2235-2988}, mesh = {Bile Acids and Salts ; Child ; Chromatography, Liquid ; Feces ; *Gastrointestinal Microbiome ; Humans ; *Non-alcoholic Fatty Liver Disease ; Tandem Mass Spectrometry ; }, abstract = {Children with nonalcoholic fatty liver disease (NAFLD) display an altered gut microbiota compared with healthy children. However, little is known about the fecal bile acid profiles and their association with gut microbiota dysbiosis in pediatric NAFLD. A total of 68 children were enrolled in this study, including 32 NAFLD patients and 36 healthy children. Fecal samples were collected and analyzed by metagenomic sequencing to determine the changes in the gut microbiota of children with NAFLD, and an ultra-performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS) system was used to quantify the concentrations of primary and secondary bile acids. The associations between the gut microbiota and concentrations of primary and secondary bile acids in the fecal samples were then analyzed. We found that children with NAFLD exhibited reduced levels of secondary bile acids and alterations in bile acid biotransforming-related bacteria in the feces. Notably, the decrease in Eubacterium and Ruminococcaceae bacteria, which express bile salt hydrolase and 7α-dehydroxylase, was significantly positively correlated with the level of fecal lithocholic acid (LCA). However, the level of fecal LCA was negatively associated with the abundance of the potential pathogen Escherichia coli that was enriched in children with NAFLD. Pediatric NAFLD is characterized by an altered profile of gut microbiota and fecal bile acids. This study demonstrates that the disease-associated gut microbiota is linked with decreased concentrations of secondary bile acids in the feces. The disease-associated gut microbiota likely inhibits the conversion of primary to secondary bile acids.}, } @article {pmid34568084, year = {2021}, author = {Oh, KY and Lee, S and Lee, MS and Lee, MJ and Shim, E and Hwang, YH and Ha, JG and Yang, YS and Hwang, IT and Park, JS}, title = {Composition of Vaginal Microbiota in Pregnant Women With Aerobic Vaginitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {677648}, pmid = {34568084}, issn = {2235-2988}, mesh = {Case-Control Studies ; Dysbiosis ; Female ; Humans ; *Microbiota ; Pregnancy ; Pregnant Women ; Vagina ; *Vaginitis ; }, abstract = {Vaginal dysbiosis, such as bacterial vaginosis (BV) and aerobic vaginitis (AV), is an important cause of premature birth in pregnant women. However, there is very little research on vaginal microbial distribution in AV compared to that in BV. This study aimed to analyze the composition of the vaginal microbiota of pregnant women with AV using microbial community analysis and identify the causative organism using each criterion of the AV scoring system. Also, we compared the quantification of aerobic bacteria using quantitative polymerase chain reaction (qPCR) and their relative abundances (RA) using metagenomics. This prospective case-control study included 228 pregnant Korean women from our previous study. A wet mount test was conducted on 159 women to diagnose AV using the AV scoring system. Vaginal samples were analyzed using metagenomics, Gram staining for Nugent score determination, conventional culture, and qPCR for Staphylococcus spp., Streptococcus spp., and Enterobacteriaceae. The relative abundances (RAs) of eleven species showed significant differences among the three groups (Normal flora (NF), mild AV, and moderate AV). Three species including Lactobacillus crispatus were significantly lower in the AV groups than in the NF group, while eight species were higher in the AV groups, particularly moderate AV. The decrease in the RA of L. crispatus was common in three criteria of the AV scoring system (Lactobacillary, WBC, and background flora grades), while it did not show a significant difference among the three grade groups of the toxic leukocyte criterion. Also, the RAs of anaerobes, such as Gardnerella and Megasphaera, were higher in the AV groups, particularly moderate AV, while the RAs of aerobes were very low (RA < 0.01). Therefore, qPCR was performed for aerobes (Staphylococcus spp., Streptococcus spp., and Enterobacteriaceae); however, their quantification did not show a higher level in the AV groups when compared to that in the NF group. Therefore, AV might be affected by the RA of Lactobacillus spp. and the main anaerobes, such as Gardnerella spp. Activation of leukocytes under specific conditions might convert them to toxic leukocytes, despite high levels of L. crispatus. Thus, the pathogenesis of AV can be evaluated under such conditions.}, } @article {pmid34564653, year = {2021}, author = {Gómez-Albarrán, C and Melguizo, C and Patiño, B and Vázquez, C and Gil-Serna, J}, title = {Diversity of Mycobiota in Spanish Grape Berries and Selection of Hanseniaspora uvarum U1 to Prevent Mycotoxin Contamination.}, journal = {Toxins}, volume = {13}, number = {9}, pages = {}, pmid = {34564653}, issn = {2072-6651}, mesh = {*Food Microbiology ; Fruit/*microbiology ; Hanseniaspora/*physiology ; *Mycobiome ; Mycotoxins/*analysis ; Spain ; Vitis/*microbiology ; }, abstract = {The occurrence of mycotoxins on grapes poses a high risk for food safety; thus, it is necessary to implement effective prevention methods. In this work, a metagenomic approach revealed the presence of important mycotoxigenic fungi in grape berries, including Aspergillus flavus, Aspergillus niger aggregate species, or Aspergillus section Circumdati. However, A. carbonarius was not detected in any sample. One of the samples was not contaminated by any mycotoxigenic species, and, therefore, it was selected for the isolation of potential biocontrol agents. In this context, Hanseniaspora uvarum U1 was selected for biocontrol in vitro assays. The results showed that this yeast is able to reduce the growth rate of the main ochratoxigenic and aflatoxigenic Aspergillus spp. occurring on grapes. Moreover, H. uvarum U1 seems to be an effective detoxifying agent for aflatoxin B1 and ochratoxin A, probably mediated by the mechanisms of adsorption to the cell wall and other active mechanisms. Therefore, H. uvarum U1 should be considered in an integrated approach to preventing AFB1 and OTA in grapes due to its potential as a biocontrol and detoxifying agent.}, } @article {pmid34563611, year = {2021}, author = {Park, SY and Faraci, G and Nanda, S and Ter-Saakyan, S and Love, TMT and Mack, WJ and Dubé, MP and Lee, HY}, title = {Gut microbiome in people living with HIV is associated with impaired thiamine and folate syntheses.}, journal = {Microbial pathogenesis}, volume = {160}, number = {}, pages = {105209}, pmid = {34563611}, issn = {1096-1208}, support = {R01 AI095066/AI/NIAID NIH HHS/United States ; }, mesh = {Folic Acid ; *Gastrointestinal Microbiome ; *HIV Infections/complications ; Humans ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Thiamine ; }, abstract = {People living with HIV have a high incidence of cardiovascular and neurological diseases as comorbid disorders that are commonly linked to inflammation. While microbial translocation can augment inflammation during HIV infection, functional microbiome shifts that may increase pro-inflammatory responses have not been fully characterized. In addition, defining HIV-induced microbiome changes has been complicated by high variability among individuals. Here we conducted functional annotation of previously-published 16S ribosomal RNA gene sequences of 305 HIV positive and 249 negative individuals, with adjustment for geographic region, sex, sexual behavior, and age. Metagenome profiles were inferred from these individuals' 16S data. HIV infection was associated with impaired microbial vitamin B synthesis; around half of the gene families in thiamine and folate biosynthesis pathways were significantly less abundant in the HIV positive group than the negative control. These results are consistent with the high prevalence of thiamine and folate deficiencies in HIV infections. These HIV-induced microbiota shifts have the potential to influence cardiovascular and neurocognitive diseases, given the documented associations between B-vitamin deficiencies, inflammation, and these diseases. We also observed that most essential amino acid biosynthesis pathways were downregulated in the microbiome of HIV-infected individuals. Microbial vitamin B and amino acid synthesis pathways were not significantly recovered by antiretroviral treatment when we compared 262 ART positive and 184 ART negative individuals. Our meta-analysis provides a new outlook for understanding vitamin B and amino acid deficiencies in HIV patients, suggesting that interventions for reversing HIV-induced microbiome shifts may aid in lessening the burdens of HIV comorbidities.}, } @article {pmid34563432, year = {2021}, author = {Turjeman, S and Koren, O}, title = {ARGuing the case for (or against) probiotics.}, journal = {Trends in microbiology}, volume = {29}, number = {11}, pages = {959-960}, doi = {10.1016/j.tim.2021.09.004}, pmid = {34563432}, issn = {1878-4380}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Microbial ; *Microbiota ; *Probiotics ; }, abstract = {Antibiotic resistance is one of the leading medical challenges with which we are currently faced. Antibiotics, while powerful medical tools, also wreak havoc on the endogenous microbiota. Many believe that probiotics can restore the microbiota following antibiotic treatment and might even suppress the spread of antibiotic-resistance genes, but a recent study (Montassier et al.) suggests otherwise.}, } @article {pmid34563039, year = {2021}, author = {Hakim, JA and Green, GBH and Watts, SA and Crowley, MR and Morrow, CD and Bej, AK}, title = {Microbial Composition and Genes for Key Metabolic Attributes in the Gut Digesta of Sea Urchins Lytechinus variegatus and Strongylocentrotus purpuratus Using Shotgun Metagenomics.}, journal = {Current issues in molecular biology}, volume = {43}, number = {2}, pages = {978-995}, pmid = {34563039}, issn = {1467-3045}, support = {P30AR050948//Comprehensive Cancer Center, University of Alabama at Birmingham/ ; P30DK0t56336efef/GF/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/*genetics/metabolism ; *Computational Biology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Lytechinus/*microbiology ; *Metagenomics ; Sequence Analysis, DNA ; Strongylocentrotus purpuratus/*microbiology ; }, abstract = {This paper describes the microbial community composition and genes for key metabolic genes, particularly the nitrogen fixation of the mucous-enveloped gut digesta of green (Lytechinus variegatus) and purple (Strongylocentrotus purpuratus) sea urchins by using the shotgun metagenomics approach. Both green and purple urchins showed high relative abundances of Gammaproteobacteria at 30% and 60%, respectively. However, Alphaproteobacteria in the green urchins had higher relative abundances (20%) than the purple urchins (2%). At the genus level, Vibrio was dominant in both green (~9%) and purple (~10%) urchins, whereas Psychromonas was prevalent only in purple urchins (~24%). An enrichment of Roseobacter and Ruegeria was found in the green urchins, whereas purple urchins revealed a higher abundance of Shewanella, Photobacterium, and Bacteroides (q-value < 0.01). Analysis of key metabolic genes at the KEGG-Level-2 categories revealed genes for amino acids (~20%), nucleotides (~5%), cofactors and vitamins (~6%), energy (~5%), carbohydrates (~13%) metabolisms, and an abundance of genes for assimilatory nitrogen reduction pathway in both urchins. Overall, the results from this study revealed the differences in the microbial community and genes designated for the metabolic processes in the nutrient-rich sea urchin gut digesta, suggesting their likely importance to the host and their environment.}, } @article {pmid34562635, year = {2021}, author = {Cheng, M and Ge, X and Zhong, C and Fu, R and Ning, K and Xu, S}, title = {Micro-coevolution of host genetics with gut microbiome in three Chinese ethnic groups.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {48}, number = {11}, pages = {972-983}, doi = {10.1016/j.jgg.2021.09.002}, pmid = {34562635}, issn = {1673-8527}, mesh = {Biodiversity ; *Biological Evolution ; China ; Computational Biology/methods ; Ethnicity/*genetics ; *Gastrointestinal Microbiome ; Genetic Background ; Genetics, Population ; Host Microbial Interactions/*genetics ; Humans ; Metagenome ; Metagenomics/methods ; }, abstract = {Understanding the micro-coevolution of the human gut microbiome with host genetics is challenging but essential in both evolutionary and medical studies. To gain insight into the interactions between host genetic variation and the gut microbiome, we analyzed both the human genome and gut microbiome collected from a cohort of 190 students in the same boarding college and representing 3 ethnic groups, Uyghur, Kazakh, and Han Chinese. We found that differences in gut microbiome were greater between genetically distinct ethnic groups than those genetically closely related ones in taxonomic composition, functional composition, enterotype stratification, and microbiome genetic differentiation. We also observed considerable correlations between host genetic variants and the abundance of a subset of gut microbial species. Notably, interactions between gut microbiome species and host genetic variants might have coordinated effects on specific human phenotypes. Bacteroides ovatus, previously reported to modulate intestinal immunity, is significantly correlated with the host genetic variant rs12899811 (meta-P = 5.55 × 10[-5]), which regulates the VPS33B expression in the colon, acting as a tumor suppressor of colorectal cancer. These results advance our understanding of the micro-coevolution of the human gut microbiome and their interactive effects with host genetic variation on phenotypic diversity.}, } @article {pmid34562162, year = {2021}, author = {de Fátima Silva Lopes, H and Tu, Z and Sumi, H and Furukawa, H and Yumoto, I}, title = {Indigofera tinctoria leaf powder as a promising additive to improve indigo fermentation prepared with sukumo (composted Polygonum tinctorium leaves).}, journal = {World journal of microbiology & biotechnology}, volume = {37}, number = {10}, pages = {179}, pmid = {34562162}, issn = {1573-0972}, support = {G-2020-3-035//Institute for Fermentation, Osaka/ ; }, mesh = {Bacteria, Anaerobic/genetics ; Coloring Agents/chemistry ; *Fermentation ; High-Throughput Nucleotide Sequencing ; Indigo Carmine/chemistry ; *Indigofera/chemistry/microbiology ; Metagenomics ; Microbiota/genetics ; Plant Extracts/chemistry ; Plant Leaves/chemistry/microbiology ; *Polygonum/chemistry/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Being insoluble in the oxidize form, indigo dye must be solubilized by reduction for it to penetrate textile. One of the procedures is the reduction by natural bacterial fermentation. Sukumo, composted leaves of Polygonum tinctorium, is a natural source of indigo in Japan. Although sukumo has an intrinsic bacterial seed, the onset of indigo reduction with this material may vary greatly. Certain additives improve indigo fermentation. Here, we studied the effects of Indigofera tinctoria leaf powder (LP) on the initiation of indigo reduction, bacterial community, redox potential (ORP), and dyeing intensity in the initial stages and in aged fermentation fluids prepared with sukumo. I. tinctoria LP markedly decreased ORP at day 1 and stabilised it during early fermentation. These effects could be explained by the phytochemicals present in I. tinctoria LP that act as oxygen scavengers and electron mediators. Using next generation sequencing results, we observed differences in the bacterial community in sukumo fermentation treated with I. tinctoria LP, which was not influenced by the bacterial community in I. tinctoria LP per se. The concomitant decrease in Bacillaceae and increase in Proteinivoraceae at the onset of fermentation, increase in the ratio of facultative to obligate anaerobes (F/O ratio), or the total abundance of facultative anaerobes (F) or obligate anaerobes (O) (designated F + O) are vital for the initiation and maintenance of indigo reduction. Hence, I. tinctoria LP improved early indigo reduction by decreasing the ORP and hasten the appropriate transitions in the bacterial community in sukumo fermentation.}, } @article {pmid34560539, year = {2021}, author = {Shah, T and Shah, Z and Baloch, Z and Cui, X}, title = {The role of microbiota in respiratory health and diseases, particularly in tuberculosis.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {143}, number = {}, pages = {112108}, doi = {10.1016/j.biopha.2021.112108}, pmid = {34560539}, issn = {1950-6007}, mesh = {Animals ; Antitubercular Agents/therapeutic use ; Dysbiosis ; *Gastrointestinal Microbiome/drug effects/immunology ; Host-Pathogen Interactions ; Humans ; Lung/drug effects/immunology/*microbiology ; Metagenome ; Mycobacterium tuberculosis/drug effects/immunology/*pathogenicity ; Tuberculosis, Pulmonary/drug therapy/immunology/*microbiology ; }, abstract = {Trillions of beneficial and hostile microorganisms live in the human respiratory and gastrointestinal tracts, which act as gatekeepers in maintaining human health, i.e., protecting the body from pathogens by colonizing mucosal surfaces with microbiota-derived antimicrobial metabolites such as short-chain fatty acids or host-derived cytokines and chemokines. It is widely accepted that the microbiome interacts with each other and with the host in a mutually beneficial relationship. Microbiota in the respiratory tract may also play a crucial role in immune homeostasis, maturation, and maintenance of respiratory physiology. Anti-TB antibiotics may cause dysbiosis in the lung and intestinal microbiota, affecting colonization resistance and making the host more susceptible to Mycobacterium tuberculosis (M. tuberculosis) infection. This review discusses recent advances in our understanding of the lung microbiota composition, the lungs and intestinal microbiota related to respiratory health and diseases, microbiome sequencing and analysis, the bloodstream, and the lymphatic system that underpin the gut-lung axis in M. tuberculosis-infected humans and animals. We also discuss the gut-lung axis interactions with the immune system, the role of the microbiome in TB pathogenesis, and the impact of anti-TB antibiotic therapy on the microbiota in animals, humans, and drug-resistant TB individuals.}, } @article {pmid34559138, year = {2021}, author = {Tanaka, T and Matsuno, Y and Torisu, T and Shibata, H and Hirano, A and Umeno, J and Kawasaki, K and Fujioka, S and Fuyuno, Y and Moriyama, T and Esaki, M and Kitazono, T}, title = {Gastric microbiota in patients with Helicobacter pylori-negative gastric MALT lymphoma.}, journal = {Medicine}, volume = {100}, number = {38}, pages = {e27287}, pmid = {34559138}, issn = {1536-5964}, mesh = {Aged ; Case-Control Studies ; Cross-Sectional Studies ; Female ; Gastric Mucosa/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Lymphoma, B-Cell, Marginal Zone/*microbiology ; Male ; Metagenomics ; Middle Aged ; Stomach Neoplasms/*microbiology ; }, abstract = {To investigate the mucosal microbiota in the stomach of patients with Helicobacter pylori-negative mucosa-associated lymphoid tissue (MALT) lymphoma by means of metagenomic analysis.Although some gastric MALT lymphomas are associated with the presence of H. pylori, other gastric MALT lymphomas occur independently of H. pylori infection. The pathogenesis of H. pylori-negative MALT lymphoma remains unclear.Mucosal biopsy specimens were collected from the gastric body from 33 MALT lymphoma patients with gastric lesions, including both H. pylori-infection naïve patients and posteradication patients, as well as 27 control participants without H. pylori infection or cancer. Subsequently, the samples were subjected to 16S rRNA gene sequencing. Quantitative insights into microbial ecology, linear discriminant analysis effect size, and phylogenetic investigation of communities by reconstruction of unobserved states softwares were used to analyze the participants' microbiota.H. pylori-negative MALT lymphoma patients had significantly lower alpha diversity (P = .04), compared with control participants. Significant differences were evident in the microbial composition (P = .04), as determined by comparison of beta diversity between the 2 groups. Taxonomic composition analysis indicated that the genera Burkholderia and Sphingomonas were significantly more abundant in MALT lymphoma patients, while the genera Prevotella and Veillonella were less abundant. Functional microbiota prediction showed that the predicted gene pathways "replication and repair," "translation," and "nucleotide metabolism" were downregulated in MALT lymphoma patients.H. pylori-negative MALT lymphoma patients exhibited altered gastric mucosal microbial compositions, suggesting that altered microbiota might be involved in the pathogenesis of H. pylori-negative MALT lymphoma.}, } @article {pmid34556654, year = {2021}, author = {Belstrøm, D and Constancias, F and Drautz-Moses, DI and Schuster, SC and Veleba, M and Mahé, F and Givskov, M}, title = {Periodontitis associates with species-specific gene expression of the oral microbiota.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {76}, pmid = {34556654}, issn = {2055-5008}, mesh = {*Diabetes Mellitus, Type 2 ; Gene Expression ; Humans ; *Microbiota/genetics ; *Periodontitis ; RNA, Ribosomal, 16S ; }, abstract = {The purpose of the present investigation was to characterize species-specific bacterial activity of the oral microbiota in periodontitis. We tested the hypotheses that chronic inflammation, i.e., periodontitis, associates with bacterial gene expression of the oral microbiota. Oral microbial samples were collected from three oral sites-subgingival plaque, tongue, and saliva from patients with periodontitis and healthy controls. Paired metagenomics and metatranscriptomics were used to perform concomitant characterization of taxonomic composition and to determine species-specific bacterial activity as expressed by the ratio of specific messenger RNA reads to their corresponding genomic DNA reads. Here, we show the association of periodontitis with bacterial gene expression of the oral microbiota. While oral site was the main determinant of taxonomic composition as well as bacterial gene expression, periodontitis was significantly associated with a reduction of carbohydrate metabolism of the oral microbiota at three oral sites (subgingival plaque, tongue, and saliva). Data from the present study revealed the association of periodontitis with bacterial gene expression of the oral microbiota. Conditions of periodontitis was associated with bacterial activity of local subgingival plaque, but also on tongue and the salivary microbiota. Collectively, data suggest that periodontitis associates with impaired carbohydrate metabolism of the oral microbiota. Future longitudinal and interventional studies are warranted to evaluate the potential pathogenic role of impaired bacterial carbohydrate metabolism not only in periodontitis but also in other diseases with low-grade inflammation, such as type 2 diabetes mellitus.}, } @article {pmid34555741, year = {2021}, author = {McDaniel, EA and Wahl, SA and Ishii, S and Pinto, A and Ziels, R and Nielsen, PH and McMahon, KD and Williams, RBH}, title = {Prospects for multi-omics in the microbial ecology of water engineering.}, journal = {Water research}, volume = {205}, number = {}, pages = {117608}, doi = {10.1016/j.watres.2021.117608}, pmid = {34555741}, issn = {1879-2448}, mesh = {Bioreactors ; Metagenomics ; *Microbiota ; Sewage ; *Water ; }, abstract = {Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions - including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful functional predictions to specific taxonomical groups with increasing fidelity. Additionally, related developments in both whole community gene expression surveys and metabolite profiling have permitted for direct surveys of community-scale functions in specific environmental settings. These advances have allowed for a shift in microbiome science away from descriptive studies and towards mechanistic and predictive frameworks for designing and harnessing microbial communities for desired beneficial outcomes. Water engineers, microbiologists, and microbial ecologists studying activated sludge, anaerobic digestion, and drinking water distribution systems have applied various (meta)omics techniques for connecting microbial community dynamics and physiologies to overall process parameters and system performance. However, the rapid pace at which new omics-based approaches are developed can appear daunting to those looking to apply these state-of-the-art practices for the first time. Here, we review how modern genome-resolved metagenomic approaches have been applied to a variety of water engineering applications from lab-scale bioreactors to full-scale systems. We describe integrated omics analysis across engineered water systems and the foundations for pairing these insights with modeling approaches. Lastly, we summarize emerging omics-based technologies that we believe will be powerful tools for water engineering applications. Overall, we provide a framework for microbial ecologists specializing in water engineering to apply cutting-edge omics approaches to their research questions to achieve novel functional insights. Successful adoption of predictive frameworks in engineered water systems could enable more economically and environmentally sustainable bioprocesses as demand for water and energy resources increases.}, } @article {pmid34555041, year = {2021}, author = {Devrim-Lanpir, A and İlktaç, HY and Wirnitzer, K and Hill, L and Rosemann, T and Knechtle, B}, title = {Vegan vs. omnivore diets paradox: A whole-metagenomic approach for defining metabolic networks during the race in ultra-marathoners- a before and after study design.}, journal = {PloS one}, volume = {16}, number = {9}, pages = {e0255952}, pmid = {34555041}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Athletic Performance/*physiology ; *Diet ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; *Marathon Running ; *Metabolic Networks and Pathways ; *Metagenome ; Middle Aged ; Nutritional Status ; Randomized Controlled Trials as Topic ; Vegans/*statistics & numerical data ; Young Adult ; }, abstract = {BACKGROUND: The effect of vegan diets on metabolic processes in the body is still controversial in ultra endurance athletes. The study aims to determine gut microbiome adaptation to extreme exercise according to vegan or omnivore diet consumed in ultra-marathoners. We also seek to evaluate long-term vegan diets' effects on redox homeostasis, and muscle fatigue, and assess energy availability.

METHODS: Seventy participants will be assigned to the study, including 35 vegan ultra-marathoners and 35 omnivores competing in the Sri-Chinmoy ultra marathon race. Research data will be collected from the participants at four steps (three visits to the research laboratory and the race day) throughout the study. At the first visit (seven days before the race), fecal samples, and anthropometric measurements will be collected. Body composition will be measured using DXA. Participants will be informed about keeping detailed food records and will be asked to record their diet data and activity logs during the entire study period. At second visit, maximum oxygen consumption will be measured on treadmill. On race day, blood samples will be collected immediately before, and 0. min, 2 hours, and 24 hours after the race. Body weight will be measured before and after the race. The blood and fecal samples will be stored at -80 C until analysis. Plasma malondialdehyde, reactive oxygen metabolites, total antioxidant capacity, Heatshockprotein-70, and serum Orosomucoid-1 will be analyzed in blood samples. Fecal samples will be analyzed with shotgun metagenomic analysis and interpreted using bioinformatics pipeline (HumanN2). Statistical tests will be analyzed using SPSS version 23.0 and R Software.

DISCUSSION: Study findings will determine the effects of the vegan diet on sports performance, revealing the multiple interactions between host and gut microbiome at the whole metagenomic level. Additionally, results will show the possible adaptation throughout the race by analyzing blood and fecal samples. Furthermore, by assessing energy availability and determining host-metabolite crosstalk for ultra-endurance athletes, possible nutritional deficiencies can be identified. Thus, advanced nutritional strategies can be developed based on metabolic needs.

TRIAL REGISTRATION: Current controlled trials, ISRCTN registry 69541705. Registered on 8 December 2019.}, } @article {pmid34554631, year = {2021}, author = {Cha, G and Meinhardt, KA and Orellana, LH and Hatt, JK and Pannu, MW and Stahl, DA and Konstantinidis, KT}, title = {The influence of alfalfa-switchgrass intercropping on microbial community structure and function.}, journal = {Environmental microbiology}, volume = {23}, number = {11}, pages = {6828-6843}, doi = {10.1111/1462-2920.15785}, pmid = {34554631}, issn = {1462-2920}, mesh = {Agriculture/methods ; Fertilizers/analysis ; Medicago sativa/microbiology ; *Microbiota/genetics ; *Mycorrhizae/chemistry ; Nitrogen/analysis ; *Panicum/microbiology ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The use of nitrogen fertilizer on bioenergy crops such as switchgrass results in increased costs, nitrogen leaching and emissions of N2 O, a potent greenhouse gas. Intercropping with nitrogen-fixing alfalfa has been proposed as an environmentally sustainable alternative, but the effects of synthetic fertilizer versus intercropping on soil microbial community functionality remain uncharacterized. We analysed 24 metagenomes from the upper soil layer of agricultural fields from Prosser, WA over two growing seasons and representing three agricultural practices: unfertilized switchgrass (control), fertilized switchgrass and switchgrass intercropped with alfalfa. The synthetic fertilization and intercropping did not result in major shifts of microbial community taxonomic and functional composition compared with the control plots, but a few significant changes were noted. Most notably, mycorrhizal fungi, ammonia-oxidizing archaea and bacteria increased in abundance with intercropping and fertilization. However, only betaproteobacterial ammonia-oxidizing bacteria abundance in fertilized plots significantly correlated to N2 O emission and companion qPCR data. Collectively, a short period of intercropping elicits minor but significant changes in the soil microbial community toward nitrogen preservation and that intercropping may be a viable alternative to synthetic fertilization.}, } @article {pmid34554392, year = {2022}, author = {Sumbula, V and Kurian, PS and Girija, D and Cherian, KA}, title = {Impact of foliar application of fungicides on tomato leaf fungal community structure revealed by metagenomic analysis.}, journal = {Folia microbiologica}, volume = {67}, number = {1}, pages = {103-108}, pmid = {34554392}, issn = {1874-9356}, mesh = {*Fungicides, Industrial/pharmacology ; *Solanum lycopersicum ; Metagenomics ; *Mycobiome ; Plant Leaves ; }, abstract = {Fungicides are commonly used to manage plant pathogens. However, little is known about their effects on the non-target fungal communities that inhabit inside and outside the plant. These fungicides may have adverse effects on beneficial microbial communities with possible consequences for plant health and productivity. Hence, a metagenomic approach, based on the ITS2 region of fungal rDNA, was used to study the impact of foliar application of two fungicides (propineb and iprodione + carbendazim) on non-target tomato leaf fungal communities, in the context of early blight disease management. Metagenomic analysis revealed that the richness and diversity of tomato leaf fungal populations were adversely affected by the chemical treatments tested. Among the two fungicides, propineb (contact fungicide) imparted less non-targeted microorganisms than iprodione + carbendazim (systemic fungicide). In addition, all samples showed association of pathogenic genera Cladosporium, Corynespora, Pseudocercospora along with early blight pathogen Alternaria on tomato leaves that otherwise were undetected. Metagenomic studies also revealed a new mode of action for fungicides and bioagents besides their direct effect that is shifting the microbial community structure so that it provides greater resistance against the pathogen.}, } @article {pmid34553243, year = {2022}, author = {Villalobos-Flores, LE and Espinosa-Torres, SD and Hernández-Quiroz, F and Piña-Escobedo, A and Cruz-Narváez, Y and Velázquez-Escobar, F and Süssmuth, R and García-Mena, J}, title = {The Bacterial and Fungal Microbiota of the Mexican Rubiaceae Family Medicinal Plant Bouvardia ternifolia.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {510-526}, pmid = {34553243}, issn = {1432-184X}, mesh = {Bacteria/genetics ; Endophytes ; Fungi/genetics ; *Mycobiome ; Plant Roots/microbiology ; *Plants, Medicinal/microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; *Rubiaceae/genetics ; Soil Microbiology ; }, abstract = {Bouvardia ternifolia is a medicinal plant considered a source of therapeutic compounds, like the antitumoral cyclohexapeptide bouvardin. It is known that large number of secondary metabolites produced by plants results from the interaction of the host and adjacent or embedded microorganisms. Using high-throughput DNA sequencing of V3-16S and V5-18S ribosomal gene libraries, we characterized the endophytic, endophytic + epiphyte bacterial, and fungal communities associated to flowers, leaves, stems, and roots, as well as the rhizosphere. The Proteobacteria (average 80.7%) and Actinobacteria (average 14.7%) were the most abundant bacterial phyla, while Leotiomycetes (average 54.8%) and Dothideomycetes (average 27.4%) were the most abundant fungal classes. Differential abundance for the bacterial endophyte group showed a predominance of Erwinia, Propionibacterium, and Microbacterium genera, while Sclerotinia, Coccomyces, and Calycina genera predominated for fungi. The predictive metagenome analysis for bacteria showed significative abundance of pathways for secondary metabolite production, while a FUNguild analysis revealed the presence of pathotroph, symbiotroph, and saprotrophs in the fungal community. Intra and inter copresence and mutual exclusion interactions were identified for bacterial and fungal kingdoms in the endophyte communities. This work provides a description of the diversity and composition of bacterial and fungal microorganisms living in flowers, leaves, stems, roots, and the rhizosphere of this medicinal plant; thus, it paves the way towards an integral understanding in the production of therapeutic metabolites.}, } @article {pmid34551799, year = {2021}, author = {Stražar, M and Mourits, VP and Koeken, VACM and de Bree, LCJ and Moorlag, SJCFM and Joosten, LAB and van Crevel, R and Vlamakis, H and Netea, MG and Xavier, RJ}, title = {The influence of the gut microbiome on BCG-induced trained immunity.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {275}, pmid = {34551799}, issn = {1474-760X}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; P30 DK043351/NH/NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; BCG Vaccine/*immunology ; Cohort Studies ; Cytokines/biosynthesis ; Female ; Firmicutes/enzymology/genetics ; Gastrointestinal Microbiome/*immunology ; Humans ; Male ; Metagenomics ; Middle Aged ; Phenylalanine/metabolism ; Young Adult ; }, abstract = {BACKGROUND: The bacillus Calmette-Guérin (BCG) vaccine protects against tuberculosis and heterologous infections but elicits high inter-individual variation in specific and nonspecific, or trained, immune responses. While the gut microbiome is increasingly recognized as an important modulator of vaccine responses and immunity in general, its potential role in BCG-induced protection is largely unknown.

RESULTS: Stool and blood were collected from 321 healthy adults before BCG vaccination, followed by blood sampling after 2 weeks and 3 months. Metagenomics based on de novo genome assembly reveals 43 immunomodulatory taxa. The nonspecific, trained immune response is detected by altered production of cytokines IL-6, IL-1β, and TNF-α upon ex vivo blood restimulation with Staphylococcus aureus and negatively correlates with abundance of Roseburia. The specific response, measured by IFN-γ production upon Mycobacterium tuberculosis stimulation, is associated positively with Ruminococcus and Eggerthella lenta. The identified immunomodulatory taxa also have the strongest effects on circulating metabolites, with Roseburia affecting phenylalanine metabolism. This is corroborated by abundances of relevant enzymes, suggesting alternate phenylalanine metabolism modules are activated in a Roseburia species-dependent manner.

CONCLUSIONS: Variability in cytokine production after BCG vaccination is associated with the abundance of microbial genomes, which in turn affect or produce metabolites in circulation. Roseburia is found to alter both trained immune responses and phenylalanine metabolism, revealing microbes and microbial products that may alter BCG-induced immunity. Together, our findings contribute to the understanding of specific and trained immune responses after BCG vaccination.}, } @article {pmid34551705, year = {2021}, author = {Bjerre, RD and Holm, JB and Palleja, A and Sølberg, J and Skov, L and Johansen, JD}, title = {Skin dysbiosis in the microbiome in atopic dermatitis is site-specific and involves bacteria, fungus and virus.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {256}, pmid = {34551705}, issn = {1471-2180}, mesh = {Adult ; Bacteria/classification/*genetics/isolation & purification/pathogenicity ; Case-Control Studies ; Dermatitis, Atopic/*microbiology/pathology ; Dysbiosis/*microbiology ; Female ; Fungi/classification/*genetics/isolation & purification/pathogenicity ; Humans ; Male ; Microbiota/*genetics ; Middle Aged ; Skin/*microbiology ; Staphylococcal Infections/*microbiology ; Staphylococcus aureus/pathogenicity ; Viruses/classification/*genetics/isolation & purification/pathogenicity ; }, abstract = {BACKGROUND: Microbial dysbiosis with increased Staphylococcus aureus (S. aureus) colonization on the skin is a hallmark of atopic dermatitis (AD), however most microbiome studies focus on bacteria in the flexures and the microbial composition at other body sites have not been studied systematically.

OBJECTIVES: The aim of the study is to characterize the skin microbiome, including bacteria, fungi and virus, at different body sites in relation to AD, lesional state, and S. aureus colonization, and to test whether the nares could be a reservoir for S. aureus strain colonization.

METHODS: Using shotgun metagenomics we characterized microbial compositions from 14 well defined skin sites from 10 patients with AD and 5 healthy controls.

RESULTS: We found clear differences in microbial composition between AD and controls at multiple skin sites, most pronounced on the flexures and neck. The flexures exhibited lower alpha-diversity and were colonized by S. aureus, accompanied by S. epidermidis in lesions. Malassezia species were absent on the neck in AD. Virus mostly constituted Propionibacterium and Staphylococcus phages, with increased abundance of Propionibacterium phages PHL041 and PHL092 and Staphylococcus epidermidis phages CNPH82 and PH15 in AD. In lesional samples, both the genus Staphylococcus and Staphylococcus phages were more abundant. S. aureus abundance was higher across all skin sites except from the feet. In samples where S. aureus was highly abundant, lower abundances of S. hominis and Cutibacterium acnes were observed. M. osloensis and M. luteus were more abundant in AD. By single nucleotide variant analysis of S. aureus we found strains to be subject specific. On skin sites some S. aureus strains were similar and some dissimilar to the ones in the nares.

CONCLUSIONS: Our data indicate a global and site-specific dysbiosis in AD, involving both bacteria, fungus and virus. When defining targeted treatment clinicians should both consider the individual and skin site and future research into potential crosstalk between microbiota in AD yields high potential.}, } @article {pmid34551287, year = {2021}, author = {Piscotta, FJ and Whitfield, ST and Nakashige, TG and Estrela, AB and Ali, T and Brady, SF}, title = {Multiplexed functional metagenomic analysis of the infant microbiome identifies effectors of NF-κB, autophagy, and cellular redox state.}, journal = {Cell reports}, volume = {36}, number = {12}, pages = {109746}, pmid = {34551287}, issn = {2211-1247}, support = {R01 AT009562/AT/NCCIH NIH HHS/United States ; }, mesh = {Amides/analysis/metabolism ; Autophagy/*genetics ; Chromatography, High Pressure Liquid ; Feces/microbiology ; Humans ; Hydrogen Sulfide/metabolism ; Infant ; Klebsiella pneumoniae/genetics ; Mass Spectrometry ; Metagenomics/*methods ; *Microbiota ; Microtubule-Associated Proteins/metabolism ; NAD/chemistry/*metabolism ; NF-kappa B/*metabolism ; }, abstract = {The human microbiota plays a critical role in host health. Proper development of the infant microbiome is particularly important. Its dysbiosis leads to both short-term health issues and long-term disorders lasting into adulthood. A central way in which the microbiome interacts with the host is through the production of effector molecules, such as proteins and small molecules. Here, a metagenomic library constructed from 14 infant stool microbiomes is analyzed for the production of effectors that modulate three distinct host pathways: immune response (nuclear factor κB [NF-κB] activation), autophagy (LC3-B puncta formation), and redox potential (NADH:NAD ratio). We identify microbiome-encoded bioactive metabolites, including commendamide and hydrogen sulfide and their associated biosynthetic genes, as well as a previously uncharacterized autophagy-inducing operon from Klebsiella spp. This work extends our understanding of microbial effector molecules that are known to influence host pathways. Parallel functional screening of metagenomic libraries can be easily expanded to investigate additional host processes.}, } @article {pmid34550975, year = {2021}, author = {Hoke, AK and Reynoso, G and Smith, MR and Gardner, MI and Lockwood, DJ and Gilbert, NE and Wilhelm, SW and Becker, IR and Brennan, GJ and Crider, KE and Farnan, SR and Mendoza, V and Poole, AC and Zimmerman, ZP and Utz, LK and Wurch, LL and Steffen, MM}, title = {Genomic signatures of Lake Erie bacteria suggest interaction in the Microcystis phycosphere.}, journal = {PloS one}, volume = {16}, number = {9}, pages = {e0257017}, pmid = {34550975}, issn = {1932-6203}, mesh = {Carbon/metabolism ; DNA, Bacterial/*genetics ; *Genome, Bacterial ; Harmful Algal Bloom/*physiology ; High-Throughput Nucleotide Sequencing ; Lakes/microbiology ; *Metagenome ; Microbiota/genetics ; Microcystis/classification/*genetics/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; Quorum Sensing/*genetics ; Signal Transduction ; United States ; }, abstract = {Microbial interactions in harmful algal bloom (HAB) communities have been examined in marine systems, but are poorly studied in fresh waters. To investigate HAB-microbe interactions, we isolated bacteria with close associations to bloom-forming cyanobacteria, Microcystis spp., during a 2017 bloom in the western basin of Lake Erie. The genomes of five isolates (Exiguobacterium sp. JMULE1, Enterobacter sp. JMULE2, Deinococcus sp. JMULE3, Paenibacillus sp. JMULE4, and Acidovorax sp. JMULE5.) were sequenced on a PacBio Sequel system. These genomes ranged in size from 3.1 Mbp (Exiguobacterium sp. JMULE1) to 5.7 Mbp (Enterobacter sp. JMULE2). The genomes were analyzed for genes relating to critical metabolic functions, including nitrogen reduction and carbon utilization. All five of the sequenced genomes contained genes that could be used in potential signaling and nutrient exchange between the bacteria and cyanobacteria such as Microcystis. Gene expression signatures of algal-derived carbon utilization for two isolates were identified in Microcystis blooms in Lake Erie and Lake Tai (Taihu) at low levels, suggesting these organisms are active and may have a functional role during Microcystis blooms in aggregates, but were largely missing from whole water samples. These findings build on the growing evidence that the bacterial microbiome associated with bloom-forming algae have the functional potential to contribute to nutrient exchange within bloom communities and interact with important bloom formers like Microcystis.}, } @article {pmid34550002, year = {2021}, author = {Cremonesi, P and Severgnini, M and Romanò, A and Sala, L and Luini, M and Castiglioni, B}, title = {Bovine Milk Microbiota: Comparison among Three Different DNA Extraction Protocols To Identify a Better Approach for Bacterial Analysis.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0037421}, pmid = {34550002}, issn = {2165-0497}, mesh = {Animals ; Bacteria/*classification/*genetics/isolation & purification ; Cattle ; DNA, Bacterial/genetics ; Dairying ; Female ; High-Throughput Nucleotide Sequencing ; Mammary Glands, Animal/*microbiology ; Mastitis, Bovine/epidemiology/microbiology ; Microbiota/*genetics ; Milk/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The bovine udder is colonized by a huge quantity of microorganisms that constitute the intramammary ecosystem, with a specific role in modulating not only udder homeostasis and mastitis susceptibility, but also the quality of the dairy products. However, generating high-quality bacterial DNA can be critical, especially starting from a complex biological matrix like milk, characterized by high fat, protein, and calcium contents. Here, bacterial DNA was recovered from a commercial ultra-high-temperature (UHT) milk sample artificially spiked with a predetermined mock community composition and from three bulk tank milk (raw milk) samples. The DNA was isolated using three different protocols to evaluate the effect of the extraction procedures on the milk microbiota composition. In the mock community experiment, the bacterial profiles generated by the three DNA extraction protocols were profoundly different, with the genera Staphylococcus, Lactobacillus, Listeria, and Salmonella underestimated by all the protocols. Only one protocol revealed values close to the expected abundances for Escherichia/Shigella spp., Bacillus spp., Enterococcus spp., and Pseudomonas spp. On the other hand, the nonspiked UHT milk sample exhibited a similar microbiota composition, revealing the prevalence of Acinetobacter spp., for all the DNA extraction protocols. For the raw milk samples, the three DNA extraction kits performed differently, revealing significant separations in both the microbial richness (alpha diversity) and composition (beta diversity). Our study highlights the presence of significant differences among these procedures, probably due to the different DNA extracting capacities and to the different properties of the milk samples, revealing that the selection of DNA extraction protocol is a critical point. IMPORTANCE The advance of high-throughput technologies has increased our knowledge of the world of microorganisms, especially of microbial populations inhabiting living animals. This study provides evidence that milk, as other complex sources, could be critical for generating high-quality DNA for microbiota analysis. In addition, it demonstrates that the microbial population highlighted by metagenomic studies changes in relation to different DNA extraction procedures, revealing that attention should be paid especially when comparing different studies.}, } @article {pmid34548111, year = {2021}, author = {Wang, L and Huang, G and Hou, R and Qi, D and Wu, Q and Nie, Y and Zuo, Z and Ma, R and Zhou, W and Ma, Y and Hu, Y and Yang, Z and Yan, L and Wei, F}, title = {Multi-omics reveals the positive leverage of plant secondary metabolites on the gut microbiota in a non-model mammal.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {192}, pmid = {34548111}, issn = {2049-2618}, mesh = {Animals ; Diet ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics ; *Ursidae ; }, abstract = {BACKGROUND: Flavonoids are important plant secondary metabolites (PSMs) that have been widely used for their health-promoting effects. However, little is known about overall flavonoid metabolism and the interactive effects between flavonoids and the gut microbiota. The flavonoid-rich bamboo and the giant panda provide an ideal system to bridge this gap.

RESULTS: Here, integrating metabolomic and metagenomic approaches, and in vitro culture experiment, we identified 97 flavonoids in bamboo and most of them have not been identified previously; the utilization of more than 70% flavonoid monomers was attributed to gut microbiota; the variation of flavonoid in bamboo leaves and shoots shaped the seasonal microbial fluctuation. The greater the flavonoid content in the diet was, the lower microbial diversity and virulence factor, but the more cellulose-degrading species.

CONCLUSIONS: Our study shows an unprecedented landscape of beneficial PSMs in a non-model mammal and reveals that PSMs remodel the gut microbiota conferring host adaptation to diet transition in an ecological context, providing a novel insight into host-microbe interaction. Video abstract.}, } @article {pmid34545840, year = {2021}, author = {Dery, KJ and Kupiec-Weglinski, JW and Dong, TS}, title = {The human microbiome in transplantation: the past, present, and future.}, journal = {Current opinion in organ transplantation}, volume = {26}, number = {6}, pages = {595-602}, doi = {10.1097/MOT.0000000000000922}, pmid = {34545840}, issn = {1531-7013}, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; *Microbiota ; }, abstract = {PURPOSE OF REVIEW: Over the past 20 years, DNA sequencing technology has transformed human microbiome research from identity characterizations to metagenomics approaches that reveal how microbials correlate with human health and disease. New studies are showing unprecedented opportunity for deep characterization of the human microbial ecosystem, with benefits to the field of organ transplantation.

RECENT FINDINGS: In the present review, we focus on past milestones of human-associated microbiota research, paying homage to microbiota pioneers. We highlight the role of sequencing efforts to provide insights beyond taxonomic identification. Recent advances in microbiome technology is now integrating high-throughput datasets, giving rise to multi'omics - a comprehensive assessment modeling dynamic biologic networks. Studies that show benefits and mechanisms in peritransplant antibiotic (Abx)-conditioned recipients are reviewed. We describe how next-generation microbial sequencing has the potential to combine with new technologies like phage therapy (PT) to translate into life-saving therapeutics.

SUMMARY: The study of the microbiome is advancing the field of transplantation by enhancing our knowledge of precision medicine. Sequencing technology has allowed the use of the microbiome as a biomarker to risk stratify patients. Further research is needed to better understand how microbiomes shape transplantation outcomes while informing immune cell - tissue crosstalk platforms.}, } @article {pmid34545693, year = {2022}, author = {Jurelevicius, D and Pereira, RDS and da Mota, FF and Cury, JC and de Oliveira, IC and Rosado, AS and Mason, OU and Jansson, JK and Seldin, L}, title = {Metagenomic analysis of microbial communities across a transect from low to highly hydrocarbon-contaminated soils in King George Island, Maritime Antarctica.}, journal = {Geobiology}, volume = {20}, number = {1}, pages = {98-111}, doi = {10.1111/gbi.12472}, pmid = {34545693}, issn = {1472-4669}, support = {//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; //Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Antarctic Regions ; Hydrocarbons/analysis ; *Microbiota ; *Petroleum/metabolism ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology ; *Soil Pollutants/analysis/metabolism ; }, abstract = {Soil samples from a transect from low to highly hydrocarbon-contaminated soils were collected around the Brazilian Antarctic Station Comandante Ferraz (EACF), located at King George Island, Antarctica. Quantitative PCR (qPCR) analysis of bacterial 16S rRNA genes, 16S rRNA gene (iTag), and shotgun metagenomic sequencing were used to characterize microbial community structure and the potential for petroleum degradation by indigenous microbes. Hydrocarbon contamination did not affect bacterial abundance in EACF soils (bacterial 16S rRNA gene qPCR). However, analysis of 16S rRNA gene sequences revealed a successive change in the microbial community along the pollution gradient. Microbial richness and diversity decreased with the increase of hydrocarbon concentration in EACF soils. The abundance of Cytophaga, Methyloversatilis, Polaromonas, and Williamsia was positively correlated (p-value = <.05) with the concentration of total petroleum hydrocarbons (TPH) and/or polycyclic aromatic hydrocarbons (PAH). Annotation of metagenomic data revealed that the most abundant hydrocarbon degradation pathway in EACF soils was related to alkyl derivative-PAH degradation (mainly methylnaphthalenes) via the CYP450 enzyme family. The abundance of genes related to nitrogen fixation increased in EACF soils as the concentration of hydrocarbons increased. The results obtained here are valuable for the future of bioremediation of petroleum hydrocarbon-contaminated soils in polar environments.}, } @article {pmid34544379, year = {2021}, author = {Zhang, W and Liang, Y and Zheng, K and Gu, C and Liu, Y and Wang, Z and Zhang, X and Shao, H and Jiang, Y and Guo, C and He, H and Wang, H and Sung, YY and Mok, WJ and Zhang, Y and McMinn, A and Wang, M}, title = {Characterization and genomic analysis of the first Oceanospirillum phage, vB_OliS_GJ44, representing a novel siphoviral cluster.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {675}, pmid = {34544379}, issn = {1471-2164}, mesh = {*Bacteriophages/genetics ; DNA, Viral/genetics ; Genome, Viral ; Genomics ; Phylogeny ; *Siphoviridae/genetics ; }, abstract = {BACKGROUND: Marine bacteriophages play key roles in the community structure of microorganisms, biogeochemical cycles, and the mediation of genetic diversity through horizontal gene transfer. Recently, traditional isolation methods, complemented by high-throughput sequencing metagenomics technology, have greatly increased our understanding of the diversity of bacteriophages. Oceanospirillum, within the order Oceanospirillales, are important symbiotic marine bacteria associated with hydrocarbon degradation and algal blooms, especially in polar regions. However, until now there has been no isolate of an Oceanospirillum bacteriophage, and so details of their metagenome has remained unknown.

RESULTS: Here, we reported the first Oceanospirillum phage, vB_OliS_GJ44, which was assembled into a 33,786 bp linear dsDNA genome, which includes abundant tail-related and recombinant proteins. The recombinant module was highly adapted to the host, according to the tetranucleotides correlations. Genomic and morphological analyses identified vB_OliS_GJ44 as a siphovirus, however, due to the distant evolutionary relationship with any other known siphovirus, it is proposed that this virus could be classified as the type phage of a new Oceanospirivirus genus within the Siphoviridae family. vB_OliS_GJ44 showed synteny with six uncultured phages, which supports its representation in uncultured environmental viral contigs from metagenomics. Homologs of several vB_OliS_GJ44 genes have mostly been found in marine metagenomes, suggesting the prevalence of this phage genus in the oceans.

CONCLUSIONS: These results describe the first Oceanospirillum phage, vB_OliS_GJ44, that represents a novel viral cluster and exhibits interesting genetic features related to phage-host interactions and evolution. Thus, we propose a new viral genus Oceanospirivirus within the Siphoviridae family to reconcile this cluster, with vB_OliS_GJ44 as a representative member.}, } @article {pmid34544375, year = {2021}, author = {Koo, H and Morrow, CD}, title = {Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {251}, pmid = {34544375}, issn = {1471-2180}, mesh = {Clostridium Infections/*prevention & control ; Fecal Microbiota Transplantation/*methods/standards ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics/*physiology ; Humans ; Immunotherapy/*adverse effects ; Longitudinal Studies ; Melanoma/immunology/therapy ; *Symbiosis ; }, abstract = {BACKGROUND: To understand inter-individual variability of fecal microbe transplantation (FMT) to enhance anti-PD-1 immunotherapy (IT) for melanoma, we analyzed the data sets from two recent publications with a microbial strain-tracking tool to determine if donor strains were dominant in the recipient feces following FMT.

RESULTS: Analysis of the Baruch et al. data set found that the presence of commensal donor microbes in recipient feces post-FMT did not correlate with the patient response to IT. From the Davar et al., data set, we found 4 patients that responded to IT had donor's related strain post-FMT, while 2 patients that did not respond to the IT also had donor's strain post-FMT. Importantly, we identified no donor microbes in the feces in one recipient post-FMT that responded to IT. Furthermore, in depth analysis from two patients who responded to IT revealed both donor and recipient strains at different times post-FMT. Colonization of the gastrointestinal tract niches is important for the interaction with the host immune system. Using a separate data set, we show that mucosa from the cecum, transverse colon, and sigmoid colon share strains, providing a large reservoir of niches containing recipient microbes.

CONCLUSIONS: We demonstrated using strain-tracking analysis individual variation with the respect to the presence of fecal dominant donor microbes in the recipient following FMT that did not correlate with the response to anti-PD-1 immunotherapy. The inter-individual differences of FMT to enhance IT might be explained by the variability of the donor microbes to occupy and outcompete recipient microbes for the gastrointestinal niches. The result from our study supports the use of new approaches to clear the niches in the gastrointestinal tract to promote donor colonization to reduce inter-individual variability of IT for melanoma and potentially other cancers.}, } @article {pmid34544076, year = {2022}, author = {Yang, M and Li, F and Zhang, R and Wu, Y and Yang, Q and Wang, F and Yu, Z and Liu, J and Cha, B and Gong, Q and Yang, B and Sun, B and Ding, H}, title = {Alteration of the Intestinal Microbial Flora and the Serum IL-17 Level in Patients with Graves' Disease Complicated with Vitamin D Deficiency.}, journal = {International archives of allergy and immunology}, volume = {183}, number = {2}, pages = {225-234}, doi = {10.1159/000518949}, pmid = {34544076}, issn = {1423-0097}, mesh = {Adult ; Biodiversity ; Biomarkers ; Case-Control Studies ; Disease Susceptibility ; Female ; Gastrointestinal Microbiome/*immunology ; Graves Disease/*blood/diagnosis/*etiology ; Humans ; Interleukin-17/*blood ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Thyroid Function Tests ; Vitamin D/blood ; Vitamin D Deficiency/blood/*complications ; }, abstract = {BACKGROUND: Intestinal flora is associated with Graves' disease (GD). This study explored the association of serum 25(OH)D with the diversity of the intestinal flora and serum IL-17 in GD patients.

METHODS: Patients newly diagnosed with GD at 2 centers between 2018 and 2021 were consecutively included. According to their 25(OH)D levels, they were divided into the deficiency group, the insufficiency group, and the sufficiency group. Some patients with vitamin D deficiency or insufficiency were randomly selected and were matched with healthy volunteers (normal control [NC]) in terms of sex, age, and case number. The diversity and differential species of the intestinal flora and serum IL-17 levels were compared.

RESULTS: Serum 25(OH)D negatively correlated with serum IL-17, the platelet/lymphocyte ratio, and TSH receptor antibody. The diversity of the intestinal flora decreased in the GD group, with noticeable differences in the composition of the intestinal flora when compared with the NC group. At the phylum level, the GD group exhibited a significantly lower abundance of Firmicutes but a higher abundance of Actinobacteria. At the genus level, the GD group exhibited higher relative abundances of Bifidobacterium, Collinsella, and Pediococcus but lower abundances of Roseburia and Dialister.

CONCLUSIONS: The changes in the vitamin D level and the composition of the intestinal flora may partially contribute to the development of GD.}, } @article {pmid34542625, year = {2022}, author = {Mallott, EK and Amato, KR}, title = {Butyrate Production Pathway Abundances Are Similar in Human and Nonhuman Primate Gut Microbiomes.}, journal = {Molecular biology and evolution}, volume = {39}, number = {1}, pages = {}, pmid = {34542625}, issn = {1537-1719}, mesh = {Animals ; Butyrates/metabolism ; Diet ; *Gastrointestinal Microbiome/genetics ; Humans ; Primates/metabolism ; }, abstract = {Over the course of human evolution, shifts in dietary practices such as meat-eating and cooking, have resulted in reduced fiber intake, a trend that has been exaggerated more recently in industrialized populations. Reduced fiber consumption is associated with a loss of gut microbial taxa that degrade fiber, particularly butyrate. Therefore, this dietary shift in humans may have altered the abundance of microbial genes involved in butyrate production. This study uses a gene-targeted alignment approach to quantify the abundance of butyrate production pathway genes from published wild nonhuman primate and human gut metagenomes. Surprisingly, humans have higher diversity and relative abundances of butyrate production pathways compared with all groups of nonhuman primates except cercopithecoids. Industrialized populations of humans also differ only slightly in butyrate pathway abundance from nonindustrialized populations. This apparent resilience of butyrate production pathways to shifts in human diet across both evolutionary and modern populations may signal an evolutionary shift in host-microbe interactions in humans that increased SCFA production. Such a shift could have contributed to meeting the increased energy requirements of humans relative to nonhuman primates.}, } @article {pmid34539647, year = {2021}, author = {Zhang, J and Tao, J and Gao, RN and Wei, ZY and He, YS and Ren, CY and Li, QC and Liu, YS and Wang, KW and Yang, G and Qian, C and Chen, JH}, title = {Cytotoxic T-Cell Trafficking Chemokine Profiles Correlate With Defined Mucosal Microbial Communities in Colorectal Cancer.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {715559}, pmid = {34539647}, issn = {1664-3224}, mesh = {Adult ; Aged ; Biomarkers ; CD8-Positive T-Lymphocytes/immunology/metabolism ; Chemokines/*metabolism ; Chemotaxis, Leukocyte/*immunology ; Colorectal Neoplasms/*etiology/*metabolism/pathology ; Computational Biology/methods ; Disease Progression ; Disease Susceptibility ; Female ; Fluorescent Antibody Technique ; Gastrointestinal Microbiome/*immunology ; Humans ; Immunohistochemistry ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Neoplasm Grading ; Neoplasm Staging ; T-Lymphocytes, Cytotoxic/*immunology/*metabolism ; }, abstract = {The involvement of gut microbiota in T-cell trafficking into tumor tissue of colorectal cancer (CRC) remains to be further elucidated. The current study aimed to evaluate the expression of major cytotoxic T-cell trafficking chemokines (CTTCs) and chemokine-associated microbiota profiles in both tumor and adjacent normal tissues during CRC progression. We analyzed the expression of chemokine C-X-C motif ligands 9, 10, and 11 (CXCL9, CXCL10, and CXCL11), and C-C motif ligand 5 (CCL5), characterized gut mucosa-associated microbiota (MAM), and investigated their correlations in CRC patients. Our results showed that the expression of CXCL9, CXCL10, and CXCL11 was significantly higher in tumor than in adjacent normal tissues in 136 CRC patients. Notably, the high expression of CXCL9 in tumor tissues was associated with enhanced CD8[+] T-cell infiltration and improved survival. Moreover, the MAM in tumor tissues showed reduction of microbial diversity and increase of oral bacteria. Microbial network analysis identified differences in microbial composition and structure between tumor and adjacent normal tissues. In addition, stronger associations between oral bacteria and other gut microbes were observed. Furthermore, the correlation analysis between the defined MAM and individual CTTCs showed that the CTTCs' correlated operational taxonomic units (OTUs) in tumor and adjacent normal tissues rarely overlap with each other. Notably, all the enriched OTUs were positively correlated with the CTTCs in either tumor or adjacent normal tissues. Our findings demonstrated stronger interactions between oral bacteria and gut microbes, and a shifted correlation pattern between MAM and major CTTCs in tumor tissues, underlining possible mechanisms of gut microbiota-host interaction in CRC.}, } @article {pmid34538688, year = {2022}, author = {Vitko, D and McQuaid, JW and Gheinani, AH and Hasegawa, K and DiMartino, S and Davis, KH and Chung, CY and Petrosino, JF and Adam, RM and Mansbach, JM and Lee, RS}, title = {Urinary Tract Infections in Children with Vesicoureteral Reflux Are Accompanied by Alterations in Urinary Microbiota and Metabolome Profiles.}, journal = {European urology}, volume = {81}, number = {2}, pages = {151-154}, doi = {10.1016/j.eururo.2021.08.022}, pmid = {34538688}, issn = {1873-7560}, mesh = {Female ; Fever/complications ; Humans ; Infant ; Male ; Metabolome ; *Microbiota ; *Urinary Tract Infections ; *Vesico-Ureteral Reflux/complications ; }, abstract = {Children with vesicoureteral reflux (VUR) are at an increased risk of recurrent urinary tract infections (UTIs) and renal scarring. Gut microbiota are associated with disease phenotypes, but there has been no study that associates urinary microbiota (uMB) and metabolic profiles with VUR pathology. To identify dominant uMB genera and metabolites associated with UTIs in VUR, urine samples collected under sterile conditions underwent 16S ribosomal RNA sequencing (n = 49) and metabolomic analysis by mass spectrometry (n = 96). Alterations in uMB and metabolomic profiles in VUR patients suggest remodeling of urinary bacterial communities after UTIs: Dorea- and Escherichia-dominant uMB profiles were more frequently identified in participants with VUR. Prevotella- and Lactobacillus-dominant uMB profiles were more prevalent in controls (p < 0.001). Microbial composition varied based on recurrent febrile UTI status (p = 0.001). A total of 243 urinary metabolites involved in energy, amino acid, nucleotide, and lipid metabolism were altered in VUR patients with UTIs (p < 0.05). Importantly, VUR specimens revealed changes in the bacteria-associated metabolic pathways such as glutamate degradation, methyl-citrate cycle, and bile acid metabolism. PATIENT SUMMARY: Differences in urinary commensal bacteria and metabolites exist between children with and without vesicoureteral reflux (VUR). These changes may be utilized to identify patients at risk of VUR-associated kidney damage.}, } @article {pmid34537643, year = {2022}, author = {Zhang, Z and Zhang, Q and Lu, T and Zhang, J and Sun, L and Hu, B and Hu, J and Peñuelas, J and Zhu, L and Qian, H}, title = {Residual chlorine disrupts the microbial communities and spreads antibiotic resistance in freshwater.}, journal = {Journal of hazardous materials}, volume = {423}, number = {Pt B}, pages = {127152}, pmid = {34537643}, issn = {1873-3336}, mesh = {Animals ; *COVID-19 ; Chlorine/toxicity ; Drug Resistance, Microbial ; Fresh Water ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; SARS-CoV-2 ; Zebrafish ; }, abstract = {Chlorine disinfection is a key global public health strategy for the prevention and control of diseases, such as COVID-19. However, little is known about effects of low levels of residual chlorine on freshwater microbial communities and antibiotic resistomes. Here, we treated freshwater microcosms with continuous low concentrations of chlorine and quantified the effects on aquatic and zebrafish intestinal microbial communities and antibiotic resistomes, using shotgun metagenome and 16S rRNA gene sequencing. Although chlorine rapidly degraded, it altered the aquatic microbial community composition over time and disrupted interactions among microbes, leading to decreases in community complexity and stability. However, community diversity was unaffected. The majority of ecological functions, particularly metabolic capacities, recovered after treatment with chlorine for 14 d, due to microbial community redundancy. There were also increased levels of antibiotic-resistance gene dissemination by horizontal and vertical gene transfer under chlorine treatment. Although the zebrafish intestinal microbial community recovered from temporary dysbiosis, growth and behavior of zebrafish adults were negatively affected by chlorine. Overall, our findings demonstrate the negative effects of residual chlorine on freshwater ecosystems and highlight a possible long-term risk to public health.}, } @article {pmid34537552, year = {2021}, author = {Jia, J and Liang, C and Wu, X and Xiong, L and Bao, P and Chen, Q and Yan, P}, title = {Effect of high proportion concentrate dietary on Ashdan Yak jejunal barrier and microbial function in cold season.}, journal = {Research in veterinary science}, volume = {140}, number = {}, pages = {259-267}, doi = {10.1016/j.rvsc.2021.09.010}, pmid = {34537552}, issn = {1532-2661}, mesh = {Animals ; Cattle ; Diet/veterinary ; Digestion ; *Jejunum ; Male ; *Microbiota ; Seasons ; }, abstract = {The intestinal health of ruminants plays a vital role in absorbing and metabolizing nutrients. In order to explore the jejunal barrier and microbiota dysfunction of Ashdan yaks, animals were fed with a high proportion of concentrated feeds in cold season. In present study, twelve Ashdan male yaks were arbitrarily separated into two categories, namely FF and CF. Compositional and functional differences in their jejunum barrier and microbiota between the FF and CF yaks were compared using metagenomics and proteomics methods. The results showed that the activity of jejunum digestive protease and microbe metabolite of forage-fed yaks were more conducive to healthy cultivation than the concentrate-fed yaks. 57 differentially expressed proteins (DEPs) were recognized using label-free MS, those could conclude to 2 principal classes: structural proteins and inflammatory factors, and 14 proteins were relatively active in those principal classes. Firmicutes were the dominant bacterial phylum in the jejunum microbiota of both the forage-fed group (24.33%) and concentrate-fed group (23.16%). As compared to forage-fed group, the concentrate-fed group showed enhanced alpha diversity and reduced beta diversity of the jejunal microbiota. The long-term high-proportion concentrate feeding inhibited the growth of Actinobacteria, Proteo-bacteria, Ascomycota, Bacteroidetes and stimulated the growth of Streptophyta, Cyanobacteria, Fusobacteria and Chlamydiae. The concentrate-fed group showed increase in the abundance of immune system process, along with decrease in the metabolic process, especially the binding process. Interestingly, the proteomics and metagenomics results were both inclined to the enrichment of jejunum mechanical barrier and inflammatory response. Overall, the study suggested that the long-term high-proportion concentrate feeding affected the expressions of specific jejunum proteins and composition of microbiota, which damaged the jejunum barrier and the function of microbiota in yaks.}, } @article {pmid34537163, year = {2021}, author = {Castillo-Álvarez, F and Pérez-Matute, P and Oteo, JA and Marzo-Sola, ME}, title = {The influence of interferon β-1b on gut microbiota composition in patients with multiple sclerosis.}, journal = {Neurologia}, volume = {36}, number = {7}, pages = {495-503}, doi = {10.1016/j.nrleng.2020.05.006}, pmid = {34537163}, issn = {2173-5808}, mesh = {Cross-Sectional Studies ; Feces ; *Gastrointestinal Microbiome ; Humans ; Interferon beta-1b/*therapeutic use ; *Multiple Sclerosis/drug therapy ; Prevotella ; }, abstract = {INTRODUCTION: The association between gut microbiota and animal models of multiple sclerosis has been well established; however, studies in humans are scarce.

METHODS: We performed a descriptive, cross-sectional study comparing the relative composition of gut microbiota in 30 patients with multiple sclerosis (15 treated with interferon β-1b, 15 not receiving this treatment) and 14 healthy controls using next generation sequencing.

RESULTS: Patients with multiple sclerosis and controls showed differences in the proportion of Euryarchaeota, Firmicutes, Proteobacteria, Actinobacteria, and Lentisphaerae phyla and in 17 bacterial species. More specifically, we found significant differences in the proportion of Firmicutes, Actinobacteria, and Lentisphaerae and 6 bacteria species between controls and untreated patients; however, these differences disappeared when compared with treated patients. Untreated patients showed a significant reduction in the proportion of Prevotella copri compared to controls, while the bacteria was significantly more abundant in patients treated with interferon β-1b than in untreated patients, with levels resembling those observed in the healthy control group.

CONCLUSION: We observed differences in gut microbiota composition between patients with multiple sclerosis and controls, and between patients treated and not treated with interferon β-1b. In most cases, no differences were observed between treated patients and healthy controls, particularly for P. copri levels. This suggests that the clinical improvements observed in patients with multiple sclerosis receiving interferon β-1b may result from the effect of the drug on gut microbiota. Longitudinal and functional studies are necessary to establish a causal relationship.}, } @article {pmid34532729, year = {2021}, author = {Gu, Z and Pei, W and Shen, Y and Wang, L and Zhu, J and Zhang, Y and Fan, S and Wu, Q and Li, L and Zhang, Z}, title = {Akkermansia muciniphila and its outer protein Amuc_1100 regulates tryptophan metabolism in colitis.}, journal = {Food & function}, volume = {12}, number = {20}, pages = {10184-10195}, doi = {10.1039/d1fo02172a}, pmid = {34532729}, issn = {2042-650X}, mesh = {Adult ; Akkermansia ; Animals ; Bacterial Outer Membrane Proteins/*pharmacology ; Colitis/drug therapy/metabolism ; Colitis, Ulcerative/blood/*drug therapy/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects ; Humans ; Kynurenine/metabolism ; Male ; Metabolomics/methods ; Metagenomics/methods ; Mice ; Mice, Inbred C57BL ; Middle Aged ; Picolinic Acids/metabolism ; Probiotics/*pharmacology ; Serotonin/metabolism ; Tryptophan/*metabolism ; }, abstract = {Dietary interventions, including dietary ingredients, nutrients and probiotics, exert anti-inflammatory effects in ulcerative colitis (UC). Our previous study showed that Akkermansia muciniphila (Akk), a promising probiotic, could protect against colitis via the regulation of the immune response. However, whether it can restore aberrant tryptophan (Trp) metabolism during colitis remains unclear. In this study, untargeted serum metabolomics of patients with UC and colitis mice showed that Trp metabolism was activated, which was confirmed by quantification of Trp metabolites from a validation cohort and animal study. Integrative analysis of faecal metagenomes and serum metabolomes revealed significant associations between Akk and three Trp metabolites. Live Akk, pasteurised Akk and Amuc_1100 failed to restore the reduction in Trp metabolites involved in the serotonin pathway in colitis mice. However, live Akk, pasteurised Akk and Amuc_1100 increased kynurenine (Kyn) but decreased 2-picolinic acid (PIC) levels and the PIC/Kyn ratio without regulating any of the genes involved in Trp metabolism, suggesting that they could suppress the Kyn pathway (KP) independent of colon tissue. In addition, they could significantly restore the enrichment of Trp metabolism mediated by faecal microbiota. Specifically, live Akk, pasteurised Akk and Amuc_1100 could significantly offset the reduction in indoleacetic acid (IAA) levels. Pasteurised Akk significantly elevated the serum levels of indole acrylic acid (IA). In addition, live Akk, pasteurised Akk and Amuc_1100 could upregulate aryl hydrocarbon receptor (AhR) targeted genes, including CYP1A1, IL-10 and IL-22, suggesting that Akk could activate AhR signaling by regulating Trp metabolism, thereby attenuating colonic inflammation.}, } @article {pmid34531862, year = {2021}, author = {Islam, SMS and Ryu, HM and Sayeed, HM and Byun, HO and Jung, JY and Kim, HA and Suh, CH and Sohn, S}, title = {Eubacterium rectale Attenuates HSV-1 Induced Systemic Inflammation in Mice by Inhibiting CD83.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {712312}, pmid = {34531862}, issn = {1664-3224}, mesh = {Administration, Oral ; Adult ; Animals ; Antigens, CD/biosynthesis/genetics ; Bacteria/classification/isolation & purification ; Behcet Syndrome/drug therapy/microbiology/*therapy ; Butyrates/metabolism/therapeutic use ; Colchicine/therapeutic use ; Combined Modality Therapy ; Dendritic Cells/immunology ; Disease Models, Animal ; Down-Regulation/drug effects ; *Eubacterium ; *Fecal Microbiota Transplantation ; Female ; *Gastrointestinal Microbiome ; Herpes Simplex/immunology/microbiology/therapy ; Herpesvirus 1, Human/*pathogenicity ; Humans ; Immunoglobulins/biosynthesis/genetics ; Inflammation/drug therapy/*therapy ; Interleukin-17/blood ; Killer Cells, Natural/immunology ; Male ; Membrane Glycoproteins/*antagonists & inhibitors/biosynthesis/genetics ; Metagenome ; Mice ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Random Allocation ; Ribotyping ; Severity of Illness Index ; CD83 Antigen ; }, abstract = {The purpose of this study was to determine whether administration of the microorganism Eubacterium rectale (E. rectale) could regulate dendritic cell (DC) activation and systemic inflammation in herpes simplex virus type 1-induced Behçet's disease (BD). E. rectale, butyrate-producing bacteria, was administered to BD mice. Peripheral blood leukocytes (PBL) and lymph node cells were isolated and analyzed by flow cytometry. 16S rRNA metagenomic analysis was performed in the feces of mice to determine the differences in the composition of the microbial population between normal and BD mice. Serum cytokine levels were measured by enzyme-linked immunosorbent assay. The frequency of DC activation marker CD83 positive cells was significantly increased in PBL of BD mice. Frequencies of CD83+ cells were also significantly increased in patients with active BD. 16S rRNA metagenomic analysis revealed different gut microbiota composition between normal and BD mice. The administration of E. rectale to BD mice reduced the frequency of CD83+ cells and significantly increased the frequency of NK1.1+ cells with the improvement of symptoms. The co-administration of colchicine and E. rectale also significantly reduced the frequency of CD83+ cells. Differences in gut microbiota were observed between normal mice and BD mice, and the administration of E. rectale downregulated the frequency of CD83, which was associated with BD deterioration. These data indicate that E. rectale could be a new therapeutic adjuvant for BD management.}, } @article {pmid34530620, year = {2021}, author = {Xu, S and Lyu, L and Zhu, H and Huang, X and Xu, W and Xu, W and Feng, Y and Fan, Y}, title = {Serum Metabolome Mediates the Antiobesity Effect of Celastrol-Induced Gut Microbial Alterations.}, journal = {Journal of proteome research}, volume = {20}, number = {10}, pages = {4840-4851}, doi = {10.1021/acs.jproteome.1c00513}, pmid = {34530620}, issn = {1535-3907}, mesh = {Animals ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; *Metabolome ; Mice ; Mice, Inbred C57BL ; Pentacyclic Triterpenes ; }, abstract = {The antiobesity effect of celastrol has been reported in numerous studies, but the underlying mechanism remains unclear. It is widely accepted that gut dysbiosis is closely related to obesity. The potential effect of celastrol on microbiota is worth exploring. In this study, the celastrol-induced weight loss was validated in high-fat diet (HFD)-induced obese mice, with the detection of reported phenotypes including a reduction in food intake, augments in dyslipidemia and glucose metabolism, and adipose thermogenesis. The anti-inflammatory effect of celastrol was also proved based on the alterations in serum cytokines. Antibiotic interference showed that gut microbiota contributes to celastrol-induced weight loss. Several key bacteria were identified using shotgun metagenomic sequencing to display the alterations of the intestinal microbiome in obese mice treated with celastrol. Meanwhile, the fecal and serum metabolic profiles were generated by pseudotargeted metabolomics, and changes in some critical metabolites related to appetite and metabolism were detected. Importantly, we applied in silico bidirectional mediation analysis to identify the precise connections among the alterations in gut microbes, serum metabolome, and host phenotypes induced by celastrol treatment for the first time. Therefore, we concluded that the celastrol-induced microbial changes partially contribute to the antiobesity effect via the serum metabolome. The mass spectrometry data are deposited on MetaboLights (ID: MTBLS3278).}, } @article {pmid34530224, year = {2021}, author = {Kim, DD and Wan, L and Cao, X and Klisarova, D and Gerdzhikov, D and Zhou, Y and Song, C and Yoon, S}, title = {Metagenomic insights into co-proliferation of Vibrio spp. and dinoflagellates Prorocentrum during a spring algal bloom in the coastal East China Sea.}, journal = {Water research}, volume = {204}, number = {}, pages = {117625}, doi = {10.1016/j.watres.2021.117625}, pmid = {34530224}, issn = {1879-2448}, mesh = {Cell Proliferation ; *Dinoflagellida/genetics ; Harmful Algal Bloom ; *Microbiota ; *Vibrio ; }, abstract = {Coastal harmful algal blooms (HABs), commonly termed 'red tides', have severe undesirable consequences to the marine ecosystems and local fishery and tourism industries. Increase in nitrogen and/or phosphorus loading is often regarded as the major culprits of increasing frequency and intensity of the coastal HAB; however, fundamental understanding is lacking as to the causes and mechanism of bloom formation despite decades of intensive investigation. In this study, we interrogated the prokaryotic microbiomes of surface water samples collected at two neighboring segments of East China Sea that contrast greatly in terms of the intensity and frequency of Prorocentrum-dominated HAB. Mantel tests identified significant correlations between the structural and functional composition of the microbiomes and the physicochemical state and the algal biomass density of the surface seawater, implying the possibility that prokaryotic microbiota may play key roles in the coastal HAB. A conspicuous feature of the microbiomes at the sites characterized with high trophic state index and eukaryotic algal cell counts was disproportionate proliferation of Vibrio spp., and their complete domination of the functional genes attributable to the dissimilatory nitrate reduction to ammonia (DNRA) pathway substantially enriched at these sites. The genes attributed to phosphorus uptake function were significantly enriched at these sites, presumably due to the Pi-deficiency induced by algal growth; however, the profiles of the phosphorus mineralization genes lacked consistency, barring any conclusive evidence with regard to contribution of prokaryotic microbiota to phosphorus bioavailability. The results of the co-occurrence network analysis performed with the core prokaryotic microbiome supported that the observed proliferation of Vibrio and HAB may be causally associated. The findings of this study suggest a previously unidentified association between Vibrio proliferation and the Prorocentrum-dominated HAB in the subtropical East China Sea, and opens a discussion regarding a theoretically unlikely, but still possible, involvement of Vibrio-mediated DNRA in Vibrio-Prorocentrum symbiosis. Further experimental substantiation of this supposed symbiotic mechanism may prove crucial in understanding the dynamics of explosive local algal growth in the region during spring algal blooms.}, } @article {pmid34530121, year = {2021}, author = {Zhang, Q and Guo, X and Xie, C and Cao, Z and Wang, X and Liu, L and Yang, P}, title = {Unraveling the metabolic pathway of choline-TMA-TMAO: Effects of gypenosides and implications for the therapy of TMAO related diseases.}, journal = {Pharmacological research}, volume = {173}, number = {}, pages = {105884}, doi = {10.1016/j.phrs.2021.105884}, pmid = {34530121}, issn = {1096-1186}, mesh = {Animals ; Brain/metabolism ; Choline/pharmacology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/drug effects/genetics ; Gynostemma ; Lipid Metabolism/drug effects ; Methylamines/blood/cerebrospinal fluid/*metabolism ; Mice, Inbred BALB C ; Microsomes, Liver/metabolism ; Oxygenases/metabolism ; Plant Extracts/pharmacology ; RNA, Ribosomal, 16S ; Mice ; }, abstract = {Trimethylamine-N-oxide (TMAO) has emerged as a promising new therapeutic target for the treatment of central nervous system diseases, atherosclerosis and other diseases. However, its origin in the brain is unclear. Gynostemma pentaphyllum (Thunb.) Makino can reduce the increase of TMAO level caused by a high fat diet. But its effective chemical composition and specific mechanism have not been reported. The study confirmed that TMA was more easily to penetrate blood brain barrier than TMAO, the MAO enzyme was partly involved in the transformation of the TMA in brain, which further supplemented the choline-TMA-TMAO pathway. Based on the above metabolic pathway, using multi-omics approaches, such as microbiodiversity, metagenomics and lipidomics, it was demonstrated that the reduction of plasma TMAO levels by gypenosides did not act on FMO3 and MAO in the pathway, but remodeled the microbiota and affected the trimethylamine lyase needed in the conversion of choline to TMA in intestinal flora. At the same time, gypenosides interfered with enzymes associated with TCA and lipid metabolism, thus affecting TMAO and lipid metabolism. Considering the bidirectional transformation of phosphatidycholine and choline, lipid metabolism and TMAO metabolism could affected each other to some extent. In conclusion, our study revealed the intrinsic correlation between long-term application of gypenosides to lipid reduction and nervous system protection, and explained why gypenosides were used to treat brain diseases, even though they had a poor ability to enter the brain. Besides, it provided a theoretical basis for clinical application of gypenosides and the development of new drugs.}, } @article {pmid34528142, year = {2022}, author = {Gorovtsov, A and Demin, K and Sushkova, S and Minkina, T and Grigoryeva, T and Dudnikova, T and Barbashev, A and Semenkov, I and Romanova, V and Laikov, A and Rajput, V and Kocharovskaya, Y}, title = {The effect of combined pollution by PAHs and heavy metals on the topsoil microbial communities of Spolic Technosols of the lake Atamanskoe, Southern Russia.}, journal = {Environmental geochemistry and health}, volume = {44}, number = {4}, pages = {1299-1315}, pmid = {34528142}, issn = {1573-2983}, support = {19-74-10046//Russian Science Foundation/ ; }, mesh = {Lakes ; *Metals, Heavy/analysis ; *Microbiota ; *Polycyclic Aromatic Hydrocarbons/analysis/toxicity ; Soil/chemistry ; Soil Microbiology ; *Soil Pollutants/analysis/toxicity ; }, abstract = {The contamination with organic and inorganic pollutants changes significantly soil microbial community structure. These shifts indicate anthropogenic pressure and help to discover new possibilities for soil remediation. In this study, the microbial community structure of Spolic Technosols formed at the territory of a former industrial sludge reservoir near the Kamensk-Shakhtinsky (Southern Russia) was studied using a metagenomics approach. The studied soils contain high concentrations of heavy metals (HM) (up to 72,900 mg kg[-1]) and 16 priority polycyclic aromatic hydrocarbons (PAHs) (up to 6670 mg kg[-1]). Its microbial communities demonstrate an excellent adaptability level reflected in their complexity and diversity. As shown by the high values of alpha diversity indices (Shannon values up to 10.1, Chao1 values from 1430 to 4273), instead of decreasing quantitatively and qualitatively on the systemic level, microbial communities tend to undergo complex redistribution. Regardless of contamination level, the share of Actinobacteria and Proteobacteria was consistently high and varied from 20 to 50%. Following the results of the Mann-Whitney U test, there were significant changes of less abundant phyla. The abundance of oligotrophic bacteria from Gemmatimonadetes and Verrucomicrobia phyla and autotrophic bacteria (e.g., Nitrospira) decreased due to the high PAH's level. And abundance of Firmicutes and amoebae-associated bacteria such as TM6 and soil Chlamydia increased in highly contaminated plots. In the Spolic Technosols studied, the influence of factors on the microbial community composition decreased from PAHs concentration to soil characteristics (organic carbon content) and phylum-phylum interactions. The high concentrations of HMs influenced weakly on the microbial community composition.}, } @article {pmid34526611, year = {2021}, author = {Garneau, JR and Legrand, V and Marbouty, M and Press, MO and Vik, DR and Fortier, LC and Sullivan, MB and Bikard, D and Monot, M}, title = {High-throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {18319}, pmid = {34526611}, issn = {2045-2322}, mesh = {Algorithms ; Bacteriophages/*genetics/physiology ; Computational Biology/methods ; Databases, Genetic ; *Genome, Viral ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Software ; *Viral Packaging Sequence ; *Virome ; Workflow ; }, abstract = {Viruses that infect bacteria (phages) are increasingly recognized for their importance in diverse ecosystems but identifying and annotating them in large-scale sequence datasets is still challenging. Although efficient scalable virus identification tools are emerging, defining the exact ends (termini) of phage genomes is still particularly difficult. The proper identification of termini is crucial, as it helps in characterizing the packaging mechanism of bacteriophages and provides information on various aspects of phage biology. Here, we introduce PhageTermVirome (PTV) as a tool for the easy and rapid high-throughput determination of phage termini and packaging mechanisms using modern large-scale metagenomics datasets. We successfully tested the PTV algorithm on a mock virome dataset and then used it on two real virome datasets to achieve the rapid identification of more than 100 phage termini and packaging mechanisms, with just a few hours of computing time. Because PTV allows the identification of free fully formed viral particles (by recognition of termini present only in encapsidated DNA), it can also complement other virus identification softwares to predict the true viral origin of contigs in viral metagenomics datasets. PTV is a novel and unique tool for high-throughput characterization of phage genomes, including phage termini identification and characterization of genome packaging mechanisms. This software should help researchers better visualize, map and study the virosphere. PTV is freely available for downloading and installation at https://gitlab.pasteur.fr/vlegrand/ptv .}, } @article {pmid34526566, year = {2021}, author = {Misra, N and Clavaud, C and Guinot, F and Bourokba, N and Nouveau, S and Mezzache, S and Palazzi, P and Appenzeller, BMR and Tenenhaus, A and Leung, MHY and Lee, PKH and Bastien, P and Aguilar, L and Cavusoglu, N}, title = {Multi-omics analysis to decipher the molecular link between chronic exposure to pollution and human skin dysfunction.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {18302}, pmid = {34526566}, issn = {2045-2322}, mesh = {*Biomarkers ; Disease Susceptibility ; Environmental Exposure/*adverse effects ; Environmental Pollution/*adverse effects ; *Genomics/methods ; Humans ; *Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Microbiota ; Skin/*metabolism/microbiology/pathology ; Skin Diseases/etiology/metabolism/pathology ; }, abstract = {Environmental pollution is composed of several factors, namely particulate matter (PM2.5, PM10), ozone and Ultra Violet (UV) rays among others and first and the most exposed tissue to these substances is the skin epidermis. It has been established that several skin disorders such as eczema, acne, lentigines and wrinkles are aggravated by exposure to atmospheric pollution. While pollutants can interact with skin surface, contamination of deep skin by ultrafine particles or Polycyclic aromatic hydrocarbons (PAH) might be explained by their presence in blood and hair cortex. Molecular mechanisms leading to skin dysfunction due to pollution exposure have been poorly explored in humans. In addition to various host skin components, cutaneous microbiome is another target of these environment aggressors and can actively contribute to visible clinical manifestation such as wrinkles and aging. The present study aimed to investigate the association between pollution exposure, skin microbiota, metabolites and skin clinical signs in women from two cities with different pollution levels. Untargeted metabolomics and targeted proteins were analyzed from D-Squame samples from healthy women (n = 67 per city), aged 25-45 years and living for at least 15 years in the Chinese cities of Baoding (used as a model of polluted area) and Dalian (control area with lower level of pollution). Additional samples by swabs were collected from the cheeks from the same population and microbiome was analysed using bacterial 16S rRNA as well as fungal ITS1 amplicon sequencing and metagenomics analysis. The level of exposure to pollution was assessed individually by the analysis of polycyclic aromatic hydrocarbons (PAH) and their metabolites in hair samples collected from each participant. All the participants of the study were assessed for the skin clinical parameters (acne, wrinkles, pigmented spots etc.). Women from the two cities (polluted and less polluted) showed distinct metabolic profiles and alterations in skin microbiome. Profiling data from 350 identified metabolites, 143 microbes and 39 PAH served to characterize biochemical events that correlate with pollution exposure. Finally, using multiblock data analysis methods, we obtained a potential molecular map consisting of multi-omics signatures that correlated with the presence of skin pigmentation dysfunction in individuals living in a polluted environment. Overall, these signatures point towards macromolecular alterations by pollution that could manifest as clinical sign of early skin pigmentation and/or other imperfections.}, } @article {pmid34526096, year = {2021}, author = {Gao, M and Xiong, C and Gao, C and Tsui, CKM and Wang, MM and Zhou, X and Zhang, AM and Cai, L}, title = {Disease-induced changes in plant microbiome assembly and functional adaptation.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {187}, pmid = {34526096}, issn = {2049-2618}, mesh = {Bacteria/genetics ; *Microbiota/genetics ; Plant Roots ; Rhizosphere ; *Soil Microbiology ; }, abstract = {BACKGROUND: The plant microbiome is an integral part of the host and increasingly recognized as playing fundamental roles in plant growth and health. Increasing evidence indicates that plant rhizosphere recruits beneficial microbes to the plant to suppress soil-borne pathogens. However, the ecological processes that govern plant microbiome assembly and functions in the below- and aboveground compartments under pathogen invasion are not fully understood. Here, we studied the bacterial and fungal communities associated with 12 compartments (e.g., soils, roots, stems, and fruits) of chili pepper (Capsicum annuum L.) using amplicons (16S and ITS) and metagenomics approaches at the main pepper production sites in China and investigated how Fusarium wilt disease (FWD) affects the assembly, co-occurrence patterns, and ecological functions of plant-associated microbiomes.

RESULTS: The amplicon data analyses revealed that FWD affected less on the microbiome of pepper reproductive organs (fruit) than vegetative organs (root and stem), with the strongest impact on the upper stem epidermis. Fungal intra-kingdom networks were less stable and their communities were more sensitive to FWD than the bacterial communities. The analysis of microbial interkingdom network further indicated that FWD destabilized the network and induced the ecological importance of fungal taxa. Although the diseased plants were more susceptible to colonization by other pathogenic fungi, their below- and aboveground compartments can also recruit potential beneficial bacteria. Some of the beneficial bacterial taxa enriched in the diseased plants were also identified as core taxa for plant microbiomes and hub taxa in networks. On the other hand, metagenomic analysis revealed significant enrichment of several functional genes involved in detoxification, biofilm formation, and plant-microbiome signaling pathways (i.e., chemotaxis) in the diseased plants.

CONCLUSIONS: Together, we demonstrate that a diseased plant could recruit beneficial bacteria and mitigate the changes in reproductive organ microbiome to facilitate host or its offspring survival. The host plants may attract the beneficial microbes through the modulation of plant-microbiome signaling pathways. These findings significantly advance our understanding on plant-microbiome interactions and could provide fundamental and important data for harnessing the plant microbiome in sustainable agriculture. Video abstract.}, } @article {pmid34525937, year = {2021}, author = {Moran-Ramos, S and Macias-Kauffer, L and López-Contreras, BE and Villamil-Ramírez, H and Ocampo-Medina, E and León-Mimila, P and Del Rio-Navarro, BE and Granados-Portillo, O and Ibarra-Gonzalez, I and Vela-Amieva, M and Tovar, AR and Torres, N and Gomez-Perez, FJ and Aguilar-Salinas, C and Canizales-Quinteros, S}, title = {A higher bacterial inward BCAA transport driven by Faecalibacterium prausnitzii is associated with lower serum levels of BCAA in early adolescents.}, journal = {Molecular medicine (Cambridge, Mass.)}, volume = {27}, number = {1}, pages = {108}, pmid = {34525937}, issn = {1528-3658}, support = {248765//consejo nacional de ciencia y tecnología/ ; }, mesh = {Adolescent ; Age Factors ; Amino Acids, Branched-Chain/*blood/metabolism ; Biomarkers ; Body Weights and Measures ; Child ; Faecalibacterium prausnitzii/*physiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Insulin Resistance ; Male ; Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Obesity/metabolism ; Public Health Surveillance ; }, abstract = {BACKGROUND: Elevations of circulating branched-chain amino acids (BCAA) are observed in humans with obesity and metabolic comorbidities, such as insulin resistance. Although it has been described that microbial metabolism contributes to the circulating pool of these amino acids, studies are still scarce, particularly in pediatric populations. Thus, we aimed to explore whether in early adolescents, gut microbiome was associated to circulating BCAA and in this way to insulin resistance.

METHODS: Shotgun sequencing was performed in DNA from fecal samples of 23 early adolescents (10-12 years old) and amino acid targeted metabolomics analysis was performed by LC-MS/MS in serum samples. By using the HUMAnN2 algorithm we explored microbiome functional profiles to identify whether bacterial metabolism contributed to serum BCAA levels and insulin resistance markers.

RESULTS: We identified that abundance of genes encoding bacterial BCAA inward transporters were negatively correlated with circulating BCAA and HOMA-IR (P < 0.01). Interestingly, Faecalibacterium prausnitzii contributed to approximately ~ 70% of bacterial BCAA transporters gene count. Moreover, Faecalibacterium prausnitzii abundance was also negatively correlated with circulating BCAA (P = 0.001) and with HOMA-IR (P = 0.018), after adjusting for age, sex and body adiposity. Finally, the association between Faecalibacterium genus and BCAA levels was replicated over an extended data set (N = 124).

CONCLUSIONS: We provide evidence that gut bacterial BCAA transport genes, mainly encoded by Faecalibacterium prausnitzii, are associated with lower circulating BCAA and lower insulin resistance. Based on the later, we propose that the relationship between Faecalibacterium prausnitzii and insulin resistance, could be through modulation of BCAA.}, } @article {pmid34524637, year = {2022}, author = {Liu, J and Zuo, X and Peng, K and He, R and Yang, L and Liu, R}, title = {Biogas and Volatile Fatty Acid Production During Anaerobic Digestion of Straw, Cellulose, and Hemicellulose with Analysis of Microbial Communities and Functions.}, journal = {Applied biochemistry and biotechnology}, volume = {194}, number = {2}, pages = {762-782}, pmid = {34524637}, issn = {1559-0291}, support = {21808010//National Natural Science Foundation of China/ ; 2018YFE111000//Key Technologies Research and Development Program/ ; }, mesh = {*Cellulose/metabolism ; *Fatty Acids, Volatile/metabolism ; *Polysaccharides/metabolism ; *Biofuels ; Anaerobiosis ; Methane/metabolism/biosynthesis ; Microbiota ; Oryza/metabolism ; }, abstract = {The anaerobic digestion efficiency and methane production of straw was limited by its complex composition and structure. In this study, rice straw (RS), cellulose, and hemicellulose were used as raw materials to study biogas production performance and changes in the volatile fatty acids (VFAs). Further, microbial communities and genetic functions were analyzed separately for each material. The biogas production potential of RS, cellulose, and hemicellulose was different, with cumulative biogas production of 283.75, 412.50, and 620.64 mL/(g·VS), respectively. The methane content of the biogas produced from cellulose and hemicellulose was approximately 10% higher than that produced from RS after the methane content stabilized. The accumulation of VFAs occurred in the early stage of anaerobic digestion in all materials, and the cumulative amount of VFAs in both cellulose and hemicellulose was relatively higher than that in RS, and the accumulation time was 12 and 14 days longer, respectively. When anaerobic digestion progressed to a stable stage, Clostridium was the dominant bacterial genus in all three anaerobic digestion systems, and the abundance of Ruminofilibacter was higher during anaerobic digestion of RS. Genetically, anaerobic digestion of all raw materials proceeded mainly via aceticlastic methanogenesis, with similar functional components. The different performance of anaerobic digestion of RS, cellulose, and hemicellulose mainly comes from the difference of composition of raw materials. Increasing the accessibility of cellulose and hemicellulose in RS feedstock by pretreatment is an effective way to improve the efficiency of anaerobic digestion. Since the similar microbial community structure will be acclimated during anaerobic digestion, there is no need to adjust the initial inoculum when the accessibility of cellulose and hemicellulose changes.}, } @article {pmid34523982, year = {2021}, author = {Guan, H and Pu, Y and Liu, C and Lou, T and Tan, S and Kong, M and Sun, Z and Mei, Z and Qi, Q and Quan, Z and Zhao, G and Zheng, Y}, title = {Comparison of Fecal Collection Methods on Variation in Gut Metagenomics and Untargeted Metabolomics.}, journal = {mSphere}, volume = {6}, number = {5}, pages = {e0063621}, pmid = {34523982}, issn = {2379-5042}, mesh = {Adult ; DNA, Bacterial ; Ethanol ; Feces/*microbiology ; Female ; Freezing ; Gastrointestinal Microbiome/*genetics ; Healthy Volunteers ; Humans ; Male ; Metabolomics/*methods ; Metagenome/genetics ; Metagenomics/*methods ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Specimen Handling/*methods ; Temperature ; Whole Genome Sequencing ; }, abstract = {Integrative analysis of high-quality metagenomics and metabolomics data from fecal samples provides novel clues for the mechanism underpinning gut microbe-human interactions. However, data regarding the influence of fecal collection methods on both metagenomics and metabolomics are sparse. Six fecal collection methods (the gold standard [GS] [i.e., immediate freezing at -80°C with no solution], 95% ethanol, RNAlater, OMNIgene Gut, fecal occult blood test [FOBT] cards, and Microlution) were used to collect 88 fecal samples from eight healthy volunteers for whole-genome shotgun sequencing (WGSS) and untargeted metabolomic profiling. Metrics assessed included the abundances of predominant phyla and α- and β-diversity at the species, gene, and pathway levels. Intraclass correlation coefficients (ICCs) were calculated for microbes and metabolites to estimate (i) stability (day 4 versus day 0 within each method), (ii) concordance (day 0 for each method versus the GS), and (iii) reliability (day 4 for each method versus the GS). For the top 4 phyla and microbial diversity metrics at the species, gene, and pathway levels, generally high stability and reliability were observed for most methods except for 95% ethanol; similar concordances were seen for different methods. For metabolomics data, 95% ethanol showed the highest stability, concordance, and reliability (median ICCs = 0.71, 0.71, and 0.65, respectively). Taken together, OMNIgene Gut, FOBT cards, RNAlater, and Microlution, but not 95% ethanol, were reliable collection methods for gut metagenomic studies. However, 95% ethanol was the best for preserving fecal metabolite profiles. We recommend using separate collecting methods for gut metagenomic sequencing and fecal metabolomic profiling in large population studies. IMPORTANCE The choice of fecal collection method is essential for studying gut microbe-human interactions in large-scale population-based research. In this study, we examined the effects of fecal collection methods and storage time at ambient temperature on variations in the gut microbiome community composition; microbial diversity metrics at the species, gene, and pathway levels; antibiotic resistance genes; and metabolome profiling. Our findings suggest using different fecal sample collection methods for different data generation purposes. OMNIgene Gut, FOBT cards, RNAlater, and Microlution, but not 95% ethanol, were reliable collection methods for gut metagenomic studies. However, 95% ethanol was the best for preserving fecal metabolite profiles.}, } @article {pmid34523979, year = {2021}, author = {Hellmann, KT and Tuura, CE and Fish, J and Patel, JM and Robinson, DA}, title = {Viability-Resolved Metagenomics Reveals Antagonistic Colonization Dynamics of Staphylococcus epidermidis Strains on Preterm Infant Skin.}, journal = {mSphere}, volume = {6}, number = {5}, pages = {e0053821}, pmid = {34523979}, issn = {2379-5042}, support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA, Bacterial/analysis ; Feces/microbiology ; Gastrointestinal Microbiome/genetics ; Humans ; Infant ; *Infant, Premature ; Metagenome ; Metagenomics/methods ; Skin/*microbiology ; Staphylococcus epidermidis/*genetics/*physiology ; }, abstract = {Preterm infants are at increased risk of infections caused by coagulase-negative staphylococci (CoNS) that colonize skin. Technical barriers in sequencing low-microbial-biomass skin swabs from preterm infants hinder attempts to gain a strain-level understanding of CoNS colonization dynamics within their developing skin microbiome. Here, the microbiome of five skin sites and available stool was studied from four preterm infants hospitalized over their first 2 months of life. We used propidium monoazide treatment of samples to enrich for the viable microbiome and metagenomic shotgun sequencing to resolve species and strains. The microbiome of different skin sites overlapped with each other, was dominated by the CoNS species Staphylococcus epidermidis and Staphylococcus capitis, and was distinct from stool. Species diversity on skin increased over time despite antibiotic exposure. Evidence of antagonism between the most common S. epidermidis strains, ST2 and ST59, included negative relationships for species correlation networks and in situ replication rates and that ST2 colonized skin earlier but was often replaced by ST59 over time. Experiments done with reference isolates showed that ST2 produced more biofilm than ST59 on plastic surfaces, which was reduced in mixed culture. We also discovered that a rare S. epidermidis strain, ST5, grew rapidly in stool in association with Stenotrophomonas maltophilia from a suspected episode of infection. Viability treatment of samples and moderate throughput shotgun sequencing provides strain-level information about CoNS colonization dynamics of preterm infant skin that ultimately might be exploited to prevent infections. IMPORTANCE The skin is a habitat for microbes that commonly infect preterm infants, but the use of sequencing for fine-scale study of the microbial communities of skin that develop in these infants has been limited by technical barriers. We treated skin swabs of preterm infants with a photoreactive dye that eliminates DNA from nonviable microbes and then sequenced the remaining DNA. We found that two strains of the most common species, Staphylococcus epidermidis, showed an antagonistic relationship on skin by cooccurring with different species, replicating fastest in different samples, and dominating skin sites at different times. Representatives of these strains also differed in their ability to stick to plastic surfaces-an important pathogenicity trait of this species. Our study shows the feasibility of gaining detailed information about strain colonization dynamics from this difficult-to-sequence body site of preterm infants, which might be used to guide novel approaches to prevent infections.}, } @article {pmid34523726, year = {2021}, author = {Lu, H and Xu, J and Hu, Y and Luo, H and Chen, Y and Xie, B and Song, X}, title = {Differences in the skin microbial community between patients with active and stable vitiligo based on 16S rRNA gene sequencing.}, journal = {The Australasian journal of dermatology}, volume = {62}, number = {4}, pages = {e516-e523}, doi = {10.1111/ajd.13721}, pmid = {34523726}, issn = {1440-0960}, support = {LGF18H110001//Basic Public Welfare Research Project of Zhejiang Province/ ; 81872517//National Natural Science Foundation of China/ ; }, mesh = {Adult ; Aged ; China ; Dysbiosis/*complications/*pathology ; Female ; Humans ; Male ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S ; Sequence Analysis, RNA ; Skin/*microbiology ; Streptococcus/isolation & purification ; Streptomyces/isolation & purification ; Vitiligo/*microbiology/*pathology ; Young Adult ; }, abstract = {BACKGROUND/OBJECTIVE: Recent studies have described an association between altered skin microbial community and epidemiology of skin diseases, such as vitiligo, atopic dermatitis and psoriasis. In this study, we conducted microbiological analysis on patients at different stages of vitiligo to determine whether the dysbiosis is associated with disease progression.

METHODS: To characterise the skin microbes in vitiligo patients, we profiled samples collected from 40 patients with active and stable vitiligo using the Novaseq sequencer. Alpha diversity was used to measure richness and uniformity, while Beta diversity (Non-Metric Multi-Dimensional Scaling) analysis was used to show the differences. Moreover, the species differences were evaluated by LEfSe analysis and the flora gene function was predicted using Statistical Analysis of Metagenomic Profiles (STAMP).

RESULTS: The alpha diversity results showed no significant differences between active vitiligo and stable vitiligo, while beta diversity and LEfSe analysis results showed the differences in community composition. Streptomyces and Streptococcus were enriched in active vitiligo compared to stable vitiligo. In addition, the flora gene function of mixed acid fermentation was more pronounced in active vitiligo, while the function of lipid IVA biosynthesis was more significant in stable vitiligo.

CONCLUSION: This study has shown the differences in epidermal microbes between active vitiligo and stable vitiligo. Our results suggest that maintaining the flora balance might be a potential therapeutic target for vitiligo.}, } @article {pmid34523579, year = {2021}, author = {Fung, AHY and Rao, S and Ngan, WY and Sekoai, PT and Touyon, L and Ho, TM and Wong, KP and Habimana, O}, title = {Exploring the optimization of aerobic food waste digestion efficiency through the engineering of functional biofilm Bio-carriers.}, journal = {Bioresource technology}, volume = {341}, number = {}, pages = {125869}, doi = {10.1016/j.biortech.2021.125869}, pmid = {34523579}, issn = {1873-2976}, mesh = {Biofilms ; Digestion ; *Food ; Microbial Consortia ; *Refuse Disposal ; }, abstract = {The possibility of breaking down cellulose-rich food waste through biofilm engineering was investigated. Six previously isolated strains from naturally degrading fruits and vegetables, screened for biofilm-forming ability and cellulolytic activity, were selected to enrich a biocarrier seeding microbial consortium. The food waste model used in this study was cabbage which was aerobically digested under repeated water rinsing and regular effluent drainage. The engineered biocarrier biofilm's functionality was evaluated by tracing microbial succession following metagenomic sequencing, quantitative PCR, scanning electron microscopy, and cellulolytic activity before and after the digestion processes. The engineered microbial consortium demonstrated superior biofilm-forming ability on biocarriers than the original microbial consortium and generally displayed a higher cellulolytic activity. The presented study provides one of the few studies of food waste aerobic digestion using engineered biofilms. Insights presented in this study could help further optimize aerobic food waste digestion.}, } @article {pmid34521917, year = {2021}, author = {Leontidou, K and Vokou, D and Sandionigi, A and Bruno, A and Lazarina, M and De Groeve, J and Li, M and Varotto, C and Girardi, M and Casiraghi, M and Cristofori, A}, title = {Plant biodiversity assessment through pollen DNA metabarcoding in Natura 2000 habitats (Italian Alps).}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {18226}, pmid = {34521917}, issn = {2045-2322}, mesh = {*Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Genome, Plant ; Magnoliopsida/*classification/genetics/physiology ; Metagenome ; Metagenomics/*methods ; Pollen/*genetics ; }, abstract = {Monitoring biodiversity is of increasing importance in natural ecosystems. Metabarcoding can be used as a powerful molecular tool to complement traditional biodiversity monitoring, as total environmental DNA can be analyzed from complex samples containing DNA of different origin. The aim of this research was to demonstrate the potential of pollen DNA metabarcoding using the chloroplast trnL partial gene sequencing to characterize plant biodiversity. Collecting airborne biological particles with gravimetric Tauber traps in four Natura 2000 habitats within the Natural Park of Paneveggio Pale di San Martino (Italian Alps), at three-time intervals in 1 year, metabarcoding identified 68 taxa belonging to 32 local plant families. Metabarcoding could identify with finer taxonomic resolution almost all non-rare families found by conventional light microscopy concurrently applied. However, compared to microscopy quantitative results, Poaceae, Betulaceae, and Oleaceae were found to contribute to a lesser extent to the plant biodiversity and Pinaceae were more represented. Temporal changes detected by metabarcoding matched the features of each pollen season, as defined by aerobiological studies running in parallel, and spatial heterogeneity was revealed between sites. Our results showcase that pollen metabarcoding is a promising approach in detecting plant species composition which could provide support to continuous monitoring required in Natura 2000 habitats for biodiversity conservation.}, } @article {pmid34520804, year = {2021}, author = {An, Y and Zhang, W and Liu, T and Wang, B and Cao, H}, title = {The intratumoural microbiota in cancer: new insights from inside.}, journal = {Biochimica et biophysica acta. Reviews on cancer}, volume = {1876}, number = {2}, pages = {188626}, doi = {10.1016/j.bbcan.2021.188626}, pmid = {34520804}, issn = {1879-2561}, mesh = {Humans ; Microbiota/*immunology ; Neoplasms/*immunology ; Tumor Microenvironment/*immunology ; }, abstract = {The human body harbors a vast array of microbiota that modulates host pathophysiological processes and modifies the risk of diseases including cancer. With the advent of metagenomic sequencing studies, the intratumoural microbiota has been found as a component of the tumor microenvironment, imperceptibly affecting the tumor progression and response to current antitumor treatments. The underlying carcinogenic mechanisms of intratumoural microbiota, mainly including inducing DNA damages, activating oncogenic signaling pathways and suppressing the immune response, differ significantly in varied organs and are not fully understood. Some native or genetically engineered microbial species can specifically accumulate and replicate within tumors to initiate antitumor immunity, which will be conducive to pursue precise cancer therapies. In this review, we summarized the community characteristics and therapeutic potential of intratumoural microbiota across diverse tumor types. It may provide new insights for a better understanding of tumor biology and hint at the significance of manipulating intratumoural microbiota.}, } @article {pmid34520120, year = {2022}, author = {Yan, L and Tang, L and Zhou, Z and Lu, W and Wang, B and Sun, Z and Jiang, X and Hu, D and Li, J and Zhang, D}, title = {Metagenomics reveals contrasting energy utilization efficiencies of captive and wild camels (Camelus ferus).}, journal = {Integrative zoology}, volume = {17}, number = {3}, pages = {333-345}, doi = {10.1111/1749-4877.12585}, pmid = {34520120}, issn = {1749-4877}, support = {2019JQ03018//Beijing Forestry University Outstanding Young Talent Cultivation Project/ ; BX20190042//Postdoctoral Innovative Talents Support Program/ ; 2020M670177//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; Animals, Wild ; *Camelus/genetics ; Feces ; *Gastrointestinal Microbiome ; Metagenomics ; }, abstract = {Captive conditions can affect the symbiotic microbiome of animals. In this study, we compared the structural and functional differences of the gastrointestinal microbiomes of wild Bactrian camels (Camelus ferus) between wild and captive populations, as well as their different host energy utilization performances through metagenomics. The results showed that wild-living camels harbored more microbial taxa related to the production of volatile fatty acids, fewer methanogens, and fewer genes encoding enzymes involved in methanogenesis, leading to higher energy utilization efficiency compared to that of captive-living camels. These findings suggest that the wild-living camel fecal microbiome demonstrates a series of adaptive characteristics that enable the host to adjust to a relatively barren field environment. Our study provides novel insights into the mechanisms of wildlife adaptations to habitats from the perspective of the microbiome.}, } @article {pmid34519857, year = {2021}, author = {Zhu, HZ and Jiang, MZ and Zhou, N and Jiang, CY and Liu, SJ}, title = {Submerged macrophytes recruit unique microbial communities and drive functional zonation in an aquatic system.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {19}, pages = {7517-7528}, pmid = {34519857}, issn = {1432-0614}, support = {NSFC grant no. 31861133002//National Natural Science Foundation of China/ ; }, mesh = {Beijing ; *Metagenomics ; *Microbiota ; }, abstract = {Aquatic and wetland systems are widely used for landscapes and water regeneration. Microbiomes and submerged macrophytes (hydrophytes) play essential roles in conversions of organic and inorganic compounds in those ecosystems. The systems were extensively investigated for microbial diversities and compositions. However, little is known about how hydrophytes recruited diverse microbiota and affected functional zonation in aquatic systems. To address this issue, epiphytic leaf and root, sediment, and surrounding water samples were collected from the dragon-shape aquatic system in Beijing Olympic Park. Metagenomic DNAs were extracted and subjected to sequencing. Results showed that epiphytic leaf and root microbiomes and metabolic marker genes were remarkably different from that of surrounding environment. Twenty indicator bacterial genera for epiphytic microbiomes were identified and 50 metabolic marker genes were applied to evaluate the function of epiphytic leaf and root, water, and sediment microbiomes. Co-occurrence analysis revealed highly modularized pattern of metabolic marker genes and indicator bacterial genera related to metabolic functions. These results suggested that hydrophytes shaped microbiomes and drove functional zonation in aquatic systems. KEY POINTS: • Microbiomes of hydrophytes and their surrounding environments were investigated. • Twenty indicator bacterial genera highly specific to epiphytic biofilms were identified. • Epiphytes recruited unique microbiomes and drove functional zonation in aquatic systems.}, } @article {pmid34519519, year = {2021}, author = {Putman, LI and Sabuda, MC and Brazelton, WJ and Kubo, MD and Hoehler, TM and McCollom, TM and Cardace, D and Schrenk, MO}, title = {Microbial Communities in a Serpentinizing Aquifer Are Assembled through Strong Concurrent Dispersal Limitation and Selection.}, journal = {mSystems}, volume = {6}, number = {5}, pages = {e0030021}, pmid = {34519519}, issn = {2379-5077}, support = {NNA15BB02A//NASA | NASA Astrobiology Institute (NAI)/ ; }, abstract = {In recent years, our appreciation of the extent of habitable environments in Earth's subsurface has greatly expanded, as has our understanding of the biodiversity contained within. Most studies have relied on single sampling points, rather than considering the long-term dynamics of subsurface environments and their microbial populations. One such habitat are aquifers associated with the aqueous alteration of ultramafic rocks through a process known as serpentinization. Ecological modeling performed on a multiyear time series of microbiology, hydrology, and geochemistry in an ultrabasic aquifer within the Coast Range Ophiolite reveals that community assembly is governed by undominated assembly (i.e., neither stochastic [random] nor deterministic [selective] processes alone govern assembly). Controls on community assembly were further assessed by characterizing aquifer hydrogeology and microbial community adaptations to the environment. These analyses show that low permeability rocks in the aquifer restrict the transmission of microbial populations between closely situated wells. Alpha and beta diversity measures and metagenomic and metatranscriptomic data from microbial communities indicate that high pH and low dissolved inorganic carbon levels impose strong environmental selection on microbial communities within individual wells. Here, we find that the interaction between strong selection imposed by extreme pH and enhanced ecological drift due to dispersal limitation imposed by slow fluid flow results in the undominated assembly signal observed throughout the site. Strong environmental selection paired with extremely low dispersal in the subsurface results in low diversity microbial communities that are well adapted to extreme pH conditions and subject to enhanced stochasticity introduced by ecological drift over time. IMPORTANCE Microbial communities existing under extreme or stressful conditions have long been thought to be structured primarily by deterministic processes. The application of macroecology theory and modeling to microbial communities in recent years has spurred assessment of assembly processes in microbial communities, revealing that both stochastic and deterministic processes are at play to different extents within natural environments. We show that low diversity microbial communities in a hard-rock serpentinizing aquifer are assembled under the influence of strong selective processes imposed by high pH and enhanced ecological drift that occurs as the result of dispersal limitation due to the slow movement of water in the low permeability aquifer. This study demonstrates the important roles that both selection and dispersal limitation play in terrestrial serpentinites, where extreme pH assembles a microbial metacommunity well adapted to alkaline conditions and dispersal limitation drives compositional differences in microbial community composition between local communities in the subsurface.}, } @article {pmid34518213, year = {2021}, author = {Six, C and Ratin, M and Marie, D and Corre, E}, title = {Marine Synechococcus picocyanobacteria: Light utilization across latitudes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {38}, pages = {}, pmid = {34518213}, issn = {1091-6490}, mesh = {Adaptation, Physiological/genetics/physiology ; Bacterial Proteins/genetics ; Cold Temperature ; Ecosystem ; Ecotype ; Light ; Metagenome/genetics ; Metagenomics/methods ; Photosynthesis/genetics/physiology ; Seawater ; Synechococcus/*genetics/*physiology ; }, abstract = {The most ubiquitous cyanobacteria, Synechococcus, have colonized different marine thermal niches through the evolutionary specialization of lineages adapted to different ranges of temperature seawater. We used the strains of Synechococcus temperature ecotypes to study how light utilization has evolved in the function of temperature. The tropical Synechococcus (clade II) was unable to grow under 16 °C but, at temperatures >25 °C, induced very high growth rates that relied on a strong synthesis of the components of the photosynthetic machinery, leading to a large increase in photosystem cross-section and electron flux. By contrast, the Synechococcus adapted to subpolar habitats (clade I) grew more slowly but was able to cope with temperatures <10 °C. We show that growth at such temperatures was accompanied by a large increase of the photoprotection capacities using the orange carotenoid protein (OCP). Metagenomic analyzes revealed that Synechococcus natural communities show the highest prevalence of the ocp genes in low-temperature niches, whereas most tropical clade II Synechococcus have lost the gene. Moreover, bioinformatic analyzes suggested that the OCP variants of the two cold-adapted Synechococcus clades I and IV have undergone evolutionary convergence through the adaptation of the molecular flexibility. Our study points to an important role of temperature in the evolution of the OCP. We, furthermore, discuss the implications of the different metabolic cost of these physiological strategies on the competitiveness of Synechococcus in a warming ocean. This study can help improve the current hypotheses and models aimed at predicting the changes in ocean carbon fluxes in response to global warming.}, } @article {pmid34517888, year = {2021}, author = {Gupta, VK and Cunningham, KY and Hur, B and Bakshi, U and Huang, H and Warrington, KJ and Taneja, V and Myasoedova, E and Davis, JM and Sung, J}, title = {Gut microbial determinants of clinically important improvement in patients with rheumatoid arthritis.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {149}, pmid = {34517888}, issn = {1756-994X}, mesh = {Aged ; Aged, 80 and over ; Arthritis, Rheumatoid/*therapy ; Clostridiales ; Cohort Studies ; Dysbiosis ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Male ; Metagenome ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S ; Retrospective Studies ; Severity of Illness Index ; }, abstract = {BACKGROUND: Rapid advances in the past decade have shown that dysbiosis of the gut microbiome is a key hallmark of rheumatoid arthritis (RA). Yet, the relationship between the gut microbiome and clinical improvement in RA disease activity remains unclear. In this study, we explored the gut microbiome of patients with RA to identify features that are associated with, as well as predictive of, minimum clinically important improvement (MCII) in disease activity.

METHODS: We conducted a retrospective, observational cohort study on patients diagnosed with RA between 1988 and 2014. Whole metagenome shotgun sequencing was performed on 64 stool samples, which were collected from 32 patients with RA at two separate time-points approximately 6-12 months apart. The Clinical Disease Activity Index (CDAI) of each patient was measured at both time-points to assess achievement of MCII; depending on this clinical status, patients were distinguished into two groups: MCII+ (who achieved MCII; n = 12) and MCII- (who did not achieve MCII; n = 20). Multiple linear regression models were used to identify microbial taxa and biochemical pathways associated with MCII while controlling for potentially confounding factors. Lastly, a deep-learning neural network was trained upon gut microbiome, clinical, and demographic data at baseline to classify patients according to MCII status, thereby enabling the prediction of whether a patient will achieve MCII at follow-up.

RESULTS: We found age to be the largest determinant of the overall compositional variance in the gut microbiome (R[2] = 7.7%, P = 0.001, PERMANOVA). Interestingly, the next factor identified to explain the most variance in the gut microbiome was MCII status (R[2] = 3.8%, P = 0.005). Additionally, by looking at patients' baseline gut microbiome profiles, we observed significantly different microbiome traits between patients who eventually showed MCII and those who did not. Taxonomic features include alpha- and beta-diversity measures, as well as several microbial taxa, such as Coprococcus, Bilophila sp. 4_1_30, and Eubacterium sp. 3_1_31. Notably, patients who achieved clinical improvement had higher alpha-diversity in their gut microbiomes at both baseline and follow-up visits. Functional profiling identified fifteen biochemical pathways, most of which were involved in the biosynthesis of L-arginine, L-methionine, and tetrahydrofolate, to be differentially abundant between the MCII patient groups. Moreover, MCII+ and MCII- groups showed significantly different fold-changes (from baseline to follow-up) in eight microbial taxa and in seven biochemical pathways. These results could suggest that, depending on the clinical course, gut microbiomes not only start at different ecological states, but also are on separate trajectories. Finally, the neural network proved to be highly effective in predicting which patients will achieve MCII (balanced accuracy = 90.0%, leave-one-out cross-validation), demonstrating potential clinical utility of gut microbiome profiles.

CONCLUSIONS: Our findings confirm the presence of taxonomic and functional signatures of the gut microbiome associated with MCII in RA patients. Ultimately, modifying the gut microbiome to enhance clinical outcome may hold promise as a future treatment for RA.}, } @article {pmid34517298, year = {2022}, author = {Han, L and Liu, T and Fang, K and Li, X and You, X and Li, Y and Wang, X and Wang, J}, title = {Indigenous functional microbial communities for the preferential degradation of chloroacetamide herbicide S-enantiomers in soil.}, journal = {Journal of hazardous materials}, volume = {423}, number = {Pt B}, pages = {127135}, doi = {10.1016/j.jhazmat.2021.127135}, pmid = {34517298}, issn = {1873-3336}, mesh = {Acetamides ; Biodegradation, Environmental ; *Herbicides ; *Microbiota ; Soil ; *Soil Pollutants/analysis ; Stereoisomerism ; }, abstract = {This study investigated indigenous functional microbial communities associated with the degradation of chloroacetamide herbicides acetochlor (ACE), S-metolachlor (S-MET) and their enantiomers in repeatedly treated soils. The results showed that biodegradation was the main process for the degradation of ACE, S-MET and their enantiomers. Eight dominant bacterial genera associated with the degradation were found: Amycolatopsis, Saccharomonospora, Mycoplasma, Myroides, Mycobacterium, Burkholderia, Afipia, and Kribbella. The S-enantiomers of ACE and S-MET were preferentially degraded, which mainly relied on Amycolatopsis, Saccharomonospora and Kribbella for the ACE S-enantiomer and Amycolatopsis and Saccharomonospora for the S-MET S-enantiomer. Importantly, the relative abundances of Amycolatopsis and Saccharomonospora increased by 146.3%-4467.2% in the S-enantiomer treatments of ACE and S-MET compared with the control, which were significantly higher than that in the corresponding R-enantiomer treatments (25.3%-4168.2%). Both metagenomic and qPCR analyses demonstrated that four genes, ppah, alkb, benA, and p450, were the dominant biodegradation genes (BDGs) potentially involved in the preferential degradation of the S-enantiomers of ACE and S-MET. Furthermore, network analysis suggested that Amycolatopsis, Saccharomonospora, Mycoplasma, Myroides, and Mycobacterium were the potential hosts of these four BDGs. Our findings indicated that Amycolatopsis and Saccharomonospora might play pivotal roles in the preferential degradation of the S-enantiomers of ACE and S-MET.}, } @article {pmid34516694, year = {2021}, author = {Takezawa, K and Fujita, K and Matsushita, M and Motooka, D and Hatano, K and Banno, E and Shimizu, N and Takao, T and Takada, S and Okada, K and Fukuhara, S and Kiuchi, H and Uemura, H and Nakamura, S and Kojima, Y and Nonomura, N}, title = {The Firmicutes/Bacteroidetes ratio of the human gut microbiota is associated with prostate enlargement.}, journal = {The Prostate}, volume = {81}, number = {16}, pages = {1287-1293}, doi = {10.1002/pros.24223}, pmid = {34516694}, issn = {1097-0045}, mesh = {Bacteroidetes/*isolation & purification ; Biopsy/methods/statistics & numerical data ; Firmicutes/*isolation & purification ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Metagenomics/methods ; Middle Aged ; Neoplasm Staging ; Organ Size ; Prostate/*pathology ; *Prostatic Hyperplasia/diagnosis/microbiology ; *Prostatic Neoplasms/microbiology/pathology/physiopathology ; RNA, Ribosomal, 16S/isolation & purification ; Risk Factors ; }, abstract = {BACKGROUND: The pathophysiology of the prostate enlargement underlying lower urinary tract symptoms is unknown. Meanwhile, the gut microbiota can contribute to various host conditions. We hypothesized that the gut microbiota plays a role in prostate enlargement.

METHODS: We included 128 patients who underwent prostate biopsies at our hospitals between December 2018 and March 2020, excluding those who had used antibiotics within the past 6 months and those who were diagnosed with prostate cancer of cT3 or higher. Patients with prostate volumes ≥30 ml were defined as the prostate-enlargement (PE) group; those with prostate volumes <30 ml were defined as the non-PE group. Their gut microbiotas were analyzed via 16S rRNA metagenomic analyses of rectal swab samples and were compared between the groups.

RESULTS: The PE group included 66 patients; the non-PE group included 62 patients. Age, body mass index, and prostate-specific antigen levels did not significantly differ between the groups. Linear discriminant analysis effect size analysis indicated a higher proportion of Firmicutes and Actinobacteria in the PE group and a higher proportion of Bacteroidetes in the non-PE group. The Firmicutes/Bacteroidetes (F/B) ratio was significantly higher in the PE group than in the non-PE group (2.21 ± 0.39 vs. 1.61 ± 0.40, p = 0.015).

CONCLUSION: The F/B ratio of the gut microbiota was associated with prostate enlargement. Although the detailed mechanisms are unclear, the gut microbiota might affect prostate enlargement.}, } @article {pmid34514619, year = {2022}, author = {Suchodolski, JS}, title = {Analysis of the gut microbiome in dogs and cats.}, journal = {Veterinary clinical pathology}, volume = {50 Suppl 1}, number = {Suppl 1}, pages = {6-17}, pmid = {34514619}, issn = {1939-165X}, mesh = {Animals ; *Cat Diseases ; Cats ; *Dog Diseases ; Dogs ; Dysbiosis/veterinary ; Feces ; *Gastrointestinal Microbiome ; }, abstract = {The gut microbiome is an important immune and metabolic organ. Intestinal bacteria produce various metabolites that influence the health of the intestine and other organ systems, including kidney, brain, and heart. Changes in the microbiome in diseased states are termed dysbiosis. The concept of dysbiosis is constantly evolving and includes changes in microbiome diversity and/or structure and functional changes (eg, altered production of bacterial metabolites). Molecular tools are now the standard for microbiome analysis. Sequencing of microbial genes provides information about the bacteria present and their functional potential but lacks standardization and analytical validation of methods and consistency in the reporting of results. This makes it difficult to compare results across studies or for individual clinical patients. The Dysbiosis Index (DI) is a validated quantitative PCR assay for canine fecal samples that measures the abundance of seven important bacterial taxa and summarizes the results as one single number. Reference intervals are established for dogs, and the DI can be used to assess the microbiome in clinical patients over time and in response to therapy (eg, fecal microbiota transplantation). In situ hybridization or immunohistochemistry allows the identification of mucosa-adherent and intracellular bacteria in animals with intestinal disease, especially granulomatous colitis. Future directions include the measurement of bacterial metabolites in feces or serum as markers for the appropriate function of the microbiome. This article summarizes different approaches to the analysis of gut microbiota and how they might be applicable to research studies and clinical practice in dogs and cats.}, } @article {pmid34512604, year = {2021}, author = {Liu, Y and Zheng, K and Liu, B and Liang, Y and You, S and Zhang, W and Zhang, X and Jie, Y and Shao, H and Jiang, Y and Guo, C and He, H and Wang, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M}, title = {Characterization and Genomic Analysis of Marinobacter Phage vB_MalS-PS3, Representing a New Lambda-Like Temperate Siphoviral Genus Infecting Algae-Associated Bacteria.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {726074}, pmid = {34512604}, issn = {1664-302X}, abstract = {Marinobacter is the abundant and important algal-associated and hydrocarbon biodegradation bacteria in the ocean. However, little knowledge about their phages has been reported. Here, a novel siphovirus, vB_MalS-PS3, infecting Marinobacter algicola DG893(T), was isolated from the surface waters of the western Pacific Ocean. Transmission electron microscopy (TEM) indicated that vB_MalS-PS3 has the morphology of siphoviruses. VB_MalS-PS3 was stable from -20 to 55°C, and with the latent and rise periods of about 80 and 10 min, respectively. The genome sequence of VB_MalS-PS3 contains a linear, double-strand 42,168-bp DNA molecule with a G + C content of 56.23% and 54 putative open reading frames (ORFs). Nineteen conserved domains were predicted by BLASTp in NCBI. We found that vB_MalS-PS3 represent an understudied viral group with only one known isolate. The phylogenetic tree based on the amino acid sequences of whole genomes revealed that vB_MalS-PS3 has a distant evolutionary relationship with other siphoviruses, and can be grouped into a novel viral genus cluster with six uncultured assembled viral genomes from metagenomics, named here as Marinovirus. This study of the Marinobacter phage vB_MalS-PS3 genome enriched the genetic database of marine bacteriophages, in addition, will provide useful information for further research on the interaction between Marinobacter phages and their hosts, and their relationship with algal blooms and hydrocarbon biodegradation in the ocean.}, } @article {pmid34509383, year = {2021}, author = {Lin, S and Zhang, T and Zhu, L and Pang, K and Lu, S and Liao, X and Ying, S and Zhu, L and Xu, X and Wu, J and Wang, X}, title = {Characteristic dysbiosis in gout and the impact of a uric acid-lowering treatment, febuxostat on the gut microbiota.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {48}, number = {9}, pages = {781-791}, doi = {10.1016/j.jgg.2021.06.009}, pmid = {34509383}, issn = {1673-8527}, mesh = {Humans ; *Febuxostat/therapeutic use/pharmacology ; *Gout/drug therapy/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Dysbiosis/microbiology ; Male ; *Uric Acid ; Middle Aged ; Female ; Gout Suppressants/therapeutic use/pharmacology ; RNA, Ribosomal, 16S/genetics ; Adult ; Aged ; Feces/microbiology ; Case-Control Studies ; }, abstract = {Gut dysbiosis is suggested to play a critical role in the pathogenesis of gout. The aim of our study was to identify the characteristic dysbiosis of the gut microbiota in gout patients and the impact of a commonly used uric acid-lowering treatment, febuxostat on gut microbiota in gout. 16S ribosomal RNA sequencing and metagenomic shotgun sequencing was performed on fecal DNA isolated from 38 untreated gout patients, 38 gout patients treated with febuxostat, and 26 healthy controls. A restriction of gut microbiota biodiversity was detected in the untreated gout patients, and the alteration was partly restored by febuxostat. Biochemical metabolic indexes involved in liver and kidney metabolism were significantly associated with the gut microbiota composition in gout patients. Functional analysis revealed that the gut microbiome of gout patients had an enriched function on carbohydrate metabolism but a lower potential for purine metabolism, which was comparatively enhanced in the febuxostat treated gout patients. A classification microbial model obtained a high mean area under the curve up to 0.973. Therefore, gut dysbiosis characterizings gout could potentially serve as a noninvasive diagnostic tool for gout and may be a promising target of future preventive interventions.}, } @article {pmid34508122, year = {2021}, author = {Suriyaphol, P and Chiu, JKH and Yimpring, N and Tunsagool, P and Mhuantong, W and Chuanchuen, R and Bessarab, I and Williams, RBH and Ong, RT and Suriyaphol, G}, title = {Dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {18091}, pmid = {34508122}, issn = {2045-2322}, mesh = {Age Factors ; Animals ; Anti-Bacterial Agents/*pharmacology ; Biodiversity ; Feces/*microbiology ; Metagenome ; Metagenomics/methods ; Microbiota/*drug effects ; Swine ; *Weaning ; }, abstract = {This study aimed to characterize the alteration of the fecal microbiome and antimicrobial resistance (AMR) determinants in 24 piglets at day 3 pre-weaning (D. - 3), weaning day (D.0), days 3 (D.3) and 8 post-weaning (D.8), using whole-genome shotgun sequencing. Distinct clusters of microbiomes and AMR determinants were observed at D.8 when Prevotella (20.9%) was the major genus, whereas at D. - 3-D.3, Alistipes (6.9-12.7%) and Bacteroides (5.2-8.5%) were the major genera. Lactobacillus and Escherichia were notably observed at D. - 3 (1.2%) and D. - 3-D.3 (0.2-0.4%), respectively. For AMR, a distinct cluster of AMR determinants was observed at D.8, mainly conferring resistance to macrolide-lincosamide-streptogramin (mefA), β-lactam (cfxA6 and aci1) and phenicol (rlmN). In contrast, at D. - 3-D.3, a high abundance of determinants with aminoglycoside (AMG) (sat, aac(6')-aph(2''), aadA and acrF), β-lactam (fus-1, cepA and mrdA), multidrug resistance (MDR) (gadW, mdtE, emrA, evgS, tolC and mdtB), phenicol (catB4 and cmlA4), and sulfonamide patterns (sul3) was observed. Canonical correlation analysis (CCA) plot associated Escherichia coli with aac(6')-aph(2''), emrA, mdtB, catB4 and cmlA4 at D. - 3, D.0 and/or D.3 whereas at D.8 associations between Prevotella and mefA, cfxA6 and aci1 were identified. The weaning age and diet factor played an important role in the microbial community composition.}, } @article {pmid34508085, year = {2021}, author = {Bramble, MS and Vashist, N and Ko, A and Priya, S and Musasa, C and Mathieu, A and Spencer, A and Lupamba Kasendue, M and Mamona Dilufwasayo, P and Karume, K and Nsibu, J and Manya, H and Uy, MNA and Colwell, B and Boivin, M and Mayambu, JPB and Okitundu, D and Droit, A and Mumba Ngoyi, D and Blekhman, R and Tshala-Katumbay, D and Vilain, E}, title = {The gut microbiome in konzo.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {5371}, pmid = {34508085}, issn = {2041-1723}, support = {D43 TW009343/TW/FIC NIH HHS/United States ; R01 ES019841/ES/NIEHS NIH HHS/United States ; R35 GM128716/GM/NIGMS NIH HHS/United States ; }, mesh = {Child ; Democratic Republic of the Congo/epidemiology ; Disease Susceptibility/*microbiology ; Feces/microbiology ; *Feeding Behavior ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Manihot/*adverse effects/chemistry ; Metagenomics ; Motor Neuron Disease/epidemiology/*microbiology ; Nitriles/adverse effects ; }, abstract = {Konzo, a distinct upper motor neuron disease associated with a cyanogenic diet and chronic malnutrition, predominately affects children and women of childbearing age in sub-Saharan Africa. While the exact biological mechanisms that cause this disease have largely remained elusive, host-genetics and environmental components such as the gut microbiome have been implicated. Using a large study population of 180 individuals from the Democratic Republic of the Congo, where konzo is most frequent, we investigate how the structure of the gut microbiome varied across geographical contexts, as well as provide the first insight into the gut flora of children affected with this debilitating disease using shotgun metagenomic sequencing. Our findings indicate that the gut microbiome structure is highly variable depending on region of sampling, but most interestingly, we identify unique enrichments of bacterial species and functional pathways that potentially modulate the susceptibility of konzo in prone regions of the Congo.}, } @article {pmid34507920, year = {2021}, author = {Velmurugan, G and Vasudevan, D}, title = {Metagenomic analysis of RNA sequencing data reveals SARS-CoV-2-mediated progressive dysbiosis of upper respiratory tract microbiota.}, journal = {Biomedical journal}, volume = {44}, number = {4}, pages = {504-507}, pmid = {34507920}, issn = {2320-2890}, mesh = {Animals ; *COVID-19 ; Dysbiosis ; Ferrets ; Humans ; *Microbiota/genetics ; RNA ; Respiratory System ; SARS-CoV-2 ; Sequence Analysis, RNA ; }, abstract = {COVID-19, an infectious disease caused by a novel coronavirus (SARS-CoV-2) has emerged as global pandemic. Here, we described the changes in microbiota of upper respiratory tract by analyzing the publically available RNA sequencing data of SARS-CoV-2-infected ferrets. The bacterial dysbiosis due to SARS-CoV-2 was largely inversely proportional to the dysbiosis caused by influenza-A virus. The bacterial taxa which are defined as healthy ecostate were significantly reduced during SARS-CoV-2 infection. Altogether, this preliminary study provides a new insight on the possible role of bacterial communities of upper respiratory tract in determining the immunity, susceptibility, and mortality for COVID-19.}, } @article {pmid34507779, year = {2021}, author = {Jia, Y and Niu, CT and Xu, X and Zheng, FY and Liu, CF and Wang, JJ and Lu, ZM and Xu, ZH and Li, Q}, title = {Metabolic potential of microbial community and distribution mechanism of Staphylococcus species during broad bean paste fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {148}, number = {}, pages = {110533}, doi = {10.1016/j.foodres.2021.110533}, pmid = {34507779}, issn = {1873-7145}, mesh = {Fermentation ; *Fermented Foods ; *Microbiota ; Staphylococcus ; *Vicia faba ; }, abstract = {Although the microbial diversity and structure in bean-based fermented foods have been widely studied, systematic studies on functional microbiota and mechanism of community forms in multi-microbial fermentation systems were still lacking. In this work, the metabolic pathway and functional potential of microbial community in broad bean paste (BBP) were investigated by metagenomics approach, and Staphylococcus, Bacillus, Weissella, Aspergillus and Zygosaccharomyces were found to be the potential predominant populations responsible for substrate alteration and flavor biosynthesis. Among them, Staphylococcus was the most abundant and widespread functional microbe, and closely related Staphylococcus species were diverse and ubiquitously distributed, with the opportunistic pathogen S. gallinarum being the most abundant Staphylococcus specie isolated from BBP. To explain the dominance status of S. gallinarum and species distributions of Staphylococcus genus, we tested the effects of abiotic and biotic factors on three Staphylococcus species using a tractable BBP model, demonstrating that adaptation to environmental conditions (environmental parameters and other functional microbes) led to the dominant position and species coexistence of Staphylococcus, and congeneric competition among Staphylococcus species further shaped ecological distributions of closely related Staphylococcus species. In general, this work revealed the metabolic potential of microbial community and distribution mechanism of Staphylococcus species during BBP fermentation, which could help traditional factories to more precisely control the safety and quality of bean-based fermented foods.}, } @article {pmid34507766, year = {2021}, author = {Liu, D and Zhang, C and Zhang, J and Xin, X and Liao, X}, title = {Metagenomics reveals the formation mechanism of flavor metabolites during the spontaneous fermentation of potherb mustard (Brassica juncea var. multiceps).}, journal = {Food research international (Ottawa, Ont.)}, volume = {148}, number = {}, pages = {110622}, doi = {10.1016/j.foodres.2021.110622}, pmid = {34507766}, issn = {1873-7145}, mesh = {Fermentation ; *Lactobacillales/genetics ; Metagenomics ; *Microbiota ; Mustard Plant/genetics ; }, abstract = {Fermented vegetable flavors are closely associated with microbial metabolism. Here, shifts in flavor metabolites and their correlations to the structure and function of fermentative microbial communities were explored during the spontaneous fermentation process of potherb mustard (Brassica juncea var. multiceps), a traditionally fermented vegetable from China. Halophilic bacteria (HAB, i.e., Halomonas, Salinivibrio, and Vibrio) and lactic acid bacteria (LAB, i.e., Lactobacillus-related genera and Weissella) became highly abundant after potherb mustard fermentation. Further, HAB and LAB abundances exhibited significant, positive correlations with metabolites important in fermented potherb mustard flavoring (e.g., organic acids, amino acids, alcohols, aldehydes, and nitriles). Metagenomic analysis indicated that Halomonas, Salinivibrio, Weissella, and Lactobacillus-related genera were likely actively engaged in pyruvate metabolism (ko00620) and citrate cycle (TCA cycle, ko00020), leading to higher lactic and acetic acid concentrations, along with lower pH, which would affect levels of volatile isothiocyanates and nitriles that contribute to flavoring of fermented potherb mustard. Further, HAB and LAB were the primary populations inferred to be responsible for amino acid and fatty acid metabolism in addition to the biosynthesis of numerous volatile flavor compounds. This study highlights the predominance and importance of LAB and HAB during spontaneous fermentation of potherb mustard and provides new insights into their roles in this process.}, } @article {pmid34502456, year = {2021}, author = {Sánchez-Alcoholado, L and Laborda-Illanes, A and Otero, A and Ordóñez, R and González-González, A and Plaza-Andrades, I and Ramos-Molina, B and Gómez-Millán, J and Queipo-Ortuño, MI}, title = {Relationships of Gut Microbiota Composition, Short-Chain Fatty Acids and Polyamines with the Pathological Response to Neoadjuvant Radiochemotherapy in Colorectal Cancer Patients.}, journal = {International journal of molecular sciences}, volume = {22}, number = {17}, pages = {}, pmid = {34502456}, issn = {1422-0067}, support = {CPI13/00003//Miguel Servet Type II" program, ISCIII, Spain; co-funded by the Fondo Europeo de Desarrollo Regional-FEDER/ ; C-0030-2018//"Nicolas Monardes" research program of the Consejería de Salud, Junta de Andalucía, Spain/ ; CP19/00098//Miguel Servet Type I" program, ISCIII, Spain; co-funded by the Fondo Europeo de Desarrollo Regional-FEDER/ ; PE-0106-2019//Predoctoral grant from the Consejería de Salud y Familia, co-funded by the Fondo Europeo de Desarrollo Regional-FEDER, Andalucia, Spain/ ; FI19-00112//predoctoral grant PFIS-ISCIII, co-funded by the Fondo Europeo de Desarrollo Regional-FEDER, Madrid, Spain./ ; PI15/00256//Institute of Health "Carlos III" (ISCIII), co-funded by the Fondo Europeo de Desarrollo Regional-FEDER/ ; }, mesh = {Aged ; Case-Control Studies ; Colorectal Neoplasms/microbiology/*therapy ; *Fatty Acids, Volatile ; Feces/chemistry/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/metabolism ; Male ; Middle Aged ; *Neoadjuvant Therapy ; Permeability ; Polyamines/*blood ; Treatment Outcome ; }, abstract = {Emerging evidence has suggested that dysbiosis of the gut microbiota may influence the drug efficacy of colorectal cancer (CRC) patients during cancer treatment by modulating drug metabolism and the host immune response. Moreover, gut microbiota can produce metabolites that may influence tumor proliferation and therapy responsiveness. In this study we have investigated the potential contribution of the gut microbiota and microbial-derived metabolites such as short chain fatty acids and polyamines to neoadjuvant radiochemotherapy (RCT) outcome in CRC patients. First, we established a profile for healthy gut microbiota by comparing the microbial diversity and composition between CRC patients and healthy controls. Second, our metagenomic analysis revealed that the gut microbiota composition of CRC patients was relatively stable over treatment time with neoadjuvant RCT. Nevertheless, treated patients who achieved clinical benefits from RTC (responders, R) had significantly higher microbial diversity and richness compared to non-responder patients (NR). Importantly, the fecal microbiota of the R was enriched in butyrate-producing bacteria and had significantly higher levels of acetic, butyric, isobutyric, and hexanoic acids than NR. In addition, NR patients exhibited higher serum levels of spermine and acetyl polyamines (oncometabolites related to CRC) as well as zonulin (gut permeability marker), and their gut microbiota was abundant in pro-inflammatory species. Finally, we identified a baseline consortium of five bacterial species that could potentially predict CRC treatment outcome. Overall, our results suggest that the gut microbiota may have an important role in the response to cancer therapies in CRC patients.}, } @article {pmid34500458, year = {2022}, author = {Cheng, L and Qi, C and Yang, H and Lu, M and Cai, Y and Fu, T and Ren, J and Jin, Q and Zhang, X}, title = {gutMGene: a comprehensive database for target genes of gut microbes and microbial metabolites.}, journal = {Nucleic acids research}, volume = {50}, number = {D1}, pages = {D795-D800}, pmid = {34500458}, issn = {1362-4962}, mesh = {Animals ; Bacteria/classification/*genetics/metabolism ; *Databases, Genetic ; Feces/microbiology ; Gastrointestinal Microbiome/genetics ; Humans ; Internet ; Metabolic Networks and Pathways/genetics ; *Metabolome ; *Metagenome ; Mice ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Software ; }, abstract = {gutMGene (http://bio-annotation.cn/gutmgene), a manually curated database, aims at providing a comprehensive resource of target genes of gut microbes and microbial metabolites in humans and mice. Metagenomic sequencing of fecal samples has identified 3.3 × 106 non-redundant microbial genes from up to 1500 different species. One of the contributions of gut microbiota to host biology is the circulating pool of bacterially derived small-molecule metabolites. It has been estimated that 10% of metabolites found in mammalian blood are derived from the gut microbiota, where they can produce systemic effects on the host through activating or inhibiting gene expression. The current version of gutMGene documents 1331 curated relationships between 332 gut microbes, 207 microbial metabolites and 223 genes in humans, and 2349 curated relationships between 209 gut microbes, 149 microbial metabolites and 544 genes in mice. Each entry in the gutMGene contains detailed information on a relationship between gut microbe, microbial metabolite and target gene, a brief description of the relationship, experiment technology and platform, literature reference and so on. gutMGene provides a user-friendly interface to browse and retrieve each entry using gut microbes, disorders and intervention measures. It also offers the option to download all the entries and submit new experimentally validated associations.}, } @article {pmid34498685, year = {2021}, author = {Wu, S and Fang, Z and Tan, J and Li, M and Wang, C and Guo, Q and Xu, C and Jiang, X and Zhu, H}, title = {DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach.}, journal = {GigaScience}, volume = {10}, number = {9}, pages = {}, pmid = {34498685}, issn = {2047-217X}, mesh = {*Bacteriophages/genetics ; *Deep Learning ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; }, abstract = {BACKGROUND: Prokaryotic viruses referred to as phages can be divided into virulent and temperate phages. Distinguishing virulent and temperate phage-derived sequences in metavirome data is important for elucidating their different roles in interactions with bacterial hosts and regulation of microbial communities. However, there is no experimental or computational approach to effectively classify their sequences in culture-independent metavirome. We present a new computational method, DeePhage, which can directly and rapidly judge each read or contig as a virulent or temperate phage-derived fragment.

FINDINGS: DeePhage uses a "one-hot" encoding form to represent DNA sequences in detail. Sequence signatures are detected via a convolutional neural network to obtain valuable local features. The accuracy of DeePhage on 5-fold cross-validation reaches as high as 89%, nearly 10% and 30% higher than that of 2 similar tools, PhagePred and PHACTS. On real metavirome, DeePhage correctly predicts the highest proportion of contigs when using BLAST as annotation, without apparent preferences. Besides, DeePhage reduces running time vs PhagePred and PHACTS by 245 and 810 times, respectively, under the same computational configuration. By direct detection of the temperate viral fragments from metagenome and metavirome, we furthermore propose a new strategy to explore phage transformations in the microbial community. The ability to detect such transformations provides us a new insight into the potential treatment for human disease.

CONCLUSIONS: DeePhage is a novel tool developed to rapidly and efficiently identify 2 kinds of phage fragments especially for metagenomics analysis. DeePhage is freely available via http://cqb.pku.edu.cn/ZhuLab/DeePhage or https://github.com/shufangwu/DeePhage.}, } @article {pmid34498139, year = {2021}, author = {Xu, X and Ran, X and Tang, J and Pradhan, S and Dai, Y and Zhuang, K and Ran, Y}, title = {Skin Microbiota in Non-inflammatory and Inflammatory Lesions of Acne Vulgaris: The Underlying Changes within the Pilosebaceous Unit.}, journal = {Mycopathologia}, volume = {186}, number = {6}, pages = {863-869}, pmid = {34498139}, issn = {1573-0832}, support = {ZYJC18033//1.3.5 project for disciplines of excellence/ ; HXYS19003//HX-Academician project (HXYS19003) of West China Hospital, Sichuan University/ ; 81773343//National Natural Science Foundation of China/ ; }, mesh = {*Acne Vulgaris ; Adolescent ; Adult ; Humans ; Malassezia ; Male ; *Microbiota ; Propionibacterium acnes ; Skin ; Young Adult ; }, abstract = {Acne vulgaris is a common chronic inflammatory skin disease of the pilosebaceous unit. Clinical manifestations include seborrhea, non-inflammatory lesions, inflammatory lesions, or scar formation. Fourteen eligible participants of either sex, aged 18-28 years old, with mild to moderate acne lesions, were recruited in this observational study. The contents of 10 pilosebaceous units of non-inflammatory (comedones) and inflammatory lesions (papules and pustules) were collected from each participant's face and examined by amplicon metagenomics sequencing and real-time Polymerase Chain Reaction (PCR). Male participants, participants with a higher body mass index (BMI) than normal, and participants younger than 20 years old, were revealed to have a higher proportion of Malassezia in their non-inflammatory lesions than that in inflammatory lesions. There was an increased abundance of Malassezia restricta (M. restricta) and Cutibacterium acnes (C. acnes) in the non-inflammatory group. Correlation analysis indicated that Staphylococcus epidermidis (S. epidermidis) and M. restricta have similar proliferation trends with C. acnes during the transformation from non-inflammatory to inflammatory lesions. M. restricta probably involve in the microecological balance within the pilosebaceous unit.}, } @article {pmid34498030, year = {2021}, author = {Gordon-Rodriguez, E and Quinn, TP and Cunningham, JP}, title = {Learning sparse log-ratios for high-throughput sequencing data.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {1}, pages = {157-163}, pmid = {34498030}, issn = {1367-4811}, support = {542963//Simons Foundation/ ; //Sloan Foundation/ ; //McKnight Endowment Fund/ ; DBI-1707398//NSF/ ; //Gatsby Charitable Foundation/ ; }, mesh = {*Software ; Algorithms ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Microbiota ; }, abstract = {MOTIVATION: The automatic discovery of sparse biomarkers that are associated with an outcome of interest is a central goal of bioinformatics. In the context of high-throughput sequencing (HTS) data, and compositional data (CoDa) more generally, an important class of biomarkers are the log-ratios between the input variables. However, identifying predictive log-ratio biomarkers from HTS data is a combinatorial optimization problem, which is computationally challenging. Existing methods are slow to run and scale poorly with the dimension of the input, which has limited their application to low- and moderate-dimensional metagenomic datasets.

RESULTS: Building on recent advances from the field of deep learning, we present CoDaCoRe, a novel learning algorithm that identifies sparse, interpretable and predictive log-ratio biomarkers. Our algorithm exploits a continuous relaxation to approximate the underlying combinatorial optimization problem. This relaxation can then be optimized efficiently using the modern ML toolbox, in particular, gradient descent. As a result, CoDaCoRe runs several orders of magnitude faster than competing methods, all while achieving state-of-the-art performance in terms of predictive accuracy and sparsity. We verify the outperformance of CoDaCoRe across a wide range of microbiome, metabolite and microRNA benchmark datasets, as well as a particularly high-dimensional dataset that is outright computationally intractable for existing sparse log-ratio selection methods.

The CoDaCoRe package is available at https://github.com/egr95/R-codacore. Code and instructions for reproducing our results are available at https://github.com/cunningham-lab/codacore.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid34496253, year = {2021}, author = {Usami, K and Niimi, K and Matsuo, A and Suyama, Y and Sakai, Y and Sato, S and Fujihashi, K and Kiyono, H and Uchino, S and Furukawa, M and Islam, J and Ito, K and Moriya, T and Kusumoto, Y and Tomura, M and Hovey, RC and Sugawara, J and Yoneyama, H and Kitazawa, H and Watanabe, K and Aso, H and Nochi, T}, title = {The gut microbiota induces Peyer's-patch-dependent secretion of maternal IgA into milk.}, journal = {Cell reports}, volume = {36}, number = {10}, pages = {109655}, doi = {10.1016/j.celrep.2021.109655}, pmid = {34496253}, issn = {2211-1247}, mesh = {Animals ; Gastrointestinal Microbiome/*immunology ; Humans ; Immunoglobulin A/immunology ; Immunoglobulin A, Secretory/immunology ; Intestinal Mucosa/*immunology ; Mice ; Milk, Human/*immunology ; Peyer's Patches/immunology ; Plasma Cells/*cytology ; }, abstract = {The evolutionary strategy of transferring maternal antibodies via milk profoundly impacts the survival, lifelong health, and wellbeing of all neonates, including a pronounced impact on human breastfeeding success and infant development. While there has been increased recognition that interorgan connectivity influences the quality of a mother's milk, potentially to personalize it for her offspring, the underlying bases for these processes are incompletely resolved. Here, we define an essential role of Peyer's patches (PPs) for the generation of plasma cells that secrete maternal immunoglobulin A (IgA) into milk. Our metagenomic analysis reveals that the presence of certain residential microorganisms in the gastrointestinal (GI) tract, such as Bacteroides acidifaciens and Prevotella buccalis, is indispensable for the programming of maternal IgA synthesis prior to lactational transfer. Our data provide important insights into how the microbiome of the maternal GI environment, specifically through PPs, can be communicated to the next generation via milk.}, } @article {pmid34496124, year = {2021}, author = {Logan, IE and Shulzhenko, N and Sharpton, TJ and Bobe, G and Liu, K and Nuss, S and Jones, ML and Miranda, CL and Vasquez-Perez, S and Pennington, JM and Leonard, SW and Choi, J and Wu, W and Gurung, M and Kim, JP and Lowry, MB and Morgun, A and Maier, CS and Stevens, JF and Gombart, AF}, title = {Xanthohumol Requires the Intestinal Microbiota to Improve Glucose Metabolism in Diet-Induced Obese Mice.}, journal = {Molecular nutrition & food research}, volume = {65}, number = {21}, pages = {e2100389}, pmid = {34496124}, issn = {1613-4133}, support = {R01 AT009168/AT/NCCIH NIH HHS/United States ; S10 RR027878/RR/NCRR NIH HHS/United States ; R01 DK103761/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Diet, High-Fat/adverse effects ; Flavonoids ; *Gastrointestinal Microbiome/genetics ; Glucose ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Obese ; Propiophenones ; RNA, Ribosomal, 16S ; }, abstract = {SCOPE: The polyphenol xanthohumol (XN) improves dysfunctional glucose and lipid metabolism in diet-induced obesity animal models. Because XN changes intestinal microbiota composition, the study hypothesizes that XN requires the microbiota to mediate its benefits.

METHODS AND RESULTS: To test the hypothesis, the study feeds conventional and germ-free male Swiss Webster mice either a low-fat diet (LFD, 10% fat derived calories), a high-fat diet (HFD, 60% fat derived calories), or a high-fat diet supplemented with XN at 60 mg kg[-1] body weight per day (HXN) for 10 weeks, and measure parameters of glucose and lipid metabolism. In conventional mice, the study discovers XN supplementation decreases plasma insulin concentrations and improves Homeostatic Model Assessment of Insulin Resistance (HOMA-IR). In germ-free mice, XN supplementation fails to improve these outcomes. Fecal sample 16S rRNA gene sequencing analysis suggests XN supplementation changes microbial composition and dramatically alters the predicted functional capacity of the intestinal microbiota. Furthermore, the intestinal microbiota metabolizes XN into bioactive compounds, including dihydroxanthohumol (DXN), an anti-obesogenic compound with improved bioavailability.

CONCLUSION: XN requires the intestinal microbiota to mediate its benefits, which involves complex diet-host-microbiota interactions with changes in both microbial composition and functional capacity. The study results warrant future metagenomic studies which will provide insight into complex microbe-microbe interactions and diet-host-microbiota interactions.}, } @article {pmid34495960, year = {2021}, author = {Li, C and Av-Shalom, TV and Tan, JWG and Kwah, JS and Chng, KR and Nagarajan, N}, title = {BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data.}, journal = {PLoS computational biology}, volume = {17}, number = {9}, pages = {e1009343}, pmid = {34495960}, issn = {1553-7358}, mesh = {Biomass ; Cross-Sectional Studies ; Datasets as Topic ; *Ecosystem ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {BEEM-Static provides new opportunities for mining ecologically interpretable interactions and systems insights from the growing corpus of microbiome data.}, } @article {pmid34495150, year = {2021}, author = {Can-Herrera, LA and Gutierrez-Canul, CD and Dzul-Cervantes, MAA and Pacheco-Salazar, OF and Chi-Cortez, JD and Carbonell, LS}, title = {Identification by molecular techniques of halophilic bacteria producing important enzymes from pristine area in Campeche, Mexico.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {83}, number = {}, pages = {e246038}, doi = {10.1590/1519-6984.246038}, pmid = {34495150}, issn = {1678-4375}, mesh = {*Archaea ; Bacteria/genetics ; Mexico ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Isla Arena is located in the coordinate 20° 70´ N - 90° 45´ W, from Campeche, Mexico. In these estuaries, the ocean mixes with fresh water, and ecosystems are concentrated where petenes and pink flamingos proliferate. Crustaceans and mollusks abound in the sea. Despite its enormous marine wealth, there are no studies carried out on which halophilic microorganisms are present in these waters. In this work, the diversity and structure of the microbial community was investigated through a metagenomics approach and corroborated for sequencing of 16S rRNA genes. It was found that the phylum Fimicutes predominates with more than 50%, in almost the same proportion of the class Bacilli and with almost 41% of relative abundance of the order Bacillales. The sequencing results showed that one of the samples presented a high percentage of similarity (99.75%) using the Nucleotide BLAST program with a peculiar microorganism: Bacillus subtilis. This microorganism is one of the best characterized bacteria among the gram-positive ones. Our results demonstrate that B. subtilis can be an efficient source of proteases, lipases and cellulases, from halophilic microbial communities located in poorly explored areas.}, } @article {pmid34494932, year = {2021}, author = {Chen, YS and Li, J and Menon, R and Jayaraman, A and Lee, K and Huang, Y and Dashwood, WM and Zhang, K and Sun, D and Dashwood, RH}, title = {Dietary spinach reshapes the gut microbiome in an Apc-mutant genetic background: mechanistic insights from integrated multi-omics.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1972756}, pmid = {34494932}, issn = {1949-0984}, support = {R01 CA122959/CA/NCI NIH HHS/United States ; }, mesh = {Adenomatous Polyposis Coli Protein/*genetics ; Adenomatous Polyps/*metabolism ; Animals ; Butyric Acid/metabolism ; Citric Acid Cycle/physiology ; Colonic Neoplasms/*diet therapy/pathology ; Diet ; Gastrointestinal Microbiome/*physiology ; Glutamic Acid/metabolism ; Linoleic Acid/metabolism ; Male ; Mitochondria/metabolism ; Neuraminic Acids/metabolism ; Rats ; Rats, Inbred F344 ; *Spinacia oleracea ; Vegetables ; }, abstract = {Complex interrelationships govern the dynamic interactions between gut microbes, the host, and exogenous drivers of disease outcome. A multi-omics approach to cancer prevention by spinach (SPI) was pursued for the first time in the polyposis in rat colon (Pirc) model. SPI fed for 26 weeks (10% w/w, freeze-dried in the diet) exhibited significant antitumor efficacy and, in the Apc-mutant genetic background, β-catenin remained highly overexpressed in adenomatous polyps. However, in both wild type and Apc-mutant rats, increased gut microbiome diversity after SPI consumption coincided with reversal of taxonomic composition. Metagenomic prediction implicated linoleate and butanoate metabolism, tricarboxylic acid cycle, and pathways in cancer, which was supported by transcriptomic and metabolomic analyses. Thus, tumor suppression by SPI involved marked reshaping of the gut microbiome along with changes in host RNA-miRNA networks. When colon polyps were compared with matched normal-looking tissues via metabolomics, anticancer outcomes were linked to SPI-derived linoleate bioactives with known anti-inflammatory/ proapoptotic mechanisms, as well as N-aceto-2-hydroxybutanoate, consistent with altered butanoate metabolism stemming from increased α-diversity of the gut microbiome. In colon tumors from SPI-fed rats, L-glutamate and N-acetylneuraminate also were reduced, implicating altered mitochondrial energetics and cell surface glycans involved in oncogenic signaling networks and immune evasion. In conclusion, a multi-omics approach to cancer prevention by SPI provided mechanistic support for linoleate and butanoate metabolism, as well as tumor-associated changes in L-glutamate and N-acetylneuraminate. Additional factors, such as the fiber content, also warrant further investigation with a view to delaying colectomy and drug intervention in at-risk patients.}, } @article {pmid34494880, year = {2021}, author = {Tavella, T and Turroni, S and Brigidi, P and Candela, M and Rampelli, S}, title = {The Human Gut Resistome up to Extreme Longevity.}, journal = {mSphere}, volume = {6}, number = {5}, pages = {e0069121}, pmid = {34494880}, issn = {2379-5042}, mesh = {Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/*administration & dosage ; Bacteria/drug effects/*genetics ; Centenarians ; Cohort Studies ; Drug Resistance, Microbial/*genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/microbiology ; Humans ; Longevity/*physiology ; Male ; Metagenomics/methods ; Middle Aged ; Young Adult ; }, abstract = {Antibiotic resistance (AR) is indisputably a major health threat which has drawn much attention in recent years. In particular, the gut microbiome has been shown to act as a pool of AR genes, potentially available to be transferred to opportunistic pathogens. Herein, we investigated for the first time changes in the human gut resistome during aging, up to extreme longevity, by analyzing shotgun metagenomics data of fecal samples from a geographically defined cohort of 62 urban individuals, stratified into four age groups: young adults, elderly, centenarians, and semisupercentenarians, i.e., individuals aged up to 109 years. According to our findings, some AR genes are similarly represented in all subjects regardless of age, potentially forming part of the core resistome. Interestingly, aging was found to be associated with a higher burden of some AR genes, including especially proteobacterial genes encoding multidrug efflux pumps. Our results warn of possible health implications and pave the way for further investigations aimed at containing AR accumulation, with the ultimate goal of promoting healthy aging. IMPORTANCE Antibiotic resistance is widespread among different ecosystems, and in humans it plays a key role in shaping the composition of the gut microbiota, enhancing the ecological fitness of certain bacterial populations when exposed to antibiotics. A considerable component of the definition of healthy aging and longevity is associated with the structure of the gut microbiota, and, in this regard, the presence of antibiotic-resistant bacteria is critical to many pathologies that come about with aging. However, the structure of the resistome has not yet been sufficiently elucidated. Here, we show distinct antibiotic resistance assets and specific microbial consortia characterizing the human gut resistome through aging.}, } @article {pmid34494564, year = {2021}, author = {Wiqoyah, N and Mertaniasih, NM and Artama, WT and Matsumoto, S}, title = {Microbiome in sputum as a potential biomarker of chronicity in pulmonary resistant to rifampicin-tuberculosis and multidrug-resistant-tuberculosis patients.}, journal = {International journal of mycobacteriology}, volume = {10}, number = {3}, pages = {260-267}, doi = {10.4103/ijmy.ijmy_132_21}, pmid = {34494564}, issn = {2212-554X}, mesh = {Antitubercular Agents/therapeutic use ; Biomarkers ; Humans ; *Microbiota ; *Mycobacterium tuberculosis/genetics ; Rifampin ; Sputum ; *Tuberculosis, Multidrug-Resistant/drug therapy ; }, abstract = {BACKGROUND: Cases of tuberculosis (TB) and multidrug-resistant TB (MDR-TB) in South-east Asia including Indonesia are still high. The presence of mixed infections in TB cases has been reported. Several studies revealed the role of the human microbiome in TB. This study purposes to characterize microbiome which can be a potential biomarker of chronicity in TB or MDR-TB.

METHODS: Sputum samples of pulmonary TB patients confirmed MDR-TB and resistant to rifampicin TB (RR-TB) were conducted Metagenomic next-generation sequencing. Principal coordinate analysis of UniFrac's showing the community structure of microbiome in MDR-TB comorbid diabetes mellitus (DM) is different from RR-TB noncomorbid DM (P = 0.003).

RESULTS: Proteobacteria microbiome in MDR-TB comorbid DM was more abundant than in RR-TB noncomorbid DM. Actinobacteria found in the small quantity in RR-TB and MDR-TB. Diversity of microbiome genera was greater in RR-TB. The linear discriminant analysis effect size analysis represents a genus biomarker whose abundance shows significant differences between groups, genus Rothia as a potential biomarker for RR-TB noncomorbid DM.

CONCLUSIONS: Interesting findings is the community structure of microbiome in MDR-TB and RR-TB. In chronic TB such as recurrent, associated MDR-TB should attention to the findings of a small number of Actinobacteria could be a biomarker of TB which is also a determinant in patient taking combined anti-TB drugs of choice.}, } @article {pmid34493428, year = {2022}, author = {Kumar, B and Lam, S and Adam, M and Gilroy, R and Pallen, MJ}, title = {The oesophageal microbiome and cancer: hope or hype?.}, journal = {Trends in microbiology}, volume = {30}, number = {4}, pages = {322-329}, doi = {10.1016/j.tim.2021.08.007}, pmid = {34493428}, issn = {1878-4380}, support = {BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Barrett Esophagus ; *Esophageal Neoplasms ; Humans ; *Microbiota ; *Neoplasms ; }, abstract = {The human oesophagus is home to a complex microbial community, the oesophageal microbiome. Despite decades of work, we still have only a poor, low-resolution view of this community, which makes it hard to distinguish hope from hype when it comes to assessing links between the oesophageal microbiome and cancer. Here we review the potential importance of this microbiome and discuss new approaches, including culturomics, metagenomics, and recovery of whole-genome sequences, that bring renewed hope for an in-depth characterisation of this community that could deliver translational impact.}, } @article {pmid34493329, year = {2021}, author = {Foley, SE and Tuohy, C and Dunford, M and Grey, MJ and De Luca, H and Cawley, C and Szabady, RL and Maldonado-Contreras, A and Houghton, JM and Ward, DV and Mrsny, RJ and McCormick, BA}, title = {Gut microbiota regulation of P-glycoprotein in the intestinal epithelium in maintenance of homeostasis.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {183}, pmid = {34493329}, issn = {2049-2618}, support = {R01 DK125407/DK/NIDDK NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; K01DK119414/NH/NIH HHS/United States ; K01 DK119414/DK/NIDDK NIH HHS/United States ; T32 AI132152/AI/NIAID NIH HHS/United States ; R01 DK109677/DK/NIDDK NIH HHS/United States ; }, mesh = {ATP Binding Cassette Transporter, Subfamily B ; ATP Binding Cassette Transporter, Subfamily B, Member 1 ; Animals ; *Gastrointestinal Microbiome/genetics ; Homeostasis ; Humans ; Intestinal Mucosa ; Mice ; }, abstract = {BACKGROUND: P-glycoprotein (P-gp) plays a critical role in protection of the intestinal epithelia by mediating efflux of drugs/xenobiotics from the intestinal mucosa into the gut lumen. Recent studies bring to light that P-gp also confers a critical link in communication between intestinal mucosal barrier function and the innate immune system. Yet, despite knowledge for over 10 years that P-gp plays a central role in gastrointestinal homeostasis, the precise molecular mechanism that controls its functional expression and regulation remains unclear. Here, we assessed how the intestinal microbiome drives P-gp expression and function.

RESULTS: We have identified a "functional core" microbiome of the intestinal gut community, specifically genera within the Clostridia and Bacilli classes, that is necessary and sufficient for P-gp induction in the intestinal epithelium in mouse models. Metagenomic analysis of this core microbial community revealed that short-chain fatty acid and secondary bile acid production positively associate with P-gp expression. We have further shown these two classes of microbiota-derived metabolites synergistically upregulate P-gp expression and function in vitro and in vivo. Moreover, in patients suffering from ulcerative colitis (UC), we find diminished P-gp expression coupled to the reduction of epithelial-derived anti-inflammatory endocannabinoids and luminal content (e.g., microbes or their metabolites) with a reduced capability to induce P-gp expression.

CONCLUSION: Overall, by means of both in vitro and in vivo studies as well as human subject sample analysis, we identify a mechanistic link between cooperative functional outputs of the complex microbial community and modulation of P-gp, an epithelial component, that functions to suppress overactive inflammation to maintain intestinal homeostasis. Hence, our data support a new cross-talk paradigm in microbiome regulation of mucosal inflammation. Video abstract.}, } @article {pmid34492446, year = {2021}, author = {Leo, S and Lazarevic, V and von Dach, E and Kaiser, L and Prendki, V and Schrenzel, J and Huttner, BD and Huttner, A}, title = {Effects of antibiotic duration on the intestinal microbiota and resistome: The PIRATE RESISTANCE project, a cohort study nested within a randomized trial.}, journal = {EBioMedicine}, volume = {71}, number = {}, pages = {103566}, pmid = {34492446}, issn = {2352-3964}, mesh = {Anti-Bacterial Agents/*administration & dosage/pharmacology/therapeutic use ; Bacteremia/drug therapy ; Drug Administration Schedule ; Drug Resistance, Bacterial/*genetics ; Gastrointestinal Microbiome/*drug effects/genetics ; Genes, Bacterial ; Gram-Negative Bacterial Infections/drug therapy ; Humans ; Metagenome/drug effects/genetics ; }, abstract = {BACKGROUND: Shortening antibiotic-treatment durations is a key recommendation of antibiotic-stewardship programmes, yet it is based on weak evidence. We investigated whether halving antibiotic courses would reduce antibiotic-resistance genes (ARG) in the intestinal microbiomes of patients treated for gram-negative bacteraemia.

METHODS: This nested prospective cohort study included adult patients hospitalized at Geneva University Hospitals (Switzerland) participating in the PIRATE randomized trial assessing non-inferiority of shorter antibiotic courses (7 versus 14 days) for gram-negative bacteraemia ('cases') and, simultaneously, hospitalized patients with similar demography and comorbidity yet no antibiotic therapy ('controls'). Stool was collected from case and control patients on days 7, 14, 30 and 90 after antibiotic initiation (day 1) and days 7 and 14 after admission, respectively, and analysed by whole-metagenome shotgun sequencing. The primary outcome was ARG abundance at day 30; secondary outcomes included microbiota-species composition and clustering over time.

FINDINGS: Forty-five patients and 11 controls were included and evaluable; ARG analyses were conducted on the 29 per-protocol patients receiving 7 (±2) days or 14 (±3) days of antibiotic therapy. At day 30, ARGs were not detected at similar abundance in patients receiving 7 and 14 days (median counts/million [mCPM]: 96 versus [vs] 71; p=.38). By day 30, total ARG content between both groups was not significantly different from that of controls at D7 (362 and 370 mCPM vs 314 mCPM, p=.24 and 0.19). There were no significant differences amongst antibiotic-treated patients at any timepoint in bacterial diversity or clustering, but Shannon species diversity was significantly reduced compared to controls through day 14 (median 3.12 and 3.24 in the 7-day and 14-day groups vs 3.61 [controls]; p=.04 and 0.012). Patients treated for 14 days had reduced faecal phage content during and after therapy compared to other patient groups.

INTERPRETATION: Reducing antibiotic durations by half did not result in decreased abundance of ARGs in patients treated for gram-negative bacteraemia, nor did it improve microbiota species diversity.

FUNDING: The study was funded by the University of Geneva's Louis-Jeantet Foundation (grant no. S04_12) and the Swiss National Science Foundation (NRP Smarter Healthcare, grant no. 407,440_167359).}, } @article {pmid34492339, year = {2022}, author = {Zhu, J and Tian, L and Chen, P and Han, M and Song, L and Tong, X and Sun, X and Yang, F and Lin, Z and Liu, X and Liu, C and Wang, X and Lin, Y and Cai, K and Hou, Y and Xu, X and Yang, H and Wang, J and Kristiansen, K and Xiao, L and Zhang, T and Jia, H and Jie, Z}, title = {Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa.}, journal = {Genomics, proteomics & bioinformatics}, volume = {20}, number = {2}, pages = {246-259}, pmid = {34492339}, issn = {2210-3244}, mesh = {Humans ; Male ; *Metagenome ; *Microbiota/genetics ; Metagenomics/methods ; Bacteria/genetics ; Feces ; }, abstract = {The oral cavity of each person is home to hundreds of bacterial species. While taxa for oral diseases have been studied using culture-based characterization as well as amplicon sequencing, metagenomic and genomic information remains scarce compared to the fecal microbiome. Here, using metagenomic shotgun data for 3346 oral metagenomic samples together with 808 published samples, we obtain 56,213 metagenome-assembled genomes (MAGs), and more than 64% of the 3589 species-level genome bins (SGBs) contain no publicly available genomes. The resulting genome collection is representative of samples around the world and contains many genomes from candidate phyla radiation (CPR) that lack monoculture. Also, it enables the discovery of new taxa such as a genus Candidatus Bgiplasma within the family Acholeplasmataceae. Large-scale metagenomic data from massive samples also allow the assembly of strains from important oral taxa such as Porphyromonas and Neisseria. The oral microbes encode genes that could potentially metabolize drugs. Apart from these findings, a strongly male-enriched Campylobacter species was identified. Oral samples would be more user-friendly collected than fecal samples and have the potential for disease diagnosis. Thus, these data lay down a genomic framework for future inquiries of the human oral microbiome.}, } @article {pmid34491886, year = {2021}, author = {Hullar, MAJ and Jenkins, IC and Randolph, TW and Curtis, KR and Monroe, KR and Ernst, T and Shepherd, JA and Stram, DO and Cheng, I and Kristal, BS and Wilkens, LR and Franke, A and Le Marchand, L and Lim, U and Lampe, JW}, title = {Associations of the gut microbiome with hepatic adiposity in the Multiethnic Cohort Adiposity Phenotype Study.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1965463}, pmid = {34491886}, issn = {1949-0984}, support = {P30 CA015704/CA/NCI NIH HHS/United States ; UL1 TR001855/TR/NCATS NIH HHS/United States ; P30 CA071789/CA/NCI NIH HHS/United States ; U01 CA164973/CA/NCI NIH HHS/United States ; P01 CA168530/CA/NCI NIH HHS/United States ; UL1 TR000130/TR/NCATS NIH HHS/United States ; }, mesh = {Adiposity/*physiology ; Aged ; Bacteria/*classification/isolation & purification ; Cross-Sectional Studies ; Endotoxins/metabolism ; Gastrointestinal Microbiome/*physiology ; Humans ; Inflammation/pathology ; Liver/pathology ; Male ; Middle Aged ; Non-alcoholic Fatty Liver Disease/*epidemiology/*ethnology ; Obesity/pathology ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; }, abstract = {Nonalcoholic fatty liver disease (NAFLD) is a risk factor for liver cancer and prevalence varies by ethnicity. Along with genetic and lifestyle factors, the gut microbiome (GM) may contribute to NAFLD and its progression to advanced liver disease. Our cross-sectional analysis assessed the association of the GM with hepatic adiposity among African American, Japanese American, White, Latino, and Native Hawaiian participants in the Multiethnic Cohort. We used MRI to measure liver fat and determine nonalcoholic fatty liver disease (NAFLD) status (n = 511 cases) in 1,544 participants, aged 60-77 years, with 12-53% overall adiposity (BMI of 17.8-46.2 kg/m[2]). The GM was measured by 16S rRNA gene sequencing and, on a subset, by metagenomic sequencing. Alpha diversity was lower overall with NAFLD and in certain ethnicities (African Americans, Whites, and Latinos). In models regressing genus on NAFLD status, 62 of 149 genera (40%) exhibited a significant interaction between NAFLD and ethnicity stratified analysis found 69 genera significantly associated with NAFLD in at least one ethnic group. No single genus was significantly associated with NAFLD across all ethnicities. In contrast, the same bacterial metabolic pathways were over-represented in participants with NAFLD regardless of ethnicity. Imputed secondary bile acid and carbohydrate pathways were associated with NAFLD, the latter of which was corroborated by metagenomics, although different genera in different ethnicities were associated with these pathways. Overall, we found that NAFLD was associated with altered bacterial composition and metabolism, and that bacterial endotoxin, assessed by plasma lipopolysaccharide binding protein (LBP), may mediate liver fat-associated systemic inflammation in a manner that seems to vary by ethnicity.}, } @article {pmid34491388, year = {2022}, author = {He, S and Xiong, Q and Tian, C and Li, L and Zhao, J and Lin, X and Guo, X and He, Y and Liang, W and Zuo, X and Ying, C}, title = {Inulin-type prebiotics reduce serum uric acid levels via gut microbiota modulation: a randomized, controlled crossover trial in peritoneal dialysis patients.}, journal = {European journal of nutrition}, volume = {61}, number = {2}, pages = {665-677}, pmid = {34491388}, issn = {1436-6215}, support = {81673161//National Natural Science Foundation of China/ ; }, mesh = {Adult ; Cross-Over Studies ; Feces ; Female ; *Gastrointestinal Microbiome ; Humans ; Inulin/pharmacology ; Male ; *Peritoneal Dialysis ; Prebiotics ; Uric Acid ; }, abstract = {PURPOSE: Increased levels of uric acid (UA), which is mainly excreted through the kidneys, are independently associated with higher mortality in end-stage renal disease (ESRD) patients. The uricolysis of gut microbiota plays an important role in extrarenal excretion of UA. This study aimed to examine the effect of inulin-type prebiotics (a type of fermentable dietary fiber) on intestinal microbiota modulation and serum UA levels in ESRD patients.

METHODS: Continuous ambulatory peritoneal dialysis (CAPD) patients were recruited to a randomized, double-blind, placebo-controlled crossover trial of 12-week inulin-type prebiotics. Participants were visited before and after treatment with prebiotics or placebo. Serum UA levels, dietary purine intake, serum xanthine oxidase (XO) activity, daily "renal excretion" of UA, and fecal UA degradation capability were measured at each visit. Fecal metagenomic analysis was conducted to assess microbial composition and function.

RESULTS: Sixteen participants (mean age = 37 y; 10 men and 6 women) completed the trial, and 64 specimens were analyzed. The average concentration of serum UA decreased by approximately 10% in the prebiotic intervention group in comparison to the placebo group (p = 0.047) without an increase in daily "renal excretion" of UA via urine and dialysate. There were no significant changes in purine intake or activity of XO. Notably, enhanced fecal UA degradation was observed after prebiotic intervention (p = 0.041), and the ratio of Firmicutes/Bacteroidetes, which was positively associated with fecal UA degradation, increased in the prebiotic period (p = 0.032). Furthermore, prebiotics enriched purine-degrading species in the gut microbiota, including unclassified_o_Clostridiales, Clostridium sp. CAG:7, Clostridium sp. FS41, Clostridium citroniae, Anaerostipes caccae, and Clostridium botulinum.

CONCLUSIONS: Inulin-type prebiotics is a promising therapeutic candidate to reduce serum UA levels in renal failure patients, and this urate-lowering effect could possibly be attributed to intestinal microbial degradation of UA.

TRIAL REGISTRY: This study was registered at the Chinese Clinical Trials Registry (http://www.chictr.org.cn/), registration ID: ChiCTR-INR-17013739, registration date: 6th Dec 2017.}, } @article {pmid34490704, year = {2021}, author = {Li, L and Zhang, Y and Speakman, JR and Hu, S and Song, Y and Qin, S}, title = {The gut microbiota and its products: Establishing causal relationships with obesity related outcomes.}, journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity}, volume = {22}, number = {12}, pages = {e13341}, doi = {10.1111/obr.13341}, pmid = {34490704}, issn = {1467-789X}, mesh = {Causality ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Obesity ; }, abstract = {Gut microorganisms not only participate in the metabolism of carbohydrate, lipids, protein, and polypeptides in the intestine but also directly affect the metabolic phenotypes of the host. Although many studies have described the apparent effects of gut microbiota on human health, the development of metagenomics and culturomics in the past decade has generated a large amount of evidence suggesting a causal relationship between gut microbiota and obesity. The interaction between the gut microbiota and host is realized by microbial metabolites with multiple biological functions. We concentrated here on several representative beneficial species connected with obesity as well as the mechanisms, with particular emphasis on microbiota-dependent metabolites. Finally, we consider the potential clinical significance of these relationships to fuel the conception and realization of novel therapeutic and preventive strategies.}, } @article {pmid34490209, year = {2021}, author = {Medvecky, M and Mandalakis, M}, title = {PepMANDIS: A Peptide Selection Tool for Designing Function-Based Targeted Proteomic Assays in Complex Microbial Systems.}, journal = {Frontiers in chemistry}, volume = {9}, number = {}, pages = {722087}, pmid = {34490209}, issn = {2296-2646}, abstract = {The majority of studies focusing on microbial functioning in various environments are based on DNA or RNA sequencing techniques that have inherent limitations and usually provide a distorted picture about the functional status of the studied system. Untargeted proteomics is better suited for that purpose, but it suffers from low efficiency when applied in complex consortia. In practice, the scanning capabilities of the currently employed LC-MS/MS systems provide limited coverage of key-acting proteins, hardly allowing a semiquantitative assessment of the most abundant ones from most prevalent species. When particular biological processes of high importance are under investigation, the analysis of specific proteins using targeted proteomics is a more appropriate strategy as it offers superior sensitivity and comes with the added benefits of increased throughput, dynamic range and selectivity. However, the development of targeted assays requires a priori knowledge regarding the optimal peptides to be screened for each protein of interest. In complex, multi-species systems, a specific biochemical process may be driven by a large number of homologous proteins having considerable differences in their amino acid sequence, complicating LC-MS/MS detection. To overcome the complexity of such systems, we have developed an automated pipeline that interrogates UniProt database or user-created protein datasets (e.g. from metagenomic studies) to gather homolog proteins with a defined functional role and extract respective peptide sequences, while it computes several protein/peptide properties and relevant statistics to deduce a small list of the most representative, process-specific and LC-MS/MS-amenable peptides for the microbial enzymatic activity of interest.}, } @article {pmid34490138, year = {2021}, author = {Lyu, X and Zheng, H and Wang, X and Zhang, H and Gao, L and Xun, Z and Zhang, Q and He, X and Hua, H and Yan, Z and Chen, F}, title = {Oral Microbiota Composition and Function Changes During Chronic Erythematous Candidiasis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {691092}, pmid = {34490138}, issn = {2235-2988}, mesh = {*Candidiasis, Oral ; Humans ; Metagenomics ; *Microbiota ; *Micrococcaceae ; }, abstract = {Oral microbiota is constantly changing with the host state, whereas the oral microbiome of chronic erythematous candidiasis remains poorly understood. The aim of this study was to compare oral microbial signatures and functional profiling between chronic erythematous candidiasis and healthy subjects. Using shotgun metagenomic sequencing, we analyzed the microbiome in 12 chronic erythematous candidiasis, 12 healthy subjects, and 2 chronic erythematous candidiasis cured by antifungal therapy. We found that the salivary microbiota of chronic erythematous candidiasis was significantly different from that of healthy subjects. Among them, Rothia mucilaginosa and Streptococcus mitis were the most abundant disease-enriched species (Mann-Whitney U-test, P < 0.05). In addition, co-occurrence network analysis showed that C. albicans formed densely connected modules with oral bacterial species and was mainly positive connected to Streptococcus species. Furthermore, we investigated the functional potentials of the microbiome and identified a set of microbial marker genes associated with chronic erythematous candidiasis. Some of these genes enriching in chronic erythematous candidiasis are involved in eukaryotic ribosome, putative glutamine transport system, and cytochrome bc1 complex respiratory unit. Altogether, this study revealed the changes of oral microbial composition, the co-occurrence between C. albicans and oral bacteria, as well as the changes of microbial marker genes during chronic erythematous candidiasis, which provides evidence of oral microbiome as a target for the treatment and prevention of chronic erythematous candidiasis.}, } @article {pmid34489372, year = {2021}, author = {Kim, S and Seo, H and Rahim, MA and Lee, S and Kim, YS and Song, HY}, title = {Changes in the Microbiome of Vaginal Fluid after Menopause in Korean Women.}, journal = {Journal of microbiology and biotechnology}, volume = {31}, number = {11}, pages = {1490-1500}, pmid = {34489372}, issn = {1738-8872}, mesh = {Adult ; Bacteria/classification ; Female ; Humans ; Metagenome ; *Microbiota ; Middle Aged ; *Postmenopause ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Vagina/*microbiology ; }, abstract = {Various microorganisms reside in the human vagina; the vaginal microbiome is closely linked to both vaginal and general health, and for this reason, microbiome studies of the vagina are an area of research. In this study, we analyzed the vaginal microbiome of women before and after menopause to further increase our understanding of the vaginal microbiome and its contribution to general health. We did a 16s rRNA gene-based metagenomic analysis on the vaginal fluids of 11 premenopausal and 19 postmenopausal women in Korea. We confirmed that the taxonomic composition was significantly different between the two groups. In postmenopausal women, species richness was significantly decreased, but species diversity was significantly increased. In particular, among the taxonomic components corresponding to all taxon ranks of the vaginal microbiome, a reduction in Lactobacillus taxa after menopause contributed the most to the difference between the two groups. In addition, we confirmed through metabolic analysis that the lactic-acid concentration was also decreased in the vaginal fluid of women after menopause. Our findings on the correlation between menopause and the microbiome could help diagnose menopause and enhance the prevention and treatment diseases related to menopause.}, } @article {pmid34488552, year = {2021}, author = {Chen, J and Wang, S and Shen, J and Hu, Q and Zhang, Y and Ma, D and Chai, K}, title = {Analysis of Gut Microbiota Composition in Lung Adenocarcinoma Patients with TCM Qi-Yin Deficiency.}, journal = {The American journal of Chinese medicine}, volume = {49}, number = {7}, pages = {1667-1682}, doi = {10.1142/S0192415X21500786}, pmid = {34488552}, issn = {1793-6853}, mesh = {Adenocarcinoma of Lung/*microbiology ; Adolescent ; Adult ; Aged ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Lung Neoplasms/*microbiology ; Medicine, Chinese Traditional ; Middle Aged ; Yin Deficiency/*microbiology ; Young Adult ; }, abstract = {In Lung adenocarcinoma (ADC), Qi-Yin deficiency syndrome (QY) is the most common Traditional Chinese medicine (TCM) syndrome. This study aimed to investigate the diversity and composition of gut microbiota in ADC patients with QY syndrome. 90 stool samples, including 30 healthy individuals (H), 30 ADC patients with QY syndrome, and 30 ADC patients with another syndrome (O) were collected. Then, 16s-RNA sequencing was used to analyze stool samples to clarify the structure of gut microbiota, and linear discriminant analysis (LDA) effect size (LEfSe) was applied to identify biomarkers for ADC with QY syndrome. Logistic regression analysis was performed to establish a diagnostic model for the diagnosis of QY syndrome in ADC patients, which was assessed with the AUC. Finally, 20 fecal samples (QY: 10; O: 10) were analyzed with Metagenomics to validate the diagnostic model. The [Formula: see text] diversity and [Formula: see text] diversity demonstrated that the structure of gut microbiota in the QY group was different from that of the H group and O group. In the QY group, the top 3 taxonomies at phylum level were Firmicutes, Bacteroidetes, and Proteobacteria, and at genus level were Faecalibacterium, Prevotella_9, and Bifidobacterium. LEfSe identified Prevotella_9 and Streptococcus might be the biomarkers for QY syndrome. A diagnostic model was constructed using those 2 genera with the AUC = 0.801, similar to the AUC based on Metagenomics (0.842). The structure of gut microbiota in ADC patients with QY syndrome was investigated, and a diagnostic model was developed for the diagnosis of QY syndrome in ADC patients, which provides a novel idea for the understanding and diagnosis of TCM syndrome.}, } @article {pmid34484688, year = {2021}, author = {Mehta, S and Crane, M and Leith, E and Batut, B and Hiltemann, S and Arntzen, MØ and Kunath, BJ and Pope, PB and Delogu, F and Sajulga, R and Kumar, P and Johnson, JE and Griffin, TJ and Jagtap, PD}, title = {ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework.}, journal = {F1000Research}, volume = {10}, number = {}, pages = {103}, pmid = {34484688}, issn = {2046-1402}, support = {U24 CA199347/CA/NCI NIH HHS/United States ; }, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Workflow ; }, abstract = {The Earth Microbiome Project (EMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the 'microbiome') and microbial diversity patterns across the habitats of our planet. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on the environment and human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). On the other hand, metatranscriptomics, the study of a microbial community's RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome. In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking. In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.}, } @article {pmid34484230, year = {2021}, author = {Que, Y and Cao, M and He, J and Zhang, Q and Chen, Q and Yan, C and Lin, A and Yang, L and Wu, Z and Zhu, D and Chen, F and Chen, Z and Xiao, C and Hou, K and Zhang, B}, title = {Gut Bacterial Characteristics of Patients With Type 2 Diabetes Mellitus and the Application Potential.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {722206}, pmid = {34484230}, issn = {1664-3224}, mesh = {Case-Control Studies ; Diabetes Mellitus, Type 2/*complications/metabolism ; Dysbiosis/*etiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; Probiotics ; RNA, Ribosomal, 16S ; ROC Curve ; }, abstract = {Type 2 diabetes mellitus (T2DM) is a complex disorder comprehensively influenced by genetic and environmental risk, and research increasingly has indicated the role of microbial dysbiosis in T2DM pathogenesis. However, studies comparing the microbiome characteristics between T2DM and healthy controls have reported inconsistent results. To further identify and describe the characteristics of the intestinal flora of T2DM patients, we performed a systematic review and meta-analysis of stool microbial profiles to discern and describe microbial dysbiosis in T2DM and to explore heterogeneity among 7 studies (600 T2DM cases, 543 controls, 1143 samples in total). Using a random effects model and a fixed effects model, we observed significant differences in beta diversity, but not alpha diversity, between individuals with T2DM and controls. We identified various operational taxonomic unit (OTUs) and bacterial genera with significant odds ratios for T2DM. The T2DM signatures derived from a single study by stepwise feature selection could be applied in other studies. By training on multiple studies, we improved the detection accuracy and disease specificity for T2DM. We also discuss the relationship between T2DM-enriched or T2DM-depleted genera and probiotics and provide new ideas for diabetes prevention and improvement.}, } @article {pmid34482702, year = {2021}, author = {Navarro, D and González, A and Saiz O Y Odriozola, A}, title = {Sample collection/stabilization and DNA/RNA extraction from swab samples for microbiome or metagenome analyses.}, journal = {BioTechniques}, volume = {71}, number = {3}, pages = {499-500}, doi = {10.2144/btn-2021-1000ap}, pmid = {34482702}, issn = {1940-9818}, mesh = {DNA, Bacterial/*isolation & purification ; *Metagenome ; *Microbiota/genetics ; RNA, Bacterial/*isolation & purification ; Specimen Handling ; }, abstract = {Good preservation and storage are essential to preserving microorganisms' genetic material in microbial communities from wide array of sample inputs and accurately represent the bacterial composition for further analysis and applications. The objective is to develop a proper preservation and storage medium to preserve DNA and RNA from those microorganisms. DANAGEN-BIOTED has developed a new product to deal with this problem. Click on the To read the full Application forum, click on the View Article button above and download the PDF.}, } @article {pmid34482027, year = {2021}, author = {Hu, X and Shen, X and Tian, J}, title = {The effects of periodontitis associated microbiota on the development of oral squamous cell carcinoma.}, journal = {Biochemical and biophysical research communications}, volume = {576}, number = {}, pages = {80-85}, doi = {10.1016/j.bbrc.2021.07.092}, pmid = {34482027}, issn = {1090-2104}, mesh = {Bacteroidaceae Infections/complications/microbiology/pathology ; Cell Line, Tumor ; Cell Movement/physiology ; Corynebacterium/genetics/isolation & purification ; Fusobacterium Infections/complications/microbiology/pathology ; Fusobacterium nucleatum/genetics/isolation & purification ; Head and Neck Neoplasms/metabolism/*microbiology/pathology ; Humans ; *Microbiota ; Neisseria sicca/genetics/isolation & purification ; Neisseriaceae Infections/complications/microbiology/pathology ; Periodontitis/*microbiology ; Porphyromonas gingivalis/genetics/isolation & purification ; Squamous Cell Carcinoma of Head and Neck/metabolism/*microbiology/pathology ; }, abstract = {Epidemiological data have shown that periodontal bacterial infection, periodontitis, and oral squamous cell carcinoma have close relationship on the disease progress and risk. However, the specific role of periodontal microbes and their mechanism in the development of oral squamous cell carcinoma is not yet clear. In our previous work, metagenomic Illumina Mi-seq analysis was used to identify tstructure and abundance of periodontital microbiome. Accoding to the results, we used Porphyromonas.spp. and Fusobacterium.spp. as the periodontitis positive microbiota; Neisseria.spp and Corynebacterium.spp as periodontitis negative microbiota (their average relative abundance were >5%). These representative strains of the above genus were used to infect OSCC cells to explore their effect on tumor cell biology behavior, and detect the expression level of the gene in related to inflammation, migration, invasion and cell cycle. We find that periodontitis positive correlated microbiota had a promoting effect on the development of oral squamous cell carcinoma in vitro by regulating mRNA and protein expression of IL-6, IL-8, MMP-9 and Cyclin-D1. Periodontitis negative correlated microbiota had suppression effect on the development of oral squamous cell carcinoma in vitro analysis.}, } @article {pmid34481302, year = {2021}, author = {Aguinaga, OE and White, KN and Dean, AP and Pittman, JK}, title = {Addition of organic acids to acid mine drainage polluted wetland sediment leads to microbial community structure and functional changes and improved water quality.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {290}, number = {}, pages = {118064}, doi = {10.1016/j.envpol.2021.118064}, pmid = {34481302}, issn = {1873-6424}, mesh = {Acids ; *Microbiota ; Mining ; Water Quality ; *Wetlands ; }, abstract = {Acid mine drainage (AMD) is a serious environmental problem worldwide that requires efficient and sustainable remediation technologies including the use of biological mechanisms. A key challenge for AMD bioremediation is to provide optimal conditions for microbial-mediated immobilisation of trace metals. Although organic carbon and oxygen can enhance treatment efficiency, the effect on microbial communities is unclear. In this study, surface sediments from a natural wetland with proven efficiency for AMD bioremediation were artificially exposed to oxygen (by aeration) and/or organic carbon (in the form of mixed organic acids) and incubated under laboratory conditions. In addition to measuring changes in water chemistry, a metagenomics approach was used to determine changes in sediment bacterial, archaeal and fungal community structure, and functional gene abundance. The addition of organic carbon produced major changes in the abundance of microorganisms related to iron and sulfur metabolism (including Geobacter and Pelobacter) and increased levels of particulate metals via sulfate reduction. Aeration resulted in an increase in Sideroxydans abundance but no significant changes in metal chemistry were observed. The study concludes that the utilisation of organic carbon by microorganisms is more important for achieving efficient AMD treatment than the availability of oxygen, yet the combination of oxygen with organic carbon addition did not inhibit the improvements to water quality.}, } @article {pmid34479875, year = {2021}, author = {Armstrong, G and Cantrell, K and Huang, S and McDonald, D and Haiminen, N and Carrieri, AP and Zhu, Q and Gonzalez, A and McGrath, I and Beck, KL and Hakim, D and Havulinna, AS and Méric, G and Niiranen, T and Lahti, L and Salomaa, V and Jain, M and Inouye, M and Swafford, AD and Kim, HC and Parida, L and Vázquez-Baeza, Y and Knight, R}, title = {Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes.}, journal = {Genome research}, volume = {31}, number = {11}, pages = {2131-2137}, pmid = {34479875}, issn = {1549-5469}, support = {CH/12/2/29428/BHF_/British Heart Foundation/United Kingdom ; R01 ES027595/ES/NIEHS NIH HHS/United States ; RG/13/13/30194/BHF_/British Heart Foundation/United Kingdom ; RG/18/13/33946/BHF_/British Heart Foundation/United Kingdom ; }, mesh = {*Microbiota/genetics ; Phylogeny ; }, abstract = {The number of publicly available microbiome samples is continually growing. As data set size increases, bottlenecks arise in standard analytical pipelines. Faith's phylogenetic diversity (Faith's PD) is a highly utilized phylogenetic alpha diversity metric that has thus far failed to effectively scale to trees with millions of vertices. Stacked Faith's phylogenetic diversity (SFPhD) enables calculation of this widely adopted diversity metric at a much larger scale by implementing a computationally efficient algorithm. The algorithm reduces the amount of computational resources required, resulting in more accessible software with a reduced carbon footprint, as compared to previous approaches. The new algorithm produces identical results to the previous method. We further demonstrate that the phylogenetic aspect of Faith's PD provides increased power in detecting diversity differences between younger and older populations in the FINRISK study's metagenomic data.}, } @article {pmid34477543, year = {2021}, author = {Tan, CCS and Acman, M and van Dorp, L and Balloux, F}, title = {Metagenomic evidence for a polymicrobial signature of sepsis.}, journal = {Microbial genomics}, volume = {7}, number = {9}, pages = {}, pmid = {34477543}, issn = {2057-5858}, mesh = {Bacteria/*genetics ; Humans ; Machine Learning ; Metagenome ; *Metagenomics ; Microbiota ; Sepsis/diagnosis/*microbiology ; }, abstract = {Our understanding of the host component of sepsis has made significant progress. However, detailed study of the microorganisms causing sepsis, either as single pathogens or microbial assemblages, has received far less attention. Metagenomic data offer opportunities to characterize the microbial communities found in septic and healthy individuals. In this study we apply gradient-boosted tree classifiers and a novel computational decontamination technique built upon SHapley Additive exPlanations (SHAP) to identify microbial hallmarks which discriminate blood metagenomic samples of septic patients from that of healthy individuals. Classifiers had high performance when using the read assignments to microbial genera [area under the receiver operating characteristic (AUROC=0.995)], including after removal of species 'culture-confirmed' as the cause of sepsis through clinical testing (AUROC=0.915). Models trained on single genera were inferior to those employing a polymicrobial model and we identified multiple co-occurring bacterial genera absent from healthy controls. While prevailing diagnostic paradigms seek to identify single pathogens, our results point to the involvement of a polymicrobial community in sepsis. We demonstrate the importance of the microbial component in characterising sepsis, which may offer new biological insights into the aetiology of sepsis, and ultimately support the development of clinical diagnostic or even prognostic tools.}, } @article {pmid34475403, year = {2021}, author = {Yan, Y and Ren, S and Duan, Y and Lu, C and Niu, Y and Wang, Z and Inglis, B and Ji, W and Zheng, Y and Si, W}, title = {Gut microbiota and metabolites of α-synuclein transgenic monkey models with early stage of Parkinson's disease.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {69}, pmid = {34475403}, issn = {2055-5008}, mesh = {Animals ; Animals, Genetically Modified ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/*physiology ; Glyceraldehyde-3-Phosphate Dehydrogenases/metabolism ; Humans ; Macaca mulatta ; Male ; Metagenomics ; Mice ; Neurodegenerative Diseases ; Parkinson Disease/*metabolism ; alpha-Synuclein/genetics/*metabolism ; }, abstract = {Parkinson's disease (PD) is the second most prevalent neurodegenerative disease. However, it is unclear whether microbiota and metabolites have demonstrated changes at early PD due to the difficulties in diagnosis and identification of early PD in clinical practice. In a previous study, we generated A53T transgenic monkeys with early Parkinson's symptoms, including anxiety and cognitive impairment. Here we analyzed the gut microbiota by metagenomic sequencing and metabolites by targeted gas chromatography. The gut microbiota analysis showed that the A53T monkeys have higher degree of diversity in gut microbiota with significantly elevated Sybergistetes, Akkermansia, and Eggerthella lenta compared with control monkeys. Prevotella significantly decreased in A53T transgenic monkeys. Glyceric acid, L-Aspartic acid, and p-Hydroxyphenylacetic acid were significantly elevated, whereas Myristic acid and 3-Methylindole were significantly decreased in A53T monkeys. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (KO0131) and the oxidative phosphorylation reaction (KO2147) were significantly increased in metabolic pathways of A53T monkeys. Our study suggested that the transgenic A53T and α-syn aggregation may affect the intestine microbiota and metabolites of rhesus monkeys, and the identified five compositional different metabolites that are mainly associated with mitochondrial dysfunction may be related to the pathogenesis of PD.}, } @article {pmid34475159, year = {2021}, author = {Deng, L and Yan, J and Xu, H and Huang, C and Lv, Y and Wu, Q and Xu, Y and Chen, X}, title = {Prediction of exacerbation frequency of AECOPD based on next-generation sequencing and its relationship with imbalance of lung and gut microbiota: a protocol of a prospective cohort study.}, journal = {BMJ open}, volume = {11}, number = {9}, pages = {e047202}, pmid = {34475159}, issn = {2044-6055}, mesh = {Disease Progression ; *Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Lung ; Phenotype ; Prospective Studies ; *Pulmonary Disease, Chronic Obstructive ; }, abstract = {INTRODUCTION: Patients with frequent acute exacerbation phenotype chronic obstructive pulmonary disease (AECOPD) have a higher hospitalisation rate than infrequent exacerbation, the disease progresses quickly and treatment is more difficult. At present, it is impossible to predict patients with COPD with frequent acute exacerbation phenotypes. The composition of the lower respiratory tract flora and the intestinal flora is closely related to AECOPD, but the specific association mechanism between them is not very clear. This study used metagenomic next-generation sequencing (mNGS) technology to explore the microbial characteristics of the intestinal tract and airways of patients with COPD, and analyse the correlation between the sequencing results and inflammatory factors, immune factors and nutritional factors.

METHODS AND ANALYSIS: This will be a prospective cohort study. We intend to recruit 152 patients with stable COPD. In the baseline, we will detect the participants' induced sputum and faecal flora through mNGS, and changes in blood immune levels, and the patient's condition is evaluated. Every 2 months, we will check the number of acute exacerbation through the phone range. After 12 months, we will check again the changes in the blood immune level, evaluate the patient's condition and count the number of episodes.

ETHICS AND DISSEMINATION: This study has been approved by the ethics committee of Guangdong Provincial Hospital of Traditional Chinese Medicine (approval number ZF2019-219-03). The results of the study will be published in peer-reviewed journals.

TRIAL REGISTRATION NUMBER: ClinicalTrials.gov Registry (ChiCTR2000032870).}, } @article {pmid34474998, year = {2021}, author = {Liu, C and Hu, J and Wu, Y and Irwin, DM and Chen, W and Zhang, Z and Yu, L}, title = {Comparative study of gut microbiota from captive and confiscated-rescued wild pangolins.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {48}, number = {9}, pages = {825-835}, doi = {10.1016/j.jgg.2021.07.009}, pmid = {34474998}, issn = {1673-8527}, mesh = {*Pangolins/microbiology ; *Gastrointestinal Microbiome/drug effects ; Animals, Wild ; Breeding ; Endangered Species ; Anti-Bacterial Agents/administration & dosage ; Diet ; RNA, Ribosomal, 16S/analysis/genetics ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Virulence Factors/analysis ; Carbohydrate Metabolism ; Enzymes/analysis ; }, abstract = {Pangolins are among the most critically endangered animals due to widespread poaching and worldwide trafficking. Captive breeding is considered to be one way to protect them and increase the sizes of their populations. However, comparative studies of captive and wild pangolins in the context of gut microbiota are rare. Here, the gut microbiome of captive and confiscated-rescued wild pangolins is compared, and the effects of different periods of captivity and captivity with and without antibiotic treatment are considered. We show that different diets and periods of captivity, as well as the application of antibiotic therapy, can alter gut community composition and abundance in pangolins. Compared to wild pangolins, captive pangolins have an increased capacity for chitin and cellulose/hemicellulose degradation, fatty acid metabolism, and short-chain fatty acid synthesis, but a reduced ability to metabolize exogenous substances. In addition to increasing the ability of the gut microbiota to metabolize nutrients in captivity, captive breeding imposes some risks for survival by resulting in a greater abundance of antibiotic resistance genes and virulence factors in captive pangolins than in wild pangolins. Our study is important for the development of guidelines for pangolin conservation, including health assessment, disease prevention, and rehabilitation of wild pangolin populations.}, } @article {pmid34473943, year = {2021}, author = {Vasquez, KS and Willis, L and Cira, NJ and Ng, KM and Pedro, MF and Aranda-Díaz, A and Rajendram, M and Yu, FB and Higginbottom, SK and Neff, N and Sherlock, G and Xavier, KB and Quake, SR and Sonnenburg, JL and Good, BH and Huang, KC}, title = {Quantifying rapid bacterial evolution and transmission within the mouse intestine.}, journal = {Cell host & microbe}, volume = {29}, number = {9}, pages = {1454-1468.e4}, pmid = {34473943}, issn = {1934-6069}, support = {R01 DK085025/DK/NIDDK NIH HHS/United States ; R35 GM131824/GM/NIGMS NIH HHS/United States ; RM1 GM135102/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Ciprofloxacin/*pharmacology ; DNA Barcoding, Taxonomic/*methods ; Escherichia coli/drug effects/*growth & development/immunology ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics ; Genetics, Population/methods ; Germ-Free Life ; Intestines/*microbiology ; Mice ; Selection, Genetic/genetics ; Whole Genome Sequencing ; }, abstract = {Due to limitations on high-resolution strain tracking, selection dynamics during gut microbiota colonization and transmission between hosts remain mostly mysterious. Here, we introduced hundreds of barcoded Escherichia coli strains into germ-free mice and quantified strain-level dynamics and metagenomic changes. Mutations in genes involved in motility and metabolite utilization are reproducibly selected within days. Even with rapid selection, coprophagy enforced similar barcode distributions across co-housed mice. Whole-genome sequencing of hundreds of isolates revealed linked alleles that demonstrate between-host transmission. A population-genetics model predicts substantial fitness advantages for certain mutants and that migration accounted for ∼10% of the resident microbiota each day. Treatment with ciprofloxacin suggests interplay between selection and transmission. While initial colonization was mostly uniform, in two mice a bottleneck reduced diversity and selected for ciprofloxacin resistance in the absence of drug. These findings highlight the interplay between environmental transmission and rapid, deterministic selection during evolution of the intestinal microbiota.}, } @article {pmid34473015, year = {2021}, author = {Kapustina, Ž and Medžiūnė, J and Alzbutas, G and Rokaitis, I and Matjošaitis, K and Mackevičius, G and Žeimytė, S and Karpus, L and Lubys, A}, title = {High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts.}, journal = {Microbial genomics}, volume = {7}, number = {9}, pages = {}, pmid = {34473015}, issn = {2057-5858}, mesh = {Bacteria/classification/genetics ; Base Sequence ; Computational Biology/methods ; DNA, Bacterial/genetics ; *Genome, Bacterial ; *Genomics ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {Sequence-based characterization of bacterial communities has long been a hostage of limitations of both 16S rRNA gene and whole metagenome sequencing. Neither approach is universally applicable, and the main efforts to resolve constraints have been devoted to improvement of computational prediction tools. Here, we present semi-targeted 16S rRNA sequencing (st16S-seq), a method designed for sequencing V1-V2 regions of the 16S rRNA gene along with the genomic locus upstream of the gene. By in silico analysis of 13 570 bacterial genome assemblies, we show that genome-linked 16S rRNA sequencing is superior to individual hypervariable regions or full-length gene sequences in terms of classification accuracy and identification of gene copy numbers. Using mock communities and soil samples we experimentally validate st16S-seq and benchmark it against the established microbial classification techniques. We show that st16S-seq delivers accurate estimation of 16S rRNA gene copy numbers, enables taxonomic resolution at the species level and closely approximates community structures obtainable by whole metagenome sequencing.}, } @article {pmid34472853, year = {2021}, author = {Wu, X and Chauhan, A and Layton, AC and Lau Vetter, MCY and Stackhouse, BT and Williams, DE and Whyte, L and Pfiffner, SM and Onstott, TC and Vishnivetskaya, TA}, title = {Comparative Metagenomics of the Active Layer and Permafrost from Low-Carbon Soil in the Canadian High Arctic.}, journal = {Environmental science & technology}, volume = {55}, number = {18}, pages = {12683-12693}, doi = {10.1021/acs.est.1c00802}, pmid = {34472853}, issn = {1520-5851}, mesh = {Arctic Regions ; Canada ; Carbon ; Metagenomics ; *Permafrost ; RNA, Ribosomal, 16S/genetics ; Soil ; Soil Microbiology ; }, abstract = {Approximately 87% of the Arctic consists of low-organic carbon mineral soil, but knowledge of microbial activity in low-carbon permafrost (PF) and active layer soils remains limited. This study investigated the taxonomic composition and genetic potential of microbial communities at contrasting depths of the active layer (5, 35, and 65 cm below surface, bls) and PF (80 cm bls). We showed microbial communities in PF to be taxonomically and functionally different from those in the active layer. 16S rRNA gene sequence analysis revealed higher biodiversity in the active layer than in PF, and biodiversity decreased significantly with depth. The reconstructed 91 metagenome-assembled genomes showed that PF was dominated by heterotrophic, fermenting Bacteroidota using nitrite as their main electron acceptor. Prevalent microbes identified in the active layer belonged to bacterial taxa, gaining energy via aerobic respiration. Gene abundance in metagenomes revealed enrichment of genes encoding the plant-derived polysaccharide degradation and metabolism of nitrate and sulfate in PF, whereas genes encoding methane/ammonia oxidation, cold-shock protein, and two-component systems were generally more abundant in the active layer, particularly at 5 cm bls. The results of this study deepen our understanding of the low-carbon Arctic soil microbiome and improve prediction of the impacts of thawing PF.}, } @article {pmid34472211, year = {2021}, author = {Lv, WQ and Lin, X and Shen, H and Liu, HM and Qiu, X and Li, BY and Shen, WD and Ge, CL and Lv, FY and Shen, J and Xiao, HM and Deng, HW}, title = {Human gut microbiome impacts skeletal muscle mass via gut microbial synthesis of the short-chain fatty acid butyrate among healthy menopausal women.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {12}, number = {6}, pages = {1860-1870}, pmid = {34472211}, issn = {2190-6009}, support = {R01AG061917/NH/NIH HHS/United States ; U54MD007595/NH/NIH HHS/United States ; R01 AR069055/AR/NIAMS NIH HHS/United States ; R01MH104680/NH/NIH HHS/United States ; U19 AG055373/AG/NIA NIH HHS/United States ; U19AG05537301/NH/NIH HHS/United States ; P20GM109036/NH/NIH HHS/United States ; R01AR069055/NH/NIH HHS/United States ; R01 AG061917/AG/NIA NIH HHS/United States ; }, mesh = {Butyrates ; Fatty Acids, Volatile ; Female ; *Gastrointestinal Microbiome ; Genome-Wide Association Study ; Humans ; Menopause ; Muscle, Skeletal ; }, abstract = {BACKGROUND: Increasing evidence suggests that human gut microbiome plays an important role in variation of skeletal muscle mass (SMM). However, specific causal mechanistic relationship of human gut microbiome with SMM remains largely unresolved. Understanding the causal mechanistic relationship may provide a basis for novel interventions for loss of SMM. This study investigated whether human gut microbiome has a causal effect on SMM among Chinese community-dwelling healthy menopausal women.

METHODS: Estimated SMM was derived from whole-body dual-energy X-ray absorptiometry. We performed integrated analyses on whole-genome sequencing, shotgun metagenomic sequencing, and serum short-chain fatty acids (SCFAs), as well as available host SMM measurements among community-dwelling healthy menopausal women (N = 482). We combined the results with summary statistics from genome-wide association analyses for human gut microbiome (N = 952) and SMM traits (N = 28 330). As a prerequisite for causality, we used a computational protocol that was proposed to measure correlations among gut metagenome, metabolome, and the host trait to investigate the relationship between human gut microbiome and SMM. Causal inference methods were applied to assess the potential causal effects of gut microbial features on SMM, through one-sample and two-sample Mendelian randomization (MR) analyses, respectively.

RESULTS: In metagenomic association analyses, the increased capacity for gut microbial synthesis of the SCFA butyrate was significantly associated with serum butyrate levels [Spearman correlation coefficient (SCC) = 0.13, P = 0.02] and skeletal muscle index (SCC = 0.084, P = 0.002). Of interest was the finding that two main butyrate-producing bacterial species were both positively associated with the increased capacity for gut microbial synthesis of butyrate [Faecalibacterium prausnitzii (SCC = 0.25, P = 6.6 × 10[-7]) and Butyricimonas virosa (SCC = 0.15, P = 0.001)] and for skeletal muscle index [F. prausnitzii (SCC = 0.16, P = 6.2 × 10[-4]) and B. virosa (SCC = 0.17, P = 2.4 × 10[-4])]. One-sample MR results showed a causal effect between gut microbial synthesis of the SCFA butyrate and appendicular lean mass (β = 0.04, 95% confidence interval 0.029 to 0.051, P = 0.003). Two-sample MR results further confirmed the causal effect between gut microbial synthesis of the SCFA butyrate and appendicular lean mass (β = 0.06, 95% confidence interval 0 to 0.13, P = 0.06).

CONCLUSIONS: Our results may help the future development of novel intervention approaches for preventing or alleviating loss of SMM.}, } @article {pmid34471330, year = {2021}, author = {Cheaib, B and Yang, P and Kazlauskaite, R and Lindsay, E and Heys, C and Dwyer, T and De Noa, M and Schaal, P and Sloan, W and Ijaz, UZ and Llewellyn, MS}, title = {Genome erosion and evidence for an intracellular niche - exploring the biology of mycoplasmas in Atlantic salmon.}, journal = {Aquaculture (Amsterdam, Netherlands)}, volume = {541}, number = {}, pages = {736772}, pmid = {34471330}, issn = {0044-8486}, abstract = {Mycoplasmas are the smallest autonomously self-replicating life form on the planet. Members of this bacterial genus are known to parasitise a wide array of metazoans including vertebrates. Whilst much research has been significant targeted at parasitic mammalian mycoplasmas, very little is known about their role in other vertebrates. In the current study, we aim to explore the biology of mycoplasmas in Atlantic Salmon, a species of major significance for aquaculture, including cellular niche, genome size structure and gene content. Using fluorescent in-situ hybridisation (FISH), mycoplasmas were targeted in epithelial tissues across the digestive tract (stomach, pyloric caecum and midgut) from different development stages (eggs, parr, subadult) of farmed Atlantic salmon (Salmo salar), and we present evidence for an intracellular niche for some of the microbes visualised. Via shotgun metagenomic sequencing, a nearly complete, albeit small, genome (~0.57 MB) as assembled from a farmed Atlantic salmon subadult. Phylogenetic analysis of the recovered genome revealed taxonomic proximity to other salmon derived mycoplasmas, as well as to the human pathogen Mycoplasma penetrans (~1.36 Mb). We annotated coding sequences and identified riboflavin pathway encoding genes and sugar transporters, the former potentially consistent with micronutrient provisioning in salmonid development. Our study provides insights into mucosal adherence, the cellular niche and gene catalog of Mycoplasma in the gut ecosystem of the Atlantic salmon, suggesting a high dependency of this minimalist bacterium on its host. Further study is required to explore and functional role of Mycoplasma in the nutrition and development of its salmonid host.}, } @article {pmid34469196, year = {2021}, author = {Yap, M and Gleeson, D and O'Toole, PW and O'Sullivan, O and Cotter, PD}, title = {Seasonality and Geography Have a Greater Influence than the Use of Chlorine-Based Cleaning Agents on the Microbiota of Bulk Tank Raw Milk.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {22}, pages = {e0108121}, pmid = {34469196}, issn = {1098-5336}, mesh = {Animals ; *Chlorine/pharmacology ; Dairying ; Disinfectants/pharmacology ; Equipment Contamination/prevention & control ; *Geography ; Ireland ; *Microbiota ; Milk/*microbiology ; *Seasons ; }, abstract = {Cleaning of the production environment is vital to ensure the safety and quality of dairy products. Although cleaning with chlorine-based agents is widely adopted, it has been associated with detrimental effects on milk quality and safety, which has garnered increasing interest in chlorine-free cleaning. However, the influence of these methods on the milk microbiota is not well documented. This study investigated the factors that influence the raw milk microbiota, with a focus on the differences when chlorine-based and chlorine-free cleaning of milking equipment are used. Bulk tank raw milk was sampled during three sampling months (April, August, and November), from farms across Ireland selected to capture the use of different cleaning methods, i.e., exclusively chlorine-based (n = 51) and chlorine-free cleaning (n = 92) and farms that used chlorine-free agents for the bulk tank and chlorine-based cleaning agents for the rest of the equipment (n = 28). Shotgun metagenomic analysis revealed the significant influence of seasonal and geographic factors on the bulk tank milk microbiota, indicated by differences in diversity, taxonomic composition, and functional characteristics. Taxonomic and functional profiles of samples collected in November clustered separately from those of samples collected in other months. In contrast, cleaning methods only accounted for 1% of the variation in the bulk tank milk bacterial community, and samples collected from farms using chlorine-based versus chlorine-free cleaning did not differ significantly, suggesting that the chlorine-free approaches used did not negatively impact microbiological quality. This study shows the value of shotgun metagenomics in advancing our knowledge of the raw milk microbiota. IMPORTANCE The microbiota of raw milk is affected by many factors that can control or promote the introduction of undesirable microorganisms. Chlorine-based cleaning agents have been commonly used due to their effectiveness in controlling undesirable microorganisms, but they have been associated with the formation of chlorine residues that are detrimental to product quality and may impact consumer health. Chlorine-free alternatives have been recommended in some countries, but the influence of cleaning agents on the milk microbiota is unknown. Here, we investigated the influence of cleaning methods and other factors on bulk tank raw milk. Results showed that season and location had a greater influence on the milk microbiota than the cleaning agents used. Indeed, the similar microbiota compositions of raw milk from farms that used chlorine-based and those that used chlorine-free cleaning methods supports the further use of chlorine-free cleaning agents in dairy production.}, } @article {pmid34469192, year = {2021}, author = {Gao, C and Xia, J and Zhou, X and Liang, Y and Jiang, Y and Wang, M and Shao, H and Shi, X and Guo, C and He, H and Wang, H and He, J and Hu, D and Wang, X and Zhao, J and Zhang, YZ and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Suttle, CA and Wang, M}, title = {Viral Characteristics of the Warm Atlantic and Cold Arctic Water Masses in the Nordic Seas.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {22}, pages = {e0116021}, pmid = {34469192}, issn = {1098-5336}, mesh = {Arctic Regions ; Atlantic Ocean ; *Metagenomics ; *Seawater/virology ; Temperature ; *Virome ; }, abstract = {Nordic Seas are the subarctic seas connecting the Arctic Ocean and North Atlantic Ocean with complex water masses, experiencing an abrupt climate change. Though knowledge of the marine virosphere has expanded rapidly, the diversity of viruses and their relationships with host cells and water masses in the Nordic Seas remain to be fully revealed. Here, we establish the Nordic Sea DNA virome (NSV) data set of 55,315 viral contigs including 1,478 unique viral populations from seven stations influenced by both the warm Atlantic and cold Arctic water masses. Caudovirales dominated in the seven NSVs, especially in the warm Atlantic waters. The major giant nucleocytoplasmic large DNA viruses (NCLDVs) contributed a significant proportion of the classified viral contigs in the NSVs (32.2%), especially in the cold Arctic waters (44.9%). The distribution patterns of Caudovirales and NCLDVs were a reflection of the community structure of their hosts in the corresponding water masses and currents. Latitude, pH, and flow speed were found to be key factors influencing the microbial communities and coinfluencing the variation of viral communities. Network analysis illustrated the tight coupling between the variation of viral communities and microbial communities in the Nordic Seas. This study suggests a probable linkage between viromes, host cells, and surface water masses from both the cool Arctic and warm Atlantic Oceans. IMPORTANCE This is a systematic study of Nordic Sea viromes using metagenomic analysis. The viral diversity, community structure, and their relationships with host cells and the complex water masses from both the cool Arctic and the warm Atlantic oceans were illustrated. The NCLDVs and Caudovirales are proposed as the viral characteristics of the cold Arctic and warm Atlantic waters, respectively. This study provides an important background for the viromes in the subarctic seas connecting the Arctic Ocean and North Atlantic Ocean and sheds light on their responses to abrupt climate change in the future.}, } @article {pmid34469017, year = {2022}, author = {Larios-Soriano, E and Zavala, RC and López, LM and Gómez-Gil, B and Ramírez, DT and Sanchez, S and Canales, K and Galaviz, MA}, title = {Soy protein concentrate effects on gut microbiota structure and digestive physiology of Totoaba macdonaldi.}, journal = {Journal of applied microbiology}, volume = {132}, number = {2}, pages = {1384-1396}, doi = {10.1111/jam.15269}, pmid = {34469017}, issn = {1365-2672}, support = {247698//SADER-CONACYT/ ; }, mesh = {Animals ; Digestive System Physiological Phenomena ; *Gastrointestinal Microbiome/genetics ; *Perciformes ; RNA, Ribosomal, 16S/genetics ; Soybean Proteins ; }, abstract = {AIMS: Examine the effect of soy protein concentrate (SPC) on allochthonous microbiota, hindgut integrity, and liver tissue of totoaba (Totoaba macdonaldi).

METHODS AND RESULTS: Four diets were prepared: control diet (100% fishmeal) and experimental diets containing partial substitution of fishmeal by SPC (15%, 30% and 45% SPC). After 90 days, samples of the hindgut contents were taken to determine the taxonomic composition of the allochthonous microbiota through sequencing of the V3-V4 region of the 16S rRNA gene. Simultaneously, liver and hindgut samples were collected for examination by histological approaches. The SPC modulated the richness and abundance of the accessory microbiota, of which the main operational taxonomic unit showed an increase corresponding to the Phylum Firmicutes (Bacillales and Lactobacillales). With the increase in SPC, a slight decrease in mucosal fold width, a decrease in goblet cells and a slight distortion of the villi in the hindgut were observed. In the liver, SPC was observed to influence hepatocytes morphology through irregular and enlarged nuclei.

CONCLUSION: The study demonstrates that Proteobacteria dominated the allochthonous microbiota of subadult totoaba, regardless of the diet. However, the SPC modulated the accessory bacteria communities and caused slight effects on the liver and gut of fish.

To our knowledge, this is the first study that analyses the effects of SPC on allochthonous microbiota of subadults T. macdonaldi through new generation techniques such as DNA sequencing for metagenomic analysis.}, } @article {pmid34468194, year = {2021}, author = {Murphy, A and Barich, D and Fennessy, MS and Slonczewski, JL}, title = {An Ohio State Scenic River Shows Elevated Antibiotic Resistance Genes, Including Acinetobacter Tetracycline and Macrolide Resistance, Downstream of Wastewater Treatment Plant Effluent.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0094121}, pmid = {34468194}, issn = {2165-0497}, mesh = {Acinetobacter baumannii/*drug effects/*genetics ; Anti-Bacterial Agents/pharmacology ; Bacteroides/drug effects/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Firmicutes/drug effects/genetics ; Humans ; Macrolides/pharmacology ; Metagenome/genetics ; Microbiota/drug effects/genetics ; Ohio ; Phylogeny ; Rivers/microbiology ; Tetracyclines/pharmacology ; Wastewater/*microbiology ; Water Purification/*methods ; }, abstract = {The entry of antibiotic resistance genes (ARGs) into aquatic systems has been documented for large municipal wastewater treatment plants (WWTPs), but there is less study of the impact of smaller plants that are situated on small rural rivers. We sampled water metagenomes for ARGs and taxa composition from the Kokosing River, a small rural river in Knox County, Ohio, which has been designated an Ohio State Scenic River for retention of natural character. Samples were obtained 1.0 km upstream, 120 m downstream, and 6.4 km downstream from the effluent release of the Mount Vernon WWTP. ARGs were identified in metagenomes using ShortBRED markers from the comprehensive antibiotic resistance database (CARD) screened against UniPROT. Through all seasons, the metagenome just downstream of the WWTP effluent showed a substantial elevation of at least 15 different ARGs, including 6 ARGs commonly associated with Acinetobacter baumannii, such as msrE, mphE (macrolide resistance), and tet(39) (tetracycline resistance). The ARGs most prevalent near the effluent pipe persisted 6.4 km downriver. Using metagenomic phylogenetic analysis (MetaPhlAn2) clade-specific marker genes, the taxa distribution near the effluent showed elevation of reads annotated as Acinetobacter species as well as gut-associated taxa, Bacteroides and Firmicutes. The ARG levels and taxa prevalence showed little dependence on seasonal chlorination of the effluent. Nitrogen and phosphorus were elevated near the effluent pipe but had no consistent correlation with ARG levels. We show that in a rural river microbiome, year-round wastewater effluent substantially elevates ARGs, including those associated with multidrug-resistant A. baumannii. IMPORTANCE Antibiotic resistance is a growing problem worldwide, with frequent transmission between pathogens and environmental organisms. Rural rivers can support high levels of recreational use by people unaware of inputs from treated wastewater, while wastewater treatment plants (WWTPs) can generate a small but significant portion of flow volume into a river surrounded by forest and agriculture. There is little information on the rural impacts of WWTP effluent on the delivery and transport of antibiotic resistance genes. In our study, the river water proximal to wastewater effluent shows evidence for the influx of multidrug-resistant Acinetobacter baumannii, an opportunistic pathogen of concern for hospitals but also widespread in natural environments. Our work highlights the importance of wastewater effluent in management of environmental antibiotic resistance, even in high quality, rural river systems.}, } @article {pmid34468193, year = {2021}, author = {Nagy-Szakal, D and Couto-Rodriguez, M and Wells, HL and Barrows, JE and Debieu, M and Butcher, K and Chen, S and Berki, A and Hager, C and Boorstein, RJ and Taylor, MK and Jonsson, CB and Mason, CE and O'Hara, NB}, title = {Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0019721}, pmid = {34468193}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents/pharmacology ; COVID-19/pathology ; Drug Resistance, Bacterial/genetics ; Genetic Variation/*genetics ; Genome, Viral/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Limit of Detection ; Macrolides/pharmacology ; Metagenomics/methods ; Microbiota/*genetics ; Nasopharynx/*microbiology ; RNA, Viral/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; SARS-CoV-2/*genetics/isolation & purification ; }, abstract = {The emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic variants that may alter viral fitness highlights the urgency of widespread next-generation sequencing (NGS) surveillance. To profile genetic variants of the entire SARS-CoV-2 genome, we developed and clinically validated a hybridization capture SARS-CoV-2 NGS assay, integrating novel methods for panel design using double-stranded DNA (dsDNA) biotin-labeled probes, and built accompanying software. This test is the first hybrid capture-based NGS assay given Food and Drug Administration (FDA) emergency use authorization for detection of the SARS-CoV-2 virus. The positive and negative percent agreement (PPA and NPA, respectively) were defined in comparison to the results for an orthogonal real-time reverse transcription polymerase chain reaction (RT-PCR) assay (PPA and NPA, 96.7 and 100%, respectively). The limit of detection was established to be 800 copies/ml with an average fold enrichment of 46,791. Furthermore, utilizing the research-use-only analysis to profile the variants, we identified 55 novel mutations, including 11 in the functionally important spike protein. Finally, we profiled the full nasopharyngeal microbiome using metagenomics and found overrepresentation of 7 taxa and evidence of macrolide resistance in SARS-CoV-2-positive patients. This hybrid capture NGS assay, coupled with optimized software, is a powerful approach to detect and comprehensively map SARS-CoV-2 genetic variants for tracking viral evolution and guiding vaccine updates. IMPORTANCE This is the first FDA emergency-use-authorized hybridization capture-based next-generation sequencing (NGS) assay to detect the SARS-CoV-2 genome. Viral metagenomics and the novel hybrid capture NGS-based assay, along with its research-use-only analysis, can provide important genetic insights into SARS-CoV-2 and other emerging pathogens and improve surveillance and early detection, potentially preventing or mitigating new outbreaks. Better understanding of the continuously evolving SARS-CoV-2 viral genome and the impact of genetic variants may provide individual risk stratification, precision therapeutic options, improved molecular diagnostics, and population-based therapeutic solutions.}, } @article {pmid34467925, year = {2021}, author = {Vilela, PB and Mendonça Neto, RP and Starling, MCVM and da S Martins, A and Pires, GFF and Souza, FAR and Amorim, CC}, title = {Metagenomic analysis of MWWTP effluent treated via solar photo-Fenton at neutral pH: Effects upon microbial community, priority pathogens, and antibiotic resistance genes.}, journal = {The Science of the total environment}, volume = {801}, number = {}, pages = {149599}, pmid = {34467925}, issn = {1879-1026}, mesh = {Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Hydrogen Peroxide ; Hydrogen-Ion Concentration ; *Microbiota ; Wastewater ; }, abstract = {The effectiveness of advanced technologies on eliminating antibiotic resistant bacteria (ARB) and resistance genes (ARGs) from wastewaters have been recently investigated. Solar photo-Fenton has been proven effective in combating ARB and ARGs from Municipal Wastewater Treatment Plant effluent (MWWTPE). However, most of these studies have relied solely on cultivable methods to assess ARB removal. This is the first study to investigate the effect of solar photo-Fenton upon ARB and ARGs in MWWTPE by high throughput metagenomic analysis (16S rDNA sequencing and Whole Genome Sequencing). Treatment efficiency upon priority pathogens and resistome profile were also investigated. Solar photo-Fenton (30 mg L[-1] of Fe[2+] intermittent additions and 50 mg L[-1] of H2O2) reached 76-86% removal of main phyla present in MWWTPE. An increase in Proteobacteria abundance was observed after solar photo-Fenton and controls in which H2O2 was present as an oxidant (Fenton, H2O2 only, solar/H2O2). Hence, tolerance mechanisms presented by this group should be further assessed. Solar photo-Fenton achieved complete removal of high priority Staphylococcus and Enterococcus, as well as Klebsiella pneumoniae and Pseudomonas aeruginosa. Substantial reduction of intrinsically multi-drug resistant bacteria was detected. Solar photo-Fenton removed nearly 60% of ARGs associated with sulfonamides, macrolides, and tetracyclines, and complete removal of ARGs related to β-lactams and fluoroquinolones. These results indicate the potential of using solar-enhanced photo-Fenton to limit the spread of antimicrobial resistance, especially in developing tropical countries.}, } @article {pmid34467883, year = {2021}, author = {Xu, S and Jiang, Y and Liu, Y and Zhang, J}, title = {Antibiotic-accelerated cyanobacterial growth and aquatic community succession towards the formation of cyanobacterial bloom in eutrophic lake water.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {290}, number = {}, pages = {118057}, doi = {10.1016/j.envpol.2021.118057}, pmid = {34467883}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents ; *Cyanobacteria ; Eutrophication ; Lakes ; *Microbiota ; Water ; }, abstract = {Antibiotics can stimulate the growth of model cyanobacterial species under pure culture conditions, but their influence on cyanobacterial blooms in natural aquatic ecosystems remains unclear. In this study, three commonly detected antibiotics (sulfamethoxazole, tetracycline, and ciprofloxacin) and their ternary mixture were proved to selectively stimulate (p < 0.05) the growth and photosynthetic activity of cyanobacteria in an aquatic microcosm at an environmentally relevant exposure dose of 300 ng/L under both oligotrophic and eutrophic conditions. Under the eutrophic condition, cyanobacteria reached a bloom density of 1.61 × 10[6] cells/mL in 15 days without antibiotics, while the cyanobacteria exposed to tetracycline, sulfamethoxazole, ciprofloxacin, and their ternary mixture exceeded this bloom density within only 10, 8, 7, and 6 days, respectively. Principal coordinate analysis indicated that the antibiotic contaminants accelerated the prokaryotic community succession towards the formation of a cyanobacterial bloom by promoting the dominance of Microcystis, Synechococcus, and Oscillatoria under the eutrophic condition. After 15 days of culture, the antibiotic exposure increased the density of cyanobacteria by 1.38-2.31-fold and 2.28-3.94-fold under eutrophic and oligotrophic conditions, respectively. Antibiotic exposure generated higher stimulatory effects on cyanobacterial growth under the oligotrophic condition, but the antibiotic(s)-treated cyanobacteria did not form a bloom due to nutrient limitation. Redundancy analysis indicated that the three target antibiotics and their ternary mixture affected the prokaryotic community structure in a similar manner, while tetracycline showed some differences compared to sulfamethoxazole, ciprofloxacin, and the ternary antibiotic mixture with regard to the regulation of the eukaryotic community structure. This study demonstrates that antibiotic contaminants accelerate the formation of cyanobacterial blooms in eutrophic lake water and provides insights into the ecological effects of antibiotics on aquatic microbial communities.}, } @article {pmid34465900, year = {2021}, author = {Sulaiman, I and Chung, M and Angel, L and Tsay, JJ and Wu, BG and Yeung, ST and Krolikowski, K and Li, Y and Duerr, R and Schluger, R and Thannickal, SA and Koide, A and Rafeq, S and Barnett, C and Postelnicu, R and Wang, C and Banakis, S and Pérez-Pérez, L and Shen, G and Jour, G and Meyn, P and Carpenito, J and Liu, X and Ji, K and Collazo, D and Labarbiera, A and Amoroso, N and Brosnahan, S and Mukherjee, V and Kaufman, D and Bakker, J and Lubinsky, A and Pradhan, D and Sterman, DH and Weiden, M and Heguy, A and Evans, L and Uyeki, TM and Clemente, JC and de Wit, E and Schmidt, AM and Shopsin, B and Desvignes, L and Wang, C and Li, H and Zhang, B and Forst, CV and Koide, S and Stapleford, KA and Khanna, KM and Ghedin, E and Segal, LN}, title = {Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome.}, journal = {Nature microbiology}, volume = {6}, number = {10}, pages = {1245-1258}, pmid = {34465900}, issn = {2058-5276}, support = {R01 CA159036/CA/NCI NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; R01 DK110014/DK/NIDDK NIH HHS/United States ; R01 AI143861/AI/NIAID NIH HHS/United States ; R01 HL125816/HL/NHLBI NIH HHS/United States ; R21 AI158997/AI/NIAID NIH HHS/United States ; R01 AI140754/AI/NIAID NIH HHS/United States ; R37 CA244775/CA/NCI NIH HHS/United States ; P20 CA252728/CA/NCI NIH HHS/United States ; T32 AI100853/AI/NIAID NIH HHS/United States ; R01 AI137336/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptive Immunity ; Adult ; Aged ; Bacteria/classification/genetics/isolation & purification ; Bacterial Load ; Bronchoalveolar Lavage Fluid/immunology/*microbiology/virology ; COVID-19/immunology/microbiology/mortality/*therapy ; Critical Illness ; Female ; Hospitalization ; Humans ; Immunity, Innate ; Male ; Microbiota ; Middle Aged ; Odds Ratio ; Prognosis ; Prospective Studies ; *Respiration, Artificial ; Respiratory System/immunology/microbiology/virology ; SARS-CoV-2/immunology/*pathogenicity ; Viral Load ; }, abstract = {Respiratory failure is associated with increased mortality in COVID-19 patients. There are no validated lower airway biomarkers to predict clinical outcome. We investigated whether bacterial respiratory infections were associated with poor clinical outcome of COVID-19 in a prospective, observational cohort of 589 critically ill adults, all of whom required mechanical ventilation. For a subset of 142 patients who underwent bronchoscopy, we quantified SARS-CoV-2 viral load, analysed the lower respiratory tract microbiome using metagenomics and metatranscriptomics and profiled the host immune response. Acquisition of a hospital-acquired respiratory pathogen was not associated with fatal outcome. Poor clinical outcome was associated with lower airway enrichment with an oral commensal (Mycoplasma salivarium). Increased SARS-CoV-2 abundance, low anti-SARS-CoV-2 antibody response and a distinct host transcriptome profile of the lower airways were most predictive of mortality. Our data provide evidence that secondary respiratory infections do not drive mortality in COVID-19 and clinical management strategies should prioritize reducing viral replication and maximizing host responses to SARS-CoV-2.}, } @article {pmid34465850, year = {2021}, author = {Guo, W and Zhang, Y and Guo, S and Mei, Z and Liao, H and Dong, H and Wu, K and Ye, H and Zhang, Y and Zhu, Y and Lang, J and Hu, L and Jin, G and Kong, X}, title = {Tumor microbiome contributes to an aggressive phenotype in the basal-like subtype of pancreatic cancer.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {1019}, pmid = {34465850}, issn = {2399-3642}, mesh = {Adenocarcinoma/microbiology/*pathology ; China ; *Microbiota ; Pancreatic Neoplasms/microbiology/*pathology ; Phenotype ; *Tumor Microenvironment ; }, abstract = {Despite the uniform mortality in pancreatic adenocarcinoma (PDAC), clinical disease heterogeneity exists with limited genomic differences. A highly aggressive tumor subtype termed 'basal-like' was identified to show worse outcomes and higher inflammatory responses. Here, we focus on the microbial effect in PDAC progression and present a comprehensive analysis of the tumor microbiome in different PDAC subtypes with resectable tumors using metagenomic sequencing. We found distinctive microbial communities in basal-like tumors and identified an increasing abundance of Acinetobacter, Pseudomonas and Sphingopyxis to be highly associated with carcinogenesis. Functional characterization of microbial genes suggested the potential to induce pathogen-related inflammation. Host-microbiota interplay analysis provided new insights into the tumorigenic role of specific microbiome compositions and demonstrated the influence of host genetics in shaping the tumor microbiome. Taken together, these findings indicated that the tumor microbiome is closely related to PDAC oncogenesis and the induction of inflammation. Additionally, our data revealed the microbial basis of PDAC heterogeneity and proved the predictive value of the microbiome, which will contribute to the intervention and treatment of disease.}, } @article {pmid34465175, year = {2021}, author = {Zhang, Y and Thompson, KN and Branck, T and Yan Yan, and Nguyen, LH and Franzosa, EA and Huttenhower, C}, title = {Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling.}, journal = {Annual review of biomedical data science}, volume = {4}, number = {}, pages = {279-311}, doi = {10.1146/annurev-biodatasci-031121-103035}, pmid = {34465175}, issn = {2574-3414}, support = {K23 DK125838/DK/NIDDK NIH HHS/United States ; R39789/VAC_/Versus Arthritis/United Kingdom ; R24 DK110499/DK/NIDDK NIH HHS/United States ; C10674/A27140/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Host Microbial Interactions ; Humans ; *Metagenomics ; *Microbiota/genetics ; Sequence Analysis, RNA ; Transcriptome ; }, abstract = {Shotgun metatranscriptomics (MTX) is an increasingly practical way to survey microbial community gene function and regulation at scale. This review begins by summarizing the motivations for community transcriptomics and the history of the field. We then explore the principles, best practices, and challenges of contemporary MTX workflows: beginning with laboratory methods for isolation and sequencing of community RNA, followed by informatics methods for quantifying RNA features, and finally statistical methods for detecting differential expression in a community context. In thesecond half of the review, we survey important biological findings from the MTX literature, drawing examples from the human microbiome, other (nonhuman) host-associated microbiomes, and the environment. Across these examples, MTX methods prove invaluable for probing microbe-microbe and host-microbe interactions, the dynamics of energy harvest and chemical cycling, and responses to environmental stresses. We conclude with a review of open challenges in the MTX field, including making assays and analyses more robust, accessible, and adaptable to new technologies; deciphering roles for millions of uncharacterized microbial transcripts; and solving applied problems such as biomarker discovery and development of microbial therapeutics.}, } @article {pmid34465064, year = {2021}, author = {Tong, T and Li, R and Chai, M and Wang, Q and Yang, Y and Xie, S}, title = {Metagenomic analysis of microbial communities continuously exposed to Bisphenol A in mangrove rhizosphere and non-rhizosphere soils.}, journal = {The Science of the total environment}, volume = {792}, number = {}, pages = {148486}, doi = {10.1016/j.scitotenv.2021.148486}, pmid = {34465064}, issn = {1879-1026}, mesh = {Benzhydryl Compounds/toxicity ; Biodegradation, Environmental ; *Microbiota ; Phenols ; *Rhizosphere ; Soil ; Soil Microbiology ; }, abstract = {Bisphenol A (BPA) is widely distributed in littoral zones and may cause adverse impacts on mangrove ecosystem. Biodegradation and phytoremediation are two primary processes for BPA dissipation in mangrove soils. However, the rhizosphere effects of different mangrove species on BPA elimination are still unresolved. In this study, three typical mangrove seedlings, namely Avicennia marina, Bruguiera gymnorrhiza (L.) and Aegiceras corniculatum, were cultivated in soil microcosms for four months and then subjected to 28-day continuous BPA amendment. Un-planted soil microcosms (as control) were also set up. The BPA residual rates and root exudates were monitored, and the metabolic pathways as well as functional microbial communities were also investigated to decipher the rhizosphere effects based on metagenomic analysis. The BPA residual rates in all planted soils were significantly lower than that in un-planted soil on day 7. Both plantation and BPA dosage had significant effects on bacterial abundance. A distinct separation of microbial structure was found between planted and un-planted soil microcosms. Genera Pseudomonas and Lutibacter got enriched with BPA addition and may play important roles in BPA biodegradation. The shifts in bacterial community structure upon BPA addition were different among the microcosms with different mangrove species. Genus Novosphingobium increased in Avicennia marina and Bruguiera gymnorrhiza (L.) rhizosphere soils but decreased in Aegiceras corniculatum rhizosphere soil. Based on KEGG annotation and binning analysis, the proposal of BPA degradation pathways and the quantification of relevant functional genes were achieved. The roles of Pseudomonas and Novosphingobium may differ in lower BPA degradation pathways. The quantity variation patterns of functional genes during the 28-day BPA amendment were different among soil microcosms and bacterial genera.}, } @article {pmid34462812, year = {2022}, author = {Greathouse, KL and Padgett, RN and Petrosino, J and Hastings-Tolsma, M and Faucher, MA}, title = {Exploration of Diet Quality by Obesity Severity in Association with Gestational Weight Gain and Distal Gut Microbiota in Pregnant African American Women: Opportunities for Intervention.}, journal = {Maternal and child health journal}, volume = {26}, number = {4}, pages = {882-894}, pmid = {34462812}, issn = {1573-6628}, support = {P30 ES030285/ES/NIEHS NIH HHS/United States ; }, mesh = {Black or African American ; Body Mass Index ; Diet ; Female ; *Gastrointestinal Microbiome ; *Gestational Weight Gain ; Humans ; Obesity ; Pregnancy ; *Pregnancy Complications ; Prospective Studies ; Vegetables ; }, abstract = {OBJECTIVE: To conduct an exploratory examination of dietary patterns and quality during pregnancy in African-American women who were class I, II, or III obese, and those women with normal pre-pregnancy body mass index (pBMI), as well to identify dietary factors associated with GWG, and changes in the distal gut microbiome. African American women represent the largest group affected by pre-pregnancy obesity, a risk factor for several adverse birth outcomes.

METHODS: This prospective study investigated the association between diet, distal gut microbiome, and GWG among African-American women (n = 21) with obesity (n = 15) compared to women with a normal pre-pregnancy body mass index (pBMI) (n = 6) at two time points, 27-29 and 37-39 weeks gestation. Dietary patterns associated with obesity severity and GWG gain were assessed using Welch's T-test and Mann-Whitney U. The association between the gut microbiome and dietary patterns was assessed using a regression-based kernel association test and the adaptive microbiome-based sum of powered score test.

RESULTS: In early pregnancy, dietary intake of Total Fruits and Greens and Beans was significantly different between pBMI and GWG groups; significance was 0.022 and 0.028 respectively. Women with Class II/III obesity and those with GWG above guidelines had Healthy Eating Index (HEI) scores below 50, meeting less than 75% of dietary guidelines, and did not meet recommendations for fruit and vegetable or fiber intake. We found no significant associations between the microbiome composition and diet (HEI Scores).

CONCLUSIONS FOR PRACTICE: Overall, the results indicate that women with pBMI obesity are not meeting minimum dietary guidelines for nutrient intakes during pregnancy, specifically fruits, vegetables, and fiber, regardless of GWG. Interventions for African-American women with pre-pregnancy obesity, with a focus on increasing consumption of fruits and vegetables, would be beneficial to control GWG and improve birth outcomes.}, } @article {pmid34462336, year = {2022}, author = {Chen, F and Dai, X and Zhou, CC and Li, KX and Zhang, YJ and Lou, XY and Zhu, YM and Sun, YL and Peng, BX and Cui, W}, title = {Integrated analysis of the faecal metagenome and serum metabolome reveals the role of gut microbiome-associated metabolites in the detection of colorectal cancer and adenoma.}, journal = {Gut}, volume = {71}, number = {7}, pages = {1315-1325}, pmid = {34462336}, issn = {1468-3288}, mesh = {*Adenoma/diagnosis ; Biomarkers, Tumor ; *Colorectal Neoplasms/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolome ; Metagenome ; }, abstract = {OBJECTIVE: To profile gut microbiome-associated metabolites in serum and investigate whether these metabolites could distinguish individuals with colorectal cancer (CRC) or adenoma from normal healthy individuals.

DESIGN: Integrated analysis of untargeted serum metabolomics by liquid chromatography-mass spectrometry and metagenome sequencing of paired faecal samples was applied to identify gut microbiome-associated metabolites with significantly altered abundance in patients with CRC and adenoma. The ability of these metabolites to discriminate between CRC and colorectal adenoma was tested by targeted metabolomic analysis. A model based on gut microbiome-associated metabolites was established and evaluated in an independent validation cohort.

RESULTS: In total, 885 serum metabolites were significantly altered in both CRC and adenoma, including eight gut microbiome-associated serum metabolites (GMSM panel) that were reproducibly detected by both targeted and untargeted metabolomics analysis and accurately discriminated CRC and adenoma from normal samples. A GMSM panel-based model to predict CRC and colorectal adenoma yielded an area under the curve (AUC) of 0.98 (95% CI 0.94 to 1.00) in the modelling cohort and an AUC of 0.92 (83.5% sensitivity, 84.9% specificity) in the validation cohort. The GMSM model was significantly superior to the clinical marker carcinoembryonic antigen among samples within the validation cohort (AUC 0.92 vs 0.72) and also showed promising diagnostic accuracy for adenomas (AUC=0.84) and early-stage CRC (AUC=0.93).

CONCLUSION: Gut microbiome reprogramming in patients with CRC is associated with alterations of the serum metabolome, and GMSMs have potential applications for CRC and adenoma detection.}, } @article {pmid34461052, year = {2022}, author = {Yang, J and Wei, H and Zhou, Y and Szeto, CH and Li, C and Lin, Y and Coker, OO and Lau, HCH and Chan, AWH and Sung, JJY and Yu, J}, title = {High-Fat Diet Promotes Colorectal Tumorigenesis Through Modulating Gut Microbiota and Metabolites.}, journal = {Gastroenterology}, volume = {162}, number = {1}, pages = {135-149.e2}, doi = {10.1053/j.gastro.2021.08.041}, pmid = {34461052}, issn = {1528-0012}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Azoxymethane ; Bacteria/drug effects/*metabolism ; Bacterial Translocation ; Cell Proliferation ; Cell Transformation, Neoplastic/metabolism/ultrastructure ; Colon/metabolism/*microbiology/ultrastructure ; Colorectal Neoplasms/chemically induced/metabolism/*microbiology/ultrastructure ; *Diet, High-Fat ; Disease Models, Animal ; Dysbiosis ; Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genes, APC ; Germ-Free Life ; Humans ; Lysophospholipids/metabolism ; Male ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Mice, Transgenic ; Permeability ; Tumor Cells, Cultured ; Mice ; }, abstract = {BACKGROUND AND AIMS: Dietary fat intake is associated with increased risk of colorectal cancer (CRC). We examined the role of high-fat diet (HFD) in driving CRC through modulating gut microbiota and metabolites.

METHODS: HFD or control diet was fed to mice littermates in CRC mouse models of an azoxymethane (AOM) model and Apc[min/+] model, with or without antibiotics cocktail treatment. Germ-free mice for fecal microbiota transplantation were used for validation. Gut microbiota and metabolites were detected using metagenomic sequencing and high-performance liquid chromatography-mass spectrometry, respectively. Gut barrier function was determined using lipopolysaccharides level and transmission electron microscopy.

RESULTS: HFD promoted colorectal tumorigenesis in both AOM-treated mice and Apc[min/+] mice compared with control diet-fed mice. Gut microbiota depletion using antibiotics attenuated colon tumor formation in HFD-fed mice. A significant shift of gut microbiota composition with increased pathogenic bacteria Alistipessp.Marseille-P5997 and Alistipessp.5CPEGH6, and depleted probiotic Parabacteroides distasonis, along with impaired gut barrier function was exhibited in HFD-fed mice. Moreover, HFD-modulated gut microbiota promotes colorectal tumorigenesis in AOM-treated germ-free mice, indicating gut microbiota was essential in HFD-associated colorectal tumorigenesis. Gut metabolites alteration, including elevated lysophosphatidic acid, which was confirmed to promote CRC cell proliferation and impair cell junction, was also observed in HFD-fed mice. Moreover, transfer of stools from HFD-fed mice to germ-free mice without interference increased colonic cell proliferation, impaired gut barrier function, and induced oncogenic genes expression.

CONCLUSIONS: HFD drives colorectal tumorigenesis through inducing gut microbial dysbiosis, metabolomic dysregulation with elevated lysophosphatidic acid, and gut barrier dysfunction in mice.}, } @article {pmid34458157, year = {2021}, author = {Chen, J and Li, H and Hird, SM and Chen, MH and Xu, W and Maas, K and Cong, X}, title = {Sex Differences in Gut Microbial Development of Preterm Infant Twins in Early Life: A Longitudinal Analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {671074}, pmid = {34458157}, issn = {2235-2988}, support = {K23 NR014674/NR/NINR NIH HHS/United States ; R01 NR016928/NR/NINR NIH HHS/United States ; }, mesh = {Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Longitudinal Studies ; Male ; Phylogeny ; *Sex Characteristics ; *Twins ; }, abstract = {Infant gut microbiota plays a vital role in immune response, mediates neurobehavioral development and health maintenance. Studies of twins' gut microbiota found that gut microbiota composition and diversity tend to be mature and stable with increasing postnatal age (PNA). Preterm infant gut microbiome shifts dramatically when they were staying in the neonatal intensive care unit (NICU). Compositions and shifting characteristics of gut microbiota among neonatal preterm twins and triplets during their early life are still unknown, which impedes a better understanding of the mechanism underpinning neurobehavioral development and precise intervention/health of preterm neonates. This longitudinal cohort study used a twins/triplets design to investigate the interaction of genetic (e.g., male vs. female) and environmental factors influencing the development of the gut microbiome in early life. We included 39 preterm infants, 12 were Female twins/triplets (Female T/T) including 3 twins pairs and 2 triplets, 12 were male twins (Male T) including 6 twins pairs, and 15 were mixed-sex twins/triplets (Mix T/T) including 6 twins pairs and 1 triplet (8 females and 7 males) during the first four weeks of NICU stay. Weekly gut microbiota patterns between females and males were compared by linear discriminant analysis (LDA) effect size (LEfSe). Metagenomics function of gut microbiota was predicted by using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Weekly function (KEGG pathways) differences between females and males were detected by using Statistical Analysis of Metagenomic Profiles (STAMP). Results found that female pairs and male pairs were significantly different in gut microbiome diversity, compositions, and predicted metabolic profiles, importantly, females and males were also significantly dissimilar within their co-twin/triplet pairs of the mixed-sex group, infants of co-twins/triplets shared more similar features than un-related infants from different twins' pair. Future research developing personalized interventions for vulnerable high-risk infants should consider sex, and the interaction of sex and environmental factors.}, } @article {pmid34455974, year = {2022}, author = {Borah, S and Sarkar, P and Sharma, HK}, title = {Zederone Improves the Fecal Microbial Profile in Dementia Induced Rat Model: A First Report.}, journal = {CNS & neurological disorders drug targets}, volume = {21}, number = {4}, pages = {335-342}, doi = {10.2174/1871527320666210827114227}, pmid = {34455974}, issn = {1996-3181}, support = {09/857 (0010)/2018-EMR-I//Council of Scientific and Industrial Research (CSIR) , India/ ; }, mesh = {Animals ; Dementia/*drug therapy ; Dysbiosis/drug therapy ; Female ; Gastrointestinal Microbiome/*drug effects ; Plaque, Amyloid/drug therapy ; Rats ; Rats, Wistar ; Sesquiterpenes/*pharmacology ; }, abstract = {BACKGROUND: Dementia correlates with Alzheimer's disease, Parkinson's disease, frontotemporal and cerebrovascular diseases. There are supporting shreds of evidence on the pharmacological activity of curcuma caesia (Zingiberaceae family) for its antioxidant, antidepressant, analgesic, anticonvulsant, and anti-acetylcholinesterase effect.

OBJECTIVE: This study aims to analyze the fecal microbial profile in Zederone treated demented rat model.

METHODS: In our study, isolation and characterization of Zederone were carried out from curcuma caesia rhizomes, followed by estimation of its memory-enhancing effect on Aluminium-induced demented rat, which was evaluated by behavioural study on radial 8 arm maze. Moreover the detection of amyloid plaque formation was carried out using fluorescent microscopy of the congo red-stained rat brain tissues of the cerebral neocortex region. This study included eighteen female Wistar Albino rats that were divided into three groups that consisted of six rats in each group. The study of fecal microbial profile by metagenomic DNA extraction followed by next-generation sequencing was carried out to establish the correlation between gut microbes and amyloid plaques in dementia.

RESULTS: Zederone could be characterized as pale yellow colored, needle-shaped crystals with 96.57% purity. This compound at 10 mg/kg body weight showed cognition improving capacity (p ≤ 0.0001) with a reduction of accumulated amyloid plaques that were detected in the demented group in fluorescence microscope and fecal microbiome study divulged an increased shift towards Lactobacillus genera in the treated group from Bacteroides in the demented group.

CONCLUSION: This sesquiterpenoid compound would assist in the modulation of gut bacterial dysbiosis and act as a better therapeutic drug for dementia and other neurological disorders.}, } @article {pmid34455391, year = {2021}, author = {Shah, S and Locca, A and Dorsett, Y and Cantoni, C and Ghezzi, L and Lin, Q and Bokoliya, S and Panier, H and Suther, C and Gormley, M and Liu, Y and Evans, E and Mikesell, R and Obert, K and Salter, A and Cross, AH and Tarr, PI and Lovett-Racke, A and Piccio, L and Zhou, Y}, title = {Alterations of the gut mycobiome in patients with MS.}, journal = {EBioMedicine}, volume = {71}, number = {}, pages = {103557}, pmid = {34455391}, issn = {2352-3964}, support = {P30 DK052574/DK/NIDDK NIH HHS/United States ; R01 NS102633/NS/NINDS NIH HHS/United States ; UL1 TR000448/TR/NCATS NIH HHS/United States ; UL1 TR002345/TR/NCATS NIH HHS/United States ; }, mesh = {Biomarkers ; Body Mass Index ; Case-Control Studies ; Computational Biology/methods ; Diet ; Disease Susceptibility ; *Dysbiosis/immunology ; Feces/microbiology ; *Gastrointestinal Microbiome/immunology ; *Host Microbial Interactions ; Humans ; Metagenome ; Metagenomics/methods ; Multiple Sclerosis/blood/*etiology/metabolism ; Mycobiome/immunology ; }, abstract = {BACKGROUND: The mycobiome is the fungal component of the gut microbiome and is implicated in several autoimmune diseases. However, its role in MS has not been studied.

METHODS: In this case-control observational study, we performed ITS sequencing and characterised the gut mycobiome in people with MS (pwMS) and healthy controls at baseline and after six months.

FINDINGS: The mycobiome had significantly higher alpha diversity and inter-subject variation in pwMS than controls. Saccharomyces and Aspergillus were over-represented in pwMS. Saccharomyces was positively correlated with circulating basophils and negatively correlated with regulatory B cells, while Aspergillus was positively correlated with activated CD16[+] dendritic cells in pwMS. Different mycobiome profiles, defined as mycotypes, were associated with different bacterial microbiome and immune cell subsets in the blood. Initial treatment with dimethyl fumarate, a common immunomodulatory therapy which also has fungicidal activity, did not cause uniform gut mycobiome changes across all pwMS.

INTERPRETATION: There is an alteration of the gut mycobiome in pwMS, compared to healthy controls. Further study is required to assess any causal association of the mycobiome with MS and its direct or indirect interactions with bacteria and autoimmunity.

FUNDING: This work was supported by the Washington University in St. Louis Institute of Clinical and Translational Sciences, funded, in part, by Grant Number # UL1 TR000448 from the National Institutes of Health, National Center for Advancing Translational Sciences, Clinical and Translational Sciences Award (Zhou Y, Piccio, L, Lovett-Racke A and Tarr PI); R01 NS102633-04 (Zhou Y, Piccio L); the Leon and Harriet Felman Fund for Human MS Research (Piccio L and Cross AH). Cantoni C. was supported by the National MS Society Career Transition Fellowship (TA-1805-31003) and by donations from Whitelaw Terry, Jr. / Valerie Terry Fund. Ghezzi L. was supported by the Italian Multiple Sclerosis Society research fellowship (FISM 2018/B/1) and the National Multiple Sclerosis Society Post-Doctoral Fellowship (FG- 1907-34474). Anne Cross was supported by The Manny & Rosalyn Rosenthal-Dr. John L. Trotter MS Center Chair in Neuroimmunology of the Barnes-Jewish Hospital Foundation. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.}, } @article {pmid34454634, year = {2021}, author = {Gupta, CL and Blum, SE and Kattusamy, K and Daniel, T and Druyan, S and Shapira, R and Krifucks, O and Zhu, YG and Zhou, XY and Su, JQ and Cytryn, E}, title = {Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {178}, pmid = {34454634}, issn = {2049-2618}, mesh = {Animals ; Anti-Bacterial Agents/*therapeutic use ; *Chickens ; Cloaca/microbiology ; *Drug Resistance, Bacterial/genetics ; Escherichia coli ; Longitudinal Studies ; *Microbiota ; Staphylococcus aureus ; }, abstract = {BACKGROUND: Therapeutic and growth-promoting antibiotics are frequently used in broiler production. Indirect evidence indicates that these practices are linked to the proliferation of antimicrobial resistance (AMR), the spread of antibiotic-resistant bacteria from food animals to humans, and the environment, but there is a lack of comprehensive experimental data supporting this. We investigated the effects of growth promotor (bacitracin) and therapeutic (enrofloxacin) antibiotic administration on AMR in broilers for the duration of a production cycle, using a holistic approach that integrated both culture-dependent and culture-independent methods. We specifically focused on pathogen-harboring families (Enterobacteriaceae, Enterococcaceae, and Staphylococcaceae).

RESULTS: Antibiotic-resistant bacteria and antibiotic resistance genes were ubiquitous in chicken cloaca and litter regardless of antibiotic administration. Environment (cloaca vs. litter) and growth stage were the primary drivers of variation in the microbiomes and resistomes, with increased bacterial diversity and a general decrease in abundance of the pathogen-harboring families with age. Bacitracin-fed groups had higher levels of bacitracin resistance genes and of vancomycin-resistant Enterococcaceae (total Enterococcaceae counts were not higher). Although metagenomic analyses classified 28-76% of the Enterococcaceae as the commensal human pathogens E. faecalis and E. faecium, culture-based analysis suggested that approximately 98% of the vancomycin-resistant Enterococcaceae were avian and not human-associated, suggesting differences in the taxonomic profiles of the resistant and non-resistant strains. Enrofloxacin treatments had varying effects, but generally facilitated increased relative abundance of multidrug-resistant Enterobacteriaceae strains, which were primarily E. coli. Metagenomic approaches revealed a diverse array of Staphylococcus spp., but the opportunistic pathogen S. aureus and methicillin resistance genes were not detected in culture-based or metagenomic analyses. Camphylobacteriaceae were significantly more abundant in the cloacal samples, especially in enrofloxacin-treated chickens, where a metagenome-assembled C. jejuni genome harboring fluoroquinolone and β-lactam resistance genes was identified.

CONCLUSIONS: Within a "farm-to-fork, one health" perspective, considering the evidence that bacitracin and enrofloxacin used in poultry production can select for resistance, we recommend their use be regulated. Furthermore, we suggest routine surveillance of ESBL E. coli, vancomycin-resistant E. faecalis and E. faecium, and fluoroquinolone-resistant C. jejuni strains considering their pathogenic nature and capacity to disseminate AMR to the environment. Video Abstract.}, } @article {pmid34454169, year = {2022}, author = {Qian, M and Liu, J and Zhao, D and Cai, P and Pan, C and Jia, W and Gao, Y and Zhang, Y and Zhang, N and Zhang, Y and Zhang, Q and Wu, D and Shan, C and Zhang, M and Schnabl, B and Yang, S and Shen, X and Wang, L}, title = {Aryl Hydrocarbon Receptor Deficiency in Intestinal Epithelial Cells Aggravates Alcohol-Related Liver Disease.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {13}, number = {1}, pages = {233-256}, pmid = {34454169}, issn = {2352-345X}, support = {P30 DK120515/DK/NIDDK NIH HHS/United States ; }, mesh = {*Alcoholism ; Animals ; Basic Helix-Loop-Helix Transcription Factors ; Epithelial Cells/metabolism ; *Gastrointestinal Microbiome ; Humans ; *Liver Diseases ; Mice ; Receptors, Aryl Hydrocarbon/agonists/genetics/metabolism ; }, abstract = {BACKGROUND & AIMS: The ligand-activated transcription factor, aryl hydrocarbon receptor (AHR) can sense xenobiotics, dietary, microbial, and metabolic cues. Roles of Ahr in intestinal epithelial cells (IECs) have been much less elucidated compared with those in intestinal innate immune cells. Here, we explored whether the IEC intrinsic Ahr could modulate the development of alcohol-related liver disease (ALD) via the gut-liver axis.

METHODS: Mice with IEC specific Ahr deficiency (Ahr[ΔIEC]) were generated and fed with a control or ethanol diet. Alterations of intestinal microbiota and metabolites were investigated by 16S ribosomal RNA sequencing, metagenomics, and untargeted metabolomics. AHR agonists were used to evaluate the therapeutic potentials of intestinal Ahr activation for ALD treatment.

RESULTS: Ahr[ΔIEC] mice showed more severe liver injury after ethanol feeding than control mice. Ahr deficiency in IECs altered the intestinal metabolite composition, creating an environment that promoted the overgrowth of Helicobacter hepaticus and Helicobacter ganmani in the gut, enhancing their translocation to mesenteric lymph nodes and liver. Among the altered metabolites, isobutyric acid was increased in the cecum of ethanol-fed Ahr[ΔIEC] mice relative to control mice. Furthermore, both H.hepaticus and isobutyric acid administration aggravated ethanol-induced liver injury in vivo and in vitro. Supplementation with AHR agonists, 6-formylindolo[3,2-b]carbazole and indole-3-carbinol, protected mice from ALD development by specifically activating intestinal Ahr without affecting liver Ahr function. Alcoholic patients showed lower intestinal AHR expression and higher H.hepaticus levels compared with healthy individuals.

CONCLUSIONS: Our results indicate that targeted restoration of IEC intrinsic Ahr function may present as a novel approach for ALD treatment.}, } @article {pmid34452845, year = {2021}, author = {Dinakis, E and Nakai, M and Gill, PA and Yiallourou, S and Sata, Y and Muir, J and Carrington, M and Head, GA and Kaye, DM and Marques, FZ}, title = {The Gut Microbiota and Their Metabolites in Human Arterial Stiffness.}, journal = {Heart, lung & circulation}, volume = {30}, number = {11}, pages = {1716-1725}, doi = {10.1016/j.hlc.2021.07.022}, pmid = {34452845}, issn = {1444-2892}, mesh = {Animals ; Blood Pressure Monitoring, Ambulatory ; Fatty Acids, Volatile ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; RNA, Ribosomal, 16S ; *Vascular Stiffness ; }, abstract = {AIM: Gut microbiota-derived metabolites, such as short-chain fatty acids (SCFAs) have vasodilator properties in animal and human ex vivo arteries. However, the role of the gut microbiota and SCFAs in arterial stiffness in humans is still unclear. Here we aimed to determine associations between the gut microbiome, SCFA and their G-protein coupled sensing receptors (GPCRs) in relation to human arterial stiffness.

METHODS: Ambulatory arterial stiffness index (AASI) was determined from ambulatory blood pressure (BP) monitoring in 69 participants from regional and metropolitan regions in Australia (55.1% women; mean, 59.8± SD, 7.26 years of age). The gut microbiome was determined by 16S rRNA sequencing, SCFA levels by gas chromatography, and GPCR expression in circulating immune cells by real-time PCR.

RESULTS: There was no association between metrics of bacterial α and β diversity and AASI or AASI quartiles in men and women. We identified two main bacteria taxa that were associated with AASI quartiles: Lactobacillus spp. was only present in the lowest quartile, while Clostridium spp. was present in all quartiles but the lowest. AASI was positively associated with higher levels of plasma, but not faecal, butyrate. Finally, we identified that the expression of GPR43 (FFAR2) and GPR41 (FFAR3) in circulating immune cells were negatively associated with AASI.

CONCLUSIONS: Our results suggest that arterial stiffness is associated with lower levels of the metabolite-sensing receptors GPR41/GPR43 in humans, blunting its response to BP-lowering metabolites such as butyrate. The role of Lactobacillus spp. and Clostridium spp., as well as butyrate-sensing receptors GPR41/GPR43, in human arterial stiffness needs to be determined.}, } @article {pmid34451490, year = {2021}, author = {Shen-Gunther, J and Xia, Q and Cai, H and Wang, Y}, title = {HPV DeepSeq: An Ultra-Fast Method of NGS Data Analysis and Visualization Using Automated Workflows and a Customized Papillomavirus Database in CLC Genomics Workbench.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {8}, pages = {}, pmid = {34451490}, issn = {2076-0817}, support = {CDMRPL-16-0-DM160469//Congressionally Directed Medical Research Programs/ ; }, abstract = {Next-generation sequencing (NGS) has actualized the human papillomavirus (HPV) virome profiling for in-depth investigation of viral evolution and pathogenesis. However, viral computational analysis remains a bottleneck due to semantic discrepancies between computational tools and curated reference genomes. To address this, we developed and tested automated workflows for HPV taxonomic profiling and visualization using a customized papillomavirus database in the CLC Microbial Genomics Module. HPV genomes from Papilloma Virus Episteme were customized and incorporated into CLC "ready-to-use" workflows for stepwise data processing to include: (1) Taxonomic Analysis, (2) Estimate Alpha/Beta Diversities, and (3) Map Reads to Reference. Low-grade (n = 95) and high-grade (n = 60) Pap smears were tested with ensuing collective runtimes: Taxonomic Analysis (36 min); Alpha/Beta Diversities (5 s); Map Reads (45 min). Tabular output conversion to visualizations entailed 1-2 keystrokes. Biodiversity analysis between low- (LSIL) and high-grade squamous intraepithelial lesions (HSIL) revealed loss of species richness and gain of dominance by HPV-16 in HSIL. Integrating clinically relevant, taxonomized HPV reference genomes within automated workflows proved to be an ultra-fast method of virome profiling. The entire process named "HPV DeepSeq" provides a simple, accurate and practical means of NGS data analysis for a broad range of applications in viral research.}, } @article {pmid34446773, year = {2021}, author = {Kobiyama, A and Rashid, J and Reza, MS and Ikeda, Y and Yamada, Y and Kudo, T and Mizusawa, N and Yanagisawa, S and Ikeda, D and Sato, S and Ogata, T and Ikeo, K and Kaga, S and Watanabe, S and Naiki, K and Kaga, Y and Segawa, S and Tada, Y and Musashi, T and Mineta, K and Gojobori, T and Watabe, S}, title = {Seasonal and annual changes in the microbial communities of Ofunato Bay, Japan, based on metagenomics.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {17277}, pmid = {34446773}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics ; Bays/*microbiology ; Cyanobacteria/classification/genetics ; Ecosystem ; Geography ; Japan ; Metagenomics/*methods ; Microbiota/*genetics ; Oxygen/metabolism ; Population Dynamics ; Salinity ; *Seasons ; Seawater/chemistry/*microbiology ; Temperature ; Whole Genome Sequencing/methods ; }, abstract = {Five years of datasets from 2015 to 2019 of whole genome shotgun sequencing for cells trapped on 0.2-µm filters of seawater collected monthly from Ofunato Bay, an enclosed bay in Japan, were analysed, which included the 2015 data that we had reported previously. Nucleotide sequences were determined for extracted DNA from three locations for both the upper (1 m) and deeper (8 or 10 m) depths. The biotic communities analysed at the domain level comprised bacteria, eukaryotes, archaea and viruses. The relative abundance of bacteria was over 60% in most months for the five years. The relative abundance of the SAR86 cluster was highest in the bacterial group, followed by Candidatus Pelagibacter and Planktomarina. The relative abundance of Ca. Pelagibacter showed no relationship with environmental factors, and those of SAR86 and Planktomarina showed positive correlations with salinity and dissolved oxygen, respectively. The bacterial community diversity showed seasonal changes, with high diversity around September and low diversity around January for all five years. Nonmetric multidimensional scaling analysis also revealed that the bacterial communities in the bay were grouped in a season-dependent manner and linked with environmental variables such as seawater temperature, salinity and dissolved oxygen.}, } @article {pmid34446072, year = {2021}, author = {Kim, CY and Lee, M and Yang, S and Kim, K and Yong, D and Kim, HR and Lee, I}, title = {Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {134}, pmid = {34446072}, issn = {1756-994X}, mesh = {Computational Biology/methods ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genetic Variation ; Host Microbial Interactions ; Humans ; India ; Japan ; Korea ; *Metagenome ; *Metagenomics/methods ; Phylogeny ; }, abstract = {BACKGROUND: Metagenome sampling bias for geographical location and lifestyle is partially responsible for the incomplete catalog of reference genomes of gut microbial species. Thus, genome assembly from currently under-represented populations may effectively expand the reference gut microbiome and improve taxonomic and functional profiling.

METHODS: We assembled genomes using public whole-metagenomic shotgun sequencing (WMS) data for 110 and 645 fecal samples from India and Japan, respectively. In addition, we assembled genomes from newly generated WMS data for 90 fecal samples collected from Korea. Expecting genome assembly for low-abundance species may require a much deeper sequencing than that usually employed, so we performed ultra-deep WMS (> 30 Gbp or > 100 million read pairs) for the fecal samples from Korea. We consequently assembled 29,082 prokaryotic genomes from 845 fecal metagenomes for the three under-represented Asian countries and combined them with the Unified Human Gastrointestinal Genome (UHGG) to generate an expanded catalog, the Human Reference Gut Microbiome (HRGM).

RESULTS: HRGM contains 232,098 non-redundant genomes for 5414 representative prokaryotic species including 780 that are novel, > 103 million unique proteins, and > 274 million single-nucleotide variants. This is an over 10% increase from the UHGG. The new 780 species were enriched for the Bacteroidaceae family, including species associated with high-fiber and seaweed-rich diets. Single-nucleotide variant density was positively associated with the speciation rate of gut commensals. We found that ultra-deep sequencing facilitated the assembly of genomes for low-abundance taxa, and deep sequencing (e.g., > 20 million read pairs) may be needed for the profiling of low-abundance taxa. Importantly, the HRGM significantly improved the taxonomic and functional classification of sequencing reads from fecal samples. Finally, analysis of human self-antigen homologs on the HRGM species genomes suggested that bacterial taxa with high cross-reactivity potential may contribute more to the pathogenesis of gut microbiome-associated diseases than those with low cross-reactivity potential by promoting inflammatory condition.

CONCLUSIONS: By including gut metagenomes from previously under-represented Asian countries, Korea, India, and Japan, we developed a substantially expanded microbiome catalog, HRGM. Information of the microbial genomes and coding genes is publicly available (www.mbiomenet.org/HRGM/). HRGM will facilitate the identification and functional analysis of disease-associated gut microbiota.}, } @article {pmid34444993, year = {2021}, author = {Tso, L and Bonham, KS and Fishbein, A and Rowland, S and Klepac-Ceraj, V}, title = {Targeted High-Resolution Taxonomic Identification of Bifidobacterium longum subsp. infantis Using Human Milk Oligosaccharide Metabolizing Genes.}, journal = {Nutrients}, volume = {13}, number = {8}, pages = {}, pmid = {34444993}, issn = {2072-6643}, support = {UG3 OD023313/GF/NIH HHS/United States ; }, mesh = {Bacterial Proteins/classification/genetics ; *Bifidobacterium longum/genetics/metabolism ; Breast Feeding ; Cohort Studies ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Genes, Bacterial/genetics ; Humans ; Infant ; Infant, Newborn ; Milk, Human/*chemistry ; Oligosaccharides/*metabolism ; }, abstract = {Bifidobacterium longum subsp. infantis (B. infantis) is one of a few microorganisms capable of metabolizing human breast milk and is a pioneer colonizer in the guts of breastfed infants. One current challenge is differentiating B. infantis from its close relatives, B. longum and B. suis. All three organisms are classified in the same species group but only B. infantis can metabolize human milk oligosaccharides (HMOs). We compared HMO-metabolizing genes across different Bifidobacterium genomes and developed B. infantis-specific primers to determine if the genes alone or the primers can be used to quickly characterize B. infantis. We showed that B. infantis is uniquely identified by the presence of five HMO-metabolizing gene clusters, tested for its prevalence in infant gut metagenomes, and validated the results using the B. infantis-specific primers. We observed that only 15 of 203 (7.4%) children under 2 years old from a cohort of US children harbored B. infantis. These results highlight the importance of developing and improving approaches to identify B. infantis. A more accurate characterization may provide insights into regional differences of B. infantis prevalence in infant gut microbiota.}, } @article {pmid34444848, year = {2021}, author = {Goris, T and Cuadrat, RRC and Braune, A}, title = {Flavonoid-Modifying Capabilities of the Human Gut Microbiome-An In Silico Study.}, journal = {Nutrients}, volume = {13}, number = {8}, pages = {}, pmid = {34444848}, issn = {2072-6643}, support = {814650//H2020 Society/ ; }, mesh = {Bacterial Proteins/*metabolism ; Computer Simulation ; Equol/metabolism ; Flavonoids/*metabolism ; Gastrointestinal Microbiome/*physiology ; Genome, Bacterial ; Humans ; Isoflavones/metabolism ; Metagenome ; Nutritional Physiological Phenomena/*physiology ; Peptide Hydrolases/metabolism ; Proteolysis ; }, abstract = {Flavonoids are a major group of dietary plant polyphenols and have a positive health impact, but their modification and degradation in the human gut is still widely unknown. Due to the rise of metagenome data of the human gut microbiome and the assembly of hundreds of thousands of bacterial metagenome-assembled genomes (MAGs), large-scale screening for potential flavonoid-modifying enzymes of human gut bacteria is now feasible. With sequences of characterized flavonoid-transforming enzymes as queries, the Unified Human Gastrointestinal Protein catalog was analyzed and genes encoding putative flavonoid-modifying enzymes were quantified. The results revealed that flavonoid-modifying enzymes are often encoded in gut bacteria hitherto not considered to modify flavonoids. The enzymes for the physiologically important daidzein-to-equol conversion, well studied in Slackiaisoflavoniconvertens, were encoded only to a minor extent in Slackia MAGs, but were more abundant in Adlercreutzia equolifaciens and an uncharacterized Eggerthellaceae species. In addition, enzymes with a sequence identity of about 35% were encoded in highly abundant MAGs of uncultivated Collinsella species, which suggests a hitherto uncharacterized daidzein-to-equol potential in these bacteria. Of all potential flavonoid modification steps, O-deglycosylation (including derhamnosylation) was by far the most abundant in this analysis. In contrast, enzymes putatively involved in C-deglycosylation were detected less often in human gut bacteria and mainly found in Agathobacter faecis (formerly Roseburia faecis). Homologs to phloretin hydrolase, flavanonol/flavanone-cleaving reductase and flavone reductase were of intermediate abundance (several hundred MAGs) and mainly prevalent in Flavonifractor plautii. This first comprehensive insight into the black box of flavonoid modification in the human gut highlights many hitherto overlooked and uncultured bacterial genera and species as potential key organisms in flavonoid modification. This could lead to a significant contribution to future biochemical-microbiological investigations on gut bacterial flavonoid transformation. In addition, our results are important for individual nutritional recommendations and for biotechnological applications that rely on novel enzymes catalyzing potentially useful flavonoid modification reactions.}, } @article {pmid34444797, year = {2021}, author = {Barber, C and Mego, M and Sabater, C and Vallejo, F and Bendezu, RA and Masihy, M and Guarner, F and Espín, JC and Margolles, A and Azpiroz, F}, title = {Differential Effects of Western and Mediterranean-Type Diets on Gut Microbiota: A Metagenomics and Metabolomics Approach.}, journal = {Nutrients}, volume = {13}, number = {8}, pages = {}, pmid = {34444797}, issn = {2072-6643}, support = {SAF 2016-76648-R//Ministerio de Economía y Competitividad/ ; PID2019-103914RB-I00//Ministerio de Ciencia e Innovacion/ ; AGL2016-78311-R//Ministerio de Ciencia e Innovación/ ; FJC2019-042125-I//Ministerio de Ciencia e Innovación/ ; }, mesh = {Adolescent ; Adult ; Biodiversity ; Colon ; Cross-Over Studies ; *Diet, Mediterranean ; *Diet, Western ; Feces/microbiology ; Flatulence ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolomics ; *Metagenomics ; Surveys and Questionnaires ; Young Adult ; }, abstract = {Our aim was to determine the effect of diet on gut microbiota, digestive function and sensations, using an integrated clinical, metagenomics and metabolomics approach. We conducted a cross-over, randomised study on the effects of a Western-type diet versus a fibre-enriched Mediterranean diet. In 20 healthy men, each diet was administered for 2 weeks preceded by a 2-week washout diet. The following outcomes were recorded: (a) number of anal gas evacuations; (b) digestive sensations; (c) volume of gas evacuated after a probe meal; (d) colonic content by magnetic resonance imaging; (e) gut microbiota taxonomy and metabolic functions by shotgun sequencing of faecal samples; (f) urinary metabolites using untargeted metabolomics. As compared to a Western diet, the Mediterranean diet was associated with (i) higher number of anal gas evacuations, (ii) sensation of flatulence and borborygmi, (iii) larger volume of gas after the meal and (iv) larger colonic content. Despite the relatively little difference in microbiota composition between both diets, microbial metabolism differed substantially, as shown by urinary metabolite profiles and the abundance of microbial metabolic pathways. The effects of the diet were less evident in individuals with robust microbiotas (higher beta-diversity). To conclude, healthy individuals tolerate dietary changes with minor microbial modifications at the composition level but with remarkable variation in microbial metabolism.}, } @article {pmid34444679, year = {2021}, author = {Juárez-Fernández, M and Román-Sagüillo, S and Porras, D and García-Mediavilla, MV and Linares, P and Ballesteros-Pomar, MD and Urioste-Fondo, A and Álvarez-Cuenllas, B and González-Gallego, J and Sánchez-Campos, S and Jorquera, F and Nistal, E}, title = {Long-Term Effects of Bariatric Surgery on Gut Microbiota Composition and Faecal Metabolome Related to Obesity Remission.}, journal = {Nutrients}, volume = {13}, number = {8}, pages = {}, pmid = {34444679}, issn = {2072-6643}, support = {BFU2017-87960-R//Ministerio de Economía y Competitividad/ ; GRS1888/A/18//Junta de Castilla y León/ ; }, mesh = {*Bariatric Surgery ; DNA/analysis ; Fatty Acids, Volatile/analysis ; Feces/*chemistry/microbiology ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; *Metabolome ; Metagenomics ; Obesity, Morbid/*microbiology/*surgery ; Weight Loss ; }, abstract = {Obesity is one of the main worldwide public health concerns whose clinical management demands new therapeutic approaches. Bariatric surgery is the most efficient treatment when other therapies have previously failed. Due to the role of gut microbiota in obesity development, the knowledge of the link between bariatric surgery and gut microbiota could elucidate new mechanistic approaches. This study aims to evaluate the long-term effects of bariatric surgery in the faecal metagenome and metabolome of patients with severe obesity. Faecal and blood samples were collected before and four years after the intervention from patients with severe obesity. Biochemical, metagenomic and metabolomic analyses were performed and faecal short-chain fatty acids were measured. Bariatric surgery improved the obesity-related status of patients and significantly reshaped gut microbiota composition. Moreover, this procedure was associated with a specific metabolome profile characterized by a reduction in energetic and amino acid metabolism. Acetate, butyrate and propionate showed a significant reduction with bariatric surgery. Finally, correlation analysis suggested the existence of a long-term compositional and functional gut microbiota profile associated with the intervention. In conclusion, bariatric surgery triggered long-lasting effects on gut microbiota composition and faecal metabolome that could be associated with the remission of obesity.}, } @article {pmid34442632, year = {2021}, author = {Thompson, AR and Roth-Monzón, AJ and Aanderud, ZT and Adams, BJ}, title = {Phagotrophic Protists and Their Associates: Evidence for Preferential Grazing in an Abiotically Driven Soil Ecosystem.}, journal = {Microorganisms}, volume = {9}, number = {8}, pages = {}, pmid = {34442632}, issn = {2076-2607}, support = {#OPP-1637708//National Science Foundation/ ; }, abstract = {The complex relationship between ecosystem function and soil food web structure is governed by species interactions, many of which remain unmapped. Phagotrophic protists structure soil food webs by grazing the microbiome, yet their involvement in intraguild competition, susceptibility to predator diversity, and grazing preferences are only vaguely known. These species-dependent interactions are contextualized by adjacent biotic and abiotic processes, and thus obfuscated by typically high soil biodiversity. Such questions may be investigated in the McMurdo Dry Valleys (MDV) of Antarctica because the physical environment strongly filters biodiversity and simplifies the influence of abiotic factors. To detect the potential interactions in the MDV, we analyzed the co-occurrence among shotgun metagenome sequences for associations suggestive of intraguild competition, predation, and preferential grazing. In order to control for confounding abiotic drivers, we tested co-occurrence patterns against various climatic and edaphic factors. Non-random co-occurrence between phagotrophic protists and other soil fauna was biotically driven, but we found no support for competition or predation. However, protists predominately associated with Proteobacteria and avoided Actinobacteria, suggesting grazing preferences were modulated by bacterial cell-wall structure and growth rate. Our study provides a critical starting-point for mapping protist interactions in native soils and highlights key trends for future targeted molecular and culture-based approaches.}, } @article {pmid34440453, year = {2021}, author = {Ruan, X and Wang, Z and Su, Y and Wang, T}, title = {Population Genomics Reveals Gene Flow and Adaptive Signature in Invasive Weed Mikania micrantha.}, journal = {Genes}, volume = {12}, number = {8}, pages = {}, pmid = {34440453}, issn = {2073-4425}, mesh = {Adaptation, Physiological/*genetics ; China ; Gene Flow/*genetics ; Introduced Species ; Metagenomics ; Mikania/*genetics/growth & development ; Plant Weeds/*genetics/growth & development ; }, abstract = {A long-standing and unresolved issue in invasion biology concerns the rapid adaptation of invaders to nonindigenous environments. Mikania micrantha is a notorious invasive weed that causes substantial economic losses and negative ecological consequences in southern China. However, the contributions of gene flow, environmental variables, and functional genes, all generally recognized as important factors driving invasive success, to its successful invasion of southern China are not fully understood. Here, we utilized a genotyping-by-sequencing approach to sequence 306 M. micrantha individuals from 21 invasive populations. Based on the obtained genome-wide single nucleotide polymorphism (SNP) data, we observed that all the populations possessed similar high levels of genetic diversity that were not constrained by longitude and latitude. Mikania micrantha was introduced multiple times and subsequently experienced rapid-range expansion with recurrent high gene flow. Using FST outliers, a latent factor mixed model, and the Bayesian method, we identified 38 outlier SNPs associated with environmental variables. The analysis of these outlier SNPs revealed that soil composition, temperature, precipitation, and ecological variables were important determinants affecting the invasive adaptation of M. micrantha. Candidate genes with outlier signatures were related to abiotic stress response. Gene family clustering analysis revealed 683 gene families unique to M. micrantha which may have significant implications for the growth, metabolism, and defense responses of M. micrantha. Forty-one genes showing significant positive selection signatures were identified. These genes mainly function in binding, DNA replication and repair, signature transduction, transcription, and cellular components. Collectively, these findings highlight the contribution of gene flow to the invasion and spread of M. micrantha and indicate the roles of adaptive loci and functional genes in invasive adaptation.}, } @article {pmid34438234, year = {2022}, author = {Konstantinidis, KT and Viver, T and Conrad, RE and Venter, SN and Rossello-Mora, R}, title = {Solar salterns as model systems to study the units of bacterial diversity that matter for ecosystem functioning.}, journal = {Current opinion in biotechnology}, volume = {73}, number = {}, pages = {151-157}, doi = {10.1016/j.copbio.2021.07.028}, pmid = {34438234}, issn = {1879-0429}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Ecosystem ; Metagenomics ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbial communities often harbor overwhelming species and gene diversity, making it challenging to determine the important units to study this diversity. We argue that the reduced, and thus tractable, microbial diversity of manmade salterns provides an ideal system to advance this cornerstone issue. We review recent time-series genomic and metagenomic studies of the saltern-dominating bacterial and archaeal taxa to show that these taxa form persistent, sequence-discrete, species-like populations. While these populations harbor extensive intra-population gene diversity, even within a single saltern site, only a small minority of these genes appear to be functionally important during environmental perturbations. We outline an approach to detect and track such populations and their ecologically important genes that should be broadly applicable.}, } @article {pmid34437844, year = {2021}, author = {Brealey, JC and Leitão, HG and Hofstede, T and Kalthoff, DC and Guschanski, K}, title = {The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans.}, journal = {Current biology : CB}, volume = {31}, number = {20}, pages = {4650-4658.e6}, doi = {10.1016/j.cub.2021.08.010}, pmid = {34437844}, issn = {1879-0445}, mesh = {Animals ; Animals, Wild ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Humans ; *Microbiota/genetics ; Sweden ; *Ursidae ; }, abstract = {Following the advent of industrial-scale antibiotic production in the 1940s,[1] antimicrobial resistance (AMR) has been on the rise and now poses a major global health threat in terms of mortality, morbidity, and economic burden.[2][,][3] Because AMR can be exchanged between humans, livestock, and wildlife, wild animals can be used as indicators of human-associated AMR contamination of the environment.[4] However, AMR is a normal function of natural environments and is present in host-associated microbiomes, which makes it challenging to distinguish between anthropogenic and natural sources.[4][,][5] One way to overcome this difficulty is to use historical samples that span the period from before the mass production of antibiotics to today. We used shotgun metagenomic sequencing of dental calculus, the calcified form of the oral microbial biofilm, to determine the abundance and repertoire of AMR genes in the oral microbiome of Swedish brown bears collected over the last 180 years. Our temporal metagenomics approach allowed us to establish a baseline of natural AMR in the pre-antibiotics era and to quantify a significant increase in total AMR load and diversity of AMR genes that is consistent with patterns of national human antibiotic use. We also demonstrated a significant decrease in total AMR load in bears in the last two decades, which coincides with Swedish strategies to mitigate AMR. Our study suggests that public health policies can be effective in limiting human-associated AMR contamination of the environment and wildlife.}, } @article {pmid34437819, year = {2021}, author = {Li, B and Zhang, J and Chen, Y and Wang, Q and Yan, L and Wang, R and Wei, Y and You, Z and Li, Y and Miao, Q and Xiao, X and Lian, M and Chen, W and Qiu, D and Fang, J and Gershwin, ME and Tang, R and Ma, X}, title = {Alterations in microbiota and their metabolites are associated with beneficial effects of bile acid sequestrant on icteric primary biliary Cholangitis.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1946366}, pmid = {34437819}, issn = {1949-0984}, mesh = {Adult ; Bacteria/*metabolism ; Bile Acids and Salts/*metabolism/*pharmacology/*therapeutic use ; China ; Cohort Studies ; Female ; Gastrointestinal Agents/metabolism/pharmacology/therapeutic use ; Gastrointestinal Microbiome/*drug effects ; Humans ; Liver Cirrhosis, Biliary/*drug therapy/*physiopathology ; Male ; Middle Aged ; }, abstract = {Background: Increasing data suggests an interaction between bile acids and intestinal microbiota in the pathogenesis of primary biliary cholangitis (PBC). Bile acid sequestrants are widely used to bind bile acids in the intestinal lumen and are therefore posited to impact gut bacteria. Herein we aimed to investigate the effects of cholestyramine on the bile acid profile and gut microbiome in a cohort of icteric PBC patients.Results: Thirty-three PBC patients were treated with cholestyramine, serum and stool samples were collected at baseline, 4 and 16 weeks. Shotgun metagenomic sequencing and targeted metabolomic profiling were performed. Following cholestyramine administration, patients exhibited a high interpersonal variability in remission of cholestasis, and were therefore dichotomized according to the decrease of total bilirubin. Gut microbial co-abundance networks showed distinct taxa interactions between subjects with superior remission (SR) and those with inferior remission (IR) at baseline. After treatment, compositional shifts of the microbiome in the SR group were characterized with enrichment of two Lachnospiraceae species, typically producing short-chain fatty acids (SCFAs). In contrast, Klebsiella pneumonia, a commensal pathobiont, was only increased in the IR group. Correspondingly, metabolome analysis demonstrated that patients with SR, but not IR, were marked by elevations of SCFAs including valeric acid and caproic acid. Finally, integrative analysis identified robust associations between the variations of microbiota, metabolites, and inflammatory cytokines in SR group, indicating potential mechanistic links.Conclusions: Beneficial responses caused by cholestyramine were closely related with compositional and functional alterations in gut commensal, highlighting the possibility of exploring bile acid-microbiota interactions for treating PBC.}, } @article {pmid34436669, year = {2022}, author = {Gopinath, D and Wie, CC and Banerjee, M and Thangavelu, L and Kumar R, P and Nallaswamy, D and Botelho, MG and Johnson, NW}, title = {Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users.}, journal = {Clinical oral investigations}, volume = {26}, number = {2}, pages = {1647-1656}, pmid = {34436669}, issn = {1436-3771}, mesh = {Bacteria/classification ; Humans ; *Microbiota ; Mouth Mucosa/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Smokers ; Tobacco Use ; *Tobacco, Smokeless ; }, abstract = {INTRODUCTION: Smoked, and especially smokeless, tobacco are major causes of oral cancer globally. Here, we examine the oral bacteriome of smokers and of smokeless tobacco users, in comparison to healthy controls, using 16S rRNA gene sequencing.

METHODS: Oral swab samples were collected from smokers, smokeless tobacco users, and healthy controls (n = 44). Microbial DNA was extracted and the 16S rRNA gene profiled using the Illumina MiSeq platform. Sequencing reads were processed using DADA2, and taxonomical classification was performed using the phylogenetic placement method. Differentially abundant taxa were identified using DESeq2, while functional metagenomes based on KEGG orthology abundance were inferred using LIMMA.

RESULTS: A significantly higher microbial diversity was observed in smokeless tobacco users and smokers relative to controls (P < 0.05). Compositional differences in microbial communities were observed in all comparisons with healthy controls (PERMANOVA P < 0.05) but not between smokers and smokeless tobacco users. Levels of Fusobacterium spp., Saccharibacterium spp., and members of Shuttleworthia were elevated in smokers when compared to controls (BH adj P < 0.01). In addition, the relative abundance of three bacterial taxa belonging to genera Fusobacterium spp., Catonella, and Fretibacterium spp. was significantly increased in smokeless tobacco users relative to controls (BH adj P < 0.01). Major functional pathways significantly increased in smokeless tobacco users relative to both controls, and smokers were similar and involved amino acid metabolism including glutamate and aspartate biosynthesis and degradation (log FC > 1.5; BH adj P < 0.01).

CONCLUSIONS: A distinct taxonomic and functional profile of oral microbiome in smokers and smokeless tobacco users as compared to healthy controls implicates a significant role of microbes and their metabolites in diseases associated with tobacco use including oral cancer.

CLINICAL RELEVANCE: Future efforts in preventive, diagnostic, curative, and prognostic strategies for diseases associated with tobacco use in smokers and smokeless tobacco users could incorporate the oral microbiome.}, } @article {pmid34433845, year = {2021}, author = {Hasrat, R and Kool, J and de Steenhuijsen Piters, WAA and Chu, MLJN and Kuiling, S and Groot, JA and van Logchem, EM and Fuentes, S and Franz, E and Bogaert, D and Bosch, T}, title = {Benchmarking laboratory processes to characterise low-biomass respiratory microbiota.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {17148}, pmid = {34433845}, issn = {2045-2322}, support = {SCAF/16/03/CSO_/Chief Scientist Office/United Kingdom ; }, mesh = {Benchmarking/*methods ; Biomass ; Humans ; Metagenomics/methods/standards ; *Microbiota ; Polymerase Chain Reaction/methods/standards ; RNA, Ribosomal, 16S/genetics ; Reagent Kits, Diagnostic/*standards ; Respiratory Mucosa/*microbiology ; Saliva/microbiology ; }, abstract = {The low biomass of respiratory samples makes it difficult to accurately characterise the microbial community composition. PCR conditions and contaminating microbial DNA can alter the biological profile. The objective of this study was to benchmark the currently available laboratory protocols to accurately analyse the microbial community of low biomass samples. To study the effect of PCR conditions on the microbial community profile, we amplified the 16S rRNA gene of respiratory samples using various bacterial loads and different number of PCR cycles. Libraries were purified by gel electrophoresis or AMPure XP and sequenced by V2 or V3 MiSeq reagent kits by Illumina sequencing. The positive control was diluted in different solvents. PCR conditions had no significant influence on the microbial community profile of low biomass samples. Purification methods and MiSeq reagent kits provided nearly similar microbiota profiles (paired Bray-Curtis dissimilarity median: 0.03 and 0.05, respectively). While profiles of positive controls were significantly influenced by the type of dilution solvent, the theoretical profile of the Zymo mock was most accurately analysed when the Zymo mock was diluted in elution buffer (difference compared to the theoretical Zymo mock: 21.6% for elution buffer, 29.2% for Milli-Q, and 79.6% for DNA/RNA shield). Microbiota profiles of DNA blanks formed a distinct cluster compared to low biomass samples, demonstrating that low biomass samples can accurately be distinguished from DNA blanks. In summary, to accurately characterise the microbial community composition we recommend 1. amplification of the obtained microbial DNA with 30 PCR cycles, 2. purifying amplicon pools by two consecutive AMPure XP steps and 3. sequence the pooled amplicons by V3 MiSeq reagent kit. The benchmarked standardized laboratory workflow presented here ensures comparability of results within and between low biomass microbiome studies.}, } @article {pmid34429455, year = {2021}, author = {Wetzels, SU and Strachan, CR and Conrady, B and Wagner, M and Burgener, IA and Virányi, Z and Selberherr, E}, title = {Wolves, dogs and humans in regular contact can mutually impact each other's skin microbiota.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {17106}, pmid = {34429455}, issn = {2045-2322}, support = {P 30704/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Dogs/*microbiology ; Domestication ; Humans ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Skin/*microbiology ; Wolves/*microbiology ; }, abstract = {In contrast to humans and dogs, the skin microbiota of wolves is yet to be described. Here, we investigated the skin microbiota of dogs and wolves kept in outdoor packs at the Wolf Science Center (WSC) via 16S rRNA gene amplicon sequencing. Skin swab samples were also collected from human care takers and their pet dogs. When comparing the three canine groups, representing different degrees of human contact to the care takers and each other, the pet dogs showed the highest level of diversity. Additionally, while human skin was dominated by a few abundant phylotypes, the skin microbiota of the care takers who had particularly close contact with the WSC animals was more similar to the microbiota of dogs and wolves compared to the humans who had less contact with these animals. Our results suggest that domestication may have an impact on the diversity of the skin microbiota, and that the canine skin microbiota can be shared with humans, depending on the level of interaction.}, } @article {pmid34429088, year = {2021}, author = {Phillips, S and Watt, R and Atkinson, T and Savva, GM and Hayhoe, A and Hall, LJ and , }, title = {The Pregnancy and EARly Life study (PEARL) - a longitudinal study to understand how gut microbes contribute to maintaining health during pregnancy and early life.}, journal = {BMC pediatrics}, volume = {21}, number = {1}, pages = {357}, pmid = {34429088}, issn = {1471-2431}, support = {BBS/E/F/00044409/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG1860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Longitudinal Studies ; *Microbiota ; Pregnancy ; Prospective Studies ; }, abstract = {BACKGROUND: The early life period represents the first step in establishing a beneficial microbial ecosystem, which in turn affects both short and longer-term health. Changes during pregnancy influence the neonatal microbiome; through transmission of maternal microbes during childbirth, and beyond, through nutritional programming. However, in-depth exploration of longitudinal maternal-infant cohorts, with sampling of multiple body sites, complemented by clinical and nutritional metadata, and use of cutting-edge experimental systems are limited. The PEARL study will increase our knowledge of; how microbes (including viruses/phages, bacteria, fungi and archaea) change in composition and functional capacity during pregnancy; transmission pathways from mother to infant; the impact of various factors on microbial communities across pregnancy and early life (e.g. diet), and how these microbes interact with other microbes and modulate host processes, including links to disease onset.

METHODS: PEARL is a longitudinal observational prospective study of 250 pregnant women and their newborns, with stool and blood samples, questionnaires and routine clinical data collected during pregnancy, labour, birth and up to 24 months post birth. Metagenomic sequencing of samples will be used to define microbiome profiles, and allow for genus, species and strain-level taxonomic identification and corresponding functional analysis. A subset of samples will be analysed for host (immune/metabolite) molecules to identify factors that alter the host gut environment. Culturing will be used to identify new strains of health-promoting bacteria, and potential pathogens. Various in vitro and in vivo experiments will probe underlying mechanisms governing microbe-microbe and microbe-host interactions.

DISCUSSION: Longitudinal studies, like PEARL, are critical if we are to define biomarkers, determine mechanisms underlying microbiome profiles in health and disease, and develop new diet- and microbe-based therapies to be tested in future studies and clinical trials.

TRIAL REGISTRATION: This study is registered in the ClinicalTrials.gov Database with ID: NCT03916874 .}, } @article {pmid34426638, year = {2021}, author = {Chen, YH and Chiang, PW and Rogozin, DY and Degermendzhy, AG and Chiu, HH and Tang, SL}, title = {Salvaging high-quality genomes of microbial species from a meromictic lake using a hybrid sequencing approach.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {996}, pmid = {34426638}, issn = {2399-3642}, mesh = {Bacteria/genetics/*isolation & purification ; *Genome, Bacterial ; *High-Throughput Nucleotide Sequencing ; Lakes/*microbiology ; *Metagenome ; *Nanopore Sequencing ; Siberia ; }, abstract = {Most of Earth's bacteria have yet to be cultivated. The metabolic and functional potentials of these uncultivated microorganisms thus remain mysterious, and the metagenome-assembled genome (MAG) approach is the most robust method for uncovering these potentials. However, MAGs discovered by conventional metagenomic assembly and binning are usually highly fragmented genomes with heterogeneous sequence contamination. In this study, we combined Illumina and Nanopore data to develop a new workflow to reconstruct 233 MAGs-six novel bacterial orders, 20 families, 66 genera, and 154 species-from Lake Shunet, a secluded meromictic lake in Siberia. With our workflow, the average N50 of reconstructed MAGs greatly increased 10-40-fold compared to when the conventional Illumina assembly and binning method were used. More importantly, six complete MAGs were recovered from our datasets. The recovery of 154 novel species MAGs from a rarely explored lake greatly expands the current bacterial genome encyclopedia.}, } @article {pmid34426398, year = {2021}, author = {Tomofuji, Y and Maeda, Y and Oguro-Igashira, E and Kishikawa, T and Yamamoto, K and Sonehara, K and Motooka, D and Matsumoto, Y and Matsuoka, H and Yoshimura, M and Yagita, M and Nii, T and Ohshima, S and Nakamura, S and Inohara, H and Takeda, K and Kumanogoh, A and Okada, Y}, title = {Metagenome-wide association study revealed disease-specific landscape of the gut microbiome of systemic lupus erythematosus in Japanese.}, journal = {Annals of the rheumatic diseases}, volume = {80}, number = {12}, pages = {1575-1583}, pmid = {34426398}, issn = {1468-2060}, mesh = {Adult ; Female ; Gastrointestinal Microbiome/*genetics ; Genes, Bacterial/*genetics ; Genome-Wide Association Study ; Humans ; Japan ; Lupus Erythematosus, Systemic/genetics/*microbiology ; Male ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Metagenomics ; Middle Aged ; Streptococcus anginosus/*genetics ; Streptococcus intermedius/*genetics ; }, abstract = {OBJECTIVE: Alteration of the gut microbiome has been linked to the pathogenesis of systemic lupus erythematosus (SLE). However, a comprehensive view of the gut microbiome in SLE and its interaction with the host remains to be revealed. This study aimed to reveal SLE-associated changes in the gut microbiome and its interaction with the host by a comprehensive metagenome-wide association study (MWAS) followed by integrative analysis.

METHODS: We performed a MWAS of SLE based on shotgun sequencing of the gut microbial DNA from Japanese individuals (Ncase=47, Ncontrol=203). We integrated the result of the MWAS with the genome-wide association study (GWAS) data and plasma metabolite data.

RESULTS: Via species level phylogenetic analysis, we identified and validated increases of Streptococcus intermedius and Streptococcus anginosus in the patients with SLE. Microbial gene analysis revealed increases of Streptococcus-derived genes including one involved in redox reaction. Additionally, microbial pathways related to sulfur metabolism and flagella assembly were altered in the patients with SLE. We identified an overlap in the enriched biological pathways between the metagenome and the germline genome by comparing the result of the MWAS and the GWAS of SLE (ie, MWAS-GWAS interaction). α-diversity and β-diversity analyses provided evidence of dysbiosis in the metagenome of the patients with SLE. Microbiome-metabolome association analysis identified positive dosage correlation of acylcarnitine with Streptococcus intermedius, an SLE-associated taxon.

CONCLUSION: Our MWAS followed by integrative analysis revealed SLE-associated changes in the gut microbiome and its interaction with the host, which contribute to our understanding of the relationship between the microbiome and SLE.}, } @article {pmid34425308, year = {2021}, author = {Turek, EM and Cox, MJ and Hunter, M and Hui, J and James, P and Willis-Owen, SAG and Cuthbertson, L and James, A and Musk, AW and Moffatt, MF and Cookson, WOCM}, title = {Airway microbial communities, smoking and asthma in a general population sample.}, journal = {EBioMedicine}, volume = {71}, number = {}, pages = {103538}, pmid = {34425308}, issn = {2352-3964}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adult ; Aged ; Asthma/*epidemiology/etiology ; Australia/epidemiology ; Computational Biology/methods ; Disease Susceptibility ; Female ; Humans ; Male ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Population Surveillance ; RNA, Ribosomal, 16S ; Respiratory Mucosa/*microbiology ; Smoking/adverse effects/*epidemiology ; Tobacco Smoking ; }, abstract = {BACKGROUND: Normal airway microbial communities play a central role in respiratory health but are poorly characterized. Cigarette smoking is the dominant global environmental influence on lung function, and asthma has become the most prevalent chronic respiratory disease worldwide. Both conditions have major microbial components that are incompletely defined.

METHODS: We investigated airway bacterial communities in a general population sample of 529 Australian adults. Posterior oropharyngeal swabs were analyzed by sequencing of the 16S rRNA gene. The microbiota were characterized according to their prevalence, abundance and network memberships.

FINDINGS: The microbiota were similar across the general population, and were strongly organized into co-abundance networks. Smoking was associated with diversity loss, negative effects on abundant taxa, profound alterations to network structure and expansion of Streptococcus spp. By contrast, the asthmatic microbiota were selectively affected by an increase in Neisseria spp. and by reduced numbers of low abundance but prevalent organisms.

INTERPRETATION: Our study shows that the healthy airway microbiota in this population were contained within a highly structured ecosystem, suggesting balanced relationships between the microbiome and human host factors. The marked abnormalities in smokers may contribute to chronic obstructive pulmonary disease (COPD) and lung cancer. The narrow spectrum of abnormalities in asthmatics encourages investigation of damaging and protective effects of specific bacteria.

FUNDING: The study was funded by the Asmarley Trust and a Wellcome Joint Senior Investigator Award to WOCC and MFM (WT096964MA and WT097117MA). The Busselton Healthy Ageing Study is supported by the Government of Western Australia (Office of Science, Department of Health) the City of Busselton, and private donations.}, } @article {pmid34424926, year = {2021}, author = {Zacho, CM and Bager, MA and Margaryan, A and Gravlund, P and Galatius, A and Rasmussen, AR and Allentoft, ME}, title = {Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes.}, journal = {PloS one}, volume = {16}, number = {8}, pages = {e0256353}, pmid = {34424926}, issn = {1932-6203}, mesh = {Animals ; *Ethanol ; *Metagenomics/methods ; *Genomics/methods ; Snakes/genetics ; Museums ; DNA, Ancient/analysis ; Genome ; Sequence Analysis, DNA/methods ; Liver/metabolism ; Preservation, Biological/methods ; Metagenome ; }, abstract = {Natural history museum collections worldwide represent a tremendous resource of information on past and present biodiversity. Fish, reptiles, amphibians and many invertebrate collections have often been preserved in ethanol for decades or centuries and our knowledge on the genomic and metagenomic research potential of such material is limited. Here, we use ancient DNA protocols, combined with shotgun sequencing to test the molecular preservation in liver, skin and bone tissue from five old (1842 to 1964) museum specimens of the common garter snake (Thamnophis sirtalis). When mapping reads to a T. sirtalis reference genome, we find that the DNA molecules are highly damaged with short average sequence lengths (38-64 bp) and high C-T deamination, ranging from 9% to 21% at the first position. Despite this, the samples displayed relatively high endogenous DNA content, ranging from 26% to 56%, revealing that genome-scale analyses are indeed possible from all specimens and tissues included here. Of the three tested types of tissue, bone shows marginally but significantly higher DNA quality in these metrics. Though at least one of the snakes had been exposed to formalin, neither the concentration nor the quality of the obtained DNA was affected. Lastly, we demonstrate that these specimens display a diverse and tissue-specific microbial genetic profile, thus offering authentic metagenomic data despite being submerged in ethanol for many years. Our results emphasize that historical museum collections continue to offer an invaluable source of information in the era of genomics.}, } @article {pmid34424588, year = {2022}, author = {Wigley, K and Egbadon, E and Carere, CR and Weaver, L and Baronian, K and Burbery, L and Dupont, PY and Bury, SJ and Gostomski, PA}, title = {RNA stable isotope probing and high-throughput sequencing to identify active microbial community members in a methane-driven denitrifying biofilm.}, journal = {Journal of applied microbiology}, volume = {132}, number = {2}, pages = {1526-1542}, doi = {10.1111/jam.15264}, pmid = {34424588}, issn = {1365-2672}, support = {//Marsden Fund Council, managed by Royal Society Te Apārangi/ ; }, mesh = {Biofilms ; High-Throughput Nucleotide Sequencing ; Isotopes ; *Methane ; *Microbiota/genetics ; Oxidation-Reduction ; Phylogeny ; RNA ; RNA Probes ; RNA, Ribosomal, 16S ; }, abstract = {AIMS: Aerobic methane oxidation coupled to denitrification (AME-D) is a promising process for removing nitrate from groundwater and yet its microbial mechanism and ecological implications are not fully understood. This study used RNA stable isotope probing (RNA-SIP) and high-throughput sequencing to identify the micro-organisms that are actively involved in aerobic methane oxidation within a denitrifying biofilm.

METHODS AND RESULTS: Two RNA-SIP experiments were conducted to investigate labelling of RNA and methane monooxygenase (pmoA) transcripts when exposed to [13] C-labelled methane over a 96-hour time period and to determine active bacteria involved in methane oxidation in a denitrifying biofilm. A third experiment was performed to ascertain the extent of [13] C labelling of RNA using isotope ratio mass spectrometry (IRMS). All experiments used biofilm from an established packed bed reactor. IRMS confirmed [13] C enrichment of the RNA. The RNA-SIP experiments confirmed selective enrichment by the shift of pmoA transcripts into heavier fractions over time. Finally, high-throughput sequencing identified the active micro-organisms enriched with [13] C.

CONCLUSIONS: Methanotrophs (Methylovulum spp. and Methylocystis spp.), methylotrophs (Methylotenera spp.) and denitrifiers (Hyphomicrobium spp.) were actively involved in AME-D.

This is the first study to use RNA-SIP and high-throughput sequencing to determine the bacteria active within an AME-D community.}, } @article {pmid34424248, year = {2021}, author = {Vieira, J and Gallagher, T and Sui, HY and Jesudasen, S and Whiteson, K and O'Toole, GA and Hanselmann, K and Lai, PS}, title = {Design and Development of a Model to Study the Effect of Supplemental Oxygen on the Cystic Fibrosis Airway Microbiome.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {174}, pages = {}, doi = {10.3791/62888}, pmid = {34424248}, issn = {1940-087X}, support = {K23 ES023700/ES/NIEHS NIH HHS/United States ; }, mesh = {*Cystic Fibrosis/therapy ; Humans ; Metagenome ; *Microbiota ; Oxygen ; Sputum ; }, abstract = {Airway microbial communities are thought to play an important role in the progression of cystic fibrosis (CF) and other chronic pulmonary diseases. Microbes have traditionally been classified based on their ability to use or tolerate oxygen. Supplemental oxygen is a common medical therapy administered to people with cystic fibrosis (pwCF); however, existing studies on oxygen and the airway microbiome have focused on how hypoxia (low oxygen) rather than hyperoxia (high oxygen) affects the predominantly aerobic and facultative anaerobic lung microbial communities. To address this critical knowledge gap, this protocol was developed using an artificial sputum medium that mimics the composition of sputum from pwCF. The use of filter sterilization, which yields a transparent medium, allows optical methods to follow the growth of single-celled microbes in suspension cultures. To create hyperoxic conditions, this model system takes advantage of established anaerobic culturing techniques to study hyperoxic conditions; instead of removing oxygen, oxygen is added to cultures by daily sparging of serum bottles with a mixture of compressed oxygen and air. Sputum from 50 pwCF underwent daily sparging for a 72-h period to verify the ability of this model to maintain differential oxygen conditions. Shotgun metagenomic sequencing was performed on cultured and uncultured sputum samples from 11 pwCF to verify the ability of this medium to support the growth of commensal and pathogenic microbes commonly found in cystic fibrosis sputum. Growth curves were obtained from 112 isolates obtained from pwCF to verify the ability of this artificial sputum medium to support the growth of common cystic fibrosis pathogens. We find that this model can culture a wide variety of pathogens and commensals in CF sputum, recovers a community highly similar to uncultured sputum under normoxic conditions, and creates different culture phenotypes under varying oxygen conditions. This new approach might lead to a better understanding of unanticipated effects induced by the use of oxygen in pwCF on airway microbial communities and common respiratory pathogens.}, } @article {pmid34418978, year = {2021}, author = {Christiansen, H and Heindler, FM and Hellemans, B and Jossart, Q and Pasotti, F and Robert, H and Verheye, M and Danis, B and Kochzius, M and Leliaert, F and Moreau, C and Patel, T and Van de Putte, AP and Vanreusel, A and Volckaert, FAM and Schön, I}, title = {Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {625}, pmid = {34418978}, issn = {1471-2164}, mesh = {Animals ; Genome ; Genomics ; Humans ; *Metagenomics ; *Research Design ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS.

RESULTS: In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA.

CONCLUSIONS: Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.}, } @article {pmid34418463, year = {2021}, author = {Brookes, ZLS and Belfield, LA and Ashworth, A and Casas-Agustench, P and Raja, M and Pollard, AJ and Bescos, R}, title = {Effects of chlorhexidine mouthwash on the oral microbiome.}, journal = {Journal of dentistry}, volume = {113}, number = {}, pages = {103768}, doi = {10.1016/j.jdent.2021.103768}, pmid = {34418463}, issn = {1879-176X}, mesh = {*Chlorhexidine/pharmacology ; *Microbiota ; Mouth ; Mouthwashes ; Nitrates ; }, abstract = {INTRODUCTION/OBJECTIVES: Chlorhexidine (CHX) is a commonly used mouthwash with potent anti-microbial effects useful for the management of oral disease. However, we are moving away from the view of simply 'killing' bacteria, towards managing oral microbial ecosystems (oral microbiome), as an integrated system, to promote oral and systemic health. Here, we aimed to review the effects of CHX mouthwash on the balance of microbial communities in the mouth in vivo in oral health and disease.

SOURCES AND STUDY SECTION: The hierarchy of evidence was applied, with systematic reviews and randomised controlled trials consulted where available and case controlled studies being described thereafter. Search terms for each subject category were entered into MEDLINE, PubMed, Google Scholar and the Cochrane database. Focussing on metagenomics studies provides unique overview of the oral microbiome as an integrated system.

DATA: Evidence was limited, but several next generation sequencing case-controlled studies suggested that in an integrated system, CHX may cause a shift towards lower bacterial diversity and abundance, in particular nitrate-reducing bacteria in vivo. CHX also appeared to alter salivary pH, lactate, nitrate and nitrite concentrations in saliva. Evidence regarding the effects of CHX on the oral microbiome during oral disease is still emerging.

CONCLUSIONS: CHX alters the composition the oral microbiome. However, as CHX use remains widespread in dentistry to manage oral disease, urgent research using metagenomics studies of microbial communities in vivo are still needed to determine CHX mouthwash is 'good', 'bad' or otherwise for bacteria, in the context of oral and systemic health.}, } @article {pmid34418188, year = {2021}, author = {Sanborn, MA and Wuertz, KM and Kim, HC and Yang, Y and Li, T and Pollett, SD and Jarman, RG and Berry, IM and Klein, TA and Hang, J}, title = {Metagenomic analysis reveals Culex mosquito virome diversity and Japanese encephalitis genotype V in the Republic of Korea.}, journal = {Molecular ecology}, volume = {30}, number = {21}, pages = {5470-5487}, doi = {10.1111/mec.16133}, pmid = {34418188}, issn = {1365-294X}, support = {P0171_21_WR//Armed Forces Health Surveillance Division, Global Emerging Infections Surveillance (GEIS)/ ; }, mesh = {Animals ; *Culex ; *Culicidae ; *Encephalitis Virus, Japanese/genetics ; *Encephalitis, Japanese/epidemiology ; Genotype ; Humans ; Metagenomics ; Phylogeny ; Retrospective Studies ; Virome ; }, abstract = {Recent outbreaks of emerging and re-emerging viruses have shown that timely detection of novel arboviruses with epidemic potential is essential to mitigate human health risks. There are rising concerns that emergent JEV genotype V (GV) is circulating in Asia, against which current vaccines may not be efficacious. To ascertain if JEV GV and other arboviruses are circulating in East Asia, we conducted next-generation sequencing on 260 pools of Culex tritaeniorhynchus and Culex bitaeniorhynchus mosquitoes (6540 specimens) collected at Camp Humphreys, Republic of Korea (ROK) in 2018. Interrogation of our data revealed a highly abundant and diverse virosphere that contained sequences from 122 distinct virus species. Our statistical and hierarchical analysis uncovered correlates of potential health, virological, and ecological relevance. Furthermore, we obtained evidence that JEV GV was circulating in Pyeongtaek and, retrospectively, in Seoul in 2016 and placed these findings within the context of human and fowl reservoir activity. Sequence-based analysis of JEV GV showed a divergent genotype that is the most distant from the GIII-derived live attenuated SA14-14-2 vaccine strain and indicated regions probably responsible for reduced antibody affinity. These results emphasize recent concerns of shifting JEV genotype in East Asia and highlight the critical need for a vaccine proven efficacious against this re-emergent virus. Together, our one-health approach to Culex viral metagenomics uncovered novel insights into virus ecology and human health.}, } @article {pmid34415535, year = {2022}, author = {Marbouty, M and Koszul, R}, title = {Metagenomes Binning Using Proximity-Ligation Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2301}, number = {}, pages = {163-181}, pmid = {34415535}, issn = {1940-6029}, mesh = {High-Throughput Nucleotide Sequencing ; *Metagenome ; Metagenomics ; Microbiota/genetics ; Sequence Analysis, DNA ; }, abstract = {Microbial communities are key components of all ecosystems, but characterization of their complete genomic structure remains challenging. Typical analysis tends to elude the complexity of the mixes in terms of species, strains, as well as extrachromosomal DNA molecules. Recently, approaches have been developed that bins DNA contigs into individual genomes and episomes according to their 3D contact frequencies. Those contacts are quantified by chromosome conformation capture experiments (3C, Hi-C), also known as proximity-ligation approaches, applied to metagenomics samples. Here, we present a simple computational pipeline that allows to recover high-quality Metagenomics Assemble Genomes (MAGs) starting from metagenomic 3C or Hi-C datasets and a metagenome assembly.}, } @article {pmid34415303, year = {2021}, author = {Li, H and Zhao, C and Yang, Y and Zhou, Z and Qi, J and Li, C}, title = {The Influence of Gut Microbiota on the Fecundity of Henosepilachna vigintioctopunctata (Coleoptera: Coccinellidae).}, journal = {Journal of insect science (Online)}, volume = {21}, number = {4}, pages = {}, pmid = {34415303}, issn = {1536-2442}, support = {31572010//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacteria/isolation & purification ; *Coleoptera/microbiology/physiology ; DNA, Bacterial ; Diet ; Female ; *Fertility ; Gastrointestinal Microbiome/*genetics ; Lipid Metabolism ; Male ; Metagenomics ; Ovary/growth & development ; Pest Control ; RNA, Ribosomal, 16S ; Testis/growth & development ; }, abstract = {The gut microbiota of insects usually plays an important role in the development and reproduction of their hosts. The fecundity of Henosepilachna vigintioctopunctata (Fabricius) varies greatly when they develop on different host plants. Whether and how the gut microbiota regulates the fecundity of H. vigintioctopunctata was unknown. To address this question, we used 16S rRNA sequencing to analyze the gut microbiomes of H. vigintioctopunctata adults fed on two host plant species (Solanum nigrum and Solanum melongena) and one artificial diet. The development of the ovaries and testes was also examined. Our results revealed that the diversity and abundance of gut microorganisms varied significantly in insects reared on different diets. The gut microbiota of H. vigintioctopunctata raised on the two host plants was similar, with Proteobacteria being the dominant phylum in both groups, whereas Firmicutes was the dominant phylum in the group reared on the artificial diet. The predominant microbiota in the S. nigrum group were Acinetobacter soli and Acinetobacter ursingii (Acinetobacter, Moraxellaceae); Moraxella osloensis (Enhydrobacter, Moraxellaceae); and Empedobacter brevis (Empedobacter, Weeksellaceae). The microbiota in this group are associated with high lipid metabolism. In addition, the beetles' ovaries and testes were more highly developed in the S. nigrum group than in the other two groups. These findings provide valuable information for elucidating the complex roles the gut microbiota play in the fecundity of H. vigintioctopunctata, and may also contribute to developing future novel control strategies involving this economically important pest.}, } @article {pmid34414130, year = {2021}, author = {Chen, H and Wang, L and Zhao, L and Luo, L and Min, S and Wen, Y and Lei, W and Shu, M and Li, Z}, title = {Alterations of Vaginal Microbiota in Women With Infertility and Chlamydia trachomatis Infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {698840}, pmid = {34414130}, issn = {2235-2988}, mesh = {Chlamydia trachomatis ; Female ; Humans ; *Infertility ; Lactobacillus ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Chlamydia trachomatis (C. trachomatis) is the most common etiological agent of bacterial sexually transmitted infections (STIs) worldwide and causes serious health sequelae such as cervicitis, pelvic inflammatory disease, and even infertility if ascending from the lower to the upper female genital tract. Previous studies have revealed the pivotal role of vaginal microbiota in susceptibility to STIs. However, alterations in the vaginal microbiota in women who are infertile and infected with C. trachomatis remain unknown. This study used metagenomic analysis of sequenced 16S rRNA gene amplicons to examine the vaginal microbial profiles of women with tubal infertility who were C. trachomatis-negative and those who were C. trachomatis-positive pre- and post-antibiotic treatment. Women who were C. trachomatis-negative and deemed healthy were recruited as references of eubiosis and dysbiosis. Women with tubal infertility and C. trachomatis infection presented a unique Lactobacillus iners-dominated vaginal microbiota rather than one dominated by Lactobacillus crispatus and displayed a decrease in Lactobacillus, Bifidobacterium, Enterobacter, Atopobium, and Streptococcus, accompanied by decreased levels of cytokines such as interferon (IFN)-γ and interleukin (IL)-10. This altered vaginal microbiota could be restored with varying degrees after standard treatment for C. trachomatis. This shift could be a predictive vaginal microbiota signature for C. trachomatis infection among females with tubal infertility, while no significant differences in phylum, class, and operational taxonomic unit (OTU) levels were observed between women with tubal infertility who were C. trachomatis-negative and healthy controls. This is the first study to provide data on the association of vaginal microbiota with C. trachomatis infection among women with tubal infertility and highlights unprecedented potential opportunities to predict C. trachomatis infection.}, } @article {pmid34414128, year = {2021}, author = {Higgins, KV and Woodie, LN and Hallowell, H and Greene, MW and Schwartz, EH}, title = {Integrative Longitudinal Analysis of Metabolic Phenotype and Microbiota Changes During the Development of Obesity.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {671926}, pmid = {34414128}, issn = {2235-2988}, mesh = {Animals ; *Diabetes Mellitus, Type 2 ; *Gastrointestinal Microbiome ; Mice ; *Microbiota ; Obesity ; Phenotype ; }, abstract = {Obesity has increased at an alarming rate over the past two decades in the United States. In addition to increased body mass, obesity is often accompanied by comorbidities such as Type II Diabetes Mellitus and metabolic dysfunction-associated fatty liver disease, with serious impacts on public health. Our understanding of the role the intestinal microbiota in obesity has rapidly advanced in recent years, especially with respect to the bacterial constituents. However, we know little of when changes in these microbial populations occur as obesity develops. Further, we know little about how other domains of the microbiota, namely bacteriophage populations, are affected during the progression of obesity. Our goal in this study was to monitor changes in the intestinal microbiome and metabolic phenotype following western diet feeding. We accomplished this by collecting metabolic data and fecal samples for shotgun metagenomic sequencing in a mouse model of diet-induced obesity. We found that after two weeks of consuming a western diet (WD), the animals weighed significantly more and were less metabolically stable than their chow fed counterparts. The western diet induced rapid changes in the intestinal microbiome with the most pronounced dissimilarity at 12 weeks. Our study highlights the dynamic nature of microbiota composition following WD feeding and puts these events in the context of the metabolic status of the mammalian host.}, } @article {pmid34412659, year = {2021}, author = {Deshpande, NP and Riordan, SM and Gorman, CJ and Nielsen, S and Russell, TL and Correa-Ospina, C and Fernando, BSM and Waters, SA and Castaño-Rodríguez, N and Man, SM and Tedla, N and Wilkins, MR and Kaakoush, NO}, title = {Multi-omics of the esophageal microenvironment identifies signatures associated with progression of Barrett's esophagus.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {133}, pmid = {34412659}, issn = {1756-994X}, mesh = {Adult ; Barrett Esophagus/*etiology/*metabolism/pathology ; *Biomarkers ; *Cellular Microenvironment/genetics ; *Disease Susceptibility ; Epithelial Cells/metabolism/pathology ; Esophagus/*metabolism/microbiology/pathology ; Female ; Gastroesophageal Reflux/complications/etiology ; Gene Expression Profiling ; Gram-Negative Bacterial Infections/complications/microbiology ; Host-Pathogen Interactions/genetics ; Humans ; Macrophages/immunology/metabolism ; Male ; Mast Cells/immunology/metabolism ; Metaplasia ; Microbiota ; Middle Aged ; Models, Biological ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: The enrichment of Gram-negative bacteria of oral origin in the esophageal microbiome has been associated with the development of metaplasia. However, to date, no study has comprehensively assessed the relationships between the esophageal microbiome and the host.

METHODS: Here, we examine the esophageal microenvironment in gastro-esophageal reflux disease and metaplasia using multi-omics strategies targeting the microbiome and host transcriptome, followed by targeted culture, comparative genomics, and host-microbial interaction studies of bacterial signatures of interest.

RESULTS: Profiling of the host transcriptome from esophageal mucosal biopsies revealed profound changes during metaplasia. Importantly, five biomarkers showed consistent longitudinal changes with disease progression from reflux disease to metaplasia. We showed for the first time that the esophageal microbiome is distinct from the salivary microbiome and the enrichment of Campylobacter species as a consistent signature in disease across two independent cohorts. Shape fitting and matrix correlation identified associations between the microbiome and host transcriptome profiles, with a novel co-exclusion relationship found between Campylobacter and napsin B aspartic peptidase. Targeted culture of Campylobacter species from the same cohort revealed a subset of isolates to have a higher capacity to survive within primary human macrophages. Comparative genomic analyses showed these isolates could be differentiated by specific genomic features, one of which was validated to be associated with intracellular fitness. Screening for these Campylobacter strain-specific signatures in shotgun metagenomics data from another cohort showed an increase in prevalence with disease progression. Comparative transcriptomic analyses of primary esophageal epithelial cells exposed to the Campylobacter isolates revealed expression changes within those infected with strains with high intracellular fitness that could explain the increased likelihood of disease progression.

CONCLUSIONS: We provide a comprehensive assessment of the esophageal microenvironment, identifying bacterial strain-specific signatures with high relevance to progression of metaplasia.}, } @article {pmid34411585, year = {2021}, author = {Didion, EM and Sabree, ZL and Kenyon, L and Nine, G and Hagan, RW and Osman, S and Benoit, JB}, title = {Microbiome reduction prevents lipid accumulation during early diapause in the northern house mosquito, Culex pipiens pipiens.}, journal = {Journal of insect physiology}, volume = {134}, number = {}, pages = {104295}, pmid = {34411585}, issn = {1879-1611}, support = {R01 AI048551/AI/NIAID NIH HHS/United States ; R01 AI148551/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification ; Carbohydrate Metabolism ; Culex/metabolism/*microbiology/physiology ; *Diapause, Insect ; Female ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Host Microbial Interactions ; Insect Proteins/metabolism ; *Lipid Metabolism ; Metagenomics/methods ; Microbiota ; RNA, Ribosomal, 16S ; Real-Time Polymerase Chain Reaction/methods ; }, abstract = {The mosquito microbiome is critical to multiple facets of their biology, including larval development and disease transmission. For mosquitoes that reside in temperate regions, periods of diapause are critical to overwintering survival, but how the microbiome impacts this state is unknown. In this study, we compared the midgut microbial communities of diapausing and non-diapausing Culex pipiens and assessed how a reduced midgut microbiome influences diapause preparation. High community variability was found within and between non-diapausing and diapausing individuals, but no specific diapause-based microbiome was noted. Emergence of adult, diapausing mosquitoes under sterile conditions generated low bacterial load (LBL) lines with nearly a 1000-fold reduction in bacteria levels. This reduction in bacterial content resulted in significantly lower survival of diapausing females after two weeks, indicating acquisition of the microbiome in adult females is critical for survival throughout diapause. LBL diapausing females had high carbohydrate levels, but did not accumulate lipid reserves, suggesting an inability to process ingested sugars necessary for diapause-associated lipid accumulation. Expression patterns of select genes associated with mosquito lipid metabolism during diapause showed no significant differences between LBL and control lines, suggesting transcriptional changes may not underlie impaired lipid accumulation. Overall, a diverse, adult-acquired microbiome is critical for diapause in C. pipiens to process sugar reserves and accumulate lipids that are necessary to survive prolonged overwintering.}, } @article {pmid34410642, year = {2021}, author = {Moore, NE and Weyrich, LS}, title = {A Standardized Approach for Shotgun Metagenomic Analysis of Ancient Dental Calculus.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2327}, number = {}, pages = {93-118}, pmid = {34410642}, issn = {1940-6029}, mesh = {DNA, Ancient ; *Dental Calculus ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics ; Microbiota/genetics ; Sequence Analysis, DNA ; }, abstract = {Ancient dental calculus provides a challenging, yet unparalleled, opportunity to reconstruct ancient oral microbial communities and trace the origins of modern microbiota-associated diseases. Metagenomic analysis of ancient dental calculus using high-throughput DNA sequencing has proven itself as an effective method to accurately reconstruct microorganisms that once lived in the mouths of ancient humans. Here, we provide the strategy, methodologies, and approaches used to establish an ancient dental calculus project, from project conception, community engagement, sampling, extracting DNA, and preparing shotgun metagenomic DNA libraries for sequencing on an Illumina platform. We also discuss techniques to minimize background or contaminant DNA by monitoring and reducing contamination in calculus data sets, utilizing appropriate protective gear, and employing the use of sample decontamination strategies. In this methodology chapter, we hope to promote transparency in the ancient dental calculus research field and encourage collaboration across the ancient DNA research community.}, } @article {pmid34410641, year = {2021}, author = {Marotz, C and Zuniga, C and Zaramela, L and Knight, R and Zengler, K}, title = {Host DNA Depletion in Saliva Samples for Improved Shotgun Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2327}, number = {}, pages = {87-92}, pmid = {34410641}, issn = {1940-6029}, mesh = {DNA/genetics ; Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Saliva ; Sequence Analysis, DNA ; }, abstract = {Host DNA makes up the majority of DNA in a saliva sample. Therefore, shotgun metagenomics can be an inefficient way to evaluate the microbial populations of saliva since often <10% of the sequencing reads are microbial. In this chapter, we describe a method to deplete human DNA from fresh or frozen saliva samples, allowing for more efficient shotgun metagenomic sequencing of the salivary microbial community.}, } @article {pmid34410638, year = {2021}, author = {Tansirichaiya, S and Reynolds, LJ and Roberts, AP}, title = {Functional Metagenomic Screening for Antimicrobial Resistance in the Oral Microbiome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2327}, number = {}, pages = {31-50}, pmid = {34410638}, issn = {1940-6029}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/drug effects/genetics ; Humans ; Metagenome ; *Metagenomics ; *Microbiota ; }, abstract = {A large proportion of bacteria, from a multitude of environments, are not yet able to be grown in the laboratory, and therefore microbiological and molecular biological investigations of these bacteria are challenging. A way to circumvent this challenge is to analyze the metagenome, the entire collection of DNA molecules that can be isolated from a particular environment or sample. This collection of DNA molecules can be sequenced and assembled to determine what is present and infer functional potential, or used as a PCR template to detect known target DNA and potentially unknown regions of DNA nearby those targets; however assigning functions to new or conserved hypothetical, functionally cryptic, genes is difficult. Functional metagenomics allows researchers to determine which genes are responsible for selectable phenotypes, such as resistance to antimicrobials and metabolic capabilities, without the prerequisite needs to grow the bacteria containing those genes or to already know which genes are of interest. It is estimated that a third of the resident species of the human oral cavity is not yet cultivable and, together with the ease of sample acquisition, makes this metagenome particularly suited to functional metagenomic studies. Here we describe the methodology related to the collection of saliva samples, extraction of metagenomic DNA, construction of metagenomic libraries, as well as the description of functional assays that have previously led to the identification of new genes conferring antimicrobial resistance.}, } @article {pmid34409759, year = {2021}, author = {Horton, MK and McCauley, K and Fadrosh, D and Fujimura, K and Graves, J and Ness, J and Wheeler, Y and Gorman, MP and Benson, LA and Weinstock-Guttman, B and Waldman, A and Rodriguez, M and Tillema, JM and Krupp, L and Belman, A and Mar, S and Rensel, M and Chitnis, T and Casper, TC and Rose, J and Hart, J and Shao, X and Tremlett, H and Lynch, SV and Barcellos, LF and Waubant, E and , }, title = {Gut microbiome is associated with multiple sclerosis activity in children.}, journal = {Annals of clinical and translational neurology}, volume = {8}, number = {9}, pages = {1867-1883}, pmid = {34409759}, issn = {2328-9503}, support = {F13NS108668/NS/NINDS NIH HHS/United States ; R01 NS071463/NS/NINDS NIH HHS/United States ; RG4861A13//National Multiple Sclerosis Society/ ; R01NS071463/NS/NINDS NIH HHS/United States ; F31 NS108668/NS/NINDS NIH HHS/United States ; HC150906233//National Multiple Sclerosis Society/ ; F13NS108668/NS/NINDS NIH HHS/United States ; R01NS071463/NS/NINDS NIH HHS/United States ; }, mesh = {Adolescent ; Child ; Female ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Humans ; Male ; Multiple Sclerosis/*microbiology/*physiopathology ; RNA, Ribosomal, 16S ; }, abstract = {OBJECTIVE: To identify features of the gut microbiome associated with multiple sclerosis activity over time.

METHODS: We used 16S ribosomal RNA sequencing from stool of 55 recently diagnosed pediatric-onset multiple sclerosis patients. Microbiome features included the abundance of individual microbes and networks identified from weighted genetic correlation network analyses. Prentice-Williams-Peterson Cox proportional hazards models estimated the associations between features and three disease activity outcomes: clinical relapses and both new/enlarging T2 lesions and new gadolinium-enhancing lesions on brain MRI. Analyses were adjusted for age, sex, and disease-modifying therapies.

RESULTS: Participants were followed, on average, 2.1 years. Five microbes were nominally associated with all three disease activity outcomes after multiple testing correction. These included butyrate producers Odoribacter (relapse hazard ratio = 0.46, 95% confidence interval: 0.24, 0.88) and Butyricicoccus (relapse hazard ratio = 0.49, 95% confidence interval: 0.28, 0.88). Two networks of co-occurring gut microbes were significantly associated with a higher hazard of both MRI outcomes (gadolinium-enhancing lesion hazard ratios (95% confidence intervals) for Modules 32 and 33 were 1.29 (1.08, 1.54) and 1.42 (1.18, 1.71), respectively; T2 lesion hazard ratios (95% confidence intervals) for Modules 32 and 33 were 1.34 (1.15, 1.56) and 1.41 (1.21, 1.64), respectively). Metagenomic predictions of these networks demonstrated enrichment for amino acid biosynthesis pathways.

INTERPRETATION: Both individual and networks of gut microbes were associated with longitudinal multiple sclerosis activity. Known functions and metagenomic predictions of these microbes suggest the important role of butyrate and amino acid biosynthesis pathways. This provides strong support for future development of personalized microbiome interventions to modify multiple sclerosis disease activity.}, } @article {pmid34409603, year = {2022}, author = {Su, H and Wang, WJ and Zheng, GD and Yin, ZP and Li, JE and Chen, LL and Zhang, QF}, title = {The anti-obesity and gut microbiota modulating effects of taxifolin in C57BL/6J mice fed with a high-fat diet.}, journal = {Journal of the science of food and agriculture}, volume = {102}, number = {4}, pages = {1598-1608}, doi = {10.1002/jsfa.11496}, pmid = {34409603}, issn = {1097-0010}, support = {32060541//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred C57BL ; Obesity/drug therapy ; Quercetin/analogs & derivatives ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Taxifolin is a natural dihydroflavonol found in many plants and health products. In the present study, its anti-obesity and gut microbiota modulating effects were studied. C57BL/6J mice were fed with a high-fat diet (HFD) supplemented with taxifolin (0, 0.5 and 1 mg mL[-1] , respectively) in drinking water for 15 weeks.

RESULTS: Taxifolin supplementation showed no influence on food and water intake. However, it decreased body weight gain, inhibited fat accumulation, and decreased total cholesterol and triacylglycerol level in mice liver. Taxifolin enhanced superoxide dismutase (SOD) activity in mice liver, which in turn protected the liver from lipid peroxidation damage. It also improved insulin resistance in obese mice. Metagenomic analysis of bacterial 16S rRNA demonstrated that HFD decreased gut microbiota diversity and caused dysbiosis. However, taxifolin improved the gut microbiota diversity and decreased the Firmicutes/Bacteroidetes ratio. In particular, it inhibited Proteobacteria from blooming, this being a signature of dysbiosis in gut microbiota.

CONCLUSION: Taxifolin ameliorated the symptoms of obesity, hepatic steatosis, lipid peroxidation, insulin resistance, and gut microbiota dysbiosis in HFD fed C57BL/6J mice. © 2021 Society of Chemical Industry.}, } @article {pmid34408730, year = {2021}, author = {Xue, CX and Lin, H and Zhu, XY and Liu, J and Zhang, Y and Rowley, G and Todd, JD and Li, M and Zhang, XH}, title = {DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {698286}, pmid = {34408730}, issn = {1664-302X}, abstract = {Metagenomics and metatranscriptomics are powerful methods to uncover key micro-organisms and processes driving biogeochemical cycling in natural ecosystems. Databases dedicated to depicting biogeochemical pathways (for example, metabolism of dimethylsulfoniopropionate (DMSP), which is an abundant organosulfur compound) from metagenomic/metatranscriptomic data are rarely seen. Additionally, a recognized normalization model to estimate the relative abundance and environmental importance of pathways from metagenomic and metatranscriptomic data has not been organized to date. These limitations impact the ability to accurately relate key microbial-driven biogeochemical processes to differences in environmental conditions. Thus, an easy-to-use, specialized tool that infers and visually compares the potential for biogeochemical processes, including DMSP cycling, is urgently required. To solve these issues, we developed DiTing, a tool wrapper to infer and compare biogeochemical pathways among a set of given metagenomic or metatranscriptomic reads in one step, based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) and a manually created DMSP cycling gene database. Accurate and specific formulae for over 100 pathways were developed to calculate their relative abundance. Output reports detail the relative abundance of biogeochemical pathways in both text and graphical format. DiTing was applied to simulated metagenomic data and resulted in consistent genetic features of simulated benchmark genomic data. Subsequently, when applied to natural metagenomic and metatranscriptomic data from hydrothermal vents and the Tara Ocean project, the functional profiles predicted by DiTing were correlated with environmental condition changes. DiTing can now be confidently applied to wider metagenomic and metatranscriptomic datasets, and it is available at https://github.com/xuechunxu/DiTing.}, } @article {pmid34407871, year = {2021}, author = {He, W and Chen, Y and Zhang, X and Peng, M and Xu, D and He, H and Gao, Y and Chen, J and Zhang, J and Li, Z and Chen, Q}, title = {Virome in adult Aedes albopictus captured during different seasons in Guangzhou City, China.}, journal = {Parasites & vectors}, volume = {14}, number = {1}, pages = {415}, pmid = {34407871}, issn = {1756-3305}, support = {2018B020241002//Key-Area Research and Development Program of Guangdong Province/ ; }, mesh = {Aedes/classification/*virology ; Animals ; China ; Female ; Male ; Metagenomics/methods ; Mosquito Vectors/*virology ; *Seasons ; Virome/*genetics ; Viruses/classification/*genetics ; }, abstract = {BACKGROUND: The mosquito Aedes albopictus is an important vector for many pathogens. Understanding the virome in Ae. albopictus is critical for assessing the risk of disease transmission, implementation of vector control measures, and health system strengthening.

METHODS: In this study, viral metagenomic and PCR methods were used to reveal the virome in adult Ae. albopictus captured in different areas and during different seasons in Guangzhou, China.

RESULTS: The viral composition of adult Ae. albopictus varied mainly between seasons. Over 50 viral families were found, which were specific to vertebrates, invertebrates, plants, fungi, bacteria, and protozoa. In rural areas, Siphoviridae (6.5%) was the most common viral family harbored by mosquitoes captured during winter and spring, while Luteoviridae (1.1%) was the most common viral family harbored by mosquitoes captured during summer and autumn. Myoviridae (7.0% and 1.3%) was the most common viral family in mosquitoes captured in urban areas during all seasons. Hepatitis B virus (HBV) was detected by PCR in a female mosquito pool. The first near full-length HBV genome from Ae. albopictus was amplified, which showed a high level of similarity with human HBV genotype B sequences. Human parechovirus (HPeV) was detected in male and female mosquito pools, and the sequences were clustered with HPeV 1 and 3 sequences.

CONCLUSIONS: Large numbers of viral species were found in adult Ae. albopictus, including viruses from vertebrates, insects, and plants. The viral composition in Ae. albopictus mainly varied between seasons. Herein, we are the first to report the detection of HPeV and HBV in mosquitoes. This study not only provides valuable information for the control and prevention of mosquito-borne diseases, but it also demonstrates the feasibility of xenosurveillance.}, } @article {pmid34407780, year = {2021}, author = {Kværner, AS and Birkeland, E and Bucher-Johannessen, C and Vinberg, E and Nordby, JI and Kangas, H and Bemanian, V and Ellonen, P and Botteri, E and Natvig, E and Rognes, T and Hovig, E and Lyle, R and Ambur, OH and de Vos, WM and Bultman, S and Hjartåker, A and Landberg, R and Song, M and Blix, HS and Ursin, G and Randel, KR and de Lange, T and Hoff, G and Holme, Ø and Berstad, P and Rounge, TB}, title = {The CRCbiome study: a large prospective cohort study examining the role of lifestyle and the gut microbiome in colorectal cancer screening participants.}, journal = {BMC cancer}, volume = {21}, number = {1}, pages = {930}, pmid = {34407780}, issn = {1471-2407}, mesh = {Aged ; Case-Control Studies ; Colonoscopy ; Colorectal Neoplasms/*diagnosis/epidemiology/microbiology ; Early Detection of Cancer/*methods ; Female ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Humans ; Incidence ; *Life Style ; Male ; Middle Aged ; Norway/epidemiology ; Occult Blood ; Prognosis ; Prospective Studies ; ROC Curve ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) screening reduces CRC incidence and mortality. However, current screening methods are either hampered by invasiveness or suboptimal performance, limiting their effectiveness as primary screening methods. To aid in the development of a non-invasive screening test with improved sensitivity and specificity, we have initiated a prospective biomarker study (CRCbiome), nested within a large randomized CRC screening trial in Norway. We aim to develop a microbiome-based classification algorithm to identify advanced colorectal lesions in screening participants testing positive for an immunochemical fecal occult blood test (FIT). We will also examine interactions with host factors, diet, lifestyle and prescription drugs. The prospective nature of the study also enables the analysis of changes in the gut microbiome following the removal of precancerous lesions.

METHODS: The CRCbiome study recruits participants enrolled in the Bowel Cancer Screening in Norway (BCSN) study, a randomized trial initiated in 2012 comparing once-only sigmoidoscopy to repeated biennial FIT, where women and men aged 50-74 years at study entry are invited to participate. Since 2017, participants randomized to FIT screening with a positive test result have been invited to join the CRCbiome study. Self-reported diet, lifestyle and demographic data are collected prior to colonoscopy after the positive FIT-test (baseline). Screening data, including colonoscopy findings are obtained from the BCSN database. Fecal samples for gut microbiome analyses are collected both before and 2 and 12 months after colonoscopy. Samples are analyzed using metagenome sequencing, with taxonomy profiles, and gene and pathway content as primary measures. CRCbiome data will also be linked to national registries to obtain information on prescription histories and cancer relevant outcomes occurring during the 10 year follow-up period.

DISCUSSION: The CRCbiome study will increase our understanding of how the gut microbiome, in combination with lifestyle and environmental factors, influences the early stages of colorectal carcinogenesis. This knowledge will be crucial to develop microbiome-based screening tools for CRC. By evaluating biomarker performance in a screening setting, using samples from the target population, the generalizability of the findings to future screening cohorts is likely to be high.

TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT01538550 .}, } @article {pmid34407769, year = {2021}, author = {Goolam Mahomed, T and Peters, R and Pretorius, G and Goolam Mahomed, A and Ueckermann, V and Kock, MM and Ehlers, MM}, title = {Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {228}, pmid = {34407769}, issn = {1471-2180}, mesh = {Aged ; Aged, 80 and over ; DNA, Bacterial/genetics ; Female ; Humans ; Lung/*microbiology ; Male ; Metagenomics/*methods/*standards ; Microbiota/*genetics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Software/*standards ; Sputum/microbiology ; }, abstract = {BACKGROUND: Targeted metagenomics and IS-Pro method are two of the many methods that have been used to study the microbiome. The two methods target different regions of the 16 S rRNA gene. The aim of this study was to compare targeted metagenomics and IS-Pro methods for the ability to discern the microbial composition of the lung microbiome of COPD patients.

METHODS: Spontaneously expectorated sputum specimens were collected from COPD patients. Bacterial DNA was extracted and used for targeted metagenomics and IS-Pro method. The analysis was performed using QIIME2 (targeted metagenomics) and IS-Pro software (IS-Pro method). Additionally, a laboratory cost per isolate and time analysis was performed for each method.

RESULTS: Statistically significant differences were observed in alpha diversity when targeted metagenomics and IS-Pro methods' data were compared using the Shannon diversity measure (p-value = 0.0006) but not with the Simpson diversity measure (p-value = 0.84). Distinct clusters with no overlap between the two technologies were observed for beta diversity. Targeted metagenomics had a lower relative abundance of phyla, such as the Proteobacteria, and higher relative abundance of phyla, such as Firmicutes when compared to the IS-Pro method. Haemophilus, Prevotella and Streptococcus were most prevalent genera across both methods. Targeted metagenomics classified 23 % (144/631) of OTUs to a species level, whereas IS-Pro method classified 86 % (55/64) of OTUs to a species level. However, unclassified OTUs accounted for a higher relative abundance when using the IS-Pro method (35 %) compared to targeted metagenomics (5 %). The two methods performed comparably in terms of cost and time; however, the IS-Pro method was more user-friendly.

CONCLUSIONS: It is essential to understand the value of different methods for characterisation of the microbiome. Targeted metagenomics and IS-Pro methods showed differences in ability in identifying and characterising OTUs, diversity and microbial composition of the lung microbiome. The IS-Pro method might miss relevant species and could inflate the abundance of Proteobacteria. However, the IS-Pro kit identified most of the important lung pathogens, such as Burkholderia and Pseudomonas and may work in a more diagnostics-orientated setting. Both methods were comparable in terms of cost and time; however, the IS-Pro method was easier to use.}, } @article {pmid34406857, year = {2021}, author = {Taylor, LJ and Dothard, MI and Rubel, MA and Allen, AA and Hwang, Y and Roche, AM and Graham-Wooten, J and Fitzgerald, AS and Khatib, LA and Ranciaro, A and Thompson, SR and Beggs, WR and Campbell, MC and Mokone, GG and Mpoloka, SW and Fokunang, C and Njamnshi, AK and Mbunwe, E and Woldemeskel, D and Belay, G and Nyambo, T and Tishkoff, SA and Collman, RG and Bushman, FD}, title = {Redondovirus Diversity and Evolution on Global, Individual, and Molecular Scales.}, journal = {Journal of virology}, volume = {95}, number = {21}, pages = {e0081721}, pmid = {34406857}, issn = {1098-5514}, support = {T32 AI007532/AI/NIAID NIH HHS/United States ; 9299//Wenner-Gren Foundation (WGF)/ ; R33HL137063-S1//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; P30 AI045008/AI/NIAID NIH HHS/United States ; BCS-1540432//National Science Foundation (NSF)/ ; R33HL137063//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; 1-19-VSN-02//American Diabetes Association/ ; 5T32AI007532-18//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R35 GM134957/GM/NIGMS NIH HHS/United States ; R33 HL137063/HL/NHLBI NIH HHS/United States ; T32AI007324//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R25 GM071745/GM/NIGMS NIH HHS/United States ; T32 AI007324/AI/NIAID NIH HHS/United States ; R25GM071745//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM134957-01//HHS | National Institutes of Health (NIH)/ ; }, mesh = {Africa/epidemiology ; Biodiversity ; Critical Illness ; DNA Virus Infections/epidemiology/*virology ; DNA Viruses/*classification/*genetics/*metabolism ; DNA-Binding Proteins/metabolism ; Evolution, Molecular ; Genome, Viral ; Humans ; Metagenomics ; Mouth/*virology ; Periodontitis/virology ; Phylogeny ; Prevalence ; Respiratory System/*virology ; Rural Population ; Saliva/*virology ; United States/epidemiology ; Viral Proteins/metabolism ; }, abstract = {Redondoviridae is a newly established family of circular Rep-encoding single-stranded (CRESS) DNA viruses found in the human ororespiratory tract. Redondoviruses were previously found in ∼15% of respiratory specimens from U.S. urban subjects; levels were elevated in individuals with periodontitis or critical illness. Here, we report higher redondovirus prevalence in saliva samples: four rural African populations showed 61 to 82% prevalence, and an urban U.S. population showed 32% prevalence. Longitudinal, limiting-dilution single-genome sequencing revealed diverse strains of both redondovirus species (Brisavirus and Vientovirus) in single individuals, persistence over time, and evidence of intergenomic recombination. Computational analysis of viral genomes identified a recombination hot spot associated with a conserved potential DNA stem-loop structure. To assess the possible role of this site in recombination, we carried out in vitro studies which showed that this potential stem-loop was cleaved by the virus-encoded Rep protein. In addition, in reconstructed reactions, a Rep-DNA covalent intermediate was shown to mediate DNA strand transfer at this site. Thus, redondoviruses are highly prevalent in humans, found in individuals on multiple continents, heterogeneous even within individuals and encode a Rep protein implicated in facilitating recombination. IMPORTANCERedondoviridae is a recently established family of DNA viruses predominantly found in the human respiratory tract and associated with multiple clinical conditions. In this study, we found high redondovirus prevalence in saliva from urban North American individuals and nonindustrialized African populations in Botswana, Cameroon, Ethiopia, and Tanzania. Individuals on both continents harbored both known redondovirus species. Global prevalence of both species suggests that redondoviruses have long been associated with humans but have remained undetected until recently due to their divergent genomes. By sequencing single redondovirus genomes in longitudinally sampled humans, we found that redondoviruses persisted over time within subjects and likely evolve by recombination. The Rep protein encoded by redondoviruses catalyzes multiple reactions in vitro, consistent with a role in mediating DNA replication and recombination. In summary, we identify high redondovirus prevalence in humans across multiple continents, longitudinal heterogeneity and persistence, and potential mechanisms of redondovirus evolution by recombination.}, } @article {pmid34406852, year = {2021}, author = {Cifuentes-Anticevic, J and Alcamán-Arias, ME and Alarcón-Schumacher, T and Tamayo-Leiva, J and Pedrós-Alió, C and Farías, L and Díez, B}, title = {Proteorhodopsin Phototrophy in Antarctic Coastal Waters.}, journal = {mSphere}, volume = {6}, number = {4}, pages = {e0052521}, pmid = {34406852}, issn = {2379-5042}, mesh = {Alphaproteobacteria/chemistry/classification/genetics ; Antarctic Regions ; Ecosystem ; Flavobacteriaceae/chemistry/classification/genetics ; Metagenomics/*methods ; Microbiota/*genetics ; *Phototrophic Processes ; Phylogeny ; Rhodopsin/metabolism ; Rhodopsins, Microbial/analysis/*genetics ; Seawater/*microbiology ; }, abstract = {Microbial proton-pumping rhodopsins are considered the simplest strategy among phototrophs to conserve energy from light. Proteorhodopsins are the most studied rhodopsins thus far because of their ubiquitous presence in the ocean, except in Antarctica, where they remain understudied. We analyzed proteorhodopsin abundance and transcriptional activity in the Western Antarctic coastal seawaters. Combining quantitative PCR (qPCR) and metagenomics, the relative abundance of proteorhodopsin-bearing bacteria accounted on average for 17, 3.5, and 29.7% of the bacterial community in Chile Bay (South Shetland Islands) during 2014, 2016, and 2017 summer-autumn, respectively. The abundance of proteorhodopsin-bearing bacteria changed in relation to environmental conditions such as chlorophyll a and temperature. Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia were the main bacteria that transcribed the proteorhodopsin gene during day and night. Although green light-absorbing proteorhodopsin genes were more abundant than blue-absorbing ones, the latter were transcribed more intensely, resulting in >50% of the proteorhodopsin transcripts during the day and night. Flavobacteriia were the most abundant proteorhodopsin-bearing bacteria in the metagenomes; however, Alphaproteobacteria and Gammaproteobacteria were more represented in the metatranscriptomes, with qPCR quantification suggesting the dominance of the active SAR11 clade. Our results show that proteorhodopsin-bearing bacteria are prevalent in Antarctic coastal waters in late austral summer and early autumn, and their ecological relevance needs to be elucidated to better understand how sunlight energy is used in this marine ecosystem. IMPORTANCE Proteorhodopsin-bearing microorganisms in the Southern Ocean have been overlooked since their discovery in 2000. The present study identify taxonomy and quantify the relative abundance of proteorhodopsin-bearing bacteria and proteorhodopsin gene transcription in the West Antarctic Peninsula's coastal waters. This information is crucial to understand better how sunlight enters this marine environment through alternative ways unrelated to chlorophyll-based strategies. The relative abundance of proteorhodopsin-bearing bacteria seems to be related to environmental parameters (e.g., chlorophyll a, temperature) that change yearly at the coastal water of the West Antarctic Peninsula during the austral late summers and early autumns. Proteorhodopsin-bearing bacteria from Antarctic coastal waters are potentially able to exploit both the green and blue spectrum of sunlight and are a prevalent group during the summer in this polar environment.}, } @article {pmid34405262, year = {2021}, author = {Ghosh, S and Pramanik, S}, title = {Structural diversity, functional aspects and future therapeutic applications of human gut microbiome.}, journal = {Archives of microbiology}, volume = {203}, number = {9}, pages = {5281-5308}, pmid = {34405262}, issn = {1432-072X}, support = {BT/PR31826BIC/101/1211/2019//Department of Biotechnology , Ministry of Science and Technology/ ; }, mesh = {*Cyanobacteria ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {The research on human gut microbiome, regarded as the black box of the human body, is still at the stage of infancy as the functional properties of the complex gut microbiome have not yet been understood. Ongoing metagenomic studies have deciphered that the predominant microbial communities belong to eubacterial phyla Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Cyanobacteria, Verrucomicrobia and archaebacterial phylum Euryarchaeota. The indigenous commensal microbial flora prevents opportunistic pathogenic infection and play undeniable roles in digestion, metabolite and signaling molecule production and controlling host's cellular health, immunity and neuropsychiatric behavior. Besides maintaining intestinal health via short-chain fatty acid (SCFA) production, gut microbes also aid in neuro-immuno-endocrine modulatory molecule production, immune cell differentiation and glucose and lipid metabolism. Interdependence of diet and intestinal microbial diversity suggests the effectiveness of pre- and pro-biotics in maintenance of gut and systemic health. Several companies worldwide have started potentially exploiting the microbial contribution to human health and have translated their use in disease management and therapeutic applications. The present review discusses the vast diversity of microorganisms playing intricate roles in human metabolism. The contribution of the intestinal microbiota to regulate systemic activities including gut-brain-immunity crosstalk has been focused. To the best of our knowledge, this review is the first of its kind to collate and discuss the companies worldwide translating the multi-therapeutic potential of human intestinal microbiota, based on the multi-omics studies, i.e. metagenomics and metabolomics, as ready solutions for several metabolic and systemic disorders.}, } @article {pmid34403368, year = {2021}, author = {Haran, JP and Bradley, E and Zeamer, AL and Cincotta, L and Salive, MC and Dutta, P and Mutaawe, S and Anya, O and Meza-Segura, M and Moormann, AM and Ward, DV and McCormick, BA and Bucci, V}, title = {Inflammation-type dysbiosis of the oral microbiome associates with the duration of COVID-19 symptoms and long COVID.}, journal = {JCI insight}, volume = {6}, number = {20}, pages = {}, pmid = {34403368}, issn = {2379-3708}, support = {RF1 AG067483/AG/NIA NIH HHS/United States ; }, mesh = {Aged ; Bacteria/classification ; COVID-19/*complications ; *Dysbiosis ; Female ; Gastrointestinal Microbiome ; Humans ; *Inflammation ; Male ; *Microbiota ; Middle Aged ; SARS-CoV-2 ; Post-Acute COVID-19 Syndrome ; }, abstract = {In the COVID-19 pandemic, caused by SARS-CoV-2, many individuals experience prolonged symptoms, termed long-lasting COVID-19 symptoms (long COVID). Long COVID is thought to be linked to immune dysregulation due to harmful inflammation, with the exact causes being unknown. Given the role of the microbiome in mediating inflammation, we aimed to examine the relationship between the oral microbiome and the duration of long COVID symptoms. Tongue swabs were collected from patients presenting with COVID-19 symptoms. Confirmed infections were followed until resolution of all symptoms. Bacterial composition was determined by metagenomic sequencing. We used random forest modeling to identify microbiota and clinical covariates that are associated with long COVID symptoms. Of the patients followed, 63% developed ongoing symptomatic COVID-19 and 37% went on to long COVID. Patients with prolonged symptoms had significantly higher abundances of microbiota that induced inflammation, such as members of the genera Prevotella and Veillonella, which, of note, are species that produce LPS. The oral microbiome of patients with long COVID was similar to that of patients with chronic fatigue syndrome. Altogether, our findings suggest an association with the oral microbiome and long COVID, revealing the possibility that dysfunction of the oral microbiome may have contributed to this draining disease.}, } @article {pmid34402617, year = {2021}, author = {Esvap, E and Ulgen, KO}, title = {Advances in Genome-Scale Metabolic Modeling toward Microbial Community Analysis of the Human Microbiome.}, journal = {ACS synthetic biology}, volume = {10}, number = {9}, pages = {2121-2137}, doi = {10.1021/acssynbio.1c00140}, pmid = {34402617}, issn = {2161-5063}, mesh = {Gastrointestinal Microbiome ; *Genomics ; Humans ; Inflammatory Bowel Diseases/microbiology/pathology ; Machine Learning ; Metabolic Networks and Pathways/genetics ; Microbiota/*genetics/physiology ; Models, Biological ; Parkinson Disease/microbiology/pathology ; Precision Medicine ; }, abstract = {A genome-scale metabolic model (GEM) represents metabolic pathways of an organism in a mathematical form and can be built using biochemistry and genome annotation data. GEMs are invaluable for understanding organisms since they analyze the metabolic capabilities and behaviors quantitatively and can predict phenotypes. The development of high-throughput data collection techniques led to an immense increase in omics data such as metagenomics, which expand our knowledge on the human microbiome, but this also created a need for systematic analysis of these data. In recent years, GEMs have also been reconstructed for microbial species, including human gut microbiota, and methods for the analysis of microbial communities have been developed to examine the interaction between the organisms or the host. The purpose of this review is to provide a comprehensive guide for the applications of GEMs in microbial community analysis. Starting with GEM repositories, automatic GEM reconstruction tools, and quality control of models, this review will give insights into microbe-microbe and microbe-host interaction predictions and optimization of microbial community models. Recent studies that utilize microbial GEMs and personalized models to infer the influence of microbiota on human diseases such as inflammatory bowel diseases (IBD) or Parkinson's disease are exemplified. Being powerful system biology tools for both species-level and community-level analysis of microbes, GEMs integrated with omics data and machine learning techniques will be indispensable for studying the microbiome and their effects on human physiology as well as for deciphering the mechanisms behind human diseases.}, } @article {pmid34400165, year = {2022}, author = {Peña-Ocaña, BA and Ovando-Ovando, CI and Puente-Sánchez, F and Tamames, J and Servín-Garcidueñas, LE and González-Toril, E and Gutiérrez-Sarmiento, W and Jasso-Chávez, R and Ruíz-Valdiviezo, VM}, title = {Metagenomic and metabolic analyses of poly-extreme microbiome from an active crater volcano lake.}, journal = {Environmental research}, volume = {203}, number = {}, pages = {111862}, doi = {10.1016/j.envres.2021.111862}, pmid = {34400165}, issn = {1096-0953}, mesh = {Archaea/genetics ; Lakes ; Metagenome ; *Metagenomics ; *Microbiota ; Phylogeny ; }, abstract = {El Chichón volcano is one of the most active volcanoes in Mexico. Previous studies have described its poly-extreme conditions and its bacterial composition, although the functional features of the complete microbiome have not been characterized yet. By using metabarcoding analysis, metagenomics, metabolomics and enzymology techniques, the microbiome of the crater lake was characterized in this study. New information is provided on the taxonomic and functional diversity of the representative Archaea phyla, Crenarchaeota and Euryarchaeota, as well as those that are representative of Bacteria, Thermotogales and Aquificae. With culture of microbial consortia and with the genetic information collected from the natural environment sampling, metabolic interactions were identified between prokaryotes, which can withstand multiple extreme conditions. The existence of a close relationship between the biogeochemical cycles of carbon and sulfur in an active volcano has been proposed, while the relationship in the energy metabolism of thermoacidophilic bacteria and archaea in this multi-extreme environment was biochemically revealed for the first time. These findings contribute towards understanding microbial metabolism under extreme conditions, and provide potential knowledge pertaining to "microbial dark matter", which can be applied to biotechnological processes and evolutionary studies.}, } @article {pmid34400128, year = {2021}, author = {Yatera, K and Noguchi, S and Mukae, H}, title = {Perspective on the clone library method for infectious diseases.}, journal = {Respiratory investigation}, volume = {59}, number = {6}, pages = {741-747}, doi = {10.1016/j.resinv.2021.07.003}, pmid = {34400128}, issn = {2212-5353}, mesh = {Child ; Clone Cells ; *Communicable Diseases ; Female ; Humans ; *Microbiota ; Middle Aged ; *Pneumonia, Bacterial ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recently, culture-independent molecular methods, such as DNA sequencing techniques targeting the 16S-ribosomal RNA (rRNA) gene and/or other housekeeping genes with Sanger method-based technologies, next generation sequencing (NGS), and metagenomic analysis, have been developed for detecting microorganisms in the human body; these can provide information on microbiomes of samples from individuals with or without infectious diseases. Determining the bacterial species is crucial in identifying causative bacteria of upper and lower respiratory tract infections, especially for Streptococcus species, but NGS analysis is often not precise enough to identify bacteria at the species level. This review briefly introduces previous observations of the microbiome of samples from various respiratory and other infections assessed using the clone library method with Sanger sequencing of the 16S-rRNA gene. On analysis of 16S-rRNA gene-sequence data of bronchoalveolar lavage fluid obtained from pneumonia lesions in patients with bacterial pneumonia and lung abscess, anaerobes are often detected in non-elderly patients with pneumonia, and the detection rate of Staphylococcus aureus in patients with hospital-acquired pneumonia is lower than that previously reported. Analysis of pleural effusion samples from patients with pleurisy indicated a more important role of anaerobes than previous believed. The other topics reviewed include microbiomes of nontuberculous mycobacteriosis and lower respiratory tract infections in children with permanent tracheostomy due to neuromuscular disorders, in nasal discharge, in bacterial vaginosis, in the intracystic fluid of postoperative maxillary cyst, and in bacterial conjunctivitis; urine microbiota in urethritis; fecal microbiota; and newly detected infectious organisms in the human respiratory tract.}, } @article {pmid34399890, year = {2021}, author = {Ramírez-Acosta, S and Arias-Borrego, A and Navarro-Roldán, F and Selma-Royo, M and Calatayud, M and Collado, MC and Huertas-Abril, PV and Abril, N and Barrera, TG}, title = {Omic methodologies for assessing metal(-loid)s-host-microbiota interplay: A review.}, journal = {Analytica chimica acta}, volume = {1176}, number = {}, pages = {338620}, doi = {10.1016/j.aca.2021.338620}, pmid = {34399890}, issn = {1873-4324}, mesh = {Mass Spectrometry ; Metabolomics ; Metals ; *Microbiota ; Proteomics ; }, abstract = {Omic methodologies have become key analytical tools in a wide number of research topics such as systems biology, environmental analysis, biomedicine or food analysis. They are especially useful when they are combined providing a new perspective and a holistic view of the analytical problem. Methodologies for microbiota analysis have been mostly focused on genome sequencing. However, information provided by these metagenomic studies is limited to the identification of the presence of genes, taxa and their inferred functionality. To achieve a deeper knowledge of microbial functionality in health and disease, especially in dysbiosis conditions related to metal and metalloid exposure, the introduction of additional meta-omic approaches including metabolomics, metallomics, metatranscriptomics and metaproteomics results essential. The possible impact of metals and metalloids on the gut microbiota and their effects on gut-brain axis (GBA) only begin to be figured out. To this end new analytical workflows combining powerful tools are claimed such as high resolution mass spectrometry and heteroatom-tagged proteomics for the absolute quantification of metal-containing biomolecules using the metal as a "tag" in a sensitive and selective detector (e.g. ICP-MS). This review focus on current analytical methodologies related with the analytical techniques and procedures available for metallomics and microbiota analysis with a special attention on their advantages and drawbacks.}, } @article {pmid34394092, year = {2021}, author = {Doaré, E and Héry-Arnaud, G and Devauchelle-Pensec, V and Alegria, GC}, title = {Healthy Patients Are Not the Best Controls for Microbiome-Based Clinical Studies: Example of Sjögren's Syndrome in a Systematic Review.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {699011}, pmid = {34394092}, issn = {1664-3224}, mesh = {*Control Groups ; *Dysbiosis ; Humans ; *Microbiota ; *Sjogren's Syndrome ; }, abstract = {INTRODUCTION: It has been hypothesized that gut and oral dysbiosis may contribute to the development of primary Sjögren's syndrome (pSS). The aim of this systematic review was to assemble available data regarding the oral and gut microbiota in pSS and to compare them to data from healthy individuals and patients with dry symptoms without a diagnosis of Sjögren's syndrome or lupus disease to identify dysbiosis and discuss the results.

METHODOLOGY: Using the PRISMA guidelines, we systematically reviewed studies that compared the oral and gut microbiota of Sjögren's patients and controls. The PubMed database and Google Scholar were searched.

RESULTS: Two-hundred and eighty-nine studies were found, and 18 studies were included: 13 referred to the oral microbiota, 4 referred to the gut microbiota, and 1 referred to both anatomical sites. The most frequent controls were healthy volunteers and patients with sicca symptoms. The most common analysis method used was 16S-targeted metagenomics. The results were mostly heterogeneous, and the results regarding diversity were not always in accordance. Dysbiosis in pSS was not confirmed, and reduced salivary secretion seems to explain more microbial changes than the underlying disease.

CONCLUSION: These heterogeneous results might be explained by the lack of a standardized methodology at each step of the process and highlight the need for guidelines. Our review provides evidence that sicca patients seem to be more relevant than healthy subjects as a control group.}, } @article {pmid34393020, year = {2021}, author = {Robertson, RC and Church, JA and Edens, TJ and Mutasa, K and Min Geum, H and Baharmand, I and Gill, SK and Ntozini, R and Chasekwa, B and Carr, L and Majo, FD and Kirkpatrick, BD and Lee, B and Moulton, LH and Humphrey, JH and Prendergast, AJ and Manges, AR and , }, title = {The fecal microbiome and rotavirus vaccine immunogenicity in rural Zimbabwean infants.}, journal = {Vaccine}, volume = {39}, number = {38}, pages = {5391-5400}, pmid = {34393020}, issn = {1873-2518}, support = {093768/Z/10/Z/WT_/Wellcome Trust/United Kingdom ; 108065/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; P20 GM125498/GM/NIGMS NIH HHS/United States ; 203905/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; R01 HD060338/HD/NICHD NIH HHS/United States ; 206455/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Antibodies, Viral ; *Gastrointestinal Microbiome ; Humans ; Immunogenicity, Vaccine ; Immunoglobulin A ; Infant ; *Rotavirus/genetics ; *Rotavirus Infections/prevention & control ; *Rotavirus Vaccines ; }, abstract = {BACKGROUND: Oral rotavirus vaccine (RVV) immunogenicity is considerably lower in low- versus high-income populations; however, the mechanisms underlying this remain unclear. Previous evidence suggests that the gut microbiota may contribute to differences in oral vaccine efficacy.

METHODS: We performed whole metagenome shotgun sequencing on stool samples and measured anti-rotavirus immunoglobulin A in plasma samples from a subset of infants enrolled in a cluster randomized 2 × 2 factorial trial of improved water, sanitation and hygiene and infant feeding in rural Zimbabwe (SHINE trial: NCT01824940). We examined taxonomic microbiome composition and functional metagenome features using random forest models, differential abundance testing and regression analyses to explored associations with RVV immunogenicity.

RESULTS: Among 158 infants with stool samples and anti-rotavirus IgA titres, 34 were RVV seroconverters. The median age at stool collection was 43 days (IQR: 35-68), corresponding to a median of 4 days before the first RVV dose. The infant microbiome was dominated by Bifidobacterium longum. The gut microbiome differed significantly between early (≤42 days) and later samples (>42 days) however, we observed no meaningful differences in alpha diversity, beta diversity, species composition or functional metagenomic features by RVV seroconversion status. Bacteroides thetaiotaomicron was the only species associated with anti-rotavirus IgA titre. Random forest models poorly classified seroconversion status by both composition and functional microbiome variables.

CONCLUSIONS: RVV immunogenicity is low in this rural Zimbabwean setting, however it was not associated with the composition or function of the early-life gut microbiome in this study. Further research is warranted to examine the mechanisms of poor oral RVV efficacy in low-income countries.}, } @article {pmid34391676, year = {2021}, author = {Chen, C and Hao, L and Zhang, Z and Tian, L and Zhang, X and Zhu, J and Jie, Z and Tong, X and Xiao, L and Zhang, T and Jin, X and Xu, X and Yang, H and Wang, J and Kristiansen, K and Jia, H}, title = {Cervicovaginal microbiome dynamics after taking oral probiotics.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {48}, number = {8}, pages = {716-726}, doi = {10.1016/j.jgg.2021.03.019}, pmid = {34391676}, issn = {1673-8527}, mesh = {Humans ; Female ; *Probiotics/administration & dosage ; *Vagina/microbiology ; *Microbiota/genetics/drug effects ; Adult ; Dysbiosis/microbiology/therapy ; Administration, Oral ; Cervix Uteri/microbiology ; Middle Aged ; }, abstract = {The vaginal microbiota is less complex than the gut microbiota, and the colonization of Lactobacillus in the female vagina is considered to be critical for reproductive health. Oral probiotics have been suggested as promising means to modulate vaginal homeostasis in the general population. In this study, 60 Chinese women were followed for over a year before, during, and after treatment with the probiotics Lactobacillus rhamnosus GR-1 and Lactobacillusreuteri RC-14. Shotgun metagenomic data of 1334 samples from multiple body sites did not support a colonization route of the probiotics from the oral cavity to the intestinal tract and then to the vagina. Our analyses enable the classification of the cervicovaginal microbiome into a stable state and a state of dysbiosis. The microbiome in the stable group steadily maintained a relatively high abundance of Lactobacilli over one year, which was not affected by probiotic intake, whereas in the dysbiosis group, the microbiota was more diverse and changed markedly over time. Data from a subset of the dysbiosis group suggests this subgroup possibly benefited from supplementation with the probiotics, indicating that probiotics supplementation can be prescribed for women in a subclinical microbiome setting of dysbiosis, providing opportunities for targeted and personalized microbiome reconstitution.}, } @article {pmid34389059, year = {2021}, author = {Boeuf, D and Eppley, JM and Mende, DR and Malmstrom, RR and Woyke, T and DeLong, EF}, title = {Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {172}, pmid = {34389059}, issn = {2049-2618}, mesh = {Bacteria/genetics ; *Microbiota ; Oceans and Seas ; Phylogeny ; *Seawater ; }, abstract = {BACKGROUND: Oceanic microbiomes play a pivotal role in the global carbon cycle and are central to the transformation and recycling of carbon and energy in the ocean's interior. SAR324 is a ubiquitous but poorly understood uncultivated clade of Deltaproteobacteria that inhabits the entire water column, from ocean surface waters to its deep interior. Although some progress has been made in elucidating potential metabolic traits of SAR324 in the dark ocean, very little is known about the ecology and the metabolic capabilities of this group in the euphotic and twilight zones. To investigate the comparative genomics, ecology, and physiological potential of the SAR324 clade, we examined the distribution and variability of key genomic features and metabolic pathways in this group from surface waters to the abyss in the North Pacific Subtropical Gyre, one of the largest biomes on Earth.

RESULTS: We leveraged a pangenomic ecological approach, combining spatio-temporally resolved single-amplified genome, metagenomic, and metatranscriptomic datasets. The data revealed substantial genomic diversity throughout the SAR324 clade, with distinct depth and temporal distributions that clearly differentiated ecotypes. Phylogenomic subclade delineation, environmental distributions, genomic feature similarities, and metabolic capacities revealed strong congruence. The four SAR324 ecotypes delineated in this study revealed striking divergence from one another with respect to their habitat-specific metabolic potentials. The ecotypes living in the dark or twilight oceans shared genomic features and metabolic capabilities consistent with a sulfur-based chemolithoautotrophic lifestyle. In contrast, those inhabiting the sunlit ocean displayed higher plasticity energy-related metabolic pathways, supporting a presumptive photoheterotrophic lifestyle. In epipelagic SAR324 ecotypes, we observed the presence of two types of proton-pumping rhodopsins, as well as genomic, transcriptomic, and ecological evidence for active photoheterotrophy, based on xanthorhodopsin-like light-harvesting proteins.

CONCLUSIONS: Combining pangenomic and both metagenomic and metatranscriptomic profiling revealed a striking divergence in the vertical distribution, genomic composition, metabolic potential, and predicted lifestyle strategies of geographically co-located members of the SAR324 bacterial clade. The results highlight the utility of metapangenomic approaches employed across environmental gradients, to decipher the properties and variation in function and ecological traits of specific phylogenetic clades within complex microbiomes. Video abstract.}, } @article {pmid34389047, year = {2021}, author = {Xiong, C and Singh, BK and He, JZ and Han, YL and Li, PP and Wan, LH and Meng, GZ and Liu, SY and Wang, JT and Wu, CF and Ge, AH and Zhang, LM}, title = {Plant developmental stage drives the differentiation in ecological role of the maize microbiome.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {171}, pmid = {34389047}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Fungi/genetics ; *Microbiota/genetics ; Plant Roots ; *Zea mays ; }, abstract = {BACKGROUND: Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how host development impacts the assembly, functions and microbial interactions of crop microbiomes are poorly understood. Here we examined both bacterial and fungal communities across soils, epiphytic and endophytic niches of leaf and root, and plastic leaf of fake plant (representing environment-originating microbes) at three developmental stages of maize at two contrasting sites, and further explored the potential function of phylloplane microbiomes based on metagenomics.

RESULTS: Our results suggested that plant developmental stage had a much stronger influence on the microbial diversity, composition and interkingdom networks in plant compartments than in soils, with the strongest effect in the phylloplane. Phylloplane microbiomes were co-shaped by both plant growth and seasonal environmental factors, with the air (represented by fake plants) as its important source. Further, we found that bacterial communities in plant compartments were more strongly driven by deterministic processes at the early stage but a similar pattern was for fungal communities at the late stage. Moreover, bacterial taxa played a more important role in microbial interkingdom network and crop yield prediction at the early stage, while fungal taxa did so at the late stage. Metagenomic analyses further indicated that phylloplane microbiomes possessed higher functional diversity at the early stage than the late stage, with functional genes related to nutrient provision enriched at the early stage and N assimilation and C degradation enriched at the late stage. Coincidently, more abundant beneficial bacterial taxa like Actinobacteria, Burkholderiaceae and Rhizobiaceae in plant microbiomes were observed at the early stage, but more saprophytic fungi at the late stage.

CONCLUSIONS: Our results suggest that host developmental stage profoundly influences plant microbiome assembly and functions, and the bacterial and fungal microbiomes take a differentiated ecological role at different stages of plant development. This study provides empirical evidence for host exerting strong effect on plant microbiomes by deterministic selection during plant growth and development. These findings have implications for the development of future tools to manipulate microbiome for sustainable increase in primary productivity. Video Abstract.}, } @article {pmid34387940, year = {2021}, author = {Ruscheweyh, HJ and Milanese, A and Paoli, L and Sintsova, A and Mende, DR and Zeller, G and Sunagawa, S}, title = {mOTUs: Profiling Taxonomic Composition, Transcriptional Activity and Strain Populations of Microbial Communities.}, journal = {Current protocols}, volume = {1}, number = {8}, pages = {e218}, doi = {10.1002/cpz1.218}, pmid = {34387940}, issn = {2691-1299}, mesh = {Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Phylogeny ; Software ; }, abstract = {The mOTU profiler, or mOTUs for short, is a software tool that enables the profiling of microbial communities in terms of their taxonomic composition, relative abundance of metabolically active members, and diversity of strain populations. To this end, it maintains a database of single-copy phylogenetic marker gene sequences, which are used as a reference to which short read metagenomic and metatranscriptomic reads are mapped for the identification and quantification of microbial taxa. Here, we describe the most common use cases of the mOTU profiler in two basic protocols. Additional supporting protocols provide information on its installation and in-depth guidance on adjusting its settings for increasing or decreasing the stringency with which taxa are detected and quantified, as well as for customizing the output file format. Guidelines for understanding the profiling results are provided, along with additional information on unique features, methodological details, and the development history of the tool. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Metagenomic and metatranscriptomic mOTU profiling Basic Protocol 2: Metagenomic SNV profiling Support Protocol 1: Installing mOTUs Support Protocol 2: Profiling pipeline-step by step Support Protocol 3: The mOTUs profiling routine using advanced parameters Support Protocol 4: Metagenomic SNV calling: advanced parameters.}, } @article {pmid34387344, year = {2021}, author = {Moura, JB and Delforno, TP and do Prado, PF and Duarte, IC}, title = {Extremophilic taxa predominate in a microbial community of photovoltaic panels in a tropical region.}, journal = {FEMS microbiology letters}, volume = {368}, number = {16}, pages = {}, doi = {10.1093/femsle/fnab105}, pmid = {34387344}, issn = {1574-6968}, mesh = {Construction Materials/microbiology ; *Cyanobacteria/genetics ; *Extremophiles/classification/genetics ; Metagenome ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Solar Energy ; Tropical Climate ; }, abstract = {Photovoltaic panels can be colonized by a highly diverse microbial diversity, despite life-threatening conditions. Although they are distributed worldwide, the microorganisms living on their surfaces have never been profiled in tropical regions using 16S rRNA high-throughput sequencing and PICRUst metagenome prediction of functional content. In this work, we investigated photovoltaic panels from two cities in southeast Brazil, Sorocaba and Itatiba, using these bioinformatics approach. Results showed that, despite significant differences in microbial diversity (p < 0.001), the taxonomic profile was very similar for both photovoltaic panels, dominated mainly by Proteobacteria, Bacteroidota and lower amounts of Cyanobacteria phyla. A predominance of Hymenobacter and Methylobacterium-Methylorubrum was observed at the genus level. We identified a microbial common core composed of Hymenobacter, Deinococcus, Sphingomonas, Methylobacterium-Methylorubrum, Craurococcus-Caldovatus, Massilia, Noviherbaspirillum and 1174-901-12 sharing genera. Predicted metabolisms focused on specific genes associated to radiation and desiccation resistance and pigments, were detected in members of the common core and among the most abundant genera. Our results suggested that taxonomic and functional profiles investigated were consistent with the harsh environment that photovoltaic panels represent. Moreover, the presence of stress genes in the predicted functional content was a preliminary evidence that microbes living there are a possibly source of metabolites with biotechnological interest.}, } @article {pmid34387003, year = {2021}, author = {Yang, S and Liebner, S and Svenning, MM and Tveit, AT}, title = {Decoupling of microbial community dynamics and functions in Arctic peat soil exposed to short term warming.}, journal = {Molecular ecology}, volume = {30}, number = {20}, pages = {5094-5104}, doi = {10.1111/mec.16118}, pmid = {34387003}, issn = {1365-294X}, mesh = {Arctic Regions ; Carbon Dioxide/analysis ; Methane ; *Microbiota/genetics ; *Soil ; Soil Microbiology ; Temperature ; }, abstract = {Temperature is an important factor governing microbe-mediated carbon feedback from permafrost soils. The link between taxonomic and functional microbial responses to temperature change remains elusive due to the lack of studies assessing both aspects of microbial ecology. Our previous study reported microbial metabolic and trophic shifts in response to short-term temperature increases in Arctic peat soil, and linked these shifts to higher CH4 and CO2 production rates (Proceedings of the National Academy of Sciences of the United States of America, 112, E2507-E2516). Here, we studied the taxonomic composition and functional potential of samples from the same experiment. We see that along a high-resolution temperature gradient (1-30°C), microbial communities change discretely, but not continuously or stochastically, in response to rising temperatures. The taxonomic variability may thus in part reflect the varied temperature responses of individual taxa and the competition between these taxa for resources. These taxonomic responses contrast the stable functional potential (metagenomic-based) across all temperatures or the previously observed metabolic or trophic shifts at key temperatures. Furthermore, with rising temperatures we observed a progressive decrease in species diversity (Shannon Index) and increased dispersion of greenhouse gas (GHG) production rates. We conclude that the taxonomic variation is decoupled from both the functional potential of the community and the previously observed temperature-dependent changes in microbial function. However, the reduced diversity at higher temperatures might help explain the higher variability in GHG production at higher temperatures.}, } @article {pmid34385112, year = {2021}, author = {Puthusseri, RM and Nair, HP and Johny, TK and Bhat, SG}, title = {Insights into the response of mangrove sediment microbiomes to heavy metal pollution: Ecological risk assessment and metagenomics perspectives.}, journal = {Journal of environmental management}, volume = {298}, number = {}, pages = {113492}, doi = {10.1016/j.jenvman.2021.113492}, pmid = {34385112}, issn = {1095-8630}, mesh = {Environmental Monitoring ; Geologic Sediments ; Metagenomics ; *Metals, Heavy/analysis ; *Microbiota/genetics ; Risk Assessment ; *Water Pollutants, Chemical/analysis ; Wetlands ; }, abstract = {Rapid urbanisation and ensuing anthropogenic pollution lead to an escalated occurrence of heavy metals and metal-resistant bacteria in the soil ecosystem. Mangrove ecosystems are particularly vulnerable to heavy metal bioaccumulation and often act as metal sinks of the coastal areas. As a consequence, the microbial population in mangrove sediments develop multifarious metal tolerance mechanisms to combat metal toxicity. In this context, metagenomic investigation of two mangroves, viz. Mangalavanam and Puthuvypin from the heavily populated metropolitan city, Cochin (Central Kerala, India) was undertaken to discern the metal resistance functions and taxonomic diversity of the microbial consortia. Estimation of heavy metal content using Inductively Coupled Plasma Atomic Emission Spectrometer (ICP-MS) identified the abundance of zinc, chromium, nickel copper, lead, arsenic, and cadmium in the mangrove sediments. Ecological risk index values indicated high cadmium contamination of the two estuarine samples. Whole metagenome shotgun sequencing of the Central Kerala mangroves and comparative analysis with mangrove metal resistomes from other geographical regions revealed the prevalence of cobalt-zinc-cadmium resistance and preponderance of Proteobacteria in all the datasets. Cation efflux system protein CusA constituted the majority of the reads at the function level. Comparative analysis of taxonomy identified the dominance of Anaeromyxobacter, Geobacter, Pseudomonas, Candidatus Solibacter, and Pelobacter in the mangrove datasets. Non-metric multidimensional scaling analysis of the metal resistance genes depicted strong geographical clustering of the function and composition of metal resistant bacteria, suggesting a strong innate resilience of microbiome towards anthropogenic perturbations. More robust studies with intensive sampling will enhance our understanding of the occurrence, interactions, and functions of microbial heavy metal resistome in mangrove ecosystems.}, } @article {pmid34384948, year = {2021}, author = {Li, W and Gao, J and Zhuang, JL and Yao, GJ and Zhang, X and Liu, YD and Liu, QK and Shapleigh, JP and Ma, L}, title = {Metagenomics and metatranscriptomics uncover the microbial community associated with high S[0] production in a denitrifying desulfurization granular sludge reactor.}, journal = {Water research}, volume = {203}, number = {}, pages = {117505}, doi = {10.1016/j.watres.2021.117505}, pmid = {34384948}, issn = {1879-2448}, mesh = {Bioreactors ; Denitrification ; Metagenomics ; *Microbiota ; Nitrates ; Oxidation-Reduction ; *Sewage ; Sulfides ; }, abstract = {The denitrification desulfurization process is a promising technology for elemental sulfur (S[0]) production from sulfide containing wastewater. However, the microbial community associated with high S[0] production still is not well studied. This study describes an efficient denitrification S[0] production bioreactor based on inoculation with anaerobic granular sludge. At an optimal S/N molar ratio of 7:2, 80 % of the influent sulfide was transformed to high quality elemental sulfur with a purity of 92.5% while the total inorganic nitrogen removal efficiency was stable at ∼80%. Metatranscriptomic analysis found that community expression of the gene encoding the sulfide-quinone reductase (SQR) was 10-fold greater than that of the flavocytochrome-c sulfide dehydrogenase subunit B (fccB). Moreover, the expression level of SQR was also significantly higher than the Dsr gene encoding for dissimilatory sulfate reductase, which encodes a critical S[0] oxidation enzyme. Metagenomic binning analysis confirmed that sulfide-oxidizing bacteria (SOB) utilizing SQR were common in the community and most likely accounted for high S[0] production. An unexpected enrichment in methanogens and high expression activity of bacteria carrying out Stickland fermentation as well as in other bacteria with reduced genomes indicated a complex community supporting stable sulfide oxidation to S[0], likely aiding in performance stability. This study establishes this treatment approach as an alternative biotechnology for sulfide containing wastewater treatment and sheds light on the microbial interactions associated with high S[0] production.}, } @article {pmid34381207, year = {2021}, author = {Fremin, BJ and Nicolaou, C and Bhatt, AS}, title = {Simultaneous ribosome profiling of hundreds of microbes from the human microbiome.}, journal = {Nature protocols}, volume = {16}, number = {10}, pages = {4676-4691}, pmid = {34381207}, issn = {1750-2799}, support = {R01 AI148623/AI/NIAID NIH HHS/United States ; U24 AG021886/AG/NIA NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; P50 AG047366/AG/NIA NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; P30 AG047366//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P30 AG066515/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; *Ribosomes/metabolism/genetics ; *Feces/microbiology ; *Microbiota/genetics ; Metagenomics/methods ; Metagenome ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing/methods ; Gastrointestinal Microbiome/genetics ; Ribosome Profiling ; }, abstract = {Ribosome profiling enables sequencing of ribosome-bound fragments of RNA, revealing which transcripts are being translated as well as the position of ribosomes along mRNAs. Although ribosome profiling has been applied to cultured bacterial isolates, its application to uncultured, mixed communities has been challenging. We present MetaRibo-Seq, a protocol that enables the application of ribosome profiling directly to the human fecal microbiome. MetaRibo-Seq is a benchmarked method that includes several modifications to existing ribosome profiling protocols, specifically addressing challenges involving fecal sample storage, purity and input requirements. We also provide a computational workflow to quality control and trim reads, de novo assemble a reference metagenome with metagenomic reads, align MetaRibo-Seq reads to the reference, and assess MetaRibo-Seq library quality (https://github.com/bhattlab/bhattlab_workflows/tree/master/metariboseq). This MetaRibo-Seq protocol enables researchers in standard molecular biology laboratories to study translation in the fecal microbiome in ~5 d.}, } @article {pmid34381036, year = {2021}, author = {Stražar, M and Temba, GS and Vlamakis, H and Kullaya, VI and Lyamuya, F and Mmbaga, BT and Joosten, LAB and van der Ven, AJAM and Netea, MG and de Mast, Q and Xavier, RJ}, title = {Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {4845}, pmid = {34381036}, issn = {2041-1723}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Arginine/metabolism ; Bacteria/immunology/isolation & purification/metabolism ; Cytokines/*immunology ; Diet ; Female ; Gastrointestinal Microbiome/immunology/*physiology ; Histidine/metabolism ; Humans ; Immunomodulation ; Male ; Metabolic Networks and Pathways ; Metabolome/immunology ; *Rural Population ; Socioeconomic Factors ; Tanzania ; *Urban Population ; Urbanization ; }, abstract = {The human gut microbiota is increasingly recognized as an important factor in modulating innate and adaptive immunity through release of ligands and metabolites that translocate into circulation. Urbanizing African populations harbor large intestinal diversity due to a range of lifestyles, providing the necessary variation to gauge immunomodulatory factors. Here, we uncover a gradient of intestinal microbial compositions from rural through urban Tanzanian, towards European samples, manifested both in relative abundance and genomic variation observed in stool metagenomics. The rural population shows increased Bacteroidetes, led by Prevotella copri, but also presence of fungi. Measured ex vivo cytokine responses were significantly associated with 34 immunomodulatory microbes, which have a larger impact on circulating metabolites than non-significant microbes. Pathway effects on cytokines, notably TNF-α and IFN-γ, differential metabolome analysis and enzyme copy number enrichment converge on histidine and arginine metabolism as potential immunomodulatory pathways mediated by Bifidobacterium longum and Akkermansia muciniphila.}, } @article {pmid34380552, year = {2021}, author = {Wicaksono, WA and Cernava, T and Berg, C and Berg, G}, title = {Bog ecosystems as a playground for plant-microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {170}, pmid = {34380552}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Bryophyta/microbiology ; *Microbiota/genetics ; Phylogeny ; *Sphagnopsida/microbiology ; *Wetlands ; }, abstract = {BACKGROUND: Bogs are unique ecosystems inhabited by distinctive, coevolved assemblages of organisms, which play a global role for carbon storage, climate stability, water quality and biodiversity. To understand ecology and plant-microbe co-occurrence in bogs, we selected 12 representative species of bryophytes and vascular plants and subjected them to a shotgun metagenomic sequencing approach. We explored specific plant-microbe associations as well as functional implications of the respective communities on their host plants and the bog ecosystem.

RESULTS: Microbial communities were shown to be functionally adapted to their plant hosts; a higher colonization specificity was found for vascular plants. Bryophytes that commonly constitute the predominant Sphagnum layer in bogs were characterized by a higher bacterial richness and diversity. Each plant group showed an enrichment of distinct phylogenetic and functional bacterial lineages. Detailed analyses of the metabolic potential of 28 metagenome-assembled genomes (MAGs) supported the observed functional specification of prevalent bacteria. We found that novel lineages of Betaproteobacteria and Actinobacteria in the bog environment harboured genes required for carbon fixation via RuBisCo. Interestingly, several of the highly abundant bacteria in both plant types harboured pathogenicity potential and carried similar virulence factors as found with corresponding human pathogens.

CONCLUSIONS: The unexpectedly high specificity of the plant microbiota reflects intimate plant-microbe interactions and coevolution in bog environments. We assume that the detected pathogenicity factors might be involved in coevolution processes, but the finding also reinforces the role of the natural plant microbiota as a potential reservoir for human pathogens. Overall, the study demonstrates how plant-microbe assemblages can ensure stability, functioning and ecosystem health in bogs. It also highlights the role of bog ecosystems as a playground for plant-microbe coevolution. Video abstract.}, } @article {pmid34380279, year = {2021}, author = {Liang, H and Wang, F and Mu, R and Huang, J and Zhao, R and Li, X and Yu, K and Li, B}, title = {Metagenomics analysis revealing the occurrence of antibiotic resistome in salt lakes.}, journal = {The Science of the total environment}, volume = {790}, number = {}, pages = {148262}, doi = {10.1016/j.scitotenv.2021.148262}, pmid = {34380279}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Lakes ; *Metagenomics ; *Microbiota ; }, abstract = {Although antimicrobial resistance genes (ARGs) in dozens of environments have been well documented, the distribution of ARGs in salt lake ecosystems has been less intensively investigated. In this study, the broad-spectrum ARG profiles, microbial community composition and the comprehensive associations between microbiome and antimicrobial resistome in four salt lakes were investigated using a metagenomic approach. A total of 175 ARG subtypes affiliated with 19 ARG types were detected, and ARGs conferring resistance to multidrug, bacitracin, and macrolide-lincosamide-streptogramin (MLS) accounted for 71.2% of the total ARG abundance. However, the abundance of ARGs significantly decreased with the increasing salinity in the lakes. Both ARG profiles and microbial community structure presented remarkable discrepancies in different lakes, as well as in different sample types. Microbes such as genera Azoarcus, Aeromonas, Pseudomonas, and Kocuria, significantly co-occurred with multiple ARGs, indicating that these bacteria are potential ARG hosts in salt lake ecosystems. Collectively, this work provides new insights into the occurrence and distribution of ARGs in salt lake ecosystems.}, } @article {pmid34380135, year = {2021}, author = {Corralo, DJ and Ev, LD and Damé-Teixeira, N and Maltz, M and Arthur, RA and Do, T and Fatturi Parolo, CC}, title = {Functionally Active Microbiome in Supragingival Biofilms in Health and Caries.}, journal = {Caries research}, volume = {55}, number = {6}, pages = {603-616}, doi = {10.1159/000518963}, pmid = {34380135}, issn = {1421-976X}, mesh = {Adolescent ; Adult ; Aged ; Biofilms ; *Dental Caries ; Dental Caries Susceptibility ; Humans ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S ; Young Adult ; }, abstract = {The oral microbiome is unique at inter and intra-individual levels at various sites due to physical and biological factors. This study aimed to compare the bacterial composition of supragingival biofilms collected from enamel sites with different caries activity, from active and inactive-caries subjects, and from caries-free (CF) subjects. Twenty-two individuals (aged between 13 and 76 years old; med = 23.5 years old) were allocated into 3 groups: caries-active (CA) (n = 10), caries-inactive (CI) (n = 6), and CF (n = 6). From the CA group, 3 sites were sampled: CA (active non-cavitated lesion), CI (inactive non-cavitated lesion), and sound enamel surface (S). From the subjects of the CI group, biofilm from a CI lesion was collected (INCL), while for the CF subjects, a pool of biofilm from sound enamel surfaces was sampled. The total RNA was extracted, and cDNA libraries were prepared and paired-end sequenced (Illumina HiSeq 3,000). Final dental biofilm samples analysed from CA was 16 (ANCL-CA = 6, INCL-CA = 4, S-CA = 6); from CI, 3 (INCL-CI = 3); and from CF, 6 (S-CF = 6) (some samples were lost by insufficient genetic material). Read sequences were processed and analysed using the Metagenomics RAST server. High-quality sequences (3,542,190) were clustered into operational taxonomic units (97% identity; SILVA SSU), representing 915 genera belonging to 29 phyla (higher abundant: Actinobacteria, Firmicutes, Bacteroidetes, and Fusobacteria). The presence of a core microbiome was observed (123 shared genera). The alpha diversity analysis showed less bacterial diversity in disease (S-CA) compared to health (S-CF). The dominant genera included Actinomyces, Corynebacterium, Capnocytophaga, Leptotrichia, Veillonella, Prevotella, Streptococcus, Eubacterium, and Neisseria. Veillonella and Leptotrichia were related with disease and Prevotella with health. Corynebacterium, Capnocytophaga, and Actinomyces clustered together presenting high abundance in health and disease. The Metric Multidimensional Scaling Ordination analysis shows that sites from active subjects (ANCL-CA, INCL-CA, and S-CA) are closer to each other than either INCL-CI subjects or S-CF subjects. In conclusion, supragingival bacterial communities presented intra-individual similarities, but inter-individual diversity and difference in bacterial composition reveal that the subject's caries activity status matters more than sites.}, } @article {pmid34378990, year = {2021}, author = {Murphy, SMC and Bautista, MA and Cramm, MA and Hubert, CRJ}, title = {Diesel and Crude Oil Biodegradation by Cold-Adapted Microbial Communities in the Labrador Sea.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {20}, pages = {e0080021}, pmid = {34378990}, issn = {1098-5336}, support = {//Alberta Innovates - Technology Futures (AITF)/ ; //ArcticNet/ ; //Association of Canadian Universities for Northern Studies (ACUNS)/ ; //Genome Alberta/ ; //Genome Canada (Génome Canada)/ ; //Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; //Marine Environmental Observation Prediction and Response Network (MEOPAR)/ ; //W. Garfield Weston Foundation/ ; }, mesh = {Adaptation, Physiological ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Cold Temperature ; Geologic Sediments/*microbiology ; Hydrocarbons/metabolism ; *Microbiota/genetics ; Newfoundland and Labrador ; Petroleum/*metabolism ; Petroleum Pollution ; RNA, Ribosomal, 16S/genetics ; Water Pollutants/*metabolism ; }, abstract = {Oil spills in the subarctic marine environment off the coast of Labrador, Canada, are increasingly likely due to potential oil production and increases in ship traffic in the region. To understand the microbiome response and how nutrient biostimulation promotes biodegradation of oil spills in this cold marine setting, marine sediment microcosms amended with diesel or crude oil were incubated at in situ temperature (4°C) for several weeks. Sequencing of 16S rRNA genes following these spill simulations revealed decreased microbial diversity and enrichment of putative hydrocarbonoclastic bacteria that differed depending on the petroleum product. Metagenomic sequencing revealed that the genus Paraperlucidibaca harbors previously unrecognized capabilities for alkane biodegradation, which were also observed in Cycloclasticus. Genomic and amplicon sequencing together suggest that Oleispira and Thalassolituus degraded alkanes from diesel, while Zhongshania and the novel PGZG01 lineage contributed to crude oil alkane biodegradation. Greater losses in PAHs from crude oil than from diesel were consistent with Marinobacter, Pseudomonas_D, and Amphritea genomes exhibiting aromatic hydrocarbon biodegradation potential. Biostimulation with nitrogen and phosphorus (4.67 mM NH4Cl and 1.47 mM KH2PO4) was effective at enhancing n-alkane and PAH degradation following low-concentration (0.1% [vol/vol]) diesel and crude oil amendments, while at higher concentrations (1% [vol/vol]) only n-alkanes in diesel were consumed, suggesting toxicity induced by compounds in unrefined crude oil. Biostimulation allowed for a more rapid shift in the microbial community in response to petroleum amendments, more than doubling the rates of CO2 increase during the first few weeks of incubation. IMPORTANCE Increases in transportation of diesel and crude oil in the Labrador Sea will pose a significant threat to remote benthic and shoreline environments, where coastal communities and wildlife are particularly vulnerable to oil spill contaminants. Whereas marine microbiology has not been incorporated into environmental assessments in the Labrador Sea, there is a growing demand for microbial biodiversity evaluations given the pronounced impact of climate change in this region. Benthic microbial communities are important to consider given that a fraction of spilled oil typically sinks such that its biodegradation occurs at the seafloor, where novel taxa with previously unrecognized potential to degrade hydrocarbons were discovered in this work. Understanding how cold-adapted microbiomes catalyze hydrocarbon degradation at low in situ temperature is crucial in the Labrador Sea, which remains relatively cold throughout the year.}, } @article {pmid34378953, year = {2021}, author = {Casar, CP and Momper, LM and Kruger, BR and Osburn, MR}, title = {Iron-Fueled Life in the Continental Subsurface: Deep Mine Microbial Observatory, South Dakota, USA.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {20}, pages = {e0083221}, pmid = {34378953}, issn = {1098-5336}, support = {80NSSC18K1267/NASA/NASA/United States ; NNH14ZDA001N//National Aeronautics and Space Administration (NASA)/ ; }, mesh = {Bacteria ; Geological Phenomena ; Iron/*metabolism ; Metagenome ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S ; South Dakota ; }, abstract = {Iron-bearing minerals are key components of the Earth's crust and potentially critical energy sources for subsurface microbial life. The Deep Mine Microbial Observatory (DeMMO) is situated in a range of iron-rich lithologies, and fracture fluids here reach concentrations as high as 8.84 mg/liter. Iron cycling is likely an important process, given the high concentrations of iron in fracture fluids and detection of putative iron-cycling taxa via marker gene surveys. However, a previous metagenomic survey detected no iron cycling potential at two DeMMO localities. Here, we revisited the potential for iron cycling at DeMMO using a new metagenomic data set including all DeMMO sites and FeGenie, a new annotation pipeline that is optimized for the detection of iron cycling genes. We annotated functional genes from whole metagenomic assemblies and metagenome-assembled genomes and characterized putative iron cycling pathways and taxa in the context of local geochemical conditions and available metabolic energy estimated from thermodynamic models. We reannotated previous metagenomic data, revealing iron cycling potential that was previously missed. Across both metagenomic data sets, we found that not only is there genetic potential for iron cycling at DeMMO, but also, iron is likely an important source of energy across the system. In response to the dramatic differences we observed between annotation approaches, we recommend the use of optimized pipelines where the detection of iron cycling genes is a major goal. IMPORTANCE We investigated iron cycling potential among microbial communities inhabiting iron-rich fracture fluids to a depth of 1.5 km in the continental crust. A previous study found no iron cycling potential in the communities despite the iron-rich nature of the system. A new tool for detecting iron cycling genes was recently published, which we used on a new data set. We combined this with a number of other approaches to get a holistic view of metabolic strategies across the communities, revealing iron cycling to be an important process here. In addition, we used the tool on the data from the previous study, revealing previously missed iron cycling potential. Iron is common in continental crust; thus, our findings are likely not unique to our study site. Our new view of important metabolic strategies underscores the importance of choosing optimized tools for detecting the potential for metabolisms like iron cycling that may otherwise be missed.}, } @article {pmid34376596, year = {2021}, author = {Yamamura, T}, title = {[Multiple Sclerosis and Gut Microbiome: Current Research and Perspective].}, journal = {Brain and nerve = Shinkei kenkyu no shinpo}, volume = {73}, number = {8}, pages = {899-903}, doi = {10.11477/mf.1416201857}, pmid = {34376596}, issn = {1881-6096}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Multiple Sclerosis ; RNA, Ribosomal, 16S ; }, abstract = {Multiple sclerosis (MS) is a neurological disease in which alterations of the gut microbiota can be confirmed by metagenomic analysis. In addition to the 16S rRNA analysis, whole metagenomic analysis, as well as, metabolomic analysis, has been applied in this field, which convincingly proved that the reduction of short chain fatty acids characterizes the intestinal environment of patients with MS. Further research is needed to elucidate the mechanisms responsible for the alterations of the gut microbiome in patients with MS. Characterization of the virome may shed light on.}, } @article {pmid34375790, year = {2021}, author = {Pan, Y and Zheng, X and Xiang, Y}, title = {Structure-function elucidation of a microbial consortium in degrading rice straw and producing acetic and butyric acids via metagenome combining 16S rDNA sequencing.}, journal = {Bioresource technology}, volume = {340}, number = {}, pages = {125709}, doi = {10.1016/j.biortech.2021.125709}, pmid = {34375790}, issn = {1873-2976}, mesh = {Butyrates ; DNA, Ribosomal ; Fermentation ; Lignin/metabolism ; Metagenome ; *Microbial Consortia ; *Oryza/metabolism ; }, abstract = {The characterized microbial consortium can efficiently degrade rice straw to produce acetic and butyric acids in high yields. The rice straw lost 86.9% in weight and degradation rates of hemicellulose, cellulose, and lignin attained were 97.1%, 86.4% and 70.3% within 12 days, respectively. During biodegradation via fermentation of rice straw, average concentrations of acetic and butyric acids reached 1570 mg/L and 1270 mg/L, accounting for 47.2% and 35.4% of the total volatile fatty acids, respectively. The consortium mainly composed of Prevotella, Cellulosilyticum, Pseudomonas, Clostridium and Ruminococcaceae, etc. Metagenomic analyses indicated that glycoside hydrolases (GHs) were the largest enzyme group with a relative abundance of 54.5%. Various lignocellulose degrading enzymes were identified in the top 30 abundant GHs, and were primarily distributed in the dominant genera (Prevotella, Cellulosilyticum and Clostridium). These results provide a new route for the commercial recycling of rice straw to produce organic acids.}, } @article {pmid34375229, year = {2021}, author = {Xia, X and Zheng, Q and Leung, SK and Wang, Y and Lee, PY and Jing, H and Jiao, N and Liu, H}, title = {Distinct metabolic strategies of the dominant heterotrophic bacterial groups associated with marine Synechococcus.}, journal = {The Science of the total environment}, volume = {798}, number = {}, pages = {149208}, doi = {10.1016/j.scitotenv.2021.149208}, pmid = {34375229}, issn = {1879-1026}, mesh = {Heterotrophic Processes ; *Microbiota ; Phylogeny ; Seawater ; *Synechococcus/genetics ; }, abstract = {The marine Synechococcus is a major primary producer in the global oceans. It is phylogenetically highly diverse, and its major phylogenetic lineages display clear spatial segregation among different marine environments. Here, we showed that the composition of the associated bacterial communities was related to the geographic origin of the different Synechococcus strains, and it was stable during long-term lab incubation. Of all the Synechococcus cultures investigated, the Rhodobacteraceae had a relatively high abundance and was the core bacterial family of the associated bacterial communities. In contrast, the Flavobacteriaceae were only abundant in the cultures collected from the South China Sea (which is warm and oligotrophic), whereas those of the Alteromonadaceae were abundant in the cultures from the coastal waters off Hong Kong and Xiamen. We also found that the Rhodobacteraceae had more ABC transporters and utilized a wider spectrum of carbon sources than did the Flavobacteriaceae and Alteromonadaceae. Moreover, the Alteromonadaceae had more transporters for importing phosphate and amino acids, but fewer transporters for importing oligosaccharides, polyol, and lipid, than the Flavobacteriaceae. Furthermore, metagenomic analysis demonstrated that bacteria involved in nitrate-ammonification prevailed in all the cultures. These results imply that networks formed by phytoplankton and heterotrophic bacteria might vary across habitats, and that different dominant bacterial groups play different roles in the phycosphere. This study provides new insight into the unique interactive and interdependent bond between phytoplankton and their associated microbiome, which may enhance our understanding of carbon and nutrient cycling in marine environments.}, } @article {pmid34375154, year = {2021}, author = {Zhang, J and Zhang, Y and Xia, Y and Sun, J}, title = {Imbalance of the intestinal virome and altered viral-bacterial interactions caused by a conditional deletion of the vitamin D receptor.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1957408}, pmid = {34375154}, issn = {1949-0984}, support = {I01 BX004824/BX/BLRD VA/United States ; R01 DK105118/DK/NIDDK NIH HHS/United States ; R01 DK114126/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Deficiency Diseases/*physiopathology ; Feces/virology ; Female ; Gastrointestinal Microbiome/*drug effects ; Intestines/*virology ; Male ; Mice ; Mice, Knockout ; Microbial Interactions/*drug effects ; Myeloid Cells/drug effects/virology ; Paneth Cells/drug effects/virology ; Receptors, Calcitriol/*deficiency ; Virome/*drug effects ; }, abstract = {Vitamin D receptor (VDR) deficiency is associated with cancer, infection, and chronic inflammation. Prior research has demonstrated VDR regulation of bacteria; however, little is known regarding VDR and viruses. We hypothesize that VDR deficiency impacts on the intestinal virome and viral-bacterial interactions. We specifically deleted VDR from intestinal epithelial cells (VDR[ΔIEC]), Paneth cells (VDR[ΔPC]), and myeloid cells (VDR[ΔLyz]) in mice. Feces were collected for shotgun metagenomic sequencing and metabolite profiling. To test the functional changes, we evaluated pattern recognition receptors (PRRs) and analyzed microbial metabolites. Vibrio phages, Lactobacillus phages, and Escherichia coli typing phages were significantly enriched in all three conditional VDR-knockout mice. In the VDR[ΔLyz] mice, the levels of eight more virus species (2 enriched, 6 depleted) were significantly changed. Altered virus species were primarily observed in female VDR[ΔLyz] (2 enriched, 3 depleted) versus male VDR[ΔLyz] (1 enriched, 1 depleted). Altered alpha and beta diversity (family to species) were found in VDR[ΔLyz]. In VDR[ΔIEC] mice, bovine viral diarrhea virus 1 was significantly enriched. A significant correlation between viral and bacterial alterations was found in conditional VDR knockout mice. There was a positive correlation between Vibrio phage JSF5 and Cutibacterium acnes in VDR[ΔPC] and VDR[ΔLyz] mice. Also, there were more altered viral species in female conditional VDR knockout mice. Notably, there were significant changes in PRRs: upregulated TLR3, TLR7, and NOD2 in VDR[ΔLyz] mice and increased CLEC4L expression in VDR[ΔIEC] and VDR[ΔPC] mice. Furthermore, we identified metabolites related to virus infection: decreased glucose in VDR[ΔIEC] mice, increased ribulose/xylulose and xylose in VDR[ΔLyz] mice, and increased long-chain fatty acids in VDR[ΔIEC] and VDR[ΔLyz] female mice. Tissue-specific deletion of VDR changes the virome and functionally changes viral receptors, which leads to dysbiosis, metabolic dysfunction, and infection risk. This study helps to elucidate VDR regulating the virome in a tissue-specific and sex-specific manner.}, } @article {pmid34374428, year = {2021}, author = {Pereira-Dias, J and Nguyen Ngoc Minh, C and Tran Thi Hong, C and Nguyen Thi Nguyen, T and Ha Thanh, T and Zellmer, C and Chung The, H and Pike, L and Higginson, EE and Baker, S}, title = {The Gut Microbiome of Healthy Vietnamese Adults and Children Is a Major Reservoir for Resistance Genes Against Critical Antimicrobials.}, journal = {The Journal of infectious diseases}, volume = {224}, number = {12 Suppl 2}, pages = {S840-S847}, pmid = {34374428}, issn = {1537-6613}, support = {218726/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 215515/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Adult ; Aged ; Animals ; Anti-Bacterial Agents/*pharmacology ; Asian People ; Child ; Child, Preschool ; Drug Resistance, Bacterial/drug effects/*genetics ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome/drug effects/genetics ; Humans ; Longitudinal Studies ; Male ; *Metagenomics ; Middle Aged ; Vietnam ; }, abstract = {Antimicrobials are a key group of therapeutic agents. Given the animal/human population density and high antimicrobial consumption rate in Southeast Asia, the region is a focal area for monitoring antimicrobial resistance (AMR). Hypothesizing that the gastrointestinal tract of healthy individuals in Vietnam is a major source of AMR genes that may be transferred to pathogens, we performed shotgun metagenomic sequencing on fecal samples from 42 healthy Vietnamese people (21 children and 21 adults). We compared their microbiome profiles by age group and determined the composition of AMR genes. An analysis of the taxonomic profiles in the gut microbiome showed a clear differentiation by age, with young children (age <2 years) exhibiting a unique structure in comparison to adults and older children. We identified a total of 132 unique AMR genes, with macrolide, lincosamide, and streptogramin class resistance genes (ermB and lnuC) and tetracycline resistance genes being almost ubiquitous across the study population. Notably, samples from younger children were significantly associated with a greater number of AMR genes than other age groups, including key signature genes associated with AMR pathogens (eg, blaCTX-M, mphA). Our data suggest that the gut microbiome of those living in Vietnam, particularly young children, is a substantial reservoir of AMR genes, which can be transferred to circulating enteric pathogens. Our data support the generation of longitudinal cohort studies of those living in urban and rural areas of developing countries to understand the behavior of these AMR reservoirs and their role in generating multidrug-resistant and extensively drug-resistant pathogens.}, } @article {pmid34373631, year = {2022}, author = {Chevallereau, A and Pons, BJ and van Houte, S and Westra, ER}, title = {Interactions between bacterial and phage communities in natural environments.}, journal = {Nature reviews. Microbiology}, volume = {20}, number = {1}, pages = {49-62}, pmid = {34373631}, issn = {1740-1534}, support = {BB/R010781/10/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S017674/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/*genetics/*metabolism ; Bacteriophages/genetics/*physiology ; Gastrointestinal Tract/microbiology/virology ; *Host Microbial Interactions ; Humans ; *Metagenome ; Metagenomics ; *Microbiota ; Oceans and Seas ; Soil ; }, abstract = {We commonly acknowledge that bacterial viruses (phages) shape the composition and evolution of bacterial communities in nature and therefore have important roles in ecosystem functioning. This view stems from studies in the 1990s to the first decade of the twenty-first century that revealed high viral abundance, high viral diversity and virus-induced microbial death in aquatic ecosystems as well as an association between collapses in bacterial density and peaks in phage abundance. The recent surge in metagenomic analyses has provided deeper insight into the abundance, genomic diversity and spatio-temporal dynamics of phages in a wide variety of ecosystems, ranging from deep oceans to soil and the mammalian digestive tract. However, the causes and consequences of variations in phage community compositions remain poorly understood. In this Review, we explore current knowledge of the composition and evolution of phage communities, as well as their roles in controlling the population and evolutionary dynamics of bacterial communities. We discuss the need for greater ecological realism in laboratory studies to capture the complexity of microbial communities that thrive in natural environments.}, } @article {pmid34373464, year = {2021}, author = {Chu, Y and Sun, S and Huang, Y and Gao, Q and Xie, X and Wang, P and Li, J and Liang, L and He, X and Jiang, Y and Wang, M and Yang, J and Chen, X and Zhou, C and Zhao, Y and Ding, F and Zhang, Y and Wu, X and Bai, X and Wu, J and Wei, X and Chen, X and Yue, Z and Fang, X and Huang, Q and Wang, Z and Huang, R}, title = {Metagenomic analysis revealed the potential role of gut microbiome in gout.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {66}, pmid = {34373464}, issn = {2055-5008}, mesh = {Adolescent ; Adult ; Aged ; Arthritis ; Bacteria/classification ; Butyrates/analysis ; Diabetes Mellitus, Type 2/genetics ; Dysbiosis/microbiology ; Fatty Acids, Volatile ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Gout/*microbiology ; Humans ; Inflammation ; Male ; Metabolic Diseases ; *Metagenome ; Metagenomics/methods ; Middle Aged ; Spondylitis, Ankylosing ; Uric Acid/blood ; Young Adult ; }, abstract = {Emerging evidence indicates an association between gut microbiome and arthritis diseases including gout. However, how and which gut bacteria affect host urate degradation and inflammation in gout remains unclear. Here we performed a metagenome analysis on 307 fecal samples from 102 gout patients and 86 healthy controls. Gout metagenomes significantly differed from those of healthy controls. The relative abundances of Prevotella, Fusobacterium, and Bacteroides were increased in gout, whereas those of Enterobacteriaceae and butyrate-producing species were decreased. Functionally, gout patients had greater abundances for genes in fructose, mannose metabolism and lipid A biosynthesis, and lower for genes in urate degradation and short chain fatty acid production. A three-pronged association between metagenomic species, functions and clinical parameters revealed that decreased abundances of species in Enterobacteriaceae were associated with reduced amino acid metabolism and environmental sensing, which together contribute to increased serum uric acid and C-reactive protein levels in gout. A random forest classifier based on three gut microbial genes showed high predictivity for gout in both discovery and validation cohorts (0.91 and 0.80 accuracy), with high specificity in the context of other chronic disorders. Longitudinal analysis showed that uric-acid-lowering and anti-inflammatory drugs partially restored gut microbiota after 24-week treatment. Comparative analysis with obesity, type 2 diabetes, ankylosing spondylitis and rheumatoid arthritis indicated that gout metagenomes were more similar to those of autoimmune than metabolic diseases. Our results suggest that gut dysbiosis was associated with dysregulated host urate degradation and systemic inflammation and may be used as non-invasive diagnostic markers for gout.}, } @article {pmid34372876, year = {2021}, author = {Yang, Z and Zhang, J and Yang, S and Wang, X and Shen, Q and Sun, G and Wang, H and Zhang, W}, title = {Virome analysis of ticks in a forest region of Liaoning, China: characterization of a novel hepe-like virus sequence.}, journal = {Virology journal}, volume = {18}, number = {1}, pages = {163}, pmid = {34372876}, issn = {1743-422X}, mesh = {Animals ; China ; Forests ; Phylogeny ; *Ticks/virology ; *Virome ; *Viruses/classification ; }, abstract = {BACKGROUND: Ticks (class Arachnida, subclass Acari) are vectors of transmitting a broad range of pathogenic microorganisms, protozoa, and viruses affecting humans and animals. Liaoning Province is rich in forests where different animals and, abundant Haemaphysalis longicornis ticks exist.

METHODS: Using viral metagenomics, we analyzed the virome in 300 Haemaphysalis longicornis ticks collected from June to August 2015 in the forested region of Liaoning Province, China.

RESULTS: From the 300 ticks, 1,218,388 high-quality reads were generated, of which 5643 (0.463%) reads showed significant sequence identity to known viruses. Sequence and phylogenetic analysis revealed that viral sequences showing a close relationship with Dabieshan tick virus, Aleutian mink disease virus, adeno-associated virus, Gokushovirus, avian gyrovirus 2 were present in the virome of these ticks. However, the significance of these viruses to human and animal health requires further investigation. Notably, an hepe-like virus, named tick-borne hepe-like virus sequence, was obtained and was highly prevalent in these ticks with a rate of 50%. Nevertheless, one constraint of our study was the limited geographical distribution of the sampled ticks.

CONCLUSION: Our study offers an overview of the virome in ticks from a forest region of Liaoning Province and provides further awareness of the viral diversity of ticks.}, } @article {pmid34372696, year = {2021}, author = {Kachroo, N and Lange, D and Penniston, KL and Stern, J and Tasian, G and Bajic, P and Wolfe, AJ and Suryavanshi, M and Ticinesi, A and Meschi, T and Monga, M and Miller, AW}, title = {Meta-analysis of Clinical Microbiome Studies in Urolithiasis Reveal Age, Stone Composition, and Study Location as the Predominant Factors in Urolithiasis-Associated Microbiome Composition.}, journal = {mBio}, volume = {12}, number = {4}, pages = {e0200721}, pmid = {34372696}, issn = {2150-7511}, mesh = {Humans ; Male ; *Metagenome ; Microbiota/*genetics/physiology ; Urinary Calculi/*chemistry ; Urinary Tract/microbiology/pathology ; Urolithiasis/*microbiology ; }, abstract = {To determine whether functionally relevant questions associated with the urinary or gut microbiome and urinary stone disease (USD) can be answered from metagenome-wide association studies (MWAS), we performed the most comprehensive meta-analysis of published clinical MWAS in USD to date, using publicly available data published prior to April 2021. Six relevant studies met inclusion criteria. For alpha-diversity, significant differences were noted between USD status, stone composition, sample type, study location, age, diet, and sex. For beta-diversity, significant differences were noted by USD status, stone composition, sample type, study location, antibiotic use (30 days and 12 months before sampling), sex, hypertension, water intake, body habitus, and age. Prevotella and Lactobacillus in the gut and urinary tract, respectively, were associated with healthy individuals, while Enterobacteriaceae was associated with USD in the urine and stones. Paradoxically, other Prevotella strains were also strongly associated with USD in the gut microbiome. When data were analyzed together, USD status, stone composition, age group, and study location were the predominant factors associated with microbiome composition. Meta-analysis showed significant microbiome differences based on USD status, stone composition, age group or study location. However, analyses were limited by a lack of public data from published studies, metadata collected, and differing study protocols. Results highlight the need for field-specific standardization of experimental protocols in terms of sample collection procedures and the anatomical niches to assess, as well as in defining clinically relevant metadata and subphenotypes such as stone composition. IMPORTANCE Studies focused on the microbiome broadly support the hypothesis that the microbiome influences the onset of chronic diseases such as urinary stone disease. However, it is unclear what environmental factors shape the microbiome in ways that increase the risk for chronic disease. In addition, it is unclear how differences in study methodology can impact the results of clinical metagenome-wide association studies. In the current meta-analysis, we show that age, stone composition, and study location are the predominant factors that associate with the microbiome and USD status. Furthermore, we reveal differences in results based on specific analytical protocols, which impacts the interpretation of any microbiome study.}, } @article {pmid34372602, year = {2021}, author = {Zakham, F and Albalawi, AE and Alanazi, AD and Truong Nguyen, P and Alouffi, AS and Alaoui, A and Sironen, T and Smura, T and Vapalahti, O}, title = {Viral RNA Metagenomics of Hyalomma Ticks Collected from Dromedary Camels in Makkah Province, Saudi Arabia.}, journal = {Viruses}, volume = {13}, number = {7}, pages = {}, pmid = {34372602}, issn = {1999-4915}, mesh = {Animals ; Camelus ; Humans ; Metagenomics/*methods ; RNA, Viral/*genetics ; Saudi Arabia ; Tick-Borne Diseases/prevention & control/*virology ; Ticks/*virology ; Virome/*genetics ; Viruses/classification/*genetics/isolation & purification ; }, abstract = {Arthropod-borne infections are a medical and economic threat to humans and livestock. Over the last three decades, several unprecedented viral outbreaks have been recorded in the Western part of the Arabian Peninsula. However, little is known about the circulation and diversity of arthropod-borne viruses in this region. To prepare for new outbreaks of vector-borne diseases, it is important to detect which viruses circulate in each vector population. In this study, we used a metagenomics approach to characterize the RNA virome of ticks infesting dromedary camels (Camelus dromedaries) in Makkah province, Saudi Arabia. Two hundred ticks of species Hyalomma dromedarii (n = 196) and Hyalomma impeltatum (n = 4) were collected from the Alkhurma district in Jeddah and Al-Taif city. Virome analysis showed the presence of several tick-specific viruses and tick-borne viruses associated with severe illness in humans. Some were identified for the first time in the Arabian Peninsula. The human disease-associated viruses detected included Crimean Congo Hemorrhagic fever virus and Tamdy virus (family Nairoviridae), Guertu virus (family Phenuiviridae), and a novel coltivirus that shares similarities with Tarumizu virus, Tai forest reovirus and Kundal virus (family Reoviridae). Furthermore, Alkhurma hemorrhagic virus (Flaviviridae) was detected in two tick pools by specific qPCR. In addition, tick-specific viruses in families Phenuiviridae (phleboviruses), Iflaviridae, Chuviridae, Totiviridae and Flaviviridae (Pestivirus) were detected. The presence of human pathogenetic viruses warrants further efforts in tick surveillance, xenosurveillence, vector control, and sero-epidemiological investigations in human and animal populations to predict, contain and mitigate future outbreaks in the region.}, } @article {pmid34371435, year = {2021}, author = {Balasubramanian, VK and Joseph Maran, MI and Ramteke, D and Vijaykumar, DS and Kottarathail Rajendran, A and Ramachandran, P and Ramachandran, R}, title = {Environmental DNA reveals aquatic biodiversity of an urban backwater area, southeast coast of India.}, journal = {Marine pollution bulletin}, volume = {171}, number = {}, pages = {112786}, doi = {10.1016/j.marpolbul.2021.112786}, pmid = {34371435}, issn = {1879-3363}, mesh = {Biodiversity ; DNA Barcoding, Taxonomic ; *DNA, Environmental ; Ecosystem ; Environmental Monitoring ; Humans ; India ; }, abstract = {Strong conservation management needs comprehensive data on biodiversity. Rapid methods that document aquatic biodiversity or assess the health condition of an ecosystem remain scarce. Herein, we have performed a metagenomics study on environmental DNA (eDNA) collected from an urban backwater area - Muttukadu, located in the southeast coast of India. Shotgun metagenomics approach using Illumina®NextSeq500 sequencing yielded 88.4 million raw reads. The processed data was assigned as 80% prokaryotes, 0.4% eukaryotes, ~2% viruses, and ~17% remain unknown. This approach has the potential to identify small micro-eukaryote, unseen species from both estuarine and marine environments. We have identified 156 eukaryote organisms represented from 21 phyla and 112 families, including those that are of conservational significance and ecological importance. Furthermore, our data also demonstrated the presence of pathogenic microorganisms due to sewage mixing with the backwaters. Given its sensitivity, we suggest this approach for an initial assessment of biodiversity structure in an ecosystem for the biomonitoring program.}, } @article {pmid34371134, year = {2021}, author = {Streit, F and Prandovszky, E and Send, T and Zillich, L and Frank, J and Sabunciyan, S and Foo, J and Sirignano, L and Lange, B and Bardtke, S and Hatfield, G and Witt, SH and Gilles, M and Rietschel, M and Deuschle, M and Yolken, R}, title = {Microbiome profiles are associated with cognitive functioning in 45-month-old children.}, journal = {Brain, behavior, and immunity}, volume = {98}, number = {}, pages = {151-160}, doi = {10.1016/j.bbi.2021.08.001}, pmid = {34371134}, issn = {1090-2139}, mesh = {Child ; Child, Preschool ; Cognition ; Feces ; Female ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Pregnancy ; RNA, Ribosomal, 16S ; }, abstract = {Prenatal, perinatal, and postnatal factors have been shown to shape neurobiological functioning and alter the risk for mental disorders later in life. The gut microbiome is established early in life, and interacts with the brain via the brain-immune-gut axis. However, little is known about how the microbiome relates to early-life cognitive functioning in children. The present study, where the fecal microbiome of 380 children was characterized using 16S rDNA and metagenomic sequencing aimed to investigate the association between the microbiota and cognitive functioning of children at the age of 45 months measured with the Wechsler Preschool and Primary Scale of Intelligence (WPPSI-III). Overall the microbiome profile showed a significant association with cognitive functioning. A strong correlation was found between cognitive functioning and the relative abundance of an unidentified genus of the family Enterobacteriaceae. Follow-up mediation analyses revealed significant mediation effects of the level of this genus on the association of maternal smoking during pregnancy and current cigarette smoking with cognitive function. Metagenomic sequencing of a subset of these samples indicated that the identified genus was most closely related to Enterobacter asburiae. Analysis of metabolic potential showed a nominally significant association of cognitive functioning with the microbial norspermidine biosynthesis pathway. Our results indicate that alteration of the gut microflora is associated with cognitive functioning in childhood. Furthermore, they suggest that the altered microflora might interact with other environmental factors such as maternal cigarette smoking. Interventions directed at altering the microbiome should be explored in terms of improving cognitive functioning in young children.}, } @article {pmid34370660, year = {2021}, author = {Gaio, D and DeMaere, MZ and Anantanawat, K and Chapman, TA and Djordjevic, SP and Darling, AE}, title = {Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes.}, journal = {Microbial genomics}, volume = {7}, number = {8}, pages = {}, pmid = {34370660}, issn = {2057-5858}, mesh = {Animals ; Gastrointestinal Microbiome/*genetics/physiology ; Genome, Bacterial ; *Metagenome ; *Metagenomics ; Phylogeny ; Proteome ; Swine ; Weaning ; }, abstract = {Using a previously described metagenomics dataset of 27 billion reads, we reconstructed over 50 000 metagenome-assembled genomes (MAGs) of organisms resident in the porcine gut, 46.5 % of which were classified as >70 % complete with a <10 % contamination rate, and 24.4 % were nearly complete genomes. Here, we describe the generation and analysis of those MAGs using time-series samples. The gut microbial communities of piglets appear to follow a highly structured developmental programme in the weeks following weaning, and this development is robust to treatments including an intramuscular antibiotic treatment and two probiotic treatments. The high resolution we obtained allowed us to identify specific taxonomic 'signatures' that characterize the gut microbial development immediately after weaning. Additionally, we characterized the carbohydrate repertoire of the organisms resident in the porcine gut. We tracked the abundance shifts of 294 carbohydrate active enzymes, and identified the species and higher-level taxonomic groups carrying each of these enzymes in their MAGs. This knowledge can contribute to the design of probiotics and prebiotic interventions as a means to modify the piglet gut microbiome.}, } @article {pmid34369983, year = {2021}, author = {Zysset-Burri, DC and Schlegel, I and Lincke, JB and Jaggi, D and Keller, I and Heller, M and Lagache, SB and Wolf, S and Zinkernagel, MS}, title = {Understanding the Interactions Between the Ocular Surface Microbiome and the Tear Proteome.}, journal = {Investigative ophthalmology & visual science}, volume = {62}, number = {10}, pages = {8}, pmid = {34369983}, issn = {1552-5783}, mesh = {Aged ; Bacteria/*genetics ; Conjunctiva/metabolism/*microbiology ; Eye Infections, Bacterial/*genetics/metabolism ; Female ; Humans ; Male ; Microbiota/*physiology ; Middle Aged ; Proteome/*genetics/metabolism ; Tears/*metabolism ; }, abstract = {PURPOSE: The purpose of this study was to explore the interplay between the ocular surface microbiome and the tear proteome in humans in order to better understand the pathogenesis of ocular surface-associated diseases.

METHODS: Twenty eyes from 20 participants were included in the study. The ocular surface microbiome was sequenced by whole-metagenome shotgun sequencing using lid and conjunctival swabs. Furthermore, the tear proteome was identified using chromatography tandem mass spectrometry. After compositional and functional profiling of the metagenome and functional characterization of the proteome by gene ontology, association studies between the ocular microbiome and tear proteome were assessed.

RESULTS: Two hundred twenty-nine taxa were identified with Actinobacteria and Proteobacteria being the most abundant phyla with significantly more Propionibacterium acnes and Staphylococcus epidermidis in lid compared to conjunctival swabs. The lid metagenomes were enriched in genes of the glycolysis lll and adenosine nucleotides de novo and L-isoleucine biosynthesis. Correlations between the phylum Firmicutes and fatty acid metabolism, between the genus Agrobacterium as well as vitamin B1 synthesis and antimicrobial activity, and between biosynthesis of heme, L-arginine, as well as L-citrulline and human vision were detected.

CONCLUSIONS: The ocular surface microbiome was found to be associated with the tear proteome with a role in human immune defense. This study has a potential impact on the development of treatment strategies for ocular surface-associated diseases.}, } @article {pmid34369304, year = {2021}, author = {Singhal, R and Donde, H and Ghare, S and Stocke, K and Zhang, J and Vadhanam, M and Reddy, S and Gobejishvili, L and Chilton, P and Joshi-Barve, S and Feng, W and McClain, C and Hoffman, K and Petrosino, J and Vital, M and Barve, S}, title = {Decrease in acetyl-CoA pathway utilizing butyrate-producing bacteria is a key pathogenic feature of alcohol-induced functional gut microbial dysbiosis and development of liver disease in mice.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1946367}, pmid = {34369304}, issn = {1949-0984}, support = {P20 GM113226/GM/NIGMS NIH HHS/United States ; P50 AA024337/AA/NIAAA NIH HHS/United States ; U01 AA022618/AA/NIAAA NIH HHS/United States ; }, mesh = {Animals ; Butyrates/*metabolism ; Chemical and Drug Induced Liver Injury/*etiology/*physiopathology ; Coenzyme A-Transferases/*metabolism ; Disease Models, Animal ; Dysbiosis/*chemically induced/physiopathology ; Ethanol/*metabolism ; Gastrointestinal Microbiome/*drug effects ; Humans ; Metabolic Networks and Pathways ; Mice ; Ruminococcus/*metabolism ; }, abstract = {Emerging research evidence has established the critical role of the gut-liver axis in the development of alcohol-associated liver disease (ALD). The present study employed 16S rRNA gene and whole genome shotgun (WGS) metagenomic analysis in combination with a revised microbial dataset to comprehensively detail the butyrate-producing microbial communities and the associated butyrate metabolic pathways affected by chronic ethanol feeding. Specifically, the data demonstrated that a decrease in several butyrate-producing bacterial genera belonging to distinct families within the Firmicutes phyla was a significant component of ethanol-induced dysbiosis. WGS analysis of total bacterial genomes encompassing butyrate synthesizing pathways provided the functional characteristics of the microbiome associated with butyrate synthesis. The data revealed that in control mice microbiome, the acetyl-coenzyme A (CoA) butyrate synthesizing pathway was the most prevalent and was significantly and maximally decreased by chronic ethanol feeding. Further WGS analysis i) validated the ethanol-induced decrease in the acetyl-CoA pathway by identifying the decrease in two critical genes but - (butyryl-CoA: acetate CoA transferase) and buk - (butyrate kinase) that encode the terminal condensing enzymes required for converting butyryl-CoA to butyrate and ii) detection of specific taxa of butyrate-producing bacteria containing but and buk genes. Notably, the administration of tributyrin (Tb) - a butyrate prodrug - significantly prevented ethanol-induced decrease in butyrate-producing bacteria, hepatic steatosis, inflammation, and injury. Taken together, our findings strongly suggest that the loss of butyrate-producing bacteria using the acetyl-CoA pathway is a significant pathogenic feature of ethanol-induced microbial dysbiosis and ALD and can be targeted for therapy.}, } @article {pmid34367180, year = {2021}, author = {Lv, L and Jiang, H and Chen, X and Wang, Q and Wang, K and Ye, J and Li, Y and Fang, D and Lu, Y and Yang, L and Gu, S and Chen, J and Diao, H and Yan, R and Li, L}, title = {The Salivary Microbiota of Patients With Primary Biliary Cholangitis Is Distinctive and Pathogenic.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {713647}, pmid = {34367180}, issn = {1664-3224}, mesh = {Biomarkers ; Case-Control Studies ; Chemokines/metabolism ; Cytokines/metabolism ; Dysbiosis/*etiology ; Female ; *Host Microbial Interactions/immunology ; Humans ; Inflammation Mediators/metabolism ; Keratinocytes/metabolism ; Liver Cirrhosis, Biliary/*complications/diagnosis/etiology/metabolism ; Liver Function Tests ; Male ; Metabolomics/methods ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Saliva/*microbiology ; }, abstract = {The role of host-microbiota interactions in primary biliary cholangitis (PBC) has received increased attention. However, the impact of PBC on the oral microbiota and contribution of the oral microbiota to PBC are unclear. In this study, thirty-nine PBC patients without other diseases and 37 healthy controls (HCs) were enrolled and tested for liver functions and haematological variables. Saliva specimens were collected before and after brushing, microbiota was determined using 16S rDNA sequencing, metabolomics was profiled using Gas Chromatography-Mass Spectrometer (GC-MS), 80 cytokines were assayed using biochips, and inflammation inducibility was evaluated using OKF6 keratinocytes and THP-1 macrophages. Finally, the effect of ultrasonic scaling on PBC was estimated. Compared with HCs, PBC saliva had enriched taxa such as Bacteroidetes, Campylobacter, Prevotella and Veillonella and depleted taxa such as Enterococcaceae, Granulicatella, Rothia and Streptococcus. PBC saliva also had enriched sCD163, enriched metabolites such as 2-aminomalonic acid and 1-dodecanol, and depleted metabolites such as dodecanoic acid and propylene glycol. sCD163, 4-hydroxybenzeneacetic acid and 2-aminomalonic acid were significantly correlated with salivary cytokines, bacteria and metabolites. Salivary Veillonellaceae members, 2-aminomalonic acid, and sCD163 were positively correlated with liver function indicators such as serum alkaline phosphatase (ALP), aspartate aminotransferase (AST) and alanine aminotransferase (ALT). PBC salivary microbes induced more soluble interleukin (IL)-6 receptor α (sIL-6Rα), sIL-6Rβ and tumour necrosis factor ligand superfamily (TNFSF)13B from OKF6 keratinocytes, and PBC salivary supernatant induced more IL-6, IL-10, granulocyte-macrophage colony-stimulating factor (GM-CSF), chemokine (C-C motif) ligand (CCL)13, C-X-C motif chemokine (CXC)L1 and CXCL16 from THP-1 macrophages. Toothbrushing significantly reduced the expression of inflammatory cytokines such as IL-1β, IL-8 and TNF-α and harmful metabolites such as cadaverine and putrescine in PBC but not HC saliva after P-value correction. The levels of ALP and bilirubin in PBC serum were decreased after ultrasonic scaling. Together, PBC patients show significant alterations in their salivary microbiota, likely representing one cause and treatment target of oral inflammation and worsening liver functions.}, } @article {pmid34367134, year = {2021}, author = {Hetemäki, I and Jian, C and Laakso, S and Mäkitie, O and Pajari, AM and de Vos, WM and Arstila, TP and Salonen, A}, title = {Fecal Bacteria Implicated in Biofilm Production Are Enriched and Associate to Gastrointestinal Symptoms in Patients With APECED - A Pilot Study.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {668219}, pmid = {34367134}, issn = {1664-3224}, mesh = {Adult ; Aged ; Antibodies, Fungal/metabolism ; Bacteria/genetics/*growth & development/immunology/metabolism ; Biofilms/*growth & development ; Case-Control Studies ; Dysbiosis ; Feces/*microbiology ; Female ; Finland ; Gastrointestinal Diseases/diagnosis/immunology/metabolism/*microbiology ; *Gastrointestinal Microbiome ; Genetic Predisposition to Disease ; Host-Pathogen Interactions ; Humans ; Immunoglobulin G/metabolism ; Intestines/*microbiology ; Lipopolysaccharides/metabolism ; Male ; Metagenome ; Middle Aged ; *Mutation ; Pilot Projects ; Polyendocrinopathies, Autoimmune/complications/diagnosis/genetics/immunology ; Saccharomyces cerevisiae/genetics/immunology ; Transcription Factors/*genetics ; Young Adult ; AIRE Protein ; }, abstract = {BACKGROUNDS AND AIMS: APECED is a rare autoimmune disease caused by mutations in the Autoimmune Regulator gene. A significant proportion of patients also have gastrointestinal symptoms, including malabsorption, chronic diarrhea, and obstipation. The pathological background of the gastrointestinal symptoms remains incompletely understood and involves multiple factors, with autoimmunity being the most common underlying cause. Patients with APECED have increased immune responses against gut commensals. Our objective was to evaluate whether the intestinal microbiota composition, predicted functions or fungal abundance differ between Finnish patients with APECED and healthy controls, and whether these associate to the patients' clinical phenotype and gastrointestinal symptoms.

METHODS: DNA was isolated from fecal samples from 15 patients with APECED (median age 46.4 years) together with 15 samples from body mass index matched healthy controls. DNA samples were subjected to analysis of the gut microbiota using 16S rRNA gene amplicon sequencing, imputed metagenomics using the PICRUSt2 algorithm, and quantitative PCR for fungi. Extensive correlations of the microbiota with patient characteristics were determined.

RESULTS: Analysis of gut microbiota indicated that both alpha- and beta-diversity were altered in patients with APECED compared to healthy controls. The fraction of Faecalibacterium was reduced in patients with APECED while that of Atopobium spp. and several gram-negative genera previously implicated in biofilm formation, e.g. Veillonella, Prevotella, Megasphaera and Heamophilus, were increased in parallel to lipopolysaccharide (LPS) synthesis in imputed metagenomics. The differences in gut microbiota were linked to patient characteristics, especially the presence of anti-Saccharomyces cerevisiae antibodies (ASCA) and severity of gastrointestinal symptoms.

CONCLUSIONS: Gut microbiota of patients with APECED is altered and enriched with predominantly gram-negative bacterial taxa that may promote biofilm formation and lead to increased exposure to LPS in the patients. The most pronounced alterations in the microbiota were associated with more severe gastrointestinal symptoms.}, } @article {pmid34365683, year = {2021}, author = {Lavaud, J and Hüssler, S and Gricourt, G and de Prost, N and Rodriguez, C and Ingen-Housz-Oro, S and Chosidow, O and Bernigaud, C and Woerther, PL}, title = {16S metagenomic assessment of the skin microbiota dynamic and possible association with the risk of infection in patients with epidermal necrolysis.}, journal = {Journal of the European Academy of Dermatology and Venereology : JEADV}, volume = {35}, number = {12}, pages = {e914-e917}, doi = {10.1111/jdv.17584}, pmid = {34365683}, issn = {1468-3083}, support = {//Société Française de Dermatologie et de Pathologie Sexuellement Transmissible/ ; }, mesh = {Humans ; *Microbiota/genetics ; Skin ; *Stevens-Johnson Syndrome/genetics ; }, } @article {pmid34363005, year = {2022}, author = {Somerville, V and Berthoud, H and Schmidt, RS and Bachmann, HP and Meng, YH and Fuchsmann, P and von Ah, U and Engel, P}, title = {Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures.}, journal = {The ISME journal}, volume = {16}, number = {2}, pages = {388-399}, pmid = {34363005}, issn = {1751-7370}, mesh = {Bacteria ; *Bacteriophages/genetics ; Food Microbiology ; Metagenomics ; *Microbiota ; }, abstract = {Undefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly controlled environments over centuries. This makes them interesting for understanding eco-evolutionary dynamics governing microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to an important Swiss cheese starter culture and analyzed historical and experimental samples reflecting 82 years of starter culture propagation. We found that the bacterial community is highly stable and dominated by only a few coexisting strains of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Genome sequencing, metabolomics analysis, and co-culturing experiments of 43 isolates show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large and diverse repertoire of matching CRISPR spacers. Our findings show that functionally equivalent strains can coexist in domesticated microbial communities and highlight an important role of bacteria-phage interactions that are different from kill-the-winner dynamics.}, } @article {pmid34362925, year = {2021}, author = {Zhang, AN and Gaston, JM and Dai, CL and Zhao, S and Poyet, M and Groussin, M and Yin, X and Li, LG and van Loosdrecht, MCM and Topp, E and Gillings, MR and Hanage, WP and Tiedje, JM and Moniz, K and Alm, EJ and Zhang, T}, title = {An omics-based framework for assessing the health risk of antimicrobial resistance genes.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {4765}, pmid = {34362925}, issn = {2041-1723}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/genetics ; Databases, Factual ; Drug Resistance, Bacterial/*drug effects/*genetics ; Gastrointestinal Microbiome/drug effects ; Genes, Bacterial/drug effects ; Genome ; Humans ; Metagenome ; Plasmids ; }, abstract = {Antibiotic resistance genes (ARGs) are widespread among bacteria. However, not all ARGs pose serious threats to public health, highlighting the importance of identifying those that are high-risk. Here, we developed an 'omics-based' framework to evaluate ARG risk considering human-associated-enrichment, gene mobility, and host pathogenicity. Our framework classifies human-associated, mobile ARGs (3.6% of all ARGs) as the highest risk, which we further differentiate as 'current threats' (Rank I; 3%) - already present among pathogens - and 'future threats' (Rank II; 0.6%) - novel resistance emerging from non-pathogens. Our framework identified 73 'current threat' ARG families. Of these, 35 were among the 37 high-risk ARGs proposed by the World Health Organization and other literature; the remaining 38 were significantly enriched in hospital plasmids. By evaluating all pathogen genomes released since framework construction, we confirmed that ARGs that recently transferred into pathogens were significantly enriched in Rank II ('future threats'). Lastly, we applied the framework to gut microbiome genomes from fecal microbiota transplantation donors. We found that although ARGs were widespread (73% of genomes), only 8.9% of genomes contained high-risk ARGs. Our framework provides an easy-to-implement approach to identify current and future antimicrobial resistance threats, with potential clinical applications including reducing risk of microbiome-based interventions.}, } @article {pmid34362459, year = {2021}, author = {Roth-Schulze, AJ and Penno, MAS and Ngui, KM and Oakey, H and Bandala-Sanchez, E and Smith, AD and Allnutt, TR and Thomson, RL and Vuillermin, PJ and Craig, ME and Rawlinson, WD and Davis, EA and Harris, M and Soldatos, G and Colman, PG and Wentworth, JM and Haynes, A and Barry, SC and Sinnott, RO and Morahan, G and Bediaga, NG and Smyth, GK and Papenfuss, AT and Couper, JJ and Harrison, LC and , }, title = {Type 1 diabetes in pregnancy is associated with distinct changes in the composition and function of the gut microbiome.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {167}, pmid = {34362459}, issn = {2049-2618}, mesh = {*Diabetes Mellitus, Type 1/microbiology ; Feces ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Intestines ; Metagenome ; Pregnancy ; Pregnancy in Diabetics/*microbiology ; }, abstract = {BACKGROUND: The gut microbiome changes in response to a range of environmental conditions, life events and disease states. Pregnancy is a natural life event that involves major physiological adaptation yet studies of the microbiome in pregnancy are limited and their findings inconsistent. Pregnancy with type 1 diabetes (T1D) is associated with increased maternal and fetal risks but the gut microbiome in this context has not been characterized. By whole metagenome sequencing (WMS), we defined the taxonomic composition and function of the gut bacterial microbiome across 70 pregnancies, 36 in women with T1D.

RESULTS: Women with and without T1D exhibited compositional and functional changes in the gut microbiome across pregnancy. Profiles in women with T1D were distinct, with an increase in bacteria that produce lipopolysaccharides and a decrease in those that produce short-chain fatty acids, especially in the third trimester. In addition, women with T1D had elevated concentrations of fecal calprotectin, a marker of intestinal inflammation, and serum intestinal fatty acid-binding protein (I-FABP), a marker of intestinal epithelial damage.

CONCLUSIONS: Women with T1D exhibit a shift towards a more pro-inflammatory gut microbiome during pregnancy, associated with evidence of intestinal inflammation. These changes could contribute to the increased risk of pregnancy complications in women with T1D and are potentially modifiable by dietary means. Video abstract.}, } @article {pmid34362295, year = {2021}, author = {Shaw, AG and Sim, K and Rose, G and Wooldridge, DJ and Li, MS and Misra, RV and Gharbia, S and Kroll, JS}, title = {Premature neonatal gut microbial community patterns supporting an epithelial TLR-mediated pathway for necrotizing enterocolitis.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {225}, pmid = {34362295}, issn = {1471-2180}, mesh = {Bayes Theorem ; DNA, Bacterial/genetics ; Enterocolitis, Necrotizing/immunology/*microbiology ; Epithelial Cells/*immunology/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Infant, Premature, Diseases/immunology/*microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Toll-Like Receptor 4/genetics/*immunology ; }, abstract = {BACKGROUND: Necrotising enterocolitis (NEC) is a devastating bowel disease, primarily affecting premature infants, with a poorly understood aetiology. Prior studies have found associations in different cases with an overabundance of particular elements of the faecal microbiota (in particular Enterobacteriaceae or Clostridium perfringens), but there has been no explanation for the different results found in different cohorts. Immunological studies have indicated that stimulation of the TLR4 receptor is involved in development of NEC, with TLR4 signalling being antagonised by the activated TLR9 receptor. We speculated that differential stimulation of these two components of the signalling pathway by different microbiota might explain the dichotomous findings of microbiota-centered NEC studies. Here we used shotgun metagenomic sequencing and qPCR to characterise the faecal microbiota community of infants prior to NEC onset and in a set of matched controls. Bayesian regression was used to segregate cases from control samples using both microbial and clinical data.

RESULTS: We found that the infants suffering from NEC fell into two groups based on their microbiota; one with low levels of CpG DNA in bacterial genomes and the other with high abundances of organisms expressing LPS. The identification of these characteristic communities was reproduced using an external metagenomic validation dataset. We propose that these two patterns represent the stimulation of a common pathway at extremes; the LPS-enriched microbiome suggesting overstimulation of TLR4, whilst a microbial community with low levels of CpG DNA suggests reduction of the counterbalance to TLR4 overstimulation.

CONCLUSIONS: The identified microbial community patterns support the concept of NEC resulting from TLR-mediated pathways. Identification of these signals suggests characteristics of the gastrointestinal microbial community to be avoided to prevent NEC. Potential pre- or pro-biotic treatments may be designed to optimise TLR signalling.}, } @article {pmid34361900, year = {2021}, author = {Panaiotov, S and Hodzhev, Y and Tsafarova, B and Tolchkov, V and Kalfin, R}, title = {Culturable and Non-Culturable Blood Microbiota of Healthy Individuals.}, journal = {Microorganisms}, volume = {9}, number = {7}, pages = {}, pmid = {34361900}, issn = {2076-2607}, support = {DN-01-4/16.12.2016//Bulgarian National Science Fund/ ; KP-06-DV/10-21.12.2019//Bulgarian National Science Fund/ ; }, abstract = {Next-generation sequencing (NGS) and metagenomics revolutionized our capacity for analysis and identification of the microbial communities in complex samples. The existence of a blood microbiome in healthy individuals has been confirmed by sequencing, but some researchers suspect that this is a cell-free circulating DNA in blood, while others have had isolated a limited number of bacterial and fungal species by culture. It is not clear what part of the blood microbiota could be resuscitated and cultured. Here, we quantitatively measured the culturable part of blood microbiota of healthy individuals by testing a medium supplemented with a high concentration of vitamin K (1 mg/mL) and culturing at 43 °C for 24 h. We applied targeted sequencing of 16S rDNA and internal transcribed spacer (ITS) markers on cultured and non-cultured blood samples from 28 healthy individuals. Dominant bacterial phyla among non-cultured samples were Proteobacteria 92.97%, Firmicutes 2.18%, Actinobacteria 1.74% and Planctomycetes 1.55%, while among cultured samples Proteobacteria were 47.83%, Firmicutes 25.85%, Actinobacteria 16.42%, Bacteroidetes 3.48%, Cyanobacteria 2.74%, and Fusobacteria 1.53%. Fungi phyla Basidiomycota, Ascomycota, and unidentified fungi were 65.08%, 17.72%, and 17.2% respectively among non-cultured samples, while among cultured samples they were 58.08%, 21.72%, and 20.2% respectively. In cultured and non-cultured samples we identified 241 OTUs belonging to 40 bacterial orders comprising 66 families and 105 genera. Fungal biodiversity accounted for 272 OTUs distributed in 61 orders, 105 families, and 133 genera. Bacterial orders that remained non-cultured, compared to blood microbiota isolated from fresh blood collection, were Sphingomonadales, Rhizobiales, and Rhodospirillales. Species of orders Bacillales, Lactobacillales, and Corynebacteriales showed the best cultivability. Fungi orders Tremellales, Polyporales, and Filobasidiales were mostly unculturable. Species of fungi orders Pleosporales, Saccharomycetales, and Helotiales were among the culturable ones. In this study, we quantified the capacity of a specific medium applied for culturing of blood microbiota in healthy individuals. Other culturing conditions and media should be tested for optimization and better characterization of blood microbiota in healthy and diseased individuals.}, } @article {pmid34356622, year = {2021}, author = {Torrell, H and Cereto-Massagué, A and Kazakova, P and García, L and Palacios, H and Canela, N}, title = {Multiomic Approach to Analyze Infant Gut Microbiota: Experimental and Analytical Method Optimization.}, journal = {Biomolecules}, volume = {11}, number = {7}, pages = {}, pmid = {34356622}, issn = {2218-273X}, mesh = {*Bacteria/classification/genetics/growth & development ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Male ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {BACKGROUND: The human intestinal microbiome plays a central role in overall health status, especially in early life stages. 16S rRNA amplicon sequencing is used to profile its taxonomic composition; however, multiomic approaches have been proposed as the most accurate methods for study of the complexity of the gut microbiota. In this study, we propose an optimized method for bacterial diversity analysis that we validated and complemented with metabolomics by analyzing fecal samples.

METHODS: Forty-eight different analytical combinations regarding (1) 16S rRNA variable region sequencing, (2) a feature selection approach, and (3) taxonomy assignment methods were tested. A total of 18 infant fecal samples grouped depending on the type of feeding were analyzed by the proposed 16S rRNA workflow and by metabolomic analysis.

RESULTS: The results showed that the sole use of V4 region sequencing with ASV identification and VSEARCH for taxonomy assignment produced the most accurate results. The application of this workflow showed clear differences between fecal samples according to the type of feeding, which correlated with changes in the fecal metabolic profile.

CONCLUSION: A multiomic approach using real fecal samples from 18 infants with different types of feeding demonstrated the effectiveness of the proposed 16S rRNA-amplicon sequencing workflow.}, } @article {pmid34356001, year = {2021}, author = {Zeng, Q and Yang, Z and Wang, F and Li, D and Liu, Y and Wang, D and Zhao, X and Li, Y and Wang, Y and Feng, X and Chen, J and Li, Y and Zheng, Y and Kenney, T and Gu, H and Feng, S and Li, S and He, Y and Xu, X and Dai, W}, title = {Association between metabolic status and gut microbiome in obese populations.}, journal = {Microbial genomics}, volume = {7}, number = {8}, pages = {}, pmid = {34356001}, issn = {2057-5858}, mesh = {Bacteria/*classification/genetics ; Biomarkers ; China ; Cohort Studies ; Diet ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolic Diseases ; Metagenome ; *Obesity ; }, abstract = {Despite that obesity is associated with many metabolic diseases, a significant proportion (10-30 %) of obese individuals is recognized as 'metabolically healthy obeses' (MHOs). The aim of the current study is to characterize the gut microbiome for MHOs as compared to 'metabolically unhealthy obeses' (MUOs). We compared the gut microbiome of 172 MHO and 138 MUO individuals from Chongqing (China) (inclined to eat red meat and food with a spicy taste), and performed validation with selected biomarkers in 40 MHOs and 33 MUOs from Quanzhou (China) (inclined to eat seafood and food with a light/bland taste). The genera Alistipes, Faecalibacterium and Odoribacter had increased abundance in both Chongqing and Quanzhou MHOs. We also observed different microbial functions in MUOs compared to MHOs, including an increased abundance of genes associated with glycan biosynthesis and metabolism. In addition, the microbial gene markers identified from the Chongqing cohort bear a moderate accuracy [AUC (area under the operating characteristic curve)=0.69] for classifying MHOs distinct from MUOs in the Quanzhou cohort. These findings indicate that gut microbiome is significantly distinct between MHOs and MUOs, implicating the potential of the gut microbiome in stratification and refined management of obesity.}, } @article {pmid34355542, year = {2021}, author = {Lee, MH}, title = {Harness the functions of gut microbiome in tumorigenesis for cancer treatment.}, journal = {Cancer communications (London, England)}, volume = {41}, number = {10}, pages = {937-967}, pmid = {34355542}, issn = {2523-3548}, support = {2020YFA0803300//National key research and development program/ ; 2018YFC0910300//National key research and development program/ ; 81630072//National Natural Science Foundation of China/ ; KQTD20170810160226082//Shenzhen Municipal Government of China/ ; 2018YFC0910300//China Association for Science and Technology/ ; 2020YFA0803300//China Association for Science and Technology/ ; }, mesh = {Carcinogenesis/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; *Neoplasms/genetics/therapy ; }, abstract = {It has been shown that gut microbiota dysbiosis leads to physiological changes and links to a number of diseases, including cancers. Thus, many cancer categories and treatment regimens should be investigated in the context of the microbiome. Owing to the availability of metagenome sequencing and multiomics studies, analyses of species characterization, host genetic changes, and metabolic profile of gut microbiota have become feasible, which has facilitated an exponential knowledge gain about microbiota composition, taxonomic alterations, and host interactions during tumorigenesis. However, the complexity of the gut microbiota, with a plethora of uncharacterized host-microbe, microbe-microbe, and environmental interactions, still contributes to the challenge of advancing our knowledge of the microbiota-cancer interactions. These interactions manifest in signaling relay, metabolism, immunity, tumor development, genetic instability, sensitivity to cancer chemotherapy and immunotherapy. This review summarizes current studies/molecular mechanisms regarding the association between the gut microbiota and the development of cancers, which provides insights into the therapeutic strategies that could be harnessed for cancer diagnosis, treatment, or prevention.}, } @article {pmid34355428, year = {2022}, author = {Diwan, AD and Harke, SN and Gopalkrishna, and Panche, AN}, title = {Aquaculture industry prospective from gut microbiome of fish and shellfish: An overview.}, journal = {Journal of animal physiology and animal nutrition}, volume = {106}, number = {2}, pages = {441-469}, doi = {10.1111/jpn.13619}, pmid = {34355428}, issn = {1439-0396}, mesh = {Animals ; Aquaculture ; *Fishes/microbiology ; *Gastrointestinal Microbiome ; *Shellfish/microbiology ; }, abstract = {The microbiome actually deals with micro-organisms that are associated with indigenous body parts and the entire gut system in all animals, including human beings. These microbes are linked with roles involving hereditary traits, defence against diseases and strengthening overall immunity, which determines the health status of an organism. Considerable efforts have been made to find out the microbiome diversity and their taxonomic identification in finfish and shellfish and its importance has been correlated with various physiological functions and activities. In recent past due to the availability of advanced molecular tools, some efforts have also been made on DNA sequencing of these microbes to understand the environmental impact and other stress factors on their genomic structural profile. There are reports on the use of next-generation sequencing (NGS) technology, including amplicon and shot-gun approaches, and associated bioinformatics tools to count and classify commensal microbiome at the species level. The microbiome present in the whole body, particularly in the gut systems of finfish and shellfish, not only contributes to digestion but also has an impact on nutrition, growth, reproduction, immune system and vulnerability of the host fish to diseases. Therefore, the study of such microbial communities is highly relevant for the development of new and innovative bio-products which will be a vital source to build bio and pharmaceutical industries, including aquaculture. In recent years, attempts have been made to discover the chemical ingredients present in these microbes in the form of biomolecules/bioactive compounds with their functions and usefulness for various health benefits, particularly for the treatment of different types of disorders in animals. Therefore, it has been speculated that microbiomes hold great promise not only as a cure for ailments but also as a preventive measure for the number of infectious diseases. This kind of exploration of new breeds of microbes with their miraculous ingredients will definitely help to accelerate the development of the drugs, pharmaceutical and other biological related industries. Probiotic research and bioinformatics skills will further escalate these opportunities in the sector. In the present review, efforts have been made to collect comprehensive information on the finfish and shellfish microbiome, their diversity and functional properties, relationship with diseases, health status, data on species-specific metagenomics, probiotic research and bioinformatics skills. Further, emphasis has also been made to carry out microbiome research on priority basis not only to keep healthy environment of the fish farming sector but also for the sustainable growth of biological related industries, including aquaculture.}, } @article {pmid34354708, year = {2021}, author = {Wang, X and Yuan, X and Su, Y and Hu, J and Ji, Q and Fu, S and Li, R and Hu, L and Dai, C}, title = {Targeting Purinergic Receptor P2RX1 Modulates Intestinal Microbiota and Alleviates Inflammation in Colitis.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {696766}, pmid = {34354708}, issn = {1664-3224}, mesh = {Animals ; Antibodies, Neutralizing/*pharmacology ; Bacteria/*metabolism ; Benzenesulfonates/*pharmacology ; Colitis/immunology/metabolism/microbiology/*prevention & control ; Colon/*drug effects/immunology/metabolism/microbiology ; Disease Models, Animal ; Drug Therapy, Combination ; Dysbiosis ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Mice, Knockout ; Purinergic P2X Receptor Antagonists/*pharmacology ; Receptors, Purinergic P2X1/genetics/*metabolism ; Signal Transduction ; Tumor Necrosis Factor Inhibitors/*pharmacology ; Mice ; }, abstract = {Inflammatory bowel disease (IBD) remains one of the most prevalent gastrointestinal diseases worldwide. Purinergic signaling has emerged as a promising therapeutic target of inflammation-associated diseases. However, little is known about the specific roles of purinergic receptors in IBD. In the present study, expression profile of purinergic receptors was screened in the public Gene Expression Omnibus (GEO) datasets, and we found that expression of P2RX1 was significantly upregulated in inflamed colon tissues. Then, purinergic receptor P2RX1 was genetically ablated in the background of C57BL/6 mice, and dextran sulfate sodium (DSS) was used to induce mice colitis. RNA sequencing results of colon tissues showed that genetic knockout of P2RX1 suppressed the inflammation responses in DSS-induced mice colitis. Flow cytometry indicated that neutrophil infiltration was inhibited in P2RX1 ablated mice. 16S ribosomal DNA sequencing revealed major differences of intestinal microbiota between WT and P2RX1 ablated mice. Functional metagenomics prediction indicated that the indole alkaloid biogenesis pathway was upregulated in P2RX1 gene ablated mice. Further studies revealed that microbiota metabolites (indole alkaloid)-involved aryl hydrocarbon receptor (AhR)/IL-22 axis was associated with the beneficial effects of P2RX1 ablation. Finally, we found that a specific P2RX1 inhibitor succeeded to improve the therapeutic efficiency of anti-TNF-α therapy in DSS-induced mice colitis. Therefore, our study suggests that targeting purinergic receptor P2RX1 may provide novel therapeutic strategy for IBD.}, } @article {pmid34354062, year = {2021}, author = {Schaan, AP and Sarquis, D and Cavalcante, GC and Magalhães, L and Sacuena, ERP and Costa, J and Fonseca, D and Mello, VJ and Guerreiro, JF and Ribeiro-Dos-Santos, Â}, title = {The structure of Brazilian Amazonian gut microbiomes in the process of urbanisation.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {65}, pmid = {34354062}, issn = {2055-5008}, mesh = {Bacteria/*classification/genetics ; Biodiversity ; Brazil ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Life Style ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; Rural Population ; Urban Population ; *Urbanization ; }, abstract = {Shifts in subsistence strategy among Native American people of the Amazon may be the cause of typically western diseases previously linked to modifications of gut microbial communities. Here, we used 16S ribosomal RNA sequencing to characterise the gut microbiome of 114 rural individuals, namely Xikrin, Suruí and Tupaiú, and urban individuals from Belém city, in the Brazilian Amazon. Our findings show the degree of potential urbanisation occurring in the gut microbiome of rural Amazonian communities characterised by the gradual loss and substitution of taxa associated with rural lifestyles, such as Treponema. Comparisons to worldwide populations indicated that Native American groups are similar to South American agricultural societies and urban groups are comparable to African urban and semi-urban populations. The transitioning profile observed among traditional populations is concerning in light of increasingly urban lifestyles. Lastly, we propose the term "tropical urban" to classify the microbiome of urban populations living in tropical zones.}, } @article {pmid34352595, year = {2021}, author = {Lin, W and Djukovic, A and Mathur, D and Xavier, JB}, title = {Listening in on the conversation between the human gut microbiome and its host.}, journal = {Current opinion in microbiology}, volume = {63}, number = {}, pages = {150-157}, doi = {10.1016/j.mib.2021.07.009}, pmid = {34352595}, issn = {1879-0364}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolomics ; Metagenomics ; *Microbiota ; }, abstract = {The gut microbiome is an ecosystem. Natural selection favored microbes fit for the gut, which can utilize and convert molecules produced by the host for their own benefit. But natural selection also favored the host's mechanisms to sense and respond to the microbial ecosystem for its own benefit. We can listen in on the host-microbiome 'conversation' in the simultaneous responses of the microbiome and the host to strong perturbations. In laboratory animals a perturbation can be done for research; in human patients a perturbation can be caused by disease or therapy. Advances in metagenomics, metabolomics and computation amplify our means to listen in on the conversation between the gut microbiome and its host.}, } @article {pmid34352239, year = {2021}, author = {Frizzera, A and Bojko, J and Cremonte, F and Vázquez, N}, title = {Symbionts of invasive and native crabs, in Argentina: The most recently invaded area on the Southwestern Atlantic coastline.}, journal = {Journal of invertebrate pathology}, volume = {184}, number = {}, pages = {107650}, doi = {10.1016/j.jip.2021.107650}, pmid = {34352239}, issn = {1096-0805}, mesh = {Animals ; Argentina ; Brachyura/*parasitology/*physiology ; *Host-Parasite Interactions ; Introduced Species ; *Symbiosis ; Trematoda/*physiology ; }, abstract = {Biological invasions have the capacity to introduce non-native parasites. This study aimed to determine whether the invasive green crab population, Carcinus spp., on the Southwestern Atlantic coast of Argentina harbours any symbionts, and whether these may spillover or spillback between native crabs, Cyrtograpsus altimanus and C. angulatus. Macroscopy, histology, and molecular analyses of some parasites were used to describe and compare their diversity across the three species of crab. We also evaluated the susceptibility of invasive Carcinus spp. to a native digenean, Maritrema madrynense, via experimental infections (exposure and cohabitation). Our results revealed that the green crab pathobiome included similar symbiotic groups to native crabs. This included putative viral, bacterial, and protozoan parasites. Haplosporidium-like observations were recorded in all crab species, and a single green crab was found to be parasitized by an Agmasoma-like microsporidium. Metagenomic analysis of one individual revealed additional symbiotic diversity (46 bacteria, 5 eukaryotic species). The green crabs were infected by more microparasite taxa than the native crabs (5:3). Wild populations of Carcinus spp. were free of metazoan parasites and are shown not to be susceptible to M. madryense under experimental conditions. Our results suggest a reduction/escape of macroparasites (trematode Maritrema madrynense; acanthocephalan Profilicollis chasmagnathi) in invasive Carcinus spp. compared to their native competitors.}, } @article {pmid34351018, year = {2021}, author = {Paul, LJ and Ericsson, AC and Andrews, FM and Keowen, ML and Morales Yniguez, F and Garza, F and Banse, HE}, title = {Gastric microbiome in horses with and without equine glandular gastric disease.}, journal = {Journal of veterinary internal medicine}, volume = {35}, number = {5}, pages = {2458-2464}, pmid = {34351018}, issn = {1939-1676}, support = {//LSU Equine Health Studies Program Charles V. Cusimano Grant/ ; }, mesh = {Animals ; Gastric Mucosa ; *Gastrointestinal Microbiome ; *Horse Diseases ; Horses ; RNA, Ribosomal, 16S/genetics ; *Stomach Diseases/veterinary ; *Stomach Ulcer/veterinary ; }, abstract = {BACKGROUND: The role of the gastric microbiome in development or persistence of equine glandular gastric disease (EGGD) remains to be investigated.

HYPOTHESIS/OBJECTIVES: The objective was to characterize the glandular mucosal and gastric fluid microbiomes of horses with and without EGGD. It was hypothesized that differences in the mucosal microbiome are associated with EGGD.

ANIMALS: Twenty-four horses were enrolled.

METHODS: Gastroscopy was performed and EGGD scores recorded (score 0, n = 6; score 1, n = 8; score ≥2, n = 10). Gastric fluid and pinch biopsies of healthy glandular mucosa and EGGD lesions were collected via gastroscope. 16S rRNA amplicon sequencing of the gastric fluid and glandular mucosal biopsies was performed. Relationships between gastric fluid and mucosal microbial community composition were evaluated among EGGD score groups (EGGD 0-BX, EGGD 1-BX, EGGD ≥2-BX) and among endoscopic appearances: controls from horses without EGGD and normal areas, hyperemic areas, and lesions from horses with EGGD.

RESULTS: Microbial community structure of mucosal biopsies differed among EGGD score groups (Jaccard similarity index; P = .009). Principal coordinate analysis showed separate clusters for EGGD 0-BX and EGGD ≥2-BX.

A modest difference was detected in the community structure of the gastric glandular mucosal microbiome in association with EGGD score.}, } @article {pmid34349022, year = {2021}, author = {Lee, S and Sieradzki, ET and Nicolas, AM and Walker, RL and Firestone, MK and Hazard, C and Nicol, GW}, title = {Methane-derived carbon flows into host-virus networks at different trophic levels in soil.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {32}, pages = {}, pmid = {34349022}, issn = {1091-6490}, mesh = {Bacteria/genetics/metabolism/*virology ; Carbon/*metabolism ; Carbon Radioisotopes/metabolism ; Clustered Regularly Interspaced Short Palindromic Repeats ; DNA Viruses/*genetics ; Genome, Bacterial ; Genome, Viral ; Metagenomics ; Methane/chemistry/*metabolism ; Microbiota ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {The concentration of atmospheric methane (CH4) continues to increase with microbial communities controlling soil-atmosphere fluxes. While there is substantial knowledge of the diversity and function of prokaryotes regulating CH4 production and consumption, their active interactions with viruses in soil have not been identified. Metagenomic sequencing of soil microbial communities enables identification of linkages between viruses and hosts. However, this does not determine if these represent current or historical interactions nor whether a virus or host are active. In this study, we identified active interactions between individual host and virus populations in situ by following the transfer of assimilated carbon. Using DNA stable-isotope probing combined with metagenomic analyses, we characterized CH4-fueled microbial networks in acidic and neutral pH soils, specifically primary and secondary utilizers, together with the recent transfer of CH4-derived carbon to viruses. A total of 63% of viral contigs from replicated soil incubations contained homologs of genes present in known methylotrophic bacteria. Genomic sequences of [13]C-enriched viruses were represented in over one-third of spacers in CRISPR arrays of multiple closely related Methylocystis populations and revealed differences in their history of viral interaction. Viruses infecting nonmethanotrophic methylotrophs and heterotrophic predatory bacteria were also identified through the analysis of shared homologous genes, demonstrating that carbon is transferred to a diverse range of viruses associated with CH4-fueled microbial food networks.}, } @article {pmid34348764, year = {2021}, author = {Browne, HP and Almeida, A and Kumar, N and Vervier, K and Adoum, AT and Viciani, E and Dawson, NJR and Forster, SC and Cormie, C and Goulding, D and Lawley, TD}, title = {Host adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {204}, pmid = {34348764}, issn = {1474-760X}, support = {/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Anaerobiosis/genetics ; Biological Evolution ; Firmicutes/*genetics/growth & development ; Gastrointestinal Microbiome/*genetics ; *Genome, Bacterial ; Host Adaptation/*genetics ; Humans ; Metagenome ; Microbiota/*genetics ; Spores, Bacterial/*genetics/growth & development ; Symbiosis/*genetics ; }, abstract = {BACKGROUND: Human-to-human transmission of symbiotic, anaerobic bacteria is a fundamental evolutionary adaptation essential for membership of the human gut microbiota. However, despite its importance, the genomic and biological adaptations underpinning symbiont transmission remain poorly understood. The Firmicutes are a dominant phylum within the intestinal microbiota that are capable of producing resistant endospores that maintain viability within the environment and germinate within the intestine to facilitate transmission. However, the impact of host transmission on the evolutionary and adaptive processes within the intestinal microbiota remains unknown.

RESULTS: We analyze 1358 genomes of Firmicutes bacteria derived from host and environment-associated habitats. Characterization of genomes as spore-forming based on the presence of sporulation-predictive genes reveals multiple losses of sporulation in many distinct lineages. Loss of sporulation in gut Firmicutes is associated with features of host-adaptation such as genome reduction and specialized metabolic capabilities. Consistent with these data, analysis of 9966 gut metagenomes from adults around the world demonstrates that bacteria now incapable of sporulation are more abundant within individuals but less prevalent in the human population compared to spore-forming bacteria.

CONCLUSIONS: Our results suggest host adaptation in gut Firmicutes is an evolutionary trade-off between transmission range and colonization abundance. We reveal host transmission as an underappreciated process that shapes the evolution, assembly, and functions of gut Firmicutes.}, } @article {pmid34347346, year = {2021}, author = {Liu, L and Wang, S and Chen, J}, title = {Anthropogenic activities change the relationship between microbial community taxonomic composition and functional attributes.}, journal = {Environmental microbiology}, volume = {23}, number = {11}, pages = {6663-6675}, doi = {10.1111/1462-2920.15702}, pmid = {34347346}, issn = {1462-2920}, mesh = {*Anthropogenic Effects ; Metagenome ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Rivers ; }, abstract = {Functional redundancy is considered common in microbial systems, but recent studies have challenged this idea. The mechanism for this contradictory result is not clear. However, in this study, we hypothesize that strong environmental filtering which links to the anthropogenic activities is able to weaken microbial functional redundancy. We used metagenome and 16S rRNA gene high-throughput sequencing to investigate planktonic microbial communities in a subtropical river. We found that the weak anthropogenic activities might result in a low selection pressure in the river upstream area. Therefore, the microbial community functional attributes were stable although the community composition changed with the water temperature and NO3 -N in upstream area (this indicates functional redundancy). However, the strong anthropogenic activities in river downstream area selected pollutant-degraded functions (e.g. nitrogen metabolism, toluene, xylenes and ethylbenzene degradation) and potentially pollutant-degraded (tolerant) microbes, and therefore caused the microbial community composition synchronously changed with the variation of community functional attributes. Our results reveal that strong environmental filtering which associates with the anthropogenic activities not only has effects on microbial community composition and community functional attributes but also on their relationships. These results provide a new insight to refine the functional redundancy idea.}, } @article {pmid34346741, year = {2021}, author = {Breitkreuz, C and Heintz-Buschart, A and Buscot, F and Wahdan, SFM and Tarkka, M and Reitz, T}, title = {Can We Estimate Functionality of Soil Microbial Communities from Structure-Derived Predictions? A Reality Test in Agricultural Soils.}, journal = {Microbiology spectrum}, volume = {9}, number = {1}, pages = {e0027821}, pmid = {34346741}, issn = {2165-0497}, mesh = {Agriculture ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Carbon/metabolism ; DNA, Bacterial/genetics ; *Microbiota ; Nitrogen/metabolism ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Computational approaches that link bacterial 16S rRNA gene amplicon data to functional genes based on prokaryotic reference genomes have emerged. This study aims to validate or refute the applicability of the functional gene prediction tools for assessment and comparison of community functionality among experimental treatments, inducing either fast or slow responses in rhizosphere microbial community composition and function. Rhizosphere samples of wheat and barley were collected in two consecutive years at active and mature growth phases from organic and conventional farming plots with ambient or future-climate treatments of the Global Change Experimental Facility. Bacterial community composition was determined by 16S rRNA gene amplicon sequencing, and the activities of five extracellular enzymes involved in carbon (β-glucosidases, cellobiohydrolase, and xylosidase), nitrogen (N-acetylglucosaminidase), and phosphorus (acid phosphatase) cycles were determined. Structural community data were used to predict functional patterns of the rhizosphere communities using Tax4Fun and PanFP. Subsequently, the predictions were compared with the measured activities. Despite the fact that different treatments mainly drove either community composition (plant growth phase) or measured enzyme activities (farming system), the predictions mirrored patterns in the treatments in a qualitative but not quantitative way. Most of the discrepancies between measured and predicted values resulted from plant growth stages (fast community response), followed by farming management and climate (slower community response). Thus, our results suggest the applicability of the prediction tools for comparative investigations of soil community functionality in less-dynamic environmental systems. IMPORTANCE Linking soil microbial community structure to its functionality, which is important for maintaining health and services of an ecosystem, is still challenging. Besides great advances in structural community analysis, functional equivalents, such as metagenomics and metatranscriptomics, are still time and cost intensive. Recent computational approaches (Tax4Fun and PanFP) aim to predict functions from structural community data based on reference genomes. Although the usability of these tools has been confirmed with metagenomic data, a comparison between predicted and measured functions is so far missing. Thus, this study comprises an expansive reality test on the performance of these tools under different environmental conditions, including relevant global change factors (land use and climate). The work provides a valuable validation of the applicability of the prediction tools for comparison of soil community functions across different sufficiently established soil ecosystems and suggest their usability to unravel the broad spectrum of functions provided by a given community structure.}, } @article {pmid34346706, year = {2021}, author = {Ma, L and Keng, J and Cheng, M and Pan, H and Feng, B and Hu, Y and Feng, T and Yang, F}, title = {Gut Microbiome and Serum Metabolome Alterations Associated with Isolated Dystonia.}, journal = {mSphere}, volume = {6}, number = {4}, pages = {e0028321}, pmid = {34346706}, issn = {2379-5042}, mesh = {Adult ; Bacteria/classification/*genetics/*metabolism ; Biosynthetic Pathways/genetics ; Dysbiosis/microbiology ; Dystonia/*blood/*etiology/microbiology/physiopathology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Mass Spectrometry ; *Metabolome ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Dystonia is a complex neurological movement disorder characterized by involuntary muscle contractions. Increasing studies implicate the microbiome as a possible key susceptibility factor for neurological disorders, but the relationship between the gut microbiota and dystonia remains poorly explored. Here, the gut microbiota of 57 patients with isolated dystonia and 27 age- and environment-matched healthy controls was analyzed by 16S rRNA gene amplicon sequencing. Further, integrative analysis of the gut microbiome and serum metabolome measured by high-performance liquid chromatography-mass spectrometry was performed. No difference in α-diversity was found, while β-diversity was significantly different, with a more heterogeneous community structure among dystonia patients than among controls. The most significant changes in dystonia highlighted an increase in Clostridiales, including Blautia obeum, Dorea longicatena, and Eubacterium hallii, and a reduction in Bacteroides vulgatus and Bacteroides plebeius. The functional analysis revealed that genes related to tryptophan and purine biosynthesis were more abundant in gut microbiota from patients with dystonia, while genes linked to citrate cycle, vitamin B6, and glycan metabolism were less abundant. The evaluation of serum metabolites revealed altered levels of l-glutamic acid, taurine, and d-tyrosine, suggesting changes in neurotransmitter metabolism. The most modified metabolites strongly inversely correlated with the abundance of members belonging to the Clostridiales, revealing the effect of the gut microbiota on neurometabolic activity. This study is the first to reveal gut microbial dysbiosis in patients with isolated dystonia and identified potential links between gut microbiota and serum neurotransmitters, providing new insight into the pathogenesis of isolated dystonia. IMPORTANCE Dystonia is the third most common movement disorder after essential tremor and Parkinson's disease. However, the cause for the majority of cases is not known. This is the first study so far that reveals significant alterations of gut microbiome and correlates the alteration of serum metabolites with gut dysbiosis in patients with isolated dystonia. We demonstrated a general overrepresentation of Clostridiales and underrepresentation of Bacteroidetes in patients with dystonia in comparison with healthy controls. The functional analysis found that genes related to the biosynthesis of tryptophan, which is the precursor of the neurotransmitter serotonin, were more active in isolated dystonia patients. Altered levels of several serum metabolites were found to be associated with microbial changes, such as d-tyrosine, taurine, and glutamate, indicating differences in neurotransmitter metabolism in isolated dystonia. Integrative analysis suggests that neurotransmitter system dysfunction may be a possible pathway by which the gut microbiome participates in the development of dystonia. The gut microbiome changes provide new insight into the pathogenesis of dystonia, suggesting new potential therapeutic directions.}, } @article {pmid34346704, year = {2021}, author = {Huang, X and Welsh, RM and Deming, C and Proctor, DM and Thomas, PJ and , and Gussin, GM and Huang, SS and Kong, HH and Bentz, ML and Vallabhaneni, S and Chiller, T and Jackson, BR and Forsberg, K and Conlan, S and Litvintseva, AP and Segre, JA}, title = {Skin Metagenomic Sequence Analysis of Early Candida auris Outbreaks in U.S. Nursing Homes.}, journal = {mSphere}, volume = {6}, number = {4}, pages = {e0028721}, pmid = {34346704}, issn = {2379-5042}, mesh = {Candida auris/*genetics ; Candidiasis/*epidemiology/microbiology ; Disease Outbreaks ; Humans ; Metagenome ; Metagenomics/*methods ; Mycobiome/genetics ; Nursing Homes/*statistics & numerical data ; Risk Factors ; Skin/*microbiology ; United States/epidemiology ; }, abstract = {Candida auris is a human fungal pathogen classified as an urgent threat to the delivery of health care due to its extensive antimicrobial resistance and the high mortality rates associated with invasive infections. Global outbreaks have occurred in health care facilities, particularly, long-term care hospitals and nursing homes. Skin is the primary site of colonization for C. auris. To accelerate research studies, we developed microbiome sequencing protocols, including amplicon and metagenomic sequencing, directly from patient samples at health care facilities with ongoing C. auris outbreaks. We characterized the skin mycobiome with a database optimized to classify Candida species and C. auris to the clade level. While Malassezia species were the predominant skin-associated fungi, nursing home residents also harbored Candida species, including C. albicans, and C. parapsilosis. Amplicon sequencing was concordant with culturing studies to identify C. auris-colonized patients and provided further resolution that distinct clades of C. auris are colonizing facilities in New York and Illinois. Shotgun metagenomic sequencing from a clinical sample with a high fungal bioburden generated a skin-associated profile of the C. auris genome. Future larger scale clinical studies are warranted to more systematically investigate the effects of commensal microbes and patient risk factors on the colonization and transmission of C. auris. IMPORTANCE Candida auris is a human pathogen of high concern due to its extensive antifungal drug resistance and high mortality rates associated with invasive infections. Candida auris skin colonization and persistence on environmental surfaces make this pathogen difficult to control once it enters a health care facility. Residents in long-term care hospitals and nursing homes are especially vulnerable. In this study, we developed microbiome sequencing protocols directly from surveillance samples, including amplicon and metagenomic sequencing, demonstrating concordance between sequencing results and culturing.}, } @article {pmid34346509, year = {2022}, author = {Song, X and Liu, L and Peng, S and Liu, T and Chen, Y and Jia, R and Zou, Y and Li, L and Zhao, X and Liang, X and Tang, H and Yin, Z}, title = {Resveratrol regulates intestinal barrier function in cyclophosphamide-induced immunosuppressed mice.}, journal = {Journal of the science of food and agriculture}, volume = {102}, number = {3}, pages = {1205-1215}, doi = {10.1002/jsfa.11458}, pmid = {34346509}, issn = {1097-0010}, mesh = {Animals ; Cyclophosphamide/*adverse effects ; Gastrointestinal Microbiome/drug effects ; Immunocompromised Host ; Interferon-gamma/genetics/immunology ; Interleukin-4/genetics/immunology ; Intestinal Mucosa/*drug effects/*immunology/microbiology ; Male ; Mice ; Mice, Inbred BALB C ; NF-kappa B/genetics ; Occludin/genetics/immunology ; Resveratrol/*administration & dosage ; Tumor Necrosis Factor-alpha/genetics/immunology ; }, abstract = {BACKGROUND: Resveratrol, a kind of polyphenolic phytoalexin, can be obtained from numerous natural foods. Although resveratrol is demonstrated to have various bioactivities, little is known about the regulation of intestinal barrier function under immunosuppression. The present study is aimed at investigating the regulatory effect of resveratrol on intestinal barrier function in immunosuppression in mice induced by cyclophosphamide.

RESULTS: The effects of resveratrol on intestinal biological barrier were evaluated by 16S rRNA and metagenome sequencing analysis. The results showed that resveratrol could improve diversity of the intestinal microbiota and intestinal flora structure by increasing the abundance of probiotics, and resveratrol regulated the function of gut microbiota to resist immunosuppression. Resveratrol could significantly upregulate the secretion of secretory immunoglobulin A and promote the transcriptional levels of test cytokines, including tumor necrosis factor α, interferon γ, interleukin 4 and interleukin 6 in jejunum and ileum mucosa, suggesting improved intestinal immune barrier by resveratrol. The mRNA and protein levels of tight junction proteins involved in intestinal physical barrier function, including zonula occludens 1 (ZO-1), claudin 1 and occludin, were increased after resveratrol treatment. The protein levels of toll-like receptor 4 (TLR4), phosphorylation nuclear factor kappa-B (NF-κB-p65) and inhibitor of nuclear factor kappa-B kinase α were decreased by resveratrol treatment when compared with the untreated group, indicating inhibition of the TLR4/NF-ĸB signaling pathway.

CONCLUSION: These results provide new insights into regulation of the intestinal barrier function by resveratrol under immunosuppression and potential applications of resveratrol in recovering intestinal function. © 2021 Society of Chemical Industry.}, } @article {pmid34346283, year = {2021}, author = {Bajaj, JS and Shamsaddini, A and Fagan, A and McGeorge, S and Gavis, E and Sikaroodi, M and Brenner, LA and Wade, JB and Gillevet, PM}, title = {Distinct gut microbial compositional and functional changes associated with impaired inhibitory control in patients with cirrhosis.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1953247}, pmid = {34346283}, issn = {1949-0984}, support = {I01 CX001076/CX/CSRD VA/United States ; R01 HS025412/HS/AHRQ HHS/United States ; R21 TR002024/TR/NCATS NIH HHS/United States ; R21 TR003095/TR/NCATS NIH HHS/United States ; }, mesh = {Aged ; *Gastrointestinal Microbiome ; Hepatic Encephalopathy/*etiology/*physiopathology ; Humans ; Liver Cirrhosis/*complications/*microbiology/*physiopathology ; Male ; Middle Aged ; Severity of Illness Index ; }, abstract = {Most cirrhosis etiologies, such as alcohol, hepatitis C, and obesity, involve behavior that require the loss of inhibitory control. Once cirrhosis develops, patients can also develop cognitive impairment due to minimal hepatic encephalopathy (MHE). Both processes could have distinct imprints on the gut-liver-brain axis. Determine the impact of inhibitory control versus traditional cirrhosis-related cognitive performance on gut microbial composition and function. Outpatients with cirrhosis underwent two tests for MHE: inhibitory control test (MHEICT, computerized associated with response inhibition) and psychometric hepatic encephalopathy score (MHEPHES, paper-pencil HE-specific associated with subcortical impairment) along with stool collection for metagenomics. MHEICT/not, MHEPHES/not, and discordant (positive on one test but negative on the other) were analyzed for demographics, bacterial species, and gut-brain modules (GBM) using multi-variable analyses. Ninety-seven patients [47 (49%) MHEPHES, 76 (78%) MHEICT, 41 discordant] were enrolled. MHEPHES/not: Cirrhosis severity was worse in MHEPHES without differences in alpha/beta diversity on bacterial species or GBMs. Pathobionts (Enterobacteriaceae) and γ-amino-butryic acid (GABA) synthesis GBM were higher in MHEPHES. MHEICT/not: We found similar cirrhosis severity and metagenomic alpha/beta diversity in MHEICT versus not. However, alpha/beta diversity of GBMs were different in MHEICT versus No-MHE patients. Alistipes ihumii, Prevotella copri, and Eubacterium spp. were higher, while Enterococcus spp. were uniquely lower in MHEICT versus no-MHE and discordant comparisons. GBMs belonging to tryptophan, menaquinone, GABA, glutamate, and short-chain fatty acid synthesis were also unique to MHEICT. Gut microbial signature of impaired inhibitory control, which is associated with addictive disorders that can lead to cirrhosis, is distinct from cirrhosis-related cognitive impairment.}, } @article {pmid34344959, year = {2021}, author = {Rouchka, EC and Chariker, JH and Alejandro, B and Adcock, RS and Singhal, R and Ramirez, J and Palmer, KE and Lasnik, AB and Carrico, R and Arnold, FW and Furmanek, S and Zhang, M and Wolf, LA and Waigel, S and Zacharias, W and Bordon, J and Chung, D}, title = {Induction of interferon response by high viral loads at early stage infection may protect against severe outcomes in COVID-19 patients.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {15715}, pmid = {34344959}, issn = {2045-2322}, support = {P20 GM103436/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Aged ; COVID-19/*pathology/virology ; Dysbiosis/etiology ; Female ; Humans ; Interferons/*metabolism ; Male ; Metagenomics ; Microbiota/genetics ; Middle Aged ; Nasopharynx/virology ; RNA, Viral/analysis ; Real-Time Polymerase Chain Reaction ; Respiratory System/microbiology/virology ; SARS-CoV-2/*genetics/isolation & purification ; Severity of Illness Index ; Transcriptome ; Up-Regulation ; Viral Load ; }, abstract = {Key elements for viral pathogenesis include viral strains, viral load, co-infection, and host responses. Several studies analyzing these factors in the function of disease severity of have been published; however, no studies have shown how all of these factors interplay within a defined cohort. To address this important question, we sought to understand how these four key components interplay in a cohort of COVID-19 patients. We determined the viral loads and gene expression using high throughput sequencing and various virological methods. We found that viral loads in the upper respiratory tract in COVID-19 patients at an early phase of infection vary widely. While the majority of nasopharyngeal (NP) samples have a viral load lower than the limit of detection of infectious viruses, there are samples with an extraordinary amount of SARS-CoV-2 RNA and a high viral titer. No specific viral factors were identified that are associated with high viral loads. Host gene expression analysis showed that viral loads were strongly correlated with cellular antiviral responses. Interestingly, however, COVID-19 patients who experience mild symptoms have a higher viral load than those with severe complications, indicating that naso-pharyngeal viral load may not be a key factor of the clinical outcomes of COVID-19. The metagenomics analysis revealed that the microflora in the upper respiratory tract of COVID-19 patients with high viral loads were dominated by SARS-CoV-2, with a high degree of dysbiosis. Finally, we found a strong inverse correlation between upregulation of interferon responses and disease severity. Overall our study suggests that a high viral load in the upper respiratory tract may not be a critical factor for severe symptoms; rather, dampened antiviral responses may be a critical factor for a severe outcome from the infection.}, } @article {pmid34344895, year = {2021}, author = {Tláskal, V and Brabcová, V and Větrovský, T and López-Mondéjar, R and Monteiro, LMO and Saraiva, JP and da Rocha, UN and Baldrian, P}, title = {Metagenomes, metatranscriptomes and microbiomes of naturally decomposing deadwood.}, journal = {Scientific data}, volume = {8}, number = {1}, pages = {198}, pmid = {34344895}, issn = {2052-4463}, mesh = {Bacteria/classification ; Czech Republic ; DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/genetics ; Ecosystem ; Fagus/*microbiology ; Forests ; Fungi/classification ; *Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Trees/microbiology ; Wood/*microbiology ; }, abstract = {Deadwood represents significant carbon (C) stock in a temperate forests. Its decomposition and C mobilization is accomplished by decomposer microorganisms - fungi and bacteria - who also supply the foodweb of commensalist microbes. Due to the ecosystem-level importance of deadwood habitat as a C and nutrient stock with significant nitrogen fixation, the deadwood microbiome composition and function are critical to understanding the microbial processes related to its decomposition. We present a comprehensive suite of data packages obtained through environmental DNA and RNA sequencing from natural deadwood. Data provide a complex picture of the composition and function of microbiome on decomposing trunks of European beech (Fagus sylvatica L.) in a natural forest. Packages include deadwood metagenomes, metatranscriptomes, sequences of total RNA, bacterial genomes resolved from metagenomic data and the 16S rRNA gene and ITS2 metabarcoding markers to characterize the bacterial and fungal communities. This project will be of use to microbiologists, environmental biologists and biogeochemists interested in the microbial processes associated with the transformation of recalcitrant plant biomass.}, } @article {pmid34343557, year = {2022}, author = {Roux, PF and Oddos, T and Stamatas, G}, title = {Deciphering the Role of Skin Surface Microbiome in Skin Health: An Integrative Multiomics Approach Reveals Three Distinct Metabolite‒Microbe Clusters.}, journal = {The Journal of investigative dermatology}, volume = {142}, number = {2}, pages = {469-479.e5}, doi = {10.1016/j.jid.2021.07.159}, pmid = {34343557}, issn = {1523-1747}, mesh = {DNA, Bacterial/isolation & purification ; Female ; Healthy Volunteers ; Humans ; Hydrogen-Ion Concentration ; Infant ; Male ; Metabolomics ; Metagenomics ; Microbiota/*physiology ; RNA, Ribosomal, 16S/genetics ; Skin/chemistry/metabolism/*microbiology ; *Skin Physiological Phenomena ; }, abstract = {The advent of 16S RNA profiling and shotgun metagenomics has enabled a holistic approach to the study of the skin microbiome composition. Despite the interesting findings in this rapidly developing scientific area, the big question remains: What role does the microbiome play in skin physiology? To begin answering this question, we employed an integrative methodology for microbiome and metabolome analysis of skin surface samples collected from the volar forearm of healthy infants aged 3-6-months. Whereas the infant skin metabolome was dominated by amino acids, lipids, and xenobiotics, the primary phyla of the microbiome were Firmicutes, Actinobacteria, and Proteobacteria. Zooming in on the species level revealed a large contribution of commensals belonging to the Cutibacterium and Staphylococcus genera, including Cutibacterium acnes, Staphylococcus epidermidis, and S. aureus. This heterogeneity was further highlighted when combining the microbiome with metabolome data. Integrative analyses delineated the coexistence of three distinct metabolite‒microbe clusters: one dominated by Cutibacterium linked to hydrophobic elements of the skin barrier, one associating Staphylococcus genus with amino acids relevant to the water holding capacity and pH regulation of the skin surface, and one characterized by Streptococcus and independent of any particular metabolomic profile.}, } @article {pmid34341764, year = {2021}, author = {Wen, M and Liu, T and Zhao, M and Dang, X and Feng, S and Ding, X and Xu, Z and Huang, X and Lin, Q and Xiang, W and Li, X and He, X and He, Q}, title = {Correlation Analysis between Gut Microbiota and Metabolites in Children with Systemic Lupus Erythematosus.}, journal = {Journal of immunology research}, volume = {2021}, number = {}, pages = {5579608}, pmid = {34341764}, issn = {2314-7156}, mesh = {Age Factors ; Biomarkers ; Case-Control Studies ; Child ; *Disease Susceptibility ; Dysbiosis ; Feces/microbiology ; Female ; Gas Chromatography-Mass Spectrometry/methods ; *Gastrointestinal Microbiome ; Humans ; Immunosuppressive Agents/therapeutic use ; Lupus Erythematosus, Systemic/drug therapy/*etiology/*metabolism/pathology ; Male ; *Metabolome ; Metabolomics/methods ; Metagenomics/methods ; }, abstract = {Systemic lupus erythematosus (SLE) is an autoimmune-mediated diffuse connective tissue disease characterized by immune inflammation with an unclear aetiology and pathogenesis. This work profiled the intestinal flora and faecal metabolome of patients with SLE using 16S RNA sequencing and gas chromatography-mass spectrometry (GC-MS). We identified unchanged alpha diversity and partially altered beta diversity of the intestinal flora. Another important finding was the increase in Proteobacteria and Enterobacteriales and the decrease in Ruminococcaceae among SLE patients. For metabolites, amino acids and short-chain fatty acids were enriched when long-chain fatty acids were downregulated in SLE faecal samples. KEGG analysis showed the significance of the protein digestion and absorption pathway, and association analysis revealed the key role of 3-phenylpropanoic acid and Sphingomonas. Sphingomonas were reported to be less abundant in healthy periodontal sites of SLE patients than in those of HCs, indicating transmission of oral species to the gut. This study contributes to the understanding of the pathogenesis of SLE disease from the perspective of intestinal microorganisms, explains the pathogenesis of SLE, and serves as a basis for exploring potential treatments for the disease.}, } @article {pmid34341379, year = {2021}, author = {Bel Lassen, P and Belda, E and Prifti, E and Dao, MC and Specque, F and Henegar, C and Rinaldi, L and Wang, X and Kennedy, SP and Zucker, JD and Calame, W and Lamarche, B and Claus, SP and Clément, K}, title = {Protein supplementation during an energy-restricted diet induces visceral fat loss and gut microbiota amino acid metabolism activation: a randomized trial.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {15620}, pmid = {34341379}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *Intra-Abdominal Fat/metabolism ; *Dietary Supplements ; Adult ; Middle Aged ; *Amino Acids/metabolism ; *Caloric Restriction/methods ; Double-Blind Method ; Dietary Proteins/administration & dosage/metabolism ; Energy Metabolism ; }, abstract = {Interactions between diet and gut microbiota are critical regulators of energy metabolism. The effects of fibre intake have been deeply studied but little is known about the impact of proteins. Here, we investigated the effects of high protein supplementation (Investigational Product, IP) in a double blind, randomised placebo-controled intervention study (NCT01755104) where 107 participants received the IP or an isocaloric normoproteic comparator (CP) alongside a mild caloric restriction. Gut microbiota profiles were explored in a patient subset (n = 53) using shotgun metagenomic sequencing. Visceral fat decreased in both groups (IP group: - 20.8 ± 23.2 cm[2]; CP group: - 14.5 ± 24.3 cm[2]) with a greater reduction (p < 0.05) with the IP supplementation in the Per Protocol population. Microbial diversity increased in individuals with a baseline low gene count (p < 0.05). The decrease in weight, fat mass and visceral fat mass significantly correlated with the increase in microbial diversity (p < 0.05). Protein supplementation had little effects on bacteria composition but major differences were seen at functional level. Protein supplementation stimulated bacterial amino acid metabolism (90% amino-acid synthesis functions enriched with IP versus 13% in CP group (p < 0.01)). Protein supplementation alongside a mild energy restriction induces visceral fat mass loss and an activation of gut microbiota amino-acid metabolism.Clinical trial registration: NCT01755104 (24/12/2012). https://clinicaltrials.gov/ct2/show/record/NCT01755104?term=NCT01755104&draw=2&rank=1 .}, } @article {pmid34340550, year = {2021}, author = {Goordial, J and D'Angelo, T and Labonté, JM and Poulton, NJ and Brown, JM and Stepanauskas, R and Früh-Green, GL and Orcutt, BN}, title = {Microbial Diversity and Function in Shallow Subsurface Sediment and Oceanic Lithosphere of the Atlantis Massif.}, journal = {mBio}, volume = {12}, number = {4}, pages = {e0049021}, pmid = {34340550}, issn = {2150-7511}, mesh = {Genomics ; Geologic Sediments/*microbiology ; Microbiota/*genetics ; *Oceans and Seas ; }, abstract = {The marine lithospheric subsurface is one of the largest biospheres on Earth; however, little is known about the identity and ecological function of microorganisms found in low abundance in this habitat, though these organisms impact global-scale biogeochemical cycling. Here, we describe the diversity and metabolic potential of sediment and endolithic (within rock) microbial communities found in ultrasmall amounts (10[1] to 10[4] cells cm[-3]) in the subsurface of the Atlantis Massif, an oceanic core complex on the Mid-Atlantic Ridge that was sampled on International Ocean Discovery Program (IODP) Expedition 357. This study used fluorescence-activated cell sorting (FACS) to enable the first amplicon, metagenomic, and single-cell genomic study of the shallow (<20 m below seafloor) subsurface of an actively serpentinizing marine system. The shallow subsurface biosphere of the Atlantis Massif was found to be distinct from communities observed in the nearby Lost City alkaline hydrothermal fluids and chimneys, yet similar to other low-temperature, aerobic subsurface settings. Genes associated with autotrophy were rare, although heterotrophy and aerobic carbon monoxide and formate cycling metabolisms were identified. Overall, this study reveals that the shallow subsurface of an oceanic core complex hosts a biosphere that is not fueled by active serpentinization reactions and by-products. IMPORTANCE The subsurface rock beneath the ocean is one of the largest biospheres on Earth, and microorganisms within influence global-scale nutrient cycles. This biosphere is difficult to study, in part due to the low concentrations of microorganisms that inhabit the vast volume of the marine lithosphere. In spite of the global significance of this biosphere, little is currently known about the microbial ecology of such rock-associated microorganisms. This study describes the identity and genomic potential of microorganisms in the subsurface rock and sediment at the Atlantis Massif, an underwater mountain near the Mid-Atlantic Ridge. To enable our analyses, fluorescence-activated cell sorting (FACS) was used as a means to concentrate cells from low biomass environmental samples for genomic analyses. We found distinct rock-associated microorganisms and found that the capacity for microorganisms to utilize organic carbon was the most prevalent form of carbon cycling. We additionally identified a potential role for carbon monoxide metabolism in the subsurface.}, } @article {pmid34339936, year = {2021}, author = {Okamura, Y and Kinoshita, M and Kono, T and Sakai, M and Hikima, JI}, title = {Deficiency of interleukin-17 receptor A1 induces microbiota disruption in the intestine of Japanese medaka, Oryzias latipes.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {40}, number = {}, pages = {100885}, doi = {10.1016/j.cbd.2021.100885}, pmid = {34339936}, issn = {1878-0407}, mesh = {Animals ; Intestines ; *Microbiota ; *Oryzias/genetics ; RNA, Ribosomal, 16S/genetics ; Receptors, Interleukin-17/genetics ; }, abstract = {The mutual relationship between the intestinal immune system and the gut microbiota has received a great deal of attention. In mammals, interleukin-17A and F (IL-17A/F) are inflammatory cytokines and key regulators of the gut microbiota. However, in teleosts, the function of IL-17A/F in controlling the gut microbiota is poorly understood. We attempted to elucidate the importance of teleost IL-17 signaling in controlling gut microbiota. We previously established a knockout (KO) of IL-17 receptor A (RA) 1, a receptor for IL-17A/F, in the Japanese medaka (Oryzias latipes) using the CRISPR-Cas9 system and performed 16S rRNA-based metagenomic analyses using the anterior and posterior sections of the intestinal tract. The number of observed OTUs in the anterior intestine was significantly decreased in IL-17RA1 KO medaka compared to that in the wild-type (WT). Furthermore, β-diversity analysis (weighted UniFrac) revealed considerably different bacterial composition in the anterior intestine of IL-17RA1 KO compared to WT, with similar findings in α-diversity. Notably, the pathogen Plesiomonas shigelloides was significantly increased in the posterior intestine of IL-17RA1 KO medaka. These findings indicate that signaling via IL-17RA1 is required to maintain a healthy gut microbiota in teleosts and mammals. The involvement of IL-17RA1 in controlling the gut microbiota has been demonstrated, resulting in microbiome dysbiosis in IL-17RA1 KO medaka.}, } @article {pmid34337850, year = {2022}, author = {Medina Ferrer, F and Rosen, MR and Feyhl-Buska, J and Russell, VV and Sønderholm, F and Loyd, S and Shapiro, R and Stamps, BW and Petryshyn, V and Demirel-Floyd, C and Bailey, JV and Johnson, HA and Spear, JR and Corsetti, FA}, title = {Potential role for microbial ureolysis in the rapid formation of carbonate tufa mounds.}, journal = {Geobiology}, volume = {20}, number = {1}, pages = {79-97}, doi = {10.1111/gbi.12467}, pmid = {34337850}, issn = {1472-4669}, mesh = {Biofilms ; Calcium Carbonate/chemistry ; *Carbonates ; Chemical Precipitation ; Lakes ; *Microbiota ; }, abstract = {Modern carbonate tufa towers in the alkaline (~pH 9.5) Big Soda Lake (BSL), Nevada, exhibit rapid precipitation rates (exceeding 3 cm/year) and host diverse microbial communities. Geochemical indicators reveal that carbonate precipitation is, in part, promoted by the mixing of calcium-rich groundwater and carbonate-rich lake water, such that a microbial role for carbonate precipitation is unknown. Here, we characterize the BSL microbial communities and evaluate their potential effects on carbonate precipitation that may influence fast carbonate precipitation rates of the active tufa mounds of BSL. Small subunit rRNA gene surveys indicate a diverse microbial community living endolithically, in interior voids, and on tufa surfaces. Metagenomic DNA sequencing shows that genes associated with metabolisms that are capable of increasing carbonate saturation (e.g., photosynthesis, ureolysis, and bicarbonate transport) are abundant. Enzyme activity assays revealed that urease and carbonic anhydrase, two microbial enzymes that promote carbonate precipitation, are active in situ in BSL tufa biofilms, and urease also increased calcium carbonate precipitation rates in laboratory incubation analyses. We propose that, although BSL tufas form partially as a result of water mixing, tufa-inhabiting microbiota promote rapid carbonate authigenesis via ureolysis, and potentially via bicarbonate dehydration and CO2 outgassing by carbonic anhydrase. Microbially induced calcium carbonate precipitation in BSL tufas may generate signatures preserved in the carbonate microfabric, such as stromatolitic layers, which could serve as models for developing potential biosignatures on Earth and elsewhere.}, } @article {pmid34336713, year = {2021}, author = {Caddey, B and De Buck, J}, title = {Meta-Analysis of Bovine Digital Dermatitis Microbiota Reveals Distinct Microbial Community Structures Associated With Lesions.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {685861}, pmid = {34336713}, issn = {2235-2988}, mesh = {Animals ; Cattle ; *Cattle Diseases ; *Digital Dermatitis ; Metagenomics ; *Microbiota ; Treponema/genetics ; }, abstract = {Bovine digital dermatitis (DD) is a significant cause of infectious lameness and economic losses in cattle production across the world. There is a lack of a consensus across different 16S metagenomic studies on DD-associated bacteria that may be potential pathogens of the disease. The goal of this meta-analysis was to identify a consistent group of DD-associated bacteria in individual DD lesions across studies, regardless of experimental design choices including sample collection and preparation, hypervariable region sequenced, and sequencing platform. A total of 6 studies were included in this meta-analysis. Raw sequences and metadata were identified on the NCBI sequence read archive and European nucleotide archive. Bacterial community structures were investigated between normal skin and DD skin samples. Random forest models were generated to classify DD status based on microbial composition, and to identify taxa that best differentiate DD status. Among all samples, members of Treponema, Mycoplasma, Porphyromonas, and Fusobacterium were consistently identified in the majority of DD lesions, and were the best genera at differentiating DD lesions from normal skin. Individual study and 16S hypervariable region sequenced had significant influence on final DD lesion microbial composition (P < 0.05). These findings indicate that members of Treponema, Mycoplasma, Porphyromonas, and/or Fusobacterium may have significant roles in DD pathogenesis, and should be studied further in respect to elucidating DD etiopathogenic mechanisms and developing more effective treatment and mitigation strategies.}, } @article {pmid34332533, year = {2021}, author = {Ammer-Herrmenau, C and Asendorf, T and Beyer, G and Buchholz, SM and Cameron, S and Damm, M and Frost, F and Henker, R and Jaster, R and Phillip, V and Placzek, M and Ratei, C and Sirtl, S and van den Berg, T and Weingarten, MJ and Woitalla, J and Mayerle, J and Ellenrieder, V and Neesse, A}, title = {Study protocol P-MAPS: microbiome as predictor of severity in acute pancreatitis-a prospective multicentre translational study.}, journal = {BMC gastroenterology}, volume = {21}, number = {1}, pages = {304}, pmid = {34332533}, issn = {1471-230X}, mesh = {Acute Disease ; Humans ; *Microbiota ; Multicenter Studies as Topic ; *Pancreatitis ; Prognosis ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; }, abstract = {BACKGROUND: Acute pancreatitis (AP) is an inflammatory disorder that causes a considerable economic health burden. While the overall mortality is low, around 20% of patients have a complicated course of disease resulting in increased morbidity and mortality. There is an emerging body of evidence that the microbiome exerts a crucial impact on the pathophysiology and course of AP. For several decades multiple clinical and laboratory parameters have been evaluated, and complex scoring systems were developed to predict the clinical course of AP upon admission. However, the majority of scoring systems are determined after several days and achieve a sensitivity around 70% for early prediction of severe AP. Thus, continued efforts are required to investigate reliable biomarkers for the early prediction of severity in order to guide early clinical management of AP patients.

METHODS: We designed a multi-center, prospective clinical-translational study to test whether the orointestinal microbiome may serve as novel early predictor of the course, severity and outcome of patients with AP. We will recruit 400 AP patients and obtain buccal and rectal swabs within 72 h of admission to the hospital. Following DNA extraction, microbiome analysis will be performed using 3rd generation sequencing Oxford Nanopore Technologies (ONT) for 16S rRNA and metagenomic sequencing. Alpha- and beta-diversity will be determined and correlated to the revised Atlanta classification and additional clinical outcome parameters such as the length of hospital stay, number and type of complications, number of interventions and 30-day mortality.

DISCUSSION: If AP patients show a distinct orointestinal microbiome dependent on the severity and course of the disease, microbiome sequencing could rapidly be implemented in the early clinical management of AP patients in the future.

TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT04777812.}, } @article {pmid34332502, year = {2021}, author = {Moeller, AH}, title = {Genomic Expansions in the Human Gut Microbiome.}, journal = {Genome biology and evolution}, volume = {13}, number = {7}, pages = {}, pmid = {34332502}, issn = {1759-6653}, support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Genome, Bacterial ; Genomics ; Humans ; Metagenome ; *Microbiota ; }, abstract = {Bacteria inhabiting the human body vary in genome size by over an order of magnitude, but the processes that generate this diversity are poorly understood. Here, we show that evolutionary forces drive divergence in genome size between bacterial lineages in the gut and their closest relatives in other body sites. Analyses of thousands of reference bacterial isolate genomes and metagenome-assembled genomes from the human microbiome indicated that transitions into the gut from other body sites have promoted genomic expansions, whereas the opposite transitions have promoted genomic contractions. Bacterial genomes in the gut are on average ∼127 kb larger than their closest congeneric relatives from other body sites. Moreover, genome size and relative abundance are positively associated within the gut but negatively associated at other body sites. These results indicate that the gut microbiome promotes expansions of bacterial genomes relative to other body sites.}, } @article {pmid34332366, year = {2021}, author = {Font-Verdera, F and Liébana, R and Aldeguer-Riquelme, B and Gangloff, V and Santos, F and Viver, T and Rosselló-Móra, R}, title = {Inverted microbial community stratification and spatial-temporal stability in hypersaline anaerobic sediments from the S'Avall solar salterns.}, journal = {Systematic and applied microbiology}, volume = {44}, number = {5}, pages = {126231}, doi = {10.1016/j.syapm.2021.126231}, pmid = {34332366}, issn = {1618-0984}, mesh = {Anaerobiosis ; *Archaea/classification/metabolism ; *Bacteria/classification/metabolism ; Geologic Sediments ; Methane ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Spatio-Temporal Analysis ; }, abstract = {The anaerobic hypersaline sediments of an ephemeral pond from the S'Avall solar salterns constituted an excellent study system because of their easy accessibility, as well as the analogy of their microbial assemblages with some known deep-sea hypersaline anaerobic brines. By means of shotgun metagenomics and 16S rRNA gene amplicon sequencing, the microbial composition of the sediment was shown to be stable in time and space. The communities were formed by prokaryote representatives with a clear inferred anaerobic metabolism, mainly related to the methane, sulfur and nitrate cycles. The most conspicuous finding was the inverted nature of the vertical stratification. Contrarily to what could be expected, a methanogenic archaeal metabolism was found to dominate in the upper layers, whereas Bacteria with fermentative and anaerobic respiration metabolisms increased with depth. We could demonstrate the methanogenic nature of the members of candidate lineages DHVE2 and MSBL1, which were present in high abundance in this system, and described, for the first time, viruses infecting these lineages. Members of the putatively active aerobic genera Salinibacter and Halorubrum were detected especially in the deepest layers for which we hypothesize that either oxygen could be sporadically available, or they could perform anaerobic metabolisms. We also report a novel repertoire of virus species thriving in these sediments, which had special relevance because of their lysogenic lifestyles.}, } @article {pmid34331556, year = {2021}, author = {Vishwakarma, A and Verma, D}, title = {Microorganisms: crucial players of smokeless tobacco for several health attributes.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {16-17}, pages = {6123-6132}, pmid = {34331556}, issn = {1432-0614}, support = {SB/YS/LS-102/2014//Science and Engineering Research Board/ ; F 30.442/2018/BSR//University Grants Commission/ ; }, mesh = {Carcinogens ; Humans ; *Microbiota ; *Nitrosamines ; *Tobacco, Smokeless ; }, abstract = {Global consumption of smokeless tobacco (SLT) reached 300 million users worldwide majorly from middle-income countries. More than 4000 chemical compounds represent it as one of the noxious consumable products by humans. Besides toxicants/carcinogens, the heavy microbial load on smokeless tobacco further keeps human health at higher risk. Several of these inhabitant microbes participate in biofilm formation and secrete endotoxin/mycotoxins and proinflammatory-like molecules, leading to several oral diseases. Tobacco-associated bacteria exhibit their role in tobacco-specific nitrosamines (TSNAs) formation and acetaldehyde production; both are well-documented carcinogens. Moreover, tobacco exhibits the potential to alter the oral microbiome and induce dysbiotic conditions that lead to the onset of several oral and systemic diseases. Traditional cultivation approaches of microbiology provide partial information of microbial communities of a habitat; therefore, microbiomics has now been employed to study the metagenomes of entire microbial communities. In the past 5 years, few NGS-based investigations have revealed that SLT harbors four dominant phyla (Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes) dominating Bacillus spp. and/or Pseudomonas spp. However, functional characterization of their genetic elements will be a more informative attribute to understand the correlation between inhabitant microbial diversity and their relatedness concerning abundance and diseases. This review provides an update on the microbial diversity of SLT and its associated attributes in human health. KEY POINTS: • Heavy microbial load on smokeless tobacco alarms for poor oral hygiene. • Inhabitant microorganisms of SLT participate in TSNA and biofilm formation. • SLTs alter the oral microbiome and causes oral dysbiosis.}, } @article {pmid34330336, year = {2021}, author = {Hiseni, P and Rudi, K and Wilson, RC and Hegge, FT and Snipen, L}, title = {HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {165}, pmid = {34330336}, issn = {2049-2618}, mesh = {*Gastrointestinal Microbiome/genetics ; Genome, Human ; Humans ; *Metagenome ; Metagenomics ; }, abstract = {BACKGROUND: A major bottleneck in the use of metagenome sequencing for human gut microbiome studies has been the lack of a comprehensive genome collection to be used as a reference database. Several recent efforts have been made to re-construct genomes from human gut metagenome data, resulting in a huge increase in the number of relevant genomes. In this work, we aimed to create a collection of the most prevalent healthy human gut prokaryotic genomes, to be used as a reference database, including both MAGs from the human gut and ordinary RefSeq genomes.

RESULTS: We screened > 5,700 healthy human gut metagenomes for the containment of > 490,000 publicly available prokaryotic genomes sourced from RefSeq and the recently announced UHGG collection. This resulted in a pool of > 381,000 genomes that were subsequently scored and ranked based on their prevalence in the healthy human metagenomes. The genomes were then clustered at a 97.5% sequence identity resolution, and cluster representatives (30,691 in total) were retained to comprise the HumGut collection. Using the Kraken2 software for classification, we find superior performance in the assignment of metagenomic reads, classifying on average 94.5% of the reads in a metagenome, as opposed to 86% with UHGG and 44% when using standard Kraken2 database. A coarser HumGut collection, consisting of genomes dereplicated at 95% sequence identity-similar to UHGG, classified 88.25% of the reads. HumGut, half the size of standard Kraken2 database and directly comparable to the UHGG size, outperforms them both.

CONCLUSIONS: The HumGut collection contains > 30,000 genomes clustered at a 97.5% sequence identity resolution and ranked by human gut prevalence. We demonstrate how metagenomes from IBD-patients map equally well to this collection, indicating this reference is relevant also for studies well outside the metagenome reference set used to obtain HumGut. All data and metadata, as well as helpful code, are available at http://arken.nmbu.no/~larssn/humgut/ . Video Abstract.}, } @article {pmid34329019, year = {2021}, author = {Kim, NK and Lee, SH and Yoon, H and Jeong, G and Jung, YJ and Hur, M and Lee, BH and Park, HD}, title = {Microbiome degrading linear alkylbenzene sulfonate in activated sludge.}, journal = {Journal of hazardous materials}, volume = {418}, number = {}, pages = {126365}, doi = {10.1016/j.jhazmat.2021.126365}, pmid = {34329019}, issn = {1873-3336}, mesh = {*Alkanesulfonic Acids ; Metagenome ; *Microbiota/genetics ; Sewage ; Surface-Active Agents ; }, abstract = {As the most widely used anionic surfactant, linear alkylbenzene sulfonate (LAS) requires biological alkane degradation when it is treated using an activated sludge (AS) process in a wastewater treatment plant because of its structural carboxylic unavailability. As consumption of LAS is gradually increasing, LAS loading into the WWTP is accordingly increasing. However, fewer studies have examined the involvement of the AS microbial community in the LAS degradation. In this study, metagenomic approaches were used to define microbiomes involved in LAS degradation in AS, with a particular focus on ω-hydroxylation. The abundance and diversity of alkane-degrading genes were investigated, and these genes were integrated with reconstructed metagenome-assembled genomes (MAGs). Additionally, the association of functional genes and MAGs with respect to LAS degradation was investigated. The results showed that alkB and cytochrome P450 genes were only shared within specific MAGs. Unique sets of genes with diverse abundances were detected in each sample. The MAGs with the alkB and cytochrome P450 genes were strongly associated with the other MAGs and involved in positive commensal interactions. The findings provided significant insights into how the AS microbiomes, which have continuously treated anionic surfactants for decades, potentially metabolize LAS and interact with commensal bacteria.}, } @article {pmid34329005, year = {2021}, author = {Li, J and Jia, C and Lu, Q and Hungate, BA and Dijkstra, P and Wang, S and Wu, C and Chen, S and Li, D and Shim, H}, title = {Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures.}, journal = {Journal of hazardous materials}, volume = {418}, number = {}, pages = {126384}, doi = {10.1016/j.jhazmat.2021.126384}, pmid = {34329005}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; Xenobiotics ; }, abstract = {Even though microbial communities can be more effective at degrading xenobiotics than cultured micro-organisms, yet little is known about the microbial strategies that underpin xenobiotic biodegradation by microbial communities. Here, we employ metagenomic community sequencing to explore the mechanisms that drive the development of 49 xenobiotic-degrading microbial communities, which were enriched from 7 contaminated soils or sediments with a range of xenobiotic compounds. We show that multiple microbial strategies likely drive the development of xenobiotic degrading communities, notably (i) presence of genes encoding catabolic enzymes to degrade xenobiotics; (ii) presence of genes encoding efflux pumps; (iii) auxiliary catabolic genes on plasmids; and (iv) positive interactions dominate microbial communities with efficient degradation. Overall, the integrated analyses of microbial ecological strategies advance our understanding of microbial processes driving the biodegradation of xenobiotics and promote the design of bioremediation systems.}, } @article {pmid34328924, year = {2021}, author = {Fu, X and Ou, Z and Zhang, M and Meng, Y and Li, Y and Chen, Q and Jiang, J and Zhang, X and Norbäck, D and Zhao, Z and Sun, Y}, title = {Classroom microbiome, functional pathways and sick-building syndrome (SBS) in urban and rural schools - Potential roles of indoor microbial amino acids and vitamin metabolites.}, journal = {The Science of the total environment}, volume = {795}, number = {}, pages = {148879}, doi = {10.1016/j.scitotenv.2021.148879}, pmid = {34328924}, issn = {1879-1026}, mesh = {*Air Pollution, Indoor/analysis ; Amino Acids ; *Asthma ; Humans ; *Microbiota ; Propionibacteriaceae ; Schools ; *Sick Building Syndrome ; Vitamins ; }, abstract = {Sick building symptoms (SBS) are defined as non-specific symptoms related to indoor exposures, including mucosal symptoms in eye, nose, throat, and skin, and general symptoms as headache and tiredness. Indoor microbial composition is associated with SBS symptoms, but the impact of microbial functional genes and potential metabolic products has not been characterized. We conducted a shotgun microbial metagenomic sequencing for vacuum dust collected in urban and rural schools in Shanxi province, China. SBS symptoms in students were surveyed, and microbial taxa and functional pathways related to the symptoms were identified using a multi-level linear regression model. SBS symptoms were common in students, and the prevalence of ocular and throat symptoms, headache, and tiredness was higher in urban than in rural areas (p < 0.05). A significant higher microbial α-diversity was found in rural areas than in urban areas (Chao1, p = 0.001; ACE, p = 0.002). Also, significant variation in microbial taxonomic and functional composition (β-diversity) was observed between urban and rural areas (p < 0.005). Five potential risk Actinobacteria species were associated with SBS symptoms (p < 0.01); students in the classrooms with a higher abundance of an unclassified Geodermatophilaceae, Geodermatophilus, Fridmanniella luteola, Microlunatus phosphovorus and Mycetocola reported more nasal and throat symptoms and tiredness. Students with a higher abundance of an unclassified flavobacteriaceae reported fewer throat symptoms and tiredness. The abundance of microbial metabolic pathways related to the synthesis of B vitamins (biotin and folate), gamma-aminobutyric acid (GABA), short-chain fatty acids (SCFAs), and peptidoglycan and were protectively (negatively) associated with SBS symptoms (FDR < 0.05). The result is consistent with human microbiota studies, which reported that these microbial products are extensively involved in immunological processes and anti-inflammatory effects. This is the first study to report the functional potential of the indoor microbiome and the occurrence of SBS, providing new insights into the potential etiologic mechanisms in chronic inflammatory diseases.}, } @article {pmid34328665, year = {2021}, author = {Marongiu, L and Landry, JJM and Rausch, T and Abba, ML and Delecluse, S and Delecluse, HJ and Allgayer, H}, title = {Metagenomic analysis of primary colorectal carcinomas and their metastases identifies potential microbial risk factors.}, journal = {Molecular oncology}, volume = {15}, number = {12}, pages = {3363-3384}, pmid = {34328665}, issn = {1878-0261}, mesh = {*Colorectal Neoplasms/genetics ; *Epstein-Barr Virus Infections ; Herpesvirus 4, Human ; Humans ; *Microbiota ; Risk Factors ; }, abstract = {The paucity of microbiome studies at intestinal tissues has contributed to a yet limited understanding of potential viral and bacterial cofactors of colorectal cancer (CRC) carcinogenesis or progression. We analysed whole-genome sequences of CRC primary tumours, their corresponding metastases and matched normal tissue for sequences of viral, phage and bacterial species. Bacteriome analysis showed Fusobacterium nucleatum, Streptococcus sanguinis, F. Hwasookii, Anaerococcus mediterraneensis and further species enriched in primary CRCs. The primary CRC of one patient was enriched for F. alocis, S. anginosus, Parvimonas micra and Gemella sp. 948. Enrichment of Escherichia coli strains IAI1, SE11, K-12 and M8 was observed in metastases together with coliphages enterobacteria phage φ80 and Escherichia phage VT2φ_272. Virome analysis showed that phages were the most preponderant viral species (46%), the main families being Myoviridae, Siphoviridae and Podoviridae. Primary CRCs were enriched for bacteriophages, showing five phages (Enterobacteria, Bacillus, Proteus, Streptococcus phages) together with their pathogenic hosts in contrast to normal tissues. The most frequently detected, and Blast-confirmed, viruses included human endogenous retrovirus K113, human herpesviruses 7 and 6B, Megavirus chilensis, cytomegalovirus (CMV) and Epstein-Barr virus (EBV), with one patient showing EBV enrichment in primary tumour and metastases. EBV was PCR-validated in 80 pairs of CRC primary tumour and their corresponding normal tissues; in 21 of these pairs (26.3%), it was detectable in primary tumours only. The number of viral species was increased and bacterial species decreased in CRCs compared with normal tissues, and we could discriminate primary CRCs from metastases and normal tissues by applying the Hutcheson t-test on the Shannon indices based on viral and bacterial species. Taken together, our results descriptively support hypotheses on microorganisms as potential (co)risk factors of CRC and extend putative suggestions on critical microbiome species in CRC metastasis.}, } @article {pmid34328191, year = {2021}, author = {Nishikawa, H and Fukunishi, S and Asai, A and Yokohama, K and Ohama, H and Nishiguchi, S and Higuchi, K}, title = {Dysbiosis and liver diseases (Review).}, journal = {International journal of molecular medicine}, volume = {48}, number = {3}, pages = {}, doi = {10.3892/ijmm.2021.5016}, pmid = {34328191}, issn = {1791-244X}, mesh = {Animals ; Disease Progression ; Dysbiosis/*complications/pathology ; *Gastrointestinal Microbiome ; Humans ; Liver/pathology ; Liver Diseases/*etiology/pathology ; }, abstract = {Dysbiosis, a qualitative and quantitative aberrancy of gut microbiota, has attracted marked attention. At present, advances in molecular biological techniques have made it possible to analyze gut microbiota at the DNA and RNA levels without culturing, and methods such as 16S ribosomal RNA targeting analysis and metagenomic analysis using next‑generation sequencers have been developed. The relationship between gut microbiota and various diseases has been extensively examined. Gut microbiota are essential for the immune system, energy intake and fat storage, and humans use them to build complex immune regulatory mechanisms and to obtain energy from food. The liver is the first organ to be nourished by the portal blood flow of intestinal origin, and liver diseases can be strongly influenced by various factors of intestinal origin, such as intestinal bacteria, bacterial components, and intestinal bacterial metabolites. Rigorous research has revealed that the composition of the gut microbiota is altered and the diversity of bacteria is reduced in liver diseases. Significance of various factors transported to the liver by portal vein blood flow from the intestine has been extensively investigated. Gut microbiota in liver disease can be associated with disease progression regardless of disease etiology and even with carcinogenesis. The relationship between gut microbiota and liver diseases (hepatitis virus‑related diseases, autoimmune liver diseases, alcoholic liver disease, non‑alcoholic fatty liver disease, non‑alcoholic steatohepatitis, liver cirrhosis and hepatocellular carcinoma) and the treatments of dysbiosis (antibiotics, prebiotics, probiotics and fecal microbiota transplantation) in liver disease are outlined based on the current evidence.}, } @article {pmid34325201, year = {2021}, author = {Wang, M and Sun, Y and Zeng, Z and Wang, Z}, title = {Metagenomics of wastewater phageome identifies an extensively cored antibiotic resistome in a swine feedlot water treatment environment.}, journal = {Ecotoxicology and environmental safety}, volume = {222}, number = {}, pages = {112552}, doi = {10.1016/j.ecoenv.2021.112552}, pmid = {34325201}, issn = {1090-2414}, mesh = {Animals ; Anti-Bacterial Agents ; Genes, Bacterial ; *Metagenomics ; Swine ; Virome ; Wastewater ; *Water Purification ; }, abstract = {Huge number of antibiotic resistance genes (ARGs) have been widely detected in phage genomes from anthropogenic environment or animal farms, whereas little is known about the dynamic changes of phage contribution to resistance under a feedlot wastewater treatment facility (WTF) pressure. Here, a metagenomics method was used to characterize the sewage phageome and identifies the antibiotic resistome. The results showed that the phage families of Siphoviridae, Myoviridae, and Podoviridae were always the most dominant. Analysis of ARGs carried by bacterial and phages showed that MLS and tetracycline resistance genes always had the highest abundances and the other ARG types also have a fixed hierarchy, showing that there is no significant change in overall ARGs abundance distribution. However, an extensively cored antibiotic resistome were specifically identified in aerobic environment. ARGs encoding ribosomal protection proteins, especially for the ARG subtypes lsaE, tet44, tetM, tetP, macB, MdlB and rpoB2, were more inclined to be selected by phages, suggesting that a more refined mechanism, such as specialized transduction and lateral transduction, was probably involved. In all, these results suggest that monitoring of dynamic changes of phage contribution to resistance should be given more attention and ARGs-carrying phage management should focus on using technologies for controlling cored ARGs rather than only the overall distribution of ARGs in phages.}, } @article {pmid34321618, year = {2022}, author = {Zhou, J and Theroux, SM and Bueno de Mesquita, CP and Hartman, WH and Tian, Y and Tringe, SG}, title = {Microbial drivers of methane emissions from unrestored industrial salt ponds.}, journal = {The ISME journal}, volume = {16}, number = {1}, pages = {284-295}, pmid = {34321618}, issn = {1751-7370}, mesh = {*Methane/metabolism ; *Microbiota ; Ponds ; RNA, Ribosomal, 16S/genetics ; Wetlands ; }, abstract = {Wetlands are important carbon (C) sinks, yet many have been destroyed and converted to other uses over the past few centuries, including industrial salt making. A renewed focus on wetland ecosystem services (e.g., flood control, and habitat) has resulted in numerous restoration efforts whose effect on microbial communities is largely unexplored. We investigated the impact of restoration on microbial community composition, metabolic functional potential, and methane flux by analyzing sediment cores from two unrestored former industrial salt ponds, a restored former industrial salt pond, and a reference wetland. We observed elevated methane emissions from unrestored salt ponds compared to the restored and reference wetlands, which was positively correlated with salinity and sulfate across all samples. 16S rRNA gene amplicon and shotgun metagenomic data revealed that the restored salt pond harbored communities more phylogenetically and functionally similar to the reference wetland than to unrestored ponds. Archaeal methanogenesis genes were positively correlated with methane flux, as were genes encoding enzymes for bacterial methylphosphonate degradation, suggesting methane is generated both from bacterial methylphosphonate degradation and archaeal methanogenesis in these sites. These observations demonstrate that restoration effectively converted industrial salt pond microbial communities back to compositions more similar to reference wetlands and lowered salinities, sulfate concentrations, and methane emissions.}, } @article {pmid34319574, year = {2021}, author = {Cezar, RM and Vezzani, FM and Kaschuk, G and Balsanelli, E and de Souza, EM and Vargas, LK and Molin, R}, title = {Crop rotation reduces the frequency of anaerobic soil bacteria in Red Latosol of Brazil.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {52}, number = {4}, pages = {2169-2177}, pmid = {34319574}, issn = {1678-4405}, mesh = {*Agriculture/methods ; Bacteria/genetics ; *Bacteria, Anaerobic/physiology ; *Biodiversity ; Brazil ; Crop Production ; Oxygen ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Crop diversity affects the processes of soil physical structuring and most likely provokes changes in the frequencies of soil microbial communities. The study was conducted for soil prokaryotic diversity sequencing 16S rDNA genes from a 25-year no-tillage experiment comprised of two crop systems: crop succession (Triticum aestivum-Glycine max) and rotation (Vicia sativa-Zea mays-Avena sativa-Glycine max-Triticum aestivum-Glycine max). The hypothesis was that a crop system with higher crop diversification (rotation) would affect the frequencies of prokaryotic taxa against a less diverse crop system (succession) altering the major soil functions guided by bacterial diversity. Soils in both crop systems were dominated by Proteobacteria (31%), Acidobacteria (23%), Actinobacteria (10%), and Gemmatimonadetes (7.2%), among other common copiotrophic soil bacteria. Crop systems did not affect the richness and diversity indexes of soil bacteria and soil archaea. However, the crop rotation system reduced only the frequencies of anaerobic metabolism bacteria Chloroacidobacteria, Holophagae, Spirochaetes, Euryarchaeota, and Crenarchaeota. It can be concluded that crop succession, a system that is poorer in root diversity over time, may have conditioned the soil to lower oxygen diffusion and built up ecological niches that suitable for anaerobic bacteria tolerating lower levels of oxygen. On the other hand, it appeared that crop rotation has restructured the soil over the years while enabling copiotrophic aerobic bacteria to dominate the soil ecosystem. The changes prompted by crop succession have implications for efficient soil organic matter decomposition, reduced greenhouse gas emissions, higher root activity, and overall soil productivity, which compromise to agriculture sustainability.}, } @article {pmid34318715, year = {2021}, author = {Rahman-Enyart, A and Yang, W and Yaggie, RE and White, BA and Welge, M and Auvil, L and Berry, M and Bushell, C and Rosen, JM and Rudick, CN and Schaeffer, AJ and Klumpp, DJ}, title = {Acyloxyacyl hydrolase is a host determinant of gut microbiome-mediated pelvic pain.}, journal = {American journal of physiology. Regulatory, integrative and comparative physiology}, volume = {321}, number = {3}, pages = {R396-R412}, pmid = {34318715}, issn = {1522-1490}, support = {R01 DK103769/DK/NIDDK NIH HHS/United States ; T32 DK062716/DK/NIDDK NIH HHS/United States ; P30 CA060553/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Carboxylic Ester Hydrolases/genetics/metabolism ; *Cystitis, Interstitial/metabolism ; Disease Models, Animal ; Dysbiosis/complications/metabolism ; *Gastrointestinal Microbiome/genetics/physiology ; Inflammation/metabolism ; *Pelvic Pain/metabolism/physiopathology ; Urinary Bladder/metabolism ; Mice ; }, abstract = {Dysbiosis of gut microbiota is associated with many pathologies, yet host factors modulating microbiota remain unclear. Interstitial cystitis/bladder pain syndrome (IC/BPS) is a debilitating condition of chronic pelvic pain often with comorbid urinary dysfunction and anxiety/depression, and recent studies find fecal dysbiosis in patients with IC/BPS. We identified the locus encoding acyloxyacyl hydrolase, Aoah, as a modulator of pelvic pain severity in a murine IC/BPS model. AOAH-deficient mice spontaneously develop rodent correlates of pelvic pain, increased responses to induced pelvic pain models, voiding dysfunction, and anxious/depressive behaviors. Here, we report that AOAH-deficient mice exhibit dysbiosis of gastrointestinal (GI) microbiota. AOAH-deficient mice exhibit an enlarged cecum, a phenotype long associated with germ-free rodents, and a "leaky gut" phenotype. AOAH-deficient ceca showed altered gene expression consistent with inflammation, Wnt signaling, and urologic disease. 16S sequencing of stool revealed altered microbiota in AOAH-deficient mice, and GC-MS identified altered metabolomes. Cohousing AOAH-deficient mice with wild-type mice resulted in converged microbiota and altered predicted metagenomes. Cohousing also abrogated the pelvic pain phenotype of AOAH-deficient mice, which was corroborated by oral gavage of AOAH-deficient mice with stool slurry of wild-type mice. Converged microbiota also alleviated comorbid anxiety-like behavior in AOAH-deficient mice. Oral gavage of AOAH-deficient mice with anaerobes cultured from IC/BPS stool resulted in exacerbation of pelvic allodynia. Together, these data indicate that AOAH is a host determinant of normal gut microbiota, and dysbiosis associated with AOAH deficiency contributes to pelvic pain. These findings suggest that the gut microbiome is a potential therapeutic target for IC/BPS.}, } @article {pmid34315772, year = {2022}, author = {Tarallo, S and Ferrero, G and De Filippis, F and Francavilla, A and Pasolli, E and Panero, V and Cordero, F and Segata, N and Grioni, S and Pensa, RG and Pardini, B and Ercolini, D and Naccarati, A}, title = {Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals.}, journal = {Gut}, volume = {71}, number = {7}, pages = {1302-1314}, pmid = {34315772}, issn = {1468-3288}, mesh = {*Diet ; *Gastrointestinal Microbiome ; Humans ; Lipids ; *MicroRNAs/genetics ; Vegetarians ; }, abstract = {OBJECTIVES: MicroRNA (miRNA) profiles have been evaluated in several biospecimens in relation to common diseases for which diet may have a considerable impact. We aimed at characterising how specific diets are associated with the miRNome in stool of vegans, vegetarians and omnivores and how this is reflected in the gut microbial composition, as this is still poorly explored.

DESIGN: We performed small RNA and shotgun metagenomic sequencing in faecal samples and dietary recording from 120 healthy volunteers, equally distributed for the different diets and matched for sex and age.

RESULTS: We found 49 miRNAs differentially expressed among vegans, vegetarians and omnivores (adj. p <0.05) and confirmed trends of expression levels of such miRNAs in vegans and vegetarians compared with an independent cohort of 45 omnivores. Two miRNAs related to lipid metabolism, miR-636 and miR-4739, were inversely correlated to the non-omnivorous diet duration, independently of subject age. Seventeen miRNAs correlated (|rho|>0.22, adj. p <0.05) with the estimated intake of nutrients, particularly animal proteins, phosphorus and, interestingly, lipids. In omnivores, higher Prevotella and Roseburia and lower Bacteroides abundances than in vegans and vegetarians were observed. Lipid metabolism-related miR-425-3p and miR-638 expression levels were associated with increased abundances of microbial species, such as Roseburia sp. CAG 182 and Akkermansia muciniphila, specific of different diets. An integrated analysis identified 25 miRNAs, 25 taxa and 7 dietary nutrients that clearly discriminated (area under the receiver operating characteristic curve=0.89) the three diets.

CONCLUSION: Stool miRNA profiles are associated with specific diets and support the role of lipids as a driver of epigenetic changes and host-microbial molecular interactions in the gut.}, } @article {pmid34313944, year = {2022}, author = {Hao, Z and Tao, K and Wu, K and Luo, Y and Lu, Y and Li, B and Shi, P and Wang, P and Zeng, X and Lin, Y}, title = {Alterations of gut microbiome and metabolite profiles in choledocholithiasis concurrent with cholangitis.}, journal = {Hepatology international}, volume = {16}, number = {2}, pages = {447-462}, pmid = {34313944}, issn = {1936-0541}, support = {81670544//the National Natural Science Foundation of China/ ; 81870416//the National Natural Science Foundation of China/ ; PWYgf2018-04//the Top-Level Clinical Discipline Project of Shanghai Pudong/ ; 19411970500//the Science and Technology Guidance Plan of Shanghai Science and Technology Commission/ ; 2019lhrcjh//the Pilot Talent Plan of Shanghai East Hospital/ ; }, mesh = {Case-Control Studies ; *Cholangitis ; *Choledocholithiasis ; *Gastrointestinal Microbiome/physiology ; Humans ; Inflammation ; }, abstract = {BACKGROUND AND AIMS: Gut microbiota and their metabolic products might play important roles in regulating the pathogenesis of choledocholithiasis concurrent with cholangitis (CC). The aim of this study was to explore the characteristic gut dysbiosis, metabolite profiles and the possible roles in patients with CC.

METHODS: A case-control study was carried out to analyze the alterations in the intestinal microbiota and their metabolites in patients with CC (n = 25) compared with healthy controls (HCs) (n = 25) by metagenomic sequencing to define the gut microbiota community and liquid chromatography/mass spectrometry (LC/MS) analysis to characterize the metabolite profiles.

RESULTS: Significantly reduced Shannon diversity index (p = 0.043) and differential overall fecal microbiota community in CCs were observed. Twelve dominant altered species were identified and analyzed (LDA score > 3.0, p < 0.05) (Q value < 0.05), including unclassified_f_Enterobacteriaceae, Escherichia_coli, Roseburia_faecis and Eubacterium rectale. Moreover, the levels of KEGG pathways related to biofilm formation of Escherichia coli, lipopolysaccharide (LPS) biosynthesis, and the metabolism of propanoate and glutathione in CCs were significantly altered. Finally, 47 markedly changed metabolites (VIP > 1.0 and p < 0.05), including low level of kynurenic acid (KYNA) and high concentration of N-palmitoylsphingosine involving tryptophan metabolism and sphingolipid signaling pathways, were identified to validate aberrant metabolic patterns in CCs, and multiple correlated metabolic modules involving bile inflammation were altered in CCs.

CONCLUSION: Our study provides novel insights into compositional and functional alterations in the gut microbiome and metabolite profiles in CC and the underlying mechanisms between gut microbiota and bile inflammation.}, } @article {pmid34313538, year = {2021}, author = {Gacesa, R and Vich Vila, A and Collij, V and Mujagic, Z and Kurilshikov, A and Voskuil, MD and Festen, EAM and Wijmenga, C and Jonkers, DMAE and Dijkstra, G and Fu, J and Zhernakova, A and Imhann, F and Weersma, RK}, title = {A combination of fecal calprotectin and human beta-defensin 2 facilitates diagnosis and monitoring of inflammatory bowel disease.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1943288}, pmid = {34313538}, issn = {1949-0984}, mesh = {Adult ; Biomarkers/analysis ; Biopsy/standards ; Cohort Studies ; Diagnosis, Differential ; Feces/*chemistry ; Female ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*diagnosis/*physiopathology ; Irritable Bowel Syndrome/*diagnosis/*physiopathology ; Leukocyte L1 Antigen Complex/*analysis ; Male ; Middle Aged ; Netherlands ; Practice Guidelines as Topic ; beta-Defensins/*analysis ; }, abstract = {Inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) show a large overlap in clinical presentation, which presents diagnostic challenges. As a consequence, invasive and burdensome endoscopies are often used to distinguish between IBD and IBS. Here, we aimed to develop a noninvasive fecal test that can distinguish between IBD and IBS and reduce the number of endoscopies.We used shotgun metagenomic sequencing to analyze the composition and function of gut microbiota of 169 IBS patients, 447 IBD patients and 1044 population controls and measured fecal Calprotectin (FCal), human beta defensin 2 (HBD2), and chromogranin A (CgA) in these samples. These measurements were used to construct training sets (75% of data) for logistic regression and machine learning models to differentiate IBS from IBD and inactive from active IBD. The results were replicated on test sets (remaining 25% of the data) and microbiome data obtained using 16S sequencing.Fecal HBD2 showed high sensitivity and specificity for differentiating between IBD and IBS (sensitivity = 0.89, specificity = 0.76), while the inclusion of microbiome data with biomarkers (HBD2 and FCal) showed a potential for improvement in predictive power (optimal sensitivity = 0.87, specificity = 0.93). Shotgun sequencing-based models produced comparable results using 16S-sequencing data. HBD2 and FCal were found to have predictive power for IBD disease activity (AUC ≈ 0.7).HBD2 is a novel biomarker for IBD in patients with gastro-intestinal complaints, especially when used in combination with FCal and potentially in combination with gut microbiome data.}, } @article {pmid34312531, year = {2021}, author = {Wippel, K and Tao, K and Niu, Y and Zgadzaj, R and Kiel, N and Guan, R and Dahms, E and Zhang, P and Jensen, DB and Logemann, E and Radutoiu, S and Schulze-Lefert, P and Garrido-Oter, R}, title = {Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota.}, journal = {Nature microbiology}, volume = {6}, number = {9}, pages = {1150-1162}, pmid = {34312531}, issn = {2058-5276}, mesh = {Arabidopsis/microbiology/*physiology ; Bacteria/classification/genetics/*isolation & purification ; Bacterial Physiological Phenomena ; Lotus/microbiology/*physiology ; *Microbiota ; Plant Roots/*microbiology/physiology ; Soil Microbiology ; *Symbiosis ; }, abstract = {Roots of different plant species are colonized by bacterial communities, that are distinct even when hosts share the same habitat. It remains unclear to what extent the host actively selects these communities and whether commensals are adapted to a specific plant species. To address this question, we assembled a sequence-indexed bacterial culture collection from roots and nodules of Lotus japonicus that contains representatives of most species previously identified using metagenomics. We analysed taxonomically paired synthetic communities from L. japonicus and Arabidopsis thaliana in a multi-species gnotobiotic system and detected signatures of host preference among commensal bacteria in a community context, but not in mono-associations. Sequential inoculation experiments revealed priority effects during root microbiota assembly, where established communities are resilient to invasion by latecomers, and that host preference of commensal bacteria confers a competitive advantage in their cognate host. Our findings show that host preference in commensal bacteria from diverse taxonomic groups is associated with their invasiveness into standing root-associated communities.}, } @article {pmid34312482, year = {2022}, author = {Coskun, ÖK and Vuillemin, A and Schubotz, F and Klein, F and Sichel, SE and Eisenreich, W and Orsi, WD}, title = {Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks.}, journal = {The ISME journal}, volume = {16}, number = {1}, pages = {257-271}, pmid = {34312482}, issn = {1751-7370}, mesh = {Carbon ; *Hydrogen ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; }, abstract = {Thermodynamic models predict that H2 is energetically favorable for seafloor microbial life, but how H2 affects anabolic processes in seafloor-associated communities is poorly understood. Here, we used quantitative [13]C DNA stable isotope probing (qSIP) to quantify the effect of H2 on carbon assimilation by microbial taxa synthesizing [13]C-labeled DNA that are associated with partially serpentinized peridotite rocks from the equatorial Mid-Atlantic Ridge. The rock-hosted seafloor community was an order of magnitude more diverse compared to the seawater community directly above the rocks. With added H2, peridotite-associated taxa increased assimilation of [13]C-bicarbonate and [13]C-acetate into 16S rRNA genes of operational taxonomic units by 146% (±29%) and 55% (±34%), respectively, which correlated with enrichment of H2-oxidizing NiFe-hydrogenases encoded in peridotite-associated metagenomes. The effect of H2 on anabolism was phylogenetically organized, with taxa affiliated with Atribacteria, Nitrospira, and Thaumarchaeota exhibiting the most significant increases in [13]C-substrate assimilation in the presence of H2. In SIP incubations with added H2, an order of magnitude higher number of peridotite rock-associated taxa assimilated [13]C-bicarbonate, [13]C-acetate, and [13]C-formate compared to taxa that were not associated with peridotites. Collectively, these findings indicate that the unique geochemical nature of the peridotite-hosted ecosystem has selected for H2-metabolizing, rock-associated taxa that can increase anabolism under high H2 concentrations. Because ultramafic rocks are widespread in slow-, and ultraslow-spreading oceanic lithosphere, continental margins, and subduction zones where H2 is formed in copious amounts, the link between H2 and carbon assimilation demonstrated here may be widespread within these geological settings.}, } @article {pmid34312252, year = {2021}, author = {Ottoni, C and Borić, D and Cheronet, O and Sparacello, V and Dori, I and Coppa, A and Antonović, D and Vujević, D and Price, TD and Pinhasi, R and Cristiani, E}, title = {Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {32}, pages = {}, pmid = {34312252}, issn = {1091-6490}, mesh = {Agriculture/*history ; Bacteria/genetics ; Balkan Peninsula ; *DNA, Ancient ; Dental Calculus/chemistry/*genetics/*microbiology ; Drug Resistance, Microbial/genetics ; Europe ; History, Ancient ; History, Medieval ; Humans ; Microbiota/*genetics ; Phylogeny ; Plants/chemistry ; }, abstract = {Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe-the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.}, } @article {pmid34312160, year = {2022}, author = {Wan, Y and Zuo, T and Xu, Z and Zhang, F and Zhan, H and Chan, D and Leung, TF and Yeoh, YK and Chan, FKL and Chan, R and Ng, SC}, title = {Underdevelopment of the gut microbiota and bacteria species as non-invasive markers of prediction in children with autism spectrum disorder.}, journal = {Gut}, volume = {71}, number = {5}, pages = {910-918}, doi = {10.1136/gutjnl-2020-324015}, pmid = {34312160}, issn = {1468-3288}, mesh = {*Autism Spectrum Disorder/complications/metabolism/microbiology ; Bacteria/genetics ; Biomarkers ; Child ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Microbiota ; }, abstract = {OBJECTIVE: The gut microbiota has been suggested to play a role in autism spectrum disorder (ASD). We postulate that children with ASD harbour an altered developmental profile of the gut microbiota distinct from that of typically developing (TD) children. Here, we aimed to characterise compositional and functional alterations in gut microbiome in association with age in children with ASD and to identify novel faecal bacterial markers for predicting ASD.

DESIGN: We performed deep metagenomic sequencing in faecal samples of 146 Chinese children (72 ASD and 74 TD children). We compared gut microbial composition and functions between children with ASD and TD children. Candidate bacteria markers were identified and validated by metagenomic analysis. Gut microbiota development in relation to chronological age was assessed using random forest model.

RESULTS: ASD and chronological age had the most significant and largest impacts on children's faecal microbiome while diet showed no correlation. Children with ASD had significant alterations in faecal microbiome composition compared with TD children characterised by increased bacterial richness (p=0.021) and altered microbiome composition (p<0.05). Five bacterial species were identified to distinguish gut microbes in ASD and TD children, with areas under the receiver operating curve (AUC) of 82.6% and 76.2% in the discovery cohort and validation cohort, respectively. Multiple neurotransmitter biosynthesis related pathways in the gut microbiome were depleted in children with ASD compared with TD children (p<0.05). Developing dynamics of growth-associated gut bacteria (age-discriminatory species) seen in TD children were lost in children with ASD across the early-life age spectrum.

CONCLUSIONS: Gut microbiome in Chinese children with ASD was altered in composition, ecological network and functionality compared with TD children. We identified novel bacterial markers for prediction of ASD and demonstrated persistent underdevelopment of the gut microbiota in children with ASD which lagged behind their respective age-matched peers.}, } @article {pmid34311761, year = {2021}, author = {Quince, C and Nurk, S and Raguideau, S and James, R and Soyer, OS and Summers, JK and Limasset, A and Eren, AM and Chikhi, R and Darling, AE}, title = {STRONG: metagenomics strain resolution on assembly graphs.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {214}, pmid = {34311761}, issn = {1474-760X}, support = {BB/R015171/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; BB/N023285/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/S037195/1/MRC_/Medical Research Council/United Kingdom ; BB/K003240/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; BB/L502029/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Algorithms ; Bayes Theorem ; Contig Mapping ; *Genome, Bacterial ; Haplotypes ; *Metagenome ; Metagenomics/methods ; Microbial Consortia/*genetics ; Sequence Analysis, DNA ; *Software ; }, abstract = {We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification. This enables the subgraphs and their unitig per-sample coverages, for individual single-copy core genes (SCGs) in each MAG, to be extracted. A Bayesian algorithm, BayesPaths, determines the number of strains present, their haplotypes or sequences on the SCGs, and abundances. STRONG is validated using synthetic communities and for a real anaerobic digestor time series generates haplotypes that match those observed from long Nanopore reads.}, } @article {pmid34310617, year = {2021}, author = {Martinez Boggio, G and Meynadier, A and Daunis-I-Estadella, P and Marie-Etancelin, C}, title = {Compositional analysis of ruminal bacteria from ewes selected for somatic cell score and milk persistency.}, journal = {PloS one}, volume = {16}, number = {7}, pages = {e0254874}, pmid = {34310617}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/genetics ; Bayes Theorem ; Diet ; Fatty Acids/*metabolism ; Female ; Lactation/genetics ; Metagenome/genetics ; Microbiota/genetics ; Milk/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sheep/*microbiology ; }, abstract = {Ruminants are dependent on their rumen microbiota to obtain energy from plants. The composition of the microbiome was well-known to be associated with health status, and production traits, but published results are difficult to reproduce due to large sources of variation. The objectives of this study were to evaluate the associations of ruminal microbiota and its association with genetic lines selected by somatic cell score (SCS) or milk persistency (PERS), as well as milk production, somatic cell score, fat and protein contents, and fatty acids and proteins of milk, using the principles of compositional data. A large sample of 700 Lacaune dairy ewes from INRAE La Fage feeding the same diet and belonging to two divergent genetic lines selected for SCS or PERS was used. The ruminal bacterial metagenome was sequenced using the 16S rRNA gene, resulting in 2,059 operational taxonomic units affiliated with 112 genera. The abundance data were centred log-transformed after the replacement of zeros with the geometric Bayesian method. Discriminant analysis of the SCS showed differences between SCS+ and SCS- ewes, while for PERS no difference was obtained. Milk traits as fat content, protein content, saturated fatty acids and caseins of milk were negatively associated with Prevotella (R = [-0.08;-0.16]), Suttonella (R = [-0.09;-0.16]) and Ruminococcus (R = [-0.08;-0.16]), and positively associated with Lachnospiraceae (R = [0.09;0.16]) and Christensenellaceae (R = [0.09;0.16]). Our findings provide an understanding of the application of compositional data to microbiome analysis, and the potential association of Prevotella, Suttonella, Ruminococcaceae and Lachnospiraceae with milk production traits such as milk fatty acids and proteins in dairy sheep.}, } @article {pmid34305834, year = {2021}, author = {Mghazli, N and Sbabou, L and Hakkou, R and Ouhammou, A and El Adnani, M and Bruneel, O}, title = {Description of Microbial Communities of Phosphate Mine Wastes in Morocco, a Semi-Arid Climate, Using High-Throughput Sequencing and Functional Prediction.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {666936}, pmid = {34305834}, issn = {1664-302X}, abstract = {Soil microbiota are vital for successful revegetation, as they play a critical role in nutrient cycles, soil functions, and plant growth and health. A rehabilitation scenario of the abandoned Kettara mine (Morocco) includes covering acidic tailings with alkaline phosphate mine wastes to limit water infiltration and hence acid mine drainage. Revegetation of phosphate wastes is the final step to this rehabilitation plan. However, revegetation is hard on this type of waste in semi-arid areas and only a few plants managed to grow naturally after 5 years on the store-and-release cover. As we know that belowground biodiversity is a key component for aboveground functioning, we sought to know if any structural problem in phosphate waste communities could explain the almost absence of plants. To test this hypothesis, bacterial and archaeal communities present in these wastes were assessed by 16S rRNA metabarcoding. Exploration of taxonomic composition revealed a quite diversified community assigned to 19 Bacterial and two Archaeal phyla, similar to other studies, that do not appear to raise any particular issues of structural problems. The dominant sequences belonged to Proteobacteria, Bacteroidetes, Actinobacteria, and Gemmatimonadetes and to the genera Massilia, Sphingomonas, and Adhaeribacter. LEfSe analysis identified 19 key genera, and metagenomic functional prediction revealed a broader phylogenetic range of taxa than expected, with all identified genera possessing at least one plant growth-promoting trait. Around 47% of the sequences were also related to genera possessing strains that facilitate plant development under biotic and environmental stress conditions, such as drought and heat.}, } @article {pmid34304905, year = {2022}, author = {Jia, B and Han, X and Kim, KH and Jeon, CO}, title = {Discovery and mining of enzymes from the human gut microbiome.}, journal = {Trends in biotechnology}, volume = {40}, number = {2}, pages = {240-254}, doi = {10.1016/j.tibtech.2021.06.008}, pmid = {34304905}, issn = {1879-3096}, mesh = {Computational Biology ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolomics ; *Microbiota ; }, abstract = {Advances in technological and bioinformatics approaches have led to the generation of a plethora of human gut metagenomic datasets. Metabolomics has also provided substantial data regarding the small metabolites produced and modified by the microbiota. Comparatively, the microbial enzymes mediating the transformation of metabolites have not been intensively investigated. Here, we discuss the recent efforts and technologies used for discovering and mining enzymes from the human gut microbiota. The wealth of knowledge on metabolites, reactions, genome sequences, and structures of proteins, may drive the development of strategies for enzyme mining. Ongoing efforts to annotate gut microbiota enzymes will explain catalytic mechanisms that may guide the clinical applications of the gut microbiome for diagnostic and therapeutic purposes.}, } @article {pmid34302622, year = {2021}, author = {Hyun, DW and Lee, JY and Kim, MS and Shin, NR and Whon, TW and Kim, KH and Kim, PS and Tak, EJ and Jung, MJ and Lee, JY and Kim, HS and Kang, W and Sung, H and Jeon, CO and Bae, JW}, title = {Pathogenomics of Streptococcus ilei sp. nov., a newly identified pathogen ubiquitous in human microbiome.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {59}, number = {8}, pages = {792-806}, pmid = {34302622}, issn = {1976-3794}, mesh = {Adult ; Animals ; Gastrointestinal Microbiome ; Humans ; Ileostomy ; Male ; Mice ; Mice, Inbred C57BL ; *Microbiota ; Phylogeny ; Streptococcal Infections/*microbiology ; Streptococcus/classification/genetics/*isolation & purification/*pathogenicity ; Virulence ; }, abstract = {Viridans group streptococci are a serious health concern because most of these bacteria cause life-threatening infections, especially in immunocompromised and hospitalized individuals. We focused on two alpha-hemolytic Streptococcus strains (I-G2 and I-P16) newly isolated from an ileostomy effluent of a colorectal cancer patient. We examined their pathogenic potential by investigating their prevalence in human and assessing their pathogenicity in a mouse model. We also predicted their virulence factors and pathogenic features by using comparative genomic analysis and in vitro tests. Using polyphasic and systematic approaches, we identified the isolates as belonging to a novel Streptococcus species and designated it as Streptococcus ilei. Metagenomic survey based on taxonomic assignment of datasets from the Human Microbiome Project revealed that S. ilei is present in most human population and at various body sites but is especially abundant in the oral cavity. Intraperitoneal injection of S. ilei was lethal to otherwise healthy C57BL/6J mice. Pathogenomics and in vitro assays revealed that S. ilei possesses a unique set of virulence factors. In agreement with the in vivo and in vitro data, which indicated that S. ilei strain I-G2 is more pathogenic than strain I-P16, only the former displayed the streptococcal group A antigen. We here newly identified S. ilei sp. nov., and described its prevalence in human, virulence factors, and pathogenicity. This will help to prevent S. ilei strain misidentification in the future, and improve the understanding and management of streptococcal infections.}, } @article {pmid34302348, year = {2021}, author = {Dong, X and Zhang, C and Li, W and Weng, S and Song, W and Li, J and Wang, Y}, title = {Functional diversity of microbial communities in inactive seafloor sulfide deposits.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {8}, pages = {}, doi = {10.1093/femsec/fiab108}, pmid = {34302348}, issn = {1574-6941}, mesh = {Bacteria/genetics ; *Hydrothermal Vents ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfides ; }, abstract = {The seafloor sulfide structures of inactive vents are known to host abundant and diverse microorganisms potentially supported by mineralogy of sulfides. However, little is known about the diversity and distribution of microbial functions. Here, we used genome-resolved metagenomics to predict microbial metabolic functions and the contribution of horizontal gene transfer to the functionality of microorganisms inhabiting several hydrothermally inactive seafloor deposits among globally distributed deep-sea vent fields. Despite of geographically distant vent fields, similar microbial community patterns were observed with the dominance of Gammaproteobacteria, Bacteroidota and previously overlooked Candidatus Patescibacteria. Metabolically flexible Gammaproteobacteria are major potential primary producers utilizing mainly sulfur, iron and hydrogen as electron donors coupled with oxygen and nitrate respiration for chemolithoautotrophic growth. In addition to heterotrophic microorganisms like free-living Bacteroidota, Ca. Patescibacteria potentially perform fermentative recycling of organic carbon. Finally, we provided evidence that many functional genes that are central to energy metabolism have been laterally transferred among members within the community and largely within the same class. Taken together, these findings shed light on microbial ecology and evolution in inactive seafloor sulfide deposits after the cessation of hydrothermal activities.}, } @article {pmid34301806, year = {2021}, author = {Xie, Y and Song, L and Yang, J and Tao, T and Yu, J and Shi, J and Jin, X}, title = {Small intestinal flora graft alters fecal flora, stool, cytokines and mood status in healthy mice.}, journal = {Life science alliance}, volume = {4}, number = {9}, pages = {}, pmid = {34301806}, issn = {2575-1077}, mesh = {*Affect ; Animals ; *Behavior, Animal ; Biomarkers ; Body Weight ; Cytokines/blood/*metabolism ; Drinking ; Eating ; *Fecal Microbiota Transplantation ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Male ; Metagenome ; Metagenomics ; Mice ; }, abstract = {Fecal microbiota transplantation is widely used. Large intestinal microbiota (LIM) is more similar to fecal microbiota than small intestinal microbiota (SIM). The SIM communities are very different from those of LIM. Therefore, SIM transplantation (SIMT) and LIM transplantation (LIMT) might exert different influences. Here, healthy adult male C57Bl/6 mice received intragastric SIMT, LIMT, or sterile PBS administration. Microbiota graft samples were collected from small/large intestine of healthy mice of the same age, sex, and strain background. Compared with PBS treatment, SIMT increased pellet number, stool wet weight, and stool water percentage; induced a fecal microbiota profile shift toward the microbial composition of the SIM graft; induced a systemic anti-inflammatory cytokines profile; and ameliorated depressive-like behaviors in recipients. LIMT, however, induced merely a slight alteration in fecal microbial composition and no significant influence on the other aspects. In sum, SIMT, rather than LIMT, affected defecation features, fecal microbial composition, cytokines profile, and depressive-like behaviors in healthy mice. This study reveals the different effects of SIMT and LIMT, providing an interesting clue for further researches involving gut microbial composition change.}, } @article {pmid34301627, year = {2021}, author = {Roodgar, M and Good, BH and Garud, NR and Martis, S and Avula, M and Zhou, W and Lancaster, SM and Lee, H and Babveyh, A and Nesamoney, S and Pollard, KS and Snyder, MP}, title = {Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment.}, journal = {Genome research}, volume = {31}, number = {8}, pages = {1433-1446}, pmid = {34301627}, issn = {1549-5469}, support = {U54 DK102556/DK/NIDDK NIH HHS/United States ; S10 OD020141/OD/NIH HHS/United States ; P30 DK116074/DK/NIDDK NIH HHS/United States ; T32 HL120824/HL/NHLBI NIH HHS/United States ; R01 AG023202/AG/NIA NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Gut microbial communities can respond to antibiotic perturbations by rapidly altering their taxonomic and functional composition. However, little is known about the strain-level processes that drive this collective response. Here, we characterize the gut microbiome of a single individual at high temporal and genetic resolution through a period of health, disease, antibiotic treatment, and recovery. We used deep, linked-read metagenomic sequencing to track the longitudinal trajectories of thousands of single nucleotide variants within 36 species, which allowed us to contrast these genetic dynamics with the ecological fluctuations at the species level. We found that antibiotics can drive rapid shifts in the genetic composition of individual species, often involving incomplete genome-wide sweeps of pre-existing variants. These genetic changes were frequently observed in species without obvious changes in species abundance, emphasizing the importance of monitoring diversity below the species level. We also found that many sweeping variants quickly reverted to their baseline levels once antibiotic treatment had concluded, demonstrating that the ecological resilience of the microbiota can sometimes extend all the way down to the genetic level. Our results provide new insights into the population genetic forces that shape individual microbiomes on therapeutically relevant timescales, with potential implications for personalized health and disease.}, } @article {pmid34301347, year = {2021}, author = {Gerb, SA and Dashek, RJ and Ericsson, AC and Griffin, R and Franklin, CL}, title = {The Effects of Ketamine on the Gut Microbiome on CD1 Mice.}, journal = {Comparative medicine}, volume = {71}, number = {4}, pages = {295-301}, pmid = {34301347}, issn = {2769-819X}, support = {T32 OD011126/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Animals ; Feces ; Female ; *Gastrointestinal Microbiome ; *Ketamine/pharmacology ; Mice ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; }, abstract = {The intestinal microbiota of an organism can significantly alter outcome data in otherwise identical experiments. Occasionally, animals may require sedation or anesthesia for scientific or health-related purposes, and certain anesthetics, such as ketamine, can profoundly affect the gastrointestinal system. While many factors can alter the gut microbiome (GM), the effects of anesthetics on the composition or diversity of the GM have not been established. The goal of the current study was to determine whether daily administration of ketamine would significantly alter the microbiome of CD1 mice. To achieve this goal, female CD1 mice received daily injections of ketamine HCl (100 mg/kg) or the equivalent volume of 0.9% saline for 10 consecutive days. Fecal samples were collected before the first administration and 24 h after the final dose of either ketamine or saline. Samples were analyzed by 16S rRNA sequencing to identify changes between groups in diversity or composition of GM. The study found no significant changes to the GM after serial ketamine administration when treated mice were housed with controls. Therefore, ketamine administration is unlikely to alter the GM of a CD1 mouse and should not serve be a confounding factor in reproducibility of research.}, } @article {pmid34299675, year = {2021}, author = {Su Mun, L and Wye Lum, S and Kong Yuiin Sze, G and Hock Yoong, C and Ching Yung, K and Kah Lok, L and Gopinath, D}, title = {Association of Microbiome with Oral Squamous Cell Carcinoma: A Systematic Review of the Metagenomic Studies.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {14}, pages = {}, pmid = {34299675}, issn = {1660-4601}, mesh = {*Carcinoma, Squamous Cell ; *Head and Neck Neoplasms ; Humans ; Metagenomics ; *Microbiota ; *Mouth Neoplasms ; Squamous Cell Carcinoma of Head and Neck ; }, abstract = {The past decade has witnessed a surge in epidemiological studies that have explored the relationship between the oral microbiome and oral cancer. Owing to the diversity of the published data, a comprehensive systematic overview of the currently available evidence is critical. This review summarises the current evidence on the metagenomic studies on the oral microbiome in oral cancer. A systematic search was conducted in Medline and Embase databases to identify original studies examining the differences in the oral microbiome of oral cancer cases and controls. A total of twenty-six studies were identified that reported differences in microbial abundance between oral squamous cell carcinoma (OSCC) and controls. Although almost all the studies identified microbial dysbiosis to be associated with oral cancer, the detailed qualitative analysis did not reveal the presence/abundance of any individual bacteria or a consortium to be consistently enriched in OSCC samples across the studies. Interestingly, few studies reported a surge of periodontopathogenic taxa, especially Fusobacteria, whereas others demonstrated a depletion of commensal taxa Streptococci. Considerable heterogeneity could be identified in the parameters used for designing the studies as well as reporting the microbial data. If microbiome data needs to be translated in the future, to complement the clinical parameters for diagnosis and prognosis of oral cancer, further studies with the integration of clinical variables, adequate statistical power, reproducible methods, and models are required.}, } @article {pmid34298350, year = {2021}, author = {Bombaywala, S and Purohit, HJ and Dafale, NA}, title = {Mobility of antibiotic resistance and its co-occurrence with metal resistance in pathogens under oxidative stress.}, journal = {Journal of environmental management}, volume = {297}, number = {}, pages = {113315}, doi = {10.1016/j.jenvman.2021.113315}, pmid = {34298350}, issn = {1095-8630}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; *Metals, Heavy/toxicity ; *Microbiota ; Oxidative Stress ; }, abstract = {The bacterial communities are challenged with oxidative stress during their exposure to bactericidal antibiotics, metals, and different levels of dissolved oxygen (DO) encountered in diverse environmental habitats. The frequency of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) co-selection is increased by selective pressure posed by oxidative stress. Hence, study of resistance acquisition is important from an evolutionary perspective. To understand the dependence of oxidative stress on the dissemination of ARGs and MRGs through a pathogenic bacterial population, 12 metagenomes belonging to gut, water and soil habitats were evaluated. The metagenome-wide analysis showed the chicken gut to pose the most diverse pool of ARGs (30.4 ppm) and pathogenic bacteria (Simpson diversity = 0.98). The most common types of resistances found in all the environmental samples were efflux pumps (13.22 ppm) and genes conferring resistance to vancomycin (12.4 ppm), tetracycline (12.1 ppm), or beta-lactam (9.4 ppm) antibiotics. Additionally, limiting DO level in soil was observed to increase the abundance of excision nucleases (uvrA and uvrB), DNA polymerase (polA), catalases (katG), and other oxidative stress response genes (OSGs). This was further evident from major variations occurred in antibiotic efflux genes due to the effect of DO concentration on two human pathogens, namely Salmonella enterica and Shigella sonnei found in all the selected habitats. In conclusion, the microbial community, when challenged with oxidative stress caused by environmental variations in oxygen level, tends to accumulate higher amounts of ARGs with increased dissemination potential through triggering non-lethal mutagenesis. Furthermore, the genetic linkage or co-occurrence of ARGs and MRGs provides evidence for selecting ARGs under high concentrations of heavy metals.}, } @article {pmid34297922, year = {2021}, author = {Lee, JWJ and Plichta, D and Hogstrom, L and Borren, NZ and Lau, H and Gregory, SM and Tan, W and Khalili, H and Clish, C and Vlamakis, H and Xavier, RJ and Ananthakrishnan, AN}, title = {Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease.}, journal = {Cell host & microbe}, volume = {29}, number = {8}, pages = {1294-1304.e4}, pmid = {34297922}, issn = {1934-6069}, support = {R01 AT009708/AT/NCCIH NIH HHS/United States ; U19 AI110495/AI/NIAID NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R21 DK127227/DK/NIDDK NIH HHS/United States ; U19 AI142784/AI/NIAID NIH HHS/United States ; }, mesh = {Antibodies, Monoclonal, Humanized ; *Biological Therapy ; Biomarkers ; Blood ; Colitis, Ulcerative/*therapy ; Crohn Disease/therapy ; Cytokines/blood/drug effects ; Feces ; Gastrointestinal Microbiome/*physiology ; Humans ; *Inflammatory Bowel Diseases/microbiology/therapy ; Infliximab ; Metabolomics ; Metagenome ; Prospective Studies ; Proteomics ; Tumor Necrosis Factor Inhibitors/therapeutic use ; }, abstract = {The intestinal microbiome is a key determinant of responses to biologic therapy in inflammatory bowel disease (IBD). However, diverse therapeutics and variable responses among IBD patients have posed challenges in predicting clinical therapeutic success. In this prospective study, we profiled baseline stool and blood in patients with moderate-to-severe Crohn's disease or ulcerative colitis initiating anti-cytokine therapy (anti-TNF or -IL12/23) or anti-integrin therapy. Patients were assessed at 14 weeks for clinical remission and 52 weeks for clinical and endoscopic remission. Baseline microbial richness indicated preferential responses to anti-cytokine therapy and correlated with the abundance of microbial species capable of 7α/β-dehydroxylation of primary to secondary bile acids. Serum signatures of immune proteins reflecting microbial diversity identified patients more likely to achieve remission with anti-cytokine therapy. Remission-associated multi-omic profiles were unique to each therapeutic class. These profiles may facilitate a priori determination of optimal therapeutics for patients and serve as targets for newer therapies.}, } @article {pmid34296337, year = {2021}, author = {Checcucci, A and Luise, D and Modesto, M and Correa, F and Bosi, P and Mattarelli, P and Trevisi, P}, title = {Assessment of Biolog Ecoplate[TM] method for functional metabolic diversity of aerotolerant pig fecal microbiota.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {14-15}, pages = {6033-6045}, pmid = {34296337}, issn = {1432-0614}, mesh = {Animals ; Feces ; *Gastrointestinal Microbiome ; Mammals ; *Microbiota ; RNA, Ribosomal, 16S ; Swine ; }, abstract = {In the last decades, gut microbiota and its role in mammal host development and health have been increasingly investigated. Metabolites produced by gut microbiota can affect intestinal homeostasis and immune system maturity and activation, and in turn, they can influence the health and growth performance of livestock. Therefore, a better understanding of the functional metabolic capability of the gut microbiota would be appreciated by the scientific community. In this study, the Biolog[TM] Ecoplates technology was applied for studying the metabolic potential of the aerotolerant microbial community of pig fecal samples, evaluating the interference of different storage conditions and cell concentrations. The length of time for which a fecal sample maintained detectable and unchanged microbial metabolic activity was also investigated. Two assays aimed to evaluate differences in the metabolic activities between fresh and snap-frozen fecal samples at different dilutions and at different lengths of times of preservation at -80°C were carried out. The biodiversity and the predicted functionality of the entire bacterial community through a targeted metagenomic approach were also explored. The results highlighted that snap freezing of fecal samples preserved the metabolic activity of the microbial community when compared to fresh feces. Sample storage at -80 °C did not significantly affect the metabolic activity of the microbial community, which was stable for 150 days. Furthermore, the highest metabolic activity was detected with 1:2 to 1:5 dilutions of the stock suspension. Biolog[TM] Ecoplates technology is a rapid and useful method to explore microbial communities' metabolism in animal fecal samples contributing to investigate host animal physiology. KEY POINTS: • Freezing of samples can preserve the functional activity of the aerotolerant microbial community for 150 days. • The concentration of microbial cells strongly influences metabolic activity detection. • Sequencing coupled with the Biolog[TM] Ecoplates could be a strategy to evaluate the metabolic potential of the microbiota of the fecal sample.}, } @article {pmid34294835, year = {2021}, author = {Wingfield, B and Lapsley, C and McDowell, A and Miliotis, G and McLafferty, M and O'Neill, SM and Coleman, S and McGinnity, TM and Bjourson, AJ and Murray, EK}, title = {Variations in the oral microbiome are associated with depression in young adults.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {15009}, pmid = {34294835}, issn = {2045-2322}, mesh = {Adolescent ; Adult ; Age Factors ; Bacteria/genetics ; *Biodiversity ; Case-Control Studies ; Depression/diagnosis/*etiology ; Female ; *Host Microbial Interactions ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth/*microbiology ; Saliva/microbiology ; Young Adult ; }, abstract = {A growing body of evidence supports an important role for alterations in the brain-gut-microbiome axis in the aetiology of depression and other psychiatric disorders. The potential role of the oral microbiome in mental health has received little attention, even though it is one of the most diverse microbiomes in the body and oral dysbiosis has been linked to systemic diseases with an underlying inflammatory aetiology. This study examines the structure and composition of the salivary microbiome for the first time in young adults who met the DSM-IV criteria for depression (n = 40) and matched controls (n = 43) using 16S rRNA gene-based next generation sequencing. Subtle but significant differences in alpha and beta diversity of the salivary microbiome were observed, with clear separation of depressed and healthy control cohorts into distinct clusters. A total of 21 bacterial taxa were found to be differentially abundant in the depressed cohort, including increased Neisseria spp. and Prevotella nigrescens, while 19 taxa had a decreased abundance. In this preliminary study we have shown that the composition of the oral microbiome is associated with depression in young adults. Further studies are now warranted, particuarly investigations into whether such shifts play any role in the underling aetiology of depression.}, } @article {pmid34294810, year = {2021}, author = {Verspecht, T and Van Holm, W and Boon, N and Bernaerts, K and Daep, CA and Zayed, N and Quirynen, M and Teughels, W}, title = {Comparison of the modulatory effects of three structurally similar potential prebiotic substrates on an in vitro multi-species oral biofilm.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {15033}, pmid = {34294810}, issn = {2045-2322}, mesh = {Biodiversity ; *Biofilms/drug effects/growth & development ; Host Microbial Interactions ; Metagenome ; Metagenomics/methods ; Microbiota ; Mouth/*microbiology ; Prebiotics/*administration & dosage ; Virulence/genetics ; }, abstract = {Previous research identified potential prebiotic substrates for oral health like the structural analogues N-acetyl-D-mannosamine (NADM) and N-acetyl-D-glucosamine (NADG). The main hypothesis of the current study was twofold. Firstly, it was hypothesized that the modulatory effects of NADM are not limited to changes in multi-species oral biofilm composition, but also include effects on metabolism, virulence, and inflammatory potential. Secondly, the presence and orientation of their N-acetyl group could play a role. Therefore, a comparison was made between the effects of NADM, NADG and D-(+)-mannose on multi-species oral biofilms. Besides a beneficial compositional shift, NADM-treated biofilms also showed an altered metabolism, a reduced virulence and a decreased inflammatory potential. At a substrate concentration of 1 M, these effects were pronounced for all biofilm aspects, whereas at ~ 0.05 M (1%(w/v)) only the effects on virulence were pronounced. When comparing between substrates, both the presence and orientation of the N-acetyl group played a role. However, this was generally only at 1 M and dependent on the biofilm aspect. Overall, NADM was found to have different effects at two concentrations that beneficially modulate in vitro multi-species oral biofilm composition, metabolism, virulence and inflammatory potential. The presence and orientation of the N-acetyl group influenced these effects.}, } @article {pmid34294783, year = {2021}, author = {Zhong, H and Zhang, J and Li, F and Chen, J}, title = {Gut microbial communities associated with phenotypically divergent populations of the striped stem borer Chilo suppressalis (Walker, 1863).}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {15010}, pmid = {34294783}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; Computational Biology/methods ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Moths/*microbiology ; Oryza/parasitology ; Plant Diseases ; RNA, Ribosomal, 16S ; }, abstract = {Chilo suppressalis (Walker, 1863) is a serious stem borer of rice and water-oat plants, and has phenotypically diverged into rice and water-oat populations. Insect gut microbiota plays an important role in the host life and understanding the dynamics of this complicated ecosystem may improve its biological control. The effect of diet and gut compartments on the gut microflora of divergent populations of C. suppressalis is not fully clear. Herein, we characterized the gut microbiota of C. suppressalis populations fed on two hosts (i.e., water-oats fruit pulps and rice seedlings), by sequencing the V3-V4 hypervariable region of the 16S rRNA gene using the Illumina MiSeq platform. Gut bacterial communities showed variation in relative abundance among C. suppressalis populations fed on water-oats fruit pulps or rice seedlings. Proteobacteria and Firmicutes became the predominant phyla, and Enterobacteriaceae, Enterococcaceae and Halomonadaceae were the predominant family in all C. suppressalis populations. The highest bacteria diversity was found in the midgut of the rice population fed on water-oat fruit pulps. Bacterial communities in the midgut were more diverse than those in the hindgut. The bacterial genera distribution showed great differences due to diet types and gut compartments among populations. Our results demonstrated that the host plants tested had a considerable impact on gut bacterial composition of C. suppressalis populations. Additionly, the unique gut morphology and physiological conditions (viz., oxygen content, enzymes) also contributed to variation in microbiomes. In conclusion, our study provided an important insight into investigation of insect-bacteria symbioses, and biocontrol of this species and other related lepidopterans.}, } @article {pmid34294041, year = {2021}, author = {Andrade, BGN and Goris, T and Afli, H and Coutinho, FH and Dávila, AMR and Cuadrat, RRC}, title = {Putative mobilized colistin resistance genes in the human gut microbiome.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {220}, pmid = {34294041}, issn = {1471-2180}, mesh = {Colistin/*pharmacology ; Computational Biology ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genetic Variation ; Humans ; Microbiota/*drug effects/*genetics ; }, abstract = {BACKGROUND: The high incidence of bacterial genes that confer resistance to last-resort antibiotics, such as colistin, caused by mobilized colistin resistance (mcr) genes, poses an unprecedented threat to human health. Understanding the spread, evolution, and distribution of such genes among human populations will help in the development of strategies to diminish their occurrence. To tackle this problem, we investigated the distribution and prevalence of potential mcr genes in the human gut microbiome using a set of bioinformatics tools to screen the Unified Human Gastrointestinal Genome (UHGG) collection for the presence, synteny and phylogeny of putative mcr genes, and co-located antibiotic resistance genes.

RESULTS: A total of 2079 antibiotic resistance genes (ARGs) were classified as mcr genes in 2046 metagenome assembled genomes (MAGs), distributed across 1596 individuals from 41 countries, of which 215 were identified in plasmidial contigs. The genera that presented the largest number of mcr-like genes were Suterella and Parasuterella. Other potential pathogens carrying mcr genes belonged to the genus Vibrio, Escherichia and Campylobacter. Finally, we identified a total of 22,746 ARGs belonging to 21 different classes in the same 2046 MAGs, suggesting multi-resistance potential in the corresponding bacterial strains, increasing the concern of ARGs impact in the clinical settings.

CONCLUSION: This study uncovers the diversity of mcr-like genes in the human gut microbiome. We demonstrated the cosmopolitan distribution of these genes in individuals worldwide and the co-presence of other antibiotic resistance genes, including Extended-spectrum Beta-Lactamases (ESBL). Also, we described mcr-like genes fused to a PAP2-like domain in S. wadsworthensis. These novel sequences increase our knowledge about the diversity and evolution of mcr-like genes. Future research should focus on activity, genetic mobility and a potential colistin resistance in the corresponding strains to experimentally validate those findings.}, } @article {pmid34294039, year = {2021}, author = {Zhang, Z and Zhang, L}, title = {METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs.}, journal = {BMC bioinformatics}, volume = {22}, number = {Suppl 10}, pages = {378}, pmid = {34294039}, issn = {1471-2105}, support = {HKBU 22201419//Early Career Scheme/ ; IRCMS/19-20/D02//Hong Kong Baptist University/ ; 2019A1515011046//Natural Science Foundation of Guangdong Province/ ; }, mesh = {Algorithms ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; Software ; }, abstract = {BACKGROUND: Due to the complexity of microbial communities, de novo assembly on next generation sequencing data is commonly unable to produce complete microbial genomes. Metagenome assembly binning becomes an essential step that could group the fragmented contigs into clusters to represent microbial genomes based on contigs' nucleotide compositions and read depths. These features work well on the long contigs, but are not stable for the short ones. Contigs can be linked by sequence overlap (assembly graph) or by the paired-end reads aligned to them (PE graph), where the linked contigs have high chance to be derived from the same clusters.

RESULTS: We developed METAMVGL, a multi-view graph-based metagenomic contig binning algorithm by integrating both assembly and PE graphs. It could strikingly rescue the short contigs and correct the binning errors from dead ends. METAMVGL learns the two graphs' weights automatically and predicts the contig labels in a uniform multi-view label propagation framework. In experiments, we observed METAMVGL made use of significantly more high-confidence edges from the combined graph and linked dead ends to the main graph. It also outperformed many state-of-the-art contig binning algorithms, including MaxBin2, MetaBAT2, MyCC, CONCOCT, SolidBin and GraphBin on the metagenomic sequencing data from simulation, two mock communities and Sharon infant fecal samples.

CONCLUSIONS: Our findings demonstrate METAMVGL outstandingly improves the short contig binning and outperforms the other existing contig binning tools on the metagenomic sequencing data from simulation, mock communities and infant fecal samples.}, } @article {pmid34292157, year = {2021}, author = {Lundberg, DS and Pramoj Na Ayutthaya, P and Strauß, A and Shirsekar, G and Lo, WS and Lahaye, T and Weigel, D}, title = {Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34292157}, issn = {2050-084X}, mesh = {Arabidopsis/microbiology ; Bacteria/classification/genetics ; Gene Library ; Host Microbial Interactions/genetics ; Humans ; Microbiota/*genetics ; Oomycetes ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; Zea mays/microbiology ; }, abstract = {The ratio of microbial population size relative to the amount of host tissue, or 'microbial load', is a fundamental metric of colonization and infection, but it cannot be directly deduced from microbial amplicon data such as 16S rRNA gene counts. Because existing methods to determine load, such as serial dilution plating, quantitative PCR, and whole metagenome sequencing add substantial cost and/or experimental burden, they are only rarely paired with amplicon sequencing. We introduce host-associated microbe PCR (hamPCR), a robust strategy to both quantify microbial load and describe interkingdom microbial community composition in a single amplicon library. We demonstrate its accuracy across multiple study systems, including nematodes and major crops, and further present a cost-saving technique to reduce host overrepresentation in the library prior to sequencing. Because hamPCR provides an accessible experimental solution to the well-known limitations and statistical challenges of compositional data, it has far-reaching potential in culture-independent microbiology.}, } @article {pmid34291461, year = {2021}, author = {Dextro, RB and Delbaje, E and Cotta, SR and Zehr, JP and Fiore, MF}, title = {Trends in Free-access Genomic Data Accelerate Advances in Cyanobacteria Taxonomy.}, journal = {Journal of phycology}, volume = {57}, number = {5}, pages = {1392-1402}, doi = {10.1111/jpy.13200}, pmid = {34291461}, issn = {1529-8817}, mesh = {*Cyanobacteria/genetics ; Genomics ; Metagenome ; *Microbiota ; Phylogeny ; }, abstract = {Free access databases of DNA sequences containing microbial genetic information have changed the way scientists look at the microbial world. Currently, the NCBI database includes about 516 distinct search results for Cyanobacterial genomes distributed in a taxonomy based on a polyphasic approach. While their classification and taxonomic relationships are widely used as is, recent proposals to alter their grouping include further exploring the relationship between Cyanobacteria and Melainabacteria. Nowadays, most cyanobacteria still are named under the Botanical Code; however, there is a proposal made by the Genome Taxonomy Database (GTDB) to harmonize cyanobacteria nomenclature with the other bacteria, an initiative to standardize microbial taxonomy based on genome phylogeny, in order to contribute to an overall better phylogenetic resolution of microbiota. Furthermore, the assembly level of the genomes and their geographical origin demonstrates some trends of cyanobacteria genomics on the scientific community, such as low availability of complete genomes and underexplored sampling locations. By describing how available cyanobacterial genomes from free-access databases fit within different taxonomic classifications, this mini-review provides a holistic view of the current knowledge of cyanobacteria and indicates some steps towards improving our efforts to create a more cohesive and inclusive classifying system, which can be greatly improved by using large-scale sequencing and metagenomic techniques.}, } @article {pmid34290346, year = {2021}, author = {de la Cruz Peña, MJ and Gonzalez-Granado, LI and Garcia-Heredia, I and Carballa, LM and Martinez-Garcia, M}, title = {Minimal-moderate variation of human oral virome and microbiome in IgA deficiency.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {14913}, pmid = {34290346}, issn = {2045-2322}, mesh = {Adolescent ; Adult ; Aged ; Child ; Female ; Humans ; IgA Deficiency/*microbiology/*virology ; Immunoglobulin A/physiology ; Immunoglobulin M/deficiency ; Male ; Metagenomics ; *Microbiota/genetics ; Middle Aged ; Mouth/*microbiology/*virology ; Saliva/microbiology/virology ; *Virome/genetics ; Young Adult ; }, abstract = {Immunoglobulin A (IgA) is the dominant antibody found in our mucosal secretions and has long been recognized to play an important role in protecting our epithelium from pathogens. Recently, IgA has been shown to be involved in gut homeostatic regulation by 'recognizing' and shaping our commensal microbes. Paradoxically, yet selective IgA-deficiency is often described as asymptomatic and there is a paucity of studies only focused on the mice and human gut microbiome context fully ignoring other niches of our body and our commensal viruses. Here, we used as a model the human oral cavity and employed a holistic view and studied the impact of IgA deficiency and also common variable IgA and IgM immunodeficiencies (CVID), on both the human virome and microbiome. Unexpectedly, metagenomic and experimental data in human IgA deficiency and CVID indicate minimal-moderate changes in microbiome and virome composition compared to healthy control group and point out to a rather functional, resilient oral commensal viruses and microbes. However, a significant depletion (two fold) of bacterial cells (p-value < 0.01) and viruses was observed in IgA-deficiency. Our results demonstrate that, within the limits of our cohort, IgA role is not critical for maintaining a rather functional salivary microbiome and suggest that IgA is not a major influence on the composition of abundant commensal microbes.}, } @article {pmid34290321, year = {2021}, author = {Sun, S and Zhu, X and Huang, X and Murff, HJ and Ness, RM and Seidner, DL and Sorgen, AA and Blakley, IC and Yu, C and Dai, Q and Azcarate-Peril, MA and Shrubsole, MJ and Fodor, AA}, title = {On the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {14828}, pmid = {34290321}, issn = {2045-2322}, support = {P30 DK034987/DK/NIDDK NIH HHS/United States ; R01 DK110166/DK/NIDDK NIH HHS/United States ; R03 CA183019/CA/NCI NIH HHS/United States ; R01CA149633/NH/NIH HHS/United States ; R03CA183019/NH/NIH HHS/United States ; UL1 TR000445/TR/NCATS NIH HHS/United States ; UL1 RR024975/RR/NCRR NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Age Factors ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents ; Anti-Inflammatory Agents, Non-Steroidal ; Bacteria/*classification/*isolation & purification ; Body Mass Index ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/*microbiology ; Male ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Rectum/*microbiology ; Sex Factors ; }, abstract = {The gut microbiota plays an important role in human health and disease. Stool, rectal swab and rectal mucosal tissue samples have been used in individual studies to survey the microbial community but the consequences of using these different sample types are not completely understood. In this study, we report differences in stool, rectal swab and rectal mucosal tissue microbial communities with shotgun metagenome sequencing of 1397 stool, swab and mucosal tissue samples from 240 participants. The taxonomic composition of stool and swab samples was distinct, but less different to each other than mucosal tissue samples. Functional profile differences between stool and swab samples are smaller, but mucosal tissue samples remained distinct from the other two types. When the taxonomic and functional profiles were used for inference in association with host phenotypes of age, sex, body mass index (BMI), antibiotics or non-steroidal anti-inflammatory drugs (NSAIDs) use, hypothesis testing using either stool or rectal swab gave broadly significantly correlated results, but inference performed on mucosal tissue samples gave results that were generally less consistent with either stool or swab. Our study represents an important resource for determination of how inference can change for taxa and pathways depending on the choice of where to sample within the human gut.}, } @article {pmid34289613, year = {2021}, author = {Šamanić, I and Kalinić, H and Fredotović, Ž and Dželalija, M and Bungur, AM and Maravić, A}, title = {Bacteria tolerant to colistin in coastal marine environment: Detection, microbiome diversity and antibiotic resistance genes' repertoire.}, journal = {Chemosphere}, volume = {281}, number = {}, pages = {130945}, doi = {10.1016/j.chemosphere.2021.130945}, pmid = {34289613}, issn = {1879-1298}, mesh = {Anti-Bacterial Agents/pharmacology ; *Colistin/pharmacology ; Croatia ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Serratia ; beta-Lactamases/genetics ; }, abstract = {The global spread of mobilized colistin resistance (mcr) genes in clinical and natural environments dangerously diminishes the effectiveness of this last-resort antibiotic, becoming an urgent health threat. We used a multidisciplinary approach to detect mcr-1 gene and colistin (CL)-resistant bacteria in seawater from two Croatian public beaches. Illumina-based sequencing of metagenomic 16S rRNA was used to assess the taxonomic, functional, and antibiotic resistance genes (ARGs) profiling of the bacterial community tolerant to CL regarding different culture-based isolation methodologies. Data revealed that the choice of methodology alters the diversity and abundance of taxa accounting for the CL-resistance phenotype. The mcr-1 gene was identified by cloning and sequencing in one sample, representing the first report of mcr-1 gene in Croatia. Culturing of CL-resistant strains revealed their resistance phenotypes and concurrent production of clinically significant β-lactamases, such as CTX-M-15, CTX-M-3 and SHV-12. We also report the first identification of blaCTX-M-15 gene in Klebsiella huaxiensis and K. michiganensis, as well as the blaTEM-1+CTX-M-3 in Serratia fonticola. ARGs profiles derived from metagenomic data and predicted by PICRUSt2, showed the highest abundance of genes encoding for multidrug efflux pumps, followed by the transporter genes accounting for the tetracycline, macrolide and phenicol resistance. Our study evidenced the multidrug resistance features of CL-tolerant bacterial communities thriving in surface beach waters. We also showed that combined application of the metagenomic approaches and culture-based techniques enabled successful detection of mcr-1 gene, which could be underreported in natural environment.}, } @article {pmid34289377, year = {2021}, author = {Zhang, XS and Yin, YS and Wang, J and Battaglia, T and Krautkramer, K and Li, WV and Li, J and Brown, M and Zhang, M and Badri, MH and Armstrong, AJS and Strauch, CM and Wang, Z and Nemet, I and Altomare, N and Devlin, JC and He, L and Morton, JT and Chalk, JA and Needles, K and Liao, V and Mount, J and Li, H and Ruggles, KV and Bonneau, RA and Dominguez-Bello, MG and Bäckhed, F and Hazen, SL and Blaser, MJ}, title = {Maternal cecal microbiota transfer rescues early-life antibiotic-induced enhancement of type 1 diabetes in mice.}, journal = {Cell host & microbe}, volume = {29}, number = {8}, pages = {1249-1265.e9}, pmid = {34289377}, issn = {1934-6069}, support = {R01 DK120679/DK/NIDDK NIH HHS/United States ; R01 DK110014/DK/NIDDK NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; R35 GM139655/GM/NIGMS NIH HHS/United States ; R01 GM128955/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Autoimmune Diseases ; Bacteria/classification/drug effects ; Cecum/*immunology/*microbiology ; Diabetes Mellitus, Type 1/*immunology ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/*drug effects/*physiology ; Gene Expression ; Histone Code ; Intestines/immunology ; Male ; Metabolic Networks and Pathways ; Metagenome ; Mice ; Mice, Inbred NOD ; MicroRNAs ; }, abstract = {Early-life antibiotic exposure perturbs the intestinal microbiota and accelerates type 1 diabetes (T1D) development in the NOD mouse model. Here, we found that maternal cecal microbiota transfer (CMT) to NOD mice after early-life antibiotic perturbation largely rescued the induced T1D enhancement. Restoration of the intestinal microbiome was significant and persistent, remediating the antibiotic-depleted diversity, relative abundance of particular taxa, and metabolic pathways. CMT also protected against perturbed metabolites and normalized innate and adaptive immune effectors. CMT restored major patterns of ileal microRNA and histone regulation of gene expression. Further experiments suggest a gut-microbiota-regulated T1D protection mechanism centered on Reg3γ, in an innate intestinal immune network involving CD44, TLR2, and Reg3γ. This regulation affects downstream immunological tone, which may lead to protection against tissue-specific T1D injury.}, } @article {pmid34287529, year = {2021}, author = {Baima, DC and Carvalho, NS and Barbuti, RC and Navarro-Rodriguez, T}, title = {ASSESSMENT OF THE INTESTINAL MICROBIOTA IN ADULTS WITH EROSIVE ESOPHAGITIS.}, journal = {Arquivos de gastroenterologia}, volume = {58}, number = {2}, pages = {168-174}, doi = {10.1590/S0004-2803.202100000-29}, pmid = {34287529}, issn = {1678-4219}, mesh = {Adolescent ; Adult ; Dysbiosis ; *Esophagitis ; Feces ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {BACKGROUND: The intestinal microbiota influences the appropriate function of the gastrointestinal tract. Intestinal dysbiosis may be associated with a higher risk of esophageal lesions, mainly due to changes in gastroesophageal motility patterns, elevation of intra-abdominal pressure, and increased frequency of transient relaxation of the lower esophageal sphincter.

OBJECTIVE: The aim of this study was to evaluate the intestinal microbiota in individuals with erosive esophagitis and in healthy individuals using metagenomics.

METHODS: A total of 22 fecal samples from adults aged between 18 and 60 years were included. Eleven individuals had esophagitis (eight men and three women) and 11 were healthy controls (10 men and one woman). The individuals were instructed to collect and store fecal material into a tube containing guanidine solution. The DNA of the microbiota was extracted from each fecal samples and PCR amplification was performed using primers for the V4 region of the 16S rRNA gene. The amplicons were sequenced using the Ion Torrent PGM platform and the data were analyzed using the QIIME™ software version 1.8. Statistical analyses were performed using the Mann-Whitney non-parametric test and the ANOSIM non-parametric method based on distance matrix.

RESULTS: The alpha-diversity and beta-diversity indices were similar between the two groups, without statistically significant differences. There was no statistically significant difference in the phylum level. However, a statistically significant difference was observed in the abundance of the family Clostridiaceae (0.3% vs 2.0%, P=0.032) and in the genus Faecaliumbacterium (10.5% vs 4.5%, P=0.045) between healthy controls and esophagitis patients.

CONCLUSION: The findings suggest that reduced abundance of the genus Faecaliumbacterium and greater abundance of the family Clostridiaceae may be risk factors for the development of erosive esophagitis. Intervention in the composition of the intestinal microbiota should be considered as an adjunct to current therapeutic strategies for this clinical condition.}, } @article {pmid34287254, year = {2021}, author = {Agrawal, R and Ajami, NJ and Malhotra, S and Chen, L and White, DL and Sharafkhaneh, A and Hoffman, KL and Graham, DY and El-Serag, HB and Petrosino, JF and Jiao, L}, title = {Habitual Sleep Duration and the Colonic Mucosa-Associated Gut Microbiota in Humans-A Pilot Study.}, journal = {Clocks & sleep}, volume = {3}, number = {3}, pages = {387-397}, pmid = {34287254}, issn = {2624-5175}, support = {CX001430.//U.S. Department of Veterans Affairs/ ; I01 CX001430/CX/CSRD VA/United States ; R01CA172880/CA/NCI NIH HHS/United States ; RP#140767//Cancer Prevention and Research Institute of Texas/ ; CIN13-413//the Houston Veterans Affairs Health Services Research Center of Innovations/ ; 0000//Golfers Against Cancer Organization/ ; 0000//Gillson Longenbaugh Foundation/ ; }, abstract = {We examined the association between the colonic adherent microbiota and nocturnal sleep duration in humans. In a cross-sectional study, 63 polyp-free adults underwent a colonoscopy and donated 206 mucosal biopsies. The gut microbiota was profiled using the 16S rRNA gene sequencing targeting the V4 region. The sequence reads were processed using UPARSE and DADA2, respectively. Lifestyle factors, including sleep habits, were obtained using an interviewer-administered questionnaire. We categorized the participants into short sleepers (<6 h per night; n = 16) and normal sleepers (6-8 h per night; n = 47) based on self-reported data. Differences in bacterial biodiversity and the taxonomic relative abundance were compared between short vs. normal sleepers, followed by multivariable analysis. A false discovery rate-adjusted p value (q value) < 0.05 indicated statistical significance. The bacterial community composition differed in short and normal sleepers. The relative abundance of Sutterella was significantly lower (0.38% vs. 1.25%) and that of Pseudomonas was significantly higher (0.14% vs. 0.08%) in short sleepers than in normal sleepers (q values < 0.01). The difference was confirmed in the multivariable analysis. Nocturnal sleep duration was associated with the bacterial community composition and structure in the colonic gut microbiota in adults.}, } @article {pmid34287009, year = {2021}, author = {Aljabr, W and Alruwaili, M and Penrice-Randal, R and Alrezaihi, A and Harrison, AJ and Ryan, Y and Bentley, E and Jones, B and Alhatlani, BY and AlShahrani, D and Mahmood, Z and Rickett, NY and Alosaimi, B and Naeem, A and Alamri, S and Alsran, H and Hamed, ME and Dong, X and Assiri, AM and Alrasheed, AR and Hamza, M and Carroll, MW and Gemmell, M and Darby, A and Donovan-Banfield, I and Stewart, JP and Matthews, DA and Davidson, AD and Hiscox, JA}, title = {Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS.}, journal = {mSphere}, volume = {6}, number = {4}, pages = {e0021921}, pmid = {34287009}, issn = {2379-5042}, support = {5F40120C00085//HHS | U.S. Food and Drug Administration (FDA)/ ; 019-003//King Fahad Medical City (KFMC)/ ; }, mesh = {Aged ; Animals ; COVID-19/virology ; Coronavirus Infections/*virology ; Female ; Humans ; Male ; Microbiota/*genetics ; Middle Aged ; Middle East Respiratory Syndrome Coronavirus/*genetics ; SARS-CoV-2/genetics ; }, abstract = {Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic infection that emerged in the Middle East in 2012. Symptoms range from mild to severe and include both respiratory and gastrointestinal illnesses. The virus is mainly present in camel populations with occasional zoonotic spill over into humans. The severity of infection in humans is influenced by numerous factors, and similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), underlying health complications can play a major role. Currently, MERS-CoV and SARS-CoV-2 are coincident in the Middle East and thus a rapid way of sequencing MERS-CoV to derive genotype information for molecular epidemiology is needed. Additionally, complicating factors in MERS-CoV infections are coinfections that require clinical management. The ability to rapidly characterize these infections would be advantageous. To rapidly sequence MERS-CoV, an amplicon-based approach was developed and coupled to Oxford Nanopore long read length sequencing. This and a metagenomic approach were evaluated with clinical samples from patients with MERS. The data illustrated that whole-genome or near-whole-genome information on MERS-CoV could be rapidly obtained. This approach provided data on both consensus genomes and the presence of minor variants, including deletion mutants. The metagenomic analysis provided information of the background microbiome. The advantage of this approach is that insertions and deletions can be identified, which are the major drivers of genotype change in coronaviruses. IMPORTANCE Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in late 2012 in Saudi Arabia. The virus is a serious threat to people not only in the Middle East but also in the world and has been detected in over 27 countries. MERS-CoV is spreading in the Middle East and neighboring countries, and approximately 35% of reported patients with this virus have died. This is the most severe coronavirus infection so far described. Saudi Arabia is a destination for many millions of people in the world who visit for religious purposes (Umrah and Hajj), and so it is a very vulnerable area, which imposes unique challenges for effective control of this epidemic. The significance of our study is that clinical samples from patients with MERS were used for rapid in-depth sequencing and metagenomic analysis using long read length sequencing.}, } @article {pmid34287005, year = {2021}, author = {Kang, Y and Sun, B and Chen, Y and Lou, Y and Zheng, M and Li, Z}, title = {Dental Plaque Microbial Resistomes of Periodontal Health and Disease and Their Changes after Scaling and Root Planing Therapy.}, journal = {mSphere}, volume = {6}, number = {4}, pages = {e0016221}, pmid = {34287005}, issn = {2379-5042}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/*genetics ; Databases, Nucleic Acid ; Dental Plaque/*microbiology ; *Dental Scaling ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial ; Humans ; Metagenome ; Metagenomics/methods ; Microbiota/drug effects/*genetics ; Periodontal Diseases/*microbiology/*therapy ; *Root Planing ; }, abstract = {The human oral microbial community has been considered a reservoir of antibiotic resistance. Currently, the effects of periodontitis and the scaling and root planing (SRP) treatment on the performance of antibiotic-resistant genes (ARGs) and metal-resistant genes (MRGs) in the dental plaque microbiota are not well characterized. To explore this issue, we selected 48 healthy-state (HS), 40 periodontitis-state (PS; before treatment), and 24 resolved-state (RS; after SRP treatment) metagenomic data of dental plaque samples from the Sequence Read Archive (SRA) database. NetShift analysis identified Fretibacterium fastidiosum, Tannerella forsythia, and Campylobacter rectus as key drivers during dental plaque microbiota alteration in the progression of periodontitis. Periodontitis and SRP treatment resulted in an increase in the number of ARGs and MRGs in dental plaque and significantly altered the composition of ARG and MRG profiles. Bacitracin, beta-lactam, macrolide-lincosamide-streptogramin (MLS), tetracycline, and multidrug resistance genes were the main classes of ARGs with high relative abundance, whereas multimetal, iron, chromium, and copper resistance genes were the primary types of MRGs in dental plaque microbiota. The cooccurrence of ARGs, MRGs, and mobile genetic elements (MGEs) indicated that a coselection phenomenon exists in the resistomes of dental plaque microbiota. Overall, our data provide new insights into the standing of the distribution of ARGs and MRGs in oral microbiota of periodontitis patients, and it was possible to contribute to the understanding of the complicated correlations among microorganisms, resistomes, and MGEs. IMPORTANCE The emergence and development of resistance to antibiotics in periodontal pathogens have affected the success rate of treatment for periodontitis. The development of new antibacterial strategies is urgently needed to help control and treat periodontal disease, and dental plaque microbiome studies offer a promising new angle of attack. In this study, we investigated the dental plaque microbiota and resistomes in periodontal health and disease states and their changes after SRP therapy. This is the first analysis of the profile of the microbial community and antibiotic and metal resistance genes in dental plaque by the metagenomic approach, to the best of our knowledge. Monitoring the profile of these resistomes has huge potential to provide reference levels for proper antibiotics use and the development of new antimicrobial strategies in periodontitis therapy and thereby improve actual efficacy of the treatment regimens.}, } @article {pmid34285074, year = {2021}, author = {Chiri, E and Nauer, PA and Lappan, R and Jirapanjawat, T and Waite, DW and Handley, KM and Hugenholtz, P and Cook, PLM and Arndt, SK and Greening, C}, title = {Termite gas emissions select for hydrogenotrophic microbial communities in termite mounds.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {30}, pages = {}, pmid = {34285074}, issn = {1091-6490}, mesh = {Animals ; Australia ; Bacteria/*metabolism ; Gases/*metabolism ; Hydrogen/metabolism ; Isoptera/*microbiology ; *Microbiota ; Oxygen Consumption ; Soil Microbiology ; }, abstract = {Organoheterotrophs are the dominant bacteria in most soils worldwide. While many of these bacteria can subsist on atmospheric hydrogen (H2), levels of this gas are generally insufficient to sustain hydrogenotrophic growth. In contrast, bacteria residing within soil-derived termite mounds are exposed to high fluxes of H2 due to fermentative production within termite guts. Here, we show through community, metagenomic, and biogeochemical profiling that termite emissions select for a community dominated by diverse hydrogenotrophic Actinobacteriota and Dormibacterota. Based on metagenomic short reads and derived genomes, uptake hydrogenase and chemosynthetic RuBisCO genes were significantly enriched in mounds compared to surrounding soils. In situ and ex situ measurements confirmed that high- and low-affinity H2-oxidizing bacteria were highly active in the mounds, such that they efficiently consumed all termite-derived H2 emissions and served as net sinks of atmospheric H2 Concordant findings were observed across the mounds of three different Australian termite species, with termite activity strongly predicting H2 oxidation rates (R[2] = 0.82). Cell-specific power calculations confirmed the potential for hydrogenotrophic growth in the mounds with most termite activity. In contrast, while methane is produced at similar rates to H2 by termites, mounds contained few methanotrophs and were net sources of methane. Altogether, these findings provide further evidence of a highly responsive terrestrial sink for H2 but not methane and suggest H2 availability shapes composition and activity of microbial communities. They also reveal a unique arthropod-bacteria interaction dependent on H2 transfer between host-associated and free-living microbial communities.}, } @article {pmid34283837, year = {2021}, author = {Velasco, C and Dunn, C and Sturdy, C and Izda, V and Martin, J and Rivas, A and McNaughton, J and Jeffries, MA}, title = {Ear wound healing in MRL/MpJ mice is associated with gut microbiome composition and is transferable to non-healer mice via microbiome transplantation.}, journal = {PloS one}, volume = {16}, number = {7}, pages = {e0248322}, pmid = {34283837}, issn = {1932-6203}, support = {K08 AR070891/AR/NIAMS NIH HHS/United States ; R33 AR078075/AR/NIAMS NIH HHS/United States ; P20 GM125528/GM/NIGMS NIH HHS/United States ; R61 AR078075/AR/NIAMS NIH HHS/United States ; R01 AR076440/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Wound Healing ; Mice ; Female ; Male ; *Mice, Inbred C57BL ; Ear/microbiology ; Fecal Microbiota Transplantation ; Cecum/microbiology ; }, abstract = {OBJECTIVE: Adult elastic cartilage has limited repair capacity. MRL/MpJ (MRL) mice, by contrast, are capable of spontaneously healing ear punctures. This study was undertaken to characterize microbiome differences between healer and non-healer mice and to evaluate whether this healing phenotype can be transferred via gut microbiome transplantation.

METHODS: We orally transplanted C57BL/6J (B6) mice with MRL/MpJ cecal contents at weaning and as adults (n = 57) and measured ear hole closure 4 weeks after a 2.0mm punch and compared to vehicle-transplanted MRL and B6 (n = 25) and B6-transplanted MRL (n = 20) mice. Sex effects, timing of transplant relative to earpunch, and transgenerational heritability were evaluated. In a subset (n = 58), cecal microbiomes were profiled by 16S sequencing and compared to ear hole closure. Microbial metagenomes were imputed using PICRUSt.

RESULTS: Transplantation of B6 mice with MRL microbiota, either in weanlings or adults, improved ear hole closure. B6-vehicle mice healed ear hole punches poorly (0.25±0.03mm, mm ear hole healing 4 weeks after a 2mm ear hole punch [2.0mm-final ear hole size], mean±SEM), whereas MRL-vehicle mice healed well (1.4±0.1mm). MRL-transplanted B6 mice healed roughly three times as well as B6-vehicle mice, and half as well as MRL-vehicle mice (0.74±0.05mm, P = 6.9E-10 vs. B6-vehicle, P = 5.2E-12 vs. MRL-vehicle). Transplantation of MRL mice with B6 cecal material did not reduce MRL healing (B6-transplanted MRL 1.3±0.1 vs. MRL-vehicle 1.4±0.1, p = 0.36). Transplantation prior to ear punch was associated with the greatest ear hole closure. Offspring of transplanted mice healed significantly better than non-transplanted control mice (offspring:0.63±0.03mm, mean±SEM vs. B6-vehicle control:0.25±0.03mm, n = 39 offspring, P = 4.6E-11). Several microbiome clades were correlated with healing, including Firmicutes (R = 0.84, P = 8.0E-7), Lactobacillales (R = 0.65, P = 1.1E-3), and Verrucomicrobia (R = -0.80, P = 9.2E-6). Females of all groups tended to heal better than males (B6-vehicle P = 0.059, MRL-transplanted B6 P = 0.096, offspring of MRL-transplanted B6 P = 0.0038, B6-transplanted MRL P = 1.6E-6, MRL-vehicle P = 0.0031). Many clades characteristic of female mouse cecal microbiota vs. males were the same as clades characteristic of MRL and MRL-transplanted B6 mice vs. B6 controls, including including increases in Clostridia and reductions in Verrucomicrobia in female mice.

CONCLUSION: In this study, we found an association between the microbiome and tissue regeneration in MRL mice and demonstrate that this trait can be transferred to non-healer mice via microbiome transplantation. We identified several microbiome clades associated with healing.}, } @article {pmid34283836, year = {2021}, author = {Huang, CY and Yu, WS and Liu, GC and Hung, SC and Chang, JH and Chang, JC and Cheng, CL and Sun, DS and Lin, MD and Lin, WY and Tzeng, YJ and Chang, HH}, title = {Opportunistic gill infection is associated with TiO2 nanoparticle-induced mortality in zebrafish.}, journal = {PloS one}, volume = {16}, number = {7}, pages = {e0247859}, pmid = {34283836}, issn = {1932-6203}, mesh = {Animals ; *Zebrafish/microbiology ; *Titanium/toxicity ; *Gills/microbiology/drug effects ; Nanoparticles/toxicity ; Opportunistic Infections/microbiology ; Fish Diseases/microbiology/chemically induced/mortality ; Bacterial Load ; Metal Nanoparticles/toxicity ; Gastrointestinal Microbiome/drug effects ; }, abstract = {The large amounts of engineered titanium dioxide nanoparticles (TiO2NPs) that have been manufactured have inevitably been released into the ecosystem. Reports have suggested that TiO2 is a relatively inert material that has low toxicity to animals. However, as various types of NPs increasingly accumulate in the ocean, their effects on aquatic life-forms remain unclear. In this study, a zebrafish model was used to investigate TiO2NP-induced injury and mortality. We found that the treatment dosages of TiO2NP are positively associated with increased motility of zebrafish and the bacterial counts in the water. Notably, gill but not dorsal fin and caudal fin of the zebrafish displayed considerably increased bacterial load. Metagenomic analysis further revealed that gut microflora, such as phyla Proteobacteria, Bacteroidetes, and Actinobacteria, involving more than 95% of total bacteria counts in the NP-injured zebrafish gill samples. These results collectively suggest that opportunistic bacterial infections are associated with TiO2NP-induced mortality in zebrafish. Infections secondary to TiO2NP-induced injury could be a neglected factor determining the detrimental effects of TiO2NPs on wild fish.}, } @article {pmid34282606, year = {2021}, author = {Choi, SJ and Kim, Y and Jeon, J and Gwak, HJ and Kim, M and Kang, K and Kim, Y and Jeong, J and Jung, YK and Lee, KG and Choi, HS and Jung, DH and Lee, SG and Lee, Y and Shin, SJ and Jang, K and Rho, M and Choi, D}, title = {Association of Microbial Dysbiosis with Gallbladder Diseases Identified by Bile Microbiome Profiling.}, journal = {Journal of Korean medical science}, volume = {36}, number = {28}, pages = {e189}, pmid = {34282606}, issn = {1598-6357}, support = {NRF-2014R1A1A1005144/NRF/National Research Foundation of Korea/Korea ; NRF-2021M3E5D1A01015177/NRF/National Research Foundation of Korea/Korea ; }, mesh = {Adult ; Bacteria/classification/*isolation & purification ; Bile/*metabolism/*microbiology ; Case-Control Studies ; Cholecystitis/microbiology/pathology ; Dysbiosis/*microbiology ; Gallbladder/*microbiology ; Gallbladder Diseases/*microbiology ; Gallbladder Neoplasms/*microbiology ; Humans ; Metagenomics ; Microbiota ; Middle Aged ; Phylogeny ; }, abstract = {BACKGROUND: Cholecystitis is an important risk factor for gallbladder cancer, but the bile microbiome and its association with gallbladder disease has not been investigated fully. We aimed to analyze the bile microbiome in normal conditions, chronic cholecystitis, and gallbladder cancer, and to identify candidate bacteria that play an important role in gallbladder carcinogenesis.

METHODS: We performed metagenome sequencing on bile samples of 10 healthy individuals, 10 patients with chronic cholecystitis, and 5 patients with gallbladder cancer, and compared the clinical, radiological, and pathological characteristics of the participants.

RESULTS: No significant bacterial signal was identified in the normal bile. The predominant dysbiotic bacteria in both chronic cholecystitis and gallbladder cancer were those belonging to the Enterobacteriaceae family. Klebsiella increased significantly in the order of normal, chronic cholecystitis, and gallbladder cancer. Patients with chronic cholecystitis and dysbiotic microbiome patterns had larger gallstones and showed marked epithelial atypia, which are considered as precancerous conditions.

CONCLUSION: We investigated the bile microbiome in normal, chronic cholecystitis, and gallbladder cancer. We suggest possible roles of Enterobacteriaceae, including Klebsiella, in gallbladder carcinogenesis. Our findings reveal a possible link between a dysbiotic bile microbiome and the development of chronic calculous cholecystitis and gallbladder cancer.}, } @article {pmid34282338, year = {2021}, author = {Vogl, T and Klompus, S and Leviatan, S and Kalka, IN and Weinberger, A and Wijmenga, C and Fu, J and Zhernakova, A and Weersma, RK and Segal, E}, title = {Population-wide diversity and stability of serum antibody epitope repertoires against human microbiota.}, journal = {Nature medicine}, volume = {27}, number = {8}, pages = {1442-1450}, pmid = {34282338}, issn = {1546-170X}, support = {J 4256/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; Epitopes/*immunology ; Female ; Humans ; Immunoglobulins/*immunology ; Infant ; Infant, Newborn ; Machine Learning ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Peptide Library ; Young Adult ; }, abstract = {Serum antibodies can recognize both pathogens and commensal gut microbiota. However, our current understanding of antibody repertoires is largely based on DNA sequencing of the corresponding B-cell receptor genes, and actual bacterial antigen targets remain incompletely characterized. Here we have profiled the serum antibody responses of 997 healthy individuals against 244,000 rationally selected peptide antigens derived from gut microbiota and pathogenic and probiotic bacteria. Leveraging phage immunoprecipitation sequencing (PhIP-Seq) based on phage-displayed synthetic oligo libraries, we detect a wide breadth of individual-specific as well as shared antibody responses against microbiota that associate with age and gender. We also demonstrate that these antibody epitope repertoires are more longitudinally stable than gut microbiome species abundances. Serum samples of more than 200 individuals collected five years apart could be accurately matched and could serve as an immunologic fingerprint. Overall, our results suggest that systemic antibody responses provide a non-redundant layer of information about microbiota beyond gut microbial species composition.}, } @article {pmid34282272, year = {2021}, author = {Malard, F and Lavelle, A and Battipaglia, G and Gaugler, B and Dulery, R and Brissot, E and Mediavilla, C and Jegou, S and Rolhion, N and Ledraa, T and Mohty, R and Sokol, H and Mohty, M}, title = {Impact of gut fungal and bacterial communities on the outcome of allogeneic hematopoietic cell transplantation.}, journal = {Mucosal immunology}, volume = {14}, number = {5}, pages = {1127-1132}, pmid = {34282272}, issn = {1935-3456}, mesh = {Adult ; Aged ; Female ; *Gastrointestinal Microbiome ; Graft vs Host Disease/diagnosis/etiology/prevention & control ; *Health Impact Assessment ; *Hematopoietic Stem Cell Transplantation/adverse effects/methods ; Histocompatibility ; Humans ; Male ; Metagenome ; Metagenomics ; *Microbial Consortia ; Middle Aged ; *Mycobiome ; Prognosis ; Proportional Hazards Models ; Transplantation Conditioning ; Transplantation, Homologous ; Treatment Outcome ; Young Adult ; }, abstract = {Patients receiving allogeneic hematopoietic cell transplantation (alloHCT) were previously shown to display a bacterial gut dysbiosis; however, limited data are available regarding the role of fungal microbiota in these patients. We evaluated the bacterial and fungal composition of the fecal microbiota at day 0 of alloHCT. Higher bacterial diversity was associated with an improved overall survival (OS) and disease-free survival (DFS). While fungal diversity had no impact on patient outcomes, we observed that high versus low relative abundance of Candida albicans in alloHCT patients at day 0 was associated with a significantly lower OS, DFS and graft-versus-host-free, relapse-free survival (GRFS) (p = 0.0008, p = 0.0064 and p = 0.026, respectively). While these results are limited by low patient numbers and low fungal read counts in some samples, they suggest a potentially important role for C albicans in alloHCT.}, } @article {pmid34281625, year = {2021}, author = {Zhong, ZP and Tian, F and Roux, S and Gazitúa, MC and Solonenko, NE and Li, YF and Davis, ME and Van Etten, JL and Mosley-Thompson, E and Rich, VI and Sullivan, MB and Thompson, LG}, title = {Glacier ice archives nearly 15,000-year-old microbes and phages.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {160}, pmid = {34281625}, issn = {2049-2618}, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; Ice Cover ; Metagenomics ; *Microbiota ; }, abstract = {BACKGROUND: Glacier ice archives information, including microbiology, that helps reveal paleoclimate histories and predict future climate change. Though glacier-ice microbes are studied using culture or amplicon approaches, more challenging metagenomic approaches, which provide access to functional, genome-resolved information and viruses, are under-utilized, partly due to low biomass and potential contamination.

RESULTS: We expand existing clean sampling procedures using controlled artificial ice-core experiments and adapted previously established low-biomass metagenomic approaches to study glacier-ice viruses. Controlled sampling experiments drastically reduced mock contaminants including bacteria, viruses, and free DNA to background levels. Amplicon sequencing from eight depths of two Tibetan Plateau ice cores revealed common glacier-ice lineages including Janthinobacterium, Polaromonas, Herminiimonas, Flavobacterium, Sphingomonas, and Methylobacterium as the dominant genera, while microbial communities were significantly different between two ice cores, associating with different climate conditions during deposition. Separately, ~355- and ~14,400-year-old ice were subject to viral enrichment and low-input quantitative sequencing, yielding genomic sequences for 33 vOTUs. These were virtually all unique to this study, representing 28 novel genera and not a single species shared with 225 environmentally diverse viromes. Further, 42.4% of the vOTUs were identifiable temperate, which is significantly higher than that in gut, soil, and marine viromes, and indicates that temperate phages are possibly favored in glacier-ice environments before being frozen. In silico host predictions linked 18 vOTUs to co-occurring abundant bacteria (Methylobacterium, Sphingomonas, and Janthinobacterium), indicating that these phages infected ice-abundant bacterial groups before being archived. Functional genome annotation revealed four virus-encoded auxiliary metabolic genes, particularly two motility genes suggest viruses potentially facilitate nutrient acquisition for their hosts. Finally, given their possible importance to methane cycling in ice, we focused on Methylobacterium viruses by contextualizing our ice-observed viruses against 123 viromes and prophages extracted from 131 Methylobacterium genomes, revealing that the archived viruses might originate from soil or plants.

CONCLUSIONS: Together, these efforts further microbial and viral sampling procedures for glacier ice and provide a first window into viral communities and functions in ancient glacier environments. Such methods and datasets can potentially enable researchers to contextualize new discoveries and begin to incorporate glacier-ice microbes and their viruses relative to past and present climate change in geographically diverse regions globally. Video Abstract.}, } @article {pmid34281401, year = {2021}, author = {Chu, ND and Crothers, JW and Nguyen, LTT and Kearney, SM and Smith, MB and Kassam, Z and Collins, C and Xavier, R and Moses, PL and Alm, EJ}, title = {Dynamic Colonization of Microbes and Their Functions after Fecal Microbiota Transplantation for Inflammatory Bowel Disease.}, journal = {mBio}, volume = {12}, number = {4}, pages = {e0097521}, pmid = {34281401}, issn = {2150-7511}, support = {P20 GM125498/GM/NIGMS NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/*metabolism ; Butyrates/analysis/metabolism ; Cohort Studies ; *Fecal Microbiota Transplantation ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/microbiology/*therapy ; Longitudinal Studies ; Metagenomics/methods ; }, abstract = {For fecal microbiota transplantation (FMT) to be successful in immune diseases like inflammatory bowel disease, it is assumed that therapeutic microbes and their beneficial functions and immune interactions must colonize a recipient patient and persist in sufficient quantity and for a sufficient period of time to produce a clinical benefit. Few studies, however, have comprehensively profiled the colonization and persistence of transferred microbes along with the transfer of their microbial functions and interactions with the host immune system. Using 16S, metagenomic, and immunoglobulin A (IgA) sequencing, we analyzed hundreds of longitudinal microbiome samples from a randomized controlled trial of 12 patients with ulcerative colitis who received fecal transplant or placebo for 12 weeks. We uncovered diverse competitive dynamics among donor and patient strains, showing that persistence of transferred microbes is far from static. Indeed, one patient experienced a dramatic loss of donor bacteria 10 weeks into the trial, coinciding with a bloom of pathogenic bacteria and worsening symptoms. We evaluated the transfer of microbial functions, including desired ones, such as butyrate production, and unintended ones, such as antibiotic resistance. By profiling bacteria coated with IgA, we identified bacteria associated with inflammation and found that microbial interactions with the host immune system can be transferred across people, which could play a role in gut microbiome therapeutics for immune-related diseases. Our findings shed light on the colonization dynamics of gut microbes and their functions in the context of FMT to treat a complex disease-information that may provide a foundation for developing more-targeted therapeutics. IMPORTANCE Fecal microbiota transplantation (FMT)-transferring fecal microbes from a healthy donor to a sick patient-has shown promise for gut diseases such as inflammatory bowel disease. Unlike pharmaceuticals, however, fecal transplants are complex mixtures of living organisms, which must then interact with the microbes and immune system of the recipient. We sought to understand these interactions by tracking the microbes of 12 inflammatory bowel disease patients who received fecal transplants for 12 weeks. We uncovered a range of dynamics. For example, one patient experienced successful transfer of donor bacteria, only to lose them after 10 weeks. We similarly evaluated transfer of microbial functions, including how they interacted with the recipient's immune system. Our findings shed light on the colonization dynamics of gut microbes, as well as their functions in the context of FMT-information that may provide a critical foundation for the development of more-targeted therapeutics.}, } @article {pmid34281236, year = {2021}, author = {Bertoldo, G and Della Lucia, MC and Squartini, A and Concheri, G and Broccanello, C and Romano, A and Ravi, S and Cagnin, M and Baglieri, A and Stevanato, P}, title = {Endophytic Microbiome Responses to Sulfur Availability in Beta vulgaris (L.).}, journal = {International journal of molecular sciences}, volume = {22}, number = {13}, pages = {}, pmid = {34281236}, issn = {1422-0067}, mesh = {Beta vulgaris/*microbiology ; *Endophytes ; Metagenome ; *Microbiota ; *Sulfur ; }, abstract = {Sulfur is an essential plant macronutrient, and its adequate supply allows an efficient root storage and sugar extractability in sugar beets (Beta&nbsp;vulgaris L.). In this study, we investigated the effect of changes in sulfur availability on the endophytic community structure of sugar beets. Plants were hydroponically grown in a complete nutrient solution (S-supplied), a nutrient solution without MgSO4 (S-deprived), and a nutrient solution without MgSO4 for six days and resupplied with 100 μM MgSO4 for 48 h (S-resupplied). The sulfur status was monitored by inductively coupled plasma ICP-OES, and combustion analysis together with the evaluation of microRNA395 as a biomarker for sulfate status. Metabarcoding of the bacterial 16S rRNA gene was carried out in order to determine leaf endophytic community structure. The Shannon diversity index significantly differed (p < 0.05) between sulfate-supplied and sulfate-deprived seedlings. Validation by Real-Time PCR showed a significant increase (p < 0.05) of Burkholderia spp. in sulfate-deprived plants as compared to sulfate-supplied ones. The study sheds new light on the effects of nutrient deficiency on the microbiome of sugar beet plants.}, } @article {pmid34280721, year = {2021}, author = {Fan, H and Wu, S and Dong, W and Li, X and Dong, Y and Wang, S and Zhu, YG and Zhuang, X}, title = {Characterization of tetracycline-resistant microbiome in soil-plant systems by combination of H2[18]O-based DNA-Stable isotope probing and metagenomics.}, journal = {Journal of hazardous materials}, volume = {420}, number = {}, pages = {126440}, doi = {10.1016/j.jhazmat.2021.126440}, pmid = {34280721}, issn = {1873-3336}, mesh = {Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents ; DNA ; Genes, Bacterial ; Isotopes ; Manure/analysis ; Metagenomics ; *Microbiota/genetics ; *Soil ; Soil Microbiology ; Tetracycline ; }, abstract = {The emergence and spread of antibiotic resistance have been considered as a global health threat. However, effective methods to identify antibiotic-resistant bacteria (ARB) in complex microbial community are lacking, and the potential transmission pathways of ARB and antibiotic resistance genes (ARGs) in the soil-plant system remain scarce. Here in this study, tetracycline was chosen as the target antibiotic due to its globally wide usage and clinical significance. DNA-based stable isotope probing with H2[18]O was applied to identify the tetracycline-resistant bacteria from soil-plant systems. Eighteen-year organic fertilization significantly changed the composition of the tetracycline-resistant microbiome in the soil-wheat system and resulted in a higher relative abundance of ARGs in the wheat endophyte. Rhizosphere harboring the most diverse ARGs and mobile genetic elements was identified as a hot spot for horizontal gene transfer and an important bridge between bulk soil and wheat endophyte. Micrococcaceae and Sphingomonadaceae carrying ARGs associated with abundant mobile genetic elements, were identified as the core bacterial taxa in long-term manure-amended and untreated soil-wheat systems, respectively. This method contributes to a more precise track of ARB in the environment, and our work depicts the high potential of ARG transfer in the rhizosphere mediated by the core species.}, } @article {pmid34276696, year = {2021}, author = {Runge, S and Rosshart, SP}, title = {The Mammalian Metaorganism: A Holistic View on How Microbes of All Kingdoms and Niches Shape Local and Systemic Immunity.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {702378}, pmid = {34276696}, issn = {1664-3224}, mesh = {Animals ; Humans ; *Immune System ; Metagenome/*immunology ; Microbiota/*immunology ; }, abstract = {The field of microbiome research has developed rapidly over the past decades and has become a topic of major interest to basic, preclinical, and clinical research, the pharmaceutical industry as well as the general public. The microbiome is a complex and diverse ecosystem and defined as the collection of all host-associated microorganisms and their genes. It is acquired through vertical transmission and environmental exposure and includes microbes of all kingdoms: bacteria, archaea, prokaryotic and eukaryotic viruses, fungi, protozoa, and the meiofauna. These microorganisms co-evolved with their respective hosts over millions of years, thereby establishing a mutually beneficial, symbiotic relationship on all epithelial barriers. Thus, the microbiome plays a pivotal role in virtually every aspect of mammalian physiology, particularly in the development, homeostasis, and function of the immune system. Consequently, the combination of the host genome and the microbial genome, together referred to as the metagenome, largely drives the mammalian phenotype. So far, the majority of studies have unilaterally focused on the gastrointestinal bacterial microbiota. However, recent work illustrating the impact of viruses, fungi, and protozoa on host immunity urges us towards a holistic view of the mammalian microbiome and the appreciation for its non-bacterial kingdoms. In addition, the importance of microbiota on epithelial barriers other than the gut as well as their systemic effects via microbially-derived biologically active compounds is increasingly recognized. Here, we want to provide a brief but comprehensive overview of the most important findings and the current knowledge on how microbes of all kingdoms and microbial niches shape local and systemic immunity in health and disease.}, } @article {pmid34276644, year = {2021}, author = {Li, Z and Lu, G and Li, Z and Wu, B and Luo, E and Qiu, X and Guo, J and Xia, Z and Zheng, C and Su, Q and Zeng, Y and Chan, WY and Su, X and Cai, Q and Xu, Y and Chen, Y and Wang, M and Poon, WS and Luo, X}, title = {Altered Actinobacteria and Firmicutes Phylum Associated Epitopes in Patients With Parkinson's Disease.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {632482}, pmid = {34276644}, issn = {1664-3224}, mesh = {Actinobacteria/classification/genetics/*immunology/metabolism ; Aged ; Biomarkers ; Biosynthetic Pathways ; Cytokines/blood ; Epitopes/*immunology ; Feces/microbiology ; Female ; Firmicutes/classification/genetics/*immunology/metabolism ; Gastrointestinal Microbiome/genetics/immunology ; Humans ; Inflammation ; Male ; Middle Aged ; Parkinson Disease/immunology/*microbiology ; }, abstract = {Recent evidence suggests that inflammation was participated in the pathogenesis of PD, thus, to understand the potential mechanism of gut microbiota in the pathogenesis of Parkinson's disease (PD), we performed a metagenomic analysis of fecal samples from PD patient and controls. Using a two-stage metagenome-wide association strategy, fecal DNA samples from 69 PD patients and 244 controls in three groups (comprising 66 spouses, 97 age-matched, and 81 normal samples, respectively) were analyzed, and differences between candidate gut microbiota and microbiota-associated epitopes (MEs) were compared. In the study, 27 candidate bacterial biomarkers and twenty-eight candidate epitope peptides were significantly different between the PD patients and control groups. Further, enriched 4 and 13 MEs in PD were positively associated with abnormal inflammatory indicators [neutrophil percentage (NEUT.1), monocyte count/percentage (MONO/MONO.1), white blood cell count (WBC)] and five candidate bacterial biomarkers (c_Actinobacteria, f_Bifidobacteriaceae, g_Bifidobacterium, o_Bifidobacteriales, p_Actinobacteria) from Actinobacteria phylum, and they were also positively associated with histidine degradation and proline biosynthesis pathways, respectively. Additionally, enriched 2 MEs and 1 ME in PD were positively associated with above inflammatory indicators and two bacteria (f_Lactobacillaceae, g_Lactobacillus) from Firmicutes phylum, and they were also positively associated with pyruvate fermentation to propanoate I and negatively associated with isopropanol biosynthesis, respectively. Of these MEs, two MEs from GROEL2, RPSC were derived from Mycobacterium tuberculosis, triggered the T cell immune response, as previously reported. Additionally, other candidate epitope peptides derived from Mycobacterium tuberculosis and Mycobacterium leprae may also have potential immune effects in PD. In all, the altered MEs in PD may relate to abnormalities in immunity and glutamate and propionate metabolism, which furthers our understanding of the pathogenesis of PD.}, } @article {pmid34274493, year = {2021}, author = {Andermann, TM and Fouladi, F and Tamburini, FB and Sahaf, B and Tkachenko, E and Greene, C and Buckley, MT and Brooks, EF and Hedlin, H and Arai, S and Mackall, CL and Miklos, D and Negrin, RS and Fodor, AA and Rezvani, AR and Bhatt, AS}, title = {A Fructo-Oligosaccharide Prebiotic Is Well Tolerated in Adults Undergoing Allogeneic Hematopoietic Stem Cell Transplantation: A Phase I Dose-Escalation Trial.}, journal = {Transplantation and cellular therapy}, volume = {27}, number = {11}, pages = {932.e1-932.e11}, pmid = {34274493}, issn = {2666-6367}, support = {K08 CA184420/CA/NCI NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; KL2 TR001083/TR/NCATS NIH HHS/United States ; UL1 TR001085/TR/NCATS NIH HHS/United States ; K23 AI163365/AI/NIAID NIH HHS/United States ; KL2 TR003143/TR/NCATS NIH HHS/United States ; UL1 TR003142/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Graft vs Host Disease/prevention & control ; *Hematopoietic Stem Cell Transplantation ; Humans ; Mice ; Oligosaccharides ; Prebiotics ; }, abstract = {Alterations of the gut microbiota after allogeneic hematopoietic cell transplantation (allo-HCT) are a key factor in the development of transplant-related complications such as graft-versus-host disease (GVHD). Interventions that preserve the gut microbiome hold promise to improve HCT-associated morbidity and mortality. Murine models demonstrate that prebiotics such as fructo-oligosaccharides (FOSs) may increase gut levels of short-chain fatty acids (SCFAs) such as butyrate and consequently induce proliferation of immunomodulatory FOXP3[+]CD4[+] regulatory T cells (Tregs), which impact GVHD risk. We conducted a pilot phase I trial to investigate the maximum tolerated dose of FOS in patients undergoing reduced-intensity allo-HCT (n = 15) compared with concurrent controls (n = 16). We administered the FOS starting at pretransplant conditioning and continuing for a total of 21 days. We characterized the gut microbiome using shotgun metagenomic sequencing, measured stool short-chain fatty acids (SCFAs) using liquid chromatography-mass spectrometry, and determined peripheral T cell concentrations using cytometry by time-of-flight. We found that FOS was safe and well-tolerated at 10 g/d without significant adverse effects in patients undergoing allo-HCT. Community-level gut microbiota composition differed significantly on the day of transplant (day 0) between patients receiving FOS and concurrent controls; however, FOS-associated alterations of the gut microbiota were not sustained after transplant. Although the impact of FOS was fleeting, transplantation itself impacted a substantial number of taxa over time. In our small pilot trial, no significant differences were observed in gut microbial metabolic pathways, stool SCFAs, or peripheral Tregs, although Tregs trended higher in those patients who received FOS. A marker of CD4[+] T cell activation (namely, CTLA4[+]) was significantly higher in patients receiving FOS, whereas a non-significant trend existed for FOP3[+]CD4[+] Treg cells, which were higher in those receiving FOS compared with controls. FOS is well tolerated at 10 g/d in patients undergoing reduced-intensity allo-HCT. Although the alterations in gut microbiota and peripheral immune cell composition in those receiving FOS are intriguing, additional studies are required to investigate the use of prebiotics in HCT recipients.}, } @article {pmid34273006, year = {2021}, author = {Dalal, N and Jalandra, R and Bayal, N and Yadav, AK and Harshulika, and Sharma, M and Makharia, GK and Kumar, P and Singh, R and Solanki, PR and Kumar, A}, title = {Gut microbiota-derived metabolites in CRC progression and causation.}, journal = {Journal of cancer research and clinical oncology}, volume = {147}, number = {11}, pages = {3141-3155}, pmid = {34273006}, issn = {1432-1335}, mesh = {Animals ; Colorectal Neoplasms/*microbiology/pathology ; Disease Progression ; Gastrointestinal Microbiome/*physiology ; Gram-Negative Bacteria/metabolism ; Gram-Positive Bacteria/metabolism ; Humans ; Metagenomics ; }, abstract = {BACKGROUND: Based on recent research reports, dysbiosis and improper concentrations of microbial metabolites in the gut may result into the carcinogenesis of colorectal cancer. Recent advancement also highlights the involvement of bacteria and their secreted metabolites in the cancer causation. Gut microbial metabolites are functional output of the host-microbiota interactions and produced by anaerobic fermentation of food components in the diet. They contribute to influence variety of biological mechanisms including inflammation, cell signaling, cell-cycle disruption which are majorly disrupted in carcinogenic activities.

PURPOSE: In this review, we intend to discuss recent updates and possible molecular mechanisms to provide the role of bacterial metabolites, gut bacteria and diet in the colorectal carcinogenesis. Recent evidences have proposed the role of bacteria, such as Fusobacterium nucleaturm, Streptococcus bovis, Helicobacter pylori, Bacteroides fragilis and Clostridium septicum, in the carcinogenesis of CRC. Metagenomic study confirmed that these bacteria are in increased abundance in CRC patient as compared to healthy individuals and can cause inflammation and DNA damage which can lead to development of cancer. These bacteria produce metabolites, such as secondary bile salts from primary bile salts, hydrogen sulfide, trimethylamine-N-oxide (TMAO), which are likely to promote inflammation and subsequently cancer development.

CONCLUSION: Recent studies suggest that gut microbiota-derived metabolites have a role in CRC progression and causation and hence, could be implicated in CRC diagnosis, prognosis and therapy.}, } @article {pmid34272286, year = {2021}, author = {Osvatic, JT and Wilkins, LGE and Leibrecht, L and Leray, M and Zauner, S and Polzin, J and Camacho, Y and Gros, O and van Gils, JA and Eisen, JA and Petersen, JM and Yuen, B}, title = {Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {29}, pages = {}, pmid = {34272286}, issn = {1091-6490}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; S10 OD010786/OD/NIH HHS/United States ; }, mesh = {Animals ; Autotrophic Processes ; Biodiversity ; Biological Evolution ; Bivalvia/classification/*microbiology/physiology ; Gammaproteobacteria/*classification/genetics/isolation & purification/*physiology ; Host Specificity ; Phylogeny ; Phylogeography ; *Symbiosis ; }, abstract = {In the ocean, most hosts acquire their symbionts from the environment. Due to the immense spatial scales involved, our understanding of the biogeography of hosts and symbionts in marine systems is patchy, although this knowledge is essential for understanding fundamental aspects of symbiosis such as host-symbiont specificity and evolution. Lucinidae is the most species-rich and widely distributed family of marine bivalves hosting autotrophic bacterial endosymbionts. Previous molecular surveys identified location-specific symbiont types that "promiscuously" form associations with multiple divergent cooccurring host species. This flexibility of host-microbe pairings is thought to underpin their global success, as it allows hosts to form associations with locally adapted symbionts. We used metagenomics to investigate the biodiversity, functional variability, and genetic exchange among the endosymbionts of 12 lucinid host species from across the globe. We report a cosmopolitan symbiont species, Candidatus Thiodiazotropha taylori, associated with multiple lucinid host species. Ca. T. taylori has achieved more success at dispersal and establishing symbioses with lucinids than any other symbiont described thus far. This discovery challenges our understanding of symbiont dispersal and location-specific colonization and suggests both symbiont and host flexibility underpin the ecological and evolutionary success of the lucinid symbiosis.}, } @article {pmid34271900, year = {2021}, author = {Oliveira, SG and Nishiyama, RR and Trigo, CAC and Mattos-Guaraldi, AL and Dávila, AMR and Jardim, R and Aguiar, FHB}, title = {Core of the saliva microbiome: an analysis of the MG-RAST data.}, journal = {BMC oral health}, volume = {21}, number = {1}, pages = {351}, pmid = {34271900}, issn = {1472-6831}, mesh = {Bacteria/genetics ; Humans ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Saliva ; }, abstract = {BACKGROUND: Oral microbiota is considered as the second most complex in the human body and its dysbiosis can be responsible for oral diseases. Interactions between the microorganism communities and the host allow establishing the microbiological proles. Identifying the core microbiome is essential to predicting diseases and changes in environmental behavior from microorganisms.

METHODS: Projects containing the term "SALIVA", deposited between 2014 and 2019 were recovered on the MG-RAST portal. Quality (Failed), taxonomic prediction (Unknown and Predicted), species richness (Rarefaction), and species diversity (Alpha) were analyzed according to sequencing approaches (Amplicon sequencing and Shotgun metagenomics). All data were checked for normality and homoscedasticity. Metagenomic projects were compared using the Mann-Whitney U test and Spearman's correlation. Microbiome cores were inferred by Principal Component Analysis. For all statistical tests, p < 0.05 was used.

RESULTS: The study was performed with 3 projects, involving 245 Amplicon and 164 Shotgun metagenome datasets. All comparisons of variables, according to the type of sequencing, showed significant differences, except for the Predicted. In Shotgun metagenomics datasets the highest correlation was between Rarefaction and Failed (r =  - 0.78) and the lowest between Alpha and Unknown (r =  - 0.12). In Amplicon sequencing datasets, the variables Rarefaction and Unknown (r = 0.63) had the highest correlation and the lowest was between Alpha and Predicted (r =  - 0.03). Shotgun metagenomics datasets showed a greater number of genera than Amplicon. Propionibacterium, Lactobacillus, and Prevotella were the most representative genera in Amplicon sequencing. In Shotgun metagenomics, the most representative genera were Escherichia, Chitinophaga, and Acinetobacter.

CONCLUSIONS: Core of the salivary microbiome and genera diversity are dependent on the sequencing approaches. Available data suggest that Shotgun metagenomics and Amplicon sequencing have similar sensitivities to detect the taxonomic level investigated, although Shotgun metagenomics allows a deeper analysis of the microorganism diversity. Microbiome studies must consider characteristics and limitations of the sequencing approaches. Were identified 20 genera in the core of saliva microbiome, regardless of the health condition of the host. Some bacteria of the core need further study to better understand their role in the oral cavity.}, } @article {pmid34270519, year = {2022}, author = {Berkowitz, E and Kopelman, Y and Kadosh, D and Carasso, S and Tiosano, B and Kesler, A and Geva-Zatorsky, N}, title = {"More Guts Than Brains?"-The Role of Gut Microbiota in Idiopathic Intracranial Hypertension.}, journal = {Journal of neuro-ophthalmology : the official journal of the North American Neuro-Ophthalmology Society}, volume = {42}, number = {1}, pages = {e70-e77}, doi = {10.1097/WNO.0000000000001330}, pmid = {34270519}, issn = {1536-5166}, mesh = {Acetazolamide ; Brain ; Female ; *Gastrointestinal Microbiome ; Humans ; Obesity ; *Papilledema ; *Pseudotumor Cerebri ; }, abstract = {BACKGROUND: Idiopathic intracranial hypertension syndrome (IIH) is most common among obese women. Weight loss is an important factor in improving papilledema. Over the last decade, growing evidence has identified gut microbiota as a potential factor in the pathophysiology of obesity. Accordingly, we investigated whether the gut microbiome is modified in IIH patients compared with healthy controls, and provide possible new treatment venues.

METHODS: Shotgun metagenomic sequencing of the gut microbiome of 25 cases of IIH patients (according to the modified Dandy criteria) and 20 healthy controls. Participants were further stratified according to their body mass index. The total DNA from each sample was extracted using the PureLink Microbiome DNA Purification Kit A29789 (Invitrogen, Thermo Fisher Scientific, US). Library preparation was performed using the Nextera DNA Flex Library Prep Kit. Samples were sequenced on the Illumina Novaseq 6000 device. A list of bacterial species that significantly differed between the IIH patients and healthy controls was produced in addition to species diversity. In addition, patients' cohort alone was analyzed, (excluding the healthy controls), and the effect of acetazolamide treatment on their gut microbiota was analyzed.

RESULTS: IIH patients have a lower diversity of bacterial species compared with healthy individuals. These bacteria, that is, Lactobacillus ruminis (L. ruminis) (p<6.95E-08), Atopobium parvulum (p<3.9E-03), Megamonas hypermegale (p<5.61E-03), Ruminococcus gnavus (p<1.29E-02), MEL.A1 (p<3.04E-02), and Streptococcus sp. I-G2 (p<3.04E-02), were previously characterized with beneficial health effects. Moreover, we found that Lactobacillus brevis, a beneficial bacterium as well, is more abundant in acetazolamide treated patients (p<7.07E-06).

CONCLUSIONS: Gut microbiota plays a potential role in IIH etiology and therefore, can provide a promising new treatment approach for this disease.}, } @article {pmid34269948, year = {2022}, author = {Sánchez-Reyes, A and Bretón-Deval, L and Mangelson, H and Salinas-Peralta, I and Sanchez-Flores, A}, title = {Hi-C deconvolution of a textile dye-related microbiome reveals novel taxonomic landscapes and links phenotypic potential to individual genomes.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {25}, number = {1}, pages = {99-110}, pmid = {34269948}, issn = {1618-1905}, mesh = {Biodegradation, Environmental ; Metagenome ; *Microbiota ; Phenotype ; Textiles ; }, abstract = {Microbial biodiversity is represented by a variety of genomic landscapes adapted to dissimilar environments on Earth. These genomic landscapes contain functional signatures connected with the community phenotypes. Here, we assess the genomic microbial diversity landscape at a high-resolution level of a polluted river-associated microbiome (Morelos, México), cultured in a medium enriched with anthraquinone Deep Blue 35 dye. We explore the resultant textile dye microbiome to infer links between predicted biodegradative functions, and metagenomic and metabolic potential, especially using the information obtained from individual reconstructed genomes. By using Hi-C proximity-ligation deconvolution method, we deconvoluted 97 genome composites (80% potentially novel species). The main taxonomic determinants were Methanobacterium, Clostridium, and Cupriavidus genera constituting 50, 22, and 11% of the total community profile. Also, we observed a rare biosphere of novel taxa without clear taxonomic standing. Removal of 50% chemical oxygen demand with 23% decolorization was observed after 30 days of dye enrichment. Genes related to catalase-peroxidase, polyphenol oxidase, and laccase enzymes were predicted as associated with textile dye biodegradation phenotype under our study conditions, highlighting the potential of metagenome-wide analysis to predict biodegradative determinants. This study prompts high-resolution screening of individual genomes within textile dye river sediment microbiomes or complex communities under environmental pressures.}, } @article {pmid34267736, year = {2021}, author = {Chanson, A and Moreau, CS and Duplais, C}, title = {Assessing Biosynthetic Gene Cluster Diversity of Specialized Metabolites in the Conserved Gut Symbionts of Herbivorous Turtle Ants.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {678100}, pmid = {34267736}, issn = {1664-302X}, abstract = {Cephalotes are herbivorous ants (>115 species) feeding on low-nitrogen food sources, and they rely on gut symbionts to supplement their diet by recycling nitrogen food waste into amino acids. These conserved gut symbionts, which encompass five bacterial orders, have been studied previously for their primary nitrogen metabolism; however, little is known about their ability to biosynthesize specialized metabolites which can play a role in bacterial interactions between communities living in close proximity in the gut. To evaluate the biosynthetic potential of their gut symbionts, we mine 14 cultured isolate genomes and gut metagenomes across 17 Cephalotes species to explore the biodiversity of biosynthetic gene clusters (BGCs) producing specialized metabolites. The diversity of BGCs across Cephalotes phylogeny was analyzed using sequence similarity networking and BGC phylogenetic reconstruction. Our results reveal that the conserved gut symbionts involved in the nutritional symbiosis possess 80% of all the 233 BGCs retrieved in this work. Furthermore, the phylogenetic analysis of BGCs reveals different patterns of distribution, suggesting different mechanisms of conservation. A siderophore BGC shows high similarity in a single symbiont across different ant host species, whereas a BGC encoding the production of non-ribosomal peptides (NRPs) found different symbionts within a single host species. Additionally, BGCs were abundant in four of the five bacterial orders of conserved symbionts co-occurring in the hindgut. However, one major symbiont localized alone in the midgut lack BGCs. Because the spatial isolation prevents direct interaction with other symbionts, this result supports the idea that BGCs are maintained in bacteria living in close proximity but are dispensable for an alone-living symbiont. These findings together pave the way for studying the mechanisms of BGC conservation and evolution in gut bacterial genomes associated with Cephalotes. This work also provides a genetic background for further study, aiming to characterize bacterial specialized metabolites and to understand their functional role in multipartite mutualisms between conserved gut symbionts and Cephalotes turtle ants.}, } @article {pmid34267241, year = {2021}, author = {Gkoutselis, G and Rohrbach, S and Harjes, J and Obst, M and Brachmann, A and Horn, MA and Rambold, G}, title = {Microplastics accumulate fungal pathogens in terrestrial ecosystems.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {13214}, pmid = {34267241}, issn = {2045-2322}, mesh = {*Ecosystem ; *Environmental Monitoring ; Fungi/*isolation & purification ; *Microplastics ; *Mycobiome ; }, abstract = {Microplastic (MP) is a pervasive pollutant in nature that is colonised by diverse groups of microbes, including potentially pathogenic species. Fungi have been largely neglected in this context, despite their affinity for plastics and their impact as pathogens. To unravel the role of MP as a carrier of fungal pathogens in terrestrial ecosystems and the immediate human environment, epiplastic mycobiomes from municipal plastic waste from Kenya were deciphered using ITS metabarcoding as well as a comprehensive meta-analysis, and visualised via scanning electron as well as confocal laser scanning microscopy. Metagenomic and microscopic findings provided complementary evidence that the terrestrial plastisphere is a suitable ecological niche for a variety of fungal organisms, including important animal and plant pathogens, which formed the plastisphere core mycobiome. We show that MPs serve as selective artificial microhabitats that not only attract distinct fungal communities, but also accumulate certain opportunistic human pathogens, such as cryptococcal and Phoma-like species. Therefore, MP must be regarded a persistent reservoir and potential vector for fungal pathogens in soil environments. Given the increasing amount of plastic waste in terrestrial ecosystems worldwide, this interrelation may have severe consequences for the trans-kingdom and multi-organismal epidemiology of fungal infections on a global scale.}, } @article {pmid34266351, year = {2022}, author = {Khattab, AR and Farag, MA}, title = {Marine and terrestrial endophytic fungi: a mine of bioactive xanthone compounds, recent progress, limitations, and novel applications.}, journal = {Critical reviews in biotechnology}, volume = {42}, number = {3}, pages = {403-430}, doi = {10.1080/07388551.2021.1940087}, pmid = {34266351}, issn = {1549-7801}, mesh = {*Endophytes/metabolism ; Fungi/metabolism ; Plants ; *Xanthones/metabolism ; }, abstract = {Endophytic fungi are a kind of fungi that colonizes living plant tissues presenting a myriad of microbial adaptations that have been developed in such a hidden environment. Owing to its large diversity and particular habituation, they present a golden mine for research in the field of drug discovery. Endophytic fungal communities possess unique biocatalytic machinery that furnishes a myriad of complex natural product scaffolds. Xanthone compounds are examples of endophytic secondary metabolic products with pronounced biological activity to include: antioxidant, antimicrobial, anti-inflammatory, antithrombotic, antiulcer, choleretic, diuretic, and monoamine oxidase inhibiting activity.The current review compiles the recent progress made on the microbiological production of xanthones using fungal endophytes obtained from both marine and terrestrial origins, with comparisons being made among both natural resources. The biosynthesis of xanthones in endophytic fungi is outlined along with its decoding enzymes. Biotransformation reactions reported to be carried out using different endophytic microbial models are also outlined for xanthones structural modification purposes and the production of novel molecules.A promising application of novel computational tools is presented as a future direction for the goal of optimizing microbial xanthones production to include establishing metabolic pathway databases and the in silico analysis of microbial interactions. Metagenomics methods and related bioinformatics platforms are highlighted as unexplored tools for the biodiversity analysis of endophytic microbial communities that are difficult to be cultured.}, } @article {pmid34265247, year = {2021}, author = {Brito, IL}, title = {The comings and goings of the healthy human gut microbiota.}, journal = {Cell host & microbe}, volume = {29}, number = {7}, pages = {1163-1164}, doi = {10.1016/j.chom.2021.06.011}, pmid = {34265247}, issn = {1934-6069}, mesh = {Bacteria ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {SNP-level analysis of 5,000+ metagenomic samples enabled Hildebrand and colleagues (2021) to identify human gut microbiota by their dispersal strategies in this issue of Cell Host & Microbe. This brings us a step closer in understanding how microbial communities are formed and maintained and also hints at ways in which microbiomes can be manipulated to improve human health.}, } @article {pmid34264786, year = {2021}, author = {Thänert, R and Thänert, A and Ou, J and Bajinting, A and Burnham, CD and Engelstad, HJ and Tecos, ME and Ndao, IM and Hall-Moore, C and Rouggly-Nickless, C and Carl, MA and Rubin, DC and Davidson, NO and Tarr, PI and Warner, BB and Dantas, G and Warner, BW}, title = {Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infections.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1940792}, pmid = {34264786}, issn = {1949-0984}, support = {U01 AI131342/AI/NIAID NIH HHS/United States ; UH3 AI083265/AI/NIAID NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; R01 DK112378/DK/NIDDK NIH HHS/United States ; UL1 TR002345/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Anti-Bacterial Agents/*therapeutic use ; Child ; Child, Preschool ; Cohort Studies ; Dysbiosis/*drug therapy/*etiology/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Male ; Missouri ; Sepsis/*drug therapy/*etiology ; Short Bowel Syndrome/*complications/microbiology ; }, abstract = {Surgical removal of the intestine, lifesaving in catastrophic gastrointestinal disorders of infancy, can result in a form of intestinal failure known as short bowel syndrome (SBS). Bloodstream infections (BSIs) are a major challenge in pediatric SBS management. BSIs require frequent antibiotic therapy, with ill-defined consequences for the gut microbiome and childhood health. Here, we combine serial stool collection, shotgun metagenomic sequencing, multivariate statistics and genome-resolved strain-tracking in a cohort of 19 patients with surgically-induced SBS to show that antibiotic-driven intestinal dysbiosis in SBS enriches for persistent intestinal colonization with BSI causative pathogens in SBS. Comparing the gut microbiome composition of SBS patients over the first 4 years of life to 19 age-matched term and 18 preterm controls, we find that SBS gut microbiota diversity and composition was persistently altered compared to controls. Commensals including Ruminococcus, Bifidobacterium, Eubacterium, and Clostridium species were depleted in SBS, while pathobionts (Enterococcus) were enriched. Integrating clinical covariates with gut microbiome composition in pediatric SBS, we identified dietary and antibiotic exposures as the main drivers of these alterations. Moreover, antibiotic resistance genes, specifically broad-spectrum efflux pumps, were at a higher abundance in SBS, while putatively beneficial microbiota functions, including amino acid and vitamin biosynthesis, were depleted. Moreover, using strain-tracking we found that the SBS gut microbiome harbors BSI causing pathogens, which can persist intestinally throughout the first years of life. The association between antibiotic-driven gut dysbiosis and enrichment of intestinal pathobionts isolated from BSI suggests that antibiotic treatment may predispose SBS patients to infection. Persistence of pathobionts and depletion of beneficial microbiota and functionalities in SBS highlights the need for microbiota-targeted interventions to prevent infection and facilitate intestinal adaptation.}, } @article {pmid34264153, year = {2021}, author = {Gilroy, R}, title = {Spotlight on the avian gut microbiome: fresh opportunities in discovery.}, journal = {Avian pathology : journal of the W.V.P.A}, volume = {50}, number = {4}, pages = {291-294}, doi = {10.1080/03079457.2021.1955826}, pmid = {34264153}, issn = {1465-3338}, mesh = {Animals ; Birds/*microbiology ; Chickens/microbiology ; *Gastrointestinal Microbiome ; }, abstract = {Chickens represent a globally ubiquitous food animal underpinning many aspects of human nutrition and health. Consumption of chicken meat continues to surge, representing a cheaper, healthier, low-carbon alternative to other livestock meats. Despite this importance, we are still unable to define what lives within the chicken gut microbiome. This complex community bridges poultry diet, health and productivity as well as providing a reservoir for zoonotic pathogens. Even with decades of intensive study, we are still discovering novel microbial species within this environment, each of which has the potential to provide an avenue for commercial microbiome modulation. The chicken gut truly represents an exhilarating challenge in turning new-found knowledge into new-won power to improve the health and wealth of poultry and people.}, } @article {pmid34261525, year = {2021}, author = {Detman, A and Laubitz, D and Chojnacka, A and Kiela, PR and Salamon, A and Barberán, A and Chen, Y and Yang, F and Błaszczyk, MK and Sikora, A}, title = {Dynamics of dark fermentation microbial communities in the light of lactate and butyrate production.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {158}, pmid = {34261525}, issn = {2049-2618}, mesh = {Bioreactors ; *Butyrates ; Fermentation ; Lactic Acid ; *Microbiota ; }, abstract = {BACKGROUND: This study focuses on the processes occurring during the acidogenic step of anaerobic digestion, especially resulting from nutritional interactions between dark fermentation (DF) bacteria and lactic acid bacteria (LAB). Previously, we have confirmed that DF microbial communities (MCs) that fed on molasses are able to convert lactate and acetate to butyrate. The aims of the study were to recognize the biodiversity of DF-MCs able and unable to convert lactate and acetate to butyrate and to define the conditions for the transformation.

RESULTS: MCs sampled from a DF bioreactor were grown anaerobically in mesophilic conditions on different media containing molasses or sucrose and/or lactate and acetate in five independent static batch experiments. The taxonomic composition (based on 16S_rRNA profiling) of each experimental MC was analysed in reference to its metabolites and pH of the digestive liquids. In the samples where the fermented media contained carbohydrates, the two main tendencies were observed: (i) a low pH (pH ≤ 4), lactate and ethanol as the main fermentation products, MCs dominated with Lactobacillus, Bifidobacterium, Leuconostoc and Fructobacillus was characterized by low biodiversity; (ii) pH in the range 5.0-6.0, butyrate dominated among the fermentation products, the MCs composed mainly of Clostridium (especially Clostridium_sensu_stricto_12), Lactobacillus, Bifidobacterium and Prevotella. The biodiversity increased with the ability to convert acetate and lactate to butyrate. The MC processing exclusively lactate and acetate showed the highest biodiversity and was dominated by Clostridium (especially Clostridium_sensu_stricto_12). LAB were reduced; other genera such as Terrisporobacter, Lachnoclostridium, Paraclostridium or Sutterella were found. Butyrate was the main metabolite and pH was 7. Shotgun metagenomic analysis of the selected butyrate-producing MCs independently on the substrate revealed C.tyrobutyricum as the dominant Clostridium species. Functional analysis confirmed the presence of genes encoding key enzymes of the fermentation routes.

CONCLUSIONS: Batch tests revealed the dynamics of metabolic activity and composition of DF-MCs dependent on fermentation conditions. The balance between LAB and the butyrate producers and the pH values were shown to be the most relevant for the process of lactate and acetate conversion to butyrate. To close the knowledge gaps is to find signalling factors responsible for the metabolic shift of the DF-MCs towards lactate fermentation. Video Abstract.}, } @article {pmid34261503, year = {2021}, author = {Karcher, N and Nigro, E and Punčochář, M and Blanco-Míguez, A and Ciciani, M and Manghi, P and Zolfo, M and Cumbo, F and Manara, S and Golzato, D and Cereseto, A and Arumugam, M and Bui, TPN and Tytgat, HLP and Valles-Colomer, M and de Vos, WM and Segata, N}, title = {Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {209}, pmid = {34261503}, issn = {1474-760X}, support = {U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {Akkermansia/classification/genetics/metabolism/virology ; Animals ; Bacteriophages/growth & development ; Clustered Regularly Interspaced Short Palindromic Repeats ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; *Genome, Bacterial ; Humans ; *Metagenome ; Mice ; Operon ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Akkermansia muciniphila is a human gut microbe with a key role in the physiology of the intestinal mucus layer and reported associations with decreased body mass and increased gut barrier function and health. Despite its biomedical relevance, the genomic diversity of A. muciniphila remains understudied and that of closely related species, except for A. glycaniphila, unexplored.

RESULTS: We present a large-scale population genomics analysis of the Akkermansia genus using 188 isolate genomes and 2226 genomes assembled from 18,600 metagenomes from humans and other animals. While we do not detect A. glycaniphila, the Akkermansia strains in the human gut can be grouped into five distinct candidate species, including A. muciniphila, that show remarkable whole-genome divergence despite surprisingly similar 16S rRNA gene sequences. These candidate species are likely human-specific, as they are detected in mice and non-human primates almost exclusively when kept in captivity. In humans, Akkermansia candidate species display ecological co-exclusion, diversified functional capabilities, and distinct patterns of associations with host body mass. Analysis of CRISPR-Cas loci reveals new variants and spacers targeting newly discovered putative bacteriophages. Remarkably, we observe an increased relative abundance of Akkermansia when cognate predicted bacteriophages are present, suggesting ecological interactions. A. muciniphila further exhibits subspecies-level genetic stratification with associated functional differences such as a putative exo/lipopolysaccharide operon.

CONCLUSIONS: We uncover a large phylogenetic and functional diversity of the Akkermansia genus in humans. This variability should be considered in the ongoing experimental and metagenomic efforts to characterize the health-associated properties of A. muciniphila and related bacteria.}, } @article {pmid34260698, year = {2021}, author = {Salazar, G and Ruscheweyh, HJ and Hildebrand, F and Acinas, SG and Sunagawa, S}, title = {mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {1}, pages = {270-272}, pmid = {34260698}, issn = {1367-4811}, support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 205321_184955//Swiss National Foundation [SNF/ ; 51NF40_180575//NCCR Microbiomes/ ; PHRT-521//ETH Zürich/ ; BB/r012490/1//BBSRC Institute Strategic Programme Gut Microbes and Health/ ; }, mesh = {Genes, rRNA ; Consensus ; Sequence Analysis, DNA/methods ; *Software ; *Microbiota/genetics ; }, abstract = {UNLABELLED: Profiling the taxonomic composition of microbial communities commonly involves the classification of ribosomal RNA gene fragments. As a trade-off to maintain high classification accuracy, existing tools are typically limited to the genus level. Here, we present mTAGs, a taxonomic profiling tool that implements the alignment of metagenomic sequencing reads to degenerate consensus reference sequences of small subunit ribosomal RNA genes. It uses DNA fragments, that is, paired-end sequencing reads, as count units and provides relative abundance profiles at multiple taxonomic ranks, including operational taxonomic units based on a 97% sequence identity cutoff. At the genus rank, mTAGs outperformed other tools across several metrics, such as the F1 score by >11% across data from different environments, and achieved competitive (F1 score) or better results (Bray-Curtis dissimilarity) at the sub-genus level.

The software tool mTAGs is implemented in Python. The source code and binaries are freely available (https://github.com/SushiLab/mTAGs). The data underlying this article are available in Zenodo, at https://doi.org/10.5281/zenodo.4352762.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid34259969, year = {2022}, author = {Nakashima, T and Fujii, K and Seki, T and Aoyama, M and Azuma, A and Kawasome, H}, title = {Novel Gut Microbiota Modulator, Which Markedly Increases Akkermansia muciniphila Occupancy, Ameliorates Experimental Colitis in Rats.}, journal = {Digestive diseases and sciences}, volume = {67}, number = {7}, pages = {2899-2911}, pmid = {34259969}, issn = {1573-2568}, mesh = {Akkermansia ; Animals ; Anti-Bacterial Agents/adverse effects ; *Colitis/chemically induced/drug therapy/microbiology ; Dextran Sulfate/pharmacology ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases/drug therapy ; Mice ; Mice, Inbred C57BL ; Mucins ; Rats ; Verrucomicrobia ; }, abstract = {BACKGROUND: Since gut microbiota is involved in the pathogenesis of inflammatory bowel disease (IBD), antibiotics or probiotics may be attractive options for the treatment of IBD. Akkermansia muciniphila is expected as a next-generation probiotic for IBD, and OPS-2071 is a novel quinolone with potent antibacterial activity against Clostridioides difficile.

AIMS: The aim of this study is to assess the potential of OPS-2071 as a gut microbiota modulator for IBD.

METHODS: Minimum inhibitory concentrations of several bacteria in the human intestinal microbiota were determined. Microbiota changes in the feces were typed using metagenomic analysis after oral administration of OPS-2071 (100 mg/kg) twice a day to normal rats. The amounts of mucin were determined using the Fecal Mucin Assay Kit. The effects of OPS-2071 (1, 3, 10 mg/kg) twice a day on fecal symptoms and fecal microbiota were evaluated in a colitis rat model induced by free access to drinking water containing 3% dextran sulfate sodium for 10 days.

RESULTS: OPS-2071 showed notably low antibacterial activity against only A. muciniphila in spite of higher antimicrobial activity against other strains of intestinal bacteria. OPS-2071 rapidly and dramatically increased the occupancy of A. muciniphila as well as the amount of mucin in the feces of normal rats. OPS-2071 (10 mg/kg) significantly suppressed the exacerbation of stool scores, especially the bloody stool score, with the increase in A. muciniphila occupancy.

CONCLUSIONS: OPS-2071 is expected to be a new therapeutic option for IBD as a gut microbiota modulator by significantly increasing A. muciniphila occupancy.}, } @article {pmid34259891, year = {2021}, author = {Yen, S and Johnson, JS}, title = {Metagenomics: a path to understanding the gut microbiome.}, journal = {Mammalian genome : official journal of the International Mammalian Genome Society}, volume = {32}, number = {4}, pages = {282-296}, pmid = {34259891}, issn = {1432-1777}, support = {/DH_/Department of Health/United Kingdom ; }, mesh = {Computational Biology/*standards ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/*standards ; Humans ; Metagenome/genetics ; *Metagenomics ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The gut microbiome is a major determinant of host health, yet it is only in the last 2 decades that the advent of next-generation sequencing has enabled it to be studied at a genomic level. Shotgun sequencing is beginning to provide insight into the prokaryotic as well as eukaryotic and viral components of the gut community, revealing not just their taxonomy, but also the functions encoded by their collective metagenome. This revolution in understanding is being driven by continued development of sequencing technologies and in consequence necessitates reciprocal development of computational approaches that can adapt to the evolving nature of sequence datasets. In this review, we provide an overview of current bioinformatic strategies for handling metagenomic sequence data and discuss their strengths and limitations. We then go on to discuss key technological developments that have the potential to once again revolutionise the way we are able to view and hence understand the microbiome.}, } @article {pmid34259622, year = {2021}, author = {Delaney, S and Do, TT and Corrigan, A and Murphy, R and Walsh, F}, title = {Investigation into the effect of mannan-rich fraction supplementation on the metagenome of broiler chickens.}, journal = {Microbial genomics}, volume = {7}, number = {7}, pages = {}, pmid = {34259622}, issn = {2057-5858}, mesh = {Animal Feed/*analysis ; Animals ; Anti-Bacterial Agents/adverse effects ; Cecum/*microbiology ; Chickens/*microbiology ; Diet/veterinary ; Dietary Supplements/*analysis ; Drug Resistance, Bacterial/genetics ; Gastrointestinal Microbiome/*drug effects/genetics ; Mannans/*pharmacology ; Metagenome/genetics ; Weight Gain/drug effects ; }, abstract = {Antibiotic resistance is regarded as one of the most serious threats to human health worldwide. The rapid increase in resistance rates has been attributed to the extensive use of antibiotics since they became commercially available. The use of antibiotics as growth promotors has been banned in numerous regions for this reason. Mannan-rich fraction (MRF) has been reported to show similar growth-promoting effects to antibiotics. We investigated the effect of MRF on the microbial community, resistome and metabolic pathways within the caecum of commercial broilers at two different timepoints within the growth of the broiler, day 27 and day 34. The data indicated an overall increase in health and economic gain for the producer with the addition of MRF to the diet of the broilers. The only significant difference across the microbial composition of the samples was in the richness of the microbial communities across all samples. While all samples harboured resistance genes conferring resistance to the same classes of antibiotics, there was significant variation in the antimicrobial resistance gene richness across time and treatment and across combinations of time and treatment. The taxa with positive correlation comprised Bacilli and Clostridia. The negative correlation taxa were also dominated by Bacilli, specifically the Streptococcus genera. The KEGG-pathway analysis identified an age-related change in the metabolism pathway abundances of the caecal microflora. We suggest that the MRF-related increases in health and weight gain in the broilers may be associated with changes in the metabolism of the microbiomes rather than the microbial composition. The resistome variations across samples were correlated with specific genera. These data may be used to further enhance the development of feed supplements to reduce the presence of antibiotic resistance genes (ARGs) within poultry. While the ARGs of greatest concern to human or animal health were not detected in this study, it has identified the potential to reduce the presence of ARGs by the increase in specific genera.}, } @article {pmid34259375, year = {2021}, author = {Liao, H and Bai, Y and Liu, C and Wen, C and Yang, Q and Chen, Z and Banerjee, S and Zhou, S and Friman, VP}, title = {Airborne and indigenous microbiomes co-drive the rebound of antibiotic resistome during compost storage.}, journal = {Environmental microbiology}, volume = {23}, number = {12}, pages = {7483-7496}, doi = {10.1111/1462-2920.15672}, pmid = {34259375}, issn = {1462-2920}, support = {BB/T010606/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; *Composting ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Manure ; *Microbiota/genetics ; }, abstract = {Composting is widely used to reduce the abundance of antibiotic resistance genes (ARGs) in solid waste. While ARG dynamics have been extensively investigated during composting, the fate and abundance of residual ARGs during the storage remain unexplored. Here, we tested experimentally how ARG and mobile genetic element (MGE) abundances change during compost storage using metagenomics, quantitative PCR and direct culturing. We found that 43.8% of ARGs and 39.9% of MGEs quickly recovered already during the first week of storage. This rebound effect was mainly driven by the regrowth of indigenous, antibiotic-resistant bacteria that survived the composting. Bacterial transmission from the surrounding air had a much smaller effect, being most evident as MGE rebound during the later stages of storage. While hyperthermophilic composting was more efficient at reducing the relative abundance of ARGs and MGEs, relatively greater ARG rebound was observed during the storage of hyperthermophilic compost, exceeding the initial levels of untreated sewage sludge. Our study reveals that residual ARGs and MGEs left in the treated compost can quickly rebound during the storage via airborne introduction and regrowth of surviving bacteria, highlighting the need to develop better storage strategies to prevent the rebound of ARGs and MGEs after composting.}, } @article {pmid34256961, year = {2021}, author = {Santiago-Rodriguez, TM and Hollister, EB}, title = {Multi 'omic data integration: A review of concepts, considerations, and approaches.}, journal = {Seminars in perinatology}, volume = {45}, number = {6}, pages = {151456}, doi = {10.1016/j.semperi.2021.151456}, pmid = {34256961}, issn = {1558-075X}, mesh = {*Genomics ; Humans ; Metabolomics ; *Microbiota ; Proteomics ; }, abstract = {The application of 'omic techniques including, but not limited to genomics/metagenomics, transcriptomics/meta-transcriptomics, proteomics/meta-proteomics, and metabolomics to generate multiple datasets from a single sample have facilitated hypothesis generation leading to the identification of biological, molecular and ecological functions and mechanisms, as well as associations and correlations. Despite their power and promise, a variety of challenges must be considered in the successful design and execution of a multi-omics study. In this review, various 'omic technologies applicable to single- and meta-organisms (i.e., host + microbiome) are described, and considerations for sample collection, storage and processing prior to data generation and analysis, as well as approaches to data storage, dissemination and analysis are discussed. Finally, case studies are included as examples of multi-omic applications providing novel insights and a more holistic understanding of biological processes.}, } @article {pmid34256809, year = {2021}, author = {Chen, P and Zhou, H and Huang, Y and Xie, Z and Zhang, M and Wei, Y and Li, J and Ma, Y and Luo, M and Ding, W and Cao, J and Jiang, T and Nan, P and Fang, J and Li, X}, title = {Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {207}, pmid = {34256809}, issn = {1474-760X}, mesh = {Aquatic Organisms/classification/genetics/*metabolism ; Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; Caudovirales/classification/genetics/*metabolism ; Ecosystem ; Fungi/classification/genetics/*metabolism ; *Geologic Sediments/microbiology/virology ; Metabolic Networks and Pathways/genetics ; Metagenome/genetics ; Microbiota/genetics ; Pacific Ocean ; Phylogeny ; Seawater/microbiology/virology ; }, abstract = {BACKGROUND: The full biosphere structure and functional exploration of the microbial communities of the Challenger Deep of the Mariana Trench, the deepest known hadal zone on Earth, lag far behind that of other marine realms.

RESULTS: We adopt a deep metagenomics approach to investigate the microbiome in the sediment of Challenger Deep, Mariana Trench. We construct 178 metagenome-assembled genomes (MAGs) representing 26 phyla, 16 of which are reported from hadal sediment for the first time. Based on the MAGs, we find the microbial community functions are marked by enrichment and prevalence of mixotrophy and facultative anaerobic metabolism. The microeukaryotic community is found to be dominated by six fungal groups that are characterized for the first time in hadal sediment to possess the assimilatory and dissimilatory nitrate/sulfate reduction, and hydrogen sulfide oxidation pathways. By metaviromic analysis, we reveal novel hadal Caudovirales clades, distinctive virus-host interactions, and specialized auxiliary metabolic genes for modulating hosts' nitrogen/sulfur metabolism. The hadal microbiome is further investigated by large-scale cultivation that cataloged 1070 bacterial and 19 fungal isolates from the Challenger Deep sediment, many of which are found to be new species specialized in the hadal habitat.

CONCLUSION: Our hadal MAGs and isolates increase the diversity of the Challenger Deep sediment microbial genomes and isolates present in the public. The deep metagenomics approach fills the knowledge gaps in structure and diversity of the hadal microbiome, and provides novel insight into the ecology and metabolism of eukaryotic and viral components in the deepest biosphere on earth.}, } @article {pmid34253790, year = {2021}, author = {Sawaswong, V and Praianantathavorn, K and Chanchaem, P and Khamwut, A and Kemthong, T and Hamada, Y and Malaivijitnond, S and Payungporn, S}, title = {Comparative analysis of oral-gut microbiota between captive and wild long-tailed macaque in Thailand.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {14280}, pmid = {34253790}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Body Weight ; Ecosystem ; Female ; Firmicutes/*metabolism ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Macaca/*microbiology/*physiology ; Male ; Metagenomics ; Microbiota ; Mouth Mucosa/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/metabolism ; Thailand ; Zoology ; }, abstract = {Long-tailed macaques (Macaca fascicularis), distributed in Southeast Asia, are generally used in biomedical research. At present, the expansion of human communities overlapping of macaques' natural habitat causes human-macaque conflicts. To mitigate this problem in Thailand, the National Primate Research Center of Thailand, Chulalongkorn University (NPRCT-CU), was granted the permit to catch the surplus wild-born macaques and transfer them to the center. Based on the fact that the diets provided and the captive environments were different, their oral-gut microbiota should be altered. Thus, we investigated and compared the oral and fecal microbiome between wild-born macaques that lived in the natural habitats and those transferred to and reared in the NPRCT-CU for 1 year. The results from 16S rRNA high-throughput sequencing showed that the captive macaques had distinct oral-gut microbiota profiles and lower bacterial richness compared to those in wild macaques. The gut of wild macaques was dominated by Firmicutes which is probably associated with lipid absorption and storage. These results implicated the effects of captivity conditions on the microbiome that might contribute to crucial metabolic functions. Our study should be applied to the animal health care program, with respect to microbial functions, for non-human primates.}, } @article {pmid34253732, year = {2021}, author = {Mehrshad, M and Lopez-Fernandez, M and Sundh, J and Bell, E and Simone, D and Buck, M and Bernier-Latmani, R and Bertilsson, S and Dopson, M}, title = {Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {4253}, pmid = {34253732}, issn = {2041-1723}, mesh = {Biodiversity ; Databases, Genetic ; *Energy Metabolism ; Gene Expression Regulation ; Groundwater/*microbiology ; Isoelectric Point ; Metagenome ; *Microbiota/genetics ; Phylogeny ; Transcription, Genetic ; Transcriptome/genetics ; }, abstract = {While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome.}, } @article {pmid34253606, year = {2021}, author = {Leonard, MM and Valitutti, F and Karathia, H and Pujolassos, M and Kenyon, V and Fanelli, B and Troisi, J and Subramanian, P and Camhi, S and Colucci, A and Serena, G and Cucchiara, S and Trovato, CM and Malamisura, B and Francavilla, R and Elli, L and Hasan, NA and Zomorrodi, AR and Colwell, R and Fasano, A and , }, title = {Microbiome signatures of progression toward celiac disease onset in at-risk children in a longitudinal prospective cohort study.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {29}, pages = {}, pmid = {34253606}, issn = {1091-6490}, support = {P30 DK040561/DK/NIDDK NIH HHS/United States ; K23 DK122127/DK/NIDDK NIH HHS/United States ; F32 DK109620/DK/NIDDK NIH HHS/United States ; R56 AI156711/AI/NIAID NIH HHS/United States ; R01 DK104344/DK/NIDDK NIH HHS/United States ; R01 AI184777/AI/NIAID NIH HHS/United States ; }, mesh = {Autoimmunity ; Biomarkers/metabolism ; Celiac Disease/metabolism/*microbiology ; Child, Preschool ; Cross-Sectional Studies ; Female ; *Gastrointestinal Microbiome/genetics ; Host Microbial Interactions ; Humans ; Infant ; Inflammation ; Longitudinal Studies ; Male ; Metabolic Networks and Pathways ; Metabolome ; Metagenomics ; Prospective Studies ; }, abstract = {Other than exposure to gluten and genetic compatibility, the gut microbiome has been suggested to be involved in celiac disease (CD) pathogenesis by mediating interactions between gluten/environmental factors and the host immune system. However, to establish disease progression markers, it is essential to assess alterations in the gut microbiota before disease onset. Here, a prospective metagenomic analysis of the gut microbiota of infants at risk of CD was done to track shifts in the microbiota before CD development. We performed cross-sectional and longitudinal analyses of gut microbiota, functional pathways, and metabolites, starting from 18 mo before CD onset, in 10 infants who developed CD and 10 matched nonaffected infants. Cross-sectional analysis at CD onset identified altered abundance of six microbial strains and several metabolites between cases and controls but no change in microbial species or pathway abundance. Conversely, results of longitudinal analysis revealed several microbial species/strains/pathways/metabolites occurring in increased abundance and detected before CD onset. These had previously been linked to autoimmune and inflammatory conditions (e.g., Dialister invisus, Parabacteroides sp., Lachnospiraceae, tryptophan metabolism, and metabolites serine and threonine). Others occurred in decreased abundance before CD onset and are known to have anti-inflammatory effects (e.g., Streptococcus thermophilus, Faecalibacterium prausnitzii, and Clostridium clostridioforme). Additionally, we uncovered previously unreported microbes/pathways/metabolites (e.g., Porphyromonas sp., high mannose-type N-glycan biosynthesis, and serine) that point to CD-specific biomarkers. Our study establishes a road map for prospective longitudinal study designs to better understand the role of gut microbiota in disease pathogenesis and therapeutic targets to reestablish tolerance and/or prevent autoimmunity.}, } @article {pmid34252627, year = {2022}, author = {Liu, Z and Zhang, T and Wu, K and Li, Z and Chen, X and Jiang, S and Du, L and Lu, S and Lin, C and Wu, J and Wang, X}, title = {Metagenomic Analysis Reveals A Possible Association Between Respiratory Infection and Periodontitis.}, journal = {Genomics, proteomics & bioinformatics}, volume = {20}, number = {2}, pages = {260-273}, pmid = {34252627}, issn = {2210-3244}, mesh = {Humans ; Adult ; Metagenome ; Metagenomics ; *Periodontitis/complications/genetics ; *Microbiota ; Dysbiosis ; Anti-Bacterial Agents ; }, abstract = {Periodontitis is an inflammatory disease that is characterized by progressive destruction of the periodontium and causes tooth loss in adults. Periodontitis is known to be associated with dysbiosis of the oral microflora, which is often linked to various diseases. However, the complexity of plaque microbial communities of periodontitis, antibiotic resistance, and enhanced virulence make this disease difficult to treat. In this study, using metagenomic shotgun sequencing, we investigated the etiology, antibiotic resistance genes (ARGs), and virulence genes (VirGs) of periodontitis. We revealed a significant shift in the composition of oral microbiota as well as several functional pathways that were represented significantly more abundantly in periodontitis patients than in controls. In addition, we observed several positively selected ARGs and VirGs with the Ka/Ks ratio > 1 by analyzing our data and a previous periodontitis dataset, indicating that ARGs and VirGs in oral microbiota may be subjected to positive selection. Moreover, 5 of 12 positively selected ARGs and VirGs in periodontitis patients were found in the genomes of respiratory tract pathogens. Of note, 91.8% of the background VirGs with at least one non-synonymous single-nucleotide polymorphism for natural selection were also from respiratory tract pathogens. These observations suggest a potential association between periodontitis and respiratory infection at the gene level. Our study enriches the knowledge of pathogens and functional pathways as well as the positive selection of antibiotic resistance and pathogen virulence in periodontitis patients, and provides evidence at the gene level for an association between periodontitis and respiratory infection.}, } @article {pmid34252569, year = {2021}, author = {van de Wouw, M and Walsh, CJ and Vigano, GMD and Lyte, JM and Boehme, M and Gual-Grau, A and Crispie, F and Walsh, AM and Clarke, G and Dinan, TG and Cotter, PD and Cryan, JF}, title = {Kefir ameliorates specific microbiota-gut-brain axis impairments in a mouse model relevant to autism spectrum disorder.}, journal = {Brain, behavior, and immunity}, volume = {97}, number = {}, pages = {119-134}, doi = {10.1016/j.bbi.2021.07.004}, pmid = {34252569}, issn = {1090-2139}, mesh = {Animals ; *Autism Spectrum Disorder ; Brain ; *Gastrointestinal Microbiome ; *Kefir ; Mice ; *Microbiota ; Quality of Life ; }, abstract = {Autism spectrum disorder (ASD) is one of the most severe developmental disorders, affecting on average 1 in 150 children worldwide. There is a great need for more effective strategies to improve quality of life in ASD subjects. The gut microbiome has emerged as a potential therapeutic target in ASD. A novel modulator of the gut microbiome, the traditionally fermented milk drink kefir, has recently been shown to modulate the microbiota and decrease repetitive behaviour, one of the hallmarks of ASD, in mice. As such, we hypothesized that kefir could ameliorate behavioural deficits in a mouse model relevant to ASD; the BTBR T[+] Itpr3[tf]/J mouse strain. To this end, adult mice were administered either kefir (UK4) or a milk control for three weeks as treatment lead-in, after which they were assessed for their behavioural phenotype using a battery of tests. In addition, we assessed systemic immunity by flow cytometry and the gut microbiome using shotgun metagenomic sequencing. We found that indeed kefir decreased repetitive behaviour in this mouse model. Furthermore, kefir prolonged stress-induced increases in corticosterone 60 min post-stress, which was accompanied by an ameliorated innate immune response as measured by LY6C[hi] monocyte levels. In addition, kefir increased the levels of anti-inflammatory Treg cells in mesenteric lymph nodes (MLNs). Kefir also increased the relative abundance of Lachnospiraceae bacterium A2, which correlated with reduced repetitive behaviour and increased Treg cells in MLNs. Functionally, kefir modulated various predicted gut microbial pathways, including the gut-brain module S-Adenosylmethionine (SAM) synthesis, as well as L-valine biosynthesis and pyruvate fermentation to isobutanol, which all correlated with repetitive behaviour. Taken together our data show that kefir modulates peripheral immunoregulation, can ameliorate specific ASD behavioural dysfunctions and modulates selective aspects of the composition and function of the gut microbiome, indicating that kefir supplementation might prove a viable strategy in improving quality of life in ASD subjects.}, } @article {pmid34252073, year = {2021}, author = {Verma, S and Dutta, SK and Firnberg, E and Phillips, L and Vinayek, R and Nair, PP}, title = {Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects.}, journal = {PloS one}, volume = {16}, number = {7}, pages = {e0251590}, pmid = {34252073}, issn = {1932-6203}, mesh = {Humans ; *Fecal Microbiota Transplantation ; Female ; Male ; *Clostridium Infections/therapy/microbiology ; Middle Aged ; *Metagenomics/methods ; Aged ; Adult ; Feces/microbiology ; Gastrointestinal Microbiome ; Clostridioides difficile/genetics/isolation & purification ; Recurrence ; Bacteria/genetics/classification/isolation & purification ; Dysbiosis/microbiology/therapy ; Metagenome ; }, abstract = {BACKGROUND: Recurrent Clostridioides diffícile infection (RCDI) is associated with major bacterial dysbiosis and colitis. Fecal microbiota transplantation (FMT) is a highly effective therapeutic modality for RCDI. While several studies have identified bacterial species associated with resolution of symptoms in patients, characterization of the fecal microbiome at the bacterial strain level in RCDI patients before and after FMT and healthy donors, has been lacking. The aim of this study was to examine the ability of bacterial strains from healthy donors to engraft in the gastrointestinal tract of patients with RCDI following FMT.

METHODS: Fecal samples were collected from 22 patients with RCDI before and after FMT and their corresponding healthy donors. Total DNA was extracted from each sample and analyzed by shotgun metagenomic sequencing. The Cosmos-ID analysis platform was used for taxonomic assignment of sequences and calculation of the relative abundance (RA) of bacterial species and strains. From these data, the total number of bacterial strains (BSI), Shannon diversity index, dysbiosis index (DI), and bacterial engraftment factor, were calculated for each strain.

FINDINGS: A marked reduction (p<0·0001) in the RA of total and specific bacterial strains, especially from phylum Firmicutes, was observed in RCDI patients prior to FMT. This change was associated with an increase in the DI (p<0·0001) and in pathobiont bacterial strains from phylum Proteobacteria, such as Escherichia coli O157:H7 and Klebsiella pneumoniae UCI 34. BSI was significantly lower in this group of patients as compared to healthy donors and correlated with the Shannon Index. (p<0·0001). Identification and engraftment of bacterial strains from healthy donors revealed a greater diversity and higher relative abundance of short-chain fatty acid (SCFA)-producing bacterial strains, including Lachnospiraceae bacterium 5_1_63FAA_u_t, Dorea formicigenerans ATCC 27755, Anaerostipes hadrusand others, in RCDI patients after FMT.

INTERPRETATION: These observations identify a group of SCFA-producing bacterial strains from healthy donors that engraft well in patients with RCDI following FMT and are associated with complete resolution of clinical symptoms and bacterial dysbiosis.}, } @article {pmid34251746, year = {2022}, author = {Garrido-Sanz, L and Senar, MÀ and Piñol, J}, title = {Relative species abundance estimation in artificial mixtures of insects using mito-metagenomics and a correction factor for the mitochondrial DNA copy number.}, journal = {Molecular ecology resources}, volume = {22}, number = {1}, pages = {153-167}, doi = {10.1111/1755-0998.13464}, pmid = {34251746}, issn = {1755-0998}, support = {TIN2017-84553-C2-1-R//Spanish Government grant/ ; 2017-SGR-1001//Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR)/ ; }, mesh = {Animals ; DNA Copy Number Variations ; *DNA, Mitochondrial/genetics ; Insecta/genetics ; *Metagenomics ; }, abstract = {Mito-metagenomics (MMG) is becoming an alternative to amplicon metabarcoding for the assessment of biodiversity in complex biological samples using high-throughput sequencing. Whereas MMG overcomes the biases introduced by the PCR step in the generation of amplicons, it is not yet a technique free of shortcomings. First, as the reads are obtained from shotgun sequencing, a very low proportion of reads map into the mitogenomes, so a high sequencing effort is needed. Second, as the number of mitogenomes per cell can vary among species, the relative species abundance (RSA) in a mixture could be wrongly estimated. Here, we challenge the MMG method to estimate the RSA using artificial libraries of 17 insect species whose complete genomes are available on public repositories. With fresh specimens of these species, we created single-species libraries to calibrate the bioinformatic pipeline and mixed-species libraries to estimate the RSA. Our results showed that the MMG approach confidently recovers the species list of the mixtures, even when they contain congeneric species. The method was also able to estimate the abundance of a species across different samples (within-species estimation) but failed to estimate the RSA within a single sample (across-species estimation) unless a correction factor accounting for the variable number of mitogenomes per cell was used. To estimate this correction factor, we used the proportion of reads mapping into mitogenomes in the single-species libraries and the lengths of the whole genomes and mitogenomes.}, } @article {pmid34249393, year = {2021}, author = {Yoon, JH and Kim, SA and Shim, WB and Seo, DC and Choi, S and Lee, SY and Kim, SR}, title = {Colonization of Listeria monocytogenes in potting soils as affected by bacterial community composition, storage temperature, and natural amendment.}, journal = {Food science and biotechnology}, volume = {30}, number = {6}, pages = {869-880}, pmid = {34249393}, issn = {2092-6456}, abstract = {UNLABELLED: This study aimed to characterize the bacterial community of commercial potting soils with or without Listeria monocytogenes inoculation at 5-35 °C using 16S metagenomic sequencing and evaluate the effect of natural amendments on the reduction L. monocytogenes in non-sterile potting soils. An increase in the expected operational taxonomic units of each sample with or without L. monocytogenes was proportional to the increasing storage temperatures after 5 days. Biodiversity was distinct among all potting soils for Shannon and inverse Simpson indices, with the highest diversity being observed in a soil sample stored at 35 °C for 5 days with L. monocytogenes. An increase in richness and diversity of soil bacterial community structure positively correlated with less survival of the invading L. monocytogenes. Particularly, garlic extract was demonstrated as a promising soil-amendment substrate, reducing L. monocytogenes by ≥ 4.50 log CFU/g in potting soils stored at 35 °C.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-021-00925-9.}, } @article {pmid34246809, year = {2021}, author = {Fan, TJ and Goeser, L and Lu, K and Faith, JJ and Hansen, JJ}, title = {Enterococcus faecalis Glucosamine Metabolism Exacerbates Experimental Colitis.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {12}, number = {4}, pages = {1373-1389}, pmid = {34246809}, issn = {2352-345X}, support = {P30 DK034987/DK/NIDDK NIH HHS/United States ; P40 OD010995/OD/NIH HHS/United States ; P40 RR018603/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Biomarkers ; Colitis/*etiology/metabolism/*pathology ; Disease Models, Animal ; Disease Progression ; *Disease Susceptibility ; Dysbiosis ; Enterococcus faecalis/genetics/*metabolism ; *Gastrointestinal Microbiome ; Gene Expression Regulation, Bacterial ; Glucosamine/*metabolism ; Host Microbial Interactions ; Inflammatory Bowel Diseases/etiology/metabolism/pathology ; Metagenome ; Metagenomics ; Mice ; Mice, Knockout ; }, abstract = {BACKGROUND & AIMS: The inflammatory bowel diseases (IBDs), Crohn's disease and ulcerative colitis, are caused in part by aberrant immune responses to resident intestinal bacteria. Certain dietary components, including carbohydrates, are associated with IBDs and alter intestinal bacterial composition. However, the effects of luminal carbohydrates on the composition and colitogenic potential of intestinal bacteria are incompletely understood. We hypothesize that carbohydrate metabolism by resident proinflammatory intestinal bacteria enhances their growth and worsens intestinal inflammation.

METHODS: We colonized germ-free, wild-type, and colitis-susceptible interleukin-10 knockout mice (Il10[-/-]) with a consortium of resident intestinal bacterial strains and quantified colon inflammation using blinded histologic scoring and spontaneous secretion of IL12/23p40 by colon explants. We measured luminal bacterial composition using real-time 16S polymerase chain reaction, bacterial gene expression using RNA sequencing and real-time polymerase chain reaction, and luminal glucosamine levels using gas chromatography-mass spectrometry.

RESULTS: We show that a consortium of 8 bacterial strains induces severe colitis in Il10[-/-] mice and up-regulates genes associated with carbohydrate metabolism during colitis. Specifically, Enterococcus faecalis strain OG1RF is proinflammatory and strongly up-regulates OG1RF_11616-11610, an operon that encodes genes of a previously undescribed phosphotransferase system that we show imports glucosamine. Experimental colitis is associated with increased levels of luminal glucosamine and OG1RF_11616 causes worse colitis, not by increasing E faecalis numbers, but rather by mechanisms that require the presence of complex microbiota.

CONCLUSIONS: Further studies of luminal carbohydrate levels and bacterial carbohydrate metabolism during intestinal inflammation will improve our understanding of the pathogenesis of IBDs and may lead to the development of novel therapies for these diseases.}, } @article {pmid34246242, year = {2021}, author = {Kameoka, S and Motooka, D and Watanabe, S and Kubo, R and Jung, N and Midorikawa, Y and Shinozaki, NO and Sawai, Y and Takeda, AK and Nakamura, S}, title = {Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1-V2 and V3-V4 primer sets.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {527}, pmid = {34246242}, issn = {1471-2164}, support = {18K08431//Ministry of Education, Culture, Sports, Science and Technology/ ; 172107106//Ministry of Internal Affairs and Communications/ ; JP18gm1010005//Japan Agency for Medical Research and Development/ ; }, mesh = {Benchmarking ; *Gastrointestinal Microbiome/genetics ; Genes, rRNA ; High-Throughput Nucleotide Sequencing ; Humans ; Japan ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: 16S rRNA gene amplicon sequencing (16S analysis) is widely used to analyze microbiota with next-generation sequencing technologies. Here, we compared fecal 16S analysis data from 192 Japanese volunteers using the modified V1-V2 (V12) and the standard V3-V4 primer (V34) sets to optimize the gut microbiota analysis protocol.

RESULTS: QIIME1 and QIIME2 analysis revealed a higher number of unclassified representative sequences in the V34 data than in the V12 data. The comparison of bacterial composition demonstrated that at the phylum level, Actinobacteria and Verrucomicrobia were detected at higher levels with V34 than with V12. Among these phyla, we observed higher relative compositions of Bifidobacterium and Akkermansia with V34. To estimate the actual abundance, we performed quantitative real-time polymerase chain reaction (qPCR) assays for Akkermansia and Bifidobacterium. We found that the abundance of Akkermansia as detected by qPCR was close to that in V12 data, but was markedly lower than that in V34 data. The abundance of Bifidobacterium detected by qPCR was higher than that in V12 and V34 data.

CONCLUSIONS: These results indicate that the bacterial composition derived from the V34 region might differ from the actual abundance for specific gut bacteria. We conclude that the use of the modified V12 primer set is more desirable in the 16S analysis of the Japanese gut microbiota.}, } @article {pmid34245762, year = {2021}, author = {Mihindukulasuriya, KA and Mars, RAT and Johnson, AJ and Ward, T and Priya, S and Lekatz, HR and Kalari, KR and Droit, L and Zheng, T and Blekhman, R and D'Amato, M and Farrugia, G and Knights, D and Handley, SA and Kashyap, PC}, title = {Multi-Omics Analyses Show Disease, Diet, and Transcriptome Interactions With the Virome.}, journal = {Gastroenterology}, volume = {161}, number = {4}, pages = {1194-1207.e8}, pmid = {34245762}, issn = {1528-0012}, support = {P30 DK084567/DK/NIDDK NIH HHS/United States ; R01 DK114007/DK/NIDDK NIH HHS/United States ; R35 GM128716/GM/NIGMS NIH HHS/United States ; RC2 DK116713/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Bacteriophages/genetics/growth & development ; Case-Control Studies ; *Diet/adverse effects ; Female ; Gastrointestinal Microbiome ; Gene Expression Profiling ; Gene Expression Regulation ; Host-Pathogen Interactions ; Humans ; Intestines/microbiology/*virology ; Irritable Bowel Syndrome/diagnosis/genetics/microbiology/*virology ; Longitudinal Studies ; Male ; Metagenome ; Metagenomics ; Middle Aged ; *Transcriptome ; Virology ; *Virome ; Viruses/genetics/*growth & development ; }, abstract = {BACKGROUND & AIMS: The gut virome includes eukaryotic viruses and bacteriophages that can shape the gut bacterial community and elicit host responses. The virome can be implicated in diseases, such as irritable bowel syndrome (IBS), where gut bacteria play an important role in pathogenesis. We provide a comprehensive and longitudinal characterization of the virome, including DNA and RNA viruses and paired multi-omics data in a cohort of healthy subjects and patients with IBS.

METHODS: We selected 2 consecutive stool samples per subject from a longitudinal study cohort and performed metagenomic sequencing on DNA and RNA viruses after enriching for viral-like particles. Viral sequence abundance was evaluated over time, as well as in the context of diet, bacterial composition and function, metabolite levels, colonic gene expression, host genetics, and IBS subsets.

RESULTS: We found that the gut virome was temporally stable and correlated with the colonic transcriptome. We identified IBS-subset-specific changes in phage populations; Microviridae, Myoviridae, and Podoviridae species were elevated in diarrhea-predominant IBS, and other Microviridae and Myoviridae species were elevated in constipation-predominant IBS compared to healthy controls. We identified correlations between subsets of the virome and bacterial composition (unclassifiable "dark matter" and phages) and diet (eukaryotic viruses).

CONCLUSIONS: We found that the gut virome is stable over time but varies among subsets of patients with IBS. It can be affected by diet and potentially influences host function via interactions with gut bacteria and/or altering host gene expression.}, } @article {pmid34245102, year = {2021}, author = {Bendia, AG and Lemos, LN and Mendes, LW and Signori, CN and Bohannan, BJM and Pellizari, VH}, title = {Metabolic potential and survival strategies of microbial communities across extreme temperature gradients on Deception Island volcano, Antarctica.}, journal = {Environmental microbiology}, volume = {23}, number = {7}, pages = {4054-4073}, doi = {10.1111/1462-2920.15649}, pmid = {34245102}, issn = {1462-2920}, mesh = {Antarctic Regions ; Archaea/genetics ; *Bacteria/genetics ; *Microbiota/genetics ; Temperature ; }, abstract = {Active volcanoes in Antarctica have remarkable temperature and geochemical gradients that could select for a wide variety of microbial adaptive mechanisms and metabolic pathways. Deception Island is a stratovolcano flooded by the sea, resulting in contrasting ecosystems such as permanent glaciers and active fumaroles, which creates steep gradients that have been shown to affect microbial diversity. In this study, we used shotgun metagenomics and metagenome-assembled genomes to explore the metabolic potentials and survival strategies of microbial communities along an extreme temperature gradient in fumarole and glacier sediments on Deception Island. We observed that communities from a 98 °C fumarole were significantly enriched in genes related to hyperthermophilic (e.g. reverse gyrase, GroEL/GroES and thermosome) and oxidative stress responses, as well as genes related to sulfate reduction, ammonification and carbon fixation. Communities from <80 °C fumaroles possessed more genes related osmotic, cold- and heat-shock responses, and diverse metabolic potentials, such as those related to sulfur oxidation and denitrification, while glacier communities showed abundant metabolic potentials mainly related to heterotrophy. Through the reconstruction of genomes, we were able to reveal the metabolic potentials and different survival strategies of underrepresented taxonomic groups, especially those related to Nanoarchaeota, Pyrodictiaceae and thermophilic ammonia-oxidizing archaeal lineages.}, } @article {pmid34244406, year = {2021}, author = {Blacher, E}, title = {Can microbes combat neurodegeneration?.}, journal = {Science (New York, N.Y.)}, volume = {373}, number = {6551}, pages = {172-173}, doi = {10.1126/science.abi9353}, pmid = {34244406}, issn = {1095-9203}, mesh = {Akkermansia/metabolism ; Amyotrophic Lateral Sclerosis/metabolism/*microbiology/*therapy ; Animals ; Bacteria/genetics/*metabolism ; Brain/*metabolism ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Metabolic Networks and Pathways ; Metagenome ; Mice ; Mice, Transgenic ; Niacinamide/administration & dosage/blood/cerebrospinal fluid/metabolism ; Probiotics ; }, } @article {pmid34239006, year = {2021}, author = {Olsen, M and Nassar, R and Senok, A and Albastaki, A and Leggett, J and Lohning, A and Campos, M and Jones, P and McKirdy, S and Tajouri, L and Alghafri, R}, title = {A pilot metagenomic study reveals that community derived mobile phones are reservoirs of viable pathogenic microbes.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {14102}, pmid = {34239006}, issn = {2045-2322}, mesh = {Bacteria/*genetics ; Bacteriophages/genetics ; Biodiversity ; *Cell Phone ; Fungi/*genetics ; Metagenome ; *Metagenomics ; Virulence Factors/metabolism ; }, abstract = {There is increasing attention focussed on the risks associated with mobile phones possibly serving as 'Trojan Horse' fomites for microbial transmission in healthcare settings. However, little is reported on the presence of microbes on community derived mobile phones which in 2021, numbered in the billions in circulation with majority being used on a daily basis. Identify viable microbial organisms swabbed from smartphones on a university campus. Entire surfaces of 5 mobile phones were swabbed and examined for their microbial content using pre-agar-based growths followed by downstream DNA metagenomic next-generation sequencing analysis. All phones were contaminated with viable microbes. 173 bacteria, 8 fungi, 8 protists, 53 bacteriophages, 317 virulence factor genes and 41 distinct antibiotic resistant genes were identified. While this research represents a pilot study, the snapshot metagenomic analysis of samples collected from the surface of mobile phones has revealed the presence of a large population of viable microbes and an array of antimicrobial resistant factors. With billions of phones in circulation, these devices might be responsible for the rise of community acquired infections. These pilot results highlight the importance of public health authorities considering mobile phones as 'Trojan Horse' devices for microbial transmission and ensure appropriate decontamination campaigns are implemented.}, } @article {pmid34234185, year = {2021}, author = {Jones, J and Reinke, SN and Ali, A and Palmer, DJ and Christophersen, CT}, title = {Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {13964}, pmid = {34234185}, issn = {2045-2322}, mesh = {Biodiversity ; Cluster Analysis ; Fatty Acids, Volatile/analysis/*metabolism ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; Microbial Viability ; Specimen Handling/*methods ; }, abstract = {Associations between the human gut microbiome and health outcomes continues to be of great interest, although fecal sample collection methods which impact microbiome studies are sometimes neglected. Here, we expand on previous work in sample optimization, to promote high quality microbiome data. To compare fecal sample collection methods, amplicons from the bacterial 16S rRNA gene (V4) and fungal (ITS2) region, as well as short chain fatty acid (SCFA) concentrations were determined in fecal material over three timepoints. We demonstrated that spot sampling of stool results in variable detection of some microbial members, and inconsistent levels of SCFA; therefore, sample homogenization prior to subsequent analysis or subsampling is recommended. We also identify a trend in microbial and metabolite composition that shifts over two consecutive stool collections less than 25 h apart. Lastly, we show significant differences in bacterial composition that result from collecting stool samples in OMNIgene·Gut tube (DNA Genotec) or Stool Nucleic Acid Collection and Preservation Tube (NORGEN) compared to immediate freezing. To assist with planning fecal sample collection and storage procedures for microbiome investigations with multiple analyses, we recommend participants to collect the first full bowel movement of the day and freeze the sample immediately after collection.}, } @article {pmid34234121, year = {2021}, author = {Lam, MMC and Wick, RR and Watts, SC and Cerdeira, LT and Wyres, KL and Holt, KE}, title = {A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {4188}, pmid = {34234121}, issn = {2041-1723}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacterial Proteins/*genetics ; Cross Infection/diagnosis/drug therapy/epidemiology/*microbiology ; Datasets as Topic ; Drug Resistance, Multiple, Bacterial/genetics ; Epidemiological Monitoring ; Gastrointestinal Microbiome/genetics ; Genome, Bacterial ; Humans ; Infant ; Infant, Newborn ; Klebsiella Infections/diagnosis/drug therapy/epidemiology/*microbiology ; Klebsiella pneumoniae/*genetics/isolation & purification/pathogenicity ; Metagenome/genetics ; Molecular Epidemiology/methods ; Molecular Typing/*methods ; Mutation ; Phylogeny ; Software ; Virulence/genetics ; Virulence Factors/genetics ; Whole Genome Sequencing ; beta-Lactamases/genetics ; }, abstract = {Klebsiella pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Its diversity and complex population structure pose challenges for analysis and interpretation of K. pneumoniae genome data. Here we introduce Kleborate, a tool for analysing genomes of K. pneumoniae and its associated species complex, which consolidates interrogation of key features of proven clinical importance. Kleborate provides a framework to support genomic surveillance and epidemiology in research, clinical and public health settings. To demonstrate its utility we apply Kleborate to analyse publicly available Klebsiella genomes, including clinical isolates from a pan-European study of carbapenemase-producing Klebsiella, highlighting global trends in AMR and virulence as examples of what could be achieved by applying this genomic framework within more systematic genomic surveillance efforts. We also demonstrate the application of Kleborate to detect and type K. pneumoniae from gut metagenomes.}, } @article {pmid34233671, year = {2021}, author = {Liu, P and Jiang, Y and Gu, S and Xue, Y and Yang, H and Li, Y and Wang, Y and Yan, C and Jia, P and Lin, X and Qi, G}, title = {Metagenome-wide association study of gut microbiome revealed potential microbial marker set for diagnosis of pediatric myasthenia gravis.}, journal = {BMC medicine}, volume = {19}, number = {1}, pages = {159}, pmid = {34233671}, issn = {1741-7015}, mesh = {Adult ; Bacteroides ; Child ; Clostridiales ; Feces ; Firmicutes ; Fusobacterium ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; *Myasthenia Gravis/diagnosis ; Prevotella ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Myasthenia gravis (MG) is an acquired immune-mediated disorder of the neuromuscular junction that causes fluctuating skeletal muscle weakness and fatigue. Pediatric MG and adult MG have many different characteristics, and current MG diagnostic methods for children are not quite fit. Previous studies indicate that alterations in the gut microbiota may be associated with adult MG. However, it has not been determined whether the gut microbiota are altered in pediatric MG patients.

METHODS: Our study recruited 53 pediatric MG patients and 46 age- and gender-matched healthy controls (HC). We sequenced the fecal samples of recruited individuals using whole-genome shotgun sequencing and analyzed the data with in-house bioinformatics pipeline.

RESULTS: We built an MG disease classifier based on the abundance of five species, Fusobacterium mortiferum, Prevotella stercorea, Prevotella copri, Megamonas funiformis, and Megamonas hypermegale. The classifier obtained 94% area under the curve (AUC) in cross-validation and 84% AUC in the independent validation cohort. Gut microbiome analysis revealed the presence of human adenovirus F/D in 10 MG patients. Significantly different pathways and gene families between MG patients and HC belonged to P. copri, Clostridium bartlettii, and Bacteroides massiliensis. Based on functional annotation, we found that the gut microbiome affects the production of short-chain fatty acids (SCFAs), and we confirmed the decrease in SCFA levels in pediatric MG patients via serum tests.

CONCLUSIONS: The study indicated that altered fecal microbiota might play vital roles in pediatric MG's pathogenesis by reducing SCFAs. The microbial markers might serve as novel diagnostic methods for pediatric MG.}, } @article {pmid34233588, year = {2021}, author = {Li, H and Wu, G and Zhao, L and Zhang, M}, title = {Suppressed inflammation in obese children induced by a high-fiber diet is associated with the attenuation of gut microbial virulence factor genes.}, journal = {Virulence}, volume = {12}, number = {1}, pages = {1754-1770}, pmid = {34233588}, issn = {2150-5608}, mesh = {Child ; Diet ; Dietary Fiber/*administration & dosage ; *Gastrointestinal Microbiome ; Humans ; *Inflammation ; *Pediatric Obesity/diet therapy ; *Prader-Willi Syndrome/diet therapy ; *Virulence Factors/genetics ; }, abstract = {In our previous study, a gut microbiota-targeted dietary intervention with a high-fiber diet improved the immune status of both genetically obese (Prader-Willi Syndrome, PWS) and simple obese (SO) children. However, PWS children had higher inflammation levels than SO children throughout the trial, the gut microbiota of the two cohorts was similar. As some virulence factors (VFs) produced by the gut microbiota play a role in triggering host inflammation, this study compared the characteristics and changes of gut microbial VF genes of the two cohorts before and after the intervention using a fecal metagenomic dataset. We found that in both cohorts, the high-fiber diet reduced the abundance of VF, and particularly pathogen-specific, genes. The composition of VF genes was also modulated, especially for offensive and defensive VF genes. Furthermore, genes belonging to invasion, T3SS (type III secretion system), and adherence classes were suppressed. Co-occurrence network analysis detected VF gene clusters closely related to host inflammation in each cohort. Though these cohort-specific clusters varied in VF gene combinations and cascade reactions affecting inflammation, they mainly contained VFs belonging to iron uptake, T3SS, and invasion classes. The PWS group had a lower abundance of VF genes before the trial, which suggested that other factors could also be responsible for the increased inflammation in this cohort. This study provides insight into the modulation of VF gene structure in the gut microbiota by a high-fiber diet, with respect to reduced inflammation in obese children, and differences in VF genes between these two cohorts.}, } @article {pmid34233229, year = {2021}, author = {Wang, R and Cai, Y and Li, J and Yau, SY and Lu, W and Stubbs, B and Su, KP and Xu, G and So, KF and Lin, K and Qi, LW}, title = {Effects of aerobic exercise on gut microbiota in adolescents with subthreshold mood syndromes and healthy adolescents: A 12-week, randomized controlled trial.}, journal = {Journal of affective disorders}, volume = {293}, number = {}, pages = {363-372}, doi = {10.1016/j.jad.2021.06.025}, pmid = {34233229}, issn = {1573-2517}, mesh = {Adolescent ; Affect ; Animals ; Exercise ; *Gastrointestinal Microbiome/genetics ; Humans ; *Microbiota ; Syndrome ; }, abstract = {BACKGROUND: Animal and human studies have revealed reciprocal association between exercise and gut-brain axis. However, the clinical evidence from randomized controlled trials (RCT) are still limited to directly assess the effects of aerobic exercise on gut microbiota. To fill this gap, we conducted this 12-week RCT in both groups of adolescents with and without sub-threshold mood symptoms.

METHODS: A total of 224 adolescents were randomized to the aerobic exercise intervention or psychoeducation-controlled arm. 49 adolescents with subthreshold symptoms and 142 clinically-well adolescents provided the sample for microbiota assessed by metagenomic sequencing. Aerobic exercise of running at the moderate-intensity for 30 min per day, 5 days a week, were conducted for 12 weeks.

RESULTS: Adolescents with subthreshold symptoms had significantly lower beta diversity than clinically-well adolescents in both the exercise intervention and psychoeducation-controlled arms (p<0.05). After intervention, no difference in gut microbiota diversity, phylum, genus, species level abundancies or gut microbial functions were found in both of the symptomatic or non-symptomatic groups. Metagenome-wide association study analysis showed no significant difference in metagenomic linkage groups.

LIMITATIONS: The sample size is relatively small. The exercise intensity we employed may be insufficient to result in observable effects on intestinal microbiota.

CONCLUSION: We conclude that a 12-week moderate-intensity aerobic exercise intervention showed no significant beneficial effect on the gut microbiota in clinically-well adolescents as well as in adolescents with subthreshold symptoms. The beta diversity of gut microbiota in adolescents with subthreshold mood syndromes may be impaired when compared with clinically-well adolescents.}, } @article {pmid34233092, year = {2022}, author = {Lee, JW and Lim, SH and Shin, JH and Lee, Y and Seo, JH}, title = {Differences in the eyelid and buccal microbiome between open-angle glaucoma and uveitic glaucoma.}, journal = {Acta ophthalmologica}, volume = {100}, number = {3}, pages = {e770-e778}, doi = {10.1111/aos.14967}, pmid = {34233092}, issn = {1755-3768}, support = {VHSMC 19022//VHS Medical Center Research Grant/ ; }, mesh = {Eyelids ; *Glaucoma ; *Glaucoma, Open-Angle ; Humans ; Intraocular Pressure ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {PURPOSE: Microbiomes have immunoregulatory functions and may be involved in the pathophysiology of eye diseases. However, the effects of microbiomes on uveitic glaucoma (UG) and open-angle glaucoma (OAG) have not been sufficiently investigated. This study analysed differences in eyelid and buccal microbiomes between UG and OAG using metagenomic technology.

METHODS: Eyelid and buccal specimens were collected from 34 UG and 62 OAG patients. The taxonomic composition of the microbiome was determined via 16S rRNA gene sequencing, operational taxonomic unit analysis and diversity analysis. Differential gene expression analysis (DEG) and principal component analyses (PCoA) determined taxon differences between the microbiomes of the UG and OAG patients. Subgroup analysis according to age and baseline IOP was performed.

RESULTS: There was no significant difference in alpha-diversity between the microbiomes of UG and OAG patients. Further, PCoA revealed no differences in eyelid microbiome between the UG and OAG groups, but significant differences were found in buccal microbiome between the groups, especially in a subgroup of OAG patients with normal IOP. DEG analysis of the eyelid microbiome revealed various taxa differences, including the enrichment of Rhodococcus in UG samples over OAG samples. Taxa such as Lactobacillus and Proteus were significantly depleted (q-value = 9.98e[-6] and q-value = 1.38 × 10[-4] , respectively) in the buccal microbiome of UG patients, whereas Enterococcus was enriched (q-value = 5.26e[-5]).

CONCLUSIONS: This study showed that the buccal microbiome in UG differs from that in OAG; reduced Lactobacillus was observed in UG. These results suggest that apart than OAG, microbiome composition may be a factor in the pathogenesis of UG.}, } @article {pmid34232064, year = {2021}, author = {Steven, B and LaReau, JC and Taerum, SJ and Zuverza-Mena, N and Cowles, RS}, title = {What's under the Christmas Tree? A Soil Sulfur Amendment Lowers Soil pH and Alters Fir Tree Rhizosphere Bacterial and Eukaryotic Communities, Their Interactions, and Functional Traits.}, journal = {Microbiology spectrum}, volume = {9}, number = {1}, pages = {e0016621}, pmid = {34232064}, issn = {2165-0497}, mesh = {Abies/*growth & development/microbiology ; Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; Eukaryota/classification/genetics/*isolation & purification ; Hydrogen-Ion Concentration ; Metagenome ; Rhizosphere ; Soil/*chemistry/*parasitology ; *Soil Microbiology ; Sulfur/*metabolism ; Trees/growth & development/microbiology ; }, abstract = {In this study, we describe the legacy effects of a soil sulfur amendment experiment performed 6 years prior and the resulting alterations to the rhizosphere communities of fir trees on a Christmas tree plantation. The pH of bulk soil was ∼1.4 pH units lower than that of untreated soils and was associated with reduced Ca, Mg, and organic matter contents. Similarly, root chemistry differed due to the treatment, with roots in sulfur-amended soils showing significantly higher Al, Mn, and Zn contents and reduced levels of B and Ca. 16S rRNA and 18S rRNA gene sequencing was pursued to characterize the bacterial/archaeal and eukaryotic communities in the rhizosphere soils. The treatment induced dramatic and significant changes in the microbial populations, with thousands of 16S rRNA gene sequence variants and hundreds of 18S rRNA gene variants being significantly different in relative abundances between the treatments. Additionally, co-occurrence networks showed that bacterial and eukaryotic interactions, network topology, and hub taxa were significantly different when constructed from the control and treated soil 16S and 18S rRNA gene amplicon libraries. Metagenome sequencing identified several genes related to transport proteins that differentiated the functional potentials of the communities between treatments, pointing to physiological adaptations in the microbial communities for living at altered pH. These data show that a legacy of soil acidification increased the heterogeneity of the soil communities as well as decreasing taxon connections, pointing to a state of ecosystem instability that has potentially persisted for 6 years. IMPORTANCE We used sulfur incorporation to investigate the legacy effects of lowered soil pH on the bacterial and eukaryotic populations in the rhizosphere of Christmas trees. Acidification of the soils drove alterations of fir tree root chemistry and large shifts in the taxonomic and functional compositions of the communities. These data demonstrate that soil pH influences are manifest across all organisms inhabiting the soil, from the host plant to the microorganisms inhabiting the rhizosphere soils. Thus, this study highlights the long-lasting influence of altering soil pH on soil and plant health as well as the status of the microbiome.}, } @article {pmid34231972, year = {2021}, author = {Wang, Z and Li, Y and Zhao, Y and Zhuang, L and Yu, Y and Wang, M and Liu, J and Wang, Q}, title = {A microbial consortium-based product promotes potato yield by recruiting rhizosphere bacteria involved in nitrogen and carbon metabolisms.}, journal = {Microbial biotechnology}, volume = {14}, number = {5}, pages = {1961-1975}, pmid = {34231972}, issn = {1751-7915}, mesh = {Bacteria/genetics ; Carbon ; Hypocreales ; Microbial Consortia ; Nitrogen ; *Rhizosphere ; Soil Microbiology ; *Solanum tuberosum ; }, abstract = {The effect of a microbial consortium-based (MCB) biocontrol product, composed of Bacillus subtilis, Trichoderma harzianum strain and diatomaceous earth as a carrier, on potato yield, and potential modes of action for its effect were investigated. The MCB product (300 kg ha[-1]) was added to furrows in which the potato seed tubers each year for 3 years (2016, 2017 and 2018), while potato planting without the MCB product treatment served as the control. A metagenomic analysis indicated that bacterial phylotypes dominated the microbial community, with a relatively small contribution of archaea and fungal taxa. The relative abundance of beneficial bacterial taxa increased significantly in response to the MCB product treatment. Notably, a higher relative abundance of bacterial taxa with carbon fixation, carbon-degrading and nitrogen metabolism properties were observed in the MCB product-treated potato rhizosphere. This was also reflected in the identification of a greater abundance of genes encoding enzymes involved in nitrogen metabolism, carbon fixation and carbon degradation pathways in the conducted metagenomic analysis. The greater relative abundance of these beneficial bacterial taxa in the rhizosphere of MCB product-treated plots, as well as the higher abundance of genes associated with the indicated cellular processes, were associated with an increase in tuber yield. The observed changes in microbial community structure at an early stage of tuber development appears to have a beneficial impact on tuber yield.}, } @article {pmid34226711, year = {2021}, author = {Montassier, E and Valdés-Mas, R and Batard, E and Zmora, N and Dori-Bachash, M and Suez, J and Elinav, E}, title = {Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner.}, journal = {Nature microbiology}, volume = {6}, number = {8}, pages = {1043-1054}, pmid = {34226711}, issn = {2058-5276}, support = {/WT_/Wellcome Trust/United Kingdom ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Adult ; Anti-Bacterial Agents/*administration & dosage ; Bacteria/classification/*drug effects/*genetics/isolation & purification ; Bacterial Proteins/*genetics/metabolism ; Cohort Studies ; *Drug Resistance, Bacterial ; Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/microbiology ; Humans ; Male ; Metagenome/drug effects ; Middle Aged ; Probiotics/*administration & dosage ; Young Adult ; }, abstract = {Antimicrobial resistance poses a substantial threat to human health. The gut microbiome is considered a reservoir for potential spread of resistance genes from commensals to pathogens, termed the gut resistome. The impact of probiotics, commonly consumed by many in health or in conjunction with the administration of antibiotics, on the gut resistome is elusive. Reanalysis of gut metagenomes from healthy antibiotics-naïve humans supplemented with an 11-probiotic-strain preparation, allowing direct assessment of the gut resistome in situ along the gastrointestinal (GI) tract, demonstrated that probiotics reduce the number of antibiotic resistance genes exclusively in the gut of colonization-permissive individuals. In mice and in a separate cohort of humans, a course of antibiotics resulted in expansion of the lower GI tract resistome, which was mitigated by autologous faecal microbiome transplantation or during spontaneous recovery. In contrast, probiotics further exacerbated resistome expansion in the GI mucosa by supporting the bloom of strains carrying vancomycin resistance genes but not resistance genes encoded by the probiotic strains. Importantly, the aforementioned effects were not reflected in stool samples, highlighting the importance of direct sampling to analyse the effect of probiotics and antibiotics on the gut resistome. Analysing antibiotic resistance gene content in additional published clinical trials with probiotics further highlighted the importance of person-specific metagenomics-based profiling of the gut resistome using direct sampling. Collectively, these findings suggest opposing person-specific and antibiotic-dependent effects of probiotics on the resistome, whose contribution to the spread of antimicrobial resistance genes along the human GI tract merit further studies.}, } @article {pmid34226572, year = {2021}, author = {Shimada, Y and Terasawa, M and Okazaki, F and Nakayama, H and Zang, L and Nishiura, K and Matsuda, K and Nishimura, N}, title = {Rhamnan sulphate from green algae Monostroma nitidum improves constipation with gut microbiome alteration in double-blind placebo-controlled trial.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {13384}, pmid = {34226572}, issn = {2045-2322}, mesh = {Adult ; Aged ; Animals ; Bacteria/*isolation & purification ; Chlorophyta/*chemistry ; Constipation/*drug therapy/microbiology ; DNA Barcoding, Taxonomic ; Double-Blind Method ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Male ; Metagenomics ; Mice ; Middle Aged ; Young Adult ; }, abstract = {Rhamnan sulphate (RS), a sulphated polysaccharide from Monostroma nitidum, possesses several biological properties that help in treating diseases such as viral infection, thrombosis, and obesity. In the present study, we first administered RS (0.25 mg/g food volume) orally to high-fat diet-treated mice for 4 weeks. RS increased the faecal volume and calorie excretion with decreased plasma lipids, which was in accordance with the results of our previous zebrafish study. Notably, as the excretion amount by RS increased in the mice, we hypothesised that RS could decrease the chance of constipation in mice and also in human subjects because RS is considered as a dietary fibre. We administrated RS (100 mg/day) to subjects with low defaecation frequencies (3-5 times/week) for 2 weeks in double-blind placebo-controlled manner. As a result, RS administration significantly increased the frequency of dejection without any side effects, although no effect was observed on the body weight and blood lipids. Moreover, we performed 16s rRNA-seq analysis of the gut microbiota in these subjects. Metagenomics profiling using PICRUSt revealed functional alternation of the KEGG pathways, which could be involved in the therapeutic effect of RS for constipation.}, } @article {pmid34226571, year = {2021}, author = {Moguel, B and Pérez, L and Alcaraz, LD and Blaz, J and Caballero, M and Muñoz-Velasco, I and Becerra, A and Laclette, JP and Ortega-Guerrero, B and Romero-Oliva, CS and Herrera-Estrella, L and Lozano-García, S}, title = {Holocene life and microbiome profiling in ancient tropical Lake Chalco, Mexico.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {13848}, pmid = {34226571}, issn = {2045-2322}, support = {/WT_/Wellcome Trust/United Kingdom ; 55005946/HHMI/Howard Hughes Medical Institute/United States ; 208934/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Carbon Cycle/genetics ; Geologic Sediments/microbiology ; Humans ; Lakes/*microbiology ; Metagenome/genetics ; Mexico ; Microbiota/*genetics ; Nitrogen/metabolism ; Phylogeny ; Tropical Climate ; }, abstract = {Metagenomic and traditional paleolimnological approaches are suitable to infer past biological and environmental changes, however, they are often applied independently, especially in tropical regions. We combined both approaches to investigate Holocene Prokaryote and Eukaryote diversity and microbial metabolic pathways in ancient Lake Chalco, Mexico. Here, we report on diversity among a large number of lineages (36,722 OTUs) and functional diversity (27,636,243 non-clustered predicted proteins, and 6,144 annotated protein-family genes). The most abundant domain is Bacteria (81%), followed by Archaea (15%) and Eukarya (3%). We also determined the diversity of protein families and their relationship to metabolic pathways. The early Holocene (> 11,000 cal years BP) lake was characterized by cool, freshwater conditions, which later became warmer and hyposaline (11,000-6,000 cal years BP). We found high abundances of cyanobacteria, and fungi groups associated with mature forests in these sediments. Bacteria and Archaea include mainly anaerobes and extremophiles that are involved in the sulfur, nitrogen, and carbon cycles. We found evidence for early human impacts, including landscape modifications and lake eutrophication, which began ~ 6,000 cal years BP. Subsaline, temperate conditions were inferred for the past 5,000 years. Finally, we found nitrogen-fixing bacteria and protein-family genes that are linked to contaminated environments, as well as several fungal pathogens of crops in near-surface sediments.}, } @article {pmid34226407, year = {2021}, author = {Wang, Y and Wang, C and Chen, Y and Chen, B and Guo, P and Cui, Z}, title = {Metagenomic Insight into Lignocellulose Degradation of the Thermophilic Microbial Consortium TMC7.}, journal = {Journal of microbiology and biotechnology}, volume = {31}, number = {8}, pages = {1123-1133}, pmid = {34226407}, issn = {1738-8872}, mesh = {Bacteria/classification/enzymology/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Cellulose/metabolism ; Lignin/*metabolism ; *Metagenome ; Metagenomics ; Microbial Consortia/*genetics ; Polysaccharides/metabolism ; }, abstract = {Biodegradation is the key process involved in natural lignocellulose biotransformation and utilization. Microbial consortia represent promising candidates for applications in lignocellulose conversion strategies for biofuel production; however, cooperation among the enzymes and the labor division of microbes in the microbial consortia remains unclear. In this study, metagenomic analysis was performed to reveal the community structure and extremozyme systems of a lignocellulolytic microbial consortium, TMC7. The taxonomic affiliation of TMC7 metagenome included members of the genera Ruminiclostridium (42.85%), Thermoanaerobacterium (18.41%), Geobacillus (10.44%), unclassified_f__Bacillaceae (7.48%), Aeribacillus (2.65%), Symbiobacterium (2.47%), Desulfotomaculum (2.33%), Caldibacillus (1.56%), Clostridium (1.26%), and others (10.55%). The carbohydrate-active enzyme annotation revealed that TMC7 encoded a broad array of enzymes responsible for cellulose and hemicellulose degradation. Ten glycoside hydrolases (GHs) endoglucanase, 4 GHs exoglucanase, and 6 GHs β-glucosidase were identified for cellulose degradation; 6 GHs endo-β-1,4-xylanase, 9 GHs β-xylosidase, and 3 GHs β-mannanase were identified for degradation of the hemicellulose main chain; 6 GHs arabinofuranosidase, 2 GHs α-mannosidase, 11 GHs galactosidase, 3 GHs α-rhamnosidase, and 4 GHs α-fucosidase were identified as xylan debranching enzymes. Furthermore, by introducing a factor named as the contribution coefficient, we found that Ruminiclostridium and Thermoanaerobacterium may be the dominant contributors, whereas Symbiobacterium and Desulfotomaculum may serve as "sugar cheaters" in lignocellulose degradation by TMC7. Our findings provide mechanistic profiles of an array of enzymes that degrade complex lignocellulosic biomass in the microbial consortium TMC7 and provide a promising approach for studying the potential contribution of microbes in microbial consortia.}, } @article {pmid34225233, year = {2021}, author = {Borsetto, C and Raguideau, S and Travis, E and Kim, DW and Lee, DH and Bottrill, A and Stark, R and Song, L and Cha, CJ and Pearson, J and Quince, C and Singer, AC and Wellington, EMH}, title = {Impact of sulfamethoxazole on a riverine microbiome.}, journal = {Water research}, volume = {201}, number = {}, pages = {117382}, doi = {10.1016/j.watres.2021.117382}, pmid = {34225233}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Genes, Bacterial ; *Microbiota ; Rivers ; *Sulfamethoxazole ; Wastewater ; }, abstract = {The continued emergence of bacterial pathogens presenting antimicrobial resistance is widely recognised as a global health threat and recent attention focused on potential environmental reservoirs of antibiotic resistance genes (ARGs). Freshwater environments such as rivers represent a potential hotspot for ARGs and antibiotic resistant bacteria as they are receiving systems for effluent discharges from wastewater treatment plants (WWTPs). Effluent also contains low levels of different antimicrobials including antibiotics and biocides. Sulfonamides are antibacterial chemicals widely used in clinical, veterinary and agricultural settings and are frequently detected in sewage sludge and manure in addition to riverine ecosystems. The impact of such exposure on ARG prevalence and diversity is unknown, so the aim of this study was to investigate the release of a sub-lethal concentration of the sulfonamide compound sulfamethoxazole (SMX) on the river bacterial microbiome using a flume system. This system was a semi-natural in vitro flume using river water (30 L) and sediment (6 kg) with circulation to mimic river flow. A combination of 'omics' approaches were conducted to study the impact of SMX exposure on the microbiomes within the flumes. Metagenomic analysis showed that the addition of low concentrations of SMX (<4 μg L[-1]) had a limited effect on the bacterial resistome in the water fraction only, with no impact observed in the sediment. Metaproteomics did not show differences in ARGs expression with SMX exposure in water. Overall, the river bacterial community was resilient to short term exposure to sub-lethal concentrations of SMX which mimics the exposure such communities experience downstream of WWTPs throughout the year.}, } @article {pmid34223947, year = {2022}, author = {Jiao, L and Kourkoumpetis, T and Hutchinson, D and Ajami, NJ and Hoffman, K and White, DL and Graham, DY and Hair, C and Shah, R and Kanwal, F and Jarbrink-Sehgal, M and Husain, N and Hernaez, R and Hou, J and Cole, R and Velez, M and Ketwaroo, G and Kramer, J and El-Serag, HB and Petrosino, JF}, title = {Spatial Characteristics of Colonic Mucosa-Associated Gut Microbiota in Humans.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {811-821}, pmid = {34223947}, issn = {1432-184X}, support = {P30 DK56338/DK/NIDDK NIH HHS/United States ; I01 CX001430/CX/CSRD VA/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; }, mesh = {Adult ; Colon/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Intestinal Mucosa/microbiology ; RNA, Ribosomal, 16S/genetics ; Verrucomicrobia/genetics ; }, abstract = {Limited data exist on the spatial distribution of the colonic bacteria in humans. We collected the colonic biopsies from five segments of 27 polyp-free adults and collected feces from 13 of them. We sequenced the V4 region of the bacterial 16S rRNA gene using the MiSeq platform. The sequencing data were assigned to the amplicon sequence variant (ASV) using SILVA. Biodiversity and the relative abundance of the ASV were compared across the colonic segments and between the rectal and fecal samples. Bacterial functional capacity was assessed using Tax4fun. Each individual had a unique bacterial community composition (Weighted Bray-Curtis P value = 0.001). There were no significant differences in richness, evenness, community composition, and the taxonomic structure across the colon segments in all the samples. Firmicutes (47%), Bacteroidetes (39%), and Proteobacteria (6%) were the major phyla in all segments, followed by Verrucomicrobia, Fusobacteria, Desulfobacterota, and Actinobacteria. There were 15 genera with relative abundance > 1%, including Bacteroides, Faecalibacterium, Escherichia/Shigella, Sutterella, Akkermansia, Parabacteroides, Prevotella, Lachnoclostridium, Alistipes, Fusobacterium, Erysipelatoclostridium, and four Lachnospiraceae family members. Intra-individually, the community compositional dissimilarity was the greatest between the cecum and the rectum. There were significant differences in biodiversity and the taxonomic structure between the rectal and fecal bacteria. The bacterial community composition and structure were homogeneous across the large intestine in adults. The inter-individual variability of the bacteria was greater than inter-segment variability. The rectal and fecal bacteria differed in the community composition and structure.}, } @article {pmid34217349, year = {2021}, author = {Liu, X and Chen, Y and Zhang, S and Dong, L}, title = {Gut microbiota-mediated immunomodulation in tumor.}, journal = {Journal of experimental & clinical cancer research : CR}, volume = {40}, number = {1}, pages = {221}, pmid = {34217349}, issn = {1756-9966}, support = {81900482//National Natural Science Foundation of China/ ; 2018ZSLC09//Zhongshan Hospital/ ; }, mesh = {Gastrointestinal Microbiome/*drug effects ; Humans ; Immunomodulation/*immunology ; Neoplasms/*drug therapy ; }, abstract = {Tumor immunity consists of various types of cells, which serve an important role in antitumor therapy. The gastrointestinal tract is colonized by trillions of microorganisms, which form the gut microbiota. In addition to pathogen defense and maintaining the intestinal ecosystem, gut microbiota also plays a pivotal role in various physiological processes. Recently, the association between these symbionts and cancer, ranging from oncogenesis and cancer progression to resistance or sensitivity to antitumor therapies, has attracted much attention. Metagenome analysis revealed a significant difference between the gut microbial composition of cancer patients and healthy individuals. Moreover, modulation of microbiome could improve therapeutic response to immune checkpoint inhibitors (ICIs). These findings suggest that microbiome is involved in cancer pathogenesis and progression through regulation of tumor immunosurveillance, although the exact mechanisms remain largely unknown. This review focuses on the interaction between the microbiome and tumor immunity, with in-depth discussion regarding the therapeutic potential of modulating gut microbiota in ICIs. Further investigations are warranted before gut microbiota can be introduced into clinical practice.}, } @article {pmid34217274, year = {2021}, author = {Kakuk, B and Wirth, R and Maróti, G and Szuhaj, M and Rakhely, G and Laczi, K and Kovács, KL and Bagi, Z}, title = {Early response of methanogenic archaea to H2 as evaluated by metagenomics and metatranscriptomics.}, journal = {Microbial cell factories}, volume = {20}, number = {1}, pages = {127}, pmid = {34217274}, issn = {1475-2859}, support = {FK123902//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; PD132145//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; FK123899//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; GINOP- 2.2.1-15-2017-00081//Nemzeti Kutatási és Technológiai Hivatal/ ; EFOP- 3.6.2-16-2017-00010//Nemzeti Kutatási és Technológiai Hivatal/ ; 2020-1.1.2-PIACI-KFI-2020-00117//Nemzeti Kutatási és Technológiai Hivatal/ ; LP2020-5/2020//Magyar Tudományos Akadémia/ ; 2020-3.1.2.-ZFR-KVG-2020-00009//nemzeti kutatási és technológiai hivatal/ ; }, mesh = {Anaerobiosis ; Bacteria/genetics/metabolism ; Carbon Dioxide/metabolism ; Fermentation ; Gene Expression Regulation, Archaeal ; Genome, Archaeal ; Hydrogen/*metabolism ; Metagenome ; Metagenomics ; Methane/*biosynthesis ; Methanomicrobiaceae/genetics/*metabolism ; Methanosarcina/genetics/*metabolism ; Microbiota ; *Transcriptome ; }, abstract = {BACKGROUND: The molecular machinery of the complex microbiological cell factory of biomethane production is not fully understood. One of the process control elements is the regulatory role of hydrogen (H2). Reduction of carbon dioxide (CO2) by H2 is rate limiting factor in methanogenesis, but the community intends to keep H2 concentration low in order to maintain the redox balance of the overall system. H2 metabolism in methanogens becomes increasingly important in the Power-to-Gas renewable energy conversion and storage technologies.

RESULTS: The early response of the mixed mesophilic microbial community to H2 gas injection was investigated with the goal of uncovering the first responses of the microbial community in the CH4 formation and CO2 mitigation Power-to-Gas process. The overall microbial composition changes, following a 10 min excessive bubbling of H2 through the reactor, was investigated via metagenome and metatranscriptome sequencing. The overall composition and taxonomic abundance of the biogas producing anaerobic community did not change appreciably 2 hours after the H2 treatment, indicating that this time period was too short to display differences in the proliferation of the members of the microbial community. There was, however, a substantial increase in the expression of genes related to hydrogenotrophic methanogenesis of certain groups of Archaea. As an early response to H2 exposure the activity of the hydrogenotrophic methanogenesis in the genus Methanoculleus was upregulated but the hydrogenotrophic pathway in genus Methanosarcina was downregulated. The RT-qPCR data corroborated the metatranscriptomic RESULTS: H2 injection also altered the metabolism of a number of microbes belonging in the kingdom Bacteria. Many Bacteria possess the enzyme sets for the Wood-Ljungdahl pathway. These and the homoacetogens are partners for syntrophic community interactions between the distinct kingdoms of Archaea and Bacteria.

CONCLUSIONS: External H2 regulates the functional activity of certain Bacteria and Archaea. The syntrophic cross-kingdom interactions in H2 metabolism are important for the efficient operation of the Power-to-Gas process. Therefore, mixed communities are recommended for the large scale Power-to-Gas process rather than single hydrogenotrophic methanogen strains. Fast and reproducible response from the microbial community can be exploited in turn-off and turn-on of the Power-to-Gas microbial cell factories.}, } @article {pmid34216067, year = {2021}, author = {Kwon, MJ and Tripathi, BM and Göckede, M and Shin, SC and Myeong, NR and Lee, YK and Kim, M}, title = {Disproportionate microbial responses to decadal drainage on a Siberian floodplain.}, journal = {Global change biology}, volume = {27}, number = {20}, pages = {5124-5140}, doi = {10.1111/gcb.15785}, pmid = {34216067}, issn = {1365-2486}, mesh = {Carbon Cycle ; Carbon Dioxide/analysis ; Methane ; *Microbiota ; *Permafrost ; Soil ; }, abstract = {Permafrost thaw induces soil hydrological changes which in turn affects carbon cycle processes in the Arctic terrestrial ecosystems. However, hydrological impacts of thawing permafrost on microbial processes and greenhouse gas (GHG) dynamics are poorly understood. This study examined changes in microbial communities using gene and genome-centric metagenomics on an Arctic floodplain subject to decadal drainage, and linked them to CO2 and CH4 flux and soil chemistry. Decadal drainage led to significant changes in the abundance, taxonomy, and functional potential of microbial communities, and these modifications well explained the changes in CO2 and CH4 fluxes between ecosystem and atmosphere-increased fungal abundances potentially increased net CO2 emission rates and highly reduced CH4 emissions in drained sites corroborated the marked decrease in the abundance of methanogens and methanotrophs. Interestingly, various microbial taxa disproportionately responded to drainage: Methanoregula, one of the key players in methanogenesis under saturated conditions, almost disappeared, and also Methylococcales methanotrophs were markedly reduced in response to drainage. Seven novel methanogen population genomes were recovered, and the metabolic reconstruction of highly correlated population genomes revealed novel syntrophic relationships between methanogenic archaea and syntrophic partners. These results provide a mechanistic view of microbial processes regulating GHG dynamics in the terrestrial carbon cycle, and disproportionate microbial responses to long-term drainage provide key information for understanding the effects of warming-induced soil drying on microbial processes in Arctic wetland ecosystems.}, } @article {pmid34215422, year = {2021}, author = {Kothe, CI and Bolotin, A and Kraïem, BF and Dridi, B and , and Renault, P}, title = {Unraveling the world of halophilic and halotolerant bacteria in cheese by combining cultural, genomic and metagenomic approaches.}, journal = {International journal of food microbiology}, volume = {358}, number = {}, pages = {109312}, doi = {10.1016/j.ijfoodmicro.2021.109312}, pmid = {34215422}, issn = {1879-3460}, mesh = {Animals ; Bacteria/genetics ; Brevibacterium ; Cattle ; *Cheese/analysis ; Metagenome ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Staphylococcus ; }, abstract = {Halophilic/halotolerant bacteria are generally assumed to live in natural environments, although they may also be found in foods such as cheese and seafood. These salt-loving bacteria have been occasionally characterized in cheese, and studies on their ecological and technological functions are still scarce. We therefore selected 13 traditional cheeses to systematically characterize these microorganisms in their rinds via cultural, genomic and metagenomic methods. Using different salt-based media, we identified 35 strains with unique 16S rRNA and rpoB gene sequences, whose whole genome was sequenced. Twenty are Gram-positive species including notably Brevibacterium aurantiacum (6) and Staphylococcus equorum (3), which are also frequently added as starters. ANI and pan-genomic analyses confirm the high genetic diversity of B. aurantiacum and reveal the presence of two subspecies in S. equorum, as well as the genetic proximity of several cheese strains to bovine isolates. Additionally, we isolated 15 Gram-negative strains, potentially defining ten new species of halophilic/halotolerant cheese bacteria, in particular for the genera Halomonas and Psychrobacter. The use of all the genomes sequenced in this study as a reference to complement those existing in the databases allowed us to study the representativeness of 66 species of halophilic/halotolerant bacteria in 74 cheese rind metagenomes. While Gram-positive strains may flourish in the different types of technologies, Gram-negative species are particularly abundant in cheeses with high moisture, such as washed-rind cheeses. Finally, analyses of co-occurrences reveal assemblies, including the frequent coexistence of several species of the same genus, forming moderately complex ecosystems with functional redundancies that probably ensure stable cheese development.}, } @article {pmid34215179, year = {2021}, author = {Lebeaux, RM and Coker, MO and Dade, EF and Palys, TJ and Morrison, HG and Ross, BD and Baker, ER and Karagas, MR and Madan, JC and Hoen, AG}, title = {The infant gut resistome is associated with E. coli and early-life exposures.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {201}, pmid = {34215179}, issn = {1471-2180}, support = {T32 AI007519/AI/NIAID NIH HHS/United States ; P20 ES018175/ES/NIEHS NIH HHS/United States ; P01 ES022832/ES/NIEHS NIH HHS/United States ; P20 GM104416/GM/NIGMS NIH HHS/United States ; R01 LM012723/LM/NLM NIH HHS/United States ; K01 LM011985/LM/NLM NIH HHS/United States ; }, mesh = {Bacteria/*classification/*genetics ; Delivery, Obstetric/statistics & numerical data ; Drug Resistance, Microbial/*genetics ; Environmental Exposure/statistics & numerical data ; Escherichia coli/*physiology ; Feces/microbiology ; Feeding Methods/statistics & numerical data ; Female ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Male ; Metagenomics ; }, abstract = {BACKGROUND: The human gut microbiome harbors a collection of bacterial antimicrobial resistance genes (ARGs) known as the resistome. The factors associated with establishment of the resistome in early life are not well understood. We investigated the early-life exposures and taxonomic signatures associated with resistome development over the first year of life in a large, prospective cohort in the United States. Shotgun metagenomic sequencing was used to profile both microbial composition and ARGs in stool samples collected at 6 weeks and 1 year of age from infants enrolled in the New Hampshire Birth Cohort Study. Negative binomial regression and statistical modeling were used to examine infant factors such as sex, delivery mode, feeding method, gestational age, antibiotic exposure, and infant gut microbiome composition in relation to the diversity and relative abundance of ARGs.

RESULTS: Metagenomic sequencing was performed on paired samples from 195 full term (at least 37 weeks' gestation) and 15 late preterm (33-36 weeks' gestation) infants. 6-week samples compared to 1-year samples had 4.37 times (95% CI: 3.54-5.39) the rate of harboring ARGs. The majority of ARGs that were at a greater relative abundance at 6 weeks (chi-squared p < 0.01) worked through the mechanism of antibiotic efflux. The overall relative abundance of the resistome was strongly correlated with Proteobacteria (Spearman correlation = 78.9%) and specifically Escherichia coli (62.2%) relative abundance in the gut microbiome. Among infant characteristics, delivery mode was most strongly associated with the diversity and relative abundance of ARGs. Infants born via cesarean delivery had a trend towards a higher risk of harboring unique ARGs [relative risk = 1.12 (95% CI: 0.97-1.29)] as well as having an increased risk for overall ARG relative abundance [relative risk = 1.43 (95% CI: 1.12-1.84)] at 1 year compared to infants born vaginally.

CONCLUSIONS: Our findings suggest that the developing infant gut resistome may be alterable by early-life exposures. Establishing the extent to which infant characteristics and early-life exposures impact the resistome can ultimately lead to interventions that decrease the transmission of ARGs and thus the risk of antibiotic resistant infections.}, } @article {pmid34213321, year = {2021}, author = {Nguyen, NA and Lin, Z and Mohanty, I and Garg, N and Schmidt, EW and Agarwal, V}, title = {An Obligate Peptidyl Brominase Underlies the Discovery of Highly Distributed Biosynthetic Gene Clusters in Marine Sponge Microbiomes.}, journal = {Journal of the American Chemical Society}, volume = {143}, number = {27}, pages = {10221-10231}, pmid = {34213321}, issn = {1520-5126}, support = {R35 GM122521/GM/NIGMS NIH HHS/United States ; R35 GM142882/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Bacteria/*enzymology ; Biological Products ; Gene Expression Regulation, Bacterial/*physiology ; Gene Expression Regulation, Enzymologic/*physiology ; Metagenome ; Microbiota/*physiology ; Multigene Family ; Porifera/*microbiology ; }, abstract = {Marine sponges are prolific sources of bioactive natural products, several of which are produced by bacteria symbiotically associated with the sponge host. Bacteria-derived natural products, and the specialized bacterial symbionts that synthesize them, are not shared among phylogenetically distant sponge hosts. This is in contrast to nonsymbiotic culturable bacteria in which the conservation of natural products and natural product biosynthetic gene clusters (BGCs) is well established. Here, we demonstrate the widespread conservation of a BGC encoding a cryptic ribosomally synthesized and post-translationally modified peptide (RiPP) in microbiomes of phylogenetically and geographically dispersed sponges from the Pacific and Atlantic oceans. Detection of this BGC was enabled by mining for halogenating enzymes in sponge metagenomes, which, in turn, allowed for the description of a broad-spectrum regiospecific peptidyl tryptophan-6-brominase which possessed no chlorination activity. In addition, we demonstrate the cyclodehydrative installation of azoline heterocycles in proteusin RiPPs. This is the first demonstration of halogenation and cyclodehydration for proteusin RiPPs and the enzymes catalyzing these transformations were found to competently interact with other previously described proteusin substrate peptides. Within a sponge microbiome, many different generalized bacterial taxa harbored this BGC with often more than 50 copies of the BGC detected in individual sponge metagenomes. Moreover, the BGC was found in all sponges queried that possess high diversity microbiomes but it was not detected in other marine invertebrate microbiomes. These data shed light on conservation of cryptic natural product biosynthetic potential in marine sponges that was not detected by traditional natural product-to-BGC (meta)genome mining.}, } @article {pmid34210980, year = {2021}, author = {Wang, J and Zhang, J and Liu, W and Zhang, H and Sun, Z}, title = {Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {55}, pmid = {34210980}, issn = {2055-5008}, mesh = {Computational Biology/methods ; *Gastrointestinal Microbiome ; *Gene Expression Profiling/methods ; Gene Expression Regulation, Bacterial ; Humans ; Lacticaseibacillus casei/*genetics ; *Metagenome ; *Metagenomics/methods ; *Transcriptome ; }, abstract = {Little is known about the replication and dynamic transcription of probiotics during their "passenger" journey in the human GI tract, which has therefore limited the understanding of their probiotic mechanisms. Here, metagenomic and metatranscriptomic sequencing was used to expose the in vivo expression patterns of the probiotic Lactobacillus casei Zhang (LcZ), which was compared with its in vitro growth transcriptomes, as well as the dynamics of the indigenous microbiome response to probiotic consumption. Extraction of the strain-specific reads revealed that replication and transcripts from the ingested LcZ were increased, while those from the resident L. casei strains remained unchanged. Mapping of all sequencing reads to LcZ genome showed that gene expression in vitro and in vivo differed dramatically. Approximately 39% of mRNAs and 45% of sRNAs of LcZ well-expressed were repressed after ingestion into human gut. The expression of ABC transporter genes and amino acid metabolism genes was induced at day 14 of ingestion, and genes for sugar and SCFA metabolism were activated at day 28 of ingestion. Expression of rli28c sRNA with peaked expression during the in vitro stationary phase was also activated in the human gut; this sRNA repressed LcZ growth and lactic acid production in vitro. However, the response of the human gut microbiome to LcZ was limited and heterogeneous. These findings implicate the ingested probiotic has to change its transcription patterns to survive and adapt in the human gut, and the time-dependent activation patterns indicate highly dynamic cross-talk between the probiotic and human gut microbes.}, } @article {pmid34210310, year = {2021}, author = {Kumar, MR and Yeap, SK and Mohamad, NE and Abdullah, JO and Masarudin, MJ and Khalid, M and Leow, ATC and Alitheen, NB}, title = {Metagenomic and phytochemical analyses of kefir water and its subchronic toxicity study in BALB/c mice.}, journal = {BMC complementary medicine and therapies}, volume = {21}, number = {1}, pages = {183}, pmid = {34210310}, issn = {2662-7671}, mesh = {Acetobacter/genetics ; Animals ; Brain/metabolism ; Chromatography, High Pressure Liquid ; Kefir/*microbiology ; Kidney/metabolism ; Lactobacillus/genetics ; Liver/metabolism ; Mass Spectrometry ; *Metagenome ; Mice, Inbred BALB C ; Microbiota ; Nitric Oxide/metabolism ; Oenococcus/genetics ; RNA, Ribosomal, 16S ; Spleen/metabolism ; Superoxide Dismutase/metabolism ; Toxicity Tests, Subchronic ; *Water Microbiology ; Mice ; }, abstract = {BACKGROUND: In recent years, researchers are interested in the discovery of active compounds from traditional remedies and natural sources, as they reveal higher therapeutic efficacies and improved toxicological profiles. Among the various traditional treatments that have been widely studied and explored for their potential therapeutic benefits, kefir, a fermented beverage, demonstrates a broad spectrum of pharmacological properties, including antioxidant, anti-inflammation, and healing activities. These health-promoting properties of kefir vary among the kefir cultures found at the different part of the world as different media and culture conditions are used for kefir maintenance and fermentation.

METHODS: This study investigated the microbial composition and readily found bioactive compounds in water kefir fermented in Malaysia using 16S rRNA microbiome and UHPLC sequencing approaches. The toxicity effects of the kefir water administration in BALB/c mice were analysed based on the mice survival, body weight index, biochemistry profile, and histopathological changes. The antioxidant activities were evaluated using SOD, FRAP, and NO assays.

RESULTS: The 16S rRNA amplicon sequencing revealed the most abundant species found in the water kefir was Lactobacillus hilgardii followed by Lactobacillus harbinensis, Acetobacter lovaniensis, Lactobacillus satsumensis, Acetobacter tropicalis, Lactobacillus zeae, and Oenococcus oeni. The UHPLC screening showed flavonoid and phenolic acid derivatives as the most important bioactive compounds present in kefir water which has been responsible for its antioxidant activities. Subchronic toxicity study showed no toxicological signs, behavioural changes, or adverse effects by administrating 10 mL/kg/day and 2.5 mL/kg/day kefir water to the mice. Antioxidants assays demonstrated enhanced SOD and FRAP activities and reduced NO level, especially in the brain and kidney samples.

CONCLUSIONS: This study will help to intensify the knowledge on the water kefir microbial composition, available phytochemicals and its toxicological and antioxidant effects on BALB/c mice since there are very limited studies on the water kefir grain fermented in Malaysia.}, } @article {pmid34210038, year = {2021}, author = {Olshan, KL and Zomorrodi, AR and Pujolassos, M and Troisi, J and Khan, N and Fanelli, B and Kenyon, V and Fasano, A and Leonard, MM}, title = {Microbiota and Metabolomic Patterns in the Breast Milk of Subjects with Celiac Disease on a Gluten-Free Diet.}, journal = {Nutrients}, volume = {13}, number = {7}, pages = {}, pmid = {34210038}, issn = {2072-6643}, support = {K23 DK122127/DK/NIDDK NIH HHS/United States ; R01 DK104344/DK/NIDDK NIH HHS/United States ; R56 AI156711/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Case-Control Studies ; Celiac Disease/diet therapy/*microbiology ; Cross-Sectional Studies ; *Diet, Gluten-Free ; Female ; Glutens/metabolism ; Humans ; Infant, Newborn ; *Metabolome ; Metabolomics ; Metagenomics ; *Microbiota ; Milk, Human/*microbiology ; Prospective Studies ; }, abstract = {The intestinal microbiome may trigger celiac disease (CD) in individuals with a genetic disposition when exposed to dietary gluten. Research demonstrates that nutrition during infancy is crucial to the intestinal microbiome engraftment. Very few studies to date have focused on the breast milk composition of subjects with a history of CD on a gluten-free diet. Here, we utilize a multi-omics approach with shotgun metagenomics to analyze the breast milk microbiome integrated with metabolome profiling of 36 subjects, 20 with CD on a gluten-free diet and 16 healthy controls. These analyses identified significant differences in bacterial and viral species/strains and functional pathways but no difference in metabolite abundance. Specifically, three bacterial strains with increased abundance were identified in subjects with CD on a gluten-free diet of which one (Rothia mucilaginosa) has been previously linked to autoimmune conditions. We also identified five pathways with increased abundance in subjects with CD on a gluten-free diet. We additionally found four bacterial and two viral species/strains with increased abundance in healthy controls. Overall, the differences observed in bacterial and viral species/strains and in functional pathways observed in our analysis may influence microbiome engraftment in neonates, which may impact their future clinical outcomes.}, } @article {pmid34207804, year = {2021}, author = {Hardouin, P and Chiron, R and Marchandin, H and Armengaud, J and Grenga, L}, title = {Metaproteomics to Decipher CF Host-Microbiota Interactions: Overview, Challenges and Future Perspectives.}, journal = {Genes}, volume = {12}, number = {6}, pages = {}, pmid = {34207804}, issn = {2073-4425}, mesh = {Animals ; Cystic Fibrosis/metabolism/*microbiology ; *Host-Pathogen Interactions ; Humans ; Metagenomics/*methods ; *Microbiota ; Proteome/genetics/metabolism ; Proteomics/*methods ; }, abstract = {Cystic fibrosis (CF) is a hereditary disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, triggering dysfunction of the anion channel in several organs including the lung and gut. The main cause of morbidity and mortality is chronic infection. The microbiota is now included among the additional factors that could contribute to the exacerbation of patient symptoms, to treatment outcome, and more generally to the phenotypic variability observed in CF patients. In recent years, various omics tools have started to shed new light on microbial communities associated with CF and host-microbiota interactions. In this context, proteomics targets the key effectors of the responses from organisms, and thus their phenotypes. Recent advances are promising in terms of gaining insights into the CF microbiota and its relation with the host. This review provides an overview of the contributions made by proteomics and metaproteomics to our knowledge of the complex host-microbiota partnership in CF. Considering the strengths and weaknesses of proteomics-based approaches in profiling the microbiota in the context of other diseases, we illustrate their potential and discuss possible strategies to overcome their limitations in monitoring both the respiratory and intestinal microbiota in sample from patients with CF.}, } @article {pmid34207047, year = {2021}, author = {Saad, N and Olmstead, JW and Varsani, A and Polston, JE and Jones, JB and Folimonova, SY and Harmon, PF}, title = {Discovery of Known and Novel Viruses in Wild and Cultivated Blueberry in Florida through Viral Metagenomic Approaches.}, journal = {Viruses}, volume = {13}, number = {6}, pages = {}, pmid = {34207047}, issn = {1999-4915}, mesh = {Blueberry Plants/*virology ; Florida ; Fruit/virology ; *Metagenome ; Metagenomics/*methods ; Plant Viruses/classification/*genetics/*isolation & purification ; *Virome ; }, abstract = {Southern highbush blueberry (interspecific hybrids of Vaccinium corymbosum L.) is cultivated near wild V. corymbosum as well as closely related species in Florida, USA. The expansion of blueberry cultivation into new areas in Florida and deployment of new cultivars containing viruses can potentially increase the diversity of viruses in wild and cultivated V. corymbosum. In this study, viral diversity in wild and cultivated blueberries (V. corymbosum) is described using a metagenomic approach. RNA viromes from V. corymbosum plants collected from six locations (two cultivated and four wild) in North Central Florida were generated by high throughput sequencing (HTS) and analyzed using a bioinformatic analysis pipeline. De novo assembled contigs obtained from viromes of both commercial and wild sites produced sequences with similarities to plant virus species from a diverse range of families (Amalgaviridae, Caulimoviridae, Endornaviridae, Ophioviridae, Phenuiviridae, and Virgaviridae). In addition, this study has enabled the identification of blueberry latent virus (BlLV) and blueberry mosaic associated ophiovirus (BlMaV) for the first time in Florida, as well as a tentative novel tepovirus (blueberry virus T) (BlVT) in blueberry. To the best of our knowledge, this is the first study that compares viral diversity in wild and cultivated blueberry using a metagenomic approach.}, } @article {pmid34205981, year = {2021}, author = {Low, A and Soh, M and Miyake, S and Aw, VZJ and Feng, J and Wong, A and Seedorf, H}, title = {Longitudinal Changes in Diet Cause Repeatable and Largely Reversible Shifts in Gut Microbial Communities of Laboratory Mice and Are Observed across Segments of the Entire Intestinal Tract.}, journal = {International journal of molecular sciences}, volume = {22}, number = {11}, pages = {}, pmid = {34205981}, issn = {1422-0067}, mesh = {Animals ; Bacteroidetes/genetics/isolation & purification ; Diet, Western/adverse effects ; Feces/microbiology ; Firmicutes/genetics/isolation & purification ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; Mice ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Dietary changes are known to alter the composition of the gut microbiome. However, it is less understood how repeatable and reversible these changes are and how diet switches affect the microbiota in the various segments of the gastrointestinal tract. Here, a treatment group of conventionally raised laboratory mice is subjected to two periods of western diet (WD) interrupted by a period of standard diet (SD) of the same duration. Beta-diversity analyses show that diet-induced microbiota changes are largely reversible (q = 0.1501; PERMANOVA, weighted-UniFrac comparison of the treatment-SD group to the control-SD group) and repeatable (q = 0.032; PERMANOVA, weighted-UniFrac comparison of both WD treatments). Furthermore, we report that diet switches alter the gut microbiota composition along the length of the intestinal tract in a segment-specific manner, leading to gut segment-specific Firmicutes/Bacteroidota ratios. We identified prevalent and distinct Amplicon Sequencing Variants (ASVs), particularly in genera of the recently described Muribaculaceae, along the gut as well as ASVs that are differentially abundant between segments of treatment and control groups. Overall, this study provides insights into the reversibility of diet-induced microbiota changes and highlights the importance of expanding sampling efforts beyond the collections of fecal samples to characterize diet-dependent and segment-specific microbiome differences.}, } @article {pmid34204939, year = {2021}, author = {Zampieri, A and Babbucci, M and Carraro, L and Milan, M and Fasolato, L and Cardazzo, B}, title = {Combining Culture-Dependent and Culture-Independent Methods: New Methodology Insight on the Vibrio Community of Ruditapes philippinarum.}, journal = {Foods (Basel, Switzerland)}, volume = {10}, number = {6}, pages = {}, pmid = {34204939}, issn = {2304-8158}, support = {C26C18000030004//Dipartimenti di Eccellenza/ ; CARD_SID18_01//Department of Comparative Biomedicine and Food Science/ ; ID 10062983//PORFESR/ ; }, abstract = {Vibrios represent a natural contaminant of seafood products. V. alginolyticus, V. cholerae, V. parahaemolyticus and V. vulnificus are the most hazardous species to human health. Given the worldwide consumption of mollusc products, reliable detection of Vibrio species is recommended to prevent human vibriosis. In this study, culture-dependent and -independent methods were compared and integrated to implement knowledge of the Manila clam Vibrio community composition. Here, 16S and recA-pyrH metabarcoding were applied to compare the microbial communities of homogenate clam samples (culture-independent method) and their culture-derived samples plated on three different media (culture-dependent method). In addition, a subset of plated clam samples was investigated using shotgun metagenomics. Homogenate metabarcoding characterized the most abundant taxa (16S) and Vibrio species (recA-pyrH). Culture-dependent metabarcoding detected the cultivable taxa, including rare species. Moreover, marine agar medium was found to be a useful substrate for the recovery of several Vibrio species, including the main human pathogenic ones. The culture-dependent shotgun metagenomics detected all the main human pathogenic Vibrio species and a higher number of vibrios with respect to the recA-pyrH metabarcoding. The study revealed that integration of culture-dependent and culture-independent methods might be a valid approach for the characterization of Vibrio biodiversity.}, } @article {pmid34202675, year = {2021}, author = {Jo, Y and Back, CG and Kim, KH and Chu, H and Lee, JH and Moh, SH and Cho, WK}, title = {Using RNA-Sequencing Data to Examine Tissue-Specific Garlic Microbiomes.}, journal = {International journal of molecular sciences}, volume = {22}, number = {13}, pages = {}, pmid = {34202675}, issn = {1422-0067}, support = {120085-3//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/ ; NRF-2018R1D1A1B07043597//National Research Foundation of Korea/ ; }, mesh = {Bacteria/classification/genetics ; Computational Biology/methods ; Garlic/*microbiology ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Organ Specificity ; Phylogeny ; Sequence Analysis, RNA ; }, abstract = {Garlic (Allium sativum) is a perennial bulbous plant. Due to its clonal propagation, various diseases threaten the yield and quality of garlic. In this study, we conducted in silico analysis to identify microorganisms, bacteria, fungi, and viruses in six different tissues using garlic RNA-sequencing data. The number of identified microbial species was the highest in inflorescences, followed by flowers and bulb cloves. With the Kraken2 tool, 57% of identified microbial reads were assigned to bacteria and 41% were assigned to viruses. Fungi only made up 1% of microbial reads. At the species level, Streptomyces lividans was the most dominant bacteria while Fusarium pseudograminearum was the most abundant fungi. Several allexiviruses were identified. Of them, the most abundant virus was garlic virus C followed by shallot virus X. We obtained a total of 14 viral genome sequences for four allexiviruses. As we expected, the microbial community varied depending on the tissue types, although there was a dominant microorganism in each tissue. In addition, we found that Kraken2 was a very powerful and efficient tool for the bacteria using RNA-sequencing data with some limitations for virome study.}, } @article {pmid34202141, year = {2021}, author = {Yuan, X and Zhang, X and Liu, X and Dong, Y and Yan, Z and Lv, D and Wang, P and Li, Y}, title = {Comparison of Gut Bacterial Communities of Grapholita molesta (Lepidoptera: Tortricidae) Reared on Different Host Plants.}, journal = {International journal of molecular sciences}, volume = {22}, number = {13}, pages = {}, pmid = {34202141}, issn = {1422-0067}, support = {31871971//National Natural Science Foundation of China/ ; 31772503//National Natural Science Foundation of China/ ; }, mesh = {Analysis of Variance ; Animals ; Computational Biology/methods ; *Gastrointestinal Microbiome ; Host-Parasite Interactions ; Lepidoptera/*microbiology ; Metagenomics/methods ; Plants/parasitology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Intestinal symbiotic bacteria have played an important role in the digestion, immunity detoxification, mating, and reproduction of insects during long-term coevolution. The oriental fruit moth, Grapholita molesta, is an important fruit tree pest worldwide. However, the composition of the G. molesta microbial community, especially of the gut microbiome, remains unclear. To explore the differences of gut microbiota of G. molesta when reared on different host plants, we determined the gut bacterial structure when G. molesta was transferred from an artificial diet to different host plants (apples, peaches, nectarines, crisp pears, plums, peach shoots) by amplicon sequencing technology. The results showed that Proteobacteria and Firmicutes are dominant in the gut microbiota of G. molesta. Plum-feeding G. molesta had the highest richness and diversity of gut microbiota, while apple-feeding G. molesta had the lowest. PCoA and PERMANOVA analysis revealed that there were significant differences in the gut microbiota structure of G. molesta on different diets. PICRUSt2 analysis indicated that most of the functional prediction pathways were concentrated in metabolic and cellular processes. Our results confirmed that gut bacterial communities of G. molesta can be influenced by host diets and may play an important role in host adaptation.}, } @article {pmid34201731, year = {2021}, author = {Bona, E and Massa, N and Toumatia, O and Novello, G and Cesaro, P and Todeschini, V and Boatti, L and Mignone, F and Titouah, H and Zitouni, A and Lingua, G and Vuolo, F and Gamalero, E}, title = {Climatic Zone and Soil Properties Determine the Biodiversity of the Soil Bacterial Communities Associated to Native Plants from Desert Areas of North-Central Algeria.}, journal = {Microorganisms}, volume = {9}, number = {7}, pages = {}, pmid = {34201731}, issn = {2076-2607}, abstract = {Algeria is the largest country in Africa characterized by semi-arid and arid sites, located in the North, and hypersaline zones in the center and South of the country. Several autochthonous plants are well known as medicinal plants, having in common tolerance to aridity, drought and salinity. In their natural environment, they live with a great amount of microbial species that altogether are indicated as plant microbiota, while the plants are now viewed as a "holobiont". In this work, the microbiota of the soil associated to the roots of fourteen economically relevant autochthonous plants from Algeria have been characterized by an innovative metagenomic approach with a dual purpose: (i) to deepen the knowledge of the arid and semi-arid environment and (ii) to characterize the composition of bacterial communities associated with indigenous plants with a strong economic/commercial interest, in order to make possible the improvement of their cultivation. The results presented in this work highlighted specific signatures which are mainly determined by climatic zone and soil properties more than by the plant species.}, } @article {pmid34201311, year = {2021}, author = {Šulčius, S and Alzbutas, G and Juknevičiūtė, V and Šimoliūnas, E and Venckus, P and Šimoliūnienė, M and Paškauskas, R}, title = {Exploring Viral Diversity in a Gypsum Karst Lake Ecosystem Using Targeted Single-Cell Genomics.}, journal = {Genes}, volume = {12}, number = {6}, pages = {}, pmid = {34201311}, issn = {2073-4425}, mesh = {Bacterial Proteins/genetics/metabolism ; Bacteriophages/*genetics/isolation & purification/pathogenicity ; Calcium Sulfate/analysis/metabolism ; Chlorobium/genetics/metabolism/*virology ; Genomics/methods ; Host-Pathogen Interactions ; Lakes/chemistry/*microbiology/virology ; Metagenome ; Single-Cell Analysis/methods ; Sulfur/metabolism ; *Virome ; }, abstract = {Little is known about the diversity and distribution of viruses infecting green sulfur bacteria (GSB) thriving in euxinic (sulfuric and anoxic) habitats, including gypsum karst lake ecosystems. In this study, we used targeted cell sorting combined with single-cell sequencing to gain insights into the gene content and genomic potential of viruses infecting sulfur-oxidizing bacteria Chlorobium clathratiforme, obtained from water samples collected during summer stratification in gypsum karst Lake Kirkilai (Lithuania). In total, 82 viral contigs were bioinformatically identified in 62 single amplified genomes (SAGs) of C. clathratiforme. The majority of viral gene and protein sequences showed little to no similarity with phage sequences in public databases, uncovering the vast diversity of previously undescribed GSB viruses. We observed a high level of lysogenization in the C. clathratiforme population, as 87% SAGs contained intact prophages. Among the thirty identified auxiliary metabolic genes (AMGs), two, thiosulfate sulfurtransferase (TST) and thioredoxin-dependent phosphoadenosine phosphosulfate (PAPS) reductase (cysH), were found to be involved in the oxidation of inorganic sulfur compounds, suggesting that viruses can influence the metabolism and cycling of this essential element. Finally, the analysis of CRISPR spacers retrieved from the consensus C. clathratiforme genome imply persistent and active virus-host interactions for several putative phages prevalent among C. clathratiforme SAGs. Overall, this study provides a glimpse into the diversity of phages associated with naturally occurring and highly abundant sulfur-oxidizing bacteria.}, } @article {pmid34199047, year = {2021}, author = {Pérez-Burillo, S and Hinojosa-Nogueira, D and Navajas-Porras, B and Blasco, T and Balzerani, F and Lerma-Aguilera, A and León, D and Pastoriza, S and Apaolaza, I and Planes, FJ and Francino, MP and Rufián-Henares, JÁ}, title = {Effect of Freezing on Gut Microbiota Composition and Functionality for In Vitro Fermentation Experiments.}, journal = {Nutrients}, volume = {13}, number = {7}, pages = {}, pmid = {34199047}, issn = {2072-6643}, support = {816303 (Stance4Health)//Research Executive Agency/ ; "Plan propio de Investigación y Transferencia" of the University of Granada under both programs "Intensificación de la Investigación, modalidad B"//Universidad de Granada/ ; "Plan propio de Investigación y Transferencia" of the University of Granada under the postdoctoral program "Perfeccionamiento de Doctores"//Universidad de Granada/ ; }, mesh = {Animals ; Cattle ; Child ; Feces/microbiology ; *Fermentation ; Food Storage ; *Freezing ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Microbiota ; Milk ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The gut microbiota has a profound effect on human health and is modulated by food and bioactive compounds. To study such interaction, in vitro batch fermentations are performed with fecal material, and some experimental designs may require that such fermentations be performed with previously frozen stools. Although it is known that freezing fecal material does not alter the composition of the microbial community in 16S rRNA gene amplicon and metagenomic sequencing studies, it is not known whether the microbial community in frozen samples could still be used for in vitro fermentations. To explore this, we undertook a pilot study in which in vitro fermentations were performed with fecal material from celiac, cow's milk allergic, obese, or lean children that was frozen (or not) with 20% glycerol. Before fermentation, the fecal material was incubated in a nutritious medium for 6 days, with the aim of giving the microbial community time to recover from the effects of freezing. An aliquot was taken daily from the stabilization vessel and used for the in vitro batch fermentation of lentils. The microbial community structure was significantly different between fresh and frozen samples, but the variation introduced by freezing a sample was always smaller than the variation among individuals, both before and after fermentation. Moreover, the potential functionality (as determined in silico by a genome-scaled metabolic reconstruction) did not differ significantly, possibly due to functional redundancy. The most affected genus was Bacteroides, a fiber degrader. In conclusion, if frozen fecal material is to be used for in vitro fermentation purposes, our preliminary analyses indicate that the functionality of microbial communities can be preserved after stabilization.}, } @article {pmid34198297, year = {2021}, author = {Miyake, T and Mori, H and Yasukawa, D and Hexun, Z and Maehira, H and Ueki, T and Kojima, M and Kaida, S and Iida, H and Shimizu, T and Ohno, M and Andoh, A and Tani, M}, title = {The Comparison of Fecal Microbiota in Left-Side and Right-Side Human Colorectal Cancer.}, journal = {European surgical research. Europaische chirurgische Forschung. Recherches chirurgicales europeennes}, volume = {62}, number = {4}, pages = {248-254}, doi = {10.1159/000516922}, pmid = {34198297}, issn = {1421-9921}, mesh = {*Colorectal Neoplasms/microbiology/pathology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/genetics ; }, abstract = {INTRODUCTION: Microbiomes play a vital role in the development and progression of cancer. The clinical status, including prognosis, genetic mutations, and sensitivity to chemotherapy, differs depending on the location of colorectal cancer (CRC); however, the association between gut microbiota and the location of CRC is not entirely understood. This study was conducted to evaluate the differences in the gut microbiota in patients with CRC according to the location of the tumor.

METHODS: Fifty-six patients who underwent surgery for CRC between August 2018 and November 2019 were included in the study. Three patients who had received neoadjuvant therapy or antibiotic treatment within 1 month before surgery were excluded. The metagenomes of microbiota in preoperative feces were assessed using the V3-V4 region of 16s rRNA amplicon sequences.

RESULTS: The beta diversity of the Bray-Curtis distance was significantly higher in left-sided than in right-sided CRC. Fusobacterium predominated in left-sided CRC according to the linear discriminant analysis effect size method. Blautia, Eryspelotrichales, Holdemanella, Faecalibacterium, Subdoligranulum, and Dorea constituted the dominant intestinal flora in right-sided CRC. Pathway analysis revealed that L-lysine fermentation and cob(II)yrinate a,c-diamide biosynthesis I were predominant in left-sided CRC.

DISCUSSION: This study demonstrated that fecal microbiota in left-sided CRC constitutionally and functionally differ from those in right-side CRC. These results will help to elucidate the biological differences according to tumor location and develop treatments for human CRC.}, } @article {pmid34198177, year = {2021}, author = {Uke, A and Nakazono-Nagaoka, E and Chuah, JA and Zain, NA and Amir, HG and Sudesh, K and Abidin, NZHAZ and Hashim, Z and Kosugi, A}, title = {Effect of decomposing oil palm trunk fibers on plant growth and soil microbial community composition.}, journal = {Journal of environmental management}, volume = {295}, number = {}, pages = {113050}, doi = {10.1016/j.jenvman.2021.113050}, pmid = {34198177}, issn = {1095-8630}, mesh = {Biomass ; Humans ; *Microbiota ; *Saccharum ; Soil ; Soil Microbiology ; *Trichoderma ; }, abstract = {Oil palm trunks (OPT) are logged for replantation and the fiber residues are disposed of into the palm plantation area. The fiber residues are expected to increase soil fertility through recycling of carbon and minerals via fiber decomposition. This study investigated the effects of OPT fiber disposal and other lignocellulosic biomass on plant growth and microbial diversity in the soil environment. Four treatment plots were tested: (A) soil+OPT fiber (1:20), (B) soil+sugarcane bagasse (1:20), (C) soil+cellulose powder (1:20), and (D) unamended soil as a negative control. Low plant height, decreased chlorophyll content, and low biomass was observed in corn grown on soil mixed with OPT fiber, cellulose, and sugarcane bagasse, when compared with those of the control. The plants grown with OPT fiber were deficient in total nitrogen and magnesium when compared with those without fiber amendment, which suggested that nitrogen and minerals in soil might be taken up by changing microflora because of the OPT fibers presence. To confirm differences in the soil microflora, metagenomics analysis was performed on untreated soil and soil from each lignocellulose treatment. The microflora of soils mixed with OPT fiber, cellulose and sugarcane bagasse revealed substantial increases in bacteria such as families Cytophagaceae and Oscillospiraceae, and two major fungal genera, Trichoderma and Trichocladium, that are involved in lignocellulose degradation. OPT fiber resulted in a drastic increase in the ratios and amounts of Trichocladium in the soil when compared with those of cellulose and sugarcane bagasse. These results indicate that unregulated disposal of OPT fiber into plantation areas could result in nutrient loss from soil by increasing the abundance of microorganisms involved in lignocellulose decomposition.}, } @article {pmid34193290, year = {2021}, author = {Huang, S and Jiang, S and Huo, D and Allaband, C and Estaki, M and Cantu, V and Belda-Ferre, P and Vázquez-Baeza, Y and Zhu, Q and Ma, C and Li, C and Zarrinpar, A and Liu, YY and Knight, R and Zhang, J}, title = {Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {151}, pmid = {34193290}, issn = {2049-2618}, support = {R01 HL148801/HL/NHLBI NIH HHS/United States ; K08 DK102902/NH/NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R21 MH117780/MH/NIMH NIH HHS/United States ; RF1 AG067744/AG/NIA NIH HHS/United States ; T32 OD017863/OD/NIH HHS/United States ; R01 AI141529/AI/NIAID NIH HHS/United States ; DP1-AT010885/AT/NCCIH NIH HHS/United States ; R03 DK114536/DK/NIDDK NIH HHS/United States ; R01 HD093761/HD/NICHD NIH HHS/United States ; K08 DK102902/DK/NIDDK NIH HHS/United States ; U19 AI095219/AI/NIAID NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; P30 DK063491/DK/NIDDK NIH HHS/United States ; 31701577//National Natural Science Foundation of China/ ; T32 GM127235/GM/NIGMS NIH HHS/United States ; P30 DK120515, P30 DK063491, and UL1 TR001442/DK/NIDDK NIH HHS/United States ; UH3 OD023268/OD/NIH HHS/United States ; R01AI141529, R01HD093761, R01AG067744/NH/NIH HHS/United States ; }, mesh = {Animals ; Bifidobacterium ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Microbiota ; *Probiotics ; Zebrafish ; }, abstract = {BACKGROUND: Improving probiotic engraftment in the human gut requires a thorough understanding of the in vivo adaptive strategies of probiotics in diverse contexts. However, for most probiotic strains, these in vivo genetic processes are still poorly characterized. Here, we investigated the effects of gut selection pressures from human, mice, and zebrafish on the genetic stability of a candidate probiotic Lactiplantibacillus plantarum HNU082 (Lp082) as well as its ecological and evolutionary impacts on the indigenous gut microbiota using shotgun metagenomic sequencing in combination with isolate resequencing methods.

RESULTS: We combined both metagenomics and isolate whole genome sequencing approaches to systematically study the gut-adaptive evolution of probiotic L. plantarum and the ecological and evolutionary changes of resident gut microbiomes in response to probiotic ingestion in multiple host species. Independent of host model, Lp082 colonized and adapted to the gut by acquiring highly consistent single-nucleotide mutations, which primarily modulated carbohydrate utilization and acid tolerance. We cultivated the probiotic mutants and validated that these gut-adapted mutations were genetically stable for at least 3 months and improved their fitness in vitro. In turn, resident gut microbial strains, especially competing strains with Lp082 (e.g., Bacteroides spp. and Bifidobacterium spp.), actively responded to Lp082 engraftment by accumulating 10-70 times more evolutionary changes than usual. Human gut microbiota exhibited a higher ecological and genetic stability than that of mice.

CONCLUSIONS: Collectively, our results suggest a highly convergent adaptation strategy of Lp082 across three different host environments. In contrast, the evolutionary changes within the resident gut microbes in response to Lp082 were more divergent and host-specific; however, these changes were not associated with any adverse outcomes. This work lays a theoretical foundation for leveraging animal models for ex vivo engineering of probiotics to improve engraftment outcomes in humans. Video abstract.}, } @article {pmid34192775, year = {2022}, author = {Vadaq, N and Schirmer, M and Tunjungputri, RN and Vlamakis, H and Chiriac, C and Ardiansyah, E and Gasem, MH and Joosten, LAB and de Groot, PG and Xavier, RJ and Netea, MG and van der Ven, AJ and de Mast, Q}, title = {Untargeted Plasma Metabolomics and Gut Microbiome Profiling Provide Novel Insights into the Regulation of Platelet Reactivity in Healthy Individuals.}, journal = {Thrombosis and haemostasis}, volume = {122}, number = {4}, pages = {529-539}, doi = {10.1055/a-1541-3706}, pmid = {34192775}, issn = {2567-689X}, mesh = {Adult ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Metabolome ; Metabolomics/methods ; Plasma ; }, abstract = {BACKGROUND: Considerable variation exists in platelet reactivity to stimulation among healthy individuals. Various metabolites and metabolic pathways influence platelet reactivity, but a comprehensive overview of these associations is missing. The gut microbiome has a strong influence on the plasma metabolome. Here, we investigated the association of platelet reactivity with results of untargeted plasma metabolomics and gut microbiome profiling.

METHODS: We used data from a cohort of 534 healthy adult Dutch volunteers (the 500 Functional Genomics study). Platelet activation and reactivity were measured by the expression of the alpha-granule protein P-selectin and the binding of fibrinogen to the activated integrin αIIbβ3, both in unstimulated blood and after ex vivo stimulation with platelet agonists. Plasma metabolome was measured using an untargeted metabolic profiling approach by quadrupole time-of-flight mass spectrometry. Gut microbiome data were measured by shotgun metagenomic sequencing from stool samples.

RESULTS: Untargeted metabolomics yielded 1,979 metabolites, of which 422 were identified to play a role in a human metabolic pathway. Overall, 92/422 (21.8%) metabolites were significantly associated with at least one readout of platelet reactivity. The majority of associations involved lipids, especially members of eicosanoids, including prostaglandins and leukotrienes. Dietary-derived polyphenols were also found to inhibit platelet reactivity. Validation of metabolic pathways with functional microbial profiles revealed two overlapping metabolic pathways ("alanine, aspartate, and glutamate metabolism" and "arginine biosynthesis") that were associated with platelet reactivity.

CONCLUSION: This comprehensive overview is an resource for understanding the regulation of platelet reactivity by the plasma metabolome and the possible contribution of the gut microbiota.}, } @article {pmid34192646, year = {2021}, author = {Karadayı, S and Arasoglu, T and Akmayan, İ and Karadayı, B}, title = {Assessment of the exclusion potential of suspects by using microbial signature in sexual assault cases: A scenario-based experimental study.}, journal = {Forensic science international}, volume = {325}, number = {}, pages = {110886}, doi = {10.1016/j.forsciint.2021.110886}, pmid = {34192646}, issn = {1872-6283}, mesh = {Adult ; *Breast ; DNA, Bacterial/genetics ; Female ; Forensic Medicine/methods ; Humans ; Male ; Microbiota ; Middle Aged ; RNA, Ribosomal, 16S ; Saliva/*microbiology ; Sequence Analysis, DNA ; *Sex Offenses ; Skin/*microbiology ; Young Adult ; }, abstract = {Sexual assault offences are one of the most serious crimes committed against a person, typically rank only second to homicide, and represent one of the major challenges in forensic sciences. In some cases of sexual assault, there may be more than one suspect and the analysis of the biological evidence with currently available methods such as human DNA analysis may not yield results. In this study using the designed experimental model (with different experimental scenarios that can be designed), it was aimed to investigate the effectiveness of the microbiome profile for the identification of the offender by comparing the microbiome structures of the suspects' saliva samples with the mixed samples on the victim (saliva transmitted on breast skin) within the first 48 h after a sexual assault. For this purpose, a total of 44 samples was collected from four healthy females and four healthy males aged 20-50 years. Microbiome profiles of 44 samples in four groups containing saliva, breast skin and mixed samples were determined with the IIlumina HiSeq platform. Differentiation between samples were calculated by beta-diversity analysis methods by using QIIME software (v1.80). To compare the differentiation among samples and groups, unweighted UniFrac distance values were applied. Eight dominant microbial genera accounted for 86.15% of the total bacterial population in male saliva samples and were composed of Fusobacterium, Haemophilus, Neisseria, Porphyromonas, Prevotella, Rothia, Streptococcus and Veillonella. These genera constituted 76.72% of the bacterial population in mixed samples, whereas they constituted 34.40% of the bacterial population in the breast skin samples. Results of this study show that bacterial DNA in saliva can be recovered from saliva transmitted breast skin within at least 48 h. In conclusion, it has been found that examination of the microbiota of the saliva transmitted to breast skin of a sexual assault victim as a forensic tool may have the potential to determine the offender of the incident among the suspects or to reduce the number of suspects. Supporting the results of this study with further studies using parameters such as different case models, different body regions, larger time periods and a higher number of participants will be beneficial to draw accurate conclusion of the judicial case.}, } @article {pmid34192637, year = {2021}, author = {Li, P and Li, K and Xu, P and Liu, X and Pu, Y}, title = {Treatment of wastewater with high carbon-to-nitrogen ratio using a waterfall aeration biofilm reactor combined with sequencing batch reactor: Microbial community structure and metabolism analysis.}, journal = {Bioresource technology}, volume = {337}, number = {}, pages = {125450}, doi = {10.1016/j.biortech.2021.125450}, pmid = {34192637}, issn = {1873-2976}, mesh = {Biofilms ; Bioreactors ; Carbon ; Denitrification ; *Microbiota ; Nitrification ; Nitrogen ; RNA, Ribosomal, 16S/genetics ; *Wastewater ; }, abstract = {A low-cost and high-efficiency waterfall aeration biofilm reactor (WABR) combined with a sequencing batch reactor (SBR) was established to treat wastewater with a C/N ratio of 50. Three WABR-SBR systems with different fillers were used. In the stable operation phase, the removal efficiency of chemical oxygen demand was R1 (approximately 99%), R2 (97-99%), and R3 (96-99%); the effluent concentration of NH4[+]-N was 0.5 mg/L without nitrite or nitrate accumulation. High-throughput 16S rRNA sequencing revealed that the dominant phyla in the microbial community structure were Proteobacteria, Bacteroidetes, and Planctomycetes. Quantitative PCR was used to quantify the nitrification and denitrification gene expressions (Nitrobacter, nirS, and nirK) to evaluate the simultaneous nitrification and denitrification processes. Both anammox and denitrifying bacteria were abundant. Metagenomic annotation of genes that revealed the metabolic pathways of carbohydrates, amino acids, and the two dominant enzymes (GH and GT) provide valuable information for microbial ecology analysis.}, } @article {pmid34191855, year = {2021}, author = {Jung, TH and Han, KS}, title = {Imbalanced dietary intake alters the colonic microbial profile in growing rats.}, journal = {PloS one}, volume = {16}, number = {6}, pages = {e0253959}, pmid = {34191855}, issn = {1932-6203}, mesh = {Animals ; Bacteria/genetics/*growth & development ; Colon/*microbiology ; DNA, Bacterial/genetics ; Diet ; *Eating ; Fatty Acids/metabolism ; Immunoglobulins/blood ; Male ; Metagenomics ; Microbiota/genetics ; Rats, Sprague-Dawley ; Sequence Analysis, DNA ; Rats ; }, abstract = {An imbalanced dietary intake is associated with alteration of intestinal ecosystem. We investigated the impact of imbalanced diets on colonic microbiota, concentrations of short chain fatty acid in colonic digesta and serum immunoglobulins (Igs) of growing rats. Compared to the control diet, consuming diets high in fat, sucrose, or processed meat, or low in iron, increased the abundance of the pathogenic bacteria such as Clostridium, Escherichia coli, and Salmonella species, and decreased the beneficial bacteria, like Bifidobacteria, Lactobacillus, Akkermansia, Phascolarctobacterium, Alistipes, and butyrate producing species of bacteria in the colon of growing rats. The heatmap of metagenomics indicated that each group was separated into distinct clusters, and the ID group in particular, showed significantly (P < 0.01) reduced alpha diversity of colonic microbiota in comparison to the control group. All experimental groups showed significantly (P < 0.05 or P < 0.01) decreased concentration of acetate and butyrate in the colonic digesta and lower levels of serum IgG or IgA, compared to the control. These results indicated that the imbalanced dietary intake negatively altered intestinal ecosystem and immunity.}, } @article {pmid34190603, year = {2021}, author = {Castro-Severyn, J and Pardo-Esté, C and Mendez, KN and Fortt, J and Marquez, S and Molina, F and Castro-Nallar, E and Remonsellez, F and Saavedra, CP}, title = {Living to the High Extreme: Unraveling the Composition, Structure, and Functional Insights of Bacterial Communities Thriving in the Arsenic-Rich Salar de Huasco Altiplanic Ecosystem.}, journal = {Microbiology spectrum}, volume = {9}, number = {1}, pages = {e0044421}, pmid = {34190603}, issn = {2165-0497}, mesh = {Arsenic/*metabolism ; Bacteria/classification/genetics/*metabolism ; Biodiversity ; Chile ; DNA, Bacterial ; *Ecosystem ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; }, abstract = {Microbial communities inhabiting extreme environments such as Salar de Huasco (SH) in northern Chile are adapted to thrive while exposed to several abiotic pressures and the presence of toxic elements such as arsenic (As). Hence, we aimed to uncover the role of As in shaping bacterial composition, structure, and functional potential in five different sites in this altiplanic wetland using a shotgun metagenomic approach. The sites exhibit wide gradients of As (9 to 321 mg/kg), and our results showed highly diverse communities and a clear dominance exerted by the Proteobacteria and Bacteroidetes phyla. Functional potential analyses show broadly convergent patterns, contrasting with their great taxonomic variability. As-related metabolism, as well as other functional categories such as those related to the CH4 and S cycles, differs among the five communities. Particularly, we found that the distribution and abundance of As-related genes increase as the As concentration rises. Approximately 75% of the detected genes for As metabolism belong to expulsion mechanisms; arsJ and arsP pumps are related to sites with higher As concentrations and are present almost exclusively in Proteobacteria. Furthermore, taxonomic diversity and functional potential are reflected in the 12 reconstructed high-quality metagenome assembled genomes (MAGs) belonging to the Bacteroidetes (5), Proteobacteria (5), Cyanobacteria (1), and Gemmatimonadetes (1) phyla. We conclude that SH microbial communities are diverse and possess a broad genetic repertoire to thrive under extreme conditions, including increasing concentrations of highly toxic As. Finally, this environment represents a reservoir of unknown and undescribed microorganisms, with great metabolic versatility, which needs further study. IMPORTANCE As microbial communities inhabiting extreme environments are fundamental for maintaining ecosystems, many studies concerning composition, functionality, and interactions have been carried out. However, much is still unknown. Here, we sampled microbial communities in the Salar de Huasco, an extreme environment subjected to several abiotic stresses (high UV radiation, salinity and arsenic; low pressure and temperatures). We found that although microbes are taxonomically diverse, functional potential seems to have an important degree of convergence, suggesting high levels of adaptation. Particularly, arsenic metabolism showed differences associated with increasing concentrations of the metalloid throughout the area, and it effectively exerts a significant pressure over these organisms. Thus, the significance of this research is that we describe highly specialized communities thriving in little-explored environments subjected to several pressures, considered analogous of early Earth and other planets, that have the potential for unraveling technologies to face the repercussions of climate change in many areas of interest.}, } @article {pmid34190385, year = {2021}, author = {Dai, Z and Zang, H and Chen, J and Fu, Y and Wang, X and Liu, H and Shen, C and Wang, J and Kuzyakov, Y and Becker, JN and Hemp, A and Barberán, A and Gunina, A and Chen, H and Luo, Y and Xu, J}, title = {Metagenomic insights into soil microbial communities involved in carbon cycling along an elevation climosequences.}, journal = {Environmental microbiology}, volume = {23}, number = {8}, pages = {4631-4645}, doi = {10.1111/1462-2920.15655}, pmid = {34190385}, issn = {1462-2920}, mesh = {Carbon ; *Microbiota/genetics ; *Soil ; Soil Microbiology ; Tanzania ; }, abstract = {Diversity and community composition of soil microorganisms along the elevation climosequences have been widely studied, while the microbial metabolic potential, particularly in regard to carbon (C) cycling, remains unclear. Here, a metagenomic analysis of C related genes along five elevations ranging from 767 to 4190 m at Mount Kilimanjaro was analysed to evaluate the microbial organic C transformation capacities in various ecosystems. The highest gene abundances for decomposition of moderate mineralizable compounds, i.e. carbohydrate esters, chitin and pectin were found at the mid-elevations with hump-shaped pattern, where the genes for decompositions of recalcitrant C (i.e. lignin) and easily mineralizable C (i.e. starch) showed the opposite trend (i.e. U-shaped pattern), due to high soil pH and seasonality in both low and high elevations. Notably, the gene abundances for the decompositions of starch, carbohydrate esters, chitin and lignin had positive relationships with corresponding C compounds, indicating the consistent responses of microbial functional profiles and metabolites to elevation climosequences. Understanding of adaptation of microbial communities, potential function and metabolites to elevation climosequences and their influencing factors provided a new insight for the regulation of terrestrial C storage.}, } @article {pmid34189610, year = {2022}, author = {Wang, X and Shang, Y and Wei, Q and Wu, X and Dou, H and Zhang, H and Zhou, S and Sha, W and Sun, G and Ma, S and Zhang, H}, title = {Comparative Analyses of the Gut Microbiome of Two Fox Species, the Red Fox (Vulpes Vulpes) and Corsac Fox (Vulpes Corsac), that Occupy Different Ecological Niches.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {753-765}, pmid = {34189610}, issn = {1432-184X}, support = {31872242//the national natural science foundation of china/ ; 31672313//the national natural science foundation of china/ ; 32070405//the national natural science foundation of china/ ; 32001228//the national natural science foundation of china/ ; 32000291//the national natural science foundation of china/ ; 61902368//the national natural science foundation of china/ ; 201404420//the Special Fund for Forest Scientific Research in the Public Welfare/ ; }, mesh = {Animals ; Ecosystem ; *Foxes ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {The gut microbiome is integral for the host's living and environmental adaptation and crucially important for understanding host adaptive mechanisms. The red fox (Vulpes vulpes) dominates a wider ecological niche and more complicated habitat than that of the corsac fox (V. corsac). However, the adaptive mechanisms (in particular, the gut microbiome responsible for this kind of difference) are still unclear. Therefore, we investigated the gut microbiome of these two species in the Hulunbuir grassland, China, and evaluated their microbiome composition, function, and adaptive mechanisms. We profiled the gut microbiome and metabolism function of red and corsac foxes via 16S rRNA gene and metagenome sequencing. The foxes harbored species-specific microbiomes and functions that were related to ecological niche and habitat. The red fox had abundant Bacteroides, which leads to significant enrichment of metabolic pathways (K12373 and K21572) and enzymes related to chitin and carbohydrate degradation that may help the red fox adapt to a wider niche. The corsac fox harbored large proportions of Blautia, Terrisporobacter, and ATP-binding cassette (ABC) transporters (K01990, K02003, and K06147) that can help maintain corsac fox health, allowing it to live in harsh habitats. These results indicate that the gut microbiome of the red and corsac foxes may have different abilities which may provide these species with differing capabilities to adapt to different ecological niches and habitats, thus providing important microbiome data for understanding the mechanisms of host adaptation to different niches and habitats.}, } @article {pmid34188136, year = {2021}, author = {Wu, C and Chen, T and Xu, W and Zhang, T and Pei, Y and Yang, Y and Zhang, F and Guo, H and Wang, Q and Wang, L and Zhao, B}, title = {The maintenance of microbial community in human fecal samples by a cost effective preservation buffer.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {13453}, pmid = {34188136}, issn = {2045-2322}, mesh = {*Cryopreservation ; Feces/*microbiology ; Humans ; *Metagenome ; Microbiota/*genetics ; *Specimen Handling ; }, abstract = {In the burgeoning microbiome field, powerful sequencing approaches and accompanied bioanalytical methods have made tremendous contributions to the discoveries of breakthroughs, which favor to unravel the intimate interplay between gut microbiota and human health. The proper preservation of samples before being processed is essential to guarantee the authenticity and reliability of microbiome studies. Hence, the development of preservation methods is extremely important to hold samples eligible for the consequent analysis, especially population cohort-based investigations or those spanning species or geography, which frequently facing difficulties in suppling freezing conditions. Although there are several commercial products available, the exploration of cost-efficient and ready-to-use preservation methods are still in a large demand. Here, we performed shotgun metagenomic sequencing and demonstrated that microbial consortia in human fecal samples were substantially preserved within a temporary storage of 4 h, independent of the storage temperature. We also verified a previous reported self-made preservation buffer (PB buffer) could not only preserve fecal microbiota at room temperature up to 4 weeks but also enable samples to endure a high temperature condition which mimics temperature variations in summer logistics. Moreover, PB buffer exhibited suitability for human saliva as well. Collectively, PB buffer may be a valuable choice to stabilize samples if neither freezing facilities nor liquid nitrogen is available.}, } @article {pmid34187542, year = {2021}, author = {Kim, JY and Yi, MH and Mahdi, AAS and Yong, TS}, title = {iSeq 100 for metagenomic pathogen screening in ticks.}, journal = {Parasites & vectors}, volume = {14}, number = {1}, pages = {346}, pmid = {34187542}, issn = {1756-3305}, support = {NRF-2019R1A2B5B01069843//National Research Foundation of Korea/ ; 2020R1I1A2074562//National Research Foundation of Korea/ ; 2020R1I1A1A0105358211//National Research Foundation of Korea/ ; }, mesh = {Animals ; Bacteria/classification/*genetics/isolation & purification/*pathogenicity ; High-Throughput Nucleotide Sequencing/*instrumentation/*methods ; Metagenomics ; Microbiota/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Ticks/*microbiology ; }, abstract = {BACKGROUND: Ticks are blood-sucking ectoparasites that play a pivotal role in the transmission of various pathogens to humans and animals. In Korea, Haemaphysalis longicornis is the predominant tick species and is recognized as the vector of pathogens causing various diseases such as babesiosis, borreliosis, rickettsiosis, and severe fever with thrombocytopenia syndrome.

METHODS: In this study, the targeted high-throughput sequencing of the 16S rRNA V4 region was performed using the state-of-the-art sequencing instrument, iSeq 100, to screen bacterial pathogens in H. longicornis, and the findings were compared with those using conventional PCR with specific primers. Microbiome analyses were performed with EzBioCloud, a commercially available ChunLab bioinformatics cloud platform. ANOVA-Like Differential Expression tool (ALDEx2) was used for differential abundance analysis.

RESULTS: Rickettsia spp. were detected in 16 out of 37 samples using iSeq 100, and this was confirmed using a PCR assay. In the phylogenetic analysis using gltA and ompA sequences of the detected Rickettsia, the highest sequence similarity was found with 'Candidatus Rickettsia jingxinensis' isolate Xian-Hl-79, 'Ca. R. jingxinensis' isolate F18, and 'Ca. R. longicornii' isolate ROK-HL727. In the microbiome study, Coxiella AB001519, a known tick symbiont, was detected in all 37 tick samples. Actinomycetospora chiangmaiensis was more abundant in Rickettsia-positive samples than in Rickettsia-negative samples.

CONCLUSIONS: In this study, iSeq 100 was used to investigate the microbiome of H. longicornis, and the potentially pathogenic Rickettsia strain was detected in 16 out of 37 ticks. We believe that this approach will aid in large-scale pathogen screening of arthropods to be used in vector-borne disease control programs.}, } @article {pmid34186487, year = {2021}, author = {Wilson, BC and Butler, ÉM and Grigg, CP and Derraik, JGB and Chiavaroli, V and Walker, N and Thampi, S and Creagh, C and Reynolds, AJ and Vatanen, T and O'Sullivan, JM and Cutfield, WS}, title = {Oral administration of maternal vaginal microbes at birth to restore gut microbiome development in infants born by caesarean section: A pilot randomised placebo-controlled trial.}, journal = {EBioMedicine}, volume = {69}, number = {}, pages = {103443}, pmid = {34186487}, issn = {2352-3964}, mesh = {Administration, Oral ; Adult ; Bacteroides/pathogenicity ; Cesarean Section/*adverse effects ; Fecal Microbiota Transplantation/adverse effects/*methods ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Infant, Newborn, Diseases/etiology/*microbiology/prevention & control ; Vagina/*microbiology ; }, abstract = {BACKGROUND: Birth by caesarean section (CS) is associated with aberrant gut microbiome development and greater disease susceptibility later in life. We investigated whether oral administration of maternal vaginal microbiota to infants born by CS could restore their gut microbiome development in a pilot single-blinded, randomised placebo-controlled trial (Australian New Zealand Clinical Trials Registry, ACTRN12618000339257).

METHODS: Pregnant women scheduled for a CS underwent comprehensive antenatal pathogen screening. At birth, healthy neonates were randomised to receive a 3 ml solution of either maternal vaginal microbes (CS-seeded, n = 12) or sterile water (CS-placebo, n = 13). Vaginally-born neonates were used as the reference control (VB, n = 22). Clinical assessments occurred within the first 2 h of birth, and at 1 month and 3 months of age. Infant stool samples and maternal vaginal extracts from CS women underwent shotgun metagenomic sequencing. The primary outcome was gut microbiome composition at 1 month of age. Secondary outcomes included maternal strain engraftment, functional potential of the gut microbiome, anthropometry, body composition, and adverse events.

FINDINGS: Despite the presence of viable microbial cells within transplant solutions, there were no observed differences in gut microbiome composition or functional potential between CS-seeded and CS-placebo infants at 1 month or 3 months of age. Both CS groups displayed the characteristic signature of low Bacteroides abundance, which contributed to a number of biosynthesis pathways being underrepresented when compared with VB microbiomes. Maternal vaginal strain engraftment was rare. Vaginal seeding had no observed effects on anthropometry or body composition. There were no serious adverse events associated with treatment.

INTERPRETATION: Our pilot findings question the value of vaginal seeding given that oral administration of maternal vaginal microbiota did not alter early gut microbiome development in CS-born infants. The limited colonisation of maternal vaginal strains suggest that other maternal sources, such as the perianal area, may play a larger role in seeding the neonatal gut microbiome.

FUNDING: Health Research Council of New Zealand, A Better Start - National Science Challenge.}, } @article {pmid34183781, year = {2021}, author = {Shi, LD and Lv, PL and McIlroy, SJ and Wang, Z and Dong, XL and Kouris, A and Lai, CY and Tyson, GW and Strous, M and Zhao, HP}, title = {Methane-dependent selenate reduction by a bacterial consortium.}, journal = {The ISME journal}, volume = {15}, number = {12}, pages = {3683-3692}, pmid = {34183781}, issn = {1751-7370}, mesh = {*Bacteria/genetics ; Bioreactors ; *Methane ; Microbial Consortia ; Oxidation-Reduction ; Selenic Acid ; }, abstract = {Methanotrophic microorganisms play a critical role in controlling the flux of methane from natural sediments into the atmosphere. Methanotrophs have been shown to couple the oxidation of methane to the reduction of diverse electron acceptors (e.g., oxygen, sulfate, nitrate, and metal oxides), either independently or in consortia with other microbial partners. Although several studies have reported the phenomenon of methane oxidation linked to selenate reduction, neither the microorganisms involved nor the underlying trophic interaction has been clearly identified. Here, we provide the first detailed evidence for interspecies electron transfer between bacterial populations in a bioreactor community where the reduction of selenate is linked to methane oxidation. Metagenomic and metaproteomic analyses of the community revealed a novel species of Methylocystis as the most abundant methanotroph, which actively expressed proteins for oxygen-dependent methane oxidation and fermentation pathways, but lacked the genetic potential for selenate reduction. Pseudoxanthomonas, Piscinibacter, and Rhodocyclaceae populations appeared to be responsible for the observed selenate reduction using proteins initially annotated as periplasmic nitrate reductases, with fermentation by-products released by the methanotrophs as electron donors. The ability for the annotated nitrate reductases to reduce selenate was confirmed by gene knockout studies in an isolate of Pseudoxanthomonas. Overall, this study provides novel insights into the metabolic flexibility of the aerobic methanotrophs that likely allows them to thrive across natural oxygen gradients, and highlights the potential role for similar microbial consortia in linking methane and other biogeochemical cycles in environments where oxygen is limited.}, } @article {pmid34183041, year = {2021}, author = {Jiang, R and Li, WV and Li, JJ}, title = {mbImpute: an accurate and robust imputation method for microbiome data.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {192}, pmid = {34183041}, issn = {1474-760X}, support = {R01 GM120507/GM/NIGMS NIH HHS/United States ; }, mesh = {Actinobacteria/classification/genetics/isolation & purification ; Bacteroidetes/classification/genetics/isolation & purification ; Case-Control Studies ; Colorectal Neoplasms/diagnosis/*microbiology/pathology ; DNA, Bacterial/*genetics ; Diabetes Mellitus, Type 2/diagnosis/*microbiology/pathology ; Firmicutes/classification/genetics/isolation & purification ; Fusobacteria/classification/genetics/isolation & purification ; Humans ; *Metagenome ; Microbiota/*genetics ; Phylogeny ; Polymerase Chain Reaction/methods ; Proteobacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Software ; Whole Genome Sequencing ; }, abstract = {A critical challenge in microbiome data analysis is the existence of many non-biological zeros, which distort taxon abundance distributions, complicate data analysis, and jeopardize the reliability of scientific discoveries. To address this issue, we propose the first imputation method for microbiome data-mbImpute-to identify and recover likely non-biological zeros by borrowing information jointly from similar samples, similar taxa, and optional metadata including sample covariates and taxon phylogeny. We demonstrate that mbImpute improves the power of identifying disease-related taxa from microbiome data of type 2 diabetes and colorectal cancer, and mbImpute preserves non-zero distributions of taxa abundances.}, } @article {pmid34180607, year = {2021}, author = {Bruggeling, CE and Garza, DR and Achouiti, S and Mes, W and Dutilh, BE and Boleij, A}, title = {Optimized bacterial DNA isolation method for microbiome analysis of human tissues.}, journal = {MicrobiologyOpen}, volume = {10}, number = {3}, pages = {e1191}, pmid = {34180607}, issn = {2045-8827}, mesh = {Bacteria/classification/*genetics/*isolation & purification ; Biopsy ; Colon/microbiology/pathology ; DNA, Bacterial/genetics/*isolation & purification ; Humans ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recent advances in microbiome sequencing have rendered new insights into the role of the microbiome in human health with potential clinical implications. Unfortunately, the presence of host DNA in tissue isolates has hampered the analysis of host-associated bacteria. Here, we present a DNA isolation protocol for tissue, optimized on biopsies from resected human colons (~2-5 mm in size), which includes reduction of human DNA without distortion of relative bacterial abundance at the phylum level. We evaluated which concentrations of Triton and saponin lyse human cells and leave bacterial cells intact, in combination with DNAse treatment to deplete released human DNA. Saponin at a concentration of 0.0125% in PBS lysed host cells, resulting in a 4.5-fold enrichment of bacterial DNA while preserving the relative abundance of Firmicutes, Bacteroidetes, γ-Proteobacteria, and Actinobacteria assessed by qPCR. Our optimized protocol was validated in the setting of two large clinical studies on 521 in vivo acquired colon biopsies of 226 patients using shotgun metagenomics. The resulting bacterial profiles exhibited alpha and beta diversities that are similar to the diversities found by 16S rRNA amplicon sequencing. A direct comparison between shotgun metagenomics and 16S rRNA amplicon sequencing of 15 forceps tissue biopsies showed similar bacterial profiles and a similar Shannon diversity index between the sequencing methods. Hereby, we present the first protocol for enriching bacterial DNA from tissue biopsies that allows efficient isolation of all bacteria. Our protocol facilitates analysis of a wide spectrum of bacteria of clinical tissue samples improving their applicability for microbiome research.}, } @article {pmid34177841, year = {2021}, author = {Selari, PJRG and Olchanheski, LR and Ferreira, AJ and Paim, TDP and Calgaro Junior, G and Claudio, FL and Alves, EM and Santos, DC and Araújo, WL and Silva, FG}, title = {Short-Term Effect in Soil Microbial Community of Two Strategies of Recovering Degraded Area in Brazilian Savanna: A Pilot Case Study.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {661410}, pmid = {34177841}, issn = {1664-302X}, abstract = {The Brazilian Cerrado is a highland tropical savanna considered a biodiversity hotspot with many endemic species of plants and animals. Over the years, most of the native areas of this biome became arable areas, and with inadequate management, some are nowadays at varying levels of degradation stage. Crop-livestock integrated systems (CLIS) are one option for the recovery of areas in degradation, improving the physicochemical and biological characteristics of the soil while increasing income and mitigating risks due to product diversification. Little is known about the effect of CLIS on the soil microbial community. Therefore, we perform this pilot case study to support further research on recovering degraded areas. The bacterial and fungal soil communities in the area with CLIS were compared to an area under moderate recovery (low-input recovering - LI) and native savanna (NS) area. Bacterial and fungal communities were investigated by 16S and ITS rRNA gene sequencing (deep rRNA sequencing). Ktedonobacteraceae and AD3 families were found predominantly in LI, confirming the relationship of the members of the Chloroflexi phylum in challenging environmental conditions, which can be evidenced in LI. The CLIS soil presented 63 exclusive bacterial families that were not found in LI or NS and presented a higher bacterial richness, which can be related to good land management. The NS area shared 21 and 6 families with CLIS and LI, respectively, suggesting that the intervention method used in the analyzed period brings microbial diversity closer to the conditions of the native area, demonstrating a trend of approximation between NS and CLIS even in the short term. The most abundant fungal phylum in NS treatment was Basidiomycota and Mucoromycota, whereas Ascomycota predominated in CLIS and LI. The fungal community needs more time to recover and to approximate from the native area than the bacterial community. However, according to the analysis of bacteria, the CLIS area behaved differently from the LI area, showing that this treatment induces a faster response to the increase in species richness, tending to more accelerated recovery. Results obtained herein encourage CLIS as a sustainable alternative for recovery and production in degraded areas.}, } @article {pmid34176489, year = {2021}, author = {Berry, ASF and Pierdon, MK and Misic, AM and Sullivan, MC and O'Brien, K and Chen, Y and Murray, SJ and Ramharack, LA and Baldassano, RN and Parsons, TD and Beiting, DP}, title = {Remodeling of the maternal gut microbiome during pregnancy is shaped by parity.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {146}, pmid = {34176489}, issn = {2049-2618}, support = {4100068710//Commonwealth Universal Research Enhancement (CURE) program/ ; }, mesh = {Animals ; Female ; *Gastrointestinal Microbiome ; Parity ; Pregnancy ; *Premature Birth ; Prevotella ; Swine ; Treponema ; }, abstract = {BACKGROUND: The maternal microbiome has emerged as an important factor in gestational health and outcome and is associated with risk of preterm birth and offspring morbidity. Epidemiological evidence also points to successive pregnancies-referred to as maternal parity-as a risk factor for preterm birth, infant mortality, and impaired neonatal growth. Despite the fact that both the maternal microbiome and parity are linked to maternal-infant health, the impact of parity on the microbiome remains largely unexplored, in part due to the challenges of studying parity in humans.

RESULTS: Using synchronized pregnancies and dense longitudinal monitoring of the microbiome in pigs, we describe a microbiome trajectory during pregnancy and determine the extent to which parity modulates this trajectory. We show that the microbiome changes reproducibly during gestation and that this remodeling occurs more rapidly as parity increases. At the time of parturition, parity was linked to the relative abundance of several bacterial species, including Treponema bryantii, Lactobacillus amylovorus, and Lactobacillus reuteri. Strain tracking carried out in 18 maternal-offspring "quadrads"-each consisting of one mother sow and three piglets-linked maternal parity to altered levels of Akkermansia muciniphila, Prevotella stercorea, and Campylobacter coli in the infant gut 10 days after birth.

CONCLUSIONS: Collectively, these results identify parity as an important environmental factor that modulates the gut microbiome during pregnancy and highlight the utility of a swine model for investigating the microbiome in maternal-infant health. In addition, our data show that the impact of parity extends beyond the mother and is associated with alterations in the community of bacteria that colonize the offspring gut early in life. The bacterial species we identified as parity-associated in the mother and offspring have been shown to influence host metabolism in other systems, raising the possibility that such changes may influence host nutrient acquisition or utilization. These findings, taken together with our observation that even subtle differences in parity are associated with microbiome changes, underscore the importance of considering parity in the design and analysis of human microbiome studies during pregnancy and in infants. Video abstract.}, } @article {pmid34175280, year = {2021}, author = {Yang, K and Niu, J and Zuo, T and Sun, Y and Xu, Z and Tang, W and Liu, Q and Zhang, J and Ng, EKW and Wong, SKH and Yeoh, YK and Chan, PKS and Chan, FKL and Miao, Y and Ng, SC}, title = {Alterations in the Gut Virome in Obesity and Type 2 Diabetes Mellitus.}, journal = {Gastroenterology}, volume = {161}, number = {4}, pages = {1257-1269.e13}, doi = {10.1053/j.gastro.2021.06.056}, pmid = {34175280}, issn = {1528-0012}, mesh = {Adolescent ; Adult ; Aged ; Case-Control Studies ; Diabetes Mellitus, Type 2/diagnosis/microbiology/*virology ; Dysbiosis ; Feces/microbiology/virology ; Female ; Gastrointestinal Microbiome ; Hong Kong ; Host-Pathogen Interactions ; Humans ; Intestines/microbiology/*virology ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Obesity/diagnosis/microbiology/*virology ; *Virome/genetics ; Young Adult ; }, abstract = {BACKGROUND & AIMS: Obesity and type 2 diabetes mellitus (T2DM) are associated with changes in the gut bacterial composition, but little is known about the role of the viral community (virome) in disease development. This study aims to characterize the gut virome alterations in obese subjects with or without T2DM.

METHODS: There were 128 obese subjects (body mass index ≥28 kg/m[2]) and 101 lean controls (body mass index ≥18.5 and <23 kg/m[2]) recruited from 2 regions in China (Hong Kong and Kunming). Fecal virome and bacteriome were profiled by shotgun metagenomic sequencing. Gut virome, bacteriome, and viral-bacterial correlations were compared between obese subjects and lean controls.

RESULTS: Obese subjects, especially those with T2DM (ObT2), had a decreased gut viral richness and diversity compared with lean controls in the Hong Kong cohort (P < .05), while no significant differences were observed in the Kunming cohort. Eleven viruses, including Escherichia phage, Geobacillus phage, and Lactobacillus phage were enriched in obese subjects (q < .1). Besides, 17 differentially abundant viruses were identified between ObT2 and lean controls (q < .1). Further ecologic analysis revealed that intensive transkingdom correlations between viruses and bacteria observed in lean controls were significantly decreased in ObT2 subjects (P < .001).

CONCLUSIONS: Obesity is characterized by altered viral taxonomic composition and weakened viral-bacterial correlations compared with lean controls. Obesity accompanied with T2DM may aggravate the obesity-associated virus signatures, signifying that the gut virome may play an important role in the development of obesity and T2DM. Geographic factors also contributed to the variations of gut virome in obesity and T2DM.}, } @article {pmid34174663, year = {2021}, author = {Wang, Y and Li, M and Liu, Z and Zhao, J and Chen, Y}, title = {Interactions between pyrene and heavy metals and their fates in a soil-maize (Zea mays L.) system: Perspectives from the root physiological functions and rhizosphere microbial community.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {287}, number = {}, pages = {117616}, doi = {10.1016/j.envpol.2021.117616}, pmid = {34174663}, issn = {1873-6424}, mesh = {Biodegradation, Environmental ; *Metals, Heavy/analysis ; *Microbiota ; Plant Roots/chemistry ; Pyrenes ; Rhizosphere ; Soil ; *Soil Pollutants/analysis ; Zea mays ; }, abstract = {The co-occurrence of polycyclic aromatic hydrocarbons (PAHs) and heavy metals in agricultural soils has become a worldwide food crop security concern. Pot experiments, rhizosphere microbial metagenomic sequencing, and root metatranscriptomic sequencing were performed to investigate the interactions among pyrene, Cu, and Cd in a soil-maize (Zea mays L.) system. This study provided direct evidence that the co-presence of PAHs and heavy metals changed the root physiological functions and the rhizosphere microbial community, which subsequently influenced the fate of the contaminants. Co-contamination at low levels tended to enhance the uptake potential and biodegradation performance of the plant, whereas increased contaminant concentrations produced opposite effects. The co-presence of 1000 mg/kg Cu decreased the abundance of Mycobacterium in the rhizosphere and reduced pyrene degradation by 12%-16%. The presence of 400-750 mg/kg pyrene altered the metabolic processes, molecular binding functions, and catalytic activity of enzymes in the maize roots, thus impeding the phytoextraction of Cu and Cd. Competitive absorption between Cu and Cd was observed for the 800-1000 mg/kg Cu and 50-100 mg/kg Cd co-treatment, in which Cu showed a competitive advantage, enhancing its root-to-shoot translocation. These findings provide important information for the production of safe crops and for the development of phytoremediation technologies.}, } @article {pmid34172822, year = {2021}, author = {Fackelmann, G and Gillingham, MAF and Schmid, J and Heni, AC and Wilhelm, K and Schwensow, N and Sommer, S}, title = {Human encroachment into wildlife gut microbiomes.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {800}, pmid = {34172822}, issn = {2399-3642}, mesh = {Adaptation, Physiological ; Animals ; Animals, Wild/*microbiology ; Ecosystem ; Gastrointestinal Microbiome/*physiology ; Humans ; Metagenome ; Microbiota ; }, abstract = {In the Anthropocene, humans, domesticated animals, wildlife, and their environments are interconnected, especially as humans advance further into wildlife habitats. Wildlife gut microbiomes play a vital role in host health. Changes to wildlife gut microbiomes due to anthropogenic disturbances, such as habitat fragmentation, can disrupt natural gut microbiota homeostasis and make animals vulnerable to infections that may become zoonotic. However, it remains unclear whether the disruption to wildlife gut microbiomes is caused by habitat fragmentation per se or the combination of habitat fragmentation with additional anthropogenic disturbances, such as contact with humans, domesticated animals, invasive species, and their pathogens. Here, we show that habitat fragmentation per se does not impact the gut microbiome of a generalist rodent species native to Central America, Tome's spiny rat Proechimys semispinosus, but additional anthropogenic disturbances do. Indeed, compared to protected continuous and fragmented forest landscapes that are largely untouched by other human activities, the gut microbiomes of spiny rats inhabiting human-disturbed fragmented landscapes revealed a reduced alpha diversity and a shifted and more dispersed beta diversity. Their microbiomes contained more taxa associated with domesticated animals and their potential pathogens, suggesting a shift in potential metagenome functions. On the one hand, the compositional shift could indicate a degree of gut microbial adaption known as metagenomic plasticity. On the other hand, the greater variation in community structure and reduced alpha diversity may signal a decline in beneficial microbial functions and illustrate that gut adaption may not catch up with anthropogenic disturbances, even in a generalist species with large phenotypic plasticity, with potentially harmful consequences to both wildlife and human health.}, } @article {pmid34172012, year = {2021}, author = {Lay, C and Chu, CW and Purbojati, RW and Acerbi, E and Drautz-Moses, DI and de Sessions, PF and Jie, S and Ho, E and Kok, YJ and Bi, X and Chen, S and Mak, SY and Chua, MC and Goh, AEN and Chiang, WC and Rao, R and Chaithongwongwatthana, S and Khemapech, N and Chongsrisawat, V and Martin, R and , and Roeselers, G and Ho, YS and Hibberd, ML and Schuster, SC and Knol, J}, title = {A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {191}, pmid = {34172012}, issn = {1471-2180}, mesh = {Bacteria/*genetics ; Biodiversity ; Cesarean Section/*adverse effects ; Double-Blind Method ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Infant ; Infant, Newborn ; Metagenome/*genetics ; }, abstract = {BACKGROUND: The compromised gut microbiome that results from C-section birth has been hypothesized as a risk factor for the development of non-communicable diseases (NCD). In a double-blind randomized controlled study, 153 infants born by elective C-section received an infant formula supplemented with either synbiotic, prebiotics, or unsupplemented from birth until 4 months old. Vaginally born infants were included as a reference group. Stool samples were collected from day 3 till week 22. Multi-omics were deployed to investigate the impact of mode of delivery and nutrition on the development of the infant gut microbiome, and uncover putative biological mechanisms underlying the role of a compromised microbiome as a risk factor for NCD.

RESULTS: As early as day 3, infants born vaginally presented a hypoxic and acidic gut environment characterized by an enrichment of strict anaerobes (Bifidobacteriaceae). Infants born by C-section presented the hallmark of a compromised microbiome driven by an enrichment of Enterobacteriaceae. This was associated with meta-omics signatures characteristic of a microbiome adapted to a more oxygen-rich gut environment, enriched with genes associated with reactive oxygen species metabolism and lipopolysaccharide biosynthesis, and depleted in genes involved in the metabolism of milk carbohydrates. The synbiotic formula modulated expression of microbial genes involved in (oligo)saccharide metabolism, which emulates the eco-physiological gut environment observed in vaginally born infants. The resulting hypoxic and acidic milieu prevented the establishment of a compromised microbiome.

CONCLUSIONS: This study deciphers the putative functional hallmarks of a compromised microbiome acquired during C-section birth, and the impact of nutrition that may counteract disturbed microbiome development.

TRIAL REGISTRATION: The study was registered in the Dutch Trial Register (Number: 2838) on 4th April 2011.}, } @article {pmid34171673, year = {2021}, author = {Noman, E and Al-Gheethi, A and Radin Mohamed, RMS and Talip, B and Al-Sahari, M and Al-Shaibani, M}, title = {Quantitative microbiological risk assessment of complex microbial community in Prawn farm wastewater and applicability of nanoparticles and probiotics for eliminating of antibiotic-resistant bacteria.}, journal = {Journal of hazardous materials}, volume = {419}, number = {}, pages = {126418}, doi = {10.1016/j.jhazmat.2021.126418}, pmid = {34171673}, issn = {1873-3336}, mesh = {Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Humans ; *Microbiota ; *Nanoparticles ; *Probiotics ; Risk Assessment ; Wastewater ; }, abstract = {The current review highlighted the quantitative microbiological risk assessment of Vibrio parahaemolyticus in Prawn farm wastewaters (PFWWs) and the applicability of nanoparticles for eliminating antibiotic-resistant bacteria (ARB). The high availability of the antibiotics in the environment and their transmission into human through the food-chain might cause unknown health effects. The aquaculture environments are considered as a reservoir for the antibiotic resistance genes (ARGs) and contributed effectively in the increasing of ABR. The metagenomic analysis is used to explore ARGs in the non-clinical environment. V. parahaemolyticus is among the pathogenic bacteria which are transmitted through sea food causing human acute gastroenteritis due to available thermostable direct hemolysin (tdh), adhesins, TDH related hemolysin (trh). The inactivation of pathogenic bacteria using nanoparticles act by disturbing the cell membrane, interrupting the transport system, DNA and mitochondria damage, and oxidizing the cellular component by reactive oxygen species (ROS). The chloramphenicol, nitrofurans, and nitroimidazole are among the prohibited drugs in fish and fishery product. The utilization of probiotics is the most effective and safe alternative for antibiotics in Prawn aquaculture. This review will ensure public understanding among the readers on how they can decrease the risk of the antimicrobial resistance distribution in the environment.}, } @article {pmid34168315, year = {2021}, author = {Nayfach, S and Páez-Espino, D and Call, L and Low, SJ and Sberro, H and Ivanova, NN and Proal, AD and Fischbach, MA and Bhatt, AS and Hugenholtz, P and Kyrpides, NC}, title = {Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome.}, journal = {Nature microbiology}, volume = {6}, number = {7}, pages = {960-970}, pmid = {34168315}, issn = {2058-5276}, support = {P30 CA124435/CA/NCI NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; }, mesh = {Archaea/virology ; Bacteria/virology ; Bacteriophages/genetics ; Catalogs as Topic ; DNA Viruses/classification/*genetics ; DNA, Viral/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Genome, Viral/*genetics ; Humans ; Metagenomics ; Phylogeny ; Viral Proteins/genetics ; }, abstract = {Bacteriophages have important roles in the ecology of the human gut microbiome but are under-represented in reference databases. To address this problem, we assembled the Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available human stool metagenomes. Over 75% of genomes represent double-stranded DNA phages that infect members of the Bacteroidia and Clostridia classes. Based on sequence clustering we identified 54,118 candidate viral species, 92% of which were not found in existing databases. The Metagenomic Gut Virus catalogue improves detection of viruses in stool metagenomes and accounts for nearly 40% of CRISPR spacers found in human gut Bacteria and Archaea. We also produced a catalogue of 459,375 viral protein clusters to explore the functional potential of the gut virome. This revealed tens of thousands of diversity-generating retroelements, which use error-prone reverse transcription to mutate target genes and may be involved in the molecular arms race between phages and their bacterial hosts.}, } @article {pmid34168163, year = {2021}, author = {Petersen, AØ and Julienne, H and Hyötyläinen, T and Sen, P and Fan, Y and Pedersen, HK and Jäntti, S and Hansen, TH and Nielsen, T and Jørgensen, T and Hansen, T and Myers, PN and Nielsen, HB and Ehrlich, SD and Orešič, M and Pedersen, O}, title = {Conjugated C-6 hydroxylated bile acids in serum relate to human metabolic health and gut Clostridia species.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {13252}, pmid = {34168163}, issn = {2045-2322}, mesh = {Adiposity ; Bile Acids and Salts/*blood ; Body Mass Index ; Cholic Acids/blood ; Chromatography, High Pressure Liquid ; Clostridium/genetics/*metabolism ; Deoxycholic Acid/blood ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Logistic Models ; Male ; Metagenomics ; Middle Aged ; Obesity/blood/microbiology ; Tandem Mass Spectrometry ; Taurocholic Acid/blood ; Waist Circumference ; }, abstract = {Knowledge about in vivo effects of human circulating C-6 hydroxylated bile acids (BAs), also called muricholic acids, is sparse. It is unsettled if the gut microbiome might contribute to their biosynthesis. Here, we measured a range of serum BAs and related them to markers of human metabolic health and the gut microbiome. We examined 283 non-obese and obese Danish adults from the MetaHit study. Fasting concentrations of serum BAs were quantified using ultra-performance liquid chromatography-tandem mass-spectrometry. The gut microbiome was characterized with shotgun metagenomic sequencing and genome-scale metabolic modeling. We find that tauro- and glycohyocholic acid correlated inversely with body mass index (P = 4.1e-03, P = 1.9e-05, respectively), waist circumference (P = 0.017, P = 1.1e-04, respectively), body fat percentage (P = 2.5e-03, P = 2.3e-06, respectively), insulin resistance (P = 0.051, P = 4.6e-4, respectively), fasting concentrations of triglycerides (P = 0.06, P = 9.2e-4, respectively) and leptin (P = 0.067, P = 9.2e-4). Tauro- and glycohyocholic acids, and tauro-a-muricholic acid were directly linked with a distinct gut microbial community primarily composed of Clostridia species (P = 0.037, P = 0.013, P = 0.027, respectively). We conclude that serum conjugated C-6-hydroxylated BAs associate with measures of human metabolic health and gut communities of Clostridia species. The findings merit preclinical interventions and human feasibility studies to explore the therapeutic potential of these BAs in obesity and type 2 diabetes.}, } @article {pmid34162081, year = {2021}, author = {Kaur, I and Gaur, VK and Regar, RK and Roy, A and Srivastava, PK and Gaur, R and Manickam, N and Barik, SK}, title = {Plants exert beneficial influence on soil microbiome in a HCH contaminated soil revealing advantage of microbe-assisted plant-based HCH remediation of a dumpsite.}, journal = {Chemosphere}, volume = {280}, number = {}, pages = {130690}, doi = {10.1016/j.chemosphere.2021.130690}, pmid = {34162081}, issn = {1879-1298}, mesh = {Biodegradation, Environmental ; Hexachlorocyclohexane/analysis ; *Microbiota ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Persistence of hexachlorocyclohexane (HCH) pesticide is a major problem for its disposal. Soil microflora plays an important role in remediating contaminated sites. Keeping concepts of microbial- and phyto-remediation together, the difference between soil microflora with and without association of HCH accumulating plant species was studied. Metagenomic analysis among the non-plant soil (BS) (∑HCH 434.19 mg/g), rhizospheric soil of shrubs (RSS) (∑HCH 157.31 mg/g), and rhizospheric soil of trees (RSD) (∑HCH 105.39 mg/g) revealed significant differences in microbial communities. Shrubs and trees occurred at a long-term dumpsite accumulated α- and β- HCH residues. Plant rhizospheric soils exhibited high richness and evenness with higher diversity indices compared to the non-plant soil. Order Rhizobiales was most abundant in all soils and Streptomycetales was absent in the BS soil. Proteobacteria and Ascomycota were highest in BS soil, while Actinobacteria was enriched in both the plant rhizospheric soil samples. In BS soil, Pseudomonas, Sordaria, Caulobacter, Magnetospirillum, Rhodospirillum were abundant. While, genera Actinoplanes, Streptomyces, Bradyrhizobium, Rhizobium, Azospirillum, Agrobacterium are abundant in RSD soil. Selected plants have accumulated HCH residues from soil and exerted positive impacts on soil microbial communities in HCH contaminated site. This study advocates microbe-assisted plant-based bioremediation strategy to remediate HCH contamination.}, } @article {pmid34161271, year = {2021}, author = {Lingappa, UF and Yeager, CM and Sharma, A and Lanza, NL and Morales, DP and Xie, G and Atencio, AD and Chadwick, GL and Monteverde, DR and Magyar, JS and Webb, SM and Valentine, JS and Hoffman, BM and Fischer, WW}, title = {An ecophysiological explanation for manganese enrichment in rock varnish.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {25}, pages = {}, pmid = {34161271}, issn = {1091-6490}, support = {P41 GM103393/GM/NIGMS NIH HHS/United States ; R01 GM111097/GM/NIGMS NIH HHS/United States ; }, mesh = {Antioxidants/metabolism ; Cyanobacteria/metabolism ; *Ecological and Environmental Phenomena ; Geologic Sediments/*chemistry/microbiology ; Manganese/*analysis ; Microbiota ; Oxidation-Reduction ; Sunlight ; Water ; }, abstract = {Desert varnish is a dark rock coating that forms in arid environments worldwide. It is highly and selectively enriched in manganese, the mechanism for which has been a long-standing geological mystery. We collected varnish samples from diverse sites across the western United States, examined them in petrographic thin section using microscale chemical imaging techniques, and investigated the associated microbial communities using 16S amplicon and shotgun metagenomic DNA sequencing. Our analyses described a material governed by sunlight, water, and manganese redox cycling that hosts an unusually aerobic microbial ecosystem characterized by a remarkable abundance of photosynthetic Cyanobacteria in the genus Chroococcidiopsis as the major autotrophic constituent. We then showed that diverse Cyanobacteria, including the relevant Chroococcidiopsis taxon, accumulate extraordinary amounts of intracellular manganese-over two orders of magnitude higher manganese content than other cells. The speciation of this manganese determined by advanced paramagnetic resonance techniques suggested that the Cyanobacteria use it as a catalytic antioxidant-a valuable adaptation for coping with the substantial oxidative stress present in this environment. Taken together, these results indicated that the manganese enrichment in varnish is related to its specific uptake and use by likely founding members of varnish microbial communities.}, } @article {pmid34161177, year = {2021}, author = {Grettenberger, CL and Hamilton, TL}, title = {Metagenome-Assembled Genomes of Novel Taxa from an Acid Mine Drainage Environment.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {17}, pages = {e0077221}, pmid = {34161177}, issn = {1098-5336}, mesh = {Acids/metabolism ; Archaea/classification/*genetics/*isolation & purification/metabolism ; Bacteria/classification/*genetics/*isolation & purification/metabolism ; Biodegradation, Environmental ; Metagenome ; Microbiota ; Mining ; Oxidation-Reduction ; Phylogeny ; Wastewater/analysis/*microbiology ; }, abstract = {Acid mine drainage (AMD) is a global problem in which iron sulfide minerals oxidize and generate acidic, metal-rich water. Bioremediation relies on understanding how microbial communities inhabiting an AMD site contribute to biogeochemical cycling. A number of studies have reported community composition in AMD sites from 16S rRNA gene amplicons, but it remains difficult to link taxa to function, especially in the absence of closely related cultured species or those with published genomes. Unfortunately, there is a paucity of genomes and cultured taxa from AMD environments. Here, we report 29 novel metagenome-assembled genomes from Cabin Branch, an AMD site in the Daniel Boone National Forest, Kentucky, USA. The genomes span 11 bacterial phyla and one archaeal phylum and include taxa that contribute to carbon, nitrogen, sulfur, and iron cycling. These data reveal overlooked taxa that contribute to carbon fixation in AMD sites as well as uncharacterized Fe(II)-oxidizing bacteria. These data provide additional context for 16S rRNA gene studies, add to our understanding of the taxa involved in biogeochemical cycling in AMD environments, and can inform bioremediation strategies. IMPORTANCE Bioremediating acid mine drainage requires understanding how microbial communities influence geochemical cycling of iron and sulfur and biologically important elements such as carbon and nitrogen. Research in this area has provided an abundance of 16S rRNA gene amplicon data. However, linking these data to metabolisms is difficult because many AMD taxa are uncultured or lack published genomes. Here, we present metagenome-assembled genomes from 29 novel AMD taxa and detail their metabolic potential. These data provide information on AMD taxa that could be important for bioremediation strategies, including taxa that are involved in cycling iron, sulfur, carbon, and nitrogen.}, } @article {pmid34160629, year = {2021}, author = {Aguirre-von-Wobeser, E and Alonso-Sánchez, A and Méndez-Bravo, A and Villanueva Espino, LA and Reverchon, F}, title = {Barks from avocado trees of different geographic locations have consistent microbial communities.}, journal = {Archives of microbiology}, volume = {203}, number = {7}, pages = {4593-4607}, pmid = {34160629}, issn = {1432-072X}, support = {CB-2014-01-242956//SEP/CONACyT/ ; }, mesh = {Archaea/genetics ; Bacteria/genetics ; *Biodiversity ; Fungi/genetics/physiology ; Metagenomics ; *Microbiota/genetics/physiology ; *Persea/microbiology ; *Plant Bark/microbiology ; Soil Microbiology ; }, abstract = {Bark is a permanent surface for microbial colonization at the interface of trees and the surrounding air, but little is known about its microbial communities. We used shotgun metagenomic sequencing to analyze the bark microbiomes of avocado trees from two orchards, and compared one of them to rhizospheric soil. It was shown that the microbial communities of avocado bark have a well-defined taxonomic structure, with consistent patterns of abundance of bacteria, fungi, and archaea, even in trees from two different locations. Bark microbial communities were distinct from rhizospheric soil, although they showed overlap in some taxa. Thus, avocado bark is a well-defined environment, providing niches for specific taxonomic groups, many of which are also found in other aerial plant tissues. The present in-depth characterization of bark microbial communities can form a basis for their future manipulation for agronomical purposes.}, } @article {pmid34160281, year = {2021}, author = {Chai, LJ and Qian, W and Zhong, XZ and Zhang, XJ and Lu, ZM and Zhang, SY and Wang, ST and Shen, CH and Shi, JS and Xu, ZH}, title = {Mining the Factors Driving the Evolution of the Pit Mud Microbiome under the Impact of Long-Term Production of Strong-Flavor Baijiu.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {17}, pages = {e0088521}, pmid = {34160281}, issn = {1098-5336}, mesh = {Archaea/classification/genetics/*isolation & purification/metabolism ; Bacteria/classification/genetics/*isolation & purification/metabolism ; China ; Clay/*microbiology ; Fermentation ; Flavoring Agents/analysis/*metabolism ; Food Storage/instrumentation ; *Microbiota ; Wine/*analysis/microbiology ; }, abstract = {The mud cellar creates a unique microenvironment for the fermentation of strong-flavor baijiu (SFB). Recent research and long-term practice have highlighted the key roles of microbes inhabiting pit mud in the formation of SFB's characteristic flavor. A positive correlation between the quality of SFB and cellar age was extracted from practice; however, the evolutionary patterns of pit mud microbiome and driving factors remain unclear. Here, based on the variation regularity analysis of microbial community structure and metabolites of samples from cellars of different ages (∼30/100/300 years), we further investigated the effects of lactate and acetate (main microbial metabolites in fermented grains) on modulating the pit mud microbiome. Esters (50.3% to 64.5%) dominated the volatile compounds identified in pit mud, and contents of the four typical acids (lactate, hexanoate, acetate, and butyrate) increased with cellar age. Bacteria (9.5 to 10.4 log10 [lg] copies/g) and archaea (8.3 to 9.1 lg copies/g) mainly constituted pit mud microbiota, respectively dominated by Clostridia (39.7% to 81.2%) and Methanomicrobia (32.8% to 92.9%). An upward trend with cellar age characterized the relative and absolute abundance of the most predominant bacterial and archaeal genera, Caproiciproducens and Methanosarcina. Correlation analysis revealed significantly (P < 0.05) positive relationships between the two genera and major metabolites. Anaerobic fermentation with acetate and lactate as carbon sources enhanced the enrichment of Clostridia, and furthermore, the relative abundance of Caproiciproducens (40.9%) significantly increased after 15-day fed-batch fermentation with lactate compared with the initial pit mud (0.22%). This work presents a directional evolutionary pattern of pit mud microbial consortia and provides an alternative way to accelerate the enrichment of functional microbes. IMPORTANCE The solid-state anaerobic fermentation in a mud cellar is the most typical feature of strong-flavor baijiu (SFB). Metabolites produced by microbes inhabiting pit mud are crucial to create the unique flavor of SFB. Accordingly, craftspeople have always highlighted the importance of the pit mud microbiome and concluded by centuries of practice that the production rate of high-quality baijiu increases with cellar age. To deepen the understanding of the pit mud microbiome, we determined the microbial community and metabolites of different-aged pit mud, inferred the main functional groups, and explored the forces driving the microbial community evolution through metagenomic, metabolomic, and multivariate statistical analyses. The results showed that the microbial consortia of pit mud presented a regular and directional evolutionary pattern under the impact of continuous batch-to-batch brewing activities. This work provides insight into the key roles of the pit mud microbiome in SFB production and supports the production optimization of high-quality pit mud.}, } @article {pmid34160270, year = {2021}, author = {Lin, Y and Zhou, B and Zhu, W}, title = {Pathogenic Escherichia coli-Specific Bacteriophages and Polyvalent Bacteriophages in Piglet Guts with Increasing Coliphage Numbers after Weaning.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {17}, pages = {e0096621}, pmid = {34160270}, issn = {1098-5336}, mesh = {Animals ; Coliphages/classification/genetics/growth & development/*isolation & purification ; Escherichia coli/*virology ; Escherichia coli Infections/microbiology/*veterinary ; Feces/microbiology/virology ; Female ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/*virology ; Male ; Swine/growth & development/microbiology/*virology ; Swine Diseases/*microbiology/virology ; Weaning ; }, abstract = {Postweaning diarrhea in pigs is mainly caused by pathogenic Escherichia coli and is a major source of revenue loss to the livestock industry. Bacteriophages dominate the gut virome and have the potential to regulate bacterial communities and thus influence the intestinal physiology. To determine the biological characterization of intestinal coliphages, we isolated and identified the fecal coliphages of healthy preweaned and postweaned piglets from the Nanjing and Chuzhou pig farms. First, ahead of coliphage isolation, 87 E. coli strains were isolated from healthy or diarrheal fecal samples from three pig farms, of which 8 were pathogenic strains, including enterotoxigenic E. coli (ETEC) and enteropathogenic E. coli (EPEC). Of the E. coli strains, 87.3% possessed drug resistance to three antibiotics. Using these 87 E. coli strains as indicator hosts, we isolated 45 coliphages and found a higher abundance in the postweaning stage than in the preweaning stage (24 versus 17 in the Nanjing and 13 versus 4 in the Chuzhou farm). Furthermore, each farm had a single most-prevalent coliphage strain. Pathogenic E. coli-specific bacteriophages were commonly detected (9/10 samples in the Nanjing farm and 7/10 in the Chuzhou farm) in guts of sampled piglets, and most had significant bacteriostatic effects (P < 0.05) on pathogenic E. coli strains. Three polyvalent bacteriophages (N24, N30, and C5) were identified. The N30 and C5 strains showed a genetic identity of 89.67%, with mild differences in infection characteristics. Our findings suggest that pathogenic E. coli-specific bacteriophages as well as polyvalent bacteriophages are commonly present in piglet guts and that weaning is an important event that affects coliphage numbers. IMPORTANCE Previous studies based on metagenomic sequencing reported that gut bacteriophages profoundly influence gut physiology but did not provide information regarding the host range and biological significance. Here, we screened coliphages from the guts of preweaned and postweaned piglets against indicator hosts, which allowed us to identify the pathogenic E. coli-specific bacteriophages and polyvalent bacteriophages in pig farms and quantify their abundance. Our approach complements sequencing methods and provides new insights into the biological characterizations of bacteriophage in the gut along with the ecological effects of intestinal bacteriophages.}, } @article {pmid34159880, year = {2021}, author = {Fouladi, F and Carroll, IM and Sharpton, TJ and Bulik-Sullivan, E and Heinberg, L and Steffen, KJ and Fodor, AA}, title = {A microbial signature following bariatric surgery is robustly consistent across multiple cohorts.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1930872}, pmid = {34159880}, issn = {1949-0984}, support = {R01 DK112585/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Bacteria/classification/genetics/*isolation & purification ; Bariatric Surgery ; Cohort Studies ; DNA, Bacterial/genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; Male ; Metagenomics ; Middle Aged ; Obesity, Morbid/*microbiology/*surgery ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bariatric surgery induces significant shifts in the gut microbiota which could potentially contribute to weight loss and metabolic benefits. The aim of this study was to characterize a microbial signature following Roux-en-Y Gastric bypass (RYGB) surgery using novel and existing gut microbiota sequence data. We generated 16S rRNA gene and metagenomic sequences from fecal samples from patients undergoing RYGB surgery (n = 61 for 16S rRNA gene and n = 135 for metagenomics) at pre-surgical baseline and one, six, and twelve-month post-surgery. We compared these data with three smaller publicly available 16S rRNA gene and one metagenomic datasets from patients who also underwent RYGB surgery. Linear mixed models and machine learning approaches were used to examine the presence of a common microbial signature across studies. Comparison of our new sequences with previous longitudinal studies revealed strikingly similar profiles in both fecal microbiota composition (r = 0.41 ± 0.10; p < .05) and metabolic pathways (r = 0.70 ± 0.05; p < .001) early after surgery across multiple datasets. Notably, Veillonella, Streptococcus, Gemella, Fusobacterium, Escherichia/Shigella, and Akkermansia increased after surgery, while Blautia decreased. Machine learning approaches revealed that the replicable gut microbiota signature associated with RYGB surgery could be used to discriminate pre- and post-surgical samples. Opportunistic pathogen abundance also increased post-surgery in a consistent manner across cohorts. Our study reveals a robust microbial signature involving many commensal and pathogenic taxa and metabolic pathways early after RYGB surgery across different studies and sites. Characterization of the effects of this robust microbial signature on outcomes of bariatric surgery could provide insights into the development of microbiome-based interventions for predicting or improving outcomes following surgery.}, } @article {pmid34158595, year = {2021}, author = {Rhoades, NS and Hendrickson, SM and Prongay, K and Haertel, A and Gill, L and Edwards, RA and Garzel, L and Slifka, MK and Messaoudi, I}, title = {Growth faltering regardless of chronic diarrhea is associated with mucosal immune dysfunction and microbial dysbiosis in the gut lumen.}, journal = {Mucosal immunology}, volume = {14}, number = {5}, pages = {1113-1126}, pmid = {34158595}, issn = {1935-3456}, support = {P51 OD011092/OD/NIH HHS/United States ; P51 OD011107/OD/NIH HHS/United States ; T32 AI007319/AI/NIAID NIH HHS/United States ; T32 AI141346/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Biodiversity ; Biomarkers ; Biopsy ; Chronic Disease ; Diarrhea/complications/etiology/*metabolism/pathology ; Disease Models, Animal ; Disease Susceptibility ; Dysbiosis/*complications/immunology ; Gastrointestinal Microbiome/*immunology ; Growth Disorders/*etiology/metabolism ; Immunity, Mucosal/genetics ; Immunohistochemistry ; Intestinal Mucosa/*immunology/metabolism/pathology ; Lymphocyte Count ; Macaca mulatta ; Metagenome ; Metagenomics/methods ; Transcriptome ; }, abstract = {Despite the impact of childhood diarrhea on morbidity and mortality, our understanding of its sequelae has been significantly hampered by the lack of studies that examine samples across the entire intestinal tract. Infant rhesus macaques are naturally susceptible to human enteric pathogens and recapitulate the hallmarks of diarrheal disease such as intestinal inflammation and growth faltering. Here, we examined intestinal biopsies, lamina propria leukocytes, luminal contents, and fecal samples from healthy infants and those experiencing growth faltering with distant acute or chronic active diarrhea. We show that growth faltering in the presence or absence of active diarrhea is associated with a heightened systemic and mucosal pro-inflammatory state centered in the colon. Moreover, polyclonal stimulation of colonic lamina propria leukocytes resulted in a dampened cytokine response, indicative of immune exhaustion. We also detected a functional and taxonomic shift in the luminal microbiome across multiple gut sites including the migration of Streptococcus and Prevotella species between the small and large intestine, suggesting a decompartmentalization of gut microbial communities. Our studies provide valuable insight into the outcomes of diarrheal diseases and growth faltering not attainable in humans and lays the groundwork to test interventions in a controlled and reproducible setting.}, } @article {pmid34158518, year = {2021}, author = {Shin, CM and Choi, YJ and Lee, DH and Moon, JS and Kim, TY and Kim, YK and Lee, WH and Yoon, H and Park, YS and Kim, N}, title = {Validity and safety of ID-JPL934 in lower gastrointestinal symptom improvement.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {13046}, pmid = {34158518}, issn = {2045-2322}, mesh = {Adult ; Cytokines/blood ; Extracellular Vesicles/drug effects/metabolism ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/drug effects ; Gastrointestinal Tract/drug effects/*pathology ; Humans ; Inflammation Mediators/blood ; Male ; Metagenomics ; Probiotics/*adverse effects/*pharmacology ; }, abstract = {The study evaluated the efficacy of ID-JPL934, a probiotic preparation containing Lactobacillus johnsonii IDCC 9203, Lactobacillus plantarum IDCC 3501 and Bifidobacterium lactis IDCC 4301, in relieving lower gastrointestinal symptoms. A total of 112 subjects with lower gastrointestinal symptoms were consecutively enrolled. They were randomized into either ID-JPL934 administration group or placebo group. Bristol stool form, stool frequency, and abnormal bowel movement symptoms were recorded at baseline and week 2, 6, and 8. Primary endpoint was improvement in overall symptoms at week 8. Fecal samples were collected to measure the probiotic levels in feces using quantitative polymerase chain reaction (qPCR), and to perform metagenomic analysis of microbiome originating from bacteria-derived extracellular vesicles and bacterial cells via 16S rDNA sequencing. Of the 112 subjects, 104 (54 in ID-JPL934 group and 50 in placebo group) completed the entire study protocol. A higher relief of overall symptoms was found in ID-JPL934 group than in placebo group (p = 0.016). Among lower gastrointestinal symptoms, abdominal pain and bloating scores were more decreased in ID-JPL934 group than in placebo group (p < 0.05). The fecal microbiome profiles of the two groups did not differ. However, the qPCR analysis showed significant increase in the levels of Lactobacillus johnsonii and Bifidobacterium lactis in feces post-treatment in ID-JPL934 group than in placebo group (p < 0.05 by repeated measure ANOVA). In conclusion, ID-JPL934 is effective in relieving lower gastrointestinal symptoms. Exposure to ID-JPL934 may increase the abundance of Lactobacillus johnsonii and Bifidobacterium lactis in the gut.Trial registration: ClinicalTrials.gov number, NCT03395626.}, } @article {pmid34158092, year = {2021}, author = {Chakaroun, RM and Massier, L and Heintz-Buschart, A and Said, N and Fallmann, J and Crane, A and Schütz, T and Dietrich, A and Blüher, M and Stumvoll, M and Musat, N and Kovacs, P}, title = {Circulating bacterial signature is linked to metabolic disease and shifts with metabolic alleviation after bariatric surgery.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {105}, pmid = {34158092}, issn = {1756-994X}, mesh = {Adult ; Bacteremia/*blood ; Bariatric Surgery/adverse effects/methods ; *Biomarkers ; Body Weight ; Computational Biology/methods ; DNA Contamination ; DNA, Bacterial ; Diabetes Mellitus, Type 2/blood ; Female ; Glucose/metabolism ; High-Throughput Nucleotide Sequencing ; Humans ; In Situ Hybridization, Fluorescence ; Male ; Metabolic Diseases/*blood/*diagnosis/etiology ; Metagenome ; Metagenomics/methods ; Microbiota ; Middle Aged ; Postoperative Period ; RNA, Ribosomal, 16S ; ROC Curve ; }, abstract = {BACKGROUND: The microbiome has emerged as an environmental factor contributing to obesity and type 2 diabetes (T2D). Increasing evidence suggests links between circulating bacterial components (i.e., bacterial DNA), cardiometabolic disease, and blunted response to metabolic interventions. In this aspect, thorough next-generation sequencing-based and contaminant-aware approaches are lacking. To address this, we tested whether bacterial DNA could be amplified in the blood of subjects with obesity and high metabolic risk under strict experimental and analytical control and whether a putative bacterial signature is related to metabolic improvement after bariatric surgery.

METHODS: Subjects undergoing bariatric surgery were recruited into sex- and BMI-matched subgroups with (n = 24) or without T2D (n = 24). Bacterial DNA in the blood was quantified and prokaryotic 16S rRNA gene amplicons were sequenced. A contaminant-aware approach was applied to derive a compositional microbial signature from bacterial sequences in all subjects at baseline and at 3 and 12 months after surgery. We modeled associations between bacterial load and composition with host metabolic and anthropometric markers. We further tested whether compositional shifts were related to weight loss response and T2D remission. Lastly, bacteria were visualized in blood samples using catalyzed reporter deposition (CARD)-fluorescence in situ hybridization (FISH).

RESULTS: The contaminant-aware blood bacterial signature was associated with metabolic health. Based on bacterial phyla and genera detected in the blood samples, a metabolic syndrome classification index score was derived and shown to robustly classify subjects along their actual clinical group. T2D was characterized by decreased bacterial richness and loss of genera associated with improved metabolic health. Weight loss and metabolic improvement following bariatric surgery were associated with an early and stable increase of these genera in parallel with improvements in key cardiometabolic risk parameters. CARD-FISH allowed the detection of living bacteria in blood samples in obesity.

CONCLUSIONS: We show that the circulating bacterial signature reflects metabolic disease and its improvement after bariatric surgery. Our work provides contaminant-aware evidence for the presence of living bacteria in the blood and suggests a putative crosstalk between components of the blood and metabolism in metabolic health regulation.}, } @article {pmid34154658, year = {2021}, author = {West, PT and Peters, SL and Olm, MR and Yu, FB and Gause, H and Lou, YC and Firek, BA and Baker, R and Johnson, AD and Morowitz, MJ and Hettich, RL and Banfield, JF}, title = {Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {142}, pmid = {34154658}, issn = {2049-2618}, support = {R01 AI049187/AI/NIAID NIH HHS/United States ; R01 AI092531/AI/NIAID NIH HHS/United States ; T32 AI060537/AI/NIAID NIH HHS/United States ; S10 OD018174/OD/NIH HHS/United States ; }, mesh = {Candida parapsilosis/genetics ; *Candidiasis ; Humans ; Infant ; Infant, Newborn ; Microbial Sensitivity Tests ; *Microbiota ; Proteomics ; Transcriptome ; }, abstract = {BACKGROUND: Candida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. parapsilosis has been primarily studied in pure culture, leaving gaps in understanding of its function in a microbiome context.

RESULTS: Here, we compare five unique C. parapsilosis genomes assembled from premature infant fecal samples, three of which are newly reconstructed, and analyze their genome structure, population diversity, and in situ activity relative to reference strains in pure culture. All five genomes contain hotspots of single nucleotide variants, some of which are shared by strains from multiple hospitals. A subset of environmental and hospital-derived genomes share variants within these hotspots suggesting derivation of that region from a common ancestor. Four of the newly reconstructed C. parapsilosis genomes have 4 to 16 copies of the gene RTA3, which encodes a lipid translocase and is implicated in antifungal resistance, potentially indicating adaptation to hospital antifungal use. Time course metatranscriptomics and metaproteomics on fecal samples from a premature infant with a C. parapsilosis blood infection revealed highly variable in situ expression patterns that are distinct from those of similar strains in pure cultures. For example, biofilm formation genes were relatively less expressed in situ, whereas genes linked to oxygen utilization were more highly expressed, indicative of growth in a relatively aerobic environment. In gut microbiome samples, C. parapsilosis co-existed with Enterococcus faecalis that shifted in relative abundance over time, accompanied by changes in bacterial and fungal gene expression and proteome composition.

CONCLUSIONS: The results reveal potentially medically relevant differences in Candida function in gut vs. laboratory environments, and constrain evolutionary processes that could contribute to hospital strain persistence and transfer into premature infant microbiomes. Video abstract.}, } @article {pmid34154652, year = {2021}, author = {Wright, RJ and Bosch, R and Langille, MGI and Gibson, MI and Christie-Oleza, JA}, title = {A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {141}, pmid = {34154652}, issn = {2049-2618}, support = {BB/M01116X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biodegradation, Environmental ; *Microbiota/genetics ; Plastics ; *Polyethylene Terephthalates ; Seawater ; }, abstract = {BACKGROUND: Plastics now pollute marine environments across the globe. On entering these environments, plastics are rapidly colonised by a diverse community of microorganisms termed the plastisphere. Members of the plastisphere have a myriad of diverse functions typically found in any biofilm but, additionally, a number of marine plastisphere studies have claimed the presence of plastic-biodegrading organisms, although with little mechanistic verification. Here, we obtained a microbial community from marine plastic debris and analysed the community succession across 6 weeks of incubation with different polyethylene terephthalate (PET) products as the sole carbon source, and further characterised the mechanisms involved in PET degradation by two bacterial isolates from the plastisphere.

RESULTS: We found that all communities differed significantly from the inoculum and were dominated by Gammaproteobacteria, i.e. Alteromonadaceae and Thalassospiraceae at early time points, Alcanivoraceae at later time points and Vibrionaceae throughout. The large number of encoded enzymes involved in PET degradation found in predicted metagenomes and the observation of polymer oxidation by FTIR analyses both suggested PET degradation was occurring. However, we were unable to detect intermediates of PET hydrolysis with metabolomic analyses, which may be attributed to their rapid depletion by the complex community. To further confirm the PET biodegrading potential within the plastisphere of marine plastic debris, we used a combined proteogenomic and metabolomic approach to characterise amorphous PET degradation by two novel marine isolates, Thioclava sp. BHET1 and Bacillus sp. BHET2. The identification of PET hydrolytic intermediates by metabolomics confirmed that both isolates were able to degrade PET. High-throughput proteomics revealed that whilst Thioclava sp. BHET1 used the degradation pathway identified in terrestrial environment counterparts, these were absent in Bacillus sp. BHET2, indicating that either the enzymes used by this bacterium share little homology with those characterised previously, or that this bacterium uses a novel pathway for PET degradation.

CONCLUSIONS: Overall, the results of our multi-OMIC characterisation of PET degradation provide a significant step forwards in our understanding of marine plastic degradation by bacterial isolates and communities and evidences the biodegrading potential extant in the plastisphere of marine plastic debris. Video abstract.}, } @article {pmid34153824, year = {2021}, author = {Chen, Z and Liu, WS and Zhong, X and Zheng, M and Fei, YH and He, H and Ding, K and Chao, Y and Tang, YT and Wang, S and Qiu, R}, title = {Genome- and community-level interaction insights into the ecological role of archaea in rare earth element mine drainage in South China.}, journal = {Water research}, volume = {201}, number = {}, pages = {117331}, doi = {10.1016/j.watres.2021.117331}, pmid = {34153824}, issn = {1879-2448}, mesh = {*Archaea/genetics ; China ; Genome, Archaeal ; Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Microbial communities play crucial roles in mine drainage generation and remediation. Despite the wide distribution of archaea in the mine ecosystem, their diversity and ecological roles remain less understood than bacteria. Here, we retrieved 56 archaeal metagenome-assembled genomes from a river impacted by rare earth element (REE) mining activities in South China. Genomic analysis showed that archaea represented four distinct lineages, including phyla of Thaumarchaeota, Micrarchaeota, Nanoarchaeota and Thermoplasmata. These archaea represented a considerable fraction (up to 40%) of the total prokaryote community, which might contribute to nitrogen and sulfur cycling in the REE mine drainage. Reconstructed metabolic potential among diverse archaea taxa revealed that archaea were involved in the network of ammonia oxidation, denitrification, sulfate redox reaction, and required substrates supplied by other community members. As the dominant driver of ammonia oxidation, Thaumarchaeota might provide substrates to support the survival of two nano-sized archaea belonging to Micrarchaeota and Nanoarchaeota. Despite the absence of biosynthesis pathways for amino acids and nucleotides, the potential capacity for nitrite reduction (nirD) was observed in Micrarchaeota, indicating that these nano-sized archaea encompassed diverse metabolisms. Moreover, Thermoplasmata, as keystone taxa in community, might be the main genetic donor for the other three archaeal phyla, transferring many environmental resistance related genes (e.g., V/A-type ATPase and Vitamin B12-transporting ATPase). The genetic interactions within archaeal community through horizontal gene transfer might be the key to the formation of archaeal resistance and functional partitioning. This study provides putative metabolic and genetic insights into the diverse archaea taxa from community-level perspectives, and highlights the ecological roles of archaea in REE contaminated aquatic environment.}, } @article {pmid34153757, year = {2021}, author = {Zhou, X and Zhang, M and Krause, SMB and Bu, X and Gu, X and Guo, Z and Jia, Z and Zhou, X and Wang, X and Chen, X and Wang, Y}, title = {Soil aeration rather than methanotrophic community drives methane uptake under drought in a subtropical forest.}, journal = {The Science of the total environment}, volume = {792}, number = {}, pages = {148292}, doi = {10.1016/j.scitotenv.2021.148292}, pmid = {34153757}, issn = {1879-1026}, mesh = {Droughts ; Forests ; Methane ; *Microbiota ; *Soil ; Soil Microbiology ; }, abstract = {Little information is available about the effects of drought on soil methane (CH4) uptake and the underlying feedback of the soil microbial community in forest biomes. More importantly, a meta-analysis of the current literature on this topic revealed that there are virtually no data available in subtropical forests. To fill the abovementioned knowledge gap, we carried out a 3-year investigation of in situ CH4 efflux under drought in a subtropical forest, and found that drought significantly increased soil CH4 uptake (P < 0.001). However, drought did not change oxidation potentials and abundances of methanotrophs, and similar methanotrophic communities were observed between the drought and ambient control sites based on metagenomic sequencing analysis. Active methanotrophic communities were dominated by the genus Methylosinus based on DNA stable-isotope probing analysis. Structural equation model analysis indicated that direct drought-derived pathway, i.e., increasing soil aerations, outweighs the indirect pathway, i.e., altering methanotrophic communities and activities, and plays a predominant role in driving soil CH4 uptake in forest ecosystems. To our knowledge, our work is the first study to investigate the effects of drought on in situ CH4 efflux and the underlying microbial mechanisms in subtropical forests.}, } @article {pmid34153055, year = {2021}, author = {Fay, M and Salazar, JK and Ramachandran, P and Stewart, D}, title = {Microbiomes of commercially-available pine nuts and sesame seeds.}, journal = {PloS one}, volume = {16}, number = {6}, pages = {e0252605}, pmid = {34153055}, issn = {1932-6203}, support = {U19 FD005322/FD/FDA HHS/United States ; }, mesh = {Alteromonadaceae/genetics/isolation & purification ; *Microbiota ; Nuts/microbiology ; Pinus/growth & development/*microbiology ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Seeds/microbiology ; Sesamum/growth & development/*microbiology ; Streptococcus/genetics/isolation & purification ; }, abstract = {Metagenomic analysis of food is becoming more routine and can provide important information pertaining to the shelf life potential and the safety of these products. However, less information is available on the microbiomes associated with low water activity foods. Pine nuts and sesame seeds, and food products which contain these ingredients, have been associated with recalls due to contamination with bacterial foodborne pathogens. The objective of this study was to identify the microbial community of pine nuts and sesame seeds using targeted 16S rRNA sequencing technology. Ten different brands of each seed type were assessed, and core microbiomes were determined. A total of 21 and 16 unique taxa with proportional abundances >1% in at least one brand were identified in the pine nuts and sesame seeds, respectively. Members of the core pine nut microbiome included the genera Alishewanella, Aminivibrio, Mycoplasma, Streptococcus, and unassigned OTUs in the families of Desulfobacteraceae and Xanthomonadaceae. For sesame seeds, the core microbiome included Aminivibrio, Chryseolina, Okibacterium, and unassigned OTUs in the family Flavobacteriaceae. The microbiomes of these seeds revealed that these products are dominated by environmental bacterial genera commonly isolated from soil, water, and plants; bacterial genera containing species known as commensal organisms were also identified. Understanding these microbiomes can aid in the risk assessment of these products by identifying food spoilage potential and community members which may co-enrich with foodborne bacterial pathogens.}, } @article {pmid34152440, year = {2021}, author = {Schmidt, BM and Erb-Downward, J and Ranjan, P and Dickson, R}, title = {Metagenomics to Identify Pathogens in Diabetic Foot Ulcers and the Potential Impact for Clinical Care.}, journal = {Current diabetes reports}, volume = {21}, number = {8}, pages = {26}, pmid = {34152440}, issn = {1539-0829}, mesh = {Adult ; *Diabetes Mellitus ; *Diabetic Foot ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Wound Healing ; }, abstract = {PURPOSE OF REVIEW: Diabetes mellitus may affect every third adult American by 2050, and about one-third will develop a diabetic foot ulcer (DFU) during their lifetime. The current standard of care results in healing of less than 50% of all DFUs. Many individuals with DFU develop limb-threatening infection which place them at risk for additional morbidity and mortality. We review research associated with culture-independent next-generation sequencing techniques pertaining to diabetic foot ulcers and their potential for clinical application.

RECENT FINDINGS: Diabetic foot ulcers are a growing problem and clinicians are limited by their reliance on conventional culture. Metagenomic sequencing technology provides an unparalleled viewpoint of the polymicrobial constituency of DFU. The microbiome techniques used to study the microbial constituency of DFU may offer insight to improve care for these patients, but without standardized approaches in research based on real-world clinical practices, a significant knowledge gap will remain.}, } @article {pmid34152425, year = {2021}, author = {Thilagavathi, R and Nakkeeran, S and Balachandar, D and Raguchander, T and Samiyappan, R}, title = {Bacterial community analysis on Sclerotium-suppressive soil.}, journal = {Archives of microbiology}, volume = {203}, number = {7}, pages = {4539-4548}, pmid = {34152425}, issn = {1432-072X}, mesh = {Antibiosis/physiology ; *Bacteria/classification/genetics ; Basidiomycota/physiology ; *Biodiversity ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Difficulties in controlling the soil-borne plant pathogenic fungus Sclerotium rolfsii favoured the analysis of its suppressive soil for better understanding. In the present study, culture-independent molecular technique was used to analyse the bacterial communities of suppressive soil and conducive soil. Hence, metagenomic DNAs from both kinds of soils were directly extracted and their sequence polymorphism was analysed by targeting hypervariable domains, V4 + V5, of the 16S rRNA gene. The results of 16S rRNA gene-driven bacterial community diversity analysis along with soil physicochemical and biological properties clearly discriminated S. rolfsii suppressive soil from conducive soil. The dominant phylogenetic group of suppressive soil is Actinobacteria followed by Proteobacteria. The other groups include Acidobacteria, Firmicutes and Cyanobacteria. In contrast, conducive soil had very few Actinobacterial sequences and was dominated by Gamma- and Betaproteobacteria. Based on the relative proportion of different bacterial communities, their diversity and species richness were observed more in suppressive soil than in conducive soil. The present study identifies the dominant bacterial community which shares S. rolfsii suppressiveness.}, } @article {pmid34152069, year = {2021}, author = {Fontana, F and Mancabelli, L and Lugli, GA and Taracchini, C and Alessandri, G and Longhi, G and Anzalone, R and Viappiani, A and Famo, R and Brognan, M and Micondo, KH and Turroni, F and Ventura, M and D'Alfonso, R and Milani, C}, title = {Investigating the infant gut microbiota in developing countries: worldwide metagenomic meta-analysis involving infants living in sub-urban areas of Côte d'Ivoire.}, journal = {Environmental microbiology reports}, volume = {13}, number = {5}, pages = {626-636}, pmid = {34152069}, issn = {1758-2229}, mesh = {Cote d'Ivoire ; Developing Countries ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In recent decades, infants' gut microbiota has aroused constant scientific interest, primarily due to early- and long-term repercussions on the host health. In this context, nutritional challenges such as those found in less developed countries can influence infants' gut microbiota development, thus generating potentially critical health outcomes. However, comprehensive investigations regarding species-level differences in the infant gut microbiota's composition between urbanized and rural countries are still missing. In this study, 16S rRNA and Shallow Shotgun metagenomics sequencing were exploited to dissect the microbial community's species-level composition of 11 faecal samples collected from infants living in a semi-urban area of Sub-Saharan Africa, i.e. Côte d'Ivoire. Moreover, the generated data were coupled with those retrieved from public available metagenomic repositories, including two rural communities and 13 urban communities of industrialized countries. The meta-analysis led to the identification of Infant Species Community States Type (ISCSTs) and microbial species covariances, which were exploited to reveal key signatures of infants living in rural and semi-urban societies. Remarkably, analysis of rural and semi-urban datasets revealed shifts from ISCSTs prevalent in urbanized populations with putative health implications. Thus, indicating the need for population-wide investigations aimed to define the factors determining such potentially harmful gut microbial communities' signatures.}, } @article {pmid34151933, year = {2021}, author = {Chen, X and Liu, L and Zhang, W and Yang, J and Wong, KC}, title = {Human host status inference from temporal microbiome changes via recurrent neural networks.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {6}, pages = {}, doi = {10.1093/bib/bbab223}, pmid = {34151933}, issn = {1477-4054}, mesh = {Algorithms ; Computational Biology/*methods ; Data Analysis ; Deep Learning ; *Host Microbial Interactions ; Humans ; Metagenomics/methods ; *Microbiota ; *Neural Networks, Computer ; RNA, Ribosomal, 16S ; }, abstract = {With the rapid increase in sequencing data, human host status inference (e.g. healthy or sick) from microbiome data has become an important issue. Existing studies are mostly based on single-point microbiome composition, while it is rare that the host status is predicted from longitudinal microbiome data. However, single-point-based methods cannot capture the dynamic patterns between the temporal changes and host status. Therefore, it remains challenging to build good predictive models as well as scaling to different microbiome contexts. On the other hand, existing methods are mainly targeted for disease prediction and seldom investigate other host statuses. To fill the gap, we propose a comprehensive deep learning-based framework that utilizes longitudinal microbiome data as input to infer the human host status. Specifically, the framework is composed of specific data preparation strategies and a recurrent neural network tailored for longitudinal microbiome data. In experiments, we evaluated the proposed method on both semi-synthetic and real datasets based on different sequencing technologies and metagenomic contexts. The results indicate that our method achieves robust performance compared to other baseline and state-of-the-art classifiers and provides a significant reduction in prediction time.}, } @article {pmid34151600, year = {2021}, author = {Jiao, N and Loomba, R and Yang, ZH and Wu, D and Fang, S and Bettencourt, R and Lan, P and Zhu, R and Zhu, L}, title = {Alterations in bile acid metabolizing gut microbiota and specific bile acid genes as a precision medicine to subclassify NAFLD.}, journal = {Physiological genomics}, volume = {53}, number = {8}, pages = {336-348}, pmid = {34151600}, issn = {1531-2267}, support = {P42 ES010337/ES/NIEHS NIH HHS/United States ; R01 DK106419/DK/NIDDK NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; }, mesh = {3-alpha-Hydroxysteroid Dehydrogenase (B-Specific)/genetics/metabolism ; Bile Acids and Salts/*genetics/*metabolism ; Case-Control Studies ; Coenzyme A Ligases/genetics/metabolism ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Humans ; Hydroxysteroid Dehydrogenases/genetics/metabolism ; Male ; Middle Aged ; Non-alcoholic Fatty Liver Disease/*genetics/metabolism/*microbiology ; Precision Medicine ; Reproducibility of Results ; }, abstract = {Multiple mechanisms for the gut microbiome contributing to the pathogenesis of nonalcoholic fatty liver disease (NAFLD) have been implicated. Here, we aim to investigate the contribution and potential application for altered bile acids (BA) metabolizing microbes in NAFLD by post hoc analysis of whole metagenome sequencing (WMS) data. The discovery cohort consisted of 86 well-characterized patients with biopsy-proven NAFLD and 38 healthy controls. Assembly-based analysis was performed to identify BA-metabolizing microbes. Statistical tests, feature selection, and microbial coabundance analysis were integrated to identify microbial alterations and markers in NAFLD. An independent validation cohort was subjected to similar analyses. NAFLD microbiota exhibited decreased diversity and microbial associations. We established a classifier model with 53 differential species exhibiting a robust diagnostic accuracy [area under the receiver-operator curve (AUC) = 0.97] for detecting NAFLD. Next, eight important differential pathway markers including secondary BA biosynthesis were identified. Specifically, increased abundance of 7α-hydroxysteroid dehydrogenase (7α-HSDH), 3α-hydroxysteroid dehydrogenase (baiA), and bile acid-coenzyme A ligase (baiB) was detected in NAFLD. Furthermore, 10 of 50 BA-metabolizing metagenome-assembled genomes (MAGs) from Bacteroides ovatus and Eubacterium biforme were dominant in NAFLD and interplayed as a synergetic ecological guild. Importantly, two subtypes of patients with NAFLD were observed according to secondary BA metabolism potentials. Elevated capability for secondary BA biosynthesis was also observed in the validation cohort. These bacterial BA-metabolizing genes and microbes identified in this study may serve as disease markers. Microbial differences in BA-metabolism and strain-specific differences among patients highlight the potential for precision medicine in NAFLD treatment.}, } @article {pmid34151454, year = {2022}, author = {Casado-Bedmar, M and de-Faria, FM and Biskou, O and Lindqvist, CM and Ranasinghe, PD and Bednarska, O and Peterson, C and Walter, SA and Carlson, M and Keita, ÅV}, title = {Elevated F-EDN correlates with mucosal eosinophil degranulation in patients with IBS-A possible association with microbiota?.}, journal = {Journal of leukocyte biology}, volume = {111}, number = {3}, pages = {655-665}, doi = {10.1002/JLB.4A0521-228R}, pmid = {34151454}, issn = {1938-3673}, mesh = {Bacteria/metabolism ; Eosinophil-Derived Neurotoxin/metabolism ; Eosinophils/metabolism ; Humans ; *Irritable Bowel Syndrome/metabolism/pathology ; *Microbiota ; Mucous Membrane/metabolism ; }, abstract = {Eosinophils have been linked to functional dyspepsia; however, less is known about their role in irritable bowel syndrome (IBS). This study tested the hypothesis of alterations in levels of fecal eosinophil-derived neurotoxin (F-EDN) and eosinophil density and degranulation within the colonic mucosa of IBS patients compared with healthy controls (HC). Colonic biopsies were collected from 37 IBS patients and 20 HC and analyzed for eosinophil numbers and local degranulation of eosinophil cationic protein (ECP) by histologic procedures. Fecal samples were collected for F-EDN and microbiota analysis. Differentiated 15HL-60 cells were used in vitro to investigate the direct effect of live bacteria on eosinophil activation measured by a colorimetric assay with o-phenylenediamine (OPD) substrate. We observed a higher number of eosinophils and increased extracellular ECP in the mucosa of IBS patients compared with HC. Moreover, F-EDN levels in IBS samples were elevated compared with HC and positively correlated to extracellular ECP. Metagenomic analysis showed significant correlations between bacterial composition and eosinophil measurements in both HC and IBS patients. In vitro experiments revealed an increased degranulation of 15HL-60 after stimulation with Salmonella typhimurium, Salmonella enterica, and Yersinia enterocolitica. To conclude, we could demonstrate alterations related to eosinophils in IBS, and, for the first time, a positive correlation between F-EDN levels and degranulated eosinophils in the colonic mucosa of IBS patients. Together our results suggest that eosinophils play a role in the pathophysiology of IBS and the mechanisms might be linked to an altered microbiota.}, } @article {pmid34150671, year = {2021}, author = {Townsend, EM and Kelly, L and Muscatt, G and Box, JD and Hargraves, N and Lilley, D and Jameson, E}, title = {The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {643214}, pmid = {34150671}, issn = {2235-2988}, support = {BB/M017982/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria ; *Bacteriophages ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Virome ; }, abstract = {The investigation of the microbial populations of the human body, known as the microbiome, has led to a revolutionary field of science, and understanding of its impacts on human development and health. The majority of microbiome research to date has focussed on bacteria and other kingdoms of life, such as fungi. Trailing behind these is the interrogation of the gut viruses, specifically the phageome. Bacteriophages, viruses that infect bacterial hosts, are known to dictate the dynamics and diversity of bacterial populations in a number of ecosystems. However, the phageome of the human gut, while of apparent importance, remains an area of many unknowns. In this paper we discuss the role of bacteriophages within the human gut microbiome. We examine the methods used to study bacteriophage populations, how this evolved over time and what we now understand about the phageome. We review the phageome development in infancy, and factors that may influence phage populations in adult life. The role and action of the phageome is then discussed at both a biological-level, and in the broader context of human health and disease.}, } @article {pmid34149688, year = {2021}, author = {Pérez-Sáez, MJ and Uffing, A and Leon, J and Murakami, N and Watanabe, A and Borges, TJ and Sabbisetti, VS and Cureton, P and Kenyon, V and Keating, L and Yee, K and Fernandes Satiro, CA and Serena, G and Hildebrandt, F and Riella, CV and Libermann, TA and Wang, M and Pascual, J and Bonventre, JV and Cravedil, P and Fasano, A and Riella, LV}, title = {Immunological Impact of a Gluten-Free Dairy-Free Diet in Children With Kidney Disease: A Feasibility Study.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {624821}, pmid = {34149688}, issn = {1664-3224}, support = {K08 DK120868/DK/NIDDK NIH HHS/United States ; R01 DK076683/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Biomarkers/blood/urine ; Child ; Child, Preschool ; Cytokines/blood ; Dairy Products/*adverse effects ; *Diet, Gluten-Free/adverse effects ; Feasibility Studies ; Female ; Gastrointestinal Microbiome ; Humans ; Infant ; Inflammation Mediators/blood ; Intestines/microbiology ; Male ; Nephrotic Syndrome/*congenital/diagnosis/diet therapy/immunology/microbiology ; Pilot Projects ; Proof of Concept Study ; Prospective Studies ; T-Lymphocytes, Regulatory/immunology/metabolism ; Th17 Cells/immunology/metabolism ; Time Factors ; Treatment Outcome ; Young Adult ; }, abstract = {Kidney disease affects 10% of the world population and is associated with increased mortality. Steroid-resistant nephrotic syndrome (SRNS) is a leading cause of end-stage kidney disease in children, often failing standard immunosuppression. Here, we report the results of a prospective study to investigate the immunological impact and safety of a gluten-free and dairy-free (GF/DF) diet in children with SRNS. The study was organized as a four-week summer camp implementing a strict GF/DF diet with prospective collection of blood, urine and stool in addition to whole exome sequencing WES of DNA of participants. Using flow cytometry, proteomic assays and microbiome metagenomics, we show that GF/DF diet had a major anti-inflammatory effect in all participants both at the protein and cellular level with 4-fold increase in T regulatory/T helper 17 cells ratio and the promotion of a favorable regulatory gut microbiota. Overall, GF/DF can have a significant anti-inflammatory effect in children with SRNS and further trials are warranted to investigate this potential dietary intervention in children with SRNS.}, } @article {pmid34149685, year = {2021}, author = {Das, Q and Shay, J and Gauthier, M and Yin, X and Hasted, TL and Ross, K and Julien, C and Yacini, H and Kennes, YM and Warriner, K and Marcone, MF and Diarra, MS}, title = {Effects of Vaccination Against Coccidiosis on Gut Microbiota and Immunity in Broiler Fed Bacitracin and Berry Pomace.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {621803}, pmid = {34149685}, issn = {1664-3224}, mesh = {Animal Feed ; Animal Nutritional Physiological Phenomena ; Animals ; Bacitracin ; Bacterial Infections/*immunology ; Bird Diseases/*immunology ; Blueberry Plants ; Cecum/*microbiology ; Chickens/*immunology ; Coccidia/*physiology ; Coccidiosis/*immunology ; Eimeria/*physiology ; Gastrointestinal Microbiome/*immunology ; Immunity, Humoral ; Lipid Metabolism ; Protozoan Vaccines/*immunology ; Vaccination ; Vaccinium macrocarpon ; }, abstract = {Feeding practices have been found to influence gut microbiota which play a major role in immunity of poultry. In the present study, changes in cecal microbiota and humoral responses resulting in the 55 ppm bacitracin (BACI), 1% each of cranberry (CP1) and wild blueberry (BP1) pomace alone or in combination (CP+BP) feeding in broiler Cobb 500 vaccinated or not against coccidiosis were investigated. In the non-vaccinated group, no significant treatment effects were observed on performance parameters. Vaccination significantly affected bird's performance parameters particularly during the growing phase from 10 to 20 days of age. In general, the prevalence of coccidiosis and necrotic enteritis (NE) was reduced by vaccination (P < 0.05). BACI-treated birds showed low intestinal lesion scores, and both CP1 and BP1 feed supplementations reduced Eimeria acervulina and Clostridium perfringens incidences similar to BACI. Vaccination induced change in serum enzymes, minerals, and lipid levels in 21-day old birds while, levels of triglyceride (TRIG) and non-esterified fatty acids (NEFA) were higher (P < 0.05) in CP1 treated non-vaccinated group than in the control. The levels of NEFA were lower in BACI- and CP1-fed birds than in the control in non-vaccinated day 28 old birds. The highest levels of all estimated three immunoglobulins (IgY, IgM, and IgA) were found in the vaccinated birds. Metagenomics analysis of the cecal bacterial community in 21-day old birds showed the presence of Firmicutes (90%), Proteobacteria (5%), Actinobacteria (2%), and Bacteroidetes (2%). In the vaccinated group, an effect of BACI was noted on Proteobacteria (P = 0.03). Vaccination and/or dietary treatments influenced the population of Lactobacillaceae, Enterobacteriaceae, Clostridiaceae, and Streptococcaceae which were among the most abundant families. Overall, this study revealed that besides their beneficial effects on performance, alike bacitracin, berry pomaces in poultry feed have profound impacts on the chicken cecal microbiota and blood metabolites that could be influenced by vaccination against coccidiosis.}, } @article {pmid34149649, year = {2021}, author = {Morrison, MD and Thissen, JB and Karouia, F and Mehta, S and Urbaniak, C and Venkateswaran, K and Smith, DJ and Jaing, C}, title = {Investigation of Spaceflight Induced Changes to Astronaut Microbiomes.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {659179}, pmid = {34149649}, issn = {1664-302X}, abstract = {The International Space Station (ISS) is a uniquely enclosed environment that has been continuously occupied for the last two decades. Throughout its operation, protecting the health of the astronauts on-board has been a high priority. The human microbiome plays a significant role in maintaining human health, and disruptions in the microbiome have been linked to various diseases. To evaluate the effects of spaceflight on the human microbiome, body swabs and saliva samples were collected from four ISS astronauts on consecutive expeditions. Astronaut samples were analyzed using shotgun metagenomic sequencing and microarrays to characterize the microbial biodiversity before, during, and after the astronauts' time onboard the ISS. Samples were evaluated at an individual and population level to identify changes in microbial diversity and abundance. No significant changes in the number or relative abundance of taxa were observed between collection time points when samples from all four astronauts were analyzed together. When the astronauts' saliva samples were analyzed individually, the saliva samples of some astronauts showed significant changes in the relative abundance of taxa during and after spaceflight. The relative abundance of Prevotella in saliva samples increased during two astronauts' time onboard the ISS while the relative abundance of other commensal taxa such as Neisseria, Rothia, and Haemophilus decreased. The abundance of some antimicrobial resistance genes within the saliva samples also showed significant changes. Most notably, elfamycin resistance gene significantly increased in all four astronauts post-flight and a CfxA6 beta-lactam marker significantly increased during spaceflight but returned to normal levels post-flight. The combination of both shotgun metagenomic sequencing and microarrays showed the benefit of both technologies in monitoring microbes on board the ISS. There were some changes in each astronaut's microbiome during spaceflight, but these changes were not universal for all four astronauts. Two antimicrobial resistance gene markers did show a significant change in abundance in the saliva samples of all four astronauts across their collection times. These results provide insight for future ISS microbial monitoring studies and targets for antimicrobial resistance screenings.}, } @article {pmid34148877, year = {2021}, author = {Shalin, TV and Jnana, A and Sriranjin, SJ and Tanwar, AS and Brand, A and Murali, TS and Satyamoorthy, K and Gangadharan, GG}, title = {Exploring the signature gut and oral microbiome in individuals of specific Ayurveda prakriti.}, journal = {Journal of biosciences}, volume = {46}, number = {}, pages = {}, pmid = {34148877}, issn = {0973-7138}, mesh = {Adult ; Bacterial Typing Techniques ; Bacteroides/classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics ; Haemophilus/classification/genetics/isolation & purification ; Healthy Volunteers ; Humans ; Male ; Medicine, Ayurvedic/*methods ; *Metagenome ; Mouth/microbiology ; Neisseria/classification/genetics/isolation & purification ; Phylogeny ; Porphyromonas/classification/genetics/isolation & purification ; Precision Medicine/*methods ; Prevotella/classification/genetics/isolation & purification ; Streptococcus/classification/genetics/isolation & purification ; Symbiosis/*physiology ; Veillonella/classification/genetics/isolation & purification ; Veillonellaceae/classification/genetics/isolation & purification ; }, abstract = {Diagnosis and treatment of various diseases in Ayurveda, the Indian system of medicine, relies on 'prakriti' phenotyping of individuals into predominantly three constitutions, kapha, pitta and vata. Recent studies propose that microbiome play an integral role in precision medicine. A study of the relationship between prakriti - the basis of personalized medicine in Ayurveda and that of gut microbiome, and possible biomarker of an individual's health, would vastly improve precision therapy. Towards this, we analyzed bacterial metagenomes from buccal (oral microbiome) and fecal (gut microbiome) samples of 272 healthy individuals of various predominant prakritis. Major bacterial genera from gut microbiome included Prevotella, Bacteroides and Dialister while oral microbiome included Streptococcus, Neisseria, Veilonella, Haemophilus, Porphyromonas and Prevotella. Though the core microbiome was shared across all individuals, we found prakriti specific signatures such as preferential presence of Paraprevotella and Christensenellaceae in vata individuals. A comparison of core gut microbiome of each prakriti with a database of 'healthy' microbes identified microbes unique to each prakriti with functional roles similar to the physiological characteristics of various prakritis as described in Ayurveda. Our findings provide evidence to Ayurvedic interventions based on prakriti phenotyping and possible microbial biomarkers that can stratify the heterogenous population and aid in precision therapy.}, } @article {pmid34143954, year = {2021}, author = {Henrick, BM and Rodriguez, L and Lakshmikanth, T and Pou, C and Henckel, E and Arzoomand, A and Olin, A and Wang, J and Mikes, J and Tan, Z and Chen, Y and Ehrlich, AM and Bernhardsson, AK and Mugabo, CH and Ambrosiani, Y and Gustafsson, A and Chew, S and Brown, HK and Prambs, J and Bohlin, K and Mitchell, RD and Underwood, MA and Smilowitz, JT and German, JB and Frese, SA and Brodin, P}, title = {Bifidobacteria-mediated immune system imprinting early in life.}, journal = {Cell}, volume = {184}, number = {15}, pages = {3884-3898.e11}, doi = {10.1016/j.cell.2021.05.030}, pmid = {34143954}, issn = {1097-4172}, support = {S10 OD018174/OD/NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bifidobacterium/*physiology ; Biomarkers/metabolism ; Breast Feeding ; CD4-Positive T-Lymphocytes/immunology ; Cell Polarity ; Cell Proliferation ; Cytokines/metabolism ; Feces/chemistry/microbiology ; Galectin 1/metabolism ; Gastrointestinal Microbiome ; Humans ; Immune System/*growth & development/*microbiology ; Indoles/metabolism ; Infant, Newborn ; Inflammation/blood/genetics ; Intestinal Mucosa/immunology ; Metabolome ; Milk, Human/chemistry ; Oligosaccharides/metabolism ; Th17 Cells/immunology ; Th2 Cells/immunology ; Water ; }, abstract = {Immune-microbe interactions early in life influence the risk of allergies, asthma, and other inflammatory diseases. Breastfeeding guides healthier immune-microbe relationships by providing nutrients to specialized microbes that in turn benefit the host's immune system. Such bacteria have co-evolved with humans but are now increasingly rare in modern societies. Here we show that a lack of bifidobacteria, and in particular depletion of genes required for human milk oligosaccharide (HMO) utilization from the metagenome, is associated with systemic inflammation and immune dysregulation early in life. In breastfed infants given Bifidobacterium infantis EVC001, which expresses all HMO-utilization genes, intestinal T helper 2 (Th2) and Th17 cytokines were silenced and interferon β (IFNβ) was induced. Fecal water from EVC001-supplemented infants contains abundant indolelactate and B. infantis-derived indole-3-lactic acid (ILA) upregulated immunoregulatory galectin-1 in Th2 and Th17 cells during polarization, providing a functional link between beneficial microbes and immunoregulation during the first months of life.}, } @article {pmid34143825, year = {2021}, author = {Onywera, H and Anejo-Okopi, J and Mwapagha, LM and Okendo, J and Williamson, AL}, title = {Predictive functional analysis reveals inferred features unique to cervicovaginal microbiota of African women with bacterial vaginosis and high-risk human papillomavirus infection.}, journal = {PloS one}, volume = {16}, number = {6}, pages = {e0253218}, pmid = {34143825}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Cervix Uteri/*microbiology ; Female ; Humans ; Lactobacillus/isolation & purification ; Microbiota/*physiology ; Papillomavirus Infections/*microbiology ; Vagina/*microbiology ; Vaginosis, Bacterial/*microbiology ; Young Adult ; }, abstract = {Mounting evidence suggests that Lactobacillus species may not necessarily be the sine qua non of healthy cervicovaginal microbiota (CVM), especially among reproductive-age African women. A majority of African women have high-diversity non-Lactobacillus-dominated CVM whose bacterial functions remain poorly characterized. Functional profiling of the CVM is vital for investigating human host-microbiota interactions in health and disease. Here, we investigated the functional potential of L. iners-dominated and high-diversity non-Lactobacillus-dominated CVM of 75 African women with and without bacterial vaginosis (BV) and high-risk human papillomavirus (HR-HPV) infection. Functional contents were predicted using PICRUSt. Microbial taxonomic diversity, BV, and HR-HPV infection statuses were correlated with the inferred functional composition of the CVM. Differentially abundant inferred functional categories were identified using linear discriminant analysis (LDA) effect size (LEfSe) (p-value <0.05 and logarithmic LDA score >2.0). Of the 75 women, 56 (74.7%), 35 (46.7%), and 29 (38.7%) had high-diversity non-Lactobacillus-dominated CVM, BV, and HR-HPV infection, respectively. Alpha diversity of the inferred functional contents (as measured by Shannon diversity index) was significantly higher in women with high-diversity non-Lactobacillus-dominated CVM and BV than their respective counterparts (H statistic ≥11.5, q-value <0.001). Ordination of the predicted functional metagenome content (using Bray-Curtis distances) showed that the samples segregated according to the extent of microbial taxonomic diversity and BV (pseudo-F statistic ≥19.6, q-value = 0.001) but not HR-HPV status (pseudo-F statistic = 1.7, q-value = 0.159). LEfSe analysis of the inferred functional categories revealed that transport systems (including ABC transporters) and transcription factors were enriched in high-diversity CVM. Interestingly, transcription factors and sporulation functional categories were uniquely associated with high-diversity CVM, BV, and HR-HPV infection. Our predictive functional analysis reveals features unique to high-diversity CVM, BV and HR-HPV infections. Such features may represent important biomarkers of BV and HR-HPV infection. Our findings require proof-of-concept functional studies to examine the relevance of these potential biomarkers in women's reproductive health and disease.}, } @article {pmid34143768, year = {2021}, author = {Prost, V and Gazut, S and Brüls, T}, title = {A zero inflated log-normal model for inference of sparse microbial association networks.}, journal = {PLoS computational biology}, volume = {17}, number = {6}, pages = {e1009089}, pmid = {34143768}, issn = {1553-7358}, mesh = {Algorithms ; Computational Biology ; Computer Simulation ; Metagenome ; Metagenomics/statistics & numerical data ; Microbial Consortia/genetics/physiology ; *Microbiota/genetics/physiology ; *Models, Biological ; Multivariate Analysis ; Normal Distribution ; Synthetic Biology ; }, abstract = {The advent of high-throughput metagenomic sequencing has prompted the development of efficient taxonomic profiling methods allowing to measure the presence, abundance and phylogeny of organisms in a wide range of environmental samples. Multivariate sequence-derived abundance data further has the potential to enable inference of ecological associations between microbial populations, but several technical issues need to be accounted for, like the compositional nature of the data, its extreme sparsity and overdispersion, as well as the frequent need to operate in under-determined regimes. The ecological network reconstruction problem is frequently cast into the paradigm of Gaussian Graphical Models (GGMs) for which efficient structure inference algorithms are available, like the graphical lasso and neighborhood selection. Unfortunately, GGMs or variants thereof can not properly account for the extremely sparse patterns occurring in real-world metagenomic taxonomic profiles. In particular, structural zeros (as opposed to sampling zeros) corresponding to true absences of biological signals fail to be properly handled by most statistical methods. We present here a zero-inflated log-normal graphical model (available at https://github.com/vincentprost/Zi-LN) specifically aimed at handling such "biological" zeros, and demonstrate significant performance gains over state-of-the-art statistical methods for the inference of microbial association networks, with most notable gains obtained when analyzing taxonomic profiles displaying sparsity levels on par with real-world metagenomic datasets.}, } @article {pmid34143307, year = {2022}, author = {Omori, M and Kato-Kogoe, N and Sakaguchi, S and Kamiya, K and Fukui, N and Gu, YH and Nakamura, S and Nakano, T and Hoshiga, M and Imagawa, A and Kit, CH and Tamaki, J and Ueno, T}, title = {Characterization of salivary microbiota in elderly patients with type 2 diabetes mellitus: a matched case-control study.}, journal = {Clinical oral investigations}, volume = {26}, number = {1}, pages = {493-504}, pmid = {34143307}, issn = {1436-3771}, mesh = {Aged ; Case-Control Studies ; *Diabetes Mellitus, Type 2 ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Saliva ; }, abstract = {OBJECTIVE: The importance of oral health in type 2 diabetes mellitus (T2DM) is widely recognized; however, oral microbiota characteristics associated with T2DM in the elderly population are not well-understood. This study was conducted to evaluate the characteristics of the salivary microbiota in elderly Japanese patients with T2DM.

METHODS: Saliva samples were collected from 42 elderly Japanese patients with T2DM and 42 age- and sex-matched subjects without T2DM (control). 16S ribosomal RNA metagenomic analysis and comparative analysis of both groups were performed. Random forest classification by machine learning was performed to discriminate between the salivary microbiota in the two groups.

RESULTS: There were significant differences in the overall salivary microbiota structure between the T2DM and control groups (beta diversity; unweighted UniFrac distances, p = 0.001; weighted UniFrac distances, p = 0.001). The phylum Firmicutes was abundant in patients with T2DM, whereas the phylum Bacteroidetes was abundant in controls. The T2DM prediction model by random forest based on salivary microbiota data was verified with a high predictive potential in five cross-validation tests (area under the curve (AUC) = 0.938 (95% CI, 0.824-1.000)).

CONCLUSION: Characterization revealed that the salivary microbiota profile of the elderly patients with T2DM is significantly distinct from that of the controls.

CLINICAL RELEVANCE: These data indicate the necessity of oral health management based on the characteristics of the salivary microbiota in elderly patients with T2DM. Our findings will contribute to future research on the development of new diagnostic and therapeutic methods for this purpose.}, } @article {pmid34140187, year = {2021}, author = {Cruz-O'Byrne, R and Piraneque-Gambasica, N and Aguirre-Forero, S}, title = {Microbial diversity associated with spontaneous coffee bean fermentation process and specialty coffee production in northern Colombia.}, journal = {International journal of food microbiology}, volume = {354}, number = {}, pages = {109282}, doi = {10.1016/j.ijfoodmicro.2021.109282}, pmid = {34140187}, issn = {1879-3460}, mesh = {Bacteria/classification/metabolism ; *Biodiversity ; *Coffea/microbiology ; Colombia ; *Fermentation ; Fungi/classification/metabolism ; *Microbiota/physiology ; *Seeds/metabolism/microbiology ; }, abstract = {Coffee fermentation involves the action of microorganisms, whose metabolism has a significant influence on the composition of the beans and, consequently, on the beverage's sensory characteristics. In this study, the microbial diversity during the wet fermentation of Coffea arabica L. in the Sierra Nevada of Santa Marta (SNSM) in Colombia was explored by high-throughput sequencing and the resulting cup quality through the standards of the Specialty Coffee Association. The taxonomic assignment of sequence reads showed a high microbial diversity comprised of 695 bacterial and 156 fungal genera. The microbial community was dominated by the Lactic Acid Bacteria (LAB) Leuconostoc, the yeast Kazachstania, and the Acetic Acid Bacteria (AAB) Acetobacter. Co-occurrence relationships suggested synergistic patterns between populations of LAB-AAB, yeasts-AAB, Leuconostoc-Prevotella, LAB-ABB-Selenomonas, and yeasts-fungi-nonLAB-nonAAB, which may result in the production of metabolites that positively impact the sensory attributes of coffee. The beverages produced were classified as specialty coffees, and their score was positively influenced by the fungal richness and the abundance of unclassified Lactobacillales, Pichia, and Pseudomonas. The findings show the richness and microbial diversity of the SNSM and serve as input for future research such as the analysis of microbial-derived metabolites and the establishment of starter cultures in coffee processing that guarantee the generation of high-quality beverages, the standardization of processes, the reduction of economic losses, and the production of value-added products that allow taking advantage of specialty coffee market.}, } @article {pmid34140026, year = {2021}, author = {Ma, W and Nguyen, LH and Song, M and Wang, DD and Franzosa, EA and Cao, Y and Joshi, A and Drew, DA and Mehta, R and Ivey, KL and Strate, LL and Giovannucci, EL and Izard, J and Garrett, W and Rimm, EB and Huttenhower, C and Chan, AT}, title = {Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {102}, pmid = {34140026}, issn = {1756-994X}, support = {K99 DK119412/DK/NIDDK NIH HHS/United States ; R01 CA202704/CA/NCI NIH HHS/United States ; R01 DK101495/DK/NIDDK NIH HHS/United States ; U01 CA152904/CA/NCI NIH HHS/United States ; U01 CA167552/CA/NCI NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; R01 HL035464/HL/NHLBI NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; R00 DK119412/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R21 AA027608/AA/NIAAA NIH HHS/United States ; P30 DK046200/DK/NIDDK NIH HHS/United States ; K24 DK098311/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Age Factors ; Aged ; Aged, 80 and over ; Biomarkers ; C-Reactive Protein ; Chronic Disease ; *Diet ; *Dietary Fiber/administration & dosage ; Disease Susceptibility ; Dysbiosis ; Feces/microbiology ; *Gastrointestinal Microbiome ; Health Personnel ; Humans ; Inflammation/*epidemiology/*etiology ; Inflammation Mediators ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Public Health Surveillance ; Sex Factors ; United States/epidemiology ; }, abstract = {BACKGROUND: A higher intake of dietary fiber is associated with a decreased risk of chronic inflammatory diseases such as cardiovascular disease and inflammatory bowel disease. This may function in part due to abrogation of chronic systemic inflammation induced by factors such as dysbiotic gut communities. Data regarding the detailed influences of long-term and recent intake of differing dietary fiber sources on the human gut microbiome are lacking.

METHODS: In a cohort of 307 generally healthy men, we examined gut microbiomes, profiled by shotgun metagenomic and metatranscriptomic sequencing, and long-term and recent dietary fiber intake in relation to plasma levels of C-reactive protein (CRP), an established biomarker for chronic inflammation. Data were analyzed using multivariate linear mixed models.

RESULTS: We found that inflammation-associated gut microbial configurations corresponded with higher CRP levels. A greater intake of dietary fiber was associated with shifts in gut microbiome composition, particularly Clostridiales, and their potential for carbohydrate utilization via polysaccharide degradation. This was particularly true for fruit fiber sources (i.e., pectin). Most striking, fiber intake was associated with significantly greater CRP reduction in individuals without substantial Prevotella copri carriage in the gut, whereas those with P. copri carriage maintained stable CRP levels regardless of fiber intake.

CONCLUSIONS: Our findings offer human evidence supporting a fiber-gut microbiota interaction, as well as a potential specific mechanism by which gut-mediated systemic inflammation may be mitigated.}, } @article {pmid34139588, year = {2021}, author = {Zhu, D and Lu, L and Zhang, Z and Qi, D and Zhang, M and O'Connor, P and Wei, F and Zhu, YG}, title = {Insights into the roles of fungi and protist in the giant panda gut microbiome and antibiotic resistome.}, journal = {Environment international}, volume = {155}, number = {}, pages = {106703}, doi = {10.1016/j.envint.2021.106703}, pmid = {34139588}, issn = {1873-6750}, mesh = {Animals ; Anti-Bacterial Agents ; Female ; Fungi/classification ; *Gastrointestinal Microbiome ; Genes, Bacterial ; Male ; *Microbiota ; *Ursidae ; }, abstract = {The mammal gut is a rich reservoir of antibiotic resistance genes (ARGs), and the relationship between bacterial communities and ARGs has been widely studied. Despite ecological significance of microeukaryotes (fungi and protists), our understanding of their roles in the mammal gut microbiome and antibiotic resistome is still limited. Here, we used amplicon sequencing, metagenomic sequencing and high-throughput quantitative PCR to examine microbiomes and antibiotic resistomes of 41 giant panda fecal samples from individuals with different genders, ages, sampling sites and diet. Our results show that diverse protists inhabit in the giant panda gut ecosystem, dominated by consumers. Higher abundance of protistan consumers was detected in the elder compared to sub-adult and adult giant pandas. Diet is the main driving factor of variation in ARGs in the giant panda gut microbiome. Weighted correlation network analysis identified two key microbial modules from multitrophic communities, which all contributed to the variation in ARGs in the giant panda gut. Protists occupied an important position in the two modules which were dominated by fungal taxa. Deterministic processes made a more important contribution to microbial community assembly of the two modules than to bacterial, fungal and protistan communities. This study sheds new light on how key microbial modules contribute to the variation in ARGs, which is crucial in understanding dynamics of antibiotic resistome in the mammal gut, particularly endangered species.}, } @article {pmid34139279, year = {2021}, author = {Aishwarya, S and Gunasekaran, K and Kumar, PS and Begum, A and Shantha, E and Jeevitha, V and Gayathri, KV}, title = {Structural, functional, resistome and pathogenicity profiling of the Cooum river.}, journal = {Microbial pathogenesis}, volume = {158}, number = {}, pages = {105048}, doi = {10.1016/j.micpath.2021.105048}, pmid = {34139279}, issn = {1096-1208}, mesh = {Bacteroides ; Bacteroidetes ; Francisella ; Humans ; *Microbiota ; *Rivers ; Virulence ; }, abstract = {The microbial community's structure and functions determine the health, quality, and anthropogenic conditions of the river ecosystems. The presence of Bacteria such as Arcobacter spp, Escherichia spp, and Campylobacters spp, have been shown to reflect the poor water quality of rivers. Apprehension of the microbial community in polluted water bodies is significant because it affects human health and the environment. Culture-independent metagenomic and metatranscriptomic approaches employed in the current study of the Cooum river unraveled the taxonomic classification of diverse microbes, including archaea, bacteria, viruses, and phages. The presence of abundant Macellibacteroides fermentans, Arcobacter bivolvorium, Arcobacter butzleri, Methanothrix soenhngeii, and Bacteroides graminisolvens were noted. Viruses and phages like Caudovirales, Human mastadenovirus C, Siphoviridae, Escherichia phage, Erwinia phage, Synechoccus phage, and Vibrio phage were relatively predominant. Various metabolic pathways like methane, sulfur, and nitrogen metabolism adopted by the microbiome confer dangerous gases. Mechanisms such as secretory systems, signal transduction, Chemotaxis, quorum sensing, transportation of chemicals and ions were significantly enriched. The microbes expressed antimicrobial resistance mechanisms as identified from the genes encoding beta-lactamase enzymes and aminoglycoside phosphotransferase enzymes. Metal resistance mechanisms against copper, tellurium, chromium, and cadmium were plentiful. Presence of human pathogens interactions with Yersinia pestis, Campylobacter jejuni, Escherichia coli, Helicobacter pylori, and Francisella tularensis subsp. tularensis suggested the possibilities of transmission of pathogenesis to humans. The current study is the first to apprehend the detailed microbiome composition of one of the highly polluted rivers in South India. The study elaborated the microbiome's structure, functions, and metabolic potential at a specific site of the polluted river.}, } @article {pmid34135898, year = {2021}, author = {Schubert, ML and Rohrbach, R and Schmitt, M and Stein-Thoeringer, CK}, title = {The Potential Role of the Intestinal Micromilieu and Individual Microbes in the Immunobiology of Chimeric Antigen Receptor T-Cell Therapy.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {670286}, pmid = {34135898}, issn = {1664-3224}, mesh = {Antigens, CD19/immunology ; Gastrointestinal Microbiome/*physiology ; Hematologic Neoplasms/*immunology/*microbiology/*therapy ; Humans ; Immunotherapy, Adoptive/*methods ; Receptors, Chimeric Antigen/therapeutic use ; }, abstract = {Cellular immunotherapy with chimeric antigen receptor (CAR)-T cells (CARTs) represents a breakthrough in the treatment of hematologic malignancies. CARTs are genetically engineered hybrid receptors that combine antigen-specificity of monoclonal antibodies with T cell function to direct patient-derived T cells to kill malignant cells expressing the target (tumor) antigen. CARTs have been introduced into clinical medicine as CD19-targeted CARTs for refractory and relapsed B cell malignancies. Despite high initial response rates, current CART therapies are limited by a long-term loss of antitumor efficacy, the occurrence of toxicities, and the lack of biomarkers for predicting therapy and toxicity outcomes. In the past decade, the gut microbiome of mammals has been extensively studied and evidence is accumulating that human health, apart from our own genome, largely depends on microbes that are living in and on the human body. The microbiome encompasses more than 1000 bacterial species who collectively encode a metagenome that guides multifaceted, bidirectional host-microbiome interactions, primarily through the action of microbial metabolites. Increasing knowledge has been accumulated on the role of the gut microbiome in T cell-driven anticancer immunotherapy. It has been shown that antibiotics, dietary components and gut microbes reciprocally affect the efficacy and toxicity of allogeneic hematopoietic cell transplantation (allo HCT) as the prototype of T cell-based immunotherapy for hematologic malignancies, and that microbiome diversity metrics can predict clinical outcomes of allo HCTs. In this review, we will provide a comprehensive overview of the principles of CD19-CART immunotherapy and major aspects of the gut microbiome and its modulators that impact antitumor T cell transfer therapies. We will outline i) the extrinsic and intrinsic variables that can contribute to the complex interaction of the gut microbiome and host in CART immunotherapy, including ii) antibiotic administration affecting loss of colonization resistance, expansion of pathobionts and disturbed mucosal and immunological homeostasis, and ii) the role of specific gut commensals and their microbial virulence factors in host immunity and inflammation. Although the role of the gut microbiome in CART immunotherapy has only been marginally explored so far, this review may open a new chapter and views on putative connections and mechanisms.}, } @article {pmid34135337, year = {2021}, author = {Makita, Y and Suzuki, S and Fushimi, K and Shimada, S and Suehisa, A and Hirata, M and Kuriyama, T and Kurihara, Y and Hamasaki, H and Okubo-Kurihara, E and Yoshitake, K and Watanabe, T and Sakuta, M and Gojobori, T and Sakami, T and Narikawa, R and Yamaguchi, H and Kawachi, M and Matsui, M}, title = {Identification of a dual orange/far-red and blue light photoreceptor from an oceanic green picoplankton.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3593}, pmid = {34135337}, issn = {2041-1723}, mesh = {Adaptation, Physiological/genetics ; Cell Nucleus/metabolism ; Chlorophyta/classification/genetics/*metabolism ; Cryptochromes/genetics/metabolism ; Evolution, Molecular ; Light ; Metagenome ; *Oceans and Seas ; Photoreceptors, Plant/genetics/*metabolism ; Phylogeny ; Phytochrome/genetics/metabolism ; Phytoplankton/classification/genetics/*metabolism ; Plant Leaves/genetics/metabolism ; Nicotiana/genetics/metabolism ; Transcription, Genetic/radiation effects ; }, abstract = {Photoreceptors are conserved in green algae to land plants and regulate various developmental stages. In the ocean, blue light penetrates deeper than red light, and blue-light sensing is key to adapting to marine environments. Here, a search for blue-light photoreceptors in the marine metagenome uncover a chimeric gene composed of a phytochrome and a cryptochrome (Dualchrome1, DUC1) in a prasinophyte, Pycnococcus provasolii. DUC1 detects light within the orange/far-red and blue spectra, and acts as a dual photoreceptor. Analyses of its genome reveal the possible mechanisms of light adaptation. Genes for the light-harvesting complex (LHC) are duplicated and transcriptionally regulated under monochromatic orange/blue light, suggesting P. provasolii has acquired environmental adaptability to a wide range of light spectra and intensities.}, } @article {pmid34133435, year = {2021}, author = {Hardmeier, I and Aeberhard, N and Qi, W and Schoenbaechler, K and Kraettli, H and Hatt, JM and Fraefel, C and Kubacki, J}, title = {Metagenomic analysis of fecal and tissue samples from 18 endemic bat species in Switzerland revealed a diverse virus composition including potentially zoonotic viruses.}, journal = {PloS one}, volume = {16}, number = {6}, pages = {e0252534}, pmid = {34133435}, issn = {1932-6203}, mesh = {Adenoviridae/classification/genetics ; Animals ; Chiroptera/classification/*virology ; Disease Reservoirs/virology ; Feces/*virology ; Genetic Variation ; Genome, Viral/genetics ; Hepevirus/classification/genetics ; Humans ; Metagenomics/*methods ; Middle East Respiratory Syndrome Coronavirus/classification/genetics ; Phylogeny ; Rotavirus/classification/genetics ; Sequence Analysis, DNA/methods ; Switzerland ; Virome/*genetics ; Viruses/classification/*genetics ; Zoonoses/*virology ; }, abstract = {Many recent disease outbreaks in humans had a zoonotic virus etiology. Bats in particular have been recognized as reservoirs to a large variety of viruses with the potential to cross-species transmission. In order to assess the risk of bats in Switzerland for such transmissions, we determined the virome of tissue and fecal samples of 14 native and 4 migrating bat species. In total, sequences belonging to 39 different virus families, 16 of which are known to infect vertebrates, were detected. Contigs of coronaviruses, adenoviruses, hepeviruses, rotaviruses A and H, and parvoviruses with potential zoonotic risk were characterized in more detail. Most interestingly, in a ground stool sample of a Vespertilio murinus colony an almost complete genome of a Middle East respiratory syndrome-related coronavirus (MERS-CoV) was detected by Next generation sequencing and confirmed by PCR. In conclusion, bats in Switzerland naturally harbour many different viruses. Metagenomic analyses of non-invasive samples like ground stool may support effective surveillance and early detection of viral zoonoses.}, } @article {pmid34132786, year = {2021}, author = {Zayed, AA and Lücking, D and Mohssen, M and Cronin, D and Bolduc, B and Gregory, AC and Hargreaves, KR and Piehowski, PD and White Iii, RA and Huang, EL and Adkins, JN and Roux, S and Moraru, C and Sullivan, MB}, title = {efam: an expanded, metaproteome-supported HMM profile database of viral protein families.}, journal = {Bioinformatics (Oxford, England)}, volume = {37}, number = {22}, pages = {4202-4208}, pmid = {34132786}, issn = {1367-4811}, mesh = {Animals ; Viral Proteins ; Software ; Metagenomics/methods ; *Viruses ; *Microbiota ; }, abstract = {MOTIVATION: Viruses infect, reprogram and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases.

RESULTS: Here, we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240 311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from 'conservative' to 'eXtremely Conservative' resulted in 37 841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ∼24% on average (up to ∼42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem.

The resources are available on the iVirus platform at (doi.org/10.25739/9vze-4143).

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid34132784, year = {2021}, author = {N'Guessan, A and Brito, IL and Serohijos, AWR and Shapiro, BJ}, title = {Mobile Gene Sequence Evolution within Individual Human Gut Microbiomes Is Better Explained by Gene-Specific Than Host-Specific Selective Pressures.}, journal = {Genome biology and evolution}, volume = {13}, number = {8}, pages = {}, pmid = {34132784}, issn = {1759-6653}, mesh = {Evolution, Molecular ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Pangenomes-the cumulative set of genes encoded by a population or species-arise from the interplay of horizontal gene transfer, drift, and selection. The balance of these forces in shaping pangenomes has been debated, and studies to date focused on ancient evolutionary time scales have suggested that pangenomes generally confer niche adaptation to their bacterial hosts. To shed light on pangenome evolution on shorter evolutionary time scales, we inferred the selective pressures acting on mobile genes within individual human microbiomes from 176 Fiji islanders. We mapped metagenomic sequence reads to a set of known mobile genes to identify single nucleotide variants (SNVs) and calculated population genetic metrics to infer deviations from a neutral evolutionary model. We found that mobile gene sequence evolution varied more by gene family than by human social attributes, such as household or village. Patterns of mobile gene sequence evolution could be qualitatively recapitulated with a simple evolutionary simulation without the need to invoke the adaptive value of mobile genes to either bacterial or human hosts. These results stand in contrast with the apparent adaptive value of pangenomes over longer evolutionary time scales. In general, the most highly mobile genes (i.e., those present in more distinct bacterial host genomes) tend to have higher metagenomic read coverage and an excess of low-frequency SNVs, consistent with their rapid spread across multiple bacterial species in the gut. However, a subset of mobile genes-including those involved in defense mechanisms and secondary metabolism-showed a contrasting signature of intermediate-frequency SNVs, indicating species-specific selective pressures or negative frequency-dependent selection on these genes. Together, our evolutionary models and population genetic data show that gene-specific selective pressures predominate over human or bacterial host-specific pressures during the relatively short time scales of a human lifetime.}, } @article {pmid34130621, year = {2021}, author = {Glickman, C and Hendrix, J and Strong, M}, title = {Simulation study and comparative evaluation of viral contiguous sequence identification tools.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {329}, pmid = {34130621}, issn = {1471-2105}, mesh = {*Bacteriophages/genetics ; Genome, Viral/genetics ; Humans ; Metagenome/genetics ; Metagenomics ; *Microbiota ; *Viruses/genetics ; }, abstract = {BACKGROUND: Viruses, including bacteriophages, are important components of environmental and human associated microbial communities. Viruses can act as extracellular reservoirs of bacterial genes, can mediate microbiome dynamics, and can influence the virulence of clinical pathogens. Various targeted metagenomic analysis techniques detect viral sequences, but these methods often exclude large and genome integrated viruses. In this study, we evaluate and compare the ability of nine state-of-the-art bioinformatic tools, including Vibrant, VirSorter, VirSorter2, VirFinder, DeepVirFinder, MetaPhinder, Kraken 2, Phybrid, and a BLAST search using identified proteins from the Earth Virome Pipeline to identify viral contiguous sequences (contigs) across simulated metagenomes with different read distributions, taxonomic compositions, and complexities.

RESULTS: Of the tools tested in this study, VirSorter achieved the best F1 score while Vibrant had the highest average F1 score at predicting integrated prophages. Though less balanced in its precision and recall, Kraken2 had the highest average precision by a substantial margin. We introduced the machine learning tool, Phybrid, which demonstrated an improvement in average F1 score over tools such as MetaPhinder. The tool utilizes machine learning with both gene content and nucleotide features. The addition of nucleotide features improves the precision and recall compared to the gene content features alone.Viral identification by all tools was not impacted by underlying read distribution but did improve with contig length. Tool performance was inversely related to taxonomic complexity and varied by the phage host. For instance, Rhizobium and Enterococcus phages were identified consistently by the tools; whereas, Neisseria prophage sequences were commonly missed in this study.

CONCLUSION: This study benchmarked the performance of nine state-of-the-art bioinformatic tools to identify viral contigs across different simulation conditions. This study explored the ability of the tools to identify integrated prophage elements traditionally excluded from targeted sequencing approaches. Our comprehensive analysis of viral identification tools to assess their performance in a variety of situations provides valuable insights to viral researchers looking to mine viral elements from publicly available metagenomic data.}, } @article {pmid34127690, year = {2021}, author = {Sousa, R and Vasconcelos, J and Vera-Escalona, I and Delgado, J and Freitas, M and González, JA and Riera, R}, title = {Major ocean currents may shape the microbiome of the topshell Phorcus sauciatus in the NE Atlantic Ocean.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {12480}, pmid = {34127690}, issn = {2045-2322}, abstract = {Studies on microbial communities are pivotal to understand the role and the evolutionary paths of the host and their associated microorganisms in the ecosystems. Meta-genomics techniques have proven to be one of the most effective tools in the identification of endosymbiotic communities of host species. The microbiome of the highly exploited topshell Phorcus sauciatus was characterized in the Northeastern Atlantic (Portugal, Madeira, Selvagens, Canaries and Azores). Alpha diversity analysis based on observed OTUs showed significant differences among regions. The Principal Coordinates Analysis of beta-diversity based on presence/absence showed three well differentiated groups, one from Azores, a second from Madeira and the third one for mainland Portugal, Selvagens and the Canaries. The microbiome results may be mainly explained by large-scale oceanographic processes of the study region, i.e., the North Atlantic Subtropical Gyre, and specifically by the Canary Current. Our results suggest the feasibility of microbiome as a model study to unravel biogeographic and evolutionary processes in marine species with high dispersive potential.}, } @article {pmid34126977, year = {2021}, author = {Liu, ZZ and Liu, QH and Liu, Z and Tang, JW and Chua, EG and Li, F and Xiong, XS and Wang, MM and Wen, PB and Shi, XY and Xi, XY and Zhang, X and Wang, L}, title = {Ethanol extract of mulberry leaves partially restores the composition of intestinal microbiota and strengthens liver glycogen fragility in type 2 diabetic rats.}, journal = {BMC complementary medicine and therapies}, volume = {21}, number = {1}, pages = {172}, pmid = {34126977}, issn = {2662-7671}, support = {2020//Jiangsu Qing-Lan Project/ ; }, mesh = {Animals ; Diabetes Mellitus, Experimental/drug therapy ; Diabetes Mellitus, Type 2/*drug therapy ; Dysbiosis/prevention & control ; Ethanol/chemistry ; Gastrointestinal Microbiome/*drug effects ; Liver Glycogen/*analysis ; Morus/*chemistry ; Plant Extracts/*pharmacology ; Plant Leaves/chemistry ; Rats, Sprague-Dawley ; Rats ; }, abstract = {BACKGROUND: Mulberry leaf as a traditional Chinese medicine is able to treat obesity, diabetes, and dyslipidemia. It is well known that diabetes leads to intestinal microbiota dysbiosis. It is also recently discovered that liver glycogen structure is impaired in diabetic animals. Since mulberry leaves are able to improve the diabetic conditions through reducing blood glucose level, it would be interesting to investigate whether they have any positive effects on intestinal microbiota and liver glycogen structure.

METHODS: In this study, we first determined the bioactive components of ethanol extract of mulberry leaves via high-performance liquid chromatography (HPLC) and liquid chromatography/mass spectrometry (LC/MS). Murine animal models were divided into three groups, normal Sprague-Dawley (SD) rats, high-fat diet (HFD) and streptozotocin (STZ) induced type 2 diabetic rats, and HFD/STZ-induced rats administered with ethanol extract of mulberry leaves (200 mg/kg/day). Composition of intestinal microbiota was analyzed via metagenomics by sequencing the V3-V4 region of 16S rDNAs. Liver glycogen structure was characterized through size exclusion chromatography (SEC). Both Student's t-test and Tukey's test were used for statistical analysis.

RESULTS: A group of type 2 diabetic rat models were successfully established. Intestinal microbiota analysis showed that ethanol extract of mulberry leaves could partially change intestinal microbiota back to normal conditions. In addition, liver glycogen was restored from fragile state to stable state through administration of ethanol extract of mulberry leaves.

CONCLUSIONS: This study confirms that the ethanol extract of mulberry leaves (MLE) ameliorates intestinal microbiota dysbiosis and strengthens liver glycogen fragility in diabetic rats. These finding can be helpful in discovering the novel therapeutic targets with the help of further investigations.}, } @article {pmid34126062, year = {2021}, author = {Nooij, S and Ducarmon, QR and Laros, JFJ and Zwittink, RD and Norman, JM and Smits, WK and Verspaget, HW and Keller, JJ and Terveer, EM and Kuijper, EJ and , }, title = {Fecal Microbiota Transplantation Influences Procarcinogenic Escherichia coli in Recipient Recurrent Clostridioides difficile Patients.}, journal = {Gastroenterology}, volume = {161}, number = {4}, pages = {1218-1228.e5}, doi = {10.1053/j.gastro.2021.06.009}, pmid = {34126062}, issn = {1528-0012}, mesh = {Adult ; Aged ; Aged, 80 and over ; Clostridioides difficile/*pathogenicity ; Clostridium Infections/diagnosis/microbiology/*therapy ; Dysbiosis ; Escherichia coli/enzymology/genetics/*growth & development ; Escherichia coli Proteins/genetics/metabolism ; *Fecal Microbiota Transplantation/adverse effects ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Polyketide Synthases/genetics/metabolism ; Reinfection ; Retrospective Studies ; Time Factors ; Treatment Outcome ; }, abstract = {BACKGROUND & AIMS: Patients with multiple recurrent Clostridioides difficile infection (rCDI) have a disturbed gut microbiota that can be restored by fecal microbiota transplantation (FMT). Despite extensive screening, healthy feces donors may carry bacteria in their intestinal tract that could have long-term health effects, such as potentially procarcinogenic polyketide synthase-positive (pks[+]) Escherichia coli. Here, we aim to determine whether the pks abundance and persistence of pks[+]E coli is influenced by pks status of the donor feces.

METHODS: In a cohort of 49 patients with rCDI treated with FMT and matching donor samples-the largest cohort of its kind, to our knowledge-we retrospectively screened fecal metagenomes for pks[+]E coli and compared the presence of pks in patients before and after treatment and to their respective donors.

RESULTS: The pks island was more prevalent (P = .026) and abundant (P < .001) in patients with rCDI (pre-FMT, 27 of 49 [55%]; median, 0.46 reads per kilobase per million [RPKM] pks) than in healthy donors (3 of 8 donors [37.5%], 11 of 38 samples [29%]; median, 0.01 RPKM pks). The pks status of patients post-FMT depended on the pks status of the donor suspension with which the patient was treated (P = .046). Particularly, persistence (8 of 9 cases) or clearance (13 of 18) of pks[+]E coli in pks[+] patients was correlated to pks in the donor (P = .004).

CONCLUSIONS: We conclude that FMT contributes to pks[+]E coli persistence or eradication in patients with rCDI but that donor-to-patient transmission of pks[+]E coli is unlikely.}, } @article {pmid34125646, year = {2021}, author = {Hong, Y and Sheng, L and Zhong, J and Tao, X and Zhu, W and Ma, J and Yan, J and Zhao, A and Zheng, X and Wu, G and Li, B and Han, B and Ding, K and Zheng, N and Jia, W and Li, H}, title = {Desulfovibrio vulgaris, a potent acetic acid-producing bacterium, attenuates nonalcoholic fatty liver disease in mice.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-20}, pmid = {34125646}, issn = {1949-0984}, mesh = {Acetic Acid/*metabolism ; Animals ; Bacteria/classification/genetics/isolation & purification/metabolism ; CD36 Antigens/genetics/metabolism ; Desulfovibrio vulgaris/growth & development/*metabolism ; Diet, High-Fat/adverse effects ; Fatty Acid Synthases/genetics/metabolism ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome ; Humans ; Liver/enzymology/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/*drug therapy/etiology/genetics/microbiology ; Probiotics/*administration & dosage ; }, abstract = {The emerging evidence supports the use of prebiotics like herb-derived polysaccharides for treating nonalcoholic fatty liver disease (NAFLD) by modulating gut microbiome. The present study was initiated on the microbiota-dependent anti-NAFLD effect of Astragalus polysaccharides (APS) extracted from Astragalus mongholicus Bunge in high-fat diet (HFD)-fed mice. However, the exact mechanisms underlying the beneficial effects of APS on NAFLD formation remain poorly understood.Co-housing experiment was used to assess the microbiota dependent anti-NAFLD effect of APS. Then, targeted metabolomics and metagenomics were adopted for determining short-chain fatty acids (SCFAs) and bacteria that were specifically enriched by APS. Further in vitro experiment was carried out to test the capacity of SCFAs-producing of identified bacterium. Finally, the anti-NAFLD efficacy of identified bacterium was tested in HFD-fed mice.Our results first demonstrated the anti-NAFLD effect of APS in HFD-fed mice and the contribution of gut microbiota. Moreover, our results indicated that SCFAs, predominantly acetic acid were elevated in APS-supplemented mice and ex vivo experiment. Metagenomics revealed that D. vulgaris from Desulfovibrio genus was not only enriched by APS, but also a potent generator of acetic acid, which showed significant anti-NAFLD effects in HFD-fed mice. In addition, D. vulgaris modulated the hepatic gene expression pattern of lipids metabolism, particularly suppressed hepatic fatty acid synthase (FASN) and CD36 protein expression.Our results demonstrate that APS enriched D. vulgaris is effective on attenuating hepatic steatosis possibly through producing acetic acid, and modulation on hepatic lipids metabolism in mice. Further studies are warranted to explore the long-term impacts of D. vulgaris on host metabolism and the underlying mechanism.}, } @article {pmid34125200, year = {2021}, author = {Haran, JP and Zeamer, A and Ward, DV and Dutta, P and Bucci, V and McCormick, BA}, title = {The Nursing Home Older Adult Gut Microbiome Composition Shows Time-dependent Dysbiosis and Is Influenced by Medication Exposures, Age, Environment, and Frailty.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {76}, number = {11}, pages = {1930-1938}, pmid = {34125200}, issn = {1758-535X}, support = {K23 AG057790/AG/NIA NIH HHS/United States ; 1R03AG056356-01/AG/NIA NIH HHS/United States ; R01 DK056754/DK/NIDDK NIH HHS/United States ; 1R15AI112985-01A1/NH/NIH HHS/United States ; RF1 AG067483/AG/NIA NIH HHS/United States ; }, mesh = {Aged ; Dysbiosis ; *Frailty ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Nursing Homes ; }, abstract = {Older adults in nursing homes (NHs) have increased frailty, medication, and antimicrobial exposures, all factors that are known to affect the composition of gut microbiota. Our objective was to define which factors have the greatest association with the NH resident gut microbiota, explore patterns of dysbiosis and compositional changes in gut microbiota over time in this environment. We collected serial stool samples from NH residents. Residents were assessed using the Mini Nutritional Assessment tool and Clinical Frailty Scale. Bacterial composition of resident stool samples was determined by metagenomic sequencing. We used mixed-effect random forest modeling to identify clinical covariates that associate with microbiota. We enrolled and followed 166 residents from 5 NHs collecting 512 stool samples and following 15 residents for > 1 year. Medications, particularly psychoactive and antihypertensive medications, had the greatest effect on the microbiota. Age and frailty also contributed, and were associated with increased and decreased diversity, respectively. The microbiota of residents who had lived in the NH for > 1 year were enriched in inflammatory and pathogenic species and reduced in anti-inflammatory and symbiotic species. We observed intraindividual stability of the microbiome among older adults who had lived in the NH already for >1 year followed with sample collections 1 year apart. Older adult NH gut microbiome is heavily influenced by medications, age, and frailty. This microbiome is influenced by the length of NH residency with dysbiosis becoming evident at 12 months, however, after this point there is demonstrated relative stability over time.}, } @article {pmid34124756, year = {2021}, author = {Schreiber, L and Fortin, N and Tremblay, J and Wasserscheid, J and Sanschagrin, S and Mason, J and Wright, CA and Spear, D and Johannessen, SC and Robinson, B and King, T and Lee, K and Greer, CW}, title = {In situ microcosms deployed at the coast of British Columbia (Canada) to study dilbit weathering and associated microbial communities under marine conditions.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {7}, pages = {}, pmid = {34124756}, issn = {1574-6941}, mesh = {Biodegradation, Environmental ; British Columbia ; Hydrocarbons ; *Microbiota ; *Polycyclic Aromatic Hydrocarbons ; *Water Pollutants, Chemical/analysis ; }, abstract = {Douglas Channel and the adjacent Hecate Strait (British Columbia, Canada) are part of a proposed route to ship diluted bitumen (dilbit). This study presents how two types of dilbit naturally degrade in this environment by using an in situ microcosm design based on dilbit-coated beads. We show that dilbit-associated n-alkanes were microbially biodegraded with estimated half-lives of 57-69 days. n-Alkanes appeared to be primarily degraded using the aerobic alkB, ladA and CYP153 pathways. The loss of dilbit polycyclic aromatic hydrocarbons (PAHs) was slower than of n-alkanes, with half-lives of 89-439 days. A biodegradation of PAHs could not be conclusively determined, although a significant enrichment of the phnAc gene (a marker for aerobic PAH biodegradation) was observed. PAH degradation appeared to be slower in Hecate Strait than in Douglas Channel. Microcosm-associated microbial communities were shaped by the presence of dilbit, deployment location and incubation time but not by dilbit type. Metagenome-assembled genomes of putative dilbit-degraders were obtained and could be divided into populations of early, late and continuous degraders. The majority of the identified MAGs could be assigned to the orders Flavobacteriales, Methylococcales, Pseudomonadales and Rhodobacterales. A high proportion of the MAGs represent currently unknown lineages or lineages with currently no cultured representative.}, } @article {pmid34122067, year = {2021}, author = {Liu, Z and Liao, W and Zhang, Z and Sun, R and Luo, Y and Chen, Q and Li, X and Lu, R and Ying, Y}, title = {Metformin Affects Gut Microbiota Composition and Diversity Associated with Amelioration of Dextran Sulfate Sodium-Induced Colitis in Mice.}, journal = {Frontiers in pharmacology}, volume = {12}, number = {}, pages = {640347}, pmid = {34122067}, issn = {1663-9812}, abstract = {Background: Inflammatory bowel disease (IBD) is an increasingly common and globally emergent immune-mediated disorder. The etiology of IBD is complex, involving multiple factors such as immune dysregulation, environmental factors, genetic mutations, and microbiota dysbiosis, exacerbated by a lack of effective clinical therapies. Recently, studies hypothesized that dysbiosis of intestinal flora might participate in the onset of IBD. Metformin is widely used to treat type 2 diabetes and has shown beneficial effects in mouse models of IBD, although its underlying mechanisms remain poorly understood. Accumulating studies found that metformin shows beneficial effects for diabetes by affecting microbiota composition. This study explores possible regulatory effects of metformin on intestinal microecology during treatment for IBD. Methods: Inflammation was induced using 3% Dextran Sulfate Sodium (DSS) solution to generate mice models of IBD. Metformin treatments were assayed by measuring body weights and colon lengths of mice and H&E staining to observe histological effects on colon tissue structures. Changes in bacterial community composition and diversity-related to IBD and metformin treatment were assessed by high-throughput metagenomic sequencing analysis. Results: Metformin administration significantly ameliorated body weight loss, inhibited colon shrinking, and contributed to preserving the integrity of colon histological structures. The gut microbiota profiles revealed that the biodiversity of intestinal flora lost during inflammation was restored under metformin treatment. Metformin administration was also associated with decreased pathogenic Escherichia shigella and increased abundance of Lactobacillus and Akkermansia. Conclusion: Metformin appears to induce anti-inflammatory effects, thus ameliorating colitis symptoms, concurrent with enrichment for beneficial taxa and restored microbial diversity, suggesting a viable strategy against IBD.}, } @article {pmid34119873, year = {2021}, author = {Batool, M and Blazier, JC and Rogovska, YV and Wang, J and Liu, S and Nebogatkin, IV and Rogovskyy, AS}, title = {Metagenomic analysis of individually analyzed ticks from Eastern Europe demonstrates regional and sex-dependent differences in the microbiota of Ixodes ricinus.}, journal = {Ticks and tick-borne diseases}, volume = {12}, number = {5}, pages = {101768}, doi = {10.1016/j.ttbdis.2021.101768}, pmid = {34119873}, issn = {1877-9603}, mesh = {Animals ; Bacteria/genetics/*isolation & purification ; Female ; Geography ; Ixodes/*microbiology ; Male ; *Metagenome ; Metagenomics ; *Microbiota ; Sex Factors ; Ukraine ; }, abstract = {Understanding the microbial ecology of disease vectors may be useful for development of novel strategies aimed at preventing transmission of vector-borne pathogens. Although Ixodes ricinus is one of the most important tick vectors, the microbiota of this tick has been examined for only limited parts of the globe. To date, the microbiota of I. ricinus ticks collected from Eastern Europe has not been defined. The objective of this study was to compare microbiota of I. ricinus ticks within (males vs. females) and between collection sites that represented three administrative regions of Ukraine, Dnipropetrovs'k (D), Kharkiv (K), and Poltava (P). A total of 89 questing I. ricinus adults were collected from region D (number of ticks, n = 29; 14 males and 15 females), region K (n = 30; 15 males and 15 females) and region P (n = 30; 15 males and 15 females). Each tick was subjected to metagenomic analysis by targeting the V6 region of 16S rRNA gene through the Illumina 4000 Hiseq sequencing. The alpha diversity analysis demonstrated that, regardless of tick sex, patterns of bacterial diversity in ticks from regions K and P were similar, whereas the microbiota of region D ticks was quite distinct. A number of inter-regional differences were detected by most beta diversity metrics for both males and females. The inter-regional variations were also supported by the principal coordinate analysis based on the unweighted UniFrac metrics with three region-specific clusters of female ticks and one distinct cluster of region D males. Lastly, numerous region- and sex-specific differences were also identified in the relative abundance of various bacterial taxa. Collectively, the present findings demonstrate that the microbiota of the I. ricinus tick can exhibit a high degree of variation between tick sexes and geographical regions.}, } @article {pmid34118976, year = {2021}, author = {Xie, F and Jin, W and Si, H and Yuan, Y and Tao, Y and Liu, J and Wang, X and Yang, C and Li, Q and Yan, X and Lin, L and Jiang, Q and Zhang, L and Guo, C and Greening, C and Heller, R and Guan, LL and Pope, PB and Tan, Z and Zhu, W and Wang, M and Qiu, Q and Li, Z and Mao, S}, title = {An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {137}, pmid = {34118976}, issn = {2049-2618}, mesh = {Animals ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Phylogeny ; Ruminants ; }, abstract = {BACKGROUND: Gastrointestinal tract (GIT) microbiomes in ruminants play major roles in host health and thus animal production. However, we lack an integrated understanding of microbial community structure and function as prior studies. are predominantly biased towards the rumen. Therefore, to acquire a microbiota inventory of the discrete GIT compartments, In this study, we used shotgun metagenomics to profile the microbiota of 370 samples that represent 10 GIT regions of seven ruminant species.

RESULTS: Our analyses reconstructed a GIT microbial reference catalog with > 154 million nonredundant genes and identified 8745 uncultured candidate species from over 10,000 metagenome-assembled genomes. The integrated gene catalog across the GIT regions demonstrates spatial associations between the microbiome and physiological adaptations, and 8745 newly characterized genomes substantially expand the genomic landscape of ruminant microbiota, particularly those from the lower gut. This substantially expands the previously known set of endogenous microbial diversity and the taxonomic classification rate of the GIT microbiome. These candidate species encode hundreds of enzymes and novel biosynthetic gene clusters that improve our understanding concerning methane production and feed efficiency in ruminants. Overall, this study expands the characterization of the ruminant GIT microbiota at unprecedented spatial resolution and offers clues for improving ruminant livestock production in the future.

CONCLUSIONS: Having access to a comprehensive gene catalog and collections of microbial genomes provides the ability to perform efficiently genome-based analysis to achieve a detailed classification of GIT microbial ecosystem composition. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production. Video abstract.}, } @article {pmid34118665, year = {2021}, author = {Zhang, L and Gong, X and Wang, L and Guo, K and Cao, S and Zhou, Y}, title = {Metagenomic insights into the effect of thermal hydrolysis pre-treatment on microbial community of an anaerobic digestion system.}, journal = {The Science of the total environment}, volume = {791}, number = {}, pages = {148096}, doi = {10.1016/j.scitotenv.2021.148096}, pmid = {34118665}, issn = {1879-1026}, mesh = {Anaerobiosis ; Bioreactors ; Hydrolysis ; *Metagenomics ; Methane ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sewage ; }, abstract = {Thermal hydrolysis process (THP) is an effective pre-treatment method to reduce solids volume and improve biogas production during anaerobic digestion (AD) via increasing the biodegradability of waste activated sludge (WAS). However, the effects of THP pre-treated sludge on microbial diversity, interspecies interactions, and metabolism in AD systems remain largely unknown. We therefore setup and operated an anaerobic digester during a long-term period to shed light on the effect of THP pre-treatment on AD microbial ecology in comparison to conventional AD via Illumina based 16S rRNA gene amplicon sequencing and genome-centric metagenomics analysis. Results showed THP sludge significantly reduced the microbial diversity, shaped the microbial community structure, and resulted in more intense microbial interactions. Compared to WAS as the feed sludge, THP sludge shaped the core functional groups, but functional redundancy ensured the system's stability. The metabolic interactions between methanogens and syntrophic bacteria as well as the specific metabolic pathways were further elucidated. Hydrogenotrophic methanogens, Methanospirillum sp. and Methanolinea sp., were the primary contributors for methane production when treating THP and WAS, respectively, which also have potential for acetate oxidation to methane. Collectively, this study provides in-depth information on the interspecies interactions to better understand how THP pre-treatment influences AD microbial community.}, } @article {pmid34118463, year = {2022}, author = {Jie, Z and Chen, C and Hao, L and Li, F and Song, L and Zhang, X and Zhu, J and Tian, L and Tong, X and Cai, K and Zhang, Z and Ju, Y and Yu, X and Li, Y and Zhou, H and Lu, H and Qiu, X and Li, Q and Liao, Y and Zhou, D and Lian, H and Zuo, Y and Chen, X and Rao, W and Ren, Y and Wang, Y and Zi, J and Wang, R and Liu, N and Wu, J and Zhang, W and Liu, X and Zong, Y and Liu, W and Xiao, L and Hou, Y and Xu, X and Yang, H and Wang, J and Kristiansen, K and Jia, H}, title = {Life History Recorded in the Vagino-cervical Microbiome Along with Multi-omes.}, journal = {Genomics, proteomics & bioinformatics}, volume = {20}, number = {2}, pages = {304-321}, pmid = {34118463}, issn = {2210-3244}, mesh = {Humans ; Female ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; *Cesarean Section ; Vagina/microbiology ; *Microbiota ; Lactobacillus/genetics ; }, abstract = {The vagina contains at least a billion microbial cells, dominated by lactobacilli. Here we perform metagenomic shotgun sequencing on cervical and fecal samples from a cohort of 516 Chinese women of reproductive age, as well as cervical, fecal, and salivary samples from a second cohort of 632 women. Factors such as pregnancyhistory, delivery history, cesarean section, and breastfeeding were all more important than menstrual cycle in shaping the microbiome, and such information would be necessary before trying to interpret differences between vagino-cervical microbiome data. Greater proportion of Bifidobacterium breve was seen with older age at sexual debut. The relative abundance of lactobacilli especially Lactobacillus crispatus was negatively associated with pregnancy history. Potential markers for lack of menstrual regularity, heavy flow, dysmenorrhea, and contraceptives were also identified. Lactobacilli were rare during breastfeeding or post-menopause. Other features such as mood fluctuations and facial speckles could potentially be predicted from the vagino-cervical microbiome. Gut and salivary microbiomes, plasma vitamins, metals, amino acids, and hormones showed associations with the vagino-cervical microbiome. Our results offer an unprecedented glimpse into the microbiota of the female reproductive tract and call for international collaborations to better understand its long-term health impact other than in the settings of infection or pre-term birth.}, } @article {pmid34117246, year = {2021}, author = {Lloréns-Rico, V and Vieira-Silva, S and Gonçalves, PJ and Falony, G and Raes, J}, title = {Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3562}, pmid = {34117246}, issn = {2041-1723}, mesh = {Benchmarking/*methods ; Classification ; Computational Biology/*methods ; Dysbiosis/microbiology ; Electronic Data Processing/methods ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Selection Bias ; }, abstract = {While metagenomic sequencing has become the tool of preference to study host-associated microbial communities, downstream analyses and clinical interpretation of microbiome data remains challenging due to the sparsity and compositionality of sequence matrices. Here, we evaluate both computational and experimental approaches proposed to mitigate the impact of these outstanding issues. Generating fecal metagenomes drawn from simulated microbial communities, we benchmark the performance of thirteen commonly used analytical approaches in terms of diversity estimation, identification of taxon-taxon associations, and assessment of taxon-metadata correlations under the challenge of varying microbial ecosystem loads. We find quantitative approaches including experimental procedures to incorporate microbial load variation in downstream analyses to perform significantly better than computational strategies designed to mitigate data compositionality and sparsity, not only improving the identification of true positive associations, but also reducing false positive detection. When analyzing simulated scenarios of low microbial load dysbiosis as observed in inflammatory pathologies, quantitative methods correcting for sampling depth show higher precision compared to uncorrected scaling. Overall, our findings advocate for a wider adoption of experimental quantitative approaches in microbiome research, yet also suggest preferred transformations for specific cases where determination of microbial load of samples is not feasible.}, } @article {pmid34116670, year = {2021}, author = {Zou, Y and Liang, N and Zhang, X and Han, C and Nan, X}, title = {Functional differentiation related to decomposing complex carbohydrates of intestinal microbes between two wild zokor species based on 16SrRNA sequences.}, journal = {BMC veterinary research}, volume = {17}, number = {1}, pages = {216}, pmid = {34116670}, issn = {1746-6148}, support = {2017YFD0600103-4-1//the National Key Program of Research and Development/ ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Carbohydrate Metabolism ; China ; Female ; *Gastrointestinal Microbiome ; Male ; Muridae/*microbiology ; RNA, Ribosomal, 16S ; Sequence Analysis, RNA ; }, abstract = {BACKGROUND: The intestinal microbes in mammals play a key role in host metabolism and adaptation. As a subterranean rodent, zokor digs tunnels for foraging and mating. These digging activities of zokors increase the energy expenditure relative to their aboveground counterparts. However, relatively little is known regarding intestinal microbes of zokor and how they make full use of limited food resources underground for high energy requirements.

RESULTS: Eospalax cansus and Eospalax rothschildi had distinct intestinal microbes. Although the composition of intestinal microbes is similar in two species, the proportion of bacterium are distinctly different between them. At phylum level, 11 phyla were shared between two species. Firmicutes and Bacteroidota were two dominant microbes in both of two species, while Eospalax cansus have a significantly high proportion of Firmicutes/Bacteroidota than that of Eospalax rothschildi. At genus level, norank_f_Muribaculaceae were dominant microbes in both of two zokor species. The relative abundance of 12 genera were significantly different between two species. Some bacterium including unclassified_f__Lachnospiraceae, Lachnospiraceae_NK4A136_group, Ruminococcus and Eubacterium_siraeum_group associated with cellulose degradation were significantly enriched in Eospalax cansus. Although alpha diversity was with no significant differences between Eospalax cansus and Eospalax rothschildi, the intestinal microbes between them are significant distinct in PCoA analysis. We have found that trapping location affected the alpha diversity values, while sex and body measurements had no effect on alpha diversity values. PICRUSt metagenome predictions revealed significant enrichment of microbial genes involved in carbohydrate metabolism in Eospalax cansus rather than Eospalax rothschildi.

CONCLUSIONS: Our results demonstrate that Eospalax cansus harbor a stronger ability of fermentation for dietary plants than Eospalax rothschildi. The stronger ability of fermentation and degradation of cellulose of intestinal microbes of Eospalax cansus may be a long-time adaptation to limited food resources underground.}, } @article {pmid34114607, year = {2021}, author = {Aevarsson, A and Kaczorowska, AK and Adalsteinsson, BT and Ahlqvist, J and Al-Karadaghi, S and Altenbuchner, J and Arsin, H and Átlasson, ÚÁ and Brandt, D and Cichowicz-Cieślak, M and Cornish, KAS and Courtin, J and Dabrowski, S and Dahle, H and Djeffane, S and Dorawa, S and Dusaucy, J and Enault, F and Fedøy, AE and Freitag-Pohl, S and Fridjonsson, OH and Galiez, C and Glomsaker, E and Guérin, M and Gundesø, SE and Gudmundsdóttir, EE and Gudmundsson, H and Håkansson, M and Henke, C and Helleux, A and Henriksen, JR and Hjörleifdóttir, S and Hreggvidsson, GO and Jasilionis, A and Jochheim, A and Jónsdóttir, I and Jónsdóttir, LB and Jurczak-Kurek, A and Kaczorowski, T and Kalinowski, J and Kozlowski, LP and Krupovic, M and Kwiatkowska-Semrau, K and Lanes, O and Lange, J and Lebrat, J and Linares-Pastén, J and Liu, Y and Lorentsen, SA and Lutterman, T and Mas, T and Merré, W and Mirdita, M and Morzywołek, A and Ndela, EO and Karlsson, EN and Olgudóttir, E and Pedersen, C and Perler, F and Pétursdóttir, SK and Plotka, M and Pohl, E and Prangishvili, D and Ray, JL and Reynisson, B and Róbertsdóttir, T and Sandaa, RA and Sczyrba, A and Skírnisdóttir, S and Söding, J and Solstad, T and Steen, IH and Stefánsson, SK and Steinegger, M and Overå, KS and Striberny, B and Svensson, A and Szadkowska, M and Tarrant, EJ and Terzian, P and Tourigny, M and Bergh, TVD and Vanhalst, J and Vincent, J and Vroling, B and Walse, B and Wang, L and Watzlawick, H and Welin, M and Werbowy, O and Wons, E and Zhang, R}, title = {Going to extremes - a metagenomic journey into the dark matter of life.}, journal = {FEMS microbiology letters}, volume = {368}, number = {12}, pages = {}, doi = {10.1093/femsle/fnab067}, pmid = {34114607}, issn = {1574-6968}, mesh = {Bioprospecting/organization & administration ; Computational Biology ; Databases, Genetic ; Europe ; Genome, Viral/*genetics ; Hydrothermal Vents/virology ; *Metagenomics ; Viral Proteins/chemistry/genetics/metabolism ; Virome/genetics ; Viruses/classification/genetics ; }, abstract = {The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms. The Virus-X Consortium, established in 2016, included experts from eight European countries. The unique approach based on high throughput bioinformatics technologies combined with structural and functional studies resulted in the development of a biodiscovery pipeline of significant capacity and scale. The activities within the Virus-X consortium cover the entire range from bioprospecting and methods development in bioinformatics to protein production and characterisation, with the final goal of translating our results into new products for the bioeconomy. The significant impact the consortium made in all of these areas was possible due to the successful cooperation between expert teams that worked together to solve a complex scientific problem using state-of-the-art technologies as well as developing novel tools to explore the virosphere, widely considered as the last great frontier of life.}, } @article {pmid34114015, year = {2021}, author = {Li, Y and Wang, DD and Satija, A and Ivey, KL and Li, J and Wilkinson, JE and Li, R and Baden, M and Chan, AT and Huttenhower, C and Rimm, EB and Hu, FB and Sun, Q}, title = {Plant-Based Diet Index and Metabolic Risk in Men: Exploring the Role of the Gut Microbiome.}, journal = {The Journal of nutrition}, volume = {151}, number = {9}, pages = {2780-2789}, pmid = {34114015}, issn = {1541-6100}, support = {R01 CA202704/CA/NCI NIH HHS/United States ; U01 CA167552/CA/NCI NIH HHS/United States ; P30 DK046200/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; K99 DK122128/DK/NIDDK NIH HHS/United States ; R00 DK119412/DK/NIDDK NIH HHS/United States ; R01 DK126698/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01HL035464/GF/NIH HHS/United States ; U01 CA152904/CA/NCI NIH HHS/United States ; R35 CA253185/CA/NCI NIH HHS/United States ; R01 HL060712/HL/NHLBI NIH HHS/United States ; }, mesh = {Aged ; Diet ; Diet, Healthy ; Diet, Vegetarian ; Feces ; *Gastrointestinal Microbiome ; Humans ; Male ; }, abstract = {BACKGROUND: Healthy plant-based diet index (hPDI) is associated with a lower risk of cardiometabolic conditions, but its association as well as interactions with microbiome have not been elucidated.

OBJECTIVES: We aimed to investigate the interrelations between hPDI, gut microbiome, and cardiometabolic risk markers.

METHODS: hPDI was derived from dietary assessments by a validated FFQ and was examined in relation to metagenomic profiles of 911 fecal samples collected from 303 men aged 71 ± 4 y with an average BMI (in kg/m2) of 25.2 ± 3.6 in the Men's Lifestyle Validation Study. Principal coordinate (PCo) analysis based on Bray-Curtis dissimilarity was conducted, and interactions between hPDI and PCo were examined by using a metabolic risk score composed of blood lipids, BMI, and glycated hemoglobin.

RESULTS: After multivariable adjustment, hPDI was significantly associated with the relative abundance of 7 species and 9 pathways. In particular, higher hPDI was significantly associated with a higher relative abundance of Bacteroides cellulosilyticus and Eubacterium eligens, amino acid biosynthesis pathways (l-isoleucine biosynthesis I and III and l-valine biosynthesis), and the pathway of pyruvate fermentation to isobutanol. A favorable association between hPDI and the metabolic risk score was more pronounced among men with a higher PCo characterized by higher abundance of Bacteroides uniformis and lower abundance of Prevotella copri. At the individual species level, a similar interaction was also observed between hPDI and P. copri, as well as with Clostridium clostridioforme or Blautia hydrogenotrophica (all P-interaction < 0.01).

CONCLUSION: A greater adherence to a healthy plant-based diet by older men was associated with a microbial profile characterized by a higher abundance of multiple species, including B. cellulosilyticus and E. eligens, as well as pathways in amino acid metabolism and pyruvate fermentation. In addition, inverse associations between healthy plant-based diet and human metabolic risk may partially depend on microbial compositions.}, } @article {pmid34112927, year = {2021}, author = {Ericsson, AC and Hart, ML and Kwan, J and Lanoue, L and Bower, LR and Araiza, R and Kent Lloyd, KC and Franklin, CL}, title = {Supplier-origin mouse microbiomes significantly influence locomotor and anxiety-related behavior, body morphology, and metabolism.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {716}, pmid = {34112927}, issn = {2399-3642}, support = {T32 OD011126/OD/NIH HHS/United States ; }, mesh = {Animals ; Anxiety/metabolism/microbiology/physiopathology ; Behavior, Animal ; Disease Models, Animal ; Exploratory Behavior ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Locomotion ; Lymphopoiesis ; Male ; Mice/anatomy & histology/*microbiology/physiology ; Mice, Inbred ICR ; }, abstract = {The mouse is the most commonly used model species in biomedical research. Just as human physical and mental health are influenced by the commensal gut bacteria, mouse models of disease are influenced by the fecal microbiome (FM). The source of mice represents one of the strongest influences on the FM and can influence the phenotype of disease models. The FM influences behavior in mice leading to the hypothesis that mice of the same genetic background from different vendors, will have different behavioral phenotypes. To test this hypothesis, colonies of CD-1 mice, rederived via embryo transfer into surrogate dams from four different suppliers, were subjected to phenotyping assays assessing behavior and physiological parameters. Significant differences in behavior, growth rate, metabolism, and hematological parameters were observed. Collectively, these findings show the profound influence of supplier-origin FMs on host behavior and physiology in healthy, genetically similar, wild-type mice maintained in identical environments.}, } @article {pmid34112903, year = {2021}, author = {Murillo-Solano, C and López-Domínguez, J and Gongora, R and Rojas-Gulloso, A and Usme-Ciro, J and Perdomo-Balaguera, E and Herrera, C and Parra-Henao, G and Dumonteil, E}, title = {Diversity and interactions among triatomine bugs, their blood feeding sources, gut microbiota and Trypanosoma cruzi in the Sierra Nevada de Santa Marta in Colombia.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {12306}, pmid = {34112903}, issn = {2045-2322}, mesh = {Animals ; Chagas Disease/genetics/parasitology/pathology ; Gastrointestinal Microbiome/*genetics ; *Genetic Variation ; Genotype ; Humans ; Insect Vectors/genetics ; Population Groups ; Rhodnius/pathogenicity ; Triatoma/classification/*genetics ; Triatominae/*genetics/parasitology ; Trypanosoma cruzi/genetics/pathogenicity ; }, abstract = {Chagas disease remains a major neglected disease in Colombia. We aimed to characterize Trypanosoma cruzi transmission networks in the Sierra Nevada de Santa Marta (SNSM) region, to shed light on disease ecology and help optimize control strategies. Triatomines were collected in rural communities and analyzed for blood feeding sources, parasite diversity and gut microbiota composition through a metagenomic and deep sequencing approach. Triatoma dimidiata predominated, followed by Rhodnius prolixus, Triatoma maculata, Rhodnius pallescens, Panstrongylus geniculatus and Eratyrus cuspidatus. Twenty-two species were identified as blood sources, resulting in an integrated transmission network with extensive connectivity among sylvatic and domestic host species. Only TcI parasites were detected, predominantly from TcIb but TcIa was also reported. The close relatedness of T. cruzi strains further supported the lack of separate transmission cycles according to habitats or triatomine species. Triatomine microbiota varied according to species, developmental stage and T. cruzi infection. Bacterial families correlated with the presence/absence of T. cruzi were identified. In conclusion, we identified a domestic transmission cycle encompassing multiple vector species and tightly connected with sylvatic hosts in the SNSM region, rather than an isolated domestic transmission cycle. Therefore, integrated interventions targeting all vector species and their contact with humans should be considered.}, } @article {pmid34112830, year = {2021}, author = {Singha, KM and Singh, B and Pandey, P}, title = {Host specific endophytic microbiome diversity and associated functions in three varieties of scented black rice are dependent on growth stage.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {12259}, pmid = {34112830}, issn = {2045-2322}, mesh = {Antioxidants ; Bacteria ; *Biodiversity ; *Endophytes/genetics/metabolism ; *Microbiota ; Oryza/*growth & development/metabolism/*microbiology ; Plant Development ; Plant Roots/growth & development/microbiology ; Symbiosis ; }, abstract = {The compositional and functional role of the endophytic bacterial community, associated with black scented rice, in correlation with its antioxidant property has been elucidated. Community dissimilarity analysis confirmed the overlapping of community in shoot and root tissues at the young stage, but not in mature plants. Proteobacteria was the most abundant phylum, in which Agrobacterium, Pleomorphomonas, Bradyrhizobium, Novasphingobium, Caulobacter were the most abundant genera, followed by Cyanobacteria and Planctomycetes in all three different varieties of the black rice. The antioxidant activity of mature plants was found to be higher in comparison to young plants. Intrinsically, the relative abundance of Pleomorphomonas and Streptomyces was positively correlated with total phenol content, while Gemmata, unclassified Pirellulaceae, unclassified Stramenopiles positively correlated with total flavonoid content and negatively correlated with Free radical scavenging activity. Accordingly, functional metagenome analysis of the endophytic microbiome revealed that naringenin -3-dioxygenase and anthocyanidin 3-O-glucosyltransferase for phenylpropanoid (flavonoid and anthocyanin) synthesis were abundant in the endophytic microbiome of mature plants. Specific enrichment of the antioxidant producing genes in the mature plant endophytic microbiome was assigned to some bacteria such as Streptomyces, Pantoea which might have contributed to the common pathway of flavonoid synthesis. The genomes of endophytic isolates Kluyvera sp.PO2S7, Bacillus subtilis AMR1 and Enterobacter sp. SES19 were sequenced and annotated, and were found to have genes for phenylpropanoid synthesis in their genomes.}, } @article {pmid34111508, year = {2021}, author = {Sano, H and Wakui, A and Kawachi, M and Washio, J and Abiko, Y and Mayanagi, G and Yamaki, K and Tanaka, K and Takahashi, N and Sato, T}, title = {Profiling system of oral microbiota utilizing polymerase chain reaction-restriction fragment length polymorphism analysis.}, journal = {Journal of oral biosciences}, volume = {63}, number = {3}, pages = {292-297}, doi = {10.1016/j.job.2021.05.003}, pmid = {34111508}, issn = {1880-3865}, mesh = {DNA Primers ; Humans ; *Microbiota/genetics ; Mouth/*microbiology ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVES: Profiling of oral microbiota has traditionally been performed using conventional methods. These methods are relatively time-consuming and labor-intensive. Metagenomic analysis of oral microbiota using high-speed next-generation sequencing is a highly promising technology. However, it is expensive. This study sought to develop a simple and cost-effective profiling method for oral microbiota using 16S rRNA gene polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of PCR-amplified 16S ribosomal RNA genes.

METHODS: Oral isolates of 59 bacterial species from human saliva, including Streptococcus, Actinomyces, and Veillonella, were cultured anaerobically on CDC Anaerobe 5% sheep blood agar plates. Genomic DNA was extracted from single colonies and 16S rRNA genes were PCR-amplified using the 27F and 1492R universal primers. The PCR products were purified and characterized by single digestion with HpaII restriction endonuclease. 16S rRNA gene sequences were obtained from the GenBank database, and the expected restriction profiles were compared with the RFLP patterns obtained from agarose gel electrophoresis.

RESULTS: Sixty-five RFLP patterns were obtained from 27 genera and 59 species. The expected fragment sizes of these species were calculated based on GenBank 16S rRNA gene sequences. Fifty-nine patterns were obtained from the analysis of GenBank sequences. The RFLP patterns produced with HpaII distinguished many oral bacterial species. RFLP patterns enabling identification of oral bacteria were generated. The 16S rRNA gene PCR-RFLP analysis did not require expensive equipment and reagents and was cost-effective.

CONCLUSION: PCR-RFLP analysis based on 16S rRNA genes could be an alternative method for oral microbiota analysis in smaller laboratories.}, } @article {pmid34111469, year = {2021}, author = {Miyoshi, J and Miyoshi, S and Delmont, TO and Cham, C and Lee, STM and Sakatani, A and Yang, K and Shan, Y and Kennedy, M and Kiefl, E and Yousef, M and Crosson, S and Sogin, M and Antonopoulos, DA and Eren, AM and Leone, V and Chang, EB}, title = {Early-Life Microbial Restitution Reduces Colitis Risk Promoted by Antibiotic-Induced Gut Dysbiosis in Interleukin 10[-/-] Mice.}, journal = {Gastroenterology}, volume = {161}, number = {3}, pages = {940-952.e15}, pmid = {34111469}, issn = {1528-0012}, support = {K01 DK111785/DK/NIDDK NIH HHS/United States ; P30 DK042086/DK/NIDDK NIH HHS/United States ; R37 DK047722/DK/NIDDK NIH HHS/United States ; RC2 DK122394/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents ; Bacteroides/*growth & development/immunology ; Colitis/immunology/metabolism/microbiology/*prevention & control ; Colon/immunology/metabolism/*microbiology/pathology ; Disease Models, Animal ; Dysbiosis ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Host-Pathogen Interactions ; Immune Tolerance ; Interleukin-10/*deficiency/genetics ; Mice, Inbred C57BL ; Mice, Knockout ; Proof of Concept Study ; Time Factors ; Mice ; }, abstract = {BACKGROUND & AIMS: Perturbations in the early-life gut microbiome are associated with increased risk for complex immune disorders like inflammatory bowel diseases. We previously showed that maternal antibiotic-induced gut dysbiosis vertically transmitted to offspring increases experimental colitis risk in interleukin (IL) 10 gene deficient (IL10[-/-]) mice, a finding that may result from the loss/lack of essential microbes needed for appropriate immunologic education early in life. Here, we aimed to identify key microbes required for proper development of the early-life gut microbiome that decrease colitis risk in genetically susceptible animals.

METHODS: Metagenomic sequencing followed by reconstruction of metagenome-assembled genomes was performed on fecal samples of IL10[-/-] mice with and without antibiotic-induced dysbiosis to identify potential missing microbial members needed for immunologic education. One high-value target strain was then engrafted early and/or late into the gut microbiomes of IL10[-/-] mice with antibiotic-induced dysbiosis.

RESULTS: Early-, but not late-, life engraftment of a single dominant Bacteroides strain of non-antibiotic-treated IL10[-/-] mice was sufficient to restore the development of the gut microbiome, promote immune tolerance, and prevent colitis in IL10[-/-] mice that had antibiotic-induced dysbiosis.

CONCLUSIONS: Restitution of a keystone microbial strain missing in the early-life antibiotic-induced gut dysbiosis results in recovery of the microbiome, proper development of immune tolerance, and reduced risk for colitis in genetically prone hosts.}, } @article {pmid34111423, year = {2021}, author = {Hildebrand, F and Gossmann, TI and Frioux, C and Özkurt, E and Myers, PN and Ferretti, P and Kuhn, M and Bahram, M and Nielsen, HB and Bork, P}, title = {Dispersal strategies shape persistence and evolution of human gut bacteria.}, journal = {Cell host & microbe}, volume = {29}, number = {7}, pages = {1167-1176.e9}, pmid = {34111423}, issn = {1934-6069}, support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /ERC_/European Research Council/International ; }, mesh = {Adult ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/*isolation & purification ; Child, Preschool ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Metagenome ; Middle Aged ; Phylogeny ; Young Adult ; }, abstract = {Human gut bacterial strains can co-exist with their hosts for decades, but little is known about how these microbes persist and disperse, and evolve thereby. Here, we examined these processes in 5,278 adult and infant fecal metagenomes, longitudinally sampled in individuals and families. Our analyses revealed that a subset of gut species is extremely persistent in individuals, families, and geographic regions, represented often by locally successful strains of the phylum Bacteroidota. These "tenacious" bacteria show high levels of genetic adaptation to the human host but a high probability of loss upon antibiotic interventions. By contrast, heredipersistent bacteria, notably Firmicutes, often rely on dispersal strategies with weak phylogeographic patterns but strong family transmissions, likely related to sporulation. These analyses describe how different dispersal strategies can lead to the long-term persistence of human gut microbes with implications for gut flora modulations.}, } @article {pmid34111395, year = {2021}, author = {Puschhof, J and Pleguezuelos-Manzano, C and Clevers, H}, title = {Organoids and organs-on-chips: Insights into human gut-microbe interactions.}, journal = {Cell host & microbe}, volume = {29}, number = {6}, pages = {867-878}, doi = {10.1016/j.chom.2021.04.002}, pmid = {34111395}, issn = {1934-6069}, mesh = {Animal Testing Alternatives ; Animals ; Coculture Techniques/methods ; *Gastrointestinal Microbiome ; *Host Microbial Interactions ; Humans ; Intestinal Mucosa ; Mice ; Microbial Interactions ; Microchip Analytical Procedures/*methods ; Microfluidics/methods ; Models, Animal ; Organoids/*microbiology ; Precision Medicine/*methods ; }, abstract = {The important and diverse roles of the gut microbiota in human health and disease are increasingly recognized. The difficulty of inferring causation from metagenomic microbiome sequencing studies and from mouse-human interspecies differences has prompted the development of sophisticated in vitro models of human gut-microbe interactions. Here, we review recent advances in the co-culture of microbes with intestinal and colonic epithelia, comparing the rapidly developing fields of organoids and organs-on-chips with other standard models. We describe how specific individual processes by which microbes and epithelia interact can be recapitulated in vitro. Using examples of bacterial, viral, and parasitic infections, we highlight the advantages of each culture model and discuss current trends and future possibilities to build more complex co-cultures.}, } @article {pmid34111242, year = {2021}, author = {Ryvchin, R and Dubinsky, V and Rabinowitz, K and Wasserberg, N and Dotan, I and Gophna, U}, title = {Alteration in Urease-producing Bacteria in the Gut Microbiomes of Patients with Inflammatory Bowel Diseases.}, journal = {Journal of Crohn's & colitis}, volume = {15}, number = {12}, pages = {2066-2077}, doi = {10.1093/ecco-jcc/jjab101}, pmid = {34111242}, issn = {1876-4479}, support = {//Leona M. and Harry B. Helmsley Charitable Trust/ ; //Israeli Ministry of Science and Technology/ ; //Tel Aviv University/ ; }, mesh = {Case-Control Studies ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Streptococcus/*metabolism ; Urease/*metabolism ; }, abstract = {BACKGROUND AND AIMS: Bacterial urease is a major virulence factor of human pathogens, and murine models have shown that it can contribute to the pathogenesis of inflammatory bowel diseases [IBD].

METHODS: The distribution of urease-producing bacteria in IBD was assessed using public faecal metagenomic data from various cohorts, including non-IBD controls [n = 55], patients with Crohn's disease [n = 291] or ulcerative colitis [n = 214], and patients with a pouch [n = 53]. The ureA gene and the taxonomic markers gyrA, rpoB, and recA were used to estimate the percentage of urease producers in each sample.

RESULTS: Levels of urease producers in patients with IBD and non-IBD controls were comparable. In non-IBD controls and most IBD patients, urease producers were primarily acetate-producing genera such as Blautia and Ruminococcus. A shift in the type of the dominant urease producers towards Proteobacteria and Bacilli was observed in a subset of all IBD subtypes, which correlated with faecal calprotectin levels in one cohort. Some patients with IBD had no detectable urease producers. In patients with a pouch, the probiotic-associated species Streptococcus thermophilus was more common as a main urease producer than in other IBD phenotypes, and it generally did not co-occur with other Bacilli or with Proteobacteria.

CONCLUSIONS: Unlike all non-IBD controls, patients with IBD often showed a shift towards Bacilli or Proteobacteria or a complete loss of urease production. Probiotics containing the species S. thermophilus may have a protective effect against colonisation by undesirable urease-producing bacteria in a subset of patients with a pouch.}, } @article {pmid34110473, year = {2021}, author = {Rivera, AJ and Tyx, RE}, title = {Microbiology of the American Smokeless Tobacco.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {12}, pages = {4843-4853}, pmid = {34110473}, issn = {1432-0614}, mesh = {Carcinogens ; Humans ; Metagenomics ; *Microbiota ; *Tobacco, Smokeless ; United States ; }, abstract = {Smokeless tobacco products (STP) contain diverse microbial communities that contribute to the formation of harmful chemical byproducts. This is concerning since 300 million individuals around the globe are users of smokeless tobacco. Significant evidence has shown that microbial metabolic activities mediate the formation of carcinogens during manufacturing. In recent years, studies have revealed a series of additional health impacts that include lesions and inflammation of the oral mucosa and the gastrointestinal tract, as well as alterations of the endogenous microbiota. These findings are due to recent developments in molecular technologies that allowed researchers to better examine the microbial component of these products. This new information illustrates the scale of the STP microbiota and its diversity in the finished product that is sold for consumption. Additionally, the application of metagenomics and metatranscriptomics has provided the tools to look at phylogenies across bacterial, viral, and eukaryotic groups, their functional capacities, and viability. Here we present key examples of tobacco microbiology research that utilizes newer approaches and strategies to define the microbial component of smokeless tobacco products. We also highlight challenges in these approaches, the knowledge gaps being filled, and those gaps that warrant further study. A better understanding of the microbiology of STP brings vast public health benefits. It will provide important information for the product consumer, impact manufacturing practices, and provide support for the development of attainable and more meaningful regulatory goals. KEY POINTS: Newer technologies allowed quicker and more comprehensive identification of microbes in tobacco samples, encapsulating microorganisms difficult or impossible to culture. Current research in smokeless tobacco microbiology is filling knowledge gaps previously unfilled due to the lack of suitable approaches. The microbial ecology of smokeless tobacco presents a clearer picture of diversity and variability not considered before.}, } @article {pmid34109451, year = {2021}, author = {Yan, Z and Xu, Q and Hsu, WH and Esser, SS and Ayala, J and Hou, R and Yao, Y and Jiang, D and Yuan, S and Wang, H}, title = {Consuming Different Structural Parts of Bamboo Induce Gut Microbiome Changes in Captive Giant Pandas.}, journal = {Current microbiology}, volume = {78}, number = {8}, pages = {2998-3009}, pmid = {34109451}, issn = {1432-0991}, support = {2017YFD0501701//National Key Research Development Program/ ; CPF2017-10//Chengdu Giant Panda Breeding Research Foundation/ ; 31470462//National Natural Science Foundation of China/ ; 17TD0037//Funds for Creative Research Groups of Sichuan Provincial Education Department/ ; 17YC357//Talent Foundation Project of China West Normal University/ ; }, mesh = {Animals ; Diet ; *Gastrointestinal Microbiome ; Metagenome ; RNA, Ribosomal, 16S/genetics ; *Ursidae ; }, abstract = {Giant pandas consume different structural parts of bamboo (shoots, leaves and culms) during different seasons. Previous research showed different bamboo parts have varying nutritional content and that a long-term diet consisting of a single part of bamboo resulted in remarkable metabolic changes within captive giant pandas. However, the effects on the gut microbiome of giant pandas, as a result of a single bamboo part diet, have not been investigated. Here, we evaluated the changes in gut microbial communities based on single bamboo part diets and their potential implications by using 16S rRNA gene-based amplicon sequencing and metagenome shotgun sequencing. We found that the composition and function of the gut microbiome from captive giant pandas fed exclusively culms were significantly different from that of individuals fed shoots or leaves. During the culm feeding period, the gut microbiome showed strongest digestive capabilities for cellulose, hemicellulose and starch, and had the highest potential abilities for the biosynthesis of bile acids, fatty acids and amino acids. This suggests the microbiome aids in breaking down culm, which is more difficult for giant pandas to digest, as a means to compensate for the nutrient poor content of the culm. Genes related to fatty acid metabolism and tricarboxylic acid cycle enzymes were more abundant during the leaf stage diet than that in the shoot and culm stages. Thus, the microbiome may help giant pandas, which typically have low lipase levels, with fat digestion. These results illustrate that adaptive changes in the gut microbiome community and function may be an important mechanism to aid giant panda digestion when consuming different structural parts of bamboo.}, } @article {pmid34108585, year = {2021}, author = {Yoshitake, K and Kimura, G and Sakami, T and Watanabe, T and Taniuchi, Y and Kakehi, S and Kuwata, A and Yamaguchi, H and Kataoka, T and Kawachi, M and Ikeo, K and Tan, E and Igarashi, Y and Ohtsubo, M and Watabe, S and Suzuki, Y and Asakawa, S and Ishino, S and Tashiro, K and Ishino, Y and Kobayashi, T and Mineta, K and Gojobori, T}, title = {Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {12222}, pmid = {34108585}, issn = {2045-2322}, mesh = {*Databases, Factual ; Japan ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; RNA, Ribosomal, 16S/*genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Although numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data (http://marine-meta.healthscience.sci.waseda.ac.jp/omd/), which provides a three-dimensional bird's-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.}, } @article {pmid34108000, year = {2021}, author = {Liu, Y and Wang, H and Yang, J and Zeng, J and Sun, GM}, title = {Virome of respiratory secretion from children with unknown etiological acute respiratory disease revealed recombinant human parechovirus and other significant viruses.}, journal = {Virology journal}, volume = {18}, number = {1}, pages = {122}, pmid = {34108000}, issn = {1743-422X}, mesh = {Child ; Genome, Viral ; Humans ; *Parechovirus/genetics ; Phylogeny ; *Picornaviridae Infections/diagnosis ; RNA, Viral ; *Respiratory Tract Diseases/diagnosis/virology ; Sequence Analysis, DNA ; *Virome ; }, abstract = {Using viral metagenomics, viral nucleic acid in 30 respiratory secretion samples collected from children with unknown etiological acute respiratory disease were investigated. Sequences showing similarity to human parainfluenza virus 1, anellovirus, bocavirus, coxsackievirus A4, human parechovirus (HPeV), and alphaflexivirus were recovered from these samples. Complete genomes of one anellovirus, one coxsackievirus A4, three parechoviruses were determined from these libraries. The anellovirus (MW267851) phylogenetically clustered with an unpublished anellovirus (MK212032) from respiratory sample of a Vietnamese patient, forming a separate branch neighboring to strains within the genus Betatorquevirus. The genome of coxsackievirus A4 (MW267852) shares the highest sequence identity of 96.4% to a coxsackievirus A4 (MN964079) which was identified in clinical samples from children with Hand, Foot, and Mouth Disease (HFMD). Two (MW267853 and MW267854) of the three parechoviruses belong to HPeV-1 and the other one (MW267855) belongs to HPeV-6. Recombination analysis indicated that an HPeV-1 (MW267854) identified in this study is a putative recombinant occurred between HPeV-1 and HPeV-3. Whether these viruses have association with specific respiratory disease calls for further investigation.}, } @article {pmid34107988, year = {2021}, author = {Flachs, A and Orkin, JD}, title = {On pickles: biological and sociocultural links between fermented foods and the human gut microbiome.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {17}, number = {1}, pages = {39}, pmid = {34107988}, issn = {1746-4269}, support = {Global Synergy Grant//College of Liberal Arts, Purdue University/ ; }, mesh = {Fermentation ; *Fermented Foods/microbiology ; *Food Microbiology ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; }, abstract = {BACKGROUND: The composition of the human microbiome varies considerably in diversity and density across communities as a function of the foods we eat and the places we live. While all foods contain microbes, humans directly shape this microbial ecology through fermentation. Fermented foods are produced from microbial reactions that depend on local environmental conditions, fermentation practices, and the manner in which foods are prepared and consumed. These interactions are of special interest to ethnobiologists because they link investigations of how people shape and know the world around them to local knowledge, food traditions, local flora, and microbial taxa.

METHODS: In this manuscript, we report on data collected at a fermentation revivalist workshop in Tennessee. To ask how fermentation traditions are learned and influence macro and micro ecologies, we conducted interviews with eleven people and participated in a four-day craft fermentation workshop. We also collected 46 fermented food products and 46 stool samples from workshop participants eating those fermented foods.

RESULTS: We identified ten major themes comprised of 29 sub-themes drawn from 326 marked codes in the transcripts. In combination, this analysis allowed us to summarize key experiences with fermentation, particularly those related to a sense of authenticity, place, health, and the discovery of tactile work. From the 605 amplicon sequence variants (ASVs) shared between food and fecal samples, we identified 25 candidate ASVs that are suspected to have been transmitted from fermented food samples to the gut microbiomes of the workshop participants. Our results indicate that many of the foods prepared and consumed during the workshop were rich sources of probiotic microbes.

CONCLUSIONS: By combining these qualitative social and quantitative microbiological data, we suggest that variation in culturally informed fermentation practices introduces variation in bacterial flora even among very similar foods, and that these food products can influence gut microbial ecology.}, } @article {pmid34107545, year = {2021}, author = {Gil-Gómez, A and Brescia, P and Rescigno, M and Romero-Gómez, M}, title = {Gut-Liver Axis in Nonalcoholic Fatty Liver Disease: the Impact of the Metagenome, End Products, and the Epithelial and Vascular Barriers.}, journal = {Seminars in liver disease}, volume = {41}, number = {2}, pages = {191-205}, doi = {10.1055/s-0041-1723752}, pmid = {34107545}, issn = {1098-8971}, support = {Spanish Ministry of Economy, Innovation, and Competition, Instituto de Salud Carlos III//PI19/00589/ ; }, mesh = {*Gastrointestinal Microbiome ; Hepatocytes ; Humans ; Metagenome ; *Non-alcoholic Fatty Liver Disease ; }, abstract = {Nonalcoholic fatty liver disease (NAFLD) is a systemic, dynamic, heterogeneous, and multiaxis entity, the pathogenesis of which is still uncertain. The gut-liver axis is regulated and stabilized by a complex network encompassing a metabolic, immune, and neuroendocrine cross-talk between the gut, the microbiota, and the liver. Changes in the gut-liver axis affect the metabolism of lipids and carbohydrates in the hepatocytes, and they impact the balance of inflammatory mediators and cause metabolic deregulation, promoting NAFLD and its progression to nonalcoholic steatohepatitis. Moreover, the microbiota and its metabolites can play direct and indirect roles in gut barrier function and fibrosis development. In this review, we will highlight findings from the recent literature focusing on the gut-liver axis and its relation to NAFLD. Finally, we will discuss the impact of technical issues, design bias, and other limitations on current knowledge of the gut microbiota in the context of NAFLD.}, } @article {pmid34105982, year = {2021}, author = {Almeida, OGG and De Martinis, ECP}, title = {Metagenome-Assembled Genomes Contribute to Unraveling of the Microbiome of Cocoa Fermentation.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {16}, pages = {e0058421}, pmid = {34105982}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/*isolation & purification/metabolism ; Cacao/metabolism/*microbiology ; Chocolate/analysis/*microbiology ; Fermentation ; Fungi/classification/genetics/*isolation & purification/metabolism ; Metagenome ; *Microbiota ; Phylogeny ; Seeds/metabolism/microbiology ; }, abstract = {Metagenomic studies about cocoa fermentation have mainly reported on the analysis of short reads for determination of operational taxonomic units. However, it is also important to determine metagenome-assembled genomes (MAGs), which are genomes deriving from the assembly of metagenomics. For this research, all the cocoa metagenomes from public databases were downloaded, resulting in five data sets: one from Ghana and four from Brazil. In addition, in silico approaches were used to describe putative phenotypes and the metabolic potential of MAGs. A total of 17 high-quality MAGs were recovered from these microbiomes, as follows: (i) for fungi, Yamadazyma tenuis (n = 1); (ii) lactic acid bacteria, Limosilactobacillus fermentum (n = 5), Liquorilactobacillus cacaonum (n = 1), Liquorilactobacillus nagelli (n = 1), Leuconostoc pseudomesenteroides (n = 1), and Lactiplantibacillus plantarum subsp. plantarum (n = 1); (iii) acetic acid bacteria, Acetobacter senegalensis (n = 2) and Kozakia baliensis (n = 1); and (iv) Bacillus subtilis (n = 1), Brevundimonas sp. (n = 2), and Pseudomonas sp. (n = 1). Medium-quality MAGs were also recovered from cocoa microbiomes, including some that, to our knowledge, were not previously detected in this environment (Liquorilactobacillus vini, Komagataeibacter saccharivorans, and Komagataeibacter maltaceti) and others previously described (Fructobacillus pseudoficulneus and Acetobacter pasteurianus). Taken together, the MAGs were useful for providing an additional description of the microbiome of cocoa fermentation, revealing previously overlooked microorganisms, with prediction of key phenotypes and biochemical pathways. IMPORTANCE The production of chocolate starts with the harvesting of cocoa fruits and the spontaneous fermentation of the seeds in a microbial succession that depends on yeasts, lactic acid bacteria, and acetic acid bacteria in order to eliminate bitter and astringent compounds present in the raw material, which will be further roasted and grinded to originate the cocoa powder that will enter the food processing industry. The microbiota of cocoa fermentation is not completely known, and yet it advanced from culture-based studies to the advent of next-generation DNA sequencing, with the generation of a myriad of data that need bioinformatic approaches to be properly analyzed. Although the majority of metagenomic studies have been based on short reads (operational taxonomic units), it is also important to analyze entire genomes to determine more precisely possible ecological roles of different species. Metagenome-assembled genomes (MAGs) are very useful for this purpose; here, MAGs from cocoa fermentation microbiomes are described, and the possible implications of their phenotypic and metabolic potentials are discussed.}, } @article {pmid34105010, year = {2022}, author = {Naidoo, Y and Valverde, A and Pierneef, RE and Cowan, DA}, title = {Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {689-701}, pmid = {34105010}, issn = {1432-184X}, support = {Free standing//National Research Foundation/ ; }, mesh = {Desert Climate ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {Precipitation is one of the major constraints influencing the diversity, structure, and activity of soil microbial communities in desert ecosystems. However, the effect of changes in precipitation on soil microbial communities in arid soil microbiomes remains unresolved. In this study, using 16S rRNA gene high-throughput sequencing and shotgun metagenome sequencing, we explored changes in taxonomic composition and functional potential across two zones in the Namib Desert with contrasting precipitation regime. We found that precipitation regime had no effect on taxonomic and functional alpha-diversity, but that microbial community composition and functional potential (beta-diversity) changed with increased precipitation. For instance, Acidobacteriota and 'resistance to antibiotics and toxic compounds' related genes were relatively more abundant in the high-rainfall zone. These changes were largely due to a small set of microbial taxa, some of which were present in low abundance (i.e. members of the rare biosphere). Overall, these results indicate that key climatic factors (i.e. precipitation) shape the taxonomic and functional attributes of the arid soil microbiome. This research provides insight into how changes in precipitation patterns associated with global climate change may impact microbial community structure and function in desert soils.}, } @article {pmid34103703, year = {2021}, author = {Wang, W and Wei, X and Wu, L and Shang, X and Cheng, F and Li, B and Zhou, X and Zhang, J}, title = {The occurrence of antibiotic resistance genes in the microbiota of yak, beef and dairy cattle characterized by a metagenomic approach.}, journal = {The Journal of antibiotics}, volume = {74}, number = {8}, pages = {508-518}, pmid = {34103703}, issn = {1881-1469}, mesh = {Animal Feed ; Animals ; Cattle/*microbiology ; Dairy Products ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Humans ; Integrons/genetics ; Interspersed Repetitive Sequences/genetics ; Meat ; Metagenomics/*methods ; Microbiota/*genetics ; Soil Microbiology ; Species Specificity ; }, abstract = {Drug resistance has been partly driven by the overuse of antimicrobials in agricultural animal feed. Better understanding of antibiotic resistance in bovine gut is needed to assess its potential effects based on metagenomic approach and analysis. In this study, we collected 40 fecal samples to explore drug resistance derived from antibiotic use in the bacterial community by an analysis of the diversities and differences of antibiotic-resistant genes (ARGs) in the gut microbiota from yak, beef, and dairy cattle. Overall, 1688 genes were annotated, including 734 ARG subtypes. The ARGs were related to tetracyclines, quinolones, β-lactam, and aminoglycosides, in accordance with the antibiotics widely used in the clinic for humans or animals. The emergence, prevalence, and differences in resistance genes in the intestines of yaks, beef, and dairy cattle may be caused by the selective pressure of different feeding patterns, where yaks were raised without antibiotics for growth promotion. In addition, the abundance of ARGs in yak was lower than in beef and dairy cattle, whereas the abundance of integron, a kind of mobile genetic elements (MGEs) was higher in yaks than those in beef and dairy cattle. Furthermore, the results of this study could provide the basis for a comprehensive profile of various ARGs among yak, beef, and dairy cattle in future.}, } @article {pmid34103263, year = {2021}, author = {Miao, Q and Ma, Y and Ling, Y and Jin, W and Su, Y and Wang, Q and Pan, J and Zhang, Y and Chen, H and Yuan, J and Wu, H and Hu, B}, title = {Evaluation of superinfection, antimicrobial usage, and airway microbiome with metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {54}, number = {5}, pages = {808-815}, pmid = {34103263}, issn = {1995-9133}, mesh = {Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/*therapeutic use ; Antimicrobial Stewardship ; *COVID-19 ; China ; Cohort Studies ; Coinfection/drug therapy ; Critical Illness ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metagenomics ; Microbiota/genetics/*physiology ; Middle Aged ; Mycoses/drug therapy ; Respiratory System/*microbiology ; Retrospective Studies ; SARS-CoV-2 ; Superinfection/*drug therapy ; }, abstract = {BACKGROUND: In COVID-19 patients, information regarding superinfection, antimicrobial assessment, and the value of metagenomic sequencing (MS) could help develop antimicrobial stewardship.

METHOD: This retrospective study analyzed 323 laboratory-confirmed COVID-19 patients for co-infection rate and antimicrobial usage in the Shanghai Public Health Clinical Center (SPHCC) from January 23rd to March 14th 2020. The microbiota composition was also investigated in patients with critically severe COVID-19.

RESULTS: The total population co-infection rate was 17/323 (5.3%) and 0/229 (0), 4/78 (5.1%), and 13/16 (81.3%) for the mild, severe, and critically severe subgroups, respectively. Proven fungal infection was significantly associated with a higher mortality rate (p = 0.029). In critically severe patients, the rate of antimicrobials and carbapenem usage were 16/16 (100%) and 13/16 (81.3%), respectively, in which the preemptive and empiric antimicrobial days accounted for 51.6% and 30.1%, respectively. Targeted therapy only accounted for 18.3%. MS was implemented to detect non-COVID-19 virus co-existence and the semi-quantitative surveillance of bacteremia, with clear clinical benefit seen in cases with MS-based precision antimicrobial management. Airway microbiome analysis suggested that the microbiota compositions in critically severe COVID-19 patients were likely due to intubation and mechanical ventilation.

CONCLUSIONS: In the SPHCC cohort, we observed a non-negligible rate of super-infection, especially for the critically ill COVID-19 patients. Fungal co-infection requires intensive attention due to the high risk of mortality, and the clinical benefit of MS in guiding antimicrobial management warrants further investigation.}, } @article {pmid34102480, year = {2021}, author = {Lu, CC and Wei, RX and Deng, DH and Luo, ZY and Abdulai, M and Liu, HH and Kang, B and Hu, SQ and Li, L and Xu, HY and Hu, JW and Wei, SH and Han, CC}, title = {Effect of different types of sugar on gut physiology and microbiota in overfed goose.}, journal = {Poultry science}, volume = {100}, number = {7}, pages = {101208}, pmid = {34102480}, issn = {1525-3171}, mesh = {Animals ; Chickens ; *Fatty Liver/veterinary ; *Gastrointestinal Microbiome ; Geese ; Sugars ; }, abstract = {To explored the difference of goose fatty liver formation induced-by different types of sugar from the intestinal physiology and the gut microflora, an integrated analysis of intestinal physiology and gut microbiota metagenomes was performed using samples collected from the geese including the normal-feeding geese and the overfed geese which were overfed with maize flour or overfeeding dietary supplementation with 10% sugar (glucose, fructose or sucrose, respectively), respectively. The results showed that the foie gras weight of the fructose group and the sucrose group was heavier (P < 0.05) than other groups. Compared with the control group, the ileum weight was significantly higher (P < 0.01), and the cecum weight was significantly lower in the sugar treatment groups (P < 0.001). Compared with the control group, the ratio of villi height to crypt depth in the fructose group was the highest in jejunum (P < 0.05); the trypsin activity of the ileum was higher in the fructose group and the sucrose group (P < 0.05). At the phylum level, Firmicutes, Proteobacteria and Bacteroidetes were the main intestinal flora of geese; and the abundance of Firmicutes in the jejunum was higher in the sugar treatment groups than that of the maize flour group. At the genus level, the abundance of Lactobacillus in the jejunum was higher (P < 0.05) in the sugar treatment groups than that of the maize flour group. In conclusion, forced-feeding diet supplementation with sugar induced stronger digestion and absorption capacity, increased the abundance of Firmicutes and Bacteroidetes and the abundance of Lactobacillus (especially fructose and sucrose) in the gut. So, the fructose and sucrose had higher induction on hepatic steatosis in goose fatty liver formation.}, } @article {pmid34102245, year = {2021}, author = {Emoto, T and Hayashi, T and Tabata, T and Yamashita, T and Watanabe, H and Takahashi, T and Gotoh, Y and Kami, K and Yoshida, N and Saito, Y and Tanaka, H and Matsumoto, K and Hayashi, T and Yamada, T and Hirata, KI}, title = {Metagenomic analysis of gut microbiota reveals its role in trimethylamine metabolism in heart failure.}, journal = {International journal of cardiology}, volume = {338}, number = {}, pages = {138-142}, doi = {10.1016/j.ijcard.2021.06.003}, pmid = {34102245}, issn = {1874-1754}, mesh = {Choline ; *Gastrointestinal Microbiome ; *Heart Failure ; Humans ; Metagenome ; Methylamines ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: We had previously reported an increase in trimethylamine N-oxide (TMAO) levels in patients with both compensated and decompensated heart failure (HF) and alteration in gut microbiota composition using 16S rRNA gene amplicon analysis. Although a metagenome-wide analysis showed that choline-TMA lyase levels increased in HF patients, which TMA generation pathway from choline, carnitine, or betaine contributes to the increase in TMAO levels in HF needs to be elucidated.

METHODS: We conducted a metagenome-wide shotgun sequencing analysis of gut microbiota and measured the TMAO levels in plasma of 22 HF patients during the compensated phase and 11 age-, sex-, and comorbidity-matched control subjects, whose gut microbiota compositions were reported in a previous 16S rRNA-based analysis.

RESULTS: The abundance of cntA/B was positively correlated with TMAO, especially in HF patients, whereas that of cutC/D or betaine reductase was not correlated either in controls or HF patients. The abundance of cntA/B was mainly derived from the genera Escherichia and Klebsiella either in controls or HF patients.

CONCLUSION: TMAO levels in plasma depend on the abundance of cntA/B in HF. Although it is difficult to exclude the involvement of confounding factors, microbial dysbiosis connecting the abundance of cntA/B in the gut and the increase of TMAO in plasma can be a therapeutic target for HF.}, } @article {pmid34100638, year = {2021}, author = {Wei, ST and Chen, YL and Wu, YW and Wu, TY and Lai, YL and Wang, PH and Ismail, W and Lee, TH and Chiang, YR}, title = {Integrated Multi-omics Investigations Reveal the Key Role of Synergistic Microbial Networks in Removing Plasticizer Di-(2-Ethylhexyl) Phthalate from Estuarine Sediments.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {e0035821}, pmid = {34100638}, issn = {2379-5077}, support = {AS-CDA-110-L13//Academia Sinica/ ; MOST 109-2221-E-001-002//Ministry of Science and Technology, Taiwan (MOST)/ ; MOST 110-2222-E-008-002//Ministry of Science and Technology, Taiwan (MOST)/ ; }, abstract = {Di-(2-ethylhexyl) phthalate (DEHP) is the most widely used plasticizer worldwide, with an annual global production of more than 8 million tons. Because of its improper disposal, endocrine-disrupting DEHP often accumulates in estuarine sediments in industrialized countries at submillimolar levels, resulting in adverse effects on both ecosystems and human beings. The microbial degraders and biodegradation pathways of DEHP in O2-limited estuarine sediments remain elusive. Here, we employed an integrated meta-omics approach to identify the DEHP degradation pathway and major degraders in this ecosystem. Estuarine sediments were treated with DEHP or its derived metabolites, o-phthalic acid and benzoic acid. The rate of DEHP degradation in denitrifying mesocosms was two times slower than that of o-phthalic acid, suggesting that side chain hydrolysis of DEHP is the rate-limiting step of anaerobic DEHP degradation. On the basis of microbial community structures, functional gene expression, and metabolite profile analysis, we proposed that DEHP biodegradation in estuarine sediments is mainly achieved through synergistic networks between denitrifying proteobacteria. Acidovorax and Sedimenticola are the major degraders of DEHP side chains; the resulting o-phthalic acid is mainly degraded by Aestuariibacter through the UbiD-dependent benzoyl coenzyme A (benzoyl-CoA) pathway. We isolated and characterized Acidovorax sp. strain 210-6 and its extracellular hydrolase, which hydrolyzes both alkyl side chains of DEHP. Interestingly, genes encoding DEHP/mono-(2-ethylhexyl) phthalate (MEHP) hydrolase and phthaloyl-CoA decarboxylase-key enzymes for side chain hydrolysis and o-phthalic acid degradation, respectively-are flanked by transposases in these proteobacterial genomes, indicating that DEHP degradation capacity is likely transferred horizontally in microbial communities. IMPORTANCE Xenobiotic phthalate esters (PAEs) have been produced on a considerably large scale for only 70 years. The occurrence of endocrine-disrupting di-(2-ethylhexyl) phthalate (DEHP) in environments has raised public concern, and estuarine sediments are major DEHP reservoirs. Our multi-omics analyses indicated that complete DEHP degradation in O2-limited estuarine sediments depends on synergistic microbial networks between diverse denitrifying proteobacteria and uncultured candidates. Our data also suggested that the side chain hydrolysis of DEHP, rather than o-phthalic acid activation, is the rate-limiting step in DEHP biodegradation within O2-limited estuarine sediments. Therefore, deciphering the bacterial ecophysiology and related biochemical mechanisms can help facilitate the practice of bioremediation in O2-limited environments. Furthermore, the DEHP hydrolase genes of active DEHP degraders can be used as molecular markers to monitor environmental DEHP degradation. Finally, future studies on the directed evolution of identified DEHP/mono-(2-ethylhexyl) phthalate (MEHP) hydrolase would bring a more catalytically efficient DEHP/MEHP hydrolase into practice.}, } @article {pmid34097462, year = {2021}, author = {Breen, P and Winters, AD and Theis, KR and Withey, JH}, title = {The Vibrio cholerae Type Six Secretion System Is Dispensable for Colonization but Affects Pathogenesis and the Structure of Zebrafish Intestinal Microbiome.}, journal = {Infection and immunity}, volume = {89}, number = {9}, pages = {e0015121}, pmid = {34097462}, issn = {1098-5522}, support = {R01 AI127390/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cholera/*microbiology ; Disease Models, Animal ; Disease Susceptibility ; *Gastrointestinal Microbiome ; *Host Microbial Interactions ; *Host-Pathogen Interactions ; Metagenomics/methods ; RNA, Ribosomal, 16S ; Type VI Secretion Systems/*physiology ; Vibrio cholerae/*physiology ; Zebrafish ; }, abstract = {Zebrafish (Danio rerio) are an attractive model organism for a variety of scientific studies, including host-microbe interactions. The organism is particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae, an intestinal pathogen. V. cholerae must colonize the intestine of an exposed host for pathogenicity to occur. While numerous studies have explored various aspects of the pathogenic effects of V. cholerae on zebrafish and other model organisms, few, if any, have examined how a V. cholerae infection alters the resident intestinal microbiome and the role of the type six secretion system (T6SS) in that process. In this study, 16S rRNA gene sequencing was utilized to investigate how strains of V. cholerae both with and without the T6SS alter the aforementioned microbial profiles following an infection. V. cholerae infection induced significant changes in the zebrafish intestinal microbiome, and while not necessary for colonization, the T6SS was important for inducing mucin secretion, a marker for diarrhea. Additional salient differences to the microbiome were observed based on the presence or absence of the T6SS in the V. cholerae utilized for challenging the zebrafish hosts. We conclude that V. cholerae significantly modulates the zebrafish intestinal microbiome to enable colonization and that the T6SS is important for pathogenesis induced by the examined V. cholerae strains. Furthermore, the presence or absence of T6SS differentially and significantly affected the composition and structure of the intestinal microbiome, with an increased abundance of other Vibrio bacteria observed in the absence of V. cholerae T6SS.}, } @article {pmid34092249, year = {2021}, author = {D'Souza, AW and Boolchandani, M and Patel, S and Galazzo, G and van Hattem, JM and Arcilla, MS and Melles, DC and de Jong, MD and Schultsz, C and , and Dantas, G and Penders, J}, title = {Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {79}, pmid = {34092249}, issn = {1756-994X}, support = {T32 GM007200/GM/NIGMS NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; }, mesh = {Bacteria/*classification/*drug effects/*genetics ; Bacterial Infections/*epidemiology/*microbiology ; Computational Biology/methods ; Databases, Genetic ; *Drug Resistance, Microbial ; Gastrointestinal Microbiome/drug effects ; Humans ; Metagenome ; Metagenomics ; Netherlands/epidemiology ; Public Health Surveillance ; *Travel-Related Illness ; beta-Lactamases/genetics ; }, abstract = {BACKGROUND: Antimicrobial-resistant bacteria and their antimicrobial resistance (AMR) genes can spread by hitchhiking in human guts. International travel can exacerbate this public health threat when travelers acquire AMR genes endemic to their destinations and bring them back to their home countries. Prior studies have demonstrated travel-related acquisition of specific opportunistic pathogens and AMR genes, but the extent and magnitude of travel's effects on the gut resistome remain largely unknown.

METHODS: Using whole metagenomic shotgun sequencing, functional metagenomics, and Dirichlet multinomial mixture models, we investigated the abundance, diversity, function, resistome architecture, and context of AMR genes in the fecal microbiomes of 190 Dutch individuals, before and after travel to diverse international locations.

RESULTS: Travel markedly increased the abundance and α-diversity of AMR genes in the travelers' gut resistome, and we determined that 56 unique AMR genes showed significant acquisition following international travel. These acquisition events were biased towards AMR genes with efflux, inactivation, and target replacement resistance mechanisms. Travel-induced shaping of the gut resistome had distinct correlations with geographical destination, so individuals returning to The Netherlands from the same destination country were more likely to have similar resistome features. Finally, we identified and detailed specific acquisition events of high-risk, mobile genetic element-associated AMR genes including qnr fluoroquinolone resistance genes, blaCTX-M family extended-spectrum β-lactamases, and the plasmid-borne mcr-1 colistin resistance gene.

CONCLUSIONS: Our results show that travel shapes the architecture of the human gut resistome and results in AMR gene acquisition against a variety of antimicrobial drug classes. These broad acquisitions highlight the putative risks that international travel poses to public health by gut resistome perturbation and the global spread of locally endemic AMR genes.}, } @article {pmid34092246, year = {2021}, author = {Wu, Y and He, F and Zhang, C and Zhang, Q and Su, X and Zhu, X and Liu, A and Shi, W and Lin, W and Jin, Z and Yang, H and Lin, J}, title = {Melatonin alleviates titanium nanoparticles induced osteolysis via activation of butyrate/GPR109A signaling pathway.}, journal = {Journal of nanobiotechnology}, volume = {19}, number = {1}, pages = {170}, pmid = {34092246}, issn = {1477-3155}, support = {81871789//National Natural Science Foundation of China/ ; 31771063//National Natural Science Foundation of China (CN)/ ; 81802200//National Natural Science Foundation of China (CN)/ ; 82171333//National Natural Science Foundation of China (CN)/ ; 82101033//National Natural Science Foundation of China (CN)/ ; BK20180052//Natural Science Foundation of Jiangsu Province (CN)/ ; GSWS2020023//Gusu Health Talents Program/ ; }, mesh = {Animals ; Butyrates/*metabolism ; Fatty Acids, Volatile ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects ; Homeostasis ; Male ; Melatonin/chemistry/metabolism/*pharmacology ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; Nanoparticles/chemistry/therapeutic use ; Osteolysis/metabolism/pathology/*prevention & control ; RNA, Ribosomal, 16S ; Receptors, G-Protein-Coupled/*genetics/*metabolism ; Signal Transduction/*drug effects ; Titanium/chemistry/metabolism/*pharmacology ; }, abstract = {BACKGROUND: Inflammatory osteolysis after total joint replacement (TJR) may cause implant failure, periprosthetic fractures, and be a severe threat to global public health. Our previous studies demonstrated that melatonin had a therapeutic effect on wear-particles induced osteolysis. Gut microbiota is closely related to bone homeostasis, and has been proven to be affected by melatonin. However, whether melatonin could play its anti-osteolysis effects through reprogramming gut microbiota remains elusive.

RESULTS: Here, we demonstrated that melatonin could alleviate Ti-particles induced osteolysis, while this therapeutic effect was blocked by antibiotic cocktail treatment. Interestingly, transplantation of fecal microbiota from mice treated with melatonin reappeared the same beneficial effect. Analysis of the 16S rRNA revealed that melatonin could reverse dysbacteriosis triggered by osteolysis, and elevate the relative abundance of some short chain fatty acid (SCFA) producing bacteria. Moreover, butyrate was enriched by exogenous melatonin administration, while acetate and propionate did not show an evident difference. This was consistent with the results of the metagenomic approach (PICRUSt2) analysis, which revealed a general increase in the synthetic enzymes of butyrate. More importantly, direct supplementation of butyrate could also recapitulate the anti-osteolysis effect of melatonin. Further analysis identified that butyrate alleviated osteolysis via activating its receptor GPR109A, and thus to suppress the activation of NLRP3 inflammasome triggered by Ti-particles.

CONCLUSIONS: Taken together, our results suggested that the benefits of melatonin mainly depend on the ability of modulating gut microbiota and regulating butyrate production.}, } @article {pmid34091278, year = {2021}, author = {Dall'Agnol, B and McCulloch, JA and Mayer, FQ and Souza, U and Webster, A and Antunes, P and Doyle, RL and Reck, J and Ferreira, CAS}, title = {Molecular characterization of bacterial communities of two neotropical tick species (Amblyomma aureolatum and Ornithodoros brasiliensis) using rDNA 16S sequencing.}, journal = {Ticks and tick-borne diseases}, volume = {12}, number = {5}, pages = {101746}, doi = {10.1016/j.ttbdis.2021.101746}, pmid = {34091278}, issn = {1877-9603}, mesh = {Amblyomma/*microbiology ; Animals ; Bacteria/genetics/isolation & purification ; Coxiella/genetics/isolation & purification ; DNA, Bacterial/isolation & purification ; Francisella/genetics/isolation & purification ; Ixodidae/microbiology ; Metagenomics ; *Microbiota ; Ornithodoros/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rickettsia/genetics/isolation & purification ; }, abstract = {Ticks are one of the main vectors of pathogens for humans and animals worldwide. However, they harbor non-pathogenic microorganisms that are important for their survival, facilitating both their nutrition and immunity. We investigated the bacterial communities associated with two neotropical tick species of human and veterinary potential health importance from Brazil: Amblyomma aureolatum and Ornithodoros brasiliensis. In A. aureolatum (adult ticks collected from wild canids from Southern Brazil), the predominant bacterial phyla were Proteobacteria (98.68%), Tenericutes (0.70%), Bacteroidetes (0.14%), Actinobacteria (0.13%), and Acidobacteria (0.05%). The predominant genera were Francisella (97.01%), Spiroplasma (0.70%), Wolbachia (0.51%), Candidatus Midichloria (0.25%), and Alkanindiges (0.13%). The predominant phyla in O. brasiliensis (adults, fed and unfed nymphs collected at the environment from Southern Brazil) were Proteobacteria (90.27%), Actinobacteria (7.38%), Firmicutes (0.77%), Bacteroidetes (0.44%), and Planctomycetes (0.22%). The predominant bacterial genera were Coxiella (87.71%), Nocardioides (1.73%), Saccharopolyspora (0.54%), Marmoricola (0.42%), and Staphylococcus (0.40%). Considering the genera with potential importance for human and animal health which can be transmitted by ticks, Coxiella sp. was found in all stages of O. brasiliensis, Francisella sp. in all stages of A. aureolatum and in unfed nymphs of O. brasiliensis, and Rickettsia sp. in females of A. aureolatum from Banhado dos Pachecos (BP) in Viamão municipality, Brazil, and in females and unfed nymphs of O. brasiliensis. These results deepen our understanding of the tick-microbiota relationship in Ixodidae and Argasidae, driving new studies with the focus on the manipulation of tick microbiota to prevent outbreaks of tick-borne diseases in South America.}, } @article {pmid34090540, year = {2021}, author = {Callahan, BJ and Grinevich, D and Thakur, S and Balamotis, MA and Yehezkel, TB}, title = {Ultra-accurate microbial amplicon sequencing with synthetic long reads.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {130}, pmid = {34090540}, issn = {2049-2618}, support = {R35 GM133745/GM/NIGMS NIH HHS/United States ; }, mesh = {*High-Throughput Nucleotide Sequencing ; Metagenome ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge.

METHODS: Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads.

RESULTS: LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens.

CONCLUSIONS: The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics. Video abstract.}, } @article {pmid34090519, year = {2021}, author = {Wilkins, D and Tong, X and Leung, MHY and Mason, CE and Lee, PKH}, title = {Diurnal variation in the human skin microbiome affects accuracy of forensic microbiome matching.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {129}, pmid = {34090519}, issn = {2049-2618}, support = {R01 AI151059/AI/NIAID NIH HHS/United States ; }, mesh = {Bayes Theorem ; Hong Kong ; Humans ; Metagenomics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: The human skin microbiome has been recently investigated as a potential forensic tool, as people leave traces of their potentially unique microbiomes on objects and surfaces with which they interact. In this metagenomic study of four people in Hong Kong, their homes, and public surfaces in their neighbourhoods, we investigated the stability and identifiability of these microbiota traces on a timescale of hours to days.

RESULTS: Using a Canberra distance-based method of comparing skin and surface microbiomes, we found that a person could be accurately matched to their household in 84% of tests and to their neighbourhood in 50% of tests, and that matching accuracy did not decay for household surfaces over the 10-day study period, although it did for public surfaces. The time of day at which a skin or surface sample was taken affected matching accuracy, and 160 species across all sites were found to have a significant variation in abundance between morning and evening samples. We hypothesised that daily routines drive a rhythm of daytime dispersal from the pooled public surface microbiome followed by normalisation of a person's microbiome by contact with their household microbial reservoir, and Dynamic Bayesian Networks (DBNs) supported dispersal from public surfaces to skin as the major dispersal route among all sites studied.

CONCLUSIONS: These results suggest that in addition to considering the decay of microbiota traces with time, diurnal patterns in microbiome exposure that contribute to the human skin microbiome assemblage must also be considered in developing this as a potential forensic method. Video Abstract.}, } @article {pmid34085924, year = {2021}, author = {Hughes, ER and Winter, MG and Alves da Silva, L and Muramatsu, MK and Jimenez, AG and Gillis, CC and Spiga, L and Chanin, RB and Santos, RL and Zhu, W and Winter, SE}, title = {Reshaping of bacterial molecular hydrogen metabolism contributes to the outgrowth of commensal E. coli during gut inflammation.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34085924}, issn = {2050-084X}, support = {R01 AI118807/AI/NIAID NIH HHS/United States ; R21 AI128151/AI/NIAID NIH HHS/United States ; T32 AI007520/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cecum/metabolism/*microbiology/pathology ; Colitis/*chemically induced/metabolism/*microbiology/pathology ; Colon/metabolism/*microbiology/pathology ; Databases, Genetic ; Dextran Sulfate ; Disease Models, Animal ; Dysbiosis ; Escherichia coli/genetics/growth & development/*metabolism ; Escherichia coli Infections/metabolism/*microbiology/pathology ; Escherichia coli Proteins/genetics/metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; Hydrogen/*metabolism ; Hydrogenase/genetics/metabolism ; Interleukin-10/genetics/metabolism ; Male ; Metagenome ; Metagenomics ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Mice, Knockout ; Piroxicam ; Mice ; }, abstract = {The composition of gut-associated microbial communities changes during intestinal inflammation, including an expansion of Enterobacteriaceae populations. The mechanisms underlying microbiota changes during inflammation are incompletely understood. Here, we analyzed previously published metagenomic datasets with a focus on microbial hydrogen metabolism. The bacterial genomes in the inflamed murine gut and in patients with inflammatory bowel disease contained more genes encoding predicted hydrogen-utilizing hydrogenases compared to communities found under non-inflamed conditions. To validate these findings, we investigated hydrogen metabolism of Escherichia coli, a representative Enterobacteriaceae, in mouse models of colitis. E. coli mutants lacking hydrogenase-1 and hydrogenase-2 displayed decreased fitness during colonization of the inflamed cecum and colon. Utilization of molecular hydrogen was in part dependent on respiration of inflammation-derived electron acceptors. This work highlights the contribution of hydrogenases to alterations of the gut microbiota in the context of non-infectious colitis.}, } @article {pmid34083731, year = {2021}, author = {Kullapanich, C and Jandang, S and Palasuk, M and Viyakarn, V and Chavanich, S and Somboonna, N}, title = {First dynamics of bacterial community during development of Acropora humilis larvae in aquaculture.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {11762}, pmid = {34083731}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/growth & development/*microbiology ; *Bacteria/classification/genetics ; High-Throughput Nucleotide Sequencing ; Larva/growth & development/*microbiology ; Life Cycle Stages ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Symbiosis ; }, abstract = {A symbiosis of bacterial community (sometimes called microbiota) play essential roles in developmental life cycle and health of coral, starting since a larva. For examples, coral bacterial holobionts function nitrogen fixation, carbon supply, sulfur cycling and antibiotic production. Yet, a study of the dynamic of bacteria associated coral larvae development is complicated owning to a vast diversity and culturable difficulty of bacteria; hence this type of study remains unexplored for Acropora humilis larvae in Thai sea. This study represented the first to utilize 16S rRNA gene sequencing to describe the timely bacterial compositions during successfully cultured and reared A. humilis larval transformation in aquaculture (gametes were collected from Sattahip Bay, Chonburi province, Thailand), from gamete spawning (0 h) and fertilization stage (1 h), to embryonic cleavage (8 h), round cell development (28, 39 and 41 h), and planula formation (48 h). The sequencing results as estimated by Good's coverage at genus level covered 99.65 ± 0.24% of total bacteria. While core phyla of bacteria were observed (Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes), changes in bacterial population structures and differential predominant core bacterial orders were denoted for each larval developmental stage, from fertilization to embryonic cleavage and subsequently from the embryonic cleavage to round cell development (P = 0.007). For instances, Pseudoalteromonas and Oceanospirillales were found prevalent at 8 h, and Rhizobiales were at 48 h. The bacterial population structures from the round cell stage, particularly at 41 h, showed gradual drift towards those of the planula formation stage, suggesting microbial selection. Overall, this study provides preliminary insights into the dynamics of bacterial community and their potentially functional association (estimated from the bacterial compositions) during the developmental embryonic A. humilis in a cultivation system in Southeast Asia region.}, } @article {pmid34083661, year = {2021}, author = {Zheng, L and Sun, R and Zhu, Y and Li, Z and She, X and Jian, X and Yu, F and Deng, X and Sai, B and Wang, L and Zhou, W and Wu, M and Li, G and Tang, J and Jia, W and Xiang, J}, title = {Lung microbiome alterations in NSCLC patients.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {11736}, pmid = {34083661}, issn = {2045-2322}, mesh = {Adult ; Aged ; Biomarkers ; Carcinoma, Non-Small-Cell Lung/*complications/diagnosis ; *Dysbiosis ; Female ; Humans ; Lung/*microbiology ; Lung Neoplasms/*complications/diagnosis ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Pneumonia/*etiology ; Risk Assessment ; Risk Factors ; }, abstract = {Lung is colonized by a diverse array of microbes and the lung microbiota is profoundly involved in the development of respiratory diseases. There is little knowledge about the role of lung microbiota dysbiosis in lung cancer. In this study, we performed metagenomic sequencing on bronchoalveolar lavage (BAL) from two different sampling methods in non-small cell lung cancer (NSCLC) patients and non-cancer controls. We found the obvious variation between bronchoscopy samples and lobectomy samples. Oral taxa can be found in both bronchoscopy and lobectomy samples and higher abundance of oral taxa can be found in bronchoscopy samples. Although the NSCLC patients had similar microbial communities with non-cancer controls, rare species such as Lactobacillus rossiae, Bacteroides pyogenes, Paenibacillus odorifer, Pseudomonas entomophila, Magnetospirillum gryphiswaldense, fungus Chaetomium globosum et al. showed obvious difference between NSCLC patients and non-cancer controls. Age-, gender-, and smoking-specific species and EGFR expression-related species in NSCLC patients were detected. There results implicated that different lung segments have differential lung microbiome composition. The oral taxa are found in the lobectomy samples suggesting that oral microbiota are the true members of lung microbiota, rather than contamination during bronchoscopy. Lung cancer does not obviously alter the global microbial composition, while rare species are altered more than common species. Certain microbes may be associated with lung cancer progression.}, } @article {pmid34083632, year = {2021}, author = {Grisnik, M and Grinath, JB and Walker, DM}, title = {The presence of Pseudogymnoascus destructans, a fungal pathogen of bats, correlates with changes in microbial metacommunity structure.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {11685}, pmid = {34083632}, issn = {2045-2322}, mesh = {Animal Diseases/*microbiology ; Animals ; *Ascomycota ; Biodiversity ; Chiroptera/*microbiology ; Computational Biology/methods ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mycoses/*veterinary ; }, abstract = {Metacommunity theory provides a framework for how community patterns arise from processes across scales, which is relevant for understanding patterns in host-associated microbial assemblages. Microbial metacommunities may have important roles in host health through interactions with pathogens; however, it is unclear how pathogens affect host microbial metacommunities. Here, we studied relationships between a fungal pathogen and a host-associated microbial metacommunity. We hypothesized that a fungal pathogen of bats, Pseudogymnoascus destructans, correlates with a shift in metacommunity structure and changes in relationships between community composition, and factors shaping these assemblages, such as ecoregion. We sampled bat cutaneous microbial assemblages in the presence/absence of P. destructans and analyzed microbial metacommunity composition and relationships with structuring variables. Absence of P. destructans correlated with a metacommunity characterized by a common core microbial group that was lacking in disease positive bats. Additionally, P. destructans presence correlated with a change in the relationship between community structure and ecoregion. Our results suggest that the fungal pathogen intensifies local processes influencing a microbial metacommunity and highlights the importance of cutaneous microbial assemblages in host-pathogen interactions.}, } @article {pmid34083435, year = {2021}, author = {Tisza, MJ and Buck, CB}, title = {A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {23}, pages = {}, pmid = {34083435}, issn = {1091-6490}, support = {ZIA BC011090/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; CRISPR-Cas Systems ; Case-Control Studies ; *Chronic Disease ; Clustered Regularly Interspaced Short Palindromic Repeats ; DNA Viruses/genetics ; Data Management ; Genome, Viral ; Genomics ; Humans ; *Metagenome ; Metagenomics ; Microbiota ; Parkinson Disease ; Virome ; Viruses/*genetics ; Young Adult ; }, abstract = {Despite remarkable strides in microbiome research, the viral component of the microbiome has generally presented a more challenging target than the bacteriome. This gap persists, even though many thousands of shotgun sequencing runs from human metagenomic samples exist in public databases, and all of them encompass large amounts of viral sequence data. The lack of a comprehensive database for human-associated viruses has historically stymied efforts to interrogate the impact of the virome on human health. This study probes thousands of datasets to uncover sequences from over 45,000 unique virus taxa, with historically high per-genome completeness. Large publicly available case-control studies are reanalyzed, and over 2,200 strong virus-disease associations are found.}, } @article {pmid34082693, year = {2021}, author = {Chen, J and Wang, A and Wang, Q}, title = {Dysbiosis of the gut microbiome is a risk factor for osteoarthritis in older female adults: a case control study.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {299}, pmid = {34082693}, issn = {1471-2105}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adult ; Aged ; Animals ; Case-Control Studies ; Dysbiosis ; Female ; *Gastrointestinal Microbiome ; Humans ; *Osteoarthritis ; Quality of Life ; Risk Factors ; }, abstract = {BACKGROUND: Osteoarthritis (OA) is a multifactorial joint degenerative disease with low-grade inflammation. The gut microbiome has recently emerged as an pathogenic factor of OA, and prebiotics supplementation could alleviate OA symptoms in animal models. However, the relationship between the gut microbiome and OA in the older female adults is hitherto not clear.

RESULTS: Here we studied the gut microbiome of 57 OA patients and their healthy controls by metagenome-wide association study based on previously published data. A significant reduction in the richness and diversity of gut microbiome were observed in OA patients. Bifidobacterium longum and Faecalibacterium prausnitzii were decreased while Clostridium spp. was increased in the OA group. The functional modules, particularly the energetic metabolism and acetate production were also decreased in the OA patients. To evaluate the diagnostic value of identified species for elderly patients with OA, we constructed a set of random forest disease classifiers based on species differences between the two groups. Among them, 9 species reached the lowest classification error in the random forest cross validation, and the area under ROC of the model was 0.81.

CONCLUSIONS: Significant alterations in the gut microbial composition and function were observed between the older patients with OA and their controls, and a random forest classifier model for OA were constructed based on the differences in our study. Our study have identified several potential gut microbial targets in the elderly females with OA, which will facilitate the treatment of OA based on gut microbiota, is of great value in alleviating pain and improving the quality of life for them.}, } @article {pmid34082069, year = {2021}, author = {Wang, Z and Hopson, LM and Singleton, SS and Yang, X and Jogunoori, W and Mazumder, R and Obias, V and Lin, P and Nguyen, BN and Yao, M and Miller, L and White, J and Rao, S and Mishra, L}, title = {Mice with dysfunctional TGF-β signaling develop altered intestinal microbiome and colorectal cancer resistant to 5FU.}, journal = {Biochimica et biophysica acta. Molecular basis of disease}, volume = {1867}, number = {10}, pages = {166179}, pmid = {34082069}, issn = {1879-260X}, support = {I01 BX003732/BX/BLRD VA/United States ; R01 AA023146/AA/NIAAA NIH HHS/United States ; R01 CA236591/CA/NCI NIH HHS/United States ; U01 CA230690/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Antineoplastic Agents/pharmacology ; Azoxymethane/pharmacology ; Colon/drug effects/metabolism/microbiology ; Colorectal Neoplasms/*drug therapy/*metabolism/microbiology ; Dextran Sulfate/pharmacology ; Female ; Fluorouracil/*pharmacology ; Gastrointestinal Microbiome/*physiology ; Male ; Mice ; Mice, Inbred C57BL ; Signal Transduction/drug effects/*physiology ; Smad4 Protein/metabolism ; Transforming Growth Factor beta/*metabolism ; }, abstract = {Emerging data show a rise in colorectal cancer (CRC) incidence in young men and women that is often chemoresistant. One potential risk factor is an alteration in the microbiome. Here, we investigated the role of TGF-β signaling on the intestinal microbiome and the efficacy of chemotherapy for CRC induced by azoxymethane and dextran sodium sulfate in mice. We used two genotypes of TGF-β-signaling-deficient mice (Smad4[+/-] and Smad4[+/-]Sptbn1[+/-]), which developed CRC with similar phenotypes and had similar alterations in the intestinal microbiome. Using these mice, we evaluated the intestinal microbiome and determined the effect of dysfunctional TGF-β signaling on the response to the chemotherapeutic agent 5-Fluoro-uracil (5FU) after induction of CRC. Using shotgun metagenomic sequencing, we determined gut microbiota composition in mice with CRC and found reduced amounts of beneficial species of Bacteroides and Parabacteroides in the mutants compared to the wild-type (WT) mice. Furthermore, the mutant mice with CRC were resistant to 5FU. Whereas the abundances of E. boltae, B.dorei, Lachnoclostridium sp., and Mordavella sp. were significantly reduced in mice with CRC, these species only recovered to basal amounts after 5FU treatment in WT mice, suggesting that the alterations in the intestinal microbiome resulting from compromised TGF-β signaling impaired the response to 5FU. These findings could have implications for inhibiting the TGF-β pathway in the treatment of CRC or other cancers.}, } @article {pmid34081399, year = {2021}, author = {Kumar, N and Hitch, TCA and Haller, D and Lagkouvardos, I and Clavel, T}, title = {MiMiC: a bioinformatic approach for generation of synthetic communities from metagenomes.}, journal = {Microbial biotechnology}, volume = {14}, number = {4}, pages = {1757-1770}, pmid = {34081399}, issn = {1751-7915}, support = {395357507//Deutsche Forschungsgemeinschaft/ ; 403224013//Deutsche Forschungsgemeinschaft/ ; SFB 1371//Deutsche Forschungsgemeinschaft/ ; SFB 1382//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Bacteria/genetics ; Computational Biology ; Humans ; *Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Environmental and host-associated microbial communities are complex ecosystems, of which many members are still unknown. Hence, it is challenging to study community dynamics and important to create model systems of reduced complexity that mimic major community functions. Therefore, we developed MiMiC, a computational approach for data-driven design of simplified communities from shotgun metagenomes. We first built a comprehensive database of species-level bacterial and archaeal genomes (n = 22 627) consisting of binary (presence/absence) vectors of protein families (Pfam = 17 929). MiMiC predicts the composition of minimal consortia using an iterative scoring system based on maximal match-to-mismatch ratios between this database and the Pfam binary vector of any input metagenome. Pfam vectorization retained enough resolution to distinguish metagenomic profiles between six environmental and host-derived microbial communities (n = 937). The calculated number of species per minimal community ranged between 5 and 11, with MiMiC selected communities better recapitulating the functional repertoire of the original samples than randomly selected species. The inferred minimal communities retained habitat-specific features and were substantially different from communities consisting of most abundant members. The use of a mixture of known microbes revealed the ability to select 23 of 25 target species from the entire genome database. MiMiC is open source and available at https://github.com/ClavelLab/MiMiC.}, } @article {pmid34081101, year = {2021}, author = {McMullen, JG and Bueno, E and Blow, F and Douglas, AE}, title = {Genome-Inferred Correspondence between Phylogeny and Metabolic Traits in the Wild Drosophila Gut Microbiome.}, journal = {Genome biology and evolution}, volume = {13}, number = {8}, pages = {}, pmid = {34081101}, issn = {1759-6653}, support = {R01 GM095372/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Drosophila/genetics ; Drosophila melanogaster/genetics/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Phylogeny ; }, abstract = {Annotated genome sequences provide valuable insight into the functional capabilities of members of microbial communities. Nevertheless, most studies on the microbiome in animal guts use metagenomic data, hampering the assignment of genes to specific microbial taxa. Here, we make use of the readily culturable bacterial communities in the gut of the fruit fly Drosophila melanogaster to obtain draft genome sequences for 96 isolates from wild flies. These include 81 new de novo assembled genomes, assigned to three orders (Enterobacterales, Lactobacillales, and Rhodospirillales) with 80% of strains identified to species level using average nucleotide identity and phylogenomic reconstruction. Based on annotations by the RAST pipeline, among-isolate variation in metabolic function partitioned strongly by bacterial order, particularly by amino acid metabolism (Rhodospirillales), fermentation, and nucleotide metabolism (Lactobacillales) and arginine, urea, and polyamine metabolism (Enterobacterales). Seven bacterial species, comprising 2-3 species in each order, were well-represented among the isolates and included ≥5 strains, permitting analysis of metabolic functions in the accessory genome (i.e., genes not present in every strain). Overall, the metabolic function in the accessory genome partitioned by bacterial order. Two species, Gluconobacter cerinus (Rhodospirillales) and Lactiplantibacillus plantarum (Lactobacillales) had large accessory genomes, and metabolic functions were dominated by amino acid metabolism (G. cerinus) and carbohydrate metabolism (La. plantarum). The patterns of variation in metabolic capabilities at multiple phylogenetic scales provide the basis for future studies of the ecological and evolutionary processes shaping the diversity of microorganisms associated with natural populations of Drosophila.}, } @article {pmid34080630, year = {2021}, author = {Gaio, D and DeMaere, MZ and Anantanawat, K and Eamens, GJ and Liu, M and Zingali, T and Falconer, L and Chapman, TA and Djordjevic, SP and Darling, AE}, title = {A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen.}, journal = {GigaScience}, volume = {10}, number = {6}, pages = {}, pmid = {34080630}, issn = {2047-217X}, mesh = {Animals ; Female ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics ; *Probiotics ; Swine ; Weaning ; }, abstract = {BACKGROUND: Early weaning and intensive farming practices predispose piglets to the development of infectious and often lethal diseases, against which antibiotics are used. Besides contributing to the build-up of antimicrobial resistance, antibiotics are known to modulate the gut microbial composition. As an alternative to antibiotic treatment, studies have previously investigated the potential of probiotics for the prevention of postweaning diarrhea. In order to describe the post-weaning gut microbiota, and to study the effects of two probiotics formulations and of intramuscular antibiotic treatment on the gut microbiota, we sampled and processed over 800 faecal time-series samples from 126 piglets and 42 sows.

RESULTS: Here we report on the largest shotgun metagenomic dataset of the pig gut lumen microbiome to date, consisting of >8 Tbp of shotgun metagenomic sequencing data. The animal trial, the workflow from sample collection to sample processing, and the preparation of libraries for sequencing, are described in detail. We provide a preliminary analysis of the dataset, centered on a taxonomic profiling of the samples, and a 16S-based beta diversity analysis of the mothers and the piglets in the first 5 weeks after weaning.

CONCLUSIONS: This study was conducted to generate a publicly available databank of the faecal metagenome of weaner piglets aged between 3 and 9 weeks old, treated with different probiotic formulations and intramuscular antibiotic treatment. Besides investigating the effects of the probiotic and intramuscular antibiotic treatment, the dataset can be explored to assess a wide range of ecological questions with regards to antimicrobial resistance, host-associated microbial and phage communities, and their dynamics during the aging of the host.}, } @article {pmid34079525, year = {2021}, author = {Sisk-Hackworth, L and Ortiz-Velez, A and Reed, MB and Kelley, ST}, title = {Compositional Data Analysis of Periodontal Disease Microbial Communities.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {617949}, pmid = {34079525}, issn = {1664-302X}, abstract = {Periodontal disease (PD) is a chronic, progressive polymicrobial disease that induces a strong host immune response. Culture-independent methods, such as next-generation sequencing (NGS) of bacteria 16S amplicon and shotgun metagenomic libraries, have greatly expanded our understanding of PD biodiversity, identified novel PD microbial associations, and shown that PD biodiversity increases with pocket depth. NGS studies have also found PD communities to be highly host-specific in terms of both biodiversity and the response of microbial communities to periodontal treatment. As with most microbiome work, the majority of PD microbiome studies use standard data normalization procedures that do not account for the compositional nature of NGS microbiome data. Here, we apply recently developed compositional data analysis (CoDA) approaches and software tools to reanalyze multiomics (16S, metagenomics, and metabolomics) data generated from previously published periodontal disease studies. CoDA methods, such as centered log-ratio (clr) transformation, compensate for the compositional nature of these data, which can not only remove spurious correlations but also allows for the identification of novel associations between microbial features and disease conditions. We validated many of the studies' original findings, but also identified new features associated with periodontal disease, including the genera Schwartzia and Aerococcus and the cytokine C-reactive protein (CRP). Furthermore, our network analysis revealed a lower connectivity among taxa in deeper periodontal pockets, potentially indicative of a more "random" microbiome. Our findings illustrate the utility of CoDA techniques in multiomics compositional data analysis of the oral microbiome.}, } @article {pmid34079079, year = {2021}, author = {Zhu, Q and Hou, Q and Huang, S and Ou, Q and Huo, D and Vázquez-Baeza, Y and Cen, C and Cantu, V and Estaki, M and Chang, H and Belda-Ferre, P and Kim, HC and Chen, K and Knight, R and Zhang, J}, title = {Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers.}, journal = {The ISME journal}, volume = {15}, number = {11}, pages = {3399-3411}, pmid = {34079079}, issn = {1751-7370}, mesh = {Biomarkers ; Feces ; *Gastrointestinal Microbiome/genetics ; *Graves Disease ; Humans ; Metagenome ; }, abstract = {Graves' Disease is the most common organ-specific autoimmune disease and has been linked in small pilot studies to taxonomic markers within the gut microbiome. Important limitations of this work include small sample sizes and low-resolution taxonomic markers. Accordingly, we studied 162 gut microbiomes of mild and severe Graves' disease (GD) patients and healthy controls. Taxonomic and functional analyses based on metagenome-assembled genomes (MAGs) and MAG-annotated genes, together with predicted metabolic functions and metabolite profiles, revealed a well-defined network of MAGs, genes and clinical indexes separating healthy from GD subjects. A supervised classification model identified a combination of biomarkers including microbial species, MAGs, genes and SNPs, with predictive power superior to models from any single biomarker type (AUC = 0.98). Global, cross-disease multi-cohort analysis of gut microbiomes revealed high specificity of these GD biomarkers, notably discriminating against Parkinson's Disease, and suggesting that non-invasive stool-based diagnostics will be useful for these diseases.}, } @article {pmid34078289, year = {2021}, author = {Moitinho-Silva, L and Wegener, M and May, S and Schrinner, F and Akhtar, A and Boysen, TJ and Schaeffer, E and Hansen, C and Schmidt, T and Rühlemann, MC and Hübenthal, M and Rausch, P and Kondakci, MT and Maetzler, W and Weidinger, S and Laudes, M and Süß, P and Schulte, D and Junker, R and Sommer, F and Weisser, B and Bang, C and Franke, A}, title = {Short-term physical exercise impacts on the human holobiont obtained by a randomised intervention study.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {162}, pmid = {34078289}, issn = {1471-2180}, support = {EXC2167//Deutsche Forschungsgemeinschaft/ ; FOR5042//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Adult ; Bacteria/classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; Diet ; *Exercise ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {BACKGROUND: Human well-being has been linked to the composition and functional capacity of the intestinal microbiota. As regular exercise is known to improve human health, it is not surprising that exercise was previously described to positively modulate the gut microbiota, too. However, most previous studies mainly focused on either elite athletes or animal models. Thus, we conducted a randomised intervention study that focused on the effects of different types of training (endurance and strength) in previously physically inactive, healthy adults in comparison to controls that did not perform regular exercise. Overall study duration was ten weeks including six weeks of intervention period. In addition to 16S rRNA gene amplicon sequencing of longitudinally sampled faecal material of participants (six time points), detailed body composition measurements and analysis of blood samples (at baseline and after the intervention) were performed to obtain overall physiological changes within the intervention period. Activity tracker devices (wrist-band wearables) provided activity status and sleeping patterns of participants as well as exercise intensity and heart measurements.

RESULTS: Different biometric responses between endurance and strength activities were identified, such as a significant increase of lymphocytes and decrease of mean corpuscular haemoglobin concentration (MCHC) only within the strength intervention group. In the endurance group, we observed a significant reduction in hip circumference and an increase in physical working capacity (PWC). Though a large variation of microbiota changes were observed between individuals of the same group, we did not find specific collective alterations in the endurance nor the strength groups, arguing for microbiome variations specific to individuals, and therefore, were not captured in our analysis.

CONCLUSIONS: We could show that different types of exercise have distinct but moderate effects on the overall physiology of humans and very distinct microbial changes in the gut. The observed overall changes during the intervention highlight the importance of physical activity on well-being. Future studies should investigate the effect of exercise on a longer timescale, investigate different training intensities and consider high-resolution shotgun metagenomics technology.

TRIAL REGISTRATION: DRKS, DRKS00015873 . Registered 12 December 2018; Retrospectively registered.}, } @article {pmid34077506, year = {2021}, author = {Hernández-Rocha, C and Borowski, K and Turpin, W and Filice, M and Nayeri, S and Raygoza Garay, JA and Stempak, JM and Silverberg, MS}, title = {Integrative Analysis of Colonic Biopsies from Inflammatory Bowel Disease Patients Identifies an Interaction Between Microbial Bile Acid-inducible Gene Abundance and Human Angiopoietin-like 4 Gene Expression.}, journal = {Journal of Crohn's & colitis}, volume = {15}, number = {12}, pages = {2078-2087}, pmid = {34077506}, issn = {1876-4479}, support = {U01 DK062423/DK/NIDDK NIH HHS/United States ; U01DK062423/NH/NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Angiopoietin-Like Protein 4/*genetics ; Bile Acids and Salts/*metabolism ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Gene Expression Regulation ; Humans ; Inflammatory Bowel Diseases/*microbiology/pathology ; Intestinal Mucosa/*microbiology/pathology ; Male ; Middle Aged ; Transcriptome ; Young Adult ; }, abstract = {BACKGROUND AND AIMS: Microbial-derived bile acids can modulate host gene expression, and their faecal abundance is decreased in active inflammatory bowel disease [IBD]. We analysed the impact of endoscopic inflammation on microbial genes involved in bile acid biotransformation, and their interaction with host transcriptome in the intestinal mucosa of IBD patients.

METHODS: Endoscopic mucosal biopsies were collected from non-inflamed and inflamed terminal ileum, ascending and sigmoid colon of IBD patients. Prediction of imputed metagenome functional content from 16S rRNA profile and real-time quantitative polymerase chain reaction [qPCR] were utsed to assess microbial bile acid biotransformation gene abundance, and RNA-seq was used for host transcriptome analysis. Linear regression and partial Spearman correlation accounting for age, sex, and IBD type were used to assess the association between microbial genes, inflammation, and host transcriptomics in each biopsy location. A Bayesian network [BN] analysis was fitted to infer the direction of interactions between IBD traits and microbial and host genes.

RESULTS: The inferred microbial gene pathway involved in secondary bile acid biosynthesis [ko00121 pathway] was depleted in inflamed terminal ileum of IBD patients compared with non-inflamed tissue. In non-inflamed sigmoid colon, the relative abundance of bile acid-inducible [baiCD] microbial genes was positively correlated with the host Angiopoietin-like 4 [Angptl4] gene expression. The BN analysis suggests that the microbial baiCD gene abundance could affect Angptl4 expression, and this interaction appears to be lost in the presence of inflammation.

CONCLUSIONS: Endoscopic inflammation affects the abundance of crucial microbial bile acid-metabolising genes and their interaction with Angptl4 in intestinal mucosa of IBD patients.}, } @article {pmid34077260, year = {2021}, author = {Cornell, CR and Zhang, Y and Van Nostrand, JD and Wagle, P and Xiao, X and Zhou, J}, title = {Temporal Changes of Virus-Like Particle Abundance and Metagenomic Comparison of Viral Communities in Cropland and Prairie Soils.}, journal = {mSphere}, volume = {6}, number = {3}, pages = {e0116020}, pmid = {34077260}, issn = {2379-5042}, mesh = {Crops, Agricultural/*virology ; *Grassland ; *Metagenome ; Metagenomics ; *Soil Microbiology ; Spatio-Temporal Analysis ; Virome/*genetics ; Viruses/*genetics ; }, abstract = {During the last several decades, viruses have been increasingly recognized for their abundance, ubiquity, and important roles in different ecosystems. Despite known contributions to aquatic systems, few studies examine viral abundance and community structure over time in terrestrial ecosystems. The effects of land conversion and land management on soil microbes have been previously investigated, but their effects on virus population are not well studied. This study examined annual dynamics of viral abundance in soils from a native tallgrass prairie and two croplands, conventional till winter wheat and no-till canola, in Oklahoma. Virus-like particle (VLP) abundance varied across sites, and showed clear seasonal shifts. VLP abundance significantly correlated with environmental variables that were generally reflective of land use, including air temperature, soil nitrogen, and plant canopy coverage. Structural equation modeling supported the effects of land use on soil communities by emphasizing interactions between management, environmental factors, and viral and bacterial abundance. Between the viral metagenomes from the prairie and tilled wheat field, 1,231 unique viral operational taxonomic units (vOTUs) were identified, and only five were shared that were rare in the contrasting field. Only 13% of the vOTUs had similarity to previously identified viruses in the RefSeq database, with only 7% having known taxonomic classification. Together, our findings indicated land use and tillage practices influence virus abundance and community structure. Analyses of viromes over time and space are vital to viral ecology in providing insight on viral communities and key information on interactions between viruses, their microbial hosts, and the environment. IMPORTANCE Conversion of land alters the physiochemical and biological environments by not only changing the aboveground community, but also modifying the soil environment for viruses and microbes. Soil microbial communities are critical to nutrient cycling, carbon mineralization, and soil quality; and viruses are known for influencing microbial abundance, community structure, and evolution. Therefore, viruses are considered an important part of soil functions in terrestrial ecosystems. In aquatic environments, virus abundance generally exceeds bacterial counts by an order of magnitude, and they are thought to be one of the greatest genetic reservoirs on the planet. However, data are extremely limited on viruses in soils, and even less is known about their responses to the disturbances associated with land use and management. The study provides important insights into the temporal dynamics of viral abundance and the structure of viral communities in response to the common practice of turning native habitats into arable soils.}, } @article {pmid34075213, year = {2021}, author = {Heilbronner, S and Krismer, B and Brötz-Oesterhelt, H and Peschel, A}, title = {The microbiome-shaping roles of bacteriocins.}, journal = {Nature reviews. Microbiology}, volume = {19}, number = {11}, pages = {726-739}, pmid = {34075213}, issn = {1740-1534}, mesh = {Bacteria/*metabolism ; Bacteriocins/*chemistry/*metabolism/pharmacology ; *Microbiota ; }, abstract = {The microbiomes on human body surfaces affect health in multiple ways. They include not only commensal or mutualistic bacteria but also potentially pathogenic bacteria, which can enter sterile tissues to cause invasive infection. Many commensal bacteria produce small antibacterial molecules termed bacteriocins that have the capacity to eliminate specific colonizing pathogens; as such, bacteriocins have attracted increased attention as potential microbiome-editing tools. Metagenome-based and activity-based screening approaches have strongly expanded our knowledge of the abundance and diversity of bacteriocin biosynthetic gene clusters and the properties of a continuously growing list of bacteriocin classes. The dynamic acquisition, diversification or loss of bacteriocin genes can shape the fitness of a bacterial strain that is in competition with bacteriocin-susceptible bacteria. However, a bacteriocin can only provide a competitive advantage if its fitness benefit exceeds the metabolic cost of production, if it spares crucial mutualistic partner strains and if major competitors cannot develop resistance. In contrast to most currently available antibiotics, many bacteriocins have only narrow activity ranges and could be attractive agents for precision therapy and prevention of infections. A common scientific strategy involving multiple disciplines is needed to uncover the immense potential of microbiome-shaping bacteriocins.}, } @article {pmid34072839, year = {2021}, author = {Mormando, R and Wolfe, AJ and Putonti, C}, title = {Discriminating between JCPyV and BKPyV in Urinary Virome Data Sets.}, journal = {Viruses}, volume = {13}, number = {6}, pages = {}, pmid = {34072839}, issn = {1999-4915}, support = {R56 DK104718/NH/NIH HHS/United States ; R01 DK104718/NH/NIH HHS/United States ; }, mesh = {BK Virus/*genetics ; *Datasets as Topic ; Humans ; JC Virus/*genetics ; Microbiota ; Polyomavirus Infections/*urine/*virology ; Urinary Tract/*virology ; Viral Load ; Virome/*genetics ; }, abstract = {Polyomaviruses are abundant in the human body. The polyomaviruses JC virus (JCPyV) and BK virus (BKPyV) are common viruses in the human urinary tract. Prior studies have estimated that JCPyV infects between 20 and 80% of adults and that BKPyV infects between 65 and 90% of individuals by age 10. However, these two viruses encode for the same six genes and share 75% nucleotide sequence identity across their genomes. While prior urinary virome studies have repeatedly reported the presence of JCPyV, we were interested in seeing how JCPyV prevalence compares to BKPyV. We retrieved all publicly available shotgun metagenomic sequencing reads from urinary microbiome and virome studies (n = 165). While one third of the data sets produced hits to JCPyV, upon further investigation were we able to determine that the majority of these were in fact BKPyV. This distinction was made by specifically mining for JCPyV and BKPyV and considering uniform coverage across the genome. This approach provides confidence in taxon calls, even between closely related viruses with significant sequence similarity.}, } @article {pmid34071172, year = {2021}, author = {Chukwuma, OB and Rafatullah, M and Tajarudin, HA and Ismail, N}, title = {Bacterial Diversity and Community Structure of a Municipal Solid Waste Landfill: A Source of Lignocellulolytic Potential.}, journal = {Life (Basel, Switzerland)}, volume = {11}, number = {6}, pages = {}, pmid = {34071172}, issn = {2075-1729}, support = {1001/PTEKIND/8011044//Universiti Sains Malaysia/ ; }, abstract = {Omics have given rise to research on sparsely studied microbial communities such as the landfill, lignocellulolytic microorganisms and enzymes. The bacterial diversity of Municipal Solid Waste sediments was determined using the illumina MiSeq system after DNA extraction and Polymerase chain reactions. Data analysis was used to determine the community's richness, diversity, and correlation with environmental factors. Physicochemical studies revealed sites with mesophilic and thermophilic temperature ranges and a mixture of acidic and alkaline pH values. Temperature and moisture content showed the highest correlation with the bacteria community. The bacterial analysis of the community DNA revealed 357,030 effective sequences and 1891 operational taxonomic units (OTUs) assigned. Forty phyla were found, with the dominant phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidota, while Aerococcus, Stenotrophomonas, and Sporosarcina were the dominant species. PICRUSt provided insight on community's metabolic function, which was narrowed down to search for lignocellulolytic enzymes' function. Cellulase, xylanase, esterase, and peroxidase were gene functions inferred from the data. This article reports on the first phylogenetic analysis of the Pulau Burung landfill bacterial community. These results will help to improve the understanding of organisms dominant in the landfill and the corresponding enzymes that contribute to lignocellulose breakdown.}, } @article {pmid34070915, year = {2021}, author = {Plachokova, AS and Andreu-Sánchez, S and Noz, MP and Fu, J and Riksen, NP}, title = {Oral Microbiome in Relation to Periodontitis Severity and Systemic Inflammation.}, journal = {International journal of molecular sciences}, volume = {22}, number = {11}, pages = {}, pmid = {34070915}, issn = {1422-0067}, support = {667837//European Union's Horizon 2020 research and innovation program/ ; CVON2018-27//Dutch Heart Foundation IN-CONTROL CVON grant/ ; 101001678]//ERC Consolidator grant/ ; 024.003.001//NWO Gravitation Netherlands Organ-on-Chip Initiative/ ; }, mesh = {Aged ; Biomarkers/metabolism ; Cardiovascular Diseases/etiology/immunology/microbiology/pathology ; Female ; Gene Expression ; Genetic Variation ; Humans ; Inflammation ; Interleukin 1 Receptor Antagonist Protein/genetics/immunology ; Interleukin-6/genetics/immunology ; Leukocytes/immunology/microbiology ; Male ; *Metagenome ; Microbiota/*genetics ; Middle Aged ; Periodontitis/complications/immunology/*microbiology/pathology ; Periodontium/immunology/*microbiology/pathology ; Phenotype ; Phylogeny ; Severity of Illness Index ; }, abstract = {Systemic inflammation induced by periodontitis is suggested to be the link between periodontitis and cardiovascular disease. The aim of this work was to explore the oral microbiome in periodontitis in relation to disease severity and systemic inflammation. The saliva and subgingival microbiome from periodontal pocket samples of patients with severe (n = 12) and mild periodontitis (n = 13) were analyzed using metagenomic shotgun sequencing. The taxa and pathways abundances were quantified. The diversity was assessed and the abundances to phenotype associations were performed using ANCOM and linear regression. A panel of inflammatory markers was measured in blood and was associated with taxa abundance. The microbial diversity and species richness did not differ between severe and mild periodontitis in either saliva or periodontal pockets. However, there were significant differences in the microbial composition between severe and mild periodontitis in the subgingival microbiome (i.e., pocket samples) and, in a lower grade, in saliva, and this is positively associated with systemic inflammatory markers. The "red complex" and "cluster B" abundances in periodontal pockets were strongly associated with inflammatory markers interleukin-6 and the white blood cell count. Our data suggest that systemic inflammation in severe periodontitis may be driven by the oral microbiome and may support the indirect (inflammatory) mechanism for the association between periodontitis and cardiovascular disease.}, } @article {pmid34069990, year = {2021}, author = {Ansorge, R and Birolo, G and James, SA and Telatin, A}, title = {Dadaist2: A Toolkit to Automate and Simplify Statistical Analysis and Plotting of Metabarcoding Experiments.}, journal = {International journal of molecular sciences}, volume = {22}, number = {10}, pages = {}, pmid = {34069990}, issn = {1422-0067}, support = {BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; BB/R506552/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/T030062/1//UK Research and Innovation/ ; }, mesh = {Algorithms ; Cluster Analysis ; Computational Biology/methods ; DNA Barcoding, Taxonomic/*statistics & numerical data ; Data Interpretation, Statistical ; High-Throughput Nucleotide Sequencing ; Metadata ; Metagenomics/*statistics & numerical data ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Software ; }, abstract = {The taxonomic composition of microbial communities can be assessed using universal marker amplicon sequencing. The most common taxonomic markers are the 16S rDNA for bacterial communities and the internal transcribed spacer (ITS) region for fungal communities, but various other markers are used for barcoding eukaryotes. A crucial step in the bioinformatic analysis of amplicon sequences is the identification of representative sequences. This can be achieved using a clustering approach or by denoising raw sequencing reads. DADA2 is a widely adopted algorithm, released as an R library, that denoises marker-specific amplicons from next-generation sequencing and produces a set of representative sequences referred to as 'Amplicon Sequence Variants' (ASV). Here, we present Dadaist2, a modular pipeline, providing a complete suite for the analysis that ranges from raw sequencing reads to the statistics of numerical ecology. Dadaist2 implements a new approach that is specifically optimised for amplicons with variable lengths, such as the fungal ITS. The pipeline focuses on streamlining the data flow from the command line to R, with multiple options for statistical analysis and plotting, both interactive and automatic.}, } @article {pmid34069916, year = {2021}, author = {Izawa, K and Okamoto-Shibayama, K and Kita, D and Tomita, S and Saito, A and Ishida, T and Ohue, M and Akiyama, Y and Ishihara, K}, title = {Taxonomic and Gene Category Analyses of Subgingival Plaques from a Group of Japanese Individuals with and without Periodontitis.}, journal = {International journal of molecular sciences}, volume = {22}, number = {10}, pages = {}, pmid = {34069916}, issn = {1422-0067}, support = {18K09559//Japan Society for Promotion of Science/ ; 45//MEXT Private University Research Branding Project/ ; }, mesh = {Adult ; Aged ; Bacteria/genetics ; Dental Plaque/genetics/*microbiology ; Dysbiosis/genetics ; Female ; Gingiva/*microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Japan/epidemiology ; Male ; Metagenome ; Microbiota/genetics ; Middle Aged ; Periodontal Pocket/genetics/microbiology ; Periodontitis/genetics/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Periodontitis is an inflammation of tooth-supporting tissues, which is caused by bacteria in the subgingival plaque (biofilm) and the host immune response. Traditionally, subgingival pathogens have been investigated using methods such as culturing, DNA probes, or PCR. The development of next-generation sequencing made it possible to investigate the whole microbiome in the subgingival plaque. Previous studies have implicated dysbiosis of the subgingival microbiome in the etiology of periodontitis. However, details are still lacking. In this study, we conducted a metagenomic analysis of subgingival plaque samples from a group of Japanese individuals with and without periodontitis. In the taxonomic composition analysis, genus Bacteroides and Mycobacterium demonstrated significantly different compositions between healthy sites and sites with periodontal pockets. The results from the relative abundance of functional gene categories, carbohydrate metabolism, glycan biosynthesis and metabolism, amino acid metabolism, replication and repair showed significant differences between healthy sites and sites with periodontal pockets. These results provide important insights into the shift in the taxonomic and functional gene category abundance caused by dysbiosis, which occurs during the progression of periodontal disease.}, } @article {pmid34065683, year = {2021}, author = {Daugrois, JH and Filloux, D and Julian, C and Claude, L and Ferdinand, R and Fernandez, E and Fontes, H and Rott, PC and Roumagnac, P}, title = {Comparison of the Virome of Quarantined Sugarcane Varieties and the Virome of Grasses Growing near the Quarantine Station.}, journal = {Viruses}, volume = {13}, number = {5}, pages = {}, pmid = {34065683}, issn = {1999-4915}, mesh = {*Metagenome ; *Metagenomics/methods ; Phylogeny ; Plant Diseases/virology ; Poaceae/*virology ; Quarantine ; Saccharum/*virology ; Virion ; *Virome ; }, abstract = {Visacane is a sugarcane quarantine station located in the South of France, far away from sugarcane growing areas. Visacane imports up to 100 sugarcane varieties per year, using safe control and confinement measures of plants and their wastes to prevent any risk of pathogen spread outside of the facilities. Viruses hosted by the imported material are either known or unknown to cause disease in cultivated sugarcane. Poaceae viruses occurring in plants surrounding the quarantine glasshouse are currently unknown. These viruses could be considered as a source of new sugarcane infections and potentially cause new sugarcane diseases in cases of confinement barrier failure. The aim of this study was to compare the plant virome inside and outside of the quarantine station to identify potential confinement failures and risks of cross infections. Leaves from quarantined sugarcane varieties and from wild Poaceae growing near the quarantine were collected and processed by a metagenomics approach based on virion-associated nucleic acids extraction and library preparation for Illumina sequencing. While viruses belonging to the same virus genus or family were identified in the sugarcane quarantine and its surroundings, no virus species was detected in both environments. Based on the data obtained in this study, no virus movement between quarantined sugarcane and nearby grassland has occurred so far, and the confinement procedures of Visacane appear to be properly implemented.}, } @article {pmid34064848, year = {2021}, author = {Eskov, AK and Zverev, AO and Abakumov, EV}, title = {Microbiomes in Suspended Soils of Vascular Epiphytes Differ from Terrestrial Soil Microbiomes and from Each Other.}, journal = {Microorganisms}, volume = {9}, number = {5}, pages = {}, pmid = {34064848}, issn = {2076-2607}, support = {21-14-00188//Russian Science Foundation/ ; }, abstract = {Microbial biodiversity parameters for tropical rainforests remain poorly understood. Whilst the soil microbiome accounts up to 95% of the total diversity of microorganisms in terrestrial ecosystems, the microbiome of suspended soils formed by vascular epiphytes remains completely unexplored. Samples of ground and suspended soils were collected in Cat Tien National Park, southern Vietnam. DNA extraction and sequencing were performed, and libraries of 16s rDNA gene sequences were analyzed. Alpha diversity indices of the microorganisms were the highest in the forest ground soil. In general, the microbiological diversity of all the soil types was found to be similar at the phylum level. Taxonomic composition of the bacterial communities in the suspended soils of plants from the same species are not closer than the taxonomic compositions of the communities in the suspended soils of different plant species. However, the beta diversity analysis revealed significant differences in the movement of mineral elements in terrestrial versus suspended soils. Our data showed that the suspended soils associated with vascular epiphytes were a depository of unique microbiological biodiversity. A contributing factor was the presence of large amounts of organic matter in the suspended soils-deposits collected by the epiphytes-which would have been degraded by termites if it had reached the ground. Further, the nutrient content of the suspended soils was prime for soil respiration activity and taxonomic microbial community biodiversity.}, } @article {pmid34064231, year = {2021}, author = {Alanin, KWS and Junco, LMF and Jørgensen, JB and Nielsen, TK and Rasmussen, MA and Kot, W and Hansen, LH}, title = {Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay.}, journal = {Viruses}, volume = {13}, number = {6}, pages = {}, pmid = {34064231}, issn = {1999-4915}, mesh = {Computational Biology ; Host Specificity ; *Metagenome ; *Metagenomics/methods ; Pseudomonas/*virology ; Pseudomonas Phages/classification/*physiology ; *Viral Plaque Assay/methods ; *Virome ; }, abstract = {Isolating single phages using plaque assays is a laborious and time-consuming process. Whether single isolated phages are the most lyse-effective, the most abundant in viromes, or those with the highest ability to make plaques in solid media is not well known. With the increasing accessibility of high-throughput sequencing, metaviromics is often used to describe viruses in environmental samples. By extracting and sequencing metaviromes from organic waste with and without exposure to a host-of-interest, we show a host-related phage community's shift, as well as identify the most enriched phages. Moreover, we isolated plaque-forming single phages using the same virome-host matrix to observe how enrichments in liquid media correspond to the metaviromic data. In this study, we observed a significant shift (p = 0.015) of the 47 identified putative Pseudomonas phages with a minimum twofold change above zero in read abundance when adding a Pseudomonas&nbsp;syringae DC3000 host. Surprisingly, it appears that only two out of five plaque-forming phages from the same organic waste sample, targeting the Pseudomonas strain, were highly abundant in the metavirome, while the other three were almost absent despite host exposure. Lastly, our sequencing results highlight how long reads from Oxford Nanopore elevates the assembly quality of metaviromes, compared to short reads alone.}, } @article {pmid34063398, year = {2021}, author = {Łoś-Rycharska, E and Gołębiewski, M and Sikora, M and Grzybowski, T and Gorzkiewicz, M and Popielarz, M and Gawryjołek, J and Krogulska, A}, title = {A Combined Analysis of Gut and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Study.}, journal = {Nutrients}, volume = {13}, number = {5}, pages = {}, pmid = {34063398}, issn = {2072-6643}, support = {2017/25/B/NZ5/00141//National Science Centre Poland/ ; }, mesh = {Bacteria/classification/genetics ; Dermatitis, Atopic/diagnosis/*microbiology ; Dysbiosis ; Feces/microbiology ; Female ; Food Hypersensitivity/*microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Immunoglobulin E/blood ; Infant ; Male ; Metagenome ; *Microbiota/genetics ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Skin/*microbiology ; }, abstract = {The gut microbiota in patients with food allergy, and the skin microbiota in atopic dermatitis patients differ from those of healthy people. We hypothesize that relationships may exist between gut and skin microbiota in patients with allergies. The aim of this study was to determine the possible relationship between gut and skin microbiota in patients with allergies, hence simultaneous analysis of the two compartments of microbiota was performed in infants with and without allergic symptoms. Fifty-nine infants with food allergy and/or atopic dermatitis and 28 healthy children were enrolled in the study. The skin and gut microbiota were evaluated using 16S rRNA gene amplicon sequencing. No significant differences in the α-diversity of dermal or fecal microbiota were observed between allergic and non-allergic infants; however, a significant relationship was found between bacterial community structure and allergy phenotypes, especially in the fecal samples. Certain clinical conditions were associated with characteristic bacterial taxa in the skin and gut microbiota. Positive correlations were found between skin and fecal samples in the abundance of Gemella among allergic infants, and Lactobacillus and Bacteroides among healthy infants. Although infants with allergies and healthy infants demonstrate microbiota with similar α-diversity, some differences in β-diversity and bacterial species abundance can be seen, which may depend on the phenotype of the allergy. For some organisms, their abundance in skin and feces samples may be correlated, and these correlations might serve as indicators of the host's allergic state.}, } @article {pmid34062889, year = {2021}, author = {Borowik, A and Wyszkowska, J and Kucharski, J}, title = {Microbiological Study in Petrol-Spiked Soil.}, journal = {Molecules (Basel, Switzerland)}, volume = {26}, number = {9}, pages = {}, pmid = {34062889}, issn = {1420-3049}, support = {30.610.006-110//University of Warmia and Mazury in Olsztyn, Faculty of Agriculture and Forestry, Department of Soil Science and Microbiology/ ; 010/RID/2018/19//Minister of Science and Higher Education in the range of the programme entitled "Regional Ini-tiative of Excellence" for the years 2019-2022/ ; }, mesh = {Actinobacteria/*metabolism ; Actinomycetales/*metabolism ; Biodegradation, Environmental ; Environmental Monitoring ; Environmental Pollutants/*analysis ; Gasoline ; Hydrocarbons ; Metagenome ; Microbiota ; *Petroleum Pollution ; *Soil Microbiology ; *Soil Pollutants ; }, abstract = {The pollution of arable lands and water with petroleum-derived products is still a valid problem, mainly due the extensive works aimed to improve their production technology to reduce fuel consumption and protect engines. An example of the upgraded fuels is the BP 98 unleaded petrol with Active technology. A pot experiment was carried out in which Eutric Cambisol soil was polluted with petrol to determine its effect on the microbiological and biochemical properties of this soil. Analyses were carried out to determine soil microbiome composition-with the incubation and metagenomic methods, the activity of seven enzymes, and cocksfoot effect on hydrocarbon degradation. The following indices were determined: colony development index (CD); ecophysiological diversity index (EP); index of cocksfoot effect on soil microorganisms and enzymes (IFG); index of petrol effect on soil microorganisms and enzymes (IFP); index of the resistance of microorganisms, enzymes, and cocksfoot to soil pollution with petrol (RS); Shannon-Weaver's index of bacterial taxa diversity (H); and Shannon-Weaver's index of hydrocarbon degradation (IDH). The soil pollution with petrol was found to increase population numbers of bacteria and fungi, and Protebacteria phylum abundance as well as to decrease the abundance of Actinobacteria and Acidobacteria phyla. The cultivation of cocksfoot on the petrol-polluted soil had an especially beneficial effect mainly on the bacteria belonging to the Ramlibacter, Pseudoxanthomonas, Mycoplana, and Sphingobium genera. The least susceptible to the soil pollution with petrol and cocksfoot cultivation were the bacteria of the following genera: Kaistobacter, Rhodoplanes, Bacillus, Streptomyces, Paenibacillus, Phenylobacterium, and Terracoccus. Cocksfoot proved effective in the phytoremediation of petrol-polluted soil, as it accelerated hydrocarbon degradation and increased the genetic diversity of bacteria. It additionally enhanced the activities of soil enzymes.}, } @article {pmid34061881, year = {2021}, author = {Ibekwe, AM and Ors, S and Ferreira, JFS and Liu, X and Suarez, DL}, title = {Influence of seasonal changes and salinity on spinach phyllosphere bacterial functional assemblage.}, journal = {PloS one}, volume = {16}, number = {6}, pages = {e0252242}, pmid = {34061881}, issn = {1932-6203}, mesh = {*Seasons ; *Spinacia oleracea/microbiology ; *Salinity ; *Plant Leaves/microbiology ; *Bacteria/genetics/metabolism/classification ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; }, abstract = {The phyllosphere is the aerial part of plants that is exposed to different environmental conditions and is also known to harbor a wide variety of bacteria including both plant and human pathogens. However, studies on phyllosphere bacterial communities have focused on bacterial composition at different stages of plant growth without correlating their functional capabilities to bacterial communities. In this study, we examined the seasonal effects and temporal variabilities driving bacterial community composition and function in spinach phyllosphere due to increasing salinity and season and estimated the functional capacity of bacterial community16S V4 rRNA gene profiles by indirectly inferring the abundance of functional genes based on metagenomics inference tool Piphillin. The experimental design involved three sets of spinach (Spinacia oleracea L., cv. Racoon) grown with saline water during different seasons. Total bacteria DNA from leaf surfaces were sequenced using MiSeq® Illumina platform. About 66.35% of bacteria detected in the phyllosphere were dominated by four phyla- Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Permutational analysis of variance (PERMANOVA) showed that phyllosphere microbiomes were significantly (P < 0.003) affected by season, but not salinity (P = 0.501). The most abundant inferred functional pathways in leaf samples were the amino acids biosynthesis, ABC transporters, ribosome, aminoacyl-tRNA biosynthesis, two-component system, carbon metabolism, purine metabolism, and pyrimidine metabolism. The photosynthesis antenna proteins pathway was significantly enriched in June leaf samples, when compared to March and May. Several genes related to toxin co-regulated pilus biosynthesis proteins were also significantly enriched in June leaf samples, when compared to March and May leaf samples. Therefore, planting and harvesting times must be considered during leafy green production due to the influence of seasons in growth and proliferation of phyllosphere microbial communities.}, } @article {pmid34061623, year = {2021}, author = {Breen, P and Winters, AD and Theis, KR and Withey, JH}, title = {Vibrio cholerae Infection Induces Strain-Specific Modulation of the Zebrafish Intestinal Microbiome.}, journal = {Infection and immunity}, volume = {89}, number = {9}, pages = {e0015721}, pmid = {34061623}, issn = {1098-5522}, support = {R01 AI127390/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cholera/*microbiology ; Disease Models, Animal ; *Disease Susceptibility ; *Gastrointestinal Microbiome ; *Host-Pathogen Interactions ; Metagenomics/methods ; *Microbial Interactions ; RNA, Ribosomal, 16S ; Vibrio cholerae/*physiology ; Zebrafish ; }, abstract = {Zebrafish (Danio rerio) is an attractive model organism to use for an array of scientific studies, including host-microbe interactions. Zebrafish contain a core (i.e., consistently detected) intestinal microbiome consisting primarily of Proteobacteria. Furthermore, this core intestinal microbiome is plastic and can be significantly altered due to external factors. Zebrafish are particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae. As an intestinal pathogen, V. cholerae must colonize the intestine of an exposed host for pathogenicity to occur. Members of the resident intestinal microbial community likely must be reduced or eliminated by V. cholerae for colonization, and subsequent disease, to occur. Many studies have explored a variety of aspects of the pathogenic effects of V. cholerae on zebrafish and other model organisms but few have researched how a V. cholerae infection changes the resident intestinal microbiome. In this study, 16S rRNA gene sequencing was used to examine how five genetically diverse V. cholerae strains alter the intestinal microbiome following an infection. We found that V. cholerae colonization induced significant changes in the zebrafish intestinal microbiome. Notably, changes in the microbial profile were significantly different from each other, based on the particular strain of V. cholerae used to infect zebrafish hosts. We conclude that V. cholerae significantly modulates the zebrafish intestinal microbiota to enable colonization and that specific microbes that are targeted depend on the V. cholerae genotype.}, } @article {pmid34061597, year = {2021}, author = {Lindstad, LJ and Lo, G and Leivers, S and Lu, Z and Michalak, L and Pereira, GV and Røhr, ÅK and Martens, EC and McKee, LS and Louis, P and Duncan, SH and Westereng, B and Pope, PB and La Rosa, SL}, title = {Human Gut Faecalibacterium prausnitzii Deploys a Highly Efficient Conserved System To Cross-Feed on β-Mannan-Derived Oligosaccharides.}, journal = {mBio}, volume = {12}, number = {3}, pages = {e0362820}, pmid = {34061597}, issn = {2150-7511}, mesh = {Bacteroides/genetics/metabolism ; Clostridiales/genetics/metabolism ; Colon/microbiology ; Diet ; Faecalibacterium prausnitzii/*genetics/growth & development/*metabolism ; Gastrointestinal Microbiome/*genetics/physiology ; Humans ; Mannans/classification/*metabolism ; Metagenomics ; Oligosaccharides/*metabolism ; }, abstract = {β-Mannans are hemicelluloses that are abundant in modern diets as components in seed endosperms and common additives in processed food. Currently, the collective understanding of β-mannan saccharification in the human colon is limited to a few keystone species, which presumably liberate low-molecular-weight mannooligosaccharide fragments that become directly available to the surrounding microbial community. Here, we show that a dominant butyrate producer in the human gut, Faecalibacterium prausnitzii, is able to acquire and degrade various β-mannooligosaccharides (β-MOS), which are derived by the primary mannanolytic activity of neighboring gut microbiota. Detailed biochemical analyses of selected protein components from their two β-MOS utilization loci (F. prausnitzii β-MOS utilization loci [FpMULs]) supported a concerted model whereby the imported β-MOS are stepwise disassembled intracellularly by highly adapted enzymes. Coculturing experiments of F. prausnitzii with the primary degraders Bacteroides ovatus and Roseburia intestinalis on polymeric β-mannan resulted in syntrophic growth, thus confirming the high efficiency of the FpMULs' uptake system. Genomic comparison with human F. prausnitzii strains and analyses of 2,441 public human metagenomes revealed that FpMULs are highly conserved and distributed worldwide. Together, our results provide a significant advance in the knowledge of β-mannan metabolism and the degree to which its degradation is mediated by cross-feeding interactions between prominent beneficial microbes in the human gut. IMPORTANCE Commensal butyrate-producing bacteria belonging to the Firmicutes phylum are abundant in the human gut and are crucial for maintaining health. Currently, insight is lacking into how they target otherwise indigestible dietary fibers and into the trophic interactions they establish with other glycan degraders in the competitive gut environment. By combining cultivation, genomic, and detailed biochemical analyses, this work reveals the mechanism enabling F. prausnitzii, as a model Ruminococcaceae within Firmicutes, to cross-feed and access β-mannan-derived oligosaccharides released in the gut ecosystem by the action of primary degraders. A comprehensive survey of human gut metagenomes shows that FpMULs are ubiquitous in human populations globally, highlighting the importance of microbial metabolism of β-mannans/β-MOS as a common dietary component. Our findings provide a mechanistic understanding of the β-MOS utilization capability by F. prausnitzii that may be exploited to select dietary formulations specifically boosting this beneficial symbiont, and thus butyrate production, in the gut.}, } @article {pmid34061229, year = {2021}, author = {de Souza, LC and Procópio, L}, title = {The profile of the soil microbiota in the Cerrado is influenced by land use.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {11}, pages = {4791-4803}, pmid = {34061229}, issn = {1432-0614}, mesh = {Acidobacteria ; Gammaproteobacteria ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Soil ; Soil Microbiology ; }, abstract = {Extensive areas of the Cerrado biome have been deforested by the rapid advance of agricultural frontiers, especially by agricultural monocultures, and cultivated pastures. The objective of this study was to characterize the soil microbial community of an environment without anthropogenic interference and to compare it with soybean soil and pasture areas. For that, metagenomic sequencing techniques of the 16S rRNA gene were employed. Consistent changes in the profiles of diversity and abundance were described between communities in relation to the type of soil. The soil microbiome of the native environment was influenced by the pH level and content of Al[3+], whereas the soil microbiomes cultivated with soybean and pasture were associated with the levels of nutrients N and P and the ions Ca[2+] and Mg[2+], respectively. The analysis of bacterial communities in the soil of the native environment showed a high abundance of members of the Proteobacteria phylum, with emphasis on the Bradyrhizobium and Burkholderia genera. In addition, significant levels of species of the Bacillus genus, and Dyella ginsengisoli, and Edaphobacter aggregans of the Acidobacteria phylum were detected. In the soil community with soybean cultivation, there was a predominance of Proteobacteria, mainly of the Sphingobium and Sphingomonas genera. In the pasture, the soil microbiota was dominated by the Firmicutes, which was almost entirely represented by the Bacillus genus. These results suggest an adaptation of the bacterial community to the soybean and pasture cultivations and will support understanding how environmental and anthropogenic factors shape the soil microbial community. KEY POINTS: • The Cerrado soil microbiota is sensitive to impacts on the biome. • Microbial communities have been altered at all taxonomic levels.}, } @article {pmid34059794, year = {2021}, author = {Sun, P and Yang, J and Wang, B and Ma, H and Zhang, Y and Guo, J and Chen, X and Zhao, J and Sun, H and Yang, J and Yang, H and Cui, Y}, title = {The effects of combined environmental factors on the intestinal flora of mice based on ground simulation experiments.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {11373}, pmid = {34059794}, issn = {2045-2322}, mesh = {Animals ; *Astronauts ; Biomarkers/metabolism ; Cluster Analysis ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Humans ; Mice ; Mice, Inbred C57BL ; *Weightlessness Simulation ; }, abstract = {The composition and function of intestinal microbial communities are important for human health. However, these intestinal floras are sensitive to changes in the environment. Adverse changes to intestinal flora can affect the health of astronauts, resulting in difficulties in implementing space missions. We randomly divided mice into three groups and placed each group in either a normal environment, simulated microgravity environment or a combined effects environment, which included simulated microgravity, low pressure and noise. Fecal samples of the mice were collected for follow-up analysis based on metagenomics technology. With the influence of different space environmental factors, the species composition at the phylum and genus levels were significantly affected by the combined effects environment, especially the abundance of the Firmicutes and Bacteroidetes. Furthermore, screening was conducted to identify biomarkers that could be regarded as environmental markers. And there have also been some noticeable changes in the function of intestinal floras. Moreover, the abundance of antibiotic resistance genes (ARGs) was also found to be changed under different environmental conditions, such as bacitracin and vancomycin. The combined effects environment could significantly affect the species composition, function, and the expression of ARGs of intestinal flora of mice which may provide a theoretical basis for space medical supervision and healthcare.}, } @article {pmid34058706, year = {2021}, author = {Hayer, J and Wille, M and Font, A and González-Aravena, M and Norder, H and Malmberg, M}, title = {Four novel picornaviruses detected in Magellanic Penguins (Spheniscus magellanicus) in Chile.}, journal = {Virology}, volume = {560}, number = {}, pages = {116-123}, doi = {10.1016/j.virol.2021.05.010}, pmid = {34058706}, issn = {1096-0341}, mesh = {Animals ; Chile/epidemiology ; Endangered Species ; Phylogeny ; Picornaviridae/*classification/genetics/*isolation & purification ; Picornaviridae Infections/*epidemiology/*veterinary ; Spheniscidae/*virology ; }, abstract = {Members of the Picornaviridae family comprise a significant burden on the poultry industry, causing diseases such as gastroenteritis and hepatitis. However, with the advent of metagenomics, a number of picornaviruses have now been revealed in apparently healthy wild birds. In this study, we identified four novel viruses belonging to the family Picornaviridae in healthy Magellanic penguins, a near threatened species. All samples were subsequently screened by RT-PCR for these new viruses, and approximately 20% of the penguins were infected with at least one of these viruses. The viruses were distantly related to members of the genera Hepatovirus, Tremovirus, Gruhelivirus and Crahelvirus. Further, they had more than 60% amino acid divergence from other picornaviruses, and therefore likely constitute novel genera. Our results demonstrate the vast undersampling of wild birds for viruses, and we expect the discovery of numerous avian viruses that are related to hepatoviruses and tremoviruses in the future.}, } @article {pmid34058528, year = {2021}, author = {Tang, XY and Gao, MX and Xiao, HH and Dai, ZQ and Yao, ZH and Dai, Y and Yao, XS}, title = {Effects of Xian-Ling-Gu-Bao capsule on the gut microbiota in ovariectomized rats: Metabolism and modulation.}, journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences}, volume = {1176}, number = {}, pages = {122771}, doi = {10.1016/j.jchromb.2021.122771}, pmid = {34058528}, issn = {1873-376X}, mesh = {Animals ; Chromatography, High Pressure Liquid/methods ; Drugs, Chinese Herbal/*pharmacology ; Female ; Gastrointestinal Microbiome/*drug effects ; *Ovariectomy ; Rats ; Rats, Sprague-Dawley ; Tandem Mass Spectrometry ; }, abstract = {Xian-Ling-Gu-Bao capsule (XLGB) has been proven to prevent and treat osteoporosis. However, as a long-term oral formula, XLGB's effects on the metabolic capacity, structure and function of gut microbiota have yet to be elucidated in ovariectomized (OVX) rats. Our objectives were to evaluate the capacity of gut microbiota for metabolizing XLGB ingredients and to assess the effect of this prescription on gut microbiota. Herein, an integrated analysis that combined ultrahigh-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) and ultrahigh-performance liquid chromatography tandem triple quadrupole mass spectrometry (UPLC-TQD-MS) was conducted to determine the metabolic capacity of gut microbiota. The effects of XLGB on gut microbiota were explored by metagenomic sequencing in OVX rats. Fecal samples from each group were collected after intragastric administration for three months. In total, 64 biotransformation products were fully characterized with rat gut microbiota from the OVX group and the XLGB group. The deglycosylation reaction was the main biotransformation pathway in core structures in the group that was incubated with XLGB. Compared with the OVX group, different biotransformation products and pathways of the XLGB group after incubation for 2 h and 8 h were described. After three months of feeding with XLGB, the domesticated gut microbiota was conducive to the production of active absorbed components via deglycosylation, such as icaritin, psoralen and isopsoralen. Comparisons of the gut microbiota of the OVX and XLGB groups showed differences in the relative abundances of the two dominant bacterial divisions, namely, Firmicutes and Bacteroidetes. The proportion of Firmicutes was significantly lower and that of Bacteroidetes was significantly higher in the XLGB group. This result demonstrated that XLGB could provide a basis for the treatment of osteoporosis by regulating lipid and bile acid metabolism. In addition, the increase in Lactobacillus, Bacteroides and Prevotella could be an important factor that led to easier production of active absorbed aglycones in the XLGB group. Our observation provided further evidence of the importance of gut microbiota in the metabolism and potential activity of XLGB.}, } @article {pmid34057024, year = {2021}, author = {Hertel, J and Heinken, A and Martinelli, F and Thiele, I}, title = {Integration of constraint-based modeling with fecal metabolomics reveals large deleterious effects of Fusobacterium spp. on community butyrate production.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-23}, pmid = {34057024}, issn = {1949-0984}, support = {RF1 AG058942/AG/NIA NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; }, mesh = {Aged ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Butyrates/*metabolism ; Case-Control Studies ; Colorectal Neoplasms/microbiology ; Feces/chemistry/*microbiology ; Female ; Fusobacterium/genetics/isolation & purification/*metabolism ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolomics ; Middle Aged ; }, abstract = {Characterizing the metabolic functions of the gut microbiome in health and disease is pivotal for translating alterations in microbial composition into clinical insights. Two major analysis paradigms have been used to explore the metabolic functions of the microbiome but not systematically integrated with each other: statistical screening approaches, such as metabolome-microbiome association studies, and computational approaches, such as constraint-based metabolic modeling. To combine the strengths of the two analysis paradigms, we herein introduce a set of theoretical concepts allowing for the population statistical treatment of constraint-based microbial community models. To demonstrate the utility of the theoretical framework, we applied it to a public metagenomic dataset consisting of 365 colorectal cancer (CRC) cases and 251 healthy controls, shining a light on the metabolic role of Fusobacterium spp. in CRC. We found that (1) glutarate production capability was significantly enriched in CRC microbiomes and mechanistically linked to lysine fermentation in Fusobacterium spp., (2) acetate and butyrate production potentials were lowered in CRC, and (3) Fusobacterium spp. presence had large negative ecological effects on community butyrate production in CRC cases and healthy controls. Validating the model predictions against fecal metabolomics, the in silico frameworks correctly predicted in vivo species metabolite correlations with high accuracy. In conclusion, highlighting the value of combining statistical association studies with in silico modeling, this study provides insights into the metabolic role of Fusobacterium spp. in the gut, while providing a proof of concept for the validity of constraint-based microbial community modeling.}, } @article {pmid34055388, year = {2021}, author = {Dudas, G and Huber, G and Wilkinson, M and Yllanes, D}, title = {Polymorphism of genetic ambigrams.}, journal = {Virus evolution}, volume = {7}, number = {1}, pages = {veab038}, pmid = {34055388}, issn = {2057-1577}, abstract = {Double synonyms in the genetic code can be used as a tool to test competing hypotheses regarding ambigrammatic narnavirus genomes. Applying the analysis to recent observations of Culex narnavirus 1 and Zhejiang mosquito virus 3 ambigrammatic viruses indicates that the open reading frame on the complementary strand of the segment coding for RNA-dependent RNA polymerase does not code for a functional protein. Culex narnavirus 1 has been shown to possess a second segment, also ambigrammatic, termed 'Robin'. We find a comparable segment for Zhejiang mosquito virus 3, a moderately diverged relative of Culex narnavirus 1. Our analysis of Robin polymorphisms suggests that its reverse open reading frame also does not code for a functional protein. We make a hypothesis about its role.}, } @article {pmid34054845, year = {2021}, author = {Bosák, J and Lexa, M and Fiedorová, K and Gadara, DC and Micenková, L and Spacil, Z and Litzman, J and Freiberger, T and Šmajs, D}, title = {Patients With Common Variable Immunodeficiency (CVID) Show Higher Gut Bacterial Diversity and Levels of Low-Abundance Genes Than the Healthy Housemates.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {671239}, pmid = {34054845}, issn = {1664-3224}, mesh = {Adenosine/metabolism ; Biodiversity ; Clostridiaceae/*physiology ; Common Variable Immunodeficiency/genetics/*microbiology ; Computational Biology/*methods ; Dysbiosis/genetics/*microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Homeostasis ; Humans ; Metabolomics ; Metagenome ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Common variable immunodeficiency (CVID) is a clinically and genetically heterogeneous disorder with inadequate antibody responses and low levels of immunoglobulins including IgA that is involved in the maintenance of the intestinal homeostasis. In this study, we analyzed the taxonomical and functional metagenome of the fecal microbiota and stool metabolome in a cohort of six CVID patients without gastroenterological symptomatology and their healthy housemates. The fecal microbiome of CVID patients contained higher numbers of bacterial species and altered abundance of thirty-four species. Hungatella hathewayi was frequent in CVID microbiome and absent in controls. Moreover, the CVID metagenome was enriched for low-abundance genes likely encoding nonessential functions, such as bacterial motility and metabolism of aromatic compounds. Metabolomics revealed dysregulation in several metabolic pathways, mostly associated with decreased levels of adenosine in CVID patients. Identified features have been consistently associated with CVID diagnosis across the patients with various immunological characteristics, length of treatment, and age. Taken together, this initial study revealed expansion of bacterial diversity in the host immunodeficient conditions and suggested several bacterial species and metabolites, which have potential to be diagnostic and/or prognostic CVID markers in the future.}, } @article {pmid34053518, year = {2021}, author = {Franciosa, I and Ferrocino, I and Giordano, M and Mounier, J and Rantsiou, K and Cocolin, L}, title = {Specific metagenomic asset drives the spontaneous fermentation of Italian sausages.}, journal = {Food research international (Ottawa, Ont.)}, volume = {144}, number = {}, pages = {110379}, doi = {10.1016/j.foodres.2021.110379}, pmid = {34053518}, issn = {1873-7145}, mesh = {Fermentation ; Food Microbiology ; Italy ; *Lactobacillus ; *Metagenomics ; }, abstract = {Metagenomics is a powerful tool to study and understand the microbial dynamics that occur during food fermentation and allows to close the link between microbial diversity and final sensory characteristics. Each food matrix can be colonized by different microbes, but also by different strains of the same species. In this study, using an innovative integrated approach combining culture-dependent method with a shotgun sequencing, we were able to show how strain-level biodiversity could influence the quality characteristics of the final product. The attention was placed on a model food fermentation process: Salame Piemonte, a Protected Geographical Indication (PGI) Italian fermented sausage. Three independent batches produced in February, March and May 2018 were analysed. The sausages were manufactured, following the production specification, in a local meat factory in the area of Turin (Italy) without the use of starter cultures. A pangenomic approach was applied in order to identify and evaluate the lactic acid bacteria (LAB) population driving the fermentation process. It was observed that all batches were characterized by the presence of few LAB species, namely Pediococcus pentosaceus, Latilactobacillus curvatus and Latilactobacillus sakei. Sausages from the different batches were different when the volatilome was taken into consideration, and a strong association between quality attributes and strains present was determined. In particular, different strains of L. sakei, showing heterogeneity at genomic level, colonized the meat at the beginning of each production and deeply influenced the fermentation process by distinctive metabolic pathways that affected the fermentation process and the final sensory aspects.}, } @article {pmid34051731, year = {2021}, author = {Kazantseva, J and Malv, E and Kaleda, A and Kallastu, A and Meikas, A}, title = {Optimisation of sample storage and DNA extraction for human gut microbiota studies .}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {158}, pmid = {34051731}, issn = {1471-2180}, support = {EU48667//Ettevõtluse Arendamise Sihtasutus/ ; }, mesh = {Bacteria/classification/*genetics/isolation & purification ; DNA, Bacterial/genetics/*isolation & purification ; Feces/microbiology ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Preservation, Biological/*methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: New developments in next-generation sequencing technologies and massive data received from this approach open wide prospects for personalised medicine and nutrition studies. Metagenomic analysis of the gut microbiota is paramount for the characterization of human health and wellbeing. Despite the intensive research, there is a huge gap and inconsistency between different studies due to the non-standardised and biased pipeline. Methodical and systemic understanding of every stage in the process is necessary to overcome all bottlenecks and grey zones of gut microbiota studies, where all details and interactions between processes are important.

RESULTS: Here we show that an inexpensive, but reliable iSeq 100 platform is an excellent tool to perform the analysis of the human gut microbiota by amplicon sequencing of the 16 S rRNA gene. Two commercial DNA extraction kits and different starting materials performed similarly regarding the taxonomic distribution of identified bacteria. DNA/RNA Shield reagent proved to be a reliable solution for stool samples collection, preservation, and storage, as the storage of faecal material in DNA/RNA Shield for three weeks at different temperatures and thawing cycles had a low impact on the bacterial distribution.

CONCLUSIONS: Altogether, a thoroughly elaborated pipeline with close attention to details ensures high reproducibility with significant biological but not technical variations.}, } @article {pmid34051218, year = {2021}, author = {Wang, H and Banerjee, N and Liang, Y and Wang, G and Hoffman, KL and Khan, MF}, title = {Gut microbiome-host interactions in driving environmental pollutant trichloroethene-mediated autoimmunity.}, journal = {Toxicology and applied pharmacology}, volume = {424}, number = {}, pages = {115597}, pmid = {34051218}, issn = {1096-0333}, support = {R01 ES016302/ES/NIEHS NIH HHS/United States ; R01 ES026887/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Autoimmunity/*drug effects ; Bacteria/*drug effects ; Drug Administration Schedule ; Environmental Pollutants/*toxicity ; Female ; Gastrointestinal Microbiome/*drug effects/physiology ; Inflammation ; Liver/drug effects ; Mice ; Mice, Inbred Strains ; Oxidative Stress ; Spleen/drug effects ; Trichloroethylene/*toxicity ; }, abstract = {Trichloroethene (TCE), a widely used industrial solvent, is associated with the development of autoimmune diseases (ADs), including systemic lupus erythematosus and autoimmune hepatitis. Increasing evidence support a linkage between altered gut microbiome composition and the onset of ADs. However, it is not clear how gut microbiome contributes to TCE-mediated autoimmunity, and initial triggers for microbiome-host interactions leading to systemic autoimmune responses remain unknown. To achieve this, female MRL+/+ mice were treated with 0.5 mg/ml TCE for 52 weeks and fecal samples were subjected to 16S rRNA sequencing to determine the microbiome composition. TCE exposure resulted in distinct bacterial community revealed by β-diversity analysis. Notably, we observed reduction in Lactobacillaceae, Rikenellaceae and Bifidobacteriaceae families, and enrichment of Akkermansiaceae and Lachnospiraceae families after TCE exposure. We also observed significantly increased colonic oxidative stress and inflammatory markers (CD14 and IL-1β), and decreased tight junction proteins (ZO-2, occludin and claudin-3). These changes were associated with increases in serum antinuclear and anti-smooth muscle antibodies and cytokines (IL-6 and IL-12), together with increased PD1 + CD4+ T cells in TCE-exposed spleen and liver tissues. Importantly, fecal microbiota transplantation (FMT) using feces from TCE-treated mice to antibiotics-treated mice induced increased anti-dsDNA antibodies and hepatic CD4+ T cell infiltration in the recipient mice. Our studies thus delineate how imbalance in gut microbiome and mucosal redox status together with gut inflammatory response and permeability changes could be the key factors in contributing to TCE-mediated ADs. Furthermore, FMT studies provide a solid support to a causal role of microbiome in TCE-mediated autoimmunity.}, } @article {pmid34051009, year = {2021}, author = {Matsushita, M and Fujita, K and Motooka, D and Hatano, K and Fukae, S and Kawamura, N and Tomiyama, E and Hayashi, Y and Banno, E and Takao, T and Takada, S and Yachida, S and Uemura, H and Nakamura, S and Nonomura, N}, title = {The gut microbiota associated with high-Gleason prostate cancer.}, journal = {Cancer science}, volume = {112}, number = {8}, pages = {3125-3135}, pmid = {34051009}, issn = {1349-7006}, support = {//Yakult Bio-Science Foundation/ ; //Japanese Urological Association/ ; }, mesh = {Aged ; Bacteria/*classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Gastrointestinal Microbiome ; Humans ; Japan ; Male ; Middle Aged ; Neoplasm Grading ; Phylogeny ; Prostatic Neoplasms/microbiology/*pathology ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {We have found that intestinal bacteria and their metabolites, short-chain fatty acids (SCFAs), promote cancer growth in prostate cancer (PCa) mouse models. To clarify the association between gut microbiota and PCa in humans, we analyzed the gut microbiota profiles of men with suspected PCa. One hundred and fifty-two Japanese men undergoing prostate biopsies (96 with cancer and 56 without cancer) were included in the study and randomly divided into two cohorts: a discovery cohort (114 samples) and a test cohort (38 samples). The gut microbiota was compared between two groups, a high-risk group (men with Grade group 2 or higher PCa) and a negative + low-risk group (men with negative biopsy or Grade group 1 PCa), using 16S rRNA gene sequencing. The relative abundances of Rikenellaceae, Alistipes, and Lachnospira, all SCFA-producing bacteria, were significantly increased in high-risk group. In receiver operating characteristic curve analysis, the index calculated from the abundance of 18 bacterial genera which were selected by least absolute shrinkage and selection operator regression detected high-risk PCa in the discovery cohort with higher accuracy than the prostate specific antigen test (area under the curve [AUC] = 0.85 vs 0.74). Validation of the index in the test cohort showed similar results (AUC = 0.81 vs 0.67). The specific bacterial taxa were associated with high-risk PCa. The gut microbiota profile could be a novel useful marker for the detection of high-risk PCa and could contribute to the carcinogenesis of PCa.}, } @article {pmid34051000, year = {2021}, author = {Arnoriaga-Rodríguez, M and Mayneris-Perxachs, J and Coll, C and Pérez-Brocal, V and Ricart, W and Moya, A and Ramió-Torrentà, L and Pamplona, R and Jové, M and Portero-Otin, M and Fernández-Real, JM}, title = {Subjects with detectable Saccharomyces cerevisiae in the gut microbiota show deficits in attention and executive function.}, journal = {Journal of internal medicine}, volume = {290}, number = {3}, pages = {740-743}, doi = {10.1111/joim.13307}, pmid = {34051000}, issn = {1365-2796}, mesh = {*Attention ; *Executive Function ; Feces ; *Gastrointestinal Microbiome ; Humans ; Metabolomics ; Saccharomyces cerevisiae/*isolation & purification ; }, } @article {pmid34050180, year = {2021}, author = {Xu, L and Dong, Z and Chiniquy, D and Pierroz, G and Deng, S and Gao, C and Diamond, S and Simmons, T and Wipf, HM and Caddell, D and Varoquaux, N and Madera, MA and Hutmacher, R and Deutschbauer, A and Dahlberg, JA and Guerinot, ML and Purdom, E and Banfield, JF and Taylor, JW and Lemaux, PG and Coleman-Derr, D}, title = {Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3209}, pmid = {34050180}, issn = {2041-1723}, support = {P42 ES007373/ES/NIEHS NIH HHS/United States ; }, mesh = {Acclimatization ; Actinobacteria/genetics/*metabolism ; Crop Production ; *Droughts ; Food Security ; Iron/*metabolism ; Metagenomics/methods ; Microbiota/*physiology ; Plant Roots/microbiology ; RNA-Seq ; Rhizosphere ; Soil Microbiology ; Sorghum/microbiology/*physiology ; Stress, Physiological ; }, abstract = {Recent studies have demonstrated that drought leads to dramatic, highly conserved shifts in the root microbiome. At present, the molecular mechanisms underlying these responses remain largely uncharacterized. Here we employ genome-resolved metagenomics and comparative genomics to demonstrate that carbohydrate and secondary metabolite transport functionalities are overrepresented within drought-enriched taxa. These data also reveal that bacterial iron transport and metabolism functionality is highly correlated with drought enrichment. Using time-series root RNA-Seq data, we demonstrate that iron homeostasis within the root is impacted by drought stress, and that loss of a plant phytosiderophore iron transporter impacts microbial community composition, leading to significant increases in the drought-enriched lineage, Actinobacteria. Finally, we show that exogenous application of iron disrupts the drought-induced enrichment of Actinobacteria, as well as their improvement in host phenotype during drought stress. Collectively, our findings implicate iron metabolism in the root microbiome's response to drought and may inform efforts to improve plant drought tolerance to increase food security.}, } @article {pmid34050176, year = {2021}, author = {Behsaz, B and Bode, E and Gurevich, A and Shi, YN and Grundmann, F and Acharya, D and Caraballo-Rodríguez, AM and Bouslimani, A and Panitchpakdi, M and Linck, A and Guan, C and Oh, J and Dorrestein, PC and Bode, HB and Pevzner, PA and Mohimani, H}, title = {Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3225}, pmid = {34050176}, issn = {2041-1723}, support = {DP2 GM126893/GM/NIGMS NIH HHS/United States ; DP2 GM137413/GM/NIGMS NIH HHS/United States ; P30 CA034196/CA/NCI NIH HHS/United States ; }, mesh = {Algorithms ; Amino Acid Sequence/genetics ; Anti-Bacterial Agents/biosynthesis/*isolation & purification ; Biological Products/*isolation & purification/metabolism ; Computational Biology/*methods ; Datasets as Topic ; Drug Discovery/*methods ; Humans ; Mass Spectrometry ; Metabolic Networks and Pathways/genetics ; Metabolomics/methods ; Metagenomics/methods ; Microbiota/genetics ; Multigene Family ; Peptide Biosynthesis ; Peptide Synthases/genetics/metabolism ; Peptides/genetics/*isolation & purification/metabolism ; Soil Microbiology ; }, abstract = {Non-Ribosomal Peptides (NRPs) represent a biomedically important class of natural products that include a multitude of antibiotics and other clinically used drugs. NRPs are not directly encoded in the genome but are instead produced by metabolic pathways encoded by biosynthetic gene clusters (BGCs). Since the existing genome mining tools predict many putative NRPs synthesized by a given BGC, it remains unclear which of these putative NRPs are correct and how to identify post-assembly modifications of amino acids in these NRPs in a blind mode, without knowing which modifications exist in the sample. To address this challenge, here we report NRPminer, a modification-tolerant tool for NRP discovery from large (meta)genomic and mass spectrometry datasets. We show that NRPminer is able to identify many NRPs from different environments, including four previously unreported NRP families from soil-associated microbes and NRPs from human microbiota. Furthermore, in this work we demonstrate the anti-parasitic activities and the structure of two of these NRP families using direct bioactivity screening and nuclear magnetic resonance spectrometry, illustrating the power of NRPminer for discovering bioactive NRPs.}, } @article {pmid34048707, year = {2021}, author = {Zhang, F and Weckhorst, JL and Assié, A and Hosea, C and Ayoub, CA and Khodakova, AS and Cabrera, ML and Vidal Vilchis, D and Félix, MA and Samuel, BS}, title = {Natural genetic variation drives microbiome selection in the Caenorhabditis elegans gut.}, journal = {Current biology : CB}, volume = {31}, number = {12}, pages = {2603-2618.e9}, pmid = {34048707}, issn = {1879-0445}, support = {P40 OD010440/OD/NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; S10 OD025251/OD/NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; DP2 DK116645/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis elegans/*microbiology ; Caenorhabditis elegans Proteins/metabolism ; *Genetic Variation ; Insulin/metabolism ; Microbiota/*genetics/*physiology ; Phylogeny ; Signal Transduction ; Transcription Factors/metabolism ; }, abstract = {Host genetic landscapes can shape microbiome assembly in the animal gut by contributing to the establishment of distinct physiological environments. However, the genetic determinants contributing to the stability and variation of these microbiome types remain largely undefined. Here, we use the free-living nematode Caenorhabditis elegans to identify natural genetic variation among wild strains of C. elegans that drives assembly of distinct microbiomes. To achieve this, we first established a diverse model microbiome that represents the strain-level phylogenetic diversity naturally encountered by C. elegans in the wild. Using this community, we show that C. elegans utilizes immune, xenobiotic, and metabolic signaling pathways to favor the assembly of different microbiome types. Variations in these pathways were associated with enrichment for specific commensals, including the Alphaproteobacteria Ochrobactrum. Using RNAi and mutant strains, we showed that host selection for Ochrobactrum is mediated specifically by host insulin signaling pathways. Ochrobactrum recruitment is blunted in the absence of DAF-2/IGFR and modulated by the competitive action of insulin signaling transcription factors DAF-16/FOXO and PQM-1/SALL2. Further, the ability of C. elegans to enrich for Ochrobactrum as adults is correlated with faster animal growth rates and larger body size at the end of development. These results highlight a new role for the highly conserved insulin signaling pathways in the regulation of gut microbiome composition in C. elegans.}, } @article {pmid34048535, year = {2021}, author = {Chen, Y and Li, HW and Cong, F and Lian, YX}, title = {Avian leukosis virus subgroup J infection alters viral composition in the chicken gut.}, journal = {FEMS microbiology letters}, volume = {368}, number = {10}, pages = {}, doi = {10.1093/femsle/fnab058}, pmid = {34048535}, issn = {1574-6968}, mesh = {Animals ; Avian Leukosis/*virology ; Avian Leukosis Virus/classification/genetics/isolation & purification/*physiology ; Chickens/virology ; Feces/virology ; Female ; Gastrointestinal Tract/*virology ; Male ; Poultry Diseases/*virology ; Virome ; Viruses/classification/genetics/isolation & purification ; }, abstract = {Chicken is one of the economically important poultry species. Avian leucosis virus subgroup J (ALV-J) has emerged as a serious cause of mortality and suboptimal performance of domestic chickens. Changes in virome may contribute to pathogenesis. Thus, it is important to investigate the effects of ALV-J infection on the composition of the virome in chicken. In the study metagenomic sequencing was used to characterize the virome of feces collected from the AVL-J infected chickens and the controls. Our results indicated that the chicken gut virome contained a diverse range of viruses that can be found in mammal, reptile, fish, and frogs. Furthermore, at the order, family and genus levels, AVL-J infection significantly altered the chicken gut virome composition. The predominant order was Herpesvirales, accounting for more than 96% of the chicken gut virome. Furthermore, the relative abundance of Caudovirales in the controls was higher than that in the AVL-J-infected chickens. At the family level, the relative abundance of Herpesviridae, Myoviridae, Alloherpesviridae, and Genomoviridae was significantly altered in the AVL-J-infected chickens compared with that in the controls. Additionally, the relative abundance of 15 genera showed a significant difference between the AVL-J-infected chickens and controls. These results will increase our understanding of the viral diversity and changes in the virome of chicken gut, with implications in chicken health.}, } @article {pmid34047390, year = {2021}, author = {Huang, MX and Yang, SY and Luo, PY and Long, J and Liu, QZ and Wang, J and He, Y and Li, L and Zhao, ZB and Lian, ZX}, title = {Gut microbiota contributes to sexual dimorphism in murine autoimmune cholangitis.}, journal = {Journal of leukocyte biology}, volume = {110}, number = {6}, pages = {1121-1130}, doi = {10.1002/JLB.3MA0321-037R}, pmid = {34047390}, issn = {1938-3673}, mesh = {Animals ; Autoimmune Diseases ; Female ; Gastrointestinal Microbiome/*physiology ; *Liver Cirrhosis, Biliary ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Receptor, Transforming Growth Factor-beta Type II/genetics ; *Sex Characteristics ; }, abstract = {The data demonstrated that a transgenic murine model of primary biliary cholangitis (PBC), expressing dominant negative TGF-β receptor Ⅱ (dnTGFβRⅡ) under the CD4 promoter, showed similarity to PBC patients that is female-dominant. Female dnTGFβRII mice developed more severe lymphocytic infiltration in the liver and had higher levels of inflammatory cytokines, including IFN-γ and TNF-α, than the male mice. Interestingly, elimination of testosterone through gonadectomy in male dnTGFβRII mice did not influence disease severity, supporting that testosterone is an unessential factor in sustaining liver immune homeostasis. Meanwhile, it was observed that treating dnTGFβRII mice with oral antibiotics markedly reduced the differences in the levels of lymphocytic infiltration and cytokines between males and females, suggesting that the commensal gut microbiome plays a role in determining the observed sexual differences in dnTGFβRII mice. Furthermore, the diversity of gut microbiota composition and their metabolic functions in the male and female groups through metagenomic sequencing analysis were identified. The results revealed a testosterone-independent and commensal gut microbiota-mediated female bias in PBC.}, } @article {pmid34047368, year = {2021}, author = {Leonardi, A and Modugno, RL and Cavarzeran, F and Rosani, U}, title = {Metagenomic analysis of the conjunctival bacterial and fungal microbiome in vernal keratoconjunctivitis.}, journal = {Allergy}, volume = {76}, number = {10}, pages = {3215-3217}, doi = {10.1111/all.14963}, pmid = {34047368}, issn = {1398-9995}, mesh = {Bacteria/genetics ; *Conjunctivitis, Allergic ; Humans ; Metagenome ; Metagenomics ; *Mycobiome ; RNA, Ribosomal, 16S ; }, } @article {pmid34044834, year = {2021}, author = {Rajeswari, G and Jacob, S and Chandel, AK and Kumar, V}, title = {Unlocking the potential of insect and ruminant host symbionts for recycling of lignocellulosic carbon with a biorefinery approach: a review.}, journal = {Microbial cell factories}, volume = {20}, number = {1}, pages = {107}, pmid = {34044834}, issn = {1475-2859}, mesh = {Animals ; *Biofuels ; Biomass ; Carbon/*metabolism ; Cellulase ; Fermentation ; *Gastrointestinal Microbiome ; Industrial Microbiology ; Insecta/microbiology ; Lignin/*metabolism ; Oxygenases ; Ruminants/microbiology ; *Symbiosis ; }, abstract = {Uprising fossil fuel depletion and deterioration of ecological reserves supply have led to the search for alternative renewable and sustainable energy sources and chemicals. Although first generation biorefinery is quite successful commercially in generating bulk of biofuels globally, the food versus fuel debate has necessitated the use of non-edible feedstocks, majorly waste biomass, for second generation production of biofuels and chemicals. A diverse class of microbes and enzymes are being exploited for biofuels production for a series of treatment process, however, the conversion efficiency of wide range of lignocellulosic biomass (LCB) and consolidated way of processing remains challenging. There were lot of research efforts in the past decade to scour for potential microbial candidate. In this context, evolution has developed the gut microbiota of several insects and ruminants that are potential LCB degraders host eco-system to overcome its host nutritional constraints, where LCB processed by microbiomes pretends to be a promising candidate. Synergistic microbial symbionts could make a significant contribution towards recycling the renewable carbon from distinctly abundant recalcitrant LCB. Several studies have assessed the bioprospection of innumerable gut symbionts and their lignocellulolytic enzymes for LCB degradation. Though, some reviews exist on molecular characterization of gut microbes, but none of them has enlightened the microbial community design coupled with various LCB valorization which intensifies the microbial diversity in biofuels application. This review provides a deep insight into the significant breakthroughs attained in enrichment strategy of gut microbial community and its molecular characterization techniques which aids in understanding the holistic microbial community dynamics. Special emphasis is placed on gut microbial role in LCB depolymerization strategies to lignocellulolytic enzymes production and its functional metagenomic data mining eventually generating the sugar platform for biofuels and renewable chemicals production.}, } @article {pmid34044757, year = {2021}, author = {Guo, J and Pang, E and Song, H and Lin, K}, title = {A tri-tuple coordinate system derived for fast and accurate analysis of the colored de Bruijn graph-based pangenomes.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {282}, pmid = {34044757}, issn = {1471-2105}, mesh = {*Algorithms ; Genome ; *Genomics ; Metagenomics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: With the rapid development of accurate sequencing and assembly technologies, an increasing number of high-quality chromosome-level and haplotype-resolved assemblies of genomic sequences have been derived, from which there will be great opportunities for computational pangenomics. Although genome graphs are among the most useful models for pangenome representation, their structural complexity makes it difficult to present genome information intuitively, such as the linear reference genome. Thus, efficiently and accurately analyzing the genome graph spatial structure and coordinating the information remains a substantial challenge.

RESULTS: We developed a new method, a colored superbubble (cSupB), that can overcome the complexity of graphs and organize a set of species- or population-specific haplotype sequences of interest. Based on this model, we propose a tri-tuple coordinate system that combines an offset value, topological structure and sample information. Additionally, cSupB provides a novel method that utilizes complete topological information and efficiently detects small indels (< 50 bp) for highly similar samples, which can be validated by simulated datasets. Moreover, we demonstrated that cSupB can adapt to the complex cycle structure.

CONCLUSIONS: Although the solution is made suitable for increasingly complex genome graphs by relaxing the constraint, the directed acyclic graph, the motif cSupB and the cSupB method can be extended to any colored directed acyclic graph. We anticipate that our method will facilitate the analysis of individual haplotype variants and population genomic diversity. We have developed a C +  + program for implementing our method that is available at https://github.com/eggleader/cSupB .}, } @article {pmid34044101, year = {2021}, author = {Gonzales-Luna, AJ and Spinler, JK and Oezguen, N and Khan, MAW and Danhof, HA and Endres, BT and Alam, MJ and Begum, K and Lancaster, C and Costa, GP and Savidge, TC and Hurdle, JG and Britton, R and Garey, KW}, title = {Systems biology evaluation of refractory Clostridioides difficile infection including multiple failures of fecal microbiota transplantation.}, journal = {Anaerobe}, volume = {70}, number = {}, pages = {102387}, pmid = {34044101}, issn = {1095-8274}, support = {F32 AI136404/AI/NIAID NIH HHS/United States ; R01 AI139261/AI/NIAID NIH HHS/United States ; U01 AI124290/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/administration & dosage ; Bacteria/classification/genetics/isolation & purification ; Clostridioides difficile/drug effects/genetics/isolation & purification/*physiology ; Clostridium Infections/drug therapy/microbiology/*therapy ; *Fecal Microbiota Transplantation ; Feces ; Female ; Gastrointestinal Microbiome/drug effects ; Humans ; Microbial Sensitivity Tests ; Polymorphism, Single Nucleotide ; Treatment Failure ; }, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) aims to cure Clostridioides difficile infection (CDI) through reestablishing a healthy microbiome and restoring colonization resistance. Although often effective after one infusion, patients with continued microbiome disruptions may require multiple FMTs. In this N-of-1 study, we use a systems biology approach to evaluate CDI in a patient receiving chronic suppressive antibiotics with four failed FMTs over two years.

METHODS: Seven stool samples were obtained between 2016-18 while the patient underwent five FMTs. Stool samples were cultured for C. difficile and underwent microbial characterization and functional gene analysis using shotgun metagenomics. C. difficile isolates were characterized through ribotyping, whole genome sequencing, metabolic pathway analysis, and minimum inhibitory concentration (MIC) determinations.

RESULTS: Growing ten strains from each sample, the index and first four recurrent cultures were single strain ribotype F078-126, the fifth was a mixed culture of ribotypes F002 and F054, and the final culture was ribotype F002. One single nucleotide polymorphism (SNP) variant was identified in the RNA polymerase (RNAP) β-subunit RpoB in the final isolated F078-126 strain when compared to previous F078-126 isolates. This SNV was associated with metabolic shifts but phenotypic differences in fidaxomicin MIC were not observed. Microbiome differences were observed over time during vancomycin therapy and after failed FMTs.

CONCLUSION: This study highlights the importance of antimicrobial stewardship in patients receiving FMT. Continued antibiotics play a destructive role on a transplanted microbiome and applies selection pressure for resistance to the few antibiotics available to treat CDI.}, } @article {pmid34044040, year = {2021}, author = {Yoo, YJ and Perinpanayagam, H and Choi, Y and Gu, Y and Chang, SW and Baek, SH and Zhu, Q and Fouad, AF and Kum, KY}, title = {Characterization of Histopathology and Microbiota in Contemporary Regenerative Endodontic Procedures: Still Coming up Short.}, journal = {Journal of endodontics}, volume = {47}, number = {8}, pages = {1285-1293.e1}, doi = {10.1016/j.joen.2021.05.006}, pmid = {34044040}, issn = {1878-3554}, mesh = {Animals ; Dental Pulp Necrosis/therapy ; Dogs ; *Microbiota ; *Periapical Periodontitis/therapy ; *Regenerative Endodontics ; Root Canal Therapy ; }, abstract = {INTRODUCTION: This study aimed to investigate microbiota and the histopathology of infected immature teeth microenvironments after disinfection with calcium hydroxide, triple antibiotic paste, and a synthetic antimicrobial peptide (synthetic human beta-defensin-3-C15) for regenerative endodontic procedures (REPs). The null hypothesis was that there is no difference among intracanal medications on disinfection in REPs.

METHODS: Pulp necrosis and periapical lesions were induced in immature beagle dog premolars. Block randomized teeth were uninfected (negative control, n = 6), left infected (positive control, n = 6), or medicated with a disinfectant (n = 6/group). After disinfection (2 weeks), teeth were reaccessed, irrigated with 17% EDTA, blood clot induced, sealed with ProRoot MTA (Dentsply Tulsa Dental, Tulsa, OK), and restored with resin-modified glass ionomer. Animals were monitored radiographically and euthanized (12 weeks) for histopathologic and metagenomic analyses.

RESULTS: REP-treated roots showed radiographic repair of periapical radiolucency (67.65%, 23/34), continued root development (73.53%, 25/34), and apical closure (70.59%, 24/34) regardless of the disinfectant used (P > .05). Canal microenvironments histologically devoid of bacteria contained new mineralized and pulp-like tissues in characteristic patterns that varied by disinfectant. Next-generation sequencing (16S ribosomal RNA) identified Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes as dominant phyla of microbiota in immature teeth. Infection-induced teeth showed changes in diversity and richness of microbiota from negative controls. Compared with positive controls, all treated teeth exhibited depleted operational taxonomic units, with lower phylogenic diversity from synthetic human beta-defensin-3-C15-treated teeth.

CONCLUSIONS: There were no differences among the medicaments investigated in radiologic treatment outcomes, but disinfectants in REPs showed altered microbiota from normal and diseased immature teeth with different histologic patterns of regeneration.}, } @article {pmid34043940, year = {2021}, author = {Danko, D and Bezdan, D and Afshin, EE and Ahsanuddin, S and Bhattacharya, C and Butler, DJ and Chng, KR and Donnellan, D and Hecht, J and Jackson, K and Kuchin, K and Karasikov, M and Lyons, A and Mak, L and Meleshko, D and Mustafa, H and Mutai, B and Neches, RY and Ng, A and Nikolayeva, O and Nikolayeva, T and Png, E and Ryon, KA and Sanchez, JL and Shaaban, H and Sierra, MA and Thomas, D and Young, B and Abudayyeh, OO and Alicea, J and Bhattacharyya, M and Blekhman, R and Castro-Nallar, E and Cañas, AM and Chatziefthimiou, AD and Crawford, RW and De Filippis, F and Deng, Y and Desnues, C and Dias-Neto, E and Dybwad, M and Elhaik, E and Ercolini, D and Frolova, A and Gankin, D and Gootenberg, JS and Graf, AB and Green, DC and Hajirasouliha, I and Hastings, JJA and Hernandez, M and Iraola, G and Jang, S and Kahles, A and Kelly, FJ and Knights, K and Kyrpides, NC and Łabaj, PP and Lee, PKH and Leung, MHY and Ljungdahl, PO and Mason-Buck, G and McGrath, K and Meydan, C and Mongodin, EF and Moraes, MO and Nagarajan, N and Nieto-Caballero, M and Noushmehr, H and Oliveira, M and Ossowski, S and Osuolale, OO and Özcan, O and Paez-Espino, D and Rascovan, N and Richard, H and Rätsch, G and Schriml, LM and Semmler, T and Sezerman, OU and Shi, L and Shi, T and Siam, R and Song, LH and Suzuki, H and Court, DS and Tighe, SW and Tong, X and Udekwu, KI and Ugalde, JA and Valentine, B and Vassilev, DI and Vayndorf, EM and Velavan, TP and Wu, J and Zambrano, MM and Zhu, J and Zhu, S and Mason, CE and , }, title = {A global metagenomic map of urban microbiomes and antimicrobial resistance.}, journal = {Cell}, volume = {184}, number = {13}, pages = {3376-3393.e17}, pmid = {34043940}, issn = {1097-4172}, support = {U01 DA053941/DA/NIDA NIH HHS/United States ; T32 GM083937/GM/NIGMS NIH HHS/United States ; MR/S019669/1/MRC_/Medical Research Council/United Kingdom ; UL1 TR000457/TR/NCATS NIH HHS/United States ; R25 EB020393/EB/NIBIB NIH HHS/United States ; R01 AI151059/AI/NIAID NIH HHS/United States ; R21 AI129851/AI/NIAID NIH HHS/United States ; R35 GM138152/GM/NIGMS NIH HHS/United States ; }, mesh = {Biodiversity ; Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Humans ; *Metagenomics ; Microbiota/*genetics ; *Urban Population ; }, abstract = {We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.}, } @article {pmid34040607, year = {2021}, author = {Gonçalves, E and Guillén, Y and Lama, JR and Sanchez, J and Brander, C and Paredes, R and Combadière, B}, title = {Host Transcriptome and Microbiota Signatures Prior to Immunization Profile Vaccine Humoral Responsiveness.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {657162}, pmid = {34040607}, issn = {1664-3224}, mesh = {Adolescent ; Adult ; Antibodies, Neutralizing/immunology ; Biodiversity ; Biomarkers ; Female ; Host Microbial Interactions/*genetics/*immunology ; Humans ; *Immunity, Humoral ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; *Transcriptome ; Vaccination ; Vaccines/*immunology ; Young Adult ; }, abstract = {The identification of new biomarkers is essential to predict responsiveness to vaccines. We investigated the whole-blood transcriptome and microbiome prior to immunization, in order to assess their involvement in induction of humoral responses two months later. We based our analyses on stool and skin microbiota, and blood transcriptome prior to immunization, in a randomized clinical study in which participants were vaccinated with the MVA-HIV clade B vaccine (MVA-B). We found that the levels of neutralizing antibody responses were correlated with abundance of Eubacterium in stool and Prevotella in skin. In addition, genus diversity and bacterial species abundance were also correlated with the expression of genes involved in B cell development prior to immunization and forecast strong responders to MVA-B. To our knowledge, this is the first study integrating host blood gene expression and microbiota that might open an avenue of research in this field and to optimize vaccination strategies and predict responsiveness to vaccines.}, } @article {pmid34039634, year = {2021}, author = {Matsushita, M and Fujita, K and Hayashi, T and Kayama, H and Motooka, D and Hase, H and Jingushi, K and Yamamichi, G and Yumiba, S and Tomiyama, E and Koh, Y and Hayashi, Y and Nakano, K and Wang, C and Ishizuya, Y and Kato, T and Hatano, K and Kawashima, A and Ujike, T and Uemura, M and Imamura, R and Rodriguez Pena, MDC and Gordetsky, JB and Netto, GJ and Tsujikawa, K and Nakamura, S and Takeda, K and Nonomura, N}, title = {Gut Microbiota-Derived Short-Chain Fatty Acids Promote Prostate Cancer Growth via IGF1 Signaling.}, journal = {Cancer research}, volume = {81}, number = {15}, pages = {4014-4026}, doi = {10.1158/0008-5472.CAN-20-4090}, pmid = {34039634}, issn = {1538-7445}, mesh = {Animals ; Disease Models, Animal ; Fatty Acids, Volatile/*metabolism ; Gastrointestinal Microbiome/*immunology ; Humans ; Insulin-Like Growth Factor I/*metabolism ; Male ; Mice ; Mice, Knockout ; Prostatic Neoplasms/*genetics ; Signal Transduction ; }, abstract = {Excessive intake of animal fat and resultant obesity are major risk factors for prostate cancer. Because the composition of the gut microbiota is known to change with dietary composition and body type, we used prostate-specific Pten knockout mice as a prostate cancer model to investigate whether there is a gut microbiota-mediated connection between animal fat intake and prostate cancer. Oral administration of an antibiotic mixture (Abx) in prostate cancer-bearing mice fed a high-fat diet containing a large proportion of lard drastically altered the composition of the gut microbiota including Rikenellaceae and Clostridiales, inhibited prostate cancer cell proliferation, and reduced prostate Igf1 expression and circulating insulin-like growth factor-1 (IGF1) levels. In prostate cancer tissue, MAPK and PI3K activities, both downstream of the IGF1 receptor, were suppressed by Abx administration. IGF1 directly promoted the proliferation of prostate cancer cell lines DU145 and 22Rv1 in vitro. Abx administration also reduced fecal levels of short-chain fatty acids (SCFA) produced by intestinal bacteria. Supplementation with SCFAs promoted tumor growth by increasing IGF1 levels. In humans, IGF1 was found to be highly expressed in prostate cancer tissue from obese patients. In conclusion, IGF1 production stimulated by SCFAs from gut microbes influences the growth of prostate cancer via activating local prostate MAPK and PI3K signaling, indicating the existence of a gut microbiota-IGF1-prostate axis. Disrupting this axis by modulating the gut microbiota may aid in prostate cancer prevention and treatment. SIGNIFICANCE: These results suggest that intestinal bacteria, acting through short-chain fatty acids, regulate systemic and local prostate IGF1 in the host, which can promote proliferation of prostate cancer cells.}, } @article {pmid34039428, year = {2021}, author = {Amar, Y and Lagkouvardos, I and Silva, RL and Ishola, OA and Foesel, BU and Kublik, S and Schöler, A and Niedermeier, S and Bleuel, R and Zink, A and Neuhaus, K and Schloter, M and Biedermann, T and Köberle, M}, title = {Pre-digest of unprotected DNA by Benzonase improves the representation of living skin bacteria and efficiently depletes host DNA.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {123}, pmid = {34039428}, issn = {2049-2618}, mesh = {*Bacteria/genetics ; DNA/genetics ; DNA, Bacterial/genetics ; Endodeoxyribonucleases ; Endoribonucleases ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Skin/*microbiology ; }, abstract = {BACKGROUND: The identification of microbiota based on next-generation sequencing (NGS) of extracted DNA has drastically improved our understanding of the role of microbial communities in health and disease. However, DNA-based microbiome analysis cannot per se differentiate between living and dead microorganisms. In environments such as the skin, host defense mechanisms including antimicrobial peptides and low cutaneous pH result in a high microbial turnover, likely resulting in high numbers of dead cells present and releasing substantial amounts of microbial DNA. NGS analyses may thus lead to inaccurate estimations of microbiome structures and consequently functional capacities.

RESULTS: We investigated in this study the feasibility of a Benzonase-based approach (BDA) to pre-digest unprotected DNA, i.e., of dead microbial cells, as a method to overcome these limitations, thus offering a more accurate assessment of the living microbiome. A skin mock community as well as skin microbiome samples were analyzed using 16S rRNA gene sequencing and metagenomics sequencing after DNA extraction with and without a Benzonase digest to assess bacterial diversity patterns. The BDA method resulted in less reads from dead bacteria both in the skin mock community and skin swabs spiked with either heat-inactivated bacteria or bacterial-free DNA. This approach also efficiently depleted host DNA reads in samples with high human-to-microbial DNA ratios, with no obvious impact on the microbiome profile. We further observed that low biomass samples generate an α-diversity bias when the bacterial load is lower than 10[5] CFU and that Benzonase digest is not sufficient to overcome this bias.

CONCLUSIONS: The BDA approach enables both a better assessment of the living microbiota and depletion of host DNA reads. Video abstract.}, } @article {pmid34039416, year = {2021}, author = {Leung, MHY and Tong, X and Bøifot, KO and Bezdan, D and Butler, DJ and Danko, DC and Gohli, J and Green, DC and Hernandez, MT and Kelly, FJ and Levy, S and Mason-Buck, G and Nieto-Caballero, M and Syndercombe-Court, D and Udekwu, K and Young, BG and Mason, CE and Dybwad, M and Lee, PKH}, title = {Characterization of the public transit air microbiome and resistome reveals geographical specificity.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {112}, pmid = {34039416}, issn = {2049-2618}, support = {U01 DA053941/DA/NIDA NIH HHS/United States ; /DH_/Department of Health/United Kingdom ; R21 AI129851/AI/NIAID NIH HHS/United States ; R01 NS076465/NS/NINDS NIH HHS/United States ; R01 MH117406/MH/NIMH NIH HHS/United States ; MR/S019669/1/MRC_/Medical Research Council/United Kingdom ; R25 EB020393/EB/NIBIB NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Geography ; Hong Kong ; Humans ; Metagenome/genetics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: The public transit is a built environment with high occupant density across the globe, and identifying factors shaping public transit air microbiomes will help design strategies to minimize the transmission of pathogens. However, the majority of microbiome works dedicated to the public transit air are limited to amplicon sequencing, and our knowledge regarding the functional potentials and the repertoire of resistance genes (i.e. resistome) is limited. Furthermore, current air microbiome investigations on public transit systems are focused on single cities, and a multi-city assessment of the public transit air microbiome will allow a greater understanding of whether and how broad environmental, building, and anthropogenic factors shape the public transit air microbiome in an international scale. Therefore, in this study, the public transit air microbiomes and resistomes of six cities across three continents (Denver, Hong Kong, London, New York City, Oslo, Stockholm) were characterized.

RESULTS: City was the sole factor associated with public transit air microbiome differences, with diverse taxa identified as drivers for geography-associated functional potentials, concomitant with geographical differences in species- and strain-level inferred growth profiles. Related bacterial strains differed among cities in genes encoding resistance, transposase, and other functions. Sourcetracking estimated that human skin, soil, and wastewater were major presumptive resistome sources of public transit air, and adjacent public transit surfaces may also be considered presumptive sources. Large proportions of detected resistance genes were co-located with mobile genetic elements including plasmids. Biosynthetic gene clusters and city-unique coding sequences were found in the metagenome-assembled genomes.

CONCLUSIONS: Overall, geographical specificity transcends multiple aspects of the public transit air microbiome, and future efforts on a global scale are warranted to increase our understanding of factors shaping the microbiome of this unique built environment.}, } @article {pmid34038319, year = {2021}, author = {Sonthiphand, P and Kraidech, S and Polart, S and Chotpantarat, S and Kusonmano, K and Uthaipaisanwong, P and Rangsiwutisak, C and Luepromchai, E}, title = {Arsenic speciation, the abundance of arsenite-oxidizing bacteria and microbial community structures in groundwater, surface water, and soil from a gold mine.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering}, volume = {56}, number = {7}, pages = {769-785}, doi = {10.1080/10934529.2021.1927421}, pmid = {34038319}, issn = {1532-4117}, mesh = {*Arsenic ; *Arsenites ; Bacteria/genetics ; Gold ; *Groundwater ; *Microbiota/genetics ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Soil ; Water ; }, abstract = {The arsenic speciation, the abundance of arsenite-oxidizing bacteria, and microbial community structures in the groundwater, surface water, and soil from a gold mining area were explored using the PHREEQC model, cloning-ddPCR of the aioA gene, and high-throughput sequencing of the 16S rRNA gene, respectively. The analysis of the aioA gene showed that arsenite-oxidizing bacteria retrieved from groundwater, surface water, and soil were associated with Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. In groundwaters from the mining area, there were relatively high ratios of aioA/total 16S rRNA gene copies and the dominance of As[5+], which suggested the presence and activity of arsenite-oxidizing bacteria. Metagenomic analysis revealed that the majority of the soil and surface water microbiomes were Proteobacteria, Actinobacteria, Bacteroidetes, and Chloroflexi, whereas the groundwater microbiomes were dominated exclusively by Betaproteobacteria and Alphaproteobacteria. Geochemical factors influencing the microbial structure in the groundwater were As, residence time, and groundwater flowrate, while those showing a positive correlation to the microbial structure in the surface water were TOC, ORP, and DO. This study provides insights into the groundwater, surface water, and soil microbiomes from a gold mine and expands the current understanding of the diversity and abundance of arsenite-oxidizing bacteria, playing a vital role in global As cycling.}, } @article {pmid34037469, year = {2021}, author = {Fulci, V and Carissimi, C and Laudadio, I}, title = {COVID-19 and Preparing for Future Ecological Crises: Hopes from Metagenomics in Facing Current and Future Viral Pandemic Challenges.}, journal = {Omics : a journal of integrative biology}, volume = {25}, number = {6}, pages = {336-341}, doi = {10.1089/omi.2021.0058}, pmid = {34037469}, issn = {1557-8100}, mesh = {Animals ; COVID-19/*diagnosis ; Ecosystem ; Humans ; Metagenomics/methods ; Pandemics/*prevention & control ; SARS-CoV-2/drug effects ; *COVID-19 Drug Treatment ; }, abstract = {The current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak demonstrates the potential of coronaviruses, especially bat-derived beta coronaviruses to rapidly escalate to a global pandemic that has caused deaths in the order of several millions already. The huge efforts put in place by the scientific community to address this emergency have disclosed how the implementation of new technologies is crucial in the prepandemic period to timely face future ecological crises. In this context, we argue that metagenomics and new approaches to understanding ecosystems and biodiversity offer veritable prospects to innovate therapeutics and diagnostics against novel and existing infectious agents. We discuss the opportunities and challenges associated with the science of metagenomics, specifically with an eye to inform and prevent future ecological crises and pandemics that are looming on the horizon in the 21st century.}, } @article {pmid34037156, year = {2021}, author = {Valença, IN and Santos, RBD and Peronni, KC and Sauvage, V and Vandenbogaert, M and Caro, V and Silva Junior, WAD and Covas, DT and Silva-Pinto, AC and Laperche, S and Kashima, S and Slavov, SN}, title = {Deep sequencing applied to the analysis of viromes in patients with beta-thalassemia.}, journal = {Revista do Instituto de Medicina Tropical de Sao Paulo}, volume = {63}, number = {}, pages = {e40}, pmid = {34037156}, issn = {1678-9946}, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; Seroepidemiologic Studies ; Virome ; *beta-Thalassemia/genetics ; }, abstract = {To date, blood banks apply routine diagnosis to a specific spectrum of transfusion-transmitted viruses. Even though this measure is considered highly efficient to control their transmission, the threat imposed by emerging viruses is increasing globally, which can impact transfusion safety, especially in the light of the accelerated viral discovery by novel sequencing technologies. One of the most important groups of patients, who may indicate the presence of emerging viruses in the field of blood transfusion, is the group of individuals who receive multiple transfusions due to hereditary hemoglobinopathies. It is possible that they harbor unknown or unsuspected parenterally-transmitted viruses. In order to elucidate this, nucleic acids from 30 patients with beta-thalassemia were analyzed by Illumina next-generation sequencing and bioinformatics analysis. Three major viral families: Anelloviridae, Flaviviridae and Hepadnaviridae were identified. Among them, anelloviruses were the most representative, being detected with high number of reads in all tested samples. Human Pegivirus 1 (HPgV-1, or GBV-C), Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV) were also identified. HBV and HCV detection was expected due to the high seroprevalence in patients with beta thalassemia. Our results do not confirm the presence of emerging or unsuspected viruses threatening the transfusion safety at present, but can be used to actively search for viruses that threaten blood transfusion safety. We believe that the application of viral metagenomics in multiple-transfused patients is highly useful to monitor possible viral transfusion threats and for the annotation of their virome composition.}, } @article {pmid34035443, year = {2021}, author = {Bay, SK and Waite, DW and Dong, X and Gillor, O and Chown, SL and Hugenholtz, P and Greening, C}, title = {Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient.}, journal = {The ISME journal}, volume = {15}, number = {11}, pages = {3339-3356}, pmid = {34035443}, issn = {1751-7370}, mesh = {*Cyanobacteria ; *Desert Climate ; Ecosystem ; Soil ; Soil Microbiology ; }, abstract = {Desert soils harbour diverse communities of aerobic bacteria despite lacking substantial organic carbon inputs from vegetation. A major question is therefore how these communities maintain their biodiversity and biomass in these resource-limiting ecosystems. Here, we investigated desert topsoils and biological soil crusts collected along an aridity gradient traversing four climatic regions (sub-humid, semi-arid, arid, and hyper-arid). Metagenomic analysis indicated these communities vary in their capacity to use sunlight, organic compounds, and inorganic compounds as energy sources. Thermoleophilia, Actinobacteria, and Acidimicrobiia were the most abundant and prevalent bacterial classes across the aridity gradient in both topsoils and biocrusts. Contrary to the classical view that these taxa are obligate organoheterotrophs, genome-resolved analysis suggested they are metabolically flexible, with the capacity to also use atmospheric H2 to support aerobic respiration and often carbon fixation. In contrast, Cyanobacteria were patchily distributed and only abundant in certain biocrusts. Activity measurements profiled how aerobic H2 oxidation, chemosynthetic CO2 fixation, and photosynthesis varied with aridity. Cell-specific rates of atmospheric H2 consumption increased 143-fold along the aridity gradient, correlating with increased abundance of high-affinity hydrogenases. Photosynthetic and chemosynthetic primary production co-occurred throughout the gradient, with photosynthesis dominant in biocrusts and chemosynthesis dominant in arid and hyper-arid soils. Altogether, these findings suggest that the major bacterial lineages inhabiting hot deserts use different strategies for energy and carbon acquisition depending on resource availability. Moreover, they highlight the previously overlooked roles of Actinobacteriota as abundant primary producers and trace gases as critical energy sources supporting productivity and resilience of desert ecosystems.}, } @article {pmid34035441, year = {2021}, author = {Teh, JJ and Berendsen, EM and Hoedt, EC and Kang, S and Zhang, J and Zhang, F and Liu, Q and Hamilton, AL and Wilson-O'Brien, A and Ching, J and Sung, JJY and Yu, J and Ng, SC and Kamm, MA and Morrison, M}, title = {Novel strain-level resolution of Crohn's disease mucosa-associated microbiota via an ex vivo combination of microbe culture and metagenomic sequencing.}, journal = {The ISME journal}, volume = {15}, number = {11}, pages = {3326-3338}, pmid = {34035441}, issn = {1751-7370}, mesh = {*Crohn Disease ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Mucous Membrane ; }, abstract = {The mucosa-associated microbiota is widely recognized as a potential trigger for Crohn's disease pathophysiology but remains largely uncharacterised beyond its taxonomic composition. Unlike stool microbiota, the functional characterisation of these communities using current DNA/RNA sequencing approaches remains constrained by the relatively small microbial density on tissue, and the overwhelming amount of human DNA recovered during sample preparation. Here, we have used a novel ex vivo approach that combines microbe culture from anaerobically preserved tissue with metagenome sequencing (MC-MGS) to reveal patient-specific and strain-level differences among these communities in post-operative Crohn's disease patients. The 16 S rRNA gene amplicon profiles showed these cultures provide a representative and holistic representation of the mucosa-associated microbiota, and MC-MGS produced both high quality metagenome-assembled genomes of recovered novel bacterial lineages. The MC-MGS approach also produced a strain-level resolution of key Enterobacteriacea and their associated virulence factors and revealed that urease activity underpins a key and diverse metabolic guild in these communities, which was confirmed by culture-based studies with axenic cultures. Collectively, these findings using MC-MGS show that the Crohn's disease mucosa-associated microbiota possesses taxonomic and functional attributes that are highly individualistic, borne at least in part by novel bacterial lineages not readily isolated or characterised from stool samples using current sequencing approaches.}, } @article {pmid34035399, year = {2021}, author = {Zhao, Z and Chu, C and Zhou, D and Wang, Q and Wu, S and Zheng, X and Song, K and Lv, W}, title = {Soil bacterial community composition in rice-fish integrated farming systems with different planting years.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {10855}, pmid = {34035399}, issn = {2045-2322}, mesh = {Agriculture ; Animals ; *Bacteria ; Biodiversity ; *Farms ; *Fishes ; Metagenome ; Metagenomics/methods ; *Microbiota ; *Oryza ; *Soil Microbiology ; }, abstract = {The high productivity and efficient nutrient utilization in rice-fish integrated farming system are well reported. However, the characteristics of soil bacterial communities and their relationship with soil nutrient availability in rice-fish field remain unclear. In this study, we selected three paddy fields, including a rice monoculture field and two rice-fish fields with different planting years, to investigate the soil bacterial community composition with Illumina MiSeq sequencing technology. The results indicated that the soil properties were significantly different among different rice farming systems. The soil bacterial community composition in the rice-fish field was significantly different from that in the rice monoculture field. Five of the top 15 phyla were observed with significant differences and Nitrospirae was the most significant one. However, no taxa observed with significance between the rice planting area and aquaculture area no matter in the 1st or 5th year of rice-fish field. RDA analysis showed that the soil bacterial community differentiation in the 5th year of rice-fish field was positively correlated with soil properties, such as AN and OM contents, EC and pH value. Although the rice yields in rice-fish field decreased, the net economic benefit of the rice-fish system enhanced obviously due to the high value of aquaculture animals.}, } @article {pmid34034165, year = {2021}, author = {Wu, X and Liu, P and Wegner, CE and Luo, Y and Xiao, KQ and Cui, Z and Zhang, F and Liesack, W and Peng, J}, title = {Deciphering microbial mechanisms underlying soil organic carbon storage in a wheat-maize rotation system.}, journal = {The Science of the total environment}, volume = {788}, number = {}, pages = {147798}, doi = {10.1016/j.scitotenv.2021.147798}, pmid = {34034165}, issn = {1879-1026}, mesh = {Agriculture ; *Carbon ; Fertilizers/analysis ; Manure ; RNA, Ribosomal, 16S ; Rotation ; *Soil ; Soil Microbiology ; Triticum ; Zea mays ; }, abstract = {A link between microbial life history strategies and soil organic carbon storage in agroecosystems is presumed, but largely unexplored at the gene level. We aimed to elucidate whether and how differential organic material amendments (manure versus peat-vermiculite) affect, relative to sole chemical fertilizer application, the link between microbial life history strategies and soil organic carbon storage in a wheat-maize rotation field experiment. To achieve this goal, we combined bacterial 16S rRNA gene and fungal ITS amplicon sequencing, metagenomics and the assembly of genomes. Fertilizer treatments had a significantly greater effect on microbial community composition than aggregate size, with soil available phosphorus and potassium being the most important community-shaping factors. Limitation in labile carbon was linked to a K-selected oligotrophic life history strategy (Gemmatimonadetes, Acidobacteria) under sole chemical fertilizer application; defined by a significant enrichment of genes involved in resource acquisition, polymer hydrolysis, and competition. By contrast, excess of labile carbon promoted an r-selected copiotrophic life history strategy (Cytophagales, Bacillales, Mortierellomycota) under manure treatment; defined by a significant enrichment of genes involved in cellular growth. A distinct life history strategy was not observed under peat-vermiculite treatment, but rather a mix of both K-selected (Acidobacteria) and r-selected (Actinobacteria, Mortierellomycota) microorganisms. Compared to sole chemical fertilizer application, soil organic carbon storage efficiency was significantly increased by 26.5% and 50.0% under manure and peat-vermiculite treatments, respectively. Taken together, our results highlight the importance of organic material amendments, but in particular a one-time peat-vermiculite application, to promote soil organic carbon storage as a potential management strategy for sustainable agriculture.}, } @article {pmid34031405, year = {2021}, author = {Roux, S and Paul, BG and Bagby, SC and Nayfach, S and Allen, MA and Attwood, G and Cavicchioli, R and Chistoserdova, L and Gruninger, RJ and Hallam, SJ and Hernandez, ME and Hess, M and Liu, WT and McAllister, TA and O'Malley, MA and Peng, X and Rich, VI and Saleska, SR and Eloe-Fadrosh, EA}, title = {Ecology and molecular targets of hypermutation in the global microbiome.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3076}, pmid = {34031405}, issn = {2041-1723}, mesh = {Bacteria/genetics ; Bacteriophages/physiology ; Biodiversity ; *Ecology ; Ecosystem ; Environmental Microbiology ; *Evolution, Molecular ; Genetic Variation ; Metagenome ; Microbiota/*genetics/*physiology ; *Mutation ; Phylogeny ; Retroelements ; }, abstract = {Changes in the sequence of an organism's genome, i.e., mutations, are the raw material of evolution. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as diversity-generating retroelements (DGRs). DGRs have been characterized from cultivated bacteria and bacteriophages, and perform error-prone reverse transcription leading to mutations being introduced in specific target genes. DGR loci were also identified in several metagenomes, but the ecological roles and evolutionary drivers of these DGRs remain poorly understood. Here, we analyze a dataset of >30,000 DGRs from public metagenomes, establish six major lineages of DGRs including three primarily encoded by phages and seemingly used to diversify host attachment proteins, and demonstrate that DGRs are broadly active and responsible for >10% of all amino acid changes in some organisms. Overall, these results highlight the constraints under which DGRs evolve, and elucidate several distinct roles these elements play in natural communities.}, } @article {pmid34030623, year = {2021}, author = {Méndez-Salazar, EO and Vázquez-Mellado, J and Casimiro-Soriguer, CS and Dopazo, J and Çubuk, C and Zamudio-Cuevas, Y and Francisco-Balderas, A and Martínez-Flores, K and Fernández-Torres, J and Lozada-Pérez, C and Pineda, C and Sánchez-González, A and Silveira, LH and Burguete-García, AI and Orbe-Orihuela, C and Lagunas-Martínez, A and Vazquez-Gomez, A and López-Reyes, A and Palacios-González, B and Martínez-Nava, GA}, title = {Taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism.}, journal = {Molecular medicine (Cambridge, Mass.)}, volume = {27}, number = {1}, pages = {50}, pmid = {34030623}, issn = {1528-3658}, mesh = {Biodiversity ; Computational Biology/methods ; *Dysbiosis ; *Gastrointestinal Microbiome ; Gout/etiology/*metabolism/pathology ; Humans ; *Metagenome ; *Metagenomics/methods ; Protein Interaction Mapping ; Protein Interaction Maps ; Uric Acid/*metabolism ; }, abstract = {OBJECTIVE: To evaluate the taxonomic composition of the gut microbiome in gout patients with and without tophi formation, and predict bacterial functions that might have an impact on urate metabolism.

METHODS: Hypervariable V3-V4 regions of the bacterial 16S rRNA gene from fecal samples of gout patients with and without tophi (n = 33 and n = 25, respectively) were sequenced and compared to fecal samples from 53 healthy controls. We explored predictive functional profiles using bioinformatics in order to identify differences in taxonomy and metabolic pathways.

RESULTS: We identified a microbiome characterized by the lowest richness and a higher abundance of Phascolarctobacterium, Bacteroides, Akkermansia, and Ruminococcus_gnavus_group genera in patients with gout without tophi when compared to controls. The Proteobacteria phylum and the Escherichia-Shigella genus were more abundant in patients with tophaceous gout than in controls. Fold change analysis detected nine genera enriched in healthy controls compared to gout groups (Bifidobacterium, Butyricicoccus, Oscillobacter, Ruminococcaceae_UCG_010, Lachnospiraceae_ND2007_group, Haemophilus, Ruminococcus_1, Clostridium_sensu_stricto_1, and Ruminococcaceae_UGC_013). We found that the core microbiota of both gout groups shared Bacteroides caccae, Bacteroides stercoris ATCC 43183, and Bacteroides coprocola DSM 17136. These bacteria might perform functions linked to one-carbon metabolism, nucleotide binding, amino acid biosynthesis, and purine biosynthesis. Finally, we observed differences in key bacterial enzymes involved in urate synthesis, degradation, and elimination.

CONCLUSION: Our findings revealed that taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism.}, } @article {pmid34030239, year = {2021}, author = {Qiao, L and Liu, X and Zhang, S and Zhang, L and Li, X and Hu, X and Zhao, Q and Wang, Q and Yu, C}, title = {Distribution of the microbial community and antibiotic resistance genes in farmland surrounding gold tailings: A metagenomics approach.}, journal = {The Science of the total environment}, volume = {779}, number = {}, pages = {146502}, doi = {10.1016/j.scitotenv.2021.146502}, pmid = {34030239}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; China ; Drug Resistance, Microbial/genetics ; Farms ; Gold ; Metagenomics ; *Metals, Heavy/analysis ; *Microbiota ; *Soil Pollutants/analysis ; }, abstract = {Metal mining has caused the accumulation of waste mine tailing dumps from abandoned mines. The pollution of farmlands surrounding metal tailings by heavy metals has been a long-recognized problem. However, the distribution of antibiotic resistance genes (ARGs) in tailings and the main factors influencing this distribution have rarely been reported. In this study, a metagenomics approach was used to investigate the microbial community and ARGs present in farmland surrounding gold tailings in northern China. The results showed that the main pollutants in the farmland were As, Pb, and Cd. Proteobacteria and Actinobacteria were the dominant phyla of microbes in farmlands surrounding gold tailings. A total of 75 ARGs with 327 ARG subtypes were detected in soil samples. Macrolide-, lincosaminide-, and streptogramin B resistant genes accounted for the majority of ARGs in this study, and Actinobacteria, Proteobacteria, and Acidobacteria were the hosts of most ARGs. Partial least squares path modeling revealed that the microbial community was the most influential driver moderating the distribution of soil ARGs near tailings, and heavy metals have direct and partially indirect effects on these ARGs. In contrast to previous analyses of ARGs, our study found that mobile gene elements had a minimal impact on ARGs. Overall, this study presents a complete ARG survey that sheds light on the distribution and fate of ARGs under heavy metal contamination in farmland around gold tailings.}, } @article {pmid34029816, year = {2021}, author = {Ramírez-Fernández, L and Orellana, LH and Johnston, ER and Konstantinidis, KT and Orlando, J}, title = {Diversity of microbial communities and genes involved in nitrous oxide emissions in Antarctic soils impacted by marine animals as revealed by metagenomics and 100 metagenome-assembled genomes.}, journal = {The Science of the total environment}, volume = {788}, number = {}, pages = {147693}, doi = {10.1016/j.scitotenv.2021.147693}, pmid = {34029816}, issn = {1879-1026}, mesh = {Animals ; Antarctic Regions ; *Metagenome ; Metagenomics ; *Microbiota ; Nitrous Oxide ; RNA, Ribosomal, 16S ; Soil ; Soil Microbiology ; }, abstract = {Antarctic soils generally have low temperatures and limited availability of liquid water and nutrients. However, animals can increase the nutrient availability of ice-free areas by transferring nutrients from marine to terrestrial ecosystems, mainly through their excreta. In this study, we employed shotgun metagenomics and population genome binning techniques to study the diversity of microbial communities in Antarctic soils impacted by marine pinnipeds and birds relative to soils with no evident animal presence. We obtained ~285,000 16S rRNA gene-carrying metagenomic reads representing ~60 phyla and 100 metagenome-assembled genomes (MAGs) representing eight phyla. Only nine of these 100 MAGs represented previously described species, revealing that these soils harbor extensive novel diversity. Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant phyla in all samples, with Rhodanobacter being one of the most abundant genera in the bird-impacted soils. Further, the relative abundance of genes related to denitrification was at least double in soils impacted by birds than soils without animal influence. These results advance our understanding of the microbial populations and their genes involved in nitrous oxide emissions in ice-free coastal Antarctic soils impacted by marine animals and reveal novel microbial diversity associated with these ecosystems.}, } @article {pmid34029658, year = {2021}, author = {Nodari, R and Drancourt, M and Barbieri, R}, title = {Paleomicrobiology of the human digestive tract: A review.}, journal = {Microbial pathogenesis}, volume = {157}, number = {}, pages = {104972}, doi = {10.1016/j.micpath.2021.104972}, pmid = {34029658}, issn = {1096-1208}, mesh = {Gastrointestinal Tract ; Humans ; *Metagenomics ; *Microbiota ; }, abstract = {The microbiota is a hot topic of research in medical microbiology, boosted by culturomics and metagenomics, with unanticipated knowledge outputs in physiology and pathology. Knowledge of the microbiota in ancient populations may therefore be of prime interest in understanding factors shaping the coevolution of the microbiota and populations. Studies on ancient human microbiomes can help us understand how the community of microorganisms presents in the oral cavity and the gut was shaped during the evolution of our species and what environmental, social or cultural changes may have changed it. This review cumulates and summarizes the discoveries in the field of the ancient human microbiota, focusing on the remains used as samples and techniques used to handle and analyze them.}, } @article {pmid34029428, year = {2021}, author = {Wang, P and Dong, Y and Jiao, J and Zuo, K and Han, C and Zhao, L and Ding, S and Yang, X and Chen, M and Li, J}, title = {Cigarette smoking status alters dysbiotic gut microbes in hypertensive patients.}, journal = {Journal of clinical hypertension (Greenwich, Conn.)}, volume = {23}, number = {7}, pages = {1431-1446}, pmid = {34029428}, issn = {1751-7176}, mesh = {*Cigarette Smoking ; Clostridiales ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; *Hypertension/epidemiology ; Tobacco Products ; }, abstract = {Smoking not only is one of the most important risk factors of hypertension (HTN), but also alters the composition of gut microbiota (GM) in previous studies. Although dysbiosis of GM has been implicated in HTN, how GM alters in patients with HTN under smoking status is still not clear. This study aimed to explore the difference in intestinal microflora among smokers with HTN (S-HTN), nonsmokers with HTN (NS-HTN), and smokers without HTN (S-CTR) and identify whether cigarette smoking led to disordered intestinal microbiota in patients with HTN. Metagenomic sequencing analysis of fecal specimens was conducted in nonsmokers without HTN (NS-CTR, n = 9), S-CTR (n = 9), NS-HTN (n = 18), and S-HTN (n = 23). Compared with S-CTR or NS-HTN, the GM in S-HTN was disordered, with lower microbial α-diversity and significant difference of β-diversity on axes as compared to S-CTR at genus and species level. The microbial enterotype in S-HTN was inclined to Prevotella-dominant type. Dramatic changes in the intestinal genera and species composition were observed in S-HTN, including reduced enrichment of Phycisphaera and Clostridium asparagiforme. Moreover, the intestinal function altered in S-HTN. Therefore, the findings of the present study revealed GM disorders in S-HTN and clarified the role of smoking in impairing the intestinal microbiome in HTN. Tobacco control is particularly important for improving GM in patients with HTN, and might be beneficial in preventing future cardiovascular events.}, } @article {pmid34028530, year = {2022}, author = {Shoemaker, WR and Chen, D and Garud, NR}, title = {Comparative Population Genetics in the Human Gut Microbiome.}, journal = {Genome biology and evolution}, volume = {14}, number = {1}, pages = {}, pmid = {34028530}, issn = {1759-6653}, mesh = {Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Genetics, Population ; Humans ; Metagenomics ; *Microbiota/genetics ; }, abstract = {Genetic variation in the human gut microbiome is responsible for conferring a number of crucial phenotypes like the ability to digest food and metabolize drugs. Yet, our understanding of how this variation arises and is maintained remains relatively poor. Thus, the microbiome remains a largely untapped resource, as the large number of coexisting species in the microbiome presents a unique opportunity to compare and contrast evolutionary processes across species to identify universal trends and deviations. Here we outline features of the human gut microbiome that, while not unique in isolation, as an assemblage make it a system with unparalleled potential for comparative population genomics studies. We consciously take a broad view of comparative population genetics, emphasizing how sampling a large number of species allows researchers to identify universal evolutionary dynamics in addition to new genes, which can then be leveraged to identify exceptional species that deviate from general patterns. To highlight the potential power of comparative population genetics in the microbiome, we reanalyze patterns of purifying selection across ∼40 prevalent species in the human gut microbiome to identify intriguing trends which highlight functional categories in the microbiome that may be under more or less constraint.}, } @article {pmid34026662, year = {2021}, author = {Chang, SC and Lin, SF and Chen, ST and Chang, PY and Yeh, YM and Lo, FS and Lu, JJ}, title = {Alterations of Gut Microbiota in Patients With Graves' Disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {663131}, pmid = {34026662}, issn = {2235-2988}, mesh = {Feces ; Firmicutes ; *Gastrointestinal Microbiome ; *Graves Disease ; Humans ; RNA, Ribosomal, 16S ; }, abstract = {Graves' disease (GD) is a systemic autoimmune disease characterized by hyperthyroidism. Evidence suggests that alterations to the gut microbiota may be involved in the development of autoimmune disorders. The aim of this study was to characterize the composition of gut microbiota in GD patients. Fecal samples were collected from 55 GD patients and 48 healthy controls. Using 16S rRNA gene amplification and sequencing, the overall bacterial richness and diversity were found to be similar between GD patients and healthy controls. However, principal coordinate analysis and partial least squares-discriminant analysis showed that the overall gut microbiota composition was significantly different (ANOSIM; p < 0.001). The linear discriminant analysis effect size revealed that Firmicutes phylum decreased in GD patients, with a corresponding increase in Bacteroidetes phylum compared to healthy controls. In addition, the families Prevotellaceae, and Veillonellaceae and the genus Prevotella_9 were closely associated with GD patients, while the families Lachnospiraceae and Ruminococcaceae and the genera Faecalibacterium, Lachnospira, and Lachnospiraceae NK4A136 were associated with healthy controls. Metagenomic profiles analysis yielded 22 statistically significant bacterial taxa: 18 taxa were increased and 4 taxa were decreased. Key bacterial taxa with different abundances between the two groups were strongly correlated with GD-associated clinical parameters using Spearman's correlation analysis. Importantly, the discriminant model based on predominant microbiota could effectively distinguish GD patients from healthy controls (AUC = 0.825). Thus, the gut microbiota composition between GD patients and healthy controls is significantly difference, indicating that gut microbiota may play a role in the pathogenesis of GD. Further studies are needed to fully elucidate the role of gut microbiota in the development of GD.}, } @article {pmid34024606, year = {2021}, author = {Song, Y and Li, F and Fischer-Tlustos, AJ and Neves, ALA and He, Z and Steele, MA and Guan, LL}, title = {Metagenomic analysis revealed the individualized shift in ileal microbiome of neonatal calves in response to delaying the first colostrum feeding.}, journal = {Journal of dairy science}, volume = {104}, number = {8}, pages = {8783-8797}, doi = {10.3168/jds.2020-20068}, pmid = {34024606}, issn = {1525-3198}, mesh = {Animals ; Animals, Newborn ; Cattle ; *Colostrum ; Female ; Ileum ; Male ; Metagenome ; *Microbiota ; Pregnancy ; }, abstract = {The aim of this study was to explore the effect of colostrum feeding time on the ileal microbiome of neonatal calves. In this study, 22 male Holstein calves were randomly assigned to different colostrum feeding time treatments: after birth (at 45 min, n = 7); at 6 h after birth (n = 8); and at 12 h after birth (TRT12h; n = 7). At 51 h after birth, calves were killed and ileum digesta was collected for microbiome analysis using shotgun metagenomic sequencing. Bacteria, archaea, eukaryotes, and viruses were identified from the ileum microbiome. For the bacteriome, Firmicutes and Proteobacteria were the predominant phyla, and Escherichia, Streptococcus, Lactobacillus were the 3 most abundant genera. For the archaeal community, Euryarchaeota and Crenarchaeota were the 2 major phyla, and Methanosarcina, Methanobrevibacter, and Methanocorpusculum were the 3 most abundant genera. In total, 116 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified from the ileal microbiome, with "biosynthesis of vancomycin group antibiotics," "biosynthesis of ansamycins," "valine, leucine, and isoleucine biosynthesis," "ribosome," and "d-alanine metabolism" as the top 5 functions. When the ileal microbiomes were compared among the 3 treatments, the relative abundance of Enterococcus was higher in TRT12h calves, suggesting that calves may have a higher abundance of opportunistic pathogens when the feeding of colostrum is delayed for 12 h. Moreover, among all KEGG pathways, the enriched "taurine and hypotaurine metabolism" (KO00430) pathway was identified in the ileal microbiome of TRT12h calves; however, future studies are needed to understand the effect on the host. Additionally, 2 distinct ileal microbial profiles were identified across all samples, indicating that that host factors may play a significant role in driving varied microbiome changes in response to colostrum feeding time. Whether such microbiome shifts affect long-term gut function and calf performance warrants future studies.}, } @article {pmid34022966, year = {2021}, author = {Matheus Carnevali, PB and Lavy, A and Thomas, AD and Crits-Christoph, A and Diamond, S and Méheust, R and Olm, MR and Sharrar, A and Lei, S and Dong, W and Falco, N and Bouskill, N and Newcomer, ME and Nico, P and Wainwright, H and Dwivedi, D and Williams, KH and Hubbard, S and Banfield, JF}, title = {Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {121}, pmid = {34022966}, issn = {2049-2618}, mesh = {Carbon ; *Microbiota/genetics ; Nitrogen ; Rivers ; *Soil ; }, abstract = {BACKGROUND: Biogeochemical exports from watersheds are modulated by the activity of microorganisms that function over micron scales. Here, we tested the hypothesis that meander-bound regions share a core microbiome and exhibit patterns of metabolic potential that broadly predict biogeochemical processes in floodplain soils along a river corridor.

RESULTS: We intensively sampled the microbiomes of floodplain soils located in the upper, middle, and lower reaches of the East River, Colorado. Despite the very high microbial diversity and complexity of the soils, we reconstructed 248 quality draft genomes representative of subspecies. Approximately one third of these bacterial subspecies was detected across all three locations at similar abundance levels, and ~ 15% of species were detected in two consecutive years. Within the meander-bound floodplains, we did not detect systematic patterns of gene abundance based on sampling position relative to the river. However, across meanders, we identified a core floodplain microbiome that is enriched in capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur. Given this, we conducted a transcriptomic analysis of the middle floodplain. In contrast to predictions made based on the prominence of gene inventories, the most highly transcribed genes were relatively rare amoCAB and nxrAB (for nitrification) genes, followed by genes involved in methanol and formate oxidation, and nitrogen and CO2 fixation. Within all three meanders, low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction. Overall, the results emphasize the importance of sulfur, one-carbon and nitrogen compound metabolism in soils of the riparian corridor.

CONCLUSIONS: The disparity between the scale of a microbial cell and the scale of a watershed currently limits the development of genomically informed predictive models describing watershed biogeochemical function. Meander-bound floodplains appear to serve as scaling motifs that predict aggregate capacities for biogeochemical transformations, providing a foundation for incorporating riparian soil microbiomes in watershed models. Widely represented genetic capacities did not predict in situ activity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change. Video abstract.}, } @article {pmid34021896, year = {2021}, author = {Sharma, R and Kumar, A and Singh, N and Sharma, K}, title = {16S rRNA gene profiling of rhizospheric microbial community of Eichhornia crassipes.}, journal = {Molecular biology reports}, volume = {48}, number = {5}, pages = {4055-4064}, pmid = {34021896}, issn = {1573-4978}, mesh = {Bacteria/genetics ; Bacteroidetes/genetics ; Biodiversity ; Eichhornia/*genetics ; Genes, rRNA/genetics ; Metagenome ; Microbiota/*genetics ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/*genetics ; Rhizosphere ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {The rhizosphere of a plant is an important interface for the plant-microbe interaction that plays a significant role in the uptake and removal of heavy metal from contaminated sites. Eichhornia crassipes is a free-floating macrophyte and a well-known metal hyperaccumulator. It is a promising plant, which harbors a diverse microbial community in its rhizosphere. Therefore it is hypothesized that it can be a good habitat for microorganisms that supports plant growth and increases its phytoremediation potential. The rhizospheric DNA was extracted from the procured plant samples. The library was prepared and sequenced using the Illumina platform. 16S rRNA data from the Next Generation Sequencing (NGS) platform was analyzed using the QIIME software package. Alpha diversity was estimated from statistical indices i.e. Shannon index, Chao1 index, and observed species. The rarefaction plots, rank abundance curve, krona graph, and heat map were generated to study the rhizospheric community in detail. Metagenome consisted of 225,408 flash reads, 185,008 non-chimeric sequences with 17,578 Operational Taxonomic Units (OTU's), and 4622 OTU's without singletons. The data of present study are available at NCBI Bioproject (PRJNA631882). The taxonomic analysis of OTU's showed that the sequences belonged to major Phyla revealing the dominance of Proteobacteria, Bacteroidetes, Cyanobacteria, and Verrucomicrobia. The most abundant Genera in the sampled rhizosphere recorded were Thiothrix and Flavobacterium.}, } @article {pmid34021225, year = {2021}, author = {Karnachuk, OV and Rusanov, II and Panova, IA and Grigoriev, MA and Zyusman, VS and Latygolets, EA and Kadyrbaev, MK and Gruzdev, EV and Beletsky, AV and Mardanov, AV and Pimenov, NV and Ravin, NV}, title = {Microbial sulfate reduction by Desulfovibrio is an important source of hydrogen sulfide from a large swine finishing facility.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {10720}, pmid = {34021225}, issn = {2045-2322}, mesh = {Animals ; Bacteria/metabolism ; *Biotransformation ; Desulfovibrio/*metabolism ; Environmental Microbiology ; Environmental Monitoring ; Farms ; Hydrogen Sulfide/analysis/*metabolism ; *Microbiota ; Soil/chemistry ; Soil Microbiology ; Sulfates/analysis/*metabolism ; Swine ; }, abstract = {There is still a lack of understanding of H2S formation in agricultural waste, which leads to poor odour prevention and control. Microbial sulfate reduction is a major process contributing to sulfide formation in natural and technogenic environments with high sulfate and low oxygen concentration. Agricultural waste can be considered a low-sulfate system with no obvious input of oxidised sulfur compounds. The purpose of this study was to characterise a microbial community participating in H2S production and estimate the microbial sulfate reduction rate (SRR) in manure slurry from a large-scale swine finishing facility in Western Siberia. In a series of manure slurry microcosms, we identified bacterial consortia by 16S rRNA gene profiling and metagenomic analysis and revealed that sulfate-reducing Desulfovibrio were key players responsible for H2S production. The SRR measured with radioactive sulfate in manure slurry was high and comprised 7.25 nmol S cm[-3] day[-1]. Gypsum may be used as a solid-phase electron acceptor for sulfate reduction. Another plausible source of sulfate is a swine diet, which often contains supplements in the form of sulfates, including lysine sulfate. Low-sulfur diet, manure treatment with iron salts, and avoiding gypsum bedding are possible ways to mitigate H2S emissions from swine manure.}, } @article {pmid34021204, year = {2021}, author = {Lima, KM and Davis, RR and Liu, SY and Greenhalgh, DG and Tran, NK}, title = {Longitudinal profiling of the burn patient cutaneous and gastrointestinal microbiota: a pilot study.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {10667}, pmid = {34021204}, issn = {2045-2322}, support = {P30 CA093373/CA/NCI NIH HHS/United States ; S10 OD010786/OD/NIH HHS/United States ; }, mesh = {Adult ; Aged ; Bacterial Infections ; Biodiversity ; Burns/complications/*epidemiology/therapy ; Computational Biology ; Female ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Skin/*microbiology ; }, abstract = {Sepsis is a leading cause of morbidity and mortality in patients that have sustained a severe burn injury. Early detection and treatment of infections improves outcomes and understanding changes in the host microbiome following injury and during treatment may aid in burn care. The loss of functional barriers, systemic inflammation, and commensal community perturbations all contribute to a burn patient's increased risk of infection. We sampled 10 burn patients to evaluate cutaneous microbial populations on the burn wound and corresponding spared skin on days 0, 3, 7, 14, 21, and 28 post-intensive care unit admission. In addition, skin samples were paired with perianal and rectal locations to evaluate changes in the burn patient gut microbiome following injury and treatment. We found significant (P = 0.011) reduction in alpha diversity on the burn wound compared to spared skin throughout the sampling period as well as reduction in common skin commensal bacteria such as Propionibacterium acnes and Staphylococcus epidermitis. Compared to healthy volunteers (n = 18), the burn patient spared skin also exhibited a significant reduction in alpha diversity (P = 0.001). Treatments such as systemic or topical antibiotic administration, skin grafting, and nutritional formulations also impact diversity and community composition at the sampling locations. When evaluating each subject individually, an increase in relative abundance of taxa isolated clinically by bacterial culture could be seen in 5/9 infections detected among the burn patient cohort.}, } @article {pmid34021052, year = {2021}, author = {Hahn, A and Burrell, A and Chaney, H and Sami, I and Koumbourlis, AC and Freishtat, RJ and Zemanick, ET and Louie, S and Crandall, KA}, title = {Importance of beta-lactam pharmacokinetics and pharmacodynamics on the recovery of microbial diversity in the airway of persons with cystic fibrosis.}, journal = {Journal of investigative medicine : the official publication of the American Federation for Clinical Research}, volume = {69}, number = {7}, pages = {1350-1359}, pmid = {34021052}, issn = {1708-8267}, support = {UL1 TR001876/TR/NCATS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacokinetics/therapeutic use ; Child ; *Cystic Fibrosis/drug therapy ; Drug Resistance, Bacterial ; Humans ; Microbial Sensitivity Tests ; *Microbiota ; Prospective Studies ; Respiratory System/*microbiology ; *beta-Lactams/pharmacokinetics/therapeutic use ; }, abstract = {Cystic fibrosis (CF) is a chronic lung disease characterized by acute pulmonary exacerbations (PExs) that are frequently treated with antibiotics. The impact of antibiotics on airway microbial diversity remains a critical knowledge gap. We sought to define the association between beta-lactam pharmacokinetic (PK) and pharmacodynamic target attainment on richness and alpha diversity. Twenty-seven children <18 years of age with CF participated in the prospective study. Airway samples were collected at hospital admission for PEx, end of antibiotic treatment (Tr), and >1 month in follow-up (FU). Metagenomic sequencing was performed to determine richness, alpha diversity, and the presence of antibiotic resistance genes. Free plasma beta-lactam levels were measured, and PK modeling was performed to determine time above the minimum inhibitory concentration (fT>MIC). 52% of study subjects had sufficient fT>MIC for optimal bacterial killing. There were no significant differences in demographics or PEx characteristics, except for F508del homozygosity. No significant differences were noted in richness or alpha diversity at individual time points, and both groups experienced a decrease in richness and alpha diversity at Tr compared with PEx. However, alpha diversity remained decreased at FU compared with PEx in those with sufficient fT>MIC but increased in those with insufficient fT>MIC (Shannon -0.222 vs +0.452, p=0.031, and inverse Simpson -1.376 vs +1.388, p=0.032). Fluoroquinolone resistance was also more frequently detected in those with insufficient fT>MIC (log2 fold change (log2FC) 2.29, p=0.025). These findings suggest sufficient beta-lactam fT>MIC is associated with suppressed recovery of alpha diversity following the antibiotic exposure period.}, } @article {pmid34020448, year = {2021}, author = {Koponen, KK and Salosensaari, A and Ruuskanen, MO and Havulinna, AS and Männistö, S and Jousilahti, P and Palmu, J and Salido, R and Sanders, K and Brennan, C and Humphrey, GC and Sanders, JG and Meric, G and Cheng, S and Inouye, M and Jain, M and Niiranen, TJ and Valsta, LM and Knight, R and Salomaa, VV}, title = {Associations of healthy food choices with gut microbiota profiles.}, journal = {The American journal of clinical nutrition}, volume = {114}, number = {2}, pages = {605-616}, pmid = {34020448}, issn = {1938-3207}, support = {P42 ES010337/ES/NIEHS NIH HHS/United States ; R01 ES027595/ES/NIEHS NIH HHS/United States ; R01ES027595/GF/NIH HHS/United States ; }, mesh = {Adult ; Aged ; Bacteria/classification ; *Choice Behavior ; Diet Surveys ; *Diet, Healthy ; Female ; *Food ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; }, abstract = {BACKGROUND: Diet has a major influence on the human gut microbiota, which has been linked to health and disease. However, epidemiological studies on associations of a healthy diet with the microbiota utilizing a whole-diet approach are still scant.

OBJECTIVES: To assess associations between healthy food choices and human gut microbiota composition, and to determine the strength of association with functional potential.

METHODS: This population-based study sample consisted of 4930 participants (ages 25-74; 53% women) in the FINRISK 2002 study. Intakes of recommended foods were assessed using a food propensity questionnaire, and responses were transformed into healthy food choices (HFC) scores. Microbial diversity (alpha diversity) and compositional differences (beta diversity) and their associations with the HFC score and its components were assessed using linear regression. Multiple permutational multivariate ANOVAs were run from whole-metagenome shallow shotgun-sequenced samples. Associations between specific taxa and HFC were analyzed using linear regression. Functional associations were derived from Kyoto Encyclopedia of Genes and Genomes orthologies with linear regression models.

RESULTS: Both microbial alpha diversity (β/SD, 0.044; SE, 6.18 × 10-5; P = 2.21 × 10-3) and beta diversity (R2, 0.12; P ≤ 1.00 × 10-3) were associated with the HFC score. For alpha diversity, the strongest associations were observed for fiber-rich breads, poultry, fruits, and low-fat cheeses (all positive). For beta diversity, the most prominent associations were observed for vegetables, followed by berries and fruits. Genera with fiber-degrading and SCFA-producing capacities were positively associated with the HFC score. The HFC score was associated positively with functions such as SCFA metabolism and synthesis, and inversely with functions such as fatty acid biosynthesis and the sulfur relay system.

CONCLUSIONS: Our results from a large, population-based survey confirm and extend findings of other, smaller-scale studies that plant- and fiber-rich dietary choices are associated with a more diverse and compositionally distinct microbiota, and with a greater potential to produce SCFAs.}, } @article {pmid34020306, year = {2021}, author = {Mohapatra, M and Yadav, R and Rajput, V and Dharne, MS and Rastogi, G}, title = {Metagenomic analysis reveals genetic insights on biogeochemical cycling, xenobiotic degradation, and stress resistance in mudflat microbiome.}, journal = {Journal of environmental management}, volume = {292}, number = {}, pages = {112738}, doi = {10.1016/j.jenvman.2021.112738}, pmid = {34020306}, issn = {1095-8630}, mesh = {Extracellular Polymeric Substance Matrix ; Geologic Sediments ; India ; *Metagenome ; *Microbiota/genetics ; Xenobiotics ; }, abstract = {Mudflats are highly productive coastal ecosystems that are dominated by halophytic vegetation. In this study, the mudflat sediment microbiome was investigated from Nalabana Island, located in a brackish water coastal wetland of India; Chilika, based on the MinION shotgun metagenomic analysis. Bacterial, archaeal, and fungal communities were mostly composed of Proteobacteria (38.3%), Actinobacteria (20.7%), Euryarchaeota (76.1%), Candidatus Bathyarchaeota (6.8%), Ascomycota (47.2%), and Basidiomycota (22.0%). Bacterial and archaeal community composition differed significantly between vegetated mudflat and un-vegetated bulk sediments. Carbon, nitrogen, sulfur metabolisms, oxidative phosphorylation, and xenobiotic biodegradation were the most common microbial functionalities in the mudflat metagenomes. Furthermore, genes involved in oxidative stresses, osmotolerance, secondary metabolite synthesis, and extracellular polymeric substance synthesis revealed adaptive mechanisms of the microbiome in mudflat habitat. Mudflat metagenome also revealed genes involved in the plant growth and development, suggesting that microbial communities could aid halophytic vegetation by providing tolerance to the abiotic stresses in a harsh mudflat environment. Canonical correspondence analysis and co-occurrence network revealed that both biotic (vegetation and microbial interactions) and abiotic factors played important role in shaping the mudflat microbiome composition. Among abiotic factors, pH accounted for the highest variance (20.10%) followed by available phosphorus (19.73%), total organic carbon (9.94%), salinity (8.28%), sediment texture (sand) (6.37%) and available nitrogen (5.53%) in the mudflat microbial communities. Overall, this first metagenomic study provided a comprehensive insight on the community structure, potential ecological interactions, and genetic potential of the mudflat microbiome in context to the cycling of organic matter, xenobiotic biodegradation, stress resistance, and in providing the ecological fitness to halophytes. These ecosystem services of the mudflat microbiome must be considered in the conservation and management plan of coastal wetlands. This study also advanced our understanding of fungal diversity which is understudied from the coastal lagoon ecosystems.}, } @article {pmid34017611, year = {2021}, author = {Costa, VA and Mifsud, JCO and Gilligan, D and Williamson, JE and Holmes, EC and Geoghegan, JL}, title = {Metagenomic sequencing reveals a lack of virus exchange between native and invasive freshwater fish across the Murray-Darling Basin, Australia.}, journal = {Virus evolution}, volume = {7}, number = {1}, pages = {veab034}, pmid = {34017611}, issn = {2057-1577}, abstract = {Biological invasions are among the biggest threats to freshwater biodiversity. This is increasingly relevant in the Murray-Darling Basin, Australia, particularly since the introduction of the common carp (Cyprinus carpio). This invasive species now occupies up to ninety per cent of fish biomass, with hugely detrimental impacts on native fauna and flora. To address the ongoing impacts of carp, cyprinid herpesvirus 3 (CyHV-3) has been proposed as a potentially effective biological control agent. Crucially, however, it is unknown whether CyHV-3 and other cyprinid herpesviruses already exist in the Murray-Darling. Further, little is known about those viruses that naturally occur in wild freshwater fauna, and the frequency with which these viruses jump species boundaries. To document the evolution and diversity of freshwater fish viromes and better understand the ecological context to the proposed introduction of CyHV-3, we performed a meta-transcriptomic viral survey of invasive and native fish across the Murray-Darling Basin, covering over 2,200 km of the river system. Across a total of thirty-six RNA libraries representing ten species, we failed to detect CyHV-3 nor any closely related viruses. Rather, meta-transcriptomic analysis identified eighteen vertebrate-associated viruses that could be assigned to the Arenaviridae, Astroviridae, Bornaviridae, Caliciviridae, Coronaviridae, Chuviridae, Flaviviridae, Hantaviridae, Hepeviridae, Paramyxoviridae, Picornaviridae, Poxviridae, Reoviridae and Rhabdoviridae families, and a further twenty-seven that were deemed to be associated with non-vertebrate hosts. Notably, we revealed a marked lack of viruses that are shared among invasive and native fish sampled here, suggesting that there is little virus transmission from common carp to native fish species, despite co-existing for over fifty years. Overall, this study provides the first data on the viruses naturally circulating in a major river system and supports the notion that fish harbour a large diversity of viruses with often deep evolutionary histories.}, } @article {pmid34017060, year = {2021}, author = {Kim, JH and Kim, K and Kim, W}, title = {Gut microbiota restoration through fecal microbiota transplantation: a new atopic dermatitis therapy.}, journal = {Experimental & molecular medicine}, volume = {53}, number = {5}, pages = {907-916}, pmid = {34017060}, issn = {2092-6413}, mesh = {Animals ; Antibodies/pharmacology ; Biomarkers ; Dermatitis, Atopic/etiology/*therapy ; Disease Management ; Disease Models, Animal ; Disease Susceptibility ; Fatty Acids, Volatile/metabolism ; *Fecal Microbiota Transplantation/methods ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/drug effects/immunology ; Immunoglobulin E/blood/immunology ; Immunomodulation ; Lymphocyte Count ; Metagenome ; Metagenomics ; Mice ; T-Lymphocyte Subsets/immunology/metabolism ; Treatment Outcome ; }, abstract = {The pathogenesis of atopic dermatitis (AD) involves complex factors, including gut microbiota and immune modulation, which remain poorly understood. The aim of this study was to restore gut microbiota via fecal microbiota transplantation (FMT) to ameliorate AD in mice. FMT was performed using stool from donor mice. The gut microbiota was characterized via 16S rRNA sequencing and analyzed using Quantitative Insights into Microbial Ecology 2 with the DADA2 plugin. Gut metabolite levels were determined by measuring fecal short-chain fatty acid (SCFA) contents. AD-induced allergic responses were evaluated by analyzing blood parameters (IgE levels and eosinophil percentage, eosinophil count, basophil percentage, and monocyte percentage), the levels of Th1 and Th2 cytokines, dermatitis score, and the number of mast cells in the ileum and skin tissues. Calprotectin level was measured to assess gut inflammation after FMT. FMT resulted in the restoration of gut microbiota to the donor state and increases in the levels of SCFAs as gut metabolites. In addition, FMT restored the Th1/Th2 balance, modulated Tregs through gut microbiota, and reduced IgE levels and the numbers of mast cells, eosinophils, and basophils. FMT is associated with restoration of gut microbiota and immunologic balance (Th1/Th2) along with suppression of AD-induced allergic responses and is thus a potential new therapy for AD.}, } @article {pmid34014265, year = {2021}, author = {Quiza, L and Tremblay, J and Greer, CW and Hemmingsen, SM and St-Arnaud, M and Pozniak, CJ and Yergeau, E}, title = {Rhizosphere shotgun metagenomic analyses fail to show differences between ancestral and modern wheat genotypes grown under low fertilizer inputs.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {6}, pages = {}, doi = {10.1093/femsec/fiab071}, pmid = {34014265}, issn = {1574-6941}, mesh = {Fertilizers ; Genotype ; Metagenome ; *Microbiota ; *Rhizosphere ; Soil ; Soil Microbiology ; Triticum ; }, abstract = {It is thought that modern wheat genotypes have lost their capacity to associate with soil microbes that would help them acquire nutrients from the soil. To test this hypothesis, ten ancestral and modern wheat genotypes were seeded in a field experiment under low fertilization conditions. The rhizosphere soil was collected, its DNA extracted and submitted to shotgun metagenomic sequencing. In contrast to our hypothesis, there was no significant difference in the global rhizosphere metagenomes of the different genotypes, and this held true when focusing the analyses on specific taxonomic or functional categories of genes. Some genes were significantly more abundant in the rhizosphere of one genotype or another, but they comprised only a small portion of the total genes identified and did not affect the global rhizosphere metagenomes. Our study shows for the first time that the rhizosphere metagenome of wheat is stable across a wide variety of genotypes when growing under nutrient poor conditions.}, } @article {pmid34012005, year = {2021}, author = {O'Sullivan, DM and Doyle, RM and Temisak, S and Redshaw, N and Whale, AS and Logan, G and Huang, J and Fischer, N and Amos, GCA and Preston, MD and Marchesi, JR and Wagner, J and Parkhill, J and Motro, Y and Denise, H and Finn, RD and Harris, KA and Kay, GL and O'Grady, J and Ransom-Jones, E and Wu, H and Laing, E and Studholme, DJ and Benavente, ED and Phelan, J and Clark, TG and Moran-Gilad, J and Huggett, JF}, title = {An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {10590}, pmid = {34012005}, issn = {2045-2322}, support = {BBS/E/F/000PR10349/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/N010469/1//MRC UK/ ; MR/R020973/1/MRC_/Medical Research Council/United Kingdom ; BBS/E/F/000PR10348/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/M01360X/1/MRC_/Medical Research Council/United Kingdom ; MR/K000551/1//MRC UK/ ; MR/N010469/1/MRC_/Medical Research Council/United Kingdom ; MR/R020973/1//MRC UK/ ; MR/M01360X/1//MRC UK/ ; BB/R013063/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/N013956/1//UK Antimicrobial Resistance Cross Council Initiative/ ; BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/N013956/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Computational Biology ; *Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Despite the advent of whole genome metagenomics, targeted approaches (such as 16S rRNA gene amplicon sequencing) continue to be valuable for determining the microbial composition of samples. Amplicon microbiome sequencing can be performed on clinical samples from a normally sterile site to determine the aetiology of an infection (usually single pathogen identification) or samples from more complex niches such as human mucosa or environmental samples where multiple microorganisms need to be identified. The methodologies are frequently applied to determine both presence of micro-organisms and their quantity or relative abundance. There are a number of technical steps required to perform microbial community profiling, many of which may have appreciable precision and bias that impacts final results. In order for these methods to be applied with the greatest accuracy, comparative studies across different laboratories are warranted. In this study we explored the impact of the bioinformatic approaches taken in different laboratories on microbiome assessment using 16S rRNA gene amplicon sequencing results. Data were generated from two mock microbial community samples which were amplified using primer sets spanning five different variable regions of 16S rRNA genes. The PCR-sequencing analysis included three technical repeats of the process to determine the repeatability of their methods. Thirteen laboratories participated in the study, and each analysed the same FASTQ files using their choice of pipeline. This study captured the methods used and the resulting sequence annotation and relative abundance output from bioinformatic analyses. Results were compared to digital PCR assessment of the absolute abundance of each target representing each organism in the mock microbial community samples and also to analyses of shotgun metagenome sequence data. This ring trial demonstrates that the choice of bioinformatic analysis pipeline alone can result in different estimations of the composition of the microbiome when using 16S rRNA gene amplicon sequencing data. The study observed differences in terms of both presence and abundance of organisms and provides a resource for ensuring reproducible pipeline development and application. The observed differences were especially prevalent when using custom databases and applying high stringency operational taxonomic unit (OTU) cut-off limits. In order to apply sequencing approaches with greater accuracy, the impact of different analytical steps needs to be clearly delineated and solutions devised to harmonise microbiome analysis results.}, } @article {pmid34009962, year = {2021}, author = {Bhagwat, G and Carbery, M and Anh Tran, TK and Grainge, I and O'Connor, W and Palanisami, T}, title = {Fingerprinting Plastic-Associated Inorganic and Organic Matter on Plastic Aged in the Marine Environment for a Decade.}, journal = {Environmental science & technology}, volume = {55}, number = {11}, pages = {7407-7417}, doi = {10.1021/acs.est.1c00262}, pmid = {34009962}, issn = {1520-5851}, mesh = {Bacteria/genetics ; Environmental Monitoring ; *Microbiota ; Plastics ; Polyethylene ; Seawater ; *Water Pollutants, Chemical/analysis ; }, abstract = {The long-term aging of plastic leads to weathering and biofouling that can influence the behavior and fate of plastic in the marine environment. This is the first study to fingerprint the contaminant profiles and bacterial communities present in plastic-associated inorganic and organic matter (PIOM) isolated from 10 year-aged plastic. Plastic sleeves were sampled from an oyster aquaculture farm and the PIOM was isolated from the intertidal, subtidal, and sediment-buried segments to investigate the levels of metal(loid)s, polyaromatic hydrocarbons (PAHs), per-fluoroalkyl substances (PFAS) and explore the microbial community composition. Results indicated that the PIOM present on long-term aged high-density polyethylene plastic harbored high concentrations of metal(loid)s, PAHs, and PFAS. Metagenomic analysis revealed that the bacterial composition in the PIOM differed by habitat type, which consisted of potentially pathogenic taxa including Vibrio, Shewanella, and Psychrobacter. This study provides new insights into PIOM as a potential sink for hazardous environmental contaminants and its role in enhancing the vector potential of plastic. Therefore, we recommend the inclusion of PIOM analysis in current biomonitoring regimes and that plastics be used with caution in aquaculture settings to safeguard valuable food resources, particularly in areas of point-source contamination.}, } @article {pmid34008933, year = {2021}, author = {Ciocan, D and Cassard, AM and Becquemont, L and Verstuyft, C and Voican, CS and El Asmar, K and Colle, R and David, D and Trabado, S and Feve, B and Chanson, P and Perlemuter, G and Corruble, E}, title = {Blood microbiota and metabolomic signature of major depression before and after antidepressant treatment: a prospective case-control study.}, journal = {Journal of psychiatry & neuroscience : JPN}, volume = {46}, number = {3}, pages = {E358-E368}, pmid = {34008933}, issn = {1488-2434}, mesh = {Adult ; Antidepressive Agents/pharmacology/*therapeutic use ; Bacteria/classification/drug effects ; Blood/drug effects/*microbiology ; Brain-Gut Axis/*drug effects ; Carbohydrate Metabolism/drug effects ; Case-Control Studies ; Depressive Disorder, Major/blood/complications/*drug therapy/*microbiology ; Dysbiosis/blood/complications/metabolism/*microbiology ; Female ; Gastrointestinal Microbiome/drug effects ; Humans ; Lipid Metabolism/drug effects ; Male ; Metabolome/*drug effects ; Microbiota/*drug effects ; }, abstract = {BACKGROUND: The microbiota interacts with the brain through the gut-brain axis, and a distinct dysbiosis may lead to major depressive episodes. Bacteria can pass through the gut barrier and be found in the blood. Using a multiomic approach, we investigated whether a distinct blood microbiome and metabolome was associated with major depressive episodes, and how it was modulated by treatment.

METHODS: In this case-control multiomic study, we analyzed the blood microbiome composition, inferred bacterial functions and metabolomic profile of 56 patients experiencing a current major depressive episode and 56 matched healthy controls, before and after treatment, using 16S rDNA sequencing and liquid chromatography coupled to tandem mass spectrometry.

RESULTS: The baseline blood microbiome in patients with a major depressive episode was distinct from that of healthy controls (patients with a major depressive episode had a higher proportion of Janthinobacterium and lower levels of Neisseria) and changed after antidepressant treatment. Predicted microbiome functions confirmed by metabolomic profiling showed that patients who were experiencing a major depressive episode had alterations in the cyanoamino acid pathway at baseline. High baseline levels of Firmicutes and low proportions of Bosea and Tetrasphaera were associated with response to antidepressant treatment. Based on inferred baseline metagenomic profiles, bacterial pathways that were significantly associated with treatment response were related to xenobiotics, amino acids, and lipid and carbohydrate metabolism, including tryptophan and drug metabolism. Metabolomic analyses showed that plasma tryptophan levels are independently associated with response to antidepressant treatment.

LIMITATIONS: Our study has some limitations, including a lack of information on blood microbiome origin and the lack of a validation cohort to confirm our results.

CONCLUSION: Patients with depression have a distinct blood microbiome and metabolomic signature that changes after treatment. Dysbiosis could be a new therapeutic target and prognostic tool for the treatment of patients who are experiencing a major depressive episode.}, } @article {pmid34008889, year = {2021}, author = {Xia, Y and Wang, J and Fang, X and Dou, T and Han, L and Yang, C}, title = {Combined analysis of metagenomic data revealed consistent changes of gut microbiome structure and function in inflammatory bowel disease.}, journal = {Journal of applied microbiology}, volume = {131}, number = {6}, pages = {3018-3031}, doi = {10.1111/jam.15154}, pmid = {34008889}, issn = {1365-2672}, support = {81603187//National Natural Science Foundation of China/ ; 2017YFC1700200//National Key Research and Development Program of China/ ; 2017YFC1702000//National Key Research and Development Program of China/ ; DUT18LK39//Fundamental Research Funds for the Central Universities/ ; DUT18RC(4)057//Fundamental Research Funds for the Central Universities/ ; DUT20RC(4)013//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Clostridiales ; Escherichia coli/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; *Inflammatory Bowel Diseases ; Metagenome ; }, abstract = {AIMS: To reveal the consistency and discrepancy in the gut microbial structure and function in inflammatory bowel disease (IBD) patients from different regions.

METHODS AND RESULTS: Gut microbes, antibiotic resistance genes (ARGs) and virulence factors genes (VFGs) were analysed using metagenome data from three cohorts. The abundance of Escherichia coli extensively increased in IBD patients, whereas Subdoligranulum unclassified decreased dramatically in IBD patients from three countries. Escherichia coli showed a positive correlation with multiple ARGs and VFGs in cohorts from China and the United States, including multidrug-related resistance genes and Capsule and LOS-related virulence factors genes. Escherichia coli biofilm synthesis pathways significantly enriched in IBD patients from three different regions. Notably, Subdoligranulum unclassified and Eubacterium hallii were negatively related to ARGs and VFGs.

CONCLUSIONS: Consistent changes of microbiome structure and function were observed in IBD patients from three different regions. As pathogenic bacteria, E. coli may accelerate IBD progression through encapsulation in biofilms by upregulating antibiotic resistance in Crohn's disease patients. Subdoligranulum unclassified and E. hallii may be beneficial for IBD patients and could serve as potential probiotics for IBD treatment.

This work dispels worries about the regional differences in gut microbial changes in IBD patients and provides useful guidance for more rational microbiome-based therapies.}, } @article {pmid34006865, year = {2021}, author = {Tierney, BT and Tan, Y and Kostic, AD and Patel, CJ}, title = {Gene-level metagenomic architectures across diseases yield high-resolution microbiome diagnostic indicators.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2907}, pmid = {34006865}, issn = {2041-1723}, support = {P30 DK036836/DK/NIDDK NIH HHS/United States ; R01 AI127250/AI/NIAID NIH HHS/United States ; T32 DK110919/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics ; Cluster Analysis ; Colorectal Neoplasms/genetics/microbiology ; Computational Biology/*methods ; Diabetes Mellitus, Type 2/genetics/microbiology ; Firmicutes/genetics/physiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Inflammatory Bowel Diseases/genetics/microbiology ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics/physiology ; Phylogeny ; Species Specificity ; }, abstract = {We propose microbiome disease "architectures": linking >1 million microbial features (species, pathways, and genes) to 7 host phenotypes from 13 cohorts using a pipeline designed to identify associations that are robust to analytical model choice. Here, we quantify conservation and heterogeneity in microbiome-disease associations, using gene-level analysis to identify strain-specific, cross-disease, positive and negative associations. We find coronary artery disease, inflammatory bowel diseases, and liver cirrhosis to share gene-level signatures ascribed to the Streptococcus genus. Type 2 diabetes, by comparison, has a distinct metagenomic signature not linked to any one specific species or genus. We additionally find that at the species-level, the prior-reported connection between Solobacterium moorei and colorectal cancer is not consistently identified across models-however, our gene-level analysis unveils a group of robust, strain-specific gene associations. Finally, we validate our findings regarding colorectal cancer and inflammatory bowel diseases in independent cohorts and identify that features inversely associated with disease tend to be less reproducible than features enriched in disease. Overall, our work is not only a step towards gene-based, cross-disease microbiome diagnostic indicators, but it also illuminates the nuances of the genetic architecture of the human microbiome, including tension between gene- and species-level associations.}, } @article {pmid34006626, year = {2021}, author = {Hwang, Y and Rahlff, J and Schulze-Makuch, D and Schloter, M and Probst, AJ}, title = {Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {}, pmid = {34006626}, issn = {2379-5077}, abstract = {Viruses play an essential role in shaping microbial community structures and serve as reservoirs for genetic diversity in many ecosystems. In hyperarid desert environments, where life itself becomes scarce and loses diversity, the interactions between viruses and host populations have remained elusive. Here, we resolved host-virus interactions in the soil metagenomes of the Atacama Desert hyperarid core, one of the harshest terrestrial environments on Earth. We show evidence of diverse viruses infecting a wide range of hosts found in sites up to 205 km apart. Viral genomes carried putative extremotolerance features (i.e., spore formation proteins) and auxiliary metabolic genes, indicating that viruses could mediate the spread of microbial resilience against environmental stress across the desert. We propose a mutualistic model of host-virus interactions in the hyperarid core where viruses seek protection in microbial cells as lysogens or pseudolysogens, while viral extremotolerance genes aid survival of their hosts. Our results suggest that the host-virus interactions in the Atacama Desert soils are dynamic and complex, shaping uniquely adapted microbiomes in this highly selective and hostile environment.IMPORTANCE Deserts are one of the largest and rapidly expanding terrestrial ecosystems characterized by low biodiversity and biomass. The hyperarid core of the Atacama Desert, previously thought to be devoid of life, is one of the harshest environments, supporting only scant biomass of highly adapted microbes. While there is growing evidence that viruses play essential roles in shaping the diversity and structure of nearly every ecosystem, very little is known about the role of viruses in desert soils, especially where viral contact with viable hosts is significantly reduced. Our results demonstrate that diverse viruses are widely dispersed across the desert, potentially spreading key stress resilience and metabolic genes to ensure host survival. The desertification accelerated by climate change expands both the ecosystem cover and the ecological significance of the desert virome. This study sheds light on the complex virus-host interplay that shapes the unique microbiome in desert soils.}, } @article {pmid34006565, year = {2021}, author = {Mueller, NT and Differding, MK and Zhang, M and Maruthur, NM and Juraschek, SP and Miller, ER and Appel, LJ and Yeh, HC}, title = {Metformin Affects Gut Microbiome Composition and Function and Circulating Short-Chain Fatty Acids: A Randomized Trial.}, journal = {Diabetes care}, volume = {44}, number = {7}, pages = {1462-1471}, pmid = {34006565}, issn = {1935-5548}, support = {827990/AHA/American Heart Association-American Stroke Association/United States ; K01 HL141589/HL/NHLBI NIH HHS/United States ; P30 CA006973/CA/NCI NIH HHS/United States ; T32 HL007024/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Fatty Acids, Volatile ; Feces ; Female ; *Gastrointestinal Microbiome ; Humans ; *Metformin/therapeutic use ; Middle Aged ; Obesity/drug therapy ; Weight Loss ; }, abstract = {OBJECTIVE: To determine the longer-term effects of metformin treatment and behavioral weight loss on gut microbiota and short-chain fatty acids (SCFAs).

RESEARCH DESIGN AND METHODS: We conducted a 3-parallel-arm, randomized trial. We enrolled overweight/obese adults who had been treated for solid tumors but had no ongoing cancer treatment and randomized them (n = 121) to either 1) metformin (up to 2,000 mg), 2) coach-directed behavioral weight loss, or 3) self-directed care (control) for 12 months. We collected stool and serum at baseline (n = 114), 6 months (n = 109), and 12 months (n = 105). From stool, we extracted microbial DNA and conducted amplicon and metagenomic sequencing. We measured SCFAs and other biochemical parameters from fasting serum.

RESULTS: Of the 121 participants, 79% were female and 46% were Black, and the mean age was 60 years. Only metformin treatment significantly altered microbiota composition. Compared with control, metformin treatment increased amplicon sequence variants for Escherichia (confirmed as Escherichia coli by metagenomic sequencing) and Ruminococcus torques and decreased Intestinibacter bartlettii at both 6 and 12 months and decreased the genus Roseburia, including R. faecis and R. intestinalis, at 12 months. Effects were similar in comparison of the metformin group with the behavioral weight loss group. Metformin versus control also increased butyrate, acetate, and valerate at 6 months (but not at 12 months). Behavioral weight loss versus control did not significantly alter microbiota composition but did increase acetate at 6 months (but not at 12 months). Increases in acetate were associated with decreases in fasting insulin. Additional whole-genome metagenomic sequencing of a subset of the metformin group showed that metformin altered 62 metagenomic functional pathways, including an acetate-producing pathway and three pathways in glucose metabolism.

CONCLUSIONS: Metformin, but not behavioral weight loss, impacted gut microbiota composition at 6 months and 12 months. Both metformin and behavioral weight loss altered circulating SCFAs at 6 months, including increasing acetate, which correlated with lower fasting insulin. Future research is needed to elucidate whether the gut microboime mediates or modifies metformin's health effects.}, } @article {pmid34006335, year = {2021}, author = {Nearing, JT and Comeau, AM and Langille, MGI}, title = {Identifying biases and their potential solutions in human microbiome studies.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {113}, pmid = {34006335}, issn = {2049-2618}, support = {2016-05039//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (CA)/ ; }, mesh = {Bias ; Humans ; *Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; Specimen Handling ; }, abstract = {Advances in DNA sequencing technology have vastly improved the ability of researchers to explore the microbial inhabitants of the human body. Unfortunately, while these studies have uncovered the importance of these microbial communities to our health, they often do not result in similar findings. One possible reason for the disagreement in these results is due to the multitude of systemic biases that are introduced during sequence-based microbiome studies. These biases begin with sample collection and continue to be introduced throughout the entire experiment leading to an observed community that is significantly altered from the true underlying microbial composition. In this review, we will highlight the various steps in typical sequence-based human microbiome studies where significant bias can be introduced, and we will review the current efforts within the field that aim to reduce the impact of these biases. Video abstract.}, } @article {pmid34006193, year = {2021}, author = {Wang, K and Zhang, Z and Mo, ZS and Yang, XH and Lin, BL and Peng, L and Xu, Y and Lei, CY and Zhuang, XD and Lu, L and Yang, RF and Chen, T and Gao, ZL}, title = {Gut microbiota as prognosis markers for patients with HBV-related acute-on-chronic liver failure.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-15}, pmid = {34006193}, issn = {1949-0984}, mesh = {Acute-On-Chronic Liver Failure/*microbiology/virology ; Adult ; Bacteria/classification/genetics/*isolation & purification ; Disease Progression ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Hepatitis B virus/physiology ; Hepatitis B, Chronic/*microbiology/virology ; Humans ; Male ; Metagenomics ; Middle Aged ; }, abstract = {The gut microbiota in the hepatitis B virus related acute-on-chronic liver failure (HBV-ACLF) is poorly defined. We aim to uncover the characteristics of the gut microbiota in HBV-ACLF and in other HBV associated pathologies. We analyzed the gut microbiome in patients with HBV-ACLF or other HBV associated pathologies and healthy individuals by 16S rRNA sequencing and metagenomic sequencing of fecal samples. 212 patients with HBV-ACLF, 252 with chronic hepatitis B (CHB), 162 with HBV-associated cirrhosis (HBV-LC) and 877 healthy individuals were recruited for the study. CHB and HBV-LC patients are grouped as HBV-Other. We discovered striking differences in the microbiome diversity between the HBV-ACLF, HBV-Other and healthy groups using 16S rRNA sequencing. The ratio of cocci to bacilli was significantly elevated in the HBV-ACLF group compared with healthy group. Further analysis within the HBV-ACLF group identified 52 genera showing distinct richness within the group where Enterococcus was enriched in the progression group whilst Faecalibacterium was enriched in the regression group. Metagenomic sequencing validated these findings and further uncovered an enrichment of Lactobacillus casei paracasei in progression group, while Alistipes senegalensis, Faecalibacterium prausnitzii and Parabacteroides merdae dominated the regression group. Importantly, our analysis revealed that there was a rapid increase of Enterococcus faecium during the progression of HBV-ACLF. The gut microbiota displayed distinct composition at different phases of HBV-ACLF. High abundance of Enterococcus is associated with progression while that of Faecalibacterium is associated with regression of HBV-ACLF. Therefore, the microbiota features hold promising potential as prognostic markers for HBV-ACLF.}, } @article {pmid34004561, year = {2021}, author = {Peng, H and Zhang, Q and Tan, B and Li, M and Zhang, W and Feng, J}, title = {A metagenomic view of how different carbon sources enhance the aniline and simultaneous nitrogen removal capacities in the aniline degradation system.}, journal = {Bioresource technology}, volume = {335}, number = {}, pages = {125277}, doi = {10.1016/j.biortech.2021.125277}, pmid = {34004561}, issn = {1873-2976}, mesh = {Aniline Compounds ; Bioreactors ; Carbon ; *Denitrification ; Heterotrophic Processes ; *Nitrogen ; }, abstract = {To cross nitrogen removal barrier, carbon sources (sodium succinate (Z1), sodium acetate (Z2) and glucose (Z3)) were applied in aniline degradation reactor to enrich heterotrophic nitrifiers and denitrifiers. The aniline was degraded almost completely and the nitrogen removal performance was improved in three systems. The total nitrogen (TN) removal efficiency of Z2 was the highest. The dominant bacteria were phylum Proteobacteria, class BetaProteobacteria, and genus Thauera (Z1, Z3), Leptothrix (Z2). Different aniline degrading bacteria, heterotrophic nitrifiers and denitrifiers were enriched, and Z2 had more high-abundance communities. Three systems followed the meta-cleavage pathway for the aniline degradation according to the genes annotation. Particularly, the contribution of each genus to nitrogen metabolism and aromatic compounds degradation in the Z2 was more evenly distributed, rather than relying mainly on the contribution of Thauera in Z1 and Z3 so that more functional genes related nitrogen metabolism and aniline degradation were more abundant in Z2.}, } @article {pmid34004416, year = {2021}, author = {Chen, O and Sudakaran, S and Blonquist, T and Mah, E and Durkee, S and Bellamine, A}, title = {Effect of arabinogalactan on the gut microbiome: A randomized, double-blind, placebo-controlled, crossover trial in healthy adults.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {90}, number = {}, pages = {111273}, doi = {10.1016/j.nut.2021.111273}, pmid = {34004416}, issn = {1873-1244}, mesh = {Adult ; Cross-Over Studies ; Galactans ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVE: Promising evidence suggests beneficial health effects of arabinogalactan, but little is known about the effect of this non-digestible carbohydrate on the gut microbiota, a crucial mediator of human health. The objective of this study was to investigate the effect of an arabinogalactan product (ResistAid) on the fecal microbiome and short-chain fatty acids and gastrointestinal tolerance in healthy adults in a randomized, double-blind, crossover trial.

METHODS: Thirty adults were randomly assigned to consume 15 g/d maltodextrin (control) or ResistAid for 6 wk.

RESULTS: At week 6, compared to placebo, ResistAid supplementation led to a significant decrease in the ratio of fecal Firmicutes to Bacteroidetes, driven by an increase in Bacteroidetes and a decrease in Firmicutes. Moreover, the relative abundance of Bifidobacterium tended to increase with ResistAid supplementation. Additionally, ResistAid significantly decreased the α-diversity of the fecal microbiome. Predicted functional abundances based on 16S rRNA sequences showed that ResistAid supplementation increased the gene abundance of the gut microbiome for α-l-rhamnosidase, β-fructosidase, and levanase, as well as tricarboxylic acid and vitamin B6 biosynthesis pathways. Fecal isovaleric, valeric, and hexanoic acids were significantly lower after ResistAid consumption. There were no statistically significant changes in bowel habit, stool consistency, gastrointestinal tolerance symptoms, chemistry profile, metabolic panel, or vitals, suggesting that consumption of 15 g daily ResistAid over 6 wk is safe.

CONCLUSION: These results demonstrate that the gut microbiome composition and predicted functions can be modulated by ResistAid consumption, perhaps suggesting a mechanistic explanation on its reported benefits in metabolic parameters and the immune system.}, } @article {pmid34002024, year = {2021}, author = {Ni, Y and Lohinai, Z and Heshiki, Y and Dome, B and Moldvay, J and Dulka, E and Galffy, G and Berta, J and Weiss, GJ and Sommer, MOA and Panagiotou, G}, title = {Distinct composition and metabolic functions of human gut microbiota are associated with cachexia in lung cancer patients.}, journal = {The ISME journal}, volume = {15}, number = {11}, pages = {3207-3220}, pmid = {34002024}, issn = {1751-7370}, support = {I 3977/FWF_/Austrian Science Fund FWF/Austria ; I 4677/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Cachexia ; *Gastrointestinal Microbiome ; Humans ; *Lung Neoplasms/complications ; Prevotella ; }, abstract = {Cachexia is associated with decreased survival in cancer patients and has a prevalence of up to 80%. The etiology of cachexia is poorly understood, and limited treatment options exist. Here, we investigated the role of the human gut microbiome in cachexia by integrating shotgun metagenomics and plasma metabolomics of 31 lung cancer patients. The cachexia group showed significant differences in the gut microbial composition, functional pathways of the metagenome, and the related plasma metabolites compared to non-cachectic patients. Branched-chain amino acids (BCAAs), methylhistamine, and vitamins were significantly depleted in the plasma of cachexia patients, which was also reflected in the depletion of relevant gut microbiota functional pathways. The enrichment of BCAAs and 3-oxocholic acid in non-cachectic patients were positively correlated with gut microbial species Prevotella copri and Lactobacillus gasseri, respectively. Furthermore, the gut microbiota capacity for lipopolysaccharides biosynthesis was significantly enriched in cachectic patients. The involvement of the gut microbiome in cachexia was further observed in a high-performance machine learning model using solely gut microbial features. Our study demonstrates the links between cachectic host metabolism and specific gut microbial species and functions in a clinical setting, suggesting that the gut microbiota could have an influence on cachexia with possible therapeutic applications.}, } @article {pmid34001974, year = {2021}, author = {Pavarina, GC and Lemos, EGM and Lima, NSM and Pizauro, JM}, title = {Characterization of a new bifunctional endo-1,4-β-xylanase/esterase found in the rumen metagenome.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {10440}, pmid = {34001974}, issn = {2045-2322}, mesh = {Animals ; Bacterial Proteins/genetics/isolation & purification/*metabolism ; Cattle ; Endo-1,4-beta Xylanases/genetics/isolation & purification/*metabolism ; Enzyme Assays ; Esterases/genetics/isolation & purification/*metabolism ; *Gastrointestinal Microbiome ; Glucuronates/biosynthesis ; Industrial Microbiology/methods ; Lignin/metabolism ; Metagenome ; Oligosaccharides/biosynthesis ; Recombinant Proteins/genetics/isolation & purification/metabolism ; Renewable Energy ; Rumen/*microbiology ; }, abstract = {Metagenomic data mining of the Nellore cattle rumen microbiota identified a new bifunctional enzyme, endo-1,4-β-xylanase/esterase, which was subsequently overexpressed in E. coli BL21 (DE3). This enzyme was stable at pH intervals of 5 to 6.5 and temperatures between 30 and 45 °C, and under the test conditions, it had a Vmax of 30.959 ± 2.334 µmol/min/mg, Km of 3.6 ± 0.6 mM and kcat of 2.323 ± 175 s[-1]. Additionally, the results showed that the enzyme is tolerant to NaCl and organic solvents and therefore is suitable for industrial environments. Xylanases are widely applicable, and the synergistic activity of endo-1,4-β-xylanase/esterase in a single molecule will improve the degradation efficiency of heteroxylans via the creation of xylanase binding sites. Therefore, this new molecule has the potential for use in lignocellulosic biomass processing and as an animal feed food additive and could improve xylooligosaccharide production efficiency.}, } @article {pmid33998505, year = {2021}, author = {Requena, T and Velasco, M}, title = {The human microbiome in sickness and in health.}, journal = {Revista clinica espanola}, volume = {221}, number = {4}, pages = {233-240}, doi = {10.1016/j.rceng.2019.07.018}, pmid = {33998505}, issn = {2254-8874}, mesh = {*Gastrointestinal Microbiome ; Humans ; Intestines ; *Microbiota ; Phylogeny ; Symbiosis ; }, abstract = {The study of the human microbiome has led to an exceptional increase in the current understanding of the importance of microbiota for health throughout all stages of life. Human microbial colonization occurs in the skin, genitourinary system and, mainly, in the oral cavity and intestinal tract. In these locations, the human microbiota establishes a symbiotic relationship with the host and helps maintain physiological homeostasis. Lifestyle, age, diet and use of antibiotics are the main regulators of the composition and functionality of human microbiota. Recent studies have indicated the reduction in microbial diversity as one of the contributors to the development of diseases. In addition to phylogenetic diversity studies, further metagenomic studies are needed at the functional level of the human microbiome to improve our understanding of its involvement in human health.}, } @article {pmid33997973, year = {2021}, author = {Anand, S and Bose, C and Kaur, H and Mande, SS}, title = {'GutFeel': an in silico method for predicting gut health status based on the metabolic functional capabilities of the resident microbiome.}, journal = {FEBS letters}, volume = {595}, number = {13}, pages = {1825-1843}, doi = {10.1002/1873-3468.14107}, pmid = {33997973}, issn = {1873-3468}, mesh = {Bacteria/*classification/isolation & purification ; Computational Biology/*methods ; Computer Simulation ; Dysbiosis/*diagnosis ; Gastrointestinal Microbiome ; Health Status ; Humans ; Life Style ; Metabolic Networks and Pathways ; Metabolomics/*methods ; Symbiosis ; }, abstract = {Dysbiosis or imbalance in the gut microbiome has been correlated with the etiology of a number of diseases/disorders. Thus, gut microbial communities can potentially be utilized for assessing the health of the human gut. Although the taxonomic composition of the microbiomes is dependent on factors such as diet, lifestyle, and geography, these microbes perform a specific set of common functions in the gut. In this study, metabolic pathway-based markers (agnostic to above-mentioned factors) specific to commensals and those specific to pathogens are utilized as indicators of gut health. Furthermore, this gut health assessment requires only a small set of features rather than complete sequencing of metagenomes. The proposed scheme can also be used to design personalized biotherapeutics, depending on functional aspects observed in an individual.}, } @article {pmid33995413, year = {2021}, author = {Alam, MS and Gangiredla, J and Hasan, NA and Barnaba, T and Tartera, C}, title = {Aging-Induced Dysbiosis of Gut Microbiota as a Risk Factor for Increased Listeria monocytogenes Infection.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {672353}, pmid = {33995413}, issn = {1664-3224}, mesh = {Aging/*physiology ; Animals ; Dysbiosis/*microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Listeria monocytogenes ; Listeriosis/*microbiology ; Mice ; Mice, Inbred C57BL ; Risk Factors ; }, abstract = {Invasive foodborne Listeria monocytogenes infection causes gastroenteritis, septicemia, meningitis, and chorioamnionitis, and is associated with high case-fatality rates in the elderly. It is unclear how aging alters gut microbiota, increases risk of listeriosis, and causes dysbiosis post-infection. We used a geriatric murine model of listeriosis as human surrogate of listeriosis for aging individuals to study the effect of aging and L. monocytogenes infection. Aging and listeriosis-induced perturbation of gut microbiota and disease severity were compared between young-adult and old mice. Young-adult and old mice were dosed intragastrically with L. monocytogenes. Fecal pellets were collected pre- and post-infection for microbiome analysis. Infected old mice had higher Listeria colonization in liver, spleen, and feces. Metagenomics analyses of fecal DNA-sequences showed increase in α-diversity as mice aged, and infection reduced its diversity. The relative abundance of major bacterial phylum like, Bacteroidetes and Firmicutes remained stable over aging or infection, while the Verrucomicrobia phylum was significantly reduced only in infected old mice. Old mice showed a marked reduction in Clostridaiceae and Lactobacillaceae bacteria even before infection when compared to uninfected young-adult mice. L. monocytogenes infection increased the abundance of Porphyromonadaceae and Prevotellaceae in young-adult mice, while members of the Ruminococcaceae and Lachnospiraceae family were significantly increased in old mice. The abundance of the genera Blautia and Alistipes were significantly reduced post-infection in young-adult and in old mice as compared to their uninfected counterparts. Butyrate producing, immune-modulating bacterial species, like Pseudoflavonifractor and Faecalibacterium were significantly increased only in old infected mice, correlating with increased intestinal inflammatory mRNA up-regulation from old mice tissue. Histologic analyses of gastric tissues showed extensive lesions in the Listeria-infected old mice, more so in the non-glandular region and fundus than in the pylorus. Commensal species like Lactobacillus, Clostridiales, and Akkermansia were only abundant in infected young-adult mice but their abundance diminished in the infected old mice. Listeriosis in old mice enhances the abundance of butyrate-producing inflammatory members of the Ruminococcaceae/Lachnospiraceae bacteria while reducing/eliminating beneficial commensals in the gut. Results of this study indicate that, aging may affect the composition of gut microbiota and increase the risk of invasive L. monocytogenes infection.}, } @article {pmid33992393, year = {2021}, author = {Fu, J and Chen, L and Yang, S and Li, Y and Jin, L and He, X and He, L and Ao, X and Liu, S and Liu, A and Yang, Y and Ma, B and Cui, X and Chen, S and Zou, L}, title = {Metagenome and analysis of metabolic potential of the microbial community in pit mud used for Chinese strong-flavor liquor production.}, journal = {Food research international (Ottawa, Ont.)}, volume = {143}, number = {}, pages = {110294}, doi = {10.1016/j.foodres.2021.110294}, pmid = {33992393}, issn = {1873-7145}, mesh = {Bacteria/genetics ; China ; Fermentation ; *Metagenome ; *Microbiota ; }, abstract = {Complex microbiomes of pit mud (PM) play significant roles in imbuing flavors and qualities of Chinese strong-flavor liquor (CSFL) during fermentation. However, understanding both of the taxonomic and functional diversity of the whole microorganisms in PM still remain a major challenge. Here, PM microbiomes were investigated based on metagenomic sequencing, assembly and binning. Metagenomic data revealed that Euryarchaeota was the predominant phylum, followed by Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria. For further functional exploration, 703 metagenome-assembled genomes (MAGs), including 304 novel strains, 197 novel species, and 94 novel genera were reconstructed. Three primary groups of Firmicutes (n = 406), Euryarchaeota (n = 130) and Bacteroidetes (n = 74), particularly genus of them Syntrophomonas, Thermacetogenium and Clostridium, methanogens (Methanobacterium, Methanoculleus, and Methanosarcina), Proteiniphilum and Prevotella, contained most of metabolic potential genes. Additionally, Chloroflexi was firstly reported to have potential to be involved in the caproic acid (CA) production. Bacteroidetes could be the key phylum to synthesize terpenes, and Armatimonadetes, Firmicutes, Ignavibacteriae and Verrucomicrobia may possess the same metabolic potential as well. Overall, this study will significantly improve our understanding of the diverse PM microbiome and help guide the future exploration of microbial resources for modifying PM fermentation processes.}, } @article {pmid33991864, year = {2021}, author = {Kalcioglu, MT and Durmaz, R and Ari, O and Celik, S and Karabudak, S}, title = {Microbiological investigation of samples collected from healthy middle ears during cochlear implant surgery.}, journal = {Diagnostic microbiology and infectious disease}, volume = {100}, number = {4}, pages = {115390}, doi = {10.1016/j.diagmicrobio.2021.115390}, pmid = {33991864}, issn = {1879-0070}, mesh = {Adult ; Bacteria/*classification/*genetics/isolation & purification ; Child, Preschool ; Cochlear Implants/*adverse effects ; Ear, Middle/*microbiology ; Genetic Variation ; Healthy Volunteers/statistics & numerical data ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Infant, Newborn ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {This study aimed to investigate the bacteriome in microscopically healthy middle ear mucosa using Next-generation sequencing (NGS) technology. A total of 60 middle ear washing fluids of pediatric and adult were obtained from 47 patients (35 children and 12 adults). Both children and adults with normal middle ears harbored diverse bacteriome. Seventeen different genera with a mean relative abundance of more than 1% were detected in all samples. Both in adult and children, the most abundant genus was Propionibacterium followed by Streptococcus, Staphylococcus, and Ralstonia. The species Propionibacterium acnes and Corynebacterium tuberculostearicum were significantly more abundant in the adult group. Although there were differences in the prevalence and relative abundance of some bacteria observed from adult and child groups, no specific genus or species was detected only in children or adults.}, } @article {pmid33990868, year = {2021}, author = {Aguirre-von-Wobeser, E}, title = {Type II Photosynthetic Reaction Center Genes of Avocado (Persea americana Mill.) Bark Microbial Communities are Dominated by Aerobic Anoxygenic Alphaproteobacteria.}, journal = {Current microbiology}, volume = {78}, number = {7}, pages = {2623-2630}, pmid = {33990868}, issn = {1432-0991}, support = {CB-2014-01-242956//SEP/CONACyT/ ; }, mesh = {*Alphaproteobacteria ; *Microbiota ; *Persea ; Photosynthesis ; *Photosynthetic Reaction Center Complex Proteins ; Plant Bark ; }, abstract = {The tree bark environment is an important microbial habitat distributed worldwide on thrillions of trees. However, the microbial communities of tree bark are largely unknown, with most studies on plant aerial surfaces focused on the leaves. Recently, we presented a metagenomic study of bark microbial communities from avocado. In these communities, oxygenic and anoxygenic photosynthesis genes were very abundant, especially when compared to rhizospheric soil from the same trees. In this work, Evolutionary Placement Algorithm analysis was performed on metagenomic reads orthologous to the PufLM gene cluster, encoding for the bacterial type II photosynthetic reaction center. These photosynthetic genes were found affiliated to different groups of bacteria, mostly aerobic anoxygenic photosynthetic Alphaproteobacteria, including Sphingomonas, Methylobacterium and several Rhodospirillales. These results suggest that anoxygenic photosynthesis in avocado bark microbial communities functions primarily as additional energy source for heterotrophic growth. Together with our previous results, showing a large abundance of cyanobacteria in these communities, a picture emerges of the tree holobiont, where light penetrating the tree canopies and reaching the inner stems, including the trunk, is probably utilized by cyanobacteria for oxygenic photosynthesis, and the far-red light aids the growth of aerobic anoxygenic photosynthetic bacteria.}, } @article {pmid33990699, year = {2021}, author = {Rasmussen, JA and Villumsen, KR and Duchêne, DA and Puetz, LC and Delmont, TO and Sveier, H and Jørgensen, LVG and Præbel, K and Martin, MD and Bojesen, AM and Gilbert, MTP and Kristiansen, K and Limborg, MT}, title = {Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {579}, pmid = {33990699}, issn = {2399-3642}, mesh = {Animals ; Gastrointestinal Microbiome/*genetics ; *Genome, Bacterial ; *Metagenome ; Mycoplasma/*genetics ; Phylogeny ; Salmonidae/*microbiology ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Salmonids are important sources of protein for a large proportion of the human population. Mycoplasma species are a major constituent of the gut microbiota of salmonids, often representing the majority of microbiota. Despite the frequent reported dominance of salmonid-related Mycoplasma species, little is known about the phylogenomic placement, functions and potential evolutionary relationships with their salmonid hosts. In this study, we utilise 2.9 billion metagenomic reads generated from 12 samples from three different salmonid host species to I) characterise and curate the first metagenome-assembled genomes (MAGs) of Mycoplasma dominating the intestines of three different salmonid species, II) establish the phylogeny of these salmonid candidate Mycoplasma species, III) perform a comprehensive pangenomic analysis of Mycoplasma, IV) decipher the putative functionalities of the salmonid MAGs and reveal specific functions expected to benefit the host. Our data provide a basis for future studies examining the composition and function of the salmonid microbiota.}, } @article {pmid33990618, year = {2021}, author = {Buck, M and Garcia, SL and Fernandez, L and Martin, G and Martinez-Rodriguez, GA and Saarenheimo, J and Zopfi, J and Bertilsson, S and Peura, S}, title = {Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds.}, journal = {Scientific data}, volume = {8}, number = {1}, pages = {131}, pmid = {33990618}, issn = {2052-4463}, support = {292251//Academy of Finland (Suomen Akatemia)/ ; 2016-00874//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/ ; }, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Carbon Cycle ; Climate Change ; Greenhouse Gases/analysis ; Lakes/chemistry/*microbiology ; *Metagenome ; Microbiota/*genetics ; Oxygen/*analysis ; Phylogeny ; Ponds/chemistry/*microbiology ; }, abstract = {Stratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the microbial communities, especially in the oxygen depleted compartments, are poorly known. Here, we present a comprehensive dataset including 267 shotgun metagenomes from 41 stratified lakes and ponds mainly located in the boreal and subarctic regions, but also including one tropical reservoir and one temperate lake. For most lakes and ponds, the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer. The majority of the samples were collected during the open water period, but also a total of 29 samples were collected from under the ice. In addition to the metagenomic sequences, the dataset includes environmental variables for the samples, such as oxygen, nutrient and organic carbon concentrations. The dataset is ideal for further exploring the microbial taxonomic and functional diversity in freshwater environments and potential climate change impacts on the functioning of these ecosystems.}, } @article {pmid33990301, year = {2021}, author = {Mota-Gutierrez, J and Ferrocino, I and Giordano, M and Suarez-Quiroz, ML and Gonzalez-Ríos, O and Cocolin, L}, title = {Influence of Taxonomic and Functional Content of Microbial Communities on the Quality of Fermented Cocoa Pulp-Bean Mass.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {14}, pages = {e0042521}, pmid = {33990301}, issn = {1098-5336}, mesh = {Adult ; Bacteria/genetics ; Cacao/*microbiology ; Female ; Fermentation ; Fungi/genetics ; Humans ; Male ; Metagenomics ; Microbiota/*genetics ; Odorants ; Taste ; Young Adult ; }, abstract = {Microbial metabolism drives changes in the physicochemical properties and, consequently, the sensory characteristics of fermented cocoa beans. In this context, information regarding the structure, function, and metabolic potential of microbial communities' present during cocoa pulp-bean mass fermentation is limited, especially concerning the formation of aromatic compounds. To bridge the gap, the metagenome of fermented cocoa pulp-bean mass (Criollo and Forastero) has been investigated using shotgun metagenomics coupled with physicochemical, microbiological, quality, and sensory analyses to explore the impact of microbial communities on the quality of fermented cocoa pulp-bean mass on one farm in one season and in one region under the same environmental conditions. Our findings showed that the metagenomic diversity in cocoa, the fermentation length, and the diversity and function of metagenome-assembled genomes (MAGs) greatly influence the resulting distinctive flavors. From the metabolic perspective, multiple indicators suggest that the heterolactic metabolism was more dominant in Criollo fermentations. KEGG genes were linked with the biosynthesis of acetic acid, ethanol, lactic acid, acetoin, and phenylacetaldehyde during Criollo and Forastero fermentations. MAGs belonging to Lactiplantibacillus plantarum, Limosilactobacillus reuteri, and Acetobacter pasteurianus were the most prevalent. Fermentation time and roasting are the most important determinants of cocoa quality, while the difference between the two varieties are relatively minor. The assessment of microbiological and chemical analysis is urgently needed for developing fermentation protocols according to regions, countries, and cocoa varieties to guarantee safety and desirable flavor development. IMPORTANCE Monitoring the composition, structure, functionalities, and metabolic potential encoded at the level of DNA of fermented cocoa pulp-bean mass metagenome is of great importance for food safety and quality implications.}, } @article {pmid33989681, year = {2021}, author = {Takewaki, D and Yamamura, T}, title = {Gut microbiome research in multiple sclerosis.}, journal = {Neuroscience research}, volume = {168}, number = {}, pages = {28-31}, doi = {10.1016/j.neures.2021.05.001}, pmid = {33989681}, issn = {1872-8111}, mesh = {Animals ; Brain ; Disease Models, Animal ; *Encephalomyelitis, Autoimmune, Experimental ; *Gastrointestinal Microbiome ; *Multiple Sclerosis ; }, abstract = {Recent studies identified specific gut microbial species linked to various human diseases, and gut-brain axis is currently attracting much attention in the field of microbiome science clinically and biologically. Research on multiple sclerosis (MS) and its mouse model, experimental autoimmune encephalomyelitis is one of the most active research subjects. Notably, recent achievements established the bidirectional causality between MS and gut microbiome. The reduction of gut microbiome-derived short chain fatty acids and the enrichment of gut-associated oxidative stress appear to be promoting for neurodegenerative processes. Also, researchers are trying to elucidate the mechanisms by which the microbiome regulates the onset and progression of MS. The new findings achieved by the analysis of the causal relationship between MS and the gut microbiome will provide a new therapeutic strategy for MS. These results will contribute to our understanding of the cause, prevention, and treatment of MS, and will lead to a complete cure for this disease in the future. In MS, for which no curative treatment has yet to be established, the unmet needs may be overcome through the analysis of gut microbiome.}, } @article {pmid33986544, year = {2021}, author = {Sun, Z and Huang, S and Zhang, M and Zhu, Q and Haiminen, N and Carrieri, AP and Vázquez-Baeza, Y and Parida, L and Kim, HC and Knight, R and Liu, YY}, title = {Challenges in benchmarking metagenomic profilers.}, journal = {Nature methods}, volume = {18}, number = {6}, pages = {618-626}, pmid = {33986544}, issn = {1548-7105}, support = {RF1 AG067744/AG/NIA NIH HHS/United States ; R01 AI141529/AI/NIAID NIH HHS/United States ; R01 HD093761/HD/NICHD NIH HHS/United States ; UH3 OD023268/OD/NIH HHS/United States ; U19 AI095219/AI/NIAID NIH HHS/United States ; U01 HL089856/HL/NHLBI NIH HHS/United States ; }, mesh = {Computational Biology/methods ; Gene Expression Profiling ; *Metagenomics ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Accurate microbial identification and abundance estimation are crucial for metagenomics analysis. Various methods for classification of metagenomic data and estimation of taxonomic profiles, broadly referred to as metagenomic profilers, have been developed. Nevertheless, benchmarking of metagenomic profilers remains challenging because some tools are designed to report relative sequence abundance while others report relative taxonomic abundance. Here we show how misleading conclusions can be drawn by neglecting this distinction between relative abundance types when benchmarking metagenomic profilers. Moreover, we show compelling evidence that interchanging sequence abundance and taxonomic abundance will influence both per-sample summary statistics and cross-sample comparisons. We suggest that the microbiome research community pay attention to potentially misleading biological conclusions arising from this issue when benchmarking metagenomic profilers, by carefully considering the type of abundance data that were analyzed and interpreted and clearly stating the strategy used for metagenomic profiling.}, } @article {pmid33986295, year = {2021}, author = {Huang, HJ and Ye, ZX and Wang, X and Yan, XT and Zhang, Y and He, YJ and Qi, YH and Zhang, XD and Zhuo, JC and Lu, G and Lu, JB and Mao, QZ and Sun, ZT and Yan, F and Chen, JP and Zhang, CX and Li, JM}, title = {Diversity and infectivity of the RNA virome among different cryptic species of an agriculturally important insect vector: whitefly Bemisia tabaci.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {43}, pmid = {33986295}, issn = {2055-5008}, mesh = {Animals ; Databases, Genetic ; Hemiptera/*virology ; Host Specificity ; Insect Vectors/virology ; Metagenome ; Metagenomics/methods ; Phylogeny ; RNA Viruses/*classification/*genetics ; RNA, Viral ; *Virome ; }, abstract = {A large number of insect-specific viruses (ISVs) have recently been discovered, mostly from hematophagous insect vectors because of their medical importance, but little attention has been paid to important plant virus vectors such as the whitefly Bemisia tabaci, which exists as a complex of cryptic species. Public SRA datasets of B. tabaci and newly generated transcriptomes of three Chinese populations are here comprehensively investigated to characterize the whitefly viromes of different cryptic species. Twenty novel ISVs were confidently identified, mostly associated with a particular cryptic species while different cryptic species harbored one or more core ISVs. Microinjection experiments showed that some ISVs might cross-infect between the two invasive whitefly cryptic species, Middle East Asia Minor 1 (MEAM1) and Mediterranean (MED), but others appeared to have a more restricted host range, reflecting the possibility of distinct long-term coevolution of these ISVs and whitefly hosts. Moreover, analysis of the profiles of virus-derived small-interfering RNAs indicated that some of the ISVs can successfully replicate in whitefly and the antiviral RNAi pathway of B. tabaci is actively involved in response to ISV infections. Our study provides a comprehensive analysis of the RNA virome, the distinct relationships and cross-cryptic species infectivity of ISVs in an agriculturally important insect vector.}, } @article {pmid33986253, year = {2021}, author = {Ma, S and Zhang, F and Zhou, F and Li, H and Ge, W and Gan, R and Nie, H and Li, B and Wang, Y and Wu, M and Li, D and Wang, D and Wang, Z and You, Y and Huang, Z}, title = {Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19.}, journal = {Signal transduction and targeted therapy}, volume = {6}, number = {1}, pages = {191}, pmid = {33986253}, issn = {2059-3635}, support = {31825008//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31422014//National Natural Science Foundation of China (National Science Foundation of China)/ ; 61872117//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Adult ; *Bacteria/classification/genetics/growth & development ; COVID-19/*microbiology ; Female ; Humans ; Male ; *Metagenomics ; *Microbiota ; Middle Aged ; Oropharynx/*microbiology ; *SARS-CoV-2 ; }, abstract = {COVID-19 remains a serious emerging global health problem, and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity. Here, we present the oropharyngeal microbiota characteristics identified by shotgun metagenomic sequencing analyses of oropharynx swab specimens from 31 COVID-19 patients, 29 influenza B patients, and 28 healthy controls. Our results revealed a distinct oropharyngeal microbiota composition in the COVID-19 patients, characterized by enrichment of opportunistic pathogens such as Veillonella and Megasphaera and depletion of Pseudopropionibacterium, Rothia, and Streptococcus. Based on the relative abundance of the oropharyngeal microbiome, we built a microbial classifier to distinguish COVID-19 patients from flu patients and healthy controls with an AUC of 0.889, in which Veillonella was identified as the most prominent biomarker for COVID-19 group. Several members of the genus Veillonella, especially Veillonella parvula which was highly enriched in the oropharynx of our COVID-19 patients, were also overrepresented in the BALF of COVID-19 patients, indicating that the oral cavity acts as a natural reservoir for pathogens to induce co-infections in the lungs of COVID-19 patients. We also found the increased ratios of Klebsiella sp., Acinetobacter sp., and Serratia sp. were correlated with both disease severity and elevated systemic inflammation markers (neutrophil-lymphocyte ratio, NLR), suggesting that these oropharynx microbiota alterations may impact COVID-19 severity by influencing the inflammatory response. Moreover, the oropharyngeal microbiome of COVID-19 patients exhibited a significant enrichment in amino acid metabolism and xenobiotic biodegradation and metabolism. In addition, all 26 drug classes of antimicrobial resistance genes were detected in the COVID-19 group, and were significantly enriched in critical cases. In conclusion, we found that oropharyngeal microbiota alterations and functional differences were associated with COVID-19 severity.}, } @article {pmid33985416, year = {2021}, author = {Engevik, MA and Herrmann, B and Ruan, W and Engevik, AC and Engevik, KA and Ihekweazu, F and Shi, Z and Luck, B and Chang-Graham, AL and Esparza, M and Venable, S and Horvath, TD and Haidacher, SJ and Hoch, KM and Haag, AM and Schady, DA and Hyser, JM and Spinler, JK and Versalovic, J}, title = {Bifidobacterium dentium-derived y-glutamylcysteine suppresses ER-mediated goblet cell stress and reduces TNBS-driven colonic inflammation.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-21}, pmid = {33985416}, issn = {1949-0984}, support = {U01 CA170930/CA/NCI NIH HHS/United States ; P30 DK123704/DK/NIDDK NIH HHS/United States ; K01 DK123195/DK/NIDDK NIH HHS/United States ; K01 DK121869/DK/NIDDK NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 DK115507/DK/NIDDK NIH HHS/United States ; F30 DK112563/DK/NIDDK NIH HHS/United States ; T32 DK007664/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bifidobacterium/*metabolism ; Colitis/chemically induced/immunology/*microbiology/*physiopathology ; Colon/*immunology/microbiology/physiopathology ; Dipeptides/*metabolism ; Endoplasmic Reticulum Chaperone BiP ; *Endoplasmic Reticulum Stress ; Gastrointestinal Microbiome ; Goblet Cells/*immunology ; Humans ; Male ; Mice ; Mucin-2/genetics/immunology ; Trinitrobenzenesulfonic Acid/adverse effects ; }, abstract = {Endoplasmic reticulum (ER) stress compromises the secretion of MUC2 from goblet cells and has been linked with inflammatory bowel disease (IBD). Although Bifidobacterium can beneficially modulate mucin production, little work has been done investigating the effects of Bifidobacterium on goblet cell ER stress. We hypothesized that secreted factors from Bifidobacterium dentium downregulate ER stress genes and modulates the unfolded protein response (UPR) to promote MUC2 secretion. We identified by mass spectrometry that B. dentium secretes the antioxidant γ-glutamylcysteine, which we speculate dampens ER stress-mediated ROS and minimizes ER stress phenotypes. B. dentium cell-free supernatant and γ-glutamylcysteine were taken up by human colonic T84 cells, increased glutathione levels, and reduced ROS generated by the ER-stressors thapsigargin and tunicamycin. Moreover, B. dentium supernatant and γ-glutamylcysteine were able to suppress NF-kB activation and IL-8 secretion. We found that B. dentium supernatant, γ-glutamylcysteine, and the positive control IL-10 attenuated the induction of UPR genes GRP78, CHOP, and sXBP1. To examine ER stress in vivo, we first examined mono-association of B. dentium in germ-free mice which increased MUC2 and IL-10 levels compared to germ-free controls. However, no changes were observed in ER stress-related genes, indicating that B. dentium can promote mucus secretion without inducing ER stress. In a TNBS-mediated ER stress model, we observed increased levels of UPR genes and pro-inflammatory cytokines in TNBS treated mice, which were reduced with addition of live B. dentium or γ-glutamylcysteine. We also observed increased colonic and serum levels of IL-10 in B. dentium- and γ-glutamylcysteine-treated mice compared to vehicle control. Immunostaining revealed retention of goblet cells and mucus secretion in both B. dentium- and γ-glutamylcysteine-treated animals. Collectively, these data demonstrate positive modulation of the UPR and MUC2 production by B. dentium-secreted compounds.}, } @article {pmid33984318, year = {2021}, author = {Stevens, BR and Pepine, CJ and Richards, EM and Kim, S and Raizada, MK}, title = {Depressive hypertension: A proposed human endotype of brain/gut microbiome dysbiosis.}, journal = {American heart journal}, volume = {239}, number = {}, pages = {27-37}, doi = {10.1016/j.ahj.2021.05.002}, pmid = {33984318}, issn = {1097-6744}, mesh = {Adult ; Affect/*physiology ; Biobehavioral Sciences ; Biota/*genetics ; *Depression/diagnosis/metabolism/physiopathology ; *Dysbiosis/diagnosis/physiopathology/psychology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Gastrointestinal Tract/microbiology/physiopathology ; Humans ; *Hypertension/diagnosis/metabolism/psychology ; Machine Learning ; Male ; Metabolic Networks and Pathways ; Metagenome ; }, abstract = {BACKGROUND: Hypertension (HTN) is frequently linked with depression (DEP) in adults with cardiovascular disease (CVD), yet the underlying mechanism and successful management remain elusive. We approached this knowledge gap through the lens that humans are eukaryote-prokaryote "meta-organisms," such that cardiovascular disease dysregulation is a mosaic disorder involving dysbiosis of the gut. We hypothesized that patients diagnosed with hypertension plus depression harbor a unique gut microbial ecology with attending functional genomics engaged with their hosts' gut/brain axis physiology.

METHODS: Stool microbiome DNA was analyzed by whole metagenome shotgun sequencing in 54 subjects parsed into cohorts diagnosed with HTN only (N = 18), DEP only (N = 7), DEP plus HTN (DEP-HTN) (N = 8), or reference subjects with neither HTN nor DEP (N = 21). A novel battery of machine-learning multivariate analyses of de-noised data yielded effect sizes and permutational covariance-based dissimilarities that significantly differentiated the cohorts (false discovery rate (FDR)-adjusted P ≤ .05); data clustering within 95% confidence interval).

RESULTS: Metagenomic significant differences extricated the four cohorts. Data of the cohort exhibiting DEP-HTN were germane to the interplay of central control of blood pressure concomitant with the neuropathology of depressive disorders. DEP-HTN gut bacterial community ecology was defined by co-occurrence of Eubacterium siraeum, Alistipes obesi, Holdemania filiformis, and Lachnospiraceae bacterium 1.1.57FAA with Streptococcus salivariu. The corresponding microbial functional genomics of DEP-HTN engaged pathways degrading GABA and beneficial short chain fatty acids (SCFA), and are associated with enhanced sodium absorption and inflammasome induction.

CONCLUSIONS: These data suggest a new putative endotype of hypertension, which we denote "depressive-hypertension" (DEP-HTN), for which we posit a model that is distinctive from either HTN alone or DEP alone. An "endotype" is a subtype of a heterogeneous pathophysiological mechanism. The DEP-HTN model incorporates a unique signature of microbial taxa and functional genomics with crosstalk that putatively intertwines host pathophysiology involving the gastrointestinal tract with disruptions in central control of blood pressure and mood. The DEP-HTN endotype model engages cardiology with gastroenterology and psychiatry, providing a proof-of-concept foundation to explore future treatments, diagnosis, and prevention of HTN-coupled mood disorders.}, } @article {pmid33980951, year = {2021}, author = {Kim, MJ and Tagele, SB and Jo, H and Kim, MC and Jung, Y and Park, YJ and So, JH and Kim, HJ and Kim, HJ and Lee, DG and Kang, S and Shin, JH}, title = {Effect of a bioconverted product of Lotus corniculatus seed on the axillary microbiome and body odor.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {10138}, pmid = {33980951}, issn = {2045-2322}, mesh = {Axilla/microbiology ; Female ; Humans ; Lotus/*chemistry ; Metagenomics/methods ; Microbiota/*drug effects ; *Odorants ; Phytochemicals/chemistry/pharmacology ; Plant Extracts/chemistry/*pharmacology ; Seeds/*chemistry ; Skin/microbiology ; }, abstract = {The skin microbiome, especially the axillary microbiome, consists of odor-causing bacteria that decompose odorless sweat into malodor compounds, which contributes to the formation of body odor. Plant-derived products are a cheap source of bioactive compounds that are common ingredients in cosmetics. Microbial bioconversion of natural products is an ecofriendly and economical method for production of new or improved biologically active compounds. Therefore, in this study, we tested the potential of a Lactobacillus acidophilus KNU-02-mediated bioconverted product (BLC) of Lotus corniculatus seed to reduce axillary malodor and its effect on the associated axillary microbiota. A chemical profile analysis revealed that benzoic acid was the most abundant chemical compound in BLC, which increased following bioconversion. Moreover, BLC treatment was found to reduce the intensity of axillary malodor. We tested the axillary microbiome of 18 study participants, divided equally into BLC and placebo groups, and revealed through 16S rRNA gene sequencing that Staphylococcus, Corynebacterium, and Anaerococcus were the dominant taxa, and some of these taxa were significantly associated with axillary malodor. After one week of BLC treatment, the abundance of Corynebacterium and Anaerococcus, which are associated with well-known odor-related genes that produce volatile fatty acids, had significantly reduced. Likewise, the identified odor-related genes decreased after the application of BLC. BLC treatment enhanced the richness and network density of the axillary microbial community. The placebo group, on the other hand, showed no difference in the microbial richness, odor associated taxa, and predicted functional genes after a week. The results demonstrated that BLC has the potential to reduce the axillary malodor and the associated odor-causing bacteria, which makes BLC a viable deodorant material in cosmetic products.}, } @article {pmid33980682, year = {2021}, author = {Xiao, K and Fan, Y and Zhang, Z and Shen, X and Li, X and Liang, X and Bi, R and Wu, Y and Zhai, J and Dai, J and Irwin, DM and Chen, W and Shen, Y}, title = {Covariation of the Fecal Microbiome with Diet in Nonpasserine Birds.}, journal = {mSphere}, volume = {6}, number = {3}, pages = {}, pmid = {33980682}, issn = {2379-5042}, mesh = {Animal Nutritional Physiological Phenomena ; Animals ; Bacteria/classification/*genetics ; Birds/*microbiology ; *Diet ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; *Metagenome ; Metagenomics ; Phylogeny ; Poultry/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Opportunistic feeding and multiple other environment factors can modulate the gut microbiome, and bias conclusions, when wild animals are used for studying the influence of phylogeny and diet on their gut microbiomes. Here, we controlled for these other confounding factors in our investigation of the magnitude of the effect of diet on the gut microbiome assemblies of nonpasserine birds. We collected fecal samples, at one point in time, from 35 species of birds in a single zoo as well as 6 species of domestic poultry from farms in Guangzhou city to minimize the influences from interfering factors. Specifically, we describe 16S rRNA amplicon data from 129 fecal samples obtained from 41 species of birds, with additional shotgun metagenomic sequencing data generated from 16 of these individuals. Our data show that diets containing native starch increase the abundance of Lactobacillus in the gut microbiome, while those containing plant-derived fiber mainly enrich the level of Clostridium Greater numbers of Fusobacteria and Proteobacteria are detected in carnivorous birds, while in birds fed a commercial corn-soybean basal diet, a stronger inner-connected microbial community containing Clostridia and Bacteroidia was enriched. Furthermore, the metagenome functions of the microbes (such as lipid metabolism and amino acid synthesis) were adapted to the different food types to achieve a beneficial state for the host. In conclusion, the covariation of diet and gut microbiome identified in our study demonstrates a modulation of the gut microbiome by dietary diversity and helps us better understand how birds live based on diet-microbiome-host interactions.IMPORTANCE Our study identified food source, rather than host phylogeny, as the main factor modulating the gut microbiome diversity of nonpasserine birds, after minimizing the effects of other complex interfering factors such as weather, season, and geography. Adaptive evolution of microbes to food types formed a dietary-microbiome-host interaction reciprocal state. The covariation of diet and gut microbiome, including the response of microbiota assembly to diet in structure and function, is important for health and nutrition in animals. Our findings help resolve the major modulators of gut microbiome diversity in nonpasserine birds, which had not previously been well studied. The diet-microbe interactions and cooccurrence patterns identified in our study may be of special interest for future health assessment and conservation in birds.}, } @article {pmid33980678, year = {2021}, author = {Pimentel, ZT and Dufault-Thompson, K and Russo, KT and Scro, AK and Smolowitz, RM and Gomez-Chiarri, M and Zhang, Y}, title = {Microbiome Analysis Reveals Diversity and Function of Mollicutes Associated with the Eastern Oyster, Crassostrea virginica.}, journal = {mSphere}, volume = {6}, number = {3}, pages = {}, pmid = {33980678}, issn = {2379-5042}, mesh = {Animals ; Bacteria/*classification/*genetics ; Crassostrea/*microbiology ; Gastrointestinal Microbiome/*genetics/physiology ; *Metagenome ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Tenericutes/classification/*genetics/metabolism ; }, abstract = {Marine invertebrate microbiomes play important roles in diverse host and ecological processes. However, a mechanistic understanding of host-microbe interactions is currently available for a small number of model organisms. Here, an integrated taxonomic and functional analysis of the microbiome of the eastern oyster, Crassostrea virginica, was performed using 16S rRNA gene-based amplicon profiling, shotgun metagenomics, and genome-scale metabolic reconstruction. Relatively high variability of the microbiome was observed across individual oysters and among different tissue types. Specifically, a significantly higher alpha diversity was observed in the inner shell than in the gut, gill, mantle, and pallial fluid samples, and a distinct microbiome composition was revealed in the gut compared to other tissues examined in this study. Targeted metagenomic sequencing of the gut microbiota led to further characterization of a dominant bacterial taxon, the class Mollicutes, which was captured by the reconstruction of a metagenome-assembled genome (MAG). Genome-scale metabolic reconstruction of the oyster Mollicutes MAG revealed a reduced set of metabolic functions and a high reliance on the uptake of host-derived nutrients. A chitin degradation and an arginine deiminase pathway were unique to the MAG compared to closely related genomes of Mollicutes isolates, indicating distinct mechanisms of carbon and energy acquisition by the oyster-associated Mollicutes A systematic reanalysis of public eastern oyster-derived microbiome data revealed a high prevalence of the Mollicutes among adult oyster guts and a significantly lower relative abundance of the Mollicutes in oyster larvae and adult oyster biodeposits.IMPORTANCE Despite their biological and ecological significance, a mechanistic characterization of microbiome function is frequently missing from many nonmodel marine invertebrates. As an initial step toward filling this gap for the eastern oyster, Crassostrea virginica, this study provides an integrated taxonomic and functional analysis of the oyster microbiome using samples from a coastal salt pond in August 2017. The study identified high variability of the microbiome across tissue types and among individual oysters, with some dominant taxa showing higher relative abundance in specific tissues. A high prevalence of Mollicutes in the adult oyster gut was revealed by comparative analysis of the gut, biodeposit, and larva microbiomes. Phylogenomic analysis and metabolic reconstruction suggested the oyster-associated Mollicutes is closely related but functionally distinct from Mollicutes isolated from other marine invertebrates. To the best of our knowledge, this study represents the first metagenomics-derived functional inference of Mollicutes in the eastern oyster microbiome.}, } @article {pmid33978940, year = {2021}, author = {Xiong, D and Muema, C and Zhang, X and Pan, X and Xiong, J and Yang, H and Yu, J and Wei, H}, title = {Enriched Opportunistic Pathogens Revealed by Metagenomic Sequencing Hint Potential Linkages between Pharyngeal Microbiota and COVID-19.}, journal = {Virologica Sinica}, volume = {36}, number = {5}, pages = {924-933}, pmid = {33978940}, issn = {1995-820X}, mesh = {Animals ; *COVID-19 ; Chlorocebus aethiops ; Humans ; Metagenomics ; *Microbiota ; SARS-CoV-2 ; Vero Cells ; }, abstract = {As a respiratory tract virus, SARS-CoV-2 infected people through contacting with the upper respiratory tract first. Previous studies indicated that microbiota could modulate immune response against pathogen infection. In the present study, we performed metagenomic sequencing of pharyngeal swabs from eleven patients with COVID-19 and eleven Non-COVID-19 patients who had similar symptoms such as fever and cough. Through metagenomic analysis of the above two groups and a healthy group from the public data, there are 6502 species identified in the samples. Specifically, the Pielou index indicated a lower evenness of the microbiota in the COVID-19 group than that in the Non-COVID-19 group. Combined with the linear discriminant analysis (LDA) and the generalized linear model, eighty-one bacterial species were found with increased abundance in the COVID-19 group, where 51 species were enriched more than 8 folds. The top three enriched genera were Streptococcus, Prevotella and Campylobacter containing some opportunistic pathogens. More interestingly, through experiments, we found that two Streptococcus strains, S. suis and S. agalactiae, could stimulate the expression of ACE2 of Vero cells in vitro, which may promote SARS-CoV-2 infection. Therefore, these enriched pathogens in the pharynxes of COVID-19 patients may involve in the virus-host interactions to affect SARS-CoV-2 infection and cause potential secondary bacterial infections through changing the expression of the viral receptor ACE2 and/or modulate the host's immune system.}, } @article {pmid33975945, year = {2021}, author = {Ruiz-Padilla, A and Rodríguez-Romero, J and Gómez-Cid, I and Pacifico, D and Ayllón, MA}, title = {Novel Mycoviruses Discovered in the Mycovirome of a Necrotrophic Fungus.}, journal = {mBio}, volume = {12}, number = {3}, pages = {}, pmid = {33975945}, issn = {2150-7511}, mesh = {Botrytis/*virology ; Fungal Viruses/*classification/*genetics/isolation & purification ; *Genome, Viral ; Italy ; *Phylogeny ; Plant Diseases/microbiology ; RNA, Viral/genetics ; *Virome ; Vitis/microbiology ; }, abstract = {Botrytis cinerea is one of the most important plant-pathogenic fungus. Products based on microorganisms can be used in biocontrol strategies alternative to chemical control, and mycoviruses have been explored as putative biological agents in such approaches. Here, we have explored the mycovirome of B. cinerea isolates from grapevine of Italy and Spain to increase the knowledge about mycoviral diversity and evolution, and to search for new widely distributed mycoviruses that could be active ingredients in biological products to control this hazardous fungus. A total of 248 B. cinerea field isolates were used for our metatranscriptomic study. Ninety-two mycoviruses were identified: 62 new mycoviral species constituting putative novel viral genera and families. Of these mycoviruses, 57 had a positive-sense single-stranded RNA (ssRNA) genome, 19 contained a double-stranded RNA (dsRNA) genome, 15 had a negative-sense ssRNA genome, and 1 contained a single-stranded DNA (ssDNA) genome. In general, ssRNA mycoviruses were widely distributed in all sampled regions, the ssDNA mycovirus was more frequently found in Spain, and dsRNA mycoviruses were scattered in some pools of both countries. Some of the identified mycoviruses belong to clades that have never been found associated with Botrytis species: Botrytis-infecting narnaviruses; alpha-like, umbra-like, and tymo-like ssRNA+ mycoviruses; trisegmented ssRNA- mycovirus; bisegmented and tetrasegmented dsRNA mycoviruses; and finally, an ssDNA mycovirus. Among the results obtained in this massive mycovirus screening, the discovery of novel bisegmented viruses, phylogenetically related to narnaviruses, is remarkable.IMPORTANCE The results obtained here have expanded our knowledge of mycoviral diversity, horizontal transfers, and putative cross-kingdom events. To date, this study presents the most extensive and wide diversity collection of mycoviruses infecting the necrotrophic fungus B. cinerea The collection included all types of mycoviruses, with dsRNA, ssRNA+, ssRNA-, and ssDNA genomes, most of which were discovered here, and some of which were previously reported as infecting B. cinerea or other plant-pathogenic fungi. Some of these mycoviruses are reported for the first time here associated with B. cinerea, as a trisegmented ssRNA- mycovirus and as an ssDNA mycovirus, but even more remarkablly, we also describe here four novel bisegmented viruses (binarnaviruses) not previously described in nature. The present findings significantly contribute to general knowledge in virology and more particularly in the field of mycovirology.}, } @article {pmid33975936, year = {2021}, author = {Sukhum, KV and Vargas, RC and Boolchandani, M and D'Souza, AW and Patel, S and Kesaraju, A and Walljasper, G and Hegde, H and Ye, Z and Valenzuela, RK and Gunderson, P and Bendixsen, C and Dantas, G and Shukla, SK}, title = {Manure Microbial Communities and Resistance Profiles Reconfigure after Transition to Manure Pits and Differ from Those in Fertilized Field Soil.}, journal = {mBio}, volume = {12}, number = {3}, pages = {}, pmid = {33975936}, issn = {2150-7511}, support = {K22 HG000045/HG/NHGRI NIH HHS/United States ; R25 GM103757/GM/NIGMS NIH HHS/United States ; T32 GM007200/GM/NIGMS NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; U54 OH008085/OH/NIOSH CDC HHS/United States ; U54OH008085/ACL/ACL HHS/United States ; R01 OH011578/OH/NIOSH CDC HHS/United States ; }, mesh = {Agriculture ; Animals ; Anti-Bacterial Agents/*pharmacology ; Cattle ; Dairying ; Drug Resistance, Microbial/genetics ; Farms ; Female ; Genes, Bacterial ; Manure/*microbiology ; Metagenome ; *Metagenomics ; Microbiota/*drug effects/*genetics ; Seasons ; *Soil Microbiology ; }, abstract = {In agricultural settings, microbes and antimicrobial resistance genes (ARGs) have the potential to be transferred across diverse environments and ecosystems. The consequences of these microbial transfers are unclear and understudied. On dairy farms, the storage of cow manure in manure pits and subsequent application to field soil as a fertilizer may facilitate the spread of the mammalian gut microbiome and its associated ARGs to the environment. To determine the extent of both taxonomic and resistance similarity during these transitions, we collected fresh manure, manure from pits, and field soil across 15 different dairy farms for three consecutive seasons. We used a combination of shotgun metagenomic sequencing and functional metagenomics to quantitatively interrogate taxonomic and ARG compositional variation on farms. We found that as the microbiome transitions from fresh dairy cow manure to manure pits, microbial taxonomic compositions and resistance profiles experience distinct restructuring, including decreases in alpha diversity and shifts in specific ARG abundances that potentially correspond to fresh manure going from a gut-structured community to an environment-structured community. Further, we did not find evidence of shared microbial community or a transfer of ARGs between manure and field soil microbiomes. Our results suggest that fresh manure experiences a compositional change in manure pits during storage and that the storage of manure in manure pits does not result in a depletion of ARGs. We did not find evidence of taxonomic or ARG restructuring of soil microbiota with the application of manure to field soils, as soil communities remained resilient to manure-induced perturbation.IMPORTANCE The addition of dairy cow manure-stored in manure pits-to field soil has the potential to introduce not only organic nutrients but also mammalian microbial communities and antimicrobial resistance genes (ARGs) to soil communities. Using shotgun sequencing paired with functional metagenomics, we showed that microbial community composition changed between fresh manure and manure pit samples with a decrease in gut-associated pathobionts, while ARG abundance and diversity remained high. However, field soil communities were distinct from those in manure in both microbial taxonomic and ARG composition. These results broaden our understanding of the transfer of microbial communities in agricultural settings and suggest that field soil microbial communities are resilient against the deposition of ARGs or microbial communities from manure.}, } @article {pmid33975870, year = {2021}, author = {Brial, F and Chilloux, J and Nielsen, T and Vieira-Silva, S and Falony, G and Andrikopoulos, P and Olanipekun, M and Hoyles, L and Djouadi, F and Neves, AL and Rodriguez-Martinez, A and Mouawad, GI and Pons, N and Forslund, S and Le-Chatelier, E and Le Lay, A and Nicholson, J and Hansen, T and Hyötyläinen, T and Clément, K and Oresic, M and Bork, P and Ehrlich, SD and Raes, J and Pedersen, OB and Gauguier, D and Dumas, ME}, title = {Human and preclinical studies of the host-gut microbiome co-metabolite hippurate as a marker and mediator of metabolic health.}, journal = {Gut}, volume = {70}, number = {11}, pages = {2105-2114}, pmid = {33975870}, issn = {1468-3288}, support = {MR/L01632X/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Biodiversity ; Biomarkers/*metabolism ; Denmark ; Female ; *Gastrointestinal Microbiome ; Hippurates/*metabolism ; Humans ; Magnetic Resonance Spectroscopy ; Male ; Metabolome ; Metagenomics ; Mice ; Middle Aged ; Phenotype ; }, abstract = {OBJECTIVE: Gut microbial products are involved in regulation of host metabolism. In human and experimental studies, we explored the potential role of hippurate, a hepatic phase 2 conjugation product of microbial benzoate, as a marker and mediator of metabolic health.

DESIGN: In 271 middle-aged non-diabetic Danish individuals, who were stratified on habitual dietary intake, we applied [1]H-nuclear magnetic resonance (NMR) spectroscopy of urine samples and shotgun-sequencing-based metagenomics of the gut microbiome to explore links between the urine level of hippurate, measures of the gut microbiome, dietary fat and markers of metabolic health. In mechanistic experiments with chronic subcutaneous infusion of hippurate to high-fat-diet-fed obese mice, we tested for causality between hippurate and metabolic phenotypes.

RESULTS: In the human study, we showed that urine hippurate positively associates with microbial gene richness and functional modules for microbial benzoate biosynthetic pathways, one of which is less prevalent in the Bacteroides 2 enterotype compared with Ruminococcaceae or Prevotella enterotypes. Through dietary stratification, we identify a subset of study participants consuming a diet rich in saturated fat in which urine hippurate concentration, independently of gene richness, accounts for links with metabolic health. In the high-fat-fed mice experiments, we demonstrate causality through chronic infusion of hippurate (20 nmol/day) resulting in improved glucose tolerance and enhanced insulin secretion.

CONCLUSION: Our human and experimental studies show that a high urine hippurate concentration is a general marker of metabolic health, and in the context of obesity induced by high-fat diets, hippurate contributes to metabolic improvements, highlighting its potential as a mediator of metabolic health.}, } @article {pmid33975103, year = {2021}, author = {Wu, D and Zhao, Y and Cheng, L and Zhou, Z and Wu, Q and Wang, Q and Yuan, Q}, title = {Activity and structure of methanogenic microbial communities in sediments of cascade hydropower reservoirs, Southwest China.}, journal = {The Science of the total environment}, volume = {786}, number = {}, pages = {147515}, doi = {10.1016/j.scitotenv.2021.147515}, pmid = {33975103}, issn = {1879-1026}, mesh = {*Archaea/genetics ; China ; Geologic Sediments ; Methane ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Freshwater reservoirs are an important source of the greenhouse gas methane (CH4). However, little is known about the activity and structure of microbial communities involved in methanogenic decomposition of sediment organic matter (SOM) in cascade hydropower reservoirs. In this study, we targeted on sediments of three cascade reservoirs in Wujiang River, Southwest China. Our results showed that the content of sediment organic carbon (SOC) was between 3% and 11%, and it's positively correlated with both C/N ratio and recalcitrant organic carbon content of SOM. Meanwhile, SOC content was positively correlated with CH4 production rates but had no significant correlation with total CO2 production rates of the sediments, when rates were normalized to sediment volume. Resultantly, the sediment anaerobic decomposition rates hardly significantly increase along with the SOC content. These results suggested that the terrestrial organic matter accumulated after damming stimulated CH4 production from the reservoir sediments even though its decomposition rate was limited. Meantime, high throughput sequencing of 16S rRNA genes indicated that not only the hydrogenotrophic and acetoclastic, but also the methylotrophic methanogens (Methanomassiliicoccus) are abundant in the reservoir sediments. Moreover, metagenomic sequencing also suggested that methylotrophic methanogenesis are potentially important in the sediment of cascade reservoirs. Finally, the hydraulic residence time of the reservoir could be the key controlling factor of the structures of bacterial and archaeal communities as well as the CH4 production rates of the reservoir sediments.}, } @article {pmid33974954, year = {2021}, author = {Lima, J and Manning, T and Rutherford, KM and Baima, ET and Dewhurst, RJ and Walsh, P and Roehe, R}, title = {Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions.}, journal = {Journal of microbiological methods}, volume = {186}, number = {}, pages = {106235}, doi = {10.1016/j.mimet.2021.106235}, pmid = {33974954}, issn = {1872-8359}, support = {BB/N01720X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S006567/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacteria/*classification/genetics/*isolation & purification ; Computational Biology/*methods ; DNA, Bacterial/genetics ; *Gastrointestinal Microbiome ; Intestines/*microbiology ; Molecular Sequence Annotation/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Swine/microbiology ; }, abstract = {Environmental microbiome studies rely on fast and accurate bioinformatics tools to characterize the taxonomic composition of samples based on the 16S rRNA gene. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology 2 (QIIME2) are two of the most popular tools available to perform this task. Their underlying algorithms differ in many aspects, and therefore the comparison of the pipelines provides insights into their best use and interpretation of the outcomes. Both of these bioinformatics tools are based on several specialized algorithms pipelined together, but whereas MG-RAST is a user-friendly webserver that clusters rRNA sequences based on their similarity to create Operational Taxonomic Units (OTU), QIIME2 employs DADA2 in the construction of Amplicon Sequence Variants (ASV) by applying an error model that considers the abundance of each sequence and its similarity to other sequences. Taxonomic compositions obtained from the analyses of amplicon sequences of DNA from swine intestinal gut and faecal microbiota samples using MG-RAST and QIIME2 were compared at domain-, phylum-, family- and genus-levels in terms of richness, relative abundance and diversity. We found significant differences between the microbiota profiles obtained from each pipeline. At domain level, bacteria were relatively more abundant using QIIME2 than MG-RAST; at phylum level, seven taxa were identified exclusively by QIIME2; at family level, samples processed in QIIME2 showed higher evenness and richness (assessed by Shannon and Simpson indices). The genus-level compositions obtained from each pipeline were used in partial least squares-discriminant analyses (PLS-DA) to discriminate between sample collection sites (caecum, colon and faeces). The results showed that different genera were found to be significant for the models, based on the Variable Importance in Projection, e.g. when using sequencing data processed by MG-RAST, the three most important genera were Acetitomaculum, Ruminococcus and Methanosphaera, whereas when data was processed using QIIME2, these were Candidatus Methanomethylophilus, Sphaerochaeta and Anaerorhabdus. Furthermore, the application of differential filtering procedures before the PLS-DA revealed higher accuracy when using non-restricted datasets obtained from MG-RAST, whereas datasets obtained from QIIME2 resulted in more accurate discrimination of sample collection sites after removing genera with low relative abundances (<1%) from the datasets. Our results highlight the differences in taxonomic compositions of samples obtained from the two separate pipelines, while underlining the impact on downstream analyses, such as biomarkers identification.}, } @article {pmid33973546, year = {2021}, author = {Breban, M and Beaufrère, M and Glatigny, S}, title = {Intestinal dysbiosis in spondyloarthritis - chicken or egg?.}, journal = {Current opinion in rheumatology}, volume = {33}, number = {4}, pages = {341-347}, doi = {10.1097/BOR.0000000000000800}, pmid = {33973546}, issn = {1531-6963}, mesh = {Dysbiosis ; *Gastrointestinal Microbiome ; HLA-B27 Antigen ; Humans ; *Inflammatory Bowel Diseases ; *Spondylarthritis ; }, abstract = {PURPOSE OF REVIEW: The well-established link between intestinal inflammation and spondyloarthritis (SpA) remains largely unexplained. Recent sequencing technologies have given access to a thorough characterization of the gut microbiota in healthy and disease conditions. This showed that inflammatory bowel disease (IBD) is associated with dysbiosis - i.e., disturbed gut microbiota composition - which may contribute to disease pathogenesis. Whether gut dysbiosis exists in SpA and could contribute to disease development or be a bystander consequence of chronic inflammation is a question of major interest.

RECENT FINDINGS: Several metagenomic studies have been performed in SpA. Most of them concerned faecal samples and showed dysbiosis consisting in a reduction of microbial biodiversity in a way similar to what has been described in IBD. They also highlighted changes in microbial taxa composition that could contribute to the inflammatory process. Likewise, healthy carriers of human leukocyte antigen (HLA)-B27 exhibited gut dysbiosis, indicating that this predisposing allele could exert its pathogenic effect by influencing microbiota composition, and possibly by driving antigen-specific cross-reactive immune response. On the other hand, SpA treatments were associated with a reduction of dysbiosis, showing that it is at least in part a consequence of inflammation.

SUMMARY: Recent insights from metagenomic studies warrant further investigations to identify the mechanisms by which microbial dysbiosis could contribute to SpA development. This would bring novel therapeutic opportunities aiming at correcting detrimental changes.}, } @article {pmid33973321, year = {2021}, author = {Lugli, GA and Alessandri, G and Milani, C and Viappiani, A and Fontana, F and Tarracchini, C and Mancabelli, L and Argentini, C and Ruiz, L and Margolles, A and van Sinderen, D and Turroni, F and Ventura, M}, title = {Genetic insights into the dark matter of the mammalian gut microbiota through targeted genome reconstruction.}, journal = {Environmental microbiology}, volume = {23}, number = {6}, pages = {3294-3305}, pmid = {33973321}, issn = {1462-2920}, mesh = {Animals ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Genome, Bacterial/genetics ; Metagenome ; Metagenomics ; }, abstract = {Whole metagenomic shotgun (WMS) sequencing has dramatically enhanced our ability to study microbial genomics. The possibility to unveil the genetic makeup of bacteria that cannot be easily isolated has significantly expanded our microbiological horizon. Here, we report an approach aimed at uncovering novel bacterial species by the use of targeted WMS sequencing. Employing in silico data retrieved from metabolic modelling to formulate a chemically defined medium (CDM), we were able to isolate and subsequently sequence the genomes of six putative novel species of bacteria from the gut of non-human primates.}, } @article {pmid33973044, year = {2021}, author = {Fadiji, AE and Kanu, JO and Babalola, OO}, title = {Impact of cropping systems on the functional diversity of rhizosphere microbial communities associated with maize plant: a shotgun approach.}, journal = {Archives of microbiology}, volume = {203}, number = {6}, pages = {3605-3613}, pmid = {33973044}, issn = {1432-072X}, support = {UID123634//National Research Foundation/ ; }, mesh = {Crops, Agricultural/*microbiology ; Metagenomics ; *Microbiota ; *Rhizosphere ; *Soil Microbiology ; Zea mays/*microbiology ; }, abstract = {Understanding the functions carried out by rhizosphere microbiomes will further explore their importance in biotechnological improvement and agricultural sustainability. This study presents one of the foremost attempts to understand the functional diversity of the rhizosphere microbiome in mono-cropping and crop rotation farming sites using shotgun metagenomic techniques. We hypothesized that the functional diversity would vary in the cropping sites and more abundant in the rotational cropping site. Hence, we carried out complete DNA extraction from the bulk and rhizospheric soils associated with maize plant cultivated on the mono-cropping farm (LT and LTc) and the crop rotation farm (VD and VDc), respectively, and sequenced employing shotgun approach. Using the SEED subsystem, our result revealed that a total of 24 functional categories dominated the rotational cropping site, while four functional categories dominated the mono-cropping sites. Alpha diversity assessment showed that no significant difference (p > 0.05) was observed across the cropping sites, while beta diversity assessment revealed a significant difference. Going by the high abundance of functional groups observed in the samples from the crop rotational site, it is evident that cropping systems influenced the functions of soil microbiomes. Worthy of note is the high abundance of unknown functions associated with these maize rhizosphere microbiomes. This is an indication that there are still some under-investigated functional genes associated with the maize rhizosphere microbiome. It is, therefore, imperative that further studies explore these functional genes for their agricultural and biotechnological potentials.}, } @article {pmid33972725, year = {2021}, author = {Jian, H and Yi, Y and Wang, J and Hao, Y and Zhang, M and Wang, S and Meng, C and Zhang, Y and Jing, H and Wang, Y and Xiao, X}, title = {Diversity and distribution of viruses inhabiting the deepest ocean on Earth.}, journal = {The ISME journal}, volume = {15}, number = {10}, pages = {3094-3110}, pmid = {33972725}, issn = {1751-7370}, mesh = {Archaea/genetics ; *Ecosystem ; Oceans and Seas ; Seawater ; *Viruses/genetics ; }, abstract = {As the most abundant biological entities on the planet, viruses significantly influence the overall functioning of marine ecosystems. The abundance, distribution, and biodiversity of viral communities in the upper ocean have been relatively well studied, but our understanding of viruses in the hadal biosphere remains poor. Here, we established the oceanic trench viral genome dataset (OTVGD) by analysing 19 microbial metagenomes derived from seawater and sediment samples of the Mariana, Yap, and Kermadec Trenches. The trench viral communities harbored remarkably high novelty, and they were predicted to infect ecologically important microbial clades, including Thaumarchaeota and Oleibacter. Significant inter-trench and intra-trench exchange of viral communities was proposed. Moreover, viral communities in different habitats (seawater/sediment and depth-stratified ocean zones) exhibited distinct niche-dependent distribution patterns and genomic properties. Notably, microbes and viruses in the hadopelagic seawater seemed to preferably adopt lysogenic lifestyles compared to those in the upper ocean. Furthermore, niche-specific auxiliary metabolic genes were identified in the hadal viral genomes, and a novel viral D-amino acid oxidase was functionally and phylogenetically characterized, suggesting the contribution of these genes in the utilization of refractory organic matter. Together, these findings highlight the genomic novelty, dynamic movement, and environment-driven diversification of viral communities in oceanic trenches, and suggest that viruses may influence the hadal ecosystem by reprogramming the metabolism of their hosts and modulating the community of keystone microbes.}, } @article {pmid33972724, year = {2021}, author = {Ücker, M and Ansorge, R and Sato, Y and Sayavedra, L and Breusing, C and Dubilier, N}, title = {Deep-sea mussels from a hybrid zone on the Mid-Atlantic Ridge host genetically indistinguishable symbionts.}, journal = {The ISME journal}, volume = {15}, number = {10}, pages = {3076-3083}, pmid = {33972724}, issn = {1751-7370}, mesh = {Animals ; Gills ; *Hydrothermal Vents ; *Microbiota/genetics ; *Mytilidae/genetics ; Symbiosis ; }, abstract = {The composition and diversity of animal microbiomes is shaped by a variety of factors, many of them interacting, such as host traits, the environment, and biogeography. Hybrid zones, in which the ranges of two host species meet and hybrids are found, provide natural experiments for determining the drivers of microbiome communities, but have not been well studied in marine environments. Here, we analysed the composition of the symbiont community in two deep-sea, Bathymodiolus mussel species along their known distribution range at hydrothermal vents on the Mid-Atlantic Ridge, with a focus on the hybrid zone where they interbreed. In-depth metagenomic analyses of the sulphur-oxidising symbionts of 30 mussels from the hybrid zone, at a resolution of single nucleotide polymorphism analyses of ~2500 orthologous genes, revealed that parental and hybrid mussels (F2-F4 generation) have genetically indistinguishable symbionts. While host genetics does not appear to affect symbiont composition in these mussels, redundancy analyses showed that geographic location of the mussels on the Mid-Atlantic Ridge explained most of the symbiont genetic variability compared to the other factors. We hypothesise that geographic structuring of the free-living symbiont population plays a major role in driving the composition of the microbiome in these deep-sea mussels.}, } @article {pmid33972424, year = {2021}, author = {Fellows Yates, JA and Velsko, IM and Aron, F and Posth, C and Hofman, CA and Austin, RM and Parker, CE and Mann, AE and Nägele, K and Arthur, KW and Arthur, JW and Bauer, CC and Crevecoeur, I and Cupillard, C and Curtis, MC and Dalén, L and Díaz-Zorita Bonilla, M and Díez Fernández-Lomana, JC and Drucker, DG and Escribano Escrivá, E and Francken, M and Gibbon, VE and González Morales, MR and Grande Mateu, A and Harvati, K and Henry, AG and Humphrey, L and Menéndez, M and Mihailović, D and Peresani, M and Rodríguez Moroder, S and Roksandic, M and Rougier, H and Sázelová, S and Stock, JT and Straus, LG and Svoboda, J and Teßmann, B and Walker, MJ and Power, RC and Lewis, CM and Sankaranarayanan, K and Guschanski, K and Wrangham, RW and Dewhirst, FE and Salazar-García, DC and Krause, J and Herbig, A and Warinner, C}, title = {The evolution and changing ecology of the African hominid oral microbiome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {20}, pages = {}, pmid = {33972424}, issn = {1091-6490}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE024468/DE/NIDCR NIH HHS/United States ; R01 GM089886/GM/NIGMS NIH HHS/United States ; R37 DE016937/DE/NIDCR NIH HHS/United States ; }, mesh = {Africa ; Animals ; Bacteria/classification/genetics ; Biofilms ; *Biological Evolution ; Dental Plaque/microbiology ; Ecology/*methods ; Geography ; Gorilla gorilla/microbiology ; Hominidae/classification/*microbiology ; Humans ; Metagenome/*genetics ; Microbiota/*genetics ; Mouth/*microbiology ; Pan troglodytes/microbiology ; Phylogeny ; }, abstract = {The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine-platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.}, } @article {pmid33970781, year = {2021}, author = {Collins, FWJ and Walsh, CJ and Gomez-Sala, B and Guijarro-García, E and Stokes, D and Jakobsdóttir, KB and Kristjánsson, K and Burns, F and Cotter, PD and Rea, MC and Hill, C and Ross, RP}, title = {The microbiome of deep-sea fish reveals new microbial species and a sparsity of antibiotic resistance genes.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-13}, pmid = {33970781}, issn = {1949-0984}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Atlantic Ocean ; Bacteria/classification/*drug effects/genetics/*isolation & purification ; Bacterial Proteins/*genetics/metabolism ; Drug Resistance, Bacterial ; Ecosystem ; Fishes/classification/*microbiology ; *Gastrointestinal Microbiome ; Intestines/microbiology ; Phylogeny ; }, abstract = {Adaptation to life in the deep-sea can be dramatic, with fish displaying behaviors and appearances unlike those seen in any other aquatic habitat. However, the extent of which adaptations may have developed at a microbial scale is not as clear. Shotgun metagenomic sequencing of the intestinal microbiome of 32 species of deep-sea fish from across the Atlantic Ocean revealed that many of the associated microbes differ extensively from those previously identified in reference databases. 111 individual metagenome-assembled genomes (MAGs) were constructed representing individual microbial species from the microbiomes of these fish, many of which are potentially novel bacterial taxa and provide a window into the microbial diversity in this underexplored environment. These MAGs also demonstrate how these microbes have adapted to deep-sea life by encoding a greater capacity for several cellular processes such as protein folding and DNA replication that can be inhibited by high pressure. Another intriguing feature was the almost complete lack of genes responsible for acquired resistance to known antibiotics in many of the samples. This highlights that deep-sea fish microbiomes may represent one of few animal-associated microbiomes with little influence from human activity. The ability of the microbes in these samples to bioluminesce is lower than expected given predictions that this trait has an important role in their life cycle at these depths. The study highlights the uniqueness, complexity and adaptation of microbial communities living in one of the largest and harshest environments on Earth.}, } @article {pmid33970544, year = {2021}, author = {Tian, J and Du, J and Zhang, S and Li, Y and Gao, X and Han, J and Lu, Z}, title = {Age-associated variation in the gut microbiota of chinstrap penguins (Pygoscelis antarctica) reveals differences in food metabolism.}, journal = {MicrobiologyOpen}, volume = {10}, number = {2}, pages = {e1190}, pmid = {33970544}, issn = {2045-8827}, support = {OT3 TR002020/TR/NCATS NIH HHS/United States ; }, mesh = {Age Factors ; Animal Feed ; Animals ; Bacteria/*classification/genetics ; DNA, Bacterial ; DNA, Ribosomal ; Feces/*microbiology ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; *Metabolism ; Metagenome ; Microbial Interactions ; Spheniscidae/*microbiology ; }, abstract = {Age is known to affect the gut microbiota in various animals; however, this relationship is poorly understood in seabirds. We investigated the temporal succession of gut microbiota in captive chinstrap penguins of different ages using high-throughput sequencing. The gut microbiota exhibited a significant age succession pattern, reaching maturity in adults and then declining with increasing age. Only 15 amplicon sequence variants were shared among the gut microbiota in chinstrap penguins at all studied ages, and these contributed to most of the age-related variations in total gut microbiota. Co-occurrence networks found that these key bacteria belonged to the genera Acinetobacter, Clostridium sensu stricto, and Fusobacterium, and more species interactions were found within the same taxonomy. Functional prediction indicated that most of the metabolic functions were more abundant in the gut microbiota in adult chinstrap penguins, except for carbohydrate metabolism, which was significantly more abundant in older individuals.}, } @article {pmid33970536, year = {2021}, author = {Tenorio-Salgado, S and Castelán-Sánchez, HG and Dávila-Ramos, S and Huerta-Saquero, A and Rodríguez-Morales, S and Merino-Pérez, E and Roa de la Fuente, LF and Solis-Pereira, SE and Pérez-Rueda, E and Lizama-Uc, G}, title = {Metagenomic analysis and antimicrobial activity of two fermented milk kefir samples.}, journal = {MicrobiologyOpen}, volume = {10}, number = {2}, pages = {e1183}, pmid = {33970536}, issn = {2045-8827}, mesh = {Animals ; Anti-Infective Agents/*metabolism/*pharmacology ; Bacteria/classification/*drug effects ; Biodiversity ; Cultured Milk Products/microbiology ; DNA, Bacterial ; DNA, Fungal ; Fermentation ; Food Microbiology ; Fungi/classification/*drug effects ; Kefir/*microbiology ; *Metagenome ; Metagenomics/methods ; Mexico ; Microbiota ; Milk/microbiology ; Peptides/pharmacology ; Polyketides/pharmacology ; Prophages/genetics ; Secondary Metabolism ; }, abstract = {In recent years, the fermented milk product kefir has been intensively studied because of its health benefits. Here, we evaluated the microbial consortia of two kefir samples, from Escarcega, Campeche, and Campeche (México). We considered a functional comparison between both samples, including fungal and bacterial inhibition; second, we applied shotgun metagenomics to assess the structure and functional diversity of the communities of microorganisms. These two samples exhibited antagonisms against bacterial and fungal pathogens. Bioactive polyketides and nonribosomal peptides were identified by LC-HRMS analysis. We also observed a high bacterial diversity and an abundance of Actinobacteria in both kefir samples, and a greater abundance of Saccharomyces species in kefir of Escarcega than in the Campeche kefir. When the prophage compositions were evaluated, the Campeche sample showed a higher diversity of prophage sequences. In Escarcega, we observed a prevalence of prophage families that infect Enterobacteria and Lactobacillus. The sequences associated with secondary metabolites, such as plipastatin, fengycin, and bacillaene, and also bacteriocins like helveticin and zoocin, were also found in different proportions, with greater diversity in the Escarcega sample. The analyses described in this work open the opportunity to understand the microbial diversity in kefir samples from two distant localities.}, } @article {pmid33970533, year = {2021}, author = {Tan, X and Chai, T and Duan, J and Wu, J and Zhang, H and Li, Y and Huang, Y and Hu, X and Zheng, P and Song, J and Ji, P and Jin, X and Zhang, H and Xie, P}, title = {Dynamic changes occur in the DNA gut virome of female cynomolgus macaques during aging.}, journal = {MicrobiologyOpen}, volume = {10}, number = {2}, pages = {e1186}, pmid = {33970533}, issn = {2045-8827}, mesh = {Aging ; Animals ; Bacteriophages/classification/genetics ; Caudovirales/drug effects/genetics ; DNA, Viral ; Feces/*virology ; Female ; *Gastrointestinal Microbiome ; Macaca fascicularis/*virology ; *Metagenome ; Metagenomics/methods ; Sequence Analysis, DNA ; *Virome ; }, abstract = {Aging is a critical factor affecting physical health and disease in mammals. Emerging evidence indicates that aging may affect the gut bacteriome in cynomolgus macaques, but little is known about whether or how the gut virome changes with age. Here, we compared the DNA gut viral composition of 16 female cynomolgus monkeys (Macaca fascicularis) at three life stages (young, adult, and old) using the shotgun metagenome sequencing method. We found that the DNA gut virome from these monkeys differed substantially among the three groups. The gut viruses were dominated by bacteriophages, the most abundant of which was the Caudovirales order (i.e., Siphoviridae, Myoviridae, and Podoviridae families). Additionally, the co-occurrence analysis revealed that the age-related bacteriophages were correlated in an extensive and complex manner with the main intestinal bacteria (i.e., Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria phyla). Furthermore, the age-related DNA gut viral functions were enriched for genetic information processing, nucleotide, and folate metabolism. Our gut virome analysis provides new insight into how aging influences the gut virome of non-human primates.}, } @article {pmid33969685, year = {2021}, author = {Zhang, T and Zhu, X and Guo, J and Gu, AZ and Li, D and Chen, J}, title = {Toxicity Assessment of Nano-ZnO Exposure on the Human Intestinal Microbiome, Metabolic Functions, and Resistome Using an In Vitro Colon Simulator.}, journal = {Environmental science & technology}, volume = {55}, number = {10}, pages = {6884-6896}, doi = {10.1021/acs.est.1c00573}, pmid = {33969685}, issn = {1520-5851}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Colon ; Drug Resistance, Microbial ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; }, abstract = {Nano-ZnO, as a commonly used nanomaterial, has been found in drinking water, food, and medicine; therefore, it poses potential health risks via the digestion system. However, little is known about the toxicity of nano-ZnO on the human intestinal microbiome, which plays critical roles in human health. This study comprehensively investigated the impact of nano-ZnO on the human gut microbiome, metabolic functions, and resistome using an in vitro colon simulator. Nano-ZnO induced concentration-dependent decreases in the production of short-chain fatty acids (SCFAs). Metagenomic analysis revealed that nano-ZnO not only led to dose-dependent shifts in the composition and diversity of the gut microbiota but also changed the key functional pathways of the gut microbiome. Although the diversity of the gut microbiota basically recovered after stopping exposure to nano-ZnO, SCFAs still showed a concentration-dependent decrease. Furthermore, although a medium concentration of nano-ZnO (2.5 mg/L) reduced the abundance of many antibiotic resistance genes (ARGs) by inhibiting the growth of related host bacteria, a low concentration of nano-ZnO (0.1 mg/L) greatly enriched the abundance of tetracycline resistance genes. Our findings provide evidence that nano-ZnO can impact the diversity, metabolism, and functional pathways of the human gut microbiome, as well as the gut resistome, highlighting the potential health effects of nanoparticles.}, } @article {pmid33968595, year = {2021}, author = {Shet, SA and Garg, S}, title = {Prokaryotic diversity of tropical coastal sand dunes ecosystem using metagenomics.}, journal = {3 Biotech}, volume = {11}, number = {5}, pages = {252}, pmid = {33968595}, issn = {2190-572X}, abstract = {UNLABELLED: Coastal sand dunes (CSDs), unique, stressed and hostile habitats act as a barrier between marine and terrestrial ecosystems. CSDs are stressed in terms of nutrition and fluctuating physio-chemical conditions. CSD is classified into several types, each of which presents different challenges for life forms. This study focuses on exploring bacterial and archaeal diversity and community structure in four CSD namely, Embryo, Fore, Gray, and Mature dunes of Keri beach, Goa along the west coast of India. The study was carried out using Next Generation Sequencing of hypervariable V3-V4 regions of the 16S rRNA gene using Illumina HiSeq platform. The present study hypothesizes that the prokaryotic communities at each dune may be different and could have different role in the ecosystem. The NGS for Embryo, Fore, Gray, and Mature dunes gave 1,045,447, 1,451,753, 1,321,867, and 1,537,758 paired-end reads, respectively, out of which 54,500, 50,032, 37,819, and 111,186 were retained through various quality filtrations. A total of 74, 63, 65, and 65% of OTUs, respectively, remained unknown at the species level. The highest bacterial and archaeal abundance was reported from Mature and Embryo dunes, respectively. Phylum Actinobacteria dominated the Embryo, Fore, and Mature dunes, whereas phylum Proteobacteria was the dominant in the Gray dune. Streptomyces was predominant in overall CSD followed by Bacillus, Acidobacterium, and Kouleothrix. The commonly and exclusively found members in each dune are cataloged. The highest species dominance, diversity, species richness, and abundance were observed in Embryo, Fore, Gray, and Mature dunes, respectively. The present study clearly elucidates that each dune has a distinct microbial community structure.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02809-5.}, } @article {pmid33966342, year = {2021}, author = {Li, P and Lu, B and Gong, J and Li, L and Chen, G and Zhang, J and Chen, Y and Tian, X and Han, B and Guo, Y and Xie, Z and Liao, Q}, title = {Chickpea Extract Ameliorates Metabolic Syndrome Symptoms via Restoring Intestinal Ecology and Metabolic Profile in Type 2 Diabetic Rats.}, journal = {Molecular nutrition & food research}, volume = {65}, number = {13}, pages = {e2100007}, doi = {10.1002/mnfr.202100007}, pmid = {33966342}, issn = {1613-4133}, mesh = {Animals ; Cicer/*chemistry ; Diabetes Mellitus, Experimental ; Diabetes Mellitus, Type 2 ; Diet, High-Fat ; Dysbiosis/drug therapy ; Gastrointestinal Microbiome/*drug effects ; Insulin Resistance ; Intestines/microbiology ; Metabolic Syndrome/*drug therapy ; *Metabolome ; Metformin ; Plant Extracts/*pharmacology ; Prebiotics ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; Streptozocin ; }, abstract = {SCOPE: Chickpeas have been recognized as a natural Uyghur medicine in Xinjiang (China) for 2500 years. Although the phenotypic effect on obesity or diabetes was authenticated, the mechanism was unclear. This work aims to study the effect of chickpea extract (CE) on metabolic syndrome induced by type 2 diabetes and to reveal its related mechanisms, focusing on intestinal flora and metabolomics.

METHODS AND RESULTS: Diabetic rats are induced by a high-fat diet and intraperitoneal injection of streptozotocin. CE supplementation (3 g kg[-1]) for 4 weeks improved the hyperglycemia, inflammatory state, and organ functions of diabetic rats. The metabolic profile trajectories of urine and faeces obtained by NMR have good separations among all groups, and CE significantly increases the contents of SCFAs in the cecum. Moreover, CE relieves intestinal dysbiosis by increasing the abundance of SCFAs-producing bacteria (e.g., Enterococcaceae) but reduces conditional pathogenic bacteria (e.g., Corynebacterium). PICRUSt predicts the functions of gut microbiome from the 16S rRNA gene sequences and metagenome, and finds that CE restored amino acids degradation, bile acids metabolism, and carbohydrate metabolism.

CONCLUSION: This study elucidates the role of CE from the perspective of metabolomics and the microbiota, which provides evidence for chickpea as a prebiotic to prevent diabetes.}, } @article {pmid33963313, year = {2021}, author = {Terrisse, S and Derosa, L and Iebba, V and Ghiringhelli, F and Vaz-Luis, I and Kroemer, G and Fidelle, M and Christodoulidis, S and Segata, N and Thomas, AM and Martin, AL and Sirven, A and Everhard, S and Aprahamian, F and Nirmalathasan, N and Aarnoutse, R and Smidt, M and Ziemons, J and Caldas, C and Loibl, S and Denkert, C and Durand, S and Iglesias, C and Pietrantonio, F and Routy, B and André, F and Pasolli, E and Delaloge, S and Zitvogel, L}, title = {Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment.}, journal = {Cell death and differentiation}, volume = {28}, number = {9}, pages = {2778-2796}, pmid = {33963313}, issn = {1476-5403}, support = {16942/CRUK_/Cancer Research UK/United Kingdom ; 29567/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Breast Neoplasms/*drug therapy ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Prognosis ; Prospective Studies ; Treatment Outcome ; }, abstract = {The prognosis of early breast cancer (BC) relies on cell autonomous and immune parameters. The impact of the intestinal microbiome on clinical outcome has not yet been evaluated. Shotgun metagenomics was used to determine the composition of the fecal microbiota in 121 specimens from 76 early BC patients, 45 of whom were paired before and after chemotherapy. These patients were enrolled in the CANTO prospective study designed to record the side effects associated with the clinical management of BC. We analyzed associations between baseline or post-chemotherapy fecal microbiota and plasma metabolomics with BC prognosis, as well as with therapy-induced side effects. We examined the clinical relevance of these findings in immunocompetent mice colonized with BC patient microbiota that were subsequently challenged with histo-compatible mouse BC and chemotherapy. We conclude that specific gut commensals that are overabundant in BC patients compared with healthy individuals negatively impact BC prognosis, are modulated by chemotherapy, and may influence weight gain and neurological side effects of BC therapies. These findings obtained in adjuvant and neoadjuvant settings warrant prospective validation.}, } @article {pmid33963194, year = {2021}, author = {Callegari, M and Crotti, E and Fusi, M and Marasco, R and Gonella, E and De Noni, I and Romano, D and Borin, S and Tsiamis, G and Cherif, A and Alma, A and Daffonchio, D}, title = {Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {42}, pmid = {33963194}, issn = {2055-5008}, mesh = {Animals ; *Bacteria/classification/ultrastructure ; *Bees ; *Biodiversity ; *Fungi/classification/ultrastructure ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; }, abstract = {The core gut microbiome of adult honeybee comprises a set of recurring bacterial phylotypes, accompanied by lineage-specific, variable, and less abundant environmental bacterial phylotypes. Several mutual interactions and functional services to the host, including the support provided for growth, hormonal signaling, and behavior, are attributed to the core and lineage-specific taxa. By contrast, the diversity and distribution of the minor environmental phylotypes and fungal members in the gut remain overlooked. In the present study, we hypothesized that the microbial components of forager honeybees (i.e., core bacteria, minor environmental phylotypes, and fungal members) are compartmentalized along the gut portions. The diversity and distribution of such three microbial components were investigated in the context of the physico-chemical conditions of different gut compartments. We observed that changes in the distribution and abundance of microbial components in the gut are consistently compartment-specific for all the three microbial components, indicating that the ecological and physiological interactions among the host and microbiome vary with changing physico-chemical and metabolic conditions of the gut.}, } @article {pmid33962692, year = {2021}, author = {Mayneris-Perxachs, J and Cardellini, M and Hoyles, L and Latorre, J and Davato, F and Moreno-Navarrete, JM and Arnoriaga-Rodríguez, M and Serino, M and Abbott, J and Barton, RH and Puig, J and Fernández-Real, X and Ricart, W and Tomlinson, C and Woodbridge, M and Gentileschi, P and Butcher, SA and Holmes, E and Nicholson, JK and Pérez-Brocal, V and Moya, A and Clain, DM and Burcelin, R and Dumas, ME and Federici, M and Fernández-Real, JM}, title = {Iron status influences non-alcoholic fatty liver disease in obesity through the gut microbiome.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {104}, pmid = {33962692}, issn = {2049-2618}, support = {MR/L01632X/1/MRC_/Medical Research Council/United Kingdom ; MR/M501797/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Iron ; Mice ; *Non-alcoholic Fatty Liver Disease ; Obesity ; }, abstract = {BACKGROUND: The gut microbiome and iron status are known to play a role in the pathophysiology of non-alcoholic fatty liver disease (NAFLD), although their complex interaction remains unclear.

RESULTS: Here, we applied an integrative systems medicine approach (faecal metagenomics, plasma and urine metabolomics, hepatic transcriptomics) in 2 well-characterised human cohorts of subjects with obesity (discovery n = 49 and validation n = 628) and an independent cohort formed by both individuals with and without obesity (n = 130), combined with in vitro and animal models. Serum ferritin levels, as a markers of liver iron stores, were positively associated with liver fat accumulation in parallel with lower gut microbial gene richness, composition and functionality. Specifically, ferritin had strong negative associations with the Pasteurellaceae, Leuconostocaceae and Micrococcaea families. It also had consistent negative associations with several Veillonella, Bifidobacterium and Lactobacillus species, but positive associations with Bacteroides and Prevotella spp. Notably, the ferritin-associated bacterial families had a strong correlation with iron-related liver genes. In addition, several bacterial functions related to iron metabolism (transport, chelation, heme and siderophore biosynthesis) and NAFLD (fatty acid and glutathione biosynthesis) were also associated with the host serum ferritin levels. This iron-related microbiome signature was linked to a transcriptomic and metabolomic signature associated to the degree of liver fat accumulation through hepatic glucose metabolism. In particular, we found a consistent association among serum ferritin, Pasteurellaceae and Micrococcacea families, bacterial functions involved in histidine transport, the host circulating histidine levels and the liver expression of GYS2 and SEC24B. Serum ferritin was also related to bacterial glycine transporters, the host glycine serum levels and the liver expression of glycine transporters. The transcriptomic findings were replicated in human primary hepatocytes, where iron supplementation also led to triglycerides accumulation and induced the expression of lipid and iron metabolism genes in synergy with palmitic acid. We further explored the direct impact of the microbiome on iron metabolism and liver fact accumulation through transplantation of faecal microbiota into recipient's mice. In line with the results in humans, transplantation from 'high ferritin donors' resulted in alterations in several genes related to iron metabolism and fatty acid accumulation in recipient's mice.

CONCLUSIONS: Altogether, a significant interplay among the gut microbiome, iron status and liver fat accumulation is revealed, with potential significance for target therapies. Video abstract.}, } @article {pmid33961733, year = {2021}, author = {Wu, YW and Singer, SW}, title = {Recovering Individual Genomes from Metagenomes Using MaxBin 2.0.}, journal = {Current protocols}, volume = {1}, number = {5}, pages = {e128}, doi = {10.1002/cpz1.128}, pmid = {33961733}, issn = {2691-1299}, support = {MOST108-2628-E-038-002-MY3//Taiwan Ministry of Science and Technology/ ; }, mesh = {Genome, Microbial ; Humans ; *Metagenome/genetics ; *Microbiota/genetics ; }, abstract = {It is critical to identify individual genomes from microbiomic samples in order to carry out analysis of the microbes. Methods based on existing databases, however, may have limited capabilities in elucidating and quantifying the microbes due to the largely unidentified microbial species in natural or human-associated environments. We thus developed a database-free method, MaxBin 2.0, to aid in the process of recovering microbial genomes from metagenomes in a de novo manner. The recovery of individual genomes allows analysis of the microbiome in terms of a collection of microbial genomes so that one can understand the functional roles of each species. The data of individual microbes may then be analyzed collectively to untangle the interactions between different microbial organisms. By reporting the genome abundance information for co-assembled metagenomes, one may also identify which microorganisms dominate the microbiome and which species may co-occur from the MaxBin 2.0 results. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Recovering genomes from one shotgun metagenome with coverage information Basic Protocol 2: Recovering genomes from one shotgun metagenome without coverage information Basic Protocol 3: Recovering genomes given multiple shotgun metagenomes with coverage information for each metagenome Basic Protocol 4: Recovering genomes given multiple shotgun metagenomes without coverage information Support Protocol 1: MaxBin installation Support Protocol 2: Assembling and co-assembling NGS reads.}, } @article {pmid33961112, year = {2021}, author = {Lim, SH and Shin, JH and Lee, JW and Lee, Y and Seo, JH}, title = {Differences in the eyelid and buccal microbiome of glaucoma patients receiving long-term administration of prostaglandin analog drops.}, journal = {Graefe's archive for clinical and experimental ophthalmology = Albrecht von Graefes Archiv fur klinische und experimentelle Ophthalmologie}, volume = {259}, number = {10}, pages = {3055-3065}, pmid = {33961112}, issn = {1435-702X}, support = {VHSMC19022//VHS Medical Center Research Grant/ ; }, mesh = {Eyelids ; *Glaucoma/drug therapy ; *Glaucoma, Open-Angle/drug therapy ; Humans ; *Microbiota ; Prostaglandins, Synthetic ; RNA, Ribosomal, 16S/genetics ; }, abstract = {PURPOSE: To investigate the differences in the eyelid and buccal microbiomes between patients receiving long-term prostaglandin analogs for open-angle glaucoma (PG-OAG) and naïve-OAG patients by using metagenomics.

METHODS: Eyelid and buccal samples were collected from 30 PG-OAG and 32 naïve-OAG patients. The taxonomic composition of the microbiome was obtained via 16S rRNA gene sequencing, operational taxonomic unit analysis, and diversity analysis. Differential gene expression analysis (DEG) and Bland-Altman (MA) plots were used to determine taxon differences between the microbiomes of PG-OAG and naïve-OAG patients.

RESULTS: The eyelid microbiome showed marginally significant differences, while the alpha-diversity of the buccal microbiome showed significant differences between PG-OAG and naïve-OAG patients. However, the beta-diversity of both eyelid and buccal microbiomes was higher in PG-OAG patients than in naïve-OAG patients. The MA plot showed cluster differences in the eyelid microbiome. DEG analysis of the eyelid microbiome revealed various taxa differences, including enrichment of Azomonas, Pseudomonas, and Granulicatella in PG-OAG patients over naïve-OAG patients, as well as significant depletion of Delftia and Rothia. In the buccal microbiome in PG-OAG patients, taxa such as Rikenella and Stenotrophomonas were significantly enriched.

CONCLUSION: Our findings suggest that the eyelid microbiome differs between PG-OAG and naïve-OAG patients, raising concerns regarding the eyelid environment in patients receiving these drugs. The overexpressed microbiome in the eyelid area suggests that microbiota may change after the administration of glaucoma medications in OAG.}, } @article {pmid33960282, year = {2021}, author = {Wang, S and Zeng, S and Egan, M and Cherry, P and Strain, C and Morais, E and Boyaval, P and Ryan, CA and M Dempsey, E and Ross, RP and Stanton, C}, title = {Metagenomic analysis of mother-infant gut microbiome reveals global distinct and shared microbial signatures.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-24}, pmid = {33960282}, issn = {1949-0984}, mesh = {Adult ; Bacteria/classification/genetics/*isolation & purification ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Infant ; Male ; Metagenome ; Metagenomics ; Mothers ; Phylogeny ; }, abstract = {Emerging evidence indicates maternal microbiota as one major reservoir for pioneering microbes in infants. However, the global distinct and identical features of mother-infant gut microbiota at various taxonomic resolutions and metabolic functions across cohorts and potential of infant microbial prediction based on their paired mother's gut microbiota remain unclear. Here, we analyzed 376 mother-infant dyads (468 mother and 1024 infant samples) of eight studies from six countries and observed higher diversity at species and strain levels in maternal gut microbiota but not their metabolic functions. A number of 290 species were shared in at least one mother-infant dyad, with 26 species (five at strain level) observed across cohorts. The profile of mother-infant shared species and strains was further influenced by delivery mode and feeding regimen. The mother-sourced species in infants exhibited similar strain heterogeneity but more metabolic functions compared to other-sourced species, suggesting the comparable stability and fitness of shared and non-shared species and the potential role of shared species in the early gut microbial community, respectively. Predictive models showed moderate performance accuracy for shared species and strains occurrences in infants. These generalized mother-infant shared species and strains may be considered as the primary targets for future work toward infant microbiome development and probiotics exploration.}, } @article {pmid33958598, year = {2021}, author = {Heinken, A and Hertel, J and Thiele, I}, title = {Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis.}, journal = {NPJ systems biology and applications}, volume = {7}, number = {1}, pages = {19}, pmid = {33958598}, issn = {2056-7189}, support = {RF1 AG058942/AG/NIA NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; }, mesh = {Child ; *Crohn Disease ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases ; Metagenomics ; }, abstract = {Inflammatory bowel diseases, such as Crohn's Disease, are characterised by an altered blood and faecal metabolome, and changes in gut microbiome composition. Here, we present an efficient, scalable, tractable systems biology framework to mechanistically link microbial strains and faecal metabolites. We retrieve strain-level relative abundances from metagenomics data from a cohort of paediatric Crohn's Disease patients with and without dysbiosis and healthy control children and construct and interrogate a personalised microbiome model for each sample. Predicted faecal secretion profiles and strain-level contributions to each metabolite vary broadly between healthy, dysbiotic, and non-dysbiotic microbiomes. The reduced microbial diversity in IBD results in reduced numbers of secreted metabolites, especially in sulfur metabolism. We demonstrate that increased potential to synthesise amino acids is linked to Proteobacteria contributions, in agreement with experimental observations. The established modelling framework yields testable hypotheses that may result in novel therapeutic and dietary interventions targeting the host-gut microbiome-diet axis.}, } @article {pmid33956889, year = {2021}, author = {Thapa, S and Venkatachalam, A and Khan, N and Naqvi, M and Balderas, M and Runge, JK and Haag, A and Hoch, KM and Glaze, DG and Luna, RA and Motil, KJ}, title = {Assessment of the gut bacterial microbiome and metabolome of girls and women with Rett Syndrome.}, journal = {PloS one}, volume = {16}, number = {5}, pages = {e0251231}, pmid = {33956889}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; Feces/chemistry/microbiology ; Female ; Gas Chromatography-Mass Spectrometry ; Gastrointestinal Diseases/etiology/metabolism/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Metabolome ; Phenotype ; RNA, Ribosomal, 16S/genetics ; Rett Syndrome/complications/metabolism/*microbiology ; Sequence Analysis, DNA ; Severity of Illness Index ; Young Adult ; }, abstract = {BACKGROUND: Gastrointestinal problems affect the health and quality of life of individuals with Rett syndrome (RTT) and pose a medical hardship for their caregivers. We hypothesized that the variability in the RTT phenotype contributes to the dysbiosis of the gut microbiome and metabolome in RTT, predisposing these individuals to gastrointestinal dysfunction.

OBJECTIVES: We characterized the gut bacterial microbiome and metabolome in girls and young women with RTT (n = 44) and unaffected controls (n = 21), and examined the relation between the composition of the microbiome and variations in the RTT phenotype.

METHODS: Demographics and clinical information, including growth and anthropometric measurements, pubertal status, symptoms, clinical severity score, bowel movement, medication use, and dietary intakes were collected from the participants. Fecal samples were collected for analysis of the gut microbiome using Illumina MiSeq-based next-generation sequencing of the 16S rRNA gene followed by bioinformatics analysis of microbial composition, diversity, and community structure. Selected end-products of microbial protein metabolism were characterized by liquid chromatography-mass spectrometry.

RESULTS: The gut bacterial microbiome differed within the RTT cohort based on pubertal status (p<0.02) and clinical severity scores (p<0.02) of the individuals and the type of diet (p<0.01) consumed. Although the composition of the gut microbiome did not differ between RTT and unaffected individuals, concentrations of protein end-products of the gut bacterial metabolome, including γ-aminobutyric acid (GABA) (p<0.001), tyrosine (p<0.02), and glutamate (p<0.06), were lower in the RTT cohort. Differences in the microbiome within RTT groups, based on symptomatic anxiety, hyperventilation, abdominal distention, or changes in stool frequency and consistency, were not detected.

CONCLUSIONS: Although variability in the RTT phenotype contributes to the dysbiosis of the gut microbiome, we presently cannot infer causality between gut bacterial dysbiosis and gastrointestinal dysfunction. Nevertheless, alterations in the gut metabolome may provide clues to the pathophysiology of gastrointestinal problems in RTT.}, } @article {pmid33955744, year = {2021}, author = {Kim, WE and Charov, K and Džunková, M and Becraft, ED and Brown, J and Schulz, F and Woyke, T and La Clair, JJ and Stepanauskas, R and Burkart, MD}, title = {Synthase-Selective Exploration of a Tunicate Microbiome by Activity-Guided Single-Cell Genomics.}, journal = {ACS chemical biology}, volume = {16}, number = {5}, pages = {813-819}, pmid = {33955744}, issn = {1554-8937}, support = {P30 NS047101/NS/NINDS NIH HHS/United States ; R01 GM095970/GM/NIGMS NIH HHS/United States ; R21 AI134037/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacillus subtilis/genetics ; Carrier Proteins/chemistry/genetics ; Ciona intestinalis/metabolism ; Computational Biology ; Escherichia coli/genetics ; Flow Cytometry ; Genomics/*methods ; Microbiota/*genetics ; Multigene Family/*genetics ; Peptide Synthases/*metabolism ; Phylogeny ; Polyketides/chemistry ; Secondary Metabolism ; Siderophores/chemistry/*genetics ; Single-Cell Analysis ; }, abstract = {While thousands of environmental metagenomes have been mined for the presence of novel biosynthetic gene clusters, such computational predictions do not provide evidence of their in vivo biosynthetic functionality. Using fluorescent in situ enzyme assay targeting carrier proteins common to polyketide (PKS) and nonribosomal peptide synthetases (NRPS), we applied fluorescence-activated cell sorting to tunicate microbiome to enrich for microbes with active secondary metabolic capabilities. Single-cell genomics uncovered the genetic basis for a wide biosynthetic diversity in the enzyme-active cells and revealed a member of marine Oceanospirillales harboring a novel NRPS gene cluster with high similarity to phylogenetically distant marine and terrestrial bacteria. Interestingly, this synthase belongs to a larger class of siderophore biosynthetic gene clusters commonly associated with pestilence and disease. This demonstrates activity-guided single-cell genomics as a tool to guide novel biosynthetic discovery.}, } @article {pmid33953365, year = {2021}, author = {Thomas, F and Le Duff, N and Wu, TD and Cébron, A and Uroz, S and Riera, P and Leroux, C and Tanguy, G and Legeay, E and Guerquin-Kern, JL}, title = {Isotopic tracing reveals single-cell assimilation of a macroalgal polysaccharide by a few marine Flavobacteria and Gammaproteobacteria.}, journal = {The ISME journal}, volume = {15}, number = {10}, pages = {3062-3075}, pmid = {33953365}, issn = {1751-7370}, mesh = {*Flavobacteriaceae ; Flavobacterium ; *Gammaproteobacteria/genetics ; *Microbiota ; Polysaccharides ; }, abstract = {Algal polysaccharides constitute a diverse and abundant reservoir of organic matter for marine heterotrophic bacteria, central to the oceanic carbon cycle. We investigated the uptake of alginate, a major brown macroalgal polysaccharide, by microbial communities from kelp-dominated coastal habitats. Congruent with cell growth and rapid substrate utilization, alginate amendments induced a decrease in bacterial diversity and a marked compositional shift towards copiotrophic bacteria. We traced [13]C derived from alginate into specific bacterial incorporators and quantified the uptake activity at the single-cell level, using halogen in situ hybridization coupled to nanoscale secondary ion mass spectrometry (HISH-SIMS) and DNA stable isotope probing (DNA-SIP). Cell-specific alginate uptake was observed for Gammaproteobacteria and Flavobacteriales, with carbon assimilation rates ranging from 0.14 to 27.50 fg C µm[-3] h[-1]. DNA-SIP revealed that only a few initially rare Flavobacteriaceae and Alteromonadales taxa incorporated [13]C from alginate into their biomass, accounting for most of the carbon assimilation based on bulk isotopic measurements. Functional screening of metagenomic libraries gave insights into the genes of alginolytic Alteromonadales active in situ. These results highlight the high degree of niche specialization in heterotrophic communities and help constraining the quantitative role of polysaccharide-degrading bacteria in coastal ecosystems.}, } @article {pmid33953314, year = {2021}, author = {Melkonian, C and Fillinger, L and Atashgahi, S and da Rocha, UN and Kuiper, E and Olivier, B and Braster, M and Gottstein, W and Helmus, R and Parsons, JR and Smidt, H and van der Waals, M and Gerritse, J and Brandt, BW and Röling, WFM and Molenaar, D and van Spanning, RJM}, title = {High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {530}, pmid = {33953314}, issn = {2399-3642}, mesh = {Bacteria/*classification/genetics/isolation & purification/metabolism ; Benzene/*metabolism ; *Biodegradation, Environmental ; *Biodiversity ; *Metagenome ; Nitrates/*metabolism ; }, abstract = {A key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and energy source and nitrate as the electron acceptor. Using genome-centric metagenomics plus metatranscriptomics, we demonstrate that most of the community members likely feed on metabolic left-overs or on necromass while only a few of them, from families Rhodocyclaceae and Peptococcaceae, are candidates to degrade benzene. We verify with an additional succession experiment using metabolomics and metabarcoding that these few community members are the actual drivers of benzene degradation. As such, we hypothesize that high species richness is maintained and the complexity of a natural community is stabilized in a controlled environment by the interdependencies between the few benzene degraders and the rest of the community members, ultimately resulting in a food web with different trophic levels.}, } @article {pmid33952659, year = {2021}, author = {Liu, K and Li, Y and Xu, R and Zhang, Y and Zheng, C and Wan, Z and Li, H and Yang, Z and Jin, X and Hao, P and Zhao, J and Zhang, C}, title = {HIV-1 Infection Alters the Viral Composition of Plasma in Men Who Have Sex with Men.}, journal = {mSphere}, volume = {6}, number = {3}, pages = {}, pmid = {33952659}, issn = {2379-5042}, mesh = {Adult ; HIV Infections/*blood/immunology/*virology ; HIV-1/*genetics/*isolation & purification ; Homosexuality, Male/*statistics & numerical data ; Humans ; Male ; Metagenomics/methods ; Viral Load/statistics & numerical data ; Virome/*genetics/immunology ; Young Adult ; }, abstract = {Altered gut virome and expanded abundance of certain viruses were found in HIV-1-infected individuals. It remains largely unknown how plasma virus composition changes during HIV-1 infection and antiretroviral therapy (ART). We performed viral metagenomic analysis on viral particles enriched from human plasma from 101 men who have sex with men (MSM) with or without HIV-1 infection and whether or not on ART and compared the differences in the plasma virome. An increased plasma viral abundance of main eukaryotic viruses was observed during HIV-1 infection in MSM, especially in AIDS patients (CD4[+] T cell counts of <200). Anellovirus, pegivirus and hepatitis B virus (HBV) were the most abundant blood-borne viruses detected among MSM and HIV-1-infected individuals, and anellovirus and pegivirus were closely related to HIV-1 infection. High diversity of anelloviruses was found mostly in HIV-1-infected MSM, and their abundance was positively correlated with the HIV-1 viral load, but negatively correlated with both CD4[+] T cell counts and CD4[+]/CD8[+] ratio; in contrast, the abundance of pegivirus showed opposite correlations. ART usage could restore the plasma virome toward that of HIV-1-negative individuals. These data showed an expansion in abundance of certain viruses during HIV-1 infection, indicating the higher risk of shedding some blood-borne viruses in these individuals. These investigations indicate that both anellovirus and pegivirus may play certain roles in HIV disease progression.IMPORTANCE Though an increasing number of studies have indicated the existence of an interaction between the virome and human health or disease, the specific role of these plasma viral components remains largely unsolved. We provide evidence here that an altered plasma virome profile is associated with different immune status of HIV-1 infection. Specific resident viruses, such as anellovirus and pegivirus, may directly or indirectly participate in the disease progression of HIV-1 infection. These results can help to determine their clinical relevance and design potential therapies.}, } @article {pmid33952388, year = {2021}, author = {Chen, YH and Yang, SH and Tandon, K and Lu, CY and Chen, HJ and Shih, CJ and Tang, SL}, title = {Potential syntrophic relationship between coral-associated Prosthecochloris and its companion sulfate-reducing bacterium unveiled by genomic analysis.}, journal = {Microbial genomics}, volume = {7}, number = {5}, pages = {}, pmid = {33952388}, issn = {2057-5858}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/classification/genetics/metabolism ; Chlorobi/*classification/*genetics/*metabolism ; DNA, Bacterial/genetics ; Desulfovibrionaceae ; Genome ; *Genomics ; Metagenome ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfates/*metabolism ; }, abstract = {Endolithic microbial symbionts in the coral skeleton may play a pivotal role in maintaining coral health. However, compared to aerobic micro-organisms, research on the roles of endolithic anaerobic micro-organisms and microbe-microbe interactions in the coral skeleton are still in their infancy. In our previous study, we showed that a group of coral-associated Prosthecochloris (CAP), a genus of anaerobic green sulphur bacteria, was dominant in the skeleton of the coral Isopora palifera. Though CAP is diverse, the 16S rRNA phylogeny presents it as a distinct clade separate from other free-living Prosthecochloris. In this study, we build on previous research and further characterize the genomic and metabolic traits of CAP by recovering two new high-quality CAP genomes - Candidatus Prosthecochloris isoporae and Candidatus Prosthecochloris sp. N1 - from the coral I. palifera endolithic cultures. Genomic analysis revealed that these two CAP genomes have high genomic similarities compared with other Prosthecochloris and harbour several CAP-unique genes. Interestingly, different CAP species harbour various pigment synthesis and sulphur metabolism genes, indicating that individual CAPs can adapt to a diversity of coral microenvironments. A novel high-quality genome of sulfate-reducing bacterium (SRB)- Candidatus Halodesulfovibrio lyudaonia - was also recovered from the same culture. The fact that CAP and various SRB co-exist in coral endolithic cultures and coral skeleton highlights the importance of SRB in the coral endolithic community. Based on functional genomic analysis of Ca. P. sp. N1, Ca. P. isoporae and Ca. H. lyudaonia, we also propose a syntrophic relationship between the SRB and CAP in the coral skeleton.}, } @article {pmid33952353, year = {2021}, author = {Newman, TM and Shively, CA and Register, TC and Appt, SE and Yadav, H and Colwell, RR and Fanelli, B and Dadlani, M and Graubics, K and Nguyen, UT and Ramamoorthy, S and Uberseder, B and Clear, KYJ and Wilson, AS and Reeves, KD and Chappell, MC and Tooze, JA and Cook, KL}, title = {Diet, obesity, and the gut microbiome as determinants modulating metabolic outcomes in a non-human primate model.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {100}, pmid = {33952353}, issn = {2049-2618}, support = {P30 AG049638/AG/NIA NIH HHS/United States ; P30 CA012197/CA/NCI NIH HHS/United States ; UL1 TR001420/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Animals ; Bacteroides ; Diet ; Feces ; Female ; *Gastrointestinal Microbiome ; Humans ; Lactobacillus ; Obesity ; Prevotella ; Primates ; }, abstract = {BACKGROUND: The objective of this study was to increase understanding of the complex interactions between diet, obesity, and the gut microbiome of adult female non-human primates (NHPs). Subjects consumed either a Western (n=15) or Mediterranean (n=14) diet designed to represent human dietary patterns for 31 months. Body composition was determined using CT, fecal samples were collected, and shotgun metagenomic sequencing was performed. Gut microbiome results were grouped by diet and adiposity.

RESULTS: Diet was the main contributor to gut microbiome bacterial diversity. Adiposity within each diet was associated with subtle shifts in the proportional abundance of several taxa. Mediterranean diet-fed NHPs with lower body fat had a greater proportion of Lactobacillus animalis than their higher body fat counterparts. Higher body fat Western diet-fed NHPs had more Ruminococcus champaneliensis and less Bacteroides uniformis than their low body fat counterparts. Western diet-fed NHPs had significantly higher levels of Prevotella copri than Mediterranean diet NHPs. Western diet-fed subjects were stratified by P. copri abundance (P. copri[HIGH] versus P. copri[LOW]), which was not associated with adiposity. Overall, Western diet-fed animals in the P. copri[HIGH] group showed greater proportional abundance of B. ovatus, B. faecis, P. stercorea, P. brevis, and Faecalibacterium prausnitzii than those in the Western P. copri[LOW] group. Western diet P. copri[LOW] subjects had a greater proportion of Eubacterium siraeum. E. siraeum negatively correlated with P. copri proportional abundance regardless of dietary consumption. In the Western diet group, Shannon diversity was significantly higher in P. copri[LOW] when compared to P. copri[HIGH] subjects. Furthermore, gut E. siraeum abundance positively correlated with HDL plasma cholesterol indicating that those in the P. copri[LOW] population may represent a more metabolically healthy population. Untargeted metabolomics on urine and plasma from Western diet-fed P. copri[HIGH] and P. copri[LOW] subjects suggest early kidney dysfunction in Western diet-fed P. copri[HIGH] subjects.

CONCLUSIONS: In summary, the data indicate diet to be the major influencer of gut bacterial diversity. However, diet and adiposity must be considered together when analyzing changes in abundance of specific bacterial taxa. Interestingly, P. copri appears to mediate metabolic dysfunction in Western diet-fed NHPs. Video abstract.}, } @article {pmid33952321, year = {2021}, author = {Minot, SS and Barry, KC and Kasman, C and Golob, JL and Willis, AD}, title = {geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {135}, pmid = {33952321}, issn = {1474-760X}, support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; }, mesh = {Genomic Islands/*genetics ; Humans ; Immune Checkpoint Inhibitors/pharmacology ; *Immunotherapy ; *Metagenomics ; Microbiota/genetics ; *Software ; Treatment Outcome ; }, abstract = {Researchers must be able to generate experimentally testable hypotheses from sequencing-based observational microbiome experiments to discover the mechanisms underlying the influence of gut microbes on human health. We describe geneshot, a novel bioinformatics tool for identifying testable hypotheses based on gene-level metagenomic analysis of WGS microbiome data. By applying geneshot to two independent previously published cohorts, we identify microbial genomic islands consistently associated with response to immune checkpoint inhibitor (ICI)-based cancer treatment in culturable type strains. The identified genomic islands are within operons involved in type II secretion, TonB-dependent transport, and bacteriophage growth.}, } @article {pmid33952319, year = {2021}, author = {Xavier, RJ}, title = {Translating the human microbiome: a path to improving health.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {78}, pmid = {33952319}, issn = {1756-994X}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Diet ; Disease Susceptibility ; Energy Metabolism ; *Homeostasis ; *Host Microbial Interactions ; Humans ; Metagenome ; Metagenomics/methods ; Microbiota/*physiology ; T-Lymphocytes/immunology/metabolism ; }, } @article {pmid33951854, year = {2021}, author = {Mohapatra, B and Saha, A and Chowdhury, AN and Kar, A and Kazy, SK and Sar, P}, title = {Geochemical, metagenomic, and physiological characterization of the multifaceted interaction between microbiome of an arsenic contaminated groundwater and aquifer sediment.}, journal = {Journal of hazardous materials}, volume = {412}, number = {}, pages = {125099}, doi = {10.1016/j.jhazmat.2021.125099}, pmid = {33951854}, issn = {1873-3336}, mesh = {*Arsenic/analysis ; Geologic Sediments ; *Groundwater ; *Microbiota ; *Water Pollutants, Chemical/analysis ; }, abstract = {Geomicrobiological details of the interactions between groundwater microbiome (GWM) and arsenic (As)-rich aquifer sediment of Bengal basin was investigated through microcosm incubations. Role of key microorganisms and their specific interactions with As-bearing minerals was demarcated under organic carbon- amended and -unamended conditions. Acinetobacter (50.8 %), Brevundimonas (7.9 %), Sideroxydans (3.4 %), Alkanindiges (3.0 %) dominated the GWM. The microbiome catalysed considerable alterations in As-bearing mineral [Fe-(hydr)oxide and aluminosilicate] phases resulting in substantial changes in overall geochemistry and release of As (65 μg/L) and Fe (118 μg/L). Synergistic roles of autotrophic, NH4[+]-oxidizing Archaea (Thaumarchaeota) and chemoheterotrophic bacteria (Stenotrophomonas, Pseudomonas, Geobacter) of diverse metabolic abilities (NH4[+]-oxidizing, NO3[-], As/Fe-reducing) were noted for observed changes. Organic carbon supported enhanced microbial growth and As mobilization (upto 403.2 μg As/L) from multiple mineral phases (hematite, magnetite, maghemite, biotite, etc.). In presence of high organic carbon, concerted actions of anaerobic, hydrocarbon-utilizing, As-, Fe-reducing Rhizobium, fermentative Escherichia, anaerobic Bacillales, metal-reducing and organic acid-utilizing Pseudomonas and Achromobacter were implicated in altering sediment mineralogy and biogeochemistry. Increase in abundance of arrA, arsC, bssA genes, and dissolution of Fe, Ca, Mg, Mn confirmed that dissimilatory-, cytosolic-As reduction, and mineral weathering fuelled by anaerobic (hydro)carbon metabolism are the predominant mechanisms of As release in aquifers of Bengal basin.}, } @article {pmid33950216, year = {2021}, author = {Hong, J and Bo, T and Xi, L and Xu, X and He, N and Zhan, Y and Li, W and Liang, P and Chen, Y and Shi, J and Li, D and Yan, F and Gu, W and Wang, W and Liu, R and Wang, J and Wang, Z and Ning, G}, title = {Reversal of Functional Brain Activity Related to Gut Microbiome and Hormones After VSG Surgery in Patients With Obesity.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {106}, number = {9}, pages = {e3619-e3633}, pmid = {33950216}, issn = {1945-7197}, mesh = {Adult ; Body Weight ; Brain/*physiopathology ; Cerebral Cortex/physiopathology ; Cohort Studies ; Eating ; Female ; Gastrectomy/*methods ; Gastrointestinal Hormones/*blood ; *Gastrointestinal Microbiome ; Ghrelin/blood ; Glucagon-Like Peptide 1/blood ; Humans ; Magnetic Resonance Imaging ; Male ; Motor Cortex/physiopathology ; Obesity/*metabolism/microbiology/*surgery ; Putamen/physiopathology ; Surveys and Questionnaires ; Treatment Outcome ; Young Adult ; }, abstract = {CONTEXT: Vertical sleeve gastrectomy (VSG) is becoming a prioritized surgical intervention for obese individuals; however, the brain circuits that mediate its effective control of food intake and predict surgical outcome remain largely unclear.

OBJECTIVE: We investigated VSG-correlated alterations of the gut-brain axis.

METHODS: In this observational cohort study, 80 patients with obesity were screened. A total of 36 patients together with 26 normal-weight subjects were enrolled and evaluated using the 21-item Three-Factor Eating Questionnaire (TFEQ), MRI scanning, plasma intestinal hormone analysis, and fecal sample sequencing. Thirty-two patients underwent VSG treatment and 19 subjects completed an average of 4-month follow-up evaluation. Data-driven regional homogeneity (ReHo) coupled with seed-based connectivity analysis were used to quantify VSG-related brain activity. Longitudinal alterations of body weight, eating behavior, brain activity, gastrointestinal hormones, and gut microbiota were detected and subjected to repeated measures correlation analysis.

RESULTS: VSG induced significant functional changes in the right putamen (PUT.R) and left supplementary motor area, both of which correlated with weight loss and TFEQ scores. Moreover, postprandial levels of active glucagon-like peptide-1 (aGLP-1) and Ghrelin were associated with ReHo of PUT.R; meanwhile, relative abundance of Clostridia increased by VSG was associated with improvements in aGLP-1 secretion, PUT.R activity, and weight loss. Importantly, VSG normalized excessive functional connectivities with PUT.R, among which baseline connectivity between PUT.R and right orbitofrontal cortex was related to postoperative weight loss.

CONCLUSION: VSG causes correlated alterations of gut-brain axis, including Clostridia, postprandial aGLP-1, PUT.R activity, and eating habits. Preoperative connectivity of PUT.R may represent a potential predictive marker of surgical outcome in patients with obesity.}, } @article {pmid33946648, year = {2021}, author = {Ferrulli, A and Drago, L and Gandini, S and Massarini, S and Bellerba, F and Senesi, P and Terruzzi, I and Luzi, L}, title = {Deep Transcranial Magnetic Stimulation Affects Gut Microbiota Composition in Obesity: Results of Randomized Clinical Trial.}, journal = {International journal of molecular sciences}, volume = {22}, number = {9}, pages = {}, pmid = {33946648}, issn = {1422-0067}, support = {RF-2011-02349303//Ministero della Salute/ ; Ricerca Corrente//IRCCS Multimedica/ ; }, mesh = {Adult ; Aged ; Autonomic Nervous System/physiopathology ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; DNA, Bacterial/genetics/isolation & purification ; Double-Blind Method ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Humans ; Male ; Middle Aged ; Models, Biological ; Norepinephrine/blood ; Obesity/*microbiology/physiopathology/*therapy ; RNA, Ribosomal, 16S/genetics ; Time Factors ; Transcranial Magnetic Stimulation/*methods ; Weight Loss ; Young Adult ; }, abstract = {Growing evidence highlights the crucial role of gut microbiota in affecting different aspects of obesity. Considering the ability of deep transcranial magnetic stimulation (dTMS) to modulate the cortical excitability, the reward system, and, indirectly, the autonomic nervous system (ANS), we hypothesized a potential role of dTMS in affecting the brain-gut communication pathways, and the gut microbiota composition in obesity. In a hospital setting, 22 subjects with obesity (5 M, 17 F; 44.9 ± 2.2 years; BMI 37.5 ± 1.0 kg/m[2]) were randomized into three groups receiving 15 sessions (3 per week for 5 weeks) of high frequency (HF), low frequency (LF) dTMS, or sham stimulation. Fecal samples were collected at baseline and after 5 weeks of treatment. Total bacterial DNA was extracted from fecal samples using the QIAamp DNA Stool Mini Kit (Qiagen, Italy) and analyzed by a metagenomics approach (Ion Torrent Personal Genome Machine). After 5 weeks, a significant weight loss was found in HF (HF: -4.1 ± 0.8%, LF: -1.9 ± 0.8%, sham: -1.3 ± 0.6%, p = 0.042) compared to LF and sham groups, associated with a decrease in norepinephrine compared to baseline (HF: -61.5 ± 15.2%, p < 0.01; LF: -31.8 ± 17.1%, p < 0.05; sham: -35.8 ± 21.0%, p > 0.05). Furthermore, an increase in Faecalibacterium (+154.3% vs. baseline, p < 0.05) and Alistipes (+153.4% vs. baseline, p < 0.05) genera, and a significant decrease in Lactobacillus (-77.1% vs. baseline, p < 0.05) were found in HF. Faecalibacterium variations were not significant compared to baseline in the other two groups (LF: +106.6%, sham: +27.6%; p > 0.05) as well as Alistipes (LF: -54.9%, sham: -15.1%; p > 0.05) and Lactobacillus (LF: -26.0%, sham: +228.3%; p > 0.05) variations. Norepinephrine change significantly correlated with Bacteroides (r[2] = 0.734; p < 0.05), Eubacterium (r[2] = 0.734; p < 0.05), and Parasutterella (r[2] = 0.618; p < 0.05) abundance variations in HF. In conclusion, HF dTMS treatment revealed to be effective in modulating gut microbiota composition in subjects with obesity, reversing obesity-associated microbiota variations, and promoting bacterial species representative of healthy subjects with anti-inflammatory properties.}, } @article {pmid33945308, year = {2021}, author = {Guo, L and He, J and Zhang, J and Zhang, X and Zhang, D and Zhou, L and Yuan, Y and Fu, S and Qiu, Y and Ye, C and Liu, Y and Wu, Z and Hu, CA}, title = {Baicalin-Aluminum Modulates the Broiler Gut Microbiome.}, journal = {DNA and cell biology}, volume = {40}, number = {7}, pages = {881-894}, doi = {10.1089/dna.2021.0080}, pmid = {33945308}, issn = {1557-7430}, mesh = {Aluminum/metabolism/pharmacology ; Animals ; Chickens/*microbiology ; China ; Colistin/pharmacology ; Flavonoids/metabolism/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Poultry/microbiology ; }, abstract = {Baicalin-aluminum regulates the gut microbiome of piglets with diarrhea. However, whether it affects poultry gut microbiome composition and function remains unknown. In this study, we used metagenomic sequencing to explore the effects of baicalin-aluminum on gut microbiome changes in poultry when compared with animals administered colistin sulfate. Our data showed that important gut microbiome components consisted of Ruminococcaceae, Subdoligranulum, Bifidobacterium, Bifidobacterium pseudolongum, and Pseudoflavonifractor when broilers were administered baicalin-aluminum compared with colistin. At the species level, Lactobacillus salivarius, Bacteroides uniformis, Oscillibacter unclassified, Bacteroides fragilis, Ruminococcus torques, and Subdoligranulum unclassified abundance were significantly upregulated upon baicalin-aluminum treatment when compared with colistin administration. In addition, Gene Ontology (GO) enrichment analysis indicated that functional differentially expressed genes, which were in the top 30 GO enrichment terms, were associated with metabolic processes, catalytic activity, and cellular processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that ABC transporters, oxidative phosphorylation, and phosphotransferase systems were the dominant signaling pathways in the baicalin-aluminum group when compared with the colistin group. Taken together, our data indicated that baicalin-aluminum modified broiler gut microbiome composition. These observations enhance our physiological insights of baicalin-aluminum-mediated functions in the broiler microbiome and potentially provide a novel therapy to manage both animal and human health.}, } @article {pmid33944776, year = {2021}, author = {Beghini, F and McIver, LJ and Blanco-Míguez, A and Dubois, L and Asnicar, F and Maharjan, S and Mailyan, A and Manghi, P and Scholz, M and Thomas, AM and Valles-Colomer, M and Weingart, G and Zhang, Y and Zolfo, M and Huttenhower, C and Franzosa, EA and Segata, N}, title = {Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {33944776}, issn = {2050-084X}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; R01 HG005220/HG/NHGRI NIH HHS/United States ; R01 CA230551/CA/NCI NIH HHS/United States ; C10674/A27140/CRUK_/Cancer Research UK/United Kingdom ; U01 CA230551/CA/NCI NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/*classification/*genetics/metabolism ; Computational Biology/*methods ; Humans ; *Metagenome ; Metagenomics/methods ; Microbiota/*genetics/*physiology ; *Phylogeny ; Research Personnel ; Ruminococcus/classification/genetics ; Workflow ; }, abstract = {Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and IBD (1635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unraveled the phylogenetic and functional structure of the common gut microbe Ruminococcus bromii, previously described by only 15 isolate genomes. With open-source implementations and cloud-deployable reproducible workflows, the bioBakery 3 platform can help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial community studies.}, } @article {pmid33944738, year = {2021}, author = {Wojno, JM and Du Toit, E and Deffur, A and Brink, A}, title = {Statement on analysis and interpretation of clinical human gastrointestinal microbiome testing using next-generation sequencing in South Africa.}, journal = {South African medical journal = Suid-Afrikaanse tydskrif vir geneeskunde}, volume = {111}, number = {3}, pages = {203-205}, doi = {10.7196/SAMJ.2021.v111i3.15336}, pmid = {33944738}, issn = {2078-5135}, mesh = {Gastrointestinal Microbiome/*genetics ; *High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; South Africa ; }, abstract = {Advances in DNA sequencing technologies and computational tools over the past few years have led to vast improvements in the metagenomic analysis of the human microbiota. While this has also significantly improved our understanding of the role of the host-microbiome interaction in health and disease, the current clinical expectation is that testing, particularly of the gastrointestinal biome, can be used to diagnose, manage and treat patients. The authors outline the available technologies and highlight current limitations of these techniques to address this clinical demand. Through understanding the limitations of and need for more research and data collection, one can improve the appropriate utilisation and interpretation, as well as the current rational clinical application of these techniques.}, } @article {pmid33942283, year = {2021}, author = {VanWallendael, A and Alvarez, M and Franks, SJ}, title = {Patterns of population genomic diversity in the invasive Japanese knotweed species complex.}, journal = {American journal of botany}, volume = {108}, number = {5}, pages = {857-868}, doi = {10.1002/ajb2.1653}, pmid = {33942283}, issn = {1537-2197}, mesh = {*Fallopia japonica ; Genetic Variation ; Genotype ; *Introduced Species ; Metagenomics ; North America ; }, abstract = {PREMISE: Invasive species are expected to undergo a reduction in genetic diversity due to founder effects, which should limit their ability to adapt to new habitats. Still, many invasive species achieve widespread distributions and dense populations. This paradox of invasions could potentially be overcome through multiple introductions or hybridization, both of which increase genetic diversity. We conducted a population genomics study of Japanese knotweed (Reynoutria japonica), which is a polyploid, clonally reproducing invasive species that has been notoriously successful worldwide despite supposedly low genetic diversity.

METHODS: We used genotyping by sequencing to collect 12,912 SNP markers from 88 samples collected at 38 locations across North America for the species complex. We used alignment-free k-mer hashing analysis in addition to traditional population genetic analyses to account for the challenges of genotyping polyploids.

RESULTS: Genotypes conformed to three genetic clusters, likely representing Japanese knotweed, giant knotweed, and hybrid bohemian knotweed. We found that, contrary to previous findings, the Japanese knotweed cluster had substantial genetic diversity, though it had no apparent genetic structure across the landscape. In contrast, giant knotweed and hybrids showed distinct population groups. We did not find evidence of isolation by distance in the species complex, likely reflecting the stochastic introduction history of this species complex.

CONCLUSIONS: The results indicate that clonal invasive species can show substantial genetic diversity and can be successful at colonizing a variety of habitats without showing evidence of local adaptation or genetic structure.}, } @article {pmid33941890, year = {2021}, author = {Chen, YJ and Leung, PM and Wood, JL and Bay, SK and Hugenholtz, P and Kessler, AJ and Shelley, G and Waite, DW and Franks, AE and Cook, PLM and Greening, C}, title = {Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem.}, journal = {The ISME journal}, volume = {15}, number = {10}, pages = {2986-3004}, pmid = {33941890}, issn = {1751-7370}, mesh = {Bacteria/genetics ; *Ecosystem ; Geologic Sediments ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Ecological theory suggests that habitat disturbance differentially influences distributions of habitat generalist and specialist species. While well-established for macroorganisms, this theory has rarely been explored for microorganisms. Here we tested these principles in permeable (sandy) sediments, ecosystems with much spatiotemporal variation in resource availability and physicochemical conditions. Microbial community composition and function were profiled in intertidal and subtidal sediments using 16S rRNA gene amplicon sequencing and metagenomics, yielding 135 metagenome-assembled genomes. Community composition and metabolic traits modestly varied with sediment depth and sampling date. Several taxa were highly abundant and prevalent in all samples, including within the orders Woeseiales and Flavobacteriales, and classified as habitat generalists; genome reconstructions indicate these taxa are highly metabolically flexible facultative anaerobes and adapt to resource variability by using different electron donors and acceptors. In contrast, obligately anaerobic taxa such as sulfate reducers and candidate lineage MBNT15 were less abundant overall and only thrived in more stable deeper sediments. We substantiated these findings by measuring three metabolic processes in these sediments; whereas the habitat generalist-associated processes of sulfide oxidation and fermentation occurred rapidly at all depths, the specialist-associated process of sulfate reduction was restricted to deeper sediments. A manipulative experiment also confirmed habitat generalists outcompete specialist taxa during simulated habitat disturbance. Together, these findings show metabolically flexible habitat generalists become dominant in highly dynamic environments, whereas metabolically constrained specialists are restricted to narrower niches. Thus, an ecological theory describing distribution patterns for macroorganisms likely extends to microorganisms. Such findings have broad ecological and biogeochemical ramifications.}, } @article {pmid33941275, year = {2021}, author = {Altabtbaei, K and Maney, P and Ganesan, SM and Dabdoub, SM and Nagaraja, HN and Kumar, PS}, title = {Anna Karenina and the subgingival microbiome associated with periodontitis.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {97}, pmid = {33941275}, issn = {2049-2618}, support = {R01 DE022579/DE/NIDCR NIH HHS/United States ; }, mesh = {*Aggressive Periodontitis ; Cross-Sectional Studies ; Humans ; Metagenome ; Metagenomics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Although localized aggressive periodontitis (LAP), generalized aggressive periodontitis (GAP), and chronic periodontitis (CP) are microbially driven diseases, our inability to separate disease-specific associations from those common to all three forms of periodontitis has hampered biomarker discovery. Therefore, we aimed to map the genomic content of, and the biological pathways encoded by, the microbiomes associated with these clinical phenotypes. We also estimated the extent to which these biomes are governed by the Anna Karenina principle (AKP), which states that eubiotic communities are similar between individuals while disease-associated communities are highly individualized.

METHODS: We collected subgingival plaque from 25 periodontally healthy individuals and diseased sites of 59 subjects with stage 3 periodontitis and used shotgun metagenomics to characterize the aggregate of bacterial genes.

RESULTS: Beta-dispersion metrics demonstrated that AKP was most evident in CP, followed by GAP and LAP. We discovered broad dysbiotic signatures spanning the three phenotypes, with over-representation of pathways that facilitate life in an oxygen-poor, protein- and heme-rich, pro-oxidant environment and enhance capacity for attachment and biofilm formation. Phenotype-specific indicators were more readily evident in LAP microbiome than GAP or CP. Genes that enable acetate-scavenging lifestyle, utilization of alternative nutritional sources, oxidative and nitrosative stress responses, and siderophore production were unique to LAP. An attenuation of virulence-related functionalities and stress response from LAP to GAP to CP was apparent. We also discovered that clinical phenotypes of disease resolved variance in the microbiome with greater clarity than the newly established grading system. Importantly, we observed that one third of the metagenome of LAP is unique to this phenotype while GAP shares significant functional and taxonomic features with both LAP and CP, suggesting either attenuation of an aggressive disease or an early-onset chronic disease.

CONCLUSION: Within the limitations of a small sample size and a cross-sectional study design, the distinctive features of the microbiomes associated with LAP and CP strongly persuade us that these are discrete disease entities, while calling into question whether GAP is a separate disease, or an artifact induced by cross-sectional study designs. Further studies on phenotype-specific microbial genes are warranted to explicate their role in disease etiology. Video Abstract.}, } @article {pmid33938389, year = {2021}, author = {Doden, HL and Wolf, PG and Gaskins, HR and Anantharaman, K and Alves, JMP and Ridlon, JM}, title = {Completion of the gut microbial epi-bile acid pathway.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-20}, pmid = {33938389}, issn = {1949-0984}, support = {R01 CA204808/CA/NCI NIH HHS/United States ; }, mesh = {Actinobacteria/genetics ; Bacterial Proteins/genetics/metabolism ; Bile Acids and Salts/*metabolism ; Clostridium/*enzymology/*genetics/*metabolism ; Clostridium Infections/microbiology ; DNA, Bacterial ; Gastrointestinal Microbiome ; Humans ; Hydroxysteroid Dehydrogenases/*genetics/*metabolism ; Lithocholic Acid/metabolism ; NADP/metabolism ; Phylogeny ; Recombinant Proteins/genetics/metabolism ; }, abstract = {Bile acids are detergent molecules that solubilize dietary lipids and lipid-soluble vitamins. Humans synthesize bile acids with α-orientation hydroxyl groups which can be biotransformed by gut microbiota to toxic, hydrophobic bile acids, such as deoxycholic acid (DCA). Gut microbiota can also convert hydroxyl groups from the α-orientation through an oxo-intermediate to the β-orientation, resulting in more hydrophilic, less toxic bile acids. This interconversion is catalyzed by regio- (C-3 vs. C-7) and stereospecific (α vs. β) hydroxysteroid dehydrogenases (HSDHs). So far, genes encoding the urso- (7α-HSDH & 7β-HSDH) and iso- (3α-HSDH & 3β-HSDH) bile acid pathways have been described. Recently, multiple human gut clostridia were reported to encode 12α-HSDH, which interconverts DCA and 12-oxolithocholic acid (12-oxoLCA). 12β-HSDH completes the epi-bile acid pathway by converting 12-oxoLCA to the 12β-bile acid denoted epiDCA; however, a gene(s) encoding this enzyme has yet to be identified. We confirmed 12β-HSDH activity in cultures of Clostridium paraputrificum ATCC 25780. From six candidate C. paraputrificum ATCC 25780 oxidoreductase genes, we discovered the first gene (DR024_RS09610) encoding bile acid 12β-HSDH. Phylogenetic analysis revealed unforeseen diversity for 12β-HSDH, leading to validation of two additional bile acid 12β-HSDHs through a synthetic biology approach. By comparison to a previous phylogenetic analysis of 12α-HSDH, we identified the first potential C-12 epimerizing strains: Collinsella tanakaei YIT 12063 and Collinsella stercoris DSM 13279. A Hidden Markov Model search against human gut metagenomes located putative 12β-HSDH genes in about 30% of subjects within the cohorts analyzed, indicating this gene is relevant in the human gut microbiome.}, } @article {pmid33936102, year = {2021}, author = {El-Far, M and Durand, M and Turcotte, I and Larouche-Anctil, E and Sylla, M and Zaidan, S and Chartrand-Lefebvre, C and Bunet, R and Ramani, H and Sadouni, M and Boldeanu, I and Chamberland, A and Lesage, S and Baril, JG and Trottier, B and Thomas, R and Gonzalez, E and Filali-Mouhim, A and Goulet, JP and Martinson, JA and Kassaye, S and Karim, R and Kizer, JR and French, AL and Gange, SJ and Ancuta, P and Routy, JP and Hanna, DB and Kaplan, RC and Chomont, N and Landay, AL and Tremblay, CL}, title = {Upregulated IL-32 Expression And Reduced Gut Short Chain Fatty Acid Caproic Acid in People Living With HIV With Subclinical Atherosclerosis.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {664371}, pmid = {33936102}, issn = {1664-3224}, support = {R01 AG054324/AG/NIA NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; PJT 148482//CIHR/Canada ; R01 HL140976/HL/NHLBI NIH HHS/United States ; R21 AG059505/AG/NIA NIH HHS/United States ; U01 HL146204/HL/NHLBI NIH HHS/United States ; R01 HL148094/HL/NHLBI NIH HHS/United States ; K01 HL137557/HL/NHLBI NIH HHS/United States ; }, mesh = {Atherosclerosis/*complications/diagnosis/etiology/metabolism ; Biomarkers ; Caproates/*metabolism ; Electrocardiography ; Fatty Acids, Volatile/*metabolism ; Female ; Gastrointestinal Microbiome ; Gastrointestinal Tract/*metabolism ; *Gene Expression Regulation ; HIV Infections/*complications/diagnosis ; Humans ; Interleukins/*genetics/metabolism ; Macrophages/immunology/metabolism ; Male ; Metagenome ; Metagenomics/methods ; Monocytes/immunology/metabolism ; T-Lymphocytes/immunology/metabolism ; Tomography, X-Ray Computed ; }, abstract = {Despite the success of antiretroviral therapy (ART), people living with HIV (PLWH) are still at higher risk for cardiovascular diseases (CVDs) that are mediated by chronic inflammation. Identification of novel inflammatory mediators with the inherent potential to be used as CVD biomarkers and also as therapeutic targets is critically needed for better risk stratification and disease management in PLWH. Here, we investigated the expression and potential role of the multi-isoform proinflammatory cytokine IL-32 in subclinical atherosclerosis in PLWH (n=49 with subclinical atherosclerosis and n=30 without) and HIV- controls (n=25 with subclinical atherosclerosis and n=24 without). While expression of all tested IL-32 isoforms (α, β, γ, D, ϵ, and θ) was significantly higher in peripheral blood from PLWH compared to HIV- controls, IL-32D and IL-32θ isoforms were further upregulated in HIV+ individuals with coronary artery atherosclerosis compared to their counterparts without. Upregulation of these two isoforms was associated with increased plasma levels of IL-18 and IL-1β and downregulation of the atheroprotective protein TRAIL, which together composed a unique atherosclerotic inflammatory signature specific for PLWH compared to HIV- controls. Logistic regression analysis demonstrated that modulation of these inflammatory variables was independent of age, smoking, and statin treatment. Furthermore, our in vitro functional data linked IL-32 to macrophage activation and production of IL-18 and downregulation of TRAIL, a mechanism previously shown to be associated with impaired cholesterol metabolism and atherosclerosis. Finally, increased expression of IL-32 isoforms in PLWH with subclinical atherosclerosis was associated with altered gut microbiome (increased pathogenic bacteria; Rothia and Eggerthella species) and lower abundance of the gut metabolite short-chain fatty acid (SCFA) caproic acid, measured in fecal samples from the study participants. Importantly, caproic acid diminished the production of IL-32, IL-18, and IL-1β in human PBMCs in response to bacterial LPS stimulation. In conclusion, our studies identified an HIV-specific atherosclerotic inflammatory signature including specific IL-32 isoforms, which is regulated by the SCFA caproic acid and that may lead to new potential therapies to prevent CVD in ART-treated PLWH.}, } @article {pmid33933813, year = {2021}, author = {Wang, B and Zhu, S and Li, W and Tang, Q and Luo, H}, title = {Effects of chromium stress on the rhizosphere microbial community composition of Cyperus alternifolius.}, journal = {Ecotoxicology and environmental safety}, volume = {218}, number = {}, pages = {112253}, doi = {10.1016/j.ecoenv.2021.112253}, pmid = {33933813}, issn = {1090-2414}, abstract = {Wetland plants are often used as the main body of soil, and the rhizosphere is a hot spot migration and transformation. Response mechanism to rhizosphere microorganisms on chromium(Cr) stressing could help improve the phytoremediation system. Cyperus alternifolius(CA) is selected as the research object by Cr-stress treatments and uncontaminated treatments with different cultivated pattern, included sole cultivated pattern(CAI), two-cultivated pattern (CAII), three-cultivated pattern (CAIII), and the un-planted blank samples (CK). 16s rRNA gene sequencing and metagenomic sequencing are performed to measure rhizosphere microbial community. And Five common enzymes in rhizosphere soils were observed: β-1,4-glucosidase (BG), β-N-acetylglucosaminidase (NAG), β-1,4-xylosidase (BX), cellobiohydrolase (CBH) and Leucine amino peptidase (LAP) in the rhizosphere. The results show that Gammaproteobacteria, Actinobacteria, Alphaproteobacteria, Gemmatimonadetes, Deltaproteobacteria are top five (63.97%) of the total sequence number. Wetland plants enriched a large amount of soil Cr in themselves, and the rhizosphere microorganisms don't show significant difference in community structure after affecting. 10.48% variation of microbial community is caused by Cr-stress. Acidovorax showed a great potential for chromium resistance. BX involvement in tolerance processes indirectly affects microbial communities (P < 0.01), there is a strong linear relationship between enzyme activity and the plants accumulating Cr and microbial community within 15.58% variant. The material accumulation and microbial quantity of CAIII are relatively low, but high biodiversity remains after affecting. These results provide references for in-depth understanding of rhizosphere microbial response to heavy metal pollution in wetland phytoremediation and interaction between wetland plants and rhizosphere microorganisms.}, } @article {pmid33931716, year = {2021}, author = {Hinsu, AT and Tulsani, NJ and Panchal, KJ and Pandit, RJ and Jyotsana, B and Dafale, NA and Patil, NV and Purohit, HJ and Joshi, CG and Jakhesara, SJ}, title = {Characterizing rumen microbiota and CAZyme profile of Indian dromedary camel (Camelus dromedarius) in response to different roughages.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {9400}, pmid = {33931716}, issn = {2045-2322}, mesh = {Animals ; Bacterial Proteins/metabolism ; Camelus/*microbiology ; *Carbohydrate Metabolism ; *Diet ; Enzymes/*metabolism ; *Microbiota ; Rumen/*microbiology ; }, abstract = {In dromedary camels, which are pseudo-ruminants, rumen or C1 section of stomach is the main compartment involved in fiber degradation, as in true ruminants. However, as camels are adapted to the harsh and scarce grazing conditions of desert, their ruminal microbiota makes an interesting target of study. The present study was undertaken to generate the rumen microbial profile of Indian camel using 16S rRNA amplicon and shotgun metagenomics. The camels were fed three diets differing in the source of roughage. The comparative metagenomic analysis revealed greater proportions of significant differences between two fractions of rumen content followed by diet associated differences. Significant differences were also observed in the rumen microbiota collected at different time-points of the feeding trial. However, fraction related differences were more highlighted as compared to diet dependent changes in microbial profile from shotgun metagenomics data. Further, 16 genera were identified as part of the core rumen microbiome of Indian camels. Moreover, glycoside hydrolases were observed to be the most abundant among all Carbohydrate-Active enzymes and were dominated by GH2, GH3, GH13 and GH43. In all, this study describes the camel rumen microbiota under different dietary conditions with focus on taxonomic, functional, and Carbohydrate-Active enzymes profiles.}, } @article {pmid33931672, year = {2021}, author = {Indu, B and Keertana, T and Ipsita, S and Jagadeeshwari, U and Sasikala, C and Ramana, CV}, title = {Uncovering the hidden bacterial ghost communities of yeast and experimental evidences demonstrates yeast as thriving hub for bacteria.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {9394}, pmid = {33931672}, issn = {2045-2322}, mesh = {Bacteria/*genetics/isolation & purification ; Candidiasis/genetics/*microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Yeasts/classification/*physiology ; }, abstract = {Our major concern was to address "yeast endobacteria" which was based on a few reports in the recent past where bacteria may find yeast as a niche for survival. In this study, we report the microbiota of twenty-nine axenic yeast cultures recovered from different habitats based on their 16S rRNA gene-amplicon metagenomes. Yeasts were identified based on D1/D2 or ITS gene sequences. Bacterial diversity was widespread, varied and rich among all yeasts except for four strains. Taxa belonging to the phylum Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes and the genera; Streptococcus, Propionibacterium were common to all the yeasts. Candida tropicalis was used as a model organism to confirm bacteria through fluorescence in situ hybridization (FISH), isolating and re-introducing the isolated bacteria into the yeast. FISH analysis confirmed the endobacteria of C. tropicalis and we have successfully isolated four bacteria only after lysis and disruption of yeast cells. These bacteria were identified as species of Pseudomonas, Chryseobacterium, Lysinibacillus and Propionibacterium. Guestimates indicate 95% of bacterial species of C. tropicalis are yet-to-be-cultivated. We have successfully reintroduced mCherry tagged Pseudomonas into C. tropicalis. Also, auto-fluorescent Prochlorococcus and Rhodopseudomonas could be introduced into C. tropicalis while mCherry tagged E. coli or Salmonella could not be introduced. FISH analysis confirmed the presence of both native and infected bacterial cells present in C. tropicalis. Our findings unveil the insights into the ghost microbiota associated with yeast, which otherwise are considered to be axenic cultures. Their inherent occurrence, together with co-cultivation experiments under laboratory conditions suggests that yeasts are a thriving hub for bacterial communities.}, } @article {pmid33927711, year = {2021}, author = {Griggs, RG and Steenwerth, KL and Mills, DA and Cantu, D and Bokulich, NA}, title = {Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {673810}, pmid = {33927711}, issn = {1664-302X}, abstract = {Microbiomes are integral to viticulture and winemaking - collectively termed winegrowing - where diverse fungi and bacteria can exert positive and negative effects on grape health and wine quality. Wine is a fermented natural product, and the vineyard serves as a key point of entry for quality-modulating microbiota, particularly in wine fermentations that are conducted without the addition of exogenous yeasts. Thus, the sources and persistence of wine-relevant microbiota in vineyards critically impact its quality. Site-specific variations in microbiota within and between vineyards may contribute to regional wine characteristics. This includes distinctions in microbiomes and microbiota at the strain level, which can contribute to wine flavor and aroma, supporting the role of microbes in the accepted notion of terroir as a biological phenomenon. Little is known about the factors driving microbial biodiversity within and between vineyards, or those that influence annual assembly of the fruit microbiome. Fruit is a seasonally ephemeral, yet annually recurrent product of vineyards, and as such, understanding the sources of microbiota in vineyards is critical to the assessment of whether or not microbial terroir persists with inter-annual stability, and is a key factor in regional wine character, as stable as the geographic distances between vineyards. This review examines the potential sources and vectors of microbiota within vineyards, general rules governing plant microbiome assembly, and how these factors combine to influence plant-microbe interactions relevant to winemaking.}, } @article {pmid33927454, year = {2021}, author = {Bae, J and Cho, HW and Jung, H and Park, J and Yun, S and Ha, S and Lee, Y and Kim, TJ}, title = {Changes in Intestinal Microbiota Due to the Expanded Polystyrene Diet of Mealworms (Tenebrio molitor).}, journal = {Indian journal of microbiology}, volume = {61}, number = {2}, pages = {130-136}, pmid = {33927454}, issn = {0046-8991}, abstract = {Expanded polystyrene (EPS), which is difficult to decompose, is usually buried or incinerated, causing the natural environment to be contaminated with microplastics and environmental hormones. Digestion of EPS by mealworms has been identified as a possible biological solution to the problem of pollution, but the complete degradation mechanism of EPS is not yet known. Intestinal microorganisms play a significant role in the degradation of EPS by mealworms, and relatively few other EPS degradation microorganisms are currently known. This study observed significant differences in the intestinal microbiota of mealworms according to the dietary results of metagenomics analysis and biodiversity indices. We have proposed two new candidates of EPS-degrading bacteria, Cronobacter sakazakii and Lactococcus garvieae, which increased significantly in the EPS feeding group population. The population change and the new two bacteria will help us understand the biological mechanism of EPS degradation and develop practical EPS degradation methods.}, } @article {pmid33926968, year = {2022}, author = {Li, J and Li, Y and Ivey, KL and Wang, DD and Wilkinson, JE and Franke, A and Lee, KH and Chan, A and Huttenhower, C and Hu, FB and Rimm, EB and Sun, Q}, title = {Interplay between diet and gut microbiome, and circulating concentrations of trimethylamine N-oxide: findings from a longitudinal cohort of US men.}, journal = {Gut}, volume = {71}, number = {4}, pages = {724-733}, pmid = {33926968}, issn = {1468-3288}, support = {K99 DK119412/DK/NIDDK NIH HHS/United States ; R00 DK122128/DK/NIDDK NIH HHS/United States ; R01 DK120870/DK/NIDDK NIH HHS/United States ; R01 DK119268/DK/NIDDK NIH HHS/United States ; U01 CA152904/CA/NCI NIH HHS/United States ; U01 CA167552/CA/NCI NIH HHS/United States ; P30 DK046200/DK/NIDDK NIH HHS/United States ; K99 DK122128/DK/NIDDK NIH HHS/United States ; R01 HL035464/HL/NHLBI NIH HHS/United States ; R01 HL060712/HL/NHLBI NIH HHS/United States ; P30 CA071789/CA/NCI NIH HHS/United States ; R00 DK119412/DK/NIDDK NIH HHS/United States ; R01 DK126698/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {*Cardiovascular Diseases ; Choline/metabolism ; Diet ; *Gastrointestinal Microbiome ; Humans ; Male ; Methylamines/metabolism ; }, abstract = {OBJECTIVES: Gut-produced trimethylamine N-oxide (TMAO) is postulated as a possible link between red meat intake and poor cardiometabolic health. We investigated whether gut microbiome could modify associations of dietary precursors with TMAO concentrations and cardiometabolic risk markers among free-living individuals.

DESIGN: We collected up to two pairs of faecal samples (n=925) and two blood samples (n=473), 6 months apart, from 307 healthy men in the Men's Lifestyle Validation Study. Diet was assessed repeatedly using food-frequency questionnaires and diet records. We profiled faecal metagenome and metatranscriptome using shotgun sequencing and identified microbial taxonomic and functional features.

RESULTS: TMAO concentrations were associated with the overall microbial compositions (permutational analysis of variance (PERMANOVA) test p=0.001). Multivariable taxa-wide association analysis identified 10 bacterial species whose abundance was significantly associated with plasma TMAO concentrations (false discovery rate <0.05). Higher habitual intake of red meat and choline was significantly associated with higher TMAO concentrations among participants who were microbial TMAO-producers (p<0.05), as characterised based on four abundant TMAO-predicting species, but not among other participants (for red meat, P-interaction=0.003; for choline, P-interaction=0.03). Among abundant TMAO-predicting species, Alistipes shahii significantly strengthened the positive association between red meat intake and HbA1c levels (P-interaction=0.01). Secondary analyses revealed that some functional features, including choline trimethylamine-lyase activating enzymes, were associated with TMAO concentrations.

CONCLUSION: We identified microbial taxa that were associated with TMAO concentrations and modified the associations of red meat intake with TMAO concentrations and cardiometabolic risk markers. Our data underscore the interplay between diet and gut microbiome in producing potentially bioactive metabolites that may modulate cardiometabolic health.}, } @article {pmid33925672, year = {2021}, author = {Altomare, A and Del Chierico, F and Rocchi, G and Emerenziani, S and Nuglio, C and Putignani, L and Angeletti, S and Lo Presti, A and Ciccozzi, M and Russo, A and Cocca, S and Ribolsi, M and Muscaritoli, M and Cicala, M and Guarino, MPL}, title = {Association between Dietary Habits and Fecal Microbiota Composition in Irritable Bowel Syndrome Patients: A Pilot Study.}, journal = {Nutrients}, volume = {13}, number = {5}, pages = {}, pmid = {33925672}, issn = {2072-6643}, support = {WFR GR-2011-02350817//Ministero della Salute (Italy)/ ; Italy, 201905_genetica_putignani to LP//RC Ministry of Health (Ministero della Salute, Italy)/ ; }, mesh = {Adult ; Aged ; Cross-Sectional Studies ; Diet/*methods/statistics & numerical data ; Feces/*microbiology ; Feeding Behavior/*physiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Irritable Bowel Syndrome/*microbiology/physiopathology ; Male ; Middle Aged ; Pilot Projects ; }, abstract = {Intestinal dysbiosis seems to play a role in the pathophysiology of irritable bowel syndrome (IBS). The present pilot study aimed to elucidate the association between nutrient intake and Mediterranean diet (MD) adherence with IBS symptoms and gut microbiota in IBS patients. The nutrient intake of 28 IBS patients and 21 controls was assessed through a food diary, the reference intake ranges (RIs) for energy-yielding macronutrients and the MD serving score (MDSS) index. MD adherence and nutrients intake were compared to IBS symptoms and fecal microbiota, obtained by 16S rRNA targeted-metagenomics. In IBS patients MDSS index was altered compared to controls (p < 0.01). IBS patients with low-MD score reported severe abdominal pain and higher flatulence point-scales. Through Linear discriminant analysis effect size (LEfSe), Erysipelotrichaceae were detected as a microbial biomarker in IBS patients with altered RIs for macronutrients intake, compared to controls. Lactobacillaceae and Lactobacillus were associated to an altered carbohydrates intake in IBS patients, while specific taxonomic biomarkers, such as Aldercreuzia, Mogibacteriaceae, Rikenellaceae, Parabacteroides and F. prausnitzii were associated with an adequate intake of nutrient in these patients. This study supports an association between dietary patterns and gut microbial biomarkers in IBS patients. Further investigations are needed to clarify these connections.}, } @article {pmid33925487, year = {2021}, author = {Nebbak, A and Monteil-Bouchard, S and Berenger, JM and Almeras, L and Parola, P and Desnues, C}, title = {Virome Diversity among Mosquito Populations in a Sub-Urban Region of Marseille, France.}, journal = {Viruses}, volume = {13}, number = {5}, pages = {}, pmid = {33925487}, issn = {1999-4915}, mesh = {Animals ; Computational Biology/methods ; Culicidae/*virology ; Humans ; Metagenome ; Metagenomics/methods ; Molecular Sequence Annotation ; Mosquito Vectors/virology ; Phylogeny ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Virome ; Viruses/*classification/genetics/ultrastructure ; }, abstract = {Some mosquito species have significant public health importance given their ability to transmit major diseases to humans and animals, making them the deadliest animals in the world. Among these, the Aedes (Ae.) genus is a vector of several viruses such as Dengue, Chikungunya, and Zika viruses that can cause serious pathologies in humans. Since 2004, Ae. albopictus has been encountered in the South of France, and autochthonous cases of Dengue, Chikungunya, and Zika diseases have recently been reported, further highlighting the need for a comprehensive survey of the mosquitoes and their associated viruses in this area. Using high throughput sequencing (HTS) techniques, we report an analysis of the DNA and RNA viral communities of three mosquito species Ae. albopictus, Culex (Cx.) pipiens, and Culiseta (Cs.) longiareolata vectors of human infectious diseases in a small sub-urban city in the South of France. Results revealed the presence of a significant diversity of viruses known to infect bacteria, plants, insects, and mammals. Several novel viruses were detected, including novel members of the Rhabdoviridae, Totiviridae, Iflaviviridae, Circoviridae, and Sobemoviridae families. No sequence related to major zoonotic viruses transmitted by mosquitoes was detected. The use of HTS on arthropod vector populations is a promising strategy for monitoring the emergence and circulation of zoonoses and epizooties. This study is a contribution to the knowledge of the mosquito microbiome.}, } @article {pmid33925168, year = {2021}, author = {François, S and Antoine-Lorquin, A and Kulikowski, M and Frayssinet, M and Filloux, D and Fernandez, E and Roumagnac, P and Froissart, R and Ogliastro, M}, title = {Characterisation of the Viral Community Associated with the Alfalfa Weevil (Hypera postica) and Its Host Plant, Alfalfa (Medicago sativa).}, journal = {Viruses}, volume = {13}, number = {5}, pages = {}, pmid = {33925168}, issn = {1999-4915}, mesh = {Agriculture ; Animals ; Biodiversity ; Ecosystem ; Medicago sativa/*parasitology/*virology ; Metagenome ; Metagenomics/methods ; Phylogeny ; Plant Diseases/virology ; *Virome ; Weevils/*virology ; }, abstract = {Advances in viral metagenomics have paved the way of virus discovery by making the exploration of viruses in any ecosystem possible. Applied to agroecosystems, such an approach opens new possibilities to explore how viruses circulate between insects and plants, which may help to optimise their management. It could also lead to identifying novel entomopathogenic viral resources potentially suitable for biocontrol strategies. We sampled the larvae of a natural population of alfalfa weevils (Hypera postica), a major herbivorous pest feeding on legumes, and its host plant alfalfa (Medicago sativa). Insect and plant samples were collected from a crop field and an adjacent meadow. We characterised the diversity and abundance of viruses associated with weevils and alfalfa, and described nine putative new virus species, including four associated with alfalfa and five with weevils. In addition, we found that trophic accumulation may result in a higher diversity of plant viruses in phytophagous pests compared to host plants.}, } @article {pmid33924545, year = {2021}, author = {García-López, R and Cornejo-Granados, F and Lopez-Zavala, AA and Cota-Huízar, A and Sotelo-Mundo, RR and Gómez-Gil, B and Ochoa-Leyva, A}, title = {OTUs and ASVs Produce Comparable Taxonomic and Diversity from Shrimp Microbiota 16S Profiles Using Tailored Abundance Filters.}, journal = {Genes}, volume = {12}, number = {4}, pages = {}, pmid = {33924545}, issn = {2073-4425}, mesh = {Animals ; Bacteria/*classification/genetics ; Computational Biology/*methods ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Gastrointestinal Microbiome ; *Genetic Variation ; Hepatopancreas/microbiology ; High-Throughput Nucleotide Sequencing ; Microbiota ; Penaeidae/genetics/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The interplay between shrimp immune system, its environment, and microbiota contributes to the organism's homeostasis and optimal production. The metagenomic composition is typically studied using 16S rDNA profiling by clustering amplicon sequences into operational taxonomic units (OTUs) and, more recently, amplicon sequence variants (ASVs). Establish the compatibility of the taxonomy, α, and β diversity described by both methods is necessary to compare past and future shrimp microbiota studies. Here, we used identical sequences to survey the V3 16S hypervariable-region using 97% and 99% OTUs and ASVs to assess the hepatopancreas and intestine microbiota of L. vannamei from two ponds under standardized rearing conditions. We found that applying filters to retain clusters >0.1% of the total abundance per sample enabled a consistent taxonomy comparison while preserving >94% of the total reads. The three sets turned comparable at the family level, whereas the 97% identity OTU set produced divergent genus and species profiles. Interestingly, the detection of organ and pond variations was robust to the clustering method's choice, producing comparable α and β-diversity profiles. For comparisons on shrimp microbiota between past and future studies, we strongly recommend that ASVs be compared at the family level to 97% identity OTUs or use 99% identity OTUs, both using tailored frequency filters.}, } @article {pmid33923841, year = {2021}, author = {van der Linde, C and Barone, M and Turroni, S and Brigidi, P and Keleszade, E and Swann, JR and Costabile, A}, title = {An In Vitro Pilot Fermentation Study on the Impact of Chlorella pyrenoidosa on Gut Microbiome Composition and Metabolites in Healthy and Coeliac Subjects.}, journal = {Molecules (Basel, Switzerland)}, volume = {26}, number = {8}, pages = {}, pmid = {33923841}, issn = {1420-3049}, mesh = {*Chlorella ; Enterobacteriaceae/classification/genetics ; Fermentation/physiology ; Gastrointestinal Microbiome/*physiology ; RNA, Ribosomal, 16S ; }, abstract = {The response of a coeliac and a healthy gut microbiota to the green algae Chlorella pyrenoidosa was evaluated using an in vitro continuous, pH controlled, gut model system, which simulated the human colon. The effect of C. pyrenoidosa on the microbial structure was determined by 16S rRNA gene sequencing and inferred metagenomics, whereas the metabolic activitywas determined by[1]H-nuclear magnetic resonancespectroscopic analysis. The addition of C. pyrenoidosa significantly increased the abundance of the genera Prevotella, Ruminococcus and Faecalibacterium in the healthy donor, while an increase in Faecalibacterium, Bifidobacterium and Megasphaera and a decrease in Enterobacteriaceae were observed in the coeliac donor. C. pyrenoidosa also altered several microbial pathways including those involved in short-chain fatty acid (SCFA) production. At the metabolic level, a significant increase from baseline was seen in butyrate and propionate (p < 0.0001) in the healthy donor, especially in vessels 2 and 3. While acetate was significantly higher in the healthy donor at baseline in vessel 3 (p < 0.001) compared to the coeliac donor, this was markedly decreased after in vitro fermentation with C. pyrenoidosa. This is the first in vitro fermentation study of C. pyrenoidosa and human gut microbiota, however, further in vivo studies are needed to prove its efficacy.}, } @article {pmid33923593, year = {2021}, author = {Fulci, V and Stronati, L and Cucchiara, S and Laudadio, I and Carissimi, C}, title = {Emerging Roles of Gut Virome in Pediatric Diseases.}, journal = {International journal of molecular sciences}, volume = {22}, number = {8}, pages = {}, pmid = {33923593}, issn = {1422-0067}, mesh = {Celiac Disease/microbiology/*virology ; Child ; Diabetes Mellitus, Type 1/microbiology/*virology ; Diarrhea/microbiology/*virology ; Humans ; Inflammatory Bowel Diseases/microbiology/*virology ; Intestinal Mucosa/microbiology/*virology ; Metagenome ; *Virome ; }, abstract = {In the last decade, the widespread application of shotgun metagenomics provided extensive characterization of the bacterial "dark matter" of the gut microbiome, propelling the development of dedicated, standardized bioinformatic pipelines and the systematic collection of metagenomic data into comprehensive databases. The advent of next-generation sequencing also unravels a previously underestimated viral population (virome) present in the human gut. Despite extensive efforts to characterize the human gut virome, to date, little is known about the childhood gut virome. However, alterations of the gut virome in children have been linked to pathological conditions such as inflammatory bowel disease, type 1 diabetes, malnutrition, diarrhea and celiac disease.}, } @article {pmid33921772, year = {2021}, author = {Park, DH and Kim, JW and Park, HJ and Hahm, DH}, title = {Comparative Analysis of the Microbiome across the Gut-Skin Axis in Atopic Dermatitis.}, journal = {International journal of molecular sciences}, volume = {22}, number = {8}, pages = {}, pmid = {33921772}, issn = {1422-0067}, support = {NRF-2020R1A4A1018598//National Research Foundation of Korea/ ; }, mesh = {Animals ; Dermatitis, Atopic/*microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Metagenomics ; Skin/microbiology ; }, abstract = {Atopic dermatitis (AD) is a refractory and relapsing skin disease with a complex and multifactorial etiology. Various congenital malformations and environmental factors are thought to be involved in the onset of the disease. The etiology of the disease has been investigated, with respect to clinical skin symptoms and systemic immune response factors. A gut microbiome-mediated connection between emotional disorders such as depression and anxiety, and dermatologic conditions such as acne, based on the comorbidities of these two seemingly unrelated disorders, has long been hypothesized. Many aspects of this gut-brain-skin integration theory have recently been revalidated to identify treatment options for AD with the recent advances in metagenomic analysis involving powerful sequencing techniques and bioinformatics that overcome the need for isolation and cultivation of individual microbial strains from the skin or gut. Comparative analysis of microbial clusters across the gut-skin axis can provide new information regarding AD research. Herein, we provide a historical perspective on the modern investigation and clinical implications of gut-skin connections in AD in terms of the integration between the two microbial clusters.}, } @article {pmid33919845, year = {2021}, author = {Thompson, HJ and Levitt, JO and McGinley, JN and Chandler, P and Guenther, PM and Huybrechts, I and Playdon, MC}, title = {Measuring Dietary Botanical Diversity as a Proxy for Phytochemical Exposure.}, journal = {Nutrients}, volume = {13}, number = {4}, pages = {}, pmid = {33919845}, issn = {2072-6643}, support = {001/WHO_/World Health Organization/International ; 5R00CA218694-03/CA/NCI NIH HHS/United States ; }, mesh = {Aged ; Algorithms ; Chronic Disease/prevention & control ; Diet Surveys/*methods/statistics & numerical data ; Feeding Behavior/*physiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Middle Aged ; *Phytochemicals ; Plants, Edible/*chemistry ; }, abstract = {The study of natural plant molecules and their medicinal properties, pharmacognosy, provides a taxonomy for botanical families that represent diverse chemical groupings with potentially distinct functions in relation to human health. Yet, this reservoir of knowledge has not been systematically applied to elucidating the role of patterns of plant food consumption on gut microbial ecology and function. All chemical classes of dietary phytochemicals can affect the composition of the microbes that colonize the gut and their function. In turn, the gut microbiome affects the host via multiple mechanisms including gut barrier function, immune function, satiety and taste regulation and the activity of biological signaling pathways that influence health and disease. Herein, we report the development of a botanical diversity index (BDI) to evaluate plant food consumption as a novel metric for identifying and quantifying phytochemicals to which an individual is exposed. A rationale is advanced for using the BDI to investigate how plant food diversity impacts gut microbial ecology and functionality.}, } @article {pmid33918473, year = {2021}, author = {Gao, B and Chi, L and Zhu, Y and Shi, X and Tu, P and Li, B and Yin, J and Gao, N and Shen, W and Schnabl, B}, title = {An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies.}, journal = {Biomolecules}, volume = {11}, number = {4}, pages = {}, pmid = {33918473}, issn = {2218-273X}, support = {R01 AA020703/AA/NIAAA NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; R37 AA020703/AA/NIAAA NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 AA026939/AA/NIAAA NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Computational Biology/*methods ; Fungi/genetics ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; RNA, Ribosomal, 16S/chemistry/metabolism ; RNA, Ribosomal, 18S/chemistry/metabolism ; Viruses/genetics ; }, abstract = {The gut microbiome is a microbial ecosystem which expresses 100 times more genes than the human host and plays an essential role in human health and disease pathogenesis. Since most intestinal microbial species are difficult to culture, next generation sequencing technologies have been widely applied to study the gut microbiome, including 16S rRNA, 18S rRNA, internal transcribed spacer (ITS) sequencing, shotgun metagenomic sequencing, metatranscriptomic sequencing and viromic sequencing. Various software tools were developed to analyze different sequencing data. In this review, we summarize commonly used computational tools for gut microbiome data analysis, which extended our understanding of the gut microbiome in health and diseases.}, } @article {pmid33917566, year = {2021}, author = {Mazier, W and Le Corf, K and Martinez, C and Tudela, H and Kissi, D and Kropp, C and Coubard, C and Soto, M and Elustondo, F and Rawadi, G and Claus, SP}, title = {A New Strain of Christensenella minuta as a Potential Biotherapy for Obesity and Associated Metabolic Diseases.}, journal = {Cells}, volume = {10}, number = {4}, pages = {}, pmid = {33917566}, issn = {2073-4409}, mesh = {Animals ; Biodiversity ; *Biological Therapy ; Biomarkers/metabolism ; Clostridiales/classification/*isolation & purification ; Diet ; Disease Models, Animal ; Epithelial Cells/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome ; Humans ; Lipid Metabolism ; Liver/metabolism ; Male ; Metabolic Diseases/*microbiology/*therapy ; Mice, Inbred C57BL ; Obesity/*microbiology/*therapy ; Phylogeny ; Mice ; }, abstract = {Obesity is associated with gut microbiota dysbiosis, characterized by a high Firmicutes/Bacteroidetes ratio. Gut-dwelling bacteria of the Christensenellaceae family have been proposed to act as keystones of the human gut ecosystem and to prevent adipogenesis. The objectives of the present study were to demonstrate the antiobesity potential of a new strain of Christensenella minuta in preclinical models and explore related mechanisms of action. The antiobesity potential of C. minuta DSM33407 was assessed in a diet-induced obesity mouse model. Changes in hepatic lipid metabolism were explored using targeted transcriptomics. Effects on gut microbiota were further assessed in a humanized Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]) model inoculated with obese fecal samples. Shotgun metagenomics was applied to study microbial community structures in both models. C. minuta DSM33407 protected from diet-induced obesity and regulated associated metabolic markers such as glycemia and leptin. It also regulated hepatic lipid metabolism through a strong inhibition of de novo lipogenesis and maintained gut epithelial integrity. In the humanized SHIME[®] model, these effects were associated with modulations of the intestinal microbiota characterized by a decreased Firmicutes/Bacteroidetes ratio. These data indicate that C. minuta DSM33407 is a convincing therapeutic candidate for the management of obesity and associated metabolic disorders.}, } @article {pmid33915727, year = {2021}, author = {Jia, B and Park, D and Chun, BH and Hahn, Y and Jeon, CO}, title = {Diet-Related Alterations of Gut Bile Salt Hydrolases Determined Using a Metagenomic Analysis of the Human Microbiome.}, journal = {International journal of molecular sciences}, volume = {22}, number = {7}, pages = {}, pmid = {33915727}, issn = {1422-0067}, support = {2017M3C1B5019250//National Research Foundation of Korea/ ; 2018R1A5A1025077//National Research Foundation of Korea/ ; }, mesh = {Amidohydrolases/chemistry/*metabolism ; Bacterial Proteins/chemistry/*metabolism ; *Diet, Ketogenic ; *Gastrointestinal Microbiome ; Humans ; Hyperphagia/*microbiology ; Metagenomics ; }, abstract = {The metabolism of bile acid by the gut microbiota is associated with host health. Bile salt hydrolases (BSHs) play a crucial role in controlling microbial bile acid metabolism. Herein, we conducted a comparative study to investigate the alterations in the abundance of BSHs using data from three human studies involving dietary interventions, which included a ketogenetic diet (KD) versus baseline diet (BD), overfeeding diet (OFD) versus underfeeding diet, and low-carbohydrate diet (LCD) versus BD. The KD increased BSH abundance compared to the BD, while the OFD and LCD did not change the total abundance of BSHs in the human gut. BSHs can be classified into seven clusters; Clusters 1 to 4 are relatively abundant in the gut. In the KD cohort, the levels of BSHs from Clusters 1, 3, and 4 increased significantly, whereas there was no notable change in the levels of BSHs from the clusters in the OFD and LCD cohorts. Taxonomic studies showed that members of the phyla Bacteroidetes, Firmicutes, and Actinobacteria predominantly produced BSHs. The KD altered the community structure of BSH-active bacteria, causing an increase in the abundance of Bacteroidetes and decrease in Actinobacteria. In contrast, the abundance of BSH-active Bacteroidetes decreased in the OFD cohort, and no significant change was observed in the LCD cohort. These results highlight that dietary patterns are associated with the abundance of BSHs and community structure of BSH-active bacteria and demonstrate the possibility of manipulating the composition of BSHs in the gut through dietary interventions to impact human health.}, } @article {pmid33913739, year = {2021}, author = {Kumar, N and Gupta, AK and Sudan, SK and Pal, D and Randhawa, V and Sahni, G and Mayilraj, S and Kumar, M}, title = {Abundance and Diversity of Phages, Microbial Taxa, and Antibiotic Resistance Genes in the Sediments of the River Ganges Through Metagenomic Approach.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {27}, number = {10}, pages = {1336-1354}, doi = {10.1089/mdr.2020.0431}, pmid = {33913739}, issn = {1931-8448}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteriophages/*genetics ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial/*genetics ; Genes, Viral/*genetics ; Geologic Sediments/*microbiology ; India ; Metagenomics ; Microbiota/*genetics ; Rivers/microbiology ; }, abstract = {In this study, we have analyzed the metagenomic DNA from the pooled sediment sample of the river Ganges to explore the abundance and diversity of phages, microbial community, and antibiotic resistance genes (ARGs). Utilizing data from Illumina platform, 4,174 (∼0.0013%) reads were classified for the 285 different DNA viruses largely dominated by the group of 260 distinctive phages (3,602 reads, ∼86.3%). Among all, Microcystis (782 hits), Haemophilus (403), Synechococcus (386), Pseudomonas (279), Enterococcus (232), Bacillus (196), Rhodococcus (166), Caulobacter (163), Salmonella (146), Enterobacteria (143), Mycobacterium and (128) phages show the highest abundance and account for ∼90% of the total identified phages. In addition, we have also identified corresponding host pertaining to these phages. Mainly, Proteobacteria (∼69.3%) dominates the microbial population structure. Primarily, orders such as Caulobacterales (∼28%), Burkholderiales (∼13.9%), Actinomycetales (∼13.7%), and Pseudomonadales (∼7.5%) signify the core section. Furthermore, 21,869 (∼0.00695%) reads were classified in 20 ARG types (classes) and 240 ARGs (subtypes), among which 4 ARG types, namely multidrug resistance (12,041 reads, ∼55%), bacitracin (3,202 reads, ∼15%), macrolide-lincosamide-streptogramin (1,744 reads, ∼7.98%), and fosmidomycin (990 reads, ∼4.53%), have the highest abundance. Simultaneously, six resistance mechanisms were also recognized with the dominance of antibiotic efflux (72.8%, 15,919 reads). The results unveil the distribution of (pro)-phages; microbial community; and various ARGs in the Ganges river sediments.}, } @article {pmid33912174, year = {2021}, author = {Wang, H and Wang, G and Banerjee, N and Liang, Y and Du, X and Boor, PJ and Hoffman, KL and Khan, MF}, title = {Aberrant Gut Microbiome Contributes to Intestinal Oxidative Stress, Barrier Dysfunction, Inflammation and Systemic Autoimmune Responses in MRL/lpr Mice.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {651191}, pmid = {33912174}, issn = {1664-3224}, support = {R01 ES016302/ES/NIEHS NIH HHS/United States ; R01 ES026887/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Disease Models, Animal ; Dysbiosis/*complications/immunology/microbiology/pathology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*immunology ; Humans ; Inflammation/immunology/microbiology/pathology ; Intestinal Mucosa/immunology/microbiology/*pathology ; Lupus Erythematosus, Systemic/*immunology/microbiology/pathology ; Mice ; Mice, Inbred MRL lpr ; Oxidative Stress/immunology ; Permeability ; }, abstract = {Microbiome composition and function have been implicated as contributing factors in the pathogenesis of autoimmune diseases (ADs), including systemic lupus erythematosus (SLE), rheumatoid arthritis and autoimmune hepatitis (AIH). Furthermore, dysbiosis of gut microbiome is associated with impaired barrier function and mucosal immune dysregulation. However, mechanisms by which gut microbiome contributes to the ADs and whether antioxidant treatment can restore gut homeostasis and ameliorate the disease outcome are not known. This study was, therefore, focused on examining the involvement of gut microbiome and host responses in the pathogenesis of SLE using unique female mouse models (C57BL/6, MRL+/+ and MRL/lpr) of 6 and 18 weeks with varying degrees of disease progression. Fecal microbiome diversity and composition, gut oxidative stress (OS), barrier function and inflammation, as well as systemic autoimmunity were determined. Interestingly, each mouse strain had distinct bacterial community as revealed by β-diversity. A lower Firmicutes/Bacteroidetes ratio in 6-week-old MRL/lpr mice was observed, evidenced by decrease in Peptostreptococcaceae under Firmicutes phylum along with enrichment of Rikenellaceae under Bacteroidetes phylum. Additionally, we observed increases in colonic OS [4-hydroxynonenal (HNE)-adducts and HNE-specific immune complexes], permeability changes (lower tight junction protein ZO-2; increased fecal albumin and IgA levels) and inflammatory responses (increased phos-NF-κB, IL-6 and IgG levels) in 18-week-old MRL/lpr mice. These changes were associated with markedly elevated AD markers (antinuclear and anti-smooth muscle antibodies) along with hepatic portal inflammation and severe glomerulonephritis. Notably, antioxidant N-acetylcysteine treatment influenced the microbial composition (decreased Rikenellaceae; increased Akkeransiaceae, Erysipelotrichaceae and Muribaculaceae) and attenuated the systemic autoimmunity in MRL/lpr mice. Our data thus show that gut microbiome dysbiosis is associated with increased colonic OS, barrier dysfunction, inflammatory responses and systemic autoimmunity markers. These findings apart from delineating a role for gut microbiome dysbiosis, also support the contribution of gut OS, permeability changes and inflammatory responses in the pathogenesis of ADs.}, } @article {pmid33911204, year = {2021}, author = {Duan, H and He, P and Shao, L and Lü, F}, title = {Functional genome-centric view of the CO-driven anaerobic microbiome.}, journal = {The ISME journal}, volume = {15}, number = {10}, pages = {2906-2919}, pmid = {33911204}, issn = {1751-7370}, mesh = {Anaerobiosis ; *Bacteria/genetics ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {CO is a promising substrate for producing biochemicals and biofuels through mixed microbial cultures, where carboxydotrophs play a crucial role. The previous investigations of mixed microbial cultures focused primarily on overall community structures, but under-characterized taxa and intricate microbial interactions have not yet been precisely explicated. Here, we undertook DNA-SIP based metagenomics to profile the anaerobic CO-driven microbiomes under 95 and 35% CO atmospheres. The time-series analysis of the isotope-labeled amplicon sequencing revealed the essential roles of Firmicutes and Proteobacteria under high and low CO pressure, respectively, and Methanobacterium was the predominant archaeal genus. The functional enrichment analysis based on the isotope-labeled metagenomes suggested that the microbial cultures under high CO pressure had greater potential in expressing carboxylate metabolism and citrate cycle pathway. The genome-centric metagenomics reconstructed 24 discovered and 24 under-characterized metagenome-assembled genomes (MAGs), covering more than 94% of the metagenomic reads. The metabolic reconstruction of the MAGs described their potential functions in the CO-driven microbiomes. Some under-characterized taxa might be versatile in multiple processes; for example, under-characterized Rhodoplanes sp. and Desulfitobacterium_A sp. could encode the complete enzymes in CO oxidation and carboxylate production, improving functional redundancy. Finally, we proposed the putative microbial interactions in the conversion of CO to carboxylates and methane.}, } @article {pmid33910647, year = {2021}, author = {Tourlousse, DM and Narita, K and Miura, T and Sakamoto, M and Ohashi, A and Shiina, K and Matsuda, M and Miura, D and Shimamura, M and Ohyama, Y and Yamazoe, A and Uchino, Y and Kameyama, K and Arioka, S and Kataoka, J and Hisada, T and Fujii, K and Takahashi, S and Kuroiwa, M and Rokushima, M and Nishiyama, M and Tanaka, Y and Fuchikami, T and Aoki, H and Kira, S and Koyanagi, R and Naito, T and Nishiwaki, M and Kumagai, H and Konda, M and Kasahara, K and Ohkuma, M and Kawasaki, H and Sekiguchi, Y and Terauchi, J}, title = {Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {95}, pmid = {33910647}, issn = {2049-2618}, mesh = {DNA ; Humans ; *Metagenomics ; *Microbiota/genetics ; Reference Standards ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Validation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization. This study set out to establish standards-based solutions to improve the accuracy and reproducibility of metagenomics-based microbiome profiling of human fecal samples.

RESULTS: In the first phase, we performed a head-to-head comparison of a wide range of protocols for DNA extraction and sequencing library construction using defined mock communities, to identify performant protocols and pinpoint sources of inaccuracy in quantification. In the second phase, we validated performant protocols with respect to their variability of measurement results within a single laboratory (that is, intermediate precision) as well as interlaboratory transferability and reproducibility through an industry-based collaborative study. We further ascertained the performance of our recommended protocols in the context of a community-wide interlaboratory study (that is, the MOSAIC Standards Challenge). Finally, we defined performance metrics to provide best practice guidance for improving measurement consistency across methods and laboratories.

CONCLUSIONS: The validated protocols and methodological guidance for DNA extraction and library construction provided in this study expand current best practices for metagenomic analyses of human fecal microbiota. Uptake of our protocols and guidelines will improve the accuracy and comparability of metagenomics-based studies of the human microbiome, thereby facilitating development and commercialization of human microbiome-based products. Video Abstract.}, } @article {pmid33906949, year = {2021}, author = {Chase, AB and Weihe, C and Martiny, JBH}, title = {Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {18}, pages = {}, pmid = {33906949}, issn = {1091-6490}, mesh = {Actinobacteria/classification/*genetics/growth & development ; Adaptation, Physiological/*genetics ; California ; *Climate Change ; Ecotype ; Genetic Variation/genetics ; Metagenome/genetics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {Microbial community responses to environmental change are largely associated with ecological processes; however, the potential for microbes to rapidly evolve and adapt remains relatively unexplored in natural environments. To assess how ecological and evolutionary processes simultaneously alter the genetic diversity of a microbiome, we conducted two concurrent experiments in the leaf litter layer of soil over 18 mo across a climate gradient in Southern California. In the first experiment, we reciprocally transplanted microbial communities from five sites to test whether ecological shifts in ecotypes of the abundant bacterium, Curtobacterium, corresponded to past adaptive differentiation. In the transplanted communities, ecotypes converged toward that of the native communities growing on a common litter substrate. Moreover, these shifts were correlated with community-weighted mean trait values of the Curtobacterium ecotypes, indicating that some of the trait variation among ecotypes could be explained by local adaptation to climate conditions. In the second experiment, we transplanted an isogenic Curtobacterium strain and tracked genomic mutations associated with the sites across the same climate gradient. Using a combination of genomic and metagenomic approaches, we identified a variety of nonrandom, parallel mutations associated with transplantation, including mutations in genes related to nutrient acquisition, stress response, and exopolysaccharide production. Together, the field experiments demonstrate how both demographic shifts of previously adapted ecotypes and contemporary evolution can alter the diversity of a soil microbiome on the same timescale.}, } @article {pmid33903636, year = {2021}, author = {Luo, L and Yao, J and Liu, W and Yang, L and Li, H and Liang, M and Ma, H and Liu, Z and Chen, Y}, title = {Comparison of bacterial communities and antibiotic resistance genes in oxidation ditches and membrane bioreactors.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {8955}, pmid = {33903636}, issn = {2045-2322}, mesh = {Bacteria/*genetics/growth & development ; Bioreactors/*microbiology ; *Drug Resistance, Multiple, Bacterial ; *Genes, Bacterial ; *Membranes, Artificial ; Microbial Consortia/*genetics ; Oxidation-Reduction ; Sewage/microbiology ; }, abstract = {Oxidation ditches (ODs) and membrane bioreactors (MBRs) are widely used in wastewater treatment plants (WWTPs) with bacteria and antibiotic resistance genes (ARGs) running through the whole system. In this study, metagenomic sequencing was used to compare the bacterial communities and ARGs in the OD and MBR systems, which received the same influent in a WWTP located in Xinjiang, China. The results showed that the removal efficiency of pollutants by the MBR process was better than that by the OD process. The composition and the relative abundance of bacteria in activated sludge were similar at the phylum and genus levels and were not affected by process type. Multidrug, fluoroquinolones and peptides were the main ARG types for the two processes, with macB being the main ARG subtype, and the relative abundance of ARG subtypes in MBR effluent was much higher than that in the OD effluent. The mobile genetic elements (MGEs) in the activated sludge were mainly transposons (tnpA) and insertion sequences (ISs; IS91). These results provide a theoretical basis for process selection and controlling the spread of ARGs.}, } @article {pmid33902743, year = {2021}, author = {Cabello-Yeves, PJ and Callieri, C and Picazo, A and Mehrshad, M and Haro-Moreno, JM and Roda-Garcia, JJ and Dzhembekova, N and Slabakova, V and Slabakova, N and Moncheva, S and Rodriguez-Valera, F}, title = {The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics.}, journal = {Environmental microbiome}, volume = {16}, number = {1}, pages = {5}, pmid = {33902743}, issn = {2524-6372}, support = {CGL2016-76273-p//Ministerio de Ciencia, Innovación y Universidades/ ; PROMETEO/2019/009//Conselleria d'Educació, Investigació, Cultura i Esport/ ; APOSTD/2019/009//Conselleria d'Educació, Investigació, Cultura i Esport/ ; D01-230/06.12.2018//Bulgarian Academy of Sciences/ ; }, abstract = {BACKGROUND: The Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former, albeit with lower salinity and temperature. Despite its well-known hydrology and physicochemical features, this enormous water mass remains poorly studied at the microbial genomics level.

RESULTS: We have sampled its different water masses and analyzed the microbiome by shotgun and genome-resolved metagenomics, generating a large number of metagenome-assembled genomes (MAGs) from them. We found various similarities with previously described Black Sea metagenomic datasets, that show remarkable stability in its microbiome. Our datasets are also comparable to other marine anoxic water columns like the Cariaco Basin. The oxic zone resembles to standard marine (e.g. Mediterranean) photic zones, with Cyanobacteria (Synechococcus but a conspicuously absent Prochlorococcus), and photoheterotrophs domination (largely again with marine relatives). The chemocline presents very different characteristics from the oxic surface with many examples of chemolithotrophic metabolism (Thioglobus) and facultatively anaerobic microbes. The euxinic anaerobic zone presents, as expected, features in common with the bottom of meromictic lakes with a massive dominance of sulfate reduction as energy-generating metabolism, a few (but detectable) methanogenesis marker genes, and a large number of "dark matter" streamlined genomes of largely unpredictable ecology.

CONCLUSIONS: The Black Sea oxic zone presents many similarities to the global ocean while the redoxcline and euxinic water masses have similarities to other similar aquatic environments of marine (Cariaco Basin or other Black Sea regions) or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environment. We are adding critical information about this unique and important ecosystem and its microbiome.}, } @article {pmid33902467, year = {2021}, author = {Wang, P and Dong, Y and Zuo, K and Han, C and Jiao, J and Yang, X and Li, J}, title = {Characteristics and variation of fecal bacterial communities and functions in isolated systolic and diastolic hypertensive patients.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {128}, pmid = {33902467}, issn = {1471-2180}, mesh = {*Biodiversity ; Feces/*microbiology ; Genes, Bacterial/genetics ; Humans ; Hypertension/*microbiology ; Microbiota/*physiology ; }, abstract = {BACKGROUND: Hypertension (HTN) is one of the major cardiovascular risk factors, which contributes to increasing target organ damages and cardiovascular morbidity and mortality worldwide. Isolated systolic HTN (ISH) and isolated diastolic HTN (IDH) are two important subtypes of HTN. Previous researches have demonstrated the alteration of fecal bacteria in HTN, but not down to these two sub-types. In order to identify whether the composition of bacterial taxa and functional modules shift in ISH and IDH, we performed a metagenomic sequencing analysis of fecal samples from 15 controls, 14 ISH, and 11 IDH.

RESULTS: Compared with control and ISH, IDH patients showed decreased gene number, bacterial richness, and evenness, although the bacterial alterations did not reach statistical significance in the Shannon index. Also, at the genus level, the β-diversity for intestinal flora in IDH was distinguishable from those with ISH. Furthermore, the taxonomic composition of ISH or IDH was different from that of healthy control at genus and species levels. Patients with IDH or ISH were confirmed to be enriched with Rothia mucilaginosa, along with reduced Clostridium sp. ASBs410. Lastly, the altered KEGG modules were significantly decreased in IDH compared with the control group, such as sodium transport system; while for ISH, functions relevant to biotin biosynthesis were decreased.

CONCLUSIONS: Overall, our results showed the disordered fecal bacteria profiles in subjects with ISH and especially IDH, emphasizing the significance of early intervention for IDH.}, } @article {pmid33901241, year = {2021}, author = {Chaudhary, P and Khati, P and Chaudhary, A and Maithani, D and Kumar, G and Sharma, A}, title = {Cultivable and metagenomic approach to study the combined impact of nanogypsum and Pseudomonas taiwanensis on maize plant health and its rhizospheric microbiome.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0250574}, pmid = {33901241}, issn = {1932-6203}, mesh = {Agriculture ; Calcium Sulfate/*pharmacology ; Crops, Agricultural/growth & development ; *Metagenomics ; *Microbiota/drug effects ; Nanoparticles/*chemistry ; Nitrogen/analysis ; Phosphorus/analysis ; Phylogeny ; Potassium/analysis ; Pseudomonas/drug effects/*physiology ; *Rhizosphere ; Soil/chemistry ; Zea mays/drug effects/*growth & development/*microbiology ; }, abstract = {In the present study we examined the effect of nanogypsum and Pseudomonas taiwanensis strain BCRC 17751on plant and soil health using conventional and metagenomics approaches. Soil physicochemical properties and agronomical parameters of maize plants were reported to be better when applied with nanogypsum and bacterial inoculum together. When compared to control a significant increase in total bacterial counts, nitrogen, phosphorus, potassium (NPK) solubilizing bacterial population and soil enzyme activities (fluorescein diacetate, alkaline phosphatase, dehydrogenase, β-glucosidase, arylesterase and amylase) was reported in treatments. The metagenomics studies revealed dominance of beneficial bacteria such as Proteobacteria, Bacteriodetes, Planctomycetes, Acidobacteria and Nitrospirae in treated soil. On the other hand some novel bacterial diversity was also reported in treated soil which was evident from presence of taxonomically unclassified sequences. Hence, it can be concluded that combined application of nanogypsum and Pseudomonas taiwanensis in maize help in improving the structure and function of soil which affects the plant health without causing any toxic effect. However, in situ validation of the prescribed treatment is required under field conditions on different crops in order to give maximum benefits to the farmers and the environment.}, } @article {pmid33901198, year = {2021}, author = {García-Bayona, L and Coyne, MJ and Comstock, LE}, title = {Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering.}, journal = {PLoS genetics}, volume = {17}, number = {4}, pages = {e1009541}, pmid = {33901198}, issn = {1553-7404}, support = {R01 AI093771/AI/NIAID NIH HHS/United States ; R01 AI120633/AI/NIAID NIH HHS/United States ; R01 AI132580/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteroides/classification/*genetics ; Cluster Analysis ; Ecosystem ; Gastrointestinal Microbiome/genetics ; Genome, Bacterial/*genetics ; Genomics ; Geography ; Humans ; Interspersed Repetitive Sequences/*genetics ; Microbiota/genetics ; Type VI Secretion Systems/classification/*genetics ; }, abstract = {The human gut microbiota is a dense microbial ecosystem with extensive opportunities for bacterial contact-dependent processes such as conjugation and Type VI secretion system (T6SS)-dependent antagonism. In the gut Bacteroidales, two distinct genetic architectures of T6SS loci, GA1 and GA2, are contained on Integrative and Conjugative Elements (ICE). Despite intense interest in the T6SSs of the gut Bacteroidales, there is only a superficial understanding of their evolutionary patterns, and of their dissemination among Bacteroidales species in human gut communities. Here, we combine extensive genomic and metagenomic analyses to better understand their ecological and evolutionary dynamics. We identify new genetic subtypes, document extensive intrapersonal transfer of these ICE to Bacteroidales species within human gut microbiomes, and most importantly, reveal frequent population fixation of these newly armed strains in multiple species within a person. We further show the distribution of each of the distinct T6SSs in human populations and show there is geographical clustering. We reveal that the GA1 T6SS ICE integrates at a minimal recombination site leading to their integration throughout genomes and their frequent interruption of genes, whereas the GA2 T6SS ICE integrate at one of three different tRNA genes. The exclusion of concurrent GA1 and GA2 T6SSs in individual strains is associated with intact T6SS loci and with an ICE-encoded gene. By performing a comprehensive analysis of mobile genetic elements (MGE) in co-resident Bacteroidales species in numerous human gut communities, we identify 74 MGE that transferred to multiple Bacteroidales species within individual gut microbiomes. We further show that only three other MGE demonstrate multi-species spread in human gut microbiomes to the degree demonstrated by the GA1 and GA2 ICE. These data underscore the ubiquity and dissemination of mobile T6SS loci within Bacteroidales communities and across human populations.}, } @article {pmid33901182, year = {2021}, author = {He, X and Yin, Q and Zhou, L and Meng, L and Hu, W and Li, F and Li, Y and Han, K and Zhang, S and Fu, S and Zhang, X and Wang, J and Xu, S and Zhang, Y and He, Y and Dong, M and Shen, X and Zhang, Z and Nie, K and Liang, G and Ma, X and Wang, H}, title = {Metagenomic sequencing reveals viral abundance and diversity in mosquitoes from the Shaanxi-Gansu-Ningxia region, China.}, journal = {PLoS neglected tropical diseases}, volume = {15}, number = {4}, pages = {e0009381}, pmid = {33901182}, issn = {1935-2735}, mesh = {Animals ; *Biodiversity ; China ; Culicidae/*virology ; High-Throughput Nucleotide Sequencing ; Host Specificity ; *Metagenomics ; Mosquito Vectors/*virology ; Viral Tropism ; Viruses/*classification/genetics/*isolation & purification ; }, abstract = {BACKGROUND: Mosquitoes host and transmit numerous arthropod-borne viruses (arboviruses) that cause disease in both humans and animals. Effective surveillance of virome profiles in mosquitoes is vital to the prevention and control of mosquito-borne diseases in northwestern China, where epidemics occur frequently.

METHODS: Mosquitoes were collected in the Shaanxi-Gansu-Ningxia region (Shaanxi Province, Gansu Province, and Ningxia Hui Autonomous Region) of China from June to August 2019. Morphological methods were used for taxonomic identification of mosquito species. High-throughput sequencing and metagenomic analysis were used to characterize mosquito viromes.

RESULTS: A total of 22,959 mosquitoes were collected, including Culex pipiens (45.7%), Culex tritaeniorhynchus (40.6%), Anopheles sinensis (8.4%), Aedes (5.2%), and Armigeres subalbatus (0.1%). In total, 3,014,183 (0.95% of clean reads) viral sequences were identified and assigned to 116 viral species (including pathogens such as Japanese encephalitis virus and Getah virus) in 31 viral families, including Flaviviridae, Togaviridae, Phasmaviridae, Phenuiviridae, and some unclassified viruses. Mosquitoes collected in July (86 species in 26 families) showed greater viral diversity than those from June and August. Culex pipiens (69 species in 25 families) and Culex tritaeniorhynchus (73 species in 24 families) carried more viral species than Anopheles sinensis (50 species in 19 families) or Aedes (38 species in 20 families) mosquitoes.

CONCLUSION: Viral diversity and abundance were affected by mosquito species and collection time. The present study elucidates the virome compositions of various mosquito species in northwestern China, improving the understanding of virus transmission dynamics for comparison with those of disease outbreaks.}, } @article {pmid33897881, year = {2021}, author = {Hu, X and Li, H and Zhao, X and Zhou, R and Liu, H and Sun, Y and Fan, Y and Shi, Y and Qiao, S and Liu, S and Liu, H and Zhang, S}, title = {Multi-omics study reveals that statin therapy is associated with restoration of gut microbiota homeostasis and improvement in outcomes in patients with acute coronary syndrome.}, journal = {Theranostics}, volume = {11}, number = {12}, pages = {5778-5793}, pmid = {33897881}, issn = {1838-7640}, mesh = {Acute Coronary Syndrome/*drug therapy/metabolism/microbiology ; Bacteria/drug effects ; Female ; Follow-Up Studies ; Gastrointestinal Microbiome/*drug effects ; Healthy Volunteers ; Homeostasis/*drug effects ; Humans ; Hydroxymethylglutaryl-CoA Reductase Inhibitors/*therapeutic use ; Male ; Metabolomics/methods ; Middle Aged ; RNA, Ribosomal, 16S/metabolism ; }, abstract = {Rationale: Prior chronic treatment with statins has been shown to be associated with more favorable outcomes in patients with acute coronary syndrome (ACS). Specific changes in the gut microbiota and microbial metabolites have been shown to influence the progression of coronary artery disease. However, the critical microbial and metabolomic changes associated with the cardiovascular protective effects of statins in ACS remain elusive. Methods: In the present study, we performed 16S rRNA sequencing and serum metabolomic analysis in 36 ACS patients who had received chronic statin treatment, 67 ACS patients who had not, and 30 healthy volunteers. A follow-up study was conducted. Metagenomic functional prediction of important bacterial taxa was achieved using PICRUSt2. Results: Statins modulated the gut microbiome of ACS patients towards a healthier status, i.e., reducing potentially pathogenic bacteria such as Parabacteroides merdae but increasing beneficial bacteria such as Bifidobacterium longum subsp. longum, Anaerostipes hadrus and Ruminococcus obeum. Moreover, prior chronic statin therapy was associated with improved outcome in ACS patients. Multi-omics analysis revealed that specific changes in bacterial taxa were associated with disease severity or outcomes either directly or by mediating metabolites such as fatty acids and prenol lipids. Finally, we discovered that important taxa associated with statins were correlated with fatty acid- and isoprenoid-related pathways that were predicted by PICRUSt2. Conclusions: Our study suggests that statin treatment might benefit ACS patients by modulating the composition and function of the gut microbiome, which might result in improved circulating metabolites and reduced metabolic risk. Our findings provide new insights for understanding the heterogenic roles of statins in ACS patients through host gut microbiota metabolic interactions.}, } @article {pmid33897703, year = {2021}, author = {Meng, KF and Ding, LG and Wu, S and Wu, ZB and Cheng, GF and Zhai, X and Sun, RH and Xu, Z}, title = {Interactions Between Commensal Microbiota and Mucosal Immunity in Teleost Fish During Viral Infection With SVCV.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {654758}, pmid = {33897703}, issn = {1664-3224}, mesh = {Animals ; Biomarkers ; Computational Biology/methods ; Dysbiosis ; Fish Diseases/*immunology/pathology/*virology ; Gene Expression ; Host-Pathogen Interactions/*immunology ; *Immunity, Mucosal ; Immunohistochemistry ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mucous Membrane/immunology/microbiology ; Rhabdoviridae/*immunology ; }, abstract = {The mucosa of vertebrates is a particularly complex but dynamic environment in which the host constantly interacts with trillions of commensal microorganisms and pathogens. Although the internal and external mucosal microbiomes with immune defense of mammals have been well investigated, the relationship between mucosal microbes and their host's immune responses has not been systematically understood in the early vertebrates. In this study, we compared the composition and distribution of mucosal microbiota in common carp (Cyprinus carpio), and found that there were significant differences of microbiota between in the internal (gut) and external mucosal (buccal mucosa, gills and skin) tissues. Next, we successfully constructed an infection model with spring viremia of carp virus (SVCV). Specifically, following viral infection, the immune and antiviral related genes showed different up-regulation in all selected mucosal tissues while significant morphological changes were only found in external tissues including buccal mucosa, gills and skin. Using 16S rRNA gene sequence, we revealed that the abundance of Proteobacteria in mucosal tissues including buccal mucosa, gills and gut showed increased trend after viral infection, whereas the abundance of Fusobacteria significantly decreased in gut. In addition, the loss of dominant commensal microorganisms and increased colonization of opportunistic bacteria were discovered in the mucosal surfaces indicating that a secondary bacterial infection might occur in these mucosal tissues after viral infection. Overall, our results firstly point out the distribution of internal and external mucosal microbiota and analyze the changes of mucosal microbiota in common carp after SVCV infection, which may indicated that the potential role of mucosal microbiota in the antiviral process in early vertebrates.}, } @article {pmid33896632, year = {2021}, author = {Saborío-Montero, A and López-García, A and Gutiérrez-Rivas, M and Atxaerandio, R and Goiri, I and García-Rodriguez, A and Jiménez-Montero, JA and González, C and Tamames, J and Puente-Sánchez, F and Varona, L and Serrano, M and Ovilo, C and González-Recio, O}, title = {A dimensional reduction approach to modulate the core ruminal microbiome associated with methane emissions via selective breeding.}, journal = {Journal of dairy science}, volume = {104}, number = {7}, pages = {8135-8151}, doi = {10.3168/jds.2020-20005}, pmid = {33896632}, issn = {1525-3198}, mesh = {Animals ; Cattle/genetics ; Female ; Fermentation ; *Methane/metabolism ; *Microbiota/genetics ; Rumen/metabolism ; Selective Breeding ; Spain ; }, abstract = {The rumen is a complex microbial system of substantial importance in terms of greenhouse gas emissions and feed efficiency. This study proposes combining metagenomic and host genomic data for selective breeding of the cow hologenome toward reduced methane emissions. We analyzed nanopore long reads from the rumen metagenome of 437 Holstein cows from 14 commercial herds in 4 northern regions in Spain. After filtering, data were treated as compositional. The large complexity of the rumen microbiota was aggregated, through principal component analysis (PCA), into few principal components (PC) that were used as proxies of the core metagenome. The PCA allowed us to condense the huge and fuzzy taxonomical and functional information from the metagenome into a few PC. Bivariate animal models were applied using these PC and methane production as phenotypes. The variability condensed in these PC is controlled by the cow genome, with heritability estimates for the first PC of ~0.30 at all taxonomic levels, with a large probability (>83%) of the posterior distribution being >0.20 and with the 95% highest posterior density interval (95%HPD) not containing zero. Most genetic correlation estimates between PC1 and methane were large (≥0.70), with most of the posterior distribution (>82%) being >0.50 and with its 95%HPD not containing zero. Enteric methane production was positively associated with relative abundance of eukaryotes (protozoa and fungi) through the first component of the PCA at phylum, class, order, family, and genus. Nanopore long reads allowed the characterization of the core rumen metagenome using whole-metagenome sequencing, and the purposed aggregated variables could be used in animal breeding programs to reduce methane emissions in future generations.}, } @article {pmid33896313, year = {2021}, author = {Beck, LC and Granger, CL and Masi, AC and Stewart, CJ}, title = {Use of omic technologies in early life gastrointestinal health and disease: from bench to bedside.}, journal = {Expert review of proteomics}, volume = {18}, number = {4}, pages = {247-259}, doi = {10.1080/14789450.2021.1922278}, pmid = {33896313}, issn = {1744-8387}, mesh = {Child ; *Gastrointestinal Microbiome ; Gastrointestinal Tract ; Humans ; Infant, Newborn ; Metabolomics ; *Metagenomics ; Proteomics ; }, abstract = {Introduction: At birth, the gastrointestinal (GI) tract is colonized by a complex community of microorganisms, forming the basis of the gut microbiome. The gut microbiome plays a fundamental role in host health, disorders of which can lead to an array of GI diseases, both short and long term. Pediatric GI diseases are responsible for significant morbidity and mortality, but many remain poorly understood. Recent advancements in high-throughput technologies have enabled deeper profiling of GI morbidities. Technologies, such as metagenomics, transcriptomics, proteomics and metabolomics, have already been used to identify associations with specific pathologies, and highlight an exciting area of research. However, since these diseases are often complex and multifactorial by nature, reliance on a single experimental approach may not capture the true biological complexity. Therefore, multi-omics aims to integrate singular omic data to further enhance our understanding of disease.Areas covered: This review will discuss and provide an overview of the main omic technologies that are used to study complex GI pathologies in early life.Expert opinion: Multi-omic technologies can help to unravel the complexities of several diseases during early life, aiding in biomarker discovery and enabling the development of novel therapeutics and augment predictive models.}, } @article {pmid33894059, year = {2021}, author = {Sun, J and Chen, YL and Ding, YC and Zhong, H and Wu, M and Liu, ZH and Ge, LP}, title = {Deposition of resistant bacteria and resistome through FMT in germ-free piglets.}, journal = {Letters in applied microbiology}, volume = {73}, number = {2}, pages = {187-196}, doi = {10.1111/lam.13490}, pmid = {33894059}, issn = {1472-765X}, support = {cstc2019jxjl80019//Chongqing Scientific Research Institute Performance Incentive and Guidance Special Project/ ; 21509(20227)//Chongqing Basic Scientific Research/ ; 20206//the Key R & D Project in Agriculture and Animal Husbandries of Rongchang/ ; }, mesh = {Age Factors ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/*classification/*drug effects ; Biodiversity ; DNA, Bacterial ; Drug Resistance, Multiple, Bacterial/*genetics ; *Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome ; Germ-Free Life ; Interspersed Repetitive Sequences ; Metagenomics ; Swine ; Virulence Factors/*genetics ; }, abstract = {Faecal microbiota transplantation (FMT) has received considerable attention in recent years due to its remarkable efficacy in restoring a normal gut microbiome. Here, we established the groups of post-FMT recipient piglets using germ-free piglets during early life to characterize the colonization of gut microbiota composition and the enrichment of resistance gene acquisition. By metagenomic analysis, we identified 115 bacterial phyla and 2111 bacterial genera that were acquired by the FMT recipients. We found that early-life microbial colonization and the spread of resistomes in recipient piglets were age dependent. A total of 425, 425 and 358 AR genes primarily belonging to 114, 114 and 102 different types were detected in the donors, post-FMT recipients in the FMT-3D group and post-FMT recipients in the FMT-15D group respectively. Genes that encoded tetracycline, macrolide and chloramphenicol resistance proteins were the most dominant AR genes, and the results corresponded with the exposure of antibiotic consumption at farm. Bacteroides, Escherichia, Clostridium, Parabacteroides, Treponema, Lactobacillus and Enterococcus were significantly correlated with the distribution of AR genes. More importantly, the relative abundance of AR genes was positively correlated with the levels of mobile genetic elements. Our results indicate that early-life microbial colonization can persistently shape the gut microbiota and antibiotic resistome.}, } @article {pmid33893765, year = {2021}, author = {Takahashi, K and Sato, H and Mizusawa, T and Tominaga, K and Ikarashi, S and Hayashi, K and Mizuno, KI and Hashimoto, S and Yokoyama, J and Terai, S}, title = {Comparison of Oral and Esophageal Microbiota in Patients with Achalasia Before and After Peroral Endoscopic Myotomy.}, journal = {The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology}, volume = {32}, number = {1}, pages = {42-52}, pmid = {33893765}, issn = {2148-5607}, mesh = {Adult ; Aged ; Aged, 80 and over ; *Esophageal Achalasia/microbiology/surgery ; *Esophageal Neoplasms/microbiology ; Esophageal Sphincter, Lower/surgery ; *Esophageal Squamous Cell Carcinoma/microbiology ; Esophagus/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Middle Aged ; Mouth/microbiology ; *Myotomy/methods ; *Natural Orifice Endoscopic Surgery/methods ; Postoperative Period ; Preoperative Period ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; }, abstract = {BACKGROUND/AIMS: Patients with achalasia have a high incidence of esophageal squamous cell carcinoma (ESCC), which may be associated with alterations in oral and esophageal microbiota caused by food stasis. This study compared the oral and esophageal microbiota of patients with achalasia before and after peroral endoscopic myotomy (POEM). It also compared patients with achalasia to those with ESCC.

MATERIALS AND METHODS: The study prospectively examined 6 patients with achalasia and 14 with superficial ESCC. Oral samples obtained from the buccal mucosa using a swab and esophageal samples obtained from the mid-esophagus using a brush via endoscopy were analyzed by 16S rRNA metagenome sequencing. Additionally, endoscopic and histological findings of patients with achalasia before and after POEM were prospectively compared.

RESULTS: In patients with achalasia, Streptococcus was most abundant in both the oral and the esophageal microbiota, and these microbiota were significantly different. Although the overall structure of the oral and esophageal microbiota did not change after POEM, the relative abundance rate of Haemophilus and Neisseria increased in the esophagus, and endoscopic findings of inflammation improved after POEM (P = .04). The relative abundance of microbiota was not different among patients with achalasia from those with ESCC.

CONCLUSIONS: The oral and esophageal microbiota were significantly different in patients with achalasia, and some of the composition of the esophageal microbiota changed after POEM. However, these findings and disease-specific microbiota should be further evaluated in large-scale studies.}, } @article {pmid33887206, year = {2021}, author = {Li, X and Stokholm, J and Brejnrod, A and Vestergaard, GA and Russel, J and Trivedi, U and Thorsen, J and Gupta, S and Hjelmsø, MH and Shah, SA and Rasmussen, MA and Bisgaard, H and Sørensen, SJ}, title = {The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition.}, journal = {Cell host & microbe}, volume = {29}, number = {6}, pages = {975-987.e4}, doi = {10.1016/j.chom.2021.03.017}, pmid = {33887206}, issn = {1934-6069}, mesh = {Anti-Bacterial Agents/*pharmacology ; Asthma/*microbiology ; Child ; Child, Preschool ; Cohort Studies ; DNA, Bacterial ; Drug Resistance, Microbial/*genetics ; Environmental Exposure/*statistics & numerical data ; Escherichia coli/drug effects/*genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Genes, Bacterial ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenomics ; Pregnancy ; Proteobacteria/drug effects ; Risk Assessment ; }, abstract = {Antimicrobial resistance (AMR) is an accelerating global threat, yet the nature of AMR in the gut microbiome and how AMR is acquired during early life remain largely unknown. In a cohort of 662 Danish children, we characterized the antibiotic resistance genes (ARGs) acquired during the first year of life and assessed the impacts of diverse environmental exposures on ARG load. Our study reveals a clear bimodal distribution of ARG richness that is driven by the composition of the gut microbiome, especially E. coli. ARG profiles were significantly affected by various environmental factors. Among these factors, the importance of antibiotics diminished with time since treatment. Finally, ARG load and ARG clusters were also associated with the maturity of the gut microbiome and a bacterial composition associated with increased risk of asthma. These findings broaden our understanding of AMR in early life and have critical implications for efforts to mitigate its spread.}, } @article {pmid33886562, year = {2021}, author = {Feher, M and Fauszt, P and Tolnai, E and Fidler, G and Pesti-Asboth, G and Stagel, A and Szucs, I and Biro, S and Remenyik, J and Paholcsek, M and Stundl, L}, title = {Effects of phytonutrient-supplemented diets on the intestinal microbiota of Cyprinus carpio.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0248537}, pmid = {33886562}, issn = {1932-6203}, mesh = {*Animal Feed/analysis ; Animals ; Aquaculture ; Carps/*microbiology ; *Dietary Supplements/analysis ; Gastrointestinal Microbiome ; Intestines/microbiology ; *Phytochemicals/analysis ; }, abstract = {In the aquaculture sector, a strategy for the more efficient use of resources and proper disease control is needed to overcome the challenges of meat production worldwide. Modulation of the gastrointestinal tract microbiota is a promising approach for promoting animal health and preventing infection. This feeding experiment was conducted to discover the phytonutrient-induced changes in the gastrointestinal tract microbiota of common carp (Cyprinus carpio). Acclimatized animals aged 7 months (30 weeks) were divided randomly into five experimental groups to investigate the effects of the applied feed additives. The dietary supplements were manufactured from anthocyanin-containing processing wastes from the food industry, specifically the production of Hungarian sour cherry extract, synbiotics from fermented corn, and fermentable oligosaccharides from Hungarian sweet red pepper seeds and carotenoids from Hungarian sweet red pepper pulps, applied at a dose of 1%. The gut contents of the animals were collected at four time points throughout the 6-week study period. To track the compositional and diversity changes in the microbiota of the carp intestinal tract, V3-V4 16S rRNA gene-based metagenomic sequencing was performed. The growth performance of common carp juveniles was not significantly affected by supplementation of the basal diet with plant extracts. Phytonutrients improve the community diversity, increase the Clostridium and Lactobacillus abundances and decrease the abundances of potentially pathogenic and spoilage bacteria, such as Shewanella, Pseudomonas, Acinetobacter and Aeromonas. The phyla Proteobacteria, Tenericutes and Chlamydiae were positively correlated with the body weight, whereas Spirochaetes and Firmicutes exhibited negatively correlations with the body weight. We hypothesize that the application of phytonutrients in aquaculture settings might be a reasonable green approach for easing the usage of antibiotics.}, } @article {pmid33886557, year = {2021}, author = {Hewson, I and Sewell, MA}, title = {Surveillance of densoviruses and mesomycetozoans inhabiting grossly normal tissues of three Aotearoa New Zealand asteroid species.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0241026}, pmid = {33886557}, issn = {1932-6203}, mesh = {Animals ; Densovirus/genetics/*isolation & purification ; Mesomycetozoea/genetics/*isolation & purification ; Metagenome ; Metagenomics ; Microbiota ; New Zealand ; Starfish/*parasitology/*virology ; }, abstract = {Asteroid wasting events and mass mortality have occurred for over a century. We currently lack a fundamental understanding of the microbial ecology of asteroid disease, with disease investigations hindered by sparse information about the microorganisms associated with grossly normal specimens. We surveilled viruses and protists associated with grossly normal specimens of three asteroid species (Patiriella regularis, Stichaster australis, Coscinasterias muricata) on the North Island / Te Ika-a-Māui, Aotearoa New Zealand, using metagenomes prepared from virus and ribosome-sized material. We discovered several densovirus-like genome fragments in our RNA and DNA metagenomic libraries. Subsequent survey of their prevalence within populations by quantitative PCR (qPCR) demonstrated their occurrence in only a few (13%) specimens (n = 36). Survey of large and small subunit rRNAs in metagenomes revealed the presence of a mesomycete (most closely matching Ichthyosporea sp.). Survey of large subunit prevalence and load by qPCR revealed that it is widely detectable (80%) and present predominately in body wall tissues across all 3 species of asteroid. Our results raise interesting questions about the roles of these microbiome constituents in host ecology and pathogenesis under changing ocean conditions.}, } @article {pmid33884825, year = {2021}, author = {Cheng, S and Lu, P and Feng, QY}, title = {[Distribution of Antibiotic Resistance Genes and Microbial Communities in a Fishery Reclamation Mining Subsidence Area].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {42}, number = {5}, pages = {2541-2549}, doi = {10.13227/j.hjkx.202009166}, pmid = {33884825}, issn = {0250-3301}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Fisheries ; Genes, Bacterial/genetics ; *Microbiota/genetics ; }, abstract = {The widespread use of antibiotics in the aquaculture industry has caused antibiotic resistance genes (ARGs) pollution. Metagenomics technology was used to detect and analyze the relative abundance of ARGs and microbial community structure in a fishery reclamation mining subsidence area. A total of 29 ARGs were detected, and bacA had the highest relative abundance in all the samples, reaching 1.96×10[-5]-1.19×10[-4]. The relative abundance of sulfonamide and tetracycline ARGs in sediments was relatively high and the relative abundance of multidrug ARGs in well water was relatively high. Proteobacteria was the most dominant bacterial phylum in all the samples, and Chloroflexi and Euryarchaeota were relatively abundant in the sediments. Thiobacillus was the most dominant bacterial genus in the sediments, and Acinetobacter and Pseudomonas were the dominant bacterial genera in the well water. The correlation analysis between the ARGs and microorganisms showed that the genera and ARGs were mainly correlated to a moderate degree, and multiple genera had significant positive correlations with ARGs. The distribution of ARGs was affected by the structure of the microbial community. The sediments and well water in the fishery reclamation mining subsidence area were both contaminated by ARGs, and corresponding control measures should be strengthened to protect the regional environment.}, } @article {pmid33884767, year = {2021}, author = {Ban, MS and Kim, Y and Lee, S and Han, B and Yu, KS and Jang, IJ and Chung, HK and Lee, S}, title = {Pharmacokinetics of Ginsenoside Compound K From a Compound K Fermentation Product, CK-30, and From Red Ginseng Extract in Healthy Korean Subjects.}, journal = {Clinical pharmacology in drug development}, volume = {10}, number = {11}, pages = {1358-1364}, doi = {10.1002/cpdd.949}, pmid = {33884767}, issn = {2160-7648}, mesh = {Adult ; Biological Availability ; Cross-Over Studies ; Extracellular Vesicles/*genetics ; *Fermentation ; Gastrointestinal Microbiome/*genetics/physiology ; Ginsenosides/metabolism/*pharmacokinetics ; Healthy Volunteers ; Humans ; Male ; Metagenomics ; Microbiota/genetics/physiology ; *Panax ; Plant Extracts/*pharmacokinetics ; Republic of Korea ; Young Adult ; }, abstract = {Natural protopanaxadiol ginsenosides exhibit low absorption in the human intestine. However, ginsenoside compound K (CK) with 1 conjugated glucose molecule exhibits favorable absorption. The purpose of this study was to compare the pharmacokinetics of ginsenoside CK from a CK fermentation product, CK-30, and from a red ginseng extract. A randomized, open-label, 2-treatment, 2×2 crossover study was conducted. The volunteers were randomly divided into 2 groups. One group received CK-30, and the other group received 2.94 g of a red ginseng extract. After a 7-day washout period, the subjects received an alternative treatment for a single dose. The pharmacokinetic parameters, including the maximum plasma concentration (Cmax) and area under the plasma concentration-time curve from time 0 to time of last measurable concentration, were calculated. The median time to reach Cmax of ginsenoside CK after administration of CK-30 was 3.0 hours, whereas the corresponding value of the red ginseng extract was 10.0 hours. Compared with the red ginseng extract, CK-30 resulted in a higher systemic exposure to ginsenoside CK, with a 118.3-fold increase in Cmax and a 135.1-fold increase in area under the plasma concentration-time curve from time 0 to time of last measurable concentration. The systemic exposure to ginsenoside CK was significantly higher after administration of CK-30 than red ginseng extract.}, } @article {pmid33883261, year = {2021}, author = {Wang, L and Rosales Rosas, AL and De Coninck, L and Shi, C and Bouckaert, J and Matthijnssens, J and Delang, L}, title = {Establishment of Culex modestus in Belgium and a Glance into the Virome of Belgian Mosquito Species.}, journal = {mSphere}, volume = {6}, number = {2}, pages = {}, pmid = {33883261}, issn = {2379-5042}, mesh = {Animals ; Belgium ; Culex/classification/*virology ; Flavivirus/physiology ; Mosquito Vectors/*virology ; Seasons ; Virome/*genetics ; Viruses/classification/*genetics/isolation & purification ; West Nile virus/physiology ; }, abstract = {Culex modestus mosquitoes are considered potential transmission vectors of West Nile virus and Usutu virus. Their presence has been reported across several European countries, including one larva detected in Belgium in 2018. In this study, mosquitoes were collected in the city of Leuven and surrounding areas in the summers of 2019 and 2020. Species identification was performed based on morphological features and partial sequences of the mitochondrial cytochrome oxidase subunit I (COI) gene. The 107 mosquitoes collected in 2019 belonged to eight mosquito species, Culex pipiens (24.3%), Cx. modestus (48.6%), Cx. torrentium (0.9%), Culiseta annulata (0.9%), Culiseta morsitans (0.9%), Aedes sticticus (14.0%), Aedes cinereus (9.3%), and Anopheles plumbeus (0.9%), suggesting the presence of an established Cx. modestus population in Belgium. The collection of Cx. modestus mosquitoes at the same locations in 2020 confirmed their establishment in the region. Haplotype network analysis of the COI sequences for Cx. modestus showed that the Belgian population is rather diverse, suggesting that it may have been established in Belgium for some time. The Belgian Cx. modestus population was most closely related to populations from the United Kingdom and Germany. Characterization of the virome of the collected mosquitoes resulted in the identification of at least 33 eukaryotic viral species. Nine (nearly) complete genomes belonging to 6 viral species were identified, all of which were closely related to known viruses. In conclusion, here, we report the presence of Cx. modestus in the surrounding areas of Leuven, Belgium. As this species is considered to be a vector of several arboviruses, the implementation of vector surveillance programs to monitor this species is recommended.IMPORTANCECulex modestus mosquitoes are considered to be a potential "bridge" vector, being able to transmit pathogens between birds as well as from birds to mammals, including humans. In Belgium, this mosquito species was considered absent until the finding of one larva in 2018 and subsequent evidence of a large population in 2019 to 2020 described here. We collected mosquitoes in the summers of 2019 and 2020 in the city of Leuven and surrounding areas. The mosquito species was identified by morphological and molecular methods, demonstrating the presence of Cx. modestus in this region. The ability of mosquitoes to transmit pathogens can depend on several factors, one of them being their natural virus composition. Therefore, we identified the mosquito-specific viruses harbored by Belgian mosquitoes. As Cx. modestus is able to transmit viruses such as West Nile virus and Usutu virus, the establishment of this mosquito species may increase the risk of virus transmission in the region. It is thus advisable to implement mosquito surveillance programs to monitor this species.}, } @article {pmid33883174, year = {2021}, author = {de Clercq, NC and van den Ende, T and Prodan, A and Hemke, R and Davids, M and Pedersen, HK and Nielsen, HB and Groen, AK and de Vos, WM and van Laarhoven, HWM and Nieuwdorp, M}, title = {Fecal Microbiota Transplantation from Overweight or Obese Donors in Cachectic Patients with Advanced Gastroesophageal Cancer: A Randomized, Double-blind, Placebo-Controlled, Phase II Study.}, journal = {Clinical cancer research : an official journal of the American Association for Cancer Research}, volume = {27}, number = {13}, pages = {3784-3792}, doi = {10.1158/1078-0432.CCR-20-4918}, pmid = {33883174}, issn = {1557-3265}, mesh = {Adult ; Aged ; Cachexia/*etiology/microbiology/*therapy ; Double-Blind Method ; Esophageal Neoplasms/*complications/microbiology/pathology ; *Fecal Microbiota Transplantation ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; Neoplasm Staging ; Obesity/microbiology ; Overweight/microbiology ; Stomach Neoplasms/*complications/microbiology/pathology ; }, abstract = {PURPOSE: Cachexia is a multifactorial syndrome, associated with poor survival in patients with cancer, and is influenced by the gut microbiota. We investigated the effects of fecal microbiota transplantation (FMT) on cachexia and treatment response in patients with advanced gastroesophageal cancer.

EXPERIMENTAL DESIGN: In a double-blind randomized placebo-controlled trial performed in the Amsterdam University Medical Center, we assigned 24 cachectic patients with metastatic HER2-negative gastroesophageal cancer to either allogenic FMT (healthy obese donor) or autologous FMT, prior to palliative chemotherapy (capecitabine and oxaliplatin). Primary objective was to assess the effect of allogenic FMT on satiety. Secondary outcomes were other features of cachexia, along with disease control rate (DCR), overall survival (OS), progression-free survival (PFS), and toxicity. Finally, exploratory analyses were performed on the effect of FMT on gut microbiota composition (metagenomic sequencing) and metabolites (untargeted metabolomics).

RESULTS: Allogenic FMT did not improve any of the cachexia outcomes. Patients in the allogenic group (n = 12) had a higher DCR at 12 weeks (P = 0.035) compared with the autologous group (n = 12), longer median OS of 365 versus 227 days [HR = 0.38; 95% confidence interval (CI), 0.14-1.05; P = 0.057] and PFS of 204 versus 93 days (HR = 0.50; 95% CI, 0.21-1.20; P = 0.092). Patients in the allogenic group showed a significant shift in fecal microbiota composition after FMT (P = 0.010) indicating proper engraftment of the donor microbiota.

CONCLUSIONS: FMT from a healthy obese donor prior to first-line chemotherapy did not affect cachexia, but may have improved response and survival in patients with metastatic gastroesophageal cancer. These results provide a rational for larger FMT trials.}, } @article {pmid33882826, year = {2021}, author = {Pan, X and Li, Z and Li, B and Zhao, C and Wang, Y and Chen, Y and Jiang, Y}, title = {Dynamics of rumen gene expression, microbiome colonization, and their interplay in goats.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {288}, pmid = {33882826}, issn = {1471-2164}, support = {31822052//National Natural Science Foundation of China/ ; 31572381//National Natural Science Foundation of China/ ; 2019M663841//Postdoctoral Research Foundation of China/ ; }, mesh = {Animal Feed/analysis ; Animals ; Diet ; Goats/genetics ; Metagenome ; *Microbiota/genetics ; *Rumen ; }, abstract = {BACKGROUND: Preweaned rumen development is vital for animal health and efficient fermentation. In this study, we integrated ruminal transcriptomic and metagenomic data to explore the dynamics of rumen functions, microbial colonization, and their functional interactions during the first 8 weeks of life in goats.

RESULTS: The dynamic rumen transcriptomic and microbial profiles both exhibited two distinct phases during early rumen development. The differentially expressed genes of the rumen transcriptome between the two phases showed that the immune-related response was enriched in the first phase and nutrient-related metabolism was enriched in the second phase, whereas the differentially expressed genes of the rumen microbiome were enriched in bacteriocin biosynthesis and glycolysis/gluconeogenesis activities. The developmental shift in the rumen transcriptome (at d 21) was earlier than the feed stimulus (at d 25) and the shift in the rumen microbiome (at d 42). Additionally, 15 temporal dynamic rumen gene modules and 20 microbial modules were revealed by coexpression network analysis. Functional correlations between the rumen and its microbiome were primarily involved in rumen pH homeostasis, nitrogen metabolism and the immune response. Rumen gene modules associated with the microbial alpha diversity index were also enriched in the immune response process.

CONCLUSIONS: The present study touched the critical developmental process of rumen functions, microbial colonization and their functional interactions during preweaned development. Taken together, these results demonstrated that rumen development at the first phase is more likely a programmed process rather than stimulation from feed and the microbiome, while the shift of rumen metagenomes was likely regulated by both the diet and host. The intensive functional correlations between rumen genes and the microbiome demonstrated that synergistic processes occurred between them during early rumen development.}, } @article {pmid33880764, year = {2021}, author = {Lin, Y and Wang, G and Yu, J and Sung, JJY}, title = {Artificial intelligence and metagenomics in intestinal diseases.}, journal = {Journal of gastroenterology and hepatology}, volume = {36}, number = {4}, pages = {841-847}, doi = {10.1111/jgh.15501}, pmid = {33880764}, issn = {1440-1746}, support = {T21-705/20-N//Research Grants Council, University Grants Committee/ ; }, mesh = {*Artificial Intelligence ; Gastrointestinal Diseases/diagnosis/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Machine Learning ; Metagenomics/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA/methods ; }, abstract = {Gut microbiota has been shown to associate with the development of gastrointestinal diseases. In the last decade, development in whole metagenome sequencing and 16S rRNA sequencing technology has dramatically accelerated the gut microbiome's research and revealed its association with gastrointestinal disorders. Because of high dimensionality and complexity's intrinsic data characteristics, traditional bioinformatical methods could only explain the most significant changes with limited prediction accuracy. In contrast, machine learning is the application of artificial intelligence that provides the computational systems to automatically learn and improve from experience (training cohort) without being explicitly programmed. It is thus capable of unwiring high dimensionality and complicated correlational hitches. With modern computation power, machine learning is widely utilized to analyze microorganisms related to disease onset and other clinical features. It could help explore and identify novel biomarkers or improve the accuracy rate of disease diagnostic. This review summarized the most recent research that utilized machine learning to reveal the role of gut microbiota in intestinal disorders.}, } @article {pmid33880762, year = {2021}, author = {Zeng, T and Yu, X and Chen, Z}, title = {Applying artificial intelligence in the microbiome for gastrointestinal diseases: A review.}, journal = {Journal of gastroenterology and hepatology}, volume = {36}, number = {4}, pages = {832-840}, doi = {10.1111/jgh.15503}, pmid = {33880762}, issn = {1440-1746}, support = {2017SHZDZX01//Shanghai Municipal Science and Technology Major Project/ ; 61803360//National Natural Science Foundation of China/ ; 11871456//National Natural Science Foundation of China/ ; XDB38050200//Strategic Priority Research Program of Chinese Academy of Sciences/ ; }, mesh = {Artificial Intelligence/*trends ; *Big Data ; Datasets as Topic ; Gastrointestinal Diseases/*etiology/*microbiology ; *Gastrointestinal Microbiome ; Information Storage and Retrieval/*methods ; }, abstract = {For a long time, gut bacteria have been recognized for their important roles in the occurrence and progression of gastrointestinal diseases like colorectal cancer, and the ever-increasing amounts of microbiome data combined with other high-quality clinical and imaging datasets are leading the study of gastrointestinal diseases into an era of biomedical big data. The "omics" technologies used for microbiome analysis continuously evolve, and the machine learning or artificial intelligence technologies are key to extract the relevant information from microbiome data. This review intends to provide a focused summary of recent research and applications of microbiome big data and to discuss the use of artificial intelligence to combat gastrointestinal diseases.}, } @article {pmid33880565, year = {2021}, author = {Golob, JL and Rao, K}, title = {Signal Versus Noise: How to Analyze the Microbiome and Make Progress on Antimicrobial Resistance.}, journal = {The Journal of infectious diseases}, volume = {223}, number = {12 Suppl 2}, pages = {S214-S221}, pmid = {33880565}, issn = {1537-6613}, support = {R01 HS027431/HS/AHRQ HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/adverse effects ; Clostridioides difficile/growth & development/pathogenicity ; Clostridium Infections/etiology/microbiology ; Disease Models, Animal ; Drug Resistance, Microbial/drug effects/*genetics ; Gastrointestinal Microbiome/drug effects/*genetics/immunology ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions ; Humans ; }, abstract = {Antimicrobial resistance has become a worldwide medical challenge [1], so impactful that vancomycin-resistant Enterococcus (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) have entered the common vernacular. We have attempted to reduce the selective pressure through antimicrobial stewardship, curtail the spread by identifying and isolating carriers and individuals with symptomatic infection, and treat antibiotic-resistant organisms (AROs) by developing novel antimicrobials. Despite these extraordinary measures, the challenge of AROs continues to grow. The gut microbiome, the ecosystem of microbes (ie, the microbiota) and metabolites present upon and within all humans, is an emerging target for both the risk for colonization and defense against infection with AROs. Here, informed from experiences and successes with understanding the role of the microbiome in mediating risk of Clostridioides difficile infection (CDI), we (1) review our understanding of the risk from ARO acquisition; (2) review our current understanding of the gut microbiome's ability to resist colonization with AROs; (3) describe how experimental model systems can test these initial, global insights to arrive at more granular, mechanistic ones; and (4) suggest a path forward to make further progress in the field.}, } @article {pmid33879801, year = {2021}, author = {Guo, N and Wu, Q and Shi, F and Niu, J and Zhang, T and Degen, AA and Fang, Q and Ding, L and Shang, Z and Zhang, Z and Long, R}, title = {Seasonal dynamics of diet-gut microbiota interaction in adaptation of yaks to life at high altitude.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {38}, pmid = {33879801}, issn = {2055-5008}, mesh = {*Acclimatization ; *Altitude ; *Animal Feed ; Animals ; Biodiversity ; Biomass ; Cattle ; Cold Temperature ; *Gastrointestinal Microbiome ; Metabolic Networks and Pathways ; Metagenome ; Metagenomics/methods ; *Seasons ; }, abstract = {Dietary selection and intake affect the survival and health of mammals under extreme environmental conditions. It has been suggested that dietary composition is a key driver of gut microbiota variation; however, how gut microbiota respond to seasonal dietary changes under extreme natural conditions remains poorly understood. Sequencing plant trnL (UAA) region and 16S rRNA gene analysis were employed to determine dietary composition and gut microbiota in freely grazing yaks on the Tibetan plateau. Dietary composition was more diverse in winter than in summer, while Gramineae and Rosaceae were consumed frequently all year. Turnover of seasonal diet and gut microbiota composition occurred consistently. Yaks shifted enterotypes in response to dietary change between warm and cold seasons to best utilize nitrogen and energy, in particular in the harsh cold season. Our findings provide insights into understanding seasonal changes of diet-microbiota linkages in the adaptation of mammals to high altitudes.}, } @article {pmid33879589, year = {2021}, author = {Yuan, MM and Kakouridis, A and Starr, E and Nguyen, N and Shi, S and Pett-Ridge, J and Nuccio, E and Zhou, J and Firestone, M}, title = {Fungal-Bacterial Cooccurrence Patterns Differ between Arbuscular Mycorrhizal Fungi and Nonmycorrhizal Fungi across Soil Niches.}, journal = {mBio}, volume = {12}, number = {2}, pages = {}, pmid = {33879589}, issn = {2150-7511}, mesh = {Bacteria/genetics/*metabolism ; Biomass ; Fungi/genetics/*metabolism ; *Microbial Interactions ; *Microbiota ; Mycorrhizae/genetics/*metabolism ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Soil bacteria and fungi are known to form niche-specific communities that differ between actively growing and decaying roots. Yet almost nothing is known about the cross-kingdom interactions that frame these communities and the environmental filtering that defines these potentially friendly or competing neighbors. We explored the temporal and spatial patterns of soil fungal (mycorrhizal and nonmycorrhizal) and bacterial cooccurrence near roots of wild oat grass, Avena fatua, growing in its naturalized soil in a greenhouse experiment. Amplicon sequences of the fungal internal transcribed spacer (ITS) and bacterial 16S rRNA genes from rhizosphere and bulk soils collected at multiple plant growth stages were used to construct covariation-based networks as a step toward identifying fungal-bacterial associations. Corresponding stable-isotope-enabled metagenome-assembled genomes (MAGs) of bacteria identified in cooccurrence networks were used to inform potential mechanisms underlying the observed links. Bacterial-fungal networks were significantly different in rhizosphere versus bulk soils and between arbuscular mycorrhizal fungi (AMF) and nonmycorrhizal fungi. Over 12 weeks of plant growth, nonmycorrhizal fungi formed increasingly complex networks with bacteria in rhizosphere soils, while AMF more frequently formed networks with bacteria in bulk soils. Analysis of network-associated bacterial MAGs suggests that some of the fungal-bacterial links that we identified are potential indicators of bacterial breakdown and consumption of fungal biomass, while others intimate shared ecological niches.IMPORTANCE Soils near living and decomposing roots form distinct niches that promote microorganisms with distinctive environmental preferences and interactions. Yet few studies have assessed the community-level cooccurrence of bacteria and fungi in these soil niches as plant roots grow and senesce. With plant growth, we observed increasingly complex cooccurrence networks between nonmycorrhizal fungi and bacteria in the rhizosphere, while mycorrhizal fungal (AMF) and bacterial cooccurrence was more pronounced in soil further from roots, in the presence of decaying root litter. This rarely documented phenomenon suggests niche sharing of nonmycorrhizal fungi and bacteria, versus niche partitioning between AMF and bacteria; both patterns are likely driven by C substrate availability and quality. Although the implications of species cooccurrence are fiercely debated, MAGs matching the bacterial nodes in our networks possess the functional potential to interact with the fungi that they are linked to, suggesting an ecological significance of fungal-bacterial cooccurrence patterns.}, } @article {pmid33878155, year = {2021}, author = {Chon, JW and Jung, JY and Ahn, Y and Bae, D and Khan, S and Seo, KH and Kim, H and Sung, K}, title = {Detection of Campylobacter jejuni from Fresh Produce: Comparison of Culture- and PCR-based Techniques, and Metagenomic Approach for Analyses of the Microbiome before and after Enrichment.}, journal = {Journal of food protection}, volume = {84}, number = {10}, pages = {1704-1712}, doi = {10.4315/JFP-20-408}, pmid = {33878155}, issn = {1944-9097}, mesh = {Animals ; *Campylobacter ; *Campylobacter jejuni/genetics ; Chickens ; Culture Media ; *Microbiota ; Real-Time Polymerase Chain Reaction ; }, abstract = {ABSTRACT: In this study, we compared the efficiency of culture-based methods with or without membrane filtration, real-time PCR, and digital droplet PCR (ddPCR) for the detection of Campylobacter in fresh produce. Alfalfa sprouts, clover sprouts, coleslaw, and lettuce salad spiked with Campylobacter jejuni were enriched in Bolton broth for 48 h, and enrichment cultures were either directly inoculated onto modified charcoal-cefoperazone-deoxycholate agar or applied on membrane filters placed on the surface of plating media. In parallel, 2-mL Bolton broth cultures were taken to extract DNA for real-time PCR and ddPCR assays and bacterial community analysis. A developed primer set for ddPCR and real-time PCR was evaluated for its inclusivity and exclusivity using pure culture of C. jejuni and non-C. jejuni strains, respectively. In pure culture, the primer set reacted only with C. jejuni strains and showed negative reaction to non-C. jejuni strains. There was no significant difference (P > 0.05) in the detection efficiency of positive Campylobacter isolates from coleslaw and lettuce salad using four detection methods. However, for sprout samples, the detection efficiency of the culture method was significantly (P < 0.05) lower than those of the two PCR assays and the filtration method. The analysis also revealed the presence of Pseudomonas and Acinetobacter as the most prevalent competing microbiota in enriched culture and only Acinetobacter on agar plates in the selective culture step.}, } @article {pmid33878111, year = {2021}, author = {Wille, M and Geoghegan, JL and Holmes, EC}, title = {How accurately can we assess zoonotic risk?.}, journal = {PLoS biology}, volume = {19}, number = {4}, pages = {e3001135}, pmid = {33878111}, issn = {1545-7885}, mesh = {Animals ; Biodiversity ; Disease Reservoirs/classification/statistics & numerical data ; *Environmental Monitoring/methods/standards ; Host Specificity/genetics ; Humans ; Metagenomics/methods/organization & administration/standards ; Phylogeny ; Risk Assessment ; Risk Factors ; Selection Bias ; *Virus Diseases/epidemiology/etiology/prevention & control/transmission ; Viruses/classification/genetics/isolation & purification/pathogenicity ; Zoonoses/epidemiology/*etiology/*prevention & control/virology ; }, abstract = {Identifying the animal reservoirs from which zoonotic viruses will likely emerge is central to understanding the determinants of disease emergence. Accordingly, there has been an increase in studies attempting zoonotic "risk assessment." Herein, we demonstrate that the virological data on which these analyses are conducted are incomplete, biased, and rapidly changing with ongoing virus discovery. Together, these shortcomings suggest that attempts to assess zoonotic risk using available virological data are likely to be inaccurate and largely only identify those host taxa that have been studied most extensively. We suggest that virus surveillance at the human-animal interface may be more productive.}, } @article {pmid33877031, year = {2021}, author = {Afridi, OK and Ali, J and Chang, JH}, title = {Resistome and microbial profiling of pediatric patient's gut infected with multidrug-resistant diarrhoeagenic Enterobacteriaceae using next-generation sequencing; the first study from Pakistan.}, journal = {The Libyan journal of medicine}, volume = {16}, number = {1}, pages = {1915615}, pmid = {33877031}, issn = {1819-6357}, mesh = {Anti-Bacterial Agents/*pharmacology ; Child, Preschool ; Cross-Sectional Studies ; Diarrhea/*microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacteriaceae/*genetics/isolation & purification ; Female ; Gastroenteritis/microbiology ; Gastrointestinal Microbiome/*genetics ; Gram-Negative Bacteria/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Microbial Sensitivity Tests ; Pakistan ; }, abstract = {A high prevalence of multidrug-resistant (MDR) pathogens has been reported in adult and pediatric populations of Pakistan. However, data describing the effect of MDR microbes on the gut microbiota is scarce. We designed a cross-sectional pediatric study to investigate the effect of MDR microbes' infection on the gut microbiome and its resistome of children using high-throughput next-generation sequencing (NGS). A cross-sectional study was conducted at a tertiary health care hospital in Peshawar Pakistan, between 5 September 2019 to 15 February 2020. Pediatric patients with acute gastroenteritis (n = 200) were enrolled. All the enrolled pediatric patients underwent initial antimicrobial resistance (AMR) screening using the disk diffusion method. Children with MDR infections were identified and selected for gut microbiome and its resistome profiling using NGS. Out of 200 enrolled pediatric patients, 80 (40%) were found infected with MDR diarrheagenic Enterobacteriaceae consisting of 50 (62.5%) infections caused by extended-spectrum beta-lactamase (ESBL) producing E. coli while 30 (37.5%) by MDR Enterobacter specie. A total of 63 and 17 antibiotic-resistant genes (ARGs) conferring resistance to 7 and 5 classes of antibiotics were identified in the resistomes of MDR diarrheagenic Enterobacteriaceae infected and healthy children, respectively. NGS-based gut microbial profiling of MDR Enterobacter spp., ESBL producing E. coli infected pediatric patients and healthy controls revealed the predominance of Proteobacteria and Actinobacteria, respectively. An increased abundance of several pathogenic gram-negative bacteria namely E. coli, Enterobacter cloacae, and Salmonella enterica was observed in the gut microbiota of children infected with MDR bacterial infections than that of the healthy controls. This work indicates that children with MDR infections have reduced microbial diversity and enriched ARGs than healthy controls. The emergence of MDR bacterial strains and their association with gut dysbiosis needs immediate attention to regulate antibiotics usage in Pakistani children.}, } @article {pmid33876546, year = {2021}, author = {Bunse, C and Koch, H and Breider, S and Simon, M and Wietz, M}, title = {Sweet spheres: succession and CAZyme expression of marine bacterial communities colonizing a mix of alginate and pectin particles.}, journal = {Environmental microbiology}, volume = {23}, number = {6}, pages = {3130-3148}, doi = {10.1111/1462-2920.15536}, pmid = {33876546}, issn = {1462-2920}, mesh = {*Alginates ; Bacteria/genetics ; *Gammaproteobacteria/genetics ; Metagenome ; Pectins ; }, abstract = {Polysaccharide particles are important substrates and microhabitats for marine bacteria. However, substrate-specific bacterial dynamics in mixtures of particle types with different polysaccharide composition, as likely occurring in natural habitats, are undescribed. Here, we studied the composition, functional diversity and gene expression of marine bacterial communities colonizing a mix of alginate and pectin particles. Amplicon, metagenome and metatranscriptome sequencing revealed that communities on alginate and pectin particles significantly differed from their free-living counterparts. Unexpectedly, microbial dynamics on alginate and pectin particles were similar, with predominance of amplicon sequence variants (ASVs) from Tenacibaculum, Colwellia, Psychrobium and Psychromonas. Corresponding metagenome-assembled genomes (MAGs) expressed diverse alginate lyases, several colocalized in polysaccharide utilization loci. Only a single, low-abundant MAG showed elevated transcript abundances of pectin-degrading enzymes. One specific Glaciecola ASV dominated the free-living fraction, possibly persisting on particle-derived oligomers through different glycoside hydrolases. Elevated ammonium uptake and metabolism signified nitrogen as an important factor for degrading carbon-rich particles, whereas elevated methylcitrate and glyoxylate cycles suggested nutrient limitation in surrounding waters. The bacterial preference for alginate, whereas pectin primarily served as colonization scaffold, illuminates substrate-driven dynamics within mixed polysaccharide pools. These insights expand our understanding of bacterial niche specialization and the biological carbon pump in macroalgae-rich habitats.}, } @article {pmid33876475, year = {2022}, author = {Wirth, R and Maróti, G and Lipták, L and Mester, M and Al Ayoubi, A and Pap, B and Madléna, M and Minárovits, J and Kovács, KL}, title = {Microbiomes in supragingival biofilms and saliva of adolescents with gingivitis and gingival health.}, journal = {Oral diseases}, volume = {28}, number = {7}, pages = {2000-2014}, doi = {10.1111/odi.13883}, pmid = {33876475}, issn = {1601-0825}, support = {GINOP-2.3.2-15-2016-00011//European Regional Development Fund/ ; GINOP-2.2.1-15-2017-00081//European Regional Development Fund/ ; GINOP-2.2.1-15-2017-00033//European Regional Development Fund/ ; EFOP-3.6.2-16-2017-00010//European Regional Development Fund/ ; PD132145//National Research, Development and Innovation Office (NKFIH), Hungary/ ; FK123899//National Research, Development and Innovation Office (NKFIH), Hungary/ ; //Hungarian Academy of Sciences/ ; }, mesh = {Adolescent ; Bacteria/genetics ; Biofilms ; *Dental Plaque/microbiology ; *Gingivitis/microbiology ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; }, abstract = {BACKGROUND: Important alterations exist in the microbiomes of supragingival biofilm and saliva samples from adolescent patients developing induced or spontaneous gingivitis relative to healthy controls. These and the relationships to dental health are not fully understood yet.

SUBJECTS AND METHODS: Supragingival biofilm samples (n = 36) were collected from the teeth of 9 adolescents with gingivitis induced by orthodontic appliances, as well as dental plaques (n = 40) from 10 adolescents with spontaneous gingivitis, in addition to similar samples (n = 36) from 9 healthy controls. The bacterial metagenomes were analyzed by 16S rRNA gene amplicon sequencing. Salivary microbiomes of the same persons were characterized by shotgun metagenome sequencing. The data sets were examined using advanced bioinformatics workflows and two reference databases.

RESULTS: The composition and diversity of bacterial communities did not differ extensively among the three study groups. Nevertheless, the relative abundances of the genera Fusobacterium, Akkermansia, Treponema, and Campylobacter were prominently higher in gingivitis patients versus controls. In contrast, the genera Lautropia, Kingella, Neisseria, Actinomyces, and Rothia were significantly more abundant in controls than in either of the two gingivitis groups.

CONCLUSIONS: The abundance pattern of certain taxa rather than individual strains shows characteristic features of potential diagnostic value. Stringent bioinformatics treatment of the sequencing data is mandatory to avoid unintentional misinterpretations.}, } @article {pmid33875673, year = {2021}, author = {Thongsripong, P and Chandler, JA and Kittayapong, P and Wilcox, BA and Kapan, DD and Bennett, SN}, title = {Metagenomic shotgun sequencing reveals host species as an important driver of virome composition in mosquitoes.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {8448}, pmid = {33875673}, issn = {2045-2322}, support = {P01 AI106695/AI/NIAID NIH HHS/United States ; P20 RR018727/RR/NCRR NIH HHS/United States ; U01 AI151788/AI/NIAID NIH HHS/United States ; U54 AI065359/AI/NIAID NIH HHS/United States ; }, mesh = {Aedes/*virology ; Animals ; Culex/*virology ; *Genome, Viral ; High-Throughput Nucleotide Sequencing ; Host Specificity ; *Metagenome ; Mosquito Vectors/*virology ; Phylogeny ; RNA Viruses/*physiology ; RNA-Seq ; Thailand ; *Virome ; }, abstract = {High-throughput nucleic acid sequencing has greatly accelerated the discovery of viruses in the environment. Mosquitoes, because of their public health importance, are among those organisms whose viromes are being intensively characterized. Despite the deluge of sequence information, our understanding of the major drivers influencing the ecology of mosquito viromes remains limited. Using methods to increase the relative proportion of microbial RNA coupled with RNA-seq we characterize RNA viruses and other symbionts of three mosquito species collected along a rural to urban habitat gradient in Thailand. The full factorial study design allows us to explicitly investigate the relative importance of host species and habitat in structuring viral communities. We found that the pattern of virus presence was defined primarily by host species rather than by geographic locations or habitats. Our result suggests that insect-associated viruses display relatively narrow host ranges but are capable of spreading through a mosquito population at the geographical scale of our study. We also detected various single-celled and multicellular microorganisms such as bacteria, alveolates, fungi, and nematodes. Our study emphasizes the importance of including ecological information in viromic studies in order to gain further insights into viral ecology in systems where host specificity is driving both viral ecology and evolution.}, } @article {pmid33875193, year = {2021}, author = {Xiao, M and Huang, T and Xu, Y and Peng, Z and Liu, Z and Guan, Q and Xie, M and Xiong, T}, title = {Metatranscriptomics reveals the gene functions and metabolic properties of the major microbial community during Chinese Sichuan Paocai fermentation.}, journal = {Food microbiology}, volume = {98}, number = {}, pages = {103573}, doi = {10.1016/j.fm.2020.103573}, pmid = {33875193}, issn = {1095-9998}, mesh = {Brassica/metabolism/*microbiology ; China ; Enterobacteriaceae/classification/genetics/*isolation & purification/*metabolism ; Fermentation ; Fermented Foods/*microbiology ; Food Microbiology ; Lactobacillaceae/classification/genetics/*isolation & purification/metabolism ; Metagenomics ; *Microbiota ; Transcriptome ; Vegetables/metabolism/*microbiology ; }, abstract = {Chinese Sichuan Paocai (CSP) is one of the world's best-known fermented vegetables with a large presence in the Chinese market. The dynamic microbial community is the main contributor to Paocai fermentation. However, little is known about the ecological distribution and functional importance of these community members. In this study, metatranscriptomics was used to comprehensively explore the active microbial community members and key transcripts with significant functions in the Paocai fermentation process. Enterobacter, Leuconostoc, and Lactobacillus dominated the three-fermentation stages (Pre-, Mid- and Lat-), respectively. Carbon metabolism was the most abundant pathway. GH (glycoside hydrolase) and GT (lycosyl transferase) were the two most highly expressed carbohydrate-active enzymes. The most highly differentially expressed genes were grouped in the biosynthesis of amino acids, followed by glycolysis. Meta-pathways in the Sichuan Paocai fermentation ecosystem were reconstructed, Lactobacillaceae and Enterobacteriaceae were the two most important metabolic contributors. In addition, the nrfA and nirB were two genes referred to distinct nitrite reductase enzymes and 9 specialized genes, such as eclo, ron and ent were expressed to produce autoinducer 2 (AI-2) kinase in response to population density. The present study revealed functional enzymes and meta-pathways of the active microbial communities, which provide a deeper understanding of their contribution to CSP products.}, } @article {pmid33874905, year = {2021}, author = {Li, YQ and Chai, YH and Wang, XS and Huang, LY and Luo, XM and Qiu, C and Liu, QH and Guan, XY}, title = {Bacterial community in saline farmland soil on the Tibetan plateau: responding to salinization while resisting extreme environments.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {119}, pmid = {33874905}, issn = {1471-2180}, mesh = {Bacteria/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; *Extreme Environments ; Farms ; Metagenomics ; Microbiota/*genetics ; Salt Tolerance ; Soil/*chemistry ; *Soil Microbiology ; Stress, Physiological/*physiology ; Tibet ; }, abstract = {BACKGROUND: Salinization damages the health of soil systems and reduces crop yields. Responses of microbial communities to salinized soils and their functional maintenance under high salt stress are valuable scientific problems. Meanwhile, the microbial community of the salinized soil in the plateau environment is less understood. Here, we applied metagenomics technology to reveal the structure and function of microorganisms in salinized soil of the Tibetan Plateau.

RESULTS: The diversity of composition and function of microbial community in saline soil have changed significantly. The abundances of chemoautotrophic and acidophilic bacteria comprising Rhodanobacter, Acidobacterium, Candidatus Nitrosotalea, and Candidatus Koribacter were significantly higher in saline soil. The potential degradation of organic carbon in the saline soil, as well as the production of NO and N2O via denitrification, and the production of sulfate by sulfur oxidation were significantly higher than the non-saline soil. Both types of soils were rich in genes encoding resistance to environmental stresses (i.e., cold, ultraviolet light, and hypoxia in Tibetan Plateau). The resistance of the soil microbial communities to the saline environment is based on the absorption of K[+] as the main mechanism, with cross-protection proteins and absorption buffer molecules as auxiliary mechanisms in our study area. Network analysis showed that functional group comprising chemoautotrophic and acidophilic bacteria had significant positive correlations with electrical conductivity and total sulfur, and significant negative correlations with the total organic carbon, pH, and available nitrogen. The soil moisture, pH, and electrical conductivity are likely to affect the bacterial carbon, nitrogen, and sulfur cycles.

CONCLUSIONS: These results indicate that the specific environment of the Tibetan Plateau and salinization jointly shape the structure and function of the soil bacterial community, and that the bacterial communities respond to complex and harsh living conditions. In addition, environmental feedback probably exacerbates greenhouse gas emissions and accelerates the reduction in the soil pH. This study will provide insights into the microbial responses to soil salinization and the potential ecological risks in the special plateau environment.}, } @article {pmid33873140, year = {2021}, author = {Das, S and Tamang, JP}, title = {Changes in microbial communities and their predictive functionalities during fermentation of toddy, an alcoholic beverage of India.}, journal = {Microbiological research}, volume = {248}, number = {}, pages = {126769}, doi = {10.1016/j.micres.2021.126769}, pmid = {33873140}, issn = {1618-0623}, mesh = {Alcoholic Beverages/analysis/*microbiology ; Alcohols/analysis/metabolism ; Ascomycota/classification/genetics/isolation & purification/*metabolism ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Fermentation ; Flowers/metabolism/microbiology ; India ; *Microbiota ; Phoeniceae/metabolism/*microbiology ; Sugars/metabolism ; }, abstract = {Toddy is a traditional mild-alcoholic drink of India, which is produced from fresh palm saps by natural fermentation. We studied the successional changes in bacterial and fungal communities during the natural fermentation (0 h-96 h) of toddy. During fermentation, alcohol content of the fermenting saps increased significantly from 0.6 %±0.15 to 5.6 %±0.02, pH decreased from 6.33 %±0.02-3.93 ± 0.01, volatile and titratable acidity acidity (g/100 mL) increased from 0.17 ± 0.02 (0 h) to 0.48 ± 0.02 (96 h) and 1.30 ± 0.005 (0 h) to 2.47 ± 0.005 (96 h), respectively. Total sugar content and ˚BRIX also decreased during the fermentation. Firmicutes (78.25 %) was the most abundant phylum followed by Proteobacteria (21.57 %). Leuconostoc was the most abundant genus in the early stages of fermentation. However, Lactobacillus and Gluconoacetobacter were found abundant with increase in pH during the later phases of fermentation (72 h-96 h). Ascomycota (99.02 %) was the most abundant fungal phylum. Hanseniaspora was the abundant yeast in the initial stages of fermentation, whereas the population of Saccharomyces increased significantly after 24 h of fermentation. Torulaspora, Lachancea and Starmerella showed their heterogeneous distribution throughout the fermentation. Computational analysis of metagenomes based on KEGG and MetaCyc databases showed different predictive functional profiles such as folate biosynthesis, glutathione metabolism, terpenoids biosynthesis and biosynthesis of amino acids with significant differences between the fresh palm saps and fermenting saps during toddy fermentation.}, } @article {pmid33872206, year = {2021}, author = {Soto-Girón, MJ and Peña-Gonzalez, A and Hatt, JK and Montero, L and Páez, M and Ortega, E and Smith, S and Cevallos, W and Trueba, G and Konstantinidis, KT and Levy, K}, title = {Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador.}, journal = {The American journal of tropical medicine and hygiene}, volume = {104}, number = {6}, pages = {2275-2285}, pmid = {33872206}, issn = {1476-1645}, support = {K01 AI103544/AI/NIAID NIH HHS/United States ; R01 AI137679/AI/NIAID NIH HHS/United States ; }, mesh = {Acute Disease/epidemiology ; Adolescent ; Adult ; Aged ; Bacteria/*classification/*genetics/isolation & purification ; Child ; Child, Preschool ; Diarrhea/epidemiology/*microbiology ; Ecuador/epidemiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Metagenomics ; Middle Aged ; Rural Population/*statistics & numerical data ; Urban Population/*statistics & numerical data ; Young Adult ; }, abstract = {Previous studies have reported lower fecal bacterial diversity in urban populations compared with those living in rural settings. However, most of these studies compare geographically distant populations from different countries and even continents. The extent of differences in the gut microbiome in adjacent rural versus urban populations, and the role of such differences, if any, during enteric infections remain poorly understood. To provide new insights into these issues, we sampled the gut microbiome of young children with and without acute diarrheal disease (ADD) living in rural and urban areas in northern Ecuador. Shotgun metagenomic analyses of non-ADD samples revealed small but significant differences in the abundance of microbial taxa, including a greater abundance of Prevotella and a lower abundance of Bacteroides and Alistipes in rural populations. Greater and more significant shifts in taxon abundance, metabolic pathway abundance, and diversity were observed between ADD and non-ADD status when comparing urban to rural sites (Welch's t-test, P < 0.05). Collectively our data show substantial functional, diversity, and taxonomic shifts in the gut microbiome of urban populations with ADD, supporting the idea that the microbiome of rural populations may be more resilient to ADD episodes.}, } @article {pmid33869074, year = {2021}, author = {Xiao, S and Zhang, G and Jiang, C and Liu, X and Wang, X and Li, Y and Cheng, M and Lv, H and Xian, F and Guo, X and Tan, Y}, title = {Deciphering Gut Microbiota Dysbiosis and Corresponding Genetic and Metabolic Dysregulation in Psoriasis Patients Using Metagenomics Sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {605825}, pmid = {33869074}, issn = {2235-2988}, mesh = {Dysbiosis ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; *Psoriasis ; RNA, Ribosomal, 16S/genetics ; Vascular Endothelial Growth Factor A ; }, abstract = {BACKGROUND: Increasing evidence has shown that alterations in the intestinal microbiota play an important role in the pathogenesis of psoriasis. The existing relevant studies focus on 16S rRNA gene sequencing, but in-depth research on gene functions and comprehensive identification of microbiota is lacking.

OBJECTIVES: To comprehensively identify characteristic gut microbial compositions, genetic functions and relative metabolites of patients with psoriasis and to reveal the potential pathogenesis of psoriasis.

METHODS: DNA was extracted from the faecal microbiota of 30 psoriatic patients and 15 healthy subjects, and metagenomics sequencing and bioinformatic analyses were performed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database, cluster of orthologous groups (COG) annotations, and metabolic analyses were used to indicate relative target genes and pathways to reveal the pathogenesis of psoriasis.

RESULTS: Compared with healthy individuals, the gut microbiota of psoriasis patients displayed an alteration in microbial taxa distribution, but no significant difference in microbial diversity. A distinct gut microbial composition in patients with psoriasis was observed, with an increased abundance of the phyla Firmicutes, Actinobacteria and Verrucomicrobia and genera Faecalibacterium, Bacteroides, Bifidobacterium, Megamonas and Roseburia and a decreased abundance of the phyla Bacteroidetes, Euryarchaeota and Proteobacteria and genera Prevotella, Alistipes, and Eubacterium. A total of 134 COGs were predicted with functional analysis, and 15 KEGG pathways, including lipopolysaccharide (LPS) biosynthesis, WNT signaling, apoptosis, bacterial secretion system, and phosphotransferase system, were significantly enriched in psoriasis patients. Five metabolites, hydrogen sulfide (H2S), isovalerate, isobutyrate, hyaluronan and hemicellulose, were significantly dysregulated in the psoriatic cohort. The dysbiosis of gut microbiota, enriched pathways and dysregulated metabolites are relevant to immune and inflammatory response, apoptosis, the vascular endothelial growth factor (VEGF) signaling pathway, gut-brain axis and brain-skin axis that play important roles in the pathogenesis of psoriasis.

CONCLUSIONS: A clear dysbiosis was displayed in the gut microbiota profile, genetic functions and relative metabolites of psoriasis patients. This study is beneficial for further understanding the inflammatory pathogenesis of psoriasis and could be used to develop microbiome-based predictions and therapeutic approaches.}, } @article {pmid33868800, year = {2021}, author = {Gilroy, R and Ravi, A and Getino, M and Pursley, I and Horton, DL and Alikhan, NF and Baker, D and Gharbi, K and Hall, N and Watson, M and Adriaenssens, EM and Foster-Nyarko, E and Jarju, S and Secka, A and Antonio, M and Oren, A and Chaudhuri, RR and La Ragione, R and Hildebrand, F and Pallen, MJ}, title = {Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e10941}, pmid = {33868800}, issn = {2167-8359}, support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community.

RESULTS: We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n = 582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes. This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from chicken faeces, documenting over forty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii.

CONCLUSIONS: Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provide a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.}, } @article {pmid33868230, year = {2021}, author = {Liu, F and Xu, X and Chao, L and Chen, K and Shao, A and Sun, D and Hong, Y and Hu, R and Jiang, P and Zhang, N and Xiao, Y and Yan, F and Feng, N}, title = {Alteration of the Gut Microbiome in Chronic Kidney Disease Patients and Its Association With Serum Free Immunoglobulin Light Chains.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {609700}, pmid = {33868230}, issn = {1664-3224}, mesh = {Biomarkers ; Case-Control Studies ; Computational Biology/methods ; Disease Susceptibility ; *Dysbiosis ; Female ; *Gastrointestinal Microbiome ; Glomerular Filtration Rate ; Humans ; Immunoglobulin Light Chains/*blood ; Kidney Function Tests ; Male ; Metabolic Networks and Pathways ; Metagenome ; Metagenomics/methods ; Renal Insufficiency, Chronic/*blood/diagnosis/*etiology ; Severity of Illness Index ; }, abstract = {OBJECTIVES: Gut dysbiosis is associated with chronic kidney disease (CKD), and serum free immunoglobulin light chains (FLCs) are biomarkers for CKD. This study aims to assess the CKD gut microbiome and to determine its impact on serum FLC levels.

METHODS: To control for confounders, 100 patients and sex- and age-matched healthy controls (HCs) were recruited. The gut microbiome was assessed by sequencing 16S rRNA gene V3-V4 hypervariable regions. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States was applied to infer functional metabolic pathways. When observing group differences in the microbiome and predicted metabolic pathways, demographic confounders were adjusted using binary logistic regression; when examining impacts of the gut microbiome and metabolic pathways on serum FLCs, factors influencing FLC levels were adjusted using multiple regression.

RESULTS: Principal coordinate analysis revealed a significantly different bacterial community between the CKD and HC groups (P < 0.05). After adjusting for confounders, lower Chao 1, observed species and Shannon indices based on binary logistic regression predicted CKD prevalence. Actinobacteria, Alistipes, Bifidobacterium and Bifidobacterium longum enrichment, upregulation of metabolic pathways of bacterial toxin, chloroalkane and chloroalkene degradation, and Staphylococcus aureus infection also predicted CKD prevalence (P < 0.05). Furthermore, depletion of Actinobacteria and Bifidobacterium and reduced chloroalkane and chloroalkene degradation predicted high levels of FLC λ (P < 0.05).

CONCLUSIONS: Gut dysbiosis in CKD patients was confirmed by controlling for confounders in the present study. Additionally, the association between gut dysbiosis and FLC λ levels demonstrates the existence of crosstalk between the microbiome and immune response in CKD.}, } @article {pmid33863919, year = {2021}, author = {Larkin, AA and Garcia, CA and Garcia, N and Brock, ML and Lee, JA and Ustick, LJ and Barbero, L and Carter, BR and Sonnerup, RE and Talley, LD and Tarran, GA and Volkov, DL and Martiny, AC}, title = {High spatial resolution global ocean metagenomes from Bio-GO-SHIP repeat hydrography transects.}, journal = {Scientific data}, volume = {8}, number = {1}, pages = {107}, pmid = {33863919}, issn = {2052-4463}, support = {OCE-1046297//National Science Foundation (NSF)/ ; OCE-1437015//National Science Foundation (NSF)/ ; NA10OAR4320143//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; OCE-1559002//National Science Foundation (NSF)/ ; OCE-1848576//National Science Foundation (NSF)/ ; T32AI141346//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; OCE-1948842//National Science Foundation (NSF)/ ; T32 AI141346/AI/NIAID NIH HHS/United States ; U8R1SE3-PRF//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; }, mesh = {Genomic Library ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Oceans and Seas ; Seawater/*microbiology ; }, abstract = {Detailed descriptions of microbial communities have lagged far behind physical and chemical measurements in the marine environment. Here, we present 971 globally distributed surface ocean metagenomes collected at high spatio-temporal resolution. Our low-cost metagenomic sequencing protocol produced 3.65 terabases of data, where the median number of base pairs per sample was 3.41 billion. The median distance between sampling stations was 26 km. The metagenomic libraries described here were collected as a part of a biological initiative for the Global Ocean Ship-based Hydrographic Investigations Program, or "Bio-GO-SHIP." One of the primary aims of GO-SHIP is to produce high spatial and vertical resolution measurements of key state variables to directly quantify climate change impacts on ocean environments. By similarly collecting marine metagenomes at high spatiotemporal resolution, we expect that this dataset will help answer questions about the link between microbial communities and biogeochemical fluxes in a changing ocean.}, } @article {pmid33863898, year = {2021}, author = {Li, X and Su, C and Jiang, Z and Yang, Y and Zhang, Y and Yang, M and Zhang, X and Du, Y and Zhang, J and Wang, L and Jiang, J and Hong, B}, title = {Berberine attenuates choline-induced atherosclerosis by inhibiting trimethylamine and trimethylamine-N-oxide production via manipulating the gut microbiome.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {36}, pmid = {33863898}, issn = {2055-5008}, mesh = {Animals ; Atherosclerosis/*etiology/*metabolism/pathology ; Berberine/*pharmacology ; Choline/*adverse effects ; Diet ; Disease Models, Animal ; Disease Susceptibility ; Dysbiosis ; Gastrointestinal Microbiome/*drug effects ; Methylamines/*metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout, ApoE ; }, abstract = {Trimethylamine-N-oxide (TMAO), a derivative from the gut microbiota metabolite trimethylamine (TMA), has been identified to be an independent risk factor for promoting atherosclerosis. Evidences suggest that berberine (BBR) could be used to treat obesity, diabetes and atherosclerosis, however, its mechanism is not clear mainly because of its poor oral bioavailability. Here, we show that BBR attenuated TMA/TMAO production in the C57BL/6J and ApoE KO mice fed with choline-supplemented chow diet, and mitigated atherosclerotic lesion areas in ApoE KO mice. Inhibition of TMA/TMAO production by BBR-modulated gut microbiota was proved by a single-dose administration of d9-choline in vivo. Metagenomic analysis of cecal contents demonstrated that BBR altered gut microbiota composition, microbiome functionality, and cutC/cntA gene abundance. Furthermore, BBR was shown to inhibit choline-to-TMA conversion in TMA-producing bacteria in vitro and in gut microbial consortium from fecal samples of choline-fed mice and human volunteers, and the result was confirmed by transplantation of TMA-producing bacteria in mice. These results offer new insights into the mechanisms responsible for the anti-atherosclerosis effects of BBR, which inhibits commensal microbial TMA production via gut microbiota remodeling.}, } @article {pmid33863892, year = {2021}, author = {Luhung, I and Uchida, A and Lim, SBY and Gaultier, NE and Kee, C and Lau, KJX and Gusareva, ES and Heinle, CE and Wong, A and Premkrishnan, BNV and Purbojati, RW and Acerbi, E and Kim, HL and Junqueira, ACM and Longford, S and Lohar, SR and Yap, ZH and Panicker, D and Koh, Y and Kushwaha, KK and Ang, PN and Putra, A and Drautz-Moses, DI and Schuster, SC}, title = {Experimental parameters defining ultra-low biomass bioaerosol analysis.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {37}, pmid = {33863892}, issn = {2055-5008}, mesh = {Air Microbiology ; *Biomass ; *Ecosystem ; *Environmental Microbiology ; Environmental Monitoring ; Metagenome ; Metagenomics/methods ; *Microbiota ; Soil Microbiology ; Water Microbiology ; }, abstract = {Investigation of the microbial ecology of terrestrial, aquatic and atmospheric ecosystems requires specific sampling and analytical technologies, owing to vastly different biomass densities typically encountered. In particular, the ultra-low biomass nature of air presents an inherent analytical challenge that is confounded by temporal fluctuations in community structure. Our ultra-low biomass pipeline advances the field of bioaerosol research by significantly reducing sampling times from days/weeks/months to minutes/hours, while maintaining the ability to perform species-level identification through direct metagenomic sequencing. The study further addresses all experimental factors contributing to analysis outcome, such as amassment, storage and extraction, as well as factors that impact on nucleic acid analysis. Quantity and quality of nucleic acid extracts from each optimisation step are evaluated using fluorometry, qPCR and sequencing. Both metagenomics and marker gene amplification-based (16S and ITS) sequencing are assessed with regard to their taxonomic resolution and inter-comparability. The pipeline is robust across a wide range of climatic settings, ranging from arctic to desert to tropical environments. Ultimately, the pipeline can be adapted to environmental settings, such as dust and surfaces, which also require ultra-low biomass analytics.}, } @article {pmid33863450, year = {2021}, author = {Correia Sales, GF and Carvalho, BF and Schwan, RF and de Figueiredo Vilela, L and Moreno Meneses, JA and Gionbelli, MP and Luiza da Silva Ávila, C}, title = {Heat stress influence the microbiota and organic acids concentration in beef cattle rumen.}, journal = {Journal of thermal biology}, volume = {97}, number = {}, pages = {102897}, doi = {10.1016/j.jtherbio.2021.102897}, pmid = {33863450}, issn = {0306-4565}, mesh = {Animals ; Bacteria/genetics/isolation & purification ; Carboxylic Acids/*metabolism ; Cattle ; Cattle Diseases/microbiology ; Female ; Heat Stress Disorders/microbiology/veterinary ; Heat-Shock Response ; Humidity ; Methanobrevibacter/genetics/isolation & purification ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Rumen/*metabolism/*microbiology ; Temperature ; }, abstract = {The objective of this study was to evaluate the effect of heat stress on meta-taxonomic and metabolic profiles of prokaryotes in beef cattle rumen. Six pure-breed Nellore heifers with ruminal cannulas were used in the study. Six treatments were tested in a 6 × 6 Latin Square with six periods of 21days. The treatments were evaluated in a 2 × 2 + 2 factorial arrangement, consisting of 4 combinations: two temperatures conditions (thermoneutral, TN: 24 °C; and heat stress, HS: 34 °C) and two dietary energy concentration [low-energy (37% non-fibrous carbohydrates - NFC, 12 Mcal of metabolizable energy per kg of dry matter) or high-energy concentration (50.5% NFC, 18.49 Mcal of metabolizable energy per kg of dry matter)] plus two additional treatments with animals maintained in TN conditions but with your intake restricted (TN-RI) to the same of the heifers in HS with the two dietary energy concentration. The meta-genome was sequenced by MiSeq Sequencing System platform, and the DNA sequences were analysed using Geneious 10.2.3 software. The metabolic profile was evaluated by liquid and gas chromatography. Animals under HS presented lower (P = 0.04) prokaryote richness than animals under TN conditions. The genera Flavonifractor (1.4%), Treponema (0.6%) and Ruminococcus (0.9%) showed the lowest (P < 0.04) and Carnobacterium (7.7%) the highest (P = 0.02) relative abundance when the animals were submitted to HS, in relation to animals in TN. A total of 49 different metabolites were identified in the ruminal samples. The concentration of isobutyric acid (4.32 mM) was highest in bovine rumen under HS conditions. Heat stress influenced the microbiota and concentration of some organic acids in beef cattle rumen. There was a reduction in the richness of rumen in cattle under heat stress, but the diversity of prokaryotes was not affected.}, } @article {pmid33860293, year = {2021}, author = {Ding, J and Ma, X and Han, L and Zhao, X and Li, A and Xin, Q and Lian, W and Li, Z and Ren, H and Ren, Z}, title = {Gut microbial alterations in neonatal jaundice pre- and post-treatment.}, journal = {Bioscience reports}, volume = {41}, number = {4}, pages = {}, pmid = {33860293}, issn = {1573-4935}, mesh = {Drugs, Chinese Herbal/pharmacology/therapeutic use ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Humans ; Infant, Newborn ; Jaundice, Neonatal/drug therapy/*microbiology ; Male ; Metagenome ; }, abstract = {Neonatal jaundice is a common disease that affects up to 60% of newborns. Herein, we performed a comparative analysis of the gut microbiome in neonatal jaundice and non-neonatal jaundice infants (NJIs) and identified gut microbial alterations in neonatal jaundice pre- and post-treatment. We prospectively collected 232 fecal samples from 51 infants at five time points (0, 1, 3, 6, and 12 months). Finally, 114 samples from 6 NJIs and 19 non-NJI completed MiSeq sequencing and analysis. We characterized the gut microbiome and identified microbial differences and gene functions. Meconium microbial diversity from NJI was decreased compared with that from non-NJI. The genus Gemella was decreased in NJI versus non-NJI. Eleven predicted microbial functions, including fructose 1,6-bisphosphatase III and pyruvate carboxylase subunit B, decreased, while three functions, including acetyl-CoA acyltransferase, increased in NJI. After treatments, the microbial community presented significant alteration-based β diversity. The phyla Firmicutes and Actinobacteria were increased, while Proteobacteria and Fusobacteria were decreased. Microbial alterations were also analyzed between 6 recovered NJI and 19 non-NJI. The gut microbiota was unique in the meconium microbiome from NJI, implying that early gut microbiome intervention could be promising for the management of neonatal jaundice. Alterations of gut microbiota from NJI can be of great value to bolster evidence-based prevention against 'bacterial dysbiosis'.}, } @article {pmid33859184, year = {2021}, author = {Couch, CE and Stagaman, K and Spaan, RS and Combrink, HJ and Sharpton, TJ and Beechler, BR and Jolles, AE}, title = {Diet and gut microbiome enterotype are associated at the population level in African buffalo.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2267}, pmid = {33859184}, issn = {2041-1723}, support = {BB/L011085/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Buffaloes/*microbiology/physiology ; Communicable Diseases/epidemiology/microbiology/*veterinary ; DNA, Bacterial/isolation & purification ; Feces/microbiology ; Feeding Behavior/*physiology ; Firmicutes/genetics/isolation & purification ; Gastrointestinal Microbiome/*immunology ; Incidence ; Metagenomics ; Phylogeny ; Planococcaceae/genetics/isolation & purification ; Prevalence ; RNA, Ribosomal, 16S/genetics ; South Africa/epidemiology ; Symbiosis/immunology ; }, abstract = {Studies in humans and laboratory animals link stable gut microbiome "enterotypes" with long-term diet and host health. Understanding how this paradigm manifests in wild herbivores could provide a mechanistic explanation of the relationships between microbiome dynamics, changes in dietary resources, and outcomes for host health. We identify two putative enterotypes in the African buffalo gut microbiome. The enterotype prevalent under resource-abundant dietary regimes, regardless of environmental conditions, has high richness, low between- and within-host beta diversity, and enrichment of genus Ruminococcaceae-UCG-005. The second enterotype, prevalent under restricted dietary conditions, has reduced richness, elevated beta diversity, and enrichment of genus Solibacillus. Population-level gamma diversity is maintained during resource restriction by increased beta diversity between individuals, suggesting a mechanism for population-level microbiome resilience. We identify three pathogens associated with microbiome variation depending on host diet, indicating that nutritional background may impact microbiome-pathogen dynamics. Overall, this study reveals diet-driven enterotype plasticity, illustrates ecological processes that maintain microbiome diversity, and identifies potential associations between diet, enterotype, and disease.}, } @article {pmid33859022, year = {2021}, author = {Lind, AL and Pollard, KS}, title = {The gut microbiomes of 180 species.}, journal = {Science (New York, N.Y.)}, volume = {372}, number = {6539}, pages = {238-239}, doi = {10.1126/science.abg9095}, pmid = {33859022}, issn = {1095-9203}, mesh = {*Gastrointestinal Microbiome ; *Graphite ; Metagenome ; RNA, Ribosomal, 16S ; }, } @article {pmid33858103, year = {2021}, author = {Zeng, H and Xu, H and Liu, G and Wei, Y and Zhang, J and Shi, H}, title = {Physiological and metagenomic strategies uncover the rhizosphere bacterial microbiome succession underlying three common environmental stresses in cassava.}, journal = {Journal of hazardous materials}, volume = {411}, number = {}, pages = {125143}, doi = {10.1016/j.jhazmat.2021.125143}, pmid = {33858103}, issn = {1873-3336}, mesh = {Bacteria/genetics ; *Manihot ; Metagenome ; Metagenomics ; *Microbiota/genetics ; Plant Roots ; Rhizosphere ; Soil Microbiology ; }, abstract = {The most common environmental pollutants such as cadmium (Cd), glyphosate and tetracycline have led to profoundly adverse impacts on plant productivity. However, how tropical crops such as cassava sense these pollutants via roots and how rhizosphere microbiome interacts with the host and pollutants remain largely unknown. In this study, we found these stresses significantly inhibited plant growth and triggered cell damage in a dosage-dependent manner, and the toxic effect on redox homeostasis was correlated with antioxidant metabolism. Using metagenomics technique, we found the rhizosphere microbiomes dynamically altered as the dose of these stresses increased. We also identified stressor-associated metagenome-assembled genomes and microbial metabolic pathways as well as mobile genetic elements in the rhizosphere microbiomes. Next, a co-occurrence network of both physiological and microbiome features was constructed to explore how these pollutants derived oxidative damage through the microbiome succession. Notably, phyllosphere transplantation of Agrobacterium tumefaciens or Pseudomonas stutzeri can significantly alleviate the negative effects of stresses on cassava growth and redox homeostasis. Collectively, this study demonstrated the dynamics of rhizosphere bacterial microbiome of cassava under three common environmental stresses, and A. tumefaciens and P. stutzeri could be developed as potential beneficial bacteria to alleviate Cd, glyphosate and tetracycline-triggered damage to cassava.}, } @article {pmid33857456, year = {2021}, author = {Shamsaddini, A and Gillevet, PM and Acharya, C and Fagan, A and Gavis, E and Sikaroodi, M and McGeorge, S and Khoruts, A and Albhaisi, S and Fuchs, M and Sterling, RK and Bajaj, JS}, title = {Impact of Antibiotic Resistance Genes in Gut Microbiome of Patients With Cirrhosis.}, journal = {Gastroenterology}, volume = {161}, number = {2}, pages = {508-521.e7}, pmid = {33857456}, issn = {1528-0012}, support = {R21 TR003095/TR/NCATS NIH HHS/United States ; R21 TR002024/TR/NCATS NIH HHS/United States ; I01 CX000176/CX/CSRD VA/United States ; I01 CX001076/CX/CSRD VA/United States ; I01 CX001761/CX/CSRD VA/United States ; R01 HS025412/HS/AHRQ HHS/United States ; }, mesh = {Adult ; Aged ; Anti-Bacterial Agents/adverse effects/*therapeutic use ; Bacteria/*drug effects/genetics ; Case-Control Studies ; Cross-Sectional Studies ; Disease Progression ; Drug Resistance, Bacterial/*genetics ; Dysbiosis ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Hospitalization ; Humans ; Intestines/*microbiology ; Liver Cirrhosis/diagnosis/*drug therapy/microbiology/mortality ; Male ; *Metagenome ; Metagenomics ; Middle Aged ; Rifaximin/adverse effects/*therapeutic use ; Risk Assessment ; Risk Factors ; Time Factors ; Treatment Outcome ; Young Adult ; }, abstract = {BACKGROUND AND AIMS: Cirrhosis is associated with changes in intestinal microbiota that can lead to hepatic encephalopathy (HE) and infections, especially with antibiotic-resistant organisms. However, the impact of gut microbial antibiotic resistance gene (ARG) burden on clinical outcomes is unclear. The aims of the study were to determine the impact of ARGs in cirrhosis-related gut metagenome on outcomes and disease progression, study the effect of rifaximin on ARG burden, and compare ARGs in cirrhosis with chronic kidney disease (CKD) and diabetes.

METHODS: In outpatients with cirrhosis who underwent metagenomics, we evaluated change in ARG abundances with progression and their multivariable impact on 90-day hospitalizations and deaths over 1 year. We also studied ARGs pre- and 8 weeks post-rifaximin in patients with compensated cirrhosis in an open-label trial. Finally, ARGs from CKD and diabetes studies were compared with cirrhosis on machine learning.

RESULTS: A total of 163 patients with cirrhosis (43 compensated, 20 ascites-only, 30 HE-only, 70 both) and 40 controls were included. ARG abundances were higher in cirrhosis versus controls and worsened with advancing cirrhosis severity; 44 patients were hospitalized and 14 died. ARG abundances were associated with hospitalizations and mortality while controlling for cirrhosis complications, medications, and demographics. Rifaximin trial: ARG abundance patterns were minimally affected in 19 patients post-rifaximin. CKD/diabetes comparison: ARG abundance patterns in cirrhosis are distinguishable on machine learning and include more gram-positive ARGs.

CONCLUSIONS: Cirrhosis is associated with high gut microbial ARG gene burden compared with controls, which worsens with disease progression and may be different from CKD and diabetes. ARGs are not affected by rifaximin and are associated with hospitalizations and death.}, } @article {pmid33853691, year = {2021}, author = {Zuo, T and Liu, Q and Zhang, F and Yeoh, YK and Wan, Y and Zhan, H and Lui, GCY and Chen, Z and Li, AYL and Cheung, CP and Chen, N and Lv, W and Ng, RWY and Tso, EYK and Fung, KSC and Chan, V and Ling, L and Joynt, G and Hui, DSC and Chan, FKL and Chan, PKS and Ng, SC}, title = {Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {91}, pmid = {33853691}, issn = {2049-2618}, mesh = {*COVID-19 ; Child, Preschool ; DNA ; *Gastrointestinal Microbiome/genetics ; Humans ; RNA ; SARS-CoV-2 ; Virome ; }, abstract = {BACKGROUND: Coronavirus disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 was isolated from fecal samples, and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively known as the virome) that play a role in regulating host immunity and disease pathophysiology. Understanding gut virome perturbation that underlies SARS-CoV-2 infection and severity is an unmet need.

METHODS: We enrolled 98 COVID-19 patients with varying disease severity (3 asymptomatic, 53 mild, 34 moderate, 5 severe, 3 critical) and 78 non-COVID-19 controls matched for gender and co-morbidities. All subjects had fecal specimens sampled at inclusion. Blood specimens were collected for COVID-19 patients at admission to test for inflammatory markers and white cell counts. Among COVID-19 cases, 37 (38%) patients had serial fecal samples collected 2 to 3 times per week from time of hospitalization until after discharge. Using shotgun metagenomics sequencing, we sequenced and profiled the fecal RNA and DNA virome. We investigated alterations and longitudinal dynamics of the gut virome in association with disease severity and blood parameters.

RESULTS: Patients with COVID-19 showed underrepresentation of Pepper mild mottle virus (RNA virus) and multiple bacteriophage lineages (DNA viruses) and enrichment of environment-derived eukaryotic DNA viruses in fecal samples, compared to non-COVID-19 subjects. Such gut virome alterations persisted up to 30 days after disease resolution. Fecal virome in SARS-CoV-2 infection harbored more stress-, inflammation-, and virulence-associated gene encoding capacities including those pertaining to bacteriophage integration, DNA repair, and metabolism and virulence associated with their bacterial host. Baseline fecal abundance of 10 virus species (1 RNA virus, pepper chlorotic spot virus, and 9 DNA virus species) inversely correlated with disease COVID-19 severity. These viruses inversely correlated with blood levels of pro-inflammatory proteins, white cells, and neutrophils. Among the 10 COVID-19 severity-associated DNA virus species, 4 showed inverse correlation with age; 5 showed persistent lower abundance both during disease course and after disease resolution relative to non-COVID-19 subjects.

CONCLUSIONS: Both enteric RNA and DNA virome in COVID-19 patients were different from non-COVID-19 subjects, which persisted after disease resolution of COVID-19. Gut virome may calibrate host immunity and regulate severity to SARS-CoV-2 infection. Our observation that gut viruses inversely correlated with both severity of COVID-19 and host age may partly explain that older subjects are prone to severe and worse COVID-19 outcomes. Altogether, our data highlight the importance of human gut virome in severity and potentially therapeutics of COVID-19. Video Abstract.}, } @article {pmid33853672, year = {2021}, author = {Mu, A and McDonald, D and Jarmusch, AK and Martino, C and Brennan, C and Bryant, M and Humphrey, GC and Toronczak, J and Schwartz, T and Nguyen, D and Ackermann, G and D'Onofrio, A and Strathdee, SA and Schooley, RT and Dorrestein, PC and Knight, R and Aslam, S}, title = {Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {92}, pmid = {33853672}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/therapeutic use ; *Bacteriophages/genetics ; Humans ; *Microbiota ; *Phage Therapy ; *Staphylococcal Infections/drug therapy ; }, abstract = {BACKGROUND: Infectious bacterial diseases exhibiting increasing resistance to antibiotics are a serious global health issue. Bacteriophage therapy is an anti-microbial alternative to treat patients with serious bacterial infections. However, the impacts to the host microbiome in response to clinical use of phage therapy are not well understood.

RESULTS: Our paper demonstrates a largely unchanged microbiota profile during 4 weeks of phage therapy when added to systemic antibiotics in a single patient with Staphylococcus aureus device infection. Metabolomic analyses suggest potential indirect cascading ecological impacts to the host (skin) microbiome. We did not detect genomes of the three phages used to treat the patient in metagenomic samples taken from saliva, stool, and skin; however, phages were detected using endpoint-PCR in patient serum.

CONCLUSION: Results from our proof-of-principal study supports the use of bacteriophages as a microbiome-sparing approach to treat bacterial infections. Video abstract.}, } @article {pmid33850115, year = {2021}, author = {Raes, EJ and Karsh, K and Sow, SLS and Ostrowski, M and Brown, MV and van de Kamp, J and Franco-Santos, RM and Bodrossy, L and Waite, AM}, title = {Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2213}, pmid = {33850115}, issn = {2041-1723}, mesh = {Bacteria/classification/*genetics ; Bacterial Physiological Phenomena ; Biodiversity ; Ecology ; Genes, Bacterial/*genetics ; Metabolic Networks and Pathways/*genetics ; Metagenome ; Metagenomics/*methods ; Pacific Ocean ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Thermodynamics ; }, abstract = {Global oceanographic monitoring initiatives originally measured abiotic essential ocean variables but are currently incorporating biological and metagenomic sampling programs. There is, however, a large knowledge gap on how to infer bacterial functions, the information sought by biogeochemists, ecologists, and modelers, from the bacterial taxonomic information (produced by bacterial marker gene surveys). Here, we provide a correlative understanding of how a bacterial marker gene (16S rRNA) can be used to infer latitudinal trends for metabolic pathways in global monitoring campaigns. From a transect spanning 7000 km in the South Pacific Ocean we infer ten metabolic pathways from 16S rRNA gene sequences and 11 corresponding metagenome samples, which relate to metabolic processes of primary productivity, temperature-regulated thermodynamic effects, coping strategies for nutrient limitation, energy metabolism, and organic matter degradation. This study demonstrates that low-cost, high-throughput bacterial marker gene data, can be used to infer shifts in the metabolic strategies at the community scale.}, } @article {pmid33849075, year = {2021}, author = {Arif, M and Zhang, C and Li, X and Güngör, C and Çakmak, B and Arslantürk, M and Tebani, A and Özcan, B and Subaş, O and Zhou, W and Piening, B and Turkez, H and Fagerberg, L and Price, N and Hood, L and Snyder, M and Nielsen, J and Uhlen, M and Mardinoglu, A}, title = {iNetModels 2.0: an interactive visualization and database of multi-omics data.}, journal = {Nucleic acids research}, volume = {49}, number = {W1}, pages = {W271-W276}, pmid = {33849075}, issn = {1362-4962}, support = {RC2 HG005805/HG/NHGRI NIH HHS/United States ; P50 GM076547/GM/NIGMS NIH HHS/United States ; P30 ES017885/ES/NIEHS NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; *Databases, Factual ; *Gastrointestinal Microbiome ; Gene Regulatory Networks ; Humans ; *Metabolomics ; *Metagenomics ; Middle Aged ; Mouth/*microbiology ; Neoplasms/genetics ; Non-alcoholic Fatty Liver Disease/blood/microbiology ; *Proteomics ; Software ; }, abstract = {It is essential to reveal the associations between various omics data for a comprehensive understanding of the altered biological process in human wellness and disease. To date, very few studies have focused on collecting and exhibiting multi-omics associations in a single database. Here, we present iNetModels, an interactive database and visualization platform of Multi-Omics Biological Networks (MOBNs). This platform describes the associations between the clinical chemistry, anthropometric parameters, plasma proteomics, plasma metabolomics, as well as metagenomics for oral and gut microbiome obtained from the same individuals. Moreover, iNetModels includes tissue- and cancer-specific Gene Co-expression Networks (GCNs) for exploring the connections between the specific genes. This platform allows the user to interactively explore a single feature's association with other omics data and customize its particular context (e.g. male/female specific). The users can also register their data for sharing and visualization of the MOBNs and GCNs. Moreover, iNetModels allows users who do not have a bioinformatics background to facilitate human wellness and disease research. iNetModels can be accessed freely at https://inetmodels.com without any limitation.}, } @article {pmid33848685, year = {2021}, author = {Canova, R and Budaszewski, RF and Weber, MN and da Silva, MS and Puhl, DE and Battisti, LO and Soares, JF and Wagner, PG and Varela, APM and Mayer, FQ and Canal, CW}, title = {Spleen and lung virome analysis of South American fur seals (Arctocephalus australis) collected on the southern Brazilian coast.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {92}, number = {}, pages = {104862}, doi = {10.1016/j.meegid.2021.104862}, pmid = {33848685}, issn = {1567-7257}, mesh = {Anelloviridae/genetics ; Animals ; Brazil ; Circovirus/genetics ; Fur Seals/*virology ; Lung/*virology ; Metagenomics/methods ; Phylogeny ; Spleen/*virology ; Virome/*genetics ; }, abstract = {South American fur seals (Arctocephalus australis) are believed to reach the coast of Rio Grande do Sul (RS) through sea currents. They live in colonies and are frequently found resting on the beach. However, it is also common to find dead pinnipeds on beaches, sharing the environment with humans, domestic animals and other wild species on the coast and facilitating the transmission of pathogens. In the present study, a metagenomic approach was applied to evaluate the viral diversity in organs of fur seals found deceased along the coast of the state of RS, southern Brazil. The lungs and spleens of 29 animals were collected, macerated individually, pooled separately (one pool for lungs and another for spleens) and sequenced using the Illumina MiSeq platform. Sequences more closely related to members of the Anelloviridae and Circoviridae families were detected. Nine putative new species of anellovirus and one putative new genus, named Nitorquevirus, were described. Additionally, the circovirus sequences found in the lungs of A. australis have a common ancestor with PCV3, a proposed swine pathogen. Our study expanded the knowledge about viral communities in pinnipeds and could be useful for monitoring new viruses and potential viral sharing among wildlife, domestic animals, and humans.}, } @article {pmid33848236, year = {2021}, author = {Perez-Mon, C and Qi, W and Vikram, S and Frossard, A and Makhalanyane, T and Cowan, D and Frey, B}, title = {Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps).}, journal = {Microbial genomics}, volume = {7}, number = {4}, pages = {}, pmid = {33848236}, issn = {2057-5858}, mesh = {Bacteria/classification/*genetics/isolation & purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Carbon/metabolism ; Carbon Cycle ; Metagenome ; Metagenomics ; *Microbiota ; Nitrogen/metabolism ; Permafrost/chemistry/*microbiology ; Phylogeny ; Soil Microbiology ; Switzerland ; }, abstract = {The warming-induced thawing of permafrost promotes microbial activity, often resulting in enhanced greenhouse gas emissions. The ability of permafrost microorganisms to survive the in situ sub-zero temperatures, their energetic strategies and their metabolic versatility in using soil organic materials determine their growth and functionality upon thawing. Hence, functional characterization of the permafrost microbiome, particularly in the underexplored mid-latitudinal alpine regions, is a crucial first step in predicting its responses to the changing climate, and the consequences for soil-climate feedbacks. In this study, for the first time, the functional potential and metabolic capabilities of a temperate mountain permafrost microbiome from central Europe has been analysed using shotgun metagenomics. Permafrost and active layers from the summit of Muot da Barba Peider (MBP) [Swiss Alps, 2979 m above sea level (a.s.l.)] revealed a strikingly high functional diversity in the permafrost (north-facing soils at a depth of 160 cm). Permafrost metagenomes were enriched in stress-response genes (e.g. cold-shock genes, chaperones), as well as in genes involved in cell defence and competition (e.g. antiviral proteins, antibiotics, motility, nutrient-uptake ABC transporters), compared with active-layer metagenomes. Permafrost also showed a higher potential for the synthesis of carbohydrate-active enzymes, and an overrepresentation of genes involved in fermentation, carbon fixation, denitrification and nitrogen reduction reactions. Collectively, these findings demonstrate the potential capabilities of permafrost microorganisms to thrive in cold and oligotrophic conditions, and highlight their metabolic versatility in carbon and nitrogen cycling. Our study provides a first insight into the high functional gene diversity of the central European mountain permafrost microbiome. Our findings extend our understanding of the microbial ecology of permafrost and represent a baseline for future investigations comparing the functional profiles of permafrost microbial communities at different latitudes.}, } @article {pmid33848166, year = {2021}, author = {Huang, W and Kane, MA}, title = {MAPLE: A Microbiome Analysis Pipeline Enabling Optimal Peptide Search and Comparative Taxonomic and Functional Analysis.}, journal = {Journal of proteome research}, volume = {20}, number = {5}, pages = {2882-2894}, doi = {10.1021/acs.jproteome.1c00114}, pmid = {33848166}, issn = {1535-3907}, mesh = {*Acer ; Humans ; *Microbiota ; Peptides ; Proteome/genetics ; Proteomics ; }, abstract = {Metaproteomics by mass spectrometry (MS) is a powerful approach to profile a large number of proteins expressed by all organisms in a highly complex biological or ecological sample, which is able to provide a direct and quantitative assessment of the functional makeup of a microbiota. The human gastrointestinal microbiota has been found playing important roles in human physiology and health, and metaproteomics has been shown to shed light on multiple novel associations between microbiota and diseases. MS-powered proteomics generally relies on genome data to define search space. However, metaproteomics, which simultaneously analyzes all proteins from hundreds to thousands of species, faces significant challenges regarding database search and interpretation of results. To overcome these obstacles, we have developed a user-friendly microbiome analysis pipeline (MAPLE, freely downloadable at http://maple.rx.umaryland.edu/), which is able to define an optimal search space by inferring proteomes specific to samples following the principle of parsimony. MAPLE facilitates highly comparable or better peptide identification compared to a sample-specific metagenome-guided search. In addition, we implemented an automated peptide-centric enrichment analysis function in MAPLE to address issues of traditional protein-centric comparison, enabling straightforward and comprehensive comparison of taxonomic and functional makeup between microbiota.}, } @article {pmid33848049, year = {2021}, author = {Thompson, TP and Kelly, SA and Skvortsov, T and Plunkett, G and Ruffell, A and Hallsworth, JE and Hopps, J and Gilmore, BF}, title = {Microbiology of a NaCl stalactite 'salticle' in Triassic halite.}, journal = {Environmental microbiology}, volume = {23}, number = {7}, pages = {3881-3895}, doi = {10.1111/1462-2920.15524}, pmid = {33848049}, issn = {1462-2920}, support = {BB/L017083/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria ; Exobiology ; *Microbiota ; *Sodium Chloride ; }, abstract = {Large regions of Earth's surface are underlain by salt deposits that evaporated from ancient oceans and are populated by extreme halophilic microbes. Some of these halophiles may have been preserved over geological timescales within hypersaline fluid inclusions, but ingresses of water and/or anthropogenic activities can lead to the formation of alternative habitats, including NaCl stalactites or other speleothems. While the microbiology of ancient evaporites has been well studied, the ecology of these recently formed structures is less-well understood. Here, the microbiology of a NaCl stalactite ('salticle') in a Triassic halite mine is characterized. The specific aims were to determine the presence of fluid inclusions, determine the microbial structure of the salticle compared with a nearby brine-pool and surficial soil, and characterize the ecophysiological capabilities of this unique ecosystem. The salticle contained fluid inclusions, and their microbiome was composed of Euryarchaetota, Proteobacteria, and Actinobacteria, with Haloarchaea in greater abundance than brine-pool or soil microbiomes. The salticle metagenome exhibited a greater abundance of genes involved in osmoregulation, anaerobic respiration, UV resistance, oxidative stress, and stress-protein synthesis relative to the soil microbiome. We discuss the potential astrobiological implications of salticles as enclosed salt-saturated habitats that are protected from ionizing radiation and have a stable water activity.}, } @article {pmid33848048, year = {2022}, author = {Chen, Z and Zhong, X and Zheng, M and Liu, WS and Fei, Y and Ding, K and Li, Y and Liu, Y and Chao, Y and Tang, YT and Wang, S and Qiu, R}, title = {Indicator species drive the key ecological functions of microbiota in a river impacted by acid mine drainage generated by rare earth elements mining in South China.}, journal = {Environmental microbiology}, volume = {24}, number = {2}, pages = {919-937}, doi = {10.1111/1462-2920.15501}, pmid = {33848048}, issn = {1462-2920}, mesh = {*Metals, Rare Earth ; *Microbiota ; Mining ; RNA, Ribosomal, 16S/genetics ; Rivers ; }, abstract = {Acid mine drainage (AMD) generated by rare earth elements (REEs) deposits exploration contains high concentrations of REEs, ammonium and sulfates, which is quite different from typical metallic AMD. Currently, microbial responses and ecological functions in REEs-AMD impacted rivers are unknown. Here, 16S rRNA analysis and genome-resolved metagenomics were performed on microbial community collected from a REEs-AMD contaminated river. The results showed that REEs-AMD significantly changed river microbial diversity and shaped unique indicator species (e.g. Thaumarchaeota, Methylophilales, Rhodospirillales and Burkholderiales). The main environmental factors regulating community were pH, ammonium and REEs, among which high concentration of REEs increased REEs-dependent enzyme-encoding genes (XoxF and ExaF/PedH). Additionally, we reconstructed 566 metagenome-assembled genomes covering 70.4% of identifying indicators. Genome-centric analysis revealed that the abundant archaea Thaumarchaeota and Xanthomonadaceae were often involved in nitrification and denitrification, while family Burkholderiaceae were capable of sulfide oxidation coupled with dissimilatory nitrate reduction to ammonium. These indicators play crucial roles in nitrogen and sulfur cycling as well as REEs immobilization in REEs-AMD contaminated rivers. This study confirmed the potential dual effect of REEs on microbial community at the functional gene level. Our investigation on the ecological roles of indicators further provided new insights for the development of REEs-AMD bioremediation.}, } @article {pmid33847922, year = {2021}, author = {Duan, M and Bau, T}, title = {Grassland fairy rings of Leucocalocybe mongolica represent the center of a rich soil microbial community.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {52}, number = {3}, pages = {1357-1369}, pmid = {33847922}, issn = {1678-4405}, mesh = {Agaricales/*growth & development ; Bacteria/genetics ; China ; Fungi/genetics ; *Grassland ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Soil ; *Soil Microbiology ; }, abstract = {BACKGROUND: The ecological phenomenon of fungal fairy rings is usually found in grasslands and caused by the growth of specific fairy ring fungi in soil. The fairy rings are classified into three zones (DARK, DEAD, and OUT), and they have the potential to increase crop yield. Among these fairy rings, distinct characteristics of type I fairy rings can be seen in the rings formed by Leucocalocybe mongolica (LM). Our studies addressed changes in the soil microbial structure due to LM fairy rings to enhance understand of this ecological phenomenon.

METHODS: In the present study, we report the soil microbial analysis results (fungi and bacteria), including those of metabarcoding (16s rRNA, ITS), microbial quantity, and metagenomics surveys of soils collected from various fairy ring zones, of 6 LM fairy rings. All sampling sites cover the grasslands of Mongolian Plateau in China.

RESULTS: First, we found through metabarcoding surveys that the difference in microbial diversity is relatively less in bacteria and that the abundance of fairy ring fungi (LM) is relatively high in DEAD zones. We also identified eight bacterial and fungal families, including Sphingobacteriaceae and Sphingomonadaceae that were enriched within the soils of fairy ring zones. Second, we found that the abundance of soil bacteria in the DEAD zones is sharply increased along with the growth of fairy ring fungi (LM). Third, we found through shotgun sequencing that fairy ring-infected zones, DARK and DEAD, exhibit greater genetic diversity than OUT zones. Finally, we showed that the fairy ring ecosystem is the center for a rich grassland microbial community.

CONCLUSIONS: The reported data can improve our understanding of type I fairy rings and will be further insightful to the research on crop production.}, } @article {pmid33846627, year = {2021}, author = {Chang, FY and Siuti, P and Laurent, S and Williams, T and Glassey, E and Sailer, AW and Gordon, DB and Hemmerle, H and Voigt, CA}, title = {Gut-inhabiting Clostridia build human GPCR ligands by conjugating neurotransmitters with diet- and human-derived fatty acids.}, journal = {Nature microbiology}, volume = {6}, number = {6}, pages = {792-805}, pmid = {33846627}, issn = {2058-5276}, mesh = {Amines/chemistry/*metabolism ; Diet ; Fatty Acids/chemistry/*metabolism ; Firmicutes/classification/genetics/*metabolism ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/metabolism/microbiology ; Humans ; Neurotransmitter Agents/chemistry/*metabolism ; Receptors, G-Protein-Coupled/genetics/metabolism ; Signal Transduction ; }, abstract = {Human physiology is regulated by endogenous signalling compounds, including fatty acid amides (FAAs), chemical mimics of which are made by bacteria. The molecules produced by human-associated microbes are difficult to identify because they may only be made in a local niche or they require a substrate sourced from the host, diet or other microbes. We identified a set of uncharacterized gene clusters in metagenomics data from the human gut microbiome. These clusters were discovered to make FAAs by fusing exogenous fatty acids with amines. Using an in vitro assay, we tested their ability to incorporate 25 fatty acids and 53 amines known to be present in the human gut, from which the production of six FAAs was deduced (oleoyl dopamine, oleoyl tyramine, lauroyl tryptamine, oleoyl aminovaleric acid, α-linolenoyl phenylethylamine and caproyl tryptamine). These molecules were screened against panels of human G-protein-coupled receptors to deduce their putative human targets. Lauroyl tryptamine is found to be an antagonist to the immunomodulatory receptor EBI2 against its native oxysterol ligand (0.98 μM half-maximal inhibitory concentration), is produced in culture by Eubacterium rectale and is present in human faecal samples. FAAs produced by Clostridia may serve as a mechanism to modulate their host by mimicking human signalling molecules.}, } @article {pmid33845910, year = {2021}, author = {Restrepo, L and Domínguez-Borbor, C and Bajaña, L and Betancourt, I and Rodríguez, J and Bayot, B and Reyes, A}, title = {Microbial community characterization of shrimp survivors to AHPND challenge test treated with an effective shrimp probiotic (Vibrio diabolicus).}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {88}, pmid = {33845910}, issn = {2049-2618}, mesh = {Animals ; Humans ; *Microbiota ; Necrosis ; *Penaeidae ; Phylogeny ; *Probiotics ; RNA, Ribosomal, 16S/genetics ; Survivors ; Vibrio ; *Vibrio parahaemolyticus/genetics ; }, abstract = {BACKGROUND: Acute hepatopancreatic necrosis disease (AHPND) is an important shrimp bacterial disease caused by some Vibrio species. The severity of the impact of this disease on aquaculture worldwide has made it necessary to develop alternatives to prophylactic antibiotics use, such as the application of probiotics. To assess the potential to use probiotics in order to limit the detrimental effects of AHNPD, we evaluated the effect of the ILI strain, a Vibrio sp. bacterium and efficient shrimp probiotic, using metabarcoding (16S rRNA gene) on the gastrointestinal microbiota of shrimp after being challenged with AHPND-causing V. parahaemolyticus.

RESULTS: We showed how the gastrointestinal microbiome of shrimp varied between healthy and infected organisms. Nevertheless, a challenge of working with AHPND-causing Vibrio pathogens and Vibrio-related bacteria as probiotics is the potential risk of the probiotic strain becoming pathogenic. Consequently, we evaluated whether ILI strain can acquire the plasmid pV-AHPND via horizontal transfer and further cause the disease in shrimp. Conjugation assays were performed resulting in a high frequency (70%) of colonies harboring the pv-AHPND. However, no shrimp mortality was observed when transconjugant colonies of the ILI strain were used in a challenge test using healthy shrimp. We sequenced the genome of the ILI strain and performed comparative genomics analyses using AHPND and non-AHPND Vibrio isolates. Using available phylogenetic and phylogenomics analyses, we reclassified the ILI strain as Vibrio diabolicus. In summary, this work represents an effort to study the role that probiotics play in the normal gastrointestinal shrimp microbiome and in AHPND-infected shrimp, showing that the ILI probiotic was able to control pathogenic bacterial populations in the host's gastrointestinal tract and stimulate the shrimp's survival. The identification of probiotic bacterial species that are effective in the host's colonization is important to promote animal health and prevent disease.

CONCLUSIONS: This study describes probiotic bacteria capable of controlling pathogenic populations of bacteria in the shrimp gastrointestinal tract. Our work provides new insights into the complex dynamics between shrimp and the changes in the microbiota. It also addresses the practical application of probiotics to solve problems with pathogens that cause high mortality-rate in shrimp farming around the world. Video Abstract.}, } @article {pmid33845884, year = {2021}, author = {Garg, S}, title = {Computational methods for chromosome-scale haplotype reconstruction.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {101}, pmid = {33845884}, issn = {1474-760X}, mesh = {*Chromosomes ; Computational Biology/*methods ; Diploidy ; Genomics/*methods ; *Haplotypes ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/methods ; Polyploidy ; Sequence Analysis, DNA/methods ; }, abstract = {High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid genomes, and metagenomes provide important insights into genetic variation associated with disease and biodiversity. However, whole-genome short read sequencing does not yield haplotype information spanning whole chromosomes directly. Computational assembly of shorter haplotype fragments is required for haplotype reconstruction, which can be challenging owing to limited fragment lengths and high haplotype and repeat variability across genomes. Recent advancements in long-read and chromosome-scale sequencing technologies, alongside computational innovations, are improving the reconstruction of haplotypes at the level of whole chromosomes. Here, we review recent and discuss methodological progress and perspectives in these areas.}, } @article {pmid33845877, year = {2021}, author = {Guerin, E and Shkoporov, AN and Stockdale, SR and Comas, JC and Khokhlova, EV and Clooney, AG and Daly, KM and Draper, LA and Stephens, N and Scholz, D and Ross, RP and Hill, C}, title = {Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {89}, pmid = {33845877}, issn = {2049-2618}, mesh = {*Bacteriophages/genetics ; Bacteroides ; *Gastrointestinal Microbiome ; Humans ; Phylogeny ; }, abstract = {BACKGROUND: The gut phageome comprises a complex phage community of thousands of individual strains, with a few highly abundant bacteriophages. CrAss-like phages, which infect bacteria of the order Bacteroidales, are the most abundant bacteriophage family in the human gut and make an important contribution to an individual's core virome. Based on metagenomic data, crAss-like phages form a family, with four sub-families and ten candidate genera. To date, only three representatives isolated in pure culture have been reported: ΦcrAss001 and two closely related phages DAC15 and DAC17; all are members of the less abundant candidate genus VI. The persistence at high levels of both crAss-like phage and their Bacteroidales hosts in the human gut has not been explained mechanistically, and this phage-host relationship can only be properly studied with isolated phage-host pairs from as many genera as possible.

RESULTS: Faeces from a healthy donor with high levels of crAss-like phage was used to initiate a faecal fermentation in a chemostat, with selected antibiotics chosen to inhibit rapidly growing bacteria and selectively enrich for Gram-negative Bacteroidales. This had the objective of promoting the simultaneous expansion of crAss-like phages on their native hosts. The levels of seven different crAss-like phages expanded during the fermentation, indicating that their hosts were also present in the fermenter. The enriched supernatant was then tested against individual Bacteroidales strains isolated from the same faecal sample. This resulted in the isolation of a previously uncharacterised crAss-like phage of candidate genus IV of the proposed Alphacrassvirinae sub-family, ΦcrAss002, that infects the gut commensal Bacteroides xylanisolvens. ΦcrAss002 does not form plaques or spots on lawns of sensitive cells, nor does it lyse liquid cultures, even at high titres. In keeping with the co-abundance of phage and host in the human gut, ΦcrAss002 and Bacteroides xylanisolvens can also co-exist at high levels when co-cultured in laboratory media.

CONCLUSIONS: We report the isolation and characterisation of ΦcrAss002, the first representative of the proposed Alphacrassvirinae sub-family of crAss-like phages. ΦcrAss002 cannot form plaques or spots on bacterial lawns but can co-exist with its host, Bacteroides xylanisolvens, at very high levels in liquid culture without impacting on bacterial numbers. Video abstract.}, } @article {pmid33845850, year = {2021}, author = {Fremin, BJ and Bhatt, AS}, title = {Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {100}, pmid = {33845850}, issn = {1474-760X}, support = {R01 AI148623/AI/NIAID NIH HHS/United States ; 1S10OD02014101/CA/NCI NIH HHS/United States ; U24 AG021886/AG/NIA NIH HHS/United States ; P30 AG066515/AG/NIA NIH HHS/United States ; P50AG047366/NH/NIH HHS/United States ; P50 AG047366/AG/NIA NIH HHS/United States ; }, mesh = {Computational Biology/methods ; Gastrointestinal Microbiome ; *Genomics/methods ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Nucleic Acid Conformation ; RNA ; Workflow ; }, abstract = {BACKGROUND: Structured RNAs play varied bioregulatory roles within microbes. To date, hundreds of candidate structured RNAs have been predicted using informatic approaches that search for motif structures in genomic sequence data. The human microbiome contains thousands of species and strains of microbes. Yet, much of the metagenomic data from the human microbiome remains unmined for structured RNA motifs primarily due to computational limitations.

RESULTS: We sought to apply a large-scale, comparative genomics approach to these organisms to identify candidate structured RNAs. With a carefully constructed, though computationally intensive automated analysis, we identify 3161 conserved candidate structured RNAs in intergenic regions, as well as 2022 additional candidate structured RNAs that may overlap coding regions. We validate the RNA expression of 177 of these candidate structures by analyzing small fragment RNA-seq data from four human fecal samples.

CONCLUSIONS: This approach identifies a wide variety of candidate structured RNAs, including tmRNAs, antitoxins, and likely ribosome protein leaders, from a wide variety of taxa. Overall, our pipeline enables conservative predictions of thousands of novel candidate structured RNAs from human microbiomes.}, } @article {pmid33841399, year = {2021}, author = {Xia, C and Jiang, C and Li, W and Wei, J and Hong, H and Li, J and Feng, L and Wei, H and Xin, H and Chen, T}, title = {A Phase II Randomized Clinical Trial and Mechanistic Studies Using Improved Probiotics to Prevent Oral Mucositis Induced by Concurrent Radiotherapy and Chemotherapy in Nasopharyngeal Carcinoma.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {618150}, pmid = {33841399}, issn = {1664-3224}, mesh = {Animals ; Chemoradiotherapy/*adverse effects/methods ; Disease Management ; Disease Models, Animal ; Disease Susceptibility ; Duration of Therapy ; Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Nasopharyngeal Neoplasms/*complications/therapy ; Probiotics/*therapeutic use ; Rats ; Severity of Illness Index ; Stomatitis/diagnosis/*etiology/*therapy ; Treatment Outcome ; }, abstract = {Earlier evidence has proven that probiotic supplements can reduce concurrent chemoradiotherapy (CCRT)-induced oral mucositis (OM) in nasopharyngeal cancer (NPC). The incidence of severe OM (grade 3 or higher) was the primary endpoint in this study. We first enrolled 85 patients with locally advanced NPC who were undergoing CCRT. Of them, 77 patients were finally selected and randomized (1:1) to receive either a probiotic cocktail or placebo. To investigate the protective effects and the mechanism of probiotic cocktail treatment on OM induced by radiotherapy and chemotherapy, we randomly divided the rats into the control (C) group, the model (M) group, and the probiotic (P) group. After treatment, samples from the tongue, blood, and fecal and proximal colon tissues on various days (7th, 14th, and 21st days) were collected and tested for the inflammatory response, cell apoptosis, intestinal permeability, and intestinal microbial changes. We found that patients taking the probiotic cocktail showed significantly lower OM. The values of the incidence of 0, 1, 2, 3, and 4 grades of OM in the placebo group and in the probiotic cocktail group were reported to be 0, 14.7, 38.2, 32.4, and 14.7% and 13.9, 36.1, 25, 22.2, and 2.8%, respectively. Furthermore, patients in the probiotic cocktail group showed a decrease in the reduction rate of CD3[+] T cells (75.5% vs. 81%, p < 0.01), CD4[+] T cells (64.53% vs. 79.53%, p < 0.01), and CD8[+] T cells (75.59 vs. 62.36%, p < 0.01) compared to the placebo group. In the rat model, the probiotic cocktail could ameliorate the severity of OM, decrease the inflammatory response, cause cell apoptosis and intestinal permeability, and restore the structure of gut microbiota to normalcy. In conclusion, the modified probiotic cocktail significantly reduces the severity of OM by enhancing the immune response of patients with NPC and modifying the structure of gut microbiota. Clinical Trial Registration: The Clinical Trial Registration should be the NCT03112837.}, } @article {pmid33839314, year = {2021}, author = {Granato, DC and Neves, LX and Trino, LD and Carnielli, CM and Lopes, AFB and Yokoo, S and Pauletti, BA and Domingues, RR and Sá, JO and Persinoti, G and Paixão, DAA and Rivera, C and de Sá Patroni, FM and Tommazetto, G and Santos-Silva, AR and Lopes, MA and de Castro, G and Brandão, TB and Prado-Ribeiro, AC and Squina, FM and Telles, GP and Paes Leme, AF}, title = {Meta-omics analysis indicates the saliva microbiome and its proteins associated with the prognosis of oral cancer patients.}, journal = {Biochimica et biophysica acta. Proteins and proteomics}, volume = {1869}, number = {8}, pages = {140659}, doi = {10.1016/j.bbapap.2021.140659}, pmid = {33839314}, issn = {1878-1454}, mesh = {Adult ; Aged ; Cohort Studies ; Female ; Humans ; Male ; Metagenomics/methods ; Microbiota/genetics ; Middle Aged ; Mouth Neoplasms/metabolism/microbiology ; Prognosis ; Proteomics/methods ; Saliva/*microbiology ; Squamous Cell Carcinoma of Head and Neck/metabolism/*microbiology ; }, abstract = {Saliva is a biofluid that maintains the health of oral tissues and the homeostasis of oral microbiota. Studies have demonstrated that Oral squamous cell carcinoma (OSCC) patients have different salivary microbiota than healthy individuals. However, the relationship between these microbial differences and clinicopathological outcomes is still far from conclusive. Herein, we investigate the capability of using metagenomic and metaproteomic saliva profiles to distinguish between Control (C), OSCC without active lesion (L0), and OSCC with active lesion (L1) patients. The results show that there are significantly distinct taxonomies and functional changes in L1 patients compared to C and L0 patients, suggesting compositional modulation of the oral microbiome, as the relative abundances of Centipeda, Veillonella, and Gemella suggested by metagenomics are correlated with tumor size, clinical stage, and active lesion. Metagenomics results also demonstrated that poor overall patient survival is associated with a higher relative abundance of Stenophotromonas, Staphylococcus, Centipeda, Selenomonas, Alloscordovia, and Acitenobacter. Finally, compositional and functional differences in the saliva content by metaproteomics analysis can distinguish healthy individuals from OSCC patients. In summary, our study suggests that oral microbiota and their protein abundance have potential diagnosis and prognosis value for oral cancer patients. Further studies are necessary to understand the role of uniquely detected metaproteins in the microbiota of healthy and OSCC patients as well as the crosstalk between saliva host proteins and the oral microbiome present in OSCC.}, } @article {pmid33839214, year = {2021}, author = {Priya, P and Aneesh, B and Harikrishnan, K}, title = {Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health.}, journal = {Journal of microbiological methods}, volume = {185}, number = {}, pages = {106215}, doi = {10.1016/j.mimet.2021.106215}, pmid = {33839214}, issn = {1872-8359}, mesh = {Agriculture/methods ; Crops, Agricultural ; Ecosystem ; Genomics/*methods ; Metagenomics ; *Microbial Interactions ; Microbiota/*genetics ; Plant Roots ; Proteomics ; *Rhizosphere ; Soil ; Soil Microbiology ; Transcriptome ; }, abstract = {Intense agricultural practices to meet rising food demands have caused ecosystem perturbations. For sustainable crop production, biological agents are gaining attention, but exploring their functional potential on a multi-layered complex ecosystem like the rhizosphere is challenging. This review explains the significance of genomics as a culture-independent molecular tool to understand the diversity and functional significance of the rhizosphere microbiome for sustainable agriculture. It discusses the recent significant studies in the rhizosphere environment carried out using evolving techniques like metagenomics, metatranscriptomics, and metaproteomics, their challenges, constraints infield application, and prospective solutions. The recent advances in techniques such as nanotechnology for the development of bioformulations and visualization techniques contemplating environmental safety were also discussed. The need for development of metagenomic data sets of regionally important crops, their plant microbial interactions and agricultural practices for narrowing down significant data from huge databases have been suggested. The role of taxonomical and functional diversity of soil microbiota in understanding soil suppression and part played by the microbial metabolites in the process have been analyzed and discussed in the context of 'omics' approach. 'Omics' studies have revealed important information about microbial diversity, their responses to various biotic and abiotic stimuli, and the physiology of disease suppression. This can be translated to crop sustainability and combinational approaches with advancing visualization and analysis methodologies fix the existing knowledge gap to a huge extend. With improved data processing and standardization of the methods, details of plant-microbe interactions can be successfully decoded to develop sustainable agricultural practices.}, } @article {pmid33838112, year = {2021}, author = {Chen, L and Wang, D and Garmaeva, S and Kurilshikov, A and Vich Vila, A and Gacesa, R and Sinha, T and , and Segal, E and Weersma, RK and Wijmenga, C and Zhernakova, A and Fu, J}, title = {The long-term genetic stability and individual specificity of the human gut microbiome.}, journal = {Cell}, volume = {184}, number = {9}, pages = {2302-2315.e12}, doi = {10.1016/j.cell.2021.03.024}, pmid = {33838112}, issn = {1097-4172}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/*genetics/isolation & purification/metabolism ; Bacterial Proteins/genetics/*metabolism ; Drug Resistance, Microbial ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Genomic Instability ; Humans ; Longitudinal Studies ; Male ; *Metabolome ; *Metagenome ; *Microbiota ; Middle Aged ; Phenotype ; Polymorphism, Single Nucleotide ; Virulence Factors/genetics/metabolism ; Young Adult ; }, abstract = {By following up the gut microbiome, 51 human phenotypes and plasma levels of 1,183 metabolites in 338 individuals after 4 years, we characterize microbial stability and variation in relation to host physiology. Using these individual-specific and temporally stable microbial profiles, including bacterial SNPs and structural variations, we develop a microbial fingerprinting method that shows up to 85% accuracy in classifying metagenomic samples taken 4 years apart. Application of our fingerprinting method to the independent HMP cohort results in 95% accuracy for samples taken 1 year apart. We further observe temporal changes in the abundance of multiple bacterial species, metabolic pathways, and structural variation, as well as strain replacement. We report 190 longitudinal microbial associations with host phenotypes and 519 associations with plasma metabolites. These associations are enriched for cardiometabolic traits, vitamin B, and uremic toxins. Finally, mediation analysis suggests that the gut microbiome may influence cardiometabolic health through its metabolites.}, } @article {pmid33837467, year = {2021}, author = {Kaushik, R and Pandit, MK and Meyerson, LA and Chaudhari, DS and Sharma, M and Dhotre, D and Shouche, YS}, title = {Contrasting Composition, Diversity and Predictive Metabolic Potential of the Rhizobacterial Microbiomes Associated with Native and Invasive Prosopis Congeners.}, journal = {Current microbiology}, volume = {78}, number = {5}, pages = {2051-2060}, pmid = {33837467}, issn = {1432-0991}, mesh = {*Microbiota ; *Prosopis ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil ; Soil Microbiology ; }, abstract = {Invasive plants are known to alter the soil microbial communities; however, the effects of co-occurring native and invasive congeners on the soil bacterial diversity and their predictive metabolic profiles are not known. Here, we compared the rhizosphere bacterial communities of invasive Prosopis juliflora and its native congener Prosopis cineraria using high-throughput sequencing of the 16S rRNA gene. Unweighted Pair Group Method with Arithmetic mean (UPGMA) based dendrogram revealed significant variation in the communities of these co-occurring Prosopis species. Additionally, Canonical Correspondence Analysis (CCA) based on microbial communities in addition to the soil physiochemical parameters viz. soil pH, electrical conductivity, moisture content and sampling depth showed ~ 80% of the variation in bacterial communities of the rhizosphere and control soil. We observed that Proteobacteria was the predominant phylum of P. juliflora rhizosphere and the control soil, while P. cineraria rhizosphere was dominated by Cyanobacteria. Notably, the invasive P. juliflora rhizosphere showed an enhanced abundance of bacterial phyla like Actinobacteria, Chloroflexi, Firmicutes and Acidobacteria compared to the native P. cineraria as well as the control soil. Predictive metagenomics revealed that the bacterial communities of the P. juliflora rhizosphere had a higher abundance of pathways involved in antimicrobial biosynthesis and degradation, suggesting probable exposure to enemy attack and an active response mechanism to counter it as compared to native P. cineraria. Interestingly, the higher antimicrobial biosynthesis predicted in the invasive rhizosphere microbiome is further corroborated by the fact that the bacterial isolates purified from the rhizosphere of P. juliflora belonged to genera like Streptomyces, Isoptericola and Brevibacterium from the phylum Actinobacteria, which are widely reported for their antibiotic production ability. In conclusion, our results demonstrate that the co-occurring native and invasive Prosopis species have significantly different rhizosphere bacterial communities in terms of composition, diversity and their predictive metabolic potentials. In addition, the rhizosphere microbiome of invasive Prosopis proffers it a fitness advantage and influences invasion success of the species.}, } @article {pmid33837203, year = {2021}, author = {Das, S and Bernasconi, E and Koutsokera, A and Wurlod, DA and Tripathi, V and Bonilla-Rosso, G and Aubert, JD and Derkenne, MF and Mercier, L and Pattaroni, C and Rapin, A and von Garnier, C and Marsland, BJ and Engel, P and Nicod, LP}, title = {A prevalent and culturable microbiota links ecological balance to clinical stability of the human lung after transplantation.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2126}, pmid = {33837203}, issn = {2041-1723}, mesh = {Adult ; Allografts/immunology/microbiology ; Bacteria/genetics/immunology/isolation & purification/pathogenicity ; Bacterial Load/immunology ; Bacteriological Techniques ; Bronchoalveolar Lavage Fluid/microbiology ; Bronchoscopy ; DNA, Bacterial/isolation & purification ; Female ; Graft Rejection/diagnosis/immunology/*microbiology ; Humans ; Immune Tolerance ; Longitudinal Studies ; Lung/immunology/*microbiology ; Lung Transplantation/*adverse effects ; Male ; Metagenomics ; Microbiota/genetics/*immunology ; Middle Aged ; Pneumonia, Bacterial/diagnosis/immunology/*microbiology ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; }, abstract = {There is accumulating evidence that the lower airway microbiota impacts lung health. However, the link between microbial community composition and lung homeostasis remains elusive. We combine amplicon sequencing and bacterial culturing to characterize the viable bacterial community in 234 longitudinal bronchoalveolar lavage samples from 64 lung transplant recipients and establish links to viral loads, host gene expression, lung function, and transplant health. We find that the lung microbiota post-transplant can be categorized into four distinct compositional states, 'pneumotypes'. The predominant 'balanced' pneumotype is characterized by a diverse bacterial community with moderate viral loads, and host gene expression profiles suggesting immune tolerance. The other three pneumotypes are characterized by being either microbiota-depleted, or dominated by potential pathogens, and are linked to increased immune activity, lower respiratory function, and increased risks of infection and rejection. Collectively, our findings establish a link between the lung microbial ecosystem, human lung function, and clinical stability post-transplant.}, } @article {pmid33837018, year = {2021}, author = {Thomas, AM and Asnicar, F and Kroemer, G and Segata, N}, title = {Genes Encoding Microbial Acyl Coenzyme A Binding Protein/Diazepam-Binding Inhibitor Orthologs Are Rare in the Human Gut Microbiome and Show No Links to Obesity.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {12}, pages = {e0047121}, pmid = {33837018}, issn = {1098-5336}, support = {R01 CA230551/CA/NCI NIH HHS/United States ; U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacterial Proteins/*genetics ; Body Mass Index ; Burkholderiaceae/genetics ; Comamonas/genetics ; Diazepam Binding Inhibitor/*genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Middle Aged ; Obesity/*microbiology ; Saccharomyces cerevisiae/genetics ; Young Adult ; }, abstract = {Acyl coenzyme A (CoA) binding protein (ACBP), also called diazepam-binding inhibitor (DBI), is a phylogenetically conserved protein that is expressed by all eukaryotic species as well as by some bacteria. Since elevated ACBP/DBI levels play a major role in the inhibition of autophagy, increase in appetite, and enhanced lipid storage that accompany obesity, we wondered whether ACBP/DBI produced by the human microbiome might affect host weight. We found that the genomes of bacterial commensals rarely contain ACBP/DBI homologues, which are rather encoded by genomes of some pathogenic or environmental taxa that were not prevalent in human feces. Exhaustive bioinformatic analyses of 1,899 gut samples from healthy individuals refuted the hypothesis that bacterial ACBP/DBI might affect the body mass index (BMI) in a physiological context. Thus, the physiological regulation of BMI is unlikely to be affected by microbial ACBP/DBI-like proteins. However, at the speculative level, it remains possible that ACBP/DBI produced by potential pathogenic bacteria might enhance their virulence by inhibiting autophagy and hence subverting innate immune responses. IMPORTANCE Acyl coenzyme A (CoA) binding protein (ACBP) can be encoded by several organisms across the domains of life, including microbes, and has shown to play major roles in human metabolic processes. However, little is known about its presence in the human gut microbiome and whether its microbial counterpart could also play a role in human metabolism. In the present study, we found that microbial ACBP/DBI sequences were rarely present in the gut microbiome across multiple metagenomic data sets. Microbes that carried ACBP/DBI in the human gut microbiome included Saccharomyces cerevisiae, Lautropia mirabilis, and Comamonas kerstersii, but these microorganisms were not associated with body mass index, further indicating an unconvincing role for microbial ACBP/DBI in human metabolism.}, } @article {pmid33836662, year = {2021}, author = {Henry, LP and Ayroles, JF}, title = {Meta-analysis suggests the microbiome responds to Evolve and Resequence experiments in Drosophila melanogaster.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {108}, pmid = {33836662}, issn = {1471-2180}, support = {R01 ES029929/ES/NIEHS NIH HHS/United States ; R35 GM124881/GM/NIGMS NIH HHS/United States ; DGE1656466//National Science Foundation/ ; }, mesh = {Adaptation, Physiological ; Animals ; Bacteria/genetics ; Biodiversity ; Drosophila melanogaster/*microbiology ; *Evolution, Molecular ; Host Microbial Interactions/*physiology ; Microbiota/genetics ; Selection, Genetic ; }, abstract = {BACKGROUND: Experimental evolution has a long history of uncovering fundamental insights into evolutionary processes, but has largely neglected one underappreciated component--the microbiome. As eukaryotic hosts evolve, the microbiome may also respond to selection. However, the microbial contribution to host evolution remains poorly understood. Here, we re-analyzed genomic data to characterize the metagenomes from ten Evolve and Resequence (E&R) experiments in Drosophila melanogaster to determine how the microbiome changed in response to host selection.

RESULTS: Bacterial diversity was significantly different in 5/10 studies, primarily in traits associated with metabolism or immunity. Duration of selection did not significantly influence bacterial diversity, highlighting the importance of associations with specific host traits.

CONCLUSIONS: Our genomic re-analysis suggests the microbiome often responds to host selection; thus, the microbiome may contribute to the response of Drosophila in E&R experiments. We outline important considerations for incorporating the microbiome into E&R experiments. The E&R approach may provide critical insights into host-microbiome interactions and fundamental insight into the genomic basis of adaptation.}, } @article {pmid33836596, year = {2021}, author = {Epihov, DZ and Saltonstall, K and Batterman, SA and Hedin, LO and Hall, JS and van Breugel, M and Leake, JR and Beerling, DJ}, title = {Legume-microbiome interactions unlock mineral nutrients in regrowing tropical forests.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {11}, pages = {}, pmid = {33836596}, issn = {1091-6490}, mesh = {Acidobacteria/classification/genetics/metabolism ; Biomass ; Carbon/analysis ; Fabaceae/growth & development/metabolism/*microbiology ; Ferric Compounds/metabolism ; *Forests ; Hydrogen-Ion Concentration ; Microbiota/genetics/*physiology ; Minerals/analysis/*metabolism ; Nitrogen/analysis/metabolism ; Nitrogen Fixation ; Nutrients/analysis/*metabolism ; Panama ; Phosphorus/metabolism ; Silicates/analysis/metabolism ; Soil/chemistry ; Soil Microbiology ; Symbiosis ; Trees/growth & development/metabolism/microbiology ; *Tropical Climate ; }, abstract = {Legume trees form an abundant and functionally important component of tropical forests worldwide with N2-fixing symbioses linked to enhanced growth and recruitment in early secondary succession. However, it remains unclear how N2-fixers meet the high demands for inorganic nutrients imposed by rapid biomass accumulation on nutrient-poor tropical soils. Here, we show that N2-fixing trees in secondary Neotropical forests triggered twofold higher in situ weathering of fresh primary silicates compared to non-N2-fixing trees and induced locally enhanced nutrient cycling by the soil microbiome community. Shotgun metagenomic data from weathered minerals support the role of enhanced nitrogen and carbon cycling in increasing acidity and weathering. Metagenomic and marker gene analyses further revealed increased microbial potential beneath N2-fixers for anaerobic iron reduction, a process regulating the pool of phosphorus bound to iron-bearing soil minerals. We find that the Fe(III)-reducing gene pool in soil is dominated by acidophilic Acidobacteria, including a highly abundant genus of previously undescribed bacteria, Candidatus Acidoferrum, genus novus. The resulting dependence of the Fe-cycling gene pool to pH determines the high iron-reducing potential encoded in the metagenome of the more acidic soils of N2-fixers and their nonfixing neighbors. We infer that by promoting the activities of a specialized local microbiome through changes in soil pH and C:N ratios, N2-fixing trees can influence the wider biogeochemical functioning of tropical forest ecosystems in a manner that enhances their ability to assimilate and store atmospheric carbon.}, } @article {pmid33834201, year = {2021}, author = {Chang, Y and Fan, Q and Hou, J and Zhang, Y and Li, J}, title = {A community-supported metaproteomic pipeline for improving peptide identifications in hydrothermal vent microbiota.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {5}, pages = {}, doi = {10.1093/bib/bbab052}, pmid = {33834201}, issn = {1477-4054}, mesh = {Amino Acid Sequence/genetics ; DNA, Ribosomal/genetics ; Databases, Genetic ; Genes, Microbial ; Hydrothermal Vents/*microbiology ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Peptides/*genetics ; Phylogeny ; Proteogenomics/*methods ; Proteome/*genetics ; }, abstract = {Microorganisms in deep-sea hydrothermal vents provide valuable insights into life under extreme conditions. Mass spectrometry-based proteomics has been widely used to identify protein expression and function. However, the metaproteomic studies in deep-sea microbiota have been constrained largely by the low identification rates of protein or peptide. To improve the efficiency of metaproteomics for hydrothermal vent microbiota, we firstly constructed a microbial gene database (HVentDB) based on 117 public metagenomic samples from hydrothermal vents and proposed a metaproteomic analysis strategy, which takes the advantages of not only the sample-matched metagenome, but also the metagenomic information released publicly in the community of hydrothermal vents. A two-stage false discovery rate method was followed up to control the risk of false positive. By applying our community-supported strategy to a hydrothermal vent sediment sample, about twice as many peptides were identified when compared with the ways against the sample-matched metagenome or the public reference database. In addition, more enriched and explainable taxonomic and functional profiles were detected by the HVentDB-based approach exclusively, as well as many important proteins involved in methane, amino acid, sugar, glycan metabolism and DNA repair, etc. The new metaproteomic analysis strategy will enhance our understanding of microbiota, including their lifestyles and metabolic capabilities in extreme environments. The database HVentDB is freely accessible from http://lilab.life.sjtu.edu.cn:8080/HventDB/main.html.}, } @article {pmid33834198, year = {2021}, author = {Yang, F and Zou, Q}, title = {DisBalance: a platform to automatically build balance-based disease prediction models and discover microbial biomarkers from microbiome data.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {5}, pages = {}, doi = {10.1093/bib/bbab094}, pmid = {33834198}, issn = {1477-4054}, mesh = {Biomarkers/analysis ; Colitis, Ulcerative/diagnosis/genetics/microbiology ; Computational Biology/*methods ; Disease/classification/genetics ; Humans ; *Internet ; Logistic Models ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Reproducibility of Results ; }, abstract = {How best to utilize the microbial taxonomic abundances in regard to the prediction and explanation of human diseases remains appealing and challenging, and the relative nature of microbiome data necessitates a proper feature selection method to resolve the compositional problem. In this study, we developed an all-in-one platform to address a series of issues in microbiome-based human disease prediction and taxonomic biomarkers discovery. We prioritize the interpretation, runtime and classification accuracy of the distal discriminative balances analysis (DBA-distal) method in selecting a set of distal discriminative balances, and develop DisBalance, a comprehensive platform, to integrate and streamline the workflows of disease model building, disease risk prediction and disease-related biomarker discovery for microbiome-based binary classifications. DisBalance allows the de novo model-building and disease risk prediction in a very fast and convenient way. To facilitate the model-driven and knowledge-driven discoveries, DisBalance dedicates multiple strategies for the mining of microbial biomarkers. The independent validation of the models constructed by the DisBalance pipeline is performed on seven microbiome datasets from the original article of DBA-distal. The implementation of the DisBalance platform is demonstrated by a complete analysis of a shotgun metagenomic dataset of Ulcerative Colitis (UC). As a free and open-source, DisBlance can be accessed at http://lab.malab.cn/soft/DisBalance. The source code and demo data for Disbalance are available at https://github.com/yangfenglong/DisBalance.}, } @article {pmid33831764, year = {2021}, author = {Pandit, PR and Kumar, R and Kumar, D and Patel, Z and Pandya, L and Kumar, M and Joshi, C}, title = {Deciphering the black box of microbial community of common effluent treatment plant through integrated metagenomics: Tackling industrial effluent.}, journal = {Journal of environmental management}, volume = {289}, number = {}, pages = {112448}, doi = {10.1016/j.jenvman.2021.112448}, pmid = {33831764}, issn = {1095-8630}, mesh = {Bacteria/genetics ; Metagenome ; *Metagenomics ; *Microbiota ; Wastewater ; }, abstract = {Identifying the microbial community and their functional potential from different stages of common effluent treatment plants (CETP) can enhance the efficiency of wastewater treatment systems. In this study, wastewater metagenomes from 8 stages of CETP were screened for microbial diversity and gene profiling along with their corresponding degradation activities. The microbial community displayed 98.46% of bacterial species, followed by Eukarya (0.10%) and Archaea 0.02%. At the Phylum level, Proteobacteria (28.8%) was dominant, followed by Bacteroidetes (16.1%), Firmicutes (11.7%), and Fusobacteria (6.9%) which are mainly capable of degrading the aromatic compounds. Klebsiella pneumoniae, Wolinella succinogenes, Pseudomonas stutzeri, Desulfovibrio vulgaris, and Clostridium sticklandii were the most prevalent species. The functional analysis further demonstrated the presence of enzymes linked with genes/pathways known to be involved in the degradation/metabolization of aromatic compounds like benzoate, bisphenol, 1,2-dichloroethane phenylalanine. This information was further validated with the whole genome analysis of the bacteria isolated from the CETP. We anticipate that integrating both shotgun and whole-genome analyses can reveal the rich reservoir for novel enzymes and genes present in CETP effluent that can contribute to designing efficient bioremediation strategies for the environment in general CETP system, in particular.}, } @article {pmid33831065, year = {2021}, author = {Crowe, SA and Simister, RL and Spence, JS and Kenward, PA and Van Slyke, AC and Lennox, P and Carr, N}, title = {Microbial community compositions in breast implant biofilms associated with contracted capsules.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0249261}, pmid = {33831065}, issn = {1932-6203}, mesh = {*Biofilms/growth & development ; *Breast Implants/microbiology/adverse effects ; Humans ; Female ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria/genetics/classification/isolation & purification ; Implant Capsular Contracture/microbiology ; Adult ; }, abstract = {Subclinical bacterial infections (biofilms) are strongly implicated in breast augmentation failure due to capsular contracture, and while these infections are generally ascribed to common skin commensals, this remains largely unsubstantiated through robust cultivation independent analyses. To determine capsule biofilm microbial community compositions, we employed amplicon sequencing of the 16S rRNA gene using DNA extracted from breast implant capsule samples. These cultivation independent analyses revealed that capsule associated biofilms are more diverse than canonical single-species infections, but have relatively low diversity (~ <100 species) compared to many host-associated microbial communities. In addition to taxa commonly associated with capsular contracture, the biofilms analyzed comprised a number of taxa that escaped detection in cultivation-dependent work. We have also isolated several key taxa identified through the culture-independent analyses. Together our analyses reveal that capsule biofilms are more diverse than cultivation studies suggest and can be heterogeneous within an individual capsule, between breasts of the same patient, across similar implant types, and over a range in severity of contracture. The complex nature of these communities requires further study across a broader suite of patients in addition to higher resolution analyses including metagenomics to better assess the fundamental role of microorganisms in capsular contracture.}, } @article {pmid33830453, year = {2021}, author = {Ishak, S and Dormontt, E and Young, JM}, title = {Microbiomes in forensic botany: a review.}, journal = {Forensic science, medicine, and pathology}, volume = {17}, number = {2}, pages = {297-307}, pmid = {33830453}, issn = {1556-2891}, mesh = {*Botany ; Crime ; Forensic Medicine ; Humans ; *Microbiota ; }, abstract = {Fragments of botanical material can often be found at crime scenes (on live and dead bodies, or on incriminating objects) and can provide circumstantial evidence on various aspects of forensic investigations such as determining crime scene locations, times of death or possession of illegal species. Morphological and genetic analysis are the most commonly applied methods to analyze plant fragment evidence but are limited by their low capacity to differentiate between potential source locations, especially at local scales. Here, we review the current applications and limitations of current plant fragment analysis for forensic investigations and introduce the potential of microbiome analysis to complement the existing forensic plant fragment analysis toolkit. The potential for plant fragment provenance identification at geographic scales meaningful to forensic investigations warrants further investigation of the phyllosphere microbiome in this context. To that end we identify three key areas of future research: 1) Retrieval of microbial DNA of sufficient quality and quantity from botanical material; 2) Variability of the phyllosphere microbiome at different taxonomic and spatial scales, with explicit reference to assignment capacity; 3) Impacts on assignment capacity of time, seasonality and movement of fragments between locations. The development of robust microbiome analysis tools for forensic purposes in botanical material could increase the evidentiary value of the botanical evidence commonly encountered in casework, aiding in the identification of crime scene locations.}, } @article {pmid33828081, year = {2021}, author = {Dove, NC and Torn, MS and Hart, SC and Taş, N}, title = {Metabolic capabilities mute positive response to direct and indirect impacts of warming throughout the soil profile.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2089}, pmid = {33828081}, issn = {2041-1723}, mesh = {Bacteria/classification/genetics ; California ; Carbon/metabolism ; Forests ; *Global Warming ; *Metagenome ; Microbiota ; Nitrogen/metabolism ; RNA, Ribosomal, 16S ; Soil/*chemistry ; *Soil Microbiology ; Temperature ; }, abstract = {Increasing global temperatures are predicted to stimulate soil microbial respiration. The direct and indirect impacts of warming on soil microbes, nevertheless, remain unclear. This is particularly true for understudied subsoil microbes. Here, we show that 4.5 years of whole-profile soil warming in a temperate mixed forest results in altered microbial community composition and metabolism in surface soils, partly due to carbon limitation. However, microbial communities in the subsoil responded differently to warming than in the surface. Throughout the soil profile-but to a greater extent in the subsoil-physiologic and genomic measurements show that phylogenetically different microbes could utilize complex organic compounds, dampening the effect of altered resource availability induced by warming. We find subsoil microbes had 20% lower carbon use efficiencies and 47% lower growth rates compared to surface soils, which constrain microbial communities. Collectively, our results show that unlike in surface soils, elevated microbial respiration in subsoils may continue without microbial community change in the near-term.}, } @article {pmid33827913, year = {2021}, author = {Benjamino, J and Leopold, B and Phillips, D and Adams, MD}, title = {Genome-Based Targeted Sequencing as a Reproducible Microbial Community Profiling Assay.}, journal = {mSphere}, volume = {6}, number = {2}, pages = {}, pmid = {33827913}, issn = {2379-5042}, mesh = {Animals ; Bacteria/*genetics ; DNA, Bacterial/genetics ; Feces/microbiology ; Gene Expression Profiling/economics/methods ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing/economics/*methods ; *Metagenome ; Mice ; Mice, Inbred C57BL ; Microbiota/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Current sequencing-based methods for profiling microbial communities rely on marker gene (e.g., 16S rRNA) or metagenome shotgun sequencing (mWGS) analysis. We present an approach based on a single-primer extension reaction using a highly multiplexed oligonucleotide probe pool. This approach, termed MA-GenTA (microbial abundances from genome tagged analysis), enables quantitative, straightforward, cost-effective microbiome profiling that combines desirable features of both 16S rRNA and mWGS strategies. The use of multiple probes per target genome and rigorous probe design criteria enabled robust determination of relative abundance. To test the utility of the MA-GenTA assay, probes were designed for 830 genome sequences representing bacteria present in mouse stool specimens. Comparison of the MA-GenTA data with mWGS data demonstrated excellent correlation down to 0.01% relative abundance and a similar number of organisms detected per sample. Despite the incompleteness of the reference database, nonmetric multidimensional scaling (NMDS) clustering based on the Bray-Curtis dissimilarity metric of sample groups was consistent between MA-GenTA, mWGS, and 16S rRNA data sets. MA-GenTA represents a potentially useful new method for microbiome community profiling based on reference genomes.IMPORTANCE New methods for profiling the microbial communities can create new approaches to understanding the composition and function of those communities. In this study, we combined bacterial genome-specific probe design with a highly multiplexed single primer extension reaction as a new method to profile microbial communities, using stool from various mouse strains as a test case. This method, termed MA-GenTA, was benchmarked against 16S rRNA gene sequencing and metagenome sequencing methods and delivered similar relative abundance and clustering data. Since the probes were generated from reference genomes, MA-GenTA was also able to provide functional pathway data for the stool microbiome in the assayed samples. The method is more informative than 16S rRNA analysis while being less costly than metagenome shotgun sequencing.}, } @article {pmid33827686, year = {2021}, author = {Ducarmon, QR and Terveer, EM and Nooij, S and Bloem, MN and Vendrik, KEW and Caljouw, MAA and Sanders, IMJG and van Dorp, SM and Wong, MC and Zwittink, RD and Kuijper, EJ}, title = {Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {54}, pmid = {33827686}, issn = {1756-994X}, mesh = {Bacteria/genetics/isolation & purification ; *Drug Resistance, Multiple, Bacterial/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Genome, Bacterial ; Humans ; Metagenome ; Microbial Sensitivity Tests ; Netherlands ; *Nursing Homes ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; Time Factors ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Nursing home residents have increased rates of intestinal colonisation with multidrug-resistant organisms (MDROs). We assessed the colonisation and spread of MDROs among this population, determined clinical risk factors for MDRO colonisation and investigated the role of the gut microbiota in providing colonisation resistance against MDROs.

METHODS: We conducted a prospective cohort study in a Dutch nursing home. Demographical, epidemiological and clinical data were collected at four time points with 2-month intervals (October 2016-April 2017). To obtain longitudinal data, faecal samples from residents were collected for at least two time points. Ultimately, twenty-seven residents were included in the study and 93 faecal samples were analysed, of which 27 (29.0%) were MDRO-positive. Twelve residents (44.4%) were colonised with an MDRO at at least one time point throughout the 6-month study.

RESULTS: Univariable generalised estimating equation logistic regression indicated that antibiotic use in the previous 2 months and hospital admittance in the previous year were associated with MDRO colonisation. Characterisation of MDRO isolates through whole-genome sequencing revealed Escherichia coli sequence type (ST)131 to be the most prevalent MDRO and ward-specific clusters of E. coli ST131 were identified. Microbiota analysis by 16S rRNA gene amplicon sequencing revealed no differences in alpha or beta diversity between MDRO-positive and negative samples, nor between residents who were ever or never colonised. Three bacterial taxa (Dorea, Atopobiaceae and Lachnospiraceae ND3007 group) were more abundant in residents never colonised with an MDRO throughout the 6-month study. An unexpectedly high abundance of Bifidobacterium was observed in several residents. Further investigation of a subset of samples with metagenomics showed that various Bifidobacterium species were highly abundant, of which B. longum strains remained identical within residents over time, but were different between residents.

CONCLUSIONS: Our study provides new evidence for the role of the gut microbiota in colonisation resistance against MDROs in the elderly living in a nursing home setting. Dorea, Atopobiaceae and Lachnospiraceae ND3007 group may be associated with protection against MDRO colonisation. Furthermore, we report a uniquely high abundance of several Bifidobacterium species in multiple residents and excluded the possibility that this was due to probiotic supplementation.}, } @article {pmid33823791, year = {2021}, author = {Okumura, T and Horiba, K and Kamei, H and Takeuchi, S and Suzuki, T and Torii, Y and Kawada, JI and Takahashi, Y and Ogura, Y and Ogi, T and Ito, Y}, title = {Temporal dynamics of the plasma microbiome in recipients at early post-liver transplantation: a retrospective study.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {104}, pmid = {33823791}, issn = {1471-2180}, mesh = {*Biodiversity ; Graft Rejection/immunology/microbiology ; Humans ; Immunocompetence ; Japan ; *Liver Transplantation ; *Microbiota/genetics/immunology ; *Plasma/microbiology ; Retrospective Studies ; Time Factors ; }, abstract = {BACKGROUND: Immunosuppression during liver transplantation (LT) enables the prevention and treatment of organ rejection but poses a risk for severe infectious diseases. Immune modulation and antimicrobials affect the plasma microbiome. Thus, determining the impact of immunosuppression on the microbiome may be important to understand immunocompetence, elucidate the source of infection, and predict the risk of infection in LT recipients. We characterized the plasma microbiome of LT recipients at early post-LT and assessed the association between the microbiome and clinical events.

RESULTS: In this study, 51 patients who received LT at Nagoya University Hospital from 2016 to 2018 were enrolled. Plasma samples were retrospectively collected at the following time points: 1) within a week after LT; 2) 4 ± 1 weeks after LT; 3) 8 ± 1 weeks after LT; and 4) within 2 days after a positive blood culture. A total of 111 plasma samples were analyzed using shotgun next-generation sequencing (NGS) with the PATHDET pipeline. Relative abundance of Anelloviridae, Nocardiaceae, Microbacteriaceae, and Enterobacteriaceae significantly changed during the postoperative period. Microbiome diversity was higher within a week after LT than that at 8 weeks after LT. Antimicrobials were significantly associated with the microbiome of LT recipients. In addition, the proportion of Enterobacteriaceae was significantly increased and the plasma microbiome diversity was significantly lower in patients with acute cellular rejection (ACR) than non-ACR patients. Sequencing reads of bacteria isolated from blood cultures were predominantly identified by NGS in 8 of 16 samples, and human herpesvirus 6 was detected as a causative pathogen in one recipient with severe clinical condition.

CONCLUSIONS: The metagenomic NGS technique has great potential in revealing the plasma microbiome and is useful as a comprehensive diagnostic procedure in clinical settings. Temporal dynamics of specific microorganisms may be used as indirect markers for the determination of immunocompetence and ACR in LT recipients.}, } @article {pmid33823666, year = {2021}, author = {Dong, F and Kuo, HC and Chen, GL and Wu, F and Shan, PF and Wang, J and Chen, D and Lei, FM and Hung, CM and Liu, Y and Yang, XJ}, title = {Population genomic, climatic and anthropogenic evidence suggest the role of human forces in endangerment of green peafowl (Pavo muticus).}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1948}, pages = {20210073}, pmid = {33823666}, issn = {1471-2954}, mesh = {Animals ; Climate Change ; Ecosystem ; Extinction, Biological ; *Genome ; Humans ; *Metagenomics ; }, abstract = {Both anthropogenic impacts and historical climate change could contribute to population decline and species extinction, but their relative importance is still unclear. Emerging approaches based on genomic, climatic and anthropogenic data provide a promising analytical framework to address this question. This study applied such an integrative approach to examine potential drivers for the endangerment of the green peafowl (Pavo muticus). Several demographic reconstructions based on population genomes congruently retrieved a drastic population declination since the mid-Holocene. Furthermore, a comparison between historical and modern genomes suggested genetic diversity decrease during the last 50 years. However, climate-based ecological niche models predicted stationary general range during these periods and imply the little impact of climate change. Further analyses suggested that human disturbance intensities were negatively correlated with the green peafowl's effective population sizes and significantly associated with its survival status (extirpation or persistence). Archaeological and historical records corroborate the critical role of humans, leaving the footprint of low genomic diversity and high inbreeding in the survival populations. This study sheds light on the potential deep-time effects of human disturbance on species endangerment and offers a multi-evidential approach in examining underlying forces for population declines.}, } @article {pmid33822948, year = {2021}, author = {Hsu, CC and Okumura, R and Motooka, D and Sasaki, R and Nakamura, S and Iida, T and Takeda, K}, title = {Alleviation of colonic inflammation by Lypd8 in a mouse model of inflammatory bowel disease.}, journal = {International immunology}, volume = {33}, number = {7}, pages = {359-372}, doi = {10.1093/intimm/dxab012}, pmid = {33822948}, issn = {1460-2377}, mesh = {Animals ; Colitis/chemically induced/metabolism ; Colon/*metabolism ; Dextran Sulfate/pharmacology ; Diet, High-Fat ; Disease Models, Animal ; Dysbiosis/chemically induced/metabolism ; Female ; GPI-Linked Proteins/*metabolism ; Gastrointestinal Microbiome/physiology ; Humans ; Inflammation/chemically induced/*metabolism ; Inflammatory Bowel Diseases/chemically induced/*metabolism ; Intestinal Mucosa/metabolism ; Mice ; Mice, Inbred C57BL ; }, abstract = {Dysfunction of the intestinal mucosal barrier causes inflammatory bowel diseases (IBDs). Indeed, mucosal barrier impairment in the gut of IBD patients results from decreased expression of barrier molecules. Ly6/Plaur domain containing 8 (Lypd8) segregates microbiota from the colonic epithelial layer. In this study, we found that Lypd8-/- mice, in which flagellated bacteria invaded the mucosal surface of the colon, developed spontaneous colitis when dysbiosis was induced by a high-fat diet (HFD). On the basis of this finding, we assessed whether the application of human LYPD8 (hLYPD8) protein exhibiting the glycan-dependent inhibition of bacterial motility is effective in a colitis model. Oral and anal treatments with hLYPD8 protein ameliorate dextran sulfate sodium-induced colitis and HFD-induced colitis in Lypd8-/- mice. These results indicate a therapeutic potential of hLYPD8 protein supplementation for IBD.}, } @article {pmid33822937, year = {2021}, author = {Pennycook, JH and Scanlan, PD}, title = {Ecological and Evolutionary responses to Antibiotic Treatment in the Human Gut Microbiota.}, journal = {FEMS microbiology reviews}, volume = {45}, number = {5}, pages = {}, pmid = {33822937}, issn = {1574-6976}, support = {//Royal Society/ ; 17/RC-PhD/3476/SFI_/Science Foundation Ireland/Ireland ; //JHP/ ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; *Microbiota ; }, abstract = {The potential for antibiotics to affect the ecology and evolution of the human gut microbiota is well recognised and has wide-ranging implications for host health. Here, we review the findings of key studies that surveyed the human gut microbiota during antibiotic treatment. We find several broad patterns including the loss of diversity, disturbance of community composition, suppression of bacteria in the Actinobacteria phylum, amplification of bacteria in the Bacteroidetes phylum, and promotion of antibiotic resistance. Such changes to the microbiota were often, but not always, recovered following the end of treatment. However, many studies reported unique and/or contradictory results, which highlights our inability to meaningfully predict or explain the effects of antibiotic treatment on the human gut microbiome. This problem arises from variation between existing studies in three major categories: differences in dose, class and combinations of antibiotic treatments used; differences in demographics, lifestyles, and locations of subjects; and differences in measurements, analyses and reporting styles used by researchers. To overcome this, we suggest two integrated approaches: (i) a top-down approach focused on building predictive models through large sample sizes, deep metagenomic sequencing, and effective collaboration; and (ii) a bottom-up reductionist approach focused on testing hypotheses using model systems.}, } @article {pmid33822893, year = {2021}, author = {Davis, ML and Huang, Y and Wang, K}, title = {Rank normalization empowers a t-test for microbiome differential abundance analysis while controlling for false discoveries.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {5}, pages = {}, pmid = {33822893}, issn = {1477-4054}, support = {P30 ES005605/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Bacterial Infections/*diagnosis/microbiology ; Benchmarking ; Biostatistics/*methods ; Case-Control Studies ; Child ; Cohort Studies ; Colorectal Neoplasms/*microbiology ; Computer Simulation ; Crohn Disease/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Mathematical Computing ; *Metagenome ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sensitivity and Specificity ; Statistics, Nonparametric ; }, abstract = {A major task in the analysis of microbiome data is to identify microbes associated with differing biological conditions. Before conducting analysis, raw data must first be adjusted so that counts from different samples are comparable. A typical approach is to estimate normalization factors by which all counts in a sample are multiplied or divided. However, the inherent variation associated with estimation of normalization factors are often not accounted for in subsequent analysis, leading to a loss of precision. Rank normalization is a nonparametric alternative to the estimation of normalization factors in which each count for a microbial feature is replaced by its intrasample rank. Although rank normalization has been successfully applied to microarray analysis in the past, it has yet to be explored for microbiome data, which is characterized by high frequencies of 0s, strongly correlated features and compositionality. We propose to use rank normalization as an alternative to the estimation of normalization factors and examine its performance when paired with a two-sample t-test. On a rigorous 3rd-party benchmarking simulation, it is shown to offer strong control over the false discovery rate, and at sample sizes greater than 50 per treatment group, to offer an improvement in performance over commonly used normalization factors paired with t-tests, Wilcoxon rank-sum tests and methodologies implemented by R packages. On two real datasets, it yielded valid and reproducible results that were strongly in agreement with the original findings and the existing literature, further demonstrating its robustness and future potential. Availability: The data underlying this article are available online along with R code and supplementary materials at https://github.com/matthewlouisdavisBioStat/Rank-Normalization-Empowers-a-T-Test.}, } @article {pmid33822891, year = {2021}, author = {Arisdakessian, CG and Nigro, OD and Steward, GF and Poisson, G and Belcaid, M}, title = {CoCoNet: an efficient deep learning tool for viral metagenome binning.}, journal = {Bioinformatics (Oxford, England)}, volume = {37}, number = {18}, pages = {2803-2810}, doi = {10.1093/bioinformatics/btab213}, pmid = {33822891}, issn = {1367-4811}, support = {1636402//National Science Foundation Division of Ocean Sciences/ ; 1557349-Ike Wai//Office of Integrative Activities/ ; 1736030-G2P//Securing Hawaii's Water Future/ ; }, mesh = {Metagenome ; Algorithms ; *Deep Learning ; Software ; *Microbiota/genetics ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; }, abstract = {MOTIVATION: Metagenomic approaches hold the potential to characterize microbial communities and unravel the intricate link between the microbiome and biological processes. Assembly is one of the most critical steps in metagenomics experiments. It consists of transforming overlapping DNA sequencing reads into sufficiently accurate representations of the community's genomes. This process is computationally difficult and commonly results in genomes fragmented across many contigs. Computational binning methods are used to mitigate fragmentation by partitioning contigs based on their sequence composition, abundance or chromosome organization into bins representing the community's genomes. Existing binning methods have been principally tuned for bacterial genomes and do not perform favorably on viral metagenomes.

RESULTS: We propose Composition and Coverage Network (CoCoNet), a new binning method for viral metagenomes that leverages the flexibility and the effectiveness of deep learning to model the co-occurrence of contigs belonging to the same viral genome and provide a rigorous framework for binning viral contigs. Our results show that CoCoNet substantially outperforms existing binning methods on viral datasets.

CoCoNet was implemented in Python and is available for download on PyPi (https://pypi.org/). The source code is hosted on GitHub at https://github.com/Puumanamana/CoCoNet and the documentation is available at https://coconet.readthedocs.io/en/latest/index.html. CoCoNet does not require extensive resources to run. For example, binning 100k contigs took about 4 h on 10 Intel CPU Cores (2.4 GHz), with a memory peak at 27 GB (see Supplementary Fig. S9). To process a large dataset, CoCoNet may need to be run on a high RAM capacity server. Such servers are typically available in high-performance or cloud computing settings.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid33820995, year = {2021}, author = {Mac Aogáin, M and Narayana, JK and Tiew, PY and Ali, NABM and Yong, VFL and Jaggi, TK and Lim, AYH and Keir, HR and Dicker, AJ and Thng, KX and Tsang, A and Ivan, FX and Poh, ME and Oriano, M and Aliberti, S and Blasi, F and Low, TB and Ong, TH and Oliver, B and Giam, YH and Tee, A and Koh, MS and Abisheganaden, JA and Tsaneva-Atanasova, K and Chalmers, JD and Chotirmall, SH}, title = {Integrative microbiomics in bronchiectasis exacerbations.}, journal = {Nature medicine}, volume = {27}, number = {4}, pages = {688-699}, pmid = {33820995}, issn = {1546-170X}, support = {SCAF/17/03/CSO_/Chief Scientist Office/United Kingdom ; }, mesh = {Bronchiectasis/*microbiology/virology ; Disease Progression ; Humans ; Metagenomics ; Microbial Interactions/genetics ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Bronchiectasis, a progressive chronic airway disease, is characterized by microbial colonization and infection. We present an approach to the multi-biome that integrates bacterial, viral and fungal communities in bronchiectasis through weighted similarity network fusion (https://integrative-microbiomics.ntu.edu.sg). Patients at greatest risk of exacerbation have less complex microbial co-occurrence networks, reduced diversity and a higher degree of antagonistic interactions in their airway microbiome. Furthermore, longitudinal interactome dynamics reveals microbial antagonism during exacerbation, which resolves following treatment in an otherwise stable multi-biome. Assessment of the Pseudomonas interactome shows that interaction networks, rather than abundance alone, are associated with exacerbation risk, and that incorporation of microbial interaction data improves clinical prediction models. Shotgun metagenomic sequencing of an independent cohort validated the multi-biome interactions detected in targeted analysis and confirmed the association with exacerbation. Integrative microbiomics captures microbial interactions to determine exacerbation risk, which cannot be appreciated by the study of a single microbial group. Antibiotic strategies probably target the interaction networks rather than individual microbes, providing a fresh approach to the understanding of respiratory infection.}, } @article {pmid33820988, year = {2021}, author = {Tourancheau, A and Mead, EA and Zhang, XS and Fang, G}, title = {Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing.}, journal = {Nature methods}, volume = {18}, number = {5}, pages = {491-498}, pmid = {33820988}, issn = {1548-7105}, support = {R01 GM128955/GM/NIGMS NIH HHS/United States ; R01 HG011095/HG/NHGRI NIH HHS/United States ; R35 GM139655/GM/NIGMS NIH HHS/United States ; R56 HG011095/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*genetics ; DNA Methylation/*physiology ; DNA, Bacterial/*genetics ; Gastrointestinal Microbiome ; Genome, Bacterial ; Metagenome ; Metagenomics/*methods ; Mice ; *Nanopore Sequencing ; }, abstract = {Bacterial DNA methylation occurs at diverse sequence contexts and plays important functional roles in cellular defense and gene regulation. Existing methods for detecting DNA modification from nanopore sequencing data do not effectively support de novo study of unknown bacterial methylomes. In this work, we observed that a nanopore sequencing signal displays complex heterogeneity across methylation events of the same type. To enable nanopore sequencing for broadly applicable methylation discovery, we generated a training dataset from an assortment of bacterial species and developed a method, named nanodisco (https://github.com/fanglab/nanodisco), that couples the identification and fine mapping of the three forms of methylation into a multi-label classification framework. We applied it to individual bacteria and the mouse gut microbiome for reliable methylation discovery. In addition, we demonstrated the use of DNA methylation for binning metagenomic contigs, associating mobile genetic elements with their host genomes and identifying misassembled metagenomic contigs.}, } @article {pmid33820946, year = {2021}, author = {Deng, Y and Huang, Y and Che, Y and Yang, Y and Yin, X and Yan, A and Dai, L and Liu, YY and Polz, M and Zhang, T}, title = {Microbiome assembly for sulfonamide subsistence and the transfer of genetic determinants.}, journal = {The ISME journal}, volume = {15}, number = {10}, pages = {2817-2829}, pmid = {33820946}, issn = {1751-7370}, support = {R01 AI141529/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Drug Resistance, Microbial ; Humans ; Metagenome ; *Microbiota/genetics ; Sulfonamides ; }, abstract = {Antibiotic subsistence in bacteria represents an alternative resistance machinery, while paradoxically, it is also a cure for environmental resistance. Antibiotic-subsisting bacteria can detoxify antibiotic-polluted environments and prevent the development of antibiotic resistance in environments. However, progress toward efficient in situ engineering of antibiotic-subsisting bacteria is hindered by the lack of mechanistic and predictive understanding of the assembly of the functioning microbiome. By top-down manipulation of wastewater microbiomes using sulfadiazine as the single limiting source, we monitored the ecological selection process that forces the wastewater microbiome to perform efficient sulfadiazine subsistence. We found that the community-level assembly selects for the same three families rising to prominence across different initial pools of microbiomes. We further analyzed the assembly patterns using a linear model. Detailed inspections of the sulfonamide metabolic gene clusters in individual genomes of isolates and assembled metagenomes reveal limited transfer potential beyond the boundaries of the Micrococcaceae lineage. Our results open up new possibilities for engineering specialist bacteria for environmental applications.}, } @article {pmid33819653, year = {2021}, author = {Zhang, Z and Wan, J and Liu, L and Ye, M and Jiang, X}, title = {Metagenomics reveals functional profiling of microbial communities in OCP contaminated sites with rapeseed oil and tartaric acid biostimulation.}, journal = {Journal of environmental management}, volume = {289}, number = {}, pages = {112515}, doi = {10.1016/j.jenvman.2021.112515}, pmid = {33819653}, issn = {1095-8630}, mesh = {Biodegradation, Environmental ; Humans ; Metagenomics ; *Microbiota ; Rapeseed Oil ; Soil Microbiology ; *Soil Pollutants/analysis ; Tartrates ; }, abstract = {Organochlorine pesticides (OCPs) contaminated sites pose great threats to both human health and environmental safety. Targeted bioremediation in these regions largely depends on microbial diversity and activity. This study applied metagenomics to characterize the microbial communities and functional groups composition features during independent or simultaneous rapeseed oil and tartaric acid applications, as well as the degradation kinetics of OCPs. Results showed that: the degradation rates of α-chlordane, β-chlordane and mirex were better when (0.50% w/w) rapeseed oil and (0.05 mol L[-1]) tartaric acid were applied simultaneously than singular use, yielding removal rates of 56.4%, 53.9%, and 49.4%, respectively. Meanwhile, bio-stimulation facilitated microbial enzyme (catalase/superoxide dismutase/peroxidase) activity in soils significantly, promoting the growth of dominant bacterial communities. Classification at phylum level showed that the relative abundance of Proteobacteria was significantly increased (p < 0.05). Network analysis showed that bio-stimulation substantially increased the dominant bacterial community's proportion, especially Proteobacteria. The functional gene results illustrated that bio-stimulation facilitated total relative abundance of degradation genes, phosphorus, carbon, nitrogen, sulfur metabolic genes, and iron transporting genes (p < 0.05). In metabolic pathways, functional genes related to methanogenesis and ammonia generation were markedly upregulated, indicating that bio-stimulation promoted the transformation of metabolic genes, such as carbon and nitrogen. This research is conducive to exploring the microbiological response mechanisms of bio-stimulation in indigenous flora, which may provide technical support for assessing the microbial ecological remediation outcomes of bio-stimulation in OCP contaminated sites.}, } @article {pmid33819509, year = {2021}, author = {Petersen, AØ and Jokinen, M and Plichta, DR and Liebisch, G and Gronwald, W and Dettmer, K and Oefner, PJ and Vlamakis, H and Chung, DC and Ranki, A and Xavier, RJ}, title = {Cytokine-specific autoantibodies shape the gut microbiome in autoimmune polyendocrine syndrome type 1.}, journal = {The Journal of allergy and clinical immunology}, volume = {148}, number = {3}, pages = {876-888}, pmid = {33819509}, issn = {1097-6825}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AT009708/AT/NCCIH NIH HHS/United States ; U19 AI110495/AI/NIAID NIH HHS/United States ; }, mesh = {Actinobacteria/genetics/isolation & purification ; Adolescent ; Adult ; Aged ; Autoantibodies/blood/*immunology ; Bacteroidetes/genetics/isolation & purification ; Child ; Child, Preschool ; Cytokines/*immunology ; Female ; *Gastrointestinal Microbiome ; Humans ; *Lacticaseibacillus rhamnosus ; Male ; Middle Aged ; Mutation ; Polyendocrinopathies, Autoimmune/blood/genetics/*immunology/*microbiology ; Probiotics/*therapeutic use ; Transcription Factors/genetics ; Young Adult ; AIRE Protein ; }, abstract = {BACKGROUND: Gastrointestinal dysfunction is a frequent and disabling manifestation of autoimmune polyendocrine syndrome type 1 (APS-1), a rare monogenic multiorgan autoimmune disease caused by the loss of central AIRE-controlled immune tolerance.

OBJECTIVES: This study aimed to understand the role of the gut microbiome in APS-1 symptoms and potentially alleviate common gastrointestinal symptoms by probiotic intervention.

METHODS: This study characterized the fecal microbiomes of 28 patients with APS-1 and searched for associations with gastrointestinal symptoms, circulating anti-cytokine autoantibodies, and tryptophan-related metabolites. Additionally, daily doses of the probiotic Lactobacillus rhamnosus GG were administered for 3 months.

RESULTS: Of 581 metagenomic operational taxonomic units (mOTUs) characterized in total, 14 were significantly associated with patients with APS-1 compared with healthy controls, with 6 mOTUs depleted and 8 enriched in patients with APS-1. Four overabundant mOTUs were significantly associated with severity of constipation. Phylogenetically conserved microbial associations with autoantibodies against cytokines were observed. After the 3-month intervention with the probiotic L rhamnosus GG, a subset of gastrointestinal symptoms were alleviated. L rhamnosus GG abundance was increased postintervention and corresponded with decreased abundances of Alistipes onderdonkii and Collinsella aerofaciens, 2 species positively associated with severity of diarrhea in patients with APS-1.

CONCLUSIONS: The APS-1 microbiome correlates with several APS-1 symptoms, some of which are alleviated after a 3-month L rhamnosus GG intervention. Autoantibodies against cytokines appear to shape the gut microbiome by positively correlating with a taxonomically consistent group of bacteria.}, } @article {pmid33817941, year = {2021}, author = {Aldeguer-Riquelme, B and Ramos-Barbero, MD and Santos, F and Antón, J}, title = {Environmental dissolved DNA harbours meaningful biological information on microbial community structure.}, journal = {Environmental microbiology}, volume = {23}, number = {5}, pages = {2669-2682}, doi = {10.1111/1462-2920.15510}, pmid = {33817941}, issn = {1462-2920}, mesh = {DNA ; *DNA, Environmental ; Metagenome ; *Microbiota/genetics ; *Viruses/genetics ; }, abstract = {Extracellular DNA (eDNA) comprises all the DNA molecules outside cells. This component of microbial ecosystems may serve as a source of nutrients and genetic information. Hypersaline environments harbour one of the highest concentrations of eDNA reported for natural systems, which has been attributed to the physicochemical preservative effect of salts and to high viral abundance. Here, we compared centrifugation and filtration protocols for the extraction of dissolved DNA (dDNA, as opposed to eDNA that also includes DNA from free viral particles) from a solar saltern crystallizer pond (CR30) water sample. The crystallizer dDNA fraction has been characterized, for the first time, and compared with cellular and viral metagenomes from the same location. High-speed centrifugation affected CR30 dDNA concentration and composition due to cell lysis, highlighting that protocol optimization should be the first step in dDNA studies. Crystallizer dDNA, which accounted for lower concentrations than those previously reported for hypersaline anoxic sediments, had a mixed viral and cellular origin, was enriched in archaeal DNA and had a distinctive taxonomic composition compared to that from the cellular assemblage of the same sample. Bioinformatic analyses indicated that nanohaloarchaeal viruses could be a cause for these differences.}, } @article {pmid33816333, year = {2021}, author = {Ye, L and Zhang, Q and Xin, F and Cao, B and Qian, L and Dong, Y}, title = {Neonatal Milk Fat Globule Membrane Supplementation During Breastfeeding Ameliorates the Deleterious Effects of Maternal High-Fat Diet on Metabolism and Modulates Gut Microbiota in Adult Mice Offspring in a Sex-Specific Way.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {621957}, pmid = {33816333}, issn = {2235-2988}, mesh = {Animals ; *Diet, High-Fat/adverse effects ; Dietary Supplements ; Female ; *Gastrointestinal Microbiome ; Glycolipids ; Glycoproteins ; Lipid Droplets ; Male ; Mice ; Mice, Inbred C57BL ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Exposure to adverse events in early life increases the risk of chronic metabolic disease in adulthood. The objective of this study was to determine the significance of milk fat globule membrane (MFGM)-mediated alterations in the gut microbiome to the metabolic health of offspring in the long-term. Female C57BL/6 mice were fed either a high-fat diet (HFD) or a control diet for 3 weeks before pregnancy and throughout pregnancy and lactation. During lactation, pups from the HFD group were breast-fed with or without 1,000 mg/kg BW/day MFGM supplementation (HFD and HFD-MS group, respectively). After weaning, the offspring in each group were divided into male and female subgroups. The weaned mice were then shifted to a control diet for 8 weeks. At the eleventh week, stool samples were collected for 16S rRNA gene sequencing. Serum biochemical parameters were analyzed, and intraperitoneal glucose and insulin tolerance tests were performed. Neonatal supplementation with MFGM ameliorated metabolic disorder and improved glucose tolerance in offspring exposed to maternal HFD in a sex-specific manner. Furthermore, maternal HFD induced gut microbiota perturbation in offspring in adulthood. Neonatal MFGM supplementation significantly enriched g-Parabacteroides, g-Bifidobacterium, g-Faecalibaculum, and g-Lactobacillus in male offspring exposed to maternal HFD, while significantly enriched g-Parabacteroides and g-Alistipes in female offspring exposed to maternal HFD. These bacteria may be associated with the favorable changes in metabolism that occur in adulthood. Sex differences in the changes of metagenomic pathways related to oxidative phosphorylation, citrate cycle, electron transfer carries, and ubiquinone biosynthesis were also observed in the offspring. Maternal HFD has an adverse effect on the metabolism of offspring in later life. Neonatal MFGM supplementation could modulate the structure of gut microbiota communities and may have long-term protective effects on lipid and glucose metabolism, but these effects are sex dimorphic.}, } @article {pmid33816323, year = {2021}, author = {Even, G and Lokmer, A and Rodrigues, J and Audebert, C and Viscogliosi, E and Ségurel, L and Chabé, M}, title = {Changes in the Human Gut Microbiota Associated With Colonization by Blastocystis sp. and Entamoeba spp. in Non-Industrialized Populations.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {533528}, pmid = {33816323}, issn = {2235-2988}, mesh = {Adult ; *Blastocystis/genetics ; *Entamoeba/genetics ; Feces ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Human gut microbial communities are mainly composed of bacteria, but also include fungi, viruses, archaea, and protozoa, whose role in the gut ecosystem has only recently begun to be recognized. For example, humans colonized by Blastocystis (a gut protozoan with controversial pathogenicity) host a more diverse bacterial microbiota than individuals not carrying it, suggesting that its presence may be beneficial for the host. In parallel, the presence of non-pathogenic Entamoeba spp. has been associated with an increased diversity and compositional shifts in the bacterial microbiota of healthy rural individuals in Cameroon. However, Entamoeba and Blastocystis, the two most prevalent human gut protozoa, have never been studied in the same individuals, preventing the study of their interaction. As Blastocystis is one of the few gut protozoa commonly found in industrialized populations, which are otherwise mostly devoid of gut eukaryotes, we need to focus on rural "traditional" populations, who harbor a higher diversity of gut eukaryotes (whether pathogenic or commensal) in order to study protozoa interactions in the gut ecosystem. To this end, we profiled the gut bacterial microbiota of 134 healthy Cameroonian adults using 16S rRNA gene amplicon sequencing data. Entamoeba and Blastocystis presence and co-occurrence pattern in the same individuals were determined using metagenomic shotgun data. We found that, when taking into account both protozoa jointly, Blastocystis was associated with both a higher richness and a higher evenness of the gut bacterial microbiota, while Entamoeba was associated only with a higher richness. We demonstrated a cumulative influence of these protozoa on bacterial microbiome diversity. Furthermore, while the abundance of several common taxa (for example, Ruminococcaceae, Coprococcus and Butyrivibrio) varied according to Blastocystis colonization, only a single Bacteroides amplicon sequence variant was found to be differentially abundant between Entamoeba-negative and Entamoeba-positive samples. Given the specific signature of each protozoan on the gut microbiota and the seemingly stronger association for Blastocystis, our results suggest that Blastocystis and Entamoeba interact with gut bacteria each in its own way, but experimental studies are needed to explore the precise mechanisms of these interactions.}, } @article {pmid33815293, year = {2021}, author = {Yuan, X and Chen, R and Zhang, Y and Lin, X and Yang, X and McCormick, KL}, title = {Gut Microbiota of Chinese Obese Children and Adolescents With and Without Insulin Resistance.}, journal = {Frontiers in endocrinology}, volume = {12}, number = {}, pages = {636272}, pmid = {33815293}, issn = {1664-2392}, mesh = {Adolescent ; Angiopoietin-Like Protein 4/*biosynthesis ; Bacteria/genetics/metabolism ; Child ; China/epidemiology ; Cross-Sectional Studies ; Cytokines/blood/metabolism ; Diet ; Feces ; Female ; *Gastrointestinal Microbiome ; Genomics ; Glucose/metabolism ; Humans ; *Insulin Resistance ; Male ; Metagenome ; Pediatric Obesity/*metabolism ; Principal Component Analysis ; RNA, Ribosomal, 16S/metabolism ; }, abstract = {OBJECTIVE: The intestinal flora of gut microbiota in obese Chinese children and adolescents with and without insulin resistance (IR) was analyzed, as well as associations between the gut microbiota and two serum cytokines related to glucose metabolism, adropin and angiopoietin-like 4 (ANGPTL4).

METHODS: Clinical data, fecal bacterial composition, glucose-related hormones, and serum adipokines (adropin and ANGPTL4) were analyzed in 65 Chinese children with exogenous obesity. The composition of the gut microbiota was determined by 16S rRNA-based metagenomics and IR was calculated using the homeostasis model assessment (HOMA).

RESULTS: The 65 obese subjects were divided into two groups: insulin sensitive (IS) (n=40, 57.5% males) or IR (n=25, 60% males). Principal coordinates analysis revealed that the gut microbiota samples from the IS group clustered together and separated partly from the IR group (p=0.008). By Mann-Whitney U-test, at a phylum level, a reduction of Firmicutes and an increase of Bacteroidetes in the IR subjects was observed. LEfSe analysis revealed that IS subject, when compared to their IR counterparts, harbored members of the order Coriobacteriales, Turicibacterales, Pasteurellales and family Turicibacteraceae, that were significantly more abundant. In contrast, the IR subjects had members of family Peptococcaceae that were significantly more prevalent than the IS subjects (all p<0.05). Spearman's correlation analysis revealed that serum ANGPTL4 was positively associated with genus Bacteroides, Butyricimonas, and Alistipes, and adropin was positively associated with genus Anaerostipes and Alistipes, and negatively associated with genus Blautia (all p<0.05).

CONCLUSION: In obese children, the gut microbiome in IR subjects was significantly discordant from the IS subjects, and the abundance of some metabolism-related bacteria correlated with the serum concentrations of adropin and ANGPTL4. These observations infer that the gut microbiota may be involved in the regulation of glucose metabolism in obesity.}, } @article {pmid33815284, year = {2021}, author = {Silamiķele, L and Silamiķelis, I and Ustinova, M and Kalniņa, Z and Elbere, I and Petrovska, R and Kalniņa, I and Kloviņš, J}, title = {Metformin Strongly Affects Gut Microbiome Composition in High-Fat Diet-Induced Type 2 Diabetes Mouse Model of Both Sexes.}, journal = {Frontiers in endocrinology}, volume = {12}, number = {}, pages = {626359}, pmid = {33815284}, issn = {1664-2392}, mesh = {Animals ; Diabetes Mellitus, Type 2/*microbiology ; *Diet, High-Fat ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/*drug effects ; Hypoglycemic Agents/*pharmacology ; Male ; Metagenome/drug effects ; Metformin/*pharmacology ; Mice ; }, abstract = {Effects of metformin, the first-line drug for type 2 diabetes therapy, on gut microbiome composition in type 2 diabetes have been described in various studies both in human subjects and animals. However, the details of the molecular mechanisms of metformin action have not been fully understood. Moreover, there is a significant lack of information on how metformin affects gut microbiome composition in female mouse models, depending on sex and metabolic status in well controlled experimental setting. Our study aimed to examine metformin-induced alterations in gut microbiome diversity, composition, and functional implications of high-fat diet-induced type 2 diabetes mouse model, using, for the first time in mice study, the shotgun metagenomic sequencing that allows estimation of microorganisms at species level. We also employed a randomized block, factorial study design, and including 24 experimental units allocated to 8 treatment groups to systematically evaluate the effect of sex and metabolic status on metformin interaction with microbiome. We used DNA obtained from fecal samples representing gut microbiome before and after ten weeks-long metformin treatment. We identified 100 metformin-related differentially abundant species in high-fat diet-fed mice before and after the treatment, with most of the species relative abundances increased. In contrast, no significant changes were observed in control diet-fed mice. Functional analysis targeted to carbohydrate, lipid, and amino acid metabolism pathways revealed 14 significantly altered hierarchies. We also observed sex-specific differences in response to metformin treatment. Males experienced more pronounced changes in metabolic markers, while in females the extent of changes in gut microbiome representatives was more marked, indicated by 53 differentially abundant species with more remarkable Log fold changes compared to the combined-sex analysis. The same pattern manifested regarding the functional analysis, where we discovered 5 significantly affected hierarchies in female groups but not in males. Our results suggest that both sexes of animals should be included in future studies focusing on metformin effects on the gut microbiome.}, } @article {pmid33813690, year = {2021}, author = {Song, Y and Liu, X and de Hoog, GS and Li, R}, title = {Disseminated Cryptococcosis Presenting as Cellulitis Diagnosed by Laser Capture Microdissection: A Case Report and Literature Review.}, journal = {Mycopathologia}, volume = {186}, number = {3}, pages = {423-433}, pmid = {33813690}, issn = {1573-0832}, support = {7194326//Beijing Natural Science Foundation/ ; }, mesh = {*Cellulitis ; *Cryptococcosis ; Cryptococcus neoformans ; Humans ; Laser Capture Microdissection ; Mycoses ; }, abstract = {Disseminated cryptococcosis primarily affects immunosuppressed patients and has a poor outcome if diagnosis and treatment are delayed. Skin lesions are rarely manifest causing misdiagnosis. We present a case of cryptococcal cellulitis with severe pain in a kidney transplant recipient on long-term immunosuppressive therapy. Multiple organs were involved, and there was cutaneous dissemination of the lesions. Histopathology revealed abundant yeast-like cells with wide capsular halos in subcutaneous tissue, suggesting Cryptococcus spp. infection. Laser capture microdissection (LCM)-PCR on skin biopsies confirmed Cryptococcus neoformans var. grubii. A literature review of 17 cases of disseminated cryptococcosis with cutaneous cellulitis or panniculitis in HIV-negative individuals found that over half the patients (52.9%, 9/17) had a history of glucocorticoid therapy, and that the most common site was the legs (76.5%, 13/17). C. neoformans was the main pathogenic species, accounting for 88.2% (15/17) of cases. Fungal cellulitis should be included in the differential diagnosis of cellulitis that fails to respond to antimicrobial therapy in HIV-negative immunosuppressed individuals. Non-culture-based molecular techniques aid in rapid pathogen identification in histologically positive, unculturable specimens.}, } @article {pmid33813595, year = {2021}, author = {Rai, A and Bhattacharjee, A}, title = {Molecular profiling of microbial community structure and their CAZymes via metagenomics, from Tsomgo lake in the Eastern Himalayas.}, journal = {Archives of microbiology}, volume = {203}, number = {6}, pages = {3135-3146}, pmid = {33813595}, issn = {1432-072X}, mesh = {*Bacteria/classification/enzymology/genetics ; *Enzymes/genetics ; India ; *Lakes/microbiology ; *Metagenomics ; *Microbiota/genetics ; Phylogeny ; *Soil Microbiology ; }, abstract = {The present study is the first of its kind which is focused on Tsomgo lake, a high-altitude lake, located in the Eastern Himalayas of Sikkim. To get a major insight into the bacterial diversity, the shotgun sequencing was carried out in Illumina platform. Our results showed that both the samples TLSS1 (soil) and TLSW1 (water), had Proteobacteria as the most abundant taxa. Cluster of Orthologous group (COG) functional category of TLSS1 has 1,46,965 predicted functions. Cluster of Orthologous Group (COG) functional category of TLSW1 has 1,34,773 predicted functions. Kyoto Encyclopedia of Gene and Genomes (KEGG) functional category of TLSS1 has 1,76,825 predicted functions, most of the sequence fall in metabolism followed by Environmental information processing function. (KEGG) functional category of TLSW1 has 1,62,696 predicted functions and it follows the same pattern as TLSS1. Our studies also provide insight into the presence of distribution of different carbohydrate-active enzymes (CAZymes) present in Tsomgo lake. We have found that in case of both the samples TLSW1 and TLSS1, GlycosylTransferases were active followed by GlycosylHydrolase. The result found, represents for the first time very important findings related to the microbial diversity and the abundance of CAZymes in Tsomgo lake one of the pristine high-altitude lakes in Sikkim.}, } @article {pmid33812983, year = {2022}, author = {Wang, F and Song, M and Lu, X and Zhu, X and Deng, J}, title = {Gut microbes in gastrointestinal cancers.}, journal = {Seminars in cancer biology}, volume = {86}, number = {Pt 2}, pages = {967-975}, doi = {10.1016/j.semcancer.2021.03.037}, pmid = {33812983}, issn = {1096-3650}, mesh = {Humans ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; *Probiotics/therapeutic use ; Metagenomics ; *Gastrointestinal Neoplasms/etiology/therapy ; }, abstract = {Gut microbes (GMs), dominated by bacteria, play important roles in many physiological processes. The structures and functions of GMs are closely related to human health, the occurrence and development of diseases and the rapid recovery of the body. Gastrointestinal cancers are the major diseases affecting human health worldwide. With the development of metagenomic technology and the wide application of new generation sequencing technology, a large number of studies suggest that complex GMs are related to the occurrence and development of gastrointestinal cancers. Fecal microbiota transplantation (FMT) and probiotics can treat and prevent the occurrence of gastrointestinal cancers. This article reviews the latest research progress of microbes in gastrointestinal cancers from the perspectives of the correlation, the influence mechanism and the application, so as to provide new directions for the prevention, early diagnosis and treatment of gastrointestinal cancers.}, } @article {pmid33812357, year = {2021}, author = {Yang, S and Huang, Y and Li, C and Jin, L and Deng, W and Zhao, S and Wu, D and He, Y and Li, B and Yu, Z and Li, T and Zhang, Z and Pan, X and Zhang, H and Zou, L}, title = {The Fecal and Serum Metabolomics of Giant Pandas Based on Untargeted Metabolomics.}, journal = {Zoological science}, volume = {38}, number = {2}, pages = {179-186}, doi = {10.2108/zs200106}, pmid = {33812357}, issn = {0289-0003}, mesh = {Aging/blood/metabolism ; Animals ; Bacteria/genetics ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome ; Male ; Metabolomics/*methods ; Metagenome ; Penicillin G/analogs & derivatives ; Ursidae/blood/*metabolism ; }, abstract = {Little is comprehensively known or understood about giant panda fecal and serum metabolites, which could serve as important indicators of the physiological metabolism of giant pandas. Therefore, we determined the contents of fecal and serum metabolites of giant pandas based on an untargeted metabolome. Four hundred and 955 metabolites were detected in the feces and serum of giant panda, respectively. Glycerophospholipid and choline metabolism were the main metabolic pathways in feces and serum. A significant correlation between the gut microbiota and fecal metabolites was found (P < 0.01). Fecal metabolites were not greatly affected by the age or gender of giant pandas, but serum metabolites were significantly affected by age and gender. The majority of different metabolites caused by age were higher in serum of younger giant pandas, including fatty acids, lipids, metabolites of bile acids, and intermediate products of vitamin D3. The majority of different metabolites caused by gender included fatty acids, phosphatidylcholine (PC), phosphatidylserine (PS), and phosphatidylethanolamine (PE). A separate feeding diet should be considered according to different ages and genders of giant panda. Therefore, our results could provide helpful suggestions to further protect captive giant pandas.}, } @article {pmid33811235, year = {2021}, author = {Farrer, AG and Wright, SL and Skelly, E and Eisenhofer, R and Dobney, K and Weyrich, LS}, title = {Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {7456}, pmid = {33811235}, issn = {2045-2322}, mesh = {Biodiversity ; DNA, Ancient/*analysis ; *Decontamination ; Dental Calculus/*genetics/*microbiology ; Environment ; Humans ; Metagenomics ; Mouth/microbiology ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {Ancient DNA analysis of human oral microbial communities within calcified dental plaque (calculus) has revealed key insights into human health, paleodemography, and cultural behaviors. However, contamination imposes a major concern for paleomicrobiological samples due to their low endogenous DNA content and exposure to environmental sources, calling into question some published results. Decontamination protocols (e.g. an ethylenediaminetetraacetic acid (EDTA) pre-digestion or ultraviolet radiation (UV) and 5% sodium hypochlorite immersion treatments) aim to minimize the exogenous content of the outer surface of ancient calculus samples prior to DNA extraction. While these protocols are widely used, no one has systematically compared them in ancient dental calculus. Here, we compare untreated dental calculus samples to samples from the same site treated with four previously published decontamination protocols: a UV only treatment; a 5% sodium hypochlorite immersion treatment; a pre-digestion in EDTA treatment; and a combined UV irradiation and 5% sodium hypochlorite immersion treatment. We examine their efficacy in ancient oral microbiota recovery by applying 16S rRNA gene amplicon and shotgun sequencing, identifying ancient oral microbiota, as well as soil and skin contaminant species. Overall, the EDTA pre-digestion and a combined UV irradiation and 5% sodium hypochlorite immersion treatment were both effective at reducing the proportion of environmental taxa and increasing oral taxa in comparison to untreated samples. This research highlights the importance of using decontamination procedures during ancient DNA analysis of dental calculus to reduce contaminant DNA.}, } @article {pmid33811041, year = {2021}, author = {Bolte, LA and Vich Vila, A and Imhann, F and Collij, V and Gacesa, R and Peters, V and Wijmenga, C and Kurilshikov, A and Campmans-Kuijpers, MJE and Fu, J and Dijkstra, G and Zhernakova, A and Weersma, RK}, title = {Long-term dietary patterns are associated with pro-inflammatory and anti-inflammatory features of the gut microbiome.}, journal = {Gut}, volume = {70}, number = {7}, pages = {1287-1298}, pmid = {33811041}, issn = {1468-3288}, mesh = {Adult ; Bacteria/isolation & purification ; *Beverages ; Colitis, Ulcerative/*microbiology ; Crohn Disease/*microbiology ; *Diet ; Feces/microbiology ; *Food ; *Gastrointestinal Microbiome ; Humans ; Inflammation/microbiology/physiopathology ; Irritable Bowel Syndrome/*microbiology ; Metagenomics ; Middle Aged ; Surveys and Questionnaires ; Time Factors ; }, abstract = {OBJECTIVE: The microbiome directly affects the balance of pro-inflammatory and anti-inflammatory responses in the gut. As microbes thrive on dietary substrates, the question arises whether we can nourish an anti-inflammatory gut ecosystem. We aim to unravel interactions between diet, gut microbiota and their functional ability to induce intestinal inflammation.

DESIGN: We investigated the relation between 173 dietary factors and the microbiome of 1425 individuals spanning four cohorts: Crohn's disease, ulcerative colitis, irritable bowel syndrome and the general population. Shotgun metagenomic sequencing was performed to profile gut microbial composition and function. Dietary intake was assessed through food frequency questionnaires. We performed unsupervised clustering to identify dietary patterns and microbial clusters. Associations between diet and microbial features were explored per cohort, followed by a meta-analysis and heterogeneity estimation.

RESULTS: We identified 38 associations between dietary patterns and microbial clusters. Moreover, 61 individual foods and nutrients were associated with 61 species and 249 metabolic pathways in the meta-analysis across healthy individuals and patients with IBS, Crohn's disease and UC (false discovery rate<0.05). Processed foods and animal-derived foods were consistently associated with higher abundances of Firmicutes, Ruminococcus species of the Blautia genus and endotoxin synthesis pathways. The opposite was found for plant foods and fish, which were positively associated with short-chain fatty acid-producing commensals and pathways of nutrient metabolism.

CONCLUSION: We identified dietary patterns that consistently correlate with groups of bacteria with shared functional roles in both, health and disease. Moreover, specific foods and nutrients were associated with species known to infer mucosal protection and anti-inflammatory effects. We propose microbial mechanisms through which the diet affects inflammatory responses in the gut as a rationale for future intervention studies.}, } @article {pmid33810955, year = {2021}, author = {Tian, R and Liu, H and Feng, S and Wang, H and Wang, Y and Wang, Y and Liang, L and Xu, H and Xing, H and Zhang, S}, title = {Gut microbiota dysbiosis in stable coronary artery disease combined with type 2 diabetes mellitus influences cardiovascular prognosis.}, journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD}, volume = {31}, number = {5}, pages = {1454-1466}, doi = {10.1016/j.numecd.2021.01.007}, pmid = {33810955}, issn = {1590-3729}, mesh = {Aged ; Bacteria/drug effects/growth & development/*metabolism ; Biomarkers/blood ; Case-Control Studies ; Clostridiales/growth & development/metabolism ; Coronary Artery Disease/blood/diagnosis/*microbiology ; Diabetes Mellitus, Type 2/blood/diagnosis/drug therapy/*microbiology ; Dysbiosis ; Female ; *Gastrointestinal Microbiome/drug effects ; Host-Pathogen Interactions ; Humans ; Hypoglycemic Agents/therapeutic use ; Intestines/*microbiology ; Male ; Metabolomics ; Metagenomics ; Metformin/therapeutic use ; Middle Aged ; Prognosis ; Prospective Studies ; }, abstract = {BACKGROUND AND AIMS: Host-microbiota interactions involving metabolic pathways have been linked to the pathogenesis of atherosclerotic disease and type 2 diabetes. As stable coronary artery disease (SCAD) patients combined with type 2 diabetes have significantly increased risk for cardiac event, we focused on elucidating the role of microbiota affecting cardiometabolic disease development.

METHODS AND RESULTS: We used multi-omics analyses (metagenomics and metabolomics) of fecal and serum samples from a prospective cohort including stable coronary artery disease combined with diabetes mellitus (SCAD + T2DM, n = 38), SCAD (n = 71), and healthy control (HC, n = 55). We linked microbiome features to disease severity in a three-pronged association analysis and identified prognostic bacterial biomarkers. We identified that bacterial and metabolic signatures varied significantly between SCAD and SCAD + T2DM groups. SCAD + T2DM individuals were characterized by increased levels of aromatic amino acids and carbohydrates, which correlate with a gut microbiome with enriched biosynthetic potential. Our study also addressed how metformin may confound gut dysbiosis and increase the potential for nitrogen metabolism. In addition, we found that specific bacterial taxa Ruminococcus torques [HR: 2.363 (08-4.56), P = 0.03] was predictive of cardiac survival outcomes.

CONCLUSION: Overall, our study identified relationships between features of the gut microbiota (GM) and circulating metabolites, providing a new direction for future studies aiming to understand the host-GM interplay in atherosclerotic cardiovascular pathogenesis.}, } @article {pmid33810609, year = {2021}, author = {Uchida, F and Oh, S and Shida, T and Suzuki, H and Yamagata, K and Mizokami, Y and Bukawa, H and Tanaka, K and Shoda, J}, title = {Effects of Exercise on the Oral Microbiota and Saliva of Patients with Non-Alcoholic Fatty Liver Disease.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {7}, pages = {}, pmid = {33810609}, issn = {1660-4601}, mesh = {Bacteria/genetics ; Humans ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; *Non-alcoholic Fatty Liver Disease ; Saliva ; }, abstract = {Exercise can be hypothesized to play an important role in non-alcoholic fatty liver disease (NAFLD) treatment by changing the oral bacterial flora and in the mechanism underlying periodontal disease. We performed salivary component analysis before and after an exercise regimen, and genome analysis of the oral bacterial flora to elucidate the underlying mechanism. Obese middle-aged men with NAFLD and periodontal disease were allocated to 12-week exercise (n = 49) or dietary restriction (n = 21) groups. We collected saliva to compare the oral microflora; performed predictive analysis of metagenomic functions; and, measured the salivary immunoglobulin A, cytokine, bacterial lipopolysaccharide (LPS), and lactoferrin concentrations. The exercise group showed improvements in the clinical indices of oral environment. Salivary component analysis revealed significant reductions in LPS, and lactoferrin during the exercise regimen. Diversity analysis of oral bacterial flora revealed higher alpha- and beta-diversity after the exercise regimen. Analysis of the microbial composition revealed that the numbers of Campylobacter (+83.9%), Corynebacterium (+142.3%), Actinomyces (+75.9%), and Lautropia (+172.9%) were significantly higher, and that of Prevotella (-28.3%) was significantly lower. The findings suggest that an exercise regimen improves the oral environment of NAFLD patients by increasing the diversity of the oral microflora and reducing the number of periodontal bacteria that produce LPS and its capability.}, } @article {pmid33810508, year = {2021}, author = {Liu, J and He, X and Sun, J and Ma, Y}, title = {A Degeneration Gradient of Poplar Trees Contributes to the Taxonomic, Functional, and Resistome Diversity of Bacterial Communities in Rhizosphere Soils.}, journal = {International journal of molecular sciences}, volume = {22}, number = {7}, pages = {}, pmid = {33810508}, issn = {1422-0067}, support = {2017ZY14//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Bacterial/*genetics ; Metagenome ; Metagenomics ; *Microbial Consortia ; Plant Roots/microbiology ; Populus/*genetics/*microbiology ; *Rhizosphere ; Soil ; Soil Microbiology ; Trees/genetics ; }, abstract = {Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.}, } @article {pmid33810171, year = {2021}, author = {Ruocco, N and Esposito, R and Bertolino, M and Zazo, G and Sonnessa, M and Andreani, F and Coppola, D and Giordano, D and Nuzzo, G and Lauritano, C and Fontana, A and Ianora, A and Verde, C and Costantini, M}, title = {A Metataxonomic Approach Reveals Diversified Bacterial Communities in Antarctic Sponges.}, journal = {Marine drugs}, volume = {19}, number = {3}, pages = {}, pmid = {33810171}, issn = {1660-3397}, mesh = {Animals ; Antarctic Regions ; Bacteria/classification/*genetics/metabolism ; *Genome, Bacterial ; *Metagenome ; *Microbiota ; Phylogeny ; Porifera/*microbiology ; Secondary Metabolism ; }, abstract = {Marine sponges commonly host a repertoire of bacterial-associated organisms, which significantly contribute to their health and survival by producing several anti-predatory molecules. Many of these compounds are produced by sponge-associated bacteria and represent an incredible source of novel bioactive metabolites with biotechnological relevance. Although most investigations are focused on tropical and temperate species, to date, few studies have described the composition of microbiota hosted by Antarctic sponges and the secondary metabolites that they produce. The investigation was conducted on four sponges collected from two different sites in the framework of the XXXIV Italian National Antarctic Research Program (PNRA) in November-December 2018. Collected species were characterized as Mycale (Oxymycale) acerata, Haliclona (Rhizoniera) dancoi, Hemigellius pilosus and Microxina sarai by morphological analysis of spicules and amplification of four molecular markers. Metataxonomic analysis of these four Antarctic sponges revealed a considerable abundance of Amplicon Sequence Variants (ASVs) belonging to the phyla Proteobacteria, Bacteroidetes, Actinobacteria and Verrucomicrobia. In particular, M. (Oxymycale) acerata, displayed several genera of great interest, such as Endozoicomonas, Rubritalea, Ulvibacter, Fulvivirga and Colwellia. On the other hand, the sponges H. pilosus and H. (Rhizoniera) dancoi hosted bacteria belonging to the genera Pseudhongella, Roseobacter and Bdellovibrio, whereas M. sarai was the sole species showing some strains affiliated to the genus Polaribacter. Considering that most of the bacteria identified in the present study are known to produce valuable secondary metabolites, the four Antarctic sponges could be proposed as potential tools for the discovery of novel pharmacologically active compounds.}, } @article {pmid33810062, year = {2021}, author = {Ding, C and Wu, C and Guo, C and Gui, J and Wei, Y and Sun, J}, title = {The Composition and Primary Metabolic Potential of Microbial Communities Inhabiting the Surface Water in the Equatorial Eastern Indian Ocean.}, journal = {Biology}, volume = {10}, number = {3}, pages = {}, pmid = {33810062}, issn = {2079-7737}, abstract = {Currently, there is scant information about the biodiversity and functional diversity of microbes in the eastern Indian Ocean (EIO). Here, we used a combination of high-throughput sequencing of 16S rRNA genes and a metagenomic approach to investigate the microbial population structure and its metabolic function in the equatorial EIO. Our results show that Cyanobacterial Prochlorococcus made up the majority of the population. Interestingly, there were fewer contributions from clades SAR11 (Alphaproteobacteria) and SAR86 (Gammaproteobacteria) to microbial communities than contributions from Prochlorococcus. Based on functional gene analysis, functional genes rbcL, narB, and nasA were relatively abundant among the relevant genes. The abundance of Prochlorococcus implies its typically ecological adaptation in the local ecosystem. The microbial metabolic potential shows that in addition to the main carbon fixation pathway Calvin cycle, the rTCA cycle and the 3-HP/4-HB cycle have potential alternative carbon fixation contributions to local ecosystems. For the nitrogen cycle, the assimilatory nitrate and nitrite reduction pathway is potentially the crucial form of nitrogen utilization; unexpectedly, nitrogen fixation activity was relatively weak. This study extends our knowledge of the roles of microbes in energy and resource cycling in the EIO and provides a foundation for revealing profound biogeochemical processes driven by the microbial community in the ocean.}, } @article {pmid33809267, year = {2021}, author = {Lee, SY and Yuk, HG and Ko, SG and Cho, SG and Moon, GS}, title = {Gut Microbiome Prolongs an Inhibitory Effect of Korean Red Ginseng on High-Fat-Diet-Induced Mouse Obesity.}, journal = {Nutrients}, volume = {13}, number = {3}, pages = {}, pmid = {33809267}, issn = {2072-6643}, support = {Not relevant//Korean Society of Ginseng/ ; }, mesh = {Animals ; Blood Glucose/analysis ; Diet, High-Fat/*adverse effects ; Fluorescent Antibody Technique ; *Gastrointestinal Microbiome/genetics/physiology ; Insulin/blood ; Leptin/blood ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Obesity/*drug therapy/microbiology/pathology ; *Panax ; Pancreas/pathology ; Phytotherapy/*methods ; Plant Extracts/*therapeutic use ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Although the anti-obesity effect of Korean red ginseng (Panax ginseng Meyer) has been revealed, its underlying mechanisms are not clearly understood. Here, we demonstrate an involvement of gut microbiome in the inhibitory effect of Korean red ginseng on high-fat-diet (HFD)-induced mouse obesity, and further provides information on the effects of saponin-containing red ginseng extract (SGE) and saponin-depleted red ginseng extract (GE). Mice were fed with either SGE or GE every third day for one month, and their food intakes, fat weights, plasma glucose, and insulin and leptin levels were measured. Immunofluorescence assays were conducted to measure pancreatic islet size. Stools from the mice were subjected to metagenomic analysis. Both SGE and GE attenuated HFD-induced gain of body weight, reducing HFD-induced increase of food intakes and fat weights. They also reduced HFD-increased plasma glucose, insulin, and leptin levels, decreased both fasting and postprandial glucose concentrations, and improved both insulin resistance and glucose intolerance. Immunofluorescence assays revealed that they blocked HFD-induced increase of pancreatic islet size. Our pyrosequencing of the 16S rRNA gene V3 region from stools revealed that both SGE and GE modulated HFD-altered composition of gut microbiota. Therefore, we conclude that Korean red ginseng inhibits HFD-induced obesity and diabetes by altering gut microbiome.}, } @article {pmid33808194, year = {2021}, author = {Lee, CB and Chae, SU and Jo, SJ and Jerng, UM and Bae, SK}, title = {The Relationship between the Gut Microbiome and Metformin as a Key for Treating Type 2 Diabetes Mellitus.}, journal = {International journal of molecular sciences}, volume = {22}, number = {7}, pages = {}, pmid = {33808194}, issn = {1422-0067}, support = {2018R1A6A1A03025108//Basic Science Research Program through the National Research Foundation/ ; HF20C0002//Korea Health Technology R&D Project/ ; 2020//Research Fund of The Catholic University of Korea/ ; }, mesh = {Bile Acids and Salts/metabolism ; Blood Glucose/metabolism ; Diabetes Mellitus, Type 2/*drug therapy/immunology/*microbiology ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/drug effects/*physiology ; Humans ; Hypoglycemic Agents/pharmacology/*therapeutic use ; Metformin/pharmacology/*therapeutic use ; }, abstract = {Metformin is the first-line pharmacotherapy for treating type 2 diabetes mellitus (T2DM); however, its mechanism of modulating glucose metabolism is elusive. Recent advances have identified the gut as a potential target of metformin. As patients with metabolic disorders exhibit dysbiosis, the gut microbiome has garnered interest as a potential target for metabolic disease. Henceforth, studies have focused on unraveling the relationship of metabolic disorders with the human gut microbiome. According to various metagenome studies, gut dysbiosis is evident in T2DM patients. Besides this, alterations in the gut microbiome were also observed in the metformin-treated T2DM patients compared to the non-treated T2DM patients. Thus, several studies on rodents have suggested potential mechanisms interacting with the gut microbiome, including regulation of glucose metabolism, an increase in short-chain fatty acids, strengthening intestinal permeability against lipopolysaccharides, modulating the immune response, and interaction with bile acids. Furthermore, human studies have demonstrated evidence substantiating the hypotheses based on rodent studies. This review discusses the current knowledge of how metformin modulates T2DM with respect to the gut microbiome and discusses the prospect of harnessing this mechanism in treating T2DM.}, } @article {pmid33807914, year = {2021}, author = {Litvinova, EA and Bets, VD and Feofanova, NA and Gvozdeva, OV and Achasova, KM and Alperina, EL and Kozhevnikova, EN}, title = {Dietary Fucose Affects Macrophage Polarization and Reproductive Performance in Mice.}, journal = {Nutrients}, volume = {13}, number = {3}, pages = {}, pmid = {33807914}, issn = {2072-6643}, support = {0259-2019-0004-C-01//Governmental project/ ; 0538-2019-0005//Budgetary funding for basic scientific research/ ; 18-015-00329//Russian Foundation for Basic Research/ ; 19-015-00169//Russian Foundation for Basic Research/ ; 20-64-47020//Russian Science Foundation/ ; 20-74-10022//Russian Science Foundation/ ; }, mesh = {Animals ; *Dietary Supplements ; Embryo Implantation/drug effects ; Female ; Fucose/*adverse effects ; Gastrointestinal Microbiome/drug effects ; Intestinal Mucosa/drug effects ; Macrophage Activation/*drug effects ; Macrophages/drug effects ; Metagenomics ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Mucin-2/*metabolism ; Mucus/drug effects ; Pregnancy ; Reproduction/*drug effects ; }, abstract = {Intestinal mucus protects epithelial and immune cells from the gut resident microorganisms, and provides growth-promoting factors as mucus-derived O-glycans for beneficial bacteria. A lack of intestinal protective mucus results in changes in the commensal microflora composition, mucosal immune system reprogramming, and inflammation. Previous work has shown that fucose, the terminal glycan chain component of the intestinal glycoprotein Mucin2, and fucoidan polysaccharides have an anti-inflammatory effect in some mouse models of colitis. This study evaluates the effect of fucose on reproductive performance in heterozygous mutant Muc2 female mice. We found that even though Muc2[+/-] females are physiologically indistinguishable from C57Bl/6 mice, they have a significantly reduced reproductive performance upon dietary fucose supplementation. Metagenomic analysis reveals that the otherwise healthy wild-type siblings of Muc2[-/-] animals have reduced numbers of some of the intestinal commensal bacterial species, compared to C57BL/6 mice. We propose that the changes in beneficial microflora affect the immune status in Muc2[+/-] mice, which causes implantation impairment. In accordance with this hypothesis, we find that macrophage polarization during pregnancy is impaired in Muc2[+/-] females upon addition of fucose. Metabolic profiling of peritoneal macrophages from Muc2[+/-] females reveals their predisposition towards anaerobic glycolysis in favor of oxidative phosphorylation, compared to C57BL/6-derived cells. In vitro experiments on phagocytosis activity and mitochondrial respiration suggest that fucose affects oxidative phosphorylation in a genotype-specific manner, which might interfere with implantation depending on the initial status of macrophages. This hypothesis is further confirmed in BALB/c female mice, where fucose caused pregnancy loss and opposed implantation-associated M2 macrophage polarization. Taken together, these data suggest that intestinal microflora affects host immunity and pregnancy outcome. At the same time, dietary fucose might act as a differential regulator of macrophage polarization during implantation, depending on the immune status of the host.}, } @article {pmid33806135, year = {2021}, author = {Saturio, S and Nogacka, AM and Suárez, M and Fernández, N and Mantecón, L and Mancabelli, L and Milani, C and Ventura, M and de Los Reyes-Gavilán, CG and Solís, G and Arboleya, S and Gueimonde, M}, title = {Early-Life Development of the Bifidobacterial Community in the Infant Gut.}, journal = {International journal of molecular sciences}, volume = {22}, number = {7}, pages = {}, pmid = {33806135}, issn = {1422-0067}, support = {EarlyMicroHealth//Joint Programming Initiative A healthy diet for a healthy life/ ; AGL2017-83653R//Agencia Estatal de Investigación/ ; 749255//FP7 People: Marie-Curie Actions/ ; IJCI-2017-32156//Ministerio de Ciencia, Innovación y Universidades/ ; }, mesh = {Bifidobacterium/*physiology ; Child Nutrition Sciences ; DNA, Intergenic/genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Male ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Temperature ; }, abstract = {The establishment of the gut microbiota poses implications for short and long-term health. Bifidobacterium is an important taxon in early life, being one of the most abundant genera in the infant intestinal microbiota and carrying out key functions for maintaining host-homeostasis. Recent metagenomic studies have shown that different factors, such as gestational age, delivery mode, or feeding habits, affect the gut microbiota establishment at high phylogenetic levels. However, their impact on the specific bifidobacterial populations is not yet well understood. Here we studied the impact of these factors on the different Bifidobacterium species and subspecies at both the quantitative and qualitative levels. Fecal samples were taken from 85 neonates at 2, 10, 30, 90 days of life, and the relative proportions of the different bifidobacterial populations were assessed by 16S rRNA-23S rRNA internal transcribed spacer (ITS) region sequencing. Absolute levels of the main species were determined by q-PCR. Our results showed that the bifidobacterial population establishment is affected by gestational age, delivery mode, and infant feeding, as it is evidenced by qualitative and quantitative changes. These data underline the need for understanding the impact of perinatal factors on the gut microbiota also at low taxonomic levels, especially in the case of relevant microbial populations such as Bifidobacterium. The data obtained provide indications for the selection of the species best suited for the development of bifidobacteria-based products for different groups of neonates and will help to develop rational strategies for favoring a healthy early microbiota development when this process is challenged.}, } @article {pmid33805379, year = {2021}, author = {Su, H and Xiao, Z and Yu, K and Zhang, Q and Lu, C and Wang, G and Wang, Y and Liang, J and Huang, W and Huang, X and Wei, F}, title = {High Diversity of β-Glucosidase-Producing Bacteria and Their Genes Associated with Scleractinian Corals.}, journal = {International journal of molecular sciences}, volume = {22}, number = {7}, pages = {}, pmid = {33805379}, issn = {1422-0067}, support = {42030502//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 41706158//National Natural Science Foundation of China/ ; AD19245121//Science and Technology Project of Guangxi/ ; AD17129019//Science and Technology Project of Guangxi/ ; AD17129063//Science and Technology Project of Guangxi/ ; AA17204074//Science and Technology Project of Guangxi/ ; AA18242026//Major Research Project of Guangxi for Science and Technology/ ; 2018GXNSFBA281101//Natural Science Foundation of Guangxi Province/ ; }, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*enzymology/genetics ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; beta-Glucosidase/*genetics/metabolism ; }, abstract = {β-Glucosidase is a microbial cellulose multienzyme that plays an important role in the regulation of the entire cellulose hydrolysis process, which is the rate-limiting step in bacterial carbon cycling in marine environments. Despite its importance in coral reefs, the diversity of β-glucosidase-producing bacteria, their genes, and enzymatic characteristics are poorly understood. In this study, 87 β-glucosidase-producing cultivable bacteria were screened from 6 genera of corals. The isolates were assigned to 21 genera, distributed among three groups: Proteobacteria, Firmicutes, and Actinobacteria. In addition, metagenomics was used to explore the genetic diversity of bacterial β-glucosidase enzymes associated with scleractinian corals, which revealed that these enzymes mainly belong to the glycosidase hydrolase family 3 (GH3). Finally, a novel recombinant β-glucosidase, referred to as Mg9373, encompassing 670 amino acids and a molecular mass of 75.2 kDa, was classified as a member of the GH3 family and successfully expressed and characterized. Mg9373 exhibited excellent tolerance to ethanol, NaCl, and glucose. Collectively, these results suggest that the diversity of β-glucosidase-producing bacteria and genes associated with scleractinian corals is high and novel, indicating great potential for applications in the food industry and agriculture.}, } @article {pmid33803228, year = {2021}, author = {Marter, P and Huang, S and Brinkmann, H and Pradella, S and Jarek, M and Rohde, M and Bunk, B and Petersen, J}, title = {Filling the Gaps in the Cyanobacterial Tree of Life-Metagenome Analysis of Stigonema ocellatum DSM 106950, Chlorogloea purpurea SAG 13.99 and Gomphosphaeria aponina DSM 107014.}, journal = {Genes}, volume = {12}, number = {3}, pages = {}, pmid = {33803228}, issn = {2073-4425}, mesh = {Cyanobacteria/*genetics ; Genome, Bacterial/genetics ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/genetics ; Phylogeny ; }, abstract = {Cyanobacteria represent one of the most important and diverse lineages of prokaryotes with an unparalleled morphological diversity ranging from unicellular cocci and characteristic colony-formers to multicellular filamentous strains with different cell types. Sequencing of more than 1200 available reference genomes was mainly driven by their ecological relevance (Prochlorococcus, Synechococcus), toxicity (Microcystis) and the availability of axenic strains. In the current study three slowly growing non-axenic cyanobacteria with a distant phylogenetic positioning were selected for metagenome sequencing in order to (i) investigate their genomes and to (ii) uncover the diversity of associated heterotrophs. High-throughput Illumina sequencing, metagenomic assembly and binning allowed us to establish nearly complete high-quality draft genomes of all three cyanobacteria and to determine their phylogenetic position. The cyanosphere of the limnic isolates comprises up to 40 heterotrophic bacteria that likely coexisted for several decades, and it is dominated by Alphaproteobacteria and Bacteriodetes. The diagnostic marker protein RpoB ensured in combination with our novel taxonomic assessment via BLASTN-dependent text-mining a reliable classification of the metagenome assembled genomes (MAGs). The detection of one new family and more than a dozen genera of uncultivated heterotrophic bacteria illustrates that non-axenic cyanobacteria are treasure troves of hidden microbial diversity.}, } @article {pmid33803225, year = {2021}, author = {Nieuwenhuijse, DF and Oude Munnink, BB and Koopmans, MPG}, title = {viromeBrowser: A Shiny App for Browsing Virome Sequencing Analysis Results.}, journal = {Viruses}, volume = {13}, number = {3}, pages = {}, pmid = {33803225}, issn = {1999-4915}, mesh = {Base Sequence/genetics ; Computational Biology/*methods ; Data Analysis ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/instrumentation/*methods ; Molecular Sequence Annotation/*methods ; Software ; Virome/*genetics ; }, abstract = {Experiments in which complex virome sequencing data is generated remain difficult to explore and unpack for scientists without a background in data science. The processing of raw sequencing data by high throughput sequencing workflows usually results in contigs in FASTA format coupled to an annotation file linking the contigs to a reference sequence or taxonomic identifier. The next step is to compare the virome of different samples based on the metadata of the experimental setup and extract sequences of interest that can be used in subsequent analyses. The viromeBrowser is an application written in the opensource R shiny framework that was developed in collaboration with end-users and is focused on three common data analysis steps. First, the application allows interactive filtering of annotations by default or custom quality thresholds. Next, multiple samples can be visualized to facilitate comparison of contig annotations based on sample specific metadata values. Last, the application makes it easy for users to extract sequences of interest in FASTA format. With the interactive features in the viromeBrowser we aim to enable scientists without a data science background to compare and extract annotation data and sequences from virome sequencing analysis results.}, } @article {pmid33798253, year = {2021}, author = {Cho, JC}, title = {Human microbiome privacy risks associated with summary statistics.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0249528}, pmid = {33798253}, issn = {1932-6203}, mesh = {*Computer Simulation ; Humans ; *Metagenomics ; *Microbiota ; *Privacy ; }, abstract = {Recognizing that microbial community composition within the human microbiome is associated with the physiological state of the host has sparked a large number of human microbiome association studies (HMAS). With the increasing size of publicly available HMAS data, the privacy risk is also increasing because HMAS metadata could contain sensitive private information. I demonstrate that a simple test statistic based on the taxonomic profiles of an individual's microbiome along with summary statistics of HMAS data can reveal the membership of the individual's microbiome in an HMAS sample. In particular, species-level taxonomic data obtained from small-scale HMAS can be highly vulnerable to privacy risk. Minimal guidelines for HMAS data privacy are suggested, and an assessment of HMAS privacy risk using the simulation method proposed is recommended at the time of study design.}, } @article {pmid33798237, year = {2021}, author = {Dizzell, S and Stearns, JC and Li, J and van Best, N and Bervoets, L and Mommers, M and Penders, J and Morrison, KM and Hutton, EK and , }, title = {Investigating colonization patterns of the infant gut microbiome during the introduction of solid food and weaning from breastmilk: A cohort study protocol.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0248924}, pmid = {33798237}, issn = {1932-6203}, support = {MOP-136811//CIHR/Canada ; IMG-143923//CIHR/Canada ; }, mesh = {Humans ; Infant ; Cohort Studies ; Diet ; *Feces/microbiology ; *Gastrointestinal Microbiome ; *Weaning ; Observational Studies as Topic ; }, abstract = {The first exposures to microbes occur during infancy and it is suggested that this initial colonization influences the adult microbiota composition. Despite the important role that the gut microbiome may have in health outcomes later in life, the factors that influence its development during infancy and early childhood have not been characterized fully. Guidelines about the introduction of solid foods and cessation of breastfeeding, which is thought to have a significant role in the transition to a more adult-like microbiota, are not based on microbiome research. There is even less understanding of approaches used to transition to solid food in the preterm population. The purpose of this study is to identify the impact of early life dietary events on gut microbiome community structures and function among infants born at term and pre-term. We plan to prospectively monitor the gut microbiome of infants during two critical timepoints in microbial development: the introduction of solid foods and cessation from breastmilk. A total of 35 participants from three primary observational birth cohorts (two full-term cohorts and one pre-term cohort) will be enrolled in this sub-study. Participants will be asked to collect stool samples and fill out a study diary before, during and after the introduction of solids and again during weaning from breastmilk. We will use frequent fecal sampling analyzed using 16S rRNA gene profiling, metagenomics, metabolomics, and targeted bacterial culturing to identify and characterize the microbial communities, as well as provide insight into the phenotypic characteristics and functional capabilities of the microbes present during these transitional periods of infancy. This study will provide a comprehensive approach to detailing the effects of dietary transition from breastmilk to a more adult-like solid food diet on the microbiome and in doing so will contribute to evidence-based infant nutrition guidance.}, } @article {pmid33796482, year = {2021}, author = {Chen, Z and Cheng, H and Cai, Z and Wei, Q and Li, J and Liang, J and Zhang, W and Yu, Z and Liu, D and Liu, L and Zhang, Z and Wang, K and Yang, L}, title = {Identification of Microbiome Etiology Associated With Drug Resistance in Pleural Empyema.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {637018}, pmid = {33796482}, issn = {2235-2988}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria ; Drug Resistance, Microbial ; *Empyema, Pleural/drug therapy ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {Identification of the offending organism and appropriate antimicrobial therapy are crucial for treating empyema. Diagnosis of empyema is largely obscured by the conventional bacterial cultivation and PCR process that has relatively low sensitivity, leading to limited understanding of the etiopathogenesis, microbiology, and role of antibiotics in the pleural cavity. To expand our understanding of its pathophysiology, we have carried out a metagenomic snapshot of the pleural effusion from 45 empyema patients by Illumina sequencing platform to assess its taxonomic, and antibiotic resistome structure. Our results showed that the variation of microbiota in the pleural effusion is generally stratified, not continuous. There are two distinct microbiome clusters observed in the forty-five samples: HA-SA type and LA-SA type. The categorization is mostly driven by species composition: HA-SA type is marked by Staphylococcus aureus as the core species, with other enriched 6 bacteria and 3 fungi, forming a low diversity and highly stable microbial community; whereas the LA-SA type has a more diverse microbial community with a distinct set of bacterial species that are assumed to be the oral origin. The microbial community does not shape the dominant antibiotic resistance classes which were common in the two types, while the increase of microbial diversity was correlated with the increase in antibiotic resistance genes. The existence of well-balanced microbial symbiotic states might respond differently to pathogen colonization and drug intake. This study provides a deeper understanding of the pathobiology of pleural empyema and suggests that potential resistance genes may hinder the antimicrobial therapy of empyema.}, } @article {pmid33795775, year = {2021}, author = {Boccella, N and Paolillo, R and Coretti, L and D'Apice, S and Lama, A and Giugliano, G and Schiattarella, GG and Cuomo, M and d'Aquino, I and Cavaliere, G and Paciello, O and Mollica, MP and Mattace Raso, G and Esposito, G and Lembo, F and Perrino, C}, title = {Transverse aortic constriction induces gut barrier alterations, microbiota remodeling and systemic inflammation.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {7404}, pmid = {33795775}, issn = {2045-2322}, mesh = {Animals ; Aortic Valve Stenosis/*complications/diagnosis ; Biomarkers ; Disease Models, Animal ; Disease Susceptibility ; Dysbiosis ; Echocardiography ; Feces/microbiology ; *Gastrointestinal Microbiome ; Heart Failure/diagnosis/etiology ; Heart Function Tests ; Inflammation/*etiology/metabolism/pathology ; Intestinal Mucosa/*metabolism/*microbiology ; Metagenome ; Metagenomics/methods ; Mice ; Permeability ; Ventricular Remodeling ; }, abstract = {Accumulating evidence suggests that modifications of gut function and microbiota composition might play a pivotal role in the pathophysiology of several cardiovascular diseases, including heart failure (HF). In this study we systematically analysed gut microbiota composition, intestinal barrier integrity, intestinal and serum cytokines and serum endotoxin levels in C57BL/6 mice undergoing pressure overload by transverse aortic constriction (TAC) for 1 and 4 weeks. Compared to sham-operated animals, TAC induced prompt and strong weakening of intestinal barrier integrity, long-lasting decrease of colon anti-inflammatory cytokine levels, significant increases of serum levels of bacterial lipopolysaccharide and proinflammatory cytokines. TAC also exerted effects on microbiota composition, inducing significant differences in bacterial genera inside Actinobacteria, Firmicutes, Proteobacteria and TM7 phyla as shown by 16S rDNA sequencing of fecal samples from TAC or sham mice. These results suggest that gut modifications represent an important element to be considered in the development and progression of cardiac dysfunction in response to TAC and support this animal model as a valuable tool to establish the role and mechanisms of gut-heart crosstalk in HF. Evidence arising in this field might identify new treatment options targeting gut integrity and microbiota components to face adverse cardiac events.}, } @article {pmid33795699, year = {2021}, author = {Kohl, C and Brinkmann, A and Radonić, A and Dabrowski, PW and Mühldorfer, K and Nitsche, A and Wibbelt, G and Kurth, A}, title = {The virome of German bats: comparing virus discovery approaches.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {7430}, pmid = {33795699}, issn = {2045-2322}, mesh = {Animals ; Chiroptera/*virology ; Chlorocebus aethiops ; *Genome, Viral ; Germany ; High-Throughput Nucleotide Sequencing ; Nairovirus/classification/genetics ; Orbivirus/classification/genetics ; Phylogeny ; Polymerase Chain Reaction ; Rotavirus/classification/genetics ; Vero Cells ; Virome/*genetics ; Viruses/classification/genetics ; }, abstract = {Bats are known to be reservoirs of several highly pathogenic viruses. Hence, the interest in bat virus discovery has been increasing rapidly over the last decade. So far, most studies have focused on a single type of virus detection method, either PCR, virus isolation or virome sequencing. Here we present a comprehensive approach in virus discovery, using all three discovery methods on samples from the same bats. By family-specific PCR screening we found sequences of paramyxoviruses, adenoviruses, herpesviruses and one coronavirus. By cell culture we isolated a novel bat adenovirus and bat orthoreovirus. Virome sequencing revealed viral sequences of ten different virus families and orders: three bat nairoviruses, three phenuiviruses, one orbivirus, one rotavirus, one orthoreovirus, one mononegavirus, five parvoviruses, seven picornaviruses, three retroviruses, one totivirus and two thymoviruses were discovered. Of all viruses identified by family-specific PCR in the original samples, none was found by metagenomic sequencing. Vice versa, none of the viruses found by the metagenomic virome approach was detected by family-specific PCRs targeting the same family. The discrepancy of detected viruses by different detection approaches suggests that a combined approach using different detection methods is necessary for virus discovery studies.}, } @article {pmid33795522, year = {2021}, author = {Wang, H and Ren, S and Lv, H and Cao, L}, title = {Gut microbiota from mice with cerebral ischemia-reperfusion injury affects the brain in healthy mice.}, journal = {Aging}, volume = {13}, number = {7}, pages = {10058-10074}, pmid = {33795522}, issn = {1945-4589}, mesh = {Animals ; Anxiety/metabolism ; Behavior, Animal/physiology ; Brain/*metabolism ; Brain Ischemia/*metabolism ; *Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/*physiology ; Male ; Memory/physiology ; Metagenome ; Mice ; Neuronal Plasticity/physiology ; Reperfusion Injury ; }, abstract = {Gut microorganisms can profoundly influence brain function in the host and their behavior. Since altered brain functional connectivity (FC) has been implicated in various cerebrovascular disorders, including cerebral ischemia-reperfusion (I/R) injury, we hypothesized that gut microbiota in mice with cerebral I/R injury would affect brain FC when transplanted into germ-free mice. Metagenomic analysis of germ-free male C57BL/6J mice colonized with microbiota from mice with and without cerebral I/R injury showed a clear distinction in microbiota composition between mice colonized with control and I/R microbiota. The I/R microbiota-colonized mice showed decreased FC in the cingulate cortex, hippocampus, and thalamus, and exhibited increased anxiety as well as diminished spatial learning and memory and short-term object recognition memory. I/R microbiota-colonized mice also had significantly reduced dendritic spine density and synaptic protein levels and exhibited increased hippocampal inflammation. These results indicate that gut microbiota components from mice with cerebral I/R injury can alter animal behavior, brain functional connectivity, hippocampal neuronal plasticity, and neuroinflammation. Moreover, they increase our understanding of the mechanisms through which the gut microbiome contributes to the pathobiology of cerebrovascular diseases.}, } @article {pmid33795009, year = {2021}, author = {Stamboulian, M and Li, S and Ye, Y}, title = {Using high-abundance proteins as guides for fast and effective peptide/protein identification from human gut metaproteomic data.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {80}, pmid = {33795009}, issn = {2049-2618}, support = {R01 AI108888/AI/NIAID NIH HHS/United States ; R01 AI143254/AI/NIAID NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; Peptides/genetics ; Proteomics ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: A few recent large efforts significantly expanded the collection of human-associated bacterial genomes, which now contains thousands of entities including reference complete/draft genomes and metagenome assembled genomes (MAGs). These genomes provide useful resource for studying the functionality of the human-associated microbiome and their relationship with human health and diseases. One application of these genomes is to provide a universal reference for database search in metaproteomic studies, when matched metagenomic/metatranscriptomic data are unavailable. However, a greater collection of reference genomes may not necessarily result in better peptide/protein identification because the increase of search space often leads to fewer spectrum-peptide matches, not to mention the drastic increase of computation time. Video Abstract METHODS: Here, we present a new approach that uses two steps to optimize the use of the reference genomes and MAGs as the universal reference for human gut metaproteomic MS/MS data analysis. The first step is to use only the high-abundance proteins (HAPs) (i.e., ribosomal proteins and elongation factors) for metaproteomic MS/MS database search and, based on the identification results, to derive the taxonomic composition of the underlying microbial community. The second step is to expand the search database by including all proteins from identified abundant species. We call our approach HAPiID (HAPs guided metaproteomics IDentification).

RESULTS: We tested our approach using human gut metaproteomic datasets from a previous study and compared it to the state-of-the-art reference database search method MetaPro-IQ for metaproteomic identification in studying human gut microbiota. Our results show that our two-steps method not only performed significantly faster but also was able to identify more peptides. We further demonstrated the application of HAPiID to revealing protein profiles of individual human-associated bacterial species, one or a few species at a time, using metaproteomic data.

CONCLUSIONS: The HAP guided profiling approach presents a novel effective way for constructing target database for metaproteomic data analysis. The HAPiID pipeline built upon this approach provides a universal tool for analyzing human gut-associated metaproteomic data.}, } @article {pmid33794735, year = {2021}, author = {Copeland, JK and Chao, G and Vanderhout, S and Acton, E and Wang, PW and Benchimol, EI and El Sohami, A and Croitoru, K and Gommerman, JL and Guttman, DS and , }, title = {The Impact of Migration on the Gut Metagenome of South Asian Canadians.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-29}, pmid = {33794735}, issn = {1949-0984}, support = {//CIHR/Canada ; }, mesh = {Adolescent ; Adult ; Asian People ; Bacteria/classification/genetics ; Biodiversity ; Canada ; Cohort Studies ; DNA, Bacterial ; Diet ; Emigrants and Immigrants ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Immune System Diseases/*microbiology ; Inflammation/*microbiology ; Male ; *Metagenome ; Metagenomics/methods ; Prevotella/classification/genetics ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {South Asian (SA) Canadian immigrants have a higher risk of developing certain immune-mediated inflammatory diseases compared to non-migrant SAs. We sought to investigate the effect of migration on the gut metagenome and to identify microbiological associations between migration and conditions that may influence the development of immune-mediated inflammatory diseases. Metagenomic analysis of 58 first-generation (GEN1) SA immigrants and 38 unrelated Canadian born children-of-immigrants (GEN2) determined that the time lived in Canada was associated with continued changes in gut microbial communities. Migration of GEN1 to Canada early in life results in a gut community with similarities to GEN2 SA Canadians and non-SA North Americans. Conversely, GEN1 immigrants who arrived recently to Canada exhibited pronounced differences from GEN2, while displaying microbial similarities to a non-migrating SA cohort. Multivariate analysis identified that community composition was primarily influenced by high abundance taxa. Prevotella copri dominated in GEN1 and non-migrant SAs. Clostridia and functionally related Bacteroidia spp. replaced P. copri dominance over generations in Canada. Mutually exclusive Dialister species occurred at differing relative abundances over time and generations in Canada. This shift in species composition is accompanied by a change in genes associated with carbohydrate utilization and short-chain fatty acid production. Total energy derived from carbohydrates compared to protein consumption was significantly higher for GEN1 recent immigrants, which may influence the functional requirements of the gut community. This study demonstrates the associations between migration and the gut microbiome, which may be further associated with the altered risk of immune-mediated inflammatory diseases observed for SA Canadians.}, } @article {pmid33794724, year = {2021}, author = {Manrique, P and Zhu, Y and van der Oost, J and Herrema, H and Nieuwdorp, M and de Vos, WM and Young, M}, title = {Gut bacteriophage dynamics during fecal microbial transplantation in subjects with metabolic syndrome.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-15}, pmid = {33794724}, issn = {1949-0984}, support = {R01 GM117361/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Aged ; Bacteria/*virology ; *Bacteriophages ; Biodiversity ; Fecal Microbiota Transplantation/*methods ; Feces/virology ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; Male ; Metabolic Syndrome/*microbiology/*therapy ; Middle Aged ; Pilot Projects ; Young Adult ; }, abstract = {Metabolic Syndrome (MetS) is a growing public health concern worldwide. Individuals with MetS have an increased risk for cardiovascular (CV) disease and type 2 diabetes (T2D). These diseases - in part preventable with the treatment of MetS - increase the chances of premature death and pose a great economic burden to health systems. A healthy gut microbiota is associated with a reduction in MetS, T2D, and CV disease. Treatment of MetS with fecal microbiota transplantation (FMT) can be effective, however, its success rate is intermediate and difficult to predict. Because bacteriophages significantly affect the microbiota membership and function, the aim of this pilot study was to explore the dynamics of the gut bacteriophage community after FMT in MetS subjects. We performed a longitudinal study of stool bacteriophages from healthy donors and MetS subjects before and after FMT treatment. Subjects were assigned to either a control group (self-stool transplant, n = 3) or a treatment group (healthy-donor-stool transplant; n-recipients = 6, n-donors = 5). Stool samples were collected over an 18-week period and bacteriophage-like particles were purified and sequenced. We found that FMT from healthy donors significantly alters the gut bacteriophage community. Subjects with better clinical outcome clustered closer to the heathy donor group, suggesting that throughout the treatment, their bacteriophage community was more similar to healthy donors. Finally, we identified bacteriophage groups that could explain these differences and we examined their prevalence in individuals from a larger cohort of MetS FMT trial.Trial information- http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=2705; NTR 2705.}, } @article {pmid33792639, year = {2021}, author = {Commichaux, S and Shah, N and Ghurye, J and Stoppel, A and Goodheart, JA and Luque, GG and Cummings, MP and Pop, M}, title = {A critical assessment of gene catalogs for metagenomic analysis.}, journal = {Bioinformatics (Oxford, England)}, volume = {37}, number = {18}, pages = {2848-2857}, pmid = {33792639}, issn = {1367-4811}, support = {ZUK 63//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Metagenome ; *Microbiota/genetics ; Metagenomics ; }, abstract = {MOTIVATION: Microbial gene catalogs are data structures that organize genes found in microbial communities, providing a reference for standardized analysis of the microbes across samples and studies. Although gene catalogs are commonly used, they have not been critically evaluated for their effectiveness as a basis for metagenomic analyses.

RESULTS: As a case study, we investigate one such catalog, the Integrated Gene Catalog (IGC), however, our observations apply broadly to most gene catalogs constructed to date. We focus on both the approach used to construct this catalog and on its effectiveness when used as a reference for microbiome studies. Our results highlight important limitations of the approach used to construct the IGC and call into question the broad usefulness of gene catalogs more generally. We also recommend best practices for the construction and use of gene catalogs in microbiome studies and highlight opportunities for future research.

All supporting scripts for our analyses can be found on GitHub: https://github.com/SethCommichaux/IGC.git. The supporting data can be downloaded from: https://obj.umiacs.umd.edu/igc-analysis/IGC_analysis_data.tar.gz.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid33791954, year = {2021}, author = {de Oliveira Santos, L and Guedes, IA and Azevedo, SMFOE and Pacheco, ABF}, title = {Occurrence and diversity of viruses associated with cyanobacterial communities in a Brazilian freshwater reservoir.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {52}, number = {2}, pages = {773-785}, pmid = {33791954}, issn = {1678-4405}, mesh = {Bacteriophages/classification/genetics/*isolation & purification ; *Biodiversity ; Brazil ; Cyanobacteria/classification/genetics/growth & development/*virology ; Fresh Water/microbiology/*virology ; Genome, Viral ; Microcystis/genetics/growth & development/virology ; Phylogeny ; Water Resources ; }, abstract = {As part of the phytoplankton of marine and freshwater environments around the world, cyanobacteria interact with viruses (cyanophages) that affect their abundance and diversity. Investigations focusing on cyanophages co-occurring with freshwater cyanobacteria are scarce, particularly in Brazil. The aim of this study was to assess the diversity of cyanophages associated with a Microcystis-dominated cyanobacterial bloom in a tropical reservoir. Samples were processed as viral fractions of water and cellular fractions, and temporal fluctuations in the abundance of Ma-LMM01-type cyanophages and their Microcystis hosts were determined by qPCR. We applied shotgun metagenomics to obtain a wider characterization of the cyanophage community. During the study period, Microcystis gene copies were quantified in all cellular fractions, and the copy number of the Ma-LMM01 phage gene tended to increase with host abundance. Metagenomic analysis demonstrated that Caudovirales was the major viral order associated with the cyanophage families Myoviridae (34-88%), Podoviridae (3-42%), and Siphoviridae (6-23%). The metagenomic analysis results confirmed the presence of Microcystis cyanophages in both viral and cellular fractions and demonstrated a high relative abundance of picocyanobacteria-related viruses and Prochlorococcus (36-52%) and Synechococcus (37-50%) phages. For other main cyanobacterial genera, no related cyanophages were identified, which was probably due to the scarce representation of cyanophage sequences in databanks. Thus, the studied reservoir hosted a diverse cyanophage community with a remarkable contribution of phages related to picoplanktonic cyanobacteria. These results provide insights that motivate future sequencing efforts to assess cyanophage diversity and recover complete genomes.}, } @article {pmid33791245, year = {2021}, author = {Li, A and Li, T and Gao, X and Yan, H and Chen, J and Huang, M and Wang, L and Yin, D and Li, H and Ma, R and Zeng, Q and Ding, S}, title = {Gut Microbiome Alterations in Patients With Thyroid Nodules.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {643968}, pmid = {33791245}, issn = {2235-2988}, mesh = {Adult ; Butyrates ; *Gastrointestinal Microbiome ; Genome-Wide Association Study ; Humans ; Metagenomics ; *Thyroid Nodule ; }, abstract = {Thyroid nodules are found in nearly half of the adult population. Accumulating evidence suggests that the gut microbiota plays an important role in thyroid metabolism, yet the association between gut microbiota capacity, thyroid nodules, and thyroid function has not been studied comprehensively. We performed a gut microbiome genome-wide association study in 196 patients with thyroid nodules and 283 controls by using whole-genome shotgun sequencing. We found that participants with high-grade thyroid nodules have decreased number of gut microbial species and gene families compared with those with lower grade nodules and controls. There are also significant alterations in the overall microbial composition in participants with high-grade thyroid nodules. The gut microbiome in participants with high-grade thyroid nodules is characterized by greater amino acid degradation and lower butyrate production. The relative abundances of multiple butyrate producing microbes are reduced in patients with high-grade thyroid nodules and the relative abundances of L-histidine metabolism pathways are associated with thyrotropin-releasing hormone. Our study describes the gut microbiome characteristics in thyroid nodules and a gut-thyroid link and highlight specific gut microbiota as a potential therapeutic target to regulate thyroid metabolism.}, } @article {pmid33791236, year = {2021}, author = {Fitzgerald, CB and Shkoporov, AN and Upadrasta, A and Khokhlova, EV and Ross, RP and Hill, C}, title = {Probing the "Dark Matter" of the Human Gut Phageome: Culture Assisted Metagenomics Enables Rapid Discovery and Host-Linking for Novel Bacteriophages.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {616918}, pmid = {33791236}, issn = {2235-2988}, mesh = {*Bacteriophages/genetics ; DNA, Viral/genetics ; Gastrointestinal Tract ; Humans ; *Metagenomics ; Virome ; }, abstract = {Recent years have been marked by the growing interest towards virulent and temperate bacteriophage populations inhabiting the human lower gastrointestinal tract - the gut phageome. A number of studies demonstrated high levels of specificity and temporal stability of individual gut phageomes, as well as their specific alterations in disease cohorts, in parallel with changes in the bacteriome. It has been speculated that phages might have an active role in shaping the taxonomic composition and functional properties of the human gut bacteriome. An overwhelming majority of gut bacteriophages, however, remain uncultured, unclassified, and their specific hosts and infection strategies are still unknown. They are often referred to as "the viral dark matter". A possible breakthrough in understanding of the phageome can only become possible when a significant proportion of the "the viral dark matter" is identified and linked to bacterial hosts. Here, we describe a method that enables rapid discovery and host-linking of novel bacteriophages in the gut via a combination of serial enrichment cultures and shotgun metagenomics of viral DNA. Using this approach dozens of novel and previously known bacteriophages were detected, including the ones infecting difficult-to-culture anaerobic bacteria. The majority of phages failed to produce lysis and propagate on host cultures in traditional assays. The newly identified phages include representatives of Siphoviridae, Myoviridae, Podoviridae, and crAss-like viruses, infecting diverse bacterial taxa of Bacteroidetes, Firmicutes, Actinobacteria, Verrucomicrobia and Proteobacteria phyla. The proposed new method has a potential for high-throughput screening applications for mass discovery of new phages in different environments.}, } @article {pmid33790324, year = {2021}, author = {Saxena, R and Mittal, P and Clavaud, C and Dhakan, DB and Roy, N and Breton, L and Misra, N and Sharma, VK}, title = {Longitudinal study of the scalp microbiome suggests coconut oil to enrich healthy scalp commensals.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {7220}, pmid = {33790324}, issn = {2045-2322}, mesh = {Administration, Topical ; Adult ; Coconut Oil/*administration & dosage ; *Dandruff/drug therapy/microbiology ; Female ; Humans ; Longitudinal Studies ; Microbiota/*drug effects ; Middle Aged ; Scalp/*microbiology ; }, abstract = {Dandruff is a recurrent chronic scalp disorder, affecting majority of the population worldwide. Recently a metagenomic study of the Indian scalp microbiome described an imperative role of bacterial commensals in providing essential vitamins and amino acids to the scalp. Coconut oil and its formulations are commonly applied on the scalp in several parts of the world to maintain scalp health. Thus, in this study we examined the effect of topical application of coconut oil on the scalp microbiome (bacterial and fungal) at the taxonomic and functional levels and their correlation with scalp physiological parameters. A 16-weeks-long time-course study was performed including 12-weeks of treatment and 4-weeks of relapse phase on a cohort of 140 (70 healthy and 70 dandruff) Indian women, resulting in ~ 900 metagenomic samples. After the treatment phase, an increase in the abundance of Cutibacterium acnes and Malassezia globosa in dandruff scalp was observed, which were negatively correlated to dandruff parameters. At the functional level, an enrichment of healthy scalp-related bacterial pathways, such as biotin metabolism and decrease in the fungal pathogenesis pathways was observed. The study provides novel insights on the effect of coconut oil in maintaining a healthy scalp and in modulating the scalp microbiome.}, } @article {pmid33790294, year = {2021}, author = {Singleton, CM and Petriglieri, F and Kristensen, JM and Kirkegaard, RH and Michaelsen, TY and Andersen, MH and Kondrotaite, Z and Karst, SM and Dueholm, MS and Nielsen, PH and Albertsen, M}, title = {Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2009}, pmid = {33790294}, issn = {2041-1723}, mesh = {Bacteria/classification/genetics ; Bioreactors/microbiology ; Denmark ; Genome, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 23S/genetics ; RNA, Ribosomal, 5S/genetics ; Sewage/*microbiology ; Wastewater/microbiology ; Water Purification/methods ; }, abstract = {Microorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.}, } @article {pmid33789570, year = {2021}, author = {Loftus, M and Hassouneh, SA and Yooseph, S}, title = {Bacterial community structure alterations within the colorectal cancer gut microbiome.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {98}, pmid = {33789570}, issn = {1471-2180}, mesh = {Bacteria/classification/*genetics ; *Biodiversity ; Colorectal Neoplasms/*microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; }, abstract = {BACKGROUND: Colorectal cancer is a leading cause of cancer-related deaths worldwide. The human gut microbiome has become an active area of research for understanding the initiation, progression, and treatment of colorectal cancer. Despite multiple studies having found significant alterations in the carriage of specific bacteria within the gut microbiome of colorectal cancer patients, no single bacterium has been unequivocally connected to all cases. Whether alterations in species carriages are the cause or outcome of cancer formation is still unclear, but what is clear is that focus should be placed on understanding changes to the bacterial community structure within the cancer-associated gut microbiome.

RESULTS: By applying a novel set of analyses on 252 previously published whole-genome shotgun sequenced fecal samples from healthy and late-stage colorectal cancer subjects, we identify taxonomic, functional, and structural changes within the cancer-associated human gut microbiome. Bacterial association networks constructed from these data exhibited widespread differences in the underlying bacterial community structure between healthy and colorectal cancer associated gut microbiomes. Within the cancer-associated ecosystem, bacterial species were found to form associations with other species that are taxonomically and functionally dissimilar to themselves, as well as form modules functionally geared towards potential changes in the tumor-associated ecosystem. Bacterial community profiling of these samples revealed a significant increase in species diversity within the cancer-associated gut microbiome, and an elevated relative abundance of species classified as originating from the oral microbiome including, but not limited to, Fusobacterium nucleatum, Peptostreptococcus stomatis, Gemella morbillorum, and Parvimonas micra. Differential abundance analyses of community functional capabilities revealed an elevation in functions linked to virulence factors and peptide degradation, and a reduction in functions involved in amino-acid biosynthesis within the colorectal cancer gut microbiome.

CONCLUSIONS: We utilize whole-genome shotgun sequenced fecal samples provided from a large cohort of late-stage colorectal cancer and healthy subjects to identify a number of potentially important taxonomic, functional, and structural alterations occurring within the colorectal cancer associated gut microbiome. Our analyses indicate that the cancer-associated ecosystem influences bacterial partner selection in the native microbiota, and we highlight specific oral bacteria and their associations as potentially relevant towards aiding tumor progression.}, } @article {pmid33786936, year = {2021}, author = {Cinek, O and Kramna, L and Odeh, R and Alassaf, A and Ibekwe, MAU and Ahmadov, G and Elmahi, BME and Mekki, H and Lebl, J and Abdullah, MA}, title = {Eukaryotic viruses in the fecal virome at the onset of type 1 diabetes: A study from four geographically distant African and Asian countries.}, journal = {Pediatric diabetes}, volume = {22}, number = {4}, pages = {558-566}, doi = {10.1111/pedi.13207}, pmid = {33786936}, issn = {1399-5448}, mesh = {Adolescent ; Azerbaijan ; Case-Control Studies ; Child ; Diabetes Mellitus, Type 1/diagnosis/*virology ; Feces/*virology ; Female ; Gastrointestinal Microbiome ; Humans ; Jordan ; Male ; Nigeria ; Sudan ; Virome ; }, abstract = {OBJECTIVES: Studies of the fecal virome in type 1 diabetes (T1D) have been limited to populations of Europe and the United States. We therefore sought to characterize the stool virome in children after onset of T1D and in matched control subjects from four geographically distant African and Asian countries.

METHODS: Samples of stool were collected from 73 children and adolescents shortly after T1D onset (Azerbaijan 19, Jordan 20, Nigeria 14, Sudan 20) and 105 matched control subjects of similar age and locale. Metagenomic sequencing of the DNA and RNA virome was performed, and virus positivity was defined as more than 0.001% of reads of the sample. Selected viruses were also quantified using real-time PCR. Conditional logistic regression was used to model associations with eukaryotic virus positivity.

RESULTS: Signals of 387 different viral species were detected; at least one eukaryotic virus was detected in 71% case and 65% control samples. Neither of observed eukaryotic virus species or genera differed in frequency between children with T1D and controls. There was a suggestive association of the total count of different viral genera per sample between cases (1.45 genera) and controls (1.10 genera, OR 1.24, 95%CI 0.98-1.57), and an unplanned subanalysis suggested marginally more frequent endogenous retrovirus signal in cases (in 28.8% vs. in 8.6% controls, OR = 4.55, 95%CI 1.72-12).

CONCLUSIONS: No clear and consistent association with T1D was observed in the fecal viromes from four distant non-European populations. The finding of borderline associations of human endogenous retroviruses merits further exploration.}, } @article {pmid33786661, year = {2021}, author = {Krishnaswamy, VG and Jaffar, MF and Sridharan, R and Ganesh, S and Kalidas, S and Palanisamy, V and Mani, K}, title = {Effect of chlorpyrifos on the earthworm Eudrilus euginae and their gut microbiome by toxicological and metagenomic analysis.}, journal = {World journal of microbiology & biotechnology}, volume = {37}, number = {5}, pages = {76}, doi = {10.1007/s11274-021-03040-3}, pmid = {33786661}, issn = {1573-0972}, support = {BT/IN/Indo-US/Foldscope/39/2015, 20/03/2018//Department of Biotechnology, Government of West Bengal/ ; }, mesh = {Animals ; Bacteria/classification/drug effects/genetics ; Chlorpyrifos/*toxicity ; Fungi/classification/drug effects/genetics ; Gastrointestinal Microbiome/*drug effects ; Insecticides/toxicity ; Metagenome ; Nanopore Sequencing ; Oligochaeta/*drug effects ; RNA, Ribosomal, 16S ; Soil ; }, abstract = {The earthworms are important soil invertebrates and play a crucial role in pedogenesis. The application of pesticides and prolonged exposure to pesticides causes mortality of earthworms apart from profoundly affecting the resident gut microbiome. The microbiome plays a significant effect on the metabolic processes associated with earthworms. The pesticide Chlorpyrifos (CPF) was studied for its toxicity on Eudrilus euginae by toxicity studies. The LC50 value of filter paper contact test and acute toxicity test was 3.8 mg/mL and 180 mg/kg. The prolonged exposure of earthworms to pesticide on reproductive toxicity resulted in the mortality of earthworms and absence of cocoon formation. Further, the effects of CPF on the whole gut microbiome of E. euginae was analyzed using a long amplicon Nanopore sequencing. Results indicated no fluctuations with Firmicutes and Bacteroidetes, that were found to be dominant at bacterial phyla level while at the genus level, remarkable differences were noticed. Clostridium dominated the earthworm gut prior to CPF exposure while Bacillus dominated after exposure. Similarly, the fungal members such as Ascomycota and Basidiomycota were observed to dominate the gut of earthworm at the phyla level before and after exposure to CPF. In contrast, Clavispora (65%) was the dominant genus before CPF exposure and Taloromyces (42%) dominated after the CPF exposure. Our study demonstrates the effect of CPF on the mortality of E. euginae while the amplicon sequencing established the unique microbiome of the gut in response to the CPF exposure.}, } @article {pmid33786001, year = {2021}, author = {Sehli, S and Allali, I and Chahboune, R and Bakri, Y and Al Idrissi, N and Hamdi, S and Nejjari, C and Amzazi, S and Ghazal, H}, title = {Metagenomics Approaches to Investigate the Gut Microbiome of COVID-19 Patients.}, journal = {Bioinformatics and biology insights}, volume = {15}, number = {}, pages = {1177932221999428}, pmid = {33786001}, issn = {1177-9322}, abstract = {Over the last decade, it has become increasingly apparent that the microbiome is a central component in human well-being and illness. However, to establish innovative therapeutic methods, it is crucial to learn more about the microbiota. Thereby, the area of metagenomics and associated bioinformatics methods and tools has become considerable in the study of the human microbiome biodiversity. The application of these metagenomics approaches to studying the gut microbiome in COVID-19 patients could be one of the promising areas of research in the fight against the SARS-CoV-2 infection and disparity. Therefore, understanding how the gut microbiome is affected by or could affect the SARS-CoV-2 is very important. Herein, we present an overview of approaches and methods used in the current published studies on COVID-19 patients and the gut microbiome. The accuracy of these researches depends on the appropriate choice and the optimal use of the metagenomics bioinformatics platforms and tools. Interestingly, most studies reported that COVID-19 patients' microbiota are enriched with opportunistic microorganisms. The choice and use of appropriate computational tools and techniques to accurately investigate the gut microbiota is therefore critical in determining the appropriate microbiome profile for diagnosis and the most reliable antiviral or preventive microbial composition.}, } @article {pmid33785906, year = {2022}, author = {Jiao, J and Dong, Y and Wang, P and Zuo, K and Han, C and Cai, J and Zhong, J and Yang, X and Li, J}, title = {Profile of gut flora in hypertensive patients with insufficient sleep duration.}, journal = {Journal of human hypertension}, volume = {36}, number = {4}, pages = {390-404}, pmid = {33785906}, issn = {1476-5527}, support = {81870308//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81670214//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81970271//National Natural Science Foundation of China (National Science Foundation of China)/ ; 7172080//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; 7204242//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; }, mesh = {Dysbiosis/complications/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Hypertension/etiology ; Sleep Deprivation/complications ; }, abstract = {Recently, the contribution of both insufficient sleep duration and gut microbiome dysbiosis to hypertension (HTN) have been revealed, yet the profile of gut flora in hypertensive patients with insufficient sleep duration remains unknown. To examine this condition, the specific shifts in the fecal microbiome of 53 participants with or without HTN were investigated. The patients were divided into those who slept short (≤6 h) or optimal (6-9 h) duration per day. Comprehensive metagenomic sequencing analysis of fecal specimens was performed in healthy controls with sufficient sleep (s-CTR, n = 10), healthy controls with insufficient sleep (ins-CTR, n = 6), hypertensive patients with sufficient sleep (s-HTN, n = 25), and HTNs complicated by short sleep duration (ins-HTN, n = 12). We found that the α-diversity and β-diversity were quite similar between s-HTN and ins-HTN. Similarities were also observed in the enterotype distribution between s-HTN and ins-HTN subjects. In addition, the enrichment of gut bacteria was evident, such as Fusobacterium mortiferum and Roseburia inulinivorans in ins-HTN subjects. Several functional modules that were distinct between s-HTN and ins-HTN subjects were identified, which were unique to hypertensive patients with insufficient sleep duration. Overall, the data demonstrated that the gut microbial features were largely maintained in hypertensive participants with insufficient sleep duration.}, } @article {pmid33785903, year = {2021}, author = {Liang, G and Bushman, FD}, title = {The human virome: assembly, composition and host interactions.}, journal = {Nature reviews. Microbiology}, volume = {19}, number = {8}, pages = {514-527}, pmid = {33785903}, issn = {1740-1534}, support = {P30 AI045008/AI/NIAID NIH HHS/United States ; R01 HL113252/HL/NHLBI NIH HHS/United States ; R61 HL137063/HL/NHLBI NIH HHS/United States ; }, mesh = {Bacteriophages/genetics ; Host-Pathogen Interactions/*genetics ; Humans ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Virome/*genetics ; }, abstract = {The human body hosts vast microbial communities, termed the microbiome. Less well known is the fact that the human body also hosts vast numbers of different viruses, collectively termed the 'virome'. Viruses are believed to be the most abundant and diverse biological entities on our planet, with an estimated 10[31] particles on Earth. The human virome is similarly vast and complex, consisting of approximately 10[13] particles per human individual, with great heterogeneity. In recent years, studies of the human virome using metagenomic sequencing and other methods have clarified aspects of human virome diversity at different body sites, the relationships to disease states and mechanisms of establishment of the human virome during early life. Despite increasing focus, it remains the case that the majority of sequence data in a typical virome study remain unidentified, highlighting the extent of unexplored viral 'dark matter'. Nevertheless, it is now clear that viral community states can be associated with adverse outcomes for the human host, whereas other states are characteristic of health. In this Review, we provide an overview of research on the human virome and highlight outstanding recent studies that explore the assembly, composition and dynamics of the human virome as well as host-virome interactions in health and disease.}, } @article {pmid33785557, year = {2022}, author = {Ng, SC and Xu, Z and Mak, JWY and Yang, K and Liu, Q and Zuo, T and Tang, W and Lau, L and Lui, RN and Wong, SH and Tse, YK and Li, AYL and Cheung, K and Ching, JYL and Wong, VWS and Kong, APS and Ma, RCW and Chow, EYK and Wong, SKH and Ho, ICH and Chan, PKS and Chan, FKL}, title = {Microbiota engraftment after faecal microbiota transplantation in obese subjects with type 2 diabetes: a 24-week, double-blind, randomised controlled trial.}, journal = {Gut}, volume = {71}, number = {4}, pages = {716-723}, doi = {10.1136/gutjnl-2020-323617}, pmid = {33785557}, issn = {1468-3288}, mesh = {*Diabetes Mellitus, Type 2/complications/therapy ; Double-Blind Method ; Fecal Microbiota Transplantation ; Feces ; *Gastrointestinal Microbiome ; Humans ; Obesity/complications/microbiology/therapy ; Treatment Outcome ; }, abstract = {OBJECTIVE: The impact of faecal microbiota transplantation (FMT) on microbiota engraftment in patients with metabolic syndrome is uncertain. We aimed to study whether combining FMT with lifestyle modification could enhance the engraftment of favourable microbiota in obese patients with type 2 diabetes mellitus (T2DM).

DESIGN: In this double-blind, randomised, placebo-controlled trial, 61 obese subjects with T2DM were randomly assigned to three parallel groups: FMT plus lifestyle intervention (LSI), FMT alone, or sham transplantation plus LSI every 4 weeks for up to week 12. FMT solution was prepared from six healthy lean donors. Faecal metagenomic sequencing was performed at baseline, weeks 4, 16 and 24. The primary outcome was the proportion of subjects acquiring ≥20% of microbiota from lean donors at week 24.

RESULTS: Proportions of subjects acquiring ≥20% of lean-associated microbiota at week 24 were 100%, 88.2% and 22% in the FMT plus LSI, FMT alone, and sham plus LSI groups, respectively (p<0.0001). Repeated FMTs significantly increased the engraftment of lean-associated microbiota (p<0.05). FMT with or without LSI increased butyrate-producing bacteria. Combining LSI and FMT led to increase in Bifidobacterium and Lactobacillus compared with FMT alone (p<0.05). FMT plus LSI group had reduced total and low-density lipoprotein cholesterol and liver stiffness at week 24 compared with baseline (p<0.05).

CONCLUSION: Repeated FMTs enhance the level and duration of microbiota engraftment in obese patients with T2DM. Combining lifestyle intervention with FMT led to more favourable changes in recipients' microbiota and improvement in lipid profile and liver stiffness.

TRIAL REGISTRATION NUMBER: NCT03127696.}, } @article {pmid33785357, year = {2021}, author = {Biegert, G and El Alam, MB and Karpinets, T and Wu, X and Sims, TT and Yoshida-Court, K and Lynn, EJ and Yue, J and Medrano, AD and Petrosino, J and Mezzari, MP and Ajami, NJ and Solley, T and Ahmed-Kaddar, M and Klopp, AH and Colbert, LE}, title = {Diversity and composition of gut microbiome of cervical cancer patients: Do results of 16S rRNA sequencing and whole genome sequencing approaches align?.}, journal = {Journal of microbiological methods}, volume = {185}, number = {}, pages = {106213}, pmid = {33785357}, issn = {1872-8359}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; T32 CA101642/CA/NCI NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Biodiversity ; DNA, Bacterial ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/methods ; Microbiota/genetics ; Middle Aged ; RNA, Ribosomal, 16S/*genetics ; Uterine Cervical Neoplasms/*genetics ; Whole Genome Sequencing/*methods ; }, abstract = {BACKGROUND: Next generation sequencing has progressed rapidly, characterizing microbial communities beyond culture-based or biochemical techniques. 16S ribosomal RNA gene sequencing (16S) produces reliable taxonomic classifications and relative abundances, while shotgun metagenome sequencing (WMS) allows higher taxonomic and functional resolution at greater cost. The purpose of this study was to determine if 16S and WMS provide congruent information for our patient population from paired fecal microbiome samples.

RESULTS: Comparative indices were highly congruent between 16S and WMS. The most abundant genera for 16S and WMS data did not overlap. Overlap was observed at the Phylum level, as expected. However, relative abundances correlated poorly between the two methodologies (all P-value>0.05). Hierarchical clustering of both sequencing analyses identified overlapping enterotypes. Both approaches were in agreement with regard to demographic variables.

CONCLUSION: Diversity, evenness and richness are comparable when using 16S and WMS techniques, however relative abundances of individual genera are not. Clinical associations with diversity and evenness metrics were similarly identified with WMS or 16S.}, } @article {pmid33785070, year = {2021}, author = {Wirbel, J and Zych, K and Essex, M and Karcher, N and Kartal, E and Salazar, G and Bork, P and Sunagawa, S and Zeller, G}, title = {Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {93}, pmid = {33785070}, issn = {1474-760X}, mesh = {Computational Biology/*methods ; Confounding Factors, Epidemiologic ; Crohn Disease/etiology ; Databases, Genetic ; Gastrointestinal Microbiome ; Humans ; *Machine Learning ; Meta-Analysis as Topic ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; Models, Statistical ; ROC Curve ; *Software ; Workflow ; }, abstract = {The human microbiome is increasingly mined for diagnostic and therapeutic biomarkers using machine learning (ML). However, metagenomics-specific software is scarce, and overoptimistic evaluation and limited cross-study generalization are prevailing issues. To address these, we developed SIAMCAT, a versatile R toolbox for ML-based comparative metagenomics. We demonstrate its capabilities in a meta-analysis of fecal metagenomic studies (10,803 samples). When naively transferred across studies, ML models lost accuracy and disease specificity, which could however be resolved by a novel training set augmentation strategy. This reveals some biomarkers to be disease-specific, with others shared across multiple conditions. SIAMCAT is freely available from siamcat.embl.de .}, } @article {pmid33784327, year = {2021}, author = {Buetti-Dinh, A and Ruinelli, M and Czerski, D and Scapozza, C and Martignier, A and Roman, S and Caminada, A and Tonolla, M}, title = {Geochemical and metagenomics study of a metal-rich, green-turquoise-coloured stream in the southern Swiss Alps.}, journal = {PloS one}, volume = {16}, number = {3}, pages = {e0248877}, pmid = {33784327}, issn = {1932-6203}, mesh = {Bacteria/classification/genetics ; Biodiversity ; Color ; *Ecosystem ; Extracellular Polymeric Substance Matrix/metabolism ; Genes, Bacterial ; Geologic Sediments/*chemistry ; *Metagenomics ; Metals/*analysis ; Nitrogen Fixation ; Phylogeny ; Rivers/*chemistry ; Switzerland ; Water/chemistry ; }, abstract = {The Swiss Alpine environments are poorly described from a microbiological perspective. Near the Greina plateau in the Camadra valley in Ticino (southern Swiss Alps), a green-turquoise-coloured water spring streams off the mountain cliffs. Geochemical profiling revealed naturally elevated concentrations of heavy metals such as copper, lithium, zinc and cadmium, which are highly unusual for the geomorphology of the region. Of particular interest, was the presence of a thick biofilm, that was revealed by microscopic analysis to be mainly composed of Cyanobacteria. A metagenome was further assembled to detail the genes found in this environment. A multitude of genes for resistance/tolerance to high heavy metal concentrations were indeed found, such as, various transport systems, and genes involved in the synthesis of extracellular polymeric substances (EPS). EPS have been evoked as a central component in photosynthetic environments rich in heavy metals, for their ability to drive the sequestration of toxic, positively-charged metal ions under high regimes of cyanobacteria-driven photosynthesis. The results of this study provide a geochemical and microbiological description of this unusual environment in the southern Swiss Alps, the role of cyanobacterial photosynthesis in metal resistance, and the potential role of such microbial community in bioremediation of metal-contaminated environments.}, } @article {pmid33783596, year = {2021}, author = {Zhao, H}, title = {The human microbiome and genetic disease: towards the integration of metagenomic and multi-omics data.}, journal = {Human genetics}, volume = {140}, number = {5}, pages = {701-702}, pmid = {33783596}, issn = {1432-1203}, mesh = {Data Analysis ; Genetic Diseases, Inborn/*microbiology ; Humans ; Metagenomics ; *Microbiota ; }, } @article {pmid33782583, year = {2021}, author = {Kachroo, N and Lange, D and Penniston, KL and Stern, J and Tasian, G and Bajic, P and Wolfe, AJ and Suryavanshi, M and Ticinesi, A and Meschi, T and Monga, M and Miller, AW}, title = {Standardization of microbiome studies for urolithiasis: an international consensus agreement.}, journal = {Nature reviews. Urology}, volume = {18}, number = {5}, pages = {303-311}, pmid = {33782583}, issn = {1759-4820}, mesh = {Humans ; Microbiological Techniques/*standards ; *Microbiota ; Urolithiasis/*microbiology ; }, abstract = {Numerous metagenome-wide association studies (MWAS) for urolithiasis have been published, leading to the discovery of potential interactions between the microbiome and urolithiasis. However, questions remain about the reproducibility, applicability and physiological relevance of these data owing to discrepancies in experimental technique and a lack of standardization in the field. One barrier to interpreting MWAS is that experimental biases can be introduced at every step of the experimental pipeline, including sample collection, preservation, storage, processing, sequencing, data analysis and validation. Thus, the introduction of standardized protocols that maintain the flexibility to achieve study-specific objectives is urgently required. To address this need, the first international consortium for microbiome in urinary stone disease - MICROCOSM - was created and consensus panel members were asked to participate in a consensus meeting to develop standardized protocols for microbiome studies if they had published an MWAS on urolithiasis. Study-specific protocols were revised until a consensus was reached. This consensus group generated standardized protocols, which are publicly available via a secure online server, for each step in the typical clinical microbiome-urolithiasis study pipeline. This standardization creates the benchmark for future studies to facilitate consistent interpretation of results and, collectively, to lead to effective interventions to prevent the onset of urolithiasis, and will also be useful for investigators interested in microbiome research in other urological diseases.}, } @article {pmid33782219, year = {2021}, author = {Jeong, M and Choi, DH and Cheon, WJ and Kim, JG}, title = {Pyrosequencing and Taxonomic Composition of the Fungal Community from Soil of Tricholoma matsutake in Gyeongju.}, journal = {Journal of microbiology and biotechnology}, volume = {31}, number = {5}, pages = {686-695}, pmid = {33782219}, issn = {1738-8872}, mesh = {Agaricales/classification/genetics/growth & development/*physiology ; Fungi/classification/genetics/growth & development/isolation & purification ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Mycobiome/*genetics ; Pinus/microbiology ; Republic of Korea ; Seasons ; *Soil Microbiology ; }, abstract = {Tricholoma matsutake is an ectomycorrhizal fungus that has a symbiotic relationship with the root of Pinus densiflora. Soil microbial communities greatly affect the growth of T. matsutake, however, few studies have examined the characteristics of these communities. In the present study, we analyzed soil fungal communities from Gyeongju and Yeongdeok using metagenomic pyrosequencing to investigate differences in fungal species diversity, richness, and taxonomic composition between the soil under T. matsutake fruiting bodies (Sample 2) and soil where the fairy ring of T. matsutake was no longer present (Sample 1). The same spot was investigated three times at intervals of four months to observe changes in the community. In the samples from Yeongdeok, the number of valid reads was lower than that at Gyeongju. The operational taxonomic units of most Sample 2 groups were less than those of Sample 1 groups, indicating that fungal diversity was low in the T. matsutakedominant soil. The soil under the T. matsutake fruiting bodies was dominated by more than 51% T. matsutake. From fall to the following spring, the ratio of T. matsutake decreased. Basidiomycota was the dominant phylum in most samples. G-F1-2, G-F2-2, and Y-F1-2 had the genera Tricholoma, Umbelopsis, Oidiodendron, Sagenomella, Cladophialophora, and Phialocephala in common. G-F1-1, G-F2-1, and Y-F1-1 had 10 genera including Umbelopsis and Sagenomella in common. From fall to the following spring, the amount of phyla Basidiomycota and Mucoromycota gradually decreased but that of phylum Ascomycota increased. We suggest that the genus Umbelopsis is positively related to T. matsutake.}, } @article {pmid33782152, year = {2021}, author = {Costantini, C and Nunzi, E and Spolzino, A and Palmieri, M and Renga, G and Zelante, T and Englmaier, L and Coufalikova, K and Spáčil, Z and Borghi, M and Bellet, MM and Acerbi, E and Puccetti, M and Giovagnoli, S and Spaccapelo, R and Talesa, VN and Lomurno, G and Merli, F and Facchini, L and Spadea, A and Melillo, L and Codeluppi, K and Marchesi, F and Marchesini, G and Valente, D and Dragonetti, G and Nadali, G and Pagano, L and Aversa, F and Romani, L}, title = {Pharyngeal Microbial Signatures Are Predictive of the Risk of Fungal Pneumonia in Hematologic Patients.}, journal = {Infection and immunity}, volume = {89}, number = {8}, pages = {e0010521}, pmid = {33782152}, issn = {1098-5522}, mesh = {Animals ; Antifungal Agents/pharmacology/therapeutic use ; Disease Models, Animal ; Hematologic Diseases/*complications ; Hematologic Neoplasms/complications ; Humans ; Metagenome ; Metagenomics/methods ; Mice ; *Microbiota ; Mycoses/diagnosis/drug therapy/*etiology ; Pharynx/*microbiology ; Pneumonia/diagnosis/drug therapy/*etiology ; Risk Assessment ; Risk Factors ; }, abstract = {The ability to predict invasive fungal infections (IFI) in patients with hematological malignancies is fundamental for successful therapy. Although gut dysbiosis is known to occur in hematological patients, whether airway dysbiosis also contributes to the risk of IFI has not been investigated. Nasal and oropharyngeal swabs were collected for functional microbiota characterization in 173 patients with hematological malignancies recruited in a multicenter, prospective, observational study and stratified according to the risk of developing IFI. A lower microbial richness and evenness were found in the pharyngeal microbiota of high-risk patients that were associated with a distinct taxonomic and metabolic profile. A murine model of IFI provided biologic plausibility for the finding that loss of protective anaerobes, such as Clostridiales and Bacteroidetes, along with an apparent restricted availability of tryptophan, is causally linked to the risk of IFI in hematologic patients and indicates avenues for antimicrobial stewardship and metabolic reequilibrium in IFI.}, } @article {pmid33781870, year = {2021}, author = {Gayathri, KV and Aishwarya, S and Kumar, PS and Rajendran, UR and Gunasekaran, K}, title = {Metabolic and molecular modelling of zebrafish gut biome to unravel antimicrobial peptides through metagenomics.}, journal = {Microbial pathogenesis}, volume = {154}, number = {}, pages = {104862}, doi = {10.1016/j.micpath.2021.104862}, pmid = {33781870}, issn = {1096-1208}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Escherichia coli ; *Gastrointestinal Microbiome ; *Metagenomics ; Microbial Sensitivity Tests ; Molecular Docking Simulation ; Pore Forming Cytotoxic Proteins ; Pseudomonas aeruginosa ; Zebrafish ; }, abstract = {Recently efforts have been taken for unravelling mysteries between host-microbe interactions in gut microbiome studies of model organisms through metagenomics. Co-existence and the co-evolution of the microorganisms is the significant cause of the growing antimicrobial menace. There needs a novel approach to develop potential antimicrobials with capabilities to act directly on the resistant microbes with reduced side effects. One such is to tap them from the natural resources, preferably the gut of the most closely related animal model. In this study, we employed metagenomics approaches to identify the large taxonomic genomes of the zebra fish gut. About 256 antimicrobial peptides were identified using gene ontology predictions from Macrel and Pubseed servers. Upon the property predictions, the top 10 antimicrobial peptides were screened based on their action against many resistant bacterial species, including Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, E. coli, and Bacillus cereus. Metabolic modelling and flux balance analysis (FBA) were computed to conclude the antibiotic such as tetracycline, cephalosporins, puromycin, neomycin biosynthesis pathways were adopted by the microbiome as protection strategies. Molecular modelling strategies, including molecular docking and dynamics, were performed to estimate the antimicrobial peptides' binding against the target-putative nucleic acid binding lipoprotein and confirm stable binding. One specific antimicrobial peptide with the sequence "MPPYLHEIQPHTASNCQTELVIKL" showed promising results with 53% hydrophobic residues and a net charge +2.5, significant for the development of antimicrobial peptides. The said peptide also showed promising interactions with the target protein and expressed stable binding with docking energy of -429.34 kcal/mol and the average root mean square deviation of 1 A[0]. The study is a novel approach focusing on tapping out potential antimicrobial peptides to be developed against most resistant bacterial species.}, } @article {pmid33781869, year = {2021}, author = {Yu, S and Xiong, Y and Fu, Y and Chen, G and Zhu, H and Mo, X and Wu, D and Xu, J}, title = {Shotgun metagenomics reveals significant gut microbiome features in different grades of acute pancreatitis.}, journal = {Microbial pathogenesis}, volume = {154}, number = {}, pages = {104849}, doi = {10.1016/j.micpath.2021.104849}, pmid = {33781869}, issn = {1096-1208}, mesh = {Acute Disease ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Pancreatitis ; }, abstract = {BACKGROUND: Acute pancreatitis (AP) has a broad spectrum of severity and is associated with considerable morbidity and mortality. Dysbiosis of gut microbiota may be associated with AP severity.

AIMS: We aimed to evaluate the composition and functional effects of gut microbiota in different grades of AP severity.

METHODS: We carried out shotgun metagenomic sequencing on rectal swab samples from three patients with mild acute pancreatitis (MAP), three with moderately severe acute pancreatitis (MSAP), three with severe acute pancreatitis (SAP) and three normal control persons (NOR). Differences analysis in gut microbiota composition and functional enrichment was performed.

RESULTS: Gut microbiota in AP patients was characterized by decreased species richness. The most representative gut microbiota in mild acute pancreatitis (MAP), moderately severe acute pancreatitis (MSAP), and severe acute pancreatitis (SAP) was Streptococcus, Escherichia-coli, and Enterococcus, respectively. Each of the three AP-associated genera could differentiate AP from healthy control population. Representative pathways associated with the glutathione metabolism, lipopolysaccharide biosynthesis, and amino acid metabolism (valine, leucine and isoleucine degradation) were enriched in MAP, MSAP, and SAP, respectively.

CONCLUSIONS: The study shows a potential association of gut microbiome composition and function to the progression of AP severity.}, } @article {pmid33781338, year = {2021}, author = {Benler, S and Yutin, N and Antipov, D and Rayko, M and Shmakov, S and Gussow, AB and Pevzner, P and Koonin, EV}, title = {Thousands of previously unknown phages discovered in whole-community human gut metagenomes.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {78}, pmid = {33781338}, issn = {2049-2618}, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; *Gastrointestinal Microbiome/genetics ; Genome, Viral/genetics ; Humans ; Metagenome ; *Microbiota ; Phylogeny ; }, abstract = {BACKGROUND: Double-stranded DNA bacteriophages (dsDNA phages) play pivotal roles in structuring human gut microbiomes; yet, the gut virome is far from being fully characterized, and additional groups of phages, including highly abundant ones, continue to be discovered by metagenome mining. A multilevel framework for taxonomic classification of viruses was recently adopted, facilitating the classification of phages into evolutionary informative taxonomic units based on hallmark genes. Together with advanced approaches for sequence assembly and powerful methods of sequence analysis, this revised framework offers the opportunity to discover and classify unknown phage taxa in the human gut.

RESULTS: A search of human gut metagenomes for circular contigs encoding phage hallmark genes resulted in the identification of 3738 apparently complete phage genomes that represent 451 putative genera. Several of these phage genera are only distantly related to previously identified phages and are likely to found new families. Two of the candidate families, "Flandersviridae" and "Quimbyviridae", include some of the most common and abundant members of the human gut virome that infect Bacteroides, Parabacteroides, and Prevotella. The third proposed family, "Gratiaviridae," consists of less abundant phages that are distantly related to the families Autographiviridae, Drexlerviridae, and Chaseviridae. Analysis of CRISPR spacers indicates that phages of all three putative families infect bacteria of the phylum Bacteroidetes. Comparative genomic analysis of the three candidate phage families revealed features without precedent in phage genomes. Some "Quimbyviridae" phages possess Diversity-Generating Retroelements (DGRs) that generate hypervariable target genes nested within defense-related genes, whereas the previously known targets of phage-encoded DGRs are structural genes. Several "Flandersviridae" phages encode enzymes of the isoprenoid pathway, a lipid biosynthesis pathway that so far has not been known to be manipulated by phages. The "Gratiaviridae" phages encode a HipA-family protein kinase and glycosyltransferase, suggesting these phages modify the host cell wall, preventing superinfection by other phages. Hundreds of phages in these three and other families are shown to encode catalases and iron-sequestering enzymes that can be predicted to enhance cellular tolerance to reactive oxygen species.

CONCLUSIONS: Analysis of phage genomes identified in whole-community human gut metagenomes resulted in the delineation of at least three new candidate families of Caudovirales and revealed diverse putative mechanisms underlying phage-host interactions in the human gut. Addition of these phylogenetically classified, diverse, and distinct phages to public databases will facilitate taxonomic decomposition and functional characterization of human gut viromes. Video abstract.}, } @article {pmid33781335, year = {2021}, author = {Zünd, M and Ruscheweyh, HJ and Field, CM and Meyer, N and Cuenca, M and Hoces, D and Hardt, WD and Sunagawa, S}, title = {High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {77}, pmid = {33781335}, issn = {2049-2618}, mesh = {Animals ; *Bacteriophages/genetics ; *Gastrointestinal Microbiome/genetics ; Genomics ; High-Throughput Nucleotide Sequencing ; Mice ; Prophages/genetics ; }, abstract = {BACKGROUND: Temperate phages influence the density, diversity and function of bacterial populations. Historically, they have been described as carriers of toxins. More recently, they have also been recognised as direct modulators of the gut microbiome, and indirectly of host health and disease. Despite recent advances in studying prophages using non-targeted sequencing approaches, methodological challenges in identifying inducible prophages in bacterial genomes and quantifying their activity have limited our understanding of prophage-host interactions.

RESULTS: We present methods for using high-throughput sequencing data to locate inducible prophages, including those previously undiscovered, to quantify prophage activity and to investigate their replication. We first used the well-established Salmonella enterica serovar Typhimurium/p22 system to validate our methods for (i) quantifying phage-to-host ratios and (ii) accurately locating inducible prophages in the reference genome based on phage-to-host ratio differences and read alignment alterations between induced and non-induced prophages. Investigating prophages in bacterial strains from a murine gut model microbiota known as Oligo-MM[12] or sDMDMm2, we located five novel inducible prophages in three strains, quantified their activity and showed signatures of lateral transduction potential for two of them. Furthermore, we show that the methods were also applicable to metagenomes of induced faecal samples from Oligo-MM[12] mice, including for strains with a relative abundance below 1%, illustrating its potential for the discovery of inducible prophages also in more complex metagenomes. Finally, we show that predictions of prophage locations in reference genomes of the strains we studied were variable and inconsistent for four bioinformatic tools we tested, which highlights the importance of their experimental validation.

CONCLUSIONS: This study demonstrates that the integration of experimental induction and bioinformatic analysis presented here is a powerful approach to accurately locate inducible prophages using high-throughput sequencing data and to quantify their activity. The ability to generate such quantitative information will be critical in helping us to gain better insights into the factors that determine phage activity and how prophage-bacteria interactions influence our microbiome and impact human health. Video abstract.}, } @article {pmid33781324, year = {2021}, author = {Snipen, L and Angell, IL and Rognes, T and Rudi, K}, title = {Reduced metagenome sequencing for strain-resolution taxonomic profiles.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {79}, pmid = {33781324}, issn = {2049-2618}, mesh = {Humans ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Studies of shifts in microbial community composition has many applications. For studies at species or subspecies levels, the 16S amplicon sequencing lacks resolution and is often replaced by full shotgun sequencing. Due to higher costs, this restricts the number of samples sequenced. As an alternative to a full shotgun sequencing we have investigated the use of Reduced Metagenome Sequencing (RMS) to estimate the composition of a microbial community. This involves the use of double-digested restriction-associated DNA sequencing, which means only a smaller fraction of the genomes are sequenced. The read sets obtained by this approach have properties different from both amplicon and shotgun data, and analysis pipelines for both can either not be used at all or not explore the full potential of RMS data.

RESULTS: We suggest a procedure for analyzing such data, based on fragment clustering and the use of a constrained ordinary least square de-convolution for estimating the relative abundance of all community members. Mock community datasets show the potential to clearly separate strains even when the 16S is 100% identical, and genome-wide differences is < 0.02, indicating RMS has a very high resolution. From a simulation study, we compare RMS to shotgun sequencing and show that we get improved abundance estimates when the community has many very closely related genomes. From a real dataset of infant guts, we show that RMS is capable of detecting a strain diversity gradient for Escherichia coli across time.

CONCLUSION: We find that RMS is a good alternative to either metabarcoding or shotgun sequencing when it comes to resolving microbial communities at the strain level. Like shotgun metagenomics, it requires a good database of reference genomes and is well suited for studies of the human gut or other communities where many reference genomes exist. A data analysis pipeline is offered, as an R package at https://github.com/larssnip/microRMS . Video abstract.}, } @article {pmid33780842, year = {2021}, author = {Jiang, X and Liu, W and Xu, H and Cui, X and Li, J and Chen, J and Zheng, B}, title = {Characterizations of heavy metal contamination, microbial community, and resistance genes in a tailing of the largest copper mine in China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {280}, number = {}, pages = {116947}, doi = {10.1016/j.envpol.2021.116947}, pmid = {33780842}, issn = {1873-6424}, mesh = {China ; Copper ; Environmental Monitoring ; *Metals, Heavy/analysis ; *Microbiota ; Soil ; *Soil Pollutants/analysis ; }, abstract = {Copper mine tailings are causing great environmental concern nowadays due to their high contents of heavy metals. These hazards may release to air, water, and soil, posing great threat to the living organisms in the surroundings. In the present work, we profiled the heavy metal contents, microbiome and resistome of a mine tailing in Dexing Copper Mine, which is the largest open-pit copper mine in China. A total of 39.75 Gb clean data was generated by metagenomics sequencing and taxonomy analysis revealed Actinobacteria, Proteobacteria, Acidobacteria, Euryarchaeota, and Nitrospirae as the most abundant phylum in this tailing. In general, 76 heavy metal resistance genes (HMRGs) and 194 antimicrobial resistance genes (ARGs) were identified with merA and rpoB2 as the most abundant HMRG and ARG, respectively. We also compared the differences of heavy metal concentrations among the six sampling sites in the same tailing and found that significant differences exited in copper and zinc. Hierarchical cluster analysis showed that the samples from the six sampling sites were clustering in two groups based on heavy metal concentrations. Accordingly, clustering based on microbial composition and relative abundances of resistance genes exhibited the same clustering pattern, indicating a possible shaping influence of heavy metals on the microbiome and resistome in this tailing. Our work presented heavy metal contents, microbial composition and resistance genes in a copper mine tailing of the largest copper mine in China, and these data will of great use in the surveillance, maintenance, and remediation of this tailing.}, } @article {pmid33780547, year = {2021}, author = {Htwe, P and Aung, H and Kywe, B and Niang, PT and Oo, TS and Monhandas, S and Kelly, L and Goldman, DL}, title = {Endotoxin Acts Synergistically With Clostridioides difficile Toxin B to Increase Interleukin 1β Production: A Potential Role for the Intestinal Biome in Modifying the Severity of C. difficile Colitis.}, journal = {The Journal of infectious diseases}, volume = {224}, number = {9}, pages = {1556-1565}, doi = {10.1093/infdis/jiab165}, pmid = {33780547}, issn = {1537-6613}, mesh = {Bacterial Proteins/genetics/*immunology ; Bacterial Toxins/genetics/*immunology ; Child ; Child, Preschool ; Clostridioides difficile/genetics/*immunology ; Colitis ; *Endotoxins ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Inflammasomes/blood ; Inflammation ; Inflammation Mediators/*metabolism ; Interleukin-1beta/*blood/metabolism ; Leukocytes, Mononuclear ; Male ; Toll-Like Receptor 4/blood ; }, abstract = {BACKGROUND: Inflammation is a crucial driver of host damage in patients with Clostridioides difficile colitis. We examined the potential for the intestinal microbiome to modify inflammation in patients with C. difficile colitis via the effects of gut-derived endotoxin on cytokine production.

METHODS: Endotoxin from Escherichia coli and Pseudomonas aeruginosa as well as stool-derived endotoxin were tested for their ability to enhance interleukin 1β (IL-1β) and tumor necrosis factor alpha (TNF-α) production by toxin B-stimulated peripheral blood mononuclear cells. Inflammasome and Toll-like receptor 4 (TLR4) blocking studies were done to discern the importance of these pathways, while metagenomic studies were done to characterize predominant organisms from stool samples.

RESULTS: Endotoxin significantly enhanced the ability of C. difficile toxin B to promote IL-1β production but not TNF-α. The magnitude of this effect varied by endotoxin type and was dependent on combined inflammasome and TLR4 activation. Stool-derived endotoxin exhibited a similar synergistic effect on IL-1β production with less synergy observed for stools that contained a high proportion of γ-proteobacteria.

CONCLUSIONS: The ability of endotoxin to enhance IL-1β production highlights a manner by which the microbiome can modify inflammation and severity of C. difficile disease. This information may be useful in devising new therapies for severe C. difficile colitis.}, } @article {pmid33779498, year = {2021}, author = {Kang, K and Imamovic, L and Misiakou, MA and Bornakke Sørensen, M and Heshiki, Y and Ni, Y and Zheng, T and Li, J and Ellabaan, MMH and Colomer-Lluch, M and Rode, AA and Bytzer, P and Panagiotou, G and Sommer, MOA}, title = {Expansion and persistence of antibiotic-specific resistance genes following antibiotic treatment.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-19}, pmid = {33779498}, issn = {1949-0984}, mesh = {Adolescent ; Adult ; Aged ; Anti-Bacterial Agents/*therapeutic use ; Bacteria/virology ; Bacteriophages/drug effects ; Biological Warfare ; Cohort Studies ; *Drug Resistance, Microbial ; Feces/*microbiology/*virology ; Gastrointestinal Microbiome/*drug effects ; Gene Transfer, Horizontal/drug effects ; Humans ; Metagenome/drug effects ; Microbiota/*drug effects ; Middle Aged ; Plasmids/drug effects ; Transcriptome/drug effects ; Virome/drug effects ; Young Adult ; }, abstract = {Oral antibiotics are commonly prescribed to non-hospitalized adults. However, antibiotic-induced changes in the human gut microbiome are often investigated in cohorts with preexisting health conditions and/or concomitant medication, leaving the effects of antibiotics not completely understood. We used a combination of omic approaches to comprehensively assess the effects of antibiotics on the gut microbiota and particularly the gut resistome of a small cohort of healthy adults. We observed that 3 to 19 species per individual proliferated during antibiotic treatment and Gram-negative species expanded significantly in relative abundance. While the overall relative abundance of antibiotic resistance gene homologs did not significantly change, antibiotic-specific gene homologs with presumed resistance toward the administered antibiotics were common in proliferating species and significantly increased in relative abundance. Virome sequencing and plasmid analysis showed an expansion of antibiotic-specific resistance gene homologs even 3 months after antibiotic administration, while paired-end read analysis suggested their dissemination among different species. These results suggest that antibiotic treatment can lead to a persistent expansion of antibiotic resistance genes in the human gut microbiota and provide further data in support of good antibiotic stewardship.Abbreviation: ARG - Antibiotic resistance gene homolog; AsRG - Antibiotic-specific resistance gene homolog; AZY - Azithromycin; CFX - Cefuroxime; CIP - Ciprofloxacin; DOX - Doxycycline; FDR - False discovery rate; GRiD - Growth rate index value; HGT - Horizontal gene transfer; NMDS - Non-metric multidimensional scaling; qPCR - Quantitative polymerase chain reaction; RPM - Reads per million mapped reads; TA - Transcriptional activity; TE - Transposable element; TPM - Transcripts per million mapped reads.}, } @article {pmid33779487, year = {2021}, author = {Prochazkova, P and Roubalova, R and Dvorak, J and Kreisinger, J and Hill, M and Tlaskalova-Hogenova, H and Tomasova, P and Pelantova, H and Cermakova, M and Kuzma, M and Bulant, J and Bilej, M and Smitka, K and Lambertova, A and Holanova, P and Papezova, H}, title = {The intestinal microbiota and metabolites in patients with anorexia nervosa.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-25}, pmid = {33779487}, issn = {1949-0984}, mesh = {Adult ; Anorexia Nervosa/*metabolism/*microbiology ; Archaea/classification/growth & development ; Bacteria/classification/growth & development/metabolism ; Body Mass Index ; Brain-Gut Axis ; Fatty Acids, Volatile/*metabolism ; Feces/microbiology ; Female ; Fungi/classification/growth & development/metabolism ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; Metagenome ; Mycobiome ; Neurotransmitter Agents/*metabolism ; Young Adult ; }, abstract = {Brain-gut microbiota interactions are intensively studied in connection with various neurological and psychiatric diseases. While anorexia nervosa (AN) pathophysiology is not entirely clear, it is presumably linked to microbiome dysbiosis. We aimed to elucidate the gut microbiota contribution in AN disease pathophysiology. We analyzed the composition and diversity of the gut microbiome of patients with AN (bacteriome and mycobiome) from stool samples before and after renourishment, and compared them to healthy controls. Further, levels of assorted neurotransmitters and short-chain fatty acids (SCFA) were analyzed in stool samples by MS and NMR, respectively. Biochemical, anthropometric, and psychometric profiles were assessed. The bacterial alpha-diversity parameter analyses revealed only increased Chao 1 index in patients with AN before the realimentation, reflecting their interindividual variation. Subsequently, core microbiota depletion signs were observed in patients with AN. Overrepresented OTUs (operation taxonomic units) in patients with AN taxonomically belonged to Alistipes, Clostridiales, Christensenellaceae, and Ruminococcaceae. Underrepresented OTUs in patients with AN were Faecalibacterium, Agathobacter, Bacteroides, Blautia, and Lachnospira. Patients exhibited greater interindividual variation in the gut bacteriome, as well as in metagenome content compared to controls, suggesting altered bacteriome functions. Patients had decreased levels of serotonin, GABA, dopamine, butyrate, and acetate in their stool samples compared to controls. Mycobiome analysis did not reveal significant differences in alpha diversity and fungal profile composition between patients with AN and healthy controls, nor any correlation of the fungal composition with the bacterial profile. Our results show the changed profile of the gut microbiome and its metabolites in patients with severe AN. Although therapeutic partial renourishment led to increased body mass index and improved psychometric parameters, SCFA, and neurotransmitter profiles, as well as microbial community compositions, did not change substantially during the hospitalization period, which can be potentially caused by only partial weight recovery.}, } @article {pmid33777844, year = {2021}, author = {Chen, X and Kang, Y and Luo, J and Pang, K and Xu, X and Wu, J and Li, X and Jin, S}, title = {Next-Generation Sequencing Reveals the Progression of COVID-19.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {632490}, pmid = {33777844}, issn = {2235-2988}, mesh = {Angiotensin-Converting Enzyme 2/genetics/metabolism ; COVID-19/*epidemiology/microbiology/transmission/virology ; Dysbiosis/virology ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome ; Pandemics ; SARS-CoV-2/*genetics ; }, abstract = {The novel coronavirus SARS-CoV-2 (causing the disease COVID-19) has caused a highly transmissible and ongoing pandemic worldwide. Due to its rapid development, next-generation sequencing plays vital roles in many aspects. Here, we summarize the current knowledge on the origin and human transmission of SARS-CoV-2 based on NGS analysis. The ACE2 expression levels in various human tissues and relevant cells were compared to provide insights into the mechanism of SAS-CoV-2 infection. Gut microbiota dysbiosis observed by metagenome sequencing and the immunogenetics of COVID-19 patients according to single-cell sequencing analysis were also highlighted. Overall, the application of these sequencing techniques could be meaningful for finding novel intermediate SARS-CoV-2 hosts to block interspecies transmission. This information will further benefit SARS-CoV-2 diagnostic development and new therapeutic target discovery. The extensive application of NGS will provide powerful support for our fight against future public health emergencies.}, } @article {pmid33775256, year = {2021}, author = {Zhao, Y and Federico, A and Faits, T and Manimaran, S and Segrè, D and Monti, S and Johnson, WE}, title = {animalcules: interactive microbiome analytics and visualization in R.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {76}, pmid = {33775256}, issn = {2049-2618}, support = {F31 DE029701/DE/NIDCR NIH HHS/United States ; R01 GM127430/GM/NIGMS NIH HHS/United States ; U01 CA220413/CA/NCI NIH HHS/United States ; }, mesh = {Data Interpretation, Statistical ; Humans ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Software ; }, abstract = {BACKGROUND: Microbial communities that live in and on the human body play a vital role in health and disease. Recent advances in sequencing technologies have enabled the study of microbial communities at unprecedented resolution. However, these advances in data generation have presented novel challenges to researchers attempting to analyze and visualize these data.

RESULTS: To address some of these challenges, we have developed animalcules, an easy-to-use interactive microbiome analysis toolkit for 16S rRNA sequencing data, shotgun DNA metagenomics data, and RNA-based metatranscriptomics profiling data. This toolkit combines novel and existing analytics, visualization methods, and machine learning models. For example, the toolkit features traditional microbiome analyses such as alpha/beta diversity and differential abundance analysis, combined with new methods for biomarker identification are. In addition, animalcules provides interactive and dynamic figures that enable users to understand their data and discover new insights. animalcules can be used as a standalone command-line R package or users can explore their data with the accompanying interactive R Shiny interface.

CONCLUSIONS: We present animalcules, an R package for interactive microbiome analysis through either an interactive interface facilitated by R Shiny or various command-line functions. It is the first microbiome analysis toolkit that supports the analysis of all 16S rRNA, DNA-based shotgun metagenomics, and RNA-sequencing based metatranscriptomics datasets. animalcules can be freely downloaded from GitHub at https://github.com/compbiomed/animalcules or installed through Bioconductor at https://www.bioconductor.org/packages/release/bioc/html/animalcules.html . Video abstract.}, } @article {pmid33775067, year = {2021}, author = {Dunaj, J and Drewnowska, J and Moniuszko-Malinowska, A and Swiecicka, I and Pancewicz, S}, title = {First metagenomic report of Borrelia americana and Borrelia carolinensis in Poland - a preliminary study.}, journal = {Annals of agricultural and environmental medicine : AAEM}, volume = {28}, number = {1}, pages = {49-55}, doi = {10.26444/aaem/118134}, pmid = {33775067}, issn = {1898-2263}, mesh = {Animals ; Dermacentor/*microbiology ; Francisella/classification/genetics/isolation & purification ; Genome, Bacterial ; Ixodes/*microbiology ; Metagenomics ; *Microbiota ; Poland ; Pseudomonas/classification/isolation & purification ; Sphingomonas/classification/genetics/isolation & purification ; Spirochaetales/classification/*genetics/isolation & purification ; }, abstract = {INTRODUCTION AND OBJECTIVE: Ixodes ricinus (I. ricinus) and Dermacentor reticulatus (D. reticulatus) are the most common ticks in Poland. These ticks contain many bacteria, which compose a microbiome with potential impact on humans. The aim of the study was to discover the microbiome of ticks in Poland.

MATERIAL AND METHODS: Ticks were collected in The Protected Landscape Area of the Bug and Nurzec Valley, Poland, in 2016-2018 by flagging. They were cleaned in 70% ethanol and damaged in mortar with PBS (without Ca[2+] and Mg[2+] ions). DNA was extracted from the homogenates with spin columns kits, and used as a matrix in end-point PCR for bacterial 16S rRNA fragments amplifications, and further for next generation sequencing (NGS) by ILLUMINA.

RESULTS: In 22 ticks (3 I. ricinus and 19 D. reticulatus) 38 microorganisms were detected. The most common were Francisella hispaniensis and Francisella novicida. In 17 ticks, Sphingomonas oligophenolica, and in 12 Rickettsia aeshlimanii were found. In 2, I. ricinus specific DNA of Borrelia americana and Borrelia carolinensis were found. In one female, D. reticulatus Anaplasma phagocytophilum and Anaplasma centrale were found. Pseudomonas lutea and Ps. moraviensis were detected in 9 and 8 ticks, respectively.

CONCLUSIONS: Polish ticks microbiome contains not only well-known tick-borne pathogens, but also other pathogenic microorganisms. For the first time in Poland, Borrelia americana and Borrelia carolinensis in I. ricinus collected from the environment were detected. The dominant pathogenic microorganisms for humans were Francisella spp. and Rickettsia spp., and non-pathogenic - Sphingomonas oligophenolica. Knowledge of a tick microbiome might be useful in tick-borne biocontrol and tick-borne diseases prevention.}, } @article {pmid33774727, year = {2021}, author = {Wani, GA and Khan, MA and Dar, MA and Shah, MA and Reshi, ZA}, title = {Next Generation High Throughput Sequencing to Assess Microbial Communities: An Application Based on Water Quality.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {106}, number = {5}, pages = {727-733}, pmid = {33774727}, issn = {1432-0800}, support = {PDF/20l8/001689//DST-SERB, Govt. of India/ ; }, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; *Microbiota ; Phylogeny ; *Water Quality ; }, abstract = {Traditional techniques to identify different contaminants (biological or chemical) in the waters are slow, laborious, and can require specialized expertise. Hence, the rapid determination of water quality using more sensitive and reliable metagenomic based approaches attains special importance. Metagenomics deals with the study of genetic material that is recovered from microbial communities present in environmental samples. In traditional techniques cultivation-based methodologies were used to describe the diversity of microorganisms in environmental samples. It has failed to function as a robust marker because of limited taxonomic and phylogenetic implications. In this backdrop, high-throughput DNA sequencing approaches have proven very powerful in microbial source tracking because of investigating the full variety of genome-based analysis such as microbial genetic diversity and population structure played by them. Next generation sequencing technologies can reveal a greater proportion of microbial communities that have not been reported earlier by traditional techniques. The present review highlights the shift from traditional techniques for the basic study of community composition to next-generation sequencing (NGS) platforms and their potential applications to the biomonitoring of water quality in relation to human health.}, } @article {pmid33773594, year = {2021}, author = {Chan, SH and Ismail, MH and Tan, CH and Rice, SA and McDougald, D}, title = {Microbial predation accelerates granulation and modulates microbial community composition.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {91}, pmid = {33773594}, issn = {1471-2180}, mesh = {Bacteria/*metabolism ; Bacteriophages/*physiology ; *Ecosystem ; Eukaryota/*physiology ; *Microbiota ; }, abstract = {BACKGROUND: Bacterial communities are responsible for biological nutrient removal and flocculation in engineered systems such as activated floccular sludge. Predators such as bacteriophage and protozoa exert significant predation pressure and cause bacterial mortality within these communities. However, the roles of bacteriophage and protozoan predation in impacting granulation process remain limited. Recent studies hypothesised that protozoa, particularly sessile ciliates, could have an important role in granulation as these ciliates were often observed in high abundance on surfaces of granules. Bacteriophages were hypothesized to contribute to granular stability through bacteriophage-mediated extracellular DNA release by lysing bacterial cells. This current study investigated the bacteriophage and protozoan communities throughout the granulation process. In addition, the importance of protozoan predation during granulation was also determined through chemical killing of protozoa in the floccular sludge.

RESULTS: Four independent bioreactors seeded with activated floccular sludge were operated for aerobic granulation for 11 weeks. Changes in the phage, protozoa and bacterial communities were characterized throughout the granulation process. The filamentous phage, Inoviridae, increased in abundance at the initiation phase of granulation. However, the abundance shifted towards lytic phages during the maturation phase. In contrast, the abundance and diversity of protozoa decreased initially, possibly due to the reduction in settling time and subsequent washout. Upon the formation of granules, ciliated protozoa from the class Oligohymenophorea were the dominant group of protozoa based on metacommunity analysis. These protozoa had a strong, positive-correlation with the initial formation of compact aggregates prior to granule development. Furthermore, chemical inhibition of these ciliates in the floccular sludge delayed the initiation of granule formation. Analysis of the bacterial communities in the thiram treated sludge demonstrated that the recovery of 'Candidatus Accumulibacter' was positively correlated with the formation of compact aggregates and granules.

CONCLUSION: Predation by bacteriophage and protozoa were positively correlated with the formation of aerobic granules. Increases in Inoviridae abundance suggested that filamentous phages may promote the structural formation of granules. Initiation of granules formation was delayed due to an absence of protozoa after chemical treatment. The presence of 'Candidatus Accumulibacter' was necessary for the formation of granules in the absence of protozoa.}, } @article {pmid33773355, year = {2021}, author = {Li, H and Fu, J and Hu, S and Li, Z and Qu, J and Wu, Z and Chen, S}, title = {Comparison of the effects of acetic acid bacteria and lactic acid bacteria on the microbial diversity of and the functional pathways in dough as revealed by high-throughput metagenomics sequencing.}, journal = {International journal of food microbiology}, volume = {346}, number = {}, pages = {109168}, doi = {10.1016/j.ijfoodmicro.2021.109168}, pmid = {33773355}, issn = {1879-3460}, mesh = {Acetic Acid/*metabolism ; Bacteria/classification/genetics/*isolation & purification/metabolism ; *Biodiversity ; Bread/*microbiology ; Fermentation ; Food Microbiology ; High-Throughput Nucleotide Sequencing ; Lactobacillales/classification/genetics/*isolation & purification/metabolism ; Metagenomics ; Triticum/metabolism/microbiology ; Yeasts/classification/genetics/isolation & purification ; }, abstract = {Knowledge of the effects of various strains of acetic acid bacteria (AAB) on sourdough remains limited. In this study, the diversity of microbial taxa in sourdoughs fermented by different starters was assessed and their functional capacity was evaluated via high-throughput metagenomics sequencing. Results showed that Erwinia (29.43%), Pantoea (45.89%), and Enterobacter (9.16%) were predominant in the blank CK treatment. Lactobacillus (91.40%), Saccharomyces (6.13%), as well as the AAB genus Acetobacter (0.61%) were the dominant microbial genera in the sourdoughs started by yeast and a strain of lactic acid bacteria (YL treatment). By contrast, the dominant genera in the sourdoughs started by yeasts and various LAB and AAB strains (YLA treatment) were Komagataeibacter (0.39%) except for the inoculated Lactobacillus (68.37%), Acetobacter (20.17%), and Saccharomyces (8.31%) species. Functional prediction of these changes in microbial community and diversity revealed that various metabolism-related pathways, including alanine, aspartate, and glutamate metabolism (21.95%), as well as amino acid biosynthesis (19.14%), were predominant in the sourdoughs started by yeast and an AAB strain (YA treatment). Moreover, arginine biosynthesis (11.65%) were the dominant pathways in the YL treatment. The fermented dough added with sourdoughs started with yeast + AAB and yeast + AAB + LAB strains had substantially higher contents (more than 48.58% in total) of essential amino acids than the dough added with sourdoughs started with yeast + LAB strain. These results demonstrated that amino acid biosynthesis has a beneficial effect on sourdoughs inoculated with an AAB strain.}, } @article {pmid33772084, year = {2021}, author = {Jang, YO and Kim, OH and Kim, SJ and Lee, SH and Yun, S and Lim, SE and Yoo, HJ and Shin, Y and Lee, SW}, title = {High-fiber diets attenuate emphysema development via modulation of gut microbiota and metabolism.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {7008}, pmid = {33772084}, issn = {2045-2322}, mesh = {Animals ; Bile Acids and Salts/biosynthesis ; Cellulose/pharmacology ; Cigarette Smoking/adverse effects ; Diet ; Dietary Fiber/*pharmacology ; Dysbiosis/prevention & control ; Emphysema/*diet therapy/*prevention & control ; Fatty Acids, Volatile/biosynthesis ; Female ; Gastrointestinal Microbiome/*physiology ; Inflammation/diet therapy/prevention & control ; Mice ; Mice, Inbred C57BL ; Pectins/pharmacology ; Prebiotics/*administration & dosage ; Sphingolipids/biosynthesis ; }, abstract = {Dietary fiber functions as a prebiotic to determine the gut microbe composition. The gut microbiota influences the metabolic functions and immune responses in human health. The gut microbiota and metabolites produced by various dietary components not only modulate immunity but also impact various organs. Although recent findings have suggested that microbial dysbiosis is associated with several respiratory diseases, including asthma, cystic fibrosis, and allergy, the role of microbiota and metabolites produced by dietary nutrients with respect to pulmonary disease remains unclear. Therefore, we explored whether the gut microbiota and metabolites produced by dietary fiber components could influence a cigarette smoking (CS)-exposed emphysema model. In this study, it was demonstrated that a high-fiber diet including non-fermentable cellulose and fermentable pectin attenuated the pathological changes associated with emphysema progression and the inflammatory response in CS-exposed emphysema mice. Moreover, we observed that different types of dietary fiber could modulate the diversity of gut microbiota and differentially impacted anabolism including the generation of short-chain fatty acids, bile acids, and sphingolipids. Overall, the results of this study indicate that high-fiber diets play a beneficial role in the gut microbiota-metabolite modulation and substantially affect CS-exposed emphysema mice. Furthermore, this study suggests the therapeutic potential of gut microbiota and metabolites from a high-fiber diet in emphysema via local and systemic inflammation inhibition, which may be useful in the development of a new COPD treatment plan.}, } @article {pmid33771219, year = {2021}, author = {Tap, J and Störsrud, S and Le Nevé, B and Cotillard, A and Pons, N and Doré, J and Öhman, L and Törnblom, H and Derrien, M and Simrén, M}, title = {Diet and gut microbiome interactions of relevance for symptoms in irritable bowel syndrome.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {74}, pmid = {33771219}, issn = {2049-2618}, mesh = {Animals ; Diet ; *Gastrointestinal Microbiome/genetics ; Humans ; Hydrogen ; *Irritable Bowel Syndrome ; *Microbiota/genetics ; }, abstract = {BACKGROUND: While several studies have documented associations between dietary habits and microbiota composition and function in healthy individuals, no study explored these associations in patients with irritable bowel syndrome (IBS), and especially with symptoms.

METHODS: Here, we used a novel approach that combined data from a 4-day food diary, integrated into a food tree, together with gut microbiota (shotgun metagenomic) for individuals with IBS (N = 149) and healthy controls (N = 52). Paired microbiota and food-based trees allowed us to detect new associations between subspecies and diet. Combining co-inertia analysis and linear regression models, exhaled gas levels and symptom severity could be predicted from metagenomic and dietary data.

RESULTS: We showed that individuals with severe IBS are characterized by a higher intake of poorer-quality food items during their main meals. Our analysis suggested that covariations between gut microbiota at subspecies level and diet could be explained with IBS symptom severity, exhaled gas, glycan metabolism, and meat/plant ratio. We provided evidence that IBS severity is associated with altered gut microbiota hydrogen function in correlation with microbiota enzymes involved in animal carbohydrate metabolism.

CONCLUSIONS: Our study provides an unprecedented resolution of diet-microbiota-symptom interactions and ultimately guides new interventional studies that aim to identify gut microbiome-based nutritional recommendations for the management of gastrointestinal symptoms.

TRIAL REGISTRATION: This trial was registered on the ClinicalTrials.gov, with the registration number NCT01252550 , on 3rd December 2010. Video abstract.}, } @article {pmid33770448, year = {2021}, author = {Shine, EE and Crawford, JM}, title = {Molecules from the Microbiome.}, journal = {Annual review of biochemistry}, volume = {90}, number = {}, pages = {789-815}, doi = {10.1146/annurev-biochem-080320-115307}, pmid = {33770448}, issn = {1545-4509}, support = {R01 CA215553/CA/NCI NIH HHS/United States ; }, mesh = {Gastrointestinal Microbiome/genetics/physiology ; Humans ; Metagenomics/*methods ; Microbiota/genetics/*physiology ; Peptides/*metabolism ; Phenotype ; Polyketides/*metabolism ; }, abstract = {The human microbiome encodes a second genome that dwarfs the genetic capacity of the host. Microbiota-derived small molecules can directly target human cells and their receptors or indirectly modulate host responses through functional interactions with other microbes in their ecological niche. Their biochemical complexity has profound implications for nutrition, immune system development, disease progression, and drug metabolism, as well as the variation in these processes that exists between individuals. While the species composition of the human microbiome has been deeply explored, detailed mechanistic studies linking specific microbial molecules to host phenotypes are still nascent. In this review, we discuss challenges in decoding these interaction networks, which require interdisciplinary approaches that combine chemical biology, microbiology, immunology, genetics, analytical chemistry, bioinformatics, and synthetic biology. We highlight important classes of microbiota-derived small molecules and notable examples. An understanding of these molecular mechanisms is central to realizing the potential of precision microbiome editing in health, disease, and therapeutic responses.}, } @article {pmid33770071, year = {2021}, author = {Pavlova, YS and Paez-Espino, D and Morozov, AY and Belalov, IS}, title = {Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling.}, journal = {PLoS computational biology}, volume = {17}, number = {3}, pages = {e1008841}, pmid = {33770071}, issn = {1553-7358}, mesh = {Archaea/genetics ; Bacteria/genetics ; Bacteriophages/genetics ; CRISPR-Cas Systems/*genetics ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics/immunology ; DNA, Intergenic/genetics ; DNA, Viral/genetics ; Metagenome/*genetics ; Metagenomics ; *Models, Genetic ; }, abstract = {Understanding CRISPR-Cas systems-the adaptive defence mechanism that about half of bacterial species and most of archaea use to neutralise viral attacks-is important for explaining the biodiversity observed in the microbial world as well as for editing animal and plant genomes effectively. The CRISPR-Cas system learns from previous viral infections and integrates small pieces from phage genomes called spacers into the microbial genome. The resulting library of spacers collected in CRISPR arrays is then compared with the DNA of potential invaders. One of the most intriguing and least well understood questions about CRISPR-Cas systems is the distribution of spacers across the microbial population. Here, using empirical data, we show that the global distribution of spacer numbers in CRISPR arrays across multiple biomes worldwide typically exhibits scale-invariant power law behaviour, and the standard deviation is greater than the sample mean. We develop a mathematical model of spacer loss and acquisition dynamics which fits observed data from almost four thousand metagenomes well. In analogy to the classical 'rich-get-richer' mechanism of power law emergence, the rate of spacer acquisition is proportional to the CRISPR array size, which allows a small proportion of CRISPRs within the population to possess a significant number of spacers. Our study provides an alternative explanation for the rarity of all-resistant super microbes in nature and why proliferation of phages can be highly successful despite the effectiveness of CRISPR-Cas systems.}, } @article {pmid33769467, year = {2021}, author = {Zhu, S and Xu, K and Jiang, Y and Zhu, C and Suo, C and Cui, M and Wang, Y and Yuan, Z and Xue, J and Wang, J and Zhang, T and Zhao, G and Ye, W and Huang, T and Lu, M and Tian, W and Jin, L and Chen, X}, title = {The gut microbiome in subclinical atherosclerosis: a population-based multiphenotype analysis.}, journal = {Rheumatology (Oxford, England)}, volume = {61}, number = {1}, pages = {258-269}, doi = {10.1093/rheumatology/keab309}, pmid = {33769467}, issn = {1462-0332}, mesh = {Atherosclerosis/*genetics/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics/*physiology ; Genomics ; Healthy Lifestyle ; Humans ; Male ; Middle Aged ; Phenotype ; }, abstract = {OBJECTIVES: An altered microbiota, which can be described quantitatively, has been identified as playing a pivotal role in host vascular physiology, and it may contribute to various diseases. The aim of this study was to better understand the role of the gut microbiota in vascular physiology in a subclinical elderly population, and to investigate how lifestyle affects the composition of host gut microbiota to further impact the pathogenesis of vascular diseases.

METHODS: We performed a population-based faecal metagenomic study over 569 elderly asymptomatic subclinical individuals in rural China. An association network was built based on clinical measurements and detailed epidemiologic questionnaires, including blood chemistry, arterial stiffness, carotid ultrasonography, and metagenomic datasets.

RESULTS: By analyzing the breadth, depth and impact of each node of the association network, we found carotid arterial atherosclerosis indices, including intima-media thickness (IMT), were essential in the network, and were significantly associated with living habits, socio-economic status, and diet. Using mediation analysis, we found that higher frequency of eating fresh fruits and vegetables, and more exercise significantly reduced carotid atherosclerosis in terms of IMT, peak systolic velocity and end-diastolic velocity values through the mediation of Alistepes, Oligella and Prevotella. Gut microbes explained 16.5% of the mediation effect of lifestyle on the pathogenesis of carotid atherosclerosis. After adjustment, Faecalicatena [odds ratio (OR) = 0.12 ∼0.65] was shown to be protective against the formation of carotid atherosclerosis, independently, while Libanicoccus (OR = 1.46 ∼4.20) was associated with increased carotid arterial IMT. KEGG/KO Kyoto Encyclopedia of Genes and Genomes/ KEGG Orthology (KEGG/KO) analyses revealed a loss of anti-inflammation function in IMT subjects.

CONCLUSION: Our study revealed a Chinese population-wide phenotype-metagenomic association network and a mediation effect of gut microbiota on carotid artery atherosclerosis, hinting at potential therapeutic and preventive uses for microbiota in vascular diseases.}, } @article {pmid33769280, year = {2021}, author = {Liu, M and Devlin, JC and Hu, J and Volkova, A and Battaglia, TW and Ho, M and Asplin, JR and Byrd, A and Loke, P and Li, H and Ruggles, KV and Tsirigos, A and Blaser, MJ and Nazzal, L}, title = {Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {33769280}, issn = {2050-084X}, support = {R01 DK110014/DK/NIDDK NIH HHS/United States ; U54 DK083908/DK/NIDDK NIH HHS/United States ; U01 AI122285/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*metabolism ; Feces/chemistry ; *Gastrointestinal Microbiome ; Homeostasis ; Humans ; Inflammatory Bowel Diseases/*metabolism/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Oxalates/*metabolism/urine ; Oxalobacter formigenes/*physiology ; }, abstract = {Over-accumulation of oxalate in humans may lead to nephrolithiasis and nephrocalcinosis. Humans lack endogenous oxalate degradation pathways (ODP), but intestinal microbes can degrade oxalate using multiple ODPs and protect against its absorption. The exact oxalate-degrading taxa in the human microbiota and their ODP have not been described. We leverage multi-omics data (>3000 samples from >1000 subjects) to show that the human microbiota primarily uses the type II ODP, rather than type I. Furthermore, among the diverse ODP-encoding microbes, an oxalate autotroph, Oxalobacter formigenes, dominates this function transcriptionally. Patients with inflammatory bowel disease (IBD) frequently suffer from disrupted oxalate homeostasis and calcium oxalate nephrolithiasis. We show that the enteric oxalate level is elevated in IBD patients, with highest levels in Crohn's disease (CD) patients with both ileal and colonic involvement consistent with known nephrolithiasis risk. We show that the microbiota ODP expression is reduced in IBD patients, which may contribute to the disrupted oxalate homeostasis. The specific changes in ODP expression by several important taxa suggest that they play distinct roles in IBD-induced nephrolithiasis risk. Lastly, we colonize mice that are maintained in the gnotobiotic facility with O. formigenes, using either a laboratory isolate or an isolate we cultured from human stools, and observed a significant reduction in host fecal and urine oxalate levels, supporting our in silico prediction of the importance of the microbiome, particularly O. formigenes in host oxalate homeostasis.}, } @article {pmid33767340, year = {2021}, author = {Cebriá-Mendoza, M and Arbona, C and Larrea, L and Díaz, W and Arnau, V and Peña, C and Bou, JV and Sanjuán, R and Cuevas, JM}, title = {Deep viral blood metagenomics reveals extensive anellovirus diversity in healthy humans.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {6921}, pmid = {33767340}, issn = {2045-2322}, mesh = {Anelloviridae/*isolation & purification ; Blood/*virology ; Healthy Volunteers ; Humans ; Metagenomics ; *Virome ; }, abstract = {Human blood metagenomics has revealed the presence of different types of viruses in apparently healthy subjects. By far, anelloviruses constitute the viral family that is more frequently found in human blood, although amplification biases and contaminations pose a major challenge in this field. To investigate this further, we subjected pooled plasma samples from 120 healthy donors in Spain to high-speed centrifugation, RNA and DNA extraction, random amplification, and massive parallel sequencing. Our results confirm the extensive presence of anelloviruses in such samples, which represented nearly 97% of the total viral sequence reads obtained. We assembled 114 different viral genomes belonging to this family, revealing remarkable diversity. Phylogenetic analysis of ORF1 suggested 28 potentially novel anellovirus species, 24 of which were validated by Sanger sequencing to discard artifacts. These findings underscore the importance of implementing more efficient purification procedures that enrich the viral fraction as an essential step in virome studies and question the suggested pathological role of anelloviruses.}, } @article {pmid33767308, year = {2021}, author = {Rodrigues, MX and Fiani, N and Bicalho, RC and Peralta, S}, title = {Preliminary functional analysis of the subgingival microbiota of cats with periodontitis and feline chronic gingivostomatitis.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {6896}, pmid = {33767308}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Cat Diseases/genetics/microbiology/*pathology ; Cats ; Chronic Periodontitis/genetics/microbiology/*veterinary ; Female ; Gingiva/metabolism/microbiology/*pathology ; Male ; *Metagenome ; *Microbiota ; Porphyromonas gingivalis/*isolation & purification ; Stomatitis/genetics/microbiology/*veterinary ; }, abstract = {The subgingival microbial communities of domestic cats remain incompletely characterized and it is unknown whether their functional profiles are associated with disease. In this study, we used a shotgun metagenomic approach to explore the functional potential of subgingival microbial communities in client-owned cats, comparing findings between periodontally healthy cats and cats with naturally occurring chronic periodontitis, aggressive periodontitis, and feline chronic gingivostomatitis. Subgingival samples were subjected to shotgun sequencing and the metagenomic datasets were analyzed using the MG-RAST metagenomic analysis server and STAMP v2.1.3 (Statistical Analysis of Metagenomic Profiles) software. The microbial composition was also described to better understand the predicted features of the communities. The Respiration category in the level 1 Subsystems database varied significantly among groups. In this category, the abundance of V-Type ATP-synthase and Biogenesis of cytochrome c oxidases were significantly enriched in the diseased and in the healthy groups, respectively. Both features have been previously described in periodontal studies in people and are in consonance with the microbial composition of feline subgingival sites. In addition, the narH (nitrate reductase) gene frequency, identified using the KEGG Orthology database, was significantly increased in the healthy group. The results of this study provide preliminary functional insights of the microbial communities associated with periodontitis in domestic cats and suggest that the ATP-synthase and nitrate-nitrite-NO pathways may represent appropriate targets for the treatment of this common disease.}, } @article {pmid33766942, year = {2021}, author = {Levin, D and Raab, N and Pinto, Y and Rothschild, D and Zanir, G and Godneva, A and Mellul, N and Futorian, D and Gal, D and Leviatan, S and Zeevi, D and Bachelet, I and Segal, E}, title = {Diversity and functional landscapes in the microbiota of animals in the wild.}, journal = {Science (New York, N.Y.)}, volume = {372}, number = {6539}, pages = {}, doi = {10.1126/science.abb5352}, pmid = {33766942}, issn = {1095-9203}, mesh = {Animals ; Animals, Wild/classification/*microbiology/physiology ; *Bacteria/classification/genetics/isolation & purification ; Bacterial Toxins/metabolism ; Behavior, Animal ; Biodiversity ; Databases, Nucleic Acid ; Diet ; Ecosystem ; Falkland Islands ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Genome, Bacterial ; Host Microbial Interactions ; Israel ; Madagascar ; *Metagenome ; Metagenomics ; Peptide Hydrolases/genetics/metabolism ; Phylogeny ; Queensland ; Uganda ; }, abstract = {Animals in the wild are able to subsist on pathogen-infected and poisonous food and show immunity to various diseases. These may be due to their microbiota, yet we have a poor understanding of animal microbial diversity and function. We used metagenomics to analyze the gut microbiota of more than 180 species in the wild, covering diverse classes, feeding behaviors, geographies, and traits. Using de novo metagenome assembly, we constructed and functionally annotated a database of more than 5000 genomes, comprising 1209 bacterial species of which 75% are unknown. The microbial composition, diversity, and functional content exhibit associations with animal taxonomy, diet, activity, social structure, and life span. We identify the gut microbiota of wild animals as a largely untapped resource for the discovery of therapeutics and biotechnology applications.}, } @article {pmid33764993, year = {2021}, author = {Tao, F and Xing, X and Wu, J and Jiang, R}, title = {Enteral nutrition modulation with n-3 PUFAs directs microbiome and lipid metabolism in mice.}, journal = {PloS one}, volume = {16}, number = {3}, pages = {e0248482}, pmid = {33764993}, issn = {1932-6203}, mesh = {Animals ; Crohn Disease/drug therapy ; Enteral Nutrition/methods ; Fatty Acids, Omega-3/*pharmacology ; Female ; Gastrointestinal Microbiome/*drug effects ; Lipid Metabolism/*drug effects ; Male ; Mice ; Mice, Inbred BALB C ; }, abstract = {Nutritional support using exclusive enteral nutrition (EEN) has been studied as primary therapy for the management of liver diseases, Crohn's disease, and cancers. EEN can also increase the number of beneficial microbiotas in the gut, improve bile acid and lipid metabolism, and decrease the number of harmful dietary micro-particles, possibly by influencing disease occurrence and increasing immunity. This study investigated the effects of EEN-n-3 polyunsaturated fatty acids (3PUFAs) (EEN-3PUFAs) on the gut microbiome, intestinal barrier, and lipid or bile acid metabolism in mice. Metagenomic sequencing technology was used to analyze the effects of EEN-3PUFAs on the composition of gut microbiome signatures. The contents of short-chain fatty acids (SCFAs) and bile acids in the feces and liver of the mice were assayed by gas chromatography and ultra-high-pressure liquid chromatography/high-resolution tandem mass spectrometry, respectively. The levels of lipopolysaccharide (LPS) and D-lactic acid in the blood were used to assess intestinal permeability. The results indicated that EEN-3PUFAs could improve the composition of gut microbiome signatures and increase the abundance of Barnesiella and Lactobacillus (genus), Porphyromonadaceae, and Bacteroidia (species), and Bacteroidetes (phylum) after EEN-3PUFAs initiation. In addition, EEN-3PUFAs induced the formation of SCFAs (mainly including acetic acid, propionic acid, and butyric acid) and increased the intestinal wall compared to the control group. In conclusion, EEN-3PUFAs modulate the alterations in gut microbiome signatures, enhanced intestinal barrier, and regulated the fatty acid composition and lipid metabolism shifts and the putative mechanisms underlying these effects.}, } @article {pmid33764980, year = {2021}, author = {Ahmad, T and Gupta, G and Sharma, A and Kaur, B and El-Sheikh, MA and Alyemeni, MN}, title = {Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake.}, journal = {PloS one}, volume = {16}, number = {3}, pages = {e0248116}, pmid = {33764980}, issn = {1932-6203}, mesh = {Altitude ; Bacteria/classification/*genetics/isolation & purification ; Genome, Bacterial ; India ; Lakes/*microbiology ; *Metagenome ; Metagenomics ; Microbiota ; }, abstract = {Freshwater lakes present an ecological border between humans and a variety of host organisms. The present study was designed to evaluate the microbiota composition and distribution in Dal Lake at Srinagar, India. The non-chimeric sequence reads were classified taxonomically into 49 phyla, 114 classes, 185 orders, 244 families and 384 genera. Proteobacteria was found to be the most abundant bacterial phylum in all the four samples. The highest number of observed species was found to be 3097 in sample taken from least populated area during summer (LPS) whereas the summer sample from highly populated area (HPS) was found most diverse among all as indicated by taxonomic diversity analysis. The QIIME output files were used for PICRUSt analysis to assign functional attributes. The samples exhibited a significant difference in their microbial community composition and structure. Comparative analysis of functional pathways indicated that the anthropogenic activities in populated areas and higher summer temperature, both decrease functional potential of the Lake microbiota. This is probably the first study to demonstrate the comparative taxonomic diversity and functional composition of an urban freshwater lake amid its highly populated and least populated areas during two extreme seasons (winter and summer).}, } @article {pmid33764826, year = {2021}, author = {Haran, JP and Ward, DV and Bhattarai, SK and Loew, E and Dutta, P and Higgins, A and McCormick, BA and Bucci, V}, title = {The high prevalence of Clostridioides difficile among nursing home elders associates with a dysbiotic microbiome.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-15}, pmid = {33764826}, issn = {1949-0984}, support = {K23 AG057790/AG/NIA NIH HHS/United States ; R03 AG056356/AG/NIA NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Asymptomatic Infections/*epidemiology ; Clostridioides difficile/growth & development/*isolation & purification ; Clostridium Infections/*epidemiology/microbiology ; Dysbiosis/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; *Nursing Homes ; Prevalence ; Proton Pump Inhibitors/therapeutic use ; }, abstract = {Clostridioides difficile disproportionally affects the elderly living in nursing homes (NHs). Our objective was to explore the prevalence of C. difficile in NH elders, over time and to determine whether the microbiome or other clinical factors are associated with C. difficile colonization.We collected serial stool samples from NH residents. C. difficile prevalence was determined by quantitative polymerase-chain reaction detection of Toxin genes tcdA and tcdB; microbiome composition was determined by shotgun metagenomic sequencing. We used mixed-effect random forest modeling machine to determine bacterial taxa whose abundance is associated with C. difficile prevalence while controlling for clinical covariates including demographics, medications, and past medical history.We enrolled 167 NH elders who contributed 506 stool samples. Of the 123 elders providing multiple samples, 30 (24.4%) elders yielded multiple samples in which C. difficile was detected and 78 (46.7%) had at least one C. difficile positive sample. Elders with C. difficile positive samples were characterized by increased abundances of pathogenic or inflammatory-associated bacterial taxa and by lower abundances of taxa with anti-inflammatory or symbiotic properties. Proton pump inhibitor (PPI) use is associated with lower prevalence of C. difficile (Odds Ratio 0.46; 95%CI, 0.22-0.99) and the abundance of bacterial species with known beneficial effects was higher in PPI users and markedly lower in elders with high C. difficile prevalence.C. difficile is prevalent among NH elders and a dysbiotic gut microbiome associates with C. difficile colonization status. Manipulating the gut microbiome may prove to be a key strategy in the reduction of C. difficile in the NH.}, } @article {pmid33762692, year = {2021}, author = {Palkova, L and Tomova, A and Repiska, G and Babinska, K and Bokor, B and Mikula, I and Minarik, G and Ostatnikova, D and Soltys, K}, title = {Evaluation of 16S rRNA primer sets for characterisation of microbiota in paediatric patients with autism spectrum disorder.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {6781}, pmid = {33762692}, issn = {2045-2322}, mesh = {Autism Spectrum Disorder/diagnosis/*etiology ; Biodiversity ; Child ; Child, Preschool ; Computational Biology/methods ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; *RNA, Ribosomal, 16S ; }, abstract = {intestinal microbiota is becoming a significant marker that reflects differences between health and disease status also in terms of gut-brain axis communication. Studies show that children with autism spectrum disorder (ASD) often have a mix of gut microbes that is distinct from the neurotypical children. Various assays are being used for microbiota investigation and were considered to be universal. However, newer studies showed that protocol for preparing DNA sequencing libraries is a key factor influencing results of microbiota investigation. The choice of DNA amplification primers seems to be the crucial for the outcome of analysis. In our study, we have tested 3 primer sets to investigate differences in outcome of sequencing analysis of microbiota in children with ASD. We found out that primers detected different portion of bacteria in samples especially at phylum level; significantly higher abundance of Bacteroides and lower Firmicutes were detected using 515f/806r compared to 27f/1492r and 27f*/1495f primers. So, the question is whether a gold standard of Firmicutes/Bacteroidetes ratio is a valuable and reliable universal marker, since two primer sets towards 16S rRNA can provide opposite information. Moreover, significantly higher relative abundance of Proteobacteria was detected using 27f/1492r. The beta diversity of sample groups differed remarkably and so the number of observed bacterial genera.}, } @article {pmid33762614, year = {2021}, author = {Moturi, J and Kim, KY and Hosseindoust, A and Lee, JH and Xuan, B and Park, J and Kim, EB and Kim, JS and Chae, BJ}, title = {Effects of Lactobacillus salivarius isolated from feces of fast-growing pigs on intestinal microbiota and morphology of suckling piglets.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {6757}, pmid = {33762614}, issn = {2045-2322}, mesh = {Animals ; *Animals, Suckling ; Biodiversity ; Biomarkers ; Body Weight ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Ligilactobacillus salivarius/*isolation & purification ; Metagenome ; Metagenomics/methods ; Swine ; }, abstract = {The study determined the effects of Lactobacillus salivarius (LS) administered early in the life of suckling piglets on their growth performance, gut morphology, and gut microbiota. Thirty litters of 3-day-old crossbreed piglets were randomly assigned to one of the three treatments, and treatments were commenced on day 3 after birth. During the whole period of the experiment, the piglets were kept with their mothers and left to suckle ad libitum while being supplemented with a milk formula with or without the bacterial probiotic supplemented. The control group (CON) was not treated with probiotics, the HLS group was treated with LS144 (HLS) screened from feces of fast-growing pigs with high body mass index (BMI) while the NLS group was supplemented with LS160 (NLS) screened from feces obtained from pigs of normal BMI. At the weaning time, a higher abundance of Actinobacteria, Lentisphaerae, and Elusimicrobia phyla were observed in NLS piglets, whereas the abundance of Fibrobacteres phylum was significantly reduced in NLS and HLS piglets compared with the CON. A greater abundance of Lactobacillus was detected in the HLS treatment compared with the CON. The abundance of Bacteroides and Fibrobacter was higher in the CON piglets compared with the HLS and NLS piglets. Compared with the CON group, the oral administration of LS significantly increased the number of Lactobacillus and villus height in the duodenum, jejunum, and ileum. Moreover, the villus height of the duodenum was significantly improved in the HLS treatment compared with the NLS treatment. Based on the findings in the neonatal piglet model, we suggest that oral supplementation of LS, particularly LS isolated from high BMI pigs, could be beneficial by improving the intestinal villus height.}, } @article {pmid33761242, year = {2021}, author = {Han, Y and Teng, Y and Wang, X and Ren, W and Wang, X and Luo, Y and Zhang, H and Christie, P}, title = {Soil Type Driven Change in Microbial Community Affects Poly(butylene adipate-co-terephthalate) Degradation Potential.}, journal = {Environmental science & technology}, volume = {55}, number = {8}, pages = {4648-4657}, doi = {10.1021/acs.est.0c04850}, pmid = {33761242}, issn = {1520-5851}, mesh = {Adipates ; Alkenes ; *Microbiota ; Phthalic Acids ; Polyesters ; *Soil ; }, abstract = {Biodegradable mulch films have been developed as a suitable alternative to conventional nondegradable polyethylene films. However, the key factors controlling the degradation speed of biodegradable mulch films in soils remain unclear. Here, we linked changes in the soil microbiome with the degradation rate of a promising biodegradable material poly(butylene adipate-co-terephthalate) (PBAT) in four soil types, a lou soil (LS), a fluvo-aquic soil (CS), a black soil (BS), and a red soil (RS), equivalent to Inceptisols (the first two soils), Mollisols, and Ultisols, using soil microcosms. The PBAT degradation rate differed with the soil type, with PBAT mineralization levels of 16, 9, 0.3, and 0.9% in LS, CS, BS, and RS, respectively, after 120 days. Metagenomic analysis showed that the microbial community in LS was more responsive to PBAT than the other three soils. PBAT hydrolase genes were significantly enriched in LS but were not significantly stimulated by PBAT in CS, BS, or RS. Several members of Proteobacteria were identified as novel potential degraders, and their enrichment extent was significantly positively correlated with PBAT degradation capacity. Overall, our results suggest that soil environments harbored a range of PBAT-degrading bacteria and the enrichment of potential degraders drives the fate of PBAT in the soils.}, } @article {pmid33760154, year = {2021}, author = {Abdulla, MH and Agarwal, D and Singh, JK and Traiki, TB and Pandey, MK and Ahmad, R and Srivastava, SK}, title = {Association of the microbiome with colorectal cancer development (Review).}, journal = {International journal of oncology}, volume = {58}, number = {5}, pages = {}, doi = {10.3892/ijo.2021.5197}, pmid = {33760154}, issn = {1791-2423}, mesh = {Bacteria/classification/metabolism/*pathogenicity ; Colorectal Neoplasms/*microbiology ; Dysbiosis/*complications ; Gastrointestinal Microbiome ; Humans ; }, abstract = {Colorectal cancer (CRC) is the second most common malignancy causing cancer‑related mortality globally. It is the third most common type of cancer detected worldwide. The recent concept of the human body supporting a diverse community of microbes has revealed the important role these microbes play synergistically in maintaining normal homeostasis. The balance between the microbiomes and epithelial cells of the human body is essential for normal physiology. Evidence from meta‑genome analysis indicates that an imbalance in the microbiome is prominent in the guts of patients with CRC. Several studies have suggested that the gut microbiota can secrete metabolites [short‑chain fatty acids (SCFAs), vitamins, polyphenols and polyamines] that modulate the susceptibility of the colon and rectum by altering inflammation and DNA damage. The state of microbiome imbalance (dysbiosis) has been reported in patients with CRC, with an increasing population of 'bad' microbes and a decrease in 'good' microbes. The 'good' microbes, also known as commensal microbes, produce butyrate; however, 'bad' microbes cause a pro‑inflammatory state. The complex association between pathological microbial communities leading to cancer progression is not yet fully understood. An altered microbial metabolite profile plays a direct role in CRC metabolism. Furthermore, diet plays an essential role in the risk of gastrointestinal cancer development. High‑fiber diets regulate the gut microbiome and reduce the risk of CRC development, and may be fruitful in the better management of therapeutics. In the present review, the current status of the microbiome in CRC development is discussed.12.}, } @article {pmid33758981, year = {2022}, author = {Campos, AB and Cavalcante, LC and de Azevedo, AR and Loiola, M and Silva, AET and Ara, A and Meirelles, PM}, title = {CPR and DPANN Have an Overlooked Role in Corals' Microbial Community Structure.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {252-255}, pmid = {33758981}, issn = {1432-184X}, support = {11268//Ministério da Ciência, Tecnologia, Inovações e Comunicações/ ; Serra-1709-17818//Instituto Serrapilheira/ ; 132261/2018-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 88887.301758/2018-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, mesh = {Animals ; *Anthozoa/microbiology ; Archaea/genetics ; Bacteria/genetics ; *Microbiota ; }, abstract = {Understanding how microbial communities are structured in coral holobionts is important to estimate local and global impacts and provide efficient environment management strategies. Several studies investigated the relationship between corals and their microbial communities, including the environmental drivers of shifts in this relationship, associated with diseases and coral cover loss. However, these studies are often geographically or taxonomically restricted and usually focused on the most abundant microbial groups, neglecting the rare biosphere, including archaea in the group DPANN and the recently discovered bacterial members of the candidate phyla radiation (CPR). Although it is known that rare microbes can play essential roles in several environments, we still lack understanding about which taxa comprise the rare biosphere of corals' microbiome. Here, we investigated the host-related and technical factors influencing coral microbial community structure and the importance of CPR and DPANN in this context by analyzing more than a hundred coral metagenomes from independent studies worldwide. We show that coral genera are the main biotic factor shaping coral microbial communities. We also detected several CPR and DPANN phyla comprising corals' rare biosphere for the first time and showed that they significantly contribute to shaping coral microbial communities.}, } @article {pmid33758906, year = {2021}, author = {Kayani, MUR and Huang, W and Feng, R and Chen, L}, title = {Genome-resolved metagenomics using environmental and clinical samples.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {5}, pages = {}, pmid = {33758906}, issn = {1477-4054}, mesh = {DNA Barcoding, Taxonomic/*methods ; Feces/microbiology ; Genitalia/microbiology ; *Genome, Microbial ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Mouth/microbiology ; Sequence Analysis, DNA ; Skin/microbiology ; Soil Microbiology ; Water Microbiology ; }, abstract = {Recent advances in high-throughput sequencing technologies and computational methods have added a new dimension to metagenomic data analysis i.e. genome-resolved metagenomics. In general terms, it refers to the recovery of draft or high-quality microbial genomes and their taxonomic classification and functional annotation. In recent years, several studies have utilized the genome-resolved metagenome analysis approach and identified previously unknown microbial species from human and environmental metagenomes. In this review, we describe genome-resolved metagenome analysis as a series of four necessary steps: (i) preprocessing of the sequencing reads, (ii) de novo metagenome assembly, (iii) genome binning and (iv) taxonomic and functional analysis of the recovered genomes. For each of these four steps, we discuss the most commonly used tools and the currently available pipelines to guide the scientific community in the recovery and subsequent analyses of genomes from any metagenome sample. Furthermore, we also discuss the tools required for validation of assembly quality as well as for improving quality of the recovered genomes. We also highlight the currently available pipelines that can be used to automate the whole analysis without having advanced bioinformatics knowledge. Finally, we will highlight the most widely adapted and actively maintained tools and pipelines that can be helpful to the scientific community in decision making before they commence the analysis.}, } @article {pmid33758359, year = {2021}, author = {Rojas-Jaimes, J and Lindo-Seminario, D and Correa-Núñez, G and Diringer, B}, title = {Characterization of the bacterial microbiome of Rhipicephalus (Boophilus) microplus collected from Pecari tajacu "Sajino" Madre de Dios, Peru.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {6661}, pmid = {33758359}, issn = {2045-2322}, mesh = {Animals ; *Bacteria/classification ; Biodiversity ; Cattle ; Ecosystem ; Farms ; Female ; Male ; *Microbiota ; Peru ; Rhipicephalus/*microbiology ; }, abstract = {Ticks are arthropods that can host and transmit pathogens to wild animals, domestic animals, and even humans. The bacterial microbiome of adult (males and females) and nymph Rhipicephalus microplus ticks collected from a collared peccary, Pecari tajacu, captured in the rural area of Botijón Village in the Amazon region of Madre de Dios, Peru, was evaluated using metagenomics. The Chao1 and Shannon-Weaver analyses indicated greater bacterial richness and diversity in female ticks (GARH; 375-4.15) and nymph ticks (GARN; 332-4.75) compared to that in male ticks (GARM; 215-3.20). Taxonomic analyses identified 185 operational taxonomic units representing 147 bacterial genera. Of the 25 most prevalent genera, Salmonella (17.5%) and Vibrio (15.0%) showed the highest relative abundance followed by several other potentially pathogenic genera, such as Paracoccus (7.8%), Staphylococcus (6.8%), Pseudomonas (6.6%), Corynebacterium (5.0%), Cloacibacterium (3.6%), and Acinetobacter (2.5%). In total, 19.7% of the detected genera are shared by GARH, GARM, and GARN, and they can be considered as the core microbiome of R. microplus. To the best of our knowledge, this study is the first to characterize the microbiome of ticks collected from P. tajacu and to report the presence of Salmonella and Vibrio in R. microplus. The pathogenic potential and the role of these bacteria in the physiology of R. microplus should be further investigated due to the possible implications for public health and animal health in populations neighboring the habitat of P. tajacu.}, } @article {pmid33758301, year = {2021}, author = {Kutsyr, O and Maestre-Carballa, L and Lluesma-Gomez, M and Martinez-Garcia, M and Cuenca, N and Lax, P}, title = {Retinitis pigmentosa is associated with shifts in the gut microbiome.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {6692}, pmid = {33758301}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Biomarkers ; Disease Models, Animal ; Disease Susceptibility ; Dysbiosis ; *Gastrointestinal Microbiome ; Immunohistochemistry ; Metagenomics/methods ; Mice ; Mice, Knockout ; RNA, Ribosomal, 16S ; Retinal Degeneration/etiology/pathology ; Retinitis Pigmentosa/*etiology/metabolism/pathology ; }, abstract = {The gut microbiome is known to influence the pathogenesis and progression of neurodegenerative diseases. However, there has been relatively little focus upon the implications of the gut microbiome in retinal diseases such as retinitis pigmentosa (RP). Here, we investigated changes in gut microbiome composition linked to RP, by assessing both retinal degeneration and gut microbiome in the rd10 mouse model of RP as compared to control C57BL/6J mice. In rd10 mice, retinal responsiveness to flashlight stimuli and visual acuity were deteriorated with respect to observed in age-matched control mice. This functional decline in dystrophic animals was accompanied by photoreceptor loss, morphologic anomalies in photoreceptor cells and retinal reactive gliosis. Furthermore, 16S rRNA gene amplicon sequencing data showed a microbial gut dysbiosis with differences in alpha and beta diversity at the genera, species and amplicon sequence variants (ASV) levels between dystrophic and control mice. Remarkably, four fairly common ASV in healthy gut microbiome belonging to Rikenella spp., Muribaculaceace spp., Prevotellaceae UCG-001 spp., and Bacilli spp. were absent in the gut microbiome of retinal disease mice, while Bacteroides caecimuris was significantly enriched in mice with RP. The results indicate that retinal degenerative changes in RP are linked to relevant gut microbiome changes. The findings suggest that microbiome shifting could be considered as potential biomarker and therapeutic target for retinal degenerative diseases.}, } @article {pmid33758228, year = {2021}, author = {Appiah, SA and Foxx, CL and Langgartner, D and Palmer, A and Zambrano, CA and Braumüller, S and Schaefer, EJ and Wachter, U and Elam, BL and Radermacher, P and Stamper, CE and Heinze, JD and Salazar, SN and Luthens, AK and Arnold, AL and Reber, SO and Huber-Lang, M and Lowry, CA and Halbgebauer, R}, title = {Evaluation of the gut microbiome in association with biological signatures of inflammation in murine polytrauma and shock.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {6665}, pmid = {33758228}, issn = {2045-2322}, support = {R01 AT010005/AT/NCCIH NIH HHS/United States ; R21 MH116263/MH/NIMH NIH HHS/United States ; R41 AT011390/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; Biodiversity ; *Biomarkers ; Disease Models, Animal ; Enzyme-Linked Immunosorbent Assay ; *Gastrointestinal Microbiome ; Inflammation/diagnosis/*etiology/*metabolism ; Male ; Metagenomics ; Mice ; Multiple Trauma/*complications/etiology ; RNA, Ribosomal, 16S ; ROC Curve ; Shock/*complications/etiology ; Supervised Machine Learning ; }, abstract = {Severe injuries are frequently accompanied by hemorrhagic shock and harbor an increased risk for complications. Local or systemic inflammation after trauma/hemorrhage may lead to a leaky intestinal epithelial barrier and subsequent translocation of gut microbiota, potentially worsening outcomes. To evaluate the extent with which trauma affects the gut microbiota composition, we performed a post hoc analysis of a murine model of polytrauma and hemorrhage. Four hours after injury, organs and plasma samples were collected, and the diversity and composition of the cecal microbiome were evaluated using 16S rRNA gene sequencing. Although cecal microbial alpha diversity and microbial community composition were not found to be different between experimental groups, norepinephrine support in shock animals resulted in increased alpha diversity, as indicated by higher numbers of distinct microbial features. We observed that the concentrations of proinflammatory mediators in plasma and intestinal tissue were associated with measures of microbial alpha and beta diversity and the presence of specific microbial drivers of inflammation, suggesting that the composition of the gut microbiome at the time of trauma, or shortly after trauma exposure, may play an important role in determining physiological outcomes. In conclusion, we found associations between measures of gut microbial alpha and beta diversity and the severity of systemic and local gut inflammation. Furthermore, our data suggest that four hours following injury is too early for development of global changes in the alpha diversity or community composition of the intestinal microbiome. Future investigations with increased temporal-spatial resolution are needed in order to fully elucidate the effects of trauma and shock on the gut microbiome, biological signatures of inflammation, and proximal and distal outcomes.}, } @article {pmid33757721, year = {2021}, author = {Choi, S and Sohn, KH and Jung, JW and Kang, MG and Yang, MS and Kim, S and Choi, JH and Cho, SH and Kang, HR and Yi, H}, title = {Lung virome: New potential biomarkers for asthma severity and exacerbation.}, journal = {The Journal of allergy and clinical immunology}, volume = {148}, number = {4}, pages = {1007-1015.e9}, doi = {10.1016/j.jaci.2021.03.017}, pmid = {33757721}, issn = {1097-6825}, mesh = {Adult ; Aged ; Asthma/physiopathology/*virology ; Biomarkers ; Disease Progression ; Female ; Herpesviridae/genetics/isolation & purification ; Humans ; Lung/physiopathology/*virology ; Male ; Middle Aged ; RNA, Ribosomal, 16S ; Respiratory Function Tests ; *Severity of Illness Index ; Sputum/virology ; *Virome/genetics ; }, abstract = {BACKGROUND: Although some respiratory virus infections are known to contribute to the development and exacerbation of asthma, commensal viromes in airway have not been extensively studied due to technical challenges.

OBJECTIVES: This study investigated the characteristics of the virome in asthmatic airways.

METHODS: Both the bacteriome and virome profiles in sputum from 12 healthy individuals, 15 patients with nonsevere asthma, and 15 patients with severe asthma were analyzed and assessed for the association with clinical characteristics such as severity, exacerbation, Asthma Control Test (ACT), and lung function.

RESULTS: While analysis of the 16S ribosomal RNA bacteriome in the airway showed no differences, clear contrasts in the diversity and composition of airway viromes were observed between healthy controls and patients with asthma. Herpesviruses were the most abundant type of virus in the asthma group (44.6 ± 4.6%), mainly with cytomegalovirus (CMV) and EBV accounting for 24.5 ± 3.3% and 16.9 ± 3.5%, respectively, in contrast to those in the healthy controls (5.4 ± 2.5% and 7.1 ± 3.0%, respectively). CMV and EBV were more abundant in patients with asthma who experienced exacerbation, and their abundance showed correlation with more severe asthma, lower ACT score, and lower lung function. On the contrary, bacteriophage that is abundant in healthy controls was severely reduced in patients with asthma in the order of nonsevere and severe asthma and presented significant positive correlation with ACT and FEV1/forced vital capacity.

CONCLUSIONS: Lung viromes, especially, CMV, EBV, and bacteriophage may be potential biomarkers of asthma severity and exacerbation.}, } @article {pmid33757515, year = {2021}, author = {Vientós-Plotts, AI and Ericsson, AC and Rindt, H and Reinero, CR}, title = {Blood cultures and blood microbiota analysis as surrogates for bronchoalveolar lavage fluid analysis in dogs with bacterial pneumonia.}, journal = {BMC veterinary research}, volume = {17}, number = {1}, pages = {129}, pmid = {33757515}, issn = {1746-6148}, mesh = {Animals ; Bacterial Typing Techniques/methods/veterinary ; Blood Culture/*veterinary ; Bronchoalveolar Lavage Fluid/*microbiology ; DNA, Bacterial ; Dog Diseases/*blood/diagnosis/microbiology ; Dogs ; Female ; High-Throughput Nucleotide Sequencing/veterinary ; Male ; *Microbiota ; Pneumonia, Bacterial/blood/diagnosis/microbiology/*veterinary ; RNA, Ribosomal, 16S ; Sensitivity and Specificity ; Sequence Analysis, DNA/veterinary ; }, abstract = {BACKGROUND: Diagnosis of canine bacterial pneumonia relies on airway lavage to confirm septic, suppurative inflammation, and a positive bacterial culture. Considering risks of bronchoalveolar lavage fluid (BALF) collection, minimally invasive methods like culture or next generation sequencing of blood would be appealing. In dogs with bacterial pneumonia, our study aims included (1): determining proportion of agreement between cultivable bacteria in BALF and blood (2); characterizing BALF, blood, and oropharyngeal (OP) microbiota and determining if bacteria cultured from BALF were present in these communities; and (3) comparing relatedness of microbial community composition at all three sites. Bacterial cultures were performed on BALF and blood. After DNA extraction of BALF, blood and OP, 16S rRNA amplicon libraries were generated, sequenced, and compared to a bacterial gene sequence database.

RESULTS: Disregarding one false positive, blood cultures were positive in 2/9 dogs (5 total isolates), all 5 isolates were present in BALF cultures (16 total isolates). Based on sequencing data, all sites had rich and diverse microbial communities. Comparing cultured BALF bacterial genera with sequenced taxa, all dogs had ≥1 cultured isolate present in their microbiota: cultured BALF isolates were found in microbiota of BALF (12/16), blood (7/16), and OP (6/11; only 7 dogs had OP swabs). Of 394 distinct taxa detected in BALF, these were present in 75% OP and 45% blood samples. BALF community composition was significantly different than OP (p = 0.0059) and blood (p = 0.0009).

CONCLUSIONS: Blood cultures are insensitive but specific for cultured BALF bacteria in canine bacterial pneumonia. Cultivable BALF bacteria were present in BALF, blood and OP microbiota to differing degrees.}, } @article {pmid33757378, year = {2021}, author = {Bellali, S and Lagier, JC and Million, M and Anani, H and Haddad, G and Francis, R and Kuete Yimagou, E and Khelaifia, S and Levasseur, A and Raoult, D and Bou Khalil, J}, title = {Running after ghosts: are dead bacteria the dark matter of the human gut microbiota?.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-12}, pmid = {33757378}, issn = {1949-0984}, mesh = {Bacteria/classification/growth & development ; *Bacterial Physiological Phenomena ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenome ; Metagenomics ; *Microbial Viability ; Phylogeny ; }, abstract = {The human gut microbiota has been explored by a wide range of culture-dependent and culture-independent methods, revealing that many microbes remain uncharacterized and uncultured. In this work, we aimed to confirm the hypothesis that some of the species present in the human gut microbiota remain uncultured not because of culture limitations, but because all members of such species are dead before reaching the end of the gastro-intestinal tract.We evaluate this phenomenon by studying the microbial viability and culturability of the human gut microbiota from the fresh fecal materials of eight healthy adults. For the first time, we applied fluorescence-activated cell sorting (FACS) combined with 16S metagenomics analysis and microbial culturomics.We identified a total of 1,020 bacterial OTUs and 495 bacterial isolates through metagenomics and culturomics, respectively. Among the FACS metagenomics results, only 735 bacterial OTUs were alive, comprising on average 42% of known species and 87% of relative abundance per individual. The remaining uncultured bacteria were rare, dead, or injured.Our strategy allowed us to shed light on the dark matter of the human gut microbiota and revealed that both metagenomics and culturomics approaches are needed for greater insight into the diversity and richness of bacteria in the human gut microbiota. Further work on culture is needed to enhance the repertoire of cultured gut bacteria by targeting low abundance bacteria and optimizing anaerobic sample conditioning and processing to preserve the viability of bacteria.}, } @article {pmid33755859, year = {2021}, author = {Das, S and Roy, G and Najar, IN and Sherpa, MT and Thakur, N}, title = {Diversity and composition of the North Sikkim hot spring mycobiome using a culture-independent method.}, journal = {Folia microbiologica}, volume = {66}, number = {3}, pages = {457-468}, pmid = {33755859}, issn = {1874-9356}, mesh = {*Biodiversity ; *Fungi/physiology ; *Hot Springs/microbiology ; Metagenomics ; *Mycobiome/physiology ; Sikkim ; }, abstract = {Fungi are considered to be the most resilient and economically important microbial community that can easily survive and optimally grow under a wide range of growth conditions. Thermophilic fungi from the geothermal sources have been less pondered upon and lie unexplored. Here, a microbiome approach was conducted to understand the concealed world of the environmental mycobiota from the two hot springs of North Sikkim district located in North-east India. The solfataric muds from the hot springs were analyzed. In both the samples, on the basis of genus level classification, genus Fusarium had the highest abundance followed by Colletotrichum, Pochonia, Pyricularia, Neurospora, etc. Analyzing the predicted genes, the functional proteins of New Yume Samdung mycobiome were found to be dominated by the genera Fusarium (22%), Trichoderma (12%), and Aspergillus (11%), whereas in the case of Old Yume Samdung, it was dominated by the genera Aspergillus (11%), Saccharomyces (6%), and Fusarium (5%). Interestingly, in the studied mycobiome, environmental yeasts were also detected. From the functional metagenomics, sulfate adenylatetransferase (SAT) proteins for sulfur assimilation were found in some of the fungal reads. Toxin protein reads such as AM-toxin biosynthesis proteins, AF-toxin biosynthesis proteins, Gliotoxin biosynthesis proteins, and aflatoxin biosynthesis proteins were detected in the mycobiomes.}, } @article {pmid33754165, year = {2021}, author = {Del Chierico, F and Manco, M and Gardini, S and Guarrasi, V and Russo, A and Bianchi, M and Tortosa, V and Quagliariello, A and Shashaj, B and Fintini, D and Putignani, L}, title = {Fecal microbiota signatures of insulin resistance, inflammation, and metabolic syndrome in youth with obesity: a pilot study.}, journal = {Acta diabetologica}, volume = {58}, number = {8}, pages = {1009-1022}, pmid = {33754165}, issn = {1432-5233}, support = {600932//European Commission (FP7 Information Communication Technologies Programme)/ ; }, mesh = {Adolescent ; Bacteria/classification/genetics ; Biomarkers/blood ; Child ; Feces/*microbiology ; Female ; Glucose Intolerance/microbiology ; Humans ; Hypertension/microbiology ; Inflammation/*microbiology ; Insulin Resistance/*physiology ; Male ; Metabolic Syndrome/*microbiology ; Metagenomics ; Microbiota/*physiology ; *Obesity/complications ; Pilot Projects ; RNA, Ribosomal, 16S/analysis ; Risk Factors ; Triglycerides/blood ; }, abstract = {AIMS: To identify fecal microbiota profiles associated with metabolic abnormalities belonging to the metabolic syndrome (MS), high count of white blood cells (WBCs) and insulin resistance (IR).

METHODS: Sixty-eight young patients with obesity were stratified for percentile distribution of MS abnormalities. A MS risk score was defined as low, medium, and high MS risk. High WBCs were defined as a count ≥ 7.0 10[3]/µL; severe obesity as body mass index Z-score ≥ 2 standard deviations; IR as homeostatic assessment model algorithm of IR (HOMA) ≥ 3.7. Stool samples were analyzed by 16S rRNA-based metagenomics.

RESULTS: We found reduced bacterial richness of fecal microbiota in patients with IR and high diastolic blood pressure (BP). Distinct microbial markers were associated to high BP (Clostridium and Clostridiaceae), low high-density lipoprotein cholesterol (Lachnospiraceae, Gemellaceae, Turicibacter), and high MS risk (Coriobacteriaceae), WBCs (Bacteroides caccae, Gemellaceae), severe obesity (Lachnospiraceae), and impaired glucose tolerance (Bacteroides ovatus and Enterobacteriaceae). Conversely, taxa such as Faecalibacterium prausnitzii, Parabacterodes, Bacteroides caccae, Oscillospira, Parabacterodes distasonis, Coprococcus, and Haemophilus parainfluenzae were associated to low MS risk score, triglycerides, fasting glucose and HOMA-IR, respectively. Supervised multilevel analysis grouped clearly "variable" patients based on the MS risk.

CONCLUSIONS: This was a proof-of-concept study opening the way at the identification of fecal microbiota signatures, precisely associated with cardiometabolic risk factors in young patients with obesity. These evidences led us to infer, while some gut bacteria have a detrimental role in exacerbating metabolic risk factors some others are beneficial ameliorating cardiovascular host health.}, } @article {pmid33754037, year = {2021}, author = {Zhong, M and Xiong, Y and Zhao, J and Gao, Z and Ma, J and Wu, Z and Song, Y and Hong, X}, title = {Candida albicans disorder is associated with gastric carcinogenesis.}, journal = {Theranostics}, volume = {11}, number = {10}, pages = {4945-4956}, pmid = {33754037}, issn = {1838-7640}, support = {26398D0016/TW/FIC NIH HHS/United States ; }, mesh = {Aged ; Aspergillus ; Basidiomycota ; *Candida albicans ; Candida glabrata ; *Carcinogenesis ; Carcinoma/*microbiology/pathology ; China ; DNA, Ribosomal/genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Hypocreales ; Male ; Metagenomics ; Middle Aged ; Mycobiome/*genetics ; Penicillium ; Sordariales ; Stomach/microbiology ; Stomach Neoplasms/*microbiology/pathology ; }, abstract = {Background: Bacterial infection is associated with gastric carcinogenesis. However, the relationship between nonbacterial components and gastric cancer (GC) has not been fully explored. We aimed to characterize the fungal microbiome in GC. Methods: We performed ITS rDNA gene analysis in cancer lesions and adjacent noncancerous tissues of 45 GC cases from Shenyang, China. Obtaining the OTUs and combining effective grouping, we carried out species identifications, alpha and beta diversity analyses, and FUNGuild functional annotation. Moreover, differences were compared and tested between groups to better investigate the composition and ecology of fungi associated with GC and find fungal indicators. Results: We observed significant gastric fungal imbalance in GC. Principal component analysis revealed separate clusters for the GC and control groups, and Venn diagram analysis indicated that the GC group showed a lower OTU abundance than the control. At the genus level, the abundances of 15 fungal biomarkers distinguished the GC group from the control, of which Candida (p = 0.000246) and Alternaria (p = 0.00341) were enriched in GC, while Saitozyma (p = 0.002324) and Thermomyces (p = 0.009158) were decreased. Combining the results of Welch's t test and Wilcoxon rank sum test, Candida albicans (C. albicans) was significantly elevated in GC. The species richness Krona pie chart further revealed that C. albicans occupied 22% and classified GC from the control with an area under the receiver operating curve (AUC) of 0.743. Random forest analysis also confirmed that C. albicans could serve as a biomarker with a certain degree of accuracy. Moreover, compared with that of the control, the alpha diversity index was significantly reduced in the GC group. The Jaccard distance index and the Bray abundance index of the PCoA clarified separate clusters between the GC and control groups at the species level (p = 0.00051). Adonis (PERMANOVA) analysis and ANOVA showed that there were significant differences in fungal structure among groups (p = 0.001). Finally, FUNGuild functional classification predicted that saprotrophs were the most abundant taxa in the GC group. Conclusions: This study revealed GC-associated mycobiome imbalance characterized by an altered fungal composition and ecology and demonstrated that C. albicans can be a fungal biomarker for GC. With the significant increase of C. albicans in GC, the abundance of Fusicolla acetilerea, Arcopilus aureus, Fusicolla aquaeductuum were increased, while Candida glabrata, Aspergillus montevidensis, Saitozyma podzolica and Penicillium arenicola were obviously decreased. In addition, C. albicans may mediate GC by reducing the diversity and richness of fungi in the stomach, contributing to the pathogenesis of GC.}, } @article {pmid33753813, year = {2021}, author = {Lyu, Z and Ghoshdastidar, S and Rekha, KR and Suresh, D and Mao, J and Bivens, N and Kannan, R and Joshi, T and Rosenfeld, CS and Upendran, A}, title = {Developmental exposure to silver nanoparticles leads to long term gut dysbiosis and neurobehavioral alterations.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {6558}, pmid = {33753813}, issn = {2045-2322}, support = {R01 ES025547/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Behavior/*drug effects ; Dysbiosis/*drug therapy ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Male ; Maze Learning ; Mental Status and Dementia Tests ; Metagenome ; Metagenomics/methods ; *Metal Nanoparticles/chemistry ; Mice ; Models, Animal ; Silver/*adverse effects/chemistry ; }, abstract = {Due to their antimicrobial properties, silver nanoparticles (AgNPs) are used in a wide range of consumer products that includes topical wound dressings, coatings for biomedical devices, and food-packaging to extend the shelf-life. Despite their beneficial antimicrobial effects, developmental exposure to such AgNPs may lead to gut dysbiosis and long-term health consequences in exposed offspring. AgNPs can cross the placenta and blood-brain-barrier to translocate in the brain of offspring. The underlying hypothesis tested in the current study was that developmental exposure of male and female mice to AgNPs disrupts the microbiome-gut-brain axis. To examine for such effects, C57BL6 female mice were exposed orally to AgNPs at a dose of 3 mg/kg BW or vehicle control 2 weeks prior to breeding and throughout gestation. Male and female offspring were tested in various mazes that measure different behavioral domains, and the gut microbial profiles were surveyed from 30 through 120 days of age. Our study results suggest that developmental exposure results in increased likelihood of engaging in repetitive behaviors and reductions in resident microglial cells. Echo-MRI results indicate increased body fat in offspring exposed to AgNPs exhibit. Coprobacillus spp., Mucispirillum spp., and Bifidobacterium spp. were reduced, while Prevotella spp., Bacillus spp., Planococcaceae, Staphylococcus spp., Enterococcus spp., and Ruminococcus spp. were increased in those developmentally exposed to NPs. These bacterial changes were linked to behavioral and metabolic alterations. In conclusion, developmental exposure of AgNPs results in long term gut dysbiosis, body fat increase and neurobehavioral alterations in offspring.}, } @article {pmid33753486, year = {2021}, author = {Geng, J and Ji, B and Li, G and López-Isunza, F and Nielsen, J}, title = {CODY enables quantitatively spatiotemporal predictions on in vivo gut microbial variability induced by diet intervention.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {13}, pages = {}, pmid = {33753486}, issn = {1091-6490}, mesh = {Adult ; Biological Variation, Individual ; Colon/microbiology/*physiology ; Cross-Sectional Studies ; Datasets as Topic ; Feces/microbiology ; Feeding Behavior/*physiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Hydrodynamics ; Infant ; Longitudinal Studies ; Metabolomics ; Metagenomics ; *Models, Biological ; Obesity/blood/*diet therapy/metabolism/microbiology ; Spatio-Temporal Analysis ; }, abstract = {Microbial variations in the human gut are harbored in temporal and spatial heterogeneity, and quantitative prediction of spatiotemporal dynamic changes in the gut microbiota is imperative for development of tailored microbiome-directed therapeutics treatments, e.g. precision nutrition. Given the high-degree complexity of microbial variations, subject to the dynamic interactions among host, microbial, and environmental factors, identifying how microbiota colonize in the gut represents an important challenge. Here we present COmputing the DYnamics of microbiota (CODY), a multiscale framework that integrates species-level modeling of microbial dynamics and ecosystem-level interactions into a mathematical model that characterizes spatial-specific in vivo microbial residence in the colon as impacted by host physiology. The framework quantifies spatiotemporal resolution of microbial variations on species-level abundance profiles across site-specific colon regions and in feces, independent of a priori knowledge. We demonstrated the effectiveness of CODY using cross-sectional data from two longitudinal metagenomics studies-the microbiota development during early infancy and during short-term diet intervention of obese adults. For each cohort, CODY correctly predicts the microbial variations in response to diet intervention, as validated by available metagenomics and metabolomics data. Model simulations provide insight into the biogeographical heterogeneity among lumen, mucus, and feces, which provides insight into how host physical forces and spatial structure are shaping microbial structure and functionality.}, } @article {pmid33752005, year = {2021}, author = {Kumar, R and Pandit, P and Kumar, D and Patel, Z and Pandya, L and Kumar, M and Joshi, C and Joshi, M}, title = {Landfill microbiome harbour plastic degrading genes: A metagenomic study of solid waste dumping site of Gujarat, India.}, journal = {The Science of the total environment}, volume = {779}, number = {}, pages = {146184}, doi = {10.1016/j.scitotenv.2021.146184}, pmid = {33752005}, issn = {1879-1026}, mesh = {India ; *Microbiota ; Plastics ; *Refuse Disposal ; Solid Waste/analysis ; Waste Disposal Facilities ; *Water Pollutants, Chemical/analysis ; }, abstract = {Globally, environmental pollution by plastic waste has become a severe ecological and social problem worldwide. The present study aimed to analyse the bacterial community structure and functional potential of the landfill site using high throughput shotgun metagenomic approach to understand plastic degrading capabilities present in the municipal solid waste (MSW) dumping site. In this study, soil, leachate and compost samples were collected from various locations (height and depth) of the Pirana landfill site in Ahmedabad city Gujarat, India. In total 30 phyla, 58 class, 125 order, 278 families, 793 genera, and 2468 species were predicted. The most dominant phyla detected were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria in the soil and compost samples. Whereas, in leachate samples, the predominant phyla belonged to Firmicutes (54.24%) followed by Actinobacteria (43.67%) and Proteobacteria (1.02%). The functional profiling revealed the presence of enzymatic groups and pathways involved in biodegradation of xenobiotics. The results also demonstrated the presence of potential genes that is associated with the biodegradation of different types of plastics such as polyethylene (PE), polyethylene terephthalate (PET), and polystyrene (PS). Present study extablishes the relationship between microbial community structure and rich sources of gene pool, which are actively involved in biodegradation of plastic waste in landfill sites.}, } @article {pmid33751971, year = {2021}, author = {Zhu, C and Zhang, J and Wang, X and Yang, Y and Chen, N and Lu, Z and Ge, Q and Jiang, R and Zhang, X and Yang, Y and Chen, T}, title = {Responses of cyanobacterial aggregate microbial communities to algal blooms.}, journal = {Water research}, volume = {196}, number = {}, pages = {117014}, doi = {10.1016/j.watres.2021.117014}, pmid = {33751971}, issn = {1879-2448}, mesh = {China ; *Cyanobacteria/genetics ; Eutrophication ; Harmful Algal Bloom ; Lakes ; Longitudinal Studies ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Freshwater lakes are threatened by harmful cyanobacterial blooms, whose basic unit is Cyanobacterial Aggregate (CA). CA-attached bacteria play a significant role through different blooming stages with substantial variation of their taxonomic structure. However, little is known about their functional variations and functional links with cyanobacteria due to the lack of reference genomes. In this longitudinal study, we collected 16 CA samples from Lake Taihu, one of China's largest freshwater lakes, from April 2015 to February 2016, and sequenced their V4 region of 16S rRNA genes, full metagenomes (MG), and metatranscriptomes (MT). The analysis of these data revealed the dynamics of microbial taxonomic and functional structure in CAs, influenced by both external environmental factors and internal metabolism. 55 OTUs, 456 genes, and 37 transcripts showed significantly differential abundance across the early, middle, and late blooming stages (ANOVA test, P < 0.05). Total nitrogen and total phosphorus were proved to be the most important environmental drivers of microbial taxonomic and functional variations in CAs (Mantel's r > 0.25, P < 0.05). We constructed 161 high-quality metagenome-assembled genomes (MAGs), out of which 22 were cyanobacterial strains with diverse energy pathways, transporters and prokaryotic defense systems. Based on these MAGs, we constructed a cyanobacteria-bacteria co-nitrogen-pathway and a cyanobacteria-bacteria co-phosphorus-pathway, by which we demonstrated how nitrogen and phosphorus influence the dynamics of the microbial structure to a certain extent by affecting these co-pathways. Overall, these results characterized the taxonomic, functional, and transcriptional variations of microbes in CAs through different blooming stages. Genome assembly and metabolic analysis of cyanobacteria and their attached bacteria suggested that the material exchange and signal transduction do, indeed, exist among them. Our understanding of the underlying molecular pathways for cyanobacterial blooms could lead to the control of blooms by interventional strategies to disrupt critical microbes' expression.}, } @article {pmid33750907, year = {2021}, author = {Oliva, M and Schneeberger, PHH and Rey, V and Cho, M and Taylor, R and Hansen, AR and Taylor, K and Hosni, A and Bayley, A and Hope, AJ and Bratman, SV and Ringash, J and Singh, S and Weinreb, I and Perez-Ordoñez, B and Chepeha, D and Waldron, J and Xu, W and Guttman, D and Siu, LL and Coburn, B and Spreafico, A}, title = {Transitions in oral and gut microbiome of HPV+ oropharyngeal squamous cell carcinoma following definitive chemoradiotherapy (ROMA LA-OPSCC study).}, journal = {British journal of cancer}, volume = {124}, number = {9}, pages = {1543-1551}, pmid = {33750907}, issn = {1532-1827}, mesh = {Carcinoma, Squamous Cell/pathology/therapy/virology ; Chemoradiotherapy/*adverse effects ; Female ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Humans ; Male ; Mouth Mucosa/drug effects/*microbiology/radiation effects ; Oropharyngeal Neoplasms/pathology/*therapy/virology ; Papillomaviridae/*isolation & purification ; Papillomavirus Infections/*complications/virology ; Prognosis ; Prospective Studies ; Saliva/drug effects/*microbiology/radiation effects ; }, abstract = {BACKGROUND: Oral and gut microbiomes have emerged as potential biomarkers in cancer. We characterised the oral and gut microbiomes in a prospective observational cohort of HPV+ oropharyngeal squamous cell carcinoma (OPSCC) patients and evaluated the impact of chemoradiotherapy (CRT).

METHODS: Saliva, oropharyngeal swabs over the tumour site and stool were collected at baseline and post-CRT. 16S RNA and shotgun metagenomic sequencing were used to generate taxonomic profiles, including relative abundance (RA), bacterial density, α-diversity and β-diversity.

RESULTS: A total of 132 samples from 22 patients were analysed. Baseline saliva and swabs had similar taxonomic composition (R[2] = 0.006; p = 0.827). Oropharyngeal swabs and stool taxonomic composition varied significantly by stage, with increased oral RA of Fusobacterium nucleatum observed in stage III disease (p < 0.05). CRT significantly reduced the species richness and increased the RA of gut-associated taxa in oropharyngeal swabs (p < 0.05), while it had no effect in stool samples. These findings remained significant when adjusted by stage, smoking status and antibiotic use.

CONCLUSIONS: Baseline oral and gut microbiomes differ by stage in this HPV+ cohort. CRT caused a shift towards a gut-like microbiome composition in oropharyngeal swabs. Stage-specific features and the transitions in oral microbiome might have prognostic and therapeutic implications.}, } @article {pmid33746944, year = {2021}, author = {Berlinberg, AJ and Regner, EH and Stahly, A and Brar, A and Reisz, JA and Gerich, ME and Fennimore, BP and Scott, FI and Freeman, AE and Kuhn, KA}, title = {Multi 'Omics Analysis of Intestinal Tissue in Ankylosing Spondylitis Identifies Alterations in the Tryptophan Metabolism Pathway.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {587119}, pmid = {33746944}, issn = {1664-3224}, support = {K08 DK107905/DK/NIDDK NIH HHS/United States ; R01 AR075033/AR/NIAMS NIH HHS/United States ; T32 AR007534/AR/NIAMS NIH HHS/United States ; U01 AI130830/AI/NIAID NIH HHS/United States ; }, mesh = {Case-Control Studies ; Computational Biology/methods ; Disease Susceptibility ; Dysbiosis ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Humans ; *Intestines ; Metabolic Networks and Pathways ; *Metabolomics ; *Metagenomics/methods ; Spondylitis, Ankylosing/*etiology/pathology ; Tryptophan/*metabolism ; }, abstract = {Intestinal microbial dysbiosis, intestinal inflammation, and Th17 immunity are all linked to the pathophysiology of spondyloarthritis (SpA); however, the mechanisms linking them remain unknown. One potential hypothesis suggests that the dysbiotic gut microbiome as a whole produces metabolites that influence human immune cells. To identify potential disease-relevant, microbiome-produced metabolites, we performed metabolomics screening and shotgun metagenomics on paired colon biopsies and fecal samples, respectively, from subjects with axial SpA (axSpA, N=21), Crohn's disease (CD, N=27), and Crohn's-axSpA overlap (CD-axSpA, N=12), as well as controls (HC, N=24). Using LC-MS based metabolomics of 4 non-inflamed pinch biopsies of the distal colon from subjects, we identified significant alterations in tryptophan pathway metabolites, including an expansion of indole-3-acetate (IAA) in axSpA and CD-axSpA compared to HC and CD and indole-3-acetaldehyde (I3Ald) in axSpA and CD-axSpA but not CD compared to HC, suggesting possible specificity to the development of axSpA. We then performed shotgun metagenomics of fecal samples to characterize gut microbial dysbiosis across these disease states. In spite of no significant differences in alpha-diversity among the 4 groups, our results confirmed differences in gene abundances of numerous enzymes involved in tryptophan metabolism. Specifically, gene abundance of indolepyruvate decarboxylase, which generates IAA and I3Ald, was significantly elevated in individuals with axSpA while gene abundances in HC demonstrated a propensity towards tryptophan synthesis. Such genetic changes were not observed in CD, again suggesting disease specificity for axSpA. Given the emerging role of tryptophan and its metabolites in immune function, altogether these data indicate that tryptophan metabolism into I3Ald and then IAA is one mechanism by which the gut microbiome potentially influences the development of axSpA.}, } @article {pmid33746613, year = {2021}, author = {Kobayashi, H and Toyoda, R and Miyamoto, H and Nakasugi, Y and Momoi, Y and Nakamura, K and Fu, Q and Maeda, H and Goda, T and Sato, K}, title = {Analysis of a Methanogen and an Actinobacterium Dominating the Thermophilic Microbial Community of an Electromethanogenic Biocathode.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2021}, number = {}, pages = {8865133}, pmid = {33746613}, issn = {1472-3654}, mesh = {*Euryarchaeota ; In Situ Hybridization, Fluorescence ; Methane ; Methanobacteriaceae ; *Microbiota ; }, abstract = {Electromethanogenesis refers to the bioelectrochemical synthesis of methane from CO2 by biocathodes. In an electromethanogenic system using thermophilic microorganisms, metagenomic analysis along with quantitative real-time polymerase chain reaction and fluorescence in situ hybridization revealed that the biocathode microbiota was dominated by the methanogen Methanothermobacter sp. strain EMTCatA1 and the actinobacterium Coriobacteriaceae sp. strain EMTCatB1. RNA sequencing was used to compare the transcriptome profiles of each strain at the methane-producing biocathodes with those in an open circuit and with the methanogenesis inhibitor 2-bromoethanesulfonate (BrES). For the methanogen, genes related to hydrogenotrophic methanogenesis were highly expressed in a manner similar to those observed under H2-limited conditions. For the actinobacterium, the expression profiles of genes encoding multiheme c-type cytochromes and membrane-bound oxidoreductases suggested that the actinobacterium directly takes up electrons from the electrode. In both strains, various stress-related genes were commonly induced in the open-circuit biocathodes and biocathodes with BrES. This study provides a molecular inventory of the dominant species of an electromethanogenic biocathode with functional insights and therefore represents the first multiomics characterization of an electromethanogenic biocathode.}, } @article {pmid33746186, year = {2021}, author = {Zhang, YZ and Jiang, DY and Zhang, C and Yang, K and Wang, HF and Xia, XW and Ding, WJ}, title = {Pathological Impact on the Phyllosphere Microbiota of Artemisia argyi by Haze.}, journal = {Journal of microbiology and biotechnology}, volume = {31}, number = {4}, pages = {510-519}, pmid = {33746186}, issn = {1738-8872}, mesh = {Air Pollution/*adverse effects ; Artemisia/*microbiology ; Bacteria/*classification/drug effects ; China ; Fungi/*classification/drug effects ; Metagenome ; *Microbiota ; Plant Leaves/microbiology ; Secondary Metabolism ; }, abstract = {The pathological impact of haze upon the phyllosphere microbiota awaits investigation. A moderate degree of haze environment and a clean control were selected in Chengdu, China. Artemisia argyi, a ubiquitously distributed and extensively applied Chinese herb, was also chosen for experiment. Total genome DNA was extracted from leaf samples, and for metagenome sequencing, an Illumina HiSeq 2500 platform was applied. The results showed that the gene numbers of phyllosphere microbiota derived from haze leaves were lower than those of the clean control. The phyllosphere microbiota derived from both haze and clean groups shared the same top ten phyla; the abundances of Proteobacteria, Actinomycetes and Anorthococcuso of the haze group were substantially increased, while Ascomycetes and Basidiomycetes decreased. At the genus level, the abundances of Nocardia, Paracoccus, Marmoricola and Knoelia from haze leaves were markedly increased, while the yeasts were statistically decreased. KEGG retrieval demonstrated that the functional genes were most annotated to metabolism. An interesting find of this work is that the phyllosphere microbiota responsible for the synthesis of primary and secondary metabolites in A. argyi were significantly increased under a haze environment. Relatively enriched genes annotated by eggNOG belong to replication, recombination and repair, and genes classified into the glycoside hydrolase and glycosyltransferase enzymes were significantly increased. In summary, we found that both structure and function of phyllosphere microbiota are globally impacted by haze, while primary and secondary metabolites responsible for haze tolerance were considerably increased. These results suggest an adaptive strategy of plants for tolerating and confronting haze damage.}, } @article {pmid33744869, year = {2021}, author = {Kurup, K and Matyi, S and Giles, CB and Wren, JD and Jones, K and Ericsson, A and Raftery, D and Wang, L and Promislow, D and Richardson, A and Unnikrishnan, A}, title = {Calorie restriction prevents age-related changes in the intestinal microbiota.}, journal = {Aging}, volume = {13}, number = {5}, pages = {6298-6329}, pmid = {33744869}, issn = {1945-4589}, support = {S10 OD021562/OD/NIH HHS/United States ; T32 AG052363/AG/NIA NIH HHS/United States ; P30 AG050911/AG/NIA NIH HHS/United States ; R21 AG062894/AG/NIA NIH HHS/United States ; K01 AG056655/AG/NIA NIH HHS/United States ; P30 AG013280/AG/NIA NIH HHS/United States ; R01 AG049494/AG/NIA NIH HHS/United States ; R01 AG045693/AG/NIA NIH HHS/United States ; IK6 BX005238/BX/BLRD VA/United States ; }, mesh = {Aging ; Animals ; *Caloric Restriction ; *Gastrointestinal Microbiome ; Intestinal Mucosa/microbiology ; Mice, Inbred C57BL ; Mice ; }, abstract = {The effect of calorie restriction (CR) on the microbiome, fecal metabolome, and colon transcriptome of adult and old male mice was compared. Life-long CR increased microbial diversity and the Bacteroidetes/Firmicutes ratio and prevented the age-related changes in the microbiota, shifting it to a younger microbial and fecal metabolite profile in both C57BL/6JN and B6D2F1 mice. Old mice fed CR were enriched in the Rikenellaceae, S24-7 and Bacteroides families. The changes in the microbiome that occur with age and CR were initiated in the cecum and further modified in the colon. Short-term CR in adult mice had a minor effect on the microbiome but a major effect on the transcriptome of the colon mucosa. These data suggest that CR has a major impact on the physiological status of the gastrointestinal system, maintaining it in a more youthful state, which in turn could result in a more diverse and youthful microbiome.}, } @article {pmid33743500, year = {2021}, author = {Romero, MF and Gallego, D and Lechuga-Jiménez, A and Martínez, JF and Barajas, HR and Hayano-Kanashiro, C and Peimbert, M and Cruz-Ortega, R and Molina-Freaner, FE and Alcaraz, LD}, title = {Metagenomics of mine tailing rhizospheric communities and its selection for plant establishment towards bioremediation.}, journal = {Microbiological research}, volume = {247}, number = {}, pages = {126732}, doi = {10.1016/j.micres.2021.126732}, pmid = {33743500}, issn = {1618-0623}, mesh = {Bacteria/classification/genetics/metabolism ; Biodegradation, Environmental ; *Metagenomics ; Metals, Heavy ; Microbiota/physiology ; Mining ; Plant Development ; Plant Roots ; Plants/*microbiology ; RNA, Ribosomal, 16S ; *Rhizosphere ; Soil ; *Soil Microbiology ; Soil Pollutants ; }, abstract = {Mining operations often generate tailing dams that contain toxic residues and are a source of contamination when left unconfined. The establishment of a plant community over the tailings has been proposed as a containment strategy known as phytostabilization. Previously, we described naturally occurring mine tailing colonizing plants such as Acacia farnesiana, Brickellia coulteri, Baccharis sarothroides, and Gnaphalium leucocephalum without finding local adaptation. We explored the rhizosphere microbes as contributors in plant establishment and described both the culturable and in situ diversity of rhizospheric bacteria using the 16S rRNA gene and metagenomic shotgun sequencing. We built a synthetic community (SC) of culturable rhizosphere bacteria from the mine tailings. The SC was then the foundation for a serial passes experiment grown in plant-derived nutrient sources, selecting for heavy metals tolerance, community cooperation, and competition. The outcome of the serial passes was named the 'final synthetic community' (FSC). Overall, diversity decreased from in situ uncultivable microbes from roots (399 bacteria genera) to the cultivated communities (291 genera), the SC (94 genera), and the lowest diversity was in the FSC (43 genera). Metagenomic diversity clustered into 94,245 protein families, where we found plant growth promotion-related genes such as the csgBAC and entCEBAH, coded in a metagenome-assembled genome named Kosakonia sp. Nacozari. Finally, we used the FSC to inoculate mine tailing colonizing plants in a greenhouse experiment. The plants with the FSC inocula observed higher relative plant growth rates in sterile substrates. The FSC presents promising features that might make it useful for phytostabilization tailored strategies.}, } @article {pmid33741616, year = {2021}, author = {Zhu, X and Feng, X and Liang, C and Li, J and Jia, J and Feng, L and Tao, Y and Chen, Y}, title = {Microbial Ecological Mechanism for Long-Term Production of High Concentrations of n-Caproate via Lactate-Driven Chain Elongation.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {11}, pages = {}, pmid = {33741616}, issn = {1098-5336}, mesh = {*Bacterial Physiological Phenomena ; Biodegradation, Environmental ; Bioreactors/*microbiology ; Caproates/*metabolism ; Clostridiales/*physiology ; Fermentation ; Lactic Acid/*chemistry ; *Microbiota ; }, abstract = {Lactate-driven chain elongation (LCE) has emerged as a new biotechnology to upgrade organic waste streams into a valuable biochemical and fuel precursor, medium-chain carboxylate, n-caproate. Considering that a low cost of downstream extraction is critical for biorefinery technology, a high concentration of n-caproate production is very important to improve the scale-up of the LCE process. We report here that in a nonsterile open environment, the n-caproate concentration was increased from the previous record of 25.7 g·liter[-1] to a new high level of 33.7 g·liter[-1] (76.8 g chemical oxygen demand [COD]·liter [-][1]), with the highest production rate being 11.5 g·liter[-1]·day[-1] (26.2 g COD·liter [-][1]·day[-1]). In addition, the LCE process remained stable, with an average concentration of n-caproate production of 20.2 ± 5.62 g·liter[-1] (46.1 ± 12.8 g COD·liter [-][1]) for 780 days. Dynamic changes in taxonomic composition integrated with metagenomic data reveal the microbial ecology for long-term production of high concentrations of n-caproate: (i) the core microbiome is related to efficient functional groups, such as Ruminococcaceae (with functional strain CPB6); (ii) the core bacteria can maintain stability for long-term operation; (iii) the microbial network has relatively low microbe-microbe interaction strength; and (iv) low relative abundance and variety of competitors. The network structure could be shaped by hydraulic retention time (HRT) over time, and long-term operation at an HRT of 8 days displayed higher efficacy.IMPORTANCE Our research revealed the microbial network of the LCE reactor microbiome for n-caproate production at high concentrations, which will provide a foundation for designing or engineering the LCE reactor microbiome to recover n-caproate from organic waste streams in the future. In addition, the hypothetical model of the reactor microbiome that we proposed may offer guidance for researchers to find the underlying microbial mechanism when they encounter low-efficiency n-caproate production from the LCE process. We anticipate that our research will rapidly advance LCE biotechnology with the goal of promoting the sustainable development of human society.}, } @article {pmid33741611, year = {2021}, author = {Palermo, CN and Shea, DW and Short, SM}, title = {Analysis of Different Size Fractions Provides a More Complete Perspective of Viral Diversity in a Freshwater Embayment.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {11}, pages = {}, pmid = {33741611}, issn = {1098-5336}, mesh = {Lakes/*virology ; Metagenome ; Ontario ; *Virome ; Viruses/classification/*isolation & purification ; }, abstract = {Inspired by recent discoveries of the prevalence of large viruses in the environment, we reassessed the longstanding approach of filtering water through small-pore-size filters to separate viruses from cells before metagenomic analysis. We collected samples from three sites in Hamilton Harbour, an embayment of Lake Ontario, and studied 6 data sets derived from <0.45-μm- and >0.45-μm-size fractions to compare the diversity of viruses in these fractions. At the level of virus order/family, we observed highly diverse and distinct virus communities in the >0.45-μm-size fractions, whereas the <0.45-μm-size fractions were composed primarily of Caudovirales The relative abundances of Caudovirales for which hosts could be inferred varied widely between size fractions, with higher relative abundances of cyanophages in the >0.45-μm-size fractions, potentially indicating replication within cells during ongoing infections. Many viruses of eukaryotes, such as Mimiviridae, Phycodnaviridae, Iridoviridae, and Poxviridae, were detected exclusively in the often-disregarded >0.45-μm-size fractions. In addition to observing unique virus communities associated with each size fraction from every site we examined, we detected viruses common to both fractions, suggesting that these are candidates for further exploration because they could be the product of ongoing or recent lytic events. Most importantly, our observations indicate that analysis of either fraction alone provides only a partial perspective of double-stranded DNA (dsDNA) viruses in the environment, highlighting the need for more comprehensive approaches for analyzing virus communities inferred from metagenomic sequencing.IMPORTANCE Most studies of aquatic virus communities analyze DNA sequences derived from the smaller-size "free-virus" fraction. Our study demonstrates that analysis of virus communities using only the smaller-size fraction can lead to erroneously low diversity estimates for many of the larger viruses such as Mimiviridae, Phycodnaviridae, Iridoviridae, and Poxviridae, whereas analyzing only the larger->0.45-μm-size fraction can lead to underestimates of Caudovirales diversity and relative abundance. Similarly, our data show that examining only the smaller-size fraction can lead to underestimations of virophage and cyanophage relative abundances that could, in turn, cause researchers to assume their limited ecological importance. Given the considerable differences we observed in this study, we recommend cautious interpretations of environmental virus community assemblages and dynamics when based on metagenomic data derived from different size fractions.}, } @article {pmid33740598, year = {2021}, author = {Calderón-Ezquerro, MDC and Serrano-Silva, N and Brunner-Mendoza, C}, title = {Aerobiological study of bacterial and fungal community composition in the atmosphere of Mexico City throughout an annual cycle.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {278}, number = {}, pages = {116858}, doi = {10.1016/j.envpol.2021.116858}, pmid = {33740598}, issn = {1873-6424}, mesh = {Air Microbiology ; Atmosphere ; Cities ; Mexico ; *Mycobiome ; }, abstract = {The atmosphere as a temporary habitat for airborne microbial communities is a valuable topic to explore, and it is through aerobiological studies that the diversity of biological particles and their release, emission, transport, deposition, and impact are assessed. Specific microorganisms are involved in meteorological processes, and phytosanitary and public health concerns. Airborne microbial composition is related to factors such as geographic region and weather conditions. In this study a metagenomic approach was used to determine the composition of bacterial and fungal communities in the air of two different land-use areas (urban area and semi-rural area), during dry and rainy seasons in Mexico City. Air sampling was carried out with a Hirst-type spore trap, collecting the samples simultaneously in both study areas. Forty-two bioaerosol samples were collected, and the DNA obtained was sequenced using Next-Generation Sequencing. The results indicated that the bacterial communities were represented mainly by the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, Cyanobacteria, and the fungal communities by the phyla Ascomycota followed by Basidiomycota. The evident changes in microbial composition were related more to seasonality than to locality, since both UA and SRA showed a high degree of urbanization, despite some differences in land use. Continuous monitoring of atmospheric bioaerosols is essential to determine the influence of meteorological factors on the composition of the aerial microbiota.}, } @article {pmid33739998, year = {2021}, author = {Silver, A and Perez, S and Gee, M and Xu, B and Garg, S and Will, K and Gill, A}, title = {Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation.}, journal = {PloS one}, volume = {16}, number = {3}, pages = {e0241529}, pmid = {33739998}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/isolation & purification ; Coleoptera/classification/*microbiology ; DNA/chemistry/metabolism ; Diet ; Intestines/microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Host-associated microbiomes can play important roles in the ecology and evolution of their insect hosts, but bacterial diversity in many insect groups remains poorly understood. Here we examine the relationship between host environment, host traits, and microbial diversity in three species in the ground beetle family (Coleoptera: Carabidae), a group of roughly 40,000 species that synthesize a wide diversity of defensive compounds. This study used 16S amplicon sequencing to profile three species that are phylogenetically distantly related, trophically distinct, and whose defensive chemical secretions differ: Anisodactylus similis LeConte, 1851, Pterostichus serripes (LeConte, 1875), and Brachinus elongatulus Chaudoir, 1876. Wild-caught beetles were compared to individuals maintained in the lab for two weeks on carnivorous, herbivorous, or starvation diets (n = 3 beetles for each species-diet combination). Metagenomic samples from two highly active tissue types-guts, and pygidial gland secretory cells (which produce defensive compounds)-were processed and sequenced separately from those of the remaining body. Bacterial composition and diversity of these ground beetles were largely resilient to controlled changes to host diet. Different tissues within the same beetle harbor unique microbial communities, and secretory cells in particular were remarkably similar across species. We also found that these three carabid species have patterns of microbial diversity similar to those previously found in carabid beetles. These results provide a baseline for future studies of the role of microbes in the diversification of carabids.}, } @article {pmid33738881, year = {2021}, author = {Xu, Y and Zhu, J and Feng, B and Lin, F and Zhou, J and Liu, J and Shi, X and Lu, X and Pan, Q and Yu, J and Zhang, Y and Li, L and Cao, H}, title = {Immunosuppressive effect of mesenchymal stem cells on lung and gut CD8[+] T cells in lipopolysaccharide-induced acute lung injury in mice.}, journal = {Cell proliferation}, volume = {54}, number = {5}, pages = {e13028}, pmid = {33738881}, issn = {1365-2184}, support = {81971756//National Natural Science Foundation of China/ ; 2016YFA0101001//National Key Research and Development Program of China/ ; }, mesh = {Acute Lung Injury/immunology/mortality/pathology/*therapy ; Animals ; Bronchoalveolar Lavage Fluid/chemistry ; CD8-Positive T-Lymphocytes/cytology/*immunology/metabolism ; Cytokines/metabolism ; Disease Models, Animal ; Gastrointestinal Microbiome ; Intestinal Mucosa/metabolism/pathology ; Intestines/*immunology/microbiology/pathology ; Lipopolysaccharides/toxicity ; Lung/*immunology/metabolism/pathology ; Male ; *Mesenchymal Stem Cell Transplantation ; Mesenchymal Stem Cells/cytology/immunology ; Mice ; Mice, Inbred C57BL ; Principal Component Analysis ; Survival Rate ; }, abstract = {OBJECTIVES: Acute lung injury (ALI) not only affects pulmonary function but also leads to intestinal dysfunction, which in turn contributes to ALI. Mesenchymal stem cell (MSC) transplantation can be a potential strategy in the treatment of ALI. However, the mechanisms of synergistic regulatory effects by MSCs on the lung and intestine in ALI need more in-depth study.

MATERIALS AND METHODS: We evaluated the therapeutic effects of MSCs on the murine model of lipopolysaccharide (LPS)-induced ALI through survival rate, histopathology and bronchoalveolar lavage fluid. Metagenomic sequencing was performed to assess the gut microbiota. The levels of pulmonary and intestinal inflammation and immune response were assessed by analysing cytokine expression and flow cytometry.

RESULTS: Mesenchymal stem cells significantly improved the survival rate of mice with ALI, alleviated histopathological lung damage, improved intestinal barrier integrity, and reduced the levels of inflammatory cytokines in the lung and gut. Furthermore, MSCs inhibited the inflammatory response by decreasing the infiltration of CD8[+] T cells in both small-intestinal lymphocytes and Peyer's patches. The gut bacterial community diversity was significantly altered by MSC transplantation. Furthermore, depletion of intestinal bacterial communities with antibiotics resulted in more severe lung and gut damages and mortality, while MSCs significantly alleviated lung injury due to their immunosuppressive effect.

CONCLUSIONS: The present research indicates that MSCs attenuate lung and gut injury partly via regulation of the immune response in the lungs and intestines and gut microbiota, providing new insights into the mechanisms underlying the therapeutic effects of MSC treatment for LPS-induced ALI.}, } @article {pmid33738808, year = {2021}, author = {Xi, W and Gao, X and Zhao, H and Luo, X and Li, J and Tan, X and Wang, L and Zhao, JB and Wang, J and Yang, G and Liu, LY and Wang, YY and Peng, L and Zou, LP and Yang, Y}, title = {Depicting the composition of gut microbiota in children with tic disorders: an exploratory study.}, journal = {Journal of child psychology and psychiatry, and allied disciplines}, volume = {62}, number = {10}, pages = {1246-1254}, doi = {10.1111/jcpp.13409}, pmid = {33738808}, issn = {1469-7610}, mesh = {Bacteroides ; Child ; *Gastrointestinal Microbiome ; Humans ; Prevotella ; Ruminococcus ; Streptococcus ; *Tic Disorders ; }, abstract = {BACKGROUND: Symptom improvement in children with tic disorder (TD) following fecal microbiota transplantation led us to investigate the gut microbiota in TD. This exploratory study aims to depict the gut microbial profile in patients with TD and explore the impact of dopamine receptor antagonist (DRA) drugs on the composition and metabolic function of the gut microbiota.

METHODS: The gut microbiota were profiled in fecal samples of 49 children with TD and 50 matched healthy controls (HC) using shotgun metagenomic sequencing. A random forest (RF) model was constructed using the gut bacterial species to distinguish TD from HC. Associations between clinical metadata and microbial abundance or function were analyzed using MaAsLin2 and Spearman correlation.

RESULTS: The gut microbiota in children with TD was featured by higher abundances of Bacteroides plebeius and Ruminococcus lactaris (a potential pro-inflammatory taxon) and lower abundances of Prevotella stercorea and Streptococcus lutetiensis compared to HC. The constructed RF model accurately distinguished TD from HC based on the gut microbiota profile, resulting in an AUC of 0.884. Significant correlations were observed between tic symptom severity and the abundances of multiple bacterial species and gut microbiota metabolic functions. Multivariate analysis identified an upregulation of 4-aminobutanoate (GABA) degradation in the gut microbiota associated with TD status. The gut microbiota of DRA-treated TD children showed a distinct gut microbiota compared to the treatment-naïve group, represented by an increase in some potential enteric pathogens such as Escherichia coli, a decline in several species including Akkermansia muciniphila, and alterations in various metabolic functions.

CONCLUSIONS: Bacterial species promoting inflammatory responses and those modulating neurotransmitters such as GABA may be involved in the pathogenesis of TD. The use of DRA drugs is likely to induce overgrowth of some enteric pathogens and alter the gut microbiota metabolism.}, } @article {pmid33736375, year = {2021}, author = {Macedo, G and van Veelen, HPJ and Hernandez-Leal, L and van der Maas, P and Heederik, D and Mevius, D and Bossers, A and Schmitt, H}, title = {Targeted metagenomics reveals inferior resilience of farm soil resistome compared to soil microbiome after manure application.}, journal = {The Science of the total environment}, volume = {770}, number = {}, pages = {145399}, doi = {10.1016/j.scitotenv.2021.145399}, pmid = {33736375}, issn = {1879-1026}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Farms ; Genes, Bacterial ; *Manure ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S ; Soil ; Soil Microbiology ; }, abstract = {Application of animal manure to soils results in the introduction of manure-derived bacteria and their antimicrobial resistance genes (ARGs) into soils. ResCap is a novel targeted-metagenomic approach that allows the detection of minority components of the resistome gene pool without the cost-prohibitive coverage depths and can provide a valuable tool to study the spread of antimicrobial resistance (AMR) in the environment. We used high-throughput sequencing and qPCR for 16S rRNA gene fragments as well as ResCap to explore the dynamics of bacteria, and ARGs introduced to soils and adjacent water ditches, both at community and individual scale, over a period of three weeks. The soil bacteriome and resistome showed strong resilience to the input of manure, as manuring did not impact the overall structure of the bacteriome, and its effects on the resistome were transient. Initially, manure application resulted in a substantial increase of ARGs in soils and adjacent waters, while not affecting the overall bacterial community composition. Still, specific families increased after manure application, either through the input of manure (e.g., Dysgonomonadaceae) or through enrichment after manuring (e.g., Pseudomonadaceae). Depending on the type of ARG, manure application resulted mostly in an increase (e.g., aph(6)-Id), but occasionally also in a decrease (e.g., dfrB3) of the absolute abundance of ARG clusters (FPKM/kg or L). This study shows that the structures of the bacteriome and resistome are shaped by different factors, where the bacterial community composition could not explain the changes in ARG diversity or abundances. Also, it highlights the potential of applying targeted metagenomic techniques, such as ResCap, to study the fate of AMR in the environment.}, } @article {pmid33735474, year = {2021}, author = {Wu, Y and Zhou, X and Zhang, X and Niu, H and Lyu, L and Liang, C and Chen, S and Gong, P and Pan, J and Li, Y and Jiang, S and Han, X and Zhang, L}, title = {Breast milk flora plays an important role in infantile eczema: cohort study in Northeast China.}, journal = {Journal of applied microbiology}, volume = {131}, number = {6}, pages = {2981-2993}, doi = {10.1111/jam.15076}, pmid = {33735474}, issn = {1365-2672}, support = {GA16B201-2//Heilongjiang province Key Sci. & Techn. Plan/ ; 2018YFC1604302//National Key Research and Development of China/ ; }, mesh = {Cohort Studies ; *Dermatitis, Atopic ; Female ; Humans ; Infant ; Metagenome ; *Microbiota ; Milk, Human ; }, abstract = {AIMS: Infantile eczema, usually coupled with a range of hypersensitive phenotypes, has come into notice with its rising prevalence and unclear pathogenesis. Recent studies show close ties between eczema and an infant's intestinal flora. To gain a further understanding of the interactions between microbiota and eczema, we studied the breast milk flora as a new factor and present the links among breast milk flora, infant intestinal flora and infantile eczema through a cohort study in Northeast China.

METHODS AND RESULTS: Fifty-two families were recruited with either an eczema or healthy infant younger than 6 months. Analysis and predictions using amplicon sequencing of microbiota found that Bifidobacterium and Bacteroidetes were enriched in healthy and eczema infant stools, respectively, consistent with previous reports. For breast milk flora, more 'positive' bacteria such as Akkermansia were enriched in breast milk from healthy infants' mothers. Further, higher bacterial delivery efficiencies were found in pairs of breast milk flora and infants' stool flora of families with eczema infants compared with families with healthy infants. Bacteroidetes, a widely known indicator of eczema, was found delivered more in eczema pairs. Further metagenomic predictions revealed that the breast milk microbiota participated significantly less in metabolism and immune system pathways, particularly in antigen processing and presentation and in Th17 cell-related pathways.

CONCLUSIONS: In conclusion, as with other components of breast milk, the breast milk microbiota closely associates with infants' health via mother-infant bacterial delivery and metabolic functions.

Our research aimed to fill the gap between the eczema and breast milk flora and describe the connections among breast milk and intestinal flora and eczema.}, } @article {pmid33734582, year = {2021}, author = {Zimmermann, M and Patil, KR and Typas, A and Maier, L}, title = {Towards a mechanistic understanding of reciprocal drug-microbiome interactions.}, journal = {Molecular systems biology}, volume = {17}, number = {3}, pages = {e10116}, pmid = {33734582}, issn = {1744-4292}, support = {MC_UU_00025/11/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Bacteria/metabolism ; Disease Models, Animal ; *Drug Interactions ; Host-Pathogen Interactions ; Humans ; Metagenomics ; *Microbiota ; Systems Biology ; }, abstract = {Broad-spectrum antibiotics target multiple gram-positive and gram-negative bacteria, and can collaterally damage the gut microbiota. Yet, our knowledge of the extent of damage, the antibiotic activity spectra, and the resistance mechanisms of gut microbes is sparse. This limits our ability to mitigate microbiome-facilitated spread of antibiotic resistance. In addition to antibiotics, non-antibiotic drugs affect the human microbiome, as shown by metagenomics as well as in vitro studies. Microbiome-drug interactions are bidirectional, as microbes can also modulate drugs. Chemical modifications of antibiotics mostly function as antimicrobial resistance mechanisms, while metabolism of non-antibiotics can also change the drugs' pharmacodynamic, pharmacokinetic, and toxic properties. Recent studies have started to unravel the extensive capacity of gut microbes to metabolize drugs, the mechanisms, and the relevance of such events for drug treatment. These findings raise the question whether and to which degree these reciprocal drug-microbiome interactions will differ across individuals, and how to take them into account in drug discovery and precision medicine. This review describes recent developments in the field and discusses future study areas that will benefit from systems biology approaches to better understand the mechanistic role of the human gut microbiota in drug actions.}, } @article {pmid33732655, year = {2021}, author = {Chong, CYL and Vatanen, T and Alexander, T and Bloomfield, FH and O'Sullivan, JM}, title = {Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {595323}, pmid = {33732655}, issn = {2235-2988}, mesh = {Cohort Studies ; Diamond ; Feces ; Female ; Humans ; Infant ; Infant, Newborn ; *Infant, Premature ; *Microbiota ; Pregnancy ; RNA, Ribosomal, 16S ; }, abstract = {The gut microbiota of preterm infants is affected by perinatal factors and, in turn, may impact upon infant health. In this study, we collected fecal samples at Day-10 (D10) and 4-months corrected-age (4M) from 227 moderate-late preterm (MLPT) babies enrolled in a randomized controlled trial of nutritional management. A total of 320 samples underwent 16S amplicon sequencing, and shotgun metagenomic sequencing was performed on 94 samples from the 4M time point. The microbiome of babies whose families lived in lower socioeconomic status (SES) areas exhibited a significantly higher microbial alpha diversity at D10 (Wilcoxon test, p = 0.021), greater abundance of Bifidobacterium (linear model, q = 0.020) at D10 and Megasphaera (q = 0.031) at 4M. Hospital of birth explained 5.2% of the observed variance in 4M samples (PERMANOVA, p = 0.038), with Staphylococcus aureus more abundant in fecal samples from babies born in Middlemore hospital (linear model, q = 0.016). Maternal antibiotic (Wilcoxon test, p = 0.013) and probiotic (p = 0.04) usage within the four-week period before sample collection was associated with a reduction in the alpha diversity of D10 samples. Infant probiotic intake explained 2.1% (PERMANOVA, p = 0.021) of the variance in the D10 microbial profile with increased Lactobacillus (linear model, q = 1.1 × 10[-10]) levels. At 4M, the microbiome of infants who were breastmilk fed had reduced alpha diversity when compared to non-breastmilk fed infants (Wilcoxon test, p < 0.05). Although causality cannot be inferred within our study, we conclude that in MLPT babies, maternal socioeconomic factors, as well as the perinatal medical environment and nutrition impact on the development of the newborn microbiome.}, } @article {pmid33731467, year = {2021}, author = {Leclerc, M and Harrison, MC and Storck, V and Planas, D and Amyot, M and Walsh, DA}, title = {Microbial Diversity and Mercury Methylation Activity in Periphytic Biofilms at a Run-of-River Hydroelectric Dam and Constructed Wetlands.}, journal = {mSphere}, volume = {6}, number = {2}, pages = {}, pmid = {33731467}, issn = {2379-5042}, mesh = {Bacteria/*classification/*genetics ; Biofilms/*growth & development ; *Genetic Variation ; Lakes/microbiology ; Mercury/*metabolism ; Methylation ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Rivers ; Water Pollutants, Chemical/analysis ; *Wetlands ; }, abstract = {Periphytic biofilms have the potential to greatly influence the microbial production of the neurotoxicant monomethylmercury in freshwaters although few studies have simultaneously assessed periphyton mercury methylation and demethylation rates and the microbial communities associated with these transformations. We performed a field study on periphyton from a river affected by run-of-river power plants and artificial wetlands in a boreal landscape (Québec, Canada). In situ incubations were performed on three sites using environmental concentrations of isotopically enriched monomethylmercury (MM[198]Hg) and inorganic mercury ([200]Hg) for demethylation and methylation rate measurements. Periphytic microbial communities were investigated through 16S rRNA gene analyses and metagenomic screenings for the hgcA gene, involved in mercury methylation. Positive mercury methylation rates ([5.9 ± 3.4] × 10[-3] day[-1]) were observed only in the wetlands, and demethylation rates averaged 1.78 ± 0.21 day[-1] for the three studied sites. The 16S rRNA gene analyses revealed Proteobacteria as the most abundant phylum across all sites (36.3% ± 1.4%), from which families associated with mercury methylation were mostly found in the wetland site. Metagenome screening for HgcA identified 24 different hgcA sequences in the constructed wetland site only, associated with 8 known families, where the iron-reducing Geobacteraceae were the most abundant. This work brings new information on mercury methylation in periphyton from habitats of impacted rivers, associating it mostly with putative iron-reducing bacteria.IMPORTANCE Monomethylmercury (MMHg) is a biomagnifiable neurotoxin of global concern with risks to human health mostly associated with fish consumption. Hydroelectric reservoirs are known to be sources of MMHg many years after their impoundment. Little is known, however, on run-of-river dams flooding smaller terrestrial areas, although their numbers are expected to increase considerably worldwide in decades to come. Production of MMHg is associated mostly with anaerobic processes, but Hg methylation has been shown to occur in periphytic biofilms located in oxic zones of the water column. Therefore, in this study, we investigated in situ production of MMHg by periphytic communities in habitats impacted by the construction of a run-of-river dam by combining transformation rate measurements with genomic approaches targeting hgcAB genes, responsible for mercury methylation. These results provide extended knowledge on mercury methylators in river ecosystems impacted by run-of-river dams in temperate habitats.}, } @article {pmid33730081, year = {2021}, author = {Szilágyi, Á and Bodor, A and Tolvai, N and Kovács, KL and Bodai, L and Wirth, R and Bagi, Z and Szepesi, Á and Markó, V and Kakuk, B and Bounedjoum, N and Rákhely, G}, title = {A comparative analysis of biogas production from tomato bio-waste in mesophilic batch and continuous anaerobic digestion systems.}, journal = {PloS one}, volume = {16}, number = {3}, pages = {e0248654}, pmid = {33730081}, issn = {1932-6203}, mesh = {Anaerobiosis ; *Biofuels ; Bioreactors/*microbiology ; *Crop Production ; Fermentation ; Solanum lycopersicum/*chemistry/microbiology ; Metagenomics ; Methane/*biosynthesis ; Microbiota/genetics ; Zea mays/chemistry/microbiology ; }, abstract = {Annually, agricultural activity produces an enormous amount of plant biomass by-product. Many studies have reported the biomethane potential of agro-industrial wastes, but only a few studies have investigated applying the substrates in both batch and continuous mode. Tomato is one of the most popular vegetables globally; its processing releases a substantial amount of by-product, such as stems and leaves. This study examined the BMP of tomato plant (Solanum lycopersicum Mill. L. cv. Alfred) waste. A comparative test revealed that the BMPs of corn stover, tomato waste,and their combination were approximately the same, around 280 mL methane/g Volatile Solid. In contrast, the relative biogas production decreased in the presence of tomato waste in a continuous mesophilic anaerobic digestion system; the daily biogas productions were 860 ± 80, 290 ± 50, and 570 ± 70 mL biogas/gVolatile Solid/day in the case of corn stover, tomato waste, and their mixture, respectively. The methane content of biogas was around 46-48%. The fermentation parameters of the continuous AD experiments were optimal in all cases; thus, TW might have an inhibitory effect on the microbial community. Tomato plant materials contain e.g. flavonoids, glycoalkaloids (such as tomatine and tomatidine), etc. known as antimicrobial and antifungal agents. The negative effect of tomatine on the biogas yield was confirmed in batch fermentation experiments. Metagenomic analysis revealed that the tomato plant waste caused significant rearrangements in the microbial communities in the continuously operated reactors. The results demonstrated that tomato waste could be a good mono-substrate in batch fermentations or a co-substrate with corn stover in a proper ratio in continuous anaerobic fermentations for biogas production. These results also point to the importance of running long-term continuous fermentations to test the suitability of a novel biomass substrate for industrial biogas production.}, } @article {pmid33726974, year = {2021}, author = {Dos Santos Bezerra, R and Bub, CB and Peronni, KC and de Figiueiredo Barros, BD and da Costa Lira, SM and Kutner, JM and Covas, DT and Kashima, S and Slavov, SN}, title = {Virome comparison of deferred blood donations obtained from different geographic regions in the Sao Paulo State, Brazil.}, journal = {Transfusion and apheresis science : official journal of the World Apheresis Association : official journal of the European Society for Haemapheresis}, volume = {60}, number = {3}, pages = {103106}, doi = {10.1016/j.transci.2021.103106}, pmid = {33726974}, issn = {1473-0502}, mesh = {Blood Donors/*statistics & numerical data ; Brazil ; Humans ; Virome/*immunology ; }, abstract = {The virome composition of blood units deferred due to symptomatic disease of the donors reported after blood donation may reveal novel or unsuspected viral agents which may have impact in the area of hemotherapy. The objective of this study was to compare the virome of blood donations obtained from two distantly located blood collecting institutions in the Saqo Paulo State and deferred from use due to post donation illness reports (PDIR). Plasma samples with PDIR due to different symptoms were collected in two cities of the Sao Paulo State (Sao Paulo city, 28 samples and Ribeirao Preto city, 11 samples). The samples were assembled in pools and sequenced in Illumina NextSeq 550 sequencer. The obtained raw sequencing data was analyzed using bioinformatic pipeline aiming viral identification. Phylogenetic classification of the most important contigs was also performed. The virome composition of the plasma samples obtained in both cities was different. This was more pronounced for some specific anellovirus types and the human pegivirus-1 (HPgV-1) which were exclusively found among donations obtained from the city of Sao Paulo. On the other hand, in PDIR samples from Ribeirao Preto, Dengue -2 reads were more abundant compared to commensal viral representatives. The obtained virome findings show that the differential viral abundance is related to geographic localization and specific disease endemicity. The virome of PDIR samples may be used to more profoundly analyze the hypothetic transfusion threats in a given location.}, } @article {pmid33725532, year = {2021}, author = {Kayani, MUR and Yu, K and Qiu, Y and Shen, Y and Gao, C and Feng, R and Zeng, X and Wang, W and Chen, L and Su, HL}, title = {Environmental concentrations of antibiotics alter the zebrafish gut microbiome structure and potential functions.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {278}, number = {}, pages = {116760}, doi = {10.1016/j.envpol.2021.116760}, pmid = {33725532}, issn = {1873-6424}, mesh = {Animals ; Anti-Bacterial Agents/toxicity ; Flavobacterium ; *Gastrointestinal Microbiome ; Zebrafish ; }, abstract = {A paradoxical impact of high rates of production and consumption of antibiotics is their widespread release in the environment. Consequently, low concentrations of antibiotics and their byproducts have been routinely identified from various environmental settings especially from aquatic environments. However, the impact of such low concentrations of antibiotics on the exposed host especially in early life remains poorly understood. We exposed zebrafish to two different environmental concentrations of oxytetracycline and sulfamethoxazole, from larval stage to adulthood (∼120 days) and characterized their impact on the taxonomic diversity, antibiotic resistance genes, and metabolic pathways of the gut microbiome using metagenomic shotgun sequencing and analysis. Long term exposure of environmental concentrations of oxytetracycline and sulfamethoxazole significantly impacted the taxonomic composition and metabolic pathways of zebrafish gut microbiome. The antibiotic exposed samples exhibited significant enrichment of multiple flavobacterial species, including Flavobacterium sp. F52, Flavobacterium johnsoniae and Flavobacterium sp. Fl, which are well known pathogenic bacteria. The relative abundance of antibiotic resistance genes, especially several tetratcycline and sulfonamide resistance genes were significantly higher in the exposed samples and showed a linear correlation with the antibiotic concentrations. Furthermore, several metabolic pathways, including folate biosynthesis, oxidative phosphorylation, and biotin metabolism pathways, showed significant enrichment in the antibiotic exposed samples. Collectively, our results suggest that early life exposure of the environmental concentrations of antibiotics can increase the abundance of unfavorable bacteria, antibiotic resistance genes and associated pathways in the gut microbiome of zebrafish.}, } @article {pmid33724519, year = {2021}, author = {Kang, WN and Jin, L and Fu, KY and Guo, WC and Li, GQ}, title = {A switch of microbial flora coupled with ontogenetic niche shift in Leptinotarsa decemlineata.}, journal = {Archives of insect biochemistry and physiology}, volume = {107}, number = {1}, pages = {e21782}, doi = {10.1002/arch.21782}, pmid = {33724519}, issn = {1520-6327}, support = {32072416//The National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacteria/classification ; Coleoptera/*microbiology/physiology ; Ecosystem ; Genes, Bacterial ; Larva/microbiology/physiology ; Metagenomics/methods ; Metamorphosis, Biological ; *Microbiota/genetics ; Pupa/*microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In Leptinotarsa decemlineata, a final-instar wandering larva typically undergoes an ontogenetic niche shift (ONS), from potato plant during the foraging stage to its pupation site below ground. Using high-throughput sequencing of the bacterial 16S ribosomal RNA gene, we determined the hypothesis that the L. decemlineata pupae harbor stage-specific bacteria to meet the physiological requirements for underground habitat. We identified 34 bacterial phyla, comprising 73 classes, 208 orders, 375 families, and 766 genera in the collected specimens. Microbes across phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were enriched in the pupae, while those in the phylum Proteobacteria, Tenericutes, Firmicutes, and Bacteroidetes dominated in the larvae and adults. A total of 18 genera, including Blastococcus, Corynebacterium_1, Gordonia, Microbacterium, Nocardia, Nocardioides, Rhodococcus, Solirubrobacter, Tsukamurella, Enterococcus, Acinetobacter, Escherichia_Shigella, Lysobacter, Pseudomonas, and Stenotrophomonas, were specifically distributed in pupae. Moreover, soil sterilizing removed a major portion of bacteria in pupae. Specifically, both Enterococcus and Pseudomonas were eliminated in the soil sterilizing and antibiotic-fed beetle groups. Furthermore, the pupation rate and fresh pupal weight were similar, whereas the emergence rate and adult weight were decreased in the antibiotic-fed beetles, compared with controls. The results demonstrate that a switch of bacterial communities occurs in the pupae; the pupal-specific bacteria genera are mainly originated from soil; this bacterial biodiversity improves pupa performance in soil. Our results provide new insight into the evolutionary fitness of L. decemlineata to different environmental niches.}, } @article {pmid33723701, year = {2022}, author = {El Mouzan, M and Al-Hussaini, A and Fanelli, B and Assiri, A and AlSaleem, B and Al Mofarreh, M and Al Sarkhy, A and Alasmi, M}, title = {Fungal Dysbiosis in Children with Celiac Disease.}, journal = {Digestive diseases and sciences}, volume = {67}, number = {1}, pages = {216-223}, pmid = {33723701}, issn = {1573-2568}, mesh = {*Celiac Disease/diagnosis/epidemiology/microbiology/physiopathology ; Child ; *Dysbiosis/diagnosis/microbiology ; Feces/microbiology ; Female ; *Fungi/classification/immunology/isolation & purification ; Humans ; Intestinal Mucosa/microbiology/pathology ; Male ; Metagenomics/methods ; Microbiological Phenomena ; *Mycobiome/genetics/immunology ; Saudi Arabia/epidemiology ; }, abstract = {BACKGROUND: Although intestinal fungi are known to interact with the immune system, the relationship between intestinal fungi and childhood celiac disease (CeD), an immune-mediated condition, has rarely been reported.

AIMS: The aim of this study was to describe gut fungal profiles in a cohort of children with new-onset CeD.

METHODS: Mucosal and fecal samples were collected from children with CeD and controls and subjected to metagenomics analysis of fungal microbiota communities. DNA libraries were sequenced using Illumina HiSeq platform 2 × 150 bp. Bioinformatic analysis was performed to quantify the relative abundance of fungi. Shannon alpha diversity metrics and beta diversity principal coordinate (PCo) analyses were calculated, and DESeq tests were performed between celiac and non-celiac groups.

RESULTS: Overall more abundant taxa in samples of children with CeD included Tricholomataceae, Saccharomycetaceae, Saccharomycetes Saccharomyces cerevisiae, and Candida, whereas less abundant taxa included Pichiaceae, Pichia kudriavzevii, Pneumocystis, and Pneumocystis jirovecii. Alpha diversity between CeD and control individuals did not differ significantly, and beta diversity PCo analysis showed overlap of samples from CeD and controls for both fecal or mucosal samples; however, there was a clear separation between mucosal and fecal overall samples CONCLUSIONS: We report fungal dysbiosis in children with CeD, suggesting a possible role in the pathogenesis of CeD. Further larger, controlled, prospective and longitudinal studies are needed to verify the results of this study and clarify the functional role of fungi in CeD.}, } @article {pmid33723324, year = {2021}, author = {Mafuna, T and Soma, P and Tsotetsi-Khambule, AM and Hefer, CA and Muchadeyi, FC and Thekisoe, OMM and Pierneef, RE}, title = {Bacterial profiling of Haemonchus contortus gut microbiome infecting Dohne Merino sheep in South Africa.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {5905}, pmid = {33723324}, issn = {2045-2322}, mesh = {Animals ; Bacteria/*classification/genetics ; Bacterial Typing Techniques ; Biodiversity ; Female ; *Gastrointestinal Microbiome ; Haemonchiasis/*veterinary ; Haemonchus/anatomy & histology/genetics/isolation & purification/*microbiology ; Male ; Phylogeny ; *Sheep ; Sheep Diseases/*parasitology ; South Africa ; }, abstract = {A metagenomic approach was used to study the gut microbiome of Haemonchus contortus field strains and that of its predilection site, the abomasum of Dohne Merino sheep. The abomasum contents and H. contortus were collected from 10 naturally infected Dohne Merino sheep. The H. contortus specimens were classified and sexually differentiated using morphometric characters and was further confirmed through molecular identification. We investigated differences and similarities between the bacterial composition of the adult male and female H. contortus gut microbiomes, which were both dominated by bacteria from the Escherichia, Shigella, Vibrio and Halomonas genera. Major abundance variations were identified between the shared adult male and female H. contortus microbiomes. The results also revealed that Succiniclasticum, Rikenellaceae RC9 gut group and Candidatus Saccharimonas were the predominant genera in the Dohne Merino abomasum. This study provides insight into the highly diverse bacterial composition of the H. contortus gut microbiome and the Dohne Merino abomasum which needs to be studied further to explore the complex interactions of different gastrointestinal nematode microbiomes with the host.}, } @article {pmid33723291, year = {2021}, author = {Desbois, AC and Ciocan, D and Saadoun, D and Perlemuter, G and Cacoub, P}, title = {Specific microbiome profile in Takayasu's arteritis and giant cell arteritis.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {5926}, pmid = {33723291}, issn = {2045-2322}, mesh = {Aged ; Aged, 80 and over ; Biomarkers/blood ; Computational Biology/methods ; *Disease Susceptibility ; Female ; Giant Cell Arteritis/drug therapy/*etiology/metabolism/pathology ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Sepsis/complications/microbiology ; Takayasu Arteritis/drug therapy/*etiology/metabolism/pathology ; }, abstract = {Recent studies have provided evidence of a close link between specific microbiota and inflammatory disorders. While the vessel wall microbiota has been recently described in large vessel vasculitis (LVV) and controls, the blood microbiome in these diseases has not been previously reported (LVV). We aimed to analyse the blood microbiome profile of LVV patients (Takayasu's arteritis [TAK], giant cell arteritis [GCA]) and healthy blood donors (HD). We studied the blood samples of 13 patients with TAK (20 samples), 9 patients with GCA (11 samples) and 15 HD patients. We assessed the blood microbiome profile by sequencing the 16S rDNA blood bacterial DNA. We used linear discriminant analysis (LDA) coupled with linear discriminant effect size measurement (LEfSe) to investigate the differences in the blood microbiome profile between TAK and GCA patients. An increase in the levels of Clostridia, Cytophagia and Deltaproteobacteria and a decrease in Bacilli at the class level were found in TAK patients compared with HD patients (LDA > 2, p < 0.05). Active TAK patients had significantly lower levels of Staphylococcus compared with inactive TAK patients. Samples of GCA patients had an increased abundance of Rhodococcus and an unidentified member of the Cytophagaceae family. Microbiota of TAK compared with GCA patients was found to show higher levels of Candidatus Aquiluna and Cloacibacterium (LDA > 2; p < 0.05). Differences highlighted in the blood microbiome were also associated with a shift of bacterial predicted metabolic functions in TAK in comparison with HD. Similar results were also found in patients with active versus inactive TAK. In conclusion, patients with TAK were found to present a specific blood microbiome profile in comparison with healthy donors and GCA subjects. Significant changes in the blood microbiome profiles of TAK patients were associated with specific metabolic functions.}, } @article {pmid33723271, year = {2021}, author = {Papa, G and Di Prisco, G and Spini, G and Puglisi, E and Negri, I}, title = {Acute and chronic effects of Titanium dioxide (TiO2) PM1 on honey bee gut microbiota under laboratory conditions.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {5946}, pmid = {33723271}, issn = {2045-2322}, mesh = {Animals ; *Bees ; Biodiversity ; Environmental Pollutants/*adverse effects ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Particulate Matter/*adverse effects ; Titanium/*adverse effects/chemistry ; }, abstract = {Apis mellifera is an important provider of ecosystem services, and during flight and foraging behaviour is exposed to environmental pollutants including airborne particulate matter (PM). While exposure to insecticides, antibiotics, and herbicides may compromise bee health through alterations of the gut microbial community, no data are available on the impacts of PM on the bee microbiota. Here we tested the effects of ultrapure Titanium dioxide (TiO2) submicrometric PM (i.e., PM1, less than 1 µm in diameter) on the gut microbiota of adult bees. TiO2 PM1 is widely used as a filler and whitening agent in a range of manufactured objects, and ultrapure TiO2 PM1 is also a common food additive, even if it has been classified by the International Agency for Research on Cancer (IARC) as a possible human carcinogen in Group 2B. Due to its ubiquitous use, honey bees may be severely exposed to TiO2 ingestion through contaminated honey and pollen. Here, we demonstrated that acute and chronic oral administration of ultrapure TiO2 PM1 to adult bees alters the bee microbial community; therefore, airborne PM may represent a further risk factor for the honey bee health, promoting sublethal effects against the gut microbiota.}, } @article {pmid33722860, year = {2021}, author = {Asnicar, F and Leeming, ER and Dimidi, E and Mazidi, M and Franks, PW and Al Khatib, H and Valdes, AM and Davies, R and Bakker, E and Francis, L and Chan, A and Gibson, R and Hadjigeorgiou, G and Wolf, J and Spector, TD and Segata, N and Berry, SE}, title = {Blue poo: impact of gut transit time on the gut microbiome using a novel marker.}, journal = {Gut}, volume = {70}, number = {9}, pages = {1665-1674}, pmid = {33722860}, issn = {1468-3288}, support = {MR/N01183X/1/MRC_/Medical Research Council/United Kingdom ; MR/N030125/1/MRC_/Medical Research Council/United Kingdom ; R01 CA230551/CA/NCI NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Akkermansia ; Bacteroides ; Bacteroidetes ; Biomarkers ; Coloring Agents ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; *Gastrointestinal Transit/genetics/physiology ; Humans ; Male ; Metagenomics ; Middle Aged ; }, abstract = {BACKGROUND AND AIMS: Gut transit time is a key modulator of host-microbiome interactions, yet this is often overlooked, partly because reliable methods are typically expensive or burdensome. The aim of this single-arm, single-blinded intervention study is to assess (1) the relationship between gut transit time and the human gut microbiome, and (2) the utility of the 'blue dye' method as an inexpensive and scalable technique to measure transit time.

METHODS: We assessed interactions between the taxonomic and functional potential profiles of the gut microbiome (profiled via shotgun metagenomic sequencing), gut transit time (measured via the blue dye method), cardiometabolic health and diet in 863 healthy individuals from the PREDICT 1 study.

RESULTS: We found that gut microbiome taxonomic composition can accurately discriminate between gut transit time classes (0.82 area under the receiver operating characteristic curve) and longer gut transit time is linked with specific microbial species such as Akkermansia muciniphila, Bacteroides spp and Alistipes spp (false discovery rate-adjusted p values <0.01). The blue dye measure of gut transit time had the strongest association with the gut microbiome over typical transit time proxies such as stool consistency and frequency.

CONCLUSIONS: Gut transit time, measured via the blue dye method, is a more informative marker of gut microbiome function than traditional measures of stool consistency and frequency. The blue dye method can be applied in large-scale epidemiological studies to advance diet-microbiome-health research. Clinical trial registry website https://clinicaltrials.gov/ct2/show/NCT03479866 and trial number NCT03479866.}, } @article {pmid33717447, year = {2021}, author = {Meucci, S and Schulte, L and Zimmermann, HH and Stoof-Leichsenring, KR and Epp, L and Bronken Eidesen, P and Herzschuh, U}, title = {Holocene chloroplast genetic variation of shrubs (Alnus alnobetula, Betula nana, Salix sp.) at the siberian tundra-taiga ecotone inferred from modern chloroplast genome assembly and sedimentary ancient DNA analyses.}, journal = {Ecology and evolution}, volume = {11}, number = {5}, pages = {2173-2193}, pmid = {33717447}, issn = {2045-7758}, abstract = {Climate warming alters plant composition and population dynamics of arctic ecosystems. In particular, an increase in relative abundance and cover of deciduous shrub species (shrubification) has been recorded. We inferred genetic variation of common shrub species (Alnus alnobetula, Betula nana, Salix sp.) through time. Chloroplast genomes were assembled from modern plants (n = 15) from the Siberian forest-tundra ecotone. Sedimentary ancient DNA (sedaDNA; n = 4) was retrieved from a lake on the southern Taymyr Peninsula and analyzed by metagenomics shotgun sequencing and a hybridization capture approach. For A. alnobetula, analyses of modern DNA showed low intraspecies genetic variability and a clear geographical structure in haplotype distribution. In contrast, B. nana showed high intraspecies genetic diversity and weak geographical structure. Analyses of sedaDNA revealed a decreasing relative abundance of Alnus since 5,400 cal yr BP, whereas Betula and Salix increased. A comparison between genetic variations identified in modern DNA and sedaDNA showed that Alnus variants were maintained over the last 6,700 years in the Taymyr region. In accordance with modern individuals, the variants retrieved from Betula and Salix sedaDNA showed higher genetic diversity. The success of the hybridization capture in retrieving diverged sequences demonstrates the high potential for future studies of plant biodiversity as well as specific genetic variation on ancient DNA from lake sediments. Overall, our results suggest that shrubification has species-specific trajectories. The low genetic diversity in A. alnobetula suggests a local population recruitment and growth response of the already present communities, whereas the higher genetic variability and lack of geographical structure in B. nana may indicate a recruitment from different populations due to more efficient seed dispersal, increasing the genetic connectivity over long distances.}, } @article {pmid33717191, year = {2021}, author = {Ancona, G and Merlini, E and Tincati, C and Barassi, A and Calcagno, A and Augello, M and Bono, V and Bai, F and Cannizzo, ES and d'Arminio Monforte, A and Marchetti, G}, title = {Long-Term Suppressive cART Is Not Sufficient to Restore Intestinal Permeability and Gut Microbiota Compositional Changes.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {639291}, pmid = {33717191}, issn = {1664-3224}, mesh = {Adult ; Anti-HIV Agents/*therapeutic use ; Female ; Gastrointestinal Microbiome/*drug effects ; HIV Infections/*drug therapy ; Humans ; Intestines/*drug effects ; Male ; Middle Aged ; Permeability/drug effects ; }, abstract = {Background: We explored the long-term effects of cART on markers of gut damage, microbial translocation, and paired gut/blood microbiota composition, with a focus on the role exerted by different drug classes. Methods: We enrolled 41 cART naïve HIV-infected subjects, undergoing blood and fecal sampling prior to cART (T0) and after 12 (T12) and 24 (T24) months of therapy. Fifteen HIV-uninfected individuals were enrolled as controls. We analyzed: (i) T-cell homeostasis (flow cytometry); (ii) microbial translocation (sCD14, EndoCab, 16S rDNA); (iii) intestinal permeability and damage markers (LAC/MAN, I-FABP, fecal calprotectin); (iv) plasma and fecal microbiota composition (alpha- and beta-diversity, relative abundance); (v) functional metagenome predictions (PICRUSt). Results: Twelve and twenty four-month successful cART resulted in a rise in EndoCAb (p = 0.0001) and I-FABP (p = 0.039) vis-à-vis stable 16S rDNA, sCD14, calprotectin and LAC/MAN, along with reduced immune activation in the periphery. Furthermore, cART did not lead to substantial modifications of microbial composition in both plasma and feces and metabolic metagenome predictions. The stratification according to cART regimens revealed a feeble effect on microbiota composition in patients on NNRTI-based or INSTI-based regimens, but not PI-based regimens. Conclusions: We hereby show that 24 months of viro-immunological effective cART, while containing peripheral hyperactivation, exerts only minor effects on the gastrointestinal tract. Persistent alteration of plasma markers indicative of gut structural and functional impairment seemingly parallels enduring fecal dysbiosis, irrespective of drug classes, with no effect on metabolic metagenome predictions.}, } @article {pmid33714730, year = {2021}, author = {Zhang, X and Yang, Y and Zhang, F and Yu, J and Sun, W and Wang, R and Wu, C}, title = {Traditional Chinese medicines differentially modulate the gut microbiota based on their nature (Yao-Xing).}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {85}, number = {}, pages = {153496}, doi = {10.1016/j.phymed.2021.153496}, pmid = {33714730}, issn = {1618-095X}, mesh = {Animals ; Drugs, Chinese Herbal/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Male ; Medicine, Chinese Traditional ; Mice ; Mice, Inbred C57BL ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Property theory is a unique principle guiding traditional Chinese medicine (TCM) that classifies various TCMs into four natures (hot, warm, cool, and cold) to reflect their medical actions on the human body. Despite successful application for thousands of years, characterizing the nature of medical TCMs by modern physiological indicators remains a challenge.

PURPOSE: In this study, we investigated the potential relationship between the nature of TCMs and their modulation of the gut microbiota.

STUDY DESIGN: We selected twelve TCMs with hot, warm, cool, or cold natures that possess antidiarrheal effects. Their aqueous extracts were orally administered to C57BL/6 mice at a clinical dose for 4 weeks. The gut microbiota was measured by 16S rRNA-based metagenomics, and the correlation between microbial composition/function and TCM nature was analyzed.

RESULTS: Antidiarrheal TCMs with different natures showed distinct impacts on the gut microbiota. Hot-natured TCMs had no influence on the gut microbiota, warm-natured TCMs had a moderate influence, cool-natured TCMs had a strong influence, and cold-natured TCMs substantially changed the structure of the gut microbial community. The abundance of Anaerotruncus, Tyzzerella and Ruminiclostridium steadily increased, while that of Ruminococcaceae_UCG-010, Parasutterella and Bifidobacterium continuously decreased as the herbal nature turned from cold to hot. Microbiome functional prediction for Cluster of Orthologous Groups (COG) of proteins and Kyoto Encyclopedia of Genes and Genomes (KEGG) categories showed that colder TCMs imposed a stronger influence on microbial functional repertoires. Specifically, the abundance of ABC transporters, key bacterial proteins involved in nutrient absorption and drug resistance, was gradually decreased by colder TCMs.

CONCLUSION: Our results demonstrated that the nature of TCMs could be reflected by their modulation of gut microbes. Cold TCMs may exert their antidiarrheal effects, at least partially, by modulating the gut microbiota, while hot TCMs may alleviate dysentery in other ways.}, } @article {pmid33713805, year = {2021}, author = {An, J and McDowell, A and Kim, YK and Kim, TB}, title = {Extracellular vesicle-derived microbiome obtained from exhaled breath condensate in patients with asthma.}, journal = {Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology}, volume = {126}, number = {6}, pages = {729-731}, doi = {10.1016/j.anai.2021.02.030}, pmid = {33713805}, issn = {1534-4436}, mesh = {Asthma/*microbiology ; Bacteria/classification/genetics ; *Breath Tests ; Exhalation ; Extracellular Vesicles/*microbiology ; Humans ; Lung/*microbiology ; Metagenomics ; *Microbiota ; }, } @article {pmid33713395, year = {2021}, author = {Gil, P and Dupuy, V and Koual, R and Exbrayat, A and Loire, E and Fall, AG and Gimonneau, G and Biteye, B and Talla Seck, M and Rakotoarivony, I and Marie, A and Frances, B and Lambert, G and Reveillaud, J and Balenghien, T and Garros, C and Albina, E and Eloit, M and Gutierrez, S}, title = {A library preparation optimized for metagenomics of RNA viruses.}, journal = {Molecular ecology resources}, volume = {21}, number = {6}, pages = {1788-1807}, doi = {10.1111/1755-0998.13378}, pmid = {33713395}, issn = {1755-0998}, support = {CuliOme/291815//Seventh Framework Programme/ ; Vmerge/613996//Seventh Framework Programme/ ; //Direction Générale de l'Alimentation/ ; }, mesh = {Animals ; *Gene Library ; Genome, Viral ; Metagenome ; *Metagenomics ; *RNA Viruses/genetics ; *Virome ; }, abstract = {Our understanding of the viral communities associated to animals has not yet reached the level attained on the bacteriome. This situation is due to, among others, technical challenges in adapting metagenomics using high-throughput sequencing to the study of RNA viromes in animals. Although important developments have been achieved in most steps of viral metagenomics, there is yet a key step that has received little attention: the library preparation. This situation differs from bacteriome studies in which developments in library preparation have largely contributed to the democratisation of metagenomics. Here, we present a library preparation optimized for metagenomics of RNA viruses from insect vectors of viral diseases. The library design allows a simple PCR-based preparation, such as those routinely used in bacterial metabarcoding, that is adapted to shotgun sequencing as required in viral metagenomics. We first optimized our library preparation using mock viral communities and then validated a full metagenomic approach incorporating our preparation in two pilot studies with field-caught insect vectors; one including a comparison with a published metagenomic protocol. Our approach provided a fold increase in virus-like sequences compared to other studies, and nearly-full genomes from new virus species. Moreover, our results suggested conserved trends in virome composition within a population of a mosquito species. Finally, the sensitivity of our approach was compared to a commercial diagnostic PCR for the detection of an arbovirus in field-caught insect vectors. Our approach could facilitate studies on viral communities from animals and the democratization of metagenomics in community ecology of viruses.}, } @article {pmid33713107, year = {2021}, author = {Kim, J and Jiang, S and Wang, Y and Xiao, G and Xie, Y and Liu, DJ and Li, Q and Koh, A and Zhan, X}, title = {MetaPrism: A versatile toolkit for joint taxa/gene analysis of metagenomic sequencing data.}, journal = {G3 (Bethesda, Md.)}, volume = {11}, number = {4}, pages = {}, pmid = {33713107}, issn = {2160-1836}, support = {R01 GM126479/GM/NIGMS NIH HHS/United States ; R56 HG011035/HG/NHGRI NIH HHS/United States ; R01 HG008983/HG/NHGRI NIH HHS/United States ; P30 CA142543/CA/NCI NIH HHS/United States ; R01 GM115473/GM/NIGMS NIH HHS/United States ; P50 CA070907/CA/NCI NIH HHS/United States ; }, mesh = {Algorithms ; Computational Biology ; Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; Software ; }, abstract = {In microbiome research, metagenomic sequencing generates enormous amounts of data. These data are typically classified into taxa for taxonomy analysis, or into genes for functional analysis. However, a joint analysis where the reads are classified into taxa-specific genes is often overlooked. To enable the analysis of this biologically meaningful feature, we developed a novel bioinformatic toolkit, MetaPrism, which can analyze sequence reads for a set of joint taxa/gene analyses to: 1) classify sequence reads and estimate the abundances for taxa-specific genes; 2) tabularize and visualize taxa-specific gene abundances; 3) compare the abundances between groups; and 4) build prediction models for clinical outcome. We illustrated these functions using a published microbiome metagenomics dataset from patients treated with immune checkpoint inhibitor therapy and showed the joint features can serve as potential biomarkers to predict therapeutic responses. MetaPrism is a toolkit for joint taxa and gene analysis. It offers biological insights on the taxa-specific genes on top of the taxa-alone or gene-alone analysis. MetaPrism is open-source software and freely available at https://github.com/jiwoongbio/MetaPrism. The example script to reproduce the manuscript is also provided in the above code repository.}, } @article {pmid33712656, year = {2021}, author = {Kim, J and Park, KY and Park, HK and Hwang, HS and Seo, MR and Kim, B and Cho, Y and Rho, M and Pai, H}, title = {High fecal carriage of blaCTX-M, blaCMY-2, and plasmid-mediated quinolone resistance genes among healthy Korean people in a metagenomic analysis.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {5874}, pmid = {33712656}, issn = {2045-2322}, mesh = {Adult ; Alleles ; Drug Resistance, Multiple, Bacterial/*genetics ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome ; *Genes, Bacterial ; *Health ; Humans ; Male ; *Metagenomics ; Middle Aged ; Phenotype ; Plasmids/*genetics ; Quinolones/*pharmacology ; Republic of Korea ; beta-Lactamases/*genetics ; }, abstract = {To characterize the carriage of antibiotic resistance genes (ARGs) in the gut microbiome of healthy individuals. Fecal carriage of ARGs was investigated in 61 healthy individuals aged 30 to 59 years through whole metagenome sequencing of the gut microbiome and a targeted metagenomic approach. The number of ARGs in the gut microbiome was counted and normalized per million predicted genes (GPM). In the Korean population, the resistome ranged from 49.7 to 292.5 GPM (median 89.7). Based on the abundance of ARGs, the subjects were categorised into high (> 120 GPM), middle (60‒120 GPM), and low (< 60 GPM) ARG groups. Individuals in the high ARG group tended to visit hospitals more often (P = 0.065), particularly for upper respiratory tract infections (P = 0.066), and carried more blaCTX-M (P = 0.008). The targeted metagenome approach for bla and plasmid-mediated quinolone resistance (PMQR) genes revealed a high fecal carriage rate; 23% or 13.1% of the subjects carried blaCTX-M or blaCMY-2, respectively. Regarding PMQR genes, 59% of the subjects carried PMQR, and 83% of them harboured 2‒4 PMQR genes (qnrB 44.3%, qnrS 47.5% etc.). The presence of blaCTX-M correlated with ARG abundance in the gut resistome, whereas PMQR genes were irrelevant to other ARGs (P = 0.176). Fecal carriage of blaCTX-M and PMQR genes was broad and multiplexed among healthy individuals.}, } @article {pmid33709132, year = {2021}, author = {Mei, Z and Chen, GC and Wang, Z and Usyk, M and Yu, B and Baeza, YV and Humphrey, G and Benitez, RS and Li, J and Williams-Nguyen, JS and Daviglus, ML and Hou, L and Cai, J and Zheng, Y and Knight, R and Burk, RD and Boerwinkle, E and Kaplan, RC and Qi, Q}, title = {Dietary factors, gut microbiota, and serum trimethylamine-N-oxide associated with cardiovascular disease in the Hispanic Community Health Study/Study of Latinos.}, journal = {The American journal of clinical nutrition}, volume = {113}, number = {6}, pages = {1503-1514}, pmid = {33709132}, issn = {1938-3207}, support = {R01 DK119268/DK/NIDDK NIH HHS/United States ; N01HC65236/HL/NHLBI NIH HHS/United States ; N01HC65235/HL/NHLBI NIH HHS/United States ; N01HC65234/HL/NHLBI NIH HHS/United States ; N01HC65233/HL/NHLBI NIH HHS/United States ; N01HC65237/HL/NHLBI NIH HHS/United States ; P60 DK020541/DK/NIDDK NIH HHS/United States ; R01 HL060712/HL/NHLBI NIH HHS/United States ; R01 DK126698/DK/NIDDK NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; P30 DK020541/DK/NIDDK NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Biomarkers ; Cardiovascular Diseases/blood/*etiology ; Cross-Sectional Studies ; *Diet ; Female ; *Gastrointestinal Microbiome ; *Hispanic or Latino ; Humans ; Male ; Methylamines/*blood ; Middle Aged ; Public Health ; }, abstract = {BACKGROUND: Trimethylamine-N-oxide (TMAO), a diet-derived and gut microbiota-related metabolite, is associated with cardiovascular disease (CVD). However, major dietary determinants and specific gut bacterial taxa related to TMAO remain to be identified in humans.

OBJECTIVES: We aimed to identify dietary and gut microbial factors associated with circulating TMAO.

METHODS: This cross-sectional study included 3972 participants (57.3% women) aged 18-74 y from the Hispanic Community Health Study/Study of Latinos in the United States. Dietary information was collected by 24-h dietary recalls at baseline interview (2008-2011), and baseline serum TMAO and its precursors were measured by an untargeted approach. Gut microbiome was profiled by shotgun metagenomic sequencing in a subset of participants (n = 626) during a follow-up visit (2016-2018). Logistic and linear regression were used to examine associations of inverse-normalized metabolites with prevalent CVD, dietary intake, and bacterial species, respectively, after adjustment for sociodemographic, behavioral, and clinical factors.

RESULTS: TMAO was positively associated with prevalent CVD (case number = 279; OR = 1.34; 95% CI: 1.17, 1.54, per 1-SD). Fish (P = 1.26 × 10-17), red meat (P = 3.33 × 10-16), and egg (P = 3.89 × 10-5) intakes were top dietary factors positively associated with TMAO. We identified 9 gut bacterial species significantly associated with TMAO (false discovery rate <0.05). All 4 species positively associated with TMAO belong to the order Clostridiales, of which 3 might have homologous genes encoding carnitine monooxygenase, an enzyme converting carnitine to trimethylamine (TMA). The red meat-TMAO association was more pronounced in participants with higher abundances of these 4 species compared with those with lower abundance (Pinteraction = 0.013), but such microbial modification was not observed for fish-TMAO or egg-TMAO associations.

CONCLUSION: In US Hispanics/Latinos, fish, red meat, and egg intakes are major dietary factors associated with serum TMAO. The identified potential TMA-producing gut microbiota and microbial modification on the red meat-TMAO association support microbial TMA production from dietary carnitine, whereas the fish-TMAO association is independent of gut microbiota.}, } @article {pmid33708211, year = {2021}, author = {Shen, S and Prame Kumar, K and Wen, SW and Shim, R and Wanrooy, BJ and Stanley, D and Moore, RJ and Van, TTH and Robert, R and Hickey, MJ and Wong, CHY}, title = {Deficiency of Dietary Fiber Modulates Gut Microbiota Composition, Neutrophil Recruitment and Worsens Experimental Colitis.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {619366}, pmid = {33708211}, issn = {1664-3224}, mesh = {Animals ; Biomarkers ; Cell Adhesion ; Chemotaxis, Leukocyte/*immunology ; Colitis/*etiology/metabolism/pathology ; Dextran Sulfate/adverse effects ; Diet ; Dietary Fiber/*deficiency ; Disease Models, Animal ; Endothelial Cells ; *Gastrointestinal Microbiome ; Leukocyte Count ; Male ; Metagenomics/methods ; Mice ; Neutrophil Infiltration/*immunology ; RNA, Ribosomal, 16S ; }, abstract = {Ulcerative colitis is an inflammatory disease of the colon that is associated with colonic neutrophil accumulation. Recent evidence indicates that diet alters the composition of the gut microbiota and influences host-pathogen interactions. Specifically, bacterial fermentation of dietary fiber produces metabolites called short-chain fatty acids (SCFAs), which have been shown to protect against various inflammatory diseases. However, the effect of fiber deficiency on the key initial steps of inflammation, such as leukocyte-endothelial cell interactions, is unknown. Moreover, the impact of fiber deficiency on neutrophil recruitment under basal conditions and during inflammation in vivo is unknown. Herein, we hypothesized that a fiber-deficient diet promotes an inflammatory state in the colon at baseline and predisposes the host to more severe colitis pathology. Mice fed a no-fiber diet for 14 days showed significant changes in the gut microbiota and exhibited increased neutrophil-endothelial interactions in the colonic microvasculature. Although mice fed a no-fiber diet alone did not have observable colitis-associated symptoms, these animals were highly susceptible to low dose (0.5%) dextran sodium sulphate (DSS)-induced model of colitis. Supplementation of the most abundant SCFA, acetate, prevented no-fiber diet-mediated enrichment of colonic neutrophils and colitis pathology. Therefore, dietary fiber, possibly through the actions of acetate, plays an important role in regulating neutrophil recruitment and host protection against inflammatory colonic damage in an experimental model of colitis.}, } @article {pmid33708192, year = {2020}, author = {Sun, Y and He, Z and Li, J and Gong, S and Yuan, S and Li, T and Ning, N and Xing, L and Zhang, L and Chen, F and Li, Z and Wang, J and Luo, D and Wang, H}, title = {Gentamicin Induced Microbiome Adaptations Associate With Increased BCAA Levels and Enhance Severity of Influenza Infection.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {608895}, pmid = {33708192}, issn = {1664-3224}, mesh = {Adaptation, Biological/*drug effects/physiology ; Amino Acids, Branched-Chain/*metabolism ; Animals ; CD11b Antigen/metabolism ; CD8-Positive T-Lymphocytes/drug effects/metabolism ; Cell Differentiation/drug effects ; Chickens ; Cytokines/metabolism ; Dendritic Cells/drug effects/metabolism ; Gastrointestinal Microbiome/*drug effects/physiology ; Gentamicins/*pharmacology ; Humans ; Inflammation/metabolism ; Mice ; Mice, Inbred BALB C ; Microbiota/drug effects ; Orthomyxoviridae/pathogenicity ; Orthomyxoviridae Infections/*metabolism ; }, abstract = {Involvement of gut microbiota in pulmonary disease by the gut-lung axis has been widely observed. However, the cross-talk messengers between respiratory mucosal immunity and gut microbiota are largely unknown. Using selective pharmacologic destruction of gut microenvironment mouse models, we found gut microbiota displayed significantly lower alpha diversity and relative abundance of bacteria in Gentamicin treated mice. Metagenomic studies revealed functional differences in gut bacteria in altering metabolic profiles in mice blood. Branched-chain amino acids (BCAAs) are the essential factors linked between gut and lung. During this process, selective destruction of gut microbiota by Gentamicin induced high levels of BCAAs, and the high levels of BCAAs impacted the lung immunity against influenza virus. In vivo, Gentamicin-treated mice or mice fed with high BCAAs diets displayed reduced survival. At the sites of infection, the number of CD11b[+]Ly6G[+] cells decreased, and CD8[+] T cells increased accompanied by exuberant expression of pro-inflammatory cytokines could result in tissue damage. CD11b[+]Ly6G[+] cells transplantation conferred remarkable protection from influenza virus infections. In vitro, BCAAs promoted bone marrow-derived cells differentiation to dendritic cells. Taken together, these findings demonstrate that Gentamicin induced disruption of the gut microbiota leads to increased BCAA levels that suppress CD11b[+]Ly6c[+] cell development in association with overactive CD8[+] T responses which may contribute to enhanced severity of the viral infection.}, } @article {pmid33707503, year = {2021}, author = {Andersen, D and Roager, HM and Zhang, L and Moll, JM and Frandsen, HL and Danneskiold-Samsøe, NB and Hansen, AK and Kristiansen, K and Licht, TR and Brix, S}, title = {Systems-wide effects of short-term feed deprivation in obese mice.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {5716}, pmid = {33707503}, issn = {2045-2322}, mesh = {Animals ; Bacteria/metabolism ; Butyric Acid/metabolism ; Cecum/metabolism ; Fermentation ; Gastrointestinal Microbiome ; Intra-Abdominal Fat/metabolism ; Male ; Mice, Inbred C57BL ; Mice, Obese ; Multivariate Analysis ; Starvation/*pathology ; *Systems Biology ; Time Factors ; Uncoupling Protein 1/metabolism ; Mice ; }, abstract = {While prolonged fasting induces significant metabolic changes in humans and mice, less is known about systems-wide metabolic changes in response to short-term feed deprivation, which is used in experimental animal studies prior to metabolic challenge tests. We here performed a systems biology-based investigation of connections between gut bacterial composition and function, inflammatory and metabolic parameters in the intestine, liver, visceral adipose tissue, blood and urine in high-fat fed, obese mice that were feed deprived up to 12 h. The systems-wide analysis revealed that feed deprivation linked to enhanced intestinal butyric acid production and expression of the gene encoding the pro-thermogenic uncoupling protein UCP1 in visceral adipose tissue of obese mice. Ucp1 expression was also positively associated with Il33 expression in ileum, colon and adipose tissue as well as with the abundance of colonic Porphyromonadaceae, the latter also correlating to cecal butyric acid levels. Collectively, the data highlighted presence of a multi-tiered system of inter-tissue communication involving intestinal, immune and metabolic functions which is affected by feed deprivation in obese mice, thus pointing to careful use of short-feed deprivation in metabolic studies using obese mice.}, } @article {pmid33706240, year = {2021}, author = {DeBofsky, A and Xie, Y and Challis, JK and Jain, N and Brinkmann, M and Jones, PD and Giesy, JP}, title = {Responses of juvenile fathead minnow (Pimephales promelas) gut microbiome to a chronic dietary exposure of benzo[a]pyrene.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {278}, number = {}, pages = {116821}, doi = {10.1016/j.envpol.2021.116821}, pmid = {33706240}, issn = {1873-6424}, mesh = {Animals ; Benzo(a)pyrene/toxicity ; *Cyprinidae ; Dietary Exposure ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; *Water Pollutants, Chemical/toxicity ; }, abstract = {The microbiome has been described as an additional host "organ" with well-established beneficial roles. However, the effects of exposures to chemicals on both structure and function of the gut microbiome of fishes are understudied. To determine effects of benzo[a]pyrene (BaP), a model persistent organic pollutant, on structural shifts of gut microbiome in juvenile fathead minnows (Pimephales promelas), fish were exposed ad libitum in the diet to concentrations of 1, 10, 100, or 1000 μg BaP g[-1] food, in addition to a vehicle control, for two weeks. To determine the link between exposure to BaP and changes in the microbial community, concentrations of metabolites of BaP were measured in fish bile and 16S rRNA amplicon sequencing was used to evaluate the microbiome. Exposure to BaP only reduced alpha-diversity at the greatest exposure concentrations. However, it did alter community composition assessed as differential abundance of taxa and reduced network complexity of the microbial community in all exposure groups. Results presented here illustrate that environmentally-relevant concentrations of BaP can alter the diversity of the gut microbiome and community network connectivity.}, } @article {pmid33705534, year = {2021}, author = {Lim, SJ and Davis, B and Gill, D and Swetenburg, J and Anderson, LC and Engel, AS and Campbell, BJ}, title = {Gill microbiome structure and function in the chemosymbiotic coastal lucinid Stewartia floridana.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {4}, pages = {}, doi = {10.1093/femsec/fiab042}, pmid = {33705534}, issn = {1574-6941}, mesh = {Animals ; Bacteria ; *Bivalvia ; Gills ; *Microbiota ; Phylogeny ; Symbiosis ; }, abstract = {Lucinid bivalves harbor environmentally acquired, chemosynthetic, gammaproteobacterial gill endosymbionts. Lucinid gill microbiomes, which may contain other gammaproteobacterial and/or spirochete taxa, remain under-sampled. To understand inter-host variability of the lucinid gill microbiome, specifically in the bacterial communities, we analyzed the microbiome content of Stewartia floridana collected from Florida. Sampled gills contained a monospecific gammaproteobacterial endosymbiont expressing lithoautotrophic, mixotrophic, diazotrophic and C1 compound oxidation-related functions previously characterized in similar lucinid species. Another low-abundance Spirochaeta-like species in ∼72% of the sampled gills was most closely related to Spirochaeta-like species in another lucinid Phacoides pectinatus and formed a clade with known marine Spirochaeta symbionts. The spirochete expressed genes were involved in heterotrophy and the transport of sugars, amino acids, peptides and other substrates. Few muscular and neurofilament genes from the host and none from the gammaproteobacterial and spirochete symbionts were differentially expressed among quadrats predominantly covered with seagrass species or 80% bare sand. Our results suggest that spirochetes are facultatively associated with S. floridana, with potential scavenging and nutrient cycling roles. Expressed stress- and defense-related functions in the host and symbionts also suggest species-species communications, which highlight the need for further study of the interactions among lucinid hosts, their microbiomes and their environment.}, } @article {pmid33704463, year = {2021}, author = {Arruda, A and Ferreira, GEM and Santos Júnior, A and Matos, NB and Carvalho, TS and Ozaki, LS and Stabeli, RG and Silva, AAE}, title = {Diversity of Culturable Bacteria Isolated From the Feces of Wild Anopheles darlingi (Diptera: Culicidae) Mosquitoes From the Brazilian Amazon.}, journal = {Journal of medical entomology}, volume = {58}, number = {4}, pages = {1900-1907}, doi = {10.1093/jme/tjab028}, pmid = {33704463}, issn = {1938-2928}, mesh = {Animals ; Anopheles/*microbiology ; *Bacteria/classification/genetics/isolation & purification ; Biological Control Agents ; Brazil ; Feces/microbiology ; Genes, Bacterial ; Malaria/prevention & control ; Metagenomics ; Microbiota/genetics ; Mosquito Control ; Mosquito Vectors/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Serratia/isolation & purification ; }, abstract = {Microorganisms living in the midgut of Anopheles mosquitoes have been studied to fight vector-borne diseases, such as malaria. Studies on the microbiota of the Neotropical Anopheles darlingi, the most important Brazilian vector for malaria, have been reported for the same purpose. Our aims were to isolate and identify culturable bacteria from An. darlingi mosquito guts through their feces and to estimate the species richness and the frequency distribution of the sampled bacteria. Sixty wild females of An. darlingi mosquitoes were captured at two rural locations, near Porto Velho, Rondônia, Brazil. Bacteria were isolated from mosquito feces, which were collected using cages which permit the collection of feces on LB nutrient agar plates. Sixty bacterial colonies were isolated and stored in glycerol at -80°C. Bacteria were identified by sequencing their 16S rRNA gene obtained using PCR and Sanger sequencing. To aid in species identification, MALDI-TOF, VITEK2, and BBL Crystal were used as complementary protocols. The sequences obtained from the 60 bacterial isolates were compared to sequences deposited in GenBank (NCBI) using BLAST. Homology greater than 97% between the query and the subject was used as the criteria for assigning the identity of each isolate. Fourteen species from eight different genera were identified among the 60 isolates. The most frequent species were Serratia liquefaciens (20%) and Serratia marcescens (15%). Due to their established apathogenicity and according to previous studies, we suggest Serratia and Pantoea species as suitable for paratransgenesis development to fight malaria in Brazilian Amazon.}, } @article {pmid33692426, year = {2021}, author = {Yadav, M and Lomash, A and Kapoor, S and Pandey, R and Chauhan, NS}, title = {Mapping of the benzoate metabolism by human gut microbiome indicates food-derived metagenome evolution.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {5561}, pmid = {33692426}, issn = {2045-2322}, mesh = {Adult ; *Bacteria/classification/genetics/metabolism ; Benzoates/*metabolism ; *Food ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; *Metagenome ; *Phylogeny ; }, abstract = {Sodium benzoate is one of the widely used food preservatives and its metabolism in the human body has been studied only with the host perspective. Despite the human gut microbiome being considered as a virtual human organ, its role in benzoate metabolism is yet to be elucidated. The current study uses a multi-omic approach to rationalize the role of human gut microbes in benzoate metabolism. Microbial diversity analysis with multiple features synchronously indicates the dominance of Bacteroidetes followed by Firmicutes, Actinobacteria, and Proteobacteria. Metagenomic exploration highlights the presence of benzoate catabolic protein features. These features were mapped on to the aerobic and anaerobic pathways of benzoate catabolism. Benzoate catabolism assays identified statistically significant metabolites (P < 0.05) associated with the protocatechuate branch of the beta-ketoadipate pathway of the benzoate metabolism. Analysis of the 201 human gut metagenomic datasets across diverse populations indicates the omnipresence of these features. Enrichment of the benzoate catabolic protein features in human gut microbes rationalizes their role in benzoate catabolism, as well as indicates food-derived microbiome evolution.}, } @article {pmid33691770, year = {2021}, author = {Zimmermann, J and Kaleta, C and Waschina, S}, title = {gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {81}, pmid = {33691770}, issn = {1474-760X}, mesh = {Bacteria/enzymology/*genetics/*metabolism ; Computational Biology/*methods ; Databases, Factual ; *Energy Metabolism ; Fermentation ; Gastrointestinal Microbiome ; Genome, Bacterial ; Genomics/methods ; Humans ; *Metabolic Networks and Pathways ; Metagenome ; Metagenomics/methods ; *Software ; Soil Microbiology ; }, abstract = {Genome-scale metabolic models of microorganisms are powerful frameworks to predict phenotypes from an organism's genotype. While manual reconstructions are laborious, automated reconstructions often fail to recapitulate known metabolic processes. Here we present gapseq (https://github.com/jotech/gapseq), a new tool to predict metabolic pathways and automatically reconstruct microbial metabolic models using a curated reaction database and a novel gap-filling algorithm. On the basis of scientific literature and experimental data for 14,931 bacterial phenotypes, we demonstrate that gapseq outperforms state-of-the-art tools in predicting enzyme activity, carbon source utilisation, fermentation products, and metabolic interactions within microbial communities.}, } @article {pmid33691464, year = {2022}, author = {Buret, AG and Allain, T and Motta, JP and Wallace, JL}, title = {Effects of Hydrogen Sulfide on the Microbiome: From Toxicity to Therapy.}, journal = {Antioxidants & redox signaling}, volume = {36}, number = {4-6}, pages = {211-219}, pmid = {33691464}, issn = {1557-7716}, support = {//CIHR/Canada ; }, mesh = {*Gastrointestinal Microbiome ; Gastrointestinal Tract ; *Hydrogen Sulfide/pharmacology ; *Microbiota ; Proteomics ; }, abstract = {Significance: Hydrogen sulfide (H2S), an important regulator of physiology and health, helps resolve inflammation and promotes tissue repair in the gastrointestinal tract. Recent Advances: Gut microbiota live as a multispecies biofilm in close interaction with the upper mucus layer lining the epithelium. The relative abundance, spatial organization, and function of these microorganisms affect a broad range of health outcomes. This article provides a state-of-the-art review of our understanding of the cross talk between H2S, the gut microbiota, and health. H2S can have toxic or therapeutic effects, depending on its concentration and source. When produced at excessive concentrations by local microbiota, H2S may cause mucus disruption and inflammation and contribute to development of cancer. In contrast, low levels of endogenous or exogenous H2S directly stabilize mucus layers, prevent fragmentation and adherence of the microbiota biofilm to the epithelium, inhibit the release of invasive pathobionts, and help resolve inflammation and tissue injury. Although scarce, research findings suggest that dietary H2S obtained from plants or ingestion of the H2S precursor, L-cysteine, may also modulate the abundance and function of microbiota. Critical Issues: A critical issue is the lack of understanding of the metagenomic, transcriptomic, and proteomic alterations that characterize the interactions between H2S and gut microbiota to shape health outcomes. Future Directions: The ambivalent roles of H2S in the gut offer a fertile ground for research on such critical issues. The findings will improve our understanding of how H2S modulates the microbiota to affect body function and will help identify novel therapeutic strategies. Antioxid. Redox Signal. 36, 211-219.}, } @article {pmid33690060, year = {2021}, author = {Ma, K and Wang, W and Liu, Y and Bao, L and Cui, Y and Kang, W and Wu, Q and Xin, X}, title = {Insight into the performance and microbial community profiles of magnetite-amended anaerobic digestion: Varying promotion effects at increased loads.}, journal = {Bioresource technology}, volume = {329}, number = {}, pages = {124928}, doi = {10.1016/j.biortech.2021.124928}, pmid = {33690060}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Bioreactors ; Ferrosoferric Oxide ; Methane ; *Microbiota ; }, abstract = {In current study, the enhancement effect of magnetite on anaerobic digestion was evaluated at increased organic loading rate (OLR) from 1.6 to 25.6 kg COD·m[-3]·d[-1]. The supplement of magnetite enhanced the methane yield by 7-483% accompanied with faster VFAs conversion. Microbial analysis suggested the varied enhancing effect achieved at different OLRs was attributed to different syntrophic interactions triggered by magnetite. More specially, an electroactive syntropy was established between Trichococcus with Methanobacterium at OLR lower than 6.4 kg COD·m[-3]·d[-1], while with the OLR increase, more acid fermentative bacteria (Propionimicrobium, Syner-01) were enriched and further enhanced methanogenesis in a syntrophic way with Methanosaeta. Overall, the incorporation of magnetite was a promising approach to achieve efficient anaerobic digestion, OLR was also critical factor affecting the methanogenesis and should be carefully regulated in future application.}, } @article {pmid33689954, year = {2021}, author = {Hitch, TCA and Afrizal, A and Riedel, T and Kioukis, A and Haller, D and Lagkouvardos, I and Overmann, J and Clavel, T}, title = {Recent advances in culture-based gut microbiome research.}, journal = {International journal of medical microbiology : IJMM}, volume = {311}, number = {3}, pages = {151485}, doi = {10.1016/j.ijmm.2021.151485}, pmid = {33689954}, issn = {1618-0607}, mesh = {Bacteria/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; }, abstract = {Gut microbes affect the physiology of their hosts. Studying their diversity and functions is thus of utmost importance as it will open new avenues towards the discovery of new biomolecules and the treatment of diseases. Gut microbiome research is currently boosted by the unification of metagenomics, which has dominated the field in the last two decades, and cultivation, which is experiencing a renaissance. Each of these approaches has advantages and drawbacks that can be overcome if used synergistically. In this brief article, we summarize recent literature and own studies on the cultivation of gut microbes, provide a succinct status quo of cultured fractions and collections of isolates, and give short opinions on challenges and next steps to take.}, } @article {pmid33689953, year = {2021}, author = {Podlesny, D and Fricke, WF}, title = {Strain inheritance and neonatal gut microbiota development: A meta-analysis.}, journal = {International journal of medical microbiology : IJMM}, volume = {311}, number = {3}, pages = {151483}, doi = {10.1016/j.ijmm.2021.151483}, pmid = {33689953}, issn = {1618-0607}, mesh = {Adolescent ; Adult ; Cesarean Section ; Child ; Feces ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Infant, Newborn ; Metagenome ; *Microbiota ; Pregnancy ; }, abstract = {As many inflammatory and metabolic disorders have been associated with structural deficits of the human gut microbiota, the principles and mechanisms that govern its initialization and development are of considerable scientific interest and clinical relevance. However, our current understanding of the developing gut microbiota dynamics remains incomplete. We carried out a large-scale, comprehensive meta-analysis of over 1900 available metagenomic shotgun samples from neonates, infants, adolescents, and their families, using our recently introduced SameStr program for strain-level microbiota profiling and the detection of microbial strain transfer and persistence. We found robust associations between fecal microbiota composition and age, as well as delivery mode, which was measurable for up to two years of life. C-section was associated with increased relative abundances of non-gut species and delayed transition from a predominantly oxygen-tolerant to intolerant microbial community. Unsupervised networks based on shared strain profiles generated family-specific clusters connecting infants, their siblings, parents and grandparents and, in one case, suggested strain transfer between neonates from the same hospital ward, but could also be used to identify potentially mislabeled metagenome samples. Vaginally delivered newborns shared more strains with their mothers than C-section infants, but strain sharing was reduced if mothers underwent antibiotic treatment. Shared strains persisted in infants throughout the first year of life and belonged to the same bacterial species as strains that were shared between adults and their parents. Irrespective of delivery type, older children shared strains with their mothers and fathers and, into adulthood, could be accurately distinguished from unrelated sample pairs. Prominent fecal commensal bacteria were both among frequently transferred (e.g. Bacteroides and Sutterella) and newly acquired taxa (e.g. Blautia, Faecalibacterium, and Ruminococcus). Our meta-analysis presents a more detailed and comprehensive picture of the highly dynamic neonatal and infant fecal microbiota development than previous studies and presents evidence for taxonomic and functional compositional differences early in life between infants born naturally or by C-section, which persist well into adolescence.}, } @article {pmid33689000, year = {2021}, author = {Ericsson, AC and Franklin, CL}, title = {The gut microbiome of laboratory mice: considerations and best practices for translational research.}, journal = {Mammalian genome : official journal of the International Mammalian Genome Society}, volume = {32}, number = {4}, pages = {239-250}, pmid = {33689000}, issn = {1432-1777}, support = {U42 OD010918/OD/NIH HHS/United States ; U42 RR014821/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Disease Models, Animal ; Gastrointestinal Microbiome/*genetics ; Humans ; Mice ; *Translational Research, Biomedical ; }, abstract = {Just as the gut microbiota (GM) is now recognized as an integral mediator of environmental influences on human physiology, susceptibility to disease, and response to pharmacological intervention, so too does the GM of laboratory mice affect the phenotype of research using mouse models. Multiple experimental factors have been shown to affect the composition of the GM in research mice, as well as the model phenotype, suggesting that the GM represents a major component in experimental reproducibility. Moreover, several recent studies suggest that manipulation of the GM of laboratory mice can substantially improve the predictive power or translatability of data generated in mouse models to the human conditions under investigation. This review provides readers with information related to these various factors and practices, and recommendations regarding methods by which issues with poor reproducibility or translatability can be transformed into discoveries.}, } @article {pmid33688048, year = {2021}, author = {Ewens, SD and Gomberg, AFS and Barnum, TP and Borton, MA and Carlson, HK and Wrighton, KC and Coates, JD}, title = {The diversity and evolution of microbial dissimilatory phosphite oxidation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {11}, pages = {}, pmid = {33688048}, issn = {1091-6490}, mesh = {Anaerobiosis ; Bacteria/classification/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; *Biodiversity ; Carbon Dioxide/metabolism ; Chemoautotrophic Growth ; Energy Metabolism ; *Evolution, Molecular ; Genetic Variation ; Genome, Bacterial/genetics ; Microbiota ; Oxidation-Reduction ; Phosphites/*metabolism ; Phylogeny ; Wastewater/microbiology ; }, abstract = {Phosphite is the most energetically favorable chemotrophic electron donor known, with a half-cell potential (E[o]') of -650 mV for the PO4[3-]/PO3[3-] couple. Since the discovery of microbial dissimilatory phosphite oxidation (DPO) in 2000, the environmental distribution, evolution, and diversity of DPO microorganisms (DPOMs) have remained enigmatic, as only two species have been identified. Here, metagenomic sequencing of phosphite-enriched microbial communities enabled the genome reconstruction and metabolic characterization of 21 additional DPOMs. These DPOMs spanned six classes of bacteria, including the Negativicutes, Desulfotomaculia, Synergistia, Syntrophia, Desulfobacteria, and Desulfomonilia_A Comparing the DPO genes from the genomes of enriched organisms with over 17,000 publicly available metagenomes revealed the global existence of this metabolism in diverse anoxic environments, including wastewaters, sediments, and subsurface aquifers. Despite their newfound environmental and taxonomic diversity, metagenomic analyses suggested that the typical DPOM is a chemolithoautotroph that occupies low-oxygen environments and specializes in phosphite oxidation coupled to CO2 reduction. Phylogenetic analyses indicated that the DPO genes form a highly conserved cluster that likely has ancient origins predating the split of monoderm and diderm bacteria. By coupling microbial cultivation strategies with metagenomics, these studies highlighted the unsampled metabolic versatility latent in microbial communities. We have uncovered the unexpected prevalence, diversity, biochemical specialization, and ancient origins of a unique metabolism central to the redox cycling of phosphorus, a primary nutrient on Earth.}, } @article {pmid33688007, year = {2021}, author = {Huang, S and He, T and Yue, F and Xu, X and Wang, L and Zhu, P and Teng, F and Sun, Z and Liu, X and Jing, G and Su, X and Jin, L and Liu, J and Xu, J}, title = {Longitudinal Multi-omics and Microbiome Meta-analysis Identify an Asymptomatic Gingival State That Links Gingivitis, Periodontitis, and Aging.}, journal = {mBio}, volume = {12}, number = {2}, pages = {}, pmid = {33688007}, issn = {2150-7511}, mesh = {*Aging ; Cohort Studies ; Cytokines/*analysis/immunology ; Dysbiosis ; Genomics ; Gingiva/*microbiology/pathology ; Gingivitis/*microbiology ; Humans ; Longitudinal Studies ; Metabolomics ; *Metagenome ; *Microbiota ; Periodontitis/*microbiology ; Proteomics ; Saliva/immunology ; }, abstract = {Most adults experience episodes of gingivitis, which can progress to the irreversible, chronic state of periodontitis, yet roles of plaque in gingivitis onset and progression to periodontitis remain elusive. Here, we longitudinally profiled the plaque metagenome, the plaque metabolome, and salivary cytokines in 40 adults who transited from naturally occurring gingivitis (NG) to healthy gingivae (baseline) and then to experimental gingivitis (EG). During EG, rapid and consistent alterations in plaque microbiota, metabolites, and salivary cytokines emerged as early as 24 to 72 h after oral-hygiene pause, defining an asymptomatic suboptimal health (SoH) stage of the gingivae. SoH features a swift, full activation of 11 salivary cytokines but a steep synergetic decrease of plaque-derived betaine and Rothia spp., suggesting an anti-gum inflammation mechanism by health-promoting symbionts. Global, cross-cohort meta-analysis revealed, at SoH, a greatly elevated microbiome-based periodontitis index driven by its convergence of both taxonomical and functional profiles toward the periodontitis microbiome. Finally, post-SoH gingivitis development accelerates oral microbiota aging by over 1 year within 28 days, with Rothia spp. depletion and Porphyromonas gingivalis elevation as hallmarks. Thus, the microbiome-defined, transient gum SoH stage is a crucial link among gingivitis, periodontitis, and aging.IMPORTANCE A significant portion of world population still fails to brush teeth daily. As a result, the majority of the global adult population is afflicted with chronic gingivitis, and if it is left untreated, some of them will eventually suffer from periodontitis. Here, we identified periodontitis-like microbiome dysbiosis in an asymptomatic SoH stage as early as 24 to 72 h after oral-hygiene pause. SoH features a swift, full activation of multiple salivary cytokines but a steep synergetic decrease of plaque-derived betaine and Rothia spp. The microbial ecology during early gingivitis is highly similar to that in periodontitis under both taxonomical and functional contexts. Unexpectedly, exposures to gingivitis can accelerate over 10-fold the normal rate of oral microbiota aging. Our findings underscore the importance of intervening at the SoH stage of gingivitis via proper oral-hygiene practices on a daily basis, so as to maintain a periodontitis-preventive plaque and ensure the healthy aging of the oral ecosystem.}, } @article {pmid33688005, year = {2021}, author = {Dmitrijeva, M and Kahlert, CR and Feigelman, R and Kleiner, RL and Nolte, O and Albrich, WC and Baty, F and von Mering, C}, title = {Strain-Resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis.}, journal = {mBio}, volume = {12}, number = {2}, pages = {}, pmid = {33688005}, issn = {2150-7511}, mesh = {Bacteria/*classification/*genetics/metabolism ; Cystic Fibrosis/*microbiology ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Longitudinal Studies ; Lung/*microbiology ; Metagenomics ; *Microbiota ; Respiratory Tract Infections ; Sputum/microbiology ; }, abstract = {In cystic fibrosis, dynamic and complex communities of microbial pathogens and commensals can colonize the lung. Cultured isolates from lung sputum reveal high inter- and intraindividual variability in pathogen strains, sequence variants, and phenotypes; disease progression likely depends on the precise combination of infecting lineages. Routine clinical protocols, however, provide a limited overview of the colonizer populations. Therefore, a more comprehensive and precise identification and characterization of infecting lineages could assist in making corresponding decisions on treatment. Here, we describe longitudinal tracking for four cystic fibrosis patients who exhibited extreme clinical phenotypes and, thus, were selected from a pilot cohort of 11 patients with repeated sampling for more than a year. Following metagenomics sequencing of lung sputum, we find that the taxonomic identity of individual colonizer lineages can be easily established. Crucially, even superficially clonal pathogens can be subdivided into multiple sublineages at the sequence level. By tracking individual allelic differences over time, an assembly-free clustering approach allows us to reconstruct multiple lineage-specific genomes with clear structural differences. Our study showcases a culture-independent shotgun metagenomics approach for longitudinal tracking of sublineage pathogen dynamics, opening up the possibility of using such methods to assist in monitoring disease progression through providing high-resolution routine characterization of the cystic fibrosis lung microbiome.IMPORTANCE Cystic fibrosis patients frequently suffer from recurring respiratory infections caused by colonizing pathogenic and commensal bacteria. Although modern therapies can sometimes alleviate respiratory symptoms by ameliorating residual function of the protein responsible for the disorder, management of chronic respiratory infections remains an issue. Here, we propose a minimally invasive and culture-independent method to monitor microbial lung content in patients with cystic fibrosis at minimal additional effort on the patient's part. Through repeated sampling and metagenomics sequencing of our selected cystic fibrosis patients, we successfully classify infecting bacterial lineages and deconvolute multiple lineage variants of the same species within a given patient. This study explores the application of modern computational methods for deconvoluting lineages in the cystic fibrosis lung microbiome, an environment known to be inhabited by a heterogeneous pathogen population that complicates management of the disorder.}, } @article {pmid33686248, year = {2021}, author = {Konishi, T and Kusakabe, S and Hino, A and Inamoto, K and Yoshifuji, K and Kiridoshi, Y and Takeshita, K and Sasajima, S and Toya, T and Igarashi, A and Najima, Y and Kobayashi, T and Doki, N and Motooka, D and Nakamura, S and Suyama, M and Suda, W and Shiota, A and Atarashi, K and Hattori, M and Honda, K and Yokota, T and Ohashi, K and Shibayama, H and Fukushima, K and Kakihana, K}, title = {Low diversity of gut microbiota in the early phase of post-bone marrow transplantation increases the risk of chronic graft-versus-host disease.}, journal = {Bone marrow transplantation}, volume = {56}, number = {7}, pages = {1728-1731}, pmid = {33686248}, issn = {1476-5365}, support = {JP19ek0510021//Japan Agency for Medical Research and Development (AMED)/ ; JP20gm0010003//Japan Agency for Medical Research and Development (AMED)/ ; }, mesh = {Bone Marrow Transplantation/adverse effects ; *Gastrointestinal Microbiome ; *Graft vs Host Disease/etiology ; *Hematopoietic Stem Cell Transplantation ; Humans ; *Microbiota ; }, } @article {pmid33686191, year = {2021}, author = {Holmfeldt, K and Nilsson, E and Simone, D and Lopez-Fernandez, M and Wu, X and de Bruijn, I and Lundin, D and Andersson, AF and Bertilsson, S and Dopson, M}, title = {The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {307}, pmid = {33686191}, issn = {2399-3642}, mesh = {Firmicutes/growth & development/virology ; Groundwater/microbiology/*virology ; Host-Pathogen Interactions ; Metagenomics ; Population Density ; Time Factors ; *Virome ; *Virus Replication ; Viruses/genetics/*growth & development/metabolism ; Water Microbiology ; }, abstract = {The deep biosphere contains members from all three domains of life along with viruses. Here we investigate the deep terrestrial virosphere by sequencing community nucleic acids from three groundwaters of contrasting chemistries, origins, and ages. These viromes constitute a highly unique community compared to other environmental viromes and sequenced viral isolates. Viral host prediction suggests that many of the viruses are associated with Firmicutes and Patescibacteria, a superphylum lacking previously described active viruses. RNA transcript-based activity implies viral predation in the shallower marine water-fed groundwater, while the deeper and more oligotrophic waters appear to be in 'metabolic standby'. Viral encoded antibiotic production and resistance systems suggest competition and antagonistic interactions. The data demonstrate a viral community with a wide range of predicted hosts that mediates nutrient recycling to support a higher microbial turnover than previously anticipated. This suggests the presence of 'kill-the-winner' oscillations creating slow motion 'boom and burst' cycles.}, } @article {pmid33685682, year = {2021}, author = {Choi, Y and Park, E and Kim, S and Ha, J and Oh, H and Kim, Y and Lee, Y and Seo, Y and Kang, J and Lee, S and Lee, H and Yoon, Y and Choi, KH}, title = {Fermented milk with Lactobacillus curvatus SMFM2016-NK alleviates periodontal and gut inflammation, and alters oral and gut microbiota.}, journal = {Journal of dairy science}, volume = {104}, number = {5}, pages = {5197-5207}, doi = {10.3168/jds.2020-19625}, pmid = {33685682}, issn = {1525-3198}, mesh = {Animals ; *Gastrointestinal Microbiome ; Inflammation/veterinary ; Lactobacillus ; Milk ; *Probiotics ; Rats ; }, abstract = {This study aimed to analyze the effect of milk fermented with Lactobacillus curvatus SMFM2016-NK on periodontal diseases and gut health in a rat model. To improve the effect of Lb. curvatus SMFM2016-NK-fermented milk administration for relieving periodontitis, the periodontitis rat models were treated with the following for 4 wk: 10% skim milk (normal), periodontitis + 10% skim milk (negative control), periodontitis + Lactobacillus rhamnosus GG-fermented milk (positive control), and periodontitis + Lb. curvatus SMFM2016-NK-fermented milk (PD+LCFM). Transcriptional analysis of inflammatory cytokines [tumor necrosis factor α (TNF-α), IL-1β, IL-6, and IL-10] was performed via quantitative reverse-transcription PCR. The changes in the oral and gut microbiomes after administering Lb. curvatus SMFM2016-NK-fermented milk were analyzed with metagenomics sequencing using DNA extracted from the oral gingival tissues and feces from the cecum of the rat models. After treatment with Lb. curvatus SMFM2016-NK-fermented milk, the relative gene expression levels of TNFA and IL1B in the gingiva decreased in the PD+LCFM group compared with those in the negative control group. In the oral microbiome, the proportion of the phylum Proteobacteria in the PD+LCFM group was lower than that in the negative control after treatment with Lb. curvatus SMFM2016-NK-fermented milk. For the effect in the gut, the relative gene expression levels of inflammatory cytokines in the colon between the normal and negative control groups were not different; however, the expression levels of TNFA and IL1B in the PD+LCFM and positive control groups, respectively, were lower than those in the negative control group. The composition and diversity of the gut microbiome differed among normal, periodontitis, and Lb. curvatus SMFM2016-NK-fermented milk treatment groups. These results indicate that Lb. curvatus SMFM2016-NK-fermented milk could alleviate periodontal and gut inflammation and change oral and gut microbiota.}, } @article {pmid33683127, year = {2021}, author = {Mehta, S and Kumar, P and Crane, M and Johnson, JE and Sajulga, R and Nguyen, DDA and McGowan, T and Arntzen, MØ and Griffin, TJ and Jagtap, PD}, title = {Updates on metaQuantome Software for Quantitative Metaproteomics.}, journal = {Journal of proteome research}, volume = {20}, number = {4}, pages = {2130-2137}, doi = {10.1021/acs.jproteome.0c00960}, pmid = {33683127}, issn = {1535-3907}, support = {U24 CA199347/CA/NCI NIH HHS/United States ; }, mesh = {Mass Spectrometry ; Metagenomics ; *Microbiota ; *Proteomics ; Software ; }, abstract = {metaQuantome is a software suite that enables the quantitative analysis, statistical evaluation. and visualization of mass-spectrometry-based metaproteomics data. In the latest update of this software, we have provided several extensions, including a step-by-step training guide, the ability to perform statistical analysis on samples from multiple conditions, and a comparative analysis of metatranscriptomics data. The training module, accessed via the Galaxy Training Network, will help users to use the suite effectively both for functional as well as for taxonomic analysis. We extend the ability of metaQuantome to now perform multi-data-point quantitative and statistical analyses so that studies with measurements across multiple conditions, such as time-course studies, can be analyzed. With an eye on the multiomics analysis of microbial communities, we have also initiated the use of metaQuantome statistical and visualization tools on outputs from metatranscriptomics data, which complements the metagenomic and metaproteomic analyses already available. For this, we have developed a tool named MT2MQ ("metatranscriptomics to metaQuantome"), which takes in outputs from the ASaiM metatranscriptomics workflow and transforms them so that the data can be used as an input for comparative statistical analysis and visualization via metaQuantome. We believe that these improvements to metaQuantome will facilitate the use of the software for quantitative metaproteomics and metatranscriptomics and will enable multipoint data analysis. These improvements will take us a step toward integrative multiomic microbiome analysis so as to understand dynamic taxonomic and functional responses of these complex systems in a variety of biological contexts. The updated metaQuantome and MT2MQ are open-source software and are available via the Galaxy Toolshed and GitHub.}, } @article {pmid33681975, year = {2021}, author = {Keller, AG and Apprill, A and Lebaron, P and Robbins, J and Romano, TA and Overton, E and Rong, Y and Yuan, R and Pollara, S and Whalen, KE}, title = {Characterizing the culturable surface microbiomes of diverse marine animals.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {4}, pages = {}, pmid = {33681975}, issn = {1574-6941}, support = {R21 AI119311/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Anthozoa ; Bacteria/genetics ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Biofilm-forming bacteria have the potential to contribute to the health, physiology, behavior and ecology of the host and serve as its first line of defense against adverse conditions in the environment. While metabarcoding and metagenomic information furthers our understanding of microbiome composition, fewer studies use cultured samples to study the diverse interactions among the host and its microbiome, as cultured representatives are often lacking. This study examines the surface microbiomes cultured from three shallow-water coral species and two whale species. These unique marine animals place strong selective pressures on their microbial symbionts and contain members under similar environmental and anthropogenic stress. We developed an intense cultivation procedure, utilizing a suite of culture conditions targeting a rich assortment of biofilm-forming microorganisms. We identified 592 microbial isolates contained within 15 bacterial orders representing 50 bacterial genera, and two fungal species. Culturable bacteria from coral and whale samples paralleled taxonomic groups identified in culture-independent surveys, including 29% of all bacterial genera identified in the Megaptera novaeangliae skin microbiome through culture-independent methods. This microbial repository provides raw material and biological input for more nuanced studies which can explore how members of the microbiome both shape their micro-niche and impact host fitness.}, } @article {pmid33680988, year = {2021}, author = {Wang, L and Yu, X and Xu, X and Ming, J and Wang, Z and Gao, B and Xing, Y and Zhou, J and Fu, J and Liu, T and Liu, X and Garstka, MA and Wang, X and Ji, Q}, title = {The Fecal Microbiota Is Already Altered in Normoglycemic Individuals Who Go on to Have Type 2 Diabetes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {598672}, pmid = {33680988}, issn = {2235-2988}, mesh = {Case-Control Studies ; Clostridiales ; *Diabetes Mellitus, Type 2 ; Humans ; *Microbiota ; Porphyromonas ; Veillonella ; }, abstract = {OBJECTIVE: Mounting evidence has suggested a link between gut microbiome characteristics and type 2 diabetes (T2D). To determine whether these alterations occur before the impairment of glucose regulation, we characterize gut microbiota in normoglycemic individuals who go on to develop T2D.

METHODS: We designed a nested case-control study, and enrolled individuals with a similar living environment. A total of 341 normoglycemic individuals were followed for 4 years, including 30 who developed T2D, 33 who developed prediabetes, and their matched controls. Fecal samples (developed T2D, developed prediabetes and controls: n=30, 33, and 63, respectively) collected at baseline underwent metagenomics sequencing.

RESULTS: Compared with matched controls, individuals who went on to develop T2D had lower abundances of Bifidobacterium longum, Coprobacillus unclassified, and Veillonella dispar and higher abundances of Roseburia hominis, Porphyromonas bennonis, and Paraprevotella unclassified. The abundance of Bifidobacterium longum was negatively correlated with follow-up blood glucose levels. Moreover, the microbial Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of carbohydrate metabolism, methane metabolism, amino acid metabolism, fatty acid metabolism, and membrane transport were changed between the two groups.

CONCLUSIONS: We found that fecal microbiota of healthy individuals who go on to develop T2D had already changed when they still were normoglycemic. These alterations of fecal microbiota might provide insights into the development of T2D and a new perspective for identifying individuals at risk of developing T2D.}, } @article {pmid33676982, year = {2021}, author = {Xiao, Y and Li, J and Wu, P and Ning, N and Li, J and Shen, Y and Huang, Q and Ni, J}, title = {An alkaline thermostable laccase from termite gut associated strain of Bacillus stratosphericus.}, journal = {International journal of biological macromolecules}, volume = {179}, number = {}, pages = {270-278}, doi = {10.1016/j.ijbiomac.2021.02.205}, pmid = {33676982}, issn = {1879-0003}, mesh = {Animals ; Bacillus/*enzymology ; Enzyme Stability ; *Gastrointestinal Microbiome ; Hydrogen-Ion Concentration ; Isoptera/*microbiology ; Kinetics ; Laccase/*chemistry ; Lignin/*metabolism ; Recombinant Proteins/chemistry ; Temperature ; }, abstract = {Laccase, an important oxidoreductase, is widely distributed in various organisms. Termites are known to decompose lignocellulose efficiently with the aid of gut microorganisms. However, few laccases have been characterized from termite or its gut microbes. We aimed to screen the strain capable of degrading lignocellulose from fungus-growing termites. In this study, Bacillus stratosphericus BCMC2 with lignocellulolytic activity was firstly isolated from the hindgut of fungus-growing termite Macrotermes barneyi. The laccase gene (BaCotA) was cloned both from the BCMC2 strain and termite intestinal metagenomic DNA. BaCotA was overexpressed in E. coli, and the recombinant BaCotA showed high specific activity (554.1 U/mg). BaCotA was thermostable with an optimum temperature of 70 °C, pH 5.0. Furthermore, BaCotA was resistant to alkali and organic solvents. The enzyme remained more than 70% residual activity at pH 8.0 for 120 min; and the organic solvents such as methanol, ethanol and acetone (10%) had no inhibitory effect on laccase activity. Additionally, BaCotA exhibited efficient decolorization ability towards indigo and crystal violet. The multiple enzymatic properties suggested the presented laccase as a potential candidate for industrial applications. Moreover, this study highlighted that termite intestine is a good resource for either new strains or enzymes.}, } @article {pmid33676490, year = {2021}, author = {Liu, Y and Liu, B and Liu, C and Hu, Y and Liu, C and Li, X and Li, X and Zhang, X and Irwin, DM and Wu, Z and Chen, Z and Jin, Q and Zhang, S}, title = {Differences in the gut microbiomes of dogs and wolves: roles of antibiotics and starch.}, journal = {BMC veterinary research}, volume = {17}, number = {1}, pages = {112}, pmid = {33676490}, issn = {1746-6148}, support = {2016YFD0500300//Ministry of Science and Technology of the People's Republic of China/ ; }, mesh = {Amylases/genetics ; Animals ; Anti-Bacterial Agents ; Bacteria/*classification/drug effects ; China ; Diet/veterinary ; Dogs/*microbiology ; Drug Resistance, Bacterial/genetics ; Gastrointestinal Microbiome/*drug effects ; RNA, Ribosomal, 16S/genetics ; Starch ; Wolves/*microbiology ; }, abstract = {BACKGROUND: Dogs are domesticated wolves. Change of living environment, such as diet and veterinary care may affect the gut bacterial flora of dogs. The aim of this study was to assess the gut bacterial diversity and function in dogs compared with captive wolves. We surveyed the gut bacterial diversity of 27 domestic dogs, which were fed commercial dog food, and 31 wolves, which were fed uncooked meat, by 16S rRNA sequencing. In addition, we collected fecal samples from 5 dogs and 5 wolves for shotgun metagenomic sequencing to explore changes in the functions of their gut microbiome.

RESULTS: Differences in the abundance of core bacterial genera were observed between dogs and wolves. Together with shotgun metagenomics, the gut microbiome of dogs was found to be enriched in bacteria resistant to clinical drugs (P < 0.001), while wolves were enriched in bacteria resistant to antibiotics used in livestock (P < 0.001). In addition, a higher abundance of putative α-amylase genes (P < 0.05; P < 0.01) was observed in the dog samples.

CONCLUSIONS: Living environment of dogs and domestic wolves has led to increased numbers of bacteria with antibiotic resistance genes, with exposure to antibiotics through direct and indirect methods. In addition, the living environment of dogs has allowed the adaptation of their microbiota to a starch-rich diet. These observations align with a domestic lifestyle for domestic dogs and captive wolves, which might have consequences for public health.}, } @article {pmid33676244, year = {2021}, author = {Du, B and Wang, Q and Yang, Q and Wang, R and Yuan, W and Yan, L}, title = {Responses of bacterial and bacteriophage communities to long-term exposure to antimicrobial agents in wastewater treatment systems.}, journal = {Journal of hazardous materials}, volume = {414}, number = {}, pages = {125486}, doi = {10.1016/j.jhazmat.2021.125486}, pmid = {33676244}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents ; *Anti-Infective Agents ; Bacteria/genetics ; *Bacteriophages/genetics ; Humans ; *Microbiota ; *Water Purification ; }, abstract = {The occurrence of antibacterial agents has received increasing concern due to their possible threats to human health. However, the effects of antibacterial residues on the evolution and dynamics between bacteria and bacteriophages in wastewater treatment systems have seldom been researched. Especially for phages, little is known about their response to antimicrobial exposure. In this study, two identical anoxic-aerobic wastewater treatment systems were established to evaluate the responses of bacterial and phage communities to long-term exposure to antimicrobial agents. The results indicated simultaneous exposure to combined antimicrobials significantly inhibited (p < 0.05) the abundance of phages and bacteria. Metagenomic sequencing analysis indicated the community of bacteria and phages changed greatly at the genus level due to combined antibacterial exposure. Additionally, long-term exposure to antimicrobial agents promoted the attachment of receptor-binding protein genes to Klebsiella, Escherichia and Salmonella (which were all members of Enterobacteriaceae). Compared to that in the control system, the numbers of receptor-binding protein genes on their possible phages (such as Lambdalikevirus and P2likevirus) were also obviously higher when the microorganisms were exposed to antimicrobials. The results are helpful to understanding the microbial communities and tracking the relationship of phage-bacterial host systems, especially under the pressure of antimicrobial exposure.}, } @article {pmid33675403, year = {2021}, author = {Arumugam, M and Sundararaju, S and Jagadesan, S and Gunasekaran, P and Rajendhran, J}, title = {Metagenomic Analysis of Microbial Community Affiliated with Termitarium Reveals High Lignocellulolytic Potential.}, journal = {Current microbiology}, volume = {78}, number = {4}, pages = {1551-1565}, pmid = {33675403}, issn = {1432-0991}, support = {No.012/RUSA/MKU/2020-2021//MKU-RUSA/ ; }, mesh = {Bacteria/genetics ; Bacteroidetes/genetics ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; }, abstract = {Termitarium (nest of termites) is a rich source of microbial populations whose resources remain untapped to date. Using the metagenomic sequencing approach, we generated 38 GB sequences comprising 808,386 contigs (896 MB) with a maximum contig size of 470 kb. The taxonomic profile obtained by BLAST against the NCBI NR database and annotation by MEGAN showed that the termitarium microbial community was dominated by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Functional annotation using the CAZY database revealed a huge diversity of glycosyl hydrolase genes from 104 families, some of which appeared to be part of polysaccharide utilization systems (PUL). Strikingly, Actinobacteria was the main contributor of the cellulolytic and hemicellulolytic GHs. Genes involving in lignin degradation were also abundantly identified in this metagenome. Comparative analysis of COG profiles of termitarium with those of other lignocellulolytic microbial communities showed a distant clustering pattern resulting from the dietary differences in carbohydrate compositions. Altogether, this study revealed that termitarium hosts a unique microbial community, which can efficiently degrade lignocelluloses.}, } @article {pmid33672887, year = {2021}, author = {Gao, B and Zhang, X and Schnabl, B}, title = {Fungi-Bacteria Correlation in Alcoholic Hepatitis Patients.}, journal = {Toxins}, volume = {13}, number = {2}, pages = {}, pmid = {33672887}, issn = {2072-6651}, support = {P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 AA026939/AA/NIAAA NIH HHS/United States ; R01 AA24726, R01AA020703, U01 AA026939/NH/NIH HHS/United States ; }, mesh = {Adult ; Aged ; Bacteria/*genetics/growth & development/metabolism ; Case-Control Studies ; Dysbiosis ; Feces/microbiology ; Female ; Fungi/*genetics/growth & development/metabolism ; *Gastrointestinal Microbiome ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Fungal ; Hepatitis, Alcoholic/diagnosis/*microbiology ; Humans ; Intestines/*microbiology ; Male ; *Metagenome ; Metagenomics ; Middle Aged ; Ribotyping ; }, abstract = {Alcohol-related liver disease is one of the most prevalent types of chronic liver diseases globally. Alcohol-related liver disease begins with fatty liver, which further develops into hepatic inflammation, hepatocyte injury, and progresses to fibrosis and cirrhosis. Compositional changes of gut bacteria and fungi were found in patients with alcohol-related liver disease. However, the functional changes of fungi and correlations between fungi and bacteria have not been investigated. In this study, we first examined the functional capacity of fungi in patients with alcohol-related liver disease using shotgun metagenomics. Among 24 MetaCyc pathways contributed by fungi, superpathway of allantoin degradation in yeast was enriched in patients with alcoholic hepatitis. Furthermore, we compared the predictive power of bacteria versus fungi and found that bacteria performed better than fungi to separate patients with alcoholic hepatitis from non-alcoholic controls and patients with alcohol use disorder. Finally, we investigated the associations between the intestinal fungi and bacteria in alcoholic hepatitis patients. Positive association between fungi and bacteria was found between Cladosporium and Gemmiger, meanwhile negative association was found between Cryptococcus and Pseudomonas in alcoholic hepatitis patients.}, } @article {pmid33671794, year = {2021}, author = {Kazarina, A and Petersone-Gordina, E and Kimsis, J and Kuzmicka, J and Zayakin, P and Griškjans, Ž and Gerhards, G and Ranka, R}, title = {The Postmedieval Latvian Oral Microbiome in the Context of Modern Dental Calculus and Modern Dental Plaque Microbial Profiles.}, journal = {Genes}, volume = {12}, number = {2}, pages = {}, pmid = {33671794}, issn = {2073-4425}, mesh = {Adolescent ; Adult ; Archaeology ; Body Remains ; Burial ; Child ; DNA, Ancient/analysis ; DNA, Bacterial/*genetics ; Dental Calculus/genetics/*microbiology ; Dental Plaque/genetics/*microbiology ; Female ; Humans ; Latvia/epidemiology ; Male ; Metagenome/genetics ; Microbiota/*genetics ; Middle Aged ; Soil Microbiology ; Young Adult ; }, abstract = {Recent advantages in paleomicrobiology have provided an opportunity to investigate the composition of ancient microbial ecologies. Here, using metagenome analysis, we investigated the microbial profiles of historic dental calculus retrieved from archaeological human remains from postmedieval Latvia dated 16-17th century AD and examined the associations of oral taxa and microbial diversity with specific characteristics. We evaluated the preservation of human oral microbiome patterns in historic samples and compared the microbial composition of historic dental calculus, modern human dental plaque, modern human dental calculus samples and burial soil microbiota. Overall, the results showed that the majority of microbial DNA in historic dental calculus originated from the oral microbiome with little impact of the burial environment. Good preservation of ancient DNA in historical dental calculus samples has provided reliable insight into the composition of the oral microbiome of postmedieval Latvian individuals. The relative stability of the classifiable oral microbiome composition was observed. Significant differences between the microbiome profiles of dental calculus and dental plaque samples were identified, suggesting microbial adaptation to a specific human body environment.}, } @article {pmid33671443, year = {2021}, author = {Zakaria, NN and Convey, P and Gomez-Fuentes, C and Zulkharnain, A and Sabri, S and Shaharuddin, NA and Ahmad, SA}, title = {Oil Bioremediation in the Marine Environment of Antarctica: A Review and Bibliometric Keyword Cluster Analysis.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, pmid = {33671443}, issn = {2076-2607}, support = {9660000, 9678900 and 9300436//Universiti Putra Malaysia/ ; 6300247//Sultan Mizan Ant-arctic Research Foundation/ ; BAS 'Biodiversity, Ecosystems and Adaptation'//Natural Environment Research Council/ ; CIMAA//Centro de Inves-tigacion y Monitoreo Ambiental Antàrctico/ ; }, abstract = {Bioremediation of hydrocarbons has received much attention in recent decades, particularly relating to fuel and other oils. While of great relevance globally, there has recently been increasing interest in hydrocarbon bioremediation in the marine environments of Antarctica. To provide an objective assessment of the research interest in this field we used VOSviewer software to analyze publication data obtained from the ScienceDirect database covering the period 1970 to the present, but with a primary focus on the years 2000-2020. A bibliometric analysis of the database allowed identification of the co-occurrence of keywords. There was an increasing trend over time for publications relating to oil bioremediation in maritime Antarctica, including both studies on marine bioremediation and of the metabolic pathways of hydrocarbon degradation. Studies of marine anaerobic degradation remain under-represented compared to those of aerobic degradation. Emerging keywords in recent years included bioprospecting, metagenomic, bioindicator, and giving insight into changing research foci, such as increasing attention to microbial diversity. The study of microbial genomes using metagenomic approaches or whole genome studies is increasing rapidly and is likely to drive emerging fields in future, including rapid expansion of bioprospecting in diverse fields of biotechnology.}, } @article {pmid33671370, year = {2021}, author = {Daliri, EB and Ofosu, FK and Chelliah, R and Lee, BH and Oh, DH}, title = {Challenges and Perspective in Integrated Multi-Omics in Gut Microbiota Studies.}, journal = {Biomolecules}, volume = {11}, number = {2}, pages = {}, pmid = {33671370}, issn = {2218-273X}, mesh = {Algorithms ; Animals ; *Gastrointestinal Microbiome ; *Genome ; Humans ; Inflammation ; Mass Spectrometry ; Metabolomics/*methods ; Microbiological Techniques ; Molecular Biology/methods ; Phylogeny ; *Proteome ; Proteomics/*methods ; *Transcriptome ; }, abstract = {The advent of omic technology has made it possible to identify viable but unculturable micro-organisms in the gut. Therefore, application of multi-omic technologies in gut microbiome studies has become invaluable for unveiling a comprehensive interaction between these commensals in health and disease. Meanwhile, despite the successful identification of many microbial and host-microbial cometabolites that have been reported so far, it remains difficult to clearly identify the origin and function of some proteins and metabolites that are detected in gut samples. However, the application of single omic techniques for studying the gut microbiome comes with its own challenges which may be overcome if a number of different omics techniques are combined. In this review, we discuss our current knowledge about multi-omic techniques, their challenges and future perspective in this field of gut microbiome studies.}, } @article {pmid33670496, year = {2021}, author = {Hernandez-Baixauli, J and Puigbò, P and Torrell, H and Palacios-Jordan, H and Ripoll, VJR and Caimari, A and Del Bas, JM and Baselga-Escudero, L and Mulero, M}, title = {A Pilot Study for Metabolic Profiling of Obesity-Associated Microbial Gut Dysbiosis in Male Wistar Rats.}, journal = {Biomolecules}, volume = {11}, number = {2}, pages = {}, pmid = {33670496}, issn = {2218-273X}, support = {TECNOMIFOOD//Centro para el Desarrollo Tecnológico Industrial/ ; }, mesh = {Animals ; Coumaric Acids/metabolism ; Dysbiosis/*metabolism/*microbiology ; Gastrointestinal Microbiome/*physiology ; Lipid Metabolism/physiology ; Male ; Metabolomics/methods ; Obesity/*metabolism/*microbiology ; Phenylalanine/metabolism ; Pilot Projects ; Rats ; Rats, Wistar ; }, abstract = {Obesity is one of the most incident and concerning disease worldwide. Definite strategies to prevent obesity and related complications remain elusive. Among the risk factors of the onset of obesity, gut microbiota might play an important role in the pathogenesis of the disease, and it has received extensive attention because it affects the host metabolism. In this study, we aimed to define a metabolic profile of the segregated obesity-associated gut dysbiosis risk factor. The study of the metabolome, in an obesity-associated gut dysbiosis model, provides a relevant way for the discrimination on the different biomarkers in the obesity onset. Thus, we developed a model of this obesity risk factors through the transference of gut microbiota from obese to non-obese male Wistar rats and performed a subsequent metabolic analysis in the receptor rats. Our results showed alterations in the lipid metabolism in plasma and in the phenylalanine metabolism in urine. In consequence, we have identified metabolic changes characterized by: (1) an increase in DG:34:2 in plasma, a decrease in hippurate, (2) an increase in 3-HPPA, and (3) an increase in o-coumaric acid. Hereby, we propose these metabolites as a metabolic profile associated to a segregated dysbiosis state related to obesity disease.}, } @article {pmid33669932, year = {2021}, author = {Pane, S and Sacco, A and Iorio, A and Romani, L and Putignani, L}, title = {Strongyloides stercoralis Infestation in a Child: How a Nematode Can Affect Gut Microbiota.}, journal = {International journal of molecular sciences}, volume = {22}, number = {4}, pages = {}, pmid = {33669932}, issn = {1422-0067}, support = {Ricerca Corrente 201905_ Genetica_Putignani and 202005_ Genetica_Putignani//Italian Ministry of Health/ ; }, mesh = {Animals ; Biodiversity ; Child ; Cluster Analysis ; Female ; *Gastrointestinal Microbiome ; Humans ; Phylogeny ; Principal Component Analysis ; Strongyloides stercoralis/genetics/isolation & purification/*physiology ; Strongyloidiasis/metabolism/*microbiology/*parasitology ; }, abstract = {Background: Strongyloidiasis is a neglected tropical disease caused by the intestinal nematode Strongyloides stercoralis and characterized by gastrointestinal and pulmonary involvement. We report a pediatric case of strongyloidiasis to underline the response of the host microbiota to the perturbation induced by the nematode. Methods: We performed a 16S rRNA-metagenomic analysis of the gut microbiota of a 7-year-old female during and after S. stercolaris infection, investigating three time-point of stool samples' ecology: T0- during parasite infection, T1- a month after parasite infection, and T2- two months after parasite infection. Targeted-metagenomics were used to investigate ecology and to predict the functional pathways of the gut microbiota. Results: an increase in the alpha-diversity indices in T0-T1 samples was observed compared to T2 and healthy controls (CTRLs). Beta-diversity analysis showed a shift in the relative abundance of specific gut bacterial species from T0 to T2 samples. Moreover, the functional prediction of the targeted-metagenomics profiles suggested an enrichment of microbial glycan and carbohydrate metabolisms in the T0 sample compared with CTRLs. Conclusions: The herein report reinforces the literature suggestion of a putative direct or immune-mediated ability of S. stercolaris to promote the increase in bacterial diversity.}, } @article {pmid33669471, year = {2021}, author = {McCauley, M and Chiarello, M and Atkinson, CL and Jackson, CR}, title = {Gut Microbiomes of Freshwater Mussels (Unionidae) Are Taxonomically and Phylogenetically Variable across Years but Remain Functionally Stable.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, pmid = {33669471}, issn = {2076-2607}, support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; DEB-1831512//National Science Foundation/ ; DEB 1831531//National Science Foundation/ ; }, abstract = {Freshwater mussels perform essential ecosystem functions, yet we have no information on how their microbiomes fluctuate over time. In this study, we examined temporal variation in the microbiome of six mussel species (Lampsilis ornata, Obovaria unicolor, Elliptio arca, Fusconaia cerina, Cyclonaias asperata, and Tritogonia verrucosa) sampled from the same river in 2016 and 2019. We examined the taxonomic, phylogenetic, and inferred functional (from 16S rRNA sequences) facets of their microbiome diversity. Significant differences between the two years were identified in five of the six species sampled. However, not all species that exhibited a temporally variable microbiome were functionally distinct across years, indicating functional redundancy within the mussel gut microbiome. Inferred biosynthesis pathways showed temporal variation in pathways involved in degradation, while pathways involved in cellular metabolism were stable. There was no evidence for phylosymbiosis across any facet of microbiome biodiversity. These results indicate that temporal variation is an important factor in the assembly of the gut microbiomes of freshwater mussels and provides further support that the mussel gut microbiome is involved in host development and activity.}, } @article {pmid33668840, year = {2021}, author = {Raethong, N and Nakphaichit, M and Suratannon, N and Sathitkowitchai, W and Weerapakorn, W and Keawsompong, S and Vongsangnak, W}, title = {Analysis of Human Gut Microbiome: Taxonomy and Metabolic Functions in Thai Adults.}, journal = {Genes}, volume = {12}, number = {3}, pages = {}, pmid = {33668840}, issn = {2073-4425}, mesh = {Adult ; Bacteria/*classification/genetics/isolation & purification ; Carbohydrate Metabolism ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics/*methods ; RNA, Ribosomal, 16S/*genetics ; Thailand ; Whole Genome Sequencing/*methods ; Young Adult ; }, abstract = {The gut microbiome plays a major role in the maintenance of human health. Characterizing the taxonomy and metabolic functions of the human gut microbiome is necessary for enhancing health. Here, we analyzed the metagenomic sequencing, assembly and construction of a meta-gene catalogue of the human gut microbiome with the overall aim of investigating the taxonomy and metabolic functions of the gut microbiome in Thai adults. As a result, the integrative analysis of 16S rRNA gene and whole metagenome shotgun (WMGS) sequencing data revealed that the dominant gut bacterial families were Lachnospiraceae and Ruminococcaceae of the Firmicutes phylum. Consistently, across 3.8 million (M) genes annotated from 163.5 gigabases (Gb) of WMGS sequencing data, a significant number of genes associated with carbohydrate metabolism of the dominant bacterial families were identified. Further identification of bacterial community-wide metabolic functions promisingly highlighted the importance of Roseburia and Faecalibacterium involvement in central carbon metabolism, sugar utilization and metabolism towards butyrate biosynthesis. This work presents an initial study of shotgun metagenomics in a Thai population-based cohort in a developing Southeast Asian country.}, } @article {pmid33668457, year = {2021}, author = {do Nascimento, WM and Machiavelli, A and Ferreira, LGE and Cruz Silveira, L and de Azevedo, SSD and Bello, G and Smith, DP and Mezzari, MP and Petrosino, JF and Delgado Duarte, RT and Zárate-Bladés, CR and Pinto, AR}, title = {Gut Microbiome Profiles and Associated Metabolic Pathways in HIV-Infected Treatment-Naïve Patients.}, journal = {Cells}, volume = {10}, number = {2}, pages = {}, pmid = {33668457}, issn = {2073-4409}, mesh = {Adult ; Bacteria/classification ; Discriminant Analysis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; HIV Infections/epidemiology/*metabolism/*microbiology/transmission ; HIV-1/physiology ; Humans ; *Metabolic Networks and Pathways ; Middle Aged ; }, abstract = {The normal composition of the intestinal microbiota is a key factor for maintaining healthy homeostasis, and accordingly, dysbiosis is well known to be present in HIV-1 patients. This article investigates the gut microbiota profile of antiretroviral therapy-naive HIV-1 patients and healthy donors living in Latin America in a cohort of 13 HIV positive patients (six elite controllers, EC, and seven non-controllers, NC) and nine healthy donors (HD). Microbiota compositions in stool samples were determined by sequencing the V3-V4 region of the bacterial 16S rRNA, and functional prediction was inferred using PICRUSt. Several taxa were enriched in EC compared to NC or HD groups, including Acidaminococcus, Clostridium methylpentosum, Barnesiella, Eubacterium coprostanoligenes, and Lachnospiraceae UCG-004. In addition, our data indicate that the route of infection is an important factor associated with changes in gut microbiome composition, and we extend these results by identifying several metabolic pathways associated with each route of infection. Importantly, we observed several bacterial taxa that might be associated with different viral subtypes, such as Succinivibrio, which were more abundant in patients infected by HIV subtype B, and Streptococcus enrichment in patients infected by subtype C. In conclusion, our data brings a significant contribution to the understanding of dysbiosis-associated changes in HIV infection and describes, for the first time, differences in microbiota composition according to HIV subtypes. These results warrant further confirmation in a larger cohort of patients.}, } @article {pmid33667869, year = {2021}, author = {Huang, Y and Lv, H and Song, Y and Sun, C and Zhang, Z and Chen, S}, title = {Community composition of cecal microbiota in commercial yellow broilers with high and low feed efficiencies.}, journal = {Poultry science}, volume = {100}, number = {4}, pages = {100996}, pmid = {33667869}, issn = {1525-3171}, mesh = {Animal Feed/analysis ; Animals ; Bacteria/classification/genetics ; Biodiversity ; *Cecum/microbiology ; Chickens ; *Gastrointestinal Microbiome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The cecal microbiota plays important roles in host food digestion and nutrient absorption, which may in part affect feed efficiency (FE). To investigate the composition and functional differences of cecal microbiota between high (n = 30) and low (n = 29) feed conversion ratio (FCR; metric for FE) groups, we performed 16S rRNA gene sequencing and predicted the metagenome function using Phylogenetic Investigation of Communities by Reconstruction of Unobserved Species in yellow broilers. The results showed that the 2 groups had the same prominent microbes but with differing abundance. Firmicutes, Bacteroidetes, and Actinobacteria were 3 prominent bacterial phyla in the cecal microbial community. Although there were no differences in microbial diversity, compositional differences related to FCR were found via linear discriminant analysis (LDA) effect size; the genus Bacteroides had a significantly higher abundance (LDA >2) in the high FE (HFE) group than in the low FE group. Furthermore, genus Bacteroides had a negative FCR-associated correlation (P < 0.05). Oscillospira was positively correlated with Bacteroides in both groups, whereas Dorea was negatively correlated with Bacteroides in the HFE group. Predictive functional analysis revealed that metabolic pathways such as "starch and sucrose metabolism," "phenylalanine, tyrosine and tryptophan biosynthesis," and "carbohydrate metabolism" were significantly enriched in the HFE group. The relatively subtle differences in FE-associated cecal microbiota composition suggest a possible link between cecal microbiota and FE. Moreover, Bacteroides may potentially be used as biomarkers for FE to improve growth performance in yellow broilers.}, } @article {pmid33666787, year = {2021}, author = {Fadiji, AE and Kanu, JO and Babalola, OO}, title = {Metagenomic profiling of rhizosphere microbial community structure and diversity associated with maize plant as affected by cropping systems.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {24}, number = {3}, pages = {325-335}, pmid = {33666787}, issn = {1618-1905}, support = {UID123634//National Research Foundation/ ; }, mesh = {Agriculture/methods ; Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biodiversity ; Fungi/classification/genetics ; Metagenomics ; *Microbiota ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S ; Rhizosphere ; Soil Microbiology ; Zea mays/*microbiology ; }, abstract = {Soil microbial diversity is believed to be vital in maintaining soil quality and health. Limited knowledge exists on the impact of cropping systems (mono-cropping and crop rotation) on the diversity of the whole soil microbiome. In this study, we investigated the effects of two cropping systems, namely crop rotation and mono-cropping, on the community structure and diversity of rhizosphere microbiome in the rhizosphere and bulk soil associated with maize plant using shotgun metagenomics. Whole DNA was extracted from bulk, and rhizosphere soils associated with maize plant from the mono-cropping (LT and LTc) and crop rotation (VD and VDc) sites, respectively, and sequenced employing shotgun metagenomics. The results obtained via the Subsystem database showed 23 bacteria, 2 fungi, and 3 archaea most abundant phyla. The major bacterial phyla are Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Gemmatimonadetes, Acidobacteria, Cyanobacteria, Spirochaetes, Aquificae, Verrucomicrobia, Chloroflexi, Planctomycetes, and Chlorobi. The major fungi phyla observed were Ascomycota and Basidiomycota, while the dominant archaea phyla are Euryarchaeota, Thaumarchaeota, and Crenarchaeota. Our diversity assessment showed that the rhizosphere microbial community was more abundant in the samples from the rotational crop site following VD>VDc>LT>LTc. Alpha diversity showed that there was no significant difference (P>0.05) in the soil microbial communities (P>0.05), while better diversity indicated that a significant difference (P = 0.01) occurred. Taken together, crop rotational practice was found to positively influence the rhizosphere microbial community associated with the maize plant.}, } @article {pmid33664461, year = {2021}, author = {von Takach, B and Penton, CE and Murphy, BP and Radford, IJ and Davies, HF and Hill, BM and Banks, SC}, title = {Population genomics and conservation management of a declining tropical rodent.}, journal = {Heredity}, volume = {126}, number = {5}, pages = {763-775}, pmid = {33664461}, issn = {1365-2540}, mesh = {Animals ; Australia ; Conservation of Natural Resources ; Genetic Variation ; *Genetics, Population ; Genome ; Genomics ; Mammals ; *Metagenomics ; *Rodentia/genetics ; }, abstract = {Conservation management is improved by incorporating information about the spatial distribution of population genetic diversity into planning strategies. Northern Australia is the location of some of the world's most severe ongoing declines of endemic mammal species, yet we have little genetic information from this regional mammal assemblage to inform a genetic perspective on conservation assessment and planning. We used next-generation sequencing data from remnant populations of the threatened brush-tailed rabbit-rat (Conilurus penicillatus) to compare patterns of genomic diversity and differentiation across the landscape and investigate standardised hierarchical genomic diversity metrics to better understand brush-tailed rabbit-rat population genomic structure. We found strong population structuring, with high levels of differentiation between populations (FST = 0.21-0.78). Two distinct genomic lineages between the Tiwi Islands and mainland are also present. Prioritisation analysis showed that one population in both lineages would need to be conserved to retain at least ~80% of alleles for the species. Analysis of standardised genomic diversity metrics showed that approximately half of the total diversity occurs among lineages (δ = 0.091 from grand total γ = 0.184). We suggest that a focus on conserving remnant island populations may not be appropriate for the preservation of species-level genomic diversity and adaptive potential, as these populations represent a small component of the total diversity and a narrow subset of the environmental conditions in which the species occurs. We also highlight the importance of considering both genomic and ecological differentiation between source and receiving populations when considering translocations for conservation purposes.}, } @article {pmid33663163, year = {2021}, author = {Zhao, CZ and Chen, Z and Li, MY}, title = {[Research progress of polymicrobial synergy and dysbiosis in periodontitis].}, journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology}, volume = {56}, number = {3}, pages = {301-305}, doi = {10.3760/cma.j.cn112144-20200429-00239}, pmid = {33663163}, issn = {1002-0098}, support = {81400501//National Natural Science Foundation of China/ ; 2021YFH0188//Science and Technology Planning Project of Sichuan Province of China/ ; }, mesh = {Dysbiosis ; Humans ; *Microbiota ; *Periodontitis ; }, abstract = {Human oral cavity is colonized by various microbial communities which play an important role in the initiation and progression of periodontitis. However, it is still not clear how these microbial communities mediate the disease. With the rise of metagenomics research, polymicrobial synergy and dysbiosis (PSD) model, a new periodontitis pathogenesis mechanism, was proposed. The importance of the microbial communities acting as a whole system in the development of periodontitis is gradually recognized. Host susceptibility, as another key factor in the initiation of the disease, is vital in PSD model. This article reviews the mechanisms of the PSD model and its research progress in periodontitis as well as some other diseases and briefly highlights the positive significance in terms of prevention and treatment of periodontitis in order to provide insights and perspectives for the future periodontal researches.}, } @article {pmid33662901, year = {2021}, author = {Zhai, Y and Pérez-Díaz, IM}, title = {Identification of potential causative agents of the CO2-mediated bloater defect in low salt cucumber fermentation.}, journal = {International journal of food microbiology}, volume = {344}, number = {}, pages = {109115}, doi = {10.1016/j.ijfoodmicro.2021.109115}, pmid = {33662901}, issn = {1879-3460}, mesh = {Calcium Chloride ; Carbon Dioxide/*analysis ; Cucumis sativus/*microbiology ; Enterobacteriaceae/*metabolism ; Fermentation ; Hydrogen-Ion Concentration ; Lactobacillaceae/*metabolism ; Leuconostocaceae/*metabolism ; Malates/metabolism ; Microbiota/physiology ; Salts ; Sodium Chloride/analysis ; }, abstract = {Development of bloater defect in cucumber fermentations is the result of carbon dioxide (CO2) production by the indigenous microbiota. The amounts of CO2 needed to cause bloater defect in cucumber fermentations brined with low salt and potential microbial contributors of the gas were identified. The carbonation of acidified cucumbers showed that 28.68 ± 6.04 mM (12%) or higher dissolved CO2 induces bloater defect. The microbiome and biochemistry of cucumber fermentations (n = 9) brined with 25 mM calcium chloride (CaCl2) and 345 mM sodium chloride (NaCl) or 1.06 M NaCl were monitored on day 0, 2, 3, 5, 8, 15 and 21 using culture dependent and independent microbiological techniques and High-Performance Liquid Chromatography. Changes in pH, CO2 concentrations and the incidence of bloater defect were also followed. The enumeration of Enterobacteriaceae on Violet Red Bile Glucose agar plates detected a cell density of 5.2 ± 0.7 log CFU/g on day 2, which declined to undetectable levels by day 8. A metagenomic analysis identified Leuconostocaceae in all fermentations at 10 to 62%. The presence of both bacterial families in fermentations brined with CaCl2 and NaCl coincided with a bloater index of 24.0 ± 10.3 to 58.8 ± 23.9. The prevalence of Lactobacillaceae in a cucumber fermentation brined with NaCl with a bloater index of 41.7 on day 5 suggests a contribution to bloater defect. This study identifies the utilization of sugars and malic acid by the cucumber indigenous Lactobacillaceae, Leuconostocaceae and Enterobacteriaceae as potential contributors to CO2 production during cucumber fermentation and the consequent bloater defect.}, } @article {pmid33662387, year = {2021}, author = {Moll, JM and Myers, PN and Zhang, C and Eriksen, C and Wolf, J and Appelberg, KS and Lindberg, G and Bahl, MI and Zhao, H and Pan-Hammarström, Q and Cai, K and Jia, H and Borte, S and Nielsen, HB and Kristiansen, K and Brix, S and Hammarström, L}, title = {Gut Microbiota Perturbation in IgA Deficiency Is Influenced by IgA-Autoantibody Status.}, journal = {Gastroenterology}, volume = {160}, number = {7}, pages = {2423-2434.e5}, doi = {10.1053/j.gastro.2021.02.053}, pmid = {33662387}, issn = {1528-0012}, mesh = {Adult ; Aged ; Autoantibodies/*metabolism ; Case-Control Studies ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*immunology ; Humans ; IgA Deficiency/*immunology/*microbiology ; Immunoglobulin A/*metabolism ; Male ; Middle Aged ; }, abstract = {BACKGROUND & AIMS: IgA exerts its primary function at mucosal surfaces, where it binds microbial antigens to regulate bacterial growth and epithelial attachment. One third of individuals with IgA deficiency (IgAD) suffers from recurrent mucosal infections, possibly related to an altered microbiota. We aimed to delineate the impact of IgAD and the IgA-autoantibody status on the composition and functional capacity of the gut microbiota.

METHODS: We performed a paired, lifestyle-balanced analysis of the effect of IgA on the gut microbiota composition and functionality based on fecal samples from individuals with IgAD and IgA-sufficient household members (n = 100), involving quantitative shotgun metagenomics, species-centric functional annotation of gut bacteria, and strain-level analyses. We supplemented the data set with 32 individuals with IgAD and examined the influence of IgA-autoantibody status on the composition and functionality of the gut microbiota.

RESULTS: The gut microbiota of individuals with IgAD exhibited decreased richness and diversity and was enriched for bacterial species encoding pathogen-related functions including multidrug and antimicrobial peptide resistance, virulence factors, and type III and VI secretion systems. These functional changes were largely attributed to Escherichia coli but were independent of E coli strain variations and most prominent in individuals with IgAD with IgA-specific autoreactive antibodies.

CONCLUSIONS: The microbiota of individuals with IgAD is enriched for species holding increased proinflammatory potential, thereby potentially decreasing the resistance to gut barrier-perturbing events. This phenotype is especially pronounced in individuals with IgAD with IgA-specific autoreactive antibodies, thus warranting a screening for IgA-specific autoreactive antibodies in IgAD to identify patients with IgAD with increased risk for gastrointestinal implications.}, } @article {pmid33662003, year = {2021}, author = {El Alam, MB and Sims, TT and Kouzy, R and Biegert, GWG and Jaoude, JABI and Karpinets, TV and Yoshida-Court, K and Wu, X and Delgado-Medrano, AY and Mezzari, MP and Ajami, NJ and Solley, T and Ahmed-Kaddar, M and Lin, LL and Ramondetta, L and Jazaeri, A and Jhingran, A and Eifel, PJ and Schmeler, KM and Wargo, J and Klopp, AH and Colbert, LE}, title = {A prospective study of the adaptive changes in the gut microbiome during standard-of-care chemoradiotherapy for gynecologic cancers.}, journal = {PloS one}, volume = {16}, number = {3}, pages = {e0247905}, pmid = {33662003}, issn = {1932-6203}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; T32 CA101642/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Antineoplastic Agents/adverse effects/therapeutic use ; Bacteria/drug effects/isolation & purification/radiation effects ; Chemoradiotherapy/adverse effects ; Female ; Gastrointestinal Microbiome/*drug effects/*radiation effects ; Genital Neoplasms, Female/*drug therapy/*radiotherapy ; Humans ; Middle Aged ; Prospective Studies ; }, abstract = {BACKGROUND: A diverse and abundant gut microbiome can improve cancer patients' treatment response; however, the effect of pelvic chemoradiotherapy (CRT) on gut diversity and composition is unclear. The purpose of this prospective study was to identify changes in the diversity and composition of the gut microbiome during and after pelvic CRT.

MATERIALS AND METHODS: Rectal swabs from 58 women with cervical, vaginal, or vulvar cancer from two institutions were prospectively analyzed before CRT (baseline), during CRT (weeks 1, 3, and 5), and at first follow-up (week 12) using 16Sv4 rRNA gene sequencing of the V4 hypervariable region of the bacterial 16S rRNA marker gene. 42 of these patients received antibiotics during the study period. Observed operational taxonomic units (OTUs; representative of richness) and Shannon, Simpson, Inverse Simpson, and Fisher diversity indices were used to characterize alpha (within-sample) diversity. Changes over time were assessed using a paired t-test, repeated measures ANOVA, and linear mixed modeling. Compositional changes in specific bacteria over time were evaluated using linear discriminant analysis effect size.

RESULTS: Gut microbiome richness and diversity levels continually decreased throughout CRT (mean Shannon diversity index, 2.52 vs. 2.91; all P <0.01), but were at or near baseline levels in 60% of patients by week 12. Patients with higher gut diversity at baseline had the steepest decline in gut microbiome diversity. Gut microbiome composition was significantly altered during CRT, with increases in Proteobacteria and decreases in Clostridiales, but adapted after CRT, with increases in Bacteroides species.

CONCLUSION: After CRT, the diversity of the gut microbiomes in this population tended to return to baseline levels by the 12 week follow-up period, but structure and composition remained significantly altered. These changes should be considered when designing studies to analyze the gut microbiome in patients who receive pelvic CRT for gynecologic cancers.}, } @article {pmid33661648, year = {2021}, author = {Verschaffelt, P and Van Den Bossche, T and Gabriel, W and Burdukiewicz, M and Soggiu, A and Martens, L and Renard, BY and Schiebenhoefer, H and Mesuere, B}, title = {MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets.}, journal = {Journal of proteome research}, volume = {20}, number = {4}, pages = {2083-2088}, doi = {10.1021/acs.jproteome.0c00926}, pmid = {33661648}, issn = {1535-3907}, mesh = {Computational Biology ; Gene Ontology ; Metagenomics ; *Microbiota ; Semantics ; *Software ; }, abstract = {The study of microbiomes has gained in importance over the past few years and has led to the emergence of the fields of metagenomics, metatranscriptomics, and metaproteomics. While initially focused on the study of biodiversity within these communities, the emphasis has increasingly shifted to the study of (changes in) the complete set of functions available in these communities. A key tool to study this functional complement of a microbiome is Gene Ontology (GO) term analysis. However, comparing large sets of GO terms is not an easy task due to the deeply branched nature of GO, which limits the utility of exact term matching. To solve this problem, we here present MegaGO, a user-friendly tool that relies on semantic similarity between GO terms to compute the functional similarity between multiple data sets. MegaGO is high performing: Each set can contain thousands of GO terms, and results are calculated in a matter of seconds. MegaGO is available as a web application at https://megago.ugent.be and is installable via pip as a standalone command line tool and reusable software library. All code is open source under the MIT license and is available at https://github.com/MEGA-GO/.}, } @article {pmid33660141, year = {2021}, author = {Krishnamoorthy, A and Gupta, A and Sar, P and Maiti, MK}, title = {Metagenomics of two gnotobiotically grown aromatic rice cultivars reveals genotype-dependent and tissue-specific colonization of endophytic bacterial communities attributing multiple plant growth promoting traits.}, journal = {World journal of microbiology & biotechnology}, volume = {37}, number = {4}, pages = {59}, pmid = {33660141}, issn = {1573-0972}, mesh = {Bacteria/classification/genetics/isolation & purification ; Bacterial Physiological Phenomena ; Biodiversity ; Endophytes/classification/isolation & purification/*physiology ; *Genotype ; *Germ-Free Life ; High-Throughput Nucleotide Sequencing ; Indoleacetic Acids ; *Metagenomics ; Microbiota/*physiology ; Nitrogen Fixation ; Oryza/growth & development/*microbiology ; *Phenotype ; *Plant Development ; Plant Roots/microbiology ; Plant Shoots/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Exploration of community structures, habitations, and potential plant growth promoting (PGP) attributes of endophytic bacteria through next generation sequencing (NGS) is a prerequisite to culturing PGP endophytic bacteria for their application in sustainable agriculture. The present study unravels the taxonomic abundance and diversity of endophytic bacteria inhabiting in vitro grown root, shoot and callus tissues of two aromatic rice cultivars through 16S rRNA gene-based Illumina NGS. Wide variability in the number of bacterial operational taxonomic units (OTUs) and genera was observed between the two samples of the root (55, 14 vs. 310, 76) and shoot (26, 12 vs. 276, 73) but not between the two callus samples (251, 61 vs. 259, 51), indicating tissue-specific and genotype-dependent bacterial community distribution in rice plant, even under similar gnotobiotic growth conditions. Sizes of core bacteriomes of the selected two rice genotypes varied from 1 to 15 genera, with Sphingomonas being the only genus detected in all six samples. Functional annotation, based upon the abundance of bacterial OTUs, revealed the presence of several PGP trait-related genes having variable relative abundance in tissue-specific and genotype-dependent manners. In silico study also documented a higher abundance of certain genes in the same biochemical pathway, such as nitrogen fixation, phosphate solubilization and indole acetic acid production; implying their crucial roles in the biosynthesis of metabolites leading to PGP. New insights on utilizing callus cultures for isolation of PGP endophytes aiming to improve rice crop productivity are presented, owing to constancy in bacterial OTUs and genera in callus tissues of both the rice genotypes.}, } @article {pmid33658300, year = {2021}, author = {Young, C and Wood, HM and Fuentes Balaguer, A and Bottomley, D and Gallop, N and Wilkinson, L and Benton, SC and Brealey, M and John, C and Burtonwood, C and Thompson, KN and Yan, Y and Barrett, JH and Morris, EJA and Huttenhower, C and Quirke, P}, title = {Microbiome Analysis of More Than 2,000 NHS Bowel Cancer Screening Programme Samples Shows the Potential to Improve Screening Accuracy.}, journal = {Clinical cancer research : an official journal of the American Association for Cancer Research}, volume = {27}, number = {8}, pages = {2246-2254}, pmid = {33658300}, issn = {1557-3265}, support = {27140/CRUK_/Cancer Research UK/United Kingdom ; P30 DK043351/DK/NIDDK NIH HHS/United States ; 203524/WT_/Wellcome Trust/United Kingdom ; A27140/CRUK_/Cancer Research UK/United Kingdom ; 203524/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Aged ; Aged, 80 and over ; Colonoscopy ; Colorectal Neoplasms/*diagnosis/microbiology ; DNA, Bacterial/isolation & purification ; Early Detection of Cancer/*methods/statistics & numerical data ; England ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; Occult Blood ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; State Medicine ; }, abstract = {PURPOSE: There is potential for fecal microbiome profiling to improve colorectal cancer screening. This has been demonstrated by research studies, but it has not been quantified at scale using samples collected and processed routinely by a national screening program.

EXPERIMENTAL DESIGN: Between 2016 and 2019, the largest of the NHS Bowel Cancer Screening Programme hubs prospectively collected processed guaiac fecal occult blood test (gFOBT) samples with subsequent colonoscopy outcomes: blood-negative [n = 491 (22%)]; colorectal cancer [n = 430 (19%)]; adenoma [n = 665 (30%)]; colonoscopy-normal [n = 300 (13%)]; nonneoplastic [n = 366 (16%)]. Samples were transported and stored at room temperature. DNA underwent 16S rRNA gene V4 amplicon sequencing. Taxonomic profiling was performed to provide features for classification via random forests (RF).

RESULTS: Samples provided 16S amplicon-based microbial profiles, which confirmed previously described colorectal cancer-microbiome associations. Microbiome-based RF models showed potential as a first-tier screen, distinguishing colorectal cancer or neoplasm (colorectal cancer or adenoma) from blood-negative with AUC 0.86 (0.82-0.89) and AUC 0.78 (0.74-0.82), respectively. Microbiome-based models also showed potential as a second-tier screen, distinguishing from among gFOBT blood-positive samples, colorectal cancer or neoplasm from colonoscopy-normal with AUC 0.79 (0.74-0.83) and AUC 0.73 (0.68-0.77), respectively. Models remained robust when restricted to 15 taxa, and performed similarly during external validation with metagenomic datasets.

CONCLUSIONS: Microbiome features can be assessed using gFOBT samples collected and processed routinely by a national colorectal cancer screening program to improve accuracy as a first- or second-tier screen. The models required as few as 15 taxa, raising the potential of an inexpensive qPCR test. This could reduce the number of colonoscopies in countries that use fecal occult blood test screening.}, } @article {pmid33657385, year = {2021}, author = {Wu, S and Jiang, P and Zhao, XM and Chen, WH}, title = {Treatment regimens may compromise gut-microbiome-derived signatures for liver cirrhosis.}, journal = {Cell metabolism}, volume = {33}, number = {3}, pages = {455-456}, doi = {10.1016/j.cmet.2021.02.012}, pmid = {33657385}, issn = {1932-7420}, mesh = {*Gastrointestinal Microbiome ; Humans ; Liver Cirrhosis ; Metagenomics ; Proton Pump Inhibitors ; }, abstract = {Many of the gut-microbiome-derived signatures for liver cirrhosis, especially the important ones, were likely under the influence of proton pump inhibitors (PPIs). Wu et al. suggest that drug usage is a confounding factor in metagenomics analysis that should be controlled for.}, } @article {pmid33657381, year = {2021}, author = {Rosario, D and Bidkhori, G and Lee, S and Bedarf, J and Hildebrand, F and Le Chatelier, E and Uhlen, M and Ehrlich, SD and Proctor, G and Wüllner, U and Mardinoglu, A and Shoaie, S}, title = {Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson's disease.}, journal = {Cell reports}, volume = {34}, number = {9}, pages = {108807}, doi = {10.1016/j.celrep.2021.108807}, pmid = {33657381}, issn = {2211-1247}, support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S016899/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Aged ; Bacteria/genetics/*metabolism ; Case-Control Studies ; Databases, Genetic ; Dysbiosis ; Folic Acid/*blood ; Folic Acid Deficiency/blood/microbiology ; *Gastrointestinal Microbiome/genetics ; Homocysteine/*blood ; Humans ; Hyperhomocysteinemia/blood/microbiology ; Intestines/*microbiology ; Male ; Metabolome ; Metabolomics ; Metagenome ; Metagenomics ; Middle Aged ; Mucins/metabolism ; Parkinson Disease/*blood/*microbiology ; Polysaccharides/metabolism ; Severity of Illness Index ; }, abstract = {Parkinson's disease (PD) is the most common progressive neurological disorder compromising motor functions. However, nonmotor symptoms, such as gastrointestinal (GI) dysfunction, precede those affecting movement. Evidence of an early involvement of the GI tract and enteric nervous system highlights the need for better understanding of the role of gut microbiota in GI complications in PD. Here, we investigate the gut microbiome of patients with PD using metagenomics and serum metabolomics. We integrate these data using metabolic modeling and construct an integrative correlation network giving insight into key microbial species linked with disease severity, GI dysfunction, and age of patients with PD. Functional analysis reveals an increased microbial capability to degrade mucin and host glycans in PD. Personalized community-level metabolic modeling reveals the microbial contribution to folate deficiency and hyperhomocysteinemia observed in patients with PD. The metabolic modeling approach could be applied to uncover gut microbial metabolic contributions to PD pathophysiology.}, } @article {pmid33656436, year = {2021}, author = {Tortelli, BA and Lewis, AL and Fay, JC}, title = {The structure and diversity of strain-level variation in vaginal bacteria.}, journal = {Microbial genomics}, volume = {7}, number = {3}, pages = {}, pmid = {33656436}, issn = {2057-5858}, support = {F30 HD094435/HD/NICHD NIH HHS/United States ; R01 AI114635/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Bacteria/classification/genetics/*isolation & purification ; Cohort Studies ; Female ; Humans ; *Microbiota ; Phylogeny ; Pregnancy ; Vagina/*microbiology ; Young Adult ; }, abstract = {The vaginal microbiome plays an important role in human health and species of vaginal bacteria have been associated with reproductive disease. Strain-level variation is also thought to be important, but the diversity, structure and evolutionary history of vaginal strains is not as well characterized. We developed and validated an approach to measure strain variation from metagenomic data based on SNPs within the core genomes for six species of vaginal bacteria: Gardnerella vaginalis, Lactobacillus crispatus, Lactobacillus iners, Lactobacillus jensenii, Lactobacillus gasseri and Atopobium vaginae. Despite inhabiting the same environment, strain diversity and structure varies across species. All species except L. iners are characterized by multiple distinct groups of strains. Even so, strain diversity is lower in the Lactobacillus species, consistent with a more recent colonization of the human vaginal microbiome. Both strain diversity and the frequency of multi-strain samples is related to species-level diversity of the microbiome in which they occur, suggesting similar ecological factors influencing diversity within the vaginal niche. We conclude that the structure of strain-level variation provides both the motivation and means of testing whether strain-level differences contribute to the function and health consequences of the vaginal microbiome.}, } @article {pmid33656283, year = {2021}, author = {Bağcı, C and Patz, S and Huson, DH}, title = {DIAMOND+MEGAN: Fast and Easy Taxonomic and Functional Analysis of Short and Long Microbiome Sequences.}, journal = {Current protocols}, volume = {1}, number = {3}, pages = {e59}, doi = {10.1002/cpz1.59}, pmid = {33656283}, issn = {2691-1299}, mesh = {Amino Acid Sequence ; Diamond ; *Metagenome ; *Microbiota ; Sequence Analysis, DNA ; }, abstract = {One main approach to computational analysis of microbiome sequences is to first align against a reference database of annotated protein sequences (NCBI-nr) and then perform taxonomic and functional binning of the sequences based on the resulting alignments. For both short and long reads (or assembled contigs), alignment is performed using DIAMOND, whereas taxonomic and functional binning, followed by inter- active exploration and analysis, is performed using MEGAN. We provide two step-by-step descriptions of this approach: © 2021 The Authors. Basic Protocol 1: Taxonomic and functional analysis of short read microbiome sequences Support Protocol 1: Preprocessing Basic Protocol 2: taxonomic and functional analysis of assembled long read microbiome sequences Support Protocol 2: Taxonomic binning and CheckM.}, } @article {pmid33653887, year = {2021}, author = {Yanuka-Golub, K and Dubinsky, V and Korenblum, E and Reshef, L and Ofek-Lalzar, M and Rishpon, J and Gophna, U}, title = {Anode Surface Bioaugmentation Enhances Deterministic Biofilm Assembly in Microbial Fuel Cells.}, journal = {mBio}, volume = {12}, number = {2}, pages = {}, pmid = {33653887}, issn = {2150-7511}, mesh = {Bacteria/genetics/growth & development ; *Biodegradation, Environmental ; Bioelectric Energy Sources/microbiology ; Biofilms/*growth & development ; *Electrodes ; *Microbiota ; Wastewater/microbiology ; Water Purification/*methods ; }, abstract = {Microbial fuel cells (MFCs) generate energy while aiding the biodegradation of waste through the activity of an electroactive mixed biofilm. Metabolic cooperation is essential for MFCs' efficiency, especially during early colonization. Thus, examining specific ecological processes that drive the assembly of anode biofilms is highly important for shortening startup times and improving MFC performance, making this technology cost-effective and sustainable. Here, we use metagenomics to show that bioaugmentation of the anode surface with a taxonomically defined electroactive consortium, dominated by Desulfuromonas, resulted in an extremely rapid current density generation. Conversely, the untreated anode surface resulted in a highly stochastic and slower biofilm assembly. Remarkably, an efficient anode colonization process was obtained only if wastewater was added, leading to a nearly complete replacement of the bioaugmented community by Geobacter lovleyi Although different approaches to improve MFC startup have been investigated, we propose that only the combination of anode bioaugmentation with wastewater inoculation can reduce stochasticity. Such an approach provides the conditions that support the growth of specific newly arriving species that positively support the fast establishment of a highly functional anode biofilm.IMPORTANCE Mixed microbial communities play important roles in treating wastewater, in producing renewable energy, and in the bioremediation of pollutants in contaminated environments. While these processes are well known, especially the community structure and biodiversity, how to efficiently and robustly manage microbial community assembly remains unknown. Moreover, it has been shown that a high degree of temporal variation in microbial community composition and structure often occurs even under identical environmental conditions. This heterogeneity is directly related to stochastic processes involved in microbial community organization, similarly during the initial stages of biofilm formation on surfaces. In this study, we show that anode surface pretreatment alone is not sufficient for a substantial improvement in startup times in microbial fuel cells (MFCs), as previously thought. Rather, we have discovered that the combination of applying a well-known consortium directly on the anode surface together with wastewater (including the bacteria that they contain) is the optimized management scheme. This allowed a selected colonization process by the wastewater species, which improved the functionality relative to that of untreated systems.}, } @article {pmid33653268, year = {2021}, author = {Casanova, A and Maroso, F and Blanco, A and Hermida, M and Ríos, N and García, G and Manuzzi, A and Zane, L and Verissimo, A and García-Marín, JL and Bouza, C and Vera, M and Martínez, P}, title = {Low impact of different SNP panels from two building-loci pipelines on RAD-Seq population genomic metrics: case study on five diverse aquatic species.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {150}, pmid = {33653268}, issn = {1471-2164}, support = {GRC2014/010//Xunta de Galicia/ ; EAPA_458/2016//Interreg/ ; MPCUdG2016/060//Universitat de Girona/ ; }, mesh = {Animals ; Genome ; *Metagenomics ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The irruption of Next-generation sequencing (NGS) and restriction site-associated DNA sequencing (RAD-seq) in the last decade has led to the identification of thousands of molecular markers and their genotyping for refined genomic screening. This approach has been especially useful for non-model organisms with limited genomic resources. Many building-loci pipelines have been developed to obtain robust single nucleotide polymorphism (SNPs) genotyping datasets using a de novo RAD-seq approach, i.e. without reference genomes. Here, the performances of two building-loci pipelines, STACKS 2 and Meyer's 2b-RAD v2.1 pipeline, were compared using a diverse set of aquatic species representing different genomic and/or population structure scenarios. Two bivalve species (Manila clam and common edible cockle) and three fish species (brown trout, silver catfish and small-spotted catshark) were studied. Four SNP panels were evaluated in each species to test both different building-loci pipelines and criteria for SNP selection. Furthermore, for Manila clam and brown trout, a reference genome approach was used as control.

RESULTS: Despite different outcomes were observed between pipelines and species with the diverse SNP calling and filtering steps tested, no remarkable differences were found on genetic diversity and differentiation within species with the SNP panels obtained with a de novo approach. The main differences were found in brown trout between the de novo and reference genome approaches. Genotyped vs missing data mismatches were the main genotyping difference detected between the two building-loci pipelines or between the de novo and reference genome comparisons.

CONCLUSIONS: Tested building-loci pipelines for selection of SNP panels seem to have low influence on population genetics inference across the diverse case-study scenarios here studied. However, preliminary trials with different bioinformatic pipelines are suggested to evaluate their influence on population parameters according with the specific goals of each study.}, } @article {pmid33652267, year = {2021}, author = {Pavlovic, J and Cavalieri, D and Mastromei, G and Pangallo, D and Perito, B and Marvasi, M}, title = {MinION technology for microbiome sequencing applications for the conservation of cultural heritage.}, journal = {Microbiological research}, volume = {247}, number = {}, pages = {126727}, doi = {10.1016/j.micres.2021.126727}, pmid = {33652267}, issn = {1618-0623}, mesh = {Bacteria/classification/genetics ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/instrumentation/*methods ; Metagenomics/instrumentation/*methods ; Microbiota/*genetics ; Paintings ; Sequence Analysis, DNA ; Textiles ; }, abstract = {The MinION single-molecule sequencing system has been attracting the attention of the community of microbiologists involved in the conservation of cultural heritage. The use of MinION for the conservation of cultural heritage is extremely recent, but surprisingly the only few applications available have been exploring many different substrates: stone, textiles, paintings and wax. The use of MinION sequencing is mainly used to address the metataxonomy (with special emphasis on non-cultivable microorganisms) with the effort to identify species involved in the degradation of the substrates. In this review, we show the current applications available on different artworks, showing how this technology can be a useful tool for microbiologists and conservators also in light of its low cost and the easy chemistry.}, } @article {pmid33651661, year = {2021}, author = {Ruuskanen, MO and Åberg, F and Männistö, V and Havulinna, AS and Méric, G and Liu, Y and Loomba, R and Vázquez-Baeza, Y and Tripathi, A and Valsta, LM and Inouye, M and Jousilahti, P and Salomaa, V and Jain, M and Knight, R and Lahti, L and Niiranen, TJ}, title = {Links between gut microbiome composition and fatty liver disease in a large population sample.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-22}, pmid = {33651661}, issn = {1949-0984}, support = {R01 ES027595/ES/NIEHS NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; P42 ES010337/ES/NIEHS NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 DK124318/DK/NIDDK NIH HHS/United States ; U01 DK061734/DK/NIDDK NIH HHS/United States ; R01 DK121378/DK/NIDDK NIH HHS/United States ; R01 DK106419/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Age Factors ; Bacteria/*classification/genetics/*growth & development/metabolism ; Clostridium/classification/genetics/growth & development/metabolism ; Cohort Studies ; Ethanol/metabolism ; Fatty Liver/*microbiology ; Female ; Fermentation ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Male ; Metagenome ; Middle Aged ; Phylogeny ; Sex Factors ; }, abstract = {Fatty liver disease is the most common liver disease in the world. Its connection with the gut microbiome has been known for at least 80 y, but this association remains mostly unstudied in the general population because of underdiagnosis and small sample sizes. To address this knowledge gap, we studied the link between the Fatty Liver Index (FLI), a well-established proxy for fatty liver disease, and gut microbiome composition in a representative, ethnically homogeneous population sample of 6,269 Finnish participants. We based our models on biometric covariates and gut microbiome compositions from shallow metagenome sequencing. Our classification models could discriminate between individuals with a high FLI (≥60, indicates likely liver steatosis) and low FLI (<60) in internal cross-region validation, consisting of 30% of the data not used in model training, with an average AUC of 0.75 and AUPRC of 0.56 (baseline at 0.30). In addition to age and sex, our models included differences in 11 microbial groups from class Clostridia, mostly belonging to orders Lachnospirales and Oscillospirales. Our models were also predictive of the high FLI group in a different Finnish cohort, consisting of 258 participants, with an average AUC of 0.77 and AUPRC of 0.51 (baseline at 0.21). Pathway analysis of representative genomes of the positively FLI-associated taxa in (NCBI) Clostridium subclusters IV and XIVa indicated the presence of, e.g., ethanol fermentation pathways. These results support several findings from smaller case-control studies, such as the role of endogenous ethanol producers in the development of the fatty liver.}, } @article {pmid33651197, year = {2021}, author = {Brubaker, L and Putonti, C and Dong, Q and Wolfe, AJ}, title = {The human urobiome.}, journal = {Mammalian genome : official journal of the International Mammalian Genome Society}, volume = {32}, number = {4}, pages = {232-238}, pmid = {33651197}, issn = {1432-1777}, support = {R01 DK104718/DK/NIDDK NIH HHS/United States ; R01 AI116706/AI/NIAID NIH HHS/United States ; }, mesh = {Female ; Humans ; Male ; *Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Urinary Bladder/*microbiology ; }, abstract = {Traditionally, the healthy urinary bladder has been considered to be sterile. Several teams have used metagenomic (DNA-dependent) and metaculturomic (culture-dependent) methods to debunk this longstanding dogma. In fact, resident microbial communities (urobiome) have been detected in both adult females and males. Although the field is young, several observations have been made. For example, the urobiome differs between men and women, likely due to anatomical and hormonal differences. Importantly, the urobiome has been associated with a variety of lower urinary tract disorders, including overactive bladder and post-operative urinary tract infection, raising the possibility that clinicians might one day treat symptoms by modifying the urobiome instead of killing the suspected uropathogen. Little is known concerning the relationship between the urobiome and host genetics; so far, only a single paper has reported such a study. However, major efforts have gone into understanding the genomics of the urobiome itself, a process facilitated by the fact that many urobiome studies have used metaculturomic methods to detect and identify microbes. In this narrative review, we will introduce the urobiome with separate sections on the female and male urobiomes, discuss challenges specific to the urobiome, describe newly discovered associations between the urobiome and lower urinary tract symptoms, and highlight the one study that has attempted to relate host genetics and the urobiome. We will finish with a section on how metagenomic surveys and whole genome sequencing of bacterial isolates are improving our understanding of the urobiome and its relationship to lower urinary tract health and disorders.}, } @article {pmid33650794, year = {2021}, author = {Dalcin Martins, P and de Jong, A and Lenstra, WK and van Helmond, NAGM and Slomp, CP and Jetten, MSM and Welte, CU and Rasigraf, O}, title = {Enrichment of novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria in an oxygen-limited methane- and iron-fed bioreactor inoculated with Bothnian Sea sediments.}, journal = {MicrobiologyOpen}, volume = {10}, number = {1}, pages = {e1175}, pmid = {33650794}, issn = {2045-8827}, mesh = {Anaerobiosis/physiology ; Bacteroidetes/growth & development/*metabolism ; Bioreactors/*microbiology ; Finland ; Geologic Sediments/*microbiology ; Iron/*metabolism ; Methane/*metabolism ; Microbiota ; Oceans and Seas ; Oxidation-Reduction ; Oxygen/metabolism ; Sweden ; Verrucomicrobia/growth & development/*metabolism ; }, abstract = {Microbial methane oxidation is a major biofilter preventing larger emissions of this powerful greenhouse gas from marine coastal areas into the atmosphere. In these zones, various electron acceptors such as sulfate, metal oxides, nitrate, or oxygen can be used. However, the key microbial players and mechanisms of methane oxidation are poorly understood. In this study, we inoculated a bioreactor with methane- and iron-rich sediments from the Bothnian Sea to investigate microbial methane and iron cycling under low oxygen concentrations. Using metagenomics, we investigated shifts in microbial community composition after approximately 2.5 years of bioreactor operation. Marker genes for methane and iron cycling, as well as respiratory and fermentative metabolism, were identified and used to infer putative microbial metabolism. Metagenome-assembled genomes representing novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria were recovered and revealed a potential for methane oxidation, organic matter degradation, and iron cycling, respectively. This work brings new hypotheses on the identity and metabolic versatility of microorganisms that may be members of such functional guilds in coastal marine sediments and highlights that microorganisms potentially composing the methane biofilter in these sediments may be more diverse than previously appreciated.}, } @article {pmid33649957, year = {2021}, author = {Milani, C}, title = {Metagenomic Analyses of Bifidobacterial Communities.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2278}, number = {}, pages = {183-193}, pmid = {33649957}, issn = {1940-6029}, mesh = {Animals ; Bifidobacterium/classification/*genetics ; Gastrointestinal Microbiome ; Gene Expression Profiling/methods ; *Genome, Bacterial ; Humans ; Metagenome ; Metagenomics/*methods ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Software ; }, abstract = {Bifidobacteria represent highly prevalent and abundant members of the gut microbiota during mammalian infancy. In this context, bifidobacterial species have been shown to be correlated with many aspects of host health by means of direct interactions with the host and cohabiting microbes. Metagenomic sequencing of fecal DNA represents a valuable approach for taxonomic and functional profiling of bacterial populations, and has allowed us to appreciate the relevance of bifidobacterial taxa in such complex bacterial communities, especially during the first stages of life.}, } @article {pmid33649949, year = {2021}, author = {McDonnell, B and Casey, E and Milani, C and Lugli, GA and Viappiani, A and Mahony, J and Ventura, M and van Sinderen, D}, title = {Phageome Analysis of Bifidobacteria-Rich Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2278}, number = {}, pages = {71-85}, pmid = {33649949}, issn = {1940-6029}, mesh = {Bacteriophages/*genetics ; Bifidobacterium/*virology ; DNA, Viral/genetics ; Feces/*microbiology ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Infant ; *Virome ; }, abstract = {Bifidobacteria are important early colonizers of the human intestinal tract. The relative abundance of bifidobacterial species may be modulated, in part, by bacteriophage activity. Metagenomic studies of these populations is a crucial step in understanding this important interaction. This chapter outlines the technical instructions required to analyze the virome of a bifidobacteria-rich sample, for example, an infant fecal sample.}, } @article {pmid33649565, year = {2021}, author = {Meyer, F and Lesker, TR and Koslicki, D and Fritz, A and Gurevich, A and Darling, AE and Sczyrba, A and Bremges, A and McHardy, AC}, title = {Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit.}, journal = {Nature protocols}, volume = {16}, number = {4}, pages = {1785-1801}, pmid = {33649565}, issn = {1750-2799}, mesh = {Animals ; Computer Simulation ; Databases, Genetic ; Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics/*methods ; Mice ; Phylogeny ; Reference Standards ; Reproducibility of Results ; *Software ; }, abstract = {Computational methods are key in microbiome research, and obtaining a quantitative and unbiased performance estimate is important for method developers and applied researchers. For meaningful comparisons between methods, to identify best practices and common use cases, and to reduce overhead in benchmarking, it is necessary to have standardized datasets, procedures and metrics for evaluation. In this tutorial, we describe emerging standards in computational meta-omics benchmarking derived and agreed upon by a larger community of researchers. Specifically, we outline recent efforts by the Critical Assessment of Metagenome Interpretation (CAMI) initiative, which supplies method developers and applied researchers with exhaustive quantitative data about software performance in realistic scenarios and organizes community-driven benchmarking challenges. We explain the most relevant evaluation metrics for assessing metagenome assembly, binning and profiling results, and provide step-by-step instructions on how to generate them. The instructions use simulated mouse gut metagenome data released in preparation for the second round of CAMI challenges and showcase the use of a repository of tool results for CAMI datasets. This tutorial will serve as a reference for the community and facilitate informative and reproducible benchmarking in microbiome research.}, } @article {pmid33649556, year = {2021}, author = {Michoud, G and Ngugi, DK and Barozzi, A and Merlino, G and Calleja, ML and Delgado-Huertas, A and Morán, XAG and Daffonchio, D}, title = {Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline.}, journal = {The ISME journal}, volume = {15}, number = {8}, pages = {2351-2365}, pmid = {33649556}, issn = {1751-7370}, mesh = {Archaea/genetics ; *Bacteria/genetics ; Indian Ocean ; *Microbiota ; Phylogeny ; Seawater ; }, abstract = {Deep-sea hypersaline anoxic basins are polyextreme environments in the ocean's interior characterized by the high density of brines that prevents mixing with the overlaying seawater, generating sharp chemoclines and redoxclines up to tens of meters thick that host a high concentration of microbial communities. Yet, a fundamental understanding of how such pycnoclines shape microbial life and the associated biogeochemical processes at a fine scale, remains elusive. Here, we applied high-precision sampling of the brine-seawater transition interface in the Suakin Deep, located at 2770 m in the central Red Sea, to reveal previously undocumented fine-scale community structuring and succession of metabolic groups along a salinity gradient only 1 m thick. Metagenomic profiling at a 10-cm-scale resolution highlighted spatial organization of key metabolic pathways and corresponding microbial functional units, emphasizing the prominent role and significance of salinity and oxygen in shaping their ecology. Nitrogen cycling processes are especially affected by the redoxcline with ammonia oxidation processes being taxa and layers specific, highlighting also the presence of novel microorganisms, such as novel Thaumarchaeota and anammox, adapted to the changing conditions of the chemocline. The findings render the transition zone as a critical niche for nitrogen cycling, with complementary metabolic networks, in turn underscoring the biogeochemical complexity of deep-sea brines.}, } @article {pmid33649554, year = {2021}, author = {Li, Z and Pan, D and Wei, G and Pi, W and Zhang, C and Wang, JH and Peng, Y and Zhang, L and Wang, Y and Hubert, CRJ and Dong, X}, title = {Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity.}, journal = {The ISME journal}, volume = {15}, number = {8}, pages = {2366-2378}, pmid = {33649554}, issn = {1751-7370}, support = {TPR 15-229/HX/HSRD VA/United States ; }, mesh = {*Geologic Sediments ; Methane ; *Microbiota ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {In marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse microbial communities, but little is known about viruses infecting these microorganisms. Here, we probed metagenomes from seven geographically diverse cold seeps across global oceans to assess viral diversity, virus-host interaction, and virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons with viruses inhabiting other ecosystems reveal that cold seep sediments harbour considerable unexplored viral diversity. Most cold seep viruses display high degrees of endemism with seep fluid flux being one of the main drivers of viral community composition. In silico predictions linked 14.2% of the viruses to microbial host populations with many belonging to poorly understood candidate bacterial and archaeal phyla. Lysis was predicted to be a predominant viral lifestyle based on lineage-specific virus/host abundance ratios. Metabolic predictions of prokaryotic host genomes and viral AMGs suggest that viruses influence microbial hydrocarbon biodegradation at cold seeps, as well as other carbon, sulfur and nitrogen cycling via virus-induced mortality and/or metabolic augmentation. Overall, these findings reveal the global diversity and biogeography of cold seep viruses and indicate how viruses may manipulate seep microbial ecology and biogeochemistry.}, } @article {pmid33648559, year = {2021}, author = {Plichta, DR and Somani, J and Pichaud, M and Wallace, ZS and Fernandes, AD and Perugino, CA and Lähdesmäki, H and Stone, JH and Vlamakis, H and Chung, DC and Khanna, D and Pillai, S and Xavier, RJ}, title = {Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {35}, pmid = {33648559}, issn = {1756-994X}, support = {UM1 AI144295/NH/NIH HHS/United States ; U19 AI110495/AI/NIAID NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; UM1 AI110557/AI/NIAID NIH HHS/United States ; K24 AR063120/NH/NIH HHS/United States ; UM1 AI144295/AI/NIAID NIH HHS/United States ; K24 AR063120/AR/NIAMS NIH HHS/United States ; }, mesh = {Bacteroidetes/physiology ; Case-Control Studies ; Cohort Studies ; Extracellular Matrix/metabolism ; Fibrosis ; Firmicutes/physiology ; *Gastrointestinal Microbiome ; Humans ; Immunoglobulin G4-Related Disease/*microbiology ; Scleroderma, Systemic/*microbiology ; Signal Transduction ; Species Specificity ; }, abstract = {BACKGROUND: Immunoglobulin G4-related disease (IgG4-RD) and systemic sclerosis (SSc) are rare autoimmune diseases characterized by the presence of CD4+ cytotoxic T cells in the blood as well as inflammation and fibrosis in various organs, but they have no established etiologies. Similar to other autoimmune diseases, the gut microbiome might encode disease-triggering or disease-sustaining factors.

METHODS: The gut microbiomes from IgG4-RD and SSc patients as well as healthy individuals with no recent antibiotic treatment were studied by metagenomic sequencing of stool DNA. De novo assembly-based taxonomic and functional characterization, followed by association and accessory gene set enrichment analysis, were applied to describe microbiome changes associated with both diseases.

RESULTS: Microbiomes of IgG4-RD and SSc patients distinctly separated from those of healthy controls: numerous opportunistic pathogenic Clostridium and typically oral Streptococcus species were significantly overabundant, while Alistipes, Bacteroides, and butyrate-producing species were depleted in the two diseases compared to healthy controls. Accessory gene content analysis in these species revealed an enrichment of Th17-activating Eggerthella lenta strains in IgG4-RD and SSc and a preferential colonization of a homocysteine-producing strain of Clostridium bolteae in SSc. Overabundance of the classical mevalonate pathway, hydroxyproline dehydratase, and fibronectin-binding protein in disease microbiomes reflects potential functional differences in host immune recognition and extracellular matrix utilization associated with fibrosis. Strikingly, the majority of species that were differentially abundant in IgG4-RD and SSc compared to controls showed the same directionality in both diseases. Compared with multiple sclerosis and rheumatoid arthritis, the gut microbiomes of IgG4-RD and SSc showed similar signatures; in contrast, the most differentially abundant taxa were not the facultative anaerobes consistently identified in inflammatory bowel diseases, suggesting the microbial signatures of IgG4-RD and SSc do not result from mucosal inflammation and decreased anaerobism.

CONCLUSIONS: These results provide an initial characterization of gut microbiome ecology in fibrosis-prone IgG4-RD and SSc and reveal microbial functions that offer insights into the pathophysiology of these rare diseases.}, } @article {pmid33648263, year = {2021}, author = {Yang, Y and Wang, ST and Lu, ZM and Zhang, XJ and Chai, LJ and Shen, CH and Shi, JS and Xu, ZH}, title = {Metagenomics unveils microbial roles involved in metabolic network of flavor development in medium-temperature daqu starter.}, journal = {Food research international (Ottawa, Ont.)}, volume = {140}, number = {}, pages = {110037}, doi = {10.1016/j.foodres.2020.110037}, pmid = {33648263}, issn = {1873-7145}, mesh = {Alcoholic Beverages/analysis ; Metabolic Networks and Pathways ; *Metagenomics ; *Microbiota/genetics ; Temperature ; }, abstract = {As a widely used Asian starter culture, the quality of daqu can significantly affect the organoleptic characteristics of the final products, yet the microbial metabolic network involved in flavor development remains unclear. This study aims to investigate that network based on the dynamics of physicochemical properties, microbial community, and volatile compounds in medium-temperature daqu (MT-daqu) during spontaneous fermentation. Analyses using the metagenomic data set facilitated the gene repertoire overview of this ecosystem, indicating that Lactobacillales (mainly Weissella, Lactobacillus, and Pediococcus), Mucorales (mainly Lichtheimia), and Eurotiales (mainly Aspergillus, Rasamsonia and Byssochlamys) were the potential predominant populations successively responsible for the production of lytic enzymes and flavor precursors/compounds in MT-daqu. Flavor-relevant pathways were found to exist in multiple species, but only bacteria showed the potential to participate in butane-2,3-diol (e.g. Weissella, Lactobacillus, and Staphylococcus) and butanoate (Thermoactinomyces) metabolism, and only fungi were potentially involved in biosynthesis of guaiacol (Byssochlamys) and 4-vinylguaiacol (Aspergillus). Furthermore, a combined analysis revealed that the acidic thermal environment present in early phases was mainly due to the catabolic activities of Lactobacillales and Lichtheimia, which could contribute to the effective self-domestication of microbiota. The study helps elucidate the different metabolic roles of microorganisms and disclose the formation mechanism of daqu's partial functions, namely providing various aromatic substances/precursors and enzymes.}, } @article {pmid33648194, year = {2021}, author = {Hu, Y and Yang, Q and Chen, D and Fu, B and Zhang, Y and Zhang, Y and Xia, X and Peng, N and Liang, Y and Zhao, S}, title = {Study on microbial communities and higher alcohol formations in the fermentation of Chinese Xiaoqu Baijiu produced by traditional and new mechanical technologies.}, journal = {Food research international (Ottawa, Ont.)}, volume = {140}, number = {}, pages = {109876}, doi = {10.1016/j.foodres.2020.109876}, pmid = {33648194}, issn = {1873-7145}, mesh = {China ; Fermentation ; *Microbiota ; Pichia ; Rhizopus ; *Saccharomyces cerevisiae/genetics ; }, abstract = {Microorganisms play an important role in the flavor formation of Chinese Baijiu. Mechanization is the way to develop Baijiu. Therefore, it is necessary to study the effects of mechanization on microbial community and flavor in Baijiu production. The microbial communities exhibited differences between two technologies with the fermentation, and the numbers of yeasts and bacteria in new mechanical technology were significantly higher than those in traditional technology at the peak of fermentation. Both metagenomic and metatranscriptomic analyses showed 5 core microorganisms in the fermentation, namely Saccharomyces cerevisiae, Rhizopus delemar, Pichia kudriavzevii, Lactobacillus helveticus, and Rhizopus oryzae. S. cerevisiae was generally regarded to be the most dominant yeast in Baijiu fermentation, but our metatranscriptomic data showed that P. kudriavzevii was more active than S. cerevisiae. These two analyses indicated that higher initiation abundance of S. cerevisiae and P. kudriavzevii and lower initiation abundance of R. delemar and R. oryzae were observed in traditional technology than in new technology, and that Lactobacillus displayed apparent advantages in traditional technology, whereas Lactobacillus and yeast exhibited obvious advantages in new technology at the end of fermentation. In addition to S. cerevisiae, other microorganisms including non-saccharomyces yeasts, molds, and bacteria were involved in higher alcohol formation. This work provides insight into the microbial dynamics and higher alcohol formation, as well as an efficient strategy for process improvement in Baijiu fermentation.}, } @article {pmid33639859, year = {2021}, author = {Stevens, V and Thijs, S and Vangronsveld, J}, title = {Diversity and plant growth-promoting potential of (un)culturable bacteria in the Hedera helix phylloplane.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {66}, pmid = {33639859}, issn = {1471-2180}, support = {08M03VGRJ//Universiteit Hasselt Methusalem/ ; G0D0916N//Fonds Wetenschappelijk Onderzoek/ ; 1166918N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {Bacteria/*classification/*genetics/isolation & purification ; Biodegradation, Environmental ; Culture Media/chemistry ; Hedera/*growth & development/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Microbiota ; *Plant Development ; Plant Leaves/microbiology ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: A diverse community of microbes naturally exists on the phylloplane, the surface of leaves. It is one of the most prevalent microbial habitats on earth and bacteria are the most abundant members, living in communities that are highly dynamic. Today, one of the key challenges for microbiologists is to develop strategies to culture the vast diversity of microorganisms that have been detected in metagenomic surveys.

RESULTS: We isolated bacteria from the phylloplane of Hedera helix (common ivy), a widespread evergreen, using five growth media: Luria-Bertani (LB), LB01, yeast extract-mannitol (YMA), yeast extract-flour (YFlour), and YEx. We also included a comparison with the uncultured phylloplane, which we showed to be dominated by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Inter-sample (beta) diversity shifted from LB and LB01 containing the highest amount of resources to YEx, YMA, and YFlour which are more selective. All growth media equally favoured Actinobacteria and Gammaproteobacteria, whereas Bacteroidetes could only be found on LB01, YEx, and YMA. LB and LB01 favoured Firmicutes and YFlour was most selective for Betaproteobacteria. At the genus level, LB favoured the growth of Bacillus and Stenotrophomonas, while YFlour was most selective for Burkholderia and Curtobacterium. The in vitro plant growth promotion (PGP) profile of 200 isolates obtained in this study indicates that previously uncultured bacteria from the phylloplane may have potential applications in phytoremediation and other plant-based biotechnologies.

CONCLUSIONS: This study gives first insights into the total bacterial community of the H. helix phylloplane, including an evaluation of its culturability using five different growth media. We further provide a collection of 200 bacterial isolates underrepresented in current databases, including the characterization of PGP profiles. Here we highlight the potential of simple strategies to obtain higher microbial diversity from environmental samples and the use of high-throughput sequencing to guide isolate selection from a variety of growth media.}, } @article {pmid33639022, year = {2021}, author = {Říhová, J and Batani, G and Rodríguez-Ruano, SM and Martinů, J and Vácha, F and Nováková, E and Hypša, V}, title = {A new symbiotic lineage related to Neisseria and Snodgrassella arises from the dynamic and diverse microbiomes in sucking lice.}, journal = {Molecular ecology}, volume = {30}, number = {9}, pages = {2178-2196}, doi = {10.1111/mec.15866}, pmid = {33639022}, issn = {1365-294X}, mesh = {Animals ; *Anoplura ; *Microbiota/genetics ; Neisseria ; *Neisseriaceae ; Phylogeny ; Symbiosis ; }, abstract = {The phylogenetic diversity of symbiotic bacteria in sucking lice suggests that lice have a complex history of symbiont acquisition, loss, and replacement throughout their evolution. These processes have resulted in the establishment of different, phylogenetically distant bacteria as obligate mutualists in different louse groups. By combining metagenomics and amplicon screening across several populations of three louse species (members of the genera Polyplax and Hoplopleura) we describe a novel louse symbiont lineage related to Neisseria and Snodgrassella, and show its independent origin in the two louse genera. While the genomes of these symbionts are highly similar, their respective distributions and status within lice microbiomes indicate that they have different functions and history. In Hoplopleura acanthopus, the Neisseriaceae-related bacterium is a dominant obligate symbiont present across several host populations. In contrast, the Polyplax microbiomes are dominated by the obligate symbiont Legionella polyplacis, with the Neisseriaceae-related bacterium co-occurring only in some samples and with much lower abundance. The results thus support the view that compared to other exclusively blood feeding insects, Anoplura possess a unique capacity to acquire symbionts from diverse groups of bacteria.}, } @article {pmid33638901, year = {2021}, author = {Shah, AS and Wakelin, SA and Moot, DJ and Blond, C and Laugraud, A and Ridgway, HJ}, title = {Trifolium repens and T. subterraneum modify their nodule microbiome in response to soil pH.}, journal = {Journal of applied microbiology}, volume = {131}, number = {4}, pages = {1858-1869}, doi = {10.1111/jam.15050}, pmid = {33638901}, issn = {1365-2672}, support = {C10X1308//Ministry of Business, Innovation and Employment/ ; }, mesh = {Hydrogen-Ion Concentration ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Rhizobium ; Root Nodules, Plant ; Soil ; Symbiosis ; *Trifolium ; }, abstract = {AIMS: The influence of soil edaphic factors on recruitment and composition of bacteria in the legume nodule is unknown. Typically, low (acidic) pH soils have a negative effect on the plant-rhizobia symbiosis and thereby reduce clover growth. However, the specific relationship between soil pH and the ecology of rhizobia is unknown, in either their free-living or nodule-inhabiting states. We used New Zealand pasture systems with soils of different pH, and white (WC) and subterranean (SC) clovers, to examine the relationship between soil pH and the diversity of bacteria that inhabit the nodules.

METHODS AND RESULTS: Amplicon sequencing (16S rRNA) assessed the bacterial community in 5299 nodules recovered from both legume species grown in 47 soils of different edaphic (including pH) properties. Fewer nodules were formed on both clovers at low soil pH. As expected, rhizobia comprised ∼ 92% of the total reads in both clovers, however 28 non-rhizobia genera were also present. Soil pH influenced the community structure of bacteria within the nodule, and this was more evident in non-Rhizobium taxa than Rhizobium. Host strongly influenced the diversity of bacteria in the nodules. The alpha diversity of nodule microbiome in SC nodules was higher than in WC nodules and SC nodules also harbored a higher relative abundance of non-Rhizobium bacteria than WC. Beta diversity of Rhizobium and non-Rhizobium bacteria was influenced more by clover species rather than edaphic factors.

CONCLUSIONS: The results indicate that these clover species modified their nodule biomes in response to pH-stress.

The non-Rhizobium bacteria may have some functional significance (such as improved clover persistence in low pH soils) in legume nodules.}, } @article {pmid33637740, year = {2021}, author = {Goyal, A and Wang, T and Dubinkina, V and Maslov, S}, title = {Ecology-guided prediction of cross-feeding interactions in the human gut microbiome.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {1335}, pmid = {33637740}, issn = {2041-1723}, mesh = {Algorithms ; Computational Biology/methods ; *Ecology ; Gastrointestinal Microbiome/*genetics/*physiology ; Humans ; Intestines/*microbiology ; Machine Learning ; Metabolome ; Metabolomics ; Metagenomics ; Models, Biological ; }, abstract = {Understanding a complex microbial ecosystem such as the human gut microbiome requires information about both microbial species and the metabolites they produce and secrete. These metabolites are exchanged via a large network of cross-feeding interactions, and are crucial for predicting the functional state of the microbiome. However, till date, we only have information for a part of this network, limited by experimental throughput. Here, we propose an ecology-based computational method, GutCP, using which we predict hundreds of new experimentally untested cross-feeding interactions in the human gut microbiome. GutCP utilizes a mechanistic model of the gut microbiome with the explicit exchange of metabolites and their effects on the growth of microbial species. To build GutCP, we combine metagenomic and metabolomic measurements from the gut microbiome with optimization techniques from machine learning. Close to 65% of the cross-feeding interactions predicted by GutCP are supported by evidence from genome annotations, which we provide for experimental testing. Our method has the potential to greatly improve existing models of the human gut microbiome, as well as our ability to predict the metabolic profile of the gut.}, } @article {pmid33634824, year = {2022}, author = {Zhou, F and He, K and Li, Q and Chapkin, RS and Ni, Y}, title = {Bayesian biclustering for microbial metagenomic sequencing data via multinomial matrix factorization.}, journal = {Biostatistics (Oxford, England)}, volume = {23}, number = {3}, pages = {891-909}, pmid = {33634824}, issn = {1468-4357}, support = {R01 ES025713/ES/NIEHS NIH HHS/United States ; R35 CA197707/CA/NCI NIH HHS/United States ; R01 CA202697/CA/NCI NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Bayes Theorem ; *Gastrointestinal Microbiome/genetics ; Humans ; *Inflammatory Bowel Diseases/genetics ; *Microbiota/genetics ; }, abstract = {High-throughput sequencing technology provides unprecedented opportunities to quantitatively explore human gut microbiome and its relation to diseases. Microbiome data are compositional, sparse, noisy, and heterogeneous, which pose serious challenges for statistical modeling. We propose an identifiable Bayesian multinomial matrix factorization model to infer overlapping clusters on both microbes and hosts. The proposed method represents the observed over-dispersed zero-inflated count matrix as Dirichlet-multinomial mixtures on which latent cluster structures are built hierarchically. Under the Bayesian framework, the number of clusters is automatically determined and available information from a taxonomic rank tree of microbes is naturally incorporated, which greatly improves the interpretability of our findings. We demonstrate the utility of the proposed approach by comparing to alternative methods in simulations. An application to a human gut microbiome data set involving patients with inflammatory bowel disease reveals interesting clusters, which contain bacteria families Bacteroidaceae, Bifidobacteriaceae, Enterobacteriaceae, Fusobacteriaceae, Lachnospiraceae, Ruminococcaceae, Pasteurellaceae, and Porphyromonadaceae that are known to be related to the inflammatory bowel disease and its subtypes according to biological literature. Our findings can help generate potential hypotheses for future investigation of the heterogeneity of the human gut microbiome.}, } @article {pmid33634788, year = {2021}, author = {Marbouty, M and Thierry, A and Millot, GA and Koszul, R}, title = {MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {33634788}, issn = {2050-084X}, mesh = {Bacteria/genetics/*virology ; Gastrointestinal Microbiome/*genetics ; *Genome, Bacterial ; *Genome, Viral ; Humans ; *Metagenome ; Metagenomics ; Prophages/genetics/*physiology ; }, abstract = {Bacteriophages play important roles in regulating the intestinal human microbiota composition, dynamics, and homeostasis, and characterizing their bacterial hosts is needed to understand their impact. We applied a metagenomic Hi-C approach on 10 healthy human gut samples to unveil a large infection network encompassing more than 6000 interactions bridging a metagenomic assembled genomes (MAGs) and a phage sequence, allowing to study in situ phage-host ratio. Whereas three-quarters of these sequences likely correspond to dormant prophages, 5% exhibit a much higher coverage than their associated MAG, representing potentially actively replicating phages. We detected 17 sequences of members of the crAss-like phage family, whose hosts diversity remained until recently relatively elusive. For each of them, a unique bacterial host was identified, all belonging to different genus of Bacteroidetes. Therefore, metaHiC deciphers infection network of microbial population with a high specificity paving the way to dynamic analysis of mobile genetic elements in complex ecosystems.}, } @article {pmid33633264, year = {2021}, author = {Staley, C and Halaweish, H and Graiziger, C and Hamilton, MJ and Kabage, AJ and Galdys, AL and Vaughn, BP and Vantanasiri, K and Suryanarayanan, R and Sadowsky, MJ and Khoruts, A}, title = {Lower endoscopic delivery of freeze-dried intestinal microbiota results in more rapid and efficient engraftment than oral administration.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4519}, pmid = {33633264}, issn = {2045-2322}, mesh = {Aged ; Aged, 80 and over ; Biodiversity ; Clostridium Infections/*microbiology/*therapy ; Disease Management ; Disease Susceptibility ; Fecal Microbiota Transplantation/*methods ; Female ; Freeze Drying ; Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Transanal Endoscopic Microsurgery/*methods ; Treatment Outcome ; }, abstract = {Fecal microbiota transplantation (FMT) is a highly effective treatment for recurrent Clostridioides difficile infection (rCDI). However, standardization of FMT products is essential for its broad implementation into clinical practice. We have developed an oral preparation of freeze-dried, encapsulated microbiota, which is ~ 80% clinically effective, but results in delayed engraftment of donor bacteria relative to administration via colonoscopy. Our objective was to measure the engraftment potential of freeze-dried microbiota without the complexity of variables associated with oral administration. We compared engraftment of identical preparations and doses of freeze-dried microbiota following colonoscopic (9 patients) versus oral administration (18 patients). Microbiota were characterized by sequencing of the 16S rRNA gene, and engraftment was determined using the SourceTracker algorithm. Oligotyping analysis was done to provide high-resolution patterns of microbiota engraftment. Colonoscopic FMT was associated with greater levels of donor engraftment within days following the procedure (ANOVA P = 0.035) and specific increases in the relative abundances of donor Lachnospiraceae, Bacteroidaceae, and Porphyromonadaceae (P ≤ 0.033). Lower relative abundances of Bacteroidaceae, Lachnospiraceae, and Ruminococcaceae families were associated with clinical failures. These results suggest that further optimization of oral capsule FMT may improve its engraftment efficiency and clinical efficacy.}, } @article {pmid33633246, year = {2021}, author = {Kang, L and Li, P and Wang, D and Wang, T and Hao, D and Qu, X}, title = {Alterations in intestinal microbiota diversity, composition, and function in patients with sarcopenia.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4628}, pmid = {33633246}, issn = {2045-2322}, mesh = {*Biodiversity ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/genetics ; Sarcopenia/*microbiology/physiopathology ; }, abstract = {16S rRNA sequencing of human fecal samples has been tremendously successful in identifying microbiome changes associated with both aging and disease. A number of studies have described microbial alterations corresponding to physical frailty and nursing home residence among aging individuals. A gut-muscle axis through which the microbiome influences skeletal muscle growth/function has been hypothesized. However, the microbiome has yet to be examined in sarcopenia. Here, we collected fecal samples of 60 healthy controls (CON) and 27 sarcopenic (Case)/possibly sarcopenic (preCase) individuals and analyzed the intestinal microbiota using 16S rRNA sequencing. We observed an overall reduction in microbial diversity in Case and preCase samples. The genera Lachnospira, Fusicantenibacter, Roseburia, Eubacterium, and Lachnoclostridium-known butyrate producers-were significantly less abundant in Case and preCase subjects while Lactobacillus was more abundant. Functional pathways underrepresented in Case subjects included numerous transporters and phenylalanine, tyrosine, and tryptophan biosynthesis suggesting that protein processing and nutrient transport may be impaired. In contrast, lipopolysaccharide biosynthesis was overrepresented in Case and PreCase subjects suggesting that sarcopenia is associated with a pro-inflammatory metagenome. These analyses demonstrate structural and functional alterations in the intestinal microbiota that may contribute to loss of skeletal muscle mass and function in sarcopenia.}, } @article {pmid33633180, year = {2021}, author = {Mishima, Y and Osaki, T and Shimada, A and Kamiya, S and Hasegawa-Ishii, S}, title = {Sex-dependent differences in the gut microbiota following chronic nasal inflammation in adult mice.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4640}, pmid = {33633180}, issn = {2045-2322}, mesh = {Animals ; Chronic Disease ; Female ; *Gastrointestinal Microbiome ; Inflammation/*pathology ; Male ; Mice ; Nasal Mucosa/*pathology ; *Sex Factors ; }, abstract = {A growing body of evidence suggests a relationship between olfactory dysfunction and the pathogenesis of mental disorders. Our previous studies indicated that chronic nasal inflammation caused loss of olfactory sensory neurons and gross atrophy of the olfactory bulb, which may lead to olfactory dysfunction. Simultaneously, increasing numbers of reports have elucidated the importance of gut microbiota to maintain brain function and that dysbiosis may be associated with neuropsychiatric disorders. Here we examined whether chronic nasal inflammation perturbed gut microbiota and whether there were sex differences in this pattern. Eight-week-old C57BL/6 mice repeatedly received bilateral nasal administration of lipopolysaccharide (LPS) 3 times/week to cause chronic nasal inflammation or saline as a control. At 9 weeks, cecal feces were used for 16S metagenomic analysis and whole blood and fresh tissue of spleen were used for ELISA analyses. Microbiome analysis demonstrated a remarkable change of the gut microbiota in male mice with chronic nasal inflammation which was different from that in female mice. In both mice, systemic inflammation did not occur. This has shown for the first time that chronic nasal inflammation correlates with sex-dependent changes in the gut microbiota. The detailed mechanism and potential alteration to brain functions await further studies.}, } @article {pmid33633172, year = {2021}, author = {Carrieri, AP and Haiminen, N and Maudsley-Barton, S and Gardiner, LJ and Murphy, B and Mayes, AE and Paterson, S and Grimshaw, S and Winn, M and Shand, C and Hadjidoukas, P and Rowe, WPM and Hawkins, S and MacGuire-Flanagan, A and Tazzioli, J and Kenny, JG and Parida, L and Hoptroff, M and Pyzer-Knapp, EO}, title = {Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4565}, pmid = {33633172}, issn = {2045-2322}, mesh = {Adult ; Aged ; Female ; Humans ; Middle Aged ; Young Adult ; Aging ; *Artificial Intelligence ; *Biodiversity ; Computational Biology/methods ; Data Analysis ; Deep Learning ; Menopause ; Metagenome ; Metagenomics/methods ; *Microbiota ; *Phenotype ; *Skin/microbiology ; Smokers ; }, abstract = {Alterations in the human microbiome have been observed in a variety of conditions such as asthma, gingivitis, dermatitis and cancer, and much remains to be learned about the links between the microbiome and human health. The fusion of artificial intelligence with rich microbiome datasets can offer an improved understanding of the microbiome's role in human health. To gain actionable insights it is essential to consider both the predictive power and the transparency of the models by providing explanations for the predictions. We combine the collection of leg skin microbiome samples from two healthy cohorts of women with the application of an explainable artificial intelligence (EAI) approach that provides accurate predictions of phenotypes with explanations. The explanations are expressed in terms of variations in the relative abundance of key microbes that drive the predictions. We predict skin hydration, subject's age, pre/post-menopausal status and smoking status from the leg skin microbiome. The changes in microbial composition linked to skin hydration can accelerate the development of personalized treatments for healthy skin, while those associated with age may offer insights into the skin aging process. The leg microbiome signatures associated with smoking and menopausal status are consistent with previous findings from oral/respiratory tract microbiomes and vaginal/gut microbiomes respectively. This suggests that easily accessible microbiome samples could be used to investigate health-related phenotypes, offering potential for non-invasive diagnosis and condition monitoring. Our EAI approach sets the stage for new work focused on understanding the complex relationships between microbial communities and phenotypes. Our approach can be applied to predict any condition from microbiome samples and has the potential to accelerate the development of microbiome-based personalized therapeutics and non-invasive diagnostics.}, } @article {pmid33631428, year = {2021}, author = {Xu, Y and Cao, J and Jiang, L and Zhang, Y}, title = {Biogeographic and Evolutionary Patterns of Trace Element Utilization in Marine Microbial World.}, journal = {Genomics, proteomics & bioinformatics}, volume = {19}, number = {6}, pages = {958-972}, pmid = {33631428}, issn = {2210-3244}, mesh = {Copper ; *Metalloproteins/genetics ; *Microbiota ; Nickel/metabolism ; Seawater/microbiology ; Selenium/metabolism ; Selenoproteins/genetics ; *Trace Elements/metabolism ; Water Microbiology ; }, abstract = {Trace elements are required by all organisms, which are key components of many enzymes catalyzing important biological reactions. Many trace element-dependent proteins have been characterized; however, little is known about their occurrence in microbial communities in diverse environments, especially the global marine ecosystem. Moreover, the relationships between trace element utilization and different types of environmental stressors are unclear. In this study, we used metagenomic data from the Global Ocean Sampling expedition project to identify the biogeographic distribution of genes encoding trace element-dependent proteins (for copper, molybdenum, cobalt, nickel, and selenium) in a variety of marine and non-marine aquatic samples. More than 56,000 metalloprotein and selenoprotein genes corresponding to nearly 100 families were predicted, becoming the largest dataset of marine metalloprotein and selenoprotein genes reported to date. In addition, samples with enriched or depleted metalloprotein/selenoprotein genes were identified, suggesting an active or inactive usage of these micronutrients in various sites. Further analysis of interactions among the elements showed significant correlations between some of them, especially those between nickel and selenium/copper. Finally, investigation of the relationships between environmental conditions and metalloprotein/selenoprotein families revealed that many environmental factors might contribute to the evolution of different metalloprotein and/or selenoprotein genes in the marine microbial world. Our data provide new insights into the utilization and biological roles of these trace elements in extant marine microbes, and might also be helpful for the understanding of how these organisms have adapted to their local environments.}, } @article {pmid33629506, year = {2021}, author = {Benítez-Páez, A and Hess, AL and Krautbauer, S and Liebisch, G and Christensen, L and Hjorth, MF and Larsen, TM and Sanz, Y and , }, title = {Sex, Food, and the Gut Microbiota: Disparate Response to Caloric Restriction Diet with Fiber Supplementation in Women and Men.}, journal = {Molecular nutrition & food research}, volume = {65}, number = {8}, pages = {e2000996}, doi = {10.1002/mnfr.202000996}, pmid = {33629506}, issn = {1613-4133}, mesh = {Bacteroidetes ; Bile Acids and Salts/metabolism ; Biomarkers ; *Caloric Restriction ; Dietary Fiber/*pharmacology ; Dietary Supplements ; Fatty Acids, Volatile/blood/metabolism ; Feces/chemistry/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Middle Aged ; Multivariate Analysis ; Sex Factors ; Weight Loss ; }, abstract = {SCOPE: Dietary-based strategies are regularly explored in controlled clinical trials to provide cost-effective therapies to tackle obesity and its comorbidities. The article presents a complementary analysis based on a multivariate multi-omics approach of a caloric restriction intervention (CRD) with fiber supplementation to unveil synergic effects on body weight control, lipid metabolism, and gut microbiota.

METHODS AND RESULTS: The study explores fecal bile acids (BAs) and short-chain fatty acids (SCFAs), plasma BAs, and fecal shotgun metagenomics on 80 overweight participants of a 12-week caloric restriction clinical trial (-500 kcal day[-1]) randomly allocated into fiber (10 g day[-1] inulin + 10 g day[-1] resistant maltodextrin) or placebo (maltodextrin) supplementation groups. The multi-omic data integration analysis uncovered the benefits of the fiber supplementation and/or the CRD (e.g., increase of Parabacteroides distasonis and fecal propionate), showing sex-specific effects on either adiposity and fasting insulin; effects thought to be linked to changes of specific gut microbiota species, functional genes, and bacterially produced metabolites like SCFAs and secondary BAs.

CONCLUSIONS: This study identifies diet-microbe-host interactions helping to design personalised interventions. It also suggests that sex perspective should be considered routinely in future studies on dietary interventions efficacy. All in all, the study uncovers that the dietary intervention is more beneficial for women than men.}, } @article {pmid33627510, year = {2021}, author = {Zhu, J and Ren, H and Zhong, H and Li, X and Zou, Y and Han, M and Li, M and Madsen, L and Kristiansen, K and Xiao, L}, title = {An Expanded Gene Catalog of Mouse Gut Metagenomes.}, journal = {mSphere}, volume = {6}, number = {1}, pages = {}, pmid = {33627510}, issn = {2379-5042}, mesh = {Animals ; Bacteria/classification/*genetics/isolation & purification ; Computational Biology/methods ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; *Genome, Bacterial ; Male ; *Metagenome ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Phylogeny ; }, abstract = {High-quality and comprehensive reference gene catalogs are essential for metagenomic research. The rather low diversity of samples used to construct existing catalogs of the mouse gut metagenome limits the numbers of identified genes in existing catalogs. We therefore established an expanded catalog of genes in the mouse gut metagenome (EMGC) containing >5.8 million genes by integrating 88 newly sequenced samples, 86 mouse gut-related bacterial genomes, and 3 existing gene catalogs. EMGC increases the number of nonredundant genes by more than 1 million genes compared to the so-far most extensive catalog. More than 60% of the genes in EMGC were assigned to Bacteria, with 54.20% being assigned to a phylum and 35.33% to a genus, while 30.39% were annotated at the KEGG orthology level. Nine hundred two metagenomic species (MGS) assigned to 122 taxa are identified based on the EMGC. The EMGC-based analysis of samples from groups of mice originating from different animal providers, housing laboratories, and genetic strains substantiated that diet is a major contributor to differences in composition and functional potential of the gut microbiota irrespective of differences in environment and genetic background. We envisage that EMGC will serve as a valuable reference data set for future metagenomic studies in mice.IMPORTANCE We established an expanded gene catalog of the mouse gut metagenome not only to increase the sample size compared to that in existing catalogs but also to provide a more comprehensive reference data set of the mouse gut microbiome for bioinformatic analysis. The expanded gene catalog comprises more than 5.8 million unique genes, as well as a wide range of taxonomic and functional information. Particularly, the analysis of metagenomic species with the expanded gene catalog reveals a great novelty of mouse gut-inhabiting microbial species. We envisage that the expanded gene catalog of the mouse gut metagenome will serve as a valuable bioinformatic resource for future gut metagenomic studies in mice.}, } @article {pmid33624268, year = {2021}, author = {Moon, K and Cho, JC}, title = {Metaviromics coupled with phage-host identification to open the viral 'black box'.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {59}, number = {3}, pages = {311-323}, pmid = {33624268}, issn = {1976-3794}, mesh = {Bacteria/genetics/*virology ; Bacteriophages/classification/*genetics/isolation & purification/physiology ; Genome, Viral ; *Virome ; Virus Physiological Phenomena ; Viruses/classification/*genetics/isolation & purification ; }, abstract = {Viruses are found in almost all biomes on Earth, with bacteriophages (phages) accounting for the majority of viral particles in most ecosystems. Phages have been isolated from natural environments using the plaque assay and liquid medium-based dilution culturing. However, phage cultivation is restricted by the current limitations in the number of culturable bacterial strains. Unlike prokaryotes, which possess universally conserved 16S rRNA genes, phages lack universal marker genes for viral taxonomy, thus restricting cultureindependent analyses of viral diversity. To circumvent these limitations, shotgun viral metagenome sequencing (i.e., metaviromics) has been developed to enable the extensive sequencing of a variety of viral particles present in the environment and is now widely used. Using metaviromics, numerous studies on viral communities have been conducted in oceans, lakes, rivers, and soils, resulting in many novel phage sequences. Furthermore, auxiliary metabolic genes such as ammonic monooxygenase C and β-lactamase have been discovered in viral contigs assembled from viral metagenomes. Current attempts to identify putative bacterial hosts of viral metagenome sequences based on sequence homology have been limited due to viral sequence variations. Therefore, culture-independent approaches have been developed to predict bacterial hosts using single-cell genomics and fluorescentlabeling. This review focuses on recent viral metagenome studies conducted in natural environments, especially in aquatic ecosystems, and their contributions to phage ecology. Here, we concluded that although metaviromics is a key tool for the study of viral ecology, this approach must be supplemented with phage-host identification, which in turn requires the cultivation of phage-bacteria systems.}, } @article {pmid33624266, year = {2021}, author = {Whon, TW and Shin, NR and Kim, JY and Roh, SW}, title = {Omics in gut microbiome analysis.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {59}, number = {3}, pages = {292-297}, pmid = {33624266}, issn = {1976-3794}, mesh = {Animals ; Bacteria/classification/*genetics/isolation & purification ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Humans ; Metagenome ; Metagenomics ; }, abstract = {Our understanding of the interactions between microbial communities and their niche in the host gut has improved owing to recent advances in environmental microbial genomics. Integration of metagenomic and metataxonomic sequencing data with other omics data to study the gut microbiome has become increasingly common, but downstream analysis after data integration and interpretation of complex omics data remain challenging. Here, we review studies that have explored the gut microbiome signature using omics approaches, including metagenomics, metataxonomics, metatranscriptomics, and metabolomics. We further discuss recent analytics programs to analyze and integrate multi-omics datasets and further utilization of omics data with other advanced techniques, such as adaptive immune receptor repertoire sequencing, microbial culturomics, and machine learning, to evaluate important microbiome characteristics in the gut.}, } @article {pmid33623780, year = {2021}, author = {Alzahrani, FM and Al-Amri, A and Shaikh, SS and Muzaheed, and Alomar, AI and Acharya, S and Aldossary, MA and Hassan, FM}, title = {Direct DNA Sequencing-Based Analysis of Microbiota Associated with Hematological Malignancies in the Eastern Province of Saudi Arabia.}, journal = {BioMed research international}, volume = {2021}, number = {}, pages = {4202019}, pmid = {33623780}, issn = {2314-6141}, mesh = {Adolescent ; Adult ; Aged ; *Bacteremia/complications/diagnosis/epidemiology/microbiology ; Bacteria/classification/genetics ; Coinfection/complications/diagnosis/epidemiology/microbiology ; DNA, Bacterial/analysis/genetics ; Female ; Hematologic Neoplasms/*complications ; Humans ; Male ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/genetics ; Middle Aged ; Molecular Diagnostic Techniques/*methods ; Saudi Arabia ; Sequence Analysis, DNA/*methods ; Young Adult ; }, abstract = {INTRODUCTION: Bloodstream infections (BSI) among patients with hematological malignancies (HM) could predispose them to higher morbidity and mortality for various underlying conditions. Several microorganisms, either pathogenic or opportunistic normal human flora, could cause severe bacteremia and septicemia. While conventional methods have their own limitations, molecular methods such as next-generation sequencing (NGS) can detect these blood infections with more reliability, specificity, and sensitivity, in addition to information on microbial population landscape. Methodology. Blood samples from HM patients (n = 50) and volunteer blood donor control individuals with no HM (n = 50) were subjected to 16S rRNA gene amplification using standard PCR protocols. A metagenomic library was prepared, and NGS was run on a MiSeq (Illumina) sequencer. Sequence reads were analyzed using MiSeq Reporter, and microbial taxa were aligned using the Green Genes library.

RESULTS: 82% of the patients showed BSI with Gram-negative bacteria as the most predominant group. E. coli comprised a major chunk of the bacterial population (19.51%), followed by K. pneumoniae (17.07%). The CoNS and Viridans Streptococci groups are 17.07% and 14.63%, respectively. Other major species were S. aureus (9.75%), P. aeruginosa (7.31%), A. baumannii (4.87%), E. cloacae (4.87%), and P. mirabilis (4.87%). 34.14% of the cases among patients showed a Gram-positive infection, while 14.63% showed polymicrobial infections.

CONCLUSION: Most of the BSI in patients were characterized by polymicrobial infections, unlike the control samples. Molecular methods like NGS showed robust, fast, and specific identification of infectious agents in BSI in HM, indicating the possibility of its application in routine follow-up of such patients for infections.}, } @article {pmid33623056, year = {2021}, author = {Berland, M and Cadiou, J and Levenez, F and Galleron, N and Quinquis, B and Thirion, F and Gauthier, F and Le Chatelier, E and Plaza Oñate, F and Schwintner, C and Rabot, S and Lepage, P and Ehrlich, D and Doré, J and Juste, C}, title = {High engraftment capacity of frozen ready-to-use human fecal microbiota transplants assessed in germ-free mice.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4365}, pmid = {33623056}, issn = {2045-2322}, mesh = {Animals ; Cryopreservation/methods ; Fecal Microbiota Transplantation/*methods ; *Gastrointestinal Microbiome ; Germ-Free Life ; Humans ; Male ; Metagenomics/methods ; Mice ; Mice, Inbred C57BL ; }, abstract = {The number of indications for fecal microbiota transplantation is expected to rise, thus increasing the needs for production of readily available frozen or freeze-dried transplants. Using shotgun metagenomics, we investigated the capacity of two novel human fecal microbiota transplants prepared in maltodextrin-trehalose solutions (abbreviated MD and TR for maltodextrin:trehalose, 3:1, w/w, and trehalose:maltodextrin 3:1, w/w, respectively), to colonize a germ-free born mouse model. Gavage with frozen-thawed MD or TR suspensions gave the taxonomic profiles of mouse feces that best resembled those obtained with the fresh inoculum (Spearman correlations based on relative abundances of metagenomic species around 0.80 and 0.75 for MD and TR respectively), while engraftment capacity of defrosted NaCl transplants most diverged (Spearman correlations around 0.63). Engraftment of members of the family Lachnospiraceae and Ruminoccocaceae was the most challenging in all groups of mice, being improved with MD and TR transplants compared to NaCl, but still lower than with the fresh preparation. Improvement of engraftment of this important group in maintaining health represents a challenge that could benefit from further research on fecal microbiota transplant manufacturing.}, } @article {pmid33622394, year = {2021}, author = {Petruschke, H and Schori, C and Canzler, S and Riesbeck, S and Poehlein, A and Daniel, R and Frei, D and Segessemann, T and Zimmerman, J and Marinos, G and Kaleta, C and Jehmlich, N and Ahrens, CH and von Bergen, M}, title = {Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {55}, pmid = {33622394}, issn = {2049-2618}, mesh = {Bacteria/classification/genetics/isolation & purification/metabolism ; Bacterial Proteins/*analysis/*chemistry/genetics ; *Cell Communication ; *Gastrointestinal Microbiome/genetics ; Humans ; Intestines/chemistry/microbiology ; Metagenome/genetics ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities.

RESULTS: We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx.

CONCLUSIONS: We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract. Video abstract.}, } @article {pmid33620469, year = {2021}, author = {You, HS and Lee, SH and Lee, YJ and Sung, HJ and Kang, HG and Hyun, SH}, title = {Microbial analyses of blood spot surfaces collected from a laboratory and the bathroom of a female single-person household under different environmental conditions.}, journal = {FEMS microbiology letters}, volume = {368}, number = {5}, pages = {}, doi = {10.1093/femsle/fnab023}, pmid = {33620469}, issn = {1574-6968}, mesh = {Adult ; Bacteria/*classification/growth & development/*isolation & purification ; Blood/*microbiology ; Female ; Forensic Medicine/methods ; Genome, Bacterial/genetics ; Humans ; Microbiota/*genetics ; Toilet Facilities ; Whole Genome Sequencing ; }, abstract = {Many people spend most of their time indoors, thereby exposing themselves to indoor environmental microbial communities that might interact with the human microbiota. These potential interactions have only been considered for personal identification; however, accumulating evidence indicates that these microbial interactions are potentially implicated with the identification of human interactions and location-specific factors including time and seasonal variations in the microbial community. To augment the potential of metagenomics-based forensic tools, we compared the composition of microbial communities in blood spot surfaces from healthy adults placed in different environments, such as in the bathroom of a female single-person household and on a laboratory, which were sampled across seasons and time points. The laboratory samples showed more changes in the bacterial community over time owing to the higher number of individuals using the laboratory, whereas the microbial communities in the bathroom samples remained relatively stable over time. Moreover, the two locations could be distinguished according to their specific bacterial community compositions. Variations were also observed related to changes in temperature and humidity, allowing for prediction of season-based microbial community. These findings offer a new perspective regarding the use of microbial community analysis in forensic science.}, } @article {pmid33619330, year = {2021}, author = {Bessey, C and Neil Jarman, S and Simpson, T and Miller, H and Stewart, T and Kenneth Keesing, J and Berry, O}, title = {Passive eDNA collection enhances aquatic biodiversity analysis.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {236}, pmid = {33619330}, issn = {2399-3642}, mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Environmental/*isolation & purification ; *Environmental Monitoring/instrumentation ; Fishes/classification/*genetics ; Membranes, Artificial ; *Metagenome ; *Metagenomics ; Oceans and Seas ; Phylogeny ; }, abstract = {Environmental DNA (eDNA) metabarcoding is a sensitive and widely used approach for species detection and biodiversity assessment. The most common eDNA collection method in aquatic systems is actively filtering water through a membrane, which is time consuming and requires specialized equipment. Ecological studies investigating species abundance or distribution often require more samples than can be practically collected with current filtration methods. Here we demonstrate how eDNA can be passively collected in both tropical and temperate marine systems by directly submerging filter membranes (positively charged nylon and non-charged cellulose ester) in the water column. Using a universal fish metabarcoding assay, we show that passive eDNA collection can detect fish as effectively as active eDNA filtration methods in temperate systems and can also provide similar estimates of total fish biodiversity. Furthermore, passive eDNA collection enables greater levels of biological sampling, which increases the range of ecological questions that eDNA metabarcoding can address.}, } @article {pmid33619320, year = {2021}, author = {Sims, TT and El Alam, MB and Karpinets, TV and Dorta-Estremera, S and Hegde, VL and Nookala, S and Yoshida-Court, K and Wu, X and Biegert, GWG and Delgado Medrano, AY and Solley, T and Ahmed-Kaddar, M and Chapman, BV and Sastry, KJ and Mezzari, MP and Petrosino, JF and Lin, LL and Ramondetta, L and Jhingran, A and Schmeler, KM and Ajami, NJ and Wargo, J and Colbert, LE and Klopp, AH}, title = {Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {237}, pmid = {33619320}, issn = {2399-3642}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; T32 CA101642/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Antigens, CD/metabolism ; Antigens, Differentiation, T-Lymphocyte/metabolism ; CD4-Positive T-Lymphocytes/immunology/metabolism ; *Chemoradiotherapy/adverse effects/mortality ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestines/*microbiology ; Ki-67 Antigen/metabolism ; Lectins, C-Type/metabolism ; Lymphocytes, Tumor-Infiltrating/immunology/metabolism ; Middle Aged ; Prospective Studies ; Time Factors ; Treatment Outcome ; Tumor Microenvironment ; Uterine Cervical Neoplasms/immunology/microbiology/mortality/*therapy ; }, abstract = {Diversity of the gut microbiome is associated with higher response rates for cancer patients receiving immunotherapy but has not been investigated in patients receiving radiation therapy. Additionally, current studies investigating the gut microbiome and outcomes in cancer patients may not have adjusted for established risk factors. Here, we sought to determine if diversity and composition of the gut microbiome was independently associated with survival in cervical cancer patients receiving chemoradiation. Our study demonstrates that the diversity of gut microbiota is associated with a favorable response to chemoradiation. Additionally, compositional variation among patients correlated with short term and long-term survival. Short term survivor fecal samples were significantly enriched in Porphyromonas, Porphyromonadaceae, and Dialister, whereas long term survivor samples were significantly enriched in Escherichia Shigella, Enterobacteriaceae, and Enterobacteriales. Moreover, analysis of immune cells from cervical tumor brush samples by flow cytometry revealed that patients with a high microbiome diversity had increased tumor infiltration of CD4+ lymphocytes as well as activated subsets of CD4 cells expressing ki67+ and CD69+ over the course of radiation therapy. Modulation of the gut microbiota before chemoradiation might provide an alternative way to enhance treatment efficacy and improve treatment outcomes in cervical cancer patients.}, } @article {pmid33619300, year = {2021}, author = {Reed, KJ and Kunz, IGZ and Scare, JA and Nielsen, MK and Turk, PJ and Coleman, RJ and Coleman, SJ}, title = {The pelvic flexure separates distinct microbial communities in the equine hindgut.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4332}, pmid = {33619300}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; *Gastrointestinal Microbiome ; *Horses ; *Intestine, Large ; Metagenome ; Metagenomics/methods ; Pelvis/*anatomy & histology ; }, abstract = {As hindgut fermenters, horses are especially dependent on the microbiota residing in their cecum and large intestines. Interactions between these microbial populations and the horse are critical for maintaining gut homeostasis, which supports proper digestion. The current project was motivated to determine if any features of the fecal microbiota are informative of the microbial communities from the cecum, ventral colon, or dorsal colon. Digesta from the cecum, ventral colon, dorsal colon and feces were collected from 6 yearling miniature horses. Microbial DNA was isolated and the microbiota from each sample was characterized by profiling the V4 region of the 16S rRNA. Principal coordinate analysis of the beta diversity results revealed significant (p = 0.0001; F = 5.2393) similarities between the microbial populations from cecal and ventral colon and the dorsal colon and fecal samples, however, there was little overlap between the proximal and distal ends of the hindgut. These distinct population structures observed in our results coincide with the pelvic flexure, which itself separates intestinal compartments with distinct roles in digestive physiology. An indicator species analysis confirmed the population differences, supported by the identification of several microbial families characteristic of the compartments upstream of the pelvic flexure that were not represented following it. Our data suggest that the fecal microbiota is not informative of the proximal hindgut but can provide insight into communities of the distal compartments. Further, our results suggest that the pelvic flexure might be an important anatomical landmark relative to the microbial communities in the equine large intestine.}, } @article {pmid33618119, year = {2021}, author = {Pu, Y and Pan, J and Yao, Y and Ngan, WY and Yang, Y and Li, M and Habimana, O}, title = {Ecotoxicological effects of erythromycin on a multispecies biofilm model, revealed by metagenomic and metabolomic approaches.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {276}, number = {}, pages = {116737}, doi = {10.1016/j.envpol.2021.116737}, pmid = {33618119}, issn = {1873-6424}, mesh = {Biofilms ; *Erythromycin/toxicity ; Metabolomics ; Metagenome ; *Microbiota ; }, abstract = {The presence of antibiotics such as erythromycin, even in trace amounts, has long been acknowledged for negatively impacting ecosystems in freshwater environments. Although many studies have focused on the impact of antibiotic pollution at a macroecological level, the impact of erythromycin on microecosystems, such as freshwater biofilms, is still not fully understood. This knowledge gap may be attributed to the lack of robust multispecies biofilm models for fundamental investigations. Here, we used a lab-cultured multispecies biofilm model to elucidate the holistic response of a microbial community to erythromycin exposure using metagenomic and metabolomic approaches. Metagenomic analyses revealed that biofilm microbial diversity did not alter following erythromycin exposure. Notably, certain predicted metabolic pathways such as cell-cell communication pathways, amino acid metabolism, and peptidoglycan biosynthesis, mainly by the phyla Actinobacteria, Alpha/Beta-proteobacteria, Bacteroidetes, and Verrucomicrobia, were found to be involved in the maintenance of homeostasis-like balance in the freshwater biofilm. Further untargeted metabolomics data highlighted changes in lipid metabolism and linoleic acid metabolism and their related molecules as a direct consequence of erythromycin exposure. Overall, the study presented a unique picture of how multispecies biofilms respond to single environmental stress exposures. Moreover, the study demonstrated the feasibility of using lab simulated multispecies biofilms for investigating their interaction and reactivity of specific bioactive compounds or pollutants at a fundamental level.}, } @article {pmid33615652, year = {2021}, author = {Mancabelli, L and Tarracchini, C and Milani, C and Lugli, GA and Fontana, F and Turroni, F and van Sinderen, D and Ventura, M}, title = {Vaginotypes of the human vaginal microbiome.}, journal = {Environmental microbiology}, volume = {23}, number = {3}, pages = {1780-1792}, doi = {10.1111/1462-2920.15441}, pmid = {33615652}, issn = {1462-2920}, mesh = {Female ; Humans ; Lactobacillus/genetics ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Vagina ; }, abstract = {The human vaginal environment harbours a community of bacteria that plays an important role in maintaining vaginal health and in protecting this environment from various urogenital infections. This bacterial population, also known as vaginal microbiota, has been demonstrated to be dominated by members of the Lactobacillus genus. Several studies employing 16S rRNA gene-based amplicon sequencing have classified the vaginal microbiota into five distinct community state types (CSTs) or vaginotypes. To deepen our understanding of the vaginal microbiota we performed an in-depth meta-analysis of 1312 publicly available datasets concerning healthy vaginal microbiome information obtained by metagenomics sequencing. The analysis confirmed the predominance of taxa belonging to the Lactobacillus genus, followed by members of the genera Gardnerella, Vibrio and Atopobium. Moreover, the statistical robustness offered by this meta-analysis allowed us to disentangle the species-level composition of dominant and accessory taxa constituting each vaginotype and to revisit and refine the previously proposed CST classification. In addition, a functional characterization of the metagenomic datasets revealed particular genetic features associated with each assigned vaginotype.}, } @article {pmid33612831, year = {2021}, author = {Santos-Medellin, C and Zinke, LA and Ter Horst, AM and Gelardi, DL and Parikh, SJ and Emerson, JB}, title = {Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities.}, journal = {The ISME journal}, volume = {15}, number = {7}, pages = {1956-1970}, pmid = {33612831}, issn = {1751-7370}, support = {S10 OD010786/OD/NIH HHS/United States ; }, mesh = {*Metagenome ; Rhizosphere ; *Soil ; Soil Microbiology ; Virome ; }, abstract = {Viruses are abundant yet understudied members of soil environments that influence terrestrial biogeochemical cycles. Here, we characterized the dsDNA viral diversity in biochar-amended agricultural soils at the preplanting and harvesting stages of a tomato growing season via paired total metagenomes and viral size fraction metagenomes (viromes). Size fractionation prior to DNA extraction reduced sources of nonviral DNA in viromes, enabling the recovery of a vaster richness of viral populations (vOTUs), greater viral taxonomic diversity, broader range of predicted hosts, and better access to the rare virosphere, relative to total metagenomes, which tended to recover only the most persistent and abundant vOTUs. Of 2961 detected vOTUs, 2684 were recovered exclusively from viromes, while only three were recovered from total metagenomes alone. Both viral and microbial communities differed significantly over time, suggesting a coupled response to rhizosphere recruitment processes and/or nitrogen amendments. Viral communities alone were also structured along an 18 m spatial gradient. Overall, our results highlight the utility of soil viromics and reveal similarities between viral and microbial community dynamics throughout the tomato growing season yet suggest a partial decoupling of the processes driving their spatial distributions, potentially due to differences in dispersal, decay rates, and/or sensitivities to soil heterogeneity.}, } @article {pmid33612553, year = {2022}, author = {Kato-Kogoe, N and Sakaguchi, S and Kamiya, K and Omori, M and Gu, YH and Ito, Y and Nakamura, S and Nakano, T and Tamaki, J and Ueno, T and Hoshiga, M}, title = {Characterization of Salivary Microbiota in Patients with Atherosclerotic Cardiovascular Disease: A Case-Control Study.}, journal = {Journal of atherosclerosis and thrombosis}, volume = {29}, number = {3}, pages = {403-421}, pmid = {33612553}, issn = {1880-3873}, mesh = {Aged ; Aged, 80 and over ; Atherosclerosis/*microbiology ; Bacteria/*isolation & purification ; Biomarkers/metabolism ; Cardiovascular Diseases/*microbiology ; Case-Control Studies ; Female ; Humans ; Male ; *Microbiota ; Middle Aged ; Saliva/*microbiology ; }, abstract = {AIMS: Oral bacteria have been reported to be associated with the pathogenesis of atherosclerosis; however, the relationship between the oral microbiota and atherosclerosis remains unclear. The present study aimed to investigate whether or not salivary microbiota of patients with atherosclerotic cardiovascular disease (ACVD) differs from that of subjects without ACVD, and to characterize the salivary microbiota of patients with ACVD.

METHODS: This study included 43 patients with ACVD and 86 age- and sex-matched non-ACVD individuals. 16S rRNA metagenomic analysis were performed using DNA isolated from the saliva samples of the participants. To select unique operational taxonomic unit (OTU) sets of ACVD, we conducted the random forest algorithm in machine learning, followed by confirmation via 10-fold cross-validation Results: There was no difference in richness or evenness between the ACVD and non-ACVD groups (alpha diversity; observed OTU index, p=0.503; Shannon's index, p=0.478). However, significant differences were found in the overall salivary microbiota structure (beta diversity; unweighted UniFrac distances, p=0.001; weighted UniFrac distances, p=0.001). The Actinobacteria phylum was highly abundant in patients with ACVD, while the Bacteroidetes phylum was less abundant. The random forest classifier identified 43 OTUs as an optimal marker set of ACVD. In a 10-fold cross validation using the validation data, an area under the curve (AUC) of 0.933 (95% CI, 0.855-1.000) was obtained.

CONCLUSIONS: The salivary microbiota in patients with ACVD was distinct from that of non-ACVD individuals, indicating that the salivary microbiota may be related to ACVD.}, } @article {pmid33610769, year = {2021}, author = {Ghosh, S and Whitley, CS and Haribabu, B and Jala, VR}, title = {Regulation of Intestinal Barrier Function by Microbial Metabolites.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {11}, number = {5}, pages = {1463-1482}, pmid = {33610769}, issn = {2352-345X}, support = {P30 ES030283/ES/NIEHS NIH HHS/United States ; R21 CA216090/CA/NCI NIH HHS/United States ; P20 GM125504/GM/NIGMS NIH HHS/United States ; T32 AI132146/AI/NIAID NIH HHS/United States ; R21 CA191683/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Cell Membrane Permeability ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/*microbiology/*physiology ; *Metabolome ; }, abstract = {The human gastrointestinal tract (GI) harbors a diverse population of microbial life that continually shapes host pathophysiological responses. Despite readily available abundant metagenomic data, the functional dynamics of gut microbiota remain to be explored in various health and disease conditions. Microbiota generate a variety of metabolites from dietary products that influence host health and pathophysiological functions. Since gut microbial metabolites are produced in close proximity to gut epithelium, presumably they have significant impact on gut barrier function and immune responses. The goal of this review is to discuss recent advances on gut microbial metabolites in the regulation of intestinal barrier function. While the mechanisms of action of these metabolites are only beginning to emerge, they mainly point to a small group of shared pathways that control gut barrier functions. Amidst expanding technology and broadening knowledge, exploitation of beneficial microbiota and their metabolites to restore pathophysiological balance will likely prove to be an extremely useful remedial tool.}, } @article {pmid33609707, year = {2021}, author = {Psonis, N and Antoniou, A and Karameta, E and Darriba, D and Stamatakis, A and Lymberakis, P and Poulakakis, N}, title = {The wall lizards of the Balkan peninsula: Tackling questions at the interface of phylogenomics and population genomics.}, journal = {Molecular phylogenetics and evolution}, volume = {159}, number = {}, pages = {107121}, doi = {10.1016/j.ympev.2021.107121}, pmid = {33609707}, issn = {1095-9513}, mesh = {Animals ; Balkan Peninsula ; DNA, Mitochondrial/genetics ; *Genetic Speciation ; *Genetics, Population ; Genomics ; Lizards/*classification ; Metagenomics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Wall lizards of the genus Podarcis (Sauria, Lacertidae) are the predominant reptile group in southern Europe, including 24 recognized species. Mitochondrial DNA data have shown that, with the exception of P. muralis, the Podarcis species distributed in the Balkan peninsula form a species group that is further sub-divided into two subgroups: the one of "P. tauricus" consisting of P. tauricus, P. milensis, P. gaigeae, and P. melisellensis, and the other of "P. erhardii" comprising P. erhardii, P. levendis, P. cretensis, and P. peloponnesiacus. In an attempt to explore the Balkan Podarcis phylogenomic relationships, assess the levels of genetic structure and to re-evaluate the number of extant species, we employed phylogenomic and admixture approaches on ddRADseq (double digested Restriction site Associated DNA sequencing) genomic data. With this efficient Next Generation Sequencing approach, we were able to obtain a large number of genomic loci randomly distributed throughout the genome and use them to resolve the previously obscure phylogenetic relationships among the different Podarcis species distributed in the Balkans. The obtained phylogenomic relationships support the monophyly of both aforementioned subgroups and revealed several divergent lineages within each subgroup, stressing the need for taxonomic re-evaluation of Podarcis' species in Balkans. The phylogenomic trees and the species delimitation analyses confirmed all recently recognized species (P. levendis, P. cretensis, and P. ionicus) and showed the presence of at least two more species, one in P. erhardii and the other in P. peloponnesiacus.}, } @article {pmid33609137, year = {2021}, author = {Neal, AL and McLaren, T and Lourenço Campolino, M and Hughes, D and Marcos Coelho, A and Gomes de Paula Lana, U and Aparecida Gomes, E and Morais de Sousa, S}, title = {Crop type exerts greater influence upon rhizosphere phosphohydrolase gene abundance and phylogenetic diversity than phosphorus fertilization.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {4}, pages = {}, doi = {10.1093/femsec/fiab033}, pmid = {33609137}, issn = {1574-6941}, support = {BBS/E/C/000I0310/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Brazil ; Fertilization ; Phosphoric Monoester Hydrolases ; *Phosphorus ; Phylogeny ; *Rhizosphere ; Soil ; Soil Microbiology ; }, abstract = {Rock phosphate is an alternative form of phosphorus (P) fertilizer; however, there is no information regarding the influence of P fertilizer sources in Brazilian Cerrado soils upon microbial genes coding for phosphohydrolase enzymes in crop rhizospheres. Here, we analyze a field experiment comparing maize and sorghum grown under different P fertilization (rock phosphate and triple superphosphate) upon crop performance, phosphatase activity and rhizosphere microbiomes at three levels of diversity: small subunit rRNA marker genes of bacteria, archaea and fungi; a suite of alkaline and acid phosphatase and phytase genes; and ecotypes of individual genes. We found no significant difference in crop performance between the fertilizer sources, but the accumulation of fertilizer P into pools of organic soil P differed. Phosphatase activity was the only biological parameter influenced by P fertilization. Differences in rhizosphere microbiomes were observed at all levels of biodiversity due to crop type, but not fertilization. Inspection of phosphohydrolase gene ecotypes responsible for differences between the crops suggests a role for lateral genetic transfer in establishing ecotype distributions. Moreover, they were not reflected in microbial community composition, suggesting that they confer competitive advantage to individual cells rather than species in the sorghum rhizosphere.}, } @article {pmid33609120, year = {2021}, author = {Gaiero, JR and Tosi, M and Bent, E and Boitt, G and Khosla, K and Turner, BL and Richardson, AE and Condron, LM and Dunfield, KE}, title = {Soil microbial communities influencing organic phosphorus mineralization in a coastal dune chronosequence in New Zealand.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {4}, pages = {}, doi = {10.1093/femsec/fiab034}, pmid = {33609120}, issn = {1574-6941}, mesh = {*Microbiota ; New Zealand ; Phosphorus/analysis ; *Soil ; Soil Microbiology ; }, abstract = {The Haast chronosequence in New Zealand is an ∼6500-year dune formation series, characterized by rapid podzol development, phosphorus (P) depletion and a decline in aboveground biomass. We examined bacterial and fungal community composition within mineral soil fractions using amplicon-based high-throughput sequencing (Illumina MiSeq). We targeted bacterial non-specific acid (class A, phoN/phoC) and alkaline (phoD) phosphomonoesterase genes and quantified specific genes and transcripts using real-time PCR. Soil bacterial diversity was greatest after 4000 years of ecosystem development and associated with an increased richness of phylotypes and a significant decline in previously dominant taxa (Firmicutes and Proteobacteria). Soil fungal communities transitioned from predominantly Basidiomycota to Ascomycota along the chronosequence and were most diverse in 290- to 392-year-old soils, coinciding with maximum tree basal area and organic P accumulation. The Bacteria:Fungi ratio decreased amid a competitive and interconnected soil community as determined by network analysis. Overall, soil microbial communities were associated with soil changes and declining P throughout pedogenesis and ecosystem succession. We identified an increased dependence on organic P mineralization, as found by the profiled acid phosphatase genes, soil acid phosphatase activity and function inference from predicted metagenomes (PICRUSt2).}, } @article {pmid33608630, year = {2021}, author = {Kim, G and Kim, M and Kim, M and Park, C and Yoon, Y and Lim, DH and Yeo, H and Kang, S and Lee, YG and Beak, NI and Lee, J and Kim, S and Kwon, JY and Choi, WW and Lee, C and Yoon, KW and Park, H and Lee, DG}, title = {Spermidine-induced recovery of human dermal structure and barrier function by skin microbiome.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {231}, pmid = {33608630}, issn = {2399-3642}, mesh = {Adult ; Collagen/metabolism ; Dysbiosis ; Elasticity ; Female ; Humans ; Lipogenesis ; Metagenome ; *Microbiota ; Phenotype ; Skin/metabolism/*microbiology ; *Skin Aging ; Spermidine/*metabolism ; Streptococcus/genetics/growth & development/*metabolism ; Young Adult ; }, abstract = {An unbalanced microbial ecosystem on the human skin is closely related to skin diseases and has been associated with inflammation and immune responses. However, little is known about the role of the skin microbiome on skin aging. Here, we report that the Streptococcus species improved the skin structure and barrier function, thereby contributing to anti-aging. Metagenomic analyses showed the abundance of Streptococcus in younger individuals or those having more elastic skin. Particularly, we isolated Streptococcus pneumoniae, Streptococcus infantis, and Streptococcus thermophilus from face of young individuals. Treatment with secretions of S. pneumoniae and S. infantis induced the expression of genes associated with the formation of skin structure and the skin barrier function in human skin cells. The application of culture supernatant including Streptococcal secretions on human skin showed marked improvements on skin phenotypes such as elasticity, hydration, and desquamation. Gene Ontology analysis revealed overlaps in spermidine biosynthetic and glycogen biosynthetic processes. Streptococcus-secreted spermidine contributed to the recovery of skin structure and barrier function through the upregulation of collagen and lipid synthesis in aged cells. Overall, our data suggest the role of skin microbiome into anti-aging and clinical applications.}, } @article {pmid33608294, year = {2021}, author = {Fortunato, CS and Butterfield, DA and Larson, B and Lawrence-Slavas, N and Algar, CK and Zeigler Allen, L and Holden, JF and Proskurowski, G and Reddington, E and Stewart, LC and Topçuoğlu, BD and Vallino, JJ and Huber, JA}, title = {Seafloor Incubation Experiment with Deep-Sea Hydrothermal Vent Fluid Reveals Effect of Pressure and Lag Time on Autotrophic Microbial Communities.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {9}, pages = {}, pmid = {33608294}, issn = {1098-5336}, mesh = {Autotrophic Processes ; Bacteria/genetics ; Bacteriological Techniques/*methods ; Base Sequence ; Hydrothermal Vents/*microbiology ; Metagenome ; Microbiota/*genetics ; Pressure ; RNA, Ribosomal, 16S/genetics ; Seawater ; Ships ; Time Factors ; }, abstract = {Depressurization and sample processing delays may impact the outcome of shipboard microbial incubations of samples collected from the deep sea. To address this knowledge gap, we developed a remotely operated vehicle (ROV)-powered incubator instrument to carry out and compare results from in situ and shipboard RNA stable isotope probing (RNA-SIP) experiments to identify the key chemolithoautotrophic microbes and metabolisms in diffuse, low-temperature venting fluids from Axial Seamount. All the incubations showed microbial uptake of labeled bicarbonate primarily by thermophilic autotrophic Epsilonbacteraeota that oxidized hydrogen coupled with nitrate reduction. However, the in situ seafloor incubations showed higher abundances of transcripts annotated for aerobic processes, suggesting that oxygen was lost from the hydrothermal fluid samples prior to shipboard analysis. Furthermore, transcripts for thermal stress proteins such as heat shock chaperones and proteases were significantly more abundant in the shipboard incubations, suggesting that depressurization induced thermal stress in the metabolically active microbes in these incubations. Together, the results indicate that while the autotrophic microbial communities in the shipboard and seafloor experiments behaved similarly, there were distinct differences that provide new insight into the activities of natural microbial assemblages under nearly native conditions in the ocean.IMPORTANCE Diverse microbial communities drive biogeochemical cycles in Earth's ocean, yet studying these organisms and processes is often limited by technological capabilities, especially in the deep ocean. In this study, we used a novel marine microbial incubator instrument capable of in situ experimentation to investigate microbial primary producers at deep-sea hydrothermal vents. We carried out identical stable isotope probing experiments coupled to RNA sequencing both on the seafloor and on the ship to examine thermophilic, microbial autotrophs in venting fluids from an active submarine volcano. Our results indicate that microbial communities were significantly impacted by the effects of depressurization and sample processing delays, with shipboard microbial communities being more stressed than seafloor incubations. Differences in metabolism were also apparent and are likely linked to the chemistry of the fluid at the beginning of the experiment. Microbial experimentation in the natural habitat provides new insights into understanding microbial activities in the ocean.}, } @article {pmid33607938, year = {2021}, author = {Siebert, JC and Saint-Cyr, M and Borengasser, SJ and Wagner, BD and Lozupone, CA and Görg, C}, title = {CANTARE: finding and visualizing network-based multi-omic predictive models.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {80}, pmid = {33607938}, issn = {1471-2105}, support = {T32 DK007658/DK/NIDDK NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Metabolomics ; Regression Analysis ; Software ; Systems Biology ; }, abstract = {BACKGROUND: One goal of multi-omic studies is to identify interpretable predictive models for outcomes of interest, with analytes drawn from multiple omes. Such findings could support refined biological insight and hypothesis generation. However, standard analytical approaches are not designed to be "ome aware." Thus, some researchers analyze data from one ome at a time, and then combine predictions across omes. Others resort to correlation studies, cataloging pairwise relationships, but lacking an obvious approach for cohesive and interpretable summaries of these catalogs.

METHODS: We present a novel workflow for building predictive regression models from network neighborhoods in multi-omic networks. First, we generate pairwise regression models across all pairs of analytes from all omes, encoding the resulting "top table" of relationships in a network. Then, we build predictive logistic regression models using the analytes in network neighborhoods of interest. We call this method CANTARE (Consolidated Analysis of Network Topology And Regression Elements).

RESULTS: We applied CANTARE to previously published data from healthy controls and patients with inflammatory bowel disease (IBD) consisting of three omes: gut microbiome, metabolomics, and microbial-derived enzymes. We identified 8 unique predictive models with AUC > 0.90. The number of predictors in these models ranged from 3 to 13. We compare the results of CANTARE to random forests and elastic-net penalized regressions, analyzing AUC, predictions, and predictors. CANTARE AUC values were competitive with those generated by random forests and  penalized regressions. The top 3 CANTARE models had a greater dynamic range of predicted probabilities than did random forests and penalized regressions (p-value = 1.35 × 10[-5]). CANTARE models were significantly more likely to prioritize predictors from multiple omes than were the alternatives (p-value = 0.005). We also showed that predictive models from a network based on pairwise models with an interaction term for IBD have higher AUC than predictive models built from a correlation network (p-value = 0.016). R scripts and a CANTARE User's Guide are available at https://sourceforge.net/projects/cytomelodics/files/CANTARE/ .

CONCLUSION: CANTARE offers a flexible approach for building parsimonious, interpretable multi-omic models. These models yield quantitative and directional effect sizes for predictors and support the generation of hypotheses for follow-up investigation.}, } @article {pmid33607296, year = {2021}, author = {Yang, Y and Wang, X and Xie, K and Zhu, C and Chen, N and Chen, T}, title = {kLDM: Inferring Multiple Metagenomic Association Networks Based on the Variation of Environmental Factors.}, journal = {Genomics, proteomics & bioinformatics}, volume = {19}, number = {5}, pages = {834-847}, pmid = {33607296}, issn = {2210-3244}, mesh = {Algorithms ; Computational Biology/methods ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Identification of significant biological relationships or patterns is central to many metagenomic studies. Methods that estimate association networks have been proposed for this purpose; however, they assume that associations are static, neglecting the fact that relationships in a microbial ecosystem may vary with changes in environmental factors (EFs), which can result in inaccurate estimations. Therefore, in this study, we propose a computational model, called the k-Lognormal-Dirichlet-Multinomial (kLDM) model, which estimates multiple association networks that correspond to specific environmental conditions, and simultaneously infers microbe-microbe and EF-microbe associations for each network. The effectiveness of the kLDM model was demonstrated on synthetic data, a colorectal cancer (CRC) dataset, the Tara Oceans dataset, and the American Gut Project dataset. The results revealed that the widely-used Spearman's rank correlation coefficient method performed much worse than the other methods, indicating the importance of separating samples by environmental conditions. Cancer fecal samples were then compared with cancer-free samples, and the estimation achieved by kLDM exhibited fewer associations among microbes but stronger associations between specific bacteria, especially five CRC-associated operational taxonomic units, indicating gut microbe translocation in cancer patients. Some EF-dependent associations were then found within a marine eukaryotic community. Finally, the gut microbial heterogeneity of inflammatory bowel disease patients was detected. These results demonstrate that kLDM can elucidate the complex associations within microbial ecosystems. The kLDM program, R, and Python scripts, together with all experimental datasets, are accessible at https://github.com/tinglab/kLDM.git.}, } @article {pmid33607218, year = {2021}, author = {Li, T and Liu, Z and Zhang, Z and Bai, H and Zong, X and Wang, F and Fan, L}, title = {Comparative analysis of the vaginal microbiome of Chinese women with Trichomonas vaginalis and mixed infection.}, journal = {Microbial pathogenesis}, volume = {154}, number = {}, pages = {104790}, doi = {10.1016/j.micpath.2021.104790}, pmid = {33607218}, issn = {1096-1208}, mesh = {China ; *Coinfection ; Female ; Humans ; *Microbiota ; *Trichomonas vaginalis ; Vagina ; }, abstract = {The high prevalence and serious long-term sequelae of Trichomonas vaginalis (TV) infection worldwide is of a particular concern; however, data regarding the differences in the composition of the vaginal microbiome in cases of single TV infection or mixed infections (i.e., presence of TV and bacterial vaginosis) are scarce. We employed metagenomic sequencing analyses to study gene expression in the vaginal microbiota of women with single TV infection and mixed infection. Women infected with only TV had significantly higher abundance of Mycoplasma, Prevotella, and Streptococcus compared to women without vaginal infection (control). Women infected with mixed infections had a significantly higher abundance of Mycoplasma, Prevotella, Streptococcus, Anaerococcus, Dialister, Peptostreptococcus, Peptoniphilus and a significantly lower abundance of Lactobacillus than TV alone. Mixed infections had a significantly higher abundance of Prevotella, Anaerococcus and Dialister. Our findings suggest that the bacterial community composition varies among healthy women, women with TV alone, and those with mixed infection, and we hypothesize that these bacterial vaginosis (BV)-associated bacterium may play a role in the pathogenesis and recurrence of TV. Probiotic pessaries may necessarily be the answer because shifting the vaginal microbiome and host responses is probably a complex undertaking.}, } @article {pmid33606979, year = {2021}, author = {Camarillo-Guerrero, LF and Almeida, A and Rangel-Pineros, G and Finn, RD and Lawley, TD}, title = {Massive expansion of human gut bacteriophage diversity.}, journal = {Cell}, volume = {184}, number = {4}, pages = {1098-1109.e9}, pmid = {33606979}, issn = {1097-4172}, support = {/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; BB/P027849/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteriophages/*genetics ; *Biodiversity ; Databases, Nucleic Acid ; *Gastrointestinal Microbiome ; Host Specificity ; Humans ; Phylogeography ; }, abstract = {Bacteriophages drive evolutionary change in bacterial communities by creating gene flow networks that fuel ecological adaptions. However, the extent of viral diversity and its prevalence in the human gut remains largely unknown. Here, we introduce the Gut Phage Database, a collection of ∼142,000 non-redundant viral genomes (>10 kb) obtained by mining a dataset of 28,060 globally distributed human gut metagenomes and 2,898 reference genomes of cultured gut bacteria. Host assignment revealed that viral diversity is highest in the Firmicutes phyla and that ∼36% of viral clusters (VCs) are not restricted to a single species, creating gene flow networks across phylogenetically distinct bacterial species. Epidemiological analysis uncovered 280 globally distributed VCs found in at least 5 continents and a highly prevalent phage clade with features reminiscent of p-crAssphage. This high-quality, large-scale catalog of phage genomes will improve future virome studies and enable ecological and evolutionary analysis of human gut bacteriophages.}, } @article {pmid33606695, year = {2021}, author = {Wyness, AJ and Fortune, I and Blight, AJ and Browne, P and Hartley, M and Holden, M and Paterson, DM}, title = {Ecosystem engineers drive differing microbial community composition in intertidal estuarine sediments.}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0240952}, pmid = {33606695}, issn = {1932-6203}, mesh = {Acidobacteria/genetics ; Animals ; Bacteria/genetics ; DNA, Bacterial/genetics ; Ecological Parameter Monitoring/*methods ; Ecosystem ; *Estuaries ; Geologic Sediments/*microbiology ; Microbiota/*genetics/physiology ; Phylogeny ; Polychaeta/genetics ; RNA, Ribosomal, 16S/genetics ; Scotland ; Sequence Analysis, DNA/methods ; Soil Microbiology ; }, abstract = {Intertidal systems are complex and dynamic environments with many interacting factors influencing biochemical characteristics and microbial communities. One key factor are the actions of resident fauna, many of which are regarded as ecosystem engineers because of their bioturbation, bioirrigation and sediment stabilising activities. The purpose of this investigation was to elucidate the evolutionary implications of the ecosystem engineering process by identifying, if any, aspects that act as selection pressures upon microbial communities. A mesocosm study was performed using the well characterised intertidal ecosystem engineers Corophium volutator, Hediste diversicolor, and microphytobenthos, in addition to manual turbation of sediments to compare effects of bioturbation, bioirrigation and stabilisation. A range of sediment functions and biogeochemical gradients were measured in conjunction with 16S rRNA sequencing and diatom taxonomy, with downstream bacterial metagenome function prediction, to identify selection pressures that incited change to microbial community composition and function. Bacterial communities were predominantly Proteobacteria, with the relative abundance of Bacteroidetes, Alphaproteobacteria and Verrucomicrobia being partially displaced by Deltaproteobacteria, Acidobacteria and Chloroflexi as dissolved oxygen concentration and redox potential decreased. Bacterial community composition was driven strongly by biogeochemistry; surface communities were affected by a combination of sediment functions and overlying water turbidity, and subsurface communities by biogeochemical gradients driven by sediment reworking. Diatom communities were dominated by Nitzschia laevis and Achnanthes sp., and assemblage composition was influenced by overlying water turbidity (manual or biogenic) rather than direct infaunal influences such as grazing.}, } @article {pmid33606522, year = {2021}, author = {Cerro-Gálvez, E and Dachs, J and Lundin, D and Fernández-Pinos, MC and Sebastián, M and Vila-Costa, M}, title = {Responses of Coastal Marine Microbiomes Exposed to Anthropogenic Dissolved Organic Carbon.}, journal = {Environmental science & technology}, volume = {55}, number = {14}, pages = {9609-9621}, pmid = {33606522}, issn = {1520-5851}, mesh = {Carbon ; *Environmental Pollutants ; Metagenomics ; *Microbiota ; Seawater ; }, abstract = {Coastal seawaters receive thousands of organic pollutants. However, we have little understanding of the response of microbiomes to this pool of anthropogenic dissolved organic carbon (ADOC). In this study, coastal microbial communities were challenged with ADOC at environmentally relevant concentrations. Experiments were performed at two Mediterranean sites with different impact by pollutants and nutrients: off the Barcelona harbor ("BCN"), and at the Blanes Bay ("BL"). ADOC additions stimulated prokaryotic leucine incorporation rates at both sites, indicating the use of ADOC as growth substrate. The percentage of "membrane-compromised" cells increased with increasing ADOC, indicating concurrent toxic effects of ADOC. Metagenomic analysis of the BCN community challenged with ADOC showed a significant growth of Methylophaga and other gammaproteobacterial taxa belonging to the rare biosphere. Gene expression profiles showed a taxon-dependent response, with significantly enrichments of transcripts from SAR11 and Glaciecola spp. in BCN and BL, respectively. Further, the relative abundance of transposon-related genes (in BCN) and transcripts (in BL) correlated with the number of differentially abundant genes (in BCN) and transcripts (in BLA), suggesting that microbial responses to pollution may be related to pre-exposure to pollutants, with transposons playing a role in adaptation to ADOC. Our results point to a taxon-specific response to low concentrations of ADOC that impact the functionality, structure and plasticity of the communities in coastal seawaters. This work contributes to address the influence of pollutants on microbiomes and their perturbation to ecosystem services and ocean health.}, } @article {pmid33606256, year = {2021}, author = {Amir, A}, title = {Microbiome Analysis Using 16S Amplicon Sequencing: From Samples to ASVs.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2243}, number = {}, pages = {123-141}, pmid = {33606256}, issn = {1940-6029}, mesh = {Algorithms ; Animals ; Bacteria/genetics ; Computational Biology/methods ; Genetic Variation/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome/genetics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; Workflow ; }, abstract = {In this chapter, we will present an outline of a typical experimental and bioinformatic workflow for identification of bacterial amplicon sequence variants (ASVs) present in a set of samples. This chapter is written from a bioinformatic point of view; therefore, the specific experimental protocols are not detailed, but rather the impact of various experimental decisions on the downstream analysis is described. Emphasis is made on the transition from reads to ASVs, describing the Deblur algorithm.}, } @article {pmid33606255, year = {2021}, author = {Joseph, TA and Pe'er, I}, title = {An Introduction to Whole-Metagenome Shotgun Sequencing Studies.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2243}, number = {}, pages = {107-122}, pmid = {33606255}, issn = {1940-6029}, mesh = {Archaea/genetics ; Bacteria/genetics ; Humans ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; Viruses/genetics ; }, abstract = {Microbial communities are found across diverse environments, including within and across the human body. As many microbes are unculturable in the lab, much of what is known about a microbiome-a collection of bacteria, fungi, archaea, and viruses inhabiting an environment--is from the sequencing of DNA from within the constituent community. Here, we provide an introduction to whole-metagenome shotgun sequencing studies, a ubiquitous approach for characterizing microbial communities, by reviewing three major research areas in metagenomics: assembly, community profiling, and functional profiling. Though not exhaustive, these areas encompass a large component of the metagenomics literature. We discuss each area in depth, the challenges posed by whole-metagenome shotgun sequencing, and approaches fundamental to the solutions of each. We conclude by discussing promising areas for future research. Though our emphasis is on the human microbiome, the methods discussed are broadly applicable across study systems.}, } @article {pmid33604305, year = {2020}, author = {Song, H and Kim, J and Guk, JH and Kim, WH and Nam, H and Suh, JG and Seong, JK and Cho, S}, title = {Metagenomic Analysis of the Gut Microbiota of Wild Mice, a Newly Identified Reservoir of Campylobacter.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {596149}, pmid = {33604305}, issn = {2235-2988}, mesh = {Animals ; Animals, Wild ; *Campylobacter/genetics ; *Campylobacter Infections/veterinary ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics ; Mice ; Multilocus Sequence Typing ; }, abstract = {Campylobacter, the most common etiologic agent of zoonotic gastroenteritis in humans, is present in many reservoirs including livestock animals, wildlife, soil, and water. Previously, we reported a novel Campylobacter jejuni strain SCJK02 (MLST ST-8388) from the gut of wild mice (Micromys minutus) using culture-dependent methods. However, due to fastidious growth conditions and the presence of viable but non-culturable Campylobacter spp., it is unclear whether M. minutus is a Campylobacter reservoir. This study aimed to: 1) determine the distribution and proportion of Campylobacter spp. in the gut microbiota of wild mice using culture-independent methods and 2) investigate the gut microbiota of wild mice and the relationship of Campylobacter spp. with other gut microbes. The gut microbiota of 38 wild mice captured from perilla fields in Korea and without any clinical symptoms (18 M. minutus and 20 Mus musculus) were analyzed. Metagenomic analysis showed that 77.8% (14 of 18) of the captured M. minutus harbored Campylobacter spp. (0.24-32.92%) in the gut metagenome, whereas none of the captured M. musculus carried Campylobacter spp. in their guts. Notably, 75% (6 of 8) of M. minutus determined to be Campylobacter-negative using culture-dependent methods showed a high proportion of Campylobacter through metagenome analysis. The results of metagenome analysis and the absence of clinical symptoms suggest that Campylobacter may be a component of the normal gut flora of wild M. minutus. Furthermore, linear discriminant analysis (LDA) showed that Campylobacter was the most enriched genus in the gut microbiota of M. minutus (LDA score, 5.37), whereas Lactobacillus was the most enriched genus in M. musculus (LDA score, -5.96). The differences in the presence of Campylobacter between the two species of wild mice may be attributed to the differential abundance of Campylobacter and Lactobacillus in their respective gut microbiota. In conclusion, the results indicate that wild M. minutus may serve as a potential Campylobacter reservoir. This study presents the first metagenomics analysis of the M. minutus gut microbiota to explore its possible role as an environmental Campylobacter reservoir and provides a basis for future studies using culture-independent methods to determine the role of environmental reservoirs in Campylobacter transmission.}, } @article {pmid33602895, year = {2021}, author = {Zhang, W and Qu, W and Wang, H and Yan, H}, title = {Antidepressants fluoxetine and amitriptyline induce alterations in intestinal microbiota and gut microbiome function in rats exposed to chronic unpredictable mild stress.}, journal = {Translational psychiatry}, volume = {11}, number = {1}, pages = {131}, pmid = {33602895}, issn = {2158-3188}, mesh = {Amitriptyline ; Animals ; Antidepressive Agents ; Fluoxetine ; *Gastrointestinal Microbiome ; Rats ; Stress, Psychological ; }, abstract = {Antidepressant medications are known to modulate the central nervous system, and gut microbiota can play a role in depression via microbiota-gut-brain axis. But the impact of antidepressants on gut microbiota function and composition remains poorly understood. Thus this study assessed the effect of serotonin reuptake inhibitor antidepressant fluoxetine (Flu) and tricyclic antidepressant amitriptyline (Ami) administration on gut microbiota composition, diversity, and species abundance, along with microbial function in a chronic unpredictable mild stress (CUMS)-induced depression rat model. Oral administration of Ami and Flu significantly altered the overall gut microbiota profile of CUMS-induced rats, as assessed using the permutational multivariate analysis of variance test. At the phylum level, 6-week of antidepressant treatment led to a decreased Firmicutes/Bacteroidetes ratio due to an enhanced Bacteroidetes and reduced Firmicutes relative abundance. Flu was more potent than Ami at altering the Firmicutes and Bacteroidetes levels in the CUMS rats. At the family level, both antidepressants significantly increased the abundance of Porphyromonadaceae. However, an increased Bacteroidaceae level was significantly associated with Ami, not Flu treatment. Furthermore, at the genus level, an increase in the relative abundance of Parabacteroides, Butyricimonas, and Alistipes was observed following Ami and Flu treatment. Subsequent metagenomics and bioinformatics analysis further indicated that Ami and Flu likely also modulated metabolic pathways, such as those involved in carbohydrate metabolism, membrane transport, and signal transduction. Additionally, both antidepressants affected antibiotic resistome, such as for aminoglycoside (aph3iiiA), multidrug (mdtK, mdtP, mdtH, mdtG, acrA), and tetracycline (tetM) resistance in CUMS rats. These data clearly illustrated the direct impact of oral administration of Flu and Ami on the gut microbiome, thus set up the foundation to reveal more insights on the therapeutic function of the antidepressants and their overall contribution to host health.}, } @article {pmid33602336, year = {2021}, author = {Bashir, AK and Wink, L and Duller, S and Schwendner, P and Cockell, C and Rettberg, P and Mahnert, A and Beblo-Vranesevic, K and Bohmeier, M and Rabbow, E and Gaboyer, F and Westall, F and Walter, N and Cabezas, P and Garcia-Descalzo, L and Gomez, F and Malki, M and Amils, R and Ehrenfreund, P and Monaghan, E and Vannier, P and Marteinsson, V and Erlacher, A and Tanski, G and Strauss, J and Bashir, M and Riedo, A and Moissl-Eichinger, C}, title = {Taxonomic and functional analyses of intact microbial communities thriving in extreme, astrobiology-relevant, anoxic sites.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {50}, pmid = {33602336}, issn = {2049-2618}, mesh = {Anaerobiosis ; Bacteria/classification/genetics/isolation & purification ; *Exobiology ; *Extreme Environments ; Metagenome ; Microbiota/genetics/*physiology ; }, abstract = {BACKGROUND: Extreme terrestrial, analogue environments are widely used models to study the limits of life and to infer habitability of extraterrestrial settings. In contrast to Earth's ecosystems, potential extraterrestrial biotopes are usually characterized by a lack of oxygen.

METHODS: In the MASE project (Mars Analogues for Space Exploration), we selected representative anoxic analogue environments (permafrost, salt-mine, acidic lake and river, sulfur springs) for the comprehensive analysis of their microbial communities. We assessed the microbiome profile of intact cells by propidium monoazide-based amplicon and shotgun metagenome sequencing, supplemented with an extensive cultivation effort.

RESULTS: The information retrieved from microbiome analyses on the intact microbial community thriving in the MASE sites, together with the isolation of 31 model microorganisms and successful binning of 15 high-quality genomes allowed us to observe principle pathways, which pinpoint specific microbial functions in the MASE sites compared to moderate environments. The microorganisms were characterized by an impressive machinery to withstand physical and chemical pressures. All levels of our analyses revealed the strong and omnipresent dependency of the microbial communities on complex organic matter. Moreover, we identified an extremotolerant cosmopolitan group of 34 poly-extremophiles thriving in all sites.

CONCLUSIONS: Our results reveal the presence of a core microbiome and microbial taxonomic similarities between saline and acidic anoxic environments. Our work further emphasizes the importance of the environmental, terrestrial parameters for the functionality of a microbial community, but also reveals a high proportion of living microorganisms in extreme environments with a high adaptation potential within habitability borders. Video abstract.}, } @article {pmid33602058, year = {2021}, author = {Coughlan, S and Das, A and O'Herlihy, E and Shanahan, F and O'Toole, PW and Jeffery, IB}, title = {The gut virome in Irritable Bowel Syndrome differs from that of controls.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-15}, pmid = {33602058}, issn = {1949-0984}, mesh = {Adolescent ; Adult ; Aged ; Bacteriophages/classification/genetics/isolation & purification ; Feces/virology ; Female ; *Gastrointestinal Microbiome ; Humans ; Irritable Bowel Syndrome/*virology ; Male ; Middle Aged ; *Virome ; Viruses/classification/genetics/isolation & purification ; Young Adult ; }, abstract = {Irritable Bowel Syndrome (IBS), the most common gastrointestinal disorder, is diagnosed solely on symptoms. Potentially diagnostic alterations in the bacterial component of the gut microbiome (the bacteriome) are associated with IBS, but despite the known role of the virome (particularly bacteriophages), in shaping the gut bacteriome, few studies have investigated the virome in IBS. We performed metagenomic sequencing of fecal Virus-Like Particles (VLPs) from 55 patients with IBS and 51 control individuals. We detected significantly lower alpha diversity of viral clusters comprising both known and novel viruses (viral 'dark matter') in IBS and a significant difference in beta diversity compared to controls, but not between IBS symptom subtypes. The three most abundant bacteriophage clusters belonged to the Siphoviridae, Myoviridae, and Podoviridae families (Order Caudovirales). A core virome (defined as a cluster present in at least 50% of samples) of 5 and 12 viral clusters was identified in IBS and control subjects, respectively. We also identified a subset of viral clusters that showed differential abundance between IBS and controls. The virome did not co-vary significantly with the bacteriome, with IBS clinical subtype, or with Bile Acid Malabsorption status. However, differences in the virome could be related back to the bacteriome as analysis of CRISPR spacers indicated that the virome alterations were at least partially related to the alterations in the bacteriome. We found no evidence for a shift from lytic to lysogenic replication of core viral clusters, a phenomenon reported for the gut virome of patients with Inflammatory Bowel Disease. Collectively, our data show alterations in the virome of patients with IBS, regardless of clinical subtype, which may facilitate development of new microbiome-based therapeutics.}, } @article {pmid33600956, year = {2021}, author = {Zhang, S and Zeng, B and Chen, Y and Yang, M and Kong, F and Wei, L and Li, F and Zhao, J and Li, Y}, title = {Gut microbiota in healthy and unhealthy long-living people.}, journal = {Gene}, volume = {779}, number = {}, pages = {145510}, doi = {10.1016/j.gene.2021.145510}, pmid = {33600956}, issn = {1879-0038}, mesh = {Aged, 80 and over ; Amino Acids/metabolism ; Asian People ; Carbohydrate Metabolism ; Drug Resistance, Microbial/genetics ; Dysbiosis/*microbiology ; Enzymes/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Metagenome ; Streptococcus/pathogenicity ; Virulence Factors/genetics ; }, abstract = {The human gut microbiota in long-living people has been characterized, however, its metabolic potential is still largely unknown in this group. In this study, the gut microbiota was assessed in 37 Chinese long-living participants (aged 90 + years) by metagenomic sequencing of stool samples. Participants were categorized into two groups, healthy long-living (n = 28) and unhealthy long-living (n = 9). Gut microbiota composition and function were compared among these two groups. We found that the gut microbiota in the healthy long-living group was significantly separated from the unhealthy group. The healthy long-living group contained a higher abundance of Bacteroidetes and more functional pathways in energy metabolism, glycan biosynthesis and metabolism, metabolism of cofactors and vitamins, and biosynthesis of other secondary metabolites. The unhealthy group contained a higher abundance of Streptococcus and other pathogenic bacteria, and also contained more functional pathways for xenobiotics biodegradation and metabolism than the healthy group. Additionally, the unhealthy group had decreased levels of carbohydrate-active enzymes, including host-glycan and fiber degrading enzymes, and an increase in starch-degrading enzymes. In conclusion, the gut microbiota of unhealthy long-living people contains more pathogenic bacteria, and the overall gut microbiota may be in an unhealthy state, "dysbiosis", which leads to a decrease in carbohydrate digestion, glycan and thiamine (B1) metabolites, and fatty acid biosynthesis.}, } @article {pmid33599321, year = {2021}, author = {Chan, WK and Wong, VW}, title = {Editorial: metagenome-assembled genomes in non-alcoholic fatty liver disease.}, journal = {Alimentary pharmacology & therapeutics}, volume = {53}, number = {6}, pages = {755-756}, doi = {10.1111/apt.16280}, pmid = {33599321}, issn = {1365-2036}, mesh = {Adult ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; *Non-alcoholic Fatty Liver Disease/epidemiology/genetics ; }, } @article {pmid33597537, year = {2021}, author = {Jensen, BAH and Holm, JB and Larsen, IS and von Burg, N and Derer, S and Sonne, SB and Pærregaard, SI and Damgaard, MV and Indrelid, SA and Rivollier, A and Agrinier, AL and Sulek, K and Arnoldussen, YJ and Fjære, E and Marette, A and Angell, IL and Rudi, K and Treebak, JT and Madsen, L and Åkesson, CP and Agace, W and Sina, C and Kleiveland, CR and Kristiansen, K and Lea, TE}, title = {Lysates of Methylococcus capsulatus Bath induce a lean-like microbiota, intestinal FoxP3[+]RORγt[+]IL-17[+] Tregs and improve metabolism.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {1093}, pmid = {33597537}, issn = {2041-1723}, support = {//CIHR/Canada ; }, mesh = {Animals ; Diet ; Forkhead Transcription Factors/immunology/metabolism ; Homeostasis/immunology ; Interleukin-17/immunology/metabolism ; Intestine, Large/*immunology/metabolism/microbiology ; Intestine, Small/*immunology/metabolism/microbiology ; Male ; Methylococcus capsulatus/chemistry/*immunology ; Mice, Inbred C57BL ; Microbiota/*immunology ; Nuclear Receptor Subfamily 1, Group F, Member 3/immunology/metabolism ; Obesity/immunology ; Proteins/*immunology/metabolism ; T-Lymphocytes, Regulatory/*immunology/metabolism ; Mice ; }, abstract = {Interactions between host and gut microbial communities are modulated by diets and play pivotal roles in immunological homeostasis and health. We show that exchanging the protein source in a high fat, high sugar, westernized diet from casein to whole-cell lysates of the non-commensal bacterium Methylococcus capsulatus Bath is sufficient to reverse western diet-induced changes in the gut microbiota to a state resembling that of lean, low fat diet-fed mice, both under mild thermal stress (T22 °C) and at thermoneutrality (T30 °C). Concomitant with microbiota changes, mice fed the Methylococcus-based western diet exhibit improved glucose regulation, reduced body and liver fat, and diminished hepatic immune infiltration. Intake of the Methylococcu-based diet markedly boosts Parabacteroides abundances in a manner depending on adaptive immunity, and upregulates triple positive (Foxp3[+]RORγt[+]IL-17[+]) regulatory T cells in the small and large intestine. Collectively, these data point to the potential for leveraging the use of McB lysates to improve immunometabolic homeostasis.}, } @article {pmid33597514, year = {2021}, author = {Chen, C and Zhou, Y and Fu, H and Xiong, X and Fang, S and Jiang, H and Wu, J and Yang, H and Gao, J and Huang, L}, title = {Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {1106}, pmid = {33597514}, issn = {2041-1723}, mesh = {Animals ; Bacteria/classification/genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Genes, Microbial/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome/*genetics ; Metagenomics/*methods ; Phylogeny ; Species Specificity ; Swine ; }, abstract = {Gut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes remains limited. Here we perform a landscape survey of the swine gut microbiome, spanning extensive sample sources by deep metagenomic sequencing resulting in an expanded gene catalog named pig integrated gene catalog (PIGC), containing 17,237,052 complete genes clustered at 90% protein identity from 787 gut metagenomes, of which 28% are unknown proteins. Using binning analysis, 6339 metagenome-assembled genomes (MAGs) were obtained, which were clustered to 2673 species-level genome bins (SGBs), among which 86% (2309) SGBs are unknown based on current databases. Using the present gene catalog and MAGs, we identified several strain-level differences between the gut microbiome of wild boars and commercial Duroc pigs. PIGC and MAGs provide expanded resources for swine gut microbiome-related research.}, } @article {pmid33597039, year = {2021}, author = {Li, Z and Xia, J and Jiang, L and Tan, Y and An, Y and Zhu, X and Ruan, J and Chen, Z and Zhen, H and Ma, Y and Jie, Z and Xiao, L and Yang, H and Wang, J and Kristiansen, K and Xu, X and Jin, L and Nie, C and Krutmann, J and Liu, X and Wang, J}, title = {Characterization of the human skin resistome and identification of two microbiota cutotypes.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {47}, pmid = {33597039}, issn = {2049-2618}, mesh = {Adult ; Aged ; Anti-Bacterial Agents/pharmacology ; China/ethnology ; Drug Resistance, Microbial/drug effects/genetics ; Ethnicity ; Female ; Genes, Bacterial/drug effects ; Humans ; Male ; Metagenomics ; *Microbiota/drug effects/genetics ; Middle Aged ; Moraxella/drug effects/*genetics/*isolation & purification ; North America/ethnology ; Propionibacteriaceae/drug effects/*genetics/*isolation & purification ; Skin/*microbiology ; Staphylococcus/drug effects/genetics/isolation & purification ; Symbiosis ; Young Adult ; }, abstract = {BACKGROUND: The human skin microbiota is considered to be essential for skin homeostasis and barrier function. Comprehensive analyses of its function would substantially benefit from a catalog of reference genes derived from metagenomic sequencing. The existing catalog for the human skin microbiome is based on samples from limited individuals from a single cohort on reference genomes, which limits the coverage of global skin microbiome diversity.

RESULTS: In the present study, we have used shotgun metagenomics to newly sequence 822 skin samples from Han Chinese, which were subsequently combined with 538 previously sequenced North American samples to construct an integrated Human Skin Microbial Gene Catalog (iHSMGC). The iHSMGC comprised 10,930,638 genes with the detection of 4,879,024 new genes. Characterization of the human skin resistome based on iHSMGC confirmed that skin commensals, such as Staphylococcus spp, are an important reservoir of antibiotic resistance genes (ARGs). Further analyses of skin microbial ARGs detected microbe-specific and skin site-specific ARG signatures. Of note, the abundance of ARGs was significantly higher in Chinese than Americans, while multidrug-resistant bacteria ("superbugs") existed on the skin of both Americans and Chinese. A detailed analysis of microbial signatures identified Moraxella osloensis as a species specific for Chinese skin. Importantly, Moraxella osloensis proved to be a signature species for one of two robust patterns of microbial networks present on Chinese skin, with Cutibacterium acnes indicating the second one. Each of such "cutotypes" was associated with distinct patterns of data-driven marker genes, functional modules, and host skin properties. The two cutotypes markedly differed in functional modules related to their metabolic characteristics, indicating that host-dependent trophic chains might underlie their development.

CONCLUSIONS: The development of the iHSMGC will facilitate further studies on the human skin microbiome. In the present study, it was used to further characterize the human skin resistome. It also allowed to discover the existence of two cutotypes on the human skin. The latter finding will contribute to a better understanding of the interpersonal complexity of the skin microbiome. Video abstract.}, } @article {pmid33597026, year = {2021}, author = {de Nies, L and Lopes, S and Busi, SB and Galata, V and Heintz-Buschart, A and Laczny, CC and May, P and Wilmes, P}, title = {PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {49}, pmid = {33597026}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/pharmacology ; Anti-Infective Agents/*pharmacology ; Drug Resistance, Bacterial/drug effects/*genetics ; *Metagenomics ; *Software ; Virulence Factors/*genetics ; }, abstract = {BACKGROUND: Pathogenic microorganisms cause disease by invading, colonizing, and damaging their host. Virulence factors including bacterial toxins contribute to pathogenicity. Additionally, antimicrobial resistance genes allow pathogens to evade otherwise curative treatments. To understand causal relationships between microbiome compositions, functioning, and disease, it is essential to identify virulence factors and antimicrobial resistance genes in situ. At present, there is a clear lack of computational approaches to simultaneously identify these factors in metagenomic datasets.

RESULTS: Here, we present PathoFact, a tool for the contextualized prediction of virulence factors, bacterial toxins, and antimicrobial resistance genes with high accuracy (0.921, 0.832 and 0.979, respectively) and specificity (0.957, 0.989 and 0.994). We evaluate the performance of PathoFact on simulated metagenomic datasets and perform a comparison to two other general workflows for the analysis of metagenomic data. PathoFact outperforms all existing workflows in predicting virulence factors and toxin genes. It performs comparably to one pipeline regarding the prediction of antimicrobial resistance while outperforming the others. We further demonstrate the performance of PathoFact on three publicly available case-control metagenomic datasets representing an actual infection as well as chronic diseases in which either pathogenic potential or bacterial toxins are hypothesized to play a role. In each case, we identify virulence factors and AMR genes which differentiated between the case and control groups, thereby revealing novel gene associations with the studied diseases.

CONCLUSION: PathoFact is an easy-to-use, modular, and reproducible pipeline for the identification of virulence factors, bacterial toxins, and antimicrobial resistance genes in metagenomic data. Additionally, our tool combines the prediction of these pathogenicity factors with the identification of mobile genetic elements. This provides further depth to the analysis by considering the genomic context of the pertinent genes. Furthermore, PathoFact's modules for virulence factors, toxins, and antimicrobial resistance genes can be applied independently, thereby making it a flexible and versatile tool. PathoFact, its models, and databases are freely available at https://pathofact.lcsb.uni.lu . Video abstract.}, } @article {pmid33596852, year = {2021}, author = {Straub, TJ and Chou, WC and Manson, AL and Schreiber, HL and Walker, BJ and Desjardins, CA and Chapman, SB and Kaspar, KL and Kahsai, OJ and Traylor, E and Dodson, KW and Hullar, MAJ and Hultgren, SJ and Khoo, C and Earl, AM}, title = {Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {53}, pmid = {33596852}, issn = {1471-2180}, support = {U01 AI095542/AI/NIAID NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; HHSN272200900018C/AI/NIAID NIH HHS/United States ; R01 DK121822/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Bacteria/classification/*drug effects/genetics ; Beverages ; Double-Blind Method ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/*genetics/physiology ; Humans ; Metagenome ; Metagenomics/methods ; Middle Aged ; Plant Extracts/*administration & dosage ; Reinfection/microbiology/prevention & control ; Urinary Tract Infections/microbiology/prevention & control ; Vaccinium macrocarpon/*chemistry ; }, abstract = {BACKGROUND: Urinary tract infections (UTIs) affect 15 million women each year in the United States, with > 20% experiencing frequent recurrent UTIs. A recent placebo-controlled clinical trial found a 39% reduction in UTI symptoms among recurrent UTI sufferers who consumed a daily cranberry beverage for 24 weeks. Using metagenomic sequencing of stool from a subset of these trial participants, we assessed the impact of cranberry consumption on the gut microbiota, a reservoir for UTI-causing pathogens such as Escherichia coli, which causes > 80% of UTIs.

RESULTS: The overall taxonomic composition, community diversity, carriage of functional pathways and gene families, and relative abundances of the vast majority of observed bacterial taxa, including E. coli, were not changed significantly by cranberry consumption. However, one unnamed Flavonifractor species (OTU41), which represented ≤1% of the overall metagenome, was significantly less abundant in cranberry consumers compared to placebo at trial completion. Given Flavonifractor's association with negative human health effects, we sought to determine OTU41 characteristic genes that may explain its differential abundance and/or relationship to key host functions. Using comparative genomic and metagenomic techniques, we identified genes in OTU41 related to transport and metabolism of various compounds, including tryptophan and cobalamin, which have been shown to play roles in host-microbe interactions.

CONCLUSION: While our results indicated that cranberry juice consumption had little impact on global measures of the microbiome, we found one unnamed Flavonifractor species differed significantly between study arms. This suggests further studies are needed to assess the role of cranberry consumption and Flavonifractor in health and wellbeing in the context of recurrent UTI.

TRIAL REGISTRATION: Clinical trial registration number: ClinicalTrials.gov NCT01776021 .}, } @article {pmid33596669, year = {2021}, author = {Shi, H and Zhang, B and Abo-Hamzy, T and Nelson, JW and Ambati, CSR and Petrosino, JF and Bryan, RM and Durgan, DJ}, title = {Restructuring the Gut Microbiota by Intermittent Fasting Lowers Blood Pressure.}, journal = {Circulation research}, volume = {128}, number = {9}, pages = {1240-1254}, pmid = {33596669}, issn = {1524-4571}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 HL134838/HL/NHLBI NIH HHS/United States ; R01 NS102594/NS/NINDS NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bile Acids and Salts/metabolism ; Cecum/microbiology ; Cholic Acid/administration & dosage ; Dysbiosis/blood/complications/metabolism/*prevention & control ; Fasting/*physiology ; Gastrointestinal Microbiome/genetics/*physiology ; Germ-Free Life ; Hypotension/etiology/*prevention & control ; Metabolome/*physiology ; Oleanolic Acid/pharmacology ; Random Allocation ; Rats ; Rats, Inbred SHR ; Rats, Inbred WKY ; Receptors, G-Protein-Coupled/agonists/blood/metabolism ; Specific Pathogen-Free Organisms ; Time Factors ; Whole Genome Sequencing ; }, abstract = {[Figure: see text].}, } @article {pmid33596519, year = {2021}, author = {Kleerebezem, R and Stouten, G and Koehorst, J and Langenhoff, A and Schaap, P and Smidt, H}, title = {Experimental infrastructure requirements for quantitative research on microbial communities.}, journal = {Current opinion in biotechnology}, volume = {67}, number = {}, pages = {158-165}, doi = {10.1016/j.copbio.2021.01.017}, pmid = {33596519}, issn = {1879-0429}, mesh = {Bacteria/genetics ; *Ecosystem ; Metagenome ; Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; }, abstract = {Natural microbial communities are composed of a large diversity of interacting microorganisms, each with a specific role in the functional properties of the ecosystem. The objectives in microbial ecology research are related to identifying, understanding and exploring the role of these different microorganisms. Because of the rapidly increasing power of DNA sequencing and the rapid increase of genomic data, main attention of microbial ecology research shifted from cultivation-oriented studies towards metagenomic studies. Despite these efforts, the direct link between the molecular properties and the measurable changes in the functional performance of the ecosystem is often poorly documented. A quantitative understanding of functional properties in relation to the molecular changes requires effective integration, standardization, and parallelization of experiments. High-resolution functional characterization is a prerequisite for interpretation of changes in metagenomic properties, and will improve our understanding of microbial communities and facilitate their exploration for health and circular economy related objectives.}, } @article {pmid33595122, year = {2021}, author = {Cai, HZ and Zhang, H and Yang, J and Zeng, J and Wang, H}, title = {Preliminary assessment of viral metagenome from cancer tissue and blood from patients with lung adenocarcinoma.}, journal = {Journal of medical virology}, volume = {93}, number = {8}, pages = {5126-5133}, doi = {10.1002/jmv.26887}, pmid = {33595122}, issn = {1096-9071}, mesh = {Adenocarcinoma of Lung/blood/pathology/*virology ; Genome, Viral/genetics ; Genotype ; Humans ; Lung Neoplasms/blood/pathology/*virology ; Metagenomics ; Pegivirus/classification/genetics/isolation & purification ; Phylogeny ; Polyomavirus/classification/genetics/isolation & purification ; Virome/*genetics ; }, abstract = {In this study, using a viral metagenomic method, we investigated the composition of virome in blood and cancer tissue samples that were collected from 25 patients with lung adenocarcinoma. Results indicated that virus sequences showing similarity to human pegivirus (HPgV), anellovirus, human endogenous retrovirus (HERV), and polyomavirus were recovered from this cohort. Three different complete genomes of HPgV were acquired from the blood samples and one complete genome of polyomavirus was determined from the cancer tissue sample. Phylogenetic analysis indicated that the three HPgV strains belonged to genotype 3 and the polyomavirus showed the highest sequence identity (99.73%) to trichodysplasia spinulosa-associated polyomavirus. PCR screening results indicated that the three HPgVs were present in 5 out of the 25 blood samples and the polyomavirus only existed in a cancer tissue sample pool. Whether infections with viruses have an association with lung cancer needs further study with a larger size of sampling.}, } @article {pmid33594055, year = {2021}, author = {Yutin, N and Benler, S and Shmakov, SA and Wolf, YI and Tolstoy, I and Rayko, M and Antipov, D and Pevzner, PA and Koonin, EV}, title = {Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {1044}, pmid = {33594055}, issn = {2041-1723}, mesh = {Bacteriophages/*genetics ; Codon/genetics ; Conserved Sequence ; DNA-Directed DNA Polymerase/metabolism ; Gastrointestinal Microbiome/*genetics ; *Genome, Viral ; Humans ; Inteins ; Introns/genetics ; *Metagenome ; Open Reading Frames/genetics ; Phylogeny ; RNA Splicing/genetics ; Transcription, Genetic ; Virome/genetics ; }, abstract = {CrAssphage is the most abundant human-associated virus and the founding member of a large group of bacteriophages, discovered in animal-associated and environmental metagenomes, that infect bacteria of the phylum Bacteroidetes. We analyze 4907 Circular Metagenome Assembled Genomes (cMAGs) of putative viruses from human gut microbiomes and identify nearly 600 genomes of crAss-like phages that account for nearly 87% of the DNA reads mapped to these cMAGs. Phylogenetic analysis of conserved genes demonstrates the monophyly of crAss-like phages, a putative virus order, and of 5 branches, potential families within that order, two of which have not been identified previously. The phage genomes in one of these families are almost twofold larger than the crAssphage genome (145-192 kilobases), with high density of self-splicing introns and inteins. Many crAss-like phages encode suppressor tRNAs that enable read-through of UGA or UAG stop-codons, mostly, in late phage genes. A distinct feature of the crAss-like phages is the recurrent switch of the phage DNA polymerase type between A and B families. Thus, comparative genomic analysis of the expanded assemblage of crAss-like phages reveals aspects of genome architecture and expression as well as phage biology that were not apparent from the previous work on phage genomics.}, } @article {pmid33593943, year = {2021}, author = {Andersen, SB and Schluter, J}, title = {A metagenomics approach to investigate microbiome sociobiology.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {10}, pages = {}, pmid = {33593943}, issn = {1091-6490}, mesh = {Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Sociobiology ; }, } @article {pmid33593881, year = {2021}, author = {Shaikh, FY and White, JR and Gills, JJ and Hakozaki, T and Richard, C and Routy, B and Okuma, Y and Usyk, M and Pandey, A and Weber, JS and Ahn, J and Lipson, EJ and Naidoo, J and Pardoll, DM and Sears, CL}, title = {A Uniform Computational Approach Improved on Existing Pipelines to Reveal Microbiome Biomarkers of Nonresponse to Immune Checkpoint Inhibitors.}, journal = {Clinical cancer research : an official journal of the American Association for Cancer Research}, volume = {27}, number = {9}, pages = {2571-2583}, pmid = {33593881}, issn = {1557-3265}, support = {KL2 TR001077/TR/NCATS NIH HHS/United States ; P30 CA006973/CA/NCI NIH HHS/United States ; T32 CA009071/CA/NCI NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics ; *Biomarkers ; *Computational Biology/methods ; Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Immune Checkpoint Inhibitors/*pharmacology/therapeutic use ; Metagenomics/methods ; Microbiota/*drug effects/genetics ; RNA, Ribosomal, 16S ; ROC Curve ; Reproducibility of Results ; Whole Genome Sequencing ; }, abstract = {PURPOSE: While immune checkpoint inhibitors (ICI) have revolutionized the treatment of cancer by producing durable antitumor responses, only 10%-30% of treated patients respond and the ability to predict clinical benefit remains elusive. Several studies, small in size and using variable analytic methods, suggest the gut microbiome may be a novel, modifiable biomarker for tumor response rates, but the specific bacteria or bacterial communities putatively impacting ICI responses have been inconsistent across the studied populations.

EXPERIMENTAL DESIGN: We have reanalyzed the available raw 16S rRNA amplicon and metagenomic sequencing data across five recently published ICI studies (n = 303 unique patients) using a uniform computational approach.

RESULTS: Herein, we identify novel bacterial signals associated with clinical responders (R) or nonresponders (NR) and develop an integrated microbiome prediction index. Unexpectedly, the NR-associated integrated index shows the strongest and most consistent signal using a random effects model and in a sensitivity and specificity analysis (P < 0.01). We subsequently tested the integrated index using validation cohorts across three distinct and diverse cancers (n = 105).

CONCLUSIONS: Our analysis highlights the development of biomarkers for nonresponse, rather than response, in predicting ICI outcomes and suggests a new approach to identify patients who would benefit from microbiome-based interventions to improve response rates.}, } @article {pmid33593778, year = {2021}, author = {Williams, AJ and Paramsothy, R and Wu, N and Ghaly, S and Leach, S and Paramsothy, S and Corte, C and O'Brien, C and Burke, C and Wark, G and Samocha-Bonet, D and Lambert, K and Ahlenstiel, G and Wasinger, V and Dutt, S and Pavli, P and Grimm, M and Lemberg, D and Connor, S and Leong, R and Hold, G}, title = {Australia IBD Microbiome (AIM) Study: protocol for a multicentre longitudinal prospective cohort study.}, journal = {BMJ open}, volume = {11}, number = {2}, pages = {e042493}, pmid = {33593778}, issn = {2044-6055}, mesh = {Australia/epidemiology ; *Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases ; *Microbiota ; Multicenter Studies as Topic ; Prospective Studies ; Proteomics ; }, abstract = {INTRODUCTION: Crohn's disease and ulcerative colitis are common chronic idiopathic inflammatory bowel diseases (IBD), which cause considerable morbidity. Although the precise mechanisms of disease remain unclear, evidence implicates a strong multidirectional interplay between diet, environmental factors, genetic determinants/immune perturbations and the gut microbiota. IBD can be brought into remission using a number of medications, which act by suppressing the immune response. However, none of the available medications address any of the underlying potential mechanisms. As we understand more about how the microbiota drives inflammation, much interest has focused on identifying microbial signals/triggers in the search for effective therapeutic targets. We describe the establishment of the Australian IBD Microbiota (AIM) Study, Australia's first longitudinal IBD bioresource, which will identify and correlate longitudinal microbial and metagenomics signals to disease activity as evaluated by validated clinical instruments, patient-reported surveys, as well as biomarkers. The AIM Study will also gather extensive demographic, clinical, lifestyle and dietary data known to influence microbial composition in order to generate a more complete understanding of the interplay between patients with IBD and their microbiota.

METHODS: The AIM Study is an Australian multicentre longitudinal prospective cohort study, which will enrol 1000 participants; 500 patients with IBD and 500 healthy controls over a 5-year period. Assessment occurs at 3 monthly intervals over a 24-month period. At each assessment oral and faecal samples are self-collected along with patient-reported outcome measures, with clinical data also collected at baseline, 12 and 24 months. Intestinal tissue will be sampled whenever a colonoscopy is performed. Dietary intake, general health and psychological state will be assessed using validated self-report questionnaires. Samples will undergo metagenomic, transcriptomic, proteomic, metabolomic and culturomic analyses. Omics data will be integrated with clinical data to identify predictive biomarkers of response to therapy, disease behaviour and environmental factors in patients with IBD.

ETHICS AND DISSEMINATION: Ethical approval for this study has been obtained from the South Eastern Sydney Local Health District Research Ethics Committee (HREC 2019/ETH11443). Findings will be reported at national and international gastroenterology meetings and published in peer-reviewed journals.

TRIAL REGISTRATION NUMBER: ACTRN12619000911190.}, } @article {pmid33593430, year = {2021}, author = {Langdon, A and Schwartz, DJ and Bulow, C and Sun, X and Hink, T and Reske, KA and Jones, C and Burnham, CD and Dubberke, ER and Dantas, G and , }, title = {Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {28}, pmid = {33593430}, issn = {1756-994X}, support = {T32 HG000045/HG/NHGRI NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; TL1 TR000449/TR/NCATS NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; TL1 TR000449/NH/NIH HHS/United States ; }, mesh = {Bacteria/genetics/*growth & development ; Clostridium Infections/*microbiology/*therapy ; *Drug Resistance, Microbial/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Intestines/*microbiology ; Phylogeny ; Principal Component Analysis ; Recurrence ; Time Factors ; Tissue Donors ; }, abstract = {BACKGROUND: Once antibiotic-resistant bacteria become established within the gut microbiota, they can cause infections in the host and be transmitted to other people and the environment. Currently, there are no effective modalities for decreasing or preventing colonization by antibiotic-resistant bacteria. Intestinal microbiota restoration can prevent Clostridioides difficile infection (CDI) recurrences. Another potential application of microbiota restoration is suppression of non-C. difficile multidrug-resistant bacteria and overall decrease in the abundance of antibiotic resistance genes (the resistome) within the gut microbiota. This study characterizes the effects of RBX2660, a microbiota-based investigational therapeutic, on the composition and abundance of the gut microbiota and resistome, as well as multidrug-resistant organism carriage, after delivery to patients suffering from recurrent CDI.

METHODS: An open-label, multi-center clinical trial in 11 centers in the USA for the safety and efficacy of RBX2660 on recurrent CDI was conducted. Fecal specimens from 29 of these subjects with recurrent CDI who received either one (N = 16) or two doses of RBX2660 (N = 13) were analyzed secondarily. Stool samples were collected prior to and at intervals up to 6 months post-therapy and analyzed in three ways: (1) 16S rRNA gene sequencing for microbiota taxonomic composition, (2) whole metagenome shotgun sequencing for functional pathways and antibiotic resistome content, and (3) selective and differential bacterial culturing followed by isolate genome sequencing to longitudinally track multidrug-resistant organisms.

RESULTS: Successful prevention of CDI recurrence with RBX2660 correlated with taxonomic convergence of patient microbiota to the donor microbiota as measured by weighted UniFrac distance. RBX2660 dramatically reduced the abundance of antibiotic-resistant Enterobacteriaceae in the 2 months after administration. Fecal antibiotic resistance gene carriage decreased in direct relationship to the degree to which donor microbiota engrafted.

CONCLUSIONS: Microbiota-based therapeutics reduce resistance gene abundance and resistant organisms in the recipient gut microbiome. This approach could potentially reduce the risk of infections caused by resistant organisms within the patient and the transfer of resistance genes or pathogens to others.

TRIAL REGISTRATION: ClinicalTrials.gov, NCT01925417 ; registered on August 19, 2013.}, } @article {pmid33593429, year = {2021}, author = {Moshkelgosha, S and Verhasselt, HL and Masetti, G and Covelli, D and Biscarini, F and Horstmann, M and Daser, A and Westendorf, AM and Jesenek, C and Philipp, S and Diaz-Cano, S and Banga, JP and Michael, D and Plummer, S and Marchesi, JR and Eckstein, A and Ludgate, M and Berchner-Pfannschmidt, U and , }, title = {Modulating gut microbiota in a mouse model of Graves' orbitopathy and its impact on induced disease.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {45}, pmid = {33593429}, issn = {2049-2618}, mesh = {Animals ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Female ; *Gastrointestinal Microbiome ; Graves Ophthalmopathy/immunology/metabolism/*microbiology/pathology ; Humans ; Mice ; Mice, Inbred BALB C ; }, abstract = {BACKGROUND: Graves' disease (GD) is an autoimmune condition in which autoantibodies to the thyrotropin receptor (TSHR) cause hyperthyroidism. About 50% of GD patients also have Graves' orbitopathy (GO), an intractable disease in which expansion of the orbital contents causes diplopia, proptosis and even blindness. Murine models of GD/GO, developed in different centres, demonstrated significant variation in gut microbiota composition which correlated with TSHR-induced disease heterogeneity. To investigate whether correlation indicates causation, we modified the gut microbiota to determine whether it has a role in thyroid autoimmunity. Female BALB/c mice were treated with either vancomycin, probiotic bacteria, human fecal material transfer (hFMT) from patients with severe GO or ddH2O from birth to immunization with TSHR-A subunit or beta-galactosidase (βgal; age ~ 6 weeks). Incidence and severity of GD (TSHR autoantibodies, thyroid histology, thyroxine level) and GO (orbital fat and muscle histology), lymphocyte phenotype, cytokine profile and gut microbiota were analysed at sacrifice (~ 22 weeks).

RESULTS: In ddH2O-TSHR mice, 84% had pathological autoantibodies, 67% elevated thyroxine, 77% hyperplastic thyroids and 70% orbital pathology. Firmicutes were increased, and Bacteroidetes reduced relative to ddH2O-βgal; CCL5 was increased. The random forest algorithm at the genus level predicted vancomycin treatment with 100% accuracy but 74% and 70% for hFMT and probiotic, respectively. Vancomycin significantly reduced gut microbiota richness and diversity compared with all other groups; the incidence and severity of both GD and GO also decreased; reduced orbital pathology correlated positively with Akkermansia spp. whilst IL-4 levels increased. Mice receiving hFMT initially inherited their GO donors' microbiota, and the severity of induced GD increased, as did the orbital brown adipose tissue volume in TSHR mice. Furthermore, genus Bacteroides, which is reduced in GD patients, was significantly increased by vancomycin but reduced in hFMT-treated mice. Probiotic treatment significantly increased CD25[+] Treg cells in orbital draining lymph nodes but exacerbated induced autoimmune hyperthyroidism and GO.

CONCLUSIONS: These results strongly support a role for the gut microbiota in TSHR-induced disease. Whilst changes to the gut microbiota have a profound effect on quantifiable GD endocrine and immune factors, the impact on GO cellular changes is more nuanced. The findings have translational potential for novel, improved treatments. Video abstract.}, } @article {pmid33592536, year = {2021}, author = {Taş, N and de Jong, AE and Li, Y and Trubl, G and Xue, Y and Dove, NC}, title = {Metagenomic tools in microbial ecology research.}, journal = {Current opinion in biotechnology}, volume = {67}, number = {}, pages = {184-191}, doi = {10.1016/j.copbio.2021.01.019}, pmid = {33592536}, issn = {1879-0429}, mesh = {Ecology ; High-Throughput Nucleotide Sequencing ; Metagenome/genetics ; *Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; }, abstract = {Ability to directly sequence DNA from the environment permanently changed microbial ecology. Here, we review the new insights to microbial life gleaned from the applications of metagenomics, as well as the extensive set of analytical tools that facilitate exploration of diversity and function of complex microbial communities. While metagenomics is shaping our understanding of microbial functions in ecosystems via gene-centric and genome-centric methods, annotating functions, metagenome assembly and binning in heterogeneous samples remains challenging. Development of new analysis and sequencing platforms generating high-throughput long-read sequences and functional screening opportunities will aid in harnessing metagenomes to increase our understanding of microbial taxonomy, function, ecology, and evolution in the environment.}, } @article {pmid33592475, year = {2021}, author = {Cao, L and Liao, L and Su, C and Mo, T and Zhu, F and Qin, R and Li, R}, title = {Metagenomic analysis revealed the microbiota and metabolic function during co-composting of food waste and residual sludge for nitrogen and phosphorus transformation.}, journal = {The Science of the total environment}, volume = {773}, number = {}, pages = {145561}, doi = {10.1016/j.scitotenv.2021.145561}, pmid = {33592475}, issn = {1879-1026}, mesh = {*Composting ; Food ; *Microbiota ; Nitrogen/analysis ; Phosphorus ; *Refuse Disposal ; Sewage ; Soil ; }, abstract = {This paper used bagasse as a composting additive and bulking agent in order to investigate the aerobic composting process of food waste and residual sludge. Accordingly, the variations of nitrogen and phosphorus nutrients, microbiota and metabolic function during the composting process were systematically explored. Three piles with residual sludge, food waste and bagasse mass ratios of 1:1:1, 2:1:1 and 4:1:1 were set. The ammonia nitrogen content in the three compost piles were 3.18 mg/g, 4.68 mg/g and 5.84 mg/g at the end of composting. The final available phosphorus content of the three piles were 3.42 mg/g, 6.70 mg/g and 11.21 mg/g, respectively. X-ray photoelectron spectroscopy (XPS) analysis showed that absorption peaks attributed to amines, amino acids and amides appeared in the 1:1:1 pile. Metagenomic analysis of the glycolysis and ammonia transformation pathways showed that the total relative abundance of key enzyme genes for the conversion of glucose to glucose-6-phosphate in the three plies were 0.326%, 0.213% and 0.248%, respectively. The total relative abundance of 2 glutamate dehydrogenase (GDH2), glud1-2 and E1,4,1,4 dehydrogenases in the three piles was 0.125%, 0.151% and 0.160%, respectively, as the main enzymes for the mutual conversion of ammonia and glutamate.}, } @article {pmid33591640, year = {2021}, author = {Huang, X and She, L and Liu, H and Liu, P and Chen, J and Chen, Y and Zhou, W and Lu, Y and Lin, J}, title = {Study of oral microorganisms contributing to non-carious cervical lesions via bacterial interaction and pH regulation.}, journal = {Journal of cellular and molecular medicine}, volume = {25}, number = {6}, pages = {3103-3112}, pmid = {33591640}, issn = {1582-4934}, support = {2017-1-62//Fujian Provincial Health Commission/ ; 2018QH1108//Fujian Medical University/ ; JAT170080//Young Teachers Education Research/ ; 2020Y0003//Fujian Science and Technology Department/ ; 2018Y9105//Joint Funds for the Innovation of Science and Technology of Fujian Province/ ; }, mesh = {*Bacteria ; Computational Biology/methods ; Disease Susceptibility ; Humans ; *Hydrogen-Ion Concentration ; Metagenome ; Metagenomics/methods ; *Microbial Viability ; *Microbiota ; Mouth/*microbiology ; RNA, Ribosomal, 16S ; Stomatognathic Diseases/*etiology ; }, abstract = {There is a lack of evidence about the relationship between microorganisms and non-carious cervical lesions (NCCLs) due to limited technologies. A group of 78 patients was enrolled for microbial 16S rRNA sequencing of dental plaques on normal and defective cervical surfaces. Parallel data from 39 patients were analysed with paired t tests, and Fusobacteriales exhibited significantly less distribution on NCCLs than on normal surfaces. As a result, Fusobacterium nucleatum, the most common oral bacterial strain belonging to the order Fusobacteriales, was selected for further research. From a scanning electron microscopy (SEM) scan, the tooth surface with Fusobacterium nucleatum and Streptococcus mutans culture was more intact than that without Fusobacterium nucleatum. Furthermore, the calcium contents in groups with Fusobacterium nucleatum were significantly higher than that without it. In further mechanistic research, Fusobacterium nucleatum was demonstrated to adhere to and disturb other organisms as well as producing alkaline secretions to neutralize the deleterious acidic environment, protecting the tooth structure. In conclusion, microorganisms and NCCLs were confirmed directly related through adherent bacterial interactions and pH regulation. The research provides a new perspective and experimental evidence for the relation between microorganisms and NCCLs, which guides clinical treatment and preventive dentistry in the future.}, } @article {pmid33589842, year = {2021}, author = {Schorn, MA and Verhoeven, S and Ridder, L and Huber, F and Acharya, DD and Aksenov, AA and Aleti, G and Moghaddam, JA and Aron, AT and Aziz, S and Bauermeister, A and Bauman, KD and Baunach, M and Beemelmanns, C and Beman, JM and Berlanga-Clavero, MV and Blacutt, AA and Bode, HB and Boullie, A and Brejnrod, A and Bugni, TS and Calteau, A and Cao, L and Carrión, VJ and Castelo-Branco, R and Chanana, S and Chase, AB and Chevrette, MG and Costa-Lotufo, LV and Crawford, JM and Currie, CR and Cuypers, B and Dang, T and de Rond, T and Demko, AM and Dittmann, E and Du, C and Drozd, C and Dujardin, JC and Dutton, RJ and Edlund, A and Fewer, DP and Garg, N and Gauglitz, JM and Gentry, EC and Gerwick, L and Glukhov, E and Gross, H and Gugger, M and Guillén Matus, DG and Helfrich, EJN and Hempel, BF and Hur, JS and Iorio, M and Jensen, PR and Kang, KB and Kaysser, L and Kelleher, NL and Kim, CS and Kim, KH and Koester, I and König, GM and Leao, T and Lee, SR and Lee, YY and Li, X and Little, JC and Maloney, KN and Männle, D and Martin H, C and McAvoy, AC and Metcalf, WW and Mohimani, H and Molina-Santiago, C and Moore, BS and Mullowney, MW and Muskat, M and Nothias, LF and O'Neill, EC and Parkinson, EI and Petras, D and Piel, J and Pierce, EC and Pires, K and Reher, R and Romero, D and Roper, MC and Rust, M and Saad, H and Saenz, C and Sanchez, LM and Sørensen, SJ and Sosio, M and Süssmuth, RD and Sweeney, D and Tahlan, K and Thomson, RJ and Tobias, NJ and Trindade-Silva, AE and van Wezel, GP and Wang, M and Weldon, KC and Zhang, F and Ziemert, N and Duncan, KR and Crüsemann, M and Rogers, S and Dorrestein, PC and Medema, MH and van der Hooft, JJJ}, title = {A community resource for paired genomic and metabolomic data mining.}, journal = {Nature chemical biology}, volume = {17}, number = {4}, pages = {363-368}, pmid = {33589842}, issn = {1552-4469}, support = {R01 GM118815/GM/NIGMS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; R35 GM138002/GM/NIGMS NIH HHS/United States ; R01 AT009143/AT/NCCIH NIH HHS/United States ; U19 AI142720/AI/NIAID NIH HHS/United States ; DP2 AT010401/AT/NCCIH NIH HHS/United States ; F32 CA221327/CA/NCI NIH HHS/United States ; U01 GM110706/GM/NIGMS NIH HHS/United States ; }, mesh = {Data Mining/*methods ; Databases, Factual ; Genomics/*methods ; Metabolomics/*methods ; }, abstract = {Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding identification of natural product biosynthetic origins and metabolite structures.}, } @article {pmid33589511, year = {2021}, author = {Bi, Y and Tu, Y and Zhang, N and Wang, S and Zhang, F and Suen, G and Shao, D and Li, S and Diao, Q}, title = {Multiomics analysis reveals the presence of a microbiome in the gut of fetal lambs.}, journal = {Gut}, volume = {70}, number = {5}, pages = {853-864}, pmid = {33589511}, issn = {1468-3288}, mesh = {Animals ; Female ; Fetus/*metabolism/*microbiology ; Gastrointestinal Microbiome/*genetics ; Gene Expression Profiling ; Metabolomics ; Metagenomics ; Models, Animal ; Pregnancy ; Sheep/*genetics/*microbiology ; }, abstract = {OBJECTIVE: Microbial exposure is critical to neonatal and infant development, growth and immunity. However, whether a microbiome is present in the fetal gut prior to birth remains debated. In this study, lambs delivered by aseptic hysterectomy at full term were used as an animal model to investigate the presence of a microbiome in the prenatal gut using a multiomics approach.

DESIGN: Lambs were euthanised immediately after aseptic caesarean section and their cecal content and umbilical cord blood samples were aseptically acquired. Cecal content samples were assessed using metagenomic and metatranscriptomic sequencing to characterise any existing microbiome. Both sample types were analysed using metabolomics in order to detect microbial metabolites.

RESULTS: We detected a low-diversity and low-biomass microbiome in the prenatal fetal gut, which was mainly composed of bacteria belonging to the phyla Proteobacteria, Actinobacteria and Firmicutes. Escherichia coli was the most abundant species in the prenatal fetal gut. We also detected multiple microbial metabolites including short chain fatty acids, deoxynojirimycin, mitomycin and tobramycin, further indicating the presence of metabolically active microbiota. Additionally, bacteriophage phiX174 and Orf virus, as well as antibiotic resistance genes, were detected in the fetal gut, suggesting that bacteriophage, viruses and bacteria carrying antibiotic resistance genes can be transmitted from the mother to the fetus during the gestation period.

CONCLUSIONS: This study provides strong evidence that the prenatal gut harbours a microbiome and that microbial colonisation of the fetal gut commences in utero.}, } @article {pmid33588951, year = {2021}, author = {Raplee, I and Walker, L and Xu, L and Surathu, A and Chockalingam, A and Stewart, S and Han, X and Rouse, R and Li, Z}, title = {Emergence of nosocomial associated opportunistic pathogens in the gut microbiome after antibiotic treatment.}, journal = {Antimicrobial resistance and infection control}, volume = {10}, number = {1}, pages = {36}, pmid = {33588951}, issn = {2047-2994}, mesh = {Animals ; Anti-Bacterial Agents/adverse effects/*pharmacology ; Bacteria/classification ; Cross Infection/*microbiology ; Dysbiosis/chemically induced ; Female ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred BALB C ; Opportunistic Infections/*microbiology ; }, abstract = {INTRODUCTION: According to the Centers for Disease Control's 2015 Hospital Acquired Infection Hospital Prevalence Survey, 1 in 31 hospital patients was infected with at least one nosocomial pathogen while being treated for unrelated issues. Many studies associate antibiotic administration with nosocomial infection occurrence. However, to our knowledge, there is little to no direct evidence of antibiotic administration selecting for nosocomial opportunistic pathogens.

AIM: This study aims to confirm gut microbiota shifts in an animal model of antibiotic treatment to determine whether antibiotic use favors pathogenic bacteria.

METHODOLOGY: We utilized next-generation sequencing and in-house metagenomic assembly and taxonomic assignment pipelines on the fecal microbiota of a urinary tract infection mouse model with and without antibiotic treatment.

RESULTS: Antibiotic therapy decreased the number of detectable species of bacteria by at least 20-fold. Furthermore, the gut microbiota of antibiotic treated mice had a significant increase of opportunistic pathogens that have been implicated in nosocomial infections, like Acinetobacter calcoaceticus/baumannii complex, Chlamydia abortus, Bacteroides fragilis, and Bacteroides thetaiotaomicron. Moreover, antibiotic treatment selected for antibiotic resistant gene enriched subpopulations for many of these opportunistic pathogens.

CONCLUSIONS: Oral antibiotic therapy may select for common opportunistic pathogens responsible for nosocomial infections. In this study opportunistic pathogens present after antibiotic therapy harbored more antibiotic resistant genes than populations of opportunistic pathogens before treatment. Our results demonstrate the effects of antibiotic therapy on induced dysbiosis and expansion of opportunistic pathogen populations and antibiotic resistant subpopulations of those pathogens. Follow-up studies with larger samples sizes and potentially controlled clinical investigations should be performed to confirm our findings.}, } @article {pmid33588422, year = {2021}, author = {Barra, WF and Sarquis, DP and Khayat, AS and Khayat, BCM and Demachki, S and Anaissi, AKM and Ishak, G and Santos, NPC and Dos Santos, SEB and Burbano, RR and Moreira, FC and de Assumpção, PP}, title = {Gastric Cancer Microbiome.}, journal = {Pathobiology : journal of immunopathology, molecular and cellular biology}, volume = {88}, number = {2}, pages = {156-169}, doi = {10.1159/000512833}, pmid = {33588422}, issn = {1423-0291}, mesh = {Computational Biology ; Gastric Mucosa/microbiology ; Gastrointestinal Microbiome/*genetics/physiology ; Helicobacter pylori/genetics/pathogenicity ; Humans ; Metabolic Networks and Pathways ; Metagenome ; Prevotella/genetics/pathogenicity ; Stomach Neoplasms/*microbiology ; }, abstract = {Identifying a microbiome pattern in gastric cancer (GC) is hugely debatable due to the variation resulting from the diversity of the studied populations, clinical scenarios, and metagenomic approach. H. pylori remains the main microorganism impacting gastric carcinogenesis and seems necessary for the initial steps of the process. Nevertheless, an additional non-H. pylori microbiome pattern is also described, mainly at the final steps of the carcinogenesis. Unfortunately, most of the presented results are not reproducible, and there are no consensual candidates to share the H. pylori protagonists. Limitations to reach a consistent interpretation of metagenomic data include contamination along every step of the process, which might cause relevant misinterpretations. In addition, the functional consequences of an altered microbiome might be addressed. Aiming to minimize methodological bias and limitations due to small sample size and the lack of standardization of bioinformatics assessment and interpretation, we carried out a comprehensive analysis of the publicly available metagenomic data from various conditions relevant to gastric carcinogenesis. Mainly, instead of just analyzing the results of each available publication, a new approach was launched, allowing the comprehensive analysis of the total sample amount, aiming to produce a reliable interpretation due to using a significant number of samples, from different origins, in a standard protocol. Among the main results, Helicobacter and Prevotella figured in the "top 6" genera of every group. Helicobacter was the first one in chronic gastritis (CG), gastric cancer (GC), and adjacent (ADJ) groups, while Prevotella was the leader among healthy control (HC) samples. Groups of bacteria are differently abundant in each clinical situation, and bacterial metabolic pathways also diverge along the carcinogenesis cascade. This information may support future microbiome interventions aiming to face the carcinogenesis process and/or reduce GC risk.}, } @article {pmid33587919, year = {2021}, author = {Honarbakhsh, M and Ericsson, A and Zhong, G and Isoherranen, N and Zhu, C and Bromberg, Y and Van Buiten, C and Malta, K and Joseph, L and Sampath, H and Lackey, AI and Storch, J and Vetriani, C and Chikindas, ML and Breslin, P and Quadro, L}, title = {Impact of vitamin A transport and storage on intestinal retinoid homeostasis and functions.}, journal = {Journal of lipid research}, volume = {62}, number = {}, pages = {100046}, pmid = {33587919}, issn = {1539-7262}, support = {R01 GM111772/GM/NIGMS NIH HHS/United States ; K01 OD019924/OD/NIH HHS/United States ; R01 DK038389/DK/NIDDK NIH HHS/United States ; R01 HD083331/HD/NICHD NIH HHS/United States ; U54 AR055073/AR/NIAMS NIH HHS/United States ; R01 HD094778/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; *Vitamin A/metabolism ; Mice ; *Homeostasis ; Vitamin A Deficiency/metabolism ; Retinoids/metabolism ; Biological Transport ; Acyltransferases/metabolism/deficiency/genetics ; Intestinal Mucosa/metabolism ; Mice, Knockout ; Gastrointestinal Microbiome ; Retinol-Binding Proteins/metabolism ; Intestines ; }, abstract = {Lecithin:retinol acyltransferase and retinol-binding protein enable vitamin A (VA) storage and transport, respectively, maintaining tissue homeostasis of retinoids (VA derivatives). The precarious VA status of the lecithin:retinol acyltransferase-deficient (Lrat[-/-]) retinol-binding protein-deficient (Rbp[-/-]) mice rapidly deteriorates upon dietary VA restriction, leading to signs of severe vitamin A deficiency (VAD). As retinoids impact gut morphology and functions, VAD is often linked to intestinal pathological conditions and microbial dysbiosis. Thus, we investigated the contribution of VA storage and transport to intestinal retinoid homeostasis and functionalities. We showed the occurrence of intestinal VAD in Lrat[-/-]Rbp[-/-] mice, demonstrating the critical role of both pathways in preserving gut retinoid homeostasis. Moreover, in the mutant colon, VAD resulted in a compromised intestinal barrier as manifested by reduced mucins and antimicrobial defense, leaky gut, increased inflammation and oxidative stress, and altered mucosal immunocytokine profiles. These perturbations were accompanied by fecal dysbiosis, revealing that the VA status (sufficient vs. deficient), rather than the amount of dietary VA per se, is likely a major initial discriminant of the intestinal microbiome. Our data also pointed to a specific fecal taxonomic profile and distinct microbial functionalities associated with VAD. Overall, our findings revealed the suitability of the Lrat[-/-]Rbp[-/-] mice as a model to study intestinal dysfunctions and dysbiosis promoted by changes in tissue retinoid homeostasis induced by the host VA status and/or intake.}, } @article {pmid33587158, year = {2021}, author = {Ma, Z and Lee, S and Fan, P and Zhai, Y and Lim, J and Galvão, KN and Nelson, C and Jeong, KC}, title = {Diverse β-lactam antibiotic-resistant bacteria and microbial community in milk from mastitic cows.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {5}, pages = {2109-2121}, pmid = {33587158}, issn = {1432-0614}, support = {2015-68003-22971//National Institute of Food and Agriculture/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/genetics ; Cattle ; Female ; Humans ; *Mastitis/drug therapy ; *Mastitis, Bovine/drug therapy ; *Microbiota ; Milk ; }, abstract = {Intramammary bacterial infection, the most common cause of mastitis, is the most costly disease in dairy cattle in the US and reason for antibiotic usage. Ceftiofur, a third-generation cephalosporin, is generally used to treat such disease, but it has a high treatment failure rate. Though the reason is not known clearly, it is hypothesized that multiple factors are associated with the treatment failure. In this study, we analyzed 169 milk samples from cows with mastitis in two independent dairy farms (Farm A and B) in which 19.4% (Farm A) and 14.3% (Farm B) of the antibiotic treated cows were not cured. The prevalence of cephalosporin-resistant bacteria (CRB) in milk was 72.0% and 42.1% in Farm A and B, respectively. Nineteen and nine bacterial genera were identified in Farm A and B respectively, with the most abundant genus being Staphylococcus (27.1%; Farm A) and Bacillus (63.5%; Farm B). However, no strong relationship between the treatment failure rate and the CRB prevalence was observed. Furthermore, the metagenomic analysis showed no significant differences in the α- and β-diversities of microbiota in milk samples from cured and uncured cows, suggesting that antibiotic-resistant bacteria were not the sole reason for the antibiotic treatment failure. KEY POINTS: • The mastitic milk samples had high prevalence of cephalosporin-resistant bacteria (CRB). • The CRB identified belong to diversified species. • Antibiotic treatment failure was not solely caused by the abundance of CRB.}, } @article {pmid33585735, year = {2021}, author = {Lin, J and Jiang, W and Shi, Y and Cai, W}, title = {Metagenomic Sequencing Revealed the Potential Pathogenic Threats of Banknotes.}, journal = {ACS omega}, volume = {6}, number = {5}, pages = {3499-3507}, pmid = {33585735}, issn = {2470-1343}, abstract = {Banknotes have long been suspected to be biologically "dirty" due to their frequent human contact, which may transmit human microbial pathogens. Still, it is an unsettled issue whether the microbes on banknotes pose a real threat to human health. In several previous studies, metagenomic sequencing was used to reveal the diversities of microbes on banknotes but live microorganism culture and functional verification were lacking. In this study, we collected banknotes of RMB in China as well as dollar bills in the United States and analyzed the microbial biodiversity and drug resistance genes carried by the identified microbes by metagenomic sequencing and in vitro culture methods. We identified eight major genera of drug-resistant bacteria through screening of 30 antibiotics, and the blood agar plate culture uncovered six pathogenic fungal species. Numerous phage and six dangerous viral sequences were also found. These results should substantiate our concern about the potential risk of banknotes to human health.}, } @article {pmid33583433, year = {2021}, author = {Raimundo, I and Silva, R and Meunier, L and Valente, SM and Lago-Lestón, A and Keller-Costa, T and Costa, R}, title = {Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {43}, pmid = {33583433}, issn = {2049-2618}, mesh = {Animals ; Anthozoa/microbiology ; Aquatic Organisms/*microbiology ; Bacteria/enzymology/genetics/*metabolism ; Chitin/*metabolism ; Chitinases/genetics/metabolism ; Geologic Sediments/*microbiology ; *Metagenomics ; *Microbiota/genetics ; Oceans and Seas ; Phylogeny ; Porifera/microbiology ; Seawater/*microbiology ; Symbiosis ; }, abstract = {BACKGROUND: Chitin ranks as the most abundant polysaccharide in the oceans yet knowledge of shifts in structure and diversity of chitin-degrading communities across marine niches is scarce. Here, we integrate cultivation-dependent and -independent approaches to shed light on the chitin processing potential within the microbiomes of marine sponges, octocorals, sediments, and seawater.

RESULTS: We found that cultivatable host-associated bacteria in the genera Aquimarina, Enterovibrio, Microbulbifer, Pseudoalteromonas, Shewanella, and Vibrio were able to degrade colloidal chitin in vitro. Congruent with enzymatic activity bioassays, genome-wide inspection of cultivated symbionts revealed that Vibrio and Aquimarina species, particularly, possess several endo- and exo-chitinase-encoding genes underlying their ability to cleave the large chitin polymer into oligomers and dimers. Conversely, Alphaproteobacteria species were found to specialize in the utilization of the chitin monomer N-acetylglucosamine more often. Phylogenetic assessments uncovered a high degree of within-genome diversification of multiple, full-length endo-chitinase genes for Aquimarina and Vibrio strains, suggestive of a versatile chitin catabolism aptitude. We then analyzed the abundance distributions of chitin metabolism-related genes across 30 Illumina-sequenced microbial metagenomes and found that the endosymbiotic consortium of Spongia officinalis is enriched in polysaccharide deacetylases, suggesting the ability of the marine sponge microbiome to convert chitin into its deacetylated-and biotechnologically versatile-form chitosan. Instead, the abundance of endo-chitinase and chitin-binding protein-encoding genes in healthy octocorals leveled up with those from the surrounding environment but was found to be depleted in necrotic octocoral tissue. Using cultivation-independent, taxonomic assignments of endo-chitinase encoding genes, we unveiled previously unsuspected richness and divergent structures of chitinolytic communities across host-associated and free-living biotopes, revealing putative roles for uncultivated Gammaproteobacteria and Chloroflexi symbionts in chitin processing within sessile marine invertebrates.

CONCLUSIONS: Our findings suggest that differential chitin degradation pathways, utilization, and turnover dictate the processing of chitin across marine micro-niches and support the hypothesis that inter-species cross-feeding could facilitate the co-existence of chitin utilizers within marine invertebrate microbiomes. We further identified chitin metabolism functions which may serve as indicators of microbiome integrity/dysbiosis in corals and reveal putative novel chitinolytic enzymes in the genus Aquimarina that may find applications in the blue biotechnology sector. Video abstract.}, } @article {pmid33583099, year = {2021}, author = {Feng, Z and Gu, M and Sun, Y and Wu, G}, title = {Potential microbial functions and quorum sensing systems in partial nitritation and anammox processes.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {93}, number = {9}, pages = {1562-1575}, doi = {10.1002/wer.1538}, pmid = {33583099}, issn = {1554-7531}, support = {51738005//National Natural Science Foundation of China/ ; }, mesh = {Bacteria/genetics ; Bioreactors ; *Microbiota ; Nitrogen ; Oxidation-Reduction ; *Quorum Sensing ; }, abstract = {Diverse microbial communities coexist in the partial nitritation-anaerobic ammonium oxidation (PNA) process, in which nitrogen metabolism and information exchange are two important microbial interactions. In the PNA process, the existence of diverse microorganisms including nitrifiers, anammox bacteria, and heterotrophs makes it challenging to achieve a balanced relationship between anaerobic ammonium oxidation bacteria and ammonia oxidizing bacteria. In this study, potential microbial functions in nitrogen conversion and acyl-homoserine lactones (AHLs)-based quorum sensing (QS) in PNA processes were examined. Candidatus_Kuenenia and Nitrosomonas were the key functional bacteria responsible for PNA, while Nitrospira was detected as the dominant nitrite oxidizing bacteria (NOB). Heterotrophs containing nxr might play a similar function to NOB. The AHLs-QS system was an important microbial communication pathway in PNA systems. N-octanoyl-L-homoserine lactone, N-decanoyl homoserine lactone, and N-dodecanoyl homoserine lactone were the main AHLs, which might be synthesized by nitrogen converting microorganisms and heterotrophs. However, only heterotrophs had the potential to sense and degrade AHLs, such as Saccharophagus (sensing) and Leptospira (degradation). These results provide comprehensive information about the possible microbial functions and interactions in the PNA system and clues for system optimization from a microbial perspective. PRACTITIONER POINTS: ●Potential functions of anammox bacteria, nitrifiers, and heterotrophs were revealed. ●Diverse nitrogen conversion and AHLs-quorum sensing related genes were detected. ●Anammox bacteria and AOB played important roles in the AHLs synthesis process. ●Heterotrophs could sense and degrade AHLs during information exchange.}, } @article {pmid33579424, year = {2021}, author = {Golonka, RM and Vijay-Kumar, M}, title = {Atypical immunometabolism and metabolic reprogramming in liver cancer: Deciphering the role of gut microbiome.}, journal = {Advances in cancer research}, volume = {149}, number = {}, pages = {171-255}, doi = {10.1016/bs.acr.2020.10.004}, pmid = {33579424}, issn = {2162-5557}, support = {R01 CA219144/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Carcinoma, Hepatocellular/immunology/*metabolism/microbiology/*pathology ; *Gastrointestinal Microbiome ; Humans ; Immune System/immunology ; Liver Neoplasms/immunology/*metabolism/microbiology/*pathology ; }, abstract = {Hepatocellular carcinoma (HCC) is the fourth leading cause of cancer-related mortality worldwide. Much recent research has delved into understanding the underlying molecular mechanisms of HCC pathogenesis, which has revealed to be heterogenous and complex. Two major hallmarks of HCC include: (i) a hijacked immunometabolism and (ii) a reprogramming in metabolic processes. We posit that the gut microbiota is a third component in an entanglement triangle contributing to HCC progression. Besides metagenomic studies highlighting the diagnostic potential in the gut microbiota profile, recent research is pinpointing the gut microbiota as an instigator, not just a mere bystander, in HCC. In this chapter, we discuss mechanistic insights on atypical immunometabolism and metabolic reprogramming in HCC, including the examination of tumor-associated macrophages and neutrophils, tumor-infiltrating lymphocytes (e.g., T-cell exhaustion, regulatory T-cells, natural killer T-cells), the Warburg effect, rewiring of the tricarboxylic acid cycle, and glutamine addiction. We further discuss the potential involvement of the gut microbiota in these characteristics of hepatocarcinogenesis. An immediate highlight is that microbiota metabolites (e.g., short chain fatty acids, secondary bile acids) can impair anti-tumor responses, which aggravates HCC. Lastly, we describe the rising 'new era' of immunotherapies (e.g., immune checkpoint inhibitors, adoptive T-cell transfer) and discuss for the potential incorporation of gut microbiota targeted therapeutics (e.g., probiotics, fecal microbiota transplantation) to alleviate HCC. Altogether, this chapter invigorates for continuous research to decipher the role of gut microbiome in HCC from its influence on immunometabolism and metabolic reprogramming.}, } @article {pmid33579191, year = {2021}, author = {Lkhagva, E and Chung, HJ and Hong, J and Tang, WHW and Lee, SI and Hong, ST and Lee, S}, title = {The regional diversity of gut microbiome along the GI tract of male C57BL/6 mice.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {44}, pmid = {33579191}, issn = {1471-2180}, support = {Grant No. HI18C2039//Korea Health Industry Development Institute/ ; }, mesh = {Animals ; Bacteria/classification/*genetics/metabolism ; Bacterial Physiological Phenomena ; *Biodiversity ; Cecum/microbiology ; Colon/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*anatomy & histology/*microbiology ; Hydrogen-Ion Concentration ; Ileum/microbiology ; Jejunum/microbiology ; Male ; *Metagenome ; Mice ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S/genetics ; Stomach/microbiology ; }, abstract = {BACKGROUND: The proliferation and survival of microbial organisms including intestinal microbes are determined by their surrounding environments. Contrary to popular myth, the nutritional and chemical compositions, water contents, O2 contents, temperatures, and pH in the gastrointestinal (GI) tract of a human are very different in a location-specific manner, implying heterogeneity of the microbial composition in a location-specific manner.

RESULTS: We first investigated the environmental conditions at 6 different locations along the GI tract and feces of ten weeks' old male SPF C57BL/6 mice. As previously known, the pH and water contents of the GI contents at the different locations of the GI tract were very different from each other in a location-specific manner, and none of which were not even similar to those of feces. After confirming the heterogeneous nature of the GI contents in specific locations and feces, we thoroughly analyzed the composition of the microbiome of the GI contents and feces. 16S rDNA-based metagenome sequencing on the GI contents and feces showed the presence of 13 different phyla. The abundance of Firmicutes gradually decreased from the stomach to feces while the abundance of Bacteroidetes gradually increased. The taxonomic α-diversities measured by ACE (Abundance-based Coverage Estimator) richness, Shannon diversity, and Fisher's alpha all indicated that the diversities of gut microbiome at colon and cecum were much higher than that of feces. The diversities of microbiome compositions were lowest in jejunum and ileum while highest in cecum and colon. Interestingly, the diversities of the fecal microbiome were lower than those of the cecum and colon. Beta diversity analyses by NMDS plots, PCA, and unsupervised hierarchical clustering all showed that the microbiome compositions were very diverse in a location-specific manner. Direct comparison of the fecal microbiome with the microbiome of the whole GI tracts by α-and β-diversities showed that the fecal microbiome did not represent the microbiome of the whole GI tract.

CONCLUSION: The fecal microbiome is different from the whole microbiome of the GI tract, contrary to a baseline assumption of contemporary microbiome research work.}, } @article {pmid33578068, year = {2021}, author = {Núñez, A and García, AM and Moreno, DA and Guantes, R}, title = {Seasonal changes dominate long-term variability of the urban air microbiome across space and time.}, journal = {Environment international}, volume = {150}, number = {}, pages = {106423}, doi = {10.1016/j.envint.2021.106423}, pmid = {33578068}, issn = {1873-6750}, mesh = {*Air Microbiology ; Cities ; Fungi ; Humans ; *Microbiota ; Seasons ; Spain ; }, abstract = {Compared to soil or aquatic ecosystems, the atmosphere is still an underexplored environment for microbial diversity. In this study, we surveyed the composition, variability and sources of microbes (bacteria and fungi) in the near surface atmosphere of a highly populated area, spanning ~ 4,000 Km[2] around the city center of Madrid (Spain), in different seasonal periods along two years. We found a core of abundant bacterial genera robust across space and time, most of soil origin, while fungi were more sensitive to environmental conditions. Microbial communities showed clear seasonal patterns driven by variability of environmental factors, mainly temperature and accumulated rain, while local sources played a minor role. We also identified taxa in both groups characteristic of seasonal periods, but not of specific sampling sites or plant coverage. The present study suggests that the near surface atmosphere of urban environments contains an ecosystem stable across relatively large spatial and temporal scales, with a rather homogenous composition, modulated by climatic variations. As such, it contributes to our understanding of the long-term changes associated to the human exposome in the air of highly populated areas.}, } @article {pmid33577875, year = {2021}, author = {Fujimoto, K and Kimura, Y and Allegretti, JR and Yamamoto, M and Zhang, YZ and Katayama, K and Tremmel, G and Kawaguchi, Y and Shimohigoshi, M and Hayashi, T and Uematsu, M and Yamaguchi, K and Furukawa, Y and Akiyama, Y and Yamaguchi, R and Crowe, SE and Ernst, PB and Miyano, S and Kiyono, H and Imoto, S and Uematsu, S}, title = {Functional Restoration of Bacteriomes and Viromes by Fecal Microbiota Transplantation.}, journal = {Gastroenterology}, volume = {160}, number = {6}, pages = {2089-2102.e12}, pmid = {33577875}, issn = {1528-0012}, support = {R01 AI079145/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Aged ; Bacteriophages ; Clostridioides difficile ; Enterocolitis, Pseudomembranous/microbiology/*therapy ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/*microbiology/virology ; Humans ; Male ; Metagenomics ; Microviridae ; Middle Aged ; Proteobacteria ; *Virome/genetics ; }, abstract = {BACKGROUND & AIMS: Fecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridioides difficile infection (rCDI). However, the overall mechanisms underlying FMT success await comprehensive elucidation, and the safety of FMT has recently become a serious concern because of the occurrence of drug-resistant bacteremia transmitted by FMT. We investigated whether functional restoration of the bacteriomes and viromes by FMT could be an indicator of successful FMT.

METHODS: The human intestinal bacteriomes and viromes from 9 patients with rCDI who had undergone successful FMT and their donors were analyzed. Prophage-based and CRISPR spacer-based host bacteria-phage associations in samples from recipients before and after FMT and in donor samples were examined. The gene functions of intestinal microorganisms affected by FMT were evaluated.

RESULTS: Metagenomic sequencing of both the viromes and bacteriomes revealed that FMT does change the characteristics of intestinal bacteriomes and viromes in recipients after FMT compared with those before FMT. In particular, many Proteobacteria, the fecal abundance of which was high before FMT, were eliminated, and the proportion of Microviridae increased in recipients. Most temperate phages also behaved in parallel with the host bacteria that were altered by FMT. Furthermore, the identification of bacterial and viral gene functions before and after FMT revealed that some distinctive pathways, including fluorobenzoate degradation and secondary bile acid biosynthesis, were significantly represented.

CONCLUSIONS: The coordinated action of phages and their host bacteria restored the recipients' intestinal flora. These findings show that the restoration of intestinal microflora functions reflects the success of FMT.}, } @article {pmid33576276, year = {2022}, author = {Schmidt, BM}, title = {Emerging Diabetic Foot Ulcer Microbiome Analysis Using Cutting Edge Technologies.}, journal = {Journal of diabetes science and technology}, volume = {16}, number = {2}, pages = {353-363}, pmid = {33576276}, issn = {1932-2968}, support = {P30 DK020572/DK/NIDDK NIH HHS/United States ; U01 DK119083/DK/NIDDK NIH HHS/United States ; }, mesh = {Amputation, Surgical ; *Diabetes Mellitus ; *Diabetic Foot ; *Foot Ulcer ; Humans ; *Microbiota ; Prognosis ; Wound Healing ; }, abstract = {One of the most prevalent complications of diabetes mellitus are diabetic foot ulcers (DFU). Diabetic foot ulcers represent a complex condition placing individuals at-risk for major lower extremity amputations and are an independent predictor of patient mortality. DFU heal poorly when standard of care therapy is applied. In fact, wound healing occurs only approximately 30% within 12 weeks and only 45% regardless of time when standard of care is utilized. Similarly, diabetic foot infections occur in half of all DFU and conventional microbiologic cultures can take several days to process before a result is known. DFU represent a significant challenge in this regard because DFU often demonstrate polymicrobial growth, become resistant to preferred antibiotic therapy, and do not inform providers about long-term prognosis. In addition, conventional culture yields may be affected by the timing of antibiotic administration and collection of tissue for analysis. This may lead to suboptimal antibiotic administration or debilitating amputations. The microbiome of DFU is a new frontier to better understand the interactions between host organisms and pathogenic ones. Newer molecular techniques are readily available to assist in analyzing the constituency of the microbiome of DFU. These emerging techniques have already been used to study the microbiome of DFU and have clinical implications that may alter standard of care practice in the near future. Here emerging molecular techniques that can provide clinicians with rapid DFU-related-information and help prognosticate outcomes in this vulnerable patient population are presented.}, } @article {pmid33573862, year = {2021}, author = {Lundy, SD and Sangwan, N and Parekh, NV and Selvam, MKP and Gupta, S and McCaffrey, P and Bessoff, K and Vala, A and Agarwal, A and Sabanegh, ES and Vij, SC and Eng, C}, title = {Functional and Taxonomic Dysbiosis of the Gut, Urine, and Semen Microbiomes in Male Infertility.}, journal = {European urology}, volume = {79}, number = {6}, pages = {826-836}, doi = {10.1016/j.eururo.2021.01.014}, pmid = {33573862}, issn = {1873-7560}, mesh = {*Dysbiosis ; Humans ; *Infertility, Male/diagnosis/genetics ; Male ; *Microbiota ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Semen ; Sperm Motility ; }, abstract = {BACKGROUND: Little is known about the role of the genitourinary and gastrointestinal microbiota in the pathogenesis of male infertility.

OBJECTIVE: To compare the taxonomic and functional profiles of the gut, semen, and urine microbiomes of infertile and fertile men.

We prospectively enrolled 25 men with primary idiopathic infertility and 12 healthy men with proven paternity, and we collected rectal swabs, semen samples, midstream urine specimens, and experimental controls.

We performed comprehensive semen analysis, 16S rRNA sequencing for quantitative high-resolution taxonomy, and shotgun metagenomics with a median of 140 million reads per sample for functional metabolic pathway profiling.

RESULTS AND LIMITATIONS: We identified a diverse semen microbiome with modest similarity to the urinary microbiome. Infertile men harbored increased seminal α-diversity and distinct β-diversity, increased seminal Aerococcus, and decreased rectal Anaerococcus. Prevotella abundance was inversely associated with sperm concentration, and Pseudomonas was directly associated with total motile sperm count. Vasectomy appeared to alter the seminal microbiome, suggesting a testicular or epididymal contribution. Anaerobes were highly over-represented in the semen of infertile men with a varicocele, but oxidative stress and leukocytospermia were associated with only subtle differences. Metagenomics data identified significant alterations in the S-adenosyl-L-methionine cycle, which may play a multifaceted role in the pathogenesis of infertility via DNA methylation, oxidative stress, and/or polyamine synthesis.

CONCLUSIONS: This pilot study represents the first comprehensive investigation into the microbiome in male infertility. These findings provide the foundation for future investigations to explore causality and identify novel microbiome-based diagnostics and therapeutics for men with this complex and emotionally devastating disease.

PATIENT SUMMARY: We explored the resident populations of bacteria living in the gut, semen, and urine of infertile and fertile men. We found several important bacterial and metabolic pathway differences with the potential to aid in diagnosing and treating male infertility in the future.}, } @article {pmid33570553, year = {2021}, author = {Jiang, H and Fang, S and Yang, H and Chen, C}, title = {Identification of the relationship between the gut microbiome and feed efficiency in a commercial pig cohort.}, journal = {Journal of animal science}, volume = {99}, number = {3}, pages = {}, pmid = {33570553}, issn = {1525-3163}, mesh = {Animal Feed/analysis ; Animals ; Feces ; *Gastrointestinal Microbiome ; Prevotella ; RNA, Ribosomal, 16S/genetics ; Swine ; }, abstract = {Feed efficiency (FE) is an economically important trait in pig production. Gut microbiota plays an important role in energy harvest, nutrient metabolism, and fermentation of dietary indigestible components. Whether and which gut microbes affect FE in pigs are largely unknown. Here, a total of 208 healthy Duroc pigs were used as experimental materials. Feces and serum samples were collected at the age of 140 d. We first performed 16S rRNA gene and metagenomic sequencing analysis to investigate the relationship between the gut microbiome and porcine residual feed intake (RFI). 16S rRNA gene sequencing analysis detected 21 operational taxonomic units showing the tendency to correlation with the RFI (P < 0.01). Metagenomic sequencing further identified that the members of Clostridiales, e.g., Ruminococcus flavefaoiens, Lachnospiraceae bacterium 28-4, and Lachnospiraceae phytofermentans, were enriched in pigs with low RFI (high-FE), while 11 bacterial species including 5 Prevotella spp., especially, the Prevotella copri, had higher abundance in pigs with high RFI. Functional capacity analysis suggested that the gut microbiome of low RFI pigs had a high abundance of the pathways related to amino acid metabolism and biosynthesis, but a low abundance of the pathways associated with monosaccharide metabolism and lipopolysaccharide biosynthesis. Serum metabolome and fecal short-chain fatty acids were determined by UPLC-QTOF/MS and gas chromatography, respectively. Propionic acid in feces and the serum metabolites related to amino acid metabolism were negatively correlated with the RFI. The results from this study may provide potential gut microbial biomarkers that could be used for improving FE in pig production industry.}, } @article {pmid33566446, year = {2022}, author = {Wang, C and Wei, S and Chen, N and Xiang, Y and Wang, Y and Jin, M}, title = {Characteristics of gut microbiota in pigs with different breeds, growth periods and genders.}, journal = {Microbial biotechnology}, volume = {15}, number = {3}, pages = {793-804}, pmid = {33566446}, issn = {1751-7915}, mesh = {Animals ; Bacteria/genetics ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Mammals/genetics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Swine ; }, abstract = {Gut microbiota plays important roles in host nutrition, metabolism and immunity, and is affected by multiple factors. However, the understandings of the gut microbiota in pigs within different breeds, growth periods and genders from a large cohort remain largely undefined. In the present study, the characteristics of the gut microbiota in 120 pigs of different breeds, growth periods and genders were investigated using the Illumina MiSeq PE300 combined with QIIME2 platform. A total of 7 388 636 raw reads and 16 411 features were obtained. Additionally, the microbial diversity, compositions and phenotypes were described. 66.53% microbiota belonged to the top 10 most abundant genera (pan gut bacteria), and 28 species were commonly identified (core gut bacteria, commonality ≥ 75%) among the pigs. Besides, the correlations within pan and core gut microbiota were firstly investigated. The metagenomic function was predicted by using PICRUSt2. Furthermore, the explanatory effects of the influencing factors suggested that growth period was the greatest contributor to the gut microbiota in pigs. These results expanded our knowledge of mammalian gut microbiota within different influencing factors and microbial-related biological features in swine, which contributes to improving animal production and assisting animal model research.}, } @article {pmid33565054, year = {2021}, author = {Gwak, HJ and Lee, SJ and Rho, M}, title = {Application of computational approaches to analyze metagenomic data.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {59}, number = {3}, pages = {233-241}, pmid = {33565054}, issn = {1976-3794}, mesh = {Animals ; Bacteria/classification/*genetics/isolation & purification ; Genome, Microbial ; Humans ; Metagenome ; *Metagenomics/methods ; Microbiota ; }, abstract = {Microorganisms play a vital role in living systems in numerous ways. In the soil or ocean environment, microbes are involved in diverse processes, such as carbon and nitrogen cycle, nutrient recycling, and energy acquisition. The relation between microbial dysbiosis and disease developments has been extensively studied. In particular, microbial communities in the human gut are associated with the pathophysiology of several chronic diseases such as inflammatory bowel disease and diabetes. Therefore, analyzing the distribution of microorganisms and their associations with the environment is a key step in understanding nature. With the advent of next-generation sequencing technology, a vast amount of metagenomic data on unculturable microbes in addition to culturable microbes has been produced. To reconstruct microbial genomes, several assembly algorithms have been developed by incorporating metagenomic features, such as uneven depth. Since it is difficult to reconstruct complete microbial genomes from metagenomic reads, contig binning approaches were suggested to collect contigs that originate from the same genome. To estimate the microbial composition in the environment, various methods have been developed to classify individual reads or contigs and profile bacterial proportions. Since microbial communities affect their hosts and environments through metabolites, metabolic profiles from metagenomic or metatranscriptomic data have been estimated. Here, we provide a comprehensive review of computational methods that can be applied to investigate microbiomes using metagenomic and metatranscriptomic sequencing data. The limitations of metagenomic studies and the key approaches to overcome such problems are discussed.}, } @article {pmid33564113, year = {2021}, author = {Tran, PQ and Bachand, SC and McIntyre, PB and Kraemer, BM and Vadeboncoeur, Y and Kimirei, IA and Tamatamah, R and McMahon, KD and Anantharaman, K}, title = {Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika.}, journal = {The ISME journal}, volume = {15}, number = {7}, pages = {1971-1986}, pmid = {33564113}, issn = {1751-7370}, mesh = {Ecosystem ; *Lakes ; Metagenome ; *Metagenomics ; Tanzania ; }, abstract = {Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth's surface. LT's mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT's 1470 meter deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 34 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change, which is predicted to bring increased stratification and anoxia to freshwater lakes.}, } @article {pmid33563544, year = {2021}, author = {Liwinski, T and Leshem, A and Elinav, E}, title = {Breakthroughs and Bottlenecks in Microbiome Research.}, journal = {Trends in molecular medicine}, volume = {27}, number = {4}, pages = {298-301}, doi = {10.1016/j.molmed.2021.01.003}, pmid = {33563544}, issn = {1471-499X}, mesh = {Diet ; Fecal Microbiota Transplantation ; Host Microbial Interactions ; Humans ; Metagenomics/methods ; *Microbiota/drug effects/genetics/immunology ; Phage Therapy ; Precision Medicine/trends ; Probiotics ; }, abstract = {Over the past 15 years, the research community has witnessed unprecedented progress in microbiome research. We review this increasing knowledge and first attempts of its clinical application, and also limitations and challenges faced by the research community, in mechanistically understanding host-microbiome interactions and integrating these insights into clinical practice.}, } @article {pmid33563315, year = {2021}, author = {Wu, G and Zhao, N and Zhang, C and Lam, YY and Zhao, L}, title = {Guild-based analysis for understanding gut microbiome in human health and diseases.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {22}, pmid = {33563315}, issn = {1756-994X}, mesh = {Databases, Genetic ; *Disease ; Female ; *Gastrointestinal Microbiome/genetics ; *Health ; Humans ; Metagenomics ; Obesity/genetics ; Phylogeny ; Polycystic Ovary Syndrome/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {To demonstrate the causative role of gut microbiome in human health and diseases, we first need to identify, via next-generation sequencing, potentially important functional members associated with specific health outcomes and disease phenotypes. However, due to the strain-level genetic complexity of the gut microbiota, microbiome datasets are highly dimensional and highly sparse in nature, making it challenging to identify putative causative agents of a particular disease phenotype. Members of an ecosystem seldomly live independently from each other. Instead, they develop local interactions and form inter-member organizations to influence the ecosystem's higher-level patterns and functions. In the ecological study of macro-organisms, members are defined as belonging to the same "guild" if they exploit the same class of resources in a similar way or work together as a coherent functional group. Translating the concept of "guild" to the study of gut microbiota, we redefine guild as a group of bacteria that show consistent co-abundant behavior and likely to work together to contribute to the same ecological function. In this opinion article, we discuss how to use guilds as the aggregation unit to reduce dimensionality and sparsity in microbiome-wide association studies for identifying candidate gut bacteria that may causatively contribute to human health and diseases.}, } @article {pmid33562073, year = {2021}, author = {Bergner, LM and Mollentze, N and Orton, RJ and Tello, C and Broos, A and Biek, R and Streicker, DG}, title = {Characterizing and Evaluating the Zoonotic Potential of Novel Viruses Discovered in Vampire Bats.}, journal = {Viruses}, volume = {13}, number = {2}, pages = {}, pmid = {33562073}, issn = {1999-4915}, support = {MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; 217221/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 102507/Z/13/A/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Chiroptera/*virology ; Disease Reservoirs/veterinary/virology ; Feces/virology ; Genome, Viral/genetics ; Humans ; Machine Learning ; Metagenomics ; Phylogeny ; Rabies virus/classification/genetics/isolation & purification ; Saliva/virology ; Viruses/classification/genetics/*isolation & purification ; Zoonoses/*virology ; }, abstract = {The contemporary surge in metagenomic sequencing has transformed knowledge of viral diversity in wildlife. However, evaluating which newly discovered viruses pose sufficient risk of infecting humans to merit detailed laboratory characterization and surveillance remains largely speculative. Machine learning algorithms have been developed to address this imbalance by ranking the relative likelihood of human infection based on viral genome sequences, but are not yet routinely applied to viruses at the time of their discovery. Here, we characterized viral genomes detected through metagenomic sequencing of feces and saliva from common vampire bats (Desmodus rotundus) and used these data as a case study in evaluating zoonotic potential using molecular sequencing data. Of 58 detected viral families, including 17 which infect mammals, the only known zoonosis detected was rabies virus; however, additional genomes were detected from the families Hepeviridae, Coronaviridae, Reoviridae, Astroviridae and Picornaviridae, all of which contain human-infecting species. In phylogenetic analyses, novel vampire bat viruses most frequently grouped with other bat viruses that are not currently known to infect humans. In agreement, machine learning models built from only phylogenetic information ranked all novel viruses similarly, yielding little insight into zoonotic potential. In contrast, genome composition-based machine learning models estimated different levels of zoonotic potential, even for closely related viruses, categorizing one out of four detected hepeviruses and two out of three picornaviruses as having high priority for further research. We highlight the value of evaluating zoonotic potential beyond ad hoc consideration of phylogeny and provide surveillance recommendations for novel viruses in a wildlife host which has frequent contact with humans and domestic animals.}, } @article {pmid33561170, year = {2021}, author = {Kurth, D and Elias, D and Rasuk, MC and Contreras, M and Farías, ME}, title = {Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile.}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0246656}, pmid = {33561170}, issn = {1932-6203}, mesh = {Bacteroidetes/genetics ; Biodiversity ; Carbon Cycle/*physiology ; Chile ; Cyanobacteria/genetics ; Geologic Sediments/microbiology ; Lakes/*microbiology ; Microbiota/genetics ; Phylogeny ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Rhodopsin/genetics/*metabolism ; Salinity ; Whole Genome Sequencing/methods ; }, abstract = {In this work, molecular diversity of two hypersaline microbial mats was compared by Whole Genome Shotgun (WGS) sequencing of environmental DNA from the mats. Brava and Tebenquiche are lakes in the Salar de Atacama, Chile, where microbial communities are growing in extreme conditions, including high salinity, high solar irradiance, and high levels of toxic metals and metaloids. Evaporation creates hypersaline conditions in these lakes and mineral precipitation is a characteristic geomicrobiological feature of these benthic ecosystems. The mat from Brava was more rich and diverse, with a higher number of different taxa and with species more evenly distributed. At the phylum level, Proteobacteria, Cyanobacteria, Chloroflexi, Bacteroidetes and Firmicutes were the most abundant, including ~75% of total sequences. At the genus level, the most abundant sequences were affilitated to anoxygenic phototropic and cyanobacterial genera. In Tebenquiche mats, Proteobacteria and Bacteroidetes covered ~70% of the sequences, and 13% of the sequences were affiliated to Salinibacter genus, thus addressing the lower diversity. Regardless of the differences at the taxonomic level, functionally the two mats were similar. Thus, similar roles could be fulfilled by different organisms. Carbon fixation through the Wood-Ljungdahl pathway was well represented in these datasets, and also in other mats from Andean lakes. In spite of presenting less taxonomic diversity, Tebenquiche mats showed increased abundance and variety of rhodopsin genes. Comparison with other metagenomes allowed identifying xantorhodopsins as hallmark genes not only from Brava and Tebenquiche mats, but also for other mats developing at high altitudes in similar environmental conditions.}, } @article {pmid33559707, year = {2021}, author = {Fromentin, M and Ricard, JD and Roux, D}, title = {Respiratory microbiome in mechanically ventilated patients: a narrative review.}, journal = {Intensive care medicine}, volume = {47}, number = {3}, pages = {292-306}, pmid = {33559707}, issn = {1432-1238}, support = {Established Investigator award//European Society of Intensive Care Medicine/ ; Basic Science Award//European Society of Intensive Care Medicine/ ; MSD/SRLF//Société de Réanimation de Langue Française/ ; Young investigator award//Société de Pathologie Infectieuse de Langue Française/ ; }, mesh = {Dysbiosis ; Humans ; *Microbiota ; *Pneumonia, Ventilator-Associated ; Respiration, Artificial/adverse effects ; *Respiratory Distress Syndrome/therapy ; }, abstract = {The respiratory microbiome has been less explored than the gut microbiome. Despite the speculated importance of dysbiosis of the microbiome in ventilator-associated pneumonia (VAP) and acute respiratory distress syndrome (ARDS), only few studies have been performed in invasively ventilated ICU patients. And only the results of small cohorts have been published. An overlap exists between bacterial populations observed in the lower respiratory tract and the oropharyngeal tract. The bacterial microbiota is characterized by relatively abundant bacteria difficult to cultivate by standard methods. Under mechanical ventilation, a dysbiosis occurs with a drop overtime in diversity. During VAP development, lung dysbiosis is characterized by a shift towards a dominant bacterial pathogen (mostly Proteobacteria) whereas enrichment of gut-associated bacteria mainly Enterobacteriaceae is the specific feature discriminating ARDS patients. However, the role of this dysbiosis in VAP and ARDS pathogenesis is not yet fully understood. A more in-depth analysis of the interplay between bacteria, virus and fungi and a better understanding of the host-microbiome interaction could provide a more comprehensive view of the role of the microbiome in VAP and ARDS pathogenesis. Priority should be given to validate a consensual and robust methodology for respiratory microbiome research and to conduct longitudinal studies. A deeper understanding of microbial interplay should be a valuable guide for care of ARDS and VAP preventive/therapeutic strategies. We present a review on the current knowledge and expose perspectives and potential clinical applications of respiratory microbiome research in mechanically ventilated patients.}, } @article {pmid33554248, year = {2021}, author = {Qi, C and Wang, P and Fu, T and Lu, M and Cai, Y and Chen, X and Cheng, L}, title = {A comprehensive review for gut microbes: technologies, interventions, metabolites and diseases.}, journal = {Briefings in functional genomics}, volume = {20}, number = {1}, pages = {42-60}, doi = {10.1093/bfgp/elaa029}, pmid = {33554248}, issn = {2041-2657}, mesh = {*Gastrointestinal Microbiome ; Homeostasis ; Humans ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Gut microbes have attracted much more attentions in the recent decade since their essential roles in the development of metabolic diseases, cancer and neurological diseases. Considerable evidence indicates that the metabolism of gut microbes exert influences on intestinal homeostasis and human diseases. Here, we first reviewed two mainstream sequencing technologies involving 16s rRNA sequencing and metagenomic sequencing for gut microbes, and data analysis methods assessing alpha and beta diversity. Next, we introduced some observational studies reflecting that many factors, such as lifestyle and intake of diets, drugs, contribute to gut microbes' quantity and diversity. Then, metabolites produced by gut microbes were presented to understand that gut microbes exert on host homeostasis in the intestinal epithelium and immune system. Finally, we focused on the molecular mechanism of gut microbes on the occurrence and development of several common diseases. In-depth knowledge of the relationship among interventions, gut microbes and diseases might provide new insights in to disease prevention and treatment.}, } @article {pmid33553973, year = {2021}, author = {Bajaj, JS and Shamsaddini, A and Fagan, A and Sterling, RK and Gavis, E and Khoruts, A and Fuchs, M and Lee, H and Sikaroodi, M and Gillevet, PM}, title = {Fecal Microbiota Transplant in Cirrhosis Reduces Gut Microbial Antibiotic Resistance Genes: Analysis of Two Trials.}, journal = {Hepatology communications}, volume = {5}, number = {2}, pages = {258-271}, pmid = {33553973}, issn = {2471-254X}, support = {R21 TR002024/TR/NCATS NIH HHS/United States ; R21 TR003095/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Aged ; Anti-Bacterial Agents/administration & dosage/*adverse effects ; *Drug Resistance, Microbial ; Fecal Microbiota Transplantation/*methods ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Lactulose/therapeutic use ; Liver Cirrhosis/pathology/*therapy ; Male ; Middle Aged ; Proton Pump Inhibitors/therapeutic use ; Rifaximin/therapeutic use ; Treatment Outcome ; Young Adult ; }, abstract = {Antibiotic resistance leads to poor outcomes in cirrhosis. Fecal microbiota transplant (FMT) is associated with reduction in antibiotic resistance gene (ARG) burden in patients without cirrhosis; however, the impact in cirrhosis is unclear. We aimed to study the effect of capsule and enema FMT on ARG abundance in fecal samples, which were collected during two published FMT trials in patients with cirrhosis on rifaximin, lactulose, and proton pump inhibitors. ARGs were identified using metagenomics and mapped against the Comprehensive Antibiotic Resistance Database. Changes in ARG abundance were studied within/between groups. The capsule FMT trial involved a one-time FMT or placebo capsule administration with stool collection at baseline and week 4 postintervention. Antibiotics+enema FMT included preprocedure antibiotics followed by FMT enema versus standard-of-care (SOC). Stool was collected at baseline, postantibiotics, and day 7/15 postintervention. Both trials included 20 patients each. There was no safety/infection signal linked to FMT. In the capsule trial, beta-lactamase (OXY/LEN) expression decreased post-FMT versus baseline. Compared to placebo, patients who were post-FMT had lower abundance of vancomycin (VanH), beta-lactamase (ACT), and rifamycin ARGs; the latter was associated with cognitive improvement. No changes were seen within patients treated with placebo. In the antibiotics+enema trial for postantibiotics at day 7 versus baseline, there was an increase in vancomycin and beta-lactamase ARGs, which decreased at day 15. However, quinolone resistance increased at day 15 versus baseline. Between SOC and FMT, day 7 had largely lower ARG (CfxA beta-lactamase, VanW, and VanX) that continued at day 15 (cepA beta-lactamase, VanW). No changes were seen within the SOC group. Conclusion: Despite differences in routes of administration and preintervention antibiotics, we found that ARG abundance is largely reduced after FMT compared to pre-FMT baseline and non-FMT groups in decompensated cirrhosis.}, } @article {pmid33550118, year = {2021}, author = {Paim, WP and Maggioli, MF and Weber, MN and Rezabek, G and Narayanan, S and Ramachandran, A and Canal, CW and Bauermann, FV}, title = {Virome characterization in serum of healthy show pigs raised in Oklahoma demonstrated great diversity of ssDNA viruses.}, journal = {Virology}, volume = {556}, number = {}, pages = {87-95}, doi = {10.1016/j.virol.2021.01.006}, pmid = {33550118}, issn = {1096-0341}, mesh = {Animals ; Animals, Domestic/*virology ; Oklahoma ; Swine/*virology ; *Virome ; }, abstract = {In the United States, show pigs are raised to compete in agricultural events. These animals are usually raised in small herds with extensive human, domestic, and wild animal contact. Therefore, pathogen monitoring in this animal category is critical for improved disease surveillance and preparedness. This study characterized the virome of healthy show pigs using high-throughput sequencing using pooled serum samples from 2018 or 2019 (200 samples each pool). Results demonstrated the presence of DNA viral families (Parvoviridae, Circoviridae, and Herpesviridae) and RNA families (Arteriviridae, Flaviviridae, and Retroviridae). Twenty-three viral species were identified, including the first detection of porcine bufavirus in the US. Moreover, important swine pathogens identified included porcine reproductive and respiratory syndrome virus, atypical porcine pestivirus, and porcine circovirus (PCV). Additionally, complete coding genomes of 17 viruses from the Parvoviridae, Anelloviridae, and Circoviridae families were retrieved and included the first near full-length genomes of US Ungulate bocaparvovirus 3 species.}, } @article {pmid33550041, year = {2021}, author = {Zhang, X and Zhang, F and Mi, Y and Liu, Y and Zheng, K and Zhou, Y and Jiang, T and Wang, M and Jiang, Y and Guo, C and Shao, H and He, H and He, J and Liang, Y and Wang, M and McMinn, A}, title = {Characterization and genome analysis of phage AL infecting Pseudoalteromonas marina.}, journal = {Virus research}, volume = {295}, number = {}, pages = {198265}, doi = {10.1016/j.virusres.2020.198265}, pmid = {33550041}, issn = {1872-7492}, mesh = {*Bacteriophages ; DNA, Viral/chemistry/genetics ; Genome, Viral ; Open Reading Frames ; Phylogeny ; *Pseudoalteromonas/genetics ; Seawater ; Sequence Analysis, DNA ; }, abstract = {Although Pseudoalteromonas is an abundant, ubiquitous, marine algae-associated bacterial genus, there is still little information on their phages. In the present study, a marine phage AL, infecting Pseudoalteromonas marina, was isolated from the coastal waters off Qingdao. The AL phage is a siphovirus with an icosahedral head of 53 ± 1 nm and a non-contractile tail, length of 99 ± 1 nm. A one-step growth curve showed that the latent period was approximately 70 min, the rise period was 50 min, and the burst size was 227 pfu/cell. The genome sequence of this phage is a 33,582 bp double-stranded DNA molecule with a GC content of 40.1 %, encoding 52 open reading frames (ORFs). The order of the functional genes, especially those related to the structure module, is highly conserved and basically follows the common pattern used by siphovirus. The stable order has been formed during the long-term evolution of phages in the siphovirus group, which has helped the phages to maintain their normal morphology and function. Phylogenetic trees based on the major capsid protein (mcp) and genome-wide sequence have shown that the AL phage is closely related to four Pseudoalteromonas phages, including PHS21, PHS3, SL25 and Pq0. Further analysis using all-to-all BLASTP also confirmed that this phage shared high sequence homology with the same four Pseudoalteromonas phages, with amino acid sequence identities ranging from 44 % to 71 %. In particular, their similarity in virion structure module may imply that these phages share common assembly mechanism characteristics and infection pathways. Pseudoalteromonas phage AL not only provides basic information for the further study of the evolution of Pseudoalteromonas phages and interactions between marine phage and host but also helps to explain the unknown viral sequences in the metagenomic databases.}, } @article {pmid33549678, year = {2021}, author = {Umirah, F and Neoh, CF and Ramasamy, K and Lim, SM}, title = {Differential gut microbiota composition between type 2 diabetes mellitus patients and healthy controls: A systematic review.}, journal = {Diabetes research and clinical practice}, volume = {173}, number = {}, pages = {108689}, doi = {10.1016/j.diabres.2021.108689}, pmid = {33549678}, issn = {1872-8227}, mesh = {Adult ; Case-Control Studies ; Diabetes Mellitus, Type 2/*physiopathology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Middle Aged ; }, abstract = {AIMS: This systematic review summarised the latest findings on differential composition of gut microbiota in T2DM.

METHODS: Literature search was performed using electronic databases. Relevant studies were identified, extracted and assessed for risk of bias. The primary outcome of this systematic review was the composition of gut microbiota in healthy controls and T2DM while the secondary outcomes included the correlation of gut microbiota with metabolic parameters.

RESULTS: Thirteen case-control studies involving 575 T2DM and 840 healthy controls were included. T2DM patients exhibited a marked increase in lactobacilli. Six studies found lactobacilli to predominate the gut of T2DM patients; however, this could be confounded by the types of antihyperglyacemic medications. Conversely, butyrate producers dominate the gut of healthy controls. In T2DM patients, butyrate producers were surprisingly higher in those taking metformin intake than those not taking the drug. Whilst lactobacilli were found to be higher with increased plasma glucose, conflicting correlations were observed between various genera and anthropometric measurements, dietary intake, lipid profiles and inflammatory markers. There were moderate to strong significant positive correlations between the class Clostridia and phylum Firmicutes with pro-inflammatory IFN-γ as well as between Negativicutes and IL-6.

CONCLUSIONS: Altogether, butyrate-producing bacteria are negatively correlated to glycaemic parameters. Lactobacilli are higher in T2DM patients and Firmicutes is correlated with inflammation.}, } @article {pmid33549667, year = {2021}, author = {Ariaeenejad, S and Kavousi, K and Mamaghani, ASA and Motahar, SFS and Nedaei, H and Salekdeh, GH}, title = {In-silico discovery of bifunctional enzymes with enhanced lignocellulose hydrolysis from microbiota big data.}, journal = {International journal of biological macromolecules}, volume = {177}, number = {}, pages = {211-220}, doi = {10.1016/j.ijbiomac.2021.02.014}, pmid = {33549667}, issn = {1879-0003}, mesh = {Animals ; Big Data ; Biomass ; Cellulase/metabolism ; Cellulose/metabolism ; Endo-1,4-beta Xylanases/metabolism ; Hydrogen-Ion Concentration ; Hydrolysis ; Lignin/*metabolism ; Metagenome/physiology ; Metagenomics/methods ; Microbiota/*physiology ; Oryza/metabolism ; Polysaccharides/metabolism ; Rumen/metabolism ; Temperature ; Thermodynamics ; }, abstract = {Due to the importance of using lignocellulosic biomass, it is always important to find an effective novel enzyme or enzyme cocktail or fusion enzymes. Identification of bifunctional enzymes through a metagenomic approach is an efficient method for converting agricultural residues and a beneficial way to reduce the cost of enzyme cocktail and fusion enzyme production. In this study, a novel stable bifunctional cellulase/xylanase, PersiCelXyn1 was identified from the rumen microbiota by the multi-stage in-silico screening pipeline and computationally assisted methodology. The enzyme exhibited the optimal activity at pH 5 and 50°C. Analyzing the enzyme activity at extreme temperature, pH, long-term storage, and presence of inhibitors and metal ions, confirmed the stability of the bifunctional enzyme under harsh conditions. Hydrolysis of the rice straw by PersiCelXyn1 showed its capability to degrade both cellulose and hemicellulose polymers. Also, the enzyme improved the degradation of various biomass substrates after 168 h of hydrolysis. Our results demonstrated the power of the multi-stage in-silico screening to identify bifunctional enzymes from metagenomic big data for effective bioconversion of lignocellulosic biomass.}, } @article {pmid33547887, year = {2021}, author = {Avitia, M and Barrón-Sandoval, A and Hernández-Terán, A and Benítez, M and Barron-Gafford, GA and Dontsova, K and Pavao-Zuckerman, MA and Escalante, AE}, title = {Soil microbial composition and carbon mineralization are associated with vegetation type and temperature regime in mesocosms of a semiarid ecosystem.}, journal = {FEMS microbiology letters}, volume = {368}, number = {4}, pages = {}, doi = {10.1093/femsle/fnab012}, pmid = {33547887}, issn = {1574-6968}, mesh = {Carbon/analysis/*metabolism ; *Ecosystem ; *Microbiota ; Plants/classification/metabolism/microbiology ; Soil/chemistry ; *Soil Microbiology ; Temperature ; }, abstract = {Transition from historic grasslands to woody plants in semiarid regions has led to questions about impacts on soil functioning, where microorganisms play a primary role. Understanding the relationship between microbes, plant diversity and soil functioning is relevant to assess such impacts. We evaluate the effect that plant type change in semiarid ecosystems has for microbial diversity and composition, and how this is related to carbon mineralization (CMIN) as a proxy for soil functioning. We followed a mesocosm experiment during 2 years within the Biosphere 2 facility in Oracle, AZ, USA. Two temperature regimes were established with two types of plants (grass or mesquite). Soil samples were analyzed for physicochemical and functional parameters, as well as microbial community composition using 16S rRNA amplicon metagenomics (Illumina MiSeq). Our results show the combined role of plant type and temperature regime in CMIN, where CMIN in grass has lower values at elevated temperatures compared with the opposite trend in mesquite. We also found a strong correlation of microbial composition with plant type but not with temperature regime. Overall, we provide evidence of the major effect of plant type in the specific composition of microbial communities as a potential result of the shrub encroachment.}, } @article {pmid33547877, year = {2021}, author = {Snelson, M and Clarke, RE and Nguyen, TV and Penfold, SA and Forbes, JM and Tan, SM and Coughlan, MT}, title = {Long Term High Protein Diet Feeding Alters the Microbiome and Increases Intestinal Permeability, Systemic Inflammation and Kidney Injury in Mice.}, journal = {Molecular nutrition & food research}, volume = {65}, number = {8}, pages = {e2000851}, doi = {10.1002/mnfr.202000851}, pmid = {33547877}, issn = {1613-4133}, mesh = {Acute Kidney Injury/*etiology/microbiology/pathology ; Albuminuria/etiology ; Animals ; Body Weight ; Chemokine CCL2/blood ; Diet, High-Protein/*adverse effects ; Fibrosis ; Gastrointestinal Microbiome/genetics/*physiology ; Gene Expression ; Inflammation/*etiology/microbiology ; Intestines/physiology ; Kidney/pathology ; Male ; Mice, Inbred C57BL ; Permeability ; Mice ; }, abstract = {SCOPE: This study evaluates the effects of a chronic high protein diet (HPD) on kidney injury, intestinal permeability and gut microbiota perturbations in a mouse model.

METHOD AND RESULTS: Mice are fed a diet containing either 20% or 52% energy from protein for 24 weeks; protein displaced an equivalent amount of wheat starch. The HPD does not alter glycemic control or body weight. The HPD induces kidney injury as evidenced by increase in albuminuria, urinary kidney injury molecule-1, blood urea nitrogen, urinary isoprostanes and renal cortical NF-κB p65 gene expression. HPD decreases intestinal occludin gene expression, increases plasma endotoxin and plasma monocyte chemoattractant protein-1, indicating intestinal leakiness and systemic inflammation. Cecal microbial analysis reveals that HPD feeding does not alter alpha diversity; however, it does alter beta diversity, indicating an altered microbial community structure with HPD feeding. Predicted metagenome pathway analysis demonstrates a reduction in branched-chain amino acid synthesis and an increase of the urea cycle with consumption of a HPD.

CONCLUSION: These results demonstrate that long term HPD consumption in mice causes albuminuria, systemic inflammation, increase in gastrointestinal permeability and is associated with gut microbiome remodeling with an increase in the urea cycle pathway, which may contribute to renal injury.}, } @article {pmid33547403, year = {2021}, author = {Rampelli, S and Turroni, S and Mallol, C and Hernandez, C and Galván, B and Sistiaga, A and Biagi, E and Astolfi, A and Brigidi, P and Benazzi, S and Lewis, CM and Warinner, C and Hofman, CA and Schnorr, SL and Candela, M}, title = {Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {169}, pmid = {33547403}, issn = {2399-3642}, support = {R01 GM089886/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Archaeology ; DNA, Ancient/isolation & purification ; Ecosystem ; Feces/*microbiology ; Fossils/microbiology ; *Gastrointestinal Microbiome ; Geologic Sediments/analysis/microbiology ; History, Ancient ; Humans ; Metagenomics ; Neanderthals/*microbiology ; Sequence Analysis, DNA ; Spain ; }, abstract = {A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.}, } @article {pmid33545322, year = {2021}, author = {Fan, S and Raychaudhuri, S and Page, R and Shahinozzaman, M and Obanda, DN}, title = {Metagenomic insights into the effects of Urtica dioica vegetable on the gut microbiota of C57BL/6J obese mice, particularly the composition of Clostridia.}, journal = {The Journal of nutritional biochemistry}, volume = {91}, number = {}, pages = {108594}, doi = {10.1016/j.jnutbio.2021.108594}, pmid = {33545322}, issn = {1873-4847}, mesh = {Animals ; Clostridium/*isolation & purification/physiology ; Dysbiosis/metabolism/microbiology/therapy ; *Functional Food ; *Gastrointestinal Microbiome ; Insulin Resistance ; Male ; Metagenome ; Mice, Inbred C57BL ; Mice, Obese ; Obesity/metabolism/microbiology/*therapy ; *Urtica dioica/metabolism ; *Vegetables/metabolism ; Mice ; }, abstract = {Urtica dioica (UT) vegetable attenuates diet induced weight gain and insulin resistance. We hypothesized that UT imparts metabolic health by impacting the gut microbiota composition. We examined effects of UT on the cecal bacterial taxonomic signature of C57BL/6J mice fed isocaloric diets: a low-fat diet (LFD) with 10% fat, a high fat diet (HFD) with 45% fat or the HFD supplemented with 9% UT (HFUT). Among Firmicutes, the HFD had no significant impact on Clostridia, but increased Bacilli particularly genus Lactococcus and Lactobacillus. HFUT lowered Lactococcus but not Lactobacillus to levels of the LFD (P<.01; n=9). Further examination of Clostridia showed that HFUT increased genus Clostridium by over 2-fold particularly the species C. vincentii and C. disporicum and increased genus Turicibacter by three-fold (P<.05; n=9). Abundance of Clostridium and Turicibacter negatively correlated with body weight (P<.05; R[2]=0.42) and HOMA-IR (P<.05; R[2]=0.45). Turicibacter and Clostridium have been shown to be more abundant in lean phenotypes compared to obese. Clostridium impacts host phenotype by inducing intestinal T cell responses. The HFUT diet had no effect on members of Actinobacteria. Among Bacteroidetes, HFUT mainly increased proliferation of Bacteroides thetaiotaomicron (P<.05; n=9) with no significant impact on other groups. Functional analysis showed that HFUT enhanced bacterial beta-alanine and D-arginine metabolism both of which are associated with a lean phenotype and enhanced insulin sensitivity. We conclude that increasing the proliferation of Clostridium and Turicibacter and altering amino acid metabolism may be contributing mechanism(s) by which Urtica dioica impacts metabolic health.}, } @article {pmid33543271, year = {2021}, author = {Rong, R and Jiang, S and Xu, L and Xiao, G and Xie, Y and Liu, DJ and Li, Q and Zhan, X}, title = {MB-GAN: Microbiome Simulation via Generative Adversarial Network.}, journal = {GigaScience}, volume = {10}, number = {2}, pages = {}, pmid = {33543271}, issn = {2047-217X}, support = {R56 HG011035/HG/NHGRI NIH HHS/United States ; R01 GM126479/GM/NIGMS NIH HHS/United States ; R01 HG008983/HG/NHGRI NIH HHS/United States ; P30 CA142543/CA/NCI NIH HHS/United States ; }, mesh = {Computer Simulation ; Humans ; Image Processing, Computer-Assisted ; *Microbiota ; *Neural Networks, Computer ; Proteins ; }, abstract = {BACKGROUND: Trillions of microbes inhabit the human body and have a profound effect on human health. The recent development of metagenome-wide association studies and other quantitative analysis methods accelerate the discovery of the associations between human microbiome and diseases. To assess the strengths and limitations of these analytical tools, simulating realistic microbiome datasets is critically important. However, simulating the real microbiome data is challenging because it is difficult to model their correlation structure using explicit statistical models.

RESULTS: To address the challenge of simulating realistic microbiome data, we designed a novel simulation framework termed MB-GAN, by using a generative adversarial network (GAN) and utilizing methodology advancements from the deep learning community. MB-GAN can automatically learn from given microbial abundances and compute simulated abundances that are indistinguishable from them. In practice, MB-GAN showed the following advantages. First, MB-GAN avoids explicit statistical modeling assumptions, and it only requires real datasets as inputs. Second, unlike the traditional GANs, MB-GAN is easily applicable and can converge efficiently.

CONCLUSIONS: By applying MB-GAN to a case-control gut microbiome study of 396 samples, we demonstrated that the simulated data and the original data had similar first-order and second-order properties, including sparsity, diversities, and taxa-taxa correlations. These advantages are suitable for further microbiome methodology development where high-fidelity microbiome data are needed.}, } @article {pmid33542492, year = {2021}, author = {Jones-Freeman, B and Chonwerawong, M and Marcelino, VR and Deshpande, AV and Forster, SC and Starkey, MR}, title = {The microbiome and host mucosal interactions in urinary tract diseases.}, journal = {Mucosal immunology}, volume = {14}, number = {4}, pages = {779-792}, pmid = {33542492}, issn = {1935-3456}, mesh = {Animals ; Disease Management ; Disease Susceptibility ; Feedback, Physiological ; Gastrointestinal Microbiome ; Homeostasis ; *Host Microbial Interactions ; *Host-Pathogen Interactions ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mucous Membrane/*microbiology ; Organ Specificity ; Urinary Tract Infections/diagnosis/*etiology/therapy ; }, abstract = {The urinary tract consists of the bladder, ureters, and kidneys, and is an essential organ system for filtration and excretion of waste products and maintaining systemic homeostasis. In this capacity, the urinary tract is impacted by its interactions with other mucosal sites, including the genitourinary and gastrointestinal systems. Each of these sites harbors diverse ecosystems of microbes termed the microbiota, that regulates complex interactions with the local and systemic immune system. It remains unclear whether changes in the microbiota and associated metabolites may be a consequence or a driver of urinary tract diseases. Here, we review the current literature, investigating the impact of the microbiota on the urinary tract in homeostasis and disease including urinary stones, acute kidney injury, chronic kidney disease, and urinary tract infection. We propose new avenues for exploration of the urinary microbiome using emerging technology and discuss the potential of microbiome-based medicine for urinary tract conditions.}, } @article {pmid33542396, year = {2021}, author = {Gavande, PV and Basak, A and Sen, S and Lepcha, K and Murmu, N and Rai, V and Mazumdar, D and Saha, SP and Das, V and Ghosh, S}, title = {Functional characterization of thermotolerant microbial consortium for lignocellulolytic enzymes with central role of Firmicutes in rice straw depolymerization.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {3032}, pmid = {33542396}, issn = {2045-2322}, mesh = {Agriculture ; Bacteroidetes/enzymology ; Biofuels ; *Biomass ; Cellulases/chemistry/genetics ; Cellulose/chemistry ; Firmicutes/enzymology ; Glycoside Hydrolases/chemistry/genetics ; Humans ; Industrial Waste ; Lignin/*chemistry/genetics ; Metagenome/*genetics ; Microbial Consortia/*genetics ; Oryza/chemistry ; }, abstract = {Rice (Oryza sativa L.) straw, an agricultural waste of high yield, is a sustainable source of fermentable sugars for biofuel and other chemicals. However, it shows recalcitrance to microbial catalysed depolymerization. We herein describe development of thermotolerant microbial consortium (RSV) from vermicompost with ability to degrade rice straw and analysis of its metagenome for bacterial diversity, and lignocellulolytic carbohydrate active enzymes (CAZymes) and their phylogenetic affiliations. RSV secretome exhibited cellulases and hemicellulases with higher activity at 60 °C. It catalysed depolymerization of chemical pretreated rice straw as revealed by scanning electron microscopy and saccharification yield of 460 mg g[-1] rice straw. Microbial diversity of RSV was distinct from other compost habitats, with predominance of members of phyla Firmicutes, Proteobacteria and Bacteroidetes; and Pseudoclostridium, Thermoanaerobacterium, Chelatococcus and Algoriphagus being most abundant genera. RSV harboured 1389 CAZyme encoding ORFs of glycoside hydrolase, carbohydrate esterase, glycosyl transferase, carbohydrate binding module and auxiliary activity functions. Microorganisms of Firmicutes showed central role in lignocellulose deconstruction with importance in hemicellulose degradation; whereas representatives of Proteobacteria and Bacteroidetes contributed to cellulose and lignin degradation, respectively. RSV consortium could be a resource for mining thermotolerant cellulolytic bacteria or enzymes and studying their synergism in deconstruction of chemically pretreated rice straw.}, } @article {pmid33542369, year = {2021}, author = {Durazzi, F and Sala, C and Castellani, G and Manfreda, G and Remondini, D and De Cesare, A}, title = {Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {3030}, pmid = {33542369}, issn = {2045-2322}, mesh = {Bacteria/classification/*genetics ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome/*genetics ; Metagenomics ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {In this paper we compared taxonomic results obtained by metataxonomics (16S rRNA gene sequencing) and metagenomics (whole shotgun metagenomic sequencing) to investigate their reliability for bacteria profiling, studying the chicken gut as a model system. The experimental conditions included two compartments of gastrointestinal tracts and two sampling times. We compared the relative abundance distributions obtained with the two sequencing strategies and then tested their capability to distinguish the experimental conditions. The results showed that 16S rRNA gene sequencing detects only part of the gut microbiota community revealed by shotgun sequencing. Specifically, when a sufficient number of reads is available, Shotgun sequencing has more power to identify less abundant taxa than 16S sequencing. Finally, we showed that the less abundant genera detected only by shotgun sequencing are biologically meaningful, being able to discriminate between the experimental conditions as much as the more abundant genera detected by both sequencing strategies.}, } @article {pmid33542351, year = {2021}, author = {Kapheim, KM and Johnson, MM and Jolley, M}, title = {Composition and acquisition of the microbiome in solitary, ground-nesting alkali bees.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2993}, pmid = {33542351}, issn = {2045-2322}, mesh = {Alkalies/metabolism ; Animals ; Bees/genetics/metabolism/*microbiology ; Cell Wall/metabolism ; Diet ; Female ; Lactobacillus/genetics/*isolation & purification ; Larva/genetics/metabolism/*microbiology ; Microbiota/*genetics ; Pollen/microbiology ; }, abstract = {Increasing evidence suggests the microbiome plays an important role in bee ecology and health. However, the relationship between bees and their bacterial symbionts has only been explored in a handful of species. We characterized the microbiome across the life cycle of solitary, ground-nesting alkali bees (Nomia melanderi). We find that feeding status is a major determinant of microbiome composition. The microbiome of feeding larvae was similar to that of pollen provisions, but the microbiome of post-feeding larvae (pre-pupae) was similar to that of the brood cell walls and newly-emerged females. Feeding larvae and pollen provisions had the lowest beta diversity, suggesting the composition of larval diet is highly uniform. Comparisons between lab-reared, newly-emerged, and nesting adult females suggest that the hindgut bacterial community is largely shaped by the external environment. However, we also identified taxa that are likely acquired in the nest or which increase or decrease in relative abundance with age. Although Lactobacillus micheneri was highly prevalent in pollen provisions, it was only detected in one lab-reared female, suggesting it is primarily acquired from environmental sources. These results provide the foundation for future research on metagenomic function and development of probiotics for these native pollinators.}, } @article {pmid33541264, year = {2021}, author = {Abe, K and Hirayama, M and Ohno, K and Shimamura, T}, title = {Hierarchical non-negative matrix factorization using clinical information for microbial communities.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {104}, pmid = {33541264}, issn = {1471-2164}, support = {19H05210//Japan Society for the Promotion of Science (JP)/ ; 20H04281//Japan Society for the Promotion of Science/ ; 20H04841//Japan Society for the Promotion of Science/ ; 20K21832//Japan Society for the Promotion of Science/ ; 20K19921//Japan Society for the Promotion of Science/ ; JP20dm0107087h0005//Japan Agency for Medical Research and Development/ ; JP20ek0109488h0001//Japan Agency for Medical Research and Development/ ; JP20km0405207h9905//Japan Agency for Medical Research and Development/ ; JP20gm1010002h0005//Japan Agency for Medical Research and Development/ ; }, mesh = {*Algorithms ; Bayes Theorem ; Computer Simulation ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {BACKGROUND: The human microbiome forms very complex communities that consist of hundreds to thousands of different microorganisms that not only affect the host, but also participate in disease processes. Several state-of-the-art methods have been proposed for learning the structure of microbial communities and to investigate the relationship between microorganisms and host environmental factors. However, these methods were mainly designed to model and analyze single microbial communities that do not interact with or depend on other communities. Such methods therefore cannot comprehend the properties between interdependent systems in communities that affect host behavior and disease processes.

RESULTS: We introduce a novel hierarchical Bayesian framework, called BALSAMICO (BAyesian Latent Semantic Analysis of MIcrobial COmmunities), which uses microbial metagenome data to discover the underlying microbial community structures and the associations between microbiota and their environmental factors. BALSAMICO models mixtures of communities in the framework of nonnegative matrix factorization, taking into account environmental factors. We proposes an efficient procedure for estimating parameters. A simulation then evaluates the accuracy of the estimated parameters. Finally, the method is used to analyze clinical data. In this analysis, we successfully detected bacteria related to colorectal cancer.

CONCLUSIONS: These results show that the method not only accurately estimates the parameters needed to analyze the connections between communities of microbiota and their environments, but also allows for the effective detection of these communities in real-world circumstances.}, } @article {pmid33540579, year = {2021}, author = {Conti, A and Corte, L and Casagrande Pierantoni, D and Robert, V and Cardinali, G}, title = {What Is the Best Lens? Comparing the Resolution Power of Genome-Derived Markers and Standard Barcodes.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, pmid = {33540579}, issn = {2076-2607}, abstract = {Fungal species delimitation was traditionally carried out with multicopy ribosomal RNA (rRNA) genes, principally for their ease of amplification. Since the efficacy of these markers has been questioned, single-copy protein-encoding genes have been proposed alone or in combination for Multi-Locus Sequence Typing (MLST). In this context, the role of the many sequences obtained with Next-Generation Sequencing (NGS) techniques, in both genomics and metagenomics, further pushes toward an analysis of the efficacy of NGS-derived markers and of the metrics to evaluate the marker efficacy in discriminating fungal species. This paper aims at proposing MeTRe (Mean Taxonomic Resolution), a novel index that could be used both for measuring marker efficacy and for assessing the actual resolution (i.e., the level of separation) between species obtained with different markers or their combinations. In this paper, we described and then employed this index to compare the efficacy of two rRNAs and four single-copy markers obtained from public databases as both an amplicon-based approach and genome-derived sequences. Two different groups of species were used, one with a pathogenic species of Candida that was characterized by relatively well-separated taxa, whereas the other, comprising some relevant species of the sensu stricto group of the genus Saccharomyces, included close species and interspecific hybrids. The results showed the ability of MeTRe to evaluate marker efficacy in general and genome-derived markers specifically.}, } @article {pmid33537122, year = {2021}, author = {Theil, S and Rifa, E}, title = {rANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsis.}, journal = {F1000Research}, volume = {10}, number = {}, pages = {7}, pmid = {33537122}, issn = {2046-1402}, mesh = {High-Throughput Nucleotide Sequencing ; *Metagenomics ; *Microbiota/genetics ; Reproducibility of Results ; Software ; Workflow ; }, abstract = {Bioinformatic tools for marker gene sequencing data analysis are continuously and rapidly evolving, thus integrating most recent techniques and tools is challenging. We present an R package for data analysis of 16S and ITS amplicons based sequencing. This workflow is based on several R functions and performs automatic treatments from fastq sequence files to diversity and differential analysis with statistical validation. The main purpose of this package is to automate bioinformatic analysis, ensure reproducibility between projects, and to be flexible enough to quickly integrate new bioinformatic tools or statistical methods. rANOMALY is an easy to install and customizable R package, that uses amplicon sequence variants (ASV) level for microbial community characterization. It integrates all assets of the latest bioinformatics methods, such as better sequence tracking, decontamination from control samples, use of multiple reference databases for taxonomic annotation, all main ecological analysis for which we propose advanced statistical tests, and a cross-validated differential analysis by four different methods. Our package produces ready to publish figures, and all of its outputs are made to be integrated in Rmarkdown code to produce automated reports.}, } @article {pmid33537012, year = {2020}, author = {Zhu, XY and Liu, J and Xue, CX and Tian, J and Zhang, XH}, title = {Shift and Metabolic Potentials of Microbial Eukaryotic Communities Across the Full Depths of the Mariana Trench.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {603692}, pmid = {33537012}, issn = {1664-302X}, abstract = {Microbial eukaryotes are widespread and play important roles in marine ecosystems. However, their ecological characteristics in the deep sea (>1,000 m), especially hadal trenches, were largely unknown. Here, we investigated the diversity and metabolic potentials of microbial eukaryotes along the whole water column of the Mariana Trench by metagenomics. Our results showed clear depth-related distribution of microbial eukaryotic community and associated metabolic potentials. Surface seawater was dominated by phototrophic/mixotrophic groups (e.g., Dinoflagellata) and genes involved in biosynthesis (photosynthesis and fatty acid biosynthesis), while deep (bathypelagic and/or hadal) seawaters were enriched with heterotrophic groups (e.g., Bicoecea) and genes related to digestion (lysosomal enzymes and V-type ATPase) and carbohydrate metabolism. Co-occurrence analysis revealed high intra-domain connectivity, indicating that microbial eukaryotic composition was more influenced by microbial eukaryotes themselves than bacteria. Increased abundance of genes associated with unsaturated fatty acid biosynthesis likely plays a role in resisting high hydrostatic pressure. Top1 and hupB genes, responsible for the formation and stabilization of DNA structure, were unique and abundant in the hadal zone and thus may be helpful to stabilize DNA structure in the deep sea. Overall, our results provide insights into the distribution and potential adaptability of microbial eukaryotes in the hadal zone.}, } @article {pmid33536562, year = {2021}, author = {Lei, WT and Huang, KY and Jhong, JH and Chen, CH and Weng, SL}, title = {Metagenomic analysis of the gut microbiome composition associated with vitamin D supplementation in Taiwanese infants.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2856}, pmid = {33536562}, issn = {2045-2322}, mesh = {Breast Feeding ; *Dietary Supplements ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Humans ; Infant ; Infant Formula/*chemistry ; Male ; Metagenome ; Metagenomics ; Milk, Human/*chemistry ; Taiwan ; Vitamin D/*administration & dosage ; }, abstract = {Early childhood is a critical stage for the foundation and development of the gut microbiome, large amounts of essential nutrients are required such as vitamin D. Vitamin D plays an important role in regulating calcium homeostasis, and deficiency can impair bone mineralization. In addition, most people know that breastfeeding is advocated to be the best thing for a newborn; however, exclusively breastfeeding infants are not easily able to absorb an adequate amount of vitamin D from breast milk. Understanding the effects of vitamin D supplementation on gut microbiome can improve the knowledge of infant health and development. A total of 62 fecal sample from healthy infants were collected in Taiwan. Of the 62 infants, 31 were exclusively breastfed infants and 31 were mixed- or formula-fed infants. For each feeding type, one subgroup of infants received 400 IU of vitamin D per day, and the remaining infants received a placebo. In total, there are 15 breastfed and 20 formula-fed infants with additional vitamin D supplementation, and 16 breastfed and 11 formula-fed infants belong to control group, respectively. We performed a comparative metagenomic analysis to investigate the distribution and diversity of infant gut microbiota among different types of feeding regimes with and without vitamin D supplementation. Our results reveal that the characteristics of infant gut microbiota not only depend on the feeding types but also on nutrients intake, and demonstrated that the vitamin D plays an important role in modulating the infant gut microbiota, especially increase the proportion of probiotics in breast-fed infants.}, } @article {pmid33535685, year = {2021}, author = {Izco, M and Vettorazzi, A and de Toro, M and Sáenz, Y and Alvarez-Erviti, L}, title = {Oral Sub-chronic Ochratoxin A Exposure Induces Gut Microbiota Alterations in Mice.}, journal = {Toxins}, volume = {13}, number = {2}, pages = {}, pmid = {33535685}, issn = {2072-6651}, support = {6FRSSABC008//European Regional Development Fund/ ; }, mesh = {Administration, Oral ; Animals ; Bacteria/*drug effects/growth & development/metabolism ; Dysbiosis ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Intestines/*microbiology ; Male ; Mice, Inbred BALB C ; Ochratoxins/administration & dosage/*toxicity ; Ribotyping ; Time Factors ; Toxicity Tests, Subchronic ; Mice ; }, abstract = {Gut microbiota plays crucial roles in maintaining host health. External factors, such as diet, medicines, and environmental toxins, influence the composition of gut microbiota. Ochratoxin A (OTA) is one of the most prevalent and relevant mycotoxins and is a highly abundant food and animal feed contaminant. In the present study, we aimed to investigate OTA gut microbiome toxicity in mice sub-chronically exposed to low doses of OTA (0.21, 0.5, and 1.5 mg/kg body weight) by daily oral gavage for 28 days. Fecal microbiota from control and OTA-treated mice was analyzed using 16S ribosomal RNA (rRNA) gene sequencing followed by metagenomics. OTA exposure caused marked changes in gut microbial community structure, including the decrease in the diversity of fecal microbiota and the relative abundance of Firmicutes, as well as the increase in the relative abundance of Bacteroidetes at the phylum level. At the family level, six bacterial families (unclassified Bacteroidales, Porphyromonadaceae, unclassified Cyanobacteria, Streptococcaceae, Enterobacteriaceae, Ruminococcaceae) were significantly altered by OTA exposure. Interestingly, OTA-induced changes were observed in the lower-dose OTA groups, while high-dose OTA group microbiota was similar to control group. Our results demonstrated that sub-chronic exposure at low doses of OTA alters the structure and diversity of the gut microbial community.}, } @article {pmid33535583, year = {2021}, author = {Oliva, M and Mulet-Margalef, N and Ochoa-De-Olza, M and Napoli, S and Mas, J and Laquente, B and Alemany, L and Duell, EJ and Nuciforo, P and Moreno, V}, title = {Tumor-Associated Microbiome: Where Do We Stand?.}, journal = {International journal of molecular sciences}, volume = {22}, number = {3}, pages = {}, pmid = {33535583}, issn = {1422-0067}, support = {27140/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Animals ; Antineoplastic Agents/pharmacology ; Carcinogenesis ; Cell Transformation, Neoplastic ; Computational Biology ; Cytoplasm/metabolism ; Disease Progression ; Dysbiosis ; Gastrointestinal Microbiome/physiology ; *Gene Expression Regulation, Bacterial ; *Gene Expression Regulation, Neoplastic ; *Gene Expression Regulation, Viral ; Humans ; Immunity ; Metagenome ; Metagenomics ; Mice ; Microbiota/*physiology ; Neoplasms/*microbiology ; RNA, Ribosomal, 16S/metabolism ; *Tumor Microenvironment ; }, abstract = {The study of the human microbiome in oncology is a growing and rapidly evolving field. In the past few years, there has been an exponential increase in the number of studies investigating associations of microbiome and cancer, from oncogenesis and cancer progression to resistance or sensitivity to specific anticancer therapies. The gut microbiome is now known to play a significant role in antitumor immune responses and in predicting the efficacy of immune-checkpoint inhibitors in cancer patients. Beyond the gut, the tumor-associated microbiome-microbe communities located either in the tumor or within its body compartment-seems to interact with the local microenvironment and the tumor immune contexture, ultimately impacting cancer progression and treatment outcome. However, pre-clinical research focusing on causality and mechanistic pathways as well as proof-of-concept studies are still needed to fully understand the potential clinical utility of microbiome in cancer patients. Moreover, there is a need for the standardization of methodology and the implementation of quality control across microbiome studies to allow for a better interpretation and greater comparability of the results reported between them. This review summarizes the accumulating evidence in the field and discusses the current and upcoming challenges of microbiome studies.}, } @article {pmid33532852, year = {2021}, author = {Molina, NM and Sola-Leyva, A and Haahr, T and Aghajanova, L and Laudanski, P and Castilla, JA and Altmäe, S}, title = {Analysing endometrial microbiome: methodological considerations and recommendations for good practice.}, journal = {Human reproduction (Oxford, England)}, volume = {36}, number = {4}, pages = {859-879}, doi = {10.1093/humrep/deab009}, pmid = {33532852}, issn = {1460-2350}, mesh = {Endometrium ; Female ; Genitalia, Female ; Humans ; *Infertility ; *Microbiota ; Uterus ; }, abstract = {There is growing evidence that the upper female genital tract is not sterile, harbouring its own microbial communities. However, the significance and the potential effect of endometrial microorganisms on reproductive functions remain to be fully elucidated. Analysing the endometrial microbiome, the microbes and their genetic material present in the endometrium, is an emerging area of study. The initial studies suggest it is associated with poor reproductive outcomes and with different gynaecological pathologies. Nevertheless, studying a low-biomass microbial niche as is endometrium, the challenge is to conduct well-designed and well-controlled experiments in order to avoid and adjust for the risk of contamination, especially from the lower genital tract. Herein, we aim to highlight methodological considerations and propose good practice recommendations for future endometrial microbiome studies.}, } @article {pmid33531396, year = {2021}, author = {Gushgari-Doyle, S and Oremland, RS and Keren, R and Baesman, SM and Akob, DM and Banfield, JF and Alvarez-Cohen, L}, title = {Acetylene-Fueled Trichloroethene Reductive Dechlorination in a Groundwater Enrichment Culture.}, journal = {mBio}, volume = {12}, number = {1}, pages = {}, pmid = {33531396}, issn = {2150-7511}, support = {P42 ES004705/ES/NIEHS NIH HHS/United States ; R01 ES024255/ES/NIEHS NIH HHS/United States ; }, mesh = {Acetylene/*metabolism ; Actinobacteria/*metabolism ; Biodegradation, Environmental ; Ethane/analogs & derivatives/metabolism ; *Groundwater/analysis ; Halogenation ; Hydrocarbons, Chlorinated/metabolism ; Metagenomics ; Microbiota ; Trichloroethylene/*metabolism ; }, abstract = {In aquifers, acetylene (C2H2) is a product of abiotic degradation of trichloroethene (TCE) catalyzed by in situ minerals. C2H2 can, in turn, inhibit multiple microbial processes including TCE dechlorination and metabolisms that commonly support dechlorination, in addition to supporting the growth of acetylenotrophic microorganisms. Previously, C2H2 was shown to support TCE reductive dechlorination in synthetic, laboratory-constructed cocultures containing the acetylenotroph Pelobacter sp. strain SFB93 and Dehalococcoides mccartyi strain 195 or strain BAV1. In this study, we demonstrate TCE and perchloroethene (PCE) reductive dechlorination by a microbial community enriched from contaminated groundwater and amended with C2H2 as the sole electron donor and organic carbon source. The metagenome of the stable, enriched community was analyzed to elucidate putative community functions. A novel anaerobic acetylenotroph in the phylum Actinobacteria was identified using metagenomic analysis. These results demonstrate that the coupling of acetylenotrophy and reductive dechlorination can occur in the environment with native bacteria and broaden our understanding of biotransformation at contaminated sites containing both TCE and C2H2IMPORTANCE Understanding the complex metabolisms of microbial communities in contaminated groundwaters is a challenge. PCE and TCE are among the most common groundwater contaminants in the United States that, when exposed to certain minerals, exhibit a unique abiotic degradation pathway in which C2H2 is a product. C2H2 can act as both an inhibitor of TCE dechlorination and of supporting metabolisms and an energy source for acetylenotrophic bacteria. Here, we combine laboratory microcosm studies with computational approaches to enrich and characterize an environmental microbial community that couples two uncommon metabolisms, demonstrating unique metabolic interactions only yet reported in synthetic, laboratory-constructed settings. Using this comprehensive approach, we have identified the first reported anaerobic acetylenotroph in the phylum Actinobacteria, demonstrating the yet-undescribed diversity of this metabolism that is widely considered to be uncommon.}, } @article {pmid33531031, year = {2021}, author = {Liem, M and Regensburg-Tuïnk, T and Henkel, C and Jansen, H and Spaink, H}, title = {Microbial diversity characterization of seawater in a pilot study using Oxford Nanopore Technologies long-read sequencing.}, journal = {BMC research notes}, volume = {14}, number = {1}, pages = {42}, pmid = {33531031}, issn = {1756-0500}, mesh = {*High-Throughput Nucleotide Sequencing ; *Nanopores ; Pilot Projects ; Seawater ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVE: Currently the majority of non-culturable microbes in sea water are yet to be discovered, Nanopore offers a solution to overcome the challenging tasks to identify the genomes and complex composition of oceanic microbiomes. In this study we evaluate the utility of Oxford Nanopore Technologies (ONT) sequencing to characterize microbial diversity in seawater from multiple locations. We compared the microbial species diversity of retrieved environmental samples from two different locations and time points.

RESULTS: With only three ONT flow cells we were able to identify thousands of organisms, including bacteriophages, from which a large part at species level. It was possible to assemble genomes from environmental samples with Flye. In several cases this resulted in > 1 Mbp contigs and in the particular case of a Thioglobus singularis species it even produced a near complete genome. k-mer analysis reveals that a large part of the data represents species of which close relatives have not yet been deposited to the database. These results show that our approach is suitable for scalable genomic investigations such as monitoring oceanic biodiversity and provides a new platform for education in biodiversity.}, } @article {pmid33528260, year = {2021}, author = {Bassignani, A and Plancade, S and Berland, M and Blein-Nicolas, M and Guillot, A and Chevret, D and Moritz, C and Huet, S and Rizkalla, S and Clément, K and Doré, J and Langella, O and Juste, C}, title = {Benefits of Iterative Searches of Large Databases to Interpret Large Human Gut Metaproteomic Data Sets.}, journal = {Journal of proteome research}, volume = {20}, number = {3}, pages = {1522-1534}, doi = {10.1021/acs.jproteome.0c00669}, pmid = {33528260}, issn = {1535-3907}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; *Microbiota ; Proteomics ; Tandem Mass Spectrometry ; }, abstract = {The gut microbiota are increasingly considered as a main partner of human health. Metaproteomics enables us to move from the functional potential revealed by metagenomics to the functions actually operating in the microbiome. However, metaproteome deciphering remains challenging. In particular, confident interpretation of a myriad of MS/MS spectra can only be pursued with smart database searches. Here, we compare the interpretation of MS/MS data sets from 48 individual human gut microbiomes using three interrogation strategies of the dedicated Integrated nonredundant Gene Catalog (IGC 9.9 million genes from 1267 individual fecal samples) together with the Homo sapiens database: the classical single-step interrogation strategy and two iterative strategies (in either two or three steps) aimed at preselecting a reduced-sized, more targeted search space for the final peptide spectrum matching. Both iterative searches outperformed the single-step classical search in terms of the number of peptides and protein clusters identified and the depth of taxonomic and functional knowledge, and this was the most convincing with the three-step approach. However, iterative searches do not help in reducing variability of repeated analyses, which is inherent to the traditional data-dependent acquisition mode, but this variability did not affect the hierarchical relationship between replicates and all other samples.}, } @article {pmid33526884, year = {2021}, author = {Peng, X and Wilken, SE and Lankiewicz, TS and Gilmore, SP and Brown, JL and Henske, JK and Swift, CL and Salamov, A and Barry, K and Grigoriev, IV and Theodorou, MK and Valentine, DL and O'Malley, MA}, title = {Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes.}, journal = {Nature microbiology}, volume = {6}, number = {4}, pages = {499-511}, pmid = {33526884}, issn = {2058-5276}, mesh = {Anaerobiosis ; Animals ; Anti-Bacterial Agents/pharmacology ; Archaea/classification/drug effects/genetics/metabolism ; Bacteria, Anaerobic/classification/drug effects/genetics/*metabolism ; Biomass ; Cellulose/metabolism ; Feces/microbiology ; Fungi/classification/genetics/*metabolism ; *Gastrointestinal Microbiome/drug effects/genetics ; Goats ; Lignin/*metabolism ; Metabolome ; Metagenome ; Methane/metabolism ; *Microbial Consortia/drug effects/genetics ; Phylogeny ; }, abstract = {The herbivore digestive tract is home to a complex community of anaerobic microbes that work together to break down lignocellulose. These microbiota are an untapped resource of strains, pathways and enzymes that could be applied to convert plant waste into sugar substrates for green biotechnology. We carried out more than 400 parallel enrichment experiments from goat faeces to determine how substrate and antibiotic selection influence membership, activity, stability and chemical productivity of herbivore gut communities. We assembled 719 high-quality metagenome-assembled genomes (MAGs) that are unique at the species level. More than 90% of these MAGs are from previously unidentified herbivore gut microorganisms. Microbial consortia dominated by anaerobic fungi outperformed bacterially dominated consortia in terms of both methane production and extent of cellulose degradation, which indicates that fungi have an important role in methane release. Metabolic pathway reconstructions from MAGs of 737 bacteria, archaea and fungi suggest that cross-domain partnerships between fungi and methanogens enabled production of acetate, formate and methane, whereas bacterially dominated consortia mainly produced short-chain fatty acids, including propionate and butyrate. Analyses of carbohydrate-active enzyme domains present in each anaerobic consortium suggest that anaerobic bacteria and fungi employ mostly complementary hydrolytic strategies. The division of labour among herbivore anaerobes to degrade plant biomass could be harnessed for industrial bioprocessing.}, } @article {pmid33526565, year = {2021}, author = {Santus, W and Devlin, JR and Behnsen, J}, title = {Crossing Kingdoms: How the Mycobiota and Fungal-Bacterial Interactions Impact Host Health and Disease.}, journal = {Infection and immunity}, volume = {89}, number = {4}, pages = {}, pmid = {33526565}, issn = {1098-5522}, support = {R01 AI143641/AI/NIAID NIH HHS/United States ; R01 DK098170/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Bacteria ; *Disease Susceptibility ; *Fungi ; *Homeostasis ; *Host Microbial Interactions/immunology ; Humans ; Immune System/immunology/metabolism ; Metagenome ; Metagenomics/methods ; *Microbial Interactions ; Microbiological Techniques ; Microbiota ; *Mycobiome ; Organ Specificity ; }, abstract = {The term "microbiota" invokes images of mucosal surfaces densely populated with bacteria. These surfaces and the luminal compartments they form indeed predominantly harbor bacteria. However, research from this past decade has started to complete the picture by focusing on important but largely neglected constituents of the microbiota: fungi, viruses, and archaea. The community of commensal fungi, also called the mycobiota, interacts with commensal bacteria and the host. It is thus not surprising that changes in the mycobiota have significant impact on host health and are associated with pathological conditions such as inflammatory bowel disease (IBD). In this review we will give an overview of why the mycobiota is an important research area and different mycobiota research tools. We will specifically focus on distinguishing transient and actively colonizing fungi of the oral and gut mycobiota and their roles in health and disease. In addition to correlative and observational studies, we will discuss mechanistic studies on specific cross-kingdom interactions of fungi, bacteria, and the host.}, } @article {pmid33524735, year = {2021}, author = {Prakash, AA and Rajasekar, A and Sarankumar, RK and AlSalhi, MS and Devanesan, S and Aljaafreh, MJ and Govarthanan, M and Sayed, SRM}, title = {Metagenomic analysis of microbial community and its role in bioelectrokinetic remediation of tannery contaminated soil.}, journal = {Journal of hazardous materials}, volume = {412}, number = {}, pages = {125133}, doi = {10.1016/j.jhazmat.2021.125133}, pmid = {33524735}, issn = {1873-3336}, mesh = {Chromium/analysis ; Iron ; Metagenome ; *Microbiota ; Soil ; *Soil Pollutants/analysis ; }, abstract = {Tanneries create a serious threat to the environment by generating a significant amount of toxic metal-containing solid waste. This study deals with the application of bio-electrokinetic remediation (Bio-EK) of tannery effluent contaminated soil (TECS). Metagenomes representing the TECS sample were sequenced using the Illumina HiSeq platform. The bioreduction of hexavalent chromium Cr(VI)to trivalent chromium Cr (III) was achieved by BIO-EK techniques. NGS-data (Next Generation Sequencing) analysis was revealed that Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Planctomycetes were identified in the bio-electrokinetic system. Proteobacteria are responsible for the bioreduction of chromium hexavalent by the formation of FeS particles. The bio-generated FeS particles can be reduced the toxic chromium (VI) to non-toxic chromium (III) in soil. Simultaneously total chromium and organic content were significantly removed in BIO-EK (40 and 290 mg kg[-1]) when compared to control soil (182 and 240 mg kg[-1]). The presence of pollutant degrading microbes such as Desulfovibrio, Pseudomonas, Bacillus, Clostridium, Halanaerobium enhanced the bioreduction of the chromium during the electrokinetic remediation. This study can be claimed that the microbial cultures assisted electrokinetic remediation of total chromium, organic and iron in the tannery effluent contaminated soil was one of the suitable efficient techniques. In addition, the viability of the new combination technology developed (Electrokinetic + Bio) to treat low-permeability polluted soils was demonstrated.}, } @article {pmid33522965, year = {2021}, author = {Dada, N and Jupatanakul, N and Minard, G and Short, SM and Akorli, J and Villegas, LM}, title = {Considerations for mosquito microbiome research from the Mosquito Microbiome Consortium.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {36}, pmid = {33522965}, issn = {2049-2618}, mesh = {Animals ; Culicidae/*microbiology ; *Metagenomics ; *Microbiota ; Reproducibility of Results ; Research/*organization & administration/*trends ; }, abstract = {In the past decade, there has been increasing interest in mosquito microbiome research, leading to large amounts of data on different mosquito species, with various underlying physiological characteristics, and from diverse geographical locations. However, guidelines and standardized methods for conducting mosquito microbiome research are lacking. To streamline methods in mosquito microbiome research and optimize data quality, reproducibility, and comparability, as well as facilitate data curation in a centralized location, we are establishing the Mosquito Microbiome Consortium, a collaborative initiative for the advancement of mosquito microbiome research. Our overall goal is to collectively work on unraveling the role of the mosquito microbiome in mosquito biology, while critically evaluating its potential for mosquito-borne disease control. This perspective serves to introduce the consortium and invite broader participation. It highlights the issues we view as most pressing to the community and proposes guidelines for conducting mosquito microbiome research. We focus on four broad areas in this piece: (1) sampling/experimental design for field, semi-field, or laboratory studies; (2) metadata collection; (3) sample processing, sequencing, and use of appropriate controls; and (4) data handling and analysis. We finally summarize current challenges and highlight future directions in mosquito microbiome research. We hope that this piece will spark discussions around this area of disease vector biology, as well as encourage careful considerations in the design and implementation of mosquito microbiome research. Video Abstract.}, } @article {pmid33519743, year = {2020}, author = {Su, Y and Yang, Y and Zhu, XY and Zhang, XH and Yu, M}, title = {Metagenomic Insights Into the Microbial Assemblage Capable of Quorum Sensing and Quorum Quenching in Particulate Organic Matter in the Yellow Sea.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {602010}, pmid = {33519743}, issn = {1664-302X}, abstract = {Quorum sensing (QS) is a density-dependent communicating mechanism that allows bacteria to regulate a wide range of biogeochemical important processes and could be inhibited by quorum quenching (QQ). Increasing researches have demonstrated that QS can affect the degradation of particulate organic matter (POM) in the photic zone. However, knowledge of the diversity and variation of microbial QS and QQ systems in sinking POM is scarce. Here, POM samples were collected from surface seawater (SW), bottom seawater (BW), and surficial sediment (SS) in the Yellow Sea of China. 16S rRNA gene amplicon and metagenome sequencing were performed to analyze the community structure of particle-associated microorganisms and distribution of QS genes [acylated homoserine lactone (AHL) synthesizing gene luxI and AHL sensing gene luxR] and QQ genes (genes encoding for AHL lactonase and acylase) in POM. Shifting community structures were observed at different sampling depths, with an increase of microbial abundance and diversity from SW to BW. Along with the variation of microbial communities, the abundances of luxI and luxR decreased slightly but were restored or even exceeded when POM arrived at SS. Comparatively, abundances of AHL lactonase and acylase remained constant during the transportation process from SW to BW but increased dramatically in SS. Correlation tests indicated that abundances of luxI and luxR were positively correlated with temperature, while those of AHL acylase were positively correlated with depth, SiO4 [2-], PO4 [3-], and NO3 [-], but negatively correlated with temperature and pH. According to phylogenetic analyses, the retrieved QS and QQ genes are more diverse and distinctive than ever experimentally identified. Besides, the vertical transmission of QS and QQ genes along with POM sinking was observed, which could be one of the key factors leading to the prevalence of QS and QQ genes in marine ecosystems. Overall, our results increase the current knowledge of QS and QQ metabolic pathways in marine environment and shed light on the intertwined interspecies relationships to better investigate their dynamics and ecological roles in POM cycling.}, } @article {pmid33518302, year = {2021}, author = {Walsh, MC and Jacquier, V and Schyns, G and Claypool, J and Tamburini, I and Blokker, B and Geremia, JM}, title = {A novel microbiome metabolic modulator improves the growth performance of broiler chickens in multiple trials and modulates targeted energy and amino acid metabolic pathways in the cecal metagenome.}, journal = {Poultry science}, volume = {100}, number = {3}, pages = {100800}, pmid = {33518302}, issn = {1525-3171}, mesh = {*Amino Acids/metabolism ; *Animal Nutritional Physiological Phenomena/drug effects ; Animals ; *Cecum/microbiology ; *Chickens/growth & development/metabolism/microbiology ; Diet/veterinary ; *Dietary Supplements/analysis ; *Energy Metabolism/drug effects ; Metagenome ; *Microbiota/drug effects ; Random Allocation ; }, abstract = {A meta-analysis of 19 floor-pen trials (579 replicate pen observations) in diverse geographies, basal diets, seasons, and medication programs was carried out to evaluate the effects of 2 precision glycan microbiome metabolic modulators (MMM1 and MMM2) on the performance of broiler chickens. In each trial, negative-control (NC) diets were compared with either MMM1 (14 trials) or MMM2 (8 trials), supplemented at an intended dose of 500 g/MT from hatch to 31 to 42 d. A dose response of MMM2 was evaluated in 8 trials at doses of 100, 250, 500, and 1,000 g/MT, not all present in each trial. Linear mixed-effect models were constructed for the final BW, cumulative feed intake, feed conversion ratio (FCR) corrected by mortality and BW (cFCR), and mortality, with Treatment as the fixed effect, nested random effects of Trial and Block, and adjustments for heterogeneity of variances. A significance level of P < 0.05 was used. In one of the studies, cecal content samples were collected at 42 d for analysis of microbiome gene abundance. Microbiome metabolic modulator 2 exhibited a reduction of the cFCR of 0.06 g feed/g BW gain compared with the NC and 0.03 g feed/g BW gain compared with MMM1, whereas MMM1 reduced the cFCR by 0.03 g feed/g BW gain compared with NC. Both MMM1 and MMM2 increased the final BW compared with the NC by 43 and 48 g/bird, respectively, with no difference among them. Compared with NC, feed intake was increased by MMM1 (+51 g/bird) and reduced by MMM2 (-74 g/bird). A one-directional dose response of the MMM2 ingredient was observed for the final BW (increasing) and cFCR (decreasing), whereas the feed intake response reached a minimum at 500 g/MT. The metagenomic analysis confirmed an increase in the abundance of genes belonging to the acrylate pathway, which is involved in propionate production, as well as arginine-N-succinyl transferase which is involved in the catabolism of arginine, in response to MMM2. Differential glycan structures of the MMM had an impact on the size and consistency of performance effects in broilers.}, } @article {pmid33518063, year = {2021}, author = {Zheng, M and Mao, P and Tian, X and Meng, L}, title = {Effects of grazing mixed-grass pastures on growth performance, immune responses, and intestinal microbiota in free-range Beijing-you chickens.}, journal = {Poultry science}, volume = {100}, number = {2}, pages = {1049-1058}, pmid = {33518063}, issn = {1525-3171}, mesh = {*Animal Feed/analysis ; Animal Husbandry ; Animals ; Beijing ; Chickens/growth & development/immunology/microbiology/*physiology ; Female ; *Gastrointestinal Microbiome ; Immunity ; *Poaceae ; RNA, Ribosomal, 16S/genetics ; Random Allocation ; }, abstract = {There is an increasing interest in free-range poultry with the increasing focus on food safety and animal welfare. This study was conducted to evaluate the effects of grazing mixed-grass pastures on growth performance, immune responses, and intestinal microbiota in free-range laying chickens. Ten-week-old female Beijing-you chickens were blocked by the BW and randomly assigned to 3 free-range systems in poplar plantations for 120 d: forage-removed paddocks with a high stocking density of 5 m[2]/hen (control [CK]); mixed-grass pastures with a low stocking density of 6 m[2]/hen ;or mixed-grass pastures with a high stocking density of 5 m[2]/hen. Intestinal microbial community analysis was performed by 16S rRNA gene sequencing using Illumina MiSeq. The results revealed that no differences (P > 0.05) were found between the 3 raising systems for the BW and ADG. Chickens grazing mixed-grass pastures exhibited decreased (P > 0.05) mortality and improved immune responses as evidenced by increased T-lymphocyte proliferation (P > 0.05) and immunoglobulin A (P > 0.05) and immunoglobulin M concentrations (P < 0.05) compared with those raised in forage-removed paddocks. Metagenomic analysis indicated that grazing mixed-grass pastures regulated the intestinal microbiota by increasing the prevalence of beneficial bacteria, such as Lactobacillus, Bacteroides, and Faecalibacterium, and reducing potentially pathogenic bacteria population, such as the Rikenellaceae_RC9_gut_group compared with the CK. Therefore, this study indicated that grazing mixed-grass pastures could positively influence intestinal microbiota that may contribute to the overall growth and immunity of free-range chickens and that a low stocking density of 6 m[2]/hen was optimal to Beijing-you chickens grazing mixed-grass pastures.}, } @article {pmid33517907, year = {2021}, author = {Blaustein, RA and Michelitsch, LM and Glawe, AJ and Lee, H and Huttelmaier, S and Hellgeth, N and Ben Maamar, S and Hartmann, EM}, title = {Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {32}, pmid = {33517907}, issn = {2049-2618}, support = {TL1 TR001423/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; *Built Environment ; Drug Resistance, Microbial/drug effects/genetics ; Humans ; Metagenome/drug effects/genetics ; *Microbiota/drug effects/genetics ; Middle Aged ; Mouth/drug effects/*microbiology ; *Toothbrushing ; Triclosan/pharmacology ; Young Adult ; }, abstract = {BACKGROUND: While indoor microbiomes impact our health and well-being, much remains unknown about taxonomic and functional transitions that occur in human-derived microbial communities once they are transferred away from human hosts. Toothbrushes are a model to investigate the potential response of oral-derived microbiota to conditions of the built environment. Here, we characterize metagenomes of toothbrushes from 34 subjects to define the toothbrush microbiome and resistome and possible influential factors.

RESULTS: Toothbrush microbiomes often comprised a dominant subset of human oral taxa and less abundant or site-specific environmental strains. Although toothbrushes contained lower taxonomic diversity than oral-associated counterparts (determined by comparison with the Human Microbiome Project), they had relatively broader antimicrobial resistance gene (ARG) profiles. Toothbrush resistomes were enriched with a variety of ARGs, notably those conferring multidrug efflux and putative resistance to triclosan, which were primarily attributable to versatile environmental taxa. Toothbrush microbial communities and resistomes correlated with a variety of factors linked to personal health, dental hygiene, and bathroom features.

CONCLUSIONS: Selective pressures in the built environment may shape the dynamic mixture of human (primarily oral-associated) and environmental microbiota that encounter each other on toothbrushes. Harboring a microbial diversity and resistome distinct from human-associated counterparts suggests toothbrushes could potentially serve as a reservoir that may enable the transfer of ARGs. Video abstract.}, } @article {pmid33517034, year = {2021}, author = {Dou, R and Sun, J and Lu, J and Deng, F and Yang, C and Lu, G and Dang, Z}, title = {Bacterial communities and functional genes stimulated during phenanthrene degradation in soil by bio-microcapsules.}, journal = {Ecotoxicology and environmental safety}, volume = {212}, number = {}, pages = {111970}, doi = {10.1016/j.ecoenv.2021.111970}, pmid = {33517034}, issn = {1090-2414}, mesh = {Bacteria/metabolism ; *Biodegradation, Environmental ; Capsules/metabolism ; Environmental Pollutants/metabolism ; Metagenomics ; Microbiota ; Phenanthrenes/*metabolism ; Polycyclic Aromatic Hydrocarbons/analysis ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/analysis/*metabolism ; }, abstract = {In this study, a taxonomic and functional metagenomic method was used to investigate the difference produced between degrading bacteria immobilized in layer-by-layer assembly (LBL) microcapsules or not during the bioremediation of a soil polluted with phenanthrene (PHE). Bioaugmentation with LBL microcapsule immobilized degrading bacteria could result in different changes of native microbial communities, shifting the functional gene constructions of polluted soils. The LBL treatment enhanced PHE degradation (initial concentration of 100 mg kg[-1] dry soil) by 60% after 25 d compared to the free bacteria (FB). The enhancing effect of PHE degradation produced by the LBL treatment was found to be significantly associated with some crucial phyla (e.g., Bacteroides, Gemmatimonadetes and Acidobacteria) and genera including Streptomyces, Ramlibacter, Mycobacterium, Phycicoccus, Gemmatirosa, Flavisolibacter, Micromonospora, Acid_Candidatus_Koribacter and Gemmatimonas. The main differences of functional metagenomics between LBL and FB treatments were observed in higher levels in metabolism of aromatic hydrocarbons and its related functions or enzymes in the former, e.g., membrane transport systems, binding, substrate transporter, cleavage enzymes, dehydrogenation, oxidase, esterase and glycosidase, greatly favoring PHE mineralization. Therefore, our results provide useful findings on understanding of how immobilization strategies can influence the taxonomic and functional gene composition in soils, as well as polycyclic aromatic hydrocarbons (PAH) degradation.}, } @article {pmid33517011, year = {2021}, author = {Jin, L and Huang, Y and Yang, S and Wu, D and Li, C and Deng, W and Zhao, K and He, Y and Li, B and Zhang, G and Xiong, Y and Wei, R and Li, G and Wu, H and Zhang, H and Zou, L}, title = {Diet, habitat environment and lifestyle conversion affect the gut microbiomes of giant pandas.}, journal = {The Science of the total environment}, volume = {770}, number = {}, pages = {145316}, doi = {10.1016/j.scitotenv.2021.145316}, pmid = {33517011}, issn = {1879-1026}, mesh = {Animals ; Diet ; Ecosystem ; *Gastrointestinal Microbiome ; Life Style ; *Ursidae ; }, abstract = {Gut microbiota (GM) are important for the health of giant pandas (GPs), in addition to the utilization of bamboo in their diets. However, it is not fully understood how diet, habitat environment and lifestyle contribute to the composition of GM in GP. Consequently, we evaluated how dietary changes, habitat environment conversions and lifestyle shifts influence the GM of GPs using high-throughput sequencing and genome-resolved metagenomics. The GM of GPs were more similar when their hosts exhibited the same diet. High fiber diets significantly increased the diversity and decreased the richness of gut bacterial communities alone or interacted with the age factor (p < 0.05). The abundances of Streptococcus, Pseudomonas, Enterococcus, Lactococcus, Acinetobacter, and Clostridium significantly increased during diet conversion process (Non-parametric factorial Kruskal-Wallis sum-rank test, LDA > 4). Reconstruction of 60 metagenome-assembled-genomes (MAGs) indicated that these bacteria were likely responsible for bamboo digestion via gene complements involved in cellulose, hemicellulose, and lignin degradation. While habitat environment may play a more important role in shaping the GM of GP, lifestyle can also greatly affect bacterial communities. The GM structure in reintroduced GPs notably converged to that of wild pandas. Importantly, the main bacterial genera of wild GPs could aid in lignin degradation, while those of reintroduced GPs were related to cellulose and hemicellulose digestion. Streptococcus, Pseudomonas, Enterococcus, Lactococcus, Acinetobacter, and Clostridium may contribute to lignocellulose digestion in GP. The results revealed that diet conversion, habitat environment and lifestyle could remarkably influence the GM of GP. In addition, results suggested that increasing the ability of lignin degradation with GM may aid to change the GM of reintroduced pandas to resemble those of wild pandas.}, } @article {pmid33515036, year = {2021}, author = {Yang, F and Zou, Q and Gao, B}, title = {GutBalance: a server for the human gut microbiome-based disease prediction and biomarker discovery with compositionality addressed.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {5}, pages = {}, doi = {10.1093/bib/bbaa436}, pmid = {33515036}, issn = {1477-4054}, mesh = {Bacteria/classification/*genetics ; Biomarkers ; *Databases, Genetic ; Disease/*genetics ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenome ; Metagenomics ; *Software ; }, abstract = {The compositionality of the microbiome data is well-known but often neglected. The compositional transformation pertains to the supervised learning of microbiome data and is a critical step that decides the performance and reliability of the disease classifiers. We value the excellent performance of the distal discriminative balance analysis (DBA) method, which selects distal balances of pairs and trios of bacteria, in addressing the classification of high-dimensional microbiome data. By applying this method to the species-level abundances of all the disease phenotypes in the GMrepo database, we build a balance-based model repository for the classification of human gut microbiome-related diseases. The model repository supports the prediction of disease risks for new sample(s). More importantly, we highlight the concept of balance-disease associations rather than the conventional microbe-disease associations and develop the human Gut Balance-Disease Association Database (GBDAD). Each predictable balance for each disease model indicates a potential biomarker-disease relationship and can be interpreted as a bacteria ratio positively or negatively correlated with the disease. Furthermore, by linking the balance-disease associations to the evidenced microbe-disease associations in MicroPhenoDB, we surprisingly found that most species-disease associations inferred from the shotgun metagenomic datasets can be validated by external evidence beyond MicroPhenoDB. The balance-based species-disease association inference will accelerate the generation of new microbe-disease association hypotheses in gastrointestinal microecology research and clinical trials. The model repository and the GBDAD database are deployed on the GutBalance server, which supports interactive visualization and systematic interrogation of the disease models, disease-related balances and disease-related species of interest.}, } @article {pmid33515008, year = {2021}, author = {Ruigrok, RAAA and Collij, V and Sureda, P and Klaassen, MAY and Bolte, LA and Jansen, BH and Voskuil, MD and Fu, J and Wijmenga, C and Zhernakova, A and Weersma, RK and Vich Vila, A}, title = {The Composition and Metabolic Potential of the Human Small Intestinal Microbiota Within the Context of Inflammatory Bowel Disease.}, journal = {Journal of Crohn's & colitis}, volume = {15}, number = {8}, pages = {1326-1338}, pmid = {33515008}, issn = {1876-4479}, support = {016.136.308//VIDI/ ; //Netherlands Organization for Scientific Research/ ; D16-14//Diagnostics Grant from the Dutch Digestive Foundation/ ; //University of Groningen/ ; GH001//Netherlands' Top Institute Food and Nutrition/ ; ERC-671274//ERC/ ; CVON 2012-03//CardioVasculair Onderzoek Nederland/ ; }, mesh = {Cohort Studies ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases ; Intestine, Small/*microbiology ; Male ; Middle Aged ; }, abstract = {BACKGROUND AND AIMS: The human gastrointestinal tract harbours distinct microbial communities essential for health. Little is known about small intestinal communities, despite the small intestine playing a fundamental role in nutrient absorption and host-microbe immune homeostasis. We aimed to explore the small intestine microbial composition and metabolic potential, in the context of inflammatory bowel disease [IBD].

METHODS: Metagenomes derived from faecal samples and extensive phenotypes were collected from 57 individuals with an ileostomy or ileoanal pouch, and compared with 1178 general population and 478 IBD faecal metagenomes. Microbiome features were identified using MetaPhAn2 and HUMAnN2, and association analyses were performed using multivariate linear regression.

RESULTS: Small intestinal samples had a significantly lower bacterial diversity, compared with the general population and, to a lesser extent, IBD samples. Comparing bacterial composition, small intestinal samples clustered furthest from general population samples and closest to IBD samples with intestinal resections. Veillonella atypica, Streptococcus salivarius, and Actinomyces graevenitzii were among the species significantly enriched in the small intestine. Predicted metabolic pathways in the small intestine are predominantly involved in simple carbohydrate and energy metabolism, but also suggest a higher pro-inflammatory potential.

CONCLUSIONS: We described the bacterial composition and metabolic potential of the small intestinal microbiota. The colonic microbiome of IBD patients, particularly with intestinal resections, showed resemblance to that of the small intestine. Moreover, several features characterising the small intestinal microbiome have been previously associated with IBD. These results highlight the importance of studying the small intestinal microbiota to gain new insight into disease pathogenesis.}, } @article {pmid33514598, year = {2021}, author = {Arnoriaga-Rodríguez, M and Mayneris-Perxachs, J and Contreras-Rodríguez, O and Burokas, A and Ortega-Sanchez, JA and Blasco, G and Coll, C and Biarnés, C and Castells-Nobau, A and Puig, J and Garre-Olmo, J and Ramos, R and Pedraza, S and Brugada, R and Vilanova, JC and Serena, J and Barretina, J and Gich, J and Pérez-Brocal, V and Moya, A and Fernández-Real, X and Ramio-Torrentà, L and Pamplona, R and Sol, J and Jové, M and Ricart, W and Portero-Otin, M and Maldonado, R and Fernández-Real, JM}, title = {Obesity-associated deficits in inhibitory control are phenocopied to mice through gut microbiota changes in one-carbon and aromatic amino acids metabolic pathways.}, journal = {Gut}, volume = {70}, number = {12}, pages = {2283-2296}, pmid = {33514598}, issn = {1468-3288}, mesh = {Adult ; Aged ; Amino Acids, Aromatic/*metabolism ; Animals ; Carbon/*metabolism ; Cross-Sectional Studies ; Fatty Liver/microbiology ; *Fecal Microbiota Transplantation ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; *Inhibition, Psychological ; Male ; Mice ; Middle Aged ; Obesity/*complications ; Phenotype ; Transcriptome ; }, abstract = {BACKGROUND: Inhibitory control (IC) is critical to keep long-term goals in everyday life. Bidirectional relationships between IC deficits and obesity are behind unhealthy eating and physical exercise habits.

METHODS: We studied gut microbiome composition and functionality, and plasma and faecal metabolomics in association with cognitive tests evaluating inhibitory control (Stroop test) and brain structure in a discovery (n=156), both cross-sectionally and longitudinally, and in an independent replication cohort (n=970). Faecal microbiota transplantation (FMT) in mice evaluated the impact on reversal learning and medial prefrontal cortex (mPFC) transcriptomics.

RESULTS: An interplay among IC, brain structure (in humans) and mPFC transcriptomics (in mice), plasma/faecal metabolomics and the gut metagenome was found. Obesity-dependent alterations in one-carbon metabolism, tryptophan and histidine pathways were associated with IC in the two independent cohorts. Bacterial functions linked to one-carbon metabolism (thyX,dut, exodeoxyribonuclease V), and the anterior cingulate cortex volume were associated with IC, cross-sectionally and longitudinally. FMT from individuals with obesity led to alterations in mice reversal learning. In an independent FMT experiment, human donor's bacterial functions related to IC deficits were associated with mPFC expression of one-carbon metabolism-related genes of recipient's mice.

CONCLUSION: These results highlight the importance of targeting obesity-related impulsive behaviour through the induction of gut microbiota shifts.}, } @article {pmid33512248, year = {2021}, author = {Shaffer, JP and Marotz, C and Belda-Ferre, P and Martino, C and Wandro, S and Estaki, M and Salido, RA and Carpenter, CS and Zaramela, LS and Minich, JJ and Bryant, M and Sanders, K and Fraraccio, S and Ackermann, G and Humphrey, G and Swafford, AD and Miller-Montgomery, S and Knight, R}, title = {A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities.}, journal = {BioTechniques}, volume = {70}, number = {3}, pages = {149-159}, pmid = {33512248}, issn = {1940-9818}, support = {K12 GM068524/GM/NIGMS NIH HHS/United States ; U01 AI124316/AI/NIAID NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; R01 HL134887/HL/NHLBI NIH HHS/United States ; RF1 AG058942/AG/NIA NIH HHS/United States ; R01 DK102932/DK/NIDDK NIH HHS/United States ; 1RF1-AG058942-01,R01DK102932,R01HL134887,R01HL140976,U01AI124316,U19AG063744/GF/NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Biodiversity ; Cats ; Chemical Fractionation/methods ; DNA, Viral/*isolation & purification ; Feces/microbiology/virology ; Female ; Fermented Foods/microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Limit of Detection ; Male ; Metagenomics/methods ; Mice ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*isolation & purification ; SARS-CoV-2/*genetics ; Saliva/microbiology/virology ; Skin/microbiology/virology ; }, abstract = {One goal of microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused by the RNA virus SARS-CoV-2, has highlighted a gap in traditional DNA-based protocols, including the high-throughput methods the authors previously established as field standards. To enable simultaneous SARS-CoV-2 and microbial community profiling, the authors compared the relative performance of two total nucleic acid extraction protocols with the authors' previously benchmarked protocol. The authors included a diverse panel of environmental and host-associated sample types, including body sites commonly swabbed for COVID-19 testing. Here the authors present results comparing the cost, processing time, DNA and RNA yield, microbial community composition, limit of detection and well-to-well contamination between these protocols.}, } @article {pmid33510238, year = {2021}, author = {Kursa, O and Tomczyk, G and Sawicka-Durkalec, A and Giza, A and Słomiany-Szwarc, M}, title = {Bacterial communities of the upper respiratory tract of turkeys.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2544}, pmid = {33510238}, issn = {2045-2322}, mesh = {Animals ; *Bacteria/classification/genetics ; Metagenome ; Metagenomics/methods ; *Microbiota ; Respiratory Mucosa/*microbiology ; Turkeys/*microbiology ; }, abstract = {The respiratory tracts of turkeys play important roles in the overall health and performance of the birds. Understanding the bacterial communities present in the respiratory tracts of turkeys can be helpful to better understand the interactions between commensal or symbiotic microorganisms and other pathogenic bacteria or viral infections. The aim of this study was the characterization of the bacterial communities of upper respiratory tracks in commercial turkeys using NGS sequencing by the amplification of 16S rRNA gene with primers designed for hypervariable regions V3 and V4 (MiSeq, Illumina). From 10 phyla identified in upper respiratory tract in turkeys, the most dominated phyla were Firmicutes and Proteobacteria. Differences in composition of bacterial diversity were found at the family and genus level. At the genus level, the turkey sequences present in respiratory tract represent 144 established bacteria. Several respiratory pathogens that contribute to the development of infections in the respiratory system of birds were identified, including the presence of Ornithobacterium and Mycoplasma OTUs. These results obtained in this study supply information about bacterial composition and diversity of the turkey upper respiratory tract. Knowledge about bacteria present in the respiratory tract and the roles they can play in infections can be useful in controlling, diagnosing and treating commercial turkey flocks.}, } @article {pmid33509508, year = {2021}, author = {Lv, XC and Chen, M and Huang, ZR and Guo, WL and Ai, LZ and Bai, WD and Yu, XD and Liu, YL and Rao, PF and Ni, L}, title = {Potential mechanisms underlying the ameliorative effect of Lactobacillus paracasei FZU103 on the lipid metabolism in hyperlipidemic mice fed a high-fat diet.}, journal = {Food research international (Ottawa, Ont.)}, volume = {139}, number = {}, pages = {109956}, doi = {10.1016/j.foodres.2020.109956}, pmid = {33509508}, issn = {1873-7145}, mesh = {Animals ; Diet, High-Fat ; *Gastrointestinal Microbiome ; *Hyperlipidemias/prevention & control ; *Lacticaseibacillus paracasei ; Lipid Metabolism ; Mice ; }, abstract = {Lactobacillus paracasei FZU103, a probiotic previously isolated from the traditional brewing process of Hongqu rice wine, may have the beneficial effect of improving the disorder of lipid metabolism. This study aimed to determine the beneficial effects of L. paracasei FZU103 on improving hepatic lipid accumulation associated with hyperlipidemia. Results indicated that L. paracasei FZU103 intervention significantly inhibited the abnormal growth of body weight and epididymal white adipose tissue (eWAT), prevented the hypertrophy of epididymal adipocytes, ameliorated the biochemical parameters of serum and liver related to lipid metabolism in HFD-fed mice. Histological analysis also showed that the excessive accumulation oflipid dropletsin the livers induced by HFD-feeding was greatly alleviated by L. paracasei FZU103 intervention. In addition, L. paracasei FZU103 also promoted the excretion of bile acids (BAs) through feces. Metagenomic analysis revealed that oral supplementation with L. paracasei FZU103 significantly increased the relative abundance of Ruminococcus, Alistipes, Pseudoflavonifractor and Helicobacter, but decreased the levels of Blautia, Staphylococcos and Tannerella in HFD-fed mice. The relationships between lipid metabolic parameters and intestinal microbial phylotypes were also revealed by correlation heatmap and network. Furthermore, ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS)-based liver metabolomics demonstrated that L. paracasei FZU103 had a significant regulatory effect on the metabolic pathways of glycerophospholipid metabolism, fatty acid degradation, fatty acid elongation, unsaturated fatty acids biosynthesis, riboflavin metabolism, glycerolipid metabolism, primary bile acid biosynthesis, arachidonic acid metabolism, etc. Additionally, L. paracasei FZU103 intervention regulated expression of hepatic genes involved in lipid metabolism and bile acid homeostasis, and promoted fecal excretion of intestinal BAs. These findings present new evidence supporting that L. paracasei FZU103 has the potential to improve lipid metabolism, and could be used as a potential functional food for the prevention of hyperlipidemia.}, } @article {pmid33509277, year = {2021}, author = {Arnold, JW and Roach, J and Fabela, S and Moorfield, E and Ding, S and Blue, E and Dagher, S and Magness, S and Tamayo, R and Bruno-Barcena, JM and Azcarate-Peril, MA}, title = {The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {31}, pmid = {33509277}, issn = {2049-2618}, support = {R01 AI107029/AI/NIAID NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; }, mesh = {Aging/drug effects/genetics/*physiology ; Animals ; Female ; Gastrointestinal Microbiome/*drug effects ; Intestines/drug effects/microbiology/physiology ; Mice ; Mice, Inbred C57BL ; Oligosaccharides/*pharmacology ; Phosphatidylinositol 3-Kinases/metabolism ; *Prebiotics ; Proto-Oncogene Proteins c-akt/metabolism ; }, abstract = {BACKGROUND: Prebiotic galacto-oligosaccharides (GOS) have an extensively demonstrated beneficial impact on intestinal health. In this study, we determined the impact of GOS diets on hallmarks of gut aging: microbiome dysbiosis, inflammation, and intestinal barrier defects ("leaky gut"). We also evaluated if short-term GOS feeding influenced how the aging gut responded to antibiotic challenges in a mouse model of Clostridioides difficile infection. Finally, we assessed if colonic organoids could reproduce the GOS responder-non-responder phenotypes observed in vivo.

RESULTS: Old animals had a distinct microbiome characterized by increased ratios of non-saccharolytic versus saccharolytic bacteria and, correspondingly, a lower abundance of β-galactosidases compared to young animals. GOS reduced the overall diversity, increased the abundance of specific saccharolytic bacteria (species of Bacteroides and Lactobacillus), increased the abundance of β-galactosidases in young and old animals, and increased the non-saccharolytic organisms; however, a robust, homogeneous bifidogenic effect was not observed. GOS reduced age-associated increased intestinal permeability and increased MUC2 expression and mucus thickness in old mice. Clyndamicin reduced the abundance Bifidobacterium while increasing Akkermansia, Clostridium, Coprococcus, Bacillus, Bacteroides, and Ruminococcus in old mice. The antibiotics were more impactful than GOS on modulating serum markers of inflammation. Higher serum levels of IL-17 and IL-6 were observed in control and GOS diets in the antibiotic groups, and within those groups, levels of IL-6 were higher in the GOS groups, regardless of age, and higher in the old compared to young animals in the control diet groups. RTqPCR revealed significantly increased gene expression of TNFα in distal colon tissue of old mice, which was decreased by the GOS diet. Colon transcriptomics analysis of mice fed GOS showed increased expression of genes involved in small-molecule metabolic processes and specifically the respirasome in old animals, which could indicate an increased oxidative metabolism and energetic efficiency. In young mice, GOS induced the expression of binding-related genes. The galectin gene Lgals1, a β-galactosyl-binding lectin that bridges molecules by their sugar moieties and is an important modulator of the immune response, and the PI3K-Akt and ECM-receptor interaction pathways were also induced in young mice. Stools from mice exhibiting variable bifidogenic response to GOS injected into colon organoids in the presence of prebiotics reproduced the response and non-response phenotypes observed in vivo suggesting that the composition and functionality of the microbiota are the main contributors to the phenotype.

CONCLUSIONS: Dietary GOS modulated homeostasis of the aging gut by promoting changes in microbiome composition and host gene expression, which was translated into decreased intestinal permeability and increased mucus production. Age was a determining factor on how prebiotics impacted the microbiome and expression of intestinal epithelial cells, especially apparent from the induction of galectin-1 in young but not old mice. Video abstract.}, } @article {pmid33509255, year = {2021}, author = {Muturi, EJ and Njoroge, TM and Dunlap, C and Cáceres, CE}, title = {Blood meal source and mixed blood-feeding influence gut bacterial community composition in Aedes aegypti.}, journal = {Parasites & vectors}, volume = {14}, number = {1}, pages = {83}, pmid = {33509255}, issn = {1756-3305}, support = {NSF DEB 1754115//National Science Foundation/ ; }, mesh = {*Aedes/microbiology/physiology ; Animals ; Bacteria/classification ; Blood ; Chickens ; *Feeding Behavior ; Gastrointestinal Microbiome/*genetics ; Genes, Bacterial ; Meals ; Metagenomics/methods ; Microbiota ; Mosquito Vectors/microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; Rabbits ; }, abstract = {BACKGROUND: The guts of blood-sucking insects host a community of bacteria that can shift dramatically in response to biotic and abiotic factors. Identifying the key factors structuring these microbial communities has important ecological and epidemiological implications.

METHODS: We used the yellow fever mosquito, Aedes aegypti, to investigate the impact of mixed blood meals on gut microbiota of vector mosquitoes. Adult females were experimentally fed on sugar or blood from chicken, rabbit or a mixture of chicken and rabbit blood, and their gut microbiota were characterized using 16S rRNA gene amplification and MiSeq sequencing.

RESULTS: The gut bacterial communities of mosquitoes fed on the three blood meal treatments clustered separately, suggesting that host species identity and mixed blood-feeding are key determinants of gut bacterial community composition in mosquitoes. Mixed blood meal had a synergistic effect on both operational taxonomic unit (OTU) richness and the Shannon diversity index, suggesting that mixed blood-feeding can offset the nutritional deficit of blood meals from certain host species. The microbial communities observed in this study were distinct from those identified from similarly fed Ae. aegypti from our previous study.

CONCLUSIONS: These findings demonstrate that vector host-feeding preferences can influence gut microbial composition and diversity, which could potentially impact pathogen acquisition and transmission by the vector. The results also demonstrate that different microenvironmental conditions within the laboratory may play an important role in structuring the microbial communities of independently reared mosquito colonies.}, } @article {pmid33509082, year = {2021}, author = {Zhu, X and Qin, J and Tan, C and Ning, K}, title = {The seasonal changes of the gut microbiome of the population living in traditional lifestyles are represented by characteristic species-level and functional-level SNP enrichment patterns.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {83}, pmid = {33509082}, issn = {1471-2164}, mesh = {Clostridiales ; Firmicutes ; *Gastrointestinal Microbiome/genetics ; Humans ; Life Style ; Seasons ; Tanzania ; }, abstract = {BACKGROUND: Most studies investigating human gut microbiome dynamics are conducted on humans living in an urban setting. However, few studies have researched the gut microbiome of the populations living traditional lifestyles. These understudied populations are arguably better subjects in answering human-gut microbiome evolution because of their lower exposure to antibiotics and higher dependence on natural resources. Hadza hunter-gatherers in Tanzania have exhibited high biodiversity and seasonal patterns in their gut microbiome composition at the family level, where some taxa disappear in one season and reappear later. Such seasonal changes have been profiled, but the nucleotide changes remain unexplored at the genome level. Thus, it is still elusive how microbial communities change with seasonal changes at the genome level.

RESULTS: In this study, we performed a strain-level single nucleotide polymorphism (SNP) analysis on 40 Hadza fecal metagenome samples spanning three seasons. With more SNP presented in the wet season, eight prevalent species have significant SNP enrichment with the increasing number of SNP calling by VarScan2, among which only three species have relatively high abundances. Eighty-three genes have the most SNP distributions between the wet season and dry season. Many of these genes are derived from Ruminococcus obeum, and mainly participated in metabolic pathways including carbon metabolism, pyruvate metabolism, and glycolysis.

CONCLUSIONS: Eight prevalent species have significant SNP enrichments with the increasing number of SNP, among which only Eubacterium biforme, Eubacterium hallii and Ruminococcus obeum have relatively high species abundances. Many genes in the microbiomes also presented characteristic SNP distributions between the wet season and the dry season. This implies that the seasonal changes might indirectly impact the mutation patterns for specific species and functions for the gut microbiome of the population that lives in traditional lifestyles through changing the diet in wet and dry seasons, indicating the role of these variants in these species' adaptation to the changing environment and diets.}, } @article {pmid33508686, year = {2021}, author = {Dionizio, A and Uyghurturk, DA and Melo, CGS and Sabino-Arias, IT and Araujo, TT and Ventura, TMS and Perles, JVCM and Zanoni, JN and Den Besten, P and Buzalaf, MAR}, title = {Intestinal changes associated with fluoride exposure in rats: Integrative morphological, proteomic and microbiome analyses.}, journal = {Chemosphere}, volume = {273}, number = {}, pages = {129607}, pmid = {33508686}, issn = {1879-1298}, support = {R01 DE013508/DE/NIDCR NIH HHS/United States ; T32 DE007306/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; Firmicutes ; *Fluorides/toxicity ; *Gastrointestinal Microbiome ; Male ; Mice ; Proteome ; Proteomics ; Rats ; }, abstract = {Gastrointestinal signs and symptoms are the first signs of toxicity due to exposure to fluoride (F). This suggests the possibility that lower levels of subchronic F exposure may affect the gut. The aim of this study was to evaluate changes in the morphology, proteome and microbiome of the ileum of rats, after subchronic exposure to F. Male rats ingested water with 0, 10, or 50 mgF/L for thirty days. Treatment with F, regardless of the dose, significantly decreased the density of HuC/D-IR neurons, whereas CGRP-IR and SP-IR varicosities were significantly increased compared to the control group. Increased VIP-IR varicosities were significantly increased only in the group treated with 50 mgF/L. A significant increase in thickness of the tunica muscularis, as well as in the total thickness of the ileum wall was observed at both F doses when compared to controls. In proteomics analysis, myosin isoforms were increased, and Gastrotopin was decreased in F-exposed mice. In the microbiome metagenomics analysis, Class Clostridia was significantly reduced upon exposure to 10 mgF/L. At the higher F dose of 50 mg/L, genus Ureaplasma was significantly reduced in comparison with controls. Morphological and proteomics alterations induced by F were marked by changes associated with inflammation, and alterations in the gut microbiome. Further studies are needed to determine whether F exposure increases inflammation with secondary effects of the gut microbiome, and/or whether primary effects of F on the gut microbiome enhance changes associated with inflammation.}, } @article {pmid33504454, year = {2021}, author = {Eetemadi, A and Tagkopoulos, I}, title = {Methane and fatty acid metabolism pathways are predictive of Low-FODMAP diet efficacy for patients with irritable bowel syndrome.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {40}, number = {6}, pages = {4414-4421}, doi = {10.1016/j.clnu.2020.12.041}, pmid = {33504454}, issn = {1532-1983}, mesh = {Bacteria/metabolism ; *Diet, Carbohydrate-Restricted ; Fatty Acids, Volatile/*metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Irritable Bowel Syndrome/*diet therapy/metabolism/microbiology ; Metabolic Networks and Pathways ; Metagenome ; Methane/*metabolism ; }, abstract = {OBJECTIVE: Identification of microbiota-based biomarkers as predictors of low-FODMAP diet response and design of a diet recommendation strategy for IBS patients.

DESIGN: We created a compendium of gut microbiome and disease severity data before and after a low-FODMAP diet treatment from published studies followed by unified data processing, statistical analysis and predictive modeling. We employed data-driven methods that solely rely on the compendium data, as well as hypothesis-driven methods that focus on methane and short chain fatty acid (SCFA) metabolism pathways that were implicated in the disease etiology.

RESULTS: The patient's response to a low-FODMAP diet was predictable using their pre-diet fecal samples with F1 accuracy scores of 0.750 and 0.875 achieved through data-driven and hypothesis-driven predictors, respectively. The fecal microbiome of patients with high response had higher abundance of methane and SCFA metabolism pathways compared to patients with no response (p-values < 6 × 10[-3]). The genera Ruminococcus 1, Ruminococcaceae UCG-002 and Anaerostipes can be used as predictive biomarkers of diet response. Furthermore, the low-FODMAP diet followers were identifiable given their microbiome data (F1-score of 0.656).

CONCLUSION: Our integrated data analysis results argue that there are two types of patients, those with high colonic methane and SCFA production, who will respond well on a low-FODMAP diet, and all others, who would benefit a dietary supplementation containing butyrate and propionate, as well as probiotics with SCFA-producing bacteria, such as lactobacillus. This work demonstrates how data integration can lead to novel discoveries and paves the way towards personalized diet recommendations for IBS.}, } @article {pmid33504360, year = {2021}, author = {Wicaksono, WA and Kusstatscher, P and Erschen, S and Reisenhofer-Graber, T and Grube, M and Cernava, T and Berg, G}, title = {Antimicrobial-specific response from resistance gene carriers studied in a natural, highly diverse microbiome.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {29}, pmid = {33504360}, issn = {2049-2618}, support = {P 29285/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Anti-Infective Agents/*pharmacology ; Ascomycota/*drug effects/*genetics ; Colistin/pharmacology ; Drug Resistance, Microbial/*drug effects/*genetics ; Glycine/analogs & derivatives/pharmacology ; Microbiota/*drug effects/*genetics ; Pyrazines/pharmacology ; RNA, Ribosomal, 16S/genetics ; Tetracycline/pharmacology ; Glyphosate ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a major threat to public health. Microorganisms equipped with AMR genes are suggested to have partially emerged from natural habitats; however, this hypothesis remains inconclusive so far. To understand the consequences of the introduction of exogenic antimicrobials into natural environments, we exposed lichen thalli of Peltigera polydactylon, which represent defined, highly diverse miniature ecosystems, to clinical (colistin, tetracycline), and non-clinical (glyphosate, alkylpyrazine) antimicrobials. We studied microbiome responses by analysing DNA- and RNA-based amplicon libraries and metagenomic datasets.

RESULTS: The analyzed samples consisted of the thallus-forming fungus that is associated with cyanobacteria as well as other diverse and abundant bacterial communities (up to 10[8] 16S rRNA gene copies ng[-1] DNA) dominated by Alphaproteobacteria and Bacteroidetes. Moreover, the natural resistome of this meta-community encompassed 728 AMR genes spanning 30 antimicrobial classes. Following 10 days of exposure to the selected antimicrobials at four different concentrations (full therapeutic dosage and a gradient of sub-therapeutic dosages), we observed statistically significant, antimicrobial-specific shifts in the structure and function but not in bacterial abundances within the microbiota. We observed a relatively lower response after the exposure to the non-clinical compared to the clinical antimicrobial compounds. Furthermore, we observed specific bacterial responders, e.g., Pseudomonas and Burkholderia to clinical antimicrobials. Interestingly, the main positive responders naturally occur in low proportions in the lichen holobiont. Moreover, metagenomic recovery of the responders' genomes suggested that they are all naturally equipped with specific genetic repertoires that allow them to thrive and bloom when exposed to antimicrobials. Of the responders, Sphingomonas, Pseudomonas, and Methylobacterium showed the highest potential.

CONCLUSIONS: Antimicrobial exposure resulted in a microbial dysbiosis due to a bloom of naturally low abundant taxa (positive responders) with specific AMR features. Overall, this study provides mechanistic insights into community-level responses of a native microbiota to antimicrobials and suggests novel strategies for AMR prediction and management. Video Abstract.}, } @article {pmid33503844, year = {2021}, author = {Raja, G and Gupta, H and Gebru, YA and Youn, GS and Choi, YR and Kim, HS and Yoon, SJ and Kim, DJ and Kim, TJ and Suk, KT}, title = {Recent Advances of Microbiome-Associated Metabolomics Profiling in Liver Disease: Principles, Mechanisms, and Applications.}, journal = {International journal of molecular sciences}, volume = {22}, number = {3}, pages = {}, pmid = {33503844}, issn = {1422-0067}, support = {Hallym University Research Fund//Hallym University Research Fund/ ; NRF-2018M3A9F3020956, NRF-2019R1I1A3A01060447, NRF-2020R1I1A3073530 and NRF-2020R1A6A1A03043026//Basic Science Research Program through the National Research Foundation of Korea funded by the Ministry of Education, Science and Technology/ ; }, mesh = {Animals ; Biomarkers ; Computational Biology/methods ; *Disease Susceptibility ; Energy Metabolism ; Gene Expression Profiling ; Genomics/methods ; Humans ; Liver Diseases/diagnosis/*etiology/*metabolism/therapy ; *Metabolome ; *Metabolomics/methods ; *Microbiota ; Phenomics ; }, abstract = {Advances in high-throughput screening of metabolic stability in liver and gut microbiota are able to identify and quantify small-molecule metabolites (metabolome) in different cellular microenvironments that are closest to their phenotypes. Metagenomics and metabolomics are largely recognized to be the "-omics" disciplines for clinical therapeutic screening. Here, metabolomics activity screening in liver disease (LD) and gut microbiomes has significantly delivered the integration of metabolomics data (i.e., a set of endogenous metabolites) with metabolic pathways in cellular environments that can be tested for biological functions (i.e., phenotypes). A growing literature in LD and gut microbiomes reports the use of metabolites as therapeutic targets or biomarkers. Although growing evidence connects liver fibrosis, cirrhosis, and hepatocellular carcinoma, the genetic and metabolic factors are still mainly unknown. Herein, we reviewed proof-of-concept mechanisms for metabolomics-based LD and gut microbiotas' role from several studies (nuclear magnetic resonance, gas/lipid chromatography, spectroscopy coupled with mass spectrometry, and capillary electrophoresis). A deeper understanding of these axes is a prerequisite for optimizing therapeutic strategies to improve liver health.}, } @article {pmid33502259, year = {2021}, author = {Mesnage, R and Teixeira, M and Mandrioli, D and Falcioni, L and Ducarmon, QR and Zwittink, RD and Mazzacuva, F and Caldwell, A and Halket, J and Amiel, C and Panoff, JM and Belpoggi, F and Antoniou, MN}, title = {Use of Shotgun Metagenomics and Metabolomics to Evaluate the Impact of Glyphosate or Roundup MON 52276 on the Gut Microbiota and Serum Metabolome of Sprague-Dawley Rats.}, journal = {Environmental health perspectives}, volume = {129}, number = {1}, pages = {17005}, pmid = {33502259}, issn = {1552-9924}, mesh = {Acinetobacter ; Animals ; Blood/*metabolism ; *Gastrointestinal Microbiome/drug effects ; Glycine/*analogs & derivatives/toxicity ; *Herbicides/toxicity ; Metabolome/drug effects ; *Metabolomics ; *Metagenomics ; Rats ; Rats, Sprague-Dawley ; Glyphosate ; }, abstract = {BACKGROUND: There is intense debate on whether glyphosate can inhibit the shikimate pathway of gastrointestinal microorganisms, with potential health implications.

OBJECTIVES: We tested whether glyphosate or its representative EU herbicide formulation Roundup MON 52276 affects the rat gut microbiome.

METHODS: We combined cecal microbiome shotgun metagenomics with serum and cecum metabolomics to assess the effects of glyphosate [0.5, 50, 175mg/kg body weight (BW) per day] or MON 52276 at the same glyphosate-equivalent doses, in a 90-d toxicity test in rats.

RESULTS: Glyphosate and MON 52276 treatment resulted in ceca accumulation of shikimic acid and 3-dehydroshikimic acid, suggesting inhibition of 5-enolpyruvylshikimate-3-phosphate synthase of the shikimate pathway in the gut microbiome. Cysteinylglycine, γ-glutamylglutamine, and valylglycine levels were elevated in the cecal microbiome following glyphosate and MON 52276 treatments. Altered cecum metabolites were not differentially expressed in serum, suggesting that the glyphosate and MON 52276 impact on gut microbial metabolism had limited consequences on physiological biochemistry. Serum metabolites differentially expressed with glyphosate treatment were associated with nicotinamide, branched-chain amino acid, methionine, cysteine, and taurine metabolism, indicative of a response to oxidative stress. MON 52276 had similar, but more pronounced, effects than glyphosate on the serum metabolome. Shotgun metagenomics of the cecum showed that treatment with glyphosate and MON 52276 resulted in higher levels of Eggerthella spp., Shinella zoogleoides, Acinetobacter johnsonii, and Akkermansia muciniphila. Shinella zoogleoides was higher only with MON 52276 exposure. In vitro culture assays with Lacticaseibacillus rhamnosus strains showed that Roundup GT plus inhibited growth at concentrations at which MON 52276 and glyphosate had no effect.

DISCUSSION: Our study highlights the power of multi-omics approaches to investigate the toxic effects of pesticides. Multi-omics revealed that glyphosate and MON 52276 inhibited the shikimate pathway in the rat gut microbiome. Our findings could be used to develop biomarkers for epidemiological studies aimed at evaluating the effects of glyphosate herbicides on humans. https://doi.org/10.1289/EHP6990.}, } @article {pmid33501716, year = {2021}, author = {Chan, S and Morrison, M and Hawley, CM and Campbell, SB and Francis, RS and Isbel, NM and Pascoe, EM and Johnson, DW}, title = {Characteristics of the gastrointestinal microbiota in paired live kidney donors and recipients.}, journal = {Nephrology (Carlton, Vic.)}, volume = {26}, number = {5}, pages = {471-478}, doi = {10.1111/nep.13853}, pmid = {33501716}, issn = {1440-1797}, support = {APP1168186//Australian Health and Medical Research Council/ ; Microba Research Grant//Microba/ ; Jacquot Research Establishment//Royal Australasian College of Physicians/ ; }, mesh = {Adult ; Cohort Studies ; Female ; *Gastrointestinal Microbiome ; Humans ; *Kidney Transplantation ; Living Donors ; Male ; Middle Aged ; Transplant Recipients ; }, abstract = {BACKGROUND: There are few studies that have examined whether dysbiosis occurs in kidney donors and transplant recipients following kidney transplant surgery.

AIM: To ascertain whether changes occur in the gastrointestinal microbiota of the kidney donor and recipient following kidney transplantation.

METHODS: Kidney transplant recipients and their donors were prospectively enrolled in a pilot study to collect one faecal sample prior to, and another faecal sample between four to eight weeks following surgery. Gastrointestinal microbiota richness, Shannon diversity measures and functional assessments of kidney donors and recipients were analysed via metagenomic sequencing.

RESULTS: The study included 12 donors (median age 56 years, 6 females) and 12 recipients (median age 51 years, 3 females). Donor microbiota showed no significant changes in gastrointestinal microbiota richness, Shannon diversity, or functional assessments before and after nephrectomy. Recipient microbiota was altered post-transplant, reflected in reductions of the mean (±SD) richness values (156 ± 46.5 to 116 ± 38.6, p = 0.002), and Shannon diversity (3.57 ± 0.49 to 3.14 ± 0.52, p = 0.007), and a dramatic increase in Roseburia spp. abundance post-transplant (26-fold increase from 0.16 ± 0.0091 to 4.6 ± 0.3; p = 0.006; FDR = 0.12). Functionally, the post-transplant microbial community shifted towards those taxa using the glycolysis pathway (1.2-fold increase; p = 0.02; FDR = 0.26) for energy metabolism, while those functions involved with reactive oxygen species degradation decreased (2.6-fold; p = 0.006; FDR = 0.14).

CONCLUSION: Live donor kidney transplantation and standard care post-transplant result in significant alterations in gut microbiota richness, diversity, composition and functional parameters in kidney transplant recipients but not in their kidney donors.}, } @article {pmid33499981, year = {2020}, author = {Wei, J and Gao, H and Yang, Y and Liu, H and Yu, H and Chen, Z and Dong, B}, title = {Seasonal dynamics and starvation impact on the gut microbiome of urochordate ascidian Halocynthia roretzi.}, journal = {Animal microbiome}, volume = {2}, number = {1}, pages = {30}, pmid = {33499981}, issn = {2524-4671}, support = {2018YFD0900705//National Key Research and Development Program of China/ ; 31970487//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Gut microbiota plays important roles in host animal metabolism, homeostasis and environmental adaptation. However, the interplay between the gut microbiome and urochordate ascidian, the most closet relative of vertebrate, remains less explored. In this study, we characterized the gut microbial communities of urochordate ascidian (Halocynthia roretzi) across the changes of season and starvation stress using a comprehensive set of omic approaches including 16S rRNA gene amplicon sequencing, shotgun metagenomics, metabolomic profiling, and transcriptome sequencing.

RESULTS: The 16S rRNA gene amplicon profiling revealed that ascidians harbor indigenous gut microbiota distinctly different to the marine microbial community and significant variations in composition and abundance of gut bacteria, with predominant bacterial orders representing each season. Depressed alpha-diversities of gut microbiota were observed across starvation stress when compared to the communities in aquafarm condition. Synechococcales involving photosynthesis and its related biosynthesis was reduced in abundance while the enrichments of Xanthomonadales and Legionellales may facilitate bile acid biosynthesis during starvation. Metabolomics analysis found that long chain fatty acids, linolenic acid, cyanoamino acid, and pigments derived from gut bacteria were upregulated, suggesting a beneficial contribution of the gut microbiome to the ascidian under starvation stress.

CONCLUSIONS: Our findings revealed seasonal variation of ascidian gut microbiota. Defense and energy-associated metabolites derived from gut microbiome may provide an adaptive interplay between gut microbiome and ascidian host that maintains a beneficial metabolic system across season and starvation stress. The diversity-generating metabolisms from both microbiota and host might lead to the co-evolution and environmental adaptation.}, } @article {pmid33498458, year = {2021}, author = {Aylward, FO and Moniruzzaman, M}, title = {ViralRecall-A Flexible Command-Line Tool for the Detection of Giant Virus Signatures in 'Omic Data.}, journal = {Viruses}, volume = {13}, number = {2}, pages = {}, pmid = {33498458}, issn = {1999-4915}, mesh = {Amino Acid Sequence ; Biodiversity ; Computational Biology/*methods ; Cytoplasm/*virology ; Eukaryotic Cells/*virology ; Gene Library ; Genome, Viral ; Giant Viruses/*classification/genetics ; *Metagenomics ; Phylogeny ; }, abstract = {Giant viruses are widespread in the biosphere and play important roles in biogeochemical cycling and host genome evolution. Also known as nucleo-cytoplasmic large DNA viruses (NCLDVs), these eukaryotic viruses harbor the largest and most complex viral genomes known. Studies have shown that NCLDVs are frequently abundant in metagenomic datasets, and that sequences derived from these viruses can also be found endogenized in diverse eukaryotic genomes. The accurate detection of sequences derived from NCLDVs is therefore of great importance, but this task is challenging owing to both the high level of sequence divergence between NCLDV families and the extraordinarily high diversity of genes encoded in their genomes, including some encoding for metabolic or translation-related functions that are typically found only in cellular lineages. Here, we present ViralRecall, a bioinformatic tool for the identification of NCLDV signatures in 'omic data. This tool leverages a library of giant virus orthologous groups (GVOGs) to identify sequences that bear signatures of NCLDVs. We demonstrate that this tool can effectively identify NCLDV sequences with high sensitivity and specificity. Moreover, we show that it can be useful both for removing contaminating sequences in metagenome-assembled viral genomes as well as the identification of eukaryotic genomic loci that derived from NCLDV. ViralRecall is written in Python 3.5 and is freely available on GitHub: https://github.com/faylward/viralrecall.}, } @article {pmid33497002, year = {2021}, author = {Nikoloudaki, O and Lemos Junior, WJF and Borruso, L and Campanaro, S and De Angelis, M and Vogel, RF and Di Cagno, R and Gobbetti, M}, title = {How multiple farming conditions correlate with the composition of the raw cow's milk lactic microbiome.}, journal = {Environmental microbiology}, volume = {23}, number = {3}, pages = {1702-1716}, doi = {10.1111/1462-2920.15407}, pmid = {33497002}, issn = {1462-2920}, mesh = {Animals ; Cattle ; Farms ; Fatty Acids ; Female ; Metagenome ; *Microbiota/genetics ; *Milk ; }, abstract = {Questionnaires on farming conditions were retrieved from 2129 dairy farms and clustered, resulting in 106 representative raw cow's milk samples analysed in winter and summer. Substantiating the efficiency of our survey, some farming conditions affected the milk physicochemical composition. Culturing identified several species of lactic acid bacteria (LAB) per milk, whose number increased through 16S ribosomal RNA (rRNA) gene sequencing and shotgun metagenome analyses. Season, indoor versus outdoor housing, cow numbers, milk substitutes, ratio cattle/rest area, house care system during lactation, and urea and medium-chain fatty acids correlated with the overall microbiome composition and the LAB diversity within it. Shotgun metagenome detected variations in gene numbers and uniqueness per milk. LAB functional pathways differed among milk samples. Focusing on amino acid metabolisms and matching the retrieved annotated genes versus non-starter lactic acid bacteria (NSLAB) references from KEGG and corresponding to those identified, all samples had the same gene spectrum for each pathway. Conversely, gene redundancy varied among samples and agreed with NSLAB diversity. Milk samples with higher numbers of NSLAB species harboured higher number of copies per pathway, which would enable steady-state towards perturbations. Some farming conditions, which affected the microbiome richness, also correlated with the NSLAB composition and functionality.}, } @article {pmid33496989, year = {2021}, author = {Nelson, JW and Phillips, SC and Ganesh, BP and Petrosino, JF and Durgan, DJ and Bryan, RM}, title = {The gut microbiome contributes to blood-brain barrier disruption in spontaneously hypertensive stroke prone rats.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {35}, number = {2}, pages = {e21201}, pmid = {33496989}, issn = {1530-6860}, support = {R21 NS094806/NS/NINDS NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R56 NS102594/NS/NINDS NIH HHS/United States ; T32 GM008231/GM/NIGMS NIH HHS/United States ; R01 HL134838/HL/NHLBI NIH HHS/United States ; R01 NS102594/NS/NINDS NIH HHS/United States ; DK56338 to the Texas Medical Center Digestive Disease Center//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; }, mesh = {Animals ; *Blood Pressure ; Blood-Brain Barrier/metabolism/*pathology ; Environment ; *Gastrointestinal Microbiome ; Ileum/microbiology/pathology ; Rats, Inbred SHR ; Rats, Inbred WKY ; Rats ; }, abstract = {In recent years, it has become apparent that the gut microbiome can influence the functioning and pathological states of organs and systems throughout the body. In this study, we tested the hypothesis that the gut microbiome has a major role in the disruption of the blood-brain barrier (BBB) in the spontaneously hypertensive stroke prone rats (SHRSP), an animal model for hypertensive cerebral small vessel disease (CSVD). Loss of BBB is thought to be an early and initiating component to the full expression of CSVD in animal models and humans. To test this hypothesis, newly born SHRSP pups were placed with foster dams of the SHRSP strain or dams of the WKY strain, the control strain that does not demonstrate BBB dysfunction or develop hypertensive CSVD. Similarly, WKY pups were placed with foster dams of the same or opposite strain. The rationale for cross fostering is that the gut microbiomes are shaped by environmental bacteria of the foster dam and the nesting surroundings. Analysis of the bacterial genera in feces, using 16S rRNA analysis, demonstrated that the gut microbiome in the rat pups was influenced by the foster dam. SHRSP offspring fostered on WKY dams had systolic blood pressures (SBPs) that were significantly decreased by 26 mmHg (P < .001) from 16-20 weeks, compared to SHRSP offspring fostered on SHRSP dams. Similarly WKY offspring fostered on SHRSP dams had significantly increased SBP compared to WKY offspring fostered on WKY dams, although the magnitude of SBP change was not as robust. At ~20 weeks of age, rats fostered on SHRSP dams showed enhanced inflammation in distal ileum regardless of the strain of the offspring. Disruption of BBB integrity, an early marker of CSVD onset, was improved in SHRSPs that were fostered on WKY dams when compared to the SHRSP rats fostered on SHRSP dams. Although SHRSP is a genetic model for CSVD, environmental factors such as the gut microbiota of the foster dam have a major influence in the loss of BBB integrity.}, } @article {pmid33495623, year = {2021}, author = {He, C and Keren, R and Whittaker, ML and Farag, IF and Doudna, JA and Cate, JHD and Banfield, JF}, title = {Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems.}, journal = {Nature microbiology}, volume = {6}, number = {3}, pages = {354-365}, pmid = {33495623}, issn = {2058-5276}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Agriculture ; Archaea/classification/*physiology/ultrastructure ; Bacteria/classification/ultrastructure ; *Bacterial Physiological Phenomena ; Cell Adhesion ; Cell Proliferation ; *Ecosystem ; Groundwater/chemistry/*microbiology ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota ; Phylogeny ; Symbiosis ; }, abstract = {Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host association of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproducibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health.}, } @article {pmid33494335, year = {2021}, author = {Baragetti, A and Severgnini, M and Olmastroni, E and Dioguardi, CC and Mattavelli, E and Angius, A and Rotta, L and Cibella, J and Caredda, G and Consolandi, C and Grigore, L and Pellegatta, F and Giavarini, F and Caruso, D and Norata, GD and Catapano, AL and Peano, C}, title = {Gut Microbiota Functional Dysbiosis Relates to Individual Diet in Subclinical Carotid Atherosclerosis.}, journal = {Nutrients}, volume = {13}, number = {2}, pages = {}, pmid = {33494335}, issn = {2072-6643}, support = {AL_RIC19ABARA_01//Vini di Batasiolo S.p.A/ ; 2020-3318//Fondazione Umberto Veronesi/ ; 2016-0852//Fondazione Cariplo/ ; GGP19146//Fondazione Telethon/ ; PRIN 2017K55HLC//Italian Ministry of Health/ ; H2020 REPROGRAM PHC-03-2015/667837-2//European Union Commission/ ; 2015-0524//Fondazione Cariplo/ ; 2015-0564//Fondazione Cariplo/ ; ERANET ER-2017-2364981//European Union Commission/ ; PRIN 2017 - LS 4 2017HTKLRF_003//Italian Ministry of Health/ ; PRIN 2017H5F943//Italian Ministry of Health/ ; GR-2011-02346974//Italian Ministry of Health-IRCCS MultiMedica/ ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/drug effects ; Carnitine/therapeutic use ; Carotid Artery Diseases/*complications/microbiology ; Choline/therapeutic use ; *Diet ; Dysbiosis/*complications/drug therapy/microbiology ; Escherichia coli ; Faecalibacterium prausnitzii ; Feces/microbiology ; Feeding Behavior ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; High-Throughput Nucleotide Sequencing ; Humans ; Life Style ; Male ; Metagenomics ; Methylamines ; Middle Aged ; Palmitates/therapeutic use ; }, abstract = {Gut Microbiota (GM) dysbiosis associates with Atherosclerotic Cardiovascular Diseases (ACVD), but whether this also holds true in subjects without clinically manifest ACVD represents a challenge of personalized prevention. We connected exposure to diet (self-reported by food diaries) and markers of Subclinical Carotid Atherosclerosis (SCA) with individual taxonomic and functional GM profiles (from fecal metagenomic DNA) of 345 subjects without previous clinically manifest ACVD. Subjects without SCA reported consuming higher amounts of cereals, starchy vegetables, milky products, yoghurts and bakery products versus those with SCA (who reported to consume more mechanically separated meats). The variety of dietary sources significantly overlapped with the separations in GM composition between subjects without SCA and those with SCA (RV coefficient between nutrients quantities and microbial relative abundances at genus level = 0.65, p-value = 0.047). Additionally, specific bacterial species (Faecalibacterium prausnitzii in the absence of SCA and Escherichia coli in the presence of SCA) are directly related to over-representation of metagenomic pathways linked to different dietary sources (sulfur oxidation and starch degradation in absence of SCA, and metabolism of amino acids, syntheses of palmitate, choline, carnitines and Trimethylamine n-oxide in presence of SCA). These findings might contribute to hypothesize future strategies of personalized dietary intervention for primary CVD prevention setting.}, } @article {pmid33493841, year = {2021}, author = {Das, J and Yadav, SK and Ghosh, S and Tyagi, K and Magotra, A and Krishnan, A and Jha, G}, title = {Enzymatic and non-enzymatic functional attributes of plant microbiome.}, journal = {Current opinion in biotechnology}, volume = {69}, number = {}, pages = {162-171}, doi = {10.1016/j.copbio.2020.12.021}, pmid = {33493841}, issn = {1879-0429}, mesh = {Agriculture ; Metagenomics ; Microbial Interactions ; *Microbiota/genetics ; Plants ; }, abstract = {Microbiome plays an important role in plant growth and adaptation to various environmental conditions. The cross-talk between host plant and microbes (including microbe-microbe interactions) plays a crucial role in shaping the microbiome. Recent studies have highlighted that plant microbiome is enriched in genes encoding enzymes and natural products. Several novel antimicrobial compounds, bioactive natural products and lytic/degrading enzymes with industrial implications are being identified from the microbiome. Moreover, advancements in metagenomics and culture techniques are facilitating the development of synthetic microbial communities to promote sustainable agriculture. We discuss the recent advancements, opportunities and challenges in harnessing the full potential of plant microbiome.}, } @article {pmid33492720, year = {2021}, author = {Gao, X and Niu, R and Zhu, X and Wang, L and Ji, J and Niu, L and Wu, C and Zhang, S and Luo, J and Cui, J}, title = {Characterization and comparison of the bacterial microbiota of Lysiphlebia japonica parasitioid wasps and their aphid host Aphis gosypii.}, journal = {Pest management science}, volume = {77}, number = {6}, pages = {2710-2718}, doi = {10.1002/ps.6299}, pmid = {33492720}, issn = {1526-4998}, support = {31572015//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Aphids ; Bacteria/genetics ; *Buchnera ; *Microbiota ; Symbiosis ; *Wasps ; }, abstract = {BACKGROUND: Endosymbiotic bacteria have been reported to mediate interactions between parasitoids and their insect hosts. How parasitic wasps influence changes in host microbial communities and the relationship between them are of great importance to the study of host-parasitoid co-evolutionary and ecological interactions. However, these interactions remain largely unreported for interactions between Aphis gossypii and Lysiphlebia japonica.

RESULTS: In this study, we characterize the bacterial microbiota of L. japonica wasps at different developmental stages and monitor changes over time in the bacterial microbiota of their parasitized and nonparasitized aphid hosts, using metagenomic analysis of 16S rDNA sequencing data. Proteobacteria, Firmicutes, and Actinobacteria were the three most abundant bacterial phyla identified in L. japonica. We found that parasitism was associated with an increased abundance of Buchnera nutritional endosymbionts, but decreased abundance of Acinetobacter, Arsenophonus, Candidatus_Hamiltonella, and Pseudomonas facultative symbionts in aphid hosts. Functional analysis of enriched pathways of parasitized aphids showed significant differences in the 'transport and metabolism of carbohydrates' and 'amino acid, lipid, and coenzyme biosynthesis' pathways. Notably, the composition of symbiotic bacteria in wasp larvae was highly similar to that of their aphid hosts, especially the high abundance of Buchnera.

CONCLUSION: The results provide a conceptual framework for L. japonica interactions with A. gossypii in which the exchange of symbiotic microbes provides a means by which microbiota can potentially serve as evolutionary drivers of complex, multilevel interactions underlying the ecology and co-evolution of these hosts and parasites. © 2021 Society of Chemical Industry.}, } @article {pmid33492552, year = {2021}, author = {Chattopadhyay, I and Dhar, R and Pethusamy, K and Seethy, A and Srivastava, T and Sah, R and Sharma, J and Karmakar, S}, title = {Exploring the Role of Gut Microbiome in Colon Cancer.}, journal = {Applied biochemistry and biotechnology}, volume = {193}, number = {6}, pages = {1780-1799}, pmid = {33492552}, issn = {1559-0291}, mesh = {Animals ; Bacteria/*metabolism ; *Colonic Neoplasms/blood supply/microbiology/therapy ; *Gastrointestinal Microbiome ; Humans ; *Neovascularization, Pathologic/microbiology/therapy ; }, abstract = {Dysbiosis of the gut microbiome has been associated with the development of colorectal cancer (CRC). Gut microbiota is involved in the metabolic transformations of dietary components into oncometabolites and tumor-suppressive metabolites that in turn affect CRC development. In a healthy colon, the major of microbial metabolism is saccharolytic fermentation pathways. The alpha-bug hypothesis suggested that oncogenic bacteria such as enterotoxigenic Bacteroides fragilis (ETBF) induce the development of CRC through direct interactions with colonic epithelial cells and alterations of microbiota composition at the colorectal site. Escherichia coli, E. faecalis, F. nucleatum, and Streptococcus gallolyticus showed higher abundance whereas Bifidobacterium, Clostridium, Faecalibacterium, and Roseburia showed reduced abundance in CRC patients. The alterations of gut microbiota may be used as potential therapeutic approaches to prevent or treat CRC. Probiotics such as Lactobacillus and Bifidobacterium inhibit the growth of CRC through inhibiting inflammation and angiogenesis and enhancing the function of the intestinal barrier through the secretion of short-chain fatty acids (SCFAs). Crosstalk between lifestyle, host genetics, and gut microbiota is well documented in the prevention and treatment of CRC. Future studies are required to understand the interaction between gut microbiota and host to the influence and prevention of CRC. However, a better understanding of bacterial dysbiosis in the heterogeneity of CRC tumors should also be considered. Metatranscriptomic and metaproteomic studies are considered a powerful omic tool to understand the anti-cancer properties of certain bacterial strains. The clinical benefits of probiotics in the CRC context remain to be determined. Metagenomic approaches along with metabolomics and immunology will open a new avenue for the treatment of CRC shortly. Dietary interventions may be suitable to modulate the growth of beneficial microbiota in the gut.}, } @article {pmid33486715, year = {2021}, author = {Fadiji, AE and Ayangbenro, AS and Babalola, OO}, title = {Unveiling the putative functional genes present in root-associated endophytic microbiome from maize plant using the shotgun approach.}, journal = {Journal of applied genetics}, volume = {62}, number = {2}, pages = {339-351}, pmid = {33486715}, issn = {2190-3883}, support = {UID123634//National Research Foundation/ ; }, mesh = {Endophytes/genetics ; Metagenomics/methods ; *Microbiota/genetics ; Nitrogen Fixation/genetics ; Plant Development ; Plant Roots/*microbiology ; Zea mays/*microbiology ; }, abstract = {To ensure food security for the ever-increasing world's population, it is important to explore other alternatives for enhancing plant productivity. This study is aimed at identifying the putative plant growth-promoting (PGP) and endophytic gene clusters in root-associated endophytic microbes from maize root and to also verify if their abundance is affected by different farming practices. To achieve this, we characterize endophytic microbiome genes involved in PGP and endophytic lifestyle inside maize root using the shotgun metagenomic approach. Our results revealed the presence of genes involved in PGP activities such as nitrogen fixation, HCN biosynthesis, siderophore, 4-hydroxybenzoate, ACC deaminase, phenazine, phosphate solubilization, butanediol, methanol utilization, acetoin, nitrogen metabolism, and IAA biosynthesis. We also identify genes involved in stress resistance such as glutathione, catalase, and peroxidase. Our results further revealed the presence of putative genes involved in endophytic behaviors such as aerotaxis, regulator proteins, motility mechanisms, flagellum biosynthesis, nitrogen regulation, regulation of carbon storage, formation of biofilm, reduction of nitric oxide, regulation of beta-lactamase resistance, type III secretion, type IV conjugal DNA, type I pilus assembly, phosphotransferase system (PTS), and ATP-binding cassette (ABC). Our study suggests a high possibility in the utilization of endophytic microbial community for plant growth promotion, biocontrol activities, and stress mitigation. Further studies in ascertaining this claim through culturing of the beneficial isolates as well as pot and field experiments are necessary.}, } @article {pmid33486428, year = {2021}, author = {Kumar, M and Kumar, A and Sahu, KP and Patel, A and Reddy, B and Sheoran, N and Krishnappa, C and Rajashekara, H and Bhagat, S and Rathour, R}, title = {Deciphering core-microbiome of rice leaf endosphere: Revelation by metagenomic and microbiological analysis of aromatic and non-aromatic genotypes grown in three geographical zones.}, journal = {Microbiological research}, volume = {246}, number = {}, pages = {126704}, doi = {10.1016/j.micres.2021.126704}, pmid = {33486428}, issn = {1618-0623}, mesh = {Biodiversity ; Endophytes/*classification/genetics ; Genome, Bacterial ; Genotype ; Geography ; India ; *Metagenomics ; *Microbiota ; Oryza/*microbiology ; Plant Leaves/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {We have deciphered the leaf endophytic-microbiome of aromatic (cv. Pusa Basmati-1) and non-aromatic (cv. BPT-5204) rice-genotypes grown in the mountain and plateau-zones of India by both metagenomic NGS (mNGS) and conventional microbiological methods. Microbiome analysis by sequencing V3-V4 region of ribosomal gene revealed marginally more bacterial operational taxonomic units (OTU) in the mountain zone at Palampur and Almora than plateau zone at Hazaribagh. Interestingly, the rice leaf endophytic microbiomes in mountain zone were found clustered separately from that of plateau-zone. The Bray-Curtis dissimilarity indices indicated influence of geographical location as compared to genotype per se for shaping rice endophytic microbiome composition. Bacterial phyla, Proteobacteria followed by Bacteroidetes, Firmicutes, and Actinobacteria were found abundant in all three locations. The core-microbiome analysis devulged association of Acidovorax; Acinetobacter; Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium; Aureimonas; Bradyrhizobium; Burkholderia-Caballeronia-Paraburkholderia; Enterobacter; Pantoea; Pseudomonas; Sphingomonas; and Stenotrophomonas with the leaf endosphere. The phyllosphere and spermosphere microbiota appears to have contributed to endophytic microbiota of rice leaf. SparCC network analysis of the endophytic-microbiome showed complex cooperative and competitive intra-microbial interactions among the microbial communities. Microbiological validation of mNGS data further confirmed the presence of core and transient genera such as Acidovorax, Alcaligenes, Bacillus, Chryseobacterium, Comamonas, Curtobacterium, Delftia, Microbacterium, Ochrobactrum, Pantoea, Pseudomonas, Rhizobium, Rhodococcus, Sphingobacterium, Staphylococcus, Stenotrophomonas, and Xanthomonas in the rice genotypes. We isolated, characterized and identified core-endophytic microbial communities of rice leaf for developing microbiome assisted crop management by microbiome reengineering in future.}, } @article {pmid33486296, year = {2021}, author = {Zhou, Z and Xu, L and Zhu, L and Liu, Y and Shuai, X and Lin, Z and Chen, H}, title = {Metagenomic analysis of microbiota and antibiotic resistome in household activated carbon drinking water purifiers.}, journal = {Environment international}, volume = {148}, number = {}, pages = {106394}, doi = {10.1016/j.envint.2021.106394}, pmid = {33486296}, issn = {1873-6750}, mesh = {Anti-Bacterial Agents/pharmacology ; Charcoal ; *Drinking Water/analysis ; Genes, Bacterial ; Metagenomics ; *Microbiota/genetics ; }, abstract = {Existing drinking water treatment systems have limited ability to control emerging contaminants such as antibiotic resistance genes (ARGs). Household activated carbon water purifiers (HWPs) are convenient measures to assure drinking water quality. However, ARGs distribution in HWPs has not been reported. Here, ARGs, mobile genetic elements (MGEs) and bacteria communities were profiled in tap water (TW), filter water (FW) and activated carbon (AC) biofilm from six kinds of HWPs after 80 days operation, using metagenomics. Results showed that the bacteria community diversities in FW and AC were higher than those in TW. A total of 88, 116 and 80 ARG subtypes were detected in TW, AC and FW, respectively. The AC structure was an important factor influencing the bacterial communities and ARG profiles in FW. The network analysis revealed the co-occurrence patterns between ARGs and bacteria. SourceTracker analyses showed AC biofilms were important contributors of microbes (29-79%) and ARGs (17-53%) in FW. Moreover, MGEs e.g. pBBta01, pMKMS02 and pMFLV01 plasmids, and ISMysp3 had significant co-occurrence patterns with ARGs in the AC biofilms. This study helps to understand the actual purification effect of HWPs and provides a theoretical reference for the management and control of ARGs pollution in domestic drinking water.}, } @article {pmid33485839, year = {2021}, author = {Khalyfa, A and Ericsson, A and Qiao, Z and Almendros, I and Farré, R and Gozal, D}, title = {Circulating exosomes and gut microbiome induced insulin resistance in mice exposed to intermittent hypoxia: Effects of physical activity.}, journal = {EBioMedicine}, volume = {64}, number = {}, pages = {103208}, pmid = {33485839}, issn = {2352-3964}, support = {R01 HL130984/HL/NHLBI NIH HHS/United States ; R56 HL140548/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Biomarkers/*blood ; Body Weight ; Cell Line ; Disease Models, Animal ; Exosomes/*metabolism ; *Gastrointestinal Microbiome ; Hypoxia/*metabolism ; Insulin/metabolism ; *Insulin Resistance ; Metabolome ; Metagenome ; Metagenomics/methods ; Mice ; *Physical Conditioning, Animal ; Sleep Apnea, Obstructive ; }, abstract = {BACKGROUND: Gut microbiota (GM) contribute to obesity and insulin resistance (IR). Obstructive sleep apnea (OSA), characterized by intermittent hypoxia (IH), promotes IR and alters GM. Since circulating exosomes are implicated in IR, we examined the effects of IH and physical activity (PA) in mice on GM, colonic epithelium permeability, systemic IR, and plasma exosome cargo, and exosome effects on visceral white adipose tissues (vWAT) IR.

METHODS: C57BL/6 mice were exposed to IH or room air (RA) for 6 weeks with and without PA (n = 12/group), and GM and systemic IR changes were assessed, as well as the effects of plasma exosomes on naïve adipocyte insulin sensitivity. Fecal microbiota transfers (FMT) were performed in naïve mice (n = 5/group), followed by fecal 16S rRNA sequencing, and systemic IR and exosome-induced effects on adipocyte insulin sensitivity were evaluated.

FINDINGS: Principal coordinate analysis (PCoA) ordinates revealed B-diversity among IH and FMT recipients that accounted for 64% principal component 1 (PC1) and 12.5% (PC2) of total variance. Dominant microbiota families and genera in IH-exposed and FMT-treated were preserved, and IH-exposed GM and IH-FMT induced increased gut permeability. Plasma exosomes from IH-exposed and IH-FMT mice decreased pAKT/AKT responses to exogenous insulin in adipocytes vs. IH+PA or RA FMT-treated mice (p = 0.001).

INTERPRETATION: IH exposures mimicking OSA induce changes in GM, increase gut permeability, and alter plasma exosome cargo, the latter inducing adipocyte dysfunction (increased IR). Furthermore, these alterations improved with PA. Thus, IH leads to perturbations of a singular GM-circulating exosome pathway that disrupts adipocyte homeostasis resulting in metabolic dysfunction, as reflected by IR.

FUNDING: This study was supported by grants from the National Institutes of Health grants HL130984 and HL140548 and University of Missouri Tier 2 grant. The study has not received any funding or grants from pharmaceutical or other industrial corporations.}, } @article {pmid33484236, year = {2021}, author = {Bergner, LM and Becker, DJ and Tello, C and Carrera, JE and Streicker, DG}, title = {Detection of Trypanosoma cruzi in the saliva of diverse neotropical bats.}, journal = {Zoonoses and public health}, volume = {68}, number = {3}, pages = {271-276}, pmid = {33484236}, issn = {1863-2378}, support = {//Wellcome Trust/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; 102507/Z/13/A/WT_/Wellcome Trust/United Kingdom ; 102507/Z/13/Z//Wellcome Senior Research Fellowship/ ; }, mesh = {Animals ; Chiroptera/*virology ; Peru ; Phylogeny ; Saliva/*virology ; Trypanosoma cruzi/genetics/*isolation & purification ; }, abstract = {Trypanosoma cruzi is widely reported in bats, yet transmission routes remain unclear. We present evidence from metagenomic sequence data that T. cruzi occurs in the saliva of diverse Neotropical bats. Phylogenetic analyses demonstrated that the bat-associated T. cruzi sequences described here formed part of a bat-specific clade, suggesting an independent transmission cycle. Our results highlight the value in repurposing metagenomic data generated for viral discovery to reveal insights into the biology of other parasites. Evaluating whether the presence of T. cruzi in the saliva of two hematophagous bat species represents an ecological route for zoonotic transmission of Chagas disease is an interesting avenue for future research.}, } @article {pmid33484150, year = {2021}, author = {Raffner Basson, A and Gomez-Nguyen, A and LaSalla, A and Buttó, L and Kulpins, D and Warner, A and Di Martino, L and Ponzani, G and Osme, A and Rodriguez-Palacios, A and Cominelli, F}, title = {Replacing Animal Protein with Soy-Pea Protein in an "American Diet" Controls Murine Crohn Disease-Like Ileitis Regardless of Firmicutes: Bacteroidetes Ratio.}, journal = {The Journal of nutrition}, volume = {151}, number = {3}, pages = {579-590}, pmid = {33484150}, issn = {1541-6100}, support = {T32 DK083251/DK/NIDDK NIH HHS/United States ; P01 DK091222/DK/NIDDK NIH HHS/United States ; P30 DK097948/DK/NIDDK NIH HHS/United States ; R01 DK055812/DK/NIDDK NIH HHS/United States ; T32 GM007250/GM/NIGMS NIH HHS/United States ; F32 DK117585/DK/NIDDK NIH HHS/United States ; R21 DK118373/DK/NIDDK NIH HHS/United States ; }, mesh = {Amino Acids/chemistry/metabolism ; Animal Feed ; Animals ; Bacteroidetes ; Colitis/chemically induced/prevention & control ; Dextran Sulfate ; Diet/veterinary ; Dietary Carbohydrates ; Dietary Fats ; Dietary Proteins/*administration & dosage ; Feces/chemistry ; Female ; Firmicutes ; Gastrointestinal Microbiome/*physiology ; Humans ; Ileitis/*prevention & control ; Male ; Mice ; Mice, Inbred C57BL ; *Pisum sativum ; *Glycine max ; Specific Pathogen-Free Organisms ; }, abstract = {BACKGROUND: The current nutritional composition of the "American diet" (AD; also known as Western diet) has been linked to the increasing incidence of chronic diseases, including inflammatory bowel disease (IBD), namely Crohn disease (CD).

OBJECTIVES: This study investigated which of the 3 major macronutrients (protein, fat, carbohydrates) in the AD has the greatest impact on preventing chronic inflammation in experimental IBD mouse models.

METHODS: We compared 5 rodent diets designed to mirror the 2011-2012 "What We Eat in America" NHANES. Each diet had 1 macronutrient dietary source replaced. The formulated diets were AD, AD-soy-pea (animal protein replaced by soy + pea protein), AD-CHO ("refined carbohydrate" by polysaccharides), AD-fat [redistribution of the ω-6:ω-3 (n-6:n-3) PUFA ratio; ∼10:1 to 1:1], and AD-mix (all 3 "healthier" macronutrients combined). In 3 separate experiments, 8-wk-old germ-free SAMP1/YitFC mice (SAMP) colonized with human gut microbiota ("hGF-SAMP") from CD or healthy donors were fed an AD, an AD-"modified," or laboratory rodent diet for 24 wk. Two subsequent dextran sodium sulfate-colitis experiments in hGF-SAMP (12-wk-old) and specific-pathogen-free (SPF) C57BL/6 (20-wk-old) mice, and a 6-wk feeding trial in 24-wk-old SPF SAMP were performed. Intestinal inflammation, gut metagenomics, and MS profiles were assessed.

RESULTS: The AD-soy-pea diet resulted in lower histology scores [mean ± SD (56.1% ± 20.7% reduction)] in all feeding trials and IBD mouse models than did other diets (P < 0.05). Compared with the AD, the AD-soy-pea correlated with increased abundance in Lactobacillaceae and Leuconostraceae (1.5-4.7 log2 and 3.0-5.1 log2 difference, respectively), glutamine (6.5 ± 0.8 compared with 3.9 ± 0.3 ng/μg stool, P = 0.0005) and butyric acid (4:0; 3.3 ± 0.5 compared with 2.54 ± 0.4 ng/μg stool, P = 0.006) concentrations, and decreased linoleic acid (18:2n-6; 5.4 ± 0.4 compared with 8.6 ± 0.3 ng/μL plasma, P = 0.01).

CONCLUSIONS: Replacement of animal protein in an AD by plant-based sources reduced the severity of experimental IBD in all mouse models studied, suggesting that similar, feasible adjustments to the daily human diet could help control/prevent IBD in humans.}, } @article {pmid33482928, year = {2021}, author = {Klassen, L and Reintjes, G and Tingley, JP and Jones, DR and Hehemann, JH and Smith, AD and Schwinghamer, TD and Arnosti, C and Jin, L and Alexander, TW and Amundsen, C and Thomas, D and Amann, R and McAllister, TA and Abbott, DW}, title = {Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {23}, pmid = {33482928}, issn = {2049-2618}, mesh = {Animals ; Bacteria/*classification/genetics/isolation & purification/*metabolism ; Cattle ; *Fluorescence ; Fluorescent Dyes/analysis ; *Gastrointestinal Microbiome ; Metagenomics ; Polysaccharides/*analysis/*metabolism ; Rumen/*microbiology ; }, abstract = {Gut microbiomes, such as the microbial community that colonizes the rumen, have vast catabolic potential and play a vital role in host health and nutrition. By expanding our understanding of metabolic pathways in these ecosystems, we will garner foundational information for manipulating microbiome structure and function to influence host physiology. Currently, our knowledge of metabolic pathways relies heavily on inferences derived from metagenomics or culturing bacteria in vitro. However, novel approaches targeting specific cell physiologies can illuminate the functional potential encoded within microbial (meta)genomes to provide accurate assessments of metabolic abilities. Using fluorescently labeled polysaccharides, we visualized carbohydrate metabolism performed by single bacterial cells in a complex rumen sample, enabling a rapid assessment of their metabolic phenotype. Specifically, we identified bovine-adapted strains of Bacteroides thetaiotaomicron that metabolized yeast mannan in the rumen microbiome ex vivo and discerned the mechanistic differences between two distinct carbohydrate foraging behaviors, referred to as "medium grower" and "high grower." Using comparative whole-genome sequencing, RNA-seq, and carbohydrate-active enzyme fingerprinting, we could elucidate the strain-level variability in carbohydrate utilization systems of the two foraging behaviors to help predict individual strategies of nutrient acquisition. Here, we present a multi-faceted study using complimentary next-generation physiology and "omics" approaches to characterize microbial adaptation to a prebiotic in the rumen ecosystem. Video abstract.}, } @article {pmid33482922, year = {2021}, author = {Okazaki, Y and Fujinaga, S and Salcher, MM and Callieri, C and Tanaka, A and Kohzu, A and Oyagi, H and Tamaki, H and Nakano, SI}, title = {Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {24}, pmid = {33482922}, issn = {2049-2618}, mesh = {Aquatic Organisms/classification/genetics/isolation & purification ; *Biodiversity ; Europe ; *Fresh Water ; Japan ; Phylogeny ; *Phylogeography ; Plankton/classification/*genetics/*isolation & purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe.

RESULTS: Our single nucleotide-resolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7-101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors or genetic drift were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion.

CONCLUSIONS: Our novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological processes underlying the ubiquity of freshwater bacterioplankton lineages. To fully exploit the performance of the method, its relatively low read throughput is the major bottleneck to be overcome in the future. Video abstract.}, } @article {pmid33482304, year = {2021}, author = {Accetto, T and Avguštin, G}, title = {Non-oral Prevotella stepping into the spotlight.}, journal = {Anaerobe}, volume = {68}, number = {}, pages = {102321}, doi = {10.1016/j.anaerobe.2021.102321}, pmid = {33482304}, issn = {1095-8274}, mesh = {Animals ; Bacteroidaceae Infections/*microbiology ; Humans ; Microbiota ; Mouth/microbiology ; Prevotella/classification/genetics/*isolation & purification ; }, abstract = {Species now affiliated to genus Prevotella have been known for decades as an integral part of human oral cavity microbiota. They were frequently isolated from patients with periodontitis or from dental root canals but also from healthy subjects. With the exception of Prevotella intermedia, they were considered opportunistic pathogens, as they were isolated also from various bacterial abscesses from the head, neck, breast, skin and various other body sites. Consequently, Prevotella were not in the focus of research activities. On the other hand, the four species found in the rumen never caused any disease and seemed early on to be numerous and important part of the rumen ecosystem indicating this genus harbored bacteria with enormously diverse habitats and lifestyles. The purpose of this review is to illustrate the main research themes performed in Prevotella on a path from less noted oral bacteria and from hard to cultivate and study rumen organisms to important mutualistic bacteria in guts of various mammals warranting major research efforts.}, } @article {pmid33482026, year = {2021}, author = {Canivet, CM and David, N and Pailhoriès, H and Briand, M and Guy, CD and Bouchez, O and Hunault, G and Fizanne, L and Lannes, A and Oberti, F and Fouchard, I and Calès, P and Diehl, AM and Barret, M and Boursier, J}, title = {Cross-linkage between bacterial taxonomy and gene functions: a study of metagenome-assembled genomes of gut microbiota in adult non-alcoholic fatty liver disease.}, journal = {Alimentary pharmacology & therapeutics}, volume = {53}, number = {6}, pages = {722-732}, doi = {10.1111/apt.16262}, pmid = {33482026}, issn = {1365-2036}, mesh = {Adult ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; *Non-alcoholic Fatty Liver Disease/genetics ; }, abstract = {BACKGROUND: The reconstruction of metagenome-assembled genomes (MAGs) has emerged as a powerful approach for combining the taxonomic and functional content of microbial populations.

AIM: To use this new approach to highlight mechanisms linking gut microbiota to NAFLD severity METHODS: Stool samples were collected from 96 NAFLD patients on the day of liver biopsy. Shotgun DNA sequencing of the gut microbiota was performed on an Illumina HiSeq3000 system. Contigs were binned into MAGs according to their co-abundances and tetranucleotide frequencies using Metabat v.0.32.4. Predicted protein-coding genes were clustered in orthologous groups (OGs) with DIAMOND against the EggNOG v4.5 database. Liver biopsies were read in accordance with the NASH CRN classification.

RESULTS: Fifty-four patients had NASH and 44 had significant fibrosis (F ≥ 2). Sequencing of DNA extracted from stools resulted in 13.8 + 3.2 million paired-end reads per sample. Of the 4,000 reconstructed MAGs, 220 in NASH patients, 192 in non-NASH patients, 203 in F ≥ 2 patients and 230 in F0-1 patients had > 70% completeness and < 5% contamination. Within these MAGs, 28 OGs were associated with NASH, 33 with significant fibrosis, and seven with both NASH and significant fibrosis. The study of MAGs showed associations between NAFLD severity and some gut bacteria with microbiota functions related to hydrogen sulfide production, citrate transport, hemicellulose degradation, aldehyde production and vitamin B12 synthesis.

CONCLUSION: Using new metagenomics methods, our study unveils potential mechanisms by which certain bacteria from the gut microbiota could protect or contribute to the development of NASH and liver fibrosis in NAFLD.}, } @article {pmid33479378, year = {2021}, author = {Glendinning, L and Genç, B and Wallace, RJ and Watson, M}, title = {Metagenomic analysis of the cow, sheep, reindeer and red deer rumen.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1990}, pmid = {33479378}, issn = {2045-2322}, support = {BB/P013759/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P013732/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004243/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; TS/J000108/1//Technology Strategy Board/ ; TS/J000116/1//Technology Strategy Board/ ; }, mesh = {Animal Feed ; Animals ; Bacteria/classification/*genetics ; Cattle ; Deer/genetics/microbiology ; Metagenomics ; Microbiota/*genetics ; Reindeer/genetics/microbiology ; Rumen/*microbiology ; Ruminants/classification/*genetics ; Sheep/genetics/microbiology ; }, abstract = {The rumen microbiota comprises a community of microorganisms which specialise in the degradation of complex carbohydrates from plant-based feed. These microbes play a highly important role in ruminant nutrition and could also act as sources of industrially useful enzymes. In this study, we performed a metagenomic analysis of samples taken from the ruminal contents of cow (Bos Taurus), sheep (Ovis aries), reindeer (Rangifer tarandus) and red deer (Cervus elaphus). We constructed 391 metagenome-assembled genomes originating from 16 microbial phyla. We compared our genomes to other publically available microbial genomes and found that they contained 279 novel species. We also found significant differences between the microbiota of different ruminant species in terms of the abundance of microbial taxonomies, carbohydrate-active enzyme genes and KEGG orthologs. We present a dataset of rumen-derived genomes which in combination with other publicly-available rumen genomes can be used as a reference dataset in future metagenomic studies.}, } @article {pmid33479326, year = {2021}, author = {Casaburi, G and Duar, RM and Brown, H and Mitchell, RD and Kazi, S and Chew, S and Cagney, O and Flannery, RL and Sylvester, KG and Frese, SA and Henrick, BM and Freeman, SL}, title = {Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1472}, pmid = {33479326}, issn = {2045-2322}, support = {S10 OD010786/OD/NIH HHS/United States ; }, mesh = {Bifidobacterium/*genetics/isolation & purification ; DNA, Bacterial/chemistry/metabolism ; Databases, Factual ; Diet ; Drug Resistance, Bacterial/genetics ; Dysbiosis ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Metagenomics/*methods ; Milk, Human/metabolism ; Oligosaccharides/metabolism ; United States ; }, abstract = {The gut microbiome plays an important role in early life, protecting newborns from enteric pathogens, promoting immune system development and providing key functions to the infant host. Currently, there are limited data to broadly assess the status of the US healthy infant gut microbiome. To address this gap, we performed a multi-state metagenomic survey and found high levels of bacteria associated with enteric inflammation (e.g. Escherichia, Klebsiella), antibiotic resistance genes, and signatures of dysbiosis, independent of location, age, and diet. Bifidobacterium were less abundant than generally expected and the species identified, including B. breve, B. longum and B. bifidum, had limited genetic capacity to metabolize human milk oligosaccharides (HMOs), while B. infantis strains with a complete capacity for HMOs utilization were found to be exceptionally rare. Considering microbiome composition and functional capacity, this survey revealed a previously unappreciated dysbiosis that is widespread in the contemporary US infant gut microbiome.}, } @article {pmid33476671, year = {2021}, author = {Brand, EC and Klaassen, MAY and Gacesa, R and Vich Vila, A and Ghosh, H and de Zoete, MR and Boomsma, DI and Hoentjen, F and Horjus Talabur Horje, CS and van de Meeberg, PC and Willemsen, G and Fu, J and Wijmenga, C and van Wijk, F and Zhernakova, A and Oldenburg, B and Weersma, RK and , }, title = {Healthy Cotwins Share Gut Microbiome Signatures With Their Inflammatory Bowel Disease Twins and Unrelated Patients.}, journal = {Gastroenterology}, volume = {160}, number = {6}, pages = {1970-1985}, doi = {10.1053/j.gastro.2021.01.030}, pmid = {33476671}, issn = {1528-0012}, mesh = {Adult ; Antigens, Bacterial/biosynthesis ; Case-Control Studies ; Cross-Sectional Studies ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/physiology ; Humans ; Inflammatory Breast Neoplasms/*epidemiology/*microbiology ; Male ; Metagenomics ; Middle Aged ; Netherlands/epidemiology ; Phenotype ; Risk Factors ; Siderophores/biosynthesis ; Twins, Dizygotic ; Twins, Monozygotic ; Young Adult ; }, abstract = {BACKGROUND & AIMS: It is currently unclear whether reported changes in the gut microbiome are cause or consequence of inflammatory bowel disease (IBD). Therefore, we studied the gut microbiome of IBD-discordant and -concordant twin pairs, which offers the unique opportunity to assess individuals at increased risk of developing IBD, namely healthy cotwins from IBD-discordant twin pairs.

METHODS: Fecal samples were obtained from 99 twins (belonging to 51 twin pairs), 495 healthy age-, sex-, and body mass index-matched controls, and 99 unrelated patients with IBD. Whole-genome metagenomic shotgun sequencing was performed. Taxonomic and functional (pathways) composition was compared among healthy cotwins, IBD-twins, unrelated patients with IBD, and healthy controls with multivariable (ie, adjusted for potential confounding) generalized linear models.

RESULTS: No significant differences were observed in the relative abundance of species and pathways between healthy cotwins and their IBD-twins (false discovery rate <0.10). Compared with healthy controls, 13, 19, and 18 species, and 78, 105, and 153 pathways were found to be differentially abundant in healthy cotwins, IBD-twins, and unrelated patients with IBD, respectively (false discovery rate <0.10). Of these, 8 (42.1%) of 19 and 1 (5.6%) of 18 species, and 37 (35.2%) of 105 and 30 (19.6%) of 153 pathways overlapped between healthy cotwins and IBD-twins, and healthy cotwins and unrelated patients with IBD, respectively. Many of the shared species and pathways have previously been associated with IBD. The shared pathways include potentially inflammation-related pathways, for example, an increase in propionate degradation and L-arginine degradation pathways.

CONCLUSIONS: The gut microbiome of healthy cotwins from IBD-discordant twin pairs displays IBD-like signatures. These IBD-like microbiome signatures might precede the onset of IBD. However, longitudinal follow-up studies are needed to infer a causal relationship.}, } @article {pmid33469669, year = {2021}, author = {Zhang, K and He, C and Xu, Y and Zhang, C and Li, C and Jing, X and Wang, M and Yang, Y and Suo, L and Kalds, P and Song, J and Wang, X and Brugger, D and Wu, Y and Chen, Y}, title = {Taxonomic and functional adaption of the gastrointestinal microbiome of goats kept at high altitude (4800 m) under intensive or extensive rearing conditions.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {3}, pages = {}, doi = {10.1093/femsec/fiab009}, pmid = {33469669}, issn = {1574-6941}, mesh = {Altitude ; Animal Feed/analysis ; Animals ; Diet/veterinary ; Fermentation ; *Gastrointestinal Microbiome ; *Goats/metabolism ; RNA, Ribosomal, 16S/genetics ; Rumen/metabolism ; }, abstract = {The gut microbiota composition is influenced by the diet as well as the environment in both wild and domestic animals. We studied the effects of two feeding systems on the rumen and hindgut microbiome of semi-feral Tibetan goats kept at high altitude (∼4800 m) using 16S rRNA gene and metagenomic sequencing. Intensive drylot feeding resulted in significantly higher zootechnical performance, narrower ruminal acetate: propionate ratios and a drop in the average rumen pH at slaughter to ∼5.04. Hindgut microbial adaption appeared to be more diverse in the drylot group suggesting a higher influx of undegraded complex non-starch polysaccharides from the rumen. Despite their higher fiber levels in the diet, grazing goats exhibited lower counts of Methanobrevibacter and genes associated with the hydrogenotrophic methanogenesis pathway, presumably reflecting the scarce dietary conditions (low energy density) when rearing goats on pasture from extreme alpine environments. These conditions appeared to promote a relevant abundance of bacitracin genes. In parallel, we recognized a significant increase in the abundance of antibiotic resistance genes in the digestive tracts of drylot animals. In summary, this study provides a deeper insight into the metataxonomic and functional adaption of the gastrointestinal microbiome of goats subject to intensive drylot and extensive pasture rearing conditions at high altitude.}, } @article {pmid33469166, year = {2021}, author = {Robbins, SJ and Song, W and Engelberts, JP and Glasl, B and Slaby, BM and Boyd, J and Marangon, E and Botté, ES and Laffy, P and Thomas, T and Webster, NS}, title = {A genomic view of the microbiome of coral reef demosponges.}, journal = {The ISME journal}, volume = {15}, number = {6}, pages = {1641-1654}, pmid = {33469166}, issn = {1751-7370}, mesh = {Animals ; *Anthozoa ; Coral Reefs ; Genomics ; Metagenome ; *Microbiota ; *Porifera ; }, abstract = {Sponges underpin the productivity of coral reefs, yet few of their microbial symbionts have been functionally characterised. Here we present an analysis of ~1200 metagenome-assembled genomes (MAGs) spanning seven sponge species and 25 microbial phyla. Compared to MAGs derived from reef seawater, sponge-associated MAGs were enriched in glycosyl hydrolases targeting components of sponge tissue, coral mucus and macroalgae, revealing a critical role for sponge symbionts in cycling reef organic matter. Further, visualisation of the distribution of these genes amongst symbiont taxa uncovered functional guilds for reef organic matter degradation. Genes for the utilisation of sialic acids and glycosaminoglycans present in sponge tissue were found in specific microbial lineages that also encoded genes for attachment to sponge-derived fibronectins and cadherins, suggesting these lineages can utilise specific structural elements of sponge tissue. Further, genes encoding CRISPR and restriction-modification systems used in defence against mobile genetic elements were enriched in sponge symbionts, along with eukaryote-like gene motifs thought to be involved in maintaining host association. Finally, we provide evidence that many of these sponge-enriched genes are laterally transferred between microbial taxa, suggesting they confer a selective advantage within the sponge niche and therefore play a critical role in host ecology and evolution.}, } @article {pmid33466668, year = {2021}, author = {Eze, MO}, title = {Metagenome Analysis of a Hydrocarbon-Degrading Bacterial Consortium Reveals the Specific Roles of BTEX Biodegraders.}, journal = {Genes}, volume = {12}, number = {1}, pages = {}, pmid = {33466668}, issn = {2073-4425}, mesh = {*Acetobacteraceae/classification/genetics/metabolism ; Biodegradation, Environmental ; DNA, Bacterial/*chemistry ; Hydrocarbons, Aromatic/*metabolism ; *Metagenome ; Microbial Consortia/*genetics ; *Sequence Analysis, DNA ; }, abstract = {Environmental contamination by petroleum hydrocarbons is of concern due to the carcinogenicity and neurotoxicity of these compounds. Successful bioremediation of organic contaminants requires bacterial populations with degradative capacity for these contaminants. Through successive enrichment of microorganisms from a petroleum-contaminated soil using diesel fuel as the sole carbon and energy source, we successfully isolated a bacterial consortium that can degrade diesel fuel hydrocarbons. Metagenome analysis revealed the specific roles of different microbial populations involved in the degradation of benzene, toluene, ethylbenzene and xylene (BTEX), and the metabolic pathways involved in these reactions. One hundred and five putative coding DNA sequences were identified as responsible for both the activation of BTEX and central metabolism (ring-cleavage) of catechol and alkylcatechols during BTEX degradation. The majority of the Coding DNA sequences (CDSs) were affiliated to Acidocella, which was also the dominant bacterial genus in the consortium. The inoculation of diesel fuel contaminated soils with the consortium resulted in approximately 70% hydrocarbon biodegradation, indicating the potential of the consortium for environmental remediation of petroleum hydrocarbons.}, } @article {pmid33466274, year = {2021}, author = {Omori, K and Miyakawa, H and Watanabe, A and Nakayama, Y and Lyu, Y and Ichikawa, N and Sasaki, H and Shibata, S}, title = {The Combined Effects of Magnesium Oxide and Inulin on Intestinal Microbiota and Cecal Short-Chain Fatty Acids.}, journal = {Nutrients}, volume = {13}, number = {1}, pages = {}, pmid = {33466274}, issn = {2072-6643}, mesh = {Animals ; Cecum ; Diet, High-Fat ; Fatty Acids, Volatile/*metabolism ; Feces/chemistry/microbiology ; Gastrointestinal Microbiome/*drug effects ; Hydrogen-Ion Concentration ; Inulin/*pharmacology ; Lipid Metabolism/*drug effects ; Magnesium Oxide/*pharmacology ; Metagenome ; Metagenomics/methods ; Mice ; }, abstract = {Constipation is a common condition that occurs in many people worldwide. While magnesium oxide (MgO) is often used as the first-line drug for chronic constipation in Japan, dietary fiber intake is also recommended. Dietary fiber is fermented by microbiota to produce short-chain fatty acids (SCFAs). SCFAs are involved in regulating systemic physiological functions and circadian rhythm. We examined the effect of combining MgO and the water-soluble dietary fiber, inulin, on cecal SCFA concentration and microbiota in mice. We also examined the MgO administration timing effect on cecal SCFAs. The cecal SCFA concentrations were measured by gas chromatography, and the microbiota was determined using next-generation sequencing. Inulin intake decreased cecal pH and increased cecal SCFA concentrations while combining MgO increased the cecal pH lowered by inulin and decreased the cecal SCFA concentrations elevated by inulin. When inulin and MgO were combined, significant changes in the microbiota composition were observed compared with inulin alone. The MgO effect on the cecal acetic acid concentration was less when administered at ZT12 than at ZT0. In conclusion, this study suggests that MgO affects cecal SCFA and microbiota during inulin feeding, and the effect on acetic acid concentration is time-dependent.}, } @article {pmid33465548, year = {2021}, author = {Nikoloudaki, O and Lemos Junior, WJF and Campanaro, S and Di Cagno, R and Gobbetti, M}, title = {Role prediction of Gram-negative species in the resistome of raw cow's milk.}, journal = {International journal of food microbiology}, volume = {340}, number = {}, pages = {109045}, doi = {10.1016/j.ijfoodmicro.2021.109045}, pmid = {33465548}, issn = {1879-3460}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Cattle ; Drug Resistance, Bacterial/*genetics ; Female ; Genes, Bacterial ; Gram-Negative Bacteria/*drug effects/genetics ; Italy ; Metagenome ; Microbiota ; Milk/*microbiology ; Pseudomonas/drug effects/genetics ; }, abstract = {Extended use of antibiotics in dairy farming for therapeutic and prophylactic reasons, but also the higher prevalence of antibiotic resistant bacteria (ARB) in the farm environment raised the concern of consuming raw cow's milk and its derived products. The aim of this study was to predict by shotgun metagenomic analyses the presence of antibiotic resistance genes (ARGs) mainly correlated with Gram-negative bacteria in antibiotic residue free raw cow's milk derived exclusively from healthy animal from South Tyrol (Northern Italy), chosen as a model system. Assessment of shotgun metagenomic data of reconstructed scaffolds, revealed the existence of Pseudomonas spp. as the most abundant Gram-negative species in the raw cow's milk samples bearing ARGs. Besides, ARGs also linked to lactic acid bacteria such as Lactococcus sp. and Lactobacillus sp. ARGs correlated to microbiome found in milk samples conferred resistance towards aminoglycoside-streptothricin, beta-lactamase, macrolide, tetracycline, carbapenem, cephalosporin, penam, peptide, penem, fluoroquinolone, chloramphenicol and elfamycin antibiotics. Further bioinformatic processing included de-novo reassembly of all metagenomic sequences from all milk samples in one, to reconstruct metagenome assembled genomes (MAGs), which were further used to investigate mobile genetic elements (MGE). Analyses of the reconstructed MAGs showed that, MAG 9 (Pseudomonas sp1.) contained the oriT gene (origin of transfer gene) needed for transferring virulent factors. Although the presence of Pseudomonas is common in raw cow's milk, pasteurization treatment reduces their survivability. Nevertheless, attention should be paid on Pseudomonas spp. due to their intrinsic resistance to antibiotics and their capability of transferring virulent factors to other bacteria.}, } @article {pmid33463854, year = {2020}, author = {Furey, PC and Lee, SS and Clemans, DL}, title = {Substratum-associated microbiota.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {92}, number = {10}, pages = {1629-1648}, doi = {10.1002/wer.1410}, pmid = {33463854}, issn = {1554-7531}, mesh = {*Cyanobacteria ; Ecology ; Fresh Water ; Metagenomics ; *Microbiota ; }, abstract = {Highlights of new, interesting, and emerging research findings on substratum-associated microbiota covered from a survey of 2019 literature from primarily freshwaters provide insight into research trends of interest to the Water Environment Federation and others interested in benthic, aquatic environments. Coverage of topics on bottom-associated or attached algae and cyanobacteria, though not comprehensive, includes new methods, taxa new-to-science, nutrient dynamics, auto- and heterotrophic interactions, grazers, bioassessment, herbicides and other pollutants, metal contaminants, and nuisance, and bloom-forming and harmful algae. Coverage of bacteria, also not comprehensive, focuses on the ecology of benthic biofilms and microbial communities, along with the ecology of microbes like Caulobacter crescentus, Rhodobacter, and other freshwater microbial species. Bacterial topics covered also include metagenomics and metatranscriptomics, toxins and pollutants, bacterial pathogens and bacteriophages, and bacterial physiology. Readers may use this literature review to learn about or renew their interest in the recent advances and discoveries regarding substratum-associated microbiota. PRACTITIONER POINTS: This review of literature from 2019 on substratum-associated microbiota presents highlights of findings on algae, cyanobacteria, and bacteria from primarily freshwaters. Coverage of algae and cyanobacteria includes findings on new methods, taxa new to science, nutrient dynamics, auto- and heterotrophic interactions, grazers, bioassessment, herbicides and other pollutants, metal contaminants, and nuisance, bloom-forming and harmful algae. Coverage of bacteria includes findings on ecology of benthic biofilms and microbial communities, the ecology of microbes, metagenomics and metatranscriptomics, toxins and pollutants, bacterial pathogens and bacteriophages, and bacterial physiology. Highlights of new, noteworthy and emerging topics build on those from 2018 and will be of relevance to the Water Environment Federation and others interested in benthic, aquatic environments.}, } @article {pmid33462508, year = {2021}, author = {Olm, MR and Crits-Christoph, A and Bouma-Gregson, K and Firek, BA and Morowitz, MJ and Banfield, JF}, title = {inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains.}, journal = {Nature biotechnology}, volume = {39}, number = {6}, pages = {727-736}, pmid = {33462508}, issn = {1546-1696}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; }, mesh = {*Biodiversity ; Humans ; Infant, Newborn ; *Metagenomics ; *Microbiota ; Polymorphism, Single Nucleotide ; }, abstract = {Coexisting microbial cells of the same species often exhibit genetic variation that can affect phenotypes ranging from nutrient preference to pathogenicity. Here we present inStrain, a program that uses metagenomic paired reads to profile intra-population genetic diversity (microdiversity) across whole genomes and compares microbial populations in a microdiversity-aware manner, greatly increasing the accuracy of genomic comparisons when benchmarked against existing methods. We use inStrain to profile >1,000 fecal metagenomes from newborn premature infants and find that siblings share significantly more strains than unrelated infants, although identical twins share no more strains than fraternal siblings. Infants born by cesarean section harbor Klebsiella with significantly higher nucleotide diversity than infants delivered vaginally, potentially reflecting acquisition from hospital rather than maternal microbiomes. Genomic loci that show diversity in individual infants include variants found between other infants, possibly reflecting inoculation from diverse hospital-associated sources. inStrain can be applied to any metagenomic dataset for microdiversity analysis and rigorous strain comparison.}, } @article {pmid33462312, year = {2021}, author = {Blifernez-Klassen, O and Klassen, V and Wibberg, D and Cebeci, E and Henke, C and Rückert, C and Chaudhari, S and Rupp, O and Blom, J and Winkler, A and Al-Dilaimi, A and Goesmann, A and Sczyrba, A and Kalinowski, J and Bräutigam, A and Kruse, O}, title = {Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1726}, pmid = {33462312}, issn = {2045-2322}, mesh = {Bacteria/genetics/*metabolism ; Biodegradation, Environmental ; Chlorophyta/*microbiology ; Ecosystem ; Eukaryota/*physiology ; Metagenome ; Microalgae ; *Microbial Consortia ; Phylogeny ; Phytoplankton/*microbiology ; Symbiosis ; }, abstract = {Bacteria occupy all major ecosystems and maintain an intensive relationship to the eukaryotes, developing together into complex biomes (i.e., phycosphere and rhizosphere). Interactions between eukaryotes and bacteria range from cooperative to competitive, with the associated microorganisms affecting their host`s development, growth and health. Since the advent of non-culture dependent analytical techniques such as metagenome sequencing, consortia have been described at the phylogenetic level but rarely functionally. Multifaceted analysis of the microbial consortium of the ancient phytoplankton Botryococcus as an attractive model food web revealed that its all abundant bacterial members belong to a niche of biotin auxotrophs, essentially depending on the microalga. In addition, hydrocarbonoclastic bacteria without vitamin auxotrophies seem adversely to affect the algal cell morphology. Synthetic rearrangement of a minimal community consisting of an alga, a mutualistic and a parasitic bacteria underpins the model of a eukaryote that maintains its own mutualistic microbial community to control its surrounding biosphere. This model of coexistence, potentially useful for defense against invaders by a eukaryotic host could represent ecologically relevant interactions that cross species boundaries. Metabolic and system reconstruction is an opportunity to unravel the relationships within the consortia and provide a blueprint for the construction of mutually beneficial synthetic ecosystems.}, } @article {pmid33462291, year = {2021}, author = {Jeong, J and Yun, K and Mun, S and Chung, WH and Choi, SY and Nam, YD and Lim, MY and Hong, CP and Park, C and Ahn, YJ and Han, K}, title = {The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1727}, pmid = {33462291}, issn = {2045-2322}, mesh = {Bacteria/*classification/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Characterizing the microbial communities inhabiting specimens is one of the primary objectives of microbiome studies. A short-read sequencing platform for reading partial regions of the 16S rRNA gene is most commonly used by reducing the cost burden of next-generation sequencing (NGS), but misclassification at the species level due to its length being too short to consider sequence similarity remains a challenge. Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S). We compared a 16S full-length-based synthetic long-read (sFL16S) and V3-V4 short-read (V3V4) methods using 24 human GUT microbiota samples. Our comparison analyses of sFL16S and V3V4 sequencing data showed that they were highly similar at all classification resolutions except the species level. At the species level, we confirmed that sFL16S showed better resolutions than V3V4 in analyses of alpha-diversity, relative abundance frequency and identification accuracy. Furthermore, we demonstrated that sFL16S could overcome the microbial misidentification caused by different sequence similarity in each 16S variable region through comparison the identification accuracy of Bifidobacterium, Bacteroides, and Alistipes strains classified from both methods. Therefore, this study suggests that the new sFL16S method is a suitable tool to overcome the weakness of the V3V4 method.}, } @article {pmid33462272, year = {2021}, author = {Jacobson, DK and Honap, TP and Ozga, AT and Meda, N and Kagoné, TS and Carabin, H and Spicer, P and Tito, RY and Obregon-Tito, AJ and Reyes, LM and Troncoso-Corzo, L and Guija-Poma, E and Sankaranarayanan, K and Lewis, CM}, title = {Analysis of global human gut metagenomes shows that metabolic resilience potential for short-chain fatty acid production is strongly influenced by lifestyle.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1724}, pmid = {33462272}, issn = {2045-2322}, support = {R01 GM089886/GM/NIGMS NIH HHS/United States ; U54 GM104938/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics ; Computational Biology/methods ; Developed Countries ; Fatty Acids, Volatile/*analysis ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; *Life Style ; Metagenome ; Phylogeny ; }, abstract = {High taxonomic diversity in non-industrial human gut microbiomes is often interpreted as beneficial; however, it is unclear if taxonomic diversity engenders ecological resilience (i.e. community stability and metabolic continuity). We estimate resilience through genus and species-level richness, phylogenetic diversity, and evenness in short-chain fatty acid (SCFA) production among a global gut metagenome panel of 12 populations (n = 451) representing industrial and non-industrial lifestyles, including novel metagenomic data from Burkina Faso (n = 90). We observe significantly higher genus-level resilience in non-industrial populations, while SCFA production in industrial populations is driven by a few phylogenetically closely related species (belonging to Bacteroides and Clostridium), meaning industrial microbiomes have low resilience potential. Additionally, database bias obfuscates resilience estimates, as we were 2-5 times more likely to identify SCFA-encoding species in industrial microbiomes compared to non-industrial. Overall, we find high phylogenetic diversity, richness, and evenness of bacteria encoding SCFAs in non-industrial gut microbiomes, signaling high potential for resilience in SCFA production, despite database biases that limit metagenomic analysis of non-industrial populations.}, } @article {pmid33461660, year = {2021}, author = {Urban, L and Holzer, A and Baronas, JJ and Hall, MB and Braeuninger-Weimer, P and Scherm, MJ and Kunz, DJ and Perera, SN and Martin-Herranz, DE and Tipper, ET and Salter, SJ and Stammnitz, MR}, title = {Freshwater monitoring by nanopore sequencing.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {33461660}, issn = {2050-084X}, support = {OpenPlant Fund (BBSRC BB/L014130/1)/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; Graduate Student Fellowship (203828/Z/16/A, 203828/Z/16/Z)/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; Graduate Student Fellowship (102453/Z/13/Z)/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/classification/genetics ; Base Sequence ; Cluster Analysis ; Computational Biology/methods ; Environmental Monitoring/methods ; Fresh Water/*microbiology ; Geography ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Nanopore Sequencing/*methods ; RNA, Ribosomal, 16S/genetics ; Rivers/microbiology ; Sequence Homology, Nucleic Acid ; Species Specificity ; United Kingdom ; *Water Microbiology ; }, abstract = {While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Here, we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices.}, } @article {pmid33455430, year = {2022}, author = {Zotta, T and Ricciardi, A and Condelli, N and Parente, E}, title = {Metataxonomic and metagenomic approaches for the study of undefined strain starters for cheese manufacture.}, journal = {Critical reviews in food science and nutrition}, volume = {62}, number = {14}, pages = {3898-3912}, doi = {10.1080/10408398.2020.1870927}, pmid = {33455430}, issn = {1549-7852}, mesh = {*Cheese/analysis ; Metagenome ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Undefined strain starters are used for the production of many traditional and artisanal cheeses. Composition of undefined starters depends on several factors, and the diversity in strains and species significantly affects cheese quality and features. Culture-dependent approaches have long been used for the microbial profiling and functionalities of undefined cultures but underestimate their diversity due to culturability biases. Recently, culture-independent methods, based on high-throughput sequencing (HTS), have been preferred, with a significant boost in resolution power and sensitivity level. Amplicon targeted (AT) metagenomics, based on 16S rRNA sequencing, returned a larger microbiota diversity at genus and, sometimes, at species levels for artisanal starters of several PDO cheeses, but was inappropriate for populations with high strain diversity, and other gene targets were tested in AT approaches. Shotgun metagenomics (total DNA) and metatranscriptomics (total RNA), although are more powerful in depicting diversity and functionality of undefined cultures, have been rarely applied because of some limitations (e.g., high costs and laboriousness, need for bioinformatics skills). The advantages of HTS technologies are undoubted, but some hurdles need to be still overcame (e.g., resolution power, discrepancy between active and inactive cells, robust analytic pipelines, cost and time reduction for integrated approaches) so that HTS become routinary and convenient for defining complexity, microbial interactions (including host-phage relationships) and evolution in cheeses of undefined starters.}, } @article {pmid33454531, year = {2021}, author = {Lu, H and Wang, J and Huang, L and Wang, X and Zhou, J and Wang, J}, title = {Effect of immobilized anthraquinone-2-sulfonate on antibiotic resistance genes and microbial community in biofilms of anaerobic reactors.}, journal = {Journal of environmental management}, volume = {282}, number = {}, pages = {111967}, doi = {10.1016/j.jenvman.2021.111967}, pmid = {33454531}, issn = {1095-8630}, mesh = {Anaerobiosis ; Anthraquinones ; *Anti-Bacterial Agents/pharmacology ; Biofilms ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microbiota ; }, abstract = {Quinone compounds could significantly accelerate anaerobic biotransformation of refractory pollutants. However, the effect of quinone compounds application on the propagation of antibiotic resistance genes (ARGs) in the bio-treatment of these pollutants-containing wastewater is not available. In this study, the catalytic performance of anthraquinone-2-sulfonate immobilized on polyurethane foam (AQS-PUF), changes of ARGs, mobile gene elements (MGEs) and microbial community structure attached on AQS-PUF and PUF in the up-flow anaerobic bioreactors were investigated. The results showed that AQS-PUF could significantly accelerate the decolorization of azo dye RR X-3B. Meanwhile, metagenomics analysis showed that the total absolute abundance of ARGs increased in the presence of the immobilized AQS. Among ARGs, the number of the efflux pump-encoding ARGs in the biofilm of AQS-PUF accounted for 35.7% of the total ARGs, which was slightly higher than that of PUF (32.1%) due to the presence of the immobilized AQS. The relative abundances of ARGs conferring resistance to MLS (macrolide, lincosamide and streptogramin), tetracycline and sulfonamide, which were deeply concerned, reduced 10%, 21.7% and 7.3% in the presence of the immobilized AQS, respectively. Moreover, the immobilized AQS resulted in the decreased relative abundance of plasmids, transposons and class I integrons. Among the detected 31 ARG subtypes located in MGEs, the relative abundances of only lnuF, msrE and mphD in the biofilm of AQS-PUF were over 2-fold higher compared with those in the biofilm of PUF. However, the three ARGs and their host Gammaproteobacteria was not dominant in microbial community. The relative abundances of more ARGs including MLS (lnuB and EreA), tetracycline (tetH) resistance genes located in MGEs decreased, which was attributed to the decreased relative abundance of their hosts. These studies showed that the addition of the immobilized AQS (around 0.25 mM) had a beneficial effect on reducing the spread of ARGs during dyeing wastewater bio-treatment.}, } @article {pmid33454444, year = {2021}, author = {Sharma, P and Tripathi, S and Chandra, R}, title = {Metagenomic analysis for profiling of microbial communities and tolerance in metal-polluted pulp and paper industry wastewater.}, journal = {Bioresource technology}, volume = {324}, number = {}, pages = {124681}, doi = {10.1016/j.biortech.2021.124681}, pmid = {33454444}, issn = {1873-2976}, mesh = {Acidobacteria ; Bacteria/genetics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Wastewater ; }, abstract = {This work aimed to study the profiling and efficiency of microbial communities and their abundance in the pulp and paper industry wastewater, which contained toxic metals, high biological oxygen demands, chemical oxygen demand, and ions contents. Sequence alignment of the 16S rRNA V3-V4 variable region zone with the Illumina MiSeq framework revealed 25356 operating taxonomical units (OTUs) derived from the wastewater sample. The major phyla identified in wastewater were Proteobacteria, Bacteroidetes, Firmicutes, Chloroflexi, Actinobacteria, Spirochetes, Patesibacteria, Acidobacteria, and others including unknown microbes. The study showed the function of microbial communities essential for the oxidation and detoxifying of complex contaminants and design of effective remediation techniques for the re-use of polluted wastewater. Findings demonstrated that the ability of different classes of microbes to adapt and survive in metal-polluted wastewater irrespective of their relative distribution, as well as further attention can be provided to its use in the bioremediation process.}, } @article {pmid33453422, year = {2021}, author = {Tao, S and Wang, Z and Quan, C and Ge, Y and Qian, Q}, title = {The effects of ALA-PDT on microbiota in pilosebaceous units of patients with severe acne: A metagenomic study.}, journal = {Photodiagnosis and photodynamic therapy}, volume = {33}, number = {}, pages = {102050}, doi = {10.1016/j.pdpdt.2020.102050}, pmid = {33453422}, issn = {1873-1597}, mesh = {*Acne Vulgaris/drug therapy ; Aminolevulinic Acid/therapeutic use ; Humans ; Longitudinal Studies ; *Microbiota ; *Photochemotherapy/methods ; Photosensitizing Agents/therapeutic use ; }, abstract = {BACKGROUND: 5-aminolevulinic acid mediated photodynamic therapy (ALA-PDT) is increasingly used to control severe acne. However, its impact on skin microbiota remains uncertain.

OBJECTIVES: We aimed to compare the makeup, diversity, and function of the microbiota in pilosebaceous units of patients with severe acne before and after ALA-PDT.

METHODS: A longitudinal cohort study was performed on 11 participants with severe facial acne. All patients were given 5%ALA-PDT every two weeks for three sessions in total. The contents of lesions were sampled for metagenomic sequencing at baseline and two weeks after the first ALA-PDT session.

RESULTS: Cutibacterium acnes was the most dominant species followed by Staphylococcus epidermidis and Pseudomonas fluorescens. Treatment with ALA-PDT led to clinical improvements in acne severity concurrent with a significant reduction in the relative abundance of C. acnes, while P. fluorescens increased significantly after ALA-PDT. No significant change was identified in other species. ALA-PDT administration was associated with an increased microbiota diversity and reductions in the relative abundance of the functional genes involved in energy metabolism and DNA replication.

CONCLUSIONS: ALA-PDT plays a therapeutic role by killing C. acnes, increasing P. fluorescens and the microbiome diversity, while inhibiting the function of microbiota in pilosebaceous units of severe acne.}, } @article {pmid33452983, year = {2021}, author = {Grigorova, EV and Belkova, NL and Nemchenko, UM and Klimenko, ES and Pogodina, AV and Romanitsa, AI and Novikova, EA and Rychkova, LV}, title = {Metasequencing of V3-V4 Variable Regions of 16S rRNA Gene in Opportunistic Microbiota and Gut Biocenosis in Obese Adolescents.}, journal = {Bulletin of experimental biology and medicine}, volume = {170}, number = {3}, pages = {321-325}, pmid = {33452983}, issn = {1573-8221}, mesh = {Enterobacteriaceae/genetics/metabolism ; Escherichia coli/genetics/metabolism ; Gastrointestinal Microbiome/genetics/physiology ; Genes, rRNA/genetics/physiology ; Microbiota/genetics/*physiology ; Obesity/*microbiology ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Opportunistic microorganisms in the gut biocenosis were studied in adolescents with normal body weight and obesity (patients consulted at the Clinical Department of Research Center of Family Health and Human Reproduction Problems). The biological material was studied by standard bacteriological methods, representatives of Enterobacteriaceae family were also characterized using metagenomic sequencing of V3-V4 variable regions of 16S gene rRNA. Gut microbiota of obese adolescents was unbalanced and was characterized by low levels of bifido- and lactoflora representatives, a spectrum of E. coli associations, and high prevalence of opportunistic microorganisms and their associations. Representatives of Enterobacteriaceae family were most often found in the gut microbiota of obese adolescents.}, } @article {pmid33452030, year = {2021}, author = {Gromala, M and Neufeld, JD and McConkey, BJ}, title = {Monitoring Microbial Populations and Antibiotic Resistance Gene Enrichment Associated with Arctic Waste Stabilization Ponds.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {7}, pages = {}, pmid = {33452030}, issn = {1098-5336}, mesh = {Bacteria/drug effects/*genetics ; Drug Resistance, Bacterial/*genetics ; *Metagenome ; Microbiota ; Nunavut ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, RNA ; *Waste Disposal, Fluid ; Wastewater/*microbiology ; }, abstract = {Wastewater management in the Canadian Arctic is challenging due to climate extremes, small population sizes, and lack of conventional infrastructure for wastewater treatment. Although many northern communities use waste stabilization ponds (WSPs) as their primary form of wastewater treatment, few studies have explored WSP microbial communities and assessed effluent impacts on receiving waters from a microbiological perspective. Here, we used 16S rRNA gene and metagenome sequencing to characterize WSP and receiving water microbial communities for two time points bracketing the spring WSP thaw in Baker Lake (Nunavut) and compared these results to other Nunavut WSPs in Cambridge Bay and Kugluktuk. Most amplicon sequence variants (ASVs) recovered from these WSP samples belonged to the phylum Proteobacteria, with considerable variation between the three locations and only six ASVs shared among the WSPs at >0.2% relative abundance. Wastewater indicator ASVs for the Baker Lake WSP were identified, and few indicator ASVs were detected in samples originating from other upstream or downstream sites. The metagenomic data revealed a strong enrichment of antibiotic resistance genes for WSP samples relative to downstream and reference samples, especially for genes associated with macrolide resistance. Together, our results provide a baseline characterization for WSP microbial communities, demonstrate how indicator ASVs can be used to monitor attenuation and dilution of effluent microorganisms, and reveal that WSPs can serve as hot spots for antibiotic resistance genes.IMPORTANCE Given that the microbial communities of Arctic waste stabilization ponds (WSPs) are poorly studied to date, our characterization of multiple WSP systems and time points provides important baseline data that will assist with ongoing monitoring of effluent impacts on downstream aquatic ecosystems in the Arctic. This research also identifies indicator amplicon sequence variants (ASVs) of WSPs that will be helpful for future monitoring for WSP effluent attenuation and demonstrates that WSP microbial communities are enriched in antibiotic resistance genes. Given operational and infrastructure changes anticipated for wastewater treatment systems in the Arctic, baseline data such as these are essential for further development of safe and effective wastewater treatment systems.}, } @article {pmid33452029, year = {2021}, author = {Nilsen, M and Lokmic, A and Angell, IL and Lødrup Carlsen, KC and Carlsen, KH and Haugen, G and Hedlin, G and Jonassen, CM and Marsland, BJ and Nordlund, B and Rehbinder, EM and Saunders, CM and Skjerven, HO and Snipen, L and Staff, AC and Söderhäll, C and Vettukattil, R and Rudi, K}, title = {Fecal Microbiota Nutrient Utilization Potential Suggests Mucins as Drivers for Initial Gut Colonization of Mother-Child-Shared Bacteria.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {6}, pages = {}, pmid = {33452029}, issn = {1098-5336}, mesh = {Bacteria ; Delivery, Obstetric ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Metagenome ; *Mother-Child Relations ; Mothers ; *Mucins ; Nutrients ; }, abstract = {The nutritional drivers for mother-child sharing of bacteria and the corresponding longitudinal trajectory of the infant gut microbiota development are not yet completely settled. We therefore aimed to characterize the mother-child sharing and the inferred nutritional utilization potential for the gut microbiota from a large unselected cohort. We analyzed in depth gut microbiota in 100 mother-child pairs enrolled antenatally from the general population-based Preventing Atopic Dermatitis and Allergies in Children (PreventADALL) cohort. Fecal samples collected at gestational week 18 for mothers and at birth (meconium), 3, 6, and 12 months for infants were analyzed by reduced metagenome sequencing to determine metagenome size and taxonomic composition. The nutrient utilization potential was determined based on the Virtual Metabolic Human (VMH, www.vmh.life) database. The estimated median metagenome size was ∼150 million base pairs (bp) for mothers and ∼20 million bp at birth for the children. Longitudinal analyses revealed mother-child sharing (P < 0.05, chi-square test) from birth up to 6 months for 3 prevalent Bacteroides species (prevalence, >25% for all age groups). In a multivariate analysis of variance (ANOVA), the mother-child-shared Bacteroides were associated with vaginal delivery (1.7% explained variance, P = 0.0001). Both vaginal delivery and mother-child sharing were associated with host-derived mucins as nutrient sources. The age-related increase in metagenome size corresponded to an increased diversity in nutrient utilization, with dietary polysaccharides as the main age-related factor. Our results support host-derived mucins as potential selection means for mother-child sharing of initial colonizers, while the age-related increase in diversity was associated with dietary polysaccharides.IMPORTANCE The initial bacterial colonization of human infants is crucial for lifelong health. Understanding the factors driving this colonization will therefore be of great importance. Here, we used a novel high-taxonomic-resolution approach to deduce the nutrient utilization potential of the infant gut microbiota in a large longitudinal mother-child cohort. We found mucins as potential selection means for the initial colonization of mother-child-shared bacteria, while the transition to a more adult-like microbiota was associated with dietary polysaccharide utilization potential. This knowledge will be important for a future understanding of the importance of diet in shaping the gut microbiota composition and development during infancy.}, } @article {pmid33452024, year = {2021}, author = {Zhu, HZ and Zhang, ZF and Zhou, N and Jiang, CY and Wang, BJ and Cai, L and Wang, HM and Liu, SJ}, title = {Bacteria and Metabolic Potential in Karst Caves Revealed by Intensive Bacterial Cultivation and Genome Assembly.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {6}, pages = {}, pmid = {33452024}, issn = {1098-5336}, mesh = {Bacteria/genetics/isolation & purification/metabolism ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Caves/*microbiology ; Coenzyme A-Transferases/genetics/metabolism ; *Genome, Bacterial ; Metagenome ; Metagenomics ; Microbiota ; Nitrogen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfur/metabolism ; }, abstract = {Karst caves are widely distributed subsurface systems, and the microbiomes therein are proposed to be the driving force for cave evolution and biogeochemical cycling. In past years, culture-independent studies on the microbiomes of cave systems have been conducted, yet intensive microbial cultivation is still needed to validate the sequence-derived hypothesis and to disclose the microbial functions in cave ecosystems. In this study, the microbiomes of two karst caves in Guizhou Province in southwest China were examined. A total of 3,562 bacterial strains were cultivated from rock, water, and sediment samples, and 329 species (including 14 newly described species) of 102 genera were found. We created a cave bacterial genome collection of 218 bacterial genomes from a karst cave microbiome through the extraction of 204 database-derived genomes and de novo sequencing of 14 new bacterial genomes. The cultivated genome collection obtained in this study and the metagenome data from previous studies were used to investigate the bacterial metabolism and potential involvement in the carbon, nitrogen, and sulfur biogeochemical cycles in the cave ecosystem. New N2-fixing Azospirillum and alkane-oxidizing Oleomonas species were documented in the karst cave microbiome. Two pcaIJ clusters of the β-ketoadipate pathway that were abundant in both the cultivated microbiomes and the metagenomic data were identified, and their representatives from the cultivated bacterial genomes were functionally demonstrated. This large-scale cultivation of a cave microbiome represents the most intensive collection of cave bacterial resources to date and provides valuable information and diverse microbial resources for future cave biogeochemical research.IMPORTANCE Karst caves are oligotrophic environments that are dark and humid and have a relatively stable annual temperature. The diversity of bacteria and their metabolisms are crucial for understanding the biogeochemical cycling in cave ecosystems. We integrated large-scale bacterial cultivation with metagenomic data mining to explore the compositions and metabolisms of the microbiomes in two karst cave systems. Our results reveal the presence of a highly diversified cave bacterial community, and 14 new bacterial species were described and their genomes sequenced. In this study, we obtained the most intensive collection of cultivated microbial resources from karst caves to date and predicted the various important routes for the biogeochemical cycling of elements in cave ecosystems.}, } @article {pmid33450352, year = {2021}, author = {Nasser, B and Saito, Y and Alarawi, M and Al-Humam, AA and Mineta, K and Gojobori, T}, title = {Characterization of microbiologically influenced corrosion by comprehensive metagenomic analysis of an inland oil field.}, journal = {Gene}, volume = {774}, number = {}, pages = {145425}, doi = {10.1016/j.gene.2021.145425}, pmid = {33450352}, issn = {1879-0038}, mesh = {Bacteria ; *Bacterial Physiological Phenomena ; Biodegradation, Environmental ; *Corrosion ; Metagenomics ; Microbiota ; Oil and Gas Fields/*microbiology ; *Soil Microbiology ; }, abstract = {Corrosion in pipelines and reservoir tanks in oil plants is a serious problem in the global energy industry because it causes substantial economic losses associated with frequent part replacement and can lead to potential damage to entire crude oil fields. Previous studies revealed that corrosion is mainly caused by microbial activities in a process currently termed microbiologically influenced corrosion or biocorrosion. Identifying the bacteria responsible for biocorrosion is crucial for its suppression. In this study, we analyzed the microbial communities present at corrosion sites in oil plant pipelines using comparative metagenomic analysis along with bioinformatics and statistics. We analyzed the microbial communities in pipelines in an oil field in which groundwater is used as injection water. We collected samples from four different facilities in the oil field. Metagenomic analysis revealed that the microbial community structures greatly differed even among samples from the same facility. Treatments such as biocide administration and demineralization at each location in the pipeline may have independently affected the microbial community structure. The results indicated that microbial inspection throughout the pipeline network is essential to prevent biocorrosion at industrial plants. By identifying the bacterial species responsible for biocorrosion, this study provides bacterial indicators to detect and classify biocorrosion. Furthermore, these species may serve as biomarkers to detect biocorrosion at an early stage. Then, appropriate management such as treatment with suitable biocides can be performed immediately and appropriately. Thus, our study will serve as a platform for obtaining microbial information related to biocorrosion to enable the development of a practical approach to prevent its occurrence.}, } @article {pmid33446604, year = {2021}, author = {Sulaiman, I and Wu, BG and Li, Y and Tsay, JC and Sauthoff, M and Scott, AS and Ji, K and Koralov, SB and Weiden, M and Clemente, JC and Jones, D and Huang, YJ and Stringer, KA and Zhang, L and Geber, A and Banakis, S and Tipton, L and Ghedin, E and Segal, LN}, title = {Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism.}, journal = {The European respiratory journal}, volume = {58}, number = {1}, pages = {}, pmid = {33446604}, issn = {1399-3003}, support = {R01 HL125816/HL/NHLBI NIH HHS/United States ; K23 AI102970/AI/NIAID NIH HHS/United States ; R37 CA244775/CA/NCI NIH HHS/United States ; R01 AI129958/AI/NIAID NIH HHS/United States ; R01 GM111400/GM/NIGMS NIH HHS/United States ; R35 GM136312/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Bacteria/genetics ; Genomics ; Metagenome ; Mice ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Microbiome studies of the lower airways based on bacterial 16S rRNA gene sequencing assess microbial community structure but can only infer functional characteristics. Microbial products, such as short-chain fatty acids (SCFAs), in the lower airways have significant impact on the host's immune tone. Thus, functional approaches to the analyses of the microbiome are necessary.

METHODS: Here we used upper and lower airway samples from a research bronchoscopy smoker cohort. In addition, we validated our results in an experimental mouse model. We extended our microbiota characterisation beyond 16S rRNA gene sequencing with the use of whole-genome shotgun (WGS) and RNA metatranscriptome sequencing. SCFAs were also measured in lower airway samples and correlated with each of the sequencing datasets. In the mouse model, 16S rRNA gene and RNA metatranscriptome sequencing were performed.

RESULTS: Functional evaluations of the lower airway microbiota using inferred metagenome, WGS and metatranscriptome data were dissimilar. Comparison with measured levels of SCFAs shows that the inferred metagenome from the 16S rRNA gene sequencing data was poorly correlated, while better correlations were noted when SCFA levels were compared with WGS and metatranscriptome data. Modelling lower airway aspiration with oral commensals in a mouse model showed that the metatranscriptome most efficiently captures transient active microbial metabolism, which was overestimated by 16S rRNA gene sequencing.

CONCLUSIONS: Functional characterisation of the lower airway microbiota through metatranscriptome data identifies metabolically active organisms capable of producing metabolites with immunomodulatory capacity, such as SCFAs.}, } @article {pmid33443810, year = {2021}, author = {Zhuang, S and Hong, H and Zhang, L and Luo, Y}, title = {Spoilage-related microbiota in fish and crustaceans during storage: Research progress and future trends.}, journal = {Comprehensive reviews in food science and food safety}, volume = {20}, number = {1}, pages = {252-288}, doi = {10.1111/1541-4337.12659}, pmid = {33443810}, issn = {1541-4337}, mesh = {Animals ; Bacteria/genetics ; Crustacea ; *Food Microbiology ; *Microbiota/genetics ; Seafood ; }, abstract = {Fish and crustaceans are highly perishable due to microbial growth and metabolism. Recent studies found that the spoilage process of fish and crustaceans is highly related to their microbiota composition. Microbiota of fish and crustaceans changes dramatically during storage and can be influenced by many factors (e.g., aquaculture environment, handling process, storage temperature, and various quality control techniques). Among them, many quality control techniques have exhibited efficient effects on inhibiting spoilage bacteria, regulating microbiota composition, and retarding quality deterioration. In this article, we elucidate the relationship between microbiota composition and fish/crustacean spoilage, demonstrate influencing factors of fish/crustaceans microbiota, and review various quality control techniques (especially plant-derived preservatives) including their preservative effects on microbiota and quality of fish and crustaceans. Besides, present and future trends of various detective methods used in microbiota analysis are also compared in this review, so as to provide guides for future microbiota studies. To conclude, novel preservation techniques (especially plant-derived preservatives) and hurdle technologies are expected to achieve comprehensive inhibitory effects on spoilage bacteria. Efficient delivery systems are promising in improving the compatibility of plant-derived preservatives with fish/crustaceans and enhancing their preservative effects. Besides, spoilage mechanisms of fishery products that involve complex metabolisms and microbial interactions need to be further elucidated, by using omics technologies like metagenomics, metatranscriptomics, and metabolomics.}, } @article {pmid33443632, year = {2021}, author = {Nkansah-Boadu, F and Hatam, I and Baldwin, SA}, title = {Microbial consortia capable of reducing selenate in the presence of nitrate enriched from coalmining-impacted environments.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {3}, pages = {1287-1300}, pmid = {33443632}, issn = {1432-0614}, support = {UPP026//Genome British Columbia/ ; }, mesh = {Microbial Consortia ; Nitrates ; Selenic Acid ; *Selenium ; *Selenium Compounds ; Wetlands ; }, abstract = {Biological treatment to remove dissolved selenium from mine-impacted water is often inhibited by the co-contaminant nitrate. In this work, we enriched microbial consortia capable of removing dissolved selenium in the presence of nitrate from native bacteria at sites influenced by coalmine seepages with elevated concentrations of Se, nitrate, and sulfate. Enrichments were collected from sediments in different vegetated or non-vegetated seepage collection ponds, and all demonstrated the potential for dissolved selenium removal. Nitrate inhibited dissolved selenium removal rates in four of these enrichments. However, microorganisms enriched from a mine seepage influenced natural vegetated marsh removed dissolved Se and nitrate simultaneously. Additionally, enrichments from one seepage collection pond achieved enhanced dissolved selenium removal in the presence of nitrate. Based on functional metagenomics, the dominant species with the metabolic capacity for selenate reduction were classified in Orders Enterobacterales and Clostridiales. Most putative selenate reductases identified as either ygfK, associated with selenoprotein synthesis or production of methylated organoselenium compounds, and narG, nitrate reductases with an affinity also for selenate.Key points• Enriched mine influenced sediment bacteria have the capacity for removal of dissolved Se species.• Consortia from a vegetated natural marsh reduced Se without inhibition from nitrate.• Nitrate stimulated the removal of Se by consortia from a disused tailing pond.}, } @article {pmid33441409, year = {2021}, author = {Fishbein, SRS and Hink, T and Reske, KA and Cass, C and Struttmann, E and Iqbal, ZH and Seiler, S and Kwon, JH and Burnham, CA and Dantas, G and Dubberke, ER}, title = {Randomized Controlled Trial of Oral Vancomycin Treatment in Clostridioides difficile-Colonized Patients.}, journal = {mSphere}, volume = {6}, number = {1}, pages = {}, pmid = {33441409}, issn = {2379-5042}, support = {T32 DK077653/DK/NIDDK NIH HHS/United States ; K23 AI137321/AI/NIAID NIH HHS/United States ; T32 HD007409/HD/NICHD NIH HHS/United States ; R01 AT009741/AT/NCCIH NIH HHS/United States ; R01 OH011578/OH/NIOSH CDC HHS/United States ; }, mesh = {Administration, Oral ; Adult ; Aged ; Anti-Bacterial Agents/*administration & dosage/adverse effects/therapeutic use ; Clostridioides difficile/*drug effects/physiology ; Clostridium Infections/*drug therapy ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Humans ; Male ; Metagenomics/methods ; Middle Aged ; Vancomycin/*administration & dosage/adverse effects/therapeutic use ; Vancomycin-Resistant Enterococci/drug effects/genetics/isolation & purification ; }, abstract = {Clostridioides difficile infection (CDI) is most commonly diagnosed using nucleic acid amplification tests (NAAT); the low positive predictive value of these assays results in patients colonized with C. difficile unnecessarily receiving CDI treatment antibiotics. The risks and benefits of antibiotic treatment in individuals with such cases are unknown. Fecal samples of NAAT-positive, toxin enzyme immunoassay (EIA)-negative patients were collected before, during, and after randomization to vancomycin (n = 8) or placebo (n = 7). C. difficile and antibiotic-resistant organisms (AROs) were selectively cultured from fecal and environmental samples. Shotgun metagenomics and comparative isolate genomics were used to understand the impact of oral vancomycin on the microbiome and environmental contamination. Overall, 80% of placebo patients and 71% of vancomycin patients were colonized with C. difficile posttreatment. One person randomized to placebo subsequently received treatment for CDI. In the vancomycin-treated group, beta-diversity (P = 0.0059) and macrolide-lincosamide-streptogramin (MLS) resistance genes (P = 0.037) increased after treatment; C. difficile and vancomycin-resistant enterococci (VRE) environmental contamination was found in 53% of patients and 26% of patients, respectively. We found that vancomycin alters the gut microbiota, does not permanently clear C. difficile, and is associated with VRE colonization/environmental contamination. (This study has been registered at ClinicalTrials.gov under registration no. NCT03388268.)IMPORTANCE A gold standard diagnostic for Clostridioides difficile infection (CDI) does not exist. An area of controversy is how to manage patients whose stool tests positive by nucleic acid amplification tests but negative by toxin enzyme immunoassay. Existing data suggest most of these patients do not have CDI, but most are treated with oral vancomycin. Potential benefits to treatment include a decreased risk for adverse outcomes if the patient does have CDI and the potential to decrease C. difficile shedding/transmission. However, oral vancomycin perturbs the intestinal microbiota and promotes antibiotic-resistant organism colonization/transmission. We conducted a double-blinded randomized controlled trial to assess the risk-benefit of oral vancomycin treatment in this population. Oral vancomycin did not result in long-term clearance of C. difficile, perturbed the microbiota, and was associated with colonization/shedding of vancomycin-resistant enterococci. This work underscores the need to better understand this population of patients in the context of C. difficile/ARO-related outcomes and transmission.}, } @article {pmid33439104, year = {2021}, author = {Manandhar, I and Alimadadi, A and Aryal, S and Munroe, PB and Joe, B and Cheng, X}, title = {Gut microbiome-based supervised machine learning for clinical diagnosis of inflammatory bowel diseases.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {320}, number = {3}, pages = {G328-G337}, pmid = {33439104}, issn = {1522-1547}, support = {R01 HL143082/HL/NHLBI NIH HHS/United States ; /DH_/Department of Health/United Kingdom ; HL143082//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; }, mesh = {Diagnosis, Computer-Assisted/*methods ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/diagnosis/*microbiology ; *Supervised Machine Learning ; }, abstract = {Despite the availability of various diagnostic tests for inflammatory bowel diseases (IBD), misdiagnosis of IBD occurs frequently, and thus, there is a clinical need to further improve the diagnosis of IBD. As gut dysbiosis is reported in patients with IBD, we hypothesized that supervised machine learning (ML) could be used to analyze gut microbiome data for predictive diagnostics of IBD. To test our hypothesis, fecal 16S metagenomic data of 729 subjects with IBD and 700 subjects without IBD from the American Gut Project were analyzed using five different ML algorithms. Fifty differential bacterial taxa were identified [linear discriminant analysis effect size (LEfSe): linear discriminant analysis (LDA) score > 3] between the IBD and non-IBD groups, and ML classifications trained with these taxonomic features using random forest (RF) achieved a testing area under the receiver operating characteristic curves (AUC) of ∼0.80. Next, we tested if operational taxonomic units (OTUs), instead of bacterial taxa, could be used as ML features for diagnostic classification of IBD. Top 500 high-variance OTUs were used for ML training, and an improved testing AUC of ∼0.82 (RF) was achieved. Lastly, we tested if supervised ML could be used for differentiating Crohn's disease (CD) and ulcerative colitis (UC). Using 331 CD and 141 UC samples, 117 differential bacterial taxa (LEfSe: LDA score > 3) were identified, and the RF model trained with differential taxonomic features or high-variance OTU features achieved a testing AUC > 0.90. In summary, our study demonstrates the promising potential of artificial intelligence via supervised ML modeling for predictive diagnostics of IBD using gut microbiome data.NEW & NOTEWORTHY Our study demonstrates the promising potential of artificial intelligence via supervised machine learning modeling for predictive diagnostics of different types of inflammatory bowel diseases using fecal gut microbiome data.}, } @article {pmid33439103, year = {2021}, author = {Cuna, A and Morowitz, MJ and Ahmed, I and Umar, S and Sampath, V}, title = {Dynamics of the preterm gut microbiome in health and disease.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {320}, number = {4}, pages = {G411-G419}, pmid = {33439103}, issn = {1522-1547}, support = {K08 DK125735/DK/NIDDK NIH HHS/United States ; R01 DK117296/DK/NIDDK NIH HHS/United States ; K08DK125735//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; }, mesh = {Animals ; Bacteria/*growth & development ; Dysbiosis ; Enterocolitis, Necrotizing/*microbiology/therapy ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Gestational Age ; Host-Pathogen Interactions ; Humans ; Infant, Newborn ; *Infant, Premature ; Intestines/*microbiology ; Neonatal Sepsis/*microbiology/therapy ; Prebiotics ; Probiotics/therapeutic use ; Prognosis ; Risk Factors ; }, abstract = {Advances in metagenomics have allowed a detailed study of the gut microbiome, and its role in human health and disease. Infants born prematurely possess a fragile gut microbial ecosystem that is vulnerable to perturbation. Alterations in the developing gut microbiome in preterm infants are linked to life-threatening diseases such as necrotizing enterocolitis (NEC) and late-onset sepsis; and may impact future risk of asthma, atopy, obesity, and psychosocial disease. In this mini-review, we summarize recent literature on the origins and patterns of development of the preterm gut microbiome in the perinatal period. The host-microbiome-environmental factors that portend development of dysbiotic intestinal microbial patterns associated with NEC and sepsis are reviewed. Strategies to manipulate the microbiome and mitigate dysbiosis, including the use of probiotics and prebiotics will also be discussed. Finally, we explore the challenges and future directions of gut microbiome research in preterm infants.}, } @article {pmid33438892, year = {2021}, author = {Peters, BA and Xue, X and Wang, Z and Usyk, M and Santoro, N and Sharma, A and Anastos, K and Tien, PC and Golub, ET and Weber, KM and Gustafson, D and Kaplan, RC and Burk, R and Qi, Q}, title = {Menopausal status and observed differences in the gut microbiome in women with and without HIV infection.}, journal = {Menopause (New York, N.Y.)}, volume = {28}, number = {5}, pages = {491-501}, pmid = {33438892}, issn = {1530-0374}, support = {U01 HL146245/HL/NHLBI NIH HHS/United States ; U01 HL146242/HL/NHLBI NIH HHS/United States ; R21 AG059505/AG/NIA NIH HHS/United States ; U01 HL146193/HL/NHLBI NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; U01 HL146204/HL/NHLBI NIH HHS/United States ; U01 HL146202/HL/NHLBI NIH HHS/United States ; }, mesh = {Cross-Sectional Studies ; Female ; *Gastrointestinal Microbiome ; *HIV Infections ; Humans ; Menopause ; Prevotella ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVE: Gut microbiota respond to host physiological phenomena, yet little is known regarding shifts in the gut microbiome due to menopausal hormonal and metabolic changes in women. HIV infection impacts menopause and may also cause gut dysbiosis. We therefore sought to determine the association between menopausal status and gut microbiome composition in women with and without HIV.

METHODS: Gut microbiome composition was assessed in stool from 432 women (99 premenopausal HIV+, 71 premenopausal HIV-, 182 postmenopausal HIV+, 80 postmenopausal HIV-) via 16S rRNA gene sequencing. We examined cross-sectional associations of menopause with gut microbiota overall diversity and composition, and taxon and inferred metagenomic pathway abundance. Models were stratified by HIV serostatus and adjusted for age, HIV-related variables, and other potential confounders.

RESULTS: Menopause, ie post- versus premenopausal status, was associated with overall microbial composition only in women with HIV (permutational MANOVA of Jensen Shannon Divergence: P = 0.01). In women with HIV, menopause was associated with enrichment of gram-negative order Enterobacteriales, depletion of highly abundant taxa within Prevotella copri, and alterations in other low-abundance taxa. Additionally, menopause in women with HIV was associated with enrichment of metagenomic pathways related to Enterobacteriales, including degradation of amino acids and phenolic compounds, biosynthesis of enterobactin, and energy metabolism pathways. Menopause-related differences in some low-abundance taxa were also observed in women without HIV.

CONCLUSIONS: A changing gut microbiome may be an overlooked phenomenon of reproductive aging in women with HIV. Longitudinal assessments across all reproductive stages are necessary to confirm these findings and identify health implications.}, } @article {pmid33436440, year = {2021}, author = {Griesenauer, B and González-Beiras, C and Fortney, KR and Lin, H and Gao, X and Godornes, C and Nelson, DE and Katz, BP and Lukehart, SA and Mitjà, O and Dong, Q and Spinola, SM}, title = {Streptococcus pyogenes Is Associated with Idiopathic Cutaneous Ulcers in Children on a Yaws-Endemic Island.}, journal = {mBio}, volume = {12}, number = {1}, pages = {}, pmid = {33436440}, issn = {2150-7511}, support = {R01 AI134727/AI/NIAID NIH HHS/United States ; T32 AI007637/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; Azithromycin/therapeutic use ; Child ; Clostridiales ; Haemophilus ducreyi ; Humans ; Metagenomics ; Microbiota ; Papua New Guinea/epidemiology ; Polymerase Chain Reaction ; Prospective Studies ; RNA, Ribosomal, 16S ; Skin Ulcer/*complications/drug therapy/epidemiology/*microbiology ; Streptococcus pyogenes/genetics/*isolation & purification ; Treponema ; Ulcer ; Yaws/*complications/drug therapy/epidemiology/*microbiology ; }, abstract = {Exudative cutaneous ulcers (CU) in yaws-endemic areas are associated with Treponema pallidum subsp. pertenue (TP) and Haemophilus ducreyi (HD), but one-third of CU cases are idiopathic (IU). Using mass drug administration (MDA) of azithromycin, a yaws eradication campaign on Lihir Island in Papua New Guinea reduced but failed to eradicate yaws; IU rates remained constant throughout the campaign. To identify potential etiologies of IU, we obtained swabs of CU lesions (n = 279) and of the skin of asymptomatic controls (AC; n = 233) from the Lihir Island cohort and characterized their microbiomes using a metagenomics approach. CU bacterial communities were less diverse than those of the AC. Using real-time multiplex PCR with pathogen-specific primers, we separated CU specimens into HD-positive (HD+), TP+, HD+TP+, and IU groups. Each CU subgroup formed a distinct bacterial community, defined by the species detected and/or the relative abundances of species within each group. Streptococcus pyogenes was the most abundant organism in IU (22.65%) and was enriched in IU compared to other ulcer groups. Follow-up samples (n = 31) were obtained from nonhealed ulcers; the average relative abundance of S. pyogenes was 30.11% in not improved ulcers and 0.88% in improved ulcers, suggesting that S. pyogenes in the not improved ulcers may be azithromycin resistant. Catonella morbi was enriched in IU that lacked S. pyogenes As some S. pyogenes and TP strains are macrolide resistant, penicillin may be the drug of choice for CU azithromycin treatment failures. Our study will aid in the design of diagnostic tests and selective therapies for CU.IMPORTANCE Cutaneous ulcers (CU) affect approximately 100,000 children in the tropics each year. While two-thirds of CU are caused by Treponema pallidum subspecies pertenue and Haemophilus ducreyi, the cause(s) of the remaining one-third is unknown. Given the failure of mass drug administration of azithromycin to eradicate CU, the World Health Organization recently proposed an integrated disease management strategy to control CU. Success of this strategy requires determining the unknown cause(s) of CU. By using 16S rRNA gene sequencing of swabs obtained from CU and the skin of asymptomatic children, we identified another possible cause of skin ulcers, Streptococcus pyogenes Although S. pyogenes is known to cause impetigo and cellulitis, this is the first report implicating the organism as a causal agent of CU. Inclusion of S. pyogenes into the integrated disease management plan will improve diagnostic testing and treatment of this painful and debilitating disease of children and strengthen elimination efforts.}, } @article {pmid33436010, year = {2021}, author = {Liu, J and Liu, C and Yue, J}, title = {Radiotherapy and the gut microbiome: facts and fiction.}, journal = {Radiation oncology (London, England)}, volume = {16}, number = {1}, pages = {9}, pmid = {33436010}, issn = {1748-717X}, support = {81871895//National Natural Science Foundation of China/ ; 2019RC003//Young Taishan Scholars and Academic Promotion Program of Shandong First Medical University/ ; }, mesh = {Animals ; Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/*radiation effects ; Humans ; Neoplasms/*radiotherapy ; Prebiotics ; Probiotics/pharmacology ; Radiation Tolerance ; Radiotherapy/*adverse effects ; }, abstract = {An ever-growing body of evidence has linked the gut microbiome with both the effectiveness and the toxicity of cancer therapies. Radiotherapy is an effective way to treat tumors, although large variations exist among patients in tumor radio-responsiveness and in the incidence and severity of radiotherapy-induced side effects. Relatively little is known about whether and how the microbiome regulates the response to radiotherapy. Gut microbiota may be an important player in modulating "hot" versus "cold" tumor microenvironment, ultimately affecting treatment efficacy. The interaction of the gut microbiome and radiotherapy is a bidirectional function, in that radiotherapy can disrupt the microbiome and those disruptions can influence the effectiveness of the anticancer treatments. Limited data have shown that interactions between the radiation and the microbiome can have positive effects on oncotherapy. On the other hand, exposure to ionizing radiation leads to changes in the gut microbiome that contribute to radiation enteropathy. The gut microbiome can influence radiation-induced gastrointestinal mucositis through two mechanisms including translocation and dysbiosis. We propose that the gut microbiome can be modified to maximize the response to treatment and minimize adverse effects through the use of personalized probiotics, prebiotics, or fecal microbial transplantation. 16S rRNA sequencing is the most commonly used approach to investigate distribution and diversity of gut microbiome between individuals though it only identifies bacteria level other than strain level. The functional gut microbiome can be studied using methods involving metagenomics, metatranscriptomics, metaproteomics, as well as metabolomics. Multiple '-omic' approaches can be applied simultaneously to the same sample to obtain integrated results. That said, challenges and remaining unknowns in the future that persist at this time include the mechanisms by which the gut microbiome affects radiosensitivity, interactions between the gut microbiome and combination treatments, the role of the gut microbiome with regard to predictive and prognostic biomarkers, the need for multi "-omic" approach for in-depth exploration of functional changes and their effects on host-microbiome interactions, and interactions between gut microbiome, microbial metabolites and immune microenvironment.}, } @article {pmid33433545, year = {2021}, author = {Ruan, S and Wang, L and Li, Y and Li, P and Ren, Y and Gao, R and Ma, H}, title = {Staple food and health: a comparative study of physiology and gut microbiota of mice fed with potato and traditional staple foods (corn, wheat and rice).}, journal = {Food & function}, volume = {12}, number = {3}, pages = {1232-1240}, doi = {10.1039/d0fo02264k}, pmid = {33433545}, issn = {2042-650X}, mesh = {Aminoacridines ; Animal Feed ; Animals ; Bacteria/classification/drug effects ; Body Weight ; Diet ; Drinking ; Eating ; Gastrointestinal Microbiome/*drug effects ; Mice ; Nitrogen Mustard Compounds ; *Oryza ; Random Allocation ; *Solanum tuberosum ; *Triticum ; *Zea mays ; }, abstract = {The effects of potato and traditional staple foods (corn, wheat and rice) on physiology and gut microbiota were investigated by feeding ICR mice for 12 months. Compared with traditional staple foods, potato significantly improved the food and water intake and survival rate, and inhibited the swelling of viscera of mice, accompanied by a decreased white blood cell count and urine bilirubin content. Furthermore, potato significantly increased the relative abundance of Bacteroides and Faecalibacterium, which are short-chain fatty acid producing bacteria and play very important roles in the maintenance of human health. Meanwhile, potato significantly decreased the relative abundance of spoilage bacteria Pseudomonas and Thiobacillus. Analysis of putative metagenomes indicated that the potato diet upregulated the gene abundance of glycan biosynthesis and metabolism, digestive system and immune system. These findings indicated that potato has the potential to be an excellent substitute for traditional staple foods owing to its good physiological function and favorable gut microbiota modulation.}, } @article {pmid33432373, year = {2021}, author = {Malakar, D and Sarathbabu, S and Borah, P and Kumar, NS}, title = {Fish gill microbiome from India's largest Brahmaputra River-a trans-border biodiversity hotspot region.}, journal = {Environmental monitoring and assessment}, volume = {193}, number = {2}, pages = {56}, pmid = {33432373}, issn = {1573-2959}, support = {No. BT/BI/12/060/2012//Department of Biotechnology, Government of India/ ; }, mesh = {Animals ; Biodiversity ; Environmental Monitoring ; Gills ; India ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Rivers ; }, abstract = {In this study, we sequenced the V3-V4 region of 16S rRNA gene amplicon using paired-end Illumina HiSeq to study the bacterial community in the gills of fish from the bank of the trans-border river of Brahmaputra, Northeast India. Metagenome data consisted of 278,784 reads, 248-bp length, and 56.48% GC content with 85% sequence having a Phred score Q = 30. Community metagenomics revealed a total of 631 genera belonging to 22 different phyla, dominated by Proteobacteria (118,222 features), Firmicutes (101,043 features), Actinobacteria (34,189 features), Bacteroidetes (17,977 features), and Cyanobacteria (2730 features). The bacterial community identified was composed of both pathogenic zoonotic and non-harmful groups. The pathway or functional analysis of the fish gill microbiome exhibited 21 different pathways which also included the pathogenic-related functions. Our data detected a wide group of bacterial communities that will be useful in further isolating and characterizing the pathogenic bacteria from the fish and also to understand the bacterial association in highly consumed fish.}, } @article {pmid33432175, year = {2021}, author = {Asnicar, F and Berry, SE and Valdes, AM and Nguyen, LH and Piccinno, G and Drew, DA and Leeming, E and Gibson, R and Le Roy, C and Khatib, HA and Francis, L and Mazidi, M and Mompeo, O and Valles-Colomer, M and Tett, A and Beghini, F and Dubois, L and Bazzani, D and Thomas, AM and Mirzayi, C and Khleborodova, A and Oh, S and Hine, R and Bonnett, C and Capdevila, J and Danzanvilliers, S and Giordano, F and Geistlinger, L and Waldron, L and Davies, R and Hadjigeorgiou, G and Wolf, J and Ordovás, JM and Gardner, C and Franks, PW and Chan, AT and Huttenhower, C and Spector, TD and Segata, N}, title = {Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals.}, journal = {Nature medicine}, volume = {27}, number = {2}, pages = {321-332}, pmid = {33432175}, issn = {1546-170X}, support = {MR/N01183X/1/MRC_/Medical Research Council/United Kingdom ; P30 DK043351/DK/NIDDK NIH HHS/United States ; MR/N030125/1/MRC_/Medical Research Council/United Kingdom ; MR/M016560/1/MRC_/Medical Research Council/United Kingdom ; K23 DK125838/DK/NIDDK NIH HHS/United States ; 212904/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; R01 CA230551/CA/NCI NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Biomarkers/metabolism ; Blastocystis/genetics ; Blood Glucose/metabolism ; Child ; Diet/adverse effects ; Fasting/metabolism ; Feeding Behavior ; Female ; Food Microbiology ; Gastrointestinal Microbiome/*genetics ; Glucose/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenome/*genetics ; Microbiota/*genetics ; Middle Aged ; Obesity/genetics/metabolism/*microbiology ; Postprandial Period/genetics ; Prevotella/genetics/isolation & purification ; }, abstract = {The gut microbiome is shaped by diet and influences host metabolism; however, these links are complex and can be unique to each individual. We performed deep metagenomic sequencing of 1,203 gut microbiomes from 1,098 individuals enrolled in the Personalised Responses to Dietary Composition Trial (PREDICT 1) study, whose detailed long-term diet information, as well as hundreds of fasting and same-meal postprandial cardiometabolic blood marker measurements were available. We found many significant associations between microbes and specific nutrients, foods, food groups and general dietary indices, which were driven especially by the presence and diversity of healthy and plant-based foods. Microbial biomarkers of obesity were reproducible across external publicly available cohorts and in agreement with circulating blood metabolites that are indicators of cardiovascular disease risk. While some microbes, such as Prevotella copri and Blastocystis spp., were indicators of favorable postprandial glucose metabolism, overall microbiome composition was predictive for a large panel of cardiometabolic blood markers including fasting and postprandial glycemic, lipemic and inflammatory indices. The panel of intestinal species associated with healthy dietary habits overlapped with those associated with favorable cardiometabolic and postprandial markers, indicating that our large-scale resource can potentially stratify the gut microbiome into generalizable health levels in individuals without clinically manifest disease.}, } @article {pmid33432149, year = {2021}, author = {Lee, SH and Cho, SY and Yoon, Y and Park, C and Sohn, J and Jeong, JJ and Jeon, BN and Jang, M and An, C and Lee, S and Kim, YY and Kim, G and Kim, S and Kim, Y and Lee, GB and Lee, EJ and Kim, SG and Kim, HS and Kim, Y and Kim, H and Yang, HS and Kim, S and Kim, S and Chung, H and Moon, MH and Nam, MH and Kwon, JY and Won, S and Park, JS and Weinstock, GM and Lee, C and Yoon, KW and Park, H}, title = {Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice.}, journal = {Nature microbiology}, volume = {6}, number = {3}, pages = {277-288}, pmid = {33432149}, issn = {2058-5276}, mesh = {Animals ; Bifidobacterium bifidum/classification/genetics/*physiology ; Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology/pathology ; Drug Therapy, Combination ; Gastrointestinal Microbiome ; Humans ; Immune Checkpoint Inhibitors/*therapeutic use ; Interferon-gamma/genetics/metabolism ; Lung Neoplasms/drug therapy/microbiology/pathology ; Metabolome/drug effects ; Mice ; Neoplasms, Experimental/drug therapy/pathology ; Probiotics/administration & dosage/*therapeutic use ; Species Specificity ; Transcriptome/drug effects ; Tryptophan/metabolism ; Tumor Burden/*drug effects ; }, abstract = {The gut microbiome can influence the development of tumours and the efficacy of cancer therapeutics[1-5]; however, the multi-omics characteristics of antitumour bacterial strains have not been fully elucidated. In this study, we integrated metagenomics, genomics and transcriptomics of bacteria, and analyses of mouse intestinal transcriptome and serum metabolome data to reveal an additional mechanism by which bacteria determine the efficacy of cancer therapeutics. In gut microbiome analyses of 96 samples from patients with non-small-cell lung cancer, Bifidobacterium bifidum was abundant in patients responsive to therapy. However, when we treated syngeneic mouse tumours with commercial strains of B. bifidum to establish relevance for potential therapeutic uses, only specific B. bifidum strains reduced tumour burden synergistically with PD-1 blockade or oxaliplatin treatment by eliciting an antitumour host immune response. In mice, these strains induced tuning of the immunological background by potentiating the production of interferon-γ, probably through the enhanced biosynthesis of immune-stimulating molecules and metabolites.}, } @article {pmid33432015, year = {2021}, author = {Debesa-Tur, G and Pérez-Brocal, V and Ruiz-Ruiz, S and Castillejo, A and Latorre, A and Soto, JL and Moya, A}, title = {Metagenomic analysis of formalin-fixed paraffin-embedded tumor and normal mucosa reveals differences in the microbiome of colorectal cancer patients.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {391}, pmid = {33432015}, issn = {2045-2322}, mesh = {Adult ; Aged ; Aged, 80 and over ; Case-Control Studies ; Cohort Studies ; Colorectal Neoplasms/*microbiology/pathology ; Female ; Formaldehyde/chemistry ; Gastrointestinal Microbiome/*genetics ; Humans ; Intestinal Mucosa/*microbiology/pathology ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Paraffin Embedding ; Tissue Fixation/methods ; }, abstract = {An increased risk of developing colorectal cancer (CRC) and other types of tumor is associated to Lynch syndrome (LS), an inherited condition caused by germline mutations in mismatch repair genes. We selected a cohort of LS patients that had developed CRC and had undergone surgical resection. Formalin-fixed paraffin embedded (FFPE) tissue blocks from matched colorectal and normal mucosa were used for genomic DNA extraction with a commercial kit and sequenced by high-throughput sequencing. A metagenomic approach enabled the taxonomic and functional identification of the microbial community and associated genes detected in the specimens. Slightly lower taxonomic diversity was observed in the tumor compared to the non-tumor tissue. Furthermore, the most remarkable differences between tumors and healthy tissue was the significant increase in the genus Fusobacterium in the former, in particular the species F. nucleatum, as well as Camplylobacter or Bacteroides fragilis, in accordance with previous studies of CRC. However, unlike prior studies, the present work is not based on directed detection by qPCR but instead uses a metagenomic approach to retrieve the whole bacterial community, and addresses the additional difficulty of using long-term stored FFPE samples.}, } @article {pmid33430705, year = {2021}, author = {Ma, C and Chen, K and Wang, Y and Cen, C and Zhai, Q and Zhang, J}, title = {Establishing a novel colorectal cancer predictive model based on unique gut microbial single nucleotide variant markers.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-6}, pmid = {33430705}, issn = {1949-0984}, mesh = {Area Under Curve ; Bacteria/classification/genetics ; Biomarkers, Tumor/genetics ; Colorectal Neoplasms/*diagnosis/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Humans ; Metagenome/genetics ; Reproducibility of Results ; }, abstract = {Current metagenomic species-based colorectal cancer (CRC) microbial biomarkers may confuse diagnosis because the genetic content of different microbial strains, even those belonging to the same species, may differ from 5% to 30%. Here, a total of 7549 non-redundant single nucleotide variants (SNVs) were annotated in 25 species from 3 CRC cohorts (n = 249). Then, 22 microbial SNV markers that contributed to distinguishing subjects with CRC from healthy subjects were identified by the random forest algorithm to construct a novel CRC predictive model. Excitingly, the predictive model showed high accuracy both in the training (AUC = 75.35%) and validation cohorts (AUC = 73.08%-88.02%). We further explored the specificity of these SNV markers in a broader background by performing a meta-analysis across 4 metabolic disease cohorts. Among these SNV markers, 3 SNVs that were enriched in CRC patients and located in the genomes of Eubacterium rectale and Faecalibacterium prausnitzii were CRC specific (AUC = 72.51%-94.07%).}, } @article {pmid33428153, year = {2021}, author = {Zhao, W and Ren, Z and Luo, Y and Cheng, J and Wang, J and Wang, Y and Yang, Z and Yao, X and Zhong, Z and Yang, W and Wu, X}, title = {Metagenomics analysis of the gut microbiome in healthy and bacterial pneumonia forest musk deer.}, journal = {Genes & genomics}, volume = {43}, number = {1}, pages = {43-53}, pmid = {33428153}, issn = {2092-9293}, mesh = {Animals ; Deer/*microbiology ; *Gastrointestinal Microbiome ; Genes, Bacterial ; *Metagenome ; Pneumonia/*microbiology/veterinary ; }, abstract = {BACKGROUND: The forest musk deer (FMD, Moschus berezovskii) is an threatened species in China. Bacterial pneumonia was found to seriously restrict the development of FMD captive breeding. Historical evidence has demonstrated the relationship between immune system and intestinal Lactobacillus in FMD.

OBJECTIVE: We sought to elucidate the differences in the gut microbiota of healthy and bacterial pneumonia FMD.

METHODS: The bacterial pneumonia FMD was demonstrated by bacterial and pathological diagnosis, and the gut microbiome of healthy and bacterial pneumonia FMD was sequenced and analysed.

RESULTS: There are three pathogens (Pseudomonas aeruginosa, Streptococcus equinus and Trueperella pyogenes) isolated from the bacterial pneumonia FMD individuals. Compared with the healthy group, the abundance of Firmicutes and Proteobacteria in the pneumonia group was changed, and a high level of Proteobacteria was found in the pneumonia group. In addition, a higher abundance of Acinetobacter (p = 0.01) was observed in the population of the pneumonia group compared with the healthy group. Several potentially harmful bacteria and disease-related KEGG subsystems were only found in the gut of the bacterial pneumonia group. Analysis of KEGG revealed that many genes related to type IV secretion system, type IV pilus, lipopolysaccharide export system, HTH-type transcriptional regulator/antitoxin MqsA, and ArsR family transcriptional regulator were significantly enriched in the metagenome of the bacterial pneumonia FMD.

CONCLUSION: Our results demonstrated that the gut microbiome was significantly altered in the bacterial pneumonia group. Overall, our research improves the understanding of the potential role of the gut microbiota in the FMD bacterial pneumonia.}, } @article {pmid33428003, year = {2021}, author = {Demirci, H and Kurt-Gur, G and Ordu, E}, title = {Microbiota profiling and screening of the lipase active halotolerant yeasts of the olive brine.}, journal = {World journal of microbiology & biotechnology}, volume = {37}, number = {2}, pages = {23}, pmid = {33428003}, issn = {1573-0972}, mesh = {Ascomycota/classification/genetics/metabolism ; Bacteria/classification/genetics/metabolism ; Biodiversity ; Candida/metabolism ; Food Microbiology ; Hydrogen-Ion Concentration ; Hydrolysis ; Lipase/*metabolism ; *Microbiota ; Olive Oil ; Saccharomycetales ; Salt Tolerance/*physiology ; *Salts ; Sequence Analysis ; Sodium Chloride ; Yeasts/genetics/*metabolism ; }, abstract = {Searching for novel enzymes that could be active in organic solvents has become an area of interest in recent years. Olive brine naturally provides a suitable environment for the survival of halophilic and acidophilic microorganisms and the resulting genome is thought to be a gene source for determining the halophilic and acidophilic proteins that are active in a non-aqueous organic solvent medium, and so it has been used in several biotechnological and industrial applications. In this study, microbial analysis of natural, cracked green olive brine from the southern region of Turkey has been made by next-generation sequencing of the brine metagenome for the first time in the literature. The number of reads assigned to fungal operational taxonomic units was the highest percentage (73.04%) with the dominant representation of Ascomycota phylum (99% of fungi). Bacterial OTU was 3.56% of the reads and Proteobacteria phylum was 65% of the reads. The lipase production capacity of the yeasts that were grown on the media containing elevated concentrations of NaCl (1-3 M) was determined on a Rhodamine B-including medium. Molecular identification of the selected yeasts was performed and 90% of sequenced yeasts had a high level of similarity with Candida diddensiae, whereas 10% showed similarity to Candida boidinii. The hydrolytic lipase activities using olive oil were analyzed and both yeasts showed cell-bound lipase activity at pH 3.0.}, } @article {pmid33425781, year = {2020}, author = {Komatsu, K and Shiba, T and Takeuchi, Y and Watanabe, T and Koyanagi, T and Nemoto, T and Shimogishi, M and Shibasaki, M and Katagiri, S and Kasugai, S and Iwata, T}, title = {Discriminating Microbial Community Structure Between Peri-Implantitis and Periodontitis With Integrated Metagenomic, Metatranscriptomic, and Network Analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {596490}, pmid = {33425781}, issn = {2235-2988}, mesh = {Firmicutes ; Humans ; *Microbiota ; *Peri-Implantitis ; *Periodontitis ; Prevotella ; }, abstract = {Peri-implantitis and periodontitis are both polymicrobial diseases induced by subgingival plaque accumulation, with some differing clinical features. Studies on the microbial and gene transcription activity of peri-implantitis microbiota are limited. This study aimed to verify the hypothesis that disease-specific microbial and gene transcription activity lead to disease-specific clinical features, using an integrated metagenomic, metatranscriptomic, and network analysis. Metagenomic data in peri-implantitis and periodontitis were obtained from the same 21 subjects and metatranscriptomic data from 12 subjects were obtained from a database. The microbial co-occurrence network based on metagenomic analysis had more diverse species taxa and correlations than the network based on the metatranscriptomic analysis. Solobacterium moorei and Prevotella denticola had high activity and were core species taxa specific to peri-implantitis in the co-occurrence network. Moreover, the activity of plasmin receptor/glyceraldehyde-3-phosphate dehydrogenase genes was higher in peri-implantitis. These activity differences may increase complexity in the peri-implantitis microbiome and distinguish clinical symptoms of the two diseases. These findings should help in exploring a novel biomarker that assist in the diagnosis and preventive treatment design of peri-implantitis.}, } @article {pmid33423396, year = {2021}, author = {Piñol, J}, title = {Genotype by sequencing: An alternative new method to amplicon metabarcoding and shotgun metagenomics for the assessment of eukaryote biodiversity.}, journal = {Molecular ecology resources}, volume = {21}, number = {4}, pages = {1001-1004}, doi = {10.1111/1755-0998.13320}, pmid = {33423396}, issn = {1755-0998}, mesh = {Animals ; Biodiversity ; *Eukaryota ; Genotype ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; }, abstract = {The use of high-throughput DNA sequencing (HTS) has revolutionized the assessment of biodiversity in plant and animal communities. There are two main approaches to estimate the identity and the relative species abundance (RSA) in complex mixtures using HTS: amplicon metabarcoding and shotgun metagenomics. While amplicon metabarcoding targets one or a few genomic regions, shotgun metagenomics randomly explores the genome of the species. In this issue of Molecular Ecology Resources, Wagemaker et al. (2021) present a new method, multi-species Genotyping by Sequencing (msGBS), as an alternative middle ground between metabarcoding and metagenomics. They apply the technique to mixtures of plant roots and report the remarkable capacity of msGBS to estimate the RSA. If validated in other laboratories and biological communities, msGBS might become a third method to explore the biodiversity of biological communities, especially of plants, where current techniques are struggling to get sufficient taxonomic resolution.}, } @article {pmid33422963, year = {2021}, author = {Pérez-Cataluña, A and Cuevas-Ferrando, E and Randazzo, W and Sánchez, G}, title = {Bias of library preparation for virome characterization in untreated and treated wastewaters.}, journal = {The Science of the total environment}, volume = {767}, number = {}, pages = {144589}, doi = {10.1016/j.scitotenv.2020.144589}, pmid = {33422963}, issn = {1879-1026}, mesh = {Gene Library ; Humans ; Metagenomics ; Virome ; *Viruses/genetics ; *Wastewater ; }, abstract = {The use of metagenomics for virome characterization and its implementation for wastewater analyses, including wastewater-based epidemiology, has increased in the last years. However, the lack of standardized methods can led to highly different results. The aim of this work was to analyze virome profiles in upstream and downstream wastewater samples collected from four wastewater treatment plants (WWTPs) using two different library preparation kits. Viral particles were enriched from wastewater concentrates using a filtration and nuclease digestion procedure prior to total nucleic acid (NA) extraction. Sequencing was performed using the ScriptSeq v2 RNA-Seq (LS) and the NEBNext Ultra II RNA (NB) library preparation kits. Cleaned reads and contigs were annotated using a curated in-house database composed by reads assigned to viruses at NCBI. Significant differences in viral families and in the ratio of detection were shown between the two library kits used. The use of LS library showed Virgaviridae, Microviridae and Siphoviridae as the most abundant families; while Ackermannviridae and Helleviridae were highly represented within the NB library. Additionally, the two sequencing libraries produced outcomes that differed in the detection of viral indicators. These results highlighted the importance of library selection for studying viruses in untreated and treated wastewater. Our results underline the need for further studies to elucidate the influence of sequencing procedures in virome profiles in wastewater matrices in order to improve the knowledge of the virome in the water environment.}, } @article {pmid33422504, year = {2021}, author = {Tan, SM and Ismail, MH and Cao, B}, title = {Biodiversity of magnetotactic bacteria in the tropical marine environment of Singapore revealed by metagenomic analysis.}, journal = {Environmental research}, volume = {194}, number = {}, pages = {110714}, doi = {10.1016/j.envres.2021.110714}, pmid = {33422504}, issn = {1096-0953}, mesh = {Asia ; Biodiversity ; *Magnetosomes ; *Metagenomics ; Phylogeny ; Rhodospirillaceae ; Singapore ; }, abstract = {Most studies on the diversity of magnetotactic bacteria (MTB) have been conducted on samples obtained from the Northern or the Southern hemispheres. The diversity of MTB in tropical Asia near the geo-equator, with a close-to-zero geomagnetic inclination, weak magnetic field and constantly high seawater temperature has never been explored. This study aims to decipher the diversity of MTB in the marine environment of Singapore through shotgun metagenomics. Although MTB has been acknowledged to be ubiquitous in aquatic environments, we did not observe magnetotactic behaviour in the samples. However, we detected the presence and determined the diversity of MTB through bioinformatic analyses. Metagenomic analysis suggested majority of the MTB in the seafloor sediments represents novel MTB taxa that cannot be classified at the species level. The relative abundance of MTB (~0.2-1.69%) in the samples collected from the marine environment of Singapore was found to be substantially lower than studies for other regions. In contrast to other studies, the genera Magnetovibrio and Desulfamplus, but not Magnetococcus, were the dominant MTB. Additionally, we recovered 3 MTB genomic bins that are unclassified at the species level, with Magnetovibrio blakemorei being the closest-associated genome. All the recovered genomic bins contain homologs of at least 5 of the 7 mam genes but lack homologs for mamI, a membrane protein suggested to take part in the magenetosome invagination. This study fills in the knowledge gap of MTB biodiversity in the tropical marine environment near the geo-equator. Our findings will facilitate future research efforts aiming to unravel the ecological roles of MTB in the tropical marine environments as well as to bioprospecting novel MTB that have been adapted to tropical marine environments for biotechnological applications.}, } @article {pmid33422152, year = {2021}, author = {Gardiner, LJ and Haiminen, N and Utro, F and Parida, L and Seabolt, E and Krishna, R and Kaufman, JH}, title = {Re-purposing software for functional characterization of the microbiome.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {4}, pmid = {33422152}, issn = {2049-2618}, mesh = {Classification/*methods ; Computational Biology/*methods ; *High-Throughput Nucleotide Sequencing ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Phylogeny ; *Software ; }, abstract = {BACKGROUND: Widespread bioinformatic resource development generates a constantly evolving and abundant landscape of workflows and software. For analysis of the microbiome, workflows typically begin with taxonomic classification of the microorganisms that are present in a given environment. Additional investigation is then required to uncover the functionality of the microbial community, in order to characterize its currently or potentially active biological processes. Such functional analysis of metagenomic data can be computationally demanding for high-throughput sequencing experiments. Instead, we can directly compare sequencing reads to a functionally annotated database. However, since reads frequently match multiple sequences equally well, analyses benefit from a hierarchical annotation tree, e.g. for taxonomic classification where reads are assigned to the lowest taxonomic unit.

RESULTS: To facilitate functional microbiome analysis, we re-purpose well-known taxonomic classification tools to allow us to perform direct functional sequencing read classification with the added benefit of a functional hierarchy. To enable this, we develop and present a tree-shaped functional hierarchy representing the molecular function subset of the Gene Ontology annotation structure. We use this functional hierarchy to replace the standard phylogenetic taxonomy used by the classification tools and assign query sequences accurately to the lowest possible molecular function in the tree. We demonstrate this with simulated and experimental datasets, where we reveal new biological insights.

CONCLUSIONS: We demonstrate that improved functional classification of metagenomic sequencing reads is possible by re-purposing a range of taxonomic classification tools that are already well-established, in conjunction with either protein or nucleotide reference databases. We leverage the advances in speed, accuracy and efficiency that have been made for taxonomic classification and translate these benefits for the rapid functional classification of microbiomes. While we focus on a specific set of commonly used methods, the functional annotation approach has broad applicability across other sequence classification tools. We hope that re-purposing becomes a routine consideration during bioinformatic resource development. Video abstract.}, } @article {pmid33421868, year = {2021}, author = {Chen, YH and Xue, F and Yu, SF and Li, XS and Liu, L and Jia, YY and Yan, WJ and Tan, QR and Wang, HN and Peng, ZW}, title = {Gut microbiota dysbiosis in depressed women: The association of symptom severity and microbiota function.}, journal = {Journal of affective disorders}, volume = {282}, number = {}, pages = {391-400}, doi = {10.1016/j.jad.2020.12.143}, pmid = {33421868}, issn = {1573-2517}, mesh = {*Depressive Disorder, Major ; Dysbiosis ; Feces ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The association between abnormal gut microbiome composition and depression is well established. However, the composition and functional capacity of the gut microbiota regarding depressed women has been poorly addressed.

METHODS: Stool samples from 62 female patients with major depressive disorder (MDD) and 46 healthy controls (Con) were analyzed by 16S rRNA gene sequencing; Twenty fecal samples from the patient group and 21 fecal samples from the Con group were further analyzed by shotgun metagenomic sequencing. Psychiatric symptoms and psychological, social, and professional functioning was also assessed.

RESULTS: Phylum Bacteroidetes, proteobaeteria, and Fusobacteria were greatly enriched in patients with MDD, while the Firmicutes and Actinobacteria phyla were consistently higher in Con. Notably, 18 microbial markers were identified on a random forest model and achieve an area under the curve of 0.92 between patients with MDD and the Con group. Forty-five species and their associated function were identified with statistically significant differences between patients with MDD and the Con group.

LIMITATIONS: The number of recruited samples, especially samples enrolled for shotgun metagenomic sequencing was relatively small, and the stool samples were collected only at baseline, making it difficult to establish a causal association between changes in gut microbiota compositions and disease remission.

CONCLUSIONS: This study characterizes the gut microbiota and their related function in female MDD. The gut microbiota-based biomarkers may be helpful in diagnosis and the altered gut microbial metabolites may contribute to the pathogenesis of MDD in women, representing potential microbial targets.}, } @article {pmid33420317, year = {2021}, author = {Koeninger, L and Osbelt, L and Berscheid, A and Wendler, J and Berger, J and Hipp, K and Lesker, TR and Pils, MC and Malek, NP and Jensen, BAH and Brötz-Oesterhelt, H and Strowig, T and Jan Wehkamp, }, title = {Curbing gastrointestinal infections by defensin fragment modifications without harming commensal microbiota.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {47}, pmid = {33420317}, issn = {2399-3642}, mesh = {Animals ; Biofilms/drug effects ; Disease Models, Animal ; Drug Resistance, Multiple, Bacterial ; Enterobacteriaceae Infections/*drug therapy ; Female ; Gastrointestinal Diseases/*drug therapy ; Gastrointestinal Microbiome/*drug effects ; Male ; Mice, Inbred C57BL ; Microbial Sensitivity Tests ; Salmonella Infections, Animal/*drug therapy ; Mice ; }, abstract = {The occurrence and spread of multidrug-resistant pathogens, especially bacteria from the ESKAPE panel, increases the risk to succumb to untreatable infections. We developed a novel antimicrobial peptide, Pam-3, with antibacterial and antibiofilm properties to counter this threat. The peptide is based on an eight-amino acid carboxyl-terminal fragment of human β-defensin 1. Pam-3 exhibited prominent antimicrobial activity against multidrug-resistant ESKAPE pathogens and additionally eradicated already established biofilms in vitro, primarily by disrupting membrane integrity of its target cell. Importantly, prolonged exposure did not result in drug-resistance to Pam-3. In mouse models, Pam-3 selectively reduced acute intestinal Salmonella and established Citrobacter infections, without compromising the core microbiota, hence displaying an added benefit to traditional broad-spectrum antibiotics. In conclusion, our data support the development of defensin-derived antimicrobial agents as a novel approach to fight multidrug-resistant bacteria, where Pam-3 appears as a particularly promising microbiota-preserving candidate.}, } @article {pmid33420281, year = {2021}, author = {Wongsaroj, L and Chanabun, R and Tunsakul, N and Prombutara, P and Panha, S and Somboonna, N}, title = {First reported quantitative microbiota in different livestock manures used as organic fertilizers in the Northeast of Thailand.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {102}, pmid = {33420281}, issn = {2045-2322}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Feces/microbiology ; Fertilizers/*microbiology/parasitology ; Livestock ; Manure/*microbiology/parasitology ; *Microbiota ; Oligochaeta/classification/genetics ; Soil/chemistry ; Thailand ; }, abstract = {Northeastern Thailand relies on agriculture as a major economic activity, and has used high levels of agrochemicals due to low facility, and salty sandy soil. To support soil recovery and sustainable agriculture, local farmers have used organic fertilizers from farmed animal feces. However, knowledge about these animal fecal manures remains minimal restricting their optimal use. Specifically, while bacteria are important for soil and plant growth, an abundance and a diversity of bacterial composition in these animal fecal manures have not been reported to allow selection and adjustment for a more effective organic fertilizer. This study thereby utilized metagenomics combined with 16S rRNA gene quantitative PCR (qPCR) and sequencing to analyze quantitative microbiota profiles in association with nutrients (N, P, K), organic matters, and the other physiochemical properties, of the commonly used earthworm manure and other manures from livestock animals (including breed and feeding diet variations) in the region. Unlike the other manures, the earthworm manure demonstrated more favorable nutrient profiles and physiochemical properties for forming fertile soil. Despite low total microbial biomass, the microbiota were enriched with maximal OTUs and Chao richness, and no plant pathogenic bacteria were found based on the VFDB database. The microbial metabolic potentials supported functions to promote crop growth, such as C, N and P cyclings, xenobiotic degradation, and synthesis of bioactive compounds. Pearson's correlation analyses indicated that the quantitative microbiota of the earthworm manure were clustered in the same direction as N, and conductivity, salinity, and water content were essential to control the microbiota of animal manures.}, } @article {pmid33420074, year = {2021}, author = {Behary, J and Amorim, N and Jiang, XT and Raposo, A and Gong, L and McGovern, E and Ibrahim, R and Chu, F and Stephens, C and Jebeili, H and Fragomeli, V and Koay, YC and Jackson, M and O'Sullivan, J and Weltman, M and McCaughan, G and El-Omar, E and Zekry, A}, title = {Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {187}, pmid = {33420074}, issn = {2041-1723}, mesh = {Aged ; Bacteria/genetics ; CD8-Positive T-Lymphocytes ; Carcinoma, Hepatocellular/genetics/*immunology/pathology ; Cytokines ; Dietary Fiber ; Dysbiosis/immunology ; Fatty Acids, Volatile/blood/metabolism ; Feces/chemistry ; Female ; Gastrointestinal Microbiome/*immunology/*physiology ; Humans ; *Immunity ; Liver/pathology ; Liver Cirrhosis ; Liver Neoplasms/*immunology/pathology ; Male ; Metabolomics ; Metagenomics ; Middle Aged ; Non-alcoholic Fatty Liver Disease/genetics/*immunology/pathology ; Phenotype ; }, abstract = {The gut microbiota is reported to modulate the immune response in hepatocellular carcinoma (HCC). Here, we employ metagenomic and metabolomic studies to characterise gut microbiota in patients with non-alcoholic fatty liver disease (NAFLD) related cirrhosis, with or without HCC, and evaluate its effect on the peripheral immune response in an ex vivo model. We find that dysbiosis characterises the microbiota of patients with NAFLD-cirrhosis, with compositional and functional shifts occurring with HCC development. Gene function of the microbiota in NAFLD-HCC supports short chain fatty acid production, and this is confirmed by metabolomic studies. Ex vivo studies show that bacterial extracts from the NAFLD-HCC microbiota, but not from the control groups, elicit a T cell immunosuppressive phenotype, characterised by expansion of regulatory T cells and attenuation of CD8 + T cells. Our study suggest that the gut microbiota in NAFLD-HCC is characterised by a distinctive microbiome/metabolomic profile, and can modulate the peripheral immune response.}, } @article {pmid33417825, year = {2021}, author = {Scharf, ME and Peterson, BF}, title = {A Century of Synergy in Termite Symbiosis Research: Linking the Past with New Genomic Insights.}, journal = {Annual review of entomology}, volume = {66}, number = {}, pages = {23-43}, doi = {10.1146/annurev-ento-022420-074746}, pmid = {33417825}, issn = {1545-4487}, mesh = {Animals ; Entomology/*history ; Genomics ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Isoptera/genetics/microbiology/*parasitology ; *Microbiota ; *Symbiosis ; }, abstract = {Termites have long been studied for their symbiotic associations with gut microbes. In the late nineteenth century, this relationship was poorly understood and captured the interest of parasitologists such as Joseph Leidy; this research led to that of twentieth-century biologists and entomologists including Cleveland, Hungate, Trager, and Lüscher. Early insights came via microscopy, organismal, and defaunation studies, which led to descriptions of microbes present, descriptions of the roles of symbionts in lignocellulose digestion, and early insights into energy gas utilization by the host termite. Focus then progressed to culture-dependent microbiology and biochemical studies of host-symbiont complementarity, which revealed specific microhabitat requirements for symbionts and noncellulosic mechanisms of symbiosis (e.g., N2 fixation). Today, knowledge on termite symbiosis has accrued exponentially thanks to omic technologies that reveal symbiont identities, functions, and interdependence, as well as intricacies of host-symbiont complementarity. Moving forward, the merging of classical twentieth-century approaches with evolving omic tools should provide even deeper insights into host-symbiont interplay.}, } @article {pmid33416984, year = {2021}, author = {Busch, P and Suleiman, M and Schäfers, C and Antranikian, G}, title = {A multi-omic screening approach for the discovery of thermoactive glycoside hydrolases.}, journal = {Extremophiles : life under extreme conditions}, volume = {25}, number = {2}, pages = {101-114}, pmid = {33416984}, issn = {1433-4909}, mesh = {Bacteria/genetics ; Glycoside Hydrolases/genetics ; Metagenome ; *Metagenomics ; *Microbiota ; }, abstract = {Next-generation sequencing and computational biology have facilitated the implementation of new combinatorial screening approaches to discover novel enzymes of biotechnological interest. In this study, we describe the successful establishment of a multi-omic approach for the identification of thermostable hydrolase-encoding genes by determination of gene expression levels. We applied this combinatorial approach using an anaerobic enrichment culture from an Azorean hot spring sample grown on green coffee beans as recalcitrant substrate. An in-depth analysis of the microbial community resulted in microorganisms capable of metabolizing the selected substrate, such as the genera Caloramator, Dictyoglomus and Thermoanaerobacter as active and abundant microorganisms. To discover glycoside hydrolases, 90,342 annotated genes were screened for specific reaction types. A total number of 106 genes encoding cellulases (EC 3.2.1.4), beta-glucosidases (EC 3.2.1.21) and endo-1,4-beta-mannosidases (EC 3.2.1.78) were selected. Mapping of RNA-Seq reads to the related metagenome led to expression levels for each gene. Amongst those, 14 genes, encoding glycoside hydrolases, showed highest expression values, and were used for further cloning. Four proteins were biochemically characterized and were identified as thermoactive glycoside hydrolases with a broad substrate range. This work demonstrated that a combinatory omic approach is a suitable strategy identifying unique thermoactive enzymes from environmental samples.}, } @article {pmid33413361, year = {2021}, author = {Ye, X and Zhou, L and Zhang, Y and Xue, S and Gan, QF and Fang, S}, title = {Effect of host breeds on gut microbiome and serum metabolome in meat rabbits.}, journal = {BMC veterinary research}, volume = {17}, number = {1}, pages = {24}, pmid = {33413361}, issn = {1746-6148}, mesh = {Animals ; Bacteria/classification/genetics ; Biomarkers ; Female ; *Gastrointestinal Microbiome ; Male ; *Metabolome ; RNA, Ribosomal, 16S ; Rabbits/*blood/genetics/*microbiology ; }, abstract = {BACKGROUND: Gut microbial compositional and functional variation can affect health and production performance of farm animals. Analysing metabolites in biological samples provides information on the basic mechanisms that affect the well-being and production traits in farm animals. However, the extent to which host breeds affect the gut microbiome and serum metabolome in meat rabbits is still unknown. In this study, the differences in phylogenetic composition and functional capacities of gut microbiota in two commercial rabbit breeds Elco and Ira were determined by 16S rRNA gene and metagenomic sequencing. The alternations in serum metabolome in the two rabbit breeds were detected using ultra-performance liquid chromatography system coupled with quadrupole time of flight mass spectrometry (UPLC-QTOFMS).

RESULTS: Sequencing results revealed that there were significant differences in the gut microbiota of the two breeds studied, suggesting that host breeds affect structure and diversity of gut microbiota. Numerous breed-associated microorganisms were identified at different taxonomic levels and most microbial taxa belonged to the families Lachnospiraceae and Ruminococcaceae. In particular, several short-chain fatty acids (SCFAs) producing species including Coprococcus comes, Ruminococcus faecis, Ruminococcus callidus, and Lachnospiraceae bacterium NK4A136 could be considered as biomarkers for improving the health and production performance in meat rabbits. Additionally, gut microbial functional capacities related to bacterial chemotaxis, ABC transporters, and metabolism of different carbohydrates, amino acids, and lipids varied greatly between rabbit breeds. Several fatty acids, amino acids, and organic acids in the serum were identified as breed-associated, where certain metabolites could be regarded as biomarkers correlated with the well-being and production traits of meat rabbits. Correlation analysis between breed-associated microbial species and serum metabolites revealed significant co-variations, indicating the existence of cross-talk among host-gut microbiome-serum metabolome.

CONCLUSIONS: Our study provides insight into how gut microbiome and serum metabolome of meat rabbits are affected by host breeds and uncovers potential biomarkers important for breed improvement of meat rabbits.}, } @article {pmid33413128, year = {2021}, author = {Mustafa, GR and Li, C and Zhao, S and Jin, L and He, X and Shabbir, MZ and He, Y and Li, T and Deng, W and Xu, L and Xiong, Y and Zhang, G and Zhang, H and Huang, Y and Zou, L}, title = {Metagenomic analysis revealed a wide distribution of antibiotic resistance genes and biosynthesis of antibiotics in the gut of giant pandas.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {15}, pmid = {33413128}, issn = {1471-2180}, support = {KLSFGAGP2020.003//Key Laboratory of SFGA on Conservation Biology of Rare Animals in the Giant Panda National Park (CCRCGP)/ ; No. 2017115//State Forestry Administration/ ; GH201709//International Cooperation project of giant panda/ ; }, mesh = {Age Factors ; Animals ; Anti-Bacterial Agents/biosynthesis/pharmacology ; Bacteria/*classification/drug effects/genetics/isolation & purification ; Bacterial Proteins/*genetics/metabolism ; Biosynthetic Pathways ; Drug Resistance, Bacterial ; Feces/microbiology ; Gastrointestinal Microbiome ; Metagenomics/*methods ; Phylogeny ; Sequence Analysis, DNA ; Ursidae/*growth & development/microbiology ; }, abstract = {BACKGROUND: The gut microbiome is essential for the host's health and serves as an essential reservoir of antibiotic resistance genes (ARGs). We investigated the effects of different factors, including the dietary shifts and age, on the functional characteristics of the giant panda's gut microbiome (GPs) through shotgun metagenome sequencing. We explored the association between gut bacterial genera and ARGs within the gut based on network analysis.

RESULTS: Fecal samples (n=60) from captive juvenile, adult, and geriatric GPs were processed, and variations were identified in the gut microbiome according to different ages, the abundance of novel ARGs and the biosynthesis of antibiotics. Among 667 ARGs identified, nine from the top ten ARGs had a higher abundance in juveniles. For 102 ARGs against bacteria, a co-occurrence pattern revealed a positive association for predominant ARGs with Streptococcus. A comparative KEGG pathways analysis revealed an abundant biosynthesis of antibiotics among three different groups of GPs, where it was more significantly observed in the juvenile group. A co-occurrence pattern further revealed a positive association for the top ten ARGs, biosynthesis of antibiotics, and metabolic pathways.

CONCLUSION: Gut of GPs serve as a reservoir for novel ARGs and biosynthesis of antibiotics. Dietary changes and age may influence the gut microbiome's functional characteristics; however, it needs further studies to ascertain the study outcomes.}, } @article {pmid33411719, year = {2021}, author = {Elmassry, MM and Kim, S and Busby, B}, title = {Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes.}, journal = {PloS one}, volume = {16}, number = {1}, pages = {e0244876}, pmid = {33411719}, issn = {1932-6203}, mesh = {Adult ; Bacteria/genetics ; Computational Biology/methods ; Data Management ; Female ; Forecasting/*methods ; Gastrointestinal Microbiome/*drug effects/genetics ; Glucuronidase/genetics/metabolism ; Humans ; Infant, Newborn ; Male ; Metagenome/drug effects/genetics ; Metagenomics/*methods ; Microbiota/drug effects/genetics ; Mothers ; }, abstract = {Characterizing the gut microbiota in terms of their capacity to interfere with drug metabolism is necessary to achieve drug efficacy and safety. Although examples of drug-microbiome interactions are well-documented, little has been reported about a computational pipeline for systematically identifying and characterizing bacterial enzymes that process particular classes of drugs. The goal of our study is to develop a computational approach that compiles drugs whose metabolism may be influenced by a particular class of microbial enzymes and that quantifies the variability in the collective level of those enzymes among individuals. The present paper describes this approach, with microbial β-glucuronidases as an example, which break down drug-glucuronide conjugates and reactivate the drugs or their metabolites. We identified 100 medications that may be metabolized by β-glucuronidases from the gut microbiome. These medications included morphine, estrogen, ibuprofen, midazolam, and their structural analogues. The analysis of metagenomic data available through the Sequence Read Archive (SRA) showed that the level of β-glucuronidase in the gut metagenomes was higher in males than in females, which provides a potential explanation for the sex-based differences in efficacy and toxicity for several drugs, reported in previous studies. Our analysis also showed that infant gut metagenomes at birth and 12 months of age have higher levels of β-glucuronidase than the metagenomes of their mothers and the implication of this observed variability was discussed in the context of breastfeeding as well as infant hyperbilirubinemia. Overall, despite important limitations discussed in this paper, our analysis provided useful insights on the role of the human gut metagenome in the variability in drug response among individuals. Importantly, this approach exploits drug and metagenome data available in public databases as well as open-source cheminformatics and bioinformatics tools to predict drug-metagenome interactions.}, } @article {pmid33410936, year = {2021}, author = {St James, AR and Lin, J and Richardson, RE}, title = {Relationship Between Peat Type and Microbial Ecology in Sphagnum-Containing Peatlands of the Adirondack Mountains, NY, USA.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {429-441}, pmid = {33410936}, issn = {1432-184X}, mesh = {Carbon ; *Microbiota ; Soil ; *Sphagnopsida ; Wetlands ; }, abstract = {Peatland microbial community composition varies with respect to a range of biological and physicochemical variables. While the extent of peat degradation (humification) has been linked to microbial community composition along vertical stratification gradients within peatland sites, across-site variations have been relatively unexplored. In this study, we compared microbial communities across ten pristine Sphagnum-containing peatlands in the Adirondack Mountains, NY, which represented three different peat types-humic fen peat, humic bog peat, and fibric bog peat. Using 16S amplicon sequencing and network correlation analysis, we demonstrate that microbial community composition is primarily linked to peat type, and that distinct taxa networks distinguish microbial communities in each type. Shotgun metagenomic sequencing of the active water table region (mesotelm) from two Sphagnum-dominated bogs-one with fibric peat and one with humic peat-revealed differences in primary carbon degradation pathways, with the fibric peat being dominated by carbohydrate metabolism and hydrogenotrophic methanogenesis, and the humic peat being dominated by aliphatic carbon metabolism and aceticlastic methanogenesis. Our results suggest that peat humification is a major factor driving microbial community dynamics across peatland ecosystems.}, } @article {pmid33410935, year = {2021}, author = {Li, W and Nelson, KE}, title = {Microbial Species that Initially Colonize the Human Gut at Birth or in Early Childhood Can Stay in Human Body for Lifetime.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {1074-1079}, pmid = {33410935}, issn = {1432-184X}, mesh = {Adult ; Child, Preschool ; *Gastrointestinal Microbiome/genetics ; *Human Body ; Humans ; Infant, Newborn ; Metagenome ; Metagenomics ; Twins, Dizygotic/genetics ; }, abstract = {In recent years, many studies have described the composition and function of the human microbiome at different body sites and suggested a role for the microbiome in various diseases and health conditions. Some studies, using longitudinal samples, have also suggested how the microbiome changes over time due to disease, diet, development, travel, and other environmental factors. However, to date, no study has demonstrated whether the microorganisms established at birth or in early childhood, either transmitted from parents or obtained from the environment, can stay in the human body until adult or senior age. To directly answer this question is difficult, because microbiome samples at childhood and at later adulthood for the same individual will need to be compared and the field is not old enough to have allowed for that type of sample collection. Here, using a metagenomic approach, we analyzed 1004 gut microbiome samples from senior adults (65 ± 7.8 years) from the TwinsUK cohort. Our data indicate that many species in the human gut acquired in early childhood can stay for a lifetime until senior ages. We identified the rare genomic variants (single nucleotide variation and indels) for 27 prevalent species with enough sequencing coverage for confident genomic variant identification. We found that for some species, twin pairs, including both monozygotic (MZ) and dizygotic (DZ) twins, share significantly more rare variants than unrelated subject pairs. But no significant difference is found between MZ and DZ twin pairs. These observations strongly suggest that these species acquired in early childhood remained in these persons until senior adulthood.}, } @article {pmid33410932, year = {2021}, author = {Hutchinson, MI and Bell, TAS and Gallegos-Graves, V and Dunbar, J and Albright, M}, title = {Merging Fungal and Bacterial Community Profiles via an Internal Control.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {484-497}, pmid = {33410932}, issn = {1432-184X}, support = {F255LANL2018//Office of Science/ ; }, mesh = {Bacteria/genetics ; DNA, Fungal/genetics ; *Fungi/genetics ; High-Throughput Nucleotide Sequencing ; *Microbiota ; }, abstract = {Integrated measurements of fungi and bacteria are critical to understand how interactions between these taxa drive key processes in ecosystems ranging from soils to animal guts. High-throughput amplicon sequencing is commonly used to census microbiomes, but the genetic markers targeted for fungi and bacteria (typically ribosomal regions) are domain-specific so profiling must be performed separately, obscuring relationships between these groups. To solve this problem, we developed a spike-in method with an internal control (IC) construct containing primer sites commonly used for bacterial and fungal taxonomic profiling. The internal control offers several advantages: estimation of absolute abundances, estimation of fungal to bacterial ratios (F:B), integration of bacterial and fungal profiles for holistic community analysis, and lower costs compared to other quantitation methods. To validate the IC as a scaling method, we compared IC-derived measures of F:B to measures from quantitative PCR (qPCR) using a commercial mock community (the ZymoBiomic Microbial Community DNA Standard II, containing two fungi and eight bacteria) and complex environmental samples. For both the mock community and the environmental samples, the IC produced F:B values that were statistically consistent with qPCR. Merging the environmental fungal and bacterial profiles based on the IC-derived F:B values revealed new relationships among samples in terms of community similarity. This IC method is the first spike-in method to employ a single construct for cross-domain amplicon sequencing, offering more reliable measurements.}, } @article {pmid33410931, year = {2021}, author = {Gomez, JA and Primm, TP}, title = {A Slimy Business: the Future of Fish Skin Microbiome Studies.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {275-287}, pmid = {33410931}, issn = {1432-184X}, mesh = {Animals ; *Bacteria/genetics ; Fishes ; Metagenomics ; *Microbiota/genetics ; Skin ; }, abstract = {Fish skin contains a mucosal microbiome for the largest and oldest group of vertebrates, a location ideal for microbial community ecology and practical applications in agriculture and veterinary medicine. These selective microbiomes are dominated by Proteobacteria, with compositions different from the surrounding water. Core taxa are a small percentage of those present and are currently functionally uncharacterized. Methods for skin sampling, DNA extraction and amplification, and sequence data processing are highly varied across the field, and reanalysis of recent studies using a consistent pipeline revealed that some conclusions did change in statistical significance. Further, the 16S gene sequencing approaches lack quantitation of microbes and copy number adjustment. Thus, consistency in the field is a serious limitation in comparing across studies. The most significant area for future study, requiring metagenomic and metabolomics data, is the biochemical pathways and functions within the microbiome community, the interactions between members, and the resulting effects on fish host health being linked to specific nutrients and microbial species. Genes linked to skin colonization, such as those for attachment or mucin degradation, need to be uncovered and explored. Skin immunity factors need to be directly linked to microbiome composition and individual taxa. The basic foundation has been laid, and many exciting future discoveries remain.}, } @article {pmid33410172, year = {2021}, author = {Ng, E and Tay, JRH and Balan, P and Ong, MMA and Bostanci, N and Belibasakis, GN and Seneviratne, CJ}, title = {Metagenomic sequencing provides new insights into the subgingival bacteriome and aetiopathology of periodontitis.}, journal = {Journal of periodontal research}, volume = {56}, number = {2}, pages = {205-218}, doi = {10.1111/jre.12811}, pmid = {33410172}, issn = {1600-0765}, support = {//National Dental Research Institute Singapore/ ; }, mesh = {*Dental Plaque ; Dysbiosis ; Humans ; *Microbiota/genetics ; *Periodontitis/genetics/therapy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {"Open-ended" molecular techniques such as 16S rRNA sequencing have revealed that the oral bacteriome of subgingival plaque is more diverse than originally thought. 16S rRNA analysis has demonstrated that constituents of the overall bacterial community are qualitatively similar in health and disease, differing mainly in their relative proportions with respect to each other. Species in low abundance can also act as critical species, leading to the concept of global community dysbiosis which relates to shifts in community structure, rather than shifts in membership. Correlation analysis suggests that coordinated interactions in the community are essential for incipient dysbiosis and disease pathogenesis. The subgingival bacteriome also provides biomarkers that are useful for disease detection and management. Combined with clinical and biological parameters, these may assist clinicians in developing and implementing effective treatment strategies to restore microbial homeostasis and monitor disease. Identification of higher risk groups or poor responders to treatment using unique subgingival bacteriome signatures may also lead to early intervention.}, } @article {pmid33410044, year = {2021}, author = {Lyu, Y and Yang, T and Liu, H and Qi, Z and Li, P and Shi, Z and Xiang, Z and Gong, D and Li, N and Zhang, Y}, title = {Enrichment and characterization of an effective hexavalent chromium-reducing microbial community YEM001.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {16}, pages = {19866-19877}, pmid = {33410044}, issn = {1614-7499}, support = {2019ABA114//Major Project for Special Technology Innovation of Hubei Province/ ; 2017ABA157//Major Project for Special Technology Innovation of Hubei Province/ ; 31370506//National Natural Science Foundation of China/ ; 21776162//National Natural Science Foundation of China/ ; 31500422//National Natural Science Foundation of China/ ; }, mesh = {Biodegradation, Environmental ; Chromium ; *Metals, Heavy ; *Microbiota ; Oxidation-Reduction ; }, abstract = {Chromium (Cr) is one of the most widely used heavy metals in industrial processes, resulting in water and soil pollution that seriously threaten environmental safety. In this paper, we have directionally enriched a Cr(VI)-reducing bacterial community YEM001 from no-Cr(VI) polluted pond sedimental sludge by selectively growing it in Cr(VI)-containing media. This community could effectively reduce Cr(VI) in laboratory rich media containing different concentrations of Cr(VI), such as 61% reduction at 435 mg/L Cr(VI), 85% reduction at 355 mg/L Cr(VI), and complete reduction at 269 mg/L Cr(VI) in 93.5 h. It was also able to completely reduce 100 mg/L and 300 mg/L Cr(VI) in landfill leachate and natural sludge in 48 h, respectively. Optimal pH for Cr(VI) reduction of the YEM001 is between 7 and 8 and the best efficiency for Cr(VI) reduction occurs at 30 °C. Metagenomic data demonstrated that the YEM001 community was composed of multiple bacteria, including well-known Cr(VI)-reducing bacteria and non-Cr(VI)-reducing bacteria. Delftia, Comamonas, Alicycliphilus, Acidovorax, Bacillus, and Clostridioides account for 83% of total community abundance. The stability of the composition of the YEM001 community and its Cr(VI)-reducing activity allows for its application in bioremediation of environmental Cr(VI) pollution.}, } @article {pmid33407663, year = {2021}, author = {Zhang, HT and Wang, H and Wu, HS and Zeng, J and Yang, Y}, title = {Comparison of viromes in vaginal secretion from pregnant women with and without vaginitis.}, journal = {Virology journal}, volume = {18}, number = {1}, pages = {11}, pmid = {33407663}, issn = {1743-422X}, mesh = {Adult ; Female ; Genome, Viral/genetics ; Humans ; Metagenomics ; Phylogeny ; Pregnancy ; *Pregnant Women ; Vagina/virology ; Vaginitis/*virology ; *Virome/genetics ; Viruses/classification/genetics/isolation & purification ; }, abstract = {BACKGROUND: Although some studies have investigated the bacterial community in vaginal tract of pregnant women, there are few reports about the viral community (virome) in this type of microenvironment.

METHODS: To investigate the composition of virome in vaginal secretion samples, 40 vaginal secretion samples from pregnant women with vaginitis and 20 vaginal secretion samples from pregnant women without vaginitis, pooled into 4 and 2 sample pools, respectively, were subjected to viral metagenomic analysis.

RESULTS: Results indicated virus sequences showing similarity to human papillomavirus (HPV), anellovirus, and norovirus were recovered from this cohort of pregnant women. Further analysis indicated that 15 different defined types and one unclassified type of HPV were detected from pregnant women with vaginitis while only 3 defined types of HPV were detected in pregnant women without vaginitis. Five different groups of viruses from the family Anelloviridae were present in pregnant women with but none of them were detected in pregnant women without vaginitis. Norovirus was detected in 3 out of the 4 sample pools from pregnant women with vaginitis but none in the pregnant women without vaginitis. Twelve complete genomes belonging to 10 different types of HPV, and 5 novel anllovirus genomes belonging 2 different genera in Anelloviridae were acquired from these libraries, based on which phylogenetical analysis and pairwise sequence comparison were performed. Phageome in these samples was also briefly characterized and compared between two groups.

CONCLUSION: Our data suggested that virome might play an important role in the progression of vaginitis in pregnant women.}, } @article {pmid33407614, year = {2021}, author = {Chi, H and Cao, W and Zhang, M and Su, D and Yang, H and Li, Z and Li, C and She, X and Wang, K and Gao, X and Ma, K and Zheng, P and Li, X and Cui, B}, title = {Environmental noise stress disturbs commensal microbiota homeostasis and induces oxi-inflammmation and AD-like neuropathology through epithelial barrier disruption in the EOAD mouse model.}, journal = {Journal of neuroinflammation}, volume = {18}, number = {1}, pages = {9}, pmid = {33407614}, issn = {1742-2094}, support = {81673136//National Natural Science Foundation of China/ ; 17JCZDJC34900//Natural Science Foundation of Tianjin City/ ; }, mesh = {Acoustic Stimulation/adverse effects ; Alzheimer Disease/etiology/genetics/*metabolism/pathology ; Animals ; Environmental Exposure/*adverse effects ; Gastrointestinal Microbiome/*physiology ; Homeostasis/*physiology ; Inflammation/etiology/metabolism/pathology ; Inflammation Mediators/*metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Noise/*adverse effects ; }, abstract = {BACKGROUND: Both genetic factors and environmental hazards, including environmental noise stress, have been associated with gut microbiome that exacerbates Alzheimer's disease (AD) pathology. However, the role and mechanism of environmental risk factors in early-onset AD (EOAD) pathogenesis remain unclear.

METHODS: The molecular pathways underlying EOAD pathophysiology following environmental noise exposure were evaluated using C57BL/6 wild-type (WT) and APP/PS1 Tg mouse models. The composition differences in intestinal microbiota were analyzed by 16S rRNA sequencing and Tax4Fun to predict the metagenome content from sequencing results. An assessment of the flora dysbiosis-triggered dyshomeostasis of oxi-inflamm-barrier and the effects of the CNS end of the gut-brain axis was conducted to explore the underlying pathological mechanisms.

RESULTS: Both WT and APP/PS1 mice showed a statistically significant relationship between environmental noise and the taxonomic composition of the corresponding gut microbiome. Bacterial-encoded functional categories in noise-exposed WT and APP/PS1 mice included phospholipid and galactose metabolism, oxidative stress, and cell senescence. These alterations corresponded with imbalanced intestinal oxidation and anti-oxidation systems and low-grade systemic inflammation following noise exposure. Mechanistically, axis-series experiments demonstrated that following noise exposure, intestinal and hippocampal tight junction protein levels reduced, whereas serum levels of inflammatory mediator were elevated. Regarding APP/PS1 overexpression, noise-induced abnormalities in the gut-brain axis may contribute to aggravation of neuropathology in the presymptomatic stage of EOAD mice model.

CONCLUSION: Our results demonstrate that noise exposure has deleterious effects on the homeostasis of oxi-inflamm-barrier in the microbiome-gut-brain axis. Therefore, at least in a genetic context, chronic noise may aggravate the progression of EOAD.}, } @article {pmid33407128, year = {2021}, author = {Xie, Y and Sun, J and Wei, L and Jiang, H and Hu, C and Yang, J and Huang, Y and Ruan, B and Zhu, B}, title = {Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {11}, pmid = {33407128}, issn = {1471-2180}, support = {81500491//Young Scientists Fund/ ; 2018ZX10715-014//Major Research Plan/ ; }, mesh = {Adult ; Antiretroviral Therapy, Highly Active/*adverse effects ; Bacteria/*classification/genetics/isolation & purification ; CD4-CD8 Ratio ; CD4-Positive T-Lymphocytes/metabolism ; CD8-Positive T-Lymphocytes/metabolism ; Case-Control Studies ; Dysbiosis/chemically induced/*immunology ; Female ; Gastrointestinal Microbiome ; HIV Infections/*drug therapy/immunology/microbiology ; Humans ; Male ; Metagenomics ; Middle Aged ; Phylogeny ; Treatment Outcome ; }, abstract = {BACKGROUND: Although gut microbiota dysbiosis has been reported in HIV infected individuals recently, the relationship between the gut microbiota and immune activation in patients with different immune responses to highly active antiretroviral therapy (HAART) is still not well understood. Gut microbiota and immune activation were studied in 36 non-HIV-infected subjects (healthy controls) and 58 HIV-infected individuals, including 28 immunological responders (IR) and 30 immunological non-responders (INR) (≥500 and < 200 CD4+ T-cell counts/μl after 2 years of HIV-1 viral suppression respectively) without comorbidities.

RESULTS: Metagenome sequencing revealed that HIV-infected immunological responders and immunological non-responders could not recover completely from the gut microbiota dysbiosis. At a 97% similarity level, the relative abundances of Fusobacterium, Ruminococcus gnavus and Megamonas were greater, whereas Faecalibacterium, Alistipes, Bifidobacterium, Eubacterium rectale and Roseburia were more depleted in the IR and INR groups than those in the healthy controls. Ruminococcaceae and Alistipes were positively correlated with nadir and current CD4+ T-cell counts, but negatively correlated with CD8 + CD57+ T-cell counts. Inflammation markers and translocation biomarkers (LPS) levels were positively correlated with the abundances of genera Ruminococcus and Fusobacterium but were negatively correlated with the genus Faecalibacterium. The relative abundances of Escherichia-Shigella and Blautia were significantly higher in the IR than those in the INR group. Escherichia-Shigella were negatively correlated with the CD4/CD8 ratio but positively correlated with the amount of CD8 + CD57+ T-cells. Roseburia and Blautia were negatively associated with nadir CD4+ T-cell and positively associated with CD8 + CD57+ T-cell counts.

CONCLUSIONS: Gut microbiota dysbiosis may be one of the factors contributing to different immune responses and treatment outcomes to HAART.}, } @article {pmid33407122, year = {2021}, author = {Li, J and Si, H and Du, H and Guo, H and Dai, H and Xu, S and Wan, J}, title = {Comparison of gut microbiota structure and Actinobacteria abundances in healthy young adults and elderly subjects: a pilot study.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {13}, pmid = {33407122}, issn = {1471-2180}, mesh = {Actinobacteria/isolation & purification ; Adult ; Age Factors ; Aged ; Bacteria/*classification/genetics/isolation & purification ; China ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; *Drug Resistance, Bacterial ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Healthy Volunteers ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metabolic Networks and Pathways ; Phylogeny ; Pilot Projects ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Young Adult ; }, abstract = {BACKGROUND: The aim was to determine the potential association of the gut microbiota composition, especially the abundance of Actinobacteria, as well as the differentiation of functional and resistance genes with age (young adults vs elderly subjects) in China.

RESULTS: The patterns of relative abundance of all bacteria isolated from fecal samples differed between young adults and elderly subjects, but the alpha diversity (Chao1 P = 0.370, Shannon P = 0.560 and Simpson P = 0.270) and beta diversity (ANOSIM R = 0.031, P = 0.226) were not significantly different. There were 3 Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways (carbon metabolism, inositol phosphate metabolism, and sesquiterpenoid and triterpenoid biosynthesis) and 7 antibiotic resistant genes (ARGs) (macrolide lincosamide-streptogramin B (MLSB), tetracycline, aminoglycoside, sulfonamide, fosmidomycin, lincomycin, and vancomycin) that showed significant differences between the 2 groups (all P < 0.05). The abundance of Actinomycetes was enriched (about 2.4-fold) in young adults. Bifidobacteria dominated in both young adults and elderly subjects, with overall higher abundances in young adults (P > 0.05). Only the Bifidobacterium_dentium species showed significant differences between the 2 groups (P = 0.013), with a higher abundance in elderly subjects but absent in young adults.

CONCLUSIONS: The present study revealed that there were 3 KEGG metabolic pathways and 7 ARGs as well as enhanced Bifidobacterium_dentium species abundance in elderly compared to young subjects.}, } @article {pmid33407112, year = {2021}, author = {Jing, G and Zhang, Y and Cui, W and Liu, L and Xu, J and Su, X}, title = {Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {9}, pmid = {33407112}, issn = {1471-2164}, support = {31771463//National Natural Science Foundation of China (CN)/ ; ZR201807060158//Natural Science Foundation of Shandong Province/ ; 2018M630807//China Postdoctoral Science Foundation/ ; 32070086//National Natural Science Foundation of China/ ; 32000389//National Natural Science Foundation of China/ ; }, mesh = {*Bacteria/genetics ; Metagenome ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Due to their much lower costs in experiment and computation than metagenomic whole-genome sequencing (WGS), 16S rRNA gene amplicons have been widely used for predicting the functional profiles of microbiome, via software tools such as PICRUSt 2. However, due to the potential PCR bias and gene profile variation among phylogenetically related genomes, functional profiles predicted from 16S amplicons may deviate from WGS-derived ones, resulting in misleading results.

RESULTS: Here we present Meta-Apo, which greatly reduces or even eliminates such deviation, thus deduces much more consistent diversity patterns between the two approaches. Tests of Meta-Apo on > 5000 16S-rRNA amplicon human microbiome samples from 4 body sites showed the deviation between the two strategies is significantly reduced by using only 15 WGS-amplicon training sample pairs. Moreover, Meta-Apo enables cross-platform functional comparison between WGS and amplicon samples, thus greatly improve 16S-based microbiome diagnosis, e.g. accuracy of gingivitis diagnosis via 16S-derived functional profiles was elevated from 65 to 95% by WGS-based classification. Therefore, with the low cost of 16S-amplicon sequencing, Meta-Apo can produce a reliable, high-resolution view of microbiome function equivalent to that offered by shotgun WGS.

CONCLUSIONS: This suggests that large-scale, function-oriented microbiome sequencing projects can probably benefit from the lower cost of 16S-amplicon strategy, without sacrificing the precision in functional reconstruction that otherwise requires WGS. An optimized C++ implementation of Meta-Apo is available on GitHub (https://github.com/qibebt-bioinfo/meta-apo) under a GNU GPL license. It takes the functional profiles of a few paired WGS:16S-amplicon samples as training, and outputs the calibrated functional profiles for the much larger number of 16S-amplicon samples.}, } @article {pmid33406160, year = {2021}, author = {Taylor, JC and Gao, X and Xu, J and Holder, M and Petrosino, J and Kumar, R and Liu, W and Höök, M and Mackenzie, C and Hillhouse, A and Brashear, W and Nunez, MP and Xu, Y}, title = {A type VII secretion system of Streptococcus gallolyticus subsp. gallolyticus contributes to gut colonization and the development of colon tumors.}, journal = {PLoS pathogens}, volume = {17}, number = {1}, pages = {e1009182}, pmid = {33406160}, issn = {1553-7374}, mesh = {Animals ; *Cell Proliferation ; Colonic Neoplasms/chemically induced/microbiology/*pathology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Mice ; Mice, Inbred A ; Streptococcal Infections/metabolism/*microbiology ; Streptococcus gallolyticus subspecies gallolyticus/*physiology ; Type VII Secretion Systems/*metabolism ; }, abstract = {Streptococcus gallolyticus subspecies gallolyticus (Sgg) has a strong clinical association with colorectal cancer (CRC) and actively promotes the development of colon tumors. However, the molecular determinants involved in Sgg pathogenicity in the gut are unknown. Bacterial type VII secretion systems (T7SS) mediate pathogen interactions with their host and are important for virulence in pathogenic mycobacteria and Staphylococcus aureus. Through genome analysis, we identified a locus in Sgg strain TX20005 that encodes a putative type VII secretion system (designated as SggT7SST05). We showed that core genes within the SggT7SST05 locus are expressed in vitro and in the colon of mice. Western blot analysis showed that SggEsxA, a protein predicted to be a T7SS secretion substrate, is detected in the bacterial culture supernatant, indicating that this SggT7SST05 is functional. Deletion of SggT7SST05 (TX20005Δesx) resulted in impaired bacterial adherence to HT29 cells and abolished the ability of Sgg to stimulate HT29 cell proliferation. Analysis of bacterial culture supernatants suggest that SggT7SST05-secreted factors are responsible for the pro-proliferative activity of Sgg, whereas Sgg adherence to host cells requires both SggT7SST05-secreted and bacterial surface-associated factors. In a murine gut colonization model, TX20005Δesx showed significantly reduced colonization compared to the parent strain. Furthermore, in a mouse model of CRC, mice exposed to TX20005 had a significantly higher tumor burden compared to saline-treated mice, whereas those exposed to TX20005Δesx did not. Examination of the Sgg load in the colon in the CRC model suggests that SggT7SST05-mediated activities are directly involved in the promotion of colon tumors. Taken together, these results reveal SggT7SST05 as a previously unrecognized pathogenicity determinant for Sgg colonization of the colon and promotion of colon tumors.}, } @article {pmid33406089, year = {2021}, author = {Patumcharoenpol, P and Nakphaichit, M and Panagiotou, G and Senavonge, A and Suratannon, N and Vongsangnak, W}, title = {MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome.}, journal = {PLoS computational biology}, volume = {17}, number = {1}, pages = {e1008487}, pmid = {33406089}, issn = {1553-7358}, mesh = {*Bacteria/enzymology/genetics/metabolism ; Bacterial Proteins/classification/genetics/metabolism ; DNA, Bacterial/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; RNA, Ribosomal, 16S/genetics ; *Software ; }, abstract = {Investigating metabolic functional capability of a human gut microbiome enables the quantification of microbiome changes, which can cause a phenotypic change of host physiology and disease. One possible way to estimate the functional capability of a microbial community is through inferring metagenomic content from 16S rRNA gene sequences. Genome-scale models (GEMs) can be used as scaffold for functional estimation analysis at a systematic level, however up to date, there is no integrative toolbox based on GEMs for uncovering metabolic functions. Here, we developed the MetGEMs (metagenome-scale models) toolbox, an open-source application for inferring metabolic functions from 16S rRNA gene sequences to facilitate the study of the human gut microbiome by the wider scientific community. The developed toolbox was validated using shotgun metagenomic data and shown to be superior in predicting functional composition in human clinical samples compared to existing state-of-the-art tools. Therefore, the MetGEMs toolbox was subsequently applied for annotating putative enzyme functions and metabolic routes related in human disease using atopic dermatitis as a case study.}, } @article {pmid33404934, year = {2021}, author = {Ali, P and Chen, F and Hassan, F and Sosa, A and Khan, S and Badshah, M and Shah, AA}, title = {Bacterial community characterization of Batura Glacier in the Karakoram Range of Pakistan.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {24}, number = {2}, pages = {183-196}, pmid = {33404934}, issn = {1618-1905}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/*isolation & purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ice Cover/*microbiology ; *Microbiota ; Pakistan ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {High-altitude cold habitats of the Karakoram are rarely explored for their bacterial community characterization and metabolite productions. In the present study, bacterial communities in ice, water, and sediments of Batura Glacier were investigated using culture-dependent and culture-independent methods. Twenty-seven cold-adapted bacterial strains (mostly psychrotrophic) were isolated using R2A, Tryptic Soy Agar (TSA), and Luria-Bertani (LB) media, at 4 °C and 15 °C. Most of the isolates exhibited growth at a wide range of temperature (4-35 °C), pH (5-12), and salinity (1-6%). Among the bacterial isolates, 52% were identified as Gram-positive and the remaining 48% represented as Gram-negative. The results of phylogenetic analysis indicated that all the culturable bacteria belonged to 3 major phylogenetic groups, i.e., Actinobacteria (48%), Bacteroidetes (26%), and Proteobacteria (22%), while Flavobacterium (26%), Arthrobacter (22%), and Pseudomonas (19%) were represented as the dominant genera. Similarly, Illumina amplicon sequencing of 16S rRNA genes after PCR amplification of DNA from the whole community revealed dominance of the same phylogenetic groups, Proteobacteria, Actinobacteria, and Bacteroidetes, while Arthrobacter, Mycoplana, Ochrobactrum, Kaistobacter, Janthinobacterium, and Flavobacterium were found as the dominant genera. Among the culturable isolates, 70% demonstrated activity for cellulases, 48% lipases, 41% proteases, 41% DNases, and only 7% for amylases. Most of the glacial isolates demonstrated antimicrobial activity against other microorganisms including the multiple-drug-resistant strains of Candida albicans, Klebsiella pneumoniae, Acinetobacter sp., and Bacillus sp. 67% of Gram-negative while 46% of Gram-positive glacial bacteria were resistant to trimethoprim/sulfamethoxazole. Resistance against methicillin and vancomycin among the Gram-positive isolates was 23% and 15%, respectively, while 11% of the Gram-negative isolates exhibited resistance against both colistin sulfate and nalidixic acid.}, } @article {pmid33401450, year = {2021}, author = {Jalili, F and Trigui, H and Guerra Maldonado, JF and Dorner, S and Zamyadi, A and Shapiro, BJ and Terrat, Y and Fortin, N and Sauvé, S and Prévost, M}, title = {Can Cyanobacterial Diversity in the Source Predict the Diversity in Sludge and the Risk of Toxin Release in a Drinking Water Treatment Plant?.}, journal = {Toxins}, volume = {13}, number = {1}, pages = {}, pmid = {33401450}, issn = {2072-6651}, support = {Genome Canada/UM RQ000607//Genome Canada and Génome Québec/International ; }, mesh = {Bacterial Toxins/*chemistry ; *Biodiversity ; Cyanobacteria/*classification ; Drinking Water/*chemistry/microbiology ; Sewage/*microbiology ; Waste Disposal Facilities ; *Water Purification ; }, abstract = {Conventional processes (coagulation, flocculation, sedimentation, and filtration) are widely used in drinking water treatment plants and are considered a good treatment strategy to eliminate cyanobacterial cells and cell-bound cyanotoxins. The diversity of cyanobacteria was investigated using taxonomic cell counts and shotgun metagenomics over two seasons in a drinking water treatment plant before, during, and after the bloom. Changes in the community structure over time at the phylum, genus, and species levels were monitored in samples retrieved from raw water (RW), sludge in the holding tank (ST), and sludge supernatant (SST). Aphanothece clathrata brevis, Microcystis aeruginosa, Dolichospermum spiroides , and Chroococcus minimus were predominant species detected in RW by taxonomic cell counts. Shotgun metagenomics revealed that Proteobacteria was the predominant phylum in RW before and after the cyanobacterial bloom. Taxonomic cell counts and shotgun metagenomic showed that the Dolichospermum bloom occurred inside the plant. Cyanobacteria and Bacteroidetes were the major bacterial phyla during the bloom. Shotgun metagenomics also showed that Synechococcus, Microcystis , and Dolichospermum were the predominant detected cyanobacterial genera in the samples. Conventional treatment removed more than 92% of cyanobacterial cells but led to cell accumulation in the sludge up to 31 times more than in the RW influx. Coagulation/sedimentation selectively removed more than 96% of Microcystis and Dolichospermum. Cyanobacterial community in the sludge varied from raw water to sludge during sludge storage (1-13 days). This variation was due to the selective removal of coagulation/sedimentation as well as the accumulation of captured cells over the period of storage time. However, the prediction of the cyanobacterial community composition in the SST remained a challenge. Among nutrient parameters, orthophosphate availability was related to community profile in RW samples, whereas communities in ST were influenced by total nitrogen, Kjeldahl nitrogen (N- Kjeldahl), total and particulate phosphorous, and total organic carbon (TOC). No trend was observed on the impact of nutrients on SST communities. This study profiled new health-related, environmental, and technical challenges for the production of drinking water due to the complex fate of cyanobacteria in cyanobacteria-laden sludge and supernatant.}, } @article {pmid33398958, year = {2020}, author = {Tan, Y and Hu, H and Li, C and Luo, X and Tan, Y and Dai, L}, title = {[Research progress and applications of strain analysis based on metagenomic data].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {36}, number = {12}, pages = {2610-2621}, doi = {10.13345/j.cjb.200380}, pmid = {33398958}, issn = {1872-2075}, mesh = {Algorithms ; Computational Biology ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; }, abstract = {Strain is the fundamental unit in microbial taxonomy. The functional diversity among strains has great influence on host phenotypes. With the development of microbiome research, knowing the composition and functional capacities of complex microbial communities at the strain level has become increasingly valuable in scientific research and clinical applications. This review introduces the principles of bioinformatics algorithms for strain analysis based on metagenomic data, the applications in microbiome research and directions of future development.}, } @article {pmid33398955, year = {2020}, author = {Zhang, Y and Cao, J and Zhao, N and Wang, J}, title = {[Virome: the next hotspot in microbiome research].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {36}, number = {12}, pages = {2566-2581}, doi = {10.13345/j.cjb.200372}, pmid = {33398955}, issn = {1872-2075}, mesh = {Animals ; Humans ; Metagenome ; Metagenomics ; *Microbiota/genetics ; Virome ; *Viruses/genetics ; }, abstract = {Virome is the collective term for the viral collection or viral metagenomes that are distributed in various environments. Viruses can be found in bodies of water, glaciers, plants, animals, and even some viruses, which are classified as eukaryotes, prokaryotes and subviruses. Viruses play very important role in maintaining environmental homeostasis and ecosystem balance, and are especially closely related to human health. In recent years, with the advancement of sequencing technology and data analysis, we are able to gain more insights into the virome and explore its potential role in the ecological niche by metagenomic sequencing. A large amount of viral data have been obtained from glaciers, oceans, and various plants and animals, and numerous unknown viruses have been discovered. Virome has been studied mainly through metagenomic data mining, as well as virus-like particles separation and enrichment. To date, several different methods for viral isolation and enrichment exist, and numerous bioinformatic analyses of the virome have been performed. However, there is a lack of specific and complete reviews on the enrichment and data analysis methods for the virome. Thus, our review will summarize viral isolation and enrichment methods and data analysis, and present some of the landmark research conducted by the enrichment method, to provide a reference for researchers of interest and further advance the field of virome research.}, } @article {pmid33398949, year = {2020}, author = {Duan, Y and Zhu, B}, title = {[Preface for microbiome sequencing and analysis].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {36}, number = {12}, pages = {2511-2515}, doi = {10.13345/j.cjb.200800}, pmid = {33398949}, issn = {1872-2075}, mesh = {Animals ; Bacteria/genetics ; China ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Microbiota/genetics ; RNA, Ribosomal, 16S ; }, abstract = {Microbes are the most important commensal organisms in humans, animals and plants, and are the major habitants in soil, sediment, water, air and other habitats. The analysis of microbiome in these habitats has become a basic research technique. As a fast developing technology in recent years, microbiome sequencing and analysis have been widely used in human health, environmental pollution control, food industry, agriculture and animal husbandry and other fields. In order to sort out and summarize the current status, development and application prospects of microbiome sequencing and analysis technologies, this special issue has prepared a collection of 16 papers in this field, that comprise sample preservation and processing, single microbe genome sequencing and analysis, and microbiome feature analysis in special habitats, microbiome related databases and algorithms, and microbiome sequencing and analysis expert consensus. It also introduced in detail the development trend of the microbiome sequencing and analysis, in order to promote the rapid development of the microbiome sequencing and analysis industry and scientific research in China, and provide necessary reference for the healthy development of related industries.}, } @article {pmid33398153, year = {2021}, author = {Nissen, JN and Johansen, J and Allesøe, RL and Sønderby, CK and Armenteros, JJA and Grønbech, CH and Jensen, LJ and Nielsen, HB and Petersen, TN and Winther, O and Rasmussen, S}, title = {Improved metagenome binning and assembly using deep variational autoencoders.}, journal = {Nature biotechnology}, volume = {39}, number = {5}, pages = {555-560}, pmid = {33398153}, issn = {1546-1696}, mesh = {Bacteroides/genetics ; Genome, Bacterial/*genetics ; Humans ; Metagenome/*genetics ; Metagenomics ; Microbiota/genetics ; *Molecular Sequence Annotation ; *Software ; }, abstract = {Despite recent advances in metagenomic binning, reconstruction of microbial species from metagenomics data remains challenging. Here we develop variational autoencoders for metagenomic binning (VAMB), a program that uses deep variational autoencoders to encode sequence coabundance and k-mer distribution information before clustering. We show that a variational autoencoder is able to integrate these two distinct data types without any previous knowledge of the datasets. VAMB outperforms existing state-of-the-art binners, reconstructing 29-98% and 45% more near-complete (NC) genomes on simulated and real data, respectively. Furthermore, VAMB is able to separate closely related strains up to 99.5% average nucleotide identity (ANI), and reconstructed 255 and 91 NC Bacteroides vulgatus and Bacteroides dorei sample-specific genomes as two distinct clusters from a dataset of 1,000 human gut microbiome samples. We use 2,606 NC bins from this dataset to show that species of the human gut microbiome have different geographical distribution patterns. VAMB can be run on standard hardware and is freely available at https://github.com/RasmussenLab/vamb .}, } @article {pmid33398096, year = {2021}, author = {Bay, SK and Dong, X and Bradley, JA and Leung, PM and Grinter, R and Jirapanjawat, T and Arndt, SK and Cook, PLM and LaRowe, DE and Nauer, PA and Chiri, E and Greening, C}, title = {Trace gas oxidizers are widespread and active members of soil microbial communities.}, journal = {Nature microbiology}, volume = {6}, number = {2}, pages = {246-256}, pmid = {33398096}, issn = {2058-5276}, mesh = {Bacteria/classification/*enzymology/genetics ; Carbon Monoxide/*metabolism ; Hydrogen/*metabolism ; Metagenomics ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; *Soil ; *Soil Microbiology ; }, abstract = {Soil microorganisms globally are thought to be sustained primarily by organic carbon sources. Certain bacteria also consume inorganic energy sources such as trace gases, but they are presumed to be rare community members, except within some oligotrophic soils. Here we combined metagenomic, biogeochemical and modelling approaches to determine how soil microbial communities meet energy and carbon needs. Analysis of 40 metagenomes and 757 derived genomes indicated that over 70% of soil bacterial taxa encode enzymes to consume inorganic energy sources. Bacteria from 19 phyla encoded enzymes to use the trace gases hydrogen and carbon monoxide as supplemental electron donors for aerobic respiration. In addition, we identified a fourth phylum (Gemmatimonadota) potentially capable of aerobic methanotrophy. Consistent with the metagenomic profiling, communities within soil profiles from diverse habitats rapidly oxidized hydrogen, carbon monoxide and to a lesser extent methane below atmospheric concentrations. Thermodynamic modelling indicated that the power generated by oxidation of these three gases is sufficient to meet the maintenance needs of the bacterial cells capable of consuming them. Diverse bacteria also encode enzymes to use trace gases as electron donors to support carbon fixation. Altogether, these findings indicate that trace gas oxidation confers a major selective advantage in soil ecosystems, where availability of preferred organic substrates limits microbial growth. The observation that inorganic energy sources may sustain most soil bacteria also has broad implications for understanding atmospheric chemistry and microbial biodiversity in a changing world.}, } @article {pmid33398049, year = {2021}, author = {Niederdorfer, R and Hausherr, D and Palomo, A and Wei, J and Magyar, P and Smets, BF and Joss, A and Bürgmann, H}, title = {Temperature modulates stress response in mainstream anammox reactors.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {23}, pmid = {33398049}, issn = {2399-3642}, mesh = {Ammonium Compounds/metabolism ; Anaerobiosis ; Bioreactors/*microbiology ; Genome, Bacterial ; Genomics ; Metagenome ; Microbial Consortia/*genetics ; *Stress, Physiological ; Temperature ; *Transcription, Genetic ; Transcriptome ; *Water Purification ; }, abstract = {Autotrophic nitrogen removal by anaerobic ammonium oxidizing (anammox) bacteria is an energy-efficient nitrogen removal process in wastewater treatment. However, full-scale deployment under mainstream conditions remains challenging for practitioners due to the high stress susceptibility of anammox bacteria towards fluctuations in dissolved oxygen (DO) and temperature. Here, we investigated the response of microbial biofilms with verified anammox activity to DO shocks under 20 °C and 14 °C. While pulse disturbances of 0.3 mg L[-1] DO prompted only moderate declines in the NH4[+] removal rates, 1.0 mg L[-1] DO led to complete but reversible inhibition of the NH4[+] removal activity in all reactors. Genome-centric metagenomics and metatranscriptomics were used to investigate the stress response on various biological levels. We show that temperature regime and strength of DO perturbations induced divergent responses from the process level down to the transcriptional profile of individual taxa. Community-wide gene expression differed significantly depending on the temperature regime in all reactors, and we found a noticeable impact of DO disturbances on genes involved in transcription, translation, replication and posttranslational modification at 20 °C but not 14 °C. Genome-centric analysis revealed that different anammox species and other key biofilm taxa differed in their transcriptional responses to distinct temperature regimes and DO disturbances.}, } @article {pmid33397500, year = {2021}, author = {LaPelusa, M and Donoviel, D and Branzini, SE and Carlson, PE and Culler, S and Cheema, AK and Kaddurah-Daouk, R and Kelly, D and de Cremoux, I and Knight, R and Krajmalnik-Brown, R and Mayo, SL and Mazmanian, SK and Mayer, EA and Petrosino, JF and Garrison, K}, title = {Microbiome for Mars: surveying microbiome connections to healthcare with implications for long-duration human spaceflight, virtual workshop, July 13, 2020.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {2}, pmid = {33397500}, issn = {2049-2618}, mesh = {Animals ; *Astronauts ; Delivery of Health Care/*trends ; Gastrointestinal Microbiome/genetics/physiology ; Humans ; *Mars ; Microbiota/genetics/*physiology ; *Space Flight ; }, abstract = {The inaugural "Microbiome for Mars" virtual workshop took place on July 13, 2020. This event assembled leaders in microbiome research and development to discuss their work and how it may relate to long-duration human space travel. The conference focused on surveying current microbiome research, future endeavors, and how this growing field could broadly impact human health and space exploration. This report summarizes each speaker's presentation in the order presented at the workshop.}, } @article {pmid33397406, year = {2021}, author = {Zhang, R and Walker, AR and Datta, S}, title = {Unraveling city-specific signature and identifying sample origin locations for the data from CAMDA MetaSUB challenge.}, journal = {Biology direct}, volume = {16}, number = {1}, pages = {1}, pmid = {33397406}, issn = {1745-6150}, support = {UL1 TR000064/TR/NCATS NIH HHS/United States ; 1UL1TR000064/TR/NCATS NIH HHS/United States ; }, mesh = {Cities ; Humans ; *Machine Learning ; *Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {BACKGROUND: Composition of microbial communities can be location-specific, and the different abundance of taxon within location could help us to unravel city-specific signature and predict the sample origin locations accurately. In this study, the whole genome shotgun (WGS) metagenomics data from samples across 16 cities around the world and samples from another 8 cities were provided as the main and mystery datasets respectively as the part of the CAMDA 2019 MetaSUB "Forensic Challenge". The feature selecting, normalization, three methods of machine learning, PCoA (Principal Coordinates Analysis) and ANCOM (Analysis of composition of microbiomes) were conducted for both the main and mystery datasets.

RESULTS: Features selecting, combined with the machines learning methods, revealed that the combination of the common features was effective for predicting the origin of the samples. The average error rates of 11.93 and 30.37% of three machine learning methods were obtained for main and mystery datasets respectively. Using the samples from main dataset to predict the labels of samples from mystery dataset, nearly 89.98% of the test samples could be correctly labeled as "mystery" samples. PCoA showed that nearly 60% of the total variability of the data could be explained by the first two PCoA axes. Although many cities overlapped, the separation of some cities was found in PCoA. The results of ANCOM, combined with importance score from the Random Forest, indicated that the common "family", "order" of the main-dataset and the common "order" of the mystery dataset provided the most efficient information for prediction respectively.

CONCLUSIONS: The results of the classification suggested that the composition of the microbiomes was distinctive across the cities, which could be used to identify the sample origins. This was also supported by the results from ANCOM and importance score from the RF. In addition, the accuracy of the prediction could be improved by more samples and better sequencing depth.}, } @article {pmid33397232, year = {2022}, author = {Hajiagha, MN and Taghizadeh, S and Asgharzadeh, M and Dao, S and Ganbarov, K and Köse, Ş and Kafil, HS}, title = {Gut Microbiota and Human Body Interactions; Its Impact on Health: A Review.}, journal = {Current pharmaceutical biotechnology}, volume = {23}, number = {1}, pages = {4-14}, doi = {10.2174/1389201022666210104115836}, pmid = {33397232}, issn = {1873-4316}, support = {65967//Faculty of Medicine and Drug Applied Research Center, Tabriz University of Medical Sciences/ ; }, mesh = {Adult ; Brain-Gut Axis ; Dysbiosis ; Female ; *Gastrointestinal Microbiome ; Human Body ; Humans ; Metagenomics ; Pregnancy ; }, abstract = {Gut microbiota (GM), as an organ of the human body, has a particular and autonomous function that is related to it. This review aims to investigate human intestinal and gut microbiota interaction and its impact on health. As a creation referable database about this dynamic and complex organ, several comprehensive projects are implemented by using culture-dependent (culturomics), culture- independent methods (e.g., metagenomics, mathematics model), and Gnotobiological together. This study was done by searching PubMed, Scopus and Google scholar database in the gut, health microbiota, and interaction keywords. The first acquired microbiota during pregnancy or childbirth is colonized in the gut by using specific and non-specific mechanisms. Its structure and shape reach relative stability with selection pressure along with host development until adulthood and keeps its resilience against external or internal variables depending on the host's genetics and negative feedback. According to research, individuals have 2 functional group microbiotas, including the core (common between vast majorities human) and flexible (transient population) microbiome. The most important role of the GM in the human body can be summarized in three basic landscapes: metabolic, immune system, and gut-brain axis interaction. So, the loss of microbial population balance will lead to disorder and disease.}, } @article {pmid33396683, year = {2020}, author = {Kuramae, EE and Dimitrov, MR and da Silva, GHR and Lucheta, AR and Mendes, LW and Luz, RL and Vet, LEM and Fernandes, TV}, title = {On-Site Blackwater Treatment Fosters Microbial Groups and Functions to Efficiently and Robustly Recover Carbon and Nutrients.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, pmid = {33396683}, issn = {2076-2607}, support = {729.004.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 2013/50351-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 206884/2014-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 99999.008090/2015-07;0622/2014//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {Wastewater is considered a renewable resource water and energy. An advantage of decentralized sanitation systems is the separation of the blackwater (BW) stream, contaminated with human pathogens, from the remaining household water. However, the composition and functions of the microbial community in BW are not known. In this study, we used shotgun metagenomics to assess the dynamics of microbial community structure and function throughout a new BW anaerobic digestion system installed at The Netherlands Institute of Ecology. Samples from the influent (BW), primary effluent (anaerobic digested BW), sludge and final effluent of the pilot upflow anaerobic sludge blanket (UASB) reactor and microalgae pilot tubular photobioreactor (PBR) were analyzed. Our results showed a decrease in microbial richness and diversity followed by a decrease in functional complexity and co-occurrence along the different modules of the bioreactor. The microbial diversity and function decrease were reflected both changes in substrate composition and wash conditions. Our wastewater treatment system also decreased microbial functions related to pathogenesis. In summary, the new sanitation system studied here fosters microbial groups and functions that allow the system to efficiently and robustly recover carbon and nutrients while reducing pathogenic groups, ultimately generating a final effluent safe for discharge and reuse.}, } @article {pmid33395690, year = {2021}, author = {Muturi, SM and Muthui, LW and Njogu, PM and Onguso, JM and Wachira, FN and Opiyo, SO and Pelle, R}, title = {Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya.}, journal = {PloS one}, volume = {16}, number = {1}, pages = {e0244755}, pmid = {33395690}, issn = {1932-6203}, mesh = {Archaea/genetics ; Bacteria/genetics ; Bacteria, Anaerobic/genetics/metabolism ; Biodiversity ; Biofuels/*microbiology ; Bioreactors/microbiology ; Euryarchaeota/metabolism ; Fermentation ; Fungi/genetics ; Kenya ; Metagenomics/*methods ; Methane/metabolism ; Methanomicrobiales/metabolism ; Microbiota/*genetics/physiology ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {The obstacle to optimal utilization of biogas technology is poor understanding of biogas microbiomes diversities over a wide geographical coverage. We performed random shotgun sequencing on twelve environmental samples. Randomized complete block design was utilized to assign the twelve treatments to four blocks, within eastern and central regions of Kenya. We obtained 42 million paired-end reads that were annotated against sixteen reference databases using two ENVO ontologies, prior to β-diversity studies. We identified 37 phyla, 65 classes and 132 orders. Bacteria dominated and comprised 28 phyla, 42 classes and 92 orders, conveying substrate's versatility in the treatments. Though, Fungi and Archaea comprised 5 phyla, the Fungi were richer; suggesting the importance of hydrolysis and fermentation in biogas production. High β-diversity within the taxa was largely linked to communities' metabolic capabilities. Clostridiales and Bacteroidales, the most prevalent guilds, metabolize organic macromolecules. The identified Cytophagales, Alteromonadales, Flavobacteriales, Fusobacteriales, Deferribacterales, Elusimicrobiales, Chlamydiales, Synergistales to mention but few, also catabolize macromolecules into smaller substrates to conserve energy. Furthermore, δ-Proteobacteria, Gloeobacteria and Clostridia affiliates syntrophically regulate PH2 and reduce metal to provide reducing equivalents. Methanomicrobiales and other Methanomicrobia species were the most prevalence Archaea, converting formate, CO2(g), acetate and methylated substrates into CH4(g). Thermococci, Thermoplasmata and Thermoprotei were among the sulfur and other metal reducing Archaea that contributed to redox balancing and other metabolism within treatments. Eukaryotes, mainly fungi were the least abundant guild, comprising largely Ascomycota and Basidiomycota species. Chytridiomycetes, Blastocladiomycetes and Mortierellomycetes were among the rare species, suggesting their metabolic and substrates limitations. Generally, we observed that environmental and treatment perturbations influenced communities' abundance, β-diversity and reactor performance largely through stochastic effect. Understanding diversity of biogas microbiomes over wide environmental variables and its' productivity provided insights into better management strategies that ameliorate biochemical limitations to effective biogas production.}, } @article {pmid33395552, year = {2021}, author = {Zhu, Z and Cao, M and Wang, W and Zhang, L and Ma, T and Liu, G and Zhang, Y and Shang, Z and Chen, X and Shi, Y and Zhang, J}, title = {Exploring the Prevalence and Distribution Patterns of Antibiotic Resistance Genes in Bovine Gut Microbiota Using a Metagenomic Approach.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {27}, number = {7}, pages = {980-990}, doi = {10.1089/mdr.2020.0271}, pmid = {33395552}, issn = {1931-8448}, mesh = {Agriculture ; Animals ; Anti-Bacterial Agents/*pharmacology ; Cattle ; Drug Resistance, Microbial/*genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Genes, Bacterial/*genetics ; Metagenomics ; Polymorphism, Single Nucleotide ; }, abstract = {Antibiotic resistance genes (ARGs) have become recognized contaminants and pose a high public health risk. The animal gut microbiota is a reservoir of ARGs, but the knowledge of the origin and dissemination of ARGs remains unclear. In this study, we provide a comprehensive profile of ARGs and mobile genetic elements in the gut microbiota from 30 bovines to study the impact of modern antibiotics on resistance. A total of 42 ARG types were detected by annotating the metagenomic sequencing data from Comprehensive Antibiotic Resistance Database (CARD). We found that the diversity and abundance of ARGs in individual yaks were significantly lower than those in dairy and beef cattle (p < 0.0001). The results of heat map and single nucleotide polymorphism clustering suggest that ARGs from dairy and beef cattle are more similar, whereas those from yaks cluster separately. The long-term use of antibiotics may contribute to this difference, suggesting that antibiotic consumption is the main cause of ARG prevalence. Furthermore, abundant insertions were also found in this study, signifying a strong potential for horizontal transfer of ARGs among microbes, especially pathogens.}, } @article {pmid33395419, year = {2021}, author = {Macher, JN and Prazeres, M and Taudien, S and Jompa, J and Sadekov, A and Renema, W}, title = {Integrating morphology and metagenomics to understand taxonomic variability of Amphisorus (Foraminifera, Miliolida) from Western Australia and Indonesia.}, journal = {PloS one}, volume = {16}, number = {1}, pages = {e0244616}, pmid = {33395419}, issn = {1932-6203}, mesh = {Biodiversity ; Dinoflagellida/genetics/physiology ; Foraminifera/classification/*genetics/physiology/ultrastructure ; Indonesia ; Metagenomics ; Symbiosis ; Western Australia ; }, abstract = {Foraminifera are a group of mostly marine protists with high taxonomic diversity. Species identification is often complex, as both morphological and molecular approaches can be challenging due to a lack of unique characters and reference sequences. An integrative approach combining state of the art morphological and molecular tools is therefore promising. In this study, we analysed large benthic Foraminifera of the genus Amphisorus from Western Australia and Indonesia. Based on previous findings on high morphological variability observed in the Soritidae and the discontinuous distribution of Amphisorus along the coast of western Australia, we expected to find multiple morphologically and genetically unique Amphisorus types. In order to gain detailed insights into the diversity of Amphisorus, we applied micro CT scanning and shotgun metagenomic sequencing. We identified four distinct morphotypes of Amphisorus, two each in Australia and Indonesia, and showed that each morphotype is a distinct genotype. Furthermore, metagenomics revealed the presence of three dinoflagellate symbiont clades. The most common symbiont was Fugacium Fr5, and we could show that its genotypes were mostly specific to Amphisorus morphotypes. Finally, we assembled the microbial taxa associated with the two Western Australian morphotypes, and analysed their microbial community composition. Even though each Amphisorus morphotype harboured distinct bacterial communities, sampling location had a stronger influence on bacterial community composition, and we infer that the prokaryotic community is primarily shaped by the microhabitat rather than host identity. The integrated approach combining analyses of host morphology and genetics, dinoflagellate symbionts, and associated microbes leads to the conclusion that we identified distinct, yet undescribed taxa of Amphisorus. We argue that the combination of morphological and molecular methods provides unprecedented insights into the diversity of foraminifera, which paves the way for a deeper understanding of their biodiversity, and facilitates future taxonomic and ecological work.}, } @article {pmid33392758, year = {2021}, author = {Liu, J and Hao, W and He, Z and Kwek, E and Zhu, H and Ma, N and Ma, KY and Chen, ZY}, title = {Blueberry and cranberry anthocyanin extracts reduce bodyweight and modulate gut microbiota in C57BL/6 J mice fed with a high-fat diet.}, journal = {European journal of nutrition}, volume = {60}, number = {5}, pages = {2735-2746}, pmid = {33392758}, issn = {1436-6215}, support = {14105820//General Research Fund/ ; }, mesh = {Animals ; Anthocyanins ; *Blueberry Plants ; Diet, High-Fat/adverse effects ; Fruit ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred C57BL ; Plant Extracts/pharmacology ; *Vaccinium macrocarpon ; }, abstract = {PURPOSE: Blueberry and cranberry are rich in anthocyanins. The present study was to investigate the effects of anthocyanin extracts from blueberry and cranberry on body weight and gut microbiota.

METHODS: C57BL/6 J Mice were divided into six groups (n = 9 each) fed one of six diets namely low-fat diet (LFD), high-fat diet (HFD), HFD with the addition of 1% blueberry extract (BL), 2% blueberry extract (BH), 1% cranberry extract (CL), and 2% cranberry extract (CH), respectively.

RESULTS: Feeding BL and BH diets significantly decreased body weight gain by 20-23%, total adipose tissue weight by 18-20%, and total liver lipids by 16-18% compared with feeding HFD. Feeding CH diet but not CL diet reduced the body weight by 27%, accompanied by a significant reduction of total plasma cholesterol by 25% and tumor necrosis factor alpha (TNF-α) by 38%. The metagenomic analysis showed that the supplementation of blueberry and cranberry anthocyanin extracts reduced plasma lipopolysaccharide concentration, accompanied by a reduction in the relative abundance of Rikenella and Rikenellaceae. Dietary supplementation of berry anthocyanin extracts promoted the growth of Lachnoclostridium, Roseburia, and Clostridium_innocuum_group in genus level, leading to a greater production of fecal short-chain fatty acids (SCFA).

CONCLUSIONS: It was concluded that both berry anthocyanins could manage the body weight and favorably modulate the gut microbiota at least in mice.}, } @article {pmid33387530, year = {2021}, author = {Kummen, M and Thingholm, LB and Rühlemann, MC and Holm, K and Hansen, SH and Moitinho-Silva, L and Liwinski, T and Zenouzi, R and Storm-Larsen, C and Midttun, Ø and McCann, A and Ueland, PM and Høivik, ML and Vesterhus, M and Trøseid, M and Laudes, M and Lieb, W and Karlsen, TH and Bang, C and Schramm, C and Franke, A and Hov, JR}, title = {Altered Gut Microbial Metabolism of Essential Nutrients in Primary Sclerosing Cholangitis.}, journal = {Gastroenterology}, volume = {160}, number = {5}, pages = {1784-1798.e0}, pmid = {33387530}, issn = {1528-0012}, support = {802544/ERC_/European Research Council/International ; }, mesh = {Adolescent ; Adult ; Aged ; Bacteria/genetics/*metabolism ; Case-Control Studies ; Cholangitis, Sclerosing/blood/diagnosis/*microbiology/surgery ; Cross-Sectional Studies ; Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Germany ; Humans ; Liver Transplantation ; Male ; *Metabolome ; Metabolomics ; *Metagenome ; Metagenomics ; Middle Aged ; Norway ; Phylogeny ; Progression-Free Survival ; Young Adult ; }, abstract = {BACKGROUND & AIMS: To influence host and disease phenotype, compositional microbiome changes, which have been demonstrated in patients with primary sclerosing cholangitis (PSC), must be accompanied by functional changes. We therefore aimed to characterize the genetic potential of the gut microbiome in patients with PSC compared with healthy controls (HCs) and patients with inflammatory bowel disease (IBD).

METHODS: Fecal DNA from 2 cohorts (1 Norwegian and 1 German), in total comprising 136 patients with PSC (58% with IBD), 158 HCs, and 93 patients with IBD without PSC, were subjected to metagenomic shotgun sequencing, generating 17 billion paired-end sequences, which were processed using HUMAnN2 and MetaPhlAn2, and analyzed using generalized linear models and random effects meta-analyses.

RESULTS: Patients with PSC had fewer microbial genes compared with HCs (P < .0001). Compared with HCs, patients with PSC showed enrichment and increased prevalence of Clostridium species and a depletion of, for example, Eubacterium spp and Ruminococcus obeum. Patients with PSC showed marked differences in the abundance of genes related to vitamin B6 synthesis and branched-chain amino acid synthesis (Qfdr < .05). Targeted metabolomics of plasma from an independent set of patients with PSC and controls found reduced concentrations of vitamin B6 and branched-chain amino acids in PSC (P < .0001), which strongly associated with reduced liver transplantation-free survival (log-rank P < .001). No taxonomic or functional differences were detected between patients with PSC with and without IBD.

CONCLUSIONS: The gut microbiome in patients with PSC exhibits large functional differences compared with that in HCs, including microbial metabolism of essential nutrients. Alterations in related circulating metabolites associated with disease course, suggesting that microbial functions may be relevant for the disease process in PSC.}, } @article {pmid33387519, year = {2021}, author = {Mehtani, R and Roy, A and Singh, V}, title = {Gut Microbial Metagenomics in ACLF: The Causality-Association Conundrum.}, journal = {Gastroenterology}, volume = {160}, number = {6}, pages = {2205}, doi = {10.1053/j.gastro.2020.12.055}, pmid = {33387519}, issn = {1528-0012}, mesh = {Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Microbiota ; }, } @article {pmid33386517, year = {2021}, author = {Ray, P and Pandey, U and Das, D and Aich, P}, title = {Vancomycin-Induced Changes in Host Immunity and Behavior: Comparative Genomic and Metagenomic Analysis in C57BL/6 and BALB/c Mice.}, journal = {Digestive diseases and sciences}, volume = {66}, number = {11}, pages = {3776-3791}, pmid = {33386517}, issn = {1573-2568}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects ; Behavior, Animal ; DNA, Bacterial ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Regulation/drug effects ; Genomics ; Immunity/*drug effects ; Male ; Metagenomics ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; RNA, Bacterial ; RNA, Ribosomal, 16S ; Vancomycin/*pharmacology ; Mice ; }, abstract = {BACKGROUND: The consequence of treatment with antibiotics on the gut microbiota can be destructive. The antibiotics, however, can be utilized to understand the role of gut microbiota on the host physiology.

AIM: Earlier, we reported the efficacy of vancomycin in gut microbiota perturbation. We continued to understand the effect of restoration kinetics of perturbed gut microbiota on the immunity and behavior of Th1 (C57BL/6)- and Th2 (BALB/c)-biased mice.

METHODS: We studied restoration kinetics of the gut microbiota for two months following the withdrawal of vancomycin treatment in both mice strains. We analyzed cecal microbiome composition, different behavioral assays, and expression of select genes associated with stress and barrier function in gut and brain.

RESULTS: Metagenomic analysis of gut microbiota revealed that the treatment with vancomycin caused a significant decrease in the relative abundance of Firmicutes and Bacteroidetes phyla with a time-dependent increase in Proteobacteria and Verrucomicrobia phyla. Maximum restoration (> 70%) of gut microbiota happened by the 15th day of withdrawal of vancomycin. BALB/c mice showed a more efficient restoration of gut microbiota compared to C57BL/6 mice. We established the correlation patterns of gut microbiota alteration and its effect on (a) the behavior of mice, (b) expression of key brain molecules, and (c) immunity-related genes.

CONCLUSIONS: The results revealed that the gut microbiome profiling, behavior, and immune responses varied significantly between Th1- and Th2-biased mice. By withdrawing the treatment with vancomycin of major gut microbes, important physiological and behavioral changes of both mice strains returned to the normal (untreated control) level.}, } @article {pmid33386513, year = {2021}, author = {Zhang, R and Zhang, Q and Yu, G and Zhang, Z}, title = {Metagenomic deep sequencing obtains taxonomic and functional profiles of Haemaphysalis longicornis that vary in response to different developmental stages and sexes.}, journal = {Experimental & applied acarology}, volume = {83}, number = {2}, pages = {285-300}, pmid = {33386513}, issn = {1572-9702}, support = {2017GSF221017//Development Plan Project of Shandong Province Science and Technology/ ; }, mesh = {Animals ; Bacteria/genetics ; Female ; High-Throughput Nucleotide Sequencing ; *Ixodidae ; Male ; Metagenome ; *Microbiota ; }, abstract = {Ticks can transmit numerous pathogens and harbor diverse microbial communities. Considerable progress has been made in the characterization of the bacterial profiles of ticks, whereas other members of tick microbiota (such as fungi and viruses) and the functional characteristics of ticks warrant further exploration. To investigate the taxonomic and functional profiles and explore potential pathogens they were carrying, samples of different developmental stages and of both sexes of Haemaphysalis longicornis were collected in the present study and the metagenomic deep sequencing method was applied. Metagenomic deep sequencing results revealed that bacteria were predominant, followed by fungi, viruses, archaea and metazoans. Proteobacteria was the dominant phylum in the microbiota of H. longicornis. The abundance of microbial species varied significantly among groups, the bacteria of nymphs and female adults demonstrated unique characteristics, and the microbial community of males overlapped with those of nymphs and females. Functional annotation results demonstrated that the metagenomic sequences of the three groups were classified under metabolism, genetic information processing, environmental information processing and cellular processes. Differences in functional characteristics were observed in both the pathways composition and abundance of carbohydrate-active enzymes. Furthermore, whole metagenome sequencing helped to elucidate the diversity of pathogens carried by H. longicornis, which may facilitate further research attempting to prevent and control tick-borne diseases.}, } @article {pmid33385834, year = {2021}, author = {Kim, N and Ahn, Y and Jo, J and Pyo, H and Lee, J and Choi, J}, title = {Soil assessment after chemical accidents using metabolic profiling and microbial community evaluation.}, journal = {Chemosphere}, volume = {268}, number = {}, pages = {129362}, doi = {10.1016/j.chemosphere.2020.129362}, pmid = {33385834}, issn = {1879-1298}, mesh = {*Chemical Hazard Release ; Metabolomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis/toxicity ; }, abstract = {This study investigated the effects of accidental contamination of soils with phenol, toluene, nitric acid, and hydrogen fluoride (HF) by simulating chemical leakage in the soil with/without rain and characterizing the resulting metabolites and microbial. In the case of acid leakage, pH and cation exchange capacity were decreased, and the content of fluoride ion was increased in case of HF leakage. Using mass spectrometry-based metabolomics analysis, phytosphingosine was detected as a distinguishing metabolite in soils contaminated with phenol and HF in rain conditions. Microbial communities were identified by 16s rRNA metagenome sequencing. Sphingomonas was one of the dominant species in soils contaminated with phenol and HF. These results suggest that phytosphingosine and Sphingomonas might be used as biomarkers to evaluate the status of soils contaminated with phenol or HF. Under simulated rain conditions, the species alpha-diversity index of soil microbes and the physicochemical properties of the soil indicated values close to those of the uncontaminated soil. Rain played an important role in the recovery of microbial and metabolic profiles after chemical accidents. Metabolic profiling and microbial community analysis can serve as a diagnostic tool for ecotoxicological research at chemical accident sites.}, } @article {pmid33384967, year = {2020}, author = {Zhao, F and Dong, T and Yuan, KY and Wang, NJ and Xia, FZ and Liu, D and Wang, ZM and Ma, R and Lu, YL and Huang, ZW}, title = {Shifts in the Bacterial Community of Supragingival Plaque Associated With Metabolic-Associated Fatty Liver Disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {581888}, pmid = {33384967}, issn = {2235-2988}, mesh = {Bacteria/genetics ; Humans ; Metagenome ; *Metagenomics ; *Microbiota ; Phylogeny ; }, abstract = {Metabolic-associated fatty liver disease (MAFLD), also known as the hepatic manifestation of metabolic disorders, has become one of the most common chronic liver diseases worldwide. The associations between some oral resident microbes and MAFLD have been described. However, changes to the oral microbial community in patients with MAFLD remain unknown. In this study, variations to the supragingival microbiota of MAFLD patients were identified. The microbial genetic profile of supragingival plaque samples from 24 MAFLD patients and 22 healthy participants were analyzed by 16S rDNA sequencing and bioinformatics analysis. Clinical variables, including indicators of insulin resistance, obesity, blood lipids, and hepatocellular damage, were evaluated with laboratory tests and physical examinations. The results showed that the diversity of the supragingival microbiota in MAFLD patients was significantly higher than that in healthy individuals. Weighted UniFrac principal coordinates analysis and partial least squares discriminant analysis showed that the samples from the MAFLD and control groups formed separate clusters (Adonis, P = 0.0120). There were 27 taxa with differential distributions (linear discriminant analysis, LDA>2.0) between two groups, among which Actinomyces spp. and Prevotella 2 spp. were over-represented in the MAFLD group with highest LDA score, while Neisseria spp. and Bergeyella spp. were more abundant in the control group. Co-occurrence networks of the top 50 abundant genera in the two groups suggested that the inter-genera relationships were also altered in the supragingival plaque of MAFLD patients. In addition, in genus level, as risk factors for the development of MAFLD, insulin resistance was positively correlated with the abundances of Granulicatella, Veillonella, Streptococcus, and Scardovia, while obesity was positively correlated to the abundances of Streptococcus, Oslenella, Scardovia, and Selenomonas. Metagenomic predictions based on Phylogenetic Investigation of Communities by Reconstruction of Unobserved States revealed that pathways related to sugar (mainly free sugar) metabolism were enriched in the supragingival plaque of the MAFLD group. In conclusion, as compared to healthy individuals, component and interactional dysbioses were observed in the supragingival microbiota of the MAFLD group.}, } @article {pmid33382948, year = {2021}, author = {Liu, W and Sun, Z and Ma, C and Zhang, J and Ma, C and Zhao, Y and Wei, H and Huang, S and Zhang, H}, title = {Exposure to soil environments during earlier life stages is distinguishable in the gut microbiome of adult mice.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-13}, pmid = {33382948}, issn = {1949-0984}, mesh = {Animals ; *Environmental Exposure ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Housing, Animal ; Life Cycle Stages/*physiology ; Metagenomics ; Mice ; Soil ; *Soil Microbiology ; }, abstract = {Environmental exposure during earlier life stages can govern the assembly and development of gut microbiota, yet it is insufficiently understood. In this study, ex-germ-free mice were cohoused with distinct soil-microbiota (from desert, steppe, and forest) beddings within 60 days after birth and subsequently transferred to new soil beddings from 60 to 90th day. Using metagenomic shotgun sequencing, firstly, we found soil microbes from natural environments (birthplace) greatly influenced the gut community assembly in the housing experiment. About 27% microbial species and 12% functional components that associated with birthplaces at Day 60 were still discriminatory of birthplaces after transferring mice to new environments. Moreover, prior soil-exposure types are associated with the magnitude of temporal microbiome change due to environmental shifts. The appropriate soil-exposure (e.g., steppe) might help mice gut microbiome adapt to changing environments or host development. Our study demonstrated the continuous soil-exposure history earlier is associated with the gut microbiome individuality and development later.}, } @article {pmid33378601, year = {2021}, author = {Faulkner, CL and Luo, YX and Isaacs, S and Rawlinson, WD and Craig, ME and Kim, KW}, title = {The virome in early life and childhood and development of islet autoimmunity and type 1 diabetes: A systematic review and meta-analysis of observational studies.}, journal = {Reviews in medical virology}, volume = {31}, number = {5}, pages = {1-14}, pmid = {33378601}, issn = {1099-1654}, mesh = {*Autoimmunity ; Child ; *Diabetes Mellitus, Type 1/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Prospective Studies ; Virome/*genetics ; }, abstract = {Viruses are postulated as primary candidate triggers of islet autoimmunity (IA) and type 1 diabetes (T1D), based on considerable epidemiological and experimental evidence. Recent studies have investigated the association between all viruses (the 'virome') and IA/T1D using metagenomic next-generation sequencing (mNGS). Current associations between the early life virome and the development of IA/T1D were analysed in a systematic review and meta-analysis of human observational studies from Medline and EMBASE (published 2000-June 2020), without language restriction. Inclusion criteria were as follows: cohort and case-control studies examining the virome using mNGS in clinical specimens of children ≤18 years who developed IA/T1D. The National Health and Medical Research Council level of evidence scale and Newcastle-Ottawa scale were used for study appraisal. Meta-analysis for exposure to specific viruses was performed using random-effects models, and the strength of association was measured using odds ratios (ORs) and 95% confidence intervals (CIs). Eligible studies (one case-control, nine nested case-control) included 1,425 participants (695 cases, 730 controls) and examined IA (n = 1,023) or T1D (n = 402). Meta-analysis identified small but significant associations between IA and number of stool samples positive for all enteroviruses (OR 1.14, 95% CI 1.00-1.29, p = 0.05; heterogeneity χ[2] = 1.51, p = 0.68, I[2] = 0%), consecutive positivity for enteroviruses (1.55, 1.09-2.20, p = 0.01; χ[2] = 0.19, p = 0.91, I[2] = 0%) and number of stool samples positive specifically for enterovirus B (1.20, 1.01-1.42, p = 0.04; χ[2] = 0.03, p = 0.86, I[2] = 0%). Virome analyses to date have demonstrated associations between enteroviruses and IA that may be clinically significant. However, larger prospective mNGS studies with more frequent sampling and follow-up from pregnancy are required to further elucidate associations between early virus exposure and IA/T1D.}, } @article {pmid33378284, year = {2020}, author = {Afolayan, AO and Ayeni, FA}, title = {Metagenomic Analysis of Bacterial Communities in Water and Soil of the Fulani and non-Fulani in Nigeria.}, journal = {Journal of infection in developing countries}, volume = {14}, number = {12}, pages = {}, doi = {10.3855/jidc.12975}, pmid = {33378284}, issn = {1972-2680}, mesh = {DNA, Bacterial ; Humans ; Metagenomics ; *Microbiota ; Nigeria ; Proteobacteria/classification/genetics ; Pseudomonas/classification/genetics ; Public Health ; RNA, Ribosomal, 16S ; Rural Population ; *Soil Microbiology ; *Water Microbiology ; }, abstract = {INTRODUCTION: Interactions between environmental factors (water and soil) and humans are inevitable, particularly in rural and semi-urbanized regions. As such, knowledge on the microbial constituents of these environmental factors is key to understanding potential risk to public health. However, the microbial profile of soil and water present in vulnerable human communities in Nigeria is currently unknown. This study sought to investigate the composition of soil and water microbiota in the environment inhabited by recently studied human communities (the Fulani nomadic group and the urbanized Jarawa ethnic group) and estimate the contribution of these environmental factors to the microbiome of the aforementioned human communities.

METHODOLOGY: Soil and water samples were collected from the Fulani and non-Fulani community in Jengre (Plateau State, Nigeria) and Jos (Plateau State, Nigeria), respectively. Genomic DNA was extracted from these environmental samples, followed by Illumina sequencing of the V4 region of the 16S rRNA gene and bioinformatics analysis via Quantitative Insights into Microbial Ecology QIIME.

RESULTS: There is abundance of Proteobacteria (43%) signature members in soil samples obtained from both human communities. Analysis of the water samples revealed the abundance of Proteobacteria, particularly in water sourced from the borehole (Fulani). Pseudomonas (30%) had higher relative abundance in the drinking water of the Fulani.

CONCLUSIONS: The drinking water of the Fulani could be a potential health risk to the studied Fulani community. Factors that increase the abundance of public health threats and health risk, such as hygiene practices, soil and water quality need to be studied further for the improvement of health in vulnerable populations.}, } @article {pmid33376062, year = {2021}, author = {Brubaker, L and Luu, S and Hoffman, K and Wood, A and Navarro Cagigas, M and Yao, Q and Petrosino, J and Fisher, W and Van Buren, G}, title = {Microbiome changes associated with acute and chronic pancreatitis: A systematic review.}, journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]}, volume = {21}, number = {1}, pages = {1-14}, pmid = {33376062}, issn = {1424-3911}, support = {T32 HL139425/HL/NHLBI NIH HHS/United States ; U01 DK108326/DK/NIDDK NIH HHS/United States ; }, mesh = {Gastrointestinal Microbiome/*physiology ; Humans ; Pancreatitis/metabolism/*microbiology ; Pancreatitis, Chronic/metabolism/microbiology ; }, abstract = {BACKGROUND: Altered intestinal microbiota has been reported in pancreatic disorders, however, it remains unclear whether these changes alter the course of disease in patients with acute (AP) and chronic pancreatitis (CP), or whether these disease states alter the environment to enable pathogenic microbial composition changes to occur. We undertook a systematic review to characterize the gut microbiome in pancreatitis patients.

METHODS: MEDLINE and EMBASE were searched for studies on microbiota in pancreatitis published from January 1, 2000 to June 5, 2020. Animal studies, reviews, case reports, and non-English articles were excluded. A frequency analysis was performed for outcomes reported in ≥2 studies and studies were analyzed for risk of bias and quality of evidence.

RESULTS: 22 papers met inclusion criteria; 15 included AP, 7 included CP. No studies were appropriately designed to assess whether alterations in the gut microbiome exacerbate pancreatitis or develop as a result of pancreatitis. We did identify several patterns of microbiome changes that are associated with pancreatitis. The gut microbiome demonstrated decreased alpha diversity in 3/3 A P studies and 3/3 C P studies. Beta diversity analysis revealed differences in bacterial community composition in the gut microbiome in 2/2 A P studies and 3/3 C P studies. Functionally, gut microbiome changes were associated with infectious pathways in AP and CP. Several studies suffered from high risk of bias and inadequate quality.

CONCLUSIONS: Detecting differences in microbial composition associated with AP and CP may represent a diagnostic tool. Appropriately controlled longitudinal studies are needed to determine whether microbiome changes are causative or reactive in pancreatitis.}, } @article {pmid33375982, year = {2021}, author = {Kalyani, DC and Reichenbach, T and Aspeborg, H and Divne, C}, title = {A homodimeric bacterial exo-β-1,3-glucanase derived from moose rumen microbiome shows a structural framework similar to yeast exo-β-1,3-glucanases.}, journal = {Enzyme and microbial technology}, volume = {143}, number = {}, pages = {109723}, doi = {10.1016/j.enzmictec.2020.109723}, pmid = {33375982}, issn = {1879-0909}, mesh = {Animals ; Glycoside Hydrolases/genetics/metabolism ; *Microbiota ; Phylogeny ; Rumen ; *Saccharomyces cerevisiae/genetics/metabolism ; Substrate Specificity ; }, abstract = {The impact of various β-glucans on the gut microbiome and immune system of vertebrates is becoming increasingly recognized. Besides the fundamental interest in understanding how β-glucans support human and animal health, enzymes that metabolize β-glucans are of interest for hemicellulose bioprocessing. Our earlier metagenomic analysis of the moose rumen microbiome identified a gene coding for a bacterial enzyme with a possible role in β-glucan metabolization. Here, we report that the enzyme, mrbExg5, has exo-β-1,3-glucanase activity on β-1,3-linked glucooligosaccharides and laminarin, but not on β-1,6- or β-1,4-glycosidic bonds. Longer oligosaccharides are good substrates, while shorter substrates are readily transglycosylated into longer products. The enzyme belongs to glycoside hydrolase subfamily GH5_44, which is a close phylogenetic neighbor of the subfamily GH5_9 exo-β-1,3-glucanases of the yeasts Saccharomyces cerevisiae and Candida albicans. The crystal structure shows that unlike the eukaryotic relatives, mrbExg5 is a functional homodimer with a binding region characterized by: (i) subsite +1 can accommodate a branched sugar on the β-1,3-glucan backbone; (ii) subsite +2 is restricted to exclude backbone substituents; and (iii) a fourth subsite (+3) formed by a unique loop. mrbExg5 is the first GH5_44 enzyme to be structurally characterized, and the first bacterial GH5 with exo-β-1,3-glucanase activity.}, } @article {pmid33374068, year = {2020}, author = {Gao, J and Zhang, SH and Wang, R and Jin, PK}, title = {[Metagenomic Insights into Salinity Build-up in Microbial Communities and Metabolism of Hydrolytic Bioreactor Treating High-color PDWW].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {41}, number = {12}, pages = {5518-5526}, doi = {10.13227/j.hjkx.202005080}, pmid = {33374068}, issn = {0250-3301}, mesh = {Bioreactors ; Coloring Agents ; Hydrolysis ; *Microbiota/genetics ; Printing, Three-Dimensional ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sewage ; Waste Disposal, Fluid ; *Wastewater ; }, abstract = {In this study, to solve the problem of salinity enrichment in industrial wastewater recycling, a hydrolytic bioreactor was continuously operated to treat high-color printing and dyeing wastewater (PDWW) with salinity build-up. Nearly complete color removal was achieved even with salinity build-ups from 0.5 to 4 g·L[-1] in the influent. Pyrosequencing of 16S rRNA genes showed that the salinity build-up results in the decrease of microbial species from 882 to 631; however, the biodiversity of the bacterial community remains stable. Metagenomic analysis indicated that salinity build-up caused no obvious effect on the overall function of the bacterial community, but altered the abundance of specific decoloring genes. Proteobacteria dominated in the bioreactor, and Methanothrix and Geobacter were the dominant genera under low salinity conditions. Proteobacteria increased in abundance with salinity build-up. Desulfovibrio and Desulfococcus were the two predominant genera in the bioreactor fed with sodium sulphate salinity build-up, demonstrating opposite responses to the sodium stress. PICRUSt functional analysis showed that the relative abundance of the decolorizing enzymes SOD1 and SOD2 decreased significantly, but the relative abundance of CAT and TYR increased, ensuring the stability of the decolorizing function of the hydrolysis biological system. From the perspective of the functional genes of hydrolysis decolorization, this study explored the effect of salinity build-up on the microbial community and function of hydrolysis, providing a theoretical basis for the study of decolorization and organic matter removal mechanism of PDWW under the condition of salinity build-up.}, } @article {pmid33373390, year = {2020}, author = {Hull, JJA and Qi, M and Montmayeur, AM and Kumar, D and Velasquez, DE and Moon, SS and Magaña, LC and Betrapally, N and Ng, TFF and Jiang, B and Marthaler, D}, title = {Metagenomic sequencing generates the whole genomes of porcine rotavirus A, C, and H from the United States.}, journal = {PloS one}, volume = {15}, number = {12}, pages = {e0244498}, pmid = {33373390}, issn = {1932-6203}, mesh = {Animals ; Evolution, Molecular ; Genome, Viral/*genetics ; Metagenomics ; Phylogeny ; Rotavirus/*genetics/isolation & purification ; Rotavirus Infections/diagnosis/prevention & control/*veterinary/virology ; Sus scrofa/*virology ; Swine ; Swine Diseases/diagnosis/prevention & control/*virology ; United States ; Virome/genetics ; Whole Genome Sequencing ; }, abstract = {The genus Rotavirus comprises eight species, designated A to H, and two recently identified tentative species I in dogs and J in bats. Species Rotavirus A, B, C and H (RVA, RVB, RVC and RVH) have been detected in humans and animals. While human and animal RVA are well characterized and defined, complete porcine genome sequences in the GenBank are limited compared to human strains. Here, we used a metagenomic approach to sequence the 11 segments of RVA, RVC and RVH strains from piglets in the United States (US) and explore the evolutionary relations of these RV species. Metagenomics identified Astroviridae, Picornaviridae, Caliciviridae, Coronoviridae in samples MN9.65 and OK5.68 while Picobirnaviridae and Arteriviridae were only identified in sample OK5.68. Whole genome sequencing and phylogenetic analyses identified multiple genotypes with the RVA of strain MN9.65 and OK5.68, with the genome constellation of G5/G9-P[7]/P[13]-I5/I5- R1/R1-C1-M1-A8-N1-T7-E1/E1-H1 and G5/G9-P[6]/P[7]-I5-R1/R1-C1-M1-A8-N1-T1/T7-E1/E1-H1, respectively. The RVA strains had a complex evolutionary relationship with other mammalian strains. The RVC strain OK5.68 had a genome constellation of G9-P[6]-I1-R1-C5-M6-A5-N1-T1-E1-H1, and shared an evolutionary relationship with porcine strains from the US. The RVH strains MN9.65 and OK5.68 had the genome constellation of G5-P1-I1-R1-C1-M1-A5-N1-T1-E4-H1 and G5-P1-I1-R1-C1-M1-A5-N1-T1-E1-H1, indicating multiple RVH genome constellations are circulating in the US. These findings allow us to understand the complexity of the enteric virome, develop improved screening methods for RVC and RVH strains, facilitate expanded rotavirus surveillance in pigs, and increase our understanding of the origin and evolution of rotavirus species.}, } @article {pmid33372909, year = {2020}, author = {Fedorov, DE and Olekhnovich, EI and Pavlenko, AV and Klimina, KM and Pokataev, IA and Manolov, AI and Konanov, DN and Veselovsky, VA and Ilina, EN}, title = {[Intestinal microbiome as a predictor of the anti-PD-1 therapy success: metagenomic data analysis].}, journal = {Biomeditsinskaia khimiia}, volume = {66}, number = {6}, pages = {502-507}, doi = {10.18097/PBMC20206606502}, pmid = {33372909}, issn = {2310-6972}, mesh = {Antibodies ; Data Analysis ; *Gastrointestinal Microbiome ; Humans ; Immunotherapy ; Metagenome ; Programmed Cell Death 1 Receptor ; }, abstract = {Anti-PD-1 immunotherapy has a large impact on cancer treatment but the rate of positive treatment outcomes is 40-45% and depends on many factors. One of the factors affecting the outcome of immunotherapy is the gut microbiota composition. This effect has been demonstrated both in model objects and in clinical patients groups. However, in order to identify clear causal relationships between microbiota and anti-PD1 immunotherapy response, it is necessary to expand the number of patients and experimental samples. This work presents an analysis of metagenomic data obtained using whole-genome sequencing of stool samples from melanoma patients (n=45) with different responses to anti-PD1 therapy. The analysis of the differential representation of microbial species has shown a difference in the composition of the microbiota between the experimental groups. Results of this study indicate existence of a strong link between the composition of the gut microbiota and the outcome of anti-PD1 therapy. Expansion of similar research may help develop additional predictive tools for the outcome of anti-PD1 cancer immunotherapy, as well as increase its effectiveness.}, } @article {pmid33372654, year = {2020}, author = {Belcour, A and Frioux, C and Aite, M and Bretaudeau, A and Hildebrand, F and Siegel, A}, title = {Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {33372654}, issn = {2050-084X}, support = {BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; ANR-10-BTBR-04//ANR/ ; BBS/E/F/000PR1035/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacteria/genetics/*metabolism ; Cattle ; Databases, Factual ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Metagenomics ; *Software ; Species Specificity ; }, abstract = {To capture the functional diversity of microbiota, one must identify metabolic functions and species of interest within hundreds or thousands of microorganisms. We present Metage2Metabo (M2M) a resource that meets the need for de novo functional screening of genome-scale metabolic networks (GSMNs) at the scale of a metagenome, and the identification of critical species with respect to metabolic cooperation. M2M comprises a flexible pipeline for the characterisation of individual metabolisms and collective metabolic complementarity. In addition, M2M identifies key species, that are meaningful members of the community for functions of interest. We demonstrate that M2M is applicable to collections of genomes as well as metagenome-assembled genomes, permits an efficient GSMN reconstruction with Pathway Tools, and assesses the cooperation potential between species. M2M identifies key organisms by reducing the complexity of a large-scale microbiota into minimal communities with equivalent properties, suitable for further analyses.}, } @article {pmid33371686, year = {2021}, author = {Jiang, L and Luo, C and Zhang, D and Song, M and Mei, W and Sun, Y and Zhang, G}, title = {Shifts in a Phenanthrene-Degrading Microbial Community are Driven by Carbohydrate Metabolism Selection in a Ryegrass Rhizosphere.}, journal = {Environmental science & technology}, volume = {55}, number = {2}, pages = {962-973}, doi = {10.1021/acs.est.0c04951}, pmid = {33371686}, issn = {1520-5851}, mesh = {Biodegradation, Environmental ; Carbohydrate Metabolism ; *Lolium ; *Microbiota ; *Phenanthrenes/analysis ; Phylogeny ; Plant Roots/chemistry ; Rhizosphere ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Plants usually promote pollutant bioremediation by several mechanisms including modifying the diversity of functional microbial species. However, conflicting results are reported that root exudates have no effects or negative effects on organic pollutant degradation. In this study, we investigated the roles of ryegrass in phenanthrene degradation in soils using DNA stable isotope probing (SIP) and metagenomics to reveal a potential explanation for conflicting results among phytoremediation studies. Phenanthrene biodegradation efficiency was improved by 8% after 14 days of cultivation. Twelve and ten operational taxonomic units (OTUs) were identified as active phenanthrene degraders in non-rhizosphere and rhizosphere soils, respectively. The active phenanthrene degraders exhibited higher average phylogenetic distances in rhizosphere soils (0.33) than non-rhizosphere soils (0.26). The Ka/Ks values (the ratio of nonsynonymous to synonymous substitutions) were about 10.37% higher in the rhizosphere treatment among >90% of all key carbohydrate metabolism-related genes, implying that ryegrass may be an important driver of microbial community variation in the rhizosphere by relieving the carbohydrate metabolism pressure and improving the survival ability of r-strategy microbes. Most Ka/Ks values of root-exudate-related metabolism genes exhibited little change, except for fumarate hydratase that increased 13-fold in the rhizosphere compared to that in the non-rhizosphere treatment. The Ka/Ks values of less than 50% phenanthrene-degradation-related genes were affected, 30% of which increased and 70% behaved oppositely. Genes with altered Ka/Ks values had a low percentage and followed an inconsistent changing tendency, indicating that phenanthrene and its metabolites are not major factors influencing the active degraders. These results suggested the importance of carbohydrate metabolism, especially fumaric acid, in rhizosphere community shift, and hinted at a new hypothesis that the rhizosphere effect on phenanthrene degradation efficiency depends on the existence of active degraders that have competitive advantages in carbohydrate and fumaric acid metabolism.}, } @article {pmid33369664, year = {2021}, author = {Díaz, L and Castellá, G and Bragulat, MR and Martorell, J and Paytuví-Gallart, A and Sanseverino, W and Cabañes, FJ}, title = {External ear canal mycobiome of some rabbit breeds.}, journal = {Medical mycology}, volume = {59}, number = {7}, pages = {683-693}, doi = {10.1093/mmy/myaa097}, pmid = {33369664}, issn = {1460-2709}, support = {//University of Alabama at Birmingham/ ; }, mesh = {Animals ; *Breeding ; DNA, Ribosomal/genetics ; Ear Canal/*microbiology ; High-Throughput Nucleotide Sequencing ; Malassezia/classification/*genetics/growth & development ; Metagenomics ; Mycobiome/*genetics ; Rabbits ; }, abstract = {UNLABELLED: The genus Malassezia is part of the normal skin mycobiota of a wide range of warm-blooded animals. In this genus, M. cuniculi is the only species described from rabbits. However, Malassezia species are rarely studied in lagomorphs. In the present study, the presence of Malassezia was assessed in samples from the external ear canal of healthy rabbits of different breeds. Cytological and culture techniques, Sanger sequencing, and Next-generation sequencing (NGS) were used to describe the ear mycobiota in the samples. Although no growth was observed in the cultured plates, cytological examination revealed the presence of round cells similar to those of Malassezia yeasts. For metagenomics analysis, the D1/D2 domain of the large subunit of the ribosomal DNA (LSU rDNA) was PCR amplified and the resulting reads were mapped against a custom-made cured database of 26S fungal sequences. NGS analysis revealed that Basidiomycota was the most abundant phylum in all the samples followed by Ascomycota. Malassezia was the most common genus presenting the highest abundance in the external ear canal. Malassezia phylotype 131 and M. cuniculi were the main sequences detected in the external auditory canal of rabbits. The study included both lop-eared and erect-eared rabbits and no differences were observed in the results when comparing both groups. This is the first attempt to study the external ear canal mycobiome of rabbits of different breeds using NGS.

LAY SUMMARY: In the present study, the presence of Malassezia was assessed in samples from the external ear canal of healthy rabbits of different breeds. Cytological and culture techniques, Sanger sequencing, and Next-generation sequencing (NGS) were used to describe the ear mycobiota in the samples.}, } @article {pmid33369241, year = {2021}, author = {Szoboszlay, M and Tebbe, CC}, title = {Hidden heterogeneity and co-occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates.}, journal = {MicrobiologyOpen}, volume = {10}, number = {1}, pages = {e1144}, pmid = {33369241}, issn = {2045-8827}, mesh = {Acidobacteria/classification/*genetics ; Archaea/classification/*genetics ; Base Sequence ; Biodiversity ; DNA, Archaeal/*genetics ; DNA, Bacterial/*genetics ; Fungi/classification/genetics ; High-Throughput Nucleotide Sequencing ; Metagenome/*genetics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Sequencing PCR-amplified gene fragments from metagenomic DNA is a widely applied method for studying the diversity and dynamics of soil microbial communities. Typically, DNA is extracted from 0.25 to 1 g of soil. These amounts, however, neglect the heterogeneity of soil present at the scale of soil aggregates and thus ignore a crucial scale for understanding the structure and functionality of soil microbial communities. Here, we show with a nitrogen-depleted agricultural soil the impact of reducing the amount of soil used for DNA extraction from 250 mg to approx. 1 mg to access spatial information on the prokaryotic community structure, as indicated by 16S rRNA gene amplicon analyses. Furthermore, we demonstrate that individual aggregates from the same soil differ in their prokaryotic community compositions. The analysis of 16S rRNA gene amplicon sequences from individual soil aggregates allowed us, in contrast to 250 mg soil samples, to construct a co-occurrence network that provides insight into the structure of microbial associations in the studied soil. Two dense clusters were apparent in the network, one dominated by Thaumarchaeota, known to be capable of ammonium oxidation at low N concentrations, and the other by Acidobacteria subgroup 6, representing an oligotrophic lifestyle to obtain energy from SOC. Overall this study demonstrates that DNA obtained from individual soil aggregates provides new insights into how microbial communities are assembled.}, } @article {pmid33369229, year = {2021}, author = {Fu, H and Zhang, L and Fan, C and Liu, C and Li, W and Cheng, Q and Zhao, X and Jia, S and Zhang, Y}, title = {Environment and host species identity shape gut microbiota diversity in sympatric herbivorous mammals.}, journal = {Microbial biotechnology}, volume = {14}, number = {4}, pages = {1300-1315}, pmid = {33369229}, issn = {1751-7915}, support = {31670394//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacteria/genetics ; Firmicutes/genetics ; *Gastrointestinal Microbiome ; *Lagomorpha ; *Microbiota ; }, abstract = {The previous studies have reported that the mammalian gut microbiota is a physiological consequence; nonetheless, the factors influencing its composition and function remain unclear. In this study, to evaluate the contributions of the host and environment to the gut microbiota, we conducted a sequencing analysis of 16S rDNA and shotgun metagenomic DNA from plateau pikas and yaks, two sympatric herbivorous mammals, and further compared the sequences in summer and winter. The results revealed that both pikas and yaks harboured considerably more distinct communities between summer and winter. We detected the over-representation of Verrucomicrobia and Proteobacteria in pikas, and Archaea and Bacteroidetes in yaks. Firmicutes and Actinobacteria, associated with energy-efficient acquisition, significantly enriched in winter. The diversity of the microbial community was determined by the interactive effects between the host and season. Metagenomic analysis revealed that methane-metabolism-related pathway of yaks was significantly enriched in summer, while some pathogenic pathways were more abundant in pikas. Both pikas and yaks had a higher capacity for lipid degradation in winter. Pika and yak shared more OTUs when food shortage occurred in winter, and this caused a convergence in gut microbial composition and function. From winter to summer, the network module number increased from one to five in pikas, which was different in yaks. Our study demonstrates that the host is a dominant factor in shaping the microbial communities and that seasonality promotes divergence or convergence based on dietary quality across host species identity.}, } @article {pmid33363050, year = {2020}, author = {Kishikawa, T and Ogawa, K and Motooka, D and Hosokawa, A and Kinoshita, M and Suzuki, K and Yamamoto, K and Masuda, T and Matsumoto, Y and Nii, T and Maeda, Y and Nakamura, S and Inohara, H and Mochizuki, H and Okuno, T and Okada, Y}, title = {A Metagenome-Wide Association Study of Gut Microbiome in Patients With Multiple Sclerosis Revealed Novel Disease Pathology.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {585973}, pmid = {33363050}, issn = {2235-2988}, mesh = {*Gastrointestinal Microbiome/genetics ; Gemella ; Genome-Wide Association Study ; Humans ; Metagenome ; *Multiple Sclerosis ; Phylogeny ; }, abstract = {While microbiome plays key roles in the etiology of multiple sclerosis (MS), its mechanism remains elusive. Here, we conducted a comprehensive metagenome-wide association study (MWAS) of the relapsing-remitting MS gut microbiome (ncase = 26, ncontrol = 77) in the Japanese population, by using whole-genome shotgun sequencing. Our MWAS consisted of three major bioinformatic analytic pipelines (phylogenetic analysis, functional gene analysis, and pathway analysis). Phylogenetic case-control association tests showed discrepancies of eight clades, most of which were related to the immune system (false discovery rate [FDR] < 0.10; e.g., Erysipelatoclostridium_sp. and Gemella morbillorum). Gene association tests found an increased abundance of one putative dehydrogenase gene (Clo1100_2356) and one ABC transporter related gene (Mahau_1952) in the MS metagenome compared with controls (FDR < 0.1). Molecular pathway analysis of the microbiome gene case-control comparisons identified enrichment of multiple Gene Ontology terms, with the most significant enrichment on cell outer membrane (P = 1.5 × 10[-7]). Interaction between the metagenome and host genome was identified by comparing biological pathway enrichment between the MS MWAS and the MS genome-wide association study (GWAS) results (i.e., MWAS-GWAS interaction). No apparent discrepancies in alpha or beta diversities of metagenome were found between MS cases and controls. Our shotgun sequencing-based MWAS highlights novel characteristics of the MS gut microbiome and its interaction with host genome, which contributes to our understanding of the microbiome's role in MS pathophysiology.}, } @article {pmid33363048, year = {2020}, author = {Shi, W and Shen, L and Zou, W and Wang, J and Yang, J and Wang, Y and Liu, B and Xie, L and Zhu, J and Zhang, Z}, title = {The Gut Microbiome Is Associated With Therapeutic Responses and Toxicities of Neoadjuvant Chemoradiotherapy in Rectal Cancer Patients-A Pilot Study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {562463}, pmid = {33363048}, issn = {2235-2988}, mesh = {*Gastrointestinal Microbiome ; Humans ; Neoadjuvant Therapy ; Phylogeny ; Pilot Projects ; *Rectal Neoplasms/therapy ; }, abstract = {Responses to neoadjuvant chemoradiotherapy (nCRT) and therapy-related toxicities in rectal cancer vary among patients. To provide the individualized therapeutic option for each patient, predictive markers of therapeutic responses and toxicities are in critical need. We aimed to identify the association of gut microbiome with and its potential predictive value for therapeutic responses and toxicities. In the present study, we collected fecal microbiome samples from patients with rectal cancer at treatment initiation and just after nCRT. Taxonomic profiling via 16S ribosomal RNA gene sequencing was performed on all samples. Patients were classified as responders versus non-responders. Patients were grouped into no or mild diarrhea and severe diarrhea. STAMP and high-dimensional class comparisons via linear discriminant analysis of effect size (LEfSe) were used to compare the compositional differences between groups. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was utilized to predict differences in metabolic function between groups. Ten patients were classified as responders and 12 patients were classified as non-responders. Fourteen patients experienced no or mild diarrhea and 8 patients experienced severe diarrhea. Several bacteria taxa with significantly different relative abundances before and after nCRT were identified. Similarly, several baseline bacteria taxa and predicted pathways with significantly different relative abundances between responders and non-responders or between patients no or mild diarrhea and severe diarrhea were identified. Specifically, Shuttleworthia was identified as enriched in responders and several bacteria taxa in the Clostridiales order etc. were identified as enriched in non-responders. Pathways including fatty acid metabolism were predicted to be enriched in responders. In addition, Bifidobacterium, Clostridia, and Bacteroides etc. were identified as enriched in patients with no or mild diarrhea. Pathways including primary bile acid biosynthesis were predicted to be enriched in patients with no or mild diarrhea. Together, the microbiota and pathway markers identified in this study may be utilized to predict the therapeutic responses and therapy-related toxicities of nCRT in patients with rectal cancer. More patient data is needed to verify the current findings and the results of metagenomic, metatranscriptomic, and metabolomic analyses will further mine key biomarkers at the compositional and functional level.}, } @article {pmid33360047, year = {2021}, author = {Pastor-Villaescusa, B and Plaza-Díaz, J and Egea-Zorrilla, A and Leis, R and Bueno, G and Hoyos, R and Vázquez-Cobela, R and Latorre, M and Cañete, MD and Caballero-Villarraso, J and Gil, Á and Cañete, R and Aguilera, CM}, title = {Evaluation of the gut microbiota after metformin intervention in children with obesity: A metagenomic study of a randomized controlled trial.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {134}, number = {}, pages = {111117}, doi = {10.1016/j.biopha.2020.111117}, pmid = {33360047}, issn = {1950-6007}, mesh = {Adolescent ; Age Factors ; Bacteria/*drug effects/genetics/growth & development ; Child ; Double-Blind Method ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Hypoglycemic Agents/*therapeutic use ; Intestines/*microbiology ; Life Style ; Male ; *Metagenome ; *Metagenomics ; Metformin/*therapeutic use ; Pediatric Obesity/diagnosis/*drug therapy/microbiology ; Spain ; Time Factors ; Treatment Outcome ; }, abstract = {BACKGROUND: Metformin, a first-line oral antidiabetic agent that has shown promising results in terms of treating childhood and adolescent obesity, might influence the composition of the gut microbiota. We aimed to evaluate whether the gut microbiota of non-diabetic children with obesity changes after a metformin intervention.

METHODS: The study was a multicenter and double-blind randomized controlled trial in 160 children with obesity. Children were randomly assigned to receive either metformin (1 g/day) or placebo for 6 months in combination with healthy lifestyle recommendations in both groups. Then, we conducted a metagenomic analysis in a subsample obtained from 33 children (15 metformin, 18 placebo). A linear mixed-effects model (LMM) was used to determine the abundance changes from baseline to six months according to treatment. To analyze the data by clusters, a principal component analysis was performed to understand whether lifestyle habits have a different influence on the microbiota depending on the treatment group.

RESULTS: Actinobacteria abundance was higher after placebo treatment compared with metformin. However, the interaction time x treatment just showed a trend to be significant (4.6% to 8.1% after placebo vs. 3.8 % to 2.6 % after metformin treatment, p = 0.055). At genus level, only the abundance of Bacillus was significantly higher after the placebo intervention compared with metformin (2.5% to 5.7% after placebo vs. 1.5 % to 0.8 % after metformin treatment, p = 0.044). Furthermore, different ensembles formed by Firmicutes, Bacteroidetes, and Verrucomicrobia were found according to the interventions under a similar food consumption.

CONCLUSION: Further studies with a large sample size controlled by lifestyle patterns are required in obese children and adolescents to clarify whether metformin might trigger gut microbiota alterations.

TRIAL REGISTRATION: Registered on the European Clinical Trials Database (EudraCT, ID: 2010-023061-21) on 14 November 2011.}, } @article {pmid33351849, year = {2020}, author = {Kempnich, MW and Sison-Mangus, MP}, title = {Presence and abundance of bacteria with the Type VI secretion system in a coastal environment and in the global oceans.}, journal = {PloS one}, volume = {15}, number = {12}, pages = {e0244217}, pmid = {33351849}, issn = {1932-6203}, mesh = {Bacteria/classification/*genetics/isolation & purification ; *Biomass ; Microbiota ; Seawater/*microbiology ; *Soil Microbiology ; Type VI Secretion Systems/*genetics ; }, abstract = {Marine bacteria employ various strategies to maintain their competitive advantage over others in a mixed community. The use of Type VI Secretion Systems (T6SS), a protein secretion apparatus used as a molecular weapon for interbacterial competition and eukaryotic interactions, is one of the competitive strategies that is least studied among heterotrophic bacteria living in the water column. To get an insight into the temporal and spatial distribution of bacteria with T6SS in this portion of the marine environment, we examine the presence and abundance of T6SS-bearing bacteria at both local and global scales through the use of metagenome data from water samples obtained from the coast of Monterey Bay and the TARA Oceans project. We also track the abundance of T6SS-harboring bacteria through a two-year time series of weekly water samples in the same coastal site to examine the environmental factors that may drive their presence and abundance. Among the twenty-one T6SS-bearing bacterial genera examined, we found several genera assume a particle-attached lifestyle, with only a few genera having a free-living lifestyle. The abundance of T6SS-harboring bacteria in both niches negatively correlates with the abundance of autotrophs. Globally, we found that T6SS genes are much more abundant in areas with low biological productivity. Our data suggest that T6SS-harboring bacteria tend to be abundant spatially and temporally when organic resources are limited. This ecological study agrees with the patterns observed from several in vitro studies; that T6SS could be an adaptive strategy employed by heterotrophic bacteria to obtain nutrients or reduce competition when resources are in limited quantity.}, } @article {pmid33350070, year = {2021}, author = {Meziti, A and Nikouli, E and Hatt, JK and Konstantinidis, KT and Kormas, KA}, title = {Time series metagenomic sampling of the Thermopyles, Greece, geothermal springs reveals stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs.}, journal = {Environmental microbiology}, volume = {23}, number = {7}, pages = {3710-3726}, doi = {10.1111/1462-2920.15373}, pmid = {33350070}, issn = {1462-2920}, mesh = {Bacteria/genetics ; Greece ; *Hot Springs ; Metagenome ; *Microbiota/genetics ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfur ; }, abstract = {Geothermal springs are essentially unaffected by environmental conditions aboveground as they are continuously supplied with subsurface water with little variability in chemistry. Therefore, changes in their microbial community composition and function, especially over a long period, are expected to be limited but this assumption has not yet been rigorously tested. Toward closing this knowledge gap, we applied whole metagenome sequencing to 17 water samples collected between 2010 and 2016 from the Thermopyles sulfur-rich geothermal springs in central Greece. As revealed by 16S rRNA gene fragments recovered in the metagenomes, Epsilonproteobacteria-related operational taxonomic units (OTUs) dominated most samples and grouping of samples based on OTU abundances exhibited no apparent seasonal pattern. Similarities between samples regarding functional gene content were high, with all samples sharing >70% similarity in functional pathways. These community-wide patterns were further confirmed by analysis of metagenome-assembled genomes (MAGs), which showed that novel species and genera of the chemoautotrophic Campylobacterales order dominated the springs. These MAGs carried different pathways for thiosulfate or sulfide oxidation coupled to carbon fixation pathways. Overall, our study showed that even in the long term, functions of microbial communities in a moderately hot terrestrial spring remain stable, presumably driving the corresponding stability in community structure.}, } @article {pmid33348106, year = {2021}, author = {Ren, X and Hao, S and Yang, C and Yuan, L and Zhou, X and Zhao, H and Yao, J}, title = {Alterations of intestinal microbiota in liver cirrhosis with muscle wasting.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {83}, number = {}, pages = {111081}, doi = {10.1016/j.nut.2020.111081}, pmid = {33348106}, issn = {1873-1244}, mesh = {Bacteroides ; Cross-Sectional Studies ; Escherichia coli ; *Gastrointestinal Microbiome ; Humans ; Liver Cirrhosis/complications/pathology ; Muscle, Skeletal/pathology ; Peptostreptococcus ; }, abstract = {OBJECTIVES: The intestinal microbiota plays an important role in the nutritional status and energy metabolism of the host. Liver cirrhosis is accompanied by muscle wasting or sarcopenia. The aim of this study was to to explore the changes in intestinal microbiota in patients with liver cirrhosis and muscle wasting by using metagenomics.

METHODS: This was a cross-sectional study of patients with (n = 30) and without (n = 30) muscle wasting and age- and sex-matched healthy controls (n = 30) to evaluate changes in intestinal microbiota by metagenomic gene sequencing. Muscle wasting was determined by the third lumbar vertebrae skeletal muscle index (L3 SMI).

RESULTS: The Shannon index, which represents species diversity, of patients in the muscle-wasting group (2.11 ± 0.88) was lower than in the non-muscle-wasting group (2.64 ± 0.68; P = 0.039), which was significantly lower than in the healthy control group (2.70 ± 0.53; P = 0.023). There were 17 microbial species with significant differences in relative abundance between the two groups (linear discriminant analysis score >2; P < 0.05). The relative abundance of Escherichia coli, Peptostreptococcus stomatis, and Bacteroides uniformis showed the most significant association with L3 SMI.

CONCLUSIONS: There were compositional alterations in intestinal microbiota in patients with liver cirrhosis and muscle wasting. L3 SMI is closely related to E. coli, P. stomatis, and B. uniformis in liver cirrhosis. Further interventional studies are needed to confirm whether improving intestinal microbiota can improve the nutritional status of patients with liver cirrhosis.}, } @article {pmid33347881, year = {2021}, author = {Iliev, ID and Cadwell, K}, title = {Effects of Intestinal Fungi and Viruses on Immune Responses and Inflammatory Bowel Diseases.}, journal = {Gastroenterology}, volume = {160}, number = {4}, pages = {1050-1066}, pmid = {33347881}, issn = {1528-0012}, support = {UL1 TR001445/TR/NCATS NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; R01 DK093668/DK/NIDDK NIH HHS/United States ; R01 HL125816/HL/NHLBI NIH HHS/United States ; R01 AI140754/AI/NIAID NIH HHS/United States ; R01 AI130945/AI/NIAID NIH HHS/United States ; R01 AI121244/AI/NIAID NIH HHS/United States ; R56 AI137157/AI/NIAID NIH HHS/United States ; R01 DK121977/DK/NIDDK NIH HHS/United States ; R21 AI146957/AI/NIAID NIH HHS/United States ; R01 DK113136/DK/NIDDK NIH HHS/United States ; R01 HL123340/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; COVID-19/complications ; Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/*physiology ; Humans ; Immunity/*immunology ; Inflammatory Bowel Diseases/*etiology ; Lectins, C-Type/physiology ; Mycobiome/*physiology ; SARS-CoV-2 ; Th1 Cells/immunology ; Virome/*physiology ; }, abstract = {The intestinal microbiota comprises diverse fungal and viral components, in addition to bacteria. These microbes interact with the immune system and affect human physiology. Advances in metagenomics have associated inflammatory and autoimmune diseases with alterations in fungal and viral species in the gut. Studies of animal models have found that commensal fungi and viruses can activate host-protective immune pathways related to epithelial barrier integrity, but can also induce reactions that contribute to events associated with inflammatory bowel disease. Changes in our environment associated with modernization and the COVID-19 pandemic have exposed humans to new fungi and viruses, with unknown consequences. We review the lessons learned from studies of animal viruses and fungi commonly detected in the human gut and how these might affect health and intestinal disease.}, } @article {pmid33342997, year = {2021}, author = {Viver, T and Conrad, RE and Orellana, LH and Urdiain, M and González-Pastor, JE and Hatt, JK and Amann, R and Antón, J and Konstantinidis, KT and Rosselló-Móra, R}, title = {Distinct ecotypes within a natural haloarchaeal population enable adaptation to changing environmental conditions without causing population sweeps.}, journal = {The ISME journal}, volume = {15}, number = {4}, pages = {1178-1191}, pmid = {33342997}, issn = {1751-7370}, mesh = {Adaptation, Physiological ; *Ecotype ; Metagenome ; *Microbiota ; Salinity ; }, abstract = {Microbial communities thriving in hypersaline brines of solar salterns are highly resistant and resilient to environmental changes, and salinity is a major factor that deterministically influences community structure. Here, we demonstrate that this resilience occurs even after rapid osmotic shocks caused by a threefold change in salinity (a reduction from 34 to 12% salts) leading to massive amounts of archaeal cell lysis. Specifically, our temporal metagenomic datasets identified two co-occurring ecotypes within the most dominant archaeal population of the brines Haloquadratum walsbyi that exhibited different salt concentration preferences. The dominant ecotype was generally more abundant and occurred in high-salt conditions (34%); the low abundance ecotype always co-occurred but was enriched at salinities around 20% or lower and carried unique gene content related to solute transport and gene regulation. Despite their apparent distinct ecological preferences, the ecotypes did not outcompete each other presumably due to weak functional differentiation between them. Further, the osmotic shock selected for a temporal increase in taxonomic and functional diversity at both the Hqr. walsbyi population and whole-community levels supporting the specialization-disturbance hypothesis, that is, the expectation that disturbance favors generalists. Altogether, our results provide new insights into how intraspecies diversity is maintained in light of substantial gene-content differences and major environmental perturbations.}, } @article {pmid33341726, year = {2021}, author = {Martínez-Gallardo, MR and López, MJ and López-González, JA and Jurado, MM and Suárez-Estrella, F and Pérez-Murcia, MD and Sáez, JA and Moral, R and Moreno, J}, title = {Microbial communities of the olive mill wastewater sludge stored in evaporation ponds: The resource for sustainable bioremediation.}, journal = {Journal of environmental management}, volume = {279}, number = {}, pages = {111810}, doi = {10.1016/j.jenvman.2020.111810}, pmid = {33341726}, issn = {1095-8630}, mesh = {Biodegradation, Environmental ; Industrial Waste/analysis ; *Microbiota ; *Olea ; Olive Oil ; Ponds ; Sewage ; Waste Disposal, Fluid ; Wastewater ; }, abstract = {Olive Mill Wastewater (OMW) is a polluting residue from the olive oil industry. It is usually stored in open-air unprotected evaporation ponds where their sediments accumulate. This study compares the characteristics of OMW sludges stored for long-time in evaporation ponds and assesses their impact on the underlying soil layer. Physicochemical parameters, toxicity bioassays, and full characterization of the microbial community were analyzed. The extension of the polluting effects was assessed by analysis of toxicity, microbial biomass carbon, and respiration. Geostatistics was used to predict their spatial distribution. Organic matter and polyphenol content besides toxicity levels determine variations between OMW sludges and have a high impact on the microbiota they contain. The microbial community was abundant, diverse, and functionally active. However, the biodegradability of the sludges was hindered by the toxicity levels. Toxicity and biomass carbon were higher on the surface of the ponds than in the soil layer revealing a reduced leach flow and depletion of contaminants. The natural microbiota might be biostimulated by means of applying sustainable and feasible biological treatments in order to favor the OMW sludges bioremediation. These results open up the possibility of solving the environmental concern caused by its storage in similar scenarios, which are common in olive oil-producing countries.}, } @article {pmid33339953, year = {2020}, author = {Kwun, JS and Kang, SH and Lee, HJ and Park, HK and Lee, WJ and Yoon, CH and Suh, JW and Cho, YS and Youn, TJ and Chae, IH}, title = {Comparison of thrombus, gut, and oral microbiomes in Korean patients with ST-elevation myocardial infarction: a case-control study.}, journal = {Experimental & molecular medicine}, volume = {52}, number = {12}, pages = {2069-2079}, pmid = {33339953}, issn = {2092-6413}, support = {2019R1C1C1006611//National Research Foundation of Korea (NRF)/ ; }, mesh = {Aged ; Case-Control Studies ; Disease Susceptibility ; Dysbiosis ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolomics/methods ; Metagenome ; Metagenomics ; *Microbiota ; Middle Aged ; Mouth/*microbiology ; Public Health Surveillance ; ST Elevation Myocardial Infarction/diagnosis/*epidemiology/*etiology ; Thrombosis/*complications/*epidemiology ; }, abstract = {ST-segment elevation myocardial infarction (STEMI) is characterized by thrombotic coronary artery occlusions caused by atherosclerotic plaque rupture. The gut microbiome potentially contributes to the pathogenesis of coronary artery diseases. This study investigated the microbial diversity and composition of coronary thrombi in STEMI patients and the composition of the thrombus microbiome relative to that of the oral and gut microbiomes. A case-control study was performed with 22 STEMI patients and 20 age- and sex-matched healthy controls. Coronary thrombi were acquired from STEMI patients via manual thrombus aspiration during primary coronary intervention. Oral swab and stool samples were collected from both groups, and 16S rRNA sequencing and metagenomic microbiome analyses were performed. Microbial DNA was detected in 4 of 22 coronary thrombi. Proteobacteria (p) and Bacteroidetes (p) were the most abundant phyla. The oral and gut microbiomes significantly differed between patients and healthy controls. The patient group presented microbial dysbiosis, as follows: a higher relative abundance of Proteobacteria (p) and Enterobacteriaceae (f) in the gut microbiome and a lower abundance of Firmicutes (p) and Haemophilus (g) in the oral microbiome. Furthermore, 4 significantly abundant genera were observed in the coronary thrombus in the patients: Escherichia, 1.25%; Parabacteroides, 0.25%; Christensenella, 0.0%; and Bacteroides, 7.48%. The present results indicate that the relative abundance of the gut and oral microbiomes was correlated with that of the thrombus microbiome.}, } @article {pmid33338226, year = {2021}, author = {Martin, G and Dang, C and Morrissey, E and Hubbart, J and Kellner, E and Kelly, C and Stephan, K and Freedman, Z}, title = {Stream sediment bacterial communities exhibit temporally-consistent and distinct thresholds to land use change in a mixed-use watershed.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {2}, pages = {}, doi = {10.1093/femsec/fiaa256}, pmid = {33338226}, issn = {1574-6941}, mesh = {Agriculture ; Bacteria/genetics ; Biodiversity ; *Ecosystem ; *Rivers ; Urbanization ; }, abstract = {Freshwater ecosystems are susceptible to biodiversity losses due to land conversion. This is particularly true for the conversion of land from forests for agriculture and urban development. Freshwater sediments harbor microorganisms that provide vital ecosystem services. In dynamic habitats like freshwater sediments, microbial communities can be shaped by many processes, although the relative contributions of environmental factors to microbial community dynamics remain unclear. Given the future projected increase in land use change, it is important to ascertain how associated changes in stream physico-chemistry will influence sediment microbiomes. Here, we characterized stream chemistry and sediment bacterial community composition along a mixed land-use gradient in West Virginia, USA across one growing season. Sediment bacterial community richness was unaffected by increasing anthropogenic land use, though microbial communities were compositionally distinct across sites. Community threshold analysis revealed greater community resilience to agricultural land use than urban land use. Further, predicted metagenomes suggest differences in potential microbial function across changes in land use. The results of this study suggest that low levels of urban land use change can alter sediment bacterial community composition and predicted functional capacity in a mixed-use watershed, which could impact stream ecosystem services in the face of global land use change.}, } @article {pmid33330938, year = {2021}, author = {Damhorst, GL and Adelman, MW and Woodworth, MH and Kraft, CS}, title = {Current Capabilities of Gut Microbiome-Based Diagnostics and the Promise of Clinical Application.}, journal = {The Journal of infectious diseases}, volume = {223}, number = {12 Suppl 2}, pages = {S270-S275}, pmid = {33330938}, issn = {1537-6613}, support = {K23 AI144036/AI/NIAID NIH HHS/United States ; UM1 AI104681/AI/NIAID NIH HHS/United States ; }, mesh = {*Clinical Laboratory Techniques ; Computational Biology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; }, abstract = {There is increasing evidence for the importance of the gut microbiome in human health and disease. Traditional and modern technologies - from cell culture to next generation sequencing - have facilitated these advances in knowledge. Each of the tools employed in measuring the microbiome exhibits unique capabilities that may be leveraged for clinical diagnostics. However, much still needs to be done to standardize the language and metrics by which a microbiome is characterized. Here we review the capabilities of gut microbiome-based diagnostics, review selected examples, and discuss the outlook towards clinical application.}, } @article {pmid33330904, year = {2021}, author = {Thänert, R and Keen, EC and Dantas, G and Warner, BB and Tarr, PI}, title = {Necrotizing Enterocolitis and the Microbiome: Current Status and Future Directions.}, journal = {The Journal of infectious diseases}, volume = {223}, number = {12 Suppl 2}, pages = {S257-S263}, pmid = {33330904}, issn = {1537-6613}, support = {P30 DK052574/DK/NIDDK NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; R01 GM099538/GM/NIGMS NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; }, mesh = {Dysbiosis/microbiology ; Enterocolitis, Necrotizing/*microbiology/therapy ; Gastrointestinal Microbiome/*physiology ; Host-Pathogen Interactions ; Humans ; Infant, Newborn ; Infant, Premature ; Risk Factors ; }, abstract = {Decades of research have failed to define the pathophysiology of necrotizing enterocolitis (NEC), a devastating pediatric gastrointestinal disorder of preterm infants. However, evidence suggests that host-microbiota interactions, in which microbial dysbiosis is followed by loss of barrier integrity, inflammation, and necrosis, are central to NEC development. Thus, greater knowledge of the preterm infant microbiome could accelerate attempts to diagnose, treat, and prevent NEC. In this article, we summarize clinical characteristics of and risk factors for NEC, the structure of the pre-event NEC microbiome, how this community interfaces with host immunology, and microbiome-based approaches that might prevent or lessen the severity of NEC in this very vulnerable population.}, } @article {pmid33329584, year = {2020}, author = {Cortés, A and Clare, S and Costain, A and Almeida, A and McCarthy, C and Harcourt, K and Brandt, C and Tolley, C and Rooney, J and Berriman, M and Lawley, T and MacDonald, AS and Rinaldi, G and Cantacessi, C}, title = {Baseline Gut Microbiota Composition Is Associated With Schistosoma mansoni Infection Burden in Rodent Models.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {593838}, pmid = {33329584}, issn = {1664-3224}, support = {/WT_/Wellcome Trust/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Antibodies, Protozoan/immunology ; Bacteria/classification/genetics ; Biodiversity ; Computational Biology/methods ; Disease Models, Animal ; Dysbiosis ; Feces/microbiology ; *Gastrointestinal Microbiome/immunology ; *Host-Parasite Interactions/immunology ; Immunomodulation ; Metagenomics/methods ; Mice ; *Parasite Load ; RNA, Ribosomal, 16S ; Schistosoma ; Schistosomiasis mansoni/*immunology/*parasitology ; }, abstract = {In spite of growing evidence supporting the occurrence of complex interactions between Schistosoma and gut bacteria in mice and humans, no data is yet available on whether worm-mediated changes in microbiota composition are dependent on the baseline gut microbial profile of the vertebrate host. In addition, the impact of such changes on the susceptibility to, and pathophysiology of, schistosomiasis remains largely unexplored. In this study, mice colonized with gut microbial populations from a human donor (HMA mice), as well as microbiota-wild type (WT) animals, were infected with Schistosoma mansoni, and alterations of their gut microbial profiles at 50 days post-infection were compared to those occurring in uninfected HMA and WT rodents, respectively. Significantly higher worm and egg burdens, together with increased specific antibody responses to parasite antigens, were observed in HMA compared to WT mice. These differences were associated to extensive dissimilarities between the gut microbial profiles of each HMA and WT groups of mice at baseline; in particular, the gut microbiota of HMA animals was characterized by low microbial alpha diversity and expanded Proteobacteria, as well as by the absence of putative immunomodulatory bacteria (e.g. Lactobacillus). Furthermore, differences in infection-associated changes in gut microbiota composition were observed between HMA and WT mice. Altogether, our findings support the hypothesis that susceptibility to S.mansoni infection in mice is partially dependent on the composition of the host baseline microbiota. Moreover, this study highlights the applicability of HMA mouse models to address key biological questions on host-parasite-microbiota relationships in human helminthiases.}, } @article {pmid33328537, year = {2020}, author = {Seferovic, MD and Mohammad, M and Pace, RM and Engevik, M and Versalovic, J and Bode, L and Haymond, M and Aagaard, KM}, title = {Maternal diet alters human milk oligosaccharide composition with implications for the milk metagenome.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {22092}, pmid = {33328537}, issn = {2045-2322}, support = {P30 DK123704/DK/NIDDK NIH HHS/United States ; R01 HD091731/HD/NICHD NIH HHS/United States ; P30 DK020593/DK/NIDDK NIH HHS/United States ; R01 DK089201/DK/NIDDK NIH HHS/United States ; R01HD091731/NH/NIH HHS/United States ; R24 DK090964/DK/NIDDK NIH HHS/United States ; K12 GM084897/GM/NIGMS NIH HHS/United States ; R01 DK055478/DK/NIDDK NIH HHS/United States ; M01 RR000188/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; *Breast Feeding ; Cross-Over Studies ; Diet ; Female ; Humans ; Infant ; Lactation/genetics ; Lactose/genetics/metabolism ; Metagenome/*genetics ; Microbiota/genetics ; Milk, Human/*chemistry/metabolism ; Nutritional Status ; Oligosaccharides/*chemistry/genetics/isolation & purification ; }, abstract = {Human milk is the optimal nutrition source for infants, and oligosaccharides represent the third most abundant component in milk after lactose and fat. Human milk oligosaccharides (HMO) are favorable macromolecules which are, interestingly, indigestible by the infant but serve as substrates for bacteria. Hypothesizing that the maternal diet itself might influence HMO composition, we sought to directly determine the effect maternal diet on HMO and the milk bacteria. Employing a human cross-over study design, we demonstrate that distinct maternal dietary carbohydrate and energy sources preferentially alter milk concentrations of HMO, including fucosylated species. We find significant associations between the concentration of HMO-bound fucose and the abundance of fucosidase (a bacterial gene that digests fucose moieties) harbored by milk bacteria. These studies reveal a successive mechanism by which the maternal diet during lactation alters milk HMO composition, which in turn shapes the functional milk microbiome prior to infant ingestion.}, } @article {pmid33328245, year = {2021}, author = {Masi, AC and Embleton, ND and Lamb, CA and Young, G and Granger, CL and Najera, J and Smith, DP and Hoffman, KL and Petrosino, JF and Bode, L and Berrington, JE and Stewart, CJ}, title = {Human milk oligosaccharide DSLNT and gut microbiome in preterm infants predicts necrotising enterocolitis.}, journal = {Gut}, volume = {70}, number = {12}, pages = {2273-2282}, pmid = {33328245}, issn = {1468-3288}, support = {P30 ES030285/ES/NIEHS NIH HHS/United States ; }, mesh = {Case-Control Studies ; Enterocolitis, Necrotizing/*microbiology/*prevention & control ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Infant, Premature ; Male ; Milk, Human/*chemistry ; Oligosaccharides/*metabolism ; }, abstract = {OBJECTIVE: Necrotising enterocolitis (NEC) is a devastating intestinal disease primarily affecting preterm infants. The underlying mechanisms are poorly understood: mother's own breast milk (MOM) is protective, possibly relating to human milk oligosaccharide (HMO) and infant gut microbiome interplay. We investigated the interaction between HMO profiles and infant gut microbiome development and its association with NEC.

DESIGN: We performed HMO profiling of MOM in a large cohort of infants with NEC (n=33) with matched controls (n=37). In a subset of 48 infants (14 with NEC), we also performed longitudinal metagenomic sequencing of infant stool (n=644).

RESULTS: Concentration of a single HMO, disialyllacto-N-tetraose (DSLNT), was significantly lower in MOM received by infants with NEC compared with controls. A MOM threshold level of 241 nmol/mL had a sensitivity and specificity of 0.9 for NEC. Metagenomic sequencing before NEC onset showed significantly lower relative abundance of Bifidobacterium longum and higher relative abundance of Enterobacter cloacae in infants with NEC. Longitudinal development of the microbiome was also impacted by low MOM DSLNT associated with reduced transition into preterm gut community types dominated by Bifidobacterium spp and typically observed in older infants. Random forest analysis combining HMO and metagenome data before disease accurately classified 87.5% of infants as healthy or having NEC.

CONCLUSION: These results demonstrate the importance of HMOs and gut microbiome in preterm infant health and disease. The findings offer potential targets for biomarker development, disease risk stratification and novel avenues for supplements that may prevent life-threatening disease.}, } @article {pmid33328144, year = {2021}, author = {Kolmeder, CA and de Vos, WM}, title = {Roadmap to functional characterization of the human intestinal microbiota in its interaction with the host.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {194}, number = {}, pages = {113751}, doi = {10.1016/j.jpba.2020.113751}, pmid = {33328144}, issn = {1873-264X}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {It is known for more than 100 years that the intestinal microbes are important for the host's health and the last decade this is being intensely studied with a focus on the mechanistic aspects. Among the fundamental functions of the intestinal microbiome are the priming of the immune system, the production of essential vitamins and the energy harvest from foods. By now, several dozens of diseases, both intestinal and non-intestinal related, have been associated with the intestinal microbiome. Initially, this was based on the description of the composition between groups of different health status or treatment arms based on phylogenetic approaches based on the 16S rRNA gene sequences. This way of analysis has mostly moved to the analysis of all the genes or transcripts of the microbiome i.e. metagenomics and meta-transcriptomics. Differences are regularly found but these have to be taken with caution as we still do not know what the majority of genes of the intestinal microbiome are capable of doing. To circumvent this caveat researchers are studying the proteins and the metabolites of the microbiome and the host via metaproteomics and metabolomics approaches. However, also here the complexity is high and only a fraction of signals obtained with high throughput instruments can be identified and assigned to a known protein or molecule. Therefore, modern microbiome research needs advancement of existing and development of new analytical techniques. The usage of model systems like intestinal organoids where samples can be taken and processed rapidly as well as microfluidics systems may help. This review aims to elucidate what we know about the functionality of the human intestinal microbiome, what technologies are advancing this knowledge, and what innovations are still required to further evolve this actively developing field.}, } @article {pmid33327517, year = {2020}, author = {Menaa, F and Wijesinghe, PAUI and Thiripuranathar, G and Uzair, B and Iqbal, H and Khan, BA and Menaa, B}, title = {Ecological and Industrial Implications of Dynamic Seaweed-Associated Microbiota Interactions.}, journal = {Marine drugs}, volume = {18}, number = {12}, pages = {}, pmid = {33327517}, issn = {1660-3397}, mesh = {Animals ; *Ecology ; Humans ; *Industry ; *Microbiota ; Seaweed/*chemistry ; }, abstract = {Seaweeds are broadly distributed and represent an important source of secondary metabolites (e.g., halogenated compounds, polyphenols) eliciting various pharmacological activities and playing a relevant ecological role in the anti-epibiosis. Importantly, host (as known as basibiont such as algae)-microbe (as known as epibiont such as bacteria) interaction (as known as halobiont) is a driving force for coevolution in the marine environment. Nevertheless, halobionts may be fundamental (harmless) or detrimental (harmful) to the functioning of the host. In addition to biotic factors, abiotic factors (e.g., pH, salinity, temperature, nutrients) regulate halobionts. Spatiotemporal and functional exploration of such dynamic interactions appear crucial. Indeed, environmental stress in a constantly changing ocean may disturb complex mutualistic relations, through mechanisms involving host chemical defense strategies (e.g., secretion of secondary metabolites and antifouling chemicals by quorum sensing). It is worth mentioning that many of bioactive compounds, such as terpenoids, previously attributed to macroalgae are in fact produced or metabolized by their associated microorganisms (e.g., bacteria, fungi, viruses, parasites). Eventually, recent metagenomics analyses suggest that microbes may have acquired seaweed associated genes because of increased seaweed in diets. This article retrospectively reviews pertinent studies on the spatiotemporal and functional seaweed-associated microbiota interactions which can lead to the production of bioactive compounds with high antifouling, theranostic, and biotechnological potential.}, } @article {pmid33326581, year = {2021}, author = {Anthony, WE and Burnham, CD and Dantas, G and Kwon, JH}, title = {The Gut Microbiome as a Reservoir for Antimicrobial Resistance.}, journal = {The Journal of infectious diseases}, volume = {223}, number = {12 Suppl 2}, pages = {S209-S213}, pmid = {33326581}, issn = {1537-6613}, support = {K23 AI137321/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Infective Agents/pharmacology ; Bacterial Infections/immunology/microbiology ; Drug Resistance, Microbial/*genetics ; Gastrointestinal Microbiome/drug effects/*genetics ; Gastrointestinal Tract/immunology/microbiology ; Genes, Microbial/genetics ; Humans ; Metagenomics ; Plasmids/drug effects/genetics ; }, abstract = {This review will consider the gut as a reservoir for antimicrobial resistance, colonization resistance, and how disruption of the microbiome can lead to colonization by pathogenic organisms. There is a focus on the gut as a reservoir for β-lactam and plasmid-mediated quinolone resistance. Finally, the role of functional metagenomics and long-read sequencing technologies to detect and understand antimicrobial resistance genes within the gut microbiome is discussed, along with the potential for future microbiome-directed methods to detect and prevent infection.}, } @article {pmid33326438, year = {2020}, author = {Schwabl, P and Maiguashca Sánchez, J and Costales, JA and Ocaña-Mayorga, S and Segovia, M and Carrasco, HJ and Hernández, C and Ramírez, JD and Lewis, MD and Grijalva, MJ and Llewellyn, MS}, title = {Culture-free genome-wide locus sequence typing (GLST) provides new perspectives on Trypanosoma cruzi dispersal and infection complexity.}, journal = {PLoS genetics}, volume = {16}, number = {12}, pages = {e1009170}, pmid = {33326438}, issn = {1553-7404}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/R021430/1/MRC_/Medical Research Council/United Kingdom ; 204820/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Costs and Cost Analysis ; DNA Barcoding, Taxonomic/economics/*methods/standards ; Disease Vectors ; *Genome, Protozoan ; Hemiptera/parasitology ; *Metagenome ; Metagenomics/economics/*methods/standards ; Polymorphism, Genetic ; Trypanosoma cruzi/*genetics/pathogenicity ; Virulence/genetics ; Whole Genome Sequencing/economics/*methods/standards ; }, abstract = {Analysis of genetic polymorphism is a powerful tool for epidemiological surveillance and research. Powerful inference from pathogen genetic variation, however, is often restrained by limited access to representative target DNA, especially in the study of obligate parasitic species for which ex vivo culture is resource-intensive or bias-prone. Modern sequence capture methods enable pathogen genetic variation to be analyzed directly from host/vector material but are often too complex and expensive for resource-poor settings where infectious diseases prevail. This study proposes a simple, cost-effective 'genome-wide locus sequence typing' (GLST) tool based on massive parallel amplification of information hotspots throughout the target pathogen genome. The multiplexed polymerase chain reaction amplifies hundreds of different, user-defined genetic targets in a single reaction tube, and subsequent agarose gel-based clean-up and barcoding completes library preparation at under 4 USD per sample. Our study generates a flexible GLST primer panel design workflow for Trypanosoma cruzi, the parasitic agent of Chagas disease. We successfully apply our 203-target GLST panel to direct, culture-free metagenomic extracts from triatomine vectors containing a minimum of 3.69 pg/μl T. cruzi DNA and further elaborate on method performance by sequencing GLST libraries from T. cruzi reference clones representing discrete typing units (DTUs) TcI, TcIII, TcIV, TcV and TcVI. The 780 SNP sites we identify in the sample set repeatably distinguish parasites infecting sympatric vectors and detect correlations between genetic and geographic distances at regional (< 150 km) as well as continental scales. The markers also clearly separate TcI, TcIII, TcIV and TcV + TcVI and appear to distinguish multiclonal infections within TcI. We discuss the advantages, limitations and prospects of our method across a spectrum of epidemiological research.}, } @article {pmid33325996, year = {2021}, author = {Lannes, R and Cavaud, L and Lopez, P and Bapteste, E}, title = {Marine Ultrasmall Prokaryotes Likely Affect the Cycling of Carbon, Methane, Nitrogen, and Sulfur.}, journal = {Genome biology and evolution}, volume = {13}, number = {1}, pages = {}, pmid = {33325996}, issn = {1759-6653}, mesh = {Acetyl Coenzyme A ; Autotrophic Processes ; Carbon/*metabolism ; Carbon Cycle ; Metabolic Networks and Pathways ; Metagenomics ; Methane/*metabolism ; Microbiota ; Nitrogen/metabolism ; Oceans and Seas ; Prokaryotic Cells/*metabolism ; Seawater/*microbiology ; Sulfur/*metabolism ; }, abstract = {Recently, we uncovered the genetic components from six carbon fixation autotrophic pathways in cleaned ultrasmall size fractions from marine samples (<0.22 µm) gathered worldwide by the Tara Oceans Expedition. This first finding suggested that prokaryotic nanoorganisms, phylogenetically distantly related to the known CPR and DPANN groups, could collectively impact carbon cycling and carbon fixation across the world's ocean. To extend our mining of the functional and taxonomic microbial dark matter from the ultrasmall size fraction from the Tara Oceans Expedition, we investigated the distribution of 28 metabolic pathways associated with the cycling of carbon, methane, nitrogen, and sulfur. For all of these pathways, we report the existence not only of novel metabolic homologs in the ultrasmall size fraction of the oceanic microbiome, associated with nanoorganisms belonging to the CPR and DPANN lineages, but also of metabolic homologs exclusively found in marine host taxa belonging to other (still unassigned) microbial lineages. Therefore, we conclude that marine nanoorganisms contribute to a greater diversity of key biogeochemical cycles than currently appreciated. In particular, we suggest that oceanic nanoorganisms may be involved in a metabolic loop around Acetyl-CoA, have an underappreciated genetic potential to degrade methane, contribute to sustaining redox-reactions by producing Coenzyme F420, and affect sulfur cycling, notably as they harbor a complete suite of homologs of enzymes of the SOX system.}, } @article {pmid33323978, year = {2021}, author = {Mirhakkak, MH and Schäuble, S and Klassert, TE and Brunke, S and Brandt, P and Loos, D and Uribe, RV and Senne de Oliveira Lino, F and Ni, Y and Vylkova, S and Slevogt, H and Hube, B and Weiss, GJ and Sommer, MOA and Panagiotou, G}, title = {Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels.}, journal = {The ISME journal}, volume = {15}, number = {5}, pages = {1257-1270}, pmid = {33323978}, issn = {1751-7370}, mesh = {Bacteria ; Bacteroidetes ; *Candida albicans/genetics ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; }, abstract = {Candida albicans is a leading cause of life-threatening hospital-acquired infections and can lead to Candidemia with sepsis-like symptoms and high mortality rates. We reconstructed a genome-scale C. albicans metabolic model to investigate bacterial-fungal metabolic interactions in the gut as determinants of fungal abundance. We optimized the predictive capacity of our model using wild type and mutant C. albicans growth data and used it for in silico metabolic interaction predictions. Our analysis of more than 900 paired fungal-bacterial metabolic models predicted key gut bacterial species modulating C. albicans colonization levels. Among the studied microbes, Alistipes putredinis was predicted to negatively affect C. albicans levels. We confirmed these findings by metagenomic sequencing of stool samples from 24 human subjects and by fungal growth experiments in bacterial spent media. Furthermore, our pairwise simulations guided us to specific metabolites with promoting or inhibitory effect to the fungus when exposed in defined media under carbon and nitrogen limitation. Our study demonstrates that in silico metabolic prediction can lead to the identification of gut microbiome features that can significantly affect potentially harmful levels of C. albicans.}, } @article {pmid33323129, year = {2020}, author = {Utter, DR and Borisy, GG and Eren, AM and Cavanaugh, CM and Mark Welch, JL}, title = {Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {293}, pmid = {33323129}, issn = {1474-760X}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; UL1 TR001102/TR/NCATS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Chromosome Mapping ; Haemophilus parainfluenzae/genetics ; Humans ; *Metagenome ; Microbiota/*genetics ; Micrococcaceae/genetics ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The increasing availability of microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic differences within related bacteria. The human oral microbiome with its diverse habitats and abundant, relatively well-characterized microbial inhabitants presents an opportunity to investigate bacterial population structures at an ecosystem scale.

RESULTS: Here, we employ a metapangenomic approach that combines public genomes with Human Microbiome Project (HMP) metagenomes to study the diversity of microbial residents of three oral habitats: tongue dorsum, buccal mucosa, and supragingival plaque. For two exemplar taxa, Haemophilus parainfluenzae and the genus Rothia, metapangenomes reveal distinct genomic groups based on shared genome content. H. parainfluenzae genomes separate into three distinct subgroups with differential abundance between oral habitats. Functional enrichment analyses identify an operon encoding oxaloacetate decarboxylase as diagnostic for the tongue-abundant subgroup. For the genus Rothia, grouping by shared genome content recapitulates species-level taxonomy and habitat preferences. However, while most R. mucilaginosa are restricted to the tongue as expected, two genomes represent a cryptic population of R. mucilaginosa in many buccal mucosa samples. For both H. parainfluenzae and the genus Rothia, we identify not only limitations in the ability of cultivated organisms to represent populations in their native environment, but also specifically which cultivar gene sequences are absent or ubiquitous.

CONCLUSIONS: Our findings provide insights into population structure and biogeography in the mouth and form specific hypotheses about habitat adaptation. These results illustrate the power of combining metagenomes and pangenomes to investigate the ecology and evolution of bacteria across analytical scales.}, } @article {pmid33323122, year = {2020}, author = {Shaiber, A and Willis, AD and Delmont, TO and Roux, S and Chen, LX and Schmid, AC and Yousef, M and Watson, AR and Lolans, K and Esen, ÖC and Lee, STM and Downey, N and Morrison, HG and Dewhirst, FE and Mark Welch, JL and Eren, AM}, title = {Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {292}, pmid = {33323122}, issn = {1474-760X}, support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; P30 DK042086/DK/NIDDK NIH HHS/United States ; R01 DE016937/DE/NIDCR NIH HHS/United States ; R35GM133420/NH/NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; DE016937/DE/NIDCR NIH HHS/United States ; DE024468/DE/NIDCR NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Adult ; Bacteria/genetics ; Female ; *Genetic Markers ; Genome, Bacterial ; Humans ; Interspersed Repetitive Sequences ; Male ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Middle Aged ; Mouth/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {INTRODUCTION: Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and intriguing patterns of site specificity amidst the lack of dispersal limitation. However, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among taxa that belong to recently discovered branches of microbial life.

RESULTS: Here, we assemble metagenomes from tongue and dental plaque samples from multiple individuals and reconstruct 790 non-redundant genomes, 43 of which resolve to TM7, a member of the Candidate Phyla Radiation, forming six monophyletic clades that distinctly associate with either plaque or tongue. Both pangenomic and phylogenomic analyses group tongue-specific clades with other host-associated TM7 genomes. In contrast, plaque-specific TM7 group with environmental TM7 genomes. Besides offering deeper insights into the ecology, evolution, and mobilome of cryptic members of the oral microbiome, our study reveals an intriguing resemblance between dental plaque and non-host environments indicated by the TM7 evolution, suggesting that plaque may have served as a stepping stone for environmental microbes to adapt to host environments for some clades of microbes. Additionally, we report that prophages are widespread among oral-associated TM7, while absent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to the host environment.

CONCLUSIONS: Our data illuminate niche partitioning of enigmatic members of the oral cavity, including TM7, SR1, and GN02, and provide genomes for poorly characterized yet prevalent members of this biome, such as uncultivated Flavobacteriaceae.}, } @article {pmid33323004, year = {2020}, author = {Van Hul, M and Le Roy, T and Prifti, E and Dao, MC and Paquot, A and Zucker, JD and Delzenne, NM and Muccioli, G and Clément, K and Cani, PD}, title = {From correlation to causality: the case of Subdoligranulum.}, journal = {Gut microbes}, volume = {12}, number = {1}, pages = {1-13}, pmid = {33323004}, issn = {1949-0984}, mesh = {Adult ; Akkermansia/isolation & purification ; Animals ; Cholesterol, HDL/blood ; Clostridiales/genetics/*metabolism ; Diabetes Mellitus/pathology ; Diet, High-Fat/adverse effects ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Insulin Resistance/physiology ; Lipid Metabolism/physiology ; Male ; Metagenome/genetics ; Mice ; Mice, Inbred C57BL ; Middle Aged ; Obesity/pathology/*prevention & control ; }, abstract = {Gut microbes are considered as major factors contributing to human health. Nowadays, the vast majority of the data available in the literature are mostly exhibiting negative or positive correlations between specific bacteria and metabolic parameters. From these observations, putative detrimental or beneficial effects are then inferred. Akkermansia muciniphila is one of the unique examples for which the correlations with health benefits have been causally validated in vivo in rodents and humans. In this study, based on available metagenomic data in overweight/obese population and clinical variables that we obtained from two cohorts of individuals (n = 108) we identified several metagenomic species (MGS) strongly associated with A. muciniphila with one standing out: Subdoligranulum. By analyzing both qPCR and shotgun metagenomic data, we discovered that the abundance of Subdoligranulum was correlated positively with microbial richness and HDL-cholesterol levels and negatively correlated with fat mass, adipocyte diameter, insulin resistance, levels of leptin, insulin, CRP, and IL6 in humans. Therefore, to further explore whether these strong correlations could be translated into causation, we investigated the effects of the unique cultivated strain of Subdoligranulum (Subdoligranulum variabile DSM 15176 [T]) in obese and diabetic mice as a proof-of-concept. Strikingly, there were no significant difference in any of the hallmarks of obesity and diabetes measured (e.g., body weight gain, fat mass gain, glucose tolerance, liver weight, plasma lipids) at the end of the 8 weeks of treatment. Therefore, the absence of effect following the supplementation with S. variabile indicates that increasing the intestinal abundance of this bacterium is not translated into beneficial effects in mice. In conclusion, we demonstrated that despite the fact that numerous strong correlations exist between a given bacteria and health, proof-of-concept experiments are required to be further validated or not in vivo. Hence, an urgent need for causality studies is warranted to move from human observations to preclinical validations.}, } @article {pmid33321431, year = {2021}, author = {Misery, B and Legendre, P and Rue, O and Bouchart, V and Guichard, H and Laplace, JM and Cretenet, M}, title = {Diversity and dynamics of bacterial and fungal communities in cider for distillation.}, journal = {International journal of food microbiology}, volume = {339}, number = {}, pages = {108987}, doi = {10.1016/j.ijfoodmicro.2020.108987}, pmid = {33321431}, issn = {1879-3460}, mesh = {Alcoholic Beverages/*microbiology ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; DNA, Ribosomal Spacer/genetics ; *Distillation ; Fermentation ; Fungi/*physiology ; Malus ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bacterial and fungal population dynamics in cider for distillation have so far been explored by culture-dependant methods. Cider for distillation can be produced by the spontaneous fermentation of apples that do not undergo any intervention during the process. In this study, cider microbiomes extracted from six tanks containing ciders for distillation from four producers in Normandy were characterized at three main stages of the fermentation process: fermentation Initiation (I), end of the alcoholic Fermentation (F) and end of the Maturation period (M). Cider samples were subjected to Illumina MiSeq sequencing (rRNA 16S V1-V3 and ITS1 region targeting) to determine bacterial and fungal communities. Yeasts (YGC), Zymomonas (mZPP) and lactic acid bacteria selective media (mMRS, mMLO, mPSM) were also used to collect 807 isolates. Alcoholic levels, glycerol, sugar content (glucose, fructose and sucrose), pH, total and volatile acidity, nitrogen, malic and lactic acid contents were determined at all sampling points. Alpha diversity indexes show significant differences (p < 0.05) in microbial populations between I, F and M. Fungal communities were characterized by microorganisms from the environment and phytopathogens at I followed by the association of yearsts with alcoholic fermentation like Saccharomyces and non-Saccharomyces yeasts (Hanseniaspora, Candida). A maturation period for cider leads to an increase of the Dekkera/Brettanomyces population, which is responsible for off-flavors in cider for all producers. Among bacterial communities, the genera community associated to malolactic fermentation (Lactobacillus sp., Leuconostoc sp., Oenococcus sp.) was the most abundant at F and M. Acetic acid bacteria such as Acetobacter sp., Komagataeibacter sp. and Gluconobacter sp. were also detected during the process. Significant differences (p < 0.05) were found in fungal and bacterial populations between the four producers and during the fermentation process. The development of microorganisms associated with cider spoilage such as Zymomonas mobilis, Lactobacillus collinoides or Brettanomyces/Dekkera sp. was anticipated by a metagenomic approach. The monitoring of microbial diversity via high throughput sequencing combined with physical-chemical analysis is an interesting approach to improve the fermentation performance of cider for distillation and therefore, the quality of Calvados.}, } @article {pmid33319778, year = {2020}, author = {Wylensek, D and Hitch, TCA and Riedel, T and Afrizal, A and Kumar, N and Wortmann, E and Liu, T and Devendran, S and Lesker, TR and Hernández, SB and Heine, V and Buhl, EM and M D'Agostino, P and Cumbo, F and Fischöder, T and Wyschkon, M and Looft, T and Parreira, VR and Abt, B and Doden, HL and Ly, L and Alves, JMP and Reichlin, M and Flisikowski, K and Suarez, LN and Neumann, AP and Suen, G and de Wouters, T and Rohn, S and Lagkouvardos, I and Allen-Vercoe, E and Spröer, C and Bunk, B and Taverne-Thiele, AJ and Giesbers, M and Wells, JM and Neuhaus, K and Schnieke, A and Cava, F and Segata, N and Elling, L and Strowig, T and Ridlon, JM and Gulder, TAM and Overmann, J and Clavel, T}, title = {A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {6389}, pmid = {33319778}, issn = {2041-1723}, mesh = {Aged, 80 and over ; Animals ; Bacteria/*classification/genetics/*isolation & purification/metabolism ; Bile Acids and Salts/metabolism ; Biodiversity ; Clostridium/classification/genetics/isolation & purification ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Genes, Bacterial/genetics ; Host Specificity ; Humans ; Intestines/*microbiology ; Male ; Metagenome ; Multigene Family ; *Phylogeny ; RNA, Ribosomal, 16S ; Swine/*microbiology ; }, abstract = {Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting functions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides. Many strains deconjugate primary bile acids in in vitro assays, and a Clostridium scindens strain produces secondary bile acids via dehydroxylation. In addition, cells of the novel species Bullifex porci are coccoidal or spherical under the culture conditions tested, in contrast with the usual helical shape of other members of the family Spirochaetaceae. The strain collection, called 'Pig intestinal bacterial collection' (PiBAC), is publicly available at www.dsmz.de/pibac and opens new avenues for functional studies of the pig gut microbiota.}, } @article {pmid33318237, year = {2021}, author = {Hosgood, HD and Cai, Q and Hua, X and Long, J and Shi, J and Wan, Y and Yang, Y and Abnet, C and Bassig, BA and Hu, W and Ji, BT and Klugman, M and Xiang, Y and Gao, YT and Wong, JY and Zheng, W and Rothman, N and Shu, XO and Lan, Q}, title = {Variation in oral microbiome is associated with future risk of lung cancer among never-smokers.}, journal = {Thorax}, volume = {76}, number = {3}, pages = {256-263}, pmid = {33318237}, issn = {1468-3296}, support = {P30 CA068485/CA/NCI NIH HHS/United States ; R01 CA207466/CA/NCI NIH HHS/United States ; UM1 CA173640/CA/NCI NIH HHS/United States ; UM1 CA182910/CA/NCI NIH HHS/United States ; }, mesh = {Case-Control Studies ; China/epidemiology ; Female ; Humans ; Incidence ; Lung Neoplasms/*epidemiology/etiology ; Male ; *Microbiota ; Middle Aged ; Mouth Mucosa/*microbiology ; Prospective Studies ; Risk Factors ; Smokers ; }, abstract = {OBJECTIVE: To prospectively investigate whether diversity in oral microbiota is associated with risk of lung cancer among never-smokers.

DESIGN AND SETTING: A nested case-control study within two prospective cohort studies, the Shanghai Women's Health Study (n=74 941) and the Shanghai Men's Health Study (n=61 480).

PARTICIPANTS: Lifetime never-smokers who had no cancer at baseline. Cases were subjects who were diagnosed with incident lung cancer (n=114) and were matched 1:1 with controls on sex, age (≤2 years), date (≤30 days) and time (morning/afternoon) of sample collection, antibiotic use during the week before sample collection (yes/no) and menopausal status (for women).

MAIN OUTCOMES AND MEASURES: Metagenomic shotgun sequencing was used to measure the community structure and abundance of the oral microbiome in pre-diagnostic oral rinse samples of each case and control. Multivariable logistic regression models were used to estimate the association of lung cancer risk with alpha diversity metrics and relative abundance of taxa. The Microbiome Regression-Based Kernel Association Test (MiRKAT) evaluated the association between risk and the microbiome beta diversity.

RESULTS: Subjects with lower microbiota alpha diversity had an increased risk of lung cancer compared with those with higher microbial alpha diversity (Shannon: ptrend=0.05; Simpson: ptrend=0.04; Observed Species: ptrend=0.64). No case-control differences were apparent for beta diversity (pMiRKAT=0.30). After accounting for multiple comparisons, a greater abundance of Spirochaetia (ORlow 1.00 (reference), ORmedium 0.61 (95% CI 0.32 to 1.18), ORhigh 0.42 (95% CI 0.21 to 0.85)) and Bacteroidetes (ORlow 1.00 (reference), ORmedium 0.66 (95% CI 0.35 to 1.25), ORhigh 0.31 (95% CI 0.15 to 0.64)) was associated with a decreased risk of lung cancer, while a greater abundance of the Bacilli class (ORlow 1.00 (reference), ORmedium 1.49 (95% CI 0.73 to 3.08), ORhigh 2.40 (95% CI 1.18 to 4.87)) and Lactobacillales order (ORlow 1.00 (reference), ORmedium 2.15 (95% CI 1.03 to 4.47), ORhigh 3.26 (95% CI 1.58 to 6.70)) was associated with an increased risk of lung cancer.

CONCLUSIONS: Our prospective study of never-smokers suggests that lower alpha diversity was associated with a greater risk of lung cancer and the abundance of certain specific taxa was associated with altered risk, providing further insight into the aetiology of lung cancer in the absence of active tobacco smoking.}, } @article {pmid33318221, year = {2020}, author = {Gao, Q and Wang, G and Xue, K and Yang, Y and Xie, J and Yu, H and Bai, S and Liu, F and He, Z and Ning, D and Hobbie, SE and Reich, PB and Zhou, J}, title = {Stimulation of soil respiration by elevated CO2 is enhanced under nitrogen limitation in a decade-long grassland study.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {52}, pages = {33317-33324}, pmid = {33318221}, issn = {1091-6490}, mesh = {Aerobiosis ; Carbon Dioxide/*pharmacology ; Computer Simulation ; *Grassland ; Nitrogen/*pharmacology ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {Whether and how CO2 and nitrogen (N) availability interact to influence carbon (C) cycling processes such as soil respiration remains a question of considerable uncertainty in projecting future C-climate feedbacks, which are strongly influenced by multiple global change drivers, including elevated atmospheric CO2 concentrations (eCO2) and increased N deposition. However, because decades of research on the responses of ecosystems to eCO2 and N enrichment have been done largely independently, their interactive effects on soil respiratory CO2 efflux remain unresolved. Here, we show that in a multifactor free-air CO2 enrichment experiment, BioCON (Biodiversity, CO2, and N deposition) in Minnesota, the positive response of soil respiration to eCO2 gradually strengthened at ambient (low) N supply but not enriched (high) N supply for the 12-y experimental period from 1998 to 2009. In contrast to earlier years, eCO2 stimulated soil respiration twice as much at low than at high N supply from 2006 to 2009. In parallel, microbial C degradation genes were significantly boosted by eCO2 at low but not high N supply. Incorporating those functional genes into a coupled C-N ecosystem model reduced model parameter uncertainty and improved the projections of the effects of different CO2 and N levels on soil respiration. If our observed results generalize to other ecosystems, they imply widely positive effects of eCO2 on soil respiration even in infertile systems.}, } @article {pmid33317323, year = {2021}, author = {Peixoto, RS and Harkins, DM and Nelson, KE}, title = {Advances in Microbiome Research for Animal Health.}, journal = {Annual review of animal biosciences}, volume = {9}, number = {}, pages = {289-311}, doi = {10.1146/annurev-animal-091020-075907}, pmid = {33317323}, issn = {2165-8110}, mesh = {Animals ; *Animals, Domestic ; *Animals, Wild ; Anthozoa ; Behavior, Animal ; Biodiversity ; COVID-19/transmission/veterinary/virology ; *Human-Animal Interaction ; Humans ; *Microbiota ; SARS-CoV-2 ; Seafood ; }, abstract = {Host-associated microbiomes contribute in many ways to the homeostasis of the metaorganism. The microbiome's contributions range from helping to provide nutrition and aiding growth, development, and behavior to protecting against pathogens and toxic compounds. Here we summarize the current knowledge of the diversity and importance of the microbiome to animals, using representative examples of wild and domesticated species. We demonstrate how the beneficial ecological roles of animal-associated microbiomes can be generally grouped into well-defined main categories and how microbe-based alternative treatments can be applied to mitigate problems for both economic and conservation purposes and to provide crucial knowledge about host-microbiota symbiotic interactions. We suggest a Customized Combination of Microbial-Based Therapies to promote animal health and contribute to the practice of sustainable husbandry. We also discuss the ecological connections and threats associated with animal biodiversity loss, microorganism extinction, and emerging diseases, such as the COVID-19 pandemic.}, } @article {pmid33317254, year = {2021}, author = {Lee, NY and Shin, MJ and Youn, GS and Yoon, SJ and Choi, YR and Kim, HS and Gupta, H and Han, SH and Kim, BK and Lee, DY and Park, TS and Sung, H and Kim, BY and Suk, KT}, title = {Lactobacillus attenuates progression of nonalcoholic fatty liver disease by lowering cholesterol and steatosis.}, journal = {Clinical and molecular hepatology}, volume = {27}, number = {1}, pages = {110-124}, pmid = {33317254}, issn = {2287-285X}, mesh = {Animals ; Cholesterol ; Female ; *Gastrointestinal Microbiome ; Humans ; Lactobacillus ; Liver ; Male ; Mice ; Mice, Inbred C57BL ; Middle Aged ; *Non-alcoholic Fatty Liver Disease ; }, abstract = {BACKGROUND/AIMS: Nonalcoholic fatty liver disease (NAFLD) is closely related to gut-microbiome. There is a paucity of research on which strains of gut microbiota affect the progression of NAFLD. This study explored the NAFLD-associated microbiome in humans and the role of Lactobacillus in the progression of NAFLD in mice.

METHODS: The gut microbiome was analyzed via next-generation sequencing in healthy people (n=37) and NAFLD patients with elevated liver enzymes (n=57). Six-week-old male C57BL/6J mice were separated into six groups (n=10 per group; normal, Western, and four Western diet + strains [109 colony-forming units/g for 8 weeks; L. acidophilus, L. fermentum, L. paracasei, and L. plantarum]). Liver/body weight ratio, liver pathology, serum analysis, and metagenomics in the mice were examined.

RESULTS: Compared to healthy subjects (1.6±4.3), NAFLD patients showed an elevated Firmicutes/Bacteroidetes ratio (25.0±29.0) and a reduced composition of Akkermansia and L. murinus (P<0.05). In the animal experiment, L. acidophilus group was associated with a significant reduction in liver/body weight ratio (5.5±0.4) compared to the Western group (6.2±0.6) (P<0.05). L. acidophilus (41.0±8.6), L. fermentum (44.3±12.6), and L. plantarum (39.0±7.6) groups showed decreased cholesterol levels compared to the Western group (85.7±8.6) (P<0.05). In comparison of steatosis, L. acidophilus (1.9±0.6), L. plantarum (2.4±0.7), and L. paracasei (2.0±0.9) groups showed significant improvement of steatosis compared to the Western group (2.6±0.5) (P<0.05).

CONCLUSION: Ingestion of Lactobacillus, such as L. acidophilus, L. fermentum, and L. plantarum, ameliorates the progression of nonalcoholic steatosis by lowering cholesterol. The use of Lactobacillus can be considered as a useful strategy for the treatment of NAFLD.}, } @article {pmid33316516, year = {2021}, author = {Tian, L and Wang, L}, title = {Multi-omics analysis reveals structure and function of biofilm microbial communities in a pre-denitrification biofilter.}, journal = {The Science of the total environment}, volume = {757}, number = {}, pages = {143908}, doi = {10.1016/j.scitotenv.2020.143908}, pmid = {33316516}, issn = {1879-1026}, mesh = {Biofilms ; Bioreactors ; China ; *Denitrification ; *Microbiota ; Nitrogen ; Wastewater ; }, abstract = {The highly complex microbial communities in biofilm play crucial roles in the pollutant removal performance of wastewater treatment plants (WWTPs). In the present study, using multi-omics analysis, we studied microbial structure, key enzymes, functional traits, and key metabolic pathways of pre-denitrification biofilter in an urban WWTP in China. The analysis results of metagenomic and metaproteomic showed that Betaproteobacteria and Flavobacteriia were dominant in biofilms. The integrated metagenomic and metaproteomic data showed that the expression of nitrogen metabolism genes was high, and the high proportion of denitrification module indicating that denitrification was the main nitrogen removal pathway. The most abundant denitrifying bacterial genera were: Dechloromonas, Acidovorax, Bosea, Polaromonas, and Chryseobacterium. And microorganisms with denitrification potential may not be able to denitrify in the actual operation of the filter. The integrated analysis of metaproteomic and metabolomic showed that there was a correlation between biofilm microorganisms and metabolites. Metabolomic analysis indicated that metabolic profiles of biofilms varied with layer height. This study provides the first detailed microbial communities and metabolic profiles in a full-scale pre-denitrification biofilter and clarifies the mechanism of denitrification.}, } @article {pmid33316292, year = {2021}, author = {Romanis, CS and Pearson, LA and Neilan, BA}, title = {Cyanobacterial blooms in wastewater treatment facilities: Significance and emerging monitoring strategies.}, journal = {Journal of microbiological methods}, volume = {180}, number = {}, pages = {106123}, doi = {10.1016/j.mimet.2020.106123}, pmid = {33316292}, issn = {1872-8359}, mesh = {Bacterial Toxins ; Bacteriological Techniques/methods ; Cyanobacteria/genetics/*growth & development ; Environmental Monitoring ; Fresh Water/microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Microbiota ; Proteomics/methods ; Sensitivity and Specificity ; Wastewater/*microbiology ; Water Purification/*methods ; }, abstract = {Municipal wastewater treatment facilities (WWTFs) are prone to the proliferation of cyanobacterial species which thrive in stable, nutrient-rich environments. Dense cyanobacterial blooms frequently disrupt treatment processes and the supply of recycled water due to their production of extracellular polymeric substances, which hinder microfiltration, and toxins, which pose a health risk to end-users. A variety of methods are employed by water utilities for the identification and monitoring of cyanobacteria and their toxins in WWTFs, including microscopy, flow cytometry, ELISA, chemoanalytical methods, and more recently, molecular methods. Here we review the literature on the occurrence and significance of cyanobacterial blooms in WWTFs and discuss the pros and cons of the various strategies for monitoring these potentially hazardous events. Particular focus is directed towards next-generation metagenomic sequencing technologies for the development of site-specific cyanobacterial bloom management strategies. Long-term multi-omic observations will enable the identification of indicator species and the development of site-specific bloom dynamics models for the mitigation and management of cyanobacterial blooms in WWTFs. While emerging metagenomic tools could potentially provide deep insight into the diversity and flux of problematic cyanobacterial species in these systems, they should be considered a complement to, rather than a replacement of, quantitative chemoanalytical approaches.}, } @article {pmid33315571, year = {2022}, author = {Liu, F and Miao, Y and Liu, Y and Hou, T}, title = {RNN-VirSeeker: A Deep Learning Method for Identification of Short Viral Sequences From Metagenomes.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {19}, number = {3}, pages = {1840-1849}, doi = {10.1109/TCBB.2020.3044575}, pmid = {33315571}, issn = {1557-9964}, mesh = {*Deep Learning ; Humans ; Metagenome/genetics ; Metagenomics/methods ; *Microbiota/genetics ; *Viruses/genetics ; }, abstract = {Viruses are the most abundant biological entities on earth, and play vital roles in many aspects of microbial communities. As major human pathogens, viruses have caused huge mortality and morbidity to human society in history. Metagenomic sequencing methods could capture all microorganisms from microbiota, with sequences of viruses mixed with these of other species. Therefore, it is necessary to identify viral sequences from metagenomes. However, existing methods perform poorly on identifying short viral sequences. To solve this problem, a deep learning based method, RNN-VirSeeker, is proposed in this paper. RNN-VirSeeker was trained by sequences of 500bp sampled from known Virus and Host RefSeq genomes. Experimental results on the testing set have shown that RNN-VirSeeker exhibited AUROC of 0.9175, recall of 0.8640 and precision of 0.9211 for sequences of 500bp, and outperformed three widely used methods, VirSorter, VirFinder, and DeepVirFinder, on identifying short viral sequences. RNN-VirSeeker was also used to identify viral sequences from a CAMI dataset and a human gut metagenome. Compared with DeepVirFinder, RNN-VirSeeker identified more viral sequences from these metagenomes and achieved greater values of AUPRC and AUROC. RNN-VirSeeker is freely available at https://github.com/crazyinter/RNN-VirSeeker.}, } @article {pmid33314800, year = {2021}, author = {Artacho, A and Isaac, S and Nayak, R and Flor-Duro, A and Alexander, M and Koo, I and Manasson, J and Smith, PB and Rosenthal, P and Homsi, Y and Gulko, P and Pons, J and Puchades-Carrasco, L and Izmirly, P and Patterson, A and Abramson, SB and Pineda-Lucena, A and Turnbaugh, PJ and Ubeda, C and Scher, JU}, title = {The Pretreatment Gut Microbiome Is Associated With Lack of Response to Methotrexate in New-Onset Rheumatoid Arthritis.}, journal = {Arthritis & rheumatology (Hoboken, N.J.)}, volume = {73}, number = {6}, pages = {931-942}, pmid = {33314800}, issn = {2326-5205}, support = {T32 AI060537/AI/NIAID NIH HHS/United States ; R01AR074500/AR/NIAMS NIH HHS/United States ; T32 AR007304/AR/NIAMS NIH HHS/United States ; R03 AR072182/AR/NIAMS NIH HHS/United States ; K08 AR073930/AR/NIAMS NIH HHS/United States ; TL1 TR001871/TR/NCATS NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; R01HL122593//National Institute of Allergy and Infectious Diseases/ ; K08AR073930/AR/NIAMS NIH HHS/United States ; R01 AR074500/AR/NIAMS NIH HHS/United States ; }, mesh = {Administration, Oral ; Adult ; Antirheumatic Agents/metabolism/*therapeutic use ; Arthritis, Rheumatoid/*drug therapy/microbiology/physiopathology ; Bacteroidetes/genetics/metabolism ; Clostridiales/genetics/metabolism ; Cohort Studies ; Escherichia/genetics/metabolism ; Euryarchaeota/genetics/metabolism ; Female ; Firmicutes/genetics/metabolism ; Gastrointestinal Microbiome/*genetics ; Humans ; Machine Learning ; Male ; Metabolomics ; Metagenomics ; Methotrexate/metabolism/*therapeutic use ; Middle Aged ; Prognosis ; RNA, Ribosomal, 16S ; Shigella/genetics/metabolism ; Treatment Outcome ; }, abstract = {OBJECTIVE: Although oral methotrexate (MTX) remains the anchor drug for rheumatoid arthritis (RA), up to 50% of patients do not achieve a clinically adequate outcome. In addition, there is a lack of prognostic tools for treatment response prior to drug initiation. This study was undertaken to investigate whether interindividual differences in the human gut microbiome can aid in the prediction of MTX efficacy in new-onset RA.

METHODS: We performed 16S ribosomal RNA gene and shotgun metagenomic sequencing on the baseline gut microbiomes of drug-naive patients with new-onset RA (n = 26). Results were validated in an additional independent cohort (n = 21). To gain insight into potential microbial mechanisms, we conducted ex vivo experiments coupled with metabolomics analysis to evaluate the association between microbiome-driven MTX depletion and clinical response.

RESULTS: Our analysis revealed significant associations of the abundance of gut bacterial taxa and their genes with future clinical response (q < 0.05), including orthologs related to purine and MTX metabolism. Machine learning techniques were applied to the metagenomic data, resulting in a microbiome-based model that predicted lack of response to MTX in an independent group of patients. Finally, MTX levels remaining after ex vivo incubation with distal gut samples from pretreatment RA patients significantly correlated with the magnitude of future clinical response, suggesting a possible direct effect of the gut microbiome on MTX metabolism and treatment outcomes.

CONCLUSION: Taken together, these findings are the first step toward predicting lack of response to oral MTX in patients with new-onset RA and support the value of the gut microbiome as a possible prognostic tool and as a potential target in RA therapeutics.}, } @article {pmid33314183, year = {2021}, author = {Chumpitazi, BP and Hoffman, KL and Smith, DP and McMeans, AR and Musaad, S and Versalovic, J and Petrosino, JF and Shulman, RJ}, title = {Fructan-sensitive children with irritable bowel syndrome have distinct gut microbiome signatures.}, journal = {Alimentary pharmacology & therapeutics}, volume = {53}, number = {4}, pages = {499-509}, pmid = {33314183}, issn = {1365-2036}, support = {K23 DK101688/DK/NIDDK NIH HHS/United States ; UH3 DK083990/DK/NIDDK NIH HHS/United States ; R03 DK117219/DK/NIDDK NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; 6250-51000-043//United States Department of Agriculture/Agriculture Research Service/ ; P30 DK056338/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Bifidobacterium ; Child ; Feces ; Fructans ; *Gastrointestinal Microbiome ; Humans ; *Irritable Bowel Syndrome ; }, abstract = {BACKGROUND: Dietary fructans may worsen gastrointestinal symptoms in children with irritable bowel syndrome (IBS).

AIM: To determine whether gut microbiome composition and function are associated with childhood IBS fructan-induced symptoms.

METHODS: Faecal samples were collected from 38 children aged 7-17 years with paediatric Rome III IBS, who previously completied a double-blind, randomised, placebo-controlled crossover (fructan vs maltodextrin) trial. Fructan sensitivity was defined as an increase of ≥30% in abdominal pain frequency during the fructan diet. Gut microbial composition was determined via 16Sv4 rDNA sequencing. LEfSe evaluated taxonomic composition differences. Tax4Fun2 predicted microbial fructan metabolic pathways.

RESULTS: At baseline, 17 fructan-sensitive (vs 21 fructan-tolerant) subjects had lower alpha diversity (q < 0.05) and were enriched in the genus Holdermania. In contrast, fructan-tolerant subjects were enriched in 14 genera from the class Clostridia. During the fructan diet, fructan-sensitive (vs tolerant) subjects were enriched in both Agathobacter (P = 0.02) and Cyanobacteria (P = 0.0001). In contrast, fructan-tolerant subjects were enriched in three genera from the Clostridia class. Comparing the fructan vs maltodextrin diet, fructan-sensitive subjects had a significantly increased relative abundance of Bifidobacterium (P = 0.02) while fructan-tolerant subjects had increased Anaerostipes (P = 0.03) during the fructan diet. Only fructan-sensitive subjects had a trend towards increased predicted β-fructofuranosidase during the fructan vs maltodextrin diet.

CONCLUSIONS: Fructan-sensitive children with IBS have distinct gut microbiome signatures. These microbiome signatures differ both at baseline and in response to a fructan challenge.}, } @article {pmid33311714, year = {2021}, author = {Lee, KS and Pereira, FC and Palatinszky, M and Behrendt, L and Alcolombri, U and Berry, D and Wagner, M and Stocker, R}, title = {Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions.}, journal = {Nature protocols}, volume = {16}, number = {2}, pages = {634-676}, pmid = {33311714}, issn = {1750-2799}, support = {GBMF3783//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 542395//Simons Foundation/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; P26127-B20//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P27831-B28//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 2019-04401//Vetenskapsrådet (Swedish Research Council)/ ; }, mesh = {Cell Separation/methods ; Flow Cytometry/*methods ; Genome/genetics ; Genomics/methods ; In Situ Hybridization, Fluorescence/methods ; Isotope Labeling/methods ; Metagenomics/methods ; Microbiota/genetics ; Microfluidics/methods ; Optical Tweezers ; Optogenetics/methods ; Single-Cell Analysis/methods ; Spectrum Analysis, Raman/*methods ; }, abstract = {Stable isotope labeling of microbial taxa of interest and their sorting provide an efficient and direct way to answer the question "who does what?" in complex microbial communities when coupled with fluorescence in situ hybridization or downstream 'omics' analyses. We have developed a platform for automated Raman-based sorting in which optical tweezers and microfluidics are used to sort individual cells of interest from microbial communities on the basis of their Raman spectra. This sorting of cells and their downstream DNA analysis, such as by mini-metagenomics or single-cell genomics, or cultivation permits a direct link to be made between the metabolic roles and the genomes of microbial cells within complex microbial communities, as well as targeted isolation of novel microbes with a specific physiology of interest. We describe a protocol from sample preparation through Raman-activated live cell sorting. Subsequent cultivation of sorted cells is described, whereas downstream DNA analysis involves well-established approaches with abundant methods available in the literature. Compared with manual sorting, this technique provides a substantially higher throughput (up to 500 cells per h). Furthermore, the platform has very high sorting accuracy (98.3 ± 1.7%) and is fully automated, thus avoiding user biases that might accompany manual sorting. We anticipate that this protocol will empower in particular environmental and host-associated microbiome research with a versatile tool to elucidate the metabolic contributions of microbial taxa within their complex communities. After a 1-d preparation of cells, sorting takes on the order of 4 h, depending on the number of cells required.}, } @article {pmid33311550, year = {2020}, author = {Aluthge, ND and Tom, WA and Bartenslager, AC and Burkey, TE and Miller, PS and Heath, KD and Kreikemeier-Bower, C and Kittana, H and Schmaltz, RJ and Ramer-Tait, AE and Fernando, SC}, title = {Differential longitudinal establishment of human fecal bacterial communities in germ-free porcine and murine models.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {760}, pmid = {33311550}, issn = {2399-3642}, mesh = {Animals ; Bacteria/classification/genetics ; Biodiversity ; Computational Biology/methods ; Disease Models, Animal ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Germ-Free Life ; Humans ; Metagenome ; Metagenomics/methods ; Mice ; Phylogeny ; Reproducibility of Results ; }, abstract = {The majority of microbiome studies focused on understanding mechanistic relationships between the host and the microbiota have used mice and other rodents as the model of choice. However, the domestic pig is a relevant model that is currently underutilized for human microbiome investigations. In this study, we performed a direct comparison of the engraftment of fecal bacterial communities from human donors between human microbiota-associated (HMA) piglet and mouse models under identical dietary conditions. Analysis of 16S rRNA genes using amplicon sequence variants (ASVs) revealed that with the exception of early microbiota from infants, the more mature microbiotas tested established better in the HMA piglets compared to HMA mice. Of interest was the greater transplantation success of members belonging to phylum Firmicutes in the HMA piglets compared to the HMA mice. Together, these results provide evidence for the HMA piglet model potentially being more broadly applicable for donors with more mature microbiotas while the HMA mouse model might be more relevant for developing microbiotas such as those of infants. This study also emphasizes the necessity to exercise caution in extrapolating findings from HMA animals to humans, since up to 28% of taxa from some donors failed to colonize either model.}, } @article {pmid33310751, year = {2021}, author = {He, X and Gao, J and Peng, L and Hu, T and Wan, Y and Zhou, M and Zhen, P and Cao, H}, title = {Bacterial O-GlcNAcase genes abundance decreases in ulcerative colitis patients and its administration ameliorates colitis in mice.}, journal = {Gut}, volume = {70}, number = {10}, pages = {1872-1883}, pmid = {33310751}, issn = {1468-3288}, mesh = {Animals ; Bacteroidetes/enzymology ; Colitis, Ulcerative/*enzymology/*genetics ; Firmicutes/enzymology ; Gastrointestinal Microbiome ; Humans ; Metagenomics ; Mice ; N-Acetylglucosaminyltransferases/*genetics/pharmacology ; }, abstract = {OBJECTIVE: O-linked N-acetylglucosaminylation (O-GlcNAcylation), controlled by O-GlcNAcase (OGA) and O-GlcNAc transferase (OGT), is an important post-translational modification of eukaryotic proteins and plays an essential role in regulating gut inflammation. Gut microbiota encode various enzymes involved in O-GlcNAcylation. However, the characteristics, abundance and function of these enzymes are unknown.

DESIGN: We first investigated the structure and taxonomic distribution of bacterial OGAs and OGTs. Then, we performed metagenomic analysis to explore the OGA genes abundance in health samples and different diseases. Finally, we employed in vitro and in vivo experiments to determine the effects and mechanisms of bacterial OGAs to hydrolyse O-GlcNAcylated proteins in host cells and suppress inflammatory response in the gut.

RESULTS: We found OGAs, instead of OGTs, are enriched in Bacteroidetes and Firmicutes, the major bacterial divisions in the human gut. Most bacterial OGAs are secreted enzymes with the same conserved catalytic domain as human OGAs. A pooled analysis on 1999 metagenomic samples encompassed six diseases revealed that bacterial OGA genes were conserved in healthy human gut with high abundance, and reduced exclusively in ulcerative colitis. In vitro studies showed that bacterial OGAs could hydrolyse O-GlcNAcylated proteins in host cells, including O-GlcNAcylated NF-κB-p65 subunit, which is important for activating NF-κB signalling. In vivo studies demonstrated that gut bacteria-derived OGAs could protect mice from chemically induced colonic inflammation through hydrolysing O-GlcNAcylated proteins.

CONCLUSION: Our results reveal a previously unrecognised enzymatic activity by which gut microbiota influence intestinal physiology and highlight bacterial OGAs as a promising therapeutic strategy in colonic inflammation.}, } @article {pmid33310084, year = {2021}, author = {Galipeau, HJ and Caminero, A and Turpin, W and Bermudez-Brito, M and Santiago, A and Libertucci, J and Constante, M and Raygoza Garay, JA and Rueda, G and Armstrong, S and Clarizio, A and Smith, MI and Surette, MG and Bercik, P and , and Croitoru, K and Verdu, EF}, title = {Novel Fecal Biomarkers That Precede Clinical Diagnosis of Ulcerative Colitis.}, journal = {Gastroenterology}, volume = {160}, number = {5}, pages = {1532-1545}, doi = {10.1053/j.gastro.2020.12.004}, pmid = {33310084}, issn = {1528-0012}, support = {143253//CIHR/Canada ; 1715-000-001//CIHR/Canada ; }, mesh = {Adolescent ; Adult ; Animals ; Bacteria/drug effects/*enzymology/genetics ; Bacterial Proteins/genetics/*metabolism ; Biomarkers/metabolism ; Case-Control Studies ; Child ; Colitis, Ulcerative/diagnosis/drug therapy/*microbiology ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome/drug effects ; Germ-Free Life ; Humans ; Male ; Metagenome ; Metagenomics ; Mice, Inbred C57BL ; Peptide Hydrolases/genetics/*metabolism ; Predictive Value of Tests ; Prospective Studies ; Protease Inhibitors/therapeutic use ; Proteolysis ; Reproducibility of Results ; Ribotyping ; Young Adult ; Mice ; }, abstract = {BACKGROUND & AIMS: Altered gut microbiota composition and function have been associated with inflammatory bowel diseases, including ulcerative colitis (UC), but the causality and mechanisms remain unknown.

METHODS: We applied 16S ribosomal RNA gene sequencing, shotgun metagenomic sequencing, in vitro functional assays, and gnotobiotic colonizations to define the microbial composition and function in fecal samples obtained from a cohort of healthy individuals at risk for inflammatory bowel diseases (pre-UC) who later developed UC (post-UC) and matched healthy control individuals (HCs).

RESULTS: Microbiota composition of post-UC samples was different from HC and pre-UC samples; however, functional analysis showed increased fecal proteolytic and elastase activity before UC onset. Metagenomics identified more than 22,000 gene families that were significantly different between HC, pre-UC, and post-UC samples. Of these, 237 related to proteases and peptidases, suggesting a bacterial component to the pre-UC proteolytic signature. Elastase activity inversely correlated with the relative abundance of Adlercreutzia and other potentially beneficial taxa and directly correlated with known proteolytic taxa, such as Bacteroides vulgatus. High elastase activity was confirmed in Bacteroides isolates from fecal samples. The bacterial contribution and functional significance of the proteolytic signature were investigated in germ-free adult mice and in dams colonized with HC, pre-UC, or post-UC microbiota. Mice colonized with or born from pre-UC-colonized dams developed higher fecal proteolytic activity and an inflammatory immune tone compared with HC-colonized mice.

CONCLUSIONS: We have identified increased fecal proteolytic activity that precedes the clinical diagnosis of UC and associates with gut microbiota changes. This proteolytic signature may constitute a noninvasive biomarker of inflammation to monitor at-risk populations that can be targeted therapeutically with antiproteases.}, } @article {pmid33308267, year = {2020}, author = {Accorsi, EK and Franzosa, EA and Hsu, T and Joice Cordy, R and Maayan-Metzger, A and Jaber, H and Reiss-Mandel, A and Kline, M and DuLong, C and Lipsitch, M and Regev-Yochay, G and Huttenhower, C}, title = {Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {301}, pmid = {33308267}, issn = {1474-760X}, support = {T32 AI007535/AI/NIAID NIH HHS/United States ; T32AI007535//National Institute of Allergy and Infectious Diseases/ ; R21AI112991//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Carnobacteriaceae ; Female ; Humans ; Infant ; Metagenomics ; *Microbiota ; Mothers ; Nose/*microbiology ; RNA, Ribosomal, 16S ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/*genetics ; Streptococcus ; }, abstract = {BACKGROUND: Staphylococcus aureus is a leading cause of healthcare- and community-associated infections and can be difficult to treat due to antimicrobial resistance. About 30% of individuals carry S. aureus asymptomatically in their nares, a risk factor for later infection, and interactions with other species in the nasal microbiome likely modulate its carriage. It is thus important to identify ecological or functional genetic elements within the maternal or infant nasal microbiomes that influence S. aureus acquisition and retention in early life.

RESULTS: We recruited 36 mother-infant pairs and profiled a subset of monthly longitudinal nasal samples from the first year after birth using shotgun metagenomic sequencing. The infant nasal microbiome is highly variable, particularly within the first 2 months. It is weakly influenced by maternal nasal microbiome composition, but primarily shaped by developmental and external factors, such as daycare. Infants display distinctive patterns of S. aureus carriage, positively associated with Acinetobacter species, Streptococcus parasanguinis, Streptococcus salivarius, and Veillonella species and inversely associated with maternal Dolosigranulum pigrum. Furthermore, we identify a gene family, likely acting as a taxonomic marker for an unclassified species, that is significantly anti-correlated with S. aureus in infants and mothers. In gene content-based strain profiling, infant S. aureus strains are more similar to maternal strains.

CONCLUSIONS: This improved understanding of S. aureus colonization is an important first step toward the development of novel, ecological therapies for controlling S. aureus carriage.}, } @article {pmid33308114, year = {2021}, author = {Wu, X and Chen, X and Lyu, X and Zheng, H}, title = {Advances in Microbiome Detection Technologies and Application in Antirheumatic Drug Design.}, journal = {Current pharmaceutical design}, volume = {27}, number = {7}, pages = {891-899}, doi = {10.2174/1381612826666201211114609}, pmid = {33308114}, issn = {1873-4286}, mesh = {*Antirheumatic Agents/pharmacology/therapeutic use ; Dysbiosis/drug therapy ; Humans ; Metagenomics ; *Microbiota ; Technology ; }, abstract = {Rheumatic diseases are a kind of chronic inflammatory and autoimmune disease affecting the connection or supporting structures of the human body, such as the most common diseases Ankylosing spondylitis (AS), gout and Systemic lupus erythematosus (SLE). Although the precise etiology and pathogenesis of the different types of rheumatic diseases remain mostly unknown, it is now commonly believed that these diseases are attributed to some complex interactions between genetics and environmental factors, especially the gut microbiome. Altered microbiome showed clinical improvement in disease symptoms and partially restored to normality after prescribing disease-modifying antirheumatic drugs (DMARDs) or other treatment strategies. Recent advances in next-generation sequencing-based microbial profiling technology, especially metagenomics, have identified alteration of the composition and function of the gut microbiota in patients. Clinical and experimental data suggest that dysbiosis may play a pivotal role in the pathogenesis of these diseases. In this paper, we provide a brief review of the advances in the microbial profiling technology and up-to-date resources for accurate taxonomic assignment of metagenomic reads, which is a key step for metagenomics studies. In addition, we review the altered gut microbiota signatures that have been reported so far across various studies, upon which diagnostics classification models can be constructed, and the drug-induced regulation of the host microbiota can be used to control disease progression and symptoms.}, } @article {pmid33307384, year = {2021}, author = {Ghemrawi, M and Torres, AR and Duncan, G and Colwell, R and Dadlani, M and McCord, B}, title = {The genital microbiome and its potential for detecting sexual assault.}, journal = {Forensic science international. Genetics}, volume = {51}, number = {}, pages = {102432}, doi = {10.1016/j.fsigen.2020.102432}, pmid = {33307384}, issn = {1878-0326}, mesh = {Adult ; Aged ; DNA, Bacterial/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Penis/*microbiology ; Pilot Projects ; Sequence Analysis, DNA ; *Sex Offenses ; Skin/microbiology ; Vagina/*microbiology ; Young Adult ; }, abstract = {Since its inception, the Human Microbiome Project (HMP) has provided key discoveries that can be applied to forensics, in addition to those of obvious medical value. Whether for postmortem interval estimation, geolocation, or human identification, there are many applications of the microbiome as an investigative lead for forensic casework. The human skin microbiome has shown great potential for use in studies of transfer and human identification, however there has been little focus on the genital microbiome, in particular penile skin which differs from other body sites. Our preliminary data on both the penile and vaginal microbiome demonstrates potential value in cases of sexual assault. In this study we describe genital microbial signatures based on the analysis of five male and five female genital samples and compare these results to those from longitudinal studies. Selected taxa, e.g., Gardnerella, Lactobacilli, Finegoldia, Peptoniphilus, and Anaerococci, are shown to be candidate constituents of the genital microbiome that merit investigation for use in sexual assault casework.}, } @article {pmid33307023, year = {2021}, author = {Britton, RA and Hoffmann, DE and Khoruts, A}, title = {Probiotics and the Microbiome-How Can We Help Patients Make Sense of Probiotics?.}, journal = {Gastroenterology}, volume = {160}, number = {2}, pages = {614-623}, doi = {10.1053/j.gastro.2020.11.047}, pmid = {33307023}, issn = {1528-0012}, mesh = {*Biomedical Research/economics/legislation & jurisprudence ; Dietary Supplements/standards ; Drug Industry/economics/legislation & jurisprudence ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; *Legislation, Drug/economics/standards ; *Probiotics/pharmacology/standards/therapeutic use ; }, abstract = {The notion of probiotics as microbes that confer health benefits has its origins in the speculative ideas that are more than a century old, yet remain largely unsubstantiated by scientific evidence. The recent advances in microbiome science have highlighted the importance of intestinal microbes in human physiology and disease pathogenesis. These developments have provided a boost to the probiotics industry, which continues to experience exponential growth driven mainly by creative marketing. Consumers, patients, and most health care providers are not able to discern the underlying science or differentiate the permitted claims that promise vague health benefits from disease-specific claims reserved for drugs. No probiotic product has been able to satisfy the regulatory requirements to be categorized as a drug, a substance intended to cure, mitigate, or prevent disease. However, patients take probiotic products in the belief that they will help to treat their intestinal or systemic diseases. Thus far, the regulators have failed to create policies that would assist to inform the public in this area. In fact, the existing regulatory regime actually creates formidable barriers to research that could provide evidence for clinical efficacy of probiotic products. We propose a potential solution to this vexing problem, where a committee created through a partnership of academia, professional organizations, and industry, but free of potential conflicts of interest, would be charged with rigorous evaluation of specific probiotic products and the evidence in support of their different claims. Companies that would submit to this process would earn the trust of consumers and healthcare providers, as well as a distinction in the marketplace.}, } @article {pmid33305509, year = {2021}, author = {Alexyuk, M and Bogoyavlenskiy, A and Alexyuk, P and Moldakhanov, Y and Berezin, V and Digel, I}, title = {Epipelagic microbiome of the Small Aral Sea: Metagenomic structure and ecological diversity.}, journal = {MicrobiologyOpen}, volume = {10}, number = {1}, pages = {e1142}, pmid = {33305509}, issn = {2045-8827}, mesh = {Archaea/*classification/genetics/isolation & purification ; Bacteria/*classification/genetics/isolation & purification ; *Biodiversity ; Kazakhstan ; Metagenome/*genetics ; Metagenomics ; Microbiota/*genetics ; Oceans and Seas ; Phylogeny ; Sequence Analysis, DNA ; Uzbekistan ; }, abstract = {Microbial diversity studies regarding the aquatic communities that experienced or are experiencing environmental problems are essential for the comprehension of the remediation dynamics. In this pilot study, we present data on the phylogenetic and ecological structure of microorganisms from epipelagic water samples collected in the Small Aral Sea (SAS). The raw data were generated by massive parallel sequencing using the shotgun approach. As expected, most of the identified DNA sequences belonged to Terrabacteria and Actinobacteria (40% and 37% of the total reads, respectively). The occurrence of Deinococcus-Thermus, Armatimonadetes, Chloroflexi in the epipelagic SAS waters was less anticipated. Surprising was also the detection of sequences, which are characteristic for strict anaerobes-Ignavibacteria, hydrogen-oxidizing bacteria, and archaeal methanogenic species. We suppose that the observed very broad range of phylogenetic and ecological features displayed by the SAS reads demonstrates a more intensive mixing of water masses originating from diverse ecological niches of the Aral-Syr Darya River basin than presumed before.}, } @article {pmid33303873, year = {2020}, author = {Yap, M and Feehily, C and Walsh, CJ and Fenelon, M and Murphy, EF and McAuliffe, FM and van Sinderen, D and O'Toole, PW and O'Sullivan, O and Cotter, PD}, title = {Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {21665}, pmid = {33303873}, issn = {2045-2322}, support = {SFI/12/RC/2273//Science Foundation Ireland/Ireland ; }, mesh = {Animals ; *Bacteria/genetics ; Cattle ; DNA/*analysis ; DNA, Bacterial/*analysis ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; *Microbiota/genetics ; Milk/metabolism/*microbiology ; Milk, Human/metabolism/*microbiology ; Sequence Analysis, DNA/*methods ; }, abstract = {Shotgun metagenomic sequencing is a valuable tool for the taxonomic and functional profiling of microbial communities. However, this approach is challenging in samples, such as milk, where a low microbial abundance, combined with high levels of host DNA, result in inefficient and uneconomical sequencing. Here we evaluate approaches to deplete host DNA or enrich microbial DNA prior to sequencing using three commercially available kits. We compared the percentage of microbial reads obtained from each kit after shotgun metagenomic sequencing. Using bovine and human milk samples, we determined that host depletion with the MolYsis complete5 kit significantly improved microbial sequencing depth compared to other approaches tested. Importantly, no biases were introduced. Additionally, the increased microbial sequencing depth allowed for further characterization of the microbiome through the generation of metagenome-assembled genomes (MAGs). Furthermore, with the use of a mock community, we compared three common classifiers and determined that Kraken2 was the optimal classifier for these samples. This evaluation shows that microbiome analysis can be performed on both bovine and human milk samples at a much greater resolution without the need for more expensive deep-sequencing approaches.}, } @article {pmid33302990, year = {2020}, author = {Chen, JC and Tyler, AD}, title = {Systematic evaluation of supervised machine learning for sample origin prediction using metagenomic sequencing data.}, journal = {Biology direct}, volume = {15}, number = {1}, pages = {29}, pmid = {33302990}, issn = {1745-6150}, mesh = {*Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*analysis ; *Supervised Machine Learning ; }, abstract = {BACKGROUND: The advent of metagenomic sequencing provides microbial abundance patterns that can be leveraged for sample origin prediction. Supervised machine learning classification approaches have been reported to predict sample origin accurately when the origin has been previously sampled. Using metagenomic datasets provided by the 2019 CAMDA challenge, we evaluated the influence of variable technical, analytical and machine learning approaches for result interpretation and novel source prediction.

RESULTS: Comparison between 16S rRNA amplicon and shotgun sequencing approaches as well as metagenomic analytical tools showed differences in normalized microbial abundance, especially for organisms present at low abundance. Shotgun sequence data analyzed using Kraken2 and Bracken, for taxonomic annotation, had higher detection sensitivity. As classification models are limited to labeling pre-trained origins, we took an alternative approach using Lasso-regularized multivariate regression to predict geographic coordinates for comparison. In both models, the prediction errors were much higher in Leave-1-city-out than in 10-fold cross validation, of which the former realistically forecasted the increased difficulty in accurately predicting samples from new origins. This challenge was further confirmed when applying the model to a set of samples obtained from new origins. Overall, the prediction performance of the regression and classification models, as measured by mean squared error, were comparable on mystery samples. Due to higher prediction error rates for samples from new origins, we provided an additional strategy based on prediction ambiguity to infer whether a sample is from a new origin. Lastly, we report increased prediction error when data from different sequencing protocols were included as training data.

CONCLUSIONS: Herein, we highlight the capacity of predicting sample origin accurately with pre-trained origins and the challenge of predicting new origins through both regression and classification models. Overall, this work provides a summary of the impact of sequencing technique, protocol, taxonomic analytical approaches, and machine learning approaches on the use of metagenomics for prediction of sample origin.}, } @article {pmid33302682, year = {2020}, author = {Zhang, M and Zhou, H and Xu, S and Liu, D and Cheng, Y and Gao, B and Li, X and Chen, J}, title = {The gut microbiome can be used to predict the gastrointestinal response and efficacy of lung cancer patients undergoing chemotherapy.}, journal = {Annals of palliative medicine}, volume = {9}, number = {6}, pages = {4211-4227}, doi = {10.21037/apm-20-2183}, pmid = {33302682}, issn = {2224-5839}, mesh = {Feces ; *Gastrointestinal Microbiome ; Humans ; *Lung Neoplasms/drug therapy ; }, abstract = {BACKGROUND: Lung cancer has the highest incidence and mortality rate of any cancer worldwide. Platinum-based combination chemotherapy is still the standard treatment for advanced lung cancer. However, the clinical efficacy of this treatment can be affected by its adverse reactions, especially gastrointestinal mucositis. The adverse reactions often lead to delayed and reduced medication. The role played by gut microbiome in the treatment of cancer is becoming clearer, and evidence suggests that regulation of the gut microbiome may affect the response to multiple types of cancer treatment.

METHODS: Sixty lung cancer patients who received chemotherapy for the first time and 17 healthy subjects were enrolled in this study. A metagenomic analysis of 137 fecal samples was performed using next-generation sequencing technology.

RESULTS: The relative abundance of Eubacterium, Ruminococcus, and Faecalibacterium was higher in the lung cancer patients than in the healthy subjects; however, the relative abundance of Prevotella, Streptococcus, Enterococcus, and Roseburia showed the opposite result. The relative abundance of each gut microbiome changed significantly during chemotherapy. At the phylum level, the relative abundance of Firmicutes and Euryarchaeota was dramatically increased after chemotherapy. Lung cancer patients with a higher relative abundance of a particular bacterial genus, such as Prevotella, Megamonas, Streptococcus, Faecalibacterium, Roseburia, Parabacteroides, Coprococcus, Oscillibacter, Dorea, or Chlamydia, at baseline were more likely to experience gastrointestinal reactions. These results show that the intestinal flora can play a role in predicting the effect of chemotherapy in lung cancer patients.

CONCLUSIONS: The gut microbiome of patients with lung cancer differs from those of healthy people. The results of this study suggest that Ruminococcus and Eubacterium may be related to the occurrence and development of lung cancer. The gut microbiome of lung cancer patients changes significantly after treatment with cytotoxic drugs, which may be associated with the gastrointestinal reaction caused by chemotherapy. The gut microbiome also can be used to predict the efficacy of chemotherapy in lung cancer patients.}, } @article {pmid33302073, year = {2021}, author = {Li, M and Zhang, C}, title = {Are silver nanoparticles better than triclosan as a daily antimicrobial? Answers from the perspectives of gut microbiome disruption and pathogenicity.}, journal = {The Science of the total environment}, volume = {756}, number = {}, pages = {143983}, doi = {10.1016/j.scitotenv.2020.143983}, pmid = {33302073}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; *Anti-Infective Agents ; *Gastrointestinal Microbiome ; Humans ; *Metal Nanoparticles/toxicity ; Silver/toxicity ; *Triclosan/toxicity ; Virulence ; }, abstract = {As an alternative to triclosan (TCS), the widespread use of silver nanoparticles (AgNPs) in daily products shows genuine potential. However, information regarding whether AgNPs are substantially better than TCS in their potential disruption of the gut microbiome and health effects is lacking. Using a simulator of the human intestinal microbial ecosystem (SHIME), we systemically compared the effects of TCS and AgNPs (at 1 μg/L and 30 μg/L) on the human gut microbiome in terms of changes in gut homeostasis, microbial community structure, antibiotic resistance profiles and abundances of opportunistic pathogens. Generally, TCS exerted more severe effects than AgNPs on gut disturbances (i.e., decreased production of short-chain fatty acids, increased contents of ammonium and total bile acids, and increased β-glucosidase activities) in a dose-dependent manner, whereas no clear dose effect was observed for the AgNP treatment because of potential nanoparticle transformation. The more serious effect of TCS than AgNPs on the microbiota composition was indicated by the dynamic increase in the Firmicutes/Bacteroidetes ratio determined using 16S rDNA sequencing. Metagenomic analyses revealed a more pronounced effect of TCS than AgNPs on the selection and dissemination of multiple resistance genes to antibiotics, TCS, and even Ag via the enrichment of genes encoding efflux pumps and mobile genetic elements. Consequently, the overgrowth of opportunistic pathogens was observed upon TCS exposure due to an imbalanced microbiome, in contrast to a slight increase in the abundance of some beneficial bacteria (i.e., Bifidobacterium) induced by the AgNP treatment. In conclusion, from the perspective of effects on gut health, AgNPs may prevail over TCS to some extent. However, the stress and potential selection of Ag resistance indicates the need for targeted surveillance of AgNP commercialization for daily use.}, } @article {pmid33301893, year = {2021}, author = {Chen, X and Li, D}, title = {Sequencing facility and DNA source associated patterns of virus-mappable reads in whole-genome sequencing data.}, journal = {Genomics}, volume = {113}, number = {1 Pt 2}, pages = {1189-1198}, pmid = {33301893}, issn = {1089-8646}, support = {R03 AI147084/AI/NIAID NIH HHS/United States ; }, mesh = {Blood/virology ; Clinical Laboratory Services/*standards ; DNA Contamination ; *Genes, Viral ; *Genome, Human ; Humans ; Metagenome ; Signal-To-Noise Ratio ; Virome ; Whole Genome Sequencing/methods/*standards ; }, abstract = {Numerous viral sequences have been reported in the whole-genome sequencing (WGS) data of human blood. However, it is not clear to what degree the virus-mappable reads represent true viral sequences rather than random-mapping or noise originating from sample preparation, sequencing processes, or other sources. Identification of patterns of virus-mappable reads may generate novel indicators for evaluating the origins of these viral sequences. We characterized paired-end unmapped reads and reads aligned to viral references in human WGS datasets, then compared patterns of the virus-mappable reads among DNA sources and sequencing facilities which produced these datasets. We then examined potential origins of the source- and facility-associated viral reads. The proportions of clean unmapped reads among the seven sequencing facilities were significantly different (P < 2 × 10[-16]). We identified 260,339 reads that were mappable to a total of 99 viral references in 2535 samples. The majority (86.7%) of these virus-mappable reads (corresponding to 47 viral references), which can be classified into four groups based on their distinct patterns, were strongly associated with sequencing facility or DNA source (adjusted P value <0.01). Possible origins of these reads include artificial sequences in library preparation, recombinant vectors in cell culture, and phages co-contaminated with their host bacteria. The sequencing facility-associated virus-mappable reads and patterns were repeatedly observed in other datasets produced in the same facilities. We have constructed an analytic framework and profiled the unmapped reads mappable to viral references. The results provide a new understanding of sequencing facility- and DNA source-associated batch effects in deep sequencing data and may facilitate improved bioinformatics filtering of reads.}, } @article {pmid33299088, year = {2021}, author = {Malard, F and Dore, J and Gaugler, B and Mohty, M}, title = {Introduction to host microbiome symbiosis in health and disease.}, journal = {Mucosal immunology}, volume = {14}, number = {3}, pages = {547-554}, pmid = {33299088}, issn = {1935-3456}, mesh = {Animals ; Dysbiosis/*therapy ; Host Microbial Interactions ; Humans ; Iatrogenic Disease/*prevention & control ; Metagenomics ; Microbiota/*physiology ; Nutrition Therapy ; Precision Medicine ; Symbiosis ; }, abstract = {Humans share a core intestinal microbiome and yet human microbiome differs by genes, species, enterotypes (ecology), and gene count (microbial diversity). Achievement of microbiota metagenomic analysis has revealed that the microbiome gene count is a key stratifier of health in several immune disorders and clinical conditions. We review here the progress of the metagenomic pipeline analysis, and how this has allowed us to define the host-microbe symbiosis associated with a healthy status. The link between host-microbe symbiosis disruption, the so-called dysbiosis and chronic diseases or iatrogenic conditions is highlighted. Finally, opportunities to use microbiota modulation, with specific nutrients and/or live microbes, as a target for personalized nutrition and therapy for the maintenance, preservation, or restoration of host-microbe symbiosis are discussed.}, } @article {pmid33299064, year = {2020}, author = {Gusareva, ES and Gaultier, NPE and Premkrishnan, BNV and Kee, C and Lim, SBY and Heinle, CE and Purbojati, RW and Nee, AP and Lohar, SR and Yanqing, K and Kharkov, VN and Drautz-Moses, DI and Stepanov, VA and Schuster, SC}, title = {Taxonomic composition and seasonal dynamics of the air microbiome in West Siberia.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {21515}, pmid = {33299064}, issn = {2045-2322}, mesh = {Actinobacteria/genetics ; Air/*analysis ; *Air Microbiology ; Ascomycota/genetics ; Bacteria/genetics ; Basidiomycota/genetics ; Ecosystem ; Environmental Monitoring/*methods ; Fungi/genetics ; Microbiota ; Proteobacteria/genetics ; Seasons ; Siberia ; }, abstract = {Here, we describe taxonomical composition, as well as seasonal and diel dynamics of airborne microbial communities in West Siberia. A total of 78 airborne biomass samples from 39 time intervals were analysed, within a temperature range of 48 °C (26 °C to - 22 °C). We observed a 5-170-fold decrease in DNA yield extracted from the airborne biomass in winter compared to summer, nevertheless, yielding sufficient material for metagenomic analysis. The airborne microbial communities included Actinobacteria and Proteobacteria, Ascomycota and Basidiomycota fungi as major components, as well as some Streptophyta plants. In summer, bacterial and fungal plant pathogens, and wood-rotting saprophytes were predominant. In winter, Ascomycota moulds and cold-related or stress environment bacterial species were enriched, while the fraction of wood-rotting and mushroom-forming Basidiomycota fungi was largely reduced. As recently reported for the tropical climate, the airborne microbial communities performed a diel cycle in summer, however, in winter diel dynamics were not observed.}, } @article {pmid33299026, year = {2020}, author = {Biagini, F and Calvigioni, M and Lapomarda, A and Vecchione, A and Magliaro, C and De Maria, C and Montemurro, F and Celandroni, F and Mazzantini, D and Mattioli-Belmonte, M and Ghelardi, E and Vozzi, G}, title = {A novel 3D in vitro model of the human gut microbiota.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {21499}, pmid = {33299026}, issn = {2045-2322}, mesh = {Bacteria/growth & development ; Biodiversity ; Biofilms/growth & development ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/microbiology ; Gelatin/chemistry ; Humans ; Microbiota/physiology ; Models, Biological ; Tissue Scaffolds/*chemistry ; }, abstract = {Clinical trials and animal studies on the gut microbiota are often limited by the difficult access to the gut, restricted possibility of in vivo monitoring, and ethical issues. An easily accessible and monitorable in vitro model of the gut microbiota represents a valid tool for a wider comprehension of the mechanisms by which microbes interact with the host and with each other. Herein, we present a novel and reliable system for culturing the human gut microbiota in vitro. An electrospun gelatin structure was biofabricated as scaffold for microbial growth. The efficiency of this structure in supporting microbial proliferation and biofilm formation was initially assessed for five microbes commonly inhabiting the human gut. The human fecal microbiota was then cultured on the scaffolds and microbial biofilms monitored by confocal laser and scanning electron microscopy and quantified over time. Metagenomic analyses and Real-Time qPCRs were performed to evaluate the stability of the cultured microbiota in terms of qualitative and quantitative composition. Our results reveal the three-dimensionality of the scaffold-adhered microbial consortia that maintain the bacterial biodiversity and richness found in the original sample. These findings demonstrate the validity of the developed electrospun gelatin-based system for in vitro culturing the human gut microbiota.}, } @article {pmid33298993, year = {2020}, author = {Wong, MK and Nakao, M and Hyodo, S}, title = {Field application of an improved protocol for environmental DNA extraction, purification, and measurement using Sterivex filter.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {21531}, pmid = {33298993}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; DNA/genetics/*isolation & purification ; DNA, Environmental/genetics/*isolation & purification ; Ecosystem ; Environmental Monitoring/methods ; Filtration/methods ; Hydrobiology/*methods ; Metagenomics/methods ; Water/analysis ; }, abstract = {Environmental DNA (eDNA) is increasingly popular as a useful non-invasive method to monitor and study biodiversity and community structure in freshwater and marine environments. To effectively extract eDNA from the filter surface is a fundamental factor determining the representativeness of the samples. We improved the eDNA extraction efficiency of an established Sterivex method by 12- to 16-fold using a larger volume of lysis buffer mix coupled with backflushing the cartridges. The DNeasy extraction column could be overloaded when the environmental sample input is high, possibly due to a higher nonspecific binding present in environmental samples, thus resulting in a relatively lower quantity measured. Therefore, we included an internal control DNA in the extraction to monitor the extraction and purification efficiencies in field samples, which is crucial for quantification of original eDNA concentration. The use of Takara Probe qPCR Mix supplemented with protein-based additives improved the robustness of the real time PCR assay on inhibitor-rich environmental samples, but prior purification by Qiagen PowerClean Pro Cleanup kit could be essential for inhibitor-rich water samples, even though the recovery rate was unexpectedly low (average 33.0%). The improved extraction and quantification complement the qualitative analyses including metabarcoding and metagenomics in field application.}, } @article {pmid33298661, year = {2021}, author = {Ito, N and Mori, N and Miyashita, NT}, title = {Rhizospheric bacterial community structure of Triticum and Aegilops revealed by pyrosequencing analysis of the 16S rRNA gene: dominance of the A genome over the B and D genomes.}, journal = {Genes & genetic systems}, volume = {95}, number = {5}, pages = {249-268}, doi = {10.1266/ggs.20-00006}, pmid = {33298661}, issn = {1880-5779}, mesh = {Aegilops/genetics/*microbiology ; *Genome, Bacterial ; *Genome, Plant ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Triticum/genetics/*microbiology ; }, abstract = {This study examined the relationship between host plant and rhizospheric bacterial community structure, including composition and diversity, in Triticum and Aegilops species (12 and two accessions, respectively) as well as three closely related species, barley, rye and oat (four accessions), to explore the possibility that wheat root and rhizosphere interaction can be utilized for wheat breeding and biotechnology in the future. For this purpose, DNA was isolated from rhizospheric soil samples and one control non-rhizospheric soil sample, and the 16S rRNA gene region was amplified and subjected to DNA pyrosequencing. A total of 132,888 amplicons were analyzed. Bacterial composition at the phylum level was similar among the 18 rhizospheric samples; however, the proportion of Acidobacteria was much lower in these samples than in the control non-rhizospheric soil sample, indicating that rhizospheres influenced the bacterial composition even at the higher taxonomic level. Across host plant genome types (three levels of ploidy and three major genomes, A, B and D), there was no detectable difference in phylum composition or species diversity. Estimated bacterial species diversity was higher in the control soil sample than in plant rhizospheric soils, implying that bacterial species diversity was reduced in rhizospheres. A PCoA plot and UPGMA dendrogram based on the bacterial species composition showed that control soil was distantly located from the plant rhizospheric samples and that Triticum, Aegilops and related species were well separated. PERMANOVA analysis detected statistically significant differentiation among these four groups. Clustering of Triticum species suggested that the A genome was dominant over the B and D genomes, with respect to the influence on rhizospheric bacterial species composition. Although the cause was not investigated in this study, these results clearly indicated that the genetic constitution of the plant host exerted a strong influence on rhizospheric bacterial community structure.}, } @article {pmid33298571, year = {2020}, author = {Nunn, KL and Clair, GC and Adkins, JN and Engbrecht, K and Fillmore, T and Forney, LJ}, title = {Amylases in the Human Vagina.}, journal = {mSphere}, volume = {5}, number = {6}, pages = {}, pmid = {33298571}, issn = {2379-5042}, support = {P30 GM103324/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Female ; Glycogen/metabolism ; Humans ; Hydrogen-Ion Concentration ; Lactic Acid/metabolism ; Lactobacillus/*growth & development/metabolism ; Metagenome ; Microbiota ; Proteomics ; Vagina/*enzymology/metabolism/*microbiology ; Vaginosis, Bacterial/diagnosis/*enzymology/*microbiology ; alpha-Amylases/*metabolism ; }, abstract = {Dominance of Lactobacillus species in vaginal communities is a hallmark of healthy conditions in the female genital tract. Key nutrients for lactobacilli include sugars produced when glycogen is degraded by α-amylase in the vagina. While α-amylase activity has been demonstrated in vaginal fluids, it is unclear whether α-amylases are produced solely by the host, bacteria in the vagina, or both. We screened cervicovaginal mucus from 23 reproductive-age women, characterized the species composition of vaginal communities, measured vaginal pH, and determined levels of amylase activity, glycogen, and lactic acid. Based on differences in these measured variables, one sample from each of four individual donors was selected for metagenomic and proteomic analyses. Of eight putative bacterial amylases identified in the assembled bacterial metagenomes, we detected four in vaginal fluids. These amylases were produced by various bacteria in different vaginal communities. Moreover, no two communities were the same in terms of which bacteria were producing amylases. Although we detected bacterial amylases in vaginal fluids, there was no clear association between the bacterial species that was dominant in a community and the level of amylase activity. This association was likely masked by the presence of human α-amylase, which was also detected in vaginal fluids. Finally, the levels of amylase activity and glycogen were only weakly associated. Our findings show, for the first time, that multiple amylases from both bacterial and human origins can be present simultaneously in the vagina. This work also suggests that the link between glycogen, amylase, and Lactobacillus in the vagina is complex.IMPORTANCE In this study, we show that multiple bacteria in the vaginal community produce amylases that hydrolyze glycogen into simpler sugars (i.e., maltose and maltotriose). These sugars serve as "common goods" that sustain bacterial populations in vaginal communities. Given the temporal changes that are observed in the human vaginal microbiome, we expect the kinds of bacterial amylases produced will also vary over time. These differences influence the pool of resources that are broadly shared and shape the species composition of the vaginal bacterial community.}, } @article {pmid33296733, year = {2021}, author = {Chen, H and Wang, Z and Liu, H and Nie, Y and Zhu, Y and Jia, Q and Ding, G and Ye, J}, title = {Variable sediment methane production in response to different source-associated sewer sediment types and hydrological patterns: Role of the sediment microbiome.}, journal = {Water research}, volume = {190}, number = {}, pages = {116670}, doi = {10.1016/j.watres.2020.116670}, pmid = {33296733}, issn = {1879-2448}, mesh = {Bacteria/genetics ; Methane ; *Microbiota ; *Sewage ; Sulfates ; }, abstract = {Production of methane (CH4), an essential anthropogenic greenhouse gas, from municipal sewer sediment is a problem deserving intensive attention. Based on long-term laboratory batch tests in conjunction with 16 s rRNA gene sequencing and metagenomics, this study provides the first detailed assessment of the variable sediment CH4 production in response to different pollution source-associated sewer sediment types and hydrological patterns, while addressing the role of the sediment microbiome. The high CH4-production capability of sanitary sewer sediment is shaped by enriched biologically active substrate and dominated by acetoclastic methanogenesis (genus Methanosaeta). Moreover, it involves syntrophic interactions among fermentation bacteria, hydrogen-producing acetogens and methanogens. Distinct source-associated microbial species, denitrifying bacteria and sulfate-reducing bacteria occur in storm sewer and illicit discharge-associated (IDA) storm sewer sediments. This reveals their insufficient microbial function capabilities to support efficient methanogenesis. Hydrogenotrophic methanogenesis (genus Methanobacterium) prevails in both these sediments. In this context, storm sewer sediment has an extremely low CH4-production capability, while IDA storm sewer sediment still shows significant carbon emission through a possibly unique mechanism. Hydrological connections promote the sewer sediment biodegradability and CH4-production capability. In contrast, hydrological disconnection facilitates the prevalence of acetoclastic methanogenesis, sulfate-reducing enzymes, denitrification enzymes and the sulfur-utilizing chemolithoautotrophic denitrifier, which drastically decreases CH4 production. Turbulent suspension of sediments results in relative stagnation of methanogenesis. This work bridges the knowledge gap and will help to stimulate and guide the resolution of 'bottom-up' system-scale carbon budgets and GHG sources, as well as the target CH4 abatement interventions.}, } @article {pmid33294135, year = {2020}, author = {Tobias, NJ and Eberhard, FE and Guarneri, AA}, title = {Enzymatic biosynthesis of B-complex vitamins is supplied by diverse microbiota in the Rhodnius prolixus anterior midgut following Trypanosoma cruzi infection.}, journal = {Computational and structural biotechnology journal}, volume = {18}, number = {}, pages = {3395-3401}, pmid = {33294135}, issn = {2001-0370}, abstract = {Trypanosoma cruzi, the causative agent of Chagas disease, colonizes the gut of triatomine insects, including Rhodnius prolixus. It is believed that this colonization upsets the microbiota that are normally present, presumably switching the environment to one more favorable for parasite survival. It was previously thought that one particular bacterium, Rhodococcus rhodnii, was essential for insect survival due to its ability to produce vital B-complex vitamins. However, these bacteria are not always identified in great abundance in studies on R. prolixus microbiota. Here we sequenced the microbiota of the insect anterior midgut using shotgun metagenomic sequencing in order to obtain a high-resolution snapshot of the microbes inside at two different time points and under two conditions; in the presence or absence of parasite and immediately following infection, or three days post-infection. We identify a total of 217 metagenomic bins, and recovered one metagenome-assembled genome, which we placed in the genus Dickeya. We show that, despite Rhodococcus being present, it is not the only microbe capable of synthesizing B-complex vitamins, with the genes required for biosynthesis present in a number of different microbes. This work helps to gain a new insight into the microbial ecology of R. prolixus.}, } @article {pmid33293686, year = {2020}, author = {West, KM and Richards, ZT and Harvey, ES and Susac, R and Grealy, A and Bunce, M}, title = {Under the karst: detecting hidden subterranean assemblages using eDNA metabarcoding in the caves of Christmas Island, Australia.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {21479}, pmid = {33293686}, issn = {2045-2322}, mesh = {Animals ; Australia ; *Biodiversity ; Cell Nucleus/genetics ; *DNA Barcoding, Taxonomic/methods ; DNA, Environmental/*genetics ; Eukaryota/genetics ; Indian Ocean ; *Metagenomics/methods ; Mitochondria/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Subterranean ecosystems are understudied and challenging to conventionally survey given the inaccessibility of underground voids and networks. In this study, we conducted a eukaryotic environmental DNA (eDNA) metabarcoding survey across the karst landscape of Christmas Island, (Indian Ocean, Australia) to evaluate the utility of this non-invasive technique to detect subterranean aquatic 'stygofauna' assemblages. Three metabarcoding assays targeting the mitochondrial 16S rRNA and nuclear 18S genes were applied to 159 water and sediment samples collected from 23 caves and springs across the island. Taken together, our assays detected a wide diversity of chordates, cnidarians, porifera, arthropods, molluscs, annelids and bryozoans from 71 families across 60 orders. We report a high level of variation between cave and spring subterranean community compositions which are significantly influenced by varying levels of salinity. Additionally, we show that dissolved oxygen and longitudinal gradients significantly affect biotic assemblages within cave communities. Lastly, we combined eDNA-derived community composition and environmental (water quality) data to predict potential underground interconnectivity across Christmas Island. We identified three cave and spring groups that showed a high degree of biotic and abiotic similarity indicating likely local connectivity. This study demonstrates the applicability of eDNA metabarcoding to detect subterranean eukaryotic communities and explore underground interconnectivity.}, } @article {pmid33293569, year = {2020}, author = {Faddetta, T and Ardizzone, F and Faillaci, F and Reina, C and Palazzotto, E and Strati, F and De Filippo, C and Spinelli, G and Puglia, AM and Gallo, G and Cavalieri, V}, title = {Composition and geographic variation of the bacterial microbiota associated with the coelomic fluid of the sea urchin Paracentrotus lividus.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {21443}, pmid = {33293569}, issn = {2045-2322}, mesh = {Animals ; Bacteria/*classification/genetics/growth & development/isolation & purification ; Bacteriological Techniques ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; High-Throughput Nucleotide Sequencing ; Microbiota ; Paracentrotus/*growth & development/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {In the present work, culture-based and culture-independent investigations were performed to determine the microbiota structure of the coelomic fluid of Mediterranean sea urchin Paracentrotus lividus individuals collected from two distinct geographical sites neighboring a high-density population bay and a nature reserve, respectively. Next Generation Sequencing analysis of 16S rRNA gene (rDNA) showed that members of the Proteobacteria, Bacteroidetes and Fusobacteria phyla, which have been previously reported to be commonly retrieved from marine invertebrates, dominate the overall population of microorganisms colonizing this liquid tissue, with minority bacterial genera exhibiting remarkable differences among individuals. Our results showed that there is a correlation between microbiota structure and geographical location of the echinoderm collection site, highlighting over-representation of metagenomic functions related to amino acid and bioactive peptides metabolism in specimens inhabiting the nature reserve. Finally, we also described the developmental delay and aberrations exhibited by sea urchin embryos exposed to distinct bacterial isolates, and showed that these defects rely upon hydrophilic compound(s) synthesized by the bacterial strains assayed. Altogether, our findings lay the groundwork to decipher the relationships of bacteria with sea urchins in their aquatic environment, also providing an additional layer of information to understand the biological roles of the coelomic fluid.}, } @article {pmid33292949, year = {2020}, author = {Song, D and Ho, CT and Zhang, X and Wu, Z and Cao, J}, title = {Modulatory effect of Cyclocarya paliurus flavonoids on the intestinal microbiota and liver clock genes of circadian rhythm disorder mice model.}, journal = {Food research international (Ottawa, Ont.)}, volume = {138}, number = {Pt A}, pages = {109769}, doi = {10.1016/j.foodres.2020.109769}, pmid = {33292949}, issn = {1873-7145}, mesh = {Animals ; *Chronobiology Disorders ; Flavonoids/pharmacology ; *Gastrointestinal Microbiome ; Intestines ; Liver ; Mice ; }, abstract = {Host circadian rhythm and gut microbiota have a bidirectional relationship, indicating that prebiotics or prebiotic-like substance is a possible way to regulate circadian rhythm. The modulatory effect of Cyclocarya paliurus flavonoids (CPF) on the intestinal microbiota and liver clock genes of a circadian rhythm disorder mouse model was investigated in the present study. 16S rDNA sequencing analysis showed that CPF ameliorated the imbalanced intestinal microbial structure induced by circadian rhythm disorder. Compared with the constant darkness (CD) group, the ratio of the relative abundance of Firmicutes to Bacteroidetes was significantly decreased after the intervention of CPF for 4 weeks. In addition, CPF significantly alleviated the disrupted diurnal oscillation and phase shift of the specific intestinal microbes and liver clock genes induced by constant darkness. Moreover, metagenomics analysis of gut microbiota showed that the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched the most differentially expressed genes (DEGs) after CPF administration includes xenobiotics biodegradation and metabolism, carbohydrate metabolism and cell motility. The results suggested that CPF may positively regulate the gut flora disturbed by host circadian rhythm disorder, including its composition, diurnal oscillation and function, as well as affect the expression of liver clock genes, thus improving the host micro-ecology and health.}, } @article {pmid33291229, year = {2020}, author = {Suskind, DL and Lee, D and Kim, YM and Wahbeh, G and Singh, N and Braly, K and Nuding, M and Nicora, CD and Purvine, SO and Lipton, MS and Jansson, JK and Nelson, WC}, title = {The Specific Carbohydrate Diet and Diet Modification as Induction Therapy for Pediatric Crohn's Disease: A Randomized Diet Controlled Trial.}, journal = {Nutrients}, volume = {12}, number = {12}, pages = {}, pmid = {33291229}, issn = {2072-6643}, support = {IBD Nutrition Grant//Kenneth Rainin Foundation/ ; Academic Enrichment Fund//Seattle Children's Center for Clinical and Translational Research/ ; UL1TR000423//National Center for Advancing Translational Sciences of the National Institutes of Health/ ; grid.436923.9//Environmental Molecular Sciences Laboratory (EMSL)/ ; }, mesh = {Adolescent ; C-Reactive Protein ; Carbohydrates ; Child ; Crohn Disease/*diet therapy/therapy ; *Diet ; *Dietary Carbohydrates ; Double-Blind Method ; Dysbiosis/*drug therapy ; Female ; Humans ; *Induction Chemotherapy ; Inflammatory Bowel Diseases ; Male ; Metabolomics ; Metagenomics ; Microbiota ; Proteomics ; }, abstract = {BACKGROUND: Crohn's disease (CD) is a chronic inflammatory intestinal disorder associated with intestinal dysbiosis. Diet modulates the intestinal microbiome and therefore has a therapeutic potential. The aim of this study is to determine the potential efficacy of three versions of the specific carbohydrate diet (SCD) in active Crohn's Disease.

METHODS: 18 patients with mild/moderate CD (PCDAI 15-45) aged 7 to 18 years were enrolled. Patients were randomized to either SCD, modified SCD(MSCD) or whole foods (WF) diet. Patients were evaluated at baseline, 2, 4, 8 and 12 weeks. PCDAI, inflammatory labs and multi-omics evaluations were assessed.

RESULTS: Mean age was 14.3 ± 2.9 years. At week 12, all participants (n = 10) who completed the study achieved clinical remission. The C-reactive protein decreased from 1.3 ± 0.7 at enrollment to 0.9 ± 0.5 at 12 weeks in the SCD group. In the MSCD group, the CRP decreased from 1.6 ± 1.1 at enrollment to 0.7 ± 0.1 at 12 weeks. In the WF group, the CRP decreased from 3.9 ± 4.3 at enrollment to 1.6 ± 1.3 at 12 weeks. In addition, the microbiome composition shifted in all patients across the study period. While the nature of the changes was largely patient specific, the predicted metabolic mode of the organisms increasing and decreasing in activity was consistent across patients.

CONCLUSIONS: This study emphasizes the impact of diet in CD. Each diet had a positive effect on symptoms and inflammatory burden; the more exclusionary diets were associated with a better resolution of inflammation.}, } @article {pmid33290720, year = {2021}, author = {Durrant, MG and Bhatt, AS}, title = {Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes.}, journal = {Cell host & microbe}, volume = {29}, number = {1}, pages = {121-131.e4}, pmid = {33290720}, issn = {1934-6069}, support = {P30 CA124435/CA/NCI NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Bacterial Proteins/genetics ; Computational Biology ; Deep Learning ; *Genome, Bacterial ; Humans ; Markov Chains ; Microbiota ; Models, Theoretical ; *Molecular Sequence Annotation ; *Open Reading Frames ; }, abstract = {Small open reading frames (smORFs) and their encoded microproteins play central roles in microbes. However, there is a vast unexplored space of smORFs within human-associated microbes. A recent bioinformatic analysis used evolutionary conservation signals to enhance prediction of small protein families. To facilitate the annotation of specific smORFs, we introduce SmORFinder. This tool combines profile hidden Markov models of each smORF family and deep learning models that better generalize to smORF families not seen in the training set, resulting in predictions enriched for Ribo-seq translation signals. Feature importance analysis reveals that the deep learning models learn to identify Shine-Dalgarno sequences, deprioritize the wobble position in each codon, and group codon synonyms found in the codon table. A core-genome analysis of 26 bacterial species identifies several core smORFs of unknown function. We pre-compute smORF annotations for thousands of RefSeq isolate genomes and Human Microbiome Project metagenomes and provide these data through a public web portal.}, } @article {pmid33289802, year = {2020}, author = {Haro-Moreno, JM and Coutinho, FH and Zaragoza-Solas, A and Picazo, A and Almagro-Moreno, S and López-Pérez, M}, title = {Dysbiosis in marine aquaculture revealed through microbiome analysis: reverse ecology for environmental sustainability.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {12}, pages = {}, doi = {10.1093/femsec/fiaa218}, pmid = {33289802}, issn = {1574-6941}, mesh = {Animals ; Aquaculture ; Bacteria/genetics ; *Dysbiosis ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {The increasing demand for products for human consumption is leading to the fast-growing expansion of numerous food sectors such as marine aquaculture (mariculture). However, excessive input of nutrients and pollutants modifies marine ecosystems. Here, we applied a metagenomic approach to investigate these perturbations in samples from marine farms of gilthead seabream cultures. Results revealed dysbiosis and functional imbalance within the net cage with a unique structure, with little interference with samples from the fish microbiota or those collected far away from the coast. Remarkably, below the cage the prokaryotic community was highly similar to the marine microbiome of photic offshore samples. We recovered 48 novel metagenome-assembled genomes. Metagenomic recruitment revealed a significant change in the microbial community which was dominated by several Proteobacteria orders (Sphingomonadales, Pseudomonadales, Caudobacterales and Rhizobiales). Genomic potential for bioremediation processes, including nitrate removal through aerobic denitrification, and degradation of aromatic compounds and other toxic products were enriched in these microbes. The detrimental side effects were the increased number of antimicrobial resistance genes and the presence of potentially emergent pathogens. Knowledge of this metabolic diversity and the microbes involved in ecological balance recovery can be used to reduce the environmental impact of these practices.}, } @article {pmid33288859, year = {2021}, author = {Pereira, O and Hochart, C and Boeuf, D and Auguet, JC and Debroas, D and Galand, PE}, title = {Seasonality of archaeal proteorhodopsin and associated Marine Group IIb ecotypes (Ca. Poseidoniales) in the North Western Mediterranean Sea.}, journal = {The ISME journal}, volume = {15}, number = {5}, pages = {1302-1316}, pmid = {33288859}, issn = {1751-7370}, mesh = {*Archaea/genetics ; *Ecotype ; Mediterranean Sea ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhodopsins, Microbial ; Seawater ; }, abstract = {The Archaea Marine Group II (MGII) is widespread in the world's ocean where it plays an important role in the carbon cycle. Despite recent discoveries on the group's metabolisms, the ecology of this newly proposed order (Candidatus Poseidoniales) remains poorly understood. Here we used a combination of time-series metagenome-assembled genomes (MAGs) and high-frequency 16S rRNA data from the NW Mediterranean Sea to test if the taxonomic diversity within the MGIIb family (Candidatus Thalassarchaeaceae) reflects the presence of different ecotypes. The MAGs' seasonality revealed a MGIIb family composed of different subclades that have distinct lifestyles and physiologies. The vitamin metabolisms were notably different between ecotypes with, in some, a possible link to sunlight's energy. Diverse archaeal proteorhodopsin variants, with unusual signature in key amino acid residues, had distinct seasonal patterns corresponding to changing day length. In addition, we show that in summer, archaea, as opposed to bacteria, disappeared completely from surface waters. Our results shed light on the diversity and the distribution of the euryarchaeotal proteorhodopsin, and highlight that MGIIb is a diverse ecological group. The work shows that time-series based studies of the taxonomy, seasonality, and metabolisms of marine prokaryotes is critical to uncover their diverse role in the ocean.}, } @article {pmid33287416, year = {2020}, author = {Averina, OV and Zorkina, YA and Yunes, RA and Kovtun, AS and Ushakova, VM and Morozova, AY and Kostyuk, GP and Danilenko, VN and Chekhonin, VP}, title = {Bacterial Metabolites of Human Gut Microbiota Correlating with Depression.}, journal = {International journal of molecular sciences}, volume = {21}, number = {23}, pages = {}, pmid = {33287416}, issn = {1422-0067}, support = {20-14-00132//Russian Science Foundation/ ; }, mesh = {Amino Acids/metabolism ; Bacteria/*metabolism ; Biomarkers ; Brain/metabolism ; Depression/*etiology/*metabolism/psychology ; Disease Susceptibility ; Energy Metabolism ; Functional Food ; *Gastrointestinal Microbiome ; Humans ; Neurotransmitter Agents/metabolism ; }, abstract = {Depression is a global threat to mental health that affects around 264 million people worldwide. Despite the considerable evolution in our understanding of the pathophysiology of depression, no reliable biomarkers that have contributed to objective diagnoses and clinical therapy currently exist. The discovery of the microbiota-gut-brain axis induced scientists to study the role of gut microbiota (GM) in the pathogenesis of depression. Over the last decade, many of studies were conducted in this field. The productions of metabolites and compounds with neuroactive and immunomodulatory properties among mechanisms such as the mediating effects of the GM on the brain, have been identified. This comprehensive review was focused on low molecular weight compounds implicated in depression as potential products of the GM. The other possible mechanisms of GM involvement in depression were presented, as well as changes in the composition of the microbiota of patients with depression. In conclusion, the therapeutic potential of functional foods and psychobiotics in relieving depression were considered. The described biomarkers associated with GM could potentially enhance the diagnostic criteria for depressive disorders in clinical practice and represent a potential future diagnostic tool based on metagenomic technologies for assessing the development of depressive disorders.}, } @article {pmid33285231, year = {2021}, author = {Zhao, X and Oduro, PK and Tong, W and Wang, Y and Gao, X and Wang, Q}, title = {Therapeutic potential of natural products against atherosclerosis: Targeting on gut microbiota.}, journal = {Pharmacological research}, volume = {163}, number = {}, pages = {105362}, doi = {10.1016/j.phrs.2020.105362}, pmid = {33285231}, issn = {1096-1186}, mesh = {Animals ; Atherosclerosis/*drug therapy/microbiology ; Biological Products/*therapeutic use ; Gastrointestinal Microbiome/*drug effects ; Humans ; }, abstract = {Gut microbiota (GM) has emerged as an essential and integral factor for maintaining human health and affecting pathological outcomes. Metagenomics and metabolomics characterization have furthered gut metagenome's understanding and unveiled that deviation of specific GM community members and GM-dependent metabolites imbalance orchestrate metabolic or cardiovascular diseases (CVDs). Restoring GM ecosystem with nutraceutical supplements keenly prebiotics and probiotics relatively decreases CVDs incidence and overall mortality. In Atherosclerosis, commensal and pathogenic gut microbes correlate with atherogenesis events. GM-dependent metabolites-trimethylamine N-oxide and short-chain fatty acids regulate atherosclerosis-related metabolic processes in opposite patterns to affect atherosclerosis outcomes. Therefore, GM might be a potential therapeutic target for atherosclerosis. In atherogenic animal models, natural products with cardioprotective properties could modulate the GM ecosystem by revitalizing healthier GM phylotypes and abrogating proatherogenic metabolites, paving future research paths for clinical therapeutics.}, } @article {pmid33282748, year = {2020}, author = {Nath, S and Kumari, N and Bandyopadhyay, D and Sinha, N and Majumder, PP and Mitra, R and Mukherjee, S}, title = {Dysbiotic Lesional Microbiome With Filaggrin Missense Variants Associate With Atopic Dermatitis in India.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {570423}, pmid = {33282748}, issn = {2235-2988}, mesh = {Adult ; Child ; *Dermatitis, Atopic/genetics ; Dysbiosis ; Filaggrin Proteins ; Humans ; India ; Intermediate Filament Proteins ; Malassezia ; *Microbiota ; Mutation ; Mutation, Missense ; S100 Proteins ; }, abstract = {Background: Atopic Dermatitis (AD) has been associated with the loss of function (LoF) mutations in Filaggrin (FLG) gene and increase in relative abundance of specific microbes in the lesional skin, predominantly in Caucasians. Our study aims to determine, in Indian AD patients, (a) the prevalence of FLG LoF and missense mutations, and (b) the nature and extent of dysbiosis and altered microbial pathways with and without mutations in FLG. AD patients (n = 34) and healthy controls (n = 54) were recruited from India in this study and shotgun sequencing was carried out in a subset of samples with adequate microbiome DNA concentration. Host DNA from the same subset of samples was subjected to FLG coding region sequencing and host-microbiome association was estimated. Results: The prevalence of FLG LoFs that are associated with AD globally were significantly lesser in our cases and controls (8.6%, 0%) than those reported in Europeans (27%, 2.6%). Staphylococcus aureus was present only on AD skin [abundance in Pediatric AD: 32.86%; Adult AD: 22.17%], but not on healthy skin on which Staphylococcus hominis (Adult controls: 16.43%, Adult AD: 0.20%; p = 0.002), Cutibacterium acnes (Adult controls:10.84%, Adult AD: 0.90%; p = 0.02), and Malassezia globosa (Adult controls: 8.89%, Adult AD: 0.005%; p = 0.001) were significantly more abundant. Microbial pathways mostly associated with skin barrier permeability, ammonia production and inflammation (Arginine and Proline metabolism, Histidine Metabolism and Staphylococcus aureus infection) were significantly enriched on AD skin metagenome. These pathways are also reported to impair antimicrobial peptide activity. Among AD patients with missense single nucleotide polymorphisms harboring "potentially damaging" alleles in FLG gene, damaging allele dosage was significantly (p < 0.02) positively correlated with relative abundance of phylum_Proteobacteria up to order_Pseudomonadales and negatively correlated with phylum_Firmicutes up to species_Staphylococcus aureus. Conclusion: Our study has provided evidence that host DNA profile is significantly associated with microbiome composition in the development of AD. Species and strain level analysis showed that the microbial pathways enriched in AD cases were mostly found in MRSA strains. These evidences can be harnessed to control AD by modulating the microbiome using a personalized strategy. Our findings on the association of FLG genotypes with the microbiome dysbiosis may pave the way for a personalized strategy to provide a more effective control of AD.}, } @article {pmid33281177, year = {2020}, author = {Hashimoto, K and Yamazaki, F and Kohyama, N and Kawakami, Y}, title = {Analysis of Fungal Flora in the Dust of Bedding in Japanese Houses and Genetic Identification of Yeasts Isolated from the Dust.}, journal = {Biocontrol science}, volume = {25}, number = {4}, pages = {193-202}, doi = {10.4265/bio.25.193}, pmid = {33281177}, issn = {1884-0205}, mesh = {Bedding and Linens/*microbiology ; Dust/*analysis ; *Environmental Microbiology ; Fungi/*classification/*genetics/isolation & purification ; Humans ; Metagenome ; Metagenomics/methods ; *Mycobiome ; }, abstract = {This study examined the fungal flora contained in the dust of bedding used in 50 houses in Japan. The result showed that the mycoflora having the largest isolation rate was yeasts, which were isolated by 42 out of 50 houses (84%), and exceeded the isolation rate of Cladosporium spp. (80%) and Aspergillus spp. (66%). In addition, the isolation rate of Alternaria, which was an important fungus causing asthma, 66% was being considered as a high isolation rate, and this result was very interesting. The isolation rate of xerophilic fungi such as Aspergillus restrictus and Wallemia often found in house dust on the floor, was not very high. Forty-one strains of yeasts isolated from each dust sample were identified, and Naganishia diffluens species complex and Filobasidium magnum had a larger number of 13 strains, respectively. Since N. diffluens was the yeasts often isolated from human skin, it was thought to be an association between the fungal skin flora and fungal flora of bed dust. Meanwhile, there was no report of isolation of F. magnum from house dust previously. To the best of our knowledge, this is the first study showing its isolation from bedding with relatively high frequency.}, } @article {pmid33277629, year = {2021}, author = {Maghini, DG and Moss, EL and Vance, SE and Bhatt, AS}, title = {Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome.}, journal = {Nature protocols}, volume = {16}, number = {1}, pages = {458-471}, pmid = {33277629}, issn = {1750-2799}, support = {P30 CA124435/CA/NCI NIH HHS/United States ; P50 AG047366/AG/NIA NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; }, mesh = {DNA/genetics/isolation & purification ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; *Microbiota ; Nanopore Sequencing/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {Short-read metagenomic sequencing and de novo genome assembly of the human gut microbiome can yield draft bacterial genomes without isolation and culture. However, bacterial genomes assembled from short-read sequencing are often fragmented. Furthermore, these metagenome-assembled genomes often exclude repeated genomic elements, such as mobile genetic elements, compromising our understanding of the contribution of these elements to important bacterial phenotypes. Although long-read sequencing has been applied successfully to the assembly of contiguous bacterial isolate genomes, extraction of DNA of sufficient molecular weight, purity and quantity for metagenomic sequencing from stool samples can be challenging. Here, we present a protocol for the extraction of microgram quantities of high-molecular-weight DNA from human stool samples that are suitable for downstream long-read sequencing applications. We also present Lathe (www.github.com/bhattlab/lathe), a computational workflow for long-read basecalling, assembly, consensus refinement with long reads or Illumina short reads and genome circularization. Altogether, this protocol can yield high-quality contiguous or circular bacterial genomes from a complex human gut sample in approximately 10 d, with 2 d of hands-on bench and computational effort.}, } @article {pmid33277504, year = {2020}, author = {Tian, L and Wang, XW and Wu, AK and Fan, Y and Friedman, J and Dahlin, A and Waldor, MK and Weinstock, GM and Weiss, ST and Liu, YY}, title = {Deciphering functional redundancy in the human microbiome.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {6217}, pmid = {33277504}, issn = {2041-1723}, support = {K01 HL130629/HL/NHLBI NIH HHS/United States ; R01 AI042347/AI/NIAID NIH HHS/United States ; U19 AI095219/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; U01 HL089856/HL/NHLBI NIH HHS/United States ; R01 AI141529/AI/NIAID NIH HHS/United States ; R01 HD093761/HD/NICHD NIH HHS/United States ; UH3 OD023268/OD/NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/classification/genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Gene Regulatory Networks ; Gene Transfer, Horizontal ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Models, Genetic ; }, abstract = {Although the taxonomic composition of the human microbiome varies tremendously across individuals, its gene composition or functional capacity is highly conserved - implying an ecological property known as functional redundancy. Such functional redundancy has been hypothesized to underlie the stability and resilience of the human microbiome, but this hypothesis has never been quantitatively tested. The origin of functional redundancy is still elusive. Here, we investigate the basis for functional redundancy in the human microbiome by analyzing its genomic content network - a bipartite graph that links microbes to the genes in their genomes. We find that this network exhibits several topological features that favor high functional redundancy. Furthermore, we develop a simple genome evolution model to generate genomic content network, finding that moderate selection pressure and high horizontal gene transfer rate are necessary to generate genomic content networks with key topological features that favor high functional redundancy. Finally, we analyze data from two published studies of fecal microbiota transplantation (FMT), finding that high functional redundancy of the recipient's pre-FMT microbiota raises barriers to donor microbiota engraftment. This work elucidates the potential ecological and evolutionary processes that create and maintain functional redundancy in the human microbiome and contribute to its resilience.}, } @article {pmid33277434, year = {2020}, author = {Reysenbach, AL and St John, E and Meneghin, J and Flores, GE and Podar, M and Dombrowski, N and Spang, A and L'Haridon, S and Humphris, SE and de Ronde, CEJ and Caratori Tontini, F and Tivey, M and Stucker, VK and Stewart, LC and Diehl, A and Bach, W}, title = {Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {51}, pages = {32627-32638}, pmid = {33277434}, issn = {1091-6490}, mesh = {Archaea/genetics ; Bacteria/genetics ; Biodiversity ; Hydrogen-Ion Concentration ; Hydrothermal Vents/*microbiology ; Metagenome ; Microbial Consortia/*physiology ; New Zealand ; Oxidation-Reduction ; Pacific Ocean ; Phylogeny ; Seawater/*microbiology ; Sulfides/chemistry ; *Volcanic Eruptions ; }, abstract = {Hydrothermally active submarine volcanoes are mineral-rich biological oases contributing significantly to chemical fluxes in the deep sea, yet little is known about the microbial communities inhabiting these systems. Here we investigate the diversity of microbial life in hydrothermal deposits and their metagenomics-inferred physiology in light of the geological history and resulting hydrothermal fluid paths in the subsurface of Brothers submarine volcano north of New Zealand on the southern Kermadec arc. From metagenome-assembled genomes we identified over 90 putative bacterial and archaeal genomic families and nearly 300 previously unknown genera, many potentially endemic to this submarine volcanic environment. While magmatically influenced hydrothermal systems on the volcanic resurgent cones of Brothers volcano harbor communities of thermoacidophiles and diverse members of the superphylum "DPANN," two distinct communities are associated with the caldera wall, likely shaped by two different types of hydrothermal circulation. The communities whose phylogenetic diversity primarily aligns with that of the cone sites and magmatically influenced hydrothermal systems elsewhere are characterized predominately by anaerobic metabolisms. These populations are probably maintained by fluids with greater magmatic inputs that have interacted with different (deeper) previously altered mineral assemblages. However, proximal (a few meters distant) communities with gene-inferred aerobic, microaerophilic, and anaerobic metabolisms are likely supported by shallower seawater-dominated circulation. Furthermore, mixing of fluids from these two distinct hydrothermal circulation systems may have an underlying imprint on the high microbial phylogenomic diversity. Collectively our results highlight the importance of considering geologic evolution and history of subsurface processes in studying microbial colonization and community dynamics in volcanic environments.}, } @article {pmid33277317, year = {2021}, author = {Zhang, X and Hoffman, KL and Wei, P and Elhor Gbito, KY and Joseph, R and Li, F and Scheet, P and Chang, S and Petrosino, JF and Daniel, CR}, title = {Baseline Oral Microbiome and All-cancer Incidence in a Cohort of Nonsmoking Mexican American Women.}, journal = {Cancer prevention research (Philadelphia, Pa.)}, volume = {14}, number = {3}, pages = {383-392}, pmid = {33277317}, issn = {1940-6215}, support = {P30 CA008748/CA/NCI NIH HHS/United States ; P30 CA016672/CA/NCI NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; R25 CA057730/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Bacteria/*pathogenicity ; Dysbiosis/*complications/microbiology ; Female ; Follow-Up Studies ; Humans ; Incidence ; Mexican Americans/*statistics & numerical data ; *Microbiota ; Middle Aged ; Mouth/*microbiology ; Neoplasms/*epidemiology/microbiology/pathology ; Prognosis ; Prospective Studies ; Texas/epidemiology ; Young Adult ; }, abstract = {Given the increasing evidence that the oral microbiome is involved in obesity, diabetes, and cancer risk, we investigated baseline oral microbiota profiles in relation to all-cancer incidence among nonsmoking women enrolled in a Texas cohort of first- and second-generation immigrants of Mexican origin. We characterized the 16Sv4 rDNA microbiome in oral mouthwash samples collected at baseline from a representative subset of 305 nonsmoking women, ages 20-75 years. We evaluated within- (alpha) and between-sample (beta) diversity by incident cancer status and applied linear discriminant analysis (LDA) effect size analysis to assess differentially abundant taxa. Diversity and candidate taxa in relation to all-cancer incidence were evaluated in multivariable-adjusted Cox regression models. Over 8.8 median years of follow-up, 31 incident cancer cases were identified and verified. Advanced age, greater acculturation, and cardiometabolic risk factors were associated with all-cancer incidence. Higher alpha diversity (age-adjusted P difference < 0.01) and distinct biological communities (P difference = 0.002) were observed by incident cancer status. Each unit increase in the Shannon diversity index yielded >8-fold increase in all-cancer and obesity-related cancer risk [multivariable-adjusted HR (95% confidence interval), 8.11 (3.14-20.94) and 10.72 (3.30-34.84), respectively] with similar findings for the inverse Simpson index. Streptococcus was enriched among women who did not develop cancer, while Fusobacterium, Prevotella, Mogibacterium, Campylobacter, Lachnoanaerobaculum, Dialister, and Atopobium were higher among women who developed cancer (LDA score ≥ 3; q-value < 0.01). This initial study of oral microbiota and overall cancer risk in nonsmoking Mexican American women suggests the readily accessible oral microbiota as a promising biomarker. PREVENTION RELEVANCE: Mexican American women suffer a disproportionate burden of chronic health conditions that increase cancer risk. Few investigations of the microbiome, a key determinant of host health, have been conducted among this group. Oral microbiota profiles may provide early and accessible cancer biomarker data on invasive bacteria or community disruptions.}, } @article {pmid33276718, year = {2020}, author = {Fan, Q and Wanapat, M and Yan, T and Hou, F}, title = {Altitude influences microbial diversity and herbage fermentation in the rumen of yaks.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {370}, pmid = {33276718}, issn = {1471-2180}, support = {2019QZKK0302//the Program for the Second Tibetan Plateau Scientific Expedition and Research: Grassland Ecosystem and Ecological Animal Husbandry/ ; 20200079//Research and Demonstration of Grassland Ecological Monitoring System in Gannan Plateau Pastoral Area/ ; IRT_17R50//Changjiang Scholars and Innovative Research Team in University/ ; }, mesh = {Altitude ; Animals ; Bacteria/classification/genetics/isolation & purification/metabolism ; Carbohydrates/analysis ; Cattle ; China ; Diet/veterinary ; Energy Metabolism/genetics ; Fatty Acids, Volatile/analysis/metabolism ; Fermentation ; Gastrointestinal Contents/chemistry ; Gastrointestinal Microbiome/genetics/*physiology ; Genes, Bacterial/physiology ; Rumen/chemistry/*metabolism/*microbiology ; }, abstract = {BACKGROUND: Rumen microbiota in ruminants are vital for sustaining good rumen ecology, health, and productivity. Currently, limited information is available regarding the response of yaks (Bos grunniens) to fluctuating environments, especially the rumen microbiome. To address this, we investigated the diet, rumen bacterial community, and volatile fatty acids (VFA) of rumen fluid of yaks raised in the great Qinghai-Tibet plateau (QTP) at 2800 (low altitude, L), 3700 (middle altitude, M), and 4700 m (high altitude, H) above sea level.

RESULTS: The results showed that despite a partial diet overlap, H yaks harbored higher fibrous fractious contents than the M and L grazing yaks. Bacteria including Christensenellaceae_R-7_group, Ruminococcus_1, Romboutsia, Alloprevotella, Eubacterium coprostanoligenes, Clostridium, Streptococcus, and Treponema were found to be enriched in the rumen of yaks grazing at H. They also showed higher rumen microbial diversity and total VFA concentrations than those shown by yaks at M and L. Principal coordinates analysis (PCoA) on weighted UniFrac distances revealed that the bacterial community structure of rumen differed between the three altitudes. Moreover, Tax4fun metagenome estimation revealed that microbial genes associated with energy requirement and carbohydrate metabolic fate were overexpressed in the rumen microbiota of H yaks.

CONCLUSIONS: Collectively, our results revealed that H yaks had a stronger herbage fermenting ability via rumen microbial fermentation. Their enhanced ability of utilizing herbage may be partly owing to a microbiota adaptation for more energy requirements in the harsh H environment, such as lower temperature and the risk of hypoxia.}, } @article {pmid33273721, year = {2021}, author = {Seyler, LM and Trembath-Reichert, E and Tully, BJ and Huber, JA}, title = {Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community.}, journal = {The ISME journal}, volume = {15}, number = {4}, pages = {1192-1206}, pmid = {33273721}, issn = {1751-7370}, mesh = {*Bacteria/genetics ; Metagenome ; *Microbiota ; Oceans and Seas ; Transcriptome ; }, abstract = {The oceanic crustal aquifer is one of the largest habitable volumes on Earth, and it harbors a reservoir of microbial life that influences global-scale biogeochemical cycles. Here, we use time series metagenomic and metatranscriptomic data from a low-temperature, ridge flank environment representative of the majority of global hydrothermal fluid circulation in the ocean to reconstruct microbial metabolic potential, transcript abundance, and community dynamics. We also present metagenome-assembled genomes from recently collected fluids that are furthest removed from drilling disturbances. Our results suggest that the microbial community in the North Pond aquifer plays an important role in the oxidation of organic carbon within the crust. This community is motile and metabolically flexible, with the ability to use both autotrophic and organotrophic pathways, as well as function under low oxygen conditions by using alternative electron acceptors such as nitrate and thiosulfate. Anaerobic processes are most abundant in subseafloor horizons deepest in the aquifer, furthest from connectivity with the deep ocean, and there was little overlap in the active microbial populations between sampling horizons. This work highlights the heterogeneity of microbial life in the subseafloor aquifer and provides new insights into biogeochemical cycling in ocean crust.}, } @article {pmid33272789, year = {2021}, author = {Muñoz-Benavent, M and Pérez-Cobas, AE and García-Ferris, C and Moya, A and Latorre, A}, title = {Insects' potential: Understanding the functional role of their gut microbiome.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {194}, number = {}, pages = {113787}, doi = {10.1016/j.jpba.2020.113787}, pmid = {33272789}, issn = {1873-264X}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Insecta ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {The study of insect-associated microbial communities is a field of great importance in agriculture, principally because of the role insects play as pests. In addition, there is a recent focus on the potential of the insect gut microbiome in areas such as biotechnology, given some microorganisms produce molecules with biotechnological and industrial applications, and also in biomedicine, since some bacteria and fungi are a reservoir of antibiotic resistance genes (ARGs). To date, most studies aiming to characterize the role of the gut microbiome of insects have been based on high-throughput sequencing of the 16S rRNA gene and/or metagenomics. However, recently functional approaches such as metatranscriptomics, metaproteomics and metabolomics have also been employed. Besides providing knowledge about the taxonomic distribution of microbial populations, these techniques also reveal their functional and metabolic capabilities. This information is essential to gain a better understanding of the role played by microbes comprising the microbial communities in their hosts, as well as to indicate their possible exploitation. This review provides an overview of how far we have come in characterizing insect gut functionality through omics, as well as the challenges and future perspectives in this field.}, } @article {pmid33272203, year = {2020}, author = {Zhang, Q and Dao, T}, title = {A distance based multisample test for high-dimensional compositional data with applications to the human microbiome.}, journal = {BMC bioinformatics}, volume = {21}, number = {Suppl 9}, pages = {205}, pmid = {33272203}, issn = {1471-2105}, mesh = {Aged ; Bayes Theorem ; Computer Simulation ; Humans ; Metagenomics ; *Microbiota ; Middle Aged ; Numerical Analysis, Computer-Assisted ; }, abstract = {BACKGROUND: Compositional data refer to the data that lie on a simplex, which are common in many scientific domains such as genomics, geology and economics. As the components in a composition must sum to one, traditional tests based on unconstrained data become inappropriate, and new statistical methods are needed to analyze this special type of data.

RESULTS: In this paper, we consider a general problem of testing for the compositional difference between K populations. Motivated by microbiome and metagenomics studies, where the data are often over-dispersed and high-dimensional, we formulate a well-posed hypothesis from a Bayesian point of view and suggest a nonparametric test based on inter-point distance to evaluate statistical significance. Unlike most existing tests for compositional data, our method does not rely on any data transformation, sparsity assumption or regularity conditions on the covariance matrix, but directly analyzes the compositions. Simulated data and two real data sets on the human microbiome are used to illustrate the promise of our method.

CONCLUSIONS: Our simulation studies and real data applications demonstrate that the proposed test is more sensitive to the compositional difference than the mean-based method, especially when the data are over-dispersed or zero-inflated. The proposed test is easy to implement and computationally efficient, facilitating its application to large-scale datasets.}, } @article {pmid33270717, year = {2020}, author = {Skarżyńska, M and Leekitcharoenphon, P and Hendriksen, RS and Aarestrup, FM and Wasyl, D}, title = {A metagenomic glimpse into the gut of wild and domestic animals: Quantification of antimicrobial resistance and more.}, journal = {PloS one}, volume = {15}, number = {12}, pages = {e0242987}, pmid = {33270717}, issn = {1932-6203}, mesh = {Animal Feed ; Animals ; Animals, Wild ; Drug Resistance, Bacterial/*genetics ; Foxes/microbiology ; Gastrointestinal Microbiome/*genetics ; *Metagenome ; Plasmids ; Poland ; Poultry/*microbiology ; Rodentia/microbiology ; Sus scrofa/microbiology ; }, abstract = {Antimicrobial resistance (AMR) in bacteria is a complex subject, why one need to look at this phenomenon from a wider and holistic perspective. The extensive use of the same antimicrobial classes in human and veterinary medicine as well as horticulture is one of the main drivers for the AMR selection. Here, we applied shotgun metagenomics to investigate the AMR epidemiology in several animal species including farm animals, which are often exposed to antimicrobial treatment opposed to an unique set of wild animals that seems not to be subjected to antimicrobial pressure. The comparison of the domestic and wild animals allowed to investigate the possible anthropogenic impact on AMR spread. Inclusion of animals with different feeding behaviors (carnivores, omnivores) enabled to further assess which AMR genes that thrives within the food chain. We tested fecal samples not only of intensively produced chickens, turkeys, and pigs, but also of wild animals such as wild boars, red foxes, and rodents. A multi-directional approach mapping obtained sequences to several databases provided insight into the occurrence of the different AMR genes. The method applied enabled also analysis of other factors that may influence AMR of intestinal microbiome such as diet. Our findings confirmed higher levels of AMR in farm animals than in wildlife. The results also revealed the potential of wildlife in the AMR dissemination. Particularly in red foxes, we found evidence of several AMR genes conferring resistance to critically important antimicrobials like quinolones and cephalosporins. In contrast, the lowest abundance of AMR was observed in rodents originating from natural environment with presumed limited exposure to antimicrobials. Shotgun metagenomics enabled us to demonstrate that discrepancies between AMR profiles found in the intestinal microbiome of various animals probably resulted from the different antimicrobial exposure, habitats, and behavior of the tested animal species.}, } @article {pmid33270378, year = {2021}, author = {Gatcliffe, C and Rao, A and Brigger, M and Dimmock, D and Hansen, C and Montgomery, J and Schlaberg, R and Coufal, NG and Farnaes, L}, title = {Metagenomic sequencing and evaluation of the host response in the pediatric aerodigestive population.}, journal = {Pediatric pulmonology}, volume = {56}, number = {2}, pages = {516-524}, doi = {10.1002/ppul.25198}, pmid = {33270378}, issn = {1099-0496}, mesh = {Bronchoalveolar Lavage Fluid/immunology/microbiology ; Child ; Child, Preschool ; Deglutition Disorders/immunology/*microbiology ; Female ; Host Microbial Interactions ; Humans ; Immunity ; Infant ; Male ; Metagenomics ; Microbiota/genetics ; Mouth/microbiology ; Respiratory Aspiration/immunology/*microbiology ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; }, abstract = {OBJECTIVES: To assess the diagnostic utility of metagenomic sequencing in pediatric aerodigestive clinic patients being evaluated for chronic aspiration. We hypothesize that using a metagenomics platform will aid in the identification of microbes not found on standard culture.

STUDY DESIGN AND METHODS: Twenty-four children referred to an aerodigestive clinic were enrolled in a prospective, single-site, cross-sectional cohort study. At the time of clinical evaluation under anesthesia, two samples were obtained: an upper airway sample and a sample from bronchoalveolar lavage (BAL). Samples were sent for routine culture and analyzed using Explify® Respiratory, a CLIA Laboratory Developed Test which identifies respiratory commensals and pathogens through RNA and DNA sequencing. Since RNA was sequenced in the course of the metagenomic analysis to identify organisms (RNA viruses and bacteria), the sequencing approach also captured host derived messenger RNA during sample analysis. This incidentally obtained host transcriptomic data were analyzed to evaluate the host immune response. The results of these studies were correlated with the clinical presentation of the research subjects.

RESULTS: In 10 patients, organisms primarily associated with oral flora were identified in the BAL. Standard culture was negative in three patients where clinical metagenomics led to a result with potential clinical significance. Transcriptomic data correlated with the presence or absence of dysphagia as identified on prior videofluoroscopic evaluation of swallowing.

CONCLUSIONS: Clinical metagenomics allows for simultaneous analysis of the microbiota and the host immune response from BAL samples. As the technologies in this field continue to advance, such testing may improve the diagnostic evaluation of patients with suspected chronic aspiration.}, } @article {pmid33268597, year = {2020}, author = {Limeta, A and Ji, B and Levin, M and Gatto, F and Nielsen, J}, title = {Meta-analysis of the gut microbiota in predicting response to cancer immunotherapy in metastatic melanoma.}, journal = {JCI insight}, volume = {5}, number = {23}, pages = {}, pmid = {33268597}, issn = {2379-3708}, mesh = {Area Under Curve ; Biomarkers, Pharmacological ; Feces ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Immunotherapy/*methods ; Melanoma/genetics/immunology/*therapy ; Metagenome ; Microbiota ; Prognosis ; Treatment Outcome ; }, abstract = {BACKGROUNDIdentifying factors conferring responses to therapy in cancer is critical to select the best treatment for patients. For immune checkpoint inhibition (ICI) therapy, mounting evidence suggests that the gut microbiome can determine patient treatment outcomes. However, the extent to which gut microbial features are applicable across different patient cohorts has not been extensively explored.METHODSWe performed a meta-analysis of 4 published shotgun metagenomic studies (Ntot = 130 patients) investigating differential microbiome composition and imputed metabolic function between responders and nonresponders to ICI.RESULTSOur analysis identified both known microbial features enriched in responders, such as Faecalibacterium as the prevailing taxa, as well as additional features, including overrepresentation of Barnesiella intestinihominis and the components of vitamin B metabolism. A classifier designed to predict responders based on these features identified responders in an independent cohort of 27 patients with the area under the receiver operating characteristic curve of 0.625 (95% CI: 0.348-0.899) and was predictive of prognosis (HR = 0.35, P = 0.081).CONCLUSIONThese results suggest the existence of a fecal microbiome signature inherent across responders that may be exploited for diagnostic or therapeutic purposes.FUNDINGThis work was funded by the Knut and Alice Wallenberg Foundation, BioGaia AB, and Cancerfonden.}, } @article {pmid33268508, year = {2020}, author = {Rom, O and Liu, Y and Liu, Z and Zhao, Y and Wu, J and Ghrayeb, A and Villacorta, L and Fan, Y and Chang, L and Wang, L and Liu, C and Yang, D and Song, J and Rech, JC and Guo, Y and Wang, H and Zhao, G and Liang, W and Koike, Y and Lu, H and Koike, T and Hayek, T and Pennathur, S and Xi, C and Wen, B and Sun, D and Garcia-Barrio, MT and Aviram, M and Gottlieb, E and Mor, I and Liu, W and Zhang, J and Chen, YE}, title = {Glycine-based treatment ameliorates NAFLD by modulating fatty acid oxidation, glutathione synthesis, and the gut microbiome.}, journal = {Science translational medicine}, volume = {12}, number = {572}, pages = {}, pmid = {33268508}, issn = {1946-6242}, support = {K99 HL150233/HL/NHLBI NIH HHS/United States ; R01 HL123333/HL/NHLBI NIH HHS/United States ; P30 DK089503/DK/NIDDK NIH HHS/United States ; P60 DK020572/DK/NIDDK NIH HHS/United States ; R01 HL134569/HL/NHLBI NIH HHS/United States ; P30 DK020572/DK/NIDDK NIH HHS/United States ; U2C DK110768/DK/NIDDK NIH HHS/United States ; R00 HL150233/HL/NHLBI NIH HHS/United States ; R01 DK106540/DK/NIDDK NIH HHS/United States ; R01 HL138139/HL/NHLBI NIH HHS/United States ; R01 HL137214/HL/NHLBI NIH HHS/United States ; P30 CA046592/CA/NCI NIH HHS/United States ; R01 HL068878/HL/NHLBI NIH HHS/United States ; R01 HL145176/HL/NHLBI NIH HHS/United States ; U24 DK097153/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Diet, High-Fat ; Fatty Acids ; *Gastrointestinal Microbiome ; Glutathione ; Glycine ; Humans ; Liver ; Mice ; Mice, Inbred C57BL ; *Non-alcoholic Fatty Liver Disease/drug therapy ; }, abstract = {Nonalcoholic fatty liver disease (NAFLD) including nonalcoholic steatohepatitis (NASH) has reached epidemic proportions with no pharmacological therapy approved. Lower circulating glycine is consistently reported in patients with NAFLD, but the causes for reduced glycine, its role as a causative factor, and its therapeutic potential remain unclear. We performed transcriptomics in livers from humans and mice with NAFLD and found suppression of glycine biosynthetic genes, primarily alanine-glyoxylate aminotransferase 1 (AGXT1). Genetic (Agxt1 [-/-] mice) and dietary approaches to limit glycine availability resulted in exacerbated diet-induced hyperlipidemia and steatohepatitis, with suppressed mitochondrial/peroxisomal fatty acid β-oxidation (FAO) and enhanced inflammation as the underlying pathways. We explored glycine-based compounds with dual lipid/glucose-lowering properties as potential therapies for NAFLD and identified a tripeptide (Gly-Gly-L-Leu, DT-109) that improved body composition and lowered circulating glucose, lipids, transaminases, proinflammatory cytokines, and steatohepatitis in mice with established NASH induced by a high-fat, cholesterol, and fructose diet. We applied metagenomics, transcriptomics, and metabolomics to explore the underlying mechanisms. The bacterial genus Clostridium sensu stricto was markedly increased in mice with NASH and decreased after DT-109 treatment. DT-109 induced hepatic FAO pathways, lowered lipotoxicity, and stimulated de novo glutathione synthesis. In turn, inflammatory infiltration and hepatic fibrosis were attenuated via suppression of NF-κB target genes and TGFβ/SMAD signaling. Unlike its effects on the gut microbiome, DT-109 stimulated FAO and glutathione synthesis independent of NASH. In conclusion, impaired glycine metabolism may play a causative role in NAFLD. Glycine-based treatment attenuates experimental NAFLD by stimulating hepatic FAO and glutathione synthesis, thus warranting clinical evaluation.}, } @article {pmid33268363, year = {2020}, author = {Yang, J and Zheng, P and Li, Y and Wu, J and Tan, X and Zhou, J and Sun, Z and Chen, X and Zhang, G and Zhang, H and Huang, Y and Chai, T and Duan, J and Liang, W and Yin, B and Lai, J and Huang, T and Du, Y and Zhang, P and Jiang, J and Xi, C and Wu, L and Lu, J and Mou, T and Xu, Y and Perry, SW and Wong, ML and Licinio, J and Hu, S and Wang, G and Xie, P}, title = {Landscapes of bacterial and metabolic signatures and their interaction in major depressive disorders.}, journal = {Science advances}, volume = {6}, number = {49}, pages = {}, pmid = {33268363}, issn = {2375-2548}, mesh = {Bacteria/genetics ; *Depressive Disorder, Major/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Gut microbiome disturbances have been implicated in major depressive disorder (MDD). However, little is known about how the gut virome, microbiome, and fecal metabolome change, and how they interact in MDD. Here, using whole-genome shotgun metagenomic and untargeted metabolomic methods, we identified 3 bacteriophages, 47 bacterial species, and 50 fecal metabolites showing notable differences in abundance between MDD patients and healthy controls (HCs). Patients with MDD were mainly characterized by increased abundance of the genus Bacteroides and decreased abundance of the genera Blautia and Eubacterium These multilevel omics alterations generated a characteristic MDD coexpression network. Disturbed microbial genes and fecal metabolites were consistently mapped to amino acid (γ-aminobutyrate, phenylalanine, and tryptophan) metabolism. Furthermore, we identified a combinatorial marker panel that robustly discriminated MDD from HC individuals in both the discovery and validation sets. Our findings provide a deep insight into understanding of the roles of disturbed gut ecosystem in MDD.}, } @article {pmid33264437, year = {2021}, author = {Kim, SS and Eun, JW and Cho, HJ and Song, DS and Kim, CW and Kim, YS and Lee, SW and Kim, YK and Yang, J and Choi, J and Yim, HJ and Cheong, JY}, title = {Microbiome as a potential diagnostic and predictive biomarker in severe alcoholic hepatitis.}, journal = {Alimentary pharmacology & therapeutics}, volume = {53}, number = {4}, pages = {540-551}, doi = {10.1111/apt.16200}, pmid = {33264437}, issn = {1365-2036}, mesh = {Biomarkers ; Dysbiosis ; *Gastrointestinal Microbiome ; *Hepatitis, Alcoholic/diagnosis/drug therapy ; Humans ; *Microbiota ; Veillonella ; }, abstract = {BACKGROUND: Severe alcoholic hepatitis (AH) is the most aggressive form of alcohol-related liver disease with high mortality. The microbiome is an emerging therapeutic target in alcohol-related liver disease.

AIMS: To investigate the microbiome composition in patients with severe AH, and to determine microbiome recovery after rifaximin treatment in gut bacteria and bacteria derived-extracellular vesicles.

METHODS: We enrolled 24 patients with severe AH and 24 healthy controls. Additional faecal samples were collected after 4 weeks in 8 patients with severe AH who completed rifaximin treatment. Treatment response was defined based on Lille score model after 7 days of treatment. Metagenomic profiling was performed using 16S ribosomal RNA amplicon sequencing.

RESULTS: Faecal microbiomes of patients with severe AH had lower alpha diversity and higher beta diversity than those of healthy controls in both gut bacteria and extracellular vesicles. Bacilli, Lactobacillales and Veillonella were significantly increased in the gut bacteria of patients with severe AH, and Veillonella, Veillonella parvula group and Lactobacillales were significantly increased in the extracellular vesicles of patients with severe AH. Eubacterium_g23, Oscillibacter and Clostridiales decreased in the gut bacteria of patients with severe AH, and Eubacterium_g23, Oscillibacter and Christensenellaceae decreased in the extracellular vesicles of patients with severe AH. After rifaximin treatment, 17 taxa in the gut bacteria and 23 taxa in extracellular vesicles were significantly restored in patients with severe AH. In common, Veillonella and Veillonella parvula group increased in patients with severe AH and decreased after rifaximin treatment, and Prevotella and Prevotellaceae decreased in patients with severe AH and increased after rifaximin treatment. Treatment non-responders showed a significantly lower abundance of Prevotella at baseline than did treatment responders.

CONCLUSION: Dysbiosis was confirmed in severe AH but was alleviated by rifaximin treatment. Taxa associated with severe AH can be candidate biomarkers or therapeutic targets.}, } @article {pmid33262957, year = {2020}, author = {de Almeida, OGG and Capizzani, CPDC and Tonani, L and Grizante Barião, PH and da Cunha, AF and De Martinis, ECP and Torres, LAGMM and von Zeska Kress, MR}, title = {The Lung Microbiome of Three Young Brazilian Patients With Cystic Fibrosis Colonized by Fungi.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {598938}, pmid = {33262957}, issn = {2235-2988}, mesh = {Brazil ; *Cystic Fibrosis/complications ; Humans ; Lung ; *Microbiota ; Sputum ; Talaromyces ; }, abstract = {Microbial communities infiltrate the respiratory tract of cystic fibrosis patients, where chronic colonization and infection lead to clinical decline. This report aims to provide an overview of the diversity of bacterial and fungal species from the airway secretion of three young CF patients with severe pulmonary disease. The bacterial and fungal microbiomes were investigated by culture isolation, metataxonomics, and metagenomics shotgun. Virulence factors and antibiotic resistance genes were also explored. A. fumigatus was isolated from cultures and identified in high incidence from patient sputum samples. Candida albicans, Penicillium sp., Hanseniaspora sp., Torulaspora delbrueckii, and Talaromyces amestolkiae were isolated sporadically. Metataxonomics and metagenomics detected fungal reads (Saccharomyces cerevisiae, A. fumigatus, and Schizophyllum sp.) in one sputum sample. The main pathogenic bacteria identified were Staphylococcus aureus, Pseudomonas aeruginosa, Burkholderia cepacia complex, and Achromobacter xylosoxidans. The canonical core CF microbiome is composed of species from the genera Streptococcus, Neisseria, Rothia, Prevotella, and Haemophilus. Thus, the airways of the three young CF patients presented dominant bacterial genera and interindividual variability in microbial community composition and diversity. Additionally, a wide diversity of virulence factors and antibiotic resistance genes were identified in the CF lung microbiomes, which may be linked to the clinical condition of the CF patients. Understanding the microbial community is crucial to improve therapy because it may have the opposite effect, restructuring the pathogenic microbiota. Future studies focusing on the influence of fungi on bacterial diversity and microbial interactions in CF microbiomes will be welcome to fulfill this huge gap of fungal influence on CF physiopathology.}, } @article {pmid33262480, year = {2020}, author = {Wang, Y and Yao, W and Li, B and Qian, S and Wei, B and Gong, S and Wang, J and Liu, M and Wei, M}, title = {Nuciferine modulates the gut microbiota and prevents obesity in high-fat diet-fed rats.}, journal = {Experimental & molecular medicine}, volume = {52}, number = {12}, pages = {1959-1975}, pmid = {33262480}, issn = {2092-6413}, support = {81703373//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Aporphines/chemistry/*pharmacology ; Diet, High-Fat/*adverse effects ; Dose-Response Relationship, Drug ; Dysbiosis/drug therapy ; Fatty Acids/metabolism ; Gastrointestinal Microbiome/*drug effects ; Lipid Metabolism ; Metabolome ; Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Obesity/*etiology/*metabolism/prevention & control ; Protective Agents/chemistry/*pharmacology ; Rats ; }, abstract = {Gut microbiota dysbiosis has a significant role in the pathogenesis of metabolic diseases, including obesity. Nuciferine (NUC) is a main bioactive component in the lotus leaf that has been used as food in China since ancient times. Here, we examined whether the anti-obesity effects of NUC are related to modulations in the gut microbiota. Using an obese rat model fed a HFD for 8 weeks, we show that NUC supplementation of HFD rats prevents weight gain, reduces fat accumulation, and ameliorates lipid metabolic disorders. Furthermore, 16S rRNA gene sequencing of the fecal microbiota suggested that NUC changed the diversity and composition of the gut microbiota in HFD-fed rats. In particular, NUC decreased the ratio of the phyla Firmicutes/Bacteroidetes, the relative abundance of the LPS-producing genus Desulfovibrio and bacteria involved in lipid metabolism, whereas it increased the relative abundance of SCFA-producing bacteria in HFD-fed rats. Predicted functional analysis of microbial communities showed that NUC modified genes involved in LPS biosynthesis and lipid metabolism. In addition, serum metabolomics analysis revealed that NUC effectively improved HFD-induced disorders of endogenous metabolism, especially lipid metabolism. Notably, NUC promoted SCFA production and enhanced intestinal integrity, leading to lower blood endotoxemia to reduce inflammation in HFD-fed rats. Together, the anti-obesity effects of NUC may be related to modulations in the composition and potential function of gut microbiota, improvement in intestinal barrier integrity and prevention of chronic low-grade inflammation. This research may provide support for the application of NUC in the prevention and treatment of obesity.}, } @article {pmid33262428, year = {2021}, author = {Gharechahi, J and Vahidi, MF and Bahram, M and Han, JL and Ding, XZ and Salekdeh, GH}, title = {Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen.}, journal = {The ISME journal}, volume = {15}, number = {4}, pages = {1108-1120}, pmid = {33262428}, issn = {1751-7370}, mesh = {Animals ; Cattle ; Fermentation ; Lignin/metabolism ; Metagenome ; *Microbiota ; *Rumen/metabolism ; }, abstract = {Rumen microbiota play a key role in the digestion and utilization of plant materials by the ruminant species, which have important implications for greenhouse gas emission. Yet, little is known about the key taxa and potential gene functions involved in the digestion process. Here, we performed a genome-centric analysis of rumen microbiota attached to six different lignocellulosic biomasses in rumen-fistulated cattle. Our metagenome sequencing provided novel genomic insights into functional potential of 523 uncultured bacteria and 15 mostly uncultured archaea in the rumen. The assembled genomes belonged mainly to Bacteroidota, Firmicutes, Verrucomicrobiota, and Fibrobacterota and were enriched for genes related to the degradation of lignocellulosic polymers and the fermentation of degraded products into short chain volatile fatty acids. We also found a shift from copiotrophic to oligotrophic taxa during the course of rumen fermentation, potentially important for the digestion of recalcitrant lignocellulosic substrates in the physiochemically complex and varying environment of the rumen. Differential colonization of forages (the incubated lignocellulosic materials) by rumen microbiota suggests that taxonomic and metabolic diversification is an evolutionary adaptation to diverse lignocellulosic substrates constituting a major component of the cattle's diet. Our data also provide novel insights into the key role of unique microbial diversity and associated gene functions in the degradation of recalcitrant lignocellulosic materials in the rumen.}, } @article {pmid33261862, year = {2021}, author = {Liu, D and Legras, JL and Zhang, P and Chen, D and Howell, K}, title = {Diversity and dynamics of fungi during spontaneous fermentations and association with unique aroma profiles in wine.}, journal = {International journal of food microbiology}, volume = {338}, number = {}, pages = {108983}, doi = {10.1016/j.ijfoodmicro.2020.108983}, pmid = {33261862}, issn = {1879-3460}, mesh = {Agriculture ; *Biodiversity ; Farms ; *Fermentation ; Fungi/chemistry/*classification/metabolism ; *Microbiota ; Odorants ; Saccharomyces cerevisiae ; Vitis/microbiology ; Wine/*microbiology ; }, abstract = {Microbial ecology is an integral part of an agricultural ecosystem and influences the quality of agricultural commodities. Microbial activity influences grapevine health and crop production, conversion of sugar to ethanol during fermentation, thus forming wine aroma and flavour. There are regionally differentiated microbial patterns in grapevines and must but how microbial patterns contribute to wine regional distinctiveness (terroir) at small scale (<100 km) is not well defined. Here we characterise fungal communities, yeast populations, and Saccharomyces cerevisiae populations during spontaneous fermentation using metagenomics and population genetics to investigate microbial distribution and fungal contributions to the resultant wine. We found differentiation of fungi, yeasts, and S. cerevisiae between geographic origins (estate/vineyard), with influences from the grape variety. Growth and dominance of S. cerevisiae during fermentation reshaped the fungal community and showed geographic structure at the strain level. Associations between fungal microbiota diversity and wine chemicals suggest that S. cerevisiae plays a primary role in determining wine aroma profiles at a sub-regional scale. The geographic distribution at scales of less than 12 km supports that differential microbial communities, including the dominant fermentative yeast S. cerevisiae can be distinct in a local setting. These findings provide further evidence for microbial contributions to wine terroir, and perspectives for sustainable agricultural practices to maintain microbial diversity and optimise fermentation function to craft beverage quality.}, } @article {pmid33260452, year = {2020}, author = {Lattos, A and Giantsis, IA and Karagiannis, D and Theodorou, JA and Michaelidis, B}, title = {Gut Symbiotic Microbial Communities in the IUCN Critically Endangered Pinna nobilis Suffering from Mass Mortalities, Revealed by 16S rRNA Amplicon NGS.}, journal = {Pathogens (Basel, Switzerland)}, volume = {9}, number = {12}, pages = {}, pmid = {33260452}, issn = {2076-0817}, abstract = {Mass mortality events due to disease outbreaks have recently affected almost every healthy population of fan mussel, Pinna nobilis in Mediterranean Sea. The devastating mortality of the species has turned the interest of the research towards the causes of these events. After the haplosporidan infestation and the infection by Mycobacterium sp., new emerging pathogens have arisen based on the latest research. In the present study, a metagenomic approach of 16S rRNA next generation sequencing (NGS) was applied in order to assess the bacterial diversity within the digestive gland of diseased individuals as well as to carry out geographical correlations among the biodiversity of microbiome in the endangered species Pinna nobilis. The specimens originated from the mortalities occurred in 2019 in the region of Greece. Together with other bacterial genera, the results confirmed the presence of Vibrio spp., assuming synergistic effects in the mortality events of the species. Alongside with the presence of Vibrio spp., numerous bacterial genera were detected as well, including Aliivibrio spp., Photobacterium spp., Pseudoalteromonas spp., Psychrilyobacter spp. and Mycoplasma spp. Bacteria of the genus Mycoplasma were in high abundance particularly in the sample originated from Limnos island representing the first time recorded in Pinna nobilis. In conclusion, apart from exclusively the Haplosporidan and the Mycobacterium parasites, the presence of potentially pathogenic bacterial taxa detected, such as Vibrio spp., Photobactrium spp. and Alivibrio spp. lead us to assume that mortality events in the endangered Fan mussel, Pinna nobilis, may be attributed to synergistic effects of more pathogens.}, } @article {pmid33259824, year = {2021}, author = {Wiemken, TL and Ericsson, AC}, title = {Chlorhexidine gluconate does not result in epidermal microbiota dysbiosis in healthy adults.}, journal = {American journal of infection control}, volume = {49}, number = {6}, pages = {769-774}, doi = {10.1016/j.ajic.2020.11.021}, pmid = {33259824}, issn = {1527-3296}, mesh = {Adult ; *Anti-Infective Agents, Local ; Chlorhexidine/analogs & derivatives ; Dysbiosis ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Chlorhexidine gluconate (CHG) and other skin antiseptics are ubiquitous in healthcare settings and are routinely used to bathe patients' skin. The commensal epidermal microbiota is believed to provide colonization resistance and other benefits to the host; yet little is known regarding the long-term stability of the epidermal microbiota, and the impact of CHG bathing. We aimed to assess the influence of CHG exposure to the epidermal microbiota and evaluate the long-term stability of the epidermal microbiota.

METHODS: The epidermal microbiota of 5 individuals was sampled using thorough swabbing of the calf, and characterized via 16S rRNA amplicon sequencing, prior to CHG bathing, and then at 30 minutes, 3 hours, 1 day, 3 days, and 7 days postbathing. Roughly 4 months later, samples were collected from the same 5 individuals, using an identical timeline but with no CHG exposure.

RESULTS: The epidermal microbiota showed no greater change 30 minutes postexposure to CHG, than was observed in the same individuals during the recovery period, likely representing the normal sample-to-sample variability. Despite that variability, the epidermal microbiota evinced a remarkable degree of intrasubject stability, even over extended periods of time.

CONCLUSION: We conclude that single applications of CHG cause minimal, if any, disruption of the epidermal microbiota, and that long-term effects of single applications of CHG on the epidermal microbiota are unlikely.}, } @article {pmid33258724, year = {2021}, author = {Dunn, KA and Connors, J and Bielawski, JP and Nearing, JT and Langille, MGI and Van Limbergen, J and Fernandez, CV and MacDonald, T and Kulkarni, K}, title = {Investigating the gut microbial community and genes in children with differing levels of change in serum asparaginase activity during pegaspargase treatment for acute lymphoblastic leukemia.}, journal = {Leukemia & lymphoma}, volume = {62}, number = {4}, pages = {927-936}, doi = {10.1080/10428194.2020.1850718}, pmid = {33258724}, issn = {1029-2403}, mesh = {*Antineoplastic Agents/therapeutic use ; Asparaginase/therapeutic use ; Child ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Polyethylene Glycols ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy/genetics ; }, abstract = {Asparaginase (ASNase) is an effective treatment of pediatric acute lymphoblastic leukemia (ALL). Changes in ASNase activity may lead to suboptimal treatment and poorer outcomes. The gut microbiome produces metabolites that could impact ASNase therapy, however, remains uninvestigated. We examined gut-microbial community and microbial-ASNase and asparagine synthetase (ASNS) genes using 16SrRNA and metagenomic sequence data from stool samples of pediatric ALL patients. Comparing ASNase activity between consecutive ASNase-doses, we found microbial communities differed between decreased- and increased-activity samples. Escherichia predominated in the decreased-activity community while Bacteroides and Streptococcus predominated in the increased-activity community. In addition microbial ASNS was significantly (p=.004) negatively correlated with change in serum ASNase activity. These preliminary findings suggest microbial communities prior to treatment could affect serum ASNase levels, although the mechanism is unknown. Replication in an independent cohort is needed, and future research on manipulation of these communities and genes could prove useful in optimizing ASNase therapy.}, } @article {pmid33256173, year = {2020}, author = {Truchado, DA and Llanos-Garrido, A and Oropesa-Olmedo, DA and Cerrada, B and Cea, P and Moens, MAJ and Gomez-Lucia, E and Doménech, A and Milá, B and Pérez-Tris, J and Cadar, D and Benítez, L}, title = {Comparative Metagenomics of Palearctic and Neotropical Avian Cloacal Viromes Reveal Geographic Bias in Virus Discovery.}, journal = {Microorganisms}, volume = {8}, number = {12}, pages = {}, pmid = {33256173}, issn = {2076-2607}, support = {CGL2013-41642-P/BOS//Spanish National Research Agency/ ; CGL2017-82117-P//Spanish National Research Agency/ ; CEBA2015-TROCSYMB//ANR/ ; CEBA:ANR-10-LABX-25-01//ANR/ ; CT27/16-CT28/16//Complutense University of Madrid/ ; }, abstract = {Our understanding about viruses carried by wild animals is still scarce. The viral diversity of wildlife may be best described with discovery-driven approaches to the study of viral diversity that broaden research efforts towards non-canonical hosts and remote geographic regions. Birds have been key organisms in the transmission of viruses causing important diseases, and wild birds are threatened by viral spillovers associated with human activities. However, our knowledge of the avian virome may be biased towards poultry and highly pathogenic diseases. We describe and compare the fecal virome of two passerine-dominated bird assemblages sampled in a remote Neotropical rainforest in French Guiana (Nouragues Natural Reserve) and a Mediterranean forest in central Spain (La Herrería). We used metagenomic data to quantify the degree of functional and genetic novelty of viruses recovered by examining if the similarity of the contigs we obtained to reference sequences differed between both locations. In general, contigs from Nouragues were significantly less similar to viruses in databases than contigs from La Herrería using Blastn but not for Blastx, suggesting that pristine regions harbor a yet unknown viral diversity with genetically more singular viruses than more studied areas. Additionally, we describe putative novel viruses of the families Picornaviridae, Reoviridae and Hepeviridae. These results highlight the importance of wild animals and remote regions as sources of novel viruses that substantially broaden the current knowledge of the global diversity of viruses.}, } @article {pmid33255677, year = {2020}, author = {Ticinesi, A and Mancabelli, L and Tagliaferri, S and Nouvenne, A and Milani, C and Del Rio, D and Lauretani, F and Maggio, MG and Ventura, M and Meschi, T}, title = {The Gut-Muscle Axis in Older Subjects with Low Muscle Mass and Performance: A Proof of Concept Study Exploring Fecal Microbiota Composition and Function with Shotgun Metagenomics Sequencing.}, journal = {International journal of molecular sciences}, volume = {21}, number = {23}, pages = {}, pmid = {33255677}, issn = {1422-0067}, support = {FIL Quota Incentivante 2016-17//University of Parma/ ; }, mesh = {Aged ; Aged, 80 and over ; Aging/*genetics/pathology ; Bacteroidetes/genetics ; Clostridiales/genetics ; Faecalibacterium prausnitzii/genetics ; Fatty Acids, Volatile/biosynthesis/genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Inflammation/genetics/microbiology/pathology ; Male ; Metabolic Networks and Pathways ; Metagenome/*genetics ; Metagenomics/methods ; Muscle, Skeletal/microbiology/physiopathology ; Sarcopenia/*genetics/microbiology/physiopathology ; }, abstract = {The gut microbiota could influence the pathophysiology of age-related sarcopenia through multiple mechanisms implying modulation of chronic inflammation and anabolic resistance. The aim of this study was to compare the fecal microbiota composition and functionality, assessed by shotgun metagenomics sequencing, between two groups of elderly outpatients, differing only for the presence of primary sarcopenia. Five sarcopenic elderly subjects and twelve non-sarcopenic controls, classified according to lower limb function and bioimpedance-derived skeletal muscle index, provided a stool sample, which was analyzed with shotgun metagenomics approaches, to determine the overall microbiota composition, the representation of bacteria at the species level, and the prediction of bacterial genes involved in functional metabolic pathways. Sarcopenic subjects displayed different fecal microbiota compositions at the species level, with significant depletion of two species known for their metabolic capacity of producing short-chain fatty acids (SCFAs), Faecalibacterium prausnitzii and Roseburia inulinivorans, and of Alistipes shahii. Additionally, their fecal metagenome had different representation of genes belonging to 108 metabolic pathways, namely, depletion of genes involved in SCFA synthesis, carotenoid and isoflavone biotransformation, and amino acid interconversion. These results support the hypothesis of an association between microbiota and sarcopenia, indicating novel possible mediators, whose clinical relevance should be investigated in future studies.}, } @article {pmid33255324, year = {2020}, author = {Pramanik, K and Das, A and Banerjee, J and Das, A and Chatterjee, S and Sharma, R and Kumar, S and Gupta, S}, title = {Metagenomic Insights into Rhizospheric Microbiome Profiling in Lentil Cultivars Unveils Differential Microbial Nitrogen and Phosphorus Metabolism under Rice-Fallow Ecology.}, journal = {International journal of molecular sciences}, volume = {21}, number = {23}, pages = {}, pmid = {33255324}, issn = {1422-0067}, mesh = {Lens Plant/*genetics/growth & development/microbiology ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Nitrogen/metabolism ; Oryza/*genetics/growth & development/microbiology ; Phosphorus/metabolism ; Plant Roots/genetics/growth & development/microbiology ; Rhizosphere ; Soil Microbiology ; }, abstract = {The plant rhizosphere interfaces an array of microbiomes related to plant growth and development. Cultivar-specific soil microbial communities with respect to their taxonomic structure and specific function have not been investigated explicitly in improving the adaptation of lentil cultivars under rice-fallow ecology. The present study was carried out to decipher the rhizosphere microbiome assembly of two lentil cultivars under rice-fallow ecology for discerning the diversity of microbial communities and for predicting the function of microbiome genes related to nitrogen (N) and phosphorus (P) cycling processes deploying high-throughput whole (meta) genome sequencing. The metagenome profile of two cultivars detected variable microbiome composition with discrete metabolic activity. Cyanobacteria, Bacteroidetes, Proteobacteria, Gemmatimonadetes, and Thaumarchaeota were abundant phyla in the "Farmer-2" rhizosphere, whereas Actinobacteria, Acidobacteria, Firmicutes, Planctomycetes, Chloroflexi, and some incompletely described procaryotes of the "Candidatus" category were found to be robustly enriched the rhizosphere of "Moitree". Functional prediction profiles of the microbial metagenomes between two cultivars revealed mostly house keeping genes with general metabolism. Additionally, the rhizosphere of "Moitree" had a high abundance of genes related to denitrification processes. Significant difference was observed regarding P cycling genes between the cultivars. "Moitree" with a profuse root system exhibited better N fixation and translocation ability due to a good "foraging strategy" for improving acquisition of native P under the nutrient depleted rice-fallow ecology. However, "Farmer-2" revealed a better "mining strategy" for enhancing P solubilization and further transportation to sinks. This study warrants comprehensive research for explaining the role of microbiome diversity and cultivar-microbe interactions towards stimulating microbiome-derived soil reactions regarding nutrient availability under rice-fallow ecology.}, } @article {pmid33254468, year = {2021}, author = {Okurowska, K and Karunakaran, E and Al-Farttoosy, A and Couto, N and Pandhal, J}, title = {Adapting the algal microbiome for growth on domestic landfill leachate.}, journal = {Bioresource technology}, volume = {319}, number = {}, pages = {124246}, doi = {10.1016/j.biortech.2020.124246}, pmid = {33254468}, issn = {1873-2976}, mesh = {Biodegradation, Environmental ; *Chlorella vulgaris ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Water Pollutants, Chemical/analysis ; }, abstract = {We aimed to improve algal growth rate on leachate by optimising the algal microbiome. An algal-bacterial consortium was enriched from landfill leachate and subjected to 24 months of adaptive laboratory evolution, increasing the growth rate of the dominant algal strain, Chlorella vulgaris, almost three-fold to 0.2 d[-1]. A dramatic reduction in nitrate production suggested a shift in biological utilisation of ammoniacal-N, supported by molecular 16S rRNA taxonomic analyses, where Nitrosomonas numbers were not detected in the adapted consortium. A PICRUSt approach predicted metagenomic functional content and revealed a high number of sequences belonging to bioremediation pathways, including degradation of aromatic compounds, benzoate and naphthalene, as well as pathways known to be involved in algal-bacterial symbiosis. This study enhances our understanding of beneficial mechanisms in algal-bacterial associations in complex effluents, and ultimately enables the bottom-up design of optimised algal microbiomes for exploitation within industry.}, } @article {pmid33252655, year = {2020}, author = {Weißbecker, C and Schnabel, B and Heintz-Buschart, A}, title = {Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology.}, journal = {GigaScience}, volume = {9}, number = {12}, pages = {}, pmid = {33252655}, issn = {2047-217X}, mesh = {High-Throughput Nucleotide Sequencing ; *Microbiota ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Software ; }, abstract = {BACKGROUND: Amplicon sequencing of phylogenetic marker genes, e.g., 16S, 18S, or ITS ribosomal RNA sequences, is still the most commonly used method to determine the composition of microbial communities. Microbial ecologists often have expert knowledge on their biological question and data analysis in general, and most research institutes have computational infrastructures to use the bioinformatics command line tools and workflows for amplicon sequencing analysis, but requirements of bioinformatics skills often limit the efficient and up-to-date use of computational resources.

RESULTS: We present dadasnake, a user-friendly, 1-command Snakemake pipeline that wraps the preprocessing of sequencing reads and the delineation of exact sequence variants by using the favorably benchmarked and widely used DADA2 algorithm with a taxonomic classification and the post-processing of the resultant tables, including hand-off in standard formats. The suitability of the provided default configurations is demonstrated using mock community data from bacteria and archaea, as well as fungi.

CONCLUSIONS: By use of Snakemake, dadasnake makes efficient use of high-performance computing infrastructures. Easy user configuration guarantees flexibility of all steps, including the processing of data from multiple sequencing platforms. It is easy to install dadasnake via conda environments. dadasnake is available at https://github.com/a-h-b/dadasnake.}, } @article {pmid33250443, year = {2021}, author = {Wei, B and Wang, S and Wang, Y and Ke, S and Jin, W and Chen, J and Zhang, H and Sun, J and Henning, SM and Wang, J and Wang, H}, title = {Gut microbiota-mediated xanthine metabolism is associated with resistance to high-fat diet-induced obesity.}, journal = {The Journal of nutritional biochemistry}, volume = {88}, number = {}, pages = {108533}, doi = {10.1016/j.jnutbio.2020.108533}, pmid = {33250443}, issn = {1873-4847}, mesh = {Animals ; Anti-Obesity Agents/metabolism ; Bacteria/genetics ; Blood Glucose/analysis ; Body Weight ; Chromatography, Liquid/methods ; Diet, High-Fat/*adverse effects ; Dysbiosis/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; Male ; Metabolomics/methods ; Mice ; Mice, Inbred C57BL ; Obesity/*metabolism ; RNA, Ribosomal, 16S/genetics ; Tandem Mass Spectrometry/methods ; Xanthine/*metabolism ; }, abstract = {Resistance to high-fat diet-induced obesity (DIR) has been observed in mice fed a high-fat diet and may provide a potential approach for anti-obesity drug discovery. However, the metabolic status, gut microbiota composition, and its associations with DIR are still unclear. Here, ultraperformance liquid chromatography-tandem mass spectrometry-based urinary metabolomic and 16S rRNA gene sequencing-based fecal microbiome analyses were conducted to investigate the relationship between metabolic profile, gut microbiota composition, and body weight of C57BL/6J mice on chow or a high-fat diet for 8 weeks. PICRUSt analysis of 16S rRNA gene sequences predicted the functional metagenomes of gut bacteria. The results demonstrated that feeding a high-fat diet increased body weight and fasting blood glucose of high-fat diet-induced obesity (DIO) mice and altered the host-microbial co-metabolism and gut microbiota composition. In DIR mice, high-fat diet did not increase body weight while fasting blood glucose was increased significantly compared to chow fed mice. In DIR mice, the urinary metabolic pattern was shifted to a distinct direction compared to DIO mice, which was mainly contributed by xanthine. Moreover, high-fat diet caused gut microbiota dysbiosis in both DIO and DIR mice, but in DIR mice, the abundance of Bifidobacteriaceae, Roseburia, and Escherichia was not affected compared to mice fed a chow diet, which played an important role in the pathway coverage of FormylTHF biosynthesis I. Meanwhile, xanthine and pathway coverage of FormylTHF biosynthesis I showed significant positive correlations with mouse body weight. These findings suggest that gut microbiota-mediated xanthine metabolism correlates with resistance to high-fat DIO.}, } @article {pmid33250435, year = {2021}, author = {Taylor, SL and Leong, LEX and Sims, SK and Keating, RL and Papanicolas, LE and Richard, A and Mobegi, FM and Wesselingh, S and Burr, LD and Rogers, GB}, title = {The cystic fibrosis gut as a potential source of multidrug resistant pathogens.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {20}, number = {3}, pages = {413-420}, doi = {10.1016/j.jcf.2020.11.009}, pmid = {33250435}, issn = {1873-5010}, mesh = {Adult ; Anti-Bacterial Agents/*pharmacology ; Case-Control Studies ; Cystic Fibrosis/*microbiology ; *Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Metagenomics ; Microbial Sensitivity Tests ; Tobramycin/pharmacology ; }, abstract = {BACKGROUND: The emergence of multidrug resistant (MDR) pathogens represents a profound threat to global health. Individuals with CF have amongst the highest cumulative antibiotic exposure of any patient group, including to critically-important last-line agents. While there is little evidence that antibiotic resistance in airway pathogens results in worse clinical outcomes for CF patients, the potential emergence of MDR pathogens in non-respiratory systems, as a consequence of CF care, represents a potential health threat to the wider population, including family and carers.

METHODS: Stool from 19 adults with CF and 16 healthy adult controls was subjected to metagenomic sequencing, to assess faecal resistome, and culture-based analysis. Resistant isolates were identified phenotypically, and genetic determinants of resistance characterised by whole genome sequencing.

RESULTS: CF and control faecal resistomes differed significantly (P = 0.0003). The proportion of reads that mapped to mobile genetic elements was significantly higher in CF (P = 0.014) and the composition was significantly different (P = 0.0001). Notably, CF patients displayed higher carriage of plasmid-mediated aminoglycoside-modifying genes ant(6)-Ib, aac(6')-Ip, and aph(3')-IIIa (P < 0.01). Culture-based analysis supported higher aminoglycoside resistance, with a higher proportion of aminoglycoside-resistant, Gram-negative bacteria (P < 0.0001). Isolated extended spectrum beta lactamase (ESBL)-positive Escherichia coli from CF stool exhibited phenotypic resistance to tobramycin and gentamicin. Genomic analysis showed co-localisation of both aminoglycoside resistance and ESBL genes, consistent with MDR emergence through horizontal gene transfer.

CONCLUSIONS: The carriage of potentially transmissible resistance within the adult CF gut microbiome is considerably greater than in healthy individuals and could contribute to the emergence and dissemination of MDR pathogens.}, } @article {pmid33250052, year = {2020}, author = {Cheng, YH and Liu, CJ and Yu, YH and Jhou, YT and Fujishima, M and Tsai, IJ and Leu, JY}, title = {Genome plasticity in Paramecium bursaria revealed by population genomics.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {180}, pmid = {33250052}, issn = {1741-7007}, support = {109-2326-B-001-015//Ministry of Science and Technology, Taiwan/International ; 105-2628-B-001-002-MY3//Ministry of Science and Technology, Taiwan/International ; AS-IA-105-L01//Academia Sinica/International ; AS-TP-107-ML06//Academia Sinica/International ; AS-CDA-107-L01//Academia Sinica/International ; }, mesh = {*Genome, Protozoan ; Macronucleus/genetics ; Metagenomics ; Paramecium/*genetics ; }, abstract = {BACKGROUND: Ciliates are an ancient and diverse eukaryotic group found in various environments. A unique feature of ciliates is their nuclear dimorphism, by which two types of nuclei, the diploid germline micronucleus (MIC) and polyploidy somatic macronucleus (MAC), are present in the same cytoplasm and serve different functions. During each sexual cycle, ciliates develop a new macronucleus in which newly fused genomes are extensively rearranged to generate functional minichromosomes. Interestingly, each ciliate species seems to have its way of processing genomes, providing a diversity of resources for studying genome plasticity and its regulation. Here, we sequenced and analyzed the macronuclear genome of different strains of Paramecium bursaria, a highly divergent species of the genus Paramecium which can stably establish endosymbioses with green algae.

RESULTS: We assembled a high-quality macronuclear genome of P. bursaria and further refined genome annotation by comparing population genomic data. We identified several species-specific expansions in protein families and gene lineages that are potentially associated with endosymbiosis. Moreover, we observed an intensive chromosome breakage pattern that occurred during or shortly after sexual reproduction and contributed to highly variable gene dosage throughout the genome. However, patterns of copy number variation were highly correlated among genetically divergent strains, suggesting that copy number is adjusted by some regulatory mechanisms or natural selection. Further analysis showed that genes with low copy number variation among populations tended to function in basic cellular pathways, whereas highly variable genes were enriched in environmental response pathways.

CONCLUSIONS: We report programmed DNA rearrangements in the P. bursaria macronuclear genome that allow cells to adjust gene copy number globally according to individual gene functions. Our results suggest that large-scale gene copy number variation may represent an ancient mechanism for cells to adapt to different environments.}, } @article {pmid33249867, year = {2022}, author = {Kumar, P and Sinha, R and Shukla, P}, title = {Artificial intelligence and synthetic biology approaches for human gut microbiome.}, journal = {Critical reviews in food science and nutrition}, volume = {62}, number = {8}, pages = {2103-2121}, doi = {10.1080/10408398.2020.1850415}, pmid = {33249867}, issn = {1549-7852}, mesh = {Artificial Intelligence ; *Gastrointestinal Microbiome/genetics ; Gene Editing/methods ; Humans ; *Microbiota ; Synthetic Biology ; }, abstract = {The gut microbiome comprises a variety of microorganisms whose genes encode proteins to carry out crucial metabolic functions that are responsible for the majority of health-related issues in human beings. The advent of the technological revolution in artificial intelligence (AI) assisted synthetic biology (SB) approaches will play a vital role in the modulating the therapeutic and nutritive potential of probiotics. This can turn human gut as a reservoir of beneficial bacterial colonies having an immense role in immunity, digestion, brain function, and other health benefits. Hence, in the present review, we have discussed the role of several gene editing tools and approaches in synthetic biology that have equipped us with novel tools like Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR-Cas) systems to precisely engineer probiotics for diagnostic, therapeutic and nutritive value. A brief discussion over the AI techniques to understand the metagenomic data from the healthy and diseased gut microbiome is also presented. Further, the role of AI in potentially impacting the pace of developments in SB and its current challenges is also discussed. The review also describes the health benefits conferred by engineered microbes through the production of biochemicals, nutraceuticals, drugs or biotherapeutics molecules etc. Finally, the review concludes with the challenges and regulatory concerns in adopting synthetic biology engineered microbes for clinical applications. Thus, the review presents a synergistic approach of AI and SB toward human gut microbiome for better health which will provide interesting clues to researchers working in the area of rapidly evolving food and nutrition science.}, } @article {pmid33249197, year = {2021}, author = {Xiao, Q and Lu, W and Kong, X and Shao, YW and Hu, Y and Wang, A and Bao, H and Cao, R and Liu, K and Wang, X and Wu, X and Zheng, S and Yuan, Y and Ding, K}, title = {Alterations of circulating bacterial DNA in colorectal cancer and adenoma: A proof-of-concept study.}, journal = {Cancer letters}, volume = {499}, number = {}, pages = {201-208}, doi = {10.1016/j.canlet.2020.11.030}, pmid = {33249197}, issn = {1872-7980}, mesh = {Adenoma/blood/*diagnosis/microbiology ; Adult ; Aged ; Aged, 80 and over ; Biomarkers, Tumor/*blood/genetics ; Case-Control Studies ; Cell-Free Nucleic Acids/*blood/genetics ; Colorectal Neoplasms/blood/*diagnosis/microbiology ; DNA, Bacterial/*blood/genetics ; Diagnosis, Differential ; Early Detection of Cancer/methods ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Healthy Volunteers ; Humans ; Male ; Mass Screening/methods ; Middle Aged ; Predictive Value of Tests ; Proof of Concept Study ; ROC Curve ; }, abstract = {The gut microbiota is closely associated with colorectal neoplasia. While most metagenomics studies utilized fecal samples, circulating bacterial DNA in colorectal neoplasia patients remained unexplored. This proof-of-concept study aims to characterize alterations of circulating bacterial DNA in colorectal neoplasia patients. We performed WGS of plasma samples from 25 colorectal cancer (CRC) patients, 10 colorectal adenoma (CRA) patients and 22 healthy controls (HC). Bacterial relative abundance was measured by removing the host genome and mapping reads into bacterial genomes. By diversity analysis, we found plasma samples required less sample size to approach saturation than fecal samples, and species diversity in HC was slightly higher compared with CRC/CRA patients. The majority of circulating bacterial DNA came from bacterial genera which commonly associated with gastrointestine and oral tract. By differential analysis, a total of 127 significant species between CRC patients and HC were identified, on which basis 28 species with top predictive ability were selected and showed promise in preliminary discrimination between CRC/CRA and HC. In CRA patients, relative abundance of the selected 28 species more closely resembled those in CRC patients than HC. By comparing with fecal metagenomics studies, we found there was moderate positive correlation between fold changes of the overlapped fecal and circulating bacterial DNA. Finally, species correlation analysis revealed that CRC and HC displayed distinct patterns of species association. In conclusion, this study demonstrated alterations of circulating bacterial DNA in colorectal neoplasia patients, which had the potential to become non-invasive biomarkers for colorectal neoplasia screening and early diagnosis.}, } @article {pmid33249136, year = {2021}, author = {Kong, G and Ellul, S and Narayana, VK and Kanojia, K and Ha, HTT and Li, S and Renoir, T and Cao, KL and Hannan, AJ}, title = {An integrated metagenomics and metabolomics approach implicates the microbiota-gut-brain axis in the pathogenesis of Huntington's disease.}, journal = {Neurobiology of disease}, volume = {148}, number = {}, pages = {105199}, doi = {10.1016/j.nbd.2020.105199}, pmid = {33249136}, issn = {1095-953X}, mesh = {Animals ; *Asymptomatic Diseases ; Brain/*metabolism ; Chromatography, Liquid ; Disease Models, Animal ; Disease Progression ; Dysbiosis/*metabolism/microbiology ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*metabolism/microbiology ; Huntington Disease/*metabolism/microbiology ; Mass Spectrometry ; *Metabolomics ; *Metagenomics ; Mice ; Mice, Transgenic ; }, abstract = {BACKGROUND: Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder with onset and severity of symptoms influenced by various environmental factors. Recent discoveries have highlighted the importance of the gastrointestinal microbiome in mediating the gut-brain-axis bidirectional communication via circulating factors. Using shotgun sequencing, we investigated the gut microbiome composition in the R6/1 transgenic mouse model of HD from 4 to 12 weeks of age (early adolescent through to adult stages). Targeted metabolomics was also performed on the blood plasma of these mice (n = 9 per group) at 12 weeks of age to investigate potential effects of gut dysbiosis on the plasma metabolome profile.

RESULTS: Modelled time profiles of each species, KEGG Orthologs and bacterial genes, revealed heightened volatility in the R6/1 mice, indicating potential early effects of the HD mutation in the gut. In addition to gut dysbiosis in R6/1 mice at 12 weeks of age, gut microbiome function was perturbed. In particular, the butanoate metabolism pathway was elevated, suggesting increased production of the protective SCFA, butyrate, in the gut. No significant alterations were found in the plasma butyrate and propionate levels in the R6/1 mice at 12 weeks of age. The statistical integration of the metagenomics and metabolomics unraveled several Bacteroides species that were negatively correlated with ATP and pipecolic acid in the plasma.

CONCLUSIONS: The present study revealed the instability of the HD gut microbiome during the pre-motor symptomatic stage of the disease which may have dire consequences on the host's health. Perturbation of the HD gut microbiome function prior to significant cognitive and motor dysfunction suggest the potential role of the gut in modulating the pathogenesis of HD, potentially via specific altered plasma metabolites which mediate gut-brain signaling.}, } @article {pmid33248775, year = {2021}, author = {Centurion, VB and Lacerda-Júnior, GV and Duarte, AWF and Silva, TR and Silva, LJ and Rosa, LH and Oliveira, VM}, title = {Dynamics of microbial stress responses driven by abiotic changes along a temporal gradient in Deception Island, Maritime Antarctica.}, journal = {The Science of the total environment}, volume = {758}, number = {}, pages = {143671}, doi = {10.1016/j.scitotenv.2020.143671}, pmid = {33248775}, issn = {1879-1026}, mesh = {Antarctic Regions ; Islands ; *Microbiota ; }, abstract = {Whalers Bay (WB), Deception Island, is an environment that can drastically change its temperature within a few meters. The main forms of life inhabiting this environment are microorganisms, which, due to the high diversity and their adaptive potential, can survive and thrive under harsh stress conditions. However, the genetic potential and mechanisms to cope with fluctuating adverse conditions as well as what extent environmental variations shape the microbial community over the years it is still unknown in Antarctic environments. In this work, sediments collected in a transect in Whalers Bay, Deception Island, during the Austral Summers of 2014, 2015 and 2017 were analyzed using shotgun metagenomics. Sequence data were further processed with the SqueezeMeta tool for assembly, gene prediction, mapping, taxonomic and functional annotations. Results showed that stress-related functions had the influence of temperatures and solar radiation observed in the years of 2015 and 2017. The most differentiated functions were the ones related to oxidative stress, comparing 2014 vs 2015 and 2014 vs 2017. The genes coding for HSP20 and oxidoreductases (nrdH, grxA, korC and korD), as well as the genes clpE, cspL, and operons mtrAB and vicKR, were differentially enriched between the years, most of them found in gram-positive bacteria. The selective pressures of temperature and radiation may have favored the growth of gram-positive bacteria in 2017, with emphasis on Arthrobacter genus. Data gathered in this work showed that temperature and solar radiation could potentially be the primary driving forces shaping the repertoire of stress-response genes for the maintenance of microbial diversity in WB Antarctic sediments.}, } @article {pmid33248757, year = {2021}, author = {Wang, Y and Hu, X and Sun, Y and Wang, C}, title = {Influence of the cold bottom water on taxonomic and functional composition and complexity of microbial communities in the southern Yellow Sea during the summer.}, journal = {The Science of the total environment}, volume = {759}, number = {}, pages = {143496}, doi = {10.1016/j.scitotenv.2020.143496}, pmid = {33248757}, issn = {1879-1026}, mesh = {Chlorophyll A ; *Microbiota ; Seasons ; *Seawater ; Water ; }, abstract = {The formation and presence of the cold bottom water (Yellow Sea Cold Water Mass, YSCWM) is a striking hydrological phenomenon in the southern Yellow Sea during the summer and has important effects on the marine ecosystem. To better understand its influence on microbial community structure and function, we compared the bacterial, archaeal and microeukaryotic communities in the cold water mass area (CWMA) and the southern area (SA) during the summer using amplicon and metagenomic sequencings. The habitat environment in the deep waters of the CWMA was characterized by higher salinity/DO/PO4-P, greater depth/distance to the coast, and lower levels of temperature/chlorophyll a/DIN/SiO3-Si/N:P ratio compared to that of the SA. Pure depth or distance to the coast explained a small portion of the microbial community variance, while environment explained a significant fraction of the variance when partialling the effects of depth and distance to the coast. Oligotrophic taxa (e.g. SAR11 clade Ia, Nitrosopumilus, Chloropicophyceae) dominated the deep water communities in the CWMA, while the common coastal taxa (e.g. Roseobacter strain HIMB11, Bacillariophyta, Noctilucophyceae) were more dominant in the deep waters of the SA, suggesting the great impact of the oligotrophic condition in the YSCWM on microbial communities. The microbial co-occurrence networks in the CWMA were less complex but contained a higher proportion of mutual exclusion relationship among prokaryotes; the prokaryotic α-diversity in the CWMA was significantly lower than in the SA while the microeukaryotic α-diversity was significantly higher in the CWMA, implying that prokaryotes and microeukaryotes respond to the cold water mass differently and the competition among prokaryotes was intensified under the impact of the YSCWM. Genes that relate to replication and repair accounted for a significantly lower proportion in the CWMA, which was likely an adaptation to the low carbon environment.}, } @article {pmid33248729, year = {2021}, author = {Vari, HK and Roslund, MI and Oikarinen, S and Nurminen, N and Puhakka, R and Parajuli, A and Grönroos, M and Siter, N and Laitinen, OH and Hyöty, H and Rajaniemi, J and Rantalainen, AL and Sinkkonen, A and , }, title = {Associations between land cover categories, gaseous PAH levels in ambient air and endocrine signaling predicted from gut bacterial metagenome of the elderly.}, journal = {Chemosphere}, volume = {265}, number = {}, pages = {128965}, doi = {10.1016/j.chemosphere.2020.128965}, pmid = {33248729}, issn = {1879-1298}, mesh = {Aged ; *Air Pollutants/analysis ; Environmental Monitoring ; Gases/analysis ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; *Polycyclic Aromatic Hydrocarbons/analysis ; }, abstract = {There is evidence that polycyclic aromatic hydrocarbons (PAHs) and human gut microbiota are associated with the modulation of endocrine signaling pathways. Independently, studies have found associations between air pollution, land cover and commensal microbiota. We are the first to estimate the interaction between land cover categories associated with air pollution or purification, PAH levels and endocrine signaling predicted from gut metagenome among urban and rural populations. The study participants were elderly people (65-79 years); 30 lived in rural and 32 in urban areas. Semi-Permeable Membrane devices were utilized to measure air PAH concentrations as they simulate the process of bioconcentration in the fatty tissues. Land cover categories were estimated using CORINE database and geographic information system. Functional orthologues for peroxisome proliferator-activated receptor (PPAR) pathway in endocrine system were analyzed from gut bacterial metagenome with Kyoto Encyclopaedia of Genes and Genomes. High coverage of broad-leaved and mixed forests around the homes were associated with decreased PAH levels in ambient air, while gut functional orthologues for PPAR pathway increased along with these forest types. The difference between urban and rural PAH concentrations was not notable. However, some rural measurements were higher than the urban average, which was due to the use of heavy equipment on active farms. The provision of air purification by forests might be an important determining factor in the context of endocrine disruption potential of PAHs. Particularly broad-leaved forests around homes may reduce PAH levels in ambient air and balance pollution-induced disturbances within commensal gut microbiota.}, } @article {pmid33248623, year = {2020}, author = {Du, W and Deng, J and Yang, Z and Zeng, L and Yang, X}, title = {Metagenomic analysis reveals linkages between cecal microbiota and feed efficiency in Xiayan chickens.}, journal = {Poultry science}, volume = {99}, number = {12}, pages = {7066-7075}, pmid = {33248623}, issn = {1525-3171}, mesh = {*Animal Feed/analysis ; Animals ; Campylobacter ; *Cecum/microbiology ; Chickens/*microbiology ; China ; Female ; *Gastrointestinal Microbiome ; Helicobacter ; Male ; *Metagenome ; RNA, Ribosomal, 16S ; }, abstract = {The cecal microbiota plays a critical role in energy harvest and nutrient digestion, influencing intestinal health and the performance of chickens. Feed efficiency (FE) is essential for improving economic efficiency and saving social resources in chicken production and may be affected by the cecal microbiota. Therefore, to investigate the composition and functional capacity of cecum microbes related to FE in Xiayan chicken, an indigenous breed in Guangxi province, metagenome sequencing was performed on chicken cecal contents. 173 male and 167 female chickens were divided into high and low FE groups according to the residual feed intake. The cecal microbial genome was extracted and sequenced. The results showed that the genera Bacteroides, Prevotella, and Alistipes were the 3 most abundant in each cecal microbiome. The linear discriminant analysis effect size revealed 6 potential biomarkers in male and 14 in female chickens. Notably, the relative abundance of Lactobacillus in the high FE group was higher than that of the low FE group both in the male and female chickens, and the species Limosilactobacillus oris has a higher score in the high FE group of male chickens. In contrast, some potentially pathogenic microorganisms such as Campylobacter avium in females and Helicobacter pullorum in males were enriched in the low FE group. Predictive functional analysis showed that the high FE group in male chickens had a greater ability of xenobiotics biodegradation and metabolism and signaling molecules and interaction. In addition, the host sex was found to exert effects on the cecal microbial composition and function associated with FE. These results increased our understanding of the cecal microbial composition and identified many potential biomarkers related to FE, which may be used to improve the FE of the chickens.}, } @article {pmid33247928, year = {2021}, author = {Pittet, LF and Bertelli, C and Scherz, V and Rochat, I and Mardegan, C and Brouillet, R and Jaton, K and Mornand, A and Kaiser, L and Posfay-Barbe, K and Asner, SA and Greub, G}, title = {Chlamydia pneumoniae and Mycoplasma pneumoniae in children with cystic fibrosis: impact on bacterial respiratory microbiota diversity.}, journal = {Pathogens and disease}, volume = {79}, number = {1}, pages = {}, pmid = {33247928}, issn = {2049-632X}, mesh = {Biodiversity ; Child ; Child, Preschool ; Chlamydophila Infections/microbiology ; Chlamydophila pneumoniae/genetics/*isolation & purification ; Cystic Fibrosis/*microbiology ; DNA, Bacterial ; Humans ; Metagenomics ; *Microbiota ; Mycoplasma pneumoniae/genetics/*isolation & purification ; Pneumonia, Mycoplasma/microbiology ; Prospective Studies ; RNA, Ribosomal, 16S ; Respiratory System/*microbiology ; Sputum/microbiology ; }, abstract = {OBJECTIVES: The contribution of intracellular and fastidious bacteria in Cystic fibrosis (CF) pulmonary exacerbations, and progressive lung function decline remains unknown. This project aimed to explore their impact on bacterial microbiota diversity over time in CF children.

METHODS: Sixty-one children enrolled in the MUCOVIB multicentre prospective cohort provided 746 samples, mostly nasopharyngeal swabs, throat swabs and sputa which were analysed using culture, specific real-time qPCRs and 16S rRNA amplicon metagenomics.

RESULTS: Chlamydia pneumoniae (n = 3) and Mycoplasma pneumoniae (n = 1) were prospectively documented in 6.6% of CF children. Microbiota alpha-diversity in children with a documented C. pneumoniae was highly variable, similarly to children infected with Staphylococcus aureus or Pseudomonas aeruginosa. The transition from routine follow-up visits to pulmonary exacerbation (n = 17) yielded variable changes in diversity indexes with some extreme loss of diversity.

CONCLUSIONS: The high rate of C. pneumoniae detection supports the need for regular screenings in CF patients. A minor impact of C. pneumoniae on the microbial community structure was documented. Although detected in a single patient, M. pneumoniae should also be considered as a possible aetiology of lung infection in CF subjects.}, } @article {pmid33246485, year = {2020}, author = {Hennart, M and Panunzi, LG and Rodrigues, C and Gaday, Q and Baines, SL and Barros-Pinkelnig, M and Carmi-Leroy, A and Dazas, M and Wehenkel, AM and Didelot, X and Toubiana, J and Badell, E and Brisse, S}, title = {Population genomics and antimicrobial resistance in Corynebacterium diphtheriae.}, journal = {Genome medicine}, volume = {12}, number = {1}, pages = {107}, pmid = {33246485}, issn = {1756-994X}, mesh = {Anti-Bacterial Agents/pharmacology ; Corynebacterium diphtheriae/classification/*drug effects/*genetics/isolation & purification ; DNA, Bacterial/genetics ; Diphtheria/microbiology ; Diphtheria Toxin/genetics ; Drug Resistance, Bacterial/*genetics ; Genes, Bacterial/*genetics ; Genome-Wide Association Study ; Genomics ; Humans ; Macrolides/pharmacology ; *Metagenomics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Phylogeny ; Prospective Studies ; }, abstract = {BACKGROUND: Corynebacterium diphtheriae, the agent of diphtheria, is a genetically diverse bacterial species. Although antimicrobial resistance has emerged against several drugs including first-line penicillin, the genomic determinants and population dynamics of resistance are largely unknown for this neglected human pathogen.

METHODS: Here, we analyzed the associations of antimicrobial susceptibility phenotypes, diphtheria toxin production, and genomic features in C. diphtheriae. We used 247 strains collected over several decades in multiple world regions, including the 163 clinical isolates collected prospectively from 2008 to 2017 in France mainland and overseas territories.

RESULTS: Phylogenetic analysis revealed multiple deep-branching sublineages, grouped into a Mitis lineage strongly associated with diphtheria toxin production and a largely toxin gene-negative Gravis lineage with few toxin-producing isolates including the 1990s ex-Soviet Union outbreak strain. The distribution of susceptibility phenotypes allowed proposing ecological cutoffs for most of the 19 agents tested, thereby defining acquired antimicrobial resistance. Penicillin resistance was found in 17.2% of prospective isolates. Seventeen (10.4%) prospective isolates were multidrug-resistant (≥ 3 antimicrobial categories), including four isolates resistant to penicillin and macrolides. Homologous recombination was frequent (r/m = 5), and horizontal gene transfer contributed to the emergence of antimicrobial resistance in multiple sublineages. Genome-wide association mapping uncovered genetic factors of resistance, including an accessory penicillin-binding protein (PBP2m) located in diverse genomic contexts. Gene pbp2m is widespread in other Corynebacterium species, and its expression in C. glutamicum demonstrated its effect against several beta-lactams. A novel 73-kb C. diphtheriae multiresistance plasmid was discovered.

CONCLUSIONS: This work uncovers the dynamics of antimicrobial resistance in C. diphtheriae in the context of phylogenetic structure, biovar, and diphtheria toxin production and provides a blueprint to analyze re-emerging diphtheria.}, } @article {pmid33246412, year = {2020}, author = {Aguilar-Marin, SB and Betancur-Murillo, CL and Isaza, GA and Mesa, H and Jovel, J}, title = {Lower methane emissions were associated with higher abundance of ruminal Prevotella in a cohort of Colombian buffalos.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {364}, pmid = {33246412}, issn = {1471-2180}, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification/metabolism ; Buffaloes ; Colombia ; Euryarchaeota/classification/genetics/isolation & purification/metabolism ; Fermentation ; Gastrointestinal Microbiome/genetics ; Hydrogen/metabolism ; Methane/*metabolism ; Prevotella/classification/genetics/isolation & purification/*metabolism ; Propionates/metabolism ; Rumen/*microbiology ; }, abstract = {BACKGROUND: Ruminants burp massive amounts of methane into the atmosphere and significantly contribute to the deposition of greenhouse gases and the consequent global warming. It is therefore urgent to devise strategies to mitigate ruminant's methane emissions to alleviate climate change. Ruminal methanogenesis is accomplished by a series of methanogen archaea in the phylum Euryarchaeota, which piggyback into carbohydrate fermentation by utilizing residual hydrogen to produce methane. Abundance of methanogens, therefore, is expected to affect methane production. Furthermore, availability of hydrogen produced by cellulolytic bacteria acting upstream of methanogens is a rate-limiting factor for methane production. The aim of our study was to identify microbes associated with the production of methane which would constitute the basis for the design of mitigation strategies.

RESULTS: Moderate differences in the abundance of methanogens were observed between groups. In addition, we present three lines of evidence suggesting an apparent higher abundance of a consortium of Prevotella species in animals with lower methane emissions. First, taxonomic classification revealed increased abundance of at least 29 species of Prevotella. Second, metagenome assembly identified increased abundance of Prevotella ruminicola and another species of Prevotella. Third, metabolic profiling of predicted proteins uncovered 25 enzymes with homology to Prevotella proteins more abundant in the low methane emissions group.

CONCLUSIONS: We propose that higher abundance of ruminal Prevotella increases the production of propionic acid and, in doing so, reduces the amount of hydrogen available for methanogenesis. However, further experimentation is required to ascertain the role of Prevotella on methane production and its potential to act as a methane production mitigator.}, } @article {pmid33246225, year = {2021}, author = {Yu, Y and Lu, J and Sun, L and Lyu, X and Chang, XY and Mi, X and Hu, MG and Wu, C and Chen, X}, title = {Akkermansia muciniphila: A potential novel mechanism of nuciferine to improve hyperlipidemia.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {133}, number = {}, pages = {111014}, doi = {10.1016/j.biopha.2020.111014}, pmid = {33246225}, issn = {1950-6007}, mesh = {Akkermansia/drug effects/genetics/growth & development ; Animals ; Anti-Bacterial Agents/pharmacology ; Aporphines/*pharmacology ; Bacteroides/drug effects/genetics/growth & development ; Biomarkers/blood ; Diet, High-Fat ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; Hyperlipidemias/blood/*drug therapy/microbiology ; Hypolipidemic Agents/*pharmacology ; Intestines/*microbiology ; Lipids/*blood ; Male ; Metagenome ; Metagenomics ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/blood/microbiology/prevention & control ; Obesity/blood/microbiology/prevention & control ; RNA-Seq ; Mice ; }, abstract = {BACKGROUND: Intestinal microbiota is a novel drug target of metabolic diseases, especially for those with poor oral bioavailability. Nuciferine, with poor bioavailability, has an anti-hyperlipidemic effect at low dosages.

PURPOSE: In the present study, we aimed to explore the role of intestinal microbiota in the anti-hyperlipidemic function of nuciferine and identify the key bacterial targets that might confer the therapeutic actions.

METHODS: The contribution of gut microbes in the anti-hyperlipidemic effect of nuciferine was evaluated by conventional and antibiotic-established pseudo-sterile mice. Whole-metagenome shotgun sequencing was used to characterize the changes in microbial communities by various agents.

RESULTS: Nuciferine exhibited potent anti-hyperlipidemic and liver steatosis-alleviating effects at the doses of 7.5-30 mg/kg. The beneficial effects of nuciferine were substantially abolished when combined with antibiotics. Metagenomic analysis showed that nuciferine significantly shifted the microbial structure, and the enrichment of Akkermansia muciniphila was closely related to the therapeutic effect of nuciferine.

CONCLUSIONS: Our results revealed that gut microbiota played an essential role in the anti-hyperlipidemic effect of nuciferine, and enrichment of Akkermansia muciniphila represented a key mechanism through which nuciferine exerted its therapeutic effects.}, } @article {pmid33246097, year = {2021}, author = {Minarovits, J}, title = {Anaerobic bacterial communities associated with oral carcinoma: Intratumoral, surface-biofilm and salivary microbiota.}, journal = {Anaerobe}, volume = {68}, number = {}, pages = {102300}, doi = {10.1016/j.anaerobe.2020.102300}, pmid = {33246097}, issn = {1095-8274}, mesh = {Anaerobiosis ; Animals ; Bacteria, Anaerobic/classification/genetics/*isolation & purification/*physiology ; Biofilms ; Humans ; *Microbiota ; Mouth Neoplasms/*microbiology ; Saliva/*microbiology ; }, abstract = {It was estimated that more than 700 bacterial species inhabit the oral cavity of healthy humans. Anaerobes comprise a significant fraction of the oral bacteriome and play an important role in the formation of multi-species biofilms attached to various anatomical sites. Bacterial biofilms are also associated with pathologic laesions of the oral cavity, including oral squamous cell carcinoma (OSCC), and distinct oral taxa could also be detected within the tumors, i.e. in deep biopsy samples. These observations suggested that certain oral bacteria or oral bacterial communities may play a causative role in oral carcinogenesis, in addition to the well characterized risk factors of oral cancer. Alternatively, it was also proposed that a subset of oral bacteria may have a growth advantage in the unique microenvironment of OSCC. Recently, a series of studies analysed the OSCC-associated bacterial communities using metataxonomic, metagenomic and metatranscriptomic approaches. This review outlines the major differences between the community structure of microbiota in tumor biopsy, surface-biofilm and salivary or oral wash samples collected from OSCC patients, compared to corresponding samples from control persons. A special emphasis is given to the anaerobic bacteria Fusobacterium nucleatum and Fusobacterium periodonticum that were characterised repeatedly as "OSCC-associated" in independent studies. Predicted microbial functions and relevant in vivo experimental models of oral carcinogenesis will also be summarized.}, } @article {pmid33244064, year = {2020}, author = {Shilts, MH and Rosas-Salazar, C and Lynch, CE and Tovchigrechko, A and Boone, HH and Russell, PB and Connolly, AS and Costello, KM and McCollum, MD and Mai, A and Wiggins, DA and Rajagopala, SV and Yooseph, S and Peebles, RS and Hartert, TV and Das, SR}, title = {Evaluation of the upper airway microbiome and immune response with nasal epithelial lining fluid absorption and nasal washes.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {20618}, pmid = {33244064}, issn = {2045-2322}, support = {K24AI77930//National Institute of Allergy and Infectious Diseases/International ; HHSN272200900007C/AI/NIAID NIH HHS/United States ; K12HD087023//Eunice Kennedy Shriver National Institute of Child Health and Human Development/International ; U19AI095227//NIAID, NIH/International ; U2CDK059637/DK/NIDDK NIH HHS/United States ; P30DK020593/DK/NIDDK NIH HHS/United States ; R21 AI149262/AI/NIAID NIH HHS/United States ; R21 AI154016/AI/NIAID NIH HHS/United States ; U19 AI110819/AI/NIAID NIH HHS/United States ; UL1 TR000445/TR/NCATS NIH HHS/United States ; UL1 RR024975/RR/NCRR NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; P30 EY008126/EY/NEI NIH HHS/United States ; G20 RR030956/RR/NCRR NIH HHS/United States ; }, mesh = {Adult ; Child ; Female ; Humans ; Immunity/genetics/immunology ; Male ; Metagenome/genetics/immunology ; Microbiota/*genetics/*immunology ; Nasal Absorption/immunology ; Nasal Cavity/immunology/microbiology ; Nasal Lavage Fluid/*immunology/*microbiology ; Nose/*immunology/*microbiology ; RNA, Ribosomal, 16S/genetics/immunology ; Specimen Handling/methods ; }, abstract = {Despite being commonly used to collect upper airway epithelial lining fluid, nasal washes are poorly reproducible, not suitable for serial sampling, and limited by a dilution effect. In contrast, nasal filters lack these limitations and are an attractive alternative. To examine whether nasal filters are superior to nasal washes as a sampling method for the characterization of the upper airway microbiome and immune response, we collected paired nasal filters and washes from a group of 40 healthy children and adults. To characterize the upper airway microbiome, we used 16S ribosomal RNA and shotgun metagenomic sequencing. To characterize the immune response, we measured total protein using a BCA assay and 53 immune mediators using multiplex magnetic bead-based assays. We conducted statistical analyses to compare common microbial ecology indices and immune-mediator median fluorescence intensities (MFIs) between sample types. In general, nasal filters were more likely to pass quality control in both children and adults. There were no significant differences in microbiome community richness, α-diversity, or structure between pediatric samples types; however, these were all highly dissimilar between adult sample types. In addition, there were significant differences in the abundance of amplicon sequence variants between sample types in children and adults. In adults, total proteins were significantly higher in nasal filters than nasal washes; consequently, the immune-mediator MFIs were not well detected in nasal washes. Based on better quality control sequencing metrics and higher immunoassay sensitivity, our results suggest that nasal filters are a superior sampling method to characterize the upper airway microbiome and immune response in both children and adults.}, } @article {pmid33243513, year = {2021}, author = {Calegario, G and Freitas, L and Appolinario, LR and Venas, T and Arruda, T and Otsuki, K and Masi, B and Omachi, C and Moreira, AP and Soares, AC and Rezende, CE and Garcia, G and Tschoeke, D and Thompson, C and Thompson, FL}, title = {Conserved rhodolith microbiomes across environmental gradients of the Great Amazon Reef.}, journal = {The Science of the total environment}, volume = {760}, number = {}, pages = {143411}, doi = {10.1016/j.scitotenv.2020.143411}, pmid = {33243513}, issn = {1879-1026}, mesh = {Coral Reefs ; Metagenome ; *Microbiota ; Photosynthesis ; *Rhodophyta ; Seawater ; }, abstract = {The Great Amazon Reef System (GARS) covers an estimated area of 56,000 km[2] off the mouth of the Amazon River. Living rhodolith holobionts are major benthic components of the GARS. However, it is unclear whether environmental conditions modulate the rhodolith microbiomes. Previous studies suggest that environmental parameters such as light, temperature, depth, and nutrients are drivers of rhodolith health. However, it is unclear whether rhodoliths from different sectors (northern, central, and southern) from the GARS have different microbiomes. We analysed metagenomes of rhodoliths (n = 10) and seawater (n = 6), obtained from the three sectors, by illumina shotgun sequencing (total read counts: 25.73 million). Suspended particulate material and isotopic composition of dissolved organic carbon (δ[13]C) indicated a strong influence of the Amazon river plume over the entire study area. However, photosynthetically active radiation at the bottom (PARb) was higher in the southern sector reefs, ranging from 10.1 to 14.3 E.m[-2] day[-1]. The coralline calcareous red algae (CCA) Corallina caespitosa, Corallina officinalis, Lithophyllum cabiochiae, and Hapalidiales were present in the three sectors and in most rhodolith samples. Rhodolith microbiomes were very homogeneous across the studied area and differed significantly from seawater microbiomes. However, some subtle differences were found when comparing the rhodolith microbiomes from the northern and central sectors to the ones from the southern. Consistent with the higher light availability, two phyla were more abundant in rhodolith microbiomes from southern sites (Bacteroidetes, and Cyanobacteria). In addition, two functional categories were enhanced in southern rhodolith microbiomes (iron acquisition and metabolism, and photosynthesis). Phycobiliprotein-coding genes were also more abundant in southern locations, while the functional categories of respiration and sulfur metabolism were enhanced in northern and central rhodolith microbiomes, consistent with higher nutrient loads. The results confirm the conserved nature of rhodolith microbiomes even under pronounced environmental gradients. Subtle taxonomic and functional differences observed in rhodolith microbiomes may enable rhodoliths to thrive in changing environmental conditions.}, } @article {pmid33240526, year = {2020}, author = {Porter, AF and Pettersson, JH and Chang, WS and Harvey, E and Rose, K and Shi, M and Eden, JS and Buchmann, J and Moritz, C and Holmes, EC}, title = {Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates.}, journal = {Virus evolution}, volume = {6}, number = {2}, pages = {veaa064}, pmid = {33240526}, issn = {2057-1577}, abstract = {The Flaviviridae family of positive-sense RNA viruses contains important pathogens of humans and other animals, including Zika virus, dengue virus, and hepatitis C virus. The Flaviviridae are currently divided into four genera-Hepacivirus, Pegivirus, Pestivirus, and Flavivirus-each with a diverse host range. Members of the genus Hepacivirus are associated with an array of animal species, including humans, non-human primates, other mammalian species, as well as birds and fish, while the closely related pegiviruses have been identified in a variety of mammalian taxa, also including humans. Using a combination of total RNA and whole-genome sequencing we identified four novel hepaci-like viruses and one novel variant of a known hepacivirus in five species of Australian wildlife. The hosts infected comprised native Australian marsupials and birds, as well as a native gecko (Gehyra lauta). From these data we identified a distinct marsupial clade of hepaci-like viruses that also included an engorged Ixodes holocyclus tick collected while feeding on Australian long-nosed bandicoots (Perameles nasuta). Distinct lineages of hepaci-like viruses associated with geckos and birds were also identified. By mining the SRA database we similarly identified three new hepaci-like viruses from avian and primate hosts, as well as two novel pegi-like viruses associated with primates. The phylogenetic history of the hepaci- and pegi-like viruses as a whole, combined with co-phylogenetic analysis, provided support for virus-host co-divergence over the course of vertebrate evolution, although with frequent cross-species virus transmission. Overall, our work highlights the diversity of the Hepacivirus and Pegivirus genera as well as the uncertain phylogenetic distinction between.}, } @article {pmid33239396, year = {2021}, author = {Baker, JL and Morton, JT and Dinis, M and Alvarez, R and Tran, NC and Knight, R and Edlund, A}, title = {Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules.}, journal = {Genome research}, volume = {31}, number = {1}, pages = {64-74}, pmid = {33239396}, issn = {1549-5469}, support = {F32 DE026947/DE/NIDCR NIH HHS/United States ; K99 DE029228/DE/NIDCR NIH HHS/United States ; R00 DE024543/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria ; *Dental Caries ; Epstein-Barr Virus Infections ; Herpesvirus 4, Human ; Humans ; *Metagenomics ; *Microbiota/genetics ; }, abstract = {Dental caries, the most common chronic infectious disease worldwide, has a complex etiology involving the interplay of microbial and host factors that are not completely understood. In this study, the oral microbiome and 38 host cytokines and chemokines were analyzed across 23 children with caries and 24 children with healthy dentition. De novo assembly of metagenomic sequencing obtained 527 metagenome-assembled genomes (MAGs), representing 150 bacterial species. Forty-two of these species had no genomes in public repositories, thereby representing novel taxa. These new genomes greatly expanded the known pangenomes of many oral clades, including the enigmatic Saccharibacteria clades G3 and G6, which had distinct functional repertoires compared to other oral Saccharibacteria. Saccharibacteria are understood to be obligate epibionts, which are dependent on host bacteria. These data suggest that the various Saccharibacteria clades may rely on their hosts for highly distinct metabolic requirements, which would have significant evolutionary and ecological implications. Across the study group, Rothia, Neisseria, and Haemophilus spp. were associated with good dental health, whereas Prevotella spp., Streptococcus mutans, and Human herpesvirus 4 (Epstein-Barr virus [EBV]) were more prevalent in children with caries. Finally, 10 of the host immunological markers were significantly elevated in the caries group, and co-occurrence analysis provided an atlas of potential relationships between microbes and host immunological molecules. Overall, this study illustrated the oral microbiome at an unprecedented resolution and contributed several leads for further study that will increase the understanding of caries pathogenesis and guide therapeutic development.}, } @article {pmid33238618, year = {2020}, author = {Zhang, X and Zhao, A and Sandhu, AK and Edirisinghe, I and Burton-Freeman, BM}, title = {Functional Deficits in Gut Microbiome of Young and Middle-Aged Adults with Prediabetes Apparent in Metabolizing Bioactive (Poly)phenols.}, journal = {Nutrients}, volume = {12}, number = {11}, pages = {}, pmid = {33238618}, issn = {2072-6643}, support = {N/A//National Processed Raspberry Council/ ; }, mesh = {Adult ; Beverages ; Female ; *Gastrointestinal Microbiome ; Humans ; Insulin Resistance ; Male ; Middle Aged ; Phenols/*metabolism ; Prediabetic State/*metabolism/*microbiology ; Rubus/*metabolism ; Young Adult ; }, abstract = {BACKGROUND: Gut microbiota metabolize select dietary (poly)phenols to absorbable metabolites that exert biological effects important in metabolic health. Microbiota composition associated with health/disease status may affect its functional capacity to yield bioactive metabolites from dietary sources. Therefore, this study assessed gut microbiome composition and its related functional capacity to metabolize fruit (poly)phenols in individuals with prediabetes and insulin resistance (PreDM-IR, n = 26) compared to a metabolically healthy Reference group (n = 10).

METHODS: Shotgun sequencing was used to characterize gut microbiome composition. Targeted quantitative metabolomic analyses of plasma and urine collected over 24 h were used to assess microbial-derived metabolites in response to a (poly)phenol-rich raspberry test drink.

RESULTS: PreDM-IR compared to the Reference group: (1) enriched Blautia obeum and Blautia wexlerae and depleted Bacteroides dorei and Coprococcus eutactus. Akkermansia muciniphila and Bacteroides spp. were depleted in the lean PreDM-IR subset; and (2) impaired microbial catabolism of select (poly)phenols resulting in lower 3,8-dihydroxy-urolithin (urolithin A), phenyl-γ-valerolactones and various phenolic acids concentrations (p < 0.05). Controlling for obesity revealed relationships with microbial species that may serve as metagenomic markers of diabetes development and therapeutic targets.

CONCLUSIONS: Data provide insight from multi-omics approaches to advance knowledge at the diet-gut-disease nexus serving as a platform for devising dietary strategies to improve metabolic health.}, } @article {pmid33233680, year = {2020}, author = {Hewson, I and Aquino, CA and DeRito, CM}, title = {Virome Variation during Sea Star Wasting Disease Progression in Pisaster ochraceus (Asteroidea, Echinodermata).}, journal = {Viruses}, volume = {12}, number = {11}, pages = {}, pmid = {33233680}, issn = {1999-4915}, mesh = {Animals ; Disease Progression ; Genetic Variation ; Longitudinal Studies ; Metagenome ; Metagenomics ; Starfish/*virology ; *Virome ; Viruses/classification/*genetics ; Wasting Syndrome/*veterinary/*virology ; }, abstract = {Sea star wasting disease (SSWD) is a condition that has affected asteroids for over 120 years, yet mechanistic understanding of this wasting etiology remains elusive. We investigated temporal virome variation in two Pisaster ochraceus specimens that wasted in the absence of external stimuli and two specimens that did not experience SSWD for the duration of our study, and compared viromes of wasting lesion margin tissues to both artificial scar margins and grossly normal tissues over time. Global assembly of all SSWD-affected tissue libraries resulted in 24 viral genome fragments represented in >1 library. Genome fragments mostly matched densoviruses and picornaviruses with fewer matching nodaviruses, and a sobemovirus. Picornavirus-like and densovirus-like genome fragments were most similar to viral genomes recovered in metagenomic study of other marine invertebrates. Read recruitment revealed only two picornavirus-like genome fragments that recruited from only SSWD-affected specimens, but neither was unique to wasting lesions. Wasting lesion margin reads recruited to a greater number of viral genotypes (i.e., richness) than did either scar tissue and grossly normal tissue reads. Taken together, these data suggest that no single viral genome fragment was associated with SSWD. Rather, wasting lesion margins may generally support viral proliferation.}, } @article {pmid33233570, year = {2020}, author = {Horne, RG and Yu, Y and Zhang, R and Abdalqadir, N and Rossi, L and Surette, M and Sherman, PM and Adeli, K}, title = {High Fat-High Fructose Diet-Induced Changes in the Gut Microbiota Associated with Dyslipidemia in Syrian Hamsters.}, journal = {Nutrients}, volume = {12}, number = {11}, pages = {}, pmid = {33233570}, issn = {2072-6643}, support = {KA:CIHR 201508FDN-353989-FDN PMS: CIHR MOP-89894 and IOP-92890/CAPMC/CIHR/Canada ; }, mesh = {Animals ; Bacteria/classification/genetics ; Cholesterol/blood ; Diet, Carbohydrate Loading/*adverse effects ; Diet, High-Fat/*adverse effects ; *Dyslipidemias ; Feces/microbiology ; Fructose/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Lipid Metabolism ; Male ; Mesocricetus ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Triglycerides/blood ; }, abstract = {Aim: The objective of this study was to characterize the early effects of high fructose diets (with and without high fat) on both the composition of the gut microbiota and lipid metabolism in Syrian hamsters, a reproducible preclinical model of diet-induced dyslipidemia. Methods: Eight-week-old male hamsters were fed diets consisting of high-fat/high-fructose, low-fat/high-fructose or a standard chow diet for 14 days. Stool was collected at baseline (day 0), day 7 and day 14. Fasting levels of plasma triglycerides and cholesterol were monitored on day 0, day 7 and day 14, and nonfasting levels were also assayed on day 15. Then, 16S rRNA sequencing of stool samples was used to determine gut microbial composition, and predictive metagenomics was performed to evaluate dietary-induced shifts in deduced microbial functions. Results: Both high-fructose diets resulted in divergent gut microbiota composition. A high-fat/high-fructose diet induced the largest shift in overall gut microbial composition, with dramatic shifts in the Firmicute/Bacteroidetes ratio, and changes in beta diversity after just seven days of dietary intervention. Significant associations between genus level taxa and dietary intervention were identified, including an association with Ruminococceace NK4A214 group in high-fat/high-fructose fed animals and an association with Butryimonas with the low-fat/high-fructose diet. High-fat/high-fructose feeding induced dyslipidemia with increases in plasma triglycerides and cholesterol, and hepatomegaly. Dietary-induced changes in several genus level taxa significantly correlated with lipid levels over the two-week period. Differences in microbial metabolic pathways between high-fat/high-fructose and low-fat/high-fructose diet fed hamsters were identified, and several of these pathways also correlated with lipid profiles in hamsters. Conclusions: The high-fat/high-fructose diet caused shifts in the host gut microbiota. These dietary-induced alterations in gut microbial composition were linked to changes in the production of secondary metabolites, which contributed to the development of metabolic syndrome in the host.}, } @article {pmid33233349, year = {2020}, author = {Santiago-Rodriguez, TM and Garoutte, A and Adams, E and Nasser, W and Ross, MC and La Reau, A and Henseler, Z and Ward, T and Knights, D and Petrosino, JF and Hollister, EB}, title = {Metagenomic Information Recovery from Human Stool Samples Is Influenced by Sequencing Depth and Profiling Method.}, journal = {Genes}, volume = {11}, number = {11}, pages = {}, pmid = {33233349}, issn = {2073-4425}, mesh = {Bacteria/genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; Genetic Markers ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Viruses/*genetics ; }, abstract = {Sequencing of the 16S rRNA gene (16S) has long been a go-to method for microbiome characterization due to its accessibility and lower cost compared to shotgun metagenomic sequencing (SMS). However, 16S sequencing rarely provides species-level resolution and cannot provide direct assessment of other taxa (e.g., viruses and fungi) or functional gene content. Shallow shotgun metagenomic sequencing (SSMS) has emerged as an approach to bridge the gap between 16S sequencing and deep metagenomic sequencing. SSMS is cost-competitive with 16S sequencing, while also providing species-level resolution and functional gene content insights. In the present study, we evaluated the effects of sequencing depth on marker gene-mapping- and alignment-based annotation of bacteria in healthy human stool samples. The number of identified taxa decreased with lower sequencing depths, particularly with the marker gene-mapping-based approach. Other annotations, including viruses and pathways, also showed a depth-dependent effect on feature recovery. These results refine the understanding of the suitability and shortcomings of SSMS, as well as annotation tools for metagenomic analyses in human stool samples. Results may also translate to other sample types and may open the opportunity to explore the effect of sequencing depth and annotation method.}, } @article {pmid33232877, year = {2021}, author = {Yan, X and He, M and Zheng, J and Zhu, T and Zou, Z and Tang, B and Yu, Y and Mai, B}, title = {Tris (1,3-dichloro-2-propyl) phosphate exposure disrupts the gut microbiome and its associated metabolites in mice.}, journal = {Environment international}, volume = {146}, number = {}, pages = {106256}, doi = {10.1016/j.envint.2020.106256}, pmid = {33232877}, issn = {1873-6750}, mesh = {Animals ; *Gastrointestinal Microbiome ; Metagenome ; Mice ; Mice, Inbred C57BL ; Phosphates ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Tris (1,3-dichloro-2-propyl) phosphate (TDCIPP) has been frequently detected in environmental media and biological samples. However, knowledge of its adverse health consequences is limited, and its impacts on the human gut microbiota, which play a key role in health and disease, remain unexplored.

OBJECTIVES: To better evaluate the potential risk of TDCIPP exposure in human health, we investigated the effects of TDCIPP on gut microbiome and gut metabolites in C57BL/6 mice.

METHODS: We applied an integrated analytical approach by combing 16S rRNA gene sequencing, metagenomic sequencing and [1]H NMR metabolomics analysis in fecal samples collected from mouse with TDCIPP exposure as well as those from controls.

RESULTS: Both 16S rRNA sequencing and metagenome sequencing showed that TDCIPP exposure significantly changed the gut microbiome, with a remarkable increased Firmicutes at the expense of Bacteroidetes after exposure. Perturbed gut metabolic profiles in the treated group were also observed and closely related with altered gut microbiome. Gene functional annotation analysis further suggested perturbed gut metabolites could be directly caused by altered gut microbiome.

CONCLUSION: TDCIPP exposure has great influence on the gut ecosystem as reflected by perturbation of microbiome community structure, microbial species, gut microbe associated gene expression and gut metabolites, which may contribute to the progression of certain uncharacterized gut microbiota related host diseases. Our findings provide novel insights into adverse effects of TDCIPP exposure on human health.}, } @article {pmid33232475, year = {2020}, author = {Ilett, EE and Jørgensen, M and Noguera-Julian, M and Nørgaard, JC and Daugaard, G and Helleberg, M and Paredes, R and Murray, DD and Lundgren, J and MacPherson, C and Reekie, J and Sengeløv, H}, title = {Associations of the gut microbiome and clinical factors with acute GVHD in allogeneic HSCT recipients.}, journal = {Blood advances}, volume = {4}, number = {22}, pages = {5797-5809}, pmid = {33232475}, issn = {2473-9537}, mesh = {Adult ; *Gastrointestinal Microbiome ; *Graft vs Host Disease/etiology ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Humans ; RNA, Ribosomal, 16S/genetics ; Transplantation Conditioning ; }, abstract = {Acute graft-versus-host disease (aGVHD) is a leading cause of transplantation-related mortality after allogeneic hematopoietic stem cell transplantation (aHSCT). 16S ribosomal RNA (16S rRNA) gene-based studies have reported that lower gut bacterial diversity and the relative abundance of certain bacteria after aHSCT are associated with aGVHD. Using shotgun metagenomic sequencing and a large cohort, we aimed to confirm and extend these observations. Adult aHSCT recipients with stool samples collected from day -30 to day 100 relative to aHSCT were included. One sample was selected per patient per period (pre-aHSCT (day -30 to day 0), early post-aHSCT (day 1 to day 28), and late post-aHSCT (day 29 to day 100)), resulting in 150 aHSCT recipients and 259 samples. Microbial and clinical factors were tested for differences between time periods and an association with subsequent aGVHD. Patients showed a decline in gut bacterial diversity posttransplant, with several patients developing a dominance of Enterococcus. A total of 36 recipients developed aGVHD at a median of 34 days (interquartile range, 26-50 days) post-aHSCT. Lower microbial gene richness (P = .02), a lower abundance of the genus Blautia (P = .05), and a lower abundance of Akkermansia muciniphila (P = .01) early post-aHSCT was observed in those who developed aGVHD. Myeloablative conditioning was associated with aGVHD along with a reduction in gene richness and abundance of Blautia and A muciniphila. These results confirm low diversity and Blautia being associated with aGVHD. Crucially, we add that pretransplant conditioning is associated with changes in gut microbiota. Investigations are warranted to determine the interplay of gut microbiota and conditioning in the development of aGVHD.}, } @article {pmid33231748, year = {2021}, author = {Noor, SO and Al-Zahrani, DA and Hussein, RM and Baeshen, MN and Moussa, TAA and Abo-Aba, SM and Al-Hejin, AM and Baeshen, NA and Huelsenbeck, JP}, title = {Assessment of fungal diversity in soil rhizosphere associated with Rhazya stricta and some desert plants using metagenomics.}, journal = {Archives of microbiology}, volume = {203}, number = {3}, pages = {1211-1219}, pmid = {33231748}, issn = {1432-072X}, support = {HiCi 1-363-1434H//King Abdulaziz University/ ; }, mesh = {*Biodiversity ; Desert Climate ; Fungi/classification/*genetics ; *Metagenomics ; Mycobiome/*genetics ; Phylogeny ; Plant Roots/microbiology ; Plants/*microbiology ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {This study aimed to compare the fungal rhizosphere communities of Rhazya stricta, Enneapogon desvauxii, Citrullus colocynthis, Senna italica, and Zygophyllum simplex, and the gut mycobiota of Poekilocerus bufonius (Orthoptera, Pyrgomorphidae, "Usherhopper"). A total of 164,485 fungal reads were observed from the five plant rhizospheres and Usherhopper gut. The highest reads were in S. italica rhizosphere (29,883 reads). Species richness in the P. bufonius gut was the highest among the six samples. Ascomycota was dominant in all samples, with the highest reads in E. desvauxii (26,734 reads) rhizosphere. Sordariomycetes and Dothideomycetes were the dominant classes detected with the highest abundance in C. colocynthis and E. desvauxii rhizospheres. Aspergillus and Ceratobasidium were the most abundant genera in the R. stricta rhizosphere, Fusarium and Penicillium in the E. desvauxii rhizosphere and P. bufonius gut, Ceratobasidium and Myrothecium in the C. colocynthis rhizosphere, Aspergillus and Fusarium in the S. italica rhizosphere, and Cochliobolus in the Z. simplex rhizosphere. Aspergillus terreus was the most abundant species in the R. stricta and S. italica rhizospheres, Fusarium sp. in E. desvauxii rhizosphere, Ceratobasidium sp. in C. colocynthis rhizosphere, Cochliobolus sp. in Z. simplex rhizosphere, and Penicillium sp. in P. bufonius gut. The phylogenetic results revealed the unclassified species were related closely to Ascomycota and the species in E. desvauxii, S. italica and Z. simplex rhizospheres were closely related, where the species in the P. bufonius gut, were closely related to the species in the R. stricta, and C. colocynthis rhizospheres.}, } @article {pmid33231228, year = {2020}, author = {Peng, M and Lee, SH and Rahaman, SO and Biswas, D}, title = {Dietary probiotic and metabolites improve intestinal homeostasis and prevent colorectal cancer.}, journal = {Food & function}, volume = {11}, number = {12}, pages = {10724-10735}, doi = {10.1039/d0fo02652b}, pmid = {33231228}, issn = {2042-650X}, mesh = {Animals ; Bacteria/classification/metabolism ; Cell Proliferation/drug effects ; Colonic Neoplasms/microbiology/*prevention & control ; Colorectal Neoplasms/microbiology/*prevention & control ; Cytokines/metabolism ; *Diet ; Dietary Supplements ; Dysbiosis ; Female ; Gastrointestinal Microbiome/drug effects/genetics ; Gastrointestinal Tract/microbiology ; Homeostasis/*drug effects ; Linoleic Acids, Conjugated/pharmacology ; Male ; Metagenome ; Mice ; Mice, Inbred BALB C ; Probiotics/*pharmacology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The excessive secretion of pro-inflammatory cytokines, uncontrolled cell proliferation, and dysbiosis in gut intestinal microbiota are involved in tumorigenesis and progression of colorectal cancer. Probiotics secrete various functional metabolites that maintain intestinal microflora balance and improve the host's gut health. This study defines the roles of dietary Lactobacillus (LC-CLA) metabolites, especially conjugated linoleic acids (CLA), in intestinal homeostasis. Based on cellular and transcriptional examination, LC-CLA cell free cultural supernatant (CFCS) significantly inhibited the viability of colorectal cancer cells (HCT-116). CFCSs containing various levels of CLA also significantly lowered the transcript levels of crucial genes for tumorous cell growth and proliferation, such as CDK1/2/6, PLK1, and SKP2. Furthermore, LC-CLA and its CFCS exhibited substantial free radical scavenging activities as well as downregulated pro-inflammatory cytokine and upregulated anti-inflammatory cytokine gene expressions. In addition, daily consumption of LC-CLA for one week modulated the composition of gut microflora by specifically reducing the relative abundance of sulfidogenic bacteria in mice. These findings reveal the potential application of CLA from probiotic origin as a dietary supplement or nutraceutical agent for improving gastrointestinal health and preventing colorectal cancer.}, } @article {pmid33228779, year = {2020}, author = {Piazzon, MC and Naya-Català, F and Perera, E and Palenzuela, O and Sitjà-Bobadilla, A and Pérez-Sánchez, J}, title = {Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {168}, pmid = {33228779}, issn = {2049-2618}, mesh = {Animals ; Diet/veterinary ; Disease Resistance/*genetics ; *Gastrointestinal Microbiome/genetics ; Intestines/*microbiology ; Male ; *Parasites ; Sea Bream/*genetics/*microbiology ; *Selection, Genetic ; }, abstract = {BACKGROUND: The key effects of intestinal microbiota in animal health have led to an increasing interest in manipulating these bacterial populations to improve animal welfare. The aquaculture sector is no exception and in the last years, many studies have described these populations in different fish species. However, this is not an easy task, as intestinal microbiota is composed of very dynamic populations that are influenced by different factors, such as diet, environment, host age, and genetics. In the current study, we aimed to determine whether the genetic background of gilthead sea bream (Sparus aurata) influences the intestinal microbial composition, how these bacterial populations are modulated by dietary changes, and the effect of selection by growth on intestinal disease resistance. To that aim, three different groups of five families of gilthead sea bream that were selected during two generations for fast, intermediate, or slow growth (F3 generation) were kept together in the same open-flow tanks and fed a control or a well-balanced plant-based diet during 9 months. Six animals per family and dietary treatment were sacrificed and the adherent bacteria from the anterior intestinal portion were sequenced. In parallel, fish of the fast- and slow-growth groups were infected with the intestinal parasite Enteromyxum leei and the disease signs, prevalence, intensity, and parasite abundance were evaluated.

RESULTS: No differences were detected in alpha diversity indexes among families, and the core bacterial architecture was the prototypical composition of gilthead sea bream intestinal microbiota, indicating no dysbiosis in any of the groups. The plant-based diet significantly changed the microbiota in the intermediate- and slow-growth families, with a much lower effect on the fast-growth group. Interestingly, the smaller changes detected in the fast-growth families potentially accounted for more changes at the metabolic level when compared with the other families. Upon parasitic infection, the fast-growth group showed significantly lower disease signs and parasite intensity and abundance than the slow-growth animals.

CONCLUSIONS: These results show a clear genome-metagenome interaction indicating that the fast-growth families harbor a microbiota that is more flexible upon dietary changes. These animals also showed a better ability to cope with intestinal infections. Video Abstract.}, } @article {pmid33228639, year = {2020}, author = {Liu, C and Ponsero, AJ and Armstrong, DG and Lipsky, BA and Hurwitz, BL}, title = {The dynamic wound microbiome.}, journal = {BMC medicine}, volume = {18}, number = {1}, pages = {358}, pmid = {33228639}, issn = {1741-7015}, support = {UL1 TR001855/TR/NCATS NIH HHS/United States ; }, mesh = {Diabetic Foot/*microbiology ; Female ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Male ; Metabolomics/*methods ; Microbiota/*physiology ; }, abstract = {BACKGROUND: Diabetic foot ulcers (DFUs) account for the majority of all limb amputations and hospitalizations due to diabetes complications. With 30 million cases of diabetes in the USA and 500,000 new diagnoses each year, DFUs are a growing health problem. Diabetes patients with limb amputations have high postoperative mortality, a high rate of secondary amputation, prolonged inpatient hospital stays, and a high incidence of re-hospitalization. DFU-associated amputations constitute a significant burden on healthcare resources that cost more than 10 billion dollars per year. Currently, there is no way to identify wounds that will heal versus those that will become severely infected and require amputation.

MAIN BODY: Accurate identification of causative pathogens in diabetic foot ulcers is a critical component of effective treatment. Compared to traditional culture-based methods, advanced sequencing technologies provide more comprehensive and unbiased profiling on wound microbiome with a higher taxonomic resolution, as well as functional annotation such as virulence and antibiotic resistance. In this review, we summarize the latest developments in defining the microbiology of diabetic foot ulcers that have been unveiled by sequencing technologies and discuss both the future promises and current limitations of these approaches. In particular, we highlight the temporal patterns and system dynamics in the diabetic foot microbiome monitored and measured during wound progression and medical intervention, and explore the feasibility of molecular diagnostics in clinics.

CONCLUSION: Molecular tests conducted during weekly office visits to clean and examine DFUs would allow clinicians to offer personalized treatment and antibiotic therapy. Personalized wound management could reduce healthcare costs, improve quality of life for patients, and recoup lost productivity that is important not only to the patient, but also to healthcare payers and providers. These efforts could also improve antibiotic stewardship and control the rise of "superbugs" vital to global health.}, } @article {pmid33227982, year = {2020}, author = {Vernocchi, P and Gili, T and Conte, F and Del Chierico, F and Conta, G and Miccheli, A and Botticelli, A and Paci, P and Caldarelli, G and Nuti, M and Marchetti, P and Putignani, L}, title = {Network Analysis of Gut Microbiome and Metabolome to Discover Microbiota-Linked Biomarkers in Patients Affected by Non-Small Cell Lung Cancer.}, journal = {International journal of molecular sciences}, volume = {21}, number = {22}, pages = {}, pmid = {33227982}, issn = {1422-0067}, mesh = {Akkermansia/classification/genetics/isolation & purification ; Alcohols/metabolism ; Aldehydes/metabolism ; Antineoplastic Agents, Immunological/therapeutic use ; Bacteroides/classification/genetics/isolation & purification ; Carcinoma, Non-Small-Cell Lung/drug therapy/*genetics/immunology/microbiology ; Clostridiaceae/classification/genetics/isolation & purification ; Databases, Genetic ; Disease Progression ; Drug Monitoring/methods ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/genetics/*immunology ; *Gene Expression Regulation, Neoplastic ; *Gene Regulatory Networks ; Humans ; Immunotherapy/methods ; Indoles/metabolism ; Lung Neoplasms/drug therapy/*genetics/immunology/microbiology ; Metabolome/genetics/*immunology ; Metagenomics/methods ; Peptostreptococcus/classification/genetics/isolation & purification ; Precision Medicine/methods ; Programmed Cell Death 1 Receptor/antagonists & inhibitors/genetics/immunology ; RNA, Ribosomal, 16S/genetics ; Signal Transduction ; }, abstract = {Several studies in recent times have linked gut microbiome (GM) diversity to the pathogenesis of cancer and its role in disease progression through immune response, inflammation and metabolism modulation. This study focused on the use of network analysis and weighted gene co-expression network analysis (WGCNA) to identify the biological interaction between the gut ecosystem and its metabolites that could impact the immunotherapy response in non-small cell lung cancer (NSCLC) patients undergoing second-line treatment with anti-PD1. Metabolomic data were merged with operational taxonomic units (OTUs) from 16S RNA-targeted metagenomics and classified by chemometric models. The traits considered for the analyses were: (i) condition: disease or control (CTRLs), and (ii) treatment: responder (R) or non-responder (NR). Network analysis indicated that indole and its derivatives, aldehydes and alcohols could play a signaling role in GM functionality. WGCNA generated, instead, strong correlations between short-chain fatty acids (SCFAs) and a healthy GM. Furthermore, commensal bacteria such as Akkermansia muciniphila, Rikenellaceae, Bacteroides, Peptostreptococcaceae, Mogibacteriaceae and Clostridiaceae were found to be more abundant in CTRLs than in NSCLC patients. Our preliminary study demonstrates that the discovery of microbiota-linked biomarkers could provide an indication on the road towards personalized management of NSCLC patients.}, } @article {pmid33226731, year = {2021}, author = {Diaz, PI}, title = {Subgingival fungi, Archaea, and viruses under the omics loupe.}, journal = {Periodontology 2000}, volume = {85}, number = {1}, pages = {82-89}, doi = {10.1111/prd.12352}, pmid = {33226731}, issn = {1600-0757}, mesh = {Archaea/genetics ; Bacteria/genetics ; DNA ; Fungi ; *Gingiva/microbiology ; Humans ; *Microbiota ; *Viruses ; }, abstract = {The microbial communities that inhabit the gingival crevice are responsible for the pathological processes that affect the periodontium. The changes in composition and function of subgingival bacteria as disease develops have been extensively studied. Subgingival communities, however, also contain fungi, Archaea, and viruses, which could contribute to the dysbiotic processes associated with periodontal diseases. High-throughput DNA sequencing has facilitated a better understanding of the mycobiome, archaeome, and virome. However, the number of studies available on the nonbacterial components of the subgingival microbiome remains limited in comparison with publications focusing on bacteria. Difficulties in characterizing fungal, archaeal, and viral populations arise from the small portion of the total metagenome mass they occupy and lack of comprehensive reference genome databases. In addition, specialized approaches potentially introducing bias are required to enrich for viral particles, while harsh methods of cell lysis are needed to recover nuclei acids from certain fungi. While the characterization of the subgingival diversity of fungi, Archaea and viruses is incomplete, emerging evidence suggests that they could contribute in different ways to subgingival dysbiosis. Certain fungi, such as Candida albicans are suggested to facilitate colonization of bacterial pathogens. Methanogenic Archaea are associated with periodontitis severity and are thought to partner synergistically with bacterial fermenters, while viruses may affect immune responses or shape microbial communities in ways incompletely understood. This review describes the manner in which omics approaches have improved our understanding of the diversity of fungi, Archaea, and viruses within subgingival communities. Further characterization of these understudied components of the subgingival microbiome is required, together with mechanistic studies to unravel their ecological role and potential contributions to dysbiosis.}, } @article {pmid33226714, year = {2021}, author = {Kumar, PS and Dabdoub, SM and Ganesan, SM}, title = {Probing periodontal microbial dark matter using metataxonomics and metagenomics.}, journal = {Periodontology 2000}, volume = {85}, number = {1}, pages = {12-27}, doi = {10.1111/prd.12349}, pmid = {33226714}, issn = {1600-0757}, mesh = {Bacteria ; Humans ; *Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; }, abstract = {Our view of the periodontal microbial community has been shaped by a century or more of cultivation-based and microscopic investigations. While these studies firmly established the infection-mediated etiology of periodontal diseases, it was apparent from the very early days that periodontal microbiology suffered from what Staley and Konopka described as the "great plate count anomaly", in that these culturable bacteria were only a minor part of what was visible under the microscope. For nearly a century, much effort has been devoted to finding the right tools to investigate this uncultivated majority, also known as "microbial dark matter". The discovery that DNA was an effective tool to "see" microbial dark matter was a significant breakthrough in environmental microbiology, and oral microbiologists were among the earliest to capitalize on these advances. By identifying the order in which nucleotides are arranged in a stretch of DNA (DNA sequencing) and creating a repository of these sequences, sequence databases were created. Computational tools that used probability-driven analysis of these sequences enabled the discovery of new and unsuspected species and ascribed novel functions to these species. This review will trace the development of DNA sequencing as a quantitative, open-ended, comprehensive approach to characterize microbial communities in their native environments, and explore how this technology has shifted traditional dogmas on how the oral microbiome promotes health and its role in disease causation and perpetuation.}, } @article {pmid33226693, year = {2021}, author = {Teles, F and Wang, Y and Hajishengallis, G and Hasturk, H and Marchesan, JT}, title = {Impact of systemic factors in shaping the periodontal microbiome.}, journal = {Periodontology 2000}, volume = {85}, number = {1}, pages = {126-160}, doi = {10.1111/prd.12356}, pmid = {33226693}, issn = {1600-0757}, support = {R01 DE024767/DE/NIDCR NIH HHS/United States ; }, mesh = {*Arthritis, Rheumatoid ; Female ; Humans ; Metagenomics ; *Microbiota ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Since 2010, next-generation sequencing platforms have laid the foundation to an exciting phase of discovery in oral microbiology as it relates to oral and systemic health and disease. Next-generation sequencing has allowed large-scale oral microbial surveys, based on informative marker genes, such as 16S ribosomal RNA, community gene inventories (metagenomics), and functional analyses (metatranscriptomics), to be undertaken. More specifically, the availability of next-generation sequencing has also paved the way for studying, in greater depth and breadth, the effect of systemic factors on the periodontal microbiome. It was natural to investigate systemic diseases, such as diabetes, in such studies, along with systemic conditions or states, , pregnancy, menopause, stress, rheumatoid arthritis, and systemic lupus erythematosus. In addition, in recent years, the relevance of systemic "variables" (ie, factors that are not necessarily diseases or conditions, but may modulate the periodontal microbiome) has been explored in detail. These include ethnicity and genetics. In the present manuscript, we describe and elaborate on the new and confirmatory findings unveiled by next-generation sequencing as it pertains to systemic factors that may shape the periodontal microbiome. We also explore the systemic and mechanistic basis for such modulation and highlight the importance of those relationships in the management and treatment of patients.}, } @article {pmid33226688, year = {2021}, author = {Duran-Pinedo, AE}, title = {Metatranscriptomic analyses of the oral microbiome.}, journal = {Periodontology 2000}, volume = {85}, number = {1}, pages = {28-45}, doi = {10.1111/prd.12350}, pmid = {33226688}, issn = {1600-0757}, support = {/DE/NIDCR NIH HHS/United States ; 2R01DE021553/NH/NIH HHS/United States ; }, mesh = {Biofilms ; *Dental Caries ; Humans ; *Microbiota/genetics ; Mouth ; *Periodontal Diseases ; }, abstract = {Although the composition of the oral human microbiome is now well studied, regulation of genes within oral microbial communities remains mostly uncharacterized. Current concepts of periodontal disease and caries highlight the importance of oral biofilms and their role as etiological agents of those diseases. Currently, there is increased interest in exploring and characterizing changes in the composition and gene-expression profiles of oral microbial communities. These efforts aim to identify changes in functional activities that could explain the transition from health to disease and the reason for the chronicity of those infections. It is now clear that the functions of distinct species within the subgingival microbiota are intimately intertwined with the rest of the microbial community. This point highlights the relevance of examining the expression profile of specific species within the subgingival microbiota in the case of periodontal disease or caries lesions, in the context of the other members of the biofilm in vivo. Metatranscriptomic analysis of the oral community is the starting point for identifying environmental signals that modulate the shift in metabolism of the community from commensal to dysbiotic. These studies give a snapshot of the expression patterns of microbial communities and also allow us to determine triggers to diseases. For example, in the case of caries, studies have unveiled a potential new pathway of sugar metabolism, namely the use of sorbitol as an additional source of carbon by Streptococcus mutans; and in the case of periodontal disease, high levels of extracellular potassium could be a signal of disease. Longitudinal studies are needed to identify the real markers of the initial stages of caries and periodontal disease. More information on the gene-expression profiles of the host, along with the patterns from the microbiome, will lead to a clearer understanding of the modulation of health and disease. This review presents a summary of these initial studies, which have opened the door to a new understanding of the dynamics of the oral community during the dysbiotic process in the oral cavity.}, } @article {pmid33226670, year = {2021}, author = {Kumar, PS}, title = {Microbiomics: Were we all wrong before?.}, journal = {Periodontology 2000}, volume = {85}, number = {1}, pages = {8-11}, doi = {10.1111/prd.12373}, pmid = {33226670}, issn = {1600-0757}, mesh = {Bacteria/genetics ; Female ; Humans ; *Metagenomics ; *Microbiota ; Proteomics ; }, abstract = {Periodontal microbiology has historically been based on an "us against them" paradigm, one that focuses mainly on identifying microbes and viruses that cause disease. However, such a bottom-up approach limits our appreciation of the incredible diversity of this ecosystem and the essential ways in which microbial interactions contribute to health and homeostasis of the subgingival niche. Microbiomics-the science of collectively characterizing and quantifying molecules responsible for the structure, function, and dynamics of a microbial community-has enabled us to study these communities in their natural habitat, thereby revolutionizing our knowledge of host-associated microbes and reconceptualizing our definition of "human." When this systems-biology approach is combined with ecologic principles, it explicates the complex relationship that exist between microbiota and between them and us, the human. In this volume of Periodontology 2000, a group of 12 female scientists take the lead in investigating how metagenomics, genomics, metatranscriptomics, proteomics, metaproteomics, and metabolomics have achieved the following: (a) widened our view of the periodontal microbiome; (b) expanded our understanding of the evolution of the human oral microbiome; (c) shone a light on not just bacteria, but also other prokaryotic and eukaryotic members of the community; (d) elucidated the effects of anthropogenic behavior and systemic diseases on shaping these communities; and (e) influenced traditional patterns of periodontal therapeutics.}, } @article {pmid33225966, year = {2020}, author = {Huang, L and Xu, C and Yang, W and Yu, R}, title = {A machine learning framework to determine geolocations from metagenomic profiling.}, journal = {Biology direct}, volume = {15}, number = {1}, pages = {27}, pmid = {33225966}, issn = {1745-6150}, mesh = {Cities ; Geography ; Humans ; *Machine Learning ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; }, abstract = {BACKGROUND: Studies on metagenomic data of environmental microbial samples found that microbial communities seem to be geolocation-specific, and the microbiome abundance profile can be a differentiating feature to identify samples' geolocations. In this paper, we present a machine learning framework to determine the geolocations from metagenomics profiling of microbial samples.

RESULTS: Our method was applied to the multi-source microbiome data from MetaSUB (The Metagenomics and Metadesign of Subways and Urban Biomes) International Consortium for the CAMDA 2019 Metagenomic Forensics Challenge (the Challenge). The goal of the Challenge is to predict the geographical origins of mystery samples by constructing microbiome fingerprints.First, we extracted features from metagenomic abundance profiles. We then randomly split the training data into training and validation sets and trained the prediction models on the training set. Prediction performance was evaluated on the validation set. By using logistic regression with L2 normalization, the prediction accuracy of the model reaches 86%, averaged over 100 random splits of training and validation datasets.The testing data consists of samples from cities that do not occur in the training data. To predict the "mystery" cities that are not sampled before for the testing data, we first defined biological coordinates for sampled cities based on the similarity of microbial samples from them. Then we performed affine transform on the map such that the distance between cities measures their biological difference rather than geographical distance. After that, we derived the probabilities of a given testing sample from unsampled cities based on its predicted probabilities on sampled cities using Kriging interpolation. Results show that this method can successfully assign high probabilities to the true cities-of-origin of testing samples.

CONCLUSION: Our framework shows good performance in predicting the geographic origin of metagenomic samples for cities where training data are available. Furthermore, we demonstrate the potential of the proposed method to predict metagenomic samples' geolocations for samples from locations that are not in the training dataset.}, } @article {pmid33225533, year = {2020}, author = {Bollmann-Giolai, A and Giolai, M and Heavens, D and Macaulay, I and Malone, J and Clark, MD}, title = {A low-cost pipeline for soil microbiome profiling.}, journal = {MicrobiologyOpen}, volume = {9}, number = {12}, pages = {e1133}, pmid = {33225533}, issn = {2045-8827}, support = {BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/J/000PR9797/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {DNA, Bacterial/*analysis/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; Microbiota/*genetics/physiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Soil ; *Soil Microbiology ; }, abstract = {Common bottlenecks in environmental and crop microbiome studies are the consumable and personnel costs necessary for genomic DNA extraction and sequencing library construction. This is harder for challenging environmental samples such as soil, which is rich in Polymerase Chain Reaction (PCR) inhibitors. To address this, we have established a low-cost genomic DNA extraction method for soil samples. We also present an Illumina-compatible 16S and ITS rRNA gene amplicon library preparation workflow that uses common laboratory equipment. We evaluated the performance of our genomic DNA extraction method against two leading commercial soil genomic DNA kits (MoBio PowerSoil® and MP Biomedicals™ FastDNA™ SPIN) and a recently published non-commercial extraction method by Zou et al. (PLoS Biology, 15, e2003916, 2017). Our benchmarking experiment used four different soil types (coniferous, broad-leafed, and mixed forest plus a standardized cereal crop compost mix) assessing the quality and quantity of the extracted genomic DNA by analyzing sequence variants of 16S V4 and ITS rRNA amplicons. We found that our genomic DNA extraction method compares well to both commercially available genomic DNA extraction kits in DNA quality and quantity. The MoBio PowerSoil® kit, which relies on silica column-based DNA extraction with extensive washing, delivered the cleanest genomic DNA, for example, best A260:A280 and A260:A230 absorbance ratios. The MP Biomedicals™ FastDNA™ SPIN kit, which uses a large amount of binding material, yielded the most genomic DNA. Our method fits between the two commercial kits, producing both good yields and clean genomic DNA with fragment sizes of approximately 10 kb. Comparative analysis of detected amplicon sequence variants shows that our method correlates well with the two commercial kits. Here, we present a low-cost genomic DNA extraction method for soil samples that can be coupled to an Illumina-compatible simple two-step amplicon library construction workflow for 16S V4 and ITS marker genes. Our method delivers high-quality genomic DNA at a fraction of the cost of commercial kits and enables cost-effective, large-scale amplicon sequencing projects. Notably, our extracted gDNA molecules are long enough to be suitable for downstream techniques such as full gene sequencing or even metagenomics shotgun approaches using long reads (PacBio or Nanopore), 10x Genomics linked reads, and Dovetail genomics.}, } @article {pmid33224899, year = {2020}, author = {Hu, Y and Xie, H and Gao, M and Huang, P and Zhou, H and Ma, Y and Zhou, M and Liang, J and Yang, J and Lv, Z}, title = {Dynamic of Composition and Diversity of Gut Microbiota in Triatoma rubrofasciata in Different Developmental Stages and Environmental Conditions.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {587708}, pmid = {33224899}, issn = {2235-2988}, mesh = {Animals ; *Chagas Disease ; *Gastrointestinal Microbiome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Triatoma ; }, abstract = {Triatoma rubrofasciata (T. rubrofasciata), one kind of triatomine insects, is the vector of Trypanosoma cruzi (T. cruzi), which lead to American trypanosomiasis. Although the gut microbiome may play an essential role in the development and susceptibility of triatomine, there is limited research on the gut microbiota of T. rubrofasciata. To elucidate the effect of the vector's developmental stages and environmental conditions on the gut microbiome, we employed 16S rRNA gene sequencing to profile the gut bacterial community diversity and composition of T. rubrofasciata. Significant shifts were observed in the overall gut microbe diversity and composition across the development of T. rubrofasciata and specific bacteria were detected in different stages. Serratia and Burkholderia-Caballeronia-Paraburkholderia were dominant in the 1[st] nymphal stage, while the abundance of Staphylococcus was low in the 1[st] nymphal stage. Oceanicaulis were undetectable in the adult stage and Odoribacter peaked in the 2[nd] nymphal stage. Moreover, Staphylococcus was correlated negatively with Serratia. Likewise, the total gut microbiota diversity and composition of T. rubrofasciata differentiated significantly by environmental conditions. The ingestion of a bloodmeal increased alpha diversity of gut bacterial communities, and Staphylococcus was more abundant in laboratory-reared bugs whereas Enterococcus enriched in wild-caught bugs. Furthermore, Pantoea was negatively correlated with Staphylococcus, and positively related to Bacillus only. The phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) algorithm showed obvious metagenomic functional differences by environmental conditions, and Chagas disease relevant pathway was enriched in wild-caught T. rubrofasciata.}, } @article {pmid33224134, year = {2020}, author = {Yu, J and He, X and Wei, A and Liu, T and Zhang, Q and Pan, Y and Hao, Z and Yang, L and Yuan, Y and Zhang, Z and Zhang, C and Hao, C and Liu, Z and Li, W}, title = {HPS1 Regulates the Maturation of Large Dense Core Vesicles and Lysozyme Secretion in Paneth Cells.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {560110}, pmid = {33224134}, issn = {1664-3224}, mesh = {Animals ; Child ; Disease Models, Animal ; Feces/microbiology ; Female ; Fluorescent Antibody Technique ; Gastrointestinal Microbiome ; Hermanski-Pudlak Syndrome/etiology/metabolism ; Humans ; Immunohistochemistry ; Intestinal Mucosa/metabolism/pathology ; Lysosomes/*metabolism ; Male ; Membrane Proteins/genetics/*metabolism ; Metagenomics/methods ; Mice ; Mice, Knockout ; Paneth Cells/*metabolism/ultrastructure ; Protein Transport ; R-SNARE Proteins/genetics/metabolism ; Secretory Vesicles/*metabolism ; }, abstract = {HPS1, a BLOC-3 subunit that acts as a guanine nucleotide exchange factor of Rab32/38, may play a role in the removal of VAMP7 during the maturation of large dense core vesicles of Paneth cells. Loss of HPS1 impairs lysozyme secretion and alters the composition of intestinal microbiota, which may explain the susceptibility of HPS-associated inflammatory bowel disease. Hermansky-Pudlak syndrome (HPS) is characterized by oculocutaneous albinism, bleeding tendency, and other chronic organ lesions due to defects in tissue-specific lysosome-related organelles (LROs). For some HPS subtypes, such as HPS-1, it is common to have symptoms of HPS-associated inflammatory bowel disease (IBD). However, its underlying mechanism is largely unknown. HPS1 is a subunit of the BLOC-3 complex which functions in the biogenesis of LROs. Large dense core vesicles (LDCVs) in Paneth cells of the intestine are a type of LROs. We here first report the abnormal LDCV morphology (increased number and enlarged size) in HPS1-deficient pale ear (ep) mice. Similar to its role in melanosome maturation, HPS1 plays an important function in the removal of VAMP7 from LDCVs to promote the maturation of LDCVs. The immature LDCVs in ep mice are defective in regulated secretion of lysozyme, a key anti-microbial peptide in the intestine. We observed changes in the composition of intestinal microbiota in both HPS-1 patients and ep mice. These findings provide insights into the underlying mechanism of HPS-associated IBD development, which may be implicated in possible therapeutic intervention of this devastating condition.}, } @article {pmid33222846, year = {2020}, author = {Wang, J and Bai, X and Peng, C and Yu, Z and Li, B and Zhang, W and Sun, Z and Zhang, H}, title = {Fermented milk containing Lactobacillus casei Zhang and Bifidobacterium animalis ssp. lactis V9 alleviated constipation symptoms through regulation of intestinal microbiota, inflammation, and metabolic pathways.}, journal = {Journal of dairy science}, volume = {103}, number = {12}, pages = {11025-11038}, doi = {10.3168/jds.2020-18639}, pmid = {33222846}, issn = {1525-3198}, mesh = {Adult ; Animals ; Bifidobacterium animalis/*physiology ; Bioreactors ; Constipation/*therapy ; Cultured Milk Products/*microbiology ; Cytokines/blood ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Inflammation/*therapy ; Lacticaseibacillus casei/*physiology ; Male ; Metabolic Networks and Pathways/physiology ; Metabolomics ; Metagenomics ; Probiotics/therapeutic use ; }, abstract = {Studies suggest that probiotics and fermented milk can improve defecation in constipated patients. However, the mechanism of fermented milk containing probiotics on constipation remains poorly understood. Volunteers with chronic constipation symptoms were recruited and given 200 g/d of fermented milk containing Lactobacillus casei Zhang and Bifidobacterium animalis ssp. lactis V9 (PFM) for 4 wk. Clinical symptoms, cytokines, metagenomics, and metabolomics were evaluated in constipated participants before and after PFM intervention. After PFM intervention, we observed significant improvement of constipation symptoms. In the serum samples, the anti-inflammatory cytokine IL-10 increased and the proinflammatory cytokine C-reactive protein and lipopolysaccharides decreased. Metagenomics results showed that the increase of B. animalis was correlated with an increase in defecation frequency. Fatty acid biosynthesis and bile acid biosynthesis in stool samples as well as carnitine shuttle, vitamin E metabolism, and ascorbate and aldarate metabolism were identified as significantly altered metabolic pathways. Acylcarnitine, located on the carnitine shuttle pathway, had a significantly positive correlation with defecation frequency. It was speculated that PFM may contribute to alleviating constipation symptoms through 3 potential mechanisms: fine-tuning gastrointestinal microbiota, fighting inflammation, and regulating metabolic pathways.}, } @article {pmid33221999, year = {2020}, author = {Liu, J and Deng, XC and Li, XY and Yang, ZB and Zhang, GY and Chen, TT}, title = {Intramuscular injection of tetracycline decreased gut microbial diversity in mouse.}, journal = {Mammalian genome : official journal of the International Mammalian Genome Society}, volume = {31}, number = {9-12}, pages = {295-308}, doi = {10.1007/s00335-020-09852-2}, pmid = {33221999}, issn = {1432-1777}, mesh = {Animals ; Anti-Bacterial Agents/administration & dosage/*pharmacology ; Biodiversity ; Computational Biology/methods ; DNA Barcoding, Taxonomic ; Gastrointestinal Microbiome/*drug effects ; Injections, Intramuscular ; Metagenome ; Metagenomics/methods ; Mice ; Phylogeny ; RNA, Ribosomal, 16S ; Tetracycline/administration & dosage/*pharmacology ; }, abstract = {Antibiotics contribute a lot to human beings and can kill bacteria effectively. However, more and more studies show that antibiotics can disturb the intestinal microbial community. It has been widely reported that oral antibiotics can reduce the diversity of intestinal microflora, but the effect of intramuscular injection on intestinal microflora is less studied. In this study, we sequenced the intestinal microflora of mice treated with tetracycline by 16SrRNA method, and found that intramuscular injection of tetracycline (TET) can also reduce the intestinal microbial richness of mice. In addition, the results showed that within a certain range (3 mg), with the increase of TET injection concentration, the wind of intestinal microflora in mice decreased significantly. When the injection concentration reached saturation, although the amount of TET injection was increased, the degree of intestinal flora affected was not increased. The results showed that the degree of diversity decrease was in direct proportion to the amount of tetracycline injection in the saturated concentration, but not positively related to the high amount of TET injection after exceeding the saturated concentration.}, } @article {pmid33219314, year = {2020}, author = {Antonson, AM and Evans, MV and Galley, JD and Chen, HJ and Rajasekera, TA and Lammers, SM and Hale, VL and Bailey, MT and Gur, TL}, title = {Unique maternal immune and functional microbial profiles during prenatal stress.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {20288}, pmid = {33219314}, issn = {2045-2322}, support = {K08 MH112892/MH/NIMH NIH HHS/United States ; R21 MH117552/MH/NIMH NIH HHS/United States ; T32 NS105864/NS/NINDS NIH HHS/United States ; 5T32DE014320/NH/NIH HHS/United States ; }, mesh = {Animals ; Brain/*embryology/immunology ; Burkholderiales/genetics/immunology ; Disease Models, Animal ; Female ; Fetal Development/*immunology ; Gastrointestinal Microbiome/genetics/*immunology ; Glucocorticoids/metabolism ; Humans ; Leukocytes, Mononuclear/immunology ; Maternal-Fetal Exchange/immunology ; Mental Health ; Metagenomics ; Mice ; Neuroimmunomodulation/immunology ; Placenta/cytology/immunology ; Pregnancy ; Pregnancy Complications/*immunology/metabolism/psychology ; Prenatal Exposure Delayed Effects/immunology ; Stress, Psychological/*immunology/metabolism/psychology ; }, abstract = {Maternal stress during pregnancy is widespread and is associated with poor offspring outcomes, including long-term mental health issues. Prenatal stress-induced fetal neuroinflammation is thought to underlie aberrant neurodevelopment and to derive from a disruption in intrauterine immune homeostasis, though the exact origins are incompletely defined. We aimed to identify divergent immune and microbial metagenome profiles of stressed gestating mice that may trigger detrimental inflammatory signaling at the maternal-fetal interface. In response to stress, maternal glucocorticoid circuit activation corresponded with indicators of systemic immunosuppression. At the maternal-fetal interface, density of placental mononuclear leukocytes decreased with stress, yet maternal whole blood leukocyte analysis indicated monocytosis and classical M1 phenotypic shifts. Genome-resolved microbial metagenomic analyses revealed reductions in genes, microbial strains, and metabolic pathways in stressed dams that are primarily associated with pro-inflammatory function. In particular, disrupted Parasutterella excrementihominis appears to be integral to inflammatory and metabolic dysregulation during prenatal stress. Overall, these perturbations in maternal immunological and microbial regulation during pregnancy may displace immune equilibrium at the maternal-fetal interface. Notably, the absence of and reduction in overt maternal inflammation during stress indicates that the signaling patterns driving fetal outcomes in this context are more nuanced and complex than originally anticipated.}, } @article {pmid33219095, year = {2020}, author = {Mostafa, HH and Fissel, JA and Fanelli, B and Bergman, Y and Gniazdowski, V and Dadlani, M and Carroll, KC and Colwell, RR and Simner, PJ}, title = {Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients.}, journal = {mBio}, volume = {11}, number = {6}, pages = {}, pmid = {33219095}, issn = {2150-7511}, mesh = {Bacteria/classification ; COVID-19/microbiology/*virology ; Coinfection/microbiology/virology ; Computational Biology ; *High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Metagenomics ; Microbiota ; Nasopharynx/*virology ; RNA, Viral/genetics ; SARS-CoV-2/*genetics ; Specimen Handling ; }, abstract = {Metagenomic next-generation sequencing (mNGS) offers an agnostic approach for emerging pathogen detection directly from clinical specimens. In contrast to targeted methods, mNGS also provides valuable information on the composition of the microbiome and might uncover coinfections that may associate with disease progression and impact prognosis. To evaluate the use of mNGS for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and/or other infecting pathogens, we applied direct Oxford Nanopore long-read third-generation metatranscriptomic and metagenomic sequencing. Nasopharyngeal (NP) swab specimens from 50 patients under investigation for CoV disease 2019 (COVID-19) were sequenced, and the data were analyzed by the CosmosID bioinformatics platform. Further, we characterized coinfections and the microbiome associated with a four-point severity index. SARS-CoV-2 was identified in 77.5% (31/40) of samples positive by RT-PCR, correlating with lower cycle threshold (Ct) values and fewer days from symptom onset. At the time of sampling, possible bacterial or viral coinfections were detected in 12.5% of SARS-CoV-2-positive specimens. A decrease in microbial diversity was observed among COVID-19-confirmed patients (Shannon diversity index, P = 0.0082; Chao richness estimate, P = 0.0097; Simpson diversity index, P = 0.018), and differences in microbial communities were linked to disease severity (P = 0.022). Furthermore, statistically significant shifts in the microbiome were identified among SARS-CoV-2-positive and -negative patients, in the latter of whom a higher abundance of Propionibacteriaceae (P = 0.028) and a reduction in the abundance of Corynebacterium accolens (P = 0.025) were observed. Our study corroborates the growing evidence that increased SARS-CoV-2 RNA detection from NP swabs is associated with the early stages rather than the severity of COVID-19. Further, we demonstrate that SARS-CoV-2 causes a significant change in the respiratory microbiome. This work illustrates the utility of mNGS for the detection of SARS-CoV-2, for diagnosing coinfections without viral target enrichment or amplification, and for the analysis of the respiratory microbiome.IMPORTANCE SARS-CoV-2 has presented a rapidly accelerating global public health crisis. The ability to detect and analyze viral RNA from minimally invasive patient specimens is critical to the public health response. Metagenomic next-generation sequencing (mNGS) offers an opportunity to detect SARS-CoV-2 from nasopharyngeal (NP) swabs. This approach also provides information on the composition of the respiratory microbiome and its relationship to coinfections or the presence of other organisms that may impact SARS-CoV-2 disease progression and prognosis. Here, using direct Oxford Nanopore long-read third-generation metatranscriptomic and metagenomic sequencing of NP swab specimens from 50 patients under investigation for COVID-19, we detected SARS-CoV-2 sequences by applying the CosmosID bioinformatics platform. Further, we characterized coinfections and detected a decrease in the diversity of the microbiomes in these patients. Statistically significant shifts in the microbiome were identified among COVID-19-positive and -negative patients, in the latter of whom a higher abundance of Propionibacteriaceae and a reduction in the abundance of Corynebacterium accolens were observed. Our study also corroborates the growing evidence that increased SARS-CoV-2 RNA detection from NP swabs is associated with the early stages of disease rather than with severity of disease. This work illustrates the utility of mNGS for the detection and analysis of SARS-CoV-2 from NP swabs without viral target enrichment or amplification and for the analysis of the respiratory microbiome.}, } @article {pmid33218999, year = {2021}, author = {Zheng, J and Reed, E and Ramachandran, P and Ottesen, A and Brown, EW and Wang, Y}, title = {Taxonomic and Functional Shifts in the Sprout Spent Irrigation Water Microbiome in Response to Salmonella Contamination of Alfalfa Seeds.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {3}, pages = {}, pmid = {33218999}, issn = {1098-5336}, mesh = {Agricultural Irrigation ; Genes, Bacterial ; Medicago sativa/*microbiology ; Metagenomics ; Microbial Interactions ; Microbiota ; Salmonella enterica/*genetics ; Seedlings/*microbiology ; Wastewater/microbiology ; }, abstract = {Despite recent advances in Salmonella-sprout research, little is known about the relationship between Salmonella and the sprout microbiome during sprouting. Sprout spent irrigation water (SSIW) provides an informative representation of the total microbiome of this primarily aquaponic crop. This study was designed to characterize the function and taxonomy of the most actively transcribed genes in SSIW from Salmonella enterica serovar Cubana-contaminated alfalfa seeds throughout the sprouting process. Genomic DNA and total RNA from SSIW was collected at regular intervals and sequenced using Illumina MiSeq and NextSeq platforms. Nucleic acid data were annotated using four different pipelines. Both metagenomic and metatranscriptomic analyses revealed a diverse and highly dynamic SSIW microbiome. A "core" SSIW microbiome comprised Klebsiella, Enterobacter, Pantoea, and Cronobacter The impact, however, of Salmonella contamination on alfalfa seeds influenced SSIW microbial community dynamics not only structurally but also functionally. Changes in genes associated with metabolism, genetic information processing, environmental information processing, and cellular processes were abundant and time dependent. At time points of 24 h, 48 h, and 96 h, totals of 541, 723, and 424 S Cubana genes, respectively, were transcribed at either higher or lower levels than at 0 h in SSIW during sprouting. An array of S Cubana genes (107) were induced at all three time points, including genes involved in biofilm formation and modulation, stress responses, and virulence and tolerance to antimicrobials. Taken together, these findings expand our understanding of the effect of Salmonella seed contamination on the sprout crop microbiome and metabolome.IMPORTANCE Interactions of human enteric pathogens like Salmonella with plants and plant microbiomes remain to be elucidated. The rapid development of next-generation sequencing technologies provides powerful tools enabling investigation of such interactions from broader and deeper perspectives. Using metagenomic and metatranscriptomic approaches, this study identified not only changes in microbiome structure of SSIW associated with sprouting but also changes in the gene expression patterns related to the sprouting process in response to Salmonella contamination of alfalfa seeds. This study advances our knowledge on Salmonella-plant (i.e., sprout) interaction.}, } @article {pmid33218339, year = {2020}, author = {Draper, LA and Ryan, FJ and Dalmasso, M and Casey, PG and McCann, A and Velayudhan, V and Ross, RP and Hill, C}, title = {Autochthonous faecal viral transfer (FVT) impacts the murine microbiome after antibiotic perturbation.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {173}, pmid = {33218339}, issn = {1741-7007}, support = {SFI/12/RC/2273/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Animals ; Anti-Bacterial Agents/administration & dosage/*adverse effects ; Bacteria/drug effects/*isolation & purification ; Bacterial Physiological Phenomena/*drug effects ; *Fecal Microbiota Transplantation ; Feces/*microbiology ; *Metagenome ; Mice ; *Microbiota ; }, abstract = {BACKGROUND: It has become increasingly accepted that establishing and maintaining a complex and diverse gut microbiota is fundamental to human health. There are growing efforts to identify means of modulating and influencing the microbiota, especially in individuals who have experienced a disruption in their native microbiota. Faecal microbiota transplantation (FMT) is one method that restores diversity to the microbiota of an individual by introducing microbes from a healthy donor. FMT introduces the total microbial load into the recipient, including the bacteria, archaea, yeasts, protists and viruses. In this study, we investigated whether an autochthonous faecal viral transfer (FVT), in the form of a sterile faecal filtrate, could impact the recovery of a bacteriome disrupted by antibiotic treatment.

RESULTS: Following antibiotic disruption of the bacteriome, test mice received an FVT harvested prior to antibiotic treatment, while control mice received a heat- and nuclease-treated FVT. In both groups of mice, the perturbed microbiome reverted over time to one more similar to the pre-treatment one. However, the bacteriomes of mice that received an FVT, in which bacteriophages predominate, separated from those of the control mice as determined by principal co-ordinate analysis (PCoA). Moreover, analysis of the differentially abundant taxa indicated a closer resemblance to the pre-treatment bacteriome in the test mice that had received an FVT. Similarly, metagenomic sequencing of the virome confirmed that faecal bacteriophages of FVT and control mice differed over time in both abundance and diversity, with the phages constituting the FVT persisting in mice that received them.

CONCLUSIONS: An autochthonous virome transfer reshaped the bacteriomes of mice post-antibiotic treatment such that they more closely resembled the pre-antibiotic microbiota profile compared to mice that received non-viable phages. Thus, FVT may have a role in addressing antibiotic-associated microbiota alterations and potentially prevent the establishment of post-antibiotic infection. Given that bacteriophages are biologically inert in the absence of their host bacteria, they could form a safe and effective alternative to whole microbiota transplants that could be delivered during/following perturbation of the gut flora.}, } @article {pmid33217332, year = {2021}, author = {Münch, PC and Franzosa, EA and Stecher, B and McHardy, AC and Huttenhower, C}, title = {Identification of Natural CRISPR Systems and Targets in the Human Microbiome.}, journal = {Cell host & microbe}, volume = {29}, number = {1}, pages = {94-106.e4}, pmid = {33217332}, issn = {1934-6069}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/*genetics/metabolism ; Bacteriophages/genetics/physiology ; CRISPR-Associated Proteins/genetics ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Gastrointestinal Microbiome/genetics ; Gene Ontology ; Genes, Bacterial ; Genome, Bacterial ; Humans ; Metagenome ; Methylation ; Microbiota/*genetics ; Mouth/microbiology ; Viral Proteins/genetics/metabolism ; Virus Physiological Phenomena ; }, abstract = {Many bacteria resist invasive DNA by incorporating sequences into CRISPR loci, which enable sequence-specific degradation. CRISPR systems have been well studied from isolate genomes, but culture-independent metagenomics provide a new window into their diversity. We profiled CRISPR loci and cas genes in the body-wide human microbiome using 2,355 metagenomes, yielding functional and taxonomic profiles for 2.9 million spacers by aligning the spacer content to each sample's metagenome and corresponding gene families. Spacer and repeat profiles agree qualitatively with those from isolate genomes but expand their diversity by approximately 13-fold, with the highest spacer load present in the oral microbiome. The taxonomy of spacer sequences parallels that of their source community, with functional targets enriched for viral elements. When coupled with cas gene systems, CRISPR-Cas subtypes are highly site and taxon specific. Our analysis provides a comprehensive collection of natural CRISPR-cas loci and targets in the human microbiome.}, } @article {pmid33216744, year = {2020}, author = {Zhao, C and Ni, H and Zhao, L and Zhou, L and Borrás-Hidalgo, O and Cui, R}, title = {High nitrogen concentration alter microbial community in Allium fistulosum rhizosphere.}, journal = {PloS one}, volume = {15}, number = {11}, pages = {e0241371}, pmid = {33216744}, issn = {1932-6203}, mesh = {Allium/*microbiology/physiology ; Bacteria/isolation & purification ; Biodiversity ; Fungi/isolation & purification ; Metagenomics ; Microbiota/*drug effects ; Nitrogen/*pharmacology ; Phylogeny ; *Rhizosphere ; Soil Microbiology ; Species Specificity ; }, abstract = {Welsh onion (Allium fistulosum L.) constitutes an important plant species cultivated in China due the benefits and applications in different areas. Moreover, nitrogen is an essential nutrient during the growth and development of plant. Here, we present the effects of nitrogen on soil microbiome in welsh onion plants. We used High-throughput sequencing analysis to determine the diversity and abundances of microbes associated to soil rhizosphere in welsh onion under the influence of nitrogen application. Nitrogen application significantly influenced in the diversity of fungal community. The relative abundance of Orbiliomycetes increased with the nitrogen concentration. Nitrogen application did not affect the diversity of bacterial community, whereas the relative abundance of Acidobacteria_Gp2, Verrucomicrobiae and Sphingobacteriia decreased with the nitrogen condition. In this work, we introduced evidences of the effect of nitrogen fertilization on microbial community in welsh onion rhizosphere, and the change of microbial community may interfere the growth and development of welsh onion.}, } @article {pmid33215702, year = {2021}, author = {Akinola, SA and Ayangbenro, AS and Babalola, OO}, title = {The diverse functional genes of maize rhizosphere microbiota assessed using shotgun metagenomics.}, journal = {Journal of the science of food and agriculture}, volume = {101}, number = {8}, pages = {3193-3201}, doi = {10.1002/jsfa.10948}, pmid = {33215702}, issn = {1097-0010}, support = {UID123634//National Research Foundation South Africa/ ; }, mesh = {Bacteria/classification/*genetics/isolation & purification ; Bacterial Proteins/*genetics/metabolism ; Metagenomics ; Microbiota ; Nitrogen Fixation ; Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; Zea mays/*growth & development/microbiology ; }, abstract = {BACKGROUND: The geographical diversification in chemical, biological and physical properties of plant biospheres instigates heterogenicity in the proliferation of important soil microbiome. Controlling functions and structure of plant rhizosphere from a better understanding and prediction of a plant's immediate environment will help assess plant-microbe interplay, improve the productivity of plant ecosystems and improve plant response to adverse soil conditions. Here we characterized functional genes of the microbial community of maize rhizosphere using a culture-independent method.

RESULTS: Our metadata showed microbial genes involved in nitrogen fixation, phosphate solubilization, quorum sensing molecules, trehalose, siderophore production, phenazine biosynthesis protein, daunorubicin resistance, acetoin, 1-aminocyclopropane-1-carboxylate deaminase, 4-hydroxybenzoate, disease control and stress-reducing genes (superoxidase dismutase, catalase, peroxidase, etc.). β-Diversity showed that there is a highly significant difference between most of the genes mined from rhizosphere soil samples and surrounding soils.

CONCLUSIONS: The high relative abundance of stress-reducing genes mined from this study showed that the sampling sites harbor not only important plant-beneficial organisms but also a hotspot for developing bio-fertilizers. Nevertheless, since most of these organisms are unculturable, mapping cultivation strategies for their growth could make them readily available as bio-inoculants and possible biotechnological applications in the future. © 2020 Society of Chemical Industry.}, } @article {pmid33215353, year = {2021}, author = {Curiel-Maciel, NF and Martínez-Morales, F and Licea-Navarro, AF and Bertrand, B and Aguilar-Guadarrama, AB and Rosas-Galván, NS and Morales-Guzmán, D and Rivera-Gómez, N and Gutiérrez-Ríos, RM and Trejo-Hernández, MR}, title = {Characterization of Enterobacter cloacae BAGM01 Producing a Thermostable and Alkaline-Tolerant Rhamnolipid Biosurfactant from the Gulf of Mexico.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {23}, number = {1}, pages = {106-126}, pmid = {33215353}, issn = {1436-2236}, support = {201441//Consejo Nacional de Ciencia y Tecnología/ ; }, mesh = {Bacteria/isolation & purification ; Enterobacter cloacae/*genetics/*metabolism ; Glycolipids/*chemistry ; Gulf of Mexico ; Microbial Consortia ; Salinity ; Surface-Active Agents/*chemistry ; }, abstract = {The search for novel biosurfactants (Bs) requires the isolation of microorganisms from different environments. The Gulf of Mexico (GoM) is a geographical area active in the exploration and exploitation of hydrocarbons. Recent metagenomic and microbiologic studies in this area suggested a potential richness for novel Bs microbial producers. In this work, nineteen bacterial consortia from the GoM were isolated at different depths of the water column and marine sediments. Bs production from four bacterial consortia was detected by the CTAB test and their capacity to reduce surface tension (ST), emulsion index (EI24), and hemolytic activity. These bacterial consortia produced Bs in media supplemented with kerosene, diesel, or sucrose. Cultivable bacteria from these consortia were isolated and identified by bacterial polyphasic characterization. In some consortia, Enterobacter cloacae was the predominant specie. E. cloacae BAGM01 presented Bs activity in minimal medium and was selected to improve its Bs production using a Taguchi and Box-Behnken experimental design; this strain was able to grow and presented Bs activity at 35 g L[-1] of NaCl. This Bs decreased ST to around 34.5 ± 0.56 mNm[-1] and presented an EI24 of 71 ± 1.27%. Other properties of this Bs were thermal stability, stability in alkaline conditions, and stability at high salinity, conferring important and desirable characteristics in multiple industries. The analysis of the genome of E. cloacae BAGM01 showed the presence of rhlAB genes that have been reported in the synthesis of rhamnolipids, and alkAB genes that are related to the degradation of alkanes. The bioactive molecule was identified as a rhamnolipid after HPLC derivatization, [1]H NMR, and UPLC-QTOF-MS analysis.}, } @article {pmid33214767, year = {2020}, author = {Das Kangabam, R and Silla, Y and Goswami, G and Barooah, M}, title = {Bacterial Operational Taxonomic Units Replace the Interactive Roles of Other Operational Taxonomic Units Under Strong Environmental Changes.}, journal = {Current genomics}, volume = {21}, number = {7}, pages = {512-524}, pmid = {33214767}, issn = {1389-2029}, abstract = {BACKGROUND: Microorganisms are an important component of an aquatic ecosystem and play a critical role in the biogeochemical cycle which influences the circulation of the materials and maintains the balance in aquatic ecosystems.

OBJECTIVE: The seasonal variation along with the impact of anthropogenic activities, water quality, bacterial community composition and dynamics in the Loktak Lake, the largest freshwater lake of North East India, located in the Indo-Burma hotspot region was assessed during post-monsoon and winter season through metagenome analysis.

METHODS: Five soil samples were collected during Post-monsoon and winter season from the Loktak Lake that had undergone different anthropogenic impacts. The metagenomic DNA of the soil samples was extracted using commercial metagenomic DNA extraction kits following the manufacturer's instruction. The extracted DNA was used to prepare the NGS library and sequenced in the Illumina MiSeq platform.

RESULTS: Metagenomics analysis reveals Proteobacteria as the predominant community followed by Acidobacteria and Actinobacteria. The presence of these groups of bacteria indicates nitrogen fixation, oxidation of iron, sulfur, methane, and source of novel antibiotic candidates. The bacterial members belonging to different groups were involved in various biogeochemical processes, including fixation of carbon and nitrogen, producing streptomycin, gramicidin and perform oxidation of sulfur, sulfide, ammonia, and methane.

CONCLUSION: The outcome of this study provides a valuable dataset representing a seasonal profile across various land use and analysis, targeting at establishing an understanding of how the microbial communities vary across the land use and the role of keystone taxa. The findings may contribute to searches for microbial bio-indicators as biodiversity markers for improving the aquatic ecosystem of the Loktak Lake.}, } @article {pmid33214748, year = {2020}, author = {Alreshidi, MM and Veettil, VN and Noumi, E and Campo, RD and Snoussi, M}, title = {Description of microbial diversity associated with ticks Hyalomma dromedarii (Acari: Ixodidae) isolated from camels in Hail region (Saudi Arabia) using massive sequencing of 16S rDNA.}, journal = {Bioinformation}, volume = {16}, number = {8}, pages = {602-610}, pmid = {33214748}, issn = {0973-2063}, abstract = {Ticks are blood feeder able to transmit a wide diversity of microbes including pathogens. Therefore, it is of our interest to detect the diversity of microorganisms residing within ticks using massive sequencing of 16S rDNA. In this study, 200 adult ticks were collected from healthy camels in two localities from Hail province (Saudi Arabia). The analysis showed high microbial diversity dominated by the two domains (Archaea and Bacteria) associated with Hyalomma dromedarii from both regions. Proteobacteria (61.3%) and Firmicutes (31.2%) dominated the ticks from the Al Khotha region. While, the microbiome of ticks from the Al Gayed region was dominated by Proteobacteria (81.2%) and Firmicutes (9.2%). Twenty-three families were identified in the DNA-pool from the Al Gayed region, and was dominated by Pseudomonadaceae (45.37%), and Marinobacteraceae (14.39%) families. Francisellaceae (46%), Staphylococcaceae (24.26%) dominated the microbiome of the ticks collected from Al Gayed region. Thus, the genera Pseudomonas, Francisella, Proteus, Marinobacter, Glutamicibacter, Pedobacter, and Staphylococcus are largely distributed in the two identified microbiomes. This study concluded that ticks collected from the studied localities contained a wide range of microbial communities. These data have a great veterinary and medical importance in near future.}, } @article {pmid33211762, year = {2020}, author = {Nascimento, FSD and Suzuki, MO and Taba, JV and de Mattos, VC and Pipek, LZ and D'Albuquerque, EMC and Iuamoto, L and Meyer, A and Andraus, W and Pinho, JRR and de Moura, EGH and Setubal, JC and Carneiro-D'Albuquerque, LA}, title = {Analysis of biliary MICRObiota in hepatoBILIOpancreatic diseases compared to healthy people [MICROBILIO]: Study protocol.}, journal = {PloS one}, volume = {15}, number = {11}, pages = {e0242553}, pmid = {33211762}, issn = {1932-6203}, mesh = {Adult ; Bile/*microbiology ; Case-Control Studies ; Cholangiopancreatography, Endoscopic Retrograde ; DNA, Bacterial/genetics ; Digestive System Diseases/*microbiology ; Female ; Humans ; Liver Transplantation ; Living Donors ; Male ; Metagenome ; *Microbiota/genetics ; Middle Aged ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Ribotyping ; Young Adult ; }, abstract = {BACKGROUND: The performance of the microbiota is observed in several digestive tract diseases. Therefore, reaching the biliary microbiota may suggest ways for studies of biomarkers, diagnoses, tests and therapies in hepatobiliopancreatic diseases.

METHODS: Bile samples will be collected in endoscopic retrograde cholangiopancreatography patients (case group) and living liver transplantation donors (control group). We will characterize the microbiome based on two types of sequence data: the V3/V4 regions of the 16S ribosomal RNA (rRNA) gene and total shotgun DNA. For 16S sequencing data a standard 16S processing pipeline based on the Amplicon Sequence Variant concept and the qiime2 software package will be employed; for shotgun data, for each sample we will assemble the reads and obtain and analyze metagenome-assembled genomes.

RESULTS: The primary expected results of the study is to characterize the specific composition of the biliary microbiota in situations of disease and health. In addition, it seeks to demonstrate the existence of changes in the case of illness and also possible disease biomarkers, diagnosis, interventions and therapies in hepatobiliopancreatic diseases.

TRIAL REGISTRATION: NCT04391426. Registered 18 May 2020, https://clinicaltrials.gov/ct2/show/NCT04391426.}, } @article {pmid33211730, year = {2020}, author = {Arunasri, K and Mahesh, M and Sai Prashanthi, G and Jayasudha, R and Kalyana Chakravarthy, S and Tyagi, M and Pappuru, RR and Shivaji, S}, title = {Mycobiome changes in the vitreous of post fever retinitis patients.}, journal = {PloS one}, volume = {15}, number = {11}, pages = {e0242138}, pmid = {33211730}, issn = {1932-6203}, mesh = {Ascomycota/*physiology ; Cluster Analysis ; Dysbiosis/microbiology ; Fever/complications/*microbiology ; Humans ; Metagenome ; *Mycobiome ; Retinitis/complications/*microbiology ; Saccharomyces/*physiology ; Uveitis/microbiology ; Vitreous Body/*microbiology ; }, abstract = {Fungi have been associated with various diseases of the eye like keratitis, uveitis and endophthalmitis. Despite this fact, fungal microbiome (mycobiome) studies compared to the bacterial microbiome studies have remained neglected. In the present study, using metagenomic sequencing, the mycobiomes of the vitreous of healthy control individuals (VC, n = 15) and individuals with post fever retinitis + non-PFR uveitis (PFR+, n = 9) were analysed and compared. The results indicated that Ascomycota was the most predominant phylum in both VC and PFR+ groups. Further, at the genera level it was observed that the abundance of 17 fungal genera were significantly different in post fever retinitis (PFR, n = 6) group compared to control group. Of these 17 genera, it was observed that 14 genera were relatively more abundant in PFR group and the remaining 3 genera in the VC group. Genus Saccharomyces, a commensal of the gut and skin, was predominantly present in the vitreous of both the cohorts, however it was significantly less abundant in PFR group. Further, significant increase in the genera that have a pathogenic interaction with the host were observed in PFR group. On the whole the mycobiome in both the groups differed significantly and formed two distinct clusters in the heatmap and Principal co-ordinate analysis. These results demonstrate significant changes in the mycobiome from the vitreous of post fever retinitis patients compared to healthy controls thus implying that dysbiotic changes in the fungal vitreous microbiome are associated with PFR.}, } @article {pmid33208821, year = {2020}, author = {Ishida, S and Kato, K and Tanaka, M and Odamaki, T and Kubo, R and Mitsuyama, E and Xiao, JZ and Yamaguchi, R and Uematsu, S and Imoto, S and Miyano, S}, title = {Genome-wide association studies and heritability analysis reveal the involvement of host genetics in the Japanese gut microbiota.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {686}, pmid = {33208821}, issn = {2399-3642}, mesh = {Adult ; Asian People/*genetics ; Bacteria/*classification/genetics ; Female ; *Gastrointestinal Microbiome ; *Genome-Wide Association Study ; Humans ; Japan ; Male ; Middle Aged ; Phylogeny ; Polymorphism, Single Nucleotide ; }, abstract = {Numerous host extrinsic and intrinsic factors affect the gut microbiota composition, but their cumulative effects do not sufficiently explain the variation in the microbiota, suggesting contributions of missing factors. The Japanese population possesses homogeneous genetic features suitable for genome-wide association study (GWAS). Here, we performed GWASs for human gut microbiota using 1068 healthy Japanese adults. To precisely evaluate genetic effects, we corrected for the impacts of numerous host extrinsic and demographic factors by introducing them as covariates, enabling us to discover five loci significantly associated with microbiome diversity measures: HS3ST4, C2CD2, 2p16.1, 10p15.1, and 18q12.2. Nevertheless, these five variants explain only a small fraction of the variation in the gut microbiota. We subsequently investigated the heritability of each of the 21 core genera and found that the abundances of six genera are heritable. We propose that the gut microbiota composition is affected by a highly polygenic architecture rather than several strongly associated variants in the Japanese population.}, } @article {pmid33208788, year = {2020}, author = {Džunková, M and Lipták, R and Vlková, B and Gardlík, R and Čierny, M and Moya, A and Celec, P}, title = {Salivary microbiome composition changes after bariatric surgery.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {20086}, pmid = {33208788}, issn = {2045-2322}, mesh = {Adult ; Bacteria/classification/genetics/*isolation & purification ; Bariatric Surgery/*methods ; Female ; Humans ; Male ; *Metagenome ; *Microbiota ; Middle Aged ; Obesity/*surgery ; RNA, Ribosomal, 16S/*analysis ; Saliva/*microbiology ; }, abstract = {Recent studies show that the salivary microbiome in subjects with obesity differ from those without obesity, but the mechanism of interaction between the salivary microbiome composition and body weight is unclear. Herein we investigate this relation by analyzing saliva samples from 35 adult patients with obesity undergoing bariatric surgery. Our aim was to describe salivary microbiome changes during body weight loss on an individual-specific level, and to elucidate the effect of bariatric surgery on the salivary microbiome which has not been studied before. Analysis of samples collected before and 1 day after surgery, as well as 3 and 12 months after surgery, showed that the salivary microbiome changed in all study participants, but these changes were heterogeneous. In the majority of participants proportions of Gemella species, Granulicatella elegans, Porphyromonas pasteri, Prevotella nanceiensis and Streptococcus oralis decreased, while Veillonella species, Megasphaera micronuciformis and Prevotella saliva increased. Nevertheless, we found participants deviating from this general trend which suggests that a variety of individual-specific factors influence the salivary microbiome composition more effectively than the body weight dynamics alone. The observed microbiome alternations could be related to dietary changes. Therefore, further studies should focus on association with altered taste preferences and potential oral health consequences.}, } @article {pmid33208514, year = {2020}, author = {Hugerth, LW and Pereira, M and Zha, Y and Seifert, M and Kaldhusdal, V and Boulund, F and Krog, MC and Bashir, Z and Hamsten, M and Fransson, E and Svarre-Nielsen, H and Schuppe-Koistinen, I and Engstrand, L}, title = {Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome.}, journal = {mSphere}, volume = {5}, number = {6}, pages = {}, pmid = {33208514}, issn = {2379-5042}, mesh = {Computational Biology ; Computer Simulation ; Databases, Genetic ; Female ; Humans ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Vagina/*microbiology ; }, abstract = {The vaginal microbiome has been connected to a wide range of health outcomes. This has led to a thriving research environment but also to the use of conflicting methodologies to study its microbial composition. Here, we systematically assessed best practices for the sequencing-based characterization of the human vaginal microbiome. As far as 16S rRNA gene sequencing is concerned, the V1-V3 region performed best in silico, but limitations of current sequencing technologies meant that the V3-V4 region performed equally well. Both approaches presented very good agreement with qPCR quantification of key taxa, provided that an appropriate bioinformatic pipeline was used. Shotgun metagenomic sequencing presents an interesting alternative to 16S rRNA gene amplification and sequencing but requires deeper sequencing and more bioinformatic expertise and infrastructure. We assessed different tools for the removal of host reads and the taxonomic annotation of metagenomic reads, including a new, easy-to-build and -use reference database of vaginal taxa. This curated database performed as well as the best-performing previously published strategies. Despite the many advantages of shotgun sequencing, none of the shotgun approaches assessed here agreed with the qPCR data as well as the 16S rRNA gene sequencing.IMPORTANCE The vaginal microbiome has been connected to various aspects of host health, including susceptibility to sexually transmitted infections as well as gynecological cancers and pregnancy outcomes. This has led to a thriving research environment but also to conflicting available methodologies, including many studies that do not report their molecular biological and bioinformatic methods in sufficient detail to be considered reproducible. This can lead to conflicting messages and delay progress from descriptive to intervention studies. By systematically assessing best practices for the characterization of the human vaginal microbiome, this study will enable past studies to be assessed more critically and assist future studies in the selection of appropriate methods for their specific research questions.}, } @article {pmid33208503, year = {2020}, author = {Claesen, J and Spagnolo, JB and Ramos, SF and Kurita, KL and Byrd, AL and Aksenov, AA and Melnik, AV and Wong, WR and Wang, S and Hernandez, RD and Donia, MS and Dorrestein, PC and Kong, HH and Segre, JA and Linington, RG and Fischbach, MA and Lemon, KP}, title = {A Cutibacterium acnes antibiotic modulates human skin microbiota composition in hair follicles.}, journal = {Science translational medicine}, volume = {12}, number = {570}, pages = {}, pmid = {33208503}, issn = {1946-6242}, support = {DP1 DK113598/DK/NIDDK NIH HHS/United States ; R01 AI101018/AI/NIAID NIH HHS/United States ; R01 DK110174/DK/NIDDK NIH HHS/United States ; U41 AT008718/AT/NCCIH NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; *Hair Follicle ; Humans ; *Microbiota ; Propionibacterium acnes ; Skin ; }, abstract = {The composition of the skin microbiota varies widely among individuals when sampled at the same body site. A key question is which molecular factors determine strain-level variability within sub-ecosystems of the skin microbiota. Here, we used a genomics-guided approach to identify an antibacterial biosynthetic gene cluster in Cutibacterium acnes (formerly Propionibacterium acnes), a human skin commensal bacterium that is widely distributed across individuals and skin sites. Experimental characterization of this biosynthetic gene cluster resulted in identification of a new thiopeptide antibiotic, cutimycin. Analysis of individual human skin hair follicles revealed that cutimycin contributed to the ecology of the skin hair follicle microbiota and helped to reduce colonization of skin hair follicles by Staphylococcus species.}, } @article {pmid33208188, year = {2020}, author = {Adamberg, K and Vilu, R and Pazienza, V}, title = {Inhibition of pyruvate dehydrogenase kinase influence microbiota and metabolomic profile in pancreatic cancer xenograft mice.}, journal = {BMC research notes}, volume = {13}, number = {1}, pages = {540}, pmid = {33208188}, issn = {1756-0500}, support = {IUT19-27//Tallinna Tehnikaülikool/ ; Ricerca Corrente (2018-2020)//Ministero della Salute/ ; IG2019-ID23006//Associazione Italiana per la Ricerca sul Cancro/ ; }, mesh = {Animals ; Cell Line, Tumor ; Dichloroacetic Acid/*pharmacology ; Humans ; Mice ; *Microbiota ; *Pancreatic Neoplasms/drug therapy ; Pyruvate Dehydrogenase Acetyl-Transferring Kinase/*antagonists & inhibitors ; Xenograft Model Antitumor Assays ; }, abstract = {OBJECTIVE: Despite recent advances in treatment options, pancreatic cancer remains the most deadly major cancer. Targeting metabolism represents an emerging anti-cancer strategy.

RESULTS: Metagenomic 16S analysis was employed to explore the effect of Dichloroacetate (DCA) on the composition of the fecal microbiota and metabolomic profile was assessed on in vivo pancreatic cancer mouse xenograft model. Pancreatic cancer xenograft mice displayed a shift of microbiota' profile as compared to control mice without DCA treatment and a significant decrease of the purine bases inosine xanthine together with their metabolically-related compound hypoxanthine were observed in the DCA treated group as compared to the control group. Two aminoacids methionine and aspartic acid resulted decreased and increased respectively. DCA affects tumor environment and studies are needed in order to understand whether DCA supplementation could be supportive as synergistic approach to enhance the efficacy of existing cancer treatments in pancreatic cancer patients.}, } @article {pmid33207267, year = {2021}, author = {Beraud-Martínez, LK and Gómez-Gil, B and Franco-Nava, MÁ and Almazán-Rueda, P and Betancourt-Lozano, M}, title = {A metagenomic assessment of microbial communities in anaerobic bioreactors and sediments: Taxonomic and functional relationships.}, journal = {Anaerobe}, volume = {68}, number = {}, pages = {102296}, doi = {10.1016/j.anaerobe.2020.102296}, pmid = {33207267}, issn = {1095-8274}, mesh = {Anaerobiosis ; Bacteria/*classification/genetics/*isolation & purification ; Bioreactors/*microbiology ; Geologic Sediments/*microbiology ; Manure/microbiology ; Metagenome ; Metagenomics ; *Microbiota ; Oxygen/metabolism ; Sewage/microbiology ; }, abstract = {The present study used metagenomic sequencing, metagenome assembly and physical-chemical analysis to describe taxonomically and functionally 3 anaerobic bioreactors treating manure (LI), brewery (BR) and cornmeal (CO) wastes, and an anaerobic estuarine sediment (ES). Proteobacteria, Firmicutes, Euryarchaeota and Bacteroidetes were the most abundant Phyla in all metagenomes. A bacteria/archaea ratio of 3.4 was found in the industrial full-scale anaerobic bioreactors BR and CO, while ratios greater than 10 were found for LI and ES. Canonical correspondence analysis showed that environmental variables such as chemical oxygen demand, lipid content, and ammonium nitrogen influenced the ordination of taxonomic groups. Mesotoga prima was linked to high-temperature conditions, particularly in the BR bioreactor, along with the presence of heat shock proteins genes. Likewise, the hydrogenotrophic methanogen, Methanoregula formicica, was associated with high ammonium concentration in LI bioreactor. The interactions of microbes with specific methanogenic pathways were identified using Clusters of Orthologous Groups (COG) functions, while metagenome-assembled genomes (MAGs) further confirmed relationships between taxa and functions. Our results provide valuable information to understand microbial processes in anaerobic environments.}, } @article {pmid33206681, year = {2020}, author = {Gureev, AP and Syromyatnikov, MY and Ignatyeva, DA and Valuyskikh, VV and Solodskikh, SA and Panevina, AV and Gryaznova, MV and Kokina, AV and Popov, VN}, title = {Effect of long-term methylene blue treatment on the composition of mouse gut microbiome and its relationship with the cognitive abilities of mice.}, journal = {PloS one}, volume = {15}, number = {11}, pages = {e0241784}, pmid = {33206681}, issn = {1932-6203}, mesh = {Animals ; Bacteroidetes/genetics/metabolism ; Cognition/drug effects/physiology ; Epsilonproteobacteria/genetics/metabolism ; Gastrointestinal Microbiome/drug effects/genetics ; High-Throughput Nucleotide Sequencing ; Maze Learning ; Methylene Blue/*pharmacology ; Mice ; Mice, Inbred C57BL ; Proteobacteria/genetics/metabolism ; }, abstract = {In recent years, methylene blue (MB) has attracted considerable interest as a potential drug for the treatment of methemoglobinemia and neurodegenerative diseases. MB is active against microorganisms from various taxonomic groups. However, no studies have yet been conducted on the effect of MB on the intestinal microbiome of model animals. The aim of this work was to study the effect of different concentrations of MB on the mouse gut microbiome and its relationship with the cognitive abilities of mice. We showed that a low MB concentration (15 mg/kg/day) did not cause significant changes in the microbiome composition. The Bacteroidetes/Firmicutes ratio decreased relative to the control on the 2nd and 3rd weeks. A slight decrease in the levels Actinobacteria was detected on the 3rd week of the experiment. Changes in the content of Delta, Gamma, and Epsilonproteobacteria have been also observed. We did not find significant alterations in the composition of intestinal microbiome, which could be an indication of the development of dysbiosis or other gut dysfunction. At the same time, a high concentration of MB (50 mg/kg/day) led to pronounced changes, primarily an increase in the levels of Delta, Gamma and Epsilonproteobacteria. Over 4 weeks of therapy, the treatment with high MB concentration has led to an increase in the median content of Proteobacteria to 7.49% vs. 1.61% in the control group. Finally, we found that MB at a concentration of 15 mg/kg/day improved the cognitive abilities of mice, while negative correlation between the content of Deferribacteres and cognitive parameters was revealed. Our data expand the understanding of the relationship between MB, cognitive abilities, and gut microbiome in respect to the antibacterial properties of MB.}, } @article {pmid33205903, year = {2020}, author = {Zhang, L and Li, C and Zhai, Y and Feng, L and Bai, K and Zhang, Z and Huang, Y and Li, T and Li, D and Li, H and Cui, P and Chen, D and Wang, H and Yang, X}, title = {Analysis of the vaginal microbiome of giant pandas using metagenomics sequencing.}, journal = {MicrobiologyOpen}, volume = {9}, number = {12}, pages = {e1131}, pmid = {33205903}, issn = {2045-8827}, mesh = {Actinobacteria/genetics/isolation & purification ; Age Factors ; Animals ; Basidiomycota/genetics/isolation & purification ; Chlamydia/genetics/isolation & purification ; Female ; Firmicutes/genetics/isolation & purification ; Geography ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Neisseria gonorrhoeae/genetics/isolation & purification ; Proteobacteria/genetics/isolation & purification ; Ursidae ; Vagina/*microbiology ; }, abstract = {In this study, a total of 14 vaginal samples (GPV1-14) from giant pandas were analyzed. These vaginal samples were divided into two groups as per the region and age of giant pandas. All the vaginal samples were analyzed using metagenomic sequencing. As per the outcomes of metagenomic analysis, Proteobacteria (39.04%), Firmicutes (5.27%), Actinobacteria (2.94%), and Basidiomycota (2.77%) were found to be the dominant phyla in the microbiome of the vaginal samples. At the genus level, Pseudomonas (21.90%) was found to be the most dominant genus, followed by Streptococcus (3.47%), Psychrobacter (1.89%), and Proteus (1.38%). Metastats analysis of the microbial species in the vaginal samples of giant pandas from Wolong Nature Reserve, Dujiangyan and Ningbo Youngor Zoo, and Ya'an Bifengxia Nature Reserve was found to be significantly different (p < 0.05). Age groups, that is, AGE1 (5-10 years old) and AGE2 (11-16 years old), also demonstrated significantly different inter-group microbial species (p < 0.05). For the first time, Chlamydia and Neisseria gonorrhoeae were detected in giant pandas' reproductive tract. GPV3 vaginal sample (2.63%) showed highest Chlamydia content followed by GPV14 (0.91%), and GPV7 (0.62%). GPV5 vaginal sample (7.17%) showed the highest Neisseria gonorrhoeae content, followed by GPV14 (7.02%), and GPV8 (6.50%). Furthermore, we employed eggNOG, CAZy, KEGG, and NCBI databases to investigate the functional significance of giant panda's vaginal microbial community. The outcomes indicated that giant panda's vaginal microbes were involved in biological processes. The data from this study will help in improving the reproductive health of giant pandas.}, } @article {pmid33204736, year = {2020}, author = {Huang, Y and Tang, J and Cai, Z and Zhou, K and Chang, L and Bai, Y and Ma, Y}, title = {Prevotella Induces the Production of Th17 Cells in the Colon of Mice.}, journal = {Journal of immunology research}, volume = {2020}, number = {}, pages = {9607328}, pmid = {33204736}, issn = {2314-7156}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Colon/*immunology/*metabolism/microbiology ; Cytokines/biosynthesis/blood ; Dendritic Cells/immunology/metabolism ; Gastrointestinal Microbiome/drug effects/*immunology ; Gene Expression Regulation ; Immunophenotyping ; Interleukin-17/genetics/metabolism ; Intestinal Mucosa/*immunology/*metabolism ; Lymphocyte Activation/drug effects/immunology ; Metagenome ; Metagenomics/methods ; Mice ; Mice, Transgenic ; Prevotella/drug effects/*immunology ; Th17 Cells/*immunology/*metabolism ; }, abstract = {Th17-mediated mucosal inflammation is related to increased Prevotella bacterial abundance. The actual involvement of Prevotella in the development and accumulation of intestinal Th17 cells at a steady state, however, remains undefined. Herein, we investigated the role of Prevotella in inducing intestinal Th17 cells in mice. Mice were treated with a combination of broad-spectrum antibiotics (including ampicillin, neomycin sulfate, vancomycin hydrochloride, and metronidazole) in their drinking water for 4 weeks and then gavaged with Prevotella for 4 weeks. After inoculation, 16S rDNA sequencing was used to verify the colonization of Prevotella in the colon of mice. The IL-17A as well as IL-17A-expressing T cells was localized and quantified by an immunofluorescence assay (IFA) of colon sections. Th17 cells in the mesenteric lymph nodes of mice were counted by flow cytometry. Systemic immune response to Prevotella colonization was evaluated based on the serum levels of IL-6, TNF-α, IL-1β, IL-17A, IL-10, IL-4, IFN-γ, and IL-2. Th17-polarizing cytokines (IL-6, TNF-α, IL-1β, and IL-2) induced by Prevotella were evaluated by stimulation of bone marrow-derived dendritic cells (BMDCs). Results revealed that after inoculation, Prevotella successfully colonized the intestine of mice and induced the production and accumulation of colonic Th17 cells in the colon. Moreover, Prevotella elevated some of the Th17-related cytokines in the serum of mice. And Th17-polarizing cytokines (IL-6 and IL-1β) produced by BMDCs were mediated mainly through the interaction between Prevotella and Toll-like receptor 2 (TLR2). In conclusion, our data suggest that Prevotella induces the production of Th17 cells in the colon of mice, thus highlighting the potential role of Prevotella in training the intestinal immune system.}, } @article {pmid33203858, year = {2020}, author = {Dong, X and Rattray, JE and Campbell, DC and Webb, J and Chakraborty, A and Adebayo, O and Matthews, S and Li, C and Fowler, M and Morrison, NM and MacDonald, A and Groves, RA and Lewis, IA and Wang, SH and Mayumi, D and Greening, C and Hubert, CRJ}, title = {Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5825}, pmid = {33203858}, issn = {2041-1723}, mesh = {Adaptation, Biological ; Alkanes/chemistry/metabolism ; Anaerobiosis ; Biodegradation, Environmental ; Biodiversity ; Chloroflexi/genetics/metabolism ; Deltaproteobacteria/genetics/metabolism ; Genome, Microbial ; Geologic Sediments/*microbiology ; Hydrocarbons/*metabolism ; Marine Biology ; Metagenome/genetics/*physiology ; Methane/metabolism ; Nova Scotia ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {At marine cold seeps, gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface. Cold seep sediments are known to host taxonomically diverse microorganisms, but little is known about their metabolic potential and depth distribution in relation to hydrocarbon and electron acceptor availability. Here we combined geophysical, geochemical, metagenomic and metabolomic measurements to profile microbial activities at a newly discovered cold seep in the deep sea. Metagenomic profiling revealed compositional and functional differentiation between near-surface sediments and deeper subsurface layers. In both sulfate-rich and sulfate-depleted depths, various archaeal and bacterial community members are actively oxidizing thermogenic hydrocarbons anaerobically. Depth distributions of hydrocarbon-oxidizing archaea revealed that they are not necessarily associated with sulfate reduction, which is especially surprising for anaerobic ethane and butane oxidizers. Overall, these findings link subseafloor microbiomes to various biochemical mechanisms for the anaerobic degradation of deeply-sourced thermogenic hydrocarbons.}, } @article {pmid33203758, year = {2020}, author = {Patin, NV and Peña-Gonzalez, A and Hatt, JK and Moe, C and Kirby, A and Konstantinidis, KT}, title = {The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study.}, journal = {mBio}, volume = {11}, number = {6}, pages = {}, pmid = {33203758}, issn = {2150-7511}, support = {K01 AI103544/AI/NIAID NIH HHS/United States ; R01 AI137679/AI/NIAID NIH HHS/United States ; }, mesh = {Asymptomatic Diseases ; Bacteroidetes/genetics/*growth & development ; Caliciviridae Infections/immunology/*prevention & control/virology ; Disease Susceptibility ; Firmicutes/genetics/*growth & development ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; Norovirus/*immunology ; Proteobacteria/genetics/*growth & development ; }, abstract = {Norovirus infections take a heavy toll on worldwide public health. While progress has been made toward understanding host responses to infection, the role of the gut microbiome in determining infection outcome is unknown. Moreover, data are lacking on the nature and duration of the microbiome response to norovirus infection, which has important implications for diagnostics and host recovery. Here, we characterized the gut microbiomes of subjects enrolled in a norovirus challenge study. We analyzed microbiome features of asymptomatic and symptomatic individuals at the genome (population) and gene levels and assessed their response over time in symptomatic individuals. We show that the preinfection microbiomes of subjects with asymptomatic infections were enriched in Bacteroidetes and depleted in Clostridia relative to the microbiomes of symptomatic subjects. These compositional differences were accompanied by differences in genes involved in the metabolism of glycans and sphingolipids that may aid in host resilience to infection. We further show that microbiomes shifted in composition following infection and that recovery times were variable among human hosts. In particular, Firmicutes increased immediately following the challenge, while Bacteroidetes and Proteobacteria decreased over the same time. Genes enriched in the microbiomes of symptomatic subjects, including the adenylyltransferase glgC, were linked to glycan metabolism and cell-cell signaling, suggesting as-yet unknown roles for these processes in determining infection outcome. These results provide important context for understanding the gut microbiome role in host susceptibility to symptomatic norovirus infection and long-term health outcomes.IMPORTANCE The role of the human gut microbiome in determining whether an individual infected with norovirus will be symptomatic is poorly understood. This study provides important data on microbes that distinguish asymptomatic from symptomatic microbiomes and links these features to infection responses in a human challenge study. The results have implications for understanding resistance to and treatment of norovirus infections.}, } @article {pmid33203567, year = {2021}, author = {Zhang, C and Du, XP and Zeng, YH and Zhu, JM and Zhang, SJ and Cai, ZH and Zhou, J}, title = {The communities and functional profiles of virioplankton along a salinity gradient in a subtropical estuary.}, journal = {The Science of the total environment}, volume = {759}, number = {}, pages = {143499}, doi = {10.1016/j.scitotenv.2020.143499}, pmid = {33203567}, issn = {1879-1026}, mesh = {Biodiversity ; China ; *Estuaries ; Rivers ; *Salinity ; }, abstract = {Viruses are the major drivers shaping microorganismal communities, and impact marine biogeochemical cycling. They are affected by various environmental parameters, such as salinity. Although the spatiotemporal distribution and dynamics of virioplankton have been extensively studied in saline environments, few detailed studies of community structure and function of viruses along salinity gradients have been conducted. Here, we used the 16S and 18S rRNA gene amplicon and metagenomic sequencing from a subtropical estuary (Pearl River Estuary, PRE; located in Shenzhen, Guangdong Province, China) to explore how viral community composition and function vary along a salinity gradient. Results showed that the detected viruses were mainly bacteriophages. The double-stranded DNA viruses were the most abundant (especially Siphoviridae, Myoviridae, Mimiviridae, Phycodnaviridae, and Podoviridae), followed by a small number of single-stranded DNA (Circoviridae) and RNA (Retroviridae) viruses. Viral biodiversity significantly declined and community structure varied greatly along the salinity gradient. The salinity, ammonium and dissolved oxygen were dominated factors influencing the community composition of viruses. Association network analysis showed that viruses had a negative effect on multiple host taxa (prokaryotic and eukaryotic species). Metagenomic data revealed that the main viral functional potential was involved in organic matter metabolism by carbohydrate-active enzymes (CAZymes). Deeper comparative functional analyses showed that viruses in the low-salinity environment had more carbohydrate-binding module and glycosidase hydrolases activities than those under high-salinity conditions. However, an opposite pattern was observed for carbohydrate esterases. These results suggest that virus-encoded CAZyme genes may alter the bacterial metabolism in estuaries. Overall, our results demonstrate that there is a spatial heterogeneity in the composition and function of virioplankton along a salinity gradient. This study enhances our understanding of viral distribution and their contribution to regulating carbon degradation throughout environments with varying salinities in subtropical estuaries.}, } @article {pmid33202695, year = {2020}, author = {Jaiani, E and Kusradze, I and Kokashvili, T and Geliashvili, N and Janelidze, N and Kotorashvili, A and Kotaria, N and Guchmanidze, A and Tediashvili, M and Prangishvili, D}, title = {Microbial Diversity and Phage-Host Interactions in the Georgian Coastal Area of the Black Sea Revealed by Whole Genome Metagenomic Sequencing.}, journal = {Marine drugs}, volume = {18}, number = {11}, pages = {}, pmid = {33202695}, issn = {1660-3397}, support = {FR 17-442//Shota Rustaveli National Science Foundation/ ; }, mesh = {Bacteria/*genetics/virology ; Bacteriophages/*genetics ; Black Sea ; DNA, Bacterial/*genetics ; DNA, Viral/*genetics ; Ecosystem ; *Genome, Bacterial ; *Genome, Viral ; Host-Pathogen Interactions ; *Metagenome ; *Metagenomics ; Microbiota ; Water Microbiology ; *Whole Genome Sequencing ; }, abstract = {Viruses have the greatest abundance and highest genetic diversity in marine ecosystems. The interactions between viruses and their hosts is one of the hot spots of marine ecology. Besides their important role in various ecosystems, viruses, especially bacteriophages and their gene pool, are of enormous interest for the development of new gene products with high innovation value. Various studies have been conducted in diverse ecosystems to understand microbial diversity and phage-host interactions; however, the Black Sea, especially the Eastern coastal area, remains among the least studied ecosystems in this regard. This study was aimed at to fill this gap by analyzing microbial diversity and bacteriophage-host interactions in the waters of Eastern Black Sea using a metagenomic approach. To this end, prokaryotic and viral metagenomic DNA from two sampling sites, Poti and Gonio, were sequenced on the Illumina Miseq platform and taxonomic and functional profiles of the metagenomes were obtained using various bioinformatics tools. Our metagenomics analyses allowed us to identify the microbial communities, with Proteobacteria, Cyanobacteria, Actinibacteria, and Firmicutes found to be the most dominant bacterial phyla and Synechococcus and Candidatus Pelagibacter phages found to be the most dominant viral groups in the Black Sea. As minor groups, putative phages specific to human pathogens were identified in the metagenomes. We also characterized interactions between the phages and prokaryotic communities by determining clustered regularly interspaced short palindromic repeats (CRISPR), prophage-like sequences, and integrase/excisionase sequences in the metagenomes, along with identification of putative horizontally transferred genes in the viral contigs. In addition, in the viral contig sequences related to peptidoglycan lytic activity were identified as well. This is the first study on phage and prokaryote diversity and their interactions in the Eastern coastal area of the Black Sea using a metagenomic approach.}, } @article {pmid33202299, year = {2021}, author = {Lu, M and Zhou, W and Ji, F and Wu, J and Nie, Y and Ren, C and Xu, Y}, title = {Profiling prokaryotic community in pit mud of Chinese strong-aroma type liquor by using oligotrophic culturing.}, journal = {International journal of food microbiology}, volume = {337}, number = {}, pages = {108951}, doi = {10.1016/j.ijfoodmicro.2020.108951}, pmid = {33202299}, issn = {1879-3460}, mesh = {Acetates/analysis/metabolism ; Alcoholic Beverages/*microbiology ; Archaea/classification/genetics/isolation & purification/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; China ; Culture Media/chemistry ; Fermentation ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Pit mud microbiota plays a key role in flavour production for Chinese strong-aroma type liquor. However, the pit mud microbiota cannot be cultured in laboratory. In this study, an oligotrophic medium with acetate as carbon source was used to enrich pit mud microbiota. The 16S rRNA gene amplicon sequencing was applied to examine the microbial dynamics of the enrichment consortia. Both methanogens and bacteria were simultaneously enriched. Euryarchaeota, Bacteroidetes and Firmicutes were the top 3 enriched phyla, and 31 genera were successfully enriched. More specifically, 11 genera (65%) out of the 17 dominant genera in pit mud were successfully enriched, including Petrimonas, Proteiniphilum, Anaerocella, Hydrogenispora, Methanosarcina, Fermentimonas, LNR_A2-18, Sedimentibacter, Lutispora, Syntrophomonas and Aminobacterium. Furthermore, 20 rare genera in the analyzed pit mud samples were also enriched. Aceticlastic Methanosaeta and Methanosarcina were found to be dominant methanogens in the enrichment consortia. Metagenomic sequencing was then applied to the enriched microbial consortia to explore the metabolic potentials of pit mud microbes. Aceticlastic methanogenesis pathway of Methanosaeta was reconstructed. Furthermore, 26 high-quality metagenome-assembled genomes (MAGs) were obtained based on the metagenomic binning analysis. Moreover, nutrients in pit mud were found to be crucial to sustain the methanogenesis of the enriched microbial consortia. These results suggested that the enrichment approach by using oligotrophic culturing can effectively cultivate the pit mud microbiota. Combined with metagenomics, the oligotrophic culturing will be greatly helpful to decipher the community composition and metabolic potentials of pit mud microbiota.}, } @article {pmid33202274, year = {2021}, author = {Ferreira-Lazarte, A and Fernández, J and Gallego-Lobillo, P and Villar, CJ and Lombó, F and Moreno, FJ and Villamiel, M}, title = {Behaviour of citrus pectin and modified citrus pectin in an azoxymethane/dextran sodium sulfate (AOM/DSS)-induced rat colorectal carcinogenesis model.}, journal = {International journal of biological macromolecules}, volume = {167}, number = {}, pages = {1349-1360}, doi = {10.1016/j.ijbiomac.2020.11.089}, pmid = {33202274}, issn = {1879-0003}, mesh = {Acetates/metabolism ; Animals ; Azoxymethane/pharmacology/*toxicity ; Bifidobacterium/isolation & purification ; Blood Glucose/drug effects ; Body Weight/drug effects ; Butyrates/metabolism ; Carcinogenesis/*drug effects/metabolism/pathology ; Chromatography, High Pressure Liquid ; Citrus/chemistry ; Colorectal Neoplasms/chemically induced/*diet therapy/metabolism/mortality ; Dextran Sulfate/pharmacology ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; Hydrogen-Ion Concentration ; Lactic Acid/metabolism ; Lactobacillaceae/isolation & purification ; Male ; Metagenomics ; Pectins/analysis/*therapeutic use ; Phylogeny ; Propionates/metabolism ; Proteobacteria/isolation & purification ; Rats ; Rats, Inbred F344 ; Triglycerides/blood ; }, abstract = {Large intestine cancer is one of the most relevant chronic diseases taking place at present. Despite therapies have evolved very positively, this pathology is still under deep investigation. One of the recent approaches is the prevention by natural compounds such as pectin. In this paper, we have assessed the impact of citrus pectin and modified citrus pectin on colorectal cancer in rats (Rattus norvegicus F344) to which azoxymethane and DSS were supplied. The lowest intake of food and body weight were detected in animals fed with citrus pectin, together with an increase in the caecum weight, probably due to the viscosity, water retention capacity and bulking properties of pectin. The most striking feature was that, neither citrus pectin nor modified citrus pectin gave rise to a tumorigenesis prevention. Moreover, in both, more than 50% of rats with cancer died, probably ascribed to a severe dysbiosis state in the gut, as shown by the metabolism and metagenomics studies carried out. This was related to a decrease of pH in caecum lumen and increase in acetate and lactic acid levels together with the absence of propionic and butyric acids. A relevant increase in Proteobacteria (Enterobacteriaceae) were thought to be one of the reasons for enteric infection that could have provoked the death of rats and the lack of cancer prevention. However, a reduction of blood glucose and triacylglycerides level and an increase of Bifidobacterium and Lactobacillaceae were found in animals that intake pectin, as compared to universal and modified citrus pectin feeding.}, } @article {pmid33201183, year = {2021}, author = {Thompson, CM and Gao, Q and Chang, P and Swanson, G}, title = {Differentiation of Milk and Whey Protein Concentrates by Microbiome Profiling Using 16S Metagenomics.}, journal = {Journal of AOAC International}, volume = {104}, number = {3}, pages = {757-764}, doi = {10.1093/jaoacint/qsaa158}, pmid = {33201183}, issn = {1944-7922}, mesh = {Animals ; *Metagenomics ; *Microbiota ; Milk/chemistry ; Milk Proteins/analysis ; Whey/chemistry ; Whey Proteins ; }, abstract = {BACKGROUND: Protein powder identification presents a challenge in quality control. There is current deliberation of the specificity of methods for the identification of milk proteins, and the consensus identification method of whey protein from the United States Pharmacopeia Food Chemical Codex relies on a combined analysis of the testing of ash, fat, lactose, loss on drying, and protein. These methods are non-specific. Milk and whey proteins both contain background DNA content. Both milk and whey proteins retain source DNA (cow), but also have bacterial DNA from natural flora, the dairy plant, and in whey protein, the cheesemaking process. The DNA in these materials is retained post-processing, even after the pasteurization process.

OBJECTIVE: By utilizing 16S metagenomics, the bacterial DNA in protein powders can be sequenced and cross-referenced to a curated library to ultimately create a microbiome profile of these raw materials. This microbiome can be measured for alpha and beta diversity, specifically how many and which species of bacteria are present.

METHOD: Using 16S metagenomics, we measure alpha and beta diversity of the microbiome profile of each protein powder and use principle coordinate analysis to produce differential groupings, providing a novel identification method for raw materials.

RESULTS: In this study, we demonstrate that the microbiome of cow proteins can be used for raw material identification, as the microbiome of milk and whey proteins differ significantly. We also demonstrate that the microbiome of whey protein concentrate can differ from supplier to supplier.

CONCLUSIONS: Microbiome profiling by 16S metagenomics can be an important forensic tool for quality control.

HIGHLIGHTS: Principle Coordinate Analysis can be used as a statistical tool for protein differentiation using the protein microbiome.}, } @article {pmid33199139, year = {2021}, author = {Li, Y and Chen, H and Song, L and Wu, J and Sun, W and Teng, Y}, title = {Effects on microbiomes and resistomes and the source-specific ecological risks of heavy metals in the sediments of an urban river.}, journal = {Journal of hazardous materials}, volume = {409}, number = {}, pages = {124472}, doi = {10.1016/j.jhazmat.2020.124472}, pmid = {33199139}, issn = {1873-3336}, mesh = {China ; Environmental Monitoring ; Geologic Sediments ; Humans ; *Metals, Heavy/analysis/toxicity ; *Microbiota/genetics ; Risk Assessment ; Rivers ; *Water Pollutants, Chemical/analysis/toxicity ; }, abstract = {This study aims to better understand the effects of heavy metal enrichment on microbiomes and resistomes and the source-specific ecological risks of metals in the sediments of an urban river. Geo-accumulation index and enrichment factor suggested the river sediments were contaminated by Cd, Cu, Pb, and Zn in varying degrees. High-throughput sequencing-based metagenomics analysis identified 430 types of antibiotic resistance genes (ARGs), dominated by the multidrug, MLS, bacitracin, quinolone, and aminoglycoside ARGs, and 52 metal resistance genes (MRGs) mainly conferring resistance to zinc, copper, cadmium, lead, mercury and multiple metals. Spearman correlation analysis and Mantel test showed the heavy metal enrichment exerted significant effects on the microbial community, ARGs and MRGs. Source apportionment using positive matrix factorization revealed that natural source (42.8%) was the largest contributor of metals in the river sediments, followed by urban activities (35.4%) and a mixed source (21.7%). However, when incorporating the apportionment results into a modified risk model to evaluate the source-specific ecological risks, results showed human activities dominated the risks of metals. Comparatively, the urban activities majorly caused moderate- and considerable- ecological risks, while the mixed source with respect to agricultural and industrial activities contributed higher percentages on high- and extremely high- ecological risks.}, } @article {pmid33195611, year = {2020}, author = {Himsworth, CG and Byers, KA and Fernando, C and Speerin, L and Lee, MJ and Hill, JE}, title = {When the Sum of the Parts Tells You More Than the Whole: The Advantage of Using Metagenomics to Characterize Bartonella spp. Infections in Norway Rats (Rattus norvegicus) and Their Fleas.}, journal = {Frontiers in veterinary science}, volume = {7}, number = {}, pages = {584724}, pmid = {33195611}, issn = {2297-1769}, abstract = {Urban Norway rats (Rattus norvegicus) are a reservoir for Bartonella spp. - a genus of zoonotic bacteria transmitted by hematophagous vectors, particularly fleas. Rats and fleas may be infected with more than one Bartonella species; however, mixed infections may be difficult to detect using culture and/or mono-locus PCR. We set out to characterize Bartonella spp. using gltA PCR and Sanger sequencing on blood (n = 480) and Nosopsyllus fasciatus flea pools (n = 200) obtained from a population of urban Norways rats from Vancouver, Canada. However, when contamination of a subset of flea pools necessitated the use of a second target (ssrA) and the results of gltA and ssrA were discordant, a metagenomic approach was used to better characterize the Bartonella spp. present in these samples and our objective transitioned to comparing data obtained via metagenomics to those from PCR/sequencing. Among the Bartonella spp.-positive rats (n = 95), 52 (55.3%), and 41 (43.6%) had Sanger sequences consistent with Bartonella tribocorum and Bartonella vinsonii, respectively. One rat had a mixed infection. All sequences from Bartonella spp.-positive flea pools (n = 85), were consistent with B. tribocorum, and re-analysis of 34 bloods of varying Bartonella spp. infection status (based gltA PCR and sequencing) using ssrA PCR showed that the assay was capable of identifying B. tribocorum but not B. vinsonii. Metagenomics analysis of a subset of PCR-positive blood samples (n = 70) and flea pools (n = 24) revealed that both B. tribocorum and B. vinsonii were circulating widely in the study population with 31/70 (44.3%) rats and 5/24 (2.1%) flea pools infected with both species. B. vinsonii, however, made up a smaller relative proportion of the reads for samples with mixed infections, which may be why it was generally not detected by genus-specific PCR and Sanger sequencing. Further analysis of 16S-23S ITS sequences amplified from a subset of samples identified the B. vinsonii strain as B. vinsonii subsp. berkhoffii type II. This demonstrates the value of a metagenomic approach for better characterizing the ecology and health risks associated with this bacterium, particularly given that the less dominant species, B. vinsonii is associated with greater pathogenicity in people.}, } @article {pmid33194990, year = {2020}, author = {González-Penagos, CE and Zamora-Briseño, JA and Cerqueda-García, D and Améndola-Pimenta, M and Pérez-Vega, JA and Hernández-Nuñez, E and Rodríguez-Canul, R}, title = {Alterations in the Gut Microbiota of Zebrafish (Danio rerio) in Response to Water-Soluble Crude Oil Components and Its Mixture With a Chemical Dispersant.}, journal = {Frontiers in public health}, volume = {8}, number = {}, pages = {584953}, pmid = {33194990}, issn = {2296-2565}, mesh = {Animals ; Ecosystem ; *Gastrointestinal Microbiome ; *Petroleum/toxicity ; Water ; *Water Pollutants, Chemical/toxicity ; Zebrafish ; }, abstract = {Crude oil spills have caused substantial impacts to aquatic ecosystems. Chemical dispersants are used to palliate the impact of oil spillages, but their use is polemic due to their additional potential toxic effect when mixed with oil-derived components. In this work, we used a 16S-based metagenomic approach to analyze the changes of the gut microbiota of adult zebrafish (Danio rerio) exposed to the water accommodated fraction (WAF) of a light crude oil (35° API gravity), and the chemically enhanced WAF (CEWAF), prepared with Nokomis 3-F4® dispersant. After 96 h of exposure, WAF induced an increase in the alpha and beta diversity, altering the relative abundance of Vibrio, Flavobacterium, and Novosphingobium. In contrast, CEWAF only caused an increase in the beta diversity, and an enrichment of the genus Pseudomona. Both treatments diminished the abundances of Aeromonas, Cetobacterium, Coxiella, Dinghuibacter, and Paucibacter. Moreover, the co-occurrence network among genera was more complex in WAF than in CEWAF, indicating a greater bacterial interaction in response to WAF. Our results indicate that short-term exposure to WAF and CEWAF can induce a dysbiosis in the gut microbiota of D. rerio, but these changes are specific in each treatment.}, } @article {pmid33194818, year = {2020}, author = {Yan, A and Butcher, J and Mack, D and Stintzi, A}, title = {Virome Sequencing of the Human Intestinal Mucosal-Luminal Interface.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {582187}, pmid = {33194818}, issn = {2235-2988}, support = {ECD-144627//CIHR/Canada ; }, mesh = {Child ; Feces ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics ; Virome ; *Viruses/genetics ; }, abstract = {While the human gut virome has been increasingly explored in recent years, nearly all studies have been limited to fecal sampling. The mucosal-luminal interface has been established as a viable sample type for profiling the microbial biogeography of the gastrointestinal tract. We have developed a protocol to extract nucleic acids from viruses at the mucosal-luminal interface of the proximal and distal colon. Colonic viromes from pediatric patients with Crohn's disease demonstrated high interpatient diversity and low but significant intrapatient variation between sites. Whole metagenomics was also performed to explore virome-bacteriome interactions and to compare the viral communities observed in virome and whole metagenomic sequencing. A site-specific study of the human gut virome is a necessary step to advance our understanding of virome-bacteriome-host interactions in human diseases.}, } @article {pmid33194817, year = {2020}, author = {Xu, C and Jia, Q and Zhang, L and Wang, Z and Zhu, S and Wang, X and Liu, Y and Li, M and Zhang, J and Wang, X and Zhang, J and Sun, Q and Wang, K and Zhu, H and Duan, L}, title = {Multiomics Study of Gut Bacteria and Host Metabolism in Irritable Bowel Syndrome and Depression Patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {580980}, pmid = {33194817}, issn = {2235-2988}, mesh = {Bacteria/genetics ; Depression ; Feces ; *Gastrointestinal Microbiome ; Humans ; *Irritable Bowel Syndrome ; }, abstract = {BACKGROUND AND AIMS: Irritable bowel syndrome (IBS) and depression have high tendencies of comorbidity. In particular, diarrhea-predominant IBS (IBS-D) and depression exhibit similar fecal microbiota signatures, yet little is known about their pathogenic mechanism. Here, we propose that the differences in structure and composition of IBS-D and depression gut microbiota give rise to different downstream functions, which lead to distinct clinical phenotypes via host metabolism and further influence the interaction of brain-gut axis.

METHODS: We performed multiomics study, including fecal metagenome-wide sequencing and serum metabolomics profiling in 65 individuals with IBS-D (n=22), depression (n=15), comorbid patients (n=13), and healthy controls (n=15). We analyzed functional genes contributed by the primary genus and evaluated their correlations with clinical indices and host metabolites.

RESULTS: Metagenomic analysis revealed 26 clusters of orthologous groups of protein (COG) categories consisting of a total of 4,631 functional genes. Trehalose and maltose hydrolase (COG1554) and fucose permease (COG0738) were the most relevant and enriched functional genes in the IBS-D patients; urease accessory proteins UreE (COG2371) was that in the depression patients. Context based genome annotation suggest that an alteration of Escherichia coli and Enterobacter cloacae in IBS-D and depression respectively may be responsible for the enrichment described above. Correlation with host metabolites, such as maltotriose and isomaltose in carbohydrate metabolism and anandamide in neuroactive metabolism, drew further connections between these findings.

CONCLUSIONS: These changes led us to propose a connection between genomic signatures and clinical differences observed in IBS-D and depression. Our findings provide further insights into the involvement of gut microbiota in diseases related to brain-gut disorder.}, } @article {pmid33194372, year = {2020}, author = {Busi, SB and Pramateftaki, P and Brandani, J and Fodelianakis, S and Peter, H and Halder, R and Wilmes, P and Battin, TJ}, title = {Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e9973}, pmid = {33194372}, issn = {2167-8359}, abstract = {Glacier-fed streams (GFS) are harsh ecosystems dominated by microbial life organized in benthic biofilms, yet the biodiversity and ecosystem functions provided by these communities remain under-appreciated. To better understand the microbial processes and communities contributing to GFS ecosystems, it is necessary to leverage high throughput sequencing. Low biomass and high inorganic particle load in GFS sediment samples may affect nucleic acid extraction efficiency using extraction methods tailored to other extreme environments such as deep-sea sediments. Here, we benchmarked the utility and efficacy of four extraction protocols, including an up-scaled phenol-chloroform protocol. We found that established protocols for comparable sample types consistently failed to yield sufficient high-quality DNA, delineating the extreme character of GFS. The methods differed in the success of downstream applications such as library preparation and sequencing. An adapted phenol-chloroform-based extraction method resulted in higher yields and better recovered the expected taxonomic profile and abundance of reconstructed genomes when compared to commercially-available methods. Affordable and straight-forward, this method consistently recapitulated the abundance and genomes of a mock community, including eukaryotes. Moreover, by increasing the amount of input sediment, the protocol is readily adjustable to the microbial load of the processed samples without compromising protocol efficiency. Our study provides a first systematic and extensive analysis of the different options for extraction of nucleic acids from glacier-fed streams for high-throughput sequencing applications, which may be applied to other extreme environments.}, } @article {pmid33189472, year = {2021}, author = {Miao, Y and Heintz, MB and Bell, CH and Johnson, NW and Polasko, AL and Favero, D and Mahendra, S}, title = {Profiling microbial community structures and functions in bioremediation strategies for treating 1,4-dioxane-contaminated groundwater.}, journal = {Journal of hazardous materials}, volume = {408}, number = {}, pages = {124457}, doi = {10.1016/j.jhazmat.2020.124457}, pmid = {33189472}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; Dioxanes ; *Groundwater ; *Microbiota ; Rhodococcus ; *Water Pollutants, Chemical ; }, abstract = {Microbial community compositions and functional profiles were analyzed in microcosms established using aquifer materials from a former automobile factory site, where 1,4-dioxane was identified as the primary contaminant of concern. Propane or oxygen biostimulation resulted in limited 1,4-dioxane degradation, which was markedly enhanced with the addition of nutrients, resulting in abundant Mycobacterium and Methyloversatilis taxa and high expressions of propane monooxygenase gene, prmA. In bioaugmented treatments, Pseudonocardia dioxanivorans CB1190 or Rhodococcus ruber ENV425 strains dominated immediately after augmentation and degraded 1,4-dioxane rapidly which was consistent with increased representation of xenobiotic and lipid metabolism-related functions. Although the bioaugmented microbes decreased due to insufficient growth substrates and microbial competition, they did continue to degrade 1,4-dioxane, presumably by indigenous propanotrophic and heterotrophic bacteria, inducing similar community structures across bioaugmentation conditions. In various treatments, functional redundancy acted as buffer capacity to ensure a stable microbiome, drove the restoration of the structure and microbial functions to original levels, and induced the decoupling between basic metabolic functions and taxonomy. The results of this study provided valuable information for design and decision-making for ex-situ bioreactors and in-situ bioremediation applications. A metagenomics-based understanding of the treatment process will enable efficient and accurate adjustments when encountering unexpected issues in bioremediation.}, } @article {pmid33188211, year = {2020}, author = {Michalak, L and Gaby, JC and Lagos, L and La Rosa, SL and Hvidsten, TR and Tétard-Jones, C and Willats, WGT and Terrapon, N and Lombard, V and Henrissat, B and Dröge, J and Arntzen, MØ and Hagen, LH and Øverland, M and Pope, PB and Westereng, B}, title = {Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5773}, pmid = {33188211}, issn = {2041-1723}, mesh = {Acetylation/drug effects ; Animals ; Butyrates/metabolism ; Cecum/metabolism ; Diet ; Dietary Fiber/*pharmacology ; Feeding Behavior/drug effects ; Female ; *Gastrointestinal Microbiome/drug effects ; Gastrointestinal Tract/drug effects/*metabolism/*microbiology ; Genome ; Male ; Mannans/pharmacology ; Metabolic Networks and Pathways/drug effects ; Metagenomics ; Principal Component Analysis ; Proteome/metabolism ; RNA, Ribosomal, 16S/genetics ; *Secondary Metabolism/drug effects ; Swine ; Wood/chemistry ; }, abstract = {Beneficial modulation of the gut microbiome has high-impact implications not only in humans, but also in livestock that sustain our current societal needs. In this context, we have tailored an acetylated galactoglucomannan (AcGGM) fibre to match unique enzymatic capabilities of Roseburia and Faecalibacterium species, both renowned butyrate-producing gut commensals. Here, we test the accuracy of AcGGM within the complex endogenous gut microbiome of pigs, wherein we resolve 355 metagenome-assembled genomes together with quantitative metaproteomes. In AcGGM-fed pigs, both target populations differentially express AcGGM-specific polysaccharide utilization loci, including novel, mannan-specific esterases that are critical to its deconstruction. However, AcGGM-inclusion also manifests a "butterfly effect", whereby numerous metabolic changes and interdependent cross-feeding pathways occur in neighboring non-mannanolytic populations that produce short-chain fatty acids. Our findings show how intricate structural features and acetylation patterns of dietary fibre can be customized to specific bacterial populations, with potential to create greater modulatory effects at large.}, } @article {pmid33188179, year = {2020}, author = {Meyer-Cifuentes, IE and Werner, J and Jehmlich, N and Will, SE and Neumann-Schaal, M and Öztürk, B}, title = {Synergistic biodegradation of aromatic-aliphatic copolyester plastic by a marine microbial consortium.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5790}, pmid = {33188179}, issn = {2041-1723}, mesh = {Aquatic Organisms/*metabolism ; Bacterial Proteins/metabolism ; Biodegradation, Environmental ; Carbon Dioxide/metabolism ; Gene Expression Regulation, Bacterial ; Genome, Bacterial ; *Microbial Consortia/genetics ; Minerals/chemistry ; Models, Biological ; Plastics/*metabolism ; Polyesters/*metabolism ; Protein Biosynthesis/genetics ; Time Factors ; }, abstract = {The degradation of synthetic polymers by marine microorganisms is not as well understood as the degradation of plastics in soil and compost. Here, we use metagenomics, metatranscriptomics and metaproteomics to study the biodegradation of an aromatic-aliphatic copolyester blend by a marine microbial enrichment culture. The culture can use the plastic film as the sole carbon source, reaching maximum conversion to CO2 and biomass in around 15 days. The consortium degrades the polymer synergistically, with different degradation steps being performed by different community members. We identify six putative PETase-like enzymes and four putative MHETase-like enzymes, with the potential to degrade aliphatic-aromatic polymers and their degradation products, respectively. Our results show that, although there are multiple genes and organisms with the potential to perform each degradation step, only a few are active during biodegradation.}, } @article {pmid33187992, year = {2021}, author = {Wu, H and Ioannou, E and Henrissat, B and Montanier, CY and Bozonnet, S and O'Donohue, MJ and Dumon, C}, title = {Multimodularity of a GH10 Xylanase Found in the Termite Gut Metagenome.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {3}, pages = {}, pmid = {33187992}, issn = {1098-5336}, mesh = {Animals ; Bacterial Proteins/genetics ; Bacteroidetes/*enzymology/genetics/isolation & purification ; *Endo-1,4-beta Xylanases/chemistry/genetics/metabolism ; Gastrointestinal Microbiome ; Isoptera/*microbiology ; Metagenome ; Xylans/metabolism ; }, abstract = {The functional screening of a Pseudacanthotermes militaris termite gut metagenomic library revealed an array of xylan-degrading enzymes, including P. militaris 25 (Pm25), a multimodular glycoside hydrolase family 10 (GH10). Sequence analysis showed details of the unusual domain organization of this enzyme. It consists of one catalytic domain, which is intercalated by two carbohydrate binding modules (CBMs) from family 4. The genes upstream of the genes encoding Pm25 are susC-susD-unk, suggesting Pm25 is a Xyn10C-like enzyme belonging to a polysaccharide utilization locus. The majority of Xyn10C-like enzymes shared the same interrupted domain architecture and were vastly distributed in different xylan utilization loci found in gut Bacteroidetes, indicating the importance of this enzyme in glycan acquisition for gut microbiota. To understand its unusual multimodularity and the possible role of the CBMs, a detailed characterization of the full-length Pm25 and truncated variants was performed. Results revealed that the GH10 catalytic module is specific toward the hydrolysis of xylan. Ligand binding results indicate that the GH10 module and the CBMs act independently, whereas the tandem CBM4s act synergistically with each other and improve enzymatic activity when assayed on insoluble polysaccharides. In addition, we show that the UNK protein upstream of Pm25 is able to bind arabinoxylan. Altogether, these findings contribute to a better understanding of the potential role of Xyn10C-like proteins in xylan utilization systems of gut bacteria.IMPORTANCE Xylan is the major hemicellulosic polysaccharide in cereals and contributes to the recalcitrance of the plant cell wall toward degradation. Members of the Bacteroidetes, one of the main phyla in rumen and human gut microbiota, have been shown to encode polysaccharide utilization loci dedicated to the degradation of xylan. Here, we present the biochemical characterization of a xylanase encoded by a Bacteroidetes strain isolated from the termite gut metagenome. This xylanase is a multimodular enzyme, the sequence of which is interrupted by the insertion of two CBMs from family 4. Our results show that this enzyme resembles homologues that were shown to be important for xylan degradation in rumen or human diet and show that the CBM insertion in the middle of the sequence seems to be a common feature in xylan utilization systems. This study shed light on our understanding of xylan degradation and plant cell wall deconstruction, which can be applied to several applications in food, feed, and bioeconomy.}, } @article {pmid33185964, year = {2021}, author = {Vik, D and Gazitúa, MC and Sun, CL and Zayed, AA and Aldunate, M and Mulholland, MR and Ulloa, O and Sullivan, MB}, title = {Genome-resolved viral ecology in a marine oxygen minimum zone.}, journal = {Environmental microbiology}, volume = {23}, number = {6}, pages = {2858-2874}, doi = {10.1111/1462-2920.15313}, pmid = {33185964}, issn = {1462-2920}, mesh = {Metagenome ; *Microbiota ; Oxygen ; Seawater ; *Viruses/genetics ; }, abstract = {Oxygen minimum zones (OMZs) are critical to marine nitrogen cycling and global climate change. While OMZ microbial communities are relatively well-studied, little is known about their viruses. Here, we assess the viral community ecology of 22 deeply sequenced viral metagenomes along a gradient of oxygenated to anoxic waters (<0.02 μmol/l O2) in the Eastern Tropical South Pacific (ETSP) OMZ. We identified 46 127 viral populations (≥5 kb), which augments the known viruses from ETSP by 10-fold. Viral communities clustered into six groups that correspond to oceanographic features. Oxygen concentration was the predominant environmental feature driving viral community structure. Alpha and beta diversity of viral communities in the anoxic zone were lower than in surface waters, which parallels the low microbial diversity seen in other studies. ETSP viruses were largely endemic, with the majority of shared viruses (87%) also present in other OMZ samples. We detected 543 putative viral-encoded auxiliary metabolic genes (AMGs), of which some have a distribution that reflects physico-chemical characteristics across depth. Together these findings provide an ecological baseline for viral community structure, drivers and population variability in OMZs that will help future studies assess the role of viruses in these climate-critical environments.}, } @article {pmid33185929, year = {2021}, author = {Bahram, M and Netherway, T and Frioux, C and Ferretti, P and Coelho, LP and Geisen, S and Bork, P and Hildebrand, F}, title = {Metagenomic assessment of the global diversity and distribution of bacteria and fungi.}, journal = {Environmental microbiology}, volume = {23}, number = {1}, pages = {316-326}, pmid = {33185929}, issn = {1462-2920}, support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacteria/classification/*genetics/isolation & purification ; *Biodiversity ; Fungi/classification/*genetics/isolation & purification ; Metagenome ; Metagenomics ; Microbiota ; Mycobiome ; Plants/microbiology ; }, abstract = {Bacteria and fungi are of uttermost importance in determining environmental and host functioning. Despite close interactions between animals, plants, their associated microbiomes, and the environment they inhabit, the distribution and role of bacteria and especially fungi across host and environments as well as the cross-habitat determinants of their community compositions remain little investigated. Using a uniquely broad global dataset of 13 483 metagenomes, we analysed the microbiome structure and function of 25 host-associated and environmental habitats, focusing on potential interactions between bacteria and fungi. We found that the metagenomic relative abundance ratio of bacteria-to-fungi is a distinctive microbial feature of habitats. Compared with fungi, the cross-habitat distribution pattern of bacteria was more strongly driven by habitat type. Fungal diversity was depleted in host-associated communities compared with those in the environment, particularly terrestrial habitats, whereas this diversity pattern was less pronounced for bacteria. The relative gene functional potential of bacteria or fungi reflected their diversity patterns and appeared to depend on a balance between substrate availability and biotic interactions. Alongside helping to identify hotspots and sources of microbial diversity, our study provides support for differences in assembly patterns and processes between bacterial and fungal communities across different habitats.}, } @article {pmid33184266, year = {2020}, author = {Zhuang, W and Yu, X and Hu, R and Luo, Z and Liu, X and Zheng, X and Xiao, F and Peng, Y and He, Q and Tian, Y and Yang, T and Wang, S and Shu, L and Yan, Q and Wang, C and He, Z}, title = {Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale.}, journal = {NPJ biofilms and microbiomes}, volume = {6}, number = {1}, pages = {52}, pmid = {33184266}, issn = {2055-5008}, mesh = {Bacteria/*classification/genetics/isolation & purification ; Bacterial Proteins/*genetics ; DNA, Ribosomal Spacer/genetics ; Fungal Proteins/*genetics ; Fungi/*classification/genetics/isolation & purification ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Fungal ; Metagenomics/*methods ; Microbiota ; Phylogeny ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Sequence Analysis, DNA ; Soil Microbiology ; Wetlands ; }, abstract = {Mangrove roots harbor a repertoire of microbial taxa that contribute to important ecological functions in mangrove ecosystems. However, the diversity, function, and assembly of mangrove root-associated microbial communities along a continuous fine-scale niche remain elusive. Here, we applied amplicon and metagenome sequencing to investigate the bacterial and fungal communities among four compartments (nonrhizosphere, rhizosphere, episphere, and endosphere) of mangrove roots. We found different distribution patterns for both bacterial and fungal communities in all four root compartments, which could be largely due to niche differentiation along the root compartments and exudation effects of mangrove roots. The functional pattern for bacterial and fungal communities was also divergent within the compartments. The endosphere harbored more genes involved in carbohydrate metabolism, lipid transport, and methane production, and fewer genes were found to be involved in sulfur reduction compared to other compartments. The dynamics of root-associated microbial communities revealed that 56-74% of endosphere bacterial taxa were derived from nonrhizosphere, whereas no fungal OTUs of nonrhizosphere were detected in the endosphere. This indicates that roots may play a more strictly selective role in the assembly of the fungal community compared to the endosphere bacterial community, which is consistent with the projections established in an amplification-selection model. This study reveals the divergence in the diversity and function of root-associated microbial communities along a continuous fine-scale niche, thereby highlighting a strictly selective role of soil-root interfaces in shaping the fungal community structure in the mangrove root systems.}, } @article {pmid33183813, year = {2021}, author = {Coutinho, FH and von Meijenfeldt, FAB and Walter, JM and Haro-Moreno, JM and Lopéz-Pérez, M and van Verk, MC and Thompson, CC and Cosenza, CAN and Appolinario, L and Paranhos, R and Cabral, A and Dutilh, BE and Thompson, FL}, title = {Ecogenomics and metabolic potential of the South Atlantic Ocean microbiome.}, journal = {The Science of the total environment}, volume = {765}, number = {}, pages = {142758}, doi = {10.1016/j.scitotenv.2020.142758}, pmid = {33183813}, issn = {1879-1026}, mesh = {Archaea/genetics ; Atlantic Ocean ; Metagenome ; Metagenomics ; *Microbiota ; *Seawater ; }, abstract = {The unique combination of depth, salinity, and water masses make the South Atlantic Ocean an ecosystem of special relevance within the global ocean. Yet, the microbiome of this ecosystem has received less attention than other regions of the global Ocean. This has hampered our understanding of the diversity and metabolic potential of the microorganisms that dwell in this habitat. To fill this knowledge gap, we analyzed a collection of 31 metagenomes from the Atlantic Ocean that spanned the epipelagic, mesopelagic and bathypelagic zones (surface to 4000 m). Read-centric and gene-centric analysis revealed the unique taxonomic and functional composition of metagenomes from each depth zone, which was driven by differences in physical and chemical parameters. In parallel, a total of 40 metagenome-assembled genomes were obtained, which recovered one third of the total community. Phylogenomic reconstruction revealed that many of these genomes are derived from poorly characterized taxa of Bacteria and Archaea. Genomes derived from heterotrophic bacteria of the aphotic zone displayed a large apparatus of genes suited for the utilization of recalcitrant organic compounds such as cellulose, chitin and alkanes. In addition, we found genomic evidence suggesting that mixotrophic bacteria from the bathypelagic zone could perform carbon fixation through the Calvin-Benson-Bassham cycle, fueled by sulfur oxidation. Finally, we found that the viral communities shifted throughout the water column regarding their targeted hosts and virus-to-microbe ratio, in response to shifts in the composition and functioning their microbial counterparts. Our findings shed light on the microbial and viral drivers of important biogeochemical processes that take place in the South Atlantic Ocean.}, } @article {pmid33182758, year = {2020}, author = {Moon, J and Yoon, CH and Choi, SH and Kim, MK}, title = {Can Gut Microbiota Affect Dry Eye Syndrome?.}, journal = {International journal of molecular sciences}, volume = {21}, number = {22}, pages = {}, pmid = {33182758}, issn = {1422-0067}, mesh = {Adaptive Immunity ; Animals ; Autoimmune Diseases/etiology/immunology/microbiology ; Autoimmunity ; Disease Models, Animal ; Dry Eye Syndromes/*etiology/immunology/microbiology ; Dysbiosis/complications/immunology/microbiology ; Gastrointestinal Microbiome/genetics/*immunology ; Homeostasis/immunology ; Host Microbial Interactions/immunology ; Humans ; Immunity, Innate ; Metagenomics ; Models, Biological ; Prebiotics ; Probiotics/therapeutic use ; Sjogren's Syndrome/etiology/immunology/microbiology ; }, abstract = {Using metagenomics, continuing evidence has elicited how intestinal microbiota trigger distant autoimmunity. Sjögren's syndrome (SS) is an autoimmune disease that affects the ocular surface, with frequently unmet therapeutic needs requiring new interventions for dry eye management. Current studies also suggest the possible relation of autoimmune dry eye with gut microbiota. Herein, we review the current knowledge of how the gut microbiota interact with the immune system in homeostasis as well as its influence on rheumatic and ocular autoimmune diseases, and compare their characteristics with SS. Both rodent and human studies regarding gut microbiota in SS and environmental dry eye are explored, and the effects of prebiotics and probiotics on dry eye are discussed. Recent clinical studies have commonly observed a correlation between gut dysbiosis and clinical manifestations of SS, while environmental dry eye portrays characteristics in between normal and autoimmune. Moreover, a decrease in both the Firmicutes/Bacteroidetes ratio and genus Faecalibacterium have most commonly been observed in SS subjects. The presumable pathways forming the "gut dysbiosis-ocular surface-lacrimal gland axis" are introduced. This review may provide perspectives into the link between the gut microbiome and dry eye, enhance our understanding of the pathogenesis in autoimmune dry eye, and be useful in the development of future interventions.}, } @article {pmid33181127, year = {2020}, author = {Miyoshi, J and Rao, MC and Chang, EB}, title = {Navigating the Human Gut Microbiome: Pathway to Success from Lessons Learned.}, journal = {Gastroenterology}, volume = {159}, number = {6}, pages = {2019-2024}, pmid = {33181127}, issn = {1528-0012}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/isolation & purification ; DNA, Bacterial/genetics/isolation & purification ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Genetic Markers ; Host Microbial Interactions/*physiology ; Humans ; Intestinal Mucosa/microbiology ; Metadata ; Metagenomics/methods ; Molecular Typing/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Specimen Handling/methods ; }, } @article {pmid33180176, year = {2021}, author = {Mima, K and Kosumi, K and Baba, Y and Hamada, T and Baba, H and Ogino, S}, title = {The microbiome, genetics, and gastrointestinal neoplasms: the evolving field of molecular pathological epidemiology to analyze the tumor-immune-microbiome interaction.}, journal = {Human genetics}, volume = {140}, number = {5}, pages = {725-746}, pmid = {33180176}, issn = {1432-1203}, support = {R35 CA197735/CA/NCI NIH HHS/United States ; R35 CA197735/NH/NIH HHS/United States ; R21 CA230873/CA/NCI NIH HHS/United States ; R01 CA248857/CA/NCI NIH HHS/United States ; R01 CA151993/CA/NCI NIH HHS/United States ; R01 CA151993/NH/NIH HHS/United States ; R01 CA248857/NH/NIH HHS/United States ; C10674/A27140//Cancer Research UK Grand Challenge Award/ ; 20K17658//Japan Society for the Promotion of Science/ ; 17H05094//Japan Society for the Promotion of Science/ ; R21 CA230873/NH/NIH HHS/United States ; }, mesh = {Adenomatous Polyposis Coli/genetics/microbiology ; Adenomatous Polyposis Coli Protein/*genetics ; Bacteroides fragilis/growth & development ; Escherichia coli/growth & development ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Neoplasms/epidemiology/*genetics/*microbiology ; Humans ; Intestinal Mucosa/*microbiology ; Molecular Epidemiology ; }, abstract = {Metagenomic studies using next-generation sequencing technologies have revealed rich human intestinal microbiome, which likely influence host immunity and health conditions including cancer. Evidence indicates a biological link between altered microbiome and cancers in the digestive system. Escherichia coli and Bacteroides fragilis have been found to be enriched in colorectal mucosal tissues from patients with familial adenomatous polyposis that is caused by germline APC mutations. In addition, recent studies have found enrichment of certain oral bacteria, viruses, and fungi in tumor tissue and fecal specimens from patients with gastrointestinal cancer. An integrative approach is required to elucidate the role of microorganisms in the pathogenic process of gastrointestinal cancers, which develop through the accumulation of somatic genetic and epigenetic alterations in neoplastic cells, influenced by host genetic variations, immunity, microbiome, and environmental exposures. The transdisciplinary field of molecular pathological epidemiology (MPE) offers research frameworks to link germline genetics and environmental factors (including diet, lifestyle, and pharmacological factors) to pathologic phenotypes. The integration of microbiology into the MPE model (microbiology-MPE) can contribute to better understanding of the interactive role of environment, tumor cells, immune cells, and microbiome in various diseases. We review major clinical and experimental studies on the microbiome, and describe emerging evidence from the microbiology-MPE research in gastrointestinal cancers. Together with basic experimental research, this new research paradigm can help us to develop new prevention and treatment strategies for gastrointestinal cancers through targeting of the microbiome.}, } @article {pmid33180172, year = {2020}, author = {Rivera, AJ and Tyx, RE and Keong, LM and Stanfill, SB and Watson, CH}, title = {Microbial communities and gene contributions in smokeless tobacco products.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {24}, pages = {10613-10629}, pmid = {33180172}, issn = {1432-0614}, support = {CC999999/ImCDC/Intramural CDC HHS/United States ; }, mesh = {Bacteria/genetics ; Metagenome ; Metagenomics ; *Microbiota ; *Tobacco, Smokeless ; }, abstract = {Smokeless tobacco products (STP) contain bacteria, mold, and fungi due to exposure from surrounding environments and tobacco processing. This has been a cause for concern since the presence of microorganisms has been linked to the formation of highly carcinogenic tobacco-specific nitrosamines. These communities have also been reported to produce toxins and other pro-inflammatory molecules that can cause mouth lesions and elicit inflammatory responses in STP users. Moreover, microbial species in these products could transfer to the mouth and gastrointestinal tract, potentially altering the established respective microbiotas of the consumer. Here, we present the first metagenomic analysis of select smokeless tobacco products, specifically US domestic moist and dry snuff. Bacterial, eukaryotic, and viral species were found in all tobacco products where 68% of the total species was comprised of Bacteria with 3 dominant phyla but also included 32% Eukarya and 1% share abundance for Archaea and Viruses. Furthermore, 693,318 genes were found to be present and included nitrate and nitrite reduction and transport enzymes, antibiotic resistance genes associated with resistance to vancomycin, β-lactamases, their derivatives, and other antibiotics, as well as genes encoding multi-drug transporters and efflux pumps. Additional analyses showed the presence of endo- and exotoxin genes in addition to other molecules associated with inflammatory responses. Our results present a novel aspect of the smokeless tobacco microbiome and provide a better understanding of these products' microbiology. KEY POINTS: • The findings presented will help understand microbial contributions to overall STP chemistries. • Gene function categorization reveals harmful constituents outside canonical forms. • Pathway genes for TSNA precursor activity may occur at early stages of production. • Bacteria in STPs carry antibiotic resistance genes and gene transfer mechanisms.}, } @article {pmid33178159, year = {2020}, author = {Maclot, F and Candresse, T and Filloux, D and Malmstrom, CM and Roumagnac, P and van der Vlugt, R and Massart, S}, title = {Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {578064}, pmid = {33178159}, issn = {1664-302X}, abstract = {The ecology of plant viruses began to be explored at the end of the 19th century. Since then, major advances have revealed mechanisms of virus-host-vector interactions in various environments. These advances have been accelerated by new technlogies for virus detection and characterization, most recently including high throughput sequencing (HTS). HTS allows investigators, for the first time, to characterize all or nearly all viruses in a sample without a priori information about which viruses might be present. This powerful approach has spurred new investigation of the viral metagenome (virome). The rich virome datasets accumulated illuminate important ecological phenomena such as virus spread among host reservoirs (wild and domestic), effects of ecosystem simplification caused by human activities (and agriculture) on the biodiversity and the emergence of new viruses in crops. To be effective, however, HTS-based virome studies must successfully navigate challenges and pitfalls at each procedural step, from plant sampling to library preparation and bioinformatic analyses. This review summarizes major advances in plant virus ecology associated with technological developments, and then presents important considerations and best practices for HTS use in virome studies.}, } @article {pmid33178147, year = {2020}, author = {Behera, BK and Chakraborty, HJ and Patra, B and Rout, AK and Dehury, B and Das, BK and Sarkar, DJ and Parida, PK and Raman, RK and Rao, AR and Rai, A and Mohapatra, T}, title = {Metagenomic Analysis Reveals Bacterial and Fungal Diversity and Their Bioremediation Potential From Sediments of River Ganga and Yamuna in India.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {556136}, pmid = {33178147}, issn = {1664-302X}, abstract = {In this study, we report the presence of a microbial community of bioremediation potential in terms of relative abundance and taxonomic biodiversity in sediment samples of river Ganga and Yamuna, India at nine different sites. Metagenomic libraries were constructed using TruSeq Nano DNA Library Prep Kit and sequenced on NextSeq 500 by Illumina Next Generation Sequencing (NGS) technology. Bioremediation bacteria belong to 45 genera with 92 species and fungi belong to 13 genera with 24 species have been classified using Kaiju taxonomical classification. The study revealed that Proteobacteria was the most dominant bacterial flora, followed by Actinobacteria, Firmicutes, and Deinococcus-Thermus. PCA analysis revealed that bioremediation bacteria viz. Streptomyces bikiniensis, Rhodococcus qingshengii, Bacillus aerophilus, Pseudomonas veronii, etc., were more dominant in highly polluted river stretch as compared to less polluted river stretch. Similarly, the relative abundance of bioremediation fungi viz. Phanerochaete chrysosporium and Rhizopus oryzae, etc., were significantly correlated with the polluted Kanpur stretch of river Ganga. Several protein domains, which play a pivotal role in bioremediation in the polluted environments, including urea ABC transporter, UrtA, UrtD, UrtE, zinc/cadmium/mercury/lead-transporting ATPase, etc., were identified using protein domain analysis. The protein domains involved in pesticide biodegradation viz. P450, short-chain dehydrogenases/reductases (SDR), etc., were also discovered in river sediment metagenomics data. This is the first report on the richness of bioremediation microbial communities in the Ganga and Yamuna riverine ecosystems, highlighting their importance in aquatic pollution management.}, } @article {pmid33176883, year = {2020}, author = {Zhang, L and Fang, X and Liao, H and Zhang, Z and Zhou, X and Han, L and Chen, Y and Qiu, Q and Li, SC}, title = {A comprehensive investigation of metagenome assembly by linked-read sequencing.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {156}, pmid = {33176883}, issn = {2049-2618}, mesh = {High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: The human microbiota are complex systems with important roles in our physiological activities and diseases. Sequencing the microbial genomes in the microbiota can help in our interpretation of their activities. The vast majority of the microbes in the microbiota cannot be isolated for individual sequencing. Current metagenomics practices use short-read sequencing to simultaneously sequence a mixture of microbial genomes. However, these results are in ambiguity during genome assembly, leading to unsatisfactory microbial genome completeness and contig continuity. Linked-read sequencing is able to remove some of these ambiguities by attaching the same barcode to the reads from a long DNA fragment (10-100 kb), thus improving metagenome assembly. However, it is not clear how the choices for several parameters in the use of linked-read sequencing affect the assembly quality.

RESULTS: We first examined the effects of read depth (C) on metagenome assembly from linked-reads in simulated data and a mock community. The results showed that C positively correlated with the length of assembled sequences but had little effect on their qualities. The latter observation was corroborated by tests using real data from the human gut microbiome, where C demonstrated minor impact on the sequence quality as well as on the proportion of bins annotated as draft genomes. On the other hand, metagenome assembly quality was susceptible to read depth per fragment (CR) and DNA fragment physical depth (CF). For the same C, deeper CR resulted in more draft genomes while deeper CF improved the quality of the draft genomes. We also found that average fragment length (μFL) had marginal effect on assemblies, while fragments per partition (NF/P) impacted the off-target reads involved in local assembly, namely, lower NF/P values would lead to better assemblies by reducing the ambiguities of the off-target reads. In general, the use of linked-reads improved the assembly for contig N50 when compared to Illumina short-reads, but not when compared to PacBio CCS (circular consensus sequencing) long-reads.

CONCLUSIONS: We investigated the influence of linked-read sequencing parameters on metagenome assembly comprehensively. While the quality of genome assembly from linked-reads cannot rival that from PacBio CCS long-reads, the case for using linked-read sequencing remains persuasive due to its low cost and high base-quality. Our study revealed that the probable best practice in using linked-reads for metagenome assembly was to merge the linked-reads from multiple libraries, where each had sufficient CR but a smaller amount of input DNA. Video Abstract.}, } @article {pmid33176699, year = {2020}, author = {Li, Z and Wei, J and Zhang, Y and Li, G and Zhu, H and Lei, N and He, Q and Geng, Y and Zhu, J}, title = {Risk factors for Keshan disease: a prospective cohort study protocol of gut flora.}, journal = {BMC cardiovascular disorders}, volume = {20}, number = {1}, pages = {481}, pmid = {33176699}, issn = {1471-2261}, support = {81870298//the National Natural Science Foundation of China/International ; }, mesh = {Adolescent ; Adult ; Aged ; Bacteria/classification/*genetics/*metabolism ; Big Data ; Biomarkers/*metabolism ; Cardiomyopathies/diagnosis/*microbiology/virology ; Case-Control Studies ; Enterovirus Infections/diagnosis/*microbiology/virology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestines/*microbiology ; Male ; *Metabolomics ; *Metagenomics ; Middle Aged ; Prospective Studies ; Research Design ; Young Adult ; }, abstract = {BACKGROUND: Keshan disease is an endemic cardiomyopathy of undefined causes. Being involved in the unclear pathogenesis of Keshan disease, a clear diagnosis, and effective treatment cannot be initiated. However, the rapid development of gut flora in cardiovascular disease combined with omics and big data platforms may promote the discovery of new diagnostic markers and provide new therapeutic options. This study aims to identify biomarkers for the early diagnosis and further explore new therapeutic targets for Keshan disease.

METHODS: This cohort study consists of two parts. Though the first part includes 300 participants, however, recruiting will be continued for the eligible participants. After rigorous screening, the blood samples, stools, electrocardiograms, and ultrasonic cardiogram data would be collected from participants to elucidate the relationship between gut flora and host. The second part includes a prospective follow-up study for every 6 months within 2 years. Finally, deep mining of big data and rapid machine learning will be employed to analyze the baseline data, experimental data, and clinical data to seek out the new biomarkers to predict the pathogenesis of Keshan disease.

DISCUSSION: Our study will clarify the distribution of gut flora in patients with Keshan disease and the abundance and population changes of gut flora in different stages of the disease. Through the big data platform analyze the relationship between environmental factors, clinical factors, and gut flora, the main factors affecting the occurrence of Keshan disease were identified, and the changed molecular pathways of gut flora were predicted. Finally, the specific gut flora and molecular pathways affecting Keshan disease were identified by metagenomics combined with metabonomic analysis.

TRIAL REGISTRATION: ChiCTR1900026639. Registered on 16 October 2019.}, } @article {pmid33176084, year = {2020}, author = {Doan, T and Worden, L and Hinterwirth, A and Arzika, AM and Maliki, R and Abdou, A and Zhong, L and Chen, C and Cook, C and Lebas, E and O'Brien, KS and Oldenburg, CE and Chow, ED and Porco, TC and Lipsitch, M and Keenan, JD and Lietman, TM}, title = {Macrolide and Nonmacrolide Resistance with Mass Azithromycin Distribution.}, journal = {The New England journal of medicine}, volume = {383}, number = {20}, pages = {1941-1950}, pmid = {33176084}, issn = {1533-4406}, mesh = {Anti-Bacterial Agents/*administration & dosage/pharmacology ; Azithromycin/*administration & dosage/pharmacology ; Child Mortality ; Child, Preschool ; Drug Resistance, Bacterial/*drug effects/genetics ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant ; Macrolides/*pharmacology/therapeutic use ; Male ; *Mass Drug Administration ; Metagenome ; Niger ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Mass distribution of azithromycin to preschool children twice yearly for 2 years has been shown to reduce childhood mortality in sub-Saharan Africa but at the cost of amplifying macrolide resistance. The effects on the gut resistome, a reservoir of antimicrobial resistance genes in the body, of twice-yearly administration of azithromycin for a longer period are unclear.

METHODS: We investigated the gut resistome of children after they received twice-yearly distributions of azithromycin for 4 years. In the Niger site of the MORDOR trial, we enrolled 30 villages in a concurrent trial in which they were randomly assigned to receive mass distribution of either azithromycin or placebo, offered to all children 1 to 59 months of age every 6 months for 4 years. Rectal swabs were collected at baseline, 36 months, and 48 months for analysis of the participants' gut resistome. The primary outcome was the ratio of macrolide-resistance determinants in the azithromycin group to those in the placebo group at 48 months.

RESULTS: Over the entire 48-month period, the mean (±SD) coverage was 86.6±12% in the villages that received placebo and 83.2±16.4% in the villages that received azithromycin. A total of 3232 samples were collected during the entire trial period; of the samples obtained at the 48-month monitoring visit, 546 samples from 15 villages that received placebo and 504 from 14 villages that received azithromycin were analyzed. Determinants of macrolide resistance were higher in the azithromycin group than in the placebo group: 7.4 times as high (95% confidence interval [CI], 4.0 to 16.7) at 36 months and 7.5 times as high (95% CI, 3.8 to 23.1) at 48 months. Continued mass azithromycin distributions also selected for determinants of nonmacrolide resistance, including resistance to beta-lactam antibiotics, an antibiotic class prescribed frequently in this region of Africa.

CONCLUSIONS: Among villages assigned to receive mass distributions of azithromycin or placebo twice yearly for 4 years, antibiotic resistance was more common in the villages that received azithromycin than in those that received placebo. This trial showed that mass azithromycin distributions may propagate antibiotic resistance. (Funded by the Bill and Melinda Gates Foundation and others; ClinicalTrials.gov number, NCT02047981.).}, } @article {pmid33172994, year = {2020}, author = {Hevroni, G and Flores-Uribe, J and Béjà, O and Philosof, A}, title = {Seasonal and diel patterns of abundance and activity of viruses in the Red Sea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {47}, pages = {29738-29747}, pmid = {33172994}, issn = {1091-6490}, mesh = {Aquatic Organisms/genetics/*virology ; DNA, Viral/isolation & purification ; Indian Ocean ; Metagenome ; Microbial Interactions/genetics ; *Seasons ; Seawater/*microbiology ; Virome/*genetics ; Viruses/classification/*genetics/isolation & purification ; }, abstract = {Virus-microbe interactions have been studied in great molecular details for many years in cultured model systems, yielding a plethora of knowledge on how viruses use and manipulate host machinery. Since the advent of molecular techniques and high-throughput sequencing, methods such as cooccurrence, nucleotide composition, and other statistical frameworks have been widely used to infer virus-microbe interactions, overcoming the limitations of culturing methods. However, their accuracy and relevance is still debatable as cooccurrence does not necessarily mean interaction. Here we introduce an ecological perspective of marine viral communities and potential interaction with their hosts, using analyses that make no prior assumptions on specific virus-host pairs. By size fractionating water samples into free viruses and microbes (i.e., also viruses inside or attached to their hosts) and looking at how viral group abundance changes over time along both fractions, we show that the viral community is undergoing a change in rank abundance across seasons, suggesting a seasonal succession of viruses in the Red Sea. We use abundance patterns in the different size fractions to classify viral clusters, indicating potential diverse interactions with their hosts and potential differences in life history traits between major viral groups. Finally, we show hourly resolved variations of intracellular abundance of similar viral groups, which might indicate differences in their infection cycles or metabolic capacities.}, } @article {pmid33172257, year = {2020}, author = {Li, M and Rong, L and Zhou, S and Xiao, X and Wu, L and Fan, Y and Lu, C and Zou, X}, title = {Dissipation of Sulfonamides in Soil Emphasizing Taxonomy and Function of Microbiomes by Metagenomic Analysis.}, journal = {Journal of agricultural and food chemistry}, volume = {68}, number = {47}, pages = {13594-13607}, doi = {10.1021/acs.jafc.0c04496}, pmid = {33172257}, issn = {1520-5118}, mesh = {Kinetics ; Metagenomics ; *Microbiota ; Soil ; *Soil Pollutants/analysis ; Sulfonamides ; }, abstract = {Sulfonamides (SAs) are widespread in soils, and their dissipation behavior is important for their fate, risk assessment, and pollution control. In this work, we investigated the dissipation behavior of different SAs in a soil under aerobic condition, focusing on revealing the relationship between overall dissipation (without sterilization and in dark) and individual abiotic (sorption, hydrolysis)/biotic (with sterilization and in dark) factors and taxonomy/function of microbiomes. The results showed that dissipation of all SAs in the soil followed the pseudo-first-order kinetic model with dissipation time at 50% removal (DT50) of 2.16-15.27 days. Based on, experimentally, abiotic/biotic processes and, theoretically, partial least-squares modeling, a relationship between overall dissipation and individual abiotic/biotic factors was developed with microbial degradation as the dominant contributor. Metagenomic analysis showed that taxonomic genera like Bradyrhizobium/Sphingomonas/Methyloferula and functions like CAZy family GT51/GH23/GT2, eggNOG category S, KEGG pathway ko02024/ko02010, and KEGG ortholog K01999/K03088 are putatively involved in SA microbial degradation in soil. Spearman correlation suggests abundant genera being multifunctional. This study provides some new insights into SA dissipation and can be applied to other antibiotics/soils in the future.}, } @article {pmid33171859, year = {2020}, author = {Webster, HJ and Emami-Khoyi, A and van Dyk, JC and Teske, PR and Jansen van Vuuren, B}, title = {Environmental DNA Metabarcoding as a Means of Estimating Species Diversity in an Urban Aquatic Ecosystem.}, journal = {Animals : an open access journal from MDPI}, volume = {10}, number = {11}, pages = {}, pmid = {33171859}, issn = {2076-2615}, abstract = {Adaptation to environments that are changing as a result of human activities is critical to species' survival. A large number of species are adapting to, and even thriving in, urban green spaces, but this diversity remains largely undocumented. In the current study, we explored the potential of environmental DNA (eDNA) to document species diversity in one of the largest green spaces in Johannesburg, South Africa. Using a novel metabarcoding approach that assembles short DNA fragments suitable for massively parallel sequencing platforms to the approximate standard ~710 bp COI barcoding fragment, we document the presence of 26 phyla, 52 classes, 134 orders, 289 families, 380 genera and 522 known species from the study site. Our results highlight the critical role that urban areas play in protecting the world's declining biodiversity.}, } @article {pmid33170893, year = {2020}, author = {Sajulga, R and Easterly, C and Riffle, M and Mesuere, B and Muth, T and Mehta, S and Kumar, P and Johnson, J and Gruening, BA and Schiebenhoefer, H and Kolmeder, CA and Fuchs, S and Nunn, BL and Rudney, J and Griffin, TJ and Jagtap, PD}, title = {Survey of metaproteomics software tools for functional microbiome analysis.}, journal = {PloS one}, volume = {15}, number = {11}, pages = {e0241503}, pmid = {33170893}, issn = {1932-6203}, support = {U24 CA199347/CA/NCI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Dysbiosis/microbiology ; Gene Ontology ; *Metagenomics ; *Microbiota ; Peptides/analysis/chemistry ; *Proteomics ; *Software ; *Surveys and Questionnaires ; Workflow ; }, abstract = {To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance of expressed microbial genes or proteins. This can be accomplished through metaproteomics, which characterizes the protein expression of microbiomes. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, to enable researchers to make informed decisions regarding software choice based on their research goals. Tandem mass spectrometry-based proteomic data obtained from dental caries plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN5, MetaGOmics, MetaProteomeAnalyzer (MPA), ProPHAnE, and Unipept to generate functional annotation through Gene Ontology (GO) terms. Among these software tools, notable differences in functional annotation were detected after comparing differentially expressed protein functional groups. Based on the generated GO terms of these tools we performed a peptide-level comparison to evaluate the quality of their functional annotations. A BLAST analysis against the NCBI non-redundant database revealed that the sensitivity and specificity of functional annotation varied between tools. For example, eggNOG-mapper mapped to the most number of GO terms, while Unipept generated more accurate GO terms. Based on our evaluation, metaproteomics researchers can choose the software according to their analytical needs and developers can use the resulting feedback to further optimize their algorithms. To make more of these tools accessible via scalable metaproteomics workflows, eggNOG-mapper and Unipept 4.0 were incorporated into the Galaxy platform.}, } @article {pmid33167991, year = {2020}, author = {Al Bataineh, MT and Dash, NR and Elkhazendar, M and Alnusairat, DMH and Darwish, IMI and Al-Hajjaj, MS and Hamid, Q}, title = {Revealing oral microbiota composition and functionality associated with heavy cigarette smoking.}, journal = {Journal of translational medicine}, volume = {18}, number = {1}, pages = {421}, pmid = {33167991}, issn = {1479-5876}, mesh = {Adult ; *Cigarette Smoking ; Fusobacterium ; Humans ; *Microbiota ; Neoplasm Recurrence, Local ; Prevotella ; Smoke ; Streptobacillus ; *Tobacco Products ; Veillonella ; }, abstract = {BACKGROUND: Heavy tobacco smoking, a hallmark feature of lung cancer, is drastically predominant in Middle Eastern populations. The precise links between nicotine dependence and the functional contribution of the oral microbiota remain unknown in these populations.

METHODS: We evaluated the composition and functional capabilities of oral microbiota with relation to cigarette smoking in 105 adults through shotgun metagenomics using buccal swabs.

RESULTS: The oral microbiota composition in our study subjects was dominated by the phyla Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes, in addition to the genera Prevotella and Veillonella, similar to previously described westernized cohorts. Furthermore, the smoker's oral microbiota represented a significant abundance of Veillonella dispar, Leptotrichia spp. and Prevotella pleuritidis when compared to non-smokers. Within the smoking groups, differential relative abundance testing unveiled relative abundance of Streptobacillus hongkongensis, Fusobacterium massiliense, Prevotella bivia in high nicotine dependent compared to low nicotine dependent profiles based on Fagerström Test for Nicotine Dependence. Functional profiling showed marked differences between smokers and non-smokers. Smokers exhibited an enrichment of Tricarballylate utilization and Lactate racemization when compared to the non-smokers. According to their nicotine dependence, enrichment of Xanthosine utilization, p-Aminobenzoyl-Glutamate utilization, and multidrug efflux pump in Campylobacter jejuni biosynthesis modules were detected in the high nicotine dependent group.

CONCLUSIONS: These compositional and functional differences may provide critical insight on how variations in the oral microbiota could predispose to respiratory illnesses and smoke cessation relapse in cigarette smokers. In particular, the observed enrichment of Fusobacterium and Prevotella in the oral microbiota possibly suggests an intriguing linkage to gut and lung cancers.}, } @article {pmid33167516, year = {2020}, author = {Mogotsi, MT and Mwangi, PN and Bester, PA and Mphahlele, MJ and Seheri, ML and O'Neill, HG and Nyaga, MM}, title = {Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic Viruses.}, journal = {Viruses}, volume = {12}, number = {11}, pages = {}, pmid = {33167516}, issn = {1999-4915}, mesh = {Cohort Studies ; Feces/virology ; Gastrointestinal Tract/*virology ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Longitudinal Studies ; *Metagenome ; Phylogeny ; RNA Viruses/classification/genetics ; RNA, Viral/*genetics ; South Africa ; *Virome ; }, abstract = {Establishing a diverse gut microbiota after birth is essential for preventing illnesses later in life. However, little knowledge exists about the total viral population (virome) present in the gut of infants during the early developmental stage, with RNA viruses being generally overlooked. Therefore, this small pilot longitudinal study investigated the diversity and changes in the enteric RNA virome in healthy infants from South Africa. Faecal samples (n = 12) were collected from four infants at three time points (on average at 8, 13, and 25 weeks), and then sequenced on an Illumina MiSeq platform. The genomic analysis revealed a diverse population of human enteric viruses from the infants' stools, and changes in the enteric virome composition were observed over time. The Reoviridae family, more specifically the Rotavirus genus, was the most common and could be linked to viral shedding due to the administration of live-attenuated oral vaccines in South Africa, followed by the Picornaviridae family including parechoviruses, echoviruses, coxsackieviruses, enteroviruses, and polioviruses. Polioviruses were also linked to vaccine-related shedding. Astroviridae (astroviruses) and Caliciviridae (noroviruses) were present at low abundance. It is evident that an infant's gut is colonized by distinct viral populations irrespective of their health state. Further characterization of the human virome (with a larger participant pool) is imperative to provide more conclusive insights into the viral community structure and diversity that has been shown in the current study, despite the smaller sample size.}, } @article {pmid33167500, year = {2020}, author = {Kuo, MT and Chao, TL and Kuo, SF and Chien, CC and Chen, A and Lai, YH and Huang, YT}, title = {A Genomic Approach to Investigating Ocular Surface Microorganisms: Monitoring Core Microbiota on Eyelid Margin with a Dot hybridization Assay.}, journal = {International journal of molecular sciences}, volume = {21}, number = {21}, pages = {}, pmid = {33167500}, issn = {1422-0067}, support = {CMRPG8F0873//Chang Gung Research Proposal/ ; CMRPG8J1091//Chang Gung Research Proposal/ ; MOST 107-2314-B-182A-091-MY2//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/therapeutic use ; Bacteria/isolation & purification ; Cataract Extraction/adverse effects ; Endophthalmitis/etiology ; Eye/microbiology ; Eye Infections, Bacterial ; Eyelids/*microbiology ; Female ; Genomics/methods ; Humans ; Male ; Microbiota/*genetics ; Middle Aged ; Nucleic Acid Hybridization/*methods ; }, abstract = {A sound ocular surface microbiota has been recognized as a part of ocular surface health following a growing body of evidence from next-generation sequencing technique and metagenomic analysis. However, even from the perspective of contemporary precision medicine, it is difficult to directly apply these new technologies to clinical practice. Therefore, we proposed a model based on dot hybridization assay (DHA) to bridge conventional culture with a metagenomic approach in investigating and monitoring ocular surface microbiota. Endophthalmitis, mostly caused by bacterial infection, is the most severe complication of many intraocular surgeries, such as cataract surgery. Hazardous microorganisms hiding and proliferating in the ocular surface microbiota not only increase the risk of endophthalmitis but also jeopardize the effectiveness of the preoperative aseptic procedure and postoperative topical antibiotics. The DHA model enables the simultaneous assessment of bacterial bioburden, detection of target pathogens and microorganisms, and surveillance of methicillin/oxacillin resistance gene mecA in the ocular surface microbiota. This assay revealed heavier bacterial bioburden in men, compatible with a higher risk of endophthalmitis in male patients who underwent cataract surgery. No occurrence of endophthalmitis for these patients was compatible with non-hazardous microorganisms identified by specific dots for target pathogens. Moreover, the mecA dot detected oxacillin-resistant strains, of which culture failed to isolate. Therefore, the DHA model could provide an alternative genomic approach to investigate and monitor ocular surface microorganisms in clinical practice nowadays.}, } @article {pmid33167293, year = {2020}, author = {Vendruscolo, ECG and Mesa, D and Rissi, DV and Meyer, BH and de Oliveira Pedrosa, F and de Souza, EM and Cruz, LM}, title = {Microbial communities network analysis of anaerobic reactors fed with bovine and swine slurry.}, journal = {The Science of the total environment}, volume = {742}, number = {}, pages = {140314}, doi = {10.1016/j.scitotenv.2020.140314}, pmid = {33167293}, issn = {1879-1026}, mesh = {Anaerobiosis ; Animals ; Archaea/genetics ; Biofuels ; *Bioreactors ; Cattle ; Methane ; *Microbiota ; RNA, Ribosomal, 16S ; Swine ; }, abstract = {Anaerobic digestion can produce biogas as an eco-friendly energy source, driven by a microbial community-dependent process and, as such, suffer influences from many biotic and abiotic factors. Understanding the players and how they interact, the mechanisms involved, what the factors are, and how they influence the biogas process and production is an important way to better control it and make it more efficient. Metagenomic approach is a powerful tool to assess microbial diversity and further, allow correlating changes in microbial communities with multiple factors in virtually all environments. In the present study, we used metagenomic approach to assess microbial community structure changes in two biodigesters, differing in their biogas production capacity, architecture, and feed. A total of 1,440,096 reads of the 16S rRNA gene V4 region were obtained and analyzed. The main bacterial phyla were Firmicutes and Bacteroidetes in both biodigesters, but the biodiversity was greater in the Upflow Anaerobic Sludge Blanket (UASB) reactor fed with bovine manure than in the Continuous Stirred Tank Reactor (CSTR) fed with swine manure, which also correlated with an increase in biogas or methane production. Microbial community structure associated with biodigesters changed seasonally and depended on animal growth stage. Random forest algorithm analysis revealed key microbial taxa for each biodigester. Candidatus Cloacomonas, Methanospirillum, and Methanosphaera were the marker taxa for UASB and the archaea groups Methanobrevibacter and Candidatus Methanoplasma were the marker taxa for CSTR. A high abundance of Candidatus Methanoplasma and Marinimicrobia SAR406 clade suggested lower increments in methane production. Network analysis pointed to negative and positive associations and specific key groups, essential in maintaining the anaerobic digestion (AD) process, as being uncultured Parcubacteria bacteria, Candidatus Cloacomonas, and Candidatus Methanoplasma groups, whose functions in AD require investigation.}, } @article {pmid33166356, year = {2020}, author = {Zhang, X and Guo, B and Yi, N}, title = {Zero-Inflated gaussian mixed models for analyzing longitudinal microbiome data.}, journal = {PloS one}, volume = {15}, number = {11}, pages = {e0242073}, pmid = {33166356}, issn = {1932-6203}, mesh = {Algorithms ; Bacteria/genetics/isolation & purification ; Bacterial Load ; Computer Simulation ; Dysbiosis/microbiology ; Humans ; Longitudinal Studies ; *Microbiota ; Normal Distribution ; RNA, Ribosomal, 16S/genetics ; Software ; }, abstract = {MOTIVATION: The human microbiome is variable and dynamic in nature. Longitudinal studies could explain the mechanisms in maintaining the microbiome in health or causing dysbiosis in disease. However, it remains challenging to properly analyze the longitudinal microbiome data from either 16S rRNA or metagenome shotgun sequencing studies, output as proportions or counts. Most microbiome data are sparse, requiring statistical models to handle zero-inflation. Moreover, longitudinal design induces correlation among the samples and thus further complicates the analysis and interpretation of the microbiome data.

RESULTS: In this article, we propose zero-inflated Gaussian mixed models (ZIGMMs) to analyze longitudinal microbiome data. ZIGMMs is a robust and flexible method which can be applicable for longitudinal microbiome proportion data or count data generated with either 16S rRNA or shotgun sequencing technologies. It can include various types of fixed effects and random effects and account for various within-subject correlation structures, and can effectively handle zero-inflation. We developed an efficient Expectation-Maximization (EM) algorithm to fit the ZIGMMs by taking advantage of the standard procedure for fitting linear mixed models. We demonstrate the computational efficiency of our EM algorithm by comparing with two other zero-inflated methods. We show that ZIGMMs outperform the previously used linear mixed models (LMMs), negative binomial mixed models (NBMMs) and zero-inflated Beta regression mixed model (ZIBR) in detecting associated effects in longitudinal microbiome data through extensive simulations. We also apply our method to two public longitudinal microbiome datasets and compare with LMMs and NBMMs in detecting dynamic effects of associated taxa.}, } @article {pmid33166187, year = {2021}, author = {Wei, B and Wang, Y and Xiang, S and Jiang, Y and Chen, R and Hu, N}, title = {Alterations of gut microbiome in patients with type 2 diabetes mellitus who had undergone cholecystectomy.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {320}, number = {1}, pages = {E113-E121}, doi = {10.1152/ajpendo.00471.2020}, pmid = {33166187}, issn = {1522-1555}, mesh = {Adult ; Aged ; Bilophila ; *Cholecystectomy ; Computational Biology ; Diabetes Mellitus, Type 2/*microbiology ; Feces/microbiology ; Female ; Fusobacterium ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; Postoperative Period ; RNA, Ribosomal, 16S/metabolism ; Thyrotropin/pharmacology ; }, abstract = {Patients with type 2 diabetes mellitus (T2DM) have a high risk of developing cholecystic disease. The gut microbiota has been shown to be strongly associated with cholecystectomy and T2DM pathogenesis. However, alterations of the gut microbiome in patients with T2DM who had undergone cholecystectomy remain unexplored. In this study, the gut microbiomes of 14 long-term patients with T2DM who had undergone cholecystectomy (T2DIIC group) and 21 age- and/or sex-matched subjects with new-onset (T2DI group) and long-term (T2DII group) T2DM without cholecystectomy were assessed using 16S rRNA gene sequencing of stool samples. It was found that cholecystectomy could alleviate the decrease in Pielou's evenness and the increase in the relative abundances of the Firmicutes phylum and Lachnospira genus in long-term patients with T2DM compared with T2DII subjects. Moreover, cholecystectomy also significantly increased the relative abundance of the Fusobacteria phylum, as well as that of the Fusobacterium and Bilophila genera. Interestingly, the T2DIIC and T2DI groups showed higher similarities than the T2DII group with respect to patterns of gut microbiota composition and predicted gut metagenomes. In summary, cholecystectomy could partially alleviate long-term diabetes-induced dysbiosis of the gut microbiota composition and function, but alterations in T2DM patient health warrant further study.NEW & NOTEWORTHY The gut microbiome of long-term T2DM patients who had undergone cholecystectomy and age- and/or sex-matched subjects of new-onset and long-term T2DM without cholecystectomy was assessed using 16S rRNA gene sequencing in stool samples. The findings suggest that, cholecystectomy could partially alleviate long-term diabetes-induced dysbiosis of gut microbiome composition and function.}, } @article {pmid33164148, year = {2020}, author = {Mandal, R and Cano, R and Davis, CD and Hayashi, D and Jackson, SA and Jones, CM and Lampe, JW and Latulippe, ME and Lin, NJ and Lippa, KA and Piotrowski, P and Da Silva, SM and Swanson, KS and Wishart, DS}, title = {Workshop report: Toward the development of a human whole stool reference material for metabolomic and metagenomic gut microbiome measurements.}, journal = {Metabolomics : Official journal of the Metabolomic Society}, volume = {16}, number = {11}, pages = {119}, pmid = {33164148}, issn = {1573-3890}, support = {R01 GM120519/GM/NIGMS NIH HHS/United States ; R25 GM061151/GM/NIGMS NIH HHS/United States ; T32 GM075774/GM/NIGMS NIH HHS/United States ; R44 GM134710/GM/NIGMS NIH HHS/United States ; T34 GM007821/GM/NIGMS NIH HHS/United States ; }, mesh = {Diet ; Feces/chemistry/*microbiology ; *Gastrointestinal Microbiome ; Humans ; *Metabolome ; Metabolomics ; *Metagenome ; Metagenomics ; }, abstract = {INTRODUCTION: To date, there has been little effort to develop standards for metabolome-based gut microbiome measurements despite the significant efforts toward standard development for DNA-based microbiome measurements.

OBJECTIVES: The National Institute of Standards and Technology (NIST), The BioCollective (TBC), and the North America Branch of the International Life Sciences Institute (ILSI North America) are collaborating to extend NIST's efforts to develop a Human Whole Stool Reference Material for the purpose of method harmonization and eventual quality control.

METHODS: The reference material will be rationally designed for adequate quality assurance and quality control (QA/QC) for underlying measurements in the study of the impact of diet and nutrition on functional aspects of the host gut microbiome and relationships of those functions to health. To identify which metabolites deserve priority in their value assignment, NIST, TBC, and ILSI North America jointly conducted a workshop on September 12, 2019 at the NIST campus in Gaithersburg, Maryland. The objective of the workshop was to identify metabolites for which evidence indicates relevance to health and disease and to decide on the appropriate course of action to develop a fit-for-purpose reference material.

RESULTS: This document represents the consensus opinions of workshop participants and co-authors of this manuscript, and provides additional supporting information. In addition to developing general criteria for metabolite selection and a preliminary list of proposed metabolites, this paper describes some of the strengths and limitations of this initiative given the current state of microbiome research.

CONCLUSIONS: Given the rapidly evolving nature of gut microbiome science and the current state of knowledge, an RM (as opposed to a CRM) measured for multiple metabolites is appropriate at this stage. As the science evolves, the RM can evolve to match the needs of the research community. Ultimately, the stool RM may exist in sequential versions. Beneficial to this evolution will be a clear line of communication between NIST and the stakeholder community to ensure alignment with current scientific understanding and community needs.}, } @article {pmid33162984, year = {2020}, author = {Hu, Y and Chen, J and Xu, Y and Zhou, H and Huang, P and Ma, Y and Gao, M and Cheng, S and Zhou, H and Lv, Z}, title = {Alterations of Gut Microbiome and Metabolite Profiling in Mice Infected by Schistosoma japonicum.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {569727}, pmid = {33162984}, issn = {1664-3224}, mesh = {Animals ; Biomarkers ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome ; Host-Parasite Interactions/*immunology ; *Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Mice ; RNA, Ribosomal, 16S/genetics ; *Schistosoma japonicum ; Schistosomiasis japonica/*immunology/*metabolism/*parasitology ; }, abstract = {Schistosoma japonicum (S. japonicum) is one of the etiological agents of schistosomiasis, a widespread zoonotic parasitic disease. However, the mechanism of the balanced co-existence between the host immune system and S. japonicum as well as their complex interaction remains unclear. In this study, 16S rRNA gene sequencing, combined with metagenomic sequencing approach as well as ultraperformance liquid chromatography-mass spectrometry metabolic profiling, was applied to demonstrate changes in the gut microbiome community structure during schistosomiasis progression, the functional interactions between the gut bacteria and S. japonicum infection in BALB/c mice, and the dynamic metabolite changes of the host. The results showed that both gut microbiome and the metabolites were significantly altered at different time points after the infection. Decrease in richness and diversity as well as differed composition of the gut microbiota was observed in the infected status when compared with the uninfected status. At the phylum level, the gut microbial communities in all samples were dominated by Firmicutes, Bacteroidetes, Proteobacteria, and Deferribacteres, while at the genus level, Lactobacillus, Lachnospiraceae NK4A136 group, Bacteroides, Staphylococcus, and Alloprevotella were the most abundant. After exposure, Roseburia, and Ruminococcaceae UCG-014 decreased, while Staphylococcus, Alistipes, and Parabacteroides increased, which could raise the risk of infections. Furthermore, LEfSe demonstrated several bacterial taxa that could discriminate between each time point of S. japonicum infection. Besides that, metagenomic analysis illuminated that the AMP-activated protein kinase (AMPK) signaling pathway and the chemokine signaling pathway were significantly perturbed after the infection. Phosphatidylcholine and colfosceril palmitate in serum as well as xanthurenic acid, naphthalenesulfonic acid, and pimelylcarnitine in urine might be metabolic biomarkers due to their promising diagnostic potential at the early stage of the infection. Alterations of glycerophospholipid and purine metabolism were also discovered in the infection. The present study might provide further understanding of the mechanisms during schistosome infection in aspects of gut microbiome and metabolites, and facilitate the discovery of new targets for early diagnosis and prognostic purposes. Further validations of potential biomarkers in human populations are necessary, and the exploration of interactions among S. japonicum, gut microbiome, and metabolites is to be deepened in the future.}, } @article {pmid33162946, year = {2020}, author = {Barajas, HR and Martínez-Sánchez, S and Romero, MF and Álvarez, CH and Servín-González, L and Peimbert, M and Cruz-Ortega, R and García-Oliva, F and Alcaraz, LD}, title = {Testing the Two-Step Model of Plant Root Microbiome Acquisition Under Multiple Plant Species and Soil Sources.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {542742}, pmid = {33162946}, issn = {1664-302X}, abstract = {The two-step model for plant root microbiomes considers soil as the primary microbial source. Active selection of the plant's bacterial inhabitants results in a biodiversity decrease toward roots. We collected sixteen samples of in situ ruderal plant roots and their soils and used these soils as the main microbial input for single genotype tomatoes grown in a greenhouse. Our main goal was to test the soil influence in the structuring of rhizosphere microbiomes, minimizing environmental variability, while testing multiple plant species. We massively sequenced the 16S rRNA and shotgun metagenomes of the soils, in situ plants, and tomato roots. We identified a total of 271,940 bacterial operational taxonomic units (OTUs) within the soils, rhizosphere and endospheric microbiomes. We annotated by homology a total of 411,432 (13.07%) of the metagenome predicted proteins. Tomato roots did follow the two-step model with lower α-diversity than soil, while ruderal plants did not. Surprisingly, ruderal plants are probably working as a microenvironmental oasis providing moisture and plant-derived nutrients, supporting larger α-diversity. Ruderal plants and their soils are closer according to their microbiome community composition than tomato and its soil, based on OTUs and protein comparisons. We expected that tomato β-diversity clustered together with their soil, if it is the main rhizosphere microbiome structuring factor. However, tomato microbiome β-diversity was associated with plant genotype in most samples (81.2%), also supported by a larger set of enriched proteins in tomato rhizosphere than soil or ruderals. The most abundant bacteria found in soils was the Actinobacteria Solirubrobacter soli, ruderals were dominated by the Proteobacteria Sphingomonas sp. URGHD0057, and tomato mainly by the Bacteroidetes Ohtaekwangia koreensis, Flavobacterium terrae, Niastella vici, and Chryseolinea serpens. We calculated a metagenomic tomato root core of 51 bacterial genera and 2,762 proteins, which could be the basis for microbiome-oriented plant breeding programs. We attributed a larger diversity in ruderal plants roots exudates as an effect of the moisture and nutrient acting as a microbial harbor. The tomato and ruderal metagenomic differences are probably due to plant domestication trade-offs, impacting plant-bacteria interactions.}, } @article {pmid33161546, year = {2021}, author = {Yeoh, YK}, title = {Removing Host-derived DNA Sequences from Microbial Metagenomes via Mapping to Reference Genomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2232}, number = {}, pages = {147-153}, doi = {10.1007/978-1-0716-1040-4_13}, pmid = {33161546}, issn = {1940-6029}, mesh = {Animals ; Arthropods/microbiology ; Base Sequence/*genetics ; Eukaryota/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota ; Plants/microbiology ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {DNA sequencing has become a common tool in environmental microbial ecology, facilitating characterization of microbial populations as well as complex microbial communities by circumventing culture bottlenecks. However, certain samples especially from host-associated environments (rhizosphere, human tissue) or complex communities (soils) can contain a high degree of DNA sequences derived from hosts (plants, human) or other organisms of non-interest (arthropods, unicellular eukaryotes). This chapter presents a simple in silico method to remove contaminating sequences in metagenomes based on aligning sequences to reference genomes of the target organism.}, } @article {pmid33161534, year = {2021}, author = {Wassermann, B and Rybakova, D and Adam, E and Zachow, C and Bernhard, M and Müller, M and Mancinelli, R and Berg, G}, title = {Studying Seed Microbiomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2232}, number = {}, pages = {1-21}, doi = {10.1007/978-1-0716-1040-4_1}, pmid = {33161534}, issn = {1940-6029}, mesh = {Endophytes/genetics/growth & development ; Germination/genetics ; In Situ Hybridization, Fluorescence/*methods ; Metagenome/genetics ; Microbiota/*genetics ; Plants/*genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; Seeds/*genetics/microbiology ; }, abstract = {Recent studies indicate that seed microbiomes affect germination and plant performance. However, the interplay between seed microbiota and plant health is still poorly understood. To get a complete picture of the system, a comprehensive analysis is required, comprising culture-dependent and culture-independent techniques. In this chapter, we provide a combination of methods that are established and optimized for the analysis of the seed microbiome. These include methods to: (1) activate and cultivate dormant seed microbiota, (2) analyze microbiota in germinated seeds (with and without substrate), (3) quantify microbial DNA via real-time PCR, (4) deplete host DNA for amplicon and metagenome analysis, and (5) visualize seed endophytes in microtomed sections using fluorescent in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM). A deep understanding of the seed microbiome and its functions can help in developing new seed treatments and breeding strategies for sustainable agriculture.}, } @article {pmid33161088, year = {2021}, author = {Kajale, S and Jani, K and Sharma, A}, title = {Contribution of archaea and bacteria in sustaining climate change by oxidizing ammonia and sulfur in an Arctic Fjord.}, journal = {Genomics}, volume = {113}, number = {1 Pt 2}, pages = {1272-1276}, doi = {10.1016/j.ygeno.2020.11.005}, pmid = {33161088}, issn = {1089-8646}, mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Arctic Regions ; Bacteria/genetics/*metabolism ; *Climate Change ; Microbiota ; Oxidation-Reduction ; Sulfur/*metabolism ; }, abstract = {The present study attempts to investigate the microbial communities and their potential to oxidize ammonia and sulfur at different sites of Arctic Fjord by targeted metagenomics. The high throughput sequencing revealed archaeal Thaumarchaeota (79.3%), Crenarchaeota (10.9%), Euryarchaeota (5.4%), and Woesearchaeota (2.9%) across different depths. In contrast, the bacterial communities depict predominance of Proteobacteria (52.6%), which comprises of dominant genera viz. Sulfurovum (11.2%) and Sulfurimonas (6.3%). Characterizing the metabolic potential of microbial communities with prime focus on the ammonia and sulfur cycling revealed the presence of amoABC and narGHYZ/ nxrAB genes encoding key enzymes. The ammonia cycling coupled with an augmentation of members of Nitrosopumilus belonging to the phylum Thaumarcheaota suggests the vital role of archaeal communities. Similarly, the persistence of chemolithoautotrophic members of Sulfurovum and Sulfurimonas along with the anaerobic genera Desulfocapsa and Desulfobulbus harboring SOX (sulfur-oxidation) system indicates the modulatory role of bacterial communities in sulfur cycling.}, } @article {pmid33160244, year = {2020}, author = {Galli, J and Calò, L and Posteraro, B and Rossi, G and Sterbini, FP and Paludetti, G and Sanguinetti, M}, title = {Pediatric oropharyngeal microbiome: Mapping in chronic tonsillitis and tonsillar hypertrophy.}, journal = {International journal of pediatric otorhinolaryngology}, volume = {139}, number = {}, pages = {110478}, doi = {10.1016/j.ijporl.2020.110478}, pmid = {33160244}, issn = {1872-8464}, mesh = {Child ; Humans ; Hypertrophy ; *Microbiota ; Palatine Tonsil ; Recurrence ; *Tonsillitis ; }, abstract = {OBJECTIVES: Aim of our study was to map the adenotonsillar lymphoid tissues' microbiome identifying its potential etiopathogenetic role in children affected by chronic tonsillitis or tonsillar hypertrophy with Obstructive Sleep Apnea Syndrome (OSAS).

METHODS: In our study, we examined tonsillar swabs from healthy children and children affected by chronic tonsillitis or by tonsillar hypertrophy with Obstructive Sleep Apnea Syndrome (OSAS). Microbiome's analysis was performed and bacterial 16Sr RNA gene was sequenced according to metagenomic principles. Variability was described according to the biodiversity concept, indicating species found in a certain environment and changes they undergo adapting to different environmental conditions.

RESULTS: The most significant differences concern variation of microbes in a single sample (alpha diversity) of some phyla in children affected by chronic tonsillitis compared with alpha diversity in healthy children and in children affected by OSAS with tonsillar hyperplasia. Proteobacteria are prevalent in chronic tonsillitis group, Fusobacteria and Spirochete in OSAS and Firmicutes, Actinobacteria, and Bacteroidetes were found in healthy children. Finally, comparison between the groups showed that children with OSAS with tonsillar hypertrophy had a higher presence of the Fusobacterium genus.

CONCLUSION: Recurrent upper airway inflammatory and/or infectious processes are polymicrobial; chronicity of such processes appear to be related to variations in microbiome's composition and interaction among various taxonomic units. Knowledge of the microbiomes' composition together with traditional clinical biomarkers can also determine relationships between oropharyngeal microbiome and systemic pathologies to determine preventive changes in lifestyle, eating habits, environmental exposure and use of probiotics.}, } @article {pmid33158461, year = {2020}, author = {Liu, L and Wang, Y and Che, Y and Chen, Y and Xia, Y and Luo, R and Cheng, SH and Zheng, C and Zhang, T}, title = {High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {155}, pmid = {33158461}, issn = {2049-2618}, mesh = {Ammonium Compounds/*metabolism ; Anaerobiosis ; Bacteria/*genetics/*metabolism ; *Chemoautotrophic Growth ; Genome, Bacterial/*genetics ; Metagenome/*genetics ; Microbiota/*genetics ; Nitrites/*metabolism ; Oxidation-Reduction ; }, abstract = {BACKGROUND: Genome-centric approaches are widely used to investigate microbial compositions, dynamics, ecology, and interactions within various environmental systems. Hundreds or even thousands of genomes could be retrieved in a single study contributed by the cost-effective short-read sequencing and developed assembly/binning pipelines. However, conventional binning methods usually yield highly fragmented draft genomes that limit our ability to comprehensively understand these microbial communities. Thus, to leverage advantage of both the long and short reads to retrieve more complete genomes from environmental samples is a must-do task to move this direction forward.

RESULTS: Here, we used an iterative hybrid assembly (IHA) approach to reconstruct 49 metagenome-assembled genomes (MAGs), including 27 high-quality (HQ) and high-contiguity (HC) genomes with contig number ≤ 5, eight of which were circular finished genomes from a partial-nitritation anammox (PNA) reactor. These 49 recovered MAGs (43 MAGs encoding full-length rRNA, average N50 of 2.2 Mbp), represented the majority (92.3%) of the bacterial community. Moreover, the workflow retrieved HQ and HC MAGs even with an extremely low coverage (relative abundance < 0.1%). Among them, 34 MAGs could not be assigned to the genus level, indicating the novelty of the genomes retrieved using the IHA method proposed in this study. Comparative analysis of HQ MAG pairs reconstructed using two methods, i.e., hybrid and short reads only, revealed that identical genes in the MAG pairs represented 87.5% and 95.5% of the total gene inventory of hybrid and short reads only assembled MAGs, respectively. In addition, the first finished anammox genome of the genus Ca. Brocadia reconstructed revealed that there were two identical hydrazine synthase (hzs) genes, providing the exact gene copy number of this crucial phylomarker of anammox at the genome level.

CONCLUSIONS: Our results showcased the high-quality and high-contiguity genome retrieval performance and demonstrated the feasibility of complete genome reconstruction using the IHA workflow from the enrichment system. These (near-) complete genomes provided a high resolution of the microbial community, which might help to understand the bacterial repertoire of anammox-associated systems. Combined with other validation experiments, the workflow can enable a detailed view of the anammox or other similar enrichment systems. Video Abstract.}, } @article {pmid33157257, year = {2021}, author = {Kelsey, CM and Prescott, S and McCulloch, JA and Trinchieri, G and Valladares, TL and Dreisbach, C and Alhusen, J and Grossmann, T}, title = {Gut microbiota composition is associated with newborn functional brain connectivity and behavioral temperament.}, journal = {Brain, behavior, and immunity}, volume = {91}, number = {}, pages = {472-486}, doi = {10.1016/j.bbi.2020.11.003}, pmid = {33157257}, issn = {1090-2139}, mesh = {Adult ; Brain ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Temperament ; }, abstract = {The gut microbiome appears to play an important role in human health and disease. However, only little is known about how variability in the gut microbiome contributes to individual differences during early and sensitive stages of brain and behavioral development. The current study examined the link between gut microbiome, brain, and behavior in newborn infants (N = 63; M [age] = 25 days). Infant gut microbiome diversity was measured from stool samples using metagenomic sequencing, infant functional brain network connectivity was assessed using a resting state functional near infrared spectroscopy (rs-fNIRS) procedure, and infant behavioral temperament was assessed using parental report. Our results show that gut microbiota composition is linked to individual variability in brain network connectivity, which in turn mediated individual differences in behavioral temperament, specifically negative emotionality, among infants. Furthermore, virulence factors, possibly indexing pathogenic activity, were associated with differences in brain network connectivity linked to negative emotionality. These findings provide novel insights into the early developmental origins of the gut microbiome-brain axis and its association with variability in important behavioral traits. This suggests that the gut microbiome is an important biological factor to consider when studying human development and health.}, } @article {pmid33155741, year = {2021}, author = {Liu, F and Kou, D and Chen, Y and Xue, K and Ernakovich, JG and Chen, L and Yang, G and Yang, Y}, title = {Altered microbial structure and function after thermokarst formation.}, journal = {Global change biology}, volume = {27}, number = {4}, pages = {823-835}, doi = {10.1111/gcb.15438}, pmid = {33155741}, issn = {1365-2486}, support = {31825006//National Natural Science Foundation of China/ ; 31988102//National Natural Science Foundation of China/ ; 91837312//National Natural Science Foundation of China/ ; 2019QZKK0106//Second Tibetan Plateau Scientific Expedition and Research/ ; 2019QZKK0302//Second Tibetan Plateau Scientific Expedition and Research/ ; QYZDB-SSW-SMC049//Chinese Academy of Sciences/ ; }, mesh = {Carbon ; *Microbiota ; *Permafrost ; Soil ; Soil Microbiology ; }, abstract = {Permafrost thaw could induce substantial carbon (C) emissions to the atmosphere, and thus trigger a positive feedback to climate warming. As the engine of biogeochemical cycling, soil microorganisms exert a critical role in mediating the direction and strength of permafrost C-climate feedback. However, our understanding about the impacts of thermokarst (abrupt permafrost thaw) on microbial structure and function remains limited. Here we employed metagenomic sequencing to analyze changes in topsoil (0-15 cm) microbial communities and functional genes along a permafrost thaw sequence (1, 10, and 16 years since permafrost collapse) on the Tibetan Plateau. By combining laboratory incubation and a two-pool model, we then explored changes in soil labile and stable C decomposition along the thaw sequence. Our results showed that topsoil microbial α-diversity decreased, while the community structure and functional gene abundance did not exhibit any significant change at the early stage of collapse (1 year since collapse) relative to non-collapsed control. However, as the time since the collapse increased, both the topsoil microbial community structure and functional genes differed from the control. Abundances of functional genes involved in labile C degradation decreased while those for stable C degradation increased at the late stage of collapse (16 years since collapse), largely driven by changes in substrate properties along the thaw sequence. Accordingly, faster stable C decomposition occurred at the late stage of collapse compared to the control, which was associated with the increase in relative abundance of functional genes for stable C degradation. These results suggest that upland thermokarst alters microbial structure and function, particularly enhances soil stable C decomposition by modulating microbial functional genes, which could reinforce a warmer climate over the decadal timescale.}, } @article {pmid33152902, year = {2020}, author = {Dalal, N and Jalandra, R and Sharma, M and Prakash, H and Makharia, GK and Solanki, PR and Singh, R and Kumar, A}, title = {Omics technologies for improved diagnosis and treatment of colorectal cancer: Technical advancement and major perspectives.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {131}, number = {}, pages = {110648}, doi = {10.1016/j.biopha.2020.110648}, pmid = {33152902}, issn = {1950-6007}, mesh = {Colorectal Neoplasms/*diagnosis/genetics/metabolism/*therapy ; Gastrointestinal Microbiome ; Humans ; Metabolomics ; Metagenomics ; Proteomics ; Transcriptome ; }, abstract = {Colorectal cancer (CRC) ranks third among the most commonly occurring cancers worldwide, and it causes half a million deaths annually. Alongside mechanistic study for CRC detection and treatment by conventional techniques, new technologies have been developed to study CRC. These technologies include genomics, transcriptomics, proteomics, and metabolomics which elucidate DNA markers, RNA transcripts, protein and, metabolites produced inside the colon and rectum part of the gut. All these approaches form the omics arena, which presents a remarkable opportunity for the discovery of novel prognostic, diagnostic and therapeutic biomarkers and also delineate the underlying mechanism of CRC causation, which may further help in devising treatment strategies. This review also mentions the latest developments in metagenomics and culturomics as emerging evidence suggests that metagenomics of gut microbiota has profound implications in the causation, prognosis, and treatment of CRC. A majority of bacteria cannot be studied as they remain unculturable, so culturomics has also been strengthened to develop culture conditions suitable for the growth of unculturable bacteria and identify unknown bacteria. The overall purpose of this review is to succinctly evaluate the application of omics technologies in colorectal cancer research for improving the diagnosis and treatment strategies.}, } @article {pmid33152096, year = {2020}, author = {Qiu, H and Gu, L and Sun, B and Zhang, J and Zhang, M and He, S and An, S and Leng, X}, title = {Metagenomic Analysis Revealed that the Terrestrial Pollutants Override the Effects of Seasonal Variation on Microbiome in River Sediments.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {105}, number = {6}, pages = {892-898}, doi = {10.1007/s00128-020-03033-2}, pmid = {33152096}, issn = {1432-0800}, support = {2017ZX07602-002//Major Science and Technology Program for Water Pollution Control and Treatment/ ; }, mesh = {Environmental Monitoring/*methods ; Environmental Pollutants ; Geologic Sediments/chemistry/*microbiology ; Microbiota/*genetics ; Rivers/chemistry ; Seasons ; Water Pollutants, Chemical/*analysis ; }, abstract = {Researching the structure and function of sediment microbiome contribute to understanding the response of microbiome to external disturbances. However, seasonal changes in sediment microbiome with different terrestrial pollutants input have not yet been clearly understood. Metagenomic sequencing was used to evaluate the effects of seasonal variations and different land use types on sediment microbiome. Results showed that the differences in structure and functions of sediment microbiome among different land use types were obviously greater than different seasons. This indicated that the terrestrial pollutants weakened the effects of seasonal variations on shaping the sediment microbiome. The significant differences in sediment properties under the input of different terrestrial pollutants was observed, but no obvious differences between seasons, which may be the reason why terrestrial pollutants override the effects of seasonal variation on the sediment microbiome. Overall, the results extended our understanding of the impacts of seasonal variation and terrestrial pollutants on river sediment microbiome.}, } @article {pmid33149234, year = {2020}, author = {Siddiqui, S and Bao, D and Doyle-Meyers, L and Dufour, J and Wu, Y and Liu, YZ and Ling, B}, title = {Alterations of the gut bacterial microbiota in rhesus macaques with SIV infection and on short- or long-term antiretroviral therapy.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {19056}, pmid = {33149234}, issn = {2045-2322}, support = {R01 MH102144/MH/NIMH NIH HHS/United States ; P51 OD011104/OD/NIH HHS/United States ; R01 MH116844/MH/NIMH NIH HHS/United States ; R01 AI093307/AI/NIAID NIH HHS/United States ; R01 NS104016/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Antiretroviral Therapy, Highly Active ; Biodiversity ; Biomarkers ; Duration of Therapy ; Dysbiosis/*etiology/immunology ; Gastrointestinal Microbiome/*drug effects/immunology ; Lipopolysaccharides/blood/metabolism ; Macaca mulatta ; Metagenome ; Metagenomics ; Simian Acquired Immunodeficiency Syndrome/*drug therapy/immunology/virology ; *Simian Immunodeficiency Virus/drug effects/immunology ; }, abstract = {Gut dysbiosis and microbial translocation are associated with chronic systemic immune activation and inflammation in HIV-1 infection. However, the extent of restoration of gut microbiota in HIV-1 patients with short or long-term antiretroviral therapy (ART) is unclear. To understand the impact of ART on the gut microbiota, we used the rhesus macaque model of SIV infection to characterize and compare the gut microbial community upon SIV infection and during ART. We observed altered taxonomic compositions of gut microbiota communities upon SIV infection and at different time points of ART. SIV-infected animals showed decreased diversity of gut microbiome composition, while the ART group appeared to recover towards the diversity level of the healthy control. Animals undergoing ART for various lengths of time were observed to have differential gut bacterial abundance across different time points. In addition, increased blood lipopolysaccharide (LPS) levels during SIV infection were reduced to near normal upon ART, indicating that microbial translocation and immune activation can be improved during therapy. In conclusion, while short ART may be related to transient increase of certain pathogenic bacterial microbiome, ART may promote microbiome diversity compromised by SIV infection, improve the gut microbiota towards the healthy compositions and alleviate immune activation.}, } @article {pmid33148984, year = {2020}, author = {Smibert, OC and Trubiano, JA and Slavin, MA and Kwong, JC}, title = {An infectious diseases perspective on the microbiome and allogeneic stem cell transplant.}, journal = {Current opinion in infectious diseases}, volume = {33}, number = {6}, pages = {426-432}, doi = {10.1097/QCO.0000000000000683}, pmid = {33148984}, issn = {1473-6527}, mesh = {Animals ; Anti-Bacterial Agents/adverse effects ; Communicable Diseases/epidemiology/*microbiology ; Gastrointestinal Microbiome ; Graft vs Host Disease/epidemiology/microbiology ; Hematopoietic Stem Cell Transplantation/adverse effects ; Humans ; Metagenomics ; *Microbiota ; Observational Studies as Topic ; Prospective Studies ; Stem Cell Transplantation/*adverse effects ; T-Lymphocytes, Regulatory/metabolism ; }, abstract = {PURPOSE OF REVIEW: The gut microbiome presents a novel source of diagnostic and therapeutic potential to modify post allogeneic stem cell transplant complications. There is an explosion of interest in microbiome research, mostly in the form of single-centre prospective time-series cohorts utilizing a variety of sampling frequencies and metagenomic technologies to sequence the microbiome. The purpose of this review is to summarize important recent publications and contextualize them within what has already been described in this rapidly growing field.

RECENT FINDING: Results from observational human cohort and animal transplant models add to the growing body of evidence that the microbiome modulates the immunopathogenesis of posttransplant complications. This is particularly the case for recipients of grafts replete with T cells where the evidence that acute graft-versus-host disease is mediated by anaerobic commensal-associated short-chain fatty acids, which interact with mucosa-associated (CD4FOXP3) T-regulatory cells.

SUMMARY: Future human research into the role of the microbiome in allogeneic stem transplant should incorporate rigorous and considered experimental design in addition to next-generation sequencing technology to better portray microbiome functional potential and active gene expression. In combination with host immune phenotyping, which would facilitate a robust understanding of the host--microbiome interaction that is required before meaningful translation into clinical diagnostics and therapeutics can be expected.}, } @article {pmid33148818, year = {2020}, author = {Garner, RE and Gregory-Eaves, I and Walsh, DA}, title = {Sediment Metagenomes as Time Capsules of Lake Microbiomes.}, journal = {mSphere}, volume = {5}, number = {6}, pages = {}, pmid = {33148818}, issn = {2379-5042}, mesh = {Bacteria/classification/*genetics/isolation & purification/virology ; Bacteriophages/genetics ; Canada ; Genetic Variation ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; *Metagenome ; Microbiota/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The reconstruction of ecological time series from lake sediment archives can retrace the environmental impact of human activities. Molecular genetic approaches in paleolimnology have provided unprecedented access to DNA time series, which record evidence of the microbial ecologies that underlaid historical lake ecosystems. Such studies often rely on single-gene surveys, and consequently, the full diversity of preserved microorganisms remains unexplored. In this study, we probed the diversity archived in contemporary and preindustrial sediments by comparative shotgun metagenomic analysis of surface water and sediment samples from three eastern Canadian lakes. In a strategy that was aimed at disentangling historical DNA from the indigenous sediment background, microbial preservation signals were captured by mapping sequence similarities between sediment metagenome reads and reference surface water metagenome assemblies. We detected preserved Cyanobacteria, diverse bacterioplankton, microeukaryotes, and viruses in sediment metagenomes. Among the preserved microorganisms were important groups never before reported in paleolimnological reconstructions, including bacteriophages (Caudovirales) and ubiquitous freshwater Betaproteobacteria (Polynucleobacter and Limnohabitans). In contrast, ultramicroscopic Actinobacteria ("Candidatus Nanopelagicales") and Alphaproteobacteria (Pelagibacterales) were apparently not well preserved in sediment metagenomes even though they were numerically dominant in surface water metagenomes. Overall, our study explored a novel application of whole-metagenome shotgun sequencing for discovering the DNA remains of a broad diversity of microorganisms preserved in lake sediments. The recovery of diverse microbial time series supports the taxonomic expansion of microbiome reconstructions and the development of novel microbial paleoindicators.IMPORTANCE Lakes are critical freshwater resources under mounting pressure from climate change and other anthropogenic stressors. The reconstruction of ecological time series from sediment archives with paleolimnological techniques has been shown to be an effective means of understanding how humans are modifying lake ecosystems over extended timescales. In this study, we combined shotgun DNA sequencing with a novel comparative analysis of surface water and sediment metagenomes to expose the diversity of microorganisms preserved in lake sediments. The detection of DNA from a broad diversity of preserved microbes serves to more fully reconstruct historical microbiomes and describe preimpact lake conditions.}, } @article {pmid33147725, year = {2020}, author = {Herak Bosnar, M and Ćetković, H and Harcet, M}, title = {Genetics of Marine Organisms Associated with Human Health.}, journal = {Marine drugs}, volume = {18}, number = {11}, pages = {}, pmid = {33147725}, issn = {1660-3397}, mesh = {Animals ; Aquatic Organisms/classification/*genetics/metabolism ; Biological Products/isolation & purification/*therapeutic use ; *Genome ; Health Status ; Humans ; Marine Toxins/*adverse effects/metabolism ; Risk Assessment ; }, abstract = {Marine habitats harbour a large variety of organisms that belong to diverse taxa; from bacteria and unicellular eukaryotes to fungi, animals, and plants. Although we have only started to understand the diversity and structure of marine communities, it is clear that numerous marine species have or might have an impact on human health. Some are a source of natural products with potential or actual medical applications, others are toxic and harmful to humans, and some are used in biomedical research to help understand the molecular basis of human diseases. New molecular genetics and genomic methods provide powerful and ever more indispensable tools for studying marine organisms and all aspects of their influence on human health. Herein, we present work using the latest research, which mostly uses genomics, to tackle the questions related with the topic of the issue.}, } @article {pmid33145903, year = {2021}, author = {Xiao, E and Cui, J and Sun, W and Jiang, S and Huang, M and Kong, D and Wu, Q and Xiao, T and Sun, X and Ning, Z}, title = {Root microbiome assembly of As-hyperaccumulator Pteris vittata and its efficacy in arsenic requisition.}, journal = {Environmental microbiology}, volume = {23}, number = {4}, pages = {1959-1971}, doi = {10.1111/1462-2920.15299}, pmid = {33145903}, issn = {1462-2920}, mesh = {*Arsenic ; Biodegradation, Environmental ; *Microbiota ; Plant Roots ; *Pteris ; *Soil Pollutants/analysis ; }, abstract = {The assemblage of root-associated microorganisms plays important roles in improving their capability to adapt to environmental stress. Metal(loid) hyperaccumulators exhibit disparate adaptive capability compared to that of non-hyperaccumulators when faced with elevated contents of metal(loid)s. However, knowledge of the assemblage of root microbes of hyperaccumulators and their ecological roles in plant growth is still scarce. The present study used Pteris vittata as a model plant to study the microbial assemblage and its beneficial role in plant growth. We demonstrated that the assemblage of microbes from the associated bulk soil to the root compartment was based on their lifestyles. We used metagenomic analysis and identified that the assembled microbes were primarily involved in root-microbe interactions in P. vittata root. Notably, we identified that the assembled root microbiome played an important role in As requisition, which promoted the fitness and growth of P. vittata. This study provides new insights into the root microbiome and potential valuable knowledge to understand how the root microbiome contributes to the fitness of its host.}, } @article {pmid33145846, year = {2021}, author = {Hohenlohe, PA and Funk, WC and Rajora, OP}, title = {Population genomics for wildlife conservation and management.}, journal = {Molecular ecology}, volume = {30}, number = {1}, pages = {62-82}, pmid = {33145846}, issn = {1365-294X}, mesh = {Animals ; Animals, Wild/genetics ; Biodiversity ; *Conservation of Natural Resources ; *Genetics, Population ; Metagenomics ; }, abstract = {Biodiversity is under threat worldwide. Over the past decade, the field of population genomics has developed across nonmodel organisms, and the results of this research have begun to be applied in conservation and management of wildlife species. Genomics tools can provide precise estimates of basic features of wildlife populations, such as effective population size, inbreeding, demographic history and population structure, that are critical for conservation efforts. Moreover, population genomics studies can identify particular genetic loci and variants responsible for inbreeding depression or adaptation to changing environments, allowing for conservation efforts to estimate the capacity of populations to evolve and adapt in response to environmental change and to manage for adaptive variation. While connections from basic research to applied wildlife conservation have been slow to develop, these connections are increasingly strengthening. Here we review the primary areas in which population genomics approaches can be applied to wildlife conservation and management, highlight examples of how they have been used, and provide recommendations for building on the progress that has been made in this field.}, } @article {pmid33145361, year = {2020}, author = {Li, R and Pang, Z and Zhou, Y and Fallah, N and Hu, C and Lin, W and Yuan, Z}, title = {Metagenomic Analysis Exploring Taxonomic and Functional Diversity of Soil Microbial Communities in Sugarcane Fields Applied with Organic Fertilizer.}, journal = {BioMed research international}, volume = {2020}, number = {}, pages = {9381506}, pmid = {33145361}, issn = {2314-6141}, mesh = {Acidobacteria/genetics/isolation & purification/metabolism ; Actinobacteria/genetics/isolation & purification/metabolism ; Bacteria/genetics/isolation & purification/metabolism ; Chloroflexi/genetics/isolation & purification/metabolism ; Crops, Agricultural/metabolism/*microbiology ; Energy Metabolism/genetics ; Humans ; Manure/*microbiology ; *Metagenome ; Microbiota/*genetics ; Nucleotides/metabolism ; Phylogeny ; Principal Component Analysis ; Proteobacteria/genetics/isolation & purification/metabolism ; Saccharum/metabolism/*microbiology ; Soil/chemistry ; *Soil Microbiology ; Sucrose/metabolism ; Sulfates/metabolism ; }, abstract = {Organic fertilizers are critically important to soil fertility, microbial communities, and sustainable agricultural strategies. We compared the effect of two fertilizer groups (organic+chemical fertilizer: OM, chemical fertilizer: CK) on sugarcane growth, by observing the difference in microbial communities and functions, soil nutrient status, and agronomic characters of sugarcane. The results showed that the sugar content and yield of sugarcane increased significantly under organic fertilizer treatment. We believe that the increased soil nutrient status and soil microorganisms are the reasons for this phenomenon. In addition, redundancy analysis (RDA) shows that the soil nutrient condition has a major impact on the soil microbial community. In comparison with CK, the species richness of Acidobacteria, Proteobacteria, Chloroflexi, and Gemmatimonadetes as well as the functional abundance of nucleotide metabolism and energy metabolism increased significantly in the OM field. Moreover, compared with CK, genes related to the absorption and biosynthesis of sulfate were more prominent in OM. Therefore, consecutive organic fertilizer application could be an effective method in reference to sustainable production of sugarcane.}, } @article {pmid33141656, year = {2020}, author = {Parras-Moltó, M and Aguirre de Cárcer, D}, title = {A comprehensive human minimal gut metagenome extends the host's metabolic potential.}, journal = {Microbial genomics}, volume = {6}, number = {11}, pages = {}, pmid = {33141656}, issn = {2057-5858}, mesh = {Bacteria/*genetics/metabolism ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metagenome/*genetics ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Accumulating evidence suggests that humans could be considered as holobionts in which the gut microbiota play essential functions. Initial metagenomic studies reported a pattern of shared genes in the gut microbiome of different individuals, leading to the definition of the minimal gut metagenome as the set of microbial genes necessary for homeostasis and present in all healthy individuals. This study analyses the minimal gut metagenome of the most comprehensive dataset available, including individuals from agriculturalist and industrialist societies, also embodying highly diverse ethnic and geographical backgrounds. The outcome, based on metagenomic predictions for community composition data, resulted in a minimal metagenome comprising 3412 genes, mapping to 1856 reactions and 128 metabolic pathways predicted to occur across all individuals. These results were substantiated by the analysis of two additional datasets describing the microbial community compositions of larger Western cohorts, as well as a substantial shotgun metagenomics dataset. Subsequent analyses showed the plausible metabolic complementarity provided by the minimal gut metagenome to the human genome.}, } @article {pmid33140419, year = {2020}, author = {Holmes, M and Flaminio, Z and Vardhan, M and Xu, F and Li, X and Devinsky, O and Saxena, D}, title = {Cross talk between drug-resistant epilepsy and the gut microbiome.}, journal = {Epilepsia}, volume = {61}, number = {12}, pages = {2619-2628}, doi = {10.1111/epi.16744}, pmid = {33140419}, issn = {1528-1167}, support = {//FACES/ ; }, mesh = {Diet, High-Protein Low-Carbohydrate ; Diet, Ketogenic ; Drug Resistant Epilepsy/diet therapy/etiology/*microbiology ; *Gastrointestinal Microbiome/physiology ; Humans ; Probiotics/therapeutic use ; }, abstract = {One-third of epilepsy patients have drug-resistant epilepsy (DRE), which is often complicated by polydrug toxicity and psychiatric and cognitive comorbidities. Advances in understanding the microbiome and gut-brain-axis are likely to shed light on epilepsy pathogenesis, anti-seizure medication (ASM) resistance, and potential therapeutic targets. Gut dysbiosis is associated with inflammation, blood-brain barrier disruption, and altered neuromodulators. High-throughput and metagenomic sequencing has advanced the characterization of microbial species and functional pathways. DRE patients show altered gut microbiome composition compared to drug-sensitive patients and healthy controls. The ketogenic and modified Atkins diets can reduce seizures in some patients with DRE. These low-carbohydrate dietary therapies alter the taxonomic and functional composition of the gut microbiome, and composition varies between diet responders and nonresponders. Murine models suggest that specific phyla are necessary to confer efficacy from the diet, and antibiotic treatment may eliminate efficacy. The impact of diet might involve alterations in microbiota, promotion of select microbial interactions, and variance in brain neurotransmitter levels that then influence seizures. Understanding the mechanics of how diet manipulates seizures may suggest novel therapies. Most ASMs act on neuronal transmission via effects on ion channels and neurotransmitters. However, ASMs may also assert their effects via the gut microbiota. In animal models, the microbiota composition (eg, abundance of certain phyla) can vary with ASM active drug metabolites. Given the developing understanding of the gut microbiome in DRE, probiotics are another potential therapy. Probiotics alter the microbiota composition, and small studies suggest that these supplements can reduce seizures in some patients. DRE has enormous consequences to patients and society, and the gut microbiome holds promise as a potential therapeutic target. However, the exact mechanism and recognition of which patients are likely to be responders remain elusive. Further studies are warranted.}, } @article {pmid33139880, year = {2021}, author = {Martínez Arbas, S and Narayanasamy, S and Herold, M and Lebrun, LA and Hoopmann, MR and Li, S and Lam, TJ and Kunath, BJ and Hicks, ND and Liu, CM and Price, LB and Laczny, CC and Gillece, JD and Schupp, JM and Keim, PS and Moritz, RL and Faust, K and Tang, H and Ye, Y and Skupin, A and May, P and Muller, EEL and Wilmes, P}, title = {Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics.}, journal = {Nature microbiology}, volume = {6}, number = {1}, pages = {123-135}, pmid = {33139880}, issn = {2058-5276}, support = {R01 AI108888/AI/NIAID NIH HHS/United States ; R01 AI143254/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*genetics/virology ; Bacteriophages/*genetics ; CRISPR-Cas Systems/*genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Genome, Bacterial/genetics ; Metagenome/genetics ; Microbial Consortia/genetics ; Microbial Interactions/*genetics/physiology ; Plasmids/*genetics ; Sewage/microbiology ; Water Purification ; }, abstract = {Viruses and plasmids (invasive mobile genetic elements (iMGEs)) have important roles in shaping microbial communities, but their dynamic interactions with CRISPR-based immunity remain unresolved. We analysed generation-resolved iMGE-host dynamics spanning one and a half years in a microbial consortium from a biological wastewater treatment plant using integrated meta-omics. We identified 31 bacterial metagenome-assembled genomes encoding complete CRISPR-Cas systems and their corresponding iMGEs. CRISPR-targeted plasmids outnumbered their bacteriophage counterparts by at least fivefold, highlighting the importance of CRISPR-mediated defence against plasmids. Linear modelling of our time-series data revealed that the variation in plasmid abundance over time explained more of the observed community dynamics than phages. Community-scale CRISPR-based plasmid-host and phage-host interaction networks revealed an increase in CRISPR-mediated interactions coinciding with a decrease in the dominant 'Candidatus Microthrix parvicella' population. Protospacers were enriched in sequences targeting genes involved in the transmission of iMGEs. Understanding the factors shaping the fitness of specific populations is necessary to devise control strategies for undesirable species and to predict or explain community-wide phenotypes.}, } @article {pmid33136284, year = {2020}, author = {Gomaa, EZ}, title = {Human gut microbiota/microbiome in health and diseases: a review.}, journal = {Antonie van Leeuwenhoek}, volume = {113}, number = {12}, pages = {2019-2040}, doi = {10.1007/s10482-020-01474-7}, pmid = {33136284}, issn = {1572-9699}, mesh = {Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Microbiota ; *Probiotics ; }, abstract = {The human gut microbiota has received considerable interest in the recent years and our knowledge of the inhabitant species and their potential applications is increased particularly after the development of metagenomic studies. Gut microbiota is highly diverse and harboring trillions of microorganisms in human digestive system. The shaping and multiplication of gut microbiome starts at birth, while the modification of their composition depends mainly on various genetic, nutritional and environmental factors. The modification in the composition and function of the gut microbiota can change intestinal permeability, digestion and metabolism as well as immune responses. The pro inflammatory state caused by alternation of gut microbiota balance lead to the onset of many diseases ranging from gastrointestinal and metabolic conditions to immunological and neuropsychiatric diseases. In this context, the present review clarifies the role of gut microbiota in maintaining host health and investigates how nutritional and environmental factors affect the gut microbial structure and function. In addition, many therapeutic strategies of gut microbiota aimed at modulating and restoring of the intestinal ecosystem balance have been surveyed.}, } @article {pmid33135936, year = {2021}, author = {Nicholson, K and Bjornevik, K and Abu-Ali, G and Chan, J and Cortese, M and Dedi, B and Jeon, M and Xavier, R and Huttenhower, C and Ascherio, A and Berry, JD}, title = {The human gut microbiota in people with amyotrophic lateral sclerosis.}, journal = {Amyotrophic lateral sclerosis & frontotemporal degeneration}, volume = {22}, number = {3-4}, pages = {186-194}, doi = {10.1080/21678421.2020.1828475}, pmid = {33135936}, issn = {2167-9223}, mesh = {*Amyotrophic Lateral Sclerosis ; Case-Control Studies ; Clostridiales ; *Gastrointestinal Microbiome/genetics ; Humans ; }, abstract = {To characterize the gut microbiota in people with amyotrophic lateral sclerosis (ALS) relative to controls and to test the hypothesis that butyrate-producing bacteria are less abundant in the gastrointestinal tracts of people with ALS (PALS). Methods: We conducted a case-control study at Massachusetts General Hospital to compare the gut microbiota in people with ALS to that in controls. Metagenomic shotgun sequencing was performed on DNA extracted from stool samples of 66 people with ALS (PALS), 61 healthy controls (HC), and 12 neurodegenerative controls (NDC). Taxonomic metagenomic profiles were analyzed for shifts in the microbial community structure between the comparator groups using per-feature univariate and multivariate association tests. Results: The relative abundance of the dominant butyrate-producing bacteria Eubacterium rectale and Roseburia intestinalis was significantly lower in ALS patients compared to HC. Adjustment for age, sex, and constipation did not materially change the results. The total abundance of 8 dominant species capable of producing butyrate was also significantly lower in ALS compared to HC (p < 0.001). Conclusions: The levels of several butyrate-producing bacteria, which are important for gut integrity and regulation of inflammation, were lower in people with ALS compared to controls. These findings lend support to the inference that the gut microbiota could be a risk factor for ALS. Further investigations are warranted, preferably earlier in the disease with corresponding dietary collection and a longitudinal design.}, } @article {pmid33135866, year = {2021}, author = {Dizman, N and Hsu, J and Bergerot, PG and Gillece, JD and Folkerts, M and Reining, L and Trent, J and Highlander, SK and Pal, SK}, title = {Randomized trial assessing impact of probiotic supplementation on gut microbiome and clinical outcome from targeted therapy in metastatic renal cell carcinoma.}, journal = {Cancer medicine}, volume = {10}, number = {1}, pages = {79-86}, pmid = {33135866}, issn = {2045-7634}, mesh = {Adult ; Aged ; Aged, 80 and over ; Antineoplastic Agents/adverse effects/*therapeutic use ; Bacteria/*growth & development ; California ; Carcinoma, Renal Cell/*drug therapy/microbiology/secondary ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Humans ; Intestines/*microbiology ; Kidney Neoplasms/*drug therapy/microbiology/pathology ; Male ; Middle Aged ; Molecular Targeted Therapy ; Probiotics/adverse effects/*therapeutic use ; Prospective Studies ; Time Factors ; Treatment Outcome ; Yogurt/*microbiology ; }, abstract = {Studies suggest a link between the gut microbiome and metastatic renal cell carcinoma (mRCC) outcomes, including evidence that mRCC patients possess a lower abundance of Bifidobacterium spp. compared to healthy adults. We sought to assess if a Bifidobacterium-containing yogurt product could modulate the gut microbiome and clinical outcome from vascular endothelial growth factor-tyrosine kinase inhibitors (VEGF-TKIs). mRCC patients initiating VEGF-TKIs, regardless of the line of therapy, were randomized to probiotic-supplemented (two 4 oz. servings of the probiotic yogurt product daily) or probiotic-restricted arms. Stool samples were collected prior to therapy and at weeks 2, 3, 4, and 12. Microbiome composition was assessed using whole-metagenome sequencing. A total of 20 patients were randomized. Bifidobacterium animalis, the active ingredient of the probiotic supplement, reached detectable levels in all patients in the probiotic-supplemented arm versus two patients in the probiotic-restricted arm. Clinical benefit rate was similar in probiotic-supplemented versus probiotic-restricted arms (70% vs. 80%, p = 0.606). Linear discriminant analysis (LDA) effect size analysis of MetaPhIAn2 abundance data predicted 25 enriched species demonstrating an LDA score >3 in either clinical benefit or no clinical benefit. In patients with clinical benefit (vs. no clinical benefit), Barnesiella intestinihominis and Akkermansia muciniphila were significantly more abundant (p = 7.4 × 10[-6] and p = 5.6 × 10[-3] , respectively). This is the first prospective randomized study demonstrating modulation of the gut microbiome with a probiotic in mRCC. Probiotic supplementation successfully increased the Bifidobacterium spp. levels. Analysis of longitudinal stool specimens identified an association between B. intestinihominis, A. muciniphila, and clinical benefit with therapy. Trial Registration: NCT02944617.}, } @article {pmid33902727, year = {2020}, author = {Bhatnagar, S and Cowley, ES and Kopf, SH and Pérez Castro, S and Kearney, S and Dawson, SC and Hanselmann, K and Ruff, SE}, title = {Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom.}, journal = {Environmental microbiome}, volume = {15}, number = {1}, pages = {3}, pmid = {33902727}, issn = {2524-6372}, abstract = {BACKGROUND: Lagoons are common along coastlines worldwide and are important for biogeochemical element cycling, coastal biodiversity, coastal erosion protection and blue carbon sequestration. These ecosystems are frequently disturbed by weather, tides, and human activities. Here, we investigated a shallow lagoon in New England. The brackish ecosystem releases hydrogen sulfide particularly upon physical disturbance, causing blooms of anoxygenic sulfur-oxidizing phototrophs. To study the habitat, microbial community structure, assembly and function we carried out in situ experiments investigating the bloom dynamics over time.

RESULTS: Phototrophic microbial mats and permanently or seasonally stratified water columns commonly contain multiple phototrophic lineages that coexist based on their light, oxygen and nutrient preferences. We describe similar coexistence patterns and ecological niches in estuarine planktonic blooms of phototrophs. The water column showed steep gradients of oxygen, pH, sulfate, sulfide, and salinity. The upper part of the bloom was dominated by aerobic phototrophic Cyanobacteria, the middle and lower parts by anoxygenic purple sulfur bacteria (Chromatiales) and green sulfur bacteria (Chlorobiales), respectively. We show stable coexistence of phototrophic lineages from five bacterial phyla and present metagenome-assembled genomes (MAGs) of two uncultured Chlorobaculum and Prosthecochloris species. In addition to genes involved in sulfur oxidation and photopigment biosynthesis the MAGs contained complete operons encoding for terminal oxidases. The metagenomes also contained numerous contigs affiliating with Microviridae viruses, potentially affecting Chlorobi. Our data suggest a short sulfur cycle within the bloom in which elemental sulfur produced by sulfide-oxidizing phototrophs is most likely reduced back to sulfide by Desulfuromonas sp.

CONCLUSIONS: The release of sulfide creates a habitat selecting for anoxygenic sulfur-oxidizing phototrophs, which in turn create a niche for sulfur reducers. Strong syntrophism between these guilds apparently drives a short sulfur cycle that may explain the rapid development of the bloom. The fast growth and high biomass yield of Chlorobi-affiliated organisms implies that the studied lineages of green sulfur bacteria can thrive in hypoxic habitats. This oxygen tolerance is corroborated by oxidases found in MAGs of uncultured Chlorobi. The findings improve our understanding of the ecology and ecophysiology of anoxygenic phototrophs and their impact on the coupled biogeochemical cycles of sulfur and carbon.}, } @article {pmid33814114, year = {2020}, author = {Hopson, LM and Singleton, SS and David, JA and Basuchoudhary, A and Prast-Nielsen, S and Klein, P and Sen, S and Mazumder, R}, title = {Bioinformatics and machine learning in gastrointestinal microbiome research and clinical application.}, journal = {Progress in molecular biology and translational science}, volume = {176}, number = {}, pages = {141-178}, doi = {10.1016/bs.pmbts.2020.08.011}, pmid = {33814114}, issn = {1878-0814}, mesh = {Computational Biology ; *Gastrointestinal Microbiome ; Humans ; Machine Learning ; Metagenomics ; }, abstract = {The scientific community currently defines the human microbiome as all the bacteria, viruses, fungi, archaea, and eukaryotes that occupy the human body. When considering the variable locations, composition, diversity, and abundance of our microbial symbionts, the sheer volume of microorganisms reaches hundreds of trillions. With the onset of next generation sequencing (NGS), also known as high-throughput sequencing (HTS) technologies, the barriers to studying the human microbiome lowered significantly, making in-depth microbiome research accessible. Certain locations on the human body, such as the gastrointestinal, oral, nasal, and skin microbiomes have been heavily studied through community-focused projects like the Human Microbiome Project (HMP). In particular, the gastrointestinal microbiome (GM) has received significant attention due to links to neurological, immunological, and metabolic diseases, as well as cancer. Though HTS technologies allow deeper exploration of the GM, data informing the functional characteristics of microbiota and resulting effects on human function or disease are still sparse. This void is compounded by microbiome variability observed among humans through factors like genetics, environment, diet, metabolic activity, and even exercise; making GM research inherently difficult to study. This chapter describes an interdisciplinary approach to GM research with the goal of mitigating the hindrances of translating findings into a clinical setting. By applying tools and knowledge from microbiology, metagenomics, bioinformatics, machine learning, predictive modeling, and clinical study data from children with treatment-resistant epilepsy, we describe a proof-of-concept approach to clinical translation and precision application of GM research.}, } @article {pmid33829126, year = {2019}, author = {Chang, WS and Eden, JS and Hartley, WJ and Shi, M and Rose, K and Holmes, EC}, title = {Metagenomic discovery and co-infection of diverse wobbly possum disease viruses and a novel hepacivirus in Australian brushtail possums.}, journal = {One health outlook}, volume = {1}, number = {}, pages = {5}, pmid = {33829126}, issn = {2524-4655}, abstract = {BACKGROUND: Australian brushtail possums (Trichosurus vulpecula) are an introduced pest species in New Zealand, but native to Australia where they are protected for biodiversity conservation. Wobbly possum disease (WPD) is a fatal neurological disease of Australian brushtail possums described in New Zealand populations that has been associated with infection by the arterivirus (Arteriviridae) wobbly possum disease virus (WPDV-NZ). Clinically, WPD-infected possums present with chronic meningoencephalitis, choroiditis and multifocal neurological symptoms including ataxia, incoordination, and abnormal gait.

METHODS: We conducted a retrospective investigation to characterise WPD in native Australian brushtail possums, and used a bulk meta-transcriptomic approach (i.e. total RNA-sequencing) to investigate its potential viral aetiology. PCR assays were developed for case diagnosis and full genome recovery in the face of extensive genetic variation.

RESULTS: We identified genetically distinct lineages of arteriviruses from archival tissues of WPD-infected possums in Australia, termed wobbly possum disease virus AU1 and AU2. Phylogenetically, WPDV-AU1 and WPDV-AU2 shared only ~ 70% nucleotide similarity to each other and the WPDV-NZ strain, suggestive of a relatively ancient divergence. Notably, we also identified a novel and divergent hepacivirus (Flaviviridae) - the first in a marsupial - in both WPD-infected and uninfected possums, indicative of virus co-infection.

CONCLUSIONS: We have identified marsupial-specific lineages of arteriviruses in mainland Australia that are genetically distinct from that in New Zealand, in some cases co-infecting animals with a novel hepacivirus. Our study provides new insight into the hidden genetic diversity of arteriviruses, the capacity for virus co-infection, and highlights the utility of meta-transcriptomics for disease investigation in a One Health context.}, } @article {pmid33404537, year = {2020}, author = {Guo, X and Zhang, X and Qin, Y and Liu, YX and Zhang, J and Zhang, N and Wu, K and Qu, B and He, Z and Wang, X and Zhang, X and Hacquard, S and Fu, X and Bai, Y}, title = {Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome.}, journal = {Plant communications}, volume = {1}, number = {1}, pages = {100003}, pmid = {33404537}, issn = {2590-3462}, mesh = {Droughts ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome ; Microbiota/genetics/*physiology ; Oryza/*microbiology ; Plant Diseases/microbiology ; Plant Roots/*microbiology ; Plasmids ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Triticum/*microbiology ; }, abstract = {Plant-associated microbes are critical for plant growth and survival under natural environmental conditions. To date, most plant microbiome studies involving high-throughput amplicon sequencing have focused on the relative abundance of microbial taxa. However, this technique does not assess the total microbial load and the abundance of individual microbes relative to the amount of host plant tissues. Here, we report the development of a host-associated quantitative abundance profiling (HA-QAP) method that can accurately examine total microbial load and colonization of individual root microbiome members relative to host plants by the copy-number ratio of microbial marker gene to plant genome. We validate the HA-QAP method using mock experiments, perturbation experiments, and metagenomic sequencing. The HA-QAP method eliminates the generation of spurious outputs in the classical method based on microbial relative abundance, and reveals the load of root microbiome to host plants. Using the HA-QAP method, we found that the copy-number ratios of microbial marker genes to plant genome range from 1.07 to 6.61 for bacterial 16S rRNA genes and from 0.40 to 2.26 for fungal internal transcribed spacers in the root microbiome samples from healthy rice and wheat. Furthermore, using HA-QAP we found that an increase in total microbial load represents a key feature of changes in root microbiome of rice plants exposed to drought stress and of wheat plants with root rot disease, which significantly influences patterns of differential taxa and species interaction networks. Given its accuracy and technical feasibility, HA-QAP would facilitate our understanding of genuine interactions between root microbiome and plants.}, } @article {pmid32742640, year = {2020}, author = {Wagner, J and Kancherla, J and Braccia, D and Matsumara, J and Felix, V and Crabtree, J and Mahurkar, A and Corrada Bravo, H}, title = {Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz.}, journal = {F1000Research}, volume = {9}, number = {}, pages = {601}, pmid = {32742640}, issn = {2046-1402}, support = {R01 GM114267/GM/NIGMS NIH HHS/United States ; U54 DK102556/DK/NIDDK NIH HHS/United States ; }, mesh = {*Data Analysis ; Data Interpretation, Statistical ; Humans ; *Microbiota ; Research Design ; }, abstract = {The rich data produced by the second phase of the Human Microbiome Project (iHMP) offers a unique opportunity to test hypotheses that interactions between microbial communities and a human host might impact an individual's health or disease status. In this work we describe infrastructure that integrates Metaviz, an interactive microbiome data analysis and visualization tool, with the iHMP Data Coordination Center web portal and the HMP2Data R/Bioconductor package. We describe integrative statistical and visual analyses of two datasets from iHMP using Metaviz along with the metagenomeSeq R/Bioconductor package for statistical analysis of differential abundance analysis. These use cases demonstrate the utility of a combined approach to access and analyze data from this resource.}, } @article {pmid33131828, year = {2021}, author = {Dean, CJ and Slizovskiy, IB and Crone, KK and Pfennig, AX and Heins, BJ and Caixeta, LS and Noyes, NR}, title = {Investigating the cow skin and teat canal microbiomes of the bovine udder using different sampling and sequencing approaches.}, journal = {Journal of dairy science}, volume = {104}, number = {1}, pages = {644-661}, doi = {10.3168/jds.2020-18277}, pmid = {33131828}, issn = {1525-3198}, mesh = {Animals ; Bacteria/classification/isolation & purification ; Cattle/*microbiology ; Female ; Mammary Glands, Animal/*microbiology ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S ; Skin/*microbiology ; Specimen Handling/veterinary ; }, abstract = {There is a need for standardized, efficient, and practical sampling methods to support large population-based studies of the internal and external epithelial microbiomes of the bovine udder. The primary objective of this study was to evaluate different sampling devices for the isolation of microbial DNA originating from the internal and external teat epithelium. Secondary objectives were to survey and compare the microbial diversity of external and teat canal epithelial microbiomes using amplicon and shotgun metagenomic sequencing approaches. To address these objectives, we enrolled a convenience sample of 24 Holstein dairy cows and collected samples from the external epithelium at the base of udder, the external teat barrel epithelium, the external teat apex epithelium, and the teat canal epithelium. Extracted DNA was quantified and subjected to PCR amplification of the V4 hypervariable region of the 16S rRNA gene and sequenced on the Illumina MiSeq platform (Illumina Inc., San Diego, CA). A subset of samples was subjected to a shallow shotgun metagenomic assay on the Illumina HiSeq platform. For samples collected from the external teat epithelium, we found that gauze squares consistently yielded more DNA than swabs, and Simpson's reciprocal index of diversity was higher for gauze than for swabs. The teat canal epithelial samples exhibited significantly lower diversity than the external sampling locations, but there were no significant differences in diversity between teat apex, teat barrel, and base of the udder samples. There were, however, differences in the microbial distribution and abundances of specific bacteria across external epithelial surfaces. The proportion of shotgun sequence reads classified as Bos taurus was highly variable between sampling locations, ranging from 0.33% in teat apex samples to 99.91% in teat canal samples. These results indicate that gauze squares should be considered for studying the microbiome of the external epithelium of the bovine udder, particularly if DNA yield must be maximized. Further, the relative proportion of host to non-host DNA present in samples collected from the internal and external teat epithelium should be considered when designing studies that utilize shotgun metagenomic sequencing.}, } @article {pmid33128571, year = {2021}, author = {Cvetkovic, L and Régis, C and Richard, C and Derosa, L and Leblond, A and Malo, J and Messaoudene, M and Desilets, A and Belkaid, W and Elkrief, A and Routy, B and Juneau, D}, title = {Physiologic colonic uptake of [18]F-FDG on PET/CT is associated with clinical response and gut microbiome composition in patients with advanced non-small cell lung cancer treated with immune checkpoint inhibitors.}, journal = {European journal of nuclear medicine and molecular imaging}, volume = {48}, number = {5}, pages = {1550-1559}, pmid = {33128571}, issn = {1619-7089}, mesh = {*Carcinoma, Non-Small-Cell Lung/diagnostic imaging/drug therapy ; Colon ; Fluorodeoxyglucose F18 ; *Gastrointestinal Microbiome ; Humans ; Immune Checkpoint Inhibitors ; *Lung Neoplasms/diagnostic imaging/drug therapy ; Positron Emission Tomography Computed Tomography ; Prognosis ; }, abstract = {BACKGROUND: Immune checkpoint inhibitors (ICI) represent the backbone treatment for advanced non-small cell lung cancer (NSCLC). Emerging data suggest that increased gut microbiome diversity is associated with favorable response to ICI and that antibiotic-induced dysbiosis is associated with deleterious outcomes. [18]F-FDG physiologic colonic uptake on PET/CT increases following treatment with antibiotics (ATB) and could act as a surrogate marker for microbiome composition and predict prognosis. The aim of this study was to determine if [18]F-FDG physiologic colonic uptake prior to ICI initiation correlates with gut microbiome profiling and clinical outcomes in patients with advanced NSCLC.

METHODS: Seventy-one patients with advanced NSCLC who underwent a PET/CT prior to ICI were identified. Blinded colonic contouring was performed for each colon segment and patients were stratified according to the median of the average colon SUVmax as well as for each segment in low vs. high SUVmax groups. Response rate, progression-free survival (PFS), and overall survival (OS) were compared in the low vs. high SUVmax groups. Gut microbiome composition was analyzed for 23 patients using metagenomics sequencing.

RESULTS: The high colon SUVmax group had a higher proportion of non-responders (p = 0.033) and significantly shorter PFS (4.1 vs. 11.3 months, HR 1.94, 95% CI 1.11-3.41, p = 0.005). High caecum SUVmax correlated with numerically shorter OS (10.8 vs. 27.6 months, HR 1.85, 95% CI 0.97-3.53, p = 0.058). Metagenomics sequencing revealed distinctive microbiome populations in each group. Patients with low caecum SUVmax had higher microbiome diversity (p = 0.046) and were enriched with Bifidobacteriaceae, Lachnospiraceae, and Bacteroidaceae.

CONCLUSIONS: Lower colon physiologic [18]F-FDG uptake on PET/CT prior to ICI initiation was associated with better clinical outcomes and higher gut microbiome diversity in patients with advanced NSCLC. Here, we propose that [18]F-FDG physiologic colonic uptake on PET/CT could serve as a potential novel marker of gut microbiome composition and may predict clinical outcomes in this population.}, } @article {pmid33128103, year = {2020}, author = {Fernandez-Bayo, JD and Simmons, CW and VanderGheynst, JS}, title = {Characterization of digestate microbial community structure following thermophilic anaerobic digestion with varying levels of green and food wastes.}, journal = {Journal of industrial microbiology & biotechnology}, volume = {47}, number = {12}, pages = {1031-1044}, pmid = {33128103}, issn = {1476-5535}, support = {201500317//UC Davis Sustainability Research and Training Program/ ; CA-D-BAE-2228-RR//National Institute of Food and Agriculture/ ; DE-AC02-05CH11231//US Department of Energy/ ; }, mesh = {*Anaerobiosis ; Archaea ; Bacteria ; Bioreactors ; Carbon ; Composting ; Food ; Microbiota ; Nitrogen/chemistry ; Refuse Disposal ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The properties of digestates generated through anaerobic digestion are influenced by interactions between the digester microbial communities, feedstock properties and digester operating conditions. This study investigated the effect of varying initial feedstock carbon to nitrogen (C/N) ratios on digestate microbiota and predicted abundance of genes encoding lignocellulolytic activity. The C/N ratio had a significant impact on the digestate microbiome. Feedstocks with intermediate C/N ratio (20-27) (where higher biomethane potential was observed) showed higher relative abundance of archaea compared to feedstocks with C/N ratios at 17 and 34. Within microbial networks, four microbial clusters and eight connector microorganisms changed significantly with the C/N ratio (P < 0.05). Feedstocks with C/N < 23 were richer in organisms from the family Thermotogaceae and genus Caldicoprobacter and enhanced potential for degradation of maltose, galactomannans, melobiose and lactose. This study provides new insights into how anaerobic digestion conditions relate to the structure and functional potential of digester microbial communities, which may be relevant to both digester performance and subsequent utilization of digestates for composting or amending soil.}, } @article {pmid33127812, year = {2021}, author = {Díaz-García, L and Huang, S and Spröer, C and Sierra-Ramírez, R and Bunk, B and Overmann, J and Jiménez, DJ}, title = {Dilution-to-Stimulation/Extinction Method: a Combination Enrichment Strategy To Develop a Minimal and Versatile Lignocellulolytic Bacterial Consortium.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {2}, pages = {}, pmid = {33127812}, issn = {1098-5336}, mesh = {Bacteria/genetics/metabolism ; Forests ; Genome, Bacterial ; Lignin/*metabolism ; Metagenomics ; *Microbial Consortia ; RNA, Ribosomal, 16S ; Soil Microbiology ; }, abstract = {The engineering of complex communities can be a successful path to understand the ecology of microbial systems and improve biotechnological processes. Here, we developed a strategy to assemble a minimal and effective lignocellulolytic microbial consortium (MELMC) using a sequential combination of dilution-to-stimulation and dilution-to-extinction approaches. The consortium was retrieved from Andean forest soil and selected through incubation in liquid medium with a mixture of three types of agricultural plant residues. After the dilution-to-stimulation phase, approximately 50 bacterial sequence types, mostly belonging to the Sphingobacteriaceae, Enterobacteriaceae, Pseudomonadaceae, and Paenibacillaceae, were significantly enriched. The dilution-to-extinction method demonstrated that only eight of the bacterial sequence types were necessary to maintain microbial growth and plant biomass consumption. After subsequent stabilization, only two bacterial species (Pseudomonas sp. and Paenibacillus sp.) became highly abundant (>99%) within the MELMC, indicating that these are the key players in degradation. Differences in the composition of bacterial communities between biological replicates indicated that selection, sampling, and/or priority effects could shape the consortium structure. The MELMC can degrade up to ∼13% of corn stover, consuming mostly its (hemi)cellulosic fraction. Tests with chromogenic substrates showed that the MELMC secretes an array of endoenzymes able to degrade xylan, arabinoxylan, carboxymethyl cellulose, and wheat straw. Additionally, the metagenomic profile inferred from the phylogenetic composition along with an analysis of carbohydrate-active enzymes of 20 bacterial genomes support the potential of the MELMC to deconstruct plant polysaccharides. This capacity was mainly attributed to the presence of Paenibacillus sp.IMPORTANCE The significance of our study mainly lies in the development of a combined top-down enrichment strategy (i.e., dilution to stimulation coupled to dilution to extinction) to build a minimal and versatile lignocellulolytic microbial consortium. We demonstrated that mainly two selectively enriched bacterial species (Pseudomonas sp. and Paenibacillus sp.) are required to drive the effective degradation of plant polymers. Our findings can guide the design of a synthetic bacterial consortium that could improve saccharification (i.e., the release of sugars from agricultural plant residues) processes in biorefineries. In addition, they can help to expand our ecological understanding of plant biomass degradation in enriched bacterial systems.}, } @article {pmid33127500, year = {2021}, author = {Woerther, PL and d'Humières, C and Lescure, X and Dubreuil, L and Rodriguez, C and Barbier, F and Fihman, V and Ruppé, E}, title = {Is the term "anti-anaerobic" still relevant?.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {102}, number = {}, pages = {178-180}, doi = {10.1016/j.ijid.2020.10.052}, pmid = {33127500}, issn = {1878-3511}, mesh = {Anaerobiosis ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria, Anaerobic/*drug effects ; Humans ; Microbiota/*drug effects ; Terminology as Topic ; }, abstract = {For decades, the term "anti-anaerobic" has been commonly used to refer to antibiotics exhibiting activity against anaerobic bacteria, also designated as anaerobes. This term is used in various situations ranging from infections associated with well-identified pathogens like Clostridioides difficile, or Fusobacterium necrophorum in Lemierre's syndrome, that require specific antibiotic treatments to polymicrobial infections generally resulting from the decreased permeability of anatomical barriers (e.g., intestinal translocation and stercoral peritonitis) or infectious secondary localizations (e.g., brain abscess and infectious pleurisy). In these cases, the causal bacteria generally remain unidentified and the antimicrobial treatment is empirical. However, major progress in the knowledge of human bacterial microbiotas in the last 10 years has shown how diverse are the species involved in these communities. Here, we sought to reappraise the concept of anti-anaerobic spectrum in the light of recent advances in the microbiota field. We first highlight that the term anaerobic itself does not represent the tremendous diversity of the bacteria it spans, and then we stress that the antibiotic susceptibility profiles for most anaerobic bacteria remain unaddressed. Furthermore, we provide examples challenging the relevance of the "anti-anaerobic" spectrum from a clinical and ecological perspective.}, } @article {pmid33127154, year = {2021}, author = {Xing, Z and Li, H and Li, M and Gao, R and Guo, C and Mi, S}, title = {Disequilibrium in chicken gut microflora with avian colibacillosis is related to microenvironment damaged by antibiotics.}, journal = {The Science of the total environment}, volume = {762}, number = {}, pages = {143058}, doi = {10.1016/j.scitotenv.2020.143058}, pmid = {33127154}, issn = {1879-1026}, mesh = {Animals ; Anti-Bacterial Agents ; Chickens ; Escherichia coli ; *Gastrointestinal Microbiome ; Humans ; *Poultry Diseases ; Virulence ; }, abstract = {The avian colibacillosis outbreak is a disease that threatens public health, poultry production, and economic interests, even after antibiotic feed addition. It is known that avian pathogenic E. coli is a major pathogenic factor; however, the systemic characteristics of gut flora in disease samples and how pathogens grow remain unknown. To study these issues in depth, we used the whole microbial genome shotgun sequencing technique to compare entire microbes in diseased and healthy broiler chickens. We found that it was not only E. coli that increased substantially, but most pathogenic flora also increased significantly in diseased samples. Subsequently, we proved that aminoglycoside antibiotic resistance genes were mainly found in non-E. coli strains. This suggests that E. coli survival under antibiotic stress was due to the cooperative resistance from non-E. coli strains. Among all these increasing strains, attaching and effacing pathogens could damage host intestinal epithelial cells to release oxygen in the gut to make the microenvironment more adaptable for E. coli strains. Furthermore, we observed that the functions of the T4SS/T6SS secretion system were dramatically enhanced, which could help E. coli to compete and enlarge their living spaces. Ultimately, pathogenic E. coli accumulated to cause avian colibacillosis. This study provides a new insight into intestinal microecology in diseased individuals, which would propose new treatment options for avian colibacillosis from a metagenome perspective.}, } @article {pmid33126925, year = {2020}, author = {Santos-Júnior, CD and Sarmento, H and de Miranda, FP and Henrique-Silva, F and Logares, R}, title = {Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {151}, pmid = {33126925}, issn = {2049-2618}, mesh = {Bacteria/*genetics/*metabolism ; *Genomics ; Microbiota/*genetics ; *Rainforest ; *Rivers ; }, abstract = {BACKGROUND: The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon River were barely known. Here, we examined the Amazon River microbiome by analysing 106 metagenomes from 30 sampling points distributed along the river.

RESULTS: We constructed the Amazon River basin Microbial non-redundant Gene Catalogue (AMnrGC) that includes ~ 3.7 million non-redundant genes, affiliating mostly to bacteria. We found that the Amazon River microbiome contains a substantial gene-novelty compared to other relevant known environments (rivers and rainforest soil). Genes encoding for proteins potentially involved in lignin degradation pathways were correlated to tripartite tricarboxylates transporters and hemicellulose degradation machinery, pointing to a possible priming effect. Based on this, we propose a model on how the degradation of recalcitrant TeOM could be modulated by labile compounds in the Amazon River waters. Our results also suggest changes of the microbial community and its genomic potential along the river course.

CONCLUSIONS: Our work contributes to expand significantly our comprehension of the world's largest river microbiome and its potential metabolism related to TeOM degradation. Furthermore, the produced gene catalogue (AMnrGC) represents an important resource for future research in tropical rivers. Video abstract.}, } @article {pmid33126862, year = {2020}, author = {Zhang, X and Yi, N}, title = {NBZIMM: negative binomial and zero-inflated mixed models, with application to microbiome/metagenomics data analysis.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {488}, pmid = {33126862}, issn = {1471-2105}, mesh = {Algorithms ; *Data Analysis ; Humans ; Metagenome ; *Metagenomics ; Microbiota/*genetics ; *Models, Statistical ; Multilevel Analysis ; }, abstract = {BACKGROUND: Microbiome/metagenomic data have specific characteristics, including varying total sequence reads, over-dispersion, and zero-inflation, which require tailored analytic tools. Many microbiome/metagenomic studies follow a longitudinal design to collect samples, which further complicates the analysis methods needed. A flexible and efficient R package is needed for analyzing processed multilevel or longitudinal microbiome/metagenomic data.

RESULTS: NBZIMM is a freely available R package that provides functions for setting up and fitting negative binomial mixed models, zero-inflated negative binomial mixed models, and zero-inflated Gaussian mixed models. It also provides functions to summarize the results from fitted models, both numerically and graphically. The main functions are built on top of the commonly used R packages nlme and MASS, allowing us to incorporate the well-developed analytic procedures into the framework for analyzing over-dispersed and zero-inflated count or proportion data with multilevel structures (e.g., longitudinal studies). The statistical methods and their implementations in NBZIMM particularly address the data characteristics and the complex designs in microbiome/metagenomic studies. The package is freely available from the public GitHub repository https://github.com/nyiuab/NBZIMM .

CONCLUSION: The NBZIMM package provides useful tools for complex microbiome/metagenomics data analysis.}, } @article {pmid33125759, year = {2021}, author = {Zheng, H and Wei, P and Zhang, G and Xu, W and Li, Y}, title = {The impact of different Saccharomyces cerevisiae strains on microbial composition and quality of Chinese rice wine fermentations.}, journal = {Yeast (Chichester, England)}, volume = {38}, number = {2}, pages = {147-156}, doi = {10.1002/yea.3523}, pmid = {33125759}, issn = {1097-0061}, mesh = {Bioreactors ; *Fermentation ; Levilactobacillus brevis/growth & development ; Metagenomics/methods ; *Microbiota/genetics/physiology ; Pantoea/growth & development ; Saccharomyces cerevisiae/*classification/genetics/*metabolism ; Volatile Organic Compounds/analysis ; Wine/*microbiology/*standards ; }, abstract = {Chinese rice wine (CRW) is a popular fermented product in China, with complicated microbial composition and flavour compounds. To reveal the effects of different strains of Saccharomyces cerevisiae (N85 and XZ11) on the microbial composition in the process of brewing, metagenomic sequencing approaches were carried out to explore the dynamic changes of bacteria and fungi. Furthermore, the volatile compounds and organic acids in CRW were identified by headspace solid phase microextraction (HS-SPME)/gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) at the end of the brewing. Our results indicated that different S. cerevisiae strains could influence microbial compositions and especially affected the growth of Lactobacillus brevis and Pantoea ananatis. The changes in the microbial community structure contributed to the remarkable difference in the content of lactic acid, esters, alcohols, and aldehydes. Moreover, functional network analysis provided insights into the biological correlations between microbial species and metabolic pathways, that is, Lactobacillus genus had negative effects on metabolic activities. This study expands the idea of improving the quality of CRW by controlling the microbiome.}, } @article {pmid33125401, year = {2020}, author = {Elbere, I and Silamikelis, I and Dindune, II and Kalnina, I and Ustinova, M and Zaharenko, L and Silamikele, L and Rovite, V and Gudra, D and Konrade, I and Sokolovska, J and Pirags, V and Klovins, J}, title = {Baseline gut microbiome composition predicts metformin therapy short-term efficacy in newly diagnosed type 2 diabetes patients.}, journal = {PloS one}, volume = {15}, number = {10}, pages = {e0241338}, pmid = {33125401}, issn = {1932-6203}, mesh = {Adult ; Bacteroidetes/drug effects ; Diabetes Mellitus, Type 2/*drug therapy/*microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Lactococcus lactis/drug effects ; Longitudinal Studies ; Male ; Metformin/*therapeutic use ; Microbiota/drug effects ; Prevotella/drug effects ; Young Adult ; }, abstract = {BACKGROUND: The study was conducted to investigate the effects of metformin treatment on the human gut microbiome's taxonomic and functional profile in the Latvian population, and to evaluate the correlation of these changes with therapeutic efficacy and tolerance.

METHODS: In this longitudinal observational study, stool samples for shotgun metagenomic sequencing-based analysis were collected in two cohorts. The first cohort included 35 healthy nondiabetic individuals (metformin dose 2x850mg/day) at three time-points during metformin administration. The second cohort was composed of 50 newly-diagnosed type 2 diabetes patients (metformin dose-determined by an endocrinologist) at two concordant times. Patients were defined as Responders if their HbA1c levels during three months of metformin therapy had decreased by ≥12.6 mmol/mol (1%), while in Non-responders HbA1c were decreased by <12.6 mmol/mol (1%).

RESULTS: Metformin reduced the alpha diversity of microbiota in healthy controls (p = 0.02) but not in T2D patients. At the species level, reduction in the abundance of Clostridium bartlettii and Barnesiella intestinihominis, as well as an increase in the abundance of Parabacteroides distasonis and Oscillibacter unclassified overlapped between both study groups. A large number of group-specific changes in taxonomic and functional profiles was observed. We identified an increased abundance of Prevotella copri (FDR = 0.01) in the Non-Responders subgroup, and enrichment of Enterococcus faecium, Lactococcus lactis, Odoribacter, and Dialister at baseline in the Responders group. Various taxonomic units were associated with the observed incidence of side effects in both cohorts.

CONCLUSIONS: Metformin effects are different in T2D patients and healthy individuals. Therapy induced changes in the composition of gut microbiome revealed possible mediators of observed short-term therapeutic effects. The baseline composition of the gut microbiome may influence metformin therapy efficacy and tolerance in T2D patients and could be used as a powerful prediction tool.}, } @article {pmid33125392, year = {2020}, author = {Sala, C and Giampieri, E and Vitali, S and Garagnani, P and Remondini, D and Bazzani, A and Franceschi, C and Castellani, GC}, title = {Gut microbiota ecology: Biodiversity estimated from hybrid neutral-niche model increases with health status and aging.}, journal = {PloS one}, volume = {15}, number = {10}, pages = {e0237207}, pmid = {33125392}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; *Aging/genetics/physiology ; Biodiversity ; Child ; Child, Preschool ; Databases, Nucleic Acid ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Health Status ; Healthy Aging/genetics/physiology ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenome ; Middle Aged ; *Models, Biological ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {In this work we propose an index to estimate the gut microbiota biodiversity using a modeling approach with the aim of describing its relationship with health and aging. The gut microbiota, a complex ecosystem that links nutrition and metabolism, has a pervasive effect on all body organs and systems, undergoes profound changes with age and life-style, and substantially contributes to the pathogenesis of age-related diseases. For these reasons, the gut microbiota is a suitable candidate for assessing and quantifying healthy aging, i.e. the capability of individuals to reach an advanced age, avoiding or postponing major age-related diseases. The importance of the gut microbiota in health and aging has been proven to be related not only to its taxonomic composition, but also to its ecological properties, namely its biodiversity. Following an ecological approach, here we intended to characterize the relationship between the gut microbiota biodiversity and healthy aging through the development a parsimonious model of gut microbiota from which biodiversity can be estimated. We analysed publicly available metagenomic data relative to subjects of different ages, countries, nutritional habits and health status and we showed that a hybrid niche-neutral model well describes the observed patterns of bacterial relative abundance. Moreover, starting from such ecological modeling, we derived an estimate of the gut microbiota biodiversity that is consistent with classical indices, while having a higher statistical power. This allowed us to unveil an increase of the gut microbiota biodiversity during aging and to provide a good predictor of health status in old age, dependent on life-style and aging disorders.}, } @article {pmid33124780, year = {2021}, author = {Chen, BD and Jia, XM and Xu, JY and Zhao, LD and Ji, JY and Wu, BX and Ma, Y and Li, H and Zuo, XX and Pan, WY and Wang, XH and Ye, S and Tsokos, GC and Wang, J and Zhang, X}, title = {An Autoimmunogenic and Proinflammatory Profile Defined by the Gut Microbiota of Patients With Untreated Systemic Lupus Erythematosus.}, journal = {Arthritis & rheumatology (Hoboken, N.J.)}, volume = {73}, number = {2}, pages = {232-243}, doi = {10.1002/art.41511}, pmid = {33124780}, issn = {2326-5205}, mesh = {Actinobacteria ; Actinomyces ; Adult ; Amino Acids, Branched-Chain/biosynthesis ; Animals ; Antirheumatic Agents/therapeutic use ; Autoantibodies/*immunology ; Autoantigens/*immunology ; Bacteroides fragilis ; Case-Control Studies ; Clostridiales ; Clostridium ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/genetics/*immunology ; Humans ; Lipopolysaccharides/biosynthesis ; Lupus Erythematosus, Systemic/drug therapy/immunology/*microbiology/physiopathology ; Male ; Metagenomics ; Mice ; Mice, Inbred MRL lpr ; Molecular Mimicry/*immunology ; Mouth/microbiology ; Polymorphism, Single Nucleotide ; Young Adult ; }, abstract = {OBJECTIVE: Changes in gut microbiota have been linked to systemic lupus erythematosus (SLE), but knowledge is limited. Our study aimed to provide an in-depth understanding of the contribution of gut microbiota to the immunopathogenesis of SLE.

METHODS: Fecal metagenomes from 117 patients with untreated SLE and 52 SLE patients posttreatment were aligned with 115 matched healthy controls and analyzed by whole-genome profiling. For comparison, we assessed the fecal metagenome of MRL/lpr mice. The oral microbiota origin of the gut species that existed in SLE patients was documented by single-nucleotide polymorphism-based strain-level analyses. Functional validation assays were performed to demonstrate the molecular mimicry of newly found microbial peptides.

RESULTS: Gut microbiota from individuals with SLE displayed significant differences in microbial composition and function compared to healthy controls. Certain species, including the Clostridium species ATCC BAA-442 as well as Atopobium rimae, Shuttleworthia satelles, Actinomyces massiliensis, Bacteroides fragilis, and Clostridium leptum, were enriched in SLE gut microbiota and reduced after treatment. Enhanced lipopolysaccharide biosynthesis aligned with reduced branched chain amino acid biosynthesis was observed in the gut of SLE patients. The findings in mice were consistent with our findings in human subjects. Interestingly, some species with an oral microbiota origin were enriched in the gut of SLE patients. Functional validation assays demonstrated the proinflammatory capacities of some microbial peptides derived from SLE-enriched species.

CONCLUSION: This study provides detailed information on the microbiota of untreated patients with SLE, including their functional signatures, similarities with murine counterparts, oral origin, and the definition of autoantigen-mimicking peptides. Our data demonstrate that microbiome-altering approaches may offer valuable adjuvant therapies in SLE.}, } @article {pmid33123966, year = {2021}, author = {Yu, Z and Pei, Y and Zhao, S and Kakade, A and Khan, A and Sharma, M and Zain, H and Feng, P and Ji, J and Zhou, T and Wang, H and Wu, J and Li, X}, title = {Metatranscriptomic analysis reveals active microbes and genes responded to short-term Cr(VI) stress.}, journal = {Ecotoxicology (London, England)}, volume = {30}, number = {8}, pages = {1527-1537}, pmid = {33123966}, issn = {1573-3017}, support = {31870082//National Natural Science Foundation of China/ ; 17ZD2WA017//Gansu Science and Technology Department/ ; lzujbky-2018-it47//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Chromium/toxicity ; Metagenomics ; *Metals, Heavy ; *Microbiota ; }, abstract = {Heavy metals have been severely polluting the environment. However, the response mechanism of microbial communities to short-term heavy metals stress remains unclear. In this study, metagenomics (MG) and metatranscriptomics (MT) was performed to observe the microbial response to short-term Cr(VI) stress. MG data showed that 99.1% of species were similar in the control and Cr(VI) treated groups. However, MT data demonstrated that 83% of the microbes were active in which 58.7% increased, while the relative abundance of 41.3% decreased after short-term Cr(VI) incubation. The MT results also revealed 9% of microbes were dormant in samples. Genes associated with oxidative stress, Cr(VI) transport, resistance, and reduction, as well as genes with unknown functions were 2-10 times upregulated after Cr(VI) treatment. To further confirm the function of unknown genes, two genes (314 and 494) were selected to detect the Cr(VI) resistance and reduction ability. The results showed that these genes significantly increased the Cr(VI) remediation ability of Escherichia coli. MT results also revealed an increase in the expression of some rare genera (at least two times) after Cr(VI) treatment, indicating these rare species played a crucial role in microbial response to short-term Cr(VI) stress. In summary, MT is an efficient way to understand the role of active and dormant microbes in specific environmental conditions.}, } @article {pmid33123103, year = {2020}, author = {Cremonesi, P and Morandi, S and Ceccarani, C and Battelli, G and Castiglioni, B and Cologna, N and Goss, A and Severgnini, M and Mazzucchi, M and Partel, E and Tamburini, A and Zanini, L and Brasca, M}, title = {Raw Milk Microbiota Modifications as Affected by Chlorine Usage for Cleaning Procedures: The Trentingrana PDO Case.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {564749}, pmid = {33123103}, issn = {1664-302X}, abstract = {Milk microbiota represents a key point in raw milk cheese production and contributes to the development of typical flavor and texture for each type of cheese. The aim of the present study was to evaluate the influence of chlorine products usage for cleaning and sanitizing the milking equipment on (i) raw milk microbiota; (ii) the deriving whey-starter microbiota; and (iii) Trentingrana Protected Designation of Origin (PDO) cheese microbiota and volatilome. Milk samples from three farms affiliated to a Trentingrana PDO cheese factory were collected three times per week during a 6-weeks period in which a sodium hypochlorite detergent (period C) was used and during a subsequent 6-weeks period of non-chlorine detergent usage (period NC). Samples were subjected to microbiological [Standard Plate Count; coliforms; coagulase-positive staphylococci; and lactic acid bacteria (LAB)] and metagenomic analysis (amplification of V3-V4 regions of 16S rRNA gene performed on Illumina MiSeq platform). In addition, cheese volatilome was determined by SPME-GC-MS. In the transition from period C to period NC, higher SPC and LAB counts in milk were recorded. Milk metagenomic analysis showed a peculiar distinctive microbiota composition for the three farms during the whole experimental period. Moreover, differences were highlighted comparing C and NC periods in each farm. A difference in microbial population related to chlorine usage in bulk milk and vat samples was evidenced. Moreover, chlorine utilization at farm level was found to affect the whey-starter population: the usually predominant Lactobacillus helveticus was significantly reduced during NC period, whereas Lactobacillus delbrueckii had the exact opposite trend. Alpha- and beta-diversity revealed a separation between the two treatment periods with a higher presence of L. helveticus, L. delbrueckii, and Streptococcus thermophilus in cheese samples after NC detergent period. Cheese volatilome analysis showed a slight decrease in lipolysis during C period in the inner part of the cheese wheel. Although preliminary, these results suggest a profound influence on milk and cheese microbiota, as well as on raw milk cheese production and quality, due to the use of chlorine. However, further studies will be needed to better understand the complex relationship between chlorine and microbiota along all the cheese production steps.}, } @article {pmid33121140, year = {2020}, author = {Gebremedhn, H and Deboutte, W and Schoonvaere, K and Demaeght, P and De Smet, L and Amssalu, B and Matthijnssens, J and de Graaf, DC}, title = {Metagenomic Approach with the NetoVIR Enrichment Protocol Reveals Virus Diversity within Ethiopian Honey Bees (Apis mellifera simensis).}, journal = {Viruses}, volume = {12}, number = {11}, pages = {}, pmid = {33121140}, issn = {1999-4915}, mesh = {Animals ; Bees/*virology ; Ethiopia ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/*methods ; Phylogeny ; Varroidae/virology ; Virology/*methods ; Virome ; Virus Diseases/transmission/*veterinary ; Viruses/*classification/isolation & purification ; }, abstract = {Metagenomics studies have accelerated the discovery of novel or divergent viruses of the honey bee. However, most of these studies predominantly focused on RNA viruses, and many suffer from the relatively low abundance of viral nucleic acids in the samples (i.e., compared to that of the host). Here, we explored the virome of the Ethiopian honey bee, Apis mellifera simensis, using an unbiased metagenomic approach in which the next-generation sequencing step was preceded by an enrichment protocol for viral particles. Our study revealed five well-known bee viruses and 25 atypical virus species, most of which have never been found in A. mellifera before. The viruses belong to Iflaviridae, Dicistroviridae, Secoviridae, Partitiviridae, Parvoviridae, Potyviridae, and taxonomically unclassified families. Fifteen of these atypical viruses were most likely plant-specific, and the remaining ten were presumed to be insect-specific. Apis mellifera filamentous virus (AmFV) was found in one sampling site out of 10. Two samples contained high read counts of a virus similar to Diatraea saccharales densovirus (DsDNV), which is a virus that causes high mortality in the sugarcane borer. AmFV and the DsDNV-like virus were the only DNA viruses found. Three viruses that primarily infect Drosophila spp. were also discovered: La Jolla virus (LJV), Kilifi virus (KiV), and Thika virus. Our study suggests that phoretic varroa mites are involved in the transmission of LJV and KiV and that both viruses replicate in mites and adult bees. We also found an overwhelming dominance of the deformed wing virus type B variant, which fits well with the apparently harmless infestation by Varroa destructor. It was suggested that Ethiopian bees have developed tolerance against virus infections as the result of natural selection.}, } @article {pmid33119247, year = {2021}, author = {Sultan, S and El-Mowafy, M and Elgaml, A and El-Mesery, M and El Shabrawi, A and Elegezy, M and Hammami, R and Mottawea, W}, title = {Alterations of the Treatment-Naive Gut Microbiome in Newly Diagnosed Hepatitis C Virus Infection.}, journal = {ACS infectious diseases}, volume = {7}, number = {5}, pages = {1059-1068}, doi = {10.1021/acsinfecdis.0c00432}, pmid = {33119247}, issn = {2373-8227}, mesh = {Dysbiosis ; *Gastrointestinal Microbiome ; Hepacivirus/genetics ; *Hepatitis C/diagnosis ; Humans ; Metagenomics ; }, abstract = {Gut microbiota dysbiosis has been linked to many heath disorders including hepatitis C virus (HCV) infection. However, profiles of the gut microbiota alterations in HCV are inconsistent in the literature and are affected by the treatment regimens. Using samples collected prior to treatment from newly diagnosed patients, we characterized the gut microbiota structure in HCV patients as compared to healthy controls. Treatment-naive HCV microbiota showed increased diversity, an increased abundance of Prevotella, Succinivibrio, Catenibacterium, Megasphaera, and Ruminococcaceae, and a lower abundance of Bacteroides, Dialister, Bilophila, Streptococcus, parabacteroides, Enterobacteriaceae, Erysipelotrichaceae, Rikenellaceae, and Alistipes. Predicted community metagenomic functions showed a depletion of carbohydrate and lipid metabolism in HCV microbiota along with perturbations of amino acid metabolism. Receiver-operating characteristic analysis identified five disease-specific operational taxonomic units (OTUs) as potential biomarkers of HCV infections. Collectively, our findings reveal the alteration of gut microbiota in treatment naive HCV patients and suggest that gut microbiota may hold diagnostic promise in HCV infection.}, } @article {pmid33119059, year = {2021}, author = {Bai, X and Ren, J and Fan, Y and Sun, F}, title = {KIMI: Knockoff Inference for Motif Identification from molecular sequences with controlled false discovery rate.}, journal = {Bioinformatics (Oxford, England)}, volume = {37}, number = {6}, pages = {759-766}, pmid = {33119059}, issn = {1367-4811}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; R01 GM131407/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Computer Simulation ; Metagenome ; *Metagenomics ; *Microbiota ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {MOTIVATION: The rapid development of sequencing technologies has enabled us to generate a large number of metagenomic reads from genetic materials in microbial communities, making it possible to gain deep insights into understanding the differences between the genetic materials of different groups of microorganisms, such as bacteria, viruses, plasmids, etc. Computational methods based on k-mer frequencies have been shown to be highly effective for classifying metagenomic sequencing reads into different groups. However, such methods usually use all the k-mers as features for prediction without selecting relevant k-mers for the different groups of sequences, i.e. unique nucleotide patterns containing biological significance.

RESULTS: To select k-mers for distinguishing different groups of sequences with guaranteed false discovery rate (FDR) control, we develop KIMI, a general framework based on model-X Knockoffs regarded as the state-of-the-art statistical method for FDR control, for sequence motif discovery with arbitrary target FDR level, such that reproducibility can be theoretically guaranteed. KIMI is shown through simulation studies to be effective in simultaneously controlling FDR and yielding high power, outperforming the broadly used Benjamini-Hochberg procedure and the q-value method for FDR control. To illustrate the usefulness of KIMI in analyzing real datasets, we take the viral motif discovery problem as an example and implement KIMI on a real dataset consisting of viral and bacterial contigs. We show that the accuracy of predicting viral and bacterial contigs can be increased by training the prediction model only on relevant k-mers selected by KIMI.

Our implementation of KIMI is available at https://github.com/xinbaiusc/KIMI.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid33115864, year = {2021}, author = {Li, Y and Altan, E and Reyes, G and Halstead, B and Deng, X and Delwart, E}, title = {Virome of Bat Guano from Nine Northern California Roosts.}, journal = {Journal of virology}, volume = {95}, number = {3}, pages = {}, pmid = {33115864}, issn = {1098-5514}, mesh = {Animals ; California ; Chiroptera/*virology ; Feces/*virology ; *Genome, Viral ; *Metagenome ; Phylogeny ; *Virome ; Viruses/classification/*genetics ; }, abstract = {Bats are hosts to a large variety of viruses, including many capable of cross-species transmissions to other mammals, including humans. We characterized the virome in guano from five common bat species in 9 Northern California roosts and from a pool of 5 individual bats. Genomes belonging to 14 viral families known to infect mammals and 17 viral families infecting insects or of unknown tropism were detected. Nearly complete or complete genomes of a novel parvovirus, astrovirus, nodavirus, circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses, and densoviruses, and more partial genomes of a novel alphacoronavirus and a bunyavirus were characterized. Lower numbers of reads with >90% amino acid identity to previously described calicivirus, circovirus, adenoviruses, hepatovirus, bocaparvoviruses, and polyomavirus in other bat species were also found, likely reflecting their wide distribution among different bats. Unexpectedly, a few sequence reads of canine parvovirus 2 and the recently described mouse kidney parvovirus were also detected and their presence confirmed by PCR; these possibly originated from guano contamination by carnivores and rodents. The majority of eukaryotic viral reads were highly divergent, indicating that numerous viruses still remain to be characterized, even from such a heavily investigated order as Chiroptera.IMPORTANCE Characterizing the bat virome is important for understanding viral diversity and detecting viral spillover between animal species. Using an unbiased metagenomics method, we characterize the virome in guano collected from multiple roosts of common Northern California bat species. We describe several novel viral genomes and report the detection of viruses with close relatives reported in other bat species, likely reflecting cross-species transmissions. Viral sequences from well-known carnivore and rodent parvoviruses were also detected, whose presence are likely the result of contamination from defecation and urination atop guano and which reflect the close interaction of these mammals in the wild.}, } @article {pmid33115723, year = {2020}, author = {Tidjani Alou, M and Naud, S and Khelaifia, S and Bonnet, M and Lagier, JC and Raoult, D}, title = {State of the Art in the Culture of the Human Microbiota: New Interests and Strategies.}, journal = {Clinical microbiology reviews}, volume = {34}, number = {1}, pages = {}, pmid = {33115723}, issn = {1098-6618}, mesh = {Bacteria/classification/*isolation & purification/metabolism ; Bacteriological Techniques/*methods ; Culture Media/*chemistry ; Flow Cytometry ; Gastrointestinal Microbiome ; Humans ; }, abstract = {The last 5 years have seen a turning point in the study of the gut microbiota with a rebirth of culture-dependent approaches to study the gut microbiota. High-throughput methods have been developed to study bacterial diversity with culture conditions aimed at mimicking the gut environment by using rich media such as YCFA (yeast extract, casein hydrolysate, fatty acids) and Gifu anaerobic medium in an anaerobic workstation, as well as media enriched with rumen and blood and coculture, to mimic the symbiosis of the gut microbiota. Other culture conditions target phenotypic and metabolic features of bacterial species to facilitate their isolation. Preexisting technologies such as next-generation sequencing and flow cytometry have also been utilized to develop innovative methods to isolate previously uncultured bacteria or explore viability in samples of interest. These techniques have been applied to isolate CPR (Candidate Phyla Radiation) among other, more classic approaches. Methanogenic archaeal and fungal cultures present different challenges than bacterial cultures. Efforts to improve the available systems to grow archaea have been successful through coculture systems. For fungi that are more easily isolated from the human microbiota, the challenge resides in the identification of the isolates, which has been approached by applying matrix-assisted laser desorption ionization-time of flight mass spectrometry technology to fungi. Bacteriotherapy represents a nonnegligible avenue in the future of medicine to correct dysbiosis and improve health or response to therapy. Although great strides have been achieved in the last 5 years, efforts in bacterial culture need to be sustained to continue deciphering the dark matter of metagenomics, particularly CPR, and extend these methods to archaea and fungi.}, } @article {pmid33115458, year = {2020}, author = {Chen, W and Jiang, Q and Yan, G and Yang, D}, title = {The oral microbiome and salivary proteins influence caries in children aged 6 to 8 years.}, journal = {BMC oral health}, volume = {20}, number = {1}, pages = {295}, pmid = {33115458}, issn = {1472-6831}, support = {31571508//National Natural Science Foundation of China/International ; 81170950//National Natural Science Foundation of China/International ; }, mesh = {Aged ; Child ; Chromatography, Liquid ; *Dental Caries ; Humans ; *Microbiota ; RNA, Ribosomal, 16S ; Saliva ; Salivary Proteins and Peptides ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: Oral microbiome and salivary proteins play a critical role in the occurrence and development of caries. In this study, we used metagenomic and metaproteomic analyses to explore the microbiological and proteinic biomarkers and investigate the etiology of caries in 6-8 years old children. Our study aims to offer a better comprehension of these factors and the relationship with caries, and these findings might facilitate caries risk assessment and provide a basis for future prevention strategies.

METHODS: Children 6 to 8 years old living in rural isolated areas including 40 caries-active subjects and 40 caries-free subjects were recruited. Supragingival plaque and unstimulated saliva were collected for 16S rDNA pyrosequencing and isobaric tags for relative and absolute quantitation (iTRAQ) technique coupled with quantitative nano-flow liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively.

RESULTS: We found 6 phyla and 13 genera predominant in all the samples, and differences in relative abundances can be observed. The Alpha diversity analysis demonstrated that the richness and diversity of the bacterial communities were similar between children with caries-free and caries-active groups; LEfSe detected differences in the bacterial community including Dialister, Selenomonas, Actinomyces, and Mogibacterium in the caries-active group (P < 0.05) and Capnocytophaga, Fusobacterium, Desulfuromonadales, Haemophilus, and Porphyromonas in the caries-free group(P < 0.05). The core microbiome was defined as 18 predominant genera in children with caries. The results of the salivary proteome identified 9135 unique peptides and 1662 proteins group from 20 salivary samples. Two hundred fifty-eight proteins were differentially expressed between the caries-free and caries-active groups.

CONCLUSIONS: The diversity of the microbial community has little effect on caries but some bacteria with different relative abundance between the caries-active and caries-free group could be considered as potential biomarkers for children with caries. In addition, as a critical host factor of caries, the salivary proteins are different in caries-free and caries-active groups.}, } @article {pmid33113351, year = {2020}, author = {Gálvez, EJC and Iljazovic, A and Amend, L and Lesker, TR and Renault, T and Thiemann, S and Hao, L and Roy, U and Gronow, A and Charpentier, E and Strowig, T}, title = {Distinct Polysaccharide Utilization Determines Interspecies Competition between Intestinal Prevotella spp.}, journal = {Cell host & microbe}, volume = {28}, number = {6}, pages = {838-852.e6}, doi = {10.1016/j.chom.2020.09.012}, pmid = {33113351}, issn = {1934-6069}, mesh = {Animals ; DNA, Bacterial ; *Gastrointestinal Microbiome ; Genetic Loci ; Genome, Bacterial ; Glycoside Hydrolases/genetics ; Glycosyltransferases/genetics ; Humans ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Phylogeny ; Polysaccharides/*metabolism ; Prevotella/classification/*growth & development/isolation & purification ; RNA, Ribosomal, 16S ; Transcriptome ; Vegans ; Whole Genome Sequencing ; Xylans/*metabolism ; }, abstract = {Prevotella spp. are a dominant bacterial genus within the human gut. Multiple Prevotella spp. co-exist in some individuals, particularly those consuming plant-based diets. Additionally, Prevotella spp. exhibit variability in the utilization of diverse complex carbohydrates. To investigate the relationship between Prevotella competition and diet, we isolated Prevotella species from the mouse gut, analyzed their genomes and transcriptomes in vivo, and performed competition experiments between species in mice. Diverse dominant Prevotella species compete for similar metabolic niches in vivo, which is linked to the upregulation of specific polysaccharide utilization loci (PULs). Complex plant-derived polysaccharides are required for Prevotella spp. expansion, with arabinoxylans having a prominent impact on species abundance. The most dominant Prevotella species encodes a specific tandem-repeat trsusC/D PUL that enables arabinoxylan utilization and is conserved in human Prevotella copri strains, particularly among those consuming a vegan diet. These findings suggest that efficient (arabino)xylan-utilization is a factor contributing to Prevotella dominance.}, } @article {pmid33113287, year = {2021}, author = {Kang, J and Park, JS and Jung, SW and Kim, HJ and Joo, HM and Kang, D and Seo, H and Kim, S and Jang, MC and Lee, KW and Jin Oh, S and Lee, S and Lee, TK}, title = {Zooming on dynamics of marine microbial communities in the phycosphere of Akashiwo sanguinea (Dinophyta) blooms.}, journal = {Molecular ecology}, volume = {30}, number = {1}, pages = {207-221}, pmid = {33113287}, issn = {1365-294X}, mesh = {*Dinoflagellida/genetics ; Harmful Algal Bloom ; *Microbiota/genetics ; Phytoplankton/genetics ; Republic of Korea ; }, abstract = {Characterizing ecological relationships between viruses, bacteria and phytoplankton in the ocean is critical to understanding the ecosystem; however, these relationships are infrequently investigated together. To understand the dynamics of microbial communities and environmental factors in harmful algal blooms (HABs), we examined the environmental factors and microbial communities during Akashiwo sanguinea HABs in the Jangmok coastal waters of South Korea by metagenomics. Specific bacterial species showed complex synergistic and antagonistic relationships with the A. sanguinea bloom. The endoparasitic dinoflagellate Amoebophrya sp. 1 controlled the bloom dynamics and correlated with HAB decline. Among nucleocytoplasmic large DNA viruses (NCLDVs), two Pandoraviruses and six Phycodnaviruses were strongly and positively correlated with the HABs. Operational taxonomic units of microbial communities and environmental factors associated with A. sanguinea were visualized by network analysis: A. sanguinea-Amoebophrya sp. 1 (r = .59, time lag: 2 days) and A. sanguinea-Ectocarpus siliculosus virus 1 in Phycodnaviridae (0.50, 4 days) relationships showed close associations. The relationship between A. sanguinea and dissolved inorganic phosphorus relationship also showed a very close correlation (0.74, 0 day). Microbial communities and the environment changed dynamically during the A. sanguinea bloom, and the rapid turnover of microorganisms responded to ecological interactions. A. sanguinea bloom dramatically changes the environments by exuding dissolved carbohydrates via autotrophic processes, followed by changes in microbial communities involving host-specific viruses, bacteria and parasitoids. Thus, the microbial communities in HAB are composed of various organisms that interact in a complex manner.}, } @article {pmid33111503, year = {2021}, author = {Zhao, Z and Fei, K and Bai, H and Wang, Z and Duan, J and Wang, J}, title = {Metagenome association study of the gut microbiome revealed biomarkers linked to chemotherapy outcomes in locally advanced and advanced lung cancer.}, journal = {Thoracic cancer}, volume = {12}, number = {1}, pages = {66-78}, pmid = {33111503}, issn = {1759-7714}, support = {KY201701//Aiyou foundation/ ; CIFMS 2016-I2M-3-008//CAMS Innovation Fund for Medical Sciences/ ; 2018PT31035//CAMS Key lab of translational research on lung cancer/ ; IRT-17R10//Ministry of Education Innovation Team development project/ ; 2019YFC1315700//National key research and development project/ ; 81630071//National Natural Sciences Foundation Key Program/ ; }, mesh = {Adult ; Aged ; Biomarkers/*metabolism ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Lung Neoplasms/*drug therapy/*genetics ; Male ; Metagenome/*genetics ; Middle Aged ; Progression-Free Survival ; }, abstract = {BACKGROUND: The gut microbiome is important in the development and immunotherapy efficacy of lung cancer. However, the relationship between the intestinal flora and chemotherapy outcomes remains unclear and was investigated in this study.

METHODS: We analyzed baseline stool samples from patients with locally advanced and advanced lung cancer before chemotherapy treatment, through metagenomics of the gut microbiota. The composition, diversity, function, and metabolic pathway analysis were compared among patients with different clinical outcomes.

RESULTS: From 64 patients, 33 responded to treatment (responders) and 31 did not (nonresponders). Streptococcus mutans and Enterococcus casseliflavus were enriched in responders (P < 0.05), while 11 bacteria including Leuconostoc lactis and Eubacterium siraeum were enriched in nonresponders (P < 0.05) by variance analysis. Responders were associated with significantly higher Acidobacteria and Granulicella, while Streptococcus oligofermentans, Megasphaera micronuciformis, and Eubacterium siraeum were more abundant in nonresponders by Lefse analysis. Streptococcus mutans and Enterococcus casseliflavus were further identified as bacterial markers relevant to responders using unsupervised clustering, and Leuconostoc lactis and Eubacterium siraeum were related to nonresponders. The L-glutamate degradation VIII pathway was enriched in responders (P = 0.014), and the C4 photosynthetic carbon assimilation cycle, reductive TCA cycle I, and hexitol fermentation to lactate, formate, ethanol, and acetate were enriched in nonresponders (P < 0.05). Additionally, significant associations of bacterial species with clinical phenotypes were observed by Spearman correlation analysis.

CONCLUSIONS: The specific gut microbiome of patients with lung cancer might be connected to the clinical outcomes of chemotherapy.

KEY POINTS: Significant findings of the study Lung cancer patients with different gut microbiome compositions and microbiome metabolic pathways have different responses to chemotherapy. Microbiome species are also associated with different lung cancer clinical phenotypes. What this study adds We have identified specific gut microbiome species that can be used as relevant biomarkers for chemotherapy outcomes. This can potentially be used to guide clinical treatment decisions.}, } @article {pmid33110490, year = {2020}, author = {Huang, C and Yu, Y and Du, W and Liu, Y and Dai, R and Tang, W and Wang, P and Zhang, C and Shi, G}, title = {Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma.}, journal = {Clinical and translational allergy}, volume = {10}, number = {}, pages = {42}, pmid = {33110490}, issn = {2045-7022}, abstract = {BACKGROUND: Fungal and bacterial microbiota play an important role in development of asthma. We aim to characterize airway microbiome (mycobiome, bacteriome) and functional genes in asthmatics and controls.

METHODS: Sputum microbiome of controls, untreated asthma patients and inhaled corticosteroid (ICS) receiving patients was detected using high throughput sequencing. Metagenomic sequencing was used to examine the functional genes of microbiome.

RESULTS: 1. Mycobiome: α diversity was lower in untreated asthma group than that in controls. Mycobiome compositions differed among the three groups. Compared with controls, untreated asthma group has higher abundance of Wallemia, Mortierella and Fusarium. Compared with untreated asthma patients, ICS receiving patients has higher abundance of Fusarium and Mortierella, lower frequency of Wallemia, Alternaria and Aspergillus. 2. Bacteriome: α diversity was lower in untreated asthma group than that in controls. There are some overlaps of bacteriome compositions between controls and untreated asthma patients which were distinct from ICS receiving patients. Untreated asthma group has higher Streptococcus than controls. 3. Potential fungal and bacterial biomarkers of asthma: Trametes, Aspergillus, Streptococcus, Gemella, Neisseria, etc. 4. Correlation network: There are dense and homogenous correlations in controls but a dramatically unbalanced network in untreated asthma and ICS receiving patients, which suggested the existence of disease-specific inter-kingdom and intra-kingdom alterations. 5. Metagenomic analysis: functional pathways were associated with the status of asthma, microbiome and functional genes showed different correlations in different environment.

CONCLUSION: We showed mycobiome and bacteriome dysbiosis in asthma featured by alterations in biodiversity, community composition, inter-kingdom and intra-kingdom network. We also observed several functional genes associated with asthma.}, } @article {pmid33110112, year = {2020}, author = {Kazemian, N and Ramezankhani, M and Sehgal, A and Khalid, FM and Kalkhoran, AHZ and Narayan, A and Wong, GK and Kao, D and Pakpour, S}, title = {The trans-kingdom battle between donor and recipient gut microbiome influences fecal microbiota transplantation outcome.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {18349}, pmid = {33110112}, issn = {2045-2322}, mesh = {Adult ; Bacteroidetes/metabolism ; Clostridiales/metabolism ; Clostridioides/metabolism ; Clostridium Infections/microbiology/therapy ; Desulfovibrio/metabolism ; *Fecal Microbiota Transplantation ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Machine Learning ; Male ; Metagenomics ; Tissue Donors ; Treatment Outcome ; }, abstract = {Fundamental restoration ecology and community ecology theories can help us better understand the underlying mechanisms of fecal microbiota transplantation (FMT) and to better design future microbial therapeutics for recurrent Clostridioides difficile infections (rCDI) and other dysbiosis-related conditions. In this study, stool samples were collected from donors and rCDI patients one week prior to FMT (pre-FMT), as well as from patients one week following FMT (post-FMT). Using metagenomic sequencing and machine learning, our results suggested that FMT outcome is not only dependent on the ecological structure of the recipients, but also the interactions between the donor and recipient microbiomes at the taxonomical and functional levels. We observed that the presence of specific bacteria in donors (Clostridioides spp., Desulfovibrio spp., Odoribacter spp. and Oscillibacter spp.) and the absence of fungi (Yarrowia spp.) and bacteria (Wigglesworthia spp.) in recipients prior to FMT could predict FMT success. Our results also suggested a series of interlocked mechanisms for FMT success, including the repair of the disturbed gut ecosystem by transient colonization of nexus species followed by secondary succession of bile acid metabolizers, sporulators, and short chain fatty acid producers.}, } @article {pmid33109755, year = {2020}, author = {Oliverio, AM and Bissett, A and McGuire, K and Saltonstall, K and Turner, BL and Fierer, N}, title = {The Role of Phosphorus Limitation in Shaping Soil Bacterial Communities and Their Metabolic Capabilities.}, journal = {mBio}, volume = {11}, number = {5}, pages = {}, pmid = {33109755}, issn = {2150-7511}, mesh = {Bacteria/classification/*metabolism ; Ecosystem ; Forests ; Metagenome ; Metagenomics ; Microbial Consortia ; Nitrogen/metabolism ; Phosphorus/*metabolism ; *Soil Microbiology ; }, abstract = {Phosphorus (P) is an essential nutrient that is often in limited supply, with P availability constraining biomass production in many terrestrial ecosystems. Despite decades of work on plant responses to P deficiency and the importance of soil microbes to terrestrial ecosystem processes, how soil microbes respond to, and cope with, P deficiencies remains poorly understood. We studied 583 soils from two independent sample sets that each span broad natural gradients in extractable soil P and collectively represent diverse biomes, including tropical forests, temperate grasslands, and arid shrublands. We paired marker gene and shotgun metagenomic analyses to determine how soil bacterial and archaeal communities respond to differences in soil P availability and to detect corresponding shifts in functional attributes. We identified microbial taxa that are consistently responsive to extractable soil P, with those taxa found in low P soils being more likely to have traits typical of oligotrophic life history strategies. Using environmental niche modeling of genes and gene pathways, we found an enriched abundance of key genes in low P soils linked to the carbon-phosphorus (C-P) lyase and phosphonotase degradation pathways, along with key components of the high-affinity phosphate-specific transporter (Pst) and phosphate regulon (Pho) systems. Taken together, these analyses suggest that catabolism of phosphonates is an important strategy used by bacteria to scavenge phosphate in P-limited soils. Surprisingly, these same pathways are important for bacterial growth in P-limited marine waters, highlighting the shared metabolic strategies used by both terrestrial and marine microbes to cope with P limitation.}, } @article {pmid33109276, year = {2020}, author = {Juma, EO and Kim, CH and Dunlap, C and Allan, BF and Stone, CM}, title = {Culex pipiens and Culex restuans egg rafts harbor diverse bacterial communities compared to their midgut tissues.}, journal = {Parasites & vectors}, volume = {13}, number = {1}, pages = {532}, pmid = {33109276}, issn = {1756-3305}, mesh = {Animals ; *Bacteria/classification/isolation & purification ; Culex/*microbiology ; Female ; Gastrointestinal Microbiome ; Genes, Bacterial ; Larva/microbiology ; Metagenomics/methods ; Microbiota ; Oviposition ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The bacterial communities associated with mosquito eggs are an essential component of the mosquito microbiota, yet there are few studies characterizing and comparing the microbiota of mosquito eggs to other host tissues.

METHODS: We sampled gravid female Culex pipiens L. and Culex restuans Theobald from the field, allowed them to oviposit in the laboratory, and characterized the bacterial communities associated with their egg rafts and midguts for comparison through MiSeq sequencing of the 16S rRNA gene.

RESULTS: Bacterial richness was higher in egg rafts than in midguts for both species, and higher in Cx pipiens than Cx. restuans. The midgut samples of Cx. pipiens and Cx. restuans were dominated by Providencia. Culex pipiens and Cx. restuans egg rafts samples were dominated by Ralstonia and Novosphingobium, respectively. NMDS ordination based on Bray-Curtis distance matrix revealed that egg-raft samples, or midgut tissues harbored similar bacterial communities regardless of the mosquito species. Within each mosquito species, there was a distinct clustering of bacterial communities between egg raft and midgut tissues.

CONCLUSION: These findings expand the list of described bacterial communities associated with Cx. pipiens and Cx. restuans and the additional characterization of the egg raft bacterial communities facilitates comparative analysis of mosquito host tissues, providing a basis for future studies seeking to understand any functional role of the bacterial communities in mosquito biology.}, } @article {pmid33108273, year = {2020}, author = {Kelly, L and Wolfson, SJ}, title = {Finding phenazine.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {33108273}, issn = {2050-084X}, mesh = {Agriculture ; Bacteria/genetics ; *Microbiota ; Phenazines ; *Soil ; }, abstract = {Analysis of genetic information from soil samples provides insights into bacteria that help to protect crops from fungal diseases by producing chemicals called phenazines.}, } @article {pmid33103254, year = {2020}, author = {Yan, X and Wang, F and Weng, P and Wu, Z}, title = {The effect of fermented Huyou juice on intestinal microbiota in a high-fat diet-induced obesity mouse model.}, journal = {Journal of food biochemistry}, volume = {44}, number = {12}, pages = {e13480}, doi = {10.1111/jfbc.13480}, pmid = {33103254}, issn = {1745-4514}, mesh = {Animals ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred C57BL ; Obesity/drug therapy/etiology ; }, abstract = {This study mainly discussed the effect of fermented Huyou juice (FHJ) on modulating the intestinal microbiota of human, and anti-obesity mechanisms. Through the way of metagenomics, the effect of FHJ on gut flora has been summarized with a mice model of obesity induced by human flora-associated (HFA) high-fat diet. The results showed that the FHJ ameliorated the gut dysbiosis caused by obesity. When receiving FHJ treatment, a dramatic decrease in Firmicutes/Bacteroidetes occurred. What's more, having experienced 8 weeks of FHJ intervention, KEGG pathways of two-component system, ATP-binding cassette (ABC) transporters, and biosynthesis of amino acids made the most differentially expressed genes more abundant, the unigene numbers are 16781,480, and 1,221, respectively. Our results may be of great significance to the use of FHJ which serves as a functional fermented beverage product with the underlying effect of treating the obesity induced by high-fat diet. The FHJ helps to improve the host health by regulating the intestinal flora and affecting some metabolic pathways. PRACTICAL APPLICATIONS: The fermentation of Huyou juice is one of the important ways to develop and utilize fruit resources. It is a common way of fruit and vegetable juice fermentation with mixed strains. After fermentation, the juice produces a large number of bioactive peptides, and sugar, toxic substances, and antinutritional material will be reduced, the nutritional value of the fruits and vegetables were improved. At the same time, the fermented juice industry could develop various functional health products, which is conducive to the transformation, upgrading, and sustainable development of Changshan Huyou.}, } @article {pmid33099131, year = {2020}, author = {Zhang, F and Yue, L and Fang, X and Wang, G and Li, C and Sun, X and Jia, X and Yang, J and Song, J and Zhang, Y and Guo, C and Ma, G and Sang, M and Chen, F and Wang, P}, title = {Altered gut microbiota in Parkinson's disease patients/healthy spouses and its association with clinical features.}, journal = {Parkinsonism & related disorders}, volume = {81}, number = {}, pages = {84-88}, doi = {10.1016/j.parkreldis.2020.10.034}, pmid = {33099131}, issn = {1873-5126}, mesh = {Aged ; Dysbiosis/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Healthy Volunteers ; Humans ; Inflammation/microbiology ; Male ; Metagenomics ; Middle Aged ; Parkinson Disease/*microbiology/physiopathology ; RNA, Ribosomal, 16S/genetics ; *Spouses ; }, abstract = {INTRODUCTION: Increasing evidence shows that gut microbiota dysbiosis may play important roles in the occurrence and progression of Parkinson's disease (PD), but the findings are inconsistent. Besides, the effect of family environment on gut microbiota dysbiosis remains unclear.

METHODS: We characterized the gut microbial compositions of 63 PD patients, 63 healthy spouses (HS) and 74 healthy people (HP) using 16S rRNA sequencing. Clinical phenotypes and microbial composition were analyzed comprehensively.

RESULTS: There were markedly different microbial compositions among PD, HS and HP samples by alpha/beta diversity. We also found differential microbial compositions among Hoehn & Yahr stage/disease duration. Eight inflammation-associated microbial genera shared a continuously increase trend with increased Hoehn & Yahr stage and disease duration, indicating characteristic bacteria associated with deterioration in PD. Additionally, seven bacterial markers were identified for accurately differentiating PD patients from the controls (area under the curve [AUC]: 0.856).

CONCLUSIONS: Our study shows altered gut microbiota in PD patients. Importantly, inflammation-associated microbial genera may play roles in PD progression. Differential microbial compositions in HS and HP samples demonstrate that the gut microbiota are also affected by family environment. Disease-associated metagenomics studies should consider the family environmental factor. Our research provides an important reference and improves the understanding of gut microbiota in PD patients.}, } @article {pmid33098556, year = {2021}, author = {Li, J and Xu, Y and Song, Q and Yang, J and Xie, L and Yu, S and Zheng, L}, title = {Polycyclic aromatic hydrocarbon and n-alkane pollution characteristics and structural and functional perturbations to the microbial community: a case-study of historically petroleum-contaminated soil.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {9}, pages = {10589-10602}, pmid = {33098556}, issn = {1614-7499}, support = {2018YFC1800901//National Key R&D Program of China/ ; 2019YFC1806004//National Key R&D Program of China/ ; PPC2018016//the Open Project Program of State Key Laboratory of Petroleum Pollution Control/ ; 41831283//National Natural Science Foundation of China/ ; }, mesh = {Alkanes/analysis ; Beijing ; Biodegradation, Environmental ; China ; *Microbiota ; *Petroleum/analysis ; *Polycyclic Aromatic Hydrocarbons/analysis ; Soil ; *Soil Pollutants/analysis ; }, abstract = {Characterization of the typical petroleum pollutants, polycyclic aromatic hydrocarbons (PAHs) and n-alkanes, and indigenous microbial community structure and function in historically contaminated soil at petrol stations is critical. Five soil samples were collected from a petrol station in Beijing, China. The concentrations of 16 PAHs and 31 n-alkanes were measured by gas chromatography-mass spectrometry. The total concentrations of PAHs and n-alkanes ranged from 973 ± 55 to 2667 ± 183 μg/kg and 6.40 ± 0.38 to 8.65 ± 0.59 mg/kg (dry weight), respectively, which increased with depth. According to the observed molecular indices, PAHs and n-alkanes originated mostly from petroleum-related sources. The levels of ΣPAHs and the total toxic benzo[a]pyrene equivalent (ranging from 6.41 to 72.54 μg/kg) might exert adverse biological effects. Shotgun metagenomic sequencing was employed to investigate the indigenous microbial community structure and function. The results revealed that Proteobacteria and Actinobacteria were the most abundant phyla, and Nocardioides and Microbacterium were the important genera. Based on COG and KEGG annotations, the highly abundant functional classes were identified, and these functions were involved in allowing microorganisms to adapt to the pressure from contaminants. Five petroleum hydrocarbon degradation-related genes were annotated, revealing the distribution of degrading microorganisms. This work facilitates the understanding of the composition, source, and potential ecological impacts of residual PAHs and n-alkanes in historically contaminated soil.}, } @article {pmid33097978, year = {2021}, author = {Forouzan, S and Hoffman, KL and Kosten, TA}, title = {Methamphetamine exposure and its cessation alter gut microbiota and induce depressive-like behavioral effects on rats.}, journal = {Psychopharmacology}, volume = {238}, number = {1}, pages = {281-292}, pmid = {33097978}, issn = {1432-2072}, mesh = {Animals ; Anxiety/*chemically induced/microbiology ; Anxiety Disorders/chemically induced/microbiology ; Behavior, Animal/*drug effects ; Brain/drug effects ; Central Nervous System Stimulants/administration & dosage/*toxicity ; Depression/chemically induced/microbiology ; Dose-Response Relationship, Drug ; Dysbiosis/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Male ; Methamphetamine/administration & dosage/*toxicity ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; Swimming ; }, abstract = {RATIONALE: Methamphetamine is a highly abused psychostimulant drug and its use remains a major public health concern worldwide with limited effective treatment options. Accumulative evidence reveals the influence of gut microbiota on the brain, behavior, and health as a part of the gut-brain axis but its involvement in modulating this substance use disorder remains poorly understood.

OBJECTIVE: We sought to determine whether methamphetamine exposure and cessation or withdrawal alter the intestinal gut microbiota as well as characterize cessation-induced behavioral changes.

METHODS: Male, Sprague-Dawley rats were administered methamphetamine (2 mg/kg; s.c.) or vehicle (n = 8 per group) twice per day for 14 consecutive days. On various days before, during, and after administration, fecal samples were collected and tests of anxiety- and depressive-like behaviors were conducted.

RESULTS: Methamphetamine administration and cessation did not alter the relative abundance of bacteria but significantly changed the composition of gut bacteria through 16S rRNA sequencing. These changes were normalized after 7 days of methamphetamine cessation. Moreover, acute methamphetamine cessation induced depressive-like behavior, with an increase in immobility in the forced swim test but did not alter anxiety-like behaviors in tests of open field test or elevated plus maze.

CONCLUSIONS: These findings provide direct evidence that methamphetamine and its cessation cause gut dysbiosis and that the latter associates with depressive-like behavior in rodents. Our observation will contribute to a better understanding of the function of gut microbiota in the process of substance use disorders and guide the choice of target therapeutics.}, } @article {pmid33097516, year = {2020}, author = {Klinsoda, J and Vötterl, J and Koger, S and Metzler-Zebeli, BU}, title = {Dietary Phytase- and Lactic Acid-Treated Cereals Caused Greater Taxonomic Adaptations than Functional Adaptations in the Cecal Metagenome of Growing Pigs.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {1}, pages = {}, pmid = {33097516}, issn = {1098-5336}, mesh = {6-Phytase/administration & dosage/*metabolism ; Animal Feed/analysis ; Animals ; Bacteria/*classification ; *Bacterial Physiological Phenomena ; Cecum/*microbiology ; Diet/veterinary ; Dietary Supplements/analysis ; Gastrointestinal Microbiome/*physiology ; Lactic Acid/administration & dosage/*metabolism ; Male ; Metagenome ; Random Allocation ; Sus scrofa/*microbiology ; }, abstract = {Phosphorus (P) is an essential nutrient for the gut bacteria and the host. Nevertheless, little information exists that indicates to what extent an improved level of P availability in the small intestine leads to functional adaptations in bacterial metabolic pathways in the large intestine. Therefore, we investigated the changes in the taxonomic and functional bacterial metagenome in cecal digesta of growing pigs fed diets containing phytase and/or cereals treated with 2.5% lactic acid (LA) for 19 days (n = 8/diet) using shotgun metagenome sequencing. The phytase supplementation resulted in strikingly distinct bacterial communities, affecting almost all major bacterial families, whereas functional changes were less dramatic among the feeding groups. While phytase treatment decreased predominant Prevotellaceae levels, it seemed that Clostridiaceae, Ruminococcaceae, and Lachnospiraceae filled the opening metabolic niches (P < 0.05). The LA-treated cereals mediated reduced levels of Bacteroidaceae and increased levels of Veillonellaceae, but those results were mainly seen when the cereals were fed as a single treatment (P < 0.05). In association with the taxonomic alterations, phytase caused changes within the major functional pathways corresponding to amino acid metabolism; translation; membrane transport; folding, sorting, and degradation; and energy metabolism, whereas the LA treatment of cereals resulted in decreased enzymatic capacities within the carbohydrate metabolism and energy metabolism pathways (P < 0.05). Metabolic dependencies corresponding to the starch and sucrose metabolism, glycolysis/gluconeogenesis, and citrate cycle pathways were indicated by diet-associated changes in enzymatic capacities related to short-chain fatty acid, methane, vitamin, and bacterial antigen synthesis. Accordingly, the present results support the idea of the importance of the availability of intestinal P for bacterial metabolism. However, the functional profiles were less different than the taxonomic profiles among the dietary treatment results, indicating a certain degree of metabolic plasticity within the cecal metagenome.IMPORTANCE Dietary strategies (e.g., phytase supplementation and lactic acid [LA] treatment of cereals) used to improve the availability of phytate-phosphorus (P) from pig feed reduce the amount of P flowing into the large intestine, whereas LA treatment-induced changes in nutrient fractions alter the substrate being available to the microbiota. In ruminants, lower intestinal P availability compromises the fibrolytic activity of the microbiome. Here, we report that the functional capacities were less dramatically affected than the taxonomic composition by phytase-supplemented and LA-treated cereals. The bacterial community appeared to be partly capable of functionally compensating for the altered flow of P by replacing taxa with higher P needs by those with lower P needs. Therefore, by acting as mucosal immune stimulants, alterations in microbiota-associated molecular patterns (MAMPs) due to the taxonomic shifts may play a greater role for host physiology and health than functional differences caused by differing intestinal P availabilities, which merits further research.}, } @article {pmid33097513, year = {2020}, author = {Dillon, KP and Correa, F and Judon, C and Sancelme, M and Fennell, DE and Delort, AM and Amato, P}, title = {Cyanobacteria and Algae in Clouds and Rain in the Area of puy de Dôme, Central France.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {1}, pages = {}, pmid = {33097513}, issn = {1098-5336}, mesh = {*Atmosphere ; *Chlorophyta ; Cyanobacteria/*isolation & purification ; Diatoms/*isolation & purification ; France ; Microbiota ; Rain/*microbiology ; }, abstract = {The atmosphere contains diverse living microbes, of which the heterotrophic community has been the best studied. Microbes with other trophic modes, such as photoautotrophy, have received much less attention. In this study, culture-independent and dependent methods were used to examine the presence and diversity of oxygenic photoautotrophic microbes in clouds and rain collected at or around puy de Dôme Mountain, central France. Cloud water was collected from the summit of puy de Dôme (1,465 m above sea level [a.s.l.]) for cultivation and metagenomic analysis. Cyanobacteria, diatoms, green algae, and other oxygenic photoautotrophs were found to be recurrent members of clouds, while green algae affiliated with the Chlorellaceae were successfully cultured from three different clouds. Additionally, rain samples were collected below the mountain from Opme meteorological station (680 m a.s.l.). The abundance of chlorophyll a-containing cells and the diversity of cyanobacteria and green algae in rain were assessed by flow cytometry and amplicon sequencing. The corresponding downward flux of chlorophyll a-containing organisms to the ground, entering surface ecosystems with rain, varied with time and was estimated to be between ∼1 and >300 cells cm[-2] day[-1] during the sampling period. Besides abundant pollen from Pinales and Rosales, cyanobacteria of the Chroococcidiopsidales and green algae of the Trebouxiales were dominant in rain samples. Certain members of these taxa are known to be ubiquitous and stress tolerant and could use the atmosphere for dispersal. Overall, our results indicate that the atmosphere carries diverse, viable oxygenic photoautotrophic microbes and acts as a dispersal vector for this microbial guild.IMPORTANCE Information regarding the diversity and abundance of oxygenic photoautotrophs in the atmosphere is limited. More information from diverse locations is needed. These airborne organisms could have important impacts upon atmospheric processes and on the ecosystems they enter after deposition. Oxygenic photoautotrophic microbes are integral to ecosystem functioning, and some have the potential to affect human health. A better understanding of the diversity and the movements of these aeolian dispersed organisms is needed to understand their ecology, as well as how they could affect ecosystems and human health.}, } @article {pmid33097506, year = {2020}, author = {Silvaraju, S and Menon, N and Fan, H and Lim, K and Kittelmann, S}, title = {Phylotype-Level Characterization of Complex Communities of Lactobacilli Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {1}, pages = {}, pmid = {33097506}, issn = {1098-5336}, mesh = {*Genes, Bacterial ; High-Throughput Nucleotide Sequencing/*methods ; Lactobacillus/classification/enzymology/*genetics ; Microbiota/*genetics ; Pediococcus/classification/enzymology/*genetics ; Phenylalanine-tRNA Ligase/*genetics ; }, abstract = {The lactobacilli identified to date encompass more than 270 closely related species that were recently reclassified into 26 genera. Because of their relevance to industry, there is a need to distinguish between closely related and yet metabolically and regulatory distinct species, e.g., during monitoring of biotechnological processes or screening of samples of unknown composition. Current available methods, such as shotgun metagenomics or rRNA gene-based amplicon sequencing, have significant limitations (high cost, low resolution, etc.). Here, we generated a phylogeny of lactobacilli based on phenylalanyl-tRNA synthetase (pheS) genes and, from it, developed a high-resolution taxonomic framework which allows for comprehensive and confident characterization of the community diversity and structure of lactobacilli at the species level. This framework is based on a total of 445 pheS gene sequences, including sequences of 276 validly described species and subspecies (of a total of 282, including the proposed L. timonensis species and the reproposed L. zeae species; coverage of 98%), and allows differentiation between 265 species-level clades of lactobacilli and the subspecies of L. sakei The methodology was validated through next-generation sequencing of mock communities. At a sequencing depth of ∼30,000 sequences, the minimum level of detection was approximately 0.02 pg per μl DNA (equaling approximately 10 genome copies per μl template DNA). The pheS approach, along with parallel sequencing of partial 16S rRNA genes, revealed considerable diversity of lactobacilli and distinct community structures across a broad range of samples from different environmental niches. This novel complementary approach may be applicable to industry and academia alike.IMPORTANCE Species formerly classified within the genera Lactobacillus and Pediococcus have been studied extensively at the genomic level. To accommodate their exceptional functional diversity, the over 270 species were recently reclassified into 26 distinct genera. Despite their relevance to both academia and industry, methods that allow detailed exploration of their ecology are still limited by low resolution, high cost, or copy number variations. The approach described here makes use of a single-copy marker gene which outperforms other markers with regard to species-level resolution and availability of reference sequences (98% coverage). The tool was validated against a mock community and used to address diversity of lactobacilli and community structure in various environmental matrices. Such analyses can now be performed at a broader scale to assess and monitor the assembly, structure, and function of communities of lactobacilli at the species level (and, in some cases, even at the subspecies level) across a wide range of academic and commercial applications.}, } @article {pmid33096423, year = {2020}, author = {Gurwara, S and Dai, A and Ajami, NJ and Graham, DY and White, DL and Chen, L and Jang, A and Chen, E and El-Serag, HB and Petrosino, JF and Jiao, L}, title = {Alcohol use alters the colonic mucosa-associated gut microbiota in humans.}, journal = {Nutrition research (New York, N.Y.)}, volume = {83}, number = {}, pages = {119-128}, pmid = {33096423}, issn = {1879-0739}, support = {I01 CX001430/CX/CSRD VA/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 CA172880/CA/NCI NIH HHS/United States ; }, mesh = {Aged ; *Alcohol Drinking ; Bacteria/classification/genetics/growth & development ; Colon/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/*microbiology ; Male ; Middle Aged ; }, abstract = {Alcohol misuse is a risk factor for many adverse health outcomes. Alcohol misuse has been associated with an imbalance of gut microbiota in preclinical models and alcoholic diseases. We hypothesized that daily alcohol use would change the community composition and structure of the human colonic gut microbiota. Thirty-four polyp-free individuals donated 97 snap-frozen colonic biopsies. Microbial DNA was sequenced for the 16S ribosomal RNA gene hypervariable region 4. The SILVA database was used for operational taxonomic unit classification. Alcohol use was assessed using a food frequency questionnaire. We compared the biodiversity and relative abundance of the taxa among never drinkers (ND, n = 9), former drinkers (FD, n = 10), current light drinkers (LD, <2 drinks daily, n = 9), and current heavy drinkers (HD, ≥2 drinks daily, n = 6). False discovery rate-adjusted P values (q values) < .05 indicated statistical significance. HD had the lowest α diversity (Shannon index q value < 0.001), and HD's microbial composition differed the most from the other groups (P value = .002). LD had the highest relative abundance of Akkermansia (q values < 0.001). HD had the lowest relative abundance of Subdoligranulum, Roseburia, and Lachnospiraceaeunc91005 but the highest relative abundance of Lachnospiraceaeunc8895 (all q values < 0.05). The multivariable negative binomial regression model supported these observations. ND and FD had a similar microbial profile. Heavy alcohol use was associated with impaired gut microbiota that may partially mediate its effect on health outcomes.}, } @article {pmid33095967, year = {2021}, author = {Zhang, L and Zhang, J and Wei, Y and Hu, W and Liu, G and Zeng, H and Shi, H}, title = {Microbiome-wide association studies reveal correlations between the structure and metabolism of the rhizosphere microbiome and disease resistance in cassava.}, journal = {Plant biotechnology journal}, volume = {19}, number = {4}, pages = {689-701}, pmid = {33095967}, issn = {1467-7652}, mesh = {Disease Resistance/genetics ; Humans ; *Manihot/genetics ; *Microbiota ; Plant Diseases ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; *Xanthomonas axonopodis/genetics ; }, abstract = {Cassava is one of the most important staple food crops in tropical regions. To date, an understanding of the relationship between microbial communities and disease resistance in cassava has remained elusive. In order to explore the relationship among microbiome and phenotypes for further targeted design of microbial community, 16S rRNA and ITS of microbiome of ten cassava varieties were analysed, and a distinctive microbial community in the rhizosphere showed significant interdependence with disease resistance. Shotgun metagenome sequencing was performed to elucidate the structure of microbiomes of cassava rhizosphere. Comprehensive microbiome studies were performed to assess the correlation between the rhizosphere microbiome and disease resistance. Subsequently, the metagenome of rhizosphere microbiome was annotated to obtain taxonomic information at species level and identify metabolic pathways that were significantly associated with cassava disease resistance. Notably, cassava disease resistance was significantly associated with Lactococcus sp., which specifically produces nisin. To definitively explain the role of nisin and underlying mechanism, analysis of nisin biosynthesis-associated genes together with in vitro and in vivo experiments highlighted the effect of nisin on inhibiting the growth of Xanthomonas axonopodis pv. manihotis (Xam) and activating immune response in cassava. The new insights between cassava rhizosphere microbiome especially Lactococcus sp. and disease resistance provide valuable information into further control of cassava disease.}, } @article {pmid33095441, year = {2021}, author = {Foroozandeh Shahraki, M and Farhadyar, K and Kavousi, K and Azarabad, MH and Boroomand, A and Ariaeenejad, S and Hosseini Salekdeh, G}, title = {A generalized machine-learning aided method for targeted identification of industrial enzymes from metagenome: A xylanase temperature dependence case study.}, journal = {Biotechnology and bioengineering}, volume = {118}, number = {2}, pages = {759-769}, doi = {10.1002/bit.27608}, pmid = {33095441}, issn = {1097-0290}, support = {//Agricultural Biotechnology Research Institute of Iran/ ; }, mesh = {Animals ; Cattle/microbiology ; *Endo-1,4-beta Xylanases/chemistry/genetics ; *Hot Temperature ; *Machine Learning ; *Metagenome ; *Microbiota ; Rumen/*microbiology ; Sheep/microbiology ; }, abstract = {Growing industrial utilization of enzymes and the increasing availability of metagenomic data highlight the demand for effective methods of targeted identification and verification of novel enzymes from various environmental microbiota. Xylanases are a class of enzymes with numerous industrial applications and are involved in the degradation of xylose, a component of lignocellulose. The optimum temperature of enzymes is an essential factor to be considered when choosing appropriate biocatalysts for a particular purpose. Therefore, in silico prediction of this attribute is a significant cost and time-effective step in the effort to characterize novel enzymes. The objective of this study was to develop a computational method to predict the thermal dependence of xylanases. This tool was then implemented for targeted screening of putative xylanases with specific thermal dependencies from metagenomic data and resulted in the identification of three novel xylanases from sheep and cow rumen microbiota. Here we present thermal activity prediction for xylanase, a new sequence-based machine learning method that has been trained using a selected combination of various protein features. This random forest classifier discriminates non-thermophilic, thermophilic, and hyper-thermophilic xylanases. The model's performance was evaluated through multiple iterations of sixfold cross-validations as well as holdout tests, and it is freely accessible as a web-service at arimees.com.}, } @article {pmid33093799, year = {2020}, author = {Jha, P and Singh, J and Vidyarthi, AS and Prasad, R}, title = {Unveiling the Biodiversity of Hyperthermophilic Archaea in Jharia Coal Mines: Potential Threat to Methanogenesis?.}, journal = {Current genomics}, volume = {21}, number = {5}, pages = {363-371}, pmid = {33093799}, issn = {1389-2029}, abstract = {AIM: To examine the biodiversity of archaeal sulfate reducers and methanogens present in the underground coal mines of Jharia using metagenomics and pyrosequencing.

OBJECTIVES: 1) Bioinformatical analysis of the metagenomic data related to a taxonomic analysis obtained from the coal to investigate complete archaeal taxonomic features of the coal bed methane (CBM) microbiome. 2) Bioinformatical analysis of the metagenomic data related to a functional analysis obtained from the coal to investigate functional features relating to taxonomic diversity of the CBM microbiome. 3) The functional attributes have been examined specifically for ORFs related to sulfite reduction and methanogenesis.The taxonomic and functional biodiversity related to euryarchaeota will help in a better understanding of the obstacles associated with methane production imposed by the sulfate reducers.

BACKGROUND: The microbial methanogenesis in the coal microbiome is a resultant of substrate utilization by primarily fermentative bacteria and methanogens. The present work reveals the biodiversity of archaeal sulfate reducers and methanogens present in the underground coal mines of Jharia using metagenomics and pyrosequencing.

METHODOLOGY: Bioinformatical analysis for structural and functional attributes was accomplished using MG-RAST. The structural analysis was accomplished using RefSeq database, whereas the functional analysis was done via CoG database with a cut off value, a sequence percent identity, and sequence alignment length cut off of 1e[-5], 60% and 45, respectively.

RESULTS: Attained communities revealed the dominance of hyperthermophilic archaea Pyrococcus furiosus along with Thermococcus kodakarensis in the coal metagenome.The obtained results also suggest the presence of dissimilatory sulfite reductase and formylmethanofuran dehydrogenase, formylmethanofuran: tetrahydromethanopterin formyltransferase involved in sulfite reduction and methanogenesis, respectively, in the microbiome.

CONCLUSION: This report is the first attempt to showcase the existence of specific euryarchaeal diversity and their related functional attributes from Jharia coal mines through high throughput sequencing. The study helps in developing a better understanding of the presence of indigenous microbes (archaea) and their functions in the coal microbiome, which can be utilized further to resolve the energy crisis.}, } @article {pmid33089329, year = {2020}, author = {Tan, JY and Wang, S and Dick, GJ and Young, VB and Sherman, DH and Burns, MA and Lin, XN}, title = {Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial 'dark matter'.}, journal = {Integrative biology : quantitative biosciences from nano to macro}, volume = {12}, number = {11}, pages = {263-274}, pmid = {33089329}, issn = {1757-9708}, support = {R21 HG005077/HG/NHGRI NIH HHS/United States ; T32 GM008353/GM/NIGMS NIH HHS/United States ; T32 GM145304/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Bioreactors ; Coculture Techniques ; Gastrointestinal Microbiome ; Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; Metagenomics/*methods ; *Microbiological Techniques ; *Microbiota ; Microfluidics ; Multigene Family ; RNA, Ribosomal, 16S/metabolism ; }, abstract = {While the 'unculturable' majority of the bacterial world is accessible with culture-independent tools, the inability to study these bacteria using culture-dependent approaches has severely limited our understanding of their ecological roles and interactions. To circumvent cultivation barriers, we utilize microfluidic droplets as localized, nanoliter-size bioreactors to co-cultivate subsets of microbial communities. This co-localization can support ecological interactions between a reduced number of encapsulated cells. We demonstrated the utility of this approach in the encapsulation and co-cultivation of droplet sub-communities from a fecal sample collected from a healthy human subject. With the whole genome amplification and metagenomic shotgun sequencing of co-cultivated sub-communities from 22 droplets, we observed that this approach provides accessibility to uncharacterized gut commensals for study. The recovery of metagenome-assembled genomes from one droplet sub-community demonstrated the capability to dissect the sub-communities with high-genomic resolution. In particular, genomic characterization of one novel member of the family Neisseriaceae revealed implications regarding its participation in fatty acid degradation and production of atherogenic intermediates in the human gut. The demonstrated genomic resolution and accessibility to the microbial 'dark matter' with this methodology can be applied to study the interactions of rare or previously uncultivated members of microbial communities.}, } @article {pmid33087359, year = {2020}, author = {Zhang, M and Chu, Y and Meng, Q and Ding, R and Shi, X and Wang, Z and He, Y and Zhang, J and Liu, J and Zhang, J and Yu, J and Kang, Y and Wang, J}, title = {A quasi-paired cohort strategy reveals the impaired detoxifying function of microbes in the gut of autistic children.}, journal = {Science advances}, volume = {6}, number = {43}, pages = {}, pmid = {33087359}, issn = {2375-2548}, mesh = {*Autism Spectrum Disorder/etiology ; *Autistic Disorder ; Child ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; }, abstract = {Growing evidence suggests that autism spectrum disorder (ASD) is strongly associated with dysbiosis in the gut microbiome, with the exact mechanisms still unclear. We have proposed a novel analytic strategy-quasi-paired cohort-and applied it to a metagenomic study of the ASD microbiome. By comparing paired samples of ASD and neurotypical subjects, we have identified significant deficiencies in ASD children in detoxifying enzymes and pathways, which show a strong correlation with biomarkers of mitochondrial dysfunction. Diagnostic models based on these detoxifying enzymes accurately distinguished ASD individuals from controls, and the dysfunction score inferred from the model increased with the clinical rating scores of ASD. In summary, our results suggest a previously undiscovered potential role of impaired intestinal microbial detoxification in toxin accumulation and mitochondrial dysfunction, a core component of ASD pathogenesis. These findings pave the way for designing future therapeutic strategies to restore microbial detoxification capabilities for patients with ASD.}, } @article {pmid33087062, year = {2020}, author = {Eng, A and Verster, AJ and Borenstein, E}, title = {MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {471}, pmid = {33087062}, issn = {1471-2105}, support = {R01DK095869/NH/NIH HHS/United States ; U19AG057377/NH/NIH HHS/United States ; 1R01GM124312/NH/NIH HHS/United States ; U19 AG057377/AG/NIA NIH HHS/United States ; 2435/19//Israel Science Foundation/ ; }, mesh = {Humans ; Metagenomics/*methods ; Microbiota ; *Software ; }, abstract = {BACKGROUND: Microbial communities have become an important subject of research across multiple disciplines in recent years. These communities are often examined via shotgun metagenomic sequencing, a technology which can offer unique insights into the genomic content of a microbial community. Functional annotation of shotgun metagenomic data has become an increasingly popular method for identifying the aggregate functional capacities encoded by the community's constituent microbes. Currently available metagenomic functional annotation pipelines, however, suffer from several shortcomings, including limited pipeline customization options, lack of standard raw sequence data pre-processing, and insufficient capabilities for integration with distributed computing systems.

RESULTS: Here we introduce MetaLAFFA, a functional annotation pipeline designed to take unfiltered shotgun metagenomic data as input and generate functional profiles. MetaLAFFA is implemented as a Snakemake pipeline, which enables convenient integration with distributed computing clusters, allowing users to take full advantage of available computing resources. Default pipeline settings allow new users to run MetaLAFFA according to common practices while a Python module-based configuration system provides advanced users with a flexible interface for pipeline customization. MetaLAFFA also generates summary statistics for each step in the pipeline so that users can better understand pre-processing and annotation quality.

CONCLUSIONS: MetaLAFFA is a new end-to-end metagenomic functional annotation pipeline with distributed computing compatibility and flexible customization options. MetaLAFFA source code is available at https://github.com/borenstein-lab/MetaLAFFA and can be installed via Conda as described in the accompanying documentation.}, } @article {pmid33086076, year = {2020}, author = {Velmurugan, G and Dinakaran, V and Rajendhran, J and Swaminathan, K}, title = {Blood Microbiota and Circulating Microbial Metabolites in Diabetes and Cardiovascular Disease.}, journal = {Trends in endocrinology and metabolism: TEM}, volume = {31}, number = {11}, pages = {835-847}, doi = {10.1016/j.tem.2020.01.013}, pmid = {33086076}, issn = {1879-3061}, mesh = {Animals ; Cardiovascular Diseases/*microbiology/physiopathology ; Diabetes Mellitus/*microbiology/physiopathology ; Humans ; Microbiota/*physiology ; Obesity/microbiology/physiopathology ; }, abstract = {Diabetes and cardiovascular disease (CVD) have evolved as the leading cause of mortality and morbidity worldwide. In addition to traditional risk factors, recent studies have established that the human microbiota, particularly gut bacteria, plays a role in the development of diabetes and CVD. Although the presence of microbes in blood has been known for centuries, mounting evidence in this metagenomic era provides new insights into the role of the blood microbiota in the pathogenesis of non-infectious diseases such as diabetes and CVD. We highlight the origin and physiology of the blood microbiota and circulating microbial metabolites in relation to the etiology and progression of diabetes and CVD. We also discuss translational perspectives targeting the blood microbiota in the diagnosis and treatment of diabetes and CVD.}, } @article {pmid33084948, year = {2021}, author = {Verma, D and Srivastava, A and Garg, PK and Akhter, Y and Dubey, AK and Mishra, S and Deo, SVS}, title = {Taxonomic profiling and functional characterization of the healthy human oral bacterial microbiome from the north Indian urban sub-population.}, journal = {Archives of microbiology}, volume = {203}, number = {3}, pages = {927-939}, pmid = {33084948}, issn = {1432-072X}, support = {SB/YS/LS-102/2014//Science and Engineering Research Board/ ; }, mesh = {Adolescent ; Adult ; Bacteria/*classification/*genetics/isolation & purification ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; India ; Male ; Metagenome ; Microbiota/*genetics ; Middle Aged ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Poor oral health has broad consequences that can be seen at personal as well as societal levels, especially in developing countries like India. We have limited information on the healthy oral cavity's inhabitant microorganisms that play a crucial role in overall oral health. In a comprehensive culture-independent approach, the bacterial composition of healthy human oral cavities was determined from a sub-population of northern India. During this study, 20 mouthwash-derived metagenomes were explored for identifying bacterial diversity using the 16S rRNA hypervariable V3 region with the MiSeq Illumina platform. On the taxonomy assignment of operational taxonomic units (OTUs), 20 assigned phyla and 162 genera were recovered among the participants. The mean relative abundance revealed that Streptococcus was the dominant genera among the participants. However, at inter-individual analysis, Neisseria and Haemophilus exhibited first-order dominance among five and three healthy individuals, respectively. Correlation studies indicate that Streptococcus shares a strong relationship with Rothia, Corynebacterium, Prevotella, and Veillonella, whereas it was negatively correlated with Neisseria, Aggregatibacter, Porphyromonas, and Fusobacteria like Gram-negative bacteria. Bacterial diversity showed insignificant differences at the level of age and gender within and between the participants. The results support several of the major findings of previous reports on the healthy oral microbiome of the Indian population, however, the present investigation further illustrates that demographic region leaves an impact on overall bacterial composition. The study will assist in a better understanding of the oral microbiome from region-specific Indian population that was otherwise highly under-represented.}, } @article {pmid33082572, year = {2021}, author = {Kroeger, ME and Meredith, LK and Meyer, KM and Webster, KD and de Camargo, PB and de Souza, LF and Tsai, SM and van Haren, J and Saleska, S and Bohannan, BJM and Rodrigues, JLM and Berenguer, E and Barlow, J and Nüsslein, K}, title = {Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon.}, journal = {The ISME journal}, volume = {15}, number = {3}, pages = {658-672}, pmid = {33082572}, issn = {1751-7370}, mesh = {Brazil ; Methane ; *Rainforest ; *Soil ; Soil Microbiology ; }, abstract = {The Amazon rainforest is a biodiversity hotspot and large terrestrial carbon sink threatened by agricultural conversion. Rainforest-to-pasture conversion stimulates the release of methane, a potent greenhouse gas. The biotic methane cycle is driven by microorganisms; therefore, this study focused on active methane-cycling microorganisms and their functions across land-use types. We collected intact soil cores from three land use types (primary rainforest, pasture, and secondary rainforest) of two geographically distinct areas of the Brazilian Amazon (Santarém, Pará and Ariquemes, Rondônia) and performed DNA stable-isotope probing coupled with metagenomics to identify the active methanotrophs and methanogens. At both locations, we observed a significant change in the composition of the isotope-labeled methane-cycling microbial community across land use types, specifically an increase in the abundance and diversity of active methanogens in pastures. We conclude that a significant increase in the abundance and activity of methanogens in pasture soils could drive increased soil methane emissions. Furthermore, we found that secondary rainforests had decreased methanogenic activity similar to primary rainforests, and thus a potential to recover as methane sinks, making it conceivable for forest restoration to offset greenhouse gas emissions in the tropics. These findings are critical for informing land management practices and global tropical rainforest conservation.}, } @article {pmid33078515, year = {2021}, author = {Ertekin, E and Meslier, V and Browning, A and Treadgold, J and DiRuggiero, J}, title = {Rock structure drives the taxonomic and functional diversity of endolithic microbial communities in extreme environments.}, journal = {Environmental microbiology}, volume = {23}, number = {7}, pages = {3937-3956}, doi = {10.1111/1462-2920.15287}, pmid = {33078515}, issn = {1462-2920}, mesh = {Calcium Sulfate ; Extreme Environments ; *Microbiota/genetics ; Phototrophic Processes ; Water ; }, abstract = {Endolithic (rock-dwelling) microbial communities are ubiquitous in hyper-arid deserts around the world and the last resort for life under extreme aridity. These communities are excellent models to explore biotic and abiotic drivers of diversity because they are of low complexity. Using high-throughput amplicon and metagenome sequencing, combined with X-ray computed tomography, we investigated how water availability and substrate architecture modulated the taxonomic and functional composition of gypsum endolithic communities in the Atacama Desert, Chile. We found that communities inhabiting gypsum rocks with a more fragmented substrate architecture had higher taxonomic and functional diversity, despite having less water available. This effect was tightly linked with community connectedness and likely the result of niche differentiation. Gypsum communities were functionally similar, yet adapted to their unique micro-habitats by modulating their carbon and energy acquisition strategies and their growth modalities. Reconstructed population genomes showed that these endolithic microbial populations encoded potential pathways for anoxygenic phototrophy and atmospheric hydrogen oxidation as supplemental energy sources.}, } @article {pmid33077849, year = {2020}, author = {Sternes, PR and Martin, TM and Paley, M and Diamond, S and Asquith, MJ and Brown, MA and Rosenbaum, JT}, title = {HLA-A alleles including HLA-A29 affect the composition of the gut microbiome: a potential clue to the pathogenesis of birdshot retinochoroidopathy.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {17636}, pmid = {33077849}, issn = {2045-2322}, support = {R01 EY029266/EY/NEI NIH HHS/United States ; EY029266/NH/NIH HHS/United States ; }, mesh = {Adult ; Aged ; *Alleles ; Birdshot Chorioretinopathy/*genetics/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; HLA-A Antigens/*genetics ; Humans ; Male ; *Metagenome ; Middle Aged ; Whole Genome Sequencing ; }, abstract = {Birdshot retinochoroidopathy occurs exclusively in individuals who are HLA-A29 positive. The mechanism to account for this association is unknown. The gut microbiome has been causally implicated in many immune-mediated diseases. We hypothesized that HLA-A29 would affect the composition of the gut microbiome, leading to a dysbiosis and immune-mediated eye disease. Fecal and intestinal biopsy samples were obtained from 107 healthy individuals from Portland, Oregon environs, 10 of whom were HLA-A29 positive, undergoing routine colonoscopy. Bacterial profiling was achieved via 16S rRNA metabarcoding. Publicly available whole meta-genome sequencing data from the Human Microbiome Project (HMP), consisting of 298 healthy controls mostly of US origin, were also interrogated. PERMANOVA and sparse partial least squares discriminant analysis (sPLSDA) demonstrated that subjects who were HLA-A29 positive differed in bacterial species composition (beta diversity) compared to HLA-A29 negative subjects in both the Portland (p = 0.019) and HMP cohorts (p = 0.0002). The Portland and HMP cohorts evidenced different subsets of bacterial species associated with HLA-A29 status, likely due to differences in the metagenomic techniques employed. The functional composition of the HMP cohort did not differ overall (p = 0.14) between HLA-A29 positive and negative subjects, although some distinct pathways such as heparan sulfate biosynthesis showed differences. As we and others have shown for various HLA alleles, the HLA allotype impacts the composition of the microbiome. We hypothesize that HLA-A29 may predispose chorioretinitis via an altered gut microbiome.}, } @article {pmid33077744, year = {2020}, author = {Kim, J and Cho, Y and Seo, MR and Bae, MH and Kim, B and Rho, M and Pai, H}, title = {Quantitative characterization of Clostridioides difficile population in the gut microbiome of patients with C. difficile infection and their association with clinical factors.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {17608}, pmid = {33077744}, issn = {2045-2322}, mesh = {Bacteroides/*isolation & purification ; Clostridioides difficile/*isolation & purification ; Clostridium Infections/*microbiology ; Diarrhea/microbiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Lactobacillus/*isolation & purification ; Male ; Metagenome ; }, abstract = {Objective was to analyse bacterial composition and abundance of Clostridioides difficile in gut microbiome of patients with C. difficile infection (CDI) in association with clinical characteristics. Whole metagenome sequencing of gut microbiome of 26 CDI patients was performed, and the relative abundance of C. difficile and its toxin genes was measured. Clinical characteristics of the patients were obtained through medical records. A strong correlation between the abundance of C. difficile and tcdB genes in CDI patients was found. The relative abundance of C. difficile in the gut microbiome ranged from undetectable to 2.8% (median 0.089). Patients with fever exhibited low abundance of C. difficile in their gut, and patients with fewer C. difficile organisms required long-term anti-CDI treatment. Abundance of Bifidobacterium and Bacteroides negatively correlated with that of C. difficile at the genus level. CDI patients were clustered using the bacterial composition of the gut: one with high population of Enterococcus (cluster 1, n = 12) and another of Bacteroides or Lactobacillus (cluster 2, n = 14). Cluster1 showed significantly lower bacterial diversity and clinical cure at the end of treatment. Additionally, patients with CDI exhibited increased ARGs; notably, blaTEM, blaSHV and blaCTX-M were enriched. C. difficile existed in variable proportion of the gut microbiome in CDI patients. CDI patients with Enterococcus-rich microbiome in the gut had lower bacterial diversity and poorer clinical cure.}, } @article {pmid33077707, year = {2020}, author = {Herold, M and Martínez Arbas, S and Narayanasamy, S and Sheik, AR and Kleine-Borgmann, LAK and Lebrun, LA and Kunath, BJ and Roume, H and Bessarab, I and Williams, RBH and Gillece, JD and Schupp, JM and Keim, PS and Jäger, C and Hoopmann, MR and Moritz, RL and Ye, Y and Li, S and Tang, H and Heintz-Buschart, A and May, P and Muller, EEL and Laczny, CC and Wilmes, P}, title = {Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5281}, pmid = {33077707}, issn = {2041-1723}, support = {R01 AI108888/AI/NIAID NIH HHS/United States ; R01 AI143254/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics/isolation & purification/*metabolism ; Bioreactors/microbiology ; Ecosystem ; Metabolomics ; Metagenome ; Metagenomics ; *Microbiota ; Proteomics ; Time Factors ; Wastewater/*microbiology ; }, abstract = {The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals. Based on 1,364 de novo metagenome-assembled genomes, we uncover four distinct fundamental niche types. Throughout the time-series, we observe a major, transient shift in community structure, coinciding with substrate availability changes. Functional omics data reveals extensive variation in gene expression and substrate usage amongst community members. Ex situ bioreactor experiments confirm that responses occur within five hours of a pulse disturbance, demonstrating rapid adaptation by specific populations. Our results show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity, and set the foundation for future ecological engineering efforts.}, } @article {pmid33077235, year = {2021}, author = {Cissell, EC and McCoy, SJ}, title = {Shotgun metagenomic sequencing reveals the full taxonomic, trophic, and functional diversity of a coral reef benthic cyanobacterial mat from Bonaire, Caribbean Netherlands.}, journal = {The Science of the total environment}, volume = {755}, number = {Pt 1}, pages = {142719}, doi = {10.1016/j.scitotenv.2020.142719}, pmid = {33077235}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa ; Caribbean Netherlands ; Coral Reefs ; *Cyanobacteria/genetics ; Ecosystem ; Humans ; Islands ; }, abstract = {Anthropogenic forcing is spurring cyanobacterial proliferation in aquatic ecosystems worldwide. While planktonic cyanobacterial blooms have received substantial research attention, benthic blooms of mat-forming cyanobacteria have received considerably less attention, especially benthic mat blooms on coral reefs. Resultingly, numerous aspects of coral reef benthic cyanobacterial bloom ecology remain unknown, including underlying biodiversity in the mat communities. Most previous characterizations of coral reef cyanobacterial mat composition have only considered the cyanobacterial component. Without an unbiased characterization of full community diversity, we cannot predict whole-community response to anthropogenic inputs or effectively determine appropriate mitigation strategies. Here, we advocate for the implementation of shotgun sequencing techniques to study coral reef cyanobacterial mats worldwide, utilizing a case study of a coral reef benthic cyanobacterial mat sampled from the island of Bonaire, Caribbean Netherlands. Read-based taxonomic profiling revealed that Cyanobacteria was present at only 47.57% relative abundance in a coral reef cyanobacterial mat, with non-cyanobacterial members of the sampled mat community, including diatoms (0.78%), fungi (0.25%), Archaea (0.34%), viruses (0.08%), and other bacteria (45.78%), co-dominating the community. We found numerous gene families for regulatory systems and for functional pathways (both aerobic and anaerobic). These gene families were involved in community coordination; photosynthesis; nutrient scavenging; and the cycling of sulfur, nitrogen, phosphorous, and iron. We also report bacteriophage (including prophage) sequences associated with this subtidal coral reef cyanobacterial mat, which could contribute to intra-mat nutrient cycling and bloom dynamics. Overall, our results suggest that Cyanobacteria-focused analysis of coral reef cyanobacterial mats underestimates mat diversity and fails to capture community members possessing broad metabolic potential for intra-mat nutrient scavenging, recycling, and retention that likely contribute to the contemporary success of cyanobacterial mats on reefs. We advocate for increased collaboration between microbiologists and coral reef ecologists to unite insights from each discipline and improve efforts to understand mat ecology.}, } @article {pmid33075172, year = {2020}, author = {Li, YH and Huang, YF and Chen, TH and Wu, SS and Tang, HC and Hsiao, CY and Huang, LC and Chang, JC and Chiu, KP and Nai, YS}, title = {Comparison of gut microbiota of healthy and diseased walking sticks, Phasmotaenia lanyuhensis.}, journal = {Archives of insect biochemistry and physiology}, volume = {105}, number = {4}, pages = {e21749}, doi = {10.1002/arch.21749}, pmid = {33075172}, issn = {1520-6327}, support = {107-2313-B-197-004-MY3//Ministry of Science and Technology, Taiwan/ ; 109-2313-B-005-048-MY3//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Animals ; Bacteria/classification/genetics ; Gastrointestinal Microbiome/*physiology ; Insecta/*microbiology ; Metagenome ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {Research on gut microbiota of phytophagous insects has shown to be important for the physiological functions of insect hosts; however, little is known about the changes in gut microbiota when they are suffering from environmental stress or pathogen infections. During rearing of Phasmotaenia lanyuhensis (Phasmatodea: Phasmatidae), sluggish locomotion was usually followed by the death of the insect with a symptom of melanization in the front part of the abdomen. Therefore, the abnormal individuals were initially classified into moribund, light- and serious-symptom based on the level of abnormal physiological circumstances and melanization. The gut microbiota of these samples were further investigated by 16S metagenomic sequencing and the differences in bacterial abundance and structure of bacterial community were analyzed. A decrease in microbiota diversity was observed in the diseased P. lanyuhensis, with the abundance of phyla Proteobacteria and Firmicute relatively higher compared to those without symptom. Interestingly, principal component analysis based on the bacterial richness was correlated to the level of melanization symptom in the diseased P. lanyuhensis, suggested the change in bacterial microbiota involved in this abnormal circumstance. However, the factor that caused the initial alternation of microbiota remains to be identified. Additionally, the lack of bacterial diversity (i.e., absence of Meiothermus and Nubsella spp.) in P. lanyuhensis might reduce the fitness for surviving. This report provided the comprehensive microbiota analysis for P. lanyuhensis and concluded that either the relative abundance or the bacterial diversity of microbiota in the insect digestive system may influence the physiological functions of phytophagous insects.}, } @article {pmid33074224, year = {2020}, author = {Marizzoni, M and Cattaneo, A and Mirabelli, P and Festari, C and Lopizzo, N and Nicolosi, V and Mombelli, E and Mazzelli, M and Luongo, D and Naviglio, D and Coppola, L and Salvatore, M and Frisoni, GB}, title = {Short-Chain Fatty Acids and Lipopolysaccharide as Mediators Between Gut Dysbiosis and Amyloid Pathology in Alzheimer's Disease.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {78}, number = {2}, pages = {683-697}, doi = {10.3233/JAD-200306}, pmid = {33074224}, issn = {1875-8908}, mesh = {Aged ; Aged, 80 and over ; Alzheimer Disease/diagnostic imaging/*metabolism/pathology ; Amyloid/*metabolism ; Biomarkers/metabolism ; Dysbiosis/diagnostic imaging/*metabolism/pathology ; Fatty Acids, Volatile/*metabolism ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Lipopolysaccharides/*metabolism ; Male ; Middle Aged ; Positron-Emission Tomography/methods ; }, abstract = {BACKGROUND: Metagenomic data support an association between certain bacterial strains and Alzheimer's disease (AD), but their functional dynamics remain elusive.

OBJECTIVE: To investigate the association between amyloid pathology, bacterial products such as lipopolysaccharide (LPS) and short chain fatty acids (SCFAs: acetate, valerate, butyrate), inflammatory mediators, and markers of endothelial dysfunction in AD.

METHODS: Eighty-nine older persons with cognitive performance from normal to dementia underwent florbetapir amyloid PET and blood collection. Brain amyloidosis was measured with standardized uptake value ratio versus cerebellum. Blood levels of LPS were measured by ELISA, SCFAs by mass spectrometry, cytokines by using real-time PCR, and biomarkers of endothelial dysfunction by flow cytometry. We investigated the association between the variables listed above with Spearman's rank test.

RESULTS: Amyloid SUVR uptake was positively associated with blood LPS (rho≥0.32, p≤0.006), acetate and valerate (rho≥0.45, p < 0.001), pro-inflammatory cytokines (rho≥0.25, p≤0.012), and biomarkers of endothelial dysfunction (rho≥0.25, p≤0.042). In contrast, it was negatively correlated with butyrate (rho≤-0.42, p≤0.020) and the anti-inflammatory cytokine IL10 (rho≤-0.26, p≤0.009). Endothelial dysfunction was positively associated with pro-inflammatory cytokines, acetate and valerate (rho≥0.25, p≤0.045) and negatively with butyrate and IL10 levels (rho≤-0.25, p≤0.038).

CONCLUSION: We report a novel association between gut microbiota-related products and systemic inflammation with brain amyloidosis via endothelial dysfunction, suggesting that SCFAs and LPS represent candidate pathophysiologic links between the gut microbiota and AD pathology.}, } @article {pmid33074097, year = {2020}, author = {Mobegi, FM and Leong, LE and Thompson, F and Taylor, SM and Harriss, LR and Choo, JM and Taylor, SL and Wesselingh, SL and McDermott, R and Ivey, KL and Rogers, GB}, title = {Intestinal microbiology shapes population health impacts of diet and lifestyle risk exposures in Torres Strait Islander communities.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {33074097}, issn = {2050-084X}, support = {GNT0631947//National Health and Medical Research Council/International ; }, mesh = {Adult ; Aged ; *Diet ; Female ; *Gastrointestinal Microbiome ; Humans ; *Life Style ; Male ; Middle Aged ; Population Health/*statistics & numerical data ; Young Adult ; }, abstract = {Poor diet and lifestyle exposures are implicated in substantial global increases in non-communicable disease burden in low-income, remote, and Indigenous communities. This observational study investigated the contribution of the fecal microbiome to influence host physiology in two Indigenous communities in the Torres Strait Islands: Mer, a remote island where a traditional diet predominates, and Waiben a more accessible island with greater access to takeaway food and alcohol. Counterintuitively, disease markers were more pronounced in Mer residents. However, island-specific differences in disease risk were explained, in part, by microbiome traits. The absence of Alistipes onderdonkii, for example, significantly (p=0.014) moderated island-specific patterns of systolic blood pressure in multivariate-adjusted models. We also report mediatory relationships between traits of the fecal metagenome, disease markers, and risk exposures. Understanding how intestinal microbiome traits influence response to disease risk exposures is critical for the development of strategies that mitigate the growing burden of cardiometabolic disease in these communities.}, } @article {pmid33068423, year = {2020}, author = {L Bräuer, S and Basiliko, N and M P Siljanen, H and H Zinder, S}, title = {Methanogenic archaea in peatlands.}, journal = {FEMS microbiology letters}, volume = {367}, number = {20}, pages = {}, doi = {10.1093/femsle/fnaa172}, pmid = {33068423}, issn = {1574-6968}, mesh = {Archaea/*classification ; Methane/metabolism ; Microbiota/physiology ; *Soil ; *Soil Microbiology ; *Wetlands ; }, abstract = {Methane emission feedbacks in wetlands are predicted to influence global climate under climate change and other anthropogenic stressors. Herein, we review the taxonomy and physiological ecology of the microorganisms responsible for methane production in peatlands. Common in peat soils are five of the eight described orders of methanogens spanning three phyla (Euryarchaeota, Halobacterota and Thermoplasmatota). The phylogenetic affiliation of sequences found in peat suggest that members of the thus-far-uncultivated group Candidatus Bathyarchaeota (representing a fourth phylum) may be involved in methane cycling, either anaerobic oxidation of methane and/or methanogenesis, as at least a few organisms within this group contain the essential gene, mcrA, according to metagenomic data. Methanogens in peatlands are notoriously challenging to enrich and isolate; thus, much remains unknown about their physiology and how methanogen communities will respond to environmental changes. Consistent patterns of changes in methanogen communities have been reported across studies in permafrost peatland thaw where the resulting degraded feature is thermokarst. However much remains to be understood regarding methanogen community feedbacks to altered hydrology and warming in other contexts, enhanced atmospheric pollution (N, S and metals) loading and direct anthropogenic disturbances to peatlands like drainage, horticultural peat extraction, forestry and agriculture, as well as post-disturbance reclamation.}, } @article {pmid33067706, year = {2020}, author = {Li, Y and Zhu, Y and Wei, H and Chen, Y and Shang, H}, title = {Study on the Diversity and Function of Gut Microbiota in Pigs Following Long-Term Antibiotic and Antibiotic-Free Breeding.}, journal = {Current microbiology}, volume = {77}, number = {12}, pages = {4114-4128}, doi = {10.1007/s00284-020-02240-8}, pmid = {33067706}, issn = {1432-0991}, support = {2017YFD0501000//National Key Research and Development Program of China/ ; 2018YFD0500600//National Key Research and Development Program of China/ ; JSGG20180507182028625//Shenzhen Key Technology Projects/ ; 81770434//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteroidetes/genetics ; Firmicutes/genetics ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Swine ; }, abstract = {In-feed antibiotics can influence intestinal microbial structures in born and early-life within a period. However, the impact of antibiotics on gut microbiota during long-term antibiotic-free and antibiotic breeding at porcine-fattening phase have not been studied extensively so far. Here, we conducted a systematic 16S rRNA gene sequencing-based study combined with metagenomic analysis to reveal the variation of diversity and function of gut microbiota between antibiotic-free (treatment group, TG) and antibiotic (a mixture of flavomycin and enramycin, control group, CG) breeding at various stages of fattening pigs. In the present study, Bacteroidetes, Firmicutes, and Proteobacteria phyla were the core microbiomes in fattening pig gut microbiota. The ratio between Firmicutes and Bacteroidetes significantly increased with age (P = 0.03). TG showed significantly higher relative abundance of Proteobacteria and Fibrobacteres phyla than CG. The microbial community can be divided into several notably clustered blocks based on cooperative and competitive correlations. These blocks centered on numerous special genera, which play essential roles in body development and disease prevention. TG showed obviously higher proportions of metabolic pathways related to metabolism, endocrine system, nervous system and excretory system, but pathways included carbohydrate metabolism and immune system diseases in CG. Collectively, this study has comprehensively demonstrated microbial diversities, differences and correlations among gut microbiota, microbial metabolism and gene functions during long-term antibiotic-free breeding. This work provides a novel resource and information with positive implications for pig husbandry production and disease prevention.}, } @article {pmid33067398, year = {2020}, author = {Shibl, AA and Isaac, A and Ochsenkühn, MA and Cárdenas, A and Fei, C and Behringer, G and Arnoux, M and Drou, N and Santos, MP and Gunsalus, KC and Voolstra, CR and Amin, SA}, title = {Diatom modulation of select bacteria through use of two unique secondary metabolites.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {44}, pages = {27445-27455}, pmid = {33067398}, issn = {1091-6490}, mesh = {Animals ; Bacteria/genetics/*growth & development ; Cinnamates/metabolism ; Depsides/metabolism ; Diatoms/genetics/*metabolism ; Dicarboxylic Acids/metabolism ; Gene Expression Profiling ; Metabolomics ; Metagenome ; Metagenomics ; Microbiota/*physiology ; Oceans and Seas ; Phytoplankton/genetics/*metabolism ; Secondary Metabolism/physiology ; *Water Microbiology ; Rosmarinic Acid ; }, abstract = {Unicellular eukaryotic phytoplankton, such as diatoms, rely on microbial communities for survival despite lacking specialized compartments to house microbiomes (e.g., animal gut). Microbial communities have been widely shown to benefit from diatom excretions that accumulate within the microenvironment surrounding phytoplankton cells, known as the phycosphere. However, mechanisms that enable diatoms and other unicellular eukaryotes to nurture specific microbiomes by fostering beneficial bacteria and repelling harmful ones are mostly unknown. We hypothesized that diatom exudates may tune microbial communities and employed an integrated multiomics approach using the ubiquitous diatom Asterionellopsis glacialis to reveal how it modulates its naturally associated bacteria. We show that A. glacialis reprograms its transcriptional and metabolic profiles in response to bacteria to secrete a suite of central metabolites and two unusual secondary metabolites, rosmarinic acid and azelaic acid. While central metabolites are utilized by potential bacterial symbionts and opportunists alike, rosmarinic acid promotes attachment of beneficial bacteria to the diatom and simultaneously suppresses the attachment of opportunists. Similarly, azelaic acid enhances growth of beneficial bacteria while simultaneously inhibiting growth of opportunistic ones. We further show that the bacterial response to azelaic acid is numerically rare but globally distributed in the world's oceans and taxonomically restricted to a handful of bacterial genera. Our results demonstrate the innate ability of an important unicellular eukaryotic group to modulate select bacteria in their microbial consortia, similar to higher eukaryotes, using unique secondary metabolites that regulate bacterial growth and behavior inversely across different bacterial populations.}, } @article {pmid33067200, year = {2020}, author = {Mori, JF and Kanaly, RA}, title = {Multispecies Diesel Fuel Biodegradation and Niche Formation Are Ignited by Pioneer Hydrocarbon-Utilizing Proteobacteria in a Soil Bacterial Consortium.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {1}, pages = {}, pmid = {33067200}, issn = {1098-5336}, mesh = {Biodegradation, Environmental ; *Gasoline ; Hydrocarbons/*metabolism ; *Microbial Consortia ; Proteobacteria/*metabolism ; *Soil Microbiology ; }, abstract = {A soil bacterial consortium that was grown on diesel fuel and consisted of more than 10 members from different genera was maintained through repetitive subculturing and was utilized as a practical model to investigate a bacterial community that was continuously exposed to petroleum hydrocarbons. Through metagenomics analyses, consortium member isolation, growth assays, and metabolite identification which supported the linkage of genomic data and functionality, two pioneering genera, Sphingobium and Pseudomonas, whose catabolic capabilities were differentiated, were found to be responsible for the creation of specialized ecological niches that were apparently occupied by other bacterial members for survival within the consortium. Coexisting genera Achromobacter and Cupriavidus maintained their existence in the consortium through metabolic dependencies by utilizing hydrocarbon biotransformation products of pioneer metabolism, which was confirmed through growth tests and identification of biotransformation products of the isolated strains. Pioneering Sphingobium and Pseudomonas spp. utilized relatively water-insoluble hydrocarbon parent compounds and facilitated the development of a consortium community structure that resulted in the creation of niches in response to diesel fuel exposure which were created through the production of more-water-soluble biotransformation products available to cocolonizers. That these and other organisms were still present in the consortium after multiple transfers spanning 15 years provided evidence for these ecological niches. Member survival through occupation of these niches led to robustness of each group within the multispecies bacterial community. Overall, these results contribute to our understanding of the complex ecological relationships that may evolve during prokaryotic hydrocarbon pollutant biodegradation.IMPORTANCE There are few metagenome studies that have explored soil consortia maintained on a complex hydrocarbon substrate after the community interrelationships were formed. A soil bacterial consortium maintained on diesel fuel was utilized as a practical model to investigate bacterial community relationships through metagenomics analyses, consortium member isolation, growth assays, and metabolite identification, which supported the linkage of genomic data and functionality. Two pioneering genera were responsible for the biodegradation of aromatics and alkanes by initiating biotransformation and thereby created specialized niches that were populated by other members. A model that represents these relationships was constructed, which contributes to our understanding of the complex ecological relationships that evolve during prokaryotic hydrocarbon pollutant biodegradation.}, } @article {pmid33065016, year = {2020}, author = {De Filippis, F and Pasolli, E and Ercolini, D}, title = {Newly Explored Faecalibacterium Diversity Is Connected to Age, Lifestyle, Geography, and Disease.}, journal = {Current biology : CB}, volume = {30}, number = {24}, pages = {4932-4943.e4}, doi = {10.1016/j.cub.2020.09.063}, pmid = {33065016}, issn = {1879-0445}, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Animals ; Child ; Child, Preschool ; Datasets as Topic ; Dysbiosis/*microbiology ; Faecalibacterium/genetics/*isolation & purification ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Geography ; Humans ; Infant ; Life Style ; Macaca ; Metagenome ; Metagenomics ; Middle Aged ; Phylogeny ; *Probiotics ; Young Adult ; }, abstract = {Faecalibacterium is prevalent in the human gut and a promising microbe for the development of next-generation probiotics (NGPs) or biotherapeutics. Analyzing reference Faecalibacterium genomes and almost 3,000 Faecalibacterium-like metagenome-assembled genomes (MAGs) reconstructed from 7,907 human and 203 non-human primate gut metagenomes, we identified the presence of 22 different Faecalibacterium-like species-level genome bins (SGBs), some further divided in different strains according to the subject geographical origin. Twelve SGBs are globally spread in the human gut and show different genomic potential in the utilization of complex polysaccharides, suggesting that higher SGB diversity may be related with increased utilization of plant-based foods. Moreover, up to 11 different species may co-occur in the same subject, with lower diversity in Western populations, as well as intestinal inflammatory states and obesity. The newly explored Faecalibacterium diversity will be able to support the choice of strains suitable as NGPs, guided by the consideration of the differences existing in their functional potential.}, } @article {pmid33063432, year = {2021}, author = {Paoli, L and Sunagawa, S}, title = {Space, time and microdiversity: towards a resolution revolution in microbiomics.}, journal = {Environmental microbiology reports}, volume = {13}, number = {1}, pages = {31-35}, pmid = {33063432}, issn = {1758-2229}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Environmental Microbiology ; Gastrointestinal Microbiome ; Humans ; *Metagenomics ; *Microbiota ; Seawater ; }, } @article {pmid33063421, year = {2021}, author = {Tiew, PY and Jaggi, TK and Chan, LLY and Chotirmall, SH}, title = {The airway microbiome in COPD, bronchiectasis and bronchiectasis-COPD overlap.}, journal = {The clinical respiratory journal}, volume = {15}, number = {2}, pages = {123-133}, doi = {10.1111/crj.13294}, pmid = {33063421}, issn = {1752-699X}, support = {NMRC/Fellowship/0049/2017//Singapore Ministry of Health's National Medical Research Council under its Research Training Fellowship/ ; MOH-000141//Singapore Ministry of Health's National Medical Research Council under its Clinician-Scientist Individual Research Grant/ ; }, mesh = {*Bronchiectasis ; Humans ; *Microbiota ; *Pulmonary Disease, Chronic Obstructive ; Severity of Illness Index ; }, abstract = {OBJECTIVE: To review the airway microbiome in chronic obstructive pulmonary disease (COPD), bronchiectasis and bronchiectasis-COPD overlap (BCO).

Relevant studies were selected from PubMed, Google scholar, EMBASE and Web of Science. All studies involving human microbiomes, published in the English language, and using the search terms "COPD", "Chronic Obstructive Pulmonary Disease", "Bronchiectasis", "BCO" or "Bronchiectasis and COPD overlap", AND "microbiome", "mycobiome" or "metagenomics" were included.

RESULTS: Despite variability in sampling methods and specimen types used, microbiome composition remains relatively comparable in COPD and bronchiectasis with prominence of Proteobacteria, Firmicutes and Bacteroidetes. Alterations to airway microbiomes occur in association to disease severity and/or exacerbations in COPD and bronchiectasis. Decreased alpha diversity and Haemophilus-predominant microbiomes are associated with poorer survival in COPD, while, in bronchiectasis, Pseudomonas-predominant microbiomes demonstrate high exacerbation frequency and greater symptom burden while Aspergillus-dominant mycobiome profiles associate with exacerbations. The role of the microbiome in BCO remains understudied.

CONCLUSION: Use of next-generation sequencing has revolutionised our detection and understanding of the airway microbiome in chronic respiratory diseases such as COPD and bronchiectasis. Targeted amplicon sequencing reveals important associations between the respiratory microbiome and disease outcome while metagenomics may elucidate functional pathways. How best to apply this information into patient care, monitoring and treatment, however, remains challenging and necessitates further study.}, } @article {pmid33063083, year = {2020}, author = {Liu, L and He, Y and Wang, K and Miao, J and Zheng, Z}, title = {Metagenomics approach to the intestinal microbiome structure and function in high fat diet-induced obesity in mice fed with conjugated linoleic acid (CLA).}, journal = {Food & function}, volume = {11}, number = {11}, pages = {9729-9739}, doi = {10.1039/d0fo02112a}, pmid = {33063083}, issn = {2042-650X}, mesh = {Animals ; Diet, High-Fat ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; Linoleic Acids, Conjugated/*pharmacology ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Obesity/*microbiology ; }, abstract = {In this study, a high fat diet induced obesity mouse model (DIO) was used to investigate the modulatory effect of high purity conjugated linoleic acid (CLA) on the intestinal microbiota. CLA was prepared by a simulated moving bed chromatography system and its influence on the gut microbes was analyzed by 16S amplicon V3-V4 region analysis. We observed a significant increase in the bacterial biodiversity and the abundance of genera of butyrate- and acetate-producing bacteria. After taking CLA for 6 weeks, the abundance of Bacteroides in the intestines of mice greatly increased, while the abundance of Firmicutes decreased. The corresponding decrease in the Firmicutes/Bacteroidetes ratio reflected a positive modulatory effect of CLA on the intestinal microbiota. In addition, KEGG pathways for the nucleotide metabolism, metabolism of terpenoids and polyketides and lipid metabolism were among the most differentially expressed genes after CLA intervention. The current study revealed that CLA can be used as a functional food component with potential therapeutic value to prevent obesity-related metabolic disorders by manipulating the intestinal microbiota.}, } @article {pmid33059593, year = {2020}, author = {Golob, JL and Minot, SS}, title = {In silico benchmarking of metagenomic tools for coding sequence detection reveals the limits of sensitivity and precision.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {459}, pmid = {33059593}, issn = {1471-2105}, support = {R01 AI134808/AI/NIAID NIH HHS/United States ; }, mesh = {Algorithms ; *Benchmarking ; *Computer Simulation ; Humans ; *Metagenome ; Metagenomics ; Microbiota/genetics ; Open Reading Frames/*genetics ; Predictive Value of Tests ; }, abstract = {BACKGROUND: High-throughput sequencing can establish the functional capacity of a microbial community by cataloging the protein-coding sequences (CDS) present in the metagenome of the community. The relative performance of different computational methods for identifying CDS from whole-genome shotgun sequencing is not fully established.

RESULTS: Here we present an automated benchmarking workflow, using synthetic shotgun sequencing reads for which we know the true CDS content of the underlying communities, to determine the relative performance (sensitivity, positive predictive value or PPV, and computational efficiency) of different metagenome analysis tools for extracting the CDS content of a microbial community. Assembly-based methods are limited by coverage depth, with poor sensitivity for CDS at < 5X depth of sequencing, but have excellent PPV. Mapping-based techniques are more sensitive at low coverage depths, but can struggle with PPV. We additionally describe an expectation maximization based iterative algorithmic approach which we show to successfully improve the PPV of a mapping based technique while retaining improved sensitivity and computational efficiency.

CONCLUSION: Our benchmarking approach reveals the trade-offs of assembly versus alignment-based approaches and the relative performance of specific implementations when one wishes to extract the protein coding capacity of microbial communities.}, } @article {pmid33059288, year = {2021}, author = {Chakraborty, J and Rajput, V and Sapkale, V and Kamble, S and Dharne, M}, title = {Spatio-temporal resolution of taxonomic and functional microbiome of Lonar soda lake of India reveals metabolic potential for bioremediation.}, journal = {Chemosphere}, volume = {264}, number = {Pt 2}, pages = {128574}, doi = {10.1016/j.chemosphere.2020.128574}, pmid = {33059288}, issn = {1879-1298}, mesh = {Biodegradation, Environmental ; India ; *Lakes ; Metagenome ; *Microbiota/genetics ; }, abstract = {Lonar Lake, India; a hypersaline and hyperalkaline extremophilic ecosystem having a unique microbial population has been rarely explored for bioremediation aspects. MinION-based shotgun sequencing was used to comprehensively compare the microbial diversity and functional potential of xenobiotic degradation pathways with seasonal changes. Proteobacteria and Firmicutes were prevalent bacterial phyla in the pre-monsoon and post-monsoon samples. Functional analysis from SEED-subsystem and KEGG database revealed 28 subsystems and 18 metabolic pathways for the metabolism of aromatic compounds and xenobiotic biodegradation respectively. Occurrence of N-phenyl alkanoic, benzoate, biphenyl, chloroaromatic, naphthalene, and phenol degradation genes depicted varied abundance in the pre-monsoon and post-monsoon samples. Further, KEGG analysis indicated nitrotoluene degradation pathway (ko00633) abundant in post-monsoon samples, and the benzoate degradation pathway (ko00362) predominant in 19LN4S (pre-monsoon) than 18LN7S (post-monsoon) samples. The abundant genes for benzoate degradation were pcaI: 3-oxoadipate CoA-transferase, alpha subunit, pcaH: protocatechuate 3,4-dioxygenase, beta subunit, and pcaB: 3-carboxy-cis, cis-muconate cycloisomerase, and 4-oxalocrotonate tautomerase. This metagenomic study provides a unique blueprint of hitherto unexplored xenobiotic biodegradation genes/pathways in terms of seasonal variations in the Lonar Lake, and warrants active exploitation of microbes for bioremediation purposes.}, } @article {pmid33058365, year = {2020}, author = {Li, J and Zuo, K and Zhang, J and Hu, C and Wang, P and Jiao, J and Liu, Z and Yin, X and Liu, X and Li, K and Yang, X}, title = {Shifts in gut microbiome and metabolome are associated with risk of recurrent atrial fibrillation.}, journal = {Journal of cellular and molecular medicine}, volume = {24}, number = {22}, pages = {13356-13369}, pmid = {33058365}, issn = {1582-4934}, mesh = {Aged ; Area Under Curve ; Atrial Fibrillation/*microbiology/*pathology ; Bacillus ; Faecalibacterium ; Female ; *Gastrointestinal Microbiome ; *Gene Expression Profiling ; Humans ; Incidence ; Kaplan-Meier Estimate ; Male ; *Metabolome ; Metabolomics ; Middle Aged ; Nitrosomonadaceae ; Recurrence ; Risk Assessment ; Treatment Outcome ; }, abstract = {Alternations of gut microbiota (GM) in atrial fibrillation (AF) with elevated diversity, perturbed composition and function have been described previously. The current work aimed to assess the association of GM composition with AF recurrence (RAF) after ablation based on metagenomic sequencing and metabolomic analyses and to construct a GM-based predictive model for RAF. Compared with non-AF controls (50 individuals), GM composition and metabolomic profile were significantly altered between patients with recurrent AF (17 individuals) and non-RAF group (23 individuals). Notably, discriminative taxa between the non-RAF and RAF groups, including the families Nitrosomonadaceae and Lentisphaeraceae, the genera Marinitoga and Rufibacter and the species Faecalibacterium spCAG:82, Bacillus gobiensis and Desulfobacterales bacterium PC51MH44, were selected to construct a taxonomic scoring system based on LASSO analysis. After incorporating the clinical factors of RAF, taxonomic score retained a significant association with RAF incidence (HR = 2.647, P = .041). An elevated AUC (0.954) and positive NRI (1.5601) for predicting RAF compared with traditional clinical scoring (AUC = 0.6918) were obtained. The GM-based taxonomic scoring system theoretically improves the model performance, and the nomogram and decision curve analysis validated the clinical value of the predicting model. These data provide novel possibility that incorporating the GM factor into future recurrent risk stratification.}, } @article {pmid33057402, year = {2020}, author = {Eriksen, AMH and Nielsen, TK and Matthiesen, H and Carøe, C and Hansen, LH and Gregory, DJ and Turner-Walker, G and Collins, MJ and Gilbert, MTP}, title = {Bone biodeterioration-The effect of marine and terrestrial depositional environments on early diagenesis and bone bacterial community.}, journal = {PloS one}, volume = {15}, number = {10}, pages = {e0240512}, pmid = {33057402}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/genetics/*growth & development ; Bone and Bones/metabolism/*microbiology/*pathology ; Environmental Exposure/*analysis ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Swine ; }, abstract = {Bacteria play an important role in the degradation of bone material. However, much remains to be learnt about the structure of their communities in degrading bone, and how the depositional environment influences their diversity throughout the exposure period. We genetically profiled the bacterial community in an experimental series of pig bone fragments (femur and humeri) deposited at different well-defined environments in Denmark. The bacterial community in the bone fragments and surrounding depositional environment were studied over one year, and correlated with the bioerosion damage patterns observed microscopically in the bones. We observed that the bacterial communities within the bones were heavily influenced by the local microbial community, and that the general bone microbial diversity increases with time after exposure. We found the presence of several known collagenase producing bacterial groups, and also observed increases in the relative abundance of several of these in bones with tunneling. We anticipate that future analyses using shotgun metagenomics on this and similar datasets will be able to provide insights into mechanisms of microbiome driven bone degradation.}, } @article {pmid33051582, year = {2021}, author = {Chen, Y and Neilson, JW and Kushwaha, P and Maier, RM and Barberán, A}, title = {Life-history strategies of soil microbial communities in an arid ecosystem.}, journal = {The ISME journal}, volume = {15}, number = {3}, pages = {649-657}, pmid = {33051582}, issn = {1751-7370}, support = {P30 ES006694/ES/NIEHS NIH HHS/United States ; P42 ES004940/ES/NIEHS NIH HHS/United States ; P42ES004940//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; }, mesh = {*Ecosystem ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Soil ; Soil Microbiology ; }, abstract = {The overwhelming taxonomic diversity and metabolic complexity of microorganisms can be simplified by a life-history classification; copiotrophs grow faster and rely on resource availability, whereas oligotrophs efficiently exploit resource at the expense of growth rate. Here, we hypothesize that community-level traits inferred from metagenomic data can distinguish copiotrophic and oligotrophic microbial communities. Moreover, we hypothesize that oligotrophic microbial communities harbor more unannotated genes. To test these hypotheses, we conducted metagenomic analyses of soil samples collected from copiotrophic vegetated areas and from oligotrophic bare ground devoid of vegetation in an arid-hyperarid region of the Sonoran Desert, Arizona, USA. Results supported our hypotheses, as we found that multiple ecologically informed life-history traits including average 16S ribosomal RNA gene copy number, codon usage bias in ribosomal genes and predicted maximum growth rate were higher for microbial communities in vegetated than bare soils, and that oligotrophic microbial communities in bare soils harbored a higher proportion of genes that are unavailable in public reference databases. Collectively, our work demonstrates that life-history traits can distill complex microbial communities into ecologically coherent units and highlights that oligotrophic microbial communities serve as a rich source of novel functions.}, } @article {pmid33051444, year = {2020}, author = {Moon, K and Kim, S and Kang, I and Cho, JC}, title = {Viral metagenomes of Lake Soyang, the largest freshwater lake in South Korea.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {349}, pmid = {33051444}, issn = {2052-4463}, support = {NRF-2019R1I1A1A01062072//National Research Foundation of Korea (NRF)/International ; NRF-2019R1I1A1A01063401//National Research Foundation of Korea (NRF)/International ; NRF-2019R1A2B5B02070538//National Research Foundation of Korea (NRF)/International ; }, mesh = {High-Throughput Nucleotide Sequencing ; Lakes/*virology ; *Metagenome ; Metagenomics ; Republic of Korea ; *Virome ; }, abstract = {A high number of viral metagenomes have revealed countless genomes of putative bacteriophages that have not yet been identified due to limitations in bacteriophage cultures. However, most virome studies have been focused on marine or gut environments, thereby leaving the viral community structure of freshwater lakes unclear. Because the lakes located around the globe have independent ecosystems with unique characteristics, viral community structures are also distinctive but comparable. Here, we present data on viral metagenomes that were seasonally collected at a depth of 1 m from Lake Soyang, the largest freshwater reservoir in South Korea. Through shotgun metagenome sequencing using the Illumina MiSeq platform, 3.08 to 5.54-Gbps of reads per virome were obtained. To predict the viral genome sequences within Lake Soyang, contigs were constructed and 648 to 1,004 putative viral contigs were obtained per sample. We expect that both viral metagenome reads and viral contigs would contribute in comparing and understanding of viral communities among different freshwater lakes depending on seasonal changes.}, } @article {pmid33050261, year = {2020}, author = {Jakobsen, RR and Haahr, T and Humaidan, P and Jensen, JS and Kot, WP and Castro-Mejia, JL and Deng, L and Leser, TD and Nielsen, DS}, title = {Characterization of the Vaginal DNA Virome in Health and Dysbiosis.}, journal = {Viruses}, volume = {12}, number = {10}, pages = {}, pmid = {33050261}, issn = {1999-4915}, mesh = {Adult ; Bacteria/classification/isolation & purification/virology ; Bacteriophages/genetics/*isolation & purification ; Cross-Sectional Studies ; Dysbiosis/*microbiology ; Female ; Humans ; Lactobacillus/isolation & purification ; Vagina/*microbiology ; Vaginosis, Bacterial/*microbiology ; Virome/*physiology ; Young Adult ; }, abstract = {Bacterial vaginosis (BV) is characterized by a reduction in Lactobacillus (L.) spp. abundance and increased abundance of facultative anaerobes, such as Gardnerella spp. BV aetiology is not fully understood; however, bacteriophages could play a pivotal role in the perturbation of the vaginal bacterial community. We investigated the vaginal viral community, including bacteriophages and the association to the bacterial community and BV-status. Vaginal samples from 48 patients undergoing IVF treatment for non-female factor infertility were subjected to metagenomic sequencing of purified virus-like particles. The vaginal viral community was characterized and correlated with the BV-status by Nugent score, bacterial community, structure, and the presence of key vaginal bacterial species. The majority of identified vaginal viruses belonged to the class of double-stranded DNA bacteriophages, with eukaryotic viruses constituting 4% of the total reads. Clear links between the viral community composition and BV (q = 0.006, R = 0.26) as well as the presence of L. crispatus (q = 0.001, R = 0.43), L. iners, Gardnerella spp., and Atopobium vaginae were found (q < 0.002, R > 0.15). The eukaryotic viral community also correlated with BV-status (q = 0.018, R = 0.20). In conclusion, the vaginal virome was clearly linked with bacterial community structure and BV-status.}, } @article {pmid33049454, year = {2020}, author = {Schots, PC and Jansen, KM and Mrazek, J and Pedersen, AM and Olsen, RL and Larsen, TS}, title = {Obesity-induced alterations in the gut microbiome in female mice fed a high-fat diet are antagonized by dietary supplementation with a novel, wax ester-rich, marine oil.}, journal = {Nutrition research (New York, N.Y.)}, volume = {83}, number = {}, pages = {94-107}, doi = {10.1016/j.nutres.2020.09.002}, pmid = {33049454}, issn = {1879-0739}, mesh = {Animals ; Anti-Obesity Agents/pharmacology ; Bacteria/classification/genetics/growth & development ; Colon/microbiology ; *Diet, High-Fat ; Dietary Fats, Unsaturated/*administration & dosage ; *Dietary Supplements ; Exenatide/pharmacology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Metagenome ; Mice ; Mice, Inbred C57BL ; Obesity/*microbiology/physiopathology/therapy ; Oils/*administration & dosage ; Weight Gain ; }, abstract = {Dietary supplementation with calanus oil, a novel wax ester-rich marine oil, has been shown to reduce adiposity in high-fat diet (HFD)-induced obese mice. Current evidence suggests that obesity and its comorbidities are intrinsically linked with unfavorable changes in the intestinal microbiome. Thus, in line with its antiobesity effect, we hypothesized that dietary supplementation with calanus oil should counteract the obesity-related deleterious changes in the gut microbiota. Seven-week-old female C57bl/6J mice received an HFD for 12 weeks to induce obesity followed by 8-week supplementation with 2% calanus oil. For comparative reasons, another group of mice was treated with exenatide, an antiobesogenic glucagon-like peptide-1 receptor agonist. Mice fed normal chow diet or nonsupplemented HFD for 20 weeks served as lean and obese controls, respectively. 16S rRNA gene sequencing was performed on fecal samples from the colon. HFD increased the abundance of the Lactococcus and Leuconostoc genera relative to normal chow diet, whereas abundances of Allobaculum and Oscillospira were decreased. Supplementation with calanus oil led to an apparent overrepresentation of Lactobacillus and Streptococcus and underrepresentation of Bilophila. Exenatide prevented the HFD-induced increase in Lactococcus and caused a decrease in the abundance of Streptococcus compared to the HFD group. Thus, HFD altered the gut microbiota composition in an unhealthy direction by increasing the abundance of proinflammatory genera while reducing those considered health-promoting. These obesity-induced changes were antagonized by both calanus oil and exenatide.}, } @article {pmid33049161, year = {2021}, author = {Khan, S and Hauptman, R and Kelly, L}, title = {Engineering the Microbiome to Prevent Adverse Events: Challenges and Opportunities.}, journal = {Annual review of pharmacology and toxicology}, volume = {61}, number = {}, pages = {159-179}, pmid = {33049161}, issn = {1545-4304}, support = {T32 AI070117/AI/NIAID NIH HHS/United States ; T32 GM007288/GM/NIGMS NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; *Microbiota ; *Pharmaceutical Preparations ; }, abstract = {In the past decade of microbiome research, we have learned about numerous adverse interactions between the microbiome and medical interventions such as drugs, radiation, and surgery. What if we could alter our microbiomes to prevent these events? In this review, we discuss potential routes to mitigate microbiome adverse events, including applications from the emerging field of microbiome engineering. We highlight cases where the microbiome acts directly on a treatment, such as via differential drug metabolism, and cases where a treatment directly harms the microbiome, such as in radiation therapy. Understanding and preventing microbiome adverse events is a difficult challenge that will require a data-driven approach involving causal statistics, multiomics techniques, and a personalized means of mitigating adverse events. We propose research considerations to encourage productive work in preventing microbiome adverse events, and we highlight the many challenges and opportunities that await.}, } @article {pmid33047445, year = {2021}, author = {Zhang, Z and Qin, F and Chen, F and Chu, X and Luo, H and Zhang, R and Du, S and Tian, Z and Zhao, Y}, title = {Culturing novel and abundant pelagiphages in the ocean.}, journal = {Environmental microbiology}, volume = {23}, number = {2}, pages = {1145-1161}, doi = {10.1111/1462-2920.15272}, pmid = {33047445}, issn = {1462-2920}, support = {41706173//NSFC/ ; }, mesh = {Alphaproteobacteria/virology ; Bacteriophages/classification/genetics/*growth & development/isolation & purification ; Genetic Variation ; Genome, Viral/genetics ; Genomics ; *Oceans and Seas ; Seawater/microbiology/*virology ; Virome/genetics ; }, abstract = {Viruses play a key role in biogeochemical cycling and host mortality, metabolism, physiology and evolution in the ocean. Viruses that infect the globally abundant SAR11 bacteria (pelagiphages) were reported to be an important component of the marine viral communities. Our current knowledge of pelagiphages is based on a few studies and therefore is limited. In this study, 10 new pelagiphages were isolated and genomically characterized. These pelagiphages represent the first cultivated representatives of four viral lineages only found in metagenomic sequencing datasets previously. Many abundant environmental viral sequences, i.e., single-virus vSAG 37-F6 and several Global Ocean Viromes (GOV) viral populations, are now further confirmed with these pelagiphages. Viromic read mapping reveals that these new pelagiphages are globally distributed in the ocean and can be detected throughout the water column. Remarkably, isolation of these pelagiphages contributed up to 12% of all viromic reads annotated in the analysed viromes. Altogether, this study has greatly broadened our understanding of pelagiphages regarding their morphology, genetic diversity, infection strategies, and distribution pattern. The availability of these newly isolated pelagiphages and their genome sequences will allow us to further explore their infectivities and ecological strategies.}, } @article {pmid33046051, year = {2020}, author = {Hasic Telalovic, J and Music, A}, title = {Using data science for medical decision making case: role of gut microbiome in multiple sclerosis.}, journal = {BMC medical informatics and decision making}, volume = {20}, number = {1}, pages = {262}, pmid = {33046051}, issn = {1472-6947}, mesh = {Bacteria/*classification/genetics/isolation & purification ; *Clinical Decision-Making ; *Data Science ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Multiple Sclerosis/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; }, abstract = {BACKGROUND: A decade ago, the advancements in the microbiome data sequencing techniques initiated the development of research of the microbiome and its relationship with the host organism. The development of sophisticated bioinformatics and data science tools for the analysis of large amounts of data followed. Since then, the analyzed gut microbiome data, where microbiome is defined as a network of microorganisms inhabiting the human intestinal system, has been associated with several conditions such as irritable bowel syndrome - IBS, colorectal cancer, diabetes, obesity, and metabolic syndrome, and lately in the study of Parkinson's and Alzheimer's diseases as well. This paper aims to provide an understanding of differences between microbial data of individuals who have been diagnosed with multiple sclerosis and those who were not by exploiting data science techniques on publicly available data.

METHODS: This study examines the relationship between multiple sclerosis (MS), an autoimmune central nervous system disease, and gut microbial community composition, using the samples acquired by 16s rRNA sequencing technique. We have used three different sets of MS samples sequenced during three independent studies (Jangi et al, Nat Commun 7:1-11, 2016), (Miyake et al, PLoS ONE 10:0137429, 2015), (McDonald et al, Msystems 3:00031-18, 2018) and this approach strengthens our results. Analyzed sequences were from healthy control and MS groups of sequences. The extracted set of statistically significant bacteria from the (Jangi et al, Nat Commun 7:1-11, 2016) dataset samples and their statistically significant predictive functions were used to develop a Random Forest classifier. In total, 8 models based on two criteria: bacteria abundance (at six taxonomic levels) and predictive functions (at two levels), were constructed and evaluated. These include using taxa abundances at different taxonomy levels as well as predictive function analysis at different hierarchical levels of KEGG pathways.

RESULTS: The highest accuracy of the classification model was obtained at the genus level of taxonomy (76.82%) and the third hierarchical level of KEGG pathways (70.95%). The second dataset's 18 MS samples (Miyake et al, PLoS ONE 10:0137429, 2015) and 18 self-reported healthy samples from the (McDonald et al, Msystems 3:00031-18, 2018) dataset were used to validate the developed classification model. The significance of this step is to show that the model is not overtrained for a specific dataset but can also be used on other independent datasets. Again, the highest classification model accuracy for both validating datasets combined was obtained at the genus level of taxonomy (70.98%) and third hierarchical level of KEGG pathways (67.24%). The accuracy of the independent set remained very relevant.

CONCLUSIONS: Our results demonstrate that the developed classification model provides a good tool that can be used to suggest the presence or absence of MS condition by collecting and analyzing gut microbiome samples. The accuracy of the model can be further increased by using sequencing methods that allow higher taxa resolution (i.e. shotgun metagenomic sequencing).}, } @article {pmid33045611, year = {2021}, author = {Zhao, R and Feng, J and Huang, J and Li, X and Li, B}, title = {Reponses of microbial community and antibiotic resistance genes to the selection pressures of ampicillin, cephalexin and chloramphenicol in activated sludge reactors.}, journal = {The Science of the total environment}, volume = {755}, number = {Pt 2}, pages = {142632}, doi = {10.1016/j.scitotenv.2020.142632}, pmid = {33045611}, issn = {1879-1026}, mesh = {Ampicillin ; Anti-Bacterial Agents/pharmacology ; Cephalexin ; Chloramphenicol ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microbiota ; *Sewage ; }, abstract = {High concentrations of antibiotics can exert strong selection pressures on the microbial community and promote the emergence and dissemination of antibiotic resistance genes (ARGs). The activated sludge reactors treating ampicillin, cephalexin and chloramphenicol production wastewater were established to investigate the responses of microbial community, ARGs and mobile genetic elements (MGEs) to antibiotics. Antibiotic selection pressures significantly declined the microbial diversity and changed microbial community structures. Based on metagenomic analysis, a total of 500 ARG subtypes affiliated with 18 ARG types were identified and 63 ARGs were shared by all samples. The substantial increase of ARG abundance and the shifts of ARG profiles were significantly correlated with antibiotic types and concentrations. The evident enrichment of non-corresponding ARG types suggested the strong co-selection effects of the target antibiotics. Additionally, metagenomic analysis revealed the occurrence of 104 MGEs belonging to various types and the five dominant MGEs were tnpA, intI1, tniA, tniB and IS91. The ARG-MGE co-occurrence associations implied the potential mobility of ARGs. Network analysis also demonstrated that five ARG types (aminoglycoside, beta-lactam, chloramphenicol, multidrug and tetracycline resistance genes) tended to co-occur internally and the obvious co-occurrence patterns among different ARG types indicated the potential for resistance co-selection. Moreover, 15 bacterial genera were speculated as the hosts of diverse ARGs. This study provides a comprehensive overview of the occurrence of ARGs and MGEs and is valuable for the risk assessment and management of antibiotic resistance.}, } @article {pmid33039712, year = {2020}, author = {Li, X and Lin, Y and Li, X and Xu, X and Zhao, Y and Xu, L and Gao, Y and Li, Y and Tan, Y and Qian, P and Huang, H}, title = {Tyrosine supplement ameliorates murine aGVHD by modulation of gut microbiome and metabolome.}, journal = {EBioMedicine}, volume = {61}, number = {}, pages = {103048}, pmid = {33039712}, issn = {2352-3964}, mesh = {Acute Disease ; Animals ; Biodiversity ; Chromatography, High Pressure Liquid ; Computational Biology/methods ; *Dietary Supplements ; Disease Management ; Disease Models, Animal ; Disease Susceptibility ; *Gastrointestinal Microbiome ; Graft vs Host Disease/diagnosis/*etiology/*metabolism/therapy ; Intestinal Mucosa ; Mass Spectrometry/methods ; *Metabolome ; Metabolomics/methods ; Metagenomics/methods ; Mice ; Phenotype ; RNA, Ribosomal, 16S/genetics ; Tyrosine/*administration & dosage ; }, abstract = {BACKGROUND: Microbial communities and their metabolic components in the gut are of vital importance for immune homeostasis and have an influence on the susceptibility of the host to a number of immune-mediated diseases like acute graft-versus-host disease (aGVHD) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). However, little is known about the functional connections between microbiome and metabolome in aGVHD due to the complexity of the gastrointestinal environment.

METHOD: Initially, gut microbiota and fecal metabolic phenotype in aGVHD murine models were unleashed by performing 16S ribosomal DNA gene sequencing and ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS)-based metabolomics.

FINDINGS: The group with aGVHD experienced a significant drop in Lachnospiraceae_unclassified but an increase in the relative abundance of Clostridium XI, Clostridium XIVa and Enterococcus. Meanwhile, a lower content of tyrosine was observed in the gut of aGVHD mice. The correlation analysis revealed that tyrosine-related metabolites were inversely correlated with Clostridium XIVa, besides, Blautia and Enterococcus also displayed the negative tendency in aGVHD condition. Apart from exploring the importance and function of tyrosine, different tyrosine diets were offered to mice during transplantation. Additional tyrosine supplements can improve overall survival, ameliorate symptoms at the early stage of aGVHD and change the structure and composition of gut microbiota and fecal metabolic phenotype. In addition, aGVHD mice deprived from tyrosine displayed worse manifestations than the vehicle diet group.

INTERPRETATION: The results demonstrated the roles and mechanisms of gut microbiota, indispensable metabolites and tyrosine in the progression of aGVHD, which can be an underlying biomarker for aGVHD diagnosis and treatment.

FUNDING: This research was funded by the International Cooperation and Exchange Program (81520108002), the National Key R&D Program of China, Stem Cell and Translation Research (2018YFA0109300), National Natural Science Foundation of China (81670169, 81670148, 81870080 and 91949115) and Natural Science Foundation of Zhejiang Province (LQ19H080006).}, } @article {pmid33039709, year = {2020}, author = {Huang, X and Hong, X and Wang, J and Sun, T and Yu, T and Yu, Y and Fang, J and Xiong, H}, title = {Metformin elicits antitumour effect by modulation of the gut microbiota and rescues Fusobacterium nucleatum-induced colorectal tumourigenesis.}, journal = {EBioMedicine}, volume = {61}, number = {}, pages = {103037}, pmid = {33039709}, issn = {2352-3964}, mesh = {Animals ; Biomarkers ; *Cell Transformation, Neoplastic/drug effects ; Colonic Neoplasms/*etiology/*metabolism/pathology ; Disease Models, Animal ; Fusobacterium Infections/*complications/microbiology ; Fusobacterium nucleatum/*physiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestinal Mucosa/metabolism/pathology ; Metagenome ; Metagenomics/methods ; Metformin/*pharmacology ; Mice ; Mice, Transgenic ; RNA, Ribosomal, 16S ; ROC Curve ; }, abstract = {BACKGROUND: The effect of metformin on gut microbiota has been reported, but whether metformin can suppress colorectal cancer (CRC) by affecting gut microbiota composition and rescue F. nucleatum-induced tumourigenicity remains unclear.

METHODS: To identify microbiota associated with both CRC occurrence and metformin treatment, first, we reanalyzed the gut microbiome of our previous data on two human cohorts of normal and CRC individuals. Subsequently, we summarized microbiota altered by metformin from published literatures. Several taxa, including Fusobacterium, were associated with both CRC occurrence and metformin treatment. We investigated the effect of metformin on APC[Min/+] mice given with or without F. nucleatum. 16S rRNA gene sequencing was performed.

FINDINGS: We summarized 131 genera altered by metformin from 18 published literatures. Five genera reported to be changed by metformin, including Bacteroides, Streptococcus, Achromobacter, Alistipes and Fusobacterium, were associated with CRC in both of our human cohorts. Metformin relieved the symptoms caused by F. nucleatum administration in APC[Min/+] mice, and showed promise in suppressing intestinal tumour formation and rescuing F. nucleatum-induced tumourigenicity. Administration of F. nucleatum and/or metformin had effect on gut microbiome structure, composition and functions of APC[Min/+] mice.

INTERPRETATION: This study pioneers in predicting critical CRC-associated taxa contributing to the antitumour effect of metformin, and correlating gut microbiome with the antitumour effect of metformin in experimental animals. We presented a basis for future investigations into metformin's potential effect on suppressing F. nucleatum-induced tumor formation in vivo.

FUNDING: This work was supported by grants from the National Natural Science Foundation of China (31701250).}, } @article {pmid33039480, year = {2021}, author = {Tay, ASL and Li, C and Nandi, T and Chng, KR and Andiappan, AK and Mettu, VS and de Cevins, C and Ravikrishnan, A and Dutertre, CA and Wong, XFCC and Ng, AHQ and Matta, SA and Ginhoux, F and Rötzschke, O and Chew, FT and Tang, MBY and Yew, YW and Nagarajan, N and Common, JEA}, title = {Atopic dermatitis microbiomes stratify into ecologic dermotypes enabling microbial virulence and disease severity.}, journal = {The Journal of allergy and clinical immunology}, volume = {147}, number = {4}, pages = {1329-1340}, doi = {10.1016/j.jaci.2020.09.031}, pmid = {33039480}, issn = {1097-6825}, mesh = {Adolescent ; Adult ; Bacteria/genetics/pathogenicity ; Biomarkers/blood ; Cytokines/blood ; Dermatitis, Atopic/blood/immunology/metabolism/*microbiology ; Female ; Humans ; Male ; *Microbiota ; Middle Aged ; Phenotype ; Severity of Illness Index ; Skin/chemistry/metabolism/*microbiology ; Skin Tests ; Virulence/genetics ; Water/metabolism ; Young Adult ; }, abstract = {BACKGROUND: Atopic dermatitis (AD) is a common skin disease affecting up to 20% of the global population, with significant clinical heterogeneity and limited information about molecular subtypes and actionable biomarkers. Although alterations in the skin microbiome have been described in subjects with AD during progression to flare state, the prognostic value of baseline microbiome configurations has not been explored.

OBJECTIVE: Our aim was to identify microbial signatures on AD skin that are predictive of disease fate.

METHODS: Nonlesional skin of patients with AD and healthy control subjects were sampled at 2 time points separated by at least 4 weeks. Using whole metagenome analysis of skin microbiomes of patients with AD and control subjects (n = 49 and 189 samples), we identified distinct microbiome configurations (dermotypes A and B). Blood was collected for immunophenotyping, and skin surface samples were analyzed for correlations with natural moisturizing factors and antimicrobial peptides.

RESULTS: Dermotypes were robust and validated across 2 additional cohorts (63 individuals), with strong enrichment of subjects with AD in dermotype B. Dermotype B was characterized by reduced microbial richness, depletion of Cutibacterium acnes, Dermacoccus and Methylobacterium species, individual-specific outlier abundance of Staphylococcus species (eg, S epidermidis, S capitis, S aureus), and enrichment in metabolic pathways (eg, branched chain amino acids and arginine biosynthesis) and virulence genes (eg, β-toxin, δ-toxin) that defined a pathogenic ecology. Skin surface and circulating host biomarkers exhibited a distinct microbial-associated signature that was further reflected in more severe itching, frequent flares, and increased disease severity in patients harboring the dermotype B microbiome.

CONCLUSION: We report distinct clusters of microbial profiles that delineate the role of microbiome configurations in AD heterogeneity, highlight a mechanism for ongoing inflammation, and provide prognostic utility toward microbiome-based disease stratification.}, } @article {pmid33037214, year = {2020}, author = {Pereira, FC and Wasmund, K and Cobankovic, I and Jehmlich, N and Herbold, CW and Lee, KS and Sziranyi, B and Vesely, C and Decker, T and Stocker, R and Warth, B and von Bergen, M and Wagner, M and Berry, D}, title = {Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5104}, pmid = {33037214}, issn = {2041-1723}, support = {W 1261/FWF_/Austrian Science Fund FWF/Austria ; P 27831/FWF_/Austrian Science Fund FWF/Austria ; P 26127/FWF_/Austrian Science Fund FWF/Austria ; P 29426/FWF_/Austrian Science Fund FWF/Austria ; ZK 57/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Acetylglucosamine/metabolism ; Animals ; Anti-Bacterial Agents ; Bacterial Proteins/metabolism ; Bacterial Toxins/metabolism ; Cell Separation/methods ; Clostridioides difficile/genetics/growth & development/*pathogenicity ; Clostridium Infections/microbiology ; Deuterium ; Female ; Gastric Mucins/chemistry/metabolism ; Gastrointestinal Microbiome/*physiology ; Intestinal Mucosa/drug effects/microbiology ; Metagenome ; Mice, Inbred C57BL ; Monosaccharides/*metabolism ; N-Acetylneuraminic Acid/metabolism ; Polysaccharides/chemistry/metabolism ; Spectrum Analysis, Raman ; }, abstract = {Many intestinal pathogens, including Clostridioides difficile, use mucus-derived sugars as crucial nutrients in the gut. Commensals that compete with pathogens for such nutrients are therefore ecological gatekeepers in healthy guts, and are attractive candidates for therapeutic interventions. Nevertheless, there is a poor understanding of which commensals use mucin-derived sugars in situ as well as their potential to impede pathogen colonization. Here, we identify mouse gut commensals that utilize mucus-derived monosaccharides within complex communities using single-cell stable isotope probing, Raman-activated cell sorting and mini-metagenomics. Sequencing of cell-sorted fractions reveals members of the underexplored family Muribaculaceae as major mucin monosaccharide foragers, followed by members of Lachnospiraceae, Rikenellaceae, and Bacteroidaceae families. Using this information, we assembled a five-member consortium of sialic acid and N-acetylglucosamine utilizers that impedes C. difficile's access to these mucosal sugars and impairs pathogen colonization in antibiotic-treated mice. Our findings underscore the value of targeted approaches to identify organisms utilizing key nutrients and to rationally design effective probiotic mixtures.}, } @article {pmid33036549, year = {2020}, author = {Gong, G and Zhou, S and Luo, R and Gesang, Z and Suolang, S}, title = {Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {302}, pmid = {33036549}, issn = {1471-2180}, support = {CARS-37//the National Beef Cattle Industrial Technology System project/ ; }, mesh = {Animals ; Bacteroidaceae/enzymology/genetics/isolation & purification ; Bacteroidetes/enzymology/genetics/isolation & purification ; Carbohydrate Metabolism ; Cattle ; Clostridiaceae/enzymology/genetics/isolation & purification ; Esterases/classification/*genetics/isolation & purification/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Gene Expression ; Genetic Variation ; Glycoside Hydrolases/classification/*genetics/isolation & purification/metabolism ; High-Throughput Nucleotide Sequencing ; Lignin/metabolism ; Metagenome ; *Metagenomics/methods ; Microbial Consortia/*genetics ; Polysaccharide-Lyases/classification/*genetics/isolation & purification/metabolism ; Prevotella/enzymology/genetics/isolation & purification ; Rumen/enzymology/*microbiology ; Ruminococcus/enzymology/genetics/isolation & purification ; }, abstract = {BACKGROUND: Yaks are able to utilize the gastrointestinal microbiota to digest plant materials. Although the cellulolytic bacteria in the yak rumen have been reported, there is still limited information on the diversity of the major microorganisms and putative carbohydrate-metabolizing enzymes for the degradation of complex lignocellulosic biomass in its gut ecosystem.

RESULTS: Here, this study aimed to decode biomass-degrading genes and genomes in the yak fecal microbiota using deep metagenome sequencing. A comprehensive catalog comprising 4.5 million microbial genes from the yak feces were established based on metagenomic assemblies from 92 Gb sequencing data. We identified a full spectrum of genes encoding carbohydrate-active enzymes, three-quarters of which were assigned to highly diversified enzyme families involved in the breakdown of complex dietary carbohydrates, including 120 families of glycoside hydrolases, 25 families of polysaccharide lyases, and 15 families of carbohydrate esterases. Inference of taxonomic assignments to the carbohydrate-degrading genes revealed the major microbial contributors were Bacteroidaceae, Ruminococcaceae, Rikenellaceae, Clostridiaceae, and Prevotellaceae. Furthermore, 68 prokaryotic genomes were reconstructed and the genes encoding glycoside hydrolases involved in plant-derived polysaccharide degradation were identified in these uncultured genomes, many of which were novel species with lignocellulolytic capability.

CONCLUSIONS: Our findings shed light on a great diversity of carbohydrate-degrading enzymes in the yak gut microbial community and uncultured species, which provides a useful genetic resource for future studies on the discovery of novel enzymes for industrial applications.}, } @article {pmid33035862, year = {2021}, author = {Chen, Q and Wang, J and Zhang, H and Shi, H and Liu, G and Che, J and Liu, B}, title = {Microbial community and function in nitrogen transformation of ectopic fermentation bed system for pig manure composting.}, journal = {Bioresource technology}, volume = {319}, number = {}, pages = {124155}, doi = {10.1016/j.biortech.2020.124155}, pmid = {33035862}, issn = {1873-2976}, mesh = {Ammonia ; Animals ; *Composting ; Fermentation ; Manure ; *Microbiota ; Nitrification ; Nitrogen ; Soil ; Swine ; }, abstract = {In this work, agricultural wastes were treated by composting in an ectopic fermentation bed system (EFBS) with a continuous nitrogen addition technique. With decreasing of NH4[+]-N concentration and increasing of NO3[-]-N concentration were observed, and activities of protease, urease and nitrate reductase changed significantly during the fermentation process. To elucidate the key microbes and their function in nitrogen-transforming, microbial diversity and clusters of orthologous groups (COGs) in composting materials were evaluated using metagenomic technology. Comparing with ammonification, the COGs involved in nitrification and denitrification were predominant in the composts. The correlation heatmap revealed that Streptomyces predominant in ammonification was significantly affected by contents of N, NH4[+]-N and NO3[-]-N. Meanwhile, ammonia-oxidizing archaea (AOA) had a positive relationship with moisture. The most abundant genera in denitrification had positive relationships with N and NO3[-]-N. The results indicated that EFBS had functionally diverse microbes and COGs for NH3 removal.}, } @article {pmid33034768, year = {2021}, author = {Xu, Y and Li, J and Han, X and Zhang, Z and Zhong, M and Hu, Z}, title = {Enteromorpha prolifera Diet Drives Intestinal Microbiome Composition in Siganus oramin.}, journal = {Current microbiology}, volume = {78}, number = {1}, pages = {229-237}, pmid = {33034768}, issn = {1432-0991}, support = {41476150//National Natural Science Foundation of China/ ; 2018KCXTD012//Guangdong Science and Technology Department/ ; 2017A020217004//Science and Technology Planning Project of Guangdong Province/ ; 2017A040403011//Science and Technology Planning Project of Guangdong Province/ ; 2019GKTSCX071//Department of Education of Guangdong Province/ ; }, mesh = {Diet ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics ; *Ulva ; }, abstract = {Enteromorpha prolifera (E. prolifera) contains complex sulfated polysaccharides that are resistant to biological degradation. Most organisms cannot digest biomass of E. prolifera, except Siganus oramin (S. oramin). This study was conducted to identify the bacteria in the intestine of S. oramin facilitating the digestion of E. prolifera polysaccharides (EPP). Metagenomic sequencing analysis of the S. oramin intestinal microbiota revealed that E. prolifera diet increased the number of Firmicutes, replacing Proteobacteria to be the dominant bacteria. The proportion of Firmicutes increased from 38.8 to 58.6%, with Bacteroidetes increasing nearly fivefold from 5 to 23.7%. 16S rDNA high-throughput sequencing showed that EPP-induced Bacteroidetes increased significantly in the intestinal flora of S. oramin cultivated in vitro. Metatranscriptome analysis showed that EPP induced more transferase, polysaccharide hydrolase, glycoside hydrolase, and esterases expressed in vitro, and most of them were taxonomically annotated to Bacteroidetes. Compared with the aggregation of GH family genes in metagenomic sequencing analysis in vivo, EPP induced more CBM32, GH2, GT2, GT30, and GH30 families gene expression in vitro. In general, We found that the bacteria in intestinal tract of S. oramin responsible for digestion of E. prolifera were Firmicutes and Bacteroidetes, while Bacteroidetes was the dominant bacteria involved in EPP degradation in vitro cultures. Compared with in vivo experiments, only GH family genes were mostly involved, we detected a more complete and complex EPP degradation pathway in vitro. The results may benefit the further study of biodegradation of E. prolifera and has potential implications for the utilization of E. prolifera for biotechnology.}, } @article {pmid33033250, year = {2020}, author = {Guo, W and Xin, M and Wang, Z and Yao, Y and Hu, Z and Song, W and Yu, K and Chen, Y and Wang, X and Guan, P and Appels, R and Peng, H and Ni, Z and Sun, Q}, title = {Origin and adaptation to high altitude of Tibetan semi-wild wheat.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5085}, pmid = {33033250}, issn = {2041-1723}, mesh = {*Adaptation, Physiological/genetics ; *Altitude ; Domestication ; Ecotype ; Genome, Plant ; Geography ; Metagenomics ; Phenotype ; Principal Component Analysis ; Tibet ; Triticum/genetics/*physiology ; }, abstract = {Tibetan wheat is grown under environmental constraints at high-altitude conditions, but its underlying adaptation mechanism remains unknown. Here, we present a draft genome sequence of a Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum Shao) accession Zang1817 and re-sequence 245 wheat accessions, including world-wide wheat landraces, cultivars as well as Tibetan landraces. We demonstrate that high-altitude environments can trigger extensive reshaping of wheat genomes, and also uncover that Tibetan wheat accessions accumulate high-altitude adapted haplotypes of related genes in response to harsh environmental constraints. Moreover, we find that Tibetan semi-wild wheat is a feral form of Tibetan landrace, and identify two associated loci, including a 0.8-Mb deletion region containing Brt1/2 homologs and a genomic region with TaQ-5A gene, responsible for rachis brittleness during the de-domestication episode. Our study provides confident evidence to support the hypothesis that Tibetan semi-wild wheat is de-domesticated from local landraces, in response to high-altitude extremes.}, } @article {pmid33032033, year = {2020}, author = {Suárez, N and Weckx, S and Minahk, C and Hebert, EM and Saavedra, L}, title = {Metagenomics-based approach for studying and selecting bioprotective strains from the bacterial community of artisanal cheeses.}, journal = {International journal of food microbiology}, volume = {335}, number = {}, pages = {108894}, doi = {10.1016/j.ijfoodmicro.2020.108894}, pmid = {33032033}, issn = {1879-3460}, mesh = {Animals ; Anti-Bacterial Agents/analysis/*biosynthesis ; Argentina ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Bacteriocins/analysis/*biosynthesis/genetics ; Cattle ; Cheese/analysis/*microbiology ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A metagenome-based approach was used to assess the taxonomic affiliation and functional potential for bacteriocin production of the bacterial community in cow's milk artisanal cheeses from Northwestern Argentina. Three different samples were analyzed by high-throughput sequencing of the V4 region of the 16S rRNA gene and shotgun metagenomics. Taxonomic analysis showed that cheese A and C were quite similar whereas cheese B displayed a rather different bacterial composition. Overall, two families, Streptococceae and Enterococceae, dominated the artisanal cheese microbiota, being the former family prevalent in cheese B and the later family the most important in samples A and C. Besides the usual species associated to cheeses, a number of bacterial taxa that have not been previously found in Argentinean artisanal cheeses were reported in the present work such as Macrococcus caseolyticus and Streptococcus macedonicus Functional metagenomics analysis using the bacteriocin mining software BAGEL3, identified 2 ORFs encoding antimicrobial peptides in cheese B and 42 different peptides in sample C. The bacteriocin genes found showed good correlation with taxonomy. Based on the microbial diversity and functional features found through shotgun metagenomic sequencing, a culture-dependent approach was applied aiming to isolate bacteriocin-producing bacteria able to inhibit the growth of the foodborne pathogen Listeria monocytogenes. From 151 bacterial colonies derived from the cheese samples, 10 were associated to high anti-Listeria activity. Based on partial 16S rRNA gene sequencing and RAPD-PCR analysis, all bacteriocinogenic isolates were identified as Enterococcus faecium. Finally, we carried out a pilot experiment with L. monocytogenes-contaminated cheese using one of the enterococcal isolates as a bioprotective adjunct culture. The use of E. faecium CRL1879 during artisanal cheese manufacturing did not alter the main organoleptic properties of the cheese and ensured an efficient control of the foodborne pathogen up to 30 days. This finding supports the use of E. faecium CRL1879 as an adjunct culture in the cheese-making process with a combination of both safety and minimal processing.}, } @article {pmid33031627, year = {2021}, author = {Zhang, M and Hill, JE and Alexander, TW and Huang, Y}, title = {The nasal viromes of cattle on arrival at western Canadian feedlots and their relationship to development of bovine respiratory disease.}, journal = {Transboundary and emerging diseases}, volume = {68}, number = {4}, pages = {2209-2218}, doi = {10.1111/tbed.13873}, pmid = {33031627}, issn = {1865-1682}, support = {//China Scholarship Council/ ; SBIF2015-109//Saskatchewan Cattlemen's Association/ ; ADF20160092//Agriculture Development Fund/ ; AMR.10.17//Beef Cattle Research Council/ ; }, mesh = {Animals ; Canada/epidemiology ; Cattle ; *Cattle Diseases/epidemiology/virology ; *Coronavirus, Bovine ; Respiratory Tract Diseases/*veterinary/virology ; Virome ; Viruses ; }, abstract = {Bovine respiratory disease (BRD) has a complex pathogenesis and aetiology, being the costliest disease affecting the cattle industry in North America. In this study, we applied Nanopore-based viral metagenomic sequencing to explore the nasal virome of cattle upon arrival at feedlot and related the findings to the development of BRD. Deep nasal swabs (DNS) from 310 cattle for which BRD outcomes were known (155 cattle developed BRD within 40 days and 155 remained healthy) were included. The most prevalent virus in on-arrival samples was bovine coronavirus (BCV) (45.2%, 140/310), followed by bovine rhinitis virus B (BRBV) (21.9%, 68/310), enterovirus E (EVE) (19.6%, 60/310), bovine parainfluenza virus 3 (BPIV3) (10.3%, 32/310), ungulate tetraparvovirus 1 (UTPV1) (9.7%, 30/310) and influenza D virus (7.1%, 22/310). No relationship was found between BRD development and the number of viruses detected, the presence of any specific individual virus or combination of viruses. Bovine kobuvirus (BKV) was detected in 2.6% of animals (8/310), being the first report of this virus in Canada. Results of this study demonstrate the diversity of viruses in bovine DNS collected upon arrival at feedlot and highlights the need for further research into prediction of BRD development in the context of mixed infections.}, } @article {pmid33030577, year = {2021}, author = {Ramne, S and Brunkwall, L and Ericson, U and Gray, N and Kuhnle, GGC and Nilsson, PM and Orho-Melander, M and Sonestedt, E}, title = {Gut microbiota composition in relation to intake of added sugar, sugar-sweetened beverages and artificially sweetened beverages in the Malmö Offspring Study.}, journal = {European journal of nutrition}, volume = {60}, number = {4}, pages = {2087-2097}, pmid = {33030577}, issn = {1436-6215}, support = {2016-01501//Vetenskapsrådet/ ; 521-2013-2756//Vetenskapsrådet/ ; 2013-210, 2014-366, 2018-02784//Vetenskapsrådet/ ; 2016-0267, 2019-0555//Hjärt-Lungfonden/ ; 2015-0427//Hjärt-Lungfonden/ ; 2013-0598, 2017-0523//Hjärt-Lungfonden/ ; 2015-338//European Foundation for the Study of Diabetes/ ; DIA 2018-358//Diabetesförbundet/ ; NNF17OC0027348, NNF18OC0034386//Novo Nordisk Fonden/ ; ERC-CoG-2014-649021/ERC_/European Research Council/International ; }, mesh = {Adolescent ; Adult ; Aged ; Artificially Sweetened Beverages ; Beverages ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Humans ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Sugar-Sweetened Beverages ; Sugars ; Sweetening Agents/adverse effects ; Young Adult ; }, abstract = {PURPOSE: It has been suggested that a high intake of sugar or sweeteners may result in an unfavorable microbiota composition; however, evidence is lacking. Hence, in this exploratory epidemiological study, we aim to examine if intake of added sugar, sugar-sweetened beverages (SSBs) or artificially sweetened beverages (ASBs) associate with the gut microbiota composition.

METHODS: Participants (18-70 years) in the Malmö Offspring Study have provided blood, urine, and fecal samples and completed both web-based 4 day food records and short food frequency questionnaires. The gut microbiota was assessed by 16S rRNA sequencing, processed in QIIME and matched to Greengenes (v.13.8), giving 64 included genera after filtering. Intake of added sugar (n = 1371) (also supported by the overnight urinary sugar biomarker in a subgroup n = 577), SSBs (n = 1086) and ASBs (n = 1085) were examined as exposures in negative binomial regressions.

RESULTS: Various genera nominally associated with intake of added sugar, SSBs, and ASBs. Only the negative association between SSB intake and Lachnobacterium remained significant after multiple testing correction. A positive association between SSB intake and the Firmicutes:Bacteroidetes ratio was also observed.

CONCLUSION: In this wide population, the cross-sectional associations between added sugar and sweet beverage intake and the gut microbiota are modest, but the results suggest that SSB intake is associated negatively with the genus Lachnobacterium and positively with the Firmicutes:Bacteroidetes ratio. Larger studies, preferably using metagenomic sequencing, are needed to further evaluate if a link exists between intake of sugars and sweeteners and the human gut microbiota.}, } @article {pmid33028395, year = {2020}, author = {Berggrund, M and Gustavsson, I and Aarnio, R and Lindberg, JH and Sanner, K and Wikström, I and Enroth, S and Bunikis, I and Olovsson, M and Gyllensten, U}, title = {Temporal changes in the vaginal microbiota in self-samples and its association with persistent HPV16 infection and CIN2.}, journal = {Virology journal}, volume = {17}, number = {1}, pages = {147}, pmid = {33028395}, issn = {1743-422X}, mesh = {Adult ; Early Detection of Cancer ; Female ; Human papillomavirus 16/genetics/isolation & purification ; Humans ; *Microbiota ; Middle Aged ; Papillomavirus Infections/diagnosis/*etiology/*microbiology ; Specimen Handling/methods ; Uterine Cervical Neoplasms/diagnosis/etiology/microbiology ; Vagina/*virology ; Vaginal Smears/*methods ; Uterine Cervical Dysplasia/diagnosis/*etiology/*microbiology ; }, abstract = {BACKGROUND: The vaginal microbiota has been reported to be associated with HPV infection and cervical cancer. This study was performed to compare the vaginal microbiota at two timepoints in women performing self-sampling and had a persistent or transient HPV16 infection. The women were tested for 12 high-risk HPV (hrHPV) types but only women with single type (HPV16) were included to reduce confounding variables.

METHODS: In total 96 women were included in this study. Of these, 26 were single positive for HPV16 in the baseline test and HPV negative in the follow-up test and 38 were single positive for HPV16 in both tests and diagnosed with CIN2+ in histology. In addition, 32 women that were negative for all 12 HPV tested were included. The samples of vaginal fluid were analyzed with the Ion 16S™ Metagenomics Kit and Ion 16S™ metagenomics module within the Ion Reporter™ software.

RESULTS: K-means clustering resulted in two Lactobacillus-dominated groups, one with Lactobacillus sp. and the other specifically with Lactobacillus iners. The two remaining clusters were dominated by a mixed non-Lactobacillus microbiota. HPV negative women had lower prevalence (28%) of the non-Lactobacill dominant cluster in the baseline test, as compared to women with HPV16 infection (42%) (p value = 0.0173). Transition between clusters were more frequent in women with persistent HPV16 infection (34%) as compared in women who cleared the HPV16 infection (19%) (p value = 0.036).

CONCLUSIONS: The vaginal microbiota showed a higher rate of transitioning between bacterial profiles in women with persistent HPV16 infection as compared to women with transient infection. This indicate an instability in the microenvironment in women with persistent HPV infection and development of CIN2+.}, } @article {pmid33027674, year = {2020}, author = {Arnoriaga-Rodríguez, M and Mayneris-Perxachs, J and Burokas, A and Contreras-Rodríguez, O and Blasco, G and Coll, C and Biarnés, C and Miranda-Olivos, R and Latorre, J and Moreno-Navarrete, JM and Castells-Nobau, A and Sabater, M and Palomo-Buitrago, ME and Puig, J and Pedraza, S and Gich, J and Pérez-Brocal, V and Ricart, W and Moya, A and Fernández-Real, X and Ramió-Torrentà, L and Pamplona, R and Sol, J and Jové, M and Portero-Otin, M and Maldonado, R and Fernández-Real, JM}, title = {Obesity Impairs Short-Term and Working Memory through Gut Microbial Metabolism of Aromatic Amino Acids.}, journal = {Cell metabolism}, volume = {32}, number = {4}, pages = {548-560.e7}, doi = {10.1016/j.cmet.2020.09.002}, pmid = {33027674}, issn = {1932-7420}, mesh = {Adult ; Aged ; Amino Acids, Aromatic/*metabolism ; Animals ; Case-Control Studies ; Cross-Sectional Studies ; Female ; *Gastrointestinal Microbiome ; Humans ; Magnetic Resonance Imaging ; Male ; *Memory, Short-Term ; Metabolomics ; Mice ; Mice, Inbred C57BL ; Middle Aged ; Obesity/*metabolism ; }, abstract = {The gut microbiome has been linked to fear extinction learning in animal models. Here, we aimed to explore the gut microbiome and memory domains according to obesity status. A specific microbiome profile associated with short-term memory, working memory, and the volume of the hippocampus and frontal regions of the brain differentially in human subjects with and without obesity. Plasma and fecal levels of aromatic amino acids, their catabolites, and vegetable-derived compounds were longitudinally associated with short-term and working memory. Functionally, microbiota transplantation from human subjects with obesity led to decreased memory scores in mice, aligning this trait from humans with that of recipient mice. RNA sequencing of the medial prefrontal cortex of mice revealed that short-term memory associated with aromatic amino acid pathways, inflammatory genes, and clusters of bacterial species. These results highlight the potential therapeutic value of targeting the gut microbiota for memory impairment, specifically in subjects with obesity.}, } @article {pmid33026068, year = {2021}, author = {Fang, X and Vázquez-Baeza, Y and Elijah, E and Vargas, F and Ackermann, G and Humphrey, G and Lau, R and Weldon, KC and Sanders, JG and Panitchpakdi, M and Carpenter, C and Jarmusch, AK and Neill, J and Miralles, A and Dulai, P and Singh, S and Tsai, M and Swafford, AD and Smarr, L and Boyle, DL and Palsson, BO and Chang, JT and Dorrestein, PC and Sandborn, WJ and Knight, R and Boland, BS}, title = {Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity.}, journal = {Inflammatory bowel diseases}, volume = {27}, number = {5}, pages = {603-616}, pmid = {33026068}, issn = {1536-4844}, support = {UL1 TR001442/TR/NCATS NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; T32 DK007202/DK/NIDDK NIH HHS/United States ; K23 DK117058/DK/NIDDK NIH HHS/United States ; K23 DK123406/DK/NIDDK NIH HHS/United States ; }, mesh = {*Crohn Disease/surgery ; *Digestive System Surgical Procedures ; Feces ; *Gastrointestinal Microbiome ; Humans ; Metabolome ; Prospective Studies ; }, abstract = {BACKGROUND: Many studies have investigated the role of the microbiome in inflammatory bowel disease (IBD), but few have focused on surgery specifically or its consequences on the metabolome that may differ by surgery type and require longitudinal sampling. Our objective was to characterize and contrast microbiome and metabolome changes after different surgeries for IBD, including ileocolonic resection and colectomy.

METHODS: The UC San Diego IBD Biobank was used to prospectively collect 332 stool samples from 129 subjects (50 ulcerative colitis; 79 Crohn's disease). Of these, 21 with Crohn's disease had ileocolonic resections, and 17 had colectomies. We used shotgun metagenomics and untargeted liquid chromatography followed by tandem mass spectrometry metabolomics to characterize the microbiomes and metabolomes of these patients up to 24 months after the initial sampling.

RESULTS: The species diversity and metabolite diversity both differed significantly among groups (species diversity: Mann-Whitney U test P value = 7.8e-17; metabolomics, P-value = 0.0043). Escherichia coli in particular expanded dramatically in relative abundance in subjects undergoing surgery. The species profile was better able to classify subjects according to surgery status than the metabolite profile (average precision 0.80 vs 0.68).

CONCLUSIONS: Intestinal surgeries seem to reduce the diversity of the gut microbiome and metabolome in IBD patients, and these changes may persist. Surgery also further destabilizes the microbiome (but not the metabolome) over time, even relative to the previously established instability in the microbiome of IBD patients. These long-term effects and their consequences for health outcomes need to be studied in prospective longitudinal trials linked to microbiome-involved phenotypes.}, } @article {pmid33025061, year = {2021}, author = {Boraks, A and Plunkett, GM and Doro, TM and Alo, F and Sam, C and Tuiwawa, M and Ticktin, T and Amend, AS}, title = {Scale-Dependent Influences of Distance and Vegetation on the Composition of Aboveground and Belowground Tropical Fungal Communities.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {874-883}, pmid = {33025061}, issn = {1432-184X}, support = {1555793//National Science Foundation (US)/ ; 1555657//National Science Foundation/ ; }, mesh = {Biodiversity ; *Ecosystem ; Fungi/genetics ; *Mycobiome ; Soil Microbiology ; Trees ; }, abstract = {Fungi provide essential ecosystem services and engage in a variety of symbiotic relationships with trees. In this study, we investigate the spatial relationship of trees and fungi at a community level. We characterized the spatial dynamics for above- and belowground fungi using a series of forest monitoring plots, at nested spatial scales, located in the tropical South Pacific, in Vanuatu. Fungal communities from different habitats were sampled using metagenomic analysis of the nuclear ribosomal ITS1 region. Fungal communities exhibited strong distance-decay of similarity across our entire sampling range (3-110,000 m) and also at small spatial scales (< 50 m). Unexpectedly, this pattern was inverted at an intermediate scale (3.7-26 km). At large scales (80-110 km), belowground and aboveground fungal communities responded inversely to increasing geographic distance. Aboveground fungal community turnover (beta diversity) was best explained, at all scales, by geographic distance. In contrast, belowground fungal community turnover was best explained by geographic distance at small scales and tree community composition at large scales. Fungal communities from various habitats respond differently to the influences of habitat and geographic distance. At large geographic distances (80-110 km), community turnover for aboveground fungi is better explained by spatial distance, whereas community turnover for belowground fungi is better explained by plant community turnover. Future syntheses of spatial dynamics among fungal communities must explicitly consider geographic scale to appropriately contextualize community turnover.}, } @article {pmid33024120, year = {2020}, author = {Zhang, Y and Gu, Y and Ren, H and Wang, S and Zhong, H and Zhao, X and Ma, J and Gu, X and Xue, Y and Huang, S and Yang, J and Chen, L and Chen, G and Qu, S and Liang, J and Qin, L and Huang, Q and Peng, Y and Li, Q and Wang, X and Kong, P and Hou, G and Gao, M and Shi, Z and Li, X and Qiu, Y and Zou, Y and Yang, H and Wang, J and Xu, G and Lai, S and Li, J and Ning, G and Wang, W}, title = {Gut microbiome-related effects of berberine and probiotics on type 2 diabetes (the PREMOTE study).}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5015}, pmid = {33024120}, issn = {2041-1723}, mesh = {Berberine/*pharmacology/therapeutic use ; Diabetes Mellitus, Type 2/*drug therapy/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/physiology ; Glycated Hemoglobin/metabolism ; Humans ; Hypoglycemic Agents/pharmacology/therapeutic use ; Male ; Metagenome/drug effects/genetics ; Middle Aged ; Placebos ; Probiotics/*therapeutic use ; Treatment Outcome ; }, abstract = {Human gut microbiome is a promising target for managing type 2 diabetes (T2D). Measures altering gut microbiota like oral intake of probiotics or berberine (BBR), a bacteriostatic agent, merit metabolic homoeostasis. We hence conducted a randomized, double-blind, placebo-controlled trial with newly diagnosed T2D patients from 20 centres in China. Four-hundred-nine eligible participants were enroled, randomly assigned (1:1:1:1) and completed a 12-week treatment of either BBR-alone, probiotics+BBR, probiotics-alone, or placebo, after a one-week run-in of gentamycin pretreatment. The changes in glycated haemoglobin, as the primary outcome, in the probiotics+BBR (least-squares mean [95% CI], -1.04[-1.19, -0.89]%) and BBR-alone group (-0.99[-1.16, -0.83]%) were significantly greater than that in the placebo and probiotics-alone groups (-0.59[-0.75, -0.44]%, -0.53[-0.68, -0.37]%, P < 0.001). BBR treatment induced more gastrointestinal side effects. Further metagenomics and metabolomic studies found that the hypoglycaemic effect of BBR is mediated by the inhibition of DCA biotransformation by Ruminococcus bromii. Therefore, our study reports a human microbial related mechanism underlying the antidiabetic effect of BBR on T2D. (Clinicaltrial.gov Identifier: NCT02861261).}, } @article {pmid33024037, year = {2020}, author = {Vuillemin, A and Vargas, S and Coskun, ÖK and Pockalny, R and Murray, RW and Smith, DC and D'Hondt, S and Orsi, WD}, title = {Atribacteria Reproducing over Millions of Years in the Atlantic Abyssal Subseafloor.}, journal = {mBio}, volume = {11}, number = {5}, pages = {}, pmid = {33024037}, issn = {2150-7511}, mesh = {Atlantic Ocean ; Bacteria/*classification/metabolism ; Ecosystem ; Geologic Sediments/*microbiology ; *Metagenome ; Microbial Viability ; *Microbiota ; Phylogeny ; Time Factors ; }, abstract = {How microbial metabolism is translated into cellular reproduction under energy-limited settings below the seafloor over long timescales is poorly understood. Here, we show that microbial abundance increases an order of magnitude over a 5 million-year-long sequence in anoxic subseafloor clay of the abyssal North Atlantic Ocean. This increase in biomass correlated with an increased number of transcribed protein-encoding genes that included those involved in cytokinesis, demonstrating that active microbial reproduction outpaces cell death in these ancient sediments. Metagenomes, metatranscriptomes, and 16S rRNA gene sequencing all show that the actively reproducing community was dominated by the candidate phylum "Candidatus Atribacteria," which exhibited patterns of gene expression consistent with fermentative, and potentially acetogenic, metabolism. "Ca. Atribacteria" dominated throughout the 8 million-year-old cored sequence, despite the detection limit for gene expression being reached in 5 million-year-old sediments. The subseafloor reproducing "Ca. Atribacteria" also expressed genes encoding a bacterial microcompartment that has potential to assist in secondary fermentation by recycling aldehydes and, thereby, harness additional power to reduce ferredoxin and NAD[+] Expression of genes encoding the Rnf complex for generation of chemiosmotic ATP synthesis were also detected from the subseafloor "Ca Atribacteria," as well as the Wood-Ljungdahl pathway that could potentially have an anabolic or catabolic function. The correlation of this metabolism with cytokinesis gene expression and a net increase in biomass over the million-year-old sampled interval indicates that the "Ca Atribacteria" can perform the necessary catabolic and anabolic functions necessary for cellular reproduction, even under energy limitation in millions-of-years-old anoxic sediments.IMPORTANCE The deep subseafloor sedimentary biosphere is one of the largest ecosystems on Earth, where microbes subsist under energy-limited conditions over long timescales. It remains poorly understood how mechanisms of microbial metabolism promote increased fitness in these settings. We discovered that the candidate bacterial phylum "Candidatus Atribacteria" dominated a deep-sea subseafloor ecosystem, where it exhibited increased transcription of genes associated with acetogenic fermentation and reproduction in million-year-old sediment. We attribute its improved fitness after burial in the seabed to its capabilities to derive energy from increasingly oxidized metabolites via a bacterial microcompartment and utilize a potentially reversible Wood-Ljungdahl pathway to help meet anabolic and catabolic requirements for growth. Our findings show that "Ca Atribacteria" can perform all the necessary catabolic and anabolic functions necessary for cellular reproduction, even under energy limitation in anoxic sediments that are millions of years old.}, } @article {pmid33022252, year = {2020}, author = {Lemon, KP}, title = {Human nasal microbiota.}, journal = {Current biology : CB}, volume = {30}, number = {19}, pages = {R1118-R1119}, doi = {10.1016/j.cub.2020.08.010}, pmid = {33022252}, issn = {1879-0445}, support = {R01 GM117174/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/*isolation & purification ; Bacterial Infections/*microbiology ; Humans ; *Microbiota ; Nasal Cavity/*microbiology ; }, abstract = {The human nasal passages host a distinct community of microbes. Katherine P. Lemon describes this distinct community, and why it matters so much for human health.}, } @article {pmid33021988, year = {2020}, author = {Behera, BK and Patra, B and Chakraborty, HJ and Sahu, P and Rout, AK and Sarkar, DJ and Parida, PK and Raman, RK and Rao, AR and Rai, A and Das, BK and Jena, J and Mohapatra, T}, title = {Metagenome analysis from the sediment of river Ganga and Yamuna: In search of beneficial microbiome.}, journal = {PloS one}, volume = {15}, number = {10}, pages = {e0239594}, pmid = {33021988}, issn = {1932-6203}, mesh = {Bacteria/classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; Geologic Sediments/*microbiology ; India ; *Metagenome ; Microbiota ; Phylogeny ; Rivers/*microbiology ; Water Microbiology ; }, abstract = {Beneficial microbes are all around us and it remains to be seen, whether all diseases and disorders can be prevented or treated with beneficial microbes. In this study, the presence of various beneficial bacteria were identified from the sediments of Indian major Rivers Ganga and Yamuna from nine different sites using a metagenomic approach. The metagenome sequence analysis using the Kaiju Web server revealed the presence of 69 beneficial bacteria. Phylogenetic analysis among these bacterial species revealed that they were highly diverse. Relative abundance analysis of these bacterial species is highly correlated with different pollution levels among the sampling sites. The PCA analysis revealed that Lactobacillus spp. group of beneficial bacteria are more associated with sediment sampling sites, KAN-2 and ND-3; whereas Bacillus spp. are more associated with sites, FAR-2 and ND-2. This is the first report revealing the richness of beneficial bacteria in the Indian rivers, Ganga and Yamuna. The study might be useful in isolating different important beneficial microorganisms from these river sediments, for possible industrial applications.}, } @article {pmid33020656, year = {2020}, author = {Kolmogorov, M and Bickhart, DM and Behsaz, B and Gurevich, A and Rayko, M and Shin, SB and Kuhn, K and Yuan, J and Polevikov, E and Smith, TPL and Pevzner, PA}, title = {metaFlye: scalable long-read metagenome assembly using repeat graphs.}, journal = {Nature methods}, volume = {17}, number = {11}, pages = {1103-1110}, pmid = {33020656}, issn = {1548-7105}, support = {P41 GM103484/GM/NIGMS NIH HHS/United States ; R25 HG011022/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Benchmarking ; Gastrointestinal Microbiome/genetics ; Genome, Bacterial/*genetics ; Genome, Human/*genetics ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; Sheep ; Software ; Species Specificity ; }, abstract = {Long-read sequencing technologies have substantially improved the assemblies of many isolate bacterial genomes as compared to fragmented short-read assemblies. However, assembling complex metagenomic datasets remains difficult even for state-of-the-art long-read assemblers. Here we present metaFlye, which addresses important long-read metagenomic assembly challenges, such as uneven bacterial composition and intra-species heterogeneity. First, we benchmarked metaFlye using simulated and mock bacterial communities and show that it consistently produces assemblies with better completeness and contiguity than state-of-the-art long-read assemblers. Second, we performed long-read sequencing of the sheep microbiome and applied metaFlye to reconstruct 63 complete or nearly complete bacterial genomes within single contigs. Finally, we show that long-read assembly of human microbiomes enables the discovery of full-length biosynthetic gene clusters that encode biomedically important natural products.}, } @article {pmid33020496, year = {2020}, author = {Natarajan, A and Bhatt, AS}, title = {Microbes and microbiomes in 2020 and beyond.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4988}, pmid = {33020496}, issn = {2041-1723}, support = {R01 AI143757/AI/NIAID NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; }, mesh = {Environmental Microbiology ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {In the next decade, advances in our understanding of microbes and microbiomes will likely transform our way of life; providing novel therapeutics, alternate energy sources, and shaping fundamental doctrines of biology. We explore the promises herein, and tools required to achieve this progress. Notably, it is critical that we improve the inclusivity and diversity of our research agendas and teams, so that science benefits people of all identities and backgrounds.}, } @article {pmid33020474, year = {2020}, author = {Lee, G and You, HJ and Bajaj, JS and Joo, SK and Yu, J and Park, S and Kang, H and Park, JH and Kim, JH and Lee, DH and Lee, S and Kim, W and Ko, G}, title = {Distinct signatures of gut microbiome and metabolites associated with significant fibrosis in non-obese NAFLD.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4982}, pmid = {33020474}, issn = {2041-1723}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Bile Acids and Salts/analysis/metabolism ; Biomarkers ; Feces/chemistry/microbiology ; Fibrosis ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Liver Cirrhosis/diagnosis/metabolism/microbiology/pathology ; Mice ; Non-alcoholic Fatty Liver Disease/metabolism/*microbiology/*pathology ; Obesity/metabolism/microbiology/pathology ; Propionates/analysis/metabolism ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; }, abstract = {Nonalcoholic fatty liver disease (NAFLD) is associated with obesity but also found in non-obese individuals. Gut microbiome profiles of 171 Asians with biopsy-proven NAFLD and 31 non-NAFLD controls are analyzed using 16S rRNA sequencing; an independent Western cohort is used for external validation. Subjects are classified into three subgroups according to histological spectra of NAFLD or fibrosis severity. Significant alterations in microbiome diversity are observed according to fibrosis severity in non-obese, but not obese, subjects. Ruminococcaceae and Veillonellaceae are the main microbiota associated with fibrosis severity in non-obese subjects. Furthermore, stool bile acids and propionate are elevated, especially in non-obese subjects with significant fibrosis. Fibrosis-related Ruminococcaceae and Veillonellaceae species undergo metagenome sequencing, and four representative species are administered in three mouse NAFLD models to evaluate their effects on liver damage. This study provides the evidence for the role of the microbiome in the liver fibrosis pathogenesis, especially in non-obese subjects.}, } @article {pmid33012229, year = {2020}, author = {Sabin, S and Yeh, HY and Pluskowski, A and Clamer, C and Mitchell, PD and Bos, KI}, title = {Estimating molecular preservation of the intestinal microbiome via metagenomic analyses of latrine sediments from two medieval cities.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1812}, pages = {20190576}, pmid = {33012229}, issn = {1471-2970}, mesh = {Cities ; Feces/*microbiology ; *Gastrointestinal Microbiome ; History, Medieval ; Israel ; Latvia ; *Metagenome ; Metagenomics ; Toilet Facilities/*history ; }, abstract = {Ancient latrine sediments, which contain the concentrated collective biological waste of past whole human communities, have the potential to be excellent proxies for human gastrointestinal health on the population level. A rich body of literature explores their use to detect the presence of gut-associated eukaryotic parasites through microscopy, immunoassays and genetics. Despite this interest, a lack of studies have explored the whole genetic content of ancient latrine sediments through consideration not only of gut-associated parasites, but also of core community gut microbiome signals that remain from the group that used the latrine. Here, we present a metagenomic analysis of bulk sediment from medieval latrines in Riga (Latvia) and Jerusalem. Our analyses reveal survival of microbial DNA representative of intestinal flora as well as numerous parasites. These data are compared against parasite taxon identifications obtained via microscopy and ELISA techniques. Together, these findings provide a first glimpse into the rich prokaryotic and eukaryotic intestinal flora of pre-industrial agricultural populations, which may give a better context for interpreting the health of modern microbiomes. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.}, } @article {pmid33012228, year = {2020}, author = {Achtman, M and Zhou, Z}, title = {Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on Streptococcus mutans and Streptococcus sobrinus.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1812}, pages = {20190573}, pmid = {33012228}, issn = {1471-2970}, support = {/WT_/Wellcome Trust/United Kingdom ; 202792/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; BB/L020319/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Dental Caries/*history/*microbiology ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, Ancient ; History, Medieval ; Humans ; *Metagenome ; *Microbiota ; Mouth/*microbiology ; Phylogeny ; Saliva/microbiology ; Streptococcus mutans/classification/*genetics ; Streptococcus sobrinus/classification/*genetics ; }, abstract = {We have recently developed bioinformatic tools to accurately assign metagenomic sequence reads to microbial taxa: SPARSE for probabilistic, taxonomic classification of sequence reads; EToKi for assembling and polishing genomes from short-read sequences; and GrapeTree, a graphic visualizer of genetic distances between large numbers of genomes. Together, these methods support comparative analyses of genomes from ancient skeletons and modern humans. Here, we illustrate these capabilities with 784 samples from historical dental calculus, modern saliva and modern dental plaque. The analyses revealed 1591 microbial species within the oral microbiome. We anticipated that the oral complexes of Socransky et al., which were defined in 1998, would predominate among taxa whose frequencies differed by source. However, although some species discriminated between sources, we could not confirm the existence of the complexes. The results also illustrate further functionality of our pipelines with two species that are associated with dental caries, Streptococcus mutans and Streptococcus sobrinus. They were rare in historical dental calculus but common in modern plaque, and even more common in saliva. Reconstructed draft genomes of these two species from metagenomic samples in which they were abundant were combined with modern public genomes to provide a detailed overview of their core genomic diversity. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.}, } @article {pmid33011259, year = {2020}, author = {Lima, RAT and De Oliveira, G and Souza, AA and Lopes, FAC and Santana, RH and Istvan, P and Quirino, BF and Barbosa, J and De Freitas, S and Garay, AV and Krüger, RH}, title = {Functional and structural characterization of a novel GH3 β-glucosidase from the gut metagenome of the Brazilian Cerrado termite Syntermes wheeleri.}, journal = {International journal of biological macromolecules}, volume = {165}, number = {Pt A}, pages = {822-834}, doi = {10.1016/j.ijbiomac.2020.09.236}, pmid = {33011259}, issn = {1879-0003}, mesh = {Animals ; Enzyme Stability ; *Gastrointestinal Microbiome ; Isoptera/*microbiology ; *Metagenome ; Substrate Specificity ; *beta-Glucosidase/chemistry/genetics ; }, abstract = {In this study, a GH3 family β-glucosidase (Bgl7226) from metagenomic sequences of the Syntermes wheeleri gut, a Brazilian Cerrado termite, was expressed, purified and characterized. The enzyme showed two optimum pHs (pH 7 and pH 10), and a maximum optimum temperature of about 40 °C using 4-Nitrophenyl β-D-glucopyranoside (pNPG) as substrate. Bgl7226 showed higher enzymatic activity at basic pH, but higher affinity (Km) at neutral pH. However, at neutral pH the Bgl7226 enzyme showed higher catalytic efficiency (kcat/Km) for pNPG substrate. Predictive analysis about the enzyme structure-function relationship by sequence alignment suggested the presence of multi-domains and conserved catalytic sites. Circular dichroism results showed that the secondary structure composition of the enzyme is pH-dependent. Small conformational changes occurred close to the optimum temperature of 40 [o] C, and seem important for the highest activity of Bgl7226 observed at pH 7 and 10. In addition, the small transition in the unfolding curves close to 40 [o] C is typical of intermediates associated with proteins structured in several domains. Bgl7226 has significant β-glucosidase activity which could be attractive for biotechnological applications, such as plant roots detoxification; specifically, our group is interested in cassava roots (Manihot esculenta) detoxification.}, } @article {pmid33010388, year = {2021}, author = {Qi, Y and Zang, SQ and Wei, J and Yu, HC and Yang, Z and Wu, HM and Kang, Y and Tao, H and Yang, MF and Jin, L and Zen, K and Wang, FY}, title = {High-throughput sequencing provides insights into oral microbiota dysbiosis in association with inflammatory bowel disease.}, journal = {Genomics}, volume = {113}, number = {1 Pt 2}, pages = {664-676}, doi = {10.1016/j.ygeno.2020.09.063}, pmid = {33010388}, issn = {1089-8646}, mesh = {Adult ; Dysbiosis/complications/epidemiology/*microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/complications/*microbiology ; Leptotrichia/genetics/pathogenicity ; Male ; *Metagenome ; Mouth/*microbiology ; Prevotella/genetics/pathogenicity ; }, abstract = {Although the prevalence of inflammatory bowel disease (IBD) has been increasing worldwide, the etiology remains elusive. Investigating oral microbiota dysbiosis is essential to understanding IBD pathogenesis. Our study evaluated variations in salivary microbiota and identified potential associations with IBD. The saliva microbiota of 22 IBD patients and 8 healthy controls (HCs) was determined using 16S ribosomal RNA (rRNA) gene sequencing and analyzed using QIIME2. A distinct saliva microbiota dysbiosis in IBD, characterized by alterations in microbiota biodiversity and composition, was identified. Saccharibacteria (TM7), Absconditabacteria (SR1), Leptotrichia, Prevotella, Bulleidia, and Atopobium, some of which are oral biofilm-forming bacteria, were significantly increased. Moreover, levels of inflammatory cytokines associated with IBD were elevated and positively correlated with TM7 and SR1. Functional variations include down-regulation of genetic information processing, while up-regulation of carbohydrate metabolism and protein processing in the endoplasmic reticulum in IBD. Our data implicate salivary microbiota dysbiosis involving in IBD pathogenesis.}, } @article {pmid33008816, year = {2020}, author = {Hammer, TJ and Dickerson, JC and McMillan, WO and Fierer, N}, title = {Heliconius Butterflies Host Characteristic and Phylogenetically Structured Adult-Stage Microbiomes.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {24}, pages = {}, pmid = {33008816}, issn = {1098-5336}, mesh = {Animals ; Bacteria/*isolation & purification ; *Bacterial Physiological Phenomena ; Butterflies/*microbiology ; Host Microbial Interactions ; *Microbiota ; Phylogeny ; Sequence Analysis, RNA/*methods ; Species Specificity ; }, abstract = {Lepidoptera (butterflies and moths) are diverse and ecologically important, yet we know little about how they interact with microbes as adults. Due to metamorphosis, the form and function of their adult-stage microbiomes might be very different from those of microbiomes in the larval stage (caterpillars). We studied adult-stage microbiomes of Heliconius and closely related passion-vine butterflies (Heliconiini), which are an important model system in evolutionary biology. To characterize the structure and dynamics of heliconiine microbiomes, we used field collections of wild butterflies, 16S rRNA gene sequencing, quantitative PCR, and shotgun metagenomics. We found that Heliconius butterflies harbor simple and abundant bacterial communities that are moderately consistent among conspecific individuals and over time. Heliconiine microbiomes also exhibited a strong signal of the host phylogeny, with a major distinction between Heliconius and other butterflies. These patterns were largely driven by differing relative abundances of bacterial phylotypes shared among host species and genera, as opposed to the presence or absence of host-specific phylotypes. We suggest that the phylogenetic structure in heliconiine microbiomes arises from conserved host traits that differentially filter microbes from the environment. While the relative importance of different traits remains unclear, our data indicate that pollen feeding (unique to Heliconius) is not a primary driver. Using shotgun metagenomics, we also discovered trypanosomatids and microsporidia to be prevalent in butterfly guts, raising the possibility of antagonistic interactions between eukaryotic parasites and colocalized gut bacteria. Our discovery of characteristic and phylogenetically structured microbiomes provides a foundation for tests of adult-stage microbiome function, a poorly understood aspect of lepidopteran biology.IMPORTANCE Many insects host microbiomes with important ecological functions. However, the prevalence of this phenomenon is unclear because in many insect taxa, microbiomes have been studied in only part of the life cycle, if at all. A prominent example is butterflies and moths, in which the composition and functional role of adult-stage microbiomes are largely unknown. We comprehensively characterized microbiomes in adult passion-vine butterflies. Butterfly-associated bacterial communities are generally abundant in guts, consistent within populations, and composed of taxa widely shared among hosts. More closely related butterflies harbor more similar microbiomes, with the most dramatic shift in microbiome composition occurring in tandem with a suite of ecological and life history traits unique to the genus Heliconius Butterflies are also frequently infected with previously undescribed eukaryotic parasites, which may interact with bacteria in important ways. These findings advance our understanding of butterfly biology and insect-microbe interactions generally.}, } @article {pmid33007604, year = {2020}, author = {Los, A and Ziuzina, D and Boehm, D and Bourke, P}, title = {Effects of cold plasma on wheat grain microbiome and antimicrobial efficacy against challenge pathogens and their resistance.}, journal = {International journal of food microbiology}, volume = {335}, number = {}, pages = {108889}, doi = {10.1016/j.ijfoodmicro.2020.108889}, pmid = {33007604}, issn = {1879-3460}, mesh = {Anti-Infective Agents/*pharmacology ; Bacteria/classification/drug effects/genetics/isolation & purification ; *Drug Resistance, Microbial ; Edible Grain/microbiology ; Fungi/classification/drug effects/genetics/isolation & purification ; Microbiota/*drug effects ; Plasma Gases/*pharmacology ; RNA, Ribosomal/genetics ; Species Specificity ; Triticum/*microbiology ; }, abstract = {The safety and quality of cereal grain supplies are adversely impacted by microbiological contamination, with novel interventions required to maximise whole grains safety and stability. The microbiological contaminants of wheat grains and the efficacy of Atmospheric Cold Plasma (ACP) for potential to control these risks were investigated. The evaluations were performed using a contained reactor dielectric barrier discharge (DBD) system; samples were treated for 0-20 min using direct and indirect plasma exposure. Amplicon-based metagenomic analysis using bacterial 16S rRNA gene and fungal 18S rRNA gene with internal transcribed spacer (ITS) region was performed to characterize the change in microbial community composition in response to ACP treatment. The antimicrobial efficacy of ACP against a range of bacterial and fungal contaminants of wheat, was assessed to include individual isolates from grains as challenge pathogens. ACP influenced wheat microbiome composition, with a higher microbial diversity as well as abundance found on the untreated control grain samples. Culture and genomic approaches revealed different trends for mycoflora detection and control. A challenge study demonstrated that using direct mode of plasma exposure with 20 min of treatment significantly reduced the concentration of all pathogens. Overall, reduction levels for B. atrophaeus vegetative cells were higher than for all fungal species tested, whereas B. atrophaeus spores were the most resistant to ACP among all microorganisms tested. Of note, repeating sub-lethal plasma treatment did not induce resistance to ACP in either B. atrophaeus or A. flavus spores. ACP process control could be tailored to address diverse microbiological risks for grain stability and safety.}, } @article {pmid33004077, year = {2020}, author = {Tauzin, AS and Pereira, MR and Van Vliet, LD and Colin, PY and Laville, E and Esque, J and Laguerre, S and Henrissat, B and Terrapon, N and Lombard, V and Leclerc, M and Doré, J and Hollfelder, F and Potocki-Veronese, G}, title = {Investigating host-microbiome interactions by droplet based microfluidics.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {141}, pmid = {33004077}, issn = {2049-2618}, mesh = {Bacteria/genetics ; *Host Microbial Interactions ; Humans ; Male ; Metagenomics ; Microbiota/genetics/*physiology ; *Microfluidics ; Middle Aged ; }, abstract = {BACKGROUND: Despite the importance of the mucosal interface between microbiota and the host in gut homeostasis, little is known about the mechanisms of bacterial gut colonization, involving foraging for glycans produced by epithelial cells. The slow pace of progress toward understanding the underlying molecular mechanisms is largely due to the lack of efficient discovery tools, especially those targeting the uncultured fraction of the microbiota.

RESULTS: Here, we introduce an ultra-high-throughput metagenomic approach based on droplet microfluidics, to screen fosmid libraries. Thousands of bacterial genomes can be covered in 1 h of work, with less than ten micrograms of substrate. Applied to the screening of the mucosal microbiota for β-N-acetylgalactosaminidase activity, this approach allowed the identification of pathways involved in the degradation of human gangliosides and milk oligosaccharides, the structural homologs of intestinal mucin glycans. These pathways, whose prevalence is associated with inflammatory bowel diseases, could be the result of horizontal gene transfers with Bacteroides species. Such pathways represent novel targets to study the microbiota-host interactions in the context of inflammatory bowel diseases, in which the integrity of the mucosal barrier is impaired.

CONCLUSION: By compartmentalizing experiments inside microfluidic droplets, this method speeds up and miniaturizes by several orders of magnitude the screening process compared to conventional approaches, to capture entire metabolic pathways from metagenomic libraries. The method is compatible with all types of (meta)genomic libraries, and employs a commercially available flow cytometer instead of a custom-made sorting system to detect intracellular or extracellular enzyme activities. This versatile and generic workflow will accelerate experimental exploration campaigns in functional metagenomics and holobiomics studies, to further decipher host-microbiota relationships. Video Abstract.}, } @article {pmid33003412, year = {2020}, author = {Reilly, AM and Tsai, AP and Lin, PB and Ericsson, AC and Oblak, AL and Ren, H}, title = {Metabolic Defects Caused by High-Fat Diet Modify Disease Risk through Inflammatory and Amyloidogenic Pathways in a Mouse Model of Alzheimer's Disease.}, journal = {Nutrients}, volume = {12}, number = {10}, pages = {}, pmid = {33003412}, issn = {2072-6643}, support = {UL1TR002529/TR/NCATS NIH HHS/United States ; R01DK120772/DK/NIDDK NIH HHS/United States ; P30DK097512/DK/NIDDK NIH HHS/United States ; T32 DK064466/DK/NIDDK NIH HHS/United States ; K01 OD019924/OD/NIH HHS/United States ; T32DK064466/DK/NIDDK NIH HHS/United States ; R00 DK098294/DK/NIDDK NIH HHS/United States ; R00DK098294/DK/NIDDK NIH HHS/United States ; P30 DK097512/DK/NIDDK NIH HHS/United States ; R01 DK120772/DK/NIDDK NIH HHS/United States ; }, mesh = {Alzheimer Disease/etiology/*metabolism ; Amyloidogenic Proteins/*metabolism ; Animals ; Apoptosis Regulatory Proteins/metabolism ; Cytokines/metabolism ; Diet, High-Fat/*adverse effects ; Disease Models, Animal ; Eating/physiology ; Energy Metabolism/physiology ; Gastrointestinal Microbiome/genetics ; Gene Expression ; Genotype ; Glucose Intolerance/blood/etiology ; Hippocampus/metabolism ; Inflammation ; Insulin/metabolism ; Lipids/blood ; Locomotion/physiology ; Male ; Mice ; Microglia/metabolism ; Neurogenic Inflammation/etiology/*metabolism ; RNA, Messenger/metabolism ; Risk Factors ; Signal Transduction/*physiology ; Synaptic Transmission/genetics ; }, abstract = {High-fat diet (HFD) has been shown to accelerate Alzheimer's disease (AD) pathology, but the exact molecular and cellular mechanisms remain incompletely understood. Moreover, it is unknown whether AD mice are more susceptible to HFD-induced metabolic dysfunctions. To address these questions, we used 5xFAD mice as an Alzheimer's disease model to study the physiological and molecular underpinning between HFD-induced metabolic defects and AD pathology. We systematically profiled the metabolic parameters, the gut microbiome composition, and hippocampal gene expression in 5xFAD and wild type (WT) mice fed normal chow diet and HFD. HFD feeding impaired energy metabolism in male 5xFAD mice, leading to increased locomotor activity, energy expenditure, and food intake. 5xFAD mice on HFD had elevated circulating lipids and worsened glucose intolerance. HFD caused profound changes in gut microbiome compositions, though no difference between genotype was detected. We measured hippocampal mRNAs related to AD neuropathology and neuroinflammation and showed that HFD elevated the expression of apoptotic, microglial, and amyloidogenic genes in 5xFAD mice. Pathway analysis revealed that differentially regulated genes were involved in insulin signaling, cytokine signaling, cellular stress, and neurotransmission. Collectively, our results showed that 5xFAD mice were more susceptible to HFD-induced metabolic dysregulation and suggest that targeting metabolic dysfunctions can ameliorate AD symptoms via effects on insulin signaling and neuroinflammation in the hippocampus.}, } @article {pmid33001506, year = {2020}, author = {Beier, S and Andersson, AF and Galand, PE and Hochart, C and Logue, JB and McMahon, K and Bertilsson, S}, title = {The environment drives microbial trait variability in aquatic habitats.}, journal = {Molecular ecology}, volume = {29}, number = {23}, pages = {4605-4617}, doi = {10.1111/mec.15656}, pmid = {33001506}, issn = {1365-294X}, mesh = {*Bacteriophages/genetics ; Lakes ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {A prerequisite to improve the predictability of microbial community dynamics is to understand the mechanisms of microbial assembly. To study factors that contribute to microbial community assembly, we examined the temporal dynamics of genes in five aquatic metagenome time-series, originating from marine offshore or coastal sites and one lake. With this trait-based approach we expected to find gene-specific patterns of temporal allele variability that depended on the seasonal metacommunity size of carrier-taxa and the variability of the milieu and the substrates to which the resulting proteins were exposed. In more detail, we hypothesized that a larger seasonal metacommunity size would result in increased temporal variability of functional units (i.e., gene alleles), as shown previously for taxonomic units. We further hypothesized that multicopy genes would feature higher temporal variability than single-copy genes, as gene multiplication can result from high variability in substrate quality and quantity. Finally, we hypothesized that direct exposure of proteins to the extracellular environment would result in increased temporal variability of the respective gene compared to intracellular proteins that are less exposed to environmental fluctuations. The first two hypotheses were confirmed in all data sets, while significant effects of the subcellular location of gene products was only seen in three of the five time-series. The gene with the highest allele variability throughout all data sets was an iron transporter, also representing a target for phage infection. Previous work has emphasized the role of phage-prokaryote interactions as a major driver of microbial diversity. Our finding therefore points to a potentially important role of iron transporter-mediated phage infections for the assembly and maintenance of diversity in aquatic prokaryotes.}, } @article {pmid33001224, year = {2021}, author = {Yavitt, JB and Roco, CA and Debenport, SJ and Barnett, SE and Shapleigh, JP}, title = {Community Organization and Metagenomics of Bacterial Assemblages Across Local Scale pH Gradients in Northern Forest Soils.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {758-769}, pmid = {33001224}, issn = {1432-184X}, support = {1007286//Agricultural Research Service/ ; }, mesh = {Bacteria/genetics ; Biodiversity ; Ecosystem ; Forests ; *Metagenomics ; Proton-Motive Force ; *Soil ; Soil Microbiology ; }, abstract = {Soil pH has shown to predict bacterial diversity, but mechanisms are still poorly understood. To investigate how bacteria distribute themselves as a function of soil pH, we assessed community composition, diversity, assembly, and gene abundance across local (ca. 1 km) scale gradients in soil pH from ~ 3.8 to 6.5 created by differences in soil parent material in three northern forests. Plant species were the same on all sites, with no evidence of agriculture in the past. Concentrations of extractable calcium, iron, and phosphorus also varied significantly across the pH gradients. Among taxa, Alphaproteobacteria and Acidobacteria were more common in soils with acidic pH values. Overall richness and diversity of OTUs peaked at intermediate pH values. Variations in OTU richness and diversity also had a quadratic fit with concentrations of extractable calcium and phosphorus. Community assembly was via homogeneous deterministic processes in soils with acidic pH values, whereas stochastic processes dominated in soils with near-neutral pH values. Although we expected selection via genes for acid tolerance response in acidic soils, genes for genetic information processing were more selective. Taxa in higher pH soils had differential abundance of transporter genes, suggesting adaptation to acquire metabolic substrates from soils. Soil bacterial communities in northern forest soils are incredibly diverse, and we still have much to learn about how soil pH and co-varying soil parameters directly drive gene selection in this critical component of ecosystem structure.}, } @article {pmid33001022, year = {2020}, author = {Maguire, F and Jia, B and Gray, KL and Lau, WYV and Beiko, RG and Brinkman, FSL}, title = {Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands.}, journal = {Microbial genomics}, volume = {6}, number = {10}, pages = {}, pmid = {33001022}, issn = {2057-5858}, support = {//CIHR/Canada ; }, mesh = {Algorithms ; Bacteria/*genetics ; Computer Simulation ; Genome, Bacterial/genetics ; Genomic Islands/*genetics ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/genetics ; Plasmids/*genetics ; Sequence Analysis, DNA ; }, abstract = {Metagenomic methods enable the simultaneous characterization of microbial communities without time-consuming and bias-inducing culturing. Metagenome-assembled genome (MAG) binning methods aim to reassemble individual genomes from this data. However, the recovery of mobile genetic elements (MGEs), such as plasmids and genomic islands (GIs), by binning has not been well characterized. Given the association of antimicrobial resistance (AMR) genes and virulence factor (VF) genes with MGEs, studying their transmission is a public-health priority. The variable copy number and sequence composition of MGEs makes them potentially problematic for MAG binning methods. To systematically investigate this issue, we simulated a low-complexity metagenome comprising 30 GI-rich and plasmid-containing bacterial genomes. MAGs were then recovered using 12 current prediction pipelines and evaluated. While 82-94 % of chromosomes could be correctly recovered and binned, only 38-44 % of GIs and 1-29 % of plasmid sequences were found. Strikingly, no plasmid-borne VF nor AMR genes were recovered, and only 0-45 % of AMR or VF genes within GIs. We conclude that short-read MAG approaches, without further optimization, are largely ineffective for the analysis of mobile genes, including those of public-health importance, such as AMR and VF genes. We propose that researchers should explore developing methods that optimize for this issue and consider also using unassembled short reads and/or long-read approaches to more fully characterize metagenomic data.}, } @article {pmid32998876, year = {2021}, author = {Bajaj, JS and Sikaroodi, M and Shamsaddini, A and Henseler, Z and Santiago-Rodriguez, T and Acharya, C and Fagan, A and Hylemon, PB and Fuchs, M and Gavis, E and Ward, T and Knights, D and Gillevet, PM}, title = {Interaction of bacterial metagenome and virome in patients with cirrhosis and hepatic encephalopathy.}, journal = {Gut}, volume = {70}, number = {6}, pages = {1162-1173}, doi = {10.1136/gutjnl-2020-322470}, pmid = {32998876}, issn = {1468-3288}, support = {R21 TR003095/TR/NCATS NIH HHS/United States ; R21 TR002024/TR/NCATS NIH HHS/United States ; R01 HS025412/HS/AHRQ HHS/United States ; }, mesh = {Aged ; Anti-Bacterial Agents/pharmacology/*therapeutic use ; Cross-Sectional Studies ; Disease Progression ; End Stage Liver Disease/etiology/*microbiology ; Faecalibacterium/genetics/virology ; Feces/microbiology ; Female ; Firmicutes/genetics/*virology ; Gastrointestinal Agents/therapeutic use ; Hepatic Encephalopathy/*microbiology ; Hospitalization ; Humans ; Lactococcus/genetics/virology ; Lactulose/therapeutic use ; Liver Cirrhosis/complications/drug therapy/*microbiology ; Male ; Metagenome/drug effects ; Metagenomics ; Microbial Interactions ; Microviridae/genetics ; Middle Aged ; Myoviridae/genetics ; Patient Acuity ; Rifaximin/pharmacology/*therapeutic use ; Streptococcus/genetics/virology ; Virome/drug effects ; }, abstract = {OBJECTIVE: Altered bacterial composition is associated with disease progression in cirrhosis but the role of virome, especially phages, is unclear.

DESIGN: Cross-sectional and pre/post rifaximin cohorts were enrolled. Cross-sectional: controls and cirrhotic outpatients (compensated, on lactulose (Cirr-L), on rifaximin (Cirr-LR)) were included and followed for 90-day hospitalisations. Pre/post: compensated cirrhotics underwent stool collection pre/post 8 weeks of rifaximin. Stool metagenomics for bacteria and phages and their correlation networks were analysed in controls versus cirrhosis, within cirrhotics, hospitalised/not and pre/post rifaximin.

RESULTS: Cross-sectional: 40 controls and 163 cirrhotics (63 compensated, 43 Cirr-L, 57 Cirr-LR) were enrolled. Cirr-L/LR groups were similar on model for end-stage liver disease (MELD) score but Cirr-L developed greater hospitalisations versus Cirr-LR (56% vs 30%, p=0.008). Bacterial alpha/beta diversity worsened from controls through Cirr-LR. While phage alpha diversity was similar, beta diversity was different between groups. Autochthonous bacteria linked negatively, pathobionts linked positively with MELD but only modest phage-MELD correlations were seen. Phage-bacterial correlation network complexity was highest in controls, lowest in Cirr-L and increased in Cirr-LR. Microviridae and Faecalibacterium phages were linked with autochthonous bacteria in Cirr-LR, but not Cirr-L hospitalised patients had greater pathobionts, lower commensal bacteria and phages focused on Streptococcus, Lactococcus and Myoviridae. Pre/post: No changes in alpha/beta diversity of phages or bacteria were seen postrifaximin. Phage-bacterial linkages centred around urease-producing Streptococcus species collapsed postrifaximin.

CONCLUSION: Unlike bacteria, faecal phages are sparsely linked with cirrhosis characteristics and 90-day outcomes. Phage and bacterial linkages centred on urease-producing, ammonia-generating Streptococcus species were affected by disease progression and rifaximin therapy and were altered in patients who experienced 90-day hospitalisations.}, } @article {pmid32998695, year = {2020}, author = {Soverini, M and Rampelli, S and Turroni, S and Brigidi, P and Biagi, E and Candela, M}, title = {Do the human gut metagenomic species possess the minimal set of core functionalities necessary for life?.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {678}, pmid = {32998695}, issn = {1471-2164}, mesh = {*Gastrointestinal Microbiome ; *Genes, Bacterial ; Genes, Essential ; Humans ; Intestinal Mucosa/metabolism/microbiology ; *Metagenome ; Metagenomics/methods/standards ; }, abstract = {BACKGROUND: Advances in bioinformatics recently allowed for the recovery of 'metagenomes assembled genomes' from human microbiome studies carried on with shotgun sequencing techniques. Such approach is used as a mean to discover new unclassified metagenomic species, putative biological entities having distinct metabolic traits.

RESULTS: In the present analysis we compare 400 genomes from isolates available on NCBI database and 10,000 human gut metagenomic species, screening all of them for the presence of a minimal set of core functionalities necessary, but not sufficient, for life. As a result, the metagenome-assembled genomes resulted systematically depleted in genes encoding for essential functions apparently needed to support autonomous bacterial life.

CONCLUSIONS: The relevant degree of lacking core functionalities that we observed in metagenome-assembled genomes raises some concerns about the effective completeness of metagenome-assembled genomes, suggesting caution in extrapolating biological information about their metabolic propensity and ecology in a complex environment like the human gastrointestinal tract.}, } @article {pmid32998681, year = {2020}, author = {Brandon-Mong, GJ and Shaw, GT and Chen, WH and Chen, CC and Wang, D}, title = {A network approach to investigating the key microbes and stability of gut microbial communities in a mouse neuropathic pain model.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {295}, pmid = {32998681}, issn = {1471-2180}, support = {MOST 108-2311-B-001-031//Ministry of Science and Technology/ ; }, mesh = {Animals ; Clostridiales/genetics/isolation & purification ; DNA, Bacterial/*genetics ; Disease Models, Animal ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Lactobacillaceae/genetics/isolation & purification ; *Metagenome ; Mice ; Mice, Inbred C57BL ; Microbial Interactions/*genetics ; Neuralgia/*microbiology/physiopathology ; Peroneal Nerve/injuries ; RNA, Ribosomal, 16S/genetics ; Staphylococcus/genetics/isolation & purification ; Sural Nerve/injuries ; }, abstract = {BACKGROUND: Neuropathic pain is an abnormally increased sensitivity to pain, especially from mechanical or thermal stimuli. To date, the current pharmacological treatments for neuropathic pain are still unsatisfactory. The gut microbiota reportedly plays important roles in inducing neuropathic pain, so probiotics have also been used to treat it. However, the underlying questions around the interactions in and stability of the gut microbiota in a spared nerve injury-induced neuropathic pain model and the key microbes (i.e., the microbes that play critical roles) involved have not been answered. We collected 66 fecal samples over 2 weeks (three mice and 11 time points in spared nerve injury-induced neuropathic pain and Sham groups). The 16S rRNA gene was polymerase chain reaction amplified, sequenced on a MiSeq platform, and analyzed using a MOTHUR- UPARSE pipeline.

RESULTS: Here we show that spared nerve injury-induced neuropathic pain alters gut microbial diversity in mice. We successfully constructed reliable microbial interaction networks using the Metagenomic Microbial Interaction Simulator (MetaMIS) and analyzed these networks based on 177,147 simulations. Interestingly, at a higher resolution, our results showed that spared nerve injury-induced neuropathic pain altered both the stability of the microbial community and the key microbes in a gut micro-ecosystem. Oscillospira, which was classified as a low-abundance and core microbe, was identified as the key microbe in the Sham group, whereas Staphylococcus, classified as a rare and non-core microbe, was identified as the key microbe in the spared nerve injury-induced neuropathic pain group.

CONCLUSIONS: In summary, our results provide novel experimental evidence that spared nerve injury-induced neuropathic pain reshapes gut microbial diversity, and alters the stability and key microbes in the gut.}, } @article {pmid32994487, year = {2020}, author = {Alvarez, AS and Tap, J and Chambaud, I and Cools-Portier, S and Quinquis, L and Bourlioux, P and Marteau, P and Guillemard, E and Schrezenmeir, J and Derrien, M}, title = {Safety and functional enrichment of gut microbiome in healthy subjects consuming a multi-strain fermented milk product: a randomised controlled trial.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15974}, pmid = {32994487}, issn = {2045-2322}, mesh = {Adult ; Bacteria/*classification/genetics/isolation & purification ; Cultured Milk Products/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Double-Blind Method ; Female ; Gastrointestinal Microbiome/*drug effects ; Healthy Volunteers ; Humans ; Lactobacillus/physiology ; Lacticaseibacillus rhamnosus/physiology ; Male ; Middle Aged ; Phylogeny ; Probiotics/*administration & dosage/pharmacology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vital Signs/drug effects ; Young Adult ; }, abstract = {Many clinical studies have evaluated the effect of probiotics, but only a few have assessed their dose effects on gut microbiota and host. We conducted a randomized, double-blind, controlled intervention clinical trial to assess the safety (primary endpoint) of and gut microbiota response (secondary endpoint) to the daily ingestion for 4 weeks of two doses (1 or 3 bottles/day) of a fermented milk product (Test) in 96 healthy adults. The Test product is a multi-strain fermented milk product, combining yogurt strains and probiotic candidate strains Lactobacillus paracasei subsp. paracasei CNCM I-1518 and CNCM I-3689 and Lactobacillus rhamnosus CNCM I-3690. We assessed the safety of the Test product on the following parameters: adverse events, vital signs, hematological and metabolic profile, hepatic, kidney or thyroid function, inflammatory markers, bowel habits and digestive symptoms. We explored the longitudinal gut microbiota response to product consumption and dose, by 16S rRNA gene sequencing and functional contribution by shotgun metagenomics. Safety results did not show any significant difference between the Test and Control products whatever the parameters assessed, at the two doses ingested daily over a 4-week-period. Probiotic candidate strains were detected only during consumption period, and at a significantly higher level for the three strains in subjects who consumed 3 products bottles/day. The global structure of the gut microbiota as assessed by alpha and beta-diversity, was not altered by consumption of the product for four weeks. A zero-inflated beta regression model with random effects (ZIBR) identified a few bacterial genera with differential responses to test product consumption dose compared to control. Shotgun metagenomics analysis revealed a functional contribution to the gut microbiome of probiotic candidates.}, } @article {pmid32994464, year = {2020}, author = {Veses, V and González-Torres, P and Carbonetto, B and Del Mar Jovani-Sancho, M and González-Martínez, R and Cortell-Ballester, I and Sheth, CC}, title = {Dental black plaque: metagenomic characterization and comparative analysis with white-plaque.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15962}, pmid = {32994464}, issn = {2045-2322}, mesh = {Adult ; Cluster Analysis ; Dental Plaque/*genetics ; Dysbiosis/genetics ; Female ; Genes, Bacterial/genetics ; Heme/genetics/metabolism ; Humans ; Male ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/*genetics ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; Spain ; }, abstract = {Extrinsic black dental staining is an external dental discoloration of bacterial origin, considered a special form of dental plaque. Currently, there is no definitive therapeutic option for eliminating black stain. This study employed 16S rRNA metagenomics to analyze black stain and white-plaque samples from 27 adult volunteers. Study objectives were to: describe the microbial diversity of adult black stain samples; characterize their taxonomic profile; compare the microbiomes of black stain versus white-plaque from adult volunteers and propose a functional map of the black stain microbiome using PICRUSt2. The black stain microbiome was poorer in species diversity as compared to white-plaque. The five most abundant genera in black stain were Capnocytophaga, Leptotrichia, Fusobacterium, Corynebacterium and Streptococcus. Functional analysis of microbial species revealed conserved and consistent clustering of functional pathways within and between black stain and white-plaque microbiomes. We describe enrichment of heme biosynthetic pathways in black stain. Our results suggest that the dysbiosis in black stain resembles "orally healthy" communities. The increased abundance of heme biosynthetic pathways suggests that heme-dependent iron sequestration and subsequent metabolism are key for black stain formation. Further research should decipher the regulation of heme biosynthetic genes and characterize the temporal sequence leading to colonization and dysbiosis.}, } @article {pmid32994415, year = {2020}, author = {Guo, X and Gao, Q and Yuan, M and Wang, G and Zhou, X and Feng, J and Shi, Z and Hale, L and Wu, L and Zhou, A and Tian, R and Liu, F and Wu, B and Chen, L and Jung, CG and Niu, S and Li, D and Xu, X and Jiang, L and Escalas, A and Wu, L and He, Z and Van Nostrand, JD and Ning, D and Liu, X and Yang, Y and Schuur, EAG and Konstantinidis, KT and Cole, JR and Penton, CR and Luo, Y and Tiedje, JM and Zhou, J}, title = {Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4897}, pmid = {32994415}, issn = {2041-1723}, mesh = {Acclimatization/genetics ; Archaea/genetics/isolation & purification/metabolism ; Bacteria/genetics/isolation & purification/metabolism ; Carbon/*analysis/metabolism ; Carbon Cycle ; Cellulose/metabolism ; DNA, Environmental/genetics/isolation & purification ; Fungi/genetics/isolation & purification/metabolism ; Global Warming ; Grassland ; Hot Temperature/adverse effects ; Metagenome/*genetics ; Metagenomics ; Microbiota/*physiology ; Models, Genetic ; Plant Roots/chemistry ; Poaceae/chemistry ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Soil microbial respiration is an important source of uncertainty in projecting future climate and carbon (C) cycle feedbacks. However, its feedbacks to climate warming and underlying microbial mechanisms are still poorly understood. Here we show that the temperature sensitivity of soil microbial respiration (Q10) in a temperate grassland ecosystem persistently decreases by 12.0 ± 3.7% across 7 years of warming. Also, the shifts of microbial communities play critical roles in regulating thermal adaptation of soil respiration. Incorporating microbial functional gene abundance data into a microbially-enabled ecosystem model significantly improves the modeling performance of soil microbial respiration by 5-19%, and reduces model parametric uncertainty by 55-71%. In addition, modeling analyses show that the microbial thermal adaptation can lead to considerably less heterotrophic respiration (11.6 ± 7.5%), and hence less soil C loss. If such microbially mediated dampening effects occur generally across different spatial and temporal scales, the potential positive feedback of soil microbial respiration in response to climate warming may be less than previously predicted.}, } @article {pmid32993936, year = {2020}, author = {Tufts, DM and Sameroff, S and Tagliafierro, T and Jain, K and Oleynik, A and VanAcker, MC and Diuk-Wasser, MA and Lipkin, WI and Tokarz, R}, title = {A metagenomic examination of the pathobiome of the invasive tick species, Haemaphysalis longicornis, collected from a New York City borough, USA.}, journal = {Ticks and tick-borne diseases}, volume = {11}, number = {6}, pages = {101516}, doi = {10.1016/j.ttbdis.2020.101516}, pmid = {32993936}, issn = {1877-9603}, mesh = {Animals ; Ixodidae/growth & development/*microbiology/virology ; Larva/growth & development/microbiology/virology ; *Metagenome ; Metagenomics ; *Microbiota ; New York City ; Nymph/growth & development/microbiology/virology ; *Virome ; }, abstract = {Haemaphysalis longicornis, the Asian longhorned tick, is an invasive tick species that has spread rapidly across the northeastern and southeastern regions of the United States in recent years. This invasive pest species, known to transmit several tick-borne pathogens in its native range, is a potential threat to wildlife, livestock, domestic animals, and humans. Questing larval (n = 25), nymph (n = 10), and adult (n = 123), along with host-derived adult (n = 25) H. longicornis ticks were collected from various locations on Staten Island, NY. The pathobiome of each specimen was examined using two different high throughput sequencing approaches, virus enrichment and shotgun metagenomics. An average of 45,828,061 total reads per sample were recovered from the virus enriched samples and an average of 11,381,144 total reads per sample were obtained using shotgun metagenomics. Aside from endogenous viral sequences, no viruses were identified through either approach. Through shotgun metagenomics, Coxiella-like bacteria, Legionella, Sphingomonas, and other bacterial species were recovered. The Coxiella-like agent was ubiquitous and present at high abundances in all samples, suggesting it may be an endosymbiont. The other bacterial agents are not known to be transmitted by ticks. From these analyses, H. longicornis do not appear to host any endemic human tick-borne pathogens in the New York City region.}, } @article {pmid32993305, year = {2021}, author = {Guarner, F}, title = {[Symbiosis in the human gastrointestinal tract].}, journal = {Nutricion hospitalaria}, volume = {37}, number = {Spec No2}, pages = {34-37}, doi = {10.20960/nh.03354}, pmid = {32993305}, issn = {1699-5198}, mesh = {Dysbiosis ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*physiology ; Genome, Bacterial ; Homeostasis ; Humans ; Symbiosis/*physiology ; }, abstract = {The human body is a planet populated by myriads of microorganisms all over its surface and in cavities connected to the outside. Experimental and clinical research is showing that microbial colonizers are a functional and essential part of the human organism. The microbial ecosystem, which is housed in the gastrointestinal tract, provides a "metagenome": genes and additional functions to the genetic resources of the species, which are involved in multiple physiological processes (somatic development, nutrition, immunity, etc.). The human intestine houses lymphoid structures specialized in the induction and regulation of adaptive immunity, and the interaction of the intestinal microbiota with the immune system of the digestive mucosa plays a key role for the individual's homeostasis with the outside world. Some chronic non-communicable inflammatory diseases in developed society are associated with dysbiosis: loss of species richness in the gut microbiota and deviation from the ancestral microbial environment. Generating and maintaining diversity in the gut microbiota is a new clinical goal for health promotion and disease prevention.}, } @article {pmid32993188, year = {2020}, author = {Peng, M and Biswas, D}, title = {Environmental Influences of High-Density Agricultural Animal Operation on Human Forearm Skin Microflora.}, journal = {Microorganisms}, volume = {8}, number = {10}, pages = {}, pmid = {32993188}, issn = {2076-2607}, support = {20185110628809//National Institute of Food and Agriculture/ ; }, abstract = {The human forearm skin microbiome ecosystem contains rich and diverse microbes, which are influenced by environmental exposures. The microbial representatives can be exchanged between human and environment, specifically animals, by which they share certain or similar epidermal microbes. Livestock and poultry are the microbial sources that are associated with the transmission of community-based pathogenic infections. Here, in this study, we proposed investigating the environmental influences introduced by livestock/poultry operations on forearm skin microflora of on-site farm workers. A total of 30 human skin swab samples were collected from 20 animal workers in dairy or integrated farms and 10 healthy volunteer controls. The skin microbiome was 16S metagenomics that were sequenced with Illumina MiSeq system. For skin microbial community analysis, the abundance of major phyla and genera as well as alpha and beta diversities were compared across groups. We identified distinctive microbial compositional patterns on skin of workers in farm with different animal commodities. Workers in integrated farms containing various animals were associated with higher abundances of epidermal Proteobacteria, especially Pseudomonas and Acinetobacter, but lower Actinobacteria, especially Corynebacterium and Propionibacterium. For those workers with frequent dairy cattle operations, their Firmicutes in the forearm skin microbiota were enriched. Furthermore, farm animal operations also reduced Staphylococcus and Streptococcus, as well as modulated the microbial biodiversity in farm workers' skin microbiome. The alterations of forearm skin microflora in farm workers, influenced by their frequent farm animal operations, may increase their risk in skin infections with unusual pathogens and epidermal diseases.}, } @article {pmid32992666, year = {2020}, author = {Grafskaia, E and Pavlova, E and Babenko, VV and Latsis, I and Malakhova, M and Lavrenova, V and Bashkirov, P and Belousov, D and Klinov, D and Lazarev, V}, title = {The Hirudo Medicinalis Microbiome Is a Source of New Antimicrobial Peptides.}, journal = {International journal of molecular sciences}, volume = {21}, number = {19}, pages = {}, pmid = {32992666}, issn = {1422-0067}, support = {20-15-00270//Russian Science Foundation/ ; }, mesh = {Amino Acid Sequence ; Animals ; Anti-Bacterial Agents/chemistry/*metabolism/pharmacology ; Antimicrobial Cationic Peptides/chemistry/*metabolism/pharmacology ; Cell Line ; Cell Survival/drug effects ; Circular Dichroism ; Drug Discovery/*methods ; Fibroblasts/drug effects ; Gram-Negative Bacteria/drug effects ; Gram-Positive Bacteria/drug effects ; Hirudo medicinalis/*metabolism/*microbiology ; Metagenome ; Mice ; Microbial Sensitivity Tests ; Microbiota/*physiology ; Protein Conformation, alpha-Helical ; }, abstract = {Antimicrobial peptides (AMPs) are considered a promising new class of anti-infectious agents. This study reports new antimicrobial peptides derived from the Hirudo medicinalis microbiome identified by a computational analysis method applied to the H. medicinalis metagenome. The identified AMPs possess a strong antimicrobial activity against Gram-positive and Gram-negative bacteria (MIC range: 5.3 to 22.4 μM), including Staphylococcus haemolyticus, an opportunistic coagulase-negative pathogen. The secondary structure analysis of peptides via CD spectroscopy showed that all the AMPs except pept_352 have mostly disordered structures that do not change under different conditions. For peptide pept_352, the α-helical content increases in the membrane environment. The examination of the mechanism of action of peptides suggests that peptide pept_352 exhibits a direct membranolytic activity. Furthermore, the cytotoxicity assay demonstrated that the nontoxic peptide pept_1545 is a promising candidate for drug development. Overall, the analysis method implemented in the study may serve as an effective tool for the identification of new AMPs.}, } @article {pmid32992213, year = {2020}, author = {Hamood Altowayti, WA and Almoalemi, H and Shahir, S and Othman, N}, title = {Comparison of culture-independent and dependent approaches for identification of native arsenic-resistant bacteria and their potential use for arsenic bioremediation.}, journal = {Ecotoxicology and environmental safety}, volume = {205}, number = {}, pages = {111267}, doi = {10.1016/j.ecoenv.2020.111267}, pmid = {32992213}, issn = {1090-2414}, mesh = {Actinobacteria/cytology/*drug effects/genetics ; Arsenic/analysis/*toxicity ; Biodegradation, Environmental ; Culture Media/chemistry ; Drug Resistance, Bacterial/drug effects ; Firmicutes/cytology/*drug effects/genetics ; Gold ; Metagenomics/*methods ; Microbial Sensitivity Tests ; Microbiota/drug effects/genetics ; Mining ; Proteobacteria/cytology/*drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/analysis/*toxicity ; }, abstract = {Arsenic is a common contaminant in gold mine soil and tailings. Microbes present an opportunity for bio-treatment of arsenic, since it is a sustainable and cost-effective approach to remove arsenic from water. However, the development of existing bio-treatment approaches depends on isolation of arsenic-resistant microbes from arsenic contaminated samples. Microbial cultures are commonly used in bio-treatment; however, it is not established whether the structure of the cultured isolates resembles the native microbial community from arsenic-contaminated soil. In this milieu, a culture-independent approach using Illumina sequencing technology was used to profile the microbial community in situ. This was coupled with a culture-dependent technique, that is, isolation using two different growth media, to analyse the microbial population in arsenic laden tailing dam sludge based on the culture-independent sequencing approach, 4 phyla and 8 genera were identified in a sample from the arsenic-rich gold mine. Firmicutes (92.23%) was the dominant phylum, followed by Proteobacteria (3.21%), Actinobacteria (2.41%), and Bacteroidetes (1.49%). The identified genera included Staphylococcus (89.8%), Pseudomonas (1.25), Corynebacterium (0.82), Prevotella (0.54%), Megamonas (0.38%) and Sphingomonas (0.36%). The Shannon index value (3.05) and Simpson index value (0.1661) indicated low diversity in arsenic laden tailing. The culture dependent method exposed significant similarities with culture independent methods at the phylum level with Firmicutes, Proteobacteria and Actinobacteria, being common, and Firmicutes was the dominant phylum whereas, at the genus level, only Pseudomonas was presented by both methods. It showed high similarities between culture independent and dependent methods at the phylum level and large differences at the genus level, highlighting the complementarity between the two methods for identification of the native population bacteria in arsenic-rich mine. As a result, the present study can be a resource on microbes for bio-treatment of arsenic in mining waste.}, } @article {pmid32992082, year = {2020}, author = {Lee, JE and Lee, SM and Jung, J}, title = {Integrated omics analysis unraveled the microbiome-mediated effects of Yijin-Tang on hepatosteatosis and insulin resistance in obese mouse.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {79}, number = {}, pages = {153354}, doi = {10.1016/j.phymed.2020.153354}, pmid = {32992082}, issn = {1618-095X}, mesh = {Animals ; Anti-Obesity Agents/*pharmacology ; Bacteroides/drug effects ; Cholesterol/adverse effects ; Diet, High-Fat/adverse effects ; Firmicutes/drug effects ; Gastrointestinal Microbiome/*drug effects/genetics/physiology ; *Insulin Resistance ; Male ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/*drug therapy/metabolism/microbiology ; Obesity/*drug therapy/etiology ; Phosphatidylglycerols/metabolism ; Plant Extracts/chemistry/*pharmacology ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Gut microbiota play important roles in insulin homeostasis and the pathogenesis of non-alcoholic fatty liver diseases (NAFLD). Yijin-Tang (YJT), a traditional Korean and Chinese medicine, is used in the treatment of gastrointestinal diseases and obesity-related disorders such as insulin resistance (IR) and NAFLD.

PURPOSE: Our aim was to identify the microbiome-mediated effects of YJT on IR and associated NAFLD by integrating metagenomics and hepatic lipid profile.

METHODS: C57BL/6J mice were fed a normal chow diet (NC) or high-fat/high-cholesterol (HFHC) diet with or without YJT treatment. Hepatic lipid profiles were analyzed using liquid chromatography/mass spectrometry, and the composition of gut microbiota was investigated using 16S rRNA sequencing. Then, hepatic lipid profiles, gut microbiome, and inflammatory marker data were integrated using multivariate analysis and bioinformatics tools.

RESULTS: YJT improved NAFLD, and 39 hepatic lipid metabolites were altered by YJT in a dose-dependent manner. YJT also altered the gut microbiome composition in HFHC-fed mice. In particular, Faecalibaculum rodentium and Bacteroides acidifaciens were altered by YJT in a dose-dependent manner. Also, we found significant correlation among hepatic phosphatidylglycerol metabolites, F. rodentium, and γδ-T cells. Moreover, interleukin (IL)-17, which is secreted by the γδ-T cell when it recognizes lipid antigens, were elevated in HFHC mice and decreased by YJT treatment. In addition, YJT increased the relative abundance of B. acidifaciens in NC or HFHC-fed mice, which is a gut microbiota that mediates anti-obesity and anti-diabetic effects by modulating the gut environment. We also confirmed that YJT ameliorated the gut tight junctions and increased short chain fatty acid (SCFA) levels in the intestine, which resulted in improved IR.

CONCLUSION: These data demonstrated that gut microbiome and hepatic lipid profiles are regulated by YJT, which improved the IR and NAFLD in mice with diet-induced obesity.}, } @article {pmid32991841, year = {2020}, author = {Ha, CWY and Martin, A and Sepich-Poore, GD and Shi, B and Wang, Y and Gouin, K and Humphrey, G and Sanders, K and Ratnayake, Y and Chan, KSL and Hendrick, G and Caldera, JR and Arias, C and Moskowitz, JE and Ho Sui, SJ and Yang, S and Underhill, D and Brady, MJ and Knott, S and Kaihara, K and Steinbaugh, MJ and Li, H and McGovern, DPB and Knight, R and Fleshner, P and Devkota, S}, title = {Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans.}, journal = {Cell}, volume = {183}, number = {3}, pages = {666-683.e17}, pmid = {32991841}, issn = {1097-4172}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; U01 DK062413/DK/NIDDK NIH HHS/United States ; R01 DK123446/DK/NIDDK NIH HHS/United States ; F30 CA243480/CA/NCI NIH HHS/United States ; P01 DK046763/DK/NIDDK NIH HHS/United States ; P30 DK020595/DK/NIDDK NIH HHS/United States ; }, mesh = {Adipose Tissue/*microbiology/pathology ; Animals ; *Bacterial Translocation ; Biodiversity ; Biomarkers/metabolism ; Cell Polarity ; Cells, Cultured ; Colitis, Ulcerative/pathology ; Crohn Disease/microbiology/pathology ; *Gastrointestinal Microbiome/genetics ; Gene Expression Regulation ; Germ-Free Life ; Humans ; Ileum/microbiology/pathology ; Lipopolysaccharides/metabolism ; Macrophages/metabolism ; Mesentery/*microbiology ; Metagenome ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Phenotype ; RNA, Ribosomal, 16S/genetics ; Stem Cells/metabolism ; }, abstract = {A mysterious feature of Crohn's disease (CD) is the extra-intestinal manifestation of "creeping fat" (CrF), defined as expansion of mesenteric adipose tissue around the inflamed and fibrotic intestine. In the current study, we explore whether microbial translocation in CD serves as a central cue for CrF development. We discovered a subset of mucosal-associated gut bacteria that consistently translocated and remained viable in CrF in CD ileal surgical resections, and identified Clostridium innocuum as a signature of this consortium with strain variation between mucosal and adipose isolates, suggesting preference for lipid-rich environments. Single-cell RNA sequencing characterized CrF as both pro-fibrotic and pro-adipogenic with a rich milieu of activated immune cells responding to microbial stimuli, which we confirm in gnotobiotic mice colonized with C. innocuum. Ex vivo validation of expression patterns suggests C. innocuum stimulates tissue remodeling via M2 macrophages, leading to an adipose tissue barrier that serves to prevent systemic dissemination of bacteria.}, } @article {pmid32991818, year = {2020}, author = {Goll, R and Johnsen, PH and Hjerde, E and Diab, J and Valle, PC and Hilpusch, F and Cavanagh, JP}, title = {Effects of fecal microbiota transplantation in subjects with irritable bowel syndrome are mirrored by changes in gut microbiome.}, journal = {Gut microbes}, volume = {12}, number = {1}, pages = {1794263}, pmid = {32991818}, issn = {1949-0984}, mesh = {Adult ; Aged ; Bacteria/classification/genetics/growth & development/metabolism ; Double-Blind Method ; *Fecal Microbiota Transplantation ; Female ; *Gastrointestinal Microbiome ; Humans ; Irritable Bowel Syndrome/*microbiology/*therapy ; Male ; Middle Aged ; Tissue Donors ; Treatment Outcome ; Young Adult ; }, abstract = {Irritable bowel syndrome (IBS) is a common disorder of the lower gastrointestinal tract. The pathophysiology is far from settled, but a gut microbial dysbiosis is hypothesized to be a contributing factor. We earlier published a randomized double-blind placebo-controlled clinical trial on fecal microbiota transplantation (FMT) for IBS - the REFIT trial. The present data set describes the engraftment and includes participants from the study who received active FMT; 14 participants with effect of FMT (Effect) and 8 without (No effect). Samples were collected at baseline, after 6 and 12 months. Samples from the transplants (Donor) served as a comparator. In total 66 recipient samples and 17 donor samples were subjected to deep metagenomic sequencing, and taxonomic and functional analyses were performed. Alpha diversity measures showed a significantly increased diversity and evenness in the IBS groups compared to the donors. Taxonomic profiles showed higher relative abundance of phylum Firmicutes, and lower relative abundance of phylum Bacteroidetes, compared to donors at baseline. This profile was shifted toward the donor profile following FMT. Imputed growth rates showed that the resulting growth pattern was a conglomerate of donor and recipient activity. Thirty-four functional subclasses showed distinct differences between baseline samples and donors, most of which were shifted toward a donor-like profile after FMT. All of these changes were less pronounced in the No effect group. We conclude that FMT induces long-term changes in gut microbiota, and these changes mirror the clinical effect of the treatment. The study was registered in ClinicalTrials.gov (NCT02154867).}, } @article {pmid32991226, year = {2020}, author = {Kumar, S and Paul, D and Bhushan, B and Wakchaure, GC and Meena, KK and Shouche, Y}, title = {Traversing the "Omic" landscape of microbial halotolerance for key molecular processes and new insights.}, journal = {Critical reviews in microbiology}, volume = {46}, number = {6}, pages = {631-653}, doi = {10.1080/1040841X.2020.1819770}, pmid = {32991226}, issn = {1549-7828}, mesh = {Bacteria/classification/*genetics/isolation & purification/*metabolism ; Ecosystem ; Metagenome ; Metagenomics ; Microbiota ; Phylogeny ; Sodium Chloride/*metabolism ; }, abstract = {Post-2005, the biology of the salt afflicted habitats is predominantly studied employing high throughput "Omic" approaches comprising metagenomics, transcriptomics, metatranscriptomics, metabolomics, and proteomics. Such "Omic-based" studies have deciphered the unfamiliar details about microbial salt-stress biology. The MAGs (Metagenome-assembled genomes) of uncultured halophilic microbial lineages such as Nanohaloarchaea and haloalkaliphilic members within CPR (Candidate Phyla Radiation) have been reconstructed from diverse hypersaline habitats. The study of MAGs of such uncultured halophilic microbial lineages has unveiled the genomic basis of salt stress tolerance in "yet to culture" microbial lineages. Furthermore, functional metagenomic approaches have been used to decipher the novel genes from uncultured microbes and their possible role in microbial salt-stress tolerance. The present review focuses on the new insights into microbial salt-stress biology gained through different "Omic" approaches. This review also summarizes the key molecular processes that underlie microbial salt-stress response, and their role in microbial salt-stress tolerance has been confirmed at more than one "Omic" levels.}, } @article {pmid32988512, year = {2020}, author = {Zhang, J and Cai, K and Mishra, R and Jha, R}, title = {In ovo supplementation of chitooligosaccharide and chlorella polysaccharide affects cecal microbial community, metabolic pathways, and fermentation metabolites in broiler chickens.}, journal = {Poultry science}, volume = {99}, number = {10}, pages = {4776-4785}, pmid = {32988512}, issn = {1525-3171}, mesh = {Animals ; Bacteria/drug effects ; *Cecum/microbiology ; *Chickens ; Chitin/administration & dosage/*analogs & derivatives/pharmacology ; Chitosan ; Chlorella/chemistry ; *Dietary Supplements ; Fermentation/drug effects ; *Metabolic Networks and Pathways/drug effects ; *Microbiota/drug effects ; Oligosaccharides ; Ovum ; Plant Extracts/pharmacology ; *Polysaccharides/pharmacology ; }, abstract = {The chitooligosaccharide (COS) and chlorella polysaccharide (CPS) have been used as feed supplements in the poultry industry for improving growth performance and immunity. However, the benefits of these prebiotics on the gut health of chickens when used in early nutrition are unknown. This study evaluated the effects of in ovo feeding of COS and CPS on the cecal microbiome, metabolic pathways, and fermentation metabolites of chickens. A total of 240 fertile eggs were divided into 6 groups (n = 4; 10 eggs/replicate): 1) no-injection control, 2) normal saline control, 3) COS 5 mg, 4) COS 20 mg, 5) CPS 5 mg, and 6) CPS 20 mg injection. On day 12.5 of egg incubation, test substrate was injected into the amniotic sac of eggs in respective treatments. The hatched chicks were raised for 21 D under standard husbandry practices. On day 3 and 21, cecal digesta were collected to determine microbiota by shotgun metagenomic sequencing and short-chain fatty acids by gas chromatography. The cecal microbial composition was not different (P > 0.05) among the treatment groups on day 3 but was different (P < 0.05) on day 21. At the species level, the polysaccharide-utilizing bacteria including Lactobacillus johnsonii, Bacteroides coprocola, and Bacteroides salanitronis were higher in the COS group, whereas the relative abundance of some opportunistic pathogenic bacteria were lower than those in the CPS and control groups. At the functional level, the pathways of gluconeogenesis, L-isoleucine degradation, L-histidine biosynthesis, and fatty acid biosynthesis were enriched in the COS group. In addition, propionic acid content was higher (P < 0.05) in the COS group. A network based on the correlation between the COS and other factors was constructed to illuminate the potential action mechanism of the COS in chicken early nutrition. In conclusion, in ovo inoculation of COS 5 mg showed positive effects on the cecal microbiota, metabolic pathways, and propionic acid, thus can be used as in ovo feeding to modulate the gut health of chickens.}, } @article {pmid32988416, year = {2020}, author = {Brown, SP and Grillo, MA and Podowski, JC and Heath, KD}, title = {Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {139}, pmid = {32988416}, issn = {2049-2618}, mesh = {*Genotype ; Medicago truncatula/anatomy & histology/*genetics/*microbiology ; *Microbiota/genetics ; Models, Biological ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; *Soil ; Soil Microbiology ; Symbiosis/genetics ; }, abstract = {BACKGROUND: Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. Legumes, which form root nodule symbioses with nitrogen-fixing rhizobia, have served as model plants for understanding the genetics and evolution of beneficial plant-microbe interactions for decades, and thus have added value as models of plant-microbiome interactions. Here we use a common garden experiment with 16S rRNA gene amplicon and shotgun metagenomic sequencing to study the drivers of microbiome diversity and composition in three genotypes of the model legume Medicago truncatula grown in two native soil communities.

RESULTS: Bacterial diversity decreased between external (rhizosphere) and internal plant compartments (root endosphere, nodule endosphere, and leaf endosphere). Community composition was shaped by strong compartment × soil origin and compartment × plant genotype interactions, driven by significant soil origin effects in the rhizosphere and significant plant genotype effects in the root endosphere. Nevertheless, all compartments were dominated by Ensifer, the genus of rhizobia that forms root nodule symbiosis with M. truncatula, and additional shotgun metagenomic sequencing suggests that the nodulating Ensifer were not genetically distinguishable from those elsewhere in the plant. We also identify a handful of OTUs that are common in nodule tissues, which are likely colonized from the root endosphere.

CONCLUSIONS: Our results demonstrate strong host filtering effects, with rhizospheres driven by soil origin and internal plant compartments driven by host genetics, and identify several key nodule-inhabiting taxa that coexist with rhizobia in the native range. Our results set the stage for future functional genetic experiments aimed at expanding our pairwise understanding of legume-rhizobium symbiosis toward a more mechanistic understanding of plant microbiomes. Video Abstract.}, } @article {pmid32987279, year = {2021}, author = {Zhang, W and Zhang, Q and Li, M and Wang, H and Li, Y and Peng, H and Feng, J}, title = {Microbial community and function evaluation in the start-up period of bioaugmented SBR fed with aniline wastewater.}, journal = {Bioresource technology}, volume = {319}, number = {}, pages = {124148}, doi = {10.1016/j.biortech.2020.124148}, pmid = {32987279}, issn = {1873-2976}, mesh = {Aniline Compounds ; Bioreactors ; Denitrification ; *Microbiota ; Nitrification ; Nitrogen ; Sewage ; Waste Disposal, Fluid ; *Wastewater ; }, abstract = {An enhanced sequencing batch reactor (SBR) system was developed to treat synthetic wastewater rich in 600 mg/L aniline. The aniline degradation efficiency was almost 100%, and the total nitrogen (TN) removal rate was more than 50%. Metagenomics technology revealed the community structure, functional genes and metabolic mechanism during the start-up of the enhanced reactor. Sequencing results showed that Proteobacteria, Bacteroidetes, Chloroflexi and Actinobacteria were dominant phylum. The proportion of degradation of aromatic compounds function increased gradually, but the proportion of nitrogen metabolism function changed little. Functional genes involved in aniline degradation including benA-xylX and dmpB/xylE were detected. The functional genes of nitrogen metabolism were involved in complete nitrification, traditional denitrification, assimilation nitrate reduction and dissimilation nitrate reduction. The functional contribution analysis and network analysis showed that the cooperation and competition of Thauera, Delftia, Diaphorobacter, Micavibrio and Azoarcus ensured the effective removal of aniline and nitrogen.}, } @article {pmid32985923, year = {2020}, author = {Ghosh, TS and Arnoux, J and O'Toole, PW}, title = {Metagenomic analysis reveals distinct patterns of gut lactobacillus prevalence, abundance, and geographical variation in health and disease.}, journal = {Gut microbes}, volume = {12}, number = {1}, pages = {1-19}, pmid = {32985923}, issn = {1949-0984}, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Aged, 80 and over ; Body Mass Index ; Child ; Child, Preschool ; Diabetes Mellitus, Type 2/microbiology ; Diet ; *Disease ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Geography ; *Health ; Humans ; Infant ; Inflammatory Bowel Diseases/microbiology ; Lactobacillus/*classification/genetics/*growth & development/isolation & purification ; Liver Diseases/microbiology ; Male ; *Metagenome ; Metagenomics ; Middle Aged ; Sex Factors ; Young Adult ; }, abstract = {Lactobacilli are exploited extensively for food fermentation and biotechnology. Some food and gut isolates have been developed as probiotics, for which species that may be commensal to the human host are considered desirable. However, the robustness of defining original niches for lactobacilli - food, environment, the gut - is questionable, and culture-independent analyses of prevalence in different human populations is lacking. Here we analyzed the abundance of lactobacilli in 6,154 subjects from a database of highly curated fecal shotgun metagenomics data spanning 25 nationalities, with ages ranging from infancy to 102 years. Twenty-five species were detected, which we assigned into low, medium, and high prevalence groups. The microbiome of apparently healthy individuals could be categorized into 6 clusters or Lactobacillotypes (LbTypes), with three of the Lbtypes being dominated by L.delbrueckii, L.ruminis, L.casei, and the other three comprising a combination of different species. These Lactobacillus clusters exhibit distinct global abundance patterns. The cluster prevalences also display distinct age-specific trends influenced by geography, with overall lactobacillus prevalence increasing significantly with age in North America and Europe but declining with age in non-Westernized societies. Regression analysis stratified by regional location identified distinct associations of the Lactobacillotypes with age, BMI, and gender. Cirrhosis, fatty-liver, , IBD and T2D were characterized by net gain of lactobacilli, whereas hypertension patients harbored depleted lactobacillus levels. Collectively these data indicate that the species abundance of gut lactobacilli is moderated by geography, diet, and interaction with the whole microbiome, and has strong interactions with diseases associated with a western lifestyle.}, } @article {pmid32984078, year = {2020}, author = {Marazzato, M and Zicari, AM and Aleandri, M and Conte, AL and Longhi, C and Vitanza, L and Bolognino, V and Zagaglia, C and De Castro, G and Brindisi, G and Schiavi, L and De Vittori, V and Reddel, S and Quagliariello, A and Del Chierico, F and Putignani, L and Duse, M and Palamara, AT and Conte, MP}, title = {16S Metagenomics Reveals Dysbiosis of Nasal Core Microbiota in Children With Chronic Nasal Inflammation: Role of Adenoid Hypertrophy and Allergic Rhinitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {458}, pmid = {32984078}, issn = {2235-2988}, mesh = {*Adenoids ; Child ; Dysbiosis ; Humans ; Hypertrophy ; Inflammation ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Rhinitis, Allergic ; }, abstract = {Allergic rhinitis (AR) and adenoid hypertrophy (AH) are, in children, the main cause of partial or complete upper airway obstruction and reduction in airflow. However, limited data exist about the impact of the increased resistance to airflow, on the nasal microbial composition of children with AR end AH. Allergic rhinitis (AR) as well as adenoid hypertrophy (AH), represent extremely common pathologies in this population. Their known inflammatory obstruction is amplified when both pathologies coexist. In our study, the microbiota of anterior nares of 75 pediatric subjects with AR, AH or both conditions, was explored by 16S rRNA-based metagenomic approach. Our data show for the first time, that in children, the inflammatory state is associated to similar changes in the microbiota composition of AR and AH subjects respect to the healthy condition. Together with such alterations, we observed a reduced variability in the between-subject biodiversity on the other hand, these same alterations resulted amplified by the nasal obstruction that could constitute a secondary risk factor for dysbiosis. Significant differences in the relative abundance of specific microbial groups were found between diseased phenotypes and the controls. Most of these taxa belonged to a stable and quantitatively dominating component of the nasal microbiota and showed marked potentials in discriminating the controls from diseased subjects. A pauperization of the nasal microbial network was observed in diseased status in respect to the number of involved taxa and connectivity. Finally, while stable co-occurrence relationships were observed within both control- and diseases-associated microbial groups, only negative correlations were present between them, suggesting that microbial subgroups potentially act as maintainer of the eubiosis state in the nasal ecosystem. In the nasal ecosystem, inflammation-associated shifts seem to impact the more intimate component of the microbiota rather than representing the mere loss of microbial diversity. The discriminatory potential showed by differentially abundant taxa provide a starting point for future research with the potential to improve patient outcomes. Overall, our results underline the association of AH and AR with the impairment of the microbial interplay leading to unbalanced ecosystems.}, } @article {pmid32979836, year = {2020}, author = {Thijssen, M and Tacke, F and Beller, L and Deboutte, W and Yinda, KC and Nevens, F and Laleman, W and Van Ranst, M and Pourkarim, MR}, title = {Clinical relevance of plasma virome dynamics in liver transplant recipients.}, journal = {EBioMedicine}, volume = {60}, number = {}, pages = {103009}, pmid = {32979836}, issn = {2352-3964}, mesh = {Adult ; Aged ; Antiviral Agents/pharmacology/therapeutic use ; Coinfection ; Computational Biology/methods ; Female ; Humans ; Liver Transplantation/*adverse effects/methods ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Phylogeny ; *Transplant Recipients ; Viremia/diagnosis/*etiology ; *Virome ; Virus Diseases/diagnosis/drug therapy/*etiology ; }, abstract = {BACKGROUND: The role of the microbiome in liver transplantation (LT) outcome has received a growing interest in the past decades. In contrast to bacteria, the role of endogenous viral communities, known as the virome, is poorly described. Here, we applied a viral metagenomic approach to study the dynamic evolution of circulating viruses in the plasma of LT recipients and its effect on the clinical course of patients.

METHODS: Patients chronically infected with hepatitis B virus (HBV) that received a LT due to endstage liver disease were included in this study. Longitudinal plasma samples were collected pre- and post-LT. Intact viral particles were isolated and sequenced on an Illumina HiSeq 2500 platform. Short read libraries were analysed with an in-house bioinformatics pipeline. Key endpoints were the dynamics of viral families and post-LT complications.

FINDINGS: The initiation of immunosuppression induced a bloom of the Anelloviridae that dominated the post-LT plasma virome. A variety of post-LT complication were observed. Nephrotoxicity was reported in 38% of the patients and was associated with a high abundance of anelloviruses. Besides nephrotoxicity, 16 (67%) patients experienced flares of viral or bacterial infections in post-transplant follow-up. These flares were recognized by an increased burden of anelloviruses (p < 0.05). Interestingly, no mortality was observed in patients infected with human pegivirus.

INTERPRETATION: These findings suggest a diagnostic potential for the Anelloviridae family in post-LT complications. Furthermore, the impact of human pegivirus infection on post-transplant survival should be further investigated.

FUNDING: This trial was supported by Gilead Sciences grant number BE-2017-000133.}, } @article {pmid32979562, year = {2021}, author = {Lai, WT and Zhao, J and Xu, SX and Deng, WF and Xu, D and Wang, MB and He, FS and Liu, YH and Guo, YY and Ye, SW and Yang, QF and Zhang, YL and Wang, S and Li, MZ and Yang, YJ and Liu, TB and Tan, ZM and Xie, XH and Rong, H}, title = {Shotgun metagenomics reveals both taxonomic and tryptophan pathway differences of gut microbiota in bipolar disorder with current major depressive episode patients.}, journal = {Journal of affective disorders}, volume = {278}, number = {}, pages = {311-319}, doi = {10.1016/j.jad.2020.09.010}, pmid = {32979562}, issn = {1573-2517}, mesh = {*Bipolar Disorder/genetics ; Cross-Sectional Studies ; *Depressive Disorder, Major/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; Tryptophan ; }, abstract = {BACKGROUND: The microbiome-gut-brain axis, especially the microbial tryptophan biosynthesis and metabolism pathway (MiTBamp), is closely connected to bipolar disorder with current major depressive episode (BPD).

METHODS: We performed shotgun metagenomics sequencing (SMS) of faecal samples from 25 BPD patients and 28 healthy controls (HCs). Except for the microbiota taxa and MiTBamp analyses, we also built a classification model using the Random Forests (RF) and Boruta algorithm to find the microbial biomarkers for BPD.

RESULTS: Compared to HCs, the phylum Bacteroidetes abundance was significantly reduced, whereas that of the Actinobacteria and Firmicutes were significantly increased in BPD patients. We also identified 38 species increased and 6 species decreased significantly in the BPD group. In the MiTBamp, we identified that two Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologies (KOs) (K00658 and K00837) were significantly lower in the BPD, and five KOs (K01696, K00382, K00626, K01667, and K03781) were significantly higher in the BPD group. We also identified significant genera and species which were closely related to these KOs. Finally, RF classification based on gut microbiota at the genus level can achieve an area under the receiver operating characteristic curve of 0.997.

LIMITATIONS: The features of cross-sectional design, limited sample size, the heterogeneity of bipolar disorders, and a lack of serum/plasma tryptophan concentration measurements.

CONCLUSIONS: The present findings enable a better understanding of changes in gastrointestinal microbiome and MiTBamp in BPD. Alterations of microbes may have potential as biomarkers for distinguishing the BPD patients form HCs.}, } @article {pmid32979472, year = {2020}, author = {Zhao, H and Liu, J and Zhu, J and Yang, F and Wu, H and Ba, Y and Cui, L and Chen, R and Chen, S}, title = {Bacterial composition and community structure of the oropharynx of adults with asthma are associated with environmental factors.}, journal = {Microbial pathogenesis}, volume = {149}, number = {}, pages = {104505}, doi = {10.1016/j.micpath.2020.104505}, pmid = {32979472}, issn = {1096-1208}, mesh = {Adult ; *Asthma ; Bacteria/genetics ; Humans ; Metagenome ; *Microbiota ; Oropharynx ; }, abstract = {The development and exacerbation of asthma are mainly attributed to inflammatory reactions caused by allergens. However, less is known about the development of asthma caused by microbial disorders in the oropharynx and induced by environmental factors. Here, the metagenome of the oropharyngeal microbiome of adults with asthma was analysed to identify their association with air pollutants. Oropharyngeal swabs from patients with asthma were collected in two winters (W1 and W2) with different environmental factor exposures. The bacterial composition and community structure of the oropharynx were analysed through high-throughput sequencing. After analysis, the α-diversity and β-diversity exhibited significant differences between the two groups. LEfSe analysis detected 8 significantly different phyla and 11 significantly different genera between the W1 and W2 groups. Multiple linear regression analyses found that the asthma status might contribute to the alteration of microbial composition. Redundancy analysis showed that NO2 was the only environmental factor that significantly affected the microbial community structure of the oropharynx. The different genera associated with NO2 were Rothia, Actinomyces, Fusobacterium and Leptotrichia. The altered taxa related to PM2.5 were Cupriavidus and Acinetobacter. Actinobacillus and Prevotella showed a highly positive correlation with O3. Moreover, network analysis was carried out to explore the co-occurrence relationships of the main genera, and PICRUSt was conducted to predict bacterial functions. This study showed that environmental factors might cause alteration in the oropharyngeal flora, which might be a potential risk factor of asthma.}, } @article {pmid32976952, year = {2021}, author = {Łoniewski, I and Misera, A and Skonieczna-Żydecka, K and Kaczmarczyk, M and Kaźmierczak-Siedlecka, K and Misiak, B and Marlicz, W and Samochowiec, J}, title = {Major Depressive Disorder and gut microbiota - Association not causation. A scoping review.}, journal = {Progress in neuro-psychopharmacology & biological psychiatry}, volume = {106}, number = {}, pages = {110111}, doi = {10.1016/j.pnpbp.2020.110111}, pmid = {32976952}, issn = {1878-4216}, mesh = {Animals ; Antidepressive Agents/adverse effects/*therapeutic use ; Brain/drug effects/*metabolism ; Brain-Gut Axis/drug effects/*physiology ; Depressive Disorder, Major/diet therapy/drug therapy/*metabolism ; Gastrointestinal Microbiome/drug effects/*physiology ; Humans ; Observational Studies as Topic/methods ; Probiotics/administration & dosage ; }, abstract = {One very promising hypothesis of Major Depressive Disorder (MDD) pathogenesis is the gut-brain axis (GBA) dysfunction, which can lead to subclinical inflammation, hypothalamic-pituitary (HPA) axis dysregulation, and altered neural, metabolic and endocrine pathways. One of the most important parts of GBA is gut microbiota, which was shown to regulate different functions in the central nervous system (CNS). The purpose of this scoping review was to present the current state of research on the relationship between MDD and gut microbiota and extract causal relationships. Further, we presented the relationship between the use of probiotics and antidepressants, and the microbiota changes. We evaluated the data from 27 studies aimed to investigate microbial fingerprints associated with depression phenotype. We abstracted data from 16 and 11 observational and clinical studies, respectively; the latter was divided into trials evaluating the effects of psychiatric treatment (n = 3) and probiotic intervention (n = 9) on the microbiome composition and function. In total, the data of 1187 individuals from observational studies were assessed. In clinical studies, there were 490 individuals analysed. In probiotic studies, 220 and 218 patients with MDD received the intervention and non-active study comparator, respectively. It was concluded that in MDD, the microbiota is altered. Although the mechanism of this relationship is unknown, we hypothesise that the taxonomic changes observed in patients with MDD are associated with bacterial proinflammatory activity, reduced Schort Chain Fatty Acids (SCFAs) production, impaired intestinal barrier integrity and neurotransmitter production, impaired carbohydrates, tryptophane and glutamate metabolic pathways. However, only in few publications this effect was confirmed by metagenomic, metabolomic analysis, or by assessment of immunological parameters or intestinal permeability markers. Future research requires standardisation process starting from patient selection, material collection, DNA sequencing, and bioinformatic analysis. We did not observe whether antidepressive medications influence on gut microbiota, but the use of psychobiotics in patients with MDD has great prospects; however, this procedure requires also standardisation and thorough mechanistic research. The microbiota should be treated as an environmental element, which considers the aetiopathogenesis of the disease and provides new possibilities for monitoring and treating patients with MDD.}, } @article {pmid32975702, year = {2021}, author = {Omori, M and Kato-Kogoe, N and Sakaguchi, S and Fukui, N and Yamamoto, K and Nakajima, Y and Inoue, K and Nakano, H and Motooka, D and Nakano, T and Nakamura, S and Ueno, T}, title = {Comparative evaluation of microbial profiles of oral samples obtained at different collection time points and using different methods.}, journal = {Clinical oral investigations}, volume = {25}, number = {5}, pages = {2779-2789}, pmid = {32975702}, issn = {1436-3771}, mesh = {Humans ; *Microbiota ; Mouthwashes ; RNA, Ribosomal, 16S/genetics ; *Saliva ; Specimen Handling ; }, abstract = {OBJECTIVES: Recently, the oral microbiome has been found to be associated with oral and general health status. Although various oral sample collection protocols are available, the potential differences between the results yielded by these protocols remain unclear. In this study, we aimed to determine the effects of different time points and methods of oral sample collection on the outcomes of microbiome analysis.

MATERIALS AND METHODS: Oral samples were collected from eight healthy individuals at four different time points: 2 h after eating, immediately after teeth brushing, immediately after waking up, and 2 h after eating on the subsequent day. Four methods of saliva collection were evaluated: spitting, gum chewing, cotton swab, and oral rinse. Oral microbiomes of these samples were compared by analyzing the bacterial 16S rRNA gene sequence data.

RESULTS: The oral microbial composition at the genus level was similar among all sample collection time points and methods. Alpha diversity was not significantly different among the groups, whereas beta diversity was different between the spitting and cotton swab methods. Compared with the between-subject variations, the weighted UniFrac distances between the groups were not minor.

CONCLUSIONS: Although the oral microbiome profiles obtained at different collection time points and using different methods were similar, some differences were detected.

CLINICAL RELEVANCE: The results of the present study suggest that although all the described protocols are useful, comparisons among microbiomes of samples collected by different methods are not appropriate. Researchers must be aware of the issues regarding the impact of saliva collection methods.}, } @article {pmid32975677, year = {2021}, author = {Ouarabi, L and Drider, D and Taminiau, B and Daube, G and Bendali, F and Lucau-Danila, A}, title = {Vaginal Microbiota: Age Dynamic and Ethnic Particularities of Algerian Women.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {1020-1029}, pmid = {32975677}, issn = {1432-184X}, mesh = {*Ethnicity ; Female ; Humans ; Lactobacillus/genetics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Vagina ; }, abstract = {The composition of the vaginal microbiota is a key element for maintaining gynecological and reproductive health. With the aim of obtaining an accurate overview of the vaginal microbiota of Algerian women, in terms of their age and ethnic group, we conducted a 16S rRNA gene targeted metagenomic analysis of 100 vaginal samples taken from healthy childbearing and menopausal women. These data were used to establish the pattern of the vaginal microbiota during reproductive and postreproductive phases. Hormone levels were correlated to changes in microbial composition for menopausal women. The ethnic comparison revealed a particular microbiota profile for Algerian women, with a dominance of CST III and CST I. A rapid qPCR method developed by the authors was successfully used to identify the vaginal bacterial pattern for a customized gynecological management.}, } @article {pmid32975580, year = {2020}, author = {Bhattacharya, S and Roy, C and Mandal, S and Sarkar, J and Rameez, MJ and Mondal, N and Mapder, T and Chatterjee, S and Pyne, P and Alam, M and Haldar, PK and Roy, R and Fernandes, S and Peketi, A and Chakraborty, R and Mazumdar, A and Ghosh, W}, title = {Aerobic microbial communities in the sediments of a marine oxygen minimum zone.}, journal = {FEMS microbiology letters}, volume = {367}, number = {19}, pages = {}, pmid = {32975580}, issn = {1574-6968}, mesh = {Aerobiosis ; Aquatic Organisms/*metabolism ; Bacteria/classification/*metabolism ; Geologic Sediments/*microbiology ; Microbiota/*physiology ; Oceans and Seas ; Oxygen/*metabolism ; }, abstract = {The ecology of aerobic microorganisms is never explored in marine oxygen minimum zone (OMZ) sediments. Here we reveal aerobic bacterial communities along ∼3 m sediment-horizons of the eastern Arabian Sea OMZ. Sulfide-containing sediment-cores retrieved from 530 mbsl (meters beneath the sea-level) and 580 mbsl were explored at 15-30 cm intervals, using metagenomics, pure-culture-isolation, genomics and metatranscriptomics. Genes for aerobic respiration, and oxidation of methane/ammonia/alcohols/thiosulfate/sulfite/organosulfur-compounds, were detected in the metagenomes from all 25 sediment-samples explored. Most probable numbers for aerobic chemolithoautotrophs and chemoorganoheterotrophs at individual sample-sites were up to 1.1 × 107 (g sediment)-1. The sediment-sample collected from 275 cmbsf (centimeters beneath the seafloor) of the 530-mbsl-core yielded many such obligately aerobic isolates belonging to Cereibacter, Guyparkeria, Halomonas, Methylophaga, Pseudomonas and Sulfitobacter which died upon anaerobic incubation, despite being provided with all possible electron acceptors and fermentative substrates. High percentages of metatranscriptomic reads from the 275 cmbsf sediment-sample, and metagenomic reads from all 25 sediment-samples, matched the isolates' genomic sequences including those for aerobic metabolisms, genetic/environmental information processing and cell division, thereby illustrating the bacteria's in-situ activity, and ubiquity across the sediment-horizons, respectively. The findings hold critical implications for organic carbon sequestration/remineralization, and inorganic compounds oxidation, within the sediment realm of global marine OMZs.}, } @article {pmid32974807, year = {2021}, author = {Xu, AA and Hoffman, K and Gurwara, S and White, DL and Kanwal, F and El-Serag, HB and Petrosino, JF and Jiao, L}, title = {Oral Health and the Altered Colonic Mucosa-Associated Gut Microbiota.}, journal = {Digestive diseases and sciences}, volume = {66}, number = {9}, pages = {2981-2991}, pmid = {32974807}, issn = {1573-2568}, support = {I01 CX001430/CX/CSRD VA/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 CA172880/CA/NCI NIH HHS/United States ; }, mesh = {Bacterial Load/methods ; Biopsy/methods ; *Colon/microbiology/pathology ; Correlation of Data ; Female ; Gastrointestinal Microbiome/genetics/immunology ; Humans ; *Inflammation/immunology/microbiology ; Life Style ; Male ; *Microbiota/genetics/immunology ; Middle Aged ; Oral Health ; *Periodontal Diseases/diagnosis/epidemiology ; RNA, Ribosomal, 16S/isolation & purification ; Sequence Analysis, DNA/methods ; *Tooth Loss/diagnosis/epidemiology ; }, abstract = {BACKGROUND: Systemic diseases have been associated with oral health and gut microbiota. We examined the association between oral health and the community composition and structure of the adherent colonic gut microbiota.

METHODS: We obtained 197 snap-frozen colonic biopsies from 62 colonoscopy-confirmed polyp-free individuals. Microbial DNA was sequenced for the 16S rRNA V4 region using the Illumina MiSeq, and the sequences were assigned to the operational taxonomic unit based on SILVA. We used a questionnaire to ascertain tooth loss, gum disease, and lifestyle factors. We compared biodiversity and relative abundance of bacterial taxa based on the amount of tooth loss and the presence of gum disease. The multivariable negative binomial regression model for panel data was used to estimate the association between the bacterial count and oral health. False discovery rate-adjusted P value (q value) < .05 indicated statistical significance.

RESULTS: More tooth loss and gum disease were associated with lower bacterial alpha diversity. The relative abundance of Faecalibacterium was lower (q values < .05) with more tooth loss. The association was significant after adjusting for age, ethnicity, obesity, smoking, alcohol use, hypertension, diabetes, and the colon segment. The relative abundance of Bacteroides was higher in those with gum disease.

CONCLUSIONS: Oral health was associated with alteration in the community composition and structure of the adherent gut bacteria in the colon. The reduced anti-inflammatory Faecalibacterium in participants with more tooth loss may indicate systemic inflammation. Future studies are warranted to confirm our findings and investigate the systemic role of Faecalibacterium.}, } @article {pmid32973805, year = {2020}, author = {Xu, R and Tan, C and He, Y and Wu, Q and Wang, H and Yin, J}, title = {Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Encephalitis: A Chinese Pilot Study.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {1994}, pmid = {32973805}, issn = {1664-3224}, mesh = {Adult ; Aged ; Biomarkers ; Blood-Brain Barrier/metabolism ; China ; *Disease Susceptibility ; *Dysbiosis ; Encephalitis/diagnosis/*etiology/*metabolism/mortality ; Fatty Acids, Volatile/*metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Permeability ; Pilot Projects ; Prognosis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Encephalitis, the inflammation of the brain, may be caused by an infection or an autoimmune reaction. However, few researches were focused on the gut microbiome characteristics in encephalitis patients.

METHODS: A prospective observational study was conducted in an academic hospital in Guangzhou from February 2017 to February 2018. Patients with encephalitis were recruited. Fecal and serum samples were collected at admission. Healthy volunteers were enrolled from a community. Disease severity scores were recorded by specialized physicians, including Glasgow Coma Scale (GCS), Sequential Organ Failure Assessment (SOFA), and Acute Physiology and Chronic Health Evaluation-II (APACHE-II). 16S rRNA sequence was performed to analyze the gut microbiome, then the α-diversities and β-diversities were estimated. Short-chain fatty acids (SCFAs) were extracted from fecal samples and determined by gas chromatography-mass spectrometry. Serum D-lactate (D-LA), intestinal fatty acid-binding protein (iFABP), lipopolysaccharide (LPS), and lipopolysaccharide-binding protein (LBP) were measured by enzyme-linked immunosorbent assay (ELISA). The associations among microbial indexes and clinical parameters were evaluated by Spearman correlation analysis.

RESULTS: In total, twenty-eight patients were recruited for analysis (median age 46 years; 82.1% male; median GCS 6.5; median SOFA 6.5; median APACHE-II 14.5). Twenty-eight age- and sex-matched healthy subjects were selected as controls. The β-diversities between patients and healthy subjects were significantly different. The α-diversities did not show significant differences between these two groups. In the patient group, the abundances of Bacteroidetes, Proteobacteria, and Bacilli were significantly enriched. Accordingly, fecal SCFA levels were decreased in the patient group, whereas serum D-LA, iFABP, LPS, and LBP levels were increased compared with those in healthy subjects. Correlation analyses showed that disease severity had positive correlations with Proteobacteria and Akkermansia but negative correlations with Firmicutes, Clostridia, and Ruminococcaceae abundances. The cerebrospinal fluid albumin-to-serum albumin ratio (CSAR) was positively related to the α-diversity but negatively correlated with the fecal butyrate concentration.

CONCLUSION: Gut microbiota disruption was observed in encephalitis patients, which manifested as pathogen dominance and health-promoting commensal depletion. Disease severity and brain damage may have associations with the gut microbiota or its metabolites. The causal relationship should be further explored in future studies.}, } @article {pmid32972462, year = {2020}, author = {Xue, Y and Lin, L and Hu, F and Zhu, W and Mao, S}, title = {Disruption of ruminal homeostasis by malnutrition involved in systemic ruminal microbiota-host interactions in a pregnant sheep model.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {138}, pmid = {32972462}, issn = {2049-2618}, mesh = {Animals ; Diet/veterinary ; Fatty Acids, Volatile/metabolism ; Female ; *Homeostasis ; *Host Microbial Interactions ; Malnutrition/*microbiology ; Microbiota/genetics/*physiology ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sheep/*microbiology ; }, abstract = {BACKGROUND: Undernutrition is a prevalent and spontaneous condition in animal production which always affects microbiota-host interaction in gastrointestinal tract. However, how undernutrition affects crosstalk homeostasis is largely unknown. Here, we discover how undernutrition affects microbial profiles and subsequently how microbial metabolism affects the signal transduction and tissue renewal in ruminal epithelium, clarifying the detrimental effect of undernutrition on ruminal homeostasis in a pregnant sheep model.

RESULTS: Sixteen pregnant ewes (115 days of gestation) were randomly and equally assigned to the control (CON) and severe feed restriction (SFR) groups. Ewes on SFR treatment were restricted to a 30% level of ad libitum feed intake while the controls were fed normally. After 15 days, all ewes were slaughtered to collect ruminal digesta for 16S rRNA gene and metagenomic sequencing and ruminal epithelium for transcriptome sequencing. Results showed that SFR diminished the levels of ruminal volatile fatty acids and microbial proteins and repressed the length, width, and surface area of ruminal papillae. The 16S rRNA gene analysis indicated that SFR altered the relative abundance of ruminal bacterial community, showing decreased bacteria about saccharide degradation (Saccharofermentans and Ruminococcus) and propionate genesis (Succiniclasticum) but increased butyrate producers (Pseudobutyrivibrio and Papillibacter). Metagenome analysis displayed that genes related to amino acid metabolism, acetate genesis, and succinate-pathway propionate production were downregulated upon SFR, while genes involved in butyrate and methane genesis and acrylate-pathway propionate production were upregulated. Transcriptome and real-time PCR analysis of ruminal epithelium showed that downregulated collagen synthesis upon SFR lowered extracellular matrix-receptor interaction, inactivated JAK3-STAT2 signaling pathway, and inhibited DNA replication and cell cycle.

CONCLUSIONS: Generally, undernutrition altered rumen bacterial community and function profile to decrease ruminal energy retention, promoted epithelial glucose and fatty acid catabolism to elevate energy supply, and inhibited the proliferation of ruminal epithelial cells. These findings provide the first insight into the systemic microbiota-host interactions that are involved in disrupting the ruminal homeostasis under a malnutrition pattern. Video Abstract.}, } @article {pmid32972018, year = {2020}, author = {Hewson, I and Johnson, MR and Tibbetts, IR}, title = {An Unconventional Flavivirus and Other RNA Viruses in the Sea Cucumber (Holothuroidea; Echinodermata) Virome.}, journal = {Viruses}, volume = {12}, number = {9}, pages = {}, pmid = {32972018}, issn = {1999-4915}, mesh = {Animals ; DNA Viruses ; Echinodermata/*virology ; Ecology ; Flavivirus/*classification/genetics ; Genome, Viral ; Metagenome ; Metagenomics ; RNA Viruses/*classification/genetics ; Sea Cucumbers/*virology ; Seawater/virology ; *Virome ; }, abstract = {Sea cucumbers (Holothuroidea; Echinodermata) are ecologically significant constituents of benthic marine habitats. We surveilled RNA viruses inhabiting eight species (representing four families) of holothurian collected from four geographically distinct locations by viral metagenomics, including a single specimen of Apostichopus californicus affected by a hitherto undocumented wasting disease. The RNA virome comprised genome fragments of both single-stranded positive sense and double stranded RNA viruses, including those assigned to the Picornavirales, Ghabrivirales, and Amarillovirales. We discovered an unconventional flavivirus genome fragment which was most similar to a shark virus. Ghabivirales-like genome fragments were most similar to fungal totiviruses in both genome architecture and homology and had likely infected mycobiome constituents. Picornavirales, which are commonly retrieved in host-associated viral metagenomes, were similar to invertebrate transcriptome-derived picorna-like viruses. The greatest number of viral genome fragments was recovered from the wasting A. californicus library compared to the asymptomatic A. californicus library. However, reads from the asymptomatic library recruited to nearly all recovered wasting genome fragments, suggesting that they were present but not well represented in the grossly normal specimen. These results expand the known host range of flaviviruses and suggest that fungi and their viruses may play a role in holothurian ecology.}, } @article {pmid32971520, year = {2021}, author = {Watts, AM and West, NP and Zhang, P and Smith, PK and Cripps, AW and Cox, AJ}, title = {The Gut Microbiome of Adults with Allergic Rhinitis Is Characterised by Reduced Diversity and an Altered Abundance of Key Microbial Taxa Compared to Controls.}, journal = {International archives of allergy and immunology}, volume = {182}, number = {2}, pages = {94-105}, doi = {10.1159/000510536}, pmid = {32971520}, issn = {1423-0097}, mesh = {Adult ; Biodiversity ; Biomarkers ; Case-Control Studies ; *Disease Susceptibility ; Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Rhinitis, Allergic/blood/diagnosis/*etiology ; Young Adult ; }, abstract = {INTRODUCTION: Unique gut microbial colonisation patterns are associated with the onset of allergic disease in infants; however, there is insufficient evidence to determine if aberrant microbial composition patterns persist in adult allergic rhinitis (AR) sufferers.

OBJECTIVE: To compare the gut microbiome composition between adult AR sufferers and controls.

METHODS: Gut microbial composition in stool samples was compared between 57 adult AR sufferers (39.06 ± 13.29 years) and 23 controls (CG; 36.55 ± 10.51 years) via next-generation sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene. Taxonomic classification and identity assignment was performed using a reference-based approach with the NCBI database of 16S rRNA gene sequences.

RESULTS: Species richness determined via the Shannon index was significantly reduced in the AR cohort compared to the CG (4.35 ± 0.59 in AR vs. 4.65 ± 0.55 in CG, p = 0.037); trends for reductions in operational taxonomic unit (OTU) counts, inverse Simpson, and CHAO1 diversity indices were also noted. Bacteroidetes (p = 0.014) was significantly more abundant in the AR group than in the CG. In contrast, the Firmicutes phylum was significantly less abundant in the AR group than in the CG (p = 0.006). An increased abundance of Parabacteroides (p = 0.008) and a reduced abundance of Oxalobacter (p = 0.001) and Clostridiales (p = 0.005) were also observed in the AR cohort compared to the CG.

CONCLUSION: Adult AR sufferers have a distinct gut microbiome profile, marked by a reduced microbial diversity and altered abundance of certain microbes compared to controls. The results of this study provide evidence that unique gut microbial patterns occur in AR sufferers in adulthood and warrant further examination in the form of mechanistic studies.}, } @article {pmid32970908, year = {2021}, author = {da Costa, AC and Moron, AF and Forney, LJ and Linhares, IM and Sabino, E and Costa, SF and Mendes-Correa, MC and Witkin, SS}, title = {Identification of bacteriophages in the vagina of pregnant women: a descriptive study.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {128}, number = {6}, pages = {976-982}, doi = {10.1111/1471-0528.16528}, pmid = {32970908}, issn = {1471-0528}, support = {//Bill and Melinda Gates Foundation/ ; //Brazilian Ministry of Health/ ; 401626/2013-0//Brazilian National Research Council/ ; }, mesh = {Adult ; *Bacteriophages/classification/genetics/isolation & purification ; Brazil ; Female ; Gestational Age ; Humans ; Metagenome ; Metagenomics/methods/statistics & numerical data ; Microbiota/*physiology ; Pregnancy ; Pregnancy Outcome/epidemiology ; Vagina/*microbiology ; }, abstract = {OBJECTIVE: To determine the presence and identity of extracellular bacteriophage (phage) families, genera and species in the vagina of pregnant women.

DESIGN: Descriptive, observational cohort study.

SETTING: São Paulo, Brazil.

POPULATION: Pregnant women at 21-24 weeks' gestation.

METHODS: Vaginal samples from 107 women whose vaginal microbiome and pregnancy outcomes were previously determined were analysed for phages by metagenomic sequencing.

MAIN OUTCOME MEASURES: Identification of phage families, genera and species.

RESULTS: Phages were detected in 96 (89.7%) of the samples. Six different phage families were identified: Siphoviridae in 69.2%, Myoviridae in 49.5%, Microviridae in 37.4%, Podoviridae in 20.6%, Herelleviridae in 10.3% and Inviridae in 1.9% of the women. Four different phage families were present in 14 women (13.1%), three families in 20 women (18.7%), two families in 31 women (29.1%) and one family in 31 women (29.1%). The most common phage species detected were Bacillus phages in 48 (43.6%), Escherichia phages in 45 (40.9%), Staphylococcus phages in 40 (36.4%), Gokushovirus in 33 (30.0%) and Lactobacillus phages in 29 (26.4%) women. In a preliminary exploratory analysis, there were no associations between a particular phage family, the number of phage families present in the vagina or any particular phage species and either gestational age at delivery or the bacterial community state type present in the vagina.

CONCLUSIONS: Multiple phages are present in the vagina of most mid-trimester pregnant women.

TWEETABLE ABSTRACT: Bacteriophages are present in the vagina of most pregnant women.}, } @article {pmid32968156, year = {2020}, author = {Laue, HE and Korrick, SA and Baker, ER and Karagas, MR and Madan, JC}, title = {Prospective associations of the infant gut microbiome and microbial function with social behaviors related to autism at age 3 years.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15515}, pmid = {32968156}, issn = {2045-2322}, support = {P42 ES007373/ES/NIEHS NIH HHS/United States ; P30 CA023108/CA/NCI NIH HHS/United States ; P01ES022832/ES/NIEHS NIH HHS/United States ; RD-83544201/EPA/EPA/United States ; P20 ES018175/ES/NIEHS NIH HHS/United States ; P01 ES022832/ES/NIEHS NIH HHS/United States ; R25 CA134286/CA/NCI NIH HHS/United States ; P20 GM104416/GM/NIGMS NIH HHS/United States ; P20GM104416/GM/NIGMS NIH HHS/United States ; UH3 OD023275/OD/NIH HHS/United States ; }, mesh = {Autism Spectrum Disorder/etiology/*microbiology/psychology ; Child, Preschool ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Infant ; Male ; Prospective Studies ; Psychological Tests ; RNA, Ribosomal, 16S/genetics ; *Social Behavior ; }, abstract = {The hypothesized link between gut bacteria and autism spectrum disorder (ASD) has been explored through animal models and human studies with microbiome assessment after ASD presentation. We aimed to prospectively characterize the association between the infant/toddler gut microbiome and ASD-related social behaviors at age 3 years. As part of an ongoing birth cohort gut bacterial diversity, structure, taxa, and function at 6 weeks (n = 166), 1 year (n = 158), 2 years (n = 129), and 3 years (n = 140) were quantified with 16S rRNA gene and shotgun metagenomic sequencing (n = 101 six weeks, n = 103 one year). ASD-related social behavior was assessed at age 3 years using Social Responsiveness Scale (SRS-2) T-scores. Covariate-adjusted linear and permutation-based models were implemented. Microbiome structure at 1 year was associated with SRS-2 total T-scores (p = 0.01). Several taxa at 1, 2, and 3 years were associated with SRS-2 performance, including many in the Lachnospiraceae family. Higher relative abundance of Adlercreutzia equolifaciens and Ruminococcus torques at 1 year related to poorer SRS-2 performance. Two functional pathways, L-ornithine and vitamin B6 biosynthesis, were associated with better social skills at 3 years. Our results support potential associations between early-childhood gut microbiome and social behaviors. Future mechanistic studies are warranted to pinpoint sensitive targets for intervention.}, } @article {pmid32968071, year = {2020}, author = {Lavrinienko, A and Tukalenko, E and Mousseau, TA and Thompson, LR and Knight, R and Mappes, T and Watts, PC}, title = {Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {312}, pmid = {32968071}, issn = {2052-4463}, support = {324605//Academy of Finland (Suomen Akatemia)/International ; }, mesh = {Animals ; Arvicolinae/*microbiology ; Bacteria/*classification ; *Gastrointestinal Microbiome ; Genome, Bacterial ; }, abstract = {Vertebrate gut microbiota provide many essential services to their host. To better understand the diversity of such services provided by gut microbiota in wild rodents, we assembled metagenome shotgun sequence data from a small mammal, the bank vole Myodes glareolus (Rodentia, Cricetidae). We were able to identify 254 metagenome assembled genomes (MAGs) that were at least 50% (n = 133 MAGs), 80% (n = 77 MAGs) or 95% (n = 44 MAGs) complete. As typical for a rodent gut microbiota, these MAGs are dominated by taxa assigned to the phyla Bacteroidetes (n = 132 MAGs) and Firmicutes (n = 80), with some Spirochaetes (n = 15) and Proteobacteria (n = 11). Based on coverage over contigs, Bacteroidetes were estimated to be most abundant group, followed by Firmicutes, Spirochaetes and Proteobacteria. These draft bacterial genomes can be used freely to determine the likely functions of gut microbiota community composition in wild rodents.}, } @article {pmid32966856, year = {2020}, author = {Hoque, MN and Istiaq, A and Rahman, MS and Islam, MR and Anwar, A and Siddiki, AMAMZ and Sultana, M and Crandall, KA and Hossain, MA}, title = {Microbiome dynamics and genomic determinants of bovine mastitis.}, journal = {Genomics}, volume = {112}, number = {6}, pages = {5188-5203}, doi = {10.1016/j.ygeno.2020.09.039}, pmid = {32966856}, issn = {1089-8646}, mesh = {Animals ; Cattle ; Drug Resistance, Microbial/genetics ; Female ; Genome, Archaeal ; Genome, Bacterial ; Genome, Viral ; Mastitis, Bovine/*microbiology/virology ; Metagenomics ; Microbiota/*genetics ; Milk/microbiology ; Virulence Factors/genetics ; }, abstract = {The milk of lactating cows presents a complex ecosystem of interconnected microbial communities which can influence the pathophysiology of mastitis. We hypothesized possible dynamic shifts of microbiome composition and genomic features with different pathological conditions of mastitis (Clinical Mastitis; CM, Recurrent CM; RCM, Subclinical Mastitis; SCM). To evaluate this hypothesis, we employed whole metagenome sequencing (WMS) in 20 milk samples (CM, 5; RCM, 6; SCM, 4; H, 5) to unravel the microbiome dynamics, interrelation, and relevant metabolic functions. The WMS data mapped to 442 bacterial, 58 archaeal and 48 viral genomes with distinct variation in microbiome composition (CM > H > RCM > SCM). Furthermore, we identified a number of microbial genomic features, including 333, 304, 183 and 50 virulence factors-associated genes (VFGs) and 48, 31, 11 and 6 antibiotic resistance genes (ARGs) in CM, RCM, SCM, and H-microbiomes, respectively. We also detected different metabolic pathway and functional genes associated with mastitis pathogenesis. Therefore, profiling microbiome dynamics in different conditions of mastitis and associated microbial genomic features contributes to developing microbiome-based diagnostics and therapeutics for bovine mastitis.}, } @article {pmid32964256, year = {2021}, author = {López-Pérez, ME and Saldaña-Robles, A and Zanor, GA and Ibarra, JE and Del Rincón-Castro, MC}, title = {Microbiomes in agricultural and mining soils contaminated with arsenic in Guanajuato, Mexico.}, journal = {Archives of microbiology}, volume = {203}, number = {2}, pages = {499-511}, pmid = {32964256}, issn = {1432-072X}, mesh = {Agriculture ; Arsenic/*toxicity ; Bacteria/classification/drug effects/*genetics ; *Biodiversity ; Fungi/classification/drug effects/*genetics ; Metagenome ; Mexico ; Microbiota/drug effects/genetics ; Mining ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants/analysis/toxicity ; }, abstract = {In this report, physical and chemical properties, and total arsenic (As) concentrations were analyzed in agricultural (MASE) and mining soils (SMI) in the State of Guanajuato, México. Additionally, a metagenomic analysis of both types of soils was the bases for the identification and selection of bacteria and fungi resistant to As. The SMI soil showed higher concentration of As (39 mg kg[-1]) as compared to MASE soil (15 mg kg[-1]). The metagenome showed a total of 175,240 reads from both soils. MASE soil showed higher diversity of bacteria, while the SMI soil showed higher diversity of fungi. 16S rRNA analysis showed that the phylum Proteobacteria showed the highest proportion (39.6% in MASE and 36.4% in SMI) and Acidobacteria was the second most representative (24.2% in SMI and 11.6% in MASE). 18S rRNA analysis, showed that the phylum Glomeromycota was found only in the SMI soils (11.6%), while Ascomycota was the most abundant, followed by Basidiomycota, and Zygomycota, in both soils. Genera Bacillus and Penicillium were able to grow in As concentrations as high as 5 and 10 mM, reduced As (V) to As (III), and removed As at 9.8% and 12.1% rates, respectively. When aoxB, arsB, ACR3(1), ACR3(2,) and arrA genes were explored, only the arsB gene was identified in Bacillus sp., B. simplex, and B. megaterium. In general, SMI soils showed more microorganisms resistant to As than MASE soils. Bacteria and fungi selected in this work may show potential to be used as bioremediation agents in As contaminated soils.}, } @article {pmid32963345, year = {2021}, author = {Zamkovaya, T and Foster, JS and de Crécy-Lagard, V and Conesa, A}, title = {A network approach to elucidate and prioritize microbial dark matter in microbial communities.}, journal = {The ISME journal}, volume = {15}, number = {1}, pages = {228-244}, pmid = {32963345}, issn = {1751-7370}, mesh = {Bacteria/genetics ; *Ecosystem ; Metagenome ; Microbial Consortia ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbes compose most of the biomass on the planet, yet the majority of taxa remain uncharacterized. These unknown microbes, often referred to as "microbial dark matter," represent a major challenge for biology. To understand the ecological contributions of these Unknown taxa, it is essential to first understand the relationship between unknown species, neighboring microbes, and their respective environment. Here, we establish a method to study the ecological significance of "microbial dark matter" by building microbial co-occurrence networks from publicly available 16S rRNA gene sequencing data of four extreme aquatic habitats. For each environment, we constructed networks including and excluding unknown organisms at multiple taxonomic levels and used network centrality measures to quantitatively compare networks. When the Unknown taxa were excluded from the networks, a significant reduction in degree and betweenness was observed for all environments. Strikingly, Unknown taxa occurred as top hubs in all environments, suggesting that "microbial dark matter" play necessary ecological roles within their respective communities. In addition, novel adaptation-related genes were detected after using 16S rRNA gene sequences from top-scoring hub taxa as probes to blast metagenome databases. This work demonstrates the broad applicability of network metrics to identify and prioritize key Unknown taxa and improve understanding of ecosystem structure across diverse habitats.}, } @article {pmid32962897, year = {2020}, author = {Albaugh, VL}, title = {Comment on: Fecal metagenomics and metabolomics reveal gut microbial changes after bariatric surgery.}, journal = {Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery}, volume = {16}, number = {11}, pages = {1782-1783}, doi = {10.1016/j.soard.2020.08.006}, pmid = {32962897}, issn = {1878-7533}, mesh = {*Bariatric Surgery ; Feces ; *Gastrointestinal Microbiome ; Humans ; Metabolomics ; Metagenomics ; }, } @article {pmid32960892, year = {2020}, author = {Crandall, SG and Gold, KM and Jiménez-Gasco, MDM and Filgueiras, CC and Willett, DS}, title = {A multi-omics approach to solving problems in plant disease ecology.}, journal = {PloS one}, volume = {15}, number = {9}, pages = {e0237975}, pmid = {32960892}, issn = {1932-6203}, mesh = {*Ecology ; Genomics/*methods ; Metabolomics/*methods ; Metagenomics/*methods ; Microbiota ; Plant Diseases/*etiology ; Plants/*immunology/metabolism ; Proteomics/*methods ; Systems Biology ; }, abstract = {The swift rise of omics-approaches allows for investigating microbial diversity and plant-microbe interactions across diverse ecological communities and spatio-temporal scales. The environment, however, is rapidly changing. The introduction of invasive species and the effects of climate change have particular impact on emerging plant diseases and managing current epidemics. It is critical, therefore, to take a holistic approach to understand how and why pathogenesis occurs in order to effectively manage for diseases given the synergies of changing environmental conditions. A multi-omics approach allows for a detailed picture of plant-microbial interactions and can ultimately allow us to build predictive models for how microbes and plants will respond to stress under environmental change. This article is designed as a primer for those interested in integrating -omic approaches into their plant disease research. We review -omics technologies salient to pathology including metabolomics, genomics, metagenomics, volatilomics, and spectranomics, and present cases where multi-omics have been successfully used for plant disease ecology. We then discuss additional limitations and pitfalls to be wary of prior to conducting an integrated research project as well as provide information about promising future directions.}, } @article {pmid32960315, year = {2021}, author = {Sodhi, KK and Kumar, M and Singh, DK}, title = {Assessing the bacterial diversity and functional profiles of the River Yamuna using Illumina MiSeq sequencing.}, journal = {Archives of microbiology}, volume = {203}, number = {1}, pages = {367-375}, pmid = {32960315}, issn = {1432-072X}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; DNA, Bacterial/genetics ; *High-Throughput Nucleotide Sequencing ; Industrial Waste ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; }, abstract = {A small percentage of the total freshwater on Earth is represented by river water. Microbes have an essential role to play in the biogeochemical cycles, mineralization of organic water, along with xenobiotics degradation. Microbial dynamics are susceptible to environmental stressors which includes pollutants such as antibiotics, metals, and other degradants. River Yamuna is polluted extensively by domestic and industrial wastes. Xenobiotics, when released into the environment, can lead to water pollution. The present study evaluates the microbial diversity in Yamuna River (28°40'5.53'' N, 77°15'0.35'' E) along with the prediction of the metagenome function. In this context, the metagenomic DNA was extracted and sequencing was done on Illumina@MiSeq platform. The total number of OTUs picked was 41,994, out of which 74% were classified within the kingdom Bacteria. 35% of the OTUs were assigned to phylum Proteobacteria, followed by Bacteriodetes (22%), whereas 26% of OTUs were unassigned. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used to predict metagenomic functions using 16S rDNA as a marker. Metagenomic reads were assigned to the Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous (COG), and Gene Ontology (GO). Functional characterization reveals the presence of methyl-accepting chemotaxis protein which is an important adaptation for the microbes in the environment. The enzymes can be mapped for the bioremediation of xenobiotics. Information obtained from the amplicon sequencing of River Yamuna, collaborated with "omic" studies, may help in the design of bioremediation strategies and can be used for environmental clean-up of pollutants.}, } @article {pmid32958861, year = {2020}, author = {Tan, SK and Granados, AC and Bouquet, J and Hoy-Schulz, YE and Green, L and Federman, S and Stryke, D and Haggerty, TD and Ley, C and Yeh, MT and Jannat, K and Maldonado, YA and Andino, R and Parsonnet, J and Chiu, CY}, title = {Metagenomic sequencing of stool samples in Bangladeshi infants: virome association with poliovirus shedding after oral poliovirus vaccination.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15392}, pmid = {32958861}, issn = {2045-2322}, support = {R01 HD088837/HD/NICHD NIH HHS/United States ; R01-HD008837/NH/NIH HHS/United States ; UL1 TR003142/TR/NCATS NIH HHS/United States ; R01 HD063142/HD/NICHD NIH HHS/United States ; UL1 RR025744/RR/NCRR NIH HHS/United States ; R01501HD063142/NH/NIH HHS/United States ; TL1 TR001084/TR/NCATS NIH HHS/United States ; Z01 HD008837/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Antibodies, Neutralizing/immunology ; Antibodies, Viral/blood ; Bangladesh/epidemiology ; Feces/virology ; Female ; Humans ; Immunization Schedule ; Infant ; Male ; Metagenome/genetics ; Metagenomics/methods ; Poliomyelitis/virology ; Poliovirus/*genetics/immunology ; Poliovirus Vaccine, Inactivated/immunology ; Poliovirus Vaccine, Oral/*immunology ; Vaccination ; Virome/genetics ; Virus Shedding/*genetics ; }, abstract = {The potential role of enteric viral infections and the developing infant virome in affecting immune responses to the oral poliovirus vaccine (OPV) is unknown. Here we performed viral metagenomic sequencing on 3 serially collected stool samples from 30 Bangladeshi infants following OPV vaccination and compared findings to stool samples from 16 age-matched infants in the United States (US). In 14 Bangladeshi infants, available post-vaccination serum samples were tested for polio-neutralizing antibodies. The abundance (p = 0.006) and richness (p = 0.013) of the eukaryotic virome increased with age and were higher than seen in age-matched US infants (p < 0.001). In contrast, phage diversity metrics remained stable and were similar to those in US infants. Non-poliovirus eukaryotic virus abundance (3.68 log10 vs. 2.25 log10, p = 0.002), particularly from potential viral pathogens (2.78log10 vs. 0.83log10, p = 0.002), and richness (p = 0.016) were inversely associated with poliovirus shedding. Following vaccination, 28.6% of 14 infants tested developed neutralizing antibodies to all three Sabin types and also exhibited higher rates of poliovirus shedding (p = 0.020). No vaccine-derived poliovirus variants were detected. These results reveal an inverse association between eukaryotic virome abundance and poliovirus shedding. Overall gut virome ecology and concurrent viral infections may impact oral vaccine responsiveness in Bangladeshi infants.}, } @article {pmid32958844, year = {2020}, author = {Dalzochio, MS and Périco, E and Dametto, N and Sahlén, G}, title = {Rapid functional traits turnover in boreal dragonfly communities (Odonata).}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15411}, pmid = {32958844}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; *Biological Evolution ; Climate Change ; Ecosystem ; *Environment ; Longitudinal Studies ; Metagenomics/methods ; Odonata/*genetics/metabolism ; Phenotype ; Sweden ; }, abstract = {All natural populations show fluctuations in space or time. This is fundamental for the maintenance of biodiversity, as it allows species to coexist. Long-term ecological studies are rare, mainly due to logistics, but studies like the one presented below recognize the dimensionality of temporal change and the ecological processes that lead to shifts in community composition over time. Here, we used three sampling occasions from a dataset spanning 20 years where dragonflies in central Sweden were monitored. Our aim was to investigate how the prevalence of ecological and biological species traits varied over time measured as Community-level Weighted Means of trait values (CWM). Most CWM values varied significantly between years. Most of the traits changed between the second and the last sampling occasion, but not between the two first ones. These changes could be linked to major changes in species abundance. Our work indicates that fundamental shifts in community structure can occur over a short time, providing environmental drivers act on species turnover. In our case, Climate change and pH levels in lakes are most likely the most important factors.}, } @article {pmid32957925, year = {2020}, author = {Zhao, Z and Cristian, A and Rosen, G}, title = {Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {412}, pmid = {32957925}, issn = {1471-2105}, mesh = {Algorithms ; Bacteria/genetics ; Bayes Theorem ; Gastrointestinal Microbiome/*genetics ; *Genome, Bacterial ; Humans ; *Machine Learning ; Metagenome ; Metagenomics/*methods ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: It is a computational challenge for current metagenomic classifiers to keep up with the pace of training data generated from genome sequencing projects, such as the exponentially-growing NCBI RefSeq bacterial genome database. When new reference sequences are added to training data, statically trained classifiers must be rerun on all data, resulting in a highly inefficient process. The rich literature of "incremental learning" addresses the need to update an existing classifier to accommodate new data without sacrificing much accuracy compared to retraining the classifier with all data.

RESULTS: We demonstrate how classification improves over time by incrementally training a classifier on progressive RefSeq snapshots and testing it on: (a) all known current genomes (as a ground truth set) and (b) a real experimental metagenomic gut sample. We demonstrate that as a classifier model's knowledge of genomes grows, classification accuracy increases. The proof-of-concept naïve Bayes implementation, when updated yearly, now runs in 1/4[th] of the non-incremental time with no accuracy loss.

CONCLUSIONS: It is evident that classification improves by having the most current knowledge at its disposal. Therefore, it is of utmost importance to make classifiers computationally tractable to keep up with the data deluge. The incremental learning classifier can be efficiently updated without the cost of reprocessing nor the access to the existing database and therefore save storage as well as computation resources.}, } @article {pmid32957679, year = {2020}, author = {Rossi, A and Treu, L and Toppo, S and Zschach, H and Campanaro, S and Dutilh, BE}, title = {Evolutionary Study of the Crassphage Virus at Gene Level.}, journal = {Viruses}, volume = {12}, number = {9}, pages = {}, pmid = {32957679}, issn = {1999-4915}, mesh = {Bacteriophages/genetics ; Capsid Proteins/genetics ; DNA Viruses/*genetics ; *Evolution, Molecular ; Feces/virology ; Gastrointestinal Microbiome ; Genome, Viral ; Humans ; Metagenome ; Metagenomics ; Phylogeny ; Viral Proteins/genetics ; Viruses/*genetics ; }, abstract = {crAss-like viruses are a putative family of bacteriophages recently discovered. The eponym of the clade, crAssphage, is an enteric bacteriophage estimated to be present in at least half of the human population and it constitutes up to 90% of the sequences in some human fecal viral metagenomic datasets. We focused on the evolutionary dynamics of the genes encoded on the crAssphage genome. By investigating the conservation of the genes, a consistent variation in the evolutionary rates across the different functional groups was found. Gene duplications in crAss-like genomes were detected. By exploring the differences among the functional categories of the genes, we confirmed that the genes encoding capsid proteins were the most ubiquitous, despite their overall low sequence conservation. It was possible to identify a core of proteins whose evolutionary trees strongly correlate with each other, suggesting their genetic interaction. This group includes the capsid proteins, which are thus established as extremely suitable for rebuilding the phylogenetic tree of this viral clade. A negative correlation between the ubiquity and the conservation of viral protein sequences was shown. Together, this study provides an in-depth picture of the evolution of different genes in crAss-like viruses.}, } @article {pmid32957565, year = {2020}, author = {Zhang, L and Luo, J and Li, X and Guo, S and Shi, D}, title = {16S rRNA Sequencing and Metagenomics Study of Gut Microbiota: Implications of BDB on Type 2 Diabetes Mellitus.}, journal = {Marine drugs}, volume = {18}, number = {9}, pages = {}, pmid = {32957565}, issn = {1660-3397}, support = {JQ201722//Shandong Provincial Natural Science Foundation for Distinguished Young Scholars/ ; 817033540, 81803344//National Natural Science Foundation of China/ ; 2017-CXZX01-1-1, 2017-CXZX01-3-9//Taishan scholar Youth Project of Shandong province, Qingdao Marine Biomedical Science and Technology Innovation Center Project/ ; U1706213//NSFC-Shan-dong Joint Fund/ ; 2019RKE27018//National Program for Support of Top-notch Young Professionals, Key research and development plan (soft science) project of Shandong province/ ; }, mesh = {Animals ; Bacteria/*drug effects/genetics/growth & development/metabolism ; Benzhydryl Compounds/isolation & purification/*pharmacology ; Biomarkers/blood ; Blood Glucose/*drug effects/metabolism ; Catechols/isolation & purification/*pharmacology ; Diabetes Mellitus, Type 2/blood/*drug therapy/microbiology ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects/genetics ; High-Throughput Nucleotide Sequencing ; Hypoglycemic Agents/isolation & purification/*pharmacology ; Male ; *Metagenomics ; Mice, Inbred C57BL ; Rhodophyta/chemistry ; *Ribotyping ; }, abstract = {Gut microbiota has a critical role in metabolic diseases, including type 2 diabetes mellitus (T2DM). 3-bromo-4,5-bis(2,3-dibromo-4,5-dihydroxybenzyl)-1,2-benzenediol (BDB) is a natural bromophenol isolated from marine red alga Rhodomela confervoides. Our latest research showed that BDB could alleviate T2DM in diabetic BKS db mice. To find out whether BDB modulates the composition of the gut microbiota during T2DM treatment, 24 BKS db diabetic mice were randomly grouped to receive BDB (n = 6), metformin (n = 6), or the vehicle (n = 6) for 7 weeks in a blinded manner. Non-diabetic BKS mice (n = 6) were used as normal control. Diabetic mice treated with BDB or metformin demonstrated significant reductions in fasting blood glucose (FBG) levels compared with the vehicle-treated mice in the 7th week. Pyrosequencing of the V3-V4 regions of the 16S rRNA gene revealed the changes of gut microbiota in response to BDB treatment. The result demonstrated short-chain acid (SCFA) producing bacteria Lachnospiraceae and Bacteroides were found to be significantly more abundant in the BDB and metformin treated group than the vehicle-treatment diabetic group. Remarkably, at the genus levels, Akkermansia elevated significantly in the BDB-treatment group. Metagenomic results indicated that BDB may alleviate the metabolic disorder of diabetic mice by promoting propanoate metabolism and inhibiting starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism. In conclusion, our study suggests that the anti-diabetic effect of BDB is closely related to the modulating structure of gut microbiota and the improvement of functional metabolism genes of intestinal microorganisms.}, } @article {pmid32956870, year = {2020}, author = {Kuijper, EJ and Vehreschild, MJGT}, title = {Clinical microbiota and infection.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {26}, number = {11}, pages = {1447}, doi = {10.1016/j.cmi.2020.09.029}, pmid = {32956870}, issn = {1469-0691}, mesh = {Communicable Diseases/microbiology/*pathology ; Drug Resistance, Bacterial ; Gene Expression Profiling ; Humans ; Metagenomics ; *Microbiota ; Periodicals as Topic ; }, } @article {pmid32956679, year = {2021}, author = {Sun, Y and Zuo, T and Cheung, CP and Gu, W and Wan, Y and Zhang, F and Chen, N and Zhan, H and Yeoh, YK and Niu, J and Du, Y and Zhang, F and Wen, Y and Yu, J and Sung, JJY and Chan, PKS and Chan, FKL and Wang, K and Ng, SC and Miao, Y}, title = {Population-Level Configurations of Gut Mycobiome Across 6 Ethnicities in Urban and Rural China.}, journal = {Gastroenterology}, volume = {160}, number = {1}, pages = {272-286.e11}, doi = {10.1053/j.gastro.2020.09.014}, pmid = {32956679}, issn = {1528-0012}, mesh = {Adult ; Body Mass Index ; China ; Diet ; *Ethnicity ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Humans ; Life Style ; Male ; Metagenomics ; *Rural Population ; *Urban Population ; }, abstract = {BACKGROUND & AIMS: Beyond bacteria, the human gastrointestinal tract is host to a vast diversity of fungi, collectively known as the gut mycobiome. Little is known of the impact of geography, ethnicity, and urbanization on the gut mycobiome at a large population level. We aim to delineate the variation of human gut mycobiome and its association with host factors, environmental factors, and diets.

METHODS: Using shotgun metagenomic sequencing, we profiled and compared the fecal mycobiome of 942 healthy individuals across different geographic regions in China (Hong Kong and Yunnan), spanning 6 ethnicities: Han, Zang, Bai, Hani, Dai, and Miao (including both urban and rural residents of each ethnicity). In parallel to fecal sampling, we collected participant metadata (environmental exposure, bowel habits, anthropometrics, and medication), diet, and clinical blood measurement results (a total of 118 variables) and investigated their impact on the gut mycobiome variation in humans.

RESULTS: The human gut mycobiome was highly variable across populations. Urbanization-related factors had the strongest impact on gut mycobiome variation, followed by geography, dietary habit, and ethnicity. The Hong Kong population (highly urbanized) had a significantly lower fungal richness compared with Yunnan population. Saccharomyces cerevisiae was highly enriched in urban compared with rural populations and showed significant inverse correlations with liver pathology-associated blood parameters, including aspartate transaminase, alanine transaminase, gamma-glutamyltransferase, and direct bilirubin. Candida dubliniensis, which was decreased in urban relative to rural populations, showed correlations with host metabolism-related parameters in blood, including a positive correlation with fasting high-density lipoprotein cholesterol levels and a negative correlation with fasting glucose levels. The fungal-blood parameter correlations were highly geography- and ethnicity-specific. Food choices had differential influences on gut mycobiome and bacterial microbiome, where taxa from the same genus tended to be coregulated by food and thereby cobloom. Ethnicity-specific fungal signatures were associated with distinct habitual foods in each ethnic group.

CONCLUSIONS: Our data highlight, for the first time to our knowledge, that geography, urbanization, ethnicity, and habitual diet play an important role in shaping the gut mycobiome composition. Gut fungal configurations in combination with population characteristics (such as residing region, ethnicity, diet, lifestyle) influence host metabolism and health.}, } @article {pmid32955994, year = {2020}, author = {Mohamed, I and Zakeer, S and Azab, M and Hanora, A}, title = {Changes in Vaginal Microbiome in Pregnant and Nonpregnant Women with Bacterial Vaginosis: Toward Microbiome Diagnostics?.}, journal = {Omics : a journal of integrative biology}, volume = {24}, number = {10}, pages = {602-614}, doi = {10.1089/omi.2020.0096}, pmid = {32955994}, issn = {1557-8100}, mesh = {Case-Control Studies ; Disease Management ; Disease Susceptibility ; Female ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Pregnancy ; Pregnancy Complications, Infectious/*diagnosis/*microbiology ; Vagina/*microbiology ; Vaginosis, Bacterial/*diagnosis/*microbiology ; }, abstract = {Bacterial vaginosis (BV) is highly common, adversely affecting the health of millions of women. New therapeutic targets and diagnostics are urgently needed for BV. Microbiome research offers new prospects in this context. We report here original findings on changes in the vaginal microbiome in pregnant and nonpregnant women with BV. Reproductive age women were recruited for this study after a clinical examination. The total sample (N = 33) included four study groups: (1) healthy nonpregnant women (n = 9), (2) nonpregnant women with symptomatic BV (n = 11), (3) healthy pregnant women without BV (n = 6), and (4) pregnant women with symptomatic BV (N = 7). The vaginal microbiota in healthy women was less diverse, with dominance of a single genus, Lactobacillus. Six major phyla appeared upon taxonomic analysis of the bacterial sequences: Firmicutes, Actinobacteria, Proteobacteria, Tenericutes, Bacteroidetes, and Fusobacteria. For instance, Firmicutes had a significantly higher abundance (98.3%) in the nonpregnant healthy group and 94.3% in pregnant healthy group, compared with nonpregnant (49.7%) and pregnant (67%) women with BV (p = 0.003). Moreover, women with BV had significant increases in representation of Actinobacteria, Fusobacteria, and Bacteroidetes (p = 0.0003, 0.004, and 0.01, respectively). Although the Lactobacillus genus was predominant in healthy women, Gardnerella, Atopobium, Sneathia, and Prevotella significantly increased in nonpregnant women with BV (p = 0.001, 0.014, 0.004, and 0.012, respectively). Dysbiosis of Lactobacillus in pregnant women with BV was accompanied by increased prevalence of the Streptococcus genus. These findings contribute new insights toward microbiome diagnostics and therapeutics innovation in BV.}, } @article {pmid32955144, year = {2021}, author = {Compant, S and Cambon, MC and Vacher, C and Mitter, B and Samad, A and Sessitsch, A}, title = {The plant endosphere world - bacterial life within plants.}, journal = {Environmental microbiology}, volume = {23}, number = {4}, pages = {1812-1829}, doi = {10.1111/1462-2920.15240}, pmid = {32955144}, issn = {1462-2920}, mesh = {*Bacteria/genetics ; Endophytes ; *Microbiota ; Plant Development ; Plant Roots ; Plants ; }, abstract = {The plant endosphere is colonized by complex microbial communities and microorganisms, which colonize the plant interior at least part of their lifetime and are termed endophytes. Their functions range from mutualism to pathogenicity. All plant organs and tissues are generally colonized by bacterial endophytes and their diversity and composition depend on the plant, the plant organ and its physiological conditions, the plant growth stage as well as on the environment. Plant-associated microorganisms, and in particular endophytes, have lately received high attention, because of the increasing awareness of the importance of host-associated microbiota for the functioning and performance of their host. Some endophyte functions are known from mostly lab assays, genome prediction and few metagenome analyses; however, we have limited understanding on in planta activities, particularly considering the diversity of micro-environments and the dynamics of conditions. In our review, we present recent findings on endosphere environments, their physiological conditions and endophyte colonization. Furthermore, we discuss microbial functions, the interaction between endophytes and plants as well as methodological limitations of endophyte research. We also provide an outlook on needs of future research to improve our understanding on the role of microbiota colonizing the endosphere on plant traits and ecosystem functioning.}, } @article {pmid32951639, year = {2020}, author = {Zhang, X and Das, S and Dunbar, S and Tang, YW}, title = {Molecular and non-molecular approaches to etiologic diagnosis of gastroenteritis.}, journal = {Advances in clinical chemistry}, volume = {99}, number = {}, pages = {49-85}, doi = {10.1016/bs.acc.2020.02.007}, pmid = {32951639}, issn = {2162-9471}, mesh = {Animals ; Feces/microbiology ; Gastroenteritis/*diagnosis/etiology/microbiology ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; Microscopy/methods ; }, abstract = {Gastroenteritis is a major cause of mortality and morbidity globally and rapid identification of the causative pathogen is important for appropriate treatment and patient management, implementation of effective infection control measures, reducing hospital length of stay, and reducing overall medical costs. Although stool culture and microscopic examination of diarrheal stool has been the primary method for laboratory diagnosis, culture-independent proteomic and genomic tests are receiving increased attention. Antigen tests for stool pathogens are routinely implemented as rapid and simple analytics whereas molecular tests are now available in various formats from high complexity to waived point-of-care tests. In addition, metagenomic next-generation sequencing stands poised for use as a method for both diagnosis and routine characterization of the gut microbiome in the very near future. Analysis of host biomarkers as indicators of infection status and pathogenesis may also become important for prediction, diagnosis, and monitoring of gastrointestinal infection. Here we review current methods and emerging technologies for the etiologic diagnosis of gastroenteritis in the clinical laboratory. Benefits and limitations of these evolving methods are highlighted.}, } @article {pmid32951609, year = {2020}, author = {Mayneris-Perxachs, J and Arnoriaga-Rodríguez, M and Luque-Córdoba, D and Priego-Capote, F and Pérez-Brocal, V and Moya, A and Burokas, A and Maldonado, R and Fernández-Real, JM}, title = {Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {136}, pmid = {32951609}, issn = {2049-2618}, mesh = {Adult ; Aged ; Animals ; Case-Control Studies ; Cross-Sectional Studies ; Female ; *Gastrointestinal Microbiome/genetics ; *Gonadal Steroid Hormones ; Humans ; Male ; *Menopause ; Mice ; Middle Aged ; *Obesity ; *Sex Characteristics ; }, abstract = {BACKGROUND: Gonadal steroid hormones have been suggested as the underlying mechanism responsible for the sexual dimorphism observed in metabolic diseases. Animal studies have also evidenced a causal role of the gut microbiome and metabolic health. However, the role of sexual dimorphism in the gut microbiota and the potential role of the microbiome in influencing sex steroid hormones and shaping sexually dimorphic susceptibility to disease have been largely overlooked. Although there is some evidence of sex-specific differences in the gut microbiota diversity, composition, and functionality, the results are inconsistent. Importantly, most of these studies have not taken into account the gonadal steroid status. Therefore, we investigated the gut microbiome composition and functionality in relation to sex, menopausal status, and circulating sex steroids.

RESULTS: No significant differences were found in alpha diversity indices among pre- and post-menopausal women and men, but beta diversity differed among groups. The gut microbiota from post-menopausal women was more similar to men than to pre-menopausal women. Metagenome functional analyses revealed no significant differences between post-menopausal women and men. Gonadal steroids were specifically associated with these differences. Hence, the gut microbiota of pre-menopausal women was more enriched in genes from the steroid biosynthesis and degradation pathways, with the former having the strongest fold change among all associated pathways. Microbial steroid pathways also had significant associations with the plasma levels of testosterone and progesterone. In addition, a specific microbiome signature was able to predict the circulating testosterone levels at baseline and after 1-year follow-up. In addition, this microbiome signature could be transmitted from humans to antibiotic-induced microbiome-depleted male mice, being able to predict donor's testosterone levels 4 weeks later, implying that the microbiota profile of the recipient mouse was influenced by the donor's gender. Finally, obesity eliminated most of the differences observed among non-obese pre-menopausal women, post-menopausal women, and men in the gut microbiota composition (Bray-Curtis and weighted unifrac beta diversity), functionality, and the gonadal steroid status.

CONCLUSIONS: The present findings evidence clear differences in the gut microbial composition and functionality between men and women, which is eliminated by both menopausal and obesity status. We also reveal a tight link between the gut microbiota composition and the circulating levels of gonadal steroids, particularly testosterone. Video Abstract.}, } @article {pmid32951554, year = {2020}, author = {Negrey, JD and Thompson, ME and Langergraber, KE and Machanda, ZP and Mitani, JC and Muller, MN and Otali, E and Owens, LA and Wrangham, RW and Goldberg, TL}, title = {Demography, life-history trade-offs, and the gastrointestinal virome of wild chimpanzees.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1811}, pages = {20190613}, pmid = {32951554}, issn = {1471-2970}, support = {R01 AG049395/AG/NIA NIH HHS/United States ; R37 AG049395/AG/NIA NIH HHS/United States ; T32 AI007414/AI/NIAID NIH HHS/United States ; }, mesh = {Age Factors ; Animals ; Feces/virology ; Female ; *Gastrointestinal Microbiome ; *Life History Traits ; Male ; Pan troglodytes/*physiology/virology ; Population Dynamics ; Sex Factors ; *Virome ; Viruses/classification/genetics/*isolation & purification ; }, abstract = {In humans, senescence increases susceptibility to viral infection. However, comparative data on viral infection in free-living non-human primates-even in our closest living relatives, chimpanzees and bonobos (Pan troglodytes and P. paniscus)-are relatively scarce, thereby constraining an evolutionary understanding of age-related patterns of viral infection. We investigated a population of wild eastern chimpanzees (P. t. schweinfurthii), using metagenomics to characterize viromes (full viral communities) in the faeces of 42 sexually mature chimpanzees (22 males, 20 females) from the Kanyawara and Ngogo communities of Kibale National Park, Uganda. We identified 12 viruses from at least four viral families possessing genomes of both single-stranded RNA and single-stranded DNA. Faecal viromes of both sexes varied with chimpanzee age, but viral richness increased with age only in males. This effect was largely due to three viruses, salivirus, porprismacovirus and chimpanzee stool-associated RNA virus (chisavirus), which occurred most frequently in samples from older males. This finding is consistent with the hypothesis that selection on males for early-life reproduction compromises investment in somatic maintenance, which has delayed consequences for health later in life, in this case reflected in viral infection and/or shedding. Faecal viromes are therefore useful for studying processes related to the divergent reproductive strategies of males and females, ageing, and sex differences in longevity. This article is part of the theme issue 'Evolution of the primate ageing process'.}, } @article {pmid32949366, year = {2021}, author = {Hemmat-Jou, MH and Safari-Sinegani, AA and Che, R and Mirzaie-Asl, A and Tahmourespour, A and Tahmasbian, I}, title = {Toxic trace element resistance genes and systems identified using the shotgun metagenomics approach in an Iranian mine soil.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {4}, pages = {4845-4856}, pmid = {32949366}, issn = {1614-7499}, mesh = {Iran ; Metagenomics ; *Metals, Heavy/analysis ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; *Trace Elements ; }, abstract = {This study aimed to identify the microbial communities, resistance genes, and resistance systems in an Iranian mine soil polluted with toxic trace elements (TTE). The polluted soil samples were collected from a mining area and compared against non-polluted (control) collected soils from the vicinity of the mine. The soil total DNA was extracted and sequenced, and bioinformatic analysis of the assembled metagenomes was conducted to identify soil microbial biodiversity, TTE resistance genes, and resistance systems. The results of the employed shotgun approach indicated that the relative abundance of Proteobacteria, Firmicutes, Bacteroidetes, and Deinococcus-Thermus was significantly higher in the TTE-polluted soils compared with those in the control soils, while the relative abundance of Actinobacteria and Acidobacteria was significantly lower in the polluted soils. The high concentration of TTE increased the ratio of archaea to bacteria and decreased the alpha diversity in the polluted soils compared with the control soils. Canonical correspondence analysis (CCA) demonstrated that heavy metal pollution was the major driving factor in shaping microbial communities compared with any other soil characteristics. In the identified heavy metal resistome (HV-resistome) of TTE-polluted soils, major functional pathways were carbohydrates metabolism, stress response, amino acid and derivative metabolism, clustering-based subsystems, iron acquisition and metabolism, cell wall synthesis and capsulation, and membrane transportation. Ten TTE resistance systems were identified in the HV-resistome of TTE-polluted soils, dominated by "P-type ATPases," "cation diffusion facilitators," and "heavy metal efflux-resistance nodulation cell division (HME-RND)." Most of the resistance genes (69%) involved in resistance systems are affiliated to cell wall, outer membrane, periplasm, and cytoplasmic membrane. The finding of this study provides insight into the microbial community in Iranian TTE-polluted soils and their resistance genes and systems.}, } @article {pmid32949277, year = {2020}, author = {Ding, X and Lan, W and Wu, J and Hong, Y and Li, Y and Ge, Q and Urzì, C and Katayama, Y and Gu, JD}, title = {Microbiome and nitrate removal processes by microorganisms on the ancient Preah Vihear temple of Cambodia revealed by metagenomics and N-15 isotope analyses.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {22}, pages = {9823-9837}, doi = {10.1007/s00253-020-10886-4}, pmid = {32949277}, issn = {1432-0614}, support = {31870100, 91851111//National Natural Science Foundation of China/ ; JCYJ20170410103015603//Shenzhen Scientific Project Fund/ ; 17302119//Research Grants Council, University Grants Committee/ ; }, mesh = {Cambodia ; Denitrification ; Metagenomics ; *Microbiota ; *Nitrates/analysis ; Nitrogen ; Nitrogen Isotopes ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Preah Vihear temple is one of the most significant representatives of the ancient Angkorian temples listed as United Nations Educational, Scientific and Cultural Organization (UNESCO) World Heritage Sites. The surfaces of this Angkor sandstone monument are covered with deteriorated materials, broadly called "sediments" here, resulting from a long time of weathering of the sandstone. The sediments might adversely affect the ancient sandstone substratum of this cultural heritage, and the potential risk from them is essential information for current strategies and on-going protection and management. The extracted DNA from the sediment samples of this temple was used for Illumina high-throughput sequencing analysis, resulting in approximately 12 Gb of metagenomic dataset. The results of this shotgun metagenomic analysis provided a thorough information of the phylogenetic groups presented in the microbiome of the sediment samples, indicating that potential metabolic activities, involving different geomicrobiological cycles, may occur in this microbiome. The phylogenetic result revealed that the majority of metagenomic reads were affiliated with Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes at the phylum level. The metabolic reconstruction results indicated that the important geomicrobiological cycling processes include carbon sequestration, and nitrogen and sulfur transformation as the potentially active ones in the sediments of the sampling sites. Specifically, the dissimilatory nitrate reduction to ammonium (DNRA) and the newly discovered complete ammonia oxidation (comammox) were retrieved from this metagenomic dataset. Furthermore, the genetic information on the presence of acid-producing processes by sulfur- and ammonia-oxidizing bacteria and archaea in this metagenomic dataset suggested that the microbial flora in these samples has the potential to participate in the degradation of sandstone cultural heritage by producing acids. N-15 isotope amendment and incubation analysis results confirmed the presence of active denitrification, but not anammox activity at this temple. These results are important for our knowledge on the microbial community composition and microbial biodeterioration processes affecting this sandstone cultural heritage and will aid in the protection and management of the ancient Preah Vihear temple.Key Points• Microbiota on Preah Viher temple was analyzed using NGS.• Nitrate-N transformation by DNRA, comammox, and denitrifcation was detected.• N-15 isotope analysis confirmed the active denitrifcation, but not Anammox.• Accumulation of nitrate is a result of less active removal by denitrification.}, } @article {pmid32948523, year = {2020}, author = {Milani, C and Alessandri, G and Mancabelli, L and Mangifesta, M and Lugli, GA and Viappiani, A and Longhi, G and Anzalone, R and Duranti, S and Turroni, F and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {Multi-omics Approaches To Decipher the Impact of Diet and Host Physiology on the Mammalian Gut Microbiome.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {23}, pages = {}, pmid = {32948523}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification/*isolation & purification ; Diet/*veterinary ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Gene Expression Profiling/veterinary ; Mammals/*microbiology/*physiology ; Metagenomics ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Species Specificity ; }, abstract = {In recent years, various studies have demonstrated that the gut microbiota influences host metabolism. However, these studies were focused primarily on a single or a limited range of host species, thus preventing a full exploration of possible taxonomic and functional adaptations by gut microbiota members as a result of host-microbe coevolution events. In the current study, the microbial taxonomic profiles of 250 fecal samples, corresponding to 77 host species that cover the mammalian branch of the tree of life, were reconstructed by 16S rRNA gene-based sequence analysis. Moreover, shotgun metagenomics was employed to investigate the metabolic potential of the fecal microbiomes of 24 mammals, and subsequent statistical analyses were performed to assess the impact of host diet and corresponding physiology of the digestive system on gut microbiota composition and functionality. Functional data were confirmed and extended through metatranscriptome assessment of gut microbial populations of eight animals, thus providing insights into the transcriptional response of gut microbiota to specific dietary lifestyles. Therefore, the analyses performed in this study support the notion that the metabolic features of the mammalian gut microbiota have adapted to maximize energy extraction from the host's diet.IMPORTANCE Diet and host physiology have been recognized as main factors affecting both taxonomic composition and functional features of the mammalian gut microbiota. However, very few studies have investigated the bacterial biodiversity of mammals by using large sample numbers that correspond to multiple mammalian species, thus resulting in an incomplete understanding of the functional aspects of their microbiome. Therefore, we investigated the bacterial taxonomic composition of 250 fecal samples belonging to 77 host species distributed along the tree of life in order to assess how diet and host physiology impact the intestinal microbial community by selecting specific microbial players. Conversely, the application of shotgun metagenomics and metatranscriptomics approaches to a group of selected fecal samples allowed us to shed light on both metabolic features and transcriptional responses of the intestinal bacterial community based on different diets.}, } @article {pmid32948522, year = {2020}, author = {Liang, Z and Shi, J and Wang, C and Li, J and Liang, D and Yong, EL and He, Z and Wang, S}, title = {Genome-Centric Metagenomic Insights into the Impact of Alkaline/Acid and Thermal Sludge Pretreatment on the Microbiome in Digestion Sludge.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {23}, pages = {}, pmid = {32948522}, issn = {1098-5336}, mesh = {Archaea/*genetics/isolation & purification ; Bacteria/*genetics/isolation & purification ; Hot Temperature ; Hydrogen-Ion Concentration ; *Metagenome ; *Microbiota ; Sewage/*chemistry/*microbiology ; Waste Disposal, Fluid/*methods ; }, abstract = {Pretreatment of waste-activated sludge (WAS) is an effective way to destabilize sludge floc structure and release organic matter for improving sludge digestion efficiency. Nonetheless, information on the impact of WAS pretreatment on digestion sludge microbiomes, as well as mechanistic insights into how sludge pretreatment improves digestion performance, remains elusive. In this study, a genome-centric metagenomic approach was employed to investigate the digestion sludge microbiome in four sludge digesters with different types of feeding sludge: WAS pretreated with 0.25 mol/liter alkaline/acid (APAD), WAS pretreated with 0.8 mol/liter alkaline/acid (HS-APAD), thermally pretreated WAS (thermal-AD), and fresh WAS (control-AD). We retrieved 254 metagenome-assembled genomes (MAGs) to identify the key functional populations involved in the methanogenic digestion process. These MAGs span 28 phyla, including 69 yet-to-be-cultivated lineages, and 30 novel lineages were characterized with metabolic potential associated with hydrolysis and fermentation. Interestingly, functional populations involving carbohydrate digestion were enriched in APAD and HS-APAD, while lineages related to protein and lipid fermentation were enriched in thermal-AD, corroborating the idea that different substrates are released from alkaline/acid and thermal pretreatments. Among the major functional populations (i.e., fermenters, syntrophic acetogens, and methanogens), significant correlations between genome sizes and abundance of the fermenters were observed, particularly in APAD and HS-APAD, which had improved digestion performance.IMPORTANCE Wastewater treatment generates large amounts of waste-activated sludge (WAS), which consists mainly of recalcitrant microbial cells and particulate organic matter. Though WAS pretreatment is an effective way to release sludge organic matter for subsequent digestion, detailed information on the impact of the sludge pretreatment on the digestion sludge microbiome remains scarce. Our study provides unprecedented genome-centric metagenomic insights into how WAS pretreatments change the digestion sludge microbiomes, as well as their metabolic networks. Moreover, digestion sludge microbiomes could be a unique source for exploring microbial dark matter. These results may inform future optimization of methanogenic sludge digestion and resource recovery.}, } @article {pmid32947866, year = {2020}, author = {Sánchez-Alcoholado, L and Ordóñez, R and Otero, A and Plaza-Andrade, I and Laborda-Illanes, A and Medina, JA and Ramos-Molina, B and Gómez-Millán, J and Queipo-Ortuño, MI}, title = {Gut Microbiota-Mediated Inflammation and Gut Permeability in Patients with Obesity and Colorectal Cancer.}, journal = {International journal of molecular sciences}, volume = {21}, number = {18}, pages = {}, pmid = {32947866}, issn = {1422-0067}, support = {PI15/00256//Institute of Health "Carlos III" (ISCIII), co-funded by the Fondo Europeo de Desarrollo Regional-FEDER/ ; CPI13/00003//Miguel Servet Type II" program, ISCIII, Spain; co-funded by the Fondo Europeo de Desarrollo Regional-FEDER/ ; C-0030-2018//Nicolas Monardes" research program of the Consejería de Salud, Junta de Andalucía, Spain/ ; PE-0106-2019//Predoctoral grant from the Consejería de Salud y Familia, co-funded by the Fondo Europeo de Desarrollo Regional-FEDER, Andalucia, Spain/ ; FI19-00112//Predoctoral grant PFIS-ISCIII, co-funded by the Fondo Europeo de Desarrollo Regional-FEDER, Madrid, Spain./ ; CP19/00098//Miguel Servet Type I" program, ISCIII, Spain; co-funded by the Fondo Europeo de Desarrollo Regional-FEDER/ ; }, mesh = {Aged ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Biomarkers ; Body Mass Index ; Colorectal Neoplasms/etiology/*microbiology/pathology/physiopathology ; Dysbiosis/complications/*microbiology/pathology/physiopathology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Haptoglobins ; Humans ; Inflammation/blood/*microbiology ; Inflammation Mediators/blood ; Interleukins/blood ; Male ; Metagenome ; Methylamines/adverse effects/blood ; Middle Aged ; Obesity/metabolism/*microbiology/pathology/physiopathology ; Permeability ; Protein Precursors/blood ; }, abstract = {Obesity is considered an important factor that increases the risk of colorectal cancer (CRC). So far, the association of gut microbiota with both obesity and cancer has been described independently. Nevertheless, a specific obesity-related microbial profile linked to CRC development has not been identified. The aim of this study was to determine the gut microbiota composition in fecal samples from CRC patients with (OB-CRC) and without obesity (L-CRC) compared to the microbiota profile present in non-obese healthy controls (L-HC), in order to unravel the possible relationship between gut microbiota and microbial-derived metabolite trimethylamine N-oxide (TMAO), the inflammatory status, and the intestinal permeability in the context of obesity-associated CRC. The presence of obesity does not induce significant changes in the diversity and richness of intestinal bacteria of CRC patients. Nevertheless, OB-CRC patients display a specific gut microbiota profile characterized by a reduction in butyrate-producing bacteria and an overabundance of opportunistic pathogens, which in turn could be responsible, at least in part, for the higher levels of proinflammatory cytokine IL-1β, the deleterious bacterial metabolite TMAO, and gut permeability found in these patients. These results suggest a possible role of obesity-related gut microbiota in the development of CRC, which could give new clues for the design of new diagnostic tools for CRC prevention.}, } @article {pmid32947654, year = {2020}, author = {Białasek, M and Miłobędzka, A}, title = {Revealing antimicrobial resistance in stormwater with MinION.}, journal = {Chemosphere}, volume = {258}, number = {}, pages = {127392}, pmid = {32947654}, issn = {1879-1298}, mesh = {Bacteria/drug effects ; Drug Resistance, Bacterial/*genetics ; Environmental Monitoring ; Feces/microbiology ; Genes, Bacterial/drug effects ; Humans ; Macrolides ; *Metagenome ; Metagenomics/methods ; Microbiota/drug effects ; Wastewater/microbiology ; beta-Lactams ; }, abstract = {Discharge of urban stormwater containing organic matter, heavy metals and sometime human feces, to the natural aquatic reservoirs without any treatment is not only an environmental problem. It can lead to prevalence of antibiotic resistant bacteria in stormwater systems and transmission of antibiotic resistance genes to the environment. We performed antibiotic resistome identification and virus detection in stormwater samples from Stockholm, using publicly available metagenomic sequencing MinION data. A MinION platform offers low-cost, precise environmental metagenomics analysis. 37 groups of antibiotic resistant bacteria (ARB), 11 resistance types with 26 resistance mechanisms - antibiotic resistance genes (ARGs) giving tolerance to the aminoglycoside, beta-lactams, fosmidomycin, MLS, multidrug and vancomycin were identified using ARGpore pipeline. The majority of the identified bacteria species were related to the natural environment such as soil and were not dangerous to human. Alarmingly, human pathogenic bacteria carrying resistance to antibiotics currently used against them (Bordetella resistant to macrolides and multidrug resistant Propionibacterium avidum) were also found in the samples. Most abundant viruses identified belonged to Caudovirales and Herpesvirales and they were not carrying ARGs. Unlike the virome, resistome and ARB were not unique for stormwater sampling points. This results underline the need for extensive monitoring of the microbial community structure in the urban stormwater systems to assess antimicrobial resistance spread.}, } @article {pmid32947608, year = {2020}, author = {Søndertoft, NB and Vogt, JK and Arumugam, M and Kristensen, M and Gøbel, RJ and Fan, Y and Lyu, L and Bahl, MI and Eriksen, C and Ängquist, L and Frøkiær, H and Hansen, TH and Brix, S and Nielsen, HB and Hansen, T and Vestergaard, H and Gupta, R and Licht, TR and Lauritzen, L and Pedersen, O}, title = {The intestinal microbiome is a co-determinant of the postprandial plasma glucose response.}, journal = {PloS one}, volume = {15}, number = {9}, pages = {e0238648}, pmid = {32947608}, issn = {1932-6203}, mesh = {Algorithms ; Blood Glucose/*metabolism ; Fasting/blood ; Female ; *Gastrointestinal Microbiome ; Humans ; Life Style ; Male ; Middle Aged ; Models, Biological ; Phenomics ; *Postprandial Period ; }, abstract = {Elevated postprandial plasma glucose is a risk factor for development of type 2 diabetes and cardiovascular disease. We hypothesized that the inter-individual postprandial plasma glucose response varies partly depending on the intestinal microbiome composition and function. We analyzed data from Danish adults (n = 106), who were self-reported healthy and attended the baseline visit of two previously reported randomized controlled cross-over trials within the Gut, Grain and Greens project. Plasma glucose concentrations at five time points were measured before and during three hours after a standardized breakfast. Based on these data, we devised machine learning algorithms integrating bio-clinical, as well as shotgun-sequencing-derived taxa and functional potentials of the intestinal microbiome to predict individual postprandial glucose excursions. In this post hoc study, we found microbial and clinical features, which predicted up to 48% of the inter-individual variance of postprandial plasma glucose responses (Pearson correlation coefficient of measured vs. predicted values, R = 0.69, 95% CI: 0.45 to 0.84, p<0.001). The features were age, fasting serum triglycerides, systolic blood pressure, BMI, fasting total serum cholesterol, abundance of Bifidobacterium genus, richness of metagenomics species and abundance of a metagenomic species annotated to Clostridiales at order level. A model based only on microbial features predicted up to 14% of the variance in postprandial plasma glucose excursions (R = 0.37, 95% CI: 0.02 to 0.64, p = 0.04). Adding fasting glycaemic measures to the model including microbial and bio-clinical features increased the predictive power to R = 0.78 (95% CI: 0.59 to 0.89, p<0.001), explaining more than 60% of the inter-individual variance of postprandial plasma glucose concentrations. The outcome of the study points to a potential role of the taxa and functional potentials of the intestinal microbiome. If validated in larger studies our findings may be included in future algorithms attempting to develop personalized nutrition, especially for prediction of individual blood glucose excursions in dys-glycaemic individuals.}, } @article {pmid32946867, year = {2020}, author = {Kumar, V and Mahajan, N and Khare, P and Kondepudi, KK and Bishnoi, M}, title = {Role of TRPV1 in colonic mucin production and gut microbiota profile.}, journal = {European journal of pharmacology}, volume = {888}, number = {}, pages = {173567}, doi = {10.1016/j.ejphar.2020.173567}, pmid = {32946867}, issn = {1879-0712}, mesh = {Ablation Techniques/methods ; Animals ; Colon/*metabolism ; Dysbiosis/genetics/metabolism ; Gastrointestinal Microbiome/*physiology ; Male ; Mucins/*antagonists & inhibitors/*biosynthesis ; Rats ; Rats, Wistar ; TRPV Cation Channels/*antagonists & inhibitors/*deficiency/genetics ; }, abstract = {This study focuses on exploring the role of sensory cation channel Transient Receptor Potential channel subfamily Vanilloid 1 (TRPV1) in gut health, specifically mucus production and microflora profile in gut. We employed resiniferatoxin (ultrapotent TRPV1 agonist) induced chemo-denervation model in rats and studied the effects of TRPV1 ablation on colonic mucus secretion patterns. Histological and transcriptional analysis showed substantial decrease in mucus production as well as in expression of genes involved in goblet cell differentiation, mucin production and glycosylation. 16S metagenome analysis revealed changes in abundance of various gut bacteria, including decrease in beneficial bacteria like Lactobacillus spp and Clostridia spp. Also, TRPV1 ablation significantly decreased the levels of short chain fatty acids, i.e. acetate and butyrate. The present study provides first evidence that systemic TRPV1 ablation leads to impairment in mucus production and causes dysbiosis in gut. Further, it suggests to address mucin production and gut microbiota related adverse effects during the development of TRPV1 antagonism/ablation-based therapeutic and preventive strategies.}, } @article {pmid32946440, year = {2020}, author = {Methe, BA and Hiltbrand, D and Roach, J and Xu, W and Gordon, SG and Goodner, BW and Stapleton, AE}, title = {Functional gene categories differentiate maize leaf drought-related microbial epiphytic communities.}, journal = {PloS one}, volume = {15}, number = {9}, pages = {e0237493}, pmid = {32946440}, issn = {1932-6203}, mesh = {Droughts ; Gene Regulatory Networks ; Genes, Plant ; Metagenomics ; Microbiota ; Molecular Sequence Annotation ; Plant Leaves/*genetics/*microbiology/physiology ; Stress, Physiological ; Water/metabolism ; Zea mays/*genetics/*microbiology/physiology ; }, abstract = {The phyllosphere epiphytic microbiome is composed of microorganisms that colonize the external aerial portions of plants. Relationships of plant responses to specific microorganisms-both pathogenic and beneficial-have been examined, but the phyllosphere microbiome functional and metabolic profile responses are not well described. Changing crop growth conditions, such as increased drought, can have profound impacts on crop productivity. Also, epiphytic microbial communities provide a new target for crop yield optimization. We compared Zea mays leaf microbiomes collected under drought and well-watered conditions by examining functional gene annotation patterns across three physically disparate locations each with and without drought treatment, through the application of short read metagenomic sequencing. Drought samples exhibited different functional sequence compositions at each of the three field sites. Maize phyllosphere functional profiles revealed a wide variety of metabolic and regulatory processes that differed in drought and normal water conditions and provide key baseline information for future selective breeding.}, } @article {pmid32945341, year = {2020}, author = {Wang, H and Chan, MWM and Chan, HH and Pang, H}, title = {Longitudinal Changes in Skin Microbiome Associated with Change in Skin Status in Patients with Psoriasis.}, journal = {Acta dermato-venereologica}, volume = {100}, number = {18}, pages = {adv00329}, pmid = {32945341}, issn = {1651-2057}, mesh = {Humans ; *Microbiota ; *Probiotics ; *Psoriasis/diagnosis ; Skin ; }, abstract = {The aim of this study was to identify key microbes associated with change in skin status (lesional vs normal). Longitudinal changes in the skin microbiome between patients with psoriasis and healthy family controls living in the same household were studied using whole genome metagenomic shotgun sequencing at 4 time-points. There were significant changes in abundance of the pathogen Campylobacter jejuni and its higher taxonomic levels when the skin status of patients with psoriasis changed. There were significant longitudinal variations in alpha diveristy (p < 0.001) and beta diversity (p < 0.05) of the skin microbiome in patients with psoriasis, but not in the healthy control group, which indicated composition of skin microbiome in patients with psoriasis was different from healthy control and was dynamically less stable. This study will serve as the basis for future temporal studies of the skin microbiome and probiotic therapeutics.}, } @article {pmid32941879, year = {2021}, author = {Solé, C and Guilly, S and Da Silva, K and Llopis, M and Le-Chatelier, E and Huelin, P and Carol, M and Moreira, R and Fabrellas, N and De Prada, G and Napoleone, L and Graupera, I and Pose, E and Juanola, A and Borruel, N and Berland, M and Toapanta, D and Casellas, F and Guarner, F and Doré, J and Solà, E and Ehrlich, SD and Ginès, P}, title = {Alterations in Gut Microbiome in Cirrhosis as Assessed by Quantitative Metagenomics: Relationship With Acute-on-Chronic Liver Failure and Prognosis.}, journal = {Gastroenterology}, volume = {160}, number = {1}, pages = {206-218.e13}, doi = {10.1053/j.gastro.2020.08.054}, pmid = {32941879}, issn = {1528-0012}, mesh = {Acute-On-Chronic Liver Failure/*etiology/mortality/*pathology ; Aged ; Case-Control Studies ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Liver Cirrhosis/*etiology/mortality/*pathology ; Male ; Metagenomics ; Middle Aged ; Prognosis ; Prospective Studies ; Survival Rate ; }, abstract = {BACKGROUND AND AIMS: Cirrhosis is associated with changes in gut microbiome composition. Although acute-on-chronic liver failure (ACLF) is the most severe clinical stage of cirrhosis, there is lack of information about gut microbiome alterations in ACLF using quantitative metagenomics. We investigated the gut microbiome in patients with cirrhosis encompassing the whole spectrum of disease (compensated, acutely decompensated without ACLF, and ACLF). A group of healthy subjects was used as control subjects.

METHODS: Stool samples were collected prospectively in 182 patients with cirrhosis. DNA library construction and sequencing were performed using the Ion Proton Sequencer (ThermoFisher Scientific, Waltham, MA). Microbial genes were grouped into clusters, denoted as metagenomic species.

RESULTS: Cirrhosis was associated with a remarkable reduction in gene and metagenomic species richness compared with healthy subjects. This loss of richness correlated with disease stages and was particularly marked in patients with ACLF and persisted after adjustment for antibiotic therapy. ACLF was associated with a significant increase of Enterococcus and Peptostreptococcus sp and a reduction of some autochthonous bacteria. Gut microbiome alterations correlated with model for end-stage liver disease and Child-Pugh scores and organ failure and was associated with some complications, particularly hepatic encephalopathy and infections. Interestingly, gut microbiome predicted 3-month survival with good stable predictors. Functional analysis showed that patients with cirrhosis had enriched pathways related to ethanol production, γ-aminobutyric acid metabolism, and endotoxin biosynthesis, among others.

CONCLUSIONS: Cirrhosis is characterized by marked alterations in gut microbiome that parallel disease stages with maximal changes in ACLF. Altered gut microbiome was associated with complications of cirrhosis and survival. Gut microbiome may contribute to disease progression and poor prognosis. These results should be confirmed in future studies.}, } @article {pmid32939880, year = {2020}, author = {Liu, S and Zhao, W and Liu, X and Cheng, L}, title = {Metagenomic analysis of the gut microbiome in atherosclerosis patients identify cross-cohort microbial signatures and potential therapeutic target.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {34}, number = {11}, pages = {14166-14181}, doi = {10.1096/fj.202000622R}, pmid = {32939880}, issn = {1530-6860}, mesh = {Aged ; Atherosclerosis/epidemiology/*genetics/metabolism/*microbiology ; Bacteria/classification/*genetics/isolation & purification ; Case-Control Studies ; China/epidemiology ; Cohort Studies ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; *Metabolome ; *Metagenome ; Middle Aged ; Sweden/epidemiology ; }, abstract = {The gut microbiota is associated with cardiovascular diseases, including atherosclerosis. However, the composition, functional capacity, and metabolites of the gut microbiome about atherosclerosis have not been comprehensively studied. Here, we reanalyzed 25 metagenomic stool samples from Sweden and 385 metagenomic stool samples from China using HUMAnN2, PanPhlAn, and MelonnPan to obtain more sufficient information. We found that the samples from atherosclerotic patients in both cohorts were depleted in Bacteroides xylanisolvens, Odoribacter splanchnicus, Eubacterium eligens, Roseburia inulinivorans, and Roseburia intestinalis. At the functional level, healthy metagenomes were both enriched in pathways of starch degradation V, glycolysis III (from glucose), CDP-diacylglycerol biosynthesis, and folate transformations. R inulinivorans and R intestinalis are major contributors to starch degradation V, while E eligens greatly contribute to the pathway CDP-diacylglycerol biosynthesis, and B xylanisolvens and B uniformis contribute to folate transformations II. The 11 marker species selected from the Chinese cohort distinguish patients from controls with an area under the receiver operating characteristics curve (AUC) of 0.86. Strain-level microbial analysis revealed a geographically associated adaptation of the strains from E eligens, B uniformis, and E coli. Two gut microbial metabolites, nicotinic acid and hydrocinnamic acid, had significantly higher predicted abundance in the control samples compared to the patients in the Chinese cohort, and interestinglynicotinic acid is already an effective lipid-lowering drug to reducing cardiovascular risk. Our results indicate intestinal bacteria such as B xylanisolvens, E eligens, and R inulinivorans could be promising probiotics and potential therapeutic target for atherosclerosis.}, } @article {pmid32939535, year = {2021}, author = {Zhang, M and Tang, YW and Xu, Y and Yonezawa, T and Shao, Y and Wang, YG and Song, ZP and Yang, J and Zhang, WJ}, title = {Concerted and birth-and-death evolution of 26S ribosomal DNA in Camellia L.}, journal = {Annals of botany}, volume = {127}, number = {1}, pages = {63-73}, pmid = {32939535}, issn = {1095-8290}, mesh = {*Camellia ; DNA, Ribosomal ; *Evolution, Molecular ; Phylogeny ; Pseudogenes ; RNA, Ribosomal ; }, abstract = {BACKGROUND AND AIMS: The ribosomal DNA (rDNA) gene family, encoding ribosomal RNA (rRNA), has long been regarded as an archetypal example illustrating the model of concerted evolution. However, controversy is arising, as rDNA in many eukaryotic species has been proved to be polymorphic. Here, a metagenomic strategy was applied to detect the intragenomic polymorphism as well as the evolutionary patterns of 26S rDNA across the genus Camellia.

METHODS: Degenerate primer pairs were designed to amplify the 26S rDNA fragments from different Camellia species. The amplicons were then paired-end sequenced on the Illumina MiSeq platform.

KEY RESULTS: An extremely high level of rDNA polymorphism existed universally in Camellia. However, functional rDNA was still the major component of the family, and was relatively conserved among different Camellia species. Sequence variations mainly came from rRNA pseudogenes and favoured regions that are rich in GC. Specifically, some rRNA pseudogenes have existed in the genome for a long time, and have even experienced several expansion events, which has greatly enriched the abundance of rDNA polymorphism.

CONCLUSIONS: Camellia represents a group in which rDNA is subjected to a mixture of concerted and birth-and-death evolution. Some rRNA pseudogenes may still have potential functions. Conversely, when released from selection constraint, they can evolve in the direction of decreasing GC content and structural stability through a methylation-induced process, and finally be eliminated from the genome.}, } @article {pmid32939014, year = {2020}, author = {Yang, J and Moon, HE and Park, HW and McDowell, A and Shin, TS and Jee, YK and Kym, S and Paek, SH and Kim, YK}, title = {Brain tumor diagnostic model and dietary effect based on extracellular vesicle microbiome data in serum.}, journal = {Experimental & molecular medicine}, volume = {52}, number = {9}, pages = {1602-1613}, pmid = {32939014}, issn = {2092-6413}, support = {NRF-2016M3A9B6901516//National Research Foundation of Korea (NRF)/ ; NRF-2020M3A9G80220292//National Research Foundation of Korea (NRF)/ ; 10050154//Ministry of Trade, Industry and Energy (Ministry of Trade, Industry and Energy, Korea)/ ; }, mesh = {Aged ; Animals ; Biomarkers, Tumor ; Brain Neoplasms/*diagnosis/*metabolism ; Case-Control Studies ; Computational Biology ; Diet ; Extracellular Vesicles/*metabolism/*microbiology ; Female ; Humans ; Machine Learning ; Male ; Metagenome ; Metagenomics/methods ; Mice ; *Microbiota ; Middle Aged ; ROC Curve ; }, abstract = {The human microbiome has been recently associated with human health and disease. Brain tumors (BTs) are a particularly difficult condition to directly link to the microbiome, as microorganisms cannot generally cross the blood-brain barrier (BBB). However, some nanosized extracellular vesicles (EVs) released from microorganisms can cross the BBB and enter the brain. Therefore, we conducted metagenomic analysis of microbial EVs in both serum (152 BT patients and 198 healthy controls (HC)) and brain tissue (5 BT patients and 5 HC) samples based on the V3-V4 regions of 16S rDNA. We then developed diagnostic models through logistic regression and machine learning algorithms using serum EV metagenomic data to assess the ability of various dietary supplements to reduce BT risk in vivo. Models incorporating the stepwise method and the linear discriminant analysis effect size (LEfSe) method yielded 12 and 29 significant genera as potential biomarkers, respectively. Models using the selected biomarkers yielded areas under the curves (AUCs) >0.93, and the model using machine learning resulted in an AUC of 0.99. In addition, Dialister and [Eubacterium] rectale were significantly lower in both blood and tissue samples of BT patients than in those of HCs. In vivo tests showed that BT risk was decreased through the addition of sorghum, brown rice oil, and garlic but conversely increased by the addition of bellflower and pear. In conclusion, serum EV metagenomics shows promise as a rich data source for highly accurate detection of BT risk, and several foods have potential for mitigating BT risk.}, } @article {pmid32938931, year = {2020}, author = {Zheng, Y and Wang, J and Zhou, S and Zhang, Y and Liu, J and Xue, CX and Williams, BT and Zhao, X and Zhao, L and Zhu, XY and Sun, C and Zhang, HH and Xiao, T and Yang, GP and Todd, JD and Zhang, XH}, title = {Bacteria are important dimethylsulfoniopropionate producers in marine aphotic and high-pressure environments.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4658}, pmid = {32938931}, issn = {2041-1723}, mesh = {Bacteria/*genetics/isolation & purification/*metabolism ; Chlorophyll A/analysis/metabolism ; Genes, Bacterial ; Geologic Sediments/chemistry ; Hydrostatic Pressure ; Marinobacter/genetics/isolation & purification/metabolism ; Metagenome ; Mutation ; Oceans and Seas ; Prochlorococcus/genetics/isolation & purification/metabolism ; RNA, Ribosomal, 16S ; Seawater/*chemistry/*microbiology ; Sulfides/analysis/metabolism ; Sulfonium Compounds/analysis/*metabolism ; Synechococcus/genetics/isolation & purification/metabolism ; }, abstract = {Dimethylsulfoniopropionate (DMSP) is an important marine osmolyte. Aphotic environments are only recently being considered as potential contributors to global DMSP production. Here, our Mariana Trench study reveals a typical seawater DMSP/dimethylsulfide (DMS) profile, with highest concentrations in the euphotic zone and decreased but consistent levels below. The genetic potential for bacterial DMSP synthesis via the dsyB gene and its transcription is greater in the deep ocean, and is highest in the sediment.s DMSP catabolic potential is present throughout the trench waters, but is less prominent below 8000 m, perhaps indicating a preference to store DMSP in the deep for stress protection. Deep ocean bacterial isolates show enhanced DMSP production under increased hydrostatic pressure. Furthermore, bacterial dsyB mutants are less tolerant of deep ocean pressures than wild-type strains. Thus, we propose a physiological function for DMSP in hydrostatic pressure protection, and that bacteria are key DMSP producers in deep seawater and sediment.}, } @article {pmid32937228, year = {2021}, author = {Zhao, Z}, title = {Comparison of microbial communities and the antibiotic resistome between prawn mono- and poly-culture systems.}, journal = {Ecotoxicology and environmental safety}, volume = {207}, number = {}, pages = {111310}, doi = {10.1016/j.ecoenv.2020.111310}, pmid = {32937228}, issn = {1090-2414}, mesh = {*Aquaculture ; Bacteria/drug effects ; Bacteriophages/drug effects/genetics ; China ; Culture ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial/drug effects ; Humans ; Metagenomics ; Microbiota/drug effects/*physiology ; }, abstract = {Antibiotic resistance genes (ARGs) in mariculture sediments pose a potential risk to public health due to their ability to transfer from environmental bacteria to human pathogens. Long term, this may reduce pathogen susceptibility to antibiotics in medical settings. In recent years, the poly-culture of multiple species has become a popular mariculture approach in China, thanks to its environmental and economic benefits. However, differences in microbial communities and antibiotic resistome between mono- and poly-culture systems are still unclear. In this study, microbial community composition and profiles of entire (microbial DNA) and mobile (plasmid and phage) ARGs in prawn mono- and poly-culture systems were investigated using metagenomics. The abundance of several viruses and human pathogens were enhanced in prawn poly-culture ponds, when compared to monoculture systems. In contrast, sediments from poly-culture systems had a lower diversity and ARG abundance when compared to mono-culture approaches. These ARG variations were predominantly related to mobile genetic elements. Prawn mariculture activities exerted a unique selectivity for ARGs in plasmids, and this selectivity was not influenced by culture methods. The findings of this study have important implications for the selection of mariculture systems in preventing pollution with ARGs.}, } @article {pmid32937127, year = {2020}, author = {Campbell, DE and Ly, LK and Ridlon, JM and Hsiao, A and Whitaker, RJ and Degnan, PH}, title = {Infection with Bacteroides Phage BV01 Alters the Host Transcriptome and Bile Acid Metabolism in a Common Human Gut Microbe.}, journal = {Cell reports}, volume = {32}, number = {11}, pages = {108142}, pmid = {32937127}, issn = {2211-1247}, support = {R35 GM124724/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/chemistry/genetics/metabolism ; Bacteriophages/genetics/*physiology ; Bacteroides/*genetics/*virology ; Bile Acids and Salts/*metabolism ; Gastrointestinal Microbiome/*genetics ; Genome, Viral ; Host-Pathogen Interactions/*genetics ; Humans ; Lysogeny ; Mice, Inbred C57BL ; Phylogeny ; Promoter Regions, Genetic/genetics ; Transcription, Genetic ; Transcriptome/*genetics ; }, abstract = {Gut-associated phages are hypothesized to alter the abundance and activity of their bacterial hosts, contributing to human health and disease. Although temperate phages constitute a significant fraction of the gut virome, the effects of lysogenic infection are underexplored. We report that the temperate phage, Bacteroides phage BV01, broadly alters its host's transcriptome, the prominent human gut symbiont Bacteroides vulgatus. This alteration occurs through phage-induced repression of a tryptophan-rich sensory protein (TspO) and represses bile acid deconjugation. Because microbially modified bile acids are important signals for the mammalian host, this is a mechanism by which a phage may influence mammalian phenotypes. Furthermore, BV01 and its relatives in the proposed phage family Salyersviridae are ubiquitous in human gut metagenomes, infecting a broad range of Bacteroides hosts. These results demonstrate the complexity of phage-bacteria-mammal relationships and emphasize a need to better understand the role of temperate phages in the gut microbiome.}, } @article {pmid32934287, year = {2020}, author = {Lee, JH and Choi, JP and Yang, J and Won, HK and Park, CS and Song, WJ and Kwon, HS and Kim, TB and Kim, YK and Park, HS and Cho, YS}, title = {Metagenome analysis using serum extracellular vesicles identified distinct microbiota in asthmatics.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15125}, pmid = {32934287}, issn = {2045-2322}, mesh = {Asthma/blood/*diagnosis/microbiology ; Bacteria/classification/*genetics/isolation & purification ; Case-Control Studies ; DNA, Bacterial/*blood/genetics ; Extracellular Vesicles/*microbiology ; Female ; Humans ; Male ; *Metagenome ; Microbiota/*genetics ; Middle Aged ; }, abstract = {Different patterns of bacterial communities have been reported in the airways and gastrointestinal tract of asthmatics when compared to healthy controls. However, the blood microbiome of asthmatics is yet to be investigated. Therefore, we aimed to determine whether a distinct serum microbiome is observed in asthmatics by metagenomic analysis of serum extracellular vesicles (EVs). We obtained serum from 190 adults with asthma and 260 healthy controls, from which EVs were isolated and analyzed. The bacterial composition of asthmatics was significantly different from that of healthy controls. Chao 1 index was significantly higher in the asthma group, while Shannon and Simpson indices were higher in the control group. At the phylum level, Bacteroidetes was more abundant in asthmatics, while Actinobacter, Verrucomicrobia, and Cyanobacteria were more abundant in healthy controls. At the genus level, 24 bacterial genera showed differences in relative abundance between asthmatics and controls, with linear discriminant analysis scores greater than 3. Further, in a diagnostic model based on these differences, a high predictive value with a sensitivity of 0.92 and a specificity of 0.93 was observed. In conclusion, we demonstrated distinct blood microbiome in asthma indicating the role of microbiome as a potential diagnostic marker of asthma.}, } @article {pmid32934239, year = {2020}, author = {Gupta, VK and Kim, M and Bakshi, U and Cunningham, KY and Davis, JM and Lazaridis, KN and Nelson, H and Chia, N and Sung, J}, title = {A predictive index for health status using species-level gut microbiome profiling.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4635}, pmid = {32934239}, issn = {2041-1723}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Health Status ; Humans ; Metagenome ; Microbiota ; }, abstract = {Providing insight into one's health status from a gut microbiome sample is an important clinical goal in current human microbiome research. Herein, we introduce the Gut Microbiome Health Index (GMHI), a biologically-interpretable mathematical formula for predicting the likelihood of disease independent of the clinical diagnosis. GMHI is formulated upon 50 microbial species associated with healthy gut ecosystems. These species are identified through a multi-study, integrative analysis on 4347 human stool metagenomes from 34 published studies across healthy and 12 different nonhealthy conditions, i.e., disease or abnormal bodyweight. When demonstrated on our population-scale meta-dataset, GMHI is the most robust and consistent predictor of disease presence (or absence) compared to α-diversity indices. Validation on 679 samples from 9 additional studies results in a balanced accuracy of 73.7% in distinguishing healthy from non-healthy groups. Our findings suggest that gut taxonomic signatures can predict health status, and highlight how data sharing efforts can provide broadly applicable discoveries.}, } @article {pmid32934151, year = {2020}, author = {Toivonen, L and Karppinen, S and Schuez-Havupalo, L and Waris, M and He, Q and Hoffman, KL and Petrosino, JF and Dumas, O and Camargo, CA and Hasegawa, K and Peltola, V}, title = {Longitudinal Changes in Early Nasal Microbiota and the Risk of Childhood Asthma.}, journal = {Pediatrics}, volume = {146}, number = {4}, pages = {}, doi = {10.1542/peds.2020-0421}, pmid = {32934151}, issn = {1098-4275}, mesh = {Aerococcaceae/isolation & purification ; Age Factors ; Asthma/diagnosis/*etiology/microbiology ; Child ; Child, Preschool ; Female ; Finland ; Follow-Up Studies ; Gene Expression Profiling/methods ; Haemophilus/isolation & purification ; Humans ; Incidence ; Infant ; Infant, Newborn ; Machine Learning ; Male ; *Microbiota/genetics ; Moraxella/isolation & purification ; Multivariate Analysis ; Nose/*microbiology ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Respiratory Tract Infections/complications/epidemiology/microbiology ; Risk ; Streptococcus/isolation & purification ; }, abstract = {OBJECTIVES: Although the airway microbiota is a highly dynamic ecology, the role of longitudinal changes in airway microbiota during early childhood in asthma development is unclear. We aimed to investigate the association of longitudinal changes in early nasal microbiota with the risk of developing asthma.

METHODS: In this prospective, population-based birth cohort study, we followed children from birth to age 7 years. The nasal microbiota was tested by using 16S ribosomal RNA gene sequencing at ages 2, 13, and 24 months. We applied an unsupervised machine learning approach to identify longitudinal nasal microbiota profiles during age 2 to 13 months (the primary exposure) and during age 2 to 24 months (the secondary exposure) and examined the association of these profiles with the risk of physician-diagnosed asthma at age 7 years.

RESULTS: Of the analytic cohort of 704 children, 57 (8%) later developed asthma. We identified 4 distinct longitudinal nasal microbiota profiles during age 2 to 13 months. In the multivariable analysis, compared with the persistent Moraxella dominance profile during age 2 to 13 months, the persistent Moraxella sparsity profile was associated with a significantly higher risk of asthma (adjusted odds ratio, 2.74; 95% confidence interval, 1.20-6.27). Similar associations were observed between the longitudinal changes in nasal microbiota during age 2 to 24 months and risk of asthma.

CONCLUSIONS: Children with an altered longitudinal pattern in the nasal microbiota during early childhood had a high risk of developing asthma. Our data guide the development of primary prevention strategies (eg, early identification of children at high risk and modification of microbiota) for childhood asthma. These observations present a new avenue for risk modification for asthma (eg, microbiota modification).}, } @article {pmid32933758, year = {2020}, author = {AlHilli, MM and Bae-Jump, V}, title = {Diet and gut microbiome interactions in gynecologic cancer.}, journal = {Gynecologic oncology}, volume = {159}, number = {2}, pages = {299-308}, doi = {10.1016/j.ygyno.2020.08.027}, pmid = {32933758}, issn = {1095-6859}, mesh = {Carcinogenesis ; Diet ; Female ; *Gastrointestinal Microbiome ; Genital Neoplasms, Female/immunology/*microbiology ; Humans ; Nutritional Physiological Phenomena ; Probiotics/therapeutic use ; Tumor Microenvironment/immunology ; }, abstract = {Over the last decade, there has been a dramatic surge in research exploring the human gut microbiome and its role in health and disease. It is now widely accepted that commensal microorganisms coexist within the human gastrointestinal tract and other organs, including those of the reproductive tract. These microorganisms, which are collectively known as the "microbiome", contribute to maintaining host physiology and to the development of pathology. Next generation sequencing and multi-'omics' technology has enriched our understanding of the complex and interdependent relationship that exists between the host and microbiome. Global changes in the microbiome are known to be influenced by dietary, genetic, lifestyle, and environmental factors. Accumulating data have shown that alterations in the gut microbiome contribute to the development, prognosis and treatment of many disease states including cancer primarily through interactions with the immune system. However, there are large gaps in knowledge regarding the association between the gut microbiome and gynecologic cancers, and research characterizing the reproductive tract microbiome is insufficient. Herein, we explore the mechanisms by which alterations in the gut and reproductive tract microbiome contribute to carcinogenesis focusing on obesity, hyperestrogenism, inflammation and altered tumor metabolism. The impact of the gut microbiome on response to anti-cancer therapy is highlighted with an emphasis on immune checkpoint inhibitor efficacy in gynecologic cancers. We discuss dietary interventions that are likely to modulate the metabolic and immunologic milieu as well as tumor microenvironment through the gut microbiome including intermittent fasting/ketogenic diet, high fiber diet, use of probiotics and the metabolic management of obesity. We conclude that enhanced understanding of the microbiome in gynecologic cancers coupled with thorough evaluation of metabolic and metagenomic analyses would enable us to integrate novel preventative strategies and adjunctive interventions into the care of women with gynecologic cancers.}, } @article {pmid32930660, year = {2020}, author = {Dar, D and Thomashow, LS and Weller, DM and Newman, DK}, title = {Global landscape of phenazine biosynthesis and biodegradation reveals species-specific colonization patterns in agricultural soils and crop microbiomes.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {32930660}, issn = {2050-084X}, support = {R01 AI127850/AI/NIAID NIH HHS/United States ; W911NF-17-1-0024//Army Research Office/International ; 1R01AI127850-01A1/NH/NIH HHS/United States ; }, mesh = {Agriculture ; Biodegradation, Environmental ; Crops, Agricultural/*microbiology ; Gammaproteobacteria/physiology ; *Metagenomics ; *Microbiota ; Phenazines/*metabolism ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants/*metabolism ; Species Specificity ; Up-Regulation ; Zea mays/microbiology ; }, abstract = {Phenazines are natural bacterial antibiotics that can protect crops from disease. However, for most crops it is unknown which producers and specific phenazines are ecologically relevant, and whether phenazine biodegradation can counter their effects. To better understand their ecology, we developed and environmentally-validated a quantitative metagenomic approach to mine for phenazine biosynthesis and biodegradation genes, applying it to >800 soil and plant-associated shotgun-metagenomes. We discover novel producer-crop associations and demonstrate that phenazine biosynthesis is prevalent across habitats and preferentially enriched in rhizospheres, whereas biodegrading bacteria are rare. We validate an association between maize and Dyella japonica, a putative producer abundant in crop microbiomes. D. japonica upregulates phenazine biosynthesis during phosphate limitation and robustly colonizes maize seedling roots. This work provides a global picture of phenazines in natural environments and highlights plant-microbe associations of agricultural potential. Our metagenomic approach may be extended to other metabolites and functional traits in diverse ecosystems.}, } @article {pmid32928304, year = {2020}, author = {Korte, SW and Dorfmeyer, RA and Franklin, CL and Ericsson, AC}, title = {Acute and long-term effects of antibiotics commonly used in laboratory animal medicine on the fecal microbiota.}, journal = {Veterinary research}, volume = {51}, number = {1}, pages = {116}, pmid = {32928304}, issn = {1297-9716}, support = {K01 OD019924/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Administration, Oral ; Administration, Topical ; Animals ; Anti-Bacterial Agents/*administration & dosage ; Bacitracin/*administration & dosage ; Enrofloxacin/*administration & dosage ; Feces/*microbiology ; Female ; Injections, Subcutaneous/veterinary ; Mice ; Mice, Inbred C57BL ; Microbiota/*drug effects ; Neomycin/*administration & dosage ; Ointments/administration & dosage ; Polymyxins/*administration & dosage ; Trimethoprim, Sulfamethoxazole Drug Combination/*administration & dosage ; }, abstract = {Biomedical research relies on the use of animal models, and the animals used in those models receive medical care, including antibiotics for brief periods of time to treat conditions such as dermatitis, fight wounds, and suspected bacterial pathogens of unknown etiology. As many mouse model phenotypes are sensitive to changes in the gut microbiota, our goal was to examine the effect of antibiotics commonly administered to mice. Therefore, four treatment groups (subcutaneous enrofloxacin for 7 days, oral enrofloxacin for 14 days, oral trimethoprim-sulfamethoxazole for 14 days, and topical triple antibiotic ointment for 14 days) alongside a fifth control group receiving no treatment (n = 12/group) were included in our study. Fecal samples were collected prior to treatment, immediately after two weeks of exposure, and four weeks after cessation of treatment, and subjected to 16S rRNA library sequencing. The entire experimental design was replicated in mice from two different suppliers. As expected, several treatments including enrofloxacin and triple antibiotic ointment substantially decreased the amount of DNA recovered from fecal material, as well as the microbial richness. Notably, many of these effects were long-lasting with diminished gut microbiota (GM) richness four weeks following exposure, in both substrains of mice. Trimethoprim-sulfamethoxazole induced minimal to no discernible changes in the taxonomic composition beyond that seen in control mice. Collectively, these data highlight the need to consider the impact on GM of brief and seemingly routine use of antibiotics in the clinical care of research animals.}, } @article {pmid32927823, year = {2020}, author = {Bose, D and Saha, P and Mondal, A and Fanelli, B and Seth, RK and Janulewicz, P and Sullivan, K and Lasley, S and Horner, R and Colwell, RR and Shetty, AK and Klimas, N and Chatterjee, S}, title = {Obesity Worsens Gulf War Illness Symptom Persistence Pathology by Linking Altered Gut Microbiome Species to Long-Term Gastrointestinal, Hepatic, and Neuronal Inflammation in a Mouse Model.}, journal = {Nutrients}, volume = {12}, number = {9}, pages = {}, pmid = {32927823}, issn = {2072-6643}, support = {W81XWH1810374//U.S. Department of Defense/ ; W81XWH-13-2-0072//U.S. Department of Defense/ ; I01 CX001923-01//U.S. Department of Veterans Affairs/ ; }, mesh = {Animals ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Dysbiosis/complications/microbiology/pathology ; Gastroenteritis/complications/microbiology/pathology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/microbiology/pathology ; Hepatitis/complications/microbiology/pathology ; Inflammation ; Liver/microbiology/pathology ; Mice ; Neuritis/complications/microbiology/pathology ; Neurons/microbiology/pathology ; Obesity/complications/*microbiology/*pathology ; Persian Gulf Syndrome/complications/*microbiology/*pathology ; }, abstract = {Persistence of Gulf War illness (GWI) pathology among deployed veterans is a clinical challenge even after almost three decades. Recent studies show a higher prevalence of obesity and metabolic disturbances among Gulf War veterans primarily due to the existence of post-traumatic stress disorder (PTSD), chronic fatigue, sedentary lifestyle, and consumption of a high-carbohydrate/high-fat diet. We test the hypothesis that obesity from a Western-style diet alters host gut microbial species and worsens gastrointestinal and neuroinflammatory symptom persistence. We used a 5 month Western diet feeding in mice that received prior Gulf War (GW) chemical exposure to mimic the home phase obese phenotype of the deployed GW veterans. The host microbial profile in the Western diet-fed GWI mice showed a significant decrease in butyrogenic and immune health-restoring bacteria. The altered microbiome was associated with increased levels of IL6 in the serum, Claudin-2, IL6, and IL1β in the distal intestine with concurrent inflammatory lesions in the liver and hyperinsulinemia. Microbial dysbiosis was also associated with frontal cortex levels of increased IL6 and IL1β, activated microglia, decreased levels of brain derived neurotrophic factor (BDNF), and higher accumulation of phosphorylated Tau, an indicator of neuroinflammation-led increased risk of cognitive deficiencies. Mechanistically, serum from Western diet-fed mice with GWI significantly increased microglial activation in transformed microglial cells, increased tyrosyl radicals, and secreted IL6. Collectively, the results suggest that an existing obese phenotype in GWI worsens persistent gastrointestinal and neuronal inflammation, which may contribute to poor outcomes in restoring cognitive function and resolving fatigue, leading to the deterioration of quality of life.}, } @article {pmid32927192, year = {2020}, author = {B Henry, A and Maung, CEH and Kim, KY}, title = {Metagenomic analysis reveals enhanced biodiversity and composting efficiency of lignocellulosic waste by thermoacidophilic effective microorganism (tEM).}, journal = {Journal of environmental management}, volume = {276}, number = {}, pages = {111252}, doi = {10.1016/j.jenvman.2020.111252}, pmid = {32927192}, issn = {1095-8630}, mesh = {Biodiversity ; *Composting ; Lignin ; Soil ; }, abstract = {Composting is a microbiological process that converts organic waste into organic soil amendment. We reveal enhanced biodiversity and microbial population with subsequent enhancement of composting efficiency of lignocellulosic waste using thermoacidophilic effective microorganisms (tEM). Composting with tEM + shading (tEMA) or tEM without shading (tEMB) increased the average microbial population by 12.0% or 6.7%, respectively compared to non-tEM composting without shading/control (C). The biodiversity in tEMA or tEMB treated groups was increased by 34.7% or 43.7%, respectively, compared to C. The highest increase in population (31.7% and 9.4%) and diversity (91.2% and 91.6%) were observed in tEMA and tEMB at 30 d, respectively. Regarding microbial structure, the most dominant phylum shifted from Proteobacteria to Bacteroidetes during composting. From 60 to 120 d, tEM notably improved the average abundance of Firmicutes (mainly Bacillus) by 166.7% and 75.8% in tEMA and tEMB groups, respectively. The overall gradation rate of large compost granules (<2 mm) increased by 36.4% and 24.7%, following tEMA and tEMB treatment, respectively. The average rate of increase in bulk density was 42.6% or 33.3% by tEMA or tEMB, respectively, compared to C. We reveal the major differences in microbial structure, including a higher abundance of beneficial microbes like Bacillus in tEM treated composts. The study revealed that tEM could improve biodiversity and population of microbes, especially during thermophilic phase (above 45 °C), with a subsequent increase in composting rate, mineralization, and product quality. The results of this study are particularly invaluable in the areas of environmental conservation and organic agriculture.}, } @article {pmid32926879, year = {2021}, author = {Vandenborght, LE and Enaud, R and Urien, C and Coron, N and Girodet, PO and Ferreira, S and Berger, P and Delhaes, L}, title = {Type 2-high asthma is associated with a specific indoor mycobiome and microbiome.}, journal = {The Journal of allergy and clinical immunology}, volume = {147}, number = {4}, pages = {1296-1305.e6}, pmid = {32926879}, issn = {1097-6825}, mesh = {Adult ; Aged ; Air Pollution, Indoor/*analysis ; Asthma/*microbiology ; DNA, Bacterial/analysis ; DNA, Fungal/analysis ; Dust/*analysis ; Environmental Monitoring ; Female ; Humans ; Male ; *Microbiota/genetics ; Middle Aged ; Severity of Illness Index ; Sputum/microbiology ; }, abstract = {BACKGROUND: The links between microbial environmental exposures and asthma are well documented, but no study has combined deep sequencing results from pulmonary and indoor microbiomes of patients with asthma with spirometry, clinical, and endotype parameters.

OBJECTIVE: The goal of this study was to investigate the links between indoor microbial exposures and pulmonary microbial communities and to document the role of microbial exposures on inflammatory and clinical outcomes of patients with severe asthma (SA).

METHODS: A total of 55 patients with SA from the national Cohort of Bronchial Obstruction and Asthma cohort were enrolled for analyzing their indoor microbial flora through the use of electrostatic dust collectors (EDCs). Among these patients, 22 were able to produce sputum during "stable" or pulmonary "exacerbation" periods and had complete pairs of EDC and sputum samples, both collected and analyzed. We used amplicon targeted metagenomics to compare microbial communities from EDC and sputum samples of patients according to type 2 (T2)-asthma endotypes.

RESULTS: Compared with patients with T2-low SA, patients with T2-high SA exhibited an increase in bacterial α-diversity and a decrease in fungal α-diversity of their indoor microbial florae, the latter being significantly correlated with fraction of exhaled nitric oxide levels. The β-diversity of the EDC mycobiome clustered significantly according to T2 endotypes. Moreover, the proportion of fungal taxa in common between the sputum and EDC samples was significantly higher when patients exhibited acute exacerbation.

CONCLUSION: These results illustrated, for the first time, a potential association between the indoor mycobiome and clinical features of patients with SA, which should renew interest in deciphering the interactions between indoor environment, fungi, and host in asthma.}, } @article {pmid32925939, year = {2020}, author = {Clark, JJ and Gilray, J and Orton, RJ and Baird, M and Wilkie, G and Filipe, ADS and Johnson, N and McInnes, CJ and Kohl, A and Biek, R}, title = {Population genomics of louping ill virus provide new insights into the evolution of tick-borne flaviviruses.}, journal = {PLoS neglected tropical diseases}, volume = {14}, number = {9}, pages = {e0008133}, pmid = {32925939}, issn = {1935-2735}, support = {MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; BB/J013854/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Cell Line ; Cricetinae ; Encephalitis Viruses, Tick-Borne/classification/*genetics ; Encephalitis, Tick-Borne/virology ; *Evolution, Molecular ; Genetics, Population ; *Genome, Viral ; Metagenomics ; Phylogeny ; Sequence Analysis, RNA ; Sheep ; United Kingdom ; }, abstract = {The emergence and spread of tick-borne arboviruses pose an increased challenge to human and animal health. In Europe this is demonstrated by the increasingly wide distribution of tick-borne encephalitis virus (TBEV, Flavivirus, Flaviviridae), which has recently been found in the United Kingdom (UK). However, much less is known about other tick-borne flaviviruses (TBFV), such as the closely related louping ill virus (LIV), an animal pathogen which is endemic to the UK and Ireland, but which has been detected in other parts of Europe including Scandinavia and Russia. The emergence and potential spatial overlap of these viruses necessitates improved understanding of LIV genomic diversity, geographic spread and evolutionary history. We sequenced a virus archive composed of 22 LIV isolates which had been sampled throughout the UK over a period of over 80 years. Combining this dataset with published virus sequences, we detected no sign of recombination and found low diversity and limited evidence for positive selection in the LIV genome. Phylogenetic analysis provided evidence of geographic clustering as well as long-distance movement, including movement events that appear recent. However, despite genomic data and an 80-year time span, we found that the data contained insufficient temporal signal to reliably estimate a molecular clock rate for LIV. Additional analyses revealed that this also applied to TBEV, albeit to a lesser extent, pointing to a general problem with phylogenetic dating for TBFV. The 22 LIV genomes generated during this study provide a more reliable LIV phylogeny, improving our knowledge of the evolution of tick-borne flaviviruses. Our inability to estimate a molecular clock rate for both LIV and TBEV suggests that temporal calibration of tick-borne flavivirus evolution should be interpreted with caution and highlight a unique aspect of these viruses which may be explained by their reliance on tick vectors.}, } @article {pmid32919472, year = {2020}, author = {Seelbinder, B and Chen, J and Brunke, S and Vazquez-Uribe, R and Santhaman, R and Meyer, AC and de Oliveira Lino, FS and Chan, KF and Loos, D and Imamovic, L and Tsang, CC and Lam, RP and Sridhar, S and Kang, K and Hube, B and Woo, PC and Sommer, MOA and Panagiotou, G}, title = {Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {133}, pmid = {32919472}, issn = {2049-2618}, mesh = {Adolescent ; Adult ; Aged ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; Fungi/*drug effects/genetics ; Gastrointestinal Microbiome/*drug effects/genetics ; Humans ; Middle Aged ; Symbiosis/*drug effects ; Time Factors ; Young Adult ; }, abstract = {BACKGROUND: Antibiotic treatment has a well-established detrimental effect on the gut bacterial composition, but effects on the fungal community are less clear. Bacteria in the lumen of the gastrointestinal tract may limit fungal colonization and invasion. Antibiotic drugs targeting bacteria are therefore seen as an important risk factor for fungal infections and induced allergies. However, antibiotic effects on gut bacterial-fungal interactions, including disruption and resilience of fungal community compositions, were not investigated in humans. We analysed stool samples collected from 14 healthy human participants over 3 months following a 6-day antibiotic administration. We integrated data from shotgun metagenomics, metatranscriptomics, metabolomics, and fungal ITS2 sequencing.

RESULTS: While the bacterial community recovered mostly over 3 months post treatment, the fungal community was shifted from mutualism at baseline to competition. Half of the bacterial-fungal interactions present before drug intervention had disappeared 3 months later. During treatment, fungal abundances were associated with the expression of bacterial genes with functions for cell growth and repair. By extending the metagenomic species approach, we revealed bacterial strains inhibiting the opportunistic fungal pathogen Candida albicans. We demonstrated in vitro how C. albicans pathogenicity and host cell damage might be controlled naturally in the human gut by bacterial metabolites such as propionate or 5-dodecenoate.

CONCLUSIONS: We demonstrated that antibacterial drugs have long-term influence on the human gut mycobiome. While bacterial communities recovered mostly 30-days post antibacterial treatment, the fungal community was shifted from mutualism towards competition. Video abstract.}, } @article {pmid32919016, year = {2020}, author = {Zhang, H and Wang, Q and Zhao, J and Liu, S and Zhang, L and Zhao, Y and Yang, H and Sun, L}, title = {Quantitative microbiome profiling links microbial community variation to the intestine regeneration rate of the sea cucumber Apostichopus japonicus.}, journal = {Genomics}, volume = {112}, number = {6}, pages = {5012-5020}, doi = {10.1016/j.ygeno.2020.09.017}, pmid = {32919016}, issn = {1089-8646}, mesh = {Animals ; *Gastrointestinal Microbiome ; Intestines/microbiology/physiology ; Metagenomics ; Regeneration ; Stichopus/*microbiology/*physiology ; }, abstract = {The intestinal microbiota may play important roles in regenerating intestine of the sea cucumber Apostichopus japonicus, the underlying mechanism remains unclear. In the present study, a germ-free sea cucumber model was developed, and the intestinal microbial differentiation of faster and slower regenerating A. japonicus individuals during intestine regeneration was analyzed. The results revealed that depletion of the intestinal microbiota resulted in elevated abundance of the potential key players Flavobacteriaceae and Rhodobacteraceae during intestine regeneration and thus promoted the intestine regeneration rate of A. japonicus. Metagenomic analysis revealed that the increased abundance of Flavobacteriaceae elevated the enrichment of genes associated with carbohydrate utilization, whereas the abundant Rhodobacteraceae-enriched genes were associated with polyhydroxybutyrate production. We identified microbiota abundance as a key driver of microbial community alterations, especially beneficial microbiota members, in the developing intestine of A. japonicus. This study provides new insights into the mechanism of host-microbiota interactions related to organ regeneration.}, } @article {pmid32918877, year = {2020}, author = {Tsai, CM and Chen, JW and Lin, WC}, title = {Effects of Acanthamoeba castellanii on the dissolved oxygen and the microbial community under the experimental aquatic model.}, journal = {Experimental parasitology}, volume = {218}, number = {}, pages = {107985}, doi = {10.1016/j.exppara.2020.107985}, pmid = {32918877}, issn = {1090-2449}, mesh = {Acanthamoeba castellanii/genetics/*physiology ; Bdellovibrio/genetics/*isolation & purification/physiology ; DNA/isolation & purification ; Legionella/genetics/*isolation & purification/pathogenicity/physiology ; Microbiota/*physiology ; Oxygen/*metabolism ; Ponds/microbiology/parasitology ; RNA, Ribosomal, 16S/chemistry ; Real-Time Polymerase Chain Reaction ; Reproducibility of Results ; Virulence ; }, abstract = {Acanthamoeba castellanii is a protist that has a high predation efficiency for bacteria in a number of monoxenic culture experiments. However, the role of A. castellanii in the microbial community is still unknown because of the lack of studies on multiple-species interactions. The aim of this study was to investigate the change of bacterial composition after A. castellanii emerges in a water environment. We added A. castellanii to an environmental water sample and incubated it for two days. Then, we performed 16S ribosomal RNA sequencing techniques to analyze the changes in bacterial composition. In this study, A. castellanii slightly increased the relative abundance of a few opportunistic pathogens, such as Legionella, Roseomonas, and Haemophilus. This result may be related to the training ground hypothesis. On the other hand, the growth of some bacteria was inhibited, such as Cyanobacteria and Firmicutes. Although A. castellanii did not drastically change the whole bacterial community, we surprisingly found the dissolved oxygen concentration was increased after incubation with A. castellanii. We applied environmental water at the laboratory scale to investigate the interactions among A. castellanii, complex microbial communities and the environment. We identified the bacteria that are sensitive to A. castellanii and further found the novel relationship between dissolved oxygen and microbial interaction. Our results helped to clarify the role of A. castellanii in microbial communities.}, } @article {pmid32918562, year = {2021}, author = {Ennis, NJ and Dharumaduri, D and Bryce, JG and Tisa, LS}, title = {Metagenome Across a Geochemical Gradient of Indian Stone Ruins Found at Historic Sites in Tamil Nadu, India.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {385-395}, pmid = {32918562}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Climate ; India ; *Metagenome ; Microbiota/*genetics ; Minerals/analysis ; Quartz/analysis ; Silicon Dioxide/*chemistry ; }, abstract = {Although stone surfaces seem unlikely to be habitable, they support microbial life. Life on these surfaces are subjected to many varying harsh conditions and require the inhabitants to exhibit resistance to environmental factors including UV irradiation, toxic metal exposure, and fluctuating temperatures and humidity. Here we report the effect of hosting stone geochemistry on the microbiome of stone ruins found in Tamil Nadu, India. The microbial communities found on the two lithologies, granite and granodiorite, hosted distinct populations of bacteria. Geochemical composition analysis of sampled stones revealed quartz mineral content as a major driver of microbial community structure, particularly promoting community richness and proportions of Cyanobacteria and Deinococcus-Thermus. Other geochemical parameters including ilmenite, albite, anorthite, and orthoclase components or elemental concentrations (Ti, Fe, Mn, Na, and K) also influenced community structure to a lesser degree than quartz. Core members of the stone microbiome community found on both lithologies were also identified and included Cyanobacteria (Chroococcidiopsaceae and Dapisostemonum CCIBt 3536), Rubrobacter, and Deinococcus. A cluster of taxa including Sphingomonas, Geodermatophilus, and Truepera were mostly found in the granodiorite samples. Community diversity correlated with quartz mineral content in these samples may indicate that the microbial communities that attach to quartz surfaces may be transient and regularly changing. This work has expanded our understanding of built-stone microbial community structure based on lithology and geochemistry.}, } @article {pmid32917913, year = {2020}, author = {Vaga, S and Lee, S and Ji, B and Andreasson, A and Talley, NJ and Agréus, L and Bidkhori, G and Kovatcheva-Datchary, P and Park, J and Lee, D and Proctor, G and Ehrlich, SD and Nielsen, J and Engstrand, L and Shoaie, S}, title = {Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {14977}, pmid = {32917913}, issn = {2045-2322}, support = {project EP/ S001301/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Bacteroides/classification/genetics/metabolism ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Ileum/*microbiology ; Intestinal Mucosa/*microbiology ; Intestine, Large/*microbiology ; Male ; }, abstract = {Gut mucosal microbes evolved closest to the host, developing specialized local communities. There is, however, insufficient knowledge of these communities as most studies have employed sequencing technologies to investigate faecal microbiota only. This work used shotgun metagenomics of mucosal biopsies to explore the microbial communities' compositions of terminal ileum and large intestine in 5 healthy individuals. Functional annotations and genome-scale metabolic modelling of selected species were then employed to identify local functional enrichments. While faecal metagenomics provided a good approximation of the average gut mucosal microbiome composition, mucosal biopsies allowed detecting the subtle variations of local microbial communities. Given their significant enrichment in the mucosal microbiota, we highlight the roles of Bacteroides species and describe the antimicrobial resistance biogeography along the intestine. We also detail which species, at which locations, are involved with the tryptophan/indole pathway, whose malfunctioning has been linked to pathologies including inflammatory bowel disease. Our study thus provides invaluable resources for investigating mechanisms connecting gut microbiota and host pathophysiology.}, } @article {pmid32917751, year = {2020}, author = {Park, SJ and Andrei, AŞ and Bulzu, PA and Kavagutti, VS and Ghai, R and Mosier, AC}, title = {Expanded Diversity and Metabolic Versatility of Marine Nitrite-Oxidizing Bacteria Revealed by Cultivation- and Genomics-Based Approaches.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {22}, pages = {}, pmid = {32917751}, issn = {1098-5336}, mesh = {Bacteria/*classification/isolation & purification/*metabolism ; Geologic Sediments/microbiology ; Metabolic Networks and Pathways ; *Microbiota ; Nitrites/*metabolism ; Oxidation-Reduction ; Republic of Korea ; Seawater/microbiology ; }, abstract = {Nitrite-oxidizing bacteria (NOB) are ubiquitous and abundant microorganisms that play key roles in global nitrogen and carbon biogeochemical cycling. Despite recent advances in understanding NOB physiology and taxonomy, currently very few cultured NOB or representative NOB genome sequences from marine environments exist. In this study, we employed enrichment culturing and genomic approaches to shed light on the phylogeny and metabolic capacity of marine NOB. We successfully enriched two marine NOB (designated MSP and DJ) and obtained a high-quality metagenome-assembled genome (MAG) from each organism. The maximum nitrite oxidation rates of the MSP and DJ enrichment cultures were 13.8 and 30.0 μM nitrite per day, respectively, with these optimum rates occurring at 0.1 mM and 0.3 mM nitrite, respectively. Each enrichment culture exhibited a different tolerance to various nitrite and salt concentrations. Based on phylogenomic position and overall genome relatedness indices, both NOB MAGs were proposed as novel taxa within the Nitrospinota and Nitrospirota phyla. Functional predictions indicated that both NOB MAGs shared many highly conserved metabolic features with other NOB. Both NOB MAGs encoded proteins for hydrogen and organic compound metabolism and defense mechanisms for oxidative stress. Additionally, these organisms may have the genetic potential to produce cobalamin (an essential enzyme cofactor that is limiting in many environments) and, thus, may play an important role in recycling cobalamin in marine sediment. Overall, this study appreciably expands our understanding of the Nitrospinota and Nitrospirota phyla and suggests that these NOB play important biogeochemical roles in marine habitats.IMPORTANCE Nitrification is a key process in the biogeochemical and global nitrogen cycle. Nitrite-oxidizing bacteria (NOB) perform the second step of aerobic nitrification (converting nitrite to nitrate), which is critical for transferring nitrogen to other organisms for assimilation or energy. Despite their ecological importance, there are few cultured or genomic representatives from marine systems. Here, we obtained two NOB (designated MSP and DJ) enriched from marine sediments and estimated the physiological and genomic traits of these marine microbes. Both NOB enrichment cultures exhibit distinct responses to various nitrite and salt concentrations. Genomic analyses suggest that these NOB are metabolically flexible (similar to other previously described NOB) yet also have individual genomic differences that likely support distinct niche distribution. In conclusion, this study provides more insights into the ecological roles of NOB in marine environments.}, } @article {pmid32917644, year = {2020}, author = {Karpinets, TV and Solley, TN and Mikkelson, MD and Dorta-Estremera, S and Nookala, SS and Medrano, AYD and Petrosino, JF and Mezzari, MP and Zhang, J and Futreal, PA and Sastry, KJ and Colbert, LE and Klopp, A}, title = {Effect of Antibiotics on Gut and Vaginal Microbiomes Associated with Cervical Cancer Development in Mice.}, journal = {Cancer prevention research (Philadelphia, Pa.)}, volume = {13}, number = {12}, pages = {997-1006}, pmid = {32917644}, issn = {1940-6215}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*classification/genetics/growth & development/isolation & purification ; Female ; *Gastrointestinal Microbiome ; Mice ; Uterine Cervical Neoplasms/drug therapy/microbiology/*pathology ; Vagina/drug effects/*microbiology ; }, abstract = {Antibiotics affect microbial diversity in the gut, leading to dysbiosis and impaired immunity. However, the impact of antibiotics on microbial communities at other sites, such as vagina is less understood. It is also not clear whether changes induced by antibiotics in both microbiomes affect the development of cervical cancer. In this study, we utilized the murine model to evaluate these questions. We show that oral application of broad-spectrum antibiotics in mice changed not only diversity, but composition and sharing of gut and vaginal microbiomes in mice and influenced cervical cancer development in an orthotopic tumor model. Antibiotics decreased richness and diversity indexes in the gut but increased them in the vagina. Some beneficial taxa, such as Bacteroides, Ruminococcaceae, and Lachnospiraceae increased their abundance in the vagina while other pathogenic species, such as Proteobacteria, were decreased. As a result of the changes, mice with greater richness and diversity of the vaginal microbiome after antibiotics exposure were less likely developed tumors. No association between richness and diversity of the gut microbiome and tumor development was identified.}, } @article {pmid32917289, year = {2020}, author = {Leonard, MM and Karathia, H and Pujolassos, M and Troisi, J and Valitutti, F and Subramanian, P and Camhi, S and Kenyon, V and Colucci, A and Serena, G and Cucchiara, S and Montuori, M and Malamisura, B and Francavilla, R and Elli, L and Fanelli, B and Colwell, R and Hasan, N and Zomorrodi, AR and Fasano, A and , }, title = {Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {130}, pmid = {32917289}, issn = {2049-2618}, support = {F32 DK109620/DK/NIDDK NIH HHS/United States ; K23 DK122127/DK/NIDDK NIH HHS/United States ; P30 DK040561/DK/NIDDK NIH HHS/United States ; R01 DK104344/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteroides/genetics/isolation & purification ; Celiac Disease/*genetics/*microbiology ; Cesarean Section ; Cross-Sectional Studies ; *Environment ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Infant, Newborn ; Longitudinal Studies ; Male ; *Metabolomics ; *Metagenomics ; Methane/metabolism ; Pregnancy ; Prospective Studies ; Risk Factors ; Thioctic Acid/metabolism ; }, abstract = {BACKGROUND: Celiac disease (CD) is an autoimmune digestive disorder that occurs in genetically susceptible individuals in response to ingesting gluten, a protein found in wheat, rye, and barley. Research shows that genetic predisposition and exposure to gluten are necessary but not sufficient to trigger the development of CD. This suggests that exposure to other environmental stimuli early in life, e.g., cesarean section delivery and exposure to antibiotics or formula feeding, may also play a key role in CD pathogenesis through yet unknown mechanisms. Here, we use multi-omics analysis to investigate how genetic and early environmental risk factors alter the development of the gut microbiota in infants at risk of CD.

RESULTS: Toward this end, we selected 31 infants from a large-scale prospective birth cohort study of infants with a first-degree relative with CD. We then performed rigorous multivariate association, cross-sectional, and longitudinal analyses using metagenomic and metabolomic data collected at birth, 3 months and 6 months of age to explore the impact of genetic predisposition and environmental risk factors on the gut microbiota composition, function, and metabolome prior to the introduction of trigger (gluten). These analyses revealed several microbial species, functional pathways, and metabolites that are associated with each genetic and environmental risk factor or that are differentially abundant between environmentally exposed and non-exposed infants or between time points. Among our significant findings, we found that cesarean section delivery is associated with a decreased abundance of Bacteroides vulgatus and Bacteroides dorei and of folate biosynthesis pathway and with an increased abundance of hydroxyphenylacetic acid, alterations that are implicated in immune system dysfunction and inflammatory conditions. Additionally, longitudinal analysis revealed that, in infants not exposed to any environmental risk factor, the abundances of Bacteroides uniformis and of metabolite 3-3-hydroxyphenylproprionic acid increase over time, while those for lipoic acid and methane metabolism pathways decrease, patterns that are linked to beneficial immunomodulatory and anti-inflammatory effects.

CONCLUSIONS: Overall, our study provides unprecedented insights into major taxonomic and functional shifts in the developing gut microbiota of infants at risk of CD linking genetic and environmental risk factors to detrimental immunomodulatory and inflammatory effects. Video Abstract.}, } @article {pmid32916104, year = {2020}, author = {Chevalier, C and Kieser, S and Çolakoğlu, M and Hadadi, N and Brun, J and Rigo, D and Suárez-Zamorano, N and Spiljar, M and Fabbiano, S and Busse, B and Ivanišević, J and Macpherson, A and Bonnet, N and Trajkovski, M}, title = {Warmth Prevents Bone Loss Through the Gut Microbiota.}, journal = {Cell metabolism}, volume = {32}, number = {4}, pages = {575-590.e7}, pmid = {32916104}, issn = {1932-7420}, support = {815962/ERC_/European Research Council/International ; }, mesh = {Animals ; Cells, Cultured ; *Gastrointestinal Microbiome ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Osteoporosis/metabolism/*prevention & control ; Ovariectomy ; }, abstract = {Osteoporosis is the most prevalent metabolic bone disease, characterized by low bone mass and microarchitectural deterioration. Here, we show that warmth exposure (34°C) protects against ovariectomy-induced bone loss by increasing trabecular bone volume, connectivity density, and thickness, leading to improved biomechanical bone strength in adult female, as well as in young male mice. Transplantation of the warm-adapted microbiota phenocopies the warmth-induced bone effects. Both warmth and warm microbiota transplantation revert the ovariectomy-induced transcriptomics changes of the tibia and increase periosteal bone formation. Combinatorial metagenomics/metabolomics analysis shows that warmth enhances bacterial polyamine biosynthesis, resulting in higher total polyamine levels in vivo. Spermine and spermidine supplementation increases bone strength, while inhibiting polyamine biosynthesis in vivo limits the beneficial warmth effects on the bone. Our data suggest warmth exposure as a potential treatment option for osteoporosis while providing a mechanistic framework for its benefits in bone disease.}, } @article {pmid32915360, year = {2020}, author = {Faria, SL and Santos, A and Magro, DO and Cazzo, E and Assalin, HB and Guadagnini, D and Vieira, FT and Dutra, ES and Saad, MJA and Ito, MK}, title = {Gut Microbiota Modifications and Weight Regain in Morbidly Obese Women After Roux-en-Y Gastric Bypass.}, journal = {Obesity surgery}, volume = {30}, number = {12}, pages = {4958-4966}, pmid = {32915360}, issn = {1708-0428}, mesh = {Brazil ; Cross-Sectional Studies ; Female ; *Gastric Bypass ; *Gastrointestinal Microbiome ; Humans ; *Obesity, Morbid/surgery ; Weight Gain ; }, abstract = {INTRODUCTION: The relationship between late post-bariatric surgery weight regain and gut microbiota is not completely understood.

OBJECTIVE: To analyze the profile of gut microbiota among patients with and without late weight regain after post-Roux-en-Y gastric bypass (RYGB) and to compare it with a control group (CG) comprised of obese Brazilian individuals.

METHODS: This is a cross-sectional study which enrolled 34 morbidly obese women divided into 3 groups: post-Roux-en-Y gastric bypass without (RYGB_non-regain), and with weight regain (RYGB_regain) at least 5 years after surgery, and a CG of preoperative individuals. Gut microbiota was determined by metagenomic analyses.

RESULTS: The alpha diversity was higher in groups RYGB non-regain and RYGB regain when compared with CG (p < 0.05). Both RYGB non-regain and RYGB regain groups showed a lower abundance of the phylum Bacteroidetes when compared with CG (p < 0.01). The genera Bacteroides and SMB53 were increased in CG (p < 0.05). Group RYGB non-regain showed more abundance of the Akkermansia genus when compared with CG and group RYGB regain (p < 0.05). RYGB non-regain showed a greater abundance of the Phascolarctobacterium genus and lower of the SMB53 genus when compared with CG (p < 0.05). RYGB non-regain showed a greater abundance of the Phascolarctobacterium genus and a lower of the SMB53 genus when compared with CG (p < 0.05).

CONCLUSION: The gut microbiota of individuals which presented late weight regain after RYGB was significantly different in comparison to individuals with a successful weight loss, a finding that points towards a significant role of gut microbiota on weight loss and maintenance after surgery.}, } @article {pmid32912585, year = {2021}, author = {Zago, M and Bardelli, T and Rossetti, L and Nazzicari, N and Carminati, D and Galli, A and Giraffa, G}, title = {Evaluation of bacterial communities of Grana Padano cheese by DNA metabarcoding and DNA fingerprinting analysis.}, journal = {Food microbiology}, volume = {93}, number = {}, pages = {103613}, doi = {10.1016/j.fm.2020.103613}, pmid = {32912585}, issn = {1095-9998}, mesh = {Bacteria/classification/genetics ; Biodiversity ; Cheese/*microbiology ; Computational Biology ; DNA Barcoding, Taxonomic/*methods ; DNA Fingerprinting/*methods ; DNA, Bacterial/genetics ; *Food Microbiology ; Genotyping Techniques ; Lactobacillus/genetics ; Microbiota/*genetics ; Random Amplified Polymorphic DNA Technique ; Streptococcus thermophilus/genetics ; Thylakoids ; }, abstract = {The composition of the bacterial community of Grana Padano (GP) cheese was evaluated by an amplicon-based metagenomic approach (DNA metabarcoding) and RAPD-PCR fingerprinting. One hundred eighteen cheeses, which included 118 dairies located in the production area of GP, were collected. Two hundred fifty-four OTUs were detected, of which 82 were further discriminated between dominant (32 OTUs; > 1% total reads) and subdominant (50 OTUs; between 0.1% and 1% total reads) taxa. Lactobacillus (L.) delbrueckii, Lacticaseibacillus (Lact.) rhamnosus, Lact. casei, Limosilactobacillus fermentum, Lactococcus (Lc.) raffinolactis, L. helveticus, Streptococcus thermophilus, and Lc. lactis were the major dominant taxa ('core microbiota'). The origin of samples significantly impacted on both richness, evenness, and the relative abundance of bacterial species, with peculiar pattern distribution among the five GP production regions. A differential analysis allowed to find bacterial species significantly associated with specific region pairings. The analysis of pattern similarity among RAPD-PCR profiles highlighted the presence of a 'core' community banding pattern present in all the GP samples, which was strictly associated with the core microbiota highlighted by DNA metabarcoding. A trend to group samples according to the five production regions was also observed. This study widened our knowledge on the bacterial composition and ecology of Grana Padano cheese.}, } @article {pmid32912581, year = {2021}, author = {de C Lima, CO and Vaz, ABM and De Castro, GM and Lobo, F and Solar, R and Rodrigues, C and Martins Pinto, LR and Vandenberghe, L and Pereira, G and Miúra da Costa, A and Benevides, RG and Azevedo, V and Trovatti Uetanabaro, AP and Soccol, CR and Góes-Neto, A}, title = {Integrating microbial metagenomics and physicochemical parameters and a new perspective on starter culture for fine cocoa fermentation.}, journal = {Food microbiology}, volume = {93}, number = {}, pages = {103608}, doi = {10.1016/j.fm.2020.103608}, pmid = {32912581}, issn = {1095-9998}, mesh = {Acetic Acid/metabolism ; Acetobacter/metabolism ; Bacteria/metabolism ; Brazil ; Cacao/*microbiology ; Chocolate ; *Fermentation ; *Fermented Foods ; Flavoring Agents ; *Food Microbiology ; Hanseniaspora/genetics/metabolism ; Metagenomics/*methods ; Microbiota/genetics ; Seeds/microbiology ; }, abstract = {Cocoa beans used for chocolate production are fermented seeds of Theobroma cacao obtained by a natural fermentation process. The flavors and chemical compounds produced during the fermentation process make this step one of the most important in fine chocolate production. Herein, an integrative analysis of the variation of microbial community structure, using a shotgun metagenomics approach and associated physicochemical features, was performed during fermentation of fine cocoa beans. Samples of Forastero variety (FOR) and a mixture of two hybrids (PS1319 and CCN51) (MIX) from Bahia, Brazil, were analyzed at 7 different times. In the beginning (0 h), the structures of microbial communities were very different between FOR and MIX, reflecting the original plant-associated microbiomes. The highest change in microbial community structures occurred at the first 24 h of fermentation, with a marked increase in temperature and acetic acid concentration, and pH decrease. At 24-48 h both microbial community structures were quite homogenous regarding temperature, acetic acid, succinic acid, pH, soluble proteins and total phenols. During 72-96 h, the community structure resembles an acidic and warmer environment, prevailing few acetic acid bacteria. Taxonomic richness and abundance at 72-144 h exhibited significant correlation with temperature, reducing sugars, succinic, and acetic acids. Finally, we recommend that dominant microbial species of spontaneous fine cocoa fermentations should be considered as inoculum in accordance with the farm/region and GMP to maintain a differential organoleptic feature for production of fine chocolate. In our study, a starter inoculum composed of Acetobacter pausterianus and Hanseniaspora opuntiae strains is indicated.}, } @article {pmid32912302, year = {2020}, author = {Saary, P and Mitchell, AL and Finn, RD}, title = {Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {244}, pmid = {32912302}, issn = {1474-760X}, support = {BB/M011755/1, BB/R015228/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Eukaryota ; *Genome, Fungal ; Metagenomics/*methods ; Skin/microbiology ; *Software ; }, abstract = {Microbial eukaryotes constitute a significant fraction of biodiversity and have recently gained more attention, but the recovery of high-quality metagenomic assembled eukaryotic genomes is limited by the current availability of tools. To help address this, we have developed EukCC, a tool for estimating the quality of eukaryotic genomes based on the automated dynamic selection of single copy marker gene sets. We demonstrate that our method outperforms current genome quality estimators, particularly for estimating contamination, and have applied EukCC to datasets derived from two different environments to enable the identification of novel eukaryote genomes, including one from the human skin.}, } @article {pmid32912225, year = {2020}, author = {LaPierre, N and Alser, M and Eskin, E and Koslicki, D and Mangul, S}, title = {Metalign: efficient alignment-based metagenomic profiling via containment min hash.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {242}, pmid = {32912225}, issn = {1474-760X}, support = {T32 EB016640/EB/NIBIB NIH HHS/United States ; K25 HL080079/HL/NHLBI NIH HHS/United States ; U01 DA024417/DA/NIDA NIH HHS/United States ; R01 GM083198/GM/NIGMS NIH HHS/United States ; R01 ES021801/ES/NIEHS NIH HHS/United States ; R01 MH101782/MH/NIMH NIH HHS/United States ; R01 ES022282/ES/NIEHS NIH HHS/United States ; }, mesh = {Metagenomics/*methods ; Microbiota ; Sequence Alignment/*methods ; }, abstract = {Metagenomic profiling, predicting the presence and relative abundances of microbes in a sample, is a critical first step in microbiome analysis. Alignment-based approaches are often considered accurate yet computationally infeasible. Here, we present a novel method, Metalign, that performs efficient and accurate alignment-based metagenomic profiling. We use a novel containment min hash approach to pre-filter the reference database prior to alignment and then process both uniquely aligned and multi-aligned reads to produce accurate abundance estimates. In performance evaluations on both real and simulated datasets, Metalign is the only method evaluated that maintained high performance and competitive running time across all datasets.}, } @article {pmid32909848, year = {2020}, author = {Aryal, S and Alimadadi, A and Manandhar, I and Joe, B and Cheng, X}, title = {Machine Learning Strategy for Gut Microbiome-Based Diagnostic Screening of Cardiovascular Disease.}, journal = {Hypertension (Dallas, Tex. : 1979)}, volume = {76}, number = {5}, pages = {1555-1562}, pmid = {32909848}, issn = {1524-4563}, support = {R01 HL143082/HL/NHLBI NIH HHS/United States ; }, mesh = {Cardiovascular Diseases/*diagnosis/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; *Machine Learning ; Mass Screening/methods ; Metagenome ; }, abstract = {Cardiovascular disease (CVD) is the number one leading cause for human mortality. Besides genetics and environmental factors, in recent years, gut microbiota has emerged as a new factor influencing CVD. Although cause-effect relationships are not clearly established, the reported associations between alterations in gut microbiota and CVD are prominent. Therefore, we hypothesized that machine learning (ML) could be used for gut microbiome-based diagnostic screening of CVD. To test our hypothesis, fecal 16S ribosomal RNA sequencing data of 478 CVD and 473 non-CVD human subjects collected through the American Gut Project were analyzed using 5 supervised ML algorithms including random forest, support vector machine, decision tree, elastic net, and neural networks. Thirty-nine differential bacterial taxa were identified between the CVD and non-CVD groups. ML modeling using these taxonomic features achieved a testing area under the receiver operating characteristic curve (0.0, perfect antidiscrimination; 0.5, random guessing; 1.0, perfect discrimination) of ≈0.58 (random forest and neural networks). Next, the ML models were trained with the top 500 high-variance features of operational taxonomic units, instead of bacterial taxa, and an improved testing area under the receiver operating characteristic curves of ≈0.65 (random forest) was achieved. Further, by limiting the selection to only the top 25 highly contributing operational taxonomic unit features, the area under the receiver operating characteristic curves was further significantly enhanced to ≈0.70. Overall, our study is the first to identify dysbiosis of gut microbiota in CVD patients as a group and apply this knowledge to develop a gut microbiome-based ML approach for diagnostic screening of CVD.}, } @article {pmid32909146, year = {2020}, author = {Punyapwar, S and Mutnuri, S}, title = {Diversity and functional annotation of microorganisms in French vertical flow constructed wetland treating greywater.}, journal = {World journal of microbiology & biotechnology}, volume = {36}, number = {10}, pages = {148}, doi = {10.1007/s11274-020-02923-1}, pmid = {32909146}, issn = {1573-0972}, mesh = {Bacteria/*classification/genetics/*metabolism ; *Biodiversity ; Biological Oxygen Demand Analysis ; Carbon/metabolism ; Ecosystem ; Metagenomics ; Nitrogen/analysis ; Phosphorus/metabolism ; Proteobacteria ; *Soil Microbiology ; Waste Disposal, Fluid ; Wastewater/*microbiology ; Water Purification/*methods ; *Wetlands ; Xenobiotics/metabolism ; }, abstract = {Constructed wetlands form a unique ecosystem having plants, soil, microbes in which microorganisms play a vital role in the transformation and degradation of pollutants from wastewater. In the present study, French type two-stage vertical flow constructed wetland (VFCW) was used for the treatment of single household greywater (GW). Pilot-scale VFCW having sand and gravel as the filter substrate was constructed with Canna indica plantation for treating GW. To understand the pollutant removal mechanism in VFCW, microbial diversity and functional annotation was carried out by metagenomics analysis of sequences obtained from illumina platform. Efficiency of VFCW was measured with respect to water quality parameters like COD, BOD5, Total Nitrogen, Nitrate, Nitrite, Ammoniacal-N, ortho-phosphate and TOC from inlet and outlet of system. The removal efficiency was 90%, 93%, 34%, 26%, 89%, 68%, 80%, and 80% for COD, BOD5, Total Nitrogen, Nitrate, Nitrite, Ammoniacal-N, ortho-phosphate and TOC respectively. Microbial diversity was much more diversified and unique in VFCW compared to GW. Metagenomes exhibited Proteobacteria and Bacteroidetes as major phyla in GW whereas Actinobacteria, Proteobacteria, Nitrospirae abundance in VFCW layers. Total of 809 and 695 genus were found in VFCW and GW respectively with minimum abundance of 10 hits. From functional annotation of sequences, VFCW microbes have the potential to transform various aromatic and xenobiotic compounds along with the removal of pollutants present in the form of Carbon, Nitrogen, and Phosphorus. These data reveal French type VFCW can efficiently treat GW and with its own unique, variable habitat VFCW harbours diverse community of microorganisms that transform and degrade the pollutants in GW.}, } @article {pmid32907957, year = {2020}, author = {Brugger, SD and Eslami, SM and Pettigrew, MM and Escapa, IF and Henke, MT and Kong, Y and Lemon, KP}, title = {Dolosigranulum pigrum Cooperation and Competition in Human Nasal Microbiota.}, journal = {mSphere}, volume = {5}, number = {5}, pages = {}, pmid = {32907957}, issn = {2379-5042}, support = {R01 DC013554/DC/NIDCD NIH HHS/United States ; R01 GM117174/GM/NIGMS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/*metabolism ; Carnobacteriaceae/genetics/*physiology ; Child, Preschool ; Genomics ; Humans ; Infant ; *Microbial Interactions ; *Microbiota ; Nasopharynx/*microbiology ; Pneumococcal Infections/microbiology ; Staphylococcus aureus/genetics/physiology ; Streptococcus pneumoniae/genetics/physiology ; }, abstract = {Multiple epidemiological studies identify Dolosigranulum pigrum as a candidate beneficial bacterium based on its positive association with health, including negative associations with nasal/nasopharyngeal colonization by the pathogenic species Staphylococcus aureus and Streptococcus pneumoniae Using a multipronged approach to gain new insights into D. pigrum function, we observed phenotypic interactions and predictions of genomic capacity that support the idea of a role for microbe-microbe interactions involving D. pigrum in shaping the composition of human nasal microbiota. We identified in vivo community-level and in vitro phenotypic cooperation by specific nasal Corynebacterium species. Also, D. pigrum inhibited S. aureus growth in vitro, whereas robust inhibition of S. pneumoniae required both D. pigrum and a nasal Corynebacterium together. D. pigrum l-lactic acid production was insufficient to account for these inhibitions. Genomic analysis of 11 strains revealed that D. pigrum has a small genome (average 1.86 Mb) and multiple predicted auxotrophies consistent with D. pigrum relying on its human host and on cocolonizing bacteria for key nutrients. Further, the accessory genome of D. pigrum harbored a diverse repertoire of biosynthetic gene clusters, some of which may have a role in microbe-microbe interactions. These new insights into D. pigrum's functions advance the field from compositional analysis to genomic and phenotypic experimentation on a potentially beneficial bacterial resident of the human upper respiratory tract and lay the foundation for future animal and clinical experiments.IMPORTANCEStaphylococcus aureus and Streptococcus pneumoniae infections cause significant morbidity and mortality in humans. For both, nasal colonization is a risk factor for infection. Studies of nasal microbiota identify Dolosigranulum pigrum as a benign bacterium present when adults are free of S. aureus or when children are free of S. pneumoniae Here, we validated these in vivo associations with functional assays. We found that D. pigrum inhibited S. aureusin vitro and, together with a specific nasal Corynebacterium species, also inhibited S. pneumoniae Furthermore, genomic analysis of D. pigrum indicated that it must obtain key nutrients from other nasal bacteria or from humans. These phenotypic interactions support the idea of a role for microbe-microbe interactions in shaping the composition of human nasal microbiota and implicate D. pigrum as a mutualist of humans. These findings support the feasibility of future development of microbe-targeted interventions to reshape nasal microbiota composition to exclude S. aureus and/or S. pneumoniae.}, } @article {pmid32907949, year = {2020}, author = {Ramírez, AL and Colmant, AMG and Warrilow, D and Huang, B and Pyke, AT and McMahon, JL and Meyer, DB and Graham, RMA and Jennison, AV and Ritchie, SA and van den Hurk, AF}, title = {Metagenomic Analysis of the Virome of Mosquito Excreta.}, journal = {mSphere}, volume = {5}, number = {5}, pages = {}, pmid = {32907949}, issn = {2379-5042}, support = {1044698/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Aedes/*virology ; Animals ; Arboviruses/classification/isolation & purification ; Australia ; Culex/*virology ; Feces/*virology ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Insect Viruses/*classification/isolation & purification ; Metagenomics ; Virome/*genetics ; }, abstract = {Traditional screening for arboviruses in mosquitoes requires a priori knowledge and the utilization of appropriate assays for their detection. Mosquitoes can also provide other valuable information, including unexpected or novel arboviruses, nonarboviral pathogens ingested from hosts they feed on, and their own genetic material. Metagenomic analysis using next-generation sequencing (NGS) is a rapidly advancing technology that allows us to potentially obtain all this information from a mosquito sample without any prior knowledge of virus, host, or vector. Moreover, it has been recently demonstrated that pathogens, including arboviruses and parasites, can be detected in mosquito excreta by molecular methods. In this study, we investigated whether RNA viruses could be detected in mosquito excreta by NGS. Excreta samples were collected from Aedes vigilax and Culex annulirostris experimentally exposed to either Ross River or West Nile viruses and from field mosquitoes collected across Queensland, Australia. Total RNA was extracted from the excreta samples, reverse transcribed to cDNA, and sequenced using the Illumina NextSeq 500 platform. Bioinformatic analyses from the generated reads demonstrate that mosquito excreta provide sufficient RNA for NGS, allowing the assembly of near-full-length viral genomes. We detected Australian Anopheles totivirus, Wuhan insect virus 33, and Hubei odonate virus 5 and identified seven potentially novel viruses closely related to members of the order Picornavirales (2/7) and to previously described, but unclassified, RNA viruses (5/7). Our results suggest that metagenomic analysis of mosquito excreta has great potential for virus discovery and for unbiased arbovirus surveillance in the near future.IMPORTANCE When a mosquito feeds on a host, it ingests not only its blood meal but also an assortment of microorganisms that are present in the blood, thus acting as an environmental sampler. By using specific tests, it is possible to detect arthropod-borne viruses (arboviruses) like dengue and West Nile viruses in mosquito excreta. Here, we explored the use of next-generation sequencing (NGS) for unbiased detection of RNA viruses present in excreta from experimentally infected and field-collected mosquitoes. We have demonstrated that mosquito excreta provide a suitable template for NGS and that it is possible to recover and assemble near-full-length genomes of both arboviruses and insect-borne viruses, including potentially novel ones. These results importantly show the direct practicality of the use of mosquito excreta for NGS, which in the future could be used for virus discovery, environmental virome sampling, and arbovirus surveillance.}, } @article {pmid32907488, year = {2020}, author = {Sibai, M and Altuntaş, E and Yıldırım, B and Öztürk, G and Yıldırım, S and Demircan, T}, title = {Microbiome and Longevity: High Abundance of Longevity-Linked Muribaculaceae in the Gut of the Long-Living Rodent Spalax leucodon.}, journal = {Omics : a journal of integrative biology}, volume = {24}, number = {10}, pages = {592-601}, doi = {10.1089/omi.2020.0116}, pmid = {32907488}, issn = {1557-8100}, mesh = {Animals ; Bacteroidetes ; Biodiversity ; Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Longevity ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S ; Spalax/*microbiology/*physiology ; }, abstract = {With a world population living longer as well as marked disparities in life expectancy, understanding the determinants of longevity is one of the priority research agendas in 21st century life sciences. To this end, the blind mole-rat (Spalax leucodon), a subterranean mammalian, has emerged as an exceptional model organism due to its astonishing features such as remarkable longevity, hypoxia and hypercapnia tolerance, and cancer resistance. The microbiome has been found to be a vital parameter for cellular physiology and it is safe to assume that it has an impact on life expectancy. Although the unique characteristics of Spalax make it an ideal experimental model for longevity research, there is limited knowledge of the bacterial composition of Spalax microbiome, which limits its in-depth utilization. In this study, using 16S rRNA amplicon sequencing, we report the gut and skin bacterial structure of Spalax for the first time. The diversity between fecal and skin samples was manifested in the distant clustering, as revealed by beta diversity analysis. Importantly, the longevity-linked Muribaculaceae bacterial family was found to be the dominating bacterial taxa in Spalax fecal samples. These new findings contribute toward further development of Spalax as a model for longevity research and potential linkages between microbiome composition and longevity.}, } @article {pmid32905861, year = {2020}, author = {Basile, A and Campanaro, S and Kovalovszki, A and Zampieri, G and Rossi, A and Angelidaki, I and Valle, G and Treu, L}, title = {Revealing metabolic mechanisms of interaction in the anaerobic digestion microbiome by flux balance analysis.}, journal = {Metabolic engineering}, volume = {62}, number = {}, pages = {138-149}, doi = {10.1016/j.ymben.2020.08.013}, pmid = {32905861}, issn = {1096-7184}, mesh = {Anaerobiosis ; Archaea ; *Bioreactors ; Metagenomics ; *Microbiota ; }, abstract = {Anaerobic digestion is a key biological process for renewable energy, yet the mechanistic knowledge on its hidden microbial dynamics is still limited. The present work charted the interaction network in the anaerobic digestion microbiome via the full characterization of pairwise interactions and the associated metabolite exchanges. To this goal, a novel collection of 836 genome-scale metabolic models was built to represent the functional capabilities of bacteria and archaea species derived from genome-centric metagenomics. Dominant microbes were shown to prefer mutualistic, parasitic and commensalistic interactions over neutralism, amensalism and competition, and are more likely to behave as metabolite importers and profiteers of the coexistence. Additionally, external hydrogen injection positively influences microbiome dynamics by promoting commensalism over amensalism. Finally, exchanges of glucogenic amino acids were shown to overcome auxotrophies caused by an incomplete tricarboxylic acid cycle. Our novel strategy predicted the most favourable growth conditions for the microbes, overall suggesting strategies to increasing the biogas production efficiency. In principle, this approach could also be applied to microbial populations of biomedical importance, such as the gut microbiome, to allow a broad inspection of the microbial interplays.}, } @article {pmid32903276, year = {2020}, author = {Radwan, S and Gilfillan, D and Eklund, B and Radwan, HM and El Menofy, NG and Lee, J and Kapuscinski, M and Abdo, Z}, title = {A comparative study of the gut microbiome in Egyptian patients with Type I and Type II diabetes.}, journal = {PloS one}, volume = {15}, number = {9}, pages = {e0238764}, pmid = {32903276}, issn = {1932-6203}, mesh = {Adult ; Biodiversity ; Case-Control Studies ; Diabetes Mellitus, Type 1/*microbiology ; Diabetes Mellitus, Type 2/*microbiology ; Egypt ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; }, abstract = {INTRODUCTION: Diabetes remains a growing public health concern in Egypt, as prevalence of Type II diabetes (TIID) has nearly tripled there in the last two decades. Egypt was ranked ninth worldwide in number of diabetes cases, with prevalence of 15.56% among adults. Recent studies have proposed that disturbance of gut microbiota could influence TIID development and indicated associations between a reduced diversity in microbiomes and Type I diabetes (TID). In the present study, we investigated the composition and abundance of the bacterial microbiome in disease state (TID and TIID) of Egyptian patients. Our goal in this study was to characterize features of the gut microbiota and possible differences associated with TID and TIID in this population.

METHODS: DNA was extracted from fecal samples taken from 22 TID and 18 TIID outpatients of Al-Hussein hospital, Cairo, Egypt. 16S rRNA amplicon sequencing was used to characterize the bacterial taxa and these reads were processed using the software mothur with analysis utilizing packages vegan, phyloseq and metagenomSeq in R.

RESULTS AND CONCLUSIONS: Our results highlighted a significant increase in abundance of Gram negative, potentially opportunistic pathogenic taxa (Pseudomonas, Prevotella) in all diabetic groups, compared to the control. Lipopolysccharide (LPS), a component of the gram-negative bacterial wall, can activate local immune response and may result in low-grade systemic inflammation contributing to insulin resistance. The gram-positive Gemella, which is associated with increased risk to diabetes, also had a significant increase in abundance in all diabetic groups, compared to the control. In contrast, the commensal bacterial taxa Turicibacter, Terrisporobacter and Clostridium were found to be more abundant in the control group than in TID. Further studies are needed to understand the role of these taxa in health and disease. Lower Richness and low Shannon diversity, though not statistically significant, were observed for TID subjects with no glucose control and with onset of liver disease or hypertension compared to other subjects. In addition, large variation in alpha diversity within the control group could also be observed. Future studies will include larger samples sizes to further elucidate these findings, as well as possible metagenomic studies to examine the intriguing function of significant microbes.}, } @article {pmid32902144, year = {2022}, author = {Arteta, AA and Milanes-Yearsley, M and Cardona-Castro, N}, title = {Cholangiocyte derived carcinomas and local microbiota.}, journal = {Journal of hepato-biliary-pancreatic sciences}, volume = {29}, number = {10}, pages = {1084-1093}, doi = {10.1002/jhbp.826}, pmid = {32902144}, issn = {1868-6982}, support = {INV.022019.003.//Instituto Colombiano de Medicina Tropical (ICMT)/ ; }, mesh = {*Carcinoma ; *Helicobacter pylori/genetics ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Stomach Neoplasms ; }, abstract = {Trillions of bacteria are present in the gastrointestinal tract as part of the local microbiota. Bacteria have been associated with a wide range of gastrointestinal diseases including malignant neoplasms. The association of bacteria in gastrointestinal and biliary tract carcinogenesis is supported in the paradigm of Helicobacter pylori and intestinal-type gastric cancer. However, the association of bacterial species to a specific carcinoma, different from intestinal-type gastric cancer is unresolved. The relationship of bacteria to a specific malignant neoplasm can drive clinical interventions. We review the classic bacteria risk factors identified using cultures and PCR (polymerase chain reaction) with new research regarding a microbiota approach through 16S rRNA (16S ribosomal ribonucleic acid gene) or metagenomic analysis for selected carcinomas in the biliary tract.}, } @article {pmid32901430, year = {2020}, author = {Borčinová, M and Pitkina, A and Marešová, H and Štěpánek, V and Palyzová, A and Kyslík, P}, title = {Characteristics of microbial community of soil subjected to industrial production of antibiotics.}, journal = {Folia microbiologica}, volume = {65}, number = {6}, pages = {1061-1072}, pmid = {32901430}, issn = {1874-9356}, support = {GAUK 1470414//Univerzita Karlova v Praze/ ; RVO 61388971//Akademie Věd České Republiky (CZ)/ ; }, mesh = {Anti-Bacterial Agents/*biosynthesis ; Bacteria/*classification/genetics/isolation & purification/*metabolism ; Biodiversity ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; Industrial Microbiology ; Metagenome ; Metagenomics ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil ; *Soil Microbiology ; Soil Pollutants ; }, abstract = {Ecosystems worldwide are exposed to pollutants connected to the industrial production of pharmaceuticals. The objective of this study was to study the composition and characteristics of the soil microbial communities that had been exposed to long-term selection pressure caused by the industrial production of penicillin G. Soil samples from four sites among the penicillin G production plant were analysed using 16S rRNA profiling via Illumina MiSeq platform and were compared with the control samples from four sites outside the plant. Total metagenomic DNA from the impacted soil was also used for the preparation of E. coli T1R-based fosmid library which was consequently qualitatively tested for the presence of penicillin G acylase (PGA)-encoding genes using the method of sequence homology. Analyses of alpha diversity revealed that the long-term antibiotic presence in the soil significantly increased the microbial diversity and richness in terms of Shannon diversity index (p = 0.002) and Chao estimates (p = 0.004). Principal component analysis showed that the two types of communities (on-site and control) could be separated at the phylum, class and genus level. The on-site soil was enriched in Betaproteobacteria, Deltaproteobacteria, Gemmatimonadetes, Acidobacteria and Planctomycetia, while a significant decrease in Actinobacteria was observed. Metagenomic fosmid library revealed high hit rates in identifying PGAs (14 different genes identified) and confirmed the biotechnological potential of soils impacted by anthropogenic activity. This study offers new insights into the changes in microbial communities of soils exposed to anthropogenic activity as well as indicates that those soils may represent a hotspot for biotechnologically interesting targets.}, } @article {pmid32900816, year = {2020}, author = {Brown, EL and Essigmann, HT and Hoffman, KL and Palm, NW and Gunter, SM and Sederstrom, JM and Petrosino, JF and Jun, G and Aguilar, D and Perkison, WB and Hanis, CL and DuPont, HL}, title = {Impact of Diabetes on the Gut and Salivary IgA Microbiomes.}, journal = {Infection and immunity}, volume = {88}, number = {12}, pages = {}, pmid = {32900816}, issn = {1098-5522}, support = {R01 DK116378/DK/NIDDK NIH HHS/United States ; R01 DK118631/DK/NIDDK NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Bacteria/classification/*genetics ; Classification ; Diabetes Mellitus, Type 2/immunology/*microbiology ; Discriminant Analysis ; Dysbiosis ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Immunoglobulin A, Secretory/*analysis/immunology ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; }, abstract = {Mucosal surfaces like those present in the lung, gut, and mouth interface with distinct external environments. These mucosal gateways are not only portals of entry for potential pathogens but also homes to microbial communities that impact host health. Secretory immunoglobulin A (SIgA) is the single most abundant acquired immune component secreted onto mucosal surfaces and, via the process of immune exclusion, shapes the architecture of these microbiomes. Not all microorganisms at mucosal surfaces are targeted by SIgA; therefore, a better understanding of the SIgA-coated fraction may identify the microbial constituents that stimulate host immune responses in the context of health and disease. Chronic diseases like type 2 diabetes are associated with altered microbial communities (dysbiosis) that in turn affect immune-mediated homeostasis. 16S rRNA gene sequencing of SIgA-coated/uncoated bacteria (IgA-Biome) was conducted on stool and saliva samples of normoglycemic participants and individuals with prediabetes or diabetes (n = 8/group). These analyses demonstrated shifts in relative abundance in the IgA-Biome profiles between normoglycemic, prediabetic, or diabetic samples distinct from that of the overall microbiome. Differences in IgA-Biome alpha diversity were apparent for both stool and saliva, while overarching bacterial community differences (beta diversity) were also observed in saliva. These data suggest that IgA-Biome analyses can be used to identify novel microbial signatures associated with diabetes and support the need for further studies exploring these communities. Ultimately, an understanding of the IgA-Biome may promote the development of novel strategies to restructure the microbiome as a means of preventing or treating diseases associated with dysbiosis at mucosal surfaces.}, } @article {pmid32899836, year = {2020}, author = {Olsen, NS and Forero-Junco, L and Kot, W and Hansen, LH}, title = {Exploring the Remarkable Diversity of Culturable Escherichia coli Phages in the Danish Wastewater Environment.}, journal = {Viruses}, volume = {12}, number = {9}, pages = {}, pmid = {32899836}, issn = {1999-4915}, mesh = {Biodiversity ; Coliphages/classification/genetics/growth & development/*isolation & purification ; Denmark ; Genome Size ; Genome, Viral ; Genomics ; Phylogeny ; Wastewater/*virology ; }, abstract = {Phages drive bacterial diversity, profoundly influencing microbial communities, from microbiomes to the drivers of global biogeochemical cycling. Aiming to broaden our understanding of Escherichiacoli (MG1655, K-12) phages, we screened 188 Danish wastewater samples and isolated 136 phages. Ninety-two of these have genomic sequences with less than 95% similarity to known phages, while most map to existing genera several represent novel lineages. The isolated phages are highly diverse, estimated to represent roughly one-third of the true diversity of culturable virulent dsDNA Escherichia phages in Danish wastewater, yet almost half (40%) are not represented in metagenomic databases, emphasising the importance of isolating phages to uncover diversity. Seven viral families, Myoviridae, Siphoviridae, Podoviridae,Drexlerviridae,Chaseviridae,Autographviridae, and Microviridae, are represented in the dataset. Their genomes vary drastically in length from 5.3 kb to 170.8 kb, with a guanine and cytosine (GC) content ranging from 35.3% to 60.0%. Hence, even for a model host bacterium, substantial diversity remains to be uncovered. These results expand and underline the range of coliphage diversity and demonstrate how far we are from fully disclosing phage diversity and ecology.}, } @article {pmid32899763, year = {2020}, author = {El-Hossary, EM and Abdel-Halim, M and Ibrahim, ES and Pimentel-Elardo, SM and Nodwell, JR and Handoussa, H and Abdelwahab, MF and Holzgrabe, U and Abdelmohsen, UR}, title = {Natural Products Repertoire of the Red Sea.}, journal = {Marine drugs}, volume = {18}, number = {9}, pages = {}, pmid = {32899763}, issn = {1660-3397}, mesh = {Animals ; Aquatic Organisms/genetics/*metabolism ; Biological Products/chemistry/isolation & purification/*pharmacology ; Humans ; Indian Ocean ; Metagenomics ; Secondary Metabolism ; }, abstract = {Marine natural products have achieved great success as an important source of new lead compounds for drug discovery. The Red Sea provides enormous diversity on the biological scale in all domains of life including micro- and macro-organisms. In this review, which covers the literature to the end of 2019, we summarize the diversity of bioactive secondary metabolites derived from Red Sea micro- and macro-organisms, and discuss their biological potential whenever applicable. Moreover, the diversity of the Red Sea organisms is highlighted as well as their genomic potential. This review is a comprehensive study that compares the natural products recovered from the Red Sea in terms of ecological role and pharmacological activities.}, } @article {pmid32899230, year = {2020}, author = {Iacono, R and Cobucci-Ponzano, B and De Lise, F and Curci, N and Maurelli, L and Moracci, M and Strazzulli, A}, title = {Spatial Metagenomics of Three Geothermal Sites in Pisciarelli Hot Spring Focusing on the Biochemical Resources of the Microbial Consortia.}, journal = {Molecules (Basel, Switzerland)}, volume = {25}, number = {17}, pages = {}, pmid = {32899230}, issn = {1420-3049}, support = {ASI N. 2019-3-U.0//Agenzia Spaziale Italiana/ ; }, mesh = {DNA/genetics/isolation & purification ; Databases, Genetic ; Enzymes/metabolism ; Hot Springs/*microbiology ; Italy ; Metagenome ; *Metagenomics ; Microbial Consortia/*genetics ; Molecular Sequence Annotation ; Phylogeny ; }, abstract = {Terrestrial hot springs are of great interest to the general public and to scientists alike due to their unique and extreme conditions. These have been sought out by geochemists, astrobiologists, and microbiologists around the globe who are interested in their chemical properties, which provide a strong selective pressure on local microorganisms. Drivers of microbial community composition in these springs include temperature, pH, in-situ chemistry, and biogeography. Microbes in these communities have evolved strategies to thrive in these conditions by converting hot spring chemicals and organic matter into cellular energy. Following our previous metagenomic analysis of Pisciarelli hot springs (Naples, Italy), we report here the comparative metagenomic study of three novel sites, formed in Pisciarelli as result of recent geothermal activity. This study adds comprehensive information about phylogenetic diversity within Pisciarelli hot springs by peeking into possible mechanisms of adaptation to biogeochemical cycles, and high applicative potential of the entire set of genes involved in the carbohydrate metabolism in this environment (CAZome). This site is an excellent model for the study of biodiversity on Earth and biosignature identification, and for the study of the origin and limits of life.}, } @article {pmid32898701, year = {2020}, author = {Pereira, AC and Cunha, MV}, title = {An effective culturomics approach to study the gut microbiota of mammals.}, journal = {Research in microbiology}, volume = {171}, number = {8}, pages = {290-300}, doi = {10.1016/j.resmic.2020.09.001}, pmid = {32898701}, issn = {1769-7123}, mesh = {Animals ; Biodiversity ; Culture Media ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Herpestidae/*microbiology ; Male ; Mammals/microbiology ; *Metagenome ; Metagenomics/*methods ; Microbiological Techniques/*methods ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {The microbial characterization of the mammal's gut is an emerging research area, wherein culturomics methodologies applied to human samples are transposed to the animal context without improvement. In this work, using Egyptian mongoose as a model, we explore wet bench conditions to define an effective experimental design based on culturomics and DNA barcoding with potential application to different mammal species. After testing a battery of solid media and enrichments, we show that YCFA-based media, in aerobic and anaerobic conditions, together with PDA supplemented with chloramphenicol, are sufficient to maximize bacterial and fungal microbiota diversity. The pasteurization of the sample enrichment before cultivation is central to gain insight into sporogenic communities. We suggest the application of this optimized culturomics strategy to accurately expand knowledge on the microbial richness of mammals' gut, maximizing the application of common laboratory resources, without dramatic time and consumables expenditure but with high resolution of microbial landscapes. The analysis of ten fecal samples proved adequate to assess the core gastrointestinal microbiota of the mesocarnivore under analysis. This approach may empower most microbiology laboratories, particularly the veterinary, to perform studies on mammal's microbiota, and, in contrast with metagenomics, enabling the recovery of live bacteria for further studies.}, } @article {pmid32897356, year = {2020}, author = {Bandini, F and Misci, C and Taskin, E and Cocconcelli, PS and Puglisi, E}, title = {Biopolymers modulate microbial communities in municipal organic waste digestion.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {10}, pages = {}, doi = {10.1093/femsec/fiaa183}, pmid = {32897356}, issn = {1574-6941}, mesh = {Anaerobiosis ; Biopolymers ; Bioreactors ; Digestion ; *Microbiota ; Phylogeny ; *Refuse Disposal ; }, abstract = {The development of biopolymers has raised issues about their recalcitrance in the environment. Their disposal is mainly carried out with the organic fraction of municipal solid waste (OFMSW) through thermophilic anaerobic digestion and aerobic composting, bioprocesses aimed at turning organic matter into biogas and compost. However, the effects of biopolymers on OFMSW treatment, on the final compost and on the microbial communities involved are partly unexplored. In this study, the OFMSW treatment was reproduced on a laboratory-scale respecting real plant conditions and testing the impacts of mixing polylactic acid (PLA) and starch-based bioplastic (SBB) separately. The dynamics of bacterial, archaeal and fungal communities during the process was screened by high-throughput sequencing (HTS) of phylogenetic amplicons. Starch-based bioplastic showed a minor and heterogeneous microbial diversity between the anaerobic and aerobic phases. Contrariwise, PLA treatment resulted in wider and more diverse bacterial and fungal communities for the compost and the aerobic biofilm. Since the biodiversity in compost may play a crucial role in its stability and safety, the modulation of environmental microbial communities induced by higher concentrations of PLA in OFMSW treatment can pose relevant issues.}, } @article {pmid32896190, year = {2021}, author = {Maity, C and Gupta PhD, AK and Saroj, DB and Biyani, A and Bagkar, P and Kulkarni, J and Dixit, Y}, title = {Impact of a Gastrointestinal Stable Probiotic Supplement Bacillus coagulans LBSC on Human Gut Microbiome Modulation.}, journal = {Journal of dietary supplements}, volume = {18}, number = {6}, pages = {577-596}, doi = {10.1080/19390211.2020.1814931}, pmid = {32896190}, issn = {1939-022X}, mesh = {*Bacillus coagulans ; *Gastrointestinal Microbiome ; Humans ; *Irritable Bowel Syndrome ; *Microbiota ; *Probiotics ; }, abstract = {Bacillus coagulans LBSC showed stability in acidic pH, bile and simulated human gastrointenstinal juices. Under static gut model, when passed through oral, gastric and intestinal phases, B. coagulans LBSC was found to be stable as free viable spores and also with various foods such as milk and baby foods, as well as American and European diets. In human studies, modulation of gut microbiota by B. coagulans LBSC was comprehended by whole genome metagenome analysis of fecal samples obtained from pre- and post-treatment of irritable bowel syndrome (IBS) patients. B. coagulans LBSC treatment showed positive modulation in gut microbiota, especially up regulation of phyla such as Actinobacteria and Firmicutes, whereas down regulation of Bacteroids, Proteobacteria, Streptophyta and Verrucomicrobia. Simultaneously, it has altered various microbiota associated metabolic pathways to create the normalcy of gut microenvironment.}, } @article {pmid32893195, year = {2020}, author = {Yamamoto, K and Matsutani, M and Shiwa, Y and Ishige, T and Sakamoto, H and Saitoh, H and Tsushima, S}, title = {Comparative Analysis of Bacterial Diversity and Community Structure in the Rhizosphere and Root Endosphere of Two Halophytes, Salicornia europaea and Glaux maritima, Collected from Two Brackish Lakes in Japan.}, journal = {Microbes and environments}, volume = {35}, number = {3}, pages = {}, pmid = {32893195}, issn = {1347-4405}, mesh = {Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Chenopodiaceae/microbiology ; Japan ; Lakes/chemistry/*microbiology ; *Microbiota ; Phylogeography ; Plant Roots/microbiology ; Primulaceae/microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Salt-Tolerant Plants/*microbiology ; }, abstract = {Microbial community structures associated with halophytes and their compositions among different habitats, particularly natural saline sites, have not yet been investigated in detail. In the present study, we examined the diversity and composition of the rhizosphere and root endosphere bacteria of two halophytes, Salicornia europaea L. and Glaux maritima L., collected from two adjacent brackish lakes, Lake Notoro and Lake Tofutsu, in Japan. The bacterial species richness and diversity indices of the two halophytes collected from both lakes showed no significant differences in the rhizosphere or root endosphere. In contrast, beta diversity and taxonomic analyses revealed significant differences in the bacterial communities from each halophyte between the two lakes even though the two locations were natural saline sites, indicating that the bacterial communities for S. europaea and G. maritima both fluctuated in a manner that depended on the geographical location. Common and abundant genera associated with each halophyte across the two lakes were then identified to verify the bacterial genera specifically inhabiting each plant species. The results obtained showed that the composition of abundant genera inhabiting each halophyte across two lakes was distinct from that reported previously in other saline soil areas. These results suggest that each halophyte in different geographical sites had an individual complex bacterial community.}, } @article {pmid32892222, year = {2020}, author = {Garey, KW and Begum, K and Lancaster, C and Gonzales-Luna, A and Bui, D and Mercier, J and Seng Yue, C and Ducharme, MP and Hu, M and Vince, B and Silverman, MH and Alam, MJ and Kankam, M}, title = {A randomized, double-blind, placebo-controlled, single and multiple ascending dose Phase 1 study to determine the safety, pharmacokinetics and food and faecal microbiome effects of ibezapolstat administered orally to healthy subjects.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {75}, number = {12}, pages = {3635-3643}, pmid = {32892222}, issn = {1460-2091}, mesh = {Administration, Oral ; *Clostridioides difficile ; *Clostridium Infections/drug therapy ; Dose-Response Relationship, Drug ; Double-Blind Method ; Female ; Healthy Volunteers ; Humans ; Male ; *Microbiota ; }, abstract = {BACKGROUND: Clostridioides difficile infection is the most common cause of healthcare-associated infections in the USA, with limited treatment options. Ibezapolstat is a novel DNA polymerase IIIC inhibitor with in vitro activity against C. difficile.

OBJECTIVES AND METHODS: Randomized, double-blind, placebo-controlled study to assess the safety, tolerability and pharmacokinetics of ibezapolstat in healthy volunteers. Microbiome changes associated with ibezapolstat were compared with vancomycin over a 10 day course using shotgun metagenomics.

RESULTS: A total of 62 subjects aged 31 ± 7 years (45% female; average BMI: 25 ± 3 kg/m2) were randomized. Ibezapolstat was well tolerated with a safety signal similar to placebo. Ibezapolstat had minimal systemic absorption with the majority of plasma concentrations less than 1 µg/mL. In the multiday, ascending dose study, ibezapolstat concentrations of 2000 µg/g of stool were observed by Day 2 and for the remainder of the dosing time period. In the multiday, multiple-dose arm, baseline microbiota was comparable between subjects that received ibezapolstat compared with vancomycin. At Day 10 of dosing, differential abundance analysis and β-diversity demonstrated a distinct difference between the microbiome in subjects given vancomycin compared with either dose of ibezapolstat (P = 0.006). α-Diversity changes were characterized as an increase in the Actinobacteria phylum in subjects that received ibezapolstat and an increase in Proteobacteria in subjects given vancomycin.

CONCLUSIONS: Ibezapolstat was shown to be safe and well tolerated, with minimal systemic exposure, high stool concentrations and a distinct microbiome profile compared with oral vancomycin. These results support further clinical development of ibezapolstat for patients with C. difficile infection.}, } @article {pmid32891158, year = {2020}, author = {Ortiz-Baez, AS and Cousins, K and Eden, JS and Chang, WS and Harvey, E and Pettersson, JH and Carver, S and Polkinghorne, A and Šlapeta, J and Rose, K and Holmes, EC}, title = {Meta-transcriptomic identification of Trypanosoma spp. in native wildlife species from Australia.}, journal = {Parasites & vectors}, volume = {13}, number = {1}, pages = {447}, pmid = {32891158}, issn = {1756-3305}, support = {FL170100022//Australian Research Council (AU)/ ; }, mesh = {Animals ; Animals, Wild/*parasitology ; Australia ; Biodiversity ; Biological Evolution ; DNA, Protozoan/genetics ; Host-Parasite Interactions ; Marsupialia/parasitology ; Metagenomics ; Passeriformes/parasitology ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Ranidae/parasitology ; Transcriptome ; *Trypanosoma/classification/genetics/isolation & purification ; Vertebrates/parasitology ; }, abstract = {BACKGROUND: Wildlife species carry a remarkable diversity of trypanosomes. The detection of trypanosome infection in native Australian fauna is central to understanding their diversity and host-parasite associations. The implementation of total RNA sequencing (meta-transcriptomics) in trypanosome surveillance and diagnosis provides a powerful methodological approach to better understand the host species distribution of this important group of parasites.

METHODS: We implemented a meta-transcriptomic approach to detect trypanosomes in a variety of tissues (brain, liver, lung, skin, gonads) sampled from native Australian wildlife, comprising four marsupials (koala, Phascolarctos cinereus; southern brown bandicoot, Isoodon obesulus; swamp wallaby, Wallabia bicolor; bare-nosed wombat, Vombatus ursinus), one bird (regent honeyeater, Anthochaera phrygia) and one amphibian (eastern dwarf tree frog, Litoria fallax). Samples corresponded to both clinically healthy and diseased individuals. Sequencing reads were de novo assembled into contigs and annotated. The evolutionary relationships among the trypanosomatid sequences identified were determined through phylogenetic analysis of 18S rRNA sequences.

RESULTS: We detected trypanosome sequences in all six species of vertebrates sampled, with positive samples in multiple organs and tissues confirmed by PCR. Phylogenetic analysis indicated that the trypanosomes infecting marsupials were related to those previously detected in placental and marsupial mammals, while the trypanosome in the regent honeyeater grouped with avian trypanosomes. In contrast, we provide the first evidence for a trypanosome in the eastern dwarf tree frog that was phylogenetically distinct from those described in other amphibians.

CONCLUSIONS: To our knowledge, this is the first meta-transcriptomic analysis of trypanosomes in native Australian wildlife, expanding the known genetic diversity of these important parasites. We demonstrated that RNA sequencing is sufficiently sensitive to detect low numbers of Trypanosoma transcripts and from diverse hosts and tissues types, thereby representing an effective means to detect trypanosomes that are divergent in genome sequence.}, } @article {pmid32890633, year = {2020}, author = {Joulian, C and Fonti, V and Chapron, S and Bryan, CG and Guezennec, AG}, title = {Bioleaching of pyritic coal wastes: bioprospecting and efficiency of selected consortia.}, journal = {Research in microbiology}, volume = {171}, number = {7}, pages = {260-270}, doi = {10.1016/j.resmic.2020.08.002}, pmid = {32890633}, issn = {1769-7123}, mesh = {Bacteria/classification/*metabolism ; *Biodegradation, Environmental ; Bioprospecting ; Bioreactors/*microbiology ; Coal/analysis ; Industrial Waste/*analysis ; Iron/*metabolism ; Microbial Consortia/physiology ; Mining ; Poland ; Sulfides/*metabolism ; Sulfur/metabolism ; }, abstract = {Pyrite-bearing coal wastes are responsible of the formation of acid mine drainage (AMD), and their management to mitigate environmental impacts is a challenge to the coal mine industry in Europe and worldwide. The European CEReS project sought to develop a generic co-processing strategy to reuse and recycle coal wastes, based on removal of AMD generating potential through bioleaching. Chemolitoautotrophic iron- and sulfur-oxidizing microbial consortia were enriched from a Polish coal waste at 30 °C and 48 °C, but not 42 °C. Pyrite leaching yield, determined from bioleaching tests in 2-L stirred bioreactors, was best with the 48 °C endogenous consortium (80%), then the 42 °C exogenous BRGM-KCC consortium (71%), and finally the 30 °C endogenous consortium (50%). 16S rRNA gene-targeted metagenomics from five surface locations on the dump waste revealed a microbial community adapted to the site context, composed of iron- and/or sulfur-oxidizing genera thriving in low pH and metal rich environments and involved in AMD generation. All together, the results confirmed the predisposition of the pyritic coal waste to bioleaching and the potential of endogenous microorganisms for efficient bioleaching at 48 °C. The good leaching yields open the perspective to optimize further and scale-up the bioleaching process.}, } @article {pmid32889498, year = {2020}, author = {Acharya, K and Halla, FF and Massawa, SM and Mgana, SM and Komar, T and Davenport, RJ and Werner, D}, title = {Chlorination effects on DNA based characterization of water microbiomes and implications for the interpretation of data from disinfected systems.}, journal = {Journal of environmental management}, volume = {276}, number = {}, pages = {111319}, doi = {10.1016/j.jenvman.2020.111319}, pmid = {32889498}, issn = {1095-8630}, mesh = {Chlorine ; *Halogenation ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Water ; Water Microbiology ; }, abstract = {Quantitative PCR (qPCR) and next generation sequencing (NGS) are nucleic acid based microbiology techniques that provide new insights into drinking water quality, but considerable uncertainty remains around their correct interpretation. We noticed the presence of bacterial DNA from various putative pathogens, including from faecal indicator bacteria (FIB), in disinfected water, when culturable FIB were absent. To understand these observations better we studied the effect of chlorination on conventional and DNA based microbial water quality assessments. Surface water chlorination reduced plate counts for various FIB by up to >6 log units, intact cell counts by flow cytometry by 3.3 log units, and 16S rRNA gene copies by qPCR by 1.5 and 1.6 log units for total bacteria and total coliforms, respectively. Nanopore sequencing of 16S rRNA amplicons with the portable MinION device revealed the DNA from several families containing putative pathogens appeared to be more resistant than that of other bacteria to degradation by chlorine disinfection. For instance, 16S rRNA genes assigned to the Enterobacteriaceae family, members of which are mostly the target of coliform tests, increased in relative abundance from 0.001 ± 0.0002% to 0.0036 ± 0.003% after chlorine treatment. Hence, metagenomic drinking water data needs to be interpreted with caution. Plate counts and flow cytometry in combination with DNA based analysis provide more robust insight than NGS or qPCR alone.}, } @article {pmid32888329, year = {2021}, author = {Yang, J and Li, F and Zhang, Y and He, Z}, title = {Metagenomic analysis of microbial community succession during the pickling process of Zhacai (preserved mustard tuber) and its correlation with Zhacai biochemical indices.}, journal = {Journal of the science of food and agriculture}, volume = {101}, number = {4}, pages = {1646-1658}, doi = {10.1002/jsfa.10785}, pmid = {32888329}, issn = {1097-0010}, support = {cstc2017jcyjAX0249//Chongqing Research Program of Basic Research and Frontier Technology/ ; XDJK2018C070 XDJK2015C135 SWU113035//Fundamental Research Funds for the Central Universities/ ; 31801529//National Natural Science Foundation of China/ ; CC18Z20//Scientific research project of Sichuan Cuisine Development Research Center, Sichuan Tourism University/ ; }, mesh = {Bacteria/classification/genetics/*isolation & purification ; Fermentation ; Fermented Foods/*microbiology ; Fungi/classification/genetics/*isolation & purification ; Metagenomics ; *Microbiota ; Mustard Plant/*microbiology ; }, abstract = {BACKGROUND: Industrial Fuling Zhacai is pickled by a method summarized as 'three times pickled and pressed', in which raw mustard tubers are subjected to three stages of pickling in different salt concentrations, with a pressing operation at the end of each stage to remove brine. This study used Illumina MiSeq technology and multivariate statistical analyses to investigate microbial community succession during the pickling process and its correlation with Zhacai biochemical indices.

RESULTS: A total of 19 phyla, 208 genera, and 295 species of bacteria were identified. Lactobacillus was the dominant genus of bacteria in all three stages and Lactobacillus sakei was the dominant species in the first and second stages. A total of six phyla, 200 genera and 301 species of fungi were also identified. According to a PICRUSt2 prediction, the main functions of the bacterial and fungal communities were carbohydrate and protein metabolism, while alcohol metabolism was also a function of fungi. Nine bacterial genera closely correlated with Zhacai biochemical indices: Acinetobacter, Pseudomonas, Pedobacter, Erwinia, Lactobacillus, Chryseobacterium, Flavobacterium, Duganella, and Paenarthrobacter. Six genera of fungi correlated closely: Penicillium, Cystobasidium, Cladosporium, Plenodomus, Aspergillus, and Simplicillium. All these genera probably originated from the surface microorganisms of raw mustard tuber.

CONCLUSION: This study reveals the succession patterns of microbial community structures during the pickling process of industrial Zhacai and infers the core functional flora, providing reference data for Zhacai pickling process control. © 2020 Society of Chemical Industry.}, } @article {pmid32887946, year = {2021}, author = {Fan, Y and Pedersen, O}, title = {Gut microbiota in human metabolic health and disease.}, journal = {Nature reviews. Microbiology}, volume = {19}, number = {1}, pages = {55-71}, pmid = {32887946}, issn = {1740-1534}, mesh = {Animals ; Biodiversity ; *Disease Susceptibility ; *Energy Metabolism ; *Gastrointestinal Microbiome ; *Health ; Humans ; Metabolic Diseases/*etiology/*metabolism ; }, abstract = {Observational findings achieved during the past two decades suggest that the intestinal microbiota may contribute to the metabolic health of the human host and, when aberrant, to the pathogenesis of various common metabolic disorders including obesity, type 2 diabetes, non-alcoholic liver disease, cardio-metabolic diseases and malnutrition. However, to gain a mechanistic understanding of how the gut microbiota affects host metabolism, research is moving from descriptive microbiota census analyses to cause-and-effect studies. Joint analyses of high-throughput human multi-omics data, including metagenomics and metabolomics data, together with measures of host physiology and mechanistic experiments in humans, animals and cells hold potential as initial steps in the identification of potential molecular mechanisms behind reported associations. In this Review, we discuss the current knowledge on how gut microbiota and derived microbial compounds may link to metabolism of the healthy host or to the pathogenesis of common metabolic diseases. We highlight examples of microbiota-targeted interventions aiming to optimize metabolic health, and we provide perspectives for future basic and translational investigations within the nascent and promising research field.}, } @article {pmid32887934, year = {2020}, author = {Choi, DH and Park, J and Choi, JK and Lee, KE and Lee, WH and Yang, J and Lee, JY and Park, YJ and Oh, C and Won, HR and Koo, BS and Chang, JW and Park, YS}, title = {Association between the microbiomes of tonsil and saliva samples isolated from pediatric patients subjected to tonsillectomy for the treatment of tonsillar hyperplasia.}, journal = {Experimental & molecular medicine}, volume = {52}, number = {9}, pages = {1564-1573}, pmid = {32887934}, issn = {2092-6413}, support = {2016M3A9B4919639//National Research Foundation of Korea (NRF)/ ; 2017R1A2B4002611//National Research Foundation of Korea (NRF)/ ; 2019M3A9H1032376//National Research Foundation of Korea (NRF)/ ; 2016R1D1A1B04932112//National Research Foundation of Korea (NRF)/ ; }, mesh = {Biomarkers ; Child ; Child, Preschool ; Female ; Humans ; Hyperplasia ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Palatine Tonsil/*microbiology/*pathology/surgery ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; Tonsillectomy ; }, abstract = {Oral microbes have the capacity to spread throughout the gastrointestinal system and are strongly associated with multiple diseases. Given that tonsils are located between the oral cavity and the laryngopharynx at the gateway of the alimentary and respiratory tracts, tonsillar tissue may also be affected by microbiota from both the oral cavity (saliva) and the alimentary tract. Here, we analyzed the distribution and association of the microbial communities in the saliva and tonsils of Korean children subjected to tonsillectomy because of tonsil hyperplasia (n = 29). The microbiome profiles of saliva and tonsils were established via 16S rRNA gene sequencing. Based on the alpha diversity indices, the microbial communities of the two groups showed high similarities. According to Spearman's ranking correlation analysis, the distribution of Treponema, the causative bacterium of periodontitis, in saliva and tonsils was found to have a significant positive correlation. Two representative microbes, Prevotella in saliva and Alloprevotella in tonsils, were negatively correlated, while Treponema 2 showed a strong positive correlation between saliva and tonsils. Taken together, strong similarities in the microbial communities of the tonsils and saliva are evident in terms of diversity and composition. The saliva microbiome is expected to significantly affect the tonsil microbiome. Furthermore, we suggest that our study creates an opportunity for tonsillar microbiome research to facilitate the development of novel microbiome-based therapeutic strategies.}, } @article {pmid32884659, year = {2020}, author = {Saccò, M and Blyth, AJ and Humphreys, WF and Cooper, SJB and Austin, AD and Hyde, J and Mazumder, D and Hua, Q and White, NE and Grice, K}, title = {Refining trophic dynamics through multi-factor Bayesian mixing models: A case study of subterranean beetles.}, journal = {Ecology and evolution}, volume = {10}, number = {16}, pages = {8815-8826}, pmid = {32884659}, issn = {2045-7758}, abstract = {Food web dynamics are vital in shaping the functional ecology of ecosystems. However, trophic ecology is still in its infancy in groundwater ecosystems due to the cryptic nature of these environments. To unravel trophic interactions between subterranean biota, we applied an interdisciplinary Bayesian mixing model design (multi-factor BMM) based on the integration of faunal C and N bulk tissue stable isotope data (δ[13]C and δ[15]N) with radiocarbon data (Δ[14]C), and prior information from metagenomic analyses. We further compared outcomes from multi-factor BMM with a conventional isotope double proxy mixing model (SIA BMM), triple proxy (δ[13]C, δ[15]N, and Δ[14]C, multi-proxy BMM), and double proxy combined with DNA prior information (SIA + DNA BMM) designs. Three species of subterranean beetles (Paroster macrosturtensis, Paroster mesosturtensis, and Paroster microsturtensis) and their main prey items Chiltoniidae amphipods (AM1: Scutachiltonia axfordi and AM2: Yilgarniella sturtensis), cyclopoids and harpacticoids from a calcrete in Western Australia were targeted. Diet estimations from stable isotope only models (SIA BMM) indicated homogeneous patterns with modest preferences for amphipods as prey items. Multi-proxy BMM suggested increased-and species-specific-predatory pressures on amphipods coupled with high rates of scavenging/predation on sister species. SIA + DNA BMM showed marked preferences for amphipods AM1 and AM2, and reduced interspecific scavenging/predation on Paroster species. Multi-factorial BMM revealed the most precise estimations (lower overall SD and very marginal beetles' interspecific interactions), indicating consistent preferences for amphipods AM1 in all the beetles' diets. Incorporation of genetic priors allowed crucial refining of the feeding preferences, while integration of more expensive radiocarbon data as a third proxy (when combined with genetic data) produced more precise outcomes but close dietary reconstruction to that from SIA + DNA BMM. Further multidisciplinary modeling from other groundwater environments will help elucidate the potential behind these designs and bring light to the feeding ecology of one the most vital ecosystems worldwide.}, } @article {pmid32883749, year = {2020}, author = {Dai, H and Guan, Y}, title = {The Nubeam reference-free approach to analyze metagenomic sequencing reads.}, journal = {Genome research}, volume = {30}, number = {9}, pages = {1364-1375}, pmid = {32883749}, issn = {1549-5469}, mesh = {Animals ; Female ; Gastrointestinal Microbiome ; Humans ; Metagenomics/*methods ; Mice ; RNA, Ribosomal, 16S ; Sequence Analysis, RNA/methods ; Vagina/microbiology ; Whole Genome Sequencing/*methods ; }, abstract = {We present Nubeam (nucleotide be a matrix) as a novel reference-free approach to analyze short sequencing reads. Nubeam represents nucleotides by matrices, transforms a read into a product of matrices, and assigns numbers to reads based on the product matrix. Nubeam capitalizes on the noncommutative property of matrix multiplication, such that different reads are assigned different numbers and similar reads similar numbers. A sample, which is a collection of reads, becomes a collection of numbers that form an empirical distribution. We demonstrate that the genetic difference between samples can be quantified by the distance between empirical distributions. Nubeam includes the k-mer method as a special case, but unlike the k-mer method, it is convenient for Nubeam to account for GC bias and nucleotide quality. As a reference-free approach, Nubeam avoids reference bias and mapping bias, and can work with organisms without reference genomes. Thus, Nubeam is ideal to analyze data sets from metagenomics whole genome shotgun (WGS) sequencing, where the amount of unmapped reads is substantial. When applied to a WGS sequencing data set to quantify distances between metagenomics samples from various human body habitats, Nubeam recapitulates findings made by mapping-based methods and sheds light on contributions of unmapped reads. Nubeam is also useful in analyzing 16S rRNA sequencing data, which is a more prevalent type of data set in metagenomics studies. In our analysis, Nubeam recapitulated the findings that natural microbiota in mouse gut are resilient under challenges, and Nubeam detected differences in vaginal microbiota between cases of polycystic ovary syndrome and healthy controls.}, } @article {pmid32883364, year = {2020}, author = {Wilkinson, T and Korir, D and Ogugo, M and Stewart, RD and Watson, M and Paxton, E and Goopy, J and Robert, C}, title = {1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {229}, pmid = {32883364}, issn = {1474-760X}, support = {BB/P013759/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/GCRF-IAA/25/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N016742/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Africa South of the Sahara ; Animals ; Cattle/*microbiology ; Food Deprivation/*physiology ; *Gastrointestinal Microbiome ; *Metagenome ; Rumen/*microbiology ; }, abstract = {BACKGROUND: The Boran (Bos indicus), indigenous Zebu cattle breed from sub-Saharan Africa, is remarkably well adapted to harsh tropical environments. Due to financial constraints and low-quality forage, African livestock are rarely fed at 100% maintenance energy requirements (MER) and the effect of sub-optimal restricted feeding on the rumen microbiome of African Zebu cattle remains largely unexplored. We collected 24 rumen fluid samples from six Boran cattle fed at sub-optimal and optimal MER levels and characterised their rumen microbial composition by performing shotgun metagenomics and de novo assembly of metagenome-assembled genomes (MAGs). These MAGs were used as reference database to investigate the effect of diet restriction on the composition and functional potential of the rumen microbiome of African cattle.

RESULTS: We report 1200 newly discovered MAGs from the rumen of Boran cattle. A total of 850 were dereplicated, and their uniqueness confirmed with pairwise comparisons (based on Mash distances) between African MAGs and other publicly available genomes from the rumen. A genome-centric investigation into sub-optimal diets highlighted a statistically significant effect on rumen microbial abundance profiles and a previously unobserved relationship between whole microbiome shifts in functional potential and taxon-level associations in metabolic pathways.

CONCLUSIONS: This study is the first to identify 1200 high-quality African rumen-specific MAGs and provides further insight into the rumen function in harsh environments with food scarcity. The genomic information from the rumen microbiome of an indigenous African cattle breed sheds light on the microbiome contribution to rumen functionality and constitutes a vital resource in addressing food security in developing countries.}, } @article {pmid32882554, year = {2021}, author = {Phulpoto, IA and Hu, B and Wang, Y and Ndayisenga, F and Li, J and Yu, Z}, title = {Effect of natural microbiome and culturable biosurfactants-producing bacterial consortia of freshwater lake on petroleum-hydrocarbon degradation.}, journal = {The Science of the total environment}, volume = {751}, number = {}, pages = {141720}, doi = {10.1016/j.scitotenv.2020.141720}, pmid = {32882554}, issn = {1879-1026}, mesh = {Bacillus ; Biodegradation, Environmental ; Hydrocarbons ; Lakes ; *Microbiota ; *Petroleum ; }, abstract = {Freshwater lake ecosystem is a reservior of valuable microbial diversity. It needs to be explored for addressing key environmental issues like petroleum-hydrocarbon contamination. In this work, the microbial communities (pre and post enriched with petroleum-hydrocarbons) from different layers of freshwater lake, i.e. surface water, sediments and deepwater, were explored through metagenomic and culture-dependent approaches. A total of 41 bacterial phyla were retrieved from pre-enriched samples, which were significantly reduced in enriched samples where Proteobacteria were dominant (87% to 100%) followed by Bacteroidetes (7.37%) and Verrucomicrobia (3.06%). The most dominant hydrocarbon-degrading genera were extensively verified as Pseudomonas (48.65%), Acinetobacter (45.38%), Stenotrophomonas (3.16%) and Brevundimonas (2.07%) in surface water (S1WCC); Acinetobacter (62.46%), Aeromonas (10.7%), Sphingobacterium (5.20%) and Pseudomonas (4.23%) in sediment (S2MCC); and Acinetobacter (46.57%), Pseudomonas (13.10%), Comamonas (12.93%), Flavobacterium (12.18%) and Enterobacter (9.62%) in deep water (S4WCC). Additionally, the maximum biodegradation of petroleum-hydrocarbons (i.e. used engine oil or UEO) was achieved by microbiome of S2MCC (67.60 ± 0.08%) followed by S4WCC (59.70 ± 0.12%), whereas only 36.80 ± 0.10% degradation was achieved by S1WCC microbiome. On the other hand, UEO degradation by cultivable biosurfactant-producing single cultures such as Pseudomonas sp. S2WE, Pseudomonas sp. S2WG, Pseudomonas sp. S2MS, Ochrobactrum sp. S1MM and Bacillus nealsonii S2MT showed 31.10 ± 0.08% to 40.50 ± 0.11% biodegradation. Comparatively, the biodegradation efficiency was found higher (i.e. 42.20 ± 0.12% to 56.10 ± 0.12%) in each consortia comprising of two, three, four, and five bacterial cultures. Conclusively, the isolated culturable biosurfactants-producing bacterial consortium of freshwater lake demonstrated >80% contribution in the total petroleum-hydrocarbons degradation by the natural microbiome of the ecosystem.}, } @article {pmid32882535, year = {2020}, author = {Turrini, P and Tescari, M and Visaggio, D and Pirolo, M and Lugli, GA and Ventura, M and Frangipani, E and Visca, P}, title = {The microbial community of a biofilm lining the wall of a pristine cave in Western New Guinea.}, journal = {Microbiological research}, volume = {241}, number = {}, pages = {126584}, doi = {10.1016/j.micres.2020.126584}, pmid = {32882535}, issn = {1618-0623}, mesh = {Acidobacteria/classification/genetics/isolation & purification ; Actinobacteria/classification/genetics/isolation & purification ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*classification/*drug effects ; Biofilms/*growth & development ; Caves/*microbiology ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Firmicutes/classification/genetics/isolation & purification ; Metagenome/genetics ; Microbial Sensitivity Tests ; Microbiota/*genetics ; New Guinea ; Proteobacteria/classification/genetics/isolation & purification ; Pseudomonas/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {Caves are extreme environments inhabited by microbial communities adapted to thrive oligotrophic conditions. Cave microbes are organised in complex ecological networks and have developed survival strategies involving the production and release of a large variety of secondary metabolites, including antibiotic-like compounds. In this study, the structure and the metabolic features of a biofilm-like microbial community lining the walls of a pristine karst cavity (the Yumugi river cave) located in a remote region of the Western New Guinea were investigated. 16S rRNA and shotgun sequence analyses highlighted the prevalence of chemoorganotrophic phyla (Proteobacteria, Actinobacteria, Firmicutes and Acidobacteria), consistent with metabolic predictions inferred from the cave metagenome analysis. Few clinically relevant antimicrobial resistance genes were detected. A culture-based approach allowed the isolation of some heterotrophic members of the bacterial community, and antimicrobial susceptibility testing revealed an overall high level of resistance to different antimicrobials classes. Isolates presumptively representing new uncharacterized members of genus Pseudomonas displayed interesting antibiotic properties against Gram-positive indicator strains. Our work supports the hypothesis that caves represent a reservoir for new bacterial species and drug discovery research.}, } @article {pmid32882233, year = {2020}, author = {Zamora-Briseño, JA and Cerqueda-García, D and Hernández-Velázquez, IM and Rivera-Bustamante, R and Huchín-Mian, JP and Briones-Fourzán, P and Lozano-Álvarez, E and Rodríguez-Canul, R}, title = {Alterations in the gut-associated microbiota of juvenile Caribbean spiny lobsters Panulirus argus (Latreille, 1804) infected with PaV1.}, journal = {Journal of invertebrate pathology}, volume = {176}, number = {}, pages = {107457}, doi = {10.1016/j.jip.2020.107457}, pmid = {32882233}, issn = {1096-0805}, mesh = {Animals ; Bacteria/classification/isolation & purification ; DNA Viruses/*physiology ; Female ; *Gastrointestinal Microbiome ; Male ; Palinuridae/*microbiology/virology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sex Factors ; }, abstract = {The spiny lobster Panulirus argus (Latreille, 1804) is currently affected by an unenveloped, icosahedral, DNA virus termed Panulirus argus virus 1 (PaV1), a virulent and pathogenic virus that produces a long-lasting infection that alters the physiology and behaviour of heavily infected lobsters. Gut-associated microbiota is crucial for lobster homeostasis and well-being, but pathogens could change microbiota composition affecting its function. In PaV1 infection, the changes of gut-associated microbiota are yet to be elucidated. In the present study, we used high-throughput 16S rRNA sequencing technology to compare the bacterial microbiota in intestines of healthy and heavily PaV1-infected male and female juveniles of spiny lobsters P. argus captured in Puerto Morelos Reef lagoon, Quintana Roo, Mexico. We found that basal gut-associated microbiota composition showed a sex-dependent bias, with females being enriched in amplicon sequence variants (ASVs) assigned to Sphingomonas, while males were enriched in the genus Candidatus Hepatoplasma and Aliiroseovarius genera. Moreover, the alpha diversity of microbiota decreased in PaV1-infected lobsters. A significant increase of the genus Candidatus Bacilloplasma was observed in infected lobsters, as well as a significant decrease in Nesterenkonia, Caldalkalibacillus, Pseudomonas, Cetobacterium and Phyllobacterium. We also observed an alteration in the abundances of Vibrio species. Results from this study suggest that PaV1 infection impacts intestinal microbiota composition in Panulirus argus in a sex-dependent manner.}, } @article {pmid32880699, year = {2020}, author = {Wei, J and Segraves, KA and Li, WZ and Yang, XK and Xue, HJ}, title = {Gut bacterial communities and their contribution to performance of specialist Altica flea beetles.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {946-959}, doi = {10.1007/s00248-020-01590-x}, pmid = {32880699}, issn = {1432-184X}, support = {31672334//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacteria/classification/isolation & purification ; *Bacterial Physiological Phenomena ; Coleoptera/*microbiology/physiology ; Female ; *Gastrointestinal Microbiome ; Male ; Metagenome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Host plant shifts are a common mode of speciation in herbivorous insects. Although insects can evolve adaptations to successfully incorporate a new host plant, it is becoming increasingly recognized that the gut bacterial community may play a significant role in allowing insects to detoxify novel plant chemical defenses. Here, we examined differences in gut bacterial communities between Altica flea beetle species that feed on phylogenetically unrelated host plants in sympatry. We surveyed the gut bacterial communities of three closely related flea beetles from multiple locations using 16S rRNA amplicon sequencing. The results showed that the beetle species shared a high proportion (80.7%) of operational taxonomic units. Alpha-diversity indicators suggested that gut bacterial diversity did not differ among host species, whereas geography had a significant effect on bacterial diversity. In contrast, analyses of beta-diversity showed significant differences in gut bacterial composition among beetle species when we used species composition and relative abundance metrics, but there was no difference in composition when species presence/absence and phylogenetic distance indices were used. Within host beetle species, gut bacterial composition varied significantly among sites. A metagenomic functionality analysis predicted that the gut microbes had functions involved in xenobiotic biodegradation and metabolism as well as metabolism of terpenoids and polyketides. These predictions, however, did not differ among beetle host species. Antibiotic curing experiments showed that development time was significantly prolonged, and there was a significant decline in body weight of newly emerged adults in beetles lacking gut bacteria, suggesting the beetles may receive a potential benefit from the gut microbe-insect interaction. On the whole, our results suggest that although the gut bacterial community did not show clear host-specific patterns among Altica species, spatiotemporal variability is an important determinant of gut bacterial communities. Furthermore, the similarity of communities among these beetle species suggests that microbial facilitation may not be a determinant of host plant shifts in Altica.}, } @article {pmid32879395, year = {2020}, author = {Richard, JC and Leis, E and Dunn, CD and Agbalog, R and Waller, D and Knowles, S and Putnam, J and Goldberg, TL}, title = {Mass mortality in freshwater mussels (Actinonaias pectorosa) in the Clinch River, USA, linked to a novel densovirus.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {14498}, pmid = {32879395}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Computational Biology ; Densovirus/*pathogenicity ; Ecosystem ; Environmental Monitoring ; Genome ; Genomics ; Open Reading Frames ; Parvoviridae Infections/mortality/*veterinary ; Phylogeny ; Rivers ; Tennessee ; Unionidae/*virology ; Viral Load ; Virginia ; }, abstract = {Freshwater mussels (order Unionida) are among the world's most biodiverse but imperiled taxa. Recent unionid mass mortality events around the world threaten ecosystem services such as water filtration, nutrient cycling, habitat stabilization, and food web enhancement, but causes have remained elusive. To examine potential infectious causes of these declines, we studied mussels in Clinch River, Virginia and Tennessee, USA, where the endemic and once-predominant pheasantshell (Actinonaias pectorosa) has suffered precipitous declines since approximately 2016. Using metagenomics, we identified 17 novel viruses in Clinch River pheasantshells. However, only one virus, a novel densovirus (Parvoviridae; Densovirinae), was epidemiologically linked to morbidity. Clinch densovirus 1 was 11.2 times more likely to be found in cases (moribund mussels) than controls (apparently healthy mussels from the same or matched sites), and cases had 2.7 (log10) times higher viral loads than controls. Densoviruses cause lethal epidemic disease in invertebrates, including shrimp, cockroaches, crickets, moths, crayfish, and sea stars. Viral infection warrants consideration as a factor in unionid mass mortality events either as a direct cause, an indirect consequence of physiological compromise, or a factor interacting with other biological and ecological stressors to precipitate mortality.}, } @article {pmid32874052, year = {2020}, author = {Yue, B and Yu, ZL and Lv, C and Geng, XL and Wang, ZT and Dou, W}, title = {Regulation of the intestinal microbiota: An emerging therapeutic strategy for inflammatory bowel disease.}, journal = {World journal of gastroenterology}, volume = {26}, number = {30}, pages = {4378-4393}, pmid = {32874052}, issn = {2219-2840}, mesh = {Animals ; *Colitis ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/therapy ; Intestines ; Mice ; *Microbiota ; }, abstract = {The rapid development of metagenomics, metabolomics, and metatranscriptomics provides novel insights into the intestinal microbiota factors linked to inflammatory bowel disease (IBD). Multiple microorganisms play a role in intestinal health; these include bacteria, fungi, and viruses that exist in a dynamic balance to maintain mucosal homeostasis. Perturbations in the intestinal microbiota disrupt mucosal homeostasis and are closely related to IBD in humans and colitis in mice. Therefore, preventing or correcting the imbalance of microbiota may serve as a novel prevention or treatment strategy for IBD. We review the most recent evidence for direct or indirect interventions targeting intestinal microbiota for treatment of IBD in order to overcome the current limitations of IBD therapies and shed light on personalized treatment options.}, } @article {pmid32873292, year = {2020}, author = {Zhu, L and Xu, F and Wan, W and Yu, B and Tang, L and Yang, Y and Du, Y and Chen, Z and Xu, H}, title = {Gut microbial characteristics of adult patients with allergy rhinitis.}, journal = {Microbial cell factories}, volume = {19}, number = {1}, pages = {171}, pmid = {32873292}, issn = {1475-2859}, support = {81900541//National Natural Science Foundation of China/ ; 2019J05005//Natural Science Foundation of Fujian Province/ ; }, mesh = {Adult ; *Biodiversity ; China/epidemiology ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Male ; Metagenome ; Quality of Life ; RNA, Ribosomal, 16S ; Rhinitis, Allergic/*microbiology ; Severity of Illness Index ; Surveys and Questionnaires ; Young Adult ; }, abstract = {BACKGROUND: Although recent studies have indicated that intestinal microbiota dweller are involved in the pathogenesis of allergy rhinitis (AR), the influence of gut microbiota on AR adult has not been fully elucidated yet. Hence, we carried out this study to uncover the distinctive bacterial taxa that differentiate allergy rhinitis patients from healthy individuals. Feces samples from thirty three AR patients and thirty one healthy individuals were analyzed by 16S rRNA gene sequencing.

RESULTS: Results showed that the bacterial diversity in AR group was significantly higher than that of the non-AR group. Bacterial communities between AR and non-AR group were significantly differentiated as revealed by Principal coordinates analysis (PCoA) and the variation within non-AR were higher than that of the counterpart. Firmicutes, Fusobacteria, Actinobacteria, Cyanobacteria and Chloroflexi were the significantly differed phyla taxa and the top significantly distinguished bacterial genus included Prevotella_9, Phascolarctobacterium, Roseburia, Megamonas, Alistipes, Lachnoclostridium and Fusobacterium. The higher network complexity in AR group were dominated by taxa belonging to Firmicutes. The predicted function, alpha linolenic acid metabolism and bacterial invasion of epithelial cells pathway were higher in non-AR group while gonadotropin-releasing hormone (GnRH) signaling pathway, Fc γ-R mediated phagocytosis and endocytosis were higher in AR patients. Although the bacterial diversity between moderate and severe AR patients showed no significant difference, the significant correlation between featured genus and total nasal symptom score or rhinoconjunctivitis quality of life questionnaire, such as Butyricicoccus and Eisenbergiella, revealed the potential to intervene the AR status by means of gut microbiota.

CONCLUSIONS: In conclusion, patients with allergy rhinitis had distinguished gut microbiota characteritics in comparison with healthy controls. The results suggest that gut microbiota might play crucial roles in influencing the course and different symptoms of AR. Trial registration ChiCTR, ChiCTR1900028613. Registered 29 December 2019, https://www.chictr.org.cn/showproj.aspx?proj=47650 .}, } @article {pmid32869496, year = {2021}, author = {Karnachuk, OV and Lukina, AP and Kadnikov, VV and Sherbakova, VA and Beletsky, AV and Mardanov, AV and Ravin, NV}, title = {Targeted isolation based on metagenome-assembled genomes reveals a phylogenetically distinct group of thermophilic spirochetes from deep biosphere.}, journal = {Environmental microbiology}, volume = {23}, number = {7}, pages = {3585-3598}, doi = {10.1111/1462-2920.15218}, pmid = {32869496}, issn = {1462-2920}, mesh = {Bacteria/genetics ; DNA, Bacterial/genetics ; *Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spirochaetales ; }, abstract = {Most microorganisms from deep terrestrial subsurface remain yet uncultured. Recent achievements in recovery of metagenome-assembled genomes (MAG) provide clues for improving cultivation via metabolic reconstructions and other genomic characteristics. Here we report the isolation in pure culture of a thermophilic spirochete with the use of MAGs binned from metagenomes of the deep (>2 km) aquifers broached by two artesian boreholes in Western Siberia. The organism constitutes a minor share in the aquifer microbial community and could not be cultivated by traditional techniques. The obtained two pure culture isolates along with three bacteria identified by MAGs represent a novel family-level lineage in the order Brevinematales. Based on genomic and phenotypic characteristics the novel spirochete is proposed to be classified as Longinema margulisiae gen. nov., sp. nov. within a novel family, Longinemaceae fam. nov. Both cultivated strains, NS[T] and N5R, are anaerobic hemoorganoheterotrophes growing by fermentation of starch and a few sugars. They can form recalcitrant round bodies under unfavourable growth conditions, which survive up to 15 min at 95°C and can revert to the original helical cells. We suggest that the round bodies may facilitate global distribution of this lineage, detected from molecular signaturesand colonization of subsurface environments.}, } @article {pmid32869063, year = {2021}, author = {Sato, N and Kakuta, M and Hasegawa, T and Yamaguchi, R and Uchino, E and Murashita, K and Nakaji, S and Imoto, S and Yanagita, M and Okuno, Y}, title = {Metagenomic profiling of gut microbiome in early chronic kidney disease.}, journal = {Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association}, volume = {36}, number = {9}, pages = {1675-1684}, doi = {10.1093/ndt/gfaa122}, pmid = {32869063}, issn = {1460-2385}, mesh = {Bacteroides ; Clostridiales ; *Gastrointestinal Microbiome ; Humans ; *Renal Insufficiency, Chronic ; Ruminococcus ; }, abstract = {BACKGROUND: The relationship between chronic kidney disease (CKD) and the gut microbiome, which interact through chronic inflammation, uraemic toxin production and immune response regulation, has gained interest in the development of CKD therapies. However, reports using shotgun metagenomic analysis of the gut microbiome are scarce, especially for early CKD. Here we characterized gut microbiome differences between non-CKD participants and ones with early CKD using metagenomic sequencing.

METHODS: In total, 74 non-CKD participants and 37 participants with early CKD were included based on propensity score matching, controlling for various factors including dietary intake. Stool samples were collected from participants and subjected to shotgun sequencing. Bacterial and pathway abundances were profiled at the species level with MetaPhlAn2 and HUMAnN2, respectively, and overall microbiome differences were determined using Bray-Curtis dissimilarities. Diabetic and non-diabetic populations were analysed separately.

RESULTS: For diabetic and non-diabetic participants, the mean estimated glomerular filtration rates of the CKD group were 53.71 [standard deviation (SD) 3.87] and 53.72 (SD 4.44), whereas those of the non-CKD group were 72.63 (SD 7.72) and 76.10 (SD 9.84), respectively. Alpha and beta diversities were not significantly different between groups. Based on taxonomic analysis, butyrate-producing species Roseburia inulinivorans, Ruminococcus torques and Ruminococcus lactaris were more abundant in the non-CKD group, whereas Bacteroides caccae and Bacteroides coprocora were more abundant in the non-diabetic CKD group.

CONCLUSIONS: Although gut microbiome changes in individuals with early CKD were subtle, the results suggest that changes related to producing short-chain fatty acids can already be observed in early CKD.}, } @article {pmid32867361, year = {2020}, author = {Xue, CX and Liu, J and Lea-Smith, DJ and Rowley, G and Lin, H and Zheng, Y and Zhu, XY and Liang, J and Ahmad, W and Todd, JD and Zhang, XH}, title = {Insights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth.}, journal = {Microorganisms}, volume = {8}, number = {9}, pages = {}, pmid = {32867361}, issn = {2076-2607}, abstract = {The Earth's oceans are a huge body of water with physicochemical properties and microbial community profiles that change with depth, which in turn influences their biogeochemical cycling potential. The differences between microbial communities and their functional potential in surface to hadopelagic water samples are only beginning to be explored. Here, we used metagenomics to investigate the microbial communities and their potential to drive biogeochemical cycling in seven different water layers down the vertical profile of the Challenger Deep (0-10,500 m) in the Mariana Trench, the deepest natural point in the Earth's oceans. We recovered 726 metagenome-assembled genomes (MAGs) affiliated to 27 phyla. Overall, biodiversity increased in line with increased depth. In addition, the genome size of MAGs at ≥4000 m layers was slightly larger compared to those at 0-2000 m. As expected, surface waters were the main source of primary production, predominantly from Cyanobacteria. Intriguingly, microbes conducting an unusual form of nitrogen metabolism were identified in the deepest waters (>10,000 m), as demonstrated by an enrichment of genes encoding proteins involved in dissimilatory nitrate to ammonia conversion (DNRA), nitrogen fixation and urea transport. These likely facilitate the survival of ammonia-oxidizing archaea α lineage, which are typically present in environments with a high ammonia concentration. In addition, the microbial potential for oxidative phosphorylation and the glyoxylate shunt was enhanced in >10,000 m waters. This study provides novel insights into how microbial communities and their genetic potential for biogeochemical cycling differs through the Challenger deep water column, and into the unique adaptive lifestyle of microbes in the Earth's deepest seawater.}, } @article {pmid32867153, year = {2020}, author = {Fart, F and Rajan, SK and Wall, R and Rangel, I and Ganda-Mall, JP and Tingö, L and Brummer, RJ and Repsilber, D and Schoultz, I and Lindqvist, CM}, title = {Differences in Gut Microbiome Composition between Senior Orienteering Athletes and Community-Dwelling Older Adults.}, journal = {Nutrients}, volume = {12}, number = {9}, pages = {}, pmid = {32867153}, issn = {2072-6643}, support = {F0514//Bo Rydins Stiftelse för Vetenskaplig Forskning/ ; 20110225//Stiftelsen för Kunskaps- och Kompetensutveckling/ ; }, mesh = {Aged ; Athletes/*statistics & numerical data ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Geriatric Assessment/*methods/*statistics & numerical data ; Humans ; Independent Living ; Male ; }, abstract = {BACKGROUND: Gastrointestinal (GI) health is an important aspect of general health. Gastrointestinal symptoms are of specific importance for the elderly, an increasing group globally. Hence, promoting the elderly's health and especially gastrointestinal health is important. Gut microbiota can influence gastrointestinal health by modulation of the immune system and the gut-brain axis. Diverse gut microbiota have been shown to be beneficial; however, for the elderly, the gut microbiota is often less diverse. Nutrition and physical activity, in particular, are two components that have been suggested to influence composition or diversity.

MATERIALS AND METHODS: In this study, we compared gut microbiota between two groups of elderly individuals: community-dwelling older adults and physically active senior orienteering athletes, where the latter group has less gastrointestinal symptoms and a reported better well-being. With this approach, we explored if certain gut microbiota were related to healthy ageing. The participant data and faecal samples were collected from these two groups and the microbiota was whole-genome sequenced and taxonomically classified with MetaPhlAn.

RESULTS: The physically active senior orienteers had a more homogeneous microbiota within the group and a higher abundance of Faecalibacterium prausnitzii compared to the community-dwelling older adults. Faecalibacterium prausnitzii has previously shown to have beneficial properties. Senior orienteers also had a lower abundance of Parasutterella excrementihominis and Bilophila unclassified, which have been associated with impaired GI health. We could not observe any difference between the groups in terms of Shannon diversity index. Interestingly, a subgroup of community-dwelling older adults showed an atypical microbiota profile as well as the parameters for gastrointestinal symptoms and well-being closer to senior orienteers.

CONCLUSIONS: Our results suggest specific composition characteristics of healthy microbiota in the elderly, and show that certain components of nutrition as well as psychological distress are not as tightly connected with composition or diversity variation in faecal microbiota samples.}, } @article {pmid32867028, year = {2020}, author = {Marin-Gómez, W and Grande, MJ and Pérez-Pulido, R and Galvez, A and Lucas, R}, title = {Changes in the Bacterial Diversity of Human Milk during Late Lactation Period (Weeks 21 to 48).}, journal = {Foods (Basel, Switzerland)}, volume = {9}, number = {9}, pages = {}, pmid = {32867028}, issn = {2304-8158}, support = {RS-AGR230//Universidad de Jaén/ ; }, abstract = {Breast milk from a single mother was collected during a 28-week lactation period. Bacterial diversity was studied by amplicon sequencing analysis of the V3-V4 variable region of the 16S rRNA gene. Firmicutes and Proteobacteria were the main phyla detected in the milk samples, followed by Actinobacteria and Bacteroidetes. The proportion of Firmicutes to Proteobacteria changed considerably depending on the sampling week. A total of 411 genera or higher taxons were detected in the set of samples. Genus Streptococcus was detected during the 28-week sampling period, at relative abundances between 2.0% and 68.8%, and it was the most abundant group in 14 of the samples. Carnobacterium and Lactobacillus had low relative abundances. At the genus level, bacterial diversity changed considerably at certain weeks within the studied period. The weeks or periods with lowest relative abundance of Streptococcus had more diverse bacterial compositions including genera belonging to Proteobacteria that were poorly represented in the rest of the samples.}, } @article {pmid32862830, year = {2020}, author = {Kwak, S and Choi, J and Hink, T and Reske, KA and Blount, K and Jones, C and Bost, MH and Sun, X and Burnham, CD and Dubberke, ER and Dantas, G and , }, title = {Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {125}, pmid = {32862830}, issn = {2049-2618}, support = {U54 CK000162/CK/NCEZID CDC HHS/United States ; }, mesh = {Aged ; Bacteria/*genetics/*isolation & purification ; *Biodiversity ; Double-Blind Method ; Drug Resistance, Microbial/*genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; *Microbiota ; Middle Aged ; }, abstract = {BACKGROUND: Intestinal microbiota restoration can be achieved by complementing a subject's perturbed microbiota with that of a healthy donor. Recurrent Clostridioides difficile infection (rCDI) is one key application of such treatment. Another emerging application of interest is reducing antibiotic-resistant genes (ARGs) and organisms (AROs). In this study, we investigated fecal specimens from a multicenter, randomized, double-blind, placebo-controlled phase 2b study of microbiota-based investigational drug RBX2660. Patients were administered either placebo, 1 dose of RBX2660 and 1 placebo, or 2 doses of RBX2660 via enema and longitudinally tracked for changes in their microbiome and antibiotic resistome.

RESULTS: All patients exhibited significant recovery of gut microbiome diversity and a decrease of ARG relative abundance during the first 7 days post-treatment. However, the microbiome and resistome shifts toward average configurations from unperturbed individuals were more significant and longer-lasting in RBX2660 recipients compared to placebo. We quantified microbiome and resistome modification by RBX2660 using a novel "transplantation index" metric. We identified taxonomic and metabolic features distinguishing the baseline microbiome of non-transplanted patients and taxa specifically enriched during the process of transplantation. We elucidated the correlation between resistome and taxonomic transplantations and post-treatment dynamics of patient-specific and RBX2660-specific ARGs. Whole genome sequencing of AROs cultured from RBX2660 product and patient samples indicate ARO eradication in patients via RBX2660 administration, but also, to a lesser extent, introduction of RBX2660-derived AROs.

CONCLUSIONS: Through shotgun metagenomic sequencing, we elucidated the effects of RBX2660 in the microbiome and resistome. Antibiotic discontinuation alone resulted in significant recovery of gut microbial diversity and reduced ARG relative abundance, but RBX2660 administration more rapidly and completely changed the composition of patients' microbiome, resistome, and ARO colonization by transplanting RBX2660 microbiota into the recipients. Although ARGs and AROs were transmitted through RBX2660, the resistome post-RBX2660 more closely resembled that of the administered product-a proxy for the donor-than an antibiotic perturbed state.

TRIAL REGISTRATION: ClinicalTrials.gov, NCT02299570 . Registered 19 November 2014 Video Abstract.}, } @article {pmid32862246, year = {2021}, author = {Starke, R and Pylro, VS and Morais, DK}, title = {16S rRNA Gene Copy Number Normalization Does Not Provide More Reliable Conclusions in Metataxonomic Surveys.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {535-539}, pmid = {32862246}, issn = {1432-184X}, support = {18-25706S//Grantová Agentura České Republiky/ ; 20-02022Y//Grantová Agentura České Republiky/ ; }, mesh = {Gene Dosage ; Gene Library ; Metagenome/genetics ; Metagenomics/*standards ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Sequencing 16S rRNA gene amplicons is the gold standard to uncover the composition of prokaryotic communities. The presence of multiple copies of this gene makes the community abundance data distorted and gene copy normalization (GCN) necessary for correction. Even though GCN of 16S data provided a picture closer to the metagenome before, it should also be compared with communities of known composition due to the fact that library preparation is prone to methodological biases. Here, we process 16S rRNA gene amplicon data from eleven simple mock communities with DADA2 and estimate the impact of GCN. In all cases, the mock community composition derived from the 16S sequencing differs from those expected, and GCN fails to improve the classification for most of the analysed communities. Our approach provides empirical evidence that GCN does not improve the 16S target sequencing analyses in real scenarios. We therefore question the use of GCN for metataxonomic surveys until a more comprehensive catalogue of copy numbers becomes available.}, } @article {pmid32861779, year = {2020}, author = {Khiaosa-Ard, R and Mahmood, M and Lerch, F and Traintinger, FP and Petri, RM and Münnich, M and Zebeli, Q}, title = {Physicochemical stressors and mixed alkaloid supplementation modulate ruminal microbiota and fermentation in vitro.}, journal = {Anaerobe}, volume = {65}, number = {}, pages = {102263}, doi = {10.1016/j.anaerobe.2020.102263}, pmid = {32861779}, issn = {1095-8274}, mesh = {Alkaloids/*administration & dosage ; Animals ; Archaea ; Bacteria ; *Dietary Supplements ; *Fermentation ; Hydrogen-Ion Concentration ; Metagenomics ; Methane/biosynthesis ; *Microbiota ; RNA, Ribosomal, 16S ; Rumen/*microbiology ; *Stress, Physiological ; Temperature ; }, abstract = {The drop of ruminal pH and heat are common physicochemical stressors challenging ruminal microbiota, nutrient digestion and cattle performance. We characterized the ruminal microbiota and digestive activity in response to different pH (6.0 and 6.6) and temperature (39.5 and 42 °C), as well as established the effective dose of alkaloid supplementation (0, 0.088 and 0.175% of feedstock DM) to modulate ruminal fermentation under these conditions. The acidotic condition decreased microbial diversity and abundances of minor bacterial families whereas most of the highly abundant families like Lactobacillaceae, Prevotellaceae, and Bifidobacteriaceae thrived under the stress. Abundances of all three methanogenic archaea taxa detected increased with heat, as did methane production. However, while Methanomassiliicoccaceae benefited from the low pH, Methanomicrobiaceae diminished and methane production decreased. The low dose of alkaloid addition shifted the fermentation to more propionate and less acetate and the high dose decreased methane and ammonia concentration under the low pH. In conclusion, physicochemical stressors shape the microbial community and function. Mixed alkaloid supplementation facilitates the activity of rumen microbial community under acidotic stress.}, } @article {pmid32861197, year = {2020}, author = {Nagpal, R and Neth, BJ and Wang, S and Mishra, SP and Craft, S and Yadav, H}, title = {Gut mycobiome and its interaction with diet, gut bacteria and alzheimer's disease markers in subjects with mild cognitive impairment: A pilot study.}, journal = {EBioMedicine}, volume = {59}, number = {}, pages = {102950}, pmid = {32861197}, issn = {2352-3964}, support = {R01 AG018915/AG/NIA NIH HHS/United States ; P30 AG049638/AG/NIA NIH HHS/United States ; UL1 TR001420/TR/NCATS NIH HHS/United States ; R01 AG055122/AG/NIA NIH HHS/United States ; P30 AG021332/AG/NIA NIH HHS/United States ; }, mesh = {Alzheimer Disease/genetics/metabolism/*psychology ; Apolipoprotein E4/genetics ; *Bacteria ; *Biomarkers ; *Cognitive Dysfunction ; Computational Biology/methods ; *Diet ; Diet, Ketogenic ; Feces/microbiology ; Female ; Fungi ; *Gastrointestinal Microbiome ; Genotype ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Pilot Projects ; }, abstract = {BACKGROUND: Recently, we reported that patients with mild cognitive impairment (MCI) harbor specific signature of bacteria in their gut and that a modified Mediterranean ketogenic diet (MMKD) improves Alzheimer's disease (AD) markers in cerebrospinal fluid (CSF) and the signatures of gut bacteria. However, other microbial population such as gut fungi (mycobiome) in relation to MCI/AD pathology, gut bacteria and diet remain unknown.

METHODS: We measure gut mycobiome by sequencing of the fungal rRNA ITS1 gene in 17 older adults (11 MCI; 6 cognitively normal [CN]) in a single-center, randomized, double-blind, crossover pilot study, before and after 6 weeks intervention of MMKD and American Heart Association Diet (AHAD), and determine its correlation with AD markers in CSF and gut bacteria.

FINDINGS: Compared to CN counterparts, patients with MCI have higher proportion of families Sclerotiniaceae, Phaffomyceteceae, Trichocomaceae, Cystofilobasidiaceae, Togniniaceae and genera Botrytis, Kazachstania, Phaeoacremonium and Cladosporium and lower abundance of Meyerozyma. Specific fungal taxa exhibit distinct correlation arrays with AD markers and gut bacteria in subjects with versus without MCI. MMKD induces broader effect on fungal diversity in subjects with MCI and increases Agaricus and Mrakia while decreasing Saccharomyces and Claviceps with differential response in subjects with or without MCI.

INTERPRETATION: The study reveals MCI-specific mycobiome signatures and demonstrates that distinct diets modulate the mycobiome in association with AD markers and fungal-bacterial co-regulation networks in patients with MCI. The findings corroborate the notion of considering gut mycobiome as a unique factor that can affect cognitive health/AD by interacting with gut bacteria and diet and facilitate better understanding of the AD and related microbiome, using unique diet or microbiome modulators.}, } @article {pmid32861142, year = {2020}, author = {Cerqueda-García, D and Améndola-Pimenta, M and Zamora-Briseño, JA and González-Penagos, CE and Árcega-Cabrera, F and Ceja-Moreno, V and Rodríguez-Canul, R}, title = {Effects of chronic exposure to water accommodated fraction (WAF) of light crude oil on gut microbiota composition of the lined sole (Achirus lineatus).}, journal = {Marine environmental research}, volume = {161}, number = {}, pages = {105116}, doi = {10.1016/j.marenvres.2020.105116}, pmid = {32861142}, issn = {1879-0291}, mesh = {Animals ; *Gastrointestinal Microbiome ; Gulf of Mexico ; *Petroleum/toxicity ; RNA, Ribosomal, 16S/genetics ; Water ; *Water Pollutants, Chemical/analysis/toxicity ; }, abstract = {Exposure of marine fish to hydrocarbon compounds from crude oil can cause physiological and ecological alterations that can result in several cytotoxic, genotoxic, and teratogenic damages. One consequence of this exposure is the dysbiosis of the gut microbiota, where the normal bacterial composition is modified. Herein, we assessed the effect of the exposure to water accommodated fraction (WAF) of a light crude oil into the gut microbiota of a native species, the lined sole Achirus lineatus, a benthonic fish widely distributed in the Gulf of Mexico (GoM). We performed a chronic bioassay using two WAF concentrations (5 and 10% v/v), collecting lined sole entire gastrointestinal tracts for microbiota analyses at two timepoints, 14 and 28 days. Changes in the gut microbiota composition were determined by high throughput amplicon sequencing of the gene 16S rRNA. Diversity analyses showed that WAF exposure produced similar changes in the microbiota composition at both concentrations. Metagenomic functional prediction showed that these alterations could result in a shift in the gut redox status, towards a more anoxygenic environment. Enrichment of bacteria capable of use hydrocarbon as carbon source seems to be fast regardless time of exposure or WAF concentrations. Our results suggest that chronic WAF exposure can cause a dysbiosis in this benthic native species from the GoM.}, } @article {pmid32860788, year = {2020}, author = {Kong, L and Lloyd-Price, J and Vatanen, T and Seksik, P and Beaugerie, L and Simon, T and Vlamakis, H and Sokol, H and Xavier, RJ}, title = {Linking Strain Engraftment in Fecal Microbiota Transplantation With Maintenance of Remission in Crohn's Disease.}, journal = {Gastroenterology}, volume = {159}, number = {6}, pages = {2193-2202.e5}, pmid = {32860788}, issn = {1528-0012}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AT009708/AT/NCCIH NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Crohn Disease/immunology/microbiology/*therapy ; Datasets as Topic ; Fecal Microbiota Transplantation/*methods ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics/immunology ; Haplotypes ; Humans ; Male ; Metagenomics ; Middle Aged ; Molecular Typing ; Phylogeny ; Remission Induction/methods ; Treatment Outcome ; Young Adult ; }, abstract = {BACKGROUND & AIMS: Crohn's disease (CD) is a chronic gastrointestinal disease resulting from the dysfunctional interplay between genetic susceptibility, the immune system, and commensal intestinal microbiota. Emerging evidence suggests that treatment by suppression of the immune response and replacement of the microbiota through fecal microbiota transplantation (FMT) is a promising approach for the treatment of CD.

METHODS: We obtained stool metagenomes from CD patients in remission and assessed gut microbiome composition before and after FMT at the species and strain levels. Longitudinal follow-up evaluation allowed us to identify the gain, loss, and strain replacement of specific species and link these events to the maintenance of remission in CD.

RESULTS: We found that FMT had a significant long-term effect on patient microbial compositions, although this was primarily driven by the engraftment of donor species, which remained at low abundance. Thirty-eight percent of FMT-driven changes were strain replacements, emphasizing the importance of detailed profiling methods, such as metagenomics. Several instances of long-term coexistence between donor and patient strains were also observed. Engraftment of some Actinobacteria, and engraftment or loss of Proteobacteria, were related to better disease outcomes in CD patients who received FMT, and transmission of Bacteroidetes was deleterious.

CONCLUSIONS: Our results suggest clades that may be beneficial to transmit/eliminate through FMT, and provide criteria that may help identify personalized FMT donors to more effectively maintain remission in CD patients. The framework established here creates a foundation for future studies centered around the application of FMT and defined microbial communities as a therapeutic approach for treating CD.}, } @article {pmid32859925, year = {2020}, author = {Jurburg, SD and Konzack, M and Eisenhauer, N and Heintz-Buschart, A}, title = {The archives are half-empty: an assessment of the availability of microbial community sequencing data.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {474}, pmid = {32859925}, issn = {2399-3642}, mesh = {Databases, Nucleic Acid ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {As DNA sequencing has become more popular, the public genetic repositories where sequences are archived have experienced explosive growth. These repositories now hold invaluable collections of sequences, e.g., for microbial ecology, but whether these data are reusable has not been evaluated. We assessed the availability and state of 16S rRNA gene amplicon sequences archived in public genetic repositories (SRA, EBI, and DDJ). We screened 26,927 publications in 17 microbiology journals, identifying 2015 16S rRNA gene sequencing studies. Of these, 7.2% had not made their data public at the time of analysis. Among a subset of 635 studies sequencing the same gene region, 40.3% contained data which was not available or not reusable, and an additional 25.5% contained faults in data formatting or data labeling, creating obstacles for data reuse. Our study reveals gaps in data availability, identifies major contributors to data loss, and offers suggestions for improving data archiving practices.}, } @article {pmid32859898, year = {2020}, author = {Metwaly, A and Dunkel, A and Waldschmitt, N and Raj, ACD and Lagkouvardos, I and Corraliza, AM and Mayorgas, A and Martinez-Medina, M and Reiter, S and Schloter, M and Hofmann, T and Allez, M and Panes, J and Salas, A and Haller, D}, title = {Integrated microbiota and metabolite profiles link Crohn's disease to sulfur metabolism.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4322}, pmid = {32859898}, issn = {2041-1723}, mesh = {Adolescent ; Adult ; Animals ; Bacteria/classification/genetics/metabolism ; Crohn Disease/drug therapy/*metabolism/*microbiology ; Disease Models, Animal ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Hematopoietic Stem Cell Transplantation ; Humans ; Interleukin-10/genetics ; Male ; Metagenome ; Mice ; Mice, Knockout ; RNA, Ribosomal, 16S/genetics ; Remission Induction ; Sulfur/*metabolism ; Young Adult ; }, abstract = {Gut microbial and metabolite alterations have been linked to the pathogenesis of inflammatory bowel diseases. Here we perform a multi-omics microbiome and metabolite analysis of a longitudinal cohort of Crohn's disease patients undergoing autologous hematopoietic stem cell transplantation, and investigational therapy that induces drug free remission in a subset of patients. Via comparison of patients who responded and maintained remission, responded but experienced disease relapse and patients who did not respond to therapy, we identify shared functional signatures that correlate with disease activity despite the variability of gut microbiota profiles at taxonomic level. These signatures reflect the disease state when transferred to gnotobiotic mice. Taken together, the integration of microbiome and metabolite profiles from human cohort and mice improves the predictive modelling of disease outcome, and allows the identification of a network of bacteria-metabolite interactions involving sulfur metabolism as a key mechanism linked to disease activity in Crohn's disease.}, } @article {pmid32859275, year = {2020}, author = {Lu, J and Salzberg, SL}, title = {Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {124}, pmid = {32859275}, issn = {2049-2618}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics/*isolation & purification ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; *Software ; Time Factors ; }, abstract = {BACKGROUND: For decades, 16S ribosomal RNA sequencing has been the primary means for identifying the bacterial species present in a sample with unknown composition. One of the most widely used tools for this purpose today is the QIIME (Quantitative Insights Into Microbial Ecology) package. Recent results have shown that the newest release, QIIME 2, has higher accuracy than QIIME, MAPseq, and mothur when classifying bacterial genera from simulated human gut, ocean, and soil metagenomes, although QIIME 2 also proved to be the most computationally expensive. Kraken, first released in 2014, has been shown to provide exceptionally fast and accurate classification for shotgun metagenomics sequencing projects. Bracken, released in 2016, then provided users with the ability to accurately estimate species or genus relative abundances using Kraken classification results. Kraken 2, which matches the accuracy and speed of Kraken 1, now supports 16S rRNA databases, allowing for direct comparisons to QIIME and similar systems.

METHODS: For a comprehensive assessment of each tool, we compare the computational resources and speed of QIIME 2's q2-feature-classifier, Kraken 2, and Bracken in generating the three main 16S rRNA databases: Greengenes, SILVA, and RDP. For an evaluation of accuracy, we evaluated each tool using the same simulated 16S rRNA reads from human gut, ocean, and soil metagenomes that were previously used to compare QIIME, MAPseq, mothur, and QIIME 2. We evaluated accuracy based on the accuracy of the final genera read counts assigned by each tool. Finally, as Kraken 2 is the only tool providing per-read taxonomic assignments, we evaluate the sensitivity and precision of Kraken 2's per-read classifications.

RESULTS: For both the Greengenes and SILVA database, Kraken 2 and Bracken are up to 100 times faster at database generation. For classification, using the same data as previous studies, Kraken 2 and Bracken are up to 300 times faster, use 100x less RAM, and generate results that more accurate at 16S rRNA profiling than QIIME 2's q2-feature-classifier.

CONCLUSION: Kraken 2 and Bracken provide a very fast, efficient, and accurate solution for 16S rRNA metataxonomic data analysis. Video Abstract.}, } @article {pmid32859198, year = {2020}, author = {Neukamm, J and Pfrengle, S and Molak, M and Seitz, A and Francken, M and Eppenberger, P and Avanzi, C and Reiter, E and Urban, C and Welte, B and Stockhammer, PW and Teßmann, B and Herbig, A and Harvati, K and Nieselt, K and Krause, J and Schuenemann, VJ}, title = {2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {108}, pmid = {32859198}, issn = {1741-7007}, support = {845479//the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie/International ; ALTF 1086-2018//European Molecular Biology Organization (EMBO) long-term fellowship/International ; }, mesh = {DNA, Ancient/analysis ; Egypt ; *Genome, Bacterial ; *Genome, Viral ; Hepatitis B virus/*genetics ; Humans ; Metagenomics ; Microbiota ; Mummies/*microbiology/virology ; Mycobacterium leprae/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Recent advances in sequencing have facilitated large-scale analyses of the metagenomic composition of different samples, including the environmental microbiome of air, water, and soil, as well as the microbiome of living humans and other animals. Analyses of the microbiome of ancient human samples may provide insights into human health and disease, as well as pathogen evolution, but the field is still in its very early stages and considered highly challenging.

RESULTS: The metagenomic and pathogen content of Egyptian mummified individuals from different time periods was investigated via genetic analysis of the microbial composition of various tissues. The analysis of the dental calculus' microbiome identified Red Complex bacteria, which are correlated with periodontal diseases. From bone and soft tissue, genomes of two ancient pathogens, a 2200-year-old Mycobacterium leprae strain and a 2000-year-old human hepatitis B virus, were successfully reconstructed.

CONCLUSIONS: The results show the reliability of metagenomic studies on Egyptian mummified individuals and the potential to use them as a source for the extraction of ancient pathogen DNA.}, } @article {pmid32858186, year = {2020}, author = {Tepaamorndech, S and Nookaew, I and Higdon, SM and Santiyanont, P and Phromson, M and Chantarasakha, K and Mhuantong, W and Plengvidhya, V and Visessanguan, W}, title = {Metagenomics in bioflocs and their effects on gut microbiome and immune responses in Pacific white shrimp.}, journal = {Fish & shellfish immunology}, volume = {106}, number = {}, pages = {733-741}, doi = {10.1016/j.fsi.2020.08.042}, pmid = {32858186}, issn = {1095-9947}, mesh = {Animals ; *Aquaculture ; Bacterial Physiological Phenomena ; *Gastrointestinal Microbiome ; Immunity, Innate ; Metagenomics ; *Penaeidae/genetics/immunology/microbiology ; RNA, Ribosomal, 16S ; }, abstract = {Biofloc systems generate and accumulate microbial aggregates known as bioflocs. The presence of bioflocs has been shown to change gut bacterial diversity and stimulate innate immunity in shrimp. The microbial niche of bioflocs may therefore have the potential to drive shifts in the shrimp gut microbiota associated with stimulation of innate immunity. We performed shotgun metagenomic analysis and 16S rRNA-based amplicon sequencing to characterize complex bacterial members in bioflocs and the shrimp digestive tract, respectively. Moreover, we determined whether biofloc-grown shrimp with discrete gut microbiomes had an elevation in local immune-related gene expression and systemic immune activities. Our findings demonstrated that the bacterial community in bioflocs changed dynamically during Pacific white shrimp cultivation. Metagenomic analysis revealed that Vibrio comprised 90% of the biofloc population, while Pseualteromonas, Photobacterium, Shewanella, Alteromonas, Bacillus, Lactobacillus, Acinetobacter, Clostridium, Marinifilum, and Pseudomonas were also detected. In the digestive tract, biofloc-grown shrimp maintained the presence of commensal bacteria including Vibrio, Photobacterium, Shewanella, Granulosicoccus, and Ruegeria similar to control shrimp. However, Vibrio and Photobacterium were significantly enriched and declined, respectively, in biofloc-grown shrimp. The presence of bioflocs upregulated immune-related genes encoding serine proteinase and prophenoloxidase in digestive organs which are routinely exposed to gut microbiota. Biofloc-grown shrimp also demonstrated a significant increase in systemic immune status. As a result, the survival rate of biofloc-grown shrimp was substantially higher than that of the control shrimp. Our findings suggested that the high relative abundance of vibrios in bioflocs enriched the number of vibrios in the digestive tract of biofloc-grown shrimp. This shift in gut microbiota composition may be partially responsible for local upregulation of immune-related gene expression in digestive organs and systemic promotion of immune status in circulating hemolymph.}, } @article {pmid32857738, year = {2020}, author = {Wang, J and Zhou, J}, title = {The effects of offshore petroleum exploitation on microbial community and antibiotic resistome of adjacent marine sediments.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {81}, number = {12}, pages = {2501-2510}, doi = {10.2166/wst.2020.289}, pmid = {32857738}, issn = {0273-1223}, mesh = {Anti-Bacterial Agents ; Bacteria/genetics ; Genes, Bacterial ; Geologic Sediments ; Humans ; *Microbiota ; *Petroleum ; }, abstract = {The exploitation of petroleum in offshore areas is becoming more prosperous due to the increasing human demand for oil. However, the effects of offshore petroleum exploitation on the microbial community in the surrounding environment are still not adequately understood. In the present study, variations in the composition, function, and antibiotic resistance of the microbial community in marine sediments adjacent to an offshore petroleum exploitation platform were analyzed by a metagenomics-based method. Significant shifts in the microbial community composition were observed in sediments impacted by offshore petroleum exploitation. Nitrosopumilales was enriched in marine sediments with the activities of offshore petroleum exploitation compared to the control sediments. The abundances of function genes involved in carbon, butanoate, methane, and fatty acid metabolism in sediment microbial communities also increased due to the offshore petroleum exploitation. Offshore petroleum exploitation resulted in the propagation of some antibiotic resistance genes (ARGs), including a multidrug transporter, smeE, and arnA, in marine sediments via horizontal gene transfer mediated by class I integrons. However, the total abundance and diversity of ARGs in marine sediments were not significantly affected by offshore petroleum exploitation. This study is the first attempt to analyze the impact of offshore petroleum exploitation on the spread of antibiotic resistance.}, } @article {pmid32857289, year = {2021}, author = {Wang, Y and Liu, F and Zhang, G and Su, Y and Sun, X and Chen, Q and Wang, C and Fu, H and He, Y and Zhu, X and Liu, X and Lv, M and Zhao, X and Zhao, X and Li, Y and Wang, Q and Huang, X and Zhang, X}, title = {Gut microbiome alterations and its link to corticosteroid resistance in immune thrombocytopenia.}, journal = {Science China. Life sciences}, volume = {64}, number = {5}, pages = {766-783}, pmid = {32857289}, issn = {1869-1889}, mesh = {Adrenal Cortex Hormones/*administration & dosage ; Drug Resistance/*genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenomics ; Protein Interaction Maps ; Purpura, Thrombocytopenic, Idiopathic/*drug therapy/*microbiology ; }, abstract = {Quantitative metagenomic studies have linked the gut microbiota to autoimmune disorders. Here, we performed deep shotgun metagenomic sequencing of fecal samples from 99 immune thrombocytopenia (ITP) patients and 52 healthy controls. Dysbiosis in the gut microbiome of ITP was detected phylogenetically and functionally, and classifier based on species markers distinguished individuals with ITP from healthy controls. In particular, the abundance of Ruminococcus gnavus, Bifidobacterium longum and Akkermansia muciniphila was markedly increased in treatment-naïve ITP patients, and the alterations of microbial species were correlated with clinical indices. Functionally, the secondary bile acid biosynthesis and flagellar assembly were depleted in the gut microbiota of ITP, which may contribute to the onset of ITP by affecting the immune system. Furthermore, we found that corticosteroid treatment affected the gut microbiome of ITP. Compared with corticosteroid-sensitive ITP patients, we identified that the corticosteroid-resistant ITP patients displayed a distinct gut microbiome, which was different from that of the treatment-naïve ITP patients. Together, we provided support for the critical role of gut microbiota in the development of ITP and established a foundation for further research characterizing gut microbiota in relation to corticosteroid resistance of ITP.}, } @article {pmid32855157, year = {2020}, author = {Peng, Z and Cheng, S and Kou, Y and Wang, Z and Jin, R and Hu, H and Zhang, X and Gong, JF and Li, J and Lu, M and Wang, X and Zhou, J and Lu, Z and Zhang, Q and Tzeng, DTW and Bi, D and Tan, Y and Shen, L}, title = {The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer.}, journal = {Cancer immunology research}, volume = {8}, number = {10}, pages = {1251-1261}, doi = {10.1158/2326-6066.CIR-19-1014}, pmid = {32855157}, issn = {2326-6074}, mesh = {B7-H1 Antigen/pharmacology ; Female ; Gastrointestinal Microbiome ; Gastrointestinal Neoplasms/*drug therapy ; Humans ; Immunotherapy/*methods ; Male ; }, abstract = {We report on a comprehensive analysis of the gut microbiomes of patients with gastrointestinal (GI) cancer receiving anti-PD-1/PD-L1 treatment. The human gut microbiota has been associated with clinical responses to anti-PD-1/PD-L1 immunotherapy in melanoma, non-small cell lung cancer, and renal cell carcinoma. We aimed to investigate this association in GI cancers. We also identified bacterial taxa with patient stratification potential. We recruited 74 patients with advanced-stage GI cancer receiving anti-PD-1/PD-L1 treatment and collected their fecal samples prior to and during immunotherapy, along with clinical evaluations. Our 16S rRNA taxonomy survey on the fecal samples revealed an elevation of the Prevotella/Bacteroides ratio in patients, with a preferred response to anti-PD-1/PD-L1 treatment, and a particular subgroup of responders harboring a significantly higher abundance of Prevotella, Ruminococcaceae, and Lachnospiraceae The shotgun metagenomes of the same samples showed that patients exhibiting different responses had differential abundance of pathways related to nucleoside and nucleotide biosynthesis, lipid biosynthesis, sugar metabolism, and fermentation to short-chain fatty acids (SCFA). Gut bacteria that were capable of SCFA production, including Eubacterium, Lactobacillus, and Streptococcus, were positively associated with anti-PD-1/PD-L1 response across different GI cancer types. We further demonstrated that the identified bacterial taxa were predictive of patient stratification in both our cohort and melanoma patients from two previously published studies. Our results thus highlight the impact of gut microbiomes on anti-PD-1/PD-L1 outcomes, at least in a subset of patients with GI cancer, and suggest the potential of the microbiome as a marker for immune-checkpoint blockade responses.See articles by Tomita et al., p. 1236, and Hakozaki et al., p. 1243.}, } @article {pmid32852361, year = {2020}, author = {Francis, F and Gough, EK and Edens, TJ and Berejena, C and Bwakura-Dangarembizi, M and Shonhai, A and Nathoo, KJ and Glass, M and Gibb, DM and Prendergast, AJ and Manges, AR}, title = {Brief Report: Cessation of Long-Term Cotrimoxazole Prophylaxis in HIV-Infected Children Does Not Alter the Carriage of Antimicrobial Resistance Genes.}, journal = {Journal of acquired immune deficiency syndromes (1999)}, volume = {85}, number = {5}, pages = {601-605}, pmid = {32852361}, issn = {1944-7884}, support = {G0300400/MRC_/Medical Research Council/United Kingdom ; MC_UU_12023/26/MRC_/Medical Research Council/United Kingdom ; //CIHR/Canada ; G1001190/MRC_/Medical Research Council/United Kingdom ; 108065/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 093768/Z/10/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Anti-Infective Agents/administration & dosage/*therapeutic use ; Child ; Child, Preschool ; Drug Resistance, Microbial/*drug effects/genetics ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; HIV Infections/*complications ; Humans ; Male ; Trimethoprim, Sulfamethoxazole Drug Combination/administration & dosage/*therapeutic use ; Zimbabwe ; }, abstract = {BACKGROUND: Cotrimoxazole (CTX) is a broad-spectrum antimicrobial, combining trimethoprim and sulfamethoxazole. CTX prophylaxis reduces mortality and morbidity among people living with HIV in regions with high prevalence of bacterial infections and malaria. The Antiretroviral research for Watoto trial evaluated the effect of stopping versus continuing CTX prophylaxis in sub-Saharan Africa.

METHODS: In this study, 72 HIV-infected Zimbabwean children, on antiretroviral therapy, provided fecal samples at 84 and 96 weeks after randomization to continue or stop CTX. DNA was extracted for whole metagenome shotgun sequencing, with sequencing reads mapped to the Comprehensive Antibiotic Resistance Database to identify CTX and other antimicrobial resistance genes.

RESULTS: There were minimal differences in the carriage of CTX resistance genes between groups. The dfrA1 gene, conferring trimethoprim resistance, was significantly higher in the continue group (P = 0.039) and the tetA(P) gene conferring resistance to tetracycline was significantly higher in the stop group (P = 0.013). CTX prophylaxis has a role in shaping the resistome; however, stopping prophylaxis does not decrease resistance gene abundance.

CONCLUSIONS: No differences were observed in resistance gene carriage between the stop and continue groups. The previously shown multi-faceted protective effects of CTX in antiretroviral research for Watoto trial clinical outcomes are not outweighed by the risk of multi-drug resistance gene selection due to prophylaxis. These findings are reassuring, given current recommendations for long-term CTX prophylaxis among children living with HIV in sub-Saharan Africa to decrease mortality and morbidity.}, } @article {pmid32850498, year = {2020}, author = {Galazzo, G and van Best, N and Benedikter, BJ and Janssen, K and Bervoets, L and Driessen, C and Oomen, M and Lucchesi, M and van Eijck, PH and Becker, HEF and Hornef, MW and Savelkoul, PH and Stassen, FRM and Wolffs, PF and Penders, J}, title = {How to Count Our Microbes? The Effect of Different Quantitative Microbiome Profiling Approaches.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {403}, pmid = {32850498}, issn = {2235-2988}, mesh = {Bacteria/genetics ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Next-generation sequencing (NGS) has instigated the research on the role of the microbiome in health and disease. The compositional nature of such microbiome datasets makes it however challenging to identify those microbial taxa that are truly associated with an intervention or health outcome. Quantitative microbiome profiling overcomes the compositional structure of microbiome sequencing data by integrating absolute quantification of microbial abundances into the NGS data. Both cell-based methods (e.g., flow cytometry) and molecular methods (qPCR) have been used to determine the absolute microbial abundances, but to what extent different quantification methods generate similar quantitative microbiome profiles has so far not been explored. Here we compared relative microbiome profiling (without incorporation of microbial quantification) to three variations of quantitative microbiome profiling: (1) microbial cell counting using flow cytometry (QMP), (2) counting of microbial cells using flow cytometry combined with Propidium Monoazide pre-treatment of fecal samples before metagenomics DNA isolation in order to only profile the microbial composition of intact cells (QMP-PMA), and (3) molecular based quantification of the microbial load using qPCR targeting the 16S rRNA gene. Although qPCR and flow cytometry both resulted in accurate and strongly correlated results when quantifying the bacterial abundance of a mock community of bacterial cells, the two methods resulted in highly divergent quantitative microbial profiles when analyzing the microbial composition of fecal samples from 16 healthy volunteers. These differences could not be attributed to the presence of free extracellular prokaryotic DNA in the fecal samples as sample pre-treatment with Propidium Monoazide did not improve the concordance between qPCR-based and flow cytometry-based QMP. Also lack of precision of qPCR was ruled out as a major cause of the disconcordant findings, since quantification of the fecal microbial load by the highly sensitive digital droplet PCR correlated strongly with qPCR. In conclusion, quantitative microbiome profiling is an elegant approach to bypass the compositional nature of microbiome NGS data, however it is important to realize that technical sources of variability may introduce substantial additional bias depending on the quantification method being used.}, } @article {pmid32848005, year = {2020}, author = {Bobay, LM and Wissel, EF and Raymann, K}, title = {Strain Structure and Dynamics Revealed by Targeted Deep Sequencing of the Honey Bee Gut Microbiome.}, journal = {mSphere}, volume = {5}, number = {4}, pages = {}, pmid = {32848005}, issn = {2379-5042}, support = {R01 GM132137/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification ; Bees/*microbiology ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; *High-Throughput Nucleotide Sequencing ; Host Microbial Interactions ; *Metagenome ; Metagenomics ; Phylogeny ; Symbiosis ; }, abstract = {Host-associated microbiomes can be critical for the health and proper development of animals and plants. The answers to many fundamental questions regarding the modes of acquisition and microevolution of microbiome communities remain to be established. Deciphering strain-level dynamics is essential to fully understand how microbial communities evolve, but the forces shaping the strain-level dynamics of microbial communities remain largely unexplored, mostly because of methodological issues and cost. Here, we used targeted strain-level deep sequencing to uncover the strain dynamics within a host-associated microbial community using the honey bee gut microbiome as a model system. Our results revealed that amplicon sequencing of conserved protein-coding gene regions using species-specific primers is a cost-effective and accurate method for exploring strain-level diversity. In fact, using this method we were able to confirm strain-level results that have been obtained from whole-genome shotgun sequencing of the honey bee gut microbiome but with a much higher resolution. Importantly, our deep sequencing approach allowed us to explore the impact of low-frequency strains (i.e., cryptic strains) on microbiome dynamics. Results show that cryptic strain diversity is not responsible for the observed variations in microbiome composition across bees. Altogether, the findings revealed new fundamental insights regarding strain dynamics of host-associated microbiomes.IMPORTANCE The factors driving fine-scale composition and dynamics of gut microbial communities are poorly understood. In this study, we used metagenomic amplicon deep sequencing to decipher the strain dynamics of two key members of the honey bee gut microbiome. Using this high-throughput and cost-effective approach, we were able to confirm results from previous large-scale whole-genome shotgun (WGS) metagenomic sequencing studies while also gaining additional insights into the community dynamics of two core members of the honey bee gut microbiome. Moreover, we were able to show that cryptic strains are not responsible for the observed variations in microbiome composition across bees.}, } @article {pmid32847820, year = {2020}, author = {Zanella, MC and Cordey, S and Kaiser, L}, title = {Beyond Cytomegalovirus and Epstein-Barr Virus: a Review of Viruses Composing the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients.}, journal = {Clinical microbiology reviews}, volume = {33}, number = {4}, pages = {}, pmid = {32847820}, issn = {1098-6618}, mesh = {Blood/*virology ; Cytomegalovirus Infections/transmission ; Epstein-Barr Virus Infections/transmission ; Hematopoietic Stem Cell Transplantation/adverse effects/*statistics & numerical data ; Humans ; Transplant Recipients/*statistics & numerical data ; Transplants/*virology ; *Virome ; Virus Diseases/blood/*transmission ; }, abstract = {Viral primary infections and reactivations are common complications in patients after solid organ transplantation (SOT) and hematopoietic stem cell transplantation (HSCT) and are associated with high morbidity and mortality. Among these patients, viral infections are frequently associated with viremia. Beyond the usual well-known viruses that are part of the routine clinical management of transplant recipients, numerous other viral signatures or genomes can be identified in the blood of these patients. The identification of novel viral species and variants by metagenomic next-generation sequencing has opened up a new field of investigation and new paradigms. Thus, there is a need to thoroughly describe the state of knowledge in this field with a review of all viral infections that should be scrutinized in high-risk populations. Here, we review the eukaryotic DNA and RNA viruses identified in blood, plasma, or serum samples of pediatric and adult SOT/HSCT recipients and the prevalence of their detection, with a particular focus on recently identified viruses and those for which their potential association with disease remains to be investigated, such as members of the Polyomaviridae, Anelloviridae, Flaviviridae, and Astroviridae families. Current knowledge of the clinical significance of these viral infections with associated viremia among transplant recipients is also discussed. To ensure a comprehensive description in these two populations, individuals described as healthy (mostly blood donors) are considered for comparative purposes. The list of viruses that should be on the clinicians' radar is certainly incomplete and will expand, but the challenge is to identify those of possible clinical significance.}, } @article {pmid32846980, year = {2020}, author = {Kubacki, J and Flacio, E and Qi, W and Guidi, V and Tonolla, M and Fraefel, C}, title = {Viral Metagenomic Analysis of Aedes albopictus Mosquitos from Southern Switzerland.}, journal = {Viruses}, volume = {12}, number = {9}, pages = {}, pmid = {32846980}, issn = {1999-4915}, mesh = {Aedes/*virology ; Animals ; Female ; Flavivirus/classification/genetics/isolation & purification ; Male ; Metagenomics ; Phylogeny ; Switzerland ; Virome/*genetics ; Viruses/classification/genetics/isolation & purification ; }, abstract = {A metagenomic study was performed on 498 female and 40 male Aedes albopictus mosquitos collected in August and September 2019 in Ticino, a region in southern Switzerland, to address the question regarding the risk of the local transmission of zoonotic viruses. A total of 13 viruses from seven different virus families and several unclassified viral taxa were identified. Reads of insect-specific flaviviruses were present in all pools, and a complete genome of aedes flavivirus was assembled and phylogenetically analysed. The most abundant virus was Wenzhou sobemo-like virus, assembled from 1.3 × 10[5] to 3.6 × 10[6] reads in each pool. In a pool of male mosquitos, a complete genome of aedes Iflavi-like virus was detected and phylogenetically analysed. Most importantly, genomes of human pathogenic viruses were not found. This is the first study to determine the virome of Ae. albopictus from Switzerland and forms a baseline for future longitudinal investigations concerning the potential role of Ae. albopictus as a vector of clinically relevant viruses.}, } @article {pmid32846589, year = {2020}, author = {Huang, ZR and Chen, M and Guo, WL and Li, TT and Liu, B and Bai, WD and Ai, LZ and Rao, PF and Ni, L and Lv, XC}, title = {Monascus purpureus-fermented common buckwheat protects against dyslipidemia and non-alcoholic fatty liver disease through the regulation of liver metabolome and intestinal microbiome.}, journal = {Food research international (Ottawa, Ont.)}, volume = {136}, number = {}, pages = {109511}, doi = {10.1016/j.foodres.2020.109511}, pmid = {32846589}, issn = {1873-7145}, mesh = {Animals ; Asia ; China ; Diet, High-Fat ; *Fagopyrum ; *Gastrointestinal Microbiome ; Metabolome ; Mice ; *Monascus ; *Non-alcoholic Fatty Liver Disease/prevention & control ; }, abstract = {Monascus-fermented rice has been used to treat digestive disorder and promote blood circulation in China and other Asian countries for centuries. However, the effects and mechanisms of Monascus purpureus-fermented common buckwheat (HQ) on non-alcoholic fatty liver disease (NAFLD) and dyslipidemia are unclear. Here, oral supplementation of HQ significantly inhibited the abnormal growth of body weight and epididymal white adipose tissue (eWAT), prevented the hypertrophy of epididymal adipocytes, ameliorated some biochemical parameters of serum and liver related to lipid metabolism in mice fed a high-fat and high-cholesterol diet (HFD). Histological analysis also showed that the excessive accumulation of lipid droplets in the livers induced by HFD-feeding was greatly alleviated by HQ supplementation. Metagenomic analysis revealed that HQ supplementation made significant structural changes in the intestinal microflora of mice fed with HFD. The Spearman's correlation analysis revealed that physiological index, serum and liver lipid profiles were positively correlated with Bacteroidales S24-7, Streptococcus, Allobaculum, and Clostridiales XIII, but negatively associated with Lactobacillus, Ruminococcaceae_NK4A214 group, Ruminiclostridium, and Alistipes. UPLC-QTOF/MS-based liver metabolomics demonstrated that HQ intervention had significant regulatory effects on the metabolic pathways of primary bile acid biosynthesis, pyrimidine metabolism, ether lipid metabolism, glutathione metabolism, glycine, serine and threonine metabolism, and amino sugar and nucleotide sugar metabolism, etc. Additionally, HQ intervention regulated the mRNA levels of hepatic genes involved in hepatic lipid metabolism and bile acid homeostasis. Collectively, these findings present new evidence supporting that HQ has the potential to ameliorate dyslipidemia and NAFLD via modulating the intestinal microbial populations and hepatic metabolite profile in hyperlipidemic mice induced by HFD.}, } @article {pmid32846568, year = {2020}, author = {Campos Calero, G and Caballero Gómez, N and Lavilla Lerma, L and Benomar, N and Knapp, CW and Abriouel, H}, title = {In silico mapping of microbial communities and stress responses in a porcine slaughterhouse and pork products through its production chain, and the efficacy of HLE disinfectant.}, journal = {Food research international (Ottawa, Ont.)}, volume = {136}, number = {}, pages = {109486}, doi = {10.1016/j.foodres.2020.109486}, pmid = {32846568}, issn = {1873-7145}, mesh = {Abattoirs ; Animals ; Computer Simulation ; *Disinfectants ; Humans ; *Meat Products ; *Microbiota ; *Red Meat ; Swine ; }, abstract = {The use of shotgun metagenomic sequencing to understand ecological-level spread of microbes and their genes has provided new insights for the prevention, surveillance and control of microbial contaminants in the slaughterhouse environment. Here, microbial samples were collected from products and surrounding areas though a porcine slaughter process; shotgun metagenomic DNA-sequencing of these samples revealed a high community diversity within the porcine slaughterhouse and pork products, in zones originating from animal arrival through to the sale zones. Bacteria were more prevalent in the first zones, such as arrival- and anesthesia-zones, and DNA viruses were prevalent in the scorching-and-whip zone, animal products and sale zone. Data revealed the dominance of Firmicutes and Proteobacteria phyla followed by Actinobacteria, with a clear shift in the relative abundance of lactic acid bacteria (mainly Lactobacillus sp.) from early slaughtering steps to Proteobacteria and then to viruses suggesting site-specific community compositions occur in the slaughterhouse. Porcine-type-C oncovirus was the main virus found in slaughterhouse, which causes malignant diseases in animals and humans. As such, to guarantee food safety in a slaughterhouse, a better decipher of ecology and adaptation strategies of microbes becomes crucial. Analysis of functional genes further revealed high abundance of diverse genes associated with stress, especially in early zones (animal and environmental surfaces of arrival zone with 57,710 and 40,806 genes, respectively); SOS responsive genes represented the most prevalent, possibly associated with genomic changes responsible of biofilm formation, stringent response, heat shock, antimicrobial production and antibiotic response. The presence of several antibiotic resistance genes suggests horizontal gene transfer, thus increasing the likelihood for resistance selection in human pathogens. These findings are of great concern, with the suggestion to focus control measures and establish good disinfection strategies to avoid gene spread and microbial contaminants (bacteria and viruses) from the animal surface into the food chain and environment, which was achieved by applying HLE disinfectant after washing with detergent.}, } @article {pmid32845369, year = {2020}, author = {Louvado, A and Coelho, FJRC and Palma, M and Tavares, LC and Ozorio, ROA and Magnoni, L and Viegas, I and Gomes, NCM}, title = {Effect of glycerol feed-supplementation on seabass metabolism and gut microbiota.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {19}, pages = {8439-8453}, pmid = {32845369}, issn = {1432-0614}, support = {PTDC/CVT-NUT/2851/2014//Fundação para a Ciência e a Tecnologia/ ; UID/AMB/50017/2019//Fundação para a Ciência e a Tecnologia/ ; UID/Multi/04423/2019//Fundação para a Ciência e a Tecnologia/ ; Centro-01-0145-FEDER-000007//European Regional Development Fund/ ; MAR-02.01.01-FEAMP-0031//European Maritime and Fisheries Fund/ ; UID/BIA/04004/2019//Fundação para a Ciência e a Tecnologia (PT)/ ; }, mesh = {Animal Feed/analysis ; Animals ; *Bass ; Dietary Supplements ; *Gastrointestinal Microbiome ; Glycerol ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Dietary glycerol supplementation in aquaculture feed is seen as an alternative and inexpensive way to fuel fish metabolism, attenuate metabolic utilization of dietary proteins and, subsequently, reduce nitrogen excretion. In this study, we evaluated the impact of dietary glycerol supplementation on nitrogen excretion of European seabass (Dicentrarchus labrax) and its effects on metabolite profile and bacterial community composition of gut digesta. These effects were evaluated in a 60-day trial with fish fed diets supplemented with 2.5% or 5% (w/w) refined glycerol and without glycerol supplementation. Nuclear magnetic resonance spectroscopy and high-throughput 16S rRNA gene sequencing were used to characterize the effects of glycerol supplementation on digesta metabolite and bacterial community composition of 6-h postprandial fish. Our results showed that ammonia excretion was not altered by dietary glycerol supplementation, and the highest glycerol dosage was associated with significant increases in amino acids and a decrease of ergogenic creatine in digesta metabolome. Concomitantly, significant decreases in putative amino acid degradation pathways were detected in the predicted metagenome analysis, suggesting a metabolic shift. Taxon-specific analysis revealed significant increases in abundance of some specific genera (e.g., Burkholderia and Vibrio) and bacterial diversity. Overall, our results indicate glycerol supplementation may decrease amino acid catabolism without adversely affecting fish gut bacterial communities.Key points• Glycerol can be an inexpensive and energetic alternative in fish feed formulations.• Glycerol did not affect nitrogen excretion and gut bacteriome composition.• Glycerol reduced uptake of amino acids and increased uptake of ergogenic creatine.• Glycerol reduced putative amino acid degradation pathways in predicted metagenome.}, } @article {pmid32845367, year = {2020}, author = {Kaster, AK and Sobol, MS}, title = {Microbial single-cell omics: the crux of the matter.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {19}, pages = {8209-8220}, pmid = {32845367}, issn = {1432-0614}, support = {320579085//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Genomics ; Metagenome ; *Metagenomics ; *Microbiota ; Phylogeny ; }, abstract = {Single-cell genomics and transcriptomics can provide reliable context for assembled genome fragments and gene expression activity on the level of individual prokaryotic genomes. These methods are rapidly emerging as an essential complement to cultivation-based, metagenomics, metatranscriptomics, and microbial community-focused research approaches by allowing direct access to information from individual microorganisms, even from deep-branching phylogenetic groups that currently lack cultured representatives. Their integration and binning with environmental 'omics data already provides unprecedented insights into microbial diversity and metabolic potential, enabling us to provide information on individual organisms and the structure and dynamics of natural microbial populations in complex environments. This review highlights the pitfalls and recent advances in the field of single-cell omics and its importance in microbiological and biotechnological studies. KEY POINTS: • Single-cell omics expands the tree of life through the discovery of novel organisms, genes, and metabolic pathways. • Disadvantages of metagenome-assembled genomes are overcome by single-cell omics. • Functional analysis of single cells explores the heterogeneity of gene expression. • Technical challenges still limit this field, thus prompting new method developments.}, } @article {pmid32845297, year = {2020}, author = {Mujica, MI and Pérez, MF and Jakalski, M and Martos, F and Selosse, MA}, title = {Soil P reduces mycorrhizal colonization while favors fungal pathogens: observational and experimental evidence in Bipinnula (Orchidaceae).}, journal = {FEMS microbiology ecology}, volume = {96}, number = {11}, pages = {}, doi = {10.1093/femsec/fiaa178}, pmid = {32845297}, issn = {1574-6941}, mesh = {*Mycobiome ; *Mycorrhizae ; *Orchidaceae ; Plant Roots ; Soil ; Soil Microbiology ; }, abstract = {Little is known about the soil factors influencing root-associated fungal communities in Orchidaceae. Limited evidence suggests that soil nutrients may modulate the association with orchid mycorrhizal fungi (OMF), but their influence on non-mycorrhizal fungi remains unexplored. To study how nutrient availability affects mycorrhizal and non-mycorrhizal fungi associated with the orchid Bipinnula fimbriata, we conducted a metagenomic investigation within a large population with variable soil conditions. Additionally, we tested the effect of phosphorus (P) addition on fungal communities and mycorrhizal colonization. Soil P negatively correlated with the abundance of OMF, but not with the abundance of non-mycorrhizal fungi. After fertilization, increments in soil P negatively affected mycorrhizal colonization; however, they had no effect on OMF richness or composition. The abundance and richness of pathotrophs were negatively related to mycorrhizal colonization and then, after fertilization, the decrease in mycorrhizal colonization correlated with an increase in pathogen richness. Our results suggest that OMF are affected by soil conditions differently from non-mycorrhizal fungi. Bipinnula fimbriata responds to fertilization by altering mycorrhizal colonization rather than by switching OMF partners in the short term, and the influence of nutrients on OMF is coupled with indirect effects on the whole fungal community and potentially on plant's health.}, } @article {pmid32844199, year = {2020}, author = {Qian, Y and Yang, X and Xu, S and Huang, P and Li, B and Du, J and He, Y and Su, B and Xu, LM and Wang, L and Huang, R and Chen, S and Xiao, Q}, title = {Gut metagenomics-derived genes as potential biomarkers of Parkinson's disease.}, journal = {Brain : a journal of neurology}, volume = {143}, number = {8}, pages = {2474-2489}, doi = {10.1093/brain/awaa201}, pmid = {32844199}, issn = {1460-2156}, mesh = {Aged ; Case-Control Studies ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; *Genetic Markers ; Humans ; Male ; Metagenomics/*methods ; Middle Aged ; Parkinson Disease/*diagnosis/*microbiology ; }, abstract = {Identification of the gut microbiome compositions associated with disease has become a research focus worldwide. Emerging evidence has revealed the presence of gut microbiota dysbiosis in Parkinson's disease. In this study, we aimed to identify the gut microbiome associated with Parkinson's disease and subsequently to screen and to validate potential diagnostic biomarkers of Parkinson's disease. This case-control study investigated gut microbial genes in faeces from 40 volunteer Chinese patients with Parkinson's disease and their healthy spouses using shotgun metagenomic sequencing. Furthermore, the identified specific gut microbial gene markers were validated with real-time PCR in an independent Chinese cohort of 78 Parkinson's disease patients, 75 control subjects, 40 patients with multiple system atrophy and 25 patients with Alzheimer's disease. We developed the first gut microbial gene catalogue associated with Parkinson's disease. Twenty-five gene markers were identified that distinguished Parkinson's disease patients from healthy control subjects, achieving an area under the receiver operating characteristic curve (AUC) of 0.896 (95% confidence interval: 83.1-96.1%). A highly accurate Parkinson's disease index, which was not influenced by disease severity or Parkinson's disease medications, was created. Testing these gene markers using quantitative PCR distinguished Parkinson's disease patients from healthy controls not only in the 40 couples (AUC = 0.922, 95% confidence interval: 86.4-98.0%), but also in an independent group of 78 patients with Parkinson's disease and 75 healthy control subjects (AUC = 0.905, 95% confidence interval: 86.0-95.1%). This classifier also performed a differential diagnosis power in discriminating these 78 patients with Parkinson's disease from a cohort of 40 patients with multiple system atrophy and 25 patients with Alzheimer's disease based on the panel of 25 biomarkers. Based on our results, the identified Parkinson's disease index based on the gene set from the gut microbiome may be a potential diagnostic biomarker of Parkinson's disease.}, } @article {pmid32841606, year = {2020}, author = {Gregory, AC and Zablocki, O and Zayed, AA and Howell, A and Bolduc, B and Sullivan, MB}, title = {The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut.}, journal = {Cell host & microbe}, volume = {28}, number = {5}, pages = {724-740.e8}, pmid = {32841606}, issn = {1934-6069}, support = {R01 HG010318/HG/NHGRI NIH HHS/United States ; T32 AI112542/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteriophages ; Databases, Factual ; Dysbiosis/virology ; Feces/virology ; Gastrointestinal Tract/*virology ; Genome, Viral ; Humans ; Longevity ; Metagenome ; Virion ; *Virome ; Virus Diseases/virology ; }, abstract = {The gut microbiome profoundly affects human health and disease, and their infecting viruses are likely as important, but often missed because of reference database limitations. Here, we (1) built a human Gut Virome Database (GVD) from 2,697 viral particle or microbial metagenomes from 1,986 individuals representing 16 countries, (2) assess its effectiveness, and (3) report a meta-analysis that reveals age-dependent patterns across healthy Westerners. The GVD contains 33,242 unique viral populations (approximately species-level taxa) and improves average viral detection rates over viral RefSeq and IMG/VR nearly 182-fold and 2.6-fold, respectively. GVD meta-analyses show highly personalized viromes, reveal that inter-study variability from technical artifacts is larger than any "disease" effect at the population level, and document how viral diversity changes from human infancy into senescence. Together, this compact foundational resource, these standardization guidelines, and these meta-analysis findings provide a systematic toolkit to help maximize our understanding of viral roles in health and disease.}, } @article {pmid32841483, year = {2020}, author = {Mammola, S and Amorim, IR and Bichuette, ME and Borges, PAV and Cheeptham, N and Cooper, SJB and Culver, DC and Deharveng, L and Eme, D and Ferreira, RL and Fišer, C and Fišer, Ž and Fong, DW and Griebler, C and Jeffery, WR and Jugovic, J and Kowalko, JE and Lilley, TM and Malard, F and Manenti, R and Martínez, A and Meierhofer, MB and Niemiller, ML and Northup, DE and Pellegrini, TG and Pipan, T and Protas, M and Reboleira, ASPS and Venarsky, MP and Wynne, JJ and Zagmajster, M and Cardoso, P}, title = {Fundamental research questions in subterranean biology.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {95}, number = {6}, pages = {1855-1872}, doi = {10.1111/brv.12642}, pmid = {32841483}, issn = {1469-185X}, support = {eLTER//Horizon 2020 Framework Programme/International ; N1-0069//Javna Agencija za Raziskovalno Dejavnost RS/International ; 15471//Villum Fonden/International ; 678193//Horizon 2020 Framework Programme/International ; RDP 00092-18//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/International ; 882221//H2020 Marie Skłodowska-Curie Actions/International ; ANR-15-CE32-0005//Agence Nationale de la Recherche/International ; 745530//H2020 Marie Skłodowska-Curie Actions/International ; CF19-0609//Carlsbergfondet/International ; }, mesh = {Adaptation, Physiological ; *Caves ; *Ecology ; Genomics ; }, abstract = {Five decades ago, a landmark paper in Science titled The Cave Environment heralded caves as ideal natural experimental laboratories in which to develop and address general questions in geology, ecology, biogeography, and evolutionary biology. Although the 'caves as laboratory' paradigm has since been advocated by subterranean biologists, there are few examples of studies that successfully translated their results into general principles. The contemporary era of big data, modelling tools, and revolutionary advances in genetics and (meta)genomics provides an opportunity to revisit unresolved questions and challenges, as well as examine promising new avenues of research in subterranean biology. Accordingly, we have developed a roadmap to guide future research endeavours in subterranean biology by adapting a well-established methodology of 'horizon scanning' to identify the highest priority research questions across six subject areas. Based on the expert opinion of 30 scientists from around the globe with complementary expertise and of different academic ages, we assembled an initial list of 258 fundamental questions concentrating on macroecology and microbial ecology, adaptation, evolution, and conservation. Subsequently, through online surveys, 130 subterranean biologists with various backgrounds assisted us in reducing our list to 50 top-priority questions. These research questions are broad in scope and ready to be addressed in the next decade. We believe this exercise will stimulate research towards a deeper understanding of subterranean biology and foster hypothesis-driven studies likely to resonate broadly from the traditional boundaries of this field.}, } @article {pmid32840567, year = {2020}, author = {Wang, Y and Zhou, R and Yu, Q and Feng, T and Li, H}, title = {Gut microbiome adaptation to extreme cold winter in wild plateau pika (Ochotona curzoniae) on the Qinghai-Tibet Plateau.}, journal = {FEMS microbiology letters}, volume = {367}, number = {16}, pages = {}, doi = {10.1093/femsle/fnaa134}, pmid = {32840567}, issn = {1574-6968}, mesh = {Adaptation, Physiological/*physiology ; Animals ; China ; *Cold Temperature ; Ecosystem ; Gastrointestinal Microbiome/*physiology ; Lagomorpha/*microbiology ; Seasons ; Tibet ; }, abstract = {The Qinghai-Tibet Plateau is a harsh environment characterized by low temperature, high altitude and hypoxia, although some native mammals may adapt well to the extreme climate. However, how animal gut microbial community structure and function adapt to extreme cold climates is not well understood. Plateau pika (Ochotona curzoniae) is an ideal animal model with which to study the effects of climate change on host adaptation by studing intestinal microorganisms. Here, we used 16S rRNA sequencing technology combined with physiological methods to investigate plateau pika gut microbiota in summer and winter. Due to limited diet resources, the pikas in winter have a lower ability of degradation and fermentation for plant-based food (reduced cellulase activity and total short-chain fatty acids) by decreasing gut microbial diversity and some functional microbes, such as fiber-degrading bacteria Oscillospira and Treponema. Metagenomic prediction showed that most of those gene functions associated with metabolism (e.g. energy metabolism and lipid metabolism) were less abundant in winter, implying that the plateau pika slows diet fermentation and weakens energy requirements in the cold season. Our results have significance for explaining the mechanism of wild plateau mammals adapting to a high-altitude cold environment from the perspective of gut microbiome.}, } @article {pmid32840024, year = {2020}, author = {Sizikov, S and Burgsdorf, I and Handley, KM and Lahyani, M and Haber, M and Steindler, L}, title = {Characterization of sponge-associated Verrucomicrobia: microcompartment-based sugar utilization and enhanced toxin-antitoxin modules as features of host-associated Opitutales.}, journal = {Environmental microbiology}, volume = {22}, number = {11}, pages = {4669-4688}, doi = {10.1111/1462-2920.15210}, pmid = {32840024}, issn = {1462-2920}, support = {1243/16//Israel Science Foundation/ ; }, mesh = {Animals ; Mediterranean Sea ; Microbiota ; Phylogeny ; Porifera/*microbiology ; Seawater/microbiology ; Sugars/*metabolism ; *Symbiosis ; Toxin-Antitoxin Systems/*genetics ; Verrucomicrobia/classification/genetics/metabolism/*physiology ; }, abstract = {Bacteria of the phylum Verrucomicrobia are ubiquitous in marine environments and can be found as free-living organisms or as symbionts of eukaryotic hosts. Little is known about host-associated Verrucomicrobia in the marine environment. Here we reconstructed two genomes of symbiotic Verrucomicrobia from bacterial metagenomes derived from the Atlanto-Mediterranean sponge Petrosia ficiformis and three genomes from strains that we isolated from offshore seawater of the Eastern Mediterranean Sea. Phylogenomic analysis of these five strains indicated that they are all members of Verrucomicrobia subdivision 4, order Opitutales. We compared these novel sponge-associated and seawater-isolated genomes to closely related Verrucomicrobia. Genomic analysis revealed that Planctomycetes-Verrucomicrobia microcompartment gene clusters are enriched in the genomes of symbiotic Opitutales including sponge symbionts but not in free-living ones. We hypothesize that in sponge symbionts these microcompartments are used for degradation of l-fucose and l-rhamnose, which are components of algal and bacterial cell walls and therefore may be found at high concentrations in the sponge tissue. Furthermore, we observed an enrichment of toxin-antitoxin modules in symbiotic Opitutales. We suggest that, in sponges, verrucomicrobial symbionts utilize these modules as a defence mechanism against antimicrobial activity deriving from the abundant microbial community co-inhabiting the host.}, } @article {pmid32839573, year = {2020}, author = {Gibbons, SM}, title = {Keystone taxa indispensable for microbiome recovery.}, journal = {Nature microbiology}, volume = {5}, number = {9}, pages = {1067-1068}, pmid = {32839573}, issn = {2058-5276}, mesh = {Anti-Bacterial Agents ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Microbiota/genetics ; }, } @article {pmid32839473, year = {2020}, author = {Duranti, S and Ruiz, L and Lugli, GA and Tames, H and Milani, C and Mancabelli, L and Mancino, W and Longhi, G and Carnevali, L and Sgoifo, A and Margolles, A and Ventura, M and Ruas-Madiedo, P and Turroni, F}, title = {Bifidobacterium adolescentis as a key member of the human gut microbiota in the production of GABA.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {14112}, pmid = {32839473}, issn = {2045-2322}, mesh = {Animals ; Anxiety/physiopathology ; Bacterial Load ; Bifidobacterium adolescentis/classification/*genetics/metabolism ; Depression/physiopathology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; Models, Animal ; Probiotics/administration & dosage ; Rats ; gamma-Aminobutyric Acid/biosynthesis/*genetics/metabolism ; }, abstract = {Gamma aminobutyric acid (GABA) is the principal inhibitory neurotransmitter playing a key role in anxiety and depression disorders in mammals. Recent studies revealed that members of the gut microbiota are able to produce GABA modulating the gut-brain axis response. Among members of the human gut microbiota, bifidobacteria are well known to establish many metabolic and physiologic interactions with the host. In this study, we performed genome analyses of more than 1,000 bifidobacterial strains publicly available revealing that Bifidobacterium adolescentis taxon might represent a model GABA producer in human gastrointestinal tract. Moreover, the in silico screening of human/animal metagenomic datasets showed an intriguing association/correlation between B. adolescentis load and mental disorders such as depression and anxiety. Interestingly, in vitro screening of 82 B. adolescentis strains allowed identifying two high GABA producers, i.e. B. adolescentis PRL2019 and B. adolescentis HD17T2H, which were employed in an in vivo trial in rats. Feeding Groningen rats with a supplementation of B. adolescentis strains, confirmed the ability of these microorganisms to stimulate the in vivo production of GABA highlighting their potential implication in gut-brain axis interactions.}, } @article {pmid32839304, year = {2020}, author = {Takewaki, D and Suda, W and Sato, W and Takayasu, L and Kumar, N and Kimura, K and Kaga, N and Mizuno, T and Miyake, S and Hattori, M and Yamamura, T}, title = {Alterations of the gut ecological and functional microenvironment in different stages of multiple sclerosis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {36}, pages = {22402-22412}, pmid = {32839304}, issn = {1091-6490}, mesh = {Adult ; Case-Control Studies ; Cysteine/metabolism ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Humans ; Male ; Metagenome/genetics ; Multiple Sclerosis, Chronic Progressive/epidemiology/*microbiology ; Multiple Sclerosis, Relapsing-Remitting/epidemiology/*microbiology ; Oxidative Stress/physiology ; Sulfur/metabolism ; }, abstract = {Multiple sclerosis (MS), an autoimmune disease of the central nervous system, generally starts as the relapsing remitting form (RRMS), but often shifts into secondary progressive MS (SPMS). SPMS represents a more advanced stage of MS, characterized by accumulating disabilities and refractoriness to medications. The aim of this study was to clarify the microbial and functional differences in gut microbiomes of the different stages of MS. Here, we compared gut microbiomes of patients with RRMS, SPMS, and two closely related disorders with healthy controls (HCs) by 16S rRNA gene and whole metagenomic sequencing data from fecal samples and by fecal metabolites. Each patient group had a number of species having significant changes in abundance in comparison with HCs, including short-chain fatty acid (SCFA)-producing bacteria reduced in MS. Changes in some species had close association with clinical severity of the patients. A marked reduction in butyrate and propionate biosynthesis and corresponding metabolic changes were confirmed in RRMS compared with HCs. Although bacterial composition analysis showed limited differences between the patient groups, metagenomic functional data disclosed an increase in microbial genes involved in DNA mismatch repair in SPMS as compared to RRMS. Together with an increased ratio of cysteine persulfide to cysteine in SPMS revealed by sulfur metabolomics, we postulate that excessive DNA oxidation could take place in the gut of SPMS. Thus, gut ecological and functional microenvironments were significantly altered in the different stages of MS. In particular, reduced SCFA biosynthesis in RRMS and elevated oxidative level in SPMS were characteristic.}, } @article {pmid32839200, year = {2021}, author = {Mokkala, K and Paulin, N and Houttu, N and Koivuniemi, E and Pellonperä, O and Khan, S and Pietilä, S and Tertti, K and Elo, LL and Laitinen, K}, title = {Metagenomics analysis of gut microbiota in response to diet intervention and gestational diabetes in overweight and obese women: a randomised, double-blind, placebo-controlled clinical trial.}, journal = {Gut}, volume = {70}, number = {2}, pages = {309-318}, doi = {10.1136/gutjnl-2020-321643}, pmid = {32839200}, issn = {1468-3288}, mesh = {Adult ; Diabetes, Gestational/*diet therapy/etiology/microbiology ; Double-Blind Method ; Female ; Fish Oils/therapeutic use ; Gastrointestinal Microbiome/*genetics ; Glucose Tolerance Test ; Humans ; Metagenome/*genetics ; Metagenomics/methods ; Obesity, Maternal/complications/*diet therapy/microbiology ; Pregnancy ; Probiotics/therapeutic use ; }, abstract = {OBJECTIVE: Gut microbiota and diet are known to contribute to human metabolism. We investigated whether the metagenomic gut microbiota composition and function changes over pregnancy are related to gestational diabetes mellitus (GDM) and can be modified by dietary supplements, fish oil and/or probiotics.

DESIGN: The gut microbiota of 270 overweight/obese women participating in a mother-infant clinical study were analysed with metagenomics approach in early (mean gestational weeks 13.9) and late (gestational weeks 35.2) pregnancy. GDM was diagnosed with a 2 hour 75 g oral glucose tolerance test.

RESULTS: Unlike women with GDM, women without GDM manifested changes in relative abundance of bacterial species over the pregnancy, particularly those receiving the fish oil + probiotics combination. The specific bacterial species or function did not predict the onset of GDM nor did it differ according to GDM status, except for the higher abundance of Ruminococcus obeum in late pregnancy in the combination group in women with GDM compared with women without GDM. In the combination group, weak decreases over the pregnancy were observed in basic bacterial housekeeping functions.

CONCLUSIONS: The specific gut microbiota species do not contribute to GDM in overweight/obese women. Nevertheless, the GDM status may disturb maternal gut microbiota flexibility and thus limit the capacity of women with GDM to respond to diet, as evidenced by alterations in gut microbiota observed only in women without GDM. These findings may be important when considering the metabolic complications during pregnancy, but further studies with larger populations are called for to verify the findings.}, } @article {pmid32835897, year = {2021}, author = {Miyoshi, J and Lee, STM and Kennedy, M and Puertolas, M and Frith, M and Koval, JC and Miyoshi, S and Antonopoulos, DA and Leone, V and Chang, EB}, title = {Metagenomic Alterations in Gut Microbiota Precede and Predict Onset of Colitis in the IL10 Gene-Deficient Murine Model.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {11}, number = {2}, pages = {491-502}, pmid = {32835897}, issn = {2352-345X}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; RC2 DK122394/DK/NIDDK NIH HHS/United States ; T32 GM007281/GM/NIGMS NIH HHS/United States ; T32 DK007074/DK/NIDDK NIH HHS/United States ; R37 DK047722/DK/NIDDK NIH HHS/United States ; K01 DK111785/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/administration & dosage ; Cefoperazone/administration & dosage ; Colitis/*diagnosis/immunology/microbiology ; Disease Models, Animal ; Dysbiosis/chemically induced/*complications/immunology/microbiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/*immunology ; Humans ; Interleukin-10/*deficiency/genetics ; Intestinal Mucosa/immunology ; Male ; Metagenome ; Metagenomics ; Mice ; Mice, Knockout ; Prognosis ; }, abstract = {BACKGROUND & AIMS: Inflammatory bowel diseases (IBD) are chronic inflammatory disorders where predictive biomarkers for the disease development and clinical course are sorely needed for development of prevention and early intervention strategies that can be implemented to improve clinical outcomes. Since gut microbiome alterations can reflect and/or contribute to impending host health changes, we examined whether gut microbiota metagenomic profiles would provide more robust measures for predicting disease outcomes in colitis-prone hosts.

METHODS: Using the interleukin (IL) 10 gene-deficient (IL10 KO) murine model where early life dysbiosis from antibiotic (cefoperozone [CPZ]) treated dams vertically transferred to pups increases risk for colitis later in life, we investigated temporal metagenomic profiles in the gut microbiota of post-weaning offspring and determined their relationship to eventual clinical outcomes.

RESULTS: Compared to controls, offspring acquiring maternal CPZ-induced dysbiosis exhibited a restructuring of intestinal microbial membership in both bacteriome and mycobiome that was associated with alterations in specific functional subsystems. Furthermore, among IL10 KO offspring from CPZ-treated dams, several functional subsystems, particularly nitrogen metabolism, diverged between mice that developed spontaneous colitis (CPZ-colitis) versus those that did not (CPZ-no-colitis) at a time point prior to eventual clinical outcome.

CONCLUSIONS: Our findings provide support that functional metagenomic profiling of gut microbes has potential and promise meriting further study for development of tools to assess risk and manage human IBD.}, } @article {pmid32835795, year = {2021}, author = {Villmones, HC and Halland, A and Stenstad, T and Ulvestad, E and Weedon-Fekjær, H and Kommedal, Ø}, title = {The cultivable microbiota of the human distal ileum.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {27}, number = {6}, pages = {912.e7-912.e13}, doi = {10.1016/j.cmi.2020.08.021}, pmid = {32835795}, issn = {1469-0691}, mesh = {Aged ; Aged, 80 and over ; Bacteria/*classification/*isolation & purification ; Bacteriological Techniques ; Female ; *Gastrointestinal Microbiome ; Humans ; Ileum/*microbiology ; Male ; Middle Aged ; }, abstract = {OBJECTIVES: The existing literature on the microbiota of the ileum is inconsistent. To further characterize the microbiota, we analysed samples obtained directly from resected ileums used for urinary diversion after radical cystectomy.

METHODS: We included 150 patients with bladder cancer operated on from March 2016 to March 2019. Samples obtained by rubbing a swab against the ileal mucosa 25 cm from the ileocecal valve were cultivated at the local laboratory. Microbial colonies were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF).

RESULTS: The microbial density of the distal ileum was low. Among our samples, 79% (95% confidence interval (CI) 71%, 84%) harboured less than 1.6 × 10[4] cfu/mL, whereas 36% (95% CI 28%, 44%) harboured less than 1.6 × 10[3] cfu/mL. The flora was dominated by viridans streptococci, Candida, Actinomyces, Rothia and Lactobacillus species. Colon-related bacteria i.e. strict anaerobic bacteria, Enterobacteriales and enterococci, were recovered from 14% of the samples. Constipation was associated with increased recovery of colon-related bacteria. Antibiotic treatment prior to surgical procedures did not affect culture results. Increased age was significantly associated with more substantial fungal growth and use of proton pump inhibitors seemed to increase both bacterial and fungal growth.

CONCLUSIONS: The microbiota of the human distal ileum is sparse and differs significantly from the colonic microbiota both quantitatively and by composition. These findings contradict recent metagenomics studies based on samples collected by retrograde colonoscopy and emphasize the crucial importance of adequate sampling techniques.}, } @article {pmid32835671, year = {2020}, author = {Badran, M and Khalyfa, A and Ericsson, A and Gozal, D}, title = {Fecal microbiota transplantation from mice exposed to chronic intermittent hypoxia elicits sleep disturbances in naïve mice.}, journal = {Experimental neurology}, volume = {334}, number = {}, pages = {113439}, pmid = {32835671}, issn = {1090-2430}, support = {R56 HL140548/HL/NHLBI NIH HHS/United States ; RF1 AG061824/AG/NIA NIH HHS/United States ; R01 HL130984/HL/NHLBI NIH HHS/United States ; K01 OD019924/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Animals ; Fecal Microbiota Transplantation/*adverse effects ; Gastrointestinal Microbiome/*physiology ; Hypoxia/*complications/*physiopathology ; Male ; Mice ; Mice, Inbred C57BL ; Sleep Wake Disorders/*etiology/*physiopathology ; }, abstract = {Obstructive sleep apnea (OSA) is a chronic prevalent condition characterized by intermittent hypoxia (IH) and sleep fragmentation (SF). Evidence suggests that OSA can alter the gut microbiome (GM) diversity and composition that may then promote the occurrence of some of the OSA-associated morbidities. However, it is unclear whether perturbations in the GM caused by IH can elicit sleep disturbances that underlie the increased sleep propensity that occurs in IH-exposed mice. To evaluate this issue, we exposed C57Bl/6 J mice to IH or room air (RA) for 6 weeks, and fecal matter was collected and frozen. C57Bl/6 J naïve mice were then randomly assigned to a fecal microbiota transfer (FMT) protocol for 3 weeks with either IH or RA fecal slur, and their GM was then analyzed using 16 s rRNA sequencing. In addition, FMT recipients underwent sleep recordings using piezoelectric approaches for 3 consecutive days. As anticipated, FMT-IH and FMT-RA mice showed different taxonomic profiles that corresponded to previous effects of IH on GM. Furthermore, FMT-IH mice exhibited increased sleep duration and the frequency of longer sleep bouts during the dark cycle, suggesting increased sleepiness (p < 0.0001 vs. FMT-RA mice). Thus, alterations of GM diversity induced by IH exposures can elicit sleep disturbances in the absence of concurrent IH, suggesting that sleep disturbances can be mediated, at least in part, by IH-induced alterations in GM.}, } @article {pmid32835181, year = {2020}, author = {Kirubakaran, R and ArulJothi, KN and Revathi, S and Shameem, N and Parray, JA}, title = {Emerging priorities for microbial metagenome research.}, journal = {Bioresource technology reports}, volume = {11}, number = {}, pages = {100485}, pmid = {32835181}, issn = {2589-014X}, abstract = {Overwhelming anthropogenic activities lead to deterioration of natural resources and the environment. The microorganisms are considered desirable, due to their suitability for easy genetic manipulation and handling. With the aid of modern biotechnological techniques, the culturable microorganisms have been widely exploited for the benefit of mankind. Metagenomics, a powerful tool to access the abundant biodiversity of the environmental samples including the unculturable microbes, to determine microbial diversity and population structure, their ecological roles and expose novel genes of interest. This review focuses on the microbial adaptations to the adverse environmental conditions, metagenomic techniques employed towards microbial biotechnology. Metagenomic approach helps to understand microbial ecology and to identify useful microbial derivatives like antibiotics, toxins, and enzymes with diverse and enhanced function. It also summarizes the application of metagenomics in clinical diagnosis, improving microbial ecology, therapeutics, xenobiotic degradation and impact on agricultural crops.}, } @article {pmid32832617, year = {2020}, author = {Villa Martín, P and Buček, A and Bourguignon, T and Pigolotti, S}, title = {Ocean currents promote rare species diversity in protists.}, journal = {Science advances}, volume = {6}, number = {29}, pages = {eaaz9037}, pmid = {32832617}, issn = {2375-2548}, mesh = {*Biodiversity ; Eukaryota/genetics ; Metagenome ; Oceans and Seas ; *Plankton/genetics ; }, abstract = {Oceans host communities of plankton composed of relatively few abundant species and many rare species. The number of rare protist species in these communities, as estimated in metagenomic studies, decays as a steep power law of their abundance. The ecological factors at the origin of this pattern remain elusive. We propose that chaotic advection by oceanic currents affects biodiversity patterns of rare species. To test this hypothesis, we introduce a spatially explicit coalescence model that reconstructs the species diversity of a sample of water. Our model predicts, in the presence of chaotic advection, a steeper power law decay of the species abundance distribution and a steeper increase of the number of observed species with sample size. A comparison of metagenomic studies of planktonic protist communities in oceans and in lakes quantitatively confirms our prediction. Our results support that oceanic currents positively affect the diversity of rare aquatic microbes.}, } @article {pmid32830371, year = {2020}, author = {Mukherjee, I and Salcher, MM and Andrei, AŞ and Kavagutti, VS and Shabarova, T and Grujčić, V and Haber, M and Layoun, P and Hodoki, Y and Nakano, SI and Šimek, K and Ghai, R}, title = {A freshwater radiation of diplonemids.}, journal = {Environmental microbiology}, volume = {22}, number = {11}, pages = {4658-4668}, doi = {10.1111/1462-2920.15209}, pmid = {32830371}, issn = {1462-2920}, support = {MSM200961801//Akademie Věd České Republiky/ ; 17-04828S//Grant Agency of the Czech Republic/ ; 19-23469S//Grant Agency of the Czech Republic/ ; 20-12496X//Grant Agency of the Czech Republic/ ; 022/2019/P//Grant Agency of the University of South Bohemia/ ; 116/2019/P//Grant Agency of the University of South Bohemia/ ; JSPS-17-17//JSPS Bilateral Japanese-Czech Joint Research Project/ ; 310030_185108/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Biodiversity ; Ecosystem ; Euglenozoa/*classification/cytology/genetics/*isolation & purification ; In Situ Hybridization, Fluorescence ; Japan ; Lakes/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Species Specificity ; }, abstract = {Diplonemids are considered marine protists and have been reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Japanese deep freshwater lakes. However, their distribution and abundances in freshwater ecosystems remain unknown. We assessed abundance and diversity of diplonemids from several geographically distant deep freshwater lakes of the world by amplicon-sequencing, shotgun metagenomics and catalysed reporter deposition-fluorescent in situ hybridization (CARD-FISH). We found diplonemids in all the studied lakes, albeit with low abundances and diversity. We assembled long 18S rRNA sequences from freshwater diplonemids and showed that they form a new lineage distinct from the diverse marine clades. Freshwater diplonemids are a sister-group to a marine clade, which are mainly isolates from coastal and bay areas, suggesting a recent habitat transition from marine to freshwater habitats. Images of CARD-FISH targeted freshwater diplonemids suggest they feed on bacteria. Our analyses of 18S rRNA sequences retrieved from single-cell genomes of marine diplonemids show they encode multiple rRNA copies that may be very divergent from each other, suggesting that marine diplonemid abundance and diversity both have been overestimated. These results have wider implications on assessing eukaryotic abundances in natural habitats by using amplicon-sequencing alone.}, } @article {pmid32829437, year = {2020}, author = {Islam, W and Noman, A and Naveed, H and Huang, Z and Chen, HYH}, title = {Role of environmental factors in shaping the soil microbiome.}, journal = {Environmental science and pollution research international}, volume = {27}, number = {33}, pages = {41225-41247}, pmid = {32829437}, issn = {1614-7499}, mesh = {Archaea/genetics ; Bacteria/genetics ; Ecosystem ; Fungi ; *Microbiota ; *Soil ; Soil Microbiology ; }, abstract = {The soil microbiome comprises one of the most important and complex components of all terrestrial ecosystems as it harbors millions of microbes including bacteria, fungi, archaea, viruses, and protozoa. Together, these microbes and environmental factors contribute to shaping the soil microbiome, both spatially and temporally. Recent advances in genomic and metagenomic analyses have enabled a more comprehensive elucidation of the soil microbiome. However, most studies have described major modulators such as fungi and bacteria while overlooking other soil microbes. This review encompasses all known microbes that may exist in a particular soil microbiome by describing their occurrence, abundance, diversity, distribution, communication, and functions. Finally, we examined the role of several abiotic factors involved in the shaping of the soil microbiome.}, } @article {pmid32828958, year = {2020}, author = {Charretier, Y and Lazarevic, V and Schrenzel, J and Ruppé, E}, title = {Messages from the Fourth International Conference on Clinical Metagenomics.}, journal = {Microbes and infection}, volume = {22}, number = {10}, pages = {635-641}, doi = {10.1016/j.micinf.2020.07.007}, pmid = {32828958}, issn = {1769-714X}, mesh = {*Clinical Laboratory Techniques/standards/trends ; Fossils/microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Joint Prosthesis/microbiology ; *Metagenomics/standards/trends ; Microbiota/genetics ; Mouth/microbiology ; Prosthesis-Related Infections/diagnosis/microbiology ; Respiratory Tract Infections/diagnosis/microbiology ; }, } @article {pmid32828012, year = {2020}, author = {Campanaro, S and Raga, R and Squartini, A}, title = {Intermittent aeration of landfill simulation bioreactors: Effects on emissions and microbial community.}, journal = {Waste management (New York, N.Y.)}, volume = {117}, number = {}, pages = {146-156}, doi = {10.1016/j.wasman.2020.08.010}, pmid = {32828012}, issn = {1879-2456}, mesh = {Bioreactors ; Carbon ; *Microbiota ; *Refuse Disposal ; Waste Disposal Facilities ; Water Pollutants, Chemical/*analysis ; }, abstract = {Landfill simulation experiments were run at lab-scale to compare the effects of intermittent and continuous aeration on the evolution of leachate composition and biogas production. The experiments were carried out using six reactors; two of them under continuous aeration, two under intermitted aeration and two anaerobic as a control. Different aeration regimes produced different effects on reactors. As expected, carbon discharge via biogas was higher in reactors under continuous aeration than under intermittent aeration. The evolution of leachate quality was affected by the aeration regimes; however, at test end very similar concentration were ascertained for relevant leachate parameters in all aerated reactors. A comprehensive description of the aerobic and anaerobic landfill microbiome is provided, using a metagenomic approach focused on the microbial genome reconstruction. A time course investigation evidenced the modification of the microbiome and revealed taxa and specific microbes more strictly connected to the environmental parameters of the reactors. Methanoculleus, Syntrophomonas and Parabacteroides were identified as the genera more strictly connected to biogas production, while numerous species belonging to Thiomonas, Nitrosomonas, Xanthomonadaceae, Myxococcales and Alcaligenaceae were found to be connected with NH4[+] oxidation.}, } @article {pmid32827548, year = {2020}, author = {Reyes, REN and Al Omran, AJ and Davies, DL and Asatryan, L}, title = {Antibiotic-induced disruption of commensal microbiome linked to increases in binge-like ethanol consumption behavior.}, journal = {Brain research}, volume = {1747}, number = {}, pages = {147067}, pmid = {32827548}, issn = {1872-6240}, support = {R01 AA022448/AA/NIAAA NIH HHS/United States ; }, mesh = {*Alcohol Drinking ; Animals ; Anti-Bacterial Agents/*pharmacology ; Ethanol/blood ; Male ; Metagenome/*drug effects ; Mice ; Microbiota/*drug effects ; }, abstract = {Research focusing on the gut-brain axis is growing, but the interplay of ethanol (alcohol molecule), the gut microbiome, the brain and behavior is poorly understood. In the current study, we remodeled the gut microbiota by providing adult male C57BL/6J mice with a non-absorbable antibiotic cocktail (ABX) in the drinking water and tested ethanol consumption behavior in a binge-like "Drinking in the Dark" model. Notably, 2 weeks of ABX pre-treatment significantly increased ethanol consumption during the 6 weeks of ethanol exposure in the DID paradigm. ABX treatment also appeared to prevent anxiety-like behavior during ethanol withdrawal period. ABX-treated mice expressed reduced bacterial diversity and modified microbiota compositions within cecal samples. There were drastically reduced levels of commensal Firmicutes and increases in the Bacteroidetes and Verrucomicrobia populations. Importantly, the relative abundance of Firmicutes inversely correlated to ethanol intake levels regardless of antibiotic treatment, whereas Bacteroidetes and Verrucomicrobia populations negatively correlated to ethanol intake levels. This is the first report demonstrating that ABX-induced disruption of the gut commensal microbiota leads to increased ethanol consumption in mice. This work reveals an important relationship between the gut microbiota and ethanol consumption behavior and supports the use of microbial-targeted approaches to study gut-brain interactions during alcohol use disorder.}, } @article {pmid32827171, year = {2020}, author = {Astudillo-García, C and Bell, JJ and Montoya, JM and Moitinho-Silva, L and Thomas, T and Webster, NS and Taylor, MW}, title = {Assessing the strength and sensitivity of the core microbiota approach on a highly diverse sponge reef.}, journal = {Environmental microbiology}, volume = {22}, number = {9}, pages = {3985-3999}, doi = {10.1111/1462-2920.15185}, pmid = {32827171}, issn = {1462-2920}, support = {//Encouraging as Supporting Innovation Doctoral Scholarship in Marine Science by the University of Auckland/International ; }, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Metagenome ; Microbiota/*genetics ; Phylogeny ; Porifera/classification/*microbiology ; }, abstract = {Marine sponge reefs usually comprise a complex array of taxonomically different sponge species, many of these hosting highly diverse microbial communities. The number of microbial species known to occupy a given sponge ranges from tens to thousands, bringing numerous challenges to their analysis. One way to deal with such complexity is to use a core microbiota approach, in which only prevalent and abundant microbes are considered. Here we aimed to test the strength and sensitivity of the core microbiota approach by applying different core definitions to 20 host sponge species. Application of increasingly stringent relative abundance and/or percentage occurrence thresholds to qualify as part of the core microbiota decreased the number of 'core' OTUs and phyla and, consequently, changed both alpha- and beta-diversity patterns. Moreover, microbial co-occurrence patterns explored using correlation networks were also affected by the core microbiota definition. The application of stricter thresholds resulted in smaller and less compartmentalized networks, with different keystone species. These results highlight that the application of different core definitions to phylogenetically disparate host species can result in the drawing of markedly different conclusions. Consequently, we recommend to assess the effects of different core community definitions on the specific system of study before considering its application.}, } @article {pmid32826214, year = {2020}, author = {Jiang, R and Wang, JG and Zhu, T and Zou, B and Wang, DQ and Rhee, SK and An, D and Ji, ZY and Quan, ZX}, title = {Use of Newly Designed Primers for Quantification of Complete Ammonia-Oxidizing (Comammox) Bacterial Clades and Strict Nitrite Oxidizers in the Genus Nitrospira.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {20}, pages = {}, pmid = {32826214}, issn = {1098-5336}, mesh = {Ammonia/*metabolism ; Bacteria/*classification/genetics/metabolism ; DNA Primers/*analysis ; Nitrites/*metabolism ; Oxidation-Reduction ; }, abstract = {Complete ammonia-oxidizing (comammox) bacteria play key roles in environmental nitrogen cycling and all belong to the genus Nitrospira, which was originally believed to include only strict nitrite-oxidizing bacteria (sNOB). Thus, differential estimation of sNOB abundance from that of comammox Nitrospira has become problematic, since both contain nitrite oxidoreductase genes that serve as common targets for sNOB detection. Herein, we developed novel comammox Nitrospira clade A- and B-specific primer sets targeting the α-subunit of the ammonia monooxygenase gene (amoA) and a sNOB-specific primer set targeting the cyanase gene (cynS) for quantitative PCR (qPCR). The high coverage and specificity of these primers were checked by use of metagenome and metatranscriptome data sets. Efficient and specific amplification with these primers was demonstrated using various environmental samples. Using the newly designed primers, we successfully estimated the abundances of comammox Nitrospira and sNOB in samples from two chloramination-treated drinking water systems and found that, in most samples, comammox Nitrospira clade A was the dominant type of Nitrospira and also served as the primary ammonia oxidizer. Compared with other ammonia oxidizers, comammox Nitrospira had a higher abundance in process water samples in these two drinking water systems. We also demonstrated that sNOB can be readily misrepresented by an earlier method, calculated by subtracting the comammox Nitrospira abundance from the total Nitrospira abundance, especially when the comammox Nitrospira proportion is relatively high. The new primer sets were successfully applied to comammox Nitrospira and sNOB quantification, which may prove useful in understanding the roles of Nitrospira in nitrification in various ecosystems.IMPORTANCENitrospira is a dominant nitrite-oxidizing bacterium in many artificial and natural environments. The discovery of complete ammonia oxidizers in the genus Nitrospira prevents the use of previously identified primers targeting the Nitrospira 16S rRNA gene or nitrite oxidoreductase (nxr) gene for differential determination of strict nitrite-oxidizing bacteria (sNOB) in the genus Nitrospira and among comammox bacteria in this genus. We designed three novel primer sets that enabled quantification of comammox Nitrospira clades A and B and sNOB with high coverage, specificity, and accuracy in various environments. With the designed primer sets, sNOB and comammox Nitrospira were differentially estimated in drinking water systems, and we found that comammox clade A predominated over sNOB and other ammonia oxidizers in process water samples. Accurate quantification of comammox Nitrospira and sNOB by use of the newly designed primers will provide essential information for evaluating the contribution of Nitrospira to nitrification in various ecosystems.}, } @article {pmid32825454, year = {2020}, author = {Zhang, Z and Li, M and Zhang, X and Zheng, N and Zhao, S and Wang, J}, title = {A Novel Urease Inhibitor of Ruminal Microbiota Screened through Molecular Docking.}, journal = {International journal of molecular sciences}, volume = {21}, number = {17}, pages = {}, pmid = {32825454}, issn = {1422-0067}, mesh = {Animals ; Bacterial Proteins/chemistry/genetics ; Caco-2 Cells ; Cattle ; Databases, Chemical ; Drug Evaluation, Preclinical/*methods ; Enzyme Inhibitors/chemistry/*pharmacology/toxicity ; Female ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Metagenome/genetics ; Molecular Docking Simulation ; Protein Conformation ; Rumen/*microbiology ; Urease/*antagonists & inhibitors/chemistry/metabolism ; }, abstract = {Inhibition of the urease activity of ruminal microbiota is not only beneficial for increasing dietary and endogenic urea-N utilization efficiency in ruminants but also might be applicable for the preservation of nitrogen fertilizer in soil and treatment of gastrointestinal and urinary tract infections caused by ureolytic bacteria. To discover urease inhibitors to efficiently target ruminal microbiota, the identified ruminal microbial metagenomic urease gene was used to construct a homology model to virtually screen urease inhibitors from the ChemDiv database by molecular docking. The GMQE and QMEAN values of the homology model were 0.85 and -0.37, respectively, indicating a good model quality. The inhibition effect of the screened urease inhibitor for ruminal urea degradation was assessed by ruminal microbial fermentation in vitro. The toxic effect of the candidate inhibitor was performed using gut Caco-2 cells in vitro. The results showed that compound 3-[1-[(aminocarbonyl)amino]-5-(4-methoxyphenyl)-1H-pyrrol-2-yl] propanoic acid (ChemDiv_ID: 6238-0047, IC50 = 65.86 μM) was found to be the most effective urease inhibitor among the candidate compounds. Compound 6238-0047 significantly lowered the amount of urea degradation and ammonia production in ruminal microbial fermentation. The 24 h degradation rate of compound 6238-0047 in ruminal microbial fermentation was 3.32%-16.00%. In addition, compound 6238-0047 (10-100 μM) had no significant adverse effect on the cell viability of Caco-2 cells. Molecular docking showed that compound 6238-0047 could interact with Asp359 in the active site and Cys318 in the flap region by the hydrogen bond and Pi-Alkyl interaction, respectively. Compound 6238-0047 could be used as a novel inhibitor for decreasing the urease activity of ruminal microbiota.}, } @article {pmid32825344, year = {2020}, author = {Said Hassane, C and Fouillaud, M and Le Goff, G and Sklirou, AD and Boyer, JB and Trougakos, IP and Jerabek, M and Bignon, J and de Voogd, NJ and Ouazzani, J and Gauvin-Bialecki, A and Dufossé, L}, title = {Microorganisms Associated with the Marine Sponge Scopalina hapalia: A Reservoir of Bioactive Molecules to Slow Down the Aging Process.}, journal = {Microorganisms}, volume = {8}, number = {9}, pages = {}, pmid = {32825344}, issn = {2076-2607}, support = {634674//H2020 European Research Council/ ; R97400235//Regional Council of Reunion Island/ ; }, abstract = {Aging research aims at developing therapies that delay normal aging processes and some related pathologies. Recently, many compounds and extracts from natural products have been shown to slow aging and/or extend lifespan. Marine sponges and their associated microorganisms have been found to produce a wide variety of bioactive secondary metabolites; however, those from the Southwest of the Indian Ocean are much less studied, especially regarding anti-aging activities. In this study, the microbial diversity of the marine sponge Scopalina hapalia was investigated by metagenomic analysis. Twenty-six bacterial and two archaeal phyla were recovered from the sponge, of which the Proteobacteria phylum was the most abundant. In addition, 30 isolates from S. hapalia were selected and cultivated for identification and secondary metabolites production. The selected isolates were affiliated to the genera Bacillus, Micromonospora, Rhodoccocus, Salinispora, Aspergillus, Chaetomium, Nigrospora and unidentified genera related to the family Thermoactinomycetaceae. Crude extracts from selected microbial cultures were found to be active against seven clinically relevant targets (elastase, tyrosinase, catalase, sirtuin 1, Cyclin-dependent kinase 7 (CDK7), Fyn kinase and proteasome). These results highlight the potential of microorganisms associated with a marine sponge from Mayotte to produce anti-aging compounds. Future work will focus on the isolation and the characterization of bioactive compounds.}, } @article {pmid32824037, year = {2020}, author = {Šimić, I and Zorec, TM and Lojkić, I and Krešić, N and Poljak, M and Cliquet, F and Picard-Meyer, E and Wasniewski, M and Zrnčić, V and Ćukušić, A and Bedeković, T}, title = {Viral Metagenomic Profiling of Croatian Bat Population Reveals Sample and Habitat Dependent Diversity.}, journal = {Viruses}, volume = {12}, number = {8}, pages = {}, pmid = {32824037}, issn = {1999-4915}, mesh = {Animals ; Chiroptera/*virology ; Croatia ; Disease Reservoirs/*veterinary/virology ; *Ecosystem ; Feces/virology ; High-Throughput Nucleotide Sequencing ; Insect Viruses/classification ; *Metagenome ; Metagenomics ; Phylogeny ; Saliva/virology ; Sequence Analysis, DNA ; Virome/*genetics ; Virus Diseases/*veterinary ; Viruses/classification/isolation & purification ; Zoonoses/virology ; }, abstract = {To date, the microbiome, as well as the virome of the Croatian populations of bats, was unknown. Here, we present the results of the first viral metagenomic analysis of guano, feces and saliva (oral swabs) of seven bat species (Myotis myotis, Miniopterus schreibersii, Rhinolophus ferrumequinum, Eptesicus serotinus, Myotis blythii, Myotis nattereri and Myotis emarginatus) conducted in Mediterranean and continental Croatia. Viral nucleic acids were extracted from sample pools, and analyzed using Illumina sequencing. The presence of 63 different viral families representing all seven Baltimore groups were confirmed, most commonly insect viruses likely reflecting the diet of insectivorous bats. Virome compositions of our samples were largely impacted by the sample type: invertebrate-infecting viruses were most frequently found in feces, bacterial viruses in guano, whereas vertebrate-infecting viruses were most common in swabs. Most vertebrate-infecting virus sequences were assigned to retroviruses, parvoviruses, iridoviruses, and poxviruses. We further report the complete genome sequence of a novel adeno-associated virus, densovirus and a near complete length genome sequence of a novel iflavirus. Additionally, one of the most interesting findings in this study was the difference in viromes between two contrasting habitats, the continental and Mediterranean Croatia.}, } @article {pmid32823659, year = {2020}, author = {Svegliati-Baroni, G and Patrício, B and Lioci, G and Macedo, MP and Gastaldelli, A}, title = {Gut-Pancreas-Liver Axis as a Target for Treatment of NAFLD/NASH.}, journal = {International journal of molecular sciences}, volume = {21}, number = {16}, pages = {}, pmid = {32823659}, issn = {1422-0067}, support = {722619//H2020 Marie Skłodowska-Curie Actions/ ; 734719//H2020 Marie Skłodowska-Curie Actions/ ; B54I19000370005//Consiglio Nazionale delle Ricerche/ ; PTDC/BIM-MET/2115/2014//Fundação para a Ciência e a Tecnologia/ ; PTDC/MEC-MET/29314/2017//Fundação para a Ciência e a Tecnologia/ ; UID/Multi/04462/2013//iNOVA4Health/ ; }, mesh = {Animals ; Gastrointestinal Microbiome ; Gastrointestinal Tract/*pathology ; Humans ; Incretins/metabolism ; Liver/*pathology ; Non-alcoholic Fatty Liver Disease/microbiology/*pathology/*therapy ; Pancreas/*pathology ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD) represents the most common form of chronic liver disease worldwide. Due to its association with obesity and diabetes and the fall in hepatitis C virus morbidity, cirrhosis in NAFLD is becoming the most frequent indication to liver transplantation, but the pathogenetic mechanisms are still not completely understood. The so-called gut-liver axis has gained enormous interest when data showed that its alteration can lead to NAFLD development and might favor the occurrence of non-alcoholic steatohepatitis (NASH). Moreover, several therapeutic approaches targeting the gut-pancreas-liver axis, e.g., incretins, showed promising results in NASH treatment. In this review, we describe the role of incretin hormones in NAFLD/NASH pathogenesis and treatment and how metagenomic/metabolomic alterations in the gut microbiota can lead to NASH in the presence of gut barrier modifications favoring the passage of bacteria or bacterial products in the portal circulation, i.e., bacterial translocation.}, } @article {pmid32822862, year = {2021}, author = {Sharma, AK}, title = {Special Issue: Mining human microbiome bringing newer paradigms to anticancer therapeutics.}, journal = {Seminars in cancer biology}, volume = {70}, number = {}, pages = {1-2}, doi = {10.1016/j.semcancer.2020.08.008}, pmid = {32822862}, issn = {1096-3650}, mesh = {Antineoplastic Agents/*therapeutic use ; *Gastrointestinal Microbiome ; *Genome, Microbial ; Humans ; *Metagenome ; *Microbiota ; Neoplasms/genetics/microbiology/*therapy ; }, } @article {pmid32822584, year = {2020}, author = {Bushman, FD and Conrad, M and Ren, Y and Zhao, C and Gu, C and Petucci, C and Kim, MS and Abbas, A and Downes, KJ and Devas, N and Mattei, LM and Breton, J and Kelsen, J and Marakos, S and Galgano, A and Kachelries, K and Erlichman, J and Hart, JL and Moraskie, M and Kim, D and Zhang, H and Hofstaedter, CE and Wu, GD and Lewis, JD and Zackular, JP and Li, H and Bittinger, K and Baldassano, R}, title = {Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease.}, journal = {Cell host & microbe}, volume = {28}, number = {3}, pages = {422-433.e7}, pmid = {32822584}, issn = {1934-6069}, support = {K22 AI137220/AI/NIAID NIH HHS/United States ; R01 HL113252/HL/NHLBI NIH HHS/United States ; L40 AI147162/AI/NIAID NIH HHS/United States ; R61 HL137063/HL/NHLBI NIH HHS/United States ; K23 DK119585/DK/NIDDK NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; }, mesh = {Adolescent ; Biomarkers ; Caproates/*metabolism ; Child ; Clostridioides difficile/genetics/*metabolism ; Clostridium Infections/*complications ; DNA, Bacterial ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*complications/microbiology ; Male ; *Metabolome ; *Metagenomics ; Taurine/*metabolism ; }, abstract = {Children with inflammatory bowel diseases (IBD) are particularly vulnerable to infection with Clostridioides difficile (CDI). IBD and IBD + CDI have overlapping symptoms but respond to distinctive treatments, highlighting the need for diagnostic biomarkers. Here, we studied pediatric patients with IBD and IBD + CDI, comparing longitudinal data on the gut microbiome, metabolome, and other measures. The microbiome is dysbiotic and heterogeneous in both disease states, but the metabolome reveals disease-specific patterns. The IBD group shows increased concentrations of markers of inflammation and tissue damage compared with healthy controls, and metabolic changes associate with susceptibility to CDI. In IBD + CDI, we detect both metabolites associated with inflammation/tissue damage and fermentation products produced by C. difficile. The most discriminating metabolite found is isocaproyltaurine, a covalent conjugate of a distinctive C. difficile fermentation product (isocaproate) and an amino acid associated with tissue damage (taurine), which may be useful as a joint marker of the two disease processes.}, } @article {pmid32820981, year = {2021}, author = {Lucyshyn, DR and Maggs, DJ and Cooper, AE and Rousseau, JD and Weese, JS}, title = {Feline conjunctival microbiota in a shelter: effects of time, upper respiratory disease and famciclovir administration.}, journal = {Journal of feline medicine and surgery}, volume = {23}, number = {4}, pages = {316-330}, pmid = {32820981}, issn = {1532-2750}, mesh = {Animals ; Bacteria/genetics ; *Cat Diseases/drug therapy ; Cats ; Conjunctiva ; Famciclovir ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVES: The aim of this study was to evaluate changes in the conjunctival microbiota of shelter-housed cats with time, upper respiratory disease (URD) and famciclovir administration.

METHODS: Cats were assigned to treatment groups on shelter entry. Healthy cats or cats with URD received ~30 mg/kg or ~90 mg/kg of famciclovir or placebo PO q12h for 7 days, or were untreated. Swabs were collected from ventral conjunctival fornices prior to (day 1) and immediately after (day 8) the treatment period. Microbiota analysis was conducted on 124 randomly selected swabs from healthy (56 swabs) or URD-affected (68 swabs) cats. Following DNA extraction and amplification of the V4 region of the 16S rRNA gene, sequences were assembled into operational taxonomic units (OTUs). Over-represented OTUs (as determined by linear discriminate analysis effect size), alpha and beta diversity, and median relative abundance of known feline ocular surface pathogens were assessed for the entire population and in 10 clinically relevant subpopulations of cats.

RESULTS: Bacteria from 33 phyla and 70 genera were identified. Considering all cats, median relative abundance of Mycoplasma increased from day 1 to day 8, while Proteobacteria decreased. Community membership and structure (beta diversity) differed between days 1 and 8 for all famciclovir-treated cats (regardless of health status or dose) and healthy or URD-affected cats (regardless of famciclovir dose). Differences in taxonomic diversity within a sample (alpha diversity) between day 1 and day 8 were not detected in any subpopulations.

CONCLUSIONS AND RELEVANCE: Within 1 week of shelter entry, there were significant changes in community structure and membership of the feline conjunctival microbiota, with a shift towards over-representation of feline ocular surface pathogens. Although famciclovir may impact beta diversity of the feline conjunctival microbiota, absence of change in alpha diversity suggests minimal shift in individual cats.}, } @article {pmid32817657, year = {2020}, author = {Milovic, A and Bassam, K and Shao, H and Chatzistamou, I and Tufts, DM and Diuk-Wasser, M and Barbour, AG}, title = {Lactobacilli and other gastrointestinal microbiota of Peromyscus leucopus, reservoir host for agents of Lyme disease and other zoonoses in North America.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0231801}, pmid = {32817657}, issn = {1932-6203}, support = {R01 AI157513/AI/NIAID NIH HHS/United States ; R21 AI136523/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Gastrointestinal Microbiome/*genetics ; Humans ; Lactobacillus/genetics/metabolism ; Lyme Disease/epidemiology/etiology ; North America ; Peromyscus/genetics/*microbiology ; Zoonoses/genetics/*microbiology ; }, abstract = {The cricetine rodent Peromyscus leucopus is an important reservoir for several human zoonoses, including Lyme disease, in North America. Akin to hamsters, the white-footed deermouse has been unevenly characterized in comparison to the murid Mus musculus. To further understanding of P. leucopus' total genomic content, we investigated gut microbiomes of an outbred colony of P. leucopus, inbred M. musculus, and a natural population of P. leucopus. Metagenome and whole genome sequencing were combined with microbiology and microscopy approaches. A focus was the genus Lactobacillus, four diverse species of which were isolated from forestomach and feces of colony P. leucopus. Three of the species-L. animalis, L. reuteri, and provisionally-named species "L. peromysci"-were identified in fecal metagenomes of wild P. leucopus but not discernibly in samples from M. musculus. L. johnsonii, the fourth species, was common in M. musculus but absent or sparse in wild P. leucopus. Also identified in both colony and natural populations were a Helicobacter sp. in feces but not stomach, and a Tritrichomonas sp. protozoan in cecum or feces. The gut metagenomes of colony P. leucopus were similar to those of colony M. musculus at the family or higher level and for major subsystems. But there were multiple differences between species and sexes within each species in their gut metagenomes at orthologous gene level. These findings provide a foundation for hypothesis-testing of functions of individual microbial species and for interventions, such as bait vaccines based on an autochthonous bacterium and targeting P. leucopus for transmission-blocking.}, } @article {pmid32816085, year = {2020}, author = {Guerrero, EB and de Villegas, RMD and Soria, MA and Santangelo, MP and Campos, E and Talia, PM}, title = {Characterization of two GH5 endoglucanases from termite microbiome using synthetic metagenomics.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {19}, pages = {8351-8366}, pmid = {32816085}, issn = {1432-0614}, support = {PICT-2013 No.1454//Fondo para la Investigación Científica y Tecnológica/ ; PICT-2018 No. 4149.//Agencia Nacional de Promoción Científica y Tecnológica/ ; PNAIyAV-1130034//Instituto Nacional de Tecnología Agropecuaria/ ; }, mesh = {Animals ; *Cellulase/genetics/metabolism ; Hydrolysis ; *Isoptera ; Metagenomics ; *Microbiota ; Substrate Specificity ; }, abstract = {Here, we characterize two novel GH5 endoglucanases (GH5CelA and GH5CelB) from an uncultured bacterium identified in termite gut microbiomes. Both genes were codon-optimized, synthetized, cloned, and expressed as recombinant proteins in Escherichia coli for subsequent purification. Both enzymes showed activity on the pNPC and barley β-glucan substrates, whereas GH5CelB also showed low activity on carboxymethyl cellulose. The optimum conditions for both enzymes were an acid pH (5) and moderate temperature (35 to 50 °C). The enzymes differed in the kinetic profiles and patterns of the generated hydrolysis products. A structural-based modeling analysis indicated that both enzymes possess a typical (β/α)8-barrel fold characteristic of GH5 family, with some differential features in the active site cleft. Also, GH5CelB presents a putative secondary binding site. Furthermore, adjacent to the active site of GH5CelA and GH5CelB, a whole subdomain rarely found in GH5 family may participate in substrate binding and thermal stability.Therefore, GH5CelA may be a good candidate for the production of cello-oligosaccharides of different degrees of polymerization applicable for feed and food industries, including prebiotics. On the other hand, GH5CelB could be useful in an enzymatic cocktail for the production of lignocellulosic bioethanol, because of the production of glucose as a hydrolysis product. Key Points • Synthetic metagenomics is a powerful approach for discovering novel enzymes. • Two novel GH5 endoglucanases from nonculturable microorganisms were characterized. • Structural differences between them and other GH5 endoglucanases were observed. • The enzymes may be good candidates for feed, food, and/or bioethanol industries.}, } @article {pmid32815317, year = {2020}, author = {Nascimento Lemos, L and Manoharan, L and William Mendes, L and Monteiro Venturini, A and Satler Pylro, V and Tsai, SM}, title = {Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils.}, journal = {Environmental microbiology reports}, volume = {12}, number = {6}, pages = {651-655}, doi = {10.1111/1758-2229.12880}, pmid = {32815317}, issn = {1758-2229}, support = {//Brazilian Microbiome Project/International ; 140032/2015-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/International ; 161931/2015-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/International ; Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/International ; 2014/50320-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/International ; 2015/13546-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/International ; 2016/18215-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/International ; 2017/09643-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/International ; 2017/24037-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/International ; //Coordination for the Improvement of Higher Education Personnel/International ; //National Council for Scientific and Technological Development/International ; //São Paulo Research Foundation/International ; }, mesh = {Bacteria/classification/*genetics/isolation & purification ; Databases, Genetic ; Genome Size ; *Genome, Bacterial ; Metagenome ; Microbiota ; Phylogeny ; *Soil Microbiology ; }, abstract = {Soil microbiome is one of the most heterogeneous biological systems. State-of-the-art molecular approaches such as those based on single-amplified genomes (SAGs) and metagenome assembled-genomes (MAGs) are now improving our capacity for disentailing soil microbial-mediated processes. Here, we analysed publicly available datasets of soil microbial genomes and MAG's reconstructed from the Amazon's tropical soil (primary forest and pasture) and active layer of permafrost, aiming to evaluate their genome size. Our results suggest that the Candidate Phyla Radiation (CPR)/Patescibacteria phyla have genomes with an average size fourfold smaller than the mean identified in the RefSoil database, which lacks any representative of this phylum. Also, by analysing the potential metabolism of 888 soil microbial genomes, we show that CPR/Patescibacteria representatives share similar functional profiles, but different from other microbial phyla and are frequently neglected in the soil microbial surveys. Finally, we argue that the use of MAGs may be a better choice over SAGs to expand the soil microbial databases, like RefSoil.}, } @article {pmid32814564, year = {2020}, author = {Vidanaarachchi, R and Shaw, M and Tang, SL and Halgamuge, S}, title = {IMPARO: inferring microbial interactions through parameter optimisation.}, journal = {BMC molecular and cell biology}, volume = {21}, number = {Suppl 1}, pages = {34}, pmid = {32814564}, issn = {2661-8850}, mesh = {Algorithms ; Bacteria/*metabolism ; Data Accuracy ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Male ; Microbial Interactions/*physiology ; *Models, Biological ; }, abstract = {BACKGROUND: Microbial Interaction Networks (MINs) provide important information for understanding bacterial communities. MINs can be inferred by examining microbial abundance profiles. Abundance profiles are often interpreted with the Lotka Volterra model in research. However existing research fails to consider a biologically meaningful underlying mathematical model for MINs or to address the possibility of multiple solutions.

RESULTS: In this paper we present IMPARO, a method for inferring microbial interactions through parameter optimisation. We use biologically meaningful models for both the abundance profile, as well as the MIN. We show how multiple MINs could be inferred with similar reconstructed abundance profile accuracy, and argue that a unique solution is not always satisfactory. Using our method, we successfully inferred clear interactions in the gut microbiome which have been previously observed in in-vitro experiments.

CONCLUSIONS: IMPARO was used to successfully infer microbial interactions in human microbiome samples as well as in a varied set of simulated data. The work also highlights the importance of considering multiple solutions for MINs.}, } @article {pmid32813756, year = {2020}, author = {Feng, G and Mikkelsen, D and Hoedt, EC and Williams, BA and Flanagan, BM and Morrison, M and Gidley, MJ}, title = {In vitro fermentation outcomes of arabinoxylan and galactoxyloglucan depend on fecal inoculum more than substrate chemistry.}, journal = {Food & function}, volume = {11}, number = {9}, pages = {7892-7904}, doi = {10.1039/d0fo01103g}, pmid = {32813756}, issn = {2042-650X}, mesh = {Adult ; Animals ; Bacteroides ; Bacteroidetes ; Diet ; Fatty Acids, Volatile ; Feces/*microbiology ; *Fermentation ; Galactose/*metabolism ; Glucans/*metabolism ; Humans ; Microbiota ; Middle Aged ; Prevotella ; Swine ; Xylans/*metabolism ; Young Adult ; }, abstract = {Using in vitro fermentation conditions, this study investigated the fermentation characteristics of arabinoxylan (AX) and xyloglucan (XG) with a fecal inoculum that was collected either from humans consuming unrestricted diets or pigs fed a semi-defined diet with cellulose being the sole non-starch polysaccharide for 10 days prior to fecal collection. Metagenomic analysis revealed that microbial communities in the two types of inoculum were distinctively different, which led to distinct fermentation characteristics with the polysaccharides. The microbial communities fermented with the porcine fecal inoculum were clustered according to the fermentation time, while those fermented with the human fecal inoculum were differentiated by the substrates. Using the porcine fecal inoculum, irrespective of the substrates, Prevotella copri and the unclassified lineage rc4-4 were the dominant operational taxonomic units (OTUs) promoted during fermentation. Fermentation of wheat AX (WAX) and galacto-XG (GXG) with the human fecal inoculum, however, promoted different OTUs, except for a shared OTU belonging to Lachnospiraceae. Specifically, WAX promoted the growth of Bacteroides plebeius and a Blautia sp., while GXG promoted an unclassified Bacteroidales, Parabacteroides distasonis, Bacteroides uniformis and Bacteroides sp. 2. These changes in bacterial communities were in accordance with the short chain fatty acid (SCFA) production, where comparable SCFA profiles were obtained from the porcine fecal fermentation while different amounts and proportions of SCFA were acquired from fermentation of WAX and GXG with the human fecal inoculum. Altogether, this study indicated that the starting inoculum composition had a greater effect than polysaccharide chemistry in driving fermentation outcomes.}, } @article {pmid32813091, year = {2020}, author = {Godlewska, U and Brzoza, P and Kwiecień, K and Kwitniewski, M and Cichy, J}, title = {Metagenomic Studies in Inflammatory Skin Diseases.}, journal = {Current microbiology}, volume = {77}, number = {11}, pages = {3201-3212}, pmid = {32813091}, issn = {1432-0991}, support = {UMO-2014/12/W/NZ6/00454//Polish National Science Center/ ; }, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Skin Diseases ; }, abstract = {Next-generation sequencing (NGS) technologies together with an improved access to compute performance led to a cost-effective genome sequencing over the past several years. This allowed researchers to fully unleash the potential of genomic and metagenomic analyses to better elucidate two-way interactions between host cells and microbiome, both in steady-state and in pathological conditions. Experimental research involving metagenomics shows that skin resident microbes can influence the cutaneous pathophysiology. Here, we review metagenome approaches to study microbiota at this barrier site. We also describe the consequences of changes in the skin microbiota burden and composition, mostly revealed by these technologies, in the development of common inflammatory skin diseases.}, } @article {pmid32812361, year = {2021}, author = {Hu, T and Dai, Q and Chen, H and Zhang, Z and Dai, Q and Gu, X and Yang, X and Yang, Z and Zhu, L}, title = {Geographic pattern of antibiotic resistance genes in the metagenomes of the giant panda.}, journal = {Microbial biotechnology}, volume = {14}, number = {1}, pages = {186-197}, pmid = {32812361}, issn = {1751-7915}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; *Gastrointestinal Microbiome ; Metagenome ; *Ursidae/genetics ; }, abstract = {The rise in infections by antibiotic-resistant bacteria poses a serious public health problem worldwide. The gut microbiome of animals is a reservoir for antibiotic resistance genes (ARGs). However, the correlation between the gut microbiome of wild animals and ARGs remains controversial. Here, based on the metagenomes of giant pandas (including three wild populations from the Qinling, Qionglai and Xiaoxiangling Mountains, and two major captive populations from Yaan and Chengdu), we investigated the potential correlation between the constitution of the gut microbiome and the composition of ARGs across the different geographic locations and living environments. We found that the types of ARGs were correlated with gut microbiome composition. The NMDS cluster analysis using Jaccard distance of the ARGs composition of the gut microbiome of wild giant pandas displayed a difference based on geographic location. Captivity also had an effect on the differences in ARGs composition. Furthermore, we found that the Qinling population exhibited profound dissimilarities of both gut microbiome composition and ARGs (the highest proportion of Clostridium and vancomycin resistance genes) when compared to the other wild and captive populations studies, which was supported by previous giant panda whole-genome sequencing analysis. In this study, we provide an example of a potential consensus pattern regarding host population genetics, symbiotic gut microbiome and ARGs. We revealed that habitat isolation impacts the ARG structure in the gut microbiome of mammals. Therefore, the difference in ARG composition between giant panda populations will provide some basic information for their conservation and management, especially for captive populations.}, } @article {pmid32811860, year = {2020}, author = {Zilius, M and Bonaglia, S and Broman, E and Chiozzini, VG and Samuiloviene, A and Nascimento, FJA and Cardini, U and Bartoli, M}, title = {N2 fixation dominates nitrogen cycling in a mangrove fiddler crab holobiont.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {13966}, pmid = {32811860}, issn = {2045-2322}, mesh = {Animals ; Biofilms/growth & development ; Brachyura/*metabolism/*microbiology ; Decapoda/metabolism/microbiology ; Ecosystem ; Microbiota/genetics ; Nitrogen/metabolism ; Nitrogen Cycle/genetics/physiology ; Nitrogen Fixation/*physiology ; RNA, Ribosomal, 16S/genetics ; Wetlands ; }, abstract = {Mangrove forests are among the most productive and diverse ecosystems on the planet, despite limited nitrogen (N) availability. Under such conditions, animal-microbe associations (holobionts) are often key to ecosystem functioning. Here, we investigated the role of fiddler crabs and their carapace-associated microbial biofilm as hotspots of microbial N transformations and sources of N within the mangrove ecosystem. 16S rRNA gene and metagenomic sequencing provided evidence of a microbial biofilm dominated by Cyanobacteria, Alphaproteobacteria, Actinobacteria, and Bacteroidota with a community encoding both aerobic and anaerobic pathways of the N cycle. Dinitrogen (N2) fixation was among the most commonly predicted process. Net N fluxes between the biofilm-covered crabs and the water and microbial N transformation rates in suspended biofilm slurries portray these holobionts as a net N2 sink, with N2 fixation exceeding N losses, and as a significant source of ammonium and dissolved organic N to the surrounding environment. N stable isotope natural abundances of fiddler crab carapace-associated biofilms were within the range expected for fixed N, further suggesting active microbial N2 fixation. These results extend our knowledge on the diversity of invertebrate-microbe associations, and provide a clear example of how animal microbiota can mediate a plethora of essential biogeochemical processes in mangrove ecosystems.}, } @article {pmid32810209, year = {2020}, author = {Hirose, Y and Shiozaki, T and Hamano, I and Yoshihara, S and Tokumoto, H and Eki, T and Harada, N}, title = {A specific combination of dual index adaptors decreases the sensitivity of amplicon sequencing with the Illumina platform.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {27}, number = {4}, pages = {}, pmid = {32810209}, issn = {1756-1663}, mesh = {DNA, Ribosomal ; Gene Library ; High-Throughput Nucleotide Sequencing/*methods/standards ; Metagenomics/methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S ; RNA, Ribosomal, 18S ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods/standards ; }, abstract = {Amplicon sequencing is a powerful approach in microbiome studies as it detects live organisms with high sensitivity. This approach determines the composition of sequence variants of marker genes using high-throughput DNA sequencers. The use of dual index adaptors is the fundamental technique for pooling DNA libraries for Illumina sequencers and is believed not to affect the results. However, here, we observed a decrease of sequence quality in samples containing a specific combination of indexes, namely N704 and S507 in Nextera kits, in multiple runs on the Illumina MiSeq sequencer operated in different facilities. This decrease was also observed when sequencing randomly fragmented DNA of Escherichia coli and was not observed when either individual adaptor was used. Each end of the DNA library with this index combination contains a complementary sequence motif, which potentially inhibits proper cluster generation and/or subsequent sequencing. Community analysis of the 16S and 18S rRNA amplicons using QIIME2 revealed significant decreases in α-diversity in the samples containing the N704/S507 index combination, resulting from loss of low-abundance sequence variants during denoising. Our data underscore the importance of quality validation of sequence reads in developing dual index techniques and suggest cautious interpretation of microbiome data containing low-quality sequence reads.}, } @article {pmid32806340, year = {2020}, author = {Banchi, E and Ametrano, CG and Tordoni, E and Stanković, D and Ongaro, S and Tretiach, M and Pallavicini, A and Muggia, L and , }, title = {Environmental DNA assessment of airborne plant and fungal seasonal diversity.}, journal = {The Science of the total environment}, volume = {738}, number = {}, pages = {140249}, doi = {10.1016/j.scitotenv.2020.140249}, pmid = {32806340}, issn = {1879-1026}, mesh = {*DNA Barcoding, Taxonomic ; *DNA, Environmental ; Fungi/genetics ; Italy ; Seasons ; }, abstract = {Environmental DNA (eDNA) metabarcoding and metagenomics analyses can improve taxonomic resolution in biodiversity studies. Only recently, these techniques have been applied in aerobiology, to target bacteria, fungi and plants in airborne samples. Here, we present a nine-month aerobiological study applying eDNA metabarcoding in which we analyzed simultaneously airborne diversity and variation of fungi and plants across five locations in North and Central Italy. We correlated species composition with the ecological characteristics of the sites and the seasons. The most abundant taxa among all sites and seasons were the fungal genera Cladosporium, Alternaria, and Epicoccum and the plant genera Brassica, Corylus, Cupressus and Linum, the latter being much more variable among sites. PERMANOVA and indicator species analyses showed that the plant diversity from air samples is significantly correlated with seasons, while that of fungi varied according to the interaction between seasons and sites. The results consolidate the performance of a new eDNA metabarcoding pipeline for the simultaneous amplification and analysis of airborne plant and fungal particles. They also highlight the promising complementarity of this approach with more traditional biomonitoring frameworks and routine reports of air quality provided by environmental agencies.}, } @article {pmid32804018, year = {2020}, author = {Sánchez-Tapia, M and Miller, AW and Granados-Portillo, O and Tovar, AR and Torres, N}, title = {The development of metabolic endotoxemia is dependent on the type of sweetener and the presence of saturated fat in the diet.}, journal = {Gut microbes}, volume = {12}, number = {1}, pages = {1801301}, pmid = {32804018}, issn = {1949-0984}, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification/metabolism ; Diet, High-Fat/adverse effects ; Endotoxemia/*etiology/metabolism/microbiology ; Fatty Acids/*adverse effects/metabolism ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome ; Humans ; Male ; Rats ; Rats, Wistar ; Sweetening Agents/*adverse effects/metabolism ; }, abstract = {Fat and sweeteners contribute to obesity. However, it is unknown whether specific bacteria are selectively modified by different caloric and noncaloric sweeteners with or without a high-fat diet (HFD). Here, we combined extensive host phenotyping and shotgun metagenomics of the gut microbiota to investigate this question. We found that the type of sweetener and its combination with an HFD selectively modified the gut microbiota. Sucralose and steviol glycosides led to the lowest α-diversity of the gut microbiota. Sucralose increased the abundance of B. fragilis in particular, resulting in a decrease in the abundance of occludin and an increase in proinflammatory cytokines, glucose intolerance, fatty acid oxidation and ketone bodies. Sucrose+HFD showed the highest metabolic endotoxemia, weight gain, body fat, total short chain fatty acids (SCFAs), serum TNFα concentration and glucose intolerance. Consumption of sucralose or sucrose resulted in enrichment of the bacterial genes involved in the synthesis of LPS and SCFAs. Notably, brown sugar and honey were associated with the absence of metabolic endotoxemia, increases in bacterial gene diversity and anti-inflammatory markers such as IL-10 and sIgA, the maintenance of glucose tolerance and energy expenditure, similar to the control group, despite the consumption of an HFD. These findings indicate that the type of sweetener and an HFD selectively modify the gut microbiota, bacterial gene enrichment of metabolic pathways involved in LPS and SCFA synthesis, and metabolic endotoxemia associated with different metabolic profiles.}, } @article {pmid32803809, year = {2020}, author = {Thompson, AR and Geisen, S and Adams, BJ}, title = {Shotgun metagenomics reveal a diverse assemblage of protists in a model Antarctic soil ecosystem.}, journal = {Environmental microbiology}, volume = {22}, number = {11}, pages = {4620-4632}, doi = {10.1111/1462-2920.15198}, pmid = {32803809}, issn = {1462-2920}, support = {#OPP-1637708//National Science Foundation/ ; NWO-VENI 016.Veni.181.078//Netherlands Organization for Scientific Research/ ; }, mesh = {Antarctic Regions ; Biodiversity ; Cercozoa/classification/genetics/isolation & purification ; Chlorophyta/classification/genetics ; Ciliophora/classification/genetics/isolation & purification ; Ecosystem ; Eukaryota/*classification/genetics/*isolation & purification ; Metagenomics ; Microbiota/*genetics ; Soil/chemistry/parasitology ; Soil Microbiology ; Stramenopiles/classification/genetics/isolation & purification ; }, abstract = {The soils of the McMurdo Dry Valleys (MDV) of Antarctica are established models for understanding fundamental processes in soil ecosystem functioning (e.g. ecological tipping points, community structuring and nutrient cycling) because the extreme physical environment drastically reduces biodiversity and ecological complexity. Understanding the functioning of MDV soils requires in-depth knowledge of the diversity of MDV soil species. Protists, which contribute significantly to soil ecosystem functioning worldwide, remain poorly characterized in the MDV. To better assess the diversity of MDV protists, we performed shotgun metagenomics on 18 sites representing a variety of landscape features and edaphic variables. Our results show MDV soil protists are diverse at both the genus (155 of 281 eukaryote genera) and family (120) levels, but comprise only 6% of eukaryotic reads. Protists are structured by moisture, total N and distance from the local coast and possess limited richness in arid (< 5% moisture) and at high elevation sites, known drivers of communities in the MDV. High relative diversity and broad distribution of protists in our study promotes these organisms as key members of MDV soil microbiomes and the MDV as a useful system for understanding the contribution of soil protists to the structure of soil microbiomes.}, } @article {pmid32803362, year = {2021}, author = {Zilius, M and Samuiloviene, A and Stanislauskienė, R and Broman, E and Bonaglia, S and Meškys, R and Zaiko, A}, title = {Depicting Temporal, Functional, and Phylogenetic Patterns in Estuarine Diazotrophic Communities from Environmental DNA and RNA.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {36-51}, pmid = {32803362}, issn = {1432-184X}, support = {P-MIP-17-126//Lietuvos Mokslo Taryba/ ; }, mesh = {Cyanobacteria/*genetics/*metabolism ; DNA, Environmental/genetics ; Estuaries ; Fresh Water/*microbiology ; Heterotrophic Processes ; Microbiota ; Nitrogen Cycle/*physiology ; Nitrogen Fixation/*physiology ; Oxidoreductases/genetics ; Phylogeny ; RNA/genetics ; Seasons ; Water Microbiology ; }, abstract = {Seasonally nitrogen-limited and phosphorus-replete temperate coastal waters generally host dense and diverse diazotrophic communities. Despite numerous studies in marine systems, little is known about diazotrophs and their functioning in oligohaline estuarine environments. Here we applied a combination of nifH transcript and metagenomic shotgun sequencing approaches to investigate temporal shifts in taxonomic composition and nifH activity of size-fractionated diazotrophic communities in a shallow and mostly freshwater coastal lagoon. Patterns in active nifH phylotypes exhibited a clear seasonal succession, which reflected their different tolerances to temperature change and nitrogen (N) availability. Thus, in spring, heterotrophic diazotrophs (Proteobacteria) dominated the nifH phylotypes, while increasing water temperature and depletion of inorganic N fostered heterocystous Cyanobacteria in summer. Metagenomic data demonstrated four main N-cycling pathways and three of them with a clear seasonal pattern: denitrification (spring) → N2 fixation (summer) → assimilative NO3[-] reduction (fall), with NH4[+] uptake into cells occurring across all seasons. Although a substantial denitrification signal was observed in spring, it could have originated from the re-suspended benthic rather than planktonic community. Our results contribute to a better understanding of the realized genetic potential of pelagic N2 fixation and its seasonal dynamics in oligohaline estuarine ecosystems, which are natural coastal biogeochemical reactors.}, } @article {pmid32803300, year = {2020}, author = {Wang, H and Huang, J and Wang, P and Li, T}, title = {Insights into the microbiota of larval and postlarval Pacific white shrimp (Penaeus vannamei) along early developmental stages: a case in pond level.}, journal = {Molecular genetics and genomics : MGG}, volume = {295}, number = {6}, pages = {1517-1528}, doi = {10.1007/s00438-020-01717-2}, pmid = {32803300}, issn = {1617-4623}, support = {QNLM201706//Pilot National Laboratory for Marine Science and Technology (Qingdao)/ ; CARS-48//China Agriculture Research System/ ; 2020TD39//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; 2018M640666//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; Bacteria/*classification/*genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Larva/growth & development/*microbiology ; Metagenomics ; Microbiota/*genetics ; Penaeidae/growth & development/*microbiology ; Ponds ; RNA, Ribosomal, 16S/*analysis/genetics ; }, abstract = {Increasing studies have revealed strong links among gut microbiota, health status, and shrimp development, but they mainly focus on the microbiota of Pacific white shrimp, Penaeus vannamei, during life stages from juveniles to adults. Little is known about shrimp microbiota dynamics at early developmental stages. In this study, with an aim to profile shrimp microbiota and its dynamics at stages nauplius, zoea, mysis, and early postlarva, we conducted a survey for the successful breeding processes in a commercial hatchery in China, sampled 33 samples including larval/postlarval shrimp, suspended substance in rearing water (SSRW), and nutrition supplements (i.e., algae and brine shrimp larvae) at stages N5, Z2, M2, and P2. The associated bacterial communities were sequenced and comparatively analyzed using high-throughput sequencing of bacterial 16S rRNA genes. Our case study results showed that bacterial community structures and compositions were strikingly different at stages N5, Z2, and P2, indicating the shift of microbiota at the three stages. Many taxa within Gamma-, Alphaproteobacteria, and Flavobacteriia classes were observed to be stage-specifically abundant and identified as taxonomic biomarkers potentially used to differentiate among shrimp at different early developmental stages. Summing up, these results shed light on larval/postlarval microbiota and its dynamics at different early developmental stages, highlighting the potential roles of shrimp development in microbiota formation and shifting.}, } @article {pmid32801139, year = {2020}, author = {Zou, M and Cai, Y and Hu, P and Cao, Y and Luo, X and Fan, X and Zhang, B and Wu, X and Jiang, N and Lin, Q and Zhou, H and Xue, Y and Gao, F}, title = {Analysis of the Composition and Functions of the Microbiome in Diabetic Foot Osteomyelitis Based on 16S rRNA and Metagenome Sequencing Technology.}, journal = {Diabetes}, volume = {69}, number = {11}, pages = {2423-2439}, doi = {10.2337/db20-0503}, pmid = {32801139}, issn = {1939-327X}, mesh = {Aged ; Diabetic Foot/*complications ; Female ; Humans ; Male ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Middle Aged ; Osteomyelitis/*microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA/methods ; }, abstract = {Metagenome sequencing has not been used in infected bone specimens. This prospective observational study explored the microbiome and its function in patients with diabetic foot osteomyelitis (DFO) and posttraumatic foot osteomyelitis (PFO) based on 16S rRNA sequencing and metagenome sequencing technologies. Spearman analysis was used to explore the correlation between dominant species and clinical indicators of patients with DFO. High-throughput sequencing showed that all the specimens were polymicrobial. The microbial diversity was significantly higher in the DFO group than in the PFO group. Firmicutes, Prevotellaceae, and Prevotella were the most abundant microbes in the DFO group. The most abundant microbes in the PFO group were Proteobacteria, Halomonadaceae, and Halomonas Prevotella denticola, Prevotella jejuni, and Prevotella fusca had positive correlation with the duration of diabetic foot infection (DFI_d). Proteus vulgaris was positively correlated with the infection index, while Bacteroides fragilis was negatively correlated. The microbial functional genes were more abundant in the DFO group than in the PFO group. Metagenome sequencing is feasible for the analysis of the microbiome in infected bone specimens. Gram-negative bacteria and anaerobes are dominant in DFO.}, } @article {pmid32800611, year = {2021}, author = {Ryan, MJ and Schloter, M and Berg, G and Kostic, T and Kinkel, LL and Eversole, K and Macklin, JA and Schelkle, B and Kazou, M and Sarand, I and Singh, BK and Fischer, D and Maguin, E and Ferrocino, I and Lima, N and McClure, RS and Charles, TC and de Souza, RSC and Kiran, GS and Krug, HL and Taffner, J and Roume, H and Selvin, J and Smith, D and Rybakova, D and Sessitsch, A}, title = {Development of Microbiome Biobanks - Challenges and Opportunities.}, journal = {Trends in microbiology}, volume = {29}, number = {2}, pages = {89-92}, doi = {10.1016/j.tim.2020.06.009}, pmid = {32800611}, issn = {1878-4380}, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification ; Biological Specimen Banks/*standards/trends ; Biomedical Research ; Humans ; Mammals/microbiology ; *Microbiota ; Plants/microbiology ; Preservation, Biological ; }, abstract = {The microbiome research field is rapidly evolving, but the required biobanking infrastructure is currently fragmented and not prepared for the biobanking of microbiomes. The rapid advancement of technologies requires an urgent assessment of how biobanks can underpin research by preserving microbiome samples and their functional potential.}, } @article {pmid32800221, year = {2020}, author = {Yadav, R and Rajput, V and Gohil, K and Khairnar, K and Dharne, M}, title = {Comprehensive metagenomic insights into a unique mass gathering and bathing event reveals transient influence on a riverine ecosystem.}, journal = {Ecotoxicology and environmental safety}, volume = {202}, number = {}, pages = {110938}, doi = {10.1016/j.ecoenv.2020.110938}, pmid = {32800221}, issn = {1090-2414}, mesh = {Drug Resistance, Microbial ; Ecosystem ; *Environmental Monitoring ; Humans ; India ; Metagenome ; Microbiota ; Rivers/*chemistry ; Water Pollution/*statistics & numerical data ; Water Quality ; }, abstract = {The religious mass gathering and bathing can pose a multitude of significant public health challenges and lead to severe alterations in the river microbial ecology. The Pandharpur Wari is an annual pilgrimage of Maharashtra, India, where millions of devotees carry the footprints of the saint-poets and pay their obeisance to Lord Vitthal on the 11th day of moon's waxing phase (Ashadi Ekadashi). As a part of the ritual, the engrossed devotees, walk over 250 km, take a first holy dip in a sacred river Indrayani at Alandi and secondly in Bhima River at Pandharpur. The MinION-based shotgun metagenomic approach was employed to examine the impact of spiritual mass bathing on environmental changes (concerning the river microbial community structure and functions); and public health aspects (in terms of changes in the pathogenic potential and antibiotic resistance). The analysis of bathing and post-bathing samples of both the rivers revealed alterations in the alpha and beta diversity, indicating significant spatiotemporal variations in the overall microbial structure and function. Furthermore, the analysis revealed up to 80% of differences in the abundance of virulence genes between the bathing and post bathing samples. We observed parallel increase of priority skin and enteric pathogens (ranging from 11% to 80%) such as Acinetobacter baumannii, Staphylococcus aureus, Streptococcus pyogenes, Mycobacterium tuberculosis, and Pseudomonas aeruginosa during the bathing event. Moreover, we observed a significant increase in the antibiotic resistance in the bathing samples of Bhima and Indrayani rivers respectively. Altogether, this is the first comprehensive metagenomic study unravelling the influence of religious mass-bathing on the riverine ecosystem.}, } @article {pmid32798955, year = {2020}, author = {Cai, Y and Chen, H and Yuan, R and Wang, F and Chen, Z and Zhou, B}, title = {Metagenomic analysis of soil microbial community under PFOA and PFOS stress.}, journal = {Environmental research}, volume = {188}, number = {}, pages = {109838}, doi = {10.1016/j.envres.2020.109838}, pmid = {32798955}, issn = {1096-0953}, mesh = {*Alkanesulfonic Acids ; Fluorocarbons ; *Microbiota ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis/toxicity ; }, abstract = {Perfluorinated compounds (PFCs) contamination of soil has attracted global attention in recent years but influences of PFCs on microorganisms in the soil environment have not been fully described. In this study, the effects of perfluorooctane sulphonate (PFOS) and perfluoroctanoic acid (PFOA) on bacterial communities were determined by Illumina Miseq sequencing and Illumina Hiseq Xten. The stimulation of PFCs pollutants on soil bacterial richness and community diversity were observed. Sequencing information indicated that Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, and Gemmatimonadetes were the dominant bacterial phyla. Two genera, Bacillus and Sphingomonas, exhibited adverse responses toward PFCs pollution. Carbohydrate-active enzymes (CAZy), Kyoto Encyclopedia of Genes and Genomes (KEGG) and NCBI databases were used to elucidate the proteins and function action of soil microbial to PFCs pollution. Pathways such as Carbohydrate metabolism, Global and overview maps and Membrane transport in the soil microbes were affected by PFCs stress. CAZy analysis revealed that glycosyl transferases (GTs) in PFCs-polluted soils showed more active, while glycoside hydrolases (GHs) were inhibited severely.}, } @article {pmid32798752, year = {2020}, author = {Luo, Y and Feng, L and Jia, R and Yang, G and Yang, Q and Mu, J}, title = {Variation in microbial populations and antibiotic resistance genes in mariculture sediments in the present of the seaweed Ulva fasciata and under selective pressure of oxytetracycline.}, journal = {Ecotoxicology and environmental safety}, volume = {204}, number = {}, pages = {111114}, doi = {10.1016/j.ecoenv.2020.111114}, pmid = {32798752}, issn = {1090-2414}, mesh = {Anti-Bacterial Agents/*toxicity ; *Aquaculture ; Bacteria/drug effects ; Biodegradation, Environmental ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; Integrons ; Microbiota/drug effects ; Oxytetracycline/analysis ; Seaweed/drug effects ; Tetracycline Resistance/drug effects ; Ulva/drug effects/*physiology ; }, abstract = {The widely distributed seaweed Ulva fasciata has nutrient absorption abilities and can be used in the bioremediation of polluted maricultural environments. This study explored microbial community and antibiotic resistance gene (ARG) variation in mariculture sediments in response to different trace levels (10, 100, and 500 μg L[-1]) of oxytetracycline (OTC) and the presence of Ulva fasciata. The increase in OTC level promoted nutrient (NO3_-N and PO4[3-]-P) removal mainly due to Ulva fasciata adsorption. The abundances of the Euryarchaeota and Planctomycetes phyla in sediments were positively related to the increase in OTC stress, while a negative correlation occurred for the Proteobacteria phylum via metagenomic analysis. Compared with the control system, the increase rates of total ARGs were 3.90%, 7.36% and 13.42% at the OTC levels of 10, 100 and 500 μg L[-1], respectively. OTC stress mainly favoured the collateral enrichment of non-corresponding polypeptide and MLS ARGs, mainly due to the enrichment of the phyla Planctomycetes and Euryarchaeota by the synergistic effect of OTC and nutrients. The results of quantitative PCR with tetracycline resistance genes (TRGs) (tetO, tetT, tetPB, tetW and otrA) and a horizontal transfer gene (intl1) demonstrated that all of genes had much higher gene numbers in sediments after 3 months of OTC stress than in those without OTC stress, which was strongly related to the variation in the phyla Bacteroidetes, Gemmatimonadetes and Acidobacteria. The significant correlation between intl1 and the target TRGs is indicative of the important role of the horizontal transfer of integron-resistant genes in the spread of TRGs.}, } @article {pmid32796856, year = {2020}, author = {Chaplin, A and Gao, H and Asase, C and Rengasamy, P and Park, B and Skander, D and Bebek, G and Rajagopalan, S and Maiseyeu, A}, title = {Systemically-delivered biodegradable PLGA alters gut microbiota and induces transcriptomic reprogramming in the liver in an obesity mouse model.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {13786}, pmid = {32796856}, issn = {2045-2322}, support = {R01 HL130516/HL/NHLBI NIH HHS/United States ; }, mesh = {Administration, Intravenous ; Animals ; Bacteroidetes/genetics/physiology ; Biocompatible Materials/administration & dosage/chemistry ; Cecum/chemistry/drug effects/microbiology ; Disease Models, Animal ; Firmicutes/genetics/physiology ; Gastrointestinal Microbiome/*drug effects/genetics/physiology ; Humans ; Hydrogen-Ion Concentration ; Liver/*drug effects/metabolism ; Mice, Inbred C57BL ; Nanoparticles/administration & dosage/chemistry ; Obesity/*genetics/metabolism ; Polylactic Acid-Polyglycolic Acid Copolymer/*administration & dosage/chemistry ; Transcriptome/*drug effects ; }, abstract = {Biodegradable materials, including the widely used poly (lactic-co-glycolic acid) (PLGA) nanoparticles contained in slow-release drug formulations, scaffolds and implants, are ubiquitous in modern biomedicine and are considered inert or capable of being metabolized through intermediates such as lactate. However, in the presence of metabolic stress, such as in obesity, the resulting degradation products may play a detrimental role, which is still not well understood. We evaluated the effect of intravenously-administered PLGA nanoparticles on the gut-liver axis under conditions of caloric excess in C57BL/6 mice. Our results show that PLGA nanoparticles accumulate and cause gut acidification in the cecum, accompanied by significant changes in the microbiome, with a marked decrease of Firmicutes and Bacteroidetes. This was associated with transcriptomic reprogramming in the liver, with a downregulation of mitochondrial function, and an increase in key enzymatic, inflammation and cell activation pathways. No changes were observed in systemic inflammation. Metagenome analysis coupled with publicly available microarray data suggested a mechanism of impaired PLGA degradation and intestinal acidification confirming an important enterohepatic axis of metabolite-microbiome interaction resulting in maintenance of metabolic homeostasis. Thus, our results have important implications for the investigation of PLGA use in metabolically-compromised clinical and experimental settings.}, } @article {pmid32793515, year = {2020}, author = {Liu, F and Fan, C and Zhang, L and Li, Y and Hou, H and Ma, Y and Fan, J and Tan, Y and Wu, T and Jia, S and Zhang, Y}, title = {Alterations of Gut Microbiome in Tibetan Patients With Coronary Heart Disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {373}, pmid = {32793515}, issn = {2235-2988}, mesh = {*Coronary Disease ; Feces ; *Gastrointestinal Microbiome ; Humans ; Lipopolysaccharides ; Risk Factors ; Tibet ; }, abstract = {Coronary heart disease (CHD) is closely related to gut microbiota, which may be significantly affected by ethnicity and the environment. Knowledge regarding the gut microbiome of Tibetan CHD patients living in the Qinghai-Tibet Plateau is very limited. In this study, we characterized the physiological parameters and gut microbiota from 23 healthy Tibetans (HT), 18 CHD patients, and 12 patients with non-stenosis coronary heart disease (NCHD). We analyzed the alterations of the gut microbiome in CHD patients and investigated the relationship between these alterations and the pathological indicators. We found no changes in trimethylamine N-oxide, however, a significant increase in lipopolysaccharides and white blood cells, and a decrease in high-density lipoprotein were observed in the blood of CHD patients, compared to that in the HT group. The gut microbiota of the NCHD group had a significantly higher Shannon index than that of the HT group. Adonis analysis showed that both microbial compositions and functions of the three groups were significantly separated. The Dialister genus was significantly lower and Blautia, Desulfovibrio, and Succinivibrio were significantly higher in abundance in CHD patients compared with the HT group, and the changes were significantly correlated with physiological indexes, such as increased lipopolysaccharides. Moreover, enrichment of genes decreased in four pathways of amino acid metabolism, such as arginine biosynthesis and histidine metabolism, although two lipid metabolism pathways, including fatty acid degradation and arachidonic acid metabolism, increased in the CHD group. Additionally, occupation and a family history of CHD were shown to be risk factors and affected the gut microbiota in Tibetans. Our study will provide insights into the understanding of CHD, leading to better diagnosis and treatment of Tibetan patients.}, } @article {pmid32793511, year = {2020}, author = {Bibbò, S and Abbondio, M and Sau, R and Tanca, A and Pira, G and Errigo, A and Manetti, R and Pes, GM and Dore, MP and Uzzau, S}, title = {Fecal Microbiota Signatures in Celiac Disease Patients With Poly-Autoimmunity.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {349}, pmid = {32793511}, issn = {2235-2988}, mesh = {*Autoimmune Diseases ; Autoimmunity ; *Celiac Disease ; Feces ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/genetics ; }, abstract = {To date, reliable tests enabling the identification of celiac disease (CD) patients at a greater risk of developing poly-autoimmune diseases are not yet available. We therefore aimed to identify non-invasive microbial biomarkers, useful to implement diagnosis of poly-autoimmunity. Twenty CD patients with poly-autoimmunity (cases) and 30 matched subjects affected exclusively by CD (controls) were selected. All patients followed a varied gluten-free diet for at least 1 year. Fecal microbiota composition was characterized using bacterial 16S ribosomal RNA gene sequencing. Significant differences in gut microbiota composition between CD patients with and without poly-autoimmune disease were found using the edgeR algorithm. Spearman correlations between gut microbiota and clinical, demographic, and anthropometric data were also examined. A significant reduction of Bacteroides, Ruminococcus, and Veillonella abundances was found in CD patients with poly-autoimmunity compared to the controls. Bifidobacterium was specifically reduced in CD patients with Hashimoto's thyroiditis and its abundance correlated negatively with abdominal circumference values in patients affected exclusively by CD. In addition, the duration of CD correlated with the abundance of Firmicutes (negatively) and Odoribacter (positively), whereas the abundance of Desulfovibrionaceae correlated positively with the duration of poly-autoimmunity. This study provides supportive evidence that specific variations of gut microbial taxa occur in CD patients with poly-autoimmune diseases. These findings open the way to future validation studies on larger cohorts, which might in turn lead to promising diagnostic applications.}, } @article {pmid32793240, year = {2020}, author = {Kaneko, K and Akagawa, S and Akagawa, Y and Kimata, T and Tsuji, S}, title = {Our Evolving Understanding of Kawasaki Disease Pathogenesis: Role of the Gut Microbiota.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {1616}, pmid = {32793240}, issn = {1664-3224}, mesh = {Animals ; *Disease Susceptibility/immunology ; Dysbiosis ; Environment ; *Gastrointestinal Microbiome/immunology ; Genetic Predisposition to Disease ; Humans ; Mucocutaneous Lymph Node Syndrome/*etiology/metabolism ; Risk Factors ; T-Lymphocyte Subsets/immunology/metabolism ; }, abstract = {Kawasaki disease (KD) was first described by Dr. Tomisaku Kawasaki in 1967. The etiology of KD has been studied comprehensively but remains largely unknown. The disease seems to result from the interplay of genetic and environmental susceptibility factors with infectious triggers, followed by a subsequent abnormal immune response characterized by increased levels of inflammatory cytokines and chemokines during the acute phase. Evidence has mounted to suggest that an imbalance between T helper 17 cells (Th17s) and regulatory T cells (Tregs) is associated with aberrant immune responses in KD. Recent advances in culture-independent techniques for detection and identification of intestinal commensal bacteria enabled the discovery that Th17 and Treg differentiation are regulated by short chain fatty acids (SCFAs), in particular butyrate, produced by the gut microbiota. This finding provided a mechanistic link between dysbiosis, defined as changes in the composition of the gut microbiota, and various inflammatory diseases. On this basis, we propose that dysbiosis, with reduced production of SCFAs leading to imbalances of Th17s/Tregs, could be involved in the etiology of KD. A pilot study supported this hypothesis, as only fecal concentrations of butyrate were significantly reduced in KD patients among SCFAs. This evolving perspective prompted us to undertake metagenomic analyses of bacterial DNA from the feces of KD patients who were antibiotic-naïve at diagnosis. Simultaneous measurements of Th17s/Tregs in peripheral blood and SCFA concentrations in feces would provide valuable information regarding the association between dysbiosis and dysregulated immune responses in KD.}, } @article {pmid32792677, year = {2020}, author = {Nieuwenhuijse, DF and Oude Munnink, BB and Phan, MVT and , and Munk, P and Venkatakrishnan, S and Aarestrup, FM and Cotten, M and Koopmans, MPG}, title = {Setting a baseline for global urban virome surveillance in sewage.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {13748}, pmid = {32792677}, issn = {2045-2322}, mesh = {Cross-Sectional Studies ; Disease Outbreaks ; Environmental Monitoring/*methods ; Food Contamination ; Humans ; Metagenome/genetics ; Metagenomics/methods ; Pilot Projects ; Sewage/*virology ; Vegetables/virology ; Virome/*genetics ; Viruses/*classification/genetics/*isolation & purification ; }, abstract = {The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective.}, } @article {pmid32791981, year = {2020}, author = {Yan, Y and Nguyen, LH and Franzosa, EA and Huttenhower, C}, title = {Strain-level epidemiology of microbial communities and the human microbiome.}, journal = {Genome medicine}, volume = {12}, number = {1}, pages = {71}, pmid = {32791981}, issn = {1756-994X}, support = {R24 DK110499/DK/NIDDK NIH HHS/United States ; R24DK110499//NIH NIDDK/International ; C10674/A27140//Cancer Research UK Grand Challenge Initiative/International ; }, mesh = {*Biodiversity ; Disease Susceptibility ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; *Metagenomics/methods ; *Microbiota ; Public Health Surveillance ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The biological importance and varied metabolic capabilities of specific microbial strains have long been established in the scientific community. Strains have, in the past, been largely defined and characterized based on microbial isolates. However, the emergence of new technologies and techniques has enabled assessments of their ecology and phenotypes within microbial communities and the human microbiome. While it is now more obvious how pathogenic strain variants are detrimental to human health, the consequences of subtle genetic variation in the microbiome have only recently been exposed. Here, we review the operational definitions of strains (e.g., genetic and structural variants) as they can now be identified from microbial communities using different high-throughput, often culture-independent techniques. We summarize the distribution and diversity of strains across the human body and their emerging links to health maintenance, disease risk and progression, and biochemical responses to perturbations, such as diet or drugs. We list methods for identifying, quantifying, and tracking strains, utilizing high-throughput sequencing along with other molecular and "culturomics" technologies. Finally, we discuss implications of population studies in bridging experimental gaps and leading to a better understanding of the health effects of strains in the human microbiome.}, } @article {pmid32791721, year = {2020}, author = {Butler, ÉM and Chiavaroli, V and Derraik, JGB and Grigg, CP and Wilson, BC and Walker, N and O'Sullivan, JM and Cutfield, WS}, title = {Maternal bacteria to correct abnormal gut microbiota in babies born by C-section.}, journal = {Medicine}, volume = {99}, number = {30}, pages = {e21315}, pmid = {32791721}, issn = {1536-5964}, mesh = {Adult ; Anthropometry/methods ; Asthma/epidemiology/etiology ; Bacterial Physiological Phenomena ; Body Composition ; Case-Control Studies ; Celiac Disease/epidemiology/etiology ; Cesarean Section/*adverse effects ; Delivery, Obstetric/trends ; Feces ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenomics/methods ; Microbiota/genetics/*physiology ; New Zealand/epidemiology ; Pediatric Obesity/epidemiology/etiology ; Placebos/*administration & dosage ; Pregnancy ; Vagina/*microbiology ; }, abstract = {INTRODUCTION: There is evidence that caesarean section (CS) is associated with increased risk of childhood obesity, asthma, and coeliac disease. The gut microbiota of CS-born babies differs to those born vaginally, possibly due to reduced exposure to maternal vaginal bacteria during birth. Vaginal seeding is a currently unproven practice intended to reduce such differences, so that the gut microbiota of CS-born babies is similar to that of babies born vaginally. Our pilot study, which uses oral administration as a novel form of vaginal seeding, will assess the degree of maternal strain transfer and overall efficacy of the procedure for establishing normal gut microbiota development.

METHODS AND ANALYSIS: Protocol for a single-blinded, randomized, placebo-controlled pilot study of a previously untested method of vaginal seeding (oral administration) in 30 CS-born babies. A sample of maternal vaginal bacteria is obtained prior to CS, and mixed with 5 ml sterile water to obtain a supernatant. Healthy babies are randomized at 1:1 to receive active treatment (3 ml supernatant) or placebo (3 ml sterile water). A reference group of 15 non-randomized vaginal-born babies are also being recruited. Babies' stool samples will undergo whole metagenomic shotgun sequencing to identify potential differences in community structure between CS babies receiving active treatment compared to those receiving placebo at age 1 month (primary outcome). Secondary outcomes include differences in overall gut community between CS groups (24 hours, 3 months); similarity of CS-seeded and placebo gut profiles to vaginally-born babies (24 hours, 1 and 3 months); degree of maternal vaginal strain transfer in CS-born babies (24 hours, 1 and 3 months); anthropometry (1 and 3 months) and body composition (3 months).

ETHICS AND DISSEMINATION: Ethics approval by the Northern A Health and Disability Ethics Committee (18/NTA/49). Results will be published in peer-reviewed journals and presented at international conferences.

REGISTRATION: Australian New Zealand Clinical Trials Registry (ACTRN12618000339257).}, } @article {pmid32791454, year = {2020}, author = {Kim, DD and Park, D and Yoon, H and Yun, T and Song, MJ and Yoon, S}, title = {Quantification of nosZ genes and transcripts in activated sludge microbiomes with novel group-specific qPCR methods validated with metagenomic analyses.}, journal = {Water research}, volume = {185}, number = {}, pages = {116261}, doi = {10.1016/j.watres.2020.116261}, pmid = {32791454}, issn = {1879-2448}, mesh = {Denitrification ; Metagenome ; *Microbiota/genetics ; Nitrous Oxide/analysis ; Republic of Korea ; *Sewage ; }, abstract = {Substantial N2O emission results from activated sludge nitrogen removal processes. N2O-reducing organisms possessing NosZ-type N2O reductases have been recognized to play crucial roles in suppressing emission of N2O produced in anoxic activated sludge via denitrification; however, which of the diverse nosZ-possessing organisms function as the major N2O sink in situ remains largely unknown. Here, nosZ genes and transcripts in wastewater microbiomes were analyzed with the group-specific qPCR assays designed de novo combining culture-based and computational approaches. A sewage sample was enriched in a batch reactor fed continuous stream of N2 containing 20-10,000 ppmv N2O with excess amount (10 mM) of acetate as the source of carbon and electrons, where 14 genera of potential N2O-reducers were identified. All available amino acid sequences of NosZ affiliated to these taxa were grouped into five subgroups (two clade I and three clade II groups), and primers/probe sets exclusively and comprehensively targeting the subgroups were designed and validated with in silico PCR. Four distinct activated sludge samples from three different wastewater treatment plants in Korea were analyzed with the qPCR assays and the results were validated with the shotgun metagenome analysis results. With these group-specific qPCR assays, the nosZ genes and transcripts of six additional activated sludge samples were analyzed and the results of the analyses clearly indicated the dominance of two clade II nosZ subgroups (Flavobacterium-like and Dechloromonas-like) among both nosZ gene and transcript pools.}, } @article {pmid32791115, year = {2020}, author = {Lang, S and Schnabl, B}, title = {Microbiota and Fatty Liver Disease-the Known, the Unknown, and the Future.}, journal = {Cell host & microbe}, volume = {28}, number = {2}, pages = {233-244}, pmid = {32791115}, issn = {1934-6069}, support = {R01 AA020703/AA/NIAAA NIH HHS/United States ; I01 BX004594/BX/BLRD VA/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 AA026939/AA/NIAAA NIH HHS/United States ; }, mesh = {Animals ; Dysbiosis/microbiology ; Fatty Liver, Alcoholic/*microbiology/*pathology/therapy ; Gastrointestinal Microbiome/*physiology ; Host Microbial Interactions/physiology ; Humans ; Intestines/microbiology/pathology ; Liver/pathology ; Mice ; Non-alcoholic Fatty Liver Disease/*microbiology/*pathology/therapy ; Probiotics/therapeutic use ; }, abstract = {The liver communicates with the intestine via the portal vein, biliary system, and mediators in the circulation. Microbes in the intestine maintain liver homeostasis but can also serve as a source of pathogens and molecules that contribute to fatty liver diseases. We review changes in the gut microbiota that can promote development or progression of alcohol-associated and non-alcoholic fatty liver disease-the most common chronic liver diseases in Western countries. We discuss how microbes and their products contribute to liver disease pathogenesis, putative microbial biomarkers of disease, and potential treatment approaches based on manipulation of the gut microbiota. Increasing our understanding of interactions between the intestinal microbiome and liver might help us identify patients with specific disease subtypes and select specific microbiota-based therapies.}, } @article {pmid32788623, year = {2020}, author = {Latorre-Pérez, A and Villalba-Bermell, P and Pascual, J and Vilanova, C}, title = {Assembly methods for nanopore-based metagenomic sequencing: a comparative study.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {13588}, pmid = {32788623}, issn = {2045-2322}, mesh = {Genome, Bacterial/genetics ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/genetics ; Nanopore Sequencing/*methods ; *Nanopores ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenomic sequencing has allowed for the recovery of previously unexplored microbial genomes. Whereas short-read sequencing platforms often result in highly fragmented metagenomes, nanopore-based sequencers could lead to more contiguous assemblies due to their potential to generate long reads. Nevertheless, there is a lack of updated and systematic studies evaluating the performance of different assembly tools on nanopore data. In this study, we have benchmarked the ability of different assemblers to reconstruct two different commercially-available mock communities that have been sequenced using Oxford Nanopore Technologies platforms. Among the tested tools, only metaFlye, Raven, and Canu performed well in all the datasets. These tools retrieved highly contiguous genomes (or even complete genomes) directly from the metagenomic data. Despite the intrinsic high error of nanopore sequencing, final assemblies reached high accuracy (~ 99.5 to 99.8% of consensus accuracy). Polishing strategies demonstrated to be necessary for reducing the number of indels, and this had an impact on the prediction of biosynthetic gene clusters. Correction with high quality short reads did not always result in higher quality draft assemblies. Overall, nanopore metagenomic sequencing data-adapted to MinION's current output-proved sufficient for assembling and characterizing low-complexity microbial communities.}, } @article {pmid32787773, year = {2020}, author = {Khurana, H and Singh, DN and Singh, A and Singh, Y and Lal, R and Negi, RK}, title = {Gut microbiome of endangered Tor putitora (Ham.) as a reservoir of antibiotic resistance genes and pathogens associated with fish health.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {249}, pmid = {32787773}, issn = {1471-2180}, support = {NBAIM/AMAAS/2017-20/GF/1a//National Bureau of Agriculturally Important Microorganisms/International ; }, mesh = {Animals ; Bacteria/*classification/genetics/isolation & purification/pathogenicity ; Bacterial Proteins/genetics ; *Drug Resistance, Bacterial ; Endangered Species ; Fishes/*microbiology ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Phylogeny ; Sequence Analysis, DNA ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Tor putitora, the largest freshwater fish of the Indian subcontinent, is an endangered species. Several factors have been attributed towards its continuous population decrease, but very little is known about the gut microbiome of this fish. Also, the fish gut microbiome serves as a reservoir of virulence factors and antibiotic resistance determinants. Therefore, the shotgun metagenomic approach was employed to investigate the taxonomic composition and functional potential of microbial communities present in the gut of Tor putitora, as well as the detection of virulence and antibiotic resistance genes in the microbiome.

RESULTS: The analysis of bacterial diversity showed that Proteobacteria was predominant phylum, followed by Chloroflexi, Bacteroidetes, and Actinobacteria. Within Proteobacteria, Aeromonas and Caulobacter were chiefly present; also, Klebsiella, Escherichia, and plant symbionts were noticeably detected. Functional characterization of gut microbes endowed the virulence determinants, while surveillance of antibiotic resistance genes showed the dominance of β-lactamase variants. The antibiotic-resistant Klebsiella pneumoniae and Escherichia coli pathovars were also detected. Microbial genome reconstruction and comparative genomics confirmed the presence of Aeromonads, the predominant fish pathogens.

CONCLUSIONS: Gut microbiome of endangered Tor putitora consisted of both commensals and opportunistic pathogens, implying that factors adversely affecting the non-pathogenic population would allow colonization and proliferation of pathogens causing diseased state in asymptomatic Tor putitora. The presence of virulence factors and antibiotic resistance genes suggested the potential risk of dissemination to other bacteria due to horizontal gene transfer, thereby posing a threat to fish and human health. The preservation of healthy gut microflora and limited use of antibiotics are some of the prerequisites for the conservation of this imperilled species.}, } @article {pmid32786562, year = {2020}, author = {Sun, X and Xu, R and Dong, Y and Li, F and Tao, W and Kong, T and Zhang, M and Qiu, L and Wang, X and Sun, W}, title = {Investigation of the Ecological Roles of Putative Keystone Taxa during Tailing Revegetation.}, journal = {Environmental science & technology}, volume = {54}, number = {18}, pages = {11258-11270}, doi = {10.1021/acs.est.0c03031}, pmid = {32786562}, issn = {1520-5851}, mesh = {Antimony ; *Arsenic ; Biodegradation, Environmental ; *Microbiota ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Metal contamination released from tailings is a global environmental concern. Although phytoremediation is a promising remediation method, its practice is often impeded by the adverse tailing geochemical conditions, which suppress biological activities. The ecosystem services provided by indigenous microorganisms could alter environmental conditions and facilitate revegetation in tailings. During the process, the keystone taxa of the microbial community are assumed an essential role in regulating the community composition and functions. The identity and the environmental functions of the keystone taxa during tailing revegetation, however, remain unelucidated. The current study compared the microbial community composition and interactions of two contrasting stibnite (Sb2S3) tailings, one revegetated and one unvegetated. The microbial interaction networks and keystone taxa were significantly different in the two tailings. Similar keystone taxa were also identified in other revegetated tailings, but not in their corresponding unvegetated tailings. Metagenome-assembled genomes (MAGs) indicated that the keystone taxa in the revegetated tailing may use both organic and inorganic energy sources (e.g., sulfur, arsenic, and antimony). They could also facilitate plant growth since a number of plant-growth-promoting genes, including phosphorus solubilization and siderophore production genes, were encoded. The current study suggests that keystone taxa may play important roles in tailing revegetation by providing nutrients, such as P and Fe, and promoting plant growth.}, } @article {pmid32785287, year = {2020}, author = {Giddings, LA and Chlipala, G and Kunstman, K and Green, S and Morillo, K and Bhave, K and Peterson, H and Driscoll, H and Maienschein-Cline, M}, title = {Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0237599}, pmid = {32785287}, issn = {1932-6203}, support = {P20 GM103449/GM/NIGMS NIH HHS/United States ; UL1 TR002003/TR/NCATS NIH HHS/United States ; }, mesh = {Acids/*chemistry ; Copper/chemistry ; Genetic Markers ; *Metagenome ; *Microbiota ; Minerals/chemistry ; *Mining ; Proteobacteria/*genetics/growth & development/*metabolism ; *Transcriptome ; }, abstract = {The microbial oxidation of metal sulfides plays a major role in the formation of acid rock drainage (ARD). We aimed to broadly characterize the ARD at Ely Brook, which drains the Ely Copper Mine Superfund site in Vermont, USA, using metagenomics and metatranscriptomics to assess the metabolic potential and seasonal ecological roles of microorganisms in water and sediment. Using Centrifuge against the NCBI "nt" database, ~25% of reads in sediment and water samples were classified as acid-tolerant Proteobacteria (61 ± 4%) belonging to the genera Pseudomonas (2.6-3.3%), Bradyrhizobium (1.7-4.1%), and Streptomyces (2.9-5.0%). Numerous genes (12%) were differentially expressed between seasons and played significant roles in iron, sulfur, carbon, and nitrogen cycling. The most abundant RNA transcript encoded the multidrug resistance protein Stp, and most expressed KEGG-annotated transcripts were involved in amino acid metabolism. Biosynthetic gene clusters involved in secondary metabolism (BGCs, 449) as well as metal- (133) and antibiotic-resistance (8501) genes were identified across the entire dataset. Several antibiotic and metal resistance genes were colocalized and coexpressed with putative BGCs, providing insight into the protective roles of the molecules BGCs produce. Our study shows that ecological stimuli, such as metal concentrations and seasonal variations, can drive ARD taxa to produce novel bioactive metabolites.}, } @article {pmid32782301, year = {2020}, author = {Chen, L and Collij, V and Jaeger, M and van den Munckhof, ICL and Vich Vila, A and Kurilshikov, A and Gacesa, R and Sinha, T and Oosting, M and Joosten, LAB and Rutten, JHW and Riksen, NP and Xavier, RJ and Kuipers, F and Wijmenga, C and Zhernakova, A and Netea, MG and Weersma, RK and Fu, J}, title = {Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4018}, pmid = {32782301}, issn = {2041-1723}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Bacteria/growth & development/isolation & purification/metabolism ; Cohort Studies ; Dysbiosis/metabolism/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Host Specificity ; Humans ; Inflammatory Bowel Diseases/metabolism/*microbiology ; Male ; Metabolic Networks and Pathways ; *Microbial Consortia ; Middle Aged ; Obesity/metabolism/*microbiology ; }, abstract = {The gut microbiome is an ecosystem that involves complex interactions. Currently, our knowledge about the role of the gut microbiome in health and disease relies mainly on differential microbial abundance, and little is known about the role of microbial interactions in the context of human disease. Here, we construct and compare microbial co-abundance networks using 2,379 metagenomes from four human cohorts: an inflammatory bowel disease (IBD) cohort, an obese cohort and two population-based cohorts. We find that the strengths of 38.6% of species co-abundances and 64.3% of pathway co-abundances vary significantly between cohorts, with 113 species and 1,050 pathway co-abundances showing IBD-specific effects and 281 pathway co-abundances showing obesity-specific effects. We can also replicate these IBD microbial co-abundances in longitudinal data from the IBD cohort of the integrative human microbiome (iHMP-IBD) project. Our study identifies several key species and pathways in IBD and obesity and provides evidence that altered microbial abundances in disease can influence their co-abundance relationship, which expands our current knowledge regarding microbial dysbiosis in disease.}, } @article {pmid32780963, year = {2021}, author = {Wijekoon, C and Quill, Z}, title = {Fungal endophyte diversity in table grapes.}, journal = {Canadian journal of microbiology}, volume = {67}, number = {1}, pages = {29-36}, doi = {10.1139/cjm-2020-0293}, pmid = {32780963}, issn = {1480-3275}, mesh = {Biodiversity ; DNA, Ribosomal Spacer/genetics ; Endophytes/classification/genetics/*isolation & purification ; Fruit/microbiology ; Fungi/classification/genetics/*isolation & purification ; Manitoba ; Microbiota/genetics ; Vitis/*microbiology ; }, abstract = {Plant fungal endophytes are diverse microbial sources that reside inside plants. Grapes (Vitis vinifera) are rich in polyphenols that have beneficial health effects, and recent research has shown that fungal endophytes in grapes may contribute to the production of these polyphenols and may serve as biocontrol agents. In this study, we determined the fungal microbial endophyte diversity in North American table grapes found at a Winnipeg, Manitoba, market. The amplicon internal transcribed spacer (ITS) metagenomics approach was used to profile the fungal communities of the fruit endophyte microbiome of three table grape types. The data supported endophyte diversity in different table grapes, including possible bioactive, saprophytic, and pathogenic fungi. Culturable endophytes were isolated and identified by morphology and ITS amplicon sequencing. The majority of the isolated culturable strains included Alternaria spp. and Cladosporium spp. The results provided evidence of the existence of diverse fungal endophytes isolated and identified from the fruit of the table grapes. These fungal endophytes may have potential in agricultural, industrial, and pharmaceutical applications.}, } @article {pmid32778754, year = {2020}, author = {Cairns, J and Jokela, R and Becks, L and Mustonen, V and Hiltunen, T}, title = {Repeatable ecological dynamics govern the response of experimental communities to antibiotic pulse perturbation.}, journal = {Nature ecology & evolution}, volume = {4}, number = {10}, pages = {1385-1394}, pmid = {32778754}, issn = {2397-334X}, mesh = {*Anti-Bacterial Agents ; Bacteria/genetics ; Metagenome ; *Microbiota ; Residence Characteristics ; }, abstract = {In an era of pervasive anthropogenic ecological disturbances, there is a pressing need to understand the factors that constitute community response and resilience. A detailed understanding of disturbance response needs to go beyond associations and incorporate features of disturbances, species traits, rapid evolution and dispersal. Multispecies microbial communities that experience antibiotic perturbation represent a key system with important medical dimensions. However, previous microbiome studies on this theme have relied on high-throughput sequencing data from uncultured species without the ability to explicitly account for the role of species traits and immigration. Here, we serially passage a 34-species defined bacterial community through different levels of pulse antibiotic disturbance, manipulating the presence or absence of species immigration. To understand the ecological community response measured using amplicon sequencing, we combine initial trait data measured for each species separately and metagenome sequencing data revealing adaptive mutations during the experiment. We found that the ecological community response was highly repeatable within the experimental treatments, which could be attributed in part to key species traits (antibiotic susceptibility and growth rate). Increasing antibiotic levels were also coupled with an increasing probability of species extinction, making species immigration critical for community resilience. Moreover, we detected signals of antibiotic-resistance evolution occurring within species at the same time scale, leaving evolutionary changes in communities despite recovery at the species compositional level. Together, these observations reveal a disturbance response that presents as classic species sorting, but is nevertheless accompanied by rapid within-species evolution.}, } @article {pmid32778056, year = {2020}, author = {Volant, S and Lechat, P and Woringer, P and Motreff, L and Campagne, P and Malabat, C and Kennedy, S and Ghozlane, A}, title = {SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {345}, pmid = {32778056}, issn = {1471-2105}, mesh = {Body Fluids/microbiology ; Child, Preschool ; *Classification ; Feces/microbiology ; Humans ; *Internet ; Metagenome ; Metagenomics/*methods ; Microbiota ; RNA, Ribosomal, 16S/genetics ; *Software ; *Statistics as Topic ; *User-Computer Interface ; Workflow ; }, abstract = {BACKGROUND: Comparing the composition of microbial communities among groups of interest (e.g., patients vs healthy individuals) is a central aspect in microbiome research. It typically involves sequencing, data processing, statistical analysis and graphical display. Such an analysis is normally obtained by using a set of different applications that require specific expertise for installation, data processing and in some cases, programming skills.

RESULTS: Here, we present SHAMAN, an interactive web application we developed in order to facilitate the use of (i) a bioinformatic workflow for metataxonomic analysis, (ii) a reliable statistical modelling and (iii) to provide the largest panel of interactive visualizations among the applications that are currently available. SHAMAN is specifically designed for non-expert users. A strong benefit is to use an integrated version of the different analytic steps underlying a proper metagenomic analysis. The application is freely accessible at http://shaman.pasteur.fr/ , and may also work as a standalone application with a Docker container (aghozlane/shaman), conda and R. The source code is written in R and is available at https://github.com/aghozlane/shaman . Using two different datasets (a mock community sequencing and a published 16S rRNA metagenomic data), we illustrate the strengths of SHAMAN in quickly performing a complete metataxonomic analysis.

CONCLUSIONS: With SHAMAN, we aim at providing the scientific community with a platform that simplifies reproducible quantitative analysis of metagenomic data.}, } @article {pmid32776951, year = {2020}, author = {Gschwind, R and Fournier, T and Kennedy, S and Tsatsaris, V and Cordier, AG and Barbut, F and Butel, MJ and Wydau-Dematteis, S}, title = {Evidence for contamination as the origin for bacteria found in human placenta rather than a microbiota.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0237232}, pmid = {32776951}, issn = {1932-6203}, mesh = {Adult ; Bacteria/genetics/*isolation & purification ; Cesarean Section ; Chorionic Villi/*microbiology ; Chorionic Villi Sampling ; DNA, Bacterial/analysis/genetics ; Delivery, Obstetric ; Extraembryonic Membranes/*microbiology ; Female ; Humans ; Microbiota ; Placenta/*microbiology ; Pregnancy ; Specimen Handling ; Umbilical Cord/*microbiology ; }, abstract = {Until recently the in utero environment of pregnant women was considered sterile. Recent high-sensitivity molecular techniques and high-throughput sequencing lead to some evidence for a low-biomass microbiome associated with the healthy placenta. Other studies failed to reveal evidence for a consistent presence of bacteria using either culture or molecular based techniques. Comparing conflicting "placental microbiome" studies is complicated by the use of varied and inconsistent protocols. Given this situation, we undertook an evaluation of the in utero environment sterility using several controlled methods, in the same study, to evaluate the presence or absence of bacteria and to explain contradictions present in the literature. Healthy pregnant women (n = 38) were recruited in three maternity wards. Placenta were collected after cesarean section with or without Alexis® and vaginal delivery births. For this study we sampled fetal membranes, umbilical cord and chorionic villi. Bacterial presence was analyzed using bacterial culture and qPCR on 34 fetal membranes, umbilical cord and chorionic villi samples. Shotgun metagenomics was performed on seven chorionic villi samples. We showed that the isolation of meaningful quantities of viable bacteria or bacterial DNA was possible only outside the placenta (fetal membranes and umbilical cords) highlighting the importance of sampling methods in studying the in utero environment. Bacterial communities described by metagenomics analysis were similar in chorionic villi samples and in negative controls and were dependent on the database chosen for the analysis. We conclude that the placenta does not harbor a specific, consistent and functional microbiota.}, } @article {pmid32774330, year = {2020}, author = {Khamis, FM and Ombura, FLO and Akutse, KS and Subramanian, S and Mohamed, SA and Fiaboe, KKM and Saijuntha, W and Van Loon, JJA and Dicke, M and Dubois, T and Ekesi, S and Tanga, CM}, title = {Insights in the Global Genetics and Gut Microbiome of Black Soldier Fly, Hermetia illucens: Implications for Animal Feed Safety Control.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1538}, pmid = {32774330}, issn = {1664-302X}, abstract = {The utilization of the black soldier fly (BSF) Hermetia illucens L. for recycling organic waste into high-quality protein and fat biomass for animal feeds has gained momentum worldwide. However, information on the genetic diversity and environmental implications on safety of the larvae is limited. This study delineates genetic variability and unravels gut microbiome complex of wild-collected and domesticated BSF populations from six continents using mitochondrial COI gene and 16S metagenomics. All sequences generated from the study linked to H. illucens accessions KM967419.1, FJ794355.1, FJ794361.1, FJ794367.1, KC192965.1, and KY817115.1 from GenBank. Phylogenetic analyses of the sequences generated from the study and rooted by GenBank accessions of Hermetia albitarsis Fabricius and Hermetia sexmaculata Macquart separated all samples into three branches, with H. illucens and H. sexmaculata being closely related. Genetic distances between H. illucens samples from the study and GenBank accessions of H. illucens ranged between 0.0091 and 0.0407 while H. sexmaculata and H. albitarsis samples clearly separated from all H. illucens by distances of 0.1745 and 0.1903, respectively. Genetic distance matrix was used to generate a principal coordinate plot that further confirmed the phylogenetic clustering. Haplotype network map demonstrated that Australia, United States 1 (Rhode Island), United States 2 (Colorado), Kenya, and China shared a haplotype, while Uganda shared a haplotype with GenBank accession KC192965 BSF from United States. All other samples analyzed had individual haplotypes. Out of 481,695 reads analyzed from 16S metagenomics, four bacterial families (Enterobactereaceae, Dysgonomonadaceae, Wohlfahrtiimonadaceae, and Enterococcaceae) were most abundant in the BSF samples. Alpha-diversity, as assessed by Shannon index, showed that the Kenyan and Thailand populations had the highest and lowest microbe diversity, respectively; while microbial diversity assessed through Bray Curtis distance showed United States 3 (Maysville) and Netherlands populations to be the most dissimilar. Our findings on genetic diversity revealed slight phylogeographic variation between BSF populations across the globe. The 16S data depicted larval gut bacterial families with economically important genera that might pose health risks to both animals and humans. This study recommends pre-treatment of feedstocks and postharvest measures of the harvested BSF larvae to minimize risk of pathogen contamination along the insect-based feed value chain.}, } @article {pmid32772914, year = {2020}, author = {Panwar, P and Allen, MA and Williams, TJ and Hancock, AM and Brazendale, S and Bevington, J and Roux, S and Páez-Espino, D and Nayfach, S and Berg, M and Schulz, F and Chen, IA and Huntemann, M and Shapiro, N and Kyrpides, NC and Woyke, T and Eloe-Fadrosh, EA and Cavicchioli, R}, title = {Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {116}, pmid = {32772914}, issn = {2049-2618}, mesh = {Antarctic Regions ; Aquatic Organisms/radiation effects/virology ; Ecosystem ; Lakes/*microbiology/*virology ; Microbiota/*radiation effects ; *Photoperiod ; *Seasons ; }, abstract = {BACKGROUND: Cold environments dominate the Earth's biosphere and microbial activity drives ecosystem processes thereby contributing greatly to global biogeochemical cycles. Polar environments differ to all other cold environments by experiencing 24-h sunlight in summer and no sunlight in winter. The Vestfold Hills in East Antarctica contains hundreds of lakes that have evolved from a marine origin only 3000-7000 years ago. Ace Lake is a meromictic (stratified) lake from this region that has been intensively studied since the 1970s. Here, a total of 120 metagenomes representing a seasonal cycle and four summers spanning a 10-year period were analyzed to determine the effects of the polar light cycle on microbial-driven nutrient cycles.

RESULTS: The lake system is characterized by complex sulfur and hydrogen cycling, especially in the anoxic layers, with multiple mechanisms for the breakdown of biopolymers present throughout the water column. The two most abundant taxa are phototrophs (green sulfur bacteria and cyanobacteria) that are highly influenced by the seasonal availability of sunlight. The extent of the Chlorobium biomass thriving at the interface in summer was captured in underwater video footage. The Chlorobium abundance dropped from up to 83% in summer to 6% in winter and 1% in spring, before rebounding to high levels. Predicted Chlorobium viruses and cyanophage were also abundant, but their levels did not negatively correlate with their hosts.

CONCLUSION: Over-wintering expeditions in Antarctica are logistically challenging, meaning insight into winter processes has been inferred from limited data. Here, we found that in contrast to chemolithoautotrophic carbon fixation potential of Southern Ocean Thaumarchaeota, this marine-derived lake evolved a reliance on photosynthesis. While viruses associated with phototrophs also have high seasonal abundance, the negative impact of viral infection on host growth appeared to be limited. The microbial community as a whole appears to have developed a capacity to generate biomass and remineralize nutrients, sufficient to sustain itself between two rounds of sunlight-driven summer-activity. In addition, this unique metagenome dataset provides considerable opportunity for future interrogation of eukaryotes and their viruses, abundant uncharacterized taxa (i.e. dark matter), and for testing hypotheses about endemic species in polar aquatic ecosystems. Video Abstract.}, } @article {pmid32772817, year = {2020}, author = {Wallace, MJ and Fishbein, SRS and Dantas, G}, title = {Antimicrobial resistance in enteric bacteria: current state and next-generation solutions.}, journal = {Gut microbes}, volume = {12}, number = {1}, pages = {1799654}, pmid = {32772817}, issn = {1949-0984}, support = {T32 CA113275/CA/NCI NIH HHS/United States ; R01 OH011578/OH/NIOSH CDC HHS/United States ; T32 DK077653/DK/NIDDK NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; T32 HD007409/HD/NICHD NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/classification/drug effects/genetics/*pathogenicity ; Biological Evolution ; *Drug Resistance, Bacterial/drug effects/genetics ; Dysbiosis/microbiology/prevention & control ; *Gastrointestinal Microbiome/drug effects/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Interspersed Repetitive Sequences/genetics ; Metagenomics ; }, abstract = {Antimicrobial resistance is one of the largest threats to global health and imposes substantial burdens in terms of morbidity, mortality, and economic costs. The gut is a key conduit for the genesis and spread of antimicrobial resistance in enteric bacterial pathogens. Distinct bacterial species that cause enteric disease can exist as invasive enteropathogens that immediately evoke gastrointestinal distress, or pathobionts that can arise from established bacterial commensals to inflict dysbiosis and disease. Furthermore, various environmental reservoirs and stressors facilitate the evolution and transmission of resistance. In this review, we present a comprehensive discussion on circulating resistance profiles and gene mobilization strategies of the most problematic species of enteric bacterial pathogens. Importantly, we present emerging approaches toward surveillance of pathogens and their resistance elements as well as promising treatment strategies that can circumvent common resistance mechanisms.}, } @article {pmid32772670, year = {2020}, author = {Moeller, AH and Sanders, JG}, title = {Roles of the gut microbiota in the adaptive evolution of mammalian species.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1808}, pages = {20190597}, pmid = {32772670}, issn = {1471-2970}, support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adaptation, Biological ; Animals ; *Biological Evolution ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; Mammals/*microbiology ; }, abstract = {Every mammalian species harbours a gut microbiota, and variation in the gut microbiota within mammalian species can have profound effects on host phenotypes. In this review, we summarize recent evidence that gut microbiotas have influenced the course of mammalian adaptation and diversification. Associations with gut microbiotas have: (i) promoted the diversification of mammalian species by enabling dietary transitions onto difficult-to-digest carbon sources and toxic food items; (ii) shaped the evolution of adaptive phenotypic plasticity in mammalian species through the amplification of signals from the external environment and from postnatal developmental processes; and (iii) generated selection for host mechanisms, including innate and adaptive immune mechanisms, to control the gut microbiota for the benefit of host fitness. The stability of specific gut microbiotas within host species lineages varies substantially across the mammalian phylogeny, and this variation may alter the ultimate evolutionary outcomes of relationships with gut microbiotas in different mammalian clades. In some mammalian species, including humans, relationships with host species-specific gut microbiotas appear to have led to the evolution of host dependence on the gut microbiota for certain functions. These studies implicate the gut microbiota as a significant environmental factor and selective agent shaping the adaptive evolution of mammalian diet, phenotypic plasticity, gastrointestinal morphology and immunity. This article is part of the theme issue 'The role of the microbiome in host evolution'.}, } @article {pmid32772242, year = {2020}, author = {Guilin, Z and Pengyu, Z and Wei, L and Fengqi, H and Chen, F and Yu, Y and Yue, H and Yuting, T}, title = {Reduction of gut microbial diversity and short chain fatty acids in BALB/c mice exposure to microcystin-LR.}, journal = {Ecotoxicology (London, England)}, volume = {29}, number = {9}, pages = {1347-1357}, doi = {10.1007/s10646-020-02254-9}, pmid = {32772242}, issn = {1573-3017}, mesh = {Animals ; Biodiversity ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*drug effects ; Marine Toxins ; Mice ; Mice, Inbred BALB C ; Microcystins/*toxicity ; }, abstract = {Gut microbiota has been shown to play critical roles in host health. The present study was to determine the toxicological effects of microcystin-LR (MCLR) on gut microbial community and metabolites using 16S rDNA sequencing and gas chromatography-mass spectrometry (GC-MS). MCLR was administered to BALB/c mice by gavage for eight weeks. Results of the microbial alpha-diversity (Sobs, Chao1, ACE and Shannon indexes) decreased in MCLR-treated group versus controls. Phylum Candidatus Saccharibacteria decreased significantly in MCLR-treated group versus controls. Correspondingly, more than thirties genera in relative abundance decreased, especially short chain fatty acid (SCFA)-producing bacteria (e.g., Alistipes and Ruminococcus). These results indicated that the gut microbial community structure was remarkably changed by MCLR. Furthermore, concentrations of SCFAs were significantly decreased after MCLR exposure (P < 0.01), where butyrate decreased as high as 4.9-fold. Consequently, sub-chronic exposure to MCLR could not only alter the microbial composition but metabolites. This study offered novel insights into the toxic mechanism of MCs from gut microbiota, and facilitated further clarification of risks to human health from MCs exposure.}, } @article {pmid32770198, year = {2021}, author = {Li, R and Huang, X and Liang, X and Su, M and Lai, KP and Chen, J}, title = {Integrated omics analysis reveals the alteration of gut microbe-metabolites in obese adults.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {3}, pages = {}, doi = {10.1093/bib/bbaa165}, pmid = {32770198}, issn = {1477-4054}, mesh = {Adult ; Body Mass Index ; Case-Control Studies ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolomics ; Obesity/blood/*metabolism/*microbiology ; }, abstract = {Obesity, a risk to health, is a global problem in modern society. The prevalence of obesity was approximately 13% among world's adult population. Recently, several reports suggested that the interference of gut microbiota composition and function is associated with metabolic disorders, including obesity. Gut microbiota produce a board range of metabolites involved in energy and glucose homeostasis, leading to the alteration in host metabolism. However, systematic evaluation of the relationship between gut microbiota, gut metabolite and host metabolite profiles in obese adults is still lacking. In this study, we used comparative metagenomics and metabolomics analysis to determine the gut microbiota and gut-host metabolite profiles in six normal and obese adults of Chinese origin, respectively. Following the functional and pathway analysis, we aimed to understand the possible impact of gut microbiota on the host metabolites via the change in gut metabolites. The result showed that the change in gut microbiota may result in the modulation of gut metabolites contributing to glycolysis, tricarboxylic acid cycle and homolactic fermentation. Furthermore, integrated metabolomic analysis demonstrated a possible positive correlation of dysregulated metabolites in the gut and host, including l-phenylalanine, l-tyrosine, uric acid, kynurenic acid, cholesterol sulfate and glucosamine, which were reported to contribute to metabolic disorders such as obesity and diabetes. The findings of this study provide the possible association between gut microbiota-metabolites and host metabolism in obese adults. The identified metabolite changes could serve as biomarkers for the evaluation of obesity and metabolic disorders.}, } @article {pmid32766782, year = {2020}, author = {Shaffer, M and Borton, MA and McGivern, BB and Zayed, AA and La Rosa, SL and Solden, LM and Liu, P and Narrowe, AB and Rodríguez-Ramos, J and Bolduc, B and Gazitúa, MC and Daly, RA and Smith, GJ and Vik, DR and Pope, PB and Sullivan, MB and Roux, S and Wrighton, KC}, title = {DRAM for distilling microbial metabolism to automate the curation of microbiome function.}, journal = {Nucleic acids research}, volume = {48}, number = {16}, pages = {8883-8900}, pmid = {32766782}, issn = {1362-4962}, support = {R01 AI143288/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*classification ; *Gastrointestinal Microbiome ; Genomics/*methods ; Humans ; Metabolomics/*methods ; Metagenome ; Molecular Sequence Annotation/methods ; *Software ; *Soil Microbiology ; Viruses/*classification ; }, abstract = {Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.}, } @article {pmid32765533, year = {2020}, author = {Gong, X and Jiang, S and Tian, H and Xiang, D and Zhang, J}, title = {Polyphenols in the Fermentation Liquid of Dendrobium candidum Relieve Intestinal Inflammation in Zebrafish Through the Intestinal Microbiome-Mediated Immune Response.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {1542}, pmid = {32765533}, issn = {1664-3224}, mesh = {Animals ; Biomarkers ; Dendrobium/*metabolism ; Fatty Acids, Volatile/metabolism ; *Fermentation ; *Gastrointestinal Microbiome/immunology ; Immunity ; Metabolome/immunology ; Oxidative Stress ; Polyphenols/*chemistry ; Zebrafish ; }, abstract = {Previous studies of Dendrobium candidum (D. candidum), which is mainly distributed in tropical areas, have mainly focused on its functional polysaccharide; the effects of D. candidum polyphenols, the chemical composition of which may be improved by fermentation, have received limited attention, especially in in vivo models, which inevitably involve interactions with intestinal microorganisms. To address this challenge, metagenomic and metabolomic techniques, were applied, and immune factors and mucosal barrier-related proteins were determined to reveal the effects of fermented D. candidum polyphenols (FDC) on intestinal inflammation induced by oxazolone in zebrafish. The results showed that fermentation significantly changed the chemical composition of D. candidum and that FDC significantly improved the intestinal immune index. After the 21st day of FDC intervention, the abundance of Lactobacillus, Faecalibacterium, and Rummeliibacillus increased, but the abundance of the genera Shewanella, Geodermatophilus, Peptostreptococcaceae, and Mycobacterium decreased. At the same time, FDC significantly increased intestinal short-chain fatty acids (SCFAs). In addition, network analysis based on multi-omics indicated that FDC intake leads to changes in intestinal microbiota and intestinal metabolites, resulting in enhanced host immune function. These results indicate that FDC can improve intestinal health by regulating the intestinal microbiota and its metabolites to treat intestinal inflammation and regulate the host immune system. The present research improved our understanding of the utilization of D. candidum polyphenols and provided new evidence for the impacts of fermented D. candidum on host health.}, } @article {pmid32764209, year = {2020}, author = {Park, YM and Ha, E and Gu, KN and Shin, GY and Lee, CK and Kim, K and Kim, HJ}, title = {Host Genetic and Gut Microbial Signatures in Familial Inflammatory Bowel Disease.}, journal = {Clinical and translational gastroenterology}, volume = {11}, number = {7}, pages = {e00213}, pmid = {32764209}, issn = {2155-384X}, mesh = {Adult ; Aged ; Colitis, Ulcerative/*genetics/immunology/microbiology ; Crohn Disease/*genetics/immunology/microbiology ; DNA, Bacterial/isolation & purification ; Dysbiosis/*diagnosis/genetics/immunology/microbiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/*immunology ; *Genetic Predisposition to Disease ; Genome-Wide Association Study ; Host Microbial Interactions/genetics/immunology ; Humans ; Male ; Medical History Taking/statistics & numerical data ; Metagenomics ; Middle Aged ; Pedigree ; Polymorphism, Single Nucleotide ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Exome Sequencing ; Young Adult ; }, abstract = {INTRODUCTION: The family history of inflammatory bowel disease (IBD) has been strongly associated with risk of developing IBD. This study aimed to identify the host genetic and gut microbial signatures in familial IBD.

METHODS: Genetic analyses using genome-wide single nucleotide polymorphism genotyping and whole exome sequencing were performed to calculate weighted genetic risk scores from known IBD-associated common variants and to identify rare deleterious protein-altering variants specific to patients with familial IBD in 8 Korean families that each included more than 2 affected first-degree relatives (FDRs) and their unaffected FDR(s). In parallel, gut microbial community was analyzed by 16S rRNA sequencing of stools from the sample individuals.

RESULTS: The risk of familial IBD was not well explained by the genetic burden from common IBD-risk variants, suggesting the presence of family-shared genetic and environmental disease-risk factors. We identified 17 genes (AC113554.1, ACE, AKAP17A, AKAP9, ANK2, ASB16, ASIC3, DNPH1, DUS3L, FAM200A, FZD10, LAMA5, NUTM2F, PKN1, PRR26, WDR66, and ZC3H4) that each contained rare, potentially deleterious variants transmitted to the affected FDRs in multiple families. In addition, metagenomic analyses revealed significantly different diversity of gut microbiota and identified a number of differentially abundant taxa in affected FDRs, highlighting 22 novel familial disease-associated taxa with large abundance changes and the previously reported gut dysbiosis including low alpha diversity in IBD and 16 known IBD-specific taxa.

DISCUSSION: This study identified familial IBD-associated rare deleterious variants and gut microbial dysbiosis in familial IBD.}, } @article {pmid32763595, year = {2020}, author = {Freitas, L and Appolinario, L and Calegario, G and Campeão, M and Tschoeke, D and Garcia, G and Venancio, IM and Cosenza, CAN and Leomil, L and Bernardes, M and Albuquerque, AL and Thompson, C and Thompson, F}, title = {Glacial-interglacial transitions in microbiomes recorded in deep-sea sediments from the western equatorial Atlantic.}, journal = {The Science of the total environment}, volume = {746}, number = {}, pages = {140904}, doi = {10.1016/j.scitotenv.2020.140904}, pmid = {32763595}, issn = {1879-1026}, mesh = {Geologic Sediments ; Metagenome ; *Microbiota ; Oceans and Seas ; Phytoplankton ; }, abstract = {In the late Quaternary, glacial-interglacial transitions are marked by major environmental changes. Glacial periods in the western equatorial Atlantic (WEA) are characterized by high continental terrigenous input, which increases the proportion of terrestrial organic matter (e.g. lignin, alkanes), nutrients (e.g. iron and sulphur), and lower primary productivity. On the other hand, interglacials are characterized by lower continental contribution and maxima in primary productivity. Microbes can serve as biosensors of past conditions, but scarce information is available on deep-sea sediments in the WEA. The hypothesis put forward in this study is that past changes in climate conditions modulated the taxonomic/functional composition of microbes from deep sediment layers. To address this hypothesis, we collected samples from a marine sediment core located in the WEA, which covered the last 130 kyr. This region is influenced by the presence of the Amazon River plume, which outputs dissolved and particulate nutrients in vast oceanic regions, as well as the Parnaiba river plume. Core GL-1248 was analysed by shotgun metagenomics and geochemical analyses (alkane, lignin, perylene, sulphur). Two clusters (glacial and interglacial-deglacial) were found based on taxonomic and functional profiles of metagenomes. The interglacial period had a higher abundance of genes belonging to several sub-systems (e.g. DNA, RNA metabolism, cell division, chemotaxis, and respiration) that are consistent with a past environment with enhanced primary productivity. On the other hand, the abundance of Alcanivorax, Marinobacter, Kangiella and aromatic compounds that may serve as energy sources for these bacteria were higher in the glacial. The glacial period was enriched in genes for the metabolism of aromatic compounds, lipids, isoprenoids, iron, and Sulphur, consistent with enhanced fluvial input during the last glacial period. In contrast, interglacials have increased contents of more labile materials originating from phytoplankton (e.g. Prochlorococcus). This study provides new insights into the microbiome as climatic archives at geological timescales.}, } @article {pmid32763188, year = {2020}, author = {Easteal, S and Arkell, RM and Balboa, RF and Bellingham, SA and Brown, AD and Calma, T and Cook, MC and Davis, M and Dawkins, HJS and Dinger, ME and Dobbie, MS and Farlow, A and Gwynne, KG and Hermes, A and Hoy, WE and Jenkins, MR and Jiang, SH and Kaplan, W and Leslie, S and Llamas, B and Mann, GJ and McMorran, BJ and McWhirter, RE and Meldrum, CJ and Nagaraj, SH and Newman, SJ and Nunn, JS and Ormond-Parker, L and Orr, NJ and Paliwal, D and Patel, HR and Pearson, G and Pratt, GR and Rambaldini, B and Russell, LW and Savarirayan, R and Silcocks, M and Skinner, JC and Souilmi, Y and Vinuesa, CG and , and Baynam, G}, title = {Equitable Expanded Carrier Screening Needs Indigenous Clinical and Population Genomic Data.}, journal = {American journal of human genetics}, volume = {107}, number = {2}, pages = {175-182}, pmid = {32763188}, issn = {1537-6605}, mesh = {Australia ; Genetic Variation/genetics ; Humans ; Metagenomics/*methods ; Population Groups/*genetics ; }, abstract = {Expanded carrier screening (ECS) for recessive monogenic diseases requires prior knowledge of genomic variation, including DNA variants that cause disease. The composition of pathogenic variants differs greatly among human populations, but historically, research about monogenic diseases has focused mainly on people with European ancestry. By comparison, less is known about pathogenic DNA variants in people from other parts of the world. Consequently, inclusion of currently underrepresented Indigenous and other minority population groups in genomic research is essential to enable equitable outcomes in ECS and other areas of genomic medicine. Here, we discuss this issue in relation to the implementation of ECS in Australia, which is currently being evaluated as part of the national Government's Genomics Health Futures Mission. We argue that significant effort is required to build an evidence base and genomic reference data so that ECS can bring significant clinical benefit for many Aboriginal and/or Torres Strait Islander Australians. These efforts are essential steps to achieving the Australian Government's objectives and its commitment "to leveraging the benefits of genomics in the health system for all Australians." They require culturally safe, community-led research and community involvement embedded within national health and medical genomics programs to ensure that new knowledge is integrated into medicine and health services in ways that address the specific and articulated cultural and health needs of Indigenous people. Until this occurs, people who do not have European ancestry are at risk of being, in relative terms, further disadvantaged.}, } @article {pmid32762019, year = {2020}, author = {Zhu, C and Miller, M and Lusskin, N and Bergk Pinto, B and Maccario, L and Häggblom, M and Vogel, T and Larose, C and Bromberg, Y}, title = {Snow microbiome functional analyses reveal novel aspects of microbial metabolism of complex organic compounds.}, journal = {MicrobiologyOpen}, volume = {9}, number = {9}, pages = {e1100}, pmid = {32762019}, issn = {2045-8827}, support = {U01 GM115486/GM/NIGMS NIH HHS/United States ; }, mesh = {Acyclic Monoterpenes/metabolism ; Bacteria/*metabolism ; Carbon/metabolism ; Fatty Acids/biosynthesis ; Metabolic Networks and Pathways ; Metagenome ; Microbiota/genetics/*physiology ; Norway ; Organic Chemicals/*metabolism ; Seasons ; Snow/*microbiology ; Styrene/metabolism ; Transcriptome ; }, abstract = {Microbes active in extreme cold are not as well explored as those of other extreme environments. Studies have revealed a substantial microbial diversity and identified cold-specific microbiome molecular functions. We analyzed the metagenomes and metatranscriptomes of 20 snow samples collected in early and late spring in Svalbard, Norway using mi-faser, our read-based computational microbiome function annotation tool. Our results reveal a more diverse microbiome functional capacity and activity in the early- vs. late-spring samples. We also find that functional dissimilarity between the same-sample metagenomes and metatranscriptomes is significantly higher in early than late spring samples. These findings suggest that early spring samples may contain a larger fraction of DNA of dormant (or dead) organisms, while late spring samples reflect a new, metabolically active community. We further show that the abundance of sequencing reads mapping to the fatty acid synthesis-related microbial pathways in late spring metagenomes and metatranscriptomes is significantly correlated with the organic acid levels measured in these samples. Similarly, the organic acid levels correlate with the pathway read abundances of geraniol degradation and inversely correlate with those of styrene degradation, suggesting a possible nutrient change. Our study thus highlights the activity of microbial degradation pathways of complex organic compounds previously unreported at low temperatures.}, } @article {pmid32761733, year = {2020}, author = {Overholt, WA and Hölzer, M and Geesink, P and Diezel, C and Marz, M and Küsel, K}, title = {Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome-assembled genomes from a complex aquifer system.}, journal = {Environmental microbiology}, volume = {22}, number = {9}, pages = {4000-4013}, doi = {10.1111/1462-2920.15186}, pmid = {32761733}, issn = {1462-2920}, support = {CRC 1076 AquaDiva//Deutsche Forschungsgemeinschaft/International ; //Joachim Herz Stiftung/International ; }, mesh = {Genome, Microbial/*genetics ; Groundwater/*microbiology/virology ; High-Throughput Nucleotide Sequencing ; Metagenome/*genetics ; Metagenomics ; *Nanopore Sequencing ; Water Microbiology ; Whole Genome Sequencing ; }, abstract = {Assembling microbial and viral genomes from metagenomes is a powerful and appealing method to understand structure-function relationships in complex environments. To compare the recovery of genomes from microorganisms and their viruses from groundwater, we generated shotgun metagenomes with Illumina sequencing accompanied by long reads derived from the Oxford Nanopore Technologies (ONT) sequencing platform. Assembly and metagenome-assembled genome (MAG) metrics for both microbes and viruses were determined from an Illumina-only assembly, ONT-only assembly, and a hybrid assembly approach. The hybrid approach recovered 2× more mid to high-quality MAGs compared to the Illumina-only approach and 4× more than the ONT-only approach. A similar number of viral genomes were reconstructed using the hybrid and ONT methods, and both recovered nearly fourfold more viral genomes than the Illumina-only approach. While yielding fewer MAGs, the ONT-only approach generated MAGs with a high probability of containing rRNA genes, 3× higher than either of the other methods. Of the shared MAGs recovered from each method, the ONT-only approach generated the longest and least fragmented MAGs, while the hybrid approach yielded the most complete. This work provides quantitative data to inform a cost-benefit analysis of the decision to supplement shotgun metagenomic projects with long reads towards the goal of recovering genomes from environmentally abundant groups.}, } @article {pmid32758760, year = {2020}, author = {Cini, A and Meriggi, N and Bacci, G and Cappa, F and Vitali, F and Cavalieri, D and Cervo, R}, title = {Gut microbial composition in different castes and developmental stages of the invasive hornet Vespa velutina nigrithorax.}, journal = {The Science of the total environment}, volume = {745}, number = {}, pages = {140873}, doi = {10.1016/j.scitotenv.2020.140873}, pmid = {32758760}, issn = {1879-1026}, mesh = {Animals ; Ecosystem ; Europe ; *Gastrointestinal Microbiome ; Introduced Species ; *Wasps ; }, abstract = {Social insects are successful animal invaders. Their survival and success, and in some cases also their impact on invaded ecosystem functioning, is often mediated by symbiosis with microorganisms. Here, we report a comprehensive comparative characterization of the gut microbial communities of different castes and developmental stages of the invasive hornet Vespa velutina nigrithorax. The species recently colonized Europe, becoming a high ecological and economic concern, as it threatens pollinator survival and competes with native hornet species. We used targeted meta-genomics to describe the yeasts and bacteria gut communities of individuals of different reproductive phenotypes (workers and future queens), life stages (larvae, newly emerged individuals and adults) and colony non-living samples (nest paper and larval faeces). Bacilli, Gammaproteobacteria, Actinobacteria, Alphaproteobacteria were the most abundant classes of bacteria, and Saccharomycetes, Dothideomycetes, Tremellomycetes and Eurotiomycetes were the most represented yeast classes. We found that the microbial compositions significantly differ across developmental stages and castes, with yeast and bacterial communities switching in frequency and abundance during ontogeny and according to reproductive phenotype. Moreover, the gut microbial communities poorly mirror those found in the nest, suggesting that hornets possess a specific microbial signature. Our results provide the first metagenomic resource of the microbiome of V. velutina in Europe and suggest the importance of considering life stages, reproductive phenotypes and nest influence in order to obtain a comprehensive picture of social insect microbial communities.}, } @article {pmid32758682, year = {2021}, author = {Andersen, TO and Kunath, BJ and Hagen, LH and Arntzen, MØ and Pope, PB}, title = {Rumen metaproteomics: Closer to linking rumen microbial function to animal productivity traits.}, journal = {Methods (San Diego, Calif.)}, volume = {186}, number = {}, pages = {42-51}, doi = {10.1016/j.ymeth.2020.07.011}, pmid = {32758682}, issn = {1095-9130}, mesh = {Animal Husbandry/*methods ; Animals ; Gastrointestinal Microbiome/*physiology ; Host Microbial Interactions/physiology ; Livestock/microbiology/physiology ; Metagenome ; Metagenomics/*methods ; Proteomics/*methods ; Quantitative Trait Loci/physiology ; Rumen/*microbiology ; Ruminants/microbiology/physiology ; }, abstract = {The rumen microbiome constitutes a dense and complex mixture of anaerobic bacteria, archaea, protozoa, virus and fungi. Collectively, rumen microbial populations interact closely in order to degrade and ferment complex plant material into nutrients for host metabolism, a process which also produces other by-products, such as methane gas. Our understanding of the rumen microbiome and its functions are of both scientific and industrial interest, as the metabolic functions are connected to animal health and nutrition, but at the same time contribute significantly to global greenhouse gas emissions. While many of the major microbial members of the rumen microbiome are acknowledged, advances in modern culture-independent meta-omic techniques, such as metaproteomics, enable deep exploration into active microbial populations involved in essential rumen metabolic functions. Meaningful and accurate metaproteomic analyses are highly dependent on representative samples, precise protein extraction and fractionation, as well as a comprehensive and high-quality protein sequence database that enables precise protein identification and quantification. This review focuses on the application of rumen metaproteomics, and its potential towards understanding the complex rumen microbiome and its metabolic functions. We present and discuss current methods in sample handling, protein extraction and data analysis for rumen metaproteomics, and finally emphasize the potential of (meta)genome-integrated metaproteomics for accurate reconstruction of active microbial populations in the rumen.}, } @article {pmid32758003, year = {2020}, author = {Elsaeed, E and Enany, S and Hanora, A and Fahmy, N}, title = {Comparative Metagenomic Screening of Aromatic Hydrocarbon Degradation and Secondary Metabolite-Producing Genes in the Red Sea, the Suez Canal, and the Mediterranean Sea.}, journal = {Omics : a journal of integrative biology}, volume = {24}, number = {9}, pages = {541-550}, doi = {10.1089/omi.2020.0070}, pmid = {32758003}, issn = {1557-8100}, mesh = {Aquatic Organisms/genetics/metabolism ; Databases, Genetic ; Ecosystem ; Hydrocarbons, Aromatic/*metabolism ; Indian Ocean ; Mediterranean Sea ; *Metagenome ; *Metagenomics/methods/standards ; *Microbiota/genetics ; Seawater ; *Secondary Metabolism ; *Water Microbiology ; Water Pollution ; }, abstract = {Marine and ecosystem pollution due to oil spills can be addressed by identifying the aromatic hydrocarbon (HC)-degrading microorganisms and their responsible genes for biodegradation. Moreover, screening for genes coding for secondary metabolites is invaluable for drug discovery. We report here, the first metagenomic study investigating the shotgun metagenome of the Suez Canal water sampled at Ismailia city concerning its aromatic HC degradation potential in comparison to the seawater sampled at Halayeb city at the Red Sea and Sallum city at the Mediterranean Sea. Moreover, for an in-depth understanding of marine biotechnology applications, we screened for the polyketide synthases (PKSs) and nonribosomal peptide synthetase (NRPS) domains in those three metagenomes. By mapping against functional protein databases, we found that 13, 6, and 3 gene classes from the SEED database; 2, 1, and 3 gene classes from the EgGNOG; and 5, 4, and 2 genes from the InterPro2GO database were identified to be differentially abundant among Halayeb, Ismailia, and Sallum metagenomes, respectively. Also, Halayeb metagenome in the Red Sea reported the highest number of PKS domains showing higher potential in secondary metabolite production in addition to the oil degradation potential.}, } @article {pmid32756645, year = {2020}, author = {Guo, Z and Hu, B and Han, H and Lei, Z and Shimizu, K and Zhang, L and Zhang, Z}, title = {Metagenomic insights into the effects of nanobubble water on the composition of gut microbiota in mice.}, journal = {Food & function}, volume = {11}, number = {8}, pages = {7175-7182}, doi = {10.1039/d0fo01592j}, pmid = {32756645}, issn = {2042-650X}, mesh = {Animals ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Hydrogen/*pharmacology ; Hydrogen-Ion Concentration ; Male ; Metagenomics ; Mice ; Mice, Inbred BALB C ; Microbubbles ; Nitrogen/*pharmacology ; RNA, Ribosomal, 16S/analysis ; Water/*chemistry/*pharmacology ; }, abstract = {The particular physicochemical and biological properties of nanobubbles (NBs) have prompted many researchers to conduct an in-depth study on their potential application in various fields. This study aims to investigate the effects of nanobubble water (NBW) on the community structure of the gut microbiota in mice. In this study, supplementation with nitrogen NBW (SD-N2 group), hydrogen NBW (SD-H2 group) and deionized water (SD-C group) to a standard diet of mice was performed for five weeks. The composition of fecal microbiota was analyzed by using 16S rRNA gene sequencing. Compared with the SD-C group, the species diversity of the fecal microbiota in mice in NBW groups was significantly increased. At the genus level, supplementation with nitrogen NBW to mice significantly increased the relative abundance of two beneficial genera Clostridium and Coprococcus (mean growth 6.3 times and 9.7 times, respectively), while supplementation with hydrogen NBW significantly decreased the relative abundance of two pathogenic genera Mucispirillum and Helicobacter (mean reduction rate 86% and 60%, respectively). These results demonstrate that supplementation with NBW might optimize the composition of gut microbiota in mice.}, } @article {pmid32755736, year = {2020}, author = {Guo, G and Hao, J and Tian, F and Liu, C and Ding, K and Xu, J and Zhou, W and Guan, Z}, title = {Decolorization and detoxification of azo dye by halo-alkaliphilic bacterial consortium: Systematic investigations of performance, pathway and metagenome.}, journal = {Ecotoxicology and environmental safety}, volume = {204}, number = {}, pages = {111073}, doi = {10.1016/j.ecoenv.2020.111073}, pmid = {32755736}, issn = {1090-2414}, mesh = {Azo Compounds/metabolism/*toxicity ; Biodegradation, Environmental ; Carbon/metabolism ; Coloring Agents/metabolism/*toxicity ; *Metagenome ; Microbiota/*drug effects/genetics ; Salinity ; Temperature ; Textile Industry ; *Wastewater/chemistry/microbiology ; Water Pollutants, Chemical/metabolism/*toxicity ; Water Purification/*methods ; }, abstract = {The high pH and salinity of textile wastewater is a major hindrance to azo dye decolorization. In this study, a mixed bacterial consortium ZW1 was enriched under saline (10% salinity) and alkaline (pH 10.0) conditions to decolorize Methanil Yellow G (MY-G). Consortium ZW1 was mainly composed of Halomonas (49.8%), Marinobacter (30.7%) and Clostridiisalibacter (19.2%). The effects of physicochemical factors were systematically investigated, along with the degradation pathway and metagenome analysis. The co-carbon source was found to be necessary, and the addition of yeast extract led to 93.3% decolorization of 100 mg/L MY-G within 16 h (compared with 1.12% for control). The optimum pH, salinity, temperature and initial dye concentration were 8.0, 5-10%, 40 °C and 100 mg/L, respectively. The typical dye-related degradation enzymes were most effective at 10% salinity. Consortium ZW1 was also able to differentially decolorize five other direct and acidic dyes in a short period. Phototoxicity tests revealed the detoxification of MY-G degradation products. Combining UV-vis, FTIR and GC-MS detection, the MY-G degradation pathway by consortium ZW1 was proposed. Furthermore, metagenomic approach was used to elucidate the functional potential of genes in MY-G biodegradation. These results signify the broad potential application of halo-alkaliphilic consortia in the bioremediation of dyeing wastewater.}, } @article {pmid32755703, year = {2020}, author = {Zhang, X and Zhao, S and He, Y and Zheng, N and Yan, X and Wang, J}, title = {Substitution of residues in UreG to investigate UreE interactions and nickel binding in a predominant urease gene cluster from the ruminal metagenome.}, journal = {International journal of biological macromolecules}, volume = {161}, number = {}, pages = {1591-1601}, doi = {10.1016/j.ijbiomac.2020.07.260}, pmid = {32755703}, issn = {1879-0003}, mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; Gene Expression ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; *Multigene Family ; Nickel/*chemistry ; Phylogeny ; Protein Binding ; Recombinant Proteins ; Ruminants/*microbiology ; Urease/*chemistry/genetics ; }, abstract = {Microbial ureases catalyze the hydrolysis of urea to ammonia, and inhibition of these enzymes in rumen has the potential to improve urea utilization efficiency and reduce urinary nitrogen excretion. Urease activity is catalyzed by a protein complex encoded by a gene cluster, and its accessory proteins (especially UreE and UreG) play important roles in transferring nickel to the active site for urease maturation. In this study, a predominant urease gene cluster (5290 bp) from the ruminal microbial metagenome was identified. Isothermal titration calorimetry (ITC) and analytical ultracentrifugation (AUC) analyses showed that the reaction of identified UreE with UreG was endothermic, and was dominated by a hydrophobic interaction, in which each UreE dimer bound 2 M equivalents of UreG monomer to form a UreE2-2UreG complex. Mutagenesis analyses showed that the UreG residues Glu-23, Asp-41, Glu-46, Glu-66, Cys-70, His-72, Asp-78, and Asp-118 were involved in the GTPase activity of UreG. Furthermore, variants of Cys-70 and His-72 involved in CPH motif of UreG, as well as the nearby Glu-66 and Asp-78, not only prevented interactions with UreE, but also prevented nickel binding. These data provide additional information regarding UreG residues that may be targeted for the design of new urease inhibitors.}, } @article {pmid32755308, year = {2020}, author = {Edwards, PT and Kashyap, PC and Preidis, GA}, title = {Microbiota on biotics: probiotics, prebiotics, and synbiotics to optimize growth and metabolism.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {319}, number = {3}, pages = {G382-G390}, pmid = {32755308}, issn = {1522-1547}, support = {K08 DK113114/DK/NIDDK NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 DK114007/DK/NIDDK NIH HHS/United States ; T32 DK007664/DK/NIDDK NIH HHS/United States ; }, mesh = {Digestive System Physiological Phenomena/*genetics ; Gastrointestinal Diseases/prevention & control ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/growth & development/*physiology ; Genomics ; Humans ; *Prebiotics ; Probiotics/*therapeutic use ; *Synbiotics ; }, abstract = {The early stages of the metagenomics era produced countless observational studies linking various human diseases to alterations in the gut microbiota. Only recently have we begun to decipher the causal roles that gut microbes play in many of these conditions. Despite an incomplete understanding of how gut microbes influence pathophysiology, clinical trials have tested empirically numerous microbiota-targeting therapies to prevent or treat disease. Unsurprisingly, these trials have yielded mixed results. Nonetheless, the consumer market for probiotics, prebiotics, and synbiotics continues to grow. This theme paper highlights recent discoveries of mechanisms underlying diet-microbial-host interactions as they pertain to growth and metabolism and discusses current and future applications of microbiota-targeting therapies in the context of child malnutrition as well as obesity and its metabolic comorbidities, including nonalcoholic fatty liver disease and cardiovascular disease. We also highlight current challenges and identify future directions to facilitate a more efficient and direct path to clinical impact.}, } @article {pmid32754885, year = {2020}, author = {Li, S and Zhang, Y and Yin, S and Wang, X and Liu, T and Deng, Z}, title = {Analysis of microbial community structure and degradation of ammonia nitrogen in groundwater in cold regions.}, journal = {Environmental science and pollution research international}, volume = {27}, number = {35}, pages = {44137-44147}, pmid = {32754885}, issn = {1614-7499}, support = {2014ZX07201010//Major Science and Technology Program for Water Pollution Control and Treatment/ ; }, mesh = {Ammonia ; China ; *Groundwater ; *Microbiota ; Nitrates/analysis ; Nitrogen/analysis ; *Water Pollutants, Chemical/analysis ; }, abstract = {Nitrogen pollution exceeding the standard because of intensive farming and cropping systems has been a widespread problem in Northeast China. This study investigated the characteristics of functional microorganisms in groundwater in the Bang River farming area. Metagenomic sequencing was used to analyze microbial community structures and Canoco was applied to reveal the response relationship between the microbial community and water environmental factors and to identify changes in the microbial population in response to the addition of electronic donors NH4[+]-N, NO2[-]-N, and NO3[-]-N. The results showed that the dominant microorganisms in groundwater belong to the genera Exiguobacterium, Citrobacter, Acinetobacter, and Pseudomonas, which accounted for more than 40% of the total microbes in the study area. When combined with the results of a water chemical factor test, the dominant bacteria were found to be correlated with Fe[2+], Mn[2+], NH4[+], NO3[-], NO2[-], HCO3[-], DOC, and pH in the water. However, the microbial population changed after the addition of the electron donor, with the genera Pseudomonas, Serratia, Enterobacter, Azomonas, and Ewingella accounting for 97.06% of the total sequences. Indigenous nitrogen-degrading bacteria suitable for low temperature, low oxygen, and oligotrophic groundwater were screened out. The total removal efficiency of NH4[+]-N, NO2[-]-N, and NO3[-]-N in 120 h was 90.83%, 75.04%, and 73.35%, respectively. According to the experimental results, the degradation reaction kinetics followed a pseudo-second-order equation. The results presented herein provide an important scientific basis for the microbial remediation of groundwater contaminated by ammonia.}, } @article {pmid32750076, year = {2020}, author = {Lee, SJ and Cho, S and La, TM and Lee, HJ and Lee, JB and Park, SY and Song, CS and Choi, IS and Lee, SW}, title = {Comparison of microbiota in the cloaca, colon, and magnum of layer chicken.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0237108}, pmid = {32750076}, issn = {1932-6203}, mesh = {Animals ; Chickens/*microbiology ; Cloaca/*microbiology ; Colon/*microbiology ; Female ; Flavobacterium/genetics/pathogenicity ; *Gastrointestinal Microbiome ; Lactobacillus/genetics/pathogenicity ; Metagenome ; Oviducts/*microbiology ; Pseudomonas/genetics/pathogenicity ; }, abstract = {Anatomically terminal parts of the urinary, reproductive, and digestive systems of birds all connect to the cloaca. As the feces drain through the cloaca in chickens, the cloacal bacteria were previously believed to represent those of the digestive system. To investigate similarities between the cloacal microbiota and the microbiota of the digestive and reproductive systems, microbiota inhabiting the colon, cloaca, and magnum, which is a portion of the chicken oviduct of 34-week-old, specific-pathogen-free hens were analyzed using a 16S rRNA metagenomic approach using the Ion torrent sequencer and the Qiime2 bioinformatics platform. Beta diversity via unweighted and weighted unifrac analyses revealed that the cloacal microbiota was significantly different from those in the colon and the magnum. Unweighted unifrac revealed that the cloacal microbiota was distal from the microbiota in the colon than from the microbiota in the magnum, whereas weighted unifrac revealed that the cloacal microbiota was located further away from the microbiota in the magnum than from the microbiota inhabiting the colon. Pseudomonas spp. were the most abundant in the cloaca, whereas Lactobacillus spp. and Flavobacterium spp. were the most abundant species in the colon and the magnum. The present results indicate that the cloaca contains a mixed population of bacteria, derived from the reproductive, urinary, and digestive systems, particularly in egg-laying hens. Therefore, sampling cloaca to study bacterial populations that inhabit the digestive system of chickens requires caution especially when applied to egg-laying hens. To further understand the physiological role of the microbiota in chicken cloaca, exploratory studies of the chicken's cloacal microbiota should be performed using chickens of different ages and types.}, } @article {pmid32749951, year = {2020}, author = {Manzari, C and Oranger, A and Fosso, B and Piancone, E and Pesole, G and D'Erchia, AM}, title = {Accurate quantification of bacterial abundance in metagenomic DNAs accounting for variable DNA integrity levels.}, journal = {Microbial genomics}, volume = {6}, number = {10}, pages = {}, pmid = {32749951}, issn = {2057-5858}, mesh = {Algorithms ; Bacteria/*classification/*genetics ; DNA, Bacterial/*genetics ; Metagenome/*genetics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The quantification of the total microbial content in metagenomic samples is critical for investigating the interplay between the microbiome and its host, as well as for assessing the accuracy and precision of the relative microbial composition which can be strongly biased in low microbial biomass samples. In the present study, we demonstrate that digital droplet PCR (ddPCR) can provide accurate quantification of the total copy number of the 16S rRNA gene, the gene usually exploited for assessing total bacterial abundance in metagenomic DNA samples. Notably, using DNA templates with different integrity levels, as measured by the DNA integrity number (DIN), we demonstrated that 16S rRNA copy number quantification is strongly affected by DNA quality and determined a precise correlation between quantification underestimation and DNA degradation levels. Therefore, we propose an input DNA mass correction, according to the observed DIN value, which could prevent inaccurate quantification of 16S copy number in degraded metagenomic DNAs. Our results highlight that a preliminary evaluation of the metagenomic DNA integrity should be considered before performing metagenomic analyses of different samples, both for the assessment of the reliability of observed differential abundances in different conditions and to obtain significant functional insights.}, } @article {pmid32747678, year = {2020}, author = {Zeng, Q and Shen, J and Chen, K and Zhou, J and Liao, Q and Lu, K and Yuan, J and Bi, F}, title = {The alteration of gut microbiome and metabolism in amyotrophic lateral sclerosis patients.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12998}, pmid = {32747678}, issn = {2045-2322}, mesh = {Adult ; Amyotrophic Lateral Sclerosis/*metabolism/*microbiology ; Bacteroidetes/genetics ; Case-Control Studies ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease accompanied with severe paralysis or even death, while the pathogenesis of ALS is still unclear and no effective therapy exists. The accumulating evidence has indicated the association between gut microbiota and various neurological diseases. Thus, to explore the potential role of gut microbiome in ALS, 20 patients diagnosed with probable or definite ALS and 20 healthy controls were enrolled and their fecal excrements were collected. The analysis of fecal community diversity with 16S rDNA sequencing showed an obvious change in microbial structure of ALS patients, where Bacteroidetes at the phylum level and several microbes at the genus level were up-regulated, while Firmicutes at the phylum level and Megamonas at the genus level were down-regulated compared to healthy controls. Additionally, decreased gene function associated with metabolic pathways was observed in ALS patients. The metagenomics further demonstrated the discrepancies in microflora at the species level and relevant metabolites thereof were also revealed when combined with metabolomics. In conclusion, the altered composition of the gut microbiota and metabolic products in ALS patients provided deeper insights into the pathogenesis of ALS, and these biomarkers might be established as potential therapeutic targets which deserve further exploration.}, } @article {pmid32747272, year = {2020}, author = {Zheng, B and Wang, T and Wang, H and Chen, L and Zhou, Z}, title = {Studies on nutritional intervention of rice starch- oleic acid complex (resistant starch type V) in rats fed by high-fat diet.}, journal = {Carbohydrate polymers}, volume = {246}, number = {}, pages = {116637}, doi = {10.1016/j.carbpol.2020.116637}, pmid = {32747272}, issn = {1879-1344}, mesh = {Actinobacteria/classification/drug effects/genetics/isolation & purification ; Animals ; Bacteroidetes/classification/drug effects/genetics/isolation & purification ; Butyrates/metabolism ; Cholesterol, LDL/metabolism ; DNA, Bacterial/*genetics ; Diet, High-Fat/adverse effects ; Firmicutes/classification/drug effects/genetics/isolation & purification ; Gastrointestinal Microbiome/*drug effects/genetics ; Gene Expression ; Glutathione Peroxidase/genetics/metabolism ; Lipid Metabolism/drug effects/genetics ; Liver/drug effects/metabolism ; Male ; Obesity/etiology/genetics/microbiology/*prevention & control ; Oleic Acid/*administration & dosage ; Phylogeny ; Proteobacteria/classification/drug effects/genetics/isolation & purification ; Rats ; Rats, Sprague-Dawley ; Resistant Starch/*administration & dosage ; Superoxide Dismutase/genetics/metabolism ; }, abstract = {In this study, rice starch-oleic acid complex with well-controlled digestibility was chosen as a supplementary diet for rats fed with high fat diet. Our results demonstrated that rice starch-oleic acid complex supplementation significantly decreased body weight, improved serum lipid profiles, hepatic metabolism and altered the composition of gut microbiota of rats, which might be related to the higher resistant starch (RS) level. Interestingly, rice starch-oleic acid complex supplementation contributed to the proliferation and growth of butyrate-producing bacteria. The Spearman's correlation analysis revealed that the genus Turicibacter and Romboutsia genus were positively correlated to HDL-c and SOD level. Meanwhile, based on the metagenomic data, Bifidobacteria genus might be a main primary degrader after rice starch-oleic acid complex intake, which was associated with the changes of key starch-degradation enzymes. Overall, our results provided basic data for the rational design of rice starch-based foods with nutritional functions and physiological benefits.}, } @article {pmid32747219, year = {2020}, author = {Yu, D and Shu, XO and Howard, EF and Long, J and English, WJ and Flynn, CR}, title = {Fecal metagenomics and metabolomics reveal gut microbial changes after bariatric surgery.}, journal = {Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery}, volume = {16}, number = {11}, pages = {1772-1782}, pmid = {32747219}, issn = {1878-7533}, support = {P30 DK058404/DK/NIDDK NIH HHS/United States ; R01 DK105847/DK/NIDDK NIH HHS/United States ; }, mesh = {*Bariatric Surgery ; Female ; *Gastric Bypass ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolomics ; Metagenomics ; Middle Aged ; Pilot Projects ; }, abstract = {BACKGROUND: Evidence from longitudinal patient studies regarding gut microbial changes after bariatric surgery is limited.

OBJECTIVE: To examine intraindividual changes in fecal microbiome and metabolites among patients undergoing Roux-en-Y gastric bypass or vertical sleeve gastrectomy.

SETTING: Observational study.

METHODS: Twenty patients were enrolled and provided stool samples before and 1 week, 1 month, and/or 3 months after surgery. Shallow shotgun metagenomics and untargeted fecal metabolomics were performed. Zero-inflated generalized additive models and linear mixed models were applied to identify fecal microbiome and metabolites changes, with adjustment for potential confounders and correction for multiple testing.

RESULTS: We enrolled 16 women and 4 men, including 16 white and 4 black participants (median age = 45 years; presurgery body mass index = 47.7 kg/m[2]). Ten patients had Roux-en-Y gastric bypass, 10 had vertical sleeve gastrectomy, and 14 patients provided postsurgery stool samples. Of 47 samples, median sequencing depth was 6.3 million reads and 1073 metabolites were identified. Microbiome alpha-diversity increased after surgery, especially at 3 months. Significant genus-level changes included increases in Odoribacter, Streptococcus, Anaerotruncus, Alistipes, Klebsiella, and Bifidobacterium, while decreases in Bacteroides, Coprocosccus, Dorea, and Faecalibacterium. Large increases in Streptococcus, Akkermansia, and Prevotella were observed at 3 months. Beta-diversity and fecal metabolites were also changed, including reduced caffeine metabolites, indoles, and butyrate.

CONCLUSIONS: Despite small sample size and missing repeated samples in some participants, our pilot study showed significant postsurgery changes in fecal microbiome and metabolites among bariatric surgery patients. Future large-scale, longitudinal studies are warranted to investigate gut microbial changes and their associations with metabolic outcomes after bariatric surgery.}, } @article {pmid32746888, year = {2020}, author = {Calgaro, M and Romualdi, C and Waldron, L and Risso, D and Vitulo, N}, title = {Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {191}, pmid = {32746888}, issn = {1474-760X}, support = {R01 CA230551/CA/NCI NIH HHS/United States ; U01 CA230551/CA/NCI NIH HHS/United States ; 1U01CA230551/CA/NCI NIH HHS/United States ; 2U24CA180996/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Metagenomics/*methods ; *Microbiota ; Sequence Analysis, RNA ; Single-Cell Analysis ; *Statistics as Topic ; }, abstract = {BACKGROUND: The correct identification of differentially abundant microbial taxa between experimental conditions is a methodological and computational challenge. Recent work has produced methods to deal with the high sparsity and compositionality characteristic of microbiome data, but independent benchmarks comparing these to alternatives developed for RNA-seq data analysis are lacking.

RESULTS: We compare methods developed for single-cell and bulk RNA-seq, and specifically for microbiome data, in terms of suitability of distributional assumptions, ability to control false discoveries, concordance, power, and correct identification of differentially abundant genera. We benchmark these methods using 100 manually curated datasets from 16S and whole metagenome shotgun sequencing.

CONCLUSIONS: The multivariate and compositional methods developed specifically for microbiome analysis did not outperform univariate methods developed for differential expression analysis of RNA-seq data. We recommend a careful exploratory data analysis prior to application of any inferential model and we present a framework to help scientists make an informed choice of analysis methods in a dataset-specific manner.}, } @article {pmid32746696, year = {2021}, author = {Baker, BJ and Appler, KE and Gong, X}, title = {New Microbial Biodiversity in Marine Sediments.}, journal = {Annual review of marine science}, volume = {13}, number = {}, pages = {161-175}, doi = {10.1146/annurev-marine-032020-014552}, pmid = {32746696}, issn = {1941-0611}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Biodiversity ; Datasets as Topic ; Geologic Sediments/*microbiology ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; Seawater/*microbiology ; }, abstract = {Microbes in marine sediments represent a large portion of the biosphere, and resolving their ecology is crucial for understanding global ocean processes. Single-gene diversity surveys have revealed several uncultured lineages that are widespread in ocean sediments and whose ecological roles are unknown, and advancements in the computational analysis of increasingly large genomic data sets have made it possible to reconstruct individual genomes from complex microbial communities. Using these metagenomic approaches to characterize sediments is transforming our view of microbial communities on the ocean floor and the biodiversity of the planet. In recent years, marine sediments have been a prominent source of new lineages in the tree of life. The incorporation of these lineages into existing phylogenies has revealed that many belong to distinct phyla, including archaeal phyla that are advancing our understanding of the origins of cellular complexity and eukaryotes. Detailed comparisons of the metabolic potentials of these new lineages have made it clear that uncultured bacteria and archaea are capable of mediating key previously undescribed steps in carbon and nutrient cycling.}, } @article {pmid32745665, year = {2020}, author = {Guindo, CO and Drancourt, M and Grine, G}, title = {Digestive tract methanodrome: Physiological roles of human microbiota-associated methanogens.}, journal = {Microbial pathogenesis}, volume = {149}, number = {}, pages = {104425}, doi = {10.1016/j.micpath.2020.104425}, pmid = {32745665}, issn = {1096-1208}, mesh = {Dysbiosis ; Gastrointestinal Tract ; Humans ; In Situ Hybridization, Fluorescence ; Metagenomics ; *Microbiota ; }, abstract = {Methanogens are the archaea most commonly found in humans, in particular in the digestive tract and are an integral part of the digestive microbiota. They are present in humans from the earliest moments of life and represent the only known source of methane production to date. They are notably detected in humans by microscopy, fluorescent in situ hybridization, molecular biology including PCR-sequencing, metagenomics, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and culture. Methanogens present in the human digestive tract play major roles, in particular the use of hydrogen from the fermentation products of bacteria, thus promoting digestion. They are also involved in the transformation of heavy metals and in the use of trimethylamine produced by intestinal bacteria, thus preventing major health problems, in particular cardiovascular diseases. Several pieces of evidence suggest their close physical contacts with bacteria support symbiotic metabolism. Their imbalance during dysbiosis is associated with many pathologies in humans, particularly digestive tract diseases such as Crohn's disease, ulcerative colitis, diverticulosis, inflammatory bowel disease, irritable bowel syndrome, colonic polyposis, and colorectal cancer. There is a huge deficit of knowledge and partially contradictory information concerning human methanogens, so much remains to be done to fully understand their physiological role in humans. It is necessary to develop new methods for the identification and culture of methanogens from clinical samples. This will permit to isolate new methanogens species as well as their phenotypic characterization, to explore their genome by sequencing and to study the population dynamics of methanogens by specifying in particular their exact role within the complex flora associated with the mucous microbiota of human.}, } @article {pmid32745120, year = {2020}, author = {Hilderbrand, RH and Keller, SR and Laperriere, SM and Santoro, AE and Cessna, J and Trott, R}, title = {Microbial communities can predict the ecological condition of headwater streams.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0236932}, pmid = {32745120}, issn = {1932-6203}, mesh = {Archaea/classification/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; Ecological Parameter Monitoring/*methods ; Ecosystem ; Environmental Monitoring/methods ; Geologic Sediments/microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; }, abstract = {Humanity's reliance on clean water and the ecosystem services provided makes identifying efficient and effective ways to assess the ecological condition of streams ever more important. We used high throughput sequencing of the 16S rRNA region to explore relationships between stream microbial communities, environmental attributes, and assessments of stream ecological condition. Bacteria and archaea in microbial community samples collected from the water column and from stream sediments during spring and summer were used to replicate standard assessments of ecological condition performed with benthic macroinvertebrate collections via the Benthic Index of Biotic Integrity (BIBI). Microbe-based condition assessments were generated at different levels of taxonomic resolution from phylum to OTU (Operational Taxonomic Units) in order to understand appropriate levels of taxonomic aggregation. Stream sediment microbial communities from both spring and summer were much better than the water column at replicating BIBI condition assessment results. Accuracies were as high as 100% on training data used to build the models and up to 80% on validation data used to assess predictions. Assessments using all OTUs usually had the highest accuracy on training data, but were lower on validation data due to overfitting. In contrast, assessments at the order-level had similar performance accuracy for validation data, and a reduced subset of orders also performed well, suggesting the method could be generalized to other watersheds. Subsets of the important orders responded similarly to environmental gradients compared to the entire community, where strong shifts in community structure occurred for known aquatic stressors such as pH, dissolved organic carbon, and nitrate nitrogen. The results suggest the stream microbes may be useful for assessing the ecological condition of streams and especially useful for stream restorations where many eukaryotic taxa have been eliminated due to prior degradation and are unable to recolonize.}, } @article {pmid32741188, year = {2020}, author = {Shao, DT and Li, MJ and Chen, R and Wei, WW}, title = {[Progress in research of influencing factors of oral microbiome and association between oral microbiome and upper gastrointestinal cancer].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {41}, number = {7}, pages = {1160-1164}, doi = {10.3760/cma.j.cn112338-20190725-00549}, pmid = {32741188}, issn = {0254-6450}, support = {2016YFC09 01400//National Key Research and Development Program of China/ ; 2016-I2M-3-001//Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences/ ; 3332019139//Fundamental Research Funds for the Central Universities of Peking Union Medical College/ ; 2018PT32012//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; }, mesh = {Biomedical Research/*trends ; Gastrointestinal Neoplasms/*epidemiology ; Humans ; *Microbiota ; Mouth/*microbiology ; Risk Factors ; }, abstract = {The composition of human oral microorganism is numerous and complex and is easily affected by many factors. With the development of metagenomic technology, the important role of oral microbiome in the development of tumor has attracted extensive attention. A literature retrieval was conducted through PubMed, Embase, CNKI and WanFang database for an analysis on the characteristics of oral bacteria and its association with oral cancer, esophageal cancer and gastric cancer. The results indicated that oral microbiome can be influenced by age, gender, race, and lifestyle. Specific oral bacteria were associated with high risk of upper gastrointestinal cancer, indicating a potential role of oral microbiota to be the biomarker for upper gastrointestinal cancer. This paper summarizes the progress in the research of the association between oral microbiome and upper gastrointestinal cancer, showing a new direction for the exploration of microbiological etiology of upper gastrointestinal cancer and providing scientific evidence for the optimization of early detection and treatment of upper gastrointestinal cancer.}, } @article {pmid32738764, year = {2020}, author = {Luiken, REC and Van Gompel, L and Bossers, A and Munk, P and Joosten, P and Hansen, RB and Knudsen, BE and García-Cobos, S and Dewulf, J and Aarestrup, FM and Wagenaar, JA and Smit, LAM and Mevius, DJ and Heederik, DJJ and Schmitt, H and , }, title = {Farm dust resistomes and bacterial microbiomes in European poultry and pig farms.}, journal = {Environment international}, volume = {143}, number = {}, pages = {105971}, doi = {10.1016/j.envint.2020.105971}, pmid = {32738764}, issn = {1873-6750}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Chickens ; Drug Resistance, Bacterial ; Dust ; Europe ; Farms ; *Microbiota ; *Poultry ; Swine ; }, abstract = {BACKGROUND: Livestock farms are a reservoir of antimicrobial resistant bacteria from feces. Airborne dust-bound bacteria can spread across the barn and to the outdoor environment. Therefore, exposure to farm dust may be of concern for animals, farmers and neighboring residents. Although dust is a potential route of transmission, little is known about the resistome and bacterial microbiome of farm dust.

OBJECTIVES: We describe the resistome and bacterial microbiome of pig and poultry farm dust and their relation with animal feces resistomes and bacterial microbiomes, and on-farm antimicrobial usage (AMU). In addition, the relation between dust and farmers' stool resistomes was explored.

METHODS: In the EFFORT-study, resistomes and bacterial microbiomes of indoor farm dust collected on Electrostatic Dust fall Collectors (EDCs), and animal feces of 35 conventional broiler and 44 farrow-to-finish pig farms from nine European countries were determined by shotgun metagenomic analysis. The analysis also included 79 stool samples from farmers working or living at 12 broiler and 19 pig farms and 46 human controls. Relative abundance of and variation in resistome and bacterial composition of farm dust was described and compared to animal feces and farmers' stool.

RESULTS: The farm dust resistome contained a large variety of antimicrobial resistance genes (ARGs); more than the animal fecal resistome. For both poultry and pigs, composition of dust resistomes finds (partly) its origin in animal feces as dust resistomes correlated significantly with fecal resistomes. The dust bacterial microbiome also correlated significantly with the dust resistome composition. A positive association between AMU in animals on the farm and the total abundance of the dust resistome was found. Occupational exposure to pig farm dust or animal feces may contribute to farmers' resistomes, however no major shifts in farmers resistome towards feces or dust resistomes were found in this study.

CONCLUSION: Poultry and pig farm dust resistomes are rich and abundant and associated with the fecal resistome of the animals and the dust bacterial microbiome.}, } @article {pmid32738030, year = {2020}, author = {Yuan, Z and Ye, X and Zhu, L and Zhang, N and An, Z and Zheng, WJ}, title = {Virome assembly and annotation in brain tissue based on next-generation sequencing.}, journal = {Cancer medicine}, volume = {9}, number = {18}, pages = {6776-6790}, pmid = {32738030}, issn = {2045-7634}, support = {R01 AG066749/AG/NIA NIH HHS/United States ; UL1 TR003167/TR/NCATS NIH HHS/United States ; }, mesh = {Brain/pathology/*virology ; Brain Neoplasms/pathology/*virology ; Case-Control Studies ; Contig Mapping ; Databases, Nucleic Acid ; Glioblastoma/pathology/*virology ; *High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; Picornaviridae/*genetics ; RNA, Viral/genetics ; RNA-Seq ; Retroviridae/*genetics ; Virome/*genetics ; }, abstract = {The glioblastoma multiforme (GBM) is one of the deadliest tumors. It has been speculated that virus plays a role in GBM but the evidences are controversy. Published researches are mainly limited to studies on the presence of human cytomegalovirus (HCMV) in GBM. No comprehensive assessment of the brain virome, the collection of viral material in the brain, based on recently sequenced data has been performed. Here, we characterized the virome from 111 GBM samples and 57 normal brain samples from eight projects in the SRA database by a tested and comprehensive assembly approach. The annotation of the assembled contigs showed that most viral sequences in the brain belong to the viral family Retroviridae. In some GBM samples, we also detected full genome sequence of a novel picornavirus recently discovered in invertebrates. Unlike previous reports, our study did not detect herpes virus such as HCMV in GBM from the data we used. However, some contigs that cannot be annotated with any known genes exhibited antibody epitopes in their sequences. These findings provide several avenues for potential cancer therapy: the newly discovered picornavirus could be a starting point to engineer novel oncolytic virus; and the exhibited antibody epitopes could be a source to explore potential drug targets for immune cancer therapy. By characterizing the virosphere in GBM and normal brain at a global level, the results from this study strengthen the link between GBM and viral infection which warrants the further investigation.}, } @article {pmid32737543, year = {2020}, author = {Deb, S and Das, L and Das, SK}, title = {Composition and functional characterization of the gut microbiome of freshwater pufferfish (Tetraodon cutcutia).}, journal = {Archives of microbiology}, volume = {202}, number = {10}, pages = {2761-2770}, doi = {10.1007/s00203-020-01997-7}, pmid = {32737543}, issn = {1432-072X}, support = {D.O.No. BT/PR7661/AAQ/3/629/2013//Department of Biotechnology, Government of India/ ; }, mesh = {Animals ; Archaea/classification/*genetics/isolation & purification ; Bacteria/classification/*genetics/isolation & purification ; Carps/microbiology ; Firmicutes/classification/*genetics/isolation & purification ; Fresh Water/microbiology ; Gastrointestinal Microbiome/genetics ; Genome, Bacterial/genetics ; Metagenome/genetics ; Salmon/microbiology ; Tetraodontiformes/*microbiology ; }, abstract = {This study describes the community composition and functions of the gut microbiome of the freshwater omnivorous pufferfish based on metagenomic approach. Metagenome sequence data showed a dominance of the class Gammaproteobacteria followed by Fusobacteria, Actinobacteria, Anerolineae, Betaproteobacteria, Deinococci, Clostridia and Deltaproteobacteria. At the order level, the most abundant groups were Aeromonadales, Fusobacteriales, Enterobacterales, Synechococcales. The genus Aeromonas was the most predominant followed by Plesiomonas and Cetobacterium. Additionally, within the domain Archaea, class Methanomicrobia was most abundant followed by Hadesarchaea, Thermoplasmata, Candidatus Altiarchaeales, Candidatus Bathyarchaeota and Thermoprotei. The metabolic profile of the bacterial community exhibited a high prevalence of genes associated with core housekeeping functions, such as synthesis of cofactors, vitamins, prosthetic groups, pigments, amino acids and its derivatives, carbohydrate and protein metabolism. Comparative analysis with other fish gut microbiome showing similarity in protein metabolism with carnivorous Salmon and carbohydrate metabolism with herbivorous grass carp respectively. This study describes the bacterial community compositions are influenced by the trophic level.}, } @article {pmid32735609, year = {2020}, author = {Steinert, RE and Rehman, A and Souto Lima, EJ and Agamennone, V and Schuren, FHJ and Gero, D and Schreiner, P and Vonlanthen, R and Ismaeil, A and Tzafos, S and Hosa, H and Vetter, D and Misselwitz, B and Bueter, M}, title = {Roux-en-Y gastric bypass surgery changes fungal and bacterial microbiota in morbidly obese patients-A pilot study.}, journal = {PloS one}, volume = {15}, number = {7}, pages = {e0236936}, pmid = {32735609}, issn = {1932-6203}, mesh = {Adult ; Bacteria/classification/genetics/isolation & purification ; DNA, Intergenic ; Feces/microbiology ; Female ; Fungi/classification/genetics/isolation & purification ; *Gastric Bypass ; *Gastrointestinal Microbiome/genetics/physiology ; Genes, Bacterial ; Genes, Fungal ; Humans ; Male ; Metagenomics ; Microbiota ; Middle Aged ; Mycobiome ; *Obesity, Morbid/microbiology/surgery ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The Roux-en-Y gastric bypass (RYGB) remains the most effective treatment for morbidly obese patients to lower body weight and improve glycemic control. There is recent evidence that the mycobiome (fungal microbiome) can aggravate disease severity in a number of diseases including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS) and hepatitis; moreover, a dysbiotic fungal microbiota has been reported in the obese. We characterized fungal and bacterial microbial composition in fecal samples of 16 morbidly obese patients before and three months after RYGB surgery and compared with nine healthy controls. We found that RYGB surgery induced a clear alteration in structure and composition of the gut fungal and bacterial microbiota. Beta diversity analysis revealed significant differences in bacterial microbiota between obese patients before surgery and healthy controls (P < 0.005) and a significant, unidirectional shift in RYGB patients after surgery (P < 0.001 vs. before surgery). In contrast, there was no significant difference in fungal microbiota between groups but individually specific changes after RYGB surgery. Interestingly, RYGB surgery induced a significant reduction in fungal alpha diversity namely Chao1, Sobs, and Shannon diversity index (P<0.05, respectively) which contrasts the trend for uniform changes in bacteria towards increased richness and diversity post-surgery. We did not observe any inter-kingdom relations in RYGB patients but in the healthy control cohort and there were several correlations between fungi and bacteria and clinical parameters (P<0.05, respectively) that warrant further research. Our study identifies changes in intestinal fungal communities in RYGB patients that are distinct to changes in the bacterial microbiota.}, } @article {pmid32734321, year = {2020}, author = {Perlińska-Lenart, U and Piłsyk, S and Gryz, E and Turło, J and Hilszczańska, D and Kruszewska, JS}, title = {Identification of bacteria and fungi inhabiting fruiting bodies of Burgundy truffle (Tuber aestivum Vittad.).}, journal = {Archives of microbiology}, volume = {202}, number = {10}, pages = {2727-2738}, pmid = {32734321}, issn = {1432-072X}, support = {OR-271.3.5.2017//the State Forests National Forest Holding/ ; }, mesh = {Ascomycota/*physiology ; Bacillus/classification/genetics/*isolation & purification ; Basidiomycota/classification/genetics/*isolation & purification ; Bradyrhizobiaceae/classification/genetics/*isolation & purification ; DNA, Ribosomal/genetics ; Fruiting Bodies, Fungal/*physiology ; High-Throughput Nucleotide Sequencing ; Microbiota ; }, abstract = {Tuber species may be regarded as complex microhabitats hosting diverse microorganisms inside their fruiting bodies. Here, we investigated the structure of microbial communities inhabiting the gleba of wild growing (in stands) T. aestivum, using Illumina sequencing and culture-based methods. The two methods used in combination allowed to extract more information on complex microbiota of Tuber aestivum gleba. Analysis of the V3-V4 region of 16S rDNA identified nine phyla of bacteria present in the gleba of T. aestivum ascomata, mostly Proteobacteria from the family Bradyrhizobiaceae. Our results ideally match the earlier data for other Tuber species where the family Bradyrhizobiaceae was the most represented. The ITS1 region of fungal rDNA represented six alien fungal species belonging to three phyla. To complement the metagenomic analysis, cultivable fungi and bacteria were obtained from the gleba of the same T. aestivum fruiting bodies. The identified fungi mostly belong to the phylum Basidiomycota and same to Ascomycota. Analysis of cultivable bacteria revealed that all the specimens were colonized by different strains of Bacillus. Fungal community inhabiting T. aestivum fruiting bodies was never shown before.}, } @article {pmid32733435, year = {2020}, author = {Omura, S and Sato, F and Park, AM and Fujita, M and Khadka, S and Nakamura, Y and Katsuki, A and Nishio, K and Gavins, FNE and Tsunoda, I}, title = {Bioinformatics Analysis of Gut Microbiota and CNS Transcriptome in Virus-Induced Acute Myelitis and Chronic Inflammatory Demyelination; Potential Association of Distinct Bacteria With CNS IgA Upregulation.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {1138}, pmid = {32733435}, issn = {1664-3224}, support = {P20 GM103433/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cardiovirus Infections/complications/immunology ; Central Nervous System Viral Diseases/*immunology/*microbiology ; Chronic Disease ; Computational Biology ; Demyelinating Autoimmune Diseases, CNS/*immunology/*microbiology ; *Gastrointestinal Microbiome ; Immunoglobulin A/immunology ; Mice ; Myelitis/*immunology/*microbiology ; Neuromuscular Diseases/*immunology/*microbiology ; Theilovirus ; Transcriptome ; Up-Regulation ; }, abstract = {Virus infections have been associated with acute and chronic inflammatory central nervous system (CNS) diseases, e.g., acute flaccid myelitis (AFM) and multiple sclerosis (MS), where animal models support the pathogenic roles of viruses. In the spinal cord, Theiler's murine encephalomyelitis virus (TMEV) induces an AFM-like disease with gray matter inflammation during the acute phase, 1 week post infection (p.i.), and an MS-like disease with white matter inflammation during the chronic phase, 1 month p.i. Although gut microbiota has been proposed to affect immune responses contributing to pathological conditions in remote organs, including the brain pathophysiology, its precise role in neuroinflammatory diseases is unclear. We infected SJL/J mice with TMEV; harvested feces and spinal cords on days 4 (before onset), 7 (acute phase), and 35 (chronic phase) p.i.; and examined fecal microbiota by 16S rRNA sequencing and CNS transcriptome by RNA sequencing. Although TMEV infection neither decreased microbial diversity nor changed overall microbiome patterns, it increased abundance of individual bacterial genera Marvinbryantia on days 7 and 35 p.i. and Coprococcus on day 35 p.i., whose pattern-matching with CNS transcriptome showed strong correlations: Marvinbryantia with eight T-cell receptor (TCR) genes on day 7 and with seven immunoglobulin (Ig) genes on day 35 p.i.; and Coprococcus with gene expressions of not only TCRs and IgG/IgA, but also major histocompatibility complex (MHC) and complements. The high gene expression of IgA, a component of mucosal immunity, in the CNS was unexpected. However, we observed substantial IgA positive cells and deposition in the CNS, as well as a strong correlation between CNS IgA gene expression and serum anti-TMEV IgA titers. Here, changes in a small number of distinct gut bacteria, but not overall gut microbiota, could affect acute and chronic immune responses, causing AFM- and MS-like lesions in the CNS. Alternatively, activated immune responses would alter the composition of gut microbiota.}, } @article {pmid32731896, year = {2020}, author = {Zuo, K and Liu, X and Wang, P and Jiao, J and Han, C and Liu, Z and Yin, X and Li, J and Yang, X}, title = {Metagenomic data-mining reveals enrichment of trimethylamine-N-oxide synthesis in gut microbiome in atrial fibrillation patients.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {526}, pmid = {32731896}, issn = {1471-2164}, support = {81670214//National Natural Science Foundation of China/ ; 81500383//National Natural Science Foundation of China/ ; 81870308//National Natural Science Foundation of China/ ; 81970271//National Natural Science Foundation of China/ ; 7172080//Natural Science Foundation of Beijing Municipality/ ; QML20170303//Beijing Hospitals Authority Youth Programme/ ; CYMY-2017-03//1351 personnel training plan/ ; }, mesh = {*Atrial Fibrillation ; Data Mining ; *Gastrointestinal Microbiome ; Humans ; Methylamines ; Oxides ; }, abstract = {BACKGROUND: The gut bacteria-derived metabolite trimethylamine-N-oxide (TMAO) has been discussed in various cardiometabolic diseases. However, evidence characterizing the microbial population responsible for TMAO accumulation in patients with atrial fibrillation (AF), an increasingly prevalent arrhythmia, is yet lacking. In order to understand the key gut microorganisms that produce TMAO in AF, trimethylamine (TMA)-synthesis enzymes and metabolic pathways, as well as the potential TMA-producers in gut microbiome were assessed based on metagenomic data-mining in a northern Chinese cohort consisting of 50 non-AF controls and 50 patients with different types of AF.

RESULTS: Compared to the control subjects, AF patients showed a marked increase in the microbial genes underlying TMA formation in the gut, which included 12 potential TMA-synthesis functional orthologs and 1 module. The specific bacterial genes, including choline-TMA lyase, carnitine monooxygenase, glycine betaine reductase, and TMAO reductase, were elevated in the gut of AF patients. Furthermore, 16 genera were assigned and significantly correlated with TMA-enzymatic genes, where 9 genera were remarkably enriched in the gut communities of AF patients. Neither of these TMA-synthesis pathways nor the microbial players showed a significant discrepancy between different types of AF in the current cohort. These gut microbes might participate in the formation of TMA by activating the key TMA-synthesis enzymes and contributing to the functional pathways in AF patients.

CONCLUSIONS: The present study provides an in-depth insight into the potential bacteria and metabolic pathways involved in TMA production in the gut of AF patients. These findings emphasize a key role of the gut bacteria in driving TMAO formation during AF pathogenesis, thereby indicating its therapeutic potential as an intervention strategy of AF by targeting TMA-synthesis pathways and dysbiotic gut microbiota.}, } @article {pmid32731153, year = {2020}, author = {Villarreal-Soto, SA and Bouajila, J and Pace, M and Leech, J and Cotter, PD and Souchard, JP and Taillandier, P and Beaufort, S}, title = {Metabolome-microbiome signatures in the fermented beverage, Kombucha.}, journal = {International journal of food microbiology}, volume = {333}, number = {}, pages = {108778}, doi = {10.1016/j.ijfoodmicro.2020.108778}, pmid = {32731153}, issn = {1879-3460}, mesh = {Antioxidants/analysis ; Bacteria/classification/genetics/isolation & purification ; Chromatography, High Pressure Liquid ; Fermentation/*physiology ; Gas Chromatography-Mass Spectrometry ; Kombucha Tea/*analysis/*microbiology ; Metabolome/physiology ; Metagenome/genetics ; Microbiota/physiology ; Phytochemicals/*analysis ; Yeasts/classification/genetics/isolation & purification ; }, abstract = {Kombucha is a fermented tea. Here we investigate the fermentation kinetics, metabolite production, microbiome and potential health promoting properties of three different kombucha consortia. Shotgun metagenomic sequencing revealed several dominant bacterial genera such as Komagataeibacter, Gluconacetobacter and Gluconobacter. Brettanomyces and Schizosaccharomyces were the most dominant yeasts identified. Species distribution reflected different patterns of sugar consumption, with S. pombe being present in samples with the highest sugar conversion. Liquid-liquid extractions were performed with organic solvents in order to obtain dried extracts, which were later characterized. HPLC-DAD and GC-MS analysis revealed differences in the production of organic acids, sugars, alcohols and phenolic compounds, where the presence of caffeine, propanoic acid and 2,3 butanediol differ greatly across the three kombuchas. Metabolomic analysis exhibited a link between the microbiota and the production of bioactive compounds in kombucha fermentation. In vitro assays were carried out in order to evaluate potential health-promoting features of the fermented teas, with notable outcomes including antioxidant ability against DPPH radical and against the 15-lipoxygenase enzyme, indicating a potential anti-inflammatory activity. These investigations considerably enhance our understanding of the relationship between the microbiota and metabolites as well as health promoting potential of kombucha and have the potential for the development of future generations of kombucha products in which these relationships are optimized.}, } @article {pmid32729971, year = {2020}, author = {Foligné, B and George, F and Standaert, A and Garat, A and Poiret, S and Peucelle, V and Ferreira, S and Sobry, H and Muharram, G and Lucau-Danila, A and Daniel, C}, title = {High-dose dietary supplementation with zinc prevents gut inflammation: Investigation of the role of metallothioneins and beyond by transcriptomic and metagenomic studies.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {34}, number = {9}, pages = {12615-12633}, doi = {10.1096/fj.202000562RR}, pmid = {32729971}, issn = {1530-6860}, mesh = {Animals ; *Colitis/drug therapy/metabolism/microbiology ; Colon/drug effects/metabolism ; Dietary Supplements ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Ileum/drug effects/metabolism ; Inflammation/*drug therapy ; Metallothionein/*metabolism ; Mice ; Mice, Inbred BALB C ; *Transcriptome ; Zinc/administration & dosage/*pharmacology ; }, abstract = {Although it is known that zinc has several beneficial roles in the context of gut inflammation, the underlying mechanisms have not been extensively characterized. Zinc (Zn) is known to be the primary physiological inducer of the expression of the metallothionein (MT) superfamily of small stress-responsive proteins. The expression of MTs in various tissues is induced or enhanced (including the gastrointestinal tract (GIT)) by a variety of stimuli, including infection and inflammation. However, the MTs' exact role in inflammation is still subject to debate. In order to establish whether or not MTs are the sole vectors in the Zn-based modulation of intestinal inflammation, we used transcriptomic and metagenomic approaches to assess the potential effect of dietary Zn, the mechanisms underlying the MTs' beneficial effects, and the induction of previously unidentified mediators. We found that the expression of endogenous MTs in the mouse GIT was stimulated by an optimized dietary supplementation with Zn. The protective effects of dietary supplementation with Zn were then evaluated in mouse models of chemically induced colitis. The potential contribution of MTs and other pathways was explored via transcriptomic analyses of the ileum and colon in Zn-treated mice. The microbiota's role was also assessed via fecal 16S rRNA sequencing. We found that high-dose dietary supplementation with Zn induced the expression of MT-encoding genes in the colon of healthy mice. We next demonstrated that the Zn diet significantly protected mice in the two models of induced colitis. When comparing Zn-treated and control mice, various genes were found to be differentially expressed in the colon and the ileum. Finally, we found that Zn supplementation did not modify the overall structure of the fecal microbiota, with the exception of (i) a significant increase in endogenous Clostridiaceae, and (ii) some subtle but specific changes at the family and genus levels. Our results emphasize the beneficial effects of excess dietary Zn on the prevention of colitis and inflammatory events in mouse models. The main underlying mechanisms were driven by the multifaceted roles of MTs and the other potential molecular mediators highlighted by our transcriptomic analyses although we cannot rule out contributions by other factors from the host and/or the microbiota.}, } @article {pmid32728075, year = {2020}, author = {Dei-Cas, I and Giliberto, F and Luce, L and Dopazo, H and Penas-Steinhardt, A}, title = {Metagenomic analysis of gut microbiota in non-treated plaque psoriasis patients stratified by disease severity: development of a new Psoriasis-Microbiome Index.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12754}, pmid = {32728075}, issn = {2045-2322}, mesh = {Adolescent ; Adult ; Bacteroides ; Bacteroidetes ; Biodiversity ; Biomarkers/metabolism ; Clostridiales ; Computational Biology ; Cross-Sectional Studies ; Faecalibacterium ; Female ; Firmicutes ; *Gastrointestinal Microbiome ; Genome, Human ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metagenomics ; Middle Aged ; Psoriasis/*diagnosis/*microbiology ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Psoriasis is an immune-mediated skin disorder. Imbalance of gut microbial populations has been implicated in many diseases. We aimed to investigate whether there were differences in gut microbiota in psoriasis patients vs non-psoriasis controls and between psoriasis severity groups. 55 psoriasis patients and 27 controls were included. V3-V4 regions of the 16S rRNA gene of fecal samples were analyzed using Illumina MiSeq. Bioinformatic analysis was performed. We found changes in gut microbiome composition depending on their psoriasis status as determined by weighted unifrac (p < 0.05), in particular an increase in Firmicutes and depletion of Bacteroidetes in psoriasis patients. Additionally, the Faecalibacterium and Blautia genus were higher in psoriasis patients while Bacteroides and Paraprevotella in non-psoriasis controls (p < 0.05, LDA score > 2). Moderate-to-severe psoriasis patients had lower biodiversity than mild psoriatic patients (p = 0.049). No differences for beta-diversity were found. We developed a Psoriasis-Microbiota Index (PMI), which discriminated among psoriasis patients and controls with sensitivity: 0.78 and specificity: 0.79. Furthermore, we performed a meta-analysis with published data to validate this index. We demonstrated gut dysbiosis in psoriasis patients, suggesting a role in psoriasis pathophysiology. Furthermore, we developed a PMI with the potential to discriminate between psoriasis patients and controls across different populations, which could be used as a biomarker in the clinical practice.}, } @article {pmid32727857, year = {2020}, author = {Auchtung, JM and Preisner, EC and Collins, J and Lerma, AI and Britton, RA}, title = {Identification of Simplified Microbial Communities That Inhibit Clostridioides difficile Infection through Dilution/Extinction.}, journal = {mSphere}, volume = {5}, number = {4}, pages = {}, pmid = {32727857}, issn = {2379-5042}, support = {R01 AI123278/AI/NIAID NIH HHS/United States ; R33 AI121522/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Animals ; Clostridioides difficile/*classification/*physiology ; Fecal Microbiota Transplantation ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Mice ; Microbiological Techniques/*methods ; Middle Aged ; }, abstract = {The gastrointestinal microbiome plays an important role in limiting susceptibility to infection with Clostridioides difficile To better understand the ecology of bacteria important for C. difficile colonization resistance, we developed an experimental platform to simplify complex communities of fecal bacteria through dilution and rapidly screen for their ability to resist C. difficile colonization after challenge, as measured by >100-fold reduction in levels of C. difficile in challenged communities. We screened 76 simplified communities diluted from cultures of six fecal donors and identified 24 simplified communities that inhibited C. difficile colonization in vitro Sequencing revealed that simplified communities were composed of 19 to 67 operational taxonomic units (OTUs) and could be partitioned into four distinct community types. One simplified community could be further simplified from 56 to 28 OTUs through dilution and retain the ability to inhibit C. difficile We tested the efficacy of seven simplified communities in a humanized microbiota mouse model. We found that four communities were able to significantly reduce the severity of the initial C. difficile infection and limit susceptibility to disease relapse. Analysis of fecal microbiomes from treated mice demonstrated that simplified communities accelerated recovery of indigenous bacteria and led to stable engraftment of 19 to 22 OTUs from simplified communities. Overall, the insights gained through the identification and characterization of these simplified communities increase our understanding of the microbial dynamics of C. difficile infection and recovery.IMPORTANCEClostridioides difficile is the leading cause of antibiotic-associated diarrhea and a significant health care burden. Fecal microbiota transplantation is highly effective at treating recurrent C. difficile disease; however, uncertainties about the undefined composition of fecal material and potential long-term unintended health consequences remain. These concerns have motivated studies to identify new communities of microbes with a simpler composition that will be effective at treating disease. This work describes a platform for rapidly identifying and screening new simplified communities for efficacy in treating C. difficile infection. Four new simplified communities of microbes with potential for development of new therapies to treat C. difficile disease are identified. While this platform was developed and validated to model infection with C. difficile, the underlying principles described in the paper could be easily modified to develop therapeutics to treat other gastrointestinal diseases.}, } @article {pmid32727371, year = {2020}, author = {Khanal, P and Maltecca, C and Schwab, C and Fix, J and Bergamaschi, M and Tiezzi, F}, title = {Modeling host-microbiome interactions for the prediction of meat quality and carcass composition traits in swine.}, journal = {Genetics, selection, evolution : GSE}, volume = {52}, number = {1}, pages = {41}, pmid = {32727371}, issn = {1297-9686}, mesh = {Animals ; Female ; *Gastrointestinal Microbiome ; Genome-Wide Association Study/*methods ; Host-Pathogen Interactions/*genetics ; Male ; Metagenome ; Models, Genetic ; Polymorphism, Single Nucleotide ; Pork Meat/*standards ; *Quantitative Trait, Heritable ; RNA, Ribosomal, 16S/genetics ; Swine/*genetics/microbiology ; }, abstract = {BACKGROUND: The objectives of this study were to evaluate genomic and microbial predictions of phenotypes for meat quality and carcass traits in swine, and to evaluate the contribution of host-microbiome interactions to the prediction. Data were collected from Duroc-sired three-way crossbred individuals (n = 1123) that were genotyped with a 60 k SNP chip. Phenotypic information and fecal 16S rRNA microbial sequences at three stages of growth (Wean, Mid-test, and Off-test) were available for all these individuals. We used fourfold cross-validation with animals grouped based on sire relatedness. Five models with three sets of predictors (full, informatively reduced, and randomly reduced) were evaluated. 'Full' included information from all genetic markers and all operational taxonomic units (OTU), while 'informatively reduced' and 'randomly reduced' represented a reduced number of markers and OTU based on significance preselection and random sampling, respectively. The baseline model included the fixed effects of dam line, sex and contemporary group and the random effect of pen. The other four models were constructed by including only genomic information, only microbiome information, both genomic and microbiome information, and microbiome and genomic information and their interaction.

RESULTS: Inclusion of microbiome information increased predictive ability of phenotype for most traits, in particular when microbiome information collected at a later growth stage was used. Inclusion of microbiome information resulted in higher accuracies and lower mean squared errors for fat-related traits (fat depth, belly weight, intramuscular fat and subjective marbling), objective color measures (Minolta a*, Minolta b* and Minolta L*) and carcass daily gain. Informative selection of markers increased predictive ability but decreasing the number of informatively reduced OTU did not improve model performance. The proportion of variation explained by the host-genome-by-microbiome interaction was highest for fat depth (~ 20% at Mid-test and Off-test) and shearing force (~ 20% consistently at Wean, Mid-test and Off-test), although the inclusion of the interaction term did not increase the accuracy of predictions significantly.

CONCLUSIONS: This study provides novel insight on the use of microbiome information for the phenotypic prediction of meat quality and carcass traits in swine. Inclusion of microbiome information in the model improved predictive ability of phenotypes for fat deposition and color traits whereas including a genome-by-microbiome term did not improve prediction accuracy significantly.}, } @article {pmid32724224, year = {2020}, author = {Vu, D and Groenewald, M and Verkley, G}, title = {Convolutional neural networks improve fungal classification.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12628}, pmid = {32724224}, issn = {2045-2322}, abstract = {Sequence classification plays an important role in metagenomics studies. We assess the deep neural network approach for fungal sequence classification as it has emerged as a successful paradigm for big data classification and clustering. Two deep learning-based classifiers, a convolutional neural network (CNN) and a deep belief network (DBN) were trained using our recently released barcode datasets. Experimental results show that CNN outperformed the traditional BLAST classification and the most accurate machine learning based Ribosomal Database Project (RDP) classifier on datasets that had many of the labels present in the training datasets. When classifying an independent dataset namely the "Top 50 Most Wanted Fungi", CNN and DBN assigned less sequences than BLAST. However, they could assign much more sequences than the RDP classifier. In terms of efficiency, it took the machine learning classifiers up to two seconds to classify a test dataset while it was 53 s for BLAST. The result of the current study will enable us to speed up the taxonomic assignments for the fungal barcode sequences generated at our institute as ~ 70% of them still need to be validated for public release. In addition, it will help to quickly provide a taxonomic profile for metagenomics samples.}, } @article {pmid32723385, year = {2020}, author = {Yuan, X and Chen, R and Zhang, Y and Lin, X and Yang, X}, title = {Sexual dimorphism of gut microbiota at different pubertal status.}, journal = {Microbial cell factories}, volume = {19}, number = {1}, pages = {152}, pmid = {32723385}, issn = {1475-2859}, support = {2016-S-wp1//Technology Innovation Team Train Project of Fuzhou Health Committee in China/ ; 201610191//key Clinical Specialty Discipline Construction Program of Fuzhou, Fujian, P.R.C/ ; }, mesh = {Adolescent ; Bacteria/*classification ; Child ; Child, Preschool ; China ; Cross-Sectional Studies ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; *Metagenomics ; *Puberty ; RNA, Ribosomal, 16S/genetics ; *Sex Characteristics ; }, abstract = {BACKGROUND: Accumulating evidence infer that gut microbiome-host relations are key mediators or modulators driving the observed sexual dimorphism in some disease onset and progression. To date, the sex-differences of gut microbiota at different pubertal status have not been reported.

OBJECTIVE: To determine the characteristics of gut microbiota of both genders at different pubertal status.

METHODS: Gut microbiota was analyzed in 89 Chinese participants aged 5-15 years. Participants were divided into pre-puberty and puberty groups for both male and female. The composition of gut microbiota was investigated by 16S rRNA-based metagenomics. Ecological representations of microbial communities were computed. The prediction of metagenomic functional content from 16S rRNA gene surveys was conducted.

RESULTS: There were 49 males (9.76 ± 2.15 years) and 40 females (9.74 ± 1.63 years); 21 males and 26 females were at puberty. At genus level, Alistipes, Megamonas, Oscillospira and Parabacteroides were more prevalent in girls than in boys (p < 0.05). There were no significantly differences of alpha-diversity between genders, which was independent of pubertal status. The beta-diversity was significantly different in pubertal subjects between genders. Using statistical analyses, we assigned genera Dorea, Megamonas, Bilophila, Parabacteroides and Phascolarctobacterium as microbial markers for pubertal subjects. The predicted metabolic profiles differ in both pubertal and pre-pubertal groups between genders.

CONCLUSION: This cross-sectional study revealed that sex differences in the gut microbiota composition and predicted metabolic profiles exist before puberty, which become more significant at puberty. The identification of novel puberty bacterial markers may disclose a potential effects of gender-related microbiota profiles on puberty onset.}, } @article {pmid32722579, year = {2020}, author = {Tsiola, A and Michoud, G and Fodelianakis, S and Karakassis, I and Kotoulas, G and Pavlidou, A and Pavloudi, C and Pitta, P and Simboura, N and Daffonchio, D and Tsapakis, M}, title = {Viral Metagenomic Content Reflects Seawater Ecological Quality in the Coastal Zone.}, journal = {Viruses}, volume = {12}, number = {8}, pages = {}, pmid = {32722579}, issn = {1999-4915}, mesh = {Bacteria/genetics ; *Ecosystem ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; Seawater/*virology ; Viral Proteins/*genetics ; *Virome ; Viruses/*genetics ; }, abstract = {Viruses interfere with their host's metabolism through the expression of auxiliary metabolic genes (AMGs) that, until now, are mostly studied under large physicochemical gradients. Here, we focus on coastal marine ecosystems and we sequence the viral metagenome (virome) of samples with discrete levels of human-driven disturbances. We aim to describe the relevance of viromics with respect to ecological quality status, defined by the classic seawater trophic index (TRIX). Neither viral (family level) nor bacterial (family level, based on 16S rRNA sequencing) community structure correlated with TRIX. AMGs involved in the Calvin and tricarboxylic acid cycles were found at stations with poor ecological quality, supporting viral lysis by modifying the host's energy supply. AMGs involved in "non-traditional" energy-production pathways (3HP, sulfur oxidation) were found irrespective of ecological quality, highlighting the importance of recognizing the prevalent metabolic paths and their intermediate byproducts. Various AMGs explained the variability between stations with poor vs. good ecological quality. Our study confirms the pivotal role of the virome content in ecosystem functioning, acting as a "pool" of available functions that may be transferred to the hosts. Further, it suggests that AMGs could be used as an ultra-sensitive metric of energy-production pathways with relevance in the vulnerable coastal zone and its ecological quality.}, } @article {pmid32719402, year = {2020}, author = {Wang, Z and Yang, Y and Yan, Z and Liu, H and Chen, B and Liang, Z and Wang, F and Miller, BE and Tal-Singer, R and Yi, X and Li, J and Stampfli, MR and Zhou, H and Brightling, CE and Brown, JR and Wu, M and Chen, R and Shu, W}, title = {Multi-omic meta-analysis identifies functional signatures of airway microbiome in chronic obstructive pulmonary disease.}, journal = {The ISME journal}, volume = {14}, number = {11}, pages = {2748-2765}, pmid = {32719402}, issn = {1751-7370}, mesh = {Humans ; Metagenome ; *Microbiota ; *Pulmonary Disease, Chronic Obstructive ; RNA, Ribosomal, 16S/genetics ; Sputum ; }, abstract = {The interaction between airway microbiome and host in chronic obstructive pulmonary disease (COPD) is poorly understood. Here we used a multi-omic meta-analysis approach to characterize the functional signature of airway microbiome in COPD. We retrieved all public COPD sputum microbiome datasets, totaling 1640 samples from 16S rRNA gene datasets and 26 samples from metagenomic datasets from across the world. We identified microbial taxonomic shifts using random effect meta-analysis and established a global classifier for COPD using 12 microbial genera. We inferred the metabolic potentials for the airway microbiome, established their molecular links to host targets, and explored their effects in a separate meta-analysis on 1340 public human airway transcriptome samples for COPD. 29.6% of differentially expressed human pathways were predicted to be targeted by microbiome metabolism. For inferred metabolite-host interactions, the flux of disease-modifying metabolites as predicted from host transcriptome was generally concordant with their predicted metabolic turnover in microbiome, suggesting a synergistic response between microbiome and host in COPD. The meta-analysis results were further validated by a pilot multi-omic study on 18 COPD patients and 10 controls, in which airway metagenome, metabolome, and host transcriptome were simultaneously characterized. 69.9% of the proposed "microbiome-metabolite-host" interaction links were validated in the independent multi-omic data. Butyrate, homocysteine, and palmitate were the microbial metabolites showing strongest interactions with COPD-associated host genes. Our meta-analysis uncovered functional properties of airway microbiome that interacted with COPD host gene signatures, and demonstrated the possibility of leveraging public multi-omic data to interrogate disease biology.}, } @article {pmid32718049, year = {2020}, author = {Altan, E and Delaney, MA and Colegrove, KM and Spraker, TR and Wheeler, EA and Deng, X and Li, Y and Gulland, FMD and Delwart, E}, title = {Complex Virome in a Mesenteric Lymph Node from a Californian Sea Lion (Zalophus Californianus) with Polyserositis and Steatitis.}, journal = {Viruses}, volume = {12}, number = {8}, pages = {}, pmid = {32718049}, issn = {1999-4915}, mesh = {Anelloviridae/classification/isolation & purification ; Animals ; Animals, Wild ; California ; Female ; Inflammation ; Lymph Nodes/*pathology/*virology ; Metagenomics ; Parvovirus/classification/isolation & purification ; Polyomavirus/classification/isolation & purification ; Sea Lions/*virology ; Serositis/*pathology/*veterinary/virology ; Steatitis/*pathology/virology ; *Virome ; }, abstract = {An emaciated subadult free-ranging California sea lion (Csl or Zalophus californianus) died following stranding with lesions similar to 11 other stranded animals characterized by chronic disseminated granulomatous inflammation with necrotizing steatitis and vasculitis, involving visceral adipose tissues in the thoracic and peritoneal cavities. Histologically, affected tissues had extensive accumulations of macrophages with perivascular lymphocytes, plasma cells, and fewer neutrophils. Using viral metagenomics on a mesenteric lymph node six mammalian viruses were identified consisting of novel parvovirus, polyomavirus, rotavirus, anellovirus, and previously described Csl adenovirus 1 and Csl bocavirus 4. The causal or contributory role of these viruses to the gross and histologic lesions of this sea lion remains to be determined.}, } @article {pmid32717520, year = {2020}, author = {Flores-Orozco, D and Patidar, R and Levin, DB and Sparling, R and Kumar, A and Çiçek, N}, title = {Effect of mesophilic anaerobic digestion on the resistome profile of dairy manure.}, journal = {Bioresource technology}, volume = {315}, number = {}, pages = {123889}, doi = {10.1016/j.biortech.2020.123889}, pmid = {32717520}, issn = {1873-2976}, mesh = {Anaerobiosis ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/drug effects ; Genes, Bacterial ; *Manure ; Microbiota/*drug effects ; }, abstract = {The effect of mesophilic anaerobic digestion (AD) on the resistome profile of manures from two different dairy farms was evaluated using a metagenomic approach. A total of 187 unique Antibiotic resistance genes (ARGs) for 17 different classes of antibiotics were detected in raw (undigested) manures. The results indicate that regardless of the origin of the dairy manure, mesophilic AD was capable of reducing or enriching the relative abundance of some ARGs. The main driver of these changes was strongly correlated with the evolution of the microbial community during the AD process. Putative ARG hosts were suggested by analyses of the co-occurrence of microbial groups and ARGs. Finally, network analyses revealed that mesophilic AD could also reduce the co-occurrence of different groups of ARGs potentially located in the same genetic elements. Our results provide valuable insights into the microbial mechanisms driving the diversity and abundance of ARGs during mesophilic AD.}, } @article {pmid32717337, year = {2021}, author = {Chadha, J and Nandi, D and Atri, Y and Nag, A}, title = {Significance of human microbiome in breast cancer: Tale of an invisible and an invincible.}, journal = {Seminars in cancer biology}, volume = {70}, number = {}, pages = {112-127}, doi = {10.1016/j.semcancer.2020.07.010}, pmid = {32717337}, issn = {1096-3650}, mesh = {Animals ; Antineoplastic Agents/*administration & dosage ; Breast Neoplasms/*drug therapy/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Prebiotics/*administration & dosage ; *Precision Medicine ; }, abstract = {The human microbiome is a mysterious treasure of the body playing endless important roles in the well-being of the host metabolism, digestion, and immunity. On the other hand, it actively participates in the development of a variety of pathological conditions including cancer. With the Human Microbiome Project initiative, metagenomics, and next-generation sequencing technologies in place, the last decade has witnessed immense explorations and investigations on the enigmatic association of breast cancer with the human microbiome. However, the connection between the human microbiome and breast cancer remains to be explored in greater detail. In fact, there are several emerging questions such as whether the host microbiota contributes to disease initiation, or is it a consequence of the disease is an irrevocably important question that demands a valid answer. Since the microbiome is an extremely complex community, gaps still remain on how this vital microbial organ plays a role in orchestrating breast cancer development. Nevertheless, undeniable evidence from studies has pinpointed the presence of specific microbial elements of the breast and gut to play a role in governing breast cancer. It is still unclear if an alteration in microbiome/dysbiosis leads to breast cancer or is it vice versa. Though specific microbial signatures have been detected to be associated with various breast cancer subtypes, the structure and composition of a core "healthy" microbiome is yet to be established. Probiotics seem to be a promising antidote for targeted prevention and treatment of breast cancer. Interestingly, these microbial communities can serve as potential biomarkers for prognosis, diagnosis, and treatment of breast cancer, thereby leading to the rise of a completely new era of personalized medicine. This review is a humble attempt to summarize the research findings on the human microbiome and its relation to breast cancer.}, } @article {pmid32712295, year = {2020}, author = {Raiyani, NM and Singh, SP}, title = {Taxonomic and functional profiling of the microbial communities of Arabian Sea: A metagenomics approach.}, journal = {Genomics}, volume = {112}, number = {6}, pages = {4361-4369}, doi = {10.1016/j.ygeno.2020.07.024}, pmid = {32712295}, issn = {1089-8646}, mesh = {Bacteria/*classification/genetics/isolation & purification ; Biodiversity ; *Metagenome ; Metagenomics ; *Microbiota ; Oceans and Seas ; Seawater/chemistry/*microbiology ; }, } @article {pmid32711340, year = {2020}, author = {Thinesh, T and Meenatchi, R and Lipton, AN and Anandham, R and Jose, PA and Tang, SL and Seghal Kiran, G and Selvin, J}, title = {Metagenomic sequencing reveals altered bacterial abundance during coral-sponge interaction: Insights into the invasive process of coral-killing sponge Terpios hoshinota.}, journal = {Microbiological research}, volume = {240}, number = {}, pages = {126553}, doi = {10.1016/j.micres.2020.126553}, pmid = {32711340}, issn = {1618-0623}, mesh = {Animals ; Anthozoa/*growth & development/*microbiology ; Bacteria/*classification/*genetics/isolation & purification ; DNA, Bacterial/genetics ; Indian Ocean ; Metagenome ; Metagenomics ; Phylogeny ; Porifera/*growth & development/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The coral-killing invasive sponge, Terpios hoshinota, causes extensive mortality to live corals and is a potential threat to reefs at different geographical locations. However, to date, the invasive mechanism remains largely unknown. In this study, we aimed to understand the bacterial competition between sponge and coral hosted bacteria when sponge outcompetes corals. We analysed the bacterial community of Terpios-invaded coral tissue, and the adjacent healthy tissue of sponge-invaded Favites colonies from Palk bay reef (South East Asia) of the Indian Ocean by using next-generation sequencing. Comparative analysis revealed similar bacterial diversity in both healthy and sponge covered coral tissues. However, relative abundance found to be differed between the groups. Terpios covered coral tissue had higher bacterial abundance than the healthy coral tissue. Bacterial phyla such as Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria, and Verrucomicrobia live both in sponge covered and healthy coral tissue. Notably, many of the lower abundant bacteria in healthy coral tissue (abundance <1%) became the most abundant in sponge-invaded tissue. In particular, the genus Neisseria, Bacteroides, and members of Pseudoalteromonas predominant in sponge-invaded tissue. Similar bacterial diversity between normal and and sponge-invaded coral tissues suggest that bacteria follow an exploitative competition, which might favoured sponge growth over corals.}, } @article {pmid32710756, year = {2020}, author = {Pedrinho, A and Mendes, LW and Merloti, LF and Andreote, FD and Tsai, SM}, title = {The natural recovery of soil microbial community and nitrogen functions after pasture abandonment in the Amazon region.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {9}, pages = {}, doi = {10.1093/femsec/fiaa149}, pmid = {32710756}, issn = {1574-6941}, mesh = {Forests ; *Microbiota ; Nitrogen/analysis ; *Soil ; Soil Microbiology ; }, abstract = {We assessed the impacts of forest-to-pasture conversion on the dynamic of soil microbial communities, especially those involved in the N-cycle, and their potential functions, using DNA-metagenomic sequencing coupled with the quantification of marker genes for N-cycling. We also evaluated whether the community's dynamic was reestablished with secondary forest growth. In general, the microbial community structure was influenced by changes in soil chemical properties. Aluminum and nitrate significantly correlated to community structure and with 12 out of 21 microbial phyla. The N-related microbial groups and their potential functions were also affected by land-use change, with pasture being clearly different from primary and secondary forest systems. The microbial community analysis demonstrated that forest-to-pasture conversion increased the abundance of different microbial groups related to nitrogen fixation, including Bacteroidetes, Chloroflexi and Firmicutes. In contrast, after pasture abandonment and with the secondary forest regeneration, there was an increase in the abundance of Proteobacteria taxa and denitrification genes. Our multi-analytical approach indicated that the secondary forest presented some signs of resilience, suggesting that the N-related microbial groups and their potential functions can be recovered over time with implications for future ecological restoration programs.}, } @article {pmid32710156, year = {2020}, author = {López, SMY and Pastorino, GN and Fernández-González, AJ and Franco, MEE and Fernández-López, M and Balatti, PA}, title = {The endosphere bacteriome of diseased and healthy tomato plants.}, journal = {Archives of microbiology}, volume = {202}, number = {10}, pages = {2629-2642}, doi = {10.1007/s00203-020-01987-9}, pmid = {32710156}, issn = {1432-072X}, support = {PICT-2016-0794//Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT) of the Ministerio de Ciencia, Tecnología e Innovación Productiva/ ; Subsidio 2017//CICBA/ ; }, mesh = {Actinobacteria/physiology ; Bacteria/classification ; *Bacterial Physiological Phenomena ; Bacteroidetes/physiology ; Endophytes/classification ; Firmicutes/physiology ; Solanum lycopersicum/*microbiology ; Microbiota/*physiology ; Plant Development ; Plant Diseases/*microbiology ; Plant Roots/microbiology ; Proteobacteria/physiology ; }, abstract = {Here we analyze the microbial community of healthy and diseased tomato plants to evaluate its impact on plant health. The organisms found in all samples mainly belonged to 4 phyla: Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The Proteobacteria were the highest relative abundant within the endophytic communities of different plant organs of diseased tomato. Among endophytic bacteria of tomato, only a few taxa could be cultured. Here we showed that only a few taxa of bacteria inhabiting tomato plants could be cultured and that all plant organs have a highly diverse endophytic bacterial, whose activity might affect plant growth and development as well as health. The roots seem to be an important barrier for microbes and leaves appear to be the organs with the higher diversity which is incidentally related to plant health. Fruits also contain a complex bacterial community that appeared to be unaffected by foliar diseases such as gray leaf spot at least under the conditions studied.}, } @article {pmid32708978, year = {2020}, author = {Wang, Y and Wang, H and Howard, AG and Meyer, KA and Tsilimigras, MCB and Avery, CL and Sha, W and Sun, S and Zhang, J and Su, C and Wang, Z and Zhang, B and Fodor, AA and Gordon-Larsen, P}, title = {Circulating Short-Chain Fatty Acids Are Positively Associated with Adiposity Measures in Chinese Adults.}, journal = {Nutrients}, volume = {12}, number = {7}, pages = {}, pmid = {32708978}, issn = {2072-6643}, support = {R01 HD030880/HD/NICHD NIH HHS/United States ; 29230-50347-466001//Sanofi/ ; R01 DK104371/DK/NIDDK NIH HHS/United States ; R01 AG065357/AG/NIA NIH HHS/United States ; R01 HD30880//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; D43 TW009077/TW/FIC NIH HHS/United States ; R01- DK104371/DK/NIDDK NIH HHS/United States ; T32HL129982/HL/NHLBI NIH HHS/United States ; P2C HD050924/HD/NICHD NIH HHS/United States ; }, mesh = {*Adiposity ; Adult ; Aged ; *Asian People ; Body Mass Index ; Colon/metabolism/microbiology ; Cross-Sectional Studies ; Diet ; Dietary Carbohydrates/administration & dosage ; Dietary Fiber/administration & dosage ; Exercise ; Fatty Acids, Volatile/*blood ; Female ; Fermentation ; Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; Overweight/blood ; Socioeconomic Factors ; Waist-Hip Ratio ; }, abstract = {Epidemiological studies suggest a positive association between obesity and fecal short-chain fatty acids (SCFAs) produced by microbial fermentation of dietary carbohydrates, while animal models suggest increased energy harvest through colonic SCFA production in obesity. However, there is a lack of human population-based studies with dietary intake data, plasma SCFAs, gut microbial, and anthropometric data. In 490 Chinese adults aged 30-68 years, we examined the associations between key plasma SCFAs (butyrate/isobutyrate, isovalerate, and valerate measured by non-targeted plasma metabolomics) with body mass index (BMI) using multivariable-adjusted linear regression. We then assessed whether overweight (BMI ≥ 24 kg/m[2]) modified the association between dietary-precursors of SCFAs (insoluble fiber, total carbohydrates, and high-fiber foods) with plasma SCFAs. In a sub-sample (n = 209) with gut metagenome data, we examined the association between gut microbial SCFA-producers with BMI. We found positive associations between butyrate/isobutyrate and BMI (p-value < 0.05). The associations between insoluble fiber and butyrate/isobutyrate differed by overweight (p-value < 0.10). There was no statistical evidence for an association between microbial SCFA-producers and BMI. In sum, plasma SCFAs were positively associated with BMI and that the colonic fermentation of fiber may differ for adults with versus without overweight.}, } @article {pmid32706816, year = {2020}, author = {Wolfe, AE and Moskowitz, JE and Franklin, CL and Wiemken, TL and Ericsson, AC}, title = {Interactions of Segmented Filamentous Bacteria (Candidatus Savagella) and bacterial drivers in colitis-associated colorectal cancer development.}, journal = {PloS one}, volume = {15}, number = {7}, pages = {e0236595}, pmid = {32706816}, issn = {1932-6203}, support = {K01 OD019924/OD/NIH HHS/United States ; T32 OD011126/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Animals ; Clostridiaceae/genetics/*pathogenicity ; Colitis/complications/*pathology ; Colorectal Neoplasms/etiology/*pathology ; Disease Models, Animal ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Helicobacter/physiology ; Male ; Mice ; Mice, Inbred BALB C ; Mice, Knockout ; Neoplasm Staging ; RNA, Ribosomal, 16S/genetics/metabolism ; Smad3 Protein/deficiency/genetics ; }, abstract = {Colorectal cancer (CRC) risk is influenced by host genetics, sex, and the gut microbiota. Using a genetically susceptible mouse model of CRC induced via inoculation with pathobiont Helicobacter spp. and demonstrating variable tumor incidence, we tested the ability of the Th17-enhancing commensal Candidatus Savagella, more commonly denoted as Segmented Filamentous Bacteria (SFB), to influence the incidence and severity of colitis-associated CRC in male and female mice. To document the composition of the gut microbiota during CRC development and identify taxa associated with disease, fecal samples were collected before and throughout disease development and characterized via 16S rRNA sequencing. While there were no significant SFB-dependent effects on disease incidence or severity, SFB was found to exert a sex-dependent protective effect in male mice. Furthermore, SFB stabilized the GM against Helicobacter-induced changes post-inoculation, resulting in a shift in disease association from Helicobacter spp. to Escherichia coli. These data support sex-dependent SFB-mediated effects on CRC risk, and highlight the complex community dynamics within the GM during exposure to inflammatory pathobionts.}, } @article {pmid32706377, year = {2020}, author = {Franklin, CL and Ericsson, AC}, title = {Complex Microbiota in Laboratory Rodents: Management Considerations.}, journal = {ILAR journal}, volume = {60}, number = {2}, pages = {289-297}, pmid = {32706377}, issn = {1930-6180}, support = {K01 OD019924/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Animals ; Gastrointestinal Microbiome/*genetics ; Genome, Microbial/*genetics ; Humans ; Models, Animal ; }, abstract = {Our bodies and those of our animal research subjects are colonized by bacterial communities that occupy virtually every organ system, including many previously considered sterile. These bacteria reside as complex communities that are collectively referred to as microbiota. Prior to the turn of the century, characterization of these communities was limited by a reliance on culture of organisms on a battery of selective media. It was recognized that the vast majority of microbes, especially those occupying unique niches of the body such as the anaerobic environment of the intestinal tract, were uncultivatable. However, with the onset and advancement of next-generation sequencing technology, we are now capable of characterizing these complex communities without the need to cultivate, and this has resulted in an explosion of information and new challenges in interpreting data generated about, and in the context of, these complex communities. We have long known that these microbial communities often exist in an intricate balance that, if disrupted (ie, dysbiosis), can lead to disease or increased susceptibility to disease. Because of many functional redundancies, the makeup of these colonies can vary dramatically within healthy individuals [1]. However, there is growing evidence that subtle differences can alter the phenotype of various animal models, which may translate to the varying susceptibility to disease seen in the human population. In this manuscript, we discuss how to include complex microbiota as a consideration in experimental design and model reproducibility and how to exploit the extensive variation that exists in contemporary rodent research colonies. Our focus will be the intestinal or gut microbiota (GM), but it should be recognized that microbial communities exist in many other body compartments and these too likely influence health and disease [2, 3]. Much like host genetics, can we one day harness the vast genetic capacity of the microbes we live with in ways that will benefit human and animal health?}, } @article {pmid32706331, year = {2020}, author = {Pérez-Cobas, AE and Gomez-Valero, L and Buchrieser, C}, title = {Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses.}, journal = {Microbial genomics}, volume = {6}, number = {8}, pages = {}, pmid = {32706331}, issn = {2057-5858}, mesh = {Computational Biology/methods ; Genetic Markers/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Software ; Whole Genome Sequencing/*methods ; }, abstract = {Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples. Whole-genome shotgun sequencing analyses the total DNA of a chosen sample to determine the presence of micro-organisms from all domains of life and their genomic content. Importantly, the whole-genome shotgun sequencing approach reveals the genomic diversity present, but can also give insights into the functional potential of the micro-organisms identified. The marker gene approach is based on the sequencing of a specific gene region. It allows one to describe the microbial composition based on the taxonomic groups present in the sample. It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge. Here we review the primary workflows and software used for both approaches and discuss the current challenges in the field.}, } @article {pmid32705341, year = {2020}, author = {Gupta, P and Vakhlu, J and Sharma, YP and Imchen, M and Kumavath, R}, title = {Metagenomic insights into the fungal assemblages of the northwest Himalayan cold desert.}, journal = {Extremophiles : life under extreme conditions}, volume = {24}, number = {5}, pages = {749-758}, pmid = {32705341}, issn = {1433-4909}, support = {DST-SERB/2018/001085//Department science and technology/ ; BT/PR11727/BCE/08/720/2008//DBT-SRF/ ; CSIR (9/100/0177) 2K13-EMR-I//CSIR-SRF/ ; }, mesh = {Antarctic Regions ; Arctic Regions ; Biodiversity ; *Fungi/genetics ; *Metagenome ; *Mycobiome ; }, abstract = {Psychrophilic fungi are a critical biotic component in cold deserts that serves a central role in nutrient recycling and biogeochemical cycles. Despite their ecological significance, culture-independent studies on psychrophilic mycobiome are limited. In the present study, the fungal diversity patterns across the Drass, an Indian cold desert in the Himalaya, were indexed by targeted amplicon pyrosequencing (ITS). In the Drass dataset, Ascomycota was represented by 92 genera, while 22 genera represented Basidiomycota. The most abundant genus was Conocybe (20.46%). Most of the identified genera were reported in the literature to be prolific extracellular hydrolytic enzyme producers. To identify whether the Drass fungal assemblages share similarities to other cold deserts, these were further compared to Antarctic and Arctic cold deserts. Comparative analysis across the three cold deserts indicated the dominance of Dikarya (Ascomycota and Basidiomycota). The observed alpha diversity, Shannon index as well as Pielou's evenness was highest in the Antarctic followed by Drass and Arctic datasets. The genera Malassezia, Preussia, Pseudogymnoascus, Cadophora, Geopora, Monodictys, Tetracladium, Titaea, Mortierella, and Cladosporium were common to all the cold deserts. Furthermore, Conocybe was represented predominantly in Drass. Interestingly, the genus Conocybe has not been previously reported from any other studies on Antarctic or Arctic biomes. To the best of our knowledge, this is the first fungal metagenome study in Drass soil. Our analysis shows that despite the similarities of low temperature among the cold deserts, a significant differential abundance of fungal communities prevails in the global cold deserts.}, } @article {pmid32704056, year = {2020}, author = {Song, CH and Kim, N and Nam, RH and Choi, SI and Lee, HN and Surh, YJ}, title = {17β-Estradiol supplementation changes gut microbiota diversity in intact and colorectal cancer-induced ICR male mice.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12283}, pmid = {32704056}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; Cell Transformation, Neoplastic ; Colorectal Neoplasms/*etiology/metabolism/pathology ; *Dietary Supplements ; Disease Models, Animal ; Disease Susceptibility ; Estradiol/*administration & dosage ; Female ; Gastrointestinal Microbiome/*drug effects ; Male ; Metagenome ; Metagenomics/methods ; Mice ; RNA, Ribosomal, 16S ; }, abstract = {The composition of the gut microbiota is influenced by sex hormones and colorectal cancer (CRC). Previously, we reported that 17β-estradiol (E2) inhibits azoxymethane/dextran sulfate sodium (AOM/DSS)-induced tumorigenesis in male mice. Here, we investigated whether the composition of the gut microbiota is different between male and female, and is regulated by estrogen as a secondary outcome of previous studies. We established four groups of mice based on the sex and estrogen status [ovariectomized (OVX) female and E2-treated male]. Additionally, three groups of males were established by treating them with AOM/DSS, and E2, after subjecting them to AOM/DSS treatment. The mice were sacrificed at 21 weeks old. The composition of the gut microbiota was analyzed using 16S rRNA metagenomics sequencing. We observed a significant increase in the microbial diversity (Chao1 index) in females, males supplemented with E2, and males treated with AOM/DSS/E2 compared with normal males. In normal physiological condition, sex difference and E2 treatment did not affect the ratio of Firmicutes/Bacteroidetes (F/B). However, in AOM/DSS-treated male mice, E2 supplementation showed significantly lower level of the F/B ratio. The ratio of commensal bacteria to opportunistic pathogens was higher in females and E2-treated males compared to normal males and females subjected to OVX. Unexpectedly, this ratio was higher in the AOM/DSS group than that determined in other males and the AOM/DSS/E2 group. Our findings suggest that estrogen alters the gut microbiota in ICR (CrljOri:CD1) mice, particularly AOM/DSS-treated males, by decreasing the F/B ratio and changing Shannon and Simpson index by supply of estrogen. This highlights another possibility that estrogen could cause changes in the gut microbiota, thereby reducing the risk of developing CRC.}, } @article {pmid32704012, year = {2020}, author = {Pascottini, OB and Van Schyndel, SJ and Spricigo, JFW and Rousseau, J and Weese, JS and LeBlanc, SJ}, title = {Dynamics of uterine microbiota in postpartum dairy cows with clinical or subclinical endometritis.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12353}, pmid = {32704012}, issn = {2045-2322}, mesh = {Animals ; *Bacteria/classification/genetics/growth & development ; Cattle ; Cattle Diseases/genetics/*microbiology/pathology ; Endometritis/genetics/*microbiology/pathology/veterinary ; Female ; *Microbiota ; }, abstract = {Our objectives were to describe and compare the uterine bacterial composition of postpartum Holstein cows diagnosed as healthy (n = 8), subclinical endometritis (SCE; n = 8), or clinical endometritis (CE; n = 5) in the fifth week postpartum. We did metagenomic analyses of 16S rRNA gene sequences from endometrial cytobrush samples at 10, 21, and 35 days in milk (DIM), and endometrial bacterial culture at 35 DIM. Uterine bacterial composition in healthy, SCE, and CE was stable at 10, 21, and 35 DIM. Alpha and beta diversities showed a different uterine microbiome from CE compared to healthy or SCE, but no differences were found between healthy and SCE cows. At the phylum level, the relative abundance of Bacteroidetes and Fusobacteria, and at genera level, of Trueperella was greater in CE than healthy or SCE cows. Trueperella pyogenes was the predominant bacteria cultured in cows with CE, and a wide variety of bacterial growth was found in healthy and SCE cows. Bacteria that grew in culture were represented within the most abundant bacterial genera based on metagenomic sequencing. The uterine microbiota was similar between SCE and healthy, but the microbiome in cows with CE had a loss of bacterial diversity.}, } @article {pmid32703166, year = {2020}, author = {Kondratenko, Y and Korobeynikov, A and Lapidus, A}, title = {CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities.}, journal = {BMC bioinformatics}, volume = {21}, number = {Suppl 12}, pages = {303}, pmid = {32703166}, issn = {1471-2105}, support = {19-16-00049//Russian Science Foundation/ ; }, mesh = {Databases, Genetic ; *High-Throughput Nucleotide Sequencing ; Humans ; Microbiota/genetics ; *Molecular Sequence Annotation ; RNA, Ribosomal, 16S/genetics ; *Software ; }, abstract = {BACKGROUND: Illumina paired-end reads are often used for 16S analysis in metagenomic studies. Since DNA fragment size is usually smaller than the sum of lengths of paired reads, reads can be merged for downstream analysis. In spite of development of several tools for merging of paired-end reads, poor quality at the 3' ends within the overlapping region prevents the accurate combining of significant portion of read pairs. Recently CD-HIT-OTU-Miseq was presented as a new approach for 16S analysis using the paired-end reads, it completely avoids the reads merging process due to separate clustering of paired reads. CD-HIT-OTU-Miseq is a set of tools which are supposed to be successively launched by auxiliary shell scripts. This launch mode is not suitable for processing of big amounts of data generated in modern omics experiments. To solve this issue we created CDSnake - Snakemake pipeline utilizing CD-HIT tools for easier consecutive launch of CD-HIT-OTU-Miseq tools for complete processing of paired end reads in metagenomic studies. Usage of pipeline make 16S analysis easier due to one-command launch and helps to yield reproducible results.

RESULTS: We benchmarked our pipeline against two commonly used pipelines for OTU retrieval, incorporated into popular workflow for microbiome analysis, QIIME2 - DADA2 and deblur. Three mock datasets having highly overlapping paired-end 2 × 250 bp reads were used for benchmarking - Balanced, HMP, and Extreme. CDSnake outputted less OTUs than DADA2 and deblur. However, on Balanced and HMP datasets number of OTUs outputted by CDSnake was closer to real number of strains which were used for mock community generation, than those outputted by DADA2 and deblur. Though generally slower than other pipelines, CDSnake outputted higher total counts, preserving more information from raw data. Inheriting this properties from original CD-HIT-OTU-MiSeq utilities, CDSnake made their usage handier due to simple scalability, easier automated runs and other Snakemake benefits.

CONCLUSIONS: We developed Snakemake pipeline for OTU-MiSeq utilities, which simplified and automated data analysis. Benchmarking showed that this approach is capable to outperform popular tools in certain conditions.}, } @article {pmid32703080, year = {2020}, author = {Ammer-Herrmenau, C and Pfisterer, N and Weingarten, MF and Neesse, A}, title = {The microbiome in pancreatic diseases: Recent advances and future perspectives.}, journal = {United European gastroenterology journal}, volume = {8}, number = {8}, pages = {878-885}, pmid = {32703080}, issn = {2050-6414}, mesh = {Biomarkers/analysis ; DNA, Bacterial/analysis/isolation & purification ; High-Throughput Nucleotide Sequencing ; Humans ; Intestinal Mucosa/immunology/*microbiology ; Metagenome ; Metagenomics/methods ; Microbiota/genetics/*immunology ; Pancreas/immunology/*microbiology/pathology ; Pancreatic Neoplasms/diagnosis/immunology/*microbiology ; Pancreatitis/diagnosis/immunology/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The human microbiota exerts multiple physiological functions such as the regulation of metabolic and inflammatory processes. High-throughput sequencing techniques such as next-generation sequencing have become widely available in preclinical and clinical settings and have exponentially increased our knowledge about the microbiome and its interaction with host cells and organisms. There is now emerging evidence that microorganisms also contribute to inflammatory and neoplastic diseases of the pancreas. This review summarizes current clinical and translational microbiome studies in acute and chronic pancreatitis as well as pancreatic cancer and provides evidence that the microbiome has a high potential for biomarker discovery. Furthermore, the intestinal and pancreas-specific microbiome may also become an integrative part of diagnostic and therapeutic approaches of pancreatic diseases in the near future.}, } @article {pmid32698001, year = {2020}, author = {McLean, JS and Bor, B and Kerns, KA and Liu, Q and To, TT and Solden, L and Hendrickson, EL and Wrighton, K and Shi, W and He, X}, title = {Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts.}, journal = {Cell reports}, volume = {32}, number = {3}, pages = {107939}, pmid = {32698001}, issn = {2211-1247}, support = {F32 DE025548/DE/NIDCR NIH HHS/United States ; R01 DE020102/DE/NIDCR NIH HHS/United States ; T90 DE021984/DE/NIDCR NIH HHS/United States ; R00 DE027719/DE/NIDCR NIH HHS/United States ; R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 DE026186/DE/NIDCR NIH HHS/United States ; }, mesh = {Acetobacteraceae/genetics ; Adaptation, Physiological/*genetics ; Animals ; Bacterial Secretion Systems/genetics ; Biodiversity ; Environmental Microbiology ; *Genome Size ; *Genome, Bacterial ; Host-Pathogen Interactions/*genetics ; Humans ; Mammals/*microbiology ; Mouth/microbiology ; Phylogeny ; Phylogeography ; Principal Component Analysis ; }, abstract = {The first cultivated representative of the enigmatic phylum Saccharibacteria (formerly TM7) was isolated from humans and revealed an ultra-small cell size (200-300 nm), a reduced genome with limited biosynthetic capabilities, and a unique parasitic lifestyle. TM7x was the only cultivated member of the candidate phyla radiation (CPR), estimated to encompass 26% of the domain Bacteria. Here we report on divergent genomes from major lineages across the Saccharibacteria phylum in humans and mammals, as well as from ancient dental calculus. These lineages are present at high prevalence within hosts. Direct imaging reveals that all groups are ultra-small in size, likely feeding off commensal bacteria. Analyses suggest that multiple acquisition events in the past led to the current wide diversity, with convergent evolution of key functions allowing Saccharibacteria from the environment to adapt to mammals. Ultra-small, parasitic CPR bacteria represent a relatively unexplored paradigm of prokaryotic interactions within mammalian microbiomes.}, } @article {pmid32696660, year = {2021}, author = {Ogai, K and Ogura, K and Ohgi, N and Park, S and Aoki, M and Urai, T and Nagase, S and Okamoto, S and Sugama, J}, title = {Stability of Skin Microbiome at Sacral Regions of Healthy Young Adults, Ambulatory Older Adults, and Bedridden Older Patients After 2 Years.}, journal = {Biological research for nursing}, volume = {23}, number = {1}, pages = {82-90}, doi = {10.1177/1099800420941151}, pmid = {32696660}, issn = {1552-4175}, mesh = {Aged ; Aged, 80 and over ; Bacteria/classification/genetics ; Bedridden Persons/*statistics & numerical data ; Female ; Gastrointestinal Microbiome ; Humans ; Male ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sacrococcygeal Region ; Skin/*microbiology/pathology ; Skin Physiological Phenomena ; Young Adult ; }, abstract = {OBJECTIVE: The sacral skin of bedridden older patients often develops a dysbiotic condition. To clarify whether the condition changes or is sustained over time, we analyzed the skin microbiome and the skin physiological functions of the sacral skin in patients who completed our 2017 study.

METHODS: In 2019, we collected the microbiome on the sacral region and measured sacral skin hydration, pH, and transepidermal water loss from 7 healthy young adults, 10 ambulatory older adults, and 8 bedridden older patients, all of whom had been recruited for the 2017 study. For microbiome analysis, 16S ribosomal RNA-based metagenomic analysis was used.

RESULTS: No significant differences in the microbial compositions or any alpha diversity metrics were found in the bedridden older patients between the 2017 and 2019 studies; the higher gut-related bacteria were still observed on the sacral skin of the bedridden older patients even after 2 years. Only skin pH showed a significant decrease, approaching normal skin condition, in the bedridden older patients over 2 years.

CONCLUSION: This study indicated that gut-related bacteria stably resided in the sacral skin in bedridden patients, even if the patient had tried to restore skin physiological functions using daily skin care. We propose the importance of skin care that focuses more on bacterial decontamination for the sacral region of bedridden older patients, in order to decrease the chances of skin/wound infection and inflammation.}, } @article {pmid32694705, year = {2020}, author = {Willis, KA and Postnikoff, CK and Freeman, A and Rezonzew, G and Nichols, K and Gaggar, A and Lal, CV}, title = {The closed eye harbours a unique microbiome in dry eye disease.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12035}, pmid = {32694705}, issn = {2045-2322}, support = {P30 AI027767/AI/NIAID NIH HHS/United States ; 17SDG32720009/AHA/American Heart Association-American Stroke Association/United States ; K08HL141652/NH/NIH HHS/United States ; UL1 TR000165/TR/NCATS NIH HHS/United States ; K08 HL141652/HL/NHLBI NIH HHS/United States ; R01 HL102371/HL/NHLBI NIH HHS/United States ; R01HL102371/NH/NIH HHS/United States ; P30 AR050948/AR/NIAMS NIH HHS/United States ; I01 CX001969/CX/CSRD VA/United States ; }, mesh = {Adult ; Case-Control Studies ; Dry Eye Syndromes/diagnosis/*etiology ; Female ; Humans ; Machine Learning ; Male ; Metagenomics/methods ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Tears/microbiology ; Trauma Severity Indices ; }, abstract = {Dry eye affects millions of individuals. In experimental models, dry eye disease is associated with T helper cell 17-mediated inflammation of the ocular surface that may cause persistent damage to the corneal epithelium. However, the initiating and perpetuating factors associated with chronic inflammation of the ocular surface remain unclear. The ocular microbiota alters ocular surface inflammation and may influence dry eye disease development and progression. Here, we collected serial samples of tears on awakening from sleep, closed eye tears, during a randomized clinical trial of a non-pharmaceutical dry eye therapy and used 16S rRNA metabarcoding to characterize the microbiome. We show the closed dry eye microbiome is distinct from the healthy closed eye microbiome, and that the microbiome remains distinct despite daily saline eye wash upon awakening. The ocular microbiome was described only recently, and this report implicates a distinct microbiome in ocular disease development. Our findings suggest an interplay between microbial commensals and inflammation on the ocular surface. This information may inform future studies of the pathophysiological mechanisms of dry eye disease.}, } @article {pmid32694128, year = {2020}, author = {Bay, SK and McGeoch, MA and Gillor, O and Wieler, N and Palmer, DJ and Baker, DJ and Chown, SL and Greening, C}, title = {Soil Bacterial Communities Exhibit Strong Biogeographic Patterns at Fine Taxonomic Resolution.}, journal = {mSystems}, volume = {5}, number = {4}, pages = {}, pmid = {32694128}, issn = {2379-5077}, abstract = {Bacteria have been inferred to exhibit relatively weak biogeographic patterns. To what extent such findings reflect true biological phenomena or methodological artifacts remains unclear. Here, we addressed this question by analyzing the turnover of soil bacterial communities from three data sets. We applied three methodological innovations: (i) design of a hierarchical sampling scheme to disentangle environmental from spatial factors driving turnover; (ii) resolution of 16S rRNA gene amplicon sequence variants to enable higher-resolution community profiling; and (iii) application of the new metric zeta diversity to analyze multisite turnover and drivers. At fine taxonomic resolution, rapid compositional turnover was observed across multiple spatial scales. Turnover was overwhelmingly driven by deterministic processes and influenced by the rare biosphere. The communities also exhibited strong distance decay patterns and taxon-area relationships, with z values within the interquartile range reported for macroorganisms. These biogeographical patterns were weakened upon applying two standard approaches to process community sequencing data: clustering sequences at 97% identity threshold and/or filtering the rare biosphere (sequences lower than 0.05% relative abundance). Comparable findings were made across local, regional, and global data sets and when using shotgun metagenomic markers. Altogether, these findings suggest that bacteria exhibit strong biogeographic patterns, but these signals can be obscured by methodological limitations. We advocate various innovations, including using zeta diversity, to advance the study of microbial biogeography.IMPORTANCE It is commonly thought that bacterial distributions show lower spatial variation than for multicellular organisms. In this article, we present evidence that these inferences are artifacts caused by methodological limitations. Through leveraging innovations in sampling design, sequence processing, and diversity analysis, we provide multifaceted evidence that bacterial communities in fact exhibit strong distribution patterns. This is driven by selection due to factors such as local soil characteristics. Altogether, these findings suggest that the processes underpinning diversity patterns are more unified across all domains of life than previously thought, which has broad implications for the understanding and management of soil biodiversity.}, } @article {pmid32694124, year = {2020}, author = {Sieradzki, ET and Koch, BJ and Greenlon, A and Sachdeva, R and Malmstrom, RR and Mau, RL and Blazewicz, SJ and Firestone, MK and Hofmockel, KS and Schwartz, E and Hungate, BA and Pett-Ridge, J}, title = {Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design.}, journal = {mSystems}, volume = {5}, number = {4}, pages = {}, pmid = {32694124}, issn = {2379-5077}, abstract = {Quantitative stable isotope probing (qSIP) estimates isotope tracer incorporation into DNA of individual microbes and can link microbial biodiversity and biogeochemistry in complex communities. As with any quantitative estimation technique, qSIP involves measurement error, and a fuller understanding of error, precision, and statistical power benefits qSIP experimental design and data interpretation. We used several qSIP data sets-from soil and seawater microbiomes-to evaluate how variance in isotope incorporation estimates depends on organism abundance and resolution of the density fractionation scheme. We assessed statistical power for replicated qSIP studies, plus sensitivity and specificity for unreplicated designs. As a taxon's abundance increases, the variance of its weighted mean density declines. Nine fractions appear to be a reasonable trade-off between cost and precision for most qSIP applications. Increasing the number of density fractions beyond that reduces variance, although the magnitude of this benefit declines with additional fractions. Our analysis suggests that, if a taxon has an isotope enrichment of 10 atom% excess, there is a 60% chance that this will be detected as significantly different from zero (with alpha 0.1). With five replicates, isotope enrichment of 5 atom% could be detected with power (0.6) and alpha (0.1). Finally, we illustrate the importance of internal standards, which can help to calibrate per sample conversions of %GC to mean weighted density. These results should benefit researchers designing future SIP experiments and provide a useful reference for metagenomic SIP applications where both financial and computational limitations constrain experimental scope.IMPORTANCE One of the biggest challenges in microbial ecology is correlating the identity of microorganisms with the roles they fulfill in natural environmental systems. Studies of microbes in pure culture reveal much about their genomic content and potential functions but may not reflect an organism's activity within its natural community. Culture-independent studies supply a community-wide view of composition and function in the context of community interactions but often fail to link the two. Quantitative stable isotope probing (qSIP) is a method that can link the identity and functional activity of specific microbes within a naturally occurring community. Here, we explore how the resolution of density gradient fractionation affects the error and precision of qSIP results, how they may be improved via additional experimental replication, and discuss cost-benefit balanced scenarios for SIP experimental design.}, } @article {pmid32692651, year = {2020}, author = {Semail, N and Suraiya, S and Calero, R and Mirabal, M and Carrillo, H and Ezzeddin Kamil, MH and Sarmiento, ME and Acosta, A and Norazmi, MN}, title = {Microbial biodiversity in the throats of pulmonary tuberculosis patients and tuberculin skin test (TST) positive and negative healthy individuals in Malaysia.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {124}, number = {}, pages = {101965}, doi = {10.1016/j.tube.2020.101965}, pmid = {32692651}, issn = {1873-281X}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Case-Control Studies ; Humans ; Malaysia ; *Microbiota ; Pharynx/*microbiology ; Predictive Value of Tests ; Ribotyping ; *Tuberculin Test ; Tuberculosis, Pulmonary/diagnosis/*microbiology ; }, abstract = {The purpose of this study was to investigate the composition of throat microbiota in pulmonary tuberculosis patients (PTB) in comparison to healthy tuberculin skin test positive (TSTp) and negative (TSTn) individuals. Throat swabs samples were collected, and the microbiota was characterized. Richer operational taxonomic units (OTUs) were present in PTB group, compared to TSTp and TSTn. Regarding alpha diversity analysis there was a higher community diversity in TSTn compared to TSTp. Beta diversity analysis showed different species composition in TSTp compared to TSTn and PTB. There was higher presence of Firmicutes in PTB and TSTn compared to TSTp group at phylum level. At the genus level, Leuconostoc and Enterococcus were higher in TSTn compared to TSTp and Pediococcus, Chryseobacterium, Bifidobacterium, Butyrivibrio, and Bulleidia were higher in PTB compared to TSTn. Streptococcus was higher in TSTn compared to PTB and Lactobacillus in PTB compared to TSTp. At species level, Streptococcus sobrinus and Bulleidia moorei were higher in PTB compared to TSTn individuals, while Lactobacillus salivarius was higher in PTB compared to TSTp. The differences in the microbiome composition could influence the resistance/susceptibility to Mtb infection.}, } @article {pmid32692360, year = {2020}, author = {Biassoni, R and Di Marco, E and Squillario, M and Barla, A and Piccolo, G and Ugolotti, E and Gatti, C and Minuto, N and Patti, G and Maghnie, M and d'Annunzio, G}, title = {Gut Microbiota in T1DM-Onset Pediatric Patients: Machine-Learning Algorithms to Classify Microorganisms as Disease Linked.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {105}, number = {9}, pages = {}, doi = {10.1210/clinem/dgaa407}, pmid = {32692360}, issn = {1945-7197}, mesh = {Adolescent ; Age of Onset ; *Algorithms ; Child ; Child, Preschool ; Cohort Studies ; Diabetes Mellitus, Type 1/*epidemiology/etiology/*microbiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; *Machine Learning ; Male ; Metagenome/physiology ; Risk Factors ; }, abstract = {AIMS: The purpose of this work is to find the gut microbial fingerprinting of pediatric patients with type 1 diabetes.

METHODS: The microbiome of 31 children with type 1 diabetes at onset and of 25 healthy children was determined using multiple polymorphic regions of the 16S ribosomal RNA. We performed machine-learning analyses and metagenome functional analysis to identify significant taxa and their metabolic pathways content.

RESULTS: Compared with healthy controls, patients showed a significantly higher relative abundance of the following most important taxa: Bacteroides stercoris, Bacteroides fragilis, Bacteroides intestinalis, Bifidobacterium bifidum, Gammaproteobacteria and its descendants, Holdemania, and Synergistetes and its descendants. On the contrary, the relative abundance of Bacteroides vulgatus, Deltaproteobacteria and its descendants, Parasutterella and the Lactobacillus, Turicibacter genera were significantly lower in patients with respect to healthy controls. The predicted metabolic pathway more associated with type 1 diabetes patients concerns "carbon metabolism," sugar and iron metabolisms in particular. Among the clinical variables considered, standardized body mass index, anti-insulin autoantibodies, glycemia, hemoglobin A1c, Tanner stage, and age at onset emerged as most significant positively or negatively correlated with specific clusters of taxa.

CONCLUSIONS: The relative abundance and supervised analyses confirmed the importance of B stercoris in type 1 diabetes patients at onset and showed a relevant role of Synergistetes and its descendants in patients with respect to healthy controls. In general the robustness and coherence of the showed results underline the relevance of studying the microbioma using multiple polymorphic regions, different types of analysis, and different approaches within each analysis.}, } @article {pmid32691653, year = {2020}, author = {Palmu, J and Salosensaari, A and Havulinna, AS and Cheng, S and Inouye, M and Jain, M and Salido, RA and Sanders, K and Brennan, C and Humphrey, GC and Sanders, JG and Vartiainen, E and Laatikainen, T and Jousilahti, P and Salomaa, V and Knight, R and Lahti, L and Niiranen, TJ}, title = {Association Between the Gut Microbiota and Blood Pressure in a Population Cohort of 6953 Individuals.}, journal = {Journal of the American Heart Association}, volume = {9}, number = {15}, pages = {e016641}, pmid = {32691653}, issn = {2047-9980}, support = {R01 ES027595/ES/NIEHS NIH HHS/United States ; S10 OD020025/OD/NIH HHS/United States ; R01 HL131532/HL/NHLBI NIH HHS/United States ; R01 HL134168/HL/NHLBI NIH HHS/United States ; R01 HL143227/HL/NHLBI NIH HHS/United States ; R01 HL142983/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Aged ; *Blood Pressure ; Cohort Studies ; Female ; *Gastrointestinal Microbiome ; Humans ; Hypertension/*microbiology ; *Lactobacillus ; Male ; Metagenome ; Middle Aged ; Sodium, Dietary/*urine ; }, abstract = {Background Several small-scale animal studies have suggested that gut microbiota and blood pressure (BP) are linked. However, results from human studies remain scarce and conflicting. We wanted to elucidate the multivariable-adjusted association between gut metagenome and BP in a large, representative, well-phenotyped population sample. We performed a focused analysis to examine the previously reported inverse associations between sodium intake and Lactobacillus abundance and between Lactobacillus abundance and BP. Methods and Results We studied a population sample of 6953 Finns aged 25 to 74 years (mean age, 49.2±12.9 years; 54.9% women). The participants underwent a health examination, which included BP measurement, stool collection, and 24-hour urine sampling (N=829). Gut microbiota was analyzed using shallow shotgun metagenome sequencing. In age- and sex-adjusted models, the α (within-sample) and β (between-sample) diversities of taxonomic composition were strongly related to BP indexes (P<0.001 for most). In multivariable-adjusted models, β diversity was only associated with diastolic BP (P=0.032). However, we observed significant, mainly positive, associations between BP indexes and 45 microbial genera (P<0.05), of which 27 belong to the phylum Firmicutes. Interestingly, we found mostly negative associations between 19 distinct Lactobacillus species and BP indexes (P<0.05). Of these, greater abundance of the known probiotic Lactobacillus paracasei was associated with lower mean arterial pressure and lower dietary sodium intake (P<0.001 for both). Conclusions Although the associations between overall gut taxonomic composition and BP are weak, individuals with hypertension demonstrate changes in several genera. We demonstrate strong negative associations of certain Lactobacillus species with sodium intake and BP, highlighting the need for experimental studies.}, } @article {pmid32691605, year = {2021}, author = {Maki, KA and Kazmi, N and Barb, JJ and Ames, N}, title = {The Oral and Gut Bacterial Microbiomes: Similarities, Differences, and Connections.}, journal = {Biological research for nursing}, volume = {23}, number = {1}, pages = {7-20}, pmid = {32691605}, issn = {1552-4175}, mesh = {Bacteria/classification/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Microbiota/genetics ; Mouth/*microbiology ; Nursing Research ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Background: The oral cavity is associated with local and systemic diseases, although oral samples are not as commonly studied as fecal samples in microbiome research. There is a gap in understanding between the similarities and differences in oral and gut microbiomes and how they may influence each other. Methods: A scoping literature review was conducted comparing oral and gut microbiome communities in healthy humans. Results: Ten manuscripts met inclusion criteria and were examined. The oral microbiome sites demonstrated great variance in differential bacterial abundance and the oral microbiome had higher alpha diversity as compared to the gut microbiome. Studies using 16S rRNA sequencing analysis resulted in overall community differences between the oral and gut microbiomes when beta diversity was analyzed. Shotgun metagenomics sequencing increased taxonomic resolution to strain level (intraspecies) and demonstrated a greater percentage of shared taxonomy and oral bacterial translocation to the gut microbiome community. Discussion: The oral and gut microbiome bacterial communities may be more similar than earlier research has suggested, when species strain is analyzed through shotgun metagenomics sequencing. The association between oral health and systemic diseases has been widely reported but many mechanisms underlying this relationship are unknown. Although future research is needed, the oral microbiome may be a novel interventional target through its downstream effects on the gut microbiome. As nurse scientists are experts in symptom characterization and phenotyping of patients, they are also well posed to lead research on the connection of the oral microbiome to the gut microbiome in health and disease.}, } @article {pmid32690973, year = {2021}, author = {Almeida, A and Nayfach, S and Boland, M and Strozzi, F and Beracochea, M and Shi, ZJ and Pollard, KS and Sakharova, E and Parks, DH and Hugenholtz, P and Segata, N and Kyrpides, NC and Finn, RD}, title = {A unified catalog of 204,938 reference genomes from the human gut microbiome.}, journal = {Nature biotechnology}, volume = {39}, number = {1}, pages = {105-114}, pmid = {32690973}, issn = {1546-1696}, support = {BB/N018354/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R015228/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/classification/genetics ; *Databases, Genetic ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/*genetics ; Humans ; Metagenome/*genetics ; Metagenomics ; Phenotype ; Phylogeny ; }, abstract = {Comprehensive, high-quality reference genomes are required for functional characterization and taxonomic assignment of the human gut microbiota. We present the Unified Human Gastrointestinal Genome (UHGG) collection, comprising 204,938 nonredundant genomes from 4,644 gut prokaryotes. These genomes encode >170 million protein sequences, which we collated in the Unified Human Gastrointestinal Protein (UHGP) catalog. The UHGP more than doubles the number of gut proteins in comparison to those present in the Integrated Gene Catalog. More than 70% of the UHGG species lack cultured representatives, and 40% of the UHGP lack functional annotations. Intraspecies genomic variation analyses revealed a large reservoir of accessory genes and single-nucleotide variants, many of which are specific to individual human populations. The UHGG and UHGP collections will enable studies linking genotypes to phenotypes in the human gut microbiome.}, } @article {pmid32690954, year = {2020}, author = {Wolf, YI and Silas, S and Wang, Y and Wu, S and Bocek, M and Kazlauskas, D and Krupovic, M and Fire, A and Dolja, VV and Koonin, EV}, title = {Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome.}, journal = {Nature microbiology}, volume = {5}, number = {10}, pages = {1262-1270}, pmid = {32690954}, issn = {2058-5276}, support = {R01 GM037706/GM/NIGMS NIH HHS/United States ; R35 GM130366/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Biodiversity ; China ; Computational Biology/methods ; Evolution, Molecular ; Gene Order ; *Genome, Viral ; *Metagenome ; *Metagenomics/methods ; Phylogeny ; RNA Viruses/*classification/*genetics ; Viral Proteins/chemistry/genetics ; Water Microbiology ; }, abstract = {RNA viruses in aquatic environments remain poorly studied. Here, we analysed the RNA virome from approximately 10 l water from Yangshan Deep-Water Harbour near the Yangtze River estuary in China and identified more than 4,500 distinct RNA viruses, doubling the previously known set of viruses. Phylogenomic analysis identified several major lineages, roughly, at the taxonomic ranks of class, order and family. The 719-member-strong Yangshan virus assemblage is the sister clade to the expansive class Alsuviricetes and consists of viruses with simple genomes that typically encode only RNA-dependent RNA polymerase (RdRP), capping enzyme and capsid protein. Several clades within the Yangshan assemblage independently evolved domain permutation in the RdRP. Another previously unknown clade shares ancestry with Potyviridae, the largest known plant virus family. The 'Aquatic picorna-like viruses/Marnaviridae' clade was greatly expanded, with more than 800 added viruses. Several RdRP-linked protein domains not previously detected in any RNA viruses were identified, such as the small ubiquitin-like modifier (SUMO) domain, phospholipase A2 and PrsW-family protease domain. Multiple viruses utilize alternative genetic codes implying protist (especially ciliate) hosts. The results reveal a vast RNA virome that includes many previously unknown groups. However, phylogenetic analysis of the RdRPs supports the previously established five-branch structure of the RNA virus evolutionary tree, with no additional phyla.}, } @article {pmid32690600, year = {2021}, author = {Zuo, T and Liu, Q and Zhang, F and Lui, GC and Tso, EY and Yeoh, YK and Chen, Z and Boon, SS and Chan, FK and Chan, PK and Ng, SC}, title = {Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19.}, journal = {Gut}, volume = {70}, number = {2}, pages = {276-284}, pmid = {32690600}, issn = {1468-3288}, mesh = {Adult ; Aged ; COVID-19/*complications/diagnosis/*microbiology ; Feces/*microbiology/*virology ; Female ; Gastrointestinal Microbiome ; Hospitalization ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; Pilot Projects ; Prospective Studies ; SARS-CoV-2/*isolation & purification ; Young Adult ; }, abstract = {OBJECTIVE: Although severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA was detected in faeces of patients with COVID-19, the activity and infectivity of the virus in the GI tract during disease course is largely unknown. We investigated temporal transcriptional activity of SARS-CoV-2 and its association with longitudinal faecal microbiome alterations in patients with COVID-19.

DESIGN: We performed RNA shotgun metagenomics sequencing on serial faecal viral extractions from 15 hospitalised patients with COVID-19. Sequencing coverage of the SARS-CoV-2 genome was quantified. We assessed faecal microbiome composition and microbiome functionality in association with signatures of faecal SARS-CoV-2 infectivity.

RESULTS: Seven (46.7%) of 15 patients with COVID-19 had stool positivity for SARS-CoV-2 by viral RNA metagenomic sequencing. Even in the absence of GI manifestations, all seven patients showed strikingly higher coverage (p=0.0261) and density (p=0.0094) of the 3' vs 5' end of SARS-CoV-2 genome in their faecal viral metagenome profile. Faecal viral metagenome of three patients continued to display active viral infection signature (higher 3' vs 5' end coverage) up to 6 days after clearance of SARS-CoV-2 from respiratory samples. Faecal samples with signature of high SARS-CoV-2 infectivity had higher abundances of bacterial species Collinsella aerofaciens, Collinsella tanakaei, Streptococcus infantis, Morganella morganii, and higher functional capacity for nucleotide de novo biosynthesis, amino acid biosynthesis and glycolysis, whereas faecal samples with signature of low-to-none SARS-CoV-2 infectivity had higher abundances of short-chain fatty acid producing bacteria, Parabacteroides merdae, Bacteroides stercoris, Alistipes onderdonkii and Lachnospiraceae bacterium 1_1_57FAA.

CONCLUSION: This pilot study provides evidence for active and prolonged 'quiescent' GI infection even in the absence of GI manifestations and after recovery from respiratory infection of SARS-CoV-2. Gut microbiota of patients with active SARS-CoV-2 GI infection was characterised by enrichment of opportunistic pathogens, loss of salutary bacteria and increased functional capacity for nucleotide and amino acid biosynthesis and carbohydrate metabolism.}, } @article {pmid32690197, year = {2020}, author = {Ramos-Barbero, MD and Martin-Cuadrado, AB and Viver, T and Santos, F and Martinez-Garcia, M and Antón, J}, title = {Corrigendum to "Recovering microbial genomes from metagenomes in hypersaline environments: The Good, the Bad and the Ugly" [Syst. Appl. Microbiol. 42 (2019) 30-40].}, journal = {Systematic and applied microbiology}, volume = {43}, number = {4}, pages = {126100}, doi = {10.1016/j.syapm.2020.126100}, pmid = {32690197}, issn = {1618-0984}, } @article {pmid32687904, year = {2020}, author = {Bi, Q and Gu, W and Meng, F and Yang, X and Zeng, L and Liang, L and Yang, M and Zhang, T and Yu, J}, title = {Pharmacological and metagenomics evidence of polysaccharide from Polygonum multiflorum in the alleviation of insulin resistance.}, journal = {International journal of biological macromolecules}, volume = {164}, number = {}, pages = {1070-1079}, doi = {10.1016/j.ijbiomac.2020.07.085}, pmid = {32687904}, issn = {1879-0003}, mesh = {AMP-Activated Protein Kinases/metabolism ; Animals ; Fallopia multiflora/*chemistry ; Fatty Acids, Volatile/metabolism ; Feces ; Gastrointestinal Microbiome/*drug effects ; Glucosides/*pharmacology ; Insulin/metabolism ; *Insulin Resistance ; Liver/metabolism ; Male ; Metagenomics ; Polysaccharides/*pharmacology ; RNA, Ribosomal, 16S/metabolism ; Rats ; Rats, Sprague-Dawley ; Receptors, G-Protein-Coupled/*metabolism ; Signal Transduction ; Stilbenes/*pharmacology ; }, abstract = {Total polysaccharide from Polygonum multiflorum (PS) and 2,3,5,4'-tetrahydroxy-stilbene-2-O-β-D-glucoside (TSG) could relieve high-fat and high-sugar diet (HF-HSD) induced rats' insulin resistance (IR) by gut microbiota and host regulation. We found that PS and TSG significantly reversed the increase of fasting blood glucose and the decrease of glucose tolerance in HF-HSD induced IR rats. PS and TSG effectively reversed the imbalance of Firmicutes/Bacteroides caused by an HF-HSD, and significantly reduced the relative abundance of Proteobacteria. It also affected the functional genes of gut microbiota and regulated short-chain fatty acids (SCFAs) and its downstream signal protein molecules. Together, these results indicated that PS and TSG alleviated HF-HSD induced IR by promoting gut microbiota and host function. Thus, PS and TSG may be promising lead substances for developing IR inhibitors that could regulate gut microbiota and its molecular messenger SCFAs to remedy IR.}, } @article {pmid32687239, year = {2020}, author = {Jensen, ET and Bertoni, AG and Crago, OL and Hoffman, KL and Wood, AC and Arzumanyan, Z and Lam, LK and Roll, K and Sandow, K and Wu, M and Rich, SS and Rotter, JI and Chen, YI and Petrosino, JF and Goodarzi, MO}, title = {Rationale, design and baseline characteristics of the Microbiome and Insulin Longitudinal Evaluation Study (MILES).}, journal = {Diabetes, obesity & metabolism}, volume = {22}, number = {11}, pages = {1976-1984}, pmid = {32687239}, issn = {1463-1326}, support = {58-3092-5-001//USDA/ARS/International ; UL1 TR001420/TR/NCATS NIH HHS/United States ; UL1 TR001881/TR/NCATS NIH HHS/United States ; P30 DK063491/DK/NIDDK NIH HHS/United States ; R01 DK109588/DK/NIDDK NIH HHS/United States ; }, mesh = {Blood Glucose ; *Diabetes Mellitus, Type 2/epidemiology ; *Gastrointestinal Microbiome ; Glucose Tolerance Test ; Humans ; Insulin ; *Insulin Resistance ; }, abstract = {AIM: To investigate the role of the gut microbiome in regulating key insulin homeostasis traits (insulin sensitivity, insulin secretion and insulin clearance) whose dysfunction leads to type 2 diabetes (T2D).

MATERIALS AND METHODS: The Microbiome and Insulin Longitudinal Evaluation Study (MILES) focuses on African American and non-Hispanic white participants aged 40-80 years without diabetes. Three study visits are planned (at baseline, 15 and 30 months). Baseline measurements include assessment of the stool microbiome and administration of an oral glucose tolerance test, which will yield indexes of insulin sensitivity, insulin secretion and insulin clearance. The gut microbiome profile (composition and function) will be determined using whole metagenome shotgun sequencing along with analyses of plasma short chain fatty acids. Additional data collected include dietary history, sociodemographic factors, health habits, anthropometry, medical history, medications and family history. Most assessments are repeated 15 and 30 months following baseline.

RESULTS: After screening 875 individuals, 129 African American and 224 non-Hispanic white participants were enrolled. At baseline, African American participants have higher blood pressure, weight, body mass index, waist and hip circumferences but similar waist-hip ratio compared with the non-Hispanic white participants. On average, African American participants are less insulin-sensitive and have higher acute insulin secretion and lower insulin clearance.

CONCLUSIONS: The longitudinal design and robust characterization of potential mediators will allow for the assessment of glucose and insulin homeostasis and gut microbiota as they change over time, improving our ability to discern causal relationships between the microbiome and the insulin homeostasis traits whose deterioration determines T2D, setting the stage for future microbiome-directed therapies to prevent and treat T2D.}, } @article {pmid32684075, year = {2020}, author = {Lang, S and Fairfied, B and Gao, B and Duan, Y and Zhang, X and Fouts, DE and Schnabl, B}, title = {Changes in the fecal bacterial microbiota associated with disease severity in alcoholic hepatitis patients.}, journal = {Gut microbes}, volume = {12}, number = {1}, pages = {1785251}, pmid = {32684075}, issn = {1949-0984}, support = {R01 AA020703/AA/NIAAA NIH HHS/United States ; I01 BX004594/BX/BLRD VA/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; R37 AA020703/AA/NIAAA NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 AA026939/AA/NIAAA NIH HHS/United States ; }, mesh = {Adult ; Aged ; Anti-Bacterial Agents/therapeutic use ; Bacteria/classification/drug effects/genetics/isolation & purification ; End Stage Liver Disease/microbiology/physiopathology ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome/drug effects ; Hepatitis, Alcoholic/drug therapy/*microbiology/*pathology ; Humans ; Liver/pathology ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Steroids/therapeutic use ; }, abstract = {BACKGROUND AND AIMS: Alcoholic hepatitis is the most severe form of alcohol-related liver disease. While the gut microbiome is known to play a role in disease development and progression, less is known about specific compositional changes of the gut bacterial microbiome associated with disease severity. Therefore, the aim of our study was to correlate gut microbiota features with disease severity in alcoholic hepatitis patients.

METHODS: We used 16S rRNA gene sequencing on fecal samples from 74 alcoholic hepatitis patients, which were enrolled at 9 centers in Europe, the United States, and Mexico in a multi-center observational study. The relative abundance of gut bacterial taxa on genus level, as well as the microbiome diversity, was correlated to various clinical, laboratory, and histologic parameters.

RESULTS: We observed a negative correlation between the model for end-stage liver disease score and Shannon diversity, independent of potentially confounding factors (Padjust = 0.046). Alcoholic hepatitis patients with more severe disease had significantly decreased relative abundances of Akkermansia while the relative abundance of Veillonella was increased. We observed a reduction in the Bacteroides abundance (Padjust = 0.048) and Shannon diversity (Padjust = 0.018) in antibiotic-treated patients and patients receiving steroids had an increase in Veillonella abundance (Padjust = 0.005), which was both independent of potentially confounding factors.

CONCLUSION: We observed distinct changes in the gut bacterial microbiome of alcoholic hepatitis patients with more severe disease. The gut bacterial microbiome might be an attractive target to prevent and treat this deadly disease.}, } @article {pmid32683292, year = {2020}, author = {Wu, Z and Luo, Y and Bao, J and Luo, Y and Yu, Z}, title = {Additives affect the distribution of metabolic profile, microbial communities and antibiotic resistance genes in high-moisture sweet corn kernel silage.}, journal = {Bioresource technology}, volume = {315}, number = {}, pages = {123821}, doi = {10.1016/j.biortech.2020.123821}, pmid = {32683292}, issn = {1873-2976}, mesh = {Anti-Bacterial Agents ; Drug Resistance, Microbial ; Fermentation ; Metabolome ; *Microbiota ; Silage/*analysis ; Zea mays ; }, abstract = {This work investigated the effects of chemical additive vanillin (V), homofermentative Lactobacillus plantarum (LP), and heterofermentative Lactobacillus brevis (LB) on the distribution of the metabolome, microbial communities, viruses, and antibiotic-resistance genes in high-moisture corn kernel silage. LP and LB improved lactic acid production, whereas V and LB inhibited protein degradation. A significant difference was observed between the metabolite profiles of silage treated with additives and a control. In silage, the Proteobacteria and Ascomycota were the main hosts of antibiotic-resistance genes, primarily antibiotic efflux. The additives significantly affected the virus content in silage, and LB-treated silage featured the lowest virus content. Overall, these findings suggest that the application of the additive LB to high-moisture corn kernel silage impacts antibiotic-resistance gene reduction and virus distribution within the silage.}, } @article {pmid32680862, year = {2020}, author = {Tomazetto, G and Pimentel, AC and Wibberg, D and Dixon, N and Squina, FM}, title = {Multi-omic Directed Discovery of Cellulosomes, Polysaccharide Utilization Loci, and Lignocellulases from an Enriched Rumen Anaerobic Consortium.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {18}, pages = {}, pmid = {32680862}, issn = {1098-5336}, mesh = {Animals ; Bacteria, Anaerobic/enzymology/*metabolism ; Bacterial Proteins/*metabolism ; Cellulases/metabolism ; Cellulose ; Cellulosomes/*metabolism ; *Gastrointestinal Microbiome ; Lignin/*metabolism ; *Microbial Consortia ; Polysaccharides/*metabolism ; Rumen/microbiology ; Saccharum ; }, abstract = {Lignocellulose is one of the most abundant renewable carbon sources, representing an alternative to petroleum for the production of fuel and chemicals. Nonetheless, the lignocellulose saccharification process, to release sugars for downstream applications, is one of the most crucial factors economically challenging to its use. The synergism required among the various carbohydrate-active enzymes (CAZymes) for efficient lignocellulose breakdown is often not satisfactorily achieved with an enzyme mixture from a single strain. To overcome this challenge, enrichment strategies can be applied to develop microbial communities with an efficient CAZyme arsenal, incorporating complementary and synergistic properties, to improve lignocellulose deconstruction. We report a comprehensive and deep analysis of an enriched rumen anaerobic consortium (ERAC) established on sugarcane bagasse (SB). The lignocellulolytic abilities of the ERAC were confirmed by analyzing the depolymerization of bagasse by scanning electron microscopy, enzymatic assays, and mass spectrometry. Taxonomic analysis based on 16S rRNA sequencing elucidated the community enrichment process, which was marked by a higher abundance of Firmicutes and Synergistetes species. Shotgun metagenomic sequencing of the ERAC disclosed 41 metagenome-assembled genomes (MAGs) harboring cellulosomes and polysaccharide utilization loci (PULs), along with a high diversity of CAZymes. The amino acid sequences of the majority of the predicted CAZymes (60% of the total) shared less than 90% identity with the sequences found in public databases. Additionally, a clostridial MAG identified in this study produced proteins during consortium development with scaffoldin domains and CAZymes appended to dockerin modules, thus representing a novel cellulosome-producing microorganism.IMPORTANCE The lignocellulolytic ERAC displays a unique set of plant polysaccharide-degrading enzymes (with multimodular characteristics), cellulosomal complexes, and PULs. The MAGs described here represent an expansion of the genetic content of rumen bacterial genomes dedicated to plant polysaccharide degradation, therefore providing a valuable resource for the development of biocatalytic toolbox strategies to be applied to lignocellulose-based biorefineries.}, } @article {pmid32679392, year = {2020}, author = {Van Gompel, L and Luiken, REC and Hansen, RB and Munk, P and Bouwknegt, M and Heres, L and Greve, GD and Scherpenisse, P and Jongerius-Gortemaker, BGM and Tersteeg-Zijderveld, MHG and García-Cobos, S and Dohmen, W and Dorado-García, A and Wagenaar, JA and Urlings, BAP and Aarestrup, FM and Mevius, DJ and Heederik, DJJ and Schmitt, H and Bossers, A and Smit, LAM}, title = {Description and determinants of the faecal resistome and microbiome of farmers and slaughterhouse workers: A metagenome-wide cross-sectional study.}, journal = {Environment international}, volume = {143}, number = {}, pages = {105939}, doi = {10.1016/j.envint.2020.105939}, pmid = {32679392}, issn = {1873-6750}, mesh = {Abattoirs ; Animals ; Anti-Bacterial Agents/pharmacology ; Chickens ; Cross-Sectional Studies ; Drug Resistance, Bacterial ; Farmers ; Humans ; Macrolides ; *Metagenome ; *Microbiota ; Netherlands ; Swine ; }, abstract = {BACKGROUND: By studying the entire human faecal resistome and associated microbiome, the diversity and abundance of faecal antimicrobial resistance genes (ARGs) can be comprehensively characterized. Prior culture-based studies have shown associations between occupational exposure to livestock and carriage of specific antimicrobial resistant bacteria. Using shotgun metagenomics, the present study investigated 194 faecal resistomes and bacteriomes from humans occupationally exposed to ARGs in livestock (i.e. pig and poultry farmers, employees and family members and pig slaughterhouse workers) and a control population (Lifelines cohort) in the Netherlands. In addition, we sought to identify determinants for the human resistome and bacteriome composition by applying a combination of multivariate (NMDS, PERMANOVA, SIMPER and DESeq2 analysis) and multivariable regression analysis techniques.

RESULTS: Pig slaughterhouse workers and pig farmers carried higher total ARG abundances in their stools compared to broiler farmers and control subjects. Tetracycline, β-lactam and macrolide resistance gene clusters dominated the resistome of all studied groups. No significant resistome alpha diversity differences were found among the four populations. However, the resistome beta diversity showed a separation of the mean resistome composition of pig and pork exposed workers from broiler farmers and controls, independent of their antimicrobial use. We demonstrated differences in resistome composition between slaughter line positions, pig versus poultry exposed workers, as well as differences between farmers and employees versus family members. In addition, we found a significant correlation between the bacteriome and resistome, and significant differences in the bacteriome composition between and within the studied subpopulations. Finally, an in-depth analysis of pig and poultry farms - of which also farm livestock resistomes were analysed - showed positive associations between the number of on-farm working hours and human faecal AMR loads.

CONCLUSION: We found that the total normalized faecal ARG carriage was larger in persons working in the Dutch pork production chain compared to poultry farmers and controls. Additionally, we showed significant differences in resistome and bacteriome composition of pig and pork exposed workers compared to a control group, as well as within-population (farms, slaughterhouse) compositional differences. The number of on-farm working hours and the farm type (pig or broiler) that persons live or work on are determinants for the human faecal resistome. Overall, our results may suggest direct or indirect livestock contact as a determinant for human ARG carriage. Future studies should further focus on the connection between the human and livestock resistome (i.e. transmission routes) to substantiate the evidence for livestock-associated resistome acquisition.}, } @article {pmid32679124, year = {2020}, author = {Ibrahim, KS and Craft, JA and Biswas, L and Spencer, J and Shu, X}, title = {Etifoxine reverses weight gain and alters the colonic bacterial community in a mouse model of obesity.}, journal = {Biochemical pharmacology}, volume = {180}, number = {}, pages = {114151}, doi = {10.1016/j.bcp.2020.114151}, pmid = {32679124}, issn = {1873-2968}, mesh = {Animals ; Anti-Anxiety Agents/pharmacology/therapeutic use ; Colon/*drug effects/microbiology/physiology ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects/physiology ; Male ; Mice ; Mice, Inbred C57BL ; Obesity/*drug therapy/etiology/physiopathology ; Oxazines/*pharmacology/*therapeutic use ; Weight Gain/*drug effects/physiology ; Weight Loss/drug effects/physiology ; }, abstract = {Obesity is intimately associated with diet and dysbiosis of gut microorganisms but anxiolytics, widely used in treatment of psychiatric conditions, frequently result in weight gain and associated metabolic disorders. We are interested in effects of the anxiolytic etifoxine, which has not been studied with respect to weight gain or effects on gut microorganisms. Here we induced obesity in mice by feeding a high-fat diet but found that intraperitoneal administration of etifoxine resulted in weight loss and decreased serum cholesterol and triglycerides. Obese mice had increased hepatic transcripts associated with lipid metabolism (cyp7a1, cyp27a1, abcg1 and LXRα) and inflammatory factors (TNFα and IL18) but these effects were reversed after etifoxine treatment other than cyp7a1. Taxonomic profiles of the organisms from the caecum were generated by 16S rRNA gene sequencing and Obese and etifoxine mice show differences by diversity metrics, Differential Abundance and functional metagenomics. Organisms in genus Oscillospira and genera from Lachnospiraceae family and Clostridiales order are higher in Control than Obese and at intermediate levels with etifoxine treatment. With respect to community metabolic potential, etifoxine mice have characteristics similar to Control and particularly with respect to metabolism of butanoate, sphingolipid, lipid biosynthesis and xenobiotic metabolism. We suggest mechanisms where-by etifoxine influences processes of host, such as on bile acid synthesis, and microbiota, such as signalling from production of butanoate and sphingosine, resulting in decreased cholesterol, lipids and inflammatory factors. We speculate that the indirect effect of etifoxine on microbial composition is mediated by microbial β-glucuronidases that metabolise excreted etifoxine glucuronides.}, } @article {pmid32676710, year = {2020}, author = {Nurul, AAN and Danish-Daniel, AM and Okomoda, VT and Asma, NA}, title = {Microbiota composition of captive bluestreak cleaner wrasse Labroides dimidiatus (Valenciennes, 1839).}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {17}, pages = {7391-7407}, doi = {10.1007/s00253-020-10781-y}, pmid = {32676710}, issn = {1432-0614}, mesh = {Animals ; Bacteria/genetics ; Bacteroidetes/genetics ; Humans ; Malaysia ; *Microbiota ; *Perciformes ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The Labroides dimidiatus is one of the most traded marine ornamental fishes worldwide, yet not much is known about the microflora associated with this fish. This study is designed to investigate the bacteria composition associated with captive L. dimidiatus and its surrounding aquarium water. The fish and carriage water were obtained from well-known ornamental fish suppliers in Terengganu Malaysia. Bacteria present on the skin and in the stomach and the aquarium water were enumerated using culture-independent approaches and next-generation sequencing (NGS) technology. A total of 3,238,564 valid reads and 828 total operational taxonomic units (OTUs) were obtained from the three metagenomic libraries using NGS analysis. Of all the 15 phyla identified in this study, Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were the most prevalent in all samples. Also, 170 families belonging to 36 bacteria classes were identified. Although many of the bacteria families were common in the skin, gut, and aquarium water (39%), about 26% of the families were exclusive to the aquarium water alone. Therefore, any substantial change in the structure and abundance of microbiota (especially pathogenic bacteria) reported in this study may serve as an early sign for disease infection in the species under captivity. KEY POINTS: • Proteobacteria was the most dominant. • The microbiota was either shared or exclusively in samples.}, } @article {pmid32676061, year = {2020}, author = {Toju, H and Abe, MS and Ishii, C and Hori, Y and Fujita, H and Fukuda, S}, title = {Scoring Species for Synthetic Community Design: Network Analyses of Functional Core Microbiomes.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1361}, pmid = {32676061}, issn = {1664-302X}, abstract = {Constructing biological communities is a major challenge in both basic and applied sciences. Although model synthetic communities with a few species have been constructed, designing systems consisting of tens or hundreds of species remains one of the most difficult goals in ecology and microbiology. By utilizing high-throughput sequencing data of interspecific association networks, we here propose a framework for exploring "functional core" species that have great impacts on whole community processes and functions. The framework allows us to score each species within a large community based on three criteria: namely, topological positions, functional portfolios, and functional balance within a target network. The criteria are measures of each species' roles in maximizing functional benefits at the community or ecosystem level. When species with potentially large contributions to ecosystem-level functions are screened, the framework also helps us design "functional core microbiomes" by focusing on properties of species groups (modules) within a network. When embedded into agroecosystems or human gut, such functional core microbiomes are expected to organize whole microbiome processes and functions. An application to a plant-associated microbiome dataset actually highlighted potential functional core microbes that were known to control rhizosphere microbiomes by suppressing pathogens. Meanwhile, an example of application in mouse gut microbiomes called attention to poorly investigated bacterial species, whose potential roles within gut microbiomes deserve future experimental studies. The framework for gaining "bird's-eye" views of functional cores within networks is applicable not only to agricultural and medical data but also to datasets produced in food processing, brewing, waste water purification, and biofuel production.}, } @article {pmid32673387, year = {2020}, author = {Zhao, F and Zhang, D and Ge, C and Zhang, L and Reinach, PS and Tian, X and Tao, C and Zhao, Z and Zhao, C and Fu, W and Zeng, C and Chen, W}, title = {Metagenomic Profiling of Ocular Surface Microbiome Changes in Meibomian Gland Dysfunction.}, journal = {Investigative ophthalmology & visual science}, volume = {61}, number = {8}, pages = {22}, pmid = {32673387}, issn = {1552-5783}, mesh = {Adult ; *Campylobacter coli/genetics/immunology/pathogenicity ; *Campylobacter jejuni/genetics/immunology/pathogenicity ; Conjunctiva/microbiology ; *Enterococcus faecium/genetics/immunology/pathogenicity ; Eyelids/*microbiology ; Female ; Gene Expression Profiling/methods ; Humans ; Immune Evasion ; Male ; *Meibomian Gland Dysfunction/metabolism/microbiology ; Metagenomics/*methods ; Microbiota/*genetics ; *Tears/metabolism/microbiology ; }, abstract = {PURPOSE: Ocular surface microbiome changes can affect meibomian gland dysfunction (MGD) development. This study aimed to delineate differences among the microbiome of eyelid skin, conjunctiva, and meibum in healthy controls (HCs) and patients afflicted with MGD.

METHODS: Shotgun metagenomic analysis was used to determine if there are differences between the microbial communities in ocular sites surrounding the meibomian gland in healthy individuals and patients afflicted with MGD.

RESULTS: The meibum bacterial content of these microbiomes was dissimilar in these two different types of individuals. Almost all of the most significant taxonomic changes in the meibum microbiome of individuals with MGD were also present in their eyelid skin, but not in the conjunctiva. Such site-specific microbe pattern changes accompany increases in the gene expression levels controlling carbohydrate and lipid metabolism. Most of the microbiomes in patients with MGD possess a microbe population capable of metabolizing benzoate. Pathogens known to underlie ocular infection were evident in these individuals. MGD meibum contained an abundance of Campylobacter coli, Campylobacter jejuni, and Enterococcus faecium pathogens, which were almost absent from HCs. Functional annotation indicated that in the microbiomes of MGD meibum their capability to undergo chemotaxis, display immune evasive virulence, and mediate type IV secretion was different than that in the microbiomes of meibum isolated from HCs.

CONCLUSIONS: MGD meibum contains distinct microbiota whose immune evasive virulence is much stronger than that in the HCs. Profiling differences between the meibum microbiome makeup in HCs and patients with MGD characterizes changes of microbial communities associated with the disease status.}, } @article {pmid32672812, year = {2020}, author = {Saak, CC and Dinh, CB and Dutton, RJ}, title = {Experimental approaches to tracking mobile genetic elements in microbial communities.}, journal = {FEMS microbiology reviews}, volume = {44}, number = {5}, pages = {606-630}, pmid = {32672812}, issn = {1574-6976}, support = {DP2 AT010401/AT/NCCIH NIH HHS/United States ; T32 GM007198/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Environmental Microbiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Microbiological Techniques/*trends ; Microbiota/*genetics ; }, abstract = {Horizontal gene transfer is an important mechanism of microbial evolution and is often driven by the movement of mobile genetic elements between cells. Due to the fact that microbes live within communities, various mechanisms of horizontal gene transfer and types of mobile elements can co-occur. However, the ways in which horizontal gene transfer impacts and is impacted by communities containing diverse mobile elements has been challenging to address. Thus, the field would benefit from incorporating community-level information and novel approaches alongside existing methods. Emerging technologies for tracking mobile elements and assigning them to host organisms provide promise for understanding the web of potential DNA transfers in diverse microbial communities more comprehensively. Compared to existing experimental approaches, chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts. We also briefly discuss how fermented food microbiomes, given their experimental tractability and moderate species complexity, make ideal models to which to apply the techniques discussed herein and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities.}, } @article {pmid32670226, year = {2020}, author = {Gubelit, YI and Grossart, HP}, title = {New Methods, New Concepts: What Can Be Applied to Freshwater Periphyton?.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1275}, pmid = {32670226}, issn = {1664-302X}, abstract = {Microbial interactions play an essential role in aquatic ecosystems and are of the great interest for both marine and freshwater ecologists. Recent development of new technologies and methods allowed to reveal many functional mechanisms and create new concepts. Yet, many fundamental aspects of microbial interactions have been almost exclusively studied for marine pelagic and benthic ecosystems. These studies resulted in a formulation of the Black Queen Hypothesis, a development of the phycosphere concept for pelagic communities, and a realization of microbial communication as a key mechanism for microbial interactions. In freshwater ecosystems, especially for periphyton communities, studies focus mainly on physiology, biodiversity, biological indication, and assessment, but the many aspects of microbial interactions are neglected to a large extent. Since periphyton plays a great role for aquatic nutrient cycling, provides the basis for water purification, and can be regarded as a hotspot of microbial biodiversity, we highlight that more in-depth studies on microbial interactions in periphyton are needed to improve our understanding on functioning of freshwater ecosystems. In this paper we first present an overview on recent concepts (e.g., the "Black Queen Hypothesis") derived from state-of-the-art OMICS methods including metagenomics, metatranscriptomics, and metabolomics. We then point to the avenues how these methods can be applied for future studies on biodiversity and the ecological role of freshwater periphyton, a yet largely neglected component of many freshwater ecosystems.}, } @article {pmid32670222, year = {2020}, author = {Zhu, Z and Sun, Y and Zhu, F and Liu, Z and Pan, R and Teng, L and Guo, S}, title = {Seasonal Variation and Sexual Dimorphism of the Microbiota in Wild Blue Sheep (Pseudois nayaur).}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1260}, pmid = {32670222}, issn = {1664-302X}, abstract = {Microbiota of the wild blue sheep (Pseudois nayaur) presents a seasonal variation due to different dietary selection and feeding strategies from different ecological niches chosen by different sex in summer. To address those issues, we analyzed the variation of gut microbiota based on the material from the feces, with 16S rRNA and meta-genome aimed to explore seasonal and gender differences. The results indicate that seasonal dietary changes and gender differentiation, as expected, cause the variation in sheep's gut microbiota structure. The variation of the former is more significant than the latter. Dominant Firmicutes exists a significantly higher abundance in summer than that in winter. Subordinate Bacteroides expresses no seasonal difference between the two seasons. Compared with the winter group, the summer group is featured by abundant enzymes digesting cellulose and generating short-chain fatty acids (SCFAs), such as beta-glucosidase (EC: 3.2.1.21) for cellulose digestion, and butyrate kinase (EC:2.7.2.7) in butyrate metabolism, implying that the changes of the composition in intestinal flora allow the sheep to adapt to the seasonalized dietary selection through alternated microbial functions to reach the goal of facilitating the efficiency of energy harvesting. The results also show that the blue sheep expresses a prominent sexual dimorphism in the components of gut microbiota, indicating that the two sexes have different adaptations to the dietary selection, and demands for physical and psychological purposes. Thus, this study provides an example of demonstrating the principles and regulations of natural selection and environmental adaptation.}, } @article {pmid32669368, year = {2020}, author = {Dirksen, P and Assié, A and Zimmermann, J and Zhang, F and Tietje, AM and Marsh, SA and Félix, MA and Shapira, M and Kaleta, C and Schulenburg, H and Samuel, BS}, title = {CeMbio - The Caenorhabditis elegans Microbiome Resource.}, journal = {G3 (Bethesda, Md.)}, volume = {10}, number = {9}, pages = {3025-3039}, pmid = {32669368}, issn = {2160-1836}, support = {DP2 DK116645/DK/NIDDK NIH HHS/United States ; P40 OD010440/OD/NIH HHS/United States ; R01 AG061302/AG/NIA NIH HHS/United States ; R01 OD024780/OD/NIH HHS/United States ; }, mesh = {Animals ; *Caenorhabditis elegans/genetics ; Metabolic Networks and Pathways ; Mice ; *Microbiota ; Models, Biological ; }, abstract = {The study of microbiomes by sequencing has revealed a plethora of correlations between microbial community composition and various life-history characteristics of the corresponding host species. However, inferring causation from correlation is often hampered by the sheer compositional complexity of microbiomes, even in simple organisms. Synthetic communities offer an effective approach to infer cause-effect relationships in host-microbiome systems. Yet the available communities suffer from several drawbacks, such as artificial (thus non-natural) choice of microbes, microbe-host mismatch (e.g., human microbes in gnotobiotic mice), or hosts lacking genetic tractability. Here we introduce CeMbio, a simplified natural Caenorhabditis elegans microbiota derived from our previous meta-analysis of the natural microbiome of this nematode. The CeMbio resource is amenable to all strengths of the C. elegans model system, strains included are readily culturable, they all colonize the worm gut individually, and comprise a robust community that distinctly affects nematode life-history. Several tools have additionally been developed for the CeMbio strains, including diagnostic PCR primers, completely sequenced genomes, and metabolic network models. With CeMbio, we provide a versatile resource and toolbox for the in-depth dissection of naturally relevant host-microbiome interactions in C. elegans.}, } @article {pmid32665602, year = {2020}, author = {Meenatchi, R and Brindangnanam, P and Hassan, S and Rathna, K and Kiran, GS and Selvin, J}, title = {Diversity of a bacterial community associated with Cliona lobata Hancock and Gelliodes pumila (Lendenfeld, 1887) sponges on the South-East coast of India.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {11558}, pmid = {32665602}, issn = {2045-2322}, mesh = {Alphaproteobacteria/classification ; Animals ; Arsenic ; Bacteria/classification ; *Biodiversity ; Cadmium ; Climate ; Cluster Analysis ; High-Throughput Nucleotide Sequencing ; India ; Lead ; Mercury ; Metagenome ; Metals, Heavy ; *Microbiota ; Phylogeny ; Porifera/*microbiology ; Quality Control ; RNA, Ribosomal, 16S/genetics ; Seaweed ; }, abstract = {Marine sponges are sources of various bioactive metabolites, including several anticancer drugs, produced mainly by sponge-associated microbes. Palk Bay, on the south-east coast of India, is an understudied, highly disturbed reef environment exposed to various anthropogenic and climatic stresses. In recent years, Palk Bay suffered from pollution due to the dumping of untreated domestic sewage, effluents from coastal aquaculture, tourism, salt pans, cultivation of exotic seaweeds, and geogenic heavy-metal pollution, especially arsenic, mercury, cadmium, and lead. Low microbial-abundant sponge species, such as Gelliodes pumila and Cliona lobata, were found to be ubiquitously present in this reef environment. Triplicate samples of each of these sponge species were subjected to Illumina MiSeq sequencing using V3-V4 region-specific primers. In both C. lobata and G. pumila, there was an overwhelming dominance (98 and 99%) of phylum Candidatus Saccharibacteria and Proteobacteria, respectively. The overall number of operational taxonomic units (OTUs) was 68 (40 and 13 OTUs unique to G. pumila and C. lobata, respectively; 15 shared OTUs). Alphaproteobacteria was the most abundant class in both the sponge species. Unclassified species of phylum Candidatus Saccharibacteria from C. lobata and Chelotivorans composti from G. pumila were the most abundant bacterial species. The predominance of Alphaproteobacteria also revealed the occurrence of various xenobiotic-degrading, surfactant-producing bacterial genera in both the sponge species, indirectly indicating the possible polluted reef status of Palk Bay. Studies on sponge microbiomes at various understudied geographical locations might be helpful in predicting the status of reef environments.}, } @article {pmid32665016, year = {2020}, author = {Le Bastard, Q and Chapelet, G and Birgand, G and Hillmann, BM and Javaudin, F and Hayatgheib, N and Bourigault, C and Bemer, P and De Decker, L and Batard, E and Lepelletier, D and Montassier, E}, title = {Gut microbiome signatures of nursing home residents carrying Enterobacteria producing extended-spectrum β-lactamases.}, journal = {Antimicrobial resistance and infection control}, volume = {9}, number = {1}, pages = {107}, pmid = {32665016}, issn = {2047-2994}, mesh = {Aged ; Aged, 80 and over ; Anti-Bacterial Agents/pharmacology ; Carrier State/microbiology ; Drug Resistance, Multiple, Bacterial ; Enterobacteriaceae/drug effects/enzymology/*genetics ; Enterobacteriaceae Infections/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Microbial Sensitivity Tests ; Nursing Homes/*statistics & numerical data ; *Transcriptome ; beta-Lactamases/*genetics ; }, abstract = {BACKGROUND: The prevalence of extended beta-lactamase producing Enterobacteriaceae (ESBL-E) has been constantly increasing over the last few decades. These microorganisms that have acquired broad antibiotic resistance are now common human pathogens. Changes in the gut microbiome, induced by antibiotics or other drugs, enable expansion of these microorganisms, but the mechanisms are not yet fully understood.

OBJECTIVES: The main objective was to identify specific bacteria and functional pathways and genes characterizing the gut microbiome of nursing home residents carrying ESBL-E, using metagenomics.

SUBJECTS AND METHODS: We included 144 residents living in two different nursing homes. All fecal samples were screened for ESBL-E and gut microbiome was characterized using shallow shotgun metagenomic DNA sequencing.

RESULTS: Ten nursing home residents were colonized by ESBL-E, namely Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae species, and were compared to non-carriers. We found that ESBL-E carriers had an alteration in within-sample diversity. Using a bootstrap algorithm, we found that the gut microbiome of ESBL-E carriers was depleted in butyrate-producing species, enriched in succinate-producing species and enriched in pathways involved in intracellular pH homeostasis compared to non-carriers individuals. Several energy metabolism pathways were overrepresented in ESBL-E carriers suggesting a greater ability to metabolize multiple microbiota and mucus layer-derived nutrients.

CONCLUSIONS: The gut microbiome of ESBL-E carriers in nursing homes harbors specific taxonomic and functional characteristics, conferring an environment that enables Enterobacteriaceae expansion. Here we describe new functional features associated with ESBL-E carriage that could help us to elucidate the complex interactions leading to colonization persistence in the human gut microbiota.}, } @article {pmid32663709, year = {2020}, author = {Yao, Y and Yan, L and Chen, H and Wu, N and Wang, W and Wang, D}, title = {Cyclocarya paliurus polysaccharides alleviate type 2 diabetic symptoms by modulating gut microbiota and short-chain fatty acids.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {77}, number = {}, pages = {153268}, doi = {10.1016/j.phymed.2020.153268}, pmid = {32663709}, issn = {1618-095X}, mesh = {Adult ; Animals ; Diabetes Mellitus, Experimental/drug therapy/metabolism/microbiology ; Diabetes Mellitus, Type 2/*drug therapy/metabolism/microbiology ; Fatty Acids, Volatile/analysis/biosynthesis ; Feces/chemistry/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Glucagon-Like Peptide 1/metabolism ; Humans ; Hypoglycemic Agents/*pharmacology ; Juglandaceae/*chemistry/microbiology ; Male ; Metabolomics ; Metagenome ; Plant Leaves/chemistry ; Plants, Medicinal/chemistry ; Polysaccharides/*pharmacology ; Rats, Sprague-Dawley ; }, abstract = {BACKGROUND: Cyclocarya paliurus polysaccharide (CCPP), a primary active component in the leaves of Cyclocarya paliurus (Batal.) Iljinsk (C. paliurus), has the ability to treat type 2 diabetes mellitus (T2DM), but cannot be digested by our digestive system. Therefore, mechanisms of regulating the gut microbiota and intestinal metabolites might exist.

PURPOSE: To reveal the potential mechanism of CCPP treatment, this study aimed to investigate the alterations of the gut microbiota and intestinal metabolites especially short chain fatty acids (SCFAs) in type 2 diabetic rats.

STUDY DESIGN AND METHODS: Type 2 diabetic rat models were developed, and the therapeutic effects of CCPP were evaluated. Metagenomics analysis was utilized to analyze the alterations to the gut microbiota, and UHPLC-QTOF/MS-based untargeted metabolomics analysis of colon contents was used to identify the differential intestinal metabolites. GC/MS was used to measure the SCFAs in rat's colon contents and human fecal inoculums. Furthermore, the expression of SCFA receptors including GPR41, GPR43 and GPR109a was verified by qRT-PCR and the concentration of glucagon-like peptide-1(GLP-1) and peptide tyrosinetyrosine (PYY) was measured by Elisa.

RESULTS: Inhibition of the blood glucose levels and improvements in glucose tolerance and serum lipid parameters were observed after CCPP treatment. Eleven SCFA-producing species including Ruminococcus_bromii, Anaerotruncus_colihominis, Clostridium_methylpentosum, Roseburia_intestinalis, Roseburia_hominis, Clostridium_asparagiforme, Pseudoflavonifractor_capillosus, Intestinimonas_butyriciproducens, Intestinimonas_sp._GD2, Oscillibacter_valericigenes and Oscillibacter_ruminantium were clearly increased in the CCPP group. Furthermore, our study indicated that CCPP increases the production of SCFAs both in vivo and in vitro, and the gut microbiota are the key factor of this process. The SCFA receptors including GPR41, GPR43 and GPR109a, were significantly stimulated in the CCPP treated rats, which was accompanied by the upregulated expression of GLP-1 and PYY.

CONCLUSION: These results demonstrated that CCPP could alleviate type 2 diabetic symptoms by increasing the SCFA-producing bacteria, promoting the production of SCFAs and upregulating SCFA-GLP1/PYY associated sensory mediators.}, } @article {pmid32663105, year = {2020}, author = {Oh, NS and Lee, JY and Kim, YT and Kim, SH and Lee, JH}, title = {Cancer-protective effect of a synbiotic combination between Lactobacillus gasseri 505 and a Cudrania tricuspidata leaf extract on colitis-associated colorectal cancer.}, journal = {Gut microbes}, volume = {12}, number = {1}, pages = {1785803}, pmid = {32663105}, issn = {1949-0984}, mesh = {Animals ; Antioxidants/metabolism ; Apoptosis/drug effects ; Cell Proliferation/drug effects ; Colitis-Associated Neoplasms/*drug therapy/immunology/microbiology/pathology ; Colon/drug effects/metabolism/microbiology/pathology ; Cultured Milk Products/analysis/microbiology ; Cytokines/metabolism ; Disease Models, Animal ; Fatty Acids, Volatile/analysis ; Feces/chemistry/microbiology ; Gastrointestinal Microbiome/drug effects ; Immunomodulation ; Inflammation ; Lactobacillus gasseri/*physiology ; Maclura/*chemistry ; Mice ; Plant Extracts/*therapeutic use ; Plant Leaves/chemistry ; *Synbiotics/administration & dosage/analysis ; }, abstract = {Previously, a synbiotic combination of probiotic Lactobacillus gasseri 505 (LG) and a new prebiotic, Cudrania tricuspidata leaf extract (CT) in fermented milk, designated FCT, showed an in vitro immunomodulatory effect and antioxidant activity. Although synbiotic combination might have cancer-protective effects, these activities have not been fully validated in vivo. Ten-week treatment of LG, CT, or FCT to azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced colitis-associated colorectal cancer (CAC) mouse model reduced both the incidence of colonic tumors and damage to the colonic mucosa effectively, suggesting a cancer-protective effect. To understand these, biomarkers associated with inflammation, colon barrier, apoptosis, and cancer cell proliferation were monitored in AOM/DSS group versus LG/CT/FCT groups. A synbiotic combination (FCT) down-regulated pro-inflammatory cytokines (TNF-α, IFN-γ, IL-1β, and IL-6) and inflammation-associated enzymes (iNOS and COX-2), and up-regulated anti-inflammatory cytokines (IL-4 and IL-10). In addition, colon barrier experiment revealed that biomarkers of mucus layer (MUC-2 and TFF3) and tight junction (occludin and ZO-1) were up-regulated. Subsequent apoptosis experiment showed that pro-apoptotic factors (p53, p21, and Bax) were up-regulated and anti-apoptotic factors (Bcl-2 and Bcl-xL) were down-regulated. Furthermore, comparative metagenome analysis of gut microbiota revealed that Staphylococcus decreased but Lactobacillus, Bifidobacterium, and Akkermansia increased, supporting their protective effects, accompanied by increased short-chain fatty acids (SCFAs). Taken together, the FCT administration showed cancer-protective effects by reducing the risk of colitis-associated colon cancer via regulation of inflammation, carcinogenesis, and compositional change of gut microbiota. Consequently, the synbiotic combination (FCT) could be a novel potential health-protective natural agent against CAC.}, } @article {pmid32663059, year = {2020}, author = {Ma, C and Wasti, S and Huang, S and Zhang, Z and Mishra, R and Jiang, S and You, Z and Wu, Y and Chang, H and Wang, Y and Huo, D and Li, C and Sun, Z and Sun, Z and Zhang, J}, title = {The gut microbiome stability is altered by probiotic ingestion and improved by the continuous supplementation of galactooligosaccharide.}, journal = {Gut microbes}, volume = {12}, number = {1}, pages = {1785252}, pmid = {32663059}, issn = {1949-0984}, mesh = {Animals ; *Dietary Supplements ; Gastrointestinal Microbiome/*drug effects/genetics ; Glycoside Hydrolases/genetics ; Lactobacillus plantarum/genetics/growth & development/metabolism ; Mice ; Mutation ; Oligosaccharides/administration & dosage/metabolism/*pharmacology ; Prebiotics/administration & dosage ; Probiotics/administration & dosage/*pharmacology ; }, abstract = {The stable gut microbiome plays a key role in sustaining host health, while the instability of gut microbiome also has been found to be a risk factor of various metabolic diseases. At the ecological and evolutionary scales, the inevitable competition between the ingested probiotic and indigenous gut microbiome can lead to an increase in the instability. It remains largely unclear if and how exogenous prebiotic can improve the overall gut microbiome stability in probiotic consumption. In this study, we used Lactobacillus plantarum HNU082 (Lp082) as a model probiotic to examine the impact of the continuous or pulsed supplementation of galactooligosaccharide (GOS) on the gut microbiome stability in mice using shotgun metagenomic sequencing. Only continuous GOS supplement promoted the growth of probiotic and decreased its single-nucleotide polymorphisms (SNPs) mutation under competitive conditions. Besides, persistent GOS supplementation increased the overall stability, reshaped the probiotic competitive interactions with Bacteroides species in the indigenous microbiome, which was also evident by over-abundance of carbohydrate-active enzymes (CAZymes) accordingly. Also, we identified a total of 793 SNPs arisen in probiotic administration in the indigenous microbiome. Over 90% of them derived from Bacteroides species, which involved genes encoding transposase, CAZymes, and membrane proteins. However, neither GOS supplementation here de-escalated the overall adaptive mutations within the indigenous microbes during probiotic intake. Collectively, our study demonstrated the beneficial effect of continuous prebiotic supplementation on the ecological and genetic stability of gut microbiomes.}, } @article {pmid32660640, year = {2020}, author = {Adegoke, A and Neff, E and Geary, A and Husser, MC and Wilson, K and Norris, SM and Dharmarajan, G and Karim, S}, title = {Laboratory colonization by Dirofilaria immitis alters the microbiome of female Aedes aegypti mosquitoes.}, journal = {Parasites & vectors}, volume = {13}, number = {1}, pages = {349}, pmid = {32660640}, issn = {1756-3305}, support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; }, mesh = {*Aedes/microbiology/parasitology ; Animals ; Bacteria/genetics/isolation & purification ; Cat Diseases/parasitology/transmission ; Cats ; DNA, Bacterial ; *Dirofilaria immitis ; Dirofilariasis/transmission ; Dog Diseases/parasitology/transmission ; Dogs ; Female ; Klebsiella oxytoca/genetics/isolation & purification ; Metagenome ; Metagenomics ; *Microbiota ; Mosquito Vectors/microbiology/parasitology ; Phylogeny ; RNA, Ribosomal, 16S ; Symbiosis ; }, abstract = {BACKGROUND: The ability of blood-feeding arthropods to successfully acquire and transmit pathogens of medical and veterinary importance has been shown to be interfered with, or enhanced by, the arthropod's native microbiome. Mosquitoes transmit viruses, protozoan and filarial nematodes, the majority of which contribute to the 17% of infectious disease cases worldwide. Dirofilaria immitis, a mosquito-transmitted filarial nematodes of dogs and cats, is vectored by several mosquito species including Aedes aegypti.

METHODS: In this study, we investigated the impact of D. immitis colonization on the microbiome of laboratory reared female Ae. aegypti. Metagenomic analysis of the V3-V4 variable region of the microbial 16S RNA gene was used for identification of the microbial differences down to species level.

RESULTS: We generated a total of 1068 OTUs representing 16 phyla, 181 genera and 271 bacterial species. Overall, in order of abundance, Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes were the most represented phylum with D. immitis-infected mosquitoes having more of Proteobacteria (71%) than uninfected mosquitoes (56.9%). An interesting finding in this study is the detection of Klebsiella oxytoca in relatively similar abundance in infected and uninfected mosquitoes, suggesting a possible endosymbiotic relationship, and has been previously shown to indirectly compete for nutrients with fungi on domestic housefly eggs and larvae. While D. immitis colonization has no effect on the overall species richness, we identified significant differences in the composition of selected bacterial genera and phyla between the two groups. We also reported distinct compositional and phylogenetic differences in the individual bacterial species when commonly identified bacteria were compared.

CONCLUSIONS: To the best of our knowledge, this is the first study to understand the impact of a filarial infection on the microbiome of its mosquito vector. Further studies are required to identify bacteria species that could play an important role in the mosquito biology. While the microbiome composition of Ae. aegypti mosquito have been previously reported, our study shows that in an effort to establish itself, a filarial nematode modifies and alters the overall microbial diversity within its mosquito host.}, } @article {pmid32660414, year = {2020}, author = {Huh, JW and Roh, TY}, title = {Opportunistic detection of Fusobacterium nucleatum as a marker for the early gut microbial dysbiosis.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {208}, pmid = {32660414}, issn = {1471-2180}, support = {NRF-2014M3C9A3064548, NRF-2017M3C9A6047625//National Research Foundation of Korea/International ; 10Z20130012243//Ministry of Education/International ; S2632274//Technology Development Program of MSS, Republic of Korea/International ; }, mesh = {Bacteria/*classification/isolation & purification ; Discriminant Analysis ; Dysbiosis/*diagnosis ; Feces/microbiology ; Female ; Fusobacterium nucleatum/*isolation & purification ; Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Logistic Models ; Longitudinal Studies ; Male ; Phylogeny ; }, abstract = {BACKGROUND: The essential roles of gut microbiome have been emphasized in modulating human health and disease. Fusobacterium nucleatum (F. nucleatum), an obligate Gram-negative microorganism residing in oral cavity, gastrointestinal tract and elsewhere, has been recently considered as a potential oncobacterium associated with human cancers. However, the consequence of its enrichment was not extensively explored in terms of microbial homeostasis and stability at the early stage of disease development.

RESULT: Our analysis on longitudinal metagenomic data generated by the Integrative Human Microbiome Project (iHMP) showed that F. nucleatum was frequently found in inflammatory bowel diseases (IBD) subjects with reduced microbial diversity. Using non-parametric logarithmic linear discriminant analysis (LDA) effect size (LEfSe) algorithm, 12 IBD- and 14 non-IBD-specific bacterial species were identified in the fecal metagenome and the IBD-specific ones were over-represented in the F. nucleatum-experienced subjects during long-term surveillance. In addition, F. nucleatum experience severely abrogated intra-personal stability of microbiome in IBD patients and induced highly variable gut microbiome between subjects. From the longitudinal comparison between microbial distributions prior and posterior to F. nucleatum detection, 41 species could be proposed as indicative "classifiers" for dysbiotic gut state. By multiple logistic regression models established on these classifiers, the high probability of experiencing F. nucleatum was significantly correlated with decreased alpha-diversity and increased number of biomarker species for IBD and colorectal cancer (CRC). Finally, microbial clustering confirmed that biomarker species for IBD and non-IBD conditions as well as CRC signature markers were well distinguishable and could be utilized for explaining gut symbiosis and dysbiosis.

CONCLUSION: F. nucleatum opportunistically appeared under early dysbiotic condition in gut, and discriminative classifier species associated with F. nucleatum were successfully applied to predict microbial alterations in both IBD and non-IBD conditions. Our prediction model and microbial classifier biomarkers for estimating gut dysbiosis should provide a novel aspect of microbial homeostasis/dynamics and useful information on non-invasive biomarker screening.}, } @article {pmid32660025, year = {2020}, author = {Palacios, T and Vitetta, L and Coulson, S and Madigan, CD and Lam, YY and Manuel, R and Briskey, D and Hendy, C and Kim, JN and Ishoey, T and Soto-Giron, MJ and Schott, EM and Toledo, G and Caterson, ID}, title = {Targeting the Intestinal Microbiota to Prevent Type 2 Diabetes and Enhance the Effect of Metformin on Glycaemia: A Randomised Controlled Pilot Study.}, journal = {Nutrients}, volume = {12}, number = {7}, pages = {}, pmid = {32660025}, issn = {2072-6643}, mesh = {Aged ; Bacteroidetes/physiology ; Blood Glucose/*analysis ; Butyrates/blood ; Diabetes Mellitus, Type 2/*blood ; Fatty Acids, Volatile/blood ; Female ; Firmicutes/physiology ; *Gastrointestinal Microbiome/drug effects ; Haptoglobins ; Humans ; Hypoglycemic Agents/*administration & dosage ; Insulin Resistance ; Male ; Metabolic Networks and Pathways/drug effects ; Metformin/*administration & dosage ; Middle Aged ; Pilot Projects ; Prediabetic State/blood ; Probiotics/*administration & dosage/adverse effects/pharmacology ; Protein Precursors/blood ; Proteobacteria/physiology ; }, abstract = {Early treatment may prevent or delay the onset of type 2 diabetes mellitus (T2DM) in individuals who are at high risk. Lifestyle interventions and the hypoglycemic drug metformin have been shown to reduce T2DM incidence. The effectiveness of such interventions may be enhanced by targeting environmental factors such as the intestinal microbiota, which has been proven to predict the response to lifestyle interventions and play a part in mediating the glucose-lowering effects of metformin. Shifts in the intestinal microbiota "towards a more balanced state" may promote glucose homeostasis by regulating short-chain fatty acids' production. This study aimed to investigate the safety and effect of a multi-strain probiotic on glycemic, inflammatory, and permeability markers in adults with prediabetes and early T2DM and to assess whether the probiotic can enhance metformin's effect on glycaemia. A randomised controlled pilot study was conducted in 60 adults with a BMI ≥ 25 kg/m[2] and with prediabetes or T2DM (within the previous 12 months). The participants were randomised to a multi-strain probiotic (L. plantarum, L. bulgaricus, L. gasseri, B. breve, B. animalis sbsp. lactis, B. bifidum, S. thermophilus, and S. boulardii) or placebo for 12 weeks. Analyses of the primary outcome (fasting plasma glucose) and secondary outcomes, including, but not limited to, circulating lipopolysaccharide, zonulin, and short chain fatty acids and a metagenomic analysis of the fecal microbiome were performed at baseline and 12 weeks post-intervention. The results showed no significant differences in the primary and secondary outcome measures between the probiotic and placebo group. An analysis of a subgroup of participants taking metformin showed a decrease in fasting plasma glucose, HbA1c, insulin resistance, and zonulin; an increase in plasma butyrate concentrations; and an enrichment of microbial butyrate-producing pathways in the probiotic group but not in the placebo group. Probiotics may act as an adjunctive to metformin by increasing the production of butyrate, which may consequently enhance glucose management.}, } @article {pmid32657325, year = {2020}, author = {Yang, F and Sun, J and Luo, H and Ren, H and Zhou, H and Lin, Y and Han, M and Chen, B and Liao, H and Brix, S and Li, J and Yang, H and Kristiansen, K and Zhong, H}, title = {Assessment of fecal DNA extraction protocols for metagenomic studies.}, journal = {GigaScience}, volume = {9}, number = {7}, pages = {}, pmid = {32657325}, issn = {2047-217X}, mesh = {Biodiversity ; Biomarkers ; Feces/*microbiology ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Shotgun metagenomic sequencing has improved our understanding of the human gut microbiota. Various DNA extraction methods have been compared to find protocols that robustly and most accurately reflect the original microbial community structures. However, these recommendations can be further refined by considering the time and cost demands in dealing with samples from very large human cohorts. Additionally, fungal DNA extraction performance has so far been little investigated.

RESULTS: We compared 6 DNA extraction protocols, MagPure Fast Stool DNA KF Kit B, Macherey Nagel™ NucleoSpin™®Soil kit, Zymo Research Quick-DNA™ Fecal/Soil Microbe kit, MOBIO DNeasy PowerSoil kit, the manual non-commercial protocol MetaHIT, and the recently published protocol Q using 1 microbial mock community (MMC) (containing 8 bacterial and 2 fungal strains) and fecal samples. All samples were manually extracted and subjected to shotgun metagenomics sequencing. Extracting DNA revealed high reproducibility within all 6 protocols, but microbial extraction efficiencies varied. The MMC results demonstrated that bead size was a determining factor for fungal and bacterial DNA yields. In human fecal samples, the MagPure bacterial extraction performed as well as the standardized protocol Q but was faster and more cost-effective. Extraction using the PowerSoil protocol resulted in a significantly higher ratio of gram-negative to gram-positive bacteria than other protocols, which might contribute to reported gut microbial differences between healthy adults.

CONCLUSIONS: We emphasize the importance of bead size selection for bacterial and fungal DNA extraction. More importantly, the performance of the novel protocol MP matched that of the recommended standardized protocol Q but consumed less time, was more cost-effective, and is recommended for further large-scale human gut metagenomic studies.}, } @article {pmid32657213, year = {2020}, author = {Jantharadej, K and Mhuantong, W and Limpiyakorn, T and Mongkolsuk, S and Sirikanchana, K and Suwannasilp, BB}, title = {Identification of sulfate-reducing and methanogenic microbial taxa in anaerobic bioreactors from industrial wastewater treatment plants using next-generation sequencing and gene clone library analyses.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering}, volume = {55}, number = {11}, pages = {1283-1293}, doi = {10.1080/10934529.2020.1789409}, pmid = {32657213}, issn = {1532-4117}, mesh = {Anaerobiosis ; Biofuels/*analysis ; Bioreactors/*microbiology ; Deltaproteobacteria/genetics/isolation & purification ; Desulfovibrio/genetics/isolation & purification ; Gene Library ; High-Throughput Nucleotide Sequencing ; Metagenome/*genetics ; Microbiota/*genetics ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; Wastewater/microbiology ; Water Purification/*methods ; }, abstract = {An understanding of microbial communities present in anaerobic bioreactors can strongly facilitate the development of approaches to control undesirable microorganisms, such as sulfate-reducing bacteria (SRB), in the system. In this study, overall microbial communities present in anaerobic bioreactors from seven industrial wastewater treatment plants (including food, pulp and paper industries) were investigated using 16S rRNA gene amplicon sequencing (MiSeq, Illumina). The dominant methanogens identified in the anaerobic bioreactors treating industrial wastewater were Methanobacterium and Methanosaeta; Methanospirillum was a predominant methanogen in the anaerobic sludge digester. Hydrogenotrophic and acetoclastic methanogens were detected at similar relative abundances in the anaerobic covered lagoons treating starch wastewater, whereas hydrogenotrophic methanogens were the predominant methanogens present in the sludge digester. SRB communities were further investigated using dsrB gene clone libraries. The results indicated the presence of SRB, such as uncultured Desulfobulbus sp., Syntrophobacter fumaroxidans, Syntrophorhabdus sp. PtaB.Bin027, and Desulfovibrio fructosivarans JJ. Incomplete-oxidizing SRB were the predominant SRB in all of the anaerobic bioreactors treating wastewater. In contrast, similar relative abundances of complete and incomplete-oxidizing SRB were observed in the sludge digester. The results of this study can further facilitate the development of SRB-controlling strategies to improve the efficiency of wastewater treatment.}, } @article {pmid32656096, year = {2020}, author = {Yang, Q and Wang, Y and Wei, X and Zhu, J and Wang, X and Xie, X and Lu, W}, title = {The Alterations of Vaginal Microbiome in HPV16 Infection as Identified by Shotgun Metagenomic Sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {286}, pmid = {32656096}, issn = {2235-2988}, mesh = {Dysbiosis ; Female ; Human papillomavirus 16/genetics ; Humans ; *Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {The association of microbiome imbalance with cancer development is being one of the research hotspots. Persistent HPV infection is a causal event in cervical cancer initiation, but, little is known about the microbiome composition and function in HPV infection. Here we identified the compositional and functional alterations on vaginal samples from 27 HPV16 positive women and 25 age-matched HPV negative controls using shotgun metagenomic sequencing, to provide a comprehensive investigation describing the microbial abundances and enriched metabolic functions in cervicovaginal metagenomes. We further employed qPCR assays to evaluate two selected gene markers of HPV16 infection in an independent validation cohort consisting of 88 HPV16 positive women and 81 controls, and six selected species markers in a subset of validation cohort of 45 HPV16 positive women and 53 controls. We found that the relative abundance of dominant Firmicutes was lower, Actinobacteria, Fusobacteria and viruses phyla were significantly higher in the HPV16-positive group; 77 genera including Gardnerella, Peptostreptococcus, and Prevotella were higher, and 20 genera including Lactobacillus and Aerococcus were lower in the HPV16-positive women. Abundance of 12 genes, 17 genera, and 7 species biomarkers showed an excellent predictive power for the HPV16-positive individuals, with 0.861, 0.819, and 0.918, respectively, of the area under the receiver-operating characteristic curve (AUC). We further characterized the microbial function, and revealed that HPV16-positive women were enriched in metabolism and membrane transport, and depleted by glycan biosynthesis and metabolism, and replication and repair. Quantitative PCR measurements validated that one gene marker and three species were significantly enriched in HPV16-positive women. These results highlight a fundamental fact that there are altered composition and function of the vaginal microbiome in HPV16-positive women, suggesting that vaginal dysbiosis may be associated with HPV infection in the female genital tract.}, } @article {pmid32655541, year = {2020}, author = {Hu, Q and Liu, C and Zhang, D and Wang, R and Qin, L and Xu, Q and Che, L and Gao, F}, title = {Effects of Low-Dose Antibiotics on Gut Immunity and Antibiotic Resistomes in Weaned Piglets.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {903}, pmid = {32655541}, issn = {1664-3224}, mesh = {Animals ; Anti-Bacterial Agents/*administration & dosage ; Bacteria/*drug effects/genetics/immunology ; Bacterial Proteins/genetics ; Colon/*drug effects/immunology/microbiology ; *Drug Resistance, Bacterial/genetics ; Female ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Profiling ; Host-Pathogen Interactions ; Ileum/*drug effects/immunology/microbiology ; Immunity, Innate/*drug effects/genetics ; Interspersed Repetitive Sequences ; Metagenomics ; Methyltransferases/genetics ; Sus scrofa ; Transcriptome ; Weaning ; }, abstract = {Widespread antibiotic use increases the risk of livestock acting as potential reservoirs of antimicrobial resistance genes (ARGs) that may be transferred to human and animal pathogens. Particularly, maternal-infant transmission of antibiotics via breastmilk represents a great concern regarding infant health. In this study, we investigated the effects of 4-week low-dose antibiotic (LDA) treatment on the host immunity and antibiotic resistomes in weaned piglets. Transcriptomic analyses of ileum tissues revealed that the affected genes were largely enriched in innate immunity-related pathways. Significantly reduced protein expression of inflammatory factors, i.e., IFN-γ, IL-6 were observed. In addition, analyses of antibiotic resistomes identified a total of 1,021 ARGs related to 39 classes of antibiotics. The samples exhibited highly individual-specific diversity and no significant difference in the structure and diversity of ARGs and mobile gene elements (MGE) after LDA exposure for both colon and ileum samples. Despite of that, there were significant changes in the abundance of two transferrable ARGs [Erm(T) and tcr3] related to the antibiotics administered, implying an increased risk of transferrable antibiotic resistance. There was a significant change in the abundance of one pathogenic species after LDA exposure in the colon samples and one in the ileum samples, but there were no significant differences in the matched ARGs. Collectively, our findings reveal considerable changes in intestinal immunity-related genes, but minimal effects on gut antibiotic resistomes (ARGs and MGEs) in weaned piglets after 4 weeks LDA exposure. Our study provides a foundation for evaluating the longer-term cumulative effects of LDA use, especially the effects of maternal-infant LDA transmission, on antibiotic resistance and risks to infant health.}, } @article {pmid32654263, year = {2020}, author = {Jiang, L and Lang, S and Duan, Y and Zhang, X and Gao, B and Chopyk, J and Schwanemann, LK and Ventura-Cots, M and Bataller, R and Bosques-Padilla, F and Verna, EC and Abraldes, JG and Brown, RS and Vargas, V and Altamirano, J and Caballería, J and Shawcross, DL and Ho, SB and Louvet, A and Lucey, MR and Mathurin, P and Garcia-Tsao, G and Kisseleva, T and Brenner, DA and Tu, XM and Stärkel, P and Pride, D and Fouts, DE and Schnabl, B}, title = {Intestinal Virome in Patients With Alcoholic Hepatitis.}, journal = {Hepatology (Baltimore, Md.)}, volume = {72}, number = {6}, pages = {2182-2196}, pmid = {32654263}, issn = {1527-3350}, support = {R01 AA020703/AA/NIAAA NIH HHS/United States ; I01 BX004594/BX/BLRD VA/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; BX004594/BX/BLRD VA/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 AA026939/AA/NIAAA NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; R01 AA24726/AA/NIAAA NIH HHS/United States ; R01AA020703/AA/NIAAA NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; }, mesh = {Adult ; Aged ; Animals ; Bacteriophages/genetics/isolation & purification ; Case-Control Studies ; DNA, Viral/isolation & purification ; End Stage Liver Disease/diagnosis/mortality/therapy/*virology ; Feces/virology ; Female ; Hepatitis, Alcoholic/diagnosis/mortality/therapy/*virology ; Herpesviridae/genetics/isolation & purification ; Humans ; Intestinal Mucosa/*virology ; Liver/pathology ; Liver Cirrhosis/diagnosis/mortality/therapy/*virology ; Male ; Metagenomics ; Middle Aged ; Parvoviridae/genetics/isolation & purification ; RNA, Viral/isolation & purification ; Severity of Illness Index ; Survival Rate ; Virome/*genetics ; }, abstract = {BACKGROUND AND AIMS: Alcoholic hepatitis (AH) is a severe manifestation of alcohol-associated liver disease (ALD) with high mortality. Although gut bacteria and fungi modulate disease severity, little is known about the effects of the viral microbiome (virome) in patients with ALD.

APPROACH AND RESULTS: We extracted virus-like particles from 89 patients with AH who were enrolled in a multicenter observational study, 36 with alcohol use disorder (AUD), and 17 persons without AUD (controls). Virus-like particles from fecal samples were fractionated using differential filtration techniques, and metagenomic sequencing was performed to characterize intestinal viromes. We observed an increased viral diversity in fecal samples from patients with ALD, with the most significant changes in samples from patients with AH. Escherichia-, Enterobacteria-, and Enterococcus phages were over-represented in fecal samples from patients with AH, along with significant increases in mammalian viruses such as Parvoviridae and Herpesviridae. Antibiotic treatment was associated with higher viral diversity. Specific viral taxa, such as Staphylococcus phages and Herpesviridae, were associated with increased disease severity, indicated by a higher median Model for End-Stage Liver Disease score, and associated with increased 90-day mortality.

CONCLUSIONS: In conclusion, intestinal viral taxa are altered in fecal samples from patients with AH and associated with disease severity and mortality. Our study describes an intestinal virome signature associated with AH.}, } @article {pmid32653000, year = {2020}, author = {Tun, HM and Li, S and Yoon, I and Meale, SJ and Azevedo, PA and Khafipour, E and Plaizier, JC}, title = {Saccharomyces cerevisiae fermentation products (SCFP) stabilize the ruminal microbiota of lactating dairy cows during periods of a depressed rumen pH.}, journal = {BMC veterinary research}, volume = {16}, number = {1}, pages = {237}, pmid = {32653000}, issn = {1746-6148}, support = {238454//NSERC/ ; ARDI10-1053//Agri-Food Research and Development Initiative/ ; }, mesh = {Acidosis/diet therapy/*veterinary ; Animal Feed/analysis ; Animals ; Cattle ; Cattle Diseases/*diet therapy ; Ciliophora ; Diet/veterinary ; Female ; Fermentation ; Gastrointestinal Microbiome ; Hydrogen-Ion Concentration ; Lactation ; RNA, Ribosomal, 16S ; Rumen/chemistry/*microbiology ; *Saccharomyces cerevisiae ; Stomach Diseases/diet therapy/microbiology/veterinary ; }, abstract = {BACKGROUND: Effects of Saccharomyces cerevisiae fermentation products (SCFP) on rumen microbiota were determined in vitro and in vivo under a high and a depressed pH. The in vitro trial determined the effects of Original XPC and NutriTek (Diamond V, Cedar Rapids, IA) at doses of 1.67 and 2.33 g/L, respectively, on the abundances of rumen bacteria under a high pH (> 6.3) and a depressed pH (5.8-6.0) using quantitative PCR (qPCR). In the in vivo trial eight rumen-cannulated lactating dairy cows were used in a cross-over design. Cows were randomly assigned to SCFP treatments (Original XPC, Diamond V, Cedar Rapids, IA) or control (No SCFP) before two 5-week experimental periods. During the second period, SCFP treatments were reversed. Cows on the SCFP treatment were supplemented with 14 g/d of SCFP and 126 g/d of ground corn. Other cows received 140 g/d ground corn. During the first 4 wk. of each period, cows received a basal diet containing 153 g/kg of starch. During week 5 of both periods, the rumen pH was depressed by a SARA challenge. This included replacing 208 g/kg of the basal diet with pellets of ground wheat and barley, resulting in a diet that contained 222 g/kg DM of starch. Microbial communities in rumen liquid digesta were examined by pyrosequencing, qPCR, and shotgun metagenomics.

RESULTS: During the in vitro experiment, XPC and NutriTek increased the relative abundances of Ruminococcus flavefaciens, and Fibrobacter succinogenes determined at both the high and the depressed pH, with NutriTek having the largest effect. The relative abundances of Prevotella brevis, R. flavefaciens, ciliate protozoa, and Bifidobacterium spp. were increased by XPC in vivo. Adverse impacts of the in vivo SARA challenge included reductions of the richness and diversity of the rumen microbial community, the abundances of Bacteroidetes and ciliate protozoa in the rumen as determined by pyrosequencing, and the predicted functionality of rumen microbiota as determined by shotgun metagenomics. These reductions were attenuated by XPC supplementation.

CONCLUSIONS: The negative effects of grain-based SARA challenges on the composition and predicted functionality of rumen microbiota are attenuated by supplementation with SCFP.}, } @article {pmid32652145, year = {2020}, author = {Lang, S and Demir, M and Martin, A and Jiang, L and Zhang, X and Duan, Y and Gao, B and Wisplinghoff, H and Kasper, P and Roderburg, C and Tacke, F and Steffen, HM and Goeser, T and Abraldes, JG and Tu, XM and Loomba, R and Stärkel, P and Pride, D and Fouts, DE and Schnabl, B}, title = {Intestinal Virome Signature Associated With Severity of Nonalcoholic Fatty Liver Disease.}, journal = {Gastroenterology}, volume = {159}, number = {5}, pages = {1839-1852}, pmid = {32652145}, issn = {1528-0012}, support = {R01 AA020703/AA/NIAAA NIH HHS/United States ; P42 ES010337/ES/NIEHS NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 AA026939/AA/NIAAA NIH HHS/United States ; R01 DK106419/DK/NIDDK NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; I01 BX004594/BX/BLRD VA/United States ; }, mesh = {Adult ; Aged ; Case-Control Studies ; Cross-Sectional Studies ; Feces/virology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestines/*virology ; Liver Cirrhosis/diagnosis/*virology ; Male ; Middle Aged ; Non-alcoholic Fatty Liver Disease/diagnosis/*virology ; Prospective Studies ; Severity of Illness Index ; *Virome ; Young Adult ; }, abstract = {BACKGROUND & AIMS: Alterations in the gut microbiome have been associated with the severity of nonalcoholic fatty liver disease (NAFLD). Previous studies focused exclusively on the bacteria in the microbiome; we investigated changes in the viral microbiome (virome) in patients with NAFLD.

METHODS: In a prospective, cross-sectional, observational study, we extracted RNA and DNA virus-like particles from fecal samples from 73 patients with NAFLD: 29 patients had an NAFLD Activity Score (NAS) of 0-4, 44 patients had an NAS of 5-8 or liver cirrhosis (LCI), 37 patients had F0-F1 fibrosis, and 36 patients had F2-F4 fibrosis. As controls, 9 individuals without liver disease and 13 patients with mild primary biliary cholangitis were included in the analysis. We performed shotgun metagenomic sequencing of virus-like particles.

RESULTS: Patients with NAFLD and NAS 5-8/LCI had a significant decrease in intestinal viral diversity compared with patients with NAFLD and NAS 0-4 or control individuals. The presence of more advanced NAFLD was associated with a significant reduction in the proportion of bacteriophages compared with other intestinal viruses. Using multivariate logistic regression analysis with leave-1-out cross validation, we developed a model, including a viral diversity index and simple clinical variables, that identified patients with NAS 5-8/LCI with an area under the curve of 0.95 (95% confidence interval, 0.91-0.99) and F2-F4 fibrosis with an area under the curve of 0.88 (95% confidence interval, 0.80-0.95). Addition of data on viral diversity significantly improved multivariate models, including those based on only clinical parameters or bacterial diversity.

CONCLUSIONS: In a study of fecal viromes from patients with NAFLD and control individuals, we associated histologic markers of NAFLD severity with significant decreases in viral diversity and proportion of bacteriophages. We developed a model based on fecal viral diversity and clinical data that identifies patients with severe NAFLD and fibrosis more accurately than models based only on clinical or bacterial data.}, } @article {pmid32652063, year = {2020}, author = {Hryckowian, AJ and Merrill, BD and Porter, NT and Van Treuren, W and Nelson, EJ and Garlena, RA and Russell, DA and Martens, EC and Sonnenburg, JL}, title = {Bacteroides thetaiotaomicron-Infecting Bacteriophage Isolates Inform Sequence-Based Host Range Predictions.}, journal = {Cell host & microbe}, volume = {28}, number = {3}, pages = {371-379.e5}, pmid = {32652063}, issn = {1934-6069}, support = {T32 GM008353/GM/NIGMS NIH HHS/United States ; DP1 AT009892/AT/NCCIH NIH HHS/United States ; R01 DK085025/DK/NIDDK NIH HHS/United States ; T32 GM145304/GM/NIGMS NIH HHS/United States ; DP5 OD019893/OD/NIH HHS/United States ; T32 AI007328/AI/NIAID NIH HHS/United States ; R01 GM099513/GM/NIGMS NIH HHS/United States ; R03 DK096023/DK/NIDDK NIH HHS/United States ; S10 RR026780/RR/NCRR NIH HHS/United States ; }, mesh = {Bacteriophages/*classification/*genetics/isolation & purification ; Bacteroides thetaiotaomicron/genetics/*virology ; Bangladesh ; Biodiversity ; Gastrointestinal Microbiome ; Genome, Viral ; Genomics ; Host Specificity/*genetics ; Humans ; Metagenome/genetics ; Phylogeny ; Sequence Analysis ; United States ; Viral Tropism/*genetics ; Whole Genome Sequencing ; }, abstract = {Our emerging view of the gut microbiome largely focuses on bacteria, while less is known about other microbial components, such as bacteriophages (phages). Though phages are abundant in the gut, very few phages have been isolated from this ecosystem. Here, we report the genomes of 27 phages from the United States and Bangladesh that infect the prevalent human gut bacterium Bacteroides thetaiotaomicron. These phages are mostly distinct from previously sequenced phages with the exception of two, which are crAss-like phages. We compare these isolates to existing human gut metagenomes, revealing similarities to previously inferred phages and additional unexplored phage diversity. Finally, we use host tropisms of these phages to identify alleles of phage structural genes associated with infectivity. This work provides a detailed view of the gut's "viral dark matter" and a framework for future efforts to further integrate isolation- and sequencing-focused efforts to understand gut-resident phages.}, } @article {pmid32652061, year = {2020}, author = {Fujimoto, K and Kimura, Y and Shimohigoshi, M and Satoh, T and Sato, S and Tremmel, G and Uematsu, M and Kawaguchi, Y and Usui, Y and Nakano, Y and Hayashi, T and Kashima, K and Yuki, Y and Yamaguchi, K and Furukawa, Y and Kakuta, M and Akiyama, Y and Yamaguchi, R and Crowe, SE and Ernst, PB and Miyano, S and Kiyono, H and Imoto, S and Uematsu, S}, title = {Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts.}, journal = {Cell host & microbe}, volume = {28}, number = {3}, pages = {380-389.e9}, doi = {10.1016/j.chom.2020.06.005}, pmid = {32652061}, issn = {1934-6069}, support = {R01 AI079145/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteriophages/*genetics/isolation & purification ; Clostridioides difficile/*virology ; Clostridium Infections/therapy ; Disease Models, Animal ; Endopeptidases/*genetics/pharmacology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial ; Genome, Viral ; Humans ; Metagenome ; Mice ; Mice, Inbred C57BL ; Phage Therapy/*methods ; Prophages/*genetics ; Sequence Analysis, DNA ; Specific Pathogen-Free Organisms ; Viral Proteins/genetics/pharmacology ; }, abstract = {The application of bacteriophages (phages) is proposed as a highly specific therapy for intestinal pathobiont elimination. However, the infectious associations between phages and bacteria in the human intestine, which is essential information for the development of phage therapies, have yet to be fully elucidated. Here, we report the intestinal viral microbiomes (viromes), together with bacterial microbiomes (bacteriomes), in 101 healthy Japanese individuals. Based on the genomic sequences of bacteriomes and viromes from the same fecal samples, the host bacteria-phage associations are illustrated for both temperate and virulent phages. To verify the usefulness of the comprehensive host bacteria-phage information, we screened Clostridioides difficile-specific phages and identified antibacterial enzymes whose activity is confirmed both in vitro and in vivo. These comprehensive metagenome analyses reveal not only host bacteria-phage associations in the human intestine but also provide vital information for the development of phage therapies against intestinal pathobionts.}, } @article {pmid32651763, year = {2020}, author = {Akobeng, AK and Singh, P and Kumar, M and Al Khodor, S}, title = {Role of the gut microbiota in the pathogenesis of coeliac disease and potential therapeutic implications.}, journal = {European journal of nutrition}, volume = {59}, number = {8}, pages = {3369-3390}, pmid = {32651763}, issn = {1436-6215}, mesh = {*Celiac Disease ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Infant ; Prebiotics ; *Probiotics ; }, abstract = {PURPOSE: Although genetic predisposition and exposure to dietary gluten are considered necessary triggers for the development of coeliac disease, alterations in the gut microbial composition may also contribute towards the pathogenesis of coeliac disease. This review aims to provide an overview of the available data on the potential mechanisms through which the gut microbiota plays a role in the causation of coeliac disease and to discuss the potential therapeutic strategies that could diminish the consequences of microbial dysbiosis.

METHOD: A search of the literature was performed using the PubMed, Embase, and JSTOR databases; relevant articles were included.

RESULTS: Recent studies in patients with coeliac disease have reported an increase in the relative amounts of gram negative bacterial genera such as Bacteroides, Prevotella, and Escherichia, and reduced amounts of protective anti-inflammatory bacteria such as Bifidobacteria and Lactobacilli. Dysbiotic microbiota may lead to a dysregulated immune response that may contribute to the pathogenesis of coeliac disease. In infancy, antibiotic use and certain infant feeding practices may lead to alterations in the developing gut microbiota to influence the immune maturation process and predispose to coeliac disease.

CONCLUSION: The induction of the intestinal immune system and gluten intolerance may be influenced by the relative abundance of certain microbiota. Factors such as infant feeding practices, diet, antibiotics, and infections, may be involved in the development of coeliac disease due to their influence on gut microbial composition. The efficacy of potential modulators of the gut microbiota such as probiotics, prebiotics, and fecal microbial transplant as adjunctive treatments to gluten-free diet in coeliac disease is unproven and requires further investigation.}, } @article {pmid32651235, year = {2021}, author = {Hu, S and Vich Vila, A and Gacesa, R and Collij, V and Stevens, C and Fu, JM and Wong, I and Talkowski, ME and Rivas, MA and Imhann, F and Bolte, L and van Dullemen, H and Dijkstra, G and Visschedijk, MC and Festen, EA and Xavier, RJ and Fu, J and Daly, MJ and Wijmenga, C and Zhernakova, A and Kurilshikov, A and Weersma, RK}, title = {Whole exome sequencing analyses reveal gene-microbiota interactions in the context of IBD.}, journal = {Gut}, volume = {70}, number = {2}, pages = {285-296}, pmid = {32651235}, issn = {1468-3288}, support = {R01 MH115957/MH/NIMH NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 HG010140/HG/NHGRI NIH HHS/United States ; U01 HG009080/HG/NHGRI NIH HHS/United States ; R56 MH115957/MH/NIMH NIH HHS/United States ; }, mesh = {Adaptor Proteins, Signal Transducing/genetics ; Adult ; Case-Control Studies ; DNA Copy Number Variations/genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Gene Frequency/genetics ; Genetic Predisposition to Disease/*genetics ; Humans ; Inflammatory Bowel Diseases/*etiology/genetics/microbiology ; Male ; Membrane Proteins/genetics ; Metagenomics ; Middle Aged ; Quantitative Trait Loci/genetics ; Receptors, Interleukin-17/genetics ; Transcription Factors/genetics ; Vesicular Transport Proteins/genetics ; *Exome Sequencing ; }, abstract = {OBJECTIVE: Both the gut microbiome and host genetics are known to play significant roles in the pathogenesis of IBD. However, the interaction between these two factors and its implications in the aetiology of IBD remain underexplored. Here, we report on the influence of host genetics on the gut microbiome in IBD.

DESIGN: To evaluate the impact of host genetics on the gut microbiota of patients with IBD, we combined whole exome sequencing of the host genome and whole genome shotgun sequencing of 1464 faecal samples from 525 patients with IBD and 939 population-based controls. We followed a four-step analysis: (1) exome-wide microbial quantitative trait loci (mbQTL) analyses, (2) a targeted approach focusing on IBD-associated genomic regions and protein truncating variants (PTVs, minor allele frequency (MAF) >5%), (3) gene-based burden tests on PTVs with MAF <5% and exome copy number variations (CNVs) with site frequency <1%, (4) joint analysis of both cohorts to identify the interactions between disease and host genetics.

RESULTS: We identified 12 mbQTLs, including variants in the IBD-associated genes IL17REL, MYRF, SEC16A and WDR78. For example, the decrease of the pathway acetyl-coenzyme A biosynthesis, which is involved in short chain fatty acids production, was associated with variants in the gene MYRF (false discovery rate <0.05). Changes in functional pathways involved in the metabolic potential were also observed in participants carrying rare PTVs or CNVs in CYP2D6, GPR151 and CD160 genes. These genes are known for their function in the immune system. Moreover, interaction analyses confirmed previously known IBD disease-specific mbQTLs in TNFSF15.

CONCLUSION: This study highlights that both common and rare genetic variants affecting the immune system are key factors in shaping the gut microbiota in the context of IBD and pinpoints towards potential mechanisms for disease treatment.}, } @article {pmid32650814, year = {2020}, author = {Wu, J and Dai, Y and Lo, ECM and Qi, Y and Zhang, Y and Li, QL and Dai, R}, title = {Using metagenomic analysis to assess the effectiveness of oral health promotion interventions in reducing risk for pneumonia among patients with stroke in acute phase: study protocol for a randomized controlled trial.}, journal = {Trials}, volume = {21}, number = {1}, pages = {634}, pmid = {32650814}, issn = {1745-6215}, support = {8170041044//Young Scientists Fund/ ; 1808085QH247//Natural Science Foundation of Anhui Province/ ; }, mesh = {China ; *Health Promotion ; Humans ; *Metagenomics ; Microbiota ; Mouth/microbiology ; *Oral Health ; Oral Hygiene ; Pneumonia/*prevention & control ; RNA, Ribosomal, 16S ; Randomized Controlled Trials as Topic ; Single-Blind Method ; Stroke/*complications ; }, abstract = {BACKGROUND: The prevalence of pneumonia complicating stroke in acute phase has a poor prognosis and higher risk for death. Oral opportunistic pathogens have been reported to be associated with pneumonia among people with compromised health. Oral health promotion is effective in reducing dental plaque among patients with stroke, which is considered as reservoirs for oral opportunistic pathogens. This study evaluates the effectiveness of oral health promotions in reducing the prevalence of pneumonia via its effects on composition and relative abundance of oral opportunistic pathogens.

METHODS/DESIGN: This study is a randomized, single-blind, parallel trial of 6 months duration. The study is being conducted at one of the largest medical teaching hospitals in Hefei, China. A total of 166 patients with stroke and free from any post-stroke complication will be recruited. After enrollment, patients will be randomized to one of the following groups: (1) oral hygiene instruction (OHI) or (2) OHI, 6-month use of powered tooth brushing, and 0.2% chlorhexidine gluconate mouth rinse (10 ml twice daily). The primary outcome is the prevalence of pneumonia complicating stroke. Patients will be monitored closely for any occurrence of pneumonia over the entire period of this trial. Oral rinse samples will be collected at baseline and multiple follow-up reviews (3, 5, 7 days, and 1, 3, 6 months after baseline). Next-generation sequencing will be employed to detect composition and relative abundances of the microorganism in the oral rinse samples. Questionnaire interviews and clinical oral examinations will be conducted at baseline and 1, 3, and 6 months after baseline.

DISCUSSION: The findings of this trial will provide evidence whether oral health promotion intervention is effective in reducing the prevalence of pneumonia complicating stroke via its effect on the oral microbiome. The analysis of the outcomes of this trial is empowered by metagenomic analysis at 16S rRNA level, which is more sensitive and comprehensive to help us detect how oral health promotion inventions affect the oral microbiome in terms of its composition, relative abundance, and interactions between species, which all may contribute to the occurrence of pneumonia complicating stroke.

TRIAL REGISTRATION: ClinicalTrials.gov NCT04095780 . Registered on 19 September 2019.}, } @article {pmid32649837, year = {2021}, author = {Ledormand, P and Desmasures, N and Dalmasso, M}, title = {Phage community involvement in fermented beverages: an open door to technological advances?.}, journal = {Critical reviews in food science and nutrition}, volume = {61}, number = {17}, pages = {2911-2920}, doi = {10.1080/10408398.2020.1790497}, pmid = {32649837}, issn = {1549-7852}, mesh = {*Bacteriophages/genetics ; Beverages ; Community Participation ; Fermentation ; *Fermented Foods ; Humans ; Metagenome ; *Microbiota ; }, abstract = {Bacteriophages (phages) are considered the most abundant biological entities on Earth. An increasing interest in understanding phage communities, also called viromes or phageomes, has arisen over the past decade especially thanks to the development and the accessibility of Next Generation Sequencing techniques. Despite the increasing amount of available metagenomic data on microbial communities in various habitats, viromes remain poorly described in the scientific literature particularly when it comes to fermented food and beverages such as wine and cider. In this review, a particular attention is paid to the current knowledge on phage communities, with a special focus on fermented food viromes and the methodological tools available to undertake their study. There is a striking lack of available data on the fermented foods and beverages viromes. As far as we know, and although a number of phages have been isolated from wine, no general study has to date been carried out to assess the diversity of viromes in fermented beverages and their possible interactions with microbiota throughout the fermentation process. With the aim of establishing connections between the currently used technologies to carry out the analysis of viromes, possible applications of current knowledge to fermented beverages are examined.}, } @article {pmid32648690, year = {2019}, author = {Deaton, J and Yu, FB and Quake, SR}, title = {Mini-Metagenomics and Nucleotide Composition Aid the Identification and Host Association of Novel Bacteriophage Sequences.}, journal = {Advanced biosystems}, volume = {3}, number = {11}, pages = {e1900108}, doi = {10.1002/adbi.201900108}, pmid = {32648690}, issn = {2366-7478}, mesh = {Bacteriophages/*genetics/isolation & purification ; *Biodiversity ; *Genome, Viral ; *Metagenomics ; *Sequence Analysis, DNA ; }, abstract = {A broad spectrum of metagenomic and single cell sequencing techniques have become popular for dissecting environmental microbial diversity, leading to the characterization of thousands of novel microbial lineages. In addition to recovering bacterial and archaeal genomes, metagenomic assembly can also produce genomes of viruses that infect microbial cells. Because of their diversity, lack of marker genes, and small genome size, identifying novel bacteriophage sequences from metagenomic data is often challenging, especially when the objective is to establish phage-host relationships. The present work describes a computational approach that uses supervised learning to classify metagenomic contigs as phage or non-phage as well as assigning phage taxonomy based on tetranucleotide frequencies. Furthermore, the method assigns phage-host relationships using co-occurrence statistics derived from a recently developed mini-metagenomic experimental technique. This work evaluates method performance at identifying viral contigs and predicting taxonomic classification using publicly available references. Then, using two mini-metagenomic datasets, over 100 novel phage contigs from hot spring samples of Yellowstone National Park are identified and assigned to putative microbial hosts. Results of this work demonstrate the value of combining viral sequence identification with mini-metagenomic experimental methods to understand the microbial ecosystem.}, } @article {pmid32648469, year = {2021}, author = {Shibata, K and Ogai, K and Ogura, K and Urai, T and Aoki, M and Arisandi, D and Takahashi, N and Okamoto, S and Sanada, H and Sugama, J}, title = {Skin Physiology and its Microbiome as Factors Associated with the Recurrence of Pressure Injuries.}, journal = {Biological research for nursing}, volume = {23}, number = {1}, pages = {75-81}, doi = {10.1177/1099800420941100}, pmid = {32648469}, issn = {1552-4175}, mesh = {Aged ; Aged, 80 and over ; Epidermis/physiology ; Female ; Humans ; Japan/epidemiology ; Long-Term Care/statistics & numerical data ; Male ; *Microbiota ; Pressure Ulcer/*microbiology/nursing/*pathology ; Prospective Studies ; Recurrence ; Skin/*microbiology/pathology ; *Skin Physiological Phenomena ; }, abstract = {BACKGROUND: Preventing recurrent pressure injuries (RPIs) is one of the important challenges faced in healthcare, but the risk factors of RPIs have not been fully revealed. This study aims to explore factors associated with RPIs, by focusing on skin physiology and its microbiome as local factors crucial for the health of healed tissue after pressure injury healing.

METHODS: This prospective observational study was conducted in a long-term care facility in Japan with patients whose PIs had healed within 1 month. Skin physiology was evaluated by stratum corneum (SC) hydration, pH, and transepidermal water loss. Skin bacteria was collected by tape stripping, followed by 16S ribosomal RNA-based metagenomics analysis. These parameters were evaluated every two weeks over a period of six weeks.

RESULTS: A total of 30 patients were included in this study, and 8 patients (26.7%) had an RPI within 6 weeks. In this study, significantly lower SC hydration and a higher rate of Staphylococcus species on the healed site were found in the RPI group.

DISCUSSION: A high rate of RPIs (about one in four) points out the necessity of a further care strategy on the healed PIs. Lower skin hydration and/or the increase in Staphylococcus bacteria may have a potential to be used as a biomarker for the prediction of RPIs, or may be an intervention point for the prevention of RPIs by, for example, skin cleansing with moisturizing care.}, } @article {pmid32647153, year = {2020}, author = {Borrego, C and Sabater, S and Proia, L}, title = {Lifestyle preferences drive the structure and diversity of bacterial and archaeal communities in a small riverine reservoir.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {11288}, pmid = {32647153}, issn = {2045-2322}, mesh = {Archaea/*classification ; Bacteria/*classification ; Biota ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Geologic Sediments/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Rivers/*microbiology ; Spain ; Water Microbiology ; }, abstract = {Spatial heterogeneity along river networks is interrupted by dams, affecting the transport, processing, and storage of organic matter, as well as the distribution of biota. We here investigated the structure of planktonic (free-living, FL), particle-attached (PA) and sediment-associated (SD) bacterial and archaeal communities within a small reservoir. We combined targeted-amplicon sequencing of bacterial and archaeal 16S rRNA genes in the DNA and RNA community fractions from FL, PA and SD, followed by imputed functional metagenomics, in order to unveil differences in their potential metabolic capabilities within the reservoir (tail, mid, and dam sections) and lifestyles (FL, PA, SD). Both bacterial and archaeal communities were structured according to their life-style preferences rather than to their location in the reservoir. Bacterial communities were richer and more diverse when attached to particles or inhabiting the sediment, while Archaea showed an opposing trend. Differences between PA and FL bacterial communities were consistent at functional level, the PA community showing higher potential capacity to degrade complex carbohydrates, aromatic compounds, and proteinaceous materials. Our results stressed that particle-attached prokaryotes were phylogenetically and metabolically distinct from their free-living counterparts, and that performed as hotspots for organic matter processing within the small reservoir.}, } @article {pmid32645241, year = {2020}, author = {Liu, Y and Jin, X and Hong, HG and Xiang, L and Jiang, Q and Ma, Y and Chen, Z and Cheng, L and Jian, Z and Wei, Z and Ai, J and Qi, S and Sun, Q and Li, H and Li, Y and Wang, K}, title = {The relationship between gut microbiota and short chain fatty acids in the renal calcium oxalate stones disease.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {34}, number = {8}, pages = {11200-11214}, doi = {10.1096/fj.202000786R}, pmid = {32645241}, issn = {1530-6860}, mesh = {Animals ; Bacteria/genetics ; Calcium Oxalate/*metabolism ; Case-Control Studies ; Fatty Acids, Volatile/*metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Kidney/*metabolism ; Kidney Calculi/*metabolism/*microbiology ; Male ; Metagenomics/methods ; Middle Aged ; Nephrolithiasis/metabolism/microbiology ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; }, abstract = {The relationship of gut microbiota and calcium oxalate stone has been limited investigated, especially with no study of gut microbiota and short chain fatty acids (SCFAs) in nephrolithiasis. We provided Sprague Dawley rats of renal calcium oxalate stones with antibiotics and examined the renal crystals deposition. We also performed a case-control study by analyzing 16S rRNA microbial profiling, shotgun metagenomics and SCFAs in 153 fecal samples from non-kidney stone (NS) controls, patients with occasional renal calcium oxalate stones (OS) and patients with recurrent stones (RS). Antibiotics reduced bacterial load in feces and could promote the formation of renal calcium crystals in model rats. In addition, both OS and RS patients exhibited higher fecal microbial diversity than NS controls. Several SCFAs-producing gut bacteria, as well as metabolic pathways associated with SCFAs production, were considerably lower in the gut microbiota among the kidney stone patients compared with the NS controls. Representation of genes involved in oxalate degradation showed no significance difference among groups. However, fecal acetic acid concentration was the highest in RS patients with high level of urinary oxalate, which was positively correlated with genes involvement in oxalate synthesis. Administration of SCFAs reduced renal crystals. These results shed new light on bacteria and SCFAs, which may promote the development of treatment strategy in nephrolithiasis.}, } @article {pmid32645030, year = {2020}, author = {Vancuren, SJ and Dos Santos, SJ and Hill, JE and , }, title = {Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling.}, journal = {PloS one}, volume = {15}, number = {7}, pages = {e0235682}, pmid = {32645030}, issn = {1932-6203}, support = {//CIHR/Canada ; }, mesh = {Bacteria/genetics ; Chaperonin 60/*genetics ; DNA Barcoding, Taxonomic/*methods ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Vagina/microbiology ; }, abstract = {Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes. Exact sequence variant calling has been proposed as an alternative to previously established methods for aggregation of sequence reads into operational taxonomic units (OTU). We investigated the utility of variant calling for cpn60 barcode sequences and determined the minimum sequence length required to provide species-level resolution. Sequence data from the 5´ region of the cpn60 barcode amplified from the human vaginal microbiome (n = 45), and a mock community were used to compare variant calling to de novo assembly of reads, and mapping to a reference sequence database in terms of number of OTU formed, and overall community composition. Variant calling resulted in microbiome profiles that were consistent in apparent composition to those generated with the other methods but with significant logistical advantages. Variant calling is rapid, achieves high resolution of taxa, and does not require reference sequence data. Our results further demonstrate that 150 bp from the 5´ end of the cpn60 barcode sequence is sufficient to provide species-level resolution of microbiota.}, } @article {pmid32643435, year = {2020}, author = {Ngo, ST and Restuadi, R and McCrae, AF and Van Eijk, RP and Garton, F and Henderson, RD and Wray, NR and McCombe, PA and Steyn, FJ}, title = {Progression and survival of patients with motor neuron disease relative to their fecal microbiota.}, journal = {Amyotrophic lateral sclerosis & frontotemporal degeneration}, volume = {21}, number = {7-8}, pages = {549-562}, doi = {10.1080/21678421.2020.1772825}, pmid = {32643435}, issn = {2167-9223}, mesh = {*Amyotrophic Lateral Sclerosis ; Feces ; Humans ; *Microbiota/genetics ; *Motor Neuron Disease/complications ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Gut microbiota studies have been well-investigated for neurodegenerative diseases such as Alzheimer's and Parkinson's disease, however, fewer studies have comprehensively examined the gut microbiome in Motor Neuron Disease (MND), with none examining its impact on disease prognosis. Here, we investigate MND prognosis and the fecal microbiota, using 16S rRNA case-control data from 100 individuals with extensive medical histories and metabolic measurements. We contrast the composition and diversity of fecal microbiome signatures from 49 MND and 51 healthy controls by combining current gold-standard 16S microbiome pipelines. Using stringent quality control thresholds, we conducted qualitative assessment approaches including; direct comparison of taxa, PICRUSt2 predicted metagenomics, Shannon and Chao1-index and Firmicutes/Bacteroidetes ratio. We show that the fecal microbiome of patients with MND is not significantly different from that of healthy controls that were matched by age, sex, and BMI, however there are distinct differences in Beta-diversity in some patients with MND. Weight, BMI, and metabolic and clinical features of disease in patients with MND were not related to the composition of their fecal microbiome, however, we observe a greater risk for earlier death in patients with MND with increased richness and diversity of the microbiome, and in those with greater Firmicutes to Bacteroidetes ratio. This was independent of anthropometric, metabolic, or clinical features of disease, and warrants support for further gut microbiota studies in MND. Given the disease heterogeneity in MND, and complexity of the gut microbiota, large studies are necessary to determine the detailed role of the gut microbiota and MND prognosis.}, } @article {pmid32640105, year = {2021}, author = {Van Olden, CC and Van de Laar, AW and Meijnikman, AS and Aydin, O and Van Olst, N and Hoozemans, JB and De Brauw, LM and Bruin, SC and Acherman, YIZ and Verheij, J and Pyykkö, JE and Hagedoorn, M and Sanderman, R and Bosma, NC and Tremaroli, V and Lundqvist, A and Olofsson, LE and Herrema, H and Lappa, D and Hjorth, S and Nielsen, J and Schwartz, T and Groen, AK and Nieuwdorp, M and Bäckhed, F and Gerdes, VEA}, title = {A systems biology approach to understand gut microbiota and host metabolism in morbid obesity: design of the BARIA Longitudinal Cohort Study.}, journal = {Journal of internal medicine}, volume = {289}, number = {3}, pages = {340-354}, pmid = {32640105}, issn = {1365-2796}, mesh = {Adult ; *Bariatric Surgery ; Biomarkers/metabolism ; Fatty Liver/metabolism ; Female ; *Gastrointestinal Microbiome ; Glucose/metabolism ; Humans ; Insulin/metabolism ; Longitudinal Studies ; Male ; Middle Aged ; Netherlands ; Obesity, Morbid/*metabolism/*surgery ; Phenotype ; *Research Design ; *Systems Biology ; Triglycerides/metabolism ; }, abstract = {INTRODUCTION: Prevalence of obesity and associated diseases, including type 2 diabetes mellitus, dyslipidaemia and non-alcoholic fatty liver disease (NAFLD), are increasing. Underlying mechanisms, especially in humans, are unclear. Bariatric surgery provides the unique opportunity to obtain biopsies and portal vein blood-samples.

METHODS: The BARIA Study aims to assess how microbiota and their metabolites affect transcription in key tissues and clinical outcome in obese subjects and how baseline anthropometric and metabolic characteristics determine weight loss and glucose homeostasis after bariatric surgery. We phenotype patients undergoing bariatric surgery (predominantly laparoscopic Roux-en-Y gastric bypass), before weight loss, with biometrics, dietary and psychological questionnaires, mixed meal test (MMT) and collect fecal-samples and intra-operative biopsies from liver, adipose tissues and jejunum. We aim to include 1500 patients. A subset (approximately 25%) will undergo intra-operative portal vein blood-sampling. Fecal-samples are analyzed with shotgun metagenomics and targeted metabolomics, fasted and postprandial plasma-samples are subjected to metabolomics, and RNA is extracted from the tissues for RNAseq-analyses. Data will be integrated using state-of-the-art neuronal networks and metabolic modeling. Patient follow-up will be ten years.

RESULTS: Preoperative MMT of 170 patients were analysed and clear differences were observed in glucose homeostasis between individuals. Repeated MMT in 10 patients showed satisfactory intra-individual reproducibility, with differences in plasma glucose, insulin and triglycerides within 20% of the mean difference.

CONCLUSION: The BARIA study can add more understanding in how gut-microbiota affect metabolism, especially with regard to obesity, glucose metabolism and NAFLD. Identification of key factors may provide diagnostic and therapeutic leads to control the obesity-associated disease epidemic.}, } @article {pmid32638044, year = {2021}, author = {Lukoseviciute, L and Lebedeva, J and Kuisiene, N}, title = {Diversity of Polyketide Synthases and Nonribosomal Peptide Synthetases Revealed Through Metagenomic Analysis of a Deep Oligotrophic Cave.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {110-121}, pmid = {32638044}, issn = {1432-184X}, mesh = {Acidobacteria/genetics ; Actinobacteria/genetics ; Bacteria/classification/*genetics/metabolism ; Caves/*microbiology ; Chloroflexi/genetics ; Firmicutes/genetics ; Geologic Sediments/*microbiology ; Georgia (Republic) ; Metagenome/genetics ; Microbiota/genetics ; Peptide Synthases/*genetics ; Polyketide Synthases/*genetics ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Secondary Metabolism/*genetics ; Soil Microbiology ; }, abstract = {Caves are considered to be extreme and challenging environments. It is believed that the ability of microorganisms to produce secondary metabolites enhances their survivability and adaptiveness in the energy-starved cave environment. Unfortunately, information on the genetic potential for the production of secondary metabolites, such as polyketides and nonribosomal peptides, is limited. In the present study, we aimed to identify and characterize genes responsible for the production of secondary metabolites in the microbial community of one of the deepest caves in the world, Krubera-Voronja Cave (43.4184 N 40.3083 E, Western Caucasus). The analysed sample materials included sediments, drinkable water from underground camps, soil and clay from the cave walls, speleothems and coloured spots from the cave walls. The type II polyketide synthases (PKSs) ketosynthases α and β and the adenylation domains of nonribosomal peptide synthetases (NRPSs) were investigated using a metagenomic approach. Taxonomic diversity analysis showed that most PKS sequences could be attributed to Actinobacteria followed by unclassified bacteria and Acidobacteria, while the NRPS sequences were more taxonomically diverse and could be assigned to Proteobacteria, Actinobacteria, Cyanobacteria, Firmicutes, Chloroflexi, etc. Only three putative metabolites could be predicted: an angucycline group polyketide, a massetolide A-like cyclic lipopeptide and a surfactin-like lipopeptide. The absolute majority of PKS and NRPS sequences showed low similarity with the sequences of the reference biosynthetic pathways, suggesting that these sequences could be involved in the production of novel secondary metabolites.}, } @article {pmid32636252, year = {2020}, author = {Naylor, D and Fansler, S and Brislawn, C and Nelson, WC and Hofmockel, KS and Jansson, JK and McClure, R}, title = {Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules.}, journal = {mBio}, volume = {11}, number = {4}, pages = {}, pmid = {32636252}, issn = {2150-7511}, mesh = {Bacteria/genetics ; Gene Expression Profiling ; Genetic Variation ; *Metabolic Networks and Pathways ; *Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {The soil microbiome represents one of the most complex microbial communities on the planet, encompassing thousands of taxa and metabolic pathways, rendering holistic analyses computationally intensive and difficult. Here, we developed an alternative approach in which the complex soil microbiome was broken into components ("functional modules"), based on metabolic capacities, for individual characterization. We hypothesized that reproducible, low-complexity communities that represent functional modules could be obtained through targeted enrichments and that, in combination, they would encompass a large extent of the soil microbiome diversity. Enrichments were performed on a starting soil inoculum with defined media based on specific carbon substrates, antibiotics, alternative electron acceptors under anaerobic conditions, or alternative growing conditions reflective of common field stresses. The resultant communities were evaluated through 16S rRNA amplicon sequencing. Less permissive modules (anaerobic conditions, complex polysaccharides, and certain stresses) resulted in more distinct community profiles with higher richness and more variability between replicates, whereas modules with simple substrates were dominated by fewer species and were more reproducible. Collectively, approximately 27% of unique taxa present in the liquid soil extract control were found across functional modules. Taxa that were underrepresented or undetected in the source soil were also enriched across the modules. Metatranscriptomic analyses were carried out on a subset of the modules to investigate differences in functional gene expression. These results demonstrate that by dissecting the soil microbiome into discrete components it is possible to obtain a more comprehensive view of the soil microbiome and its biochemical potential than would be possible using more holistic analyses.IMPORTANCE The taxonomic and functional diversity inherent to the soil microbiome complicate assessments of the metabolic potential carried out by the community members. An alternative approach is to break down the soil microbiome into reduced-complexity subsets based on metabolic capacities (functional modules) prior to sequencing and analysis. Here, we demonstrate that this approach successfully identified specific phylogenetic and biochemical traits of the soil microbiome that otherwise remained hidden from a more top-down analysis.}, } @article {pmid32634615, year = {2020}, author = {Xiaoting, L and Shanshan, L and Qiuhong, W and Weichen, D and Haixue, K}, title = {Metagenomics approach the intestinal microbiome structure and function in the anti-H1N1 of a traditional chinese medicine acid polysaccharide.}, journal = {Microbial pathogenesis}, volume = {147}, number = {}, pages = {104351}, doi = {10.1016/j.micpath.2020.104351}, pmid = {32634615}, issn = {1096-1208}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Influenza A Virus, H1N1 Subtype ; Medicine, Chinese Traditional ; Metagenomics ; Mice ; Polysaccharides ; }, abstract = {Ephedra sinica Stapf polysaccharide is a pure acidic uniform polysaccharide extracted from the traditional Chinese medicine Ephedra sinica Stapf. In our past research, it was found that it has anti-inflammatory response and suppresses immunity. Therefore, in this experiment, mice were infected with FM1 virus, treated with Ephedra sinica Stapf polysaccharide, and metagene sequencing was used to sequence the mouse intestinal contents. As a result, we found that Ephedra sinica Stapf polysaccharide has obvious therapeutic effect on acute lung injury caused by H1N1. In the intestinal flora, the abundance of Lactobacillales and Bifidobacteriaceae increased significantly, and the metabolome increased significantly in the KEGG pathway. The intestinal flora may be an important target of Ephedra sinica Stapf polysaccharides metabolism against H1N1.}, } @article {pmid32634417, year = {2020}, author = {Kwong, WK}, title = {Microbiome Evolution: Having the Guts to Be Different.}, journal = {Current biology : CB}, volume = {30}, number = {13}, pages = {R766-R768}, doi = {10.1016/j.cub.2020.05.040}, pmid = {32634417}, issn = {1879-0445}, mesh = {Animals ; Bees ; *Gastrointestinal Microbiome ; *Microbiota ; }, abstract = {Metagenomic sequencing of the gut microbial communities of two closely related bee species, the Western honey bee (Apis mellifera) and the Eastern honey bee (Apis cerana), show that organisms with similar characteristics can harbor unexpected differences in their microbiomes.}, } @article {pmid32633956, year = {2020}, author = {Bas-Bellver, C and Andrés, C and Seguí, L and Barrera, C and Jiménez-Hernández, N and Artacho, A and Betoret, N and Gosalbes, MJ}, title = {Valorization of Persimmon and Blueberry Byproducts to Obtain Functional Powders: In Vitro Digestion and Fermentation by Gut Microbiota.}, journal = {Journal of agricultural and food chemistry}, volume = {68}, number = {30}, pages = {8080-8090}, doi = {10.1021/acs.jafc.0c02088}, pmid = {32633956}, issn = {1520-5118}, mesh = {Bacteria/metabolism ; Blueberry Plants/*chemistry/metabolism ; Diospyros/*chemistry/metabolism ; Fermentation ; Fruit/chemistry/metabolism ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/metabolism/microbiology ; Humans ; Models, Biological ; Plant Preparations/*chemistry/metabolism ; Powders/analysis/metabolism ; Waste Products/analysis ; }, abstract = {Globalization of fruit and vegetable markets generates overproduction, surpluses, and potentially valuable residues. The valorization of these byproducts constitutes a challenge, to ensure sustainability and reintroduce them into the food chain. This work focuses on blueberry and persimmon residues, rich in polyphenols and carotenoids, to obtain powders with high added value to be used as ingredients in food formulation. These powders have been characterized, and the changes in the bioactive compounds in in vitro gastrointestinal digestion have been evaluated. The results indicated that the type of residue, the drying process, as well as the content and type of fiber determine the release of antioxidants during digestion. In vitro colonic fermentations were also performed, and it was observed that the characteristics of digested powders had an effect on the composition of the growing microbial community. Thus, carotenoids and anthocyanins maintain an interplay with microbiota that could be beneficial for human health.}, } @article {pmid32633756, year = {2020}, author = {Tovo, A and Menzel, P and Krogh, A and Cosentino Lagomarsino, M and Suweis, S}, title = {Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju.}, journal = {Nucleic acids research}, volume = {48}, number = {16}, pages = {e93}, pmid = {32633756}, issn = {1362-4962}, mesh = {Bacteria/*classification/genetics ; Computational Biology ; DNA, Bacterial/genetics ; Databases, Protein ; Gastrointestinal Microbiome/*genetics ; Genetic Markers ; Humans ; *Metagenome ; Metagenomics/*methods ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {Characterizing species diversity and composition of bacteria hosted by biota is revolutionizing our understanding of the role of symbiotic interactions in ecosystems. Determining microbiomes diversity implies the assignment of individual reads to taxa by comparison to reference databases. Although computational methods aimed at identifying the microbe(s) taxa are available, it is well known that inferences using different methods can vary widely depending on various biases. In this study, we first apply and compare different bioinformatics methods based on 16S ribosomal RNA gene and shotgun sequencing to three mock communities of bacteria, of which the compositions are known. We show that none of these methods can infer both the true number of taxa and their abundances. We thus propose a novel approach, named Core-Kaiju, which combines the power of shotgun metagenomics data with a more focused marker gene classification method similar to 16S, but based on emergent statistics of core protein domain families. We thus test the proposed method on various mock communities and we show that Core-Kaiju reliably predicts both number of taxa and abundances. Finally, we apply our method on human gut samples, showing how Core-Kaiju may give more accurate ecological characterization and a fresh view on real microbiomes.}, } @article {pmid32633011, year = {2020}, author = {Meijnikman, AS and Aydin, O and Prodan, A and Tremaroli, V and Herrema, H and Levin, E and Acherman, Y and Bruin, S and Gerdes, VE and Backhed, F and Groen, AK and Nieuwdorp, M}, title = {Distinct differences in gut microbial composition and functional potential from lean to morbidly obese subjects.}, journal = {Journal of internal medicine}, volume = {288}, number = {6}, pages = {699-710}, doi = {10.1111/joim.13137}, pmid = {32633011}, issn = {1365-2796}, mesh = {Adult ; Amino Acids/metabolism ; Body Mass Index ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Machine Learning ; Metabolic Networks and Pathways ; Metagenomics ; Middle Aged ; Obesity, Morbid/metabolism/*microbiology ; Thinness/metabolism/*microbiology ; }, abstract = {INTRODUCTION: The gut microbiome may contribute to the development of obesity. So far, the extent of microbiome variation in people with obesity has not been determined in large cohorts and for a wide range of body mass index (BMI). Here, we aimed to investigate whether the faecal microbial metagenome can explain the variance in several clinical phenotypes associated with morbid obesity.

METHODS: Caucasian subjects were recruited at our hospital. Blood pressure and anthropometric measurements were taken. Dietary intake was determined using questionnaires. Shotgun metagenomic sequencing was performed on faecal samples from 177 subjects.

RESULTS: Subjects without obesity (n = 82, BMI 24.7 ± 2.9 kg m[-2]) and subjects with obesity (n = 95, BMI 38.6 ± 5.1 kg m[-2]) could be clearly distinguished based on microbial composition and microbial metabolic pathways. A total number of 52 bacterial species differed significantly in people with and without obesity. Independent of dietary intake, we found that microbial pathways involved in biosynthesis of amino acids were enriched in subjects with obesity, whereas pathways involved in the degradation of amino acids were depleted. Machine learning models showed that more than half of the variance in body fat composition followed by BMI could be explained by the gut microbiome, composition and microbial metabolic pathways, compared with 6% of variation explained in triglycerides and 9% in HDL.

CONCLUSION: Based on the faecal microbiota composition, we were able to separate subjects with and without obesity. In addition, we found strong associations between gut microbial amino acid metabolism and specific microbial species in relation to clinical features of obesity.}, } @article {pmid32632261, year = {2020}, author = {Chng, KR and Ghosh, TS and Tan, YH and Nandi, T and Lee, IR and Ng, AHQ and Li, C and Ravikrishnan, A and Lim, KM and Lye, D and Barkham, T and Raman, K and Chen, SL and Chai, L and Young, B and Gan, YH and Nagarajan, N}, title = {Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut.}, journal = {Nature ecology & evolution}, volume = {4}, number = {9}, pages = {1256-1267}, pmid = {32632261}, issn = {2397-334X}, mesh = {Animals ; Anti-Bacterial Agents ; Bacteria/genetics ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Mice ; *Microbiota ; }, abstract = {Loss of diversity in the gut microbiome can persist for extended periods after antibiotic treatment, impacting microbiome function, antimicrobial resistance and probably host health. Despite widespread antibiotic use, our understanding of the species and metabolic functions contributing to gut microbiome recovery is limited. Using data from 4 discovery cohorts in 3 continents comprising >500 microbiome profiles from 117 individuals, we identified 21 bacterial species exhibiting robust association with ecological recovery post antibiotic therapy. Functional and growth-rate analysis showed that recovery is supported by enrichment in specific carbohydrate-degradation and energy-production pathways. Association rule mining on 782 microbiome profiles from the MEDUSA database enabled reconstruction of the gut microbial 'food web', identifying many recovery-associated bacteria as keystone species, with the ability to use host- and diet-derived energy sources, and support repopulation of other gut species. Experiments in a mouse model recapitulated the ability of recovery-associated bacteria (Bacteroides thetaiotaomicron and Bifidobacterium adolescentis) to promote recovery with synergistic effects, providing a boost of two orders of magnitude to microbial abundance in early time points and faster maturation of microbial diversity. The identification of specific species and metabolic functions promoting recovery opens up opportunities for rationally determining pre- and probiotic formulations offering protection from long-term consequences of frequent antibiotic usage.}, } @article {pmid32632193, year = {2020}, author = {Keohane, DM and Ghosh, TS and Jeffery, IB and Molloy, MG and O'Toole, PW and Shanahan, F}, title = {Microbiome and health implications for ethnic minorities after enforced lifestyle changes.}, journal = {Nature medicine}, volume = {26}, number = {7}, pages = {1089-1095}, pmid = {32632193}, issn = {1546-170X}, mesh = {Adult ; Chronic Disease/*epidemiology ; Ethnicity/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics/immunology ; Genetics, Population ; Humans ; Immune System/*immunology/microbiology ; Ireland/epidemiology ; *Life Style ; Male ; Metagenomics/methods ; Microbiota/genetics/immunology ; Phylogeny ; Roma/genetics ; Transients and Migrants ; }, abstract = {Modern lifestyles increase the risk of chronic diseases, in part by modifying the microbiome, but the health effects of lifestyles enforced on ethnic minorities are understudied[1-3]. Lifestyle affects the microbiome early in life, when the microbiome is assembled and the immune system is undergoing maturation[4-6]. Moreover, the influence of lifestyle has been separated from genetic and geographic factors by studies of genetically similar populations and ethnically distinct groups living in the same geographic location[7-11]. The lifestyle of Irish Travellers, an ethnically distinct subpopulation, changed with legislation in 2002 that effectively ended nomadism and altered their living conditions. Comparative metagenomics of gut microbiomes shows that Irish Travellers retain a microbiota similar to that of non-industrialized societies. Their microbiota is associated with non-dietary factors and is proportionately linked with risk of microbiome-related metabolic disease. Our findings suggest there are microbiome-related public health implications when ethnic minorities are pressured to change lifestyles.}, } @article {pmid32631930, year = {2020}, author = {Nelson, MT and Wolter, DJ and Eng, A and Weiss, EJ and Vo, AT and Brittnacher, MJ and Hayden, HS and Ravishankar, S and Bautista, G and Ratjen, A and Blackledge, M and McNamara, S and Nay, L and Majors, C and Miller, SI and Borenstein, E and Simon, RH and LiPuma, JJ and Hoffman, LR}, title = {Maintenance tobramycin primarily affects untargeted bacteria in the CF sputum microbiome.}, journal = {Thorax}, volume = {75}, number = {9}, pages = {780-790}, pmid = {32631930}, issn = {1468-3296}, support = {K24 HL141669/HL/NHLBI NIH HHS/United States ; P30 DK089507/DK/NIDDK NIH HHS/United States ; T32 AI055396/AI/NIAID NIH HHS/United States ; }, mesh = {Administration, Inhalation ; Adolescent ; Adult ; Aged ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; *Bacteria/genetics/isolation & purification ; Bacterial Infections/prevention & control ; Child ; Cystic Fibrosis/*microbiology/physiopathology ; Forced Expiratory Volume ; Humans ; Maintenance Chemotherapy ; Metagenome/drug effects ; Microbiota/*drug effects ; Middle Aged ; Severity of Illness Index ; Sputum/*microbiology ; Time Factors ; Tobramycin/*pharmacology/therapeutic use ; Young Adult ; }, abstract = {RATIONALE: The most common antibiotic used to treat people with cystic fibrosis (PWCF) is inhaled tobramycin, administered as maintenance therapy for chronic Pseudomonas aeruginosa lung infections. While the effects of inhaled tobramycin on P. aeruginosa abundance and lung function diminish with continued therapy, this maintenance treatment is known to improve long-term outcomes, underscoring how little is known about why antibiotics work in CF infections, what their effects are on complex CF sputum microbiomes and how to improve these treatments.

OBJECTIVES: To rigorously define the effect of maintenance tobramycin on CF sputum microbiome characteristics.

METHODS AND MEASUREMENTS: We collected sputum from 30 PWCF at standardised times before, during and after a single month-long course of maintenance inhaled tobramycin. We used traditional culture, quantitative PCR and metagenomic sequencing to define the dynamic effects of this treatment on sputum microbiomes, including abundance changes in both clinically targeted and untargeted bacteria, as well as functional gene categories.

MAIN RESULTS: CF sputum microbiota changed most markedly by 1 week of antibiotic therapy and plateaued thereafter, and this shift was largely driven by changes in non-dominant taxa. The genetically conferred functional capacities (ie, metagenomes) of subjects' sputum communities changed little with antibiotic perturbation, despite taxonomic shifts, suggesting functional redundancy within the CF sputum microbiome.

CONCLUSIONS: Maintenance treatment with inhaled tobramycin, an antibiotic with demonstrated long-term mortality benefit, primarily impacted clinically untargeted bacteria in CF sputum, highlighting the importance of monitoring the non-canonical effects of antibiotics and other treatments to accurately define and improve their clinical impact.}, } @article {pmid32630711, year = {2020}, author = {Williams, SH and Levy, A and Yates, RA and Somaweera, N and Neville, PJ and Nicholson, J and Lindsay, MDA and Mackenzie, JS and Jain, K and Imrie, A and Smith, DW and Lipkin, WI}, title = {The Diversity and Distribution of Viruses Associated with Culex annulirostris Mosquitoes from the Kimberley Region of Western Australia.}, journal = {Viruses}, volume = {12}, number = {7}, pages = {}, pmid = {32630711}, issn = {1999-4915}, support = {U19AI109761/NH/NIH HHS/United States ; }, mesh = {Animals ; Culex/*virology ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Mosquito Vectors/*virology ; *Virome ; Viruses/*classification/isolation & purification ; Western Australia ; }, abstract = {Metagenomics revealed an impressive breadth of previously unrecognized viruses. Here, we report the virome of the Culex annulirostris Skuse mosquito, an important vector of pathogenic arboviruses in Australia. Mosquitoes were collected from three sites in the Kimberley region of Western Australia. Unbiased high-throughput sequencing (HTS) revealed the presence of 16 novel viral sequences that share less than 90% identity with known viruses. None were closely related to pathogenic arboviruses. Viruses were distributed unevenly across sites, indicating a heterogeneous Cx. annulirostris virome. Polymerase chain reaction assays confirmed HTS data and identified marked variation between the virus prevalence identified at each site.}, } @article {pmid32627750, year = {2020}, author = {Yang, J and Howe, A and Lee, J and Yoo, K and Park, J}, title = {An Improved Approach to Identify Bacterial Pathogens to Human in Environmental Metagenome.}, journal = {Journal of microbiology and biotechnology}, volume = {30}, number = {9}, pages = {1335-1342}, pmid = {32627750}, issn = {1738-8872}, mesh = {Bacteria/classification/genetics/isolation & purification/pathogenicity ; Databases, Genetic ; *Environmental Microbiology ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/genetics ; Systems Integration ; }, abstract = {The identification of bacterial pathogens to humans is critical for environmental microbial risk assessment. However, current methods for identifying pathogens in environmental samples are limited in their ability to detect highly diverse bacterial communities and accurately differentiate pathogens from commensal bacteria. In the present study, we suggest an improved approach using a combination of identification results obtained from multiple databases, including the multilocus sequence typing (MLST) database, virulence factor database (VFDB), and pathosystems resource integration center (PATRIC) databases to resolve current challenges. By integrating the identification results from multiple databases, potential bacterial pathogens in metagenomes were identified and classified into eight different groups. Based on the distribution of genes in each group, we proposed an equation to calculate the metagenomic pathogen identification index (MPII) of each metagenome based on the weighted abundance of identified sequences in each database. We found that the accuracy of pathogen identification was improved by using combinations of multiple databases compared to that of individual databases. When the approach was applied to environmental metagenomes, metagenomes associated with activated sludge were estimated with higher MPII than other environments (i.e., drinking water, ocean water, ocean sediment, and freshwater sediment). The calculated MPII values were statistically distinguishable among different environments (p<0.05). These results demonstrate that the suggested approach allows more for more accurate identification of the pathogens associated with metagenomes.}, } @article {pmid32626665, year = {2020}, author = {Huston, WM and Tachedjian, G}, title = {Editorial: Interplay of Infection and Microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {304}, doi = {10.3389/fcimb.2020.00304}, pmid = {32626665}, issn = {2235-2988}, mesh = {High-Throughput Nucleotide Sequencing ; Metagenomics ; *Microbiota ; }, } @article {pmid32624568, year = {2020}, author = {Quiroga, R and Nistal, E and Estébanez, B and Porras, D and Juárez-Fernández, M and Martínez-Flórez, S and García-Mediavilla, MV and de Paz, JA and González-Gallego, J and Sánchez-Campos, S and Cuevas, MJ}, title = {Exercise training modulates the gut microbiota profile and impairs inflammatory signaling pathways in obese children.}, journal = {Experimental & molecular medicine}, volume = {52}, number = {7}, pages = {1048-1061}, pmid = {32624568}, issn = {2092-6413}, support = {FPU15/05051//Ministerio de Educación, Cultura y Deporte (Ministry of Education, Culture and Sports, Spain)/International ; FPU18/06257//Ministerio de Educación, Cultura y Deporte (Ministry of Education, Culture and Sports, Spain)/International ; }, mesh = {Case-Control Studies ; Child ; Endurance Training ; Exercise/*physiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Inflammation/*microbiology ; Male ; Metabolomics ; Pediatric Obesity/blood/*metabolism/*microbiology/*physiopathology ; Phylogeny ; Principal Component Analysis ; *Signal Transduction ; }, abstract = {Childhood obesity has reached epidemic levels and is a serious health concern associated with metabolic syndrome, nonalcoholic fatty liver disease, and gut microbiota alterations. Physical exercise is known to counteract obesity progression and modulate the gut microbiota composition. This study aims to determine the effect of a 12-week strength and endurance combined training program on gut microbiota and inflammation in obese pediatric patients. Thirty-nine obese children were assigned randomly to the control or training group. Anthropometric and biochemical parameters, muscular strength, and inflammatory signaling pathways in mononuclear cells were evaluated. Bacterial composition and functionality were determined by massive sequencing and metabolomic analysis. Exercise reduced plasma glucose levels and increased dynamic strength in the upper and lower extremities compared with the obese control group. Metagenomic analysis revealed a bacterial composition associated with obesity, showing changes at the phylum, class, and genus levels. Exercise counteracted this profile, significantly reducing the Proteobacteria phylum and Gammaproteobacteria class. Moreover, physical activity tended to increase some genera, such as Blautia, Dialister, and Roseburia, leading to a microbiota profile similar to that of healthy children. Metabolomic analysis revealed changes in short-chain fatty acids, branched-chain amino acids, and several sugars in response to exercise, in correlation with a specific microbiota profile. Finally, the training protocol significantly inhibited the activation of the obesity-associated NLRP3 signaling pathway. Our data suggest the existence of an obesity-related deleterious microbiota profile that is positively modified by physical activity intervention. Exercise training could be considered an efficient nonpharmacological therapy, reducing inflammatory signaling pathways induced by obesity in children via microbiota modulation.}, } @article {pmid32623494, year = {2020}, author = {Wang, TY and Zhang, XQ and Chen, AL and Zhang, J and Lv, BH and Ma, MH and Lian, J and Wu, YX and Zhou, YT and Ma, CC and Dong, RJ and Ge, DY and Gao, SH and Jiang, GJ}, title = {A comparative study of microbial community and functions of type 2 diabetes mellitus patients with obesity and healthy people.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {16}, pages = {7143-7153}, doi = {10.1007/s00253-020-10689-7}, pmid = {32623494}, issn = {1432-0614}, support = {81774171//National Natural Science Foundation of China/ ; 18130219A//Tangshan Science and Technology Innovation TeamTraining Program/ ; CYXC1719//collaborative innovation project of Chaoyang District in Beijing/ ; }, mesh = {Adult ; Bacteria/*classification/metabolism ; Computational Biology ; Diabetes Mellitus, Type 2/*microbiology/physiopathology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Male ; *Metagenome ; Metagenomics ; Middle Aged ; Obesity/*microbiology ; }, abstract = {The gut microbiota is crucial in the pathogenesis of type 2 diabetes mellitus (T2DM). However, the metabolism of T2DM patients is not well-understood. We aimed to identify the differences on composition and function of gut microbiota between T2DM patients with obesity and healthy people. In this study, 6 T2DM patients with obesity and 6 healthy volunteers were recruited, and metagenomic approach and bioinformatics analysis methods were used to understand the composition of the gut microbiota and the metabolic network. We found a decrease in the abundance of Firmicutes, Oribacterium, and Paenibacillus; this may be attributed to a possible mechanism and biological basis of T2DM; moreover, we identified three critical bacterial taxa, Bacteroides plebeius, Phascolarctobacterium sp. CAG207, and the order Acidaminococcales that can potentially be used for T2DM treatment. We also revealed the composition of the microbiota through functional annotation based on multiple databases and found that carbohydrate metabolism contributed greatly to the pathogenesis of T2DM. This study helps in elucidating the different metabolic roles of microbes in T2DM patients with obesity.}, } @article {pmid32623173, year = {2020}, author = {Li, J and Liang, Y and Miao, Y and Wang, D and Jia, S and Liu, CH}, title = {Metagenomic insights into aniline effects on microbial community and biological sulfate reduction pathways during anaerobic treatment of high-sulfate wastewater.}, journal = {The Science of the total environment}, volume = {742}, number = {}, pages = {140537}, doi = {10.1016/j.scitotenv.2020.140537}, pmid = {32623173}, issn = {1879-1026}, mesh = {Anaerobiosis ; Aniline Compounds ; Bioreactors ; *Microbiota ; Sewage ; Sulfates ; Waste Disposal, Fluid ; *Wastewater ; }, abstract = {For comprehensive insights into the change of sulfate reduction pathway responding to the toxic stress and the shift of microbial community and performance of sulfate reduction, we built a laboratory-scale expanded granular sludge bed reactor (EGSB) treating high-sulfate wastewater with elevated aniline concentrations from 0 to 480 mg/L. High-throughput sequencing and metagenomic approaches were applied to decipher the molecular mechanisms of sulfate reduction under aniline stress through taxonomic and functional profiles. The increasing aniline in the anaerobic system induced the accumulation of volatile fatty acids (VFA), further turned the bioreactor into acidification, which was the principal reason for the deterioration of system performance and finally resulted in the accumulation of toxic free sulfide. Moreover, aniline triggered the change of bacterial community and genes relating to sulfate reduction pathways. The increase of aniline from 0 to 320 mg/L enriched total sulfate-reducing bacteria (SRB), and the most abundant genus was Desulfomicrobium, accounting for 66.85-91.25% of total SRB. The assimilatory sulfate reduction pathway was obviously inhibited when aniline was over 160 mg/L, while genes associated with dissimilatory sulfate reduction pathways all exhibited an upward tendency with the increasing aniline content. The enrichment of aniline-resistant SRB (e.g. Desulfomicrobium) carrying genes associated with the dissimilatory sulfate reduction pathway also confirmed the underlying mechanism that sulfate reduction turned into dissimilation under high aniline condition. Taken together, these results comprehensively provided solid evidence for the effects of aniline on the biological sulfate reduction processes treating high-sulfate wastewater and the underlying molecular mechanisms which may highlight the important roles of SRB and related sulfate reduction genes during treatment.}, } @article {pmid32622559, year = {2021}, author = {Khan Mirzaei, M and Xue, J and Costa, R and Ru, J and Schulz, S and Taranu, ZE and Deng, L}, title = {Challenges of Studying the Human Virome - Relevant Emerging Technologies.}, journal = {Trends in microbiology}, volume = {29}, number = {2}, pages = {171-181}, doi = {10.1016/j.tim.2020.05.021}, pmid = {32622559}, issn = {1878-4380}, mesh = {Bacteriophages/classification/*genetics/isolation & purification ; Genome, Viral ; Humans ; Metagenomics/*methods/trends ; *Virome ; Viruses/classification/*genetics/isolation & purification ; }, abstract = {In this review we provide an overview of current challenges and advances in bacteriophage research within the growing field of viromics. In particular, we discuss, from a human virome study perspective, the current and emerging technologies available, their limitations in terms of de novo discoveries, and possible solutions to overcome present experimental and computational biases associated with low abundance of viral DNA or RNA. We summarize recent breakthroughs in metagenomics assembling tools and single-cell analysis, which have the potential to increase our understanding of phage biology, diversity, and interactions with both the microbial community and the human body. We expect that these recent and future advances in the field of viromics will have a strong impact on how we develop phage-based therapeutic approaches.}, } @article {pmid32621033, year = {2020}, author = {Ramos, RT and Sodré, CS and de Sousa Rodrigues, PMGR and da Silva, AMP and Fuly, MS and Dos Santos, HF and Gonçalves, LS and de Carvalho Ferreira, D and Ribeiro, MG}, title = {High-throughput nucleotide sequencing for bacteriome studies in oral squamous cell carcinoma: a systematic review.}, journal = {Oral and maxillofacial surgery}, volume = {24}, number = {4}, pages = {387-401}, doi = {10.1007/s10006-020-00873-4}, pmid = {32621033}, issn = {1865-1569}, mesh = {*Carcinoma, Squamous Cell/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota/genetics ; *Mouth Neoplasms/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {PURPOSE: Dysbiosis has been identified in oral squamous cell carcinoma (OSCC). The aim of this study was to carry out a systematic review of an electronic research that was carried out on articles published between January 2008 and September 2018.

METHODS: Eight studies were selected after applying the inclusion and exclusion criteria.

RESULTS: All articles targeted the hypervariable regions of the 16S rRNA gene. At the phylum level, it was found reduction of Bacteroidetes (2/8 studies) and increase of Firmicutes (2/8 studies). At the genus level, Rothia increased (1/8 studies) and decreased (2/8 studies) in tumor samples, and Streptococcus also was found increased (3/8 studies) and reduced (3/8 studies). Fusobacterium only increased in OSCC samples (3/8 studies). At species level, an increase in F. nucleatum subsp. polymorphum was more associated to OSCC (2/8 studies) than with controls, as was P. aeruginosa (3/8 studies).

CONCLUSION: In summary, the results corroborated dysbiosis in OSCC patients, with enrichment of microbial taxa that are associated with inflammation and production of acetaldehyde. However, variations of study design and sample size were observed among the studies, as well as a shortage of more detailed analyses of possible correlations between risk habits and OSCC. This lack of more detailed analysis may be the cause of the inconsistencies in regard of the alterations reported for certain genera and species. In conclusion, there is an association between OSCC and oral microbiota dysbiosis, but its role in oral carcinogenesis needs to be clarified in more detail.}, } @article {pmid32620143, year = {2020}, author = {Creswell, R and Tan, J and Leff, JW and Brooks, B and Mahowald, MA and Thieroff-Ekerdt, R and Gerber, GK}, title = {High-resolution temporal profiling of the human gut microbiome reveals consistent and cascading alterations in response to dietary glycans.}, journal = {Genome medicine}, volume = {12}, number = {1}, pages = {59}, pmid = {32620143}, issn = {1756-994X}, support = {R01 GM130777/GM/NIGMS NIH HHS/United States ; 1R01GM130777/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Bayes Theorem ; Biodiversity ; Computational Biology/methods ; *Diet ; Feces/microbiology ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; *Metagenome ; *Metagenomics/methods ; Models, Theoretical ; Polysaccharides/*metabolism ; Software ; }, abstract = {BACKGROUND: Dietary glycans, widely used as food ingredients and not directly digested by humans, are of intense interest for their beneficial roles in human health through shaping the microbiome. Characterizing the consistency and temporal responses of the gut microbiome to glycans is critical for rationally developing and deploying these compounds as therapeutics.

METHODS: We investigated the effect of two chemically distinct glycans (fructooligosaccharides and polydextrose) through three clinical studies conducted with 80 healthy volunteers. Stool samples, collected at dense temporal resolution (~ 4 times per week over 10 weeks) and analyzed using shotgun metagenomic sequencing, enabled detailed characterization of participants' microbiomes. For analyzing the microbiome time-series data, we developed MC-TIMME2 (Microbial Counts Trajectories Infinite Mixture Model Engine 2.0), a purpose-built computational tool based on nonparametric Bayesian methods that infer temporal patterns induced by perturbations and groups of microbes sharing these patterns.

RESULTS: Overall microbiome structure as well as individual taxa showed rapid, consistent, and durable alterations across participants, regardless of compound dose or the order in which glycans were consumed. Significant changes also occurred in the abundances of microbial carbohydrate utilization genes in response to polydextrose, but not in response to fructooligosaccharides. Using MC-TIMME2, we produced detailed, high-resolution temporal maps of the microbiota in response to glycans within and across microbiomes.

CONCLUSIONS: Our findings indicate that dietary glycans cause reproducible, dynamic, and differential alterations to the community structure of the human microbiome.}, } @article {pmid32619440, year = {2020}, author = {Reitmeier, S and Kiessling, S and Clavel, T and List, M and Almeida, EL and Ghosh, TS and Neuhaus, K and Grallert, H and Linseisen, J and Skurk, T and Brandl, B and Breuninger, TA and Troll, M and Rathmann, W and Linkohr, B and Hauner, H and Laudes, M and Franke, A and Le Roy, CI and Bell, JT and Spector, T and Baumbach, J and O'Toole, PW and Peters, A and Haller, D}, title = {Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes.}, journal = {Cell host & microbe}, volume = {28}, number = {2}, pages = {258-272.e6}, doi = {10.1016/j.chom.2020.06.004}, pmid = {32619440}, issn = {1934-6069}, support = {MR/N030125/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; Circadian Clocks/physiology ; Circadian Rhythm/*physiology ; Diabetes Mellitus, Type 2/epidemiology/microbiology/*pathology ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Germany/epidemiology ; Humans ; Metagenome/genetics ; Metagenomics/methods ; Obesity/microbiology/*pathology ; }, abstract = {Lifestyle, obesity, and the gut microbiome are important risk factors for metabolic disorders. We demonstrate in 1,976 subjects of a German population cohort (KORA) that specific microbiota members show 24-h oscillations in their relative abundance and identified 13 taxa with disrupted rhythmicity in type 2 diabetes (T2D). Cross-validated prediction models based on this signature similarly classified T2D. In an independent cohort (FoCus), disruption of microbial oscillation and the model for T2D classification was confirmed in 1,363 subjects. This arrhythmic risk signature was able to predict T2D in 699 KORA subjects 5 years after initial sampling, being most effective in combination with BMI. Shotgun metagenomic analysis functionally linked 26 metabolic pathways to the diurnal oscillation of gut bacteria. Thus, a cohort-specific risk pattern of arrhythmic taxa enables classification and prediction of T2D, suggesting a functional link between circadian rhythms and the microbiome in metabolic diseases.}, } @article {pmid32617960, year = {2021}, author = {Guk, J and Guedj, J and Burdet, C and Andremont, A and de Gunzburg, J and Ducher, A and Mentré, F}, title = {Modeling the Effect of DAV132, a Novel Colon-Targeted Adsorbent, on Fecal Concentrations of Moxifloxacin and Gut Microbiota Diversity in Healthy Volunteers.}, journal = {Clinical pharmacology and therapeutics}, volume = {109}, number = {4}, pages = {1045-1054}, doi = {10.1002/cpt.1977}, pmid = {32617960}, issn = {1532-6535}, mesh = {Adolescent ; Adsorption/physiology ; Adult ; Colon/*drug effects ; Dose-Response Relationship, Drug ; Feces/*chemistry ; Female ; Gastrointestinal Microbiome/*drug effects ; Healthy Volunteers ; Humans ; Male ; Metagenomics ; Middle Aged ; Models, Biological ; Moxifloxacin/administration & dosage/*pharmacokinetics ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {To prevent antibiotic-induced perturbations on gut microbiota, DAV132, a novel colon-targeted adsorbent, which sequesters antibiotic residues in the lower gastrointestinal tract, was developed. We built an integrated pharmacological model of how DAV132 reduces fecal free moxifloxacin and preserves gut microbiota. We used plasma and fecal free moxifloxacin concentrations, and Shannon diversity index from 16S ribosomal RNA gene metagenomics analysis of fecal microbiota, of 143 healthy volunteers assigned randomly to receive moxifloxacin only, or with 10 DAV132 dose regimens, or to a control group. We modeled reduced fecal moxifloxacin concentrations using a transit model for DAV132 kinetics and a Michaelis-Menten model with an effect of the amount of activated charcoal on adsorption efficacy. Changes in moxifloxacin-induced perturbations on gut microbiota diversity were then quantified through a turnover model with the Emax model. With the developed model, the efficiency of pharmacokinetic antagonism and its consequences on gut microbiota diversity were quantified.}, } @article {pmid32617829, year = {2021}, author = {Huang, G and Wang, X and Hu, Y and Wu, Q and Nie, Y and Dong, J and Ding, Y and Yan, L and Wei, F}, title = {Diet drives convergent evolution of gut microbiomes in bamboo-eating species.}, journal = {Science China. Life sciences}, volume = {64}, number = {1}, pages = {88-95}, pmid = {32617829}, issn = {1869-1889}, mesh = {Ailuridae/classification/*genetics/microbiology ; Animals ; Bacteria/classification/genetics ; Bambusa/physiology ; Carnivora/classification/*genetics/microbiology ; *Diet ; *Evolution, Molecular ; Feces/microbiology ; Feeding Behavior/physiology ; Gastrointestinal Microbiome/*genetics ; *Genetic Variation ; Metagenomics/methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Ursidae/classification/*genetics/microbiology ; }, abstract = {Gut microbiota plays a critical role in host physiology and health. The coevolution between the host and its gut microbes facilitates animal adaptation to its specific ecological niche. Multiple factors such as host diet and phylogeny modulate the structure and function of gut microbiota. However, the relative contribution of each factor in shaping the structure of gut microbiota remains unclear. The giant (Ailuropoda melanoleuca) and red (Ailurus styani) pandas belong to different families of order Carnivora. They have evolved as obligate bamboo-feeders and can be used as a model system for studying the gut microbiome convergent evolution. Here, we compare the structure and function of gut microbiota of the two pandas with their carnivorous relatives using 16S rRNA and metagenome sequencing. We found that both panda species share more similarities in their gut microbiota structure with each other than each species shares with its carnivorous relatives. This indicates that the specialized herbivorous diet rather than host phylogeny is the dominant driver of gut microbiome convergence within Arctoidea. Metagenomic analysis revealed that the symbiotic gut microbiota of both pandas possesses a high level of starch and sucrose metabolism and vitamin B12 biosynthesis. These findings suggest a diet-driven convergence of gut microbiomes and provide new insight into host-microbiota coevolution of these endangered species.}, } @article {pmid32616517, year = {2020}, author = {Seppey, M and Manni, M and Zdobnov, EM}, title = {LEMMI: a continuous benchmarking platform for metagenomics classifiers.}, journal = {Genome research}, volume = {30}, number = {8}, pages = {1208-1216}, pmid = {32616517}, issn = {1549-5469}, mesh = {Algorithms ; Bacteria/*classification/*genetics ; Computational Biology/*methods ; Genome, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {Studies of microbiomes are booming, along with the diversity of computational approaches to make sense out of the sequencing data and the volumes of accumulated microbial genotypes. A swift evaluation of newly published methods and their improvements against established tools is necessary to reduce the time between the methods' release and their adoption in microbiome analyses. The LEMMI platform offers a novel approach for benchmarking software dedicated to metagenome composition assessments based on read classification. It enables the integration of newly published methods in an independent and centralized benchmark designed to be continuously open to new submissions. This allows developers to be proactive regarding comparative evaluations and guarantees that any promising methods can be assessed side by side with established tools quickly after their release. Moreover, LEMMI enforces an effective distribution through software containers to ensure long-term availability of all methods. Here, we detail the LEMMI workflow and discuss the performances of some previously unevaluated tools. We see this platform eventually as a community-driven effort in which method developers can showcase novel approaches and get unbiased benchmarks for publications, and users can make informed choices and obtain standardized and easy-to-use tools.}, } @article {pmid32615432, year = {2020}, author = {Yang, L and Hou, K and Zhang, B and Ouyang, C and Lin, A and Xu, S and Ke, D and Fang, L and Chen, Q and Wu, J and Yan, C and Lian, Y and Jiang, T and He, J and Wang, H and Fu, Y and Xiao, C and Chen, Z}, title = {Preservation of the fecal samples at ambient temperature for microbiota analysis with a cost-effective and reliable stabilizer EffcGut.}, journal = {The Science of the total environment}, volume = {741}, number = {}, pages = {140423}, doi = {10.1016/j.scitotenv.2020.140423}, pmid = {32615432}, issn = {1879-1026}, mesh = {Cost-Benefit Analysis ; Feces ; Humans ; *Microbiota ; RNA, Ribosomal, 16S ; *Specimen Handling ; Temperature ; }, abstract = {With the increasing researches on the role of gut microbiota in human health and disease, appropriate storage method of fecal samples at ambient temperature would conveniently guarantee the precise and reliable microbiota results. Nevertheless, less choice of stabilizer that is cost-efficient and feasible to be used in longer preservation period obstructed the large-scale metagenomics studies. Here, we evaluated the efficacy of a guanidine isothiocyanate-based reagent method EffcGut and compared it with the other already used storage method by means of 16S rRNA gene sequencing technology. We found that guanidine isothiocyanate-based reagent method at ambient temperature was not inferior to OMNIgene·GUT OM-200 and it could retain the similar bacterial community as that of -80 °C within 24 weeks. Furthermore, bacterial diversity and community structure difference were compared among different sample fraction (supernatant, suspension and precipitate) preserved in EffcGut and -80 °C. We found that supernatant under the preservation of EffcGut retained the similar community structure and composition as that of the low temperature preservation method.}, } @article {pmid32615270, year = {2021}, author = {Guilloux, CA and Lamoureux, C and Beauruelle, C and Héry-Arnaud, G}, title = {Porphyromonas: A neglected potential key genus in human microbiomes.}, journal = {Anaerobe}, volume = {68}, number = {}, pages = {102230}, doi = {10.1016/j.anaerobe.2020.102230}, pmid = {32615270}, issn = {1095-8274}, mesh = {Bacteroidaceae Infections/*microbiology ; Humans ; *Microbiota ; Phylogeny ; Porphyromonas/classification/genetics/growth & development/*isolation & purification ; }, abstract = {Anaerobes form a large part of microbial communities, and have begun to be specifically studied in both healthy and pathologic contexts. Porphyromonas is one of the top ten anaerobic taxa in the microbiome (anaerobiome) in healthy subjects. However, to date, most studies focused on the deleterious role of P. gingivalis, the most widely described species. Interestingly, targeted metagenomics reveals Porphyromonas other than gingivalis (POTG), highlighting other species such as P. catoniae or P. pasteri as potential biomarkers in disease progression or pathogen colonization susceptibility. From the sparse data, it appears that the Porphyromonas genus may also be a relevant target of investigation in several pulmonary diseases. Moreover, deciphering cutaneous, gastric and oral microbiomes hint that Porphyromonas may be a genus of interest in non-pulmonary diseases. This review aims to summarize the major data on POTG and to report their impact on the various human microbiomes in different clinical states.}, } @article {pmid32614993, year = {2021}, author = {Williams, SC and Frew, JW and Krueger, JG}, title = {A systematic review and critical appraisal of metagenomic and culture studies in hidradenitis suppurativa.}, journal = {Experimental dermatology}, volume = {30}, number = {10}, pages = {1388-1397}, pmid = {32614993}, issn = {1600-0625}, support = {T32 GM007739/GM/NIGMS NIH HHS/United States ; UL1 TR001866/TR/NCATS NIH HHS/United States ; }, mesh = {Hidradenitis Suppurativa/*genetics/*microbiology ; Humans ; Metagenomics ; *Microbiota ; Skin/*microbiology ; }, abstract = {Hidradenitis suppurativa (HS), also known as acne inversa, is a chronic inflammatory skin disease with still largely unknown pathogenesis. While infectious organisms have been identified in lesions of the disease since the 1980s, questions remain over the role that bacteria and microbiome play. Recent studies using 16S ribosomal RNA gene sequencing and larger culture-based studies have begun to paint a clearer picture of the microbial world of HS. With this systematic review, we summarize all the work that has been done to date in HS bacteriology, analyse potential pitfalls and limitations of the current studies, and address future directions of investigation. This systematic review attempted to collate and analyse all bacteriology studies done to date. This review was prospectively registered with PROSPERO (1670769) performed in line with the PRISMA checklist. Twenty two studies were identified comprising 862 individual HS patients for culture studies and 206 HS patients for 16S rRNA gene sequencing studies. Methodology tended to be varied, with different sampling, culturing and sequencing methods as well as amount of analysis and stratification of patients. Bacteria identified as elevated in HS lesions in sequencing studies as well as grown from HS lesions in culture studies are identified and discussed. These primarily included the anerobic Gram-negative bacilli Prevotella, Porphyromonas and Fusibacterium, the Gram-positive bacilli Corynebacterium, and the Gram-positive cocci Staphylococcus, Streptococcus and Parvimonas. Potential interactions, as well as work in other disease models with related bacteria are also discussed. Areas of further investigation include in vitro studies of interactions between bacteria and keratinocytes, gut and oral microbiome studies and deep sequencing studies for virulence and phage factors.}, } @article {pmid32613749, year = {2020}, author = {Szeinbaum, N and Nunn, BL and Cavazos, AR and Crowe, SA and Stewart, FJ and DiChristina, TJ and Reinhard, CT and Glass, JB}, title = {Novel insights into the taxonomic diversity and molecular mechanisms of bacterial Mn(III) reduction.}, journal = {Environmental microbiology reports}, volume = {12}, number = {5}, pages = {583-593}, pmid = {32613749}, issn = {1758-2229}, support = {NNX14AJ87G/NASA/NASA/United States ; //NASA Astrobiology Postdoctoral Fellowship/International ; NSF-CDEBI OCE-0939564//Center for Dark Energy Biosphere Investigations/International ; NNA15BB03A//NASA Astrobiology Institute/International ; //NSERC CRC, CFI, and Discovery/International ; }, mesh = {Bacteria/*classification/genetics/isolation & purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; *Biodiversity ; Indonesia ; Iron/metabolism ; Lakes/*microbiology ; Manganese/*metabolism ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Soluble ligand-bound Mn(III) can support anaerobic microbial respiration in diverse aquatic environments. Thus far, Mn(III) reduction has only been associated with certain Gammaproteobacteria. Here, we characterized microbial communities enriched from Mn-replete sediments of Lake Matano, Indonesia. Our results provide the first evidence for the biological reduction of soluble Mn(III) outside the Gammaproteobacteria. Metagenome assembly and binning revealed a novel betaproteobacterium, which we designate 'Candidatus Dechloromonas occultata.' This organism dominated the enrichment and expressed a porin-cytochrome c complex typically associated with iron-oxidizing Betaproteobacteria and a novel cytochrome c-rich protein cluster (Occ), including an undecaheme putatively involved in extracellular electron transfer. This occ gene cluster was also detected in diverse aquatic bacteria, including uncultivated Betaproteobacteria from the deep subsurface. These observations provide new insight into the taxonomic and functional diversity of microbially driven Mn(III) reduction in natural environments.}, } @article {pmid32612960, year = {2020}, author = {Jayasinghe, TN and Vatanen, T and Chiavaroli, V and Jayan, S and McKenzie, EJ and Adriaenssens, E and Derraik, JGB and Ekblad, C and Schierding, W and Battin, MR and Thorstensen, EB and Cameron-Smith, D and Forbes-Blom, E and Hofman, PL and Roy, NC and Tannock, GW and Vickers, MH and Cutfield, WS and O'Sullivan, JM}, title = {Differences in Compositions of Gut Bacterial Populations and Bacteriophages in 5-11 Year-Olds Born Preterm Compared to Full Term.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {276}, pmid = {32612960}, issn = {2235-2988}, support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Bacteriophages ; Child ; Cross-Sectional Studies ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Preterm infants are exposed to major perinatal, post-natal, and early infancy events that could impact on the gut microbiome. These events include infection, steroid and antibiotic exposure, parenteral nutrition, necrotizing enterocolitis, and stress. Studies have shown that there are differences in the gut microbiome during the early months of life in preterm infants. We hypothesized that differences in the gut microbial composition and metabolites in children born very preterm persist into mid-childhood. Participants were healthy prepubertal children aged 5-11 years who were born very preterm (≤32 weeks of gestation; n = 51) or at term (37-41 weeks; n = 50). We recorded the gestational age, birth weight, mode of feeding, mode of birth, age, sex, and the current height and weight of our cohort. We performed a multi'omics [i.e., 16S rRNA amplicon and shotgun metagenomic sequencing, SPME-GCMS (solid-phase microextraction followed by gas chromatography-mass spectrometry)] analysis to investigate the structure and function of the fecal microbiome (as a proxy of the gut microbiota) in our cross-sectional cohort. Children born very preterm were younger (7.8 vs. 8.3 years; p = 0.034), shorter [height-standard deviation score (SDS) 0.31 vs. 0.92; p = 0.0006) and leaner [BMI (body mass index) SDS -0.20 vs. 0.29; p < 0.0001] than the term group. Children born very preterm had higher fecal calprotectin levels, decreased fecal phage richness, lower plasma arginine, lower fecal branched-chain amino acids and higher fecal volatile (i.e., 3-methyl-butanoic acid, butyrolactone, butanoic acid and pentanoic acid) profiles. The bacterial microbiomes did not differ between preterm and term groups. We speculate that the observed very preterm-specific changes were established in early infancy and may impact on the capacity of the very preterm children to respond to environmental changes.}, } @article {pmid32612216, year = {2020}, author = {Hofmeyr, S and Egan, R and Georganas, E and Copeland, AC and Riley, R and Clum, A and Eloe-Fadrosh, E and Roux, S and Goltsman, E and Buluç, A and Rokhsar, D and Oliker, L and Yelick, K}, title = {Terabase-scale metagenome coassembly with MetaHipMer.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {10689}, pmid = {32612216}, issn = {2045-2322}, mesh = {Algorithms ; Computational Biology/*methods ; Computers ; Genome, Bacterial/*genetics ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/genetics ; Pseudoalteromonas/genetics/isolation & purification ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenome sequence datasets can contain terabytes of reads, too many to be coassembled together on a single shared-memory computer; consequently, they have only been assembled sample by sample (multiassembly) and combining the results is challenging. We can now perform coassembly of the largest datasets using MetaHipMer, a metagenome assembler designed to run on supercomputers and large clusters of compute nodes. We have reported on the implementation of MetaHipMer previously; in this paper we focus on analyzing the impact of very large coassembly. In particular, we show that coassembly recovers a larger genome fraction than multiassembly and enables the discovery of more complete genomes, with lower error rates, whereas multiassembly recovers more dominant strain variation. Being able to coassemble a large dataset does not preclude one from multiassembly; rather, having a fast, scalable metagenome assembler enables a user to more easily perform coassembly and multiassembly, and assemble both abundant, high strain variation genomes, and low-abundance, rare genomes. We present several assemblies of terabyte datasets that could never be coassembled before, demonstrating MetaHipMer's scaling power. MetaHipMer is available for public use under an open source license and all datasets used in the paper are available for public download.}, } @article {pmid32611986, year = {2021}, author = {Parbie, PK and Mizutani, T and Ishizaka, A and Kawana-Tachikawa, A and Runtuwene, LR and Seki, S and Abana, CZ and Kushitor, D and Bonney, EY and Ofori, SB and Uematsu, S and Imoto, S and Kimura, Y and Kiyono, H and Ishikawa, K and Ampofo, WK and Matano, T}, title = {Fecal Microbiome Composition in Healthy Adults in Ghana.}, journal = {Japanese journal of infectious diseases}, volume = {74}, number = {1}, pages = {42-47}, doi = {10.7883/yoken.JJID.2020.469}, pmid = {32611986}, issn = {1884-2836}, mesh = {Adult ; Bacteroidetes/genetics ; Cross-Sectional Studies ; Feces/*microbiology ; Female ; Firmicutes/genetics ; Gastrointestinal Microbiome/*genetics ; Ghana ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; Microbiota ; Middle Aged ; Proteobacteria/genetics ; RNA, Bacterial/isolation & purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recent studies have indicated an association between gut microbiome composition and various disorders, including infectious diseases. The composition of the microbiome differs among ethnicities and countries, possibly resulting in diversified interactions between host immunity and the gut microbiome. Characterization of baseline microbiome composition in healthy people is an essential step for better understanding of the biological interactions associated with individual populations. However, data on the gut/fecal microbiome have not been accumulated for individuals in West Africa. In the present study, we examined the fecal microbiome composition in healthy adults in Ghana. Toward this, 16S rRNA gene libraries were prepared using bacterial fractions derived from 55 Ghanaian adults, which were then subjected to next-generation sequencing. The fecal microbiome of the Ghanaian adults was dominated by Firmicutes (Faecalibacterium, Subdoligranulum, and Ruminococcaceae UCG-014), Proteobacteria (Escherichia-Shigella and Klebsiella), and Bacteroidetes (Prevotella 9 and Bacteroides), consistent with previous observations in African cohorts. Further, our analysis revealed differences in microbiome composition and a lower diversity of the fecal microbiome in the Ghanaian cohort compared with those reported in non-African countries. This is the first study to describe substantial fecal microbiome data obtained using high-throughput metagenomic tools on samples derived from a cohort in Ghana. The data may provide a valuable basis for determining the association between the fecal microbiome and progression of various diseases in West African populations.}, } @article {pmid32610345, year = {2021}, author = {Levade, I and Saber, MM and Midani, FS and Chowdhury, F and Khan, AI and Begum, YA and Ryan, ET and David, LA and Calderwood, SB and Harris, JB and LaRocque, RC and Qadri, F and Shapiro, BJ and Weil, AA}, title = {Predicting Vibrio cholerae Infection and Disease Severity Using Metagenomics in a Prospective Cohort Study.}, journal = {The Journal of infectious diseases}, volume = {223}, number = {2}, pages = {342-351}, pmid = {32610345}, issn = {1537-6613}, support = {R01 AI103055/AI/NIAID NIH HHS/United States ; T32A1070611976/AI/NIAID NIH HHS/United States ; K08 AI123494/AI/NIAID NIH HHS/United States ; R01 AI137164/AI/NIAID NIH HHS/United States ; R01 AI099243/AI/NIAID NIH HHS/United States ; U01 AI058935/AI/NIAID NIH HHS/United States ; R56 AI106878/AI/NIAID NIH HHS/United States ; R37 AI106878/AI/NIAID NIH HHS/United States ; }, mesh = {Biomarkers ; Cholera/*diagnosis/*microbiology ; Disease Susceptibility ; Gastrointestinal Microbiome ; Metagenome ; *Metagenomics/methods ; Phylogeny ; Prognosis ; ROC Curve ; Severity of Illness Index ; Vibrio cholerae/*physiology ; }, abstract = {BACKGROUND: Susceptibility to Vibrio cholerae infection is affected by blood group, age, and preexisting immunity, but these factors only partially explain who becomes infected. A recent study used 16S ribosomal RNA amplicon sequencing to quantify the composition of the gut microbiome and identify predictive biomarkers of infection with limited taxonomic resolution.

METHODS: To achieve increased resolution of gut microbial factors associated with V. cholerae susceptibility and identify predictors of symptomatic disease, we applied deep shotgun metagenomic sequencing to a cohort of household contacts of patients with cholera.

RESULTS: Using machine learning, we resolved species, strains, gene families, and cellular pathways in the microbiome at the time of exposure to V. cholerae to identify markers that predict infection and symptoms. Use of metagenomic features improved the precision and accuracy of prediction relative to 16S sequencing. We also predicted disease severity, although with greater uncertainty than our infection prediction. Species within the genera Prevotella and Bifidobacterium predicted protection from infection, and genes involved in iron metabolism were also correlated with protection.

CONCLUSION: Our results highlight the power of metagenomics to predict disease outcomes and suggest specific species and genes for experimental testing to investigate mechanisms of microbiome-related protection from cholera.}, } @article {pmid32610095, year = {2020}, author = {Oh, TG and Kim, SM and Caussy, C and Fu, T and Guo, J and Bassirian, S and Singh, S and Madamba, EV and Bettencourt, R and Richards, L and Yu, RT and Atkins, AR and Huan, T and Brenner, DA and Sirlin, CB and Downes, M and Evans, RM and Loomba, R}, title = {A Universal Gut-Microbiome-Derived Signature Predicts Cirrhosis.}, journal = {Cell metabolism}, volume = {32}, number = {5}, pages = {878-888.e6}, pmid = {32610095}, issn = {1932-7420}, support = {P01 HL088093/HL/NHLBI NIH HHS/United States ; R01 HL105278/HL/NHLBI NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 DK124318/DK/NIDDK NIH HHS/United States ; R37 DK057978/DK/NIDDK NIH HHS/United States ; U01 DK061734/DK/NIDDK NIH HHS/United States ; P01 HL147835/HL/NHLBI NIH HHS/United States ; R01 DK121378/DK/NIDDK NIH HHS/United States ; R01 DK106419/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; P42 ES010337/ES/NIEHS NIH HHS/United States ; R01 DK057978/DK/NIDDK NIH HHS/United States ; P30 CA014195/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Aspartate Aminotransferases/*blood ; Cohort Studies ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Liver Cirrhosis/*diagnosis ; Male ; Metabolome ; Metagenome ; Middle Aged ; Non-alcoholic Fatty Liver Disease/*pathology ; Serum Albumin, Human/*analysis ; }, abstract = {Dysregulation of the gut microbiome has been implicated in the progression of non-alcoholic fatty liver disease (NAFLD) to advanced fibrosis and cirrhosis. To determine the diagnostic capacity of this association, we compared stool microbiomes across 163 well-characterized participants encompassing non-NAFLD controls, NAFLD-cirrhosis patients, and their first-degree relatives. Interrogation of shotgun metagenomic and untargeted metabolomic profiles by using the random forest machine learning algorithm and differential abundance analysis identified discrete metagenomic and metabolomic signatures that were similarly effective in detecting cirrhosis (diagnostic accuracy 0.91, area under curve [AUC]). Combining the metagenomic signature with age and serum albumin levels accurately distinguished cirrhosis in etiologically and genetically distinct cohorts from geographically separated regions. Additional inclusion of serum aspartate aminotransferase levels, which are increased in cirrhosis patients, enabled discrimination of cirrhosis from earlier stages of fibrosis. These findings demonstrate that a core set of gut microbiome species might offer universal utility as a non-invasive diagnostic test for cirrhosis.}, } @article {pmid32609272, year = {2020}, author = {Horodesky, A and Castilho-Westphal, GG and Pont, GD and Faoro, H and Balsanelli, E and Tadra-Sfeir, MZ and Cozer, N and Pie, MR and Ostrensky, A}, title = {Metagenomic analysis of the bacterial microbiota associated with cultured oysters (Crassostrea sp.) in estuarine environments.}, journal = {Anais da Academia Brasileira de Ciencias}, volume = {92}, number = {suppl 1}, pages = {e20180432}, doi = {10.1590/0001-3765202020180432}, pmid = {32609272}, issn = {1678-2690}, mesh = {Animals ; Bacteria ; Brazil ; *Crassostrea ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {In this work, we identified the bacterial microbiota associated with farmed oystersin estuarine regions of four states in the north eastern region of Brazil. During the drought and rainy seasons, for eight months, twenty oysters were sampled seasonally from seven different marine farms. In the laboratory, DNA extraction, amplification, and sequencing of the 16S rRNA gene were performed to establish the taxonomic units. We identified 106 genera of bacteria belonging to 103 families, 70 orders, 39 classes, and 21 phyla. Out of the total, 40 of the genera represented bacteria potentially pathogenic to humans; of these, nine are known to cause foodborne diseases and six are potentially pathogenic to oysters. The most prevalent genera were Mycoplasma, Propionigenium, Psychrilyobacter, and Arcobacter. The results indicate the need for more systematic monitoring of bacteria of the genus Mycoplasma in oyster farming operations in the Brazilian north eastern region. Currently, Mycoplasma is not one of the microorganisms analysed and monitored by order of Brazilian legislation during the oyster production and/or commercialization process, even though this genus was the most prevalent at all sampling points and presents pathogenic potential both for oysters and for consumers.}, } @article {pmid32608067, year = {2020}, author = {Doane, M and Haggerty, JM and da Silva Lopes, CR and Yates, P and Edwards, R and Dinsdale, E and Lopes, FAC and Bruce, T}, title = {Latitude and chlorophyll a density drive the distribution of carbohydrate-active enzymes in the planktonic microbial fraction of the epipelagic zone.}, journal = {Environmental microbiology reports}, volume = {12}, number = {5}, pages = {473-485}, doi = {10.1111/1758-2229.12865}, pmid = {32608067}, issn = {1758-2229}, support = {23038.009420/2012-71//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/International ; 1323809//National Science Foundation/International ; 1330800//National Science Foundation/International ; }, mesh = {Bacteria/classification/*enzymology/genetics/metabolism ; Bacterial Proteins/genetics/*metabolism ; Biodiversity ; Carbohydrate Metabolism ; Carbon Cycle ; Chlorophyll/*analysis/metabolism ; Ecosystem ; Glycoside Hydrolases/genetics/*metabolism ; Metagenome ; Microbiota ; Oceans and Seas ; Plankton ; Salinity ; Seawater/chemistry/*microbiology ; Temperature ; }, abstract = {Microbes drive the majority of the global carbon cycle. The effect of environmental conditions on selecting microbial functional diversity is well established, and recent studies have revealed the effects of geographic distances on selecting the functional components of marine microbial communities. Our study is the first attempt at establishing the effects of environmental factors on driving the marine carbohydrate-active enzyme (CAZyme) distribution. We characterized the diversity of CAZyme genes and investigated the correlations between their distributions and biogeographic parameters (latitude, longitude, distance from the equator, site depth, water depth, chlorophyll density, salinity and temperature). Therefore, we accessed a subset of surface water samples (38 metagenomes) from the Global Ocean Sampling project. Only chlorophyll and latitude altered the distribution patterns of CAZymes, revealing the existence of two latitudinal gradients (positive and negative) of marine CAZyme abundance. Considering the importance of carbohydrates in microbial life, characterization of the spatial patterns of the genetic repertoire involved in carbohydrate metabolism represents an important step in improving our understanding of the metabolic strategies associated with the microbial marine carbon cycle and their effects on the productivity of marine ecosystems.}, } @article {pmid32607646, year = {2020}, author = {Stultiens, K and van Kessel, MAHJ and Frank, J and Fischer, P and Pelzer, C and van Alen, TA and Kartal, B and Op den Camp, HJM and Jetten, MSM}, title = {Diversity, enrichment, and genomic potential of anaerobic methane- and ammonium-oxidizing microorganisms from a brewery wastewater treatment plant.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {16}, pages = {7201-7212}, pmid = {32607646}, issn = {1432-0614}, support = {669371//H2020 European Research Council/ ; 6400422//H2020 European Research Council/ ; 339880//H2020 European Research Council/ ; 13146//Stichting voor de Technische Wetenschappen/ ; 016.veni.192.062//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 024002002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, mesh = {Ammonium Compounds/*metabolism ; Anaerobiosis ; Bacteria/*classification/metabolism ; *Biodiversity ; Bioreactors/*microbiology ; Metagenomics ; Methane/*metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Water Purification ; }, abstract = {Anaerobic wastewater treatment offers several advantages; however, the effluent of anaerobic digesters still contains high levels of ammonium and dissolved methane that need to be removed before these effluents can be discharged to surface waters. The simultaneous anaerobic removal of methane and ammonium by denitrifying (N-damo) methanotrophs in combination with anaerobic ammonium-oxidizing (anammox) bacteria could be a potential solution to this challenge. After a molecular survey of a wastewater plant treating brewery effluent, indicating the presence of both N-damo and anammox bacteria, we started an anaerobic bioreactor with a continuous supply of methane, ammonium, and nitrite to enrich these anaerobic microorganisms. After 14 months of operation, a stable enrichment culture containing two types of 'Candidatus Methylomirabilis oxyfera' bacteria and two strains of 'Ca. Brocadia'-like anammox bacteria was achieved. In this community, anammox bacteria converted 80% of the nitrite with ammonium, while 'Ca. Methylomirabilis' contributed to 20% of the nitrite consumption. The analysis of metagenomic 16S rRNA reads and fluorescence in situ hybridization (FISH) correlated well and showed that, after 14 months, 'Ca. Methylomirabilis' and anammox bacteria constituted approximately 30 and 20% of the total microbial community. In addition, a substantial part (10%) of the community consisted of Phycisphaera-related planctomycetes. Assembly and binning of the metagenomic sequences resulted in high-quality draft genome of two 'Ca. Methylomirabilis' species containing the marker genes pmoCAB, xoxF, and nirS and putative NO dismutase genes. The anammox draft genomes most closely related to 'Ca. Brocadia fulgida' included the marker genes hzsABC, hao, and hdh. Whole-reactor and batch anaerobic activity measurements with methane, ammonium, nitrite, and nitrate revealed an average anaerobic methane oxidation rate of 0.12 mmol h[-1] L[-1] and ammonium oxidation rate of 0.5 mmol h[-1] L[-1]. Together, this study describes the enrichment and draft genomes of anaerobic methanotrophs from a brewery wastewater treatment plant, where these organisms together with anammox bacteria can contribute significantly to the removal of methane and ammonium in a more sustainable way. KEY POINTS: • An enrichment culture containing both N-damo and anammox bacteria was obtained. • Simultaneous consumption of ammonia, nitrite, and methane under anoxic conditions. • In-depth metagenomic biodiversity analysis of inoculum and enrichment culture.}, } @article {pmid32606383, year = {2020}, author = {Neal, AL and Bacq-Labreuil, A and Zhang, X and Clark, IM and Coleman, K and Mooney, SJ and Ritz, K and Crawford, JW}, title = {Soil as an extended composite phenotype of the microbial metagenome.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {10649}, pmid = {32606383}, issn = {2045-2322}, support = {BBS/E/C/000I0330/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/C/000J0300/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/C/000I0310/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Carbon Cycle ; *Metagenome ; *Microbiota ; Phenotype ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {We use a unique set of terrestrial experiments to demonstrate how soil management practises result in emergence of distinct associations between physical structure and biological functions. These associations have a significant effect on the flux, resilience and efficiency of nutrient delivery to plants (including water). Physical structure, determining the air-water balance in soil as well as transport rates, is influenced by nutrient and physical interventions. Contrasting emergent soil structures exert selective pressures upon the microbiome metagenome. These selective pressures are associated with the quality of organic carbon inputs, the prevalence of anaerobic microsites and delivery of nutrients to microorganisms attached to soil surfaces. This variety results in distinctive gene assemblages characterising each state. The nature of the interactions provide evidence that soil behaves as an extended composite phenotype of the resident microbiome, responsive to the input and turnover of plant-derived organic carbon. We provide new evidence supporting the theory that soil-microbe systems are self-organising states with organic carbon acting as a critical determining parameter. This perspective leads us to propose carbon flux, rather than soil organic carbon content as the critical factor in soil systems, and we present evidence to support this view.}, } @article {pmid32605986, year = {2020}, author = {Cao, H and Shimura, Y and Steffen, MM and Yang, Z and Lu, J and Joel, A and Jenkins, L and Kawachi, M and Yin, Y and Garcia-Pichel, F}, title = {The Trait Repertoire Enabling Cyanobacteria to Bloom Assessed through Comparative Genomic Complexity and Metatranscriptomics.}, journal = {mBio}, volume = {11}, number = {3}, pages = {}, pmid = {32605986}, issn = {2150-7511}, mesh = {Cyanobacteria/*genetics/physiology ; Ecosystem ; *Eutrophication ; *Gene Expression Profiling ; *Genome, Bacterial ; Genomics ; Lakes/*microbiology ; Metabolic Networks and Pathways ; Metagenomics ; Phenotype ; }, abstract = {Water bloom development due to eutrophication constitutes a case of niche specialization among planktonic cyanobacteria, but the genomic repertoire allowing bloom formation in only some species has not been fully characterized. We posited that the habitat relevance of a trait begets its underlying genomic complexity, so that traits within the repertoire would be differentially more complex in species successfully thriving in that habitat than in close species that cannot. To test this for the case of bloom-forming cyanobacteria, we curated 17 potentially relevant query metabolic pathways and five core pathways selected according to existing ecophysiological literature. The available 113 genomes were split into those of blooming (45) or nonblooming (68) strains, and an index of genomic complexity for each strain's version of each pathway was derived. We show that strain versions of all query pathways were significantly more complex in bloomers, with complexity in fact correlating positively with strain blooming incidence in 14 of those pathways. Five core pathways, relevant everywhere, showed no differential complexity or correlations. Gas vesicle, toxin and fatty acid synthesis, amino acid uptake, and C, N, and S acquisition systems were most strikingly relevant in the blooming repertoire. Further, we validated our findings using metagenomic gene expression analyses of blooming and nonblooming cyanobacteria in natural settings, where pathways in the repertoire were differentially overexpressed according to their relative complexity in bloomers, but not in nonbloomers. We expect that this approach may find applications to other habitats and organismal groups.IMPORTANCE We pragmatically delineate the trait repertoire that enables organismal niche specialization. We based our approach on the tenet, derived from evolutionary and complex-system considerations, that genomic units that can significantly contribute to fitness in a certain habitat will be comparatively more complex in organisms specialized to that habitat than their genomic homologs found in organisms from other habitats. We tested this in cyanobacteria forming harmful water blooms, for which decades-long efforts in ecological physiology and genomics exist. Our results essentially confirm that genomics and ecology can be linked through comparative complexity analyses, providing a tool that should be of general applicability for any group of organisms and any habitat, and enabling the posing of grounded hypotheses regarding the ecogenomic basis for diversification.}, } @article {pmid32605604, year = {2020}, author = {Hou, J and Sievert, SM and Wang, Y and Seewald, JS and Natarajan, VP and Wang, F and Xiao, X}, title = {Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {102}, pmid = {32605604}, issn = {2049-2618}, support = {DY135-B2-12//China Ocean Mineral Resources Research and Development Association (CN)/International ; 91751205//National Natural Science Foundation of China/International ; 41530967//National Natural Science Foundation of China/International ; 41921006//National Natural Science Foundation of China/International ; KEXUE2019GZ06//Senior User Project of RV KEXUE/International ; OCE-1136727//US National Science Foundation/International ; }, mesh = {*Biodiversity ; *Biological Evolution ; Hydrothermal Vents/*microbiology ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Sulfides/*metabolism ; *Water Microbiology ; }, abstract = {BACKGROUND: Deep-sea hydrothermal vents are highly productive biodiversity hotspots in the deep ocean supported by chemosynthetic microorganisms. Prominent features of these systems are sulfide chimneys emanating high-temperature hydrothermal fluids. While several studies have investigated the microbial diversity in both active and inactive sulfide chimneys that have been extinct for up to thousands of years, little is known about chimneys that have ceased activity more recently, as well as the microbial succession occurring during the transition from active to inactive chimneys.

RESULTS: Genome-resolved metagenomics was applied to an active and a recently extinct (~ 7 years) sulfide chimney from the 9-10° N hydrothermal vent field on the East Pacific Rise. Full-length 16S rRNA gene and a total of 173 high-quality metagenome assembled genomes (MAGs) were retrieved for comparative analysis. In the active chimney (L-vent), sulfide- and/or hydrogen-oxidizing Campylobacteria and Aquificae with the potential for denitrification were identified as the dominant community members and primary producers, fixing carbon through the reductive tricarboxylic acid (rTCA) cycle. In contrast, the microbiome of the recently extinct chimney (M-vent) was largely composed of heterotrophs from various bacterial phyla, including Delta-/Beta-/Alphaproteobacteria and Bacteroidetes. Gammaproteobacteria were identified as the main primary producers, using the oxidation of metal sulfides and/or iron oxidation coupled to nitrate reduction to fix carbon through the Calvin-Benson-Bassham (CBB) cycle. Further analysis revealed a phylogenetically distinct Nitrospirae cluster that has the potential to oxidize sulfide minerals coupled to oxygen and/or nitrite reduction, as well as for sulfate reduction, and that might serve as an indicator for the early stages of chimneys after venting has ceased.

CONCLUSIONS: This study sheds light on the composition, metabolic functions, and succession of microbial communities inhabiting deep-sea hydrothermal vent sulfide chimneys. Collectively, microbial succession during the life span of a chimney could be described to proceed from a "fluid-shaped" microbial community in newly formed and actively venting chimneys supported by the oxidation of reductants in the hydrothermal fluid to a "mineral-shaped" community supported by the oxidation of minerals after hydrothermal activity has ceased. Remarkably, the transition appears to occur within the first few years, after which the communities stay stable for thousands of years. Video Abstract.}, } @article {pmid32604176, year = {2020}, author = {Qian, XB and Chen, T and Xu, YP and Chen, L and Sun, FX and Lu, MP and Liu, YX}, title = {A guide to human microbiome research: study design, sample collection, and bioinformatics analysis.}, journal = {Chinese medical journal}, volume = {133}, number = {15}, pages = {1844-1855}, pmid = {32604176}, issn = {2542-5641}, mesh = {*Computational Biology ; Humans ; *Microbiota/genetics ; Reproducibility of Results ; Research Design ; Specimen Handling ; }, abstract = {The purpose of this review is to provide medical researchers, especially those without a bioinformatics background, with an easy-to-understand summary of the concepts and technologies used in microbiome research. First, we define primary concepts such as microbiota, microbiome, and metagenome. Then, we discuss study design schemes, the methods of sample size calculation, and the methods for improving the reliability of research. We emphasize the importance of negative and positive controls in this section. Next, we discuss statistical analysis methods used in microbiome research, focusing on problems with multiple comparisons and ways to compare β-diversity between groups. Finally, we provide step-by-step pipelines for bioinformatics analysis. In summary, the meticulous study design is a key step to obtaining meaningful results, and appropriate statistical methods are important for accurate interpretation of microbiome data. The step-by-step pipelines provide researchers with insights into newly developed bioinformatics analysis methods.}, } @article {pmid32603623, year = {2020}, author = {New, FN and Brito, IL}, title = {What Is Metagenomics Teaching Us, and What Is Missed?.}, journal = {Annual review of microbiology}, volume = {74}, number = {}, pages = {117-135}, doi = {10.1146/annurev-micro-012520-072314}, pmid = {32603623}, issn = {1545-3251}, support = {R01 DK093595/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Computational Biology/methods/standards ; High-Throughput Nucleotide Sequencing/methods/standards ; *Metagenome ; *Metagenomics ; Microbiota/*genetics ; }, abstract = {Shotgun metagenomic sequencing has revolutionized our ability to detect and characterize the diversity and function of complex microbial communities. In this review, we highlight the benefits of using metagenomics as well as the breadth of conclusions that can be made using currently available analytical tools, such as greater resolution of species and strains across phyla and functional content, while highlighting challenges of metagenomic data analysis. Major challenges remain in annotating function, given the dearth of functional databases for environmental bacteria compared to model organisms, and the technical difficulties of metagenome assembly and phasing in heterogeneous environmental samples. In the future, improvements and innovation in technology and methodology will lead to lowered costs. Data integration using multiple technological platforms will lead to a better understanding of how to harness metagenomes. Subsequently, we will be able not only to characterize complex microbiomes but also to manipulate communities to achieve prosperous outcomes for health, agriculture, and environmental sustainability.}, } @article {pmid32602643, year = {2020}, author = {Mahadevan, P and Middlebrooks, ML}, title = {Bacterial diversity in the clarki ecotype of the photosynthetic sacoglossan, Elysia crispata.}, journal = {MicrobiologyOpen}, volume = {9}, number = {9}, pages = {e1098}, pmid = {32602643}, issn = {2045-8827}, mesh = {Amino Acids/metabolism ; Animals ; Bacteria/*classification/genetics/isolation & purification/*metabolism ; Carbohydrate Metabolism ; Ecotype ; Gastropoda/classification/metabolism/*microbiology ; Lipid Metabolism ; Metabolic Networks and Pathways ; Metabolome ; *Microbiota ; Nucleotides/metabolism ; Photosynthesis ; Phylogeny ; Symbiosis ; }, abstract = {Few studies have examined the bacterial communities associated with photosynthetic sacoglossan sea slugs. In this study, we determined the bacterial diversity in the clarki ecotype, Elysia crispata using 16S rRNA sequencing. Computational analysis using QIIME2 revealed variability between individual samples, with the Spirochaetes and Bacteroidetes phyla dominating most samples. Tenericutes and Proteobacteria were also found, among other phyla. Computational metabolic profiling of the bacteria revealed a variety of metabolic pathways involving carbohydrate metabolism, lipid metabolism, nucleotide metabolism, and amino acid metabolism. Although associated bacteria may be involved in mutually beneficial metabolic pathways, there was a high degree of variation in the bacterial community of individual slugs. This suggests that many of these relationships are likely opportunistic rather than obligate and that many of these bacteria may live commensally providing no major benefit to the slugs.}, } @article {pmid32602257, year = {2021}, author = {Delbeke, H and Younas, S and Casteels, I and Joossens, M}, title = {Current knowledge on the human eye microbiome: a systematic review of available amplicon and metagenomic sequencing data.}, journal = {Acta ophthalmologica}, volume = {99}, number = {1}, pages = {16-25}, doi = {10.1111/aos.14508}, pmid = {32602257}, issn = {1755-3768}, mesh = {Bacteria/*genetics ; DNA, Bacterial/*genetics ; Eye Infections, Bacterial/*genetics/microbiology ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {Insights in the ocular surface microbiome are still at an early stage and many more questions remain unanswered compared with other human-associated microbial communities. The current knowledge on the human microbiome changed our viewpoint on bacteria and human health and significantly enhanced our understanding of human pathophysiology. Also in ocular medicine, microbiome research might impact treatment. Here, we summarize the current knowledge on ocular microbiome research with a particular focus on potential confounding factors and their effects on microbiome composition. Moreover, we present the ocular surface core microbiome based on current available data and defined it as genera present in almost half of the published control cohorts with a relative abundance of at least 1%.}, } @article {pmid32602070, year = {2020}, author = {Starý, L and Mezerová, K and Vysloužil, K and Zbořil, P and Skalický, P and Stašek, M and Raclavský, V}, title = {Candida albicans culture from a rectal swab can be associated with newly diagnosed colorectal cancer.}, journal = {Folia microbiologica}, volume = {65}, number = {6}, pages = {989-994}, pmid = {32602070}, issn = {1874-9356}, support = {IGA_LF_2020_021//Univerzita Palackého v Olomouci/ ; 61989592//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; FNOl 00098892//Ministerstvo Zdravotnictví Ceské Republiky/ ; NV19-03-00069//Ministerstvo Zdravotnictví Ceské Republiky/ ; }, mesh = {Adenoma/diagnosis/*microbiology ; Bacteria ; *Candida albicans/isolation & purification ; Colorectal Neoplasms/diagnosis/*microbiology ; Female ; Humans ; Male ; Microbiota ; Middle Aged ; Risk Factors ; }, abstract = {Plenty of metagenomic studies have suggested possible associations between microbiome composition and colorectal cancer (CRC). However, these techniques are not economic enough for routine use so far. Therefore, we explored the possibility to detect species associated with colorectal cancer by conventional culture from rectal swab. Fifty-two patients newly diagnosed for adenoma/CRC and 52 age-matched controls were recruited and sampled. Rectal swabs were inoculated on several types of plates and incubated appropriately under both aerobic and anaerobic conditions. All colonial morphotypes were subcultured and identified using MALDI-ToF MS. Although no bacterial species was significantly associated with CRC in our study, we surprisingly observed a strong and significant overrepresentation of the yeast Candida albicans in cases (P = 0.0066, odds ratio 5.444 [95% CI 1.449-20.462]). Potential confounding factors were associated neither with CRC (history of CRC in first-degree relatives, a personal history of appendectomy and cholecystectomy, increased BMI (body mass index), and the percentage of males) nor with C. albicans presence (preexisting diabetes and PPI medication) in our cohort. A growing body of evidence supports the view that C. albicans does cause cancer in humans. We hypothesize that presence of C. albicans in the gut may induce or facilitate some part of the sporadic CRC cases. Our observation should be a strong incentive to verify the potential usefulness of the easily culturable C. albicans yeast as a screening marker for patients at risk of CRC or those suffering an early asymptomatic stage of CRC.}, } @article {pmid32601270, year = {2020}, author = {Fremin, BJ and Sberro, H and Bhatt, AS}, title = {MetaRibo-Seq measures translation in microbiomes.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {3268}, pmid = {32601270}, issn = {2041-1723}, support = {P30 AG066515/AG/NIA NIH HHS/United States ; P50 AG047366/AG/NIA NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; U24 AG021886/AG/NIA NIH HHS/United States ; }, mesh = {Metagenomics ; Microbiota/*genetics ; Protein Biosynthesis/genetics ; RNA-Seq/*methods ; }, abstract = {No method exists to measure large-scale translation of genes in uncultured organisms in microbiomes. To overcome this limitation, we develop MetaRibo-Seq, a method for simultaneous ribosome profiling of tens to hundreds of organisms in microbiome samples. MetaRibo-Seq was benchmarked against gold-standard Ribo-Seq in a mock microbial community and applied to five different human fecal samples. Unlike RNA-Seq, Ribo-Seq signal of a predicted gene suggests it encodes a translated protein. We demonstrate two applications of this technique: First, MetaRibo-Seq identifies small genes, whose identification until now has been challenging. For example, MetaRibo-Seq identifies 2,091 translated, previously unannotated small protein families from five fecal samples, more than doubling the number of small proteins predicted to exist in this niche. Second, the combined application of RNA-Seq and MetaRibo-Seq identifies differences in the translation of transcripts. In summary, MetaRibo-Seq enables comprehensive translational profiling in microbiomes and identifies previously unannotated small proteins.}, } @article {pmid32600361, year = {2020}, author = {Moskowitz, JE and Doran, AG and Lei, Z and Busi, SB and Hart, ML and Franklin, CL and Sumner, LW and Keane, TM and Amos-Landgraf, JM}, title = {Integration of genomics, metagenomics, and metabolomics to identify interplay between susceptibility alleles and microbiota in adenoma initiation.}, journal = {BMC cancer}, volume = {20}, number = {1}, pages = {600}, pmid = {32600361}, issn = {1471-2407}, support = {MR/R017565/1/MRC_/Medical Research Council/United Kingdom ; T32 OD011126/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; U42 OD010918/CD/ODCDC CDC HHS/United States ; }, mesh = {Adenoma/*genetics/metabolism/microbiology ; Adenomatous Polyposis Coli Protein/genetics ; Alleles ; Animals ; Colorectal Neoplasms/*genetics/metabolism/microbiology ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/*physiology ; *Genetic Predisposition to Disease ; Humans ; Male ; Metabolomics ; Metagenomics ; Mice ; Mutation ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is a multifactorial disease resulting from both genetic predisposition and environmental factors including the gut microbiota (GM), but deciphering the influence of genetic variants, environmental variables, and interactions with the GM is exceedingly difficult. We previously observed significant differences in intestinal adenoma multiplicity between C57BL/6 J-Apc[Min] (B6-Min/J) from The Jackson Laboratory (JAX), and original founder strain C57BL/6JD-Apc[Min] (B6-Min/D) from the University of Wisconsin.

METHODS: To resolve genetic and environmental interactions and determine their contributions we utilized two genetically inbred, independently isolated Apc[Min] mouse colonies that have been separated for over 20 generations. Whole genome sequencing was used to identify genetic variants unique to the two substrains. To determine the influence of genetic variants and the impact of differences in the GM on phenotypic variability, we used complex microbiota targeted rederivation to generate two Apc mutant mouse colonies harboring complex GMs from two different sources (GMJAX originally from JAX or GMHSD originally from Envigo), creating four Apc[Min] groups. Untargeted metabolomics were used to characterize shifts in the fecal metabolite profile based on genetic variation and differences in the GM.

RESULTS: WGS revealed several thousand high quality variants unique to the two substrains. No homozygous variants were present in coding regions, with the vast majority of variants residing in noncoding regions. Host genetic divergence between Min/J and Min/D and the complex GM additively determined differential adenoma susceptibility. Untargeted metabolomics revealed that both genetic lineage and the GM collectively determined the fecal metabolite profile, and that each differentially regulates bile acid (BA) metabolism. Metabolomics pathway analysis facilitated identification of a functionally relevant private noncoding variant associated with the bile acid transporter Fatty acid binding protein 6 (Fabp6). Expression studies demonstrated differential expression of Fabp6 between Min/J and Min/D, and the variant correlates with adenoma multiplicity in backcrossed mice.

CONCLUSIONS: We found that both genetic variation and differences in microbiota influences the quantitiative adenoma phenotype in Apc[Min] mice. These findings demonstrate how the use of metabolomics datasets can aid as a functional genomic tool, and furthermore illustrate the power of a multi-omics approach to dissect complex disease susceptibility of noncoding variants.}, } @article {pmid32598884, year = {2020}, author = {Zuo, T and Zhan, H and Zhang, F and Liu, Q and Tso, EYK and Lui, GCY and Chen, N and Li, A and Lu, W and Chan, FKL and Chan, PKS and Ng, SC}, title = {Alterations in Fecal Fungal Microbiome of Patients With COVID-19 During Time of Hospitalization until Discharge.}, journal = {Gastroenterology}, volume = {159}, number = {4}, pages = {1302-1310.e5}, pmid = {32598884}, issn = {1528-0012}, mesh = {Adult ; Aged ; Aspergillus flavus/genetics/isolation & purification ; Aspergillus niger/genetics/isolation & purification ; Betacoronavirus ; COVID-19 ; Candida/genetics/isolation & purification ; Candida albicans/genetics/isolation & purification ; Case-Control Studies ; Community-Acquired Infections/microbiology ; Coronavirus Infections/*microbiology ; DNA, Fungal/analysis ; Feces/*microbiology ; Female ; Fungi/genetics/*isolation & purification ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Middle Aged ; *Mycobiome ; Nasopharynx/virology ; Pandemics ; Patient Discharge ; Pneumonia/microbiology ; Pneumonia, Viral/*microbiology ; SARS-CoV-2 ; Time Factors ; Young Adult ; }, abstract = {BACKGROUND & AIMS: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects intestinal cells, and might affect the intestinal microbiota. We investigated changes in the fecal fungal microbiomes (mycobiome) of patients with SARS-CoV-2 infection during hospitalization and on recovery.

METHODS: We performed deep shotgun metagenomic sequencing analysis of fecal samples from 30 patients with coronavirus disease 2019 (COVID-19) in Hong Kong, from February 5 through May 12, 2020. Fecal samples were collected 2 to 3 times per week from time of hospitalization until discharge. We compared fecal mycobiome compositions of patients with COVID-19 with those from 9 subjects with community-acquired pneumonia and 30 healthy individuals (controls). We assessed fecal mycobiome profiles throughout time of hospitalization until clearance of SARS-CoV-2 from nasopharyngeal samples.

RESULTS: Patients with COVID-19 had significant alterations in their fecal mycobiomes compared with controls, characterized by enrichment of Candia albicans and a highly heterogeneous mycobiome configuration, at time of hospitalization. Although fecal mycobiomes of 22 patients with COVID-19 did not differ significantly from those of controls during times of hospitalization, 8 of 30 patients with COVID-19 had continued significant differences in fecal mycobiome composition, through the last sample collected. The diversity of the fecal mycobiome of the last sample collected from patients with COVID-19 was 2.5-fold higher than that of controls (P < .05). Samples collected at all timepoints from patients with COVID-19 had increased proportions of opportunistic fungal pathogens, Candida albicans, Candida auris, and Aspergillus flavus compared with controls. Two respiratory-associated fungal pathogens, A. flavus and Aspergillus niger, were detected in fecal samples from a subset of patients with COVID-19, even after clearance of SARS-CoV-2 from nasopharyngeal samples and resolution of respiratory symptoms.

CONCLUSIONS: In a pilot study, we found heterogeneous configurations of the fecal mycobiome, with enrichment of fungal pathogens from the genera Candida and Aspergillus, during hospitalization of 30 patients with COVID-19 compared with controls. Unstable gut mycobiomes and prolonged dysbiosis persisted in a subset of patients with COVID-19 up to 12 days after nasopharyngeal clearance of SARS-CoV-2. Studies are needed to determine whether alterations in intestinal fungi contribute to or result from SARS-CoV-2 infection, and the effects of these changes in disease progression.}, } @article {pmid32593021, year = {2020}, author = {Cerqueira, F and Christou, A and Fatta-Kassinos, D and Vila-Costa, M and Bayona, JM and Piña, B}, title = {Effects of prescription antibiotics on soil- and root-associated microbiomes and resistomes in an agricultural context.}, journal = {Journal of hazardous materials}, volume = {400}, number = {}, pages = {123208}, doi = {10.1016/j.jhazmat.2020.123208}, pmid = {32593021}, issn = {1873-3336}, mesh = {*Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; *Microbiota ; Prescriptions ; Soil ; Soil Microbiology ; }, abstract = {The use of treated wastewater for crop irrigation is rapidly increasing to respond to the ever-growing demands for water and food resources. However, this practice may contribute to the spread of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in agricultural settings. To evaluate this potential risk, we analyzed microbiomes and resistomes of soil and Lactuca sativa L. (lettuce) root samples from pots irrigated with tap water spiked with 0, 20, or 100 μg L[-1] of a mixture of three antibiotics (Trimethoprim, Ofloxacin, Sulfamethoxazole). The presence of antibiotics induced changes in bacterial populations, particularly in soil, as revealed by 16S rDNA sequence analysis. Parallel shotgun sequencing identified a total of 56 different ARGs conferring resistance against 14 antibiotic families. Antibiotic -treated samples showed increased loads of ARGs implicated in mutidrug resistance or in both direct and indirect acquired resistance. These changes correlated with the prevalence of Xantomonadales species in the root microbiomes. We interpret these data as indicating different strategies of soil and root microbiomes to cope with the presence of antibiotics, and as a warning that their presence may increase the loads of ARBs and ARGs in edible plant parts, therefore constituting a potential risk for human consumers.}, } @article {pmid32591381, year = {2020}, author = {Luo, Y and Huang, Y and Xu, RX and Qian, B and Zhou, JW and Xia, XL}, title = {Primary and Secondary Succession Mediate the Accumulation of Biogenic Amines during Industrial Semidry Chinese Rice Wine Fermentation.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {17}, pages = {}, pmid = {32591381}, issn = {1098-5336}, mesh = {Bacteria/isolation & purification ; Biogenic Amines/*metabolism ; China ; *Fermentation ; Microbiota/*physiology ; Wine/*microbiology ; }, abstract = {The use of exogenous functional microorganisms to regulate biogenic amine (BA) content is a common approach in fermentation systems. Here, to better understand the microbial traits of succession trajectories in resource-based and biotic interference systems, the BA-related primary and secondary succession were tracked during industrial semidry Chinese rice wine (CRW) fermentation. Dominant abundance and BA-associated microbial functionality based on phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) indicated that Citrobacter, Acinetobacter, Lactobacillus, Exiguobacterium, Bacillus, Pseudomonas, and Enterobacter spp. prominently contributed to the decarboxylase gene family in CRW. The expression levels of tyrosine decarboxylase (tyrDC), ornithine decarboxylase (odc), and agmatine deiminase (aguA) genes were assessed by quantitative PCR (qPCR). The transcription levels of these genes did not correlate with the BA formation rate during postfermentation, indicating that acidification and carbon source depletion upregulated the expression and microbes launch the dormancy strategy to respond to unfavorable conditions. Furthermore, microbial interference with CRW fermentation by Lactobacillus plantarum (ACBC271) and Staphylococcus xylosus (CGMCC1.8382) coinoculated at a ratio of 1:2 exhibited the best synergetic control of BA content. Spearman correlations revealed that Lactobacillus and Staphylococcus exhibited influence on BA-associated microbiota (|ρ| > 0), Exiguobacterium and Pseudomonas were strongly suppressed by Lactobacillus (ρ = -0.867 and ρ = -0.782, respectively; P < 0.05), and Staphylococcus showed the strongest inhibitory effect toward Lactobacillus (ρ = -0.115) and Citrobacter (ρ = -0.188) in the coinoculated 1:2 group. The high inhibitory effect of exogenous added strains on specific bacteria presented evidence for the obtained BA-associated contributors. Overall, this work provides important insight into the microbial traits that rely on resource usage and functional microbiota within food microbial ecology.IMPORTANCE Understanding the shifting patterns of substance usage and microbial interactions is a fundamental objective within microbiology and ecology. Analyses of primary and secondary microbial succession allow for determinations of taxonomic diversity, community traits, and functional transformations over time or after a disturbance. The kinetics of BA generation and the patterns of resource consumption, functional metagenome prediction, and microbial interactions were profiled to elucidate the equilibrium mechanism of microbial systems. Secondary succession after a disturbance triggers a change in resource usage, which in turn affects primary succession and metabolism. In this study, the functional potential of exogenous microorganisms under disturbance synergized with secondary succession strategies, including rebalancing and dormancy, which ultimately reduced BA accumulation. Thus, this succession system could facilitate the settling of essential issues with respect to microbial traits that rely on resource usage and microbial interactions that occur in natural ecosystems.}, } @article {pmid32591376, year = {2020}, author = {Moeller, AH and Ivey, K and Cornwall, MB and Herr, K and Rede, J and Taylor, EN and Gunderson, AR}, title = {The Lizard Gut Microbiome Changes with Temperature and Is Associated with Heat Tolerance.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {17}, pages = {}, pmid = {32591376}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification ; California ; Female ; Gastrointestinal Microbiome/*physiology ; Lizards/*microbiology/*physiology ; Male ; Temperature ; *Thermotolerance ; }, abstract = {Vertebrates harbor trillions of microorganisms in the gut, collectively termed the gut microbiota, which affect a wide range of host functions. Recent experiments in lab-reared vertebrates have shown that changes in environmental temperature can induce shifts in the gut microbiota, and in some cases these shifts have been shown to affect host thermal physiology. However, there is a lack of information about the effects of temperature on the gut microbiota of wild-caught vertebrates. Moreover, in ectotherms, which are particularly vulnerable to changing temperature regimens, the extent to which microbiota composition is shaped by temperature and associated with host thermal tolerance has not been investigated. To address these issues, we monitored the gut microbiota composition of wild-caught western fence lizards (Sceloporus occidentalis) experimentally exposed to a cool-to-warm temperature transition. Comparing experimentally exposed and control lizards indicated that warm temperatures altered and destabilized the composition of the S. occidentalis gut microbiota. Warming drove a significant reduction in the relative abundances of a clade of Firmicutes, a significant increase in the rate of compositional turnover in the gut microbiota within individual lizards, and increases in the abundances of bacteria from predicted pathogenic clades. In addition, the composition of the microbiota was significantly associated with the thermal tolerance of lizards measured at the end of the experiment. These results suggest that temperature can alter the lizard gut microbiota, with potential implications for the physiological performance and fitness of natural populations.IMPORTANCE Gut microbial communities affect their animal hosts in numerous ways, motivating investigations of the factors that shape the gut microbiota and the consequences of gut microbiota variation for host traits. In this study, we tested the effects of increases in environmental temperatures on the gut microbiota of fence lizards, a vertebrate ectotherm threatened by warming climates. By monitoring lizards and their gut microbes during an experimental temperature treatment, we showed that the warming altered and destabilized the lizard gut microbiota. Moreover, measuring thermal performance of lizard hosts at the end of the experiment indicated that the composition of the gut microbiota was associated with host thermal tolerance. These results indicate that warming temperatures can alter the gut microbiota of vertebrate ectotherms and suggest relationships between variation in the gut microbiota and the thermal physiology of natural host populations.}, } @article {pmid32591016, year = {2020}, author = {Amos, GCA and Logan, A and Anwar, S and Fritzsche, M and Mate, R and Bleazard, T and Rijpkema, S}, title = {Developing standards for the microbiome field.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {98}, pmid = {32591016}, issn = {2049-2618}, mesh = {Genomics/*methods/*standards ; High-Throughput Nucleotide Sequencing/*standards ; Metagenome/*genetics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Reference Standards ; }, abstract = {BACKGROUND: Effective standardisation of methodologies to analyse the microbiome is essential to the entire microbiome community. Despite the microbiome field being established for over a decade, there are no accredited or certified reference materials available to the wider community. In this study, we describe the development of the first reference reagents produced by the National Institute for Biological Standards and Control (NIBSC) for microbiome analysis by next-generation sequencing. These can act as global working standards and will be evaluated as candidate World Health Organization International Reference Reagents.

RESULTS: We developed the NIBSC DNA reference reagents Gut-Mix-RR and Gut-HiLo-RR and a four-measure framework for evaluation of bioinformatics tool and pipeline bias. Using these reagents and reporting system, we performed an independent evaluation of a variety of bioinformatics tools by analysing shotgun sequencing and 16S rRNA sequencing data generated from the Gut-Mix-RR and Gut-HiLo-RR. We demonstrate that key measures of microbiome health, such as diversity estimates, are largely inflated by the majority of bioinformatics tools. Across all tested tools, biases were present, with a clear trade-off occurring between sensitivity and the relative abundance of false positives in the final dataset. Using commercially available mock communities, we investigated how the composition of reference reagents may impact benchmarking studies. Reporting measures consistently changed when the same bioinformatics tools were used on different community compositions. This was influenced by both community complexity and taxonomy of species present. Both NIBSC reference reagents, which consisted of gut commensal species, proved to be the most challenging for the majority of bioinformatics tools tested. Going forward, we recommend the field uses site-specific reagents of a high complexity to ensure pipeline benchmarking is fit for purpose.

CONCLUSIONS: If a consensus of acceptable levels of error can be agreed on, widespread adoption of these reference reagents will standardise downstream gut microbiome analyses. We propose to do this through a large open-invite collaborative study for multiple laboratories in 2020. Video Abstract.}, } @article {pmid32591010, year = {2020}, author = {Leung, MHY and Tong, X and Bastien, P and Guinot, F and Tenenhaus, A and Appenzeller, BMR and Betts, RJ and Mezzache, S and Li, J and Bourokba, N and Breton, L and Clavaud, C and Lee, PKH}, title = {Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {100}, pmid = {32591010}, issn = {2049-2618}, mesh = {Adult ; China ; Cities ; Environmental Monitoring ; Environmental Pollutants/administration & dosage/*pharmacology ; Female ; Humans ; Microbiota/*drug effects ; Middle Aged ; Polycyclic Aromatic Hydrocarbons/administration & dosage/*pharmacology ; Skin/*drug effects/*microbiology ; }, abstract = {BACKGROUND: Polycyclic aromatic hydrocarbons (PAHs) are of environmental and public health concerns and contribute to adverse skin attributes such as premature skin aging and pigmentary disorder. However, little information is available on the potential roles of chronic urban PAH pollutant exposure on the cutaneous microbiota. Given the roles of the skin microbiota have on healthy and undesirable skin phenotypes and the relationships between PAHs and skin properties, we hypothesize that exposure of PAHs may be associated with changes in the cutaneous microbiota. In this study, the skin microbiota of over two hundred Chinese individuals from two cities in China with varying exposure levels of PAHs were characterized by bacterial and fungal amplicon and shotgun metagenomics sequencing.

RESULTS: Skin site and city were strong parameters in changing microbial communities and their assembly processes. Reductions of bacterial-fungal microbial network structural integrity and stability were associated with skin conditions (acne and dandruff). Multivariate analysis revealed associations between abundances of Propionibacterium and Malassezia with host properties and pollutant exposure levels. Shannon diversity increase was correlated to exposure levels of PAHs in a dose-dependent manner. Shotgun metagenomics analysis of samples (n = 32) from individuals of the lowest and highest exposure levels of PAHs further highlighted associations between the PAHs quantified and decrease in abundances of skin commensals and increase in oral bacteria. Functional analysis identified associations between levels of PAHs and abundance of microbial genes of metabolic and other pathways with potential importance in host-microbe interactions as well as degradation of aromatic compounds.

CONCLUSIONS: The results in this study demonstrated the changes in composition and functional capacities of the cutaneous microbiota associated with chronic exposure levels of PAHs. Findings from this study will aid the development of strategies to harness the microbiota in protecting the skin against pollutants. Video Abstract.}, } @article {pmid32589701, year = {2021}, author = {Solbach, P and Chhatwal, P and Woltemate, S and Tacconelli, E and Buhl, M and Autenrieth, IB and Vehreschild, MJGT and Jazmati, N and Gerhard, M and Stein-Thoeringer, CK and Rupp, J and Ulm, K and Ott, A and Lasch, F and Koch, A and Manns, MP and Suerbaum, S and Bachmann, O}, title = {Microbiota-associated Risk Factors for Clostridioides difficile Acquisition in Hospitalized Patients: A Prospective, Multicentric Study.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {73}, number = {9}, pages = {e2625-e2634}, doi = {10.1093/cid/ciaa871}, pmid = {32589701}, issn = {1537-6591}, support = {//German Center for Infection Research/ ; 2889//State of Lower Saxony/ ; }, mesh = {*Bacterial Toxins/genetics ; Bacteroidetes ; Clostridioides ; *Clostridioides difficile/genetics ; *Clostridium Infections/epidemiology ; Feces ; Humans ; *Microbiota ; Prospective Studies ; Risk Factors ; Ruminococcus ; }, abstract = {BACKGROUND: Asymptomatic C. difficile colonization is believed to predispose to subsequent C. difficile infection (CDI). While emerging insights into the role of the commensal microbiota in mediating colonization resistance against C. difficile have associated CDI with specific microbial components, corresponding prospectively collected data on colonization with C. difficile are largely unavailable.

METHODS: C. difficile status was assessed by GDH EIA and real-time PCR targeting the toxin A (tcdA) and B (tcdB) genes. 16S V3 and V4 gene sequencing results from fecal samples of patients tested positive for C. difficile were analyzed by assessing alpha and beta diversity, LefSe, and the Piphillin functional inference approach to estimate functional capacity.

RESULTS: 1506 patients were recruited into a prospective observational study (DRKS00005335) upon admission into one of five academic hospitals. 936 of them provided fecal samples on admission and at discharge and were thus available for longitudinal analysis. Upon hospital admission, 5.5% (83/1506) and 3.7% (56/1506) of patients were colonized with toxigenic (TCD) and non-toxigenic C. difficile (NTCD), respectively. During hospitalization, 1.7% (16/936) acquired TCD. Risk factors for acquisition of TCD included pre-existing lung diseases, lower GI endoscopy and antibiotics. Species protecting against hospital-related C. difficile acquisition included Gemmiger spp., Odoribacter splanchnicus, Ruminococcus bromii and other Ruminococcus spp. Metagenomic pathway analysis identified steroid biosynthesis as the most underrepresented metabolic pathway in patients who later acquire C. difficile colonization.

CONCLUSIONS: Gemmiger spp., Odoribacter splanchnicus, Ruminococcus bromii and other Ruminococci were associated with a decreased risk of C. difficile acquisition.

CLINICAL TRIALS REGISTRATION: DRKS00005335.}, } @article {pmid32589643, year = {2020}, author = {Ajene, IJ and Khamis, FM and van Asch, B and Pietersen, G and Rasowo, BA and Ombura, FL and Wairimu, AW and Akutse, KS and Sétamou, M and Mohamed, S and Ekesi, S}, title = {Microbiome diversity in Diaphorina citri populations from Kenya and Tanzania shows links to China.}, journal = {PloS one}, volume = {15}, number = {6}, pages = {e0235348}, pmid = {32589643}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; China ; Drug Resistance, Microbial/genetics ; Hemiptera/*microbiology ; Insect Vectors/microbiology ; Kenya ; *Microbiota/drug effects/genetics ; *Phylogeny ; Plant Diseases/microbiology ; Sequence Analysis ; Symbiosis ; Tanzania ; }, abstract = {The Asian citrus psyllid (Diaphorina citri) is a key pest of Citrus spp. worldwide, as it acts as a vector for "Candidatus Liberibacter asiaticus (Las)", the bacterial pathogen associated with the destructive Huanglongbing (HLB) disease. Recent detection of D. citri in Africa and reports of Las-associated HLB in Ethiopia suggest that the citrus industry on the continent is under imminent threat. Endosymbionts and gut bacteria play key roles in the biology of arthropods, especially with regards to vector-pathogen interactions and resistance to antibiotics. Thus, we aim to profile the bacterial genera and to identify antibiotic resistance genes within the microbiome of different populations worldwide of D. citri. The metagenome of D. citri was sequenced using the Oxford Nanopore full-length 16S metagenomics protocol, and the "What's in my pot" (WIMP) analysis pipeline. Microbial diversity within and between D. citri populations was assessed, and antibiotic resistance genes were identified using the WIMP-ARMA workflow. The most abundant genera were key endosymbionts of D. citri ("Candidatus Carsonella", "Candidatus Profftella", and Wolbachia). The Shannon diversity index showed that D. citri from Tanzania had the highest diversity of bacterial genera (1.92), and D. citri from China had the lowest (1.34). The Bray-Curtis dissimilarity showed that China and Kenya represented the most diverged populations, while the populations from Kenya and Tanzania were the least diverged. The WIMP-ARMA analyses generated 48 CARD genes from 13 bacterial species in each of the populations. Spectinomycin resistance genes were the most frequently found, with an average of 65.98% in all the populations. These findings add to the knowledge on the diversity of the African D. citri populations and the probable introduction source of the psyllid in these African countries.}, } @article {pmid32588473, year = {2020}, author = {Schoster, A and Weese, JS and Gerber, V and Nicole Graubner, C}, title = {Dysbiosis is not present in horses with fecal water syndrome when compared to controls in spring and autumn.}, journal = {Journal of veterinary internal medicine}, volume = {34}, number = {4}, pages = {1614-1621}, pmid = {32588473}, issn = {1939-1676}, mesh = {Animals ; Bacteria/classification ; Case-Control Studies ; Diarrhea/etiology/microbiology/*veterinary ; Dysbiosis/*veterinary ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome ; Horse Diseases/etiology/*microbiology ; Horses ; Male ; Prospective Studies ; Seasons ; }, abstract = {BACKGROUND: Fecal water syndrome (FWS) is long-standing and common in horses, particularly in central Europe. No large epidemiological data sets exist, and the cause remains elusive. Dysbiosis could play a role in pathogenesis.

OBJECTIVES: To evaluate whether dysbiosis is present in horses with FWS when compared to stable-matched control horses in spring and autumn.

ANIMALS: Fecal samples were collected from horses with FWS (n = 16; 9 mares, 7 geldings) and controls (n = 15; 8 mares, 7 geldings).

METHODS: The bacterial microbiome of samples collected in spring and autumn of 2016 was analyzed using high-throughput sequencing. Differences in relative abundance of bacterial taxa, alpha diversity, and beta diversity indices were assessed between horses with FWS and controls based on season.

RESULTS: Differences in microbial community composition based on time point and health status were not observed on any taxonomic level. Limited differences were seen on linear discriminant analysis effect size analysis. No difference in alpha diversity indices was observed including richness, diversity based on health status, or time point. No effect of health status on microbial community membership structure was observed.

Limited differences were found in the bacterial microbiota of horses with and without FWS, regardless of season. Further research is needed to elucidate the role of microbiota in the development of FWS.}, } @article {pmid32588084, year = {2020}, author = {Zambounis, A and Ganopoulos, I and Tsaftaris, A and Valasiadis, D and Madesis, P}, title = {Metagenomics analysis of fungal communities associated with postharvest diseases in pear fruits under the effect of management practices.}, journal = {Archives of microbiology}, volume = {202}, number = {9}, pages = {2391-2400}, doi = {10.1007/s00203-020-01960-6}, pmid = {32588084}, issn = {1432-072X}, mesh = {*Food Microbiology ; Fruit/*microbiology ; *Fungi/classification/drug effects/genetics ; Fungicides, Industrial/pharmacology ; *Metagenomics ; *Mycobiome/drug effects/genetics ; Pyrus/*microbiology ; }, abstract = {An amplicon metagenomic approach based on the ITS1 region of fungal rDNA was employed to identify the composition of fungal communities associated with diseases of pear fruits during postharvest storage. The sampled fruits were harvested at an orchard using routine management practices involving treatments with various chemical fungicides and were transferred to a storage packinghouse. Effective tags of reading sequences clustered into 53 OTUs whereas Ascomycota was the dominant phylum (83.4%) followed by Basidiomycota (15.8%). Our results revealed that four genera, Penicillium, Rhodotorula, Alternaria and Cladosporium were the most abundant representing 59-95% of the relative abundance per sample. The interruption of chemical treatments during the last month before harvest altered the structure of the fungal community of fruits among untreated and treated samples, mainly in cases of relative abundance of Penicillium and Rhodotorula genera. We hypothesize that various antagonistic interactions might occur on fruit surfaces among the detected fungal genera whose relative abundances were affected by fungicide treatments. Interestingly, some common pre- and postharvest pear fungal pathogens were either less present (such as Moniliana), or undetected (such as Aspergillus, Venturia and Septoria) in untreated and treated samples.}, } @article {pmid32588072, year = {2021}, author = {Zhou, X and Wang, JT and Wang, WH and Tsui, CK and Cai, L}, title = {Changes in Bacterial and Fungal Microbiomes Associated with Tomatoes of Healthy and Infected by Fusarium oxysporum f. sp. lycopersici.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {1004-1017}, pmid = {32588072}, issn = {1432-184X}, support = {NSFC 31725001//National Natural Science Foundation of China/ ; QYZDB-SSW-SMC044//Key Research Program of Frontier Sciences,CAS/ ; }, mesh = {Bacteria/genetics ; *Fusarium/genetics ; *Solanum lycopersicum ; *Mycobiome ; Plant Diseases ; }, abstract = {Fusarium wilt of tomato caused by the pathogen Fusarium oxysporum f. sp. lycopersici (Fol) is one of the most devastating soilborne diseases of tomato. To evaluate whether microbial community composition associated with Fol-infected tomato is different from healthy tomato, we analyzed the tomato-associated microbes in both healthy and Fol-infected tomato plants at both the taxonomic and functional levels; both bacterial and fungal communities have been characterized from bulk soil, rhizosphere, rhizoplane, and endosphere of tomatoes using metabarcoding and metagenomics approaches. The microbial community (bacteria and fungi) composition of healthy tomato was significantly different from that of diseased tomato, despite similar soil physicochemical characteristics. Both fungal and bacterial diversities were significantly higher in the tomato plants that remained healthy than in those that became diseased; microbial diversities were also negatively correlated with the concentration of Fol pathogen. Network analysis revealed the microbial community of healthy tomato formed a larger and more complex network than that of diseased tomato, probably providing a more stable community beneficial to plant health. Our findings also suggested that healthy tomato contained significantly greater microbial consortia, including some well-known biocontrol agents (BCAs), and enriched more functional genes than diseased tomato. The microbial taxa enriched in healthy tomato plants are recognized as potential suppressors of Fol pathogen invasion.}, } @article {pmid32588040, year = {2020}, author = {Yang, F and Zou, Q}, title = {mAML: an automated machine learning pipeline with a microbiome repository for human disease classification.}, journal = {Database : the journal of biological databases and curation}, volume = {2020}, number = {}, pages = {}, pmid = {32588040}, issn = {1758-0463}, mesh = {Computational Biology/*methods ; Databases, Factual ; Disease/*classification ; *Gastrointestinal Microbiome ; Humans ; *Machine Learning ; *Software ; }, abstract = {Due to the concerted efforts to utilize the microbial features to improve disease prediction capabilities, automated machine learning (AutoML) systems aiming to get rid of the tediousness in manually performing ML tasks are in great demand. Here we developed mAML, an ML model-building pipeline, which can automatically and rapidly generate optimized and interpretable models for personalized microbiome-based classification tasks in a reproducible way. The pipeline is deployed on a web-based platform, while the server is user-friendly and flexible and has been designed to be scalable according to the specific requirements. This pipeline exhibits high performance for 13 benchmark datasets including both binary and multi-class classification tasks. In addition, to facilitate the application of mAML and expand the human disease-related microbiome learning repository, we developed GMrepo ML repository (GMrepo Microbiome Learning repository) from the GMrepo database. The repository involves 120 microbiome-based classification tasks for 85 human-disease phenotypes referring to 12 429 metagenomic samples and 38 643 amplicon samples. The mAML pipeline and the GMrepo ML repository are expected to be important resources for researches in microbiology and algorithm developments. Database URL: http://lab.malab.cn/soft/mAML.}, } @article {pmid32587239, year = {2020}, author = {Li, H and Xu, H and Li, Y and Jiang, Y and Hu, Y and Liu, T and Tian, X and Zhao, X and Zhu, Y and Wang, S and Zhang, C and Ge, J and Wang, X and Wen, H and Bai, C and Sun, Y and Song, L and Zhang, Y and Hui, R and Cai, J and Chen, J}, title = {Alterations of gut microbiota contribute to the progression of unruptured intracranial aneurysms.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {3218}, pmid = {32587239}, issn = {2041-1723}, mesh = {Animals ; Case-Control Studies ; Clostridiaceae/*metabolism ; Cohort Studies ; Disease Progression ; Fecal Microbiota Transplantation ; Female ; *Gastrointestinal Microbiome ; Humans ; *Intracranial Aneurysm/microbiology/pathology ; Male ; Mice ; Prognosis ; Risk Factors ; Taurine/*metabolism ; }, abstract = {Unruptured intracranial aneurysm (UIA) is a life-threatening cerebrovascular condition. Whether changes in gut microbial composition participate in the development of UIAs remains largely unknown. We perform a case-control metagenome-wide association study in two cohorts of Chinese UIA patients and control individuals and mice that receive fecal transplants from human donors. After fecal transplantation, the UIA microbiota is sufficient to induce UIAs in mice. We identify UIA-associated gut microbial species link to changes in circulating taurine. Specifically, the abundance of Hungatella hathewayi is markedly decreased and positively correlated with the circulating taurine concentration in both humans and mice. Consistently, gavage with H. hathewayi normalizes the taurine levels in serum and protects mice against the formation and rupture of intracranial aneurysms. Taurine supplementation also reverses the progression of intracranial aneurysms. Our findings provide insights into a potential role of H. hathewayi-associated taurine depletion as a key factor in the pathogenesis of UIAs.}, } @article {pmid32586278, year = {2020}, author = {Weiß, CL and Gansauge, MT and Aximu-Petri, A and Meyer, M and Burbano, HA}, title = {Mining ancient microbiomes using selective enrichment of damaged DNA molecules.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {432}, pmid = {32586278}, issn = {1471-2164}, support = {Presidential Innovation Fund//Max-Planck-Gesellschaft/ ; }, mesh = {Animals ; Bacteria/*classification/genetics ; DNA, Ancient/*analysis/chemistry ; DNA, Bacterial/genetics ; Data Mining ; Fossils/*microbiology ; Gene Library ; Metagenomics ; Microbiota ; Neanderthals/microbiology ; Plants/microbiology ; Sequence Analysis, DNA/*methods ; Uracil/*chemistry ; }, abstract = {BACKGROUND: The identification of bona fide microbial taxa in microbiomes derived from ancient and historical samples is complicated by the unavoidable mixture between DNA from ante- and post-mortem microbial colonizers. One possibility to distinguish between these sources of microbial DNA is querying for the presence of age-associated degradation patterns typical of ancient DNA (aDNA). The presence of uracils, resulting from cytosine deamination, has been detected ubiquitously in aDNA retrieved from diverse sources, and used as an authentication criterion. Here, we employ a library preparation method that separates molecules that carry uracils from those that do not for a set of samples that includes Neandertal remains, herbarium specimens and archaeological plant remains.

RESULTS: We show that sequencing DNA libraries enriched in molecules carrying uracils effectively amplifies age associated degradation patterns in microbial mixtures of ancient and historical origin. This facilitates the discovery of authentic ancient microbial taxa in cases where degradation patterns are difficult to detect due to large sequence divergence in microbial mixtures. Additionally, the relative enrichment of taxa in the uracil enriched fraction can help to identify bona fide ancient microbial taxa that could be missed using a more targeted approach.

CONCLUSIONS: Our experiments show, that in addition to its use in enriching authentic endogenous DNA of organisms of interest, the selective enrichment of damaged DNA molecules can be a valuable tool in the discovery of ancient microbial taxa.}, } @article {pmid32583287, year = {2020}, author = {Park, C and Yun, KE and Chu, JM and Lee, JY and Hong, CP and Nam, YD and Jeong, J and Han, K and Ahn, YJ}, title = {Performance comparison of fecal preservative and stock solutions for gut microbiome storage at room temperature.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {58}, number = {8}, pages = {703-710}, doi = {10.1007/s12275-020-0092-6}, pmid = {32583287}, issn = {1976-3794}, mesh = {Adult ; Bacteria/*classification/*drug effects/genetics ; Bacteroidetes/drug effects ; Ethanol/*pharmacology ; Feces/microbiology ; Female ; Firmicutes/drug effects ; Gastrointestinal Microbiome/*drug effects ; Humans ; Male ; Proteobacteria/drug effects ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Specimen Handling/*methods ; Young Adult ; }, abstract = {The gut microbiome, which is symbiotic within the human body, assists in human digestion. It plays significant roles in identifying intestinal disease as well as in maintaining a healthy body with functional immune and metabolic activities. To confirm the consistency of fecal intestinal microbial research, it is necessary to study the changes in intestinal microbial flora according to the fecal collection solution and storage period. We collected fecal samples from three healthy Korean adults. To examine the efficacy of fecal collection solution, we used NBgene-Gut, OMNIgene-Gut, 70% ethanol (Ethanol-70%), and RNAlater. The samples were stored for up to two months at room temperature using three different methods, and we observed changes in microbial communities over time. We analyzed clusters of changes in the microbial flora by observing fecal stock solutions and metagenome sequencing performed over time. In particular, we confirmed the profiling of alpha and beta diversity and microbial classification according to the differences in intestinal environment among individuals. We also confirmed that the microbial profile remained stable for two months and that the microbial profile did not change significantly over time. In addition, our results suggest the possibility of verifying microbial profiling even for long-term storage of a single sample. In conclusion, collecting fecal samples using a stock solution rather than freezing feces seems to be relatively reproducible and stable for GUT metagenome analysis. Therefore, stock solution tubes in intestinal microbial research can be used without problems.}, } @article {pmid32580987, year = {2020}, author = {Volery, M and Scherz, V and Jakob, W and Bandeira, D and Deggim-Messmer, V and Lauber-Biason, A and Wildhaber, J and Falquet, L and Curtis, N and Zimmermann, P}, title = {Study protocol for the ABERRANT study: antibiotic-induced disruption of the maternal and infant microbiome and adverse health outcomes - a prospective cohort study among children born at term.}, journal = {BMJ open}, volume = {10}, number = {6}, pages = {e036275}, pmid = {32580987}, issn = {2044-6055}, mesh = {Anti-Bacterial Agents/*adverse effects ; Clinical Protocols ; Drug Resistance, Bacterial ; Eczema/epidemiology ; Female ; Gastrointestinal Microbiome/*drug effects/genetics/physiology ; Humans ; Hypersensitivity/epidemiology ; Infant ; Infant, Newborn ; Metagenomics ; Milk, Human/chemistry/microbiology ; Otitis Media/epidemiology ; Pregnancy ; Prenatal Exposure Delayed Effects/*chemically induced ; Prospective Studies ; Respiratory Tract Diseases/epidemiology ; }, abstract = {INTRODUCTION: There is compositional overlap between the maternal intestinal microbiome, the breast milk microbiome and the infant oral and intestinal microbiome. Antibiotics cause profound changes in the microbiome. However, the effect of intrapartum and early-life antibiotics on the maternal intestinal and breast milk microbiome, and the infant oral and intestinal microbiome, and whether effects are only short term or persist long term remain uncertain.

METHODS AND ANALYSES: In this prospective cohort study, we will use metagenomic sequencing to determine: (1) the effect of intrapartum antibiotics on the composition of the breast milk, and the infant oral and intestinal microbiome, including the development and persistence of antibiotic resistance; (2) the effect of antibiotic exposure in the first year of life on the composition of the infant oral and intestinal microbiome, including the development and persistence of antibiotic resistance; (3) the effect of disruption of the infant oral and intestinal microbiome on health outcomes and (4) the compositional overlap between the maternal intestinal microbiome, the breast milk microbiome and the infant oral and intestinal microbiome.

ETHICS AND DISSEMINATION: The ABERRANT study has been approved by the commission cantonale d'éthique de la recherche sur l'être humain (CER-VD) du Canton de Vaud (#2019-01567). Outcomes will be disseminated through publication and will be presented at scientific conferences.

TRIAL REGISTRATION NUMBER: NCT04091282.}, } @article {pmid32580896, year = {2020}, author = {Metwally, AA and Ascoli, C and Turturice, B and Rani, A and Ranjan, R and Chen, Y and Schott, C and Faro, A and Ferkol, TW and Finn, PW and Perkins, DL}, title = {Pediatric lung transplantation: Dynamics of the microbiome and bronchiolitis obliterans in cystic fibrosis.}, journal = {The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation}, volume = {39}, number = {8}, pages = {824-834}, pmid = {32580896}, issn = {1557-3117}, support = {F30 HL136001/HL/NHLBI NIH HHS/United States ; F30 HL137267/HL/NHLBI NIH HHS/United States ; T32 HL082547/HL/NHLBI NIH HHS/United States ; R01 HL138628/HL/NHLBI NIH HHS/United States ; U01 AI132898/AI/NIAID NIH HHS/United States ; UL1 TR002003/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Bronchiolitis Obliterans/diagnosis/*surgery ; Bronchoalveolar Lavage Fluid/microbiology ; Bronchoscopy ; Child ; Cystic Fibrosis/diagnosis/*surgery ; Female ; Follow-Up Studies ; Humans ; Lung/*microbiology ; Lung Transplantation/*methods ; Male ; *Microbiota ; Prospective Studies ; }, abstract = {BACKGROUND: Compositional changes in the microbiome are associated with the development of bronchiolitis obliterans (BO) after lung transplantation (LTx) in adults with cystic fibrosis (CF). The association between the lower airway bacterial community and BO after LTx in children with CF remains largely unexplored and is possibly influenced by frequent antibiotic therapy. The objectives of this study were to examine the relationship between bacterial community dynamics and the development of BO and analyze antibiotic resistance trends in children after LTx for CF.

METHODS: For 3 years from the time of transplant, 12 LTx recipients were followed longitudinally, with 5 subjects developing BO during the study period. A total of 82 longitudinal bronchoalveolar lavage samples were collected during standard of care bronchoscopies. Metagenomic shotgun sequencing was performed on the extracted microbial DNA from bronchoalveolar lavage specimens. Taxonomic profiling was constructed using WEVOTE pipeline. The longitudinal association between development of BO and temporal changes in bacterial diversity and abundance were evaluated with MetaLonDA. The analysis of antibiotic resistance genes was performed with the ARGs-OAP v2.0 pipeline.

RESULTS: All recipients demonstrated a Proteobacteria-predominant lower airways community. Temporal reduction in bacterial diversity was significantly associated with the development of BO and associated with neutrophilia and antibiotic therapy. Conversely, an increasing abundance of the phylum Actinobacteria and the orders Neisseriales and Pseudonocardiales in the lower airways was significantly associated with resilience to BO. A more diverse bacterial community was related to a higher expression of multidrug resistance genes and increased proteobacterial abundance.

CONCLUSIONS: Decreased diversity within bacterial communities may suggest a contribution to pediatric lung allograft rejection in CF.}, } @article {pmid32580805, year = {2020}, author = {Garber, A and Hastie, PM and Farci, V and McGuinness, D and Bulmer, L and Alzahal, O and Murray, JMD}, title = {The effect of supplementing pony diets with yeast on 2. The faecal microbiome.}, journal = {Animal : an international journal of animal bioscience}, volume = {14}, number = {12}, pages = {2493-2502}, doi = {10.1017/S1751731120001512}, pmid = {32580805}, issn = {1751-732X}, mesh = {Animal Feed/analysis ; Animals ; Diet/veterinary ; Feces ; Horses ; Male ; *Microbiota ; *Saccharomyces cerevisiae ; }, abstract = {There is a need to develop feeding strategies to prevent the adverse effect of concentrate feeding in high-performance horses fed energy-dense diets aiming to maintain their health and welfare. The objective of this study is to determine the effect of a VistaEQ product containing 4% live yeast Saccharomyces cerevisiae (S. cerevisiae), with activity 5 × 108 colony-forming unit/g and fed 2 g/pony per day, on faecal microbial populations when supplemented with high-starch and high-fibre diets using Illumina next generation sequencing of the V3-V4 region of the 16S ribosomal RNA gene. The four treatments were allocated to eight mature Welsh section A pony geldings enrolled in a 4-period × 8 animal crossover design. Each 19-day experimental period consisted of an 18-day adaptation phase and a single collection day, followed by a 7-day wash out period. After DNA extraction from faeces and library preparation, α-diversity and linear discriminant analysis effect size were performed using 16S metagenomics pipeline in Quantitative Insights Into Microbial Ecology (QIIME™) and Galaxy/Hutlab. Differences between the groups were considered significant when linear discriminant analysis score was >2 corresponding to P < 0.05. The present study showed that S. cerevisiae used was able to induce positive changes in the equine microbiota when supplemented to a high-fibre diet: it increased relative abundance (RA) of Lachnospiraceae and Dehalobacteriaceae family members associated with a healthy core microbiome. Yeast supplementation also increased the RA of fibrolytic bacteria (Ruminococcus) when fed with a high-fibre diet and reduced the RA of lactate producing bacteria (Streptococcus) when a high-starch diet was fed. In addition, yeast increased the RA of acetic, succinic acid producing bacterial family (Succinivibrionaceae) and butyrate producing bacterial genus (Roseburia) when fed with high-starch and high-fibre diets, respectively. VistaEQ supplementation to equine diets can be potentially used to prevent acidosis and increase fibre digestibility. It may help to meet the energy requirements of performance horses while maintaining gut health.}, } @article {pmid32580027, year = {2020}, author = {Weber, MN and Mosena, ACS and da Silva, MS and Canova, R and de Lorenzo, C and Olegário, JC and Budaszewski, RF and Baumbach, LF and Soares, JF and Sonne, L and Varela, APM and Mayer, FQ and de Oliveira, LGS and Canal, CW}, title = {Virome of crab-eating (Cerdocyon thous) and pampas foxes (Lycalopex gymnocercus) from southern Brazil and Uruguay.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {85}, number = {}, pages = {104421}, pmid = {32580027}, issn = {1567-7257}, mesh = {Anelloviridae/classification/genetics ; Animals ; Bocavirus/classification/genetics ; Brazil ; DNA Viruses/classification/genetics ; DNA, Viral ; Distemper Virus, Canine/classification/genetics ; Dogs/*virology ; Foxes/*virology ; High-Throughput Nucleotide Sequencing ; Lymph Nodes/virology ; Metagenomics ; Paramyxoviridae/classification/genetics ; Parvoviridae/classification/genetics ; Parvovirus, Canine/classification/genetics ; Phylogeny ; RNA, Viral ; Spleen/virology ; Uruguay ; *Virome ; Virus Diseases/veterinary/virology ; Viruses/*classification/*genetics/isolation & purification ; }, abstract = {Crab-eating (Cerdocyon thous) and Pampas foxes (Lycalopex gymnocercus) are wild canids distributed in South America. Domestic dogs (Canis lupus familiaris) and wild canids may share viral pathogens, including rabies virus (RABV), canine distemper virus (CDV), and canine parvovirus 2 (CPV-2). To characterize the virome of these wild canid species, the present work evaluated the spleen and mesenteric lymph node virome of 17 crab-eating and five Pampas foxes using high-throughput sequencing (HTS). Organ samples were pooled and sequenced using an Illumina MiSeq platform. Additional PCR analyses were performed to identify the frequencies and host origin for each virus detected by HTS. Sequences more closely related to the Paramyxoviridae, Parvoviridae and Anelloviridae families were detected, as well as circular Rep-encoding single-stranded (CRESS) DNA viruses. CDV was found only in crab-eating foxes, whereas CPV-2 was found in both canid species; both viruses were closely related to sequences reported in domestic dogs from southern Brazil. Moreover, the present work reported the detection of canine bocavirus (CBoV) strains that were genetically divergent from CBoV-1 and 2 lineages. Finally, we also characterized CRESS DNA viruses and anelloviruses with marked diversity. The results of this study contribute to the body of knowledge regarding wild canid viruses that can potentially be shared with domestic canids or other species.}, } @article {pmid32578861, year = {2020}, author = {Li, Z and Shen, J and Xu, Y and Zhu, W}, title = {Metagenomic analysis reveals significant differences in microbiome and metabolic profiles in the rumen of sheep fed low N diet with increased urea supplementation.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {10}, pages = {}, doi = {10.1093/femsec/fiaa117}, pmid = {32578861}, issn = {1574-6941}, mesh = {Animal Feed/analysis ; Animals ; Diet/veterinary ; Dietary Supplements ; Fermentation ; Male ; Metabolome ; *Microbiota ; *Rumen/metabolism ; Sheep ; Urea/metabolism ; }, abstract = {Urea is a cost-effective replacement for feed proteins in ruminant diets. However, its metabolism by the rumen microbiome is not fully understood. Here, rumen contents were collected from 18 male sheep fed one of the following three treatments: a low N basal diet with no urea (UC, 0 g/kg dry matter (DM)), low urea (LU, 10 g/kg DM) and high urea (HU, 30 g/kg DM). Principal coordinate analysis showed that the microbial composition and functional profiles of the LU treatment significantly differed from the UC and HU treatments. The genera Prevotella, Succinivibrio, Succinatimonas and Megasphaera were higher in the LU rumen, while the genera Clostridium, Ruminococcus and Butyrivibrio were enriched in the UC and HU rumen. The aspartate-glutamate and arginine-proline metabolic pathways and valine, leucine and isoleucine biosynthesis were higher in the LU rumen. The cysteine and methionine metabolism, lysine degradation and fructose and pentose phosphate metabolism pathways were higher in the UC and HU rumen. The protozoa population in the HU treatment was higher than in the UC and LU treatments. These findings suggest that the rumen microbiome of sheep fed low N diet with different urea supplementation are significantly different.}, } @article {pmid32578244, year = {2020}, author = {Sun, Y and Fu, X and Li, Y and Yuan, Q and Ou, Z and Lindgren, T and Deng, Y and Norbäck, D}, title = {Shotgun metagenomics of dust microbiome from flight deck and cabin in civil aviation aircraft.}, journal = {Indoor air}, volume = {30}, number = {6}, pages = {1199-1212}, doi = {10.1111/ina.12707}, pmid = {32578244}, issn = {1600-0668}, mesh = {*Air Microbiology ; Air Pollution, Indoor ; *Aircraft ; Aviation ; Comamonadaceae ; Dust/*analysis ; Environmental Monitoring ; Floors and Floorcoverings ; Humans ; *Metagenomics ; Microbiota ; }, abstract = {Microbial exposure is related to the health of passengers on commercial aircraft, but no studies characterized the microbial composition at the species level and identified their ecological determinants. We collected vacuum dust from floor and seat surfaces in flight decks and cabins of 18 aircraft, and amplification-free shotgun metagenomics was conducted to characterize the microbial composition. In total, 7437 microbial taxa were identified. The relative abundance for bacteria, eukaryote, viruses, and archaea was 96.9%, 1.8%, 0.3%, and 0.03%, respectively. The top bacterial species mainly derived from outdoor air and human skin included Sphingomonas, Corynebacterium, Micrococcus luteus, Variovorax paradoxus, Paracoccus dentrificans, and Propionibacterium acnes. The abundance of NIAID-defined pathogens was low, accounted for only 0.23% of total microbes. The microbial species and functional composition were structured by the indoor surface type (R[2] = 0.38, Adonis), followed by the manufacturer of the aircraft (R[2] = 0.12) and flight duration (R[2] = 0.07). Indoor surfaces affected species derived from different habitats; the abundance of dry skin and desiccated species was higher on textile surfaces, whereas the abundance of moist and oily skin species was higher on leather surfaces. The growth rates for most microbes were stopped and almost stopped.}, } @article {pmid32577746, year = {2021}, author = {Comin, M and Di Camillo, B and Pizzi, C and Vandin, F}, title = {Comparison of microbiome samples: methods and computational challenges.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {1}, pages = {88-95}, doi = {10.1093/bib/bbaa121}, pmid = {32577746}, issn = {1477-4054}, mesh = {Animals ; High-Throughput Nucleotide Sequencing/methods/standards ; Humans ; Metagenomics/*methods/standards ; Microbiota/*genetics ; }, abstract = {The study of microbial communities crucially relies on the comparison of metagenomic next-generation sequencing data sets, for which several methods have been designed in recent years. Here, we review three key challenges in the comparison of such data sets: species identification and quantification, the efficient computation of distances between metagenomic samples and the identification of metagenomic features associated with a phenotype such as disease status. We present current solutions for such challenges, considering both reference-based methods relying on a database of reference genomes and reference-free methods working directly on all sequencing reads from the samples.}, } @article {pmid32576522, year = {2020}, author = {Lopetuso, LR and Quagliariello, A and Schiavoni, M and Petito, V and Russo, A and Reddel, S and Del Chierico, F and Ianiro, G and Scaldaferri, F and Neri, M and Cammarota, G and Putignani, L and Gasbarrini, A}, title = {Towards a disease-associated common trait of gut microbiota dysbiosis: The pivotal role of Akkermansia muciniphila.}, journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver}, volume = {52}, number = {9}, pages = {1002-1010}, doi = {10.1016/j.dld.2020.05.020}, pmid = {32576522}, issn = {1878-3562}, mesh = {Akkermansia/physiology ; Case-Control Studies ; Dysbiosis/metabolism/*physiopathology ; Feces/*microbiology ; Gastrointestinal Diseases/metabolism/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Intestinal Mucosa/*metabolism/microbiology ; Permeability ; Phenotype ; }, abstract = {BACKGROUND: Gut microbiota exerts a crucial role in gastrointestinal (GI) and extra-intestinal (EI) disorders. In this context, Akkermansia muciniphila is pivotal for the maintenance of host health and has been correlated with several disorders.

AIM: To explore the potential role of A. muciniphila as common dysbiotic marker linked to the disease status.

METHODS: A cohort of patients affected by GI and EI disorders was enrolled and compared to healthy controls (CTRLs). A targeted-metagenomics approach combined to unsupervised cluster and machine learning (ML) analyses provided microbiota signatures.

RESULTS: Microbiota composition was associated to disease phenotype, therapies, diet and anthropometric features, identifying phenotype and therapies as the most impacting variables on microbiota ecology. Unsupervised cluster analyses identified one cluster composed by the majority of patients. DESeq2 algorithm identified ten microbial discriminatory features of patients and CTRLs clusters. Among these microbes, Akkermansia muciniphila resulted the discriminating ML node between patients and CTRLs, independently of specific GI/EI disease or confounding effects. A. muciniphila decrease represented a transversal signature of gut microbiota alteration, showing also an inverse correlation with α-diversity.

CONCLUSION: Overall, A. muciniphila decline may have a crucial role in affecting microbial ecology and in discriminating patients from healthy subjects. Its grading may be considered as a gut dysbiosis feature associated to disease-related microbiota profile.}, } @article {pmid32576288, year = {2020}, author = {Hosoda, S and Nishijima, S and Fukunaga, T and Hattori, M and Hamada, M}, title = {Revealing the microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {95}, pmid = {32576288}, issn = {2049-2618}, mesh = {Bacteria/classification/genetics/isolation & purification ; Butyrates/metabolism ; Datasets as Topic ; Gastrointestinal Microbiome/*genetics ; Humans ; *Latent Class Analysis ; *Metagenome ; }, abstract = {BACKGROUND: The human gut microbiome has been suggested to affect human health and thus has received considerable attention. To clarify the structure of the human gut microbiome, clustering methods are frequently applied to human gut taxonomic profiles. Enterotypes, i.e., clusters of individuals with similar microbiome composition, are well-studied and characterized. However, only a few detailed studies on assemblages, i.e., clusters of co-occurring bacterial taxa, have been conducted. Particularly, the relationship between the enterotype and assemblage is not well-understood.

RESULTS: In this study, we detected gut microbiome assemblages using a latent Dirichlet allocation (LDA) method. We applied LDA to a large-scale human gut metagenome dataset and found that a 4-assemblage LDA model could represent relationships between enterotypes and assemblages with high interpretability. This model indicated that each individual tends to have several assemblages, three of which corresponded to the three classically recognized enterotypes. Conversely, the fourth assemblage corresponded to no enterotypes and emerged in all enterotypes. Interestingly, the dominant genera of this assemblage (Clostridium, Eubacterium, Faecalibacterium, Roseburia, Coprococcus, and Butyrivibrio) included butyrate-producing species such as Faecalibacterium prausnitzii. Indeed, the fourth assemblage significantly positively correlated with three butyrate-producing functions.

CONCLUSIONS: We conducted an assemblage analysis on a large-scale human gut metagenome dataset using LDA. The present study revealed that there is an enterotype-independent assemblage. Video Abstract.}, } @article {pmid32576248, year = {2020}, author = {Podell, S and Blanton, JM and Oliver, A and Schorn, MA and Agarwal, V and Biggs, JS and Moore, BS and Allen, EE}, title = {A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {97}, pmid = {32576248}, issn = {2049-2618}, support = {R00 ES026620/ES/NIEHS NIH HHS/United States ; R01 ES030316/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/*genetics/isolation & purification/*metabolism ; Biodiversity ; Genomics ; Metagenome/*genetics ; Microbiota/*genetics ; *Phylogeny ; Porifera/*classification/metabolism/*microbiology ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {BACKGROUND: Marine sponges and their microbiomes contribute significantly to carbon and nutrient cycling in global reefs, processing and remineralizing dissolved and particulate organic matter. Lamellodysidea herbacea sponges obtain additional energy from abundant photosynthetic Hormoscilla cyanobacterial symbionts, which also produce polybrominated diphenyl ethers (PBDEs) chemically similar to anthropogenic pollutants of environmental concern. Potential contributions of non-Hormoscilla bacteria to Lamellodysidea microbiome metabolism and the synthesis and degradation of additional secondary metabolites are currently unknown.

RESULTS: This study has determined relative abundance, taxonomic novelty, metabolic capacities, and secondary metabolite potential in 21 previously uncharacterized, uncultured Lamellodysidea-associated microbial populations by reconstructing near-complete metagenome-assembled genomes (MAGs) to complement 16S rRNA gene amplicon studies. Microbial community compositions aligned with sponge host subgroup phylogeny in 16 samples from four host clades collected from multiple sites in Guam over a 3-year period, including representatives of Alphaproteobacteria, Gammaproteobacteria, Oligoflexia, and Bacteroidetes as well as Cyanobacteria (Hormoscilla). Unexpectedly, microbiomes from one host clade also included Cyanobacteria from the prolific secondary metabolite-producer genus Prochloron, a common tunicate symbiont. Two novel Alphaproteobacteria MAGs encoded pathways diagnostic for methylotrophic metabolism as well as type III secretion systems, and have been provisionally assigned to a new order, designated Candidatus Methylospongiales. MAGs from other taxonomic groups encoded light-driven energy production pathways using not only chlorophyll, but also bacteriochlorophyll and proteorhodopsin. Diverse heterotrophic capabilities favoring aerobic versus anaerobic conditions included pathways for degrading chitin, eukaryotic extracellular matrix polymers, phosphonates, dimethylsulfoniopropionate, trimethylamine, and benzoate. Genetic evidence identified an aerobic catabolic pathway for halogenated aromatics that may enable endogenous PBDEs to be used as a carbon and energy source.

CONCLUSIONS: The reconstruction of high-quality MAGs from all microbial taxa comprising greater than 0.1% of the sponge microbiome enabled species-specific assignment of unique metabolic features that could not have been predicted from taxonomic data alone. This information will promote more representative models of marine invertebrate microbiome contributions to host bioenergetics, the identification of potential new sponge parasites and pathogens based on conserved metabolic and physiological markers, and a better understanding of biosynthetic and degradative pathways for secondary metabolites and halogenated compounds in sponge-associated microbiota. Video Abstract.}, } @article {pmid32574649, year = {2020}, author = {Van Borm, S and Fu, Q and Winand, R and Vanneste, K and Hakhverdyan, M and Höper, D and Vandenbussche, F}, title = {Evaluation of a commercial exogenous internal process control for diagnostic RNA virus metagenomics from different animal clinical samples.}, journal = {Journal of virological methods}, volume = {283}, number = {}, pages = {113916}, doi = {10.1016/j.jviromet.2020.113916}, pmid = {32574649}, issn = {1879-0984}, mesh = {Animals ; Feces/virology ; High-Throughput Nucleotide Sequencing/methods ; Mengovirus/genetics/isolation & purification ; Metagenomics/*methods ; RNA Virus Infections/*diagnosis/*virology ; RNA Viruses/genetics/*isolation & purification ; RNA, Viral/genetics/isolation & purification ; Sensitivity and Specificity ; Swine ; Swine Diseases/virology ; Virome ; }, abstract = {Metagenomic next generation sequencing (mNGS) is increasingly recognized as an important complementary tool to targeted human and animal infectious disease diagnostics. It is, however, sensitive to biases and errors that are currently not systematically evaluated by the implementation of quality controls (QC) for the diagnostic use of mNGS. We evaluated a commercial reagent (Mengovirus extraction control kit, CeraamTools, bioMérieux) as an exogenous internal control for mNGS. It validates the integrity of reagents and workflow, the efficient isolation of viral nucleic acids and the absence of inhibitors in individual samples (verified using a specific qRT-PCR). Moreover, it validates the efficient generation of viral sequence data in individual samples (verified by normalized mengoviral read counts in the metagenomic analysis). We show that when using a completely random metagenomics workflow: (1) Mengovirus RNA can be reproducibly detected in different animal sample types (swine feces and sera, wild bird cloacal swabs), except for tissue samples (swine lung); (2) the Mengovirus control kit does not contain other contaminating viruses that may affect metagenomic experiments (using a cutoff of minimum 1 Kraken classified read per million (RPM)); (3) the addition of 2.17 × 10[6]Mengovirus copies/mL of sample does not affect the virome composition of pig fecal samples or wild bird cloacal swab samples; (4) Mengovirus Cq values (using as cutoff the upper limit of the 99 % confidence interval of Cq values for a given sample matrix) allow the identification of samples with poor viral RNA extraction or high inhibitor load; (5) Mengovirus normalized read counts (cutoff RPM > 1) allow the identification of samples where the viral sequences are outcompeted by host or bacterial target sequences in the random metagenomic workflow. The implementation of two QC testing points, a first one after RNA extraction (Mengoviral qRT-PCR) and a second one after metagenomic data analysis provide valuable information for the validation of individual samples and results. Their implementation in addition to external controls validating runs or experiments should be carefully considered for a given sample type and workflow.}, } @article {pmid32572576, year = {2020}, author = {Park, H and Choi, IG}, title = {Genomic and transcriptomic perspectives on mycoremediation of polycyclic aromatic hydrocarbons.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {16}, pages = {6919-6928}, doi = {10.1007/s00253-020-10746-1}, pmid = {32572576}, issn = {1432-0614}, support = {PJ01337602//Rural Development Administration/ ; 20173010092460//Korea Institute of Energy Technology Evaluation and Planning/ ; }, mesh = {Basidiomycota/*genetics/*metabolism ; *Biodegradation, Environmental ; *Gene Expression Profiling ; *Metagenomics ; Microbial Consortia ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Soil Microbiology ; Soil Pollutants/metabolism ; Transcriptome ; }, abstract = {Mycoremediation holds great potential in remedying toxic environments contaminated with polyaromatic organic pollutants. To harness the natural process for practical applications, understanding the genetic and molecular basis of the remediation process is prerequisite. Compared to known bacterial degradation pathways of aromatic pollutants, however, the fungal degradation system is less studied and understanding of the genetic basis for biochemical activity is still incomplete. In this review, we surveyed recent findings from genomic and transcriptomic approaches to mycoremediation of aromatic pollutants, in company with the genomic basis of polycyclic aromatic hydrocarbon (PAH) degradation by basidiomycete fungi, Dentipellis sp. KUC8613. Unique features in the fungal degradation of PAHs were outlined by multiple cellular processes: (i) the initial oxidation of recalcitrant contaminants by various oxidoreductases including mono- and dioxygenases, (ii) the following detoxification, and (iii) the mineralization of activated pollutants that are common metabolism in many fungi. Along with the genomic data, the transcriptomic analysis not only posits a full repertoire of inducible genes that are common or specific to metabolize different PAHs but also leads to the discovery of uncharacterized genes with potential functions for bioremediation processes. In addition, the metagenomic study accesses community level of mycoremediation process to seek for the potential species or a microbial consortium in the natural environments. The comprehensive understanding of fungal degradation in multiple levels will accelerate practical application of mycoremediation. Key points • Mycoremediation of polyaromatic pollutants exploits a potent fungal degrader. • Fungal genomics provides a full repository of potential genes and enzymes. • Mycoremediation is a concerted cellular process involved with many novel genes. • Multi-omics approach enables the genome-scale reconstruction of remedying pathways.}, } @article {pmid32572536, year = {2020}, author = {Díaz-García, L and Bugg, TDH and Jiménez, DJ}, title = {Exploring the Lignin Catabolism Potential of Soil-Derived Lignocellulolytic Microbial Consortia by a Gene-Centric Metagenomic Approach.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {885-896}, doi = {10.1007/s00248-020-01546-1}, pmid = {32572536}, issn = {1432-184X}, support = {PR.3.2018.5287//Universidad de Los Andes/ ; BB/P01738X/1//BBSRC/ ; }, mesh = {Bacteria/*enzymology/genetics ; Biomass ; Lignin/*metabolism ; *Metagenome ; Metagenomics ; *Microbial Consortia ; Panicum/microbiology ; *Soil Microbiology ; Triticum/microbiology ; Zea mays/microbiology ; }, abstract = {An exploration of the ligninolytic potential of lignocellulolytic microbial consortia can improve our understanding of the eco-enzymology of lignin conversion in nature. In this study, we aimed to detect enriched lignin-transforming enzymes on metagenomes from three soil-derived microbial consortia that were cultivated on "pre-digested" plant biomass (wheat straw, WS1-M; switchgrass, SG-M; and corn stover, CS-M). Of 60 selected enzyme-encoding genes putatively involved in lignin catabolism, 20 genes were significantly abundant in WS1-M, CS-M, and/or SG-M consortia compared with the initial forest soil inoculum metagenome (FS1). These genes could be involved in lignin oxidation (e.g., superoxide dismutases), oxidative stress responses (e.g., catalase/peroxidases), generation of protocatechuate (e.g., vanAB genes), catabolism of gentisate, catechol and 3-phenylpropionic acid (e.g., gentisate 1,2-dioxygenases, muconate cycloisomerases, and hcaAB genes), the beta-ketoadipate pathway (e.g., pcaIJ genes), and tolerance to lignocellulose-derived inhibitors (e.g., thymidylate synthases). The taxonomic affiliation of 22 selected lignin-transforming enzymes from WS1-M and CS-M consortia metagenomes revealed that Pseudomonadaceae, Alcaligenaceae, Sphingomonadaceae, Caulobacteraceae, Comamonadaceae, and Xanthomonadaceae are the key bacterial families in the catabolism of lignin. A predictive "model" was sketched out, where each microbial population has the potential to metabolize an array of aromatic compounds through different pathways, suggesting that lignin catabolism can follow a "task division" strategy. Here, we have established an association between functions and taxonomy, allowing a better understanding of lignin transformations in soil-derived lignocellulolytic microbial consortia, and pinpointing some bacterial taxa and catabolic genes as ligninolytic trait-markers.}, } @article {pmid32572149, year = {2020}, author = {Wutthi-In, M and Cheevadhanarak, S and Yasom, S and Kerdphoo, S and Thiennimitr, P and Phrommintikul, A and Chattipakorn, N and Kittichotirat, W and Chattipakorn, S}, title = {Gut Microbiota Profiles of Treated Metabolic Syndrome Patients and their Relationship with Metabolic Health.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {10085}, pmid = {32572149}, issn = {2045-2322}, mesh = {Aged ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/*genetics/physiology ; Humans ; Male ; Metabolic Syndrome/classification/*microbiology ; Metagenome ; Metagenomics/methods ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Stress, Physiological/physiology ; Thailand ; }, abstract = {Metabolic syndrome (MetS) has become a worldwide health issue. Recent studies reveal that the human gut microbiota exerts a significant role in the pathogenesis of this disease. While drug treatments may greatly improve metabolic symptoms, little is known about the gut microbiota composition of these treated MetS patients. This study aimed to characterize the gut microbiota composition of treated-MetS patients and analyse the possibility of using gut microbiota as an indicator of metabolic conditions. 16S rRNA metagenomic sequencing approach was used to profile gut microbiota of 111 treated MetS patients from The Cohort of patients at a high Risk of Cardiovascular Events (CORE)-Thailand registry. Our results show that the gut microbiota profiles of MetS patients are diverse across individuals, but can be classified based on their similarity into three groups or enterotypes. We also showed several associations between species abundance and metabolic parameters that are enterotype specific. These findings suggest that information on the gut microbiota can be useful for assessing treatment options for MetS patients. In addition, any correlations between species abundance and human properties are likely specific to each microbial community.}, } @article {pmid32570702, year = {2020}, author = {Sánchez, B and Cobo, A and Hidalgo, M and Martínez-Rodríguez, AM and Prieto, I and Gálvez, A and Martínez-Cañamero, M}, title = {Prevalence of an Intestinal ST40 Enterococcus faecalis over Other E. faecalis Strains in the Gut Environment of Mice Fed Different High Fat Diets.}, journal = {International journal of molecular sciences}, volume = {21}, number = {12}, pages = {}, pmid = {32570702}, issn = {1422-0067}, support = {PI Excelencia_2010 AGR 6340//Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía/ ; PP2009/13/03//Universidad de Jaén/ ; }, mesh = {Animals ; Bacterial Proteins/*metabolism ; Diet, High-Fat/*adverse effects/classification ; Enterococcus faecalis/*classification/drug effects/genetics/isolation & purification ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects ; Genotype ; Male ; Mice ; Multilocus Sequence Typing/*methods ; Prevalence ; Proteomics ; }, abstract = {E. faecalis is a commensal bacterium with specific strains involved in opportunistic and nosocomial infections. Therefore, it is important to know how the strains of this species are selected in the gut. In this study, fifteen E. faecalis strains, isolated over twelve weeks from the faeces of mice fed standard chow or one of three high fat diets enriched with extra virgin olive oil, refined olive oil or butter were subjected to a genetic "Multilocus Sequence Typing" study that revealed the presence of mainly two genotypes, ST9 and ST40, the latter one prevailing at the end of the research. A V3-V5 sequence comparison of the predominant ST40 strain (12B3-5) in a metagenomic study showed that this sequence was the only E. faecalis present in the mouse cohort after twelve weeks. The strain was subjected to a comparative proteomic study with a ST9 strain by 2D electrophoresis and mass spectrometry. After comparing the results with a E. faecalis database, unshared entries were compared and 12B3-5 showed higher antimicrobial production as well as greater protection from environmental factors such as xenobiotics, oxidative stress and metabolite accumulation, which could be the reason for its ability to outcompete other possible rivals in an intestinal niche.}, } @article {pmid32569776, year = {2020}, author = {Coker, OO and Wu, WKK and Wong, SH and Sung, JJY and Yu, J}, title = {Altered Gut Archaea Composition and Interaction With Bacteria Are Associated With Colorectal Cancer.}, journal = {Gastroenterology}, volume = {159}, number = {4}, pages = {1459-1470.e5}, doi = {10.1053/j.gastro.2020.06.042}, pmid = {32569776}, issn = {1528-0012}, mesh = {Adenoma/*microbiology/*pathology ; Aged ; Archaea/*isolation & purification ; Case-Control Studies ; Cohort Studies ; Colorectal Neoplasms/*microbiology/*pathology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; Sensitivity and Specificity ; }, abstract = {BACKGROUND & AIMS: Changes in the intestinal microbiota have been associated with development and progression of colorectal cancer (CRC). Archaea are stable components of the microbiota, but little is known about their composition or contribution to colorectal carcinogenesis. We analyzed archaea in fecal microbiomes of 2 large cohorts of patients with CRC.

METHODS: We performed shotgun metagenomic analyses of fecal samples from 585 participants (184 patients with CRC, 197 patients with adenomas, and 204 healthy individuals) from discovery (165 individuals) and validation (420 individuals) cohorts. Assignment of taxonomies was performed by exact k-mer alignment against an integrated microbial reference genome database.

RESULTS: Principal component analysis of archaeomes showed distinct clusters in fecal samples from patients with CRC, patients with adenomas, and control individuals (P < .001), indicating an alteration in the composition of enteric archaea during tumorigenesis. Fecal samples from patients with CRC had significant enrichment of halophilic and depletion of methanogenic archaea. The halophilic Natrinema sp. J7-2 increased progressively in samples from control individuals, to patients with adenomas, to patients with CRC. Abundances of 9 archaea species that were enriched in fecal samples from patients with CRC distinguished them from control individuals with areas under the receiver operating characteristic curve of 0.82 in the discovery cohort and 0.83 in the validation cohort. An association between archaea and bacteria diversities was observed in fecal samples from control individuals but not from patients with CRC. Archaea that were enriched in fecal samples from patients with CRC had an extensive mutual association with bacteria that were enriched in the same samples and exclusivity with bacteria that were lost from these samples.

CONCLUSIONS: Archaeomes of fecal samples from patients with CRC are characterized by enrichment of halophiles and depletion of methanogens. Studies are needed to determine whether associations between specific archaea and bacteria species in samples from patients with CRC contribute to or are a response to colorectal tumorigenesis.}, } @article {pmid32569375, year = {2021}, author = {Gambardella, J and Castellanos, V and Santulli, G}, title = {Standardizing translational microbiome studies and metagenomic analyses.}, journal = {Cardiovascular research}, volume = {117}, number = {3}, pages = {640-642}, pmid = {32569375}, issn = {1755-3245}, support = {R00 DK107895/DK/NIDDK NIH HHS/United States ; R01 DK123259/DK/NIDDK NIH HHS/United States ; R01 HL146691/HL/NHLBI NIH HHS/United States ; R01 DK033823/DK/NIDDK NIH HHS/United States ; }, mesh = {Metagenome ; *Metagenomics ; *Microbiota ; }, } @article {pmid32568184, year = {2020}, author = {Pi, H and Huang, L and Liu, H and Liang, S and Mei, J}, title = {Effects of PD-1/PD-L1 signaling pathway on intestinal flora in patients with colorectal cancer.}, journal = {Cancer biomarkers : section A of Disease markers}, volume = {28}, number = {4}, pages = {529-535}, doi = {10.3233/CBM-201606}, pmid = {32568184}, issn = {1875-8592}, mesh = {Aged ; Animals ; Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use ; B7-H1 Antigen/immunology/metabolism ; Cell Line, Tumor ; Colorectal Neoplasms/*drug therapy/immunology/microbiology/mortality ; DNA, Bacterial/isolation & purification ; Disease Models, Animal ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/drug effects/genetics/*immunology ; Humans ; Immune Checkpoint Inhibitors/*pharmacology/therapeutic use ; Immunologic Surveillance/drug effects ; Intestinal Mucosa/immunology/microbiology ; Male ; Metagenomics ; Mice ; Middle Aged ; Programmed Cell Death 1 Receptor/*antagonists & inhibitors/immunology/metabolism ; Progression-Free Survival ; RNA, Ribosomal, 16S/genetics ; Signal Transduction/drug effects/immunology ; }, abstract = {OBJECTIVE: To explore the effects of the programmed death-1/programmed death-ligand 1 (PD-1/PD-L1) signaling pathway on the intestinal flora in patients with colorectal cancer (CRC).

METHODS: A total of 30 CRC patients treated with PD-1 monoclonal antibody therapy in the Oncology Department of our hospital from January 2018 to January 2019, and another 30 patients treated with routine non-immune therapy were enrolled. The feces specimens were collected for sequencing, the CRC model was established, and the 16S rRNA gene sequences in intestinal flora in feces specimens of mice were analyzed.

RESULTS: The 3-month progression-free survival could not be predicted through the gene count or abundance of metagenomic species (MGS) in intestinal microflora of patients. The gene count or MGS abundance was related to the clinical progression-free response. There were abundant unclassified Escherichia coli, s_lactobacillus and s_unclassified parasutterella in patients treated with PD-1. The reflection curve of microbiota had an obvious difference in richness (Chao1), but had no apparent difference in diversity (Shannon).

CONCLUSION: The PD-1/PD-L1 signaling pathway can regulate the metabolic activity of intestinal flora, thereby promoting immune surveillance of tumors.}, } @article {pmid32564657, year = {2020}, author = {Hamilton, AL and Kamm, MA and De Cruz, P and Wright, EK and Feng, H and Wagner, J and Sung, JJY and Kirkwood, CD and Inouye, M and Teo, SM}, title = {Luminal microbiota related to Crohn's disease recurrence after surgery.}, journal = {Gut microbes}, volume = {11}, number = {6}, pages = {1713-1728}, pmid = {32564657}, issn = {1949-0984}, mesh = {Adult ; Bacteria/classification/genetics/*isolation & purification ; Crohn Disease/*microbiology/*surgery ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Ileum/microbiology ; Male ; Middle Aged ; Prospective Studies ; Recurrence ; }, abstract = {BACKGROUND: Microbial factors are likely to be involved in the recurrence of Crohn's disease (CD) after bowel resection. We investigated the luminal microbiota before and longitudinally after surgery, in relation to disease recurrence, using 16S metagenomic techniques.

METHODS: In the prospective Post-Operative Crohn's Endoscopic Recurrence (POCER) study, fecal samples were obtained before surgery and 6, 12, and 18 months after surgery from 130 CD patients. Endoscopy was undertaken to detect disease recurrence, defined as Rutgeerts score ≥i2, at 6 months in two-thirds of patients and all patients at 18 months after surgery. The V2 region of the 16S rRNA gene was sequenced using Illumina MiSeq. Cluster analysis was performed at family level, assessing microbiome community differences between patients with and without recurrence.

RESULTS: Six microbial cluster groups were identified. The cluster associated with maintenance of remission was enriched for the Lachnospiraceae family [adjusted OR 0.47 (0.27-0.82), P = .007]. The OTU diversity of Lachnospiraceae within this cluster was significantly greater than in all other clusters. The cluster enriched for Enterobacteriaceae was associated with an increased risk of disease recurrence [adjusted OR 6.35 (1.24-32.44), P = .026]. OTU diversity of Enterobacteriaceae within this cluster was significantly greater than in other clusters.

CONCLUSIONS: Luminal bacterial communities are associated with protection from, and the occurrence of, Crohn's disease recurrence after surgery. Recurrence may relate to a higher abundance of facultatively anaerobic pathobionts from the Enterobacteriaceae family. The ecologic change of depleted Lachnospiraceae, a genus of butyrate-producing bacteria, may permit expansion of Enterobacteriaceae through luminal environmental perturbation.}, } @article {pmid32564244, year = {2020}, author = {Mokkala, K and Houttu, N and Koivuniemi, E and Sørensen, N and Nielsen, HB and Laitinen, K}, title = {GlycA, a novel marker for low grade inflammation, reflects gut microbiome diversity and is more accurate than high sensitive CRP in reflecting metabolomic profile.}, journal = {Metabolomics : Official journal of the Metabolomic Society}, volume = {16}, number = {7}, pages = {76}, pmid = {32564244}, issn = {1573-3890}, mesh = {Acetylglucosamine/blood ; Adult ; Biomarkers/blood ; C-Reactive Protein/metabolism ; Cardiovascular Diseases/blood/metabolism ; Cross-Sectional Studies ; Feces/chemistry ; Female ; Fibrinogen/metabolism ; Gastrointestinal Microbiome/*physiology ; Glycoproteins/blood ; Haptoglobins/metabolism ; Humans ; Inflammation/blood/*metabolism ; Metabolomics/methods ; Obesity/blood/metabolism ; Pregnancy ; Serum Amyloid A Protein/metabolism ; }, abstract = {INTRODUCTION: Gut microbiota is, along with adipose tissue, recognized as a source for many metabolic and inflammatory disturbances that may contribute to the individual's state of health.

OBJECTIVES: We investigated in cross-sectional setting the feasibility of utilizing GlycA, a novel low grade inflammatory marker, and traditional low grade inflammatory marker, high sensitivity CRP (hsCRP), in reflecting serum metabolomics status and gut microbiome diversity.

METHODS: Fasting serum samples of overweight/obese pregnant women (n = 335, gestational weeks: mean 13.8) were analysed for hsCRP by immunoassay, GlycA and metabolomics status by NMR metabolomics and faecal samples for gut microbiome diversity by metagenomics. The benefits of GlycA as a metabolic marker were investigated against hsCRP.

RESULTS: The GlycA concentration correlated with more of the metabolomics markers (144 out of 157), than hsCRP (55 out of 157) (FDR < 0.05). The results remained essentially the same when potential confounding factors known to associate with GlycA and hsCRP levels were taken into account (P < 0.05). This was attributable to the detected correlations between GlycA and the constituents and concentrations of several sized VLDL-particles and branched chain amino acids, which were statistically non-significant with regard to hsCRP. GlycA, but not hsCRP, correlated inversely with gut microbiome diversity.

CONCLUSION: GlycA is a superior marker than hsCRP in assessing the metabolomic profile and gut microbiome diversity. It is proposed that GlycA may act as a novel marker that reflects both the gut microbiome and adipose tissue originated metabolic aberrations; this proposal will need to be verified with regard to clinical outcomes.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, NCT01922791, August 14, 2013.}, } @article {pmid32564086, year = {2020}, author = {Ohno, H}, title = {The impact of metabolites derived from the gut microbiota on immune regulation and diseases.}, journal = {International immunology}, volume = {32}, number = {10}, pages = {629-636}, doi = {10.1093/intimm/dxaa041}, pmid = {32564086}, issn = {1460-2377}, mesh = {Animals ; Bifidobacteriales Infections/*immunology/metabolism ; Dysbiosis/immunology/metabolism ; Gastrointestinal Microbiome/*immunology ; Humans ; T-Lymphocytes, Regulatory/*immunology/metabolism ; }, abstract = {The gut microbiota strongly impacts the physiology and pathology in the host. To understand the complex interactions between host and gut microbiota, an 'integrated omics' approach has been employed, where exhaustive analyses for the different layers of cellular functions, such as epigenomics, transcriptomics and metabolomics, in addition to metagenomics, are combined. With this approach, the mechanisms whereby short-chain fatty acids (SCFAs) regulate host defense and the immune system have been elucidated. In a gnotobiotic mouse model of enterohemorrhagic Escherichia coli infection, Bifidobacterium-derived acetate can protect from infection-mediated death by changing the gene expression profile of colonic epithelial cells. It has also been shown that gut microbiota-derived butyrate enhances colonic regulatory T-cell differentiation through its epigenetic modulatory ability via histone deacetylase inhibition. SCFAs are involved in many other immunomodulatory effects as well as host pathophysiological conditions. Dysbiosis in the gut has been implicated in the pathogenesis of many diseases. Although the causal relationship of gut microbial dysbiosis and/or metabolites with pathogenesis is mostly unknown, mechanistic insights have been elucidated in some cases. Metabolism in the gut microbiota and host liver produces trimethylamine N-oxide, which is known to aggravate atherosclerosis, and a secondary bile acid deoxycholate, which reportedly induces non-alcoholic steatohepatitis-related hepatocellular carcinoma. It has been reported that secondary bile acids could also induce the differentiation of peripherally derived regulatory T cells in the gut. Further studies on the interactions between the host and gut microbiota could lead to the development of new therapeutic strategies as well as in preventive medicine.}, } @article {pmid32563694, year = {2020}, author = {Tschoeke, DA and Coutinho, FH and Leomil, L and Cavalcanti, G and Silva, BS and Garcia, GD and Dos Anjos, LC and Nascimento, LB and Moreira, LS and Otsuki, K and Cordeiro, RC and Rezende, CE and Thompson, FL and Thompson, CC}, title = {New bacterial and archaeal lineages discovered in organic rich sediments of a large tropical Bay.}, journal = {Marine genomics}, volume = {54}, number = {}, pages = {100789}, doi = {10.1016/j.margen.2020.100789}, pmid = {32563694}, issn = {1876-7478}, mesh = {Archaea/classification/genetics/*isolation & purification ; Bacteria/classification/genetics/*isolation & purification ; Bays/*microbiology ; Brazil ; Geologic Sediments/*microbiology ; *Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; }, abstract = {The nutrient and oxygen gradient present in marine sediments promotes high levels of microbial diversity. We applied metagenomics and biogeochemical tools to analyze microbial communities in different sediment depths (0-4 m below sea floor, mbsf) from Guanabara Bay, Brazil, a brackish tropical ecosystem with a history of massive anthropogenic impacts, and a largely unknown sediment microbial diversity. Methanogens (e.g. Methanosarcinales, Methanomicrobiales) were more abundant at 1 mbsf, while sulphate-reducing microbes (Desulfurococcales, Thermoprotales, and Sulfolobales) were more abundant at deeper layers (4 mbsf; corresponding to 3 K Radiocarbon years before present, Holocene Epoch). Taxonomic analyzes and functional gene identification associated with anaerobic methane oxidation (e.g. monomethylamine methyltransferase (mtmB), trimethylamine methyltransferase (mttB) and CO dehydrogenase/acetyl-CoA synthase delta subunit) and sulfate reduction indicated the dominance of Campylobacteria (Sulfurimonas) at deeper sediment layers. Gene sequences related to assimilation of inorganic sulfur increased with depth, while organic sulfur related sequences decrease, accompanying the clear reduction in the concentration of sulfur, organic carbon and chla torwards deeper layers. Analyzes of metagenome assembled genomes also led to the discovery of a novel order within the phylum Acidobacteriota, named Guanabacteria. This novel order had several in silico phenotyping features that differentiate it from closely related phylogenetic neighbors (e.g. Acidobacteria, Aminicenantes, and Thermoanaerobaculum), including several genes (carbon monoxide dehydrogenase, CO dehydrogenase/CO-methylating acetyl-CoA synthase complex subunit beta, heterodisulfide reductase, sulfite exporter TauE/SafE family protein, sulfurtransferase) that relevant for the S and C cycles. Furthermore, the recovered Bathyarchaeota genome SS9 illustrates the methanogenic potential in deeper sediment layer.}, } @article {pmid32563005, year = {2020}, author = {Perazza, LR and Mitchell, PL and Jensen, BAH and Daniel, N and Boyer, M and Varin, TV and Bouchareb, R and Nachbar, RT and Bouchard, M and Blais, M and Gagné, A and Joubert, P and Sweeney, G and Roy, D and Arsenault, BJ and Mathieu, P and Marette, A}, title = {Dietary sucrose induces metabolic inflammation and atherosclerotic cardiovascular diseases more than dietary fat in LDLr[-/-]ApoB[100/100] mice.}, journal = {Atherosclerosis}, volume = {304}, number = {}, pages = {9-21}, doi = {10.1016/j.atherosclerosis.2020.05.002}, pmid = {32563005}, issn = {1879-1484}, support = {FDN#143247//CIHR/Canada ; }, mesh = {Animals ; Apolipoprotein B-100 ; *Atherosclerosis ; *Cardiovascular Diseases ; Diet, High-Fat ; Dietary Fats/adverse effects ; Dietary Sucrose/*adverse effects ; Gastrointestinal Microbiome ; Hyperlipidemias ; *Inflammation ; *Insulin Resistance ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND AND AIMS: Poor dietary habits contribute to the obesity pandemic and related cardiovascular diseases but the respective impact of high saturated fat versus added sugar consumption remains debated. Herein, we aimed to disentangle the individual role of dietary fat versus sugar in cardiometabolic disease progression.

METHODS: We fed pro-atherogenic LDLr[-/-]ApoB[100/100] mice either a low-fat/high-sucrose (LFHS) or a high-fat/low-sucrose (HFLS) diet for 24 weeks. Weekly body weight gain was registered. 16S rRNA gene-based gut microbial analysis was performed to investigate gut microbial modulations. Intraperitoneal insulin (ipITT) and oral glucose tolerance test (oGTT) were conducted to assess glucose homeostasis and insulin sensitivity. Cytokines were assessed in fasted plasma, epididymal white adipose tissue and liver lysates. Heart function was evaluated by echocardiography. Aortic atheroma lesions were quantified according to the en face technique.

RESULTS: HFLS feeding increased obesity, insulin resistance and dyslipidemia compared to LFHS feeding. Conversely, high sucrose consumption decreased gut microbial diversity while augmenting inflammation and the adaptative immune defense against metabolic endotoxemia and reduced macrophage cholesterol efflux capacity. This led to more severe cardiovascular complications as revealed by remarkably high level of atherosclerotic lesions and the early development of cardiac dysfunction in LFHS vs HFLS fed mice.

CONCLUSIONS: We uncoupled obesity-associated insulin resistance from cardiovascular diseases and provided novel evidence that dietary sucrose, not fat, is the main driver of metabolic inflammation accelerating severe atherosclerosis in hyperlipidemic mice.}, } @article {pmid32562822, year = {2020}, author = {Lu, Y and Ocaña-Pallarès, E and López-Escardó, D and Dennis, SR and Monaghan, MT and Ruiz-Trillo, I and Spaak, P and Wolinska, J}, title = {Revisiting the phylogenetic position of Caullerya mesnili (Ichthyosporea), a common Daphnia parasite, based on 22 protein-coding genes.}, journal = {Molecular phylogenetics and evolution}, volume = {151}, number = {}, pages = {106891}, doi = {10.1016/j.ympev.2020.106891}, pmid = {32562822}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Biological Evolution ; Daphnia/*parasitology ; Likelihood Functions ; Mesomycetozoea/*classification/*genetics ; Open Reading Frames/*genetics ; Parasites/*classification/*genetics ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Caullerya mesnili is a common and virulent parasite of the water flea, Daphnia. It was classified within the Haplosporidia (Rhizaria) for over a century. However, a recent molecular phylogeny based on the 18S rRNA gene suggested it belonged to the Ichthyosporea, a class of protists closely related to animals within the Opisthokonta clade. The exact phylogenetic position of C. mesnili remained uncertain because it appeared in the 18S rRNA tree with a very long branch and separated from all other taxa, suggesting that its position could be artifactual. A better understanding of its phylogenetic position has been constrained by a lack of molecular markers and the difficulty of obtaining a suitable quantity and quality of DNA from in vitro cultures, as this intracellular parasite cannot be cultured without its host. We isolated and collected spores of C. mesnili and sequenced genomic libraries. Phylogenetic analyses of a newly generated multi-protein data set (22 proteins, 4998 amino acids) and of sequences from the 18S rRNA gene both placed C. mesnili within the Ichthyophonida sub-clade of Ichthyosporea, as sister-taxon to Abeoforma whisleri and Pirum gemmata. Our study highlights the utility of metagenomic approaches for obtaining genomic information from intracellular parasites and for more accurate phylogenetic placement in evolutionary studies.}, } @article {pmid32557173, year = {2020}, author = {Hinsu, AT and Patel, AB and Pandit, RJ and Thakkar, JR and Shah, RK and Jakhesara, SJ and Koringa, PG and Joshi, CG}, title = {MetaRNAseq analysis of surti buffalo rumen content reveals that transcriptionally active microorganisms need not be abundant.}, journal = {Molecular biology reports}, volume = {47}, number = {7}, pages = {5101-5114}, doi = {10.1007/s11033-020-05581-6}, pmid = {32557173}, issn = {1573-4978}, support = {AAU/GVC/CPCSEA-IAEC/108/2013 dated 05/10/2013//Indian Council of Agricultural Research/ ; }, mesh = {Animals ; Buffaloes/genetics/*microbiology ; Carbohydrate Metabolism ; *Gastrointestinal Microbiome ; *Metagenome ; RNA-Seq ; Rumen/metabolism/*microbiology ; *Transcriptome ; }, abstract = {The present study describes rumen microbiota composition and their functional profiles in Indian Surti buffaloes by metagenomic (MG) and metatranscriptomic (MT) approaches. The study compares samples from buffaloes fed three different proportion of roughages; green and dry type of roughage; and different rumen liquor fractions. Irrespective of sample, Bacteroidetes and Firmicutes were the most predominant bacterial phyla, followed by Proteobacteria, Fibrobacteres and Actinobacteria while, Prevotella, Bacteroides, Ruminococcus and Clostridium were the most abundant genera. Different proportions of taxa were observed in both MG and MT approaches indicating the differences in organisms present and organisms active in the rumen. Higher proportions of fungal taxa were observed in MT while important organisms like Fibrobacter and Butyrivibrio and abundant organisms like Bacteroides and Prevotella were underrepresented in MT data. Functionally, higher proportions of genes involved in Carbohydrate metabolism, Amino acid metabolism and Translation were observed in both data. Genes involved in Metabolism were observed to be underrepresented in MT data while, those involved in Genetic information processing were overrepresented in MT data. Further, genes involved in Carbohydrate metabolism were overexpressed compared to genes involved in Amino acid metabolism in MT data compared to MG data which had higher proportion of genes involved in Amino acid metabolism than Carbohydrate metabolism. In all significant differences were observed between both approaches, different fractions of rumen liquor (liquid and solid) and different proportions of roughage in diet.}, } @article {pmid32556390, year = {2020}, author = {Khan, S and Chen, N and Zhang, C and Wang, L and Han, C and Lu, K and Li, Y and Rafiq, M and Iqbal, A and Zhao, C}, title = {Soil fungal taxonomic diversity along an elevation gradient on the semi-arid Xinglong Mountain, Northwest China.}, journal = {Archives of microbiology}, volume = {202}, number = {8}, pages = {2291-2302}, doi = {10.1007/s00203-020-01948-2}, pmid = {32556390}, issn = {1432-072X}, support = {31522013//National Natural Science Foundation of China/ ; }, mesh = {*Biodiversity ; China ; Fungi/*classification ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Elevation gradients, often regarded as "natural experiments or laboratories", can be used to study changes in the distribution of microbial diversity related to changes in environmental conditions that typically occur over small geographical scales. We exploited this feature by characterizing fungal composition and diversity along an elevation gradient on Xinglong Mountain, northwest China. For this, we used MiSeq sequencing to obtain fungal sequences and clustered them into operational taxonomic units (OTUs). In total, we obtained 1,203,302 reads, 133,700 on average in each sample of soil collected at three selected elevations (2807, 3046, and 3536 m). The reads were assigned to 2192 OTUs. Inconsistent variations were observed in fungal alpha-diversity in samples from the three elevations. However, Principal Coordinate Analysis based on Bray-Curtis and UniFrac (weighted and unweighted) distance metrics revealed that fungal communities in soil samples from 3046 and 3536 m elevations were most similar. Principal Component Analysis based on relative abundances of shared OTUs confirmed that OTUs in samples from 3536 m elevation were more closely related to OTUs from 3046 m than samples from 2807 m elevation. Ascomycota, Basidiomycota, Glomeromycota, Cercozoa and Chytridiomycota were the most abundant fungal phyla across the elevation gradient. Our study also provides valuable indications of relations between fungal communities and an array of soil chemical properties, and variations in fungal taxonomic diversity across a substantial elevation gradient.}, } @article {pmid32556166, year = {2020}, author = {De Filippis, F and Pasolli, E and Ercolini, D}, title = {The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health.}, journal = {FEMS microbiology reviews}, volume = {44}, number = {4}, pages = {454-489}, pmid = {32556166}, issn = {1574-6976}, mesh = {*Food Microbiology ; *Gastrointestinal Microbiome ; *Health ; Humans ; Lactobacillales/*physiology ; }, abstract = {Lactic acid bacteria (LAB) are present in foods, the environment and the animal gut, although fermented foods (FFs) are recognized as the primary niche of LAB activity. Several LAB strains have been studied for their health-promoting properties and are employed as probiotics. FFs are recognized for their potential beneficial effects, which we review in this article. They are also an important source of LAB, which are ingested daily upon FF consumption. In this review, we describe the diversity of LAB and their occurrence in food as well as the gut microbiome. We discuss the opportunities to study LAB diversity and functional properties by considering the availability of both genomic and metagenomic data in public repositories, as well as the different latest computational tools for data analysis. In addition, we discuss the role of LAB as potential probiotics by reporting the prevalence of key genomic features in public genomes and by surveying the outcomes of LAB use in clinical trials involving human subjects. Finally, we highlight the need for further studies aimed at improving our knowledge of the link between LAB-fermented foods and the human gut from the perspective of health promotion.}, } @article {pmid32555605, year = {2020}, author = {Shamsaddini, A and Dadkhah, K and Gillevet, PM}, title = {BiomMiner: An advanced exploratory microbiome analysis and visualization pipeline.}, journal = {PloS one}, volume = {15}, number = {6}, pages = {e0234860}, pmid = {32555605}, issn = {1932-6203}, mesh = {Animals ; Bacteria/*classification/genetics ; Computational Biology/*methods ; Datasets as Topic ; *Gastrointestinal Microbiome ; Metagenomics/*methods ; Mice ; RNA, Ribosomal, 16S/genetics ; *Software ; }, abstract = {Current microbiome applications require substantial bioinformatics expertise to execute. As microbiome clinical diagnostics are being developed, there is a critical need to implement computational tools and applications that are user-friendly for the medical community to understand microbiome correlation with the health. To address this need, we have developed BiomMiner (pronounced as "biominer"), an automated pipeline that provides a comprehensive analysis of microbiome data. The pipeline finds taxonomic signatures of microbiome data and compiles actionable clinical report that allows clinicians and biomedical scientists to efficiently perform statistical analysis and data mining on the large microbiome datasets. BiomMiner generates web-enabled visualization of the analysis results and is specifically designed to facilitate the use of microbiome datasets in clinical applications.}, } @article {pmid32554942, year = {2020}, author = {Takebe, H and Tominaga, K and Fujiwara, K and Yamamoto, K and Yoshida, T}, title = {Differential Responses of a Coastal Prokaryotic Community to Phytoplanktonic Organic Matter Derived from Cellular Components and Exudates.}, journal = {Microbes and environments}, volume = {35}, number = {3}, pages = {}, pmid = {32554942}, issn = {1347-4405}, mesh = {Bacteria/classification/genetics/growth & development/metabolism ; Biodiversity ; Eutrophication ; Exudates and Transudates/*metabolism ; *Microbiota ; Phylogeny ; Phytoplankton/*metabolism ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Stramenopiles/metabolism ; }, abstract = {The phytoplanktonic production and prokaryotic consumption of organic matter significantly contribute to marine carbon cycling. Organic matter released from phytoplankton via three processes (exudation of living cells, cell disruption through grazing, and viral lysis) shows distinct chemical properties. We herein investigated the effects of phytoplanktonic whole-cell fractions (WF) (representing cell disruption by grazing) and extracellular fractions (EF) (representing exudates) prepared from Heterosigma akashiwo, a bloom-forming Raphidophyceae, on prokaryotic communities using culture-based experiments. We analyzed prokaryotic community changes for two weeks. The shift in cell abundance by both treatments showed similar dynamics, reaching the first peak (~4.1×10[6]‍ ‍cells‍ ‍mL[-1]) on day 3 and second peak (~1.1×10[6]‍ ‍cells‍ ‍mL[-1]) on day 13. We classified the sequences obtained into operational taxonomic units (OTUs). A Bray-Curtis dissimilarity analysis revealed that the OTU-level community structure changed distinctively with the two treatments. Ten and 13 OTUs were specifically abundant in the WF and EF treatments, respectively. These OTUs were assigned as heterotrophic bacteria mainly belonging to the Alteromonadales (Gammaproteobacteria) and Bacteroidetes clades and showed successive dynamics following the addition of organic matter. We also analyzed the dynamics of these OTUs in the ocean using publicly available metagenomic data from a natural coastal bloom in Monterey Bay, USA. At least two WF treatment OTUs showed co-occurrence with H. akashiwo, indicating that the blooms of H. akashiwo also affect these OTUs in the ocean. The present results strongly suggest that the thriving and dead cells of uninfected phytoplankton differentially influence the marine prokaryotic community.}, } @article {pmid32554026, year = {2020}, author = {Appolinario, LR and Tschoeke, D and Calegario, G and Barbosa, LH and Moreira, MA and Albuquerque, ALS and Thompson, CC and Thompson, FL}, title = {Oil leakage induces changes in microbiomes of deep-sea sediments of Campos Basin (Brazil).}, journal = {The Science of the total environment}, volume = {740}, number = {}, pages = {139556}, doi = {10.1016/j.scitotenv.2020.139556}, pmid = {32554026}, issn = {1879-1026}, mesh = {Brazil ; Geologic Sediments ; Hydrocarbons ; Metagenomics ; *Microbiota ; *Petroleum ; }, abstract = {The Campos Basin (100,000 km[2]) is located on the continental shelf of southeastern Brazil. Despite the significant oil and gas industrial activities underway in the Campos Basin, scarce information is available regarding the hydrocarbon contents and microbial communities in the deep-sea sediments. To gain new insights on these aspects, we first obtained deep-sea sediment samples with different degrees of oil exposure. We obtained samples from a seabed fissure (N = 28), surroundings (250 m to 500 m from the fissure; N = 24), and a control area (N = 4). We used shotgun metagenomics to characterize the taxonomic and metabolic diversity and analyzed biogeochemical parameters (metal and oil concentration) of all samples. The high levels of unresolved complex mixture of hydrocarbons in the fissure indicate a potentially recent petrogenic contribution in these sediments. The fissure area was found to have a higher abundance of hydrocarbonoclastic bacterial genera and hydrocarbon degradation genes. These bacteria may be used as biosensors of sediment contamination. The effects of oil contamination, mainly around the fissure, are less clear at 250 m and 500 m, suggesting that the surroundings may not have been heavily affected by the oil leakage. Our study demonstrates that metagenomics can disclose biosensors for environmental monitoring.}, } @article {pmid32552447, year = {2020}, author = {Hu, Y and Cheng, M and Liu, B and Dong, J and Sun, L and Yang, J and Yang, F and Chen, X and Jin, Q}, title = {Metagenomic analysis of the lung microbiome in pulmonary tuberculosis - a pilot study.}, journal = {Emerging microbes & infections}, volume = {9}, number = {1}, pages = {1444-1452}, pmid = {32552447}, issn = {2222-1751}, mesh = {Bacteria/classification/genetics/isolation & purification ; Bronchoalveolar Lavage Fluid/microbiology ; Humans ; Lung/*microbiology ; Metagenome ; Metagenomics ; *Microbiota ; Mycobacterium tuberculosis/genetics/*physiology ; Pilot Projects ; Tuberculosis, Pulmonary/diagnosis/*microbiology ; }, abstract = {The lung microbiome plays an important role in the pathophysiological processes associated with pulmonary tuberculosis (PTB). However, only a few studies using 16S rDNA amplicon sequencing have been reported, and the interactions between Mycobacterium tuberculosis (MTB) and the lung microbiome remain poorly understood. Patients with respiratory symptoms and imaging abnormalities compatible with tuberculosis (TB) were enrolled. We analyzed the lung microbiome in bronchoalveolar lavage (BAL) samples from 30 MTB-positive (MTB+) subjects and 30 MTB negative (MTB-) subjects by shotgun metagenomic sequencing. Alpha diversity tended to be lower in the MTB+ group than in the MTB- group. There was a significant difference in beta diversity between the MTB+ and MTB- subjects. MTB+ lung samples were dominated by MTB, while MTB- samples were enriched with Streptococcus, Prevotella, Nesseria, Selenomonas and Bifidobacterium, which more closely resemble the microbial composition of a healthy lung. Network analysis suggested that MTB could greatly impact the microbial community structure. MTB+ and MTB- communities showed distinct functional signatures. Fungal communities were also found to be associated with the presence or absence of MTB. Furthermore, it was confirmed that 16S rDNA amplicon sequencing underrepresents Mycobacterium. This pilot study is the first to explore the interplay between MTB and the host microbiome by using metagenomic sequencing. MTB dominates the lung microbiome of MTB+ subjects, while MTB- subjects have a Streptococcus-enriched microbiome. The 16S approach underrepresents Mycobacterium and is not the best way to study the TB-associated microbiome.}, } @article {pmid32550611, year = {2020}, author = {Hamilton, M and Ma, X and McCrea, BA and Carrisosa, M and Macklin, KS and Zhang, C and Wang, X and Hauck, R}, title = {Influence of Eimeria spp. Infection on Chicken Jejunal Microbiota and the Efficacy of Two Alternative Products Against the Infection.}, journal = {Avian diseases}, volume = {64}, number = {2}, pages = {123-129}, doi = {10.1637/0005-2086-64.2.123}, pmid = {32550611}, issn = {1938-4351}, mesh = {Acetic Acid/chemistry ; Amprolium/pharmacology ; Animals ; *Chickens ; Coccidiosis/parasitology/prevention & control/*veterinary ; Coccidiostats/chemistry/*pharmacology ; Eimeria/*physiology ; Eimeria tenella/physiology ; Fruit and Vegetable Juices ; Gastrointestinal Microbiome/*physiology ; Jejunum/microbiology ; Malus/chemistry ; Poultry Diseases/parasitology/*prevention & control ; Tea/chemistry ; }, abstract = {Eimeria spp. are important intestinal pathogens of chickens (Gallus gallus domesticus). Anticoccidial feed additives, chemicals, and ionophores have traditionally been used to control Eimeria infections in broiler production. Thus, the trend toward antibiotic-free and organic production requires new approaches to coccidiosis prevention. Two not mutually exclusive methods are the use of plant extracts with antiparasitic activity and manipulation of the intestinal microbiota by pre- and probiotics. In the present study, birds were inoculated with a combination of Eimeria acervulina, Eimeria maxima, and Eimeria tenella. We profiled the jejunal microbiome at multiple time points postinfection to investigate the changes in jejunum microbiota and to identify the time point of the maximum difference between infected and noninfected birds. Additionally, we assessed the anticoccidial effects of two anecdotal treatment methods, green tea and apple cider vinegar, as well as amprolium. Green tea and apple cider vinegar had no effect on oocyst shedding, but green tea reduced the mild unspecific lesions in coccidia-infected birds; there was no influence on unspecific lesions in uninfected controls. Jejunal contents were collected on the day of the infection and 1, 2, 4, 6, 10, and 14 days postinfection (dpi) for investigation of the intestinal microbiota by 16S ribosomal (r)RNA gene sequencing. Comparison of the untreated-uninfected and the untreated-infected groups showed a maximum community dissimilarity of 10 dpi. From 4 days after infection, Clostridiales were significantly enriched at the expense of Lactobacillales in infected compared with uninfected birds. Interestingly, treatment with green tea prevented proliferation of Clostridiales induced by the coccidia and increased the relative abundance of Melainabacteria.}, } @article {pmid32546614, year = {2020}, author = {Sharrar, AM and Crits-Christoph, A and Méheust, R and Diamond, S and Starr, EP and Banfield, JF}, title = {Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type.}, journal = {mBio}, volume = {11}, number = {3}, pages = {}, pmid = {32546614}, issn = {2150-7511}, mesh = {Bacteria/classification/*metabolism ; Biosynthetic Pathways ; California ; Metagenome ; *Microbiota ; Multigene Family ; Phylogeny ; *Secondary Metabolism ; *Soil ; *Soil Microbiology ; Trees ; }, abstract = {Bacteria isolated from soils are major sources of specialized metabolites, including antibiotics and other compounds with clinical value that likely shape interactions among microbial community members and impact biogeochemical cycles. Yet, isolated lineages represent a small fraction of all soil bacterial diversity. It remains unclear how the production of specialized metabolites varies across the phylogenetic diversity of bacterial species in soils and whether the genetic potential for production of these metabolites differs with soil depth and vegetation type within a geographic region. We sampled soils and saprolite from three sites in a northern California Critical Zone Observatory with various vegetation and bedrock characteristics and reconstructed 1,334 metagenome-assembled genomes containing diverse biosynthetic gene clusters (BGCs) for secondary metabolite production. We obtained genomes for prolific producers of secondary metabolites, including novel groups within the Actinobacteria, Chloroflexi, and candidate phylum "Candidatus Dormibacteraeota." Surprisingly, one genome of a candidate phyla radiation (CPR) bacterium coded for a ribosomally synthesized linear azole/azoline-containing peptide, a capacity we found in other publicly available CPR bacterial genomes. Overall, bacteria with higher biosynthetic potential were enriched in shallow soils and grassland soils, with patterns of abundance of BGC type varying by taxonomy.IMPORTANCE Microbes produce specialized compounds to compete or communicate with one another and their environment. Some of these compounds, such as antibiotics, are also useful in medicine and biotechnology. Historically, most antibiotics have come from soil bacteria which can be isolated and grown in the lab. Though the vast majority of soil bacteria cannot be isolated, we can extract their genetic information and search it for genes which produce these specialized compounds. These understudied soil bacteria offer a wealth of potential for the discovery of new and important microbial products. Here, we identified the ability to produce these specialized compounds in diverse and novel bacteria in a range of soil environments. This information will be useful to other researchers who wish to isolate certain products. Beyond their use to humans, understanding the distribution and function of microbial products is key to understanding microbial communities and their effects on biogeochemical cycles.}, } @article {pmid32545455, year = {2020}, author = {Klimina, KM and Voroshilova, VN and Poluektova, EU and Veselovsky, VA and Yunes, RA and Kovtun, AS and Kudryavtseva, AV and Kasianov, AS and Danilenko, VN}, title = {Toxin-Antitoxin Systems: A Tool for Taxonomic Analysis of Human Intestinal Microbiota.}, journal = {Toxins}, volume = {12}, number = {6}, pages = {}, pmid = {32545455}, issn = {2072-6651}, support = {18-34-00011//Russian Foundation for Basic Research/International ; 19-74-00146//Russian Science Foundation/International ; }, mesh = {Bacteria/classification/*genetics ; Databases, Genetic ; Feces/microbiology ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Humans ; Intestines/*microbiology ; *Metagenome ; *Metagenomics ; Ribotyping ; Toxin-Antitoxin Systems/*genetics ; }, abstract = {The human gastrointestinal microbiota (HGM) is known for its rich diversity of bacterial species and strains. Yet many studies stop at characterizing the HGM at the family level. This is mainly due to lack of adequate methods for a high-resolution profiling of the HGM. One way to characterize the strain diversity of the HGM is to look for strain-specific functional markers. Here, we propose using type II toxin-antitoxin systems (TAS). To identify TAS systems in the HGM, we previously developed the software TAGMA. This software was designed to detect the TAS systems, MazEF and RelBE, in lactobacilli and bifidobacteria. In this study, we updated the gene catalog created previously and used it to test our software anew on 1346 strains of bacteria, which belonged to 489 species and 49 genera. We also sequenced the genomes of 20 fecal samples and analyzed the results with TAGMA. Although some differences were detected at the strain level, the results showed no particular difference in the bacterial species between our method and other classic analysis software. These results support the use of the updated catalog of genes encoding type II TAS as a useful tool for computer-assisted species and strain characterization of the HGM.}, } @article {pmid32544460, year = {2020}, author = {Kenny, DJ and Plichta, DR and Shungin, D and Koppel, N and Hall, AB and Fu, B and Vasan, RS and Shaw, SY and Vlamakis, H and Balskus, EP and Xavier, RJ}, title = {Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level.}, journal = {Cell host & microbe}, volume = {28}, number = {2}, pages = {245-257.e6}, pmid = {32544460}, issn = {1934-6069}, support = {R01 HL131015/HL/NHLBI NIH HHS/United States ; R01 HL092577/HL/NHLBI NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; HHSN268201500001I/HL/NHLBI NIH HHS/United States ; T32 GM095450/GM/NIGMS NIH HHS/United States ; N01HC25195/HL/NHLBI NIH HHS/United States ; F32 MH095450/MH/NIMH NIH HHS/United States ; 75N92019D00031/HL/NHLBI NIH HHS/United States ; HHSN268201500001C/HL/NHLBI NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/enzymology/genetics/*metabolism ; Cholestanol/*biosynthesis ; Cholesterol/*blood/*metabolism ; Feces/chemistry/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Lipid Metabolism/physiology ; Metabolomics ; Metagenomics ; Oxidoreductases/genetics/*metabolism ; }, abstract = {The human microbiome encodes extensive metabolic capabilities, but our understanding of the mechanisms linking gut microbes to human metabolism remains limited. Here, we focus on the conversion of cholesterol to the poorly absorbed sterol coprostanol by the gut microbiota to develop a framework for the identification of functional enzymes and microbes. By integrating paired metagenomics and metabolomics data from existing cohorts with biochemical knowledge and experimentation, we predict and validate a group of microbial cholesterol dehydrogenases that contribute to coprostanol formation. These enzymes are encoded by ismA genes in a clade of uncultured microorganisms, which are prevalent in geographically diverse human cohorts. Individuals harboring coprostanol-forming microbes have significantly lower fecal cholesterol levels and lower serum total cholesterol with effects comparable to those attributed to variations in lipid homeostasis genes. Thus, cholesterol metabolism by these microbes may play important roles in reducing intestinal and serum cholesterol concentrations, directly impacting human health.}, } @article {pmid32544224, year = {2020}, author = {Saghaï, A and Zivanovic, Y and Moreira, D and Tavera, R and López-García, P}, title = {A Novel Microbialite-Associated Phototrophic Chloroflexi Lineage Exhibiting a Quasi-Clonal Pattern along Depth.}, journal = {Genome biology and evolution}, volume = {12}, number = {7}, pages = {1207-1216}, pmid = {32544224}, issn = {1759-6653}, mesh = {Adaptation, Biological ; Anaerobiosis ; Bacterial Proteins ; Carotenoids/metabolism ; Chloroflexi/*genetics/metabolism ; Ecosystem ; Electron Transport ; Genetic Variation ; *Genome, Bacterial ; Lakes/*microbiology ; Metagenome ; Mexico ; Microbial Consortia ; Nitrogen/metabolism ; Phylogeny ; Sulfur/metabolism ; }, abstract = {Chloroflexales (Chloroflexi) are typical members of the anoxygenic photosynthesizing component of microbial mats and have mostly been characterized from communities associated to hot springs. Here, we report the assembly of five metagenome-assembled genomes (MAGs) of a novel lineage of Chloroflexales found in mesophilic lithifying microbial mats (microbialites) in Lake Alchichica (Mexico). Genomic and phylogenetic analyses revealed that the bins shared 92% of their genes, and these genes were nearly identical despite being assembled from samples collected along a depth gradient (1-15 m depth). We tentatively name this lineage Candidatus Lithoflexus mexicanus. Metabolic predictions based on the MAGs suggest that these chlorosome-lacking mixotrophs share features in central carbon metabolism, electron transport, and adaptations to life under oxic and anoxic conditions, with members of two related lineages, Chloroflexineae and Roseiflexineae. Contrasting with the other diverse microbialite community members, which display much lower genomic conservation along the depth gradient, Ca. L. mexicanus MAGs exhibit remarkable similarity. This might reflect a particular flexibility to acclimate to varying light conditions with depth or the capacity to occupy a very specific spatial ecological niche in microbialites from different depths. Alternatively, Ca. L. mexicanus may also have the ability to modulate its gene expression as a function of the local environmental conditions during diel cycles in microbialites along the depth gradient.}, } @article {pmid32543662, year = {2020}, author = {Kang, Y and Zhang, H and Hu, M and Ma, Y and Chen, P and Zhao, Z and Li, J and Ye, Y and Zheng, M and Lou, Y}, title = {Alterations in the Ocular Surface Microbiome in Traumatic Corneal Ulcer Patients.}, journal = {Investigative ophthalmology & visual science}, volume = {61}, number = {6}, pages = {35}, pmid = {32543662}, issn = {1552-5783}, mesh = {Adult ; Aged ; Aged, 80 and over ; Cornea/*microbiology ; Corneal Injuries/*complications/diagnosis ; Corneal Ulcer/etiology/*microbiology ; Eye Infections, Bacterial/etiology/*microbiology ; Female ; Humans ; Male ; *Microbiota ; Middle Aged ; Pseudomonas aeruginosa/*isolation & purification ; }, abstract = {PURPOSE: Corneal ulcers are a common eye inflammatory disease that can cause visual impairment or even blindness if not treated promptly. Ocular trauma is a major risk factor for corneal ulcers, and corneal trauma in agricultural work can rapidly progress to corneal ulcers. This study aims to evaluate the changes in the ocular surface (OS) microbiome of patients with traumatic corneal ulcer (TCU).

METHODS: Among 20 healthy control (HC) subjects and 22 patients with TCU, 42 eyes were examined to investigate the OS microbial flora using metagenomic shotgun sequencing.

RESULTS: At the taxonomic composition level, our findings showed that dysbiosis (alterations in richness and community structure) occurs in the OS microbiome of patients with TCU. Notably, Pseudomonas was present at a greater than 30% relative abundance in all individuals in the TCU group. At the species level, the abundance of Pseudomonas fluorescens and Pseudomonas aeruginosa was significantly elevated in the TCU group compared to the HC group. At the functional level, we identified significant differences in the HC and TCU groups. We observed that inflammation-related pathways involved in bacterial chemotaxis, flagellar assembly, and biofilm formation were significantly more abundant in the TCU group. Besides, the pathways related to biosynthesis, degradation, and metabolism were also increased significantly in the TCU group.

CONCLUSIONS: These findings indicate an altered OS microbiome in the affected eyes of patients with TCU. Further research is needed to determine whether these alterations contribute to the pathogenesis of TCU or impact disease progression.}, } @article {pmid32541790, year = {2020}, author = {Diakite, A and Dubourg, G and Dione, N and Afouda, P and Bellali, S and Ngom, II and Valles, C and Tall, ML and Lagier, JC and Raoult, D}, title = {Optimization and standardization of the culturomics technique for human microbiome exploration.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {9674}, pmid = {32541790}, issn = {2045-2322}, mesh = {Bacteria/*classification/*growth & development/isolation & purification ; Bacteriological Techniques/methods/*standards ; Culture Media/chemistry ; Feces/*microbiology ; Humans ; Microbiota ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Workflow ; }, abstract = {Culturomics is a high-throughput culture approach that has dramatically contributed to the recent renewal of culture. While metagenomics enabled substantial advances in exploring the microbiota, culturomics significantly expanded our knowledge regarding the bacterial gut repertoire through the discovery and the description of hundreds of new taxa. While this approach relies on the variation of culture conditions and media, we have tested so far more than 300 conditions since the beginning of culturomics studies. In this context, we aimed herein to identify the most profitable conditions for optimizing culturomics approach. For this purpose, we have analysed a set of 58 culturomics conditions that were previously applied to 8 faecal specimens, enabling the isolation of 497 bacterial species. As a result, we were able to reduce the number of conditions used to isolate these 497 of more than a half (i.e. to 25 culture conditions). We have also established a list of the 16 conditions that allowed to capture 98% of the total number of species previously isolated. These data constitute a methodological starting point for culture-based microbiota studies by improving the culturomics workflow without any loss of captured bacterial diversity.}, } @article {pmid32539969, year = {2020}, author = {Belleggia, L and Aquilanti, L and Ferrocino, I and Milanović, V and Garofalo, C and Clementi, F and Cocolin, L and Mozzon, M and Foligni, R and Haouet, MN and Scuota, S and Framboas, M and Osimani, A}, title = {Discovering microbiota and volatile compounds of surströmming, the traditional Swedish sour herring.}, journal = {Food microbiology}, volume = {91}, number = {}, pages = {103503}, doi = {10.1016/j.fm.2020.103503}, pmid = {32539969}, issn = {1095-9998}, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification/metabolism ; Colony Count, Microbial ; Fermentation ; *Fermented Foods/analysis/microbiology ; Fishes/*microbiology ; Food Microbiology ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Seafood/analysis/microbiology ; Sweden ; Volatile Organic Compounds/*analysis/chemistry ; }, abstract = {In this study, the microbiota of ready-to-eat surströmming from three Swedish producers were studied using a combined approach. The pH values of the samples ranged between 6.67 ± 0.01 and 6.98 ± 0.01, whereas their aw values were between 0.911 ± 0.001 and 0.940 ± 0.001. The acetic acid concentration was between 0.289 ± 0.009 g/100 g and 0.556 ± 0.036 g/100 g. Very low concentrations of lactic acid were measured. Viable counting revealed the presence of mesophilic aerobes, mesophilic lactobacilli and lactococci as well as halophilic lactobacilli and lactococci, coagulase-negative staphylococci, halophilic aerobes and anaerobes. Negligible counts for Enterobacteriaceae, Pseudomonadaceae and total eumycetes were observed, whereas no sulfite-reducing anaerobes were detected. Listeria monocytogenes and Salmonella spp. were absent in all samples. Multiplex real-time PCR revealed the absence of the bont/A, bont/B, bont/E, bont/F, and 4gyrB (CP) genes, which encode botulinic toxins, in all the samples analyzed. Metagenomic sequencing revealed the presence of a core microbiota dominated by Halanaerobium praevalens, Alkalibacterium gilvum, Carnobacterium spp., Tetragenococcus halophilus, Clostridiisalibacter spp. and Porphyromonadaceae. Psychrobacter celer, Ruminococcaceae, Marinilactibacillus psychrotolerans, Streptococcus infantis and Salinivibrio costicola were detected as minor OTUs. GC-MS analysis of volatile components revealed the massive presence of trimethylamine and sulphur compounds. Moreover, 1,2,4-trithiolane, phenols, ketones, aldehydes, alcohols, esters and long chain aliphatic hydrocarbons were also detected. The data obtained allowed pro-technological bacteria, which are well-adapted to saline environments, to be discovered for the first time. Further analyses are needed to better clarify the extent of the contribution of either the microbiota or autolytic enzymes of the fish flesh in the aroma definition.}, } @article {pmid32539965, year = {2020}, author = {Benítez-Cabello, A and Calero-Delgado, B and Rodríguez-Gómez, F and Bautista-Gallego, J and Garrido-Fernández, A and Jiménez-Díaz, R and Arroyo-López, FN}, title = {The use of multifunctional yeast-lactobacilli starter cultures improves fermentation performance of Spanish-style green table olives.}, journal = {Food microbiology}, volume = {91}, number = {}, pages = {103497}, doi = {10.1016/j.fm.2020.103497}, pmid = {32539965}, issn = {1095-9998}, mesh = {Bacteria/classification/genetics/isolation & purification/metabolism ; Biofilms/growth & development ; Coculture Techniques ; Fermentation ; Fermented Foods/analysis/*microbiology ; Food Microbiology ; Fruit/microbiology ; Homoserine/analogs & derivatives/analysis/biosynthesis ; Lactobacillus/classification/growth & development/*metabolism ; Lactones/analysis ; Microbiota/genetics ; Olea/*microbiology ; Saccharomycetales/growth & development/*metabolism ; }, abstract = {In this work, Lactobacillus pentosus LPG1, Lactobacillus pentosus Lp13, Lactobacillus plantarum Lpl15, and Wickerhanomyces anomalous Y12, all of them previously isolated from fermented table olive biofilms, were used (alone or in combination) as multifunctional starters for Manzanilla Spanish-style green table olive fermentations. Their performances were evaluated through the changes in the key physico-chemical and microbiological parameters, correlation between AI-2 production and biofilm formation, inoculum imposition, metataxonomic analysis and sensory characteristics of the finished products. Inoculation only with lactic acid bacteria (LAB) strains led to higher titratable acidities and lower pH values than the spontaneous fermentation (non-inoculated control), mainly during the first steps of processing. However, the sequential inoculation of the yeast and then the combination of the 3 LAB strains showed the most favourable evolution. LPG1 strain and, particularly Lp13, were excellent biofilms former and showed the major imposition on the fruit epidermis, as corroborated by rep-PCR analysis. Production of AI-2 was lower in the treatment inoculated exclusively with yeast Y12 but had the highest presence in the sequential yeast-LAB inoculum, with its maximum concentration and maximum LAB population on fruits (19th days) strongly related. Metataxonomic analysis of the biofilms at the end of the fermentation revealed, in addition to Lactobacillus, high proportions of sequences from genera Marinilactobacillus, Alkalibacterium, Halolactobacillus, and low levels of Halomonas and Aerococcus. Compositional data analysis of the omics data revealed that Lpl15 was scarcely efficient for controlling the spontaneous microbiota since its treatment presented the highest proportions of Aerococcus genus. Finally, the sensory analysis showed similar characteristics for the treatment inoculated with LPG1 and the spontaneous process, with olives inoculated with the yeast (alone or in combination with Lactobacillus strains) showing attractive scores. Then, inoculation of Spanish-style table olive fermentations with a sequential yeast and LAB combination could be an advisable practice.}, } @article {pmid32539695, year = {2020}, author = {Philips, A and Stolarek, I and Handschuh, L and Nowis, K and Juras, A and Trzciński, D and Nowaczewska, W and Wrzesińska, A and Potempa, J and Figlerowicz, M}, title = {Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {402}, pmid = {32539695}, issn = {1471-2164}, support = {R21 DE026280/DE/NIDCR NIH HHS/United States ; R21DE026280/DE/NIDCR NIH HHS/United States ; }, mesh = {Body Remains/*microbiology ; Fossils/*microbiology ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Genomics ; Humans ; Metagenome ; Mouth/*microbiology ; Periodontitis/microbiology ; Periodontium/microbiology ; Tannerella forsythia/*genetics/*pathogenicity ; Tooth/microbiology ; Virulence Factors/*genetics ; }, abstract = {BACKGROUND: Recent advances in the next-generation sequencing (NGS) allowed the metagenomic analyses of DNA from many different environments and sources, including thousands of years old skeletal remains. It has been shown that most of the DNA extracted from ancient samples is microbial. There are several reports demonstrating that the considerable fraction of extracted DNA belonged to the bacteria accompanying the studied individuals before their death.

RESULTS: In this study we scanned 344 microbiomes from 1000- and 2000- year-old human teeth. The datasets originated from our previous studies on human ancient DNA (aDNA) and on microbial DNA accompanying human remains. We previously noticed that in many samples infection-related species have been identified, among them Tannerella forsythia, one of the most prevalent oral human pathogens. Samples containing sufficient amount of T. forsythia aDNA for a complete genome assembly were selected for thorough analyses. We confirmed that the T. forsythia-containing samples have higher amounts of the periodontitis-associated species than the control samples. Despites, other pathogens-derived aDNA was found in the tested samples it was too fragmented and damaged to allow any reasonable reconstruction of these bacteria genomes. The anthropological examination of ancient skulls from which the T. forsythia-containing samples were obtained revealed the pathogenic alveolar bone loss in tooth areas characteristic for advanced periodontitis. Finally, we analyzed the genetic material of ancient T. forsythia strains. As a result, we assembled four ancient T. forsythia genomes - one 2000- and three 1000- year-old. Their comparison with contemporary T. forsythia genomes revealed a lower genetic diversity within the four ancient strains than within contemporary strains. We also investigated the genes of T. forsythia virulence factors and found that several of them (KLIKK protease and bspA genes) differ significantly between ancient and modern bacteria.

CONCLUSIONS: In summary, we showed that NGS screening of the ancient human microbiome is a valid approach for the identification of disease-associated microbes. Following this protocol, we provided a new set of information on the emergence, evolution and virulence factors of T. forsythia, the member of the oral dysbiotic microbiome.}, } @article {pmid32536582, year = {2021}, author = {Jian, C and Luukkonen, P and Sädevirta, S and Yki-Järvinen, H and Salonen, A}, title = {Impact of short-term overfeeding of saturated or unsaturated fat or sugars on the gut microbiota in relation to liver fat in obese and overweight adults.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {40}, number = {1}, pages = {207-216}, doi = {10.1016/j.clnu.2020.05.008}, pmid = {32536582}, issn = {1532-1983}, mesh = {Body Mass Index ; Diet, High-Fat/*adverse effects ; Dietary Sugars/administration & dosage ; Eating/physiology ; Fasting/blood ; Fats, Unsaturated/administration & dosage ; Fatty Acids/administration & dosage ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Liver/metabolism ; Male ; Middle Aged ; Non-alcoholic Fatty Liver Disease/*etiology ; Obesity/complications/*metabolism ; Overweight/complications/*metabolism ; }, abstract = {BACKGROUNDS & AIMS: Intestinal microbiota may be causally involved in the pathogenesis of non-alcoholic fatty liver disease (NAFLD). We aimed to study the effect of short-term overfeeding on human gut microbiota in relation to baseline and overfeeding-induced liver steatosis. We also asked whether the baseline microbiota composition is associated to the overfeeding-induced increase in liver fat.

METHODS: In a randomized trial, 38 overweight and obese subjects were assigned to consume an excess of 1000 kcal/day of diets rich in either saturated fat, unsaturated fat, or simple sugars for 3 weeks. Fasting blood samples and [1]H-MR spectroscopy were used for extensive clinical phenotyping as previously reported (PMID: 29844096). Fecal samples were collected for the analysis of the gut microbiota using 16S rRNA amplicon sequencing, imputed metagenomics and qPCR. Microbiota results were correlated with dietary intakes and clinical measurements before and during overfeeding.

RESULTS: The overall community structure of the microbiota remained highly stable and personalized during overfeeding based on between-sample Bray-Curtis dissimilarity, but the relative abundances of individual taxa were altered in a diet-specific manner: overfeeding saturated fat increased Proteobacteria, while unsaturated fat increased butyrate producers. Sugar overfeeding increased Lactococcus and Escherichia coli. Imputed functions of the gut microbiota were not affected by overfeeding. Several taxa affected by overfeeding significantly correlated with the changes in host metabolic markers. The baseline levels of proteobacterial family Desulfovibrionaceae, and especially genus Bilophila, were significantly associated to overfeeding-induced liver fat increase independently of the diet arm. In general, limited overlap was observed between the overfeeding-induced microbiota changes and the liver fat-associated microbiota features at baseline.

CONCLUSIONS: Our work indicates that the human gut microbiota is resilient to short-term overfeeding on community level, but specific taxa are altered on diet composition-dependent manner. Generalizable microbiota signatures directly associated with liver steatosis could not be identified. Instead, the carriage of Bilophila was identified as a potential novel risk factor for diet-induced liver steatosis in humans. Clinical trial registry number: NCT02133144 listed on NIH website: ClinicalTrials.gov.}, } @article {pmid32535444, year = {2020}, author = {Barak, H and Brenner, A and Sivan, A and Kushmaro, A}, title = {Temporal distribution of microbial community in an industrial wastewater treatment system following crash and during recovery periods.}, journal = {Chemosphere}, volume = {258}, number = {}, pages = {127271}, doi = {10.1016/j.chemosphere.2020.127271}, pmid = {32535444}, issn = {1879-1298}, mesh = {Biodegradation, Environmental ; Bioreactors/*microbiology ; Gammaproteobacteria/drug effects/genetics ; Industrial Waste/analysis ; Membranes, Artificial ; Metagenomics ; Microbiota/*drug effects/genetics ; Sewage/microbiology ; *Wastewater/chemistry/microbiology ; Water Purification/*methods ; }, abstract = {Water and soil contamination by industrial wastes is a global concern. Biological treatment of industrial wastewater using bioreactors allows the removal of organic matter and nutrients and enables either reuse or safe discharge. Wastewater bioremediation depends in part on the microbial communities present in the bioreactor. To ascertain which communities may play a role in the remediation process, the present study investigates the microbial community structure and diversity of microorganisms found in a full-scale membrane bioreactor (MBR) for industrial wastewater treatment. The study was carried out using high-throughput data observations following a failure (crash) of the MBR and during the extended recovery of the process. Results revealed a positive correlation between the MBR's ability to remove organic matter and its microbial community richness. The significant changes in relative microbial abundance between crash and recovery periods of the MBR revealed the important role of specific bacterial genera in wastewater treatment processes. A whole-genome metagenomics based comparison showed a clear difference in microbial makeup between two functional periods of MBR activity. The crash period was characterized by abundance in bacteria belonging to Achromobacter, Acinetobacter, Halomonas, Pseudomonas and an uncultured MBAE14. The recovery period on the other hand was characterized by Aquamicrobium and by Wenzhouxiangella marina. Our study also revealed some interesting functional pathways characterizing the microbial communities from the two periods of bioreactor function, such as Nitrate and Sulfate reduction pathways. These differences indicate the connection between the bacterial diversity of the MBR and its efficiency to remove TOC.}, } @article {pmid32535435, year = {2020}, author = {Kotoky, R and Pandey, P}, title = {Difference in the rhizosphere microbiome of Melia azedarach during removal of benzo(a)pyrene from cadmium co-contaminated soil.}, journal = {Chemosphere}, volume = {258}, number = {}, pages = {127175}, doi = {10.1016/j.chemosphere.2020.127175}, pmid = {32535435}, issn = {1879-1298}, mesh = {Bacteria/genetics/isolation & purification/metabolism ; Benzo(a)pyrene/*metabolism/toxicity ; Biodegradation, Environmental ; Cadmium/*toxicity ; Melia azedarach/*metabolism/microbiology ; Metagenome ; *Microbiota/drug effects/genetics ; *Rhizosphere ; Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {Benzo(a)pyrene (BaP) is a highly persistent biohazard polyaromatic hydrocarbon and often reported to be present in soils co-contaminated with heavy metals. The present study explains the rhizodegradation of BaP using bacterial consortium in the rhizosphere of Melia azedarach, along with a change in taxonomical and functional properties of the rhizosphere microbiome. The relative abundance of most dominant phylum Proteobacteria was 2% higher with BaP, while in the presence of both BaP and Cd, its abundance was 2.2% lower. Functional metagenome analysis also revealed the shifting of microbial community and functional gene abundance in the favor of xenobiotic compound degradation upon augmentation of bacterial consortium. Interestingly, upon the addition of BaP the range of functional abundance for genes of PAH degradation (0.165-0.19%), was found to be decreasing. However, augmentation of a bacterial consortium led to an increase in its abundance including genes for degradation of benzoate (0.55-0.64%), toluene (0.2-0.22%), naphthalene (0.25-0.295%) irrespective of the addition of BaP and Cd. Moreover, under greenhouse condition, the application of M. azedarach-bacterial consortium enhanced the degradation of BaP in the rhizosphere (88%) after 60 days, significantly higher than degradation in bulk soil (68.22%). The analysis also showed an increase in degradation of BaP by 15% with plant-native microbe association than in bulk soil. Therefore, the association of M. azedarach-bacterial consortium enhanced the degradation of BaP in soil along with the taxonomical and functional attributes of the rhizosphere microbiome.}, } @article {pmid32534767, year = {2020}, author = {Szemplinski, KL and Thompson, A and Cherry, N and Guay, K and Smith, WB and Brady, J and Jones, T}, title = {Transporting and Exercising Unconditioned Horses: Effects on Microflora Populations.}, journal = {Journal of equine veterinary science}, volume = {90}, number = {}, pages = {102988}, doi = {10.1016/j.jevs.2020.102988}, pmid = {32534767}, issn = {0737-0806}, mesh = {Animals ; Feces ; Firmicutes ; Horses ; Metagenome ; *Microbiota ; *Physical Conditioning, Animal ; }, abstract = {The objective of this study was to determine if transportation and exercise stress in horses affect the microflora populations in the equine hindgut. Four horses were subjected to three transport periods (0, 3, and 6 hours) with a 7-d rest period between each transport. Horses were fed 0.91 kg/day of Purina Impact All Stages 12% and had ad libitum access to Cynodon dactylon (Coastal Bermudagrass) hay. Fecal samples were collected before (0 hours) and after (48 hours) transport. In addition, three horses underwent a different standardized exercise test with a 7-d rest period between each exercise. Standardized exercise test intensity was determined by heart rate to validate if the horse was in aerobic or anaerobic work. The protocol for fecal sample collection after exercise was the same as for transport. Prokaryotic community profiling was conducted by 16S metagenomic analysis. After DNA evaluation, differences were found in the microbiome at transport 0 hours and grouped transport 3 hours time 48 and transport 6 hours time 48 (PERMANOVA P = .037) where Bacteroidetes increased 48 hours after transport and Firmicutes decreased 48 hours after transport. Exercise microbial communities showed no difference in either alpha or beta diversity when compared with controls (0 hours). In the present study, difference in microflora may have resulted from stress duration of transport rather than stress duration of exercise.}, } @article {pmid32534596, year = {2020}, author = {Doane, MP and Morris, MM and Papudeshi, B and Allen, L and Pande, D and Haggerty, JM and Johri, S and Turnlund, AC and Peterson, M and Kacev, D and Nosal, A and Ramirez, D and Hovel, K and Ledbetter, J and Alker, A and Avalos, J and Baker, K and Bhide, S and Billings, E and Byrum, S and Clemens, M and Demery, AJ and Lima, LFO and Gomez, O and Gutierrez, O and Hinton, S and Kieu, D and Kim, A and Loaiza, R and Martinez, A and McGhee, J and Nguyen, K and Parlan, S and Pham, A and Price-Waldman, R and Edwards, RA and Dinsdale, EA}, title = {The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {93}, pmid = {32534596}, issn = {2049-2618}, support = {1323809//National Science Foundation/International ; 1330800//National Science Foundation/International ; }, mesh = {Animals ; Bacteria/genetics/isolation & purification ; Elasmobranchii/*microbiology ; Fishes/*microbiology ; Integumentary System/*microbiology ; *Metagenomics ; Microbiota/*genetics ; *Phylogeny ; *Symbiosis ; }, abstract = {BACKGROUND: The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes are covered in scales and are mucous rich. The divergence time among these two fish groups is hypothesized to result in predictable variation among symbionts. Here, using shotgun metagenomics, we test if patterns of diversity in the skin surface microbiome across the two fish clades match predictions made by phylosymbiosis theory. We hypothesize (1) the skin microbiome will be host and clade-specific, (2) evolutionary difference in elasmobranch and teleost will correspond with a concomitant increase in host-microbiome dissimilarity, and (3) the skin structure of the two groups will affect the taxonomic and functional composition of the microbiomes.

RESULTS: We show that the taxonomic and functional composition of the microbiomes is host-specific. Teleost fish had lower average microbiome within clade similarity compared to among clade comparison, but their composition is not different among clade in a null based model. Elasmobranch's average similarity within clade was not different than across clade and not different in a null based model of comparison. In the comparison of host distance with microbiome distance, we found that the taxonomic composition of the microbiome was related to host distance for the elasmobranchs, but not the teleost fishes. In comparison, the gene function composition was not related to the host-organism distance for elasmobranchs but was negatively correlated with host distance for teleost fishes.

CONCLUSION: Our results show the patterns of phylosymbiosis are not consistent across both fish clades, with the elasmobranchs showing phylosymbiosis, while the teleost fish are not. The discrepancy may be linked to alternative processes underpinning microbiome assemblage, including possible historical host-microbiome evolution of the elasmobranchs and convergent evolution in the teleost which filter specific microbial groups. Our comparison of the microbiomes among fishes represents an investigation into the microbial relationships of the oldest divergence of extant vertebrate hosts and reveals that microbial relationships are not consistent across evolutionary timescales. Video abstract.}, } @article {pmid32534383, year = {2020}, author = {Muccee, F and Ejaz, S}, title = {Whole genome shotgun sequencing of POPs degrading bacterial community dwelling tannery effluents and petrol contaminated soil.}, journal = {Microbiological research}, volume = {238}, number = {}, pages = {126504}, doi = {10.1016/j.micres.2020.126504}, pmid = {32534383}, issn = {1618-0623}, mesh = {Bacteria/*classification/*metabolism ; *Biodegradation, Environmental ; DNA, Bacterial ; Gasoline/microbiology ; Metabolic Networks and Pathways ; Metagenome ; Persistent Organic Pollutants/*metabolism ; *Petroleum Pollution ; Soil Microbiology ; Soil Pollutants/metabolism ; Wastewater/microbiology ; Whole Genome Sequencing ; }, abstract = {The present study involved identification of genes which are present in the genome of native bacteria to make them effective tools for bioremediation of persistent organic pollutants (POPs). During this study, forty-one POPs (naphthalene, toluene and petrol) metabolizing bacteria were isolated from tannery effluents and petrol contaminated soil samples by successive enrichment culturing. The taxonomic diversity and gene repertoire conferring POPs degradation ability to the isolated bacterial community were studied through whole genome shotgun sequencing of DNA consortium. The DNA consortium contained equimolar concentration of DNA extracted from each bacterial isolate using organic method. To add a double layer of confirmation the established DNA consortium was subjected to 16S rRNA metagenome sequencing and whole genome shotgun sequencing analysis. Biodiversity analysis revealed that the consortium was composed of phyla Firmicutes (80 %), Proteobacteria (12 %) and Actinobacteria (5%). Genera found included Bacillus (45 %), Burkholderia (25 %), Brevibacillus (9%) and Geobacillus (4%). Functional profiling of consortium helped us to identify genes associated with degradation pathways of a variety of organic compounds including toluene, naphthalene, caprolactam, benzoate, aminobenzoate, xylene, 4-hydroxyphenyl acetic acid, biphenyl, anthracene, aminobenzoate, chlorocyclohexane, chlorobenzene, n-phenylalkanoic acid, phenylpropanoid, salicylate, gentisate, central meta cleavage of aromatic compounds, cinnamic acid, catechol and procatechuate branch of β-ketoadipate pathway, phenyl-acetyl CoA and homogentisate catabolic pathway. The information thus generated has ensured not only biodegradation potential but also revealed many possible future applications of the isolated bacteria.}, } @article {pmid32533650, year = {2020}, author = {Jiang, HY and Pan, LY and Zhang, X and Zhang, Z and Zhou, YY and Ruan, B}, title = {Altered gut bacterial-fungal interkingdom networks in patients with current depressive episode.}, journal = {Brain and behavior}, volume = {10}, number = {8}, pages = {e01677}, pmid = {32533650}, issn = {2162-3279}, support = {LY20H090012//Natural Science Foundation of Zhejiang Province/ ; 2013CB531401//National Key Stone Basic Research Program (973 Program) of China/ ; }, mesh = {Adult ; Bacteria/genetics ; Dysbiosis ; Female ; Fungi/genetics ; *Gastrointestinal Microbiome ; Humans ; Male ; RNA, Ribosomal, 16S/genetics ; }, abstract = {INTRODUCTION: Bacterial dysbiosis has been described in patients with current depressive episode (CDE); however, the fungal composition in the gut has not been investigated in these patients.

METHODS: Here, we characterized the fungal gut mycobiota in patients with CDE. We systematically characterized the microbiota and mycobiota in fecal samples obtained from 24 patients with CDE and 16 healthy controls (HC) using 16S rRNA gene- and ITS1-based DNA sequencing, respectively.

RESULTS: In patients with CDE, bacterial dysbiosis was characterized by an altered composition and reduced correlation network density, and the gut mycobiota was characterized by a relative reduction in alpha diversity and altered composition. Most notably, the CDE group had higher levels of Candida and lower level of Penicillium than the HC group. Compared with the HC group, the gut microbiota in patients with CDE displayed a significant disruption in the bacteria-fungi correlation network suggestive of altered interkingdom interactions. Furthermore, a gut microbial index based on the combination of eight genera (four bacterial and four fungal CDE-associated genera) distinguished CDE patients from controls with an area under the curve of approximately 0.84, suggesting that the gut microbiome signature is a promising tool for disease classification.

CONCLUSIONS: Our findings suggest that both bacteria and fungi contribute to gut dysbiosis in patients with CDE. Future studies involving larger cohorts and metagenomic or metabolomic analyses may clarify the structure and potential roles and functions of the gut mycobiome and its impact on the development of CDE.}, } @article {pmid32531490, year = {2020}, author = {Deng, Q and Wan, L and Li, X and Cao, X and Zhou, Y and Song, C}, title = {Metagenomic evidence reveals denitrifying community diversity rather than abundance drives nitrate removal in stormwater biofilters amended with different organic and inorganic electron donors.}, journal = {Chemosphere}, volume = {257}, number = {}, pages = {127269}, doi = {10.1016/j.chemosphere.2020.127269}, pmid = {32531490}, issn = {1879-1298}, mesh = {Bacteria ; Bioreactors/*microbiology ; Carbon ; Denitrification/*physiology ; Electrons ; Metagenome ; *Microbiota ; Nitrates ; Nitrogen ; Nitrogen Oxides ; Sulfur ; }, abstract = {Various sole and mixed electron donors were tested to promote the denitrification rate and nitrate removal efficiency in biofilter systems with high phosphate and ammonia removal efficiency (92.6% and 95.3% respectively). Compared to sole electron donors, complex organic carbon (bits of wood and straw) substantially improved the denitrification rate and nitrate removal efficiency (from 6.3%-18.5% to35.4%) by shifting the denitrifying microbial community composition, even though the relative abundance of functional genes mediating denitrification decreased. The mixed electron donor combining complex organic carbon with sulfur, iron and CH4 further promoted nitrate removal efficiency by 37.2%. The significantly higher abundance and diversity of bacteria mediating organic carbon decomposition in the treatments with complex organic carbon indicated the continuous production of organic carbon with small molecular weights, which provided sustainable and effective electron donor for denitrification. However, sole sulfur or iron did not effectively promote the denitrification rate and nitrogen removal efficiency, even though the related microbial community had been formed.}, } @article {pmid32531290, year = {2020}, author = {Khoruts, A and Hoffmann, DE and Britton, RA}, title = {Probiotics: Promise, Evidence, and Hope.}, journal = {Gastroenterology}, volume = {159}, number = {2}, pages = {409-413}, doi = {10.1053/j.gastro.2020.05.058}, pmid = {32531290}, issn = {1528-0012}, mesh = {Digestive System Diseases/*diet therapy/microbiology/prevention & control ; Gastrointestinal Microbiome/*physiology ; Humans ; Probiotics/*administration & dosage/adverse effects ; }, } @article {pmid32531278, year = {2020}, author = {Ellegaard, KM and Suenami, S and Miyazaki, R and Engel, P}, title = {Vast Differences in Strain-Level Diversity in the Gut Microbiota of Two Closely Related Honey Bee Species.}, journal = {Current biology : CB}, volume = {30}, number = {13}, pages = {2520-2531.e7}, pmid = {32531278}, issn = {1879-0445}, mesh = {Animals ; Bacteria/classification/*genetics/isolation & purification ; Bees/*microbiology ; *Gastrointestinal Microbiome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Species Specificity ; }, abstract = {Most bacterial species encompass strains with vastly different gene content. Strain diversity in microbial communities is therefore considered to be of functional importance. Yet little is known about the extent to which related microbial communities differ in diversity at this level and which underlying mechanisms may constrain and maintain strain-level diversity. Here, we used shotgun metagenomics to characterize and compare the gut microbiota of two honey bee species, Apis mellifera and Apis cerana, which diverged about 6 mya. Although the host species are colonized largely by the same bacterial 16S rRNA phylotypes, we find that their communities are host specific when analyzed with genomic resolution. Moreover, despite their similar ecology, A. mellifera displayed a much higher diversity of strains and functional gene content in the microbiota compared to A. cerana, both per colony and per individual bee. In particular, the gene repertoire for polysaccharide degradation was massively expanded in the microbiota of A. mellifera relative to A. cerana. Bee management practices, divergent ecological adaptation, or habitat size may have contributed to the observed differences in microbiota genomic diversity of these key pollinator species. Our results illustrate that the gut microbiota of closely related animal hosts can differ vastly in genomic diversity while displaying similar levels of diversity based on the 16S rRNA gene. Such differences are likely to have consequences for gut microbiota functioning and host-symbiont interactions, highlighting the need for metagenomic studies to understand the ecology and evolution of microbial communities.}, } @article {pmid32530501, year = {2021}, author = {Alferink, LJM and Radjabzadeh, D and Erler, NS and Vojinovic, D and Medina-Gomez, C and Uitterlinden, AG and de Knegt, RJ and Amin, N and Ikram, MA and Janssen, HLA and Kiefte-de Jong, JC and Metselaar, HJ and van Duijn, CM and Kraaij, R and Darwish Murad, S}, title = {Microbiomics, Metabolomics, Predicted Metagenomics, and Hepatic Steatosis in a Population-Based Study of 1,355 Adults.}, journal = {Hepatology (Baltimore, Md.)}, volume = {73}, number = {3}, pages = {968-982}, doi = {10.1002/hep.31417}, pmid = {32530501}, issn = {1527-3350}, mesh = {Cross-Sectional Studies ; Fatty Liver/*etiology/genetics/metabolism/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Metabolomics ; Metagenome/genetics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; Ruminococcus/metabolism ; }, abstract = {BACKGROUND AND AIMS: Previous small studies have appraised the gut microbiome (GM) in steatosis, but large-scale studies are lacking. We studied the association of the GM diversity and composition, plasma metabolites, predicted functional metagenomics, and steatosis.

APPROACH AND RESULTS: This is a cross-sectional analysis of the prospective population-based Rotterdam Study. We used 16S ribosomal RNA gene sequencing and determined taxonomy using the SILVA reference database. Alpha diversity and beta diversity were calculated using the Shannon diversity index and Bray-Curtis dissimilarities. Differences were tested across steatosis using permutational multivariate analysis of variance. Hepatic steatosis was diagnosed by ultrasonography. We subsequently selected genera using regularized regression. The functional metagenome was predicted based on the GM using Kyoto Encyclopedia of Genes and Genomes pathways. Serum metabolomics were assessed using high-throughput proton nuclear magnetic resonance. All analyses were adjusted for age, sex, body mass index, alcohol, diet, and proton-pump inhibitors. We included 1,355 participants, of whom 472 had steatosis. Alpha diversity was lower in steatosis (P = 1.1∙10[-9]), and beta diversity varied across steatosis strata (P = 0.001). Lasso selected 37 genera of which three remained significantly associated after adjustment (Coprococcus3: β = -65; Ruminococcus Gauvreauiigroup: β = 62; and Ruminococcus Gnavusgroup: β = 45, Q-value = 0.037). Predicted metagenome analyses revealed that pathways of secondary bile-acid synthesis and biotin metabolism were present, and D-alanine metabolism was absent in steatosis. Metabolic profiles showed positive associations for aromatic and branched chain amino acids and glycoprotein acetyls with steatosis and R. Gnavusgroup, whereas these metabolites were inversely associated with alpha diversity and Coprococcus3.

CONCLUSIONS: We confirmed, on a large-scale, the lower microbial diversity and association of Coprococcus and Ruminococcus Gnavus with steatosis. We additionally showed that steatosis and alpha diversity share opposite metabolic profiles.}, } @article {pmid32526207, year = {2020}, author = {Javdan, B and Lopez, JG and Chankhamjon, P and Lee, YJ and Hull, R and Wu, Q and Wang, X and Chatterjee, S and Donia, MS}, title = {Personalized Mapping of Drug Metabolism by the Human Gut Microbiome.}, journal = {Cell}, volume = {181}, number = {7}, pages = {1661-1679.e22}, pmid = {32526207}, issn = {1097-4172}, support = {DP2 AI124441/AI/NIAID NIH HHS/United States ; T32 GM007388/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Animals ; Bacteria/classification ; Biomarkers, Pharmacological/metabolism ; Drug Evaluation, Preclinical/*methods ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Healthy Volunteers ; Humans ; Male ; Metagenome/genetics ; Metagenomics/methods ; Mice ; Mice, Inbred C57BL ; Microbiota/*drug effects/genetics ; Pharmaceutical Preparations/metabolism ; Precision Medicine/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The human gut microbiome harbors hundreds of bacterial species with diverse biochemical capabilities. Dozens of drugs have been shown to be metabolized by single isolates from the gut microbiome, but the extent of this phenomenon is rarely explored in the context of microbial communities. Here, we develop a quantitative experimental framework for mapping the ability of the human gut microbiome to metabolize small molecule drugs: Microbiome-Derived Metabolism (MDM)-Screen. Included are a batch culturing system for sustained growth of subject-specific gut microbial communities, an ex vivo drug metabolism screen, and targeted and untargeted functional metagenomic screens to identify microbiome-encoded genes responsible for specific metabolic events. Our framework identifies novel drug-microbiome interactions that vary between individuals and demonstrates how the gut microbiome might be used in drug development and personalized medicine.}, } @article {pmid32525961, year = {2020}, author = {Miller-Ensminger, T and Mormando, R and Maskeri, L and Shapiro, JW and Wolfe, AJ and Putonti, C}, title = {Introducing Lu-1, a Novel Lactobacillus jensenii Phage Abundant in the Urogenital Tract.}, journal = {PloS one}, volume = {15}, number = {6}, pages = {e0234159}, pmid = {32525961}, issn = {1932-6203}, mesh = {Bacteriophages/genetics/*isolation & purification ; Computational Biology ; Female ; Humans ; Lactobacillus/*virology ; Microbiota ; Perineum/*microbiology ; Vagina/*microbiology ; }, abstract = {Bacteriophages (phages) play a key role in shaping microbial communities, including those of the human body. Phages are abundant members of the urogenital tract, most often persisting through the lysogenic life cycle as prophages integrated within the genomes of their bacterial hosts. While numerous studies of the urogenital microbiota have focused on the most abundant bacterial member of this niche-Lactobacillus species-very little is known about Lactobacillus phages. Focusing on Lactobacillus jensenii strains from the urinary tract, we identified numerous prophages related to the previously characterized Lv-1 phage from a vaginal L. jensenii strain. Furthermore, we identified a new L. jensenii phage, Lu-1. Evidence suggests that both phages are abundant within the urogenital tract. CRISPR spacer sequences matching to Lv-1 and Lu-1 prophages were identified. While first detected in urinary isolates, the Lu-1 phage was also discovered in L. jensenii isolates from vaginal and perineal swabs, and both phages were found in metagenomic data sets. The prevalence of these phages in the isolates suggests that both phages are active members of the urogenital microbiota.}, } @article {pmid32524948, year = {2020}, author = {Hinterwirth, A and Sié, A and Coulibaly, B and Ouermi, L and Dah, C and Tapsoba, C and Zhong, L and Chen, C and Lietman, TM and Keenan, JD and Doan, T and Oldenburg, CE}, title = {Rapid Reduction of Campylobacter Species in the Gut Microbiome of Preschool Children after Oral Azithromycin: A Randomized Controlled Trial.}, journal = {The American journal of tropical medicine and hygiene}, volume = {103}, number = {3}, pages = {1266-1269}, pmid = {32524948}, issn = {1476-1645}, support = {R25 MH083620/MH/NIMH NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*therapeutic use ; Azithromycin/*therapeutic use ; Burkina Faso/epidemiology ; Campylobacter/genetics/*isolation & purification ; Campylobacter Infections/epidemiology/microbiology/*mortality ; Child Mortality ; Child, Preschool ; *Gastrointestinal Microbiome ; Humans ; Infant ; Metagenomics ; Sequence Analysis, DNA ; }, abstract = {Campylobacter has emerged as a potential important cause of childhood morbidity in sub-Saharan Africa. Biannual mass azithromycin distribution has previously been shown to reduce all-cause child mortality in sub-Saharan Africa. We conducted a randomized controlled trial in Burkina Faso in which children were randomized in a 1:1 fashion to a 5-day course of azithromycin or placebo to investigate the effect of oral antibiotics on the gut microbiome. We evaluated the changes in the gut microbiome of preschool children treated with azithromycin using metagenomic DNA sequencing. We found that three Campylobacter species were reduced with azithromycin treatment compared with placebo. These results were consistent with other studies that have shown decreases in Campylobacter species after azithromycin treatment, generating the hypothesis that a decrease in Campylobacter may contribute to observations of reduction in mortality following azithromycin distribution.}, } @article {pmid32524177, year = {2020}, author = {Dekaboruah, E and Suryavanshi, MV and Chettri, D and Verma, AK}, title = {Human microbiome: an academic update on human body site specific surveillance and its possible role.}, journal = {Archives of microbiology}, volume = {202}, number = {8}, pages = {2147-2167}, pmid = {32524177}, issn = {1432-072X}, mesh = {Computational Biology/*trends ; Disease ; *Human Body ; Humans ; Microbiota/*physiology ; }, abstract = {Human body is inhabited by vast number of microorganisms which form a complex ecological community and influence the human physiology, in the aspect of both health and diseases. These microbes show a relationship with the human immune system based on coevolution and, therefore, have a tremendous potential to contribute to the metabolic function, protection against the pathogen and in providing nutrients and energy. However, of these microbes, many carry out some functions that play a crucial role in the host physiology and may even cause diseases. The introduction of new molecular technologies such as transcriptomics, metagenomics and metabolomics has contributed to the upliftment on the findings of the microbiome linked to the humans in the recent past. These rapidly developing technologies are boosting our capacity to understand about the human body-associated microbiome and its association with the human health. The highlights of this review are inclusion of how to derive microbiome data and the interaction between human and associated microbiome to provide an insight on the role played by the microbiome in biological processes of the human body as well as the development of major human diseases.}, } @article {pmid32522967, year = {2020}, author = {MsangoSoko, K and Gandotra, S and Chandel, RK and Sharma, K and Ramakrishinan, B and Subramanian, S}, title = {Composition and Diversity of Gut Bacteria Associated with the Eri Silk Moth, Samia ricini, (Lepidoptera: Saturniidae) as Revealed by Culture-Dependent and Metagenomics Analysis.}, journal = {Journal of microbiology and biotechnology}, volume = {30}, number = {9}, pages = {1367-1378}, pmid = {32522967}, issn = {1738-8872}, mesh = {Animals ; Bacteria, Aerobic/isolation & purification/metabolism ; Bacteria, Anaerobic/isolation & purification/metabolism ; Bombyx/*metabolism/*microbiology ; Colony Count, Microbial ; DNA, Bacterial/genetics/isolation & purification ; Firmicutes/isolation & purification/metabolism ; *Gastrointestinal Microbiome ; Larva/metabolism/microbiology ; *Metagenomics ; Phylogeny ; Proteobacteria/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics/*isolation & purification ; }, abstract = {The polyphagous eri silk moth, Samia ricini, is associated with various symbiotic gut bacteria believed to provide several benefits to the host. The larvae of S. ricini were subjected to isolation of gut bacteria using culture-dependent 16S rRNA generic characterization, metagenomics analysis and qualitative enzymatic assays. Sixty culturable aerobic gut bacterial isolates comprising Firmicutes (54%) and Proteobacteria (46%); and twelve culturable facultative anaerobic bacteria comprising Proteobacteria (92%) and Firmicutes (8%) were identified inhabiting the gut of S. ricini. The results of metagenomics analysis revealed the presence of a diverse community of both culturable and un-culturable gut bacteria belonging to Proteobacteria (60%) and Firmicutes (20%) associated with seven orders. An analysis of the results of culturable isolation indicates that these bacterial isolates inhabited all the three compartments of the gut. Investigation on persistence of bacteria coupled with metagenomics analysis of the fifth instar suggested that bacteria persist in the gut across the different instar stages. In addition, enzymatic assays indicated that 48 and 75% of culturable aerobic, and 75% of anaerobic gut bacterial isolates had cellulolytic, lipolytic and nitrate reductase activities, thus suggesting that they may be involved in food digestion and nutritional provision to the host. These bacterial isolates may be good sources for profiling novel genes and biomolecules for biotechnological application.}, } @article {pmid32522544, year = {2020}, author = {Xu, M and Mo, X and Huang, H and Chen, X and Liu, H and Peng, Z and Chen, L and Rong, S and Yang, W and Xu, S and Liu, L}, title = {Yeast β-glucan alleviates cognitive deficit by regulating gut microbiota and metabolites in Aβ1-42-induced AD-like mice.}, journal = {International journal of biological macromolecules}, volume = {161}, number = {}, pages = {258-270}, doi = {10.1016/j.ijbiomac.2020.05.180}, pmid = {32522544}, issn = {1879-0003}, mesh = {Alzheimer Disease/etiology/metabolism/pathology ; Amyloid beta-Peptides/*adverse effects ; Animals ; Biomarkers ; Cognition/*drug effects ; Disease Models, Animal ; Fungal Polysaccharides/*chemistry/pharmacology ; Gastrointestinal Microbiome/*drug effects ; Hippocampus/metabolism ; Insulin/metabolism ; Male ; Metagenome ; Metagenomics ; Mice ; Peptide Fragments/*adverse effects ; Prebiotics ; RNA, Ribosomal, 16S ; beta-Glucans/*chemistry/pharmacology ; }, abstract = {Alzheimer's disease (AD) is a neurodegenerative disease that remarkably imposes a huge global public health burden. Yeast β-glucans have been incorporated in functional foods and used in prophylactic applications owing to their biological effects. However, few studies had investigated the effects of yeast β-glucans on neurodegenerative diseases. Here, gut microbiota and metabolites SCFAs were analyzed through high-throughput 16S rRNA gene sequencing and GC-MS, respectively. Results indicated that yeast β-glucans could prominently shape the intestinal flora and produce SCFAs. Aβ1-42-induced AD mice treated with small-molecular yeast β-glucan (S-β-Glu) or macro-molecular yeast β-glucan (M-β-Glu) exhibited evident alterations of the composition of the gut microbiota, especially in some beneficial bacteria and inflammatory-related bacteria such as Lactobacillus, Bifidobacterium, Desulfovibrio, Oscillibacter, Mucispirillum, Alistipes, Anaerotruncus, and Rikenella. M-β-Glu regulated gut microbiota act as prebiotics better than S-β-Glu. Correlation analysis demonstrated the key microbiota closely associated with AD-related pathologies and cognition. Moreover, M-β-Glu and S-β-Glu ameliorated neuroinflammation and brain insulin resistance (IR), which played a central role in the process of AD pathology. This study broadened the underlying applications of yeast β-glucans as a novel dietary supplementation to prevent early-stage pathologies associated with AD by regulating gut microbiota and the potential mechanism might be ameliorating brain IR.}, } @article {pmid32521370, year = {2020}, author = {Kang, X and Cui, Y and Shen, T and Yan, M and Tu, W and Shoaib, M and Xiang, Q and Zhao, K and Gu, Y and Chen, Q and Li, S and Liang, Y and Ma, M and Zou, L and Yu, X}, title = {Changes of root microbial populations of natively grown plants during natural attenuation of V-Ti magnetite tailings.}, journal = {Ecotoxicology and environmental safety}, volume = {201}, number = {}, pages = {110816}, doi = {10.1016/j.ecoenv.2020.110816}, pmid = {32521370}, issn = {1090-2414}, mesh = {Biodegradation, Environmental ; China ; Ferrosoferric Oxide/analysis/*toxicity ; Metagenomics ; Microbiota/*drug effects/genetics ; Mining ; Plant Roots/*microbiology ; Poaceae/growth & development/microbiology ; Rhizobium ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/analysis/*toxicity ; Titanium/analysis/*toxicity ; Typhaceae/growth & development/microbiology ; Vanadium/analysis/*toxicity ; }, abstract = {Mine tailings contain dangerously high levels of toxic metals which pose a constant threat to local ecosystems. Few naturally grown native plants can colonize tailings site and the existence of their root-associated microbial populations is poorly understood. The objective of this study was to give further insights into the interactions between native plants and their microbiota during natural attenuation of abandoned V-Ti magnetite mine tailings. In the present work, we first examined the native plants' potential for phytoremediation using plant/soil analytical methods and then investigated the root microbial communities and their inferred functions using 16 S rRNA-based metagenomics. It was found that in V-Ti magnetite mine tailings the two dominant plants Bothriochloa ischaemum and Typha angustifolia were able to increase available nitrogen in the rhizosphere soil by 23.3% and 53.7% respectively. The translocation factors (TF) for both plants indicated that B. ischaemum was able to accumulate Pb (TF = 1.212), while T. angustifolia was an accumulator of Mn (TF = 2.502). The microbial community structure was more complex in the soil associated with T. angustifolia than with B. ischaemum. The presence of both plants significantly reduced the population of Acinetobacter. Specifically, B. ischaemum enriched Massilia, Opitutus and Hydrogenophaga species while T. angustifolia significantly increased rhizobia species. Multivariate analyses revealed that among all tested soil variables Fe and total organic carbon (TOC) could be the key factors in shaping the microbial structure. The putative functional analysis indicated that soil sample of B. ischaemum was abundant with nitrate/nitrite reduction-related functions while that of T. angustifolia was rich in nitrogen fixing functions. The results indicate that these native plants host a diverse range of soil microbes, whose community structure can be shaped by plant types and soil variables. It is also possible that these plants can be used to improve soil nitrogen content and serve as bioaccumulators for Pb or Mn for phytoremediation purposes.}, } @article {pmid32520351, year = {2020}, author = {Reddington, K and Eccles, D and O'Grady, J and Drown, DM and Hansen, LH and Nielsen, TK and Ducluzeau, AL and Leggett, RM and Heavens, D and Peel, N and Snutch, TP and Bayega, A and Oikonomopoulos, S and Ragoussis, I and Barry, T and van der Helm, E and Jolic, D and Richardson, H and Jansen, H and Tyson, JR and Jain, M and Brown, BL}, title = {Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function.}, journal = {GigaScience}, volume = {9}, number = {6}, pages = {}, pmid = {32520351}, issn = {2047-217X}, support = {BB/M011216/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; TL4 GM118992/GM/NIGMS NIH HHS/United States ; UL1 GM118991/GM/NIGMS NIH HHS/United States ; RL5 GM118990/GM/NIGMS NIH HHS/United States ; BB/J004669/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CSP17270/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; P20 GM103395/GM/NIGMS NIH HHS/United States ; 10677//CIHR/Canada ; MR/N013956/1/MRC_/Medical Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biodiversity ; *Metagenome ; Metagenomics/*methods ; *Microbial Consortia ; *Microbiota ; Nanopore Sequencing ; Plankton/*genetics ; Rivers/microbiology ; Water Microbiology ; }, abstract = {BACKGROUND: Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments. Because rivers are used extensively for anthropogenic purposes (drinking water, recreation, agriculture, and industry), it is essential to understand how these activities affect the composition of river microbial consortia. Recent studies have shown that river metagenomes vary considerably, suggesting that microbial community data should be included in broad-scale river ecosystem models. But such ecogenomic studies have not been applied on a broad "aquascape" scale, and few if any have applied the newest nanopore technology.

RESULTS: We investigated the metagenomes of 11 rivers across 3 continents using MinION nanopore sequencing, a portable platform that could be useful for future global river monitoring. Up to 10 Gb of data per run were generated with average read lengths of 3.4 kb. Diversity and diagnosis of river function potential was accomplished with 0.5-1.0 ⋅ 106 long reads. Our observations for 7 of the 11 rivers conformed to other river-omic findings, and we exposed previously unrecognized microbial biodiversity in the other 4 rivers.

CONCLUSIONS: Deeper understanding that emerged is that river microbial consortia and the ecological functions they fulfil did not align with geographic location but instead implicated ecological responses of microbes to urban and other anthropogenic effects, and that changes in taxa manifested over a very short geographic space.}, } @article {pmid32519942, year = {2020}, author = {François, S and Pybus, OG}, title = {Towards an understanding of the avian virome.}, journal = {The Journal of general virology}, volume = {101}, number = {8}, pages = {785-790}, pmid = {32519942}, issn = {1465-2099}, support = {BB/T008806/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Animals, Wild/virology ; Birds/*virology ; Genome, Viral/genetics ; Humans ; Poultry Diseases/virology ; Virome/*genetics ; Virus Diseases/virology ; }, abstract = {The last two decades have seen the rise of viromics, the study of viral communities through the detection and characterization of virus genome sequences. Here we systematically review and summarize the scope and limitations of our current understanding of avian viromes, in both domesticated and wild-bird populations. We compare this viromic work to the broader literature on avian prokaryotic microbiomes, and highlight the growing importance of structured sampling and experimental design for testing explanatory hypotheses. We provide a number of recommendations for sample collection and preliminary data analysis to guide the development of avian viromics. Avian viromes have the potential to inform disease surveillance in poultry and improve our understanding of the risk of zoonotic viruses to human health.}, } @article {pmid32519746, year = {2020}, author = {Su, X and Zhao, Y and Li, Y and Ma, S and Wang, Z}, title = {Gut dysbiosis is associated with primary hypothyroidism with interaction on gut-thyroid axis.}, journal = {Clinical science (London, England : 1979)}, volume = {134}, number = {12}, pages = {1521-1535}, doi = {10.1042/CS20200475}, pmid = {32519746}, issn = {1470-8736}, mesh = {Adult ; Animals ; Case-Control Studies ; Dysbiosis/*complications ; Fatty Acids/metabolism ; Fecal Microbiota Transplantation ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*pathology ; Humans ; Hypothyroidism/*complications ; Male ; Metagenomics ; Mice, Inbred BALB C ; Phylogeny ; ROC Curve ; Thyroid Gland/*pathology ; }, abstract = {Background Previous studies have shown that the gut microbiome is associated with thyroid diseases, including Graves' disease, Hashimoto's disease, thyroid nodules, and thyroid cancer. However, the association between intestinal flora and primary hypothyroidism remains elusive. We aimed to characterize gut microbiome in primary hypothyroidism patients. Methods Fifty-two primary hypothyroidism patients and 40 healthy controls were recruited. The differences in gut microbiota between the two groups were analyzed by 16S rRNA sequencing technology. Fecal microbiota transplantation (FMT) was performed in mice using flora from both groups; changes in thyroid function were then assessed in the mice. Results There were significant differences in α and β diversities of gut microbiota between primary hypothyroidism patients and healthy individuals. The random forest analysis indicated that four intestinal bacteria (Veillonella, Paraprevotella, Neisseria, and Rheinheimera) could distinguish untreated primary hypothyroidism patients from healthy individuals with the highest accuracy; this was confirmed by receiver operator characteristic curve analysis. The short chain fatty acid producing ability of the primary hypothyroidism patients' gut was significantly decreased, which resulted in the increased serum lipopolysaccharide (LPS) levels. The FMT showed that mice receiving the transplant from primary hypothyroidism patients displayed decreased total thyroxine levels. Conclusions Our study suggests that primary hypothyroidism causes changes in gut microbiome. In turn, an altered flora can affect thyroid function in mice. These findings could help understand the development of primary hypothyroidism and might be further used to develop potential probiotics to facilitate the adjuvant treatment of this disease.}, } @article {pmid32518820, year = {2020}, author = {Ganesan, SM and Dabdoub, SM and Nagaraja, HN and Scott, ML and Pamulapati, S and Berman, ML and Shields, PG and Wewers, ME and Kumar, PS}, title = {Adverse effects of electronic cigarettes on the disease-naive oral microbiome.}, journal = {Science advances}, volume = {6}, number = {22}, pages = {eaaz0108}, pmid = {32518820}, issn = {2375-2548}, support = {R01 DE027857/DE/NIDCR NIH HHS/United States ; }, mesh = {*Electronic Nicotine Delivery Systems ; Humans ; *Microbiota ; Smoking ; *Tobacco Products/adverse effects ; United States ; *Volatile Organic Compounds ; }, abstract = {Six percent of Americans, including 3 million high schoolers, use e-cigarettes, which contain potentially toxic substances, volatile organic compounds, and metals. We present the first human study on the effects of e-cigarette exposure in the oral cavity. By interrogating both immunoinflammatory responses and microbial functional dynamics, we discovered pathogen overrepresentation, higher virulence signatures, and a brisk proinflammatory signal in clinically healthy e-cigarette users, equivalent to patients with severe periodontitis. Using RNA sequencing and confocal and electron microscopy to validate these findings, we demonstrate that the carbon-rich glycol/glycerol vehicle is an important catalyst in transforming biofilm architecture within 24 hours of exposure. Last, a machine-learning classifier trained on the metagenomic signatures of e-cigarettes identified as e-cigarette users both those individuals who used e-cigarettes to quit smoking, and those who use both e-cigarettes and cigarettes. The present study questions the safety of e-cigarettes and the harm reduction narrative promoted by advertising campaigns.}, } @article {pmid32518251, year = {2020}, author = {Bovo, S and Utzeri, VJ and Ribani, A and Cabbri, R and Fontanesi, L}, title = {Shotgun sequencing of honey DNA can describe honey bee derived environmental signatures and the honey bee hologenome complexity.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {9279}, pmid = {32518251}, issn = {2045-2322}, mesh = {Animals ; Bacteria/genetics ; Bees ; DNA, Environmental/*analysis/genetics ; Gastrointestinal Microbiome/genetics ; Genome, Bacterial/genetics ; Genome, Fungal/genetics ; Genome, Plant/genetics ; Genome, Protozoan/genetics ; Genome, Viral/genetics ; Honey/*analysis ; *Metagenomics ; Sequence Analysis, DNA ; }, abstract = {Honey bees are large-scale monitoring tools due to their extensive environmental exploration. In their activities and from the hive ecosystem complex, they get in close contact with many organisms whose traces can be transferred into the honey, which can represent an interesting reservoir of environmental DNA (eDNA) signatures and information useful to analyse the honey bee hologenome complexity. In this study, we tested a deep shotgun sequencing approach of honey DNA coupled with a specifically adapted bioinformatic pipeline. This methodology was applied to a few honey samples pointing out DNA sequences from 191 organisms spanning different kingdoms or phyla (viruses, bacteria, plants, fungi, protozoans, arthropods, mammals). Bacteria included the largest number of species. These multi-kingdom signatures listed common hive and honey bee gut microorganisms, honey bee pathogens, parasites and pests, which resembled a complex interplay that might provide a general picture of the honey bee pathosphere. Based on the Apis mellifera filamentous virus genome diversity (the most abundant detected DNA source) we obtained information that could define the origin of the honey at the apiary level. Mining Apis mellifera sequences made it possible to identify the honey bee subspecies both at the mitochondrial and nuclear genome levels.}, } @article {pmid32516966, year = {2020}, author = {Tilocca, B and Pieroni, L and Soggiu, A and Britti, D and Bonizzi, L and Roncada, P and Greco, V}, title = {Gut-Brain Axis and Neurodegeneration: State-of-the-Art of Meta-Omics Sciences for Microbiota Characterization.}, journal = {International journal of molecular sciences}, volume = {21}, number = {11}, pages = {}, pmid = {32516966}, issn = {1422-0067}, mesh = {Animals ; Brain/*physiology ; *Disease Susceptibility ; *Feedback, Physiological ; Gastrointestinal Tract/*physiology ; Genomics/methods ; Humans ; Metabolomics/methods ; Metagenomics/methods ; Microbiota ; Neurodegenerative Diseases/*etiology/*metabolism ; Proteomics/methods ; }, abstract = {Recent advances in the field of meta-omics sciences and related bioinformatics tools have allowed a comprehensive investigation of human-associated microbiota and its contribution to achieving and maintaining the homeostatic balance. Bioactive compounds from the microbial community harboring the human gut are involved in a finely tuned network of interconnections with the host, orchestrating a wide variety of physiological processes. These includes the bi-directional crosstalk between the central nervous system, the enteric nervous system, and the gastrointestinal tract (i.e., gut-brain axis). The increasing accumulation of evidence suggest a pivotal role of the composition and activity of the gut microbiota in neurodegeneration. In the present review we aim to provide an overview of the state-of-the-art of meta-omics sciences including metagenomics for the study of microbial genomes and taxa strains, metatranscriptomics for gene expression, metaproteomics and metabolomics to identify and/or quantify microbial proteins and metabolites, respectively. The potential and limitations of each discipline were highlighted, as well as the advantages of an integrated approach (multi-omics) to predict microbial functions and molecular mechanisms related to human diseases. Particular emphasis is given to the latest results obtained with these approaches in an attempt to elucidate the link between the gut microbiota and the most common neurodegenerative diseases, such as multiple sclerosis (MS), Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS).}, } @article {pmid32514171, year = {2020}, author = {Chng, KR and Li, C and Bertrand, D and Ng, AHQ and Kwah, JS and Low, HM and Tong, C and Natrajan, M and Zhang, MH and Xu, L and Ko, KKK and Ho, EXP and Av-Shalom, TV and Teo, JWP and Khor, CC and , and Chen, SL and Mason, CE and Ng, OT and Marimuthu, K and Ang, B and Nagarajan, N}, title = {Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment.}, journal = {Nature medicine}, volume = {26}, number = {6}, pages = {941-951}, pmid = {32514171}, issn = {1546-170X}, support = {MR/L01341X/1/MRC_/Medical Research Council/United Kingdom ; MR/S019669/1/MRC_/Medical Research Council/United Kingdom ; MR/S020810/1/MRC_/Medical Research Council/United Kingdom ; MR/S020810/2/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Beds/microbiology ; Biofilms ; Cross Infection/drug therapy/*microbiology/transmission ; Disinfection ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Equipment Contamination ; Equipment and Supplies, Hospital/*microbiology ; Geographic Mapping ; Humans ; *Infection Control ; Metagenomics ; Microbiota/*genetics ; Opportunistic Infections/drug therapy/microbiology/transmission ; Patients' Rooms ; Singapore ; Spatio-Temporal Analysis ; Tertiary Care Centers ; }, abstract = {Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections.}, } @article {pmid32513234, year = {2020}, author = {Karcher, N and Pasolli, E and Asnicar, F and Huang, KD and Tett, A and Manara, S and Armanini, F and Bain, D and Duncan, SH and Louis, P and Zolfo, M and Manghi, P and Valles-Colomer, M and Raffaetà, R and Rota-Stabelli, O and Collado, MC and Zeller, G and Falush, D and Maixner, F and Walker, AW and Huttenhower, C and Segata, N}, title = {Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {138}, pmid = {32513234}, issn = {1474-760X}, support = {U54 DE023798/DE/NIDCR NIH HHS/United States ; R01 HG005220/HG/NHGRI NIH HHS/United States ; U01 CA230551/CA/NCI NIH HHS/United States ; R01 CA230551/CA/NCI NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Carbohydrate Metabolism/genetics ; Child ; Child, Preschool ; Eubacterium/*genetics ; *Gastrointestinal Microbiome ; *Genome, Bacterial ; Glycosyltransferases/genetics ; Humans ; Infant ; Metagenome ; Middle Aged ; Phylogeography ; Young Adult ; }, abstract = {BACKGROUND: Eubacterium rectale is one of the most prevalent human gut bacteria, but its diversity and population genetics are not well understood because large-scale whole-genome investigations of this microbe have not been carried out.

RESULTS: Here, we leverage metagenomic assembly followed by a reference-based binning strategy to screen over 6500 gut metagenomes spanning geography and lifestyle and reconstruct over 1300 E. rectale high-quality genomes from metagenomes. We extend previous results of biogeographic stratification, identifying a new subspecies predominantly found in African individuals and showing that closely related non-human primates do not harbor E. rectale. Comparison of pairwise genetic and geographic distances between subspecies suggests that isolation by distance and co-dispersal with human populations might have contributed to shaping the contemporary population structure of E. rectale. We confirm that a relatively recently diverged E. rectale subspecies specific to Europe consistently lacks motility operons and that it is immotile in vitro, probably due to ancestral genetic loss. The same subspecies exhibits expansion of its carbohydrate metabolism gene repertoire including the acquisition of a genomic island strongly enriched in glycosyltransferase genes involved in exopolysaccharide synthesis.

CONCLUSIONS: Our study provides new insights into the population structure and ecology of E. rectale and shows that shotgun metagenomes can enable population genomics studies of microbiota members at a resolution and scale previously attainable only by extensive isolate sequencing.}, } @article {pmid32512689, year = {2020}, author = {Iizuka, K and Yabe, D}, title = {The Role of Metagenomics in Precision Nutrition.}, journal = {Nutrients}, volume = {12}, number = {6}, pages = {}, pmid = {32512689}, issn = {2072-6643}, support = {20K11645//Japan Society for the Promotion of Science/ ; 19-049//Suzuken Memorial Foundation/ ; }, mesh = {Gastrointestinal Microbiome ; Humans ; *Metagenomics ; *Nutrigenomics ; *Nutrition Policy ; *Nutritional Status ; *Precision Medicine ; }, abstract = {Conventional recommendations for dietary intervention have been generally based on population groups divided by gender and age [...].}, } @article {pmid32512648, year = {2020}, author = {Sureshkumar, S and Jung, SK and Kim, D and Oh, KB and Yang, H and Lee, HC and Jo, YJ and Lee, HS and Lee, S and Byun, SJ}, title = {Administration of L. salivarius expressing 3D8 scFv as a feed additive improved the growth performance, immune homeostasis, and gut microbiota of chickens.}, journal = {Animal science journal = Nihon chikusan Gakkaiho}, volume = {91}, number = {1}, pages = {e13399}, doi = {10.1111/asj.13399}, pmid = {32512648}, issn = {1740-0929}, support = {PJ01328303//Cooperative Research Program for Agriculture Science & Technology Development of the Rural Development Administration, Republic of Korea/International ; }, mesh = {*Animal Feed ; *Animal Nutritional Physiological Phenomena ; Animals ; Chickens/*growth & development/*immunology/*microbiology ; Cytokines/blood ; Diet/*veterinary ; *Dietary Supplements ; Female ; *Gastrointestinal Microbiome ; *Homeostasis ; *Ligilactobacillus salivarius ; Single-Chain Antibodies/*administration & dosage ; }, abstract = {Probiotics have been defined as live microorganisms that are administered in an appropriate amount to provide health benefits to the host animal. In this study, we investigated the effect of L. salivarius DJ-sa-01 secreting the 3D8 single-chain variable fragment (3D8 scFv) on the growth performance, cytokine secretion, and intestinal microbial flora of chickens. The experiment was divided into the control group and L. salivarius expressing 3D8 scFv experimental group. Chicken was fed 10[9] colony-forming units (CFUs) of wild-type (WT) L. salivarius or 3D8 scFv-secreting L. salivarius daily for 35 days. The administration of L. salivarius expressing 3D8 scFv significantly improved the body weight of chickens compared with the administration of WT L. salivarius. A 16S ribosomal RNA metagenomic analysis showed that Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla in both experimental groups. At the genus level, Lactobacillus was more abundant (22.82%) in the L. salivarius/3D8 group compared with the WT L. salivarius group. The serum levels of cytokines, such as IL-8, TNF-α, IL-1β, IFN-γ, IL-4, and IGF1, were significantly reduced in the L. salivarius/3D8-treated chickens. In summary, our results suggest that L. salivarius expressing 3D8 scFv could be considered a feed additive for improving the growth performance, immune function, and disease resistance of poultry.}, } @article {pmid32512428, year = {2020}, author = {Estrella-González, MJ and Suárez-Estrella, F and Jurado, MM and López, MJ and López-González, JA and Siles-Castellano, AB and Muñoz-Mérida, A and Moreno, J}, title = {Uncovering new indicators to predict stability, maturity and biodiversity of compost on an industrial scale.}, journal = {Bioresource technology}, volume = {313}, number = {}, pages = {123557}, doi = {10.1016/j.biortech.2020.123557}, pmid = {32512428}, issn = {1873-2976}, mesh = {Biodiversity ; *Composting ; Soil ; }, abstract = {Currently, the metagenomic study of the composting process has gained great importance since it has allowed the identification of the existence of microorganisms that, until now, had not been isolated during the process by traditional techniques. However, it is still complex to determine which bioindicators could reveal the degree of maturity and stability of a particular compost. Thereby, the main objective of this work was to demonstrate the possible correlation between traditional parameters of maturity and stability of compost, with other indicators of biodiversity in products highly heterogeneous from composting processes on an industrial scale. The results demonstrated the enormous influence of the raw materials in characterizing the products obtained. Even so, important relationships were established between the Chao1 and Shannon indexes, and certain parameters related to the maturity, stability and toxicity of the samples, such as nitrification index, humification rate, phenolic content, germination index or oxygen consumption.}, } @article {pmid32508155, year = {2020}, author = {Mercer, KE and Yeruva, L and Pack, L and Graham, JL and Stanhope, KL and Chintapalli, SV and Wankhade, UD and Shankar, K and Havel, PJ and Adams, SH and Piccolo, BD}, title = {Xenometabolite signatures in the UC Davis type 2 diabetes mellitus rat model revealed using a metabolomics platform enriched with microbe-derived metabolites.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {319}, number = {2}, pages = {G157-G169}, pmid = {32508155}, issn = {1522-1547}, support = {RC1DK087307//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/International ; 6026-51000-010-05S//U.S. Department of Agriculture (USDA)/International ; R01 HL121324/HL/NHLBI NIH HHS/United States ; R01HL107256//HHS | NIH | National Heart, Lung, and Blood Institute (NHBLI)/International ; R01DK095060//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/International ; U24DK092933//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/International ; R01HL091333//HHS | NIH | National Heart, Lung, and Blood Institute (NHBLI)/International ; RO1HL121324//HHS | NIH | National Heart, Lung, and Blood Institute (NHBLI)/International ; }, mesh = {Animals ; Bacteria/classification/isolation & purification ; Cecum/microbiology ; Diabetes Mellitus, Type 2/*metabolism ; Gastrointestinal Microbiome/*physiology ; Male ; Metabolic Networks and Pathways ; *Metabolomics ; Rats ; Rats, Sprague-Dawley ; }, abstract = {The gut microbiome has the potential to create or modify xenometabolites (i.e., nonhost-derived metabolites) through de novo synthesis or modification of exogenous and endogenous compounds. While there are isolated examples of xenometabolites influencing host health and disease, wide-scale characterization of these metabolites remains limited. We developed a metabolomics platform ("XenoScan") using liquid chromatography-mass spectrometry to characterize a range of known and suspected xenometabolites and their derivatives. This assay currently applies authentic standards for 190 molecules, enriched for metabolites of microbial origin. As a proof-of-principle, we characterized the cecal content xenometabolomics profile in adult male lean Sprague-Dawley (LSD) and University of California, Davis type 2 diabetes mellitus (UCD-T2DM) rats at different stages of diabetes. These results were correlated to specific bacterial species generated via shotgun metagenomic sequencing. UCD-T2DM rats had a unique xenometabolite profile compared with LSD rats, regardless of diabetes status, suggesting that at least some of the variation is associated with host genetics. Furthermore, modeling approaches revealed that several xenometabolites discriminated UCD-T2DM rats at early stages of diabetes versus those at 3 mo postdiabetes onset. Several xenometabolite hubs correlated with specific bacterial species in both LSD and UCD-T2DM rats. For example, indole-3-propionic acid negatively correlated with species within the Oscillibacter genus in UCD-T2DM rats considered to be prediabetic or recently diagnosed diabetic, in contrast to gluconic acid and trimethylamine, which were positively correlated with Oscillibacter species. The application of a xenometabolite-enriched metabolomics assay in relevant milieus will enable rapid identification of a wide variety of gut-derived metabolites, their derivatives, and their potential biochemical origins of xenometabolites in relationship to host gastrointestinal microbial ecology.NEW & NOTEWORTHY We debut a liquid chromatography-mass spectrometry (LC/MS) platform called the XenoScan, which is a metabolomics platform for xenometabolites (nonself-originating metabolites). This assay has 190 in-house standards with the majority enriched for microbe-derived metabolites. As a proof-of-principle, we used the XenoScan to discriminate genetic differences from cecal samples associated with different rat lineages, in addition to characterizing diabetes progression in rat model of type 2 diabetes. Complementing microbial sequencing data with xenometabolites uncovered novel microbial metabolism in targeted organisms.}, } @article {pmid32506557, year = {2020}, author = {Chiu, CY and Chou, HC and Chang, LC and Fan, WL and Dinh, MCV and Kuo, YL and Chung, WH and Lai, HC and Hsieh, WP and Su, SC}, title = {Integration of metagenomics-metabolomics reveals specific signatures and functions of airway microbiota in mite-sensitized childhood asthma.}, journal = {Allergy}, volume = {75}, number = {11}, pages = {2846-2857}, doi = {10.1111/all.14438}, pmid = {32506557}, issn = {1398-9995}, mesh = {Animals ; *Asthma/diagnosis ; Child ; Humans ; Metabolomics ; Metagenomics ; *Microbiota ; *Mites ; Prevotella ; }, abstract = {BACKGROUND: Childhood asthma is a multifactorial inflammatory condition of the airways, associated with specific changes in respiratory microbiome and circulating metabolome.

METHODS: To explore the functional capacity of asthmatic microbiome and its intricate connection with the host, we performed shotgun sequencing of airway microbiome and untargeted metabolomics profiling of serum samples in a cohort of children with mite-sensitized asthma and non-asthmatic controls.

RESULTS: We observed higher gene counts and sample-to-sample dissimilarities in asthmatic microbiomes, indicating a more heterogeneous community structure and functionality among the cases than in controls. Moreover, we identified airway microbial species linked to changes in circulating metabolites and IgE responses of the host, including a positive correlation between Prevotella sp oral taxon 306 and dimethylglycine that were both decreased in patients. Several control-enriched species (Eubacterium sulci, Prevotella pallens, and Prevotella sp oral taxon 306) were inversely correlated with total and allergen-specific IgE levels. Genes related to microbial carbohydrate, amino acid, and lipid metabolism were differentially enriched, suggesting that changes in microbial metabolism may contribute to respiratory health in asthmatics. Pathway modules relevant to allergic responses were differentially abundant in asthmatic microbiome, such as enrichments for biofilm formation by Pseudomonas aeruginosa, membrane trafficking, histidine metabolism, and glycosaminoglycan degradation, and depletions for polycyclic aromatic hydrocarbon degradation. Further, we identified metagenomic and metabolomic markers (eg, Eubacterium sulci) to discriminate cases from the non-asthmatic controls.

CONCLUSIONS: Our dual-omics data reveal the connections between respiratory microbes and circulating metabolites perturbed in mite-sensitized pediatric asthma, which may be of etiological and diagnostic implications.}, } @article {pmid32506266, year = {2020}, author = {Kang, Y and Wan, C and Lu, S and Fu, Z and Chen, AK and Lu, Z}, title = {A new metagenome binning method based on gene uniqueness.}, journal = {Genes & genomics}, volume = {42}, number = {8}, pages = {883-892}, doi = {10.1007/s13258-020-00956-2}, pmid = {32506266}, issn = {2092-9293}, mesh = {Algorithms ; Cluster Analysis ; DNA Barcoding, Taxonomic/methods ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/*genetics ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The human gut microbiome contains millions of genes and many undetected bacteria species. Recovering bacterial genomes from large complex metagenomes remains highly challenging, and current binning methods show insufficient recall rates.

OBJECTIVE: This study was performed to put forward a new metagenome binning method with promising recall rate and accuracy.

METHODS: We found that more than 85% of the genes could be aligned to only one bacteria species by using strict BLAST parameters (identity > 90% and aligning length > 100 bp). This phenomenon was called "the gene uniqueness", which indicated that the most bacterial genes could be exclusive to the species' taxonomy. In our new metagenome binning method, we could cluster contigs based on gene similarity via a graph model. Any contig shared with same gene under Strict Blast parameters would be clustered into one bin.

RESULTS: we obtained 1,131 bins and reconstructed the genomes of 12 unknown species for MetaHIT data Our method exhibited a more promising recall rate, faster running speed and lower time complexity than the current methods.

CONCLUSIONS: The present new metagenome binning method based on gene uniqueness had high recall rate and low error, which could be applied to assemble the bacterial genomes efficiently in complex metagenome.}, } @article {pmid32505886, year = {2020}, author = {Wang, C and Wang, Y and Wang, Y and Cheung, KK and Ju, F and Xia, Y and Zhang, T}, title = {Genome-centric microbiome analysis reveals solid retention time (SRT)-shaped species interactions and niche differentiation in food waste and sludge co-digesters.}, journal = {Water research}, volume = {181}, number = {}, pages = {115858}, doi = {10.1016/j.watres.2020.115858}, pmid = {32505886}, issn = {1879-2448}, mesh = {Anaerobiosis ; Bioreactors ; Food ; Methane ; *Microbiota ; *Refuse Disposal ; Sewage ; }, abstract = {Co-digestion of food waste with sewage sludge is widely applied for waste stabilization and energy recovery around the world. However, the effect of solid retention time (SRT) on the microbial population dynamics, metabolism and interspecies interaction have not been fully elucidated. Here, the influence of SRTs (5-25 days) on the performance of the co-digestion system was investigated and state-of-the-art genome-centric metagenomic analysis was employed to uncover the dynamics and metabolic network of the key players underlying the well-functioned and poorly-functioned co-digestion microbial communities. The results of the microbial analyses indicated that SRT largely shaped microbial community structure by enriching the syntrophic specialist Syntrophomonas and CO2/H2 (formate)-using methanogen Methanocorpusculum in the well-functioned co-digester operated at SRT of 25 days, while selecting acid-tolerant populations Lactobacillus at SRT of 5 days. The metagenome assembled genomes (MAGs) of key players, such as Syntrophomonadaceae, Methanocorpusculum, and Mesotoga, were retrieved, additionally, the syntrophic acetate oxidation plus hydrogenotrophic methanogenesis (SAO-HM) were proposed as the dominant pathway for methane production. The metabolic interaction in the co-digestion microbial consortia was profiled by assigning MAGs into functional guilds. Functional redundancy was found in the bacterial groups in hydrolysis step, and the members in these groups reduced the direct competition by niche differentiation.}, } @article {pmid32505835, year = {2020}, author = {Wang, L and Liu, L and Liu, X and Xiang, M and Zhou, L and Huang, C and Shen, Z and Miao, L}, title = {The gut microbes, Enterococcus and Escherichia-Shigella, affect the responses of heart valve replacement patients to the anticoagulant warfarin.}, journal = {Pharmacological research}, volume = {159}, number = {}, pages = {104979}, doi = {10.1016/j.phrs.2020.104979}, pmid = {32505835}, issn = {1096-1186}, mesh = {Adult ; Aged ; Anticoagulants/adverse effects/*therapeutic use ; Blood Coagulation/*drug effects ; Enterococcus/genetics/metabolism/*physiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; *Heart Valve Prosthesis Implantation/adverse effects ; Hemorrhage/chemically induced/microbiology ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions ; Humans ; Intestines/*microbiology ; Male ; Metagenomics ; Middle Aged ; Ribotyping ; Shiga-Toxigenic Escherichia coli/genetics/metabolism/*physiology ; Thromboembolism/etiology/microbiology/*prevention & control ; Treatment Outcome ; Vitamin K 2/metabolism ; Warfarin/adverse effects/*therapeutic use ; }, abstract = {Numerous algorithms based on patient genetic variants have been established with the aim of reducing the risk of GI bleeding and thromboembolism during warfarin administration. However, approximately 35 % of individual warfarin sensitivity still remains unexplained. Few of warfarin algorithms take into account gut microbiota profiles. The identification of certain microbiome will provide new targets and new strategies for reducing the risk of bleeding and thromboembolism during warfarin administration. In this study, we collected plasma and stool samples from 200 inpatients undergoing heart valve replacement (HVR), which were classified as low responder (LR), high responder (HR) and normal responder (NR). Significant differences were observed in the diversity and relative abundance of the gut microbiota among the three groups. The genus Escherichia-Shigella was enriched significantly in the LRs (P = 3.189e[-11]), while the genus Enterococcus was enriched significantly in the HRs (P = 1.249e[-11]). The amount of VK2 synthesized by gut microbiota in LR group was much higher than that in HR group (P = 0.005). Whole genome shotgun sequencing indicated that the relative abundance of enzymes and modules associated with VK biosynthesis was significantly higher in LRs than in HRs or NRs. The 12 microbial markers were identified through tenfold cross-validation with a random forest model. The results provided a new microbial diagnostic model that can be used to inform modulation of warfarin dosage on the basis of patient intestinal flora composition.}, } @article {pmid32505584, year = {2021}, author = {Raita, Y and Toivonen, L and Schuez-Havupalo, L and Karppinen, S and Waris, M and Hoffman, KL and Camargo, CA and Peltola, V and Hasegawa, K}, title = {Maturation of nasal microbiota and antibiotic exposures during early childhood: a population-based cohort study.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {27}, number = {2}, pages = {283.e1-283.e7}, doi = {10.1016/j.cmi.2020.05.033}, pmid = {32505584}, issn = {1469-0691}, mesh = {Age Factors ; Anti-Bacterial Agents/*administration & dosage/pharmacology ; Bacteria/*classification/drug effects/genetics/isolation & purification ; Child, Preschool ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Finland ; Humans ; Infant ; Infant, Newborn ; Longitudinal Studies ; Male ; Microbiota/drug effects ; Neural Networks, Computer ; Nose/drug effects/*microbiology ; Phylogeny ; Prospective Studies ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {OBJECTIVES: Little is known about maturation of the airway microbiota during early childhood and the consequences of early-life antibiotic exposure.

METHODS: In a population-based birth cohort of 902 healthy Finnish children, we applied deep neural network models to investigate the relationship between the nasal microbiota (measured by 16S rRNA gene sequencing at up to three time points) and child age during the first 24 months. We also performed stratified analyses according to antibiotic exposure during the age period 0-2 months.

RESULTS: The dense deep neural network analysis successfully modelled the relationship between 232 bacterial genera and child age with a mean absolute error of 4.3 (95%CI 4.0-4.7) months. Similarly, the recurrent neural network analysis also successfully modelled the relationship between 215 genera and child age with a mean absolute error of 0.45 (95%CI 0.42-0.47) months. Among the genera, Staphylococcus spp. and members of the Corynebacteriaceae decreased with age, while Dolosigranulum and Moraxella increased with age in the first 2 years of life (all false discovery rate (FDR) = 0.001). In children without early-life antibiotic exposure, Dolosigranulum increased with age (FDR = 0.001). By contrast, in those with early-life antibiotic exposure, Haemophilus increased with age (FDR = 0.002).

CONCLUSIONS: In this prospective birth cohort of healthy children, we demonstrated the development of the nasal microbiota, with shifts in specific genera constituting maturation, in the first 2 years of life. Antibiotic exposures during early infancy were related to different age-discriminatory bacteria.}, } @article {pmid32504490, year = {2020}, author = {Kobayashi, R and Ogawa, Y and Hashizume-Takizawa, T and Kurita-Ochiai, T}, title = {Oral bacteria affect the gut microbiome and intestinal immunity.}, journal = {Pathogens and disease}, volume = {78}, number = {3}, pages = {}, doi = {10.1093/femspd/ftaa024}, pmid = {32504490}, issn = {2049-632X}, mesh = {Animals ; Dysbiosis/microbiology ; Feces ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Immunity ; Immunoglobulin A/immunology ; Intestines/*immunology ; Macrophages/immunology ; Male ; Metagenome ; Mice ; Mice, Inbred C57BL ; Mouth/*microbiology ; *Porphyromonas ; RNA, Ribosomal, 16S ; *Streptococcus ; T-Lymphocytes, Regulatory/immunology ; Th17 Cells/immunology ; }, abstract = {Recently, it has been suggested that the oral administration of Porphyromonas gingivalis, a keystone pathogen for periodontal disease, induces dysbiosis of the mouse intestinal microbiota and affects intestinal barrier function. Since oral streptococci are the predominant oral bacterial group, we compared the effect of their oral administration on the intestinal tract compared to that of P. gingivalis. Swallowing oral bacteria caused gut dysbiosis, due to increased Bacteroides and Staphylococcus and decreased Lactobacillus spp. Furthermore, oral bacterial infection caused an increase in lactate and decreases in succinate and n-butyrate contents. In the small intestine, the decrease in Th17 cells was considered to be a result of oral bacterial infection, although the population of Treg cells remained unaffected. In addition, oral bacterial challenge increased the M1/M2 macrophage ratio and decreased the immunoglobulin A (IgA) antibody titer in feces. These results suggest that gut dysbiosis caused by oral bacteria may cause a decrease in Th17 cells and fecal IgA levels and an increase in the M1/M2 macrophage ratio, thereby promoting chronic inflammation.}, } @article {pmid32504470, year = {2020}, author = {Avetisov, SE and Abramova, ND and Gogoleva, NE and Gusev, OA and Mitichkina, TS and Novikov, IA and Subbot, AM and Shagimardanova, EI}, title = {[Rational strategy for studying microbiome of the ocular surface of people using hard contact lenses by method of 16S rRNA gene metabarcoding].}, journal = {Vestnik oftalmologii}, volume = {136}, number = {3}, pages = {3-9}, doi = {10.17116/oftalma20201360313}, pmid = {32504470}, issn = {0042-465X}, mesh = {*Contact Lenses ; DNA, Bacterial ; Humans ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {UNLABELLED: The study is based on the hypothesis that high taxonomic diversity of bacteria detectable on the eye surface by molecular genetic methods is attributed to the high level of its contamination by skin microflora. Such contamination would make it problematic to identify the fractions of real ocular surface microbiome, which remains behind the one-percent cut-off threshold adopted in the metagenomic analysis. Hard contact lenses for long-wearing act as a physical filter preventing DNA contamination from random microorganisms, and at the same time providing adhesion to the living cells of bacteria and fungi. To confirm this assumption, a detailed analysis of references was carried out, supplemented by original laboratory research.

MATERIAL AND METHODS: The analysis included 16 hard contact lenses obtained from 11 patients with impaired refraction (myopia). Additionally, conjunctival mucosa scrapings were collected from 42 patients. Samples were cross-analyzed by 16S rRNA gene sequencing using 454 GS Junior (Ion Torrent) and Illumina MiSeq platforms.

RESULTS: Results obtained by the Illumina platform (analysis of the V3-V4 variable region of the 16S rRNA gene) showed better convergence with the data of culture tests reported in the literature. The major microorganism groups found were: Acinetobacter (39%), Gluconacetobacter (10.8%), Propionibacterium (9.3%), Corynebacterium (9.3%), Staphylococcus (7.2%), Streptococcus (7%), Pseudomonas (4.1%), Micrococcus (3.3%), Yersinia (3%), Chondromyces (2.4%), Serratia (2.3%), and Bacillus (2.1%). Analysis of the samples obtained directly from the mucosa revealed dominance of typical skin-associated microorganisms.

CONCLUSION: The present study proposes a contamination-reduction algorithm for microbiological testing of the ocular surface using hard contact lenses for prolonged wearing as a carrier for microbial DNA.}, } @article {pmid32501768, year = {2020}, author = {Gotkine, M and Kviatcovsky, D and Elinav, E}, title = {Amyotrophic lateral sclerosis and intestinal microbiota-toward establishing cause and effect.}, journal = {Gut microbes}, volume = {11}, number = {6}, pages = {1833-1841}, pmid = {32501768}, issn = {1949-0984}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Amyotrophic Lateral Sclerosis/*microbiology ; Animals ; Bacteria/classification/genetics/isolation & purification ; Disease Models, Animal ; Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {The intestinal microbiota may be involved, through metabolic gut-brain interactions, in a variety of neurological conditions. In this addendum, we summarize the findings of our recent study investigating the potentially modulatory influence of the microbiome in a transgenic ALS mouse model, and the possible application to human disease. We found that transgenic mice show evidence of dysbiosis, even at the pre-symptomatic stage, and have a more severe disease course under germ-free conditions or after receiving broad-spectrum antibiotics. We demonstrated that Akkermansia muciniphila ameliorated the disease in mice and that this may be due to the production of nicotinamide. We then conducted a preliminary study in human ALS and identified functionally similar alterations within the metagenome. Furthermore, we found that patients with ALS had lower systemic and CSF levels of nicotinamide, suggesting that the changes observed in the mouse model may be relevant to human disease.}, } @article {pmid32500037, year = {2020}, author = {Hasain, Z and Mokhtar, NM and Kamaruddin, NA and Mohamed Ismail, NA and Razalli, NH and Gnanou, JV and Raja Ali, RA}, title = {Gut Microbiota and Gestational Diabetes Mellitus: A Review of Host-Gut Microbiota Interactions and Their Therapeutic Potential.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {188}, pmid = {32500037}, issn = {2235-2988}, mesh = {Bacteroidetes ; *Diabetes Mellitus, Type 2/therapy ; *Diabetes, Gestational/therapy ; Female ; *Gastrointestinal Microbiome ; Humans ; Pregnancy ; }, abstract = {Gestational diabetes mellitus (GDM) is defined as impaired glucose tolerance recognized during pregnancy. GDM is associated with metabolic disorder phenotypes, such as obesity, low-grade inflammation, and insulin resistance. Following delivery, nearly half of the women with a history of GDM have persistent postpartum glucose intolerance and an increased risk of developing type 2 diabetes mellitus (T2DM), as much as 7-fold. The alarming upward trend may worsen the socioeconomic burden worldwide. Accumulating evidence strongly associates gut microbiota dysbiosis in women with GDM, similar to the T2DM profile. Several metagenomics studies have shown gut microbiota, such as Ruminococcaceae, Parabacteroides distasonis, and Prevotella, were enriched in women with GDM. These microbiota populations are associated with metabolic pathways for carbohydrate metabolism and insulin signaling, suggesting a potential "gut microbiota signature" in women with GDM. Furthermore, elevated expression of serum zonulin, a marker of gut epithelial permeability, during early pregnancy in women with GDM indicates a possible link between gut microbiota and GDM. Nevertheless, few studies have revealed discrepant results, and the interplay between gut microbiota dysbiosis and host metabolism in women with GDM is yet to be elucidated. Lifestyle modification and pharmacological treatment with metformin showed evidence of modulation of gut microbiota and proved to be beneficial to maintain glucose homeostasis in T2DM. Nonetheless, post-GDM women have poor compliance toward lifestyle modification after delivery, and metformin treatment remains controversial as a T2DM preventive strategy. We hypothesized modulation of the composition of gut microbiota with probiotics supplementation may reverse postpartum glucose intolerance in post-GDM women. In this review, we addressed gut microbiota dysbiosis and the possible mechanistic links between the host and gut microbiota in women with GDM. Furthermore, this review highlights the potential therapeutic use of probiotics in post-GDM women as a T2DM preventive strategy.}, } @article {pmid32499497, year = {2020}, author = {Van Rossum, T and Ferretti, P and Maistrenko, OM and Bork, P}, title = {Diversity within species: interpreting strains in microbiomes.}, journal = {Nature reviews. Microbiology}, volume = {18}, number = {9}, pages = {491-506}, pmid = {32499497}, issn = {1740-1534}, support = {669830/ERC_/European Research Council/International ; }, mesh = {Bacteria/genetics ; Evolution, Molecular ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {Studying within-species variation has traditionally been limited to culturable bacterial isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing and technical advances have enabled culture-free, high-resolution strain and subspecies analyses at high throughput and in complex environments. This holds great scientific promise but has also led to an overwhelming number of methods and terms to describe infraspecific variation. This Review aims to clarify these advances by focusing on the diversity within bacterial and archaeal species in the context of microbiomics. We cover foundational microevolutionary concepts relevant to population genetics and summarize how within-species variation can be studied and stratified directly within microbial communities with a focus on metagenomics. Finally, we describe how common applications of within-species variation can be achieved using metagenomic data. We aim to guide the selection of appropriate terms and analytical approaches to facilitate researchers in benefiting from the increasing availability of large, high-resolution microbiome genetic sequencing data.}, } @article {pmid32497331, year = {2020}, author = {Mérot, C}, title = {Making the most of population genomic data to understand the importance of chromosomal inversions for adaptation and speciation.}, journal = {Molecular ecology}, volume = {29}, number = {14}, pages = {2513-2516}, doi = {10.1111/mec.15500}, pmid = {32497331}, issn = {1365-294X}, mesh = {Adaptation, Physiological ; *Chromosome Inversion ; Ecotype ; *Helianthus ; Humans ; Metagenomics ; }, abstract = {Chromosomal inversions are increasingly found to differentiate locally adapted populations. This adaptive role is predictable because reduced recombination protects allelic combinations from gene flow. However, we are far from understanding how frequently inversions contribute to local adaptation and how widespread this phenomenon is across species. In a "From the Cover" article in this issue of Molecular Ecology, Huang, Andrew, Owens, Ostevik, and Rieseberg (2020) provide an important step towards this goal not only by finding adaptive inversions in a sunflower ecotype, but also by reversing the approach used to investigate the link between adaptation and inversions. Most studies compare two phenotypes and uncover divergence at a few regions, of which some can subsequently be identified as inversions. In contrast, Huang et al first catalogue putative inversions and then test genotype-environment associations, which allows them to ask systematically whether inversions may be adaptive and in which ecological contexts. They achieve that by revisiting a previous reduced-representation sequencing (RAD-sequencing) data set, demonstrating the suitability of this method to detect inversions in species with limited genomic resources. As such, Huang et al pave the way for a better understanding of the evolutionary role of structural genomic variation and highlight that accounting for inversions in population genomics is now possible, and much needed, in a wider range of organisms.}, } @article {pmid32497143, year = {2020}, author = {Wang, S and Yan, Z and Wang, P and Zheng, X and Fan, J}, title = {Comparative metagenomics reveals the microbial diversity and metabolic potentials in the sediments and surrounding seawaters of Qinhuangdao mariculture area.}, journal = {PloS one}, volume = {15}, number = {6}, pages = {e0234128}, pmid = {32497143}, issn = {1932-6203}, mesh = {Bacteria/classification/*genetics/*metabolism ; *Biodiversity ; China ; Geologic Sediments/*microbiology ; *Metagenomics ; Seawater/*microbiology ; }, abstract = {Qinhuangdao coastal area is an important mariculture area in North China. Microbial communities play an important role in driving biogeochemical cycle and energy flow. It is necessary to identify the microbial communities and their functions in the coastal mariculture area of Qinhuangdao. In this study, the microbial community compositions and their metabolic potentials in the sediments and their surrounding seawaters of Qinhuangdao mariculture area were uncovered by the 16S rRNA gene amplicon sequencing and metagenomic shotgun sequencing approaches. The results of amplicon sequencing showed that Gammaproteobacteria and Alphaproteobacteria were predominant classes. Our datasets showed a clear shift in microbial taxonomic groups and the metabolic pathways in the sediments and surrounding seawaters. Metagenomic analysis showed that purine metabolism, ABC transporters, and pyrimidine metabolism were the most abundant pathways. Genes related to two-component system, TCA cycle and nitrogen metabolism exhibited higher abundance in sediments compared with those in seawaters. The presence of cadmium-resistant genes and ABC transporters suggested the ability of microorganisms to resist the toxicity of cadmium. In summary, this study provides comprehensive and significant differential signatures in the microbial community and metabolic pathways in Qinhuangdao mariculture area, and can develop effective microbial indicators to monitor mariculture area in the future.}, } @article {pmid32496513, year = {2021}, author = {Zhang, Q and Yu, K and Li, S and Zhang, X and Zhao, Q and Zhao, X and Liu, Z and Cheng, H and Liu, ZX and Li, X}, title = {gutMEGA: a database of the human gut MEtaGenome Atlas.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {3}, pages = {}, doi = {10.1093/bib/bbaa082}, pmid = {32496513}, issn = {1477-4054}, mesh = {*Databases, Genetic ; Gastrointestinal Microbiome/*genetics ; Humans ; Internet ; *Metagenome ; Phenotype ; Software ; }, abstract = {The gut microbiota plays important roles in human health through regulating both physiological homeostasis and disease emergence. The accumulation of metagenomic sequencing studies enables us to better understand the temporal and spatial variations of the gut microbiota under different physiological and pathological conditions. However, it is inconvenient for scientists to query and retrieve published data; thus, a comprehensive resource for the quantitative gut metagenome is urgently needed. In this study, we developed gut MEtaGenome Atlas (gutMEGA), a well-annotated comprehensive database, to curate and host published quantitative gut microbiota datasets from Homo sapiens. By carefully curating the gut microbiota composition, phenotypes and experimental information, gutMEGA finally integrated 59 132 quantification events for 6457 taxa at seven different levels (kingdom, phylum, class, order, family, genus and species) under 776 conditions. Moreover, with various browsing and search functions, gutMEGA provides a fast and simple way for users to obtain the relative abundances of intestinal microbes among phenotypes. Overall, gutMEGA is a convenient and comprehensive resource for gut metagenome research, which can be freely accessed at http://gutmega.omicsbio.info.}, } @article {pmid32495495, year = {2020}, author = {Rodriguez-R, LM and Tsementzi, D and Luo, C and Konstantinidis, KT}, title = {Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences.}, journal = {Environmental microbiology}, volume = {22}, number = {8}, pages = {3394-3412}, doi = {10.1111/1462-2920.15112}, pmid = {32495495}, issn = {1462-2920}, support = {1241046//National Science Foundation/International ; 1759831//National Science Foundation/International ; }, mesh = {Chloroflexi/*classification/genetics/*isolation & purification ; Databases, Genetic ; Genome, Bacterial/*genetics ; Lakes/*microbiology ; Metagenome/genetics ; Metagenomics ; Microbiota/genetics ; }, abstract = {Recent advances in sequencing technology and bioinformatic pipelines have allowed unprecedented access to the genomes of yet-uncultivated microorganisms from diverse environments. However, the catalogue of freshwater genomes remains limited, and most genome recovery attempts in freshwater ecosystems have only targeted specific taxa. Here, we present a genome recovery pipeline incorporating iterative subtractive binning, and apply it to a time series of 100 metagenomic datasets from seven connected lakes and estuaries along the Chattahoochee River (Southeastern USA). Our set of metagenome-assembled genomes (MAGs) represents >400 yet-unnamed genomospecies, substantially increasing the number of high-quality MAGs from freshwater lakes. We propose names for two novel species: 'Candidatus Elulimicrobium humile' ('Ca. Elulimicrobiota', 'Patescibacteria') and 'Candidatus Aquidulcis frankliniae' ('Chloroflexi'). Collectively, our MAGs represented about half of the total microbial community at any sampling point. To evaluate the prevalence of these genomospecies in the chronoseries, we introduce methodologies to estimate relative abundance and habitat preference that control for uneven genome quality and sample representation. We demonstrate high degrees of habitat-specialization and endemicity for most genomospecies in the Chattahoochee lakes. Wider ecological ranges characterized smaller genomes with higher coding densities, indicating an overall advantage of smaller, more compact genomes for cosmopolitan distributions.}, } @article {pmid32493439, year = {2020}, author = {Carrión, O and Gibson, L and Elias, DMO and McNamara, NP and van Alen, TA and Op den Camp, HJM and Supramaniam, CV and McGenity, TJ and Murrell, JC}, title = {Diversity of isoprene-degrading bacteria in phyllosphere and soil communities from a high isoprene-emitting environment: a Malaysian oil palm plantation.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {81}, pmid = {32493439}, issn = {2049-2618}, support = {694578-IsoMet//H2020 European Research Council/International ; }, mesh = {Bacteria/classification/metabolism ; *Biodiversity ; Butadienes/metabolism ; *Hemiterpenes/metabolism ; Malaysia ; *Plant Leaves/microbiology ; *Soil ; *Soil Microbiology ; }, abstract = {BACKGROUND: Isoprene is the most abundantly produced biogenic volatile organic compound (BVOC) on Earth, with annual global emissions almost equal to those of methane. Despite its importance in atmospheric chemistry and climate, little is known about the biological degradation of isoprene in the environment. The largest source of isoprene is terrestrial plants, and oil palms, the cultivation of which is expanding rapidly, are among the highest isoprene-producing trees.

RESULTS: DNA stable isotope probing (DNA-SIP) to study the microbial isoprene-degrading community associated with oil palm trees revealed novel genera of isoprene-utilising bacteria including Novosphingobium, Pelomonas, Rhodoblastus, Sphingomonas and Zoogloea in both oil palm soils and on leaves. Amplicon sequencing of isoA genes, which encode the α-subunit of the isoprene monooxygenase (IsoMO), a key enzyme in isoprene metabolism, confirmed that oil palm trees harbour a novel diversity of isoA sequences. In addition, metagenome-assembled genomes (MAGs) were reconstructed from oil palm soil and leaf metagenomes and putative isoprene degradation genes were identified. Analysis of unenriched metagenomes showed that isoA-containing bacteria are more abundant in soils than in the oil palm phyllosphere.

CONCLUSION: This study greatly expands the known diversity of bacteria that can metabolise isoprene and contributes to a better understanding of the biological degradation of this important but neglected climate-active gas. Video abstract.}, } @article {pmid32492805, year = {2020}, author = {Haudum, C and Lindheim, L and Ascani, A and Trummer, C and Horvath, A and Münzker, J and Obermayer-Pietsch, B}, title = {Impact of Short-Term Isoflavone Intervention in Polycystic Ovary Syndrome (PCOS) Patients on Microbiota Composition and Metagenomics.}, journal = {Nutrients}, volume = {12}, number = {6}, pages = {}, pmid = {32492805}, issn = {2072-6643}, support = {W1241//Austrian Science Fund/ ; FFG844609//Österreichische Forschungsförderungsgesellschaft/ ; }, mesh = {Adult ; Equol/metabolism ; Female ; Gastrointestinal Microbiome/*physiology ; Glucose/metabolism ; Humans ; Isoflavones/metabolism/*pharmacology/*therapeutic use ; *Metagenomics ; *Phytotherapy ; Polycystic Ovary Syndrome/*drug therapy/etiology/metabolism/*microbiology ; Receptors, Estrogen/metabolism ; Soy Milk ; Young Adult ; }, abstract = {BACKGROUND: Polycystic ovary syndrome (PCOS) affects 5-20% of women of reproductive age worldwide and is associated with disorders of glucose metabolism. Hormone and metabolic signaling may be influenced by phytoestrogens, such as isoflavones. Their endocrine effects may modify symptom penetrance in PCOS. Equol is one of the most active isoflavone metabolites, produced by intestinal bacteria, and acts as a selective estrogen receptor modulator.

METHOD: In this interventional study of clinical and biochemical characterization, urine isoflavone levels were measured in PCOS and control women before and three days after a defined isoflavone intervention via soy milk. In this interventional study, bacterial equol production was evaluated using the log(equol: daidzein ratio) and microbiome, metabolic, and predicted metagenome analyses were performed.

RESULTS: After isoflavone intervention, predicted stool metagenomic pathways, microbial alpha diversity, and glucose homeostasis in PCOS improved resembling the profile of the control group at baseline. In the whole cohort, larger equol production was associated with lower androgen as well as fertility markers.

CONCLUSION: The dynamics in our metabolic, microbiome, and predicted metagenomic profiles underline the importance of external phytohormones on PCOS characteristics and a potential therapeutic approach or prebiotic in the future.}, } @article {pmid32090172, year = {2020}, author = {Brunker, K and Jaswant, G and Thumbi, SM and Lushasi, K and Lugelo, A and Czupryna, AM and Ade, F and Wambura, G and Chuchu, V and Steenson, R and Ngeleja, C and Bautista, C and Manalo, DL and Gomez, MRR and Chu, MYJV and Miranda, ME and Kamat, M and Rysava, K and Espineda, J and Silo, EAV and Aringo, AM and Bernales, RP and Adonay, FF and Tildesley, MJ and Marston, DA and Jennings, DL and Fooks, AR and Zhu, W and Meredith, LW and Hill, SC and Poplawski, R and Gifford, RJ and Singer, JB and Maturi, M and Mwatondo, A and Biek, R and Hampson, K}, title = {Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes.}, journal = {Wellcome open research}, volume = {5}, number = {}, pages = {3}, pmid = {32090172}, issn = {2398-502X}, support = {MR/R025649/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; 110330/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; 207569/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; EP-C-15-008/EPA/EPA/United States ; /WT_/Wellcome Trust/United Kingdom ; }, abstract = {Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.}, } @article {pmid32492369, year = {2020}, author = {Sorbara, MT and Littmann, ER and Fontana, E and Moody, TU and Kohout, CE and Gjonbalaj, M and Eaton, V and Seok, R and Leiner, IM and Pamer, EG}, title = {Functional and Genomic Variation between Human-Derived Isolates of Lachnospiraceae Reveals Inter- and Intra-Species Diversity.}, journal = {Cell host & microbe}, volume = {28}, number = {1}, pages = {134-146.e4}, pmid = {32492369}, issn = {1934-6069}, support = {P30 CA008748/CA/NCI NIH HHS/United States ; R01 AI042135/AI/NIAID NIH HHS/United States ; R01 AI095706/AI/NIAID NIH HHS/United States ; U01 AI124275/AI/NIAID NIH HHS/United States ; }, mesh = {Clostridiales/*classification/*genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; *Genetic Variation ; Genome, Bacterial ; Humans ; Metabolic Networks and Pathways/*genetics ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Whole Genome Sequencing ; }, abstract = {Bacteria belonging to the Lachnospiraceae family are abundant, obligate anaerobic members of the microbiota in healthy humans. Lachnospiraceae impact their hosts by producing short-chain fatty acids, converting primary to secondary bile acids, and facilitating colonization resistance against intestinal pathogens. To increase our understanding of genomic and functional diversity between members of this family, we cultured 273 Lachnospiraceae isolates representing 11 genera and 27 species from human donors and performed whole-genome sequencing assembly and annotation. This analysis revealed substantial inter- and intra-species diversity in pathways that likely influence an isolate's ability to impact host health. These differences are likely to impact colonization resistance through lantibiotic expression or intestinal acidification, influence host mucosal immune cells and enterocytes via butyrate production, or contribute to synergism within a consortium by heterogenous polysaccharide metabolism. Identification of these specific functions could facilitate development of probiotic bacterial consortia that drive and/or restore in vivo microbiome functions.}, } @article {pmid32488118, year = {2020}, author = {Tan, SC and Chong, CW and Yap, IKS and Thong, KL and Teh, CSJ}, title = {Comparative assessment of faecal microbial composition and metabonome of swine, farmers and human control.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {8997}, pmid = {32488118}, issn = {2045-2322}, mesh = {Animals ; Butyrates/analysis ; Case-Control Studies ; *Farmers ; Feces/*microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Malaysia ; Metabolome/*physiology ; Metagenome/genetics ; Methylamines/analysis ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S ; Sus scrofa/*microbiology ; }, abstract = {The gastrointestinal tract of humans and swine consist of a wide range of bacteria which interact with hosts metabolism. Due to the differences in co-evolution and co-adaptation, a large fraction of the gut microbiome is host-specific. In this study, we evaluated the effect of close human-animal interaction to the faecal metagenome and metabonome of swine, farmer and human control. Three distinct clusters were observed based on T-RFLP-derived faecal microbial composition. However, 16S-inferred faecal microbiota and metabolic profiles showed that only human control was significantly different from the swine (P < 0.05). The metabonome of farmers and human controls were highly similar. Notably, higher trimethylamine N-oxide (TMAO) and butyrate were detected in human control and swine, respectively. The relative abundance of TMAO was positively correlated with Prevotella copri. Overall, we compared and established the relationship between the metabolites and microbiota composition of swine, farmers and human control. Based on the data obtained, we deduced that long term occupational exposure to swine and farm environment had affected the gut bacterial composition of farmers. Nonetheless, the effect was less prominent in the metabolite profiles, suggesting the gut bacteria expressed high functional plasticity and are therefore resilience to the level of community shift detected.}, } @article {pmid32487781, year = {2020}, author = {Ma, S and Qin, J and Hao, Y and Fu, L}, title = {Association of gut microbiota composition and function with an aged rat model of senile osteoporosis using 16S rRNA and metagenomic sequencing analysis.}, journal = {Aging}, volume = {12}, number = {11}, pages = {10795-10808}, pmid = {32487781}, issn = {1945-4589}, mesh = {Animals ; Bone Density ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Metabolic Networks and Pathways ; Metagenomics ; Osteoporosis/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; }, abstract = {Recently, more interest has been paid to the association between bone mass and gut microecological dysbiosis. The results of clinical studies comparing gut microbiota (GM) in osteoporosis patients have been inconsistent due to different inclusion and exclusion criteria. To date, the association between the GM and senile osteoporosis remains poorly understood. Here, we utilized an aged rat model (22 months old) of senile osteoporosis to study the association of the composition and function of the GM with osteoporosis by 16S rRNA and metagenomic sequencing. The results showed that there was a significant reduction in alpha diversity and the F/B (Firmicutes/Bacteroidetes) ratio in aged rats. At the genus level, the enrichment of Helicobacter was potentially related to osteoporosis as a risk factor. Metagenomics results based on two databases indicated that shifts in the GM contribute to senile osteoporosis through metabolic pathways and subsequent immune disorders. In conclusion, our study reveals the association of gut microbiota composition and function with senile osteoporosis in an aged rat model in a brand new way, and variations in the GM might contribute to senile osteoporosis through metabolic pathways.}, } @article {pmid32487246, year = {2020}, author = {Sánchez-Reyes, A and Bretón-Deval, L and Mangelson, H and Sanchez-Flores, A}, title = {Draft genome sequence of "Candidatus Afipia apatlaquensis" sp. nov., IBT-C3, a potential strain for decolorization of textile dyes.}, journal = {BMC research notes}, volume = {13}, number = {1}, pages = {265}, pmid = {32487246}, issn = {1756-0500}, mesh = {Afipia/*genetics ; *Biodegradation, Environmental ; *Coloring Agents ; Genome, Bacterial/*genetics ; Metagenome/genetics ; Mexico ; Microbiota/genetics ; *Phylogeny ; *Textiles ; }, abstract = {OBJECTIVES: In order to characterize a river-associated, enriched microbiome capable of degrading an anthraquinone dye from the oil blue family, as well as assessing its functional potential, we performed a taxa-specific metagenomic deconvolution analysis based on contact probability maps at the chromosomal level. This study will allow associating the genomic content of "Candidatus Afipia apatlaquensis" strain IBT-C3 with its phenotypic potential in the context of bioremediation of textile dyes. We anticipate that this resource will be very useful in comparative genomic clinical studies, contributing to understanding the genomic basis of Afipia pathogenicity.

DATA DESCRIPTION: Here, we report the first draft genome sequence of "Candidatus Afipia apatlaquensis" sp. nov., strain IBT-C3, obtained by deconvolution of a textile-dye degrader microbiome in Mexico. The genome composite was deconvoluted using a Hi-C proximity ligation method. Whole-genome-based comparisons and phylogenomics reconstruction indicate that strain IBT-C3 represents a new species of the genus Afipia. The assembly completeness was 92.5% with 5,604,749 bp in length and 60.72% G+C content. The genome complement of IBT-C3 suggests a functional potential for decolorization of textile dyes, contrasting with previous reports of Afipia genus focused on its pathogenic potential.}, } @article {pmid32486022, year = {2020}, author = {Koike, Y and Kuwatsuka, S and Nishimoto, K and Motooka, D and Murota, H}, title = {Skin Mycobiome of Psoriasis Patients is Retained during Treatment with TNF and IL-17 Inhibitors.}, journal = {International journal of molecular sciences}, volume = {21}, number = {11}, pages = {}, pmid = {32486022}, issn = {1422-0067}, support = {KHKS20190401015//Kyowa Hakko Kirin/ ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Biodiversity ; Biological Products ; DNA, Fungal/genetics ; DNA, Intergenic/genetics ; Female ; Humans ; Interleukin-17/*antagonists & inhibitors ; Malassezia ; Male ; Metagenomics ; Middle Aged ; *Mycobiome ; Pore Forming Cytotoxic Proteins/pharmacology ; Psoriasis/*drug therapy/*microbiology ; Skin/*microbiology ; Tumor Necrosis Factor Inhibitors/*therapeutic use ; Young Adult ; }, abstract = {BACKGROUND: Biological treatment relieves refractory skin lesions in patients with psoriasis; however, changes in the fungal microbiome (the mycobiome) on the skin are unclear.

METHODS: The skin mycobiome of psoriasis patients treated with TNF inhibitors (TNFi, n = 5) and IL-17 inhibitors (IL-17i, n = 7) was compared with that of patients not receiving systemic therapy (n = 7). Skin swab samples were collected from non-lesional post-auricular areas. Fungal DNA was sequenced by ITS1 metagenomic analysis and taxonomic classification was performed.

RESULTS: An average of 37543 reads/sample were analyzed and fungi belonging to 31 genera were detected. The genus Malassezia accounted for >90% of reads in 7/7 samples from the no-therapy group, 4/5 from the TNFi group, and 5/7 from the IL-17i group. Biodiversity was low in those three groups. Few members of the genus trichophyton were detected; the genus Candida was not detected at all. Among the Malassezia species, M. restricta was the major species in 6/7 samples from the no-therapy group, 4/5 from the TNFi group, and 5/7 from the IL-17i group whose the other largest species revealed M. globosa.

CONCLUSIONS: The mycobiome is retained on post-auricular skin during systemic treatment with TNF and IL-17 inhibitors.}, } @article {pmid32485282, year = {2020}, author = {Wang, MX and Lin, L and Chen, YD and Zhong, YP and Lin, YX and Li, P and Tian, X and Han, B and Xie, ZY and Liao, QF}, title = {Evodiamine has therapeutic efficacy in ulcerative colitis by increasing Lactobacillus acidophilus levels and acetate production.}, journal = {Pharmacological research}, volume = {159}, number = {}, pages = {104978}, doi = {10.1016/j.phrs.2020.104978}, pmid = {32485282}, issn = {1096-1186}, mesh = {Acetates/*metabolism ; Animals ; Colitis, Ulcerative/chemically induced/*drug therapy/metabolism/microbiology ; Colon/metabolism/*microbiology ; Cytokines/metabolism ; Dextran Sulfate ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Feces/microbiology ; Gastrointestinal Agents/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Inflammation Mediators/metabolism ; Intestinal Mucosa/metabolism/microbiology ; Lactobacillus acidophilus/*drug effects/genetics/growth & development/metabolism ; Male ; Metabolomics ; Quinazolines/*pharmacology ; Rats, Sprague-Dawley ; Ribotyping ; }, abstract = {Emerging evidence implicates gut microbiota have an important role in ulcerative colitis (UC). Previous study indicated that Evodiamine (EVO) can alleviate colitis through downregulating inflammatory pathways. However, specific relationship between EVO-treated colitis relief and regulation of gut microbiota is still unclear. Here, our goal was to determine the potential role of gut microbiota in the relief of UC by EVO. By using pathology-related indicators, 16S rRNA sequencing and metabolomics profiling, we assessed the pharmacological effect of EVO on dextran sulfate sodium (DSS)-induced colitis rats as well as on the change of gut microbiota and metabolism. Fecal derived from EVO-treated rats was transplanted into colitis rats to verify the effect of EVO on gut microbiota, and 'driver bacteria' was found and validated by 16S rRNA sequencing, metagenome and qRT-PCR. The effect of Lactobacillus acidophilus (L. acidophilus) was investigated by vivo experiment, microbiota analysis, Short-chain fatty acids (SCFAs) quantification and colon transcriptomics. EVO reduced the susceptibility to DSS-induced destruction of epithelial integrity and severe inflammatory response, and regulated the gut microbiota and metabolites. Fecal Microbiota Transplantation (FMT) alleviated DSS-induced colitis, increased the abundance of L. acidophilus and the level of acetate. Furthermore, gavaged with L. acidophilus reduced pro-inflammatory cytokines, promoted the increase of goblet cells and the secretion of antimicrobial peptides, regulated the ratio of Firmicutes/Bacteroidetes and increased the level of acetate. Our results indicated that EVO mitigation of DSS-induced colitis is associated with increased in L. acidophilus and protective acetate production, which may be a promising strategy for treating UC.}, } @article {pmid32484785, year = {2020}, author = {Ma, S and Qin, J and Hao, Y and Shi, Y and Fu, L}, title = {Structural and functional changes of gut microbiota in ovariectomized rats and their correlations with altered bone mass.}, journal = {Aging}, volume = {12}, number = {11}, pages = {10736-10753}, pmid = {32484785}, issn = {1945-4589}, mesh = {Animals ; Biomechanical Phenomena ; Bone Development/*physiology ; Bone and Bones/*metabolism ; Disease Models, Animal ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Osteoporosis, Postmenopausal/*metabolism ; Ovariectomy ; RNA, Ribosomal, 16S/analysis ; Rats ; Rats, Sprague-Dawley ; Ruminococcus/isolation & purification ; }, abstract = {As a critical factor involved in the maintenance of physiological homeostasis, the gut microbiota (GM) reportedly plays a key role in bone development. To date, the association between the GM and steroid deficiency-induced osteoporosis remains poorly understood. Forty female Sprague Dawley rats were divided into an ovariectomy (OVX) or control group. We performed 16S rRNA and metagenome sequencing, to compare diversity, taxonomic differences, and functional genes. The GM composition did not change in the control group and the number of operational taxonomic units increased significantly following ovariectomy. Alpha diversity, determined by ACE estimator, CHAO estimator, the Shannon index, and the Simpson index showed an increasing trend after ovariectomy. Samples in the OVX group were well clustered both pre- and post-ovariectomy, as demonstrated by principal coordinate 1 (PC1) and PC2. Functional genes of GM, including those involved in synthesis and metabolism of carbohydrates and nucleotides, microbial structure, and heme, as well as hemin uptake and utilization, increased at the early stage of osteoporosis. We observed that Ruminococcus flavefaciens exhibited the greatest variation in abundance among the GM and this was also associated with osteoclastic indicators and the estrobolome. Specific changes in fecal microbiota are associated with the pathogenesis of steroid deficiency-induced osteoporosis.}, } @article {pmid32482859, year = {2020}, author = {Roach, TNF and Little, M and Arts, MGI and Huckeba, J and Haas, AF and George, EE and Quinn, RA and Cobián-Güemes, AG and Naliboff, DS and Silveira, CB and Vermeij, MJA and Kelly, LW and Dorrestein, PC and Rohwer, F}, title = {A multiomic analysis of in situ coral-turf algal interactions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {24}, pages = {13588-13595}, pmid = {32482859}, issn = {1091-6490}, mesh = {Animals ; Anthozoa/chemistry/*metabolism/microbiology/parasitology ; Bacteria/classification/genetics/isolation & purification/metabolism ; Chlorophyta/chemistry/*metabolism ; Coral Reefs ; Ecosystem ; Metagenomics ; Microbiota ; }, abstract = {Viruses, microbes, and host macroorganisms form ecological units called holobionts. Here, a combination of metagenomic sequencing, metabolomic profiling, and epifluorescence microscopy was used to investigate how the different components of the holobiont including bacteria, viruses, and their associated metabolites mediate ecological interactions between corals and turf algae. The data demonstrate that there was a microbial assemblage unique to the coral-turf algae interface displaying higher microbial abundances and larger microbial cells. This was consistent with previous studies showing that turf algae exudates feed interface and coral-associated microbial communities, often at the detriment of the coral. Further supporting this hypothesis, when the metabolites were assigned a nominal oxidation state of carbon (NOSC), we found that the turf algal metabolites were significantly more reduced (i.e., have higher potential energy) compared to the corals and interfaces. The algae feeding hypothesis was further supported when the ecological outcomes of interactions (e.g., whether coral was winning or losing) were considered. For example, coral holobionts losing the competition with turf algae had higher Bacteroidetes-to-Firmicutes ratios and an elevated abundance of genes involved in bacterial growth and division. These changes were similar to trends observed in the obese human gut microbiome, where overfeeding of the microbiome creates a dysbiosis detrimental to the long-term health of the metazoan host. Together these results show that there are specific biogeochemical changes at coral-turf algal interfaces that predict the competitive outcomes between holobionts and are consistent with algal exudates feeding coral-associated microbes.}, } @article {pmid32482258, year = {2020}, author = {Chu, W and Han, Q and Xu, J and Wang, J and Sun, Y and Li, W and Chen, ZJ and Du, Y}, title = {Metagenomic analysis identified microbiome alterations and pathological association between intestinal microbiota and polycystic ovary syndrome.}, journal = {Fertility and sterility}, volume = {113}, number = {6}, pages = {1286-1298.e4}, doi = {10.1016/j.fertnstert.2020.01.027}, pmid = {32482258}, issn = {1556-5653}, mesh = {Adult ; Bacteria/classification/*genetics ; Case-Control Studies ; Cross-Sectional Studies ; Dysbiosis ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Intestines/*microbiology ; Metagenomics ; Polycystic Ovary Syndrome/diagnosis/*microbiology/physiopathology ; Young Adult ; }, abstract = {OBJECTIVE: To identify different microbial species in women with polycystic ovary syndrome (PCOS) and reveal a possible relationship between gut dysbiosis and pathological changes.

DESIGN: Cross-sectional study.

SETTING: Academic institution.

PATIENT(S): Reproductive-aged women with PCOS (n = 14) and controls (n = 14) from the Centre for Reproductive Medicine.

INTERVENTION(S): Shotgun metagenomic sequencing on fecal samples from patients, and clinical parameters (including body mass index, endocrine hormone levels, and glycemia level) gathered for correlation analysis.

MAIN OUTCOME MEASURE(S): Identification of different gut microbial strains and relativity between microbiota and clinical parameters.

RESULT(S): We found several microbial strains were statistically significantly more abundant in the PCOS group, including Parabacteroides merdae, Bacteroides fragilis, and strains of Escherichia and Shigella, whereas Faecalibacterium prausnitzii was enriched in the control group. Metagenomic species (MGS) analysis revealed that the microbes of the PCOS group were negatively correlated with those of the control group. Of note, we observed a positive correlation between MGS relevant to PCOS and endocrine disorders, including body mass index and elevated levels of serum testosterone, luteinizing hormone, and antimüllerian hormone. Functional alterations, reflected by Kyoto Encyclopedia of Genes and Genomes orthologues, could imply potential mechanisms of microbial involvement in the developmental progress of PCOS.

CONCLUSION(S): Our findings suggest an intimate association and potential mechanisms linking microbial dysbiosis and the pathophysiologic changes of PCOS. We address the importance of monitoring and modulating microbial composition and functional shifts in future clinical practice.}, } @article {pmid32482169, year = {2020}, author = {Zhong, H and Lehtovirta-Morley, L and Liu, J and Zheng, Y and Lin, H and Song, D and Todd, JD and Tian, J and Zhang, XH}, title = {Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {78}, pmid = {32482169}, issn = {2049-2618}, support = {91751202//National Natural Science Foundation of China/International ; 41730530//National Natural Science Foundation of China/International ; 41476112//National Natural Science Foundation of China/International ; }, mesh = {*Adaptation, Physiological ; *Aquatic Organisms/metabolism ; *Archaea/genetics/metabolism ; *Metagenome ; Oceans and Seas ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; }, abstract = {BACKGROUND: Marine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans-the hadal zone (depth > 6000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the "shallower" deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water.

RESULTS: In this study, metagenomic data were obtained from 0-10,500 m deep seawater samples from the Mariana Trench. The distribution patterns of Thaumarchaeota derived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance of Thaumarchaeota peaked in bathypelagic zone (depth 1000-4000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics, we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H[+] and Na[+] respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition. We also found that hadal MGI have the genetic potential to import a far higher range of organic compounds than their shallower water counterparts. Despite this trait, hadal MDI ammonia oxidation and carbon fixation genes are highly transcribed providing evidence they are likely autotrophic, contributing to the primary production in the aphotic deep sea.

CONCLUSIONS: Our study reveals potentially novel adaptation mechanisms of deep-sea thaumarchaeotal clades and suggests key functions of deep-sea Thaumarchaeota in carbon and nitrogen cycling. Video Abstract.}, } @article {pmid32482164, year = {2020}, author = {Costa, OYA and de Hollander, M and Pijl, A and Liu, B and Kuramae, EE}, title = {Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {76}, pmid = {32482164}, issn = {2049-2618}, support = {729.004.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/International ; 202496/2015-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/International ; }, mesh = {Bacteria/enzymology/genetics ; Biodegradation, Environmental ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; *Polymers/metabolism ; }, abstract = {BACKGROUND: Cultivation-independent methods, including metagenomics, are tools for the exploration and discovery of biotechnological compounds produced by microbes in natural environments. Glycoside hydrolases (GHs) enzymes are extremely desired and important in the industry of production for goods and biofuel and removal of problematic biofilms and exopolysaccharide (EPS). Biofilms and EPS are complex, requiring a wide range of enzymes for a complete degradation. The aim of this study was to identify potential GH microbial producers and GH genes with biotechnological potential, using EPS-complex structure (WH15EPS) of Acidobacteria Granulicella sp. strain WH15 as an enrichment factor, in cultivation-independent and cultivation-dependent methods. We performed stable isotope probing (SIP) combined with metagenomics on topsoil litter amended with WH15EPS and coupled solid culture-EPS amended medium with metagenomics.

RESULTS: SIP metagenome analysis of the soil litter demonstrated that phyla Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes were the most abundant in WH15EPS amended and unamended treatments. The enrichment cultures in solid culture medium coupled to metagenomics demonstrated an enrichment in Proteobacteria, and the metagenome assembly of this enrichment cultures resulted in 4 metagenome-assembled genomes (MAGs) of microbes with low identity (42-86%) to known microorganisms. Among all carbohydrate-active enzymes (CAZymes) retrieved genes, glycoside transferase (GT) was the most abundant family, either in culture-independent or culture-based metagenome datasets. Within the glycoside hydrolases (GHs), GH13 was the most abundant family in both metagenome datasets. In the "heavy" fraction of the culture-independent metagenome SIP dataset, GH109 (α-N-acetylgalactosaminidases), GH117 (agarases), GH50 (agarases), GH32 (invertases and inulinases), GH17 (endoglucanases), and GH71 (mutanases) families were more abundant in comparison with the controls. Those GH families are affiliated to microorganism that are probably capable to degrade WH15EPS and potentially applicable for biofilm deconstruction. Subsequent in culture-based metagenome, the assembled 4 MAGs (unclassified Proteobacteria) also contained GH families of interest, involving mannosidases, lysozymes, galactosidases, and chitinases.

CONCLUSIONS: We demonstrated that functional diversity induced by the presence of WH15EPS in both culture-independent and culture-dependent approaches was enriched in GHs, such as amylases and endoglucanases that could be applied in chemical, pharmaceutical, and food industrial sectors. Furthermore, WH15EPS may be used for the investigation and isolation of yet unknown taxa, such as unclassified Proteobacteria and Planctomycetes, increasing the number of current cultured bacterial representatives with potential biotechnological traits. Video Abstract.}, } @article {pmid32479018, year = {2020}, author = {Asad, F and Anwar, H and Yassine, HM and Ullah, MI and Rahman, A and Kamran, Z and Sohail, MU}, title = {White Button Mushroom, Agaricus bisporus (Agaricomycetes), and a Probiotics Mixture Supplementation Correct Dyslipidemia without Influencing the Colon Microbiome Profile in Hypercholesterolemic Rats.}, journal = {International journal of medicinal mushrooms}, volume = {22}, number = {3}, pages = {235-244}, doi = {10.1615/IntJMedMushrooms.2020033807}, pmid = {32479018}, issn = {1940-4344}, mesh = {*Agaricus ; Animals ; Bacteria/classification/isolation & purification ; Cholesterol/blood ; Diet, High-Fat ; *Dietary Supplements ; Dyslipidemias/*therapy ; Female ; *Gastrointestinal Microbiome ; Hypercholesterolemia/*therapy ; Male ; Metagenomics ; Oxidative Stress ; Phylogeny ; Probiotics/*therapeutic use ; Rats ; Rats, Wistar ; Triglycerides/blood ; }, abstract = {Consumption of foods rich in dietary fiber has attracted considerable attention for lowering blood cholesterol and triglycerides through attenuation of gut microbiome. Diets rich in fiber may provide substrates for microbes to digest and proliferate. In response, products of microbial digestion enter systemic circulation and support host energy homeostasis. In the present study, rats with hypercholesterolemia (HC) were supplemented with probiotics (PB) and Agaricus bisporus mushroom to examine the antidyslipidemia effects. Forty adult rats were divided into five treatment groups. The rats in the control group were fed only a chow maintenance diet (CON; n = 8), whereas an atherogenic diet (chow diet supplemented with 1.5% cholesterol and 0.5% cholic acid) was offered to the remaining rats to induce hypercholesterolemia (HC group; n = 32). Rats developed HC following a 24-day continuous supplementation with the atherogenic diet. From day 25 onward, the HC group was further divided into HC-CON, HC-PB (supplemented with PB at 1 mg/rat/day), HC-AB (supplemented with A. bisporus at 5% of diet), and HC-AB.PB (supplemented with both A. bisporus and PB). After 6 weeks of supplementation, rats were killed to collect blood to determine serum lipid profile, oxidative stress, and for metagenomics analysis of colon contents. Results showed that all supplementations corrected HC-induced oxidative stress. Furthermore, A. bisporus supplementation corrected HC-induced dyslipidemia (P ≤ .05). Blautia and Bifidobacterium were the most dominant bacterial genera in HC-AB and HC-PB groups, respectively. Phylum Firmicutes and class Clostridia predominantly occupied the gut microbiome in all groups. However, no significant differences were observed in microbiome diversity and clustering patterns among study groups. In conclusion, supplementation of A. bisporus mushroom and probiotics can lower oxidative stress and dyslipidemia with partial effects on the phylogenetic makeup in the gut microbiome.}, } @article {pmid32477962, year = {2020}, author = {Duan, J and Meng, X and Liu, S and Zhou, P and Zeng, C and Fu, C and Dou, Q and Wu, A and Li, C}, title = {Gut Microbiota Composition Associated With Clostridium difficile-Positive Diarrhea and C. difficile Type in ICU Patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {190}, pmid = {32477962}, issn = {2235-2988}, mesh = {*Clostridioides difficile/genetics ; *Clostridium Infections ; Diarrhea ; *Gastrointestinal Microbiome ; Humans ; Intensive Care Units ; Prospective Studies ; }, abstract = {The gut microbiota composition of intensive care unit (ICU) patients suffering from Clostridium difficile-positive diarrhea (CDpD) is poorly understood. This prospective study aims to use 16S rDNA (and metagenome) sequencing to compare the microbiota composition of 58 (and 5) ICU patients with CDpD (CDpD group), 33 (and 4) ICU patients with C. difficile-negative diarrhea (CDnD group), and 21 (and 5) healthy control subjects (control group), as well as CDpD patients in the A[+]B[+] (N = 34; A/B: C. difficile TcdA/B), A[-]B[+] (N = 7), and A[-]B[-] (N = 17) subgroups. For 16S rDNA data, OTU clustering (tool: UPARSE), taxonomic assignment (tool: RDP classifier), α-diversity, and β-diversity analyses (tool: QIIME) were conducted. For metagenome data, metagenome assembly (tool: SOAPdenovo), gene calling (tools: MetaGeneMark, CD-HIT, and SoapAligner), unigene alignment (tool: DIAMOND), taxon difference analysis (tool: Metastats), and gene annotation (tool: DIAMOND) were performed. The microbial diversity of the CDpD group was lower than that of the CDnD and control groups. The abundances of 10 taxa (e.g., Deferribacteres, Cryptomycota, Acetothermia) were significantly higher in the CDpD group than in the CDnD group. The abundances of Saccharomycetes and Clostridia were significantly lower in CDpD in comparison with control. Some taxa were significantly different between the A[+]B[+] and A[-]B[-] subgroups. CDpD might relate to a decrease in beneficial taxa (i.e., Saccharomycetes and Clostridia) and an increase in harmful taxa (e.g., Deferribacteres, Cryptomycota, Acetothermia) in gut microbiota of ICU patients. C. difficile toxin type might be slightly associated with gut microbiota composition.}, } @article {pmid32477320, year = {2020}, author = {Sharma, P and Rani, J and Chauhan, C and Kumari, S and Tevatiya, S and Das De, T and Savargaonkar, D and Pandey, KC and Dixit, R}, title = {Altered Gut Microbiota and Immunity Defines Plasmodium vivax Survival in Anopheles stephensi.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {609}, pmid = {32477320}, issn = {1664-3224}, mesh = {Animals ; Anopheles/immunology/microbiology/*parasitology ; Gastrointestinal Microbiome/*physiology ; Plasmodium vivax/*growth & development ; RNA-Seq ; Symbiosis ; }, abstract = {Blood-feeding enriched gut-microbiota boosts mosquitoes' anti-Plasmodium immunity. Here, we ask how Plasmodium vivax alters gut-microbiota, anti-Plasmodial immunity, and impacts tripartite Plasmodium-mosquito-microbiota interactions in the gut lumen. We used a metagenomics and RNAseq strategy to address these questions. In naïve mosquitoes, Elizabethkingia meningitis and Pseudomonas spp. are the dominant bacteria and blood-feeding leads to a heightened detection of Elizabethkingia, Pseudomonas and Serratia 16S rRNA. A parallel RNAseq analysis of blood-fed midguts also shows the presence of Elizabethkingia-related transcripts. After, P. vivax infected blood-meal, however, we do not detect bacterial 16S rRNA until circa 36 h. Intriguingly, the transcriptional expression of a selected array of antimicrobial arsenal cecropins 1-2, defensin-1, and gambicin remained low during the first 36 h-a time frame when ookinetes/early oocysts invaded the gut. We conclude during the preinvasive phase, P. vivax outcompetes midgut-microbiota. This microbial suppression likely negates the impact of mosquito immunity which in turn may enhance the survival of P. vivax. Detection of sequences matching to mosquito-associated Wolbachia opens a new inquiry for its exploration as an agent for "paratransgenesis-based" mosquito control.}, } @article {pmid32475373, year = {2020}, author = {Zheng, J and Hoffman, KL and Chen, JS and Shivappa, N and Sood, A and Browman, GJ and Dirba, DD and Hanash, S and Wei, P and Hebert, JR and Petrosino, JF and Schembre, SM and Daniel, CR}, title = {Dietary inflammatory potential in relation to the gut microbiome: results from a cross-sectional study.}, journal = {The British journal of nutrition}, volume = {124}, number = {9}, pages = {931-942}, pmid = {32475373}, issn = {1475-2662}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; R25 CA056452/CA/NCI NIH HHS/United States ; R25 CA057730/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Biomarkers/blood ; Cross-Sectional Studies ; Diet/*adverse effects ; Diet Surveys ; Diet, Healthy/*statistics & numerical data ; Fasting/blood ; Female ; Gastrointestinal Microbiome/*physiology ; Healthy Volunteers ; Humans ; Inflammation/etiology/*microbiology ; Inflammation Mediators/*blood ; Linear Models ; Male ; Middle Aged ; RNA, Ribosomal, 16S/analysis ; Statistics, Nonparametric ; }, abstract = {Diet has direct and indirect effects on health through inflammation and the gut microbiome. We investigated total dietary inflammatory potential via the literature-derived index (Dietary Inflammatory Index (DII®)) with gut microbiota diversity, composition and function. In cancer-free patient volunteers initially approached at colonoscopy and healthy volunteers recruited from the medical centre community, we assessed 16S ribosomal DNA in all subjects who provided dietary assessments and stool samples (n 101) and the gut metagenome in a subset of patients with residual fasting blood samples (n 34). Associations of energy-adjusted DII scores with microbial diversity and composition were examined using linear regression, permutational multivariate ANOVA and linear discriminant analysis. Spearman correlation was used to evaluate associations of species and pathways with DII and circulating inflammatory markers. Across DII levels, α- and β-diversity did not significantly differ; however, Ruminococcus torques, Eubacterium nodatum, Acidaminococcus intestini and Clostridium leptum were more abundant in the most pro-inflammatory diet group, while Akkermansia muciniphila was enriched in the most anti-inflammatory diet group. With adjustment for age and BMI, R. torques, E. nodatum and A. intestini remained significantly associated with a more pro-inflammatory diet. In the metagenomic and fasting blood subset, A. intestini was correlated with circulating plasminogen activator inhibitor-1, a pro-inflammatory marker (rho = 0·40), but no associations remained significant upon correction for multiple testing. An index reflecting overall inflammatory potential of the diet was associated with specific microbes, but not overall diversity of the gut microbiome in our study. Findings from this preliminary study warrant further research in larger samples and prospective cohorts.}, } @article {pmid32473013, year = {2020}, author = {Li, J and Zhong, H and Ramayo-Caldas, Y and Terrapon, N and Lombard, V and Potocki-Veronese, G and Estellé, J and Popova, M and Yang, Z and Zhang, H and Li, F and Tang, S and Yang, F and Chen, W and Chen, B and Li, J and Guo, J and Martin, C and Maguin, E and Xu, X and Yang, H and Wang, J and Madsen, L and Kristiansen, K and Henrissat, B and Ehrlich, SD and Morgavi, DP}, title = {A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment.}, journal = {GigaScience}, volume = {9}, number = {6}, pages = {}, pmid = {32473013}, issn = {2047-217X}, support = {322820/ERC_/European Research Council/International ; }, mesh = {Animals ; Biomass ; Cattle ; Diet ; Digestion ; Drug Resistance, Microbial ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenome ; *Metagenomics/methods ; Mice ; Microbiota/*genetics ; Rumen/*microbiology ; Swine ; }, abstract = {BACKGROUND: The rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen.

RESULTS: Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig, and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. The catalog expands the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only <0.1% of genes were shared by all animals, which contrast with a large overlap for functions, i.e., 63% for KEGG functions. Different diets induced differences in the relative abundance rather than the presence or absence of genes, which explains the great adaptability of cattle to rapidly adjust to dietary changes.

CONCLUSIONS: These data bring new insights into functions, carbohydrate-degrading enzymes, and microbes of the rumen to complement the available information on microbial genomes. The catalog is a significant biological resource enabling deeper understanding of phenotypes and biological processes and will be expanded as new data are made available.}, } @article {pmid32471941, year = {2020}, author = {Vollmar, S and Wellmann, R and Borda-Molina, D and Rodehutscord, M and Camarinha-Silva, A and Bennewitz, J}, title = {The Gut Microbial Architecture of Efficiency Traits in the Domestic Poultry Model Species Japanese Quail (Coturnix japonica) Assessed by Mixed Linear Models.}, journal = {G3 (Bethesda, Md.)}, volume = {10}, number = {7}, pages = {2553-2562}, pmid = {32471941}, issn = {2160-1836}, mesh = {Animals ; *Coturnix/genetics ; *Gastrointestinal Microbiome/genetics ; Linear Models ; Poultry ; RNA, Ribosomal, 16S/genetics ; }, abstract = {It is well known that mammals and avian gut microbiota compositions are shaped by the host genomes and affect quantitative traits. The microbial architecture describes the impact of the microbiota composition on quantitative trait variation and the number and effect distribution of microbiota features. In the present study the gut microbial architecture of feed-related traits phosphorus and calcium utilization, daily gain, feed intake and feed per gain ratio in the domestic poultry model species Japanese quail were assessed by mixed linear models. The ileum microbiota composition was characterized by 16S rRNA amplicon sequencing techniques of growing individuals. The microbiability of the traits was on a similar level as the narrow sense heritability and was highly significant except for calcium utilization. The animal microbial correlation of the traits was substantial. Microbiome-wide association analyses revealed several traits associated and highly significant microbiota features, both on the bacteria genera as well as on the operational taxonomic unit level. Most features were significant for more than one trait, which explained the high microbial correlations. It can be concluded that the traits are polymicrobial determined with some microbiota features with larger effects and many with small effects. The results are important for the development of hologenomic selection schemes for feed-related traits in avian breeding programs that are targeting the host genome and the metagenome simultaneously.}, } @article {pmid32471901, year = {2022}, author = {Kitamura, K and Shionoya, H and Terato, K and Suzuki, S and Fukai, R and Uda, S and Abe, C and Takemori, H and Nishimura, K and Baba, H and Waritani, T and Katayama, K}, title = {Comment on: 'Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population' by Kishikawa et al.}, journal = {Annals of the rheumatic diseases}, volume = {81}, number = {5}, pages = {e71}, doi = {10.1136/annrheumdis-2020-217808}, pmid = {32471901}, issn = {1468-2060}, mesh = {*Arthritis, Rheumatoid/etiology ; *Gastrointestinal Microbiome ; Humans ; Japan ; Metagenome ; Metagenomics ; }, } @article {pmid32471897, year = {2022}, author = {Kishikawa, T and Maeda, Y and Nii, T and Okada, Y}, title = {Response to: 'Comment on 'Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population' by Kishikawa et al.' by Kitamura et al.}, journal = {Annals of the rheumatic diseases}, volume = {81}, number = {5}, pages = {e72}, doi = {10.1136/annrheumdis-2020-217897}, pmid = {32471897}, issn = {1468-2060}, mesh = {*Arthritis, Rheumatoid/genetics ; *Gastrointestinal Microbiome/physiology ; Humans ; Japan/epidemiology ; Metagenome ; Metagenomics ; }, } @article {pmid32471482, year = {2020}, author = {Zlitni, S and Bishara, A and Moss, EL and Tkachenko, E and Kang, JB and Culver, RN and Andermann, TM and Weng, Z and Wood, C and Handy, C and Ji, HP and Batzoglou, S and Bhatt, AS}, title = {Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale.}, journal = {Genome medicine}, volume = {12}, number = {1}, pages = {50}, pmid = {32471482}, issn = {1756-994X}, support = {R01 HG006137/HG/NHGRI NIH HHS/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; P01 HG000205/HG/NHGRI NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; K08 CA184420/CA/NCI NIH HHS/United States ; }, mesh = {Anti-Infective Agents/pharmacology ; Azacitidine/pharmacology ; Azithromycin/pharmacology ; Bacteria/classification/drug effects/*genetics/isolation & purification ; Ciprofloxacin/pharmacology ; DNA, Bacterial ; Diet ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/*genetics ; Genome, Bacterial ; Hematopoietic Stem Cell Transplantation ; Humans ; Immunosuppressive Agents/pharmacology ; Male ; Metagenome ; Middle Aged ; Myelodysplastic Syndromes/microbiology/therapy ; Primary Myelofibrosis/microbiology/therapy ; RNA-Seq ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Populations of closely related microbial strains can be simultaneously present in bacterial communities such as the human gut microbiome. We recently developed a de novo genome assembly approach that uses read cloud sequencing to provide more complete microbial genome drafts, enabling precise differentiation and tracking of strain-level dynamics across metagenomic samples. In this case study, we present a proof-of-concept using read cloud sequencing to describe bacterial strain diversity in the gut microbiome of one hematopoietic cell transplantation patient over a 2-month time course and highlight temporal strain variation of gut microbes during therapy. The treatment was accompanied by diet changes and administration of multiple immunosuppressants and antimicrobials.

METHODS: We conducted short-read and read cloud metagenomic sequencing of DNA extracted from four longitudinal stool samples collected during the course of treatment of one hematopoietic cell transplantation (HCT) patient. After applying read cloud metagenomic assembly to discover strain-level sequence variants in these complex microbiome samples, we performed metatranscriptomic analysis to investigate differential expression of antibiotic resistance genes. Finally, we validated predictions from the genomic and metatranscriptomic findings through in vitro antibiotic susceptibility testing and whole genome sequencing of isolates derived from the patient stool samples.

RESULTS: During the 56-day longitudinal time course that was studied, the patient's microbiome was profoundly disrupted and eventually dominated by Bacteroides caccae. Comparative analysis of B. caccae genomes obtained using read cloud sequencing together with metagenomic RNA sequencing allowed us to identify differences in substrain populations over time. Based on this, we predicted that particular mobile element integrations likely resulted in increased antibiotic resistance, which we further supported using in vitro antibiotic susceptibility testing.

CONCLUSIONS: We find read cloud assembly to be useful in identifying key structural genomic strain variants within a metagenomic sample. These strains have fluctuating relative abundance over relatively short time periods in human microbiomes. We also find specific structural genomic variations that are associated with increased antibiotic resistance over the course of clinical treatment.}, } @article {pmid32470263, year = {2020}, author = {Uberos, J}, title = {Perinatal microbiota: review of its importance in newborn health.}, journal = {Archivos argentinos de pediatria}, volume = {118}, number = {3}, pages = {e265-e270}, doi = {10.5546/aap.2020.eng.e265}, pmid = {32470263}, issn = {1668-3501}, mesh = {Breast Feeding ; Delivery, Obstetric/adverse effects/methods ; Female ; *Gastrointestinal Microbiome ; Humans ; *Infant Health ; Infant, Newborn ; Pregnancy ; }, abstract = {The use of metagenomics in the study of gut bacterial ecosystems has helped to define a standard, functional genetic profile in newborn infants, so that a bacterial ecosystem will be deemed more "normal" the more similar its functional genetic profile is to a standard. The development of a specific functional enterotype in the first days of life after birth is critical for the priming of the immune system with certain bacterial antigens. Regardless of whether the first gut bacteria are acquired before or just after birth, the newborn microbiota will result from the symbiosis with the environmental microbial flora, especially with the bacterial flora of the mother. The type of delivery, the administration of perinatal antibiotics, the environment, and nutritional exposure, especially breastfeeding, have demonstrated an important relationship with the prevalent gut microbiome.}, } @article {pmid32468578, year = {2020}, author = {Xie, J and Yu, R and Qi, J and Zhang, G and Peng, X and Luo, J}, title = {Pectin and inulin stimulated the mucus formation at a similar level: An omics-based comparative analysis.}, journal = {Journal of food science}, volume = {85}, number = {6}, pages = {1939-1947}, doi = {10.1111/1750-3841.15163}, pmid = {32468578}, issn = {1750-3841}, support = {31801543//National Natural Science Foundation of China/ ; 2018M643368//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; Bacteria/classification/genetics/metabolism ; Cecum/metabolism/microbiology ; Gastrointestinal Microbiome ; Inulin/*metabolism ; Male ; Mucin-2/metabolism ; Mucus/*metabolism/microbiology ; Pectins/*metabolism ; Polysaccharides/metabolism ; Rats ; Rats, Wistar ; }, abstract = {Mucin 2 (MUC2) is the skeleton of colonic mucus that comprises the physical intestinal barrier. Different dietary polysaccharides may affect colonic mucus at different extents. The effect of pectin on MUC2 production is contradictory. To investigate whether and how pectin affected hosts' colonic mucus, the amount of MUC2 in colon, the cecal, mucosal microbiota, and metabolites profiles were analyzed and compared with inulin. The results showed pectin stimulated the production of MUC2 at a similar level to inulin. Both interventions increased the abundance of cecal Lachnospira and Christensenellaceae_R-7_group, and enhanced the production of specific metabolites including soyasapogenol B 24-O-b-d-glucoside, lucyoside Q, trans-EKODE-(E)-Ib, and 1,26-dicaffeoylhexacosanediol. Additionally, pectin increased the relative abundance (RA) of cecal Lactobacillus, and induced less RA of potentially harmful bacteria such as Helicobacter in mucosal microbiota than inulin. In conclusion, we first reported that pectin and inulin stimulated the mucus formation at a similar level. Two genera of cecal bacteria and four metabolites may play an important role in enhancing the production of MUC2. Moreover, the MUC2 production may be unrelated to several traditional health-beneficial bacteria; pectin possibly performed as good as or better than the inulin in rats' gut.}, } @article {pmid32467975, year = {2020}, author = {Brealey, JC and Leitão, HG and van der Valk, T and Xu, W and Bougiouri, K and Dalén, L and Guschanski, K}, title = {Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome.}, journal = {Molecular biology and evolution}, volume = {37}, number = {10}, pages = {3003-3022}, pmid = {32467975}, issn = {1537-1719}, mesh = {Animals ; Biological Evolution ; Dental Calculus/*microbiology ; Diet ; Drug Resistance, Microbial/genetics ; Gorilla gorilla ; Mammals/*microbiology ; Metagenome ; *Microbiota ; Mouth/*microbiology ; Reindeer ; Ursidae ; }, abstract = {Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.}, } @article {pmid32466801, year = {2020}, author = {Jian, X and Zhu, Y and Ouyang, J and Wang, Y and Lei, Q and Xia, J and Guan, Y and Zhang, J and Guo, J and He, Y and Wang, J and Li, J and Lin, J and Su, M and Li, G and Wu, M and Qiu, L and Xiang, J and Xie, L and Jia, W and Zhou, W}, title = {Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {74}, pmid = {32466801}, issn = {2049-2618}, support = {31900102//National Natural Science Foundation of China/International ; 81570205, 81630007//National Natural Science Foundation of China/International ; 81800209//National Natural Science Foundation of China/International ; 2019M652792//China Postdoctoral Science Foundation/International ; ZLXD2017004//Strategic Priority Research Program of Central South University/International ; }, mesh = {Animals ; Bacteria/genetics ; *Biodiversity ; China ; Disease Progression ; Fecal Microbiota Transplantation ; Female ; *Gastrointestinal Microbiome/genetics ; Glutamine/metabolism ; *Host Microbial Interactions ; Humans ; Klebsiella/physiology ; Metagenome ; Mice ; *Multiple Myeloma/microbiology/therapy ; Streptococcus/metabolism ; }, abstract = {BACKGROUND: Gut microbiome alterations are closely related to human health and linked to a variety of diseases. Although great efforts have been made to understand the risk factors for multiple myeloma (MM), little is known about the role of the gut microbiome and alterations of its metabolic functions in the development of MM.

RESULTS: Here, in a cohort of newly diagnosed patients with MM and healthy controls (HCs), significant differences in metagenomic composition were discovered, for the first time, with higher bacterial diversity in MM. Specifically, nitrogen-recycling bacteria such as Klebsiella and Streptococcus were significantly enriched in MM. Also, the bacteria enriched in MM were significantly correlated with the host metabolome, suggesting strong metabolic interactions between microbes and the host. In addition, the MM-enriched bacteria likely result from the regulation of urea nitrogen accumulated during MM progression. Furthermore, by performing fecal microbiota transplantation (FMT) into 5TGM1 mice, we proposed a mechanistic explanation for the interaction between MM-enriched bacteria and MM progression via recycling urea nitrogen. Further experiments validated that Klebsiella pneumoniae promoted MM progression via de novo synthesis of glutamine in mice and that the mice fed with glutamine-deficient diet exhibited slower MM progression.

CONCLUSIONS: Overall, our findings unveil a novel function of the altered gut microbiome in accelerating the malignant progression of MM and open new avenues for novel treatment strategies via manipulation of the intestinal microbiota of MM patients. Video abstract.}, } @article {pmid32466531, year = {2020}, author = {Martínez-Núñez, MA and Rodríguez-Escamilla, Z}, title = {Mining the Yucatan Coastal Microbiome for the Identification of Non-Ribosomal Peptides Synthetase (NRPS) Genes.}, journal = {Toxins}, volume = {12}, number = {6}, pages = {}, pmid = {32466531}, issn = {2072-6651}, support = {IA205417; IA203719//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/International ; Ciencia Básica A1-S-16959//Consejo Nacional de Ciencia y Tecnología/International ; }, mesh = {Bacteria/classification/enzymology/*genetics ; Bacterial Proteins/*genetics/metabolism ; Geologic Sediments/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Microbiota ; Peptide Biosynthesis, Nucleic Acid-Independent/*genetics ; Peptide Synthases/*genetics/metabolism ; Phylogeny ; *Transcriptome ; Wetlands ; }, abstract = {Prokaryotes represent a source of both biotechnological and pharmaceutical molecules of importance, such as nonribosomal peptides (NRPs). NRPs are secondary metabolites which their synthesis is independent of ribosomes. Traditionally, obtaining NRPs had focused on organisms from terrestrial environments, but in recent years marine and coastal environments have emerged as an important source for the search and obtaining of nonribosomal compounds. In this study, we carried out a metataxonomic analysis of sediment of the coast of Yucatan in order to evaluate the potential of the microbial communities to contain bacteria involved in the synthesis of NRPs in two sites: one contaminated and the other conserved. As well as a metatranscriptomic analysis to discover nonribosomal peptide synthetases (NRPSs) genes. We found that the phyla with the highest representation of NRPs producing organisms were the Proteobacteria and Firmicutes present in the sediments of the conserved site. Similarly, the metatranscriptomic analysis showed that 52% of the sequences identified as catalytic domains of NRPSs were found in the conserved site sample, mostly (82%) belonging to Proteobacteria and Firmicutes; while the representation of Actinobacteria traditionally described as the major producers of secondary metabolites was low. It is important to highlight the prediction of metabolic pathways for siderophores production, as well as the identification of NRPS's condensation domain in organisms of the Archaea domain. Because this opens the possibility to the search for new nonribosomal structures in these organisms. This is the first mining study using high throughput sequencing technologies conducted in the sediments of the Yucatan coast to search for bacteria producing NRPs, and genes that encode NRPSs enzymes.}, } @article {pmid32466241, year = {2020}, author = {Li, Z and Tian, J and Lai, Y and Lee, CH and Cai, Z and Yu, CF}, title = {Puffer Fish Gut Microbiota Studies Revealed Unique Bacterial Co-Occurrence Patterns and New Insights on Tetrodotoxin Producers.}, journal = {Marine drugs}, volume = {18}, number = {5}, pages = {}, pmid = {32466241}, issn = {1660-3397}, support = {UGC/FDS25/M03/15//Hong Kong Research Grants Council/ ; R201907/R201711//Research grants of Beijing Normal University - Hong Kong Baptist University United International College/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/analysis ; Symbiosis ; *Tetraodontiformes ; Tetrodotoxin/*metabolism ; }, abstract = {Tetrodotoxin (TTX) is a potent neurotoxin isolated mainly from toxic puffer fish. To date, the TTX biosynthetic mechanism inside its hosts remains unresolved. Here, we hypothesize the TTX synthesis relies on the host gut microbiota, including the neglected non-culturable bacteria. In these studies, we collected the gut contents from 5 puffer fish species of the genus Takifugu including one suspected hybrid species for gut microbiota study by 16S rRNA amplicon metagenomics approach. Their gut samples were divided into toxic and non-toxic groups based on the TTX concentrations in the livers detected by LC-MS/MS. Bacterial diversity studies showed that gut microbiota structures were significantly different between toxic and non-toxic species. Vibrio and Cyanobacteria centered at the gut bacterial co-occurrence network, suggesting their importance in TTX biosynthesis. The results of PICRUSt2 metagenomic prediction and gene set enrichment analysis provided new support of arginine-precursor required in TTX biosynthesis. This is the first study to profile the gut microbiota in toxic and non-toxic puffer fish species by 16S rRNA amplicon metagenomic approach, defining significant microbial co-occurrence patterns in their gut environment. Our data supported the proposed biosynthesis of TTX inside the hosts by their gut bacterial symbionts using arginine as a precursor.}, } @article {pmid32463954, year = {2020}, author = {Fontaine, SS and Kohl, KD}, title = {Gut microbiota of invasive bullfrog tadpoles responds more rapidly to temperature than a noninvasive congener.}, journal = {Molecular ecology}, volume = {29}, number = {13}, pages = {2449-2462}, doi = {10.1111/mec.15487}, pmid = {32463954}, issn = {1365-294X}, mesh = {Animals ; Bacteria ; *Gastrointestinal Microbiome ; Introduced Species ; Larva ; Rana catesbeiana/*microbiology ; *Temperature ; }, abstract = {Environmental temperature can alter the composition, diversity, and function of ectothermic vertebrate gut microbial communities, which may result in negative consequences for host physiology, or conversely, increase phenotypic plasticity and persistence in harsh conditions. The magnitude of either of these effects will depend on the length of time animals are exposed to extreme temperatures, and how quickly the composition and function of the gut microbiota can respond to temperature change. However, the temporal effects of temperature on gut microbiota are currently unknown. Here, we investigated the length of time required for increased temperature to alter the composition of gut bacterial communities in tadpoles of two frog species, the green frog, Lithobates clamitans, and its congener, the globally invasive American bullfrog, L. catesbeianus. We also explored the potential functional consequences of these changes by comparing predicted metagenomic profiles across temperature treatments at the last experimental time point. Bullfrog-associated microbial communities were more plastic than those of the green frog. Specifically, bullfrog communities were altered by increased temperature within hours, while green frog communities took multiple days to exhibit significant changes. Further, over ten times more bullfrog bacterial functional pathways were temperature-dependent compared to the green frog. These results support our hypothesis that bullfrog gut microbial communities would respond more rapidly to temperature change, potentially bolstering their ability to exploit novel environments. More broadly, we have revealed that even short-term increases in environmental temperature, expected to occur frequently under global climate change, can alter the gut microbiota of ectothermic vertebrates.}, } @article {pmid32461640, year = {2020}, author = {Liang, G and Zhao, C and Zhang, H and Mattei, L and Sherrill-Mix, S and Bittinger, K and Kessler, LR and Wu, GD and Baldassano, RN and DeRusso, P and Ford, E and Elovitz, MA and Kelly, MS and Patel, MZ and Mazhani, T and Gerber, JS and Kelly, A and Zemel, BS and Bushman, FD}, title = {The stepwise assembly of the neonatal virome is modulated by breastfeeding.}, journal = {Nature}, volume = {581}, number = {7809}, pages = {470-474}, pmid = {32461640}, issn = {1476-4687}, support = {R01 HL113252/HL/NHLBI NIH HHS/United States ; UL1 TR001878/TR/NCATS NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; UL1 TR000003/TR/NCATS NIH HHS/United States ; R61 HL137063/HL/NHLBI NIH HHS/United States ; K23 AI135090/AI/NIAID NIH HHS/United States ; R01 DK107565/DK/NIDDK NIH HHS/United States ; P30 AI064518/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Bacteriolysis ; Bacteriophages/genetics/isolation & purification ; *Breast Feeding ; Feces/virology ; Female ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/*virology ; Humans ; Infant ; Infant, Newborn ; Lysogeny ; Male ; Meconium/virology ; Prophages/genetics/isolation & purification ; Viruses/genetics/*isolation & purification ; }, abstract = {The gut of healthy human neonates is usually devoid of viruses at birth, but quickly becomes colonized, which-in some cases-leads to gastrointestinal disorders[1-4]. Here we show that the assembly of the viral community in neonates takes place in distinct steps. Fluorescent staining of virus-like particles purified from infant meconium or early stool samples shows few or no particles, but by one month of life particle numbers increase to 10[9] per gram, and these numbers seem to persist throughout life[5-7]. We investigated the origin of these viral populations using shotgun metagenomic sequencing of virus-enriched preparations and whole microbial communities, followed by targeted microbiological analyses. Results indicate that, early after birth, pioneer bacteria colonize the infant gut and by one month prophages induced from these bacteria provide the predominant population of virus-like particles. By four months of life, identifiable viruses that replicate in human cells become more prominent. Multiple human viruses were more abundant in stool samples from babies who were exclusively fed on formula milk compared with those fed partially or fully on breast milk, paralleling reports that breast milk can be protective against viral infections[8-10]. Bacteriophage populations also differed depending on whether or not the infant was breastfed. We show that the colonization of the infant gut is stepwise, first mainly by temperate bacteriophages induced from pioneer bacteria, and later by viruses that replicate in human cells; this second phase is modulated by breastfeeding.}, } @article {pmid32461638, year = {2020}, author = {Polster, SP and Sharma, A and Tanes, C and Tang, AT and Mericko, P and Cao, Y and Carrión-Penagos, J and Girard, R and Koskimäki, J and Zhang, D and Stadnik, A and Romanos, SG and Lyne, SB and Shenkar, R and Yan, K and Lee, C and Akers, A and Morrison, L and Robinson, M and Zafar, A and Bittinger, K and Kim, H and Gilbert, JA and Kahn, ML and Shen, L and Awad, IA}, title = {Permissive microbiome characterizes human subjects with a neurovascular disease cavernous angioma.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2659}, pmid = {32461638}, issn = {2041-1723}, support = {P01 NS092521/NS/NINDS NIH HHS/United States ; R01 NS100949/NS/NINDS NIH HHS/United States ; U54 NS065705/NS/NINDS NIH HHS/United States ; R01 HL094326/HL/NHLBI NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; F30 NS100252/NS/NINDS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Biomarkers/blood ; Brain Neoplasms/complications/diagnosis/microbiology ; DNA, Bacterial/genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Hemangioma, Cavernous/*complications/diagnosis ; Humans ; Intestines/microbiology/pathology ; Male ; Metagenomics ; Middle Aged ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Cavernous angiomas (CA) are common vascular anomalies causing brain hemorrhage. Based on mouse studies, roles of gram-negative bacteria and altered intestinal homeostasis have been implicated in CA pathogenesis, and pilot study had suggested potential microbiome differences between non-CA and CA individuals based on 16S rRNA gene sequencing. We here assess microbiome differences in a larger cohort of human subjects with and without CA, and among subjects with different clinical features, and conduct more definitive microbial analyses using metagenomic shotgun sequencing. Relative abundance of distinct bacterial species in CA patients is shown, consistent with postulated permissive microbiome driving CA lesion genesis via lipopolysaccharide signaling, in humans as in mice. Other microbiome differences are related to CA clinical behavior. Weighted combinations of microbiome signatures and plasma inflammatory biomarkers enhance associations with disease severity and hemorrhage. This is the first demonstration of a sensitive and specific diagnostic microbiome in a human neurovascular disease.}, } @article {pmid32460612, year = {2020}, author = {Joseph, G and Zhang, B and Harrison, SH and Graves, JL and Thomas, MD and Panchagavi, R and Ewunkem, JAJ and Wang, L}, title = {Microbial community dynamics during anaerobic co-digestion of corn stover and swine manure at different solid content, carbon to nitrogen ratio and effluent volumetric percentages.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering}, volume = {55}, number = {9}, pages = {1111-1124}, doi = {10.1080/10934529.2020.1771975}, pmid = {32460612}, issn = {1532-4117}, mesh = {Anaerobiosis ; Animals ; Archaea/growth & development ; Bacteria, Anaerobic/growth & development ; Biofuels/analysis ; Bioreactors/*microbiology ; Carbon/analysis ; Manure/*analysis ; Methane/*biosynthesis ; *Microbiota ; Models, Theoretical ; Nitrogen/analysis ; Solid Waste/*analysis ; Swine ; Zea mays/*chemistry ; }, abstract = {The methane production and the microbial community dynamics of thermophilic anaerobic co-digestion (AD) of corn stover, swine manure and effluent were conducted at total solid (TS) content of 5%, 10% and 15%, the carbon to nitrogen ratio (C/N) of 20, 30 and 40 and the effluent volumetric percentage (EVP) of 20%, 40% and 60%. For batches with 5% TS, the highest methane yield of 238.5-283.1 mL g[-1] volatile solid (VS) and the specific methane productivity of 138.5-152.2 mL g[-1] initial VS were obtained at the C/N ratios of 20 and 30. For the mixtures with 10% and 15% TS, the highest methane yield was 341.9 mL g[-1] VS and 351.2 mL g[-1] VS, respectively, when the C/N ratio of 20% and 60% EVP conditions were maintained. Co-digestion of swine manure with corn stover caused an obvious shift in microbial population, in which the archaeal population changed from 0.3% to 2.8% and the bacterial community changed from 97.2% to 99.7%. The experimental batches with the highest relative abundance of the archaeal population (2.00% of total microbial population for 5% TS, 1.74% for 10% TS and 2.76% for 15% TS) had the highest rate of methanogenesis subsequently enhancing methane production (283.08 mL g[-1] VS for 5% TS, 341.91 mL g[-1] VS for 10% TS and 351.23 mL g[-1] VS for 15% TS). The results of microbiome analysis enabled understanding the key populations in biomethane generation.}, } @article {pmid32459982, year = {2020}, author = {Monaghan, TM and Sloan, TJ and Stockdale, SR and Blanchard, AM and Emes, RD and Wilcox, M and Biswas, R and Nashine, R and Manke, S and Gandhi, J and Jain, P and Bhotmange, S and Ambalkar, S and Satav, A and Draper, LA and Hill, C and Kashyap, RS}, title = {Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome.}, journal = {Gut microbes}, volume = {12}, number = {1}, pages = {1752605}, pmid = {32459982}, issn = {1949-0984}, support = {/DH_/Department of Health/United Kingdom ; }, mesh = {Adult ; Aged ; Anti-Bacterial Agents/therapeutic use ; Bacteria/*classification/*isolation & purification/virology ; Carbapenems/therapeutic use ; Cephalosporins/therapeutic use ; Clostridioides difficile/drug effects/isolation & purification ; Diarrhea/*epidemiology/microbiology ; Enterocolitis, Pseudomembranous/drug therapy/*epidemiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; India/epidemiology ; Male ; Metagenomics ; Middle Aged ; Rural Population ; Urban Population ; Young Adult ; }, abstract = {BACKGROUND: The Central Indian gut microbiome remains grossly understudied. Herein, we sought to investigate the burden of antimicrobial resistance and diarrheal diseases, particularly Clostridioides difficile, in rural-agricultural and urban populations in Central India, where there is widespread unregulated antibiotic use. We utilized shotgun metagenomics to comprehensively characterize the bacterial and viral fractions of the gut microbiome and their encoded functions in 105 participants.

RESULTS: We observed distinct rural-urban differences in bacterial and viral populations, with geography exhibiting a greater influence than diarrheal status. Clostridioides difficile disease was more commonly observed in urban subjects, and their microbiomes were enriched in metabolic pathways relating to the metabolism of industrial compounds and genes encoding resistance to 3[rd] generation cephalosporins and carbapenems. By linking phages present in the microbiome to their bacterial hosts through CRISPR spacers, phage variation could be directly related to shifts in bacterial populations, with the auxiliary metabolic potential of rural-associated phages enriched for carbon and amino acid energy metabolism.

CONCLUSIONS: We report distinct differences in antimicrobial resistance gene profiles, enrichment of metabolic pathways and phage composition between rural and urban populations, as well as a higher burden of Clostridioides difficile disease in the urban population. Our results reveal that geography is the key driver of variation in urban and rural Indian microbiomes, with acute diarrheal disease, including C. difficile disease exerting a lesser impact. Future studies will be required to understand the potential role of dietary, cultural, and genetic factors in contributing to microbiome differences between rural and urban populations.}, } @article {pmid32457850, year = {2020}, author = {Guizzo, MG and Neupane, S and Kucera, M and Perner, J and Frantová, H and da Silva Vaz, I and de Oliveira, PL and Kopacek, P and Zurek, L}, title = {Poor Unstable Midgut Microbiome of Hard Ticks Contrasts With Abundant and Stable Monospecific Microbiome in Ovaries.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {211}, pmid = {32457850}, issn = {2235-2988}, mesh = {Animals ; Female ; Humans ; *Ixodes ; *Ixodidae ; *Microbiota ; Ovary ; *Rhipicephalus ; }, abstract = {Culture-independent metagenomic methodologies have enabled detection and identification of microorganisms in various biological systems and often revealed complex and unknown microbiomes. In many organisms, the microbiome outnumbers the host cells and greatly affects the host biology and fitness. Ticks are hematophagous ectoparasites with a wide host range. They vector a number of human and animal pathogens and also directly cause major economic losses in livestock. Although several reports on a tick midgut microbiota show a diverse bacterial community, in most cases the size of the bacterial population has not been determined. In this study, the microbiome was quantified in the midgut and ovaries of the ticks Ixodes ricinus and Rhipicephalus microplus before, during, and after blood feeding. Although the size of bacterial community in the midgut fluctuated with blood feeding, it was overall extremely low in comparison to that of other hematophagous arthropods. In addition, the tick ovarian microbiome of both tick species exceeded the midgut 16S rDNA copy numbers by several orders of magnitude. This indicates that the ratio of a tick midgut/ovary microbiome represents an exception to the general biology of other metazoans. In addition to the very low abundance, the tick midgut diversity in I. ricinus was variable and that is in contrast to that found in the tick ovary. The ovary of I. ricinus had a very low bacterial diversity and a very high and stable bacterial abundance with the dominant endosymbiont, Midichloria sp. The elucidation of this aspect of tick biology highlights a unique tissue-specific microbial-invertebrate host interaction.}, } @article {pmid32457482, year = {2020}, author = {Ruff, WE and Greiling, TM and Kriegel, MA}, title = {Host-microbiota interactions in immune-mediated diseases.}, journal = {Nature reviews. Microbiology}, volume = {18}, number = {9}, pages = {521-538}, pmid = {32457482}, issn = {1740-1534}, support = {K08 AI095318/AI/NIAID NIH HHS/United States ; R01 AI118855/AI/NIAID NIH HHS/United States ; T32 DK007017/DK/NIDDK NIH HHS/United States ; P30 DK079310/DK/NIDDK NIH HHS/United States ; P30 AR053495/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; Host Microbial Interactions/genetics/*physiology ; Humans ; Immune System/*immunology ; Microbiota/*immunology/*physiology ; }, abstract = {Host-microbiota interactions are fundamental for the development of the immune system. Drastic changes in modern environments and lifestyles have led to an imbalance of this evolutionarily ancient process, coinciding with a steep rise in immune-mediated diseases such as autoimmune, allergic and chronic inflammatory disorders. There is an urgent need to better understand these diseases in the context of mucosal and skin microbiota. This Review discusses the mechanisms of how the microbiota contributes to the predisposition, initiation and perpetuation of immune-mediated diseases in the context of a genetically prone host. It is timely owing to the wealth of new studies that recently contributed to this field, ranging from metagenomic studies in humans and mechanistic studies of host-microorganism interactions in gnotobiotic models and in vitro systems, to molecular mechanisms with broader implications across immune-mediated diseases. We focus on the general principles, such as breaches in immune tolerance and barriers, leading to the promotion of immune-mediated diseases by gut, oral and skin microbiota. Lastly, the therapeutic avenues that either target the microbiota, the barrier surfaces or the host immune system to restore tolerance and homeostasis will be explored.}, } @article {pmid32457278, year = {2021}, author = {Lee, SM and Kim, N and Yoon, H and Kim, YS and Choi, SI and Park, JH and Lee, DH}, title = {Compositional and Functional Changes in the Gut Microbiota in Irritable Bowel Syndrome Patients.}, journal = {Gut and liver}, volume = {15}, number = {2}, pages = {253-261}, pmid = {32457278}, issn = {2005-1212}, mesh = {Diarrhea ; Feces ; *Gastrointestinal Microbiome ; Humans ; *Irritable Bowel Syndrome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND/AIMS: This study aimed to characterize the changes in the gut microbiota of irritable bowel syndrome (IBS) patients and to investigate the consequent alterations in bacterial functions.

METHODS: We performed 16S rRNA metagenomic sequencing and a phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analyses using fecal samples from control (n=12) and diarrhea-dominant IBS patients (n=7).

RESULTS: The samples were clustered by the principal coordinates analysis depending on the presence of IBS (p=0.003). In the IBS patients, the abundances of Acidaminococcaceae, Sutterellaceae, and Desulfovibrionaceae were significantly increased, while those of Enterococcaceae, Leuconostocaceae, Clostridiaceae, Peptostreptococcaceae, and Lachnospiraceae were significantly decreased. The PICRUSt results indicated that two orthologues involved in secondary bile acid biosynthesis were significantly decreased in IBS patients. Modules involved in multidrug resistance, lipopolysaccharide biosynthesis, the reductive citrate cycle, and the citrate cycle were significantly increased in the IBS patients. In contrast, modules involved in cationic antimicrobial peptide resistance, and some transport systems were more abundant in controls than in IBS patients.

CONCLUSIONS: Changes in the gut microbiota composition in IBS patients lead to alterations in bacterial functions, such as bile acid transformation and the induction of inflammation, which is a known pathophysiological mechanism of IBS.}, } @article {pmid32451391, year = {2020}, author = {Pasolli, E and De Filippis, F and Mauriello, IE and Cumbo, F and Walsh, AM and Leech, J and Cotter, PD and Segata, N and Ercolini, D}, title = {Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2610}, pmid = {32451391}, issn = {2041-1723}, mesh = {Animals ; Databases, Genetic ; Fermented Foods/microbiology ; *Food Microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Lactobacillales/*genetics/*isolation & purification ; Lactococcus lactis/genetics/isolation & purification ; Life Style ; Metagenome ; Primates/microbiology ; Probiotics ; Streptococcus thermophilus/genetics/isolation & purification ; }, abstract = {Lactic acid bacteria (LAB) are fundamental in the production of fermented foods and several strains are regarded as probiotics. Large quantities of live LAB are consumed within fermented foods, but it is not yet known to what extent the LAB we ingest become members of the gut microbiome. By analysis of 9445 metagenomes from human samples, we demonstrate that the prevalence and abundance of LAB species in stool samples is generally low and linked to age, lifestyle, and geography, with Streptococcus thermophilus and Lactococcus lactis being most prevalent. Moreover, we identify genome-based differences between food and gut microbes by considering 666 metagenome-assembled genomes (MAGs) newly reconstructed from fermented food microbiomes along with 154,723 human MAGs and 193,078 reference genomes. Our large-scale genome-wide analysis demonstrates that closely related LAB strains occur in both food and gut environments and provides unprecedented evidence that fermented foods can be indeed regarded as a possible source of LAB for the gut microbiome.}, } @article {pmid32451027, year = {2020}, author = {Timsit, E and McMullen, C and Amat, S and Alexander, TW}, title = {Respiratory Bacterial Microbiota in Cattle: From Development to Modulation to Enhance Respiratory Health.}, journal = {The Veterinary clinics of North America. Food animal practice}, volume = {36}, number = {2}, pages = {297-320}, doi = {10.1016/j.cvfa.2020.03.001}, pmid = {32451027}, issn = {1558-4240}, mesh = {Animals ; Bacteria/genetics ; Cattle ; Cattle Diseases/*microbiology ; Microbiota/*physiology ; Respiratory System/*microbiology ; Respiratory Tract Diseases/microbiology/*veterinary ; }, abstract = {The respiratory tract of cattle is colonized by complex bacterial ecosystems also known as bacterial microbiotas. These microbiotas evolve over time and are shaped by numerous factors, including maternal vaginal microbiota, environment, age, diet, parenteral antimicrobials, and stressful events. The resulting microbiota can be diverse and enriched with known beneficial bacteria that can provide colonization resistance against bacterial pathogens or, on the contrary, with opportunistic pathogens that can predispose cattle to respiratory disease. The respiratory microbiota can be modulated by nonantimicrobial approaches to promote health, creating new potential strategies for prevention and treatment of bovine respiratory disease.}, } @article {pmid32450885, year = {2020}, author = {Rubel, MA and Abbas, A and Taylor, LJ and Connell, A and Tanes, C and Bittinger, K and Ndze, VN and Fonsah, JY and Ngwang, E and Essiane, A and Fokunang, C and Njamnshi, AK and Bushman, FD and Tishkoff, SA}, title = {Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {122}, pmid = {32450885}, issn = {1474-760X}, support = {R61-HL137063/NH/NIH HHS/United States ; R01-HL113252/NH/NIH HHS/United States ; 5T32AI007532-18/NH/NIH HHS/United States ; K24 HL115354/HL/NHLBI NIH HHS/United States ; R01 GM113657/GM/NIGMS NIH HHS/United States ; K24-HL115354/NH/NIH HHS/United States ; R35 GM134957/GM/NIGMS NIH HHS/United States ; 1R01DK104339-01/NH/NIH HHS/United States ; 1R01GM113657-01)/NH/NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; R01-HL087115/NH/NIH HHS/United States ; U01-HL098957/NH/NIH HHS/United States ; }, mesh = {Animals ; Cameroon ; Diet, Paleolithic ; Farmers/*statistics & numerical data ; *Gastrointestinal Microbiome ; Host-Parasite Interactions/*immunology ; Humans ; Life Style ; Machine Learning ; Metagenome ; Nematoda/*physiology ; *Parasite Load ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: African populations provide a unique opportunity to interrogate host-microbe co-evolution and its impact on adaptive phenotypes due to their genomic, phenotypic, and cultural diversity. We integrate gut microbiome 16S rRNA amplicon and shotgun metagenomic sequence data with quantification of pathogen burden and measures of immune parameters for 575 ethnically diverse Africans from Cameroon. Subjects followed pastoralist, agropastoralist, and hunter-gatherer lifestyles and were compared to an urban US population from Philadelphia.

RESULTS: We observe significant differences in gut microbiome composition across populations that correlate with subsistence strategy and country. After these, the variable most strongly associated with gut microbiome structure in Cameroonians is the presence of gut parasites. Hunter-gatherers have high frequencies of parasites relative to agropastoralists and pastoralists. Ascaris lumbricoides, Necator americanus, Trichuris trichiura, and Strongyloides stercoralis soil-transmitted helminths ("ANTS" parasites) significantly co-occur, and increased frequency of gut parasites correlates with increased gut microbial diversity. Gut microbiome composition predicts ANTS positivity with 80% accuracy. Colonization with ANTS, in turn, is associated with elevated levels of TH1, TH2, and proinflammatory cytokines, indicating an association with multiple immune mechanisms. The unprecedented size of this dataset allowed interrogation of additional questions-for example, we find that Fulani pastoralists, who consume high levels of milk, possess an enrichment of gut bacteria that catabolize galactose, an end product of lactose metabolism, and of bacteria that metabolize lipids.

CONCLUSIONS: These data document associations of bacterial microbiota and eukaryotic parasites with each other and with host immune responses; each of these is further correlated with subsistence practices.}, } @article {pmid32450738, year = {2020}, author = {Chakraborty, S and Mandal, J and Cheng, X and Galla, S and Hindupur, A and Saha, P and Yeoh, BS and Mell, B and Yeo, JY and Vijay-Kumar, M and Yang, T and Joe, B}, title = {Diurnal Timing Dependent Alterations in Gut Microbial Composition Are Synchronously Linked to Salt-Sensitive Hypertension and Renal Damage.}, journal = {Hypertension (Dallas, Tex. : 1979)}, volume = {76}, number = {1}, pages = {59-72}, pmid = {32450738}, issn = {1524-4563}, support = {R01 CA219144/CA/NCI NIH HHS/United States ; R01 HL143082/HL/NHLBI NIH HHS/United States ; }, mesh = {3-Hydroxybutyric Acid/blood ; Animals ; Base Sequence ; Blood Pressure/drug effects/*physiology ; Circadian Rhythm/*physiology ; Diet, Sodium-Restricted ; Energy Metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/*physiology ; Genes, Bacterial ; Hypertension/etiology/*microbiology/physiopathology ; Kidney/*drug effects ; Male ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Inbred Dahl ; Sodium Chloride, Dietary/*administration & dosage/adverse effects ; }, abstract = {Alterations of diurnal rhythms of blood pressure (BP) and reshaping of gut microbiota are both independently associated with hypertension. However, the relationships between biorhythms of BP and gut microbial composition are unknown. We hypothesized that diurnal timing-associated alterations of microbial compositions are synchronous with diurnal rhythmicity, dip in BP, and renal function. To test this hypothesis, Dahl salt-sensitive (S) rats on low- and high-salt diets were examined for time of day effects on gut microbiota, BP, and indicators of renal damage. Major shifts in night and day patterns of specific groups of microbiota were observed between the dark (active) and light (rest) phases, which correlated with diurnal rhythmicity of BP. The diurnal abundance of Firmicutes, Bacteroidetes, and Actinobacteria were independently associated with BP. Discrete bacterial taxa were observed to correlate independently or interactively with one or more of the following 3 factors: (1) BP rhythm, (2) dietary salt, and (3) dip in BP. Phylogenetic Investigation of Communities revealed diurnal timing effects on microbial pathways, characterized by upregulated biosynthetic processes during the active phase of host, and upregulated degradation pathways of metabolites in the resting phase. Additional metagenomics functional pathways with rhythm variations were noted for aromatic amino acid metabolism and taurine metabolism. These diurnal timing dependent changes in microbiota, their functional pathways, and BP dip were associated with concerted effects of the levels of renal lipocalin 2 and kidney injury molecule-1 expression. These data provide evidence for a firm and concerted diurnal timing effects of BP, renal damage, and select microbial communities.}, } @article {pmid32448763, year = {2021}, author = {Carr, VR and Shkoporov, A and Hill, C and Mullany, P and Moyes, DL}, title = {Probing the Mobilome: Discoveries in the Dynamic Microbiome.}, journal = {Trends in microbiology}, volume = {29}, number = {2}, pages = {158-170}, doi = {10.1016/j.tim.2020.05.003}, pmid = {32448763}, issn = {1878-4380}, mesh = {Animals ; Bacteria/classification/*genetics/isolation & purification ; Humans ; Interspersed Repetitive Sequences ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {There has been an explosion of metagenomic data representing human, animal, and environmental microbiomes. This provides an unprecedented opportunity for comparative and longitudinal studies of many functional aspects of the microbiome that go beyond taxonomic classification, such as profiling genetic determinants of antimicrobial resistance, interactions with the host, potentially clinically relevant functions, and the role of mobile genetic elements (MGEs). One of the most important but least studied of these aspects are the MGEs, collectively referred to as the 'mobilome'. Here we elaborate on the benefits and limitations of using different metagenomic protocols, discuss the relative merits of various sequencing technologies, and highlight relevant bioinformatics tools and pipelines to predict the presence of MGEs and their microbial hosts.}, } @article {pmid32448430, year = {2020}, author = {Pan, S and Chen, R}, title = {Metaproteomic analysis of human gut microbiome in digestive and metabolic diseases.}, journal = {Advances in clinical chemistry}, volume = {97}, number = {}, pages = {1-12}, pmid = {32448430}, issn = {2162-9471}, support = {R01 CA180949/CA/NCI NIH HHS/United States ; R01 CA211892/CA/NCI NIH HHS/United States ; }, mesh = {Digestive System Diseases/*metabolism ; *Gastrointestinal Microbiome ; Humans ; Metabolic Diseases/*metabolism ; Proteins/*metabolism ; *Proteomics ; }, abstract = {Metaproteomics, as a subfield of proteomics, has quickly emerged as a pivotal tool for global characterization of a microbiome system at a functional level. It has been increasingly applied in studying human digestive and metabolic diseases, and provides information-rich data to identify the dysbiosis of human gut microbiome related to healthy or disease states to elucidate the molecular events underlying host-microbiota interplays. While significant technical challenges still exist, this emerging technology has been demonstrated to provide essential information in interrogating functional changes in the human gut microbiome, complementary to metagenomics and metatranscriptomics. This chapter overviews the overall metaproteomic work flow and its recent applications in studying human gut microbiome relevant to digestive and metabolic diseases.}, } @article {pmid32447634, year = {2020}, author = {Davies, N and O'Sullivan, JM and Plank, LD and Murphy, R}, title = {Gut Microbial Predictors of Type 2 Diabetes Remission Following Bariatric Surgery.}, journal = {Obesity surgery}, volume = {30}, number = {9}, pages = {3536-3548}, pmid = {32447634}, issn = {1708-0428}, support = {Project grant//Auckland Medical Research Foundation/ ; Flexible funding//Maurice Wilkins Centre/ ; }, mesh = {Bacteroidetes ; *Bariatric Surgery ; *Diabetes Mellitus, Type 2/surgery ; Gastrectomy ; *Gastric Bypass ; *Gastrointestinal Microbiome ; Humans ; *Obesity, Morbid/surgery ; Weight Loss ; }, abstract = {PURPOSE: Distinct anatomical rearrangements of the gastrointestinal tract achieved by various types of bariatric surgery cause changes in nutrient intake and gut microbiota. The contribution of such gut microbiota changes to remission of type 2 diabetes (T2D) remains unclear.

AIM: We examined gut microbiota changes following banded Roux-en-Y gastric bypass (RYGB) or sleeve gastrectomy (SG) in a randomised study, in relation to T2D remission.

MATERIALS AND METHODS: Whole-metagenome shotgun sequencing was carried out on paired stool samples at pre- and 1-year post-surgery collected from 44 participants with T2D randomised to banded Roux-en-Y gastric bypass (RYGB) or sleeve gastrectomy (SG). Taxonomic composition and predicted functional potential of the gut bacteria were identified using HUMANn2, and annotated using MetaCyc. Five-day dietary records (analysed using FoodWorks v8.0), body weight and diabetes status were recorded at both time points.

RESULTS: RYGB participants had higher percentage excess weight loss than SG (p = 0.01), even though dietary intake was similar at 1-year post-surgery. Similar proportions achieved diabetes remission (HbA1c < 48 mmol/mol without medications) after either RYGB (68%) or SG (59%). RYGB resulted in increased abundances of Firmicutes and Proteobacteria, while SG resulted in increased Bacteroidetes. Pre-surgery, an increased abundance of Eubacteriaceae (p = 0.01) and Alistipes putredinis (p = 0.01) was observed in those who went on to remit from T2D post-surgery. Following surgery, Lachnospiraceae (p = 0.04) and Roseburia (p = 0.01) species were more abundant in those who had achieved T2D remission.

CONCLUSIONS: Specific stool bacterial taxa may signal likelihood of T2D remission after bariatric surgery which is potentially mediated by increases in Lachnospiraceae and Roseburia.}, } @article {pmid32445473, year = {2020}, author = {Ishizawa, H and Kuroda, M and Inoue, D and Morikawa, M and Ike, M}, title = {Community dynamics of duckweed-associated bacteria upon inoculation of plant growth-promoting bacteria.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {7}, pages = {}, doi = {10.1093/femsec/fiaa101}, pmid = {32445473}, issn = {1574-6941}, mesh = {*Araceae ; Bacteria/genetics ; Betaproteobacteria ; *Microbiota ; Plant Development ; Plant Roots ; }, abstract = {Plant growth-promoting bacteria (PGPB) have recently been demonstrated as a promising agent to improve wastewater treatment and biomass production efficiency of duckweed hydrocultures. With a view to their reliable use in aqueous environments, this study analysed the plant colonization dynamics of PGPB and the ecological consequences for the entire duckweed-associated bacterial community. A PGPB strain, Aquitalea magnusonii H3, was inoculated to duckweed at different cell densities or timings in the presence of three environmental bacterial communities. The results showed that strain H3 improved duckweed growth by 11.7-32.1% in five out of nine experiments. Quantitative-PCR and amplicon sequencing analyses showed that strain H3 successfully colonized duckweed after 1 and 3 d of inoculation in all cultivation tests. However, it significantly decreased in number after 7 d, and similar bacterial communities were observed on duckweed regardless of H3 inoculation. Predicted metagenome analysis suggested that genes related to bacterial chemotactic motility and surface attachment systems are consistently enriched through community assembly on duckweed. Taken together, strain H3 dominantly colonized duckweed for a short period and improved duckweed growth. However, the inoculation of the PGPB did not have a lasting impact due to the strong resilience of the natural duckweed microbiome.}, } @article {pmid32442592, year = {2020}, author = {Wang, Z and Liang, Y and Yu, J and Zhang, D and Ren, L and Zhang, Z and Liu, Y and Wu, X and Liu, L and Tang, Z}, title = {Guchang Zhixie Wan protects mice against dextran sulfate sodium-induced colitis through modulating the gut microbiota in colon.}, journal = {Journal of ethnopharmacology}, volume = {260}, number = {}, pages = {112991}, doi = {10.1016/j.jep.2020.112991}, pmid = {32442592}, issn = {1872-7573}, mesh = {Animals ; Colitis/*prevention & control ; Colon/drug effects/pathology ; Cytokines/metabolism ; Dextran Sulfate ; Disease Models, Animal ; Dose-Response Relationship, Drug ; Drugs, Chinese Herbal/administration & dosage/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Inflammation/drug therapy/pathology ; Male ; Mice ; Sulfasalazine/pharmacology ; }, abstract = {Guchang Zhixie Wan (GC) is a traditional Chinese patent medicine used in the treatment of colitis in clinical trials. Though the notable effect of GC on colitis, the concrete mechanism of GC remain elusive. Emerging evidence showed that the imbalances of inflammatory cytokines and gut microbiota were both closely related to the initiation and progression of colitis.

AIM OF THE STUDY: To elucidate the relationship between the protective effects of GC on colitis and gut microbiota.

MATERIALS AND METHODS: Male Kunming (KM) mice were enrolled in our work to establish colitis model induced by dextran sulfate sodium (DSS). The colitis mice were randomly divided into different groups and treated orally with 125 mg/kg of sulfasalazine (positive control) and 25, 50, 100 mg/kg of GC for 7 days, respectively. Inflammation cytokines of IL-1β, IL-4, IL-6, IL-8, IL-11, IL-12 and TNF-α were detected by ELISA analysis and the histological changes were detected by H&E staining. Gut microbiota diversity was analyzed by 16S rDNA sequencing. Metagenomes analysis were also conducted to reflect the protective effects of GC on colitis.

RESULTS: The results of CAS (Clinical Activity Score) confirmed the protective effects of GC on colitis. After administration of GC, the levels of pro-inflammatory cytokines IL-1β, IL-6, IL-8, IL-11, IL-12 and TNF-α were all decreased while the anti-inflammatory cytokines IL-4 was slightly increased, indicating that GC could down regulate pro-inflammatory cytokines. H&E staining revealed that GC could improve the histopathological structure of the colon tissue. The results of 16S rDNA sequences analysis showed that GC could decrease the relative abundance of Turicibacter and increase the relative abundance of Ruminococcaceae_UCG-005.

CONCLUSION: GC greatly improve the health condition of colitis mice induced by DSS through improving the imbalances of inflammatory cytokines and gut microbiota.}, } @article {pmid32442562, year = {2020}, author = {Zuo, T and Zhang, F and Lui, GCY and Yeoh, YK and Li, AYL and Zhan, H and Wan, Y and Chung, ACK and Cheung, CP and Chen, N and Lai, CKC and Chen, Z and Tso, EYK and Fung, KSC and Chan, V and Ling, L and Joynt, G and Hui, DSC and Chan, FKL and Chan, PKS and Ng, SC}, title = {Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization.}, journal = {Gastroenterology}, volume = {159}, number = {3}, pages = {944-955.e8}, pmid = {32442562}, issn = {1528-0012}, mesh = {Adult ; Aged ; *Betacoronavirus ; COVID-19 ; Coronavirus Infections/*microbiology ; Dysbiosis/*virology ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/microbiology ; Hong Kong/epidemiology ; Hospitalization/statistics & numerical data ; Humans ; Male ; Middle Aged ; Pandemics ; Pilot Projects ; Pneumonia, Viral/*microbiology ; SARS-CoV-2 ; }, abstract = {BACKGROUND & AIMS: Although severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects gastrointestinal tissues, little is known about the roles of gut commensal microbes in susceptibility to and severity of infection. We investigated changes in fecal microbiomes of patients with SARS-CoV-2 infection during hospitalization and associations with severity and fecal shedding of virus.

METHODS: We performed shotgun metagenomic sequencing analyses of fecal samples from 15 patients with Coronavirus Disease 2019 (COVID-19) in Hong Kong, from February 5 through March 17, 2020. Fecal samples were collected 2 or 3 times per week from time of hospitalization until discharge; disease was categorized as mild (no radiographic evidence of pneumonia), moderate (pneumonia was present), severe (respiratory rate ≥30/min, or oxygen saturation ≤93% when breathing ambient air), or critical (respiratory failure requiring mechanical ventilation, shock, or organ failure requiring intensive care). We compared microbiome data with those from 6 subjects with community-acquired pneumonia and 15 healthy individuals (controls). We assessed gut microbiome profiles in association with disease severity and changes in fecal shedding of SARS-CoV-2.

RESULTS: Patients with COVID-19 had significant alterations in fecal microbiomes compared with controls, characterized by enrichment of opportunistic pathogens and depletion of beneficial commensals, at time of hospitalization and at all timepoints during hospitalization. Depleted symbionts and gut dysbiosis persisted even after clearance of SARS-CoV-2 (determined from throat swabs) and resolution of respiratory symptoms. The baseline abundance of Coprobacillus, Clostridium ramosum, and Clostridium hathewayi correlated with COVID-19 severity; there was an inverse correlation between abundance of Faecalibacterium prausnitzii (an anti-inflammatory bacterium) and disease severity. Over the course of hospitalization, Bacteroides dorei, Bacteroides thetaiotaomicron, Bacteroides massiliensis, and Bacteroides ovatus, which downregulate expression of angiotensin-converting enzyme 2 (ACE2) in murine gut, correlated inversely with SARS-CoV-2 load in fecal samples from patients.

CONCLUSIONS: In a pilot study of 15 patients with COVID-19, we found persistent alterations in the fecal microbiome during the time of hospitalization, compared with controls. Fecal microbiota alterations were associated with fecal levels of SARS-CoV-2 and COVID-19 severity. Strategies to alter the intestinal microbiota might reduce disease severity.}, } @article {pmid32442018, year = {2020}, author = {Ritchie, AI and Singanayagam, A}, title = {Metagenomic Characterization of the Respiratory Microbiome. A Pièce de Résistance.}, journal = {American journal of respiratory and critical care medicine}, volume = {202}, number = {3}, pages = {321-322}, pmid = {32442018}, issn = {1535-4970}, mesh = {Anti-Bacterial Agents ; Macrolides ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; }, } @article {pmid32440704, year = {2020}, author = {Wang, G and Wang, Y and Man, H and Lee, YW and Shi, J and Xu, J}, title = {Metabolomics-guided analysis reveals a two-step epimerization of deoxynivalenol catalyzed by the bacterial consortium IFSN-C1.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {13}, pages = {6045-6056}, pmid = {32440704}, issn = {1432-0614}, support = {U1604234//National Natural Science Foundation of China/ ; 31901805//National Natural Science Foundation of China/ ; 31872914//National Natural Science Foundation of China/ ; CX(17)1003//Jiangsu Agricultural Science and Technology Independent Innovation Fund/ ; 2019-02-08-00-12-F01148//Shanghai Agriculture Applied Technology Development Program/ ; }, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; Biodegradation, Environmental ; Inactivation, Metabolic ; Metabolomics ; Metagenomics ; Microbial Consortia/genetics/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Trichothecenes/chemistry/*metabolism ; Triticum/microbiology ; }, abstract = {Deoxynivalenol (DON) is commonly found in wheat and wheat-derived foods, posing a threat to human health. Biodegradation is an efficient and eco-friendly measure for mycotoxin detoxification. Understanding the mechanism of DON biodegradation is hence of great importance. Herein, we report the application of metabolomics methods for the analysis of DON degradation by a bacterial consortium isolated from wheat leaves collected in Jiangsu Province. Metabolomics analysis combined with a nuclear magnetic resonance analysis revealed the main degradation product, 3-keto-DON, and a minor degradation product, 3-epi-DON. Further study illustrated that DON underwent a two-step epimerization through the intermediate 3-keto-DON. Sequencing analysis of the 16S rRNA metagenome of the microorganismal community suggested that the abundance of three bacterial genera, Achromobacter, Sphingopyxis, and Sphingomonas, substantially increased during the coculture of bacterial consortium and DON. Further investigation revealed that Devosia sp. might be responsible for the epimerization of 3-keto-DON. These findings shed light on the catabolic pathways of DON during biodegradation and illustrate the potential of using metabolomics approaches in biodegradation studies.Key Points• A bacterial consortium was isolated with good deoxynivalenol-degrading potential. • Metabolomics approaches were successfully used to interpret the degradation pathway. • A trace-amount degradation product was determined by metabolomics and NMR analysis. Graphical Abstract .}, } @article {pmid32439449, year = {2020}, author = {Yao, H and Wang, L and Tang, X and Yang, Z and Li, H and Sun, C and Wu, X and Xu, D}, title = {Two novel polysaccharides from Solanum nigrum L. exert potential prebiotic effects in an in vitro fermentation model.}, journal = {International journal of biological macromolecules}, volume = {159}, number = {}, pages = {648-658}, doi = {10.1016/j.ijbiomac.2020.05.121}, pmid = {32439449}, issn = {1879-0003}, mesh = {Chromatography, Gas ; Fatty Acids, Volatile/biosynthesis ; Feces/chemistry/microbiology ; *Fermentation ; Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; Molecular Weight ; Monosaccharides/chemistry ; Polysaccharides/*chemistry/isolation & purification ; *Prebiotics ; Solanum nigrum/*chemistry ; }, abstract = {In this research, two novel polysaccharides (S1 and S2) from Solanum nigrum L were extracted and purified. Then homogeneity, molecular weights, major chemical contents and monosaccharide compositions of S1 and S2 were determined. Then, the effects of S1 and S2 on human faecal microbial community and short-chain fatty acid production were investigated using an in vitro fermentation model. Results showed that S1 and S2 have different impacts on human gut microbiota in vitro. S1 selectively promoted the abundance of 9 genera and the production of propionic acid, butyric acid, isobutyric acid, valeric acid and isovaleric acid; while S2 selectively promoted the abundance of 8 genera and the production of acetic acid, propionic acid, butyric acid, isobutyric acid, valeric acid, isovaleric acid and succinic acid. Also, S1 group had higher abundance of genera Butyricimonas and Megamonas and higher levels of lactic acid than S2; while S2 group had higher abundance of Megaphaera and higher levels of butyric acid, valeric acid, isobutyric acid, isovaleric acid and succinic acid comparably. We concluded that S1 and S2 may have potential prebiotic functions.}, } @article {pmid32439117, year = {2020}, author = {Pammi, M and Hollister, E and Neu, J}, title = {Gut Injury and the Microbiome in Neonates.}, journal = {Clinics in perinatology}, volume = {47}, number = {2}, pages = {369-382}, doi = {10.1016/j.clp.2020.02.010}, pmid = {32439117}, issn = {1557-9840}, mesh = {Dysbiosis/*congenital/*immunology ; Enterocolitis, Necrotizing/congenital/immunology ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Intestinal Diseases/*congenital/*immunology ; Risk Factors ; }, abstract = {The causes of neonatal gut injury are multifactorial and include ischemia, tissue hypoxia due to anemia, excessive inflammation, deficiency of growth factors, and food protein sensitivity. The developing intestinal microbiome plays a role in some of these forms of intestinal injury but knowledge of its relative role in each remains poorly understood. Commensal bacteria are required for normal immune development and immune tolerance. Dysbiosis in the neonatal gut that alters the patterns of commensal and pathogenic bacteria may accentuate gut injury.}, } @article {pmid32438916, year = {2020}, author = {Lajoie, G and Maglione, R and Kembel, SW}, title = {Adaptive matching between phyllosphere bacteria and their tree hosts in a neotropical forest.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {70}, pmid = {32438916}, issn = {2049-2618}, support = {CGS-D//Natural Sciences and Engineering Research Council of Canada/International ; Discovery Grant//Natural Sciences and Engineering Research Council of Canada/International ; }, mesh = {Adaptation, Physiological ; *Bacteria/genetics ; Biodiversity ; Forests ; *Microbiota ; Phylogeny ; *Plant Leaves/microbiology ; *Trees/microbiology ; Tropical Climate ; }, abstract = {BACKGROUND: The phyllosphere is an important microbial habitat, but our understanding of how plant hosts drive the composition of their associated leaf microbial communities and whether taxonomic associations between plants and phyllosphere microbes represent adaptive matching remains limited. In this study, we quantify bacterial functional diversity in the phyllosphere of 17 tree species in a diverse neotropical forest using metagenomic shotgun sequencing. We ask how hosts drive the functional composition of phyllosphere communities and their turnover across tree species, using host functional traits and phylogeny.

RESULTS: Neotropical tree phyllosphere communities are dominated by functions related to the metabolism of carbohydrates, amino acids, and energy acquisition, along with environmental signalling pathways involved in membrane transport. While most functional variation was observed within communities, there is non-random assembly of microbial functions across host species possessing different leaf traits. Metabolic functions related to biosynthesis and degradation of secondary compounds, along with signal transduction and cell-cell adhesion, were particularly important in driving the match between microbial functions and host traits. These microbial functions were also evolutionarily conserved across the host phylogeny.

CONCLUSIONS: Functional profiling based on metagenomic shotgun sequencing offers evidence for the presence of a core functional microbiota across phyllosphere communities of neotropical trees. While functional turnover across phyllosphere communities is relatively small, the association between microbial functions and leaf trait gradients among host species supports a significant role for plant hosts as selective filters on phyllosphere community assembly. This interpretation is supported by the presence of phylogenetic signal for the microbial traits driving inter-community variation across the host phylogeny. Taken together, our results suggest that there is adaptive matching between phyllosphere microbes and their plant hosts. Video abstract.}, } @article {pmid32438915, year = {2020}, author = {Zolti, A and Green, SJ and Sela, N and Hadar, Y and Minz, D}, title = {The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {71}, pmid = {32438915}, issn = {2049-2618}, support = {IS- 4662-13//United States - Israel Binational Agricultural Research and Development Fund/International ; M34-011//USAID-MERK/International ; 821-0142-13//Ministry of Agriculture and Rural Development (IL)/International ; }, mesh = {*Biosensing Techniques ; *Host Microbial Interactions ; Metagenomics ; *Microbiota/genetics ; *Plant Roots/microbiology ; Soil Microbiology ; *Stress, Physiological ; }, abstract = {BACKGROUND: Microbial communities are highly responsive to environmental cues, and both their structure and activity can be altered in response to changing conditions. We hypothesized that host-associated microbial communities, particularly those colonizing host surfaces, can serve as in situ sensors to reveal environmental conditions experienced by both microorganisms and the host. For a proof-of-concept, we studied a model plant-soil system and employed a non-deterministic gene-centric approach. A holistic analysis was performed using plants of two species and irrigation with water of low quality to induce host stress. Our analyses examined the genetic potential (DNA) and gene expression patterns (RNA) of plant-associated microbial communities, as well as transcriptional profiling of host plants.

RESULTS: Transcriptional analysis of plants irrigated with treated wastewater revealed significant enrichment of general stress-associated root transcripts relative to plants irrigated with fresh water. Metagenomic analysis of root-associated microbial communities in treated wastewater-irrigated plants, however, revealed enrichment of more specific stress-associated genes relating to high levels of salt, high pH and lower levels of oxygen. Meta-analysis of these differentially abundant genes obtained from other metagenome studies, provided evidence of the link between environmental factors such as pH and oxygen and these genes. Analysis of microbial transcriptional response demonstrated that enriched gene content was actively expressed, which implies contemporary response to elevated levels of pH and salt.

CONCLUSIONS: We demonstrate here that microbial profiling can elucidate stress signals that cannot be observed even through interrogation of host transcriptome, leading to an alternate mechanism for evaluating in situ conditions experienced by host organisms. This study is a proof-of-concept for the use of microbial communities as microsensors, with great potential for interrogation of a wide range of host systems. Video Abstract.}, } @article {pmid32437658, year = {2020}, author = {Ang, QY and Alexander, M and Newman, JC and Tian, Y and Cai, J and Upadhyay, V and Turnbaugh, JA and Verdin, E and Hall, KD and Leibel, RL and Ravussin, E and Rosenbaum, M and Patterson, AD and Turnbaugh, PJ}, title = {Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells.}, journal = {Cell}, volume = {181}, number = {6}, pages = {1263-1275.e16}, pmid = {32437658}, issn = {1097-4172}, support = {T32 AI060537/AI/NIAID NIH HHS/United States ; R21 CA227232/CA/NCI NIH HHS/United States ; U54 GM104940/GM/NIGMS NIH HHS/United States ; M01 RR001271/RR/NCRR NIH HHS/United States ; P30 DK098722/DK/NIDDK NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; P30 DK072476/DK/NIDDK NIH HHS/United States ; K08 AG048354/AG/NIA NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Animals ; Diet, High-Fat/methods ; Diet, Ketogenic/methods ; Female ; Gastrointestinal Microbiome/*immunology/*physiology ; Humans ; Intestines/*immunology/*microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Microbiota/immunology/physiology ; Middle Aged ; Th17 Cells/*immunology/microbiology/*physiology ; Young Adult ; }, abstract = {Very low-carbohydrate, high-fat ketogenic diets (KDs) induce a pronounced shift in metabolic fuel utilization that elevates circulating ketone bodies; however, the consequences of these compounds for host-microbiome interactions remain unknown. Here, we show that KDs alter the human and mouse gut microbiota in a manner distinct from high-fat diets (HFDs). Metagenomic and metabolomic analyses of stool samples from an 8-week inpatient study revealed marked shifts in gut microbial community structure and function during the KD. Gradient diet experiments in mice confirmed the unique impact of KDs relative to HFDs with a reproducible depletion of bifidobacteria. In vitro and in vivo experiments showed that ketone bodies selectively inhibited bifidobacterial growth. Finally, mono-colonizations and human microbiome transplantations into germ-free mice revealed that the KD-associated gut microbiota reduces the levels of intestinal pro-inflammatory Th17 cells. Together, these results highlight the importance of trans-kingdom chemical dialogs for mediating the host response to dietary interventions.}, } @article {pmid32434845, year = {2020}, author = {Evans, JT and Denef, VJ}, title = {To Dereplicate or Not To Dereplicate?.}, journal = {mSphere}, volume = {5}, number = {3}, pages = {}, pmid = {32434845}, issn = {2379-5042}, mesh = {*Metagenome ; Metagenomics ; Microbiota ; Phylogeny ; *Software ; }, abstract = {Metagenome-assembled genomes (MAGs) expand our understanding of microbial diversity, evolution, and ecology. Concerns have been raised on how sequencing, assembly, binning, and quality assessment tools may result in MAGs that do not reflect single populations in nature. Here, we reflect on another issue, i.e., how to handle highly similar MAGs assembled from independent data sets. Obtaining multiple genomic representatives for a species is highly valuable, as it allows for population genomic analyses; however, when retaining genomes of closely related populations, it complicates MAG quality assessment and abundance inferences. We show that (i) published data sets contain a large fraction of MAGs sharing >99% average nucleotide identity, (ii) different software packages and parameters used to resolve this redundancy remove very different numbers of MAGs, and (iii) the removal of closely related genomes leads to losses of population-specific auxiliary genes. Finally, we highlight some approaches that can infer strain-specific dynamics across a sample series without dereplication.}, } @article {pmid32434436, year = {2020}, author = {Seneviratne, CJ and Balan, P and Suriyanarayanan, T and Lakshmanan, M and Lee, DY and Rho, M and Jakubovics, N and Brandt, B and Crielaard, W and Zaura, E}, title = {Oral microbiome-systemic link studies: perspectives on current limitations and future artificial intelligence-based approaches.}, journal = {Critical reviews in microbiology}, volume = {46}, number = {3}, pages = {288-299}, doi = {10.1080/1040841X.2020.1766414}, pmid = {32434436}, issn = {1549-7828}, mesh = {Arthritis, Rheumatoid/diagnosis/microbiology ; *Artificial Intelligence ; Atherosclerosis/diagnosis/microbiology ; Diabetes Mellitus, Type 2/diagnosis/microbiology ; *Diagnosis ; *Disease ; Female ; Humans ; Metagenomics ; *Microbiota ; Mouth/*microbiology ; Neural Networks, Computer ; Pancreatic Neoplasms/diagnosis/microbiology ; Pregnancy ; }, abstract = {In the past decade, there has been a tremendous increase in studies on the link between oral microbiome and systemic diseases. However, variations in study design and confounding variables across studies often lead to inconsistent observations. In this narrative review, we have discussed the potential influence of study design and confounding variables on the current sequencing-based oral microbiome-systemic disease link studies. The current limitations of oral microbiome-systemic link studies on type 2 diabetes mellitus, rheumatoid arthritis, pregnancy, atherosclerosis, and pancreatic cancer are discussed in this review, followed by our perspective on how artificial intelligence (AI), particularly machine learning and deep learning approaches, can be employed for predicting systemic disease and host metadata from the oral microbiome. The application of AI for predicting systemic disease as well as host metadata requires the establishment of a global database repository with microbiome sequences and annotated host metadata. However, this task requires collective efforts from researchers working in the field of oral microbiome to establish more comprehensive datasets with appropriate host metadata. Development of AI-based models by incorporating consistent host metadata will allow prediction of systemic diseases with higher accuracies, bringing considerable clinical benefits.}, } @article {pmid32433701, year = {2020}, author = {Taylor, WS and Pearson, J and Miller, A and Schmeier, S and Frizelle, FA and Purcell, RV}, title = {MinION Sequencing of colorectal cancer tumour microbiomes-A comparison with amplicon-based and RNA-Sequencing.}, journal = {PloS one}, volume = {15}, number = {5}, pages = {e0233170}, pmid = {32433701}, issn = {1932-6203}, mesh = {*Bacteria/classification/genetics ; Colorectal Neoplasms/genetics/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; *Metagenome ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA ; }, abstract = {BACKGROUND: Recent evidence suggests a role for the gut microbiome in the development and progression of many diseases and many studies have been carried out to analyse the microbiome using a variety of methods. In this study, we compare MinION sequencing with meta-transcriptomics and amplicon-based sequencing for microbiome analysis of colorectal tumour tissue samples.

METHODS: DNA and RNA were extracted from 11 colorectal tumour samples. 16S rRNA amplicon sequencing and MinION sequencing was carried out using genomic DNA, and RNA-Sequencing for meta-transcriptomic analysis. Non-human MinION and RNA-Sequencing reads, and 16S rRNA amplicon sequencing reads were taxonomically classified using a database built from available RefSeq bacterial and archaeal genomes and a k-mer based algorithm in Kraken2. Concordance between the three platforms at different taxonomic levels was tested on a per-sample basis using Spearman's rank correlation.

RESULTS: The average number of reads per sample using RNA-Sequencing was greater than 129 times that generated using MinION sequencing. However, the average read length of MinION sequences was more than 13 times that of RNA or 16S rRNA amplicon sequencing. Taxonomic assignment using 16S sequencing was less reliable beyond the genus level, and both RNA-Sequencing and MinION sequencing could detect greater numbers of phyla and genera in the same samples, compared to 16S sequencing. Bacterial species associated with colorectal cancer, Fusobacterium nucleatum, Parvimonas micra, Bacteroides fragilis and Porphyromonas gingivalis, were detectable using MinION, RNA-Sequencing and 16S rRNA amplicon sequencing data.

CONCLUSIONS: Long-read sequences generated using MinION sequencing can compensate for low numbers of reads for bacterial classification. MinION sequencing can discriminate between bacterial strains and plasmids and shows potential as a cost-effective tool for rapid microbiome sequencing in a clinical setting.}, } @article {pmid32433607, year = {2020}, author = {Vieira-Silva, S and Falony, G and Belda, E and Nielsen, T and Aron-Wisnewsky, J and Chakaroun, R and Forslund, SK and Assmann, K and Valles-Colomer, M and Nguyen, TTD and Proost, S and Prifti, E and Tremaroli, V and Pons, N and Le Chatelier, E and Andreelli, F and Bastard, JP and Coelho, LP and Galleron, N and Hansen, TH and Hulot, JS and Lewinter, C and Pedersen, HK and Quinquis, B and Rouault, C and Roume, H and Salem, JE and Søndertoft, NB and Touch, S and , and Dumas, ME and Ehrlich, SD and Galan, P and Gøtze, JP and Hansen, T and Holst, JJ and Køber, L and Letunic, I and Nielsen, J and Oppert, JM and Stumvoll, M and Vestergaard, H and Zucker, JD and Bork, P and Pedersen, O and Bäckhed, F and Clément, K and Raes, J}, title = {Statin therapy is associated with lower prevalence of gut microbiota dysbiosis.}, journal = {Nature}, volume = {581}, number = {7808}, pages = {310-315}, pmid = {32433607}, issn = {1476-4687}, mesh = {Bacteroides/isolation & purification ; Cohort Studies ; Cross-Sectional Studies ; Dysbiosis/*epidemiology/*prevention & control ; Faecalibacterium/isolation & purification ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Hydroxymethylglutaryl-CoA Reductase Inhibitors/administration & dosage/*pharmacology/therapeutic use ; Inflammatory Bowel Diseases/microbiology ; Male ; Obesity/microbiology ; Prevalence ; }, abstract = {Microbiome community typing analyses have recently identified the Bacteroides2 (Bact2) enterotype, an intestinal microbiota configuration that is associated with systemic inflammation and has a high prevalence in loose stools in humans[1,2]. Bact2 is characterized by a high proportion of Bacteroides, a low proportion of Faecalibacterium and low microbial cell densities[1,2], and its prevalence varies from 13% in a general population cohort to as high as 78% in patients with inflammatory bowel disease[2]. Reported changes in stool consistency[3] and inflammation status[4] during the progression towards obesity and metabolic comorbidities led us to propose that these developments might similarly correlate with an increased prevalence of the potentially dysbiotic Bact2 enterotype. Here, by exploring obesity-associated microbiota alterations in the quantitative faecal metagenomes of the cross-sectional MetaCardis Body Mass Index Spectrum cohort (n = 888), we identify statin therapy as a key covariate of microbiome diversification. By focusing on a subcohort of participants that are not medicated with statins, we find that the prevalence of Bact2 correlates with body mass index, increasing from 3.90% in lean or overweight participants to 17.73% in obese participants. Systemic inflammation levels in Bact2-enterotyped individuals are higher than predicted on the basis of their obesity status, indicative of Bact2 as a dysbiotic microbiome constellation. We also observe that obesity-associated microbiota dysbiosis is negatively associated with statin treatment, resulting in a lower Bact2 prevalence of 5.88% in statin-medicated obese participants. This finding is validated in both the accompanying MetaCardis cardiovascular disease dataset (n = 282) and the independent Flemish Gut Flora Project population cohort (n = 2,345). The potential benefits of statins in this context will require further evaluation in a prospective clinical trial to ascertain whether the effect is reproducible in a randomized population and before considering their application as microbiota-modulating therapeutics.}, } @article {pmid32433519, year = {2020}, author = {Mahnic, A and Auchtung, JM and Poklar Ulrih, N and Britton, RA and Rupnik, M}, title = {Microbiota in vitro modulated with polyphenols shows decreased colonization resistance against Clostridioides difficile but can neutralize cytotoxicity.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {8358}, pmid = {32433519}, issn = {2045-2322}, mesh = {Actinobacteria/immunology ; Bacterial Toxins/metabolism/*toxicity ; Biological Assay ; Bioreactors/microbiology ; Clindamycin/adverse effects ; Clostridioides difficile/growth & development/metabolism ; Clostridium/immunology ; Clostridium Infections/immunology/microbiology/*prevention & control ; Disease Resistance/*drug effects/immunology ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/*immunology ; Humans ; Polyphenols/*pharmacology ; }, abstract = {While the knowledge on gut microbiota - C. difficile interactions has improved over the years, the understanding of the underlying mechanisms providing colonization resistance as well as preventative measures against the infection remain incomplete. In this study the antibiotic clindamycin and polyphenol extracts from pomegranate and blueberries were used individually and in combination to modulate fecal microbial communities in minibioreactor arrays (MBRA). Modulated communities were inoculated with C. difficile (ribotype 027). Subsequent 7-day periodical monitoring included evaluation of C. difficile growth and activity of toxins TcdA and TcdB as well as analysis of MBRA bacterial community structure (V3V4 16 S metagenomics). Polyphenols affected multiple commensal bacterial groups and showed different synergistic and antagonistic effects in combination with clindamycin. Exposure to either clindamycin or polyphenols led to the loss of colonization resistance against C. difficile. The successful growth of C. difficile was most significantly correlated with the decrease in Collinsella and Lachnospiraceae. Additionally, we demonstrated that Clostridium sporogenes decreased the activity of both C. difficile toxins TcdA and TcdB. The feature was shown to be common among distinct C. sporogenes strains and could potentially be applicable as a non-antibiotic agent for the alleviation of C. difficile infection.}, } @article {pmid32433514, year = {2021}, author = {Iljazovic, A and Roy, U and Gálvez, EJC and Lesker, TR and Zhao, B and Gronow, A and Amend, L and Will, SE and Hofmann, JD and Pils, MC and Schmidt-Hohagen, K and Neumann-Schaal, M and Strowig, T}, title = {Perturbation of the gut microbiome by Prevotella spp. enhances host susceptibility to mucosal inflammation.}, journal = {Mucosal immunology}, volume = {14}, number = {1}, pages = {113-124}, pmid = {32433514}, issn = {1935-3456}, mesh = {Adaptive Immunity ; Animals ; Bacteroidaceae Infections/*immunology/*microbiology ; Cytokines/metabolism ; Disease Models, Animal ; Disease Susceptibility ; Gastrointestinal Microbiome/*immunology ; Host-Pathogen Interactions/*immunology ; Inflammation Mediators/metabolism ; Intestinal Mucosa/*immunology/metabolism/*microbiology/pathology ; Metagenome ; Metagenomics/methods ; Mice ; Mice, Knockout ; Mucositis/etiology/metabolism/pathology ; Prevotella/*immunology ; }, abstract = {Diverse microbial signatures within the intestinal microbiota have been associated with intestinal and systemic inflammatory diseases, but whether these candidate microbes actively modulate host phenotypes or passively expand within the altered microbial ecosystem is frequently not known. Here we demonstrate that colonization of mice with a member of the genus Prevotella, which has been previously associated to colitis in mice, exacerbates intestinal inflammation. Our analysis revealed that Prevotella intestinalis alters composition and function of the ecosystem resulting in a reduction of short-chain fatty acids, specifically acetate, and consequently a decrease in intestinal IL-18 levels during steady state. Supplementation of IL-18 to Prevotella-colonized mice was sufficient to reduce intestinal inflammation. Hence, we conclude that intestinal Prevotella colonization results in metabolic changes in the microbiota, which reduce IL-18 production and consequently exacerbate intestinal inflammation, and potential systemic autoimmunity.}, } @article {pmid32431114, year = {2021}, author = {Dash, NR and Al Bataineh, MT}, title = {Metagenomic Analysis of the Gut Microbiome Reveals Enrichment of Menaquinones (Vitamin K2) Pathway in Diabetes Mellitus.}, journal = {Diabetes & metabolism journal}, volume = {45}, number = {1}, pages = {77-85}, pmid = {32431114}, issn = {2233-6087}, mesh = {*Diabetes Mellitus, Type 2/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics ; Vitamin K 2 ; }, abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM) is a chronic metabolic disease with a high prevalence worldwide, especially among overweight and obese populations. T2DM is multifactorial with several genetic and acquired risk factors that lead to insulin resistance. Mounting evidence indicates that alteration of gut microbiome composition contribute to insulin resistance and inflammation. However, the precise link between T2DM and gut microbiome role and composition remains unknown.

METHODS: We evaluated the metabolic capabilities of the gut microbiome of twelve T2DM and six healthy individuals through shotgun metagenomics using MiSeq platform.

RESULTS: We identified no significant differences in the overall taxonomic composition between healthy and T2DM subjects when controlling for differences in diet. However, results showed that T2DM enriched in metabolic pathways involved in menaquinone (vitamin K2) superpathway biosynthesis (PWY-5838) as compared to healthy individuals. Covariance analysis between the bacterial genera and metabolic pathways displaying difference in abundance (analysis of variance P<0.05) in T2DM as compared to healthy subjects revealed that genera belonging Firmicutes, Actinobacteria, and Bacteroidetes phyla contribute significantly to vitamin K2 biosynthesis. Further, the microbiome corresponding to T2DM with high glycosylated hemoglobin (HbA1c) (>6.5%) exhibit high abundance of genes involved in lysine biosynthesis and low abundance of genes involved in creatinine degradation as compared to T2DM with lower HbA1c (<6.5%).

CONCLUSION: The identified differences in metabolic capabilities provide important information that may eventually lead to the development of novel biomarkers and more effective management strategies to treat T2DM.}, } @article {pmid32424779, year = {2020}, author = {Cao, J and Liu, F and Zhu, B and Shi, Y and Gao, GF}, title = {Diversity and abundance of resistome in rhizosphere soil.}, journal = {Science China. Life sciences}, volume = {63}, number = {12}, pages = {1946-1949}, pmid = {32424779}, issn = {1869-1889}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/isolation & purification ; Biodiversity ; Citrus/microbiology ; Drug Resistance, Bacterial/drug effects/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Metagenome/*genetics ; Phylogeny ; *Rhizosphere ; *Soil Microbiology ; }, } @article {pmid32424436, year = {2020}, author = {Zemskaya, TI and Cabello-Yeves, PJ and Pavlova, ON and Rodriguez-Valera, F}, title = {Microorganisms of Lake Baikal-the deepest and most ancient lake on Earth.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {14}, pages = {6079-6090}, pmid = {32424436}, issn = {1432-0614}, support = {"VIREVO" CGL2016-76273-P [MCI/AEI/FEDER, EU]//Ministerio de Ciencia e Innovación (ES)/ ; "HIDRAS3" PROMETEO/2019/009//Generalitat Valenciana/ ; APOSTD/2019/009 Post-Doctoral fellowship//Generalitat Valenciana/ ; 0345-2019-0007//Ministry of Education and Science of the Russian Federation/ ; Ofi-m 17-29-05040//Российский Фонд Фундаментальных Исследований (РФФИ)/ ; }, mesh = {Climate ; Geography ; In Situ Hybridization, Fluorescence ; Lakes/chemistry/*microbiology ; Metagenomics ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Russia ; *Water Microbiology ; }, abstract = {Lake Baikal (Russia) is the largest (by volume) and deepest lake on Earth. The lake remains relatively pristine due to the low population density around its basin. Being very distant from any marine water body but having a remarkable number of similarities to oceans (depth, oxygen content, oligotrophy) provides a unique model of pelagic microbiota that is submitted to marine-like conditions minus the salt content of the water. It is also a model of lakes located at high latitudes and submitted to yearly ice cover (from January to April). The analysis by different approaches has indeed provided a view of the microbiota of this lake. It contains novel microbes that are closely related to marine groups not known to be present in freshwater like Chloroflexi or Pelagibacter. The deep water mass contains large communities of chemolithotrophs that use ammonia generated in the photic zone or methane from the sediments. KEY POINTS: • The chemical composition and limnic features of the deepest lake on Earth determine the vital activity of microorganisms. • The diversity, ecology, and role of individual taxa of microorganisms were studied using cultivation and molecular methods. • Data of large metagenomic datasets in the epipelagic and bathypelagic layers of the water column in southern Baikal were discussed.}, } @article {pmid32424337, year = {2020}, author = {Morris, RM and Cain, KR and Hvorecny, KL and Kollman, JM}, title = {Lysogenic host-virus interactions in SAR11 marine bacteria.}, journal = {Nature microbiology}, volume = {5}, number = {8}, pages = {1011-1015}, pmid = {32424337}, issn = {2058-5276}, support = {F32 AI145111/AI/NIAID NIH HHS/United States ; R01 GM127648/GM/NIGMS NIH HHS/United States ; }, mesh = {Alphaproteobacteria/*virology ; Bacteriophages/*metabolism ; *Genome, Viral ; Heterotrophic Processes ; *Host Microbial Interactions ; *Lysogeny ; Metagenomics ; Microbiota ; Oceans and Seas ; Prophages/*metabolism ; Seawater/microbiology/virology ; Sequence Alignment ; Sequence Analysis, DNA ; Viral Proteins/*genetics/metabolism ; }, abstract = {Host-virus interactions structure microbial communities, drive biogeochemical cycles and enhance genetic diversity in nature[1,2]. Hypotheses proposed to explain the range of interactions that mediate these processes often invoke lysogeny[3-6], a latent infection strategy used by temperate bacterial viruses to replicate in host cells until an induction event triggers the production and lytic release of free viruses. Most cultured bacteria harbour temperate viruses in their genomes (prophage)[7]. The absence of prophages in cultures of the dominant lineages of marine bacteria has contributed to an ongoing debate over the ecological significance of lysogeny and other viral life strategies in nature[6,8-15]. Here, we report the discovery of prophages in cultured SAR11, the ocean's most abundant clade of heterotrophic bacteria[16,17]. We show the concurrent production of cells and viruses, with enhanced virus production under carbon-limiting growth conditions. Evidence that related prophages are broadly distributed in the oceans suggests that similar interactions have contributed to the evolutionary success of SAR11 in nutrient-limited systems.}, } @article {pmid32423436, year = {2020}, author = {van de Wouw, M and Walsh, AM and Crispie, F and van Leuven, L and Lyte, JM and Boehme, M and Clarke, G and Dinan, TG and Cotter, PD and Cryan, JF}, title = {Distinct actions of the fermented beverage kefir on host behaviour, immunity and microbiome gut-brain modules in the mouse.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {67}, pmid = {32423436}, issn = {2049-2618}, support = {SFI/12/RC/2273/SFI_/Science Foundation Ireland/Ireland ; 15/JP-HDHL/3270/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Animals ; *Behavior, Animal ; *Gastrointestinal Microbiome ; *Host Microbial Interactions/physiology ; *Kefir/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Microbial Interactions ; *Microbiota ; }, abstract = {BACKGROUND: Mounting evidence suggests a role for the gut microbiota in modulating brain physiology and behaviour, through bi-directional communication, along the gut-brain axis. As such, the gut microbiota represents a potential therapeutic target for influencing centrally mediated events and host behaviour. It is thus notable that the fermented milk beverage kefir has recently been shown to modulate the composition of the gut microbiota in mice. It is unclear whether kefirs have differential effects on microbiota-gut-brain axis and whether they can modulate host behaviour per se.

METHODS: To address this, two distinct kefirs (Fr1 and UK4), or unfermented milk control, were administered to mice that underwent a battery of tests to characterise their behavioural phenotype. In addition, shotgun metagenomic sequencing of ileal, caecal and faecal matter was performed, as was faecal metabolome analysis. Finally, systemic immunity measures and gut serotonin levels were assessed. Statistical analyses were performed by ANOVA followed by Dunnett's post hoc test or Kruskal-Wallis test followed by Mann-Whitney U test.

RESULTS: Fr1 ameliorated the stress-induced decrease in serotonergic signalling in the colon and reward-seeking behaviour in the saccharin preference test. On the other hand, UK4 decreased repetitive behaviour and ameliorated stress-induced deficits in reward-seeking behaviour. Furthermore, UK4 increased fear-dependent contextual memory, yet decreased milk gavage-induced improvements in long-term spatial learning. In the peripheral immune system, UK4 increased the prevalence of Treg cells and interleukin 10 levels, whereas Fr1 ameliorated the milk gavage stress-induced elevation in neutrophil levels and CXCL1 levels. Analysis of the gut microbiota revealed that both kefirs significantly changed the composition and functional capacity of the host microbiota, where specific bacterial species were changed in a kefir-dependent manner. Furthermore, both kefirs increased the capacity of the gut microbiota to produce GABA, which was linked to an increased prevalence in Lactobacillus reuteri.

CONCLUSIONS: Altogether, these data show that kefir can signal through the microbiota-gut-immune-brain axis and modulate host behaviour. In addition, different kefirs may direct the microbiota toward distinct immunological and behavioural modulatory effects. These results indicate that kefir can positively modulate specific aspects of the microbiota-gut-brain axis and support the broadening of the definition of psychobiotic to include kefir fermented foods. Video abstract.}, } @article {pmid32421558, year = {2020}, author = {Jurado, MM and Camelo-Castillo, AJ and Suárez-Estrella, F and López, MJ and López-González, JA and Estrella-González, MJ and Síles-Castellano, AB and Moreno, J}, title = {Integral approach using bacterial microbiome to stabilize municipal solid waste.}, journal = {Journal of environmental management}, volume = {265}, number = {}, pages = {110528}, doi = {10.1016/j.jenvman.2020.110528}, pmid = {32421558}, issn = {1095-8630}, mesh = {*Composting ; Fertilizers ; *Microbiota ; *Refuse Disposal ; Soil ; Solid Waste ; *Waste Management ; }, abstract = {Biological transformation of municipal solid waste is an environment-friendly management strategy against recalcitrant residues. The bacterial biome that inhabit said residues are responsible of decomposing both simple and complex materials. For this reason, processes such as composting, which favor the acceleration of the transformation of organic matter, can contribute to the degradation of municipal solid waste. Not only as mere fertilizer for crops, but also as methods for the recovery of solid waste. However, the control of the conditions necessary to achieve an optimal process on an industrial scale is a great concern. Thus, the aim of this work focuses on the characterization of the bacterial microbiome on three municipal solid waste facilities in order to deepen the role of microorganisms in the state of the final product obtained. For it, an intensive metagenomic analysis as well as a battery of physicochemical determinations were carried out. The lack of adequate thermophilic phases was decisive in finding certain bacterial genera, such as Lactobacillus, which was significant through these processes. Biodiversity did not follow a common pattern in the three processes, neither in abundance nor in richness but, in general, it was greater during the bio-oxidative stage. Despite the different trend in terms of the degradation of carbon fractions in these wastes, at the end of the biodegradation treatments, a sufficient degree of bioestabilization of the organic matter was reached. The results offer the opportunity to obtain a level of detail unprecedented of the structure, dynamics and function of the bacterial community in real conditions, without the control offered by laboratory conditions or pilot plants.}, } @article {pmid32417556, year = {2020}, author = {Gallego, S and Barkay, T and Fahrenfeld, NL}, title = {Tagging the vanA gene in wastewater microbial communities for cell sorting and taxonomy of vanA carrying cells.}, journal = {The Science of the total environment}, volume = {732}, number = {}, pages = {138865}, doi = {10.1016/j.scitotenv.2020.138865}, pmid = {32417556}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Bacterial Proteins ; Carbon-Oxygen Ligases ; In Situ Hybridization, Fluorescence ; Microbial Sensitivity Tests ; *Microbiota ; Phylogeny ; Wastewater ; }, abstract = {Failure to understand the microbial ecology driving the proliferation of antibiotic resistance in the environment prevents us from developing strategies to limit the spread of antibiotic resistant infectious disease. In this study, we developed for the first time a tyramide signal amplification-fluorescence in situ hybridization-fluorescence-activated cell sorting protocol (TSA-FISH-FACS) for the characterization of all vanA carrying bacteria in wastewater samples. Firstly, we validated the TSA-FISH protocol through microscopy in pure cultures and wastewater influent. Then, samples were sorted and quantified by FACS and qPCR. Significantly higher percentage tagging of cells was detected in vanA carrying pure cultures and wastewater samples spiked with vanA carrying cells as compared to vanA negative Gram positive strains and non-spiked wastewater samples respectively. qPCR analysis targeting vanZ, a regulating gene in the vanA cluster, showed its relative abundance was significantly greater in Enterococcus faecium ATCC 700221-spiked and positively sorted samples compared to the E. faecium spiked and negatively sorted samples. Phylogenetic analysis was then performed. Although further efforts are needed to overcome technical problems, we have, for the first time, demonstrated sorting bacterial-cells carrying antibiotic resistance genes from wastewater samples through a TSA-FISH-FACS protocol and provided insight into the microbial ecology of vancomycin resistant bacteria. Future potential applications using this approach will include the separation of members of an environmental microbial community (cultured and hard-to-culture) to allow for metagenomics on single cells or, in the case of clumping, targeting a smaller portion of the community with a priori knowledge that the target gene is present.}, } @article {pmid32417519, year = {2020}, author = {Luan, X and Zhang, H and Tian, Z and Yang, M and Wen, X and Zhang, Y}, title = {Microbial community functional structure in an aerobic biofilm reactor: Impact of streptomycin and recovery.}, journal = {Chemosphere}, volume = {255}, number = {}, pages = {127032}, doi = {10.1016/j.chemosphere.2020.127032}, pmid = {32417519}, issn = {1879-1298}, mesh = {Aerobiosis ; Anti-Bacterial Agents/analysis/*toxicity ; Biofilms/*drug effects/growth & development ; Bioreactors/*microbiology ; Carbon/metabolism ; Drug Resistance, Bacterial/drug effects/genetics ; Metagenome/drug effects ; Microbiota/*drug effects/genetics ; Nitrification ; Nitrogen/metabolism ; Streptomycin/analysis/*toxicity ; Wastewater/chemistry/microbiology ; Water Pollutants, Chemical/analysis/*toxicity ; Water Purification/*methods ; }, abstract = {Antibiotics can affect microbial community structure and promote antibiotic resistance. However, the course of microbial community recovery in wastewater treatment systems after antibiotic disturbance remains unclear. Herein, multiple molecular biology tools, including 16S amplicon sequencing, GeoChip 5.0, quantitative polymerase chain reaction (qPCR), and metagenomic sequencing, were used to investigate the year-long (352 d) recovery of the microbial community functional structure in an aerobic biofilm reactor. Nitrification was completely inhibited under 50 mg/L of streptomycin spiking (STM_50) due to the significant reduction of ammonia-oxidizing bacteria, but recovered to original pre-disturbance levels after streptomycin removal, indicating the high resilience of ammonia-oxidizing bacteria. Bacterial community richness and diversity decreased significantly under STM_50 (p < 0.05), but recovered to levels similar to those observed before disturbance after 352 d. In contrast, bacterial composition did not recover to the original structure. The carbon degradation and nitrogen cycling functional community significantly changed after recovery compared to that observed pre-disturbance (p < 0.05), thus indicating functional redundancy. Additionally, levels of aminoglycoside and total antibiotic resistance genes under STM_50 (relative abundance, 0.33 and 0.80, respectively) and after one year of recovery (0.12 and 0.29, respectively) were higher than the levels detected pre-disturbance (0.04 and 0.24, respectively). This study provides an overall depiction of the recovery of the microbial community functional structure after antibiotic exposure. Our findings give notice that recovery caused by antibiotic disturbance in the water environment should be taken more seriously, and that engineering control strategies should be implemented to prevent the antibiotic pollution of wastewater.}, } @article {pmid32417229, year = {2020}, author = {Pratama, AA and Terpstra, J and de Oliveria, ALM and Salles, JF}, title = {The Role of Rhizosphere Bacteriophages in Plant Health.}, journal = {Trends in microbiology}, volume = {28}, number = {9}, pages = {709-718}, doi = {10.1016/j.tim.2020.04.005}, pmid = {32417229}, issn = {1878-4380}, mesh = {Bacteria/*virology ; Bacteriophages/*physiology ; Biodiversity ; Host Microbial Interactions ; Metagenomics ; Plants/*microbiology/*virology ; *Rhizosphere ; Soil Microbiology ; *Virome ; }, abstract = {Microbiomes and their hosts influence each other; for instance, the microbiome improves host fitness, whereas the host supports microbiome nutrition. Most studies on this topic have focused on the role of bacteria and fungi, although research on viruses that infect bacteria, known as 'bacteriophages' (phages), has gained importance due to the potential role bacteriophages play in the resilience and functionality of the gut microbiome. Like the gut microbiome, the rhizosphere harbors a complex microbiome, but little is known about the role of phages in this ecosystem. In this opinion, we extend the knowledge gained in human gut virus metagenomics (viromics) to disentangle the potential role of phages in driving the resilience and functionality of the rhizosphere microbiome. We propose that future comparative studies across environments are necessary to unravel the underlying mechanisms through which phages drive the composition and functionality of the rhizosphere microbiome and its interaction with the plant host. Importantly, such understanding might generate strategies to improve plant resistance and resilience in the context of climate change.}, } @article {pmid32416615, year = {2021}, author = {Cordier, T and Alonso-Sáez, L and Apothéloz-Perret-Gentil, L and Aylagas, E and Bohan, DA and Bouchez, A and Chariton, A and Creer, S and Frühe, L and Keck, F and Keeley, N and Laroche, O and Leese, F and Pochon, X and Stoeck, T and Pawlowski, J and Lanzén, A}, title = {Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap.}, journal = {Molecular ecology}, volume = {30}, number = {13}, pages = {2937-2958}, pmid = {32416615}, issn = {1365-294X}, mesh = {Biodiversity ; DNA Barcoding, Taxonomic ; *Ecosystem ; Environmental Monitoring ; *Metagenomics ; }, abstract = {A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.}, } @article {pmid32414415, year = {2020}, author = {F Escapa, I and Huang, Y and Chen, T and Lin, M and Kokaras, A and Dewhirst, FE and Lemon, KP}, title = {Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {65}, pmid = {32414415}, issn = {2049-2618}, support = {R01 AI101018/AI/NIAID NIH HHS/United States ; R01 DE024468/DE/NIDCR NIH HHS/United States ; R01 DE016937/DE/NIDCR NIH HHS/United States ; R01GM117174//National Institute of General Medical Sciences (US)/International ; R01AI101018//Division of Intramural Research, National Institute of Allergy and Infectious Diseases/International ; R37 DE016937/DE/NIDCR NIH HHS/United States ; UL1 TR001102/TR/NCATS NIH HHS/United States ; R01DE024468/DE/NIDCR NIH HHS/United States ; R01 GM117174/GM/NIGMS NIH HHS/United States ; R37DE016937/DE/NIDCR NIH HHS/United States ; }, mesh = {*Bacteria/genetics ; Bayes Theorem ; *Computational Biology/methods ; Gastrointestinal Microbiome/genetics ; Humans ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: The low cost of 16S rRNA gene sequencing facilitates population-scale molecular epidemiological studies. Existing computational algorithms can resolve 16S rRNA gene sequences into high-resolution amplicon sequence variants (ASVs), which represent consistent labels comparable across studies. Assigning these ASVs to species-level taxonomy strengthens the ecological and/or clinical relevance of 16S rRNA gene-based microbiota studies and further facilitates data comparison across studies.

RESULTS: To achieve this, we developed a broadly applicable method for constructing high-resolution training sets based on the phylogenic relationships among microbes found in a habitat of interest. When used with the naïve Bayesian Ribosomal Database Project (RDP) Classifier, this training set achieved species/supraspecies-level taxonomic assignment of 16S rRNA gene-derived ASVs. The key steps for generating such a training set are (1) constructing an accurate and comprehensive phylogenetic-based, habitat-specific database; (2) compiling multiple 16S rRNA gene sequences to represent the natural sequence variability of each taxon in the database; (3) trimming the training set to match the sequenced regions, if necessary; and (4) placing species sharing closely related sequences into a training-set-specific supraspecies taxonomic level to preserve subgenus-level resolution. As proof of principle, we developed a V1-V3 region training set for the bacterial microbiota of the human aerodigestive tract using the full-length 16S rRNA gene reference sequences compiled in our expanded Human Oral Microbiome Database (eHOMD). We also overcame technical limitations to successfully use Illumina sequences for the 16S rRNA gene V1-V3 region, the most informative segment for classifying bacteria native to the human aerodigestive tract. Finally, we generated a full-length eHOMD 16S rRNA gene training set, which we used in conjunction with an independent PacBio single molecule, real-time (SMRT)-sequenced sinonasal dataset to validate the representation of species in our training set. This also established the effectiveness of a full-length training set for assigning taxonomy of long-read 16S rRNA gene datasets.

CONCLUSION: Here, we present a systematic approach for constructing a phylogeny-based, high-resolution, habitat-specific training set that permits species/supraspecies-level taxonomic assignment to short- and long-read 16S rRNA gene-derived ASVs. This advancement enhances the ecological and/or clinical relevance of 16S rRNA gene-based microbiota studies. Video Abstract.}, } @article {pmid32414080, year = {2020}, author = {Nagpal, R and Mishra, SP and Yadav, H}, title = {Unique Gut Microbiome Signatures Depict Diet-Versus Genetically Induced Obesity in Mice.}, journal = {International journal of molecular sciences}, volume = {21}, number = {10}, pages = {}, pmid = {32414080}, issn = {1422-0067}, support = {R01AG018915/NH/NIH HHS/United States ; UL1TR001420/NH/NIH HHS/United States ; W81XWH-19-1-0236//Congressionally Directed Medical Research Programs/ ; W81XWH-18-1-0118//Congressionally Directed Medical Research Programs/ ; P30 AG021332/AG/NIA NIH HHS/United States ; R01 AG018915/AG/NIA NIH HHS/United States ; P30AG21332/NH/NIH HHS/United States ; }, mesh = {Animals ; Diabetes Mellitus, Type 2/genetics/*microbiology ; Diet, High-Fat/adverse effects ; Gastrointestinal Microbiome/*genetics ; Humans ; Leptin/deficiency/*genetics ; Male ; Mice ; Mice, Inbred NOD/genetics ; Obesity/genetics/*microbiology/pathology ; Receptors, Leptin/deficiency/*genetics ; }, abstract = {The gut microbiome plays an important role in obesity and Type 2 diabetes (T2D); however, it remains unclear whether the gut microbiome could clarify the dietary versus genetic origin of these ailments. Moreover, studies examining the gut microbiome in diet- versus genetically induced obesity/T2D in the same experimental set-up are lacking. We herein characterized the gut microbiomes in three of the most widely used mouse models of obesity/T2D, i.e., genetically induced (leptin-deficient i.e., Lep[ob/ob]; and leptin-receptor-deficient i.e., Lep[db/db]) and high-fat diet (HFD)-induced obese (DIO)/T2D mice, with reference to their normal chow-fed (NC) and low-fat-diet-fed (LF) control counterparts. In terms of β-diversity, Lep[ob/ob] and Lep[db/db] mice showed similarity to NC mice, whereas DIO and LF mice appeared as distinct clusters. The phylum- and genus-level compositions were relatively similar in NC, Lep[ob/ob], and Lep[db/db] mice, whereas DIO and LF mice demonstrated distinct compositions. Further analyses revealed several unique bacterial taxa, metagenomic functional features, and their correlation patterns in these models. The data revealed that obesity/T2D driven by diet as opposed to genetics presents distinct gut microbiome signatures enriched with distinct functional capacities, and indicated that these signatures can distinguish diet- versus genetically induced obesity/T2D and, if extrapolated to humans, might offer translational potential in devising dietary and/or genetics-based therapies against these maladies.}, } @article {pmid32414048, year = {2020}, author = {Kuramae, EE and Derksen, S and Schlemper, TR and Dimitrov, MR and Costa, OYA and Silveira, APDD}, title = {Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics.}, journal = {Microorganisms}, volume = {8}, number = {5}, pages = {}, pmid = {32414048}, issn = {2076-2607}, support = {729.004.013//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 456420/2013-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Bacteria from the genera Paraburkholderia and Herbaspirillum can promote the growth of Sorghum bicolor, but the underlying mechanisms are not yet known. In a pot experiment, sorghum plants grown on sterilized substrate were inoculated with Paraburkholderia tropica strain IAC/BECa 135 and Herbaspirillum frisingense strain IAC/BECa 152 under phosphate-deficient conditions. These strains significantly increased Sorghum bicolor cultivar SRN-39 root and shoot biomass. Shotgun metagenomic analysis of the rhizosphere revealed successful colonization by both strains; however, the incidence of colonization was higher in plants inoculated with P. tropica strain IAC/BECa 135 than in those inoculated with H. frisingense strain IAC/BECa 152. Conversely, plants inoculated with H. frisingense strain IAC/BECa 152 showed the highest increase in biomass. Genomic analysis of the two inoculants implied a high degree of rhizosphere fitness of P. tropica strain IAC/BECa 135 through environmental signal processing, biofilm formation, and nutrient acquisition. Both genomes contained genes related to plant growth-promoting bacterial (PGPB) traits, including genes related to indole-3-acetate (IAA) synthesis, nitrogen fixation, nodulation, siderophore production, and phosphate solubilization, although the P. tropica strain IAC/BECa 135 genome contained a slightly more extensive repertoire. This study provides evidence that complementary mechanisms of growth promotion in Sorghum might occur, i.e., that P. tropica strain IAC/BECa 135 acts in the rhizosphere and increases the availability of nutrients, while H. frisingense strain IAC/BECa 152 influences plant hormone signaling. While the functional and taxonomic profiles of the rhizobiomes were similar in all treatments, significant differences in plant biomass were observed, indicating that the rhizobiome and the endophytic microbial community may play equally important roles in the complicated plant-microbial interplay underlying increased host plant growth.}, } @article {pmid32411648, year = {2020}, author = {Jain, N}, title = {The Need for Personalized Approaches to Microbiome Modulation.}, journal = {Frontiers in public health}, volume = {8}, number = {}, pages = {144}, pmid = {32411648}, issn = {2296-2565}, mesh = {Metagenomics ; *Microbiota ; }, } @article {pmid32411616, year = {2020}, author = {Hahn, A and Whiteson, K and Davis, TJ and Phan, J and Sami, I and Koumbourlis, AC and Freishtat, RJ and Crandall, KA and Bean, HD}, title = {Longitudinal Associations of the Cystic Fibrosis Airway Microbiome and Volatile Metabolites: A Case Study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {174}, pmid = {32411616}, issn = {2235-2988}, support = {R56 HL139846/HL/NHLBI NIH HHS/United States ; UL1 TR000075/TR/NCATS NIH HHS/United States ; }, mesh = {*Cystic Fibrosis ; Humans ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sputum ; }, abstract = {The identification of 16S rDNA biomarkers from respiratory samples to describe the continuum of clinical disease states within persons having cystic fibrosis (CF) has remained elusive. We sought to combine 16S, metagenomics, and metabolomics data to describe multiple transitions between clinical disease states in 14 samples collected over a 12-month period in a single person with CF. We hypothesized that each clinical disease state would have a unique combination of bacterial genera and volatile metabolites as a potential signature that could be utilized as a biomarker of clinical disease state. Taxonomy identified by 16S sequencing corroborated clinical culture results, with the majority of the 109 PCR amplicons belonging to the bacteria grown in clinical cultures (Escherichia coli and Staphylococcus aureus). While alpha diversity measures fluctuated across disease states, no significant trends were present. Principle coordinates analysis showed that treatment samples trended toward a different community composition than baseline and exacerbation samples. This was driven by the phylum Bacteroidetes (less abundant in treatment, log2 fold difference -3.29, p = 0.015) and the genus Stenotrophomonas (more abundant in treatment, log2 fold difference 6.26, p = 0.003). Across all sputum samples, 466 distinct volatile metabolites were identified with total intensity varying across clinical disease state. Baseline and exacerbation samples were rather uniform in chemical composition and similar to one another, while treatment samples were highly variable and differed from the other two disease states. When utilizing a combination of the microbiome and metabolome data, we observed associations between samples dominated Staphylococcus and Escherichia and higher relative abundances of alcohols, while samples dominated by Achromobacter correlated with a metabolomics shift toward more oxidized volatiles. However, the microbiome and metabolome data were not tightly correlated; examining both the metagenomics and metabolomics allows for more context to examine changes across clinical disease states. In our study, combining the sputum microbiome and metabolome data revealed stability in the sputum composition through the first exacerbation and treatment episode, and into the second exacerbation. However, the second treatment ushered in a prolonged period of instability, which after three additional exacerbations and treatments culminated in a new lung microbiome and metabolome.}, } @article {pmid32410629, year = {2020}, author = {Fang, S and Chen, X and Pan, J and Chen, Q and Zhou, L and Wang, C and Xiao, T and Gan, QF}, title = {Dynamic distribution of gut microbiota in meat rabbits at different growth stages and relationship with average daily gain (ADG).}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {116}, pmid = {32410629}, issn = {1471-2180}, mesh = {Animals ; Bacteria/*classification/genetics/isolation & purification ; Body Weight ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Feces/microbiology ; Gastrointestinal Microbiome ; Meat/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Rabbits ; Sequence Analysis, DNA/*methods ; Weaning ; }, abstract = {BACKGROUND: The mammalian intestinal tract harbors diverse and dynamic microbial communities that play pivotal roles in host health, metabolism, immunity, and development. Average daily gain (ADG) is an important growth trait in meat rabbit industry. The effects of gut microbiota on ADG in meat rabbits are still unknown.

RESULTS: In this study, we investigated the dynamic distribution of gut microbiota in commercial Ira rabbits from weaning to finishing and uncover the relationship between the microbiota and average daily gain (ADG) via 16S rRNA gene sequencing. The results indicated that the richness and diversity of gut microbiota significantly increased with age. Gut microbial structure was less variable among finishing rabbits than among weaning rabbits. The relative abundances of the dominant phyla Firmicutes, Bacteroidetes, Verrucomicrobia and Cyanobacteria, and the 15 predominant genera significantly varied with age. Metagenomic prediction analysis showed that both KOs and KEGG pathways related to the metabolism of monosaccharides and vitamins were enriched in the weaning rabbits, while those related to the metabolism of amino acids and polysaccharides were more abundant in the finishing rabbits. We identified 34 OTUs, 125 KOs, and 25 KEGG pathways that were significantly associated with ADG. OTUs annotation suggested that butyrate producing bacteria belong to the family Ruminococcaceae and Bacteroidales_S24-7_group were positively associated with ADG. Conversely, Eubacterium_coprostanoligenes_group, Christensenellaceae_R-7_group, and opportunistic pathogens were negatively associated with ADG. Both KOs and KEGG pathways correlated with the metabolism of vitamins, basic amino acids, and short chain fatty acids (SCFAs) showed positive correlations with ADG, while those correlated with aromatic amino acids metabolism and immune response exhibited negative correlations with ADG. In addition, our results suggested that 10.42% of the variation in weaning weight could be explained by the gut microbiome.

CONCLUSIONS: Our findings give a glimpse into the dynamic shifts in gut microbiota of meat rabbits and provide a theoretical basis for gut microbiota modulation to improve ADG in the meat rabbit industry.}, } @article {pmid32410031, year = {2020}, author = {Zhang, F and Weckhorst, JL and Assié, A and Khodakova, AS and Loeza-Cabrera, M and Vidal, D and Samuel, BS}, title = {High-Throughput Assessment of Changes in the Caenorhabditis elegans Gut Microbiome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2144}, number = {}, pages = {131-144}, doi = {10.1007/978-1-0716-0592-9_12}, pmid = {32410031}, issn = {1940-6029}, support = {DP2 DK116645/DK/NIDDK NIH HHS/United States ; }, mesh = {Aging/*genetics ; Animals ; Caenorhabditis elegans/growth & development/*microbiology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Screening Assays/*methods ; Longevity/genetics ; }, abstract = {The gut microbiome is an important driver of host physiology and development. Altered abundance or membership of this microbe community can influence host health and disease progression, including the determination of host lifespan and healthspan. Here, we describe a robust pipeline to measure microbiome abundance and composition in the C. elegans gut that can be applied to examine the role of the microbiome on host aging or other physiologic processes.}, } @article {pmid32408110, year = {2020}, author = {Wei, M and Huang, F and Zhao, L and Zhang, Y and Yang, W and Wang, S and Li, M and Han, X and Ge, K and Qu, C and Rajani, C and Xie, G and Zheng, X and Zhao, A and Bian, Z and Jia, W}, title = {A dysregulated bile acid-gut microbiota axis contributes to obesity susceptibility.}, journal = {EBioMedicine}, volume = {55}, number = {}, pages = {102766}, pmid = {32408110}, issn = {2352-3964}, support = {U01 CA188387/CA/NCI NIH HHS/United States ; }, mesh = {Adipose Tissue, Brown/metabolism ; Animals ; Body Mass Index ; Chenodeoxycholic Acid/*metabolism ; Cholestenones/metabolism ; Clostridiales/metabolism/pathogenicity ; Cohort Studies ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Disease Susceptibility ; *Gastrointestinal Microbiome ; Gene Expression Regulation ; Glucagon-Like Peptide 1/genetics/metabolism ; Humans ; Ileum/metabolism/*microbiology ; Lithocholic Acid/*metabolism ; Male ; Metagenomics/methods ; Mice ; Mice, Inbred C57BL ; Obesity/etiology/genetics/metabolism/*microbiology ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/genetics/metabolism ; Uncoupling Protein 1/genetics/metabolism ; Ursodeoxycholic Acid/*metabolism ; }, abstract = {BACKGROUND: The composition of the bile acid (BA) pool is closely associated with obesity and is modified by gut microbiota. Perturbations of gut microbiota shape the BA composition, which, in turn, may alter important BA signaling and affect host metabolism.

METHODS: We investigated BA composition of high BMI subjects from a human cohort study and a high fat diet (HFD) obesity prone (HF-OP) / HFD obesity resistant (HF-OR) mice model. Gut microbiota was analysed by metagenomics sequencing. GLP-1 secretion and gene regulation studies involved ELISA, qPCR, Western blot, Immunohistochemistry, and Immunofluorescence staining.

FINDINGS: We found that the proportion of non-12-OH BAs was significantly decreased in the unhealthy high BMI subjects. The HF-OR mice had an enhanced level of non-12-OH BAs. Non-12-OH BAs including ursodeoxycholate (UDCA), chenodeoxycholate (CDCA), and lithocholate (LCA) were decreased in the HF-OP mice and associated with altered gut microbiota. Clostridium scindens was decreased in HF-OP mice and had a positive correlation with UDCA and LCA. Gavage of Clostridium scindens in mice increased the levels of hepatic non-12-OH BAs, accompanied by elevated serum 7α-hydroxy-4-cholesten-3-one (C4) levels. In HF-OP mice, altered BA composition was associated with significantly downregulated expression of GLP-1 in ileum and PGC1α, UCP1 in brown adipose tissue. In addition, we identified that UDCA attenuated the high fat diet-induced obesity via enhancing levels of non-12-OH BAs.

INTERPRETATION: Our study highlights that dysregulated BA signaling mediated by gut microbiota contributes to obesity susceptibility, suggesting modulation of BAs could be a promising strategy for obesity therapy.}, } @article {pmid32406906, year = {2020}, author = {Liang, G and Conrad, MA and Kelsen, JR and Kessler, LR and Breton, J and Albenberg, LG and Marakos, S and Galgano, A and Devas, N and Erlichman, J and Zhang, H and Mattei, L and Bittinger, K and Baldassano, RN and Bushman, FD}, title = {Dynamics of the Stool Virome in Very Early-Onset Inflammatory Bowel Disease.}, journal = {Journal of Crohn's & colitis}, volume = {14}, number = {11}, pages = {1600-1610}, pmid = {32406906}, issn = {1876-4479}, support = {K23 DK100461/DK/NIDDK NIH HHS/United States ; K23 DK119585/DK/NIDDK NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; }, mesh = {Age of Onset ; Anelloviridae/*isolation & purification ; Biomarkers, Pharmacological/analysis ; Child, Preschool ; Correlation of Data ; Feces/*virology ; Female ; Gastrointestinal Microbiome/physiology ; Humans ; Immunosuppressive Agents/*therapeutic use ; *Inflammatory Bowel Diseases/epidemiology/physiopathology/virology ; Male ; Metagenome/immunology ; Risk Factors ; United States/epidemiology ; Virome/*physiology ; Viruses/classification/isolation & purification ; }, abstract = {BACKGROUND AND AIMS: Dysbiosis of the gut microbiota is a well-known correlate of the pathogenesis of inflammatory bowel disease [IBD]. However, few studies have examined the microbiome in very early-onset [VEO] IBD, which is defined as onset of IBD before 6 years of age. Here we focus on the viral portion of the microbiome-the virome-to assess possible viral associations with disease processes, reasoning that any viruses potentially associated with IBD might grow more robustly in younger subjects, and so be more detectable.

METHODS: Virus-like particles [VLPs] were purified from stool samples collected from patients with VEO-IBD [n = 54] and healthy controls [n = 23], and characterized by DNA and RNA sequencing and VLP particle counts.

RESULTS: The total number of VLPs was not significantly different between VEO-IBD and healthy controls. For bacterial viruses, the VEO-IBD subjects were found to have a higher ratio of Caudovirales vs to Microviridae compared to healthy controls. An increase in Caudovirales was also associated with immunosuppressive therapy. For viruses infecting human cells, Anelloviridae showed higher prevalence in VEO-IBD compared to healthy controls. Within the VEO-IBD group, higher levels of Anelloviridae DNA were also positively associated with immunosuppressive treatment. To search for new viruses, short sequences enriched in VEO-IBD samples were identified, and some could be validated in an independent cohort, although none was clearly viral; this provides sequence tags to interrogate in future studies.

CONCLUSIONS: These data thus document perturbations to normal viral populations associated with VEO-IBD, and provide a biomarker-Anelloviridae DNA levels-potentially useful for reporting the effectiveness of immunosuppression.}, } @article {pmid32404904, year = {2020}, author = {Pascual-García, A and Bell, T}, title = {Community-level signatures of ecological succession in natural bacterial communities.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2386}, pmid = {32404904}, issn = {2041-1723}, mesh = {Bacteria/classification/genetics/*growth & development ; *Biodiversity ; *Biota ; DNA, Bacterial/genetics ; Ecosystem ; Metagenome/genetics ; Microbiota ; Phylogeny ; Population Dynamics ; RNA, Ribosomal, 16S/*genetics ; Stochastic Processes ; }, abstract = {A central goal in microbial ecology is to simplify the extraordinary biodiversity that inhabits natural environments into ecologically coherent units. We profiled (16S rRNA sequencing) > 700 semi-aquatic bacterial communities while measuring their functional capacity when grown in laboratory conditions. This approach allowed us to investigate the relationship between composition and function excluding confounding environmental factors. Simulated data allowed us to reject the hypothesis that stochastic processes were responsible for community assembly, suggesting that niche effects prevailed. Consistent with this idea we identified six distinct community classes that contained samples collected from distant locations. Structural equation models showed there was a functional signature associated with each community class. We obtained a more mechanistic understanding of the classes using metagenomic predictions (PiCRUST). This approach allowed us to show that the classes contained distinct genetic repertoires reflecting community-level ecological strategies. The ecological strategies resemble the classical distinction between r- and K-strategists, suggesting that bacterial community assembly may be explained by simple ecological mechanisms.}, } @article {pmid32404017, year = {2020}, author = {Engevik, MA and Banks, LD and Engevik, KA and Chang-Graham, AL and Perry, JL and Hutchinson, DS and Ajami, NJ and Petrosino, JF and Hyser, JM}, title = {Rotavirus infection induces glycan availability to promote ileum-specific changes in the microbiome aiding rotavirus virulence.}, journal = {Gut microbes}, volume = {11}, number = {5}, pages = {1324-1347}, pmid = {32404017}, issn = {1949-0984}, support = {P30 DK123704/DK/NIDDK NIH HHS/United States ; K12 GM084897/GM/NIGMS NIH HHS/United States ; R21 AI137710/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R03 DK110270/DK/NIDDK NIH HHS/United States ; F30 DK112563/DK/NIDDK NIH HHS/United States ; T32 DK007664/DK/NIDDK NIH HHS/United States ; R01 DK115507/DK/NIDDK NIH HHS/United States ; P20 GM103423/GM/NIGMS NIH HHS/United States ; }, mesh = {Akkermansia/growth & development/metabolism ; Animals ; Animals, Newborn ; Bacteria/classification/growth & development ; Bacteroides/growth & development/metabolism ; *Gastrointestinal Microbiome ; Goblet Cells/physiology ; Ileum/*microbiology/pathology ; Intestine, Small/microbiology/pathology ; Lactobacillus/growth & development ; Mice ; Mice, Inbred BALB C ; Mucins/metabolism ; Polysaccharides/*metabolism ; RNA, Ribosomal, 16S/genetics ; Rotavirus/*pathogenicity ; Rotavirus Infections/microbiology/*pathology/*virology ; Virulence ; }, abstract = {Multiple studies have identified changes within the gut microbiome in response to diarrheal-inducing bacterial pathogens. However, examination of the microbiome in response to viral pathogens remains understudied. Compounding this, many studies use fecal samples to assess microbiome composition; which may not accurately mirror changes within the small intestine, the primary site for most enteric virus infections. As a result, the functional significance of small intestinal microbiome shifts during infection is not well defined. To address these gaps, rotavirus-infected neonatal mice were examined for changes in bacterial community dynamics, host gene expression, and tissue recovery during infection. Profiling bacterial communities using 16S rRNA sequencing suggested significant and distinct changes in ileal communities in response to rotavirus infection, with no significant changes for other gastrointestinal (GI) compartments. At 1-d post-infection, we observed a loss in Lactobacillus species from the ileum, but an increase in Bacteroides and Akkermansia, both of which exhibit mucin-digesting capabilities. Concomitant with the bacterial community shifts, we observed a loss of mucin-filled goblet cells in the small intestine at d 1, with recovery occurring by d 3. Rotavirus infection of mucin-producing cell lines and human intestinal enteroids (HIEs) stimulated release of stored mucin granules, similar to in vivo findings. In vitro, incubation of mucins with Bacteroides or Akkermansia members resulted in significant glycan degradation, which altered the binding capacity of rotavirus in silico and in vitro. Taken together, these data suggest that the response to and recovery from rotavirus-diarrhea is unique between sub-compartments of the GI tract and may be influenced by mucin-degrading microbes.}, } @article {pmid32403302, year = {2020}, author = {Françoise, A and Héry-Arnaud, G}, title = {The Microbiome in Cystic Fibrosis Pulmonary Disease.}, journal = {Genes}, volume = {11}, number = {5}, pages = {}, pmid = {32403302}, issn = {2073-4425}, mesh = {Aminophenols/pharmacology ; Animals ; Archaea/isolation & purification ; Bacteria/isolation & purification ; Biomarkers ; Cystic Fibrosis/genetics/*microbiology/pathology ; Cystic Fibrosis Transmembrane Conductance Regulator/deficiency/drug effects/genetics ; Disease Models, Animal ; Disease Progression ; Dysbiosis/*complications ; Fungi/isolation & purification ; Gastrointestinal Microbiome/drug effects ; Genotype ; High-Throughput Nucleotide Sequencing ; Humans ; Lung/microbiology/pathology/virology ; Mammals ; Metagenomics ; *Microbiota/drug effects ; Organ Specificity ; Prognosis ; Quinolones/pharmacology ; Viruses/isolation & purification ; }, abstract = {Cystic fibrosis (CF) is a genetic disease with mutational changes leading to profound dysbiosis, both pulmonary and intestinal, from a very young age. This dysbiosis plays an important role in clinical manifestations, particularly in the lungs, affected by chronic infection. The range of microbiological tools has recently been enriched by metagenomics based on next-generation sequencing (NGS). Currently applied essentially in a gene-targeted manner, metagenomics has enabled very exhaustive description of bacterial communities in the CF lung niche and, to a lesser extent, the fungi. Aided by progress in bioinformatics, this now makes it possible to envisage shotgun sequencing and opens the door to other areas of the microbial world, the virome, and the archaeome, for which almost everything remains to be described in cystic fibrosis. Paradoxically, applying NGS in microbiology has seen a rebirth of bacterial culture, but in an extended manner (culturomics), which has proved to be a perfectly complementary approach to NGS. Animal models have also proved indispensable for validating microbiome pathophysiological hypotheses. Description of pathological microbiomes and correlation with clinical status and therapeutics (antibiotic therapy, cystic fibrosis transmembrane conductance regulator (CFTR) modulators) revealed the richness of microbiome data, enabling description of predictive and follow-up biomarkers. Although monogenic, CF is a multifactorial disease, and both genotype and microbiome profiles are crucial interconnected factors in disease progression. Microbiome-genome interactions are thus important to decipher.}, } @article {pmid32401138, year = {2020}, author = {Kulecka, M and Fraczek, B and Mikula, M and Zeber-Lubecka, N and Karczmarski, J and Paziewska, A and Ambrozkiewicz, F and Jagusztyn-Krynicka, K and Cieszczyk, P and Ostrowski, J}, title = {The composition and richness of the gut microbiota differentiate the top Polish endurance athletes from sedentary controls.}, journal = {Gut microbes}, volume = {11}, number = {5}, pages = {1374-1384}, pmid = {32401138}, issn = {1949-0984}, mesh = {Adolescent ; Adult ; Aged ; *Athletes ; Bacteria/*classification/genetics/growth & development ; Bacteroides/growth & development ; Diet ; Dietary Fiber/administration & dosage ; Dietary Sucrose/administration & dosage ; *Endurance Training ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Genes, rRNA ; Humans ; Male ; *Marathon Running ; Middle Aged ; Physical Endurance ; Poland ; Prevotella/growth & development ; RNA, Ribosomal, 16S ; Sedentary Behavior ; *Skiing ; Young Adult ; }, abstract = {BACKGROUND: Little data are available on the subject of gut microbiota composition in endurance athletes as well as connections between diet and specific bacteria abundance. However, most studies suggest that athletes' microbiota undergoes major alterations, which may contribute to increased physical performance. Therefore, we decided to investigate differences in gut microbiota between healthy controls and endurance athletes.

MATERIALS AND METHODS: Stools samples were collected from 14 marathon runners, 11 cross-country skiers and 46 sedentary healthy controls. The athletes' diet evaluation was performed with 24-h diet recall, using the Aliant programme. The 16S gene sequencing was performed using the Ion 16S Metagenomics Kit on Ion Torrent PGM sequencer. Taxonomic classification and diversity indices computation was performed with Mothur.

RESULTS: 20 and 5 taxa differentiated healthy controls from marathon runners and cross-country skiers, respectively. Both groups presented a lowered abundance of major gut microbiota genus, Bacteroidetes and higher abundance of Prevotella. The athletes' microbiome was also more diverse in cross-country skiers than the one of sedentary controls (Simpson index p-value at 0.025). Thirty-one strong correlations (Spearman's coefficient > 0.6) were uncovered between bacteria abundance and diet, including inverse correlation of Prevotella with sucrose intake, Phascolarctobacterium with polyunsaturated fatty acids as well as positive correlation of Christensenellaceae with folic acid intake and Agathobacter with fiber amount in diet.

CONCLUSIONS: The excessive training associates with both differences in composition and promotion of higher bacterial diversity. Taxons enriched in athletes are known to participate in fiber fermentation.}, } @article {pmid32400910, year = {2020}, author = {Moore, RL and Geraghty, AA and Feehily, C and Saldova, R and Murphy, EF and Van Sinderen, D and Cotter, PD and McAuliffe, FM}, title = {Can a probiotic supplement in pregnancy result in transfer to the neonatal gut: A systematic review.}, journal = {Acta obstetricia et gynecologica Scandinavica}, volume = {99}, number = {10}, pages = {1269-1277}, doi = {10.1111/aogs.13899}, pmid = {32400910}, issn = {1600-0412}, mesh = {Feces/microbiology ; Female ; Fetal Development ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Maternal-Fetal Exchange ; Polymerase Chain Reaction ; Pregnancy ; *Prenatal Care ; Probiotics/*administration & dosage ; RNA, Ribosomal, 16S ; Sequence Analysis ; }, abstract = {INTRODUCTION: The establishment of the neonatal gut microbiome is a crucial step that may have lifelong health implications. We aimed to systematically review evidence on maternal probiotic supplementation during pregnancy and vertical transfer of the corresponding strain to the infant gut.

MATERIAL AND METHODS: Medline, CINAHL, Embase, Web of Science, and OVID were searched from inception to September 2018. Studies of maternal probiotic supplementation for a minimum duration of 2 weeks and analyses of neonatal stool samples were included. The primary outcome was presence of the specific probiotic strain in the infant stool. Electronic databases were searched for relevant studies and references were cross-checked. Risk of bias among included studies was assessed and data were extracted independently by two authors.

RESULTS: Three studies were included in the review. Only one study was identified involving prenatal maternal probiotic supplementation alone. Neonatal colonization with the maternally administered probiotic was not demonstrated but supplementation with the probiotic influenced levels of a bacterial strain other than that found in the probiotic product. The other two studies identified included both prenatal and postnatal supplementation of either mother or infant. All three studies reported employing strain-specific isolation methodology to isolate the supplemented bacterial strain in infant stool but none used whole metagenome shotgun sequencing.

CONCLUSIONS: Few studies investigating transfer of a specific probiotic bacterial strain from mother to infant were identified, showing inconclusive evidence of vertical transfer.}, } @article {pmid32400083, year = {2020}, author = {Piñar, G and Tafer, H and Schreiner, M and Miklas, H and Sterflinger, K}, title = {Decoding the biological information contained in two ancient Slavonic parchment codices: an added historical value.}, journal = {Environmental microbiology}, volume = {22}, number = {8}, pages = {3218-3233}, pmid = {32400083}, issn = {1462-2920}, support = {//(FWF)/International ; P29892//Austrian Science Fund/International ; }, mesh = {Animals ; Biodegradation, Environmental ; Conservation of Natural Resources ; *DNA, Ancient/isolation & purification ; Europe, Eastern ; History, Ancient ; Humans ; Manuscripts as Topic/*history ; *Microbiota ; Saccharopolyspora ; Skin/microbiology ; }, abstract = {This study provides an example in the emerging field of biocodicology showing how metagenomics can help answer relevant questions that may contribute to a better understanding of the history of ancient manuscripts. To this end, two Slavonic codices dating from the 11th century were investigated through shotgun metagenomics. Endogenous DNA enabled to infer the animal origin of the skins used in the manufacture of the two codices, while nucleic sequences recovered from viruses were investigated for the first time in this material, opening up new possibilities in the field of biocodicology. In addition, the microbiomes colonizing the surface of the parchments served to determine their conservation status and their latent risk of deterioration. The saline environment provided by the parchments selected halophilic and halotolerant microorganisms, which are known to be responsible for the biodegradation of parchment. Species of Nocardiopsis, Gracilibacillus and Saccharopolyspora, but also members of the Aspergillaceae family were detected in this study, all possessing enzymatic capabilities for the biodeterioration of this material. Finally, a relative abundance of microorganisms originating from the human skin microbiome were identified, most probably related to the intensive manipulation of the manuscripts throughout the centuries, which should be taken with caution as they can be potential pathogens.}, } @article {pmid32398126, year = {2020}, author = {Xue, MY and Sun, HZ and Wu, XH and Liu, JX and Guan, LL}, title = {Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {64}, pmid = {32398126}, issn = {2049-2618}, mesh = {Animals ; Cattle ; Dairying ; Female ; *Lactation ; *Metabolome ; *Microbiota ; *Milk ; Prevotella/isolation & purification/metabolism ; Rumen/*microbiology ; }, abstract = {BACKGROUND: Recently, we reported that some dairy cows could produce high amounts of milk with high amounts of protein (defined as milk protein yield [MPY]) when a population was raised under the same nutritional and management condition, a potential new trait that can be used to increase high-quality milk production. It is unknown to what extent the rumen microbiome and its metabolites, as well as the host metabolism, contribute to MPY. Here, analysis of rumen metagenomics and metabolomics, together with serum metabolomics was performed to identify potential regulatory mechanisms of MPY at both the rumen microbiome and host levels.

RESULTS: Metagenomics analysis revealed that several Prevotella species were significantly more abundant in the rumen of high-MPY cows, contributing to improved functions related to branched-chain amino acid biosynthesis. In addition, the rumen microbiome of high-MPY cows had lower relative abundances of organisms with methanogen and methanogenesis functions, suggesting that these cows may produce less methane. Metabolomics analysis revealed that the relative concentrations of rumen microbial metabolites (mainly amino acids, carboxylic acids, and fatty acids) and the absolute concentrations of volatile fatty acids were higher in the high-MPY cows. By associating the rumen microbiome with the rumen metabolome, we found that specific microbial taxa (mainly Prevotella species) were positively correlated with ruminal microbial metabolites, including the amino acids and carbohydrates involved in glutathione, phenylalanine, starch, sucrose, and galactose metabolism. To detect the interactions between the rumen microbiome and host metabolism, we associated the rumen microbiome with the host serum metabolome and found that Prevotella species may affect the host's metabolism of amino acids (including glycine, serine, threonine, alanine, aspartate, glutamate, cysteine, and methionine). Further analysis using the linear mixed effect model estimated contributions to the variation in MPY based on different omics and revealed that the rumen microbial composition, functions, and metabolites, and the serum metabolites contributed 17.81, 21.56, 29.76, and 26.78%, respectively, to the host MPY.

CONCLUSIONS: These findings provide a fundamental understanding of how the microbiome-dependent and host-dependent mechanisms contribute to varied individualized performance in the milk production quality of dairy cows under the same management condition. This fundamental information is vital for the development of potential manipulation strategies to improve milk quality and production through precision feeding. Video Abstract.}, } @article {pmid32398103, year = {2020}, author = {Mohr, AE and Jäger, R and Carpenter, KC and Kerksick, CM and Purpura, M and Townsend, JR and West, NP and Black, K and Gleeson, M and Pyne, DB and Wells, SD and Arent, SM and Kreider, RB and Campbell, BI and Bannock, L and Scheiman, J and Wissent, CJ and Pane, M and Kalman, DS and Pugh, JN and Ortega-Santos, CP and Ter Haar, JA and Arciero, PJ and Antonio, J}, title = {The athletic gut microbiota.}, journal = {Journal of the International Society of Sports Nutrition}, volume = {17}, number = {1}, pages = {24}, pmid = {32398103}, issn = {1550-2783}, mesh = {Athletic Performance/*physiology ; *Diet ; Exercise/*physiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Sports Nutritional Physiological Phenomena ; }, abstract = {The microorganisms in the gastrointestinal tract play a significant role in nutrient uptake, vitamin synthesis, energy harvest, inflammatory modulation, and host immune response, collectively contributing to human health. Important factors such as age, birth method, antibiotic use, and diet have been established as formative factors that shape the gut microbiota. Yet, less described is the role that exercise plays, particularly how associated factors and stressors, such as sport/exercise-specific diet, environment, and their interactions, may influence the gut microbiota. In particular, high-level athletes offer remarkable physiology and metabolism (including muscular strength/power, aerobic capacity, energy expenditure, and heat production) compared to sedentary individuals, and provide unique insight in gut microbiota research. In addition, the gut microbiota with its ability to harvest energy, modulate the immune system, and influence gastrointestinal health, likely plays an important role in athlete health, wellbeing, and sports performance. Therefore, understanding the mechanisms in which the gut microbiota could play in the role of influencing athletic performance is of considerable interest to athletes who work to improve their results in competition as well as reduce recovery time during training. Ultimately this research is expected to extend beyond athletics as understanding optimal fitness has applications for overall health and wellness in larger communities. Therefore, the purpose of this narrative review is to summarize current knowledge of the athletic gut microbiota and the factors that shape it. Exercise, associated dietary factors, and the athletic classification promote a more "health-associated" gut microbiota. Such features include a higher abundance of health-promoting bacterial species, increased microbial diversity, functional metabolic capacity, and microbial-associated metabolites, stimulation of bacterial abundance that can modulate mucosal immunity, and improved gastrointestinal barrier function.}, } @article {pmid32396115, year = {2020}, author = {Reiman, D and Metwally, AA and Sun, J and Dai, Y}, title = {PopPhy-CNN: A Phylogenetic Tree Embedded Architecture for Convolutional Neural Networks to Predict Host Phenotype From Metagenomic Data.}, journal = {IEEE journal of biomedical and health informatics}, volume = {24}, number = {10}, pages = {2993-3001}, doi = {10.1109/JBHI.2020.2993761}, pmid = {32396115}, issn = {2168-2208}, support = {UL1 TR002003/TR/NCATS NIH HHS/United States ; }, mesh = {Algorithms ; Databases, Genetic ; Deep Learning ; Gastrointestinal Microbiome/*genetics ; Genetic Predisposition to Disease/classification/*genetics ; Metagenomics/*methods ; *Neural Networks, Computer ; Phenotype ; Phylogeny ; }, abstract = {Accurate prediction of the host phenotype from a metagenomic sample and identification of the associated microbial markers are important in understanding potential host-microbiome interactions related to disease initiation and progression. We introduce PopPhy-CNN, a novel convolutional neural network (CNN) learning framework that effectively exploits phylogenetic structure in microbial taxa for host phenotype prediction. Our approach takes an input format of a 2D matrix representing the phylogenetic tree populated with the relative abundance of microbial taxa in a metagenomic sample. This conversion empowers CNNs to explore the spatial relationship of the taxonomic annotations on the tree and their quantitative characteristics in metagenomic data. We show the competitiveness of our model compared to other available methods using nine metagenomic datasets of moderate size for binary classification. With synthetic and biological datasets, we show the superior and robust performance of our model for multi-class classification. Furthermore, we design a novel scheme for feature extraction from the learned CNN models and demonstrate improved performance when the extracted features. PopPhy-CNN is a practical deep learning framework for the prediction of host phenotype with the ability of facilitating the retrieval of predictive microbial taxa.}, } @article {pmid32394199, year = {2021}, author = {Liu, YX and Qin, Y and Chen, T and Lu, M and Qian, X and Guo, X and Bai, Y}, title = {A practical guide to amplicon and metagenomic analysis of microbiome data.}, journal = {Protein & cell}, volume = {12}, number = {5}, pages = {315-330}, pmid = {32394199}, issn = {1674-8018}, mesh = {*Algorithms ; Computational Biology ; *High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics ; Microbiota/*genetics ; *Software ; }, abstract = {Advances in high-throughput sequencing (HTS) have fostered rapid developments in the field of microbiome research, and massive microbiome datasets are now being generated. However, the diversity of software tools and the complexity of analysis pipelines make it difficult to access this field. Here, we systematically summarize the advantages and limitations of microbiome methods. Then, we recommend specific pipelines for amplicon and metagenomic analyses, and describe commonly-used software and databases, to help researchers select the appropriate tools. Furthermore, we introduce statistical and visualization methods suitable for microbiome analysis, including alpha- and beta-diversity, taxonomic composition, difference comparisons, correlation, networks, machine learning, evolution, source tracing, and common visualization styles to help researchers make informed choices. Finally, a step-by-step reproducible analysis guide is introduced. We hope this review will allow researchers to carry out data analysis more effectively and to quickly select the appropriate tools in order to efficiently mine the biological significance behind the data.}, } @article {pmid32393180, year = {2020}, author = {Jiang, P and Lai, S and Wu, S and Zhao, XM and Chen, WH}, title = {Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {348}, pmid = {32393180}, issn = {1471-2164}, support = {2018YFC0910502//National Key Research and Development Program of China/ ; 61932008//National Natural Science Foundation of China/ ; 61772368//National Natural Science Foundation of China/ ; 61572363//National Natural Science Foundation of China/ ; 2018YFC0910500//National Key R&D Program of China/ ; 17ZR1445600//Natural Science Foundation of Shanghai/ ; 2018SHZDZX01//Shanghai Municipal Science and Technology Major Project/ ; }, mesh = {Antibodies, Monoclonal/therapeutic use ; Biomarkers/*metabolism ; Colorectal Neoplasms/*diagnosis/genetics/pathology ; Crohn Disease/*diagnosis/drug therapy/genetics/pathology ; DNA/*metabolism ; Dysbiosis ; Feces/*chemistry ; Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/metabolism ; Leukocyte L1 Antigen Complex/metabolism ; Machine Learning ; Metagenomics/methods ; Treatment Outcome ; }, abstract = {BACKGROUND: Compromised intestinal barrier (CIB) has been associated with many enteropathies, including colorectal cancer (CRC) and inflammatory bowel disease (IBD). We hypothesized that CIB could lead to increased host-derived contents including epithelial cells into the gut, change its physio-metabolic properties, and globally alter microbial community and metabolic capacities.

RESULTS: Consistently, we found host DNA contents (HDCs), calculated as the percentage of metagenomic sequencing reads mapped to the host genome, were significantly elevated in patients of CRC and Crohn's disease (CD). Consistent with our hypothesis, we found that HDC correlated with microbial- and metabolic-biomarkers of these diseases, contributed significantly to machine-learning models for patient stratification and was consequently ranked as a top contributor. CD patients with treatment could partially reverse the changes of many CD-signature species over time, with reduced HDC and fecal calprotectin (FCP) levels. Strikingly, HDC showed stronger correlations with the reversing changes of the CD-related species than FCP, and contributed greatly in classifying treatment responses, suggesting that it was also a biomarker for effective treatment.

CONCLUSIONS: Together, we revealed that association between HDCs and gut dysbiosis, and identified HDC as a novel biomarker from fecal metagenomics for diagnosis and effective treatment of intestinal diseases; our results also suggested that host-derived contents may have greater impact on gut microbiota than previously anticipated.}, } @article {pmid32392682, year = {2020}, author = {Lee, S and Suits, M and Wituszynski, D and Winston, R and Martin, J and Lee, J}, title = {Residential urban stormwater runoff: A comprehensive profile of microbiome and antibiotic resistance.}, journal = {The Science of the total environment}, volume = {723}, number = {}, pages = {138033}, doi = {10.1016/j.scitotenv.2020.138033}, pmid = {32392682}, issn = {1879-1026}, mesh = {Drug Resistance, Microbial ; Environmental Monitoring ; Escherichia coli ; *Microbiota ; Ohio ; Rain ; *Water Microbiology ; }, abstract = {Non-point stormwater runoff is a major contamination source of receiving waterbodies. Heightened incidence of waterborne disease outbreaks related to recreational use and source water contamination is associated with extreme rainfall events. Such extreme events are predicted to increase in some regions due to climate change. Consequently, municipal separate storm sewer systems (MS4s) conveying pathogens to receiving waters are a growing public health concern. In addition, the spread of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria in various environmental matrices, including urban runoff, is an emerging threat. The resistome and microbiota profile of MS4 discharges has yet to be fully characterized. To address this knowledge gap, we first analyzed the relationship between rainfall depth and intensity and E. coli densities (fecal indicator) in stormwater from four MS4 outflows in Columbus, Ohio, USA during the spring and summer of 2017. Microbial source tracking (MST) was conducted to examine major fecal contamination sources in the study sewersheds. A subset of samples was analyzed for microbial and resistome profiles using a metagenomic approach. The results showed a significant positive relationship between outflow E. coli density and rainfall intensity. MST results indicate prevalent fecal contamination from ruminant populations in the study sites (91% positive among the samples tested). Protobacteria and Actinobacteria were two dominant bacteria at a phylum level. A diverse array of ARGs and potentially pathogenic bacteria (e.g. Salmonella enterica Typhimurium), fungi (e.g. Scedosporium apiospermum), and protists (e.g. Acanthamoeba palestinensis) were found in urban stormwater outflows that discharge into adjacent streams. The most prevalent ARGs among samples were β-lactam resistance genes and the most predominant virulence genes within bacterial community were related with Staphylococcus aureus. A comprehensive contamination profile indicates a need for sustainable strategies to manage urban stormwater runoff amid increasingly intense rainfall events to protect public and environmental health.}, } @article {pmid32392124, year = {2020}, author = {Edwards, A and Cameron, KA and Cook, JM and Debbonaire, AR and Furness, E and Hay, MC and Rassner, SME}, title = {Microbial genomics amidst the Arctic crisis.}, journal = {Microbial genomics}, volume = {6}, number = {5}, pages = {}, pmid = {32392124}, issn = {2057-5858}, mesh = {Arctic Regions ; Evolution, Molecular ; Genomics/*methods ; Global Warming ; *Microbiota ; Permafrost/*microbiology ; Soil Microbiology ; }, abstract = {The Arctic is warming - fast. Microbes in the Arctic play pivotal roles in feedbacks that magnify the impacts of Arctic change. Understanding the genome evolution, diversity and dynamics of Arctic microbes can provide insights relevant for both fundamental microbiology and interdisciplinary Arctic science. Within this synthesis, we highlight four key areas where genomic insights to the microbial dimensions of Arctic change are urgently required: the changing Arctic Ocean, greenhouse gas release from the thawing permafrost, 'biological darkening' of glacial surfaces, and human activities within the Arctic. Furthermore, we identify four principal challenges that provide opportunities for timely innovation in Arctic microbial genomics. These range from insufficient genomic data to develop unifying concepts or model organisms for Arctic microbiology to challenges in gaining authentic insights to the structure and function of low-biomass microbiota and integration of data on the causes and consequences of microbial feedbacks across scales. We contend that our insights to date on the genomics of Arctic microbes are limited in these key areas, and we identify priorities and new ways of working to help ensure microbial genomics is in the vanguard of the scientific response to the Arctic crisis.}, } @article {pmid32391909, year = {2020}, author = {Cuadrat, RRC and Sorokina, M and Andrade, BG and Goris, T and Dávila, AMR}, title = {Global ocean resistome revealed: Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samples.}, journal = {GigaScience}, volume = {9}, number = {5}, pages = {}, pmid = {32391909}, issn = {2047-217X}, mesh = {Algorithms ; Anti-Bacterial Agents/pharmacology ; Anti-Infective Agents/*pharmacology ; Computational Biology/methods ; DNA Barcoding, Taxonomic ; *Drug Resistance, Microbial ; Genes, Bacterial ; Humans ; Metagenome ; Metagenomics/methods ; Oceans and Seas ; Plasmids ; *Water Microbiology ; }, abstract = {BACKGROUND: The rise of antibiotic resistance (AR) in clinical settings is of great concern. Therefore, the understanding of AR mechanisms, evolution, and global distribution is a priority for patient survival. Despite all efforts in the elucidation of AR mechanisms in clinical strains, little is known about its prevalence and evolution in environmental microorganisms. We used 293 metagenomic samples from the TARA Oceans project to detect and quantify environmental antibiotic resistance genes (ARGs) using machine learning tools.

RESULTS: After manual curation of ARGs, their abundance and distribution in the global ocean are presented. Additionally, the potential of horizontal ARG transfer by plasmids and their correlation with environmental and geographical parameters is shown. A total of 99,205 environmental open reading frames (ORFs) were classified as 1 of 560 different ARGs conferring resistance to 26 antibiotic classes. We found 24,567 ORFs in putative plasmid sequences, suggesting the importance of mobile genetic elements in the dynamics of environmental ARG transmission. Moreover, 4,804 contigs with >=2 putative ARGs were found, including 2 plasmid-like contigs with 5 different ARGs, highlighting the potential presence of multi-resistant microorganisms in the natural ocean environment. Finally, we identified ARGs conferring resistance to some of the most relevant clinical antibiotics, revealing the presence of 15 ARGs similar to mobilized colistin resistance genes (mcr) with high abundance on polar biomes. Of these, 5 are assigned to Psychrobacter, a genus including opportunistic human pathogens.

CONCLUSIONS: This study uncovers the diversity and abundance of ARGs in the global ocean metagenome. Our results are available on Zenodo in MySQL database dump format, and all the code used for the analyses, including a Jupyter notebook js avaliable on Github. We also developed a dashboard web application (http://www.resistomedb.com) for data visualization.}, } @article {pmid32390250, year = {2021}, author = {Zhang, Y and Qi, Y and Lo, ECM and McGrath, C and Mei, ML and Dai, R}, title = {Using next-generation sequencing to detect oral microbiome change following periodontal interventions: A systematic review.}, journal = {Oral diseases}, volume = {27}, number = {5}, pages = {1073-1089}, pmid = {32390250}, issn = {1601-0825}, support = {1808085QH247//Anhui Province Natural Science Foundation/ ; 81701036//National Natural Science Foundation of China/ ; }, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Periodontitis ; }, abstract = {OBJECTIVES: This systematic review was to evaluate the change of oral microbiome based on next-generation sequencing (NGS)-metagenomic analysis following periodontal interventions among systematically healthy subjects.

MATERIALS AND METHODS: A structured search strategy consisting of "metagenomics" and "oral diseases" was applied to PubMed, EMBASE, and Web of Science to identify effective papers. The included studies were original studies published in English, using metagenomic approach to analyze the effectiveness of periodontal intervention on oral microbiome among systematically healthy human subjects with periodontitis.

RESULTS: A total of 12 papers were included in this review. Due to the heterogeneity of selected study, quantitative analysis was not performed. The findings as to how alpha diversity changed after interventions were not consistent across studies. Six studies illustrated clear separation of microbial composition between dental plaque samples collected before and after intervention using principal coordinates/component analysis. The most commonly detected genera before intervention were Porphyromonas, Treponema, Tannerella, and Prevotella, while Streptococcus and Actinomyces usually increased and became the dominant genera after intervention. Correlation network analysis revealed that after intervention, the topology of network was different compared to the corresponding pre-interventional samples.

CONCLUSION: Existing evidence of metagenomic studies depicts a complex change in oral microbiome after periodontal intervention.}, } @article {pmid32389951, year = {2020}, author = {Shinohara, M and Kiyosue, M and Tochio, T and Kimura, S and Koga, Y}, title = {Activation of butyrate-producing bacteria as well as bifidobacteria in the cat intestinal microbiota by the administration of 1-kestose, the smallest component of fructo-oligosaccharide.}, journal = {The Journal of veterinary medical science}, volume = {82}, number = {7}, pages = {866-874}, pmid = {32389951}, issn = {1347-7439}, mesh = {Animal Feed/analysis ; Animals ; Bacteria/classification/genetics ; Bifidobacterium/isolation & purification ; Butyrates/metabolism ; Cats/*microbiology ; Diet/veterinary ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Lactobacillus/isolation & purification ; Male ; Megasphaera/isolation & purification ; Prebiotics/administration & dosage ; RNA, Ribosomal, 16S/genetics ; Trisaccharides/*administration & dosage ; }, abstract = {1-kestose is a structural component of fructo-oligosaccharides and is composed of 2 fructose residues bound to sucrose through β2-1 bonds. In the present study, the influence of the ingestion of 1-kestose on the intestinal microbiota was investigated in cats. Six healthy cats were administered 1 g/day of 1-kestose for 8 weeks followed by a 2-week wash-out period. Fecal samples were collected from cats after 0, 4, 8, and 10 weeks. The intestinal microbiota was examined by a 16S rRNA gene metagenomic analysis and real-time PCR. Short-chain fatty acids were measured by GC/MS. The results suggested that the intestinal bacterial community structure in feline assigned to this study was divided into 2 types: one group mainly composed of the genus Lactobacillus (GA) and the other mainly composed of the genus Blautia with very few bacteria of Lactobacillus (GB). Furthermore, the number of Bifidobacterium slightly increased after the administration of 1-kestose (at 4 and 8 weeks) (P<0.1). The administration of 1-kestose also increased the abundance of Megasphaera, the butyric acid-producing bacteria, at 4 and 8 weeks (P<0.1). Furthermore, an increase in butyric acid levels was observed after the administration of 1-kestose for 4 weeks (P<0.1). These results suggest that 1-kestose activated butyrate-producing bacteria as well as bifidobacteria and propose its potential as a new generation prebiotic.}, } @article {pmid32389290, year = {2020}, author = {Fomina, M and Hong, JW and Gadd, GM}, title = {Effect of depleted uranium on a soil microcosm fungal community and influence of a plant-ectomycorrhizal association.}, journal = {Fungal biology}, volume = {124}, number = {5}, pages = {289-296}, doi = {10.1016/j.funbio.2019.08.001}, pmid = {32389290}, issn = {1878-6146}, mesh = {Basidiomycota/genetics/metabolism ; DNA, Fungal/genetics ; *Mycobiome/drug effects ; *Mycorrhizae/genetics/metabolism ; *Pinus/microbiology ; Plant Roots/microbiology ; Soil/chemistry ; Soil Microbiology ; *Uranium/toxicity ; }, abstract = {Fungi are one of the most biogeochemically active components of the soil microbiome, becoming particularly important in metal polluted terrestrial environments. There is scant information on the mycobiota of uranium (U) polluted sites and the effect of metallic depleted uranium (DU) stress on fungal communities in soil has not been reported. The present study aimed to establish the effect of DU contamination on a fungal community in soil using a culture-independent approach, fungal ribosomal intergenic spacer analysis (F-RISA). Experimental soil microcosms also included variants with plants (Pinus silvestris) and P. silvestris/Rhizopogon rubescens ectomycorrhizal associations. Soil contamination with DU resulted in the appearance of RISA bands of the ITS fragments of fungal metagenomic DNA that were characteristic of the genus Mortierella (Mortierellomycotina: Mucoromycota) in pine-free microcosms and for ectomycorrhizal fungi of the genus Scleroderma (Basidiomycota) in microcosms with mycorrhizal pines. The precise taxonomic affinity of the ITS fragments from the band appearing for non-mycorrhizal pines combined with DU remained uncertain, the most likely being related to the subphylum Zoopagomycotina. Thus, soil contamination by thermodynamically unstable metallic depleted uranium can cause a significant change in a soil fungal community under experimental conditions. These changes were also strongly affected by the presence of pine seedlings and their mycorrhizal status which impacted on DU biocorrosion and the release of bioavailable uranium species.}, } @article {pmid32388577, year = {2020}, author = {Seward, J and Carson, MA and Lamit, LJ and Basiliko, N and Yavitt, JB and Lilleskov, E and Schadt, CW and Smith, DS and Mclaughlin, J and Mykytczuk, N and Willims-Johnson, S and Roulet, N and Moore, T and Harris, L and Bräuer, S}, title = {Peatland Microbial Community Composition Is Driven by a Natural Climate Gradient.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {593-602}, doi = {10.1007/s00248-020-01510-z}, pmid = {32388577}, issn = {1432-184X}, mesh = {Archaea/*isolation & purification ; Bacteria/*isolation & purification ; *Climate ; *Microbiota ; Ontario ; Soil Microbiology ; United States ; *Wetlands ; }, abstract = {Peatlands are important players in climate change-biosphere feedbacks via long-term net carbon (C) accumulation in soil organic matter and as potential net C sources including the potent greenhouse gas methane (CH4). Interactions of climate, site-hydrology, plant community, and groundwater chemical factors influence peatland development and functioning, including C dioxide (CO2) and CH4 fluxes, but the role of microbial community composition is not well understood. To assess microbial functional and taxonomic dissimilarities, we used high throughput sequencing of the small subunit ribosomal DNA (SSU rDNA) to determine bacterial and archaeal community composition in soils from twenty North American peatlands. Targeted DNA metabarcoding showed that although Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla on average, intermediate and rich fens hosted greater diversity and taxonomic richness, as well as an array of candidate phyla when compared with acidic and nutrient-poor poor fens and bogs. Moreover, pH was revealed to be the strongest predictor of microbial community structure across sites. Predictive metagenome content (PICRUSt) showed increases in specific genes, such as purine/pyrimidine and amino-acid metabolism in mid-latitude peatlands from 38 to 45° N, suggesting a shift toward utilization of microbial biomass over utilization of initial plant biomass in these microbial communities. Overall, there appears to be noticeable differences in community structure between peatland classes, as well as differences in microbial metabolic activity between latitudes. These findings are in line with a predicted increase in the decomposition and accelerated C turnover, and suggest that peatlands north of 37° latitude may be particularly vulnerable to climate change.}, } @article {pmid32388254, year = {2020}, author = {Zhou, J and Tang, L and Shen, CL and Wang, JS}, title = {Green tea polyphenols boost gut-microbiota-dependent mitochondrial TCA and urea cycles in Sprague-Dawley rats.}, journal = {The Journal of nutritional biochemistry}, volume = {81}, number = {}, pages = {108395}, doi = {10.1016/j.jnutbio.2020.108395}, pmid = {32388254}, issn = {1873-4847}, support = {U01 AT006691/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; Chromatography, Liquid/methods ; Citric Acid Cycle/*drug effects ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Metabolomics ; Metagenomics ; Microbiota ; Mitochondria/*metabolism ; Polyphenols/administration & dosage/*pharmacology ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; Tea/*chemistry ; Urea/*metabolism ; }, abstract = {Green tea polyphenols (GTPs) were found to boost mammal energy conversion by modulating gut-microbial community structure, gene orthologs and metabolic pathways. Here we examined the metabolites present in the gut-microbiota-dependent mitochondrial tricarboxylic acid (TCA) cycle and urea cycle using hydrophilic interaction liquid chromatography (HILIC)-heated electrospray ionization (HESI)-tandem liquid chromatogram mass spectrometry (LC-MS). Six groups (n=12) of Sprague-Dawley rats (6-mo, ~250 g) were administered with water containing 0%, 0.5%, and 1.5% GTPs (wt/vol or g/dL). Gut-content samples were collected at 3- and 6-mo. Untargeted metabolomics detected 2177 features, with 91 features demonstrating significant dose- and time-dependencies on the GTPs treatment. Targeted metabolomics analysis revealed remarkable changes of 39 metabolites in the mitochondrial TCA cycle and urea cycle, including argininosuccunic acid (0.9-fold vs control), dihydrouracil (1.14-fold vs control), fumaric acid (1.19-fold vs control), malic acid (2.17-fold vs control), citrulline (1.86-fold vs control), and succinic acid (0.4-fold vs control). The untargeted metabolomics data were mined using bioinformatics approaches, such as analysis of variance-simultaneous component analysis (ASCA), enrichment pathway analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway mapping analysis. The results of 16S rRNA survey, metagenomics analysis, and metabolomics analysis were extrapolated and integrated using databases of Integrated Microbial Genomes and Microbiomes (IMG/M) and KEGG. Our analysis demonstrates that GTPs enhance energy conversion by boosting mitochondrial TCA cycle and urea cycle of gut-microbiota in rats. This metabolic modulation is achieved by enriching many gene orthologs, following the increase of beneficial microbials in families C. Ruminococcaceae, C. Lachnospiraceae and B. Bacteroidaceae.}, } @article {pmid32387495, year = {2020}, author = {Zhao, R and Coker, OO and Wu, J and Zhou, Y and Zhao, L and Nakatsu, G and Bian, X and Wei, H and Chan, AWH and Sung, JJY and Chan, FKL and El-Omar, E and Yu, J}, title = {Aspirin Reduces Colorectal Tumor Development in Mice and Gut Microbes Reduce its Bioavailability and Chemopreventive Effects.}, journal = {Gastroenterology}, volume = {159}, number = {3}, pages = {969-983.e4}, doi = {10.1053/j.gastro.2020.05.004}, pmid = {32387495}, issn = {1528-0012}, mesh = {Adenomatous Polyposis Coli Protein/genetics ; Animals ; Anti-Bacterial Agents/adverse effects ; Anticarcinogenic Agents/administration & dosage/*pharmacokinetics ; Aspirin/administration & dosage/*pharmacokinetics ; Azoxymethane/toxicity ; Bacillaceae/genetics/isolation & purification/metabolism ; Bacteroides fragilis/genetics/isolation & purification/metabolism ; Bacteroidetes/genetics/isolation & purification/metabolism ; Biological Availability ; Carcinogenesis/chemically induced/drug effects ; Colitis/chemically induced/genetics ; Colon/drug effects/metabolism/microbiology/pathology ; Colorectal Neoplasms/etiology/pathology/*prevention & control ; DNA, Bacterial/isolation & purification ; Dextran Sulfate/toxicity ; Disease Models, Animal ; Dose-Response Relationship, Drug ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/*physiology ; Germ-Free Life ; Humans ; Intestinal Mucosa/drug effects/metabolism/microbiology/pathology ; Male ; Mice ; Mice, Transgenic ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND & AIMS: Alterations in the intestinal microbiota affect development of colorectal cancer and drug metabolism. We studied whether the intestinal microbiota affect the ability of aspirin to reduce colon tumor development in mice.

METHODS: We performed studies with APC[min/+] mice and mice given azoxymethane and dextran sulfate sodium to induce colorectal carcinogenesis. Some mice were given antibiotics to deplete intestinal microbes, with or without aspirin, throughout the entire experiment. Germ-free mice were studied in validation experiments. Colon tissues were collected and analyzed by histopathology, quantitative reverse-transcription polymerase chain reaction, and immunoblots. Blood samples and gut luminal contents were analyzed by liquid chromatography/mass spectrometry and an arylesterase activity assay. Fecal samples were analyzed by 16S ribosomal RNA gene and shotgun metagenome sequencing.

RESULTS: Administration of aspirin to mice reduced colorectal tumor number and load in APC[min/+] mice and mice given azoxymethane and dextran sulfate sodium that had been given antibiotics (depleted gut microbiota), but not in mice with intact microbiota. Germ-free mice given aspirin developed fewer colorectal tumors than conventionalized germ-free mice given aspirin. Plasma levels of aspirin were higher in mice given antibiotics than in mice with intact gut microbiota. Analyses of luminal contents revealed that aerobic gut microbes, including Lysinibacillus sphaericus, degrade aspirin. Germ-free mice fed L sphaericus had lower plasma levels of aspirin than germ-free mice that were not fed this bacterium. There was an inverse correlation between aspirin dose and colorectal tumor development in conventional mice, but this correlation was lost with increased abundance of L sphaericus. Fecal samples from mice fed aspirin were enriched in Bifidobacterium and Lactobacillus genera, which are considered beneficial, and had reductions in Alistipes finegoldii and Bacteroides fragili, which are considered pathogenic.

CONCLUSIONS: Aspirin reduces development of colorectal tumors in APC[min/+] mice and mice given azoxymethane and dextran sulfate sodium, depending on the presence of intestinal microbes. L sphaericus in the gut degrades aspirin and reduced its chemopreventive effects in mice. Fecal samples from mice fed aspirin were enriched in beneficial bacteria, with reductions in pathogenic bacteria.}, } @article {pmid32385374, year = {2020}, author = {Liu, PY and Cheng, AC and Huang, SW and Lu, HP and Oshida, T and Liu, W and Yu, HT}, title = {Body-size Scaling is Related to Gut Microbial Diversity, Metabolism and Dietary Niche of Arboreal Folivorous Flying Squirrels.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {7809}, pmid = {32385374}, issn = {2045-2322}, mesh = {Animals ; Bacteroidetes/genetics ; Body Size ; Diet ; Feces/microbiology ; Firmicutes/genetics ; Gastrointestinal Microbiome/*genetics ; *Genetic Variation ; Metagenome/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sciuridae/genetics/metabolism/*microbiology ; }, abstract = {Thermal homeostasis of mammals is constrained by body-size scaling. Consequently, small mammals require considerable energy to maintain a high mass-specific metabolic rate (MSMR) and sustain target body temperature. In association with gut microbiota, mammalian hosts acquire absorbable molecules and fulfill their metabolic requirements. Our objective was to characterize gut microbes in wild mammals and relate those findings to host body-size scaling. Two large (Petaurista philippensis grandis and P. alborufus lena), one medium (Trogopterus xanthipes) and one small (Pteromys volans orii) species of flying squirrels (FS) were studied. Using 16S rRNA genes, 1,104 OTUs were detected from four FS, with 1.99% of OTUs shared among all FS. Although all FS gut microbiota were dominated by Firmicutes, they were constituted by different bacterial families. Moreover, Bacteroidetes accounted for up to 19% of gut microbiota in small FS, but was absent in large FS. Finally, based on metagenome predictions, carbohydrate and amino acid metabolism genes were enriched in small body-size FS. In conclusion, gut microbiota compositions and predictive metabolic functions were characteristic of body-size in FS, consistent with their adaptations to folivorous dietary niches.}, } @article {pmid32382536, year = {2020}, author = {Kibegwa, FM and Bett, RC and Gachuiri, CK and Stomeo, F and Mujibi, FD}, title = {A Comparison of Two DNA Metagenomic Bioinformatic Pipelines While Evaluating the Microbial Diversity in Feces of Tanzanian Small Holder Dairy Cattle.}, journal = {BioMed research international}, volume = {2020}, number = {}, pages = {2348560}, pmid = {32382536}, issn = {2314-6141}, mesh = {Animals ; *Archaea/classification/genetics ; *Bacteria/classification/genetics ; Cattle/*microbiology ; Computational Biology ; Feces/*microbiology ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; }, abstract = {Analysis of shotgun metagenomic data generated from next generation sequencing platforms can be done through a variety of bioinformatic pipelines. These pipelines employ different sets of sophisticated bioinformatics algorithms which may affect the results of this analysis. In this study, we compared two commonly used pipelines for shotgun metagenomic analysis: MG-RAST and Kraken 2, in terms of taxonomic classification, diversity analysis, and usability using their primarily default parameters. Overall, the two pipelines detected similar abundance distributions in the three most abundant taxa Proteobacteria, Firmicutes, and Bacteroidetes. Within bacterial domain, 497 genera were identified by both pipelines, while an additional 694 and 98 genera were solely identified by Kraken 2 and MG-RAST, respectively. 933 species were detected by the two algorithms. Kraken 2 solely detected 3550 species, while MG-RAST identified 557 species uniquely. For archaea, Kraken 2 generated 105 and 236 genera and species, respectively, while MG-RAST detected 60 genera and 88 species. 54 genera and 72 species were commonly detected by the two methods. Kraken 2 had a quicker analysis time (~4 hours) while MG-RAST took approximately 2 days per sample. This study revealed that Kraken 2 and MG-RAST generate comparable results and that a reliable high-level overview of sample is generated irrespective of the pipeline selected. However, Kraken 2 generated a more accurate taxonomic identification given the higher number of "Unclassified" reads in MG-RAST. The observed variations at the genus level show that a main restriction is using different databases for classification of the metagenomic data. The results of this research indicate that a more inclusive and representative classification of microbiomes may be achieved through creation of the combined pipelines.}, } @article {pmid32382098, year = {2020}, author = {Berlemont, R and Winans, N and Talamantes, D and Dang, H and Tsai, HW}, title = {MetaGeneHunt for protein domain annotation in short-read metagenomes.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {7712}, pmid = {32382098}, issn = {2045-2322}, support = {RL5 GM118978/GM/NIGMS NIH HHS/United States ; UL1 GM118979/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*genetics ; Computational Biology ; Databases, Genetic ; Genome, Microbial/genetics ; Metagenome/*genetics ; Metagenomics/methods ; Mice ; Microbiota/genetics ; Molecular Sequence Annotation ; Protein Domains/*genetics ; Sequence Analysis ; *Software ; }, abstract = {The annotation of short-reads metagenomes is an essential process to understand the functional potential of sequenced microbial communities. Annotation techniques based solely on the identification of local matches tend to confound local sequence similarity and overall protein homology and thus don't mirror the complex multidomain architecture and the shuffling of functional domains in many protein families. Here, we present MetaGeneHunt to identify specific protein domains and to normalize the hit-counts based on the domain length. We used MetaGeneHunt to investigate the potential for carbohydrate processing in the mouse gastrointestinal tract. We sampled, sequenced, and analyzed the microbial communities associated with the bolus in the stomach, intestine, cecum, and colon of five captive mice. Focusing on Glycoside Hydrolases (GHs) we found that, across samples, 58.3% of the 4,726,023 short-read sequences matching with a GH domain-containing protein were located outside the domain of interest. Next, before comparing the samples, the counts of localized hits matching the domains of interest were normalized to account for the corresponding domain length. Microbial communities in the intestine and cecum displayed characteristic GH profiles matching distinct microbial assemblages. Conversely, the stomach and colon were associated with structurally and functionally more diverse and variable microbial communities. Across samples, despite fluctuations, changes in the functional potential for carbohydrate processing correlated with changes in community composition. Overall MetaGeneHunt is a new way to quickly and precisely identify discrete protein domains in sequenced metagenomes processed with MG-RAST. In addition, using the sister program "GeneHunt" to create custom Reference Annotation Table, MetaGeneHunt provides an unprecedented way to (re)investigate the precise distribution of any protein domain in short-reads metagenomes.}, } @article {pmid32381633, year = {2020}, author = {Ericsson, AC}, title = {Bronchopulmonary dysplasia: a crime of opportunity?.}, journal = {The European respiratory journal}, volume = {55}, number = {5}, pages = {}, doi = {10.1183/13993003.00551-2020}, pmid = {32381633}, issn = {1399-3003}, support = {MR/M022552/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Bronchopulmonary Dysplasia/epidemiology/therapy ; Crime ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; }, } @article {pmid32381601, year = {2020}, author = {Denburg, MR and Koepsell, K and Lee, JJ and Gerber, J and Bittinger, K and Tasian, GE}, title = {Perturbations of the Gut Microbiome and Metabolome in Children with Calcium Oxalate Kidney Stone Disease.}, journal = {Journal of the American Society of Nephrology : JASN}, volume = {31}, number = {6}, pages = {1358-1369}, pmid = {32381601}, issn = {1533-3450}, support = {K23 DK106428/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Bacteria/metabolism ; Calcium Oxalate/metabolism ; Case-Control Studies ; Child ; Child, Preschool ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Kidney Calculi/*etiology/metabolism/microbiology ; Male ; *Metabolome ; Nephrolithiasis/*etiology/metabolism/microbiology ; }, abstract = {BACKGROUND: The relationship between the composition and function of gut microbial communities and early-onset calcium oxalate kidney stone disease is unknown.

METHODS: We conducted a case-control study of 88 individuals aged 4-18 years, which included 44 individuals with kidney stones containing ≥50% calcium oxalate and 44 controls matched for age, sex, and race. Shotgun metagenomic sequencing and untargeted metabolomics were performed on stool samples.

RESULTS: Participants who were kidney stone formers had a significantly less diverse gut microbiome compared with controls. Among bacterial taxa with a prevalence >0.1%, 31 taxa were less abundant among individuals with nephrolithiasis. These included seven taxa that produce butyrate and three taxa that degrade oxalate. The lower abundance of these bacteria was reflected in decreased abundance of the gene encoding butyryl-coA dehydrogenase (P=0.02). The relative abundance of these bacteria was correlated with the levels of 18 fecal metabolites, and levels of these metabolites differed in individuals with kidney stones compared with controls. The oxalate-degrading bacterial taxa identified as decreased in those who were kidney stone formers were components of a larger abundance correlation network that included Eggerthella lenta and several Lactobacillus species. The microbial (α) diversity was associated with age of stone onset, first decreasing and then increasing with age. For the individuals who were stone formers, we found the lowest α diversity among individuals who first formed stones at age 9-14 years, whereas controls displayed no age-related differences in diversity.

CONCLUSIONS: Loss of gut bacteria, particularly loss of those that produce butyrate and degrade oxalate, associates with perturbations of the metabolome that may be upstream determinants of early-onset calcium oxalate kidney stone disease.}, } @article {pmid32380596, year = {2019}, author = {Francini-Filho, RB and Cordeiro, MC and Omachi, CY and Rocha, AM and Bahiense, L and Garcia, GD and Tschoeke, D and de Almeida, MG and Rangel, TP and De Oliveira, BCV and de Almeida, DQR and Menezes, R and Mazzei, EF and Joyeux, JC and Rezende, CE and Thompson, CC and Thompson, FL}, title = {Remote sensing, isotopic composition and metagenomics analyses revealed Doce River ore plume reached the southern Abrolhos Bank Reefs.}, journal = {The Science of the total environment}, volume = {697}, number = {}, pages = {134038}, doi = {10.1016/j.scitotenv.2019.134038}, pmid = {32380596}, issn = {1879-1026}, mesh = {Animals ; Anthozoa ; Brazil ; *Coral Reefs ; Ecosystem ; Isotopes/analysis ; *Metagenomics ; *Remote Sensing Technology ; Rivers/*chemistry ; Water Pollutants/*analysis ; }, abstract = {On November 5th, 2015, the Fundão dam rupture released >50 million m[3] of ore tailings into the Doce River, Minas Gerais State, Brazil. The huge volume of mud spread along the river and reached the sea, 17 days after the disaster, in Regência, Espírito Santo State (ES). In 2018, after three years of the disaster, the impacts of the ore tailings in the marine environment are still unclear. This study aims to investigate possible short-term impacts in marine biodiversity caused by the ore tailings' mud over the reef ecosystems that are closest to the disaster area: i.e. recently discovered reefs in the southern Abrolhos Bank. A remote sensing surveillance including winds, sea surface temperature, total suspended material and watercolor (MODIS Aqua data) indicated that the iron tailings plume reached the southern portion of Abrolhos Bank on June 16th, 2016. Subsequently, to obtain further evidence of the presence of the tailings in the coral reefs, water samples were collected in a gradient spanning from the river estuary to the reefs in southern Abrolhos Bank, we also analyzed the isotopic and microbial composition of the samples, as well as the reef benthic composition. Despite no clues of negative impact on benthic (coral) communities, isotopic analysis confirmed the presence of the plume over the reefs area. This study serves as a baseline for future long-term impact assessments of the health of coral reefs in the Abrolhos Bank.}, } @article {pmid32377412, year = {2020}, author = {Fan, C and Yang, B and Huang, Y}, title = {Efficacy of 0.5% Levofloxacin and 5.0% Povidone-Iodine Eyedrops in Reducing Conjunctival Bacterial Flora: Metagenomic Analysis.}, journal = {Journal of ophthalmology}, volume = {2020}, number = {}, pages = {1780498}, pmid = {32377412}, issn = {2090-004X}, abstract = {Bacteria associated with postoperative endophthalmitis mostly originate from the normal bacterial flora of the patient's conjunctiva and eyelids, so the incidence of endophthalmitis may be reduced by eliminating the ocular and adnexal flora before surgery. We assessed the effectiveness of eyedrops of 0.5% levofloxacin and 5.0% povidone-iodine (PVI) in reducing conjunctival bacterial flora by metagenomic analysis. A total of 2.4 × 10[6] high-quality sequencing reads were generated from 93 conjunctival samples obtained from 31 eyes scheduled for cataract surgery before prophylactic therapy (group 1), after administration of 0.5% levofloxacin eyedrops into the conjunctival sac 8 times before surgery (group 2), and at 3 minutes after instillation of 5.0% PVI solution in the conjunctival sac (group 3) followed by surgery irrigation. The alpha diversity and beta diversity results demonstrated that group 3 had the least richness and biodiversity. Corynebacterium, Pseudomonas, Staphylococcus, Acinetobacter, and Streptococcus were predominant in all samples. The relative abundance of these bacterial species was 30.94%, 27.48%, 5.26%, 4.55%, and 2.61% in group 1, 16.32%, 44.10%, 2.19%, 5.39%, and 0.97% in group 2, and 5.90%, 65.55%, 0.39%, 5.36%, and 0.10% in group 3, respectively. The most easily and difficultly eliminated were Corynebacterium and Pseudomonas, respectively. In conclusion, the metagenomic analysis using high-throughput sequencing provides a scientific way for evaluating the effectiveness of a disinfection method from the perspective of analyzing the composition and diversity of the conjunctival microbiome. Despite the use of preoperative antisepsis regimens, the ocular surface of patients receiving cataract surgery could not be rendered completely aseptic, indicating that more strict disinfection methods need to be adopted to reduce the risk for anterior chamber contamination and endophthalmitis after cataract surgery.}, } @article {pmid32377002, year = {2020}, author = {Li, M and Liu, S and Wang, M and Hu, H and Yin, J and Liu, C and Huang, Y}, title = {Gut Microbiota Dysbiosis Associated with Bile Acid Metabolism in Neonatal Cholestasis Disease.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {7686}, pmid = {32377002}, issn = {2045-2322}, mesh = {Bile Acids and Salts/*metabolism ; Biomarkers ; Cholestasis/diagnosis/*etiology/*metabolism ; Disease Susceptibility ; *Dysbiosis ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Liver/metabolism ; Liver Function Tests ; Metagenome ; Metagenomics/methods ; Prognosis ; }, abstract = {Neonatal cholestasis disease (NCD) is a complex and easily mis-diagnosed condition. We analyzed microbiota community structure in feces and measured short-chain fatty acids, bile acids (BAs) and liver function of 12 healthy, 13 NCD, and 13 treated infants after diagnosis. Based on 16S rRNA gene amplicon sequencing and gas-chromatographic-mass-spectrometric analysis of secondary BAs, we identified microbial genera and metabolites that associate with abnormal bile secretion. Streptococcus gallolyticus and Parabacteroides distasonis, and Lactobacillus gasseri had higher relative abundance in healthy and NCD infants respectively. Compared to NCD patients, healthy infants had higher LCA, CDCA and GCDCA fecal concentrations. The three microbial species and three secondary bile acids were selected as potential non-invasive combined biomarkers to diagnose NCD. We propose that microbiota-metabolite combined biomarkers could be used for diagnosis of NCD, and this may contribute to improved early clinical diagnosis of NCD in the future.}, } @article {pmid32376136, year = {2020}, author = {Derosa, L and Routy, B and Fidelle, M and Iebba, V and Alla, L and Pasolli, E and Segata, N and Desnoyer, A and Pietrantonio, F and Ferrere, G and Fahrner, JE and Le Chatellier, E and Pons, N and Galleron, N and Roume, H and Duong, CPM and Mondragón, L and Iribarren, K and Bonvalet, M and Terrisse, S and Rauber, C and Goubet, AG and Daillère, R and Lemaitre, F and Reni, A and Casu, B and Alou, MT and Alves Costa Silva, C and Raoult, D and Fizazi, K and Escudier, B and Kroemer, G and Albiges, L and Zitvogel, L}, title = {Gut Bacteria Composition Drives Primary Resistance to Cancer Immunotherapy in Renal Cell Carcinoma Patients.}, journal = {European urology}, volume = {78}, number = {2}, pages = {195-206}, doi = {10.1016/j.eururo.2020.04.044}, pmid = {32376136}, issn = {1873-7560}, mesh = {Animals ; Carcinoma, Renal Cell/*drug therapy/*microbiology ; *Drug Resistance, Neoplasm ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Immune Checkpoint Inhibitors/*therapeutic use ; Kidney Neoplasms/*drug therapy/*microbiology ; Mice ; Nivolumab/*therapeutic use ; Predictive Value of Tests ; Prospective Studies ; }, abstract = {BACKGROUND: The development of immune checkpoint blockade (ICB) has revolutionized the clinical outcome of renal cell carcinoma (RCC). Nevertheless, improvement of durability and prediction of responses remain unmet medical needs. While it has been recognized that antibiotics (ATBs) decrease the clinical activity of ICB across various malignancies, little is known about the direct impact of distinct intestinal nonpathogenic bacteria (commensals) on therapeutic outcomes of ICB in RCC.

OBJECTIVE: To evaluate the predictive value of stool bacteria composition for ICB efficacy in a cohort of advanced RCC patients.

We prospectively collected fecal samples from 69 advanced RCC patients treated with nivolumab and enrolled in the GETUG-AFU 26 NIVOREN microbiota translational substudy phase 2 trial (NCT03013335) at Gustave Roussy. We recorded patient characteristics including ATB use, prior systemic therapies, and response criteria. We analyzed 2994 samples of feces from healthy volunteers (HVs). In parallel, preclinical studies performed in RCC-bearing mice that received fecal transplant (FMT) from RCC patients resistant to ICB (NR-FMT) allowed us to draw a cause-effect relationship between gut bacteria composition and clinical outcomes for ICB. The influence of tyrosine kinase inhibitors (TKIs) taken before starting nivolumab on the microbiota composition has also been assessed.

Metagenomic data (MG) from whole genome sequencing (WGS) were analyzed by multivariate and pairwise comparisons/fold ratio to identify bacterial fingerprints related to ATB or prior TKI exposure and patients' therapeutic response (overall response and progression-free survival), and compared with the data from cancer-free donors.

RESULTS AND LIMITATIONS: Recent ATB use (n = 11; 16%) reduced objective response rates (from 28% to 9%, p < 0.03) and markedly affected the composition of the microbiota, facilitating the dominance of distinct species such as Clostridium hathewayi, which were also preferentially over-represented in stools from RCC patients compared with HVs. Importantly, TKIs taken prior to nivolumab had implications in shifting the microbiota composition. To establish a cause-effect relationship between gut bacteria composition and ICB efficacy, NR-FMT mice were successfully compensated with either FMT from responding RCC patients or beneficial commensals identified by WGS-MG (Akkermansia muciniphila and Bacteroides salyersiae).

CONCLUSIONS: The composition of the microbiota is influenced by TKIs and ATBs, and impacts the success of immunotherapy. Future studies will help sharpen the role of these specific bacteria and their potential as new biomarkers.

PATIENT SUMMARY: We used quantitative shotgun DNA sequencing of fecal microbes as well as preclinical models of fecal or bacterial transfer to study the association between stool composition and (pre)clinical outcome to immune checkpoint blockade. Novel insights into the pathophysiological relevance of intestinal dysbiosis in the prognosis of kidney cancer may lead to innovative therapeutic solutions, such as supplementation with probiotics to prevent primary resistance to therapy.}, } @article {pmid32375874, year = {2020}, author = {Rifkin, RF and Vikram, S and Ramond, JB and Rey-Iglesia, A and Brand, TB and Porraz, G and Val, A and Hall, G and Woodborne, S and Le Bailly, M and Potgieter, M and Underdown, SJ and Koopman, JE and Cowan, DA and Van de Peer, Y and Willerslev, E and Hansen, AJ}, title = {Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the 'ancestral' sub-Saharan African intestinal microbiome.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {62}, pmid = {32375874}, issn = {2049-2618}, mesh = {Africa South of the Sahara ; *Archaeology ; Feces/*microbiology ; *Gastrointestinal Microbiome ; History, 15th Century ; Humans ; Metagenomics ; }, abstract = {BACKGROUND: The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen.

METHODS: Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM.

RESULTS: Our results indicate that the distal IM of the Neolithic 'Middle Iron Age' (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Ötzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to 'Western' diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants.

CONCLUSIONS: Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000 years ago. Video Abtract.}, } @article {pmid32375386, year = {2020}, author = {Li, Y and Gordon, E and Idle, A and Altan, E and Seguin, MA and Estrada, M and Deng, X and Delwart, E}, title = {Virome of a Feline Outbreak of Diarrhea and Vomiting Includes Bocaviruses and a Novel Chapparvovirus.}, journal = {Viruses}, volume = {12}, number = {5}, pages = {}, pmid = {32375386}, issn = {1999-4915}, mesh = {Animals ; Bocavirus/classification/genetics/*isolation & purification/physiology ; British Columbia/epidemiology ; Cat Diseases/epidemiology/*virology ; Cats ; Diarrhea/epidemiology/*veterinary/virology ; Disease Outbreaks ; Feces/virology ; Female ; Genome, Viral ; Male ; Parvovirinae/classification/genetics/*isolation & purification/physiology ; Phylogeny ; *Virome ; Vomiting/epidemiology/*veterinary/virology ; }, abstract = {An unexplained outbreak of feline diarrhea and vomiting, negative for common enteric viral and bacterial pathogens, was subjected to viral metagenomics and PCR. We characterized from fecal samples the genome of a novel chapparvovirus we named fechavirus that was shed by 8/17 affected cats and identified three different feline bocaviruses shed by 9/17 cats. Also detected were nucleic acids from attenuated vaccine viruses, members of the normal feline virome, viruses found in only one or two cases, and viruses likely derived from ingested food products. Epidemiological investigation of disease signs, time of onset, and transfers of affected cats between three facilities support a possible role for this new chapparvovirus in a highly contagious feline diarrhea and vomiting disease.}, } @article {pmid32373553, year = {2020}, author = {Xu, Z and Xie, Z and Sun, J and Huang, S and Chen, Y and Li, C and Sun, X and Xia, B and Tian, L and Guo, C and Li, F and Pi, G}, title = {Gut Microbiome Reveals Specific Dysbiosis in Primary Osteoporosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {160}, pmid = {32373553}, issn = {2235-2988}, mesh = {DNA, Ribosomal ; Dysbiosis ; Feces ; *Gastrointestinal Microbiome ; Humans ; *Osteoporosis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Object: Primary osteoporosis (PO) is the most common bone disease, which is characterized by decreased bone mass, damage of bone tissue microstructure, increased bone fragility, and is prone to fracture. Gut microbiome may be involved in bone metabolism of PO through gut-brain axis regulation of immune system and endocrine system, however, the specific mechanism is still unclear. The purpose of this study was to characterize the gut microbiome of patients with PO and its possible role in the occurrence and development of the disease. Methods: Fecal samples were collected from 48 PO patients and 48 healthy controls (HC). The composition of gut microbiome community was analyzed by 16s rDNA amplification sequencing, and the difference of gut microbiome composition between PO patients and HC individuals was compared. PICRUSt was also used to predict the biological function of gut microbiome in patients with PO, and to explore its possible role in the occurrence and development of this disease. The classification model is constructed by random forest algorithm so as to screen the key biomarkers. Result: The diversity of gut microorganisms in PO patients was significantly higher than that in HC group (p < 0.05) and there was significant difference in microbial composition in PO group. The abundance of Dialister (0.036 vs. 0.004, p < 0.001) and Faecalibacterium (0.331 vs. 0.132, p < 0.001) were significantly enriched which were the key flora related to PO. Although no significant correlation between bone mineral density and the richness of microbial communities are found, PICRUST results show that there are a wide range of potential pathways between gut microbiome and PO patients, including genetic information processing, metabolism, environmental information processing, cellular processes, human diseases, and organic systems. Notably, the discriminant model based on dominant microflora can effectively distinguish PO from HC (AUC = 93.56). Conclusions: The findings show that PO is related to the change of gut microbiome, especially the enriched Dialister and Faecalibacterium genera, which give new clues to understand the disease and provide markers for the diagnosis and new strategies for intervention treatment of the disease.}, } @article {pmid32373220, year = {2020}, author = {Wu, IW and Gao, SS and Chou, HC and Yang, HY and Chang, LC and Kuo, YL and Dinh, MCV and Chung, WH and Yang, CW and Lai, HC and Hsieh, WP and Su, SC}, title = {Integrative metagenomic and metabolomic analyses reveal severity-specific signatures of gut microbiota in chronic kidney disease.}, journal = {Theranostics}, volume = {10}, number = {12}, pages = {5398-5411}, pmid = {32373220}, issn = {1838-7640}, mesh = {Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/genetics/physiology ; Humans ; Metabolomics/*methods ; Renal Insufficiency, Chronic/*metabolism/*microbiology ; }, abstract = {UNLABELLED: Chronic kidney disease (CKD) is a serious healthcare dilemma, associated with specific changes in gut microbiota and circulating metabolome. Yet, the functional capacity of CKD microbiome and its intricate relationship with the host metabolism at different stages of disease are less understood.

METHODS: Here, shotgun sequencing of fecal samples and targeted metabolomics profiling of serum bile acids, short- and medium-chain fatty acids, and uremic solutes were performed in a cohort of CKD patients with different severities and non-CKD controls.

RESULTS: We identified that levels of 13 microbial species and 6 circulating metabolites were significantly altered across early to advanced stages or only in particular stage(s). Among these, Prevotella sp. 885 (decreased) was associated with urea excretion, while caproic acid (decreased) and p-cresyl sulfate (elevated) were positively and negatively correlated with the glomerular filtration rate, respectively. In addition, we identified gut microbial species linked to changes in circulating metabolites. Microbial genes related to secondary bile acid biosynthesis were differentially abundant at the early stage, while pathway modules related to lipid metabolism and lipopolysaccharide biosynthesis were enriched in the CKD microbiome at the advanced stage, suggesting that changes in microbial metabolism and host inflammation may contribute to renal health. Further, we identified metagenomic and metabolomic markers to discriminate cases of different severities from the controls, among which Bacteroides eggerthii individually was of particular value in early diagnosis.

CONCLUSIONS: Our dual-omics data reveal the connections between intestinal microbes and circulating metabolites perturbed in CKD, which may be of etiological and diagnostic importance.}, } @article {pmid32369165, year = {2020}, author = {Lim, SK and Kim, D and Moon, DC and Cho, Y and Rho, M}, title = {Antibiotic resistomes discovered in the gut microbiomes of Korean swine and cattle.}, journal = {GigaScience}, volume = {9}, number = {5}, pages = {}, pmid = {32369165}, issn = {2047-217X}, mesh = {Animals ; Anti-Infective Agents/*pharmacology ; Bacteria/drug effects/genetics ; Cattle ; Computational Biology ; *Drug Resistance, Microbial ; Farms ; Gastrointestinal Microbiome/*drug effects ; Metagenome ; Metagenomics/methods ; Microbial Sensitivity Tests ; Republic of Korea ; Swine ; }, abstract = {BACKGROUND: Antibiotics administered to farm animals have led to increasing prevalence of resistance genes in different microbiomes and environments. While antibiotic treatments help cure infectious diseases in farm animals, the possibility of spreading antibiotic resistance genes into the environment and human microbiomes raises significant concerns. Through long-term evolution, antibiotic resistance genes have mutated, thereby complicating the resistance problems.

RESULTS: In this study, we performed deep sequencing of the gut microbiomes of 36 swine and 41 cattle in Korean farms, and metagenomic analysis to understand the diversity and prevalence of antibiotic resistance genes. We found that aminoglycoside, β-lactam, lincosamide, streptogramin, and tetracycline were the prevalent resistance determinants in both swine and cattle. Tetracycline resistance was abundant and prevalent in cattle and swine. Specifically, tetQ, tetW, tetO, tet32, and tet44 were the 5 most abundant and prevalent tetracycline resistance genes. Their prevalence was almost 100% in swine and cattle. While tetQ was similarly abundant in both swine and cattle, tetW was more abundant in swine than in cattle. Aminoglycoside was the second highest abundant resistance determinant in swine, but not in cattle. In particular, ANT(6) and APH(3'') were the dominant resistance gene families in swine. β-lactam was also an abundant resistance determinant in both swine and cattle. Cfx was the major contributing gene family conferring resistance against β-lactams.

CONCLUSIONS: Antibiotic resistome was more pervasive in swine than in cattle. Specifically, prevalent antibiotic resistance genes (prevalence >50%) were found more in swine than in cattle. Genomic investigation of specific resistance genes from the gut microbiomes of swine and cattle in this study should provide opportunities to better understand the exchange of antibiotic resistance genes in farm animals.}, } @article {pmid32369006, year = {2020}, author = {Shah, S and Donze-Reiner, T and Shah, V}, title = {Diversity of navel microbiome in young adults.}, journal = {Journal of medical microbiology}, volume = {69}, number = {5}, pages = {721-727}, doi = {10.1099/jmm.0.001192}, pmid = {32369006}, issn = {1473-5644}, mesh = {Adolescent ; Adult ; Body Piercing ; Cluster Analysis ; DNA Barcoding, Taxonomic ; Female ; Humans ; Male ; Metagenomics/methods ; *Microbiota ; Opportunistic Infections/microbiology ; RNA, Ribosomal, 16S/genetics ; Sex Factors ; Skin/*microbiology ; Young Adult ; }, abstract = {Introduction. Human skin microbial communities represent a tremendous source of genetic diversity that evolves as a function of human age. Microbiota differs between regions of oily and moist skin, and appears to stabilize with age.Aim. We have a minimal understanding of the time frame required for the stabilization of skin microbiota, and the role played by gender. In the current study, we examined the microbiota present in the navel region of college-attending young adults in the age group of 18-25 years and investigated if diversity is associated with gender (male and female).Method. The study involved 16 female and six male subjects. Isolated DNA samples from navel swabs were processed using the Nextera XT library preparation kit and sequenced using the MiSeq platform. Data were analysed using QIIME and statistical analysis performed in R.Results. Microbiota of navel skin is dominated by Corynebacterium and Staphylococcus and includes opportunistic pathogens like Clostridium and Pseudomonas. Also present as the major component of the flora were the organisms normally associated with the gastrointestinal tract such as Acinetobacter, Campylobacter, Klebsiella and organisms from the Enterobacteriaceae and Moraxellaceae families. Comparison of alpha and beta diversity of the microbiota in the male and female navel regions suggests that the flora is not statistically different (P>0.05). However, pairwise comparison suggests that the abundance of 12 specific genera varied with gender, including higher abundance of Klebsiella and Enterobacter in females.Conclusion. Our findings indicate that the navel skin microbiota of young adults has a core microbiota of Corynebacterium and Staphylococcus. We also noted the presence of a significant number of opportunistic pathogens. A minor gender difference in the abundance of individual organisms was also observed.}, } @article {pmid32365167, year = {2020}, author = {Hillmann, B and Al-Ghalith, GA and Shields-Cutler, RR and Zhu, Q and Knight, R and Knights, D}, title = {SHOGUN: a modular, accurate and scalable framework for microbiome quantification.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {13}, pages = {4088-4090}, pmid = {32365167}, issn = {1367-4811}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; R01 AI121383/AI/NIAID NIH HHS/United States ; }, mesh = {Bayes Theorem ; Data Analysis ; Metagenomics ; *Microbiota/genetics ; *Software ; }, abstract = {SUMMARY: The software pipeline SHOGUN profiles known taxonomic and gene abundances of short-read shotgun metagenomics sequencing data. The pipeline is scalable, modular and flexible. Data analysis and transformation steps can be run individually or together in an automated workflow. Users can easily create new reference databases and can select one of three DNA alignment tools, ranging from ultra-fast low-RAM k-mer-based database search to fully exhaustive gapped DNA alignment, to best fit their analysis needs and computational resources. The pipeline includes an implementation of a published method for taxonomy assignment disambiguation with empirical Bayesian redistribution. The software is installable via the conda resource management framework, has plugins for the QIIME2 and QIITA packages and produces both taxonomy and gene abundance profile tables with a single command, thus promoting convenient and reproducible metagenomics research.

https://github.com/knights-lab/SHOGUN.}, } @article {pmid32360228, year = {2019}, author = {Myers, B and Brownstone, N and Reddy, V and Chan, S and Thibodeaux, Q and Truong, A and Bhutani, T and Chang, HW and Liao, W}, title = {The gut microbiome in psoriasis and psoriatic arthritis.}, journal = {Best practice & research. Clinical rheumatology}, volume = {33}, number = {6}, pages = {101494}, doi = {10.1016/j.berh.2020.101494}, pmid = {32360228}, issn = {1532-1770}, mesh = {*Arthritis, Psoriatic/microbiology ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; *Psoriasis ; }, abstract = {This review summarizes existing research on the gut microbiome composition and function in psoriasis and psoriatic arthritis, exploring potential roles in disease pathogenesis, progression, and management. A strong relationship between skin, joint, and gastrointestinal inflammation exists, as demonstrated by an increased prevalence of psoriasis, psoriatic arthritis, and inflammatory bowel disease co-occurring together; however, the link between them has not been fully elucidated. Studies analyzing the gut microbiome in psoriasis and psoriatic arthritis reveal a unique pattern of dysbiosis. With regard to the gut microbiome's role in psoriasis and psoriatic arthritis pathogenesis, we discuss several theories including intestinal permeability, altered immune homeostasis, and imbalance of short- and medium-chain fatty acid-producing bacteria. We also discuss how the gut microbiome affects patient risk of psoriatic arthritis and other serious comorbidities, and how fecal microbes could be used clinically as therapeutic targets or markers of disease.}, } @article {pmid32360114, year = {2020}, author = {Farin, W and Oñate, FP and Plassais, J and Bonny, C and Beglinger, C and Woelnerhanssen, B and Nocca, D and Magoules, F and Le Chatelier, E and Pons, N and Cervino, ACL and Ehrlich, SD}, title = {Impact of laparoscopic Roux-en-Y gastric bypass and sleeve gastrectomy on gut microbiota: a metagenomic comparative analysis.}, journal = {Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery}, volume = {16}, number = {7}, pages = {852-862}, doi = {10.1016/j.soard.2020.03.014}, pmid = {32360114}, issn = {1878-7533}, mesh = {France ; Gastrectomy ; *Gastric Bypass ; *Gastrointestinal Microbiome ; Humans ; *Laparoscopy ; *Obesity, Morbid/surgery ; Switzerland ; }, abstract = {BACKGROUND: Bariatric surgery is an effective therapeutic procedure for morbidly obese patients. The 2 most common interventions are sleeve gastrectomy (SG) and laparoscopic Roux-en-Y gastric bypass (LRYGB).

OBJECTIVES: The aim of this study was to compare microbiome long-term microbiome after SG and LRYGB surgery in obese patients.

SETTING: University Hospital, France; University Hospital, United States; and University Hospital, Switzerland.

METHODS: Eighty-nine and 108 patients who underwent SG and LRYGB, respectively, were recruited. Stools were collected before and 6 months after surgery. Microbial DNA was analyzed with shotgun metagenomic sequencing (SOLiD 5500 xl Wildfire). MSPminer, a novel innovative tool to characterize new in silico biological entities, was used to identify 715 Metagenomic Species Pan-genome. One hundred forty-eight functional modules were analyzed using GOmixer and KEGG database.

RESULTS: Both interventions resulted in a similar increase of Shannon's diversity index and gene richness of gut microbiota, in parallel with weight loss, but the changes of microbial composition were different. LRYGB led to higher relative abundance of aero-tolerant bacteria, such as Escherichia coli and buccal species, such as Streptococcus and Veillonella spp. In contrast, anaerobes, such as Clostridium, were more abundant after SG, suggesting better conservation of anaerobic conditions in the gut. Enrichment of Akkermansia muciniphila was also observed after both surgeries. Function-level changes included higher potential for bacterial use of supplements, such as vitamin B12, B1, and iron upon LRYGB.

CONCLUSION: Microbiota changes after bariatric surgery depend on the nature of the intervention. LRYGB induces greater taxonomic and functional changes in gut microbiota than SG. Possible long-term health consequences of these alterations remain to be established.}, } @article {pmid32356546, year = {2020}, author = {He, WS and Li, L and Rui, J and Li, J and Sun, Y and Cui, D and Xu, B}, title = {Tomato seed oil attenuates hyperlipidemia and modulates gut microbiota in C57BL/6J mice.}, journal = {Food & function}, volume = {11}, number = {5}, pages = {4275-4290}, doi = {10.1039/d0fo00133c}, pmid = {32356546}, issn = {2042-650X}, mesh = {Animals ; Diet, High-Fat ; Gastrointestinal Microbiome/*drug effects ; Hyperlipidemias/drug therapy ; Hypolipidemic Agents/*pharmacology/therapeutic use ; *Solanum lycopersicum ; Male ; Mice ; Mice, Inbred C57BL ; Phytotherapy ; Plant Oils/*pharmacology/therapeutic use ; Seeds ; }, abstract = {In this study we aimed to investigate the role of tomato seed oil (TSO) in the alleviation of hyperlipidemia and the regulation of gut microbiota in C57BL/6J mice. Mice were divided into the following four diet-based groups: low-fat diet (LF, n = 8), high-fat diet (HF, n = 6), HF diet with TSO replacing one-third of lard (TL, n = 8), and HF diet with TSO replacing two-thirds of lard (TH, n = 8). The results showed that TH significantly reduced weight gain, relative adipose tissue weights, plasma cholesterol, triacylglycerol, low-density lipoprotein cholesterol (LDL-C), ratio of LDL-C to high-density lipoprotein cholesterol (HDL-C), hepatic cholesterol, and total fatty acids, and markedly increased plasma HDL-C. TSO supplementation also dose-dependently increased fecal cholesterol excretion and reduced fecal total fatty acids. This was accompanied by upregulation of the gene expression of hepatic PPARα, ACADL, CYP7A1, LXRα, ABCA1, and SR-B1. Metagenomic analyses demonstrated that TSO tended to reduce the Firmicutes/Bacteroidetes ratio, significantly increased the relative abundance of the genus Lactobacillus, and reduced the relative abundance of the genera Rikenella, Enterorhabdus, unclassified_o_Clostridiales and Ruminococcaceae_UCG-009. These results proved that TSO was effective in attenuating hyperlipidemia in C57BL/6J mice by enhancing fatty acid β-oxidation, reducing cholesterol absorption, promoting cholesterol efflux, and favorably modulating the gut microbiota.}, } @article {pmid32356337, year = {2020}, author = {Shin, NR and Bose, S and Wang, JH and Nam, YD and Song, EJ and Lim, DW and Kim, HB and Lim, YS and Choi, HS and Kim, H}, title = {Chemically or surgically induced thyroid dysfunction altered gut microbiota in rat models.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {34}, number = {6}, pages = {8686-8701}, doi = {10.1096/fj.201903091RR}, pmid = {32356337}, issn = {1530-6860}, mesh = {Animals ; Bacteria/genetics ; Bacteroidetes/genetics ; Disease Models, Animal ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Hypothyroidism/microbiology/pathology ; Male ; Metagenomics/methods ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; Thyroid Gland/*microbiology/*pathology ; }, abstract = {Thyroid hormones are essential for the regulation of energy homeostasis and metabolic processes. However, the relationship between thyroid function and host gut microbial communities is not properly understood. To determine whether and how gut microbiota is associated with thyroid function, metagenomics analysis of the bacterial population in fecal samples of rat models of hyperthyroidism (induced by levothyroxine) and hypothyroidism (induced by propylthiouracil or thyroidectomy) was conducted through 16S rRNA gene sequencing. Our results revealed that all thyroid dysfunction models were definitely established and gut microbial composition varied according to different thyroid functional status. The relative abundance of Ruminococcus was significantly higher in the hyperthyroidism group (HE) vs both the normal and hypothyroidism groups (HO) while S24-7 was significantly higher in the HO group. The population of Prevotellaceae and Prevotella were significantly lower in the HO group vs the normal. Firmicutes and Oscillospira were significantly higher in the SHO (surgery-induced hypothyroidism) group, while Prevotellaceae and Prevotella showed lower abundance in the SHO group than the SHAM group. Present results suggest that thyroid functions may have the potential to influence the profile of gut microbiota and could be used as foundation to investigate interaction mechanism between thyroid and gut microbiome.}, } @article {pmid32354993, year = {2020}, author = {Chakraborty, A and Ruff, SE and Dong, X and Ellefson, ED and Li, C and Brooks, JM and McBee, J and Bernard, BB and Hubert, CRJ}, title = {Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {20}, pages = {11029-11037}, pmid = {32354993}, issn = {1091-6490}, mesh = {Alkanes/metabolism ; Archaea/classification/metabolism ; Bacteria/classification/metabolism ; Biodiversity ; Geologic Sediments/chemistry/*microbiology ; Gulf of Mexico ; Hydrocarbons/*metabolism ; Metagenome ; Metagenomics ; Microbiota/*physiology ; Petroleum/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; }, abstract = {Marine cold seeps transmit fluids between the subseafloor and seafloor biospheres through upward migration of hydrocarbons that originate in deep sediment layers. It remains unclear how geofluids influence the composition of the seabed microbiome and if they transport deep subsurface life up to the surface. Here we analyzed 172 marine surficial sediments from the deep-water Eastern Gulf of Mexico to assess whether hydrocarbon fluid migration is a mechanism for upward microbial dispersal. While 132 of these sediments contained migrated liquid hydrocarbons, evidence of continuous advective transport of thermogenic alkane gases was observed in 11 sediments. Gas seeps harbored distinct microbial communities featuring bacteria and archaea that are well-known inhabitants of deep biosphere sediments. Specifically, 25 distinct sequence variants within the uncultivated bacterial phyla Atribacteria and Aminicenantes and the archaeal order Thermoprofundales occurred in significantly greater relative sequence abundance along with well-known seep-colonizing members of the bacterial genus Sulfurovum, in the gas-positive sediments. Metabolic predictions guided by metagenome-assembled genomes suggested these organisms are anaerobic heterotrophs capable of nonrespiratory breakdown of organic matter, likely enabling them to inhabit energy-limited deep subseafloor ecosystems. These results point to petroleum geofluids as a vector for the advection-assisted upward dispersal of deep biosphere microbes from subsurface to surface environments, shaping the microbiome of cold seep sediments and providing a general mechanism for the maintenance of microbial diversity in the deep sea.}, } @article {pmid32354259, year = {2020}, author = {Lee, J and d'Aigle, J and Atadja, L and Quaicoe, V and Honarpisheh, P and Ganesh, BP and Hassan, A and Graf, J and Petrosino, J and Putluri, N and Zhu, L and Durgan, DJ and Bryan, RM and McCullough, LD and Venna, VR}, title = {Gut Microbiota-Derived Short-Chain Fatty Acids Promote Poststroke Recovery in Aged Mice.}, journal = {Circulation research}, volume = {127}, number = {4}, pages = {453-465}, pmid = {32354259}, issn = {1524-4571}, support = {R01 NS094543/NS/NINDS NIH HHS/United States ; TL1 TR003169/TR/NCATS NIH HHS/United States ; R01 NS103592/NS/NINDS NIH HHS/United States ; UL1 TR003167/TR/NCATS NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 HL134838/HL/NHLBI NIH HHS/United States ; RF1 AG058463/AG/NIA NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; }, mesh = {Age Factors ; Animals ; Bifidobacterium longum/metabolism ; Brain Chemistry ; Clostridium symbiosum/metabolism ; Faecalibacterium prausnitzii/metabolism ; Fatty Acids, Volatile/analysis/*biosynthesis/blood ; *Fecal Microbiota Transplantation ; Feces/chemistry ; Gastrointestinal Microbiome/*physiology ; Infarction, Middle Cerebral Artery/*therapy ; Interleukin-17/biosynthesis ; Intestines/chemistry ; Intraepithelial Lymphocytes/physiology ; Ischemic Stroke/*therapy ; Limosilactobacillus fermentum/metabolism ; Male ; Mice ; Mucin-2/metabolism ; Mucin-4/metabolism ; T-Lymphocytes, Regulatory/physiology ; }, abstract = {RATIONALE: The elderly experience profound systemic responses after stroke, which contribute to higher mortality and more severe long-term disability. Recent studies have revealed that stroke outcomes can be influenced by the composition of gut microbiome. However, the potential benefits of manipulating the gut microbiome after injury is unknown.

OBJECTIVE: To determine if restoring youthful gut microbiota after stroke aids in recovery in aged subjects, we altered the gut microbiome through young fecal transplant gavage in aged mice after experimental stroke. Further, the effect of direct enrichment of selective bacteria producing short-chain fatty acids (SCFAs) was tested as a more targeted and refined microbiome therapy.

METHODS AND RESULTS: Aged male mice (18-20 months) were subjected to ischemic stroke by middle cerebral artery occlusion. We performed fecal transplant gavage 3 days after middle cerebral artery occlusion using young donor biome (2-3 months) or aged biome (18-20 months). At day 14 after stroke, aged stroke mice receiving young fecal transplant gavage had less behavioral impairment, and reduced brain and gut inflammation. Based on data from microbial sequencing and metabolomics analysis demonstrating that young fecal transplants contained much higher SCFA levels and related bacterial strains, we selected 4 SCFA-producers (Bifidobacterium longum, Clostridium symbiosum, Faecalibacterium prausnitzii, and Lactobacillus fermentum) for transplantation. These SCFA-producers alleviated poststroke neurological deficits and inflammation, and elevated gut, brain and plasma SCFA concentrations in aged stroke mice.

CONCLUSIONS: This is the first study suggesting that the poor stroke recovery in aged mice can be reversed via poststroke bacteriotherapy following the replenishment of youthful gut microbiome via modulation of immunologic, microbial, and metabolomic profiles in the host.}, } @article {pmid32354152, year = {2020}, author = {Reider, SJ and Moosmang, S and Tragust, J and Trgovec-Greif, L and Tragust, S and Perschy, L and Przysiecki, N and Sturm, S and Tilg, H and Stuppner, H and Rattei, T and Moschen, AR}, title = {Prebiotic Effects of Partially Hydrolyzed Guar Gum on the Composition and Function of the Human Microbiota-Results from the PAGODA Trial.}, journal = {Nutrients}, volume = {12}, number = {5}, pages = {}, pmid = {32354152}, issn = {2072-6643}, support = {17605//Oesterreichische Nationalbank/ ; CD Laboratory for Mucosal Immunology//Christian Doppler Forschungsgesellschaft/ ; }, mesh = {Acetates/metabolism ; Bacteroides/isolation & purification ; Butyrates/metabolism ; Dietary Fiber/*administration & dosage/*pharmacology ; Faecalibacterium/isolation & purification ; Feces/*microbiology ; Female ; Galactans/*administration & dosage/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; *Healthy Volunteers ; Humans ; Hydrolysis ; Male ; Mannans/*administration & dosage/*pharmacology ; Plant Gums/*administration & dosage/*pharmacology ; *Prebiotics ; Ruminococcus/isolation & purification ; Solubility ; }, abstract = {(1) Background: Alterations in the structural composition of the human gut microbiota have been identified in various disease entities along with exciting mechanistic clues by reductionist gnotobiotic modeling. Improving health by beneficially modulating an altered microbiota is a promising treatment approach. Prebiotics, substrates selectively used by host microorganisms conferring a health benefit, are broadly used for dietary and clinical interventions. Herein, we sought to investigate the microbiota-modelling effects of the soluble fiber, partially hydrolyzed guar gum (PHGG). (2) Methods: We performed a 9 week clinical trial in 20 healthy volunteers that included three weeks of a lead-in period, followed by three weeks of an intervention phase, wherein study subjects received 5 g PHGG up to three times per day, and concluding with a three-week washout period. A stool diary was kept on a daily basis, and clinical data along with serum/plasma and stool samples were collected on a weekly basis. PHGG-induced alterations of the gut microbiota were studied by 16S metagenomics of the V1-V3 and V3-V4 regions. To gain functional insight, we further studied stool metabolites using nuclear magnetic resonance (NMR) spectroscopy. (3) Results: In healthy subjects, PHGG had significant effects on stool frequency and consistency. These effects were paralleled by changes in α- (species evenness) and β-diversity (Bray-Curtis distances), along with increasing abundances of metabolites including butyrate, acetate and various amino acids. On a taxonomic level, PHGG intake was associated with a bloom in Ruminococcus, Fusicatenibacter, Faecalibacterium and Bacteroides and a reduction in Roseburia, Lachnospiracea and Blautia. The majority of effects disappeared after stopping the prebiotic and most effects tended to be more pronounced in male participants. (4) Conclusions: Herein, we describe novel aspects of the prebiotic PHGG on compositional and functional properties of the healthy human microbiota.}, } @article {pmid32353491, year = {2021}, author = {Abdel-Aziz, MI and Brinkman, P and Vijverberg, SJH and Neerincx, AH and Riley, JH and Bates, S and Hashimoto, S and Kermani, NZ and Chung, KF and Djukanovic, R and Dahlén, SE and Adcock, IM and Howarth, PH and Sterk, PJ and Kraneveld, AD and Maitland-van der Zee, AH and , }, title = {Sputum microbiome profiles identify severe asthma phenotypes of relative stability at 12 to 18 months.}, journal = {The Journal of allergy and clinical immunology}, volume = {147}, number = {1}, pages = {123-134}, doi = {10.1016/j.jaci.2020.04.018}, pmid = {32353491}, issn = {1097-6825}, mesh = {Asthma/*microbiology ; Female ; Follow-Up Studies ; Humans ; Male ; *Microbiota ; Middle Aged ; Severity of Illness Index ; Specimen Handling ; Sputum/*microbiology ; Time Factors ; }, abstract = {BACKGROUND: Asthma is a heterogeneous disease characterized by distinct phenotypes with associated microbial dysbiosis.

OBJECTIVES: Our aim was to identify severe asthma phenotypes based on sputum microbiome profiles and assess their stability after 12 to 18 months. A further aim was to evaluate clusters' robustness after inclusion of an independent cohort of patients with mild-to-moderate asthma.

METHODS: In this longitudinal multicenter cohort study, sputum samples were collected for microbiome profiling from a subset of the Unbiased Biomarkers in Prediction of Respiratory Disease Outcomes adult patient cohort at baseline and after 12 to 18 months of follow-up. Unsupervised hierarchical clustering was performed by using the Bray-Curtis β-diversity measure of microbial profiles. For internal validation, partitioning around medoids, consensus cluster distribution, bootstrapping, and topological data analysis were applied. Follow-up samples were studied to evaluate within-patient clustering stability in patients with severe asthma. Cluster robustness was evaluated by using an independent cohort of patients with mild-to-moderate asthma.

RESULTS: Data were available for 100 subjects with severe asthma (median age 55 years; 42% males). Two microbiome-driven clusters were identified; they were characterized by differences in asthma onset, smoking status, residential locations, percentage of blood and/or sputum neutrophils and macrophages, lung spirometry results, and concurrent asthma medications (all P values < .05). The cluster 2 patients displayed a commensal-deficient bacterial profile that was associated with worse asthma outcomes than those of the cluster 1 patients. Longitudinal clusters revealed high relative stability after 12 to 18 months in those with severe asthma. Further inclusion of an independent cohort of 24 patients with mild-to-moderate asthma was consistent with the clustering assignments.

CONCLUSION: Unbiased microbiome-driven clustering revealed 2 distinct robust phenotypes of severe asthma that exhibited relative overtime stability. This suggests that the sputum microbiome may serve as a biomarker for better characterizing asthma phenotypes.}, } @article {pmid32352657, year = {2020}, author = {Rosado, T and Dias, L and Lança, M and Nogueira, C and Santos, R and Martins, MR and Candeias, A and Mirão, J and Caldeira, AT}, title = {Assessment of microbiota present on a Portuguese historical stone convent using high-throughput sequencing approaches.}, journal = {MicrobiologyOpen}, volume = {9}, number = {6}, pages = {1067-1084}, pmid = {32352657}, issn = {2045-8827}, mesh = {Archaeology ; Bacteria/*classification/genetics/metabolism ; *Biodegradation, Environmental ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; Fungi/*classification/genetics/metabolism ; Geologic Sediments/*microbiology ; High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; Portugal ; }, abstract = {The study performed on the stone materials from the Convent of Christ revealed the presence of a complex microbial ecosystem, emphasizing the determinant role of microorganisms on the biodecay of this built cultural heritage. In this case study, the presence of Rubrobacter sp., Arthrobacter sp., Roseomonas sp., and Marinobacter sp. seems to be responsible for colored stains and biofilm formation while Ulocladium sp., Cladosporium sp., and Dirina sp. may be related to structural damages. The implementation of high-throughput sequencing approaches on the Convent of Christ's biodecay assessment allowed us to explore, compare, and characterize the microbial communities, overcoming the limitations of culture-dependent techniques, which only identify the cultivable population. The application of these different tools and insights gave us a panoramic view of the microbiota thriving on the Convent of Christ and signalize the main biodeteriogenic agents acting on the biodecay of stone materials. This finding highlighted the importance of performing metagenomic studies due to the improvements and the reduced amount of sample DNA needed, promoting a deeper and more detailed knowledge of the microbiota present on these dynamic repositories that support microbial life. This will further enable us to perform prospective studies in quarry and applied stone context, monitoring biogenic and nonbiogenic agents, and also to define long-term mitigation strategies to prevent biodegradation/biodeterioration processes.}, } @article {pmid32350078, year = {2020}, author = {Call, L and Molina, T and Stoll, B and Guthrie, G and Chacko, S and Plat, J and Robinson, J and Lin, S and Vonderohe, C and Mohammad, M and Kunichoff, D and Cruz, S and Lau, P and Premkumar, M and Nielsen, J and Fang, Z and Olutoye, O and Thymann, T and Britton, R and Sangild, P and Burrin, D}, title = {Parenteral lipids shape gut bile acid pools and microbiota profiles in the prevention of cholestasis in preterm pigs.}, journal = {Journal of lipid research}, volume = {61}, number = {7}, pages = {1038-1051}, pmid = {32350078}, issn = {1539-7262}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 DK094616/DK/NIDDK NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; T32 GM088129/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bile Acids and Salts/*metabolism ; Cholestasis/complications/*metabolism/*microbiology ; *Lipid Metabolism ; *Microbiota ; Parenteral Nutrition ; Premature Birth/*metabolism/*microbiology ; Swine ; }, abstract = {Multi-component lipid emulsions, rather than soy-oil emulsions, prevent cholestasis by an unknown mechanism. Here, we quantified liver function, bile acid pools, and gut microbial and metabolite profiles in premature parenterally fed pigs given a soy-oil lipid emulsion, Intralipid (IL), a multi component lipid emulsion, SMOFlipid (SMOF), a novel emulsion with a modified fatty-acid composition [experimental emulsion (EXP)], or a control enteral diet (ENT) for 22 days. We assayed serum cholestasis markers, measured total bile acid levels in plasma, liver, and gut contents, and analyzed colonic bacterial 16S rRNA gene sequences and metabolomic profiles. Serum cholestasis markers (i.e., bilirubin, bile acids, and γ-glutamyl transferase) were highest in IL-fed pigs and normalized in those given SMOF, EXP, or ENT. Gut bile acid pools were lowest in the IL treatment and were increased in the SMOF and EXP treatments and comparable to ENT. Multiple bile acids, especially their conjugated forms, were higher in the colon contents of SMOF and EXP than in IL pigs. The colonic microbial communities of SMOF and EXP pigs had lower relative abundance of several gram-positive anaerobes, including Clostridrium XIVa, and higher abundance of Enterobacteriaceae than those of IL and ENT pigs. Differences in lipid and microbial-derived compounds were also observed in colon metabolite profiles. These results indicate that multi-component lipid emulsions prevent cholestasis and restore enterohepatic bile flow in association with gut microbial and metabolomic changes. We conclude that sustained bile flow induced by multi-component lipid emulsions likely exerts a dominant effect in reducing bile acid-sensitive gram-positive bacteria.}, } @article {pmid32348781, year = {2020}, author = {Bisanz, JE and Soto-Perez, P and Noecker, C and Aksenov, AA and Lam, KN and Kenney, GE and Bess, EN and Haiser, HJ and Kyaw, TS and Yu, FB and Rekdal, VM and Ha, CWY and Devkota, S and Balskus, EP and Dorrestein, PC and Allen-Vercoe, E and Turnbaugh, PJ}, title = {A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria.}, journal = {Cell host & microbe}, volume = {27}, number = {6}, pages = {1001-1013.e9}, pmid = {32348781}, issn = {1934-6069}, support = {T32 GM007810/GM/NIGMS NIH HHS/United States ; T32 AI060537/AI/NIAID NIH HHS/United States ; R21 CA227232/CA/NCI NIH HHS/United States ; T32 GM007618/GM/NIGMS NIH HHS/United States ; M01 RR001271/RR/NCRR NIH HHS/United States ; P30 DK098722/DK/NIDDK NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; R01 AR074500/AR/NIAMS NIH HHS/United States ; }, mesh = {Actinobacteria/classification/drug effects/genetics/isolation & purification ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/*genetics/*isolation & purification ; Dissection/*methods ; Gastrointestinal Microbiome/*genetics/physiology ; Gastrointestinal Tract/microbiology ; Genes, Bacterial/genetics ; *Genomics ; Germ-Free Life ; Humans ; Metagenome ; Metagenomics ; Mice ; Microbial Sensitivity Tests ; Multigene Family ; Phenotype ; Polymorphism, Genetic ; }, abstract = {Despite the remarkable microbial diversity found within humans, our ability to link genes to phenotypes is based upon a handful of model microorganisms. We report a comparative genomics platform for Eggerthella lenta and other Coriobacteriia, a neglected taxon broadly relevant to human health and disease. We uncover extensive genetic and metabolic diversity and validate a tool for mapping phenotypes to genes and sequence variants. We also present a tool for the quantification of strains from metagenomic sequencing data, enabling the identification of genes that predict bacterial fitness. Competitive growth is reproducible under laboratory conditions and attributable to intrinsic growth rates and resource utilization. Unique signatures of in vivo competition in gnotobiotic mice include an adhesin enriched in poor colonizers. Together, these computational and experimental resources represent a strong foundation for the continued mechanistic dissection of the Coriobacteriia and a template that can be applied to study other genetically intractable taxa.}, } @article {pmid32348348, year = {2020}, author = {Avila-Herrera, A and Thissen, J and Urbaniak, C and Be, NA and Smith, DJ and Karouia, F and Mehta, S and Venkateswaran, K and Jaing, C}, title = {Crewmember microbiome may influence microbial composition of ISS habitable surfaces.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0231838}, pmid = {32348348}, issn = {1932-6203}, mesh = {*Astronauts ; DNA, Bacterial/genetics/isolation & purification ; *Ecological Systems, Closed ; Environmental Monitoring/methods ; Humans ; Metagenome/genetics ; Microbiota/*genetics ; Saliva/microbiology ; Skin/microbiology ; Space Flight/*instrumentation ; *Spacecraft ; Time Factors ; }, abstract = {The International Space Station (ISS) is a complex built environment physically isolated from Earth. Assessing the interplay between the microbial community of the ISS and its crew is important for preventing biomedical and structural complications for long term human spaceflight missions. In this study, we describe one crewmember's microbial profile from body swabs of mouth, nose, ear, skin and saliva that were collected at eight different time points pre-, during and post-flight. Additionally, environmental surface samples from eight different habitable locations in the ISS were collected from two flights. Environmental samples from one flight were collected by the crewmember and samples from the next flight were collected after the crewmember departed. The microbial composition in both environment and crewmember samples was measured using shotgun metagenomic sequencing and processed using the Livermore Metagenomics Analysis Toolkit. Ordination of sample to sample distances showed that of the eight crew body sites analyzed, skin, nostril, and ear samples are more similar in microbial composition to the ISS surfaces than mouth and saliva samples; and that the microbial composition of the crewmember's skin samples are more closely related to the ISS surface samples collected by the crewmember on the same flight than ISS surface samples collected by other crewmembers on different flights. In these collections, species alpha diversity in saliva samples appears to decrease during flight and rebound after returning to Earth. This is the first study to compare the ISS microbiome to a crewmember's microbiome via shotgun metagenomic sequencing. We observed that the microbiome of the surfaces inside the ISS resemble those of the crew's skin. These data support future crew and ISS microbial surveillance efforts and the design of preventive measures to maintain crew habitat onboard spacecraft destined for long term space travel.}, } @article {pmid32346574, year = {2020}, author = {Ajilogba, CF and Babalola, OO}, title = {Bambara groundnut soil metagenomics data.}, journal = {Data in brief}, volume = {30}, number = {}, pages = {105542}, pmid = {32346574}, issn = {2352-3409}, abstract = {Metagenomics analysis was carried out on extracted DNA of Rhizospheric soil samples from Bambara groundnut. This dataset presented reports on the bacterial communities at the different growth stages of Bambara groundnut and the bulk soil. Paired-end Illumina-Miseq sequencing of 16S rRNA genes was carried on the soil samples of the bacterial community with the phyla dominated by Actinobacteria (30.1%), Proteobacteria (22%), Acidobacteria (20.9%), Bacteroides (8.4%), Chloroflex (4.5%) and Firmicutes (4.4%) in all the soil samples. Samples from the bulk soil had the least average percent phyla, while samples at seed maturity stage had the highest average percent phyla. The alpha diversity at p = 0.05 was highest at this stage compared to the others and the control. Rubrobacter was the most predominant genera, after which is Acidobacterium and Skermanella. The biodiversity profile generated from the metagenomics analysis is useful in increasing knowledge of the drought-tolerance ability of Bambara groundnut. The data generated can be used to compare bacterial diversity at different growth stages of plants.}, } @article {pmid32345639, year = {2020}, author = {Neugent, ML and Hulyalkar, NV and Nguyen, VH and Zimmern, PE and De Nisco, NJ}, title = {Advances in Understanding the Human Urinary Microbiome and Its Potential Role in Urinary Tract Infection.}, journal = {mBio}, volume = {11}, number = {2}, pages = {}, pmid = {32345639}, issn = {2150-7511}, mesh = {Female ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; *Microbiota/drug effects/genetics ; Probiotics/therapeutic use ; Urinary Tract/*microbiology ; *Urinary Tract Infections/diagnosis/microbiology/prevention & control/therapy ; Urine/microbiology ; }, abstract = {Recent advances in the analysis of microbial communities colonizing the human body have identified a resident microbial community in the human urinary tract (UT). Compared to many other microbial niches, the human UT harbors a relatively low biomass. Studies have identified many genera and species that may constitute a core urinary microbiome. However, the contribution of the UT microbiome to urinary tract infection (UTI) and recurrent UTI (rUTI) pathobiology is not yet clearly understood. Evidence suggests that commensal species within the UT and urogenital tract (UGT) microbiomes, such as Lactobacillus crispatus, may act to protect against colonization with uropathogens. However, the mechanisms and fundamental biology of the urinary microbiome-host relationship are not understood. The ability to measure and characterize the urinary microbiome has been enabled through the development of next-generation sequencing and bioinformatic platforms that allow for the unbiased detection of resident microbial DNA. Translating technological advances into clinical insight will require further study of the microbial and genomic ecology of the urinary microbiome in both health and disease. Future diagnostic, prognostic, and therapeutic options for the management of UTI may soon incorporate efforts to measure, restore, and/or preserve the native, healthy ecology of the urinary microbiomes.}, } @article {pmid32345342, year = {2020}, author = {Zhang, Q and Hu, J and Feng, JW and Hu, XT and Wang, T and Gong, WX and Huang, K and Guo, YX and Zou, Z and Lin, X and Zhou, R and Yuan, YQ and Zhang, AD and Wei, H and Cao, G and Liu, C and Chen, LL and Jin, ML}, title = {Influenza infection elicits an expansion of gut population of endogenous Bifidobacterium animalis which protects mice against infection.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {99}, pmid = {32345342}, issn = {1474-760X}, mesh = {Animals ; Bifidobacterium/isolation & purification ; *Bifidobacterium animalis/isolation & purification/physiology ; Coenzyme A/therapeutic use ; Feces/microbiology ; *Gastrointestinal Microbiome ; Influenza A Virus, H7N9 Subtype ; Lethal Dose 50 ; Lung/pathology ; Mice ; Mice, Inbred C57BL ; Orthomyxoviridae Infections/microbiology/pathology/*prevention & control ; Valine/therapeutic use ; }, abstract = {BACKGROUND: Influenza is a severe respiratory illness that continually threatens global health. It has been widely known that gut microbiota modulates the host response to protect against influenza infection, but mechanistic details remain largely unknown. Here, we took advantage of the phenomenon of lethal dose 50 (LD50) and metagenomic sequencing analysis to identify specific anti-influenza gut microbes and analyze the underlying mechanism.

RESULTS: Transferring fecal microbes from mice that survive virulent influenza H7N9 infection into antibiotic-treated mice confers resistance to infection. Some gut microbes exhibit differential features to lethal influenza infection depending on the infection outcome. Bifidobacterium pseudolongum and Bifidobacterium animalis levels are significantly elevated in surviving mice when compared to dead or mock-infected mice. Oral administration of B. animalis alone or the combination of both significantly reduces the severity of H7N9 infection in both antibiotic-treated and germ-free mice. Functional metagenomic analysis suggests that B. animalis mediates the anti-influenza effect via several specific metabolic molecules. In vivo tests confirm valine and coenzyme A produce an anti-influenza effect.

CONCLUSIONS: These findings show that the severity of influenza infection is closely related to the heterogeneous responses of the gut microbiota. We demonstrate the anti-influenza effect of B. animalis, and also find that the gut population of endogenous B. animalis can expand to enhance host influenza resistance when lethal influenza infection occurs, representing a novel interaction between host and gut microbiota. Further, our data suggest the potential utility of Bifidobacterium in the prevention and as a prognostic predictor of influenza.}, } @article {pmid32345218, year = {2020}, author = {Loo, EXL and Zain, A and Yap, GC and Purbojati, RW and Drautz-Moses, DI and Koh, YQ and Chong, YS and Tan, KH and Gluckman, PD and Yap, F and Eriksson, JG and Tham, E and Shek, LP and Kjelleberg, S and Schuster, SC and Banerjee, R and Lee, BW}, title = {Longitudinal assessment of antibiotic resistance gene profiles in gut microbiomes of infants at risk of eczema.}, journal = {BMC infectious diseases}, volume = {20}, number = {1}, pages = {312}, pmid = {32345218}, issn = {1471-2334}, support = {(R-178-000-222-511)//NMRC/ ; NMRC/TCR/004-NUS/2008; NMRC/TCR/012-NUHS/2014.//NMRC/ ; }, mesh = {Aminoglycosides/pharmacology ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Eczema/*diagnosis/etiology ; Escherichia coli/drug effects/enzymology/isolation & purification ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant ; Infant, Newborn ; Klebsiella pneumoniae/drug effects/enzymology/isolation & purification ; Longitudinal Studies ; Male ; Risk ; beta-Lactamases/genetics/metabolism ; beta-Lactams/pharmacology ; }, abstract = {BACKGROUND: While there is increasing knowledge about the gut microbiome, the factors influencing and the significance of the gut resistome are still not well understood. Infant gut commensals risk transferring multidrug-resistant antibiotic resistance genes (ARGs) to pathogenic bacteria. The rapid spread of multidrug-resistant pathogenic bacteria is a worldwide public health concern. Better understanding of the naïve infant gut resistome may build the evidence base for antimicrobial stewardship in both humans and in the food industry. Given the high carriage rate of extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in Asia, we aimed to evaluate community prevalence, dynamics, and longitudinal changes in antibiotic resistance gene (ARG) profiles and prevalence of ESBL-producing E. coli and K. pneumoniae in the intestinal microbiome of infants participating in the Growing Up in Singapore Towards Healthy Outcomes (GUSTO) study, a longitudinal cohort study of pregnant women and their infants.

METHODS: We analysed ARGs in the first year of life among 75 infants at risk of eczema who had stool samples collected at multiple timepoints using metagenomics.

RESULTS: The mean number of ARGs per infant increased with age. The most common ARGs identified confer resistance to aminoglycoside, beta-lactam, macrolide and tetracycline antibiotics; all infants harboured these antibiotic resistance genes at some point in the first year of life. Few ARGs persisted throughout the first year of life. Beta-lactam resistant Escherichia coli and Klebsiella pneumoniae were detected in 4 (5.3%) and 32 (42.7%) of subjects respectively.

CONCLUSION: In this longitudinal cohort study of infants living in a region with high endemic antibacterial resistance, we demonstrate that majority of the infants harboured several antibiotic resistance genes in their gut and showed that the infant gut resistome is diverse and dynamic over the first year of life.}, } @article {pmid32343737, year = {2020}, author = {Angebault, C and Payen, M and Woerther, PL and Rodriguez, C and Botterel, F}, title = {Combined bacterial and fungal targeted amplicon sequencing of respiratory samples: Does the DNA extraction method matter?.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0232215}, pmid = {32343737}, issn = {1932-6203}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Biodiversity ; DNA, Bacterial/genetics/*isolation & purification ; DNA, Fungal/genetics/*isolation & purification ; France ; Fungi/classification/*genetics/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; Microbiota/genetics ; Real-Time Polymerase Chain Reaction ; Respiratory System/*microbiology ; Sequence Analysis, DNA/methods ; Sputum/microbiology ; }, abstract = {BACKGROUND: High-throughput sequencing techniques are used to analyse the diversity of the respiratory microbiota in health and disease. Although extensive data are available regarding bacterial respiratory microbiota, its fungal component remains poorly studied. This is partly due to the technical issues associated with fungal metagenomics analyses. In this study, we compared two DNA extraction protocols and two fungal amplification targets for combined bacterial and fungal targeted amplicon sequencing analyses of the respiratory microbiota.

METHODS: Six sputa, randomly selected from routine samples in Mondor Hospital (Creteil, France) and treated anonymously, were tested after bacterial and fungal routine culture. Two of which were spiked with Aspergillus Fumigati and Aspergillus Nigri (105 conidia/mL). After mechanical lysis, DNA was extracted using automated QIAsymphony® extraction (AQE) or manual PowerSoil® MoBio extraction (MPE). DNA yield and purity were compared. DNA extracted from spiked sputa was subjected to (i) real-time PCR for Aspergillus DNA detection and (ii) combined metagenomic analyses targeting barcoded primers for fungal ITS1 and ITS2, and bacterial V1-V2 and V3-V4 16S regions. Amplicon libraries were prepared using MiSeq Reagent V3 kit on Illumina platform. Data were analysed using PyroMIC© and SHAMAN software, and compared with culture results.

RESULTS: AQE extraction provided a higher yield of DNA (AQE/MPE DNA ratio = 4.5 [1.3-11]) in a shorter time. The yield of Aspergillus DNA detected by qPCR was similar for spiked sputa regardless of extraction protocol. The extraction moderately impacted the diversity or relative abundances of bacterial communities using targeted amplicon sequencing (2/43 taxa impacted). For fungi, the relative abundances of 4/11 major taxa were impacted and AQE results were closer to culture results. The V1-V2 or V3-V4 and ITS1 or ITS2 targets assessed similarly the diversity of bacterial and fungal major taxa, but ITS2 and V3-V4 detected more minor taxa.

CONCLUSION: Our results showed the importance of DNA extraction for combined bacterial and fungal targeted metagenomics of respiratory samples. The extraction protocol can affect DNA yield and the relative abundances of few bacterial but more fungal taxa. For fungal analysis, ITS2 allowed the detection of a greater number of minor taxa compared with ITS1.}, } @article {pmid32343490, year = {2020}, author = {Estaki, M and Jiang, L and Bokulich, NA and McDonald, D and González, A and Kosciolek, T and Martino, C and Zhu, Q and Birmingham, A and Vázquez-Baeza, Y and Dillon, MR and Bolyen, E and Caporaso, JG and Knight, R}, title = {QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data.}, journal = {Current protocols in bioinformatics}, volume = {70}, number = {1}, pages = {e100}, pmid = {32343490}, issn = {1934-340X}, support = {UL1 TR001442/TR/NCATS NIH HHS/United States ; }, mesh = {Biodiversity ; *Databases as Topic ; Linear Models ; *Microbiota ; Phylogeny ; *Software ; }, abstract = {QIIME 2 is a completely re-engineered microbiome bioinformatics platform based on the popular QIIME platform, which it has replaced. QIIME 2 facilitates comprehensive and fully reproducible microbiome data science, improving accessibility to diverse users by adding multiple user interfaces. QIIME 2 can be combined with Qiita, an open-source web-based platform, to re-use available data for meta-analysis. The following basic protocol describes how to install QIIME 2 on a single computer and analyze microbiome sequence data, from processing of raw DNA sequence reads through generating publishable interactive figures. These interactive figures allow readers of a study to interact with data with the same ease as its authors, advancing microbiome science transparency and reproducibility. We also show how plug-ins developed by the community to add analysis capabilities can be installed and used with QIIME 2, enhancing various aspects of microbiome analyses-e.g., improving taxonomic classification accuracy. Finally, we illustrate how users can perform meta-analyses combining different datasets using readily available public data through Qiita. In this tutorial, we analyze a subset of the Early Childhood Antibiotics and the Microbiome (ECAM) study, which tracked the microbiome composition and development of 43 infants in the United States from birth to 2 years of age, identifying microbiome associations with antibiotic exposure, delivery mode, and diet. For more information about QIIME 2, see https://qiime2.org. To troubleshoot or ask questions about QIIME 2 and microbiome analysis, join the active community at https://forum.qiime2.org. © 2020 The Authors. Basic Protocol: Using QIIME 2 with microbiome data Support Protocol: Further microbiome analyses.}, } @article {pmid32341166, year = {2020}, author = {Deboutte, W and Beller, L and Yinda, CK and Maes, P and de Graaf, DC and Matthijnssens, J}, title = {Honey-bee-associated prokaryotic viral communities reveal wide viral diversity and a profound metabolic coding potential.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {19}, pages = {10511-10519}, pmid = {32341166}, issn = {1091-6490}, mesh = {Animals ; Bacteria/genetics ; Bacteriophages/*genetics/metabolism ; Bees/genetics/*metabolism/*virology ; Biodiversity ; Ecosystem ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Phylogeny ; Pollination/genetics ; Symbiosis/genetics ; }, abstract = {Honey bees (Apis mellifera) produce an enormous economic value through their pollination activities and play a central role in the biodiversity of entire ecosystems. Recent efforts have revealed the substantial influence that the gut microbiota exert on bee development, food digestion, and homeostasis in general. In this study, deep sequencing was used to characterize prokaryotic viral communities associated with honey bees, which was a blind spot in research up until now. The vast majority of the prokaryotic viral populations are novel at the genus level, and most of the encoded proteins comprise unknown functions. Nevertheless, genomes of bacteriophages were predicted to infect nearly every major bee-gut bacterium, and functional annotation and auxiliary metabolic gene discovery imply the potential to influence microbial metabolism. Furthermore, undiscovered genes involved in the synthesis of secondary metabolic biosynthetic gene clusters reflect a wealth of previously untapped enzymatic resources hidden in the bee bacteriophage community.}, } @article {pmid32340923, year = {2019}, author = {Gotschlich, EC and Colbert, RA and Gill, T}, title = {Methods in microbiome research: Past, present, and future.}, journal = {Best practice & research. Clinical rheumatology}, volume = {33}, number = {6}, pages = {101498}, pmid = {32340923}, issn = {1532-1770}, support = {ZIA AR041184/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Dysbiosis ; Humans ; *Microbiota ; Research/trends ; }, abstract = {The human microbiome is impressively immense and participates in many aspects of our health and wellness, particularly involving the development and maintenance of a healthy immune system. Not only do our microbes teach the immune system to fight infection, they also teach immune tolerance and help maintain homeostasis. From this knowledge, we have learned that the loss of tolerance to microbiota in both innate and adaptive processes plays an important role in immune-mediated and autoimmune disease. In this chapter, we will be discussing about methods used to study the microbiome, both old and new methods, fundamental concepts that have taken hold within the field, and how these principles relate to rheumatology, including thoughts on how microbiome research may be focused in the next decade.}, } @article {pmid32340697, year = {2020}, author = {Dumas, E and Venken, K and Rosenbaum, JT and Elewaut, D}, title = {Intestinal Microbiota, HLA-B27, and Spondyloarthritis: Dangerous Liaisons.}, journal = {Rheumatic diseases clinics of North America}, volume = {46}, number = {2}, pages = {213-224}, doi = {10.1016/j.rdc.2020.01.007}, pmid = {32340697}, issn = {1558-3163}, mesh = {Disease Progression ; *Gastrointestinal Microbiome/genetics/immunology ; *HLA-B27 Antigen/genetics/immunology ; Humans ; *Spondylarthritis/complications/genetics/immunology ; }, abstract = {Spondyloarthritis, although primarily a joint-centered disease, is associated with extra-articular features, such as gut inflammation, psoriasis, and/or uveitis. Evidence points to underlying genetic predisposing factors and/or environmental factors. This is most clear in the gut, with progress through 16S and metagenomics sequencing studies and the results of functional studies in preclinical arthritis models. Translation of these findings to the clinic is making progress based on encouraging results of fecal microbial transplant studies in several human diseases. This review elaborates on novel trends in host-microbial interplay in spondyloarthritis, focusing on microbiota, immune dysregulation, and disease progression, and modulation by HLA-B27.}, } @article {pmid32340468, year = {2020}, author = {Liu, X and Tao, J and Li, J and Cao, X and Li, Y and Gao, X and Fu, Y}, title = {Dysbiosis of Fecal Microbiota in Allergic Rhinitis Patients.}, journal = {American journal of rhinology & allergy}, volume = {34}, number = {5}, pages = {650-660}, doi = {10.1177/1945892420920477}, pmid = {32340468}, issn = {1945-8932}, mesh = {*Dysbiosis/complications ; Humans ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; *Rhinitis, Allergic/complications ; }, abstract = {BACKGROUND: The gut microbiota plays an important role in shaping the immune system and may be closely connected to the development of allergic diseases.

OBJECTIVE: This study aimed to determine the gut microbiota composition in Chinese allergic rhinitis (AR) patients as compared with healthy controls (HCs).

METHODS: We collected stool samples from 93 AR patients and 72 age- and sex-matched HCs. Gut microbiota composition was analyzed using QIIME targeting the 16S rRNA gene. Functional pathways were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. Statistical analysis was performed using the R program, linear discriminant analysis effect size (LefSe), analysis of QIIME, and statistical analysis of metagenomic profiles, among other tests.

RESULTS: Compared with HCs, AR patients had significantly lower gut-microbiota α-diversity (P < .001). The gut microbiota composition significantly differed between the 2 study groups. At the phylum level, the relative abundance of Bacteroidetes was higher while those of Actinobacteria and Proteobacteria were lower in the AR group than in the HC group (P < .001, q < 0.001). At the genus level, Escherichia-Shigella, Prevotella, and Parabacteroides (P < .001, q < 0.001) had significantly higher relative abundances in the AR group than in the HC group. LefSe analysis indicated that Escherichia-Shigella, Lachnoclostridium, Parabacteroides, and Dialister were potential biomarkers for AR. In addition, predictive metagenome functional analysis showed that pyruvate, porphyrin, chlorophyll, purine metabolism, and peptidoglycan biosynthesis significantly differed between the AR and HC groups.

CONCLUSION: A comparison of the gut microbiota of AR patients and HCs suggested that dysbiosis of the fecal microbiota is involved in the development of AR. The present results may reveal key differences and identify targets for preventive or therapeutic intervention.}, } @article {pmid32339246, year = {2020}, author = {Kuballa, A and Geraci, M and Johnston, M and Sorrentino, D}, title = {The Gut Microbial Profile of Preclinical Crohn's Disease Is Similar to That of Healthy Controls.}, journal = {Inflammatory bowel diseases}, volume = {26}, number = {11}, pages = {1682-1690}, doi = {10.1093/ibd/izaa072}, pmid = {32339246}, issn = {1536-4844}, mesh = {Adult ; Case-Control Studies ; Crohn Disease/*genetics/*microbiology ; Dysbiosis/complications/*genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metagenomics ; Middle Aged ; *Phylogeny ; }, abstract = {BACKGROUND AND AIMS: It is unclear whether microbial dysbiosis plays an etiologic role in Crohn's disease (CD) or is the result of protracted inflammation. Here, we test the hypothesis that dysbiosis predates clinical CD in asymptomatic first-degree relatives (FDRs) of CD patients: normal (FDR1), with borderline inflammation (FDR2), and with frank, very early inflammation (FDR3).

METHODS: The gut microbial diversity was tested in ileocecal biopsies through next generation sequencing of the 16S rRNA gene in 10 healthy controls (HCs), 22 patients with active, untreated CD, and 25 FDRs (9 FDR1; 12 FDR2; 4 FDR3). The metagenomic functions of 41 microbiome-related processes were inferred by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis.

RESULTS: Compared with HCs, alpha diversity in CD patients was decreased, with an observed decrease in Faecalibacterium prausnitzii and increase in Bacteroides fragilis. In FDRs, microbial diversity was unchanged compared with HCs. In Operational Taxonomic Units and PICRUSt Principal coordinates and component analyses, the ellipse centroid of FDRs was diagonally opposed to that of CD patients, but close to the HC centroid. In both analyses, statistically significant differences in terms of beta diversity were found between CD and HC but not between FDR and HC.

CONCLUSIONS: In FDRs (including FDR3-who bear preclinical/biologic onset disease), we found that the microbial profile is remarkably similar to HC. If confirmed in larger studies, this finding suggests that clinical CD-associated dysbiosis could result from the changed microenvironment due to disease evolution over time.}, } @article {pmid32338757, year = {2020}, author = {Nagpal, S and Singh, R and Yadav, D and Mande, SS}, title = {MetagenoNets: comprehensive inference and meta-insights for microbial correlation networks.}, journal = {Nucleic acids research}, volume = {48}, number = {W1}, pages = {W572-W579}, pmid = {32338757}, issn = {1362-4962}, mesh = {Algorithms ; Humans ; Inflammatory Bowel Diseases/microbiology ; Metagenomics ; *Microbiota ; *Software ; }, abstract = {Microbial association networks are frequently used for understanding and comparing community dynamics from microbiome datasets. Inferring microbial correlations for such networks and obtaining meaningful biological insights, however, requires a lengthy data management workflow, choice of appropriate methods, statistical computations, followed by a different pipeline for suitably visualizing, reporting and comparing the associations. The complexity is further increased with the added dimension of multi-group 'meta-data' and 'inter-omic' functional profiles that are often associated with microbiome studies. This not only necessitates the need for categorical networks, but also integrated and bi-partite networks. Multiple options of network inference algorithms further add to the efforts required for performing correlation-based microbiome interaction studies. We present MetagenoNets, a web-based application, which accepts multi-environment microbial abundance as well as functional profiles, intelligently segregates 'continuous and categorical' meta-data and allows inference as well as visualization of categorical, integrated (inter-omic) and bi-partite networks. Modular structure of MetagenoNets ensures logical flow of analysis (inference, integration, exploration and comparison) in an intuitive and interactive personalized dashboard driven framework. Dynamic choice of filtration, normalization, data transformation and correlation algorithms ensures, that end-users get a one-stop solution for microbial network analysis. MetagenoNets is freely available at https://web.rniapps.net/metagenonets.}, } @article {pmid32337748, year = {2020}, author = {Gao, R and Wang, Z and Li, H and Cao, Z and Gao, Z and Chen, H and Zhang, X and Pan, D and Yang, R and Zhong, H and Shen, R and Yin, L and Jia, Z and Shen, T and Qin, N and Hu, Z and Qin, H}, title = {Gut microbiota dysbiosis signature is associated with the colorectal carcinogenesis sequence and improves the diagnosis of colorectal lesions.}, journal = {Journal of gastroenterology and hepatology}, volume = {35}, number = {12}, pages = {2109-2121}, doi = {10.1111/jgh.15077}, pmid = {32337748}, issn = {1440-1746}, support = {81730102, 81230057 and 81472262//the National Natural Science Foundation of China/ ; 2018SYPDRC030//"Climbing" plan of Shanghai Tenth People's Hospital/ ; 20194Y0483//Special project for Clinical Research in Health Industry of Shanghai Municipal Health Commission/ ; SYGZRPY2017024//Training program of the National Natural Science Foundation of China of Shanghai Tenth People's Hospital/ ; 20194Y0483//Special Project for Clinical Research in the Health Industry of the Shanghai Municipal Health Commission/ ; 22120180575//the Fundamental Research Funds for the Central Universities/ ; 162385//Tongji University Subject Pilot Program/ ; SHDC12017112//Emerging Cutting-Edge Technology Joint Research Projects of Shanghai/ ; }, mesh = {*Biomarkers, Tumor ; Cohort Studies ; Colorectal Neoplasms/*diagnosis/*microbiology ; *Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Humans ; Male ; Precancerous Conditions/diagnosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; }, abstract = {BACKGROUND AND AIM: The gut microbiota is associated with colorectal lesions in cases of precancer and colorectal cancer (CRC). However, there are apparent differences in studies on the gut microbiota in the pathogenic sequence from precancer to cancer. Here, we characterize the gut microbiota signatures of colorectal precancer and cancer and test their utility in detecting colorectal lesions in two independent Chinese cohorts.

METHODS: Stool samples collected from patients with precancer and CRC were subjected to 16S ribosomal RNA gene sequencing and metagenomic shotgun sequencing analyses, which revealed the microbial signatures of the two disease stages.

RESULTS: In comparison with healthy controls, lower microbial richness and diversity were observed in precancer and intensive interbacterial associations were found in CRC. We identified 41 bacteria that showed gradual increases while 12 bacteria showed gradual decreases at the genus level gradually during the development of CRC. Novel CRC-associated pathogenetic species were identified. Species units that contributed to altered microbial functions were identified in CRC patients and healthy controls. The microbial panel showed a comparable ability to fecal immunochemical test (FIT) in detecting CRC. However, the combination of microbes and FIT significantly improved the detection ability and sensitivity of colon lesions based on 18 genera. Microbial network analysis revealed a significant positive correlation among beneficial microbes and a negative correlation in detrimental phenotypes.

CONCLUSIONS: Microbial dysbiosis was revealed in colorectal lesions. The combination of microbial markers and FIT improved the CRC detection ability, which might assist in the early diagnosis of CRC.}, } @article {pmid32334626, year = {2020}, author = {Liu, Q and Wang, H and Ling, Y and Yang, SX and Wang, XC and Zhou, R and Xiao, YQ and Chen, X and Yang, J and Fu, WG and Zhang, W and Qi, GL}, title = {Viral metagenomics revealed diverse CRESS-DNA virus genomes in faeces of forest musk deer.}, journal = {Virology journal}, volume = {17}, number = {1}, pages = {61}, pmid = {32334626}, issn = {1743-422X}, mesh = {Animals ; China ; DNA Viruses/*classification/genetics ; DNA, Viral/genetics ; Deer/*virology ; Feces/*virology ; Metagenomics ; Phylogeny ; *Virome ; }, abstract = {BACKGROUND: Musk deer can produce musk which has high medicinal value and is closely related to human health. Viruses in forest musk deer both threaten the health of forest musk deer and human beings.

METHODS: Using viral metagenomics we investigated the virome in 85 faeces samples collected from forest musk deer.

RESULTS: In this article, eight novel CRESS-DNA viruses were characterized, whole genomes were 2148 nt-3852 nt in length. Phylogenetic analysis indicated that some viral genomes were part of four different groups of CRESS-DNA virus belonging in the unclassified CRESS-DNA virus, Smacoviridae, pCPa-like virus and pPAPh2-like virus. UJSL001 (MN621482), UJSL003 (MN621469) and UJSL017 (MN621476) fall into the branch of unclassified CRESS-DNA virus (CRESSV1-2), UJSL002 (MN621468), UJSL004 (MN621481) and UJSL007 (MN621470) belong to the cluster of Smacoviridae, UJSL005 (MN604398) showing close relationship with pCPa-like (pCRESS4-8) clusters and UJSL006 (MN621480) clustered into the branch of pPAPh2-like (pCRESS9) virus, respectively.

CONCLUSION: The virome in faeces samples of forest musk deer from Chengdu, Sichuan province, China was revealed, which further characterized the diversity of viruses in forest musk deer intestinal tract.}, } @article {pmid32334231, year = {2020}, author = {Zhang, H and Zhang, Q and Chen, S and Zhang, Z and Song, J and Long, Z and Yu, Y and Fang, H}, title = {Enterobacteriaceae predominate in the endophytic microbiome and contribute to the resistome of strawberry.}, journal = {The Science of the total environment}, volume = {727}, number = {}, pages = {138708}, doi = {10.1016/j.scitotenv.2020.138708}, pmid = {32334231}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/drug effects ; Enterobacteriaceae ; *Fragaria ; Genes, Bacterial/drug effects ; Humans ; Metagenome/drug effects ; Microbiota/*drug effects ; }, abstract = {Antibiotic resistance genes (ARGs) harbored by plant microbiomes have been implicated as a potential risk to public health via food chain, especially directly edible fruits and vegetables. Here, we investigated the microbiome and antibiotic resistome in soil-strawberry ecosystem using shotgun metagenomic sequencing. The results showed that the enterobacterial population dominated the endophytes of strawberry fruits. Moreover, 85 subtypes of ARGs, including several clinically important ARGs, were detected in the strawberry fruit metagenomes. Additionally, host tracking analysis in combination with antibiotic-resistant bacterial isolate screening suggested that fruit-borne ARGs were mainly carried by members of the Enterobacteriaceae family. Unexpectedly, most of fruit-borne isolates were found to be resistant to several clinically important antimicrobials, e.g., erythromycin and cephalexin. Our findings provide broad insights into endophytic antibiotic resistomes of direct edible strawberry fruits and their potential hosts, and highlight the potential exposure risks of plant microbiomes to the human food chain.}, } @article {pmid32332864, year = {2020}, author = {Spasov, E and Tsuji, JM and Hug, LA and Doxey, AC and Sauder, LA and Parker, WJ and Neufeld, JD}, title = {High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant.}, journal = {The ISME journal}, volume = {14}, number = {7}, pages = {1857-1872}, pmid = {32332864}, issn = {1751-7370}, mesh = {Ammonia ; Archaea/genetics ; Bacteria/genetics ; *Biological Products ; Canada ; *Microbiota ; Nitrification ; Nitrites ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; *Water Purification ; }, abstract = {Nitrification, the oxidation of ammonia to nitrate via nitrite, is an important process in municipal wastewater treatment plants (WWTPs). Members of the Nitrospira genus that contribute to complete ammonia oxidation (comammox) have only recently been discovered and their relevance to engineered water treatment systems is poorly understood. This study investigated distributions of Nitrospira, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in biofilm samples collected from tertiary rotating biological contactors (RBCs) of a municipal WWTP in Guelph, Ontario, Canada. Using quantitative PCR (qPCR), 16S rRNA gene sequencing, and metagenomics, our results demonstrate that Nitrospira species strongly dominate RBC biofilm samples and that comammox Nitrospira outnumber all other nitrifiers. Genome bins recovered from assembled metagenomes reveal multiple populations of comammox Nitrospira with distinct spatial and temporal distributions, including several taxa that are distinct from previously characterized Nitrospira members. Diverse functional profiles imply a high level of niche heterogeneity among comammox Nitrospira, in contrast to the sole detected AOA representative that was previously cultivated and characterized from the same RBC biofilm. Our metagenome bins also reveal two cyanase-encoding populations of comammox Nitrospira, suggesting an ability to degrade cyanate, which has only been shown previously for several Nitrospira representatives that are strict nitrite oxidizers. This study demonstrates the importance of RBCs as model systems for continued investigation of environmental factors that control the distributions and activities of AOB, AOA, comammox Nitrospira, and other nitrite oxidizers.}, } @article {pmid32331776, year = {2020}, author = {Lee, CG and Baba, Y and Asano, R and Fukuda, Y and Tada, C and Nakai, Y}, title = {Identification of bacteria involved in the decomposition of lignocellulosic biomass treated with cow rumen fluid by metagenomic analysis.}, journal = {Journal of bioscience and bioengineering}, volume = {130}, number = {2}, pages = {137-141}, doi = {10.1016/j.jbiosc.2020.03.010}, pmid = {32331776}, issn = {1347-4421}, mesh = {Animals ; Bacteria/*classification/*enzymology/genetics/isolation & purification ; Biodiversity ; Biomass ; Cattle ; Cellulase/genetics/metabolism ; Fatty Acids, Volatile ; Glycoside Hydrolases/genetics/metabolism ; *Industrial Microbiology ; Lignin/*metabolism ; *Metagenome ; Methane/biosynthesis ; Rumen/*microbiology ; }, abstract = {We had developed a new pretreatment system using cow rumen fluid to improve the methane production from lignocellulosic substrates. However, the pretreatment conditions differ from the in-situ rumen environment, therefore different microbes may be involved in plant cell wall decomposition. In the current study, shotgun metagenomic analysis using MiSeq platform was performed to elucidate the bacteria which produce cellulase and hemicellulase in this pretreatment system. The rumen fluid which contained waste paper pieces (0.1% w/v) were incubated at 37°C during 120 h. The fluid samples were collected from the reactor at each time-point and analyzed for chemical properties. Rumen microbial DNA was extracted from 0-h and 60-h samples and subjected to shotgun-metagenomic analysis. After pretreatment, approximately half of cellulose and hemicellulose contents of the waste paper were decomposed and some volatile fatty acids were accumulated. Clostridia (e.g., Ruminococcus and Clostridium) were the predominant bacteria before and after 60-h pretreatment, and their relative abundance was increased during pretreatment. However, Prevotella and Fibrobacter, one of the most dominant bacteria in-situ rumen fluid, were observed less than 3% before incubation and they were decreased after pretreatment. Genes encoding cellulase and hemicellulase were mainly found in Ruminococcus, Clostridium, and Caldicellulosiruptor. Calicellulosiruptor, which had not been previously identified as the predominant genus in lignocellulose decomposition in in-situ rumen conditions, might be considered as the main fibrolytic bacterium in this system. Thus, this study demonstrated that the composition of fibrolytic bacteria in this system was greatly different from those in the in-situ rumen.}, } @article {pmid32329665, year = {2020}, author = {Jia, B and Park, D and Hahn, Y and Jeon, CO}, title = {Metagenomic analysis of the human microbiome reveals the association between the abundance of gut bile salt hydrolases and host health.}, journal = {Gut microbes}, volume = {11}, number = {5}, pages = {1300-1313}, pmid = {32329665}, issn = {1949-0984}, mesh = {Amidohydrolases/chemistry/classification/*metabolism ; Bacteria/*enzymology ; Bile Acids and Salts/*metabolism ; Cardiovascular Diseases/enzymology/microbiology ; Diabetes Mellitus, Type 2/enzymology/microbiology ; Gastrointestinal Diseases/enzymology/microbiology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology ; Humans ; Liver Diseases/enzymology/microbiology ; Metagenome ; Metagenomics ; Microbiota/*physiology ; Nervous System Diseases/enzymology/microbiology ; Phylogeny ; }, abstract = {Bile acid metabolism by the gut microbiome exerts both beneficial and harmful effects on host health. Microbial bile salt hydrolases (BSHs), which initiate bile acid metabolism, exhibit both positive and negative effects on host physiology. In this study, 5,790 BSH homologs were collected and classified into seven clusters based on a sequence similarity network. Next, the abundance and distribution of BSH in 380 metagenomes from healthy participants were analyzed. It was observed that different clusters occupied diverse ecological niches in the human microbiome and that the clusters with signal peptides were relatively abundant in the gut. Then, the association between BSH clusters and 12 human diseases was analyzed by comparing the abundances of BSH genes in patients (n = 1,605) and healthy controls (n = 1,540). The analysis identified a significant association between BSH gene abundance and 10 human diseases, including gastrointestinal diseases, obesity, type 2 diabetes, liver diseases, cardiovascular diseases, and neurological diseases. The associations were further validated by separate cohorts with inflammatory bowel diseases and colorectal cancer. These large-scale studies of enzyme sequences combined with metagenomic data provide a reproducible assessment of the association between gut BSHs and human diseases. This information can contribute to future diagnostic and therapeutic applications of BSH-active bacteria for improving human health.}, } @article {pmid32328670, year = {2020}, author = {Hanya, G and Tackmann, J and Sawada, A and Lee, W and Pokharel, SS and de Castro Maciel, VG and Toge, A and Kuroki, K and Otsuka, R and Mabuchi, R and Liu, J and Hatakeyama, M and Yamasaki, E and von Mering, C and Shimizu-Inatsugi, R and Hayakawa, T and Shimizu, KK and Ushida, K}, title = {Fermentation Ability of Gut Microbiota of Wild Japanese Macaques in the Highland and Lowland Yakushima: In Vitro Fermentation Assay and Genetic Analyses.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {459-474}, doi = {10.1007/s00248-020-01515-8}, pmid = {32328670}, issn = {1432-184X}, support = {15KK0256//MEXT Grant-in-Aid for Promotion of Joint International Research (Fostering Joint International Research)/ ; 19KK0186//MEXT Grant-in-Aid for Promotion of Joint International Research (Fostering Joint International Research)/ ; 25291100//MEXT Grant-in-Aid for Scientific Research B/ ; 18H02508//MEXT Grant-in-Aid for Scientific Research B/ ; }, mesh = {Animals ; Bacteria/genetics/*metabolism ; Diet ; *Digestion ; *Feeding Behavior ; Fermentation ; Gastrointestinal Microbiome/*physiology ; Macaca fuscata/*microbiology/*physiology ; Metagenome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Wild Japanese macaques (Macaca fuscata Blyth) living in the highland and lowland areas of Yakushima are known to have different diets, with highland individuals consuming more leaves. We aim to clarify whether and how these differences in diet are also reflected by gut microbial composition and fermentation ability. Therefore, we conduct an in vitro fermentation assay using fresh feces from macaques as inoculum and dry leaf powder of Eurya japonica Thunb. as a substrate. Fermentation activity was higher for feces collected in the highland, as evidenced by higher gas and butyric acid production and lower pH. Genetic analysis indicated separation of highland and lowland in terms of both community structure and function of the gut microbiota. Comparison of feces and suspension after fermentation indicated that the community structure changed during fermentation, and the change was larger for lowland samples. Analysis of the 16S rRNA V3-V4 barcoding region of the gut microbiota showed that community structure was clearly clustered between the two areas. Furthermore, metagenomic analysis indicated separation by gene and pathway abundance patterns. Two pathways (glycogen biosynthesis I and D-galacturonate degradation I) were enriched in lowland samples, possibly related to the fruit-eating lifestyle in the lowland. Overall, we demonstrated that the more leaf-eating highland Japanese macaques harbor gut microbiota with higher leaf fermentation ability compared with the more fruit-eating lowland ones. Broad, non-specific taxonomic and functional gut microbiome differences suggest that this pattern may be driven by a complex interplay between many taxa and pathways rather than single functional traits.}, } @article {pmid32327694, year = {2020}, author = {Yang, H and Zhang, J and Xue, Z and Zhao, C and Lei, L and Wen, Y and Dong, Y and Yang, J and Zhang, L}, title = {Potential Pathogenic Bacteria in Seminal Microbiota of Patients with Different Types of Dysspermatism.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {6876}, pmid = {32327694}, issn = {2045-2322}, mesh = {Adult ; Asthenozoospermia/microbiology ; Bacteria/metabolism/pathogenicity ; Biodiversity ; Biomarkers/metabolism ; Case-Control Studies ; Discriminant Analysis ; Humans ; Infertility, Male/*microbiology ; Male ; Metagenome ; *Microbiota/genetics ; Oligospermia/microbiology ; Phylogeny ; Principal Component Analysis ; Semen/*microbiology ; }, abstract = {Human microbiota play an important role in the health of their human hosts. Recent studies have demonstrated that microbiota exist in seminal plasma. The current study aims to elucidate whether seminal microbiota exist in patients with different types of dysspermatism and whether bacterial biomarkers can be identified for them. A total of 159 study participants were recruited, including 22 patients with oligoasthenospermia, 58 patients with asthenospermia, 8 patients with azoospermia, 13 patients with oligospermia, and 58 matched healthy controls. Seminal microbiota composition was analyzed using 16S rRNA gene-based sequencing. The results showed that the composition of seminal microbiota of patients with dysspermatism differed from those of healthy controls. Comparison of the microbiota composition in semen samples from patients with different types of dysspermatism showed that microbiota in patients with asthenospermia and oligoasthenospermia were distinct from healthy controls in beta diversity (P < 0.05). Characteristic biomarkers, including Ureaplasma, Bacteroides, Anaerococcus, Finegoldia, Lactobacillus and Acinetobacter lwoffii, were identified based on LEfSe analysis. Inferred functional analysis based on seminal microbiome data further indicated the presence of potential pathogenic biomarkers in patients with asthenospermia and oligoasthenospermia. These results provided profiles of seminal microbiota exhibited in different types of dysspermatism, thus providing new insights into their pathogenesis.}, } @article {pmid32325376, year = {2020}, author = {Dai, X and Lv, J and Yan, G and Chen, C and Guo, S and Fu, P}, title = {Bioremediation of intertidal zones polluted by heavy oil spilling using immobilized laccase-bacteria consortium.}, journal = {Bioresource technology}, volume = {309}, number = {}, pages = {123305}, doi = {10.1016/j.biortech.2020.123305}, pmid = {32325376}, issn = {1873-2976}, mesh = {Bacteria ; Biodegradation, Environmental ; Laccase ; *Petroleum ; *Petroleum Pollution ; *Polycyclic Aromatic Hydrocarbons ; }, abstract = {Heavy oil pollution in the intertidal zones has become a worldwide environmental problem. In this study, bioremediation on heavy oil pollutants in the intertidal zones using an immobilized laccase-bacteria consortium system was evaluated with the aid of intertidal experimental pools built in the coastal area. It is found that degradation efficiency of the immobilized laccase-bacteria consortium for heavy oil was 66.5% after 100 days remediation, with the reaction rate constant of 0.018 d[-1]. Gas Chromatograph-Mass Spectrometer analysis shows that degradation efficiency of saturated hydrocarbons and aromatic hydrocarbons were 79.2% and 78.7%, which were 64.9% and 65.1% higher than control. It is further seen that degradation of long-chain n-alkanes of C26-C35 and polycyclic aromatic hydrocarbons with more than three rings were significant. Metagenomic analysis indicates that the immobilized laccase-bacterial consortium has not only increased the biodiversity of heavy oil degrading bacteria, but also accelerated the degradation of heavy oil.}, } @article {pmid32322441, year = {2020}, author = {Riley, NG and Goller, CC and Leggett, ZH and Lewis, DM and Ciccone, K and Dunn, RR}, title = {Catalyzing rapid discovery of gold-precipitating bacterial lineages with university students.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e8925}, pmid = {32322441}, issn = {2167-8359}, abstract = {Intriguing and potentially commercially useful microorganisms are found in our surroundings and new tools allow us to learn about their genetic potential and evolutionary history. Engaging students from different disciplines and courses in the search for microbes requires an exciting project with innovative but straightforward procedures and goals. Here we describe an interdisciplinary program to engage students from different courses in the sampling, identification and analysis of the DNA sequences of a unique yet common microbe, Delftia spp. A campus-wide challenge was created to identify the prevalence of this genus, able to precipitate gold, involving introductory level environmental and life science courses, upper-level advanced laboratory modules taken by undergraduate students (juniors and seniors), graduate students and staff from the campus. The number of participants involved allowed for extensive sampling while undergraduate researchers and students in lab-based courses participated in the sample processing and analyses, helping contextualize and solidify their learning of the molecular biology techniques. The results were shared at each step through publicly accessible websites and workshops. This model allows for the rapid discovery of Delftia presence and prevalence and is adaptable to different campuses and experimental questions.}, } @article {pmid32320621, year = {2020}, author = {Mac Aogáin, M and Lau, KJX and Cai, Z and Kumar Narayana, J and Purbojati, RW and Drautz-Moses, DI and Gaultier, NE and Jaggi, TK and Tiew, PY and Ong, TH and Siyue Koh, M and Lim Yick Hou, A and Abisheganaden, JA and Tsaneva-Atanasova, K and Schuster, SC and Chotirmall, SH}, title = {Metagenomics Reveals a Core Macrolide Resistome Related to Microbiota in Chronic Respiratory Disease.}, journal = {American journal of respiratory and critical care medicine}, volume = {202}, number = {3}, pages = {433-447}, pmid = {32320621}, issn = {1535-4970}, mesh = {Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents ; Asthma/*microbiology ; Bronchiectasis/*microbiology ; Case-Control Studies ; Drug Resistance, Bacterial/*genetics ; Dysbiosis/*microbiology ; Female ; Fluoroquinolones ; Humans ; *Macrolides ; Male ; *Metagenomics ; Microbiota/*genetics ; Middle Aged ; Nebulizers and Vaporizers/microbiology ; Pulmonary Disease, Chronic Obstructive/*microbiology ; Severity of Illness Index ; Tetracycline Resistance/genetics ; beta-Lactam Resistance/genetics ; }, abstract = {Rationale: Long-term antibiotic use for managing chronic respiratory disease is increasing; however, the role of the airway resistome and its relationship to host microbiomes remains unknown.Objectives: To evaluate airway resistomes and relate them to host and environmental microbiomes using ultradeep metagenomic shotgun sequencing.Methods: Airway specimens from 85 individuals with and without chronic respiratory disease (severe asthma, chronic obstructive pulmonary disease, and bronchiectasis) were subjected to metagenomic sequencing to an average depth exceeding 20 million reads. Respiratory and device-associated microbiomes were evaluated on the basis of taxonomical classification and functional annotation including the Comprehensive Antibiotic Resistance Database to determine airway resistomes. Co-occurrence networks of gene-microbe association were constructed to determine potential microbial sources of the airway resistome. Paired patient-inhaler metagenomes were compared (n = 31) to assess for the presence of airway-environment overlap in microbiomes and/or resistomes.Measurements and Main Results: Airway metagenomes exhibit taxonomic and metabolic diversity and distinct antimicrobial resistance patterns. A "core" airway resistome dominated by macrolide but with high prevalence of β-lactam, fluoroquinolone, and tetracycline resistance genes exists and is independent of disease status or antibiotic exposure. Streptococcus and Actinomyces are key potential microbial reservoirs of macrolide resistance including the ermX, ermF, and msrD genes. Significant patient-inhaler overlap in airway microbiomes and their resistomes is identified where the latter may be a proxy for airway microbiome assessment in chronic respiratory disease.Conclusions: Metagenomic analysis of the airway reveals a core macrolide resistome harbored by the host microbiome.}, } @article {pmid32320412, year = {2020}, author = {Morant, D and Picazo, A and Rochera, C and Santamans, AC and Miralles-Lorenzo, J and Camacho-Santamans, A and Ibañez, C and Martínez-Eixarch, M and Camacho, A}, title = {Carbon metabolic rates and GHG emissions in different wetland types of the Ebro Delta.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0231713}, pmid = {32320412}, issn = {1932-6203}, mesh = {Agriculture ; Carbon/*metabolism ; Carbon Dioxide ; Carbon Sequestration ; Chenopodiaceae/*metabolism ; Climate Change ; Greenhouse Gases/*metabolism ; Metagenome ; Methane/metabolism ; Microbiota/*physiology ; Nutrients/metabolism ; RNA, Ribosomal, 16S/genetics ; Rivers ; Salinity ; Soil/chemistry ; Soil Microbiology ; Spain ; *Wetlands ; }, abstract = {Deltaic wetlands are highly productive ecosystems, which characteristically can act as C-sinks. However, they are among the most threatened ecosystems, being very vulnerable to global change, and require special attention towards its conservation. Knowing their climate change mitigating potential, conservation measures should also be oriented with a climatic approach, to strengthen their regulatory services. In this work we studied the carbon biogeochemistry and the specific relevance of certain microbial guilds on carbon metabolisms of the three main types of deltaic wetlands located in the Ebro Delta, north-eastern Spain, as well as how they deal with human pressures and climate change effects. We estimated the metabolic rates of the main carbon-related metabolisms (primary production and respiration) and the resulting carbon and global warming potential balances in sites with a different salinity range and trophic status. With the results obtained, we tried to define the influence of possible changes in salinity and trophic level linked to the main impacts currently threatening deltaic wetlands, on the C-metabolisms and GHG emissions, for a better understanding of the mitigating capacity and their possible enhancement when applying specific management actions. Metabolic rates showed a pattern highly influenced by the salinity range and nutrients inputs. Freshwater and brackish wetlands, with higher nutrient inputs from agricultural runoff, showed higher C-capture capacity (around 220-250 g C m-2 y-1), but also higher rates of degradative metabolisms (aerobic respiration and CH4 emissions). Contrastingly, the rates of C-related metabolisms and C-retention of Salicornia-type coastal salt marshes were lower (42 g C m-2 y-1). The study of the microbial metacommunity composition by the16S RNA gene sequencing revealed a significant higher presence of methanogens in the salt marsh, and also higher metabolic potential, where there was significantly more organic matter content in sediment. Salinity inhibition, however, explained the lower respiration rates, both aerobic and anaerobic, and prevented higher rates of methanogenesis despite the major presence of methanogens. Conservation measures for these wetlands would require, overall, maintaining the sediment contributions of the river basin intending to overcome the regression of the Delta and its salt marshes in a climate change scenario. Particularly, for reducing degradative metabolisms, and favour C-retention, nutrient inputs should be controlled in freshwater and brackish wetlands in order to reduce eutrophication. In salt marshes, the reduction of salinity should be avoided to control increases in methanogenesis and CH4 emissions.}, } @article {pmid32320134, year = {2020}, author = {Bieker, VC and Sánchez Barreiro, F and Rasmussen, JA and Brunier, M and Wales, N and Martin, MD}, title = {Metagenomic analysis of historical herbarium specimens reveals a postmortem microbial community.}, journal = {Molecular ecology resources}, volume = {20}, number = {5}, pages = {1206-1219}, doi = {10.1111/1755-0998.13174}, pmid = {32320134}, issn = {1755-0998}, support = {//NTNU/ ; }, mesh = {Alternaria ; Ambrosia ; Arabidopsis ; Fungi/genetics ; *Microbiota ; Museums ; *Plants/genetics/microbiology ; Sequence Analysis, DNA ; }, abstract = {Advances in DNA extraction and next-generation sequencing have made a vast number of historical herbarium specimens available for genomic investigation. These specimens contain not only genomic information from the individual plants themselves, but also from associated microorganisms such as bacteria and fungi. These microorganisms may have colonized the living plant (e.g., pathogens or host-associated commensal taxa) or may result from postmortem colonization that may include decomposition processes or contamination during sample handling. Here we characterize the metagenomic profile from shotgun sequencing data from herbarium specimens of two widespread plant species (Ambrosia artemisiifolia and Arabidopsis thaliana) collected up to 180 years ago. We used blast searching in combination with megan and were able to infer the metagenomic community even from the oldest herbarium sample. Through comparison with contemporary plant collections, we identify three microbial species that are nearly exclusive to herbarium specimens, including the fungus Alternaria alternata, which can comprise up to 7% of the total sequencing reads. This species probably colonizes the herbarium specimens during preparation for mounting or during storage. By removing the probable contaminating taxa, we observe a temporal shift in the metagenomic composition of the invasive weed Am. artemisiifolia. Our findings demonstrate that it is generally possible to use herbarium specimens for metagenomic analyses, but that the results should be treated with caution, as some of the identified species may be herbarium contaminants rather than representing the natural metagenomic community of the host plant.}, } @article {pmid32319677, year = {2020}, author = {Li, Z and Zhu, H and Guo, Y and Du, X and Qin, C}, title = {Gut microbiota regulate cognitive deficits and amyloid deposition in a model of Alzheimer's disease.}, journal = {Journal of neurochemistry}, volume = {155}, number = {4}, pages = {448-461}, doi = {10.1111/jnc.15031}, pmid = {32319677}, issn = {1471-4159}, mesh = {Alzheimer Disease/*metabolism/pathology/psychology ; Amyloid beta-Protein Precursor/*metabolism ; Animals ; Cognition Disorders/*metabolism/pathology/psychology ; *Disease Models, Animal ; Female ; Gastrointestinal Microbiome/*physiology ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; }, abstract = {Gut microbiota, comprising a vast number of microorganism species with complex metagenome, are known to be associated with Alzheimer's disease (AD) and amyloid deposition. However, studies related to gut microbiota have been mostly restricted to comparisons of amyloid deposits, while investigations on neurobehavioral changes and the pathogenesis of AD are limited. Therefore, we aimed to identify the relationship between changes in the intestinal microbiome and the pathogenesis of AD. APP[swe] /PS1[ΔE9] (PAP) transgenic mice and wild-type (WT) mice of different age groups were used. The composition of intestinal bacterial communities in the mice was determined by 16S ribosomal RNA sequencing (16S rRNA Seq), and the Y maze was used to measure cognitive function. Transcriptome sequencing (RNA Seq) and Gene Expression Omnibus (GEO) database (GSE 36980) were used to filter differentially expressed genes (DEGs) between specific pathogen-free (SPF) and germ-free (GF) mice. Quantitative reverse-transcriptase PCR (qRT-PCR) and western blot (WB) were used to verify the results. We found that the intestinal microbiota was significantly different between 5-month-old PAP and WT mice and the cognition of SPF PAP mice was diminished compared to GF PAP and SPF WT mice. DEGs in 5-month-old SPF and GF mice were enriched in the MAPK signalling pathway, and expression of amyloid precursor protein and amyloid deposition increased in 5-month-old SPF PAP mice. Results from this study showed that changes in intestinal microbiota were correlated with impairment of cognitive function and might promote amyloid deposition by stimulating the MAPK signalling pathway in the brain.}, } @article {pmid32317321, year = {2020}, author = {Price, TK and Wolff, B and Halverson, T and Limeira, R and Brubaker, L and Dong, Q and Mueller, ER and Wolfe, AJ}, title = {Temporal Dynamics of the Adult Female Lower Urinary Tract Microbiota.}, journal = {mBio}, volume = {11}, number = {2}, pages = {}, pmid = {32317321}, issn = {2150-7511}, support = {R01 DK104718/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Biodiversity ; Female ; Humans ; Metagenomics ; *Microbiota ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; Urinary Tract/*microbiology ; Urinary Tract Infections/microbiology ; }, abstract = {Temporal dynamics of certain human microbiotas have been described in longitudinal studies; variability often relates to modifiable factors or behaviors. Early studies of the urinary microbiota preferentially used samples obtained by transurethral catheterization to minimize vulvovaginal microbial contributions. Whereas voided specimens are preferred for longitudinal studies, the few studies that reported longitudinal data were limited to women with lower urinary tract (LUT) symptoms, due to ease of accessing a clinical population for sampling and the impracticality and risk of collecting repeated catheterized urine specimens in a nonclinical population. Here, we studied the microbiota of the LUT of nonsymptomatic, premenopausal women using midstream voided urine (MSU) specimens to investigate relationships between microbial dynamics and personal factors. Using 16S rRNA gene sequencing and a metaculturomics method called expanded quantitative urine culture (EQUC), we characterized the microbiotas of MSU and periurethral swab specimens collected daily for approximately 3 months from a small cohort of adult women. Participants were screened for eligibility, including the ability to self-collect paired urogenital specimens prior to enrollment. In this population, we found that measures of microbial dynamics related to specific participant-reported factors, particularly menstruation and vaginal intercourse. Further investigation of the trends revealed differences in the composition and diversity of LUT microbiotas within and across participants. These data, in combination with previous studies showing relationships between the LUT microbiota and LUT symptoms, suggest that personal factors relating to the genitourinary system may be an important consideration in the etiology, prevention, and/or treatment of LUT disorders.IMPORTANCE Following the discovery of the collective human urinary microbiota, important knowledge gaps remain, including the stability and variability of this microbial niche over time. Initial urinary studies preferentially utilized samples obtained by transurethral catheterization to minimize contributions from vulvovaginal microbes. However, catheterization has the potential to alter the urinary microbiota; therefore, voided specimens are preferred for longitudinal studies. In this report, we describe microbial findings obtained by daily assessment over 3 months in a small cohort of adult women. We found that, similarly to vaginal microbiotas, lower urinary tract (LUT) microbiotas are dynamic, with changes relating to several factors, particularly menstruation and vaginal intercourse. Our study results show that LUT microbiotas are both dynamic and resilient. They also offer novel opportunities to target LUT microbiotas by preventative or therapeutic means, through risk and/or protective factor modification.}, } @article {pmid32317019, year = {2020}, author = {Guibert, I and Lecellier, G and Torda, G and Pochon, X and Berteaux-Lecellier, V}, title = {Metabarcoding reveals distinct microbiotypes in the giant clam Tridacna maxima.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {57}, pmid = {32317019}, issn = {2049-2618}, mesh = {Animals ; *Anthozoa/microbiology/physiology ; Bacteria/classification/growth & development ; *Bivalvia/microbiology/physiology ; *Coral Reefs ; *DNA Barcoding, Taxonomic ; Dinoflagellida/classification/growth & development ; *Microbiota ; Symbiosis ; Temperature ; }, abstract = {BACKGROUND: Giant clams and scleractinian (reef-building) corals are keystone species of coral reef ecosystems. The basis of their ecological success is a complex and fine-tuned symbiotic relationship with microbes. While the effect of environmental change on the composition of the coral microbiome has been heavily studied, we know very little about the composition and sensitivity of the microbiome associated with clams. Here, we explore the influence of increasing temperature on the microbial community (bacteria and dinoflagellates from the family Symbiodiniaceae) harbored by giant clams, maintained either in isolation or exposed to other reef species. We created artificial benthic assemblages using two coral species (Pocillopora damicornis and Acropora cytherea) and one giant clam species (Tridacna maxima) and studied the microbial community in the latter using metagenomics.

RESULTS: Our results led to three major conclusions. First, the health status of giant clams depended on the composition of the benthic species assemblages. Second, we discovered distinct microbiotypes in the studied T. maxima population, one of which was disproportionately dominated by Vibrionaceae and directly linked to clam mortality. Third, neither the increase in water temperature nor the composition of the benthic assemblage had a significant effect on the composition of the Symbiodiniaceae and bacterial communities of T. maxima.

CONCLUSIONS: Altogether, our results suggest that at least three microbiotypes naturally exist in the studied clam populations, regardless of water temperature. These microbiotypes plausibly provide similar functions to the clam host via alternate molecular pathways as well as microbiotype-specific functions. This redundancy in functions among microbiotypes together with their specificities provides hope that giant clam populations can tolerate some levels of environmental variation such as increased temperature. Importantly, the composition of the benthic assemblage could make clams susceptible to infections by Vibrionaceae, especially when water temperature increases. Video abstract.}, } @article {pmid32313992, year = {2020}, author = {Lu, Y and Zhang, E and Hong, M and Yin, X and Cai, H and Yuan, L and Yuan, F and Li, L and Zhao, K and Lan, X}, title = {Analysis of endophytic and rhizosphere bacterial diversity and function in the endangered plant Paeonia ludlowii.}, journal = {Archives of microbiology}, volume = {202}, number = {7}, pages = {1717-1728}, pmid = {32313992}, issn = {1432-072X}, support = {XZ2017ZRG-22//Tibet Department of Science and Technology General Scientific Research Project/ ; 502219005//The coordinated innovation program for the research and development of Tibet characteristic agricultural and animal resources/ ; 2060302-1702-13//Research and formulating of standards for the construction of China wild traditional Chinese medicine resources protection base (Tibet region)/ ; 20190411-542222//State Administration of Traditional Chinese Medicine of the People's Republic of China/ ; }, mesh = {*Biodiversity ; Cyanobacteria/genetics/isolation & purification ; DNA, Ribosomal/genetics ; *Endangered Species ; Endophytes/*classification/genetics/*physiology ; High-Throughput Nucleotide Sequencing ; Paeonia/*microbiology ; Plant Roots/microbiology ; Proteobacteria/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; *Soil Microbiology ; Tibet ; }, abstract = {Paeonia ludlowii is indigenous to Tibet and has an important ecological and economic value in China. In Tibet, P. ludlowii has been used in folk medicine with relative success. Plant microbial endophytes play an important role in plant growth, health and ecological function. The diversity of endophytic bacteria associated with P. ludlowii remains poorly understood. In this study, the structure of the endophytic bacterial communities associated with different tissues, including fruits, flowers, leaves, stems, and roots, and rhizosphere soils was analyzed with Illumina MiSeq sequencing of bacterial 16S rDNA. A total of 426,240 sequences and 4847 operational taxonomic units (OTUs) were obtained. The OTUs abundance of roots was higher than that of other tissues; however, the OTUs abundance was similar among different deep soil samples. In the plant tissues, Cyanobacteria was the most abundant bacterial phylum, followed by Proteobacteria; however, the most abundant phyla were Proteobacteria and Acidobacteria in soil samples from three different layers. In addition, the diversity and richness of the microorganisms in the soil were very similar to those in roots but higher than those in other tissues of P. ludlowii. Predictive metagenome analysis revealed that endophytic bacteria play critical functional roles in P. ludlowii. This conclusion could facilitate the study of the ecological functions of endophytic bacteria and their interactions with P. ludlowii to analyze the reasons why this important medicinal plant is becoming endangered.}, } @article {pmid32312186, year = {2020}, author = {Dan, Z and Mao, X and Liu, Q and Guo, M and Zhuang, Y and Liu, Z and Chen, K and Chen, J and Xu, R and Tang, J and Qin, L and Gu, B and Liu, K and Su, C and Zhang, F and Xia, Y and Hu, Z and Liu, X}, title = {Altered gut microbial profile is associated with abnormal metabolism activity of Autism Spectrum Disorder.}, journal = {Gut microbes}, volume = {11}, number = {5}, pages = {1246-1267}, pmid = {32312186}, issn = {1949-0984}, mesh = {Adolescent ; Autism Spectrum Disorder/complications/*metabolism/*microbiology ; Bacteria/classification/genetics/*growth & development/metabolism ; Child ; Child, Preschool ; Cohort Studies ; Constipation/complications/microbiology ; Feces/chemistry/microbiology ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; Metabolome ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Autism Spectrum Disorder (ASD) is a severe neurodevelopmental disorder. To enhance the understanding of the gut microbiota structure in ASD children at different ages as well as the relationship between gut microbiota and fecal metabolites, we first used the 16S rRNA sequencing to evaluate the gut microbial population in a cohort of 143 children aged 2-13 years old. We found that the α-diversity of ASD group showed no significant change with age, while the TD group showed increased α-diversity with age, which indicates that the compositional development of the gut microbiota in ASD varies at different ages in ways that are not consistent with TD group. Recent studies have shown that chronic constipation is one of the most commonly obvious gastrointestinal (GI) symptoms along with ASD core symptoms. To further investigate the potential interaction effects between ASD and GI symptoms, the 30 C-ASD and their aged-matched TD were picked out to perform metagenomics analysis. We observed that C-ASD group displayed decreased diversity, depletion of species of Sutterella, Prevotella, and Bacteroides as well as dysregulation of associated metabolism activities, which may involve in the pathogenesis of C-ASD. Consistent with metagenomic analysis, liquid chromatography-mass spectrometry (LC/MS) revealed some of the differential metabolites between C-ASD and TD group were involved in the metabolic network of neurotransmitters including serotonin, dopamine, histidine, and GABA. Furthermore, we found these differences in metabolites were associated with altered abundance of specific bacteria. The study suggested possible future modalities for ASD intervention through targeting the specific bacteria associated with neurotransmitter metabolism.}, } @article {pmid32307861, year = {2021}, author = {Uritskiy, G and Tisza, MJ and Gelsinger, DR and Munn, A and Taylor, J and DiRuggiero, J}, title = {Cellular life from the three domains and viruses are transcriptionally active in a hypersaline desert community.}, journal = {Environmental microbiology}, volume = {23}, number = {7}, pages = {3401-3417}, doi = {10.1111/1462-2920.15023}, pmid = {32307861}, issn = {1462-2920}, mesh = {*Cyanobacteria/genetics ; Desert Climate ; Metagenome/genetics ; *Microbiota/genetics ; *Viruses/genetics ; }, abstract = {Microbial communities play essential roles in the biosphere and understanding the mechanisms underlying their functional adaptations to environmental conditions is critical for predicting their behaviour. This aspect of microbiome function has not been well characterized in natural high-salt environments. To address this knowledge gap, and to build a general framework relating the genomic and transcriptomic components in a microbiome, we performed a meta-omic survey of extremophile communities inhabiting halite (salt) nodules in the Atacama Desert. We found that the major phyla of this halophilic community have different levels of total transcriptional activity, at the selected time-points, and that different metabolic pathways were activated in their transcriptomes. We report that a novel Dolichomastix alga-the only eukaryote found in this system-was the most active community member. It produced the vast majority of the community's photosynthetic transcripts despite being outnumbered by Cyanobacteria. The divergence in the transcriptional landscapes of these segregated communities, compared with the relatively stable metagenomic functional potential, suggests that microbiomes in each salt nodule undergo unique transcriptional adjustments to adapt to local conditions. We also report the characterization of several previously unknown halophilic viruses, many of which exhibit transcriptional activity indicative of host infection.}, } @article {pmid32307604, year = {2020}, author = {Jiang, T and Guo, C and Wang, M and Wang, M and You, S and Liu, Y and Zhang, X and Liu, H and Jiang, Y and Shao, H and Liang, Y and McMinn, A}, title = {Isolation and complete genome sequence of a novel cyanophage, S-B05, infecting an estuarine Synechococcus strain: insights into environmental adaptation.}, journal = {Archives of virology}, volume = {165}, number = {6}, pages = {1397-1407}, doi = {10.1007/s00705-020-04595-6}, pmid = {32307604}, issn = {1432-8798}, support = {No. 41906126//Natural Science Foundation of China/ ; No.41976117//Natural Science Foundation of China/ ; No.41676178//Natural Science Foundation of China/ ; LMB20091001//Open research fund of LMB/ ; }, mesh = {Base Composition ; Base Sequence ; China ; *Genome, Viral ; Host Specificity ; Metagenomics ; Myoviridae/*classification/*isolation & purification/ultrastructure ; Open Reading Frames ; Pacific Ocean ; Phylogeny ; Seawater/*virology ; Synechococcus/*virology ; Water Microbiology ; Whole Genome Sequencing ; }, abstract = {A new cyanophage, S-B05, infecting a phycoerythrin-enriched (PE-type) Synechococcus strain was isolated by the liquid infection method, and its morphology and genetic features were examined. Phylogenetic analysis and morphological observation confirmed that S-B05 belongs to the family Myoviridae of the order Caudovirales. Its genome was fully sequenced, and found to be 208,857 bp in length with a G + C content of 39.9%. It contained 280 potential open reading frames and 123 conserved domains. Ninety-eight functional genes responsible for cyanophage structuring and packaging, DNA replication and regulation, and photosynthesis were identified, as well as genes encoding 172 hypothetical proteins. The genome of S-B05 is most similar to that of Prochlorococcus phage P-TIM68. Homologues of open reading frames of S-B05 can be found in various marine environments, as revealed by comparison of the S-B05 genome sequence to sequences in marine viral metagenomic databases. The presence of auxiliary metabolic genes (AMGs) related to photosynthesis, carbon metabolism, and phosphorus assimilation, as well as the phylogenetic relationships based on AMGs and the complete genome sequence, reflect the phage-host interaction mechanism or the specific adaptation strategy of the host to environmental conditions. The genome sequence information reported here will provide an important basis for further study of the adaptive evolution and ecological role of cyanophages and their hosts in the marine environment.}, } @article {pmid32306993, year = {2020}, author = {Mejia, R and Damania, A and Jeun, R and Bryan, PE and Vargas, P and Juarez, M and Cajal, PS and Nasser, J and Krolewiecki, A and Lefoulon, E and Long, C and Drake, E and Cimino, RO and Slatko, B}, title = {Impact of intestinal parasites on microbiota and cobalamin gene sequences: a pilot study.}, journal = {Parasites & vectors}, volume = {13}, number = {1}, pages = {200}, pmid = {32306993}, issn = {1756-3305}, support = {D34HP31024/HRSA/HRSA HHS/United States ; }, mesh = {Animals ; Child ; Child, Preschool ; *Coinfection/microbiology/parasitology ; Cross-Sectional Studies ; DNA, Helminth ; DNA, Protozoan ; Female ; Gastrointestinal Microbiome/*genetics ; Genes, Bacterial ; Giardia lamblia/classification/genetics/isolation & purification ; Helminths/classification/genetics/isolation & purification ; Humans ; *Intestines/microbiology/parasitology ; Male ; Metagenomics ; Parasites/classification/*genetics/isolation & purification ; Pilot Projects ; Real-Time Polymerase Chain Reaction ; Vitamin B 12/*genetics/metabolism ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Approximately 30% of children worldwide are infected with gastrointestinal parasites. Depending on the species, parasites can disrupt intestinal bacterial microbiota affecting essential vitamin biosynthesis.

METHODS: Stool samples were collected from 37 asymptomatic children from a previous cross-sectional Argentinian study. A multi-parallel real-time quantitative PCR was implemented for Ascaris lumbricoides, Ancylostoma duodenale, Necator americanus, Strongyloides stercoralis, Trichuris trichiura, Cryptosporidium spp., Entamoeba histolytica and Giardia duodenalis. In addition, whole-genome sequencing analysis was conducted for bacterial microbiota on all samples and analyzed using Livermore Metagenomic Analysis Toolkit and DIAMOND software. Separate analyses were carried out for uninfected, Giardia-only, Giardia + helminth co-infections, and helminth-only groups.

RESULTS: For Giardia-only infected children compared to uninfected children, DNA sequencing data showed a decrease in microbiota biodiversity that correlated with increasing Giardia burden and was statistically significant using Shannon's alpha diversity (Giardia-only > 1 fg/µl 2.346; non-infected group 3.253, P = 0.0317). An increase in diversity was observed for helminth-only infections with a decrease in diversity for Giardia + helminth co-infections (P = 0.00178). In Giardia-only infections, microbiome taxonomy changed from Firmicutes towards increasing proportions of Prevotella, with the degree of change related to the intensity of infection compared to uninfected (P = 0.0317). The abundance of Prevotella bacteria was decreased in the helminths-only group but increased for Giardia + helminth co-infections (P = 0.0262). Metagenomic analysis determined cobalamin synthesis was decreased in the Giardia > 1 fg/µl group compared to both the Giardia < 1 fg/µl and the uninfected group (P = 0.0369). Giardia + helminth group also had a decrease in cobalamin CbiM genes from helminth-only infections (P = 0.000754).

CONCLUSION: The study results may provide evidence for an effect of parasitic infections enabling the permissive growth of anaerobic bacteria such as Prevotella, suggesting an altered capacity of vitamin B12 (cobalamin) biosynthesis and potential impact on growth and development in children .}, } @article {pmid32305646, year = {2020}, author = {Wang, P and Gao, J and Ke, W and Wang, J and Li, D and Liu, R and Jia, Y and Wang, X and Chen, X and Chen, F and Hu, X}, title = {Resveratrol reduces obesity in high-fat diet-fed mice via modulating the composition and metabolic function of the gut microbiota.}, journal = {Free radical biology & medicine}, volume = {156}, number = {}, pages = {83-98}, doi = {10.1016/j.freeradbiomed.2020.04.013}, pmid = {32305646}, issn = {1873-4596}, mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred C57BL ; Obesity/drug therapy/etiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Resveratrol ; }, abstract = {Resveratrol (RSV) is a natural polyphenol with anti-obesity effects. However, the mechanisms of anti-obesity remain unclear due to its low bioavailability. Recent evidence demonstrates that gut microbiota plays a key role in obesity. This spurred us to investigate whether the anti-obesity effects of RSV are related to modulations in the gut microbiota and metabolic functions. Here, RSV significantly improved metabolic phenotype and intestinal oxidative stress in the high-fat diet (HFD)-fed mice. A multi-omics approach was used to systematically profile the microbial signatures at both the phylogenetic and functional levels using 16S rRNA gene sequencing and metagenome. At the phylogenetic level, RSV treatment significantly modulated the gut microbiota composition in HFD-fed mice, characterized with increased Blautia abundance and decreased Desulfovibrio and Lachnospiraceae_NK4A136_group abundance. At the functional level, RSV significantly decreased the enrichment of pathways linked to host metabolic disease and increased the enrichment of pathways involved in the generation of small metabolites. Besides, the fecal microbiota transplantation experiment showed anti-obesity and microbiota-modulating effects similar to those observed in the oral RSV-feeding experiment. Furthermore, metabolomic analysis and antibiotic treatment verified that 4-hydroxyphenylacetic acid (4-HPA) and 3-hydroxyphenylpropionic acid (3-HPP) were the two gut metabolites of RSV, which contribute to improving lipid metabolism in vitro. Moreover, the content of 4-HPA and 3-HPP exhibited strong correlation with the intestinal oxidative state. We concluded that the RSV-mediated alteration of gut microbiota, related gut metabolites and redox state of the intestinal environment contributed to prevention of metabolic syndrome in HFD-fed mice.}, } @article {pmid32304259, year = {2020}, author = {Silva, EN and Martins, TVF and Miyauchi-Tavares, TM and Miranda, BAE and Dos Santos, GA and Rosa, CP and Santos, JA and Novaes, RD and de Almeida, LA and Corsetti, PP}, title = {Amoxicillin-induced gut dysbiosis influences estrous cycle in mice and cytokine expression in the ovary and the caecum.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {84}, number = {1}, pages = {e13247}, doi = {10.1111/aji.13247}, pmid = {32304259}, issn = {1600-0897}, mesh = {Amoxicillin/*adverse effects ; Animals ; Anti-Bacterial Agents/*adverse effects ; Cecum/*physiology ; Cytokines/metabolism ; Drug-Related Side Effects and Adverse Reactions/*immunology ; Dysbiosis/etiology/*immunology ; Estrous Cycle/*drug effects ; Female ; Gastrointestinal Microbiome/drug effects ; Gene Expression Regulation ; Humans ; Interleukin-10/genetics/metabolism ; Interleukin-1beta/metabolism ; Mice ; Mice, 129 Strain ; Ovary/*physiology ; }, abstract = {PROBLEM: Gut dysbiosis is caused by several factors, including the use of antibiotics. Since intestinal dysbiosis is associated with a wide range of immunopathological and reproductive conditions, the main goal of this study was to evaluate amoxicillin-induced gut dysbiosis and its influence on the oestrous cycle in mice.

METHOD OF STUDY: Mice were treated with amoxicillin or PBS, and faecal microbiota was evaluated by 16S rDNA metagenomic sequencing. The oestrous cycle was evaluated by vaginal cytology, vaginal opening and flow cytometry. After the induction of gut dysbiosis, the ovaries and the caecum were analysed to differential expression of IL-1β and IL-10 genes and histological analysis.

RESULTS: Amoxicillin-treated mice presented differing bacterial groups in the faecal microbiota when compared to the PBS-treated group indicating that amoxicillin treatment-induced gut dysbiosis and they gained weight. The vaginal cytology analysis showed that amoxicillin-induced gut dysbiosis decreased the number of cells but increased the relative number of leucocytes and altered the oestrous cycle. IL-1β was shown to be upregulated in the caecum and in the ovary of the dysbiotic mice. On the other hand, IL-10 expression was shown to be diminished in both organs of the dysbiotic mice. The oocyte area from dysbiotic group presented lower than non-dysbiotic mice with increasing thickness of the pellucid zone. The follicular teak from dysbiotic mice showed lower thickness than non-dysbiotic mice.

CONCLUSION: The results indicate that amoxicillin induces gut dysbiosis and influences the oestrous cycle and the inflammatory status of the ovary and the caecum.}, } @article {pmid32303552, year = {2020}, author = {Milani, C and Fontana, F and Alessandri, G and Mancabelli, L and Lugli, GA and Longhi, G and Anzalone, R and Viappiani, A and Duranti, S and Turroni, F and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {Ecology of Lactobacilli Present in Italian Cheeses Produced from Raw Milk.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {12}, pages = {}, pmid = {32303552}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification ; Cheese/*microbiology ; Italy ; Lactobacillus/classification/genetics/isolation & purification/*physiology ; Microbiota ; Milk/*microbiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Among the bacterial genera that are used for cheese production, Lactobacillus is a key taxon of high industrial relevance that is commonly present in commercial starter cultures for dairy fermentations. Certain lactobacilli play a defining role in the development of the organoleptic features during the ripening stages of particular cheeses. We performed an in-depth 16S rRNA gene-based microbiota analysis coupled with internally transcribed spacer-mediated Lactobacillus compositional profiling of 21 common Italian cheeses produced from raw milk in order to evaluate the ecological distribution of lactobacilli associated with this food matrix. Statistical analysis of the collected data revealed the existence of putative Lactobacillus community state types (LCSTs), which consist of clusters of Lactobacillus (sub)species. Each LCST is dominated by one or two taxa that appear to represent keystone elements of an elaborate network of positive and negative interactions with minor components of the cheese microbiota. The results obtained in this study reveal the existence of peculiar cheese microbiota assemblies that represent intriguing targets for further functional studies aimed at dissecting the species-specific role of bacteria in cheese manufacturing.IMPORTANCE The microbiota is known to play a key role in the development of the organoleptic features of dairy products. Lactobacilli have been reported to represent one of the main components of the nonstarter bacterial population, i.e., bacteria that are not deliberately added to the milk, harbored by cheese, although the species-level composition of this microbial population has never been assessed in detail. In the present study, we applied a recently developed metagenomic approach that employs an internally transcribed spacer to profile the Lactobacillus population harbored by cheese produced from raw milk at the (sub)species level. The obtained data revealed the existence of particular Lactobacillus community state types consisting of clusters of Lactobacillus (sub)species that tend to cooccur in the screened cheeses. Moreover, analysis of covariances between members of this genus indicate that these taxa form an elaborate network of positive and negative interactions that define specific clusters of covariant lactobacilli.}, } @article {pmid32303546, year = {2020}, author = {Allaway, D and Haydock, R and Lonsdale, ZN and Deusch, OD and O'Flynn, C and Hughes, KR}, title = {Rapid Reconstitution of the Fecal Microbiome after Extended Diet-Induced Changes Indicates a Stable Gut Microbiome in Healthy Adult Dogs.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {13}, pages = {}, pmid = {32303546}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification/*isolation & purification ; Diet/*veterinary ; Dogs ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Male ; Metagenome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; }, abstract = {The gut microbiome has an important role in health, and diet represents a key lever for shaping the gut microbiome across all stages of life. Maternal milk consumption in neonates leads to long-term health effects, indicating that pliability in the infant gut microbiome in response to diet can drive enduring change. The ability of diet to drive lasting changes in the adult gut microbiome is less understood. We studied the effect of an extreme dietary shift on the fecal microbiome of 46 Labrador retriever dogs (mean age, 4.6 years) over 11 months. Dogs were fed a nutritionally complete, commercially available complex diet (CD) for a minimum of 5 weeks, followed by highly purified diets (PDs) for 36 weeks, and the initial CD for at least a further 4 weeks. Fecal samples were collected at regular intervals for DNA extraction. By analyzing 16S rRNA genes and the metagenomes, we observed minor effects on microbial diversity but significant changes in bacterial taxa and genetic potential when a PD was fed. Specifically, metagenomics identified an enrichment of quinone- and GABA-related pathways on PD, providing insights into dietary effects on cross-feeding strategies impacting community structure. When dogs returned to the CD, no significant differences were found with the initial time point. These findings are consistent with the gut microbiome being rapidly adaptable but capable of being reconstituted when provided with similar diets. These data highlight that long-term changes in the adult dog gut microbiome may only be achieved through long-term maintenance on a specified diet, rather than through feeding a transitionary diet.IMPORTANCE Diet can influence the adult gut microbiome (the community of bacteria) and health outcomes, but the ability to make changes persisting beyond feeding of a particular diet is poorly understood. We investigated whether feeding highly purified diets to adult dogs for 36 weeks would alter bacterial populations sufficiently to result in a persistent change following the dogs' return to a commercial diet. As expected, the microbiome changed when the purified diet was fed, but the original microbiome was reconstituted within weeks of the dogs returning to the commercial diet. The significance of these findings is in identifying an intrinsic stability of the host microbiome in healthy dogs, suggesting that dietary changes to support adult dog health through modifying the gut microbiome may be achieved only through maintenance on a specified diet, rather than through feeding transitionary diets.}, } @article {pmid32299221, year = {2020}, author = {Sijbers, AM and Schoemaker, RJW and Nauta, A and Alkema, W}, title = {Revealing new leads for the impact of galacto-oligosaccharides on gut commensals and gut health benefits through text mining.}, journal = {Beneficial microbes}, volume = {11}, number = {3}, pages = {283-302}, doi = {10.3920/BM2019.0105}, pmid = {32299221}, issn = {1876-2891}, mesh = {Bifidobacterium/growth & development/physiology ; *Data Mining ; Feces/microbiology ; Fermentation ; *Galactose ; *Gastrointestinal Microbiome ; Health ; Humans ; Oligosaccharides/*administration & dosage ; Prebiotics/*analysis ; *Symbiosis ; }, abstract = {Galacto-oligosaccharides (GOS) are linked to various health benefits, such as the relief of symptoms of constipation. Part of the beneficial effects of GOS are thought to be the consequence of their bifidogenic effect, stimulating the growth of several Bifidobacterium species in vivo. However, GOS may exert additional effects by directly stimulating other bacterial species or by effects that bifidobacteria may have on other commensals in the gut. To get a better insight into the potential health effects induced by GOS, a good understanding of the gut ecosystem, the role of GOS and bifidobacteria is important. An increasing number of 16S DNA profiling and metagenomics studies have led to an expanding inventory of genera, species and strains that can be found in the human gut. To investigate the potential connection of these commensals with GOS and bifidobacteria, we have undertaken a text-mining study to chart the literature landscape around these commensals. To this end, we created controlled vocabularies describing GOS, a large set of gut commensals and a number of terms related to gut health, which were used to mine the entire MEDLINE database. Co-occurrence text-mining revealed that a large number of commensals found in the gut have a connection with Bifidobacterium species and with gut health effects. Word frequency analysis provided more insight into the functional nature of these relationships. Combined co-occurrence search results pointed to putative novel health benefits indirectly linked to bifidobacteria and GOS. The potential beneficial effects of GOS on the protection of epithelial function and epithelial barrier impairment and appendicitis are interesting novel leads. The text-mining approach reported here revealed a number of novel leads through which GOS could exert health effects and that could be investigated in dedicated studies.}, } @article {pmid32298617, year = {2020}, author = {Ternes, D and Karta, J and Tsenkova, M and Wilmes, P and Haan, S and Letellier, E}, title = {Microbiome in Colorectal Cancer: How to Get from Meta-omics to Mechanism?.}, journal = {Trends in microbiology}, volume = {28}, number = {5}, pages = {401-423}, doi = {10.1016/j.tim.2020.01.001}, pmid = {32298617}, issn = {1878-4380}, mesh = {Animals ; Bacteria/*classification/isolation & purification ; Colorectal Neoplasms/*microbiology/*pathology ; Dysbiosis/*microbiology ; Gastrointestinal Microbiome/physiology ; Gastrointestinal Tract/microbiology/pathology ; Host-Pathogen Interactions/*physiology ; Humans ; Mice ; }, abstract = {Mounting evidence from metagenomic analyses suggests that a state of pathological microbial imbalance or dysbiosis is prevalent in the gut of patients with colorectal cancer. Several bacterial taxa have been identified of which representative isolate cultures interact with human cancer cells in vitro and trigger disease pathways in animal models. However, how the complex interrelationships in dysbiotic communities may be involved in cancer pathogenesis remains a crucial question. Here, we provide a survey of current knowledge of the gut microbiome in colorectal cancer. Moving beyond observational studies, we outline new experimental approaches for gaining ecosystem-level mechanistic understanding of the gut microbiome's role in cancer pathogenesis.}, } @article {pmid32298613, year = {2020}, author = {Koonin, EV and Yutin, N}, title = {The crAss-like Phage Group: How Metagenomics Reshaped the Human Virome.}, journal = {Trends in microbiology}, volume = {28}, number = {5}, pages = {349-359}, doi = {10.1016/j.tim.2020.01.010}, pmid = {32298613}, issn = {1878-4380}, mesh = {Bacteriophages/classification/*genetics ; Bacteroides/*virology ; Gastrointestinal Microbiome/genetics ; Genome, Viral/genetics ; Humans ; Metagenomics ; Viral Replicase Complex Proteins/*genetics/metabolism ; Virome/*genetics ; }, abstract = {Metagenomics is currently the primary means for identifying new viruses. One of the most impactful metagenomic discoveries is that of crAssphage, the most abundant human-associated virus that is found in about 50% of human gut viromes where it can comprise up to 90% of the virus sequences. Although initial genome analysis of crAssphage failed to detect related phages, or functionally annotate most of the genes, subsequent reanalysis with powerful computational methods and larger databases led to the identification of an expansive group of crAss-like phages. The functions of most crAssphage proteins were predicted, including unusual ones such as giant RNA polymerase polyproteins. The host range of the crAss-like phages consists of various members of the bacterial phylum Bacteroidetes as demonstrated by CRISPR spacer analysis and by analysis of genes acquired by phages from the hosts. New metagenomic studies vastly expanded the crAss-like phage group and demonstrated its global spread and ancient association with primates. The first members of the crAss-like group was recently isolated and shown to infect the bacterium Bacteroides intestinales. Characterization of this phage validated the predicted podovirus-like virion structure and the identity of the major capsid protein and other predicted virion proteins, including three RNA polymerase subunits.}, } @article {pmid32296838, year = {2020}, author = {Lin, TY and Wu, PH and Lin, YT and Hung, SC}, title = {Characterization of Gut Microbiota Composition in Hemodialysis Patients With Normal Weight Obesity.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {105}, number = {6}, pages = {}, doi = {10.1210/clinem/dgaa166}, pmid = {32296838}, issn = {1945-7197}, mesh = {Aged ; Biomarkers/analysis ; *Body Mass Index ; Case-Control Studies ; Female ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Humans ; Male ; *Metagenome ; Obesity/genetics/*microbiology ; Overweight/genetics/*microbiology ; Prognosis ; RNA, Ribosomal, 16S/analysis/genetics ; Renal Dialysis/*methods ; }, abstract = {BACKGROUND: Normal weight obesity (NWO), defined by a normal body mass index (BMI) but increased body fat percentage (BF%), is associated with an increased risk of cardiovascular disease and mortality. NWO is characterized by inflammation and muscle wasting in chronic kidney disease (CKD), but the underlying mechanisms remain largely unknown. Gut microbiota has been implicated in the regulation of host metabolism and may play important roles in the development of NWO in CKD.

METHODS: In this case-control study, we examined the gut microbial diversity and taxonomy in 96 hemodialysis patients with normal weight (BMI < 25 kg/m2 and BF% ≤ 25% for men or ≤ 35% for women; n = 32), NWO (BMI < 25 kg/m2 and BF% > 25% for men or > 35% for women; n = 32), and overweight/obesity (BMI ≥ 25 kg/m2; n = 32), matched for age, gender, and diabetes. BF% was measured using bioimpedance spectroscopy device. Gut microbiota was determined by 16S rRNA sequencing.

RESULTS: We found that α-diversity was significantly different among the 3 adiposity phenotypes, with NWO being the least diverse. α-diversity was positively correlated with BMI, subjective global assessment score, and physical activity, but negatively correlated with interleukin-6 and tumor necrosis factor-α. Patients with or without NWO were distinguished with respect to principal coordinate analysis of β-diversity. Notably, the relative abundance of butyrate-producing bacteria, such as Faecalibacterium prausnitzii and Coprococcus, was markedly reduced in patients with NWO.

CONCLUSION: Our findings support associations between gut dysbiosis and a proinflammatory and catabolic state in hemodialysis patients with NWO.}, } @article {pmid32296425, year = {2020}, author = {Escobar, MF and Hincapie, MA and Barona, JS}, title = {Immunological Role of the Maternal Uterine Microbiota in Postpartum Hemorrhage.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {504}, pmid = {32296425}, issn = {1664-3224}, mesh = {Animals ; Dysbiosis/*immunology ; Female ; Humans ; Microbiota/*immunology ; Postpartum Hemorrhage/*immunology ; Pregnancy ; Uterus/*immunology/*microbiology ; }, abstract = {Recent metagenomics and microbiology studies have identified microorganisms that are typical of the fetoplacental unit. Considering this emerging evidence, the placenta, uterus, and the amniotic cavity are not sterile and not immune privileged. However, there is evidence for a beneficial interaction between active maternal immune system and the presence of commensal pathogens, which lead to an immune-tolerant state, thereby preventing fetal rejection. Multiple conditions associated with the loss of the normal flora are described (dysbiosis), which could result in perinatal and puerperal adverse events, including, directly or indirectly, postpartum hemorrhage. Altered flora when associated with a severe proinflammatory state and combined with patient's genetic and environmental factors confers a high-risk adverse outcome. Better understanding of the adverse role of dysbiosis in pregnancy outcome will improve maternal outcome.}, } @article {pmid32296109, year = {2020}, author = {Calderón-Pérez, L and Gosalbes, MJ and Yuste, S and Valls, RM and Pedret, A and Llauradó, E and Jimenez-Hernandez, N and Artacho, A and Pla-Pagà, L and Companys, J and Ludwig, I and Romero, MP and Rubió, L and Solà, R}, title = {Gut metagenomic and short chain fatty acids signature in hypertension: a cross-sectional study.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {6436}, pmid = {32296109}, issn = {2045-2322}, mesh = {Adult ; Blood Pressure/physiology ; Cross-Sectional Studies ; DNA, Bacterial/isolation & purification ; Fatty Acids, Volatile/*analysis ; Feces/chemistry/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Hypertension/blood/*diagnosis/metabolism/microbiology ; Male ; Metabolomics ; Metagenome ; Methylamines/*blood ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Hypertension is an independent and preventable risk factor for the development of cardiovascular diseases, however, little is known about the impact of gut microbiota composition in its development. We carried out comprehensive gut microbiota analysis and targeted metabolomics in a cross-sectional study of 29 non-treated hypertensive (HT) and 32 normotensive (NT) subjects. We determined fecal microbiota composition by 16S rRNA gene sequencing and bacterial functions by metagenomic analysis. The microbial metabolites analysed were short chain fatty acids (SCFA) both in plasma and feces, and trimethylamine N-oxide (TMAO) in plasma. The overall bacterial composition and diversity of bacterial community in the two groups were not significantly different. However, Ruminococcaceae NK4A214, Ruminococcaceae_UCG-010, Christensenellaceae_R-7, Faecalibacterium prausnitzii and Roseburia hominis were found to be significantly enriched in NT group, whereas, Bacteroides coprocola, Bacteroides plebeius and genera of Lachnospiraceae were increased in HT patients. We found a positive correlation between the HT-associated species and systolic and diastolic blood pressure after adjusted for measured confounders. SCFA showed antagonistic results in plasma and feces, detecting in HT subjects significant higher levels in feces and lower levels in plasma, which could indicate a less efficient SCFA absorption. Overall, our results present a disease classifier based on microbiota and bacterial metabolites to discriminate HT individuals from NT controls in a first disease grade prior to drug treatment.}, } @article {pmid32294307, year = {2020}, author = {Goller, CC and Ott, LE}, title = {Evolution of an 8-week upper-division metagenomics course: Diagramming a learning path from observational to quantitative microbiome analysis.}, journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology}, volume = {48}, number = {4}, pages = {391-403}, doi = {10.1002/bmb.21349}, pmid = {32294307}, issn = {1539-3429}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Computational Biology/*methods ; Genome, Bacterial ; Humans ; Metagenomics/*education/methods ; *Microbiota ; Problem-Based Learning/*methods ; RNA, Bacterial/*analysis/genetics ; RNA, Ribosomal, 16S/*analysis/genetics ; Soil Microbiology ; Students ; }, abstract = {Metagenomics is a tool that enables researchers to study genetic material recovered directly from microbial communities or microbiomes. Fueled by advances in sequencing technologies, bioinformatics tools, and sample processing, metagenomics studies promise to expand our understanding of human health and the use of microorganisms for agriculture and industry. Therefore, teaching students about metagenomics is crucial to prepare them for modern careers in the life sciences. However, the increasing number of different approaches makes teaching metagenomics to students a challenge. This 8-week metagenomics laboratory course has the objective of introducing upper-level undergraduate and graduate students to strategies for designing, executing, and analyzing microbiome investigations. The laboratory component begins with sample processing, library preparation, and submission for high-throughput sequencing before transitioning to computer-based activities, which include an introduction to several fundamental computational metagenomics tools. Students analyze their sequencing results and deposit findings in sequence databases. The laboratory component is complemented by a weekly lecture, where active learning sessions promote retrieval practice and allow students to reflect on and diagram processes performed in the laboratory. Attainment of student learning outcomes was assessed through the completion of various course assignments: laboratory reports, presentations, and a cumulative final exam. Further, students' perceptions of their gains relevant to the learning outcomes were evaluated using pre- and postcourse surveys. Collectively, these data demonstrate that this course results in the attainment of the learning outcomes and that this approach provides an adaptable way to expose students to the cutting-edge field of metagenomics.}, } @article {pmid32293597, year = {2020}, author = {Zhang, X and Liu, X and Zhang, M}, title = {Performance and microbial community of the CANON process in a sequencing batch membrane bioreactor with elevated COD/N ratios.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {81}, number = {1}, pages = {138-147}, doi = {10.2166/wst.2020.089}, pmid = {32293597}, issn = {0273-1223}, mesh = {Ammonia ; Biological Oxygen Demand Analysis ; Bioreactors ; Denitrification ; *Microbiota ; Nitrification ; Nitrites ; *Nitrogen ; }, abstract = {In this study, the effects of elevated chemical oxygen demand/nitrogen (COD/N) ratios on nitrogen removal, production and composition of the extracellular polymer substances (EPS) and microbial community of a completely autotrophic nitrogen removal via nitrite (CANON) process were studied in a sequencing batch membrane bioreactor (SBMBR). The whole experiment was divided into two stages: the CANON stage (without organic matter in influent) and the simultaneous partial nitrification, anaerobic ammonia oxidation and denitrification (SNAD) stage (with organic matter in influent). When the inflow ammonia nitrogen was 420 mg/L and the COD/N ratio was no higher than 0.8, the addition of COD was helpful to the CANON process; the total nitrogen removal efficiency (TNE) was improved from approximately 65% to more than 75%, and the nitrogen removal rate (NRR) was improved from approximately 0.255 kgN/(m[3]·d) to approximately 0.278 kgN/(m[3]•d), while the TNE decreased to 60%, and the NRR decreased to 0.236 kgN/(m[3]•d) when the COD/N ratio was elevated to 1.0. For the EPS, the amounts of soluble EPS (SEPS) and loosely bound EPS (LB-EPS) were both higher in the CANON stage than in the SNAD stage, while the amount of tightly bound EPS (TB-EPS) in the SNAD stage was significantly higher due to the proliferation of heterotrophic bacteria. The metagenome sequencing technique was used to analyse the microbial community in the SBMBR. The results showed that the addition of COD altered the structure of the bacterial community in the SBMBR. The amounts of Candidatus 'Anammoxoglobus' of anaerobic ammonia oxidation bacteria (AAOB) and Nitrosomonas of ammonia oxidizing bacteria (AOB) both decreased significantly, and Nitrospira of nitrite oxidizing bacteria (NOB) was always in the reactor, although the amount changed slightly. A proliferation of denitrifiers related to the genera of Thauera, Dokdonella and Azospira was found in the SBMBR.}, } @article {pmid32293504, year = {2020}, author = {Raspini, B and Porri, D and De Giuseppe, R and Chieppa, M and Liso, M and Cerbo, RM and Civardi, E and Garofoli, F and Monti, MC and Vacca, M and De Angelis, M and Cena, H}, title = {Prenatal and postnatal determinants in shaping offspring's microbiome in the first 1000 days: study protocol and preliminary results at one month of life.}, journal = {Italian journal of pediatrics}, volume = {46}, number = {1}, pages = {45}, pmid = {32293504}, issn = {1824-7288}, mesh = {Adult ; Child Development/*physiology ; Female ; Fetal Development/*physiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Infant ; Infant, Newborn ; Italy ; Longitudinal Studies ; Male ; *Maternal Health ; Pregnancy ; Prospective Studies ; }, abstract = {BACKGROUND: Fetal programming during in utero life defines the set point of physiological and metabolic responses that lead into adulthood; events happening in "the first 1,000 days" (from conception to 2-years of age), play a role in the development of non-communicable diseases (NCDs). The infant gut microbiome is a highly dynamic organ, which is sensitive to maternal and environmental factors and is one of the elements driving intergenerational NCDs' transmission. The A.MA.MI (Alimentazione MAmma e bambino nei primi MIlle giorni) project aims at investigating the correlation between several factors, from conception to the first year of life, and infant gut microbiome composition. We described the study design of the A.MA.MI study and presented some preliminary results.

METHODS: A.MA.MI is a longitudinal, prospective, observational study conducted on a group of mother-infant pairs (n = 60) attending the Neonatal Unit, Fondazione IRCCS Policlinico San Matteo, Pavia (Italy). The study was planned to provide data collected at T0, T1, T2 and T3, respectively before discharge, 1,6 and 12 months after birth. Maternal and infant anthropometric measurements were assessed at each time. Other variables evaluated were: pre-pregnancy/gestational weight status (T0), maternal dietary habits/physical activity (T1-T3); infant medical history, type of feeding, antibiotics/probiotics/supplements use, environment exposures (e.g cigarette smoking, pets, environmental temperature) (T1-T3). Infant stool samples were planned to be collected at each time and analyzed using metagenomics 16S ribosomal RNA gene sequence-based methods.

RESULTS: Birth mode (cesarean section vs. vaginal delivery) and maternal pre pregnancy BMI (BMI < 25 Kg/m[2] vs. BMI ≥ 25 Kg/m[2]), significant differences were found at genera and species levels (T0). Concerning type of feeding (breastfed vs. formula-fed), gut microbiota composition differed significantly at genus and species level (T1).

CONCLUSION: These preliminary and explorative results confirmed that pre-pregnancy, mode of delivery and infant factors likely impact infant microbiota composition at different levels.

TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT04122612.}, } @article {pmid32289594, year = {2020}, author = {Boullerne, AI and Adami, GR and Schwartz, JL and Skias, D and Maienschein-Cline, M and Green, SJ and Feinstein, DL}, title = {Deep DNA metagenomic sequencing reveals oral microbiome divergence between monozygotic twins discordant for multiple sclerosis severity.}, journal = {Journal of neuroimmunology}, volume = {343}, number = {}, pages = {577237}, pmid = {32289594}, issn = {1872-8421}, support = {I01 BX002625/BX/BLRD VA/United States ; IK6 BX004852/BX/BLRD VA/United States ; UL1 TR002003/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Demyelinating Diseases/*microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Microbiota ; Mouth/*microbiology ; Multiple Sclerosis, Relapsing-Remitting/*microbiology ; Twins, Monozygotic ; }, abstract = {In contrast to gut, the oral microbiome of MS patients has not been characterized. Deep sequencing of saliva DNA from a pair of monozygotic twins (MSF1 with relapsing remitting MS; MSF2 with clinically isolated syndrome) identified 2036 bacterial species. Relative abundances of 3 phyla were higher, and 3 lower in MSF1 versus MSF2. Species diversity was greater in MSF2, and 20 abundant species differed at least 2-fold. Pathway analysis identified 116 functional hierarchies differing 50% or more. Although limited to one pair of twins, our data suggests that oral microbiome analysis may be useful for diagnosis or monitoring therapeutic efficacy.}, } @article {pmid32286907, year = {2020}, author = {Wade, WG and Prosdocimi, EM}, title = {Profiling of Oral Bacterial Communities.}, journal = {Journal of dental research}, volume = {99}, number = {6}, pages = {621-629}, pmid = {32286907}, issn = {1544-0591}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R37 DE016937/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/classification ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota/genetics ; Mouth/*microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The profiling of bacterial communities by the sequencing of housekeeping genes such as that encoding the small subunit ribosomal RNA has revealed the extensive diversity of bacterial life on earth. Standard protocols have been developed and are widely used for this application, but individual habitats may require modification of methods. This review discusses the sequencing and analysis methods most appropriate for the study of the bacterial component of the human oral microbiota. If possible, DNA should be extracted from samples soon after collection. If samples have to be stored for practical reasons, precautions to avoid DNA degradation on freezing should be taken. A critical aspect of profiling oral bacterial communities is the choice of region of the 16S rRNA gene for sequencing. The V1-V2 region provides the best discrimination between species of the genus Streptococcus, the most common genus in the mouth and important in health and disease. The MiSeq platform is most commonly used for sequencing, but long-read technologies are now becoming available that should improve the resolution of analyses. There are a variety of well-established data analysis pipelines available, including mothur and QIIME, which identify sequence reads as phylotypes by comparing them to reference data sets or grouping them into operational taxonomic units. DADA2 has improved sequence error correction capabilities and resolves reads to unique variants. Two curated oral 16S rRNA databases are available: HOMD and CORE. Expert interpretation of community profiles is required, both to detect the presence of contaminating DNA, which is commonly present in the reagents used in analysis, and to differentiate oral and nonoral bacteria and determine the significance of findings. Despite advances in shotgun whole-genome metagenomic methods, oral bacterial community profiling via 16S rRNA sequence analysis remains a valuable technique for the characterization of oral bacterial populations.}, } @article {pmid32285557, year = {2020}, author = {Kobayashi, R and Nagaoka, K and Nishimura, N and Koike, S and Takahashi, E and Niimi, K and Murase, H and Kinjo, T and Tsukahara, T and Inoue, R}, title = {Comparison of the fecal microbiota of two monogastric herbivorous and five omnivorous mammals.}, journal = {Animal science journal = Nihon chikusan Gakkaiho}, volume = {91}, number = {1}, pages = {e13366}, pmid = {32285557}, issn = {1740-0929}, mesh = {Animals ; Bacteria/genetics/isolation & purification ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Mammals/*microbiology ; Metagenome ; RNA, Ribosomal, 16S ; }, abstract = {Fecal microbiota in seven different monogastric animal species, elephant, horse, human, marmoset, mouse, pig and, rat were compared using the same analytical protocol of 16S rRNA metagenome. Fecal microbiota in herbivores showed higher alpha diversity than omnivores except for pigs. Additionally, principal coordinate analysis based on weighted UniFrac distance demonstrated that herbivores and pigs clustered together, whereas other animal species were separately aggregated. In view of butyrate- and lactate-producing bacteria, predominant genera were different depending on animal species. For example, the abundance of Faecalibacterium, a known butyrate producer, was 8.02% ± 3.22% in human while it was less than 1% in other animal species. Additionally, Bifidobacterium was a predominant lactate producer in human and marmoset, while it was rarely detected in other omnivores. The abundance of lactate-producing bacteria in herbivores was notably lower than omnivores. On the other hand, herbivores as well as pig possess Fibrobacter, a cellulolytic bacterium. This study demonstrated that fecal microbiota in herbivorous animals is similar, sharing some common features such as higher alpha diversity and higher abundance of cellulolytic bacterium. On the other hand, omnivorous animals seem to possess unique fecal microbiota. It is of interest that pigs, although omnivore, have fecal microbiota showing some common features with herbivores.}, } @article {pmid32284564, year = {2020}, author = {Bittinger, K and Zhao, C and Li, Y and Ford, E and Friedman, ES and Ni, J and Kulkarni, CV and Cai, J and Tian, Y and Liu, Q and Patterson, AD and Sarkar, D and Chan, SHJ and Maranas, C and Saha-Shah, A and Lund, P and Garcia, BA and Mattei, LM and Gerber, JS and Elovitz, MA and Kelly, A and DeRusso, P and Kim, D and Hofstaedter, CE and Goulian, M and Li, H and Bushman, FD and Zemel, BS and Wu, GD}, title = {Bacterial colonization reprograms the neonatal gut metabolome.}, journal = {Nature microbiology}, volume = {5}, number = {6}, pages = {838-847}, pmid = {32284564}, issn = {2058-5276}, support = {UL1 TR001878/TR/NCATS NIH HHS/United States ; P30 DK050306/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; T32 CA009140/CA/NCI NIH HHS/United States ; R01 GM080279/GM/NIGMS NIH HHS/United States ; R01 DK107565/DK/NIDDK NIH HHS/United States ; }, mesh = {*Bacteria/classification/genetics ; Cohort Effect ; Computational Biology/methods ; Feces/microbiology ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Infant, Newborn ; Metabolome ; Metabolomics/methods ; Metagenomics/methods ; Phylogeny ; Proteomics/methods ; }, abstract = {Initial microbial colonization and later succession in the gut of human infants are linked to health and disease later in life. The timing of the appearance of the first gut microbiome, and the consequences for the early life metabolome, are just starting to be defined. Here, we evaluated the gut microbiome, proteome and metabolome in 88 African-American newborns using faecal samples collected in the first few days of life. Gut bacteria became detectable using molecular methods by 16 h after birth. Detailed analysis of the three most common species, Escherichia coli, Enterococcus faecalis and Bacteroides vulgatus, did not suggest a genomic signature for neonatal gut colonization. The appearance of bacteria was associated with reduced abundance of approximately 50 human proteins, decreased levels of free amino acids and an increase in products of bacterial fermentation, including acetate and succinate. Using flux balance modelling and in vitro experiments, we provide evidence that fermentation of amino acids provides a mechanism for the initial growth of E. coli, the most common early colonizer, under anaerobic conditions. These results provide a deep characterization of the first microbes in the human gut and show how the biochemical environment is altered by their appearance.}, } @article {pmid32284502, year = {2020}, author = {Bassi, D and Orrù, L and Cabanillas Vasquez, J and Cocconcelli, PS and Fontana, C}, title = {Peruvian chicha: A Focus on the Microbial Populations of This Ancient Maize-Based Fermented Beverage.}, journal = {Microorganisms}, volume = {8}, number = {1}, pages = {}, pmid = {32284502}, issn = {2076-2607}, abstract = {Peruvian chicha de jora is one of the most ancient traditional beverages produced through maize fermentation, still popular to modern consumers, but less studied in terms of microbial compositions. In this work, the bacterial biodiversity of 27 chicha samples collected from 14 different "chicherias" in seven provinces of Peru was investigated by Next-Generation Sequencing (NGS). A large dissimilarity in chicha microbial composition was a direct consequence of ingredients, manufacturing processes and geographical influences. The core microbiome was represented by six main genera, belonging to Lactic Acid Bacteria (LAB) and Acetic Acid Bacteria (AAB). Lactobacillus prevailed (more than 50% of sequences belong to this genus) followed by Weissella, Leuconostoc, Lactococcus and Streptococcus. Acetobacter was the only AAB genus identified in chicha. The occurrence of sequences associated to spoiling and pathogenic bacteria, such as Bacillus, Clostridium, and Enterobacteriaceae, was observed only in a few samples, validating the safety of this beverage. Predictive functional annotation of metagenomic sequences revealed that carbohydrate and amino acid metabolisms and coenzyme transport are the main KEGG categories associated to chicha fermentation pathways. The old recipes and traditional processing of each chicherias helps maintain native microorganisms as a resource of biodiversity with potential technological and health-beneficial properties.}, } @article {pmid32283670, year = {2020}, author = {Bolatti, EM and Zorec, TM and Montani, ME and Hošnjak, L and Chouhy, D and Viarengo, G and Casal, PE and Barquez, RM and Poljak, M and Giri, AA}, title = {A Preliminary Study of the Virome of the South American Free-Tailed Bats (Tadarida brasiliensis) and Identification of Two Novel Mammalian Viruses.}, journal = {Viruses}, volume = {12}, number = {4}, pages = {}, pmid = {32283670}, issn = {1999-4915}, mesh = {Animals ; Argentina ; Chiroptera/*virology ; Gene Order ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; Open Reading Frames ; Papillomaviridae/classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; *Virome ; Whole Genome Sequencing ; Workflow ; }, abstract = {Bats provide important ecosystem services as pollinators, seed dispersers, and/or insect controllers, but they have also been found harboring different viruses with zoonotic potential. Virome studies in bats distributed in Asia, Africa, Europe, and North America have increased dramatically over the past decade, whereas information on viruses infecting South American species is scarce. We explored the virome of Tadarida brasiliensis, an insectivorous New World bat species inhabiting a maternity colony in Rosario (Argentina), by a metagenomic approach. The analysis of five pooled oral/anal swab samples indicated the presence of 43 different taxonomic viral families infecting a wide range of hosts. By conventional nucleic acid detection techniques and/or bioinformatics approaches, the genomes of two novel viruses were completely covered clustering into the Papillomaviridae (Tadarida brasiliensis papillomavirus type 1, TbraPV1) and Genomoviridae (Tadarida brasiliensis gemykibivirus 1, TbGkyV1) families. TbraPV1 is the first papillomavirus type identified in this host and the prototype of a novel genus. TbGkyV1 is the first genomovirus reported in New World bats and constitutes a new species within the genus Gemykibivirus. Our findings extend the knowledge about oral/anal viromes of a South American bat species and contribute to understand the evolution and genetic diversity of the novel characterized viruses.}, } @article {pmid32282803, year = {2020}, author = {Dillon, ML and Hawes, I and Jungblut, AD and Mackey, TJ and Eisen, JA and Doran, PT and Sumner, DY}, title = {Environmental control on the distribution of metabolic strategies of benthic microbial mats in Lake Fryxell, Antarctica.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0231053}, pmid = {32282803}, issn = {1932-6203}, mesh = {Antarctic Regions ; Bacteria/classification/*genetics ; Carbon Cycle/genetics ; Geologic Sediments/microbiology ; Lakes/microbiology ; Metagenome/*genetics ; Microbiota/*genetics ; Oxygen/metabolism ; Photosynthesis/*genetics ; Phylogeny ; }, abstract = {Ecological theories posit that heterogeneity in environmental conditions greatly affects community structure and function. However, the degree to which ecological theory developed using plant- and animal-dominated systems applies to microbiomes is unclear. Investigating the metabolic strategies found in microbiomes are particularly informative for testing the universality of ecological theories because microorganisms have far wider metabolic capacity than plants and animals. We used metagenomic analyses to explore the relationships between the energy and physicochemical gradients in Lake Fryxell and the metabolic capacity of its benthic microbiome. Statistical analysis of the relative abundance of metabolic marker genes and gene family diversity shows that oxygenic photosynthesis, carbon fixation, and flavin-based electron bifurcation differentiate mats growing in different environmental conditions. The pattern of gene family diversity points to the likely importance of temporal environmental heterogeneity in addition to resource gradients. Overall, we found that the environmental heterogeneity of photosynthetically active radiation (PAR) and oxygen concentration ([O2]) in Lake Fryxell provide the framework by which metabolic diversity and composition of the community is structured, in accordance with its phylogenetic structure. The organization of the resulting microbial ecosystems are consistent with the maximum power principle and the species sorting model.}, } @article {pmid32281239, year = {2020}, author = {Schultz, D and Zühlke, D and Bernhardt, J and Francis, TB and Albrecht, D and Hirschfeld, C and Markert, S and Riedel, K}, title = {An optimized metaproteomics protocol for a holistic taxonomic and functional characterization of microbial communities from marine particles.}, journal = {Environmental microbiology reports}, volume = {12}, number = {4}, pages = {367-376}, doi = {10.1111/1758-2229.12842}, pmid = {32281239}, issn = {1758-2229}, support = {RI 969/9-1//Deutsche Forschungsgemeinschaft DFG - German Research Foundation/International ; }, mesh = {Bacteria/chemistry/*classification/genetics/*isolation & purification ; Bacterial Proteins/chemistry/genetics ; Chromatography, Liquid ; Eutrophication ; Metagenome ; *Microbiota ; North Sea ; Proteomics/*methods ; Seawater/microbiology ; Tandem Mass Spectrometry ; }, abstract = {This study aimed to establish a robust and reliable metaproteomics protocol for an in-depth characterization of marine particle-associated (PA) bacteria. To this end, we compared six well-established protein extraction protocols together with different MS-sample preparation techniques using particles sampled during a North Sea spring algae bloom in 2009. In the final optimized workflow, proteins are extracted using a combination of SDS-containing lysis buffer and cell disruption by bead-beating, separated by SDS-PAGE, in-gel digested and analysed by LC-MS/MS, before MASCOT search against a metagenome-based database and data processing/visualization with the in-house-developed bioinformatics tools Prophane and Paver. As an application example, free-living (FL) and particulate communities sampled in April 2009 were analysed, resulting in an as yet unprecedented number of 9354 and 5034 identified protein groups for FL and PA bacteria, respectively. Our data suggest that FL and PA communities appeared similar in their taxonomic distribution, with notable exceptions: eukaryotic proteins and proteins assigned to Flavobacteriia, Cyanobacteria, and some proteobacterial genera were found more abundant on particles, whilst overall proteins belonging to Proteobacteria were more dominant in the FL fraction. Furthermore, our data points to functional differences including proteins involved in polysaccharide degradation, sugar- and phosphorus uptake, adhesion, motility, and stress response.}, } @article {pmid32281049, year = {2020}, author = {Yimagou, EK and Baudoin, JP and Abdallah, RA and Di Pinto, F and Bou Khalil, JY and Raoult, D}, title = {Full-repertoire comparison of the microscopic objects composing the human gut microbiome with sequenced and cultured communities.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {58}, number = {5}, pages = {377-386}, pmid = {32281049}, issn = {1976-3794}, mesh = {*Bacteria/classification/ultrastructure ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; }, abstract = {The study of the human gut microbiome is essential in microbiology and infectious diseases as specific alterations in the gut microbiome might be associated with various pathologies, such as chronic inflammatory disease, intestinal infection and colorectal cancer. To identify such dysregulations, several strategies are being used to create a repertoire of the microorganisms composing the human gut microbiome. In this study, we used the "microscomics" approach, which consists of creating an ultrastructural repertoire of all the cell-like objects composing stool samples from healthy donors using transmission electron microscopy (TEM). We used TEM to screen ultrathin sections of 8 resin-embedded stool samples. After exploring hundreds of micrographs, we managed to elaborate ultrastructural categories based on morphological criteria or features. This approach explained many inconsistencies observed with other techniques, such as metagenomics and culturomics. We highlighted the value of our culture-independent approach by comparing our microscopic images to those of cultured bacteria and those reported in the literature. This study helped to detect "minimicrobes" Candidate Phyla Radiation (CPR) for the first time in human stool samples. This "microscomics" approach is non-exhaustive but complements already existing approaches and adds important data to the puzzle of the microbiota.}, } @article {pmid32279325, year = {2020}, author = {Bahram, M and Netherway, T and Hildebrand, F and Pritsch, K and Drenkhan, R and Loit, K and Anslan, S and Bork, P and Tedersoo, L}, title = {Plant nutrient-acquisition strategies drive topsoil microbiome structure and function.}, journal = {The New phytologist}, volume = {227}, number = {4}, pages = {1189-1199}, doi = {10.1111/nph.16598}, pmid = {32279325}, issn = {1469-8137}, support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Microbiota ; *Mycorrhizae ; Nutrients ; Soil ; Soil Microbiology ; }, abstract = {Plant nutrient-acquisition strategies drive soil processes and vegetation performance, but their effect on the soil microbiome remains poorly understood. This knowledge is important to predict the shifts in microbial diversity and functions due to increasing changes in vegetation traits under global change. Here we documented the topsoil microbiomes of 145 boreal and temperate terrestrial sites in the Baltic region that broadly differed in vegetation type and nutritional traits, such as mycorrhizal types and symbiotic nitrogen-fixation. We found that sites dominated by arbuscular mycorrhizal (AM) vegetation harbor relatively more AM fungi, bacteria, fungal saprotrophs, and pathogens in the topsoil compared with sites dominated by ectomycorrhizal (EM) plants. These differences in microbiome composition reflect the rapid nutrient cycling and negative plant-soil feedback in AM soils. Lower fungal diversity and bacteria : fungi ratios in EM-dominated habitats are driven by monodominance of woody vegetation as well as soil acidification by EM fungi, which are associated with greater diversity and relative abundance of carbohydrate-active enzymes. Our study suggests that shifts in vegetation related to global change and land use may strongly alter the topsoil microbiome structure and function.}, } @article {pmid32278134, year = {2020}, author = {Quadros, DL and Zanella, R and Bondan, C and Zanella, GC and Facioli, FL and da Silva, AN and Zanella, EL}, title = {Study of vaginal microbiota of Holstein cows submitted to an estrus synchronization protocol with the use of intravaginal progesterone device.}, journal = {Research in veterinary science}, volume = {131}, number = {}, pages = {1-6}, doi = {10.1016/j.rvsc.2020.03.027}, pmid = {32278134}, issn = {1532-2661}, mesh = {Administration, Intravaginal ; Animals ; *Cattle ; Estrus Synchronization/*methods ; Female ; Insemination, Artificial/veterinary ; Microbiota/*drug effects ; Progesterone/administration & dosage/*pharmacology ; Progestins/administration & dosage/pharmacology ; Reproduction ; Vagina/*microbiology ; }, abstract = {The characterization of vaginal microbiota will help to understand some of the reproductive problems and mechanisms to improve cattle reproduction. The objective of this study was to characterize the vaginal microbiota of cyclical Holstein cows with different parturition orders using 16S rDNA sequencing. Animals were submitted to an estrus synchronization protocol with the use of intravaginal progesterone (P4) implants and were treated or not with ceftiofur hydrochloride. DNA samples were extracted from vaginal swabs on day 0 and 10 of the synchronization, and sequenced with the Illumina MiSeq platform with an average coverage rate of 10.000 reads per samples using a Single-End library for fragments of 300 bp. The main bacterial phyla found in the vaginal tract of Holstein cows, were Firmicutes (37.61%), Tenericutes (29.45%), Proteobacteria (17.47%) and Bacteriodetes (13.73%), followed by Actinobacteria (0.82%) and Spirochaetae (0.45%). The use of intravaginal P4 devices has increased the relative abundance of the genera Family XIII AD3011 and Family XIII unclassified (p < .049). We have also observed an effect of the number of calving on the vaginal microbiota composition, showing that multiparous cows have a greater bacterial diversity than primiparous animals (p < .05). The use of ceftiofur hydrochloride was effective to reduce the vaginal bacteria proliferation. This study describes for the first time the vaginal microbiota of cows synchronized with intravaginal progesterone devices, different from the traditional methods such as microbiological culture and biochemical tests. We have identified a large number of microorganisms commonly found in the gastrointestinal tract of cows, colonizing the vaginal microbiota.}, } @article {pmid32275297, year = {2020}, author = {Simonin, M and Dasilva, C and Terzi, V and Ngonkeu, ELM and Diouf, D and Kane, A and Béna, G and Moulin, L}, title = {Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European soils.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {6}, pages = {}, doi = {10.1093/femsec/fiaa067}, pmid = {32275297}, issn = {1574-6941}, mesh = {France ; Fungi ; Genotype ; Italy ; *Microbiota ; Plant Roots ; *Rhizosphere ; Soil ; Soil Microbiology ; Triticum ; }, abstract = {Here, we assessed the relative influence of wheat genotype, agricultural practices (conventional vs organic) and soil type on the rhizosphere microbiome. We characterized the prokaryotic (archaea and bacteria) and eukaryotic (fungi and protists) communities in soils from four different countries (Cameroon, France, Italy, Senegal) and determined if a rhizosphere core microbiome existed across these different countries. The wheat genotype had a limited effect on the rhizosphere microbiome (2% of variance) as the majority of the microbial taxa were consistently associated to multiple wheat genotypes grown in the same soil. Large differences in taxa richness and in community structure were observed between the eight soils studied (57% variance) and the two agricultural practices (10% variance). Despite these differences between soils, we observed that 177 taxa (2 archaea, 103 bacteria, 41 fungi and 31 protists) were consistently detected in the rhizosphere, constituting a core microbiome. In addition to being prevalent, these core taxa were highly abundant and collectively represented 50% of the reads in our data set. Based on these results, we identify a list of key taxa as future targets of culturomics, metagenomics and wheat synthetic microbiomes. Additionally, we show that protists are an integral part of the wheat holobiont that is currently overlooked.}, } @article {pmid32273998, year = {2020}, author = {French, BJ and Lim, YW and Zgliczynski, BJ and Edwards, RA and Rohwer, F and Sandin, SA}, title = {Decoding diversity in a coral reef fish species complex with restricted range using metagenomic sequencing of gut contents.}, journal = {Ecology and evolution}, volume = {10}, number = {7}, pages = {3413-3423}, pmid = {32273998}, issn = {2045-7758}, abstract = {AIM: Identification of the processes that generate and maintain species diversity within the same region can provide insight into biogeographic patterns at broader spatiotemporal scales. Hawkfishes in the genus Paracirrhites are a unique taxon to explore with respect to niche differentiation, exhibiting diagnostic differences in coloration, and an apparent center of distribution outside of the Indo-Malay-Philippine (IMP) biodiversity hotspot for coral reef fishes. Our aim is to use next-generation sequencing methods to leverage samples of a taxon at their center of maximum diversity to explore phylogenetic relationships and a possible mechanism of coexistence.

LOCATION: Flint Island, Southern Line Islands, Republic of Kiribati.

METHODS: A comprehensive review of museum records, the primary literature, and unpublished field survey records was undertaken to determine ranges for four "arc-eye" hawkfish species in the Paracirrhites species complex and a potential hybrid. Fish from four Paracirrhites species were collected from Flint Island in the Southern Line Islands, Republic of Kiribati. Hindgut contents were sequenced, and subsequent metagenomic analyses were used to assess the phylogenetic relatedness of the host fish, the microbiome community structure, and prey remains for each species.

RESULTS: Phylogenetic analyses conducted with recovered mitochondrial genomes revealed clustering of P. bicolor with P. arcatus and P. xanthus with P. nisus, which were unexpected on the basis of previous morphological work in this species complex. Differences in taxonomic composition of gut microbial communities and presumed prey remains indicate likely separation of foraging niches.

MAIN CONCLUSIONS: Our findings point toward previously unidentified relationships in this cryptic species complex at its proposed center of distribution. The three species endemic to the Polynesian province (P. nisus, P. xanthus, and P. bicolor) cluster separately from the more broadly distributed P. arcatus on the basis of relative abundance of metazoan sequences in the gut (presumed prey remains). Discordance between gut microbial communities and phylogeny of the host fish further reinforce the hypothesis of niche separation.}, } @article {pmid32272146, year = {2020}, author = {Verma, SK and Sharma, PC}, title = {NGS-based characterization of microbial diversity and functional profiling of solid tannery waste metagenomes.}, journal = {Genomics}, volume = {112}, number = {4}, pages = {2903-2913}, doi = {10.1016/j.ygeno.2020.04.002}, pmid = {32272146}, issn = {1089-8646}, mesh = {Biodiversity ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Open Reading Frames ; Peptide Hydrolases/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Solid Waste ; *Tanning ; }, abstract = {Tanneries pose a serious threat to the environment by generating large amount of solid tannery waste (STW). Two metagenomes representing tannery waste dumpsites Jajmau (JJK) and Unnao (UNK) were sequenced using Illumina HiSeq platform. Microbial diversity analysis revealed domination of Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Planctomycetes in both metagenomes. Presence of pollutant degrading microbes such as Bacillus, Clostridium, Halanaerobium and Pseudomonas strongly indicated their bioremediation ability. KEGG and SEED annotated main functional categories included carbohydrate metabolism, amino acids metabolism, and protein metabolism. KEGG displayed 5848 and 9633 proteases encoding ORFs compared to 5159 and 8044 ORFs displayed by SEED classification in JJK and UNK metagenomes, respectively. Abundantly present serine- and metallo-proteases belonging to Bacillaceae, Clostridiaceae, Xanthomonadaceae, Flavobacteriaceae and Chitinophagaceae families exhibited proteinaceous waste degrading ability of these metagenomes. Further structural and functional analysis of metagenome encoded enzymes may facilitate the discovery of novel proteases useful in bioremediation of STW.}, } @article {pmid32271799, year = {2020}, author = {Brumfield, KD and Hasan, NA and Leddy, MB and Cotruvo, JA and Rashed, SM and Colwell, RR and Huq, A}, title = {A comparative analysis of drinking water employing metagenomics.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0231210}, pmid = {32271799}, issn = {1932-6203}, support = {R01 ES030317/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/genetics/pathogenicity ; Colony Count, Microbial ; DNA/genetics ; Drinking Water/*microbiology/*parasitology ; Genes, Bacterial ; *Metagenomics ; Microbiota/genetics ; Principal Component Analysis ; Virulence/genetics ; }, abstract = {The microbiological content of drinking water traditionally is determined by employing culture-dependent methods that are unable to detect all microorganisms, especially those that are not culturable. High-throughput sequencing now makes it possible to determine the microbiome of drinking water. Thus, the natural microbiota of water and water distribution systems can now be determined more accurately and analyzed in significantly greater detail, providing comprehensive understanding of the microbial community of drinking water applicable to public health. In this study, shotgun metagenomic analysis was performed to determine the microbiological content of drinking water and to provide a preliminary assessment of tap, drinking fountain, sparkling natural mineral, and non-mineral bottled water. Predominant bacterial species detected were members of the phyla Actinobacteria and Proteobacteria, notably the genera Alishewanella, Salmonella, and Propionibacterium in non-carbonated non-mineral bottled water, Methyloversatilis and Methylibium in sparkling natural mineral water, and Mycobacterium and Afipia in tap and drinking fountain water. Fecal indicator bacteria, i.e., Escherichia coli or enterococci, were not detected in any samples examined in this study. Bacteriophages and DNA encoding a few virulence-associated factors were detected but determined to be present only at low abundance. Antibiotic resistance markers were detected only at abundance values below our threshold of confidence. DNA of opportunistic plant and animal pathogens was identified in some samples and these included bacteria (Mycobacterium spp.), protozoa (Acanthamoeba mauritaniensis and Acanthamoeba palestinensis), and fungi (Melampsora pinitorqua and Chryosporium queenslandicum). Archaeal DNA (Candidatus Nitrosoarchaeum) was detected only in sparkling natural mineral water. This preliminary study reports the complete microbiome (bacteria, viruses, fungi, and protists) of selected types of drinking water employing whole-genome high-throughput sequencing and bioinformatics. Investigation into activity and function of the organisms detected is in progress.}, } @article {pmid32271249, year = {2020}, author = {Li, Y and Altan, E and Pilcher, C and Hartogensis, W and Hecht, FM and Deng, X and Delwart, E}, title = {Semen virome of men with HIV on or off antiretroviral treatment.}, journal = {AIDS (London, England)}, volume = {34}, number = {6}, pages = {827-832}, doi = {10.1097/QAD.0000000000002497}, pmid = {32271249}, issn = {1473-5571}, mesh = {Anelloviridae/isolation & purification ; Anti-HIV Agents/*therapeutic use ; Antiretroviral Therapy, Highly Active ; Blood/virology ; CD4 Lymphocyte Count ; Cytomegalovirus/isolation & purification ; DNA, Viral/genetics/isolation & purification ; Genotype ; HIV Infections/diagnosis/*drug therapy/*virology ; HIV-1/genetics/*isolation & purification ; Humans ; Male ; Metagenomics ; RNA, Viral ; San Francisco ; Semen/*virology ; *Virome ; Virus Shedding ; }, abstract = {OBJECTIVES: Improving immune status of people living with HIV through antiretroviral therapy (ART) may also reduce shedding of other viruses in semen. We characterized the seminal fluid virome of men with HIV and tested potential associations between viruses present and CD4 T-cell count, HIV viremia, and antiretroviral therapy (ART) status.

DESIGN AND METHODS: Metagenomics was used to enrich and sequence viral nucleic acids from the seminal fluid of 55 semen samples from 42 men living with HIV from San Francisco with a median age of 33 (IQR, 28.7-45) and median CD4 T-cell counts of 837 cells/μl (IQR, 258-1571 cells/μl). All samples were collected between 2005 and 2015, and ART status was ascertained from medical records.

RESULTS: Anelloviruses, cytomegalovirus (CMV), and multiple genotypes of human papillomaviruses were detected. Participants shed from 0 to 4 distinct human viruses. Longitudinally collected seminal fluid samples showed changes in the viruses shed. Viruses were more frequently shed by individuals with detectable HIV viremia (43.7 vs. 15.4%, P = 0.042). A trend was seen for increased shedding by individuals who were not on ART (42.8 vs. 17.8%, P = 0.082) or with CD4 T-cell count less than 350 cells/μl (35.3 vs. 20%, P = 0.27).

CONCLUSION: Seminal fluid from men with HIV from San Francisco contains nucleic acids from three different DNA viral families. A greater number of viruses, particularly CMV, were shed by participants with detectable HIV viremia (18.9 vs. 0%, P = 0.022). Control of viremia through ART may lower shedding of other viruses in semen in addition to HIV.}, } @article {pmid32270658, year = {2020}, author = {Ku, HJ and Kim, YT and Lee, JH}, title = {Microbiome Study of Initial Gut Microbiota from Newborn Infants to Children Reveals that Diet Determines Its Compositional Development.}, journal = {Journal of microbiology and biotechnology}, volume = {30}, number = {7}, pages = {1067-1071}, pmid = {32270658}, issn = {1738-8872}, mesh = {*Breast Feeding ; Child, Preschool ; *Diet ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Infant ; Infant, Newborn ; Klebsiella ; Male ; Milk, Human/*microbiology ; Serratia ; }, abstract = {To understand the formation of initial gut microbiota, three initial fecal samples were collected from two groups of two breast milk-fed (BM1) and seven formula milk-fed (FM1) infants, and the compositional changes in gut microbiota were determined using metagenomics. Compositional change analysis during week one showed that Bifidobacterium increased from the first to the third fecal samples in the BM1 group (1.3% to 35.1%), while Klebsiella and Serratia were detected in the third fecal sample of the FM1 group (4.4% and 34.2%, respectively), suggesting the beneficial effect of breast milk intake. To further understand the compositional changes during progression from infancy to childhood (i.e., from three weeks to five years of age), additional fecal samples were collected from four groups of two breast milk-fed infants (BM2), one formula milk-fed toddler (FM2), three weaning food-fed toddlers (WF), and three solid food-fed children (SF). Subsequent compositional change analysis and principal coordinates analysis (PCoA) revealed that the composition of the gut microbiota changed from an infant-like composition to an adult-like one in conjunction with dietary changes. Interestingly, overall gut microbiota composition analyses during the period of progression from infancy to childhood suggested increasing complexity of gut microbiota as well as emergence of a new species of bacteria capable of digesting complex carbohydrates in WF and SF groups, substantiating that diet type is a key factor in determining the composition of gut microbiota. Consequently, this study may be useful as a guide to understanding the development of initial gut microbiota based on diet.}, } @article {pmid32267865, year = {2020}, author = {Kaur, K and Khatri, I and Akhtar, A and Subramanian, S and Ramya, TNC}, title = {Metagenomics analysis reveals features unique to Indian distal gut microbiota.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0231197}, pmid = {32267865}, issn = {1932-6203}, mesh = {Adult ; Bifidobacterium/*genetics ; Body Mass Index ; Carbohydrate Metabolism/physiology ; DNA, Bacterial/genetics ; Diet ; Eating ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Healthy Volunteers ; Humans ; India ; Male ; Metagenomics/*methods ; Phylogeny ; Prevotella/*genetics ; Whole Genome Sequencing ; }, abstract = {Various factors including diet, age, geography, culture and socio-economic status have a role in determining the composition of the human gut microbiota. The human gut microbial composition is known to be altered in disease conditions. Considering the important role of the gut microbiome in maintaining homeostasis and overall health, it is important to understand the microbial diversity and the functional metagenome of the healthy gut. Here, we characterized the microbiota of 31 fecal samples from healthy individuals of Indian ethnic tribes from Ladakh, Jaisalmer and Khargone by shotgun metagenomic sequencing. Sequence analysis revealed that Bifidobacterium and Prevotella were the key microbes contributing to the differences among Jaisalmer, Khargone and Ladakh samples at the genus level. Our correlation network study identified carbohydrate-active enzymes and carbohydrate binding proteins that are associated with specific genera in the different Indian geographical regions studied. Network analysis of carbohydrate-active enzymes and genus abundance revealed that the presence of different carbohydrate-active enzymes is driven by differential abundance of genera. The correlation networks were different in the different geographical regions, and these interactions suggest the role of less abundant genera in shaping the gut environment. We compared our data with samples from different countries and found significant differences in taxonomic composition and abundance of carbohydrate-active enzymes in the gut microbiota as compared to the other countries.}, } @article {pmid32266563, year = {2020}, author = {Huan, Z and Yao, Y and Yu, J and Chen, H and Li, M and Yang, C and Zhao, B and Ni, Q and Zhang, M and Xie, M and Xu, H}, title = {Differences in the gut microbiota between Cercopithecinae and Colobinae in captivity.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {58}, number = {5}, pages = {367-376}, pmid = {32266563}, issn = {1976-3794}, mesh = {Animals ; Bacteria/*classification ; Biodiversity ; Cercopithecinae/*microbiology ; Colobinae/*microbiology ; Diet ; *Gastrointestinal Microbiome ; Metagenome ; }, abstract = {The gut microbiome of captive primates can provide a window into their health and disease status. The diversity and composition of gut microbiota are influenced by not only host phylogeny, but also host diet. Old World monkeys (Cercopithecidae) are divided into two subfamilies: Cercopithecinae and Colobinae. The diet and physiological digestive features differ between these two subfamilies. Accordingly, highthroughput sequencing was used to examine gut microbiota differences between these two subfamilies, using data from 29 Cercopithecinae individuals and 19 Colobinae individuals raised in captivity. Through a comparative analysis of operational taxonomic units (OTUs), significant differences in the diversity and composition of gut microbiota were observed between Cercopithecinae and Colobinae. In particular, the gut microbiota of captive Old World monkeys clustered strongly by the two subfamilies. The Colobinae microbial diversity was higher than that of Cercopithecinae. Additionally, Firmicutes, Lactobacillaceae, Veillonellaceae, and Prevotella abundance were higher in Cercopithecinae, while Bacteroidetes, Ruminococcaceae, Christensenellaceae, Bacteroidaceae, and Acidaminococcaceae abundance were higher in Colobinae. PICRUSt analysis revealed that the predicted metagenomes of metabolic pathways associated with proteins, carbohydrates, and amino acids were significantly higher in Colobinae. In the context of host phylogeny, these differences between Cercopithecinae and Colobinae could reflect adaptations associated with their respective diets. This well-organized dataset is a valuable resource for future related research on primates and gut microbiota. Moreover, this study may provide useful insight into animal management practices and primate conservation.}, } @article {pmid32266159, year = {2020}, author = {Arredondo-Hernández, R and Schmulson, M and Orduña, P and López-Leal, G and Zarate, AM and Alanis-Funes, G and Alcaraz, LD and Santiago-Cruz, R and Cevallos, MA and Villa, AR and Ponce-de-León Rosales, S and López-Vidal, Y and , }, title = {Mucosal Microbiome Profiles Polygenic Irritable Bowel Syndrome in Mestizo Individuals.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {72}, pmid = {32266159}, issn = {2235-2988}, mesh = {Adult ; Bacteria/*classification/genetics ; Brain/metabolism ; Colon/*microbiology ; Diet ; *Ethnicity/genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gene Frequency ; Humans ; Immunity/genetics ; Intestinal Mucosa/microbiology ; Irritable Bowel Syndrome/*genetics/*microbiology ; Male ; Metagenome ; Middle Aged ; *Multifactorial Inheritance ; Polymorphism, Single Nucleotide ; Young Adult ; }, abstract = {Irritable bowel syndrome (IBS) is the most frequent functional gastrointestinal disorder, worldwide, with a high prevalence among Mestizo Latin Americans. Because several inflammatory disorders appear to affect this population, a further understanding of host genomic background variants, in conjunction with colonic mucosa dysbiosis, is necessary to determine IBS physiopathology and the effects of environmental pressures. Using a simple polygenic model, host single nucleotide polymorphisms (SNPs) and the taxonomic compositions of microbiota were compared between IBS patients and healthy subjects. As proof of concept, five IBS-Rome III patients and five healthy controls (HCs) were systematically studied. The human and bacterial intestinal metagenome of each subject was taxonomically annotated and screened for previously annotated IBS, ulcerative colitis, and Crohn's disease-associated SNPs or taxon abundance. Dietary data and fecal markers were collected and associated with the intestinal microbiome. However, more than 1,000 variants were found, and at least 76 SNPs differentiated IBS patients from HCs, as did associations with 4 phyla and 10 bacterial genera. In this study, we found elements supporting a polygenic background, with frequent variants, among the Mestizo population, and the colonic mucosal enrichment of Bacteroides, Alteromonas, Neisseria, Streptococcus, and Microbacterium, may serve as a hallmark for IBS.}, } @article {pmid32265914, year = {2020}, author = {Pan, X and Zhang, D and Nguyen, DN and Wei, W and Yu, X and Gao, F and Sangild, PT}, title = {Postnatal Gut Immunity and Microbiota Development Is Minimally Affected by Prenatal Inflammation in Preterm Pigs.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {420}, pmid = {32265914}, issn = {1664-3224}, mesh = {Animals ; Animals, Newborn ; *Chorioamnionitis ; Female ; Gastrointestinal Microbiome/*physiology ; Inflammation/immunology/microbiology ; Intestines/*immunology/*microbiology ; Pregnancy ; Premature Birth ; Swine ; }, abstract = {Chorioamnionitis (CA), resulting from intra-amniotic inflammation, is a frequent cause of preterm birth and exposes the immature intestine to bacterial toxins and/or inflammatory mediators before birth via fetal swallowing. This may affect intestinal immune development, interacting with the effects of enteral feeding and gut microbiota colonization just after birth. Using preterm pigs as model for preterm infants, we hypothesized that prenatal exposure to gram-negative endotoxin influences postnatal bacterial colonization and gut immune development. Pig fetuses were given intra-amniotic lipopolysaccharide (LPS) 3 days before preterm delivery by cesarean section and were compared with littermate controls (CON) at birth and after 5 days of formula feeding and spontaneous bacterial colonization. Amniotic fluid was collected for analysis of leukocyte counts and cytokines, and the distal small intestine was analyzed for endotoxin level, morphology, and immune cell counts. Intestinal gene expression and microbiota were analyzed by transcriptomics and metagenomics, respectively. At birth, LPS-exposed pigs showed higher intestinal endotoxin, neutrophil/macrophage density, and shorter villi. About 1.0% of intestinal genes were affected at birth, and DMBT1, a regulator of mucosal immune defense, was identified as the hub gene in the co-expression network. Genes related to innate immune response (TLR2, LBP, CD14, C3, SFTPD), neutrophil chemotaxis (C5AR1, CSF3R, CCL5), and antigen processing (MHC II genes and CD4) were also affected, and expression levels correlated with intestinal neutrophil/macrophage density and amniotic fluid cytokine levels. On day 5, LPS and CON pigs showed similar sensitivity to necrotizing enterocolitis, endotoxin levels, morphology, immune cell counts, gene expressions, and microbiota composition (except for difference in some low-abundant species). Our results show that CA markedly affects intestinal genes at preterm birth, including genes related to immune cell infiltration. However, a few days later, following the physiological adaptations to preterm birth, CA had limited effects on intestinal structure, function, gene expression, bacterial colonization, and necrotizing enterocolitis sensitivity. We conclude that short-term, prenatal intra-amniotic inflammation is unlikely to exert marked effects on intestinal immune development in preterm neonates beyond the immediate neonatal period.}, } @article {pmid32265336, year = {2020}, author = {Déjean, G and Tamura, K and Cabrera, A and Jain, N and Pudlo, NA and Pereira, G and Viborg, AH and Van Petegem, F and Martens, EC and Brumer, H}, title = {Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides.}, journal = {mBio}, volume = {11}, number = {2}, pages = {}, pmid = {32265336}, issn = {2150-7511}, support = {P41 GM103393/GM/NIGMS NIH HHS/United States ; R01 DK118024/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacterial Proteins/metabolism ; Bacteroides/*enzymology ; Carrier Proteins/*metabolism ; Cell Membrane/enzymology ; Cohort Studies ; Crystallography, X-Ray ; *Dietary Fiber ; Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Glycoside Hydrolases/*metabolism ; Humans ; Substrate Specificity ; beta-Glucans/*metabolism ; }, abstract = {The human gut microbiota (HGM) has far-reaching impacts on human health and nutrition, which are fueled primarily by the metabolism of otherwise indigestible complex carbohydrates commonly known as dietary fiber. However, the molecular basis of the ability of individual taxa of the HGM to address specific dietary glycan structures remains largely unclear. In particular, the utilization of β(1,3)-glucans, which are widespread in the human diet as yeast, seaweed, and plant cell walls, had not previously been resolved. Through a systems-based approach, here we show that the symbiont Bacteroides uniformis deploys a single, exemplar polysaccharide utilization locus (PUL) to access yeast β(1,3)-glucan, brown seaweed β(1,3)-glucan (laminarin), and cereal mixed-linkage β(1,3)/β(1,4)-glucan. Combined biochemical, enzymatic, and structural analysis of PUL-encoded glycoside hydrolases (GHs) and surface glycan-binding proteins (SGBPs) illuminates a concerted molecular system by which B. uniformis recognizes and saccharifies these distinct β-glucans. Strikingly, the functional characterization of homologous β(1,3)-glucan utilization loci (1,3GUL) in other Bacteroides further demonstrated that the ability of individual taxa to utilize β(1,3)-glucan variants and/or β(1,3)/β(1,4)-glucans arises combinatorially from the individual specificities of SGBPs and GHs at the cell surface, which feed corresponding signals to periplasmic hybrid two-component sensors (HTCSs) via TonB-dependent transporters (TBDTs). These data reveal the importance of cooperativity in the adaptive evolution of GH and SGBP cohorts to address individual polysaccharide structures. We anticipate that this fine-grained knowledge of PUL function will inform metabolic network analysis and proactive manipulation of the HGM. Indeed, a survey of 2,441 public human metagenomes revealed the international, yet individual-specific, distribution of each 1,3GUL.IMPORTANCEBacteroidetes are a dominant phylum of the human gut microbiota (HGM) that target otherwise indigestible dietary fiber with an arsenal of polysaccharide utilization loci (PULs), each of which is dedicated to the utilization of a specific complex carbohydrate. Here, we provide novel insight into this paradigm through functional characterization of homologous PULs from three autochthonous Bacteroides species, which target the family of dietary β(1,3)-glucans. Through detailed biochemical and protein structural analysis, we observed an unexpected diversity in the substrate specificity of PUL glycosidases and glycan-binding proteins with regard to β(1,3)-glucan linkage and branching patterns. In combination, these individual enzyme and protein specificities support taxon-specific growth on individual β(1,3)-glucans. This detailed metabolic insight, together with a comprehensive survey of individual 1,3GULs across human populations, further expands the fundamental roadmap of the HGM, with potential application to the future development of microbial intervention therapies.}, } @article {pmid32265327, year = {2020}, author = {Malki, K and Rosario, K and Sawaya, NA and Székely, AJ and Tisza, MJ and Breitbart, M}, title = {Prokaryotic and Viral Community Composition of Freshwater Springs in Florida, USA.}, journal = {mBio}, volume = {11}, number = {2}, pages = {}, pmid = {32265327}, issn = {2150-7511}, mesh = {Bacteria/*classification ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Viral/genetics ; Ecosystem ; Florida ; Fresh Water/microbiology/virology ; *Metagenome ; Natural Springs/*microbiology/*virology ; Phylogeny ; Sequence Analysis, DNA ; Viruses/*classification ; }, abstract = {Aquifers, which are essential underground freshwater reservoirs worldwide, are understudied ecosystems that harbor diverse forms of microbial life. This study investigated the abundance and composition of prokaryotic and viral communities in the outflow of five springs across northern Florida, USA, as a proxy of microbial communities found in one of the most productive aquifers in the world, the Floridan aquifer. The average abundances of virus-like particles and prokaryotic cells were slightly lower than those reported from other groundwater systems, ranging from 9.6 × 10[3] ml[-1] to 1.1 × 10[5] ml[-1] and 2.2 × 10[3] ml[-1] to 3.4 × 10[4] ml[-1], respectively. Despite all of the springs being fed by the Floridan aquifer, sequencing of 16S rRNA genes and viral metagenomes (viromes) revealed unique communities in each spring, suggesting that groundwater microbial communities are influenced by land usage in recharge zones. The prokaryotic communities were dominated by Bacteria, and though the most abundant phyla (Proteobacteria, Cyanobacteria, and Bacteroidetes) were found in relatively high abundance across springs, variation was seen at finer taxonomic resolution. The viral sequences were most similar to those described from other aquatic environments. Sequencing resulted in the completion of 58 novel viral genomes representing members of the order Caudovirales as well as prokaryotic and eukaryotic single-stranded DNA (ssDNA) viruses. Sequences similar to those of ssDNA viruses were detected at all spring sites and dominated the identifiable sequences at one spring site, showing that these small viruses merit further investigation in groundwater systems.IMPORTANCE Aquifer systems may hold up to 40% of the total microbial biomass on Earth. However, little is known about the composition of microbial communities within these critical freshwater ecosystems. Here, we took advantage of Florida's first-magnitude springs (the highest spring classification based on water discharge), each discharging at least 246 million liters of water each day from the Floridan aquifer system (FAS), to investigate prokaryotic and viral communities from the aquifer. The FAS serves as a major source of potable water in the Southeastern United States, providing water for large cities and citizens in three states. Unfortunately, the health of the FAS and its associated springs has declined in the past few decades due to nutrient loading, increased urbanization and agricultural activity in aquifer recharge zones, and saltwater intrusion. This is the first study to describe the prokaryotic and viral communities in Florida's first-magnitude springs, providing a baseline against which to compare future ecosystem change.}, } @article {pmid32259760, year = {2020}, author = {An, X and Chen, Y and Chen, G and Feng, L and Zhang, Q}, title = {Integrated metagenomic and metaproteomic analyses reveal potential degradation mechanism of azo dye-Direct Black G by thermophilic microflora.}, journal = {Ecotoxicology and environmental safety}, volume = {196}, number = {}, pages = {110557}, doi = {10.1016/j.ecoenv.2020.110557}, pmid = {32259760}, issn = {1090-2414}, mesh = {Azo Compounds/*analysis ; Biodegradation, Environmental ; Ecosystem ; Gene Expression Profiling ; Gene Library ; Gene Ontology ; Metagenome/*genetics ; Metagenomics ; Microbiota/*genetics ; Proteome/*genetics ; Water Pollutants, Chemical/*analysis ; }, abstract = {Direct Black G (DBG) is a typical toxic azo dye with extensive applications but it poses a serious threat to the aquatic ecosystem and humans. It is necessary to efficiently and safely remove DBG from environments by the application of various treatment technologies. A thermophilic microflora previously isolated from the soil can effectively metabolize DBG. However, the molecular basis of DBG degradation by this thermophilic microflora remains unknown. In this study, metagenomic sequencing technology and qRT-PCR have been used to elucidate the functional potential of genes and their modes of action on DBG. A quantitative metaproteomic method was further utilized to identify the relative functional proteins involved. Subsequently, the possible co-metabolic molecular mechanisms of DBG degradation by candidate genes and functional proteins of the thermophilic microflora were illustrated. The combination of metagenomics and metaproteomics to investigate the degradation of DBG by a microflora was reported for the first time in recent literature; this can further provide a deep insight into the molecular degradation mechanism of dye pollutants by natural microflora.}, } @article {pmid32256492, year = {2020}, author = {Okamura, Y and Morimoto, N and Ikeda, D and Mizusawa, N and Watabe, S and Miyanishi, H and Saeki, Y and Takeyama, H and Aoki, T and Kinoshita, M and Kono, T and Sakai, M and Hikima, JI}, title = {Interleukin-17A/F1 Deficiency Reduces Antimicrobial Gene Expression and Contributes to Microbiome Alterations in Intestines of Japanese medaka (Oryzias latipes).}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {425}, pmid = {32256492}, issn = {1664-3224}, mesh = {Animals ; Fish Proteins/*immunology ; Gastrointestinal Microbiome/*immunology ; Gene Expression ; Immunity, Mucosal/*immunology ; Interleukin-17/deficiency/*immunology ; Oryzias/*immunology ; }, abstract = {In mammals, interleukin (IL)-17A and F are hallmark inflammatory cytokines that play key roles in protection against infection and intestinal mucosal immunity. In the gastrointestinal tract (GI), the induction of antimicrobial peptide (AMP) production via Paneth cells is a fundamental role of IL-17A and F in maintaining homeostasis of the GI microbiome and health. Although mammalian IL-17A and F homologs (referred to as IL-17A/F1-3) have been identified in several fish species, their function in the intestine is poorly understood. Additionally, the fish intestine lacks Paneth cells, and its GI structure is very different from that of mammals. Therefore, the GI microbiome modulatory mechanism via IL-17A/F genes has not been fully elucidated. In this study, Japanese medaka (Oryzias latipes) were used as a teleost model, and IL-17A/F1-knockout (IL-17A/F1-KO) medaka were established using the CRISPR/Cas9 genome editing technique. Furthermore, two IL-17A/F1-deficient medaka strains were generated, including one strain containing a 7-bp deletion (-7) and another with an 11-bp addition (+11). After establishing F2 homozygous KO medaka, transcriptome analysis (RNA-seq) was conducted to elucidate IL-17A/F1-dependent gene induction in the intestine. Results of RNA-seq and real-time PCR (qPCR) demonstrated down-regulation of immune-related genes, including interleukin-1β (IL-1β), complement 1q subunit C (C1qc), transferrin a (Tfa), and G-type lysozyme (LyzG), in IL-17A/F1-KO medaka. Interestingly, protein and lipid digestive enzyme genes, including phospholipase A2, group IB (pla2g1b), and elastase-1-like (CELA1), were also downregulated in the intestines of IL-17A/F1-KO medaka. Furthermore, to reveal the influence of these downregulated genes on the gut microbiome in IL-17A/F1-KO, 16S rRNA-based metagenomic sequencing analysis was conducted to analyze the microbiome constitution. Under a non-exposed state, the intestinal microbiome of IL-17A/F1-KO medaka differed at the phylum level from wild-type, with significantly higher levels of Verrucomicrobia and Planctomycetes. Additionally, at the operational taxonomic unit (OTU) level of the human and fish pathogens, the Enterobacteriaceae Plesiomonas shigelloides was the dominant species in IL-17A/F1-KO medaka. These findings suggest that IL-17A/F1 is involved in the maintenance of a healthy gut microbiome.}, } @article {pmid32255488, year = {2021}, author = {McGovern, BH and Ford, CB and Henn, MR and Pardi, DS and Khanna, S and Hohmann, EL and O'Brien, EJ and Desjardins, CA and Bernardo, P and Wortman, JR and Lombardo, MJ and Litcofsky, KD and Winkler, JA and McChalicher, CWJ and Li, SS and Tomlinson, AD and Nandakumar, M and Cook, DN and Pomerantz, RJ and Auninš, JG and Trucksis, M}, title = {SER-109, an Investigational Microbiome Drug to Reduce Recurrence After Clostridioides difficile Infection: Lessons Learned From a Phase 2 Trial.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {72}, number = {12}, pages = {2132-2140}, pmid = {32255488}, issn = {1537-6591}, mesh = {Aged ; Clostridioides ; *Clostridioides difficile ; *Clostridium Infections/drug therapy/prevention & control ; Drugs, Investigational ; Female ; Humans ; Male ; *Microbiota ; Recurrence ; }, abstract = {BACKGROUND: Recurrent Clostridioides difficile infection (rCDI) is associated with loss of microbial diversity and microbe-derived secondary bile acids, which inhibit C. difficile germination and growth. SER-109, an investigational microbiome drug of donor-derived, purified spores, reduced recurrence in a dose-ranging, phase (P) 1 study in subjects with multiple rCDIs.

METHODS: In a P2 double-blind trial, subjects with clinical resolution on standard-of-care antibiotics were stratified by age (< or ≥65 years) and randomized 2:1 to single-dose SER-109 or placebo. Subjects were diagnosed at study entry by PCR or toxin testing. Safety, C. difficile-positive diarrhea through week 8, SER-109 engraftment, and bile acid changes were assessed.

RESULTS: 89 subjects enrolled (67% female; 80.9% diagnosed by PCR). rCDI rates were lower in the SER-109 arm than placebo (44.1% vs 53.3%) but did not meet statistical significance. In a preplanned analysis, rates were reduced among subjects ≥65 years (45.2% vs 80%, respectively; RR, 1.77; 95% CI, 1.11-2.81), while the <65 group showed no benefit. Early engraftment of SER-109 was associated with nonrecurrence (P < .05) and increased secondary bile acid concentrations (P < .0001). Whole-metagenomic sequencing from this study and the P1 study revealed previously unappreciated dose-dependent engraftment kinetics and confirmed an association between early engraftment and nonrecurrence. Engraftment kinetics suggest that P2 dosing was suboptimal. Adverse events were generally mild to moderate in severity.

CONCLUSIONS: Early SER-109 engraftment was associated with reduced CDI recurrence and favorable safety was observed. A higher dose of SER-109 and requirements for toxin testing were implemented in the current P3 trial.

CLINICAL TRIALS REGISTRATION: NCT02437487, https://clinicaltrials.gov/ct2/show/NCT02437487?term=SER-109&draw= 2&rank=4.}, } @article {pmid32252812, year = {2020}, author = {Zhou, Y and Coventry, DR and Gupta, VVSR and Fuentes, D and Merchant, A and Kaiser, BN and Li, J and Wei, Y and Liu, H and Wang, Y and Gan, S and Denton, MD}, title = {The preceding root system drives the composition and function of the rhizosphere microbiome.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {89}, pmid = {32252812}, issn = {1474-760X}, mesh = {Cicer/microbiology ; Genes, Microbial ; Metagenome ; Metagenomics ; *Microbiota ; Molecular Sequence Annotation ; Plant Roots/growth & development/microbiology ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; Symbiosis ; Triticum/microbiology ; }, abstract = {BACKGROUND: The soil environment is responsible for sustaining most terrestrial plant life, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere, and how it responds to agricultural management such as crop rotations and soil tillage, is vital for improving global food production.

RESULTS: This study establishes an in-depth soil microbial gene catalogue based on the living-decaying rhizosphere niches in a cropping soil. The detritusphere microbiome regulates the composition and function of the rhizosphere microbiome to a greater extent than plant type: rhizosphere microbiomes of wheat and chickpea were homogenous (65-87% similarity) in the presence of decaying root (DR) systems but were heterogeneous (3-24% similarity) where DR was disrupted by tillage. When the microbiomes of the rhizosphere and the detritusphere interact in the presence of DR, there is significant degradation of plant root exudates by the rhizosphere microbiome, and genes associated with membrane transporters, carbohydrate and amino acid metabolism are enriched.

CONCLUSIONS: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the detritusphere microbiome in determining the metagenome of developing root systems. Modifications in root microbial function through soil management can ultimately govern plant health, productivity and food security.}, } @article {pmid32251667, year = {2020}, author = {Pickert, G and Wirtz, S and Matzner, J and Ashfaq-Khan, M and Heck, R and Rosigkeit, S and Thies, D and Surabattula, R and Ehmann, D and Wehkamp, J and Aslam, M and He, G and Weigert, A and Foerster, F and Klotz, L and Frick, JS and Becker, C and Bockamp, E and Schuppan, D}, title = {Wheat Consumption Aggravates Colitis in Mice via Amylase Trypsin Inhibitor-mediated Dysbiosis.}, journal = {Gastroenterology}, volume = {159}, number = {1}, pages = {257-272.e17}, doi = {10.1053/j.gastro.2020.03.064}, pmid = {32251667}, issn = {1528-0012}, mesh = {Animal Feed/adverse effects ; Animals ; Colitis/chemically induced/diagnosis/*immunology/microbiology ; Dextran Sulfate/toxicity ; Disease Models, Animal ; Dysbiosis/complications/diagnosis/*immunology/microbiology ; Fecal Microbiota Transplantation ; Feces/microbiology ; Gastrointestinal Microbiome/immunology ; Humans ; Immunity, Innate ; Inflammatory Bowel Diseases/chemically induced/diagnosis/*immunology/microbiology ; Male ; Mice ; Mice, Knockout ; Plant Proteins, Dietary/*adverse effects/immunology ; Severity of Illness Index ; Signal Transduction/genetics/immunology ; Toll-Like Receptor 4/genetics/metabolism ; Triticum/*immunology ; Trypsin Inhibitors/adverse effects/immunology ; }, abstract = {BACKGROUND & AIMS: Wheat has become the world's major staple and its consumption correlates with prevalence of noncommunicable disorders such as inflammatory bowel diseases. Amylase trypsin inhibitors (ATIs), a component of wheat, activate the intestine's innate immune response via toll-like receptor 4 (TLR4). We investigated the effects of wheat and ATIs on severity of colitis and fecal microbiota in mice.

METHODS: C57BL/6 wild-type and Tlr4[-/-] mice were fed wheat- or ATI-containing diets or a wheat-free (control) diet and then given dextran sodium sulfate to induce colitis; we also studied Il10[-/-] mice, which develop spontaneous colitis. Changes in fecal bacteria were assessed by taxa-specific quantitative polymerase chain reaction and 16S ribosomal RNA metagenomic sequencing. Feces were collected from mice on wheat-containing, ATI-containing, control diets and transplanted to intestines of mice with and without colitis on control or on ATI-containing diets. Intestinal tissues were collected and analyzed by histology, immunohistochemistry, and flow cytometry. Bacteria with reported immunomodulatory effects were incubated with ATIs and analyzed in radial diffusion assays.

RESULTS: The wheat- or ATI-containing diets equally increased inflammation in intestinal tissues of C57BL/6 mice with colitis, compared with mice on control diets. The ATI-containing diet promoted expansion of taxa associated with development of colitis comparable to the wheat-containing diet. ATIs inhibited proliferation of specific human commensal bacteria in radial diffusion assays. Transplantation of microbiota from feces of mice fed the wheat- or ATI-containing diets to intestines of mice on control diets increased the severity of colitis in these mice. The ATI-containing diet did not increase the severity of colitis in Tlr4[-/-] mice.

CONCLUSIONS: Consumption of wheat or wheat ATIs increases intestinal inflammation in mice with colitis, via TLR4, and alters their fecal microbiota. Wheat-based, ATI-containing diets therefore activate TLR4 signaling and promote intestinal dysbiosis.}, } @article {pmid32251665, year = {2020}, author = {Kappel, BA and De Angelis, L and Heiser, M and Ballanti, M and Stoehr, R and Goettsch, C and Mavilio, M and Artati, A and Paoluzi, OA and Adamski, J and Mingrone, G and Staels, B and Burcelin, R and Monteleone, G and Menghini, R and Marx, N and Federici, M}, title = {Cross-omics analysis revealed gut microbiome-related metabolic pathways underlying atherosclerosis development after antibiotics treatment.}, journal = {Molecular metabolism}, volume = {36}, number = {}, pages = {100976}, pmid = {32251665}, issn = {2212-8778}, mesh = {Aged ; Animals ; Anti-Bacterial Agents/metabolism/pharmacology ; Atherosclerosis/*metabolism/*microbiology ; Bacteria/genetics ; Cecum/microbiology ; Disease Progression ; Feces ; Female ; Gastrointestinal Microbiome/drug effects/*genetics ; Humans ; Male ; Metabolic Networks and Pathways ; Metabolome ; Metabolomics/methods ; Mice ; Mice, Knockout, ApoE ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Serum/chemistry ; }, abstract = {OBJECTIVE: The metabolic influence of gut microbiota plays a pivotal role in the pathogenesis of cardiometabolic diseases. Antibiotics affect intestinal bacterial diversity, and long-term usage has been identified as an independent risk factor for atherosclerosis-driven events. The aim of this study was to explore the interaction between gut dysbiosis by antibiotics and metabolic pathways with the impact on atherosclerosis development.

METHODS: We combined oral antibiotics with different diets in an Apolipoprotein E-knockout mouse model linking gut microbiota to atherosclerotic lesion development via an integrative cross-omics approach including serum metabolomics and cecal 16S rRNA targeted metagenomic sequencing. We further investigated patients with carotid atherosclerosis compared to control subjects with comparable cardiovascular risk.

RESULTS: Here, we show that increased atherosclerosis by antibiotics was connected to a loss of intestinal diversity and alterations of microbial metabolic functional capacity with a major impact on the host serum metabolome. Pathways that were modulated by antibiotics and connected to atherosclerosis included diminished tryptophan and disturbed lipid metabolism. These pathways were related to the reduction of certain members of Bacteroidetes and Clostridia by antibiotics in the gut. Patients with atherosclerosis presented a similar metabolic signature as those induced by antibiotics in our mouse model.

CONCLUSION: Taken together, this work provides insights into the complex interaction between intestinal microbiota and host metabolism. Our data highlight that detrimental effects of antibiotics on the gut flora are connected to a pro-atherogenic metabolic phenotype beyond classical risk factors.}, } @article {pmid32251334, year = {2020}, author = {Baskaran, V and Patil, PK and Antony, ML and Avunje, S and Nagaraju, VT and Ghate, SD and Nathamuni, S and Dineshkumar, N and Alavandi, SV and Vijayan, KK}, title = {Microbial community profiling of ammonia and nitrite oxidizing bacterial enrichments from brackishwater ecosystems for mitigating nitrogen species.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {5201}, pmid = {32251334}, issn = {2045-2322}, mesh = {Ammonia/*metabolism/pharmacology ; Autotrophic Processes ; Bacteria/classification/drug effects/*isolation & purification/metabolism ; Heterotrophic Processes ; Metabolic Networks and Pathways ; Metagenome ; *Microbiota ; *Nitrification ; Nitrites/*metabolism/pharmacology ; Nitrogen Cycle ; Oxidation-Reduction ; Ribotyping ; *Saline Waters ; Species Specificity ; *Water Microbiology ; }, abstract = {Nitrogen species such as ammonia and nitrite are considered as major stressors in modern aquaculture practices. We developed enrichments of ammonia oxidising bacteria (AOB) and nitrite oxidising bacteria (NOB) for effective mitigation of nitrogenous wastes in the shrimp culture operations. The objective of this study was to understand the microbial community composition of AOB and NOB enrichments using the V3-V4 region of the 16S rDNA gene by Illumina MiSeq sequencing. The analysis revealed 2948 and 1069 OTUs at 97% similarity index and Shannon alpha diversity index of 7.64 and 4.85 for AOB and NOB enrichments, respectively. Comparative analysis showed that a total of 887 OTUs were common among AOB and NOB enrichments. The AOB and NOB enrichment were dominated by Eubacteria at 96% and 99.7% respectively. Proteobacterial phylum constituted 31.46% (AOB) and 39.75% (NOB) and dominated by α-Proteobacteria (20%) in AOB and γ-Proteobacteria (16%) in NOB. Among the species in AOB enrichment (2,948) two sequences were assigned to ammonia oxidising bacterial group belonging to Nitrosomonas, and Nitrosococcus genera and two belonged to archaeon group comprising Nitrosopumilus and Candidatus Nitrososphaeraea genera. The NOB enrichment was predominated by Nitrospiraceae and Thermodesulfovibrionaceae. Further, the data revealed the presence of heterotrophic bacteria contributing to the process of nitrification and form microcosm with the AOB and NOB. PICRUSt analysis predicted the presence of 24 different nitrogen cycling genes involved in nitrification, denitrification, ammonia and nitrogen transporter family, nitrate reduction and ammonia assimilation. The study confirms the presence of many lesser known nitrifying bacteria along with well characterised nitrifiers.}, } @article {pmid32250964, year = {2020}, author = {Byrd, DA and Sinha, R and Hoffman, KL and Chen, J and Hua, X and Shi, J and Chia, N and Petrosino, J and Vogtmann, E}, title = {Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing.}, journal = {mSphere}, volume = {5}, number = {1}, pages = {}, pmid = {32250964}, issn = {2379-5042}, support = {P42 ES010349/ES/NIEHS NIH HHS/United States ; R01 CA179243/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; DNA, Bacterial ; Ethanol ; Feces/*microbiology ; Female ; Freezing ; Gastrointestinal Microbiome/*genetics ; Healthy Volunteers ; Humans ; Male ; *Metagenome ; Metagenomics/*methods ; Middle Aged ; Preservation, Biological/methods ; RNA, Ribosomal, 16S/genetics ; Specimen Handling/*methods ; Temperature ; *Whole Genome Sequencing ; }, abstract = {Few previous studies have assessed stability and "gold-standard" concordance of fecal sample collection methods for whole-genome shotgun metagenomic sequencing (WGSS), an increasingly popular method for studying the gut microbiome. We used WGSS data to investigate ambient temperature stability and putative gold-standard concordance of microbial profiles in fecal samples collected and stored using fecal occult blood test (FOBT) cards, fecal immunochemical test (FIT) tubes, 95% ethanol, or RNAlater. Among 15 Mayo Clinic employees, for each collection method, we calculated intraclass correlation coefficients (ICCs) to estimate stability of fecal microbial profiles after storage for 4 days at ambient temperature and concordance with immediately frozen, no-solution samples (i.e., the putative gold standard). ICCs were estimated for multiple metrics, including relative abundances of select phyla, species, KEGG k-genes (representing any coding sequence that had >70% identity and >70% query coverage with respect to a known KEGG ortholog), KEGG modules, and KEGG pathways; species and k-gene alpha diversity; and Bray-Curtis and Jaccard species beta diversity. ICCs for microbial profile stability were excellent (≥90%) for fecal samples collected via most of the collection methods, except those preserved in 95% ethanol. Concordance with the immediately frozen, no-solution samples varied for all collection methods, but the number of observed species and the beta diversity metrics tended to have higher concordance than other metrics. Our findings, taken together with previous studies and feasibility considerations, indicated that FOBT cards, FIT tubes, and RNAlater are acceptable choices for fecal sample collection methods in future WGSS studies.IMPORTANCE A major direction for future microbiome research is implementation of fecal sample collections in large-scale, prospective epidemiologic studies. Studying microbiome-disease associations likely requires microbial data to be pooled from multiple studies. Our findings suggest collection methods that are most optimal to be used standardly across future WGSS microbiome studies.}, } @article {pmid32249550, year = {2020}, author = {Sabuda, MC and Brazelton, WJ and Putman, LI and McCollom, TM and Hoehler, TM and Kubo, MDY and Cardace, D and Schrenk, MO}, title = {A dynamic microbial sulfur cycle in a serpentinizing continental ophiolite.}, journal = {Environmental microbiology}, volume = {22}, number = {6}, pages = {2329-2345}, doi = {10.1111/1462-2920.15006}, pmid = {32249550}, issn = {1462-2920}, support = {NNA15BB02A//NASA Astrobiology Institute/International ; DE-AC02-05CH11231//U.S. Department of Energy/International ; 2011-12-01//Alfred P. Sloan Foundation Deep Carbon Observatory/International ; }, mesh = {*Geological Phenomena ; Microbiota ; Oxidation-Reduction ; Sulfur ; Sulfur Compounds/*metabolism ; *Water Microbiology ; }, abstract = {Serpentinization is the hydration and oxidation of ultramafic rock, which occurs as oceanic lithosphere is emplaced onto continental margins (ophiolites), and along the seafloor as faulting exposes this mantle-derived material to circulating hydrothermal fluids. This process leads to distinctive fluid chemistries as molecular hydrogen (H2) and hydroxyl ions (OH[-]) are produced and reduced carbon compounds are mobilized. Serpentinizing ophiolites also serve as a vector to transport sulfur compounds from the seafloor onto the continents. We investigated hyperalkaline, sulfur-rich, brackish groundwater in a serpentinizing continental ophiolite to elucidate the role of sulfur compounds in fuelling in situ microbial activities. Here we illustrate that key sulfur-cycling taxa, including Dethiobacter, Desulfitispora and 'Desulforudis', persist throughout this extreme environment. Biologically catalysed redox reactions involving sulfate, sulfide and intermediate sulfur compounds are thermodynamically favourable in the groundwater, which indicates they may be vital to sustaining life in these characteristically oxidant- and energy-limited systems. Furthermore, metagenomic and metatranscriptomic analyses reveal a complex network involving sulfate reduction, sulfide oxidation and thiosulfate reactions. Our findings highlight the importance of the complete inorganic sulfur cycle in serpentinizing fluids and suggest sulfur biogeochemistry provides a key link between terrestrial serpentinizing ecosystems and their submarine heritage.}, } @article {pmid32249395, year = {2020}, author = {Joshi, N and Sharma, M and Singh, SP}, title = {Characterization of a novel xylanase from an extreme temperature hot spring metagenome for xylooligosaccharide production.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {11}, pages = {4889-4901}, doi = {10.1007/s00253-020-10562-7}, pmid = {32249395}, issn = {1432-0614}, support = {BT/PR17586/PFN/20/1195//Department of Biotechnology , Ministry of Science and Technology/ ; }, mesh = {Biocatalysis ; Endo-1,4-beta Xylanases/*genetics/isolation & purification/*metabolism ; Enzyme Stability ; Escherichia coli/genetics ; Glucuronates/*biosynthesis ; Glycoside Hydrolases/genetics/isolation & purification/metabolism ; *Hot Springs ; *Hot Temperature ; Hydrogen-Ion Concentration ; Kinetics ; *Metagenome ; Microbiota/genetics/physiology ; Oligosaccharides/*biosynthesis ; Xylans/metabolism ; }, abstract = {In this study, the metagenomic resource generated from an aquatic habitat of extreme temperature was screened for the identification of a novel xylanase, XynM1. Gene sequence analysis designated it as a member of glycoside hydrolase (GH) family 10. The metagenomic DNA fragment was cloned, expressed in Escherichia coli, and the purified protein was biochemically characterized. The optimum temperature and pH for the XynM1 xylanase were found to be at 80 °C and 7, respectively. It exhibited worthwhile pH stability by retaining about 70% activity in the range of pH 6 to 9 after the exposure for 12 h at 25 °C. Thermostability analysis established considerable heat tolerance in XynM1 protein at elevated temperatures, displaying about 50% residual activity after the exposure of 40 °C, 50 °C, 60 °C, and 70 °C for 20 h, 12 h, 6 h, and 1.5 h, respectively. The effects of additives such as metals, surfactants, and organic solvents were evaluated on the activity of XynM1. It was able to retain about 50% of its initial activity in the presence of NaCl concentration of 1 to 5 M. The novel xylanase was capable of hydrolyzing the hemicellulosic polymer, derived from diverse biomass sources, e.g., beechwood xylan, wheat arabinoxylan, corncob xylan, and sweet sorghum xylan. The XynM1-treated beechwood xylan manifested catalytic release of xylooligosaccharides (XOS) of 2-6 DP. The novel GH10 xylanase is a promising biocatalyst that could be ascribed for biomass conversion and production of prebiotic XOS biomolecules.}, } @article {pmid32247981, year = {2020}, author = {Yue, Y and Shao, T and Long, X and He, T and Gao, X and Zhou, Z and Liu, Z and Rengel, Z}, title = {Microbiome structure and function in rhizosphere of Jerusalem artichoke grown in saline land.}, journal = {The Science of the total environment}, volume = {724}, number = {}, pages = {138259}, doi = {10.1016/j.scitotenv.2020.138259}, pmid = {32247981}, issn = {1879-1026}, mesh = {*Helianthus ; *Microbiota ; Rhizosphere ; Soil ; Soil Microbiology ; }, abstract = {The improvement and development of saline-alkali soils is currently a hot economic and scientific issue, and exploring the correlation between rhizosphere microorganisms of plants growing on saline-alkali soils and their salt tolerance has become the key point of related research. In our study, the community structure of microorganism and various properties of saline soils were characterized in which Jerusalem artichoke grown along a soil salinity gradient. A variety of basic soil properties were measured and the amplicon was performed as well as metagenomic sequencing on coastal saline soils using various techniques (such as RDA analysis and the assembly of genomes) to evaluate microbial functions. In addition, WGCNA (Weighted gene coexpression network analysis) method was used to identify the species related to salt stress and the sequence binning to assemble two enriched putative bacterial genomes. The research showed the cultivation of Jerusalem artichoke on saline soil changed soil physico-chemical and enzymatic properties; most of the rapidly changing as well as the long-term stable properties differed significantly between the rhizosphere and bulk soils. The amplicon and metagenomic sequencing revealed the function and structure of microorganisms varied between the rhizosphere and bulk soils, with greater microbial diversity in the rhizosphere. Catalase activity and the moisture content were the factors with the greatest impact on microorganisms. The putative genomes of two species of microorganisms (belong to Nitrospira and Gemmatimonas) were assembled, identified microbial species that were highly responsive to salt stress and that may play a key role in saline soil, stressed the important role of archaea in microbial communities in response to salt stress. The study provides a comprehensive understanding of the microbial community structure in the rhizosphere of Jerusalem artichoke to enable the improvement and economic development of saline land.}, } @article {pmid32247457, year = {2020}, author = {Zhao, CC and Eun, JB}, title = {Shotgun metagenomics approach reveals the bacterial community and metabolic pathways in commercial hongeo product, a traditional Korean fermented skate product.}, journal = {Food research international (Ottawa, Ont.)}, volume = {131}, number = {}, pages = {109030}, doi = {10.1016/j.foodres.2020.109030}, pmid = {32247457}, issn = {1873-7145}, mesh = {Ammonia/metabolism ; Animals ; Bacteria/*classification/genetics/*metabolism ; Fermentation ; Fermented Foods/*microbiology ; Lactobacillales/metabolism ; *Metabolic Networks and Pathways ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; Republic of Korea ; Seafood/*microbiology ; *Skates, Fish ; }, abstract = {The aim of this study was to investigate the microbial diversity and microbial metabolic pathways using a metagenomic approach in commercial hongeo samples collected from five different fish processing plants. Community comparison analysis indicated that hongeo samples from different fish processing plants have a similar microbial structure at genus level, but the relative abundance of these genera showed a significant difference among different hongeo samples. Four bacterial genera including Psychrobacter, Pseudomonas, Clostridium, and Oblitimonas were detected in all hongeo samples with a high relative abundance, which associated with the nitrogen compound accumulation and ammonia flavor formation in hongeo samples. In addition, some alkaliphilic marine lactic acid bacteria (LAB) belonging to the genera Marinilactibacillus and Jeotgalibaca were detected in hongeo samples, indicating that this product might be a useful source for finding novel bacteria and possibly marine LAB. Through functional profiling analysis, it was found that hongeo samples had higher bacterial gene content related to amino acid metabolism, followed by carbohydrate metabolism and inorganic ion metabolism. The results of this study provide an important information for understanding the mechanism of quality characteristics and ammonia flavor formation in hongeo products.}, } @article {pmid32247371, year = {2020}, author = {Keshavarzian, A and Engen, P and Bonvegna, S and Cilia, R}, title = {The gut microbiome in Parkinson's disease: A culprit or a bystander?.}, journal = {Progress in brain research}, volume = {252}, number = {}, pages = {357-450}, doi = {10.1016/bs.pbr.2020.01.004}, pmid = {32247371}, issn = {1875-7855}, mesh = {Animals ; Dopamine Agents/*pharmacology ; *Dysbiosis/immunology/metabolism/microbiology ; *Gastrointestinal Microbiome/immunology ; Humans ; *Inflammation/immunology/metabolism/microbiology ; *Life Style ; *Parkinson Disease/drug therapy/immunology/metabolism/microbiology ; *alpha-Synuclein/metabolism ; }, abstract = {In recent years, large-scale metagenomics projects such as the Human Microbiome Project placed the gut microbiota under the spotlight of research on its role in health and in the pathogenesis several diseases, as it can be a target for novel therapeutical approaches. The emerging concept of a microbiota modulation of the gut-brain axis in the pathogenesis of neurodegenerative disorders has been explored in several studies in animal models, as well as in human subjects. Particularly, research on changes in the composition of gut microbiota as a potential trigger for alpha-synuclein (α-syn) pathology in Parkinson's disease (PD) has gained increasing interest. In the present review, we first provide the basis to the understanding of the role of gut microbiota in healthy subjects and the molecular basis of the gut-brain interaction, focusing on metabolic and neuroinflammatory factors that could trigger the alpha-synuclein conformational changes and aggregation. Then, we critically explored preclinical and clinical studies reporting on the changes in gut microbiota in PD, as compared to healthy subjects. Furthermore, we examined the relationship between the gut microbiota and PD clinical features, discussing data consistently reported across studies, as well as the potential sources of inconsistencies. As a further step toward understanding the effects of gut microbiota on PD, we discussed the relationship between dysbiosis and response to dopamine replacement therapy, focusing on Levodopa metabolism. We conclude that further studies are needed to determine whether the gut microbiota changes observed so far in PD patients is the cause or, instead, it is merely a consequence of lifestyle changes associated with the disease. Regardless, studies so far strongly suggest that changes in microbiota appears to be impactful in pathogenesis of neuroinflammation. Thus, dysbiotic microbiota in PD could influence the disease course and response to medication, especially Levodopa. Future research will assess the impact of microbiota-directed therapeutic intervention in PD patients.}, } @article {pmid32245390, year = {2020}, author = {Levy Karin, E and Mirdita, M and Söding, J}, title = {MetaEuk-sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {48}, pmid = {32245390}, issn = {2049-2618}, mesh = {*Algorithms ; Computational Biology/methods ; Databases, Genetic ; Eukaryota/*genetics ; High-Throughput Screening Assays ; Metagenome ; Metagenomics/instrumentation/*methods ; *Microbiota ; Molecular Sequence Annotation/*methods ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Metagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, allowing us to investigate by direct sequencing a tremendous diversity of organisms without the need for prior cultivation. Unicellular eukaryotes play essential roles in most microbial communities as chief predators, decomposers, phototrophs, bacterial hosts, symbionts, and parasites to plants and animals. Investigating their roles is therefore of great interest to ecology, biotechnology, human health, and evolution. However, the generally lower sequencing coverage, their more complex gene and genome architectures, and a lack of eukaryote-specific experimental and computational procedures have kept them on the sidelines of metagenomics.

RESULTS: MetaEuk is a toolkit for high-throughput, reference-based discovery, and annotation of protein-coding genes in eukaryotic metagenomic contigs. It performs fast searches with 6-frame-translated fragments covering all possible exons and optimally combines matches into multi-exon proteins. We used a benchmark of seven diverse, annotated genomes to show that MetaEuk is highly sensitive even under conditions of low sequence similarity to the reference database. To demonstrate MetaEuk's power to discover novel eukaryotic proteins in large-scale metagenomic data, we assembled contigs from 912 samples of the Tara Oceans project. MetaEuk predicted >12,000,000 protein-coding genes in 8 days on ten 16-core servers. Most of the discovered proteins are highly diverged from known proteins and originate from very sparsely sampled eukaryotic supergroups.

CONCLUSION: The open-source (GPLv3) MetaEuk software (https://github.com/soedinglab/metaeuk) enables large-scale eukaryotic metagenomics through reference-based, sensitive taxonomic and functional annotation. Video abstract.}, } @article {pmid32245246, year = {2020}, author = {Chandrarathna, HPSU and Liyanage, TD and Edirisinghe, SL and Dananjaya, SHS and Thulshan, EHT and Nikapitiya, C and Oh, C and Kang, DH and De Zoysa, M}, title = {Marine Microalgae, Spirulina maxima-Derived Modified Pectin and Modified Pectin Nanoparticles Modulate the Gut Microbiota and Trigger Immune Responses in Mice.}, journal = {Marine drugs}, volume = {18}, number = {3}, pages = {}, pmid = {32245246}, issn = {1660-3397}, support = {PN68031//National Research Foundation of Korea/ ; PE99621 and PE99722//Korea Institute of Ocean Science and Technology (KIOST)/ ; }, mesh = {Animals ; Antimicrobial Cationic Peptides/analysis/metabolism ; Bacteroidetes/genetics/isolation & purification ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/genetics ; Immunity, Innate/drug effects ; Immunity, Mucosal/drug effects ; Intestinal Mucosa/drug effects/immunology/metabolism/microbiology ; Male ; Metagenomics ; Mice ; Microalgae/*chemistry ; Models, Animal ; Mucins/analysis/metabolism ; Nanoparticles/*administration & dosage ; Pectins/*administration & dosage/isolation & purification ; Prebiotics/*administration & dosage ; Spirulina/*chemistry ; }, abstract = {This study evaluated the modulation of gut microbiota, immune responses, and gut morphometry in C57BL/6 mice, upon oral administration of S. maxima-derived modified pectin (SmP, 7.5 mg/mL) and pectin nanoparticles (SmPNPs; 7.5 mg/mL). Metagenomics analysis was conducted using fecal samples, and mice duodenum and jejunum were used for analyzing the immune response and gut morphometry, respectively. The results of metagenomics analysis revealed that the abundance of Bacteroidetes in the gut increased in response to both modified SmP and SmPNPs (75%) as compared with that in the control group (66%), while that of Firmicutes decreased in (20%) as compared with that in the control group (30%). The mRNA levels of mucin, antimicrobial peptide, and antiviral and gut permeability-related genes in the duodenum were significantly (p < 0.05) upregulated (> 2-fold) upon modified SmP and SmPNPs feeding. Protein level of intestinal alkaline phosphatase was increased (1.9-fold) in the duodenum of modified SmPNPs feeding, evidenced by significantly increased goblet cell density (0.5 ± 0.03 cells/1000 µm[2]) and villi height (352 ± 10 µm). Our results suggest that both modified SmP and SmPNPs have the potential to modulate gut microbial community, enhance the expression of immune related genes, and improve gut morphology.}, } @article {pmid32245128, year = {2020}, author = {Nishiyama, M and Ohtake, N and Kaneko, A and Tsuchiya, N and Imamura, S and Iizuka, S and Ishizawa, S and Nishi, A and Yamamoto, M and Taketomi, A and Kono, T}, title = {Increase of Akkermansia muciniphila by a Diet Containing Japanese Traditional Medicine Bofutsushosan in a Mouse Model of Non-Alcoholic Fatty Liver Disease.}, journal = {Nutrients}, volume = {12}, number = {3}, pages = {}, pmid = {32245128}, issn = {2072-6643}, mesh = {Akkermansia ; *Animal Feed/microbiology ; Animals ; Biodiversity ; Biomarkers ; Biopsy ; Body Weight ; Dietary Supplements ; Disease Models, Animal ; Drugs, Chinese Herbal/*administration & dosage ; Eating ; Gastrointestinal Microbiome ; Humans ; Immunohistochemistry ; Metagenome ; Metagenomics/methods ; Mice ; Mice, Obese ; Non-alcoholic Fatty Liver Disease/*etiology/metabolism/pathology/prevention & control ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD) is considered a worldwide healthcare problem that mirrors the increased prevalence of obesity. Gut microbiota plays a crucial role in the progression and treatment of NAFLD. Bofutsushosan (BTS), a pharmaceutical-grade Japanese traditional medicine, has long been prescribed in Japan for obesity and obesity-related syndrome. Although BTS has been reported to exert an anti-obesity effect in obese patients as well as various obesity-model animals, its effect on gut microbiota is unknown. Here, the effects of BTS on obesity, liver damage, and the gut microbiome in genetically obese mice, ob/ob, were studied. Seven-week-old ob/ob mice were fed a standard diet with (BTS group) or without (CONT group) 5% BTS for 4 weeks. By comparison to the CONT group, the BTS group showed reduced body weight gain and hyperlipidemia as well as improved liver function. Moreover, gut microbiota in the CONT and BTS group formed a significantly different cluster. Specifically, the genera Akkermansia, Bacteroides and an unknown genus of the family Enterobacteriaceae expanded dramatically in the BTS group. Noteworthy, the population of Akkermansia muciniphila, which is reported to elicit an anti-obesity effect and improve various metabolic abnormalities, was markedly increased (93-fold) compared with the CONT group. These results imply that BTS may be a promising agent for treating NAFLD.}, } @article {pmid32243481, year = {2020}, author = {Hess, MK and Rowe, SJ and Van Stijn, TC and Henry, HM and Hickey, SM and Brauning, R and McCulloch, AF and Hess, AS and Kirk, MR and Kumar, S and Pinares-Patiño, C and Kittelmann, S and Wood, GR and Janssen, PH and McEwan, JC}, title = {A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0219882}, pmid = {32243481}, issn = {1932-6203}, mesh = {Animals ; Bacteria/genetics ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/economics/*methods ; Male ; Metagenome ; Metagenomics/economics/*methods ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sheep/*microbiology ; }, abstract = {Microbial community profiles have been associated with a variety of traits, including methane emissions in livestock. These profiles can be difficult and expensive to obtain for thousands of samples (e.g. for accurate association of microbial profiles with traits), therefore the objective of this work was to develop a low-cost, high-throughput approach to capture the diversity of the rumen microbiome. Restriction enzyme reduced representation sequencing (RE-RRS) using ApeKI or PstI, and two bioinformatic pipelines (reference-based and reference-free) were compared to bacterial 16S rRNA gene sequencing using repeated samples collected two weeks apart from 118 sheep that were phenotypically extreme (60 high and 58 low) for methane emitted per kg dry matter intake (n = 236). DNA was extracted from freeze-dried rumen samples using a phenol chloroform and bead-beating protocol prior to RE-RRS. The resulting sequences were used to investigate the repeatability of the rumen microbial community profiles, the effect of laboratory and analytical method, and the relationship with methane production. The results suggested that the best method was PstI RE-RRS analyzed with the reference-free approach, which accounted for 53.3±5.9% of reads, and had repeatabilities of 0.49±0.07 and 0.50±0.07 for the first two principal components (PC1 and PC2), phenotypic correlations with methane yield of 0.43±0.06 and 0.46±0.06 for PC1 and PC2, and explained 41±8% of the variation in methane yield. These results were significantly better than for bacterial 16S rRNA gene sequencing of the same samples (p<0.05) except for the correlation between PC2 and methane yield. A Sensitivity study suggested approximately 2000 samples could be sequenced in a single lane on an Illumina HiSeq 2500, meaning the current work using 118 samples/lane and future proposed 384 samples/lane are well within that threshold. With minor adaptations, our approach could be used to obtain microbial profiles from other metagenomic samples.}, } @article {pmid32242065, year = {2020}, author = {Osakunor, DNM and Munk, P and Mduluza, T and Petersen, TN and Brinch, C and Ivens, A and Chimponda, T and Amanfo, SA and Murray, J and Woolhouse, MEJ and Aarestrup, FM and Mutapi, F}, title = {The gut microbiome but not the resistome is associated with urogenital schistosomiasis in preschool-aged children.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {155}, pmid = {32242065}, issn = {2399-3642}, support = {/WT_/Wellcome Trust/United Kingdom ; 108061/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Age Factors ; Animals ; Bacteria/classification/genetics/*growth & development ; Case-Control Studies ; Child, Preschool ; Cross-Sectional Studies ; Female ; *Gastrointestinal Microbiome ; Host-Parasite Interactions ; Humans ; Infant ; Intestines/*microbiology ; Male ; Metagenome ; Metagenomics ; Schistosoma haematobium/*pathogenicity ; Schistosomiasis haematobia/diagnosis/*microbiology/*parasitology ; Zimbabwe ; }, abstract = {Helminth parasites have been shown to have systemic effects in the host. Using shotgun metagenomic sequencing, we characterise the gut microbiome and resistome of 113 Zimbabwean preschool-aged children (1-5 years). We test the hypothesis that infection with the human helminth parasite, Schistosoma haematobium, is associated with changes in gut microbial and antimicrobial resistance gene abundance/diversity. Here, we show that bacteria phyla Bacteroidetes, Firmicutes, Proteobacteria, and fungi phyla Ascomycota, Microsporidia, Zoopagomycota dominate the microbiome. The abundance of Proteobacteria, Ascomycota, and Basidiomycota differ between schistosome-infected versus uninfected children. Specifically, infection is associated with increases in Pseudomonas, Stenotrophomonas, Derxia, Thalassospira, Aspergillus, Tricholoma, and Periglandula, with a decrease in Azospirillum. We find 262 AMR genes, from 12 functional drug classes, but no association with individual-specific data. To our knowledge, we describe a novel metagenomic dataset of Zimbabwean preschool-aged children, indicating an association between urogenital schistosome infection and changes in the gut microbiome.}, } @article {pmid32241293, year = {2020}, author = {Sun, S and Jones, RB and Fodor, AA}, title = {Inference-based accuracy of metagenome prediction tools varies across sample types and functional categories.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {46}, pmid = {32241293}, issn = {2049-2618}, mesh = {Animals ; Chickens ; Computational Biology/*methods ; Databases, Factual ; Gorilla gorilla ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics/*methods ; Mice ; *Microbiota ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; *Software ; *Soil Microbiology ; }, abstract = {BACKGROUND: Despite recent decreases in the cost of sequencing, shotgun metagenome sequencing remains more expensive compared with 16S rRNA amplicon sequencing. Methods have been developed to predict the functional profiles of microbial communities based on their taxonomic composition. In this study, we evaluated the performance of three commonly used metagenome prediction tools (PICRUSt, PICRUSt2, and Tax4Fun) by comparing the significance of the differential abundance of predicted functional gene profiles to those from shotgun metagenome sequencing across different environments.

RESULTS: We selected 7 datasets of human, non-human animal, and environmental (soil) samples that have publicly available 16S rRNA and shotgun metagenome sequences. As we would expect based on previous literature, strong Spearman correlations were observed between predicted gene compositions and gene relative abundance measured with shotgun metagenome sequencing. However, these strong correlations were preserved even when the abundance of genes were permuted across samples. This suggests that simple correlation coefficient is a highly unreliable measure for the performance of metagenome prediction tools. As an alternative, we compared the performance of genes predicted with PICRUSt, PICRUSt2, and Tax4Fun to sequenced metagenome genes in inference models associated with metadata within each dataset. With this approach, we found reasonable performance for human datasets, with the metagenome prediction tools performing better for inference on genes related to "housekeeping" functions. However, their performance degraded sharply outside of human datasets when used for inference.

CONCLUSION: We conclude that the utility of PICRUSt, PICRUSt2, and Tax4Fun for inference with the default database is likely limited outside of human samples and that development of tools for gene prediction specific to different non-human and environmental samples is warranted. Video abstract.}, } @article {pmid32241287, year = {2020}, author = {Cao, S and Zhang, W and Ding, W and Wang, M and Fan, S and Yang, B and Mcminn, A and Wang, M and Xie, BB and Qin, QL and Chen, XL and He, J and Zhang, YZ}, title = {Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {47}, pmid = {32241287}, issn = {2049-2618}, mesh = {Antarctic Regions ; Arctic Regions ; Bacteria/*classification ; *Metagenomics ; Microbiota/*genetics ; Oceans and Seas ; Phylogeny ; Seawater/*microbiology ; }, abstract = {BACKGROUND: The Arctic and Antarctic are the two most geographically distant bioregions on earth. Recent sampling efforts and following metagenomics have shed light on the global ocean microbial diversity and function, yet the microbiota of polar regions has not been included in such global analyses.

RESULTS: Here a metagenomic study of seawater samples (n = 60) collected from different depths at 28 locations in the Arctic and Antarctic zones was performed, together with metagenomes from the Tara Oceans. More than 7500 (19%) polar seawater-derived operational taxonomic units could not be identified in the Tara Oceans datasets, and more than 3,900,000 protein-coding gene orthologs had no hits in the Ocean Microbial Reference Gene Catalog. Analysis of 214 metagenome assembled genomes (MAGs) recovered from the polar seawater microbiomes, revealed strains that are prevalent in the polar regions while nearly undetectable in temperate seawater. Metabolic pathway reconstruction for these microbes suggested versatility for saccharide and lipids biosynthesis, nitrate and sulfate reduction, and CO2 fixation. Comparison between the Arctic and Antarctic microbiomes revealed that antibiotic resistance genes were enriched in the Arctic while functions like DNA recombination were enriched in the Antarctic.

CONCLUSIONS: Our data highlight the occurrence of dominant and locally enriched microbes in the Arctic and Antarctic seawater with unique functional traits for environmental adaption, and provide a foundation for analyzing the global ocean microbiome in a more complete perspective. Video abstract.}, } @article {pmid32240601, year = {2020}, author = {Yan, Y and Drew, DA and Markowitz, A and Lloyd-Price, J and Abu-Ali, G and Nguyen, LH and Tran, C and Chung, DC and Gilpin, KK and Meixell, D and Parziale, M and Schuck, M and Patel, Z and Richter, JM and Kelsey, PB and Garrett, WS and Chan, AT and Stadler, ZK and Huttenhower, C}, title = {Structure of the Mucosal and Stool Microbiome in Lynch Syndrome.}, journal = {Cell host & microbe}, volume = {27}, number = {4}, pages = {585-600.e4}, pmid = {32240601}, issn = {1934-6069}, support = {27140/CRUK_/Cancer Research UK/United Kingdom ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 CA202704/CA/NCI NIH HHS/United States ; L30 CA209764/CA/NCI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; R01 CA154426/CA/NCI NIH HHS/United States ; T32 CA009001/CA/NCI NIH HHS/United States ; K01 DK120742/DK/NIDDK NIH HHS/United States ; }, mesh = {Adenoma/microbiology ; Adult ; Aged ; Aged, 80 and over ; Colectomy/adverse effects ; Colonic Neoplasms/diagnosis/*microbiology/pathology ; Colorectal Neoplasms, Hereditary Nonpolyposis/diagnosis/*microbiology/pathology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metagenomics ; Middle Aged ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Transcriptome ; Tumor Microenvironment ; }, abstract = {The gut microbiota has been associated with colorectal cancer (CRC), but causal alterations preceding CRC have not been elucidated. To prospectively assess microbiome changes prior to colorectal neoplasia, we investigated samples from 100 Lynch syndrome patients using 16S rRNA gene sequencing of colon biopsies, coupled with metagenomic and metatranscriptomic sequencing of feces. Colectomy and CRC history represented the largest effects on microbiome profiles. A subset of Clostridiaceae were depleted in stool corresponding with baseline adenomas, while Desulfovibrio was enriched both in stool and in mucosal biopsies. A classifier leveraging stool metatranscriptomes resulted in modest power to predict interval development of preneoplastic colonic adenoma. Predictive transcripts corresponded with a shift in flagellin contributors and oxidative metabolic microenvironment, potentially factors in local CRC pathogenesis. This suggests that the effectiveness of prospective microbiome monitoring for adenomas may be limited but supports the potential causality of these consistent, early microbial changes in colonic neoplasia.}, } @article {pmid32240475, year = {2021}, author = {Wang, YG and Gao, Y and Feng, J and Dou, YQ}, title = {Effect of Modified Xijiao Dihuang Decoction () on Intestinal Flora and Th17/Treg in Rats with Radiation Enteritis.}, journal = {Chinese journal of integrative medicine}, volume = {27}, number = {3}, pages = {198-205}, pmid = {32240475}, issn = {1993-0402}, mesh = {Animals ; *Enteritis/drug therapy ; Female ; Forkhead Transcription Factors ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; T-Lymphocytes, Regulatory ; Th17 Cells ; }, abstract = {OBJECTIVE: To observe the effect of Modified Xijiao Dihuang Decoction (, MXDD) on rats with radiation enteritis, and explore its action mechanism.

METHODS: Thirty female Sprague Dawley rats were divided into the control, model, dexamethasone (DXM), golden bifid (GB) and MXDD groups using random number table, 6 rats in each group. Except the control group, the other rats were developed into radiation enteritis model by exposing to a single [60]Co-γ ray at a dose of 11 Gy. The rats in the DXM, GB and MXDD groups were treated with DXM (1.425 mg/kg), GB (0.8 g/kg) and MXDD (36.0 g/kg) for 3 days, respectively. Body weight and diarrhea condition of rats were evaluated daily. On day 3, the feces of rats were collected for intestinal flora detection and the small intestinal tissues were also collected. Bacterial species annotation, alpha and beta diversities as well as composition of intestinal flora were detected and compared. The protein and mRNA expressions of interleukin 17 (IL-17), retinoid-related orphan nuclear receptor gamma t (ROR-γt) and forkhead/ winged helix transcription factor p3 (FoxP3) were determined by Western blot and polymerase chain reaction, respectively. The abundance and diversity of intestinal flora as well as the proportion at the phylum and genus levels were assayed by 16S rRNA metagenome sequencing. Correlation between intestinal flora and Th17/Treg was analyzed by heatmap method.

RESULTS: On day 1 to 3 after radiation, compared with the control group, the body weight in model group was decreased (P<0.05 or P<0.01). Compared with the model group, MXDD could alleviate weight loss and diarrhea caused by irradiation. At the phylum level, MXDD cause a significant increase in Firmicutes, and a decrease in Proteobacteria (P<0.05 or P<0.01). At the genus level, MXDD reduced the proportion of Escherichia Shigella (P<0.01). In addition, IL-17 and FoxP3 mRNA and protein expression levels were down-regulated and ROR-γt was up-regulated by MXDD treatment (P<0.05). Besides, Firmicutes and Lactobacillus were positively correlated with FoxP3 (r=0.73, 0.79, respectively; P<0.01), negatively correlated with IL-17 (r=0.66, 0.64, respectively; P<0.01 or P<0.05) and ROR-γt (r0.73, 0.81, respectively; P<0.01). Proteobacteria and Escherichia Shigella both had positive correlation with IL-17 (r 0.77, 0.57, respectively; P<0.01 or P<0.05) and ROR-γt (r=0.94, 0.79, respectively; P<0.01) and negative correlation with FoxP3 (r0.74, 0.65; P<0.01).

CONCLUSION: MXDD could improve the survival status of irradiated rats by regulating the richness, diversity and composition of intestinal flora, and restoring the balance of Th17/Treg.}, } @article {pmid32239170, year = {2021}, author = {Li, W and Tapiainen, T and Brinkac, L and Lorenzi, HA and Moncera, K and Tejesvi, MV and Salo, J and Nelson, KE}, title = {Vertical Transmission of Gut Microbiome and Antimicrobial Resistance Genes in Infants Exposed to Antibiotics at Birth.}, journal = {The Journal of infectious diseases}, volume = {224}, number = {7}, pages = {1236-1246}, pmid = {32239170}, issn = {1537-6613}, support = {U19 AI110819/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/adverse effects/*pharmacology ; Case-Control Studies ; Drug Resistance, Bacterial/drug effects/*genetics ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/drug effects/*genetics ; Humans ; Infant ; Infant, Newborn ; *Infectious Disease Transmission, Vertical ; Metagenomics ; Parturition ; Pregnancy ; }, abstract = {Vertical transmission of maternal microbes is a major route for establishing the gut microbiome in newborns. The impact of perinatal antibiotics on vertical transmission of microbes and antimicrobial resistance is not well understood. Using a metagenomic approach, we analyzed the fecal samples from mothers and vaginally delivered infants from a control group (10 pairs) and a treatment group (10 pairs) receiving perinatal antibiotics. Antibiotic-usage had a significant impact on the main source of inoculum in the gut microbiome of newborns. The control group had significantly more species transmitted from mothers to infants (P = .03) than the antibiotic-treated group. Approximately 72% of the gut microbial population of infants at 3-7 days after birth in the control group was transmitted from their mothers, versus only 25% in the antibiotic-treated group. In conclusion, perinatal antibiotics markedly disturbed vertical transmission and changed the source of gut colonization towards horizontal transfer from the environment to the infants.}, } @article {pmid32238913, year = {2020}, author = {Greene, LK and Williams, CV and Junge, RE and Mahefarisoa, KL and Rajaonarivelo, T and Rakotondrainibe, H and O'Connell, TM and Drea, CM}, title = {A role for gut microbiota in host niche differentiation.}, journal = {The ISME journal}, volume = {14}, number = {7}, pages = {1675-1687}, pmid = {32238913}, issn = {1751-7370}, mesh = {Feces ; *Gastrointestinal Microbiome ; Gastrointestinal Tract ; Metagenome ; *Microbiota ; }, abstract = {If gut microbes influence host behavioral ecology in the short term, over evolutionary time, they could drive host niche differentiation. We explored this possibility by comparing the gut microbiota of Madagascar's folivorous lemurs from Indriidae and Lepilemuridae. Occurring sympatrically in the eastern rainforest, our four, target species have different dietary specializations, including frugo-folivory (sifakas), young-leaf folivory (indri and woolly lemurs), and mature-leaf folivory (sportive lemurs). We collected fecal samples, from 2013 to 2017, and used amplicon sequencing, metagenomic sequencing, and nuclear magnetic resonance spectroscopy, respectively, to integrate analyses of gut microbiome structure and function with analysis of the colonic metabolome. The lemurs harbored species-specific microbiomes, metagenomes, and metabolomes that were tuned to their dietary specializations: Frugo-folivores had greater microbial and metagenomic diversity, and harbored generalist taxa. Mature-leaf folivores had greater individual microbiome variation, and taxa and metabolites putatively involved in cellulolysis. The consortia even differed between related, young-leaf specialists, with indri prioritizing metabolism of fiber and plant secondary compounds, and woolly lemurs prioritizing amino-acid cycling. Specialized gut microbiota and associated gastrointestinal morphologies enable folivores to variably tolerate resource fluctuation and support nutrient extraction from challenging resources (e.g., by metabolizing plant secondary compounds or recalcitrant fibers), perhaps ultimately facilitating host species' diversity and specialized feeding ecologies.}, } @article {pmid32238866, year = {2020}, author = {Zhao, R and Summers, ZM and Christman, GD and Yoshimura, KM and Biddle, JF}, title = {Metagenomic views of microbial dynamics influenced by hydrocarbon seepage in sediments of the Gulf of Mexico.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {5772}, pmid = {32238866}, issn = {2045-2322}, support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaea/*genetics/isolation & purification ; Bacteria/*genetics/isolation & purification ; Geologic Sediments/analysis/*microbiology ; Gulf of Mexico ; Hydrocarbons/analysis ; *Metagenome ; Microbiota ; Nitrogen Fixation ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/analysis/microbiology ; }, abstract = {Microbial cells in the seabed are thought to persist by slow population turnover rates and extremely low energy requirements. External stimulations such as seafloor hydrocarbon seeps have been demonstrated to significantly boost microbial growth; however, the microbial community response has not been fully understood. Here we report a comparative metagenomic study of microbial response to natural hydrocarbon seeps in the Gulf of Mexico. Subsurface sediments (10-15 cm below seafloor) were collected from five natural seep sites and two reference sites. The resulting metagenome sequencing datasets were analyzed with both gene-based and genome-based approaches. 16S rRNA gene-based analyses suggest that the seep samples are distinct from the references by both 16S rRNA fractional content and phylogeny, with the former dominated by ANME-1 archaea (~50% of total) and Desulfobacterales, and the latter dominated by the Deltaproteobacteria, Planctomycetes, and Chloroflexi phyla. Sulfate-reducing bacteria (SRB) are present in both types of samples, with higher relative abundances in seep samples than the references. Genes for nitrogen fixation were predominantly found in the seep sites, whereas the reference sites showed a dominant signal for anaerobic ammonium oxidation (anammox). We recovered 49 metagenome-assembled genomes and assessed the microbial functional potentials in both types of samples. By this genome-based analysis, the seep samples were dominated by ANME-1 archaea and SRB, with the capacity for methane oxidation coupled to sulfate reduction, which is consistent with the 16S rRNA-gene based characterization. Although ANME-1 archaea and SRB are present in low relative abundances, genome bins from the reference sites are dominated by uncultured members of NC10 and anammox Scalindua, suggesting a prevalence of nitrogen transformations for energy in non-seep pelagic sediments. This study suggests that hydrocarbon seeps can greatly change the microbial community structure by stimulating nitrogen fixation, inherently shifting the nitrogen metabolism compared to those of the reference sediments.}, } @article {pmid32235930, year = {2020}, author = {Basolo, A and Hohenadel, M and Ang, QY and Piaggi, P and Heinitz, S and Walter, M and Walter, P and Parrington, S and Trinidad, DD and von Schwartzenberg, RJ and Turnbaugh, PJ and Krakoff, J}, title = {Effects of underfeeding and oral vancomycin on gut microbiome and nutrient absorption in humans.}, journal = {Nature medicine}, volume = {26}, number = {4}, pages = {589-598}, pmid = {32235930}, issn = {1546-170X}, support = {T32 AI060537/AI/NIAID NIH HHS/United States ; R21 CA227232/CA/NCI NIH HHS/United States ; P30 DK098722/DK/NIDDK NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; }, mesh = {Administration, Oral ; Adolescent ; Adult ; Caloric Restriction ; Cross-Over Studies ; Diet ; Double-Blind Method ; Energy Metabolism/drug effects ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestinal Absorption/*drug effects ; Male ; Malnutrition/*metabolism/*microbiology ; Middle Aged ; Nutrients/*pharmacokinetics ; Vancomycin/*administration & dosage/pharmacology ; Verrucomicrobia/isolation & purification ; Young Adult ; }, abstract = {Direct evidence in humans for the impact of the microbiome on nutrient absorption is lacking. We conducted an extended inpatient study using two interventions that we hypothesized would alter the gut microbiome and nutrient absorption. In each, stool calorie loss, a direct proxy of nutrient absorption, was measured. The first phase was a randomized cross-over dietary intervention in which all participants underwent in random order 3 d of over- and underfeeding. The second was a randomized, double-blind, placebo-controlled pharmacologic intervention using oral vancomycin or matching placebo (NCT02037295). Twenty-seven volunteers (17 men and 10 women, age 35.1 ± 7.3, BMI 32.3 ± 8.0), who were healthy other than having impaired glucose tolerance and obesity, were enrolled and 25 completed the entire trial. The primary endpoints were the effects of dietary and pharmacological intervention on stool calorie loss. We hypothesized that stool calories expressed as percentage of caloric intake would increase with underfeeding compared with overfeeding and increase during oral vancomycin treatment. Both primary endpoints were met. Greater stool calorie loss was observed during underfeeding relative to overfeeding and during vancomycin treatment compared with placebo. Key secondary endpoints were to evaluate the changes in gut microbial community structure as evidenced by amplicon sequencing and metagenomics. We observed only a modest perturbation of gut microbial community structure with under- versus overfeeding but a more widespread change in community structure with reduced diversity with oral vancomycin. Increase in Akkermansia muciniphila was common to both interventions that resulted in greater stool calorie loss. These results indicate that nutrient absorption is sensitive to environmental perturbations and support the translational relevance of preclinical models demonstrating a possible causal role for the gut microbiome in dietary energy harvest.}, } @article {pmid32235826, year = {2020}, author = {Zhu, F and Ju, Y and Wang, W and Wang, Q and Guo, R and Ma, Q and Sun, Q and Fan, Y and Xie, Y and Yang, Z and Jie, Z and Zhao, B and Xiao, L and Yang, L and Zhang, T and Feng, J and Guo, L and He, X and Chen, Y and Chen, C and Gao, C and Xu, X and Yang, H and Wang, J and Dang, Y and Madsen, L and Brix, S and Kristiansen, K and Jia, H and Ma, X}, title = {Metagenome-wide association of gut microbiome features for schizophrenia.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {1612}, pmid = {32235826}, issn = {2041-1723}, mesh = {Animals ; Bacteria/classification/genetics ; Behavior, Animal ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Male ; *Metagenome ; Metagenomics/methods ; Mice ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S ; ROC Curve ; Risk Factors ; Schizophrenia/*metabolism/*microbiology ; Social Behavior ; Streptococcus ; }, abstract = {Evidence is mounting that the gut-brain axis plays an important role in mental diseases fueling mechanistic investigations to provide a basis for future targeted interventions. However, shotgun metagenomic data from treatment-naïve patients are scarce hampering comprehensive analyses of the complex interaction between the gut microbiota and the brain. Here we explore the fecal microbiome based on 90 medication-free schizophrenia patients and 81 controls and identify a microbial species classifier distinguishing patients from controls with an area under the receiver operating characteristic curve (AUC) of 0.896, and replicate the microbiome-based disease classifier in 45 patients and 45 controls (AUC = 0.765). Functional potentials associated with schizophrenia include differences in short-chain fatty acids synthesis, tryptophan metabolism, and synthesis/degradation of neurotransmitters. Transplantation of a schizophrenia-enriched bacterium, Streptococcus vestibularis, appear to induces deficits in social behaviors, and alters neurotransmitter levels in peripheral tissues in recipient mice. Our findings provide new leads for further investigations in cohort studies and animal models.}, } @article {pmid32235279, year = {2020}, author = {Lundy, SD and Vij, SC and Rezk, AH and Cohen, JA and Bajic, P and Ramasamy, R}, title = {The microbiome of the infertile male.}, journal = {Current opinion in urology}, volume = {30}, number = {3}, pages = {355-362}, pmid = {32235279}, issn = {1473-6586}, mesh = {Humans ; Infertility, Male/*microbiology ; Male ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S ; Semen/*microbiology ; Semen Analysis ; }, abstract = {PURPOSE OF REVIEW: Contrary to historic dogma, many tissues and organs in the human body contain a resident population of bacteria, fungi, and viruses collectively known as the microbiome. The microbiome plays a role in both homeostatic symbiosis and also pathogenic dysbiosis in a wide array of diseases. Our understanding of the relationship between the microbiome and male factor infertility is in its infancy but is slowly evolving.

RECENT FINDINGS: Recent literature indicates that semen (and likely the testis) is not sterile and contains a distinct microbiome, and these changes in its composition are associated with alterations in semen quality and fertility status. Preliminary investigation indicates that manipulating the human microbiome may have implications in improving semen parameters and fertility.

SUMMARY: In this review, we describe relationships between the microbiome and the genitourinary system, discuss the prior work on the relationship among bacteriospermia, leukocytospermia and male factor infertility, and summarize the current literature utilizing 16s rRNA-based next-generation sequencing on the seminal and testicular microbiome. We explore the specific microbial taxa implicated in various aspects of spermatic dysfunction and introduce preliminary evidence for therapeutic approaches to alter the microbiome and improve fertility status.}, } @article {pmid32233325, year = {2019}, author = {Barbut, F and Couturier, J}, title = {[Interactions between intestinal microbiota and Clostridioides difficile].}, journal = {La Revue du praticien}, volume = {69}, number = {7}, pages = {784-791}, pmid = {32233325}, issn = {2101-017X}, mesh = {*Clostridioides difficile/pathogenicity ; *Clostridium Infections ; Diarrhea ; France ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Interactions between intestinal microbiota and clostridioides difficile. Clostridioides difficile is a spore-forming anaerobic Gram-positive bacillus that is responsible for diarrhea and post-antibiotic colitis. Approximately 20,000 inpatients are infected by C. difficile in France per year. This bacterium is recognized as an emerging pathogen responsible for community-acquired diarrhea. Antibiotic therapy is the main risk factor for C. difficile infection (CDI) because it leads to intestinal dysbiosis and loss of "colonization resistance". C. difficile from endogenous or exogenous origin can then establish, multiply and produce its two toxins causing enterocyte lesions and a significant inflammatory reaction. The loss of colonization resistance has been associated with the loss of microbial diversity, particularly of some taxa that play a protective role. These variations of bacterial communities lead to changes in functions that can be explored by metabolomic or metagenomic approaches. Data from these experiments led to mechanistic assumptions about resistance or susceptibility to CDI. Microbiota studies have also pushed physicians to develop therapeutic approaches based on biotherapies. These therapies aim at repopulating the colon by a healthy microbiota either by fecal microbiota transplantation or by the administration of strains and cocktails of strains to restore the colonization resistance effect.}, } @article {pmid32233019, year = {2020}, author = {Mai, BHA and Drancourt, M and Aboudharam, G}, title = {Ancient dental pulp: Masterpiece tissue for paleomicrobiology.}, journal = {Molecular genetics & genomic medicine}, volume = {8}, number = {6}, pages = {e1202}, pmid = {32233019}, issn = {2324-9269}, mesh = {Bacterial Infections/epidemiology/*microbiology ; *DNA, Ancient ; Dental Pulp/*microbiology ; Fossils/*microbiology ; Humans ; Metagenome ; Microbiota ; }, abstract = {INTRODUCTION: Dental pulp with special structure has become a good reference sample in paleomicrobiology-related blood-borne diseases, many pathogens were detected by different methods based on the diagnosis of nucleic acids and proteins.

OBJECTIVES: This review aims to propose the preparation process from ancient teeth collection to organic molecule extraction of dental pulp and summary, analyze the methods that have been applied to detect septicemic pathogens through ancient dental pulps during the past 20 years following the first detection of an ancient microbe.

METHODS: The papers used in this review with two main objectives were obtained from PubMed and Google scholar with combining keywords: "ancient," "dental pulp," "teeth," "anatomy," "structure," "collection," "preservation," "selection," "photography," "radiography," "contamination," "decontamination," "DNA," "protein," "extraction," "bone," "paleomicrobiology," "bacteria," "virus," "pathogen," "molecular biology," "proteomics," "PCR," "MALDI-TOF," "LC/MS," "ELISA," "immunology," "immunochromatography," "genome," "microbiome," "metagenomics."

RESULTS: The analysis of ancient dental pulp should have a careful preparation process with many different steps to give highly accurate results, each step complies with the rules in archaeology and paleomicrobiology. After the collection of organic molecules from dental pulp, they were investigated for pathogen identification based on the analysis of DNA and protein. Actually, DNA approach takes a principal role in diagnosis while the protein approach is more and more used. A total of seven techniques was used and ten bacteria (Yersinia pestis, Bartonella quintana, Salmonella enterica serovar Typhi, Salmonella enterica serovar Paratyphi C, Mycobacterium leprae, Mycobacterium tuberculosis, Rickettsia prowazeki, Staphylococcus aureus, Borrelia recurrentis, Bartonella henselae) and one virus (Anelloviridae) were identified. Y. pestis had the most published in quantity and all methods were investigated for this pathogen, S. aureus and B. recurrentis were identified by three different methods and others only by one. The combining methods interestingly increase the positive rate with ELISA, PCR and iPCR in Yersinia pestis diagnosis. Twenty-seven ancient genomes of Y. pestis and one ancient genome of B. recurrentis were reconstructed. Comparing to the ancient bone, ancient teeth showed more advantage in septicemic diagnosis. Beside pathogen identification, ancient pulp help to distinguish species.

CONCLUSIONS: Dental pulp with specific tissue is a suitable sample for detection of the blood infection in the past through DNA and protein identification with the correct preparation process, furthermore, it helps to more understand the pathogens of historic diseases and epidemics.}, } @article {pmid32232443, year = {2020}, author = {Bartolomaeus, H and Avery, EG and Bartolomaeus, TUP and Kozhakhmetov, S and Zhumadilov, Z and Müller, DN and Wilck, N and Kushugulova, A and Forslund, SK}, title = {Blood pressure changes correlate with short-chain fatty acid production potential shifts under a synbiotic intervention.}, journal = {Cardiovascular research}, volume = {116}, number = {7}, pages = {1252-1253}, doi = {10.1093/cvr/cvaa083}, pmid = {32232443}, issn = {1755-3245}, mesh = {Bacteria/genetics/*metabolism ; *Blood Pressure ; Databases, Genetic ; Fatty Acids/*blood ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolic Syndrome/blood/*diet therapy/microbiology/physiopathology ; Metagenomics ; Randomized Controlled Trials as Topic ; Synbiotics/*administration & dosage ; Treatment Outcome ; }, } @article {pmid32231240, year = {2020}, author = {Chaudhari, DS and Dhotre, DP and Agarwal, DM and Gaike, AH and Bhalerao, D and Jadhav, P and Mongad, D and Lubree, H and Sinkar, VP and Patil, UK and Salvi, S and Bavdekar, A and Juvekar, SK and Shouche, YS}, title = {Gut, oral and skin microbiome of Indian patrilineal families reveal perceptible association with age.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {5685}, pmid = {32231240}, issn = {2045-2322}, mesh = {Adolescent ; Adult ; *Age Factors ; Aged ; Aged, 80 and over ; Bacteria/genetics ; Child ; Child, Preschool ; Family ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics ; Humans ; India/epidemiology ; Male ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/*genetics ; Middle Aged ; Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Skin/microbiology ; }, abstract = {The human microbiome plays a key role in maintaining host homeostasis and is influenced by age, geography, diet, and other factors. Traditionally, India has an established convention of extended family arrangements wherein three or more generations, bound by genetic relatedness, stay in the same household. In the present study, we have utilized this unique family arrangement to understand the association of age with the microbiome. We characterized stool, oral and skin microbiome of 54 healthy individuals from six joint families by 16S rRNA gene-based metagenomics. In total, 69 (1.03%), 293 (2.68%) and 190 (8.66%) differentially abundant OTUs were detected across three generations in the gut, skin and oral microbiome, respectively. Age-associated changes in the gut and oral microbiome of patrilineal families showed positive correlations in the abundance of phyla Proteobacteria and Fusobacteria, respectively. Genera Treponema and Fusobacterium showed a positive correlation with age while Granulicatella and Streptococcus showed a negative correlation with age in the oral microbiome. Members of genus Prevotella illustrated high abundance and prevalence as a core OTUs in the gut and oral microbiome. In conclusion, this study highlights that precise and perceptible association of age with microbiome can be drawn when other causal factors are kept constant.}, } @article {pmid32230931, year = {2020}, author = {Leitão, AL and Costa, MC and Gabriel, AF and Enguita, FJ}, title = {Interspecies Communication in Holobionts by Non-Coding RNA Exchange.}, journal = {International journal of molecular sciences}, volume = {21}, number = {7}, pages = {}, pmid = {32230931}, issn = {1422-0067}, mesh = {Animals ; Anthozoa/physiology ; Bacteria ; Bacterial Physiological Phenomena ; Cell Communication/*genetics/*physiology ; Dysbiosis ; Mammals ; Metagenome ; MicroRNAs ; Microbiota/physiology ; Plant Physiological Phenomena ; Plants ; RNA, Untranslated/*genetics/*metabolism ; *Signal Transduction ; Symbiosis/genetics/physiology ; Transcriptome ; }, abstract = {Complex organisms are associations of different cells that coexist and collaborate creating a living consortium, the holobiont. The relationships between the holobiont members are essential for proper homeostasis of the organisms, and they are founded on the establishment of complex inter-connections between all the cells. Non-coding RNAs are regulatory molecules that can also act as communication signals between cells, being involved in either homeostasis or dysbiosis of the holobionts. Eukaryotic and prokaryotic cells can transmit signals via non-coding RNAs while using specific extracellular conveyors that travel to the target cell and can be translated into a regulatory response by dedicated molecular machinery. Within holobionts, non-coding RNA regulatory signaling is involved in symbiotic and pathogenic relationships among the cells. This review analyzes current knowledge regarding the role of non-coding RNAs in cell-to-cell communication, with a special focus on the signaling between cells in multi-organism consortia.}, } @article {pmid32229362, year = {2020}, author = {Czaplicki, LM and Redfern, LK and Cooper, EM and Ferguson, PL and Vilgalys, R and Gunsch, CK}, title = {Investigating the mycobiome of the Holcomb Creosote Superfund Site.}, journal = {Chemosphere}, volume = {252}, number = {}, pages = {126208}, pmid = {32229362}, issn = {1879-1298}, support = {P42 ES010356/ES/NIEHS NIH HHS/United States ; }, mesh = {Ascomycota/metabolism ; Bacteria/metabolism ; Biodegradation, Environmental ; Creosote/*analysis ; *Hazardous Waste Sites ; Microbiota ; *Mycobiome ; Polycyclic Aromatic Hydrocarbons/analysis ; *Soil Microbiology ; Soil Pollutants/*analysis ; }, abstract = {Even though many fungi are known to degrade a range of organic chemicals and may be advantageous for targeting hydrophobic chemicals with low bioavailability due to their ability to secrete extracellular enzymes, fungi are not commonly leveraged in the context of bioremediation. Here we sought to examine the fungal microbiome (mycobiome) at a model creosote polluted site to determine if fungi were prevalent under high PAH contamination conditions as well as to identify potential mycostimulation targets. Several significant positive associations were detected between OTUs and mid-to high-molecular weight PAHs. Several OTUs were closely related to taxa that have previously been identified in culture-based studies as PAH degraders. In particular, members belonging to the Ascomycota phylum were the most diverse at higher PAH concentrations suggesting this phylum may be promising biostimulation targets. There were nearly three times more positive correlations as compared to negative correlations, suggesting that creosote-tolerance is more common than creosote-sensitivity in the fungal community. Future work including shotgun metagenomic analysis would help confirm the presence of specific degradation genes. Overall this study suggests that mycobiome and bacterial microbiome analyses should be performed in parallel to devise the most optimal in situ biostimulation treatment strategies.}, } @article {pmid32228448, year = {2020}, author = {Xu, L and Surathu, A and Raplee, I and Chockalingam, A and Stewart, S and Walker, L and Sacks, L and Patel, V and Li, Z and Rouse, R}, title = {The effect of antibiotics on the gut microbiome: a metagenomics analysis of microbial shift and gut antibiotic resistance in antibiotic treated mice.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {263}, pmid = {32228448}, issn = {1471-2164}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Microbial/genetics ; Gastrointestinal Microbiome/drug effects/genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Mice ; Mice, Inbred BALB C ; }, abstract = {BACKGROUND: Emergence of antibiotic resistance is a global public health concern. The relationships between antibiotic use, the gut community composition, normal physiology and metabolism, and individual and public health are still being defined. Shifts in composition of bacteria, antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) after antibiotic treatment are not well-understood.

METHODS: This project used next-generation sequencing, custom-built metagenomics pipeline and differential abundance analysis to study the effect of antibiotic monotherapy on resistome and taxonomic composition in the gut of Balb/c mice infected with E. coli via transurethral catheterization to investigate the evolution and emergence of antibiotic resistance.

RESULTS: There is a longitudinal decrease of gut microbiota diversity after antibiotic treatment. Various ARGs are enriched within the gut microbiota despite an overall reduction of the diversity and total amount of bacteria after antibiotic treatment. Sometimes treatment with a specific class of antibiotics selected for ARGs that resist antibiotics of a completely different class (e.g. treatment of ciprofloxacin or fosfomycin selected for cepA that resists ampicillin). Relative abundance of some MGEs increased substantially after antibiotic treatment (e.g. transposases in the ciprofloxacin group).

CONCLUSIONS: Antibiotic treatment caused a remarkable reduction in diversity of gut bacterial microbiota but enrichment of certain types of ARGs and MGEs. These results demonstrate an emergence of cross-resistance as well as a profound change in the gut resistome following oral treatment of antibiotics.}, } @article {pmid32227463, year = {2020}, author = {Lu, X and Wang, K and Sun, S and Mou, X}, title = {Metatranscriptomic identification of polyamine-transforming bacterioplankton in the Gulf of Mexico.}, journal = {Environmental microbiology reports}, volume = {12}, number = {3}, pages = {258-266}, doi = {10.1111/1758-2229.12841}, pmid = {32227463}, issn = {1758-2229}, support = {OCE1029697//National Science Foundation/International ; }, mesh = {Actinobacteria/classification/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; Bacteroidetes/classification/genetics/isolation & purification ; Cyanobacteria/classification/genetics/isolation & purification ; Gulf of Mexico ; Metagenomics ; Microbiota ; Nitrogen/metabolism ; Phylogeny ; Planctomycetales/classification/genetics/isolation & purification ; *Plankton/metabolism/microbiology ; Polyamines/*metabolism ; Proteobacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; Transcriptome ; }, abstract = {The importance of short-chained aliphatic polyamines (PAs) to bacterioplankton-mediated carbon and nitrogen cycles has been repeatedly proposed. However, bacterial taxa and genes involved in the transformations of different PA compounds and their potential spatial variations remain unclear. This study collected surface bacterioplankton from nearshore, offshore, and open ocean stations in the Gulf of Mexico and examined how metatranscriptomes responded to additions of three single PA model compounds (i.e. putrescine, spermidine, or spermine). Our data showed an overrepresentation of genes affiliated with γ-glutamylation and spermidine cleavage pathways in metatranscriptomes received PA amendments and the expression level of each pathway varied among different PA compounds and sampling locations. PA-transforming taxa were affiliated with Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, and Proteobacteria and their relative importance was also compound and location specific. These findings suggest that PAs are transformed via multiple pathways and by a diversity of marine bacterioplankton in the Gulf of Mexico. The relative importance of different PA transforming pathways and composition of functional microbial communities may be regulated by nutrient status of local environments.}, } @article {pmid32226996, year = {2020}, author = {Chen, M and Guo, WL and Li, QY and Xu, JX and Cao, YJ and Liu, B and Yu, XD and Rao, PF and Ni, L and Lv, XC}, title = {The protective mechanism of Lactobacillus plantarum FZU3013 against non-alcoholic fatty liver associated with hyperlipidemia in mice fed a high-fat diet.}, journal = {Food & function}, volume = {11}, number = {4}, pages = {3316-3331}, doi = {10.1039/c9fo03003d}, pmid = {32226996}, issn = {2042-650X}, mesh = {Adipose Tissue/metabolism ; Animals ; Bile Acids and Salts/metabolism ; Body Weight ; Cholesterol/blood ; Cholesterol 7-alpha-Hydroxylase/metabolism ; Diet, High-Fat/*adverse effects ; Feces/microbiology ; Gastrointestinal Microbiome ; Hyperlipidemias/*drug therapy ; Lactobacillus plantarum/*physiology ; Lipid Metabolism/drug effects ; Lipid Metabolism Disorders ; Lipogenesis ; Liver/metabolism/pathology ; Male ; Mice ; Non-alcoholic Fatty Liver Disease/*drug therapy ; Probiotics/*pharmacology ; Triglycerides/blood ; }, abstract = {Lactobacillus plantarum FZU3013, a probiotic previously isolated from the traditional brewing process of Hongqu rice wine, may have the beneficial effect of improving the disorders of lipid metabolism. This study aimed to investigate the role of L. plantarum FZU3013 in improving non-alcoholic fatty liver (NAFL) associated with hyperlipidemia in mice fed a high-fat diet. The results indicated that L. plantarum FZU3013 intervention significantly reduced the HFD-induced body weight gain and the abnormal levels of serum total triglycerides (TG), total cholesterol (TC) and low-density lipoprotein (LDL-C), and inhibited the excessive accumulation of liver lipids. In addition, L. plantarum FZU3013 also promoted the excretion of bile acids through feces. Metagenomic and multivariate statistical analysis revealed that L. plantarum FZU3013 made significant structural changes in the intestinal microbiome of the mice fed with HFD, in particular by modulating the relative abundance of some function related microbial phylotypes. Furthermore, ultra-performance liquid chromatography with quadruple-time of flight mass spectrometry (UPLC-QTOF/MS)-based liver metabolomics demonstrated that L. plantarum FZU3013 had a significant regulatory effect on the composition of liver metabolites in hyperlipidemic mice, especially on the levels of some important biomarkers involved in the pathways of glycerophospholipid metabolism, fatty acid degradation, fatty acid elongation, glycerolipid metabolism, primary bile acid biosynthesis, arachidonic acid metabolism, etc. Moreover, L. plantarum FZU3013 regulated the mRNA expression levels of the genes responsible for liver lipid and cholesterol metabolism. L. plantarum FZU3013 intervention increased the hepatic mRNA levels of cholesterol 7α-hydroxylase (CYP7A1) and the bile salt export pump (BSEP), suggesting enhanced bile acid synthesis and excretion from the liver. These findings present new evidence supporting that L. plantarum FZU3013 has the potential to improve lipid metabolism disorders through modulating specific intestinal microbial phylotypes and regulating hepatic lipid metabolism related genes, therefore it could be used as a potential functional food for the prevention of NAFL and hyperlipidemia.}, } @article {pmid32221908, year = {2020}, author = {Caraballo Guzmán, A and González Hurtado, MI and Cuesta-Astroz, Y and Torres, G}, title = {Metagenomic characterization of bacterial biofilm in four food processing plants in Colombia.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {51}, number = {3}, pages = {1259-1267}, pmid = {32221908}, issn = {1678-4405}, support = {55965//Colciencias/ ; }, mesh = {Bacteria/classification/*genetics/isolation & purification ; *Biofilms ; Colombia ; Disinfection ; Equipment Contamination/*statistics & numerical data ; Food Handling/*instrumentation ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Bacteria inside biofilms are more persistent and resistant to stress conditions found in the production environment of food processing plants, thus representing a constant risk for product safety and quality. Therefore, the aim of this study was to characterize, using 16S rRNA sequencing, the bacterial communities from biofilms found in four food processing plants (P1, P2, P3, and P4). In total, 50 samples from these four processing plants were taken after cleaning and disinfection processes. Four phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroides represented over 94% of the operational taxonomic units found across these four plants. A total of 102 families and 189 genera were identified. Two genera, Pseudomonas spp. and Acinetobacter spp., were the most frequently found (93.47%) across the four plants. In P1, Pseudomonas spp. and Lactobacillus spp. were the dominant genera, whereas Lactobacillus spp. and Streptococcus spp. were identified in P2. On the other hand, biofilms found in P3 and P4 mainly consisted of Pseudomonas spp. and Acinetobacter spp. Our results indicate that different bacterial genera of interest to the food industry due to their ability to form biofilm and affect food quality can coexist inside biofilms, and as such, persist in production environments, representing a constant risk for manufactured foods. In addition, the core microbiota identified across processing plants evaluated was probably influenced by type of food produced and cleaning and disinfection processes performed in each one of these.}, } @article {pmid32216046, year = {2020}, author = {Sandoz, FA and Bindschedler, S and Dauphin, B and Farinelli, L and Grant, JR and Hervé, V}, title = {Biotic and abiotic factors shape arbuscular mycorrhizal fungal communities associated with the roots of the widespread fern Botrychium lunaria (Ophioglossaceae).}, journal = {Environmental microbiology reports}, volume = {12}, number = {3}, pages = {342-354}, doi = {10.1111/1758-2229.12840}, pmid = {32216046}, issn = {1758-2229}, support = {//Fonds Wuthrich Mathey-Dupraz/International ; 31003A_156456//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/International ; CR32I2-149853/1//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/International ; CR32I2-149853/1 31003A_156456/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Ferns/*microbiology ; Genes, Fungal ; Glomeromycota/classification/genetics/isolation & purification ; Grassland ; Metagenomics ; Microbial Interactions ; Microbiota ; Mycobiome/*genetics ; Mycorrhizae/*genetics ; Phylogeny ; Plant Roots/microbiology ; Soil Microbiology ; Switzerland ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) play central roles in terrestrial ecosystems by interacting with both above and belowground communities as well as by influencing edaphic properties. The AMF communities associated with the roots of the fern Botrychium lunaria (Ophioglossaceae) were sampled in four transects at 2400 m a.s.l. in the Swiss Alps and analyzed using metabarcoding. Members of five Glomeromycota genera were identified across the 71 samples. Our analyses revealed the existence of a core microbiome composed of four abundant Glomus operational taxonomic units (OTUs), as well as a low OTU turnover between samples. The AMF communities were not spatially structured, which contrasts with most studies on AMF associated with angiosperms. pH, microbial connectivity and humus cover significantly shaped AMF beta diversity but only explained a minor fraction of variation in beta diversity. AMF OTUs associations were found to be significant by both cohesion and co-occurrence analyses, suggesting a role for fungus-fungus interactions in AMF community assembly. In particular, OTU co-occurrences were more frequent between different genera than among the same genus, rising the hypothesis of functional complementarity among the AMF associated to B. lunaria. Altogether, our results provide new insights into the ecology of fern symbionts in alpine grasslands.}, } @article {pmid32213246, year = {2020}, author = {Averina, OV and Kovtun, AS and Polyakova, SI and Savilova, AM and Rebrikov, DV and Danilenko, VN}, title = {The bacterial neurometabolic signature of the gut microbiota of young children with autism spectrum disorders.}, journal = {Journal of medical microbiology}, volume = {69}, number = {4}, pages = {558-571}, doi = {10.1099/jmm.0.001178}, pmid = {32213246}, issn = {1473-5644}, mesh = {Autism Spectrum Disorder/*microbiology ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Butyric Acid/metabolism ; Child, Preschool ; Cohort Studies ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Melatonin/metabolism ; Metagenome ; }, abstract = {Introduction. The human gut microbiota is currently seen as an important factor that can promote autism spectrum disorder (ASD) development in children.Aim. This study aimed to detect differences in the taxonomic composition and content of bacterial genes encoding key enzymes involved in the metabolism of neuroactive biomarker compounds in the metagenomes of gut microbiota of children with ASD and neurotypical children.Methodology. A whole metagenome sequencing approach was used to obtain metagenomic data on faecal specimens of 36 children with ASD and 21 healthy neurotypical children of 3-5 years old. Taxonomic analysis was conducted using MetaPhlAn2. The developed bioinformatics algorithm and created catalogue of the orthologues were applied to identify bacterial genes of neuroactive compounds in the metagenomes. For the identification of metagenomic signatures of children with ASD, Wilcoxon's test and adjustment for multiple comparisons were used.Results. Statistically significant differences with decreases in average abundance in the microbiota of ASD children were found for the genera Barnesiella and Parabacteroides and species Alistipes putredinis, B. caccae, Bacteroides intestinihominis, Eubacterium rectale, Parabacteroides distasonis and Ruminococcus lactaris. Average relative abundances of the detected genes and neurometabolic signature approach did not reveal many significant differences in the metagenomes of the groups that were compared. We noted decreases in the abundance of genes linked to production of GABA, melatonine and butyric acid in the ASD metagenomes.Conclusion. For the first time, the neurometabolic signature of the gut microbiota of young children with ASD is presented. The data can help to provide a comparative assessment of the transcriptional and metabolomic activity of the identified genes.}, } @article {pmid32211345, year = {2020}, author = {Walkenhorst, MS and Reyes, L and Perez, G and Progulske-Fox, A and Brown, MB and Phillips, PL}, title = {A Uniquely Altered Oral Microbiome Composition Was Observed in Pregnant Rats With Porphyromonas gingivalis Induced Periodontal Disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {92}, pmid = {32211345}, issn = {2235-2988}, support = {R15 HD081439/HD/NICHD NIH HHS/United States ; }, mesh = {Alveolar Bone Loss/etiology ; Animals ; Antibodies, Bacterial/blood ; Bacteroidaceae Infections/*microbiology ; Dysbiosis/microbiology ; Female ; Immunity, Humoral ; Metagenome ; *Microbiota/physiology ; Mouth/*microbiology ; Periodontitis/*microbiology ; Pilot Projects ; *Porphyromonas gingivalis/immunology ; Pregnancy ; Pregnancy Complications, Infectious/*microbiology ; Rats ; }, abstract = {Porphyromonas gingivalis is an anaerobic bacterium commonly found in the oral cavity and associated with the development of periodontal disease. P. gingivalis has also been linked to several systemic vascular and inflammatory diseases including poor pregnancy outcomes. Little is known about the changes in the oral flora during pregnancy in connection to P. gingivalis infection. This pilot study aims to explore changes in the oral microbiome due to P. gingivalis inoculation and pregnancy in an in vivo rat model of periodontal disease. A metagenomic sequencing analysis targeting seven of the 16S rRNA gene variable regions was performed for oral samples collected at the following time points: baseline control (week 0), P. gingivalis inoculated (week 11), P. gingivalis inoculated and pregnant rat at necropsy (week 16). A second set of animals were also sampled to generate a sham-inoculated (week 11) control group. We found that the rat oral microbiome profiles were more similar to that of the human oral cavity compared to previous reports targeting one or two 16S variable regions. Overall, there appears to be a relatively stable core microbiome in the oral cavity. As expected, P. gingivalis induced periodontal disease resulted in oral microbiome dysbiosis. During pregnancy, some aspects of the oral microbiome shifted toward a more baseline-like profile. However, population analyses in terms of dissimilarity measures and especially metagenomic based predictions of select characteristics such as cell morphology, oxygen requirement, and major metabolite synthesis showed that pregnancy did not restore the composition of the oral microbiome. Rather, a uniquely altered oral microbiome composition was observed in pregnant rats with pre-established periodontal disease.}, } @article {pmid32210237, year = {2020}, author = {Long, S and Yang, Y and Shen, C and Wang, Y and Deng, A and Qin, Q and Qiao, L}, title = {Metaproteomics characterizes human gut microbiome function in colorectal cancer.}, journal = {NPJ biofilms and microbiomes}, volume = {6}, number = {1}, pages = {14}, pmid = {32210237}, issn = {2055-5008}, mesh = {Bacteria/*classification/isolation & purification/metabolism ; Bacterial Proteins/*analysis ; Case-Control Studies ; Chromatography, Liquid ; Colorectal Neoplasms/*microbiology ; DNA Replication ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Iron/metabolism ; Male ; Oxidative Stress ; Phylogeny ; Proteomics/*methods ; Tandem Mass Spectrometry ; }, abstract = {Pathogenesis of colorectal cancer (CRC) is associated with alterations in gut microbiome. Previous studies have focused on the changes of taxonomic abundances by metagenomics. Variations of the function of intestinal bacteria in CRC patients compared to healthy crowds remain largely unknown. Here we collected fecal samples from CRC patients and healthy volunteers and characterized their microbiome using quantitative metaproteomic method. We have identified and quantified 91,902 peptides, 30,062 gut microbial protein groups, and 195 genera of microbes. Among the proteins, 341 were found significantly different in abundance between the CRC patients and the healthy volunteers. Microbial proteins related to iron intake/transport; oxidative stress; and DNA replication, recombination, and repair were significantly alternated in abundance as a result of high local concentration of iron and high oxidative stress in the large intestine of CRC patients. Our study shows that metaproteomics can provide functional information on intestinal microflora that is of great value for pathogenesis research, and can help guide clinical diagnosis in the future.}, } @article {pmid32210160, year = {2020}, author = {Melnikova, DI and Magarlamov, TY}, title = {The Microbial Community of Tetrodotoxin-Bearing and Non-Tetrodotoxin-Bearing Ribbon Worms (Nemertea) from the Sea of Japan.}, journal = {Marine drugs}, volume = {18}, number = {3}, pages = {}, pmid = {32210160}, issn = {1660-3397}, mesh = {Animals ; Aquatic Organisms/*microbiology ; DNA, Bacterial/isolation & purification ; Invertebrates/*microbiology ; Microbiota/*physiology ; Oceans and Seas ; RNA, Ribosomal, 16S/genetics ; Tetrodotoxin/*metabolism ; }, abstract = {A potent marine toxin, tetrodotoxin (TTX), found in a great variety of marine and some terrestrial species, leaves intriguing questions about its origin and distribution in marine ecosystems. TTX-producing bacteria were found in the cultivable microflora of many TTX-bearing hosts, thereby providing strong support for the hypothesis that the toxin is of bacterial origin in these species. However, metagenomic studies of TTX-bearing animals addressing the whole microbial composition and estimating the contribution of TTX-producing bacteria to the overall toxicity of the host were not conducted. The present study is the first to characterize and compare the 16S rRNA gene data obtained from four TTX-bearing and four non-TTX-bearing species of marine ribbon worms. The statistical analysis showed that different nemertean species harbor distinct bacterial communities, while members of the same species mostly share more similar microbiomes. The bacterial species historically associated with TTX production were found in all studied samples but predominated in TTX-bearing nemertean species. This suggests that deeper knowledge of the microbiome of TTX-bearing animals is a key to understanding the origin of TTX in marine ecosystems.}, } @article {pmid32209692, year = {2020}, author = {Storey, MA and Andreassend, SK and Bracegirdle, J and Brown, A and Keyzers, RA and Ackerley, DF and Northcote, PT and Owen, JG}, title = {Metagenomic Exploration of the Marine Sponge Mycale hentscheli Uncovers Multiple Polyketide-Producing Bacterial Symbionts.}, journal = {mBio}, volume = {11}, number = {2}, pages = {}, pmid = {32209692}, issn = {2150-7511}, mesh = {Animals ; Aquatic Organisms/microbiology ; Bacteria/*classification/isolation & purification ; Biosynthetic Pathways ; Metabolome ; *Metagenomics ; Microbiota ; Multigene Family ; Phylogeny ; Polyketides/*metabolism ; Porifera/*microbiology ; Secondary Metabolism ; *Symbiosis ; }, abstract = {Marine sponges have been a prolific source of unique bioactive compounds that are presumed to act as a deterrent to predation. Many of these compounds have potential therapeutic applications; however, the lack of efficient and sustainable synthetic routes frequently limits clinical development. Here, we describe a metagenomic investigation of Mycale hentscheli, a chemically gifted marine sponge that possesses multiple distinct chemotypes. We applied shotgun metagenomic sequencing, hybrid assembly of short- and long-read data, and metagenomic binning to obtain a comprehensive picture of the microbiome of five specimens, spanning three chemotypes. Our data revealed multiple producing species, each having relatively modest secondary metabolomes, that contribute collectively to the chemical arsenal of the holobiont. We assembled complete genomes for multiple new genera, including two species that produce the cytotoxic polyketides pateamine and mycalamide, as well as a third high-abundance symbiont harboring a proteusin-type biosynthetic pathway that appears to encode a new polytheonamide-like compound. We also identified an additional 188 biosynthetic gene clusters, including a pathway for biosynthesis of peloruside. These results suggest that multiple species cooperatively contribute to defensive symbiosis in M. hentscheli and reveal that the taxonomic diversity of secondary-metabolite-producing sponge symbionts is larger and richer than previously recognized.IMPORTANCEMycale hentscheli is a marine sponge that is rich in bioactive small molecules. Here, we use direct metagenomic sequencing to elucidate highly complete and contiguous genomes for the major symbiotic bacteria of this sponge. We identify complete biosynthetic pathways for the three potent cytotoxic polyketides which have previously been isolated from M. hentscheli Remarkably, and in contrast to previous studies of marine sponges, we attribute each of these metabolites to a different producing microbe. We also find that the microbiome of M. hentscheli is stably maintained among individuals, even over long periods of time. Collectively, our data suggest a cooperative mode of defensive symbiosis in which multiple symbiotic bacterial species cooperatively contribute to the defensive chemical arsenal of the holobiont.}, } @article {pmid32209031, year = {2020}, author = {Sarma, SJ and Lei, Z and Rosenfeld, CS and Ericsson, A and Sumner, LW}, title = {Nontargeted fecal metabolomics: an emerging tool to probe the role of the gut microbiome in host health.}, journal = {Bioanalysis}, volume = {12}, number = {6}, pages = {351-353}, doi = {10.4155/bio-2020-0010}, pmid = {32209031}, issn = {1757-6199}, support = {R01 ES025547/ES/NIEHS NIH HHS/United States ; }, mesh = {Feces/*chemistry ; Gastrointestinal Microbiome/*physiology ; Humans ; Metabolomics/*methods ; }, } @article {pmid32208434, year = {2020}, author = {Jangid, A and Fukuda, S and Seki, M and Horiuchi, T and Suzuki, Y and Taylor, TD and Ohno, H and Prakash, T}, title = {Association of colitis with gut-microbiota dysbiosis in clathrin adapter AP-1B knockout mice.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0228358}, pmid = {32208434}, issn = {1932-6203}, mesh = {Adaptor Protein Complex 1/*deficiency/*genetics ; Animals ; Colitis/complications/*genetics/*microbiology ; Dysbiosis/complications/*microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; Mice ; }, abstract = {Inflammatory bowel disease results from alterations in the immune system and intestinal microbiota. The role of intestinal epithelial cells (IECs) in maintaining gut homeostasis is well known and its perturbation often causes gastrointestinal disorders including IBD. The epithelial specific adaptor protein (AP)-1B is involved in the establishment of the polarity of IECs. Deficiency of the AP-1B μ subunit (Ap1m2-/-) leads to the development of chronic colitis in mice. However, how this deficiency affects the gut microbes and its potential functions remains elusive. To gain insights into the gut microbiome of Ap1m2-/- mice having the colitis phenotype, we undertook shotgun metagenomic sequencing analysis of knockout mice. We found important links to the microbial features involved in altering various physiological pathways, including carbohydrate metabolism, nutrient transportation, oxidative stress, and bacterial pathogenesis (cell motility). In addition, an increased abundance of sulfur-reducing and lactate-producing bacteria has been observed which may aggravate the colitis condition.}, } @article {pmid32207614, year = {2020}, author = {Hu, W and Liang, J and Ju, F and Wang, Q and Liu, R and Bai, Y and Liu, H and Qu, J}, title = {Metagenomics Unravels Differential Microbiome Composition and Metabolic Potential in Rapid Sand Filters Purifying Surface Water Versus Groundwater.}, journal = {Environmental science & technology}, volume = {54}, number = {8}, pages = {5197-5206}, doi = {10.1021/acs.est.9b07143}, pmid = {32207614}, issn = {1520-5851}, mesh = {Filtration ; *Groundwater ; Metagenomics ; *Microbiota ; Oxidation-Reduction ; Sand ; *Water Purification ; }, abstract = {Designed for retaining suspended particles, rapid sand filters (RSFs) are widely used in drinking water treatment. There is increasing evidence that microbial processes within RSFs contribute to the transformation and removal of organic carbon, nitrogen, and metal pollutants. Here, we linked microbial composition and functional profiles with the treatment performance of 12 different RSFs that significantly removed influent ammonium and manganese (Mn). Metagenomic analyses showed that chemoautotrophic or methanotrophic bacteria were prevalent in the groundwater filters, and chemoheterotrophic bacteria encoding more carbohydrate- and xenobiotic-metabolizing genes were more abundant in the surface water filters. Approximately 92% of ammonium was transformed into nitrate, with a critical contribution from comammox Nitrospira. The composition of comammox amoA differed between groundwater and surface water filters, with clade A dominating groundwater filters (78.0 ± 12.0%) and clade B dominating surface water filters (91.9 ± 8.9%). Further, we identified six bacterial genera encoding known Mn(II)-oxidizing genes in the RSFs, with Pseudomonas accounting for 71.1%. These Mn(II)-oxidizing bacteria might promote Mn(II) oxidation and thus increase the removal of influent Mn. Overall, our study gave a comprehensive investigation of microbiome in RSFs and highlighted the roles of comammox and Mn(II)-oxidizing bacteria in water purification.}, } @article {pmid32207218, year = {2020}, author = {Newberry, E and Bhandari, R and Kemble, J and Sikora, E and Potnis, N}, title = {Genome-resolved metagenomics to study co-occurrence patterns and intraspecific heterogeneity among plant pathogen metapopulations.}, journal = {Environmental microbiology}, volume = {22}, number = {7}, pages = {2693-2708}, doi = {10.1111/1462-2920.14989}, pmid = {32207218}, issn = {1462-2920}, support = {//Alabama Agricultural Experiment Station/International ; //National Institute of Food and Agriculture/International ; }, mesh = {Base Sequence ; Genome, Bacterial/*genetics ; Genomics ; Genotype ; Humans ; Solanum lycopersicum/*microbiology ; Metagenomics ; Microbiota/genetics ; Plant Diseases/*microbiology ; Plant Leaves/microbiology ; Pseudomonas/*genetics ; Sequence Analysis, DNA ; Xanthomonas/*genetics ; }, abstract = {Assessment of pathogen diversity in agricultural fields is essential for informing management decisions and the development of resistant plant varieties. However, many population genomic studies have relied on culture-based approaches that do not provide quantitative assessment of pathogen populations at the field-level or the associated host microbiome. Here, we applied whole-genome shotgun sequencing of microbial DNA extracted directly from the washings of pooled leaf samples, collected from individual tomato and pepper fields in Alabama that displayed the classical symptoms of bacterial spot disease caused by Xanthomonas spp. Our results revealed that while the occurrence of both X. perforans and X. euvesicatoria within fields was limited, evidence of co-occurrence of up to three distinct X. perforans genotypes was obtained in 7 of 10 tomato fields sampled. These population dynamics were accompanied by the corresponding type 3 secreted effector repertoires associated with the co-occurring X. perforans genotypes, indicating that metapopulation structure within fields should be considered when assessing the adaptive potential of X. perforans. Finally, analysis of microbial community composition revealed that co-occurrence of the bacterial spot pathogens Pseudomonas cichorii and Xanthomonas spp. is common in Alabama fields and provided evidence for the non-random association of several other human and plant opportunists.}, } @article {pmid32206831, year = {2020}, author = {Mehta, O and Ghosh, TS and Kothidar, A and Gowtham, MR and Mitra, R and Kshetrapal, P and Wadhwa, N and Thiruvengadam, R and , and Nair, GB and Bhatnagar, S and Das, B}, title = {Vaginal Microbiome of Pregnant Indian Women: Insights into the Genome of Dominant Lactobacillus Species.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {487-499}, doi = {10.1007/s00248-020-01501-0}, pmid = {32206831}, issn = {1432-184X}, support = {No.BT/PR9983/MED/97/194/2013//Department of Biotechnology, Government of India/ ; }, mesh = {Adult ; Bacteria/isolation & purification ; Female ; Genome, Bacterial/*physiology ; Humans ; India ; Lactobacillus/genetics/*physiology ; *Microbiota ; Pregnancy ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Vagina/*microbiology ; Young Adult ; }, abstract = {The trillions of microorganisms residing in the human body display varying degrees of compositional and functional diversities within and between individuals and contribute significantly to host physiology and susceptibility to disease. Microbial species present in the vaginal milieu of reproductive age women showed a large personal component and varies widely in different ethnic groups at the taxonomic, genomic, and functional levels. Lactobacillus iners, L. crispatus, L. gasseri, L. jensenii, and L. johnsonii are most frequently detected bacterial species in the vaginal milieu of reproductive age women. However, we currently lack (i) an understanding of the baseline vaginal microbiota of reproductive age Indian women, (ii) the extent of taxonomic and functional variations of vaginal microbiota between individuals and (iii) the genomic repertoires of the dominant vaginal microbiota associated with the Indian subjects. In our study, we analyzed the metagenome of high vaginal swab (HVS) samples collected from 40 pregnant Indian women enrolled in the GARBH-Ini cohort. Composition and abundance of bacterial species was characterized by pyrosequencing 16S rRNA gene. We identified 3067 OTUs with ≥ 10 reads from four different bacterial phyla. Several species of lactobacilli were clustered into three community state types (CSTs). L. iners, L. crispatus, L. gasseri, and L. jensenii are the most frequently detected Lactobacillus species in the vaginal environment of Indian women. Other than Lactobacillus, several species of Halomonas were also identified in the vaginal environment of most of the women sampled. To gain genomic and functional insights, we isolated several Lactobacillus species from the HVS samples and explored their whole genome sequences by shotgun sequencing. We analyzed the genome of dominant Lactobacillus species, L. iners, L. crispatus, L. gasseri, and L. paragesseri to represent the CSTs and identify functions that may influence the composition of complex vaginal microbial ecology. This study reports for the first time the vaginal microbial ecology of Indian women and genomic insights into L. iners, L. crispatus, L. gasseri, and L. paragesseri commonly found in the genital tract of reproductive age women.}, } @article {pmid32205368, year = {2020}, author = {Vorobev, A and Dupouy, M and Carradec, Q and Delmont, TO and Annamalé, A and Wincker, P and Pelletier, E}, title = {Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics.}, journal = {Genome research}, volume = {30}, number = {4}, pages = {647-659}, pmid = {32205368}, issn = {1549-5469}, mesh = {Biodiversity ; Computational Biology/*methods ; Eukaryota/classification/*genetics ; *Gene Expression Profiling/methods ; *Metagenome ; *Metagenomics/methods ; Phylogeny ; Plankton/classification/*genetics ; *Transcriptome ; }, abstract = {Large-scale metagenomic and metatranscriptomic data analyses are often restricted by their gene-centric approach, limiting the ability to understand organismal and community biology. De novo assembly of large and mosaic eukaryotic genomes from complex meta-omics data remains a challenging task, especially in comparison with more straightforward bacterial and archaeal systems. Here, we use a transcriptome reconstruction method based on clustering co-abundant genes across a series of metagenomic samples. We investigated the co-abundance patterns of ∼37 million eukaryotic unigenes across 365 metagenomic samples collected during the Tara Oceans expeditions to assess the diversity and functional profiles of marine plankton. We identified ∼12,000 co-abundant gene groups (CAGs), encompassing ∼7 million unigenes, including 924 metagenomics-based transcriptomes (MGTs, CAGs larger than 500 unigenes). We demonstrated the biological validity of the MGT collection by comparing individual MGTs with available references. We identified several key eukaryotic organisms involved in dimethylsulfoniopropionate (DMSP) biosynthesis and catabolism in different oceanic provinces, thus demonstrating the potential of the MGT collection to provide functional insights on eukaryotic plankton. We established the ability of the MGT approach to capture interspecies associations through the analysis of a nitrogen-fixing haptophyte-cyanobacterial symbiotic association. This MGT collection provides a valuable resource for analyses of eukaryotic plankton in the open ocean by giving access to the genomic content and functional potential of many ecologically relevant eukaryotic species.}, } @article {pmid32204538, year = {2020}, author = {Tsai, MC and Liu, YY and Lin, CC and Wang, CC and Wu, YJ and Yong, CC and Chen, KD and Chuah, SK and Yao, CC and Huang, PY and Chen, CH and Hu, TH and Chen, CL}, title = {Gut Microbiota Dysbiosis in Patients with Biopsy-Proven Nonalcoholic Fatty Liver Disease: A Cross-Sectional Study in Taiwan.}, journal = {Nutrients}, volume = {12}, number = {3}, pages = {}, pmid = {32204538}, issn = {2072-6643}, support = {CMRPG8H1111//Kaohsiung Chang Gung Memorial Hospital/ ; CMRPG8J1571//Kaohsiung Chang Gung Memorial Hospital/ ; CMRPG8K0661//Kaohsiung Chang Gung Memorial Hospital/ ; }, mesh = {Adolescent ; Adult ; Aged ; Biomarkers ; Biopsy ; Case-Control Studies ; Cross-Sectional Studies ; *Dysbiosis ; Female ; *Gastrointestinal Microbiome ; Humans ; Liver/metabolism/pathology ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Non-alcoholic Fatty Liver Disease/diagnosis/*epidemiology/*etiology ; Public Health Surveillance ; Taiwan/epidemiology ; Young Adult ; }, abstract = {The gut microbiota plays a role in nonalcoholic fatty liver disease (NAFLD), but data about gut dysbiosis in Asians with NAFLD remains scarce. We analyzed the differences in fecal microbiota between adults with and without NAFLD. This cross-sectional study examined adults with histology-proven NAFLD (25 nonalcoholic fatty liver (NAFL) patients, 25 nonalcoholic steatohepatitis (NASH) patients, and 25 living liver donors (healthy controls)). The taxonomic composition of the gut microbiota was determined by 16S ribosomal RNA gene sequencing of stool samples. The NAFL and NASH groups showed lower total bacterial diversity and richness than the controls. NAFLD patients had higher levels of the phylum Bacteroidetes and lower levels of Firmicutes than controls. The genus Ruminococcaceae UCG-010, family Ruminococcaceae, order Clostridiales, and class Clostridia were less abundant in patients with NAFL or NASH than healthy individuals. The lipopolysaccharide biosynthesis pathway was differentially enriched in the NASH group. This study examined the largest number of Asian patients with biopsy-proven NAFL and NASH in terms of dysbiosis of the gut microbiota in NAFLD patients. NAFLD patients had higher levels of Bacteroidetes and lower levels of Firmicutes. These results are different from research from western countries and could provide different targets for therapies by region.}, } @article {pmid32203124, year = {2020}, author = {Liang, JL and Liu, J and Jia, P and Yang, TT and Zeng, QW and Zhang, SC and Liao, B and Shu, WS and Li, JT}, title = {Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining.}, journal = {The ISME journal}, volume = {14}, number = {6}, pages = {1600-1613}, pmid = {32203124}, issn = {1751-7370}, mesh = {Bacteria/genetics ; China ; Microbiota ; *Mining ; Phosphates/metabolism ; Phosphorus/*metabolism ; Plants/metabolism ; Soil ; *Soil Microbiology ; }, abstract = {Little is known about the changes in soil microbial phosphorus (P) cycling potential during terrestrial ecosystem management and restoration, although much research aims to enhance soil P cycling. Here, we used metagenomic sequencing to analyse 18 soil microbial communities at a P-deficient degraded mine site in southern China where ecological restoration was implemented using two soil ameliorants and eight plant species. Our results show that the relative abundances of key genes governing soil microbial P-cycling potential were higher at the restored site than at the unrestored site, indicating enhancement of soil P cycling following restoration. The gcd gene, encoding an enzyme that mediates inorganic P solubilization, was predominant across soil samples and was a major determinant of bioavailable soil P. We reconstructed 39 near-complete bacterial genomes harboring gcd, which represented diverse novel phosphate-solubilizing microbial taxa. Strong correlations were found between the relative abundance of these genomes and bioavailable soil P, suggesting their contributions to the enhancement of soil P cycling. Moreover, 84 mobile genetic elements were detected in the scaffolds containing gcd in the 39 genomes, providing evidence for the role of phage-related horizontal gene transfer in assisting soil microbes to acquire new metabolic potential related to P cycling.}, } @article {pmid32203121, year = {2020}, author = {Campbell, TP and Sun, X and Patel, VH and Sanz, C and Morgan, D and Dantas, G}, title = {The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography.}, journal = {The ISME journal}, volume = {14}, number = {6}, pages = {1584-1599}, pmid = {32203121}, issn = {1751-7370}, support = {DP2 DK098089/DK/NIDDK NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial ; Gastrointestinal Microbiome/drug effects ; Geography ; Gorilla gorilla/*microbiology ; Humans ; Life Style ; Metagenomics ; *Microbiota ; Pan troglodytes/*microbiology ; }, abstract = {The gut microbiome can vary across differences in host lifestyle, geography, and host species. By comparing closely related host species across varying lifestyles and geography, we can evaluate the relative contributions of these factors in structuring the composition and functions of the microbiome. Here we show that the gut microbial taxa, microbial gene family composition, and resistomes of great apes and humans are more related by host lifestyle than geography. We show that captive chimpanzees and gorillas are enriched for microbial genera commonly found in non-Westernized humans. Captive ape microbiomes also had up to ~34-fold higher abundance and up to ~5-fold higher richness of all antibiotic resistance genes compared with wild apes. Through functional metagenomics, we identified a number of novel antibiotic resistance genes, including a gene conferring resistance to colistin, an antibiotic of last resort. Finally, by comparing our study cohorts to human and ape gut microbiomes from a diverse range of environments and lifestyles, we find that the influence of host lifestyle is robust to various geographic locations.}, } @article {pmid32202696, year = {2020}, author = {Zhang, X and Ma, C and Zhang, W and Li, W and Yu, J and Xue, D and Wu, X and Deng, G}, title = {Shifts in microbial community, pathogenicity-related genes and antibiotic resistance genes during dairy manure piled up.}, journal = {Microbial biotechnology}, volume = {13}, number = {4}, pages = {1039-1053}, pmid = {32202696}, issn = {1751-7915}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; Drug Resistance, Microbial/genetics ; Female ; Genes, Bacterial ; Humans ; *Manure ; *Microbiota ; Soil ; Soil Microbiology ; Virulence ; }, abstract = {The uncomposted faeces of dairy cow are usually stacked on cow breeding farms, dried under natural conditions and then used as cow bedding material or they may be continuously piled up. However, no information is available to evaluate variations in the human and animal pathogen genes and antibiotic resistance during the accumulation of fresh faeces of dairy cow to manure. Here, we present the metagenomic analysis of fresh faeces and manure from a dairy farm in Ning Xia, showing a unique enrichment of human and animal pathogen genes and antibiotic resistance genes (ARGs) in manure. We found that manure accumulation could significantly increase the diversity and abundance of the pathogenic constituents. Furthermore, pathogens from manure could spread to the plant environment and enphytotic pathogens could affect the yield and quality of crops during the use of manure as a fertilizer. Levels of virulence genes and ARGs increased with the enrichment of microbes and pathogens when faeces accumulated to manure. Accumulated manure was also the transfer station of ARGs to enrich the ARGs in the environment, indicating the ubiquitous presence of environmental antibiotic resistance genes. Our results demonstrate that manure accumulation and usage without effective manure management is an unreasonable approach that could enrich pathogenic microorganisms and ARGs in the environment. The manure metagenome structure allows us to appreciate the overall influence and interaction of animal waste on water, soil and other areas impacted by faecal accumulation and the factors that influence pathogen occurrence in products from dairy cows.}, } @article {pmid32200751, year = {2020}, author = {Quistad, SD and Doulcier, G and Rainey, PB}, title = {Experimental manipulation of selfish genetic elements links genes to microbial community function.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1798}, pages = {20190681}, pmid = {32200751}, issn = {1471-2970}, mesh = {Bacteria/*genetics ; Metagenome ; Metagenomics ; Microbiota/*genetics ; *Repetitive Sequences, Nucleic Acid ; *Soil Microbiology ; }, abstract = {Microbial communities underpin the Earth's biological and geochemical processes, but their complexity hampers understanding. Motivated by the challenge of diversity and the need to forge ways of capturing dynamical behaviour connecting genes to function, biologically independent experimental communities comprising hundreds of microbial genera were established from garden compost and propagated on nitrogen-limited minimal medium with cellulose (paper) as sole carbon source. After 1 year of bi-weekly transfer, communities retained hundreds of genera. To connect genes to function, we used a simple experimental manipulation that involved the periodic collection of selfish genetic elements (SGEs) from separate communities, followed by pooling and redistribution across communities. The treatment was predicted to promote amplification and dissemination of SGEs and thus horizontal gene transfer. Confirmation came from comparative metagenomics, which showed the substantive movement of ecologically significant genes whose dynamic across space and time could be followed. Enrichment of genes implicated in nitrogen metabolism, and particularly ammonification, prompted biochemical assays that revealed a measurable impact on community function. Our simple experimental strategy offers a conceptually new approach for unravelling dynamical processes affecting microbial community function. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.}, } @article {pmid32200748, year = {2020}, author = {VanInsberghe, D and Arevalo, P and Chien, D and Polz, MF}, title = {How can microbial population genomics inform community ecology?.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1798}, pages = {20190253}, pmid = {32200748}, issn = {1471-2970}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Gene Flow ; *Metagenomics ; Microbiota/*genetics ; }, abstract = {Populations are fundamental units of ecology and evolution, but can we define them for bacteria and archaea in a biologically meaningful way? Here, we review why population structure is difficult to recognize in microbes and how recent advances in measuring contemporary gene flow allow us to identify clearly delineated populations among collections of closely related genomes. Such structure can arise from preferential gene flow caused by coexistence and genetic similarity, defining populations based on biological mechanisms. We show that such gene flow units are sufficiently genetically isolated for specific adaptations to spread, making them also ecological units that are differentially adapted compared to their closest relatives. We discuss the implications of these observations for measuring bacterial and archaeal diversity in the environment. We show that operational taxonomic units defined by 16S rRNA gene sequencing have woefully poor resolution for ecologically defined populations and propose monophyletic clusters of nearly identical ribosomal protein genes as an alternative measure for population mapping in community ecological studies employing metagenomics. These population-based approaches have the potential to provide much-needed clarity in interpreting the vast microbial diversity in human and environmental microbiomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.}, } @article {pmid32200740, year = {2020}, author = {Garcia, CA and Hagstrom, GI and Larkin, AA and Ustick, LJ and Levin, SA and Lomas, MW and Martiny, AC}, title = {Linking regional shifts in microbial genome adaptation with surface ocean biogeochemistry.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1798}, pages = {20190254}, pmid = {32200740}, issn = {1471-2970}, support = {T32 AI141346/AI/NIAID NIH HHS/United States ; }, mesh = {*Adaptation, Biological ; Atlantic Ocean ; Genome, Microbial/*physiology ; Indian Ocean ; *Metagenome ; Microbiota/*genetics ; Pacific Ocean ; Seawater/*chemistry ; }, abstract = {Linking 'omics measurements with biogeochemical cycles is a widespread challenge in microbial community ecology. Here, we propose applying genomic adaptation as 'biosensors' for microbial investments to overcome nutrient stress. We then integrate this genomic information with a trait-based model to predict regional shifts in the elemental composition of marine plankton communities. We evaluated this approach using metagenomic and particulate organic matter samples from the Atlantic, Indian and Pacific Oceans. We find that our genome-based trait model significantly improves our prediction of particulate C : P (carbon : phosphorus) across ocean regions. Furthermore, we detect previously unrecognized ocean areas of iron, nitrogen and phosphorus stress. In many ecosystems, it can be very challenging to quantify microbial stress. Thus, a carefully calibrated genomic approach could become a widespread tool for understanding microbial responses to environmental changes and the biogeochemical outcomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.}, } @article {pmid32200735, year = {2020}, author = {Rainey, PB and Quistad, SD}, title = {Toward a dynamical understanding of microbial communities.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1798}, pages = {20190248}, pmid = {32200735}, issn = {1471-2970}, mesh = {Bacteria/*genetics ; *Bacterial Physiological Phenomena/genetics ; *Biological Evolution ; *Gene Transfer, Horizontal ; *Metagenome ; *Microbiota ; }, abstract = {The challenge of moving beyond descriptions of microbial community composition to the point where understanding underlying eco-evolutionary dynamics emerges is daunting. While it is tempting to simplify through use of model communities composed of a small number of types, there is a risk that such strategies fail to capture processes that might be specific and intrinsic to complexity of the community itself. Here, we describe approaches that embrace this complexity and show that, in combination with metagenomic strategies, dynamical insight is increasingly possible. Arising from these studies is mounting evidence of rapid eco-evolutionary change among lineages and a sense that processes, particularly those mediated by horizontal gene transfer, not only are integral to system function, but are central to long-term persistence. That such dynamic, systems-level insight is now possible, means that the study and manipulation of microbial communities can move to new levels of inquiry. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.}, } @article {pmid32200314, year = {2020}, author = {Wang, Y and Hu, Y and Liu, F and Cao, J and Lv, N and Zhu, B and Zhang, G and Gao, GF}, title = {Integrated metagenomic and metatranscriptomic profiling reveals differentially expressed resistomes in human, chicken, and pig gut microbiomes.}, journal = {Environment international}, volume = {138}, number = {}, pages = {105649}, doi = {10.1016/j.envint.2020.105649}, pmid = {32200314}, issn = {1873-6750}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Chickens ; China ; *Gastrointestinal Microbiome/genetics ; Genes, Bacterial ; Humans ; Metagenomics ; Swine ; }, abstract = {Gut microbiota is a reservoir of antibiotic resistance genes (ARGs). Yet, limited information is available regarding the presence (metagenomic DNA level) and expression profiles (metatranscriptomic RNA level) of ARGs in gut microbiota. Here, we used both metagenomic and metatranscriptomic approaches to comprehensively reveal the abundance, diversity, and expression of ARGs in human, chicken, and pig gut microbiomes in China. Based on deep sequencing data and ARG databases, a total of 330 ARGs associated with 21 antibiotic classes were identified in 18 human, chicken, and pig fecal samples. Metatranscriptomic analysis revealed that 49.4, 66.5, and 56.6% of ARGs identified in human, chicken, and pig gut microbiota, respectively, were expressed, indicating that a large proportion of ARGs were not transcriptionally active. Further analysis demonstrated that transcript abundance of tetracycline, aminoglycoside, and beta-lactam resistance genes was mainly contributed by acquired ARGs. We also found that various biocide, chemical, and metal resistance genes were actively transcribed in human and animal guts. The combination of metagenomic and metatranscriptomic analysis in this study allowed us to specifically link ARGs to their transcripts, providing a comprehensive view of the prevalence and expression of ARGs in gut microbiota. Taken together, these data deepen our understanding of the distribution, evolution, and dissemination of ARGs and metal resistance genes in human, chicken, and pig gut microbiota.}, } @article {pmid32200249, year = {2020}, author = {Santos, A and Rachid, C and Pacheco, AB and Magalhães, V}, title = {Biotic and abiotic factors affect microcystin-LR concentrations in water/sediment interface.}, journal = {Microbiological research}, volume = {236}, number = {}, pages = {126452}, doi = {10.1016/j.micres.2020.126452}, pmid = {32200249}, issn = {1618-0623}, mesh = {Biodegradation, Environmental ; Cyanobacteria/*metabolism ; Genes, Bacterial ; Geologic Sediments/analysis/*microbiology ; *Harmful Algal Bloom ; Humans ; Hydrogen-Ion Concentration ; Lakes/microbiology ; Marine Toxins ; Metagenomics ; Microbiota/*genetics ; *Microcystins/analysis ; RNA, Ribosomal, 16S/genetics ; Temperature ; Water/analysis ; Water Pollutants, Chemical/*analysis ; }, abstract = {Harmful cyanobacterial blooms are increasingly common in aquatic environments. This can lead to higher concentrations of cyanotoxins, such as microcystins (MCs), posing a great risk to diverse organisms, including humans. MCs are among the most commonly reported cyanotoxins in freshwater environments worldwide, where they may have different fates. MCs can adsorb to suspended particles into the water column and deposit onto the sediment where they can be affected by physical factors (e.g. winds in shallow lakes causing sediment resuspension) or biological factors (e.g. biodegradation). Here we focused on the conditions of a coastal shallow lagoon contaminated by MCs aiming to estimate the return of pre-existing MCs from the sediment to the water column, to evaluate the adsorption of dissolved MC-LR to the sediment and to verify the occurrence of biodegradation. In experiments with sediment, desorption and adsorption were tested under the influence of temperature, pH and aeration, reproducing conditions observed in the lagoon. MC-desorption was not detected under the tested conditions. Spiking MC-LR into lagoon water samples in the presence of sediment resulted in a 50 % reduction of soluble MC-LR concentration in control conditions (25 °C, pH 8.0, no aeration). Increasing temperature (45 °C) or introducing aeration further stimulated MC-LR removal from the water. Biodegradation was observed in sediment samples and interstitial water (even with tetracycline). The composition of the bacterial community differed in sediment and interstitial water: major phyla were Chloroflexi, Proteobacteria, Firmicutes, and OP3. From the assigned OTUs, we identified genera already described as MC degrading bacteria. Thus, the sediment is a key factor influencing the fate of MC-LR in this shallow coastal lake contributing to stable adsorption and biodegradation.}, } @article {pmid32200181, year = {2020}, author = {Samson, R and Rajput, V and Shah, M and Yadav, R and Sarode, P and Dastager, SG and Dharne, MS and Khairnar, K}, title = {Deciphering taxonomic and functional diversity of fungi as potential bioindicators within confluence stretch of Ganges and Yamuna Rivers, impacted by anthropogenic activities.}, journal = {Chemosphere}, volume = {252}, number = {}, pages = {126507}, doi = {10.1016/j.chemosphere.2020.126507}, pmid = {32200181}, issn = {1879-1298}, mesh = {*Environmental Biomarkers ; Environmental Monitoring/*methods ; Fungi ; Metagenomics ; *Microbiota ; Rivers/chemistry/microbiology ; *Water Microbiology ; }, abstract = {River confluences are interesting ecological niche with limited information in respect of the structure and the functions of diverse microbial communities. Fungi are gaining global attention as promising biological spectacles for defining the trophic status of riverine systems. We condense existing knowledge in confluence diversity in two Indian rivers (i.e. Ganges and Yamuna), by combining sediment metagenomics using long read aided MinION nanopore sequencing. A total of 63 OTU's were observed, of which top 20 OTU's were considered based on relative abundance of each OTU at a particular location. Fungal genera such as Aspergillus, Penicillium, Kluveromyces, Lodderomyces, and Nakaseomyces were deciphered as potential bio indicators of river pollution and eutrophication in the confluent zone. In silico functional gene analysis uncovered hits for neurodegenerative diseases and xenobiotic degradation potential, supporting bioindication of river pollution in wake of anthropogenic intervention.}, } @article {pmid32198176, year = {2020}, author = {Kanik, M and Munro-Ehrlich, M and Fernandes-Martins, MC and Payne, D and Gianoulias, K and Keller, L and Kubacki, A and Lindsay, MR and Baxter, BK and Vanden Berg, MD and Colman, DR and Boyd, ES}, title = {Unexpected Abundance and Diversity of Phototrophs in Mats from Morphologically Variable Microbialites in Great Salt Lake, Utah.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {10}, pages = {}, pmid = {32198176}, issn = {1098-5336}, mesh = {Bacteria/*classification ; *Bacterial Physiological Phenomena ; Cyanobacteria/classification/physiology ; Lakes/*microbiology ; *Microbiota ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Salinity ; Utah ; }, abstract = {Microbial mat communities are associated with extensive (∼700 km[2]) and morphologically variable carbonate structures, termed microbialites, in the hypersaline Great Salt Lake (GSL), Utah. However, whether the composition of GSL mat communities covaries with microbialite morphology and lake environment is unknown. Moreover, the potential adaptations that allow the establishment of these extensive mat communities at high salinity (14% to 17% total salts) are poorly understood. To address these questions, microbial mats were sampled from seven locations in the south arm of GSL representing different lake environments and microbialite morphologies. Despite the morphological differences, microbialite-associated mats were taxonomically similar and were dominated by the cyanobacterium Euhalothece and several heterotrophic bacteria. Metagenomic sequencing of a representative mat revealed Euhalothece and subdominant Thiohalocapsa populations that harbor the Calvin cycle and nitrogenase, suggesting they supply fixed carbon and nitrogen to heterotrophic bacteria. Fifteen of the next sixteen most abundant taxa are inferred to be aerobic heterotrophs and, surprisingly, harbor reaction center, rhodopsin, and/or bacteriochlorophyll biosynthesis proteins, suggesting aerobic photoheterotrophic (APH) capabilities. Importantly, proteins involved in APH are enriched in the GSL community relative to that in microbialite mat communities from lower salinity environments. These findings indicate that the ability to integrate light into energy metabolism is a key adaptation allowing for robust mat development in the hypersaline GSL.IMPORTANCE The earliest evidence of life on Earth is from organosedimentary structures, termed microbialites, preserved in 3.481-billion-year-old (Ga) rocks. Phototrophic microbial mats form in association with an ∼700-km[2] expanse of morphologically diverse microbialites in the hypersaline Great Salt Lake (GSL), Utah. Here, we show taxonomically similar microbial mat communities are associated with morphologically diverse microbialites across the lake. Metagenomic sequencing reveals an abundance and diversity of autotrophic and heterotrophic taxa capable of harvesting light energy to drive metabolism. The unexpected abundance of and diversity in the mechanisms of harvesting light energy observed in GSL mat populations likely function to minimize niche overlap among coinhabiting taxa, provide a mechanism(s) to increase energy yield and osmotic balance during salt stress, and enhance fitness. Together, these physiological benefits promote the formation of robust mats that, in turn, influence the formation of morphologically diverse microbialite structures that can be imprinted in the rock record.}, } @article {pmid32198072, year = {2020}, author = {Wang, Y and Zhou, Y and Xiao, X and Zheng, J and Zhou, H}, title = {Metaproteomics: A strategy to study the taxonomy and functionality of the gut microbiota.}, journal = {Journal of proteomics}, volume = {219}, number = {}, pages = {103737}, doi = {10.1016/j.jprot.2020.103737}, pmid = {32198072}, issn = {1876-7737}, mesh = {*Gastrointestinal Microbiome ; Humans ; Mass Spectrometry ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {The gut microbiota is the largest and most complex microbial community in the human body. Host-gut microbiota interactions have significant implications on health and disease. The development of genome-sequencing technologies, especially the application of next-generation sequencing (NGS), has accelerated the study of the gut microbiota. Most gut microbiota studies rely on 16S rRNA sequencing, metagenomics, and metatranscriptomics, but metaproteomics, based on mass spectrometry (MS), provides functional information on the signaling and metabolic pathways in the gut microbiota. This review is intended to introduce different research methods to study the gut microbiota, with a specific focus on the current progress and application of metaproteomics. SIGNIFICANCE: The gut microbiota plays a key role in human health and disease. In this review, different research methods are described and compared in the field of the gut microbiota. Among these research methods, metaproteomics reveals the taxonomy and functionality of the gut microbiota, especially the functional pathways associated with diseases. Thus, the current progress and application of metaproteomics are summarized, in order to enhance a comprehensive depiction of metaproteomics.}, } @article {pmid32197656, year = {2020}, author = {Dai, Z and Sevillano-Rivera, MC and Calus, ST and Bautista-de Los Santos, QM and Eren, AM and van der Wielen, PWJJ and Ijaz, UZ and Pinto, AJ}, title = {Disinfection exhibits systematic impacts on the drinking water microbiome.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {42}, pmid = {32197656}, issn = {2049-2618}, mesh = {Archaea/classification/drug effects ; Bacteria/classification/drug effects ; Disinfectants/*pharmacology ; *Disinfection ; Drinking Water/analysis/*microbiology ; Eukaryota/classification/drug effects ; Metagenomics ; *Microbiota ; Water Purification ; }, abstract = {Limiting microbial growth during drinking water distribution is achieved either by maintaining a disinfectant residual or through nutrient limitation without using a disinfectant. The impact of these contrasting approaches on the drinking water microbiome is not systematically understood. We use genome-resolved metagenomics to compare the structure, metabolic traits, and population genomes of drinking water microbiome samples from bulk drinking water across multiple full-scale disinfected and non-disinfected drinking water systems. Microbial communities cluster at the structural- and functional potential-level based on the presence/absence of a disinfectant residual. Disinfectant residual alone explained 17 and 6.5% of the variance in structure and functional potential of the drinking water microbiome, respectively, despite including multiple drinking water systems with variable source waters and source water communities and treatment strategies. The drinking water microbiome is structurally and functionally less diverse and variable across disinfected compared to non-disinfected systems. While bacteria were the most abundant domain, archaea and eukaryota were more abundant in non-disinfected and disinfected systems, respectively. Community-level differences in functional potential were driven by enrichment of genes associated with carbon and nitrogen fixation in non-disinfected systems and γ-aminobutyrate metabolism in disinfected systems likely associated with the recycling of amino acids. Genome-level analyses for a subset of phylogenetically-related microorganisms suggests that disinfection selects for microorganisms capable of using fatty acids, presumably from microbial decay products, via the glyoxylate cycle. Overall, we find that disinfection exhibits systematic selective pressures on the drinking water microbiome and may select for microorganisms able to utilize microbial decay products originating from disinfection-inactivated microorganisms. Video abstract.}, } @article {pmid32197644, year = {2020}, author = {Böhm, ME and Razavi, M and Marathe, NP and Flach, CF and Larsson, DGJ}, title = {Discovery of a novel integron-borne aminoglycoside resistance gene present in clinical pathogens by screening environmental bacterial communities.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {41}, pmid = {32197644}, issn = {2049-2618}, mesh = {Aminoglycosides/*pharmacology ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/drug effects ; *Integrons ; Metagenomics ; Microbial Sensitivity Tests ; *Microbiota ; Wastewater/*microbiology ; }, abstract = {BACKGROUND: New antibiotic resistance determinants are generally discovered too late, long after they have irreversibly emerged in pathogens and spread widely. Early discovery of resistance genes, before or soon after their transfer to pathogens could allow more effective measures to monitor and reduce spread, and facilitate genetics-based diagnostics.

RESULTS: We modified a functional metagenomics approach followed by in silico filtering of known resistance genes to discover novel, mobilised resistance genes in class 1 integrons in wastewater-impacted environments. We identified an integron-borne gene cassette encoding a protein that conveys high-level resistance against aminoglycosides with a garosamine moiety when expressed in E. coli. The gene is named gar (garosamine-specific aminoglycoside resistance) after its specificity. It contains none of the functional domains of known aminoglycoside modifying enzymes, but bears characteristics of a kinase. By searching public databases, we found that the gene occurs in three sequenced, multi-resistant clinical isolates (two Pseudomonas aeruginosa and one Luteimonas sp.) from Italy and China, respectively, as well as in two food-borne Salmonella enterica isolates from the USA. In all cases, gar has escaped discovery until now.

CONCLUSION: To the best of our knowledge, this is the first time a novel resistance gene, present in clinical isolates, has been discovered by exploring the environmental microbiome. The gar gene has spread horizontally to different species on at least three continents, further limiting treatment options for bacterial infections. Its specificity to garosamine-containing aminoglycosides may reduce the usefulness of the newest semisynthetic aminoglycoside plazomicin, which is designed to avoid common aminoglycoside resistance mechanisms. Since the gene appears to be not yet common in the clinics, the data presented here enables early surveillance and maybe even mitigation of its spread.}, } @article {pmid32196626, year = {2020}, author = {Nicoletti, A and Ponziani, FR and Nardella, E and Ianiro, G and Gasbarrini, A and Zileri Dal Verme, L}, title = {Biliary tract microbiota: a new kid on the block of liver diseases?.}, journal = {European review for medical and pharmacological sciences}, volume = {24}, number = {5}, pages = {2750-2775}, doi = {10.26355/eurrev_202003_20548}, pmid = {32196626}, issn = {2284-0729}, mesh = {Biliary Tract/*microbiology ; Humans ; Liver Diseases/*microbiology ; Microbiota ; }, abstract = {The microbiome plays a crucial role in maintaining the homeostasis of the organism. Recent evidence has provided novel insights for understanding the interaction between the microbiota and the host. However, the vast majority of such studies have analyzed the interactions taking place in the intestinal tract. The biliary tree has traditionally been considered sterile under normal conditions. However, the advent of metagenomic techniques has revealed an unexpectedly rich bacterial community in the biliary tract. Associations between specific microbiological patterns and inflammatory biliary diseases and cancer have been recently described. Hence, biliary dysbiosis may be a primary trigger in the pathogenesis of biliary diseases. In particular, recent studies have suggested that microorganisms could play a significant role in the development of gallstones, pathogenesis of autoimmune cholangiopathies and biliary carcinogenesis. Moreover, the intimate connection between the biliary tract, liver and pancreas, could reveal hidden influences on the development of diseases of these organs. Further studies are needed to deepen the comprehension of the influence of the biliary microbiota in human pathology. This knowledge could lead to the formulation of strategies for modulating the biliary microbiota in order to treat and prevent these pathological conditions.}, } @article {pmid32196510, year = {2020}, author = {Farhana, L and Sarkar, S and Nangia-Makker, P and Yu, Y and Khosla, P and Levi, E and Azmi, A and Majumdar, APN}, title = {Natural agents inhibit colon cancer cell proliferation and alter microbial diversity in mice.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0229823}, pmid = {32196510}, issn = {1932-6203}, support = {I01 BX001927/BX/BLRD VA/United States ; R21 CA175916/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Biological Products/*pharmacology/therapeutic use ; Cell Proliferation/drug effects ; Colonic Neoplasms/*drug therapy/pathology ; Curcuma ; Curcumin/*pharmacology/therapeutic use ; Gastrointestinal Microbiome/*drug effects ; HCT116 Cells ; Humans ; Mice ; Mice, SCID ; Plant Extracts/*pharmacology/therapeutic use ; Tocotrienols/*pharmacology/therapeutic use ; Xenograft Model Antitumor Assays ; }, abstract = {The current study was undertaken to investigate the effect of differentially formulated polyphenolic compound Essential Turmeric Oil-Curcumin (ETO-Cur), and Tocotrienol-rich fraction (TRF) of vitamin E isomers on colorectal cancer (CRC) cells that produce aggressive tumors. Combinations of ETO-Cur and TRF were used to determine the combinatorial effects of ETO-Cur and TRF-mediated inhibition of growth of CRC cells in vitro and HCT-116 cells xenograft in SCID mice. 16S rRNA gene sequence profiling was performed to determine the outcome of gut microbial communities in mice feces between control and ETO-Cur-TRF groups. Bacterial identifications were validated by performing SYBR-based Real Time (RT) PCR. For metagenomics analysis to characterize the microbial communities, multiple software/tools were used, including Quantitative Insights into Microbial Ecology (QIIME) processing tool. We found ETO-Cur and TRF to synergize and that the combination of ETO-Cur-TRF significantly inhibited growth of HCT-116 xenografts in SCID mice. This was associated with a marked alteration in microbial communities and increased microbial OTU (operation taxonomic unit) number. The relative abundance of taxa was increased and the level of microbial diversity after 34 days of combinatorial treatment was found to be 44% higher over the control. Shifting of microbial family composition was observed in ETO-Cur-TRF treated mice as evidenced by marked reductions in Bacteroidaceae, Ruminococcaceae, Clostridiales, Firmicutes and Parabacteroids families, compared to controls. Interestingly, during the inhibition of tumor growth in ETO-Cur treated mice, probiotic Lactobacillaceae and Bifidobacteriaceae were increased by 20-fold and 6-fold, respectively. The relative abundance of anti-inflammatory Clostridium XIVa was also increased in ETO-Cur-TRF treated mice when compared with the control. Our data suggest that ETO-Cur-TRF show synergistic effects in inhibiting colorectal cancer cell proliferation in vitro and in mouse xenografts in vivo, and might induce changes in microbial diversity in mice.}, } @article {pmid32196448, year = {2020}, author = {Boutin, S and Dalpke, AH}, title = {The Microbiome: A Reservoir to Discover New Antimicrobials Agents.}, journal = {Current topics in medicinal chemistry}, volume = {20}, number = {14}, pages = {1291-1299}, doi = {10.2174/1568026620666200320112731}, pmid = {32196448}, issn = {1873-4294}, mesh = {Anti-Infective Agents/*chemistry/*pharmacology ; Biological Products/*chemistry/*pharmacology ; Computational Biology ; Drug Evaluation, Preclinical ; Drug Resistance, Microbial ; Gene Expression Regulation, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; Microbiota/*genetics ; Multigene Family/genetics ; }, abstract = {Nature offered mankind the first golden era of discovery of novel antimicrobials based on the ability of eukaryotes or micro-organisms to produce such compounds. The microbial world proved to be a huge reservoir of such antimicrobial compounds which play important functional roles in every environment. However, most of those organisms are still uncultivable in a classical way, and therefore, the use of extended culture or DNA based methods (metagenomics) to discover novel compounds promises usefulness. In the past decades, the advances in next-generation sequencing and bioinformatics revealed the enormous diversity of the microbial worlds and the functional repertoire available for studies. Thus, data-mining becomes of particular interest in the context of the increased need for new antibiotics due to antimicrobial resistance and the rush in antimicrobial discovery. In this review, an overview of principles will be presented to discover new natural compounds from the microbiome. We describe culture-based and culture-independent (metagenomic) approaches that have been developed to identify new antimicrobials and the input of those methods in the field as well as their limitations.}, } @article {pmid32196394, year = {2020}, author = {Liu, G and Wu, C and Abrams, WR and Li, Y}, title = {Structural and Functional Characteristics of the Microbiome in Deep-Dentin Caries.}, journal = {Journal of dental research}, volume = {99}, number = {6}, pages = {713-720}, doi = {10.1177/0022034520913248}, pmid = {32196394}, issn = {1544-0591}, mesh = {Adolescent ; Child ; *Dental Caries ; Dentin ; Humans ; Metagenome ; *Microbiota/genetics ; Streptococcus ; }, abstract = {Dental caries is a cariogenic bacteria-mediated, fermentable carbohydrate-driven dynamic disease. The new ecological hypothesis for dentin caries suggests that an alteration in the microbial community and the presence of specific metabolic pathway genes contribute to the initiation and progression of caries. This study aimed to determine the structural and functional characteristics of a microbial community of human deep-dentin carious lesions. Sixteen deep-dentin carious lesions were obtained from the first permanent molars of 8 patients aged 9 to 18 y. Shotgun metagenomic sequencing was used to measure the microbial composition and abundance at the phylum, class, order, family, genus, and species levels. Functional analysis of the DNA sequencing data set was also performed and compared among different layers of the lesions using DIAMOND software against the Kyoto Encyclopedia of Genes and Genomes database. This study found that in the deep-dentin carious lesions, Actinobacteria (35.8%) and Firmicutes (31.2%) were the most prevalent phyla, followed by Bacteroidetes (13.6%), Proteobacteria (3.6%), and Fusobacteria (2.5%). The microbial composition varied among the individuals, but there were no significant differences in the distribution of the relative microbial abundance between the superficial layers and the deep layers. Although 14.5% of the top 10 taxa were identified as Lactobacillus at the genus level, only 25% of the deep-dentin carious samples showed Lactobacillus as the most abundant genus. Other abundant taxa included Actinomyces (10.5%), Olsenella (9.4%), Prevotella (8.8%), Propionibacterium (7.2%), Streptococcus (3.9%), Selenomonas (3.7%), Corynebacterium (1.9%), Leptotrichia (1.4%), and Parascardovia (1.1%). The most abundant pathway identified in the KEGG database was the metabolic pathway containing 101,427 annotated genes, which consisted of 51.4% of all annotated genes. The carbohydrate metabolism pathway, amino acid metabolism, and membrane transport were the functional traits of the level 2 pathways. These findings suggest that the potent interaction within the microbial communities in deep-dentin carious lesions may play a fundamental role in caries etiology.}, } @article {pmid32196076, year = {2020}, author = {Deyett, E and Rolshausen, PE}, title = {Endophytic microbial assemblage in grapevine.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {5}, pages = {}, doi = {10.1093/femsec/fiaa053}, pmid = {32196076}, issn = {1574-6941}, mesh = {Bacteria/genetics ; *Microbiota ; Plant Roots ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; *Soil Microbiology ; }, abstract = {The plant vascular system has remained an underexplored niche despite its potential for hosting beneficial microbes. The aim of this work was to determine the origin of the microbial endophytes inhabiting grapevine. We focused on a single commercial vineyard in California over a two-year period and used an amplicon metagenomics approach to profile the bacterial (16S-V4) and fungal (ITS) communities of the microbiome across a continuum of six grapevine compartments: bulk soil, rhizosphere, root, cordon, cane and sap. Our data supported that roots are a bottleneck to microbial richness and that they are mostly colonized with soilborne microbes, including plant growth-promoting bacteria recruited by the host, but also saprophytic and pathogenic fungal invaders. A core group of taxa was identified throughout the vine; however, there was clear partitioning of the microbiome with niche adaptation of distinct taxonomic groups. Above- and belowground plant tissues displayed distinct microbial fingerprints and were intermixed in a limited capacity mostly by way of the plant sap. We discuss how cultural practices and human contact may shape the endosphere microbiome and identify potential channels for transmission of its residents.}, } @article {pmid32193482, year = {2020}, author = {Ghanbari Maman, L and Palizban, F and Fallah Atanaki, F and Elmi Ghiasi, N and Ariaeenejad, S and Ghaffari, MR and Hosseini Salekdeh, G and Kavousi, K}, title = {Co-abundance analysis reveals hidden players associated with high methane yield phenotype in sheep rumen microbiome.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {4995}, pmid = {32193482}, issn = {2045-2322}, mesh = {Animals ; Dietary Carbohydrates/metabolism ; Dietary Fiber ; Methane/*metabolism ; Microbiota/*genetics/*physiology ; *Phenotype ; Rumen/metabolism/*microbiology ; Sheep/*microbiology ; }, abstract = {Rumen microbial environment hosts a variety of microorganisms that interact with each other to carry out the feed digestion and generation of several by-products especially methane, which plays an essential role in global warming as a greenhouse gas. However, due to its multi-factorial nature, the exact cause of methane production in the rumen has not yet been fully determined. The current study is an attempt to use system modeling to analyze the relationship between interacting components of rumen microbiome and its role in methane production. Metagenomic data of sheep rumen, with equal numbers of high methane yield (HMY) and low methane yield (LMY) samples, were used. As a well-known approach for the systematic comparative study of complex traits, the co-abundance networks were constructed in both operational taxonomic unit (OTU) and gene levels. A gene-catalog of 1,444 different rumen microbial strains was developed as a reference to measure gene abundances. The results from both types of co-abundance networks showed that methanogens, which are the main ruminal source for methanogenesis, need other microbial species to accomplish the task of methane production through producing the main precursor molecules like H2 and acetate for methanogenesis pathway as their byproducts. KEGG Orthology(KO) analysis of the current study shows that the metabolism and growth rate of methanogens will be increased due to the higher rate of the metabolism and carbohydrate/fiber digestion pathways in the hidden elements. This finding proposes that any ruminant methane yield alteration strategy should consider complex interactions of rumen microbiome components as one tightly integrated unit rather than several separate parts.}, } @article {pmid32193245, year = {2020}, author = {Valdés, N and Gonzalez, A and Garcia, V and Tello, M}, title = {Analysis of the Microbiome of Rainbow Trout (Oncorhynchus mykiss) Exposed to the Pathogen Flavobacterium psychrophilum 10094.}, journal = {Microbiology resource announcements}, volume = {9}, number = {12}, pages = {}, pmid = {32193245}, issn = {2576-098X}, abstract = {Rainbow trout that were resistant or susceptible to Flavobacterium psychrophilum infection were compared with respect to their microbial composition by using 16S rRNA V3-V4 sequencing. The differences occurred in gills, where resistant fish displayed a greater abundance of the phylum Proteobacteria and a smaller proportion of Firmicutes relative to those of susceptible fish.}, } @article {pmid32190998, year = {2020}, author = {Naboka, YL and Gudima, IA and Mordanov, SV and Krakhotkin, DV and Ilyash, AV and Kogan, MI and Ibishev, KS}, title = {[Virusuria as a component of the urine microbiota and its significance for assessing the health of the urinary tract: a descriptive clinical study].}, journal = {Urologiia (Moscow, Russia : 1999)}, volume = {}, number = {1}, pages = {12-18}, pmid = {32190998}, issn = {1728-2985}, mesh = {Adult ; Bacteria ; Escherichia coli ; Female ; Humans ; Male ; *Microbiota ; *Urinary Tract Infections ; Young Adult ; }, abstract = {AIM: To determine the frequency of occurrence of oportunistic pathogenic bacterial flora and viral pathogens in the urine of healthy people with the establishment of the association between them.

MATERIALS AND METHODS: 40 healthy sexually active women and men were examined, which are divided by gender into equivalent groups: Group I - healthy women (n=19), Group II - healthy men (n=21). The age of the subjects ranged from 20 to 25 years, the average age was 22.4+/-1.2 years. In both groups, the average portion of morning urine was taken for a study after a proper hygienic procedure with self-urination of the subjects in a sterile plastic container (Sterile Uricol for urine sample collection "HiMedia"). In addition to the nutrient media regulated by the Clinical Guidelines, additional HiMedia chromogenic media were used to cultivate facultative anaerobic (FAB) and non-clostridial anaerobic bacteria (NAB). Detection of viruses was performed by PCR with detection in "real time". DNA isolation was carried out by the sorption method using the AmpliPrime DNA-Sorb-B ("NextBio") kit from urine samples, with preliminary concentration.

RESULTS: In all 40 cases, normative leukocyturia was detected in the urine. According to the results of bacteriological examination of urine, healthy men and women in all cases found aerobic-anaerobic associations. Coagulase-negative staphylococci (CNS) and Corynebacterium spp. Dominated in the cluster of aerobic taxa of microbiota. (75.0%, 55.0% respectively). The spectrum of CNS was represented by five species: S.epidermidis (30.0%), S.haemolyticus (27.5%), and S.warneri (25.0%), S.saprophyticus and S.lentus (15.0%). Enterococcus spp. were recorded in the urine in 32.5% of cases. Representatives of the Enterobacteriaceae family were represented by 4 taxa: E. coli (10.0%), Klebsiella spp., Proteus spp. (5.0% each), Enterobacter spp., Citrobacter spp. (2.5%). In a cluster of anaerobic bacteria in the urine, Eubacterium spp. (60.0%) and almost half of healthy individuals recorded Lactobacillus spp. and Peptococcus spp. (42.5% each). When analyzing the frequencies of detection of various microbiota taxa, it was found that women significantly more frequently recorded urine Corynebacterium spp., Eubacterium spp. and Lactobacillus spp., as well as Enterococcus spp. and Peptococcus spp. Peptostreptococcus spp. and Veillonella spp. were significantly more often determined (p<0.05) in the urine of men. HHV6 (10.0%), HPV18 and B19 parvovirus (2,5%) were determined in the urine of healthy people. It should be noted that the studied viruses were more often recorded in men, in particular, HPV18 and parvovirus B19 - only in men, and HHV6 more often in men (7.5%), less often in women (2.5%). Significant associations of some genera of microorganisms with the sex of the participants were revealed for E. faecalis and Lactobacillus spp., which were more often found in the urine of healthy women Reliably significant associations were found for three taxa: viruses HPV6, HPV18 and parvoviruses B19 (16.7%) were determined in the presence of Bacteroides spp., Bifidobacterium spp., and Prevotella spp., in urine. Accordingly, in 83.3% of cases, these viruses were detected in the absence of the above-listed taxa of microorganisms in the urine.

CONCLUSIONS: The normal urinary microbiota of healthy women and men has differences: Lactobacillus spp and Candida spp are absent in the urine of men while Streptococcus spp in urine of women. HHV6, HPV18, parvoviruses B19 are found in urine of healthy people and more often in men. Data about the virobiota and microbiota of urine in healthy people can highlight on the pathogenesis of urinary tract infections of various localization and develop targeted approaches in personalized therapy of this group of diseases.}, } @article {pmid32190661, year = {2020}, author = {Sha, Y and Hu, J and Shi, B and Dingkao, R and Wang, J and Li, S and Zhang, W and Luo, Y and Liu, X}, title = {Characteristics and Functions of the Rumen Microbial Community of Cattle-Yak at Different Ages.}, journal = {BioMed research international}, volume = {2020}, number = {}, pages = {3482692}, pmid = {32190661}, issn = {2314-6141}, mesh = {Age Factors ; Animals ; Bacteria/*classification/genetics ; Cattle ; China ; Genome, Bacterial ; Lignin/metabolism ; Male ; Metagenome ; Microbiota/genetics/*physiology ; Rumen/*microbiology ; }, abstract = {A cattle-yak, which is a hybrid between a yak (Bos grunniens) and cattle (Bos taurus), is an important livestock animal, but basic questions regarding its physiology and environmental adaptation remain unanswered. To address this issue, the present study examined the species composition and functional characteristics of rumen microorganisms in the cattle-yak of different ages (2 and 3 years old) by metagenomic analysis. We found that rumen microbial community composition was similar at the two ages. Firmicutes, Fibrobacteres, Euryarchaeota, Bacteroidetes, and Proteobacteria were the predominant phyla, with Firmicutes accounting for the highest percentage of bacteria in 2-year-old (48%) and 3-year-old (46%) animals. Bacterial species involved in lignocellulose degradation were detected in the rumen of adult cattle-yaks including Ruminococcus flavefaciens, Ruminococcus albus, Fibrobacter succinogenes, and Prevotella ruminicola, with F. succinogenes being the most abundant. A total of 145,489 genes were annotated according to the Carbohydrate-active Enzyme database, which identified glycoside hydrolases as the most highly represented enzyme family. Further functional annotation revealed specific microflora and genes in the adult rumen that are potentially related to plateau adaptability. These results could explain the heterosis of the cattle-yak and provide insight into mechanisms of physiologic adaptation in plateau animals.}, } @article {pmid32190648, year = {2020}, author = {Li, K and Peng, W and Zhou, Y and Ren, Y and Zhao, J and Fu, X and Nie, Y}, title = {Host Genetic and Environmental Factors Shape the Composition and Function of Gut Microbiota in Populations Living at High Altitude.}, journal = {BioMed research international}, volume = {2020}, number = {}, pages = {1482109}, pmid = {32190648}, issn = {2314-6141}, mesh = {Actinobacteria/genetics/isolation & purification/metabolism ; Adult ; *Altitude ; Anti-Bacterial Agents/administration & dosage ; Asian People ; Bacteroidetes/genetics/isolation & purification/metabolism ; Body Mass Index ; China ; Cyanobacteria/genetics/isolation & purification/metabolism ; DNA, Bacterial/genetics/isolation & purification ; Diet ; Drug Resistance, Multiple, Bacterial/genetics ; Feces/microbiology ; Female ; Firmicutes/genetics/isolation & purification/metabolism ; *Gastrointestinal Microbiome ; Health Behavior ; Humans ; Male ; Metagenome ; Proteobacteria/genetics/isolation & purification/metabolism ; Sequence Analysis, DNA ; Tenericutes/genetics/isolation & purification/metabolism ; Tibet ; }, abstract = {The human gut microbiota is affected by genetic and environmental factors. It remains unclear how host genetic and environmental factors affect the composition and function of gut microbiota in populations living at high altitudes. We used a metagenome-wide analysis to investigate the gut microbiota composition in 15 native Tibetans and 12 Hans living on the Tibetan Plateau. The composition of gut microbiota differed significantly between these two groups (P < 0.05). The Planctomycetes was the most abundant phyla both in native Tibetans and in Hans. Furthermore, the most relatively abundant phyla for native Tibetans were Bacteroidetes (15.66%), Firmicutes (11.10%), Proteobacteria (1.32%), Actinobacteria (1.10%), and Tenericutes (0.35%), while the most relatively abundant phyla for Hans were Bacteroidetes (16.28%), Firmicutes (8.41%), Proteobacteria (2.93%), Actinobacteria (0.49%), and Cyanobacteria (0.21%). The abundance of the majority of genera was significantly higher in Tibetans than in Hans (P < 0.01). The number of microbial genes was 4.9 times higher in Tibetans than in Hans. The metabolic pathways and clusters of orthologous groups differed significantly between the two populations (P < 0.05). The abundance of carbohydrate-active enzyme modules and antibiotic resistance genes was significantly lower in Tibetans compared to Hans (P < 0.05). Our results suggest that different genetic factors (race) and environmental factors (diets and consumption of antibiotics) may play important roles in shaping the composition and function of gut microbiota in populations living at high altitudes.}, } @article {pmid32188862, year = {2020}, author = {Sun, J and Liao, XP and D'Souza, AW and Boolchandani, M and Li, SH and Cheng, K and Luis Martínez, J and Li, L and Feng, YJ and Fang, LX and Huang, T and Xia, J and Yu, Y and Zhou, YF and Sun, YX and Deng, XB and Zeng, ZL and Jiang, HX and Fang, BH and Tang, YZ and Lian, XL and Zhang, RM and Fang, ZW and Yan, QL and Dantas, G and Liu, YH}, title = {Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {1427}, pmid = {32188862}, issn = {2041-1723}, support = {DP2 DK098089/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics/isolation & purification ; *Drug Resistance, Bacterial ; Farms ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Humans ; Male ; Occupational Exposure ; Schools, Veterinary ; Students/statistics & numerical data ; Swine/*microbiology ; Young Adult ; }, abstract = {Anthropogenic environments have been implicated in enrichment and exchange of antibiotic resistance genes and bacteria. Here we study the impact of confined and controlled swine farm environments on temporal changes in the gut microbiome and resistome of veterinary students with occupational exposure for 3 months. By analyzing 16S rRNA and whole metagenome shotgun sequencing data in tandem with culture-based methods, we show that farm exposure shapes the gut microbiome of students, resulting in enrichment of potentially pathogenic taxa and antimicrobial resistance genes. Comparison of students' gut microbiomes and resistomes to farm workers' and environmental samples revealed extensive sharing of resistance genes and bacteria following exposure and after three months of their visit. Notably, antibiotic resistance genes were found in similar genetic contexts in student samples and farm environmental samples. Dynamic Bayesian network modeling predicted that the observed changes partially reverse over a 4-6 month period. Our results indicate that acute changes in a human's living environment can persistently shape their gut microbiota and antibiotic resistome.}, } @article {pmid32188747, year = {2020}, author = {Zuo, K and Yin, X and Li, K and Zhang, J and Wang, P and Jiao, J and Liu, Z and Liu, X and Liu, J and Li, J and Yang, X}, title = {Different Types of Atrial Fibrillation Share Patterns of Gut Microbiota Dysbiosis.}, journal = {mSphere}, volume = {5}, number = {2}, pages = {}, pmid = {32188747}, issn = {2379-5042}, mesh = {Aged ; Atrial Fibrillation/classification/*etiology ; Cohort Studies ; Dysbiosis/metabolism/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolomics ; Metagenomics ; Middle Aged ; }, abstract = {Dysbiotic gut microbiota (GM) and disordered metabolic patterns are known to be involved in the clinical expression of atrial fibrillation (AF). However, little evidence has been reported in characterizing the specific changes in fecal microbiota in paroxysmal AF (PAF) and persistent AF (psAF). To provide a comprehensive understanding of GM dysbiosis in AF types, we assessed the GM signatures of 30 PAF patients, 20 psAF patients, and 50 non-AF controls based on metagenomic and metabolomic analyses. Compared with control subjects, similar changes of GM were identified in PAF and psAF patients, with elevated microbial diversity and similar alteration in the microbiota composition. PAF and psAF patients shared the majority of differential taxa compared with non-AF controls. Moreover, the similarity was also illuminated in microbial function and associated metabolic alterations. Additionally, minor disparity was observed in PAF compared with psAF. Several distinctive taxa between PAF and psAF were correlated with certain metabolites and atrial diameter, which might play a role in the pathogenesis of atrial remodeling. Our findings characterized the presence of many common features in GM shared by PAF and psAF, which occurred at the self-terminating PAF. Preventative and therapeutic measures targeting GM for early intervention to postpone the progression of AF are highly warranted.IMPORTANCE Atrial fibrillation has been identified to be associated with disordered gut microbiota. Notably, atrial fibrillation is a progressive disease and could be categorized as paroxysmal and persistent based on the duration of the episodes. The persistent atrial fibrillation patients are accompanied by higher risk of stroke and lower success rate of rhythm control. However, the microbial signatures of different categories of atrial fibrillation patients remain unknown. We sought to determine whether disordered gut microbiota occurs in the self-terminating PAF or intestinal flora develops dynamically during atrial fibrillation progression. We found that different types of atrial fibrillation show a limited degree of gut microbiota shift. Gut microbiota dysbiosis has already occurred in mild stages of atrial fibrillation, which might act as an early modulator of disease, and therefore may be regarded as a potential target to postpone atrial fibrillation progression.}, } @article {pmid32188136, year = {2020}, author = {Focardi, A and Ostrowski, M and Goossen, K and Brown, MV and Paulsen, I}, title = {Investigating the Diversity of Marine Bacteriophage in Contrasting Water Masses Associated with the East Australian Current (EAC) System.}, journal = {Viruses}, volume = {12}, number = {3}, pages = {}, pmid = {32188136}, issn = {1999-4915}, mesh = {Australia ; Bacteriophages/*classification/*genetics/isolation & purification ; *Biodiversity ; DNA Viruses/genetics ; DNA, Viral ; Genes, Viral/genetics ; Metagenome ; Microbiota ; Oceans and Seas ; Phylogeny ; Seawater/*virology ; }, abstract = {Virus- and bacteriophage-induced mortality can have a significant impact on marine productivity and alter the flux of nutrients in marine microbial food-webs. Viral mediated horizontal gene transfer can also influence host fitness and community composition. However, there are very few studies of marine viral diversity in the Southern Hemisphere, which hampers our ability to fully understand the complex interplay of biotic and abiotic factors that shape microbial communities. We carried out the first genetic study of bacteriophage communities within a dynamic western boundary current (WBC) system, the east Australian current (EAC). Virus DNA sequences were extracted from 63 assembled metagenomes and six metaviromes obtained from various depths at 24 different locations. More than 1700 bacteriophage genomic fragments (>9 kbps) were recovered from the assembled sequences. Bacteriophage diversity displayed distinct depth and regional patterns. There were clear differences in the bacteriophage populations associated with the EAC and Tasman Sea euphotic zones, at both the taxonomic and functional level. In contrast, bathypelagic phages were similar across the two oceanic regions. These data provide the first characterisation of viral diversity across a dynamic western boundary current, which is an emerging model for studying the response of microbial communities to climate change.}, } @article {pmid32186690, year = {2020}, author = {Chen, L}, title = {powmic: an R package for power assessment in microbiome case-control studies.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {11}, pages = {3563-3565}, doi = {10.1093/bioinformatics/btaa197}, pmid = {32186690}, issn = {1367-4811}, mesh = {Case-Control Studies ; *Microbiota/genetics ; Software ; }, abstract = {SUMMARY: Power analysis is essential to decide the sample size of metagenomic sequencing experiments in a case-control study for identifying differentially abundant (DA) microbes. However, the complexity of microbial data characteristics, such as excessive zeros, over-dispersion, compositionality, intrinsically microbial correlations and variable sequencing depths, makes the power analysis particularly challenging because the analytical form is usually unavailable. Here, we develop a simulation-based power assessment strategy and R package powmic, which considers the complexity of microbial data characteristics. A real data example demonstrates the usage of powmic.

powmic R package and online tutorial are available at https://github.com/lichen-lab/powmic.

CONTACT: chen61@iu.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid32185431, year = {2020}, author = {Pentimone, I and Colagiero, M and Rosso, LC and Ciancio, A}, title = {Omics applications: towards a sustainable protection of tomato.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {10}, pages = {4185-4195}, doi = {10.1007/s00253-020-10500-7}, pmid = {32185431}, issn = {1432-0614}, mesh = {Gene Expression Profiling ; Gene Expression Regulation, Plant ; High-Throughput Nucleotide Sequencing ; Solanum lycopersicum/*genetics ; *Metabolomics ; *Metagenomics ; MicroRNAs ; *Proteomics ; Rhizosphere ; Transcriptome ; }, abstract = {Transcriptome data and gene expression analysis have a huge potential in the study of multiple relationships involving plants, pathogens, and pests, including the interactions with beneficial microorganisms such as endophytes or other functional groups. Next-generation sequencing (NGS) and other recent long-read-based sequencing approaches (i.e., nanopore and others) provide unprecedented tools allowing the fast identification of plant information processing systems, in situ and in real time, fundamental for crop management and pest regulation. Other -omics approaches such as metagenomics and metatranscriptomics allow high-resolution insights on the rhizosphere ecology. They may highlight key factors affecting belowground biodiversity or processes, modulating the expression of stress-responsive pathways. The application of miRNAs and other small RNAs is a relatively new field of application, with enormous potential for the selective activation of defense pathways. However, limitations concerning the stability of the RNA molecules and their effective delivery must be overcome.}, } @article {pmid32184999, year = {2020}, author = {Moore, G and Tessler, M and Cunningham, SW and Betancourt, J and Harbert, R}, title = {Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA.}, journal = {Ecology and evolution}, volume = {10}, number = {5}, pages = {2530-2544}, pmid = {32184999}, issn = {2045-7758}, abstract = {Fossil rodent middens are powerful tools in paleoecology. In arid parts of western North America, packrat (Neotoma spp.) middens preserve plant and animal remains for tens of thousands of years. Midden contents are so well preserved that fragments of endogenous ancient DNA (aDNA) can be extracted and analyzed across millennia. Here, we explore the use of shotgun metagenomics to study the aDNA obtained from packrat middens up to 32,000 C[14] years old. Eleven Illumina HiSeq 2500 libraries were successfully sequenced, and between 0.11% and 6.7% of reads were classified using Centrifuge against the NCBI "nt" database. Eukaryotic taxa identified belonged primarily to vascular plants with smaller proportions mapping to ascomycete fungi, arthropods, chordates, and nematodes. Plant taxonomic diversity in the middens is shown to change through time and tracks changes in assemblages determined by morphological examination of the plant remains. Amplicon sequencing of ITS2 and rbcL provided minimal data for some middens, but failed at amplifying the highly fragmented DNA present in others. With repeated sampling and deep sequencing, analysis of packrat midden aDNA from well-preserved midden material can provide highly detailed characterizations of past communities of plants, animals, bacteria, and fungi present as trace DNA fossils. The prospects for gaining more paleoecological insights from aDNA for rodent middens will continue to improve with optimization of laboratory methods, decreasing sequencing costs, and increasing computational power.}, } @article {pmid32184182, year = {2021}, author = {Borren, NZ and Plichta, D and Joshi, AD and Bonilla, G and Peng, V and Colizzo, FP and Luther, J and Khalili, H and Garber, JJ and Janneke van der Woude, C and Sadreyev, R and Vlamakis, H and Xavier, RJ and Ananthakrishnan, AN}, title = {Alterations in Fecal Microbiomes and Serum Metabolomes of Fatigued Patients With Quiescent Inflammatory Bowel Diseases.}, journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association}, volume = {19}, number = {3}, pages = {519-527.e5}, doi = {10.1016/j.cgh.2020.03.013}, pmid = {32184182}, issn = {1542-7714}, support = {K01 DK110267/DK/NIDDK NIH HHS/United States ; R01 DK103039/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Clostridiales ; *Colitis, Ulcerative/complications ; Fatigue ; Feces ; Female ; *Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases/complications ; Male ; Metabolome ; Proteomics ; }, abstract = {BACKGROUND & AIMS: Fatigue is frequent and disabling in patients with inflammatory bowel diseases (IBD) but its mechanisms are poorly understood. We investigated alterations in fecal microbiomes and serum metabolomes and proteomes in patients with quiescent IBD, with vs without fatigue.

METHODS: We performed a prospective observational study of patients (44% women; mean age, 39.8 y) with clinically and endoscopically quiescent Crohn's disease (n = 106) or ulcerative colitis (n = 60) at a tertiary hospital, from March 2016 through December 2018. Fatigue was assessed using the functional assessment of chronic illness therapy-fatigue scoring system and defined as a score of 43 or less. We performed metabolomic analysis of serum samples using liquid chromatography-mass spectrometry methods and proteomic analysis using multiplex proximity extension assay (PEA) technology. Stool samples were obtained from 50 patients and analyzed by shotgun metagenomic sequencing on Illumina HiSeq platform.

RESULTS: Of the 166 study participants, 91 (55%) were fatigued. Serum samples from patients with fatigue (n = 59) did not have significant increases in levels of inflammatory cytokines compared with serum samples from nonfatigued patients (n = 72). We found a statistically significant difference in a cluster of 18 serum metabolites between patients with fatigue (n = 84) vs without fatigue (n = 72) (P = .033); serum samples from patients with fatigue had significant reductions in levels of methionine (P = .020), tryptophan (P = .042), proline (P = .017), and sarcosine (P = .047). Fecal samples from patients with fatigue had a less diverse gut microbiome, with significant reductions in butyrate-producing bacteria, including Faecalibacterium prausnitzii (P = .0002, q =.007) and Roseburia hominis (P = .0079, q = 0.105). This fatigue-like microbiome was associated with fatigue scales and correlated with progressive depletion of metabolites from serum samples.

CONCLUSIONS: In an analysis of fecal and serum samples from 166 patients with IBD, we found alterations in serum metabolites and fecal microbes that were associated with fatigue.}, } @article {pmid32183717, year = {2020}, author = {Chen, Q and Zhao, H and Wen, M and Li, J and Zhou, H and Wang, J and Zhou, Y and Liu, Y and Du, L and Kang, H and Zhang, J and Cao, R and Xu, X and Zhou, JJ and Ren, B and Wang, Y}, title = {Genome of the webworm Hyphantria cunea unveils genetic adaptations supporting its rapid invasion and spread.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {242}, pmid = {32183717}, issn = {1471-2164}, support = {No. 130028684//Open Project Program of the Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization/ ; No. 1300289103//Open Project Program of the Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization/ ; No. 31501890//National Natural Science Foundation of China/ ; No. 20160204023NY//Natural Science Foundation of Jilin Province/ ; No. 20170204003NY//Natural Science Foundation of Jilin Province/ ; No. 20180101005JC//Natural Science Foundation of Jilin Province/ ; No. 20190301047NY//Natural Science Foundation of Jilin Province/ ; No. 2017E0272//Foundation of Xinjiang Uygur Autonomous Region/ ; No. 11SSXT153//The Fundamental Research Funds for the Central Universities/ ; No. 2412015KJ015//The Fundamental Research Funds for the Central Universities/ ; No. 2412019FZ022//The Fundamental Research Funds for the Central Universities/ ; No. J1210070//Fund for Fostering Talents in Basic Science of the National Natural Science/ ; NO. 131004003//Undergraduate teaching quality and teaching reform project of Northeast Normal University/ ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; Base Sequence ; Gene Expression Profiling ; Genome ; *Introduced Species ; Moths/*classification/*genetics ; Phylogeny ; }, abstract = {BACKGROUND: The fall webworm Hyphantria cunea is an invasive and polyphagous defoliator pest that feeds on nearly any type of deciduous tree worldwide. The silk web of H. cunea aids its aggregating behavior, provides thermal regulation and is regarded as one of causes for its rapid spread. In addition, both chemosensory and detoxification genes are vital for host adaptation in insects.

RESULTS: Here, a high-quality genome of H. cunea was obtained. Silk-web-related genes were identified from the genome, and successful silencing of the silk protein gene HcunFib-H resulted in a significant decrease in silk web shelter production. The CAFE analysis showed that some chemosensory and detoxification gene families, such as CSPs, CCEs, GSTs and UGTs, were expanded. A transcriptome analysis using the newly sequenced H. cunea genome showed that most chemosensory genes were specifically expressed in the antennae, while most detoxification genes were highly expressed during the feeding peak. Moreover, we found that many nutrient-related genes and one detoxification gene, HcunP450 (CYP306A1), were under significant positive selection, suggesting a crucial role of these genes in host adaptation in H. cunea. At the metagenomic level, several microbial communities in H. cunea gut and their metabolic pathways might be beneficial to H. cunea for nutrient metabolism and detoxification, and might also contribute to its host adaptation.

CONCLUSIONS: These findings explain the host and environmental adaptations of H. cunea at the genetic level and provide partial evidence for the cause of its rapid invasion and potential gene targets for innovative pest management strategies.}, } @article {pmid32182740, year = {2020}, author = {Islam, MM and Ekuni, D and Toyama, N and Kobayashi, T and Fujimori, K and Uchida, Y and Fukuhara, D and Taniguchi-Tabata, A and Kataoka, K and Iwasaki, Y and Morita, M}, title = {Relationship of Salivary Microbiome with the Worsening of the Periodontal Health Status in Young Adults: A 3-Year Cohort Study.}, journal = {International journal of environmental research and public health}, volume = {17}, number = {5}, pages = {}, pmid = {32182740}, issn = {1660-4601}, mesh = {Cohort Studies ; *Health Status ; Humans ; Male ; *Microbiota ; Periodontal Index ; Prospective Studies ; Saliva ; Young Adult ; }, abstract = {The purpose of this prospective cohort study was to investigate the influence of the salivary microbiome on the worsening of the periodontal health status among Japanese young adults. We assessed the data of systemically healthy and non-smoking young (18-22 years) university students (n = 457) from Okayama University at baseline (2013) and follow-up (2016). The worsening group was defined based on an increase in the percentage of bleeding on probing (%BOP) or an increase in probing pocket depth (PPD) from <4 mm to ≥4 mm. Unstimulated saliva samples were randomly collected from 69 students for microbiome analysis at follow-up. The salivary microbiome was assessed through 16S rRNA metagenomic sequencing. The type of community in the salivary microbiome clustered by statistical analysis and diversity was not significantly associated with the worsening of the periodontal health status in cases of increasing %BOP and PPD (p > 0.05). The prevalence of some species was significantly higher in the worsening group than in the non-worsening group (p < 0.05) in both cases. The worsening of the periodontal health status was associated with some species, but not the type of community and diversity in the salivary microbiome among Japanese young adults.}, } @article {pmid32182280, year = {2020}, author = {Ivanova, AA and Zhelezova, AD and Chernov, TI and Dedysh, SN}, title = {Linking ecology and systematics of acidobacteria: Distinct habitat preferences of the Acidobacteriia and Blastocatellia in tundra soils.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0230157}, pmid = {32182280}, issn = {1932-6203}, mesh = {*Acidobacteria/classification/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Carbon/analysis ; Classification ; DNA, Bacterial ; Ecosystem ; Metagenomics ; Nitrogen/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; *Tundra ; }, abstract = {The Acidobacteria is one of the major bacterial phyla in soils and peatlands. The currently explored diversity within this phylum is assigned to 15 class-level units, five of which contain described members. The ecologically relevant traits of acidobacteria from different classes remain poorly understood. Here, we compared the patterns of acidobacterial diversity in sandy soils of tundra, along a gradient of increasing vegetation-unfixed aeolian sand, semi-fixed surfaces with mosses and lichens, and mature soil under fully developed plant cover. The Acidobacteria-affiliated 16S rRNA gene sequences retrieved from these soils comprised 11 to 33% of total bacterial reads and belonged mostly to members of the classes Acidobacteriia and Blastocatellia, which displayed opposite habitat preferences. The relative abundance of the Blastocatellia was maximal in unfixed sands and declined in soils of vegetated plots, showing positive correlation with soil pH and negative correlation with carbon and nitrogen availability. An opposite tendency was characteristic for the Acidobacteriia. Most Blastocatellia-affiliated reads belonged to as-yet-undescribed members of the family Arenimicrobiaceae, which appears to be characteristic for dry, depleted in organic matter soil habitats. The pool of Acidobacteriia-affiliated sequences, apart from Acidobacteriaceae- and Bryobacteraceae-related reads, had a large proportion of sequences from as-yet-undescribed families, which seem to specialize in degrading plant-derived organic matter. This analysis reveals sandy soils of tundra as a source of novel acidobacterial diversity and provides an insight into the ecological preferences of different taxonomic groups within this phylum.}, } @article {pmid32182269, year = {2020}, author = {Herren, GL and Habraken, J and Waeyenberge, L and Haegeman, A and Viaene, N and Cougnon, M and Reheul, D and Steel, H and Bert, W}, title = {Effects of synthetic fertilizer and farm compost on soil nematode community in long-term crop rotation plots: A morphological and metabarcoding approach.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0230153}, pmid = {32182269}, issn = {1932-6203}, mesh = {Animals ; *Composting ; Crop Production/methods ; Ecosystem ; *Fertilizers ; Food Chain ; Metagenomics ; *Nematoda/anatomy & histology/classification/genetics/growth & development ; Nitrogen Compounds ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Soil biodiversity plays a key regulation role in the ecosystem services that underpin regenerative sustainable agriculture. It can be impacted by agricultural management techniques, both positively (through measures such as compost application) and negatively (through, for example, application of synthetic nitrogen). As one of the most numerous members of the soil biota, nematodes are well established as indicators for the soil food web. However, compost application also includes the addition of nematodes present in compost and their subsequent survival in soil is unknown. Nematode communities within the compost applied to soil, and nematode communities in the soil of a multi-year rotational cropping field trial in Melle (Belgium) were studied using morphological and metabarcoding techniques. Compost (C) and nitrogen fertilizer (NF) treated plots were compared. Three replicate plots were investigated for each of the following treatments: C application only; C and NF application; NF only; no C and no NF (control). Plots were sampled six times between 2015-2017, before and after C or NF were added each spring and after crop harvest (except for 2017). NF treatment resulted in a significant decrease of fungal feeding and predatory nematodes, while herbivorous nematodes were positively affected. Remarkably, we did not find compost addition to exert any noticeable effects on the soil nematode community. The morphological and metabarcoding data resulted in different results of the nematode community composition. However, trends and patterns in the two data sets were congruent when observed with NMDS plots and using the nematode maturity index. Metabarcoding of individual compost nematode taxa demonstrated that nematodes originating from compost did not persist in soil.}, } @article {pmid32179734, year = {2020}, author = {Mas-Lloret, J and Obón-Santacana, M and Ibáñez-Sanz, G and Guinó, E and Pato, ML and Rodriguez-Moranta, F and Mata, A and García-Rodríguez, A and Moreno, V and Pimenoff, VN}, title = {Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {92}, pmid = {32179734}, issn = {2052-4463}, mesh = {*Colon ; Cross-Sectional Studies ; *Feces ; Female ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The gut microbiome has a fundamental role in human health and disease. However, studying the complex structure and function of the gut microbiome using next generation sequencing is challenging and prone to reproducibility problems. Here, we obtained cross-sectional colon biopsies and faecal samples from nine participants in our COLSCREEN study and sequenced them in high coverage using Illumina pair-end shotgun (for faecal samples) and IonTorrent 16S (for paired feces and colon biopsies) technologies. The metagenomes consisted of between 47 and 92 million reads per sample and the targeted sequencing covered more than 300 k reads per sample across seven hypervariable regions of the 16S gene. Our data is freely available and coupled with code for the presented metagenomic analysis using up-to-date bioinformatics algorithms. These results will add up to the informed insights into designing comprehensive microbiome analysis and also provide data for further testing for unambiguous gut microbiome analysis.}, } @article {pmid32179689, year = {2020}, author = {Bonilla-Rosso, G and Steiner, T and Wichmann, F and Bexkens, E and Engel, P}, title = {Honey bees harbor a diverse gut virome engaging in nested strain-level interactions with the microbiota.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {13}, pages = {7355-7362}, pmid = {32179689}, issn = {1091-6490}, mesh = {Animals ; Bacteria/genetics ; Bacteriophages/genetics ; Bees/genetics/*microbiology/*virology ; Bifidobacterium/isolation & purification/virology ; Gastrointestinal Microbiome ; Metagenome ; Microbiota ; Symbiosis/physiology ; }, abstract = {The honey bee gut microbiota influences bee health and has become an important model to study the ecology and evolution of microbiota-host interactions. Yet, little is known about the phage community associated with the bee gut, despite its potential to modulate bacterial diversity or to govern important symbiotic functions. Here we analyzed two metagenomes derived from virus-like particles, analyzed the prevalence of the identified phages across 73 bacterial metagenomes from individual bees, and tested the host range of isolated phages. Our results show that the honey bee gut virome is composed of at least 118 distinct clusters corresponding to both temperate and lytic phages and representing novel genera with a large repertoire of unknown gene functions. We find that the phage community is prevalent in honey bees across space and time and targets the core members of the bee gut microbiota. The large number and high genetic diversity of the viral clusters seems to mirror the high extent of strain-level diversity in the bee gut microbiota. We isolated eight lytic phages that target the core microbiota member Bifidobacterium asteroides, but that exhibited different host ranges at the strain level, resulting in a nested interaction network of coexisting phages and bacterial strains. Collectively, our results show that the honey bee gut virome consists of a complex and diverse phage community that likely plays an important role in regulating strain-level diversity in the bee gut and that holds promise as an experimental model to study bacteria-phage dynamics in natural microbial communities.}, } @article {pmid32179266, year = {2020}, author = {Perez-Fernandez, C and Morales-Navas, M and Aguilera-Sáez, LM and Abreu, AC and Guardia-Escote, L and Fernández, I and Garrido-Cárdenas, JA and Colomina, MT and Giménez, E and Sánchez-Santed, F}, title = {Medium and long-term effects of low doses of Chlorpyrifos during the postnatal, preweaning developmental stage on sociability, dominance, gut microbiota and plasma metabolites.}, journal = {Environmental research}, volume = {184}, number = {}, pages = {109341}, doi = {10.1016/j.envres.2020.109341}, pmid = {32179266}, issn = {1096-0953}, mesh = {Adult ; Animals ; *Autism Spectrum Disorder/chemically induced ; *Chlorpyrifos/toxicity ; Female ; *Gastrointestinal Microbiome ; Humans ; *Insecticides/toxicity ; Mice ; Rats ; Social Behavior ; }, abstract = {Autism spectrum disorder (ASD) is a complex neurodevelopmental pathology characterized by altered verbalizations, reduced social interaction behavior, and stereotypies. Environmental factors have been associated with its development. Some researchers have focused on pesticide exposure. Chlorpyrifos (CPF) is the most used Organophosphate. Previous developmental studies with CPF showed decreased, enhanced or no effect on social outcomes eminently in mice. The study of CPF exposure during preweaning stages on social behavior is sparse in mice and non-existent in rats. d stressors could be at the basis of ASD development, and around postnatal day 10 in the rat is equivalent to the human birthday in neurodevelopmental terms. We explored the effects of exposure to low doses (1mg/kg/mL/day) of CPF during this stage regarding: sociability, dominance gut microbiome and plasma metabolomic profile, since alterations in these systems have also been linked to ASD. There was a modest influence of CPF on social behavior in adulthood, with null effects during adolescence. Dominance and hierarchical status were not affected by exposure. Dominance status explained the significant reduction in reaction to social novelty observed on the sociability test. CPF induced a significant gut microbiome dysbiosis and triggered a hyperlipidemic, hypoglycemic/hypogluconeogenesis and a general altered cell energy production in females. These behavioral results in rats extend and complement previous studies with mice and show novel influences on gut metagenomics and plasma lipid profile and metabolomics, but do not stablish a relation between the exposure to CPF and the ASD phenotype. The effects of dominance status on reaction to social novelty have an important methodological meaning for future research on sociability.}, } @article {pmid32179121, year = {2020}, author = {Maleki, M and Shahraki, MF and Kavousi, K and Ariaeenejad, S and Hosseini Salekdeh, G}, title = {A novel thermostable cellulase cocktail enhances lignocellulosic bioconversion and biorefining in a broad range of pH.}, journal = {International journal of biological macromolecules}, volume = {154}, number = {}, pages = {349-360}, doi = {10.1016/j.ijbiomac.2020.03.100}, pmid = {32179121}, issn = {1879-0003}, mesh = {Animals ; Bacteria/*enzymology ; Beta vulgaris/metabolism ; Camelus ; Cellulases/*chemistry ; *Gastrointestinal Microbiome ; Hydrolysis ; Kinetics ; Lignin/*metabolism ; Oryza/metabolism ; Recombinant Proteins ; Rumen/*microbiology ; }, abstract = {Lignocellulose is the most abundant biomass in nature, and the effective biorefining of them is dependent upon enzymes with high catalytic activity and stability in extreme pH and high temperatures. Due to the molecular constraints for a single enzyme, obtaining a more excellent active pH range can be more easily achievable through the simultaneous activity of two or more enzymes in a cocktail. To address this, we attempted to develop a cocktail of novel thermostable cellulases with high hydrolytic ability and stability. Two cellulases were mined, identified, cloned, and expressed from the camel rumen microbiota. The PersiCel1 demonstrated its maximum relative activity at the pH of 8, and the temperature of 60 °C and the PersiCel2 was optimally active at the pH of 5 and the temperature of 50 °C. Furthermore, utilization of the enzyme cocktail implies the synergistic relationship and significantly increased the saccharification yield of lignocellulosic substrates up to 71.7% for sugar-beet pulp (active pH range of 4-9) and 138.7% for rice-straw (active pH range of 5-8), compared to maximum hydrolysis of Persicel1 or PersiCel2 separately at 55 °C. Our results indicate the probable applicability of PersiCel1, PersiCel2, and their cocktail in numerous industries, specifically biorefineries and lignocellulose bioconversion based technologies.}, } @article {pmid32176535, year = {2020}, author = {Haley, BJ and Kim, SW and Salaheen, S and Hovingh, E and Van Kessel, JAS}, title = {Differences in the Microbial Community and Resistome Structures of Feces from Preweaned Calves and Lactating Dairy Cows in Commercial Dairy Herds.}, journal = {Foodborne pathogens and disease}, volume = {17}, number = {8}, pages = {494-503}, doi = {10.1089/fpd.2019.2768}, pmid = {32176535}, issn = {1556-7125}, mesh = {Animals ; Animals, Suckling/microbiology ; Bacteria/*classification/drug effects ; Cattle ; Dairying ; Drug Resistance, Bacterial/*genetics ; Feces/*microbiology ; Female ; Lactation ; *Microbiota ; }, abstract = {Preweaned dairy calves and lactating dairy cows are known reservoirs of antibiotic-resistant bacteria. To further understand the differences in the resistomes and microbial communities between the two, we sequenced the metagenomes of fecal composite samples from preweaned dairy calves and lactating dairy cows on 17 commercial dairy farms (n = 34 samples). Results indicated significant differences in the structures of the microbial communities (analysis of similarities [ANOSIM] R = 0.81, p = 0.001) and resistomes (ANOSIM R = 0.93 to 0.96, p = 0.001) between the two age groups. Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria were the predominant members of the communities, but when the groups were compared, Bacteroidetes and Verrumicrobia were significantly more abundant in calf fecal composite samples, whereas Firmicutes, Spirochaetes, Deinococcus-Thermus, Lentisphaerae, Planctomycetes, Chlorofexi, and Saccharibacteria-(TM7) were more abundant in lactating cow samples. Diverse suites of antibiotic resistance genes (ARGs) were identified in all samples, with the most frequently detected being assigned to tetracycline and aminoglycoside resistance. When the two groups were compared, ARGs were significantly more abundant in composite fecal samples from calves than those from lactating cows (calf median ARG abundance = 1.8 × 10[0] ARG/16S ribosomal RNA [rRNA], cow median ARG abundance = 1.7 × 10[-1] ARG/16S rRNA) and at the antibiotic resistance class level, the relative abundance of tetracycline, trimethoprim, aminoglycoside, macrolide-lincosamide-streptogramin B, β-lactam, and phenicol resistance genes was significantly higher in calf samples than in cow samples. Results of this study indicate that composite feces from preweaned calves harbor different bacterial communities and resistomes than composite feces from lactating cows, with a greater abundance of resistance genes detected in preweaned calf feces.}, } @article {pmid32174200, year = {2020}, author = {Lohmann, P and Schäpe, SS and Haange, SB and Oliphant, K and Allen-Vercoe, E and Jehmlich, N and Von Bergen, M}, title = {Function is what counts: how microbial community complexity affects species, proteome and pathway coverage in metaproteomics.}, journal = {Expert review of proteomics}, volume = {17}, number = {2}, pages = {163-173}, doi = {10.1080/14789450.2020.1738931}, pmid = {32174200}, issn = {1744-8387}, mesh = {Metabolic Networks and Pathways ; Metabolomics/*methods/standards ; Metagenome ; Metagenomics/*methods/standards ; *Microbiota ; Proteome/genetics/metabolism ; Proteomics/*methods/standards ; }, abstract = {Introduction: Metaproteomics is an established method to obtain a comprehensive taxonomic and functional view of microbial communities. After more than a decade, we are now able to describe the promise, reality, and perspectives of metaproteomics and provide useful information about the choice of method, applications, and potential improvement strategies.Areas covered: In this article, we will discuss current challenges of species and proteome coverage, and also highlight functional aspects of metaproteomics analysis of microbial communities with different levels of complexity. To do this, we re-analyzed data from microbial communities with low to high complexity (8, 72, 200 and >300 species). High species diversity leads to a reduced number of protein group identifications in a complex community, and thus the number of species resolved is underestimated. Ultimately, low abundance species remain undiscovered in complex communities. However, we observed that the main functional categories were better represented within complex microbiomes when compared to species coverage.Expert opinion: Our findings showed that even with low species coverage, metaproteomics has the potential to reveal habitat-specific functional features. Finally, we exploit this information to highlight future research avenues that are urgently needed to enhance our understanding of taxonomic composition and functions of complex microbiomes.}, } @article {pmid32173258, year = {2019}, author = {Breban, M and Beaufrère, M and Glatigny, S}, title = {The microbiome in spondyloarthritis.}, journal = {Best practice & research. Clinical rheumatology}, volume = {33}, number = {6}, pages = {101495}, doi = {10.1016/j.berh.2020.101495}, pmid = {32173258}, issn = {1532-1770}, mesh = {Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; *Spondylarthritis/microbiology ; *Spondylitis, Ankylosing ; }, abstract = {A causal link between the wealth of microbes that populate our body surfaces, designated as microbiota, and inflammatory disorders, including ankylosing spondylitis and the related spondyloarthritis (SpA) has been suspected for decades. This specially concerns the gut microbiota that became only recently accessible to thorough description thanks to massive sequencing methods or metagenomics. Here, we review evidences supporting the existence of microbiota imbalance or dysbiosis in the context of SpA. We also discuss currently existing evidences for a causal relationship between such dysbiosis and disease development, as well as putative therapeutic implications.}, } @article {pmid32171248, year = {2020}, author = {Liu, T and Chen, CY and Chen-Deng, A and Chen, YL and Wang, JY and Hou, YI and Lin, MC}, title = {Joining Illumina paired-end reads for classifying phylogenetic marker sequences.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {105}, pmid = {32171248}, issn = {1471-2105}, support = {107-2221-E-006-198-MY2//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Asthma/microbiology ; Bacteria/genetics ; Child ; Cluster Analysis ; Genetic Markers ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome ; Metagenomics/methods ; Microbiota/genetics ; *Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Illumina sequencing of a marker gene is popular in metagenomic studies. However, Illumina paired-end (PE) reads sometimes cannot be merged into single reads for subsequent analysis. When mergeable PE reads are limited, one can simply use only first reads for taxonomy annotation, but that wastes information in the second reads. Presumably, including second reads should improve taxonomy annotation. However, a rigorous investigation of how best to do this and how much can be gained has not been reported.

RESULTS: We evaluated two methods of joining as opposed to merging PE reads into single reads for taxonomy annotation using simulated data with sequencing errors. Our rigorous evaluation involved several top classifiers (RDP classifier, SINTAX, and two alignment-based methods) and realistic benchmark datasets. For most classifiers, read joining ameliorated the impact of sequencing errors and improved the accuracy of taxonomy predictions. For alignment-based top-hit classifiers, rearranging the reference sequences is recommended to avoid improper alignments of joined reads. For word-counting classifiers, joined reads could be compared to the original reference for classification. We also applied read joining to our own real MiSeq PE data of nasal microbiota of asthmatic children. Before joining, trimming low quality bases was necessary for optimizing taxonomy annotation and sequence clustering. We then showed that read joining increased the amount of effective data for taxonomy annotation. Using these joined trimmed reads, we were able to identify two promising bacterial genera that might be associated with asthma exacerbation.

CONCLUSIONS: When mergeable PE reads are limited, joining them into single reads for taxonomy annotation is always recommended. Reference sequences may need to be rearranged accordingly depending on the classifier. Read joining also relaxes the constraint on primer selection, and thus may unleash the full capacity of Illumina PE data for taxonomy annotation. Our work provides guidance for fully utilizing PE data of a marker gene when mergeable reads are limited.}, } @article {pmid32170305, year = {2021}, author = {Toivonen, L and Schuez-Havupalo, L and Karppinen, S and Waris, M and Hoffman, KL and Camargo, CA and Hasegawa, K and Peltola, V}, title = {Antibiotic Treatments During Infancy, Changes in Nasal Microbiota, and Asthma Development: Population-based Cohort Study.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {72}, number = {9}, pages = {1546-1554}, pmid = {32170305}, issn = {1537-6591}, mesh = {Anti-Bacterial Agents/adverse effects ; *Asthma/epidemiology ; Child ; Child, Preschool ; Cohort Studies ; Finland/epidemiology ; Humans ; Infant ; Infant, Newborn ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Early-life exposures to antibiotics may increase the risk of developing childhood asthma. However, little is known about the mechanisms linking antibiotic exposures to asthma. We hypothesized that changes in the nasal airway microbiota serve as a causal mediator in the antibiotics-asthma link.

METHODS: In a population-based birth-cohort study in Finland, we identified longitudinal nasal microbiota profiles during age 2-24 months using 16S rRNA gene sequencing and an unsupervised machine learning approach. We performed a causal mediation analysis to estimate the natural direct effect of systemic antibiotic treatments during age 0-11 months on risks of developing physician-diagnosed asthma by age 7 years and the natural indirect (causal mediation) effect through longitudinal changes in nasal microbiota.

RESULTS: In our birth cohort of 697 children, 8.0% later developed asthma. Exposure to ≥2 antibiotic treatments during age 0-11 months was associated with a 4.0% increase in the absolute risk of developing asthma (absolute increase, 95% CI, .9-7.2%; P = .006). The unsupervised clustering approach identified 6 longitudinal nasal microbiota profiles. Infants with a larger number of antibiotic treatments had a higher risk of having a profile with early Moraxella sparsity (per each antibiotic treatment, adjusted RRR, 1.38; 95% CI, 1.15-1.66; P < .001). This effect of antibiotics on asthma was partly mediated by longitudinal changes in the nasal microbiota (natural indirect effect, P = .008), accounting for 16% of the total effect.

CONCLUSIONS: Early exposures to antibiotics were associated with increased risk of asthma; the effect was mediated, in part, by longitudinal changes in the nasal airway microbiota.}, } @article {pmid32170201, year = {2020}, author = {Alneberg, J and Bennke, C and Beier, S and Bunse, C and Quince, C and Ininbergs, K and Riemann, L and Ekman, M and Jürgens, K and Labrenz, M and Pinhassi, J and Andersson, AF}, title = {Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {119}, pmid = {32170201}, issn = {2399-3642}, mesh = {Aquatic Organisms/*genetics ; Archaea/genetics ; Bacteria/genetics ; Base Sequence ; Ecology ; *Ecosystem ; *Genome, Archaeal ; *Genome, Bacterial ; Machine Learning ; *Metagenome ; Metagenomics/*methods ; Phylogeny ; Plankton/microbiology ; Sequence Analysis, DNA/methods ; }, abstract = {The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes' placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data.}, } @article {pmid32169939, year = {2020}, author = {Props, R and Denef, VJ}, title = {Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater Genus Limnohabitans.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {10}, pages = {}, pmid = {32169939}, issn = {1098-5336}, mesh = {Comamonadaceae/classification/*genetics/*physiology ; *Gene Expression ; *Genes, Bacterial ; *Genetic Variation ; Lakes/microbiology ; Michigan ; Microbiota ; Nutrients ; Temperature ; }, abstract = {Most freshwater bacterial communities are characterized by a few dominant taxa that are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic diversity within these taxonomic groups is limited to a subset of taxa. Here, we investigated the genomic diversity that enables Limnohabitans, a freshwater genus key in funneling carbon from primary producers to higher trophic levels, to achieve abundance and ubiquity. We reconstructed eight putative Limnohabitans metagenome-assembled genomes (MAGs) from stations located along broad environmental gradients existing in Lake Michigan, part of Earth's largest surface freshwater system. De novo strain inference analysis resolved a total of 23 strains from these MAGs, which strongly partitioned into two habitat-specific clusters with cooccurring strains from different lineages. The largest number of strains belonged to the abundant LimB lineage, for which robust in situ strain delineation had not previously been achieved. Our data show that temperature and nutrient levels may be important environmental parameters associated with microdiversification within the Limnohabitans genus. In addition, strains predominant in low- and high-phosphorus conditions had larger genomic divergence than strains abundant under different temperatures. Comparative genomics and gene expression analysis yielded evidence for the ability of LimB populations to exhibit cellular motility and chemotaxis, a phenotype not yet associated with available Limnohabitans isolates. Our findings broaden historical marker gene-based surveys of Limnohabitans microdiversification and provide in situ evidence of genome diversity and its functional implications across freshwater gradients.IMPORTANCELimnohabitans is an important bacterial taxonomic group for cycling carbon in freshwater ecosystems worldwide. Here, we examined the genomic diversity of different Limnohabitans lineages. We focused on the LimB lineage of this genus, which is globally distributed and often abundant, and its abundance has shown to be largely invariant to environmental change. Our data show that the LimB lineage is actually comprised of multiple cooccurring populations for which the composition and genomic characteristics are associated with variations in temperature and nutrient levels. The gene expression profiles of this lineage suggest the importance of chemotaxis and motility, traits that had not yet been associated with the Limnohabitans genus, in adapting to environmental conditions.}, } @article {pmid32168729, year = {2020}, author = {Todorov, H and Kollar, B and Bayer, F and Brandão, I and Mann, A and Mohr, J and Pontarollo, G and Formes, H and Stauber, R and Kittner, JM and Endres, K and Watzer, B and Nockher, WA and Sommer, F and Gerber, S and Reinhardt, C}, title = {α-Linolenic Acid-Rich Diet Influences Microbiota Composition and Villus Morphology of the Mouse Small Intestine.}, journal = {Nutrients}, volume = {12}, number = {3}, pages = {}, pmid = {32168729}, issn = {2072-6643}, support = {Novel and neglected cardiovascular risk factors//Boehringer Ingelheim Stiftung/ ; RE 3450/5-2//Deutsche Forschungsgemeinschaft/ ; 01EO1003 and 01EO1503//Bundesministerium für Bildung und Forschung/ ; -//Naturwissenschaftlich-Medizinische Forschungszentrum (NMFZ)/ ; -//Inneruniversitäre Forschungsförderung (Stufe 1)/ ; }, mesh = {*Animal Feed/analysis ; Animals ; *Biodiversity ; Fatty Acids/metabolism ; Feces/microbiology ; Food Analysis ; *Gastrointestinal Microbiome ; Immunohistochemistry ; Intestinal Mucosa/cytology/*microbiology ; Intestine, Small/*metabolism/*microbiology ; Lipid Metabolism ; Male ; Metagenome ; Metagenomics/methods ; Mice ; alpha-Linolenic Acid/analysis/*metabolism ; }, abstract = {α-Linolenic acid (ALA) is well-known for its anti-inflammatory activity. In contrast, the influence of an ALA-rich diet on intestinal microbiota composition and its impact on small intestine morphology are not fully understood. In the current study, we kept adult C57BL/6J mice for 4 weeks on an ALA-rich or control diet. Characterization of the microbial composition of the small intestine revealed that the ALA diet was associated with an enrichment in Prevotella and Parabacteroides. In contrast, taxa belonging to the Firmicutes phylum, including Lactobacillus, Clostridium cluster XIVa, Lachnospiraceae and Streptococcus, had significantly lower abundance compared to control diet. Metagenome prediction indicated an enrichment in functional pathways such as bacterial secretion system in the ALA group, whereas the two-component system and ALA metabolism pathways were downregulated. We also observed increased levels of ALA and its metabolites eicosapentanoic and docosahexanoic acid, but reduced levels of arachidonic acid in the intestinal tissue of ALA-fed mice. Furthermore, intestinal morphology in the ALA group was characterized by elongated villus structures with increased counts of epithelial cells and reduced epithelial proliferation rate. Interestingly, the ALA diet reduced relative goblet and Paneth cell counts. Of note, high-fat Western-type diet feeding resulted in a comparable adaptation of the small intestine. Collectively, our study demonstrates the impact of ALA on the gut microbiome and reveals the nutritional regulation of gut morphology.}, } @article {pmid32167528, year = {2020}, author = {Mallawaarachchi, V and Wickramarachchi, A and Lin, Y}, title = {GraphBin: refined binning of metagenomic contigs using assembly graphs.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {11}, pages = {3307-3313}, doi = {10.1093/bioinformatics/btaa180}, pmid = {32167528}, issn = {1367-4811}, mesh = {Algorithms ; *Metagenome ; Metagenomics ; *Microbiota ; Sequence Analysis, DNA ; Software ; }, abstract = {MOTIVATION: The field of metagenomics has provided valuable insights into the structure, diversity and ecology within microbial communities. One key step in metagenomics analysis is to assemble reads into longer contigs which are then binned into groups of contigs that belong to different species present in the metagenomic sample. Binning of contigs plays an important role in metagenomics and most available binning algorithms bin contigs using genomic features such as oligonucleotide/k-mer composition and contig coverage. As metagenomic contigs are derived from the assembly process, they are output from the underlying assembly graph which contains valuable connectivity information between contigs that can be used for binning.

RESULTS: We propose GraphBin, a new binning method that makes use of the assembly graph and applies a label propagation algorithm to refine the binning result of existing tools. We show that GraphBin can make use of the assembly graphs constructed from both the de Bruijn graph and the overlap-layout-consensus approach. Moreover, we demonstrate improved experimental results from GraphBin in terms of identifying mis-binned contigs and binning of contigs discarded by existing binning tools. To the best of our knowledge, this is the first time that the information from the assembly graph has been used in a tool for the binning of metagenomic contigs.

The source code of GraphBin is available at https://github.com/Vini2/GraphBin.

CONTACT: vijini.mallawaarachchi@anu.edu.au or yu.lin@anu.edu.au.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid32165294, year = {2020}, author = {Kieran, TJ}, title = {Mitochondrial, metagenomic, and phylogenetic analysis of the ground beetle Harpalus pensylvanicus (Coleoptera: Carabidae).}, journal = {Gene}, volume = {740}, number = {}, pages = {144540}, doi = {10.1016/j.gene.2020.144540}, pmid = {32165294}, issn = {1879-0038}, mesh = {Animals ; Coleoptera/classification/*genetics ; Genome, Mitochondrial/genetics ; *Metagenomics ; Microbiota/genetics ; }, abstract = {Harpalus pensylvanicus (Coloptera: Carabidae) is a weed seed predator common throughout the United States. While Carabidae is a very large group of beetles, limited genomic resources exist, especially mitochondrial genomes. This study expands research in this area by assembling and annotating the complete mitochondrial genome of H. pensylvanicus and performs phylogenetic analyses with closely related species. Further use of the metagenomic data was made to characterize microbial taxa and clusters of orthologous groups of proteins. The complete mitochondrial genome is 16,434 bp in length, AT rich, and consist of 13 protein coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region. Phylogenetic analyses were congruent with the Harpalinae and Pterostichinae clade together. Microbial classification shows a predominance of Gamma- (37.77%) and Alpha-proteobacteria (33.97%).}, } @article {pmid32164527, year = {2020}, author = {Kobus, R and Abuín, JM and Müller, A and Hellmann, SL and Pichel, JC and Pena, TF and Hildebrandt, A and Hankeln, T and Schmidt, B}, title = {A big data approach to metagenomics for all-food-sequencing.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {102}, pmid = {32164527}, issn = {1471-2105}, support = {HySim//Deutsche Forschungsgemeinschaft/ ; RTI2018-093336-B-C21//Ministerio de Econom?a y Competitividad/ ; ED481B 2018/013 and ED431C 2018/19//Xunta de Galicia/ ; 2816503814//Federal O?ce for Agriculture and Food/ ; }, mesh = {*Big Data ; Biosurveillance ; Food Analysis/*methods ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Software ; Whole Genome Sequencing/*methods ; }, abstract = {BACKGROUND: All-Food-Sequencing (AFS) is an untargeted metagenomic sequencing method that allows for the detection and quantification of food ingredients including animals, plants, and microbiota. While this approach avoids some of the shortcomings of targeted PCR-based methods, it requires the comparison of sequence reads to large collections of reference genomes. The steadily increasing amount of available reference genomes establishes the need for efficient big data approaches.

RESULTS: We introduce an alignment-free k-mer based method for detection and quantification of species composition in food and other complex biological matters. It is orders-of-magnitude faster than our previous alignment-based AFS pipeline. In comparison to the established tools CLARK, Kraken2, and Kraken2+Bracken it is superior in terms of false-positive rate and quantification accuracy. Furthermore, the usage of an efficient database partitioning scheme allows for the processing of massive collections of reference genomes with reduced memory requirements on a workstation (AFS-MetaCache) or on a Spark-based compute cluster (MetaCacheSpark).

CONCLUSIONS: We present a fast yet accurate screening method for whole genome shotgun sequencing-based biosurveillance applications such as food testing. By relying on a big data approach it can scale efficiently towards large-scale collections of complex eukaryotic and bacterial reference genomes. AFS-MetaCache and MetaCacheSpark are suitable tools for broad-scale metagenomic screening applications. They are available at https://muellan.github.io/metacache/afs.html (C++ version for a workstation) and https://github.com/jmabuin/MetaCacheSpark (Spark version for big data clusters).}, } @article {pmid32163141, year = {2020}, author = {Greshake Tzovaras, B and Segers, FHID and Bicker, A and Dal Grande, F and Otte, J and Anvar, SY and Hankeln, T and Schmitt, I and Ebersberger, I}, title = {What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen.}, journal = {Genome biology and evolution}, volume = {12}, number = {4}, pages = {309-324}, pmid = {32163141}, issn = {1759-6653}, mesh = {Ascomycota/*genetics/growth & development ; *Genome, Fungal ; Lichens/*genetics/growth & development ; *Metagenome ; Phylogeny ; *Symbiosis ; }, abstract = {Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are poor candidates for experimentation. Obtaining contiguous, high-quality genomes for such symbiotic communities is technically challenging. Here, we present the first assembly of a lichen holo-genome from metagenomic whole-genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis-the fungus Umbilicaria pustulata (33 Mb) and the green alga Trebouxia sp. (53 Mb)-were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative abundance of fungal to algal nuclei of ∼20:1. Gap-free, circular sequences for all organellar genomes were obtained. The bacterial community is dominated by Acidobacteriaceae and encompasses strains closely related to bacteria isolated from other lichens. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that GC-rich inverted repeats paired with nonrandom sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.}, } @article {pmid32163040, year = {2020}, author = {Hunter, P and Greco, E and Cross, K and Perry, J}, title = {Topical Oxygen Therapy Shifts Microbiome Dynamics in Chronic Diabetic Foot Ulcers.}, journal = {Wounds : a compendium of clinical research and practice}, volume = {32}, number = {3}, pages = {81-85}, pmid = {32163040}, issn = {1943-2704}, mesh = {Administration, Cutaneous ; Bacteria, Aerobic/classification/genetics/isolation & purification ; Bacteria, Anaerobic/classification/genetics/isolation & purification ; Cohort Studies ; Diabetic Foot/*microbiology/*therapy ; Humans ; Microbiota/*genetics ; Oxygen/administration & dosage/*therapeutic use ; *Wound Healing ; }, abstract = {INTRODUCTION: Bacterial biofilm in wounds prevents healing by acting as a physical barrier to wound closure and hyperactivating local inflammatory processes, thus making its removal a high priority. The authors previously have shown that adding topical oxygen to standard wound care increased healing of Texas Grade II and III diabetic foot ulcers (DFUs), which they hypothesized was a result of alterations of the wound microbiome/biofilm.

OBJECTIVE: This study aims to determine the mechanism of action of topical oxygen in DFUs by examining the diversity of bacterial genera present in DFUs treated with topical oxygen.

MATERIALS AND METHODS: Six patients with chronic DFUs had their wounds swabbed weekly over an 8-week period of continuous topical oxygen treatment, and microbiome diversity was assessed by metagenomic 16S rDNA sequencing using a next-generation sequencing platform.

RESULTS: The wound microbiome shifted toward a diverse flora dominated by aerobes and facultative anaerobes with oxygen therapy in 5 healed wounds. In contrast, anaerobic flora persisted in a single nonhealing ulcer in the present study cohort.

CONCLUSIONS: Although the sample size was small, this study suggests topical oxygen therapy may have the ability to encourage the growth of aerobic members of the wound microbiome and be an effective alternative to antibiotics in this area.}, } @article {pmid32161947, year = {2020}, author = {Zafeiropoulos, H and Viet, HQ and Vasileiadou, K and Potirakis, A and Arvanitidis, C and Topalis, P and Pavloudi, C and Pafilis, E}, title = {PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes.}, journal = {GigaScience}, volume = {9}, number = {3}, pages = {}, pmid = {32161947}, issn = {2047-217X}, mesh = {Animals ; Archaea ; Bacteria ; DNA Barcoding, Taxonomic/*methods/standards ; DNA, Environmental/chemistry/*genetics ; Electron Transport Complex IV/genetics ; Fungi ; Metagenomics/*methods/standards ; Plants ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Reference Standards ; Sensitivity and Specificity ; Software ; }, abstract = {BACKGROUND: Environmental DNA and metabarcoding allow the identification of a mixture of species and launch a new era in bio- and eco-assessment. Many steps are required to obtain taxonomically assigned matrices from raw data. For most of these, a plethora of tools are available; each tool's execution parameters need to be tailored to reflect each experiment's idiosyncrasy. Adding to this complexity, the computation capacity of high-performance computing systems is frequently required for such analyses. To address the difficulties, bioinformatic pipelines need to combine state-of-the art technologies and algorithms with an easy to get-set-use framework, allowing researchers to tune each study. Software containerization technologies ease the sharing and running of software packages across operating systems; thus, they strongly facilitate pipeline development and usage. Likewise programming languages specialized for big data pipelines incorporate features like roll-back checkpoints and on-demand partial pipeline execution.

FINDINGS: PEMA is a containerized assembly of key metabarcoding analysis tools that requires low effort in setting up, running, and customizing to researchers' needs. Based on third-party tools, PEMA performs read pre-processing, (molecular) operational taxonomic unit clustering, amplicon sequence variant inference, and taxonomy assignment for 16S and 18S ribosomal RNA, as well as ITS and COI marker gene data. Owing to its simplified parameterization and checkpoint support, PEMA allows users to explore alternative algorithms for specific steps of the pipeline without the need of a complete re-execution. PEMA was evaluated against both mock communities and previously published datasets and achieved results of comparable quality.

CONCLUSIONS: A high-performance computing-based approach was used to develop PEMA; however, it can be used in personal computers as well. PEMA's time-efficient performance and good results will allow it to be used for accurate environmental DNA metabarcoding analysis, thus enhancing the applicability of next-generation biodiversity assessment studies.}, } @article {pmid32159537, year = {2020}, author = {Zhang, M and Zhu, J and Zhang, X and Zhao, DG and Ma, YY and Li, D and Ho, CT and Huang, Q}, title = {Aged citrus peel (chenpi) extract causes dynamic alteration of colonic microbiota in high-fat diet induced obese mice.}, journal = {Food & function}, volume = {11}, number = {3}, pages = {2667-2678}, doi = {10.1039/c9fo02907a}, pmid = {32159537}, issn = {2042-650X}, mesh = {Adipose Tissue/drug effects ; Animals ; Bacteria/*drug effects/genetics ; Citrus/chemistry ; *Diet, High-Fat ; Drugs, Chinese Herbal/*pharmacology ; Fruit/chemistry ; Gastrointestinal Microbiome/*drug effects/genetics ; Male ; Metagenome/drug effects/genetics ; Mice ; Mice, Inbred C57BL ; Mice, Obese ; }, abstract = {Aged citrus peels (chenpi) have been used as a dietary supplement for gastrointestinal health maintenance in China. Recently, it was reported to exhibit anti-obesity activity. However, the relationship between the modulation effect of chenpi on gut microbiota and obesity prevention is not clearly understood. In this study, mice were fed with a high-fat diet (HFD), HFD supplemented with 0.25%- and 0.5%-chenpi extract, and normal diet, respectively, for 11 weeks. Chenpi extract significantly increased fecal short chain fatty acids by 43% for acetic acid and 86% for propionic acid. In addition, chenpi could decrease the prevalence of Proteobacteria and the ratio of Firmicutes to Bacteroidetes by about 88% and 70%, respectively. Moreover, this study was the first work to demonstrate the dynamics of two beneficial bacteria-Akkermansia spp. and Allobaculum spp. in a dose- and time-dependent manner for chenpi treatment via monitoring the dynamic change of the gut microbiota. Metagenomic analysis of the gut microbiota showed that several pathways, such as a two-component system, a tight junction, Staphylococcus aureus infection and others, were enhanced dynamically. The improved biological process of metabolism especially in benzoate derivatives might refer to the increased metabolic transformation of polymethoxyflavones from chenpi in the colon. Our study indicated that the modulation effect of chenpi on the gut microbiota may be an important pathway for its anti-obesity mechanisms.}, } @article {pmid32159510, year = {2020}, author = {Ghosh, TS and Das, M and Jeffery, IB and O'Toole, PW}, title = {Adjusting for age improves identification of gut microbiome alterations in multiple diseases.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {32159510}, issn = {2050-084X}, support = {APC/SFI/12/RC/2273/SFI_/Science Foundation Ireland/Ireland ; 13/SIRG/2128/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Adult ; Age Factors ; Aged ; Aged, 80 and over ; Computational Biology ; Data Interpretation, Statistical ; *Disease Susceptibility ; *Dysbiosis ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Microbiota ; Middle Aged ; Reproducibility of Results ; Young Adult ; }, abstract = {Interaction between disease-microbiome associations and ageing has not been explored in detail. Here, using age/region-matched sub-sets, we analysed the gut microbiome differences across five major diseases in a multi-cohort dataset constituting more than 2500 individuals from 20 to 89 years old. We show that disease-microbiome associations display specific age-centric trends. Ageing-associated microbiome alterations towards a disease-like configuration occur in colorectal cancer patients, thereby masking disease signatures. We identified a microbiome disease response shared across multiple diseases in elderly subjects that is distinct from that in young/middle-aged individuals, but also a novel set of taxa consistently gained in disease across all age groups. A subset of these taxa was associated with increased frailty in subjects from the ELDERMET cohort. The relevant taxa differentially encode specific functions that are known to have disease associations.}, } @article {pmid32158700, year = {2020}, author = {Romani, L and Del Chierico, F and Chiriaco, M and Foligno, S and Reddel, S and Salvatori, G and Cifaldi, C and Faraci, S and Finocchi, A and Rossi, P and Bagolan, P and D'Argenio, P and Putignani, L and Fusaro, F}, title = {Gut Mucosal and Fecal Microbiota Profiling Combined to Intestinal Immune System in Neonates Affected by Intestinal Ischemic Injuries.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {59}, pmid = {32158700}, issn = {2235-2988}, mesh = {Feces ; *Gastrointestinal Microbiome ; Gastrointestinal Tract ; Humans ; Immune System ; Infant, Newborn ; *Microbiota ; }, abstract = {Background and Purpose: Early life microbiota plays a crucial role in human health by acting as a barrier from pathogens' invasion and maintaining the intestinal immune homoeostasis. Altered fecal microbiota (FM) ecology was reported in newborns affected by intestinal ischemia. Our purpose was to describe, in these patients, the FM, the mucosal microbiota (MM) and the mucosal immunity. Methods: Fourteen newborns underwent intestinal resection because of intestinal ischemia. FM and MM were determined through targeted-metagenomics, diversity assignment and Kruskal-Wallis analyses of Operational taxonomic units (OTUs). The mucosal immune cells were analyzed through cytofluorimetry. Results and Conclusion: Based on the severity intestinal injueris we identified two groups: extensive (EII) and focal intestinal ischemia (FII). FM and MM varied in EII and FII groups, showing in the EII group the predominance of Proteobacteria and Enterobacteriaceae and the reduction of Bacteroidetes and Verrucomicrobia for both microbiota. The MM was characterized by a statistically significant reduction of Bacteroides, Lachnospiraceae and Ruminococcaceae and by a higher diversity in the EII compared to FII group. FM showed a prevalence of Proteobacteria, while the Shannon index was lower in the EII compared to FII group. An overall increment in B- and T-lymphocytes and Natural killer (NK) T-like cells was found for EII mucosal samples associated to an increment of TNF-α and INF-γ expressing cells, compared to FII group. FM and MM carry specific signatures of intestinal ischemic lesions. Further research may be crucial to address the role of specific taxa in EII, expecially with reference to inflammation grade and ischemia extension.}, } @article {pmid32157805, year = {2020}, author = {Reñé, A and Auladell, A and Reboul, G and Moreira, D and López-García, P}, title = {Performance of the melting seawater-ice elution method on the metabarcoding characterization of benthic protist communities.}, journal = {Environmental microbiology reports}, volume = {12}, number = {3}, pages = {314-323}, doi = {10.1111/1758-2229.12834}, pmid = {32157805}, issn = {1758-2229}, support = {ProtistWorld Grant 322669//H2020 European Research Council/International ; COPAS CTM2017-86121-R//Ministerio de Economía y Competitividad/International ; José Castillejo Grant CAS17/00237//Ministerio de Educación, Cultura y Deporte/International ; }, mesh = {Biodiversity ; Ciliophora/genetics/isolation & purification ; Dinoflagellida/genetics/isolation & purification ; *Eukaryota/genetics/isolation & purification ; Fungi/genetics/isolation & purification ; Geologic Sediments/microbiology ; Metagenomics/*methods ; RNA, Ribosomal, 18S/genetics ; Seawater/*microbiology ; }, abstract = {Massive amplicon sequencing approaches to characterize the diversity of microbial eukaryotes in sediments are scarce and controls about the effects introduced by different methods to recover DNA are lacking. In this study, we compare the performance of the melting seawater-ice elution method on the characterization of benthic protist communities by 18S rRNA gene metabarcoding with results obtained by direct cell lysis and DNA purification from sediments. Even though the most abundant operational taxonomic units were recovered by both methods, eluted samples yielded higher richness than samples undergoing direct lysis. Both treatments allowed recovering the same taxonomic groups, although we observed significant differences in terms of relative abundance for some of them. Dinoflagellata and Ciliophora strongly dominated the community in eluted samples (> 80% reads). In directly lysed samples, they only represented 37%, while groups like Fungi and Ochrophytes were highly represented (> 20% reads respectively). Our results show that the elution process yields a higher protist richness estimation, most likely as a result of the higher sample volume used to recover organisms as compared to commonly used volumes for direct benthic DNA purification. Motile groups, like dinoflagellates and ciliates, are logically more enriched during the elution process.}, } @article {pmid32157603, year = {2020}, author = {Zhao, T and Gong, H and Shen, X and Zhang, W and Shan, T and Yu, X and Wang, SJ and Cui, L}, title = {Comparison of Viromes in Ticks from Different Domestic Animals in China.}, journal = {Virologica Sinica}, volume = {35}, number = {4}, pages = {398-406}, pmid = {32157603}, issn = {1995-820X}, mesh = {Animals ; Animals, Domestic/*parasitology ; Cattle/parasitology ; China ; Dogs/parasitology ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Sheep/parasitology ; Tick Infestations/*veterinary/virology ; Ticks/classification/*virology ; *Virome ; Viruses/*classification/isolation & purification ; }, abstract = {Ticks are involved in the transmission of various arboviruses and some tick-borne viruses pose significant threats to the health of humans or livestock. This study aimed to investigate the geographical distribution of tick species and tick-associated viruses in central and eastern China. Total 573 ticks from domestic animals including dogs, sheep and cattle were collected in 2017. Two genera of ticks were identified including Rhipicephalus and Haemaphysalis. Sequencing was performed on Miseq Illumina platform to characterize the tick viromes from the four different sampling locations. Following trimming, 13,640 reads were obtained and annotated to 19 virus families. From these sequences, above 37.74% of the viral reads were related to the RNA viruses. Virome comparison study revealed that the tick viral diversity was considerably different in the two identified tick genera. The viral diversity of R. microplus was significantly different from that of other Rhipicephalus species. On the other hand, substantial overlap in viral species was observed between the same genera. In addition, we found no evidence that the natural host played a major role in shaping virus diversity based on the comparison of their viromes. Rather, the geographic location seems to significantly influence the viral families. Phylogenetic study indicated that the novel negative-sense RNA viruses identified in this study was closely related to Bole tick virus 1 and 3 viruses. In conclusion, the present study provides a baseline for comparing viruses detected in ticks, according to species, natural hosts, and geographic locations.}, } @article {pmid32157464, year = {2020}, author = {Casalone, E and Cavalieri, D and Daly, G and Vitali, F and Perito, B}, title = {Propolis hosts a diversemicrobial community.}, journal = {World journal of microbiology & biotechnology}, volume = {36}, number = {3}, pages = {50}, pmid = {32157464}, issn = {1573-0972}, support = {prot.2012RCEZWH_001//Programmi di Ricerca di Rilevante Interesse Nazionale (PRIN) 2012/ ; }, mesh = {Animals ; Anti-Infective Agents/pharmacology ; Bacteria/*classification/drug effects/isolation & purification ; Bees ; DNA, Ribosomal/genetics ; Fungi/*classification/drug effects/isolation & purification ; Gastrointestinal Microbiome ; Microbial Sensitivity Tests ; *Microbiota/drug effects ; Phylogeny ; Propolis/*pharmacology ; }, abstract = {Despite the deep knowledge of the honey bee (Apis mellifera) gut microbiome, information on the microbial communities of other hive components is still scarce. Propolis originates from a natural resinous mixture that honeybees collect from different plants sources and modify; it is used mainly to ensure the hygiene of the hive. By virtue of its antimicrobial properties, propolis has been considered relatively aseptic, yet its ability to harbor microorganisms has not been previously investigated. In this study we report the first description of the diversity of the microbial community of propolis by both targeted-metagenomics analysis and cultivation. We demonstrated that propolis hosts a variety of microbial strains belonging to taxa already described in other hive components. Some of them are cultivable in standard laboratory conditions, and show metabolic characteristics compatible with their persistence in different physiological states inside propolis. Isolated bacteria produce antimicrobials against Gram-negative and Gram-positive bacteria, and entomopathogenic fungi, with different spectra of inhibition. Metagenomics analysis shows the presence of bacteria and fungi with great potential to outcompete potentially harmful microorganisms. These findings suggest that the characterized microbiota could contribute to the overall antimicrobial properties of propolis and to its ecological role as "disinfectant" within the hive.}, } @article {pmid32156316, year = {2020}, author = {Huang, Z and Zeng, S and Xiong, J and Hou, D and Zhou, R and Xing, C and Wei, D and Deng, X and Yu, L and Wang, H and Deng, Z and Weng, S and Kriengkrai, S and Ning, D and Zhou, J and He, J}, title = {Microecological Koch's postulates reveal that intestinal microbiota dysbiosis contributes to shrimp white feces syndrome.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {32}, pmid = {32156316}, issn = {2049-2618}, mesh = {Animals ; Bacteria/classification/isolation & purification ; Dysbiosis/*microbiology ; Fecal Microbiota Transplantation/*veterinary ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genetic Variation ; Intestines/*microbiology/physiopathology ; Penaeidae/*microbiology ; }, abstract = {BACKGROUND: Recently, increasing evidence supports that some complex diseases are not attributed to a given pathogen, but dysbiosis in the host intestinal microbiota (IM). The full intestinal ecosystem alterations, rather than a single pathogen, are associated with white feces syndrome (WFS), a globally severe non-infectious shrimp disease, while no experimental evidence to explore the causality. Herein, we conducted comprehensive metagenomic and metabolomic analysis, and intestinal microbiota transplantation (IMT) to investigate the causal relationship between IM dysbiosis and WFS.

RESULTS: Compared to the Control shrimp, we found dramatically decreased microbial richness and diversity in WFS shrimp. Ten genera, such as Vibrio, Candidatus Bacilloplasma, Photobacterium, and Aeromonas, were overrepresented in WFS, whereas 11 genera, including Shewanella, Chitinibacter, and Rhodobacter were enriched in control. The divergent changes in these populations might contribute the observation that a decline of pathways conferring lipoic acid metabolism and mineral absorption in WFS. Meanwhile, some sorts of metabolites, especially lipids and organic acids, were found to be related to the IM alteration in WFS. Integrated with multiomics and IMT, we demonstrated that significant alterations in the community composition, functional potentials, and metabolites of IM were closely linked to shrimp WFS. The distinguished metabolites which were attributed to the IM dysbiosis were validated by feed-supplementary challenge. Both homogenous selection and heterogeneous selection process were less pronounced in WFS microbial community assembly. Notably, IMT shrimp from WFS donors eventually developed WFS clinical signs, while the dysbiotic IM can be recharacterized in recipient shrimp.

CONCLUSIONS: Collectively, our findings offer solid evidence of the causality between IM dysbiosis and shrimp WFS, which exemplify the 'microecological Koch's postulates' (an intestinal microbiota dysbiosis, a disease) in disease etiology, and inspire our cogitation on etiology from an ecological perspective. Video abstract.}, } @article {pmid32155753, year = {2020}, author = {Ottati, S and Chiapello, M and Galetto, L and Bosco, D and Marzachì, C and Abbà, S}, title = {New Viral Sequences Identified in the Flavescence Dorée Phytoplasma Vector Scaphoideus titanus.}, journal = {Viruses}, volume = {12}, number = {3}, pages = {}, pmid = {32155753}, issn = {1999-4915}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Hemiptera/*microbiology/*virology ; *Metagenome ; *Metagenomics/methods ; Phylogeny ; Phytoplasma ; RNA Viruses/genetics ; RNA, Double-Stranded ; *Virome ; }, abstract = {The leafhopper Scaphoideus titanus is the primary vector of Flavescence dorée phytoplasma (FDp) in European vineyards. Flavescence dorée is one of the most severely damaging diseases of Vitis vinifera and, consequently, a major threat to grape and wine production in several European countries. Control measures are compulsory, but they mainly involve large-scale insecticide treatments, with detrimental impacts on the environment. One possible solution is to exploit the largely unexplored genetic diversity of viruses infecting S. titanus as highly specific and environmentally benign tools for biological control. (2)Methods: A metatranscriptomic approach was adopted to identify viruses that may infect individuals caught in the wild in both its native (United States) and invasive (Europe) areas. Reverse transcription PCR was used to confirm their presence in RNA pools and explore their prevalence. (3)Results: We described nine new RNA viruses, including members of "Picorna-Calici", "Permutotetra", "Bunya-Arena", "Reo", "Partiti-Picobirna", "Luteo-Sobemo" and "Toti-Chryso" clades. A marked difference in the diversity and abundance of the viral species was observed between the US population and the European ones. (4)Conclusions: This work represents the first survey to assess the viral community of a phytoplasma insect vector. The possibility to exploit these naturally occurring viruses as specific and targeted biocontrol agents of S. titanus could be the answer to increasing demand for a more sustainable viticulture.}, } @article {pmid32148761, year = {2019}, author = {Williams, J and Bravo, HC and Tom, J and Paulson, JN}, title = {microbiomeDASim: Simulating longitudinal differential abundance for microbiome data.}, journal = {F1000Research}, volume = {8}, number = {}, pages = {1769}, pmid = {32148761}, issn = {2046-1402}, mesh = {*Microbiota ; Sequence Analysis, DNA ; *Software ; }, abstract = {An increasing emphasis on understanding the dynamics of microbial communities in various settings has led to the proliferation of longitudinal metagenomic sampling studies. Data from whole metagenomic shotgun sequencing and marker-gene survey studies have characteristics that drive novel statistical methodological development for estimating time intervals of differential abundance. In designing a study and the frequency of collection prior to a study, one may wish to model the ability to detect an effect, e.g., there may be issues with respect to cost, ease of access, etc. Additionally, while every study is unique, it is possible that in certain scenarios one statistical framework may be more appropriate than another. Here, we present a simulation paradigm implemented in the R Bioconductor software package microbiomeDASim available at http://bioconductor.org/packages/microbiomeDASim microbiomeDASim. microbiomeDASim allows investigators to simulate longitudinal differential abundant microbiome features with a variety of known functional forms with flexible parameters to control desired signal-to-noise ratio. We present metrics of success results on one particular method called metaSplines.}, } @article {pmid32155560, year = {2020}, author = {Duan, JL and Sun, JW and Ji, MM and Ma, Y and Cui, ZT and Tian, RK and Xu, PC and Sun, WL and Yuan, XZ}, title = {Indicatory bacteria and chemical composition related to sulfur distribution in the river-lake systems.}, journal = {Microbiological research}, volume = {236}, number = {}, pages = {126453}, doi = {10.1016/j.micres.2020.126453}, pmid = {32155560}, issn = {1618-0623}, mesh = {*Bacteria/classification/genetics ; Biodiversity ; China ; Genes, Bacterial ; Geologic Sediments/chemistry/microbiology ; Lakes/*chemistry/microbiology ; Metagenomics ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S ; Rivers/*chemistry/microbiology ; *Sentinel Species/classification/genetics ; Sulfur/*analysis ; Water Pollutants, Chemical/analysis ; }, abstract = {Sulfate related water quality and trophic status are crucial to operation of water diversion. Though the sulfur geochemistry in the lake sediment have been well studied, the effective indicator of surrounding environment conditions related to sulfur in river-lake systems are still unknown. In this study, Dongping Lake (DPH), Weishan Lake (WSH), and Hanzhuang trunk canal (HZQ) were selected as the typical river-lake systems in the eastern of China. Different spatial variations in sedimentary sulfate, total sulfur, and elemental composition of sediments were investigated in these areas. The relatively high sulfate in surface water and sediments appeared in portions of WSH. The biodiversity of HZQ and WSH surface sediments was much higher than that of DPH. Pseudomonas, Acinetobacter, and Thiobacillus were the dominant genera of the river-lake systems. Among the different genera in distribution, genera such as Malikia, Sulfurovum and Lysinibacillus were significantly negatively correlated with sulfur related environmental factors. While the genera such as Pseudomonas, Vogesella and Acinetobacter were significantly positively correlated with these factors. Compared with connectivity in the largest interaction network, bacteria such as Proteus, Acidobacter and Chlorobacteria were identified as indicatory taxa to infer sulfate related conditions in the river-lake systems.}, } @article {pmid32155347, year = {2020}, author = {Ali, S and Saldias, S and Weerasuriya, N and Delaney, K and Kandasamy, S and Lazarovits, G}, title = {Corn microbial diversity and its relationship to yield.}, journal = {Canadian journal of microbiology}, volume = {66}, number = {8}, pages = {457-473}, doi = {10.1139/cjm-2020-0002}, pmid = {32155347}, issn = {1480-3275}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Farms ; *Microbiota ; Polymorphism, Restriction Fragment Length ; Soil Microbiology ; Zea mays/growth & development/*microbiology ; }, abstract = {This study aimed to identify possible relationships between corn (Zea mays L.) productivity and its endosphere microbial community. Any insights would be used to develop testable hypotheses at the farm level. Sap was collected from 14 fields in 2014 and 10 fields in 2017, with a yield range of 10.1 to 21.7 tonnes per hectare (t/ha). The microbial sap communities were analyzed using terminal restriction fragment length polymorphism (TRFLP) and identified using an internal pure culture reference database and BLAST. This technique is rapid and inexpensive and is suitable for use at the grower level. Diversity, richness, and normalized abundances of each bacterial population in corn sap samples were evaluated to link the microbiome of a specific field to its yield. A negative trend was observed (r = -0.60), with higher-yielding fields having lower terminal restriction fragment (TRF) richness. A partial least square regression analysis of TRF intensity and binary data from 2014 identified 10 TRFs (bacterial genera) that positively, or negatively, correlated with corn yields, when either absent or present at certain levels or ratios. Using these observations, a model was developed that accommodated criteria for each of the 10 microbes and assigned a score for each field out of 10. Data collected in 2014 showed that sites with higher model scores were highly correlated with larger yields (r = 0.83). This correlation was also seen when the 2017 data set was used (r = 0.87). We were able to conclude that a positive significant effect was seen with the model score and yield (adjusted R[2] = 0.67, F[1,22] = 46.7, p < 0.001) when combining 2014 and 2017 data. The results of this study are being expanded to identify the key microbes in the corn sap community that potentially impact corn yield, regardless of corn variety, geographic factors, or edaphic factors.}, } @article {pmid32155146, year = {2020}, author = {Ramiro, RS and Durão, P and Bank, C and Gordo, I}, title = {Low mutational load and high mutation rate variation in gut commensal bacteria.}, journal = {PLoS biology}, volume = {18}, number = {3}, pages = {e3000617}, pmid = {32155146}, issn = {1545-7885}, mesh = {Adaptation, Physiological/genetics ; Animals ; Anti-Bacterial Agents/pharmacology ; DNA Polymerase III/genetics ; Escherichia coli/genetics ; Escherichia coli Proteins/genetics ; Gastrointestinal Microbiome/drug effects/*genetics ; Male ; Mice, Inbred C57BL ; Microorganisms, Genetically-Modified ; *Mutation Rate ; Selection, Genetic ; }, abstract = {Bacteria generally live in species-rich communities, such as the gut microbiota. Yet little is known about bacterial evolution in natural ecosystems. Here, we followed the long-term evolution of commensal Escherichia coli in the mouse gut. We observe the emergence of mutation rate polymorphism, ranging from wild-type levels to 1,000-fold higher. By combining experiments, whole-genome sequencing, and in silico simulations, we identify the molecular causes and explore the evolutionary conditions allowing these hypermutators to emerge and coexist within the microbiota. The hypermutator phenotype is caused by mutations in DNA polymerase III proofreading and catalytic subunits, which increase mutation rate by approximately 1,000-fold and stabilise hypermutator fitness, respectively. Strong mutation rate variation persists for >1,000 generations, with coexistence between lineages carrying 4 to >600 mutations. The in vivo molecular evolution pattern is consistent with fitness effects of deleterious mutations sd ≤ 10-4/generation, assuming a constant effect or exponentially distributed effects with a constant mean. Such effects are lower than typical in vitro estimates, leading to a low mutational load, an inference that is observed in in vivo and in vitro competitions. Despite large numbers of deleterious mutations, we identify multiple beneficial mutations that do not reach fixation over long periods of time. This indicates that the dynamics of beneficial mutations are not shaped by constant positive Darwinian selection but could be explained by other evolutionary mechanisms that maintain genetic diversity. Thus, microbial evolution in the gut is likely characterised by partial sweeps of beneficial mutations combined with hitchhiking of slightly deleterious mutations, which take a long time to be purged because they impose a low mutational load. The combination of these two processes could allow for the long-term maintenance of intraspecies genetic diversity, including mutation rate polymorphism. These results are consistent with the pattern of genetic polymorphism that is emerging from metagenomics studies of the human gut microbiota, suggesting that we have identified key evolutionary processes shaping the genetic composition of this community.}, } @article {pmid32153535, year = {2020}, author = {Stokke, R and Reeves, EP and Dahle, H and Fedøy, AE and Viflot, T and Lie Onstad, S and Vulcano, F and Pedersen, RB and Eijsink, VGH and Steen, IH}, title = {Tailoring Hydrothermal Vent Biodiversity Toward Improved Biodiscovery Using a Novel in situ Enrichment Strategy.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {249}, pmid = {32153535}, issn = {1664-302X}, abstract = {Deep-sea hydrothermal vents are amongst the most extreme environments on Earth and represent interesting targets for marine bioprospecting and biodiscovery. The microbial communities in hydrothermal vents are often dominated by chemolithoautotrophs utilizing simple chemical compounds, though the full extent of their heterotrophic abilities is still being explored. In the bioprocessing industry, where degradation of complex organic materials often is a major challenge, new microbial solutions are heavily needed. To meet these needs, we have developed novel in situ incubators and tested if deployment of recalcitrant materials from fish farming and wood-pulping industries introduced changes in the microbial community structure in hot marine hydrothermal sediments. The incubation chambers were deployed in sediments at the Bruse vent site located within the Jan Mayen vent field for 1 year, after which the microbial populations in the chambers were profiled by 16S rRNA Ion Torrent amplicon sequencing. A total of 921 operational taxonomic units (OTUs) were assigned into 74 different phyla where differences in community structure were observed depending on the incubated material, chamber depth below the sea floor and/or temperature. A high fraction of putative heterotrophic microbial lineages related to cultivated members within the Thermotogales were observed. However, considerable fractions of previously uncultivated and novel Thermotogales and Bacteroidetes were also identified. Moreover, several novel lineages (e.g., members within the DPANN superphylum, unidentified archaeal lineages, unclassified Thermoplasmatales and Candidatus division BRC-1 bacterium) of as-yet uncultivated thermophilic archaea and bacteria were identified. Overall, our data illustrate that amendment of hydrothermal vent communities by in situ incubation of biomass induces shifts in community structure toward increased fractions of heterotrophic microorganisms. The technologies utilized here could aid in subsequent metagenomics-based enzyme discovery for diverse industries.}, } @article {pmid32152478, year = {2020}, author = {Aron-Wisnewsky, J and Vigliotti, C and Witjes, J and Le, P and Holleboom, AG and Verheij, J and Nieuwdorp, M and Clément, K}, title = {Gut microbiota and human NAFLD: disentangling microbial signatures from metabolic disorders.}, journal = {Nature reviews. Gastroenterology & hepatology}, volume = {17}, number = {5}, pages = {279-297}, pmid = {32152478}, issn = {1759-5053}, mesh = {Animals ; Diabetes Mellitus, Type 2/microbiology ; Digestive System Diseases/microbiology ; Dysbiosis/immunology/microbiology ; Gastrointestinal Microbiome/*immunology ; Humans ; Non-alcoholic Fatty Liver Disease/immunology/*microbiology ; Obesity/microbiology ; Signal Transduction ; }, abstract = {Gut microbiota dysbiosis has been repeatedly observed in obesity and type 2 diabetes mellitus, two metabolic diseases strongly intertwined with non-alcoholic fatty liver disease (NAFLD). Animal studies have demonstrated a potential causal role of gut microbiota in NAFLD. Human studies have started to describe microbiota alterations in NAFLD and have found a few consistent microbiome signatures discriminating healthy individuals from those with NAFLD, non-alcoholic steatohepatitis or cirrhosis. However, patients with NAFLD often present with obesity and/or insulin resistance and type 2 diabetes mellitus, and these metabolic confounding factors for dysbiosis have not always been considered. Patients with different NAFLD severity stages often present with heterogeneous lesions and variable demographic characteristics (including age, sex and ethnicity), which are known to affect the gut microbiome and have been overlooked in most studies. Finally, multiple gut microbiome sequencing tools and NAFLD diagnostic methods have been used across studies that could account for discrepant microbiome signatures. This Review provides a broad insight into microbiome signatures for human NAFLD and explores issues with disentangling these signatures from underlying metabolic disorders. More advanced metagenomics and multi-omics studies using system biology approaches are needed to improve microbiome biomarkers.}, } @article {pmid32152415, year = {2020}, author = {Giron, LB and Tanes, CE and Schleimann, MH and Engen, PA and Mattei, LM and Anzurez, A and Damra, M and Zhang, H and Bittinger, K and Bushman, F and Kossenkov, A and Denton, PW and Tateno, H and Keshavarzian, A and Landay, AL and Abdel-Mohsen, M}, title = {Sialylation and fucosylation modulate inflammasome-activating eIF2 Signaling and microbial translocation during HIV infection.}, journal = {Mucosal immunology}, volume = {13}, number = {5}, pages = {753-766}, pmid = {32152415}, issn = {1935-3456}, support = {R21 NS106970/NS/NINDS NIH HHS/United States ; R01 AG062383/AG/NIA NIH HHS/United States ; R01 DK123733/DK/NIDDK NIH HHS/United States ; R21 AI143385/AI/NIAID NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; R21 AI129636/AI/NIAID NIH HHS/United States ; }, mesh = {Antiretroviral Therapy, Highly Active ; Biodiversity ; Colon, Sigmoid/immunology/metabolism/microbiology ; Dysbiosis ; Epitopes, T-Lymphocyte/immunology ; Eukaryotic Initiation Factor-2/*metabolism ; *Gastrointestinal Microbiome/immunology ; Glycosylation ; HIV Infections/drug therapy/immunology/*metabolism/virology ; Humans ; Immunocompromised Host ; Inflammasomes/*metabolism ; Intestinal Mucosa/immunology/metabolism/microbiology/pathology ; Metagenome ; Metagenomics/methods ; Protein Processing, Post-Translational ; *Signal Transduction ; Viral Load ; }, abstract = {An emerging paradigm suggests that gut glycosylation is a key force in maintaining the homeostatic relationship between the gut and its microbiota. Nevertheless, it is unclear how gut glycosylation contributes to the HIV-associated microbial translocation and inflammation that persist despite viral suppression and contribute to the development of several comorbidities. We examined terminal ileum, right colon, and sigmoid colon biopsies from HIV-infected virally-suppressed individuals and found that gut glycomic patterns are associated with distinct microbial compositions and differential levels of chronic inflammation and HIV persistence. In particular, high levels of the pro-inflammatory hypo-sialylated T-antigen glycans and low levels of the anti-inflammatory fucosylated glycans were associated with higher abundance of glycan-degrading microbial species (in particular, Bacteroides vulgatus), a less diverse microbiome, higher levels of inflammation, and higher levels of ileum-associated HIV DNA. These findings are linked to the activation of the inflammasome-mediating eIF2 signaling pathway. Our study thus provides the first proof-of-concept evidence that a previously unappreciated factor, gut glycosylation, is a force that may impact the vicious cycle between HIV infection, microbial translocation, and chronic inflammation.}, } @article {pmid32150601, year = {2020}, author = {Prifti, E and Chevaleyre, Y and Hanczar, B and Belda, E and Danchin, A and Clément, K and Zucker, JD}, title = {Interpretable and accurate prediction models for metagenomics data.}, journal = {GigaScience}, volume = {9}, number = {3}, pages = {}, pmid = {32150601}, issn = {2047-217X}, mesh = {Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenome ; Metagenomics/*methods ; Models, Genetic ; Support Vector Machine ; }, abstract = {BACKGROUND: Microbiome biomarker discovery for patient diagnosis, prognosis, and risk evaluation is attracting broad interest. Selected groups of microbial features provide signatures that characterize host disease states such as cancer or cardio-metabolic diseases. Yet, the current predictive models stemming from machine learning still behave as black boxes and seldom generalize well. Their interpretation is challenging for physicians and biologists, which makes them difficult to trust and use routinely in the physician-patient decision-making process. Novel methods that provide interpretability and biological insight are needed. Here, we introduce "predomics", an original machine learning approach inspired by microbial ecosystem interactions that is tailored for metagenomics data. It discovers accurate predictive signatures and provides unprecedented interpretability. The decision provided by the predictive model is based on a simple, yet powerful score computed by adding, subtracting, or dividing cumulative abundance of microbiome measurements.

RESULTS: Tested on >100 datasets, we demonstrate that predomics models are simple and highly interpretable. Even with such simplicity, they are at least as accurate as state-of-the-art methods. The family of best models, discovered during the learning process, offers the ability to distil biological information and to decipher the predictability signatures of the studied condition. In a proof-of-concept experiment, we successfully predicted body corpulence and metabolic improvement after bariatric surgery using pre-surgery microbiome data.

CONCLUSIONS: Predomics is a new algorithm that helps in providing reliable and trustworthy diagnostic decisions in the microbiome field. Predomics is in accord with societal and legal requirements that plead for an explainable artificial intelligence approach in the medical field.}, } @article {pmid32145354, year = {2020}, author = {Zhang, Z and Cao, H and Song, N and Zhang, L and Cao, Y and Tai, J}, title = {Long-term hexavalent chromium exposure facilitates colorectal cancer in mice associated with changes in gut microbiota composition.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {138}, number = {}, pages = {111237}, doi = {10.1016/j.fct.2020.111237}, pmid = {32145354}, issn = {1873-6351}, mesh = {Animals ; Body Weight ; Chromium/*adverse effects ; Colorectal Neoplasms/*chemically induced ; Dimethylhydrazines/*adverse effects ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/*drug effects ; Mice ; Mice, Inbred C57BL ; Oxidative Stress/drug effects ; }, abstract = {Colorectal cancer (CRC) is among the leading causes of cancer-related mortality worldwide. Hexavalent chromium [Cr(VI)] is often present in groundwater. Chronic Cr(VI) exposure is suggested to be one of the main factors inducing cancer. However, the correlation between Cr(VI) and CRC remains unclear. In this study, we investigated the role of Cr(VI) in CRC by establishing a mouse CRC model induced by 1, 2-dimethylhydrazine (DMH). The results showed that Cr(VI) increased weight loss in DMH-induced mice and promoted the formation of tumors. Cr(VI) also increased DMH-induced proliferating cell nuclear antigen (PCNA) levels. Investigation of the underlying mechanisms found that Cr(VI) significantly decreased DMH-induced SOD, GSH and CAT levels, while, the MDA level increased. Metagenomic analyses found that the abundance of Firmicutes and Bacteroidetes in the DMH + Cr group was down-regulated. Interestingly, the combination of Cr(VI) and DMH significantly increased the abundance of Verrucomicrobia. At the family and genus levels, families Akkermansiaceae and Saccharimonadaceae and genus Akkermansia were more abundant in the DMH + Cr group, whereas the abundance of short-chain fatty acid (SCFA)-producing bacteria (family Muribaculaceae, family Lachnosipiraceae, genus Lachnospiraceae_NK4A136_group, and genus Roseburia) decreased. These results indicate that Cr(VI) might aggravate CRC by altering the composition of the gut microflora.}, } @article {pmid32145224, year = {2020}, author = {Worden, L}, title = {Conservation of community functional structure across changes in composition in consumer-resource models.}, journal = {Journal of theoretical biology}, volume = {493}, number = {}, pages = {110239}, pmid = {32145224}, issn = {1095-8541}, support = {R01 GM130900/GM/NIGMS NIH HHS/United States ; U01 GM087728/GM/NIGMS NIH HHS/United States ; }, mesh = {Ecosystem ; *Metagenomics ; *Microbiota ; Phylogeny ; }, abstract = {High-throughput sequencing techniques such as metagenomic and metatranscriptomic technologies allow cataloguing of functional characteristics of microbial community members as well as their phylogenetic identity. Such studies have found that a community's makeup in terms of ecologically relevant functional traits or guilds can be conserved more strictly across varying settings than its composition is in terms of taxa. I use a standard ecological resource-consumer model to examine the dynamics of traits relevant to resource consumption, and analyze determinants of functional structure. This model demonstrates that interaction with essential resources can regulate the community-wide abundances of ecologically relevant traits, keeping them at consistent levels despite large changes in the abundances of the species housing those traits in response to changes in the environment, and across variation between communities in species composition. Functional structure is shown to be able to track differences in environmental conditions faithfully across differences in species composition. Mathematical conditions on consumers' vital rates and functional responses necessary and sufficient to produce conservation of functional community structure across differences in species composition in these models are presented. These conditions imply a nongeneric relation between biochemical rates, and avenues for further research are discussed.}, } @article {pmid32144784, year = {2020}, author = {Shah, AA and Wu, J and Qian, C and Liu, Z and Mobashar, M and Tao, Z and Zhang, X and Zhong, X}, title = {Ensiling of whole-plant hybrid pennisetum with natamycin and Lactobacillus plantarum impacts on fermentation characteristics and meta-genomic microbial community at low temperature.}, journal = {Journal of the science of food and agriculture}, volume = {100}, number = {8}, pages = {3378-3385}, doi = {10.1002/jsfa.10371}, pmid = {32144784}, issn = {1097-0010}, mesh = {Acetic Acid/metabolism ; Ammonia/analysis/metabolism ; Fermentation/drug effects ; Genomics ; Lactic Acid/metabolism ; Lactobacillales/classification/drug effects/genetics/*metabolism ; Lactobacillus plantarum/drug effects/*metabolism ; *Microbiota/drug effects ; Natamycin/*pharmacology ; Pennisetum/metabolism/*microbiology ; Silage/analysis/microbiology ; Yeasts/classification/drug effects/genetics/metabolism ; }, abstract = {BACKGROUND: The aim of the current research was to clarify the impacts of the ensiling of whole-plant hybrid pennisetum with natamycin and Lactobacillus plantarum on fermentation characteristics and the meta-genomic microbial community at low temperatures.

RESULTS: During the ensiling process, lactic acid (LA) and lactic acid bacteria (LAB) significantly (P < 0.05) increased and acetic acid (AA), water-soluble carbohydrate (WSC), ammonia total nitrogen (NH3-N), and yeast significantly (P < 0.05) reduced in treatments as compared to controls. Different treatments and different ensiling days led to variations in the bacterial community at family and genus levels. The family Lactobacillaceae and genera Lactobacillus and Pediococcus are dominant communities in treatment silage. The family and genus levels bacterial ecology and fermentation quality were analyzed by principal component analysis (PCA). The PCO1, and PCO2 can be explained by 10.81% and 72.14% of the whole variance regularly, similarly in PCO1 and PCO2 can be explained 24.23% and 52.06% regularly. The core bacterial micro-biome operational taxonomic unit (OTU) numbers increased in treatments, as compared to controls, on different hybrid pennisetum ensiling days.

CONCLUSIONS: The inoculation of L. plantarum alone and combined with natamycin influenced the fermentation quality and reduced undesirable microorganisms during the fermentation of hybrid pennisetum silage. Natamycin alone did not significantly enhance the concentration of organic acid but numerically enhanced in treatments group as compared to control. © 2020 Society of Chemical Industry.}, } @article {pmid32144387, year = {2020}, author = {De Angelis, M and Ferrocino, I and Calabrese, FM and De Filippis, F and Cavallo, N and Siragusa, S and Rampelli, S and Di Cagno, R and Rantsiou, K and Vannini, L and Pellegrini, N and Lazzi, C and Turroni, S and Lorusso, N and Ventura, M and Chieppa, M and Neviani, E and Brigidi, P and O'Toole, PW and Ercolini, D and Gobbetti, M and Cocolin, L}, title = {Diet influences the functions of the human intestinal microbiome.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {4247}, pmid = {32144387}, issn = {2045-2322}, mesh = {Cell Line, Tumor ; Computational Biology/methods ; *Diet ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metabolic Networks and Pathways ; Metagenome ; Metagenomics/methods ; Nitrogen/metabolism ; }, abstract = {Gut microbes programme their metabolism to suit intestinal conditions and convert dietary components into a panel of small molecules that ultimately affect host physiology. To unveil what is behind the effects of key dietary components on microbial functions and the way they modulate host-microbe interaction, we used for the first time a multi-omic approach that goes behind the mere gut phylogenetic composition and provides an overall picture of the functional repertoire in 27 fecal samples from omnivorous, vegan and vegetarian volunteers. Based on our data, vegan and vegetarian diets were associated to the highest abundance of microbial genes/proteins responsible for cell motility, carbohydrate- and protein-hydrolyzing enzymes, transport systems and the synthesis of essential amino acids and vitamins. A positive correlation was observed when intake of fiber and the relative fecal abundance of flagellin were compared. Microbial cells and flagellin extracted from fecal samples of 61 healthy donors modulated the viability of the human (HT29) colon carcinoma cells and the host response through the stimulation of the expression of Toll-like receptor 5, lectin RegIIIα and three interleukins (IL-8, IL-22 and IL-23). Our findings concretize a further and relevant milestone on how the diet may prevent/mitigate disease risk.}, } @article {pmid32144104, year = {2020}, author = {Matthews, MK and Wilcox, H and Hughes, R and Veloz, M and Hammer, A and Banks, B and Walters, A and Schneider, KJ and Sexton, CE and Chaston, JM}, title = {Genetic Influences of the Microbiota on the Life Span of Drosophila melanogaster.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {10}, pages = {}, pmid = {32144104}, issn = {1098-5336}, mesh = {Animals ; Drosophila melanogaster/*microbiology/*physiology ; Genome-Wide Association Study ; Longevity/physiology ; Metabolome/genetics ; Metagenome/physiology ; Microbiota/genetics/*physiology ; }, abstract = {To better understand how associated microorganisms ("microbiota") influence organismal aging, we focused on the model organism Drosophila melanogaster We conducted a metagenome-wide association (MGWA) as a screen to identify bacterial genes associated with variation in the D. melanogaster life span. The results of the MGWA predicted that bacterial cysteine and methionine metabolism genes influence fruit fly longevity. A mutant analysis, in which flies were inoculated with Escherichia coli strains bearing mutations in various methionine cycle genes, confirmed a role for some methionine cycle genes in extending or shortening fruit fly life span. Initially, we predicted these genes might influence longevity by mimicking or opposing methionine restriction, an established mechanism for life span extension in fruit flies. However, follow-up transcriptome sequencing (RNA-seq) and metabolomic experiments were generally inconsistent with this conclusion and instead implicated glucose and vitamin B6 metabolism in these influences. We then tested if bacteria could influence life span through methionine restriction using a different set of bacterial strains. Flies reared with a bacterial strain that ectopically expressed bacterial transsulfuration genes and lowered the methionine content of the fly diet also extended female D. melanogaster life span. Taken together, the microbial influences shown here overlap with established host genetic mechanisms for aging and therefore suggest overlapping roles for host and microbial metabolism genes in organismal aging.IMPORTANCE Associated microorganisms ("microbiota") are intimately connected to the behavior and physiology of their animal hosts, and defining the mechanisms of these interactions is an urgent imperative. This study focuses on how microorganisms influence the life span of a model host, the fruit fly Drosophila melanogaster First, we performed a screen that suggested a strong influence of bacterial methionine metabolism on host life span. Follow-up analyses of gene expression and metabolite abundance identified stronger roles for vitamin B6 and glucose than methionine metabolism among the tested mutants, possibly suggesting a more limited role for bacterial methionine metabolism genes in host life span effects. In a parallel set of experiments, we created a distinct bacterial strain that expressed life span-extending methionine metabolism genes and showed that this strain can extend fly life span. Therefore, this work identifies specific bacterial genes that influence host life span, including in ways that are consistent with the expectations of methionine restriction.}, } @article {pmid32142706, year = {2020}, author = {Dharamshi, JE and Tamarit, D and Eme, L and Stairs, CW and Martijn, J and Homa, F and Jørgensen, SL and Spang, A and Ettema, TJG}, title = {Marine Sediments Illuminate Chlamydiae Diversity and Evolution.}, journal = {Current biology : CB}, volume = {30}, number = {6}, pages = {1032-1048.e7}, doi = {10.1016/j.cub.2020.02.016}, pmid = {32142706}, issn = {1879-0445}, mesh = {Aquatic Organisms/classification/genetics/isolation & purification ; Arctic Regions ; *Biological Evolution ; Chlamydiales/classification/genetics/isolation & purification ; Geologic Sediments/*microbiology ; Gram-Negative Bacteria/classification/genetics/*isolation & purification ; *Microbiota ; Oceans and Seas ; }, abstract = {The bacterial phylum Chlamydiae is so far composed of obligate symbionts of eukaryotic hosts. Well known for Chlamydiaceae, pathogens of humans and other animals, Chlamydiae also include so-called environmental lineages that primarily infect microbial eukaryotes. Environmental surveys indicate that Chlamydiae are found in a wider range of environments than anticipated previously. However, the vast majority of this chlamydial diversity has been underexplored, biasing our current understanding of their biology, ecological importance, and evolution. Here, we report that previously undetected and active chlamydial lineages dominate microbial communities in deep anoxic marine sediments taken from the Arctic Mid-Ocean Ridge. Reaching relative abundances of up to 43% of the bacterial community, and a maximum diversity of 163 different species-level taxonomic units, these Chlamydiae represent important community members. Using genome-resolved metagenomics, we reconstructed 24 draft chlamydial genomes, expanding by over a third the known genomic diversity in this phylum. Phylogenomic analyses revealed several novel clades across the phylum, including a previously unknown sister lineage of the Chlamydiaceae, providing new insights into the origin of pathogenicity in this family. We were unable to identify putative eukaryotic hosts for these marine sediment chlamydiae, despite identifying genomic features that may be indicative of host-association. The high abundance and genomic diversity of Chlamydiae in these anoxic marine sediments indicate that some members could play an important, and thus far overlooked, ecological role in such environments and may indicate alternate lifestyle strategies.}, } @article {pmid32141148, year = {2020}, author = {Alessi, AM and Gray, V and Farquharson, FM and Flores-López, A and Shaw, S and Stead, D and Wegmann, U and Shearman, C and Gasson, M and Collie-Duguid, ESR and Flint, HJ and Louis, P}, title = {β-Glucan is a major growth substrate for human gut bacteria related to Coprococcus eutactus.}, journal = {Environmental microbiology}, volume = {22}, number = {6}, pages = {2150-2164}, doi = {10.1111/1462-2920.14977}, pmid = {32141148}, issn = {1462-2920}, support = {//University of Aberdeen Rowett Institute/International ; //Institute of Food Research/International ; //ScottishGovernment Rural and Environment Science and Analytical Services Division/International ; }, mesh = {Bacterial Proteins/genetics ; Clostridiales/genetics/*growth & development ; *Gastrointestinal Microbiome ; Gene Expression ; Glucans/pharmacology ; Glycoside Hydrolases/genetics ; Humans ; Proteomics ; *beta-Glucans ; }, abstract = {A clone encoding carboxymethyl cellulase activity was isolated during functional screening of a human gut metagenomic library using Lactococcus lactis MG1363 as heterologous host. The insert carried a glycoside hydrolase family 9 (GH9) catalytic domain with sequence similarity to a gene from Coprococcus eutactus ART55/1. Genome surveys indicated a limited distribution of GH9 domains among dominant human colonic anaerobes. Genomes of C. eutactus-related strains harboured two GH9-encoding and four GH5-encoding genes, but the strains did not appear to degrade cellulose. Instead, they grew well on β-glucans and one of the strains also grew on galactomannan, galactan, glucomannan and starch. Coprococcus comes and Coprococcus catus strains did not harbour GH9 genes and were not able to grow on β-glucans. Gene expression and proteomic analysis of C. eutactus ART55/1 grown on cellobiose, β-glucan and lichenan revealed similar changes in expression in comparison to glucose. On β-glucan and lichenan only, one of the four GH5 genes was strongly upregulated. Growth on glucomannan led to a transcriptional response of many genes, in particular a strong upregulation of glycoside hydrolases involved in mannan degradation. Thus, β-glucans are a major growth substrate for species related to C. eutactus, with glucomannan and galactans alternative substrates for some strains.}, } @article {pmid32140945, year = {2020}, author = {Leite, GGS and Weitsman, S and Parodi, G and Celly, S and Sedighi, R and Sanchez, M and Morales, W and Villanueva-Millan, MJ and Barlow, GM and Mathur, R and Lo, SK and Jamil, LH and Paski, S and Rezaie, A and Pimentel, M}, title = {Mapping the Segmental Microbiomes in the Human Small Bowel in Comparison with Stool: A REIMAGINE Study.}, journal = {Digestive diseases and sciences}, volume = {65}, number = {9}, pages = {2595-2604}, pmid = {32140945}, issn = {1573-2568}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacteria/*classification/genetics ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestine, Small/*microbiology ; Male ; Metagenomics ; Middle Aged ; Prospective Studies ; Ribotyping ; Young Adult ; }, abstract = {BACKGROUND: Most gut microbiome studies have been performed using stool samples. However, the small intestine is of central importance to digestion, nutrient absorption, and immune function, and characterizing its microbial populations is essential for elucidating their roles in human health and disease.

AIMS: To characterize the microbial populations of different small intestinal segments and contrast these to the stool microbiome.

METHODS: Male and female subjects undergoing esophagogastroduodenoscopy without colon preparation were prospectively recruited. Luminal aspirates were obtained from the duodenum, jejunum, and farthest distance reached. A subset also provided stool samples. 16S rRNA sequencing was performed and analyses were carried out using CLC Genomics Workbench.

RESULTS: 16S rRNA sequencing identified differences in more than 2000 operational taxonomic units between the small intestinal and stool microbiomes. Firmicutes and Proteobacteria were the most abundant phyla in the small intestine, and Bacteroidetes were less abundant. In the small intestine, phylum Firmicutes was primarily represented by lactic acid bacteria, including families Streptococcaceae, Lactobacillaceae, and Carnobacteriaceae, and Proteobacteria was represented by families Neisseriaceae, Pasteurellaceae, and Enterobacteriaceae. The duodenal and FD microbial signatures were markedly different from each other, but there were overlaps between duodenal and jejunal and between jejunal and FD microbial signatures. In stool, Firmicutes were represented by families Ruminococcaceae, Lachnospiraceae, Christensenellaceae, and Proteobacteria by class Deltaproteobacteria.

CONCLUSIONS: The small bowel microbiome is markedly different from that in stool and also varies between segments. These findings may be important in determining how compositional changes in small intestinal microbiota contribute to human disease states.}, } @article {pmid32139706, year = {2020}, author = {Allamin, IA and Halmi, MIE and Yasid, NA and Ahmad, SA and Abdullah, SRS and Shukor, Y}, title = {Rhizodegradation of Petroleum Oily Sludge-contaminated Soil Using Cajanus cajan Increases the Diversity of Soil Microbial Community.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {4094}, pmid = {32139706}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics/*metabolism ; *Biodegradation, Environmental ; Biodiversity ; Cajanus/growth & development/*metabolism/microbiology ; Environmental Monitoring ; Microbiota ; Petroleum/*metabolism ; Plant Roots/growth & development/metabolism/microbiology ; Rhizosphere ; Sewage/*analysis ; Soil/*chemistry ; Soil Pollutants/isolation & purification/*metabolism ; }, abstract = {Most components of petroleum oily sludge (POS) are toxic, mutagenic and cancer-causing. Often bioremediation using microorganisms is hindered by the toxicity of POS. Under this circumstance, phytoremediation is the main option as it can overcome the toxicity of POS. Cajanus cajan a legume plant, was evaluated as a phyto-remediating agent for petroleum oily sludge-spiked soil. Culture dependent and independent methods were used to determine the rhizosphere microorganisms' composition. Degradation rates were estimated gravimetrically. The population of total heterotrophic bacteria (THRB) was significantly higher in the uncontaminated soil compared to the contaminated rhizosphere soil with C. cajan, but the population of hydrocarbon-utilizing bacteria (HUB) was higher in the contaminated rhizosphere soil. The results show that for 1 to 3% oily sludge concentrations, an increase in microbial counts for all treatments from day 0 to 90 d was observed with the contaminated rhizosphere CR showing the highest significant increase (p < 0.05) in microbial counts compared to other treatments. The metagenomic study focused on the POS of 3% (w/w) and based on the calculated bacterial community abundance indices showed an increase in the values for Ace, Cho, Shannon (Shannon-Weaver) and the Simpson's (measured as InvSimpson) indices in CR3 compared to CN3. Both the Simpson's and the Shannon values for CR3 were higher than CN3 indicating an increase in diversity upon the introduction of C. cajan into the contaminated soil. The PCoA plot revealed community-level differences between the contaminated non-rhizosphere control and contaminated rhizosphere microbiota. The PCoA differentiated the two treatments based on the presence or absence of plant. The composition and taxonomic analysis of microbiota-amplified sequences were categorized into eight phyla for the contaminated non-rhizosphere and ten phyla for the contaminated rhizosphere. The overall bacterial composition of the two treatments varied, as the distribution shows a similar variation between the two treatments in the phylum distribution. The percentage removal of total petroleum hydrocarbon (TPH) after 90 days of treatments with 1, 2, 3, 4, and 5% (w/w) of POS were 92, 90, 89, 68.3 and 47.3%, respectively, indicating removal inhibition at higher POS concentrations. As the search for more eco-friendly and sustainable remediating green plant continues, C. cajan shows great potential in reclaiming POS contaminated soil. Our findings will provide solutions to POS polluted soils and subsequent re-vegetation.}, } @article {pmid32139564, year = {2020}, author = {Coleine, C and Albanese, D and Onofri, S and Tringe, SG and Pennacchio, C and Donati, C and Stajich, JE and Selbmann, L}, title = {Metagenomes in the Borderline Ecosystems of the Antarctic Cryptoendolithic Communities.}, journal = {Microbiology resource announcements}, volume = {9}, number = {10}, pages = {}, pmid = {32139564}, issn = {2576-098X}, support = {S10 OD016290/OD/NIH HHS/United States ; }, abstract = {Antarctic cryptoendolithic communities are microbial ecosystems dwelling inside rocks of the Antarctic desert. We present the first 18 shotgun metagenomes from these communities to further characterize their composition, biodiversity, functionality, and adaptation. Future studies will integrate taxonomic and functional annotations to examine the pathways necessary for life to evolve in the extremes.}, } @article {pmid32138779, year = {2020}, author = {Heshiki, Y and Vazquez-Uribe, R and Li, J and Ni, Y and Quainoo, S and Imamovic, L and Li, J and Sørensen, M and Chow, BKC and Weiss, GJ and Xu, A and Sommer, MOA and Panagiotou, G}, title = {Predictable modulation of cancer treatment outcomes by the gut microbiota.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {28}, pmid = {32138779}, issn = {2049-2618}, mesh = {Adult ; Aged ; Animals ; Bacteria/*classification ; Disease Models, Animal ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Genetic Variation ; Humans ; Longitudinal Studies ; Lung Neoplasms/drug therapy ; Male ; *Metagenomics ; Mice ; Mice, Inbred C57BL ; Middle Aged ; Neoplasms/*drug therapy/*microbiology ; Prognosis ; Treatment Outcome ; }, abstract = {The gut microbiota has the potential to influence the efficacy of cancer therapy. Here, we investigated the contribution of the intestinal microbiome on treatment outcomes in a heterogeneous cohort that included multiple cancer types to identify microbes with a global impact on immune response. Human gut metagenomic analysis revealed that responder patients had significantly higher microbial diversity and different microbiota compositions compared to non-responders. A machine-learning model was developed and validated in an independent cohort to predict treatment outcomes based on gut microbiota composition and functional repertoires of responders and non-responders. Specific species, Bacteroides ovatus and Bacteroides xylanisolvens, were positively correlated with treatment outcomes. Oral gavage of these responder bacteria significantly increased the efficacy of erlotinib and induced the expression of CXCL9 and IFN-γ in a murine lung cancer model. These data suggest a predictable impact of specific constituents of the microbiota on tumor growth and cancer treatment outcomes with implications for both prognosis and therapy.}, } @article {pmid32135388, year = {2020}, author = {Fouladi, F and Bailey, MJ and Patterson, WB and Sioda, M and Blakley, IC and Fodor, AA and Jones, RB and Chen, Z and Kim, JS and Lurmann, F and Martino, C and Knight, R and Gilliland, FD and Alderete, TL}, title = {Air pollution exposure is associated with the gut microbiome as revealed by shotgun metagenomic sequencing.}, journal = {Environment international}, volume = {138}, number = {}, pages = {105604}, pmid = {32135388}, issn = {1873-6750}, support = {P30 ES007048/ES/NIEHS NIH HHS/United States ; P30 DK048520/DK/NIDDK NIH HHS/United States ; P01 ES022845/ES/NIEHS NIH HHS/United States ; T32 ES013678/ES/NIEHS NIH HHS/United States ; R00 ES027853/ES/NIEHS NIH HHS/United States ; }, mesh = {*Air Pollutants/analysis/toxicity ; *Air Pollution/adverse effects/analysis ; Animals ; Bacteroides ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Young Adult ; }, abstract = {Animal work indicates exposure to air pollutants may alter the composition of the gut microbiota. This study examined relationships between air pollutants and the gut microbiome in young adults residing in Southern California. Our results demonstrate significant associations between exposure to air pollutants and the composition of the gut microbiome using whole-genome sequencing. Higher exposure to 24-hour O3 was associated with lower Shannon diversity index, higher Bacteroides caecimuris, and multiple gene pathways, including L-ornithine de novo biosynthesis as well as pantothenate and coenzyme A biosynthesis I. Among other pollutants, higher NO2 exposure was associated with fewer taxa, including higher Firmicutes. The percent variation in gut bacterial composition that was explained by air pollution exposure was up to 11.2% for O3 concentrations, which is large compared to the effect size for many other covariates reported in healthy populations. This study provides the first evidence of significant associations between exposure to air pollutants and the compositional and functional profile of the human gut microbiome. These results identify O3 as an important pollutant that may alter the human gut microbiome.}, } @article {pmid32135365, year = {2020}, author = {Hu, Y and Chen, N and Liu, T and Feng, C and Ma, L and Chen, S and Li, M}, title = {The mechanism of nitrate-Cr(VI) reduction mediated by microbial under different initial pHs.}, journal = {Journal of hazardous materials}, volume = {393}, number = {}, pages = {122434}, doi = {10.1016/j.jhazmat.2020.122434}, pmid = {32135365}, issn = {1873-3336}, mesh = {Bacteria/metabolism ; Biodegradation, Environmental ; Bioreactors ; Chromium/*metabolism ; Hydrogen-Ion Concentration ; Metabolic Networks and Pathways ; Microbiota ; Nitrates/*metabolism ; Oxidation-Reduction ; Water Pollutants, Chemical/*metabolism ; }, abstract = {To date, comparatively little research is known about the role of pH conditions in bioremediation of Cr(VI) contaminated aquifers. This study explored microbial Cr(VI) reduction and denitrification under different initial pHs. The underlying mechanism was also investigated. When testing 50 mg/L-N nitrate and 10 mg/L Cr(VI), complete contaminants removal was observed at initial pH 10.0 and 11.0, and only 10 %-30 % of removal achieved under other conditions, which might be ascribe to the significant up-regulation of functional genes narG (8.31 and 10.46 folds) and azoR (24.90 and 15.96 folds) at initial pH 10.0 and 11.0. Metagenomic sequencing showed that alkali tolerant bacteria played major roles in the NO3[-]-Cr(VI) reduction (i.e. Pannonibacter increased by 13.08 % and 25.24 % at initial pH 10.0 and 11.0), and metabolic pathways of Degradation and Energy were found of increased abundant. Furthermore, a significative study suggested that potential interspecies cooperation existed at initial pH 11.0 to facilitating the simultaneous removal of contaminants, and Pannonibacter indicus might be an important participant in the degradation of contaminants. The results of this study will fully understand the metabolic patterns of bacteria under alkaline conditions, expand the range of available functional bacteria, and enhance the practical aspects of co-contaminants remediation.}, } @article {pmid32135180, year = {2020}, author = {Gordon, CA and Krause, L and McManus, DP and Morrison, M and Weerakoon, KG and Connor, MC and Olveda, RM and Ross, AG and Gobert, GN}, title = {Helminths, polyparasitism, and the gut microbiome in the Philippines.}, journal = {International journal for parasitology}, volume = {50}, number = {3}, pages = {217-225}, doi = {10.1016/j.ijpara.2019.12.008}, pmid = {32135180}, issn = {1879-0135}, mesh = {Adolescent ; Adult ; Albendazole/therapeutic use ; Ancylostoma/isolation & purification ; Ancylostomatoidea/isolation & purification ; Animals ; Ascaris/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; Child ; Child, Preschool ; Cohort Studies ; *Coinfection/microbiology/parasitology ; Feces/microbiology/parasitology ; Female ; Gastrointestinal Microbiome/*genetics ; Genes, Bacterial ; Helminthiasis/drug therapy/*epidemiology ; Helminths/genetics/*isolation & purification ; Host-Parasite Interactions ; Humans ; Male ; Metagenomics ; Microbial Interactions ; Middle Aged ; Pathology, Molecular ; Philippines/epidemiology ; Schistosoma/isolation & purification ; Schistosomiasis/drug therapy/*epidemiology ; Soil/parasitology ; Trichuris/isolation & purification ; Young Adult ; }, abstract = {Polyparasitism, involving soil-transmitted helminths. and Schistosoma blood flukes, is common in low to middle income countries. These helminths impact on the gut environment and can cause changes to the gut microbiome composition. Here we examined the gut microbiome in individuals with polyparasitism from two human cohorts in the Philippines utilising DNA sequencing-based profiling. Multiple helminth species infections were high with 70.3% of study participants harbouring at least two parasite species, and 16% harbouring at least five species. Increased numbers of helminth co-infections, in particular with the gut-resident soil-transmitted helminths, were significantly associated with increased bacterial diversity; however no significant parasite-gut microbiome associations were evident for individuals infected only with Schistosoma japonicum. In general, a healthy gut is associated with high bacterial diversity, which in these human cohorts may be the result of helminth-mediated immune modulation, or due to changes in the gut environment caused by these parasitic helminths.}, } @article {pmid32134020, year = {2020}, author = {Agnihotry, S and Sarangi, AN and Aggarwal, R}, title = {Construction & assessment of a unified curated reference database for improving the taxonomic classification of bacteria using 16S rRNA sequence data.}, journal = {The Indian journal of medical research}, volume = {151}, number = {1}, pages = {93-103}, pmid = {32134020}, issn = {0971-5916}, mesh = {Bacteria/classification/*genetics ; *Classification ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenomics/classification ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND & OBJECTIVES: For bacterial community analysis, 16S rRNA sequences are subjected to taxonomic classification through comparison with one of the three commonly used databases [Greengenes, SILVA and Ribosomal Database Project (RDP)]. It was hypothesized that a unified database containing fully annotated, non-redundant sequences from all the three databases, might provide better taxonomic classification during analysis of 16S rRNA sequence data. Hence, a unified 16S rRNA database was constructed and its performance was assessed by using it with four different taxonomic assignment methods, and for data from various hypervariable regions (HVRs) of 16S rRNA gene.

METHODS: We constructed a unified 16S rRNA database (16S-UDb) by merging non-ambiguous, fully annotated, full-length 16S rRNA sequences from the three databases and compared its performance in taxonomy assignment with that of three original databases. This was done using four different taxonomy assignment methods [mothur Naïve Bayesian Classifier (mothur-nbc), RDP Naïve Bayesian Classifier (rdp-nbc), UCLUST, SortMeRNA] and data from 13 regions of 16S rRNA [seven hypervariable regions (HVR) (V2-V8) and six pairs of adjacent HVRs].

RESULTS: Our unified 16S rRNA database contained 13,078 full-length, fully annotated 16S rRNA sequences. It could assign genus and species to larger proportions (90.05 and 46.82%, respectively, when used with mothur-nbc classifier and the V2+V3 region) of sequences in the test database than the three original 16S rRNA databases (70.88-87.20% and 10.23-24.28%, respectively, with the same classifier and region).

Our results indicate that for analysis of bacterial mixtures, sequencing of V2-V3 region of 16S rRNA followed by analysis of the data using the mothur-nbc classifier and our 16S-UDb database may be preferred.}, } @article {pmid32132981, year = {2020}, author = {Song, D and Zhang, Y and Liu, J and Zhong, H and Zheng, Y and Zhou, S and Yu, M and Todd, JD and Zhang, XH}, title = {Metagenomic Insights Into the Cycling of Dimethylsulfoniopropionate and Related Molecules in the Eastern China Marginal Seas.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {157}, pmid = {32132981}, issn = {1664-302X}, abstract = {The microbial cycling of dimethylsulfoniopropionate (DMSP) and its gaseous catabolites dimethylsulfide (DMS) and methanethiol (MeSH) are important processes in the global sulfur cycle, marine microbial food webs, signaling pathways, atmospheric chemistry, and potentially climate regulation. Many functional genes have been identified and used to study the genetic potential of microbes to produce and catabolize these organosulfur compounds in different marine environments. Here, we sampled seawater, marine sediment and hydrothermal sediment, and polymetallic sulfide in the eastern Chinese marginal seas and analyzed their microbial communities for the genetic potential to cycle DMSP, DMS, and MeSH using metagenomics. DMSP was abundant in all sediment samples, but was fivefold less prominent in those from hydrothermal samples. Indeed, Yellow Sea (YS) sediment samples had DMSP concentrations two orders of magnitude higher than in surface water samples. Bacterial genetic potential to synthesize DMSP (mainly in Rhodobacteraceae bacteria) was far higher than for phytoplankton in all samples, but particularly in the sediment where no algal DMSP synthesis genes were detected. Thus, we propose bacteria as important DMSP producers in these marine sediments. DMSP catabolic pathways mediated by the DMSP lyase DddP (prominent in Pseudomonas and Mesorhizobium bacteria) and DMSP demethylase DmdA enzymes (prominent in Rhodobacteraceae bacteria) and MddA-mediated MeSH S-methylation were very abundant in Bohai Sea and Yellow Sea sediments (BYSS) samples. In contrast, the genetic potential for DMSP degradation was very low in the hydrothermal sediment samples-dddP was the only catabolic gene detected and in only one sample. However, the potential for DMS production from MeSH (mddA) and DMS oxidation (dmoA and ddhA) was relatively abundant. This metagenomics study does not provide conclusive evidence for DMSP cycling; however, it does highlight the potential importance of bacteria in the synthesis and catabolism of DMSP and related compounds in diverse sediment environments.}, } @article {pmid32130896, year = {2020}, author = {Lesker, TR and Durairaj, AC and Gálvez, EJC and Lagkouvardos, I and Baines, JF and Clavel, T and Sczyrba, A and McHardy, AC and Strowig, T}, title = {An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome.}, journal = {Cell reports}, volume = {30}, number = {9}, pages = {2909-2922.e6}, pmid = {32130896}, issn = {2211-1247}, mesh = {Animals ; Base Sequence ; Biodiversity ; Female ; Gastrointestinal Microbiome/*genetics ; Male ; Metagenome/*genetics ; Mice, Inbred C57BL ; Models, Genetic ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The complexity of host-associated microbial ecosystems requires host-specific reference catalogs to survey the functions and diversity of these communities. We generate a comprehensive resource, the integrated mouse gut metagenome catalog (iMGMC), comprising 4.6 million unique genes and 660 metagenome-assembled genomes (MAGs), many (485 MAGs, 73%) of which are linked to reconstructed full-length 16S rRNA gene sequences. iMGMC enables unprecedented coverage and taxonomic resolution of the mouse gut microbiota; i.e., more than 92% of MAGs lack species-level representatives in public repositories (<95% ANI match). The integration of MAGs and 16S rRNA gene data allows more accurate prediction of functional profiles of communities than predictions based on 16S rRNA amplicons alone. Accompanying iMGMC, we provide a set of MAGs representing 1,296 gut bacteria obtained through complementary assembly strategies. We envision that integrated resources such as iMGMC, together with MAG collections, will enhance the resolution of numerous existing and future sequencing-based studies.}, } @article {pmid32130504, year = {2020}, author = {Gallo-Franco, JJ and Toro-Perea, N}, title = {Variations in the Bacterial Communities in Anastrepha obliqua (Diptera: Tephritidae) According to the Insect Life Stage and Host Plant.}, journal = {Current microbiology}, volume = {77}, number = {7}, pages = {1283-1291}, doi = {10.1007/s00284-020-01939-y}, pmid = {32130504}, issn = {1432-0991}, mesh = {Animals ; Bacteria/classification/genetics ; Fruit/microbiology ; Larva/*microbiology ; Magnoliopsida/*microbiology ; Metagenome/*genetics ; Microbiota/*genetics ; Tephritidae/*microbiology ; }, abstract = {Insects have established close relationships with a wide variety of microorganisms, which play a key role in insect ecology and evolution. Fruit flies in the Tephritidae family have economic importance at the global level, including species such as Anastrepha obliqua, which is an important pest in the neotropical region. Although several studies have been performed on the microbiota associated with fruit flies, there are still large gaps in our knowledge about the bacterial communities on the genus Anastrepha. During this study, we used high-throughput sequencing to characterize the bacterial communities of the polyphagous fly A. obliqua, and we evaluated the effect of the life stage (larvae and adults) and host plant (three plant species) on the structure of these communities. Our results show that the bacterial communities in A. obliqua appears to be structured according to the insect life stage and the host plant. The predominant genera belonging to the phylum Proteobacteria were Wolbachia and Enterobacter in both larvae and adults, and they displayed differences in abundance between them, with Wolbachia sp. being more abundant in larvae and Enterobacter sp. being more abundant in adults. Differences in the structures of the bacterial communities were also observed according to the host plant with higher abundance of Enterobacter and Acetobacter bacteria in mango and plum fruits. Based on our results, it can be hypothesized that the bacterial communities on A. obliqua reorganize according to the needs of these insects during their different life stages and could also play an important role in the establishment of this fly species on different host plants. This study represents the first approach to understanding microorganism-insect interactions in fruit flies in Colombia.}, } @article {pmid32130435, year = {2020}, author = {Tikariha, H and Purohit, HJ}, title = {Unfolding microbial community intelligence in aerobic and anaerobic biodegradation processes using metagenomics.}, journal = {Archives of microbiology}, volume = {202}, number = {6}, pages = {1269-1274}, pmid = {32130435}, issn = {1432-072X}, mesh = {Aerobiosis ; Anaerobiosis ; *Biodegradation, Environmental ; Bioreactors/*microbiology ; *Metagenomics ; Microbiota/*physiology ; Sewage/*microbiology ; Wastewater/*microbiology ; }, abstract = {Environmental factors and available nutrients influence microbial communities, and with that, there exists a dynamic shift in community structure and hierarchy in wastewater treatment systems. Of the various factors, the availability and gradient of oxygen selectively enrich a typical microbial community and also form the community stratification which could be established through metagenomics studies. In recent years, metagenomics with various sets of bioinformatics tools has assisted in exploration and better insight into the organization and relation of the taxonomical and functional composition and associate physiological intelligence of the microbial communities. The microbial communities, under defined conditions acquire a typical hierarchy with flexible but active network of the metabolic route, which ensures the survival needs of every member residing in that community and their abundance. This knowledge of community functional organization defines the rule in designing and improving biodegradation processes in case of both aerobic and anaerobic systems.}, } @article {pmid32130257, year = {2020}, author = {Sher, Y and Olm, MR and Raveh-Sadka, T and Brown, CT and Sher, R and Firek, B and Baker, R and Morowitz, MJ and Banfield, JF}, title = {Combined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0229537}, pmid = {32130257}, issn = {1932-6203}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; }, mesh = {Case-Control Studies ; Databases, Genetic ; Digestive System/microbiology ; Digestive System Physiological Phenomena ; Electron Transport Complex IV/genetics ; Enterocolitis, Necrotizing/diagnosis/genetics/microbiology ; Escherichia/genetics/isolation & purification ; Female ; Gastrointestinal Microbiome/*genetics/*physiology ; Genes, Bacterial ; Humans ; Infant, Newborn ; Infant, Premature/*physiology ; Male ; Metagenome ; Microbiota/genetics ; Transcriptome ; }, abstract = {Microbes alter their transcriptomic profiles in response to the environment. The physiological conditions experienced by a microbial community can thus be inferred using meta-transcriptomic sequencing by comparing transcription levels of specifically chosen genes. However, this analysis requires accurate reference genomes to identify the specific genes from which RNA reads originate. In addition, such an analysis should avoid biases in transcript counts related to differences in organism abundance. In this study we describe an approach to address these difficulties. Sample-specific meta-genomic assembled genomes (MAGs) were used as reference genomes to accurately identify the origin of RNA reads, and transcript ratios of genes with opposite transcription responses were compared to eliminate biases related to differences in organismal abundance, an approach hereafter named the "diametric ratio" method. We used this approach to probe the environmental conditions experienced by Escherichia spp. in the gut of 4 premature infants, 2 of whom developed necrotizing enterocolitis (NEC), a severe inflammatory intestinal disease. We analyzed twenty fecal samples taken from four premature infants (4-6 time points from each infant), and found significantly higher diametric ratios of genes associated with low oxygen levels in samples of infants later diagnosed with NEC than in samples without NEC. We also show this method can be used for examining other physiological conditions, such as exposure to nitric oxide and osmotic pressure. These study results should be treated with caution, due to the presence of confounding factors that might also distinguish between NEC and control infants. Nevertheless, together with benchmarking analyses, we show here that the diametric ratio approach can be applied for evaluating the physiological conditions experienced by microbes in situ. Results from similar studies can be further applied for designing diagnostic methods to detect NEC in its early developmental stages.}, } @article {pmid32128982, year = {2020}, author = {Tu, Q}, title = {Random sampling in metagenomic sequencing leads to overestimated spatial scaling of microbial diversity.}, journal = {Environmental microbiology}, volume = {22}, number = {6}, pages = {2140-2149}, doi = {10.1111/1462-2920.14973}, pmid = {32128982}, issn = {1462-2920}, support = {31700427//National Natural Science Foundation of China/International ; 31971446//National Natural Science Foundation of China/International ; LQ17D060002//Zhejiang Provincial Natural Science Foundation of China/International ; kf2016002//Open Project of Key Laboratory of Environmental Biotechnology, CAS/International ; SKYAM002-2016//Open Funding of State Key Laboratory of Applied Microbiology Southern China/International ; 2017C82218//Bureau of Science and Technology of Zhoushan/International ; //Qilu Young Scholarship of Shandong University/International ; }, mesh = {*Biodiversity ; Forests ; Geography ; Metagenome ; Metagenomics ; Microbiota/*genetics ; Random Allocation ; *Soil Microbiology ; }, abstract = {Revealing the spatial scaling patterns of microbial diversity is of special interest in microbial ecology. One critical question is whether the observed spatial turnover rate truly reflect the actual spatial patterns of extremely diverse microbial communities. Using simulated mock communities, this study suggested that the currently observed microbial spatial turnover rates were overestimated by random sampling processes associated with high-throughput metagenomic sequencing. The observed z values were largely contributed by accumulated microbial taxa due to cumulative number of samples. This is a crucial issue because microbial communities already have very low spatial turnover rate due to the small size and potential cosmopolitism nature of microorganisms. Further investigations suggested a linear relationship between the observed and expected z values, which can be applied to remove random sampling noises from the observed z values. Adjustment of z values for data sets from six American forests showed much lower spatial turnover rate than that before adjustment. However, the patterns of z values among these six forests remained unchanged. This study suggested that our current understanding of microbial taxa-area relationships could be inaccurate. Therefore, cautions and efforts should be made for more accurate estimation and interpretation of microbial spatial patterns.}, } @article {pmid32127450, year = {2020}, author = {Lima, LFO and Weissman, M and Reed, M and Papudeshi, B and Alker, AT and Morris, MM and Edwards, RA and de Putron, SJ and Vaidya, NK and Dinsdale, EA}, title = {Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network.}, journal = {mBio}, volume = {11}, number = {2}, pages = {}, pmid = {32127450}, issn = {2150-7511}, support = {T32 GM128596/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anthozoa/*microbiology ; Bermuda ; Metagenomics ; Microbial Interactions ; *Microbiota ; *Models, Theoretical ; Mucus/microbiology ; *Temperature ; }, abstract = {Host-associated microbial communities are shaped by extrinsic and intrinsic factors to the holobiont organism. Environmental factors and microbe-microbe interactions act simultaneously on the microbial community structure, making the microbiome dynamics challenging to predict. The coral microbiome is essential to the health of coral reefs and sensitive to environmental changes. Here, we develop a dynamic model to determine the microbial community structure associated with the surface mucus layer (SML) of corals using temperature as an extrinsic factor and microbial network as an intrinsic factor. The model was validated by comparing the predicted relative abundances of microbial taxa to the relative abundances of microbial taxa from the sample data. The SML microbiome from Pseudodiploria strigosa was collected across reef zones in Bermuda, where inner and outer reefs are exposed to distinct thermal profiles. A shotgun metagenomics approach was used to describe the taxonomic composition and the microbial network of the coral SML microbiome. By simulating the annual temperature fluctuations at each reef zone, the model output is statistically identical to the observed data. The model was further applied to six scenarios that combined different profiles of temperature and microbial network to investigate the influence of each of these two factors on the model accuracy. The SML microbiome was best predicted by model scenarios with the temperature profile that was closest to the local thermal environment, regardless of the microbial network profile. Our model shows that the SML microbiome of P. strigosa in Bermuda is primarily structured by seasonal fluctuations in temperature at a reef scale, while the microbial network is a secondary driver.IMPORTANCE Coral microbiome dysbiosis (i.e., shifts in the microbial community structure or complete loss of microbial symbionts) caused by environmental changes is a key player in the decline of coral health worldwide. Multiple factors in the water column and the surrounding biological community influence the dynamics of the coral microbiome. However, by including only temperature as an external factor, our model proved to be successful in describing the microbial community associated with the surface mucus layer (SML) of the coral P. strigosa The dynamic model developed and validated in this study is a potential tool to predict the coral microbiome under different temperature conditions.}, } @article {pmid32127018, year = {2020}, author = {Qin, N and Liang, P and Wu, C and Wang, G and Xu, Q and Xiong, X and Wang, T and Zolfo, M and Segata, N and Qin, H and Knight, R and Gilbert, JA and Zhu, TF}, title = {Longitudinal survey of microbiome associated with particulate matter in a megacity.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {55}, pmid = {32127018}, issn = {1474-760X}, mesh = {*Air Pollution ; China ; Cities ; Environmental Monitoring/methods ; *Metagenome ; Metagenomics/methods ; *Microbiota ; *Smog ; }, abstract = {BACKGROUND: While the physical and chemical properties of airborne particulate matter (PM) have been extensively studied, their associated microbiome remains largely unexplored. Here, we performed a longitudinal metagenomic survey of 106 samples of airborne PM2.5 and PM10 in Beijing over a period of 6 months in 2012 and 2013, including those from several historically severe smog events.

RESULTS: We observed that the microbiome composition and functional potential were conserved between PM2.5 and PM10, although considerable temporal variations existed. Among the airborne microorganisms, Propionibacterium acnes, Escherichia coli, Acinetobacter lwoffii, Lactobacillus amylovorus, and Lactobacillus reuteri dominated, along with several viral species. We further identified an extensive repertoire of genes involved in antibiotic resistance and detoxification, including transporters, transpeptidases, and thioredoxins. Sample stratification based on Air Quality Index (AQI) demonstrated that many microbial species, including those associated with human, dog, and mouse feces, exhibit AQI-dependent incidence dynamics. The phylogenetic and functional diversity of air microbiome is comparable to those of soil and water environments, as its composition likely derives from a wide variety of sources.

CONCLUSIONS: Airborne particulate matter accommodates rich and dynamic microbial communities, including a range of microbial elements that are associated with potential health consequences.}, } @article {pmid32123319, year = {2020}, author = {Lax, S and Abreu, CI and Gore, J}, title = {Higher temperatures generically favour slower-growing bacterial species in multispecies communities.}, journal = {Nature ecology & evolution}, volume = {4}, number = {4}, pages = {560-567}, pmid = {32123319}, issn = {2397-334X}, support = {R01 GM102311/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteria ; Hot Temperature ; *Microbiota ; Temperature ; }, abstract = {Temperature is one of the fundamental environmental variables that determine the composition and function of microbial communities. However, a predictive understanding of how microbial communities respond to changes in temperature is lacking, partly because it is not obvious which aspects of microbial physiology determine whether a species could benefit from a change in the temperature. Here we incorporate how microbial growth rates change with temperature into a modified Lotka-Volterra competition model and predict that higher temperatures should-in general-favour the slower-growing species in a bacterial community. We experimentally confirm this prediction in pairwise cocultures assembled from a diverse set of species and show that these changes to pairwise outcomes with temperature are also predictive of changing outcomes in three-species communities, suggesting that our theory may be applicable to more-complex assemblages. Our results demonstrate that it is possible to predict how bacterial communities will shift with temperature knowing only the growth rates of the community members. These results provide a testable hypothesis for future studies of more-complex natural communities and we hope that this work will help to bridge the gap between ecological theory and the complex dynamics observed in metagenomic surveys.}, } @article {pmid32123297, year = {2020}, author = {Glasl, B and Robbins, S and Frade, PR and Marangon, E and Laffy, PW and Bourne, DG and Webster, NS}, title = {Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes.}, journal = {The ISME journal}, volume = {14}, number = {6}, pages = {1435-1450}, pmid = {32123297}, issn = {1751-7370}, mesh = {Animals ; Archaea/genetics ; Bacteria/classification/*genetics/isolation & purification ; Biomass ; Coral Reefs ; Metagenome ; *Microbiota ; Porifera/*microbiology ; Seasons ; Seawater/microbiology ; Seaweed/classification/*genetics ; }, abstract = {Microbially mediated processes contribute to coral reef resilience yet, despite extensive characterisation of microbial community variation following environmental perturbation, the effect on microbiome function is poorly understood. We undertook metagenomic sequencing of sponge, macroalgae and seawater microbiomes from a macroalgae-dominated inshore coral reef to define their functional potential and evaluate seasonal shifts in microbially mediated processes. In total, 125 high-quality metagenome-assembled genomes were reconstructed, spanning 15 bacterial and 3 archaeal phyla. Multivariate analysis of the genomes relative abundance revealed changes in the functional potential of reef microbiomes in relation to seasonal environmental fluctuations (e.g. macroalgae biomass, temperature). For example, a shift from Alphaproteobacteria to Bacteroidota-dominated seawater microbiomes occurred during summer, resulting in an increased genomic potential to degrade macroalgal-derived polysaccharides. An 85% reduction of Chloroflexota was observed in the sponge microbiome during summer, with potential consequences for nutrition, waste product removal, and detoxification in the sponge holobiont. A shift in the Firmicutes:Bacteroidota ratio was detected on macroalgae over summer with potential implications for polysaccharide degradation in macroalgal microbiomes. These results highlight that seasonal shifts in the dominant microbial taxa alter the functional repertoire of host-associated and seawater microbiomes, and highlight how environmental perturbation can affect microbially mediated processes in coral reef ecosystems.}, } @article {pmid32123275, year = {2020}, author = {Romero Victorica, M and Soria, MA and Batista-García, RA and Ceja-Navarro, JA and Vikram, S and Ortiz, M and Ontañon, O and Ghio, S and Martínez-Ávila, L and Quintero García, OJ and Etcheverry, C and Campos, E and Cowan, D and Arneodo, J and Talia, PM}, title = {Neotropical termite microbiomes as sources of novel plant cell wall degrading enzymes.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {3864}, pmid = {32123275}, issn = {2045-2322}, mesh = {Animals ; Bacteria/*enzymology/genetics ; Bacterial Proteins/genetics/*metabolism ; Cell Wall ; Cellulose/*chemistry ; Gastrointestinal Microbiome/*physiology ; Glycoside Hydrolases/genetics/*metabolism ; Isoptera/metabolism/*microbiology ; Plant Cells ; Species Specificity ; *Wood ; }, abstract = {In this study, we used shotgun metagenomic sequencing to characterise the microbial metabolic potential for lignocellulose transformation in the gut of two colonies of Argentine higher termite species with different feeding habits, Cortaritermes fulviceps and Nasutitermes aquilinus. Our goal was to assess the microbial community compositions and metabolic capacity, and to identify genes involved in lignocellulose degradation. Individuals from both termite species contained the same five dominant bacterial phyla (Spirochaetes, Firmicutes, Proteobacteria, Fibrobacteres and Bacteroidetes) although with different relative abundances. However, detected functional capacity varied, with C. fulviceps (a grass-wood-feeder) gut microbiome samples containing more genes related to amino acid metabolism, whereas N. aquilinus (a wood-feeder) gut microbiome samples were enriched in genes involved in carbohydrate metabolism and cellulose degradation. The C. fulviceps gut microbiome was enriched specifically in genes coding for debranching- and oligosaccharide-degrading enzymes. These findings suggest an association between the primary food source and the predicted categories of the enzymes present in the gut microbiomes of each species. To further investigate the termite microbiomes as sources of biotechnologically relevant glycosyl hydrolases, a putative GH10 endo-β-1,4-xylanase, Xyl10E, was cloned and expressed in Escherichia coli. Functional analysis of the recombinant metagenome-derived enzyme showed high specificity towards beechwood xylan (288.1 IU/mg), with the optimum activity at 50 °C and a pH-activity range from 5 to 10. These characteristics suggest that Xy110E may be a promising candidate for further development in lignocellulose deconstruction applications.}, } @article {pmid32123204, year = {2020}, author = {Lo Sasso, G and Phillips, BW and Sewer, A and Battey, JND and Kondylis, A and Talikka, M and Titz, B and Guedj, E and Peric, D and Bornand, D and Dulize, R and Merg, C and Corciulo, M and Ouadi, S and Yanuar, R and Tung, CK and Ivanov, NV and Peitsch, MC and Hoeng, J}, title = {The reduction of DSS-induced colitis severity in mice exposed to cigarette smoke is linked to immune modulation and microbial shifts.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {3829}, pmid = {32123204}, issn = {2045-2322}, mesh = {Animals ; Colitis/chemically induced/*immunology/*microbiology ; Dextran Sulfate/*pharmacology ; Male ; Mice ; Mice, Inbred C57BL ; Microbiota/drug effects ; Smoke/*adverse effects ; Tobacco Products/*adverse effects ; }, abstract = {Exposure to cigarette smoke (CS) causes detrimental health effects, increasing the risk of cardiovascular, pulmonary diseases and carcinogenesis in exposed individuals. The impact of CS on Inflammatory Bowel Disease (IBD) has been established by a number of epidemiological and clinical studies. In fact, CS is associated with a higher risk of developing Crohn's disease (CD) while inversely correlates with the development, disease risks, and relapse rate of ulcerative colitis (UC). To investigate the effect of CS exposure on experimental colitis, we performed a comprehensive and integrated comparative analysis of colon transcriptome and microbiome in mice exposed to dextran sodium sulfate (DSS) and CS. Colon transcriptome analysis revealed that CS downregulated specific pathways in a concentration-dependent manner, affecting both the inflammatory state and composition of the gut microbiome. Metagenomics analysis demonstrated that CS can modulate DSS-induced dysbiosis of specific bacterial genera, contributing to resolve the inflammation or accelerate recovery. The risks of smoking far outweigh any possible benefit, thus smoking cessation must always be encouraged because of its significant health benefits. However, the inverse association between active smoking and the development of UC cannot be ignored and the present study lays the foundation for investigating potential molecular mechanisms responsible for the attenuation of colitis by certain compounds of tobacco when decoupled from combustion.}, } @article {pmid32122398, year = {2020}, author = {Cao, J and Hu, Y and Liu, F and Wang, Y and Bi, Y and Lv, N and Li, J and Zhu, B and Gao, GF}, title = {Metagenomic analysis reveals the microbiome and resistome in migratory birds.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {26}, pmid = {32122398}, issn = {2049-2618}, mesh = {Animal Migration ; Animals ; Anti-Bacterial Agents ; Bacteria/*classification ; Birds/*microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genes, MDR ; *Metagenome ; Phylogeny ; }, abstract = {BACKGROUND: Antibiotic-resistant pathogens pose high risks to human and animal health worldwide. In recent years, the role of gut microbiota as a reservoir of antibiotic resistance genes (ARGs) in humans and animals has been increasingly investigated. However, the structure and function of the gut bacterial community, as well as the ARGs they carry in migratory birds remain unknown.

RESULTS: Here, we collected samples from migratory bird species and their associated environments and characterized their gut microbiomes and resistomes using shotgun metagenomic sequencing. We found that migratory birds vary greatly in gut bacterial composition but are similar in their microbiome metabolism and function. Birds from the same environment tend to harbor similar bacterial communities. In total, 1030 different ARGs (202 resistance types) conferring resistance to tetracycline, aminoglycoside, β-lactam, sulphonamide, chloramphenicol, macrolide-lincosamide-streptogramin (MLS), and quinolone are identified. Procrustes analysis indicated that microbial community structure is not correlated with the resistome in migratory birds. Moreover, metagenomic assembly-based host tracking revealed that most of the ARG-carrying contigs originate from Proteobacteria. Co-occurrence patterns revealed by network analysis showed that emrD, emrY, ANT(6)-Ia, and tetO, the hubs of ARG type network, are indicators of other co-occurring ARG types. Compared with the microbiomes and resistomes in the environment, migratory birds harbor a lower phylogenetic diversity but have more antibiotic resistance proteins. Interestingly, we found that the mcr-1 resistance gene is widespread among different birds, accounting for 50% of the total samples. Meanwhile, a large number of novel β-lactamase genes are also reconstructed from bird metagenomic assemblies based on fARGene software.

CONCLUSIONS: Our study provides a comprehensive overview of the diversity and abundance of ARGs in migratory birds and highlights the possible role of migratory birds as ARG disseminators into the environment. Video abstract.}, } @article {pmid32121402, year = {2020}, author = {Birnberg, L and Temmam, S and Aranda, C and Correa-Fiz, F and Talavera, S and Bigot, T and Eloit, M and Busquets, N}, title = {Viromics on Honey-Baited FTA Cards as a New Tool for the Detection of Circulating Viruses in Mosquitoes.}, journal = {Viruses}, volume = {12}, number = {3}, pages = {}, pmid = {32121402}, issn = {1999-4915}, mesh = {Animals ; Culicidae/*virology ; *Environmental Microbiology ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; *Honey ; Metagenomics/*methods ; Mosquito Vectors/virology ; Phylogeny ; Polymerase Chain Reaction ; RNA, Viral ; Sequence Analysis, DNA ; Spain ; *Virome ; Virus Diseases/transmission ; Viruses/classification/genetics ; }, abstract = {Worldwide, emerging and re-emerging infectious diseases (EIDs) are a major burden on public and animal health. Arthropod vectors, with mosquitoes being the main contributors of global disease, transmit more than 70% of the recognized EIDs. To assess new alternatives for arthropod-borne viral diseases surveillance, and for the detection of new viruses, honey-baited Flinders Technology Associates (FTA) cards were used as sugar bait in mosquito traps during entomological surveys at the Llobregat River Delta (Catalonia, Spain). Next generation sequencing (NGS) metagenomics analysis was applied on honey-baited FTA cards, which had been exposed to field-captured mosquitoes to characterize their associated virome. Arthropod- and plant-infecting viruses governed the virome profile on FTA cards. Twelve near-complete viral genomes were successfully obtained, suggesting good quality preservation of viral RNAs. Mosquito pools linked to the FTA cards were screened for the detection of mosquito-associated viruses by specific RT-PCRs to confirm the presence of these viruses. The circulation of viruses related to Alphamesonivirus, Quaranjavirus and unclassified Bunyavirales was detected in mosquitoes, and phylogenetic analyses revealed their similarities to viruses previously reported in other continents. To the best our knowledge, our findings constitute the first distribution record of these viruses in European mosquitoes and the first hint of insect-specific viruses in mosquitoes' saliva in field conditions, demonstrating the feasibility of this approach to monitor the transmissible fraction of the mosquitoes' virome. In conclusion, this pilot viromics study on honey-baited FTA cards was shown to be a valid approach for the detection of viruses circulating in mosquitoes, thereby setting up an alternative tool for arbovirus surveillance and control programs.}, } @article {pmid32121094, year = {2020}, author = {Faizah, AN and Kobayashi, D and Isawa, H and Amoa-Bosompem, M and Murota, K and Higa, Y and Futami, K and Shimada, S and Kim, KS and Itokawa, K and Watanabe, M and Tsuda, Y and Minakawa, N and Miura, K and Hirayama, K and Sawabe, K}, title = {Deciphering the Virome of Culex vishnui Subgroup Mosquitoes, the Major Vectors of Japanese Encephalitis, in Japan.}, journal = {Viruses}, volume = {12}, number = {3}, pages = {}, pmid = {32121094}, issn = {1999-4915}, mesh = {Animals ; Biodiversity ; Culex/classification/*virology ; Encephalitis Viruses, Japanese/*physiology ; Encephalitis, Japanese/epidemiology/*transmission/*virology ; Genome, Viral ; Geography, Medical ; Japan/epidemiology ; Metagenome ; Metagenomics/methods ; Mosquito Vectors/classification/*virology ; Phylogeny ; Public Health Surveillance ; *Virome ; Viruses/classification/genetics ; }, abstract = {Japanese encephalitis (JE) remains a public health concern in several countries, and the Culex mosquito plays a central role in its transmission cycle. Culex mosquitoes harbor a wide range of viruses, including insect-specific viruses (ISVs), and can transmit a variety of arthropod-borne viruses (arboviruses) that cause human and animal diseases. The current trend of studies displays enhanced efforts to characterize the mosquito virome through bulk RNA sequencing due to possible arbovirus-ISV interactions; however, the extent of viral diversity in the mosquito taxon is still poorly understood, particularly in some disease vectors. In this study, arboviral screening and RNA virome analysis of Culex tritaeniorhynchus and C. pseudovishnui, which are part of the Culex vishnui subgroup mosquitoes, were performed. Results from these two mosquito species, known as the major vectors of JE virus (JEV) in Asia, collected in three prefectures in Japan were also compared with the sympatric species C. inatomii. A total of 27 viruses, including JEV, were detected from these Culex mosquitoes. Molecular and phylogenetic analyses of the detected viruses classified 15 of the 27 viruses as novel species, notably belonging to the Flaviviridae, Rhabdoviridae, Totiviridae, and Iflaviridae families. The successful isolation of JEV genotype I confirmed its continuous presence in Japan, suggesting the need for periodic surveillance. Aside from JEV, this study has also reported the diversity of the RNA virome of disease vectors and broadened the knowledge on mosquito virome profiles containing both arbovirus and ISV. Mosquito taxon seemed to contribute largely to the virome structure (e.g., virome composition, diversity, and abundance) as opposed to the geographical location of the mosquito species. This study therefore offers notable insights into the ecology and evolution of each identified virus and viral family. To the authors' knowledge, this is the first study to characterize the viromes of the major JE vectors in Japan.}, } @article {pmid32120990, year = {2020}, author = {Zou, H and Wang, D and Ren, H and Cai, K and Chen, P and Fang, C and Shi, Z and Zhang, P and Wang, J and Yang, H and Zhong, H}, title = {Effect of Caloric Restriction on BMI, Gut Microbiota, and Blood Amino Acid Levels in Non-Obese Adults.}, journal = {Nutrients}, volume = {12}, number = {3}, pages = {}, pmid = {32120990}, issn = {2072-6643}, support = {NO.2018YFC1313800, No. JCYJ20170817145809215 and No. CXB201108250098A//the National Key Research and Development Program of China, the Shenzhen Municipal Government of China/ ; }, mesh = {Adult ; Amino Acids/*blood ; Bacteroides ; *Body Mass Index ; *Caloric Restriction ; Female ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; Male ; Prevotella ; }, abstract = {Adequate calorie restriction (CR) as a healthy lifestyle is recommended not only for people with metabolic disorders but also for healthy adults. Previous studies have mainly focused on the beneficial metabolic effects of CR on obese subjects, while its effects on non-obese subjects are still scarce. Here, we conducted a three-week non-controlled CR intervention in 41 subjects, with approximately 40% fewer calories than the recommended daily energy intake. We measured BMI, and applied targeted metabolic profiling on fasting blood samples and shotgun metagenomic sequencing on fecal samples, before and after intervention. Subjects were stratified into two enterotypes according to their baseline microbial composition, including 28 enterotype Bacteroides (ETB) subjects and 13 enterotype Prevotella (ETP) subjects. CR decreased BMI in most subjects, and ETP subjects exhibited a significantly higher BMI loss ratio than the ETB subjects. Additionally, CR induced limited changes in gut microbial composition but substantial microbial-independent changes in blood AAs, including a significant increase in 3-methylhistidine, a biomarker of the skeletal muscle protein turnover. Finally, baseline abundances of seven microbial species, rather than baseline AA levels, could well predict CR-induced BMI loss. This non-controlled intervention study revealed associations between baseline gut microbiota and CR-induced BMI loss and provided evidence to accelerate the application of microbiome stratification in future personalized nutrition intervention.}, } @article {pmid32114713, year = {2020}, author = {Wang, Y and Xu, J and Kong, L and Li, B and Li, H and Huang, WE and Zheng, C}, title = {Raman-activated sorting of antibiotic-resistant bacteria in human gut microbiota.}, journal = {Environmental microbiology}, volume = {22}, number = {7}, pages = {2613-2624}, pmid = {32114713}, issn = {1462-2920}, support = {EP/M002403/1//Engineering and Physical Sciences Research Council/International ; EP/M02833X/1//Engineering and Physical Sciences Research Council/International ; NE/M002934/1//Natural Environment Research Council UK/International ; 41890852//National Natural Science Foundation of China/International ; 41931292//National Natural Science Foundation of China/International ; }, mesh = {Adult ; Amoxicillin/pharmacology ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/*genetics ; Cephalexin/pharmacology ; Drug Resistance, Bacterial/*genetics ; Gastrointestinal Microbiome/*drug effects/genetics ; Humans ; Metagenome/genetics ; Metagenomics ; Nonlinear Optical Microscopy ; Sequence Analysis, DNA ; Tetracycline/pharmacology ; Thiamphenicol/analogs & derivatives/pharmacology ; Vancomycin/pharmacology ; }, abstract = {The antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) in human gut microbiota have significant impact on human health. While high throughput metagenomic sequencing reveals genotypes of microbial communities, the functionality, phenotype and heterogeneity of human gut microbiota are still elusive. In this study, we applied Raman microscopy and deuterium isotope probing (Raman-DIP) to detect metabolic active ARB (MA-ARB) in situ at the single-cell level in human gut microbiota from two healthy adults. We analysed the relative abundances of MA-ARB under different concentrations of amoxicillin, cephalexin, tetracycline, florfenicol and vancomycin. To establish the link between phenotypes and genotypes of the MA-ARB, Raman-activated cell sorting (RACS) was used to sort MA-ARB from human gut microbiota, and mini-metagenomic DNA of the sorted bacteria was amplified, sequenced and analysed. The sorted MA-ARB and their associated ARGs were identified. Our results suggest a strong relation between ARB in human gut microbiota and personal medical history. This study demonstrates that the toolkit of Raman-DIP, RACS and DNA sequencing can be useful to unravel both phenotypes and genotypes of ARB in human gut microbiota at the single-cell level.}, } @article {pmid32114693, year = {2020}, author = {Karthikeyan, S and Rodriguez-R, LM and Heritier-Robbins, P and Hatt, JK and Huettel, M and Kostka, JE and Konstantinidis, KT}, title = {Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil-associated microbes.}, journal = {Environmental microbiology}, volume = {22}, number = {6}, pages = {2094-2106}, doi = {10.1111/1462-2920.14966}, pmid = {32114693}, issn = {1462-2920}, support = {No 321611-00//Gulf of Mexico Research Initiative/International ; //Georgia Institute of Technology/International ; }, mesh = {*Biodegradation, Environmental ; *Databases, Genetic ; Gulf of Mexico ; Hydrocarbons/metabolism ; Metagenome/genetics ; Metagenomics ; Microbiota/genetics ; Oil and Gas Fields/*microbiology ; Petroleum/metabolism/*microbiology ; Petroleum Pollution/*analysis ; }, abstract = {Microbial communities ultimately control the fate of petroleum hydrocarbons (PHCs) that enter the natural environment, but the interactions of microbes with PHCs and the environment are highly complex and poorly understood. Genome-resolved metagenomics can help unravel these complex interactions. However, the lack of a comprehensive database that integrates existing genomic/metagenomic data from oil environments with physicochemical parameters known to regulate the fate of PHCs currently limits data analysis and interpretations. Here, we curated a comprehensive, searchable database that documents microbial populations in natural oil ecosystems and oil spills, along with available underlying physicochemical data, geocoded via geographic information system to reveal their geographic distribution patterns. Analysis of the ~2000 metagenome-assembled genomes (MAGs) available in the database revealed strong ecological niche specialization within habitats. Over 95% of the recovered MAGs represented novel taxa underscoring the limited representation of cultured organisms from oil-contaminated and oil reservoir ecosystems. The majority of MAGs linked to oil-contaminated ecosystems were detectable in non-oiled samples from the Gulf of Mexico but not in comparable samples from elsewhere, indicating that the Gulf is primed for oil biodegradation. The repository should facilitate future work toward a predictive understanding of the microbial taxa and their activities that control the fate of oil spills.}, } @article {pmid32114362, year = {2020}, author = {Zeng, B and Zhang, S and Xu, H and Kong, F and Yu, X and Wang, P and Yang, M and Li, D and Zhang, M and Ni, Q and Li, Y and Fan, X and Yang, D and Ning, R and Zhao, J and Li, Y}, title = {Gut microbiota of Tibetans and Tibetan pigs varies between high and low altitude environments.}, journal = {Microbiological research}, volume = {235}, number = {}, pages = {126447}, doi = {10.1016/j.micres.2020.126447}, pmid = {32114362}, issn = {1618-0623}, mesh = {Acclimatization ; *Altitude ; Animals ; Asian People ; Bacteria/*classification ; *Energy Metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Macaca mulatta/microbiology ; Metabolic Networks and Pathways ; Metabolome ; Metagenome ; Rabbits/microbiology ; Swine/microbiology ; Tibet ; }, abstract = {This study set out to investigate the relationship between gut microbiota composition and host adaptation to high altitude conditions. Fecal samples from both high and low altitude humans and pigs were studied using multi-omics methods. 16S ribosomal meta-analysis results showed significant differences in bacterial diversity and composition between high and low altitude members of the same species, as well as between different species. Acinetobacter, Pseudomonas, and Sphingobacterium were the three most abundant bacterial genera found in high altitude fecal samples of both humans and pigs. The alpha diversities of microbiota from Chinese people were found to be relatively lower than those of people in other countries. We found significant convergent trends in microbial metagenome compositions between Tibetans and Tibetan pigs living at high altitudes, and significant differences between these and their low-altitude counterparts. Metabolic pathways related to energy metabolism, amino-acid metabolism, and carbohydrate metabolism were consistently enriched at high altitudes, in both Tibetans and Tibetan pigs. Propanoic acid and octadecanoic acid were significantly elevated in high-altitude Tibetan pigs, and genes related to these two metabolites were also up-regulated. Thus, this study revealed that unique gut bacteriomes and their functions may be closely related to environmental host adaptation in high altitude conditions, such as those in the Tibetan plateau.}, } @article {pmid32111636, year = {2020}, author = {Seyed Tabib, NS and Madgwick, M and Sudhakar, P and Verstockt, B and Korcsmaros, T and Vermeire, S}, title = {Big data in IBD: big progress for clinical practice.}, journal = {Gut}, volume = {69}, number = {8}, pages = {1520-1532}, pmid = {32111636}, issn = {1468-3288}, support = {BB/S50743X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004529/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CSP17270/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P016774/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Big Data ; Gastrointestinal Microbiome ; Gene Expression Profiling ; *Genomics ; Humans ; Image Interpretation, Computer-Assisted ; Inflammatory Bowel Diseases/diagnosis/drug therapy/*genetics/*metabolism ; *Machine Learning ; Metagenomics ; Precision Medicine ; Prognosis ; Proteomics ; Risk Assessment ; Translational Research, Biomedical ; }, abstract = {IBD is a complex multifactorial inflammatory disease of the gut driven by extrinsic and intrinsic factors, including host genetics, the immune system, environmental factors and the gut microbiome. Technological advancements such as next-generation sequencing, high-throughput omics data generation and molecular networks have catalysed IBD research. The advent of artificial intelligence, in particular, machine learning, and systems biology has opened the avenue for the efficient integration and interpretation of big datasets for discovering clinically translatable knowledge. In this narrative review, we discuss how big data integration and machine learning have been applied to translational IBD research. Approaches such as machine learning may enable patient stratification, prediction of disease progression and therapy responses for fine-tuning treatment options with positive impacts on cost, health and safety. We also outline the challenges and opportunities presented by machine learning and big data in clinical IBD research.}, } @article {pmid32111593, year = {2020}, author = {Li, X and Islam, MM and Chen, L and Wang, L and Zheng, X}, title = {Metagenomics-Guided Discovery of Potential Bacterial Metallothionein Genes from the Soil Microbiome That Confer Cu and/or Cd Resistance.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {9}, pages = {}, pmid = {32111593}, issn = {1098-5336}, mesh = {Bacteria/drug effects/*genetics ; Cadmium/*adverse effects ; Copper/*adverse effects ; Drug Resistance, Bacterial/*genetics ; Genes, Bacterial ; *Metagenome ; Metagenomics ; Metallothionein/*genetics/metabolism ; Microbiota/drug effects/*genetics ; Soil Microbiology ; Soil Pollutants/adverse effects ; }, abstract = {Metallothionein (MT) genes are valuable genetic materials for developing metal bioremediation tools. Currently, a limited number of prokaryotic MTs have been experimentally identified, which necessitates the expansion of bacterial MT diversity. In this study, we conducted a metagenomics-guided analysis for the discovery of potential bacterial MT genes from the soil microbiome. More specifically, we combined resistance gene enrichment through diversity loss, metagenomic mining with a dedicated MT database, evolutionary trace analysis, DNA chemical synthesis, and functional genomic validation to identify novel MTs. Results showed that Cu stress induced a compositional change in the soil microbiome, with an enrichment of metal-resistant bacteria in soils with higher Cu concentrations. Shotgun metagenomic sequencing was performed to obtain the gene pool of environmental DNA (eDNA), which was subjected to a local BLAST search against an MT database for detecting putative MT genes. Evolutional trace analysis led to the identification of 27 potential MTs with conserved cysteine/histidine motifs different from those of known prokaryotic MTs. Following chemical synthesis of these 27 potential MT genes and heterologous expression in Escherichia coli, six of them were found to improve the hosts' growth substantially and enhanced the hosts' sorption of Cu, Cd, and Zn, among which MT5 led to a 13.7-fold increase in Cd accumulation. Furthermore, four of them restored Cu and/or Cd resistance in two metal-sensitive E. coli strains.IMPORTANCE The metagenomics-guided procedure developed here bypasses the difficulties encountered in classic PCR-based approaches and led to the discovery of novel MT genes, which may be useful in developing bioremediation tools. The procedure used here expands our knowledge on the diversity of bacterial MTs in the environment and may also be applicable to identify other functional genes from eDNA.}, } @article {pmid32111519, year = {2020}, author = {Chen, CC and Wu, WK and Chang, CM and Panyod, S and Lu, TP and Liou, JM and Fang, YJ and Chuang, EY and Wu, MS}, title = {Comparison of DNA stabilizers and storage conditions on preserving fecal microbiota profiles.}, journal = {Journal of the Formosan Medical Association = Taiwan yi zhi}, volume = {119}, number = {12}, pages = {1791-1798}, doi = {10.1016/j.jfma.2020.01.013}, pmid = {32111519}, issn = {0929-6646}, mesh = {DNA ; Feces ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; Temperature ; }, abstract = {BACKGROUND/PURPOSE: Appropriate storage of fecal samples is a critical step for the unbiased analysis of microbial communities in metagenomic studies. Rapid freezing at -80 °C is usually considered to be best practice, but this approach is challenging. DNA stabilizing kits may provide a more convenient method to preserve and store clinical samples. We evaluated the reliability of two collection kits (Stratec stool collection tube with stabilizer, #1038111200 and OMNIgene.GUT OMR-200) on preserving fecal microbiota.

METHODS: Samples were collected from two locations of the fecal specimen, in four healthy volunteers. The samples were sub-aliquoted and stored in a -80 °C freezer, in Stratec and OMNIgene.GUT (incubation at ambient temperature for 0, 3, or 7 days). The fecal microbial composition was assessed by 16S rRNA sequencing.

RESULTS: We found that alpha diversity was not significantly affected by storage conditions. Samples stored in DNA stabilizers were still representative of the original microbial community after 7 days at ambient temperature. Individual differences were found to have a greater contribution to the differences in microbial community composition than storage conditions or sampling location. Samples subjected to stabilizers displayed microbial community shifts compared with immediately frozen samples. A linear discriminant analysis effect size (LEfSe) analysis showed that the relative abundances of Faecalibacterium were significantly higher in samples stored in Stratec kits.

CONCLUSION: Our study reveals that both Stratec and OMNIgene.GUT kits provide good microbiome preservation for up to 7 days in ambient temperature and would represent good options for fecal sample collection in large scale, population-based studies.}, } @article {pmid32109809, year = {2020}, author = {Zhang, L and Zhang, Y and Patterson, J and Arslan, M and Zhang, Y and Gamal El-Din, M}, title = {Biofiltration of oil sands process water in fixed-bed biofilm reactors shapes microbial community structure for enhanced degradation of naphthenic acids.}, journal = {The Science of the total environment}, volume = {718}, number = {}, pages = {137028}, doi = {10.1016/j.scitotenv.2020.137028}, pmid = {32109809}, issn = {1879-1026}, mesh = {Biodegradation, Environmental ; Biofilms ; Carboxylic Acids ; Filtration ; *Microbiota ; Oil and Gas Fields ; Ozone ; Water Pollutants, Chemical ; }, abstract = {Naphthenic acids (NAs) are a complex mixture of carboxylic acids present in oil sands process water (OSPW). Their recalcitrant nature makes them difficult to be removed from the environment using conventional remediation strategies. This study hypothesized that, upon continuous operation, biofiltration of OSPW in fixed-bed biofilm reactors would allow the development of NA-degrading microbial community within the biofilter following successful removal. Both raw and ozonated OSPW were treated in the biofilters and changes in microbial community were tested via 16S/18S amplicon sequencing and metatranscriptomics. Through switch from suspended growth to attached growth, a shift in indigenous microbial community was seen following by an increase in alpha diversity. Concomitantly, improved degradation of NAs was monitored, i.e., 35.8% and 69.4% of NAs were removed from raw and ozonated OSPW, respectively. Metatranscriptomics analysis suggested the presence of genes involved in the degradation of organic acids and petroleum-related compounds. Specifically, functional abundance of aromatic compounds' metabolism improved from 0.05% to 0.76%; whereas abundance of benzoate transport and degradation pathway increased from 0.04% to 0.64%. These changes conclude that continuous operation of OSPW in the bioreactors was in favor of shaping the overall microbiome towards better NA degradation.}, } @article {pmid32108314, year = {2020}, author = {Jo, J and Oh, J and Park, C}, title = {Microbial community analysis using high-throughput sequencing technology: a beginner's guide for microbiologists.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {58}, number = {3}, pages = {176-192}, pmid = {32108314}, issn = {1976-3794}, mesh = {Animals ; *Bacteria/classification/genetics ; Computational Biology/methods ; Datasets as Topic ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Programmed Instructions as Topic ; Seawater/microbiology ; Sequence Analysis, DNA/*methods ; *Software ; Soil Microbiology ; Stichopus/microbiology ; }, abstract = {Microbial communities present in diverse environments from deep seas to human body niches play significant roles in the complex ecosystem and human health. Characterizing their structural and functional diversities is indispensable, and many approaches, such as microscopic observation, DNA fingerprinting, and PCR-based marker gene analysis, have been successfully applied to identify microorganisms. Since the revolutionary improvement of DNA sequencing technologies, direct and high-throughput analysis of genomic DNA from a whole environmental community without prior cultivation has become the mainstream approach, overcoming the constraints of the classical approaches. Here, we first briefly review the history of environmental DNA analysis applications with a focus on profiling the taxonomic composition and functional potentials of microbial communities. To this end, we aim to introduce the shotgun metagenomic sequencing (SMS) approach, which is used for the untargeted ("shotgun") sequencing of all ("meta") microbial genomes ("genomic") present in a sample. SMS data analyses are performed in silico using various software programs; however, in silico analysis is typically regarded as a burden on wet-lab experimental microbiologists. Therefore, in this review, we present microbiologists who are unfamiliar with in silico analyses with a basic and practical SMS data analysis protocol. This protocol covers all the bioinformatics processes of the SMS analysis in terms of data preprocessing, taxonomic profiling, functional annotation, and visualization.}, } @article {pmid32108159, year = {2020}, author = {Soret, P and Vandenborght, LE and Francis, F and Coron, N and Enaud, R and Avalos, M and Schaeverbeke, T and Berger, P and Fayon, M and Thiebaut, R and Delhaes, L and , }, title = {Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {3589}, pmid = {32108159}, issn = {2045-2322}, mesh = {Acute Disease ; Adult ; Aspergillus/*physiology ; Candida/*physiology ; Cystic Fibrosis/*microbiology ; Disease Progression ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Lung/*microbiology ; Male ; Microbiota/*genetics ; Pseudomonas/*physiology ; RNA, Ribosomal, 16S/*genetics ; Respiratory Tract Infections/*microbiology ; Scedosporium/*physiology ; Sequence Analysis, DNA ; Sputum/microbiology ; Young Adult ; }, abstract = {Lung infections play a critical role in cystic fibrosis (CF) pathogenesis. CF respiratory tract is now considered to be a polymicrobial niche and advances in high-throughput sequencing allowed to analyze its microbiota and mycobiota. However, no NGS studies until now have characterized both communities during CF pulmonary exacerbation (CFPE). Thirty-three sputa isolated from patients with and without CFPE were used for metagenomic high-throughput sequencing targeting 16S and ITS2 regions of bacterial and fungal rRNA. We built inter-kingdom network and adapted Phy-Lasso method to highlight correlations in compositional data. The decline in respiratory function was associated with a decrease in bacterial diversity. The inter-kingdom network revealed three main clusters organized around Aspergillus, Candida, and Scedosporium genera. Using Phy-Lasso method, we identified Aspergillus and Malassezia as relevantly associated with CFPE, and Scedosporium plus Pseudomonas with a decline in lung function. We corroborated in vitro the cross-domain interactions between Aspergillus and Streptococcus predicted by the correlation network. For the first time, we included documented mycobiome data into a version of the ecological Climax/Attack model that opens new lines of thoughts about the physiopathology of CF lung disease and future perspectives to improve its therapeutic management.}, } @article {pmid32106534, year = {2020}, author = {D'Aquila, P and Carelli, LL and De Rango, F and Passarino, G and Bellizzi, D}, title = {Gut Microbiota as Important Mediator Between Diet and DNA Methylation and Histone Modifications in the Host.}, journal = {Nutrients}, volume = {12}, number = {3}, pages = {}, pmid = {32106534}, issn = {2072-6643}, mesh = {Animals ; Brain/metabolism ; DNA Methylation/physiology ; Epigenesis, Genetic/*physiology ; Feeding Behavior/*physiology ; Gastrointestinal Microbiome/*physiology ; Histone Code/physiology ; Host Microbial Interactions/*genetics ; Humans ; Intestinal Mucosa/immunology/metabolism ; Metagenome/*physiology ; Models, Animal ; }, abstract = {The human gut microbiota is a complex ecosystem consisting of trillions of microorganisms that inhabit symbiotically on and in the human intestine. They carry out, through the production of a series of metabolites, many important metabolic functions that complement the activity of mammalian enzymes and play an essential role in host digestion. Interindividual variability of microbiota structure, and consequently of the expression of its genes (microbiome), was largely ascribed to the nutritional regime. Diet influences microbiota composition and function with short- and long-term effects. In spite of the vast literature, molecular mechanisms underlying these effects still remain elusive. In this review, we summarized the current evidence on the role exerted by gut microbiota and, more specifically, by its metabolites in the establishment of the host epigenome. The interest in this topic stems from the fact that, by modulating DNA methylation and histone modifications, the gut microbiota does affect the cell activities of the hosting organism.}, } @article {pmid32106294, year = {2020}, author = {Deng, Y and Wen, X and Hu, X and Zou, Y and Zhao, C and Chen, X and Miao, L and Li, X and Deng, X and Bible, PW and Ke, H and Situ, J and Guo, S and Liang, J and Chen, T and Zou, B and Liu, Y and Chen, W and Wu, K and Zhang, M and Jin, ZB and Liang, L and Wei, L}, title = {Geographic Difference Shaped Human Ocular Surface Metagenome of Young Han Chinese From Beijing, Wenzhou, and Guangzhou Cities.}, journal = {Investigative ophthalmology & visual science}, volume = {61}, number = {2}, pages = {47}, pmid = {32106294}, issn = {1552-5783}, mesh = {Age Factors ; China ; Conjunctiva/*microbiology ; DNA, Bacterial/analysis ; DNA, Fungal/analysis ; DNA, Viral/analysis ; Female ; Humans ; Male ; Metagenome ; *Microbiota ; Sex Factors ; }, abstract = {PURPOSE: Microbial ecosystems interact with the human body and affect human health. The microbial community on the ocular surface remains an underexplored territory despite its importance as the first line of defense barrier that protects the eye and ultimately sight. We investigated how age and sex affected human ocular surface microbiome, and in the present study wanted to understand how geographic difference shaped the microbiome in the ocular surface.

METHODS: We collected conjunctival specimens of 172 eyes from 86 healthy volunteers living in three Chinese cities, namely, Guangzhou, Wenzhou, and Beijing. Using the direct metagenomic shotgun sequencing approach, we characterized how geographic difference affected the human ocular microbiome.

RESULTS: We surveyed the taxonomic composition and metabolic function of the microbiota on human ocular surface. We showed that the ocular surface microbiota was composed of bacteria, viruses, and fungi. A geographical difference in both composition and function of the conjunctival microbiome suggests that the environment people lived in shapes their conjunctival microbiome, especially the dominate species.

CONCLUSIONS: Our study provides a reference catalog of the healthy conjunctival metagenome and raises a concern for environmental influences on the ocular surface microbiome.}, } @article {pmid32106051, year = {2020}, author = {Valeriani, F and Gianfranceschi, G and Romano Spica, V}, title = {The microbiota as a candidate biomarker for SPA pools and SPA thermal spring stability after seismic events.}, journal = {Environment international}, volume = {137}, number = {}, pages = {105595}, doi = {10.1016/j.envint.2020.105595}, pmid = {32106051}, issn = {1873-6750}, mesh = {*Bacteria ; Biodiversity ; Biomarkers ; Fresh Water ; *Hot Springs ; *Microbiota ; Water Microbiology ; }, abstract = {Worldwide, the location of thermal springs overlaps seismic areas, and the higher occurrence of earthquakes may impact on water stability and safety. The hydrogeological perturbations pose environmental and public health risks that can be monitored by well-established chemical, physical and biological parameters. Specific health concerns involve the exposure of the population to the medical or wellness uses of SPA thermal waters, e.g. in respiratory or hydropinic treatments as well as during rehabilitative or recreational activities in pools. Since SPA waters are characterized by their own microbiota, we analysed by 16S amplicon sequencing the dynamics of water microbial communities after the August 2017 Ischia island earthquake. For the first time, we report the impact of a seismic event on a thermal spring water, whose microbiota was deeply characterized before and immediately after the natural disaster. The biodiversity stability of the water underwent a dramatic disturbance following the earthquake, as summarized by a Shannon index moving from 1.300 during May 2016-July 2017, up to 1.600 during the first 20-70 h after the event and slightly slowing down to 1.500 after 30 days and to 1.400 after 6 months. Microbiota analysis showed a sudden reduction of the relative abundance of autochthone thermophilic species within the first 20 h and a parallel increase of other thermophilic species as well as of ectopic bacteria from soil, sediments, sea, freshwater and wastewaters. Cultivable mesophilic bacteria were observed only in the first 20 h sample (7 × 10[3]/L), even if the presence of faecal contamination traces was detected by Real Time PCR also up to 70 h after the disaster. OTUs analysis of putative metabolic functions showed several changes between pre and post event, such as in the distribution of Sulphur metabolizing and Carbon fixation species. The restoration of the original pattern followed a slow trend, requiring over six months. The observed results confirm the impact of the earthquake on the microbiota structure of the underground thermal spring water, suggesting further perspectives for monitoring water stability and safety issues by a metagenomic approach.}, } @article {pmid32105997, year = {2020}, author = {Dias, MF and da Rocha Fernandes, G and Cristina de Paiva, M and Christina de Matos Salim, A and Santos, AB and Amaral Nascimento, AM}, title = {Exploring the resistome, virulome and microbiome of drinking water in environmental and clinical settings.}, journal = {Water research}, volume = {174}, number = {}, pages = {115630}, doi = {10.1016/j.watres.2020.115630}, pmid = {32105997}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; *Drinking Water ; Drug Resistance, Microbial ; Genes, Bacterial ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {Aquatic ecosystems harbor a vast pool of antibiotic resistance genes (ARGs), which can suffer mutation, recombination and selection events. Here, we explored the diversity of ARGs, virulence factors and the bacterial community composition in water samples before (surface raw water, RW) and after (disinfected water, DW) drinking water conventional treatment, as well as in tap water (TW) and ultrafiltration membranes (UM, recovered from hemodialysis equipment) through metagenomics. A total of 852 different ARGs were identified, 21.8% of them only in RW, which might reflect the impact of human activities on the river at the sampling point. Although a similar resistance profile has been observed between the samples, significant differences in the frequency of clinically relevant antibiotic classes (penam and peptide) were identified. Resistance determinants to last resort antibiotics, including sequences related to mcr, optrA and poxtA and clinically relevant beta-lactamase genes (i.e. blaKPC, blaGES, blaIMP, blaVIM, blaSPM and blaNDM) were detected. 830 coding sequences (CDSs - related to 217 different ARGs) were embedded in contigs associated with mobile genetic elements, specially plasmids, of which 68% in RW, DW and TW, suggesting the importance of water environments in resistance dissemination. Shifts in bacterial pathogens genera were observed, such as a significant increase in Mycobacterium after treatment and distribution. In UM, the potentially pathogenic genus Halomonas predominated. Its draft genome was closely related to H. stevensii, hosting mainly multidrug efflux pumps. These results broaden our understanding of the global ARGs diversity and stress the importance of tracking the ever-expanding environmental resistome.}, } @article {pmid32103130, year = {2020}, author = {Xu, P and Shi, Y and Liu, P and Yang, Y and Zhou, C and Li, G and Luo, J and Zhang, C and Cao, H and Hu, G and Guo, X}, title = {16S rRNA gene sequencing reveals an altered composition of the gut microbiota in chickens infected with a nephropathogenic infectious bronchitis virus.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {3556}, pmid = {32103130}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Chickens ; Computational Biology/methods ; Coronavirus Infections/*veterinary ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; *Infectious bronchitis virus/physiology ; Intestinal Mucosa/metabolism/microbiology/pathology ; *Metagenome ; *Metagenomics/methods ; Poultry Diseases/*etiology ; *RNA, Ribosomal, 16S ; Viral Load ; }, abstract = {Infectious bronchitis virus (IBV), a member of the Coronaviridae family, causes serious losses to the poultry industry. Intestinal microbiota play an important role in chicken health and contribute to the defence against colonization by invading pathogens. The aim of this study was to investigate the link between the intestinal microbiome and nephropathogenic IBV (NIBV) infection. Initially, chickens were randomly distributed into 2 groups: the normal group (INC) and the infected group (IIBV). The ilea were collected for morphological assessment, and the ileal contents were collected for 16S rRNA gene sequencing analysis. The results of the IIBV group analyses showed a significant decrease in the ratio of villus height to crypt depth (P < 0.05), while the goblet cells increased compared to those in the INC group. Furthermore, the microbial diversity in the ilea decreased and overrepresentation of Enterobacteriaceae and underrepresentation of Chloroplast and Clostridia was found in the NIBV-infected chickens. In conclusion, these results showed that the significant separation of the two groups and the characterization of the gut microbiome profiles of the chickens with NIBV infection may provide valuable information and promising biomarkers for the diagnosis of this disease.}, } @article {pmid32103005, year = {2020}, author = {Ma, B and France, MT and Crabtree, J and Holm, JB and Humphrys, MS and Brotman, RM and Ravel, J}, title = {A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {940}, pmid = {32103005}, issn = {2041-1723}, support = {R01 NR015495/NR/NINR NIH HHS/United States ; R01 AI116799/AI/NIAID NIH HHS/United States ; U19 AI084044/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*classification/*genetics/isolation & purification ; Female ; Gene Expression Profiling ; Gene Library ; Humans ; Metagenome/genetics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Transcriptome/*genetics ; Vagina/*microbiology ; }, abstract = {Analysis of metagenomic and metatranscriptomic data is complicated and typically requires extensive computational resources. Leveraging a curated reference database of genes encoded by members of the target microbiome can make these analyses more tractable. In this study, we assemble a comprehensive human vaginal non-redundant gene catalog (VIRGO) that includes 0.95 million non-redundant genes. The gene catalog is functionally and taxonomically annotated. We also construct a vaginal orthologous groups (VOG) from VIRGO. The gene-centric design of VIRGO and VOG provides an easily accessible tool to comprehensively characterize the structure and function of vaginal metagenome and metatranscriptome datasets. To highlight the utility of VIRGO, we analyze 1,507 additional vaginal metagenomes, and identify a high degree of intraspecies diversity within and across vaginal microbiota. VIRGO offers a convenient reference database and toolkit that will facilitate a more in-depth understanding of the role of vaginal microorganisms in women's health and reproductive outcomes.}, } @article {pmid32101703, year = {2020}, author = {Sinha, SR and Haileselassie, Y and Nguyen, LP and Tropini, C and Wang, M and Becker, LS and Sim, D and Jarr, K and Spear, ET and Singh, G and Namkoong, H and Bittinger, K and Fischbach, MA and Sonnenburg, JL and Habtezion, A}, title = {Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation.}, journal = {Cell host & microbe}, volume = {27}, number = {4}, pages = {659-670.e5}, pmid = {32101703}, issn = {1934-6069}, support = {R01 DK101119/DK/NIDDK NIH HHS/United States ; R01 DK085025/DK/NIDDK NIH HHS/United States ; L30 DK106876/DK/NIDDK NIH HHS/United States ; UL1 TR001085/TR/NCATS NIH HHS/United States ; KL2 TR001083/TR/NCATS NIH HHS/United States ; KL2 TR003143/TR/NCATS NIH HHS/United States ; UL1 TR003142/TR/NCATS NIH HHS/United States ; }, mesh = {Adenomatous Polyposis Coli/microbiology ; Animals ; Bile Acids and Salts/*metabolism/pharmacology ; Colitis/etiology/microbiology ; Colonic Pouches/*microbiology ; Disease Models, Animal ; Dysbiosis/*complications ; Feces/*microbiology ; Humans ; Inflammation/drug therapy/etiology ; Intestines/drug effects/pathology ; Metagenome ; Mice ; Microbiota ; Receptors, G-Protein-Coupled/drug effects/*metabolism ; Ruminococcus/isolation & purification ; Transcriptome ; }, abstract = {Secondary bile acids (SBAs) are derived from primary bile acids (PBAs) in a process reliant on biosynthetic capabilities possessed by few microbes. To evaluate the role of BAs in intestinal inflammation, we performed metabolomic, microbiome, metagenomic, and transcriptomic profiling of stool from ileal pouches (surgically created resevoirs) in colectomy-treated patients with ulcerative colitis (UC) versus controls (familial adenomatous polyposis [FAP]). We show that relative to FAP, UC pouches have reduced levels of lithocholic acid and deoxycholic acid (normally the most abundant gut SBAs), genes required to convert PBAs to SBAs, and Ruminococcaceae (one of few taxa known to include SBA-producing bacteria). In three murine colitis models, SBA supplementation reduces intestinal inflammation. This anti-inflammatory effect is in part dependent on the TGR5 bile acid receptor. These data suggest that dysbiosis induces SBA deficiency in inflammatory-prone UC patients, which promotes a pro-inflammatory state within the intestine that may be treated by SBA restoration.}, } @article {pmid32099013, year = {2020}, author = {Fidler, G and Tolnai, E and Stagel, A and Remenyik, J and Stundl, L and Gal, F and Biro, S and Paholcsek, M}, title = {Tendentious effects of automated and manual metagenomic DNA purification protocols on broiler gut microbiome taxonomic profiling.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {3419}, pmid = {32099013}, issn = {2045-2322}, mesh = {Animals ; Chickens/*microbiology ; *DNA, Bacterial/chemistry/genetics/isolation & purification ; *Gastrointestinal Microbiome ; *Gram-Negative Bacteria/classification/genetics ; *Metagenome ; *Metagenomics ; }, abstract = {Here, we developed protocols to improve sensitivity, rigor and comparability of 16S rRNA gene amplification-based next-generation sequencing (NGS) results. A thorough study was performed by evaluating extraction efficiency with respect to the yield, purity, fragmentation of the purified DNA, and sequencing metrics considering the number of quality reads, amplicon sequence variants (ASVs), community structure and biodiversity. We identified batch-effects that significantly bias broiler gastrointestinal tract (GIT) community compositions and made recommendations to improve sensitivity, consistency, and cross-study comparability. We found that the purity of the extracted nucleic acid had a strong effect on the success rate of downstream library preparations. The preparation of stool bacterial suspensions from feces showed a significant positive influence on community biodiversity by enriching Gram-negative bacteria and cataloguing low abundant taxa with greater success than direct processing of fecal material. Applications relying on the automated Roche MagNa Pure 24 magnetic-bead based method provided results with high consistency therefore it seems to be the optimal choice in large-scale studies for investigating broiler GIT microbiota.}, } @article {pmid32098813, year = {2020}, author = {Waterworth, SC and Flórez, LV and Rees, ER and Hertweck, C and Kaltenpoth, M and Kwan, JC}, title = {Horizontal Gene Transfer to a Defensive Symbiont with a Reduced Genome in a Multipartite Beetle Microbiome.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {32098813}, issn = {2150-7511}, support = {T32 GM008349/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; Biological Products ; Burkholderia/genetics ; Coleoptera/*microbiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome Size ; Genome, Bacterial/*genetics ; Metagenomics ; Microbiota/*genetics ; Multigene Family ; Symbiosis/*genetics/physiology ; }, abstract = {Symbiotic mutualisms of bacteria and animals are ubiquitous in nature, running a continuum from facultative to obligate from the perspectives of both partners. The loss of functions required for living independently but not within a host gives rise to reduced genomes in many symbionts. Although the phenomenon of genome reduction can be explained by existing evolutionary models, the initiation of the process is not well understood. Here, we describe the microbiome associated with the eggs of the beetle Lagria villosa, consisting of multiple bacterial symbionts related to Burkholderia gladioli, including a reduced-genome symbiont thought to be the exclusive producer of the defensive compound lagriamide. We show that the putative lagriamide-producing symbiont is the only member of the microbiome undergoing genome reduction and that it has already lost the majority of its primary metabolism and DNA repair pathways. The key step preceding genome reduction in the symbiont was likely the horizontal acquisition of the putative lagriamide lga biosynthetic gene cluster. Unexpectedly, we uncovered evidence of additional horizontal transfers to the symbiont's genome while genome reduction was occurring and despite a current lack of genes needed for homologous recombination. These gene gains may have given the genome-reduced symbiont a selective advantage in the microbiome, especially given the maintenance of the large lga gene cluster despite ongoing genome reduction.IMPORTANCE Associations between microorganisms and an animal, plant, or fungal host can result in increased dependence over time. This process is due partly to the bacterium not needing to produce nutrients that the host provides, leading to loss of genes that it would need to live independently and to a consequent reduction in genome size. It is often thought that genome reduction is aided by genetic isolation-bacteria that live in monocultures in special host organs, or inside host cells, have less access to other bacterial species from which they can obtain genes. Here, we describe exposure of a genome-reduced beetle symbiont to a community of related bacteria with nonreduced genomes. We show that the symbiont has acquired genes from other bacteria despite going through genome reduction, suggesting that isolation has not yet played a major role in this case of genome reduction, with horizontal gene gains still offering a potential route for adaptation.}, } @article {pmid32097599, year = {2020}, author = {Kang, D and Douglas, AE}, title = {Functional traits of the gut microbiome correlated with host lipid content in a natural population of Drosophila melanogaster.}, journal = {Biology letters}, volume = {16}, number = {2}, pages = {20190803}, pmid = {32097599}, issn = {1744-957X}, support = {R01 GM095372/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Drosophila melanogaster ; *Gastrointestinal Microbiome ; *Gastrointestinal Tract ; Lipids ; Phenotype ; }, abstract = {Most research on the nutritional significance of the gut microbiome is conducted on laboratory animals, and its relevance to wild animals is largely unknown. This study investigated the microbiome correlates of lipid content in individual wild fruit flies, Drosophila melanogaster. Lipid content varied 3.6-fold among the flies and was significantly correlated with the abundance of gut-derived bacterial DNA sequences that were assigned to genes contributing to 16 KEGG pathways. These included genes encoding sugar transporters and enzymes in glycolysis/gluconeogenesis, potentially promoting sugar consumption by the gut microbiome and, thereby, a lean fly phenotype. Furthermore, the lipid content of wild flies was significantly lower than laboratory flies, indicating that, as for some mammalian models, certain laboratory protocols might be obesogenic for Drosophila. This study demonstrates the value of research on natural populations to identify candidate microbial genes that influence ecologically important host traits.}, } @article {pmid32093782, year = {2020}, author = {Rajan, R and Chunduri, AR and Lima, A and Mamillapalli, A}, title = {16S rRNA sequence data of Bombyx mori gut bacteriome after spermidine supplementation.}, journal = {BMC research notes}, volume = {13}, number = {1}, pages = {94}, pmid = {32093782}, issn = {1756-0500}, support = {BT/PR15319/TDS/121/12/2015//Department of Biotechnology, Ministry of Science and Technology/ ; }, mesh = {Actinobacteria/classification/genetics ; Animals ; Bacteria/classification/*genetics ; Bacteroidetes/classification/genetics ; Bombyx/*microbiology ; DNA, Bacterial/analysis/genetics ; Firmicutes/classification/genetics ; Gastrointestinal Microbiome/*drug effects/genetics ; Genetic Variation ; High-Throughput Nucleotide Sequencing/methods ; Larva/microbiology ; Morus/chemistry ; Plant Leaves/chemistry ; Plant Preparations/*pharmacology ; Proteobacteria/classification/genetics ; RNA, Ribosomal, 16S/*genetics ; Spermidine/*pharmacology ; }, abstract = {OBJECTIVES: The silkworm Bombyx mori (B. mori) is an important domesticated lepidopteran model for basic and applied research. They produce silk fibres that have great economic value. The gut microbiome plays an important role in the growth of organisms. Spermidine (Spd) is shown to be important for the growth of all living cells. The effect of spermidine feeding on the gut microbiome of 5th instar B. mori larvae was checked. The B. mori gut samples from control and spermidine fed larvae were subjected to next-generation sequencing analysis to unravel changes in the bacterial community upon spermidine supplementation.

DATA DESCRIPTION: The changes in gut bacteriota after spermidine feeding is not studied before. B. mori larvae were divided into two groups of 50 worms each and were fed with normal mulberry leaves and mulberry leaves fortified with 50 µM spermidine. The gut tissues were isolated aseptically and total genomic DNA was extracted, 16S rRNA region amplified and sequenced using Illumina platform. The spermidine fed gut samples were shown to have abundance and diversity of the phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria.}, } @article {pmid32093762, year = {2020}, author = {Nazeen, S and Yu, YW and Berger, B}, title = {Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {47}, pmid = {32093762}, issn = {1474-760X}, support = {R01 GM108348/GM/NIGMS NIH HHS/United States ; T15 LM007092/LM/NLM NIH HHS/United States ; }, mesh = {Crohn Disease/genetics/microbiology ; Diabetes Mellitus, Type 2/genetics/microbiology ; Gastrointestinal Microbiome/*genetics ; Genome, Human ; Humans ; Metabolic Networks and Pathways ; *Metagenome ; Metagenomics/*methods ; Parkinson Disease/genetics/microbiology ; *Software ; }, abstract = {Microbial populations exhibit functional changes in response to different ambient environments. Although whole metagenome sequencing promises enough raw data to study those changes, existing tools are limited in their ability to directly compare microbial metabolic function across samples and studies. We introduce Carnelian, an end-to-end pipeline for metabolic functional profiling uniquely suited to finding functional trends across diverse datasets. Carnelian is able to find shared metabolic pathways, concordant functional dysbioses, and distinguish Enzyme Commission (EC) terms missed by existing methodologies. We demonstrate Carnelian's effectiveness on type 2 diabetes, Crohn's disease, Parkinson's disease, and industrialized and non-industrialized gut microbiome cohorts.}, } @article {pmid32093685, year = {2020}, author = {Fernández, J and de la Fuente, VG and García, MTF and Sánchez, JG and Redondo, BI and Villar, CJ and Lombó, F}, title = {A diet based on cured acorn-fed ham with oleic acid content promotes anti-inflammatory gut microbiota and prevents ulcerative colitis in an animal model.}, journal = {Lipids in health and disease}, volume = {19}, number = {1}, pages = {28}, pmid = {32093685}, issn = {1476-511X}, support = {IDI/2018/000120//Gobierno del Principado de Asturias/ ; FUO-222-16//Cárnicas Joselito/ ; }, mesh = {*Animal Feed ; Animals ; Anti-Inflammatory Agents/chemistry/*therapeutic use ; Colitis, Ulcerative/*drug therapy/microbiology ; Colon/microbiology ; Cytokines/blood ; Disease Models, Animal ; Gas Chromatography-Mass Spectrometry ; Gastrointestinal Microbiome/*drug effects ; Intestinal Mucosa/microbiology ; Male ; Oleic Acid/chemistry/*therapeutic use ; Phylogeny ; RNA, Ribosomal, 16S/metabolism ; Rats ; Rats, Inbred F344 ; }, abstract = {BACKGROUND: Diets based on meat products are not recommended in the case of ulcerative colitis (UC). The objective here is to test if some traditional cured meat products, as acorn-fed ham (high levels of oleic acid), may be useful for controlling inflammatory diseases as UC in animal models, which could represent a new dietary complementary intervention in the prevention of this inflammatory disease in humans.

METHODS: Two rat cohorts have been used: conventional vegetable rat feed and acorn-fed ham. UC was induced with DSS in drinking water ad libitum for 1 week. Short-chain fatty acids (SCFAs) and 16S rRNA metagenomics from bacterial populations were analyzed in cecum samples. Colon samples were analyzed for histological parameters.

RESULTS: Acorn-fed ham diet induced changes in gut microbiota composition, with pronounced enrichments in anti-inflammatory bacterial genera (Alistipes, Blautia, Dorea, Parabacteroides). The animals with this diet showed a strong reduction in most parameters associated to ulcerative colitis: disease activity index, macroscopic score of colitis, epitelium alteration in colon mucosa, inflammatory cell density in colon, myeloperoxidase titers in colon, proinflammatory cytokines (IL-17, IFN-γ). Also, acorn-fed ham diet animals showed increased total antioxidant activity an oleic acid levels in plasma, as well as higher short-chain fatty acid concentrations in cecum (isobutyric, isovaleric and valeric).

CONCLUSIONS: In the acorn-fed ham cohort, as a result of the dietary intake of oleic acid and low intake of omega-6 fatty acids, a strong preventive effect against UC symptoms was observed.}, } @article {pmid32092934, year = {2020}, author = {Mohanty, I and Podell, S and Biggs, JS and Garg, N and Allen, EE and Agarwal, V}, title = {Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors.}, journal = {Marine drugs}, volume = {18}, number = {2}, pages = {}, pmid = {32092934}, issn = {1660-3397}, support = {R01 ES030316/ES/NIEHS NIH HHS/United States ; R01-ES030316/NH/NIH HHS/United States ; R00-ES026620/NH/NIH HHS/United States ; OCE-1837116//National Science Foundation/ ; }, mesh = {Animals ; *Ecosystem ; *Metabolomics ; *Microbiota ; Phylogeny ; Porifera/genetics/*metabolism/*microbiology ; }, abstract = {Marine sponge holobionts, defined as filter-feeding sponge hosts together with their associated microbiomes, are prolific sources of natural products. The inventory of natural products that have been isolated from marine sponges is extensive. Here, using untargeted mass spectrometry, we demonstrate that sponges harbor a far greater diversity of low-abundance natural products that have evaded discovery. While these low-abundance natural products may not be feasible to isolate, insights into their chemical structures can be gleaned by careful curation of mass fragmentation spectra. Sponges are also some of the most complex, multi-organismal holobiont communities in the oceans. We overlay sponge metabolomes with their microbiome structures and detailed metagenomic characterization to discover candidate gene clusters that encode production of sponge-derived natural products. The multi-omic profiling strategy for sponges that we describe here enables quantitative comparison of sponge metabolomes and microbiomes to address, among other questions, the ecological relevance of sponge natural products and for the phylochemical assignment of previously undescribed sponge identities.}, } @article {pmid32090489, year = {2020}, author = {Villar, E and Cabrol, L and Heimbürger-Boavida, LE}, title = {Widespread microbial mercury methylation genes in the global ocean.}, journal = {Environmental microbiology reports}, volume = {12}, number = {3}, pages = {277-287}, doi = {10.1111/1758-2229.12829}, pmid = {32090489}, issn = {1758-2229}, support = {ANR-15-CE02-0011//Agence Nationale de la Recherche/International ; }, mesh = {*Bacteria/classification/genetics/isolation & purification/metabolism ; Chloroflexi/classification/genetics/isolation & purification/metabolism ; Deltaproteobacteria/classification/genetics/isolation & purification/metabolism ; Firmicutes/classification/genetics/isolation & purification/metabolism ; Genes, Bacterial ; Mercury/metabolism ; Metagenomics ; Methylation ; Methylmercury Compounds/*metabolism ; Microbiota ; Oceans and Seas ; Phylogeny ; *Seawater/chemistry/microbiology ; Transcriptome ; }, abstract = {Methylmercury is a neurotoxin that bioaccumulates from seawater to high concentrations in marine fish, putting human and ecosystem health at risk. High methylmercury levels have been found in the oxic subsurface waters of all oceans, but only anaerobic microorganisms have been shown to efficiently produce methylmercury in anoxic environments. The microaerophilic nitrite-oxidizing bacteria Nitrospina have previously been suggested as possible mercury methylating bacteria in Antarctic sea ice. However, the microorganisms responsible for processing inorganic mercury into methylmercury in oxic seawater remain unknown. Here, we show metagenomic and metatranscriptomic evidence that the genetic potential for microbial methylmercury production is widespread in oxic seawater. We find high abundance and expression of the key mercury methylating genes hgcAB across all ocean basins, corresponding to the taxonomic relatives of known mercury methylating bacteria from Deltaproteobacteria, Firmicutes and Chloroflexi. Our results identify Nitrospina as the predominant and widespread microorganism carrying and actively expressing hgcAB. The highest hgcAB abundance and expression occurs in the oxic subsurface waters of the global ocean where the highest MeHg concentrations are typically observed.}, } @article {pmid32089582, year = {2020}, author = {Maoloni, A and Milanović, V and Cardinali, F and Mangia, NP and Murgia, MA and Garofalo, C and Clementi, F and Osimani, A and Aquilanti, L}, title = {Bacterial and Fungal Communities of Gioddu as Revealed by PCR-DGGE Analysis.}, journal = {Indian journal of microbiology}, volume = {60}, number = {1}, pages = {119-123}, pmid = {32089582}, issn = {0046-8991}, abstract = {Gioddu is the sole variety of fermented milk originating in Italy. Despite the long history of consumption, Gioddu still represents an undisclosed source of microbial diversity. The present study was aimed to get an insight into the bacterial and fungal diversity of Gioddu samples collected from two artisan producers located in Sardinia. To this end 3 batches of Gioddu were collected from each producer and subjected to Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) analyses. Gioddu was produced with sheep milk in accordance with the local tradition. Regarding the bacterial population, a low biodiversity emerged. In more detail, the sole species Lactobacillus delbrueckii subsp. bulgaricus was detected in all the samples, irrespective of the producer or the batch. A more ample microbial diversity was highlighted for the fungal population that included closest relatives to Pichia cactophila, Kluyveromyces marxianus and Galactomyces candidum. Based on the results, the detected bacterial and fungal species generally clustered in accordance with the producer, irrespective of the batch considered. It is noteworthy that, Gioddu revealed several microbiological similarities with kefir beverage, thus suggesting, by analogy, potential health benefits related to its consumption. More research is needed to better clarify the microbiota composition of Gioddu by using more powerful metagenomic techniques.}, } @article {pmid32088998, year = {2020}, author = {Kim, S and Rigatto, K and Gazzana, MB and Knorst, MM and Richards, EM and Pepine, CJ and Raizada, MK}, title = {Altered Gut Microbiome Profile in Patients With Pulmonary Arterial Hypertension.}, journal = {Hypertension (Dallas, Tex. : 1979)}, volume = {75}, number = {4}, pages = {1063-1071}, pmid = {32088998}, issn = {1524-4563}, support = {R01 HL091005/HL/NHLBI NIH HHS/United States ; R01 HL102033/HL/NHLBI NIH HHS/United States ; R01 HL146158/HL/NHLBI NIH HHS/United States ; UL1 TR000064/TR/NCATS NIH HHS/United States ; U01 HL087366/HL/NHLBI NIH HHS/United States ; U01 HL064924/HL/NHLBI NIH HHS/United States ; R01 HL132448/HL/NHLBI NIH HHS/United States ; UM1 HL087366/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Metagenomics ; Middle Aged ; Pulmonary Arterial Hypertension/*microbiology ; }, abstract = {Pulmonary arterial hypertension (PAH) is considered a disease of the pulmonary vasculature. Limited progress has been made in preventing or arresting progression of PAH despite extensive efforts. Our previous studies indicated that PAH could be considered a systemic disease since its pathology involves interplay of multiple organs. This, coupled with increasing implication of the gut and its microbiome in chronic diseases, led us to hypothesize that patients with PAH exhibit a distinct gut microbiome that contributes to, and predicts, the disease. Fecal microbiome of 18 type 1 PAH patients (mean pulmonary arterial pressure, 57.4, SD 16.7 mm Hg) and 13 reference subjects were compared by shotgun metagenomics to evaluate this hypothesis. Significant taxonomic and functional changes in microbial communities in the PAH cohort were observed. Pathways for the synthesis of arginine, proline, and ornithine were increased in PAH cohort compared with reference cohort. Additionally, groups of bacterial communities associated with trimethylamine/ trimethylamine N-oxide and purine metabolism were increased in PAH cohort. In contrast, butyrate-and propionate-producing bacteria such as Coprococcus, Butyrivibrio, Lachnospiraceae, Eubacterium, Akkermansia, and Bacteroides were increased in reference cohort. A random forest model predicted PAH from the composition of the gut microbiome with 83% accuracy. Finally, virome analysis showed enrichment of Enterococcal and relative depletion of Lactococcal phages in the PAH cohort. In conclusion, patients with PAH exhibit a unique microbiome profile that has the high predictive potential for PAH. This highlights previously unknown roles of gut bacteria in this disease and could lead to new therapeutic, diagnostic, or management paradigms for PAH.}, } @article {pmid32088206, year = {2020}, author = {Schneider, AM and Cook, LC and Zhan, X and Banerjee, K and Cong, Z and Imamura-Kawasawa, Y and Gettle, SL and Longenecker, AL and Kirby, JS and Nelson, AM}, title = {Response to Ring et al.: In Silico Predictive Metagenomic Analyses Highlight Key Metabolic Pathways Impacted in the Hidradenitis Suppurativa Skin Microbiome.}, journal = {The Journal of investigative dermatology}, volume = {140}, number = {7}, pages = {1476-1479}, doi = {10.1016/j.jid.2020.02.003}, pmid = {32088206}, issn = {1523-1747}, mesh = {Computer Simulation ; *Hidradenitis Suppurativa/genetics ; Humans ; Metabolic Networks and Pathways/genetics ; *Microbiota/genetics ; Skin ; }, } @article {pmid32086815, year = {2020}, author = {Rashidi, A and Herman, A and Gomes, ALC and Peled, JU and Jenq, RR and Brereton, DG and Staley, C and Blazar, BR and Weisdorf, DJ}, title = {An alpha-defensin gene single nucleotide polymorphism modulates the gut microbiota and may alter the risk of acute graft-versus-host disease.}, journal = {British journal of haematology}, volume = {189}, number = {5}, pages = {926-930}, pmid = {32086815}, issn = {1365-2141}, support = {UL1 TR002494/TR/NCATS NIH HHS/United States ; R01 HL118979/HL/NHLBI NIH HHS/United States ; R37 AI034495/AI/NIAID NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; KL2 TR002492/TR/NCATS NIH HHS/United States ; K08 HL143189/HL/NHLBI NIH HHS/United States ; }, mesh = {Acute Disease ; Adolescent ; Adult ; Allografts ; Bacteroidetes/*isolation & purification/physiology ; Bone Marrow Transplantation/adverse effects ; Cord Blood Stem Cell Transplantation/adverse effects ; Dysbiosis/*genetics ; Female ; *Gastrointestinal Microbiome ; Graft vs Host Disease/*genetics/microbiology/prevention & control ; Humans ; Male ; Metagenome ; Paneth Cells/*metabolism ; Peripheral Blood Stem Cell Transplantation/adverse effects ; *Polymorphism, Single Nucleotide ; Risk ; Symbiosis ; Young Adult ; alpha-Defensins/*genetics ; }, abstract = {We previously reported a protective association between single nucleotide polymorphisms (SNPs; rs4415345G and rs4610776A alleles) of Paneth cell α-defensin-5 against acute graft-versus-host disease (aGVHD). Because dysbiosis has been associated with aGVHD, we hypothesized that these SNPs may have a gut microbiota signature. In Lasso regression analysis of 248 healthy individuals, rs4415345G was associated with a higher abundance of Odoribacter splanchnicus, an anaerobic butyrogenic commensal. In multivariable analysis of data from 613 allogeneic haematopoietic cell transplant recipients, peri-engraftment presence of O. splanchnicus was associated with ~50% lower risk for grade II-IV aGVHD (hazard ratio 0·53, 95% confidence interval 0·28-1·00, P = 0·05). O. splanchnicus may protect rs4415345G individuals against aGVHD.}, } @article {pmid32084485, year = {2020}, author = {Lei, S and Li, X and Liu, L and Zheng, M and Chang, Q and Zhang, Y and Zeng, H}, title = {Effect of lotus seed resistant starch on tolerance of mice fecal microbiota to bile salt.}, journal = {International journal of biological macromolecules}, volume = {151}, number = {}, pages = {384-393}, doi = {10.1016/j.ijbiomac.2020.02.197}, pmid = {32084485}, issn = {1879-0003}, mesh = {Animals ; Bile Acids and Salts/*chemistry ; Biodiversity ; Cluster Analysis ; Feces/*microbiology ; *Gastrointestinal Microbiome/drug effects ; Lotus/*chemistry ; Metagenomics/methods ; Mice ; Seeds/*chemistry ; Starch/*chemistry ; }, abstract = {We investigated the effect of lotus seed resistant starch (LRS) on mice fecal microbiota tolerance to bile salt by culturing organisms compared to inulin (INU) glucose (GLU) and waxy corn starch (WAX). Operational taxonomic units (OTUs) and diversity indices in LRS and INU groups were increased in the presence of 0.03% to 0.3% bile salt, while they were decreased in GLU, and OTUs were decreased in WAX. Specifically, LRS promoted proliferation of Lactobacillus, which potentially used bile acid, and inhibited growth of the potentially harmful bacteria Enterococcus and Staphylococcus. Moreover, Lactobacillus was negatively correlated with Salinicoccus and Granulicatella in GLU, LRS and INU groups at 1.5% bile salt. With LRS, amino acid metabolic pathways were increased while pathogens causing certain diseases were decreased. LRS increased the tolerance of mice fecal microbiota to bile salt by promoting the proliferation of bacteria utilizing bile acid and inhibiting the growth of harmful bacteria.}, } @article {pmid32083024, year = {2019}, author = {Chen, J and Wang, Q and Wang, A and Lin, Z}, title = {Structural and Functional Characterization of the Gut Microbiota in Elderly Women With Migraine.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {470}, pmid = {32083024}, issn = {2235-2988}, support = {/WT_/Wellcome Trust/United Kingdom ; 105022/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; /DH_/Department of Health/United Kingdom ; }, mesh = {Adenosine/analogs & derivatives/metabolism ; Aged ; Bacteria/classification/*metabolism ; Bifidobacterium adolescentis/metabolism ; Faecalibacterium prausnitzii/metabolism ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenome ; Methanobrevibacter/metabolism ; Migraine Disorders/*therapy ; Prognosis ; Quinolinic Acid/metabolism ; Spermidine/analogs & derivatives/metabolism ; }, abstract = {Migraine is a very common, multifactorial, and recurrent central nervous system disorder that causes throbbing headache, photophobia, phonophobia, nausea, and disability. Migraine occurs more often in females, and its complex physiopathology is not yet fully understood. An increasing number of gastrointestinal disorders have been linked to the occurrence of migraine suggesting that gut microbiota might play a pivotal role in migraine through the gut-brain axis. In the present work, we performed a metagenome-wide association study (MWAS) to determine the relationship between gut microbiota and migraine by analyzing 108 shotgun-sequenced fecal samples obtained from elderly women who suffer from migraine and matched healthy controls. Notably, the alpha diversity was significantly decreased in the migraine group at species, genus, and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologous levels. Firmicutes, especially the "unfriendly" Clostridium spp., were significantly enriched in the migraine group. Conversely, the healthy controls held more beneficial microorganisms, such as Faecalibacterium prausnitzii, Bifidobacterium adolescentis, and Methanobrevibacter smithii. For functional modules, the migraine group was enriched in gut-brain modules (GBMs) including kynurenine degradation and γ-aminobutyric acid (GABA) synthesis. However, the healthy controls held higher gut metabolic modules (GMMs) including glycolysis, homoacetogenesis, and GBMs including quinolinic acid degradation and S-adenosyl methionine (SAM) synthesis. The differences in gut microbiota composition and function between the migraine and healthy groups provided new information as well as novel therapeutic targets and strategies for migraine treatment, which could help to improve the early diagnosis of the disease, as well as the long-term prognosis and the life quality of patients suffering from migraine.}, } @article {pmid32081987, year = {2020}, author = {Afshari, R and Pillidge, CJ and Read, E and Rochfort, S and Dias, DA and Osborn, AM and Gill, H}, title = {New insights into cheddar cheese microbiota-metabolome relationships revealed by integrative analysis of multi-omics data.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {3164}, pmid = {32081987}, issn = {2045-2322}, mesh = {Biodiversity ; Cheese/*microbiology ; DNA, Bacterial/metabolism ; *Food Analysis ; *Food Microbiology ; Lactobacillus ; Lactococcus ; *Metabolome ; Metabolomics ; Metagenomics ; *Microbiota ; Principal Component Analysis ; RNA, Ribosomal, 16S/metabolism ; Streptococcus ; }, abstract = {Cheese microbiota and metabolites and their inter-relationships that underpin specific cheese quality attributes remain poorly understood. Here we report that multi-omics and integrative data analysis (multiple co-inertia analysis, MCIA) can be used to gain deeper insights into these relationships and identify microbiota and metabolite fingerprints that could be used to monitor product quality and authenticity. Our study into different brands of artisanal and industrial cheddar cheeses showed that Streptococcus, Lactococcus and Lactobacillus were the dominant taxa with overall microbial community structures differing not only between industrial and artisanal cheeses but also among different cheese brands. Metabolome analysis also revealed qualitative and semi-quantitative differences in metabolites between different cheeses. This also included the presence of two compounds (3-hydroxy propanoic acid and O-methoxycatechol-O-sulphate) in artisanal cheese that have not been previously reported in any type of cheese. Integrative analysis of multi-omics datasets revealed that highly similar cheeses, identical in age and appearance, could be distinctively clustered according to cheese type and brand. Furthermore, the analysis detected strong relationships, some previously unknown, which existed between the cheese microbiota and metabolome, and uncovered specific taxa and metabolites that contributed to these relationships. These results highlight the potential of this approach for identifying product specific microbe/metabolite signatures that could be used to monitor and control cheese quality and product authenticity.}, } @article {pmid32079472, year = {2020}, author = {Zhang, J and Zhao, J and Jin, H and Lv, R and Shi, H and De, G and Yang, B and Sun, Z and Zhang, H}, title = {Probiotics maintain the intestinal microbiome homeostasis of the sailors during a long sea voyage.}, journal = {Gut microbes}, volume = {11}, number = {4}, pages = {930-943}, pmid = {32079472}, issn = {1949-0984}, mesh = {Bacteria/classification/genetics/*growth & development/isolation & purification ; Bifidobacterium/classification/genetics/growth & development/isolation & purification ; Feces/microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Homeostasis ; Humans ; Klebsiella pneumoniae/classification/genetics/growth & development/isolation & purification ; Longitudinal Studies ; Metagenome ; Metagenomics ; *Military Personnel ; Naval Medicine ; Probiotics/*administration & dosage ; Ships ; Streptococcus gordonii/classification/genetics/growth & development/isolation & purification ; }, abstract = {The challenging conditions encountered during long sea voyages increase the risk of health-threatening physiological and psychological stress for sailors compared with land-based workers. However, how the intestinal microbiota responds to a long sea voyage and whether there is a feasible approach for protecting gut health during sea voyage are still unexplored. Here, we designed a 30-d longitudinal study including a placebo group (n = 42) and a probiotic group (n = 40) and used shotgun metagenomic sequencing to explore the impacts of sea voyage on the intestinal microbiome of sailors. By comparing the intestinal microbiome of subjects in the placebo group at baseline (d 0) and at the end of the sea voyage (d 30), we observed an alteration in the intestinal microbiome during the long sea voyage based on the microbial structure; the results revealed an increase in the species Streptococcus gordonii and Klebsiella pneumoniae as well as a decrease in some functional features. However, the change in the microbial structure of sailors in the probiotic group between d 0 and d 30 was limited, which indicated a maintenance effect of probiotics on intestinal microbiome homeostasis. At the metagenomic strain level, a generally positive correlation was observed between probiotics and the strains belonging to Bifidobacterium longum and Bifidobacterium animalis, whereas a common negative correlation was observed between probiotics and Clostridium leptum; this result revealed the potential mechanism of maintaining intestinal microbiome homeostasis by probiotics. The present study provided a feasible approach for protecting gut health during a long sea voyage.}, } @article {pmid32075887, year = {2020}, author = {Meslier, V and Laiola, M and Roager, HM and De Filippis, F and Roume, H and Quinquis, B and Giacco, R and Mennella, I and Ferracane, R and Pons, N and Pasolli, E and Rivellese, A and Dragsted, LO and Vitaglione, P and Ehrlich, SD and Ercolini, D}, title = {Mediterranean diet intervention in overweight and obese subjects lowers plasma cholesterol and causes changes in the gut microbiome and metabolome independently of energy intake.}, journal = {Gut}, volume = {69}, number = {7}, pages = {1258-1268}, pmid = {32075887}, issn = {1468-3288}, mesh = {Adult ; Cholesterol/*blood ; *Diet, Mediterranean ; Energy Intake ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; *Metabolome ; Obesity/blood/*diet therapy/microbiology ; Overweight/blood/*diet therapy/microbiology ; }, abstract = {OBJECTIVES: This study aimed to explore the effects of an isocaloric Mediterranean diet (MD) intervention on metabolic health, gut microbiome and systemic metabolome in subjects with lifestyle risk factors for metabolic disease.

DESIGN: Eighty-two healthy overweight and obese subjects with a habitually low intake of fruit and vegetables and a sedentary lifestyle participated in a parallel 8-week randomised controlled trial. Forty-three participants consumed an MD tailored to their habitual energy intakes (MedD), and 39 maintained their regular diets (ConD). Dietary adherence, metabolic parameters, gut microbiome and systemic metabolome were monitored over the study period.

RESULTS: Increased MD adherence in the MedD group successfully reprogrammed subjects' intake of fibre and animal proteins. Compliance was confirmed by lowered levels of carnitine in plasma and urine. Significant reductions in plasma cholesterol (primary outcome) and faecal bile acids occurred in the MedD compared with the ConD group. Shotgun metagenomics showed gut microbiome changes that reflected individual MD adherence and increase in gene richness in participants who reduced systemic inflammation over the intervention. The MD intervention led to increased levels of the fibre-degrading Faecalibacterium prausnitzii and of genes for microbial carbohydrate degradation linked to butyrate metabolism. The dietary changes in the MedD group led to increased urinary urolithins, faecal bile acid degradation and insulin sensitivity that co-varied with specific microbial taxa.

CONCLUSION: Switching subjects to an MD while maintaining their energy intake reduced their blood cholesterol and caused multiple changes in their microbiome and metabolome that are relevant in future strategies for the improvement of metabolic health.}, } @article {pmid32073995, year = {2020}, author = {Laudadio, I and Cesi, V and Carissimi, C}, title = {Metagenomics in Italy and Europe: Three Actionable Challenges/Prospects in 2020.}, journal = {Omics : a journal of integrative biology}, volume = {24}, number = {3}, pages = {122-123}, doi = {10.1089/omi.2020.0006}, pmid = {32073995}, issn = {1557-8100}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Bacteriocins/*therapeutic use ; Drug Resistance, Multiple, Bacterial/*drug effects/genetics ; Europe ; Humans ; Metagenomics/*trends ; Microbiota/genetics ; Probiotics/administration & dosage ; }, } @article {pmid32071370, year = {2020}, author = {Kim, DJ and Yang, J and Seo, H and Lee, WH and Ho Lee, D and Kym, S and Park, YS and Kim, JG and Jang, IJ and Kim, YK and Cho, JY}, title = {Colorectal cancer diagnostic model utilizing metagenomic and metabolomic data of stool microbial extracellular vesicles.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {2860}, pmid = {32071370}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics ; Colorectal Neoplasms/*diagnosis/genetics/microbiology/pathology ; Dysbiosis/genetics/microbiology/pathology ; Extracellular Vesicles/*genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/genetics ; Gene Expression Regulation, Neoplastic/genetics ; Humans ; *Metabolomics ; Metagenome/genetics ; Metagenomics ; }, abstract = {Colorectal cancer (CRC) is the most common type cancers in the world. CRC occurs sporadically in the majority of cases, indicating the predominant cause of the disease are environmental factors. Diet-induced changes in gut-microbiome are recently supposed to contribute on epidemics of CRC. This study was aimed to investigate the association of metagenomics and metabolomics in gut extracellular vesicles (EVs) of CRC and healthy subjects. A total of 40 healthy volunteers and 32 patients with CRC were enrolled in this study. Metagenomic profiling by sequencing 16 S rDNA was performed for assessing microbial codiversity. We explored the small molecule metabolites using gas chromatography-time-of-flight mass spectrometry. In total, stool EVs were prepared from 40 healthy volunteers and 32 patients with CRC. Metagenomic profiling demonstrated that bacterial phyla, particularly of Firmicutes and Proteobacteria, were significantly altered in patients with colorectal cancer. Through metabolomics profiling, we determined seven amino acids, four carboxylic acids, and four fatty acids; including short-chain to long chain fatty acids that altered in the disease group. Binary logistic regression was further tested to evaluate the diagnostic performance. In summary, the present findings suggest that gut flora dysbiosis may result in alternation of amino acid metabolism, which may be correlated with the pathogenesis of CRC.}, } @article {pmid32071270, year = {2020}, author = {Zheng, Q and Wang, Y and Lu, J and Lin, W and Chen, F and Jiao, N}, title = {Metagenomic and Metaproteomic Insights into Photoautotrophic and Heterotrophic Interactions in a Synechococcus Culture.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {32071270}, issn = {2150-7511}, mesh = {Bacteria/classification/genetics/metabolism ; Bacterial Physiological Phenomena ; Bacterial Secretion Systems ; Biochemical Phenomena/*physiology ; Ecosystem ; Glycogen/metabolism ; Heterotrophic Processes/*physiology ; *Metagenome ; Microbiota/genetics/physiology ; Nutrients ; Oceans and Seas ; Oxidative Stress ; Photosynthesis ; *Proteomics ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Synechococcus/*genetics/*metabolism ; }, abstract = {Microbial photoautotroph-heterotroph interactions underlie marine food webs and shape ecosystem diversity and structure in upper ocean environments. Here, bacterial community composition, lifestyle preference, and genomic- and proteomic-level metabolic characteristics were investigated for an open ocean Synechococcus ecotype and its associated heterotrophs over 91 days of cocultivation. The associated heterotrophic bacterial assembly mostly constituted five classes, including Flavobacteria, Bacteroidetes, Phycisphaerae, Gammaproteobacteria, and Alphaproteobacteria The seven most abundant taxa/genera comprised >90% of the total heterotrophic bacterial community, and five of these displayed distinct lifestyle preferences (free-living or attached) and responses to Synechococcus growth phases. Six high-quality genomes, including Synechococcus and the five dominant heterotrophic bacteria, were reconstructed. The only primary producer of the coculture system, Synechococcus, displayed metabolic processes primarily involved in inorganic nutrient uptake, photosynthesis, and organic matter biosynthesis and release. Two of the flavobacterial populations, Muricauda and Winogradskyella, and an SM1A02 population, displayed preferences for initial degradation of complex compounds and biopolymers, as evinced by high abundances of TonB-dependent transporters (TBDTs), glycoside hydrolase, and peptidase proteins. Polysaccharide utilization loci present in the flavobacterial genomes influence their lifestyle preferences and close associations with phytoplankton. In contrast, the alphaproteobacterium Oricola sp. population mainly utilized low-molecular-weight dissolved organic carbon (DOC) through ATP-binding cassette (ABC), tripartite ATP-independent periplasmic (TRAP), and tripartite tricarboxylate transporter (TTT) transport systems. The heterotrophic bacterial populations exhibited complementary mechanisms for degrading Synechococcus-derived organic matter and driving nutrient cycling. In addition to nutrient exchange, removal of reactive oxygen species and vitamin trafficking might also contribute to the maintenance of the Synechococcus-heterotroph coculture system and the interactions shaping the system.IMPORTANCE The high complexity of in situ ecosystems renders it difficult to study marine microbial photoautotroph-heterotroph interactions. Two-member coculture systems of picocyanobacteria and single heterotrophic bacterial strains have been thoroughly investigated. However, in situ interactions comprise far more diverse heterotrophic bacterial associations with single photoautotrophic organisms. In the present study, combined metagenomic and metaproteomic data supplied the metabolic potentials and activities of uncultured dominant bacterial populations in the coculture system. The results of this study shed light on the nature of interactions between photoautotrophs and heterotrophs, improving our understanding of the complexity of in situ environments.}, } @article {pmid32065891, year = {2020}, author = {Santos, SS and Schöler, A and Nielsen, TK and Hansen, LH and Schloter, M and Winding, A}, title = {Land use as a driver for protist community structure in soils under agricultural use across Europe.}, journal = {The Science of the total environment}, volume = {717}, number = {}, pages = {137228}, doi = {10.1016/j.scitotenv.2020.137228}, pmid = {32065891}, issn = {1879-1026}, mesh = {Animals ; Biodiversity ; Europe ; *Soil ; Soil Microbiology ; }, abstract = {Soil biodiversity is threatened by intensification of land use. The consequences of different land use on belowground biodiversity remain insufficiently explored for soil protists. Alongside being abundant and extremely diverse in soil, protists provide many ecosystem services: key players in the microbial loop, turnover of organic matter and stimulation of plant growth-promoting rhizobacteria. However, we lack knowledge of effects of site, land use intensity and management on diversity of soil protists. Here we assessed protist communities in four European arable sites with contrasting land use intensities at each site: Lusignan, France; Moskanjci, Slovenia; Castro Verde, Portugal and Scheyern, Germany as well as two grassland sites: Hainich, Germany and Lancaster, UK. Each site has consistent agricultural management history of low and high land use intensities quantified in terms of land use index (LUI). We employed high-throughput sequencing of environmental DNA, targeting the V4 region of the 18S rRNA gene. By assigning the protist composition to trophic groups, we inspected for effects of management, and other biotic and abiotic variables. While overall protist richness was unaffected by LUI within sites, specific trophic groups such as plant pathogens and saprotrophs were affected. Effects on protist biome across land uses and sites were also observed. LUI sensitive taxa were taxonomically diverse in each plot, and their trophic groups responded in specific patterns to specific practices. The most abundant trophic group was phagotrophs (73%), followed by photoautotrophs (16%), plant pathogens (4%), animal parasites (2%) and saprotrophs (1%). Community compositions and factors affecting the structure of individual trophic groups differed between land uses and management systems. The agricultural management selected for distinct protist populations as well as specific functional traits, and the protist community and diversity were indeed affected by site, LUI and management, which indicates the ecological significance of protists in the soil food web.}, } @article {pmid32065512, year = {2020}, author = {van der Heyde, M and Bunce, M and Wardell-Johnson, G and Fernandes, K and White, NE and Nevill, P}, title = {Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding.}, journal = {Molecular ecology resources}, volume = {20}, number = {3}, pages = {}, doi = {10.1111/1755-0998.13148}, pmid = {32065512}, issn = {1755-0998}, support = {ICI150100041//ARC Centre for Mine Site Restoration/ ; }, mesh = {Animals ; Arthropods/genetics ; Biodiversity ; Climate ; DNA/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Environmental/*genetics ; Ecosystem ; Environmental Monitoring/*methods ; Invertebrates/genetics ; Metagenomics/methods ; Plants/genetics ; Soil ; }, abstract = {Biological surveys based on visual identification of the biota are challenging, expensive and time consuming, yet crucial for effective biomonitoring. DNA metabarcoding is a rapidly developing technology that can also facilitate biological surveys. This method involves the use of next generation sequencing technology to determine the community composition of a sample. However, it is uncertain as to what biological substrate should be the primary focus of metabarcoding surveys. This study aims to test multiple sample substrates (soil, scat, plant material and bulk arthropods) to determine what organisms can be detected from each and where they overlap. Samples (n = 200) were collected in the Pilbara (hot desert climate) and Swan Coastal Plain (hot Mediterranean climate) regions of Western Australia. Soil samples yielded little plant or animal DNA, especially in the Pilbara, probably due to conditions not conducive to long-term preservation. In contrast, scat samples contained the highest overall diversity with 131 plant, vertebrate and invertebrate families detected. Invertebrate and plant sequences were detected in the plant (86 families), pitfall (127 families) and vane trap (126 families) samples. In total, 278 families were recovered from the survey, 217 in the Swan Coastal Plain and 156 in the Pilbara. Aside from soil, 22%-43% of the families detected were unique to the particular substrate, and community composition varied significantly between substrates. These results demonstrate the importance of selecting appropriate metabarcoding substrates when undertaking terrestrial surveys. If the aim is to broadly capture all biota then multiple substrates will be required.}, } @article {pmid32065492, year = {2020}, author = {Obiol, A and Giner, CR and Sánchez, P and Duarte, CM and Acinas, SG and Massana, R}, title = {A metagenomic assessment of microbial eukaryotic diversity in the global ocean.}, journal = {Molecular ecology resources}, volume = {20}, number = {3}, pages = {}, doi = {10.1111/1755-0998.13147}, pmid = {32065492}, issn = {1755-0998}, support = {3362//King Abdullah University of Science and Technology (KAUST)/ ; CSD2008-00077//Spanish Ministry of Economy and Competitiveness projects Malaspina-2010/ ; CTM2016-75083-R//ALLFLAGS/ ; //Spanish FPI/ ; }, mesh = {Biodiversity ; DNA, Ribosomal/genetics ; Eukaryota/*genetics ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Oceans and Seas ; Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Surveying microbial diversity and function is accomplished by combining complementary molecular tools. Among them, metagenomics is a PCR free approach that contains all genetic information from microbial assemblages and is today performed at a relatively large scale and reasonable cost, mostly based on very short reads. Here, we investigated the potential of metagenomics to provide taxonomic reports of marine microbial eukaryotes. We prepared a curated database with reference sequences of the V4 region of 18S rDNA clustered at 97% similarity and used this database to extract and classify metagenomic reads. More than half of them were unambiguously affiliated to a unique reference whilst the rest could be assigned to a given taxonomic group. The overall diversity reported by metagenomics was similar to that obtained by amplicon sequencing of the V4 and V9 regions of the 18S rRNA gene, although either one or both of these amplicon surveys performed poorly for groups like Excavata, Amoebozoa, Fungi and Haptophyta. We then studied the diversity of picoeukaryotes and nanoeukaryotes using 91 metagenomes from surface down to bathypelagic layers in different oceans, unveiling a clear taxonomic separation between size fractions and depth layers. Finally, we retrieved long rDNA sequences from assembled metagenomes that improved phylogenetic reconstructions of particular groups. Overall, this study shows metagenomics as an excellent resource for taxonomic exploration of marine microbial eukaryotes.}, } @article {pmid32062778, year = {2020}, author = {Nkongolo, KK and Narendrula-Kotha, R}, title = {Advances in monitoring soil microbial community dynamic and function.}, journal = {Journal of applied genetics}, volume = {61}, number = {2}, pages = {249-263}, pmid = {32062778}, issn = {2190-3883}, support = {CRDP-J- 470535-2014//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Bacteria/*genetics/isolation & purification ; *Environmental Monitoring ; High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; Polymorphism, Restriction Fragment Length/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Microorganisms are vital to the overall ecosystem functioning, stability, and sustainability. Soil fertility and health depend on chemical composition and also on the qualitative and quantitative nature of microorganisms inhabiting it. Historically, denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE), single-strand conformation polymorphism, DNA amplification fingerprinting, amplified ribosomal DNA restriction analysis, terminal restriction fragment length polymorphism, length heterogeneity PCR, and ribosomal intergenic spacer analysis were used to assess soil microbial community structure (SMCS), abundance, and diversity. However, these methods had significant shortcomings and limitations for application in land reclamation monitoring. SMCS has been primarily determined by phospholipid fatty acid (PLFA) analysis. This method provides a direct measure of viable biomass in addition to a biochemical profile of the microbial community. PLFA has limitations such as overlap in the composition of microorganisms and the specificity of PLFAs signature. In recent years, high-throughput next-generation sequencing has dramatically increased the resolution and detectable spectrum of diverse microbial phylotypes from environmental samples and it plays a significant role in microbial ecology studies. Next-generation sequencings using 454, Illumina, SOLiD, and Ion Torrent platforms are rapid and flexible. The two methods, PLFA and next-generation sequencing, are useful in detecting changes in microbial community diversity and structure in different ecosystems. Single-molecule real-time (SMRT) and nanopore sequencing technologies represent third-generation sequencing (TGS) platforms that have been developed to address the shortcomings of second-generation sequencing (SGS). Enzymatic and soil respiration analyses are performed to further determine soil quality and microbial activities. Other valuable methods that are being recently applied to microbial function and structures include NanoSIM, GeoChip, and DNA stable staple isotope probing (DNA-SIP) technologies. They are powerful metagenomics tool for analyzing microbial communities, including their structure, metabolic potential, diversity, and their impact on ecosystem functions. This review is a critical analysis of current methods used in monitoring soil microbial community dynamic and functions.}, } @article {pmid32062353, year = {2020}, author = {Trøseid, M and Andersen, GØ and Broch, K and Hov, JR}, title = {The gut microbiome in coronary artery disease and heart failure: Current knowledge and future directions.}, journal = {EBioMedicine}, volume = {52}, number = {}, pages = {102649}, pmid = {32062353}, issn = {2352-3964}, mesh = {Animals ; Butyrates/metabolism ; Coronary Artery Disease/*etiology/*metabolism ; Diet ; *Disease Susceptibility ; Dysbiosis/metabolism ; Fatty Acids, Volatile/biosynthesis ; *Gastrointestinal Microbiome ; Heart Failure/*etiology/*metabolism ; Humans ; Intestinal Mucosa/immunology/metabolism/pathology ; Lipopolysaccharides/metabolism ; Metagenome ; Metagenomics ; Signal Transduction ; }, abstract = {Host-microbiota interactions involving inflammatory and metabolic pathways have been linked to the pathogenesis of multiple immune-mediated diseases and metabolic conditions like diabetes and obesity. Accumulating evidence suggests that alterations in the gut microbiome could play a role in cardiovascular disease. This review focuses on recent advances in our understanding of the interplay between diet, gut microbiota and cardiovascular disease, with emphasis on heart failure and coronary artery disease. Whereas much of the literature has focused on the circulating levels of the diet- and microbiota-dependent metabolite trimethylamine-N-oxide (TMAO), several recent sequencing-based studies have demonstrated compositional and functional alterations in the gut microbiomes in both diseases. Some microbiota characteristics are consistent across several study cohorts, such as a decreased abundance of microbes with capacity for producing butyrate. However, the published gut microbiota studies generally lack essential covariates like diet and clinical data, are too small to capture the substantial variation in the gut microbiome, and lack parallel plasma samples, limiting the ability to translate the functional capacity of the gut microbiomes to actual function reflected by circulating microbiota-related metabolites. This review attempts to give directions for future studies in order to demonstrate clinical utility of the gut-heart axis.}, } @article {pmid32062351, year = {2020}, author = {Loughman, A and Ponsonby, AL and O'Hely, M and Symeonides, C and Collier, F and Tang, MLK and Carlin, J and Ranganathan, S and Allen, K and Pezic, A and Saffery, R and Jacka, F and Harrison, LC and Sly, PD and Vuillermin, P and , }, title = {Gut microbiota composition during infancy and subsequent behavioural outcomes.}, journal = {EBioMedicine}, volume = {52}, number = {}, pages = {102640}, pmid = {32062351}, issn = {2352-3964}, mesh = {Adult ; Age Factors ; Anti-Bacterial Agents/pharmacology ; Australia ; Biodiversity ; Brain/physiology ; Child ; *Child Behavior ; Child, Preschool ; Cohort Studies ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/drug effects ; Humans ; Infant ; *Infant Behavior ; Male ; Metagenome ; Metagenomics/methods ; *Neurogenesis ; RNA, Ribosomal, 16S ; Risk Factors ; }, abstract = {BACKGROUND: Despite intense interest in the relationship between gut microbiota and brain development, longitudinal data from human studies are lacking. This study aimed to investigate the relationship between the composition of gut microbiota during infancy and subsequent behavioural outcomes.

METHODS: A subcohort of 201 children with behavioural outcome measures was identified within a longitudinal, Australian birth-cohort study. The faecal microbiota were analysed at 1, 6, and 12 months of age. Behavioural outcomes were measured at 2 years of age.

FINDINGS: In an unselected birth cohort, we found a clear association between decreased normalised abundance of Prevotella in faecal samples collected at 12 months of age and increased behavioural problems at 2 years, in particular Internalizing Problem scores. This association appeared independent of multiple potentially confounding variables, including maternal mental health. Recent exposure to antibiotics was the best predictor of decreased Prevotella.

INTERPRETATION: Our findings demonstrate a strong association between the composition of the gut microbiota in infancy and subsequent behavioural outcomes; and support the importance of responsible use of antibiotics during early life.

FUNDING: This study was funded by the National Health and Medical Research Council of Australia (1082307, 1147980, 1129813), The Murdoch Children's Research Institute, Barwon Health, Deakin University, Perpetual Trustees, and The Shepherd Foundation. The funders had no involvement in the data collection, analysis or interpretation, trial design, recruitment or any other aspect pertinent to the study.}, } @article {pmid32061677, year = {2020}, author = {Rios-Arce, ND and Schepper, JD and Dagenais, A and Schaefer, L and Daly-Seiler, CS and Gardinier, JD and Britton, RA and McCabe, LR and Parameswaran, N}, title = {Post-antibiotic gut dysbiosis-induced trabecular bone loss is dependent on lymphocytes.}, journal = {Bone}, volume = {134}, number = {}, pages = {115269}, pmid = {32061677}, issn = {1873-2763}, support = {P30 DK020572/DK/NIDDK NIH HHS/United States ; R01 AT007695/AT/NCCIH NIH HHS/United States ; R01 DK101050/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Anti-Bacterial Agents ; *Bone Resorption/microbiology ; Cancellous Bone ; *Dysbiosis/chemically induced ; *Gastrointestinal Microbiome ; Lymphocytes ; Mice ; Mice, Inbred C57BL ; }, abstract = {Recent studies in mouse models have shown that gut microbiota significantly influences bone health. We demonstrated that 2-week oral treatment with broad spectrum antibiotics followed by 4 weeks of recovery of the gut microbiota results in dysbiosis (microbiota imbalance)-induced bone loss in mice. Because gut microbiota is critical for the development of the immune system and since both microbiota and the immune system can regulate bone health, in this study, we tested the role of the immune system in mediating post-antibiotic dysbiosis-induced bone loss. For this, we treated wild-type (WT) and lymphocyte deficient Rag2 knockout (KO) mice with ampicillin/neomycin cocktail in water for 2 weeks followed by 4 weeks of water without antibiotics. This led to a significant bone loss (31% decrease from control) in WT mice. Interestingly, no bone loss was observed in the KO mice suggesting that lymphocytes are required for dysbiosis-induced bone loss. Bray-Curtis diversity metrics showed similar microbiota changes in both the WT and KO post-antibiotic treated groups. However, several operational taxonomic units (OTUs) classified as Lactobacillales were significantly higher in the repopulated KO when compared to the WT mice, suggesting that these bacteria might play a protective role in preventing bone loss in the KO mice after antibiotic treatment. The effect of dysbiosis on bone was therefore examined in the WT mice in the presence or absence of oral Lactobacillus reuteri treatment for 4 weeks (post-ABX treatment). As hypothesized, mice treated with L. reuteri did not display bone loss, suggesting a bone protective role for this group of bacteria. Taken together, our studies elucidate an important role for lymphocytes in regulating post-antibiotic dysbiosis-induced bone loss.}, } @article {pmid32061251, year = {2020}, author = {Zhu, X and Campanaro, S and Treu, L and Seshadri, R and Ivanova, N and Kougias, PG and Kyrpides, N and Angelidaki, I}, title = {Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {22}, pmid = {32061251}, issn = {2049-2618}, mesh = {Acetates/metabolism ; Anaerobiosis ; Bacteria/classification/*metabolism ; Bioreactors ; Chemoautotrophic Growth ; Ecosystem ; Gene Expression Profiling ; Hydrogen/metabolism ; *Metabolic Networks and Pathways ; Metagenomics ; Methane/*biosynthesis ; Methanosarcina/metabolism ; *Microbiota ; }, abstract = {Methanogenesis, a biological process mediated by complex microbial communities, has attracted great attention due to its contribution to global warming and potential in biotechnological applications. The current study unveiled the core microbial methanogenic metabolisms in anaerobic vessel ecosystems by applying combined genome-centric metagenomics and metatranscriptomics. Here, we demonstrate that an enriched natural system, fueled only with acetate, could support a bacteria-dominated microbiota employing a multi-trophic methanogenic process. Moreover, significant changes, in terms of microbial structure and function, were recorded after the system was supplemented with additional H2. Methanosarcina thermophila, the predominant methanogen prior to H2 addition, simultaneously performed acetoclastic, hydrogenotrophic, and methylotrophic methanogenesis. The methanogenic pattern changed after the addition of H2, which immediately stimulated Methanomicrobia-activity and was followed by a slow enrichment of Methanobacteria members. Interestingly, the essential genes involved in the Wood-Ljungdahl pathway were not expressed in bacterial members. The high expression of a glycine cleavage system indicated the activation of alternative metabolic pathways for acetate metabolism, which were reconstructed in the most abundant bacterial genomes. Moreover, as evidenced by predicted auxotrophies, we propose that specific microbes of the community were forming symbiotic relationships, thus reducing the biosynthetic burden of individual members. These results provide new information that will facilitate future microbial ecology studies of interspecies competition and symbiosis in methanogenic niches. Video abstract.}, } @article {pmid32060494, year = {2020}, author = {Louca, P and Menni, C and Padmanabhan, S}, title = {Genomic Determinants of Hypertension With a Focus on Metabolomics and the Gut Microbiome.}, journal = {American journal of hypertension}, volume = {33}, number = {6}, pages = {473-481}, pmid = {32060494}, issn = {1941-7225}, support = {CS/16/1/31878/BHF_/British Heart Foundation/United Kingdom ; MR/M016560/1/MRC_/Medical Research Council/United Kingdom ; SP/14/8/31352/BHF_/British Heart Foundation/United Kingdom ; RE/18/6/34217/BHF_/British Heart Foundation/United Kingdom ; }, mesh = {Animals ; Bacteria/*metabolism ; *Blood Pressure ; Diet ; Essential Hypertension/*genetics/*microbiology/physiopathology ; *Gastrointestinal Microbiome ; Gene-Environment Interaction ; Genetic Predisposition to Disease ; *Genetic Variation ; Humans ; *Metabolomics ; Risk Factors ; }, abstract = {Epidemiologic and genomic studies have progressively improved our understanding of the causation of hypertension and the complex relationship with diet and environment. The majority of Mendelian forms of syndromic hypotension and hypertension (HTN) have all been linked to mutations in genes whose encoded proteins regulate salt-water balance in the kidney, supporting the primacy of the kidneys in blood pressure regulation. There are more than 1,477 single nucleotide polymorphisms associated with blood pressure and hypertension and the challenge is establishing a causal role for these variants. Hypertension is a complex multifactorial phenotype and it is likely to be influenced by multiple factors including interactions between diet and lifestyle factors, microbiome, and epigenetics. Given the finite genetic variability that is possible in humans, it is likely that incremental gains from single marker analyses have now plateaued and a greater leap in our understanding of the genetic basis of disease will come from integration of other omics and the interacting environmental factors. In this review, we focus on emerging results from the microbiome and metabolomics and discuss how leveraging these findings may facilitate a deeper understanding of the interrelationships between genomics, diet, and microbial ecology in humans in the causation of essential hypertension.}, } @article {pmid32060329, year = {2020}, author = {Gao, J and Yan, KT and Wang, JX and Dou, J and Wang, J and Ren, M and Ma, J and Zhang, X and Liu, Y}, title = {Gut microbial taxa as potential predictive biomarkers for acute coronary syndrome and post-STEMI cardiovascular events.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {2639}, pmid = {32060329}, issn = {2045-2322}, mesh = {Acute Coronary Syndrome/blood/diagnosis/*microbiology ; Adult ; Biomarkers/blood ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Methylamines/blood ; Middle Aged ; Prognosis ; Prospective Studies ; ST Elevation Myocardial Infarction/blood/diagnosis/*microbiology ; }, abstract = {UNLABELLED: Plasma trimethylamine N-oxide (TMAO) is associated with coronary atherosclerotic plaque and cardiovascular disease risk, but associations between gut microbes in acute coronary syndrome (ACS) and post-ST-segment elevation myocardial infarction (post-STEMI) events are unknown. We investigated associations between gut microbial taxa and systemic TMAO levels and the possible TMAO contribution to incident post-STEMI cardiovascular events.

PATIENTS AND METHODS: A total of 60 patients, including 30 with unstable angina pectoris (UAP), 30 post-STEMI and 30 healthy controls, were enrolled from June to November 2017. Metagenomic sequencing was performed and TMAO and IL-6 were detected.

RESULTS: Minimal discriminators of gut microbial taxa (top 40) distinguished ACS patients from controls. Serum TMAO levels were positively associated with increased abundance of Aerococcaceae, Ruminococcaceae_UCG.005, Ruminococcaceae_UCC.014 and X. Eubacterium_fissicatena, and decreased abundance of Lachnospiraceae_FCS020 (P < 0.05). Elevated serum TMAO levels correlated independently with ACS (P < 0.05). Risk stratification for incident major adverse cardiovascular events (MACE) improved at one year in patients with serum TMAO levels ≦2.19 µM. Serum interleukin-6 levels were not significantly increased in patients with ACS and post-STEMI MACE.

CONCLUSIONS: ACS and incident post-STEMI MACE may be associated with the gut bacteria choline metabolite TMAO. The specific gut microbial taxa identified in association with serum TMAO levels may be potential predictive biomarkers for accurate diagnosis of ACS onset.}, } @article {pmid32058642, year = {2020}, author = {Sunwoo, J and Ji, SC and Kim, AH and Yu, KS and Cho, JY and Jang, IJ and Lee, S}, title = {Impact of Vancomycin-Induced Changes in the Intestinal Microbiota on the Pharmacokinetics of Simvastatin.}, journal = {Clinical and translational science}, volume = {13}, number = {4}, pages = {752-760}, pmid = {32058642}, issn = {1752-8062}, mesh = {Administration, Oral ; Adult ; Anti-Bacterial Agents/*administration & dosage ; Bacteroidetes/drug effects/isolation & purification/metabolism ; Cross-Over Studies ; Drug Interactions ; Feces/chemistry/microbiology ; Gastrointestinal Microbiome/*drug effects/physiology ; Glucuronic Acid/isolation & purification/metabolism ; Healthy Volunteers ; Humans ; Hydroxymethylglutaryl-CoA Reductase Inhibitors ; Male ; Metabolomics ; Middle Aged ; Proteobacteria/drug effects/isolation & purification/metabolism ; Simvastatin/administration & dosage/*pharmacokinetics ; Vancomycin/*administration & dosage ; Young Adult ; }, abstract = {The pharmacokinetic (PK) properties of drugs are affected in several ways by interactions with microbiota. The aim of this study was to investigate the effects of oral vancomycin on the gut microbiota and, consequently, on the PKs of simvastatin. An open-label, single arm, sequential crossover study was conducted in six healthy Korean male subjects. After 6 days on a control diet, simvastatin 40 mg was orally administered to the subjects before and after 1 week of oral vancomycin treatment. Blood samples for PK analysis and fecal samples for metagenomic and metabolomic analyses were collected. After vancomycin treatment, the richness of microbiota considerably decreased, and the composition was altered. In particular, the relative abundance of Bacteroidetes decreased, whereas that of proteobacteria increased. In addition, changes in fecal metabolites, including D-glucuronic acid, were observed. However, systemic exposure of simvastatin was not changed whereas that of hydroxysimvastatin showed a tendency to increase. The relationship between the change of PKs of simvastatin and the change of gut microbiota and fecal metabolites were not clearly observed.}, } @article {pmid32058299, year = {2020}, author = {Khachatryan, L and de Leeuw, RH and Kraakman, MEM and Pappas, N and Te Raa, M and Mei, H and de Knijff, P and Laros, JFJ}, title = {Taxonomic classification and abundance estimation using 16S and WGS-A comparison using controlled reference samples.}, journal = {Forensic science international. Genetics}, volume = {46}, number = {}, pages = {102257}, doi = {10.1016/j.fsigen.2020.102257}, pmid = {32058299}, issn = {1878-0326}, mesh = {Bacteria/*classification/*genetics ; Datasets as Topic ; High-Throughput Nucleotide Sequencing ; Metagenomics ; RNA, Ribosomal, 16S/*genetics ; Real-Time Polymerase Chain Reaction ; *Whole Genome Sequencing ; }, abstract = {The assessment of microbiome biodiversity is the most common application of metagenomics. While 16S sequencing remains standard procedure for taxonomic profiling of metagenomic data, a growing number of studies have clearly demonstrated biases associated with this method. By using Whole Genome Shotgun sequencing (WGS) metagenomics, most of the known restrictions associated with 16S data are alleviated. However, due to the computationally intensive data analyses and higher sequencing costs, WGS based metagenomics remains a less popular option. Selecting the experiment type that provides a comprehensive, yet manageable amount of information is a challenge encountered in many metagenomics studies. In this work, we created a series of artificial bacterial mixes, each with a different distribution of skin-associated microbial species. These mixes were used to estimate the resolution of two different metagenomic experiments - 16S and WGS - and to evaluate several different bioinformatics approaches for taxonomic read classification. In all test cases, WGS approaches provide much more accurate results, in terms of taxa prediction and abundance estimation, in comparison to those of 16S. Furthermore, we demonstrate that a 16S dataset, analysed using different state of the art techniques and reference databases, can produce widely different results. In light of the fact that most forensic metagenomic analysis are still performed using 16S data, our results are especially important.}, } @article {pmid32056780, year = {2020}, author = {Madan, A and Thompson, D and Fowler, JC and Ajami, NJ and Salas, R and Frueh, BC and Bradshaw, MR and Weinstein, BL and Oldham, JM and Petrosino, JF}, title = {The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness.}, journal = {Journal of affective disorders}, volume = {264}, number = {}, pages = {98-106}, doi = {10.1016/j.jad.2019.12.020}, pmid = {32056780}, issn = {1573-2517}, mesh = {Adult ; Animals ; Anxiety ; Anxiety Disorders ; *Gastrointestinal Microbiome/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; }, abstract = {BACKGROUND: Emerging evidence implicates the gut microbiota in central nervous system functioning via its effects on inflammation, the hypothalamic-pituitary axis, and/or neurotransmission. Our understanding of the cellular underpinnings of the brain-gut relationship is based almost exclusively on animal models with some small-scale human studies. This study examined the relationship between the gut microbiota and psychiatric symptom severity and treatment response among inpatients with serious mental illness.

METHOD: We collected data from adult inpatients (N = 111). Measures of diagnoses, suicide severity, trauma, depression, and anxiety were collected shortly after admission, while self-collected fecal swabs were collected early in the course of hospitalization and processed using 16S rRNA gene sequencing and whole genome shotgun sequencing methods.

RESULTS: Results indicate that depression and anxiety severity shortly after admission were negatively associated with bacterial richness and alpha diversity. Additional analyses revealed a number of bacterial taxa associated with depression and anxiety severity. Gut microbiota richness and alpha diversity early in the course of hospitalization was a significant predictor of depression remission at discharge.

CONCLUSIONS: This study is among the first to demonstrate a gut microbiota relationship with symptom severity among psychiatric inpatients as well as a relationship to remission of depression post-treatment. These findings are consistent with animal models and limited human studies as well as with the broader literature implicating inflammation in the pathophysiology of depression. These findings offer the foundation for further studies of novel therapeutic approaches to the treatment, prevention of, or recurrence of serious mental illness.}, } @article {pmid32056227, year = {2020}, author = {Smirnova, E and Puri, P and Muthiah, MD and Daitya, K and Brown, R and Chalasani, N and Liangpunsakul, S and Shah, VH and Gelow, K and Siddiqui, MS and Boyett, S and Mirshahi, F and Sikaroodi, M and Gillevet, P and Sanyal, AJ}, title = {Fecal Microbiome Distinguishes Alcohol Consumption From Alcoholic Hepatitis But Does Not Discriminate Disease Severity.}, journal = {Hepatology (Baltimore, Md.)}, volume = {72}, number = {1}, pages = {271-286}, pmid = {32056227}, issn = {1527-3350}, support = {UL1 TR002649/TR/NCATS NIH HHS/United States ; UO1 AA021891-01/NH/NIH HHS/United States ; U01 AA021891/AA/NIAAA NIH HHS/United States ; T32 DK07150-40/NH/NIH HHS/United States ; CTSA UL1TR002649/NH/NIH HHS/United States ; KL2 TR002648/TR/NCATS NIH HHS/United States ; T32 DK007150/DK/NIDDK NIH HHS/United States ; K23 AA021179/AA/NIAAA NIH HHS/United States ; }, mesh = {Adult ; *Alcohol Drinking ; Diagnosis, Differential ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Hepatitis, Alcoholic/*diagnosis/*microbiology ; Humans ; Male ; Middle Aged ; Severity of Illness Index ; }, abstract = {BACKGROUND AND AIMS: The role of the intestinal microbiome in alcoholic hepatitis is not established. The aims of this study were to (1) characterize the fecal microbial ecology associated with alcoholic hepatitis, (2) relate microbiome changes to disease severity, and (3) infer the functional relevance of shifts in microbial ecology.

APPROACH AND RESULTS: The fecal microbiome in patients with moderate alcoholic hepatitis (MAH) or severe alcoholic hepatitis (SAH) was compared with healthy controls (HCs) and heavy drinking controls (HDCs). Microbial taxa were identified by 16S pyrosequencing. Functional metagenomics was performed using PICRUSt. Fecal short chain fatty acids (SCFAs) were measured using a liquid chromatography-mass spectrometry platform. A total of 78 participants (HC, n = 24; HDC, n = 20; MAH, n = 10; SAH, n = 24) were studied. HDC had a distinct signature compared with HC with depletion of Bacteroidetes (46% vs. 26%; P = 0.01). Alcoholic hepatitis was associated with a distinct microbiome signature compared with HDC (area under the curve = 0.826); differential abundance of Ruminococcaceae, Veillonellaceae, Lachnospiraceae, Porphyromonadaceae, and Rikenellaceae families were the key contributors to these differences. The beta diversity was significantly different among the groups (permutational multivariate analysis of variance [PERMANOVA] P < 0.001). SAH was associated with increased Proteobacteria (SAH 14% vs. HDC 7% and SAH vs. HC 2%, P = 0.20 and 0.01, respectively). Firmicutes abundance declined from HDC to MAH to SAH (63% vs. 53% vs. 48%, respectively; P = 0.09, HDC vs. SAH). Microbial taxa did not distinguish between MAH and SAH (PERMANOVA P = 0.785). SCFAs producing bacteria (Lachnospiraceae and Ruminococcaceae) were decreased in alcoholic hepatitis, and a similar decrease was observed in fecal SCFAs among alcoholic hepatitis patients.

CONCLUSIONS: There are distinct changes in fecal microbiome associated with the development, but not severity, of alcoholic hepatitis.}, } @article {pmid32054085, year = {2020}, author = {Langan, EA and Recke, A and Bokor-Billmann, T and Billmann, F and Kahle, BK and Zillikens, D}, title = {The Role of the Cutaneous Microbiome in Hidradenitis Suppurativa-Light at the End of the Microbiological Tunnel.}, journal = {International journal of molecular sciences}, volume = {21}, number = {4}, pages = {}, pmid = {32054085}, issn = {1422-0067}, mesh = {Animals ; Bacteria/genetics/isolation & purification ; Dysbiosis/complications/microbiology/physiopathology ; Hidradenitis Suppurativa/complications/*microbiology/physiopathology ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; Microbiota ; Skin/*microbiology/physiopathology ; }, abstract = {The development of next generation sequencing, coupled with advances in bio-informatics, has provided new insights into the role of the cutaneous microbiome in the pathophysiology of a range of inflammatory skin diseases. In fact, it has even been suggested that the identification of specific skin microbial signatures may not only be useful in terms of diagnosis of skin diseases but they may also ultimately help inform personalised treatment strategies. To date, research investigating the role of microbiota in the development of inflammatory skin diseases has largely focused on atopic eczema and psoriasis vulgaris. The role of the microbiome in Hidradenits suppurativa (HS)-also known as acne inversa-a chronic auto-inflammatory skin disease associated with significant morbidity, has received comparatively little attention. This is despite the fact that antimicrobial therapy plays a central role in the treatment of HS. After briefly outlining the clinical features of HS and current treatment strategies, we move on to review the evidence of microbial dysbiosis in HS pathophysiology. We conclude by outlining the potential for metagenomic studies to deepen our understanding of HS biology but more importantly to identify novel and much needed treatment strategies.}, } @article {pmid32053789, year = {2020}, author = {Khan Mirzaei, M and Khan, MAA and Ghosh, P and Taranu, ZE and Taguer, M and Ru, J and Chowdhury, R and Kabir, MM and Deng, L and Mondal, D and Maurice, CF}, title = {Bacteriophages Isolated from Stunted Children Can Regulate Gut Bacterial Communities in an Age-Specific Manner.}, journal = {Cell host & microbe}, volume = {27}, number = {2}, pages = {199-212.e5}, pmid = {32053789}, issn = {1934-6069}, mesh = {Age Factors ; Bacteria/classification/genetics/isolation & purification/virology ; Bacteriophages/classification/genetics/*isolation & purification ; Child, Preschool ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Genes, Bacterial ; Genes, Viral ; Growth Disorders/*microbiology/*virology ; Host Microbial Interactions ; Humans ; Infant ; Male ; Metagenomics ; Proteobacteria/classification/genetics/isolation & purification/virology ; RNA, Ribosomal, 16S ; }, abstract = {Stunting, a severe and multigenerational growth impairment, globally affects 22% of children under the age of 5 years. Stunted children have altered gut bacterial communities with higher proportions of Proteobacteria, a phylum with several known human pathogens. Despite the links between an altered gut microbiota and stunting, the role of bacteriophages, highly abundant bacterial viruses, is unknown. Here, we describe the gut bacterial and bacteriophage communities of Bangladeshi stunted children younger than 38 months. We show that these children harbor distinct gut bacteriophages relative to their non-stunted counterparts. In vitro, these gut bacteriophages are infectious and can regulate bacterial abundance and composition in an age-specific manner, highlighting their possible role in the pathophysiology of child stunting. Specifically, Proteobacteria from non-stunted children increased in the presence of phages from younger stunted children, suggesting that phages could contribute to the bacterial community changes observed in child stunting.}, } @article {pmid32053145, year = {2020}, author = {Corrêa, PS and Mendes, LW and Lemos, LN and Crouzoulon, P and Niderkorn, V and Hoste, H and Costa-Júnior, LM and Tsai, SM and Faciola, AP and Abdalla, AL and Louvandini, H}, title = {Tannin supplementation modulates the composition and function of ruminal microbiome in lambs infected with gastrointestinal nematodes.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {3}, pages = {}, doi = {10.1093/femsec/fiaa024}, pmid = {32053145}, issn = {1574-6941}, mesh = {Animal Feed/analysis ; Animals ; Diet/veterinary ; Dietary Supplements ; Fermentation ; *Microbiota ; *Nematoda ; Rumen/metabolism ; Sheep ; Tannins/metabolism ; }, abstract = {This study was carried out to evaluate the effects of tannin supplementation on ruminal microbiota of sixteen lambs infected and non-infected with Haemonchus contortus and Trichostrongylus colubriformis. Animals were fed with hay, concentrate and supplemented with Acacia mearnsii (A. mearnsii). The animals were divided into four treatments: two control groups without infection, either receiving A. mearnsii (C+) or not (C-), and two infected groups, one with A. mearnsii (I+) and another without A. mearnsii (I-). Ruminal short-chain fatty acids (SCFA) and metagenome sequencing of ruminal microbiota were used to evaluate the effect of tannin and infection on ruminal microbiome. For SCFA, differences were observed only with A. mearnsii. Total SCFA and acetate molar percentage were decreased in C+ and I+ (P<0.05). Butyrate, valerate and isovalerate were higher in lambs that received A. mearnsii in the diet (P<0.05). The infection changed the microbiome structure and decreased the abundance of butyrate-producing microorganisms. In addition, A. mearnsii supplementation also affected the structure the microbial community, increasing the diversity and abundance of the butyrate-producing and probiotics bacteria, amino acid metabolic pathways, purine, pyrimidine and sphingolipid metabolism. Together, our findings indicate that A. mearnsii supplementation modulates important groups related to nitrogen, amino acid, purine and pyrimidine metabolism, in rumen microbiome, affected by gastrointestinal nematodes infection in lambs.}, } @article {pmid32052588, year = {2020}, author = {Li, X and Xu, M and Li, X and Christie, P and Wagg, C and Zhang, J}, title = {Linkages between changes in plant and mycorrhizal fungal community composition at high versus low elevation in alpine ecosystems.}, journal = {Environmental microbiology reports}, volume = {12}, number = {2}, pages = {229-240}, doi = {10.1111/1758-2229.12827}, pmid = {32052588}, issn = {1758-2229}, support = {31272251//National Natural Science Foundation of China/International ; 31872182//National Natural Science Foundation of China/International ; 31702002//National Natural Science Foundation of China/International ; }, mesh = {*Altitude ; Biodiversity ; Biomass ; Ecosystem ; Genes, Fungal ; Metagenome ; Metagenomics/methods ; Mycobiome ; *Mycorrhizae/classification/genetics ; Phylogeny ; Plants/*microbiology ; Soil/chemistry ; Soil Microbiology ; Tibet ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) play an important role in maintaining plant diversity and productivity in grassland ecosystems. However, very few studies have investigated how AMF and plant communities co-vary between contrasting environments in natural ecosystems. Intensive sampling (50 soil samples) was conducted in natural open grasslands at both 3570 and 4556 m on Mount Segrila on the Southeast Tibetan Plateau. We used 454-pyrosequencing to investigate soil AMF communities and to explore relationships between AMF diversity and plant richness, productivity and community composition. AMF diversity was negatively correlated with plant richness at 3570 m but positively at 4556 m. Differences in AMF community composition between elevations were attributable to plant community composition, soil pH and available phosphorus concentration. The AMF community was more phylogenetically clustered at the higher elevation than the lower elevation. However, greater phylogenetic clustering (under dispersion) of AMF communities at the two elevations was positively correlated with above-ground biomass. Our results indicate that plant community composition and environmental filtering are the primary drivers structuring the AMF community. Phylogenetic relatedness may be important in explaining the function of AMF communities in alpine ecosystems.}, } @article {pmid32051648, year = {2020}, author = {Cook, KV and Li, C and Cai, H and Krumholz, LR and Hambright, KD and Paerl, HW and Steffen, MM and Wilson, AE and Burford, MA and Grossart, HP and Hamilton, DP and Jiang, H and Sukenik, A and Latour, D and Meyer, EI and Padisák, J and Qin, B and Zamor, RM and Zhu, G}, title = {The global Microcystis interactome.}, journal = {Limnology and oceanography}, volume = {65}, number = {Suppl 1}, pages = {S194-S207}, pmid = {32051648}, issn = {0024-3590}, support = {P01 ES028939/ES/NIEHS NIH HHS/United States ; }, abstract = {Bacteria play key roles in the function and diversity of aquatic systems, but aside from study of specific bloom systems, little is known about the diversity or biogeography of bacteria associated with harmful cyanobacterial blooms (cyanoHABs). CyanoHAB species are known to shape bacterial community composition and to rely on functions provided by the associated bacteria, leading to the hypothesized cyanoHAB interactome, a coevolved community of synergistic and interacting bacteria species, each necessary for the success of the others. Here, we surveyed the microbiome associated with Microcystis aeruginosa during blooms in 12 lakes spanning four continents as an initial test of the hypothesized Microcystis interactome. We predicted that microbiome composition and functional potential would be similar across blooms globally. Our results, as revealed by 16S rRNA sequence similarity, indicate that M. aeruginosa is cosmopolitan in lakes across a 280° longitudinal and 90° latitudinal gradient. The microbiome communities were represented by a wide range of operational taxonomic units and relative abundances. Highly abundant taxa were more related and shared across most sites and did not vary with geographic distance, thus, like Microcystis, revealing no evidence for dispersal limitation. High phylogenetic relatedness, both within and across lakes, indicates that microbiome bacteria with similar functional potential were associated with all blooms. While Microcystis and the microbiome bacteria shared many genes, whole-community metagenomic analysis revealed a suite of biochemical pathways that could be considered complementary. Our results demonstrate a high degree of similarity across global Microcystis blooms, thereby providing initial support for the hypothesized Microcystis interactome.}, } @article {pmid32051429, year = {2020}, author = {Dam, P and Rodriguez-R, LM and Luo, C and Hatt, J and Tsementzi, D and Konstantinidis, KT and Voit, EO}, title = {Model-based Comparisons of the Abundance Dynamics of Bacterial Communities in Two Lakes.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {2423}, pmid = {32051429}, issn = {2045-2322}, mesh = {Bacteria/*genetics/isolation & purification ; Biodiversity ; Georgia ; Lakes/*microbiology ; Metagenome ; *Microbiota ; Models, Biological ; Phylogeny ; Plankton/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Seasons ; Wisconsin ; }, abstract = {Lake Lanier (Georgia, USA) is home to more than 11,000 microbial Operational Taxonomic Units (OTUs), many of which exhibit clear annual abundance patterns. To assess the dynamics of this microbial community, we collected time series data of 16S and 18S rRNA gene sequences, recovered from 29 planktonic shotgun metagenomic datasets. Based on these data, we constructed a dynamic mathematical model of bacterial interactions in the lake and used it to analyze changes in the abundances of OTUs. The model accounts for interactions among 14 sub-communities (SCs), which are composed of OTUs blooming at the same time of the year, and three environmental factors. It captures the seasonal variations in abundances of the SCs quite well. Simulation results suggest that changes in water temperature affect the various SCs differentially and that the timing of perturbations is critical. We compared the model results with published results from Lake Mendota (Wisconsin, USA). These comparative analyses between lakes in two very different geographical locations revealed substantially more cooperation and less competition among species in the warmer Lake Lanier than in Lake Mendota.}, } @article {pmid32051205, year = {2020}, author = {Yeoh, YK and Chen, Z and Wong, MCS and Hui, M and Yu, J and Ng, SC and Sung, JJY and Chan, FKL and Chan, PKS}, title = {Southern Chinese populations harbour non-nucleatum Fusobacteria possessing homologues of the colorectal cancer-associated FadA virulence factor.}, journal = {Gut}, volume = {69}, number = {11}, pages = {1998-2007}, pmid = {32051205}, issn = {1468-3288}, mesh = {Adult ; Aged ; *Asian People ; China ; Cohort Studies ; Colorectal Neoplasms/epidemiology/*microbiology/*pathology ; Feces/microbiology ; Female ; Fusobacterium/*isolation & purification ; Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; Phylogeny ; }, abstract = {OBJECTIVE: Fusobacteria are not common nor relatively abundant in non-colorectal cancer (CRC) populations, however, we identified multiple Fusobacterium taxa nearly absent in western and rural populations to be comparatively more prevalent and relatively abundant in southern Chinese populations. We investigated whether these represented known or novel lineages in the Fusobacterium genus, and assessed their genomes for features implicated in development of cancer.

METHODS: Prevalence and relative abundances of fusobacterial species were calculated from 3157 CRC and non-CRC gut metagenomes representing 16 populations from various biogeographies. Microbial genomes were assembled and compared with existing reference genomes to assess novel fusobacterial diversity. Phylogenetic distribution of virulence genes implicated in CRC was investigated.

RESULTS: Irrespective of CRC disease status, southern Chinese populations harboured increased prevalence (maximum 39% vs 7%) and relative abundances (average 0.4% vs 0.04% of gut community) of multiple recognised and novel fusobacterial taxa phylogenetically distinct from Fusobacterium nucleatum. Genomes assembled from southern Chinese gut metagenomes increased existing fusobacterial diversity by 14.3%. Homologues of the FadA adhesin linked to CRC were consistently detected in several monophyletic lineages sister to and inclusive of F. varium and F. ulcerans, but not F. mortiferum. We also detected increased prevalence and relative abundances of F. varium in CRC compared with non-CRC cohorts, which together with distribution of FadA homologues supports a possible association with gut disease.

CONCLUSION: The proportion of fusobacteria in guts of southern Chinese populations are higher compared with several western and rural populations in line with the notion of environment/biogeography driving human gut microbiome composition. Several non-nucleatum taxa possess FadA homologues and were enriched in CRC cohorts; whether this imposes a risk in developing CRC and other gut diseases deserves further investigation.}, } @article {pmid32051016, year = {2020}, author = {Glendinning, L and Stewart, RD and Pallen, MJ and Watson, KA and Watson, M}, title = {Assembly of hundreds of novel bacterial genomes from the chicken caecum.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {34}, pmid = {32051016}, issn = {1474-760X}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; BBS/E/F/000PR10351/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P013759/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P013732/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/D/20320000/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004243/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Cecum/microbiology ; Chickens/*microbiology ; *Gastrointestinal Microbiome ; *Genome, Bacterial ; *Metagenome ; }, abstract = {BACKGROUND: Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short-chain fatty acids, nitrogen recycling, and amino acid production. In this study, we sequence DNA from caecal content samples taken from 24 chickens belonging to either a fast or a slower growing breed consuming either a vegetable-only diet or a diet containing fish meal.

RESULTS: We utilise 1.6 T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species, and 42 novel genera. We compare our genomes to data from 9 European Union countries and show that these genomes are abundant within European chicken flocks. We also compare the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed- and diet-specific microbiomes, as well as an overlapping core microbiome.

CONCLUSIONS: This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.}, } @article {pmid32050766, year = {2020}, author = {Panyod, S and Wu, WK and Lu, KH and Liu, CT and Chu, YL and Ho, CT and Hsiao, WW and Lai, YS and Chen, WC and Lin, YE and Lin, SH and Wu, MS and Sheen, LY}, title = {Allicin Modifies the Composition and Function of the Gut Microbiota in Alcoholic Hepatic Steatosis Mice.}, journal = {Journal of agricultural and food chemistry}, volume = {68}, number = {10}, pages = {3088-3098}, doi = {10.1021/acs.jafc.9b07555}, pmid = {32050766}, issn = {1520-5118}, mesh = {Animals ; Disulfides ; Ethanol/adverse effects ; Fatty Liver, Alcoholic/*drug therapy/immunology/microbiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Interleukin-1beta/genetics/immunology ; Interleukin-6/genetics/immunology ; Liver/drug effects/immunology ; Male ; Mice ; Mice, Inbred C57BL ; Sulfinic Acids/*administration & dosage ; Toll-Like Receptor 4/genetics/immunology ; Tumor Necrosis Factor-alpha/genetics/immunology ; }, abstract = {The intestinal microbiome plays an important role in the pathogenesis of liver diseases. Alcohol intake induces gut microbiota dysbiosis and alters its function. This study investigated the antibiotic effect of allicin in mice with hepatic steatosis. Male C57BL/6 mice were administered an ethanol diet supplemented with allicin (5 and 20 mg/(kg bw day)) for 4 weeks. Allicin modified the gut microbiota composition. Cecal microbiota exhibited a positive correlation with alcohol and hepatic triacylglycerol, but were suppressed with allicin. Ethanol diet with 5 mg of allicin induced a lower intestinal permeability compared to the ethanol diet alone. Allicin mediated the lipopolysaccharide (LPS)-CD14-toll-like receptor 4 (TLR4)-induced hepatic inflammation pathway by reducing LPS, CD14, TLR4, and pro-inflammatory cytokines-tumor necrosis factor (TNF)-α, interleukin (IL)-1β, and IL-6. However, hepatic inflammation primarily resulted from alcohol toxicity rather than LPS production in the gut. The prediction of functional profiles from metagenomic 16S ribosomal RNA (rRNA) data revealed different functional profiles in each group. The predicted aldehyde dehydrogenase tended to increase in alcoholic mice administered allicin. The predicted LPS-related pathway and LPS biosynthesis protein results exhibited a similar trend as plasma LPS levels. Thus, alcohol and allicin intake shapes the gut microbiota and its functional profile and improves the CD14-TLR4 pathway to alleviate inflammation in the liver.}, } @article {pmid32050330, year = {2020}, author = {Huang, W and Gong, B and He, L and Wang, Y and Zhou, J}, title = {Intensified nutrients removal in a modified sequencing batch reactor at low temperature: Metagenomic approach reveals the microbial community structure and mechanisms.}, journal = {Chemosphere}, volume = {244}, number = {}, pages = {125513}, doi = {10.1016/j.chemosphere.2019.125513}, pmid = {32050330}, issn = {1879-1298}, mesh = {Ammonia/metabolism ; Ammonium Compounds ; Betaproteobacteria/metabolism ; Bioreactors/*microbiology ; Carbon/metabolism ; Cold Temperature ; Denitrification ; Hydroxybutyrates ; Metagenome ; Microbiota ; Nitrites/metabolism ; Nitrogen/analysis/metabolism ; Phosphorus/analysis/metabolism ; Polyesters ; Sewage/chemistry ; Temperature ; Waste Disposal, Fluid/*methods ; Water Pollutants/analysis/metabolism ; }, abstract = {To achieve efficient biological nutrients removal at low temperature, a modified sequencing batch reactor (SBR) was developed at 10 °C by extending sludge retention time (SRT), shortening aerobic stage and compensating anoxic stage. The average removal rates of ammonium (NH4[+]-N), total nitrogen (TN) and total phosphorus (TP) were 98.82%, 94.12% and 96.04%, respectively. Variation of carbon source in a typical cycle demonstrated the maximum synthesis of poly-β-hydroxybutyrate (PHB) (60 mg/L) occurred after feast period. Furthermore, the TP in sludge reached 50.4 mg/g mixed liquor suspended solids (MLSS) (78.4% was inorganic phosphorus and 21.6% was organic phosphorus) after 120 days of operation, indicating an excellent P-accumulating capacity was achieved in this system. Ammonia oxidizing bacteria (AOB) activity inhibition test verified both AOB and ammonia oxidizing archaea (AOA) were involved in ammonia-oxidizing process and the latter accounted for 17%-19%. Metagenomic-based taxonomy revealed the dominant genera were Candidatus Accumulibacter (12.18%), Dechloromonas (7.54%), Haliangium (6.69%) and Candidatus Contendobacter (3.40%). As described from the denitrifying genes perspective, with the exception of nitrite reduction (performed by denitrifiers), denitrifying phosphorus-accumulating organisms (DPAOs) played a leading role in denitrification pathway, showing that poly-β-hydroxyalkanoates (PHA)-driven nutrients removal was the dominate process.}, } @article {pmid32050327, year = {2020}, author = {Tan, S and Ge, W and Wang, J and Liu, W and Zhao, Y and Shen, W and Li, L}, title = {Zearalenone-induced aberration in the composition of the gut microbiome and function impacts the ovary reserve.}, journal = {Chemosphere}, volume = {244}, number = {}, pages = {125493}, doi = {10.1016/j.chemosphere.2019.125493}, pmid = {32050327}, issn = {1879-1298}, mesh = {Animals ; Bacteria/drug effects ; Female ; Gastrointestinal Microbiome/*drug effects ; Glycerophospholipids/metabolism ; Lysophospholipids/blood ; Mice ; Ovarian Follicle/drug effects ; Ovarian Reserve/*drug effects ; Ovary/drug effects ; Zearalenone/*toxicity ; }, abstract = {Zearalenone (ZEA), as a contaminant commonly found in our daily diet, has been widely studied for its toxicity. However, the exact mechanism underlying ZEA induced reproduction disorders remains unclear. Our study aimed to elucidate the underlying relationship between aberrations in the gut microbiota and the degeneration of the ovarian reserve following exposure to ZEA. Four-week-old mice were treated with different doses (0, 20, 40 μg/kg bw/day) of ZEA for 2 weeks and it was found that the primordial follicles were dramatically decreased when compared to untreated controls. Moreover, we applied metagenomic shotgun sequencing to investigate the effects of ZEA exposure on the population composition and function of gut microbiota. The results showed that the abundance of three susceptible bacterial strains, parabacteroides, bacteroides and lachnospiraceae were increased in a dose-dependent manner after ZEA exposure, whereas the bacterial glycerophospholipid metabolism pathway was greatly suppressed. Of note, utilizing LC/MS we found lysophosphatidylcholines (LPCs), important metabolites in the process of glycerophospholipid metabolism, were markedly decreased in the plasma of the ZEA treated mice. In conclusion, our findings here provide evidences that the dysfunction in gut microbiome after ZEA exposure may affect the ovarian reserve.}, } @article {pmid32047891, year = {2021}, author = {Liu, Z and Ma, A and Mathé, E and Merling, M and Ma, Q and Liu, B}, title = {Network analyses in microbiome based on high-throughput multi-omics data.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {2}, pages = {1639-1655}, pmid = {32047891}, issn = {1477-4054}, support = {UL1 TR002733/TR/NCATS NIH HHS/United States ; }, mesh = {High-Throughput Screening Assays/*methods ; Humans ; Metabolomics/*methods ; Metagenomics/*methods ; *Microbiota ; Proteomics/*methods ; *Transcriptome ; }, abstract = {Together with various hosts and environments, ubiquitous microbes interact closely with each other forming an intertwined system or community. Of interest, shifts of the relationships between microbes and their hosts or environments are associated with critical diseases and ecological changes. While advances in high-throughput Omics technologies offer a great opportunity for understanding the structures and functions of microbiome, it is still challenging to analyse and interpret the omics data. Specifically, the heterogeneity and diversity of microbial communities, compounded with the large size of the datasets, impose a tremendous challenge to mechanistically elucidate the complex communities. Fortunately, network analyses provide an efficient way to tackle this problem, and several network approaches have been proposed to improve this understanding recently. Here, we systemically illustrate these network theories that have been used in biological and biomedical research. Then, we review existing network modelling methods of microbial studies at multiple layers from metagenomics to metabolomics and further to multi-omics. Lastly, we discuss the limitations of present studies and provide a perspective for further directions in support of the understanding of microbial communities.}, } @article {pmid32047192, year = {2020}, author = {Fiore, CL and Jarett, JK and Steinert, G and Lesser, MP}, title = {Trait-Based Comparison of Coral and Sponge Microbiomes.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {2340}, pmid = {32047192}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/genetics/growth & development/*microbiology ; Bacteria/*classification/genetics/isolation & purification ; Biodiversity ; Host-Pathogen Interactions ; Metabolic Networks and Pathways ; *Metagenome ; *Microbiota ; Phylogeny ; Porifera/genetics/growth & development/*microbiology ; RNA, Ribosomal, 16S/*analysis ; *Symbiosis ; }, abstract = {Corals and sponges harbor diverse microbial communities that are integral to the functioning of the host. While the taxonomic diversity of their microbiomes has been well-established for corals and sponges, their functional roles are less well-understood. It is unclear if the similarities of symbiosis in an invertebrate host would result in functionally similar microbiomes, or if differences in host phylogeny and environmentally driven microhabitats within each host would shape functionally distinct communities. Here we addressed this question, using metatranscriptomic and 16S rRNA gene profiling techniques to compare the microbiomes of two host organisms from different phyla. Our results indicate functional similarity in carbon, nitrogen, and sulfur assimilation, and aerobic nitrogen cycling. Additionally, there were few statistical differences in pathway coverage or abundance between the two hosts. For example, we observed higher coverage of phosphonate and siderophore metabolic pathways in the star coral, Montastraea cavernosa, while there was higher coverage of chloroalkane metabolism in the giant barrel sponge, Xestospongia muta. Higher abundance of genes associated with carbon fixation pathways was also observed in M. cavernosa, while in X. muta there was higher abundance of fatty acid metabolic pathways. Metagenomic predictions based on 16S rRNA gene profiling analysis were similar, and there was high correlation between the metatranscriptome and metagenome predictions for both hosts. Our results highlight several metabolic pathways that exhibit functional similarity in these coral and sponge microbiomes despite the taxonomic differences between the two microbiomes, as well as potential specialization of some microbially based metabolism within each host.}, } @article {pmid32046772, year = {2020}, author = {Chen, HL and Zhao, XY and Zhao, GX and Huang, HB and Li, HR and Shi, CW and Yang, WT and Jiang, YL and Wang, JZ and Ye, LP and Zhao, Q and Wang, CF and Yang, GL}, title = {Dissection of the cecal microbial community in chickens after Eimeria tenella infection.}, journal = {Parasites & vectors}, volume = {13}, number = {1}, pages = {56}, pmid = {32046772}, issn = {1756-3305}, support = {2017YFD0500400//The National Key Research and Development Program of China/ ; 2017YFD0501200//The National Key Research and Development Program of China/ ; 31672528//the National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacteria/classification/isolation & purification ; Cecum/microbiology/parasitology/pathology ; *Chickens/microbiology/parasitology ; Coccidiosis/therapy/*veterinary ; *Eimeria tenella/genetics/parasitology ; Gastrointestinal Microbiome/*genetics ; Metagenomics ; Poultry Diseases/*parasitology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Eimeria spp. are responsible for chicken coccidiosis which is the most important enteric protozoan disease resulting in tremendous economic losses in the poultry industry. Understanding the interaction between the avian cecal microbiota and coccidia is of interest in the development of alternative treatments that do not rely on chemotherapeutics and do not lead to drug resistance.

METHODS: We utilized 16S rRNA gene sequencing to detect the dynamics of the cecal microbial community in AA broilers challenged with Eimeria tenella. Histopathological analysis of the cecum was also conducted.

RESULTS: We found that microbial shifts occur during the infection. Lactobacillus, Faecalibacterium, Ruminococcaceae UCG-013, Romboutsia and Shuttleworthia decreased in abundance. However, the opportunistic pathogens Enterococcus and Streptococcus increased in abundance over time in response to the infection.

CONCLUSIONS: Eimeria tenella disrupts the integrity of the cecal microbiota and could promote the establishment and growth of potentially pathogenic bacteria. Defining bacterial populations affected by coccidial infection might help identify bacterial markers for intestinal disease as well as populations or species that could be beneficial in maintaining and restoring gut homeostasis during and after infection with E. tenella.}, } @article {pmid32043695, year = {2020}, author = {He, Z and Pan, L and Zhang, M and Zhang, M and Huang, F and Gao, S}, title = {Metagenomic comparison of structure and function of microbial community between water, effluent and shrimp intestine of higher place Litopenaeus vannamei ponds.}, journal = {Journal of applied microbiology}, volume = {129}, number = {2}, pages = {243-255}, doi = {10.1111/jam.14610}, pmid = {32043695}, issn = {1365-2672}, support = {KLM2017005//Key Laboratory of Mariculture, Ministry Education, Ocean University of China (OUC)/ ; 20160359//Bio-Form Biotechnology Co. LTD/ ; }, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification ; Intestines/*microbiology ; Metagenome ; Microbiota/genetics/*physiology ; Penaeidae/*microbiology ; Ponds/*microbiology ; RNA, Ribosomal, 16S/genetics ; Shellfish/*microbiology ; Wastewater/microbiology ; }, abstract = {AIMS: The present study aimed to reveal microbial relationship between shrimp intestine and ambient in higher place shrimp ponds from the aspects of composition and function.

METHODS AND RESULTS: Metagenome and 16S rRNA gene sequencing were used to compare microbial compositions and functions of water, effluent and shrimp intestine in higher place Litopenaeus vannamei ponds. Although the three groups had similar dominant phyla, such as Proteobacteria, Bacteroidetes and Tenericutes, their bacterial compositions at the genus level were obviously different. Compared to effluent and intestine, the relative abundance of Vibrio as common opportunistic pathogen for shrimp was significantly higher in water. However, cluster analysis showed that intestinal microbial composition was more similar to that of effluent than water. Metagenomic data showed that the predominant microbial functions in the three groups were mostly related to energy production and biosynthesis, while carbohydrate metabolism was relatively enriched in intestinal microbiota. More importantly, Proteobacteria played a critical role in carbon metabolism and biosynthesis of amino acids in the three habitats, and Vibrio had the most functions related to bacterial virulence and infection.

CONCLUSIONS: Shrimp intestinal microbiota had a close correlation with the ambient microbiota in both structure and function. As the most dominant phylum, Proteobacteria was very important for microbiota communication and nutrient cycling in higher place shrimp ponds. Moreover, due to the pathogenicity, it was necessary to monitor the abundant changes of Vibrio in water to decrease the risk of shrimp disease outbreaks.

These above results may be helpful to comprehensively understand the characteristics and functions of microbiota in higher place shrimp ponds, thereby providing basic information for developing the management strategies of entire microbiota to sustain shrimp health.}, } @article {pmid32042898, year = {2020}, author = {Oliverio, AM and Geisen, S and Delgado-Baquerizo, M and Maestre, FT and Turner, BL and Fierer, N}, title = {The global-scale distributions of soil protists and their contributions to belowground systems.}, journal = {Science advances}, volume = {6}, number = {4}, pages = {eaax8787}, pmid = {32042898}, issn = {2375-2548}, mesh = {Archaea/classification/*growth & development ; Bacteria/classification/*growth & development ; *Biodiversity ; Microbiota/*physiology ; *Soil ; *Soil Microbiology ; }, abstract = {Protists are ubiquitous in soil, where they are key contributors to nutrient cycling and energy transfer. However, protists have received far less attention than other components of the soil microbiome. We used amplicon sequencing of soils from 180 locations across six continents to investigate the ecological preferences of protists and their functional contributions to belowground systems. We complemented these analyses with shotgun metagenomic sequencing of 46 soils to validate the identities of the more abundant protist lineages. We found that most soils are dominated by consumers, although parasites and phototrophs are particularly abundant in tropical and arid ecosystems, respectively. The best predictors of protist composition (primarily annual precipitation) are fundamentally distinct from those shaping bacterial and archaeal communities (namely, soil pH). Some protists and bacteria co-occur globally, highlighting the potential importance of these largely undescribed belowground interactions. Together, this study allowed us to identify the most abundant and ubiquitous protists living in soil, with our work providing a cross-ecosystem perspective on the factors structuring soil protist communities and their likely contributions to soil functioning.}, } @article {pmid32042169, year = {2020}, author = {Moss, EL and Maghini, DG and Bhatt, AS}, title = {Complete, closed bacterial genomes from microbiomes using nanopore sequencing.}, journal = {Nature biotechnology}, volume = {38}, number = {6}, pages = {701-707}, pmid = {32042169}, issn = {1546-1696}, support = {R01 AI148623/AI/NIAID NIH HHS/United States ; P30 AG066515/AG/NIA NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; P50 AG047366/AG/NIA NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Animals ; DNA, Bacterial/analysis/genetics ; Dogs ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/*genetics ; Humans ; Metagenomics/*methods ; Mice ; Nanopore Sequencing/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {Microbial genomes can be assembled from short-read sequencing data, but the assembly contiguity of these metagenome-assembled genomes is constrained by repeat elements. Correct assignment of genomic positions of repeats is crucial for understanding the effect of genome structure on genome function. We applied nanopore sequencing and our workflow, named Lathe, which incorporates long-read assembly and short-read error correction, to assemble closed bacterial genomes from complex microbiomes. We validated our approach with a synthetic mixture of 12 bacterial species. Seven genomes were completely assembled into single contigs and three genomes were assembled into four or fewer contigs. Next, we used our methods to analyze metagenomics data from 13 human stool samples. We assembled 20 circular genomes, including genomes of Prevotella copri and a candidate Cibiobacter sp. Despite the decreased nucleotide accuracy compared with alternative sequencing and assembly approaches, our methods improved assembly contiguity, allowing for investigation of the role of repeat elements in microbial function and adaptation.}, } @article {pmid32041654, year = {2020}, author = {Cheaib, B and Seghouani, H and Ijaz, UZ and Derome, N}, title = {Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbations.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {14}, pmid = {32041654}, issn = {2049-2618}, mesh = {Animals ; Bacteria/*classification/drug effects/pathogenicity ; Bioaccumulation ; Cadmium Chloride/*pharmacology ; High-Throughput Nucleotide Sequencing ; Liver/metabolism ; Metagenomics ; Microbiota/*drug effects ; Perches/metabolism/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Stress, Physiological ; }, abstract = {BACKGROUND: The eco-evolutionary processes ruling post-disturbance microbial assembly remain poorly studied, particularly in host-microbiome systems. The community recovery depends not only on the type, duration, intensity, and gradient of disturbance, but also on the initial community structure, phylogenetic composition, legacy, and habitat (soil, water, host). In this study, yellow perch (Perca flavescens) juveniles were exposed over 90 days to constant and gradual sublethal doses of cadmium chloride. Afterward, the exposure of aquaria tank system to cadmium was ceased for 60 days. The skin, gut and water tank microbiomes in control and treatment groups, were characterized before, during and after the cadmium exposure using 16s rDNA libraries and high throughput sequencing technology (Illumina, Miseq).

RESULTS: Our data exhibited long-term bioaccumulation of cadmium salts in the liver even after two months since ceasing the exposure. The gradient of cadmium disturbance had differential effects on the perch microbiota recovery, including increases in evenness, taxonomic composition shifts, as well as functional and phylogenetic divergence. The perch microbiome reached an alternative stable state in the skin and nearly complete recovery trajectories in the gut communities. The recovery of skin communities showed a significant proliferation of opportunistic fish pathogens (i.e., Flavobacterium). Our findings provide evidence that neutral processes were a much more significant contributor to microbial community turnover in control treatments than in those treated with cadmium, suggesting the role of selective processes in driving community recovery.

CONCLUSIONS: The short-term metallic disturbance of fish development has important long-term implications for host health. The recovery of microbial communities after metallic exposure depends on the magnitude of exposure (constant, gradual), and the nature of the ecological niche (water, skin, and gut). The skin and gut microbiota of fish exposed to constant concentrations of cadmium (CC) were closer to the control negative than those exposed to the gradual concentrations (CV). Overall, our results show that the microbial assembly during the community recovery were both orchestrated by neutral and deterministic processes. Video Abtract.}, } @article {pmid32041001, year = {2020}, author = {Wang, Y and Liu, L and Yang, J and Duan, Y and Luo, Y and Taherzadeh, MJ and Li, Y and Li, H and Awasthi, MK and Zhao, Z}, title = {The diversity of microbial community and function varied in response to different agricultural residues composting.}, journal = {The Science of the total environment}, volume = {715}, number = {}, pages = {136983}, doi = {10.1016/j.scitotenv.2020.136983}, pmid = {32041001}, issn = {1879-1026}, mesh = {China ; *Composting ; Microbiota ; Soil ; *Soil Microbiology ; }, abstract = {Microbial activities are the dynamic core in the soil nutrient cycle. To improve the knowledges about the responses of soil microbial community structure and potential function to long-term cover crops practice. The co-occurrence patterns of soil microbial community structure and functional genes were evaluated using 16SrRNA, ITS and metagenomic technique in 13 years cover crops of orchard grass (OG, Dactylis glomerata L.) with high C/N and white clover (WC, Trifolium repens L.) with low C/N. Conventional tillage (CT) was control. The experiment was implemented in an apple orchard located on the Loess Plateau, China, from 2006 to 2018. We also measured soil physicochemical properties and enzyme activities related to carbon and nitrogen cycling. The conclusions showed that the dominant bacterial phyla were Actinobacteria 27.68% in OG treatment and Proteobacteria 25.89% in WC treatment. Organic matter inputs stimulated growth of the phyla of Actinobacteria, Firmicutes, Chloroflexi, Ascomycota and genera of Bacillus, Blastococcus, Streptomyces and Penicillium. Interestingly, the OG and WC treatments promoted the fungal and bacterial alpha-diversity compared to CT treatment, respectively. In addition, compared to CT treatment, OG treatment was beneficial to the increase of C-cycle enzyme activity, while WC treatment tended to increase the N-cycle enzyme activity. Notably, compared to CT treatment, they both enriched carbon fixation and cycle pathways genes, while WC treatment increased the nitrogen metabolism pathway genes. Moreover, OG treatment was more conducive to the enrichment of carbohydrate enzymes genes involved in the hydrolysis of cellulose and hemicellulose compared to WC treatment. Overall, different quality of plant residues stimulated the specific expressions of soil microbial community structure and function. Long-term planted white clover was effective strategy to improve soil quality.}, } @article {pmid32039051, year = {2019}, author = {Tong, Y and Zheng, L and Qing, P and Zhao, H and Li, Y and Su, L and Zhang, Q and Zhao, Y and Luo, Y and Liu, Y}, title = {Oral Microbiota Perturbations Are Linked to High Risk for Rheumatoid Arthritis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {475}, pmid = {32039051}, issn = {2235-2988}, mesh = {Arthritis, Rheumatoid/*epidemiology ; Bacteria/classification/genetics ; Biodiversity ; Case-Control Studies ; China ; Dysbiosis/*complications ; Female ; *Host Microbial Interactions ; Humans ; Male ; Metagenomics ; Middle Aged ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; Risk Assessment ; }, abstract = {Oral microbial dysbiosis is known to increase susceptibility of an individual to develop rheumatoid arthritis (RA). Individuals at-risk of RA may undergo different phases of disease progression. In this study, we aim to investigate whether and whereby the oral microbiome communities alter prior to symptoms of RA. Seventy-nine saliva samples were collected from 29 high-risk individuals, who were positive for anti-citrullinated protein antibodies (ACPA) and have no clinical arthritis, 27 RA patients and 23 healthy controls (HCs). The salivary microbiome was examined using 16S ribosomal RNA gene sequencing. Alpha and beta diversity analysis and the linear discriminant analysis were applied to examine the bacterial diversity, community structure and discriminatory taxa between three groups, respectively. The correlation between salivary bacteria and autoantibodies were analyzed. In the "pre-clinical" stages, salivary microbial diversity was significantly reduced comparing to RA patients and HCs. In contrast to HCs, like RA patients, individuals at high-risk for RA showed a reduction in the abundance of genus Defluviitaleaceae_UCG-011 and the species Neisseria oralis, but an expansion of Prevotella_6. Unexpectedly, the relative abundance of Porphyromonas gingivalis, reported as opportunistic pathogens for RA development, was significantly decreased in high-risk individuals. Additionally, we identified four genera in the saliva from high-risk individuals positively correlated with serum ACPA titers, and the other two genera inversely displayed. In summary, we observed a characteristic compositional change of salivary microbes in individuals at high-risk for RA, suggesting that oral microbiota dysbiosis occurs in the "pre-clinical" stage of RA and are correlated with systemic autoimmune features.}, } @article {pmid32031567, year = {2021}, author = {Zhu, M and Kang, K and Ning, K}, title = {Meta-Prism: Ultra-fast and highly accurate microbial community structure search utilizing dual indexing and parallel computation.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {1}, pages = {557-567}, doi = {10.1093/bib/bbaa009}, pmid = {32031567}, issn = {1477-4054}, mesh = {Humans ; Metagenomics/*methods/standards ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; Software/standards ; }, abstract = {Microbiome samples are accumulating at an unprecedented speed. As a result, a massive amount of samples have become available for the mining of the intrinsic patterns among them. However, due to the lack of advanced computational tools, fast yet accurate comparisons and searches among thousands to millions of samples are still in urgent need. In this work, we proposed the Meta-Prism method for comparing and searching the microbial community structures amongst tens of thousands of samples. Meta-Prism is at least 10 times faster than contemporary methods serving the same purpose and can provide very accurate search results. The method is based on three computational techniques: dual-indexing approach for sample subgrouping, refined scoring function that could scrutinize the minute differences among samples, and parallel computation on CPU or GPU. The superiority of Meta-Prism on speed and accuracy for multiple sample searches is proven based on searching against ten thousand samples derived from both human and environments. Therefore, Meta-Prism could facilitate similarity search and in-depth understanding among massive number of heterogenous samples in the microbiome universe. The codes of Meta-Prism are available at: https://github.com/HUST-NingKang-Lab/metaPrism.}, } @article {pmid32031212, year = {2020}, author = {Fenske, GJ and Ghimire, S and Antony, L and Christopher-Hennings, J and Scaria, J}, title = {Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {3}, pages = {}, doi = {10.1093/femsec/fiaa022}, pmid = {32031212}, issn = {1574-6941}, mesh = {Animals ; Bacteroidetes/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Swine ; }, abstract = {Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.}, } @article {pmid32028248, year = {2020}, author = {Zhou, J and Zhang, BY and Yu, K and Du, XP and Zhu, JM and Zeng, YH and Cai, ZH}, title = {Functional profiles of phycospheric microorganisms during a marine dinoflagellate bloom.}, journal = {Water research}, volume = {173}, number = {}, pages = {115554}, doi = {10.1016/j.watres.2020.115554}, pmid = {32028248}, issn = {1879-2448}, mesh = {*Dinoflagellida ; Harmful Algal Bloom ; *Microbiota ; Nitrogen ; Phosphorus ; }, abstract = {Harmful algal blooms (HABs) are an ecological concern but relatively few studies have investigated the functional potential of bacterioplankton over a complete algal bloom cycle, which is critical for determining their contribution to the fate of algal blooms. To address this point, we carried out a time-series metagenomic analysis of the functional features of microbial communities at three different Gymnodinium catenatum bloom stages (pre-, peak-, and post-bloom). Different microbial composition were observed during the blooming stages. The environmental parameters and correlation networks co-contribute to microbial variability, and the former explained 38.4% of total variations of the bacterioplankton community composition. Functionally, a range of pathways involved in carbon, nitrogen, phosphorus and sulfur cycling were significantly different during the various HAB stages. Genes associated with carbohydrate-active enzymes, denitrification, and iron oxidation were enriched at the pre-bloom stage; genes involved in reductive citrate cycle for carbon fixation, carbon degradation, nitrification and phosphate transport were enhanced at the peak stage; and relative gene abundance related to sulfur oxidation, vitamin synthesis, and iron transport and storage was increased at the post-bloom stage. The ecological linkage analysis has shown that microbial functional potential especially the C/P/Fe metabolism were significantly linked to the fate of the algal blooms. Taken together, our results demonstrated that microorganisms displayed successional patterns not only at the community level, but also in the metabolic potential on HAB's progression. This work contributes to a growing understanding of microbial structural elasticity and functional plasticity and shed light on the potential mechanisms of microbial-mediated HAB trajectory.}, } @article {pmid32027927, year = {2020}, author = {Fadiji, AE and Babalola, OO}, title = {Metagenomics methods for the study of plant-associated microbial communities: A review.}, journal = {Journal of microbiological methods}, volume = {170}, number = {}, pages = {105860}, doi = {10.1016/j.mimet.2020.105860}, pmid = {32027927}, issn = {1872-8359}, mesh = {Computational Biology/*methods ; Endophytes/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; Zea mays/growth & development/*microbiology ; }, abstract = {Plant microbiota have different effects on the plant which can be beneficial or pathogenic. In this study, we concentrated on beneficial microbes associated with plants using endophytic microbes as a case study. Detailed knowledge of the microbial diversity, abundance, composition, functional genes patterns, and metabolic pathways at genome level could assist in understanding the contributions of microbial community towards plant growth and health. Recently, the study of microbial community has improved greatly with the discovery of next-generation sequencing and bioinformatics technologies. Analysis of next generation sequencing data and a proper computational method plays a key role in examining microbial metagenome. This review presents the general metagenomics and computational methods used in processing plant associated metagenomes with concentration on endophytes. This includes 1) introduction of plant-associated microbiota and the factors driving their diversity. 2) plant metagenome focusing on DNA extraction, verification and quality control. 3) metagenomics methods used in community analysis of endophytes focusing on maize plant and, 4) computational methods used in the study of endophytic microbiomes. Limitations and future prospects of metagenomics and computational methods for the analysis of plant-associated metagenome (endophytic metagenome) were also discussed with the aim of fostering its development. We conclude that there is need to adopt advanced genomic features such as k-mers of random size, which do not depend on annotation and can represent other sequence alternatives.}, } @article {pmid32024572, year = {2020}, author = {Newbold, CJ and Ramos-Morales, E}, title = {Review: Ruminal microbiome and microbial metabolome: effects of diet and ruminant host.}, journal = {Animal : an international journal of animal bioscience}, volume = {14}, number = {S1}, pages = {s78-s86}, doi = {10.1017/S1751731119003252}, pmid = {32024572}, issn = {1751-732X}, mesh = {Animals ; Diet/veterinary ; Fermentation ; *Gastrointestinal Microbiome ; Gene Expression Profiling/veterinary ; *Metabolome ; Metabolomics ; *Metagenome ; Metagenomics ; Methane/*metabolism ; Nitrogen/metabolism ; Phylogeny ; Plant Extracts/metabolism ; *Proteome ; Proteomics ; Rumen/metabolism ; Ruminants/metabolism/*microbiology ; *Transcriptome ; }, abstract = {The rumen contains a great diversity of prokaryotic and eukaryotic microorganisms that allow the ruminant to utilize ligno-cellulose material and to convert non-protein nitrogen into microbial protein to obtain energy and amino acids. However, rumen fermentation also has potential deleterious consequences associated with the emissions of greenhouse gases, excessive nitrogen excreted in manure and may also adversely influence the nutritional value of ruminant products. While several strategies for optimizing the energy and nitrogen use by ruminants have been suggested, a better understanding of the key microorganisms involved and their activities is essential to manipulate rumen processes successfully. Diet is the most obvious factor influencing the rumen microbiome and fermentation. Among dietary interventions, the ban of antimicrobial growth promoters in animal production systems has led to an increasing interest in the use of plant extracts to manipulate the rumen. Plant extracts (e.g. saponins, polyphenol compounds, essential oils) have shown potential to decrease methane emissions and improve the efficiency of nitrogen utilization; however, there are limitations such as inconsistency, transient and adverse effects for their use as feed additives for ruminants. It has been proved that the host animal may also influence the rumen microbial population both as a heritable trait and through the effect of early-life nutrition on microbial population structure and function in adult ruminants. Recent developments have allowed phylogenetic information to be upscaled to metabolic information; however, research effort on cultivation of microorganisms for an in-depth study and characterization is needed. The introduction and integration of metagenomic, transcriptomic, proteomic and metabolomic techniques is offering the greatest potential of reaching a truly systems-level understanding of the rumen; studies have been focused on the prokaryotic population and a broader approach needs to be considered.}, } @article {pmid32024435, year = {2020}, author = {Gough, EK and Bourke, CD and Berejena, C and Shonhai, A and Bwakura-Dangarembizi, M and Prendergast, AJ and Manges, AR}, title = {Strain-level analysis of gut-resident pro-inflammatory viridans group Streptococci suppressed by long-term cotrimoxazole prophylaxis among HIV-positive children in Zimbabwe.}, journal = {Gut microbes}, volume = {11}, number = {4}, pages = {1104-1115}, pmid = {32024435}, issn = {1949-0984}, support = {G0300400/MRC_/Medical Research Council/United Kingdom ; 206225/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; //CIHR/Canada ; MC_U122886353/MRC_/Medical Research Council/United Kingdom ; 108065/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; MC_EX_G0300400/MRC_/Medical Research Council/United Kingdom ; MC_UU_12023/26/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 093768/Z/10/Z/WT_/Wellcome Trust/United Kingdom ; MC_UU_12023/17/MRC_/Medical Research Council/United Kingdom ; G1001190/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; Anti-HIV Agents/therapeutic use ; *Antibiotic Prophylaxis ; Child ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; HIV Infections/drug therapy/*microbiology ; Humans ; Inflammation/microbiology/prevention & control ; Intestines/immunology/microbiology ; Species Specificity ; Streptococcus salivarius/classification/*drug effects/physiology ; Trimethoprim, Sulfamethoxazole Drug Combination/*therapeutic use ; Viridans Streptococci/classification/*drug effects/physiology ; Zimbabwe ; }, abstract = {Antimicrobials have become a mainstay of healthcare in the past century due to their activity against pathogens. More recently, it has become clear that they can also affect health via their impact on the microbiota and inflammation. This may explain some of their clinical benefits despite global increases in antimicrobial resistance (AMR) and reduced antimicrobial effectiveness. We showed in a randomized controlled trial of stopping versus continuing cotrimoxazole prophylaxis among HIV-positive Zimbabwean children taking antiretroviral therapy (ART), that continuation of cotrimoxazole persistently suppressed gut-resident viridans group streptococcal species (VGS) that were associated with intestinal inflammation. In this addendum, we provide a broader overview of how antibiotics can shape the microbiota and use high read-depth whole metagenome sequencing data from our published study to investigate whether (i) the impact of cotrimoxazole on gut VGS and (ii) VGS associated inflammation, is attributable to strain-level variability. We focus on S. salivarius, the VGS species that was most prevalent in the cohort and for which there was sufficient genome coverage to differentiate strains. We demonstrate that suppression of S. salivarius by cotrimoxazole is not strain specific, nor did stool concentration of the pro-inflammatory mediator myeloperoxidase vary by S. salivarius strain. We also show that gut-resident S. salivarius strains present in this study population are distinct from common oral strains. This is the first analysis of how cotrimoxazole prophylaxis used according to international treatment guidelines for children living with HIV influences the gut microbiome at the strain-level. We also provide a detailed review of the literature on the mechanisms by which suppression of VGS may act synergistically with cotrimoxazole's anti-inflammatory effects to reduce gut inflammation. A greater understanding of the sub-clinical effects of antibiotics offers new insights into their responsible clinical use.}, } @article {pmid32023871, year = {2020}, author = {Panyukov, VV and Kiselev, SS and Ozoline, ON}, title = {Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling.}, journal = {International journal of molecular sciences}, volume = {21}, number = {3}, pages = {}, pmid = {32023871}, issn = {1422-0067}, support = {18-14-00348//Russian Science Foundation/ ; 18-07-00899//Российский Фонд Фундаментальных Исследований (РФФИ)/ ; }, mesh = {Algorithms ; Case-Control Studies ; Computational Biology ; Crohn Disease/*genetics/microbiology ; DNA Barcoding, Taxonomic/*methods ; Escherichia coli/classification/*genetics/isolation & purification ; Escherichia coli Infections/*genetics/microbiology ; *Genes, Bacterial ; *Genome, Bacterial ; Humans ; Metagenome ; *Microbiota ; }, abstract = {The need for a comparative analysis of natural metagenomes stimulated the development of new methods for their taxonomic profiling. Alignment-free approaches based on the search for marker k-mers turned out to be capable of identifying not only species, but also strains of microorganisms with known genomes. Here, we evaluated the ability of genus-specific k-mers to distinguish eight phylogroups of Escherichia coli (A, B1, C, E, D, F, G, B2) and assessed the presence of their unique 22-mers in clinical samples from microbiomes of four healthy people and four patients with Crohn's disease. We found that a phylogenetic tree inferred from the pairwise distance matrix for unique 18-mers and 22-mers of 124 genomes was fully consistent with the topology of the tree, obtained with concatenated aligned sequences of orthologous genes. Therefore, we propose strain-specific "barcodes" for rapid phylotyping. Using unique 22-mers for taxonomic analysis, we detected microbes of all groups in human microbiomes; however, their presence in the five samples was significantly different. Pointing to the intraspecies heterogeneity of E. coli in the natural microflora, this also indicates the feasibility of further studies of the role of this heterogeneity in maintaining population homeostasis.}, } @article {pmid32023788, year = {2020}, author = {Wang, M and Xie, X and Wang, M and Wu, J and Zhou, Q and Sun, Y}, title = {The bacterial microbiota in florfenicol contaminated soils: The antibiotic resistome and the nitrogen cycle.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {259}, number = {}, pages = {113901}, doi = {10.1016/j.envpol.2019.113901}, pmid = {32023788}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents/analysis/pharmacology ; *Bacteria/drug effects/genetics ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial/genetics ; *Microbiota ; Nitrogen Cycle ; Soil/chemistry ; *Soil Microbiology ; Thiamphenicol/*analogs & derivatives/analysis/pharmacology ; }, abstract = {Soil antibiotic resistome and the nitrogen cycle are affected by florfenicol addition to manured soils but their interactions have not been fully described. In the present study, antibiotic resistance genes (ARGs) and nitrogen cycle genes possessed by soil bacteria were characterized using real-time fluorescence quantification PCR (qPCR) and metagenomic sequencing in a short-term (30 d) soil model experiment. Florfenicol significantly changed in the abundance of genes conferring resistance to aminoglycosides, β-lactams, tetracyclines and macrolides. And the abundance of Sphingomonadaceae, the protein metabolic and nitrogen metabolic functions, as well as NO reductase, nitrate reductase, nitrite reductase and N2O reductase can also be affected by florfenicol. In this way, ARG types of genes conferring resistance to aminoglycosides, β-lactamases, tetracyclines, colistin, fosfomycin, phenicols and trimethoprim were closely associated with multiple nitrogen cycle genes. Actinobacteria, Chlorobi, Firmicutes, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia played an important role in spreading of ARGs. Moreover, soil physicochemical properties were important factors affecting the distribution of soil flora. This study provides a theoretical basis for further exploration of the transmission regularity and interference mechanism of ARGs in soil bacteria responsible for nitrogen cycle.}, } @article {pmid32023487, year = {2020}, author = {Wang, GH and Berdy, BM and Velasquez, O and Jovanovic, N and Alkhalifa, S and Minbiole, KPC and Brucker, RM}, title = {Changes in Microbiome Confer Multigenerational Host Resistance after Sub-toxic Pesticide Exposure.}, journal = {Cell host & microbe}, volume = {27}, number = {2}, pages = {213-224.e7}, doi = {10.1016/j.chom.2020.01.009}, pmid = {32023487}, issn = {1934-6069}, mesh = {Animals ; Atrazine/metabolism/toxicity ; Bacteria/genetics/isolation & purification/metabolism ; Directed Molecular Evolution ; Drug Resistance/genetics ; *Gastrointestinal Microbiome/drug effects/genetics ; Genes, Bacterial ; Maternal Inheritance ; Metagenomics ; Pesticides/metabolism/*toxicity ; Pseudomonas/genetics/isolation & purification/metabolism ; Serratia marcescens/genetics/isolation & purification/metabolism ; Wasps/drug effects/*microbiology ; Xenobiotics/metabolism/toxicity ; }, abstract = {The gut is a first point of contact with ingested xenobiotics, where chemicals are metabolized directly by the host or microbiota. Atrazine is a widely used pesticide, but the role of the microbiome metabolism of this xenobiotic and the impact on host responses is unclear. We exposed successive generations of the wasp Nasonia vitripennis to subtoxic levels of atrazine and observed changes in the structure and function of the gut microbiome that conveyed atrazine resistance. This microbiome-mediated resistance was maternally inherited and increased over successive generations, while also heightening the rate of host genome selection. The rare gut bacteria Serratia marcescens and Pseudomonas protegens contributed to atrazine metabolism. Both of these bacteria contain genes that are linked to atrazine degradation and were sufficient to confer resistance in experimental wasp populations. Thus, pesticide exposure causes functional, inherited changes in the microbiome that should be considered when assessing xenobiotic exposure and as potential countermeasures to toxicity.}, } @article {pmid32019923, year = {2020}, author = {Carr, VR and Witherden, EA and Lee, S and Shoaie, S and Mullany, P and Proctor, GB and Gomez-Cabrero, D and Moyes, DL}, title = {Abundance and diversity of resistomes differ between healthy human oral cavities and gut.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {693}, pmid = {32019923}, issn = {2041-1723}, support = {EP/S001301/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/International ; BB/M009513/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/International ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/*genetics/isolation & purification ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; *Drug Resistance, Bacterial ; Feces/microbiology ; Gastrointestinal Microbiome ; Humans ; Intestines/*microbiology ; Metagenome ; Mouth/*microbiology ; Phylogeny ; }, abstract = {The global threat of antimicrobial resistance has driven the use of high-throughput sequencing techniques to monitor the profile of resistance genes, known as the resistome, in microbial populations. The human oral cavity contains a poorly explored reservoir of these genes. Here we analyse and compare the resistome profiles of 788 oral cavities worldwide with paired stool metagenomes. We find country and body site-specific differences in the prevalence of antimicrobial resistance genes, classes and mechanisms in oral and stool samples. Within individuals, the highest abundances of antimicrobial resistance genes are found in the oral cavity, but the oral cavity contains a lower diversity of resistance genes compared to the gut. Additionally, co-occurrence analysis shows contrasting ARG-species associations between saliva and stool samples. Maintenance and persistence of antimicrobial resistance is likely to vary across different body sites. Thus, we highlight the importance of characterising the resistome across body sites to uncover the antimicrobial resistance potential in the human body.}, } @article {pmid32019901, year = {2020}, author = {Mancini, N and Peri, F and Rescigno, M and Zanoni, I}, title = {Microbiome studies in the medical sciences and the need for closer multidisciplinary interplay.}, journal = {Science signaling}, volume = {13}, number = {617}, pages = {}, doi = {10.1126/scisignal.aba9911}, pmid = {32019901}, issn = {1937-9145}, support = {R01 AI121066/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metabolic Syndrome/*genetics/metabolism/microbiology ; Metabolomics/methods ; Metagenomics/methods ; Proteomics/methods ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Next-generation sequencing techniques have enabled identification of the microorganisms colonizing mucosal tissues. The International Congress "MicrobiotaMi 2020" (Milan, February 2020) will focus on the mechanisms of microbiota-related functions in health and disease and their clinical application.}, } @article {pmid32019803, year = {2020}, author = {Ruaud, A and Esquivel-Elizondo, S and de la Cuesta-Zuluaga, J and Waters, JL and Angenent, LT and Youngblut, ND and Ley, RE}, title = {Syntrophy via Interspecies H2 Transfer between Christensenella and Methanobrevibacter Underlies Their Global Cooccurrence in the Human Gut.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {32019803}, issn = {2150-7511}, support = {R01 DK093595/DK/NIDDK NIH HHS/United States ; }, mesh = {Acetates/metabolism ; *Body Mass Index ; Butyrates/metabolism ; Clostridiales/genetics/*metabolism ; Feces/microbiology ; Fermentation ; *Gastrointestinal Microbiome ; Humans ; Hydrogen/*metabolism ; Meta-Analysis as Topic ; Methane/metabolism ; Methanobrevibacter/genetics/*metabolism ; Microbial Interactions ; Obesity/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Across human populations, 16S rRNA gene-based surveys of gut microbiomes have revealed that the bacterial family Christensenellaceae and the archaeal family Methanobacteriaceae cooccur and are enriched in individuals with a lean, compared to an obese, body mass index (BMI). Whether these association patterns reflect interactions between metabolic partners, as well as whether these associations play a role in the lean host phenotype with which they associate, remains to be ascertained. Here, we validated previously reported cooccurrence patterns of the two families and their association with a lean BMI with a meta-analysis of 1,821 metagenomes derived from 10 independent studies. Furthermore, we report positive associations at the genus and species levels between Christensenella spp. and Methanobrevibacter smithii, the most abundant methanogen of the human gut. By coculturing three Christensenella spp. with M. smithii, we show that Christensenella spp. efficiently support the metabolism of M. smithii via H2 production far better than Bacteroides thetaiotaomicron does. Christensenella minuta forms flocs colonized by M. smithii even when H2 is in excess. In culture with C. minuta, H2 consumption by M. smithii shifts the metabolic output of C. minuta's fermentation toward acetate rather than butyrate. Together, these results indicate that the widespread cooccurrence of these microorganisms is underpinned by both physical and metabolic interactions. Their combined metabolic activity may provide insights into their association with a lean host BMI.IMPORTANCE The human gut microbiome is made of trillions of microbial cells, most of which are Bacteria, with a subset of Archaea The bacterial family Christensenellaceae and the archaeal family Methanobacteriaceae are widespread in human guts. They correlate with each other and with a lean body type. Whether species of these two families interact and how they affect the body type are unanswered questions. Here, we show that species within these families correlate with each other across people. We also demonstrate that particular species of these two families grow together in dense flocs, wherein the bacteria provide hydrogen gas to the archaea, which then make methane. When the archaea are present, the ratio of bacterial products (which are nutrients for humans) is changed. These observations indicate that when these species grow together, their products have the potential to affect the physiology of their human host.}, } @article {pmid32019684, year = {2020}, author = {Johnson, BM and Gaudreau, MC and Gudi, R and Brown, R and Gilkeson, G and Vasu, C}, title = {Gut microbiota differently contributes to intestinal immune phenotype and systemic autoimmune progression in female and male lupus-prone mice.}, journal = {Journal of autoimmunity}, volume = {108}, number = {}, pages = {102420}, pmid = {32019684}, issn = {1095-9157}, support = {P60 AR062755/AR/NIAMS NIH HHS/United States ; R01 AI073858/AI/NIAID NIH HHS/United States ; R01 AI138511/AI/NIAID NIH HHS/United States ; R21 AI136339/AI/NIAID NIH HHS/United States ; }, mesh = {Age Factors ; Animals ; *Autoimmunity ; Biomarkers ; Disease Models, Animal ; Disease Progression ; Female ; Gastrointestinal Microbiome/*immunology ; Inflammation Mediators/metabolism ; Lupus Erythematosus, Systemic/*etiology/*pathology ; Male ; Metagenome ; Metagenomics/methods ; Mice ; *Phenotype ; Sex Factors ; Transcriptome ; }, abstract = {The risk of developing systemic lupus erythematosus (SLE) is about 9 times higher in women as compared to men. Our recent report, which used (SWRxNZB) F1 (SNF1) mouse model of spontaneous lupus, showed a potential link between immune response initiated in the gut mucosa at juvenile age (sex hormone independent) and SLE susceptibility. Here, using this mouse model, we show that gut microbiota contributes differently to pro-inflammatory immune response in the intestine and autoimmune progression in lupus-prone males and females. We found that gut microbiota composition in male and female littermates are significantly different only at adult ages. However, depletion of gut microbes causes suppression of autoimmune progression only in females. In agreement, microbiota depletion suppressed the pro-inflammatory cytokine response of gut mucosa in juvenile and adult females. Nevertheless, microbiota from females and males showed, upon cross-transfer, contrasting abilities to modulate disease progression. Furthermore, orchidectomy (castration) not only caused changes in the composition of gut microbiota, but also a modest acceleration of autoimmune progression. Overall, our work shows that microbiota-dependent pro-inflammatory immune response in the gut mucosa of females initiated at juvenile ages and androgen-dependent protection of males contribute to gender differences in the intestinal immune phenotype and systemic autoimmune progression.}, } @article {pmid32018061, year = {2020}, author = {Kusakabe, S and Fukushima, K and Yokota, T and Hino, A and Fujita, J and Motooka, D and Nakamura, S and Shibayama, H and Kanakura, Y}, title = {Enterococcus: A Predictor of Ravaged Microbiota and Poor Prognosis after Allogeneic Hematopoietic Stem Cell Transplantation.}, journal = {Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation}, volume = {26}, number = {5}, pages = {1028-1033}, doi = {10.1016/j.bbmt.2020.01.019}, pmid = {32018061}, issn = {1523-6536}, mesh = {Enterococcus/genetics ; *Gastrointestinal Microbiome ; *Hematopoietic Stem Cell Transplantation ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Intestinal flora plays an essential role in regulating immune responses. Changes in the gut flora are associated with poor prognosis after allogeneic hematopoietic stem cell transplantation (HSCT). We aimed to investigate the impact of diverse intestinal flora on survival after allogeneic HSCT. Using next-generation sequencing of the bacterial 16S ribosomal RNA (rRNA) gene, we found that the intestinal microbiota of patients undergoing allogeneic HSCT differed significantly from that of healthy controls. Furthermore, dysbiosis persisted for at least 1 year after transplantation. Interestingly, increased abundance of the genus Enterococcus detected by 16S rRNA sequencing as early as 1 month after transplantation was correlated with poor survival (overall survival at 2 years post-HSCT, 83.9% for patients with <1% relative abundance of Enterococcus and 47.6% for those with ≥1% relative abundance of Enterococcus), which was undetectable by conventional standard stool culture. These findings suggest that detection of Enterococcus by 16S rRNA analysis reflects compromised intestinal flora and may be a promising prognostic indicator.}, } @article {pmid32015529, year = {2020}, author = {Dion, MB and Oechslin, F and Moineau, S}, title = {Phage diversity, genomics and phylogeny.}, journal = {Nature reviews. Microbiology}, volume = {18}, number = {3}, pages = {125-138}, pmid = {32015529}, issn = {1740-1534}, mesh = {Bacteriophages/*classification/*genetics/ultrastructure ; *Biodiversity ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Viral ; Host Microbial Interactions ; Metagenomics ; *Phylogeny ; Recombination, Genetic ; Viral Proteins/genetics ; Virion/ultrastructure ; }, abstract = {Recent advances in viral metagenomics have enabled the rapid discovery of an unprecedented catalogue of phages in numerous environments, from the human gut to the deep ocean. Although these advances have expanded our understanding of phage genomic diversity, they also revealed that we have only scratched the surface in the discovery of novel viruses. Yet, despite the remarkable diversity of phages at the nucleotide sequence level, the structural proteins that form viral particles show strong similarities and conservation. Phages are uniquely interconnected from an evolutionary perspective and undergo multiple events of genetic exchange in response to the selective pressure of their hosts, which drives their diversity. In this Review, we explore phage diversity at the structural, genomic and community levels as well as the complex evolutionary relationships between phages, moulded by the mosaicity of their genomes.}, } @article {pmid32014483, year = {2020}, author = {Li, M and Yue, H and Wang, Y and Guo, C and Du, Z and Jin, C and Ding, K}, title = {Intestinal microbes derived butyrate is related to the immunomodulatory activities of Dendrobium officinale polysaccharide.}, journal = {International journal of biological macromolecules}, volume = {149}, number = {}, pages = {717-723}, doi = {10.1016/j.ijbiomac.2020.01.305}, pmid = {32014483}, issn = {1879-0003}, mesh = {Animals ; Bacteria/classification/drug effects/genetics ; Butyrates/*metabolism/*pharmacology ; Colon/microbiology/pathology ; Dendrobium/*chemistry ; Dietary Carbohydrates ; Fatty Acids, Volatile/analysis ; Female ; Gastrointestinal Microbiome/drug effects ; Glucose ; Glucuronic Acid ; Immunity ; Immunoglobulin M ; Immunologic Factors/*metabolism ; Interleukin-10 ; Intestines/immunology/*microbiology/pathology ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Molecular Weight ; Monosaccharides ; Plant Extracts/chemistry/*pharmacology ; Polysaccharides/*chemistry/isolation & purification/*pharmacology ; Tumor Necrosis Factor-alpha ; }, abstract = {Although immunomodulatory activities of Dendrobium officinale polysaccharide has been investigated for many years, yet the potential contribution of its metabolite derived from intestinal microbes on immunoregulation effect has not been reported. In this study, polysaccharide DOW-5B with average molecular weight of 39.4 kDa was isolated from the stem of Dendrobium officinale Kimura et Migo. The carbohydrate content was 91.97% and no protein was detected. The monosaccharide analysis showed this polysaccharide was composed of glucuronic acid and glucose at a molar ratio (M/G) of 1.2:19.4. Animal test indicated DOW-5B increased the diversity of gut microbiota on mice. Beneficial microbes such as Ruminococcus, Eubacterium, Clostridium, Bifidobacterium, Parabacteroides and Akkermansiamuciniphila increased while harmful bacteria in Proteobacteria decreased. Surprisingly, DOW-5B promoted gut microbes to generate more butyrate and mainly produced by Parabacteroides_sp_HGS0025. Further, we found the health of large intestine as well as immunity response of mice was improved. In addition, Parabacteroides_sp_HGS0025 positively correlated with butyrate, IgM, IL-10, and TNF-α products in intestine and mice blood, respectively. The data suggested that Dendrobium officinale polysaccharide has function on immunity may be mediated by butyrate. It adds new evidence to support the basis of how herbal polysaccharides affect immunity.}, } @article {pmid32013116, year = {2020}, author = {Han, Y and Park, H and Choi, BR and Ji, Y and Kwon, EY and Choi, MS}, title = {Alteration of Microbiome Profile by D-Allulose in Amelioration of High-Fat-Diet-Induced Obesity in Mice.}, journal = {Nutrients}, volume = {12}, number = {2}, pages = {}, pmid = {32013116}, issn = {2072-6643}, support = {NRF-2016R1A2B4011329//National Research Foundation of Korea/ ; 22A20130000161//National Research Foundation of Korea/ ; }, mesh = {Animals ; Diet, High-Fat/*adverse effects ; Dietary Supplements ; Fructose/*administration & dosage/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Male ; Mice ; Mice, Inbred C57BL ; Obesity/*chemically induced/*drug therapy ; }, abstract = {Recently, there has been a global shift in diet towards an increased intake of energy-dense foods that are high in sugars. D-allulose has received attention as a sugar substitute and has been reported as one of the anti-obesity food components; however, its correlation with the intestinal microbial community is not yet completely understood. Thirty-six C57BL/6J mice were divided in to four dietary groups and fed a normal diet (ND), a high-fat diet (HFD, 20% fat, 1% cholesterol, w/w), and a HFD with 5% erythritol (ERY) and D-allulose (ALL) supplement for 16 weeks. A pair-feeding approach was used so that all groups receiving the high-fat diet would have the same calorie intake. As a result, body weight and body fat mass in the ALL group were significantly decreased toward the level of the normal group with a simultaneous decrease in plasma leptin and resistin. Fecal short-chain fatty acid (SCFA) production analysis revealed that ALL induced elevated total SCFA production compared to the other groups. Also, ALL supplement induced the change in the microbial community that could be responsible for improving the obesity based on 16S rRNA gene sequence analysis, and ALL significantly increased the energy expenditure in Day(6a.m to 6pm). Taken together, our findings suggest that 5% dietary ALL led to an improvement in HFD-induced obesity by altering the microbiome community.}, } @article {pmid32011231, year = {2020}, author = {Cepko, LCS and Garling, EE and Dinsdale, MJ and Scott, WP and Bandy, L and Nice, T and Faber-Hammond, J and Mellies, JL}, title = {Myoviridae phage PDX kills enteroaggregative Escherichia coli without human microbiome dysbiosis.}, journal = {Journal of medical microbiology}, volume = {69}, number = {2}, pages = {309-323}, pmid = {32011231}, issn = {1473-5644}, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification ; Bacteriophages/classification/genetics/isolation & purification/*physiology ; Dysbiosis/microbiology ; Escherichia coli/physiology/*virology ; Escherichia coli Infections/microbiology/*therapy ; Female ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Microbiota ; Myoviridae/classification/genetics/isolation & purification/*physiology ; Phylogeny ; }, abstract = {Introduction. Bacteriophage therapy can be developed to target emerging diarrhoeal pathogens, but doing so in the absence of microbiome disruption, which occurs with antibiotic treatment, has not been established.Aim. Identify a therapeutic bacteriophage that kills diarrhoeagenic enteroaggregative Escherichia coli (EAEC) while leaving the human microbiome intact.Methodology. Phages from wastewater in Portland, OR, USA were screened for bacteriolytic activity by overlay assay. One isolated phage, PDX, was classified by electron microscopy and genome sequencing. A mouse model of infection determined whether the phage was therapeutic against EAEC. 16S metagenomic analysis of anaerobic cultures determined whether a normal human microbiome was altered by treatment.Results. Escherichia virus PDX, a member of the strictly lytic family Myoviridae, killed a case-associated EAEC isolate from a child in rural Tennessee in a dose-dependent manner, and killed EAEC isolates from Columbian children. A single dose of PDX (multiplicity of infection: 100) 1 day post-infection reduced EAEC recovered from mouse faeces. PDX also killed EAEC when cultured anaerobically in the presence of human faecal bacteria. While the addition of EAEC reduced the β-diversity of the human microbiota, that of the cultures with either faeces alone, faeces with EAEC and PDX, or with just PDX phage was not different statistically.Conclusion. PDX killed EAEC isolate EN1E-0007 in vivo and in vitro, while not altering the diversity of normal human microbiota in anaerobic culture, and thus could be part of an effective therapy for children in developing countries and those suffering from EAEC-mediated traveller's diarrhoea without causing dysbiosis.}, } @article {pmid32010064, year = {2019}, author = {Saha, M and Ferguson, RMW and Dove, S and Künzel, S and Meichssner, R and Neulinger, SC and Petersen, FO and Weinberger, F}, title = {Salinity and Time Can Alter Epibacterial Communities of an Invasive Seaweed.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2870}, pmid = {32010064}, issn = {1664-302X}, abstract = {The establishment of epibacterial communities is fundamental to seaweed health and fitness, in modulating ecological interactions and may also facilitate adaptation to new environments. Abiotic factors like salinity can determine bacterial abundance, growth and community composition. However, influence of salinity as a driver of epibacterial community composition (until species level) has not been investigated for seaweeds and especially under long time scales. We also do not know how abiotic stressors may influence the 'core' bacterial species of seaweeds. Following an initial (immediately after field collection) sampling of epibacterial community of an invasive red seaweed Agarophyton vermicullophylum, we conducted a long term mesocosm experiment for 5 months, to examine the influence of three different salinities (low, medium and high) at two different time points (3 months after start of experiment and 5 months, i.e., at the end of experiment) on the epibacterial community richness and composition of Agarophyton. Metagenomic sequencing showed that epibacterial communities changed significantly according to salinity and time points sampled. Epibacterial richness was significantly different between low and high salinities at both time points. Epibacterial richness also varied significantly between 3 months (after start of experiment) and 5 months (end of experiment) within low, medium and high salinity level. Irrespective of salinity levels and time points sampled 727 taxa consistently appeared in all Agarophyton samples hinting at the presence of core bacterial species on the surface of the alga. Our results indicate that both salinity and time can be major driving forces in structuring epibacterial communities of seaweeds with respect to richness and β-diversity. We highlight the necessity of conducting long term experiments allowing us to detect and understand epibacterial succession over time on seaweeds.}, } @article {pmid32008578, year = {2020}, author = {Scotti, R and Southern, S and Boinett, C and Jenkins, TP and Cortés, A and Cantacessi, C}, title = {MICHELINdb: a web-based tool for mining of helminth-microbiota interaction datasets, and a meta-analysis of current research.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {10}, pmid = {32008578}, issn = {2049-2618}, mesh = {Animals ; Bacteria/genetics/metabolism ; Data Mining ; Datasets as Topic ; Feces/microbiology ; *Gastrointestinal Microbiome ; Helminthiasis/microbiology/parasitology ; Helminthiasis, Animal/microbiology ; Helminths/*genetics/*physiology ; Humans ; Intestinal Diseases, Parasitic/parasitology ; Metagenome ; Microbiota/*genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; *Software ; }, abstract = {BACKGROUND: The complex network of interactions occurring between gastrointestinal (GI) and extra-intestinal (EI) parasitic helminths of humans and animals and the resident gut microbial flora is attracting increasing attention from biomedical researchers, because of the likely implications for the pathophysiology of helminth infection and disease. Nevertheless, the vast heterogeneity of study designs and microbial community profiling strategies, and of bioinformatic and biostatistical approaches for analyses of metagenomic sequence datasets hinder the identification of bacterial targets for follow-up experimental investigations of helminth-microbiota cross-talk. Furthermore, comparative analyses of published datasets are made difficult by the unavailability of a unique repository for metagenomic sequence data and associated metadata linked to studies aimed to explore potential changes in the composition of the vertebrate gut microbiota in response to GI and/or EI helminth infections.

RESULTS: Here, we undertake a meta-analysis of available metagenomic sequence data linked to published studies on helminth-microbiota cross-talk in humans and veterinary species using a single bioinformatic pipeline, and introduce the 'MICrobiome HELminth INteractions database' (MICHELINdb), an online resource for mining of published sequence datasets, and corresponding metadata, generated in these investigations.

CONCLUSIONS: By increasing data accessibility, we aim to provide the scientific community with a platform to identify gut microbial populations with potential roles in the pathophysiology of helminth disease and parasite-mediated suppression of host inflammatory responses, and facilitate the design of experiments aimed to disentangle the cause(s) and effect(s) of helminth-microbiota relationships. Video abstract.}, } @article {pmid32007775, year = {2020}, author = {Li, G and Xia, X and Zhao, S and Shi, M and Liu, F and Zhu, Y}, title = {The physiological and toxicological effects of antibiotics on an interspecies insect model.}, journal = {Chemosphere}, volume = {248}, number = {}, pages = {126019}, doi = {10.1016/j.chemosphere.2020.126019}, pmid = {32007775}, issn = {1879-1298}, mesh = {Animals ; Anti-Bacterial Agents/*toxicity ; Bacteria/genetics ; Bombyx/drug effects ; Gastrointestinal Microbiome/drug effects ; Gene Expression ; Insect Proteins ; *Insecta ; Intestines/microbiology ; Models, Biological ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Toxicity Tests ; }, abstract = {Silkworm (Bombyx mori L.) has a clear genetic background, parts of which are highly homologous to certain genes related to human hereditary diseases. Thus, the species presents an excellent interspecies model for drug screening and microbe-host interaction studies. Chloramphenicol (CAM) and vancomycin (VCM) are antibiotics commonly used to treat specific bacterial infections in medical care, animal husbandry, and agriculture. However, inappropriate dosages and prolonged therapy increase their risk of toxicity. In this work, we investigated the physiological and toxicological responses of silkworm to combined oral administration of CAM and VCM. Results showed that antibiotics promote the feeding behavior of silkworm and significantly reduce (P < 0.05) intestinal cultivable bacterial counts. Moreover, antibiotics decreased the antioxidant enzyme activities of superoxide dismutase, catalase, glutathione S-transferase, and thioredoxin reductase and caused oxidative damage to the silkworm intestine; the degree of damage was confirmed by histopathology analysis. The gene expression levels of antimicrobial peptides (attacin, lysozyme, and cecropins) were also perturbed by antibiotics. After antibiotic exposure, 16S rRNA metagenomic sequencing revealed increases in the relative abundance of Sphingobium, Burkholderia, Barnesiella, Bacteroides, Bradyrhizobium, Acinetobacter, Phenylobacterium, Plesiomonas, Escherichia/Shigella, and unclassified bacteria, as well as a reduction of Enterococcus. The metabolic and functional profiles of intestinal microbiota, particularly metabolic processes, such as energy, cofactors and vitamins, lipid, amino acid, and carbohydrate metabolisms, changed after antibiotic exposure. In conclusion, our findings reveal that antibiotics exert substantial effects on silkworm. The present study may promote the applications of silkworm as an interspecies model in the medical and pharmaceutical fields.}, } @article {pmid32007505, year = {2020}, author = {Heravi, FS and Zakrzewski, M and Vickery, K and Hu, H}, title = {Host DNA depletion efficiency of microbiome DNA enrichment methods in infected tissue samples.}, journal = {Journal of microbiological methods}, volume = {170}, number = {}, pages = {105856}, doi = {10.1016/j.mimet.2020.105856}, pmid = {32007505}, issn = {1872-8359}, mesh = {Bacteria/classification/*genetics/isolation & purification ; DNA, Bacterial/*genetics ; Diabetic Foot/*microbiology/pathology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Infections/*diagnosis/microbiology ; Metagenomics/methods ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/*methods ; }, abstract = {Shotgun metagenomic sequencing or metagenomic whole genome sequencing is a genome-wide sequencing approach to explore bacterial communities directly from their habitat or sites of infection. However, host DNA contamination in metagenomic sequencing overwhelm low biomass of microbial signals and decrease sensitivity for microbial detection. In this study, we evaluated the host DNA depletion efficiency of four different microbiome DNA enrichment methods (NEBNext Microbiome DNA Enrichment kit, Molzym Ultra-Deep Microbiome Prep, QIAamp DNA Microbiome kit and Zymo HostZERO microbial DNA kit) in diabetic foot infection (DFI) tissue samples using quantitative real-time PCR and their effect on bacterial community composition by 16S ribosomal RNA amplicon sequencing. The host DNA depletion ratio (18S/16S rRNA), the percentage of bacterial DNA component and the microbial community profile of DFI were compared before (control) and after each microbiome DNA enrichment method. There was a significant difference in the 18S/16S rRNA ratio among different microbiome DNA enrichment methods (p <.001). QIAamp and HostZERO method reduced 18S/16S rRNA ratio by 32 and 57 fold than control method respectively. The percentage of bacterial DNA component increased more than ten-fold in QiaAmp (71.0 ± 2.7%) and HostZERO (79.9 ± 3.1%) method respectively than those in control method without host DNA depletion (6.7 ± 0.1%). It demonstrated the host DNA contamination was efficiently depleted and bacterial DNA was effectively enriched in HostZERO and QIAamp methods, attesting to the efficacy of these two methods in shotgun metagenomic sequencing studies. Overall, bacterial community composition of DFI samples was similar between control and microbiome enriched DNA samples.}, } @article {pmid32007292, year = {2020}, author = {Santos-Cortez, RLP and Bhutta, MF and Earl, JP and Hafrén, L and Jennings, M and Mell, JC and Pichichero, ME and Ryan, AF and Tateossian, H and Ehrlich, GD}, title = {Panel 3: Genomics, precision medicine and targeted therapies.}, journal = {International journal of pediatric otorhinolaryngology}, volume = {130 Suppl 1}, number = {Suppl 1}, pages = {109835}, pmid = {32007292}, issn = {1872-8464}, support = {R01 DC015688/DC/NIDCD NIH HHS/United States ; R01 DC012595/DC/NIDCD NIH HHS/United States ; R01 DC002148/DC/NIDCD NIH HHS/United States ; R01 DC000129/DC/NIDCD NIH HHS/United States ; MC_UP_1503/1/MRC_/Medical Research Council/United Kingdom ; R01 DC015004/DC/NIDCD NIH HHS/United States ; R01 AI080935/AI/NIAID NIH HHS/United States ; R13 DC017389/DC/NIDCD NIH HHS/United States ; }, mesh = {Animals ; Ear, Middle/*microbiology ; Genetic Predisposition to Disease/*genetics ; Genomics ; Humans ; Microbiota/genetics ; Otitis Media/drug therapy/*genetics/*microbiology/prevention & control ; Precision Medicine ; }, abstract = {OBJECTIVE: To review the most recent advances in human and bacterial genomics as applied to pathogenesis and clinical management of otitis media.

DATA SOURCES: PubMed articles published since the last meeting in June 2015 up to June 2019.

REVIEW METHODS: A panel of experts in human and bacterial genomics of otitis media was formed. Each panel member reviewed the literature in their respective fields and wrote draft reviews. The reviews were shared with all panel members, and a merged draft was created. The panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019, discussed the review and refined the content. A final draft was made, circulated, and approved by the panel members.

CONCLUSION: Trans-disciplinary approaches applying pan-omic technologies to identify human susceptibility to otitis media and to understand microbial population dynamics, patho-adaptation and virulence mechanisms are crucial to the development of novel, personalized therapeutics and prevention strategies for otitis media.

IMPLICATIONS FOR PRACTICE: In the future otitis media prevention strategies may be augmented by mucosal immunization, combination vaccines targeting multiple pathogens, and modulation of the middle ear microbiome. Both treatment and vaccination may be tailored to an individual's otitis media phenotype as defined by molecular profiles obtained by using rapidly developing techniques in microbial and host genomics.}, } @article {pmid32006845, year = {2020}, author = {Wu, F and You, Y and Werner, D and Jiao, S and Hu, J and Zhang, X and Wan, Y and Liu, J and Wang, B and Wang, X}, title = {Carbon nanomaterials affect carbon cycle-related functions of the soil microbial community and the coupling of nutrient cycles.}, journal = {Journal of hazardous materials}, volume = {390}, number = {}, pages = {122144}, doi = {10.1016/j.jhazmat.2020.122144}, pmid = {32006845}, issn = {1873-3336}, mesh = {Carbon/*administration & dosage ; Carbon Cycle/*drug effects ; Escherichia coli/drug effects ; Microbiota/*drug effects ; Nanostructures/*administration & dosage ; Nitrogen/metabolism ; Nitrogen Fixation ; Phosphorus/metabolism ; Soil Microbiology ; Sulfur/metabolism ; }, abstract = {Many studies have examined changes in soil microbial community structure and composition by carbon nanomaterials (CNMs). Few, however, have investigated their impact on microbial community functions. This study explored how fullerene (C60) and multi-walled carbon nanotubes (M50) altered functionality of an agricultural soil microbial community (Archaea, Bacteria and Eukarya), using microcosm experiments combined with GeoChip microarray. M50 had a stronger effect than C60 on alpha diversity of microbial functional genes; both CNMs increased beta diversity, resulting in functional profiles distinct from the control. M50 exerted a broader, severer impact on microbially mediated nutrient cycles. Together, these two CNMs affected CO2 fixation pathways, microbial degradation of diverse carbohydrates, secondary plant metabolites, lipids and phospholipids, proteins, as well as methanogenesis and methane oxidation. They also suppressed nitrogen fixation, nitrification, dissimilatory nitrogen reduction, eukaryotic assimilatory nitrogen reduction, and anaerobic ammonium oxidation (anammox). Phosphorus and sulfur cycles were less vulnerable; only phytic acid hydrolysis and sulfite reduction were inhibited by M50 but not C60. Network analysis suggested decoupling of nutrient cycles by CNMs, manifesting closer and more hierarchical gene networks. This work reinforces profound impact of CNMs on soil microbial community functions and ecosystem services, laying a path for future investigation in this direction.}, } @article {pmid32006353, year = {2020}, author = {Sadan, T and Aravindakshan, TV and Radhika, G and Anand, LF and Ally, K}, title = {Metagenomic analysis exploring taxonomic diversity of rumen microbial communities in Vechur and crossbred cattle of Kerala state, India.}, journal = {Journal of applied genetics}, volume = {61}, number = {2}, pages = {287-297}, pmid = {32006353}, issn = {2190-3883}, support = {CB/51/81/MVM/2016/GT//Kerala Veterinary and Animal Sciences University/ ; }, mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Cattle ; Classification ; Genetic Variation/*genetics ; India ; Metagenome/*genetics ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; }, abstract = {Rumen, one of the most productive diverse microbial habitats plays a vital role in the breakdown of feed to produce energy for maintenance and milk production in cattle. Culture-based procedures could identify only 10% of microbial species present in the rumen. Kerala, one of the southern states of India, owns only one native cattle breed, the Vechur cattle, which is noted for its short stature, disease resistance and adaptability to hot humid climate. Lower population density and decreased milk production potential of Vechur cattle led to the development of crossbred cattle of Kerala, with higher milk yield. A study was conducted to assess the rumen microbial profile of low productive Vechur cattle and high productive crossbred cattle for a better understanding of the relationship between the host and microbial community. DNA isolated from rumen liquor of five cattle each from both genetic groups maintained on standard ration (forage, concentrate ratio of 50:50) was subjected to whole metagenome sequencing. Bioinformatics and statistical analysis revealed that bacteria followed by archaea and eukaryota dominated in the Vechur cattle as well as the crossbred cattle rumen. Bacterial community was dominated by Bacteroidetes and Firmicutes phyla in both genetic groups with a higher Firmicutes to Bacteroidetes ratio of 0.45 in Vechur cattle. Among archaea, Euryarchaeota was more abundant, which constitute methanogens, contributing 98% of total archaeal reads. Prevalent protozoal genus found in the Vechur cattle rumen was Entodinium and in crossbred cattle rumen was Entamoeba. In Vechur and crossbred cattle rumen, 1086 and 1262 microbial species were observed exclusively and 4731 species were shared between habitats. There was a significant difference in total microbial species abundance between the two genetic groups and Vechur cattle displayed significantly higher microbial diversity compared to crossbred. As per literature, this is presumably the first report of rumen metagenome profile of Vechur cattle, a unique short breed of India.}, } @article {pmid32006175, year = {2020}, author = {Yıldırım, S and Shoskes, D and Kulkarni, S and Laguna, P}, title = {Urinary microbiome in uncomplicated and interstitial cystitis: is there any similarity?.}, journal = {World journal of urology}, volume = {38}, number = {11}, pages = {2721-2731}, pmid = {32006175}, issn = {1433-8726}, mesh = {Acute Disease ; Cystitis/*microbiology ; Cystitis, Interstitial/microbiology ; Humans ; *Microbiota ; }, abstract = {PURPOSE: Acute/uncomplicated cystitis is the most common bacterial infection causing inflammation in the bladder tissues and predominantly diagnosed in women. Interstitial cystitis may too, cause inflammation in the bladder but its etiology has been elusive. Even though the site and symptoms of both diseases are largely shared, state of the urinary microbiome in these disorders have not been comparatively evaluated before. The purpose of this review is to assess and qualitatively compare structure and composition of the urinary microbiome in acute/uncomplicated cystitis and interstitial cystitis.

METHODS AND RESULTS: The available literature in MEDLINE are extensively searched using keywords and screened. Pertinent evidence is carefully assessed and synthesized. We included the original studies with a cohort of medically stable, non-pregnant women with otherwise functionally normal urinary tract and excluded the original articles if the infection in a patient's cohort is accompanied by urinary syndromes such as incontinence and overactive bladder syndrome. A total of six original papers reporting on the urinary microbiome in acute cystitis and nine papers on the interstitial cystitis met the selection criteria.

CONCLUSION: The evidence we have gleaned from the literature on the urinary microbiome associated with the acute and interstitial cystitis does not point to convergence of microbiome similarities between the two diseases. More studies with direct sampling of the bladder tissues besides sampling bladder surfaces are warranted for accurate comparison of microbiome similarity between the two conditions. The future research on interstitial cystitis microbiome should include stratified cohorts with prospective design.}, } @article {pmid32005736, year = {2020}, author = {Alessandri, G and Milani, C and Mancabelli, L and Longhi, G and Anzalone, R and Lugli, GA and Duranti, S and Turroni, F and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {Deciphering the Bifidobacterial Populations within the Canine and Feline Gut Microbiota.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {7}, pages = {}, pmid = {32005736}, issn = {1098-5336}, mesh = {Animals ; Bifidobacterium/*isolation & purification ; Cats/*microbiology ; DNA, Ribosomal Spacer/analysis ; Dogs/*microbiology ; *Gastrointestinal Microbiome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; }, abstract = {During the course of evolution, dogs and cats have been subjected to extensive domestication, becoming the principal companion animals for humans. For this reason, their health care, including their intestinal microbiota, is considered of considerable importance. However, the canine and feline gut microbiota still represent a largely unexplored research area. In the present work, we profiled the microbiota of 23 feline fecal samples by 16S rRNA gene and bifidobacterial internally transcribed spacer (ITS) approaches and compared this information with previously reported data from 138 canine fecal samples. The obtained data allowed the reconstruction of the core gut microbiota of the above-mentioned samples coupled with their classification into distinct community state types at both genus and species levels, identifying Bacteroides, Fusobacterium, and Prevotella 9 as the main bacterial components of the canine and feline gut microbiota. At the species level, the intestinal bifidobacterial gut communities of dogs and cats differed in terms of both species number and composition, as emphasized by a covariance analysis. Together, our findings show that the intestinal populations of cats and dogs are similar in terms of genus-level taxonomical composition, while at the bifidobacterial species level, clear differences were observed, indicative of host-specific colonization behavior by particular bifidobacterial taxa.IMPORTANCE Currently, domesticated dogs and cats are the most cherished companion animals for humans, and concerns about their health and well-being are therefore important. In this context, the gut microbiota plays a crucial role in maintaining and promoting host health. However, despite the social relevance of domesticated dogs and cats, their intestinal microbial communities are still far from being completely understood. In this study, the taxonomical composition of canine and feline gut microbiota was explored at genus and bifidobacterial species levels, allowing classification of these microbial populations into distinct gut community state types at either of the two investigated taxonomic levels. Furthermore, the reconstruction of core gut microbiota coupled with covariance network analysis based on bifidobacterial internally transcribed spacer (ITS) profiling revealed differences in the bifidobacterial compositions of canine and feline gut microbiota, suggesting that particular bifidobacterial species have developed a selective ability to colonize a specific host.}, } @article {pmid32005194, year = {2020}, author = {Crusell, MKW and Brink, LR and Nielsen, T and Allin, KH and Hansen, T and Damm, P and Lauenborg, J and Hansen, TH and Pedersen, O}, title = {Gestational diabetes and the human salivary microbiota: a longitudinal study during pregnancy and postpartum.}, journal = {BMC pregnancy and childbirth}, volume = {20}, number = {1}, pages = {69}, pmid = {32005194}, issn = {1471-2393}, support = {13-4608//Augustinus Fonden/ ; 10-001605//Aase og Ejnar Danielsens Fond/ ; }, mesh = {Adult ; Blood Glucose ; Body Mass Index ; Diabetes, Gestational/*microbiology ; Female ; Glucose Tolerance Test ; Humans ; Longitudinal Studies ; *Microbiota ; Postpartum Period/*blood ; Pregnancy ; Pregnancy Trimester, Third/*blood ; RNA, Ribosomal, 16S ; Saliva/*microbiology ; }, abstract = {BACKGROUND: An aberrant composition of the salivary microbiota has been found in individuals with type 2 diabetes, and in pregnant women salivary microbiota composition has been associated with preeclampsia and pre-term birth. Pregnant women, who develop gestational diabetes (GDM), have a high risk of developing type 2 diabetes after pregnancy. In the present study we assessed whether GDM is linked to variation in the oral microbial community by examining the diversity and composition of the salivary microbiota.

METHOD: In this observational study the salivary microbiota of pregnant women with GDM (n = 50) and normal glucose regulation (n = 160) in third trimester and 9 months postpartum was assessed by 16S rRNA gene amplicon sequencing of the V1-V3 region. GDM was diagnosed in accordance with the International Association of the Diabetes and Pregnancy Study Groups (IADPSG) criteria. Cross-sectional difference in alpha diversity was assessed using Student's t-test and longitudinal changes were assessed by mixed linear regression. Cross-sectional and longitudinal difference in beta diversity was assessed by permutational multivariate analyses of variance. Differentially abundant genera and OTUs were identified by negative binomial regression.

RESULTS: In the third trimester, two species-level operational taxonomic units (OTUs), while eight OTUs postpartum were differentially abundant in women with GDM compared with normoglycaemic women. OTU richness, Shannon diversity and Pielou evenness decreased from late pregnancy to 9 months after delivery regardless of glycaemic status.

CONCLUSION: GDM is associated with a minor aberration of the salivary microbiota during late pregnancy and postpartum. For unknown reasons richness of the salivary microbiota decreased from late pregnancy to postpartum, which might be explained by the physiological changes of the immune system during human pregnancy.}, } @article {pmid32005134, year = {2020}, author = {Krotman, Y and Yergaliyev, TM and Alexander Shani, R and Avrahami, Y and Szitenberg, A}, title = {Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {9}, pmid = {32005134}, issn = {2049-2618}, mesh = {Animals ; Bacteria/*classification/metabolism ; DNA Barcoding, Taxonomic ; Dysbiosis ; Environmental Pollution/analysis ; Fishes/*microbiology ; Fresh Water/microbiology ; Genetic Variation ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Salinity ; Skin/*microbiology ; Temperature ; }, abstract = {BACKGROUND: Fish skin microbiomes are rarely studied in inland water systems, in spite of their importance for fish health and ecology. This is mainly because fish species distribution often covaries with other biotic and abiotic factors, complicating the study design. We tackled this issue in the northern part of the Jordan River system, in which a few fish species geographically overlap, across steep gradients of water temperature and salinity.

RESULTS: Using 16S rRNA metabarcoding, we studied the water properties that shape the skin bacterial communities, and their interaction with fish taxonomy. To better characterise the indigenous skin community, we excluded bacteria that were equally abundant in the skin samples and in the water samples, from our analysis of the skin samples. With this in mind, we found alpha diversity of the skin communities to be stable across sites, but higher in benthic loaches, compared to other fish. Beta diversity was found to be different among sites and to weakly covary with the dissolved oxygen, when treated skin communities were considered. In contrast, water temperature and conductivity were strong factors explaining beta diversity in the untreated skin communities. Beta diversity differences between co-occurring fish species emerged only for the treated skin communities. Metagenomics predictions highlighted the microbiome functional implications of excluding the water community contamination from the fish skin communities. Finally, we found that human-induced eutrophication promotes dysbiosis of the fish skin community, with signatures relating to fish health.

CONCLUSIONS: Consideration of the background water microbiome when studying fish skin microbiomes, across varying fish species and water properties, exposes patterns otherwise undetected and highlight among-fish-species differences. We suggest that sporadic nutrient pollution events, otherwise undetected, drive fish skin communities to dysbiosis. This finding is in line with a recent study, showing that biofilms capture sporadic pollution events, undetectable by interspersed water monitoring. Video abstract.}, } @article {pmid32004459, year = {2020}, author = {Zhou, W and Spoto, M and Hardy, R and Guan, C and Fleming, E and Larson, PJ and Brown, JS and Oh, J}, title = {Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin.}, journal = {Cell}, volume = {180}, number = {3}, pages = {454-470.e18}, pmid = {32004459}, issn = {1097-4172}, support = {U19 AI142733/AI/NIAID NIH HHS/United States ; P30 CA034196/CA/NCI NIH HHS/United States ; R43 AR073562/AR/NIAMS NIH HHS/United States ; F30 DE027870/DE/NIDCR NIH HHS/United States ; R90 DE022526/DE/NIDCR NIH HHS/United States ; T90 DE021989/DE/NIDCR NIH HHS/United States ; K22 AI119231/AI/NIAID NIH HHS/United States ; U54 NS105539/NS/NINDS NIH HHS/United States ; R21 AR075174/AR/NIAMS NIH HHS/United States ; DP2 GM126893/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; *Evolution, Molecular ; Female ; *Gene Transfer, Horizontal ; Healthy Volunteers ; Host Microbial Interactions/*genetics ; Humans ; Male ; Microbiota/*genetics ; Middle Aged ; Phylogeny ; *Polymorphism, Single Nucleotide ; Skin/*microbiology ; Staphylococcus epidermidis/*genetics/isolation & purification/pathogenicity ; Virulence/genetics ; Young Adult ; }, abstract = {Metagenomic inferences of bacterial strain diversity and infectious disease transmission studies largely assume a dominant, within-individual haplotype. We hypothesize that within-individual bacterial population diversity is critical for homeostasis of a healthy microbiome and infection risk. We characterized the evolutionary trajectory and functional distribution of Staphylococcus epidermidis-a keystone skin microbe and opportunistic pathogen. Analyzing 1,482 S. epidermidis genomes from 5 healthy individuals, we found that skin S. epidermidis isolates coalesce into multiple founder lineages rather than a single colonizer. Transmission events, natural selection, and pervasive horizontal gene transfer result in population admixture within skin sites and dissemination of antibiotic resistance genes within-individual. We provide experimental evidence for how admixture can modulate virulence and metabolism. Leveraging data on the contextual microbiome, we assess how interspecies interactions can shape genetic diversity and mobile gene elements. Our study provides insights into how within-individual evolution of human skin microbes shapes their functional diversification.}, } @article {pmid32002757, year = {2020}, author = {Galloway-Peña, J and Hanson, B}, title = {Tools for Analysis of the Microbiome.}, journal = {Digestive diseases and sciences}, volume = {65}, number = {3}, pages = {674-685}, pmid = {32002757}, issn = {1573-2568}, support = {K01 AI143881/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/*methods/trends ; High-Throughput Nucleotide Sequencing/*methods/trends ; Humans ; Machine Learning/trends ; Metagenomics/*methods/trends ; Microbiota/*physiology ; Sequence Analysis, DNA/*methods/trends ; }, abstract = {Over the past decade, it has become exceedingly clear that the microbiome is a critical factor in human health and disease and thus should be investigated to develop innovative treatment strategies. The field of metagenomics has come a long way in leveraging the advances of next-generation sequencing technologies resulting in the capability to identify and quantify all microorganisms present in human specimens. However, the field of metagenomics is still in its infancy, specifically in regard to the limitations in computational analysis, statistical assessments, standardization, and validation due to vast variability in the cohorts themselves, experimental design, and bioinformatic workflows. This review summarizes the methods, technologies, computational tools, and model systems for characterizing and studying the microbiome. We also discuss important considerations investigators must make when interrogating the involvement of the microbiome in health and disease in order to establish robust results and mechanistic insights before moving into therapeutic design and intervention.}, } @article {pmid32000795, year = {2020}, author = {Mohammad, HA and Madi, NM and Al-Nakib, W}, title = {Analysis of viral diversity in stool samples from infants and children with acute gastroenteritis in Kuwait using Metagenomics approach.}, journal = {Virology journal}, volume = {17}, number = {1}, pages = {10}, pmid = {32000795}, issn = {1743-422X}, mesh = {Acute Disease ; Child ; Child, Preschool ; Diarrhea/virology ; Feces/*virology ; Female ; Gastroenteritis/*virology ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Kuwait ; Male ; *Metagenomics ; RNA, Viral/genetics ; Real-Time Polymerase Chain Reaction ; *Virome ; Viruses/*classification/genetics ; }, abstract = {BACKGROUND: Current molecular target-dependent methods are used to detect only known viruses. However, metagenomics based on next-generation sequencing (NGS) technique is a target-independent assay that enables simultaneous detection and genomic characterisation of all microorganisms present in a sample. In this study, we aimed to develop a metagenomics approach using NGS to identify and characterise viruses in stool samples from infants and children with Acute Gastroenteritis (AGE) in Kuwait.

METHODS: We have investigated 84 stool samples from infants and children aged one month to ten years old with signs and symptoms of gastroenteritis who attended Mubarak Al-Kabeer and Al-Amiri hospitals in Kuwait from January to December 2017. A metagenomics approach using NGS to characterise viruses in clinical samples was used. Also, the commercial Real-Time PCR assay was used to detect viruses causing gastroenteritis.

RESULTS: Metagenomics analysis revealed an average of 280,768 reads in which 5% of the reads were derived from viruses. The analysis of viral sequences verified that single infection of human adenovirus was the leading cause of gastroenteritis among infants and children, which was detected in 23.2% of the patients, followed by a mixed infection of human adenovirus and other viruses, which was detected in 20.9% of patients. Also, the newly discovered viruses known to cause gastroenteritis were detected, such as astrovirus MLB2, primate bocaparvovirus-1, Aichivirus A, cardiovirus, parechovirus A, astrovirus VA4, cosavirus-F, and bufavirus-3. Our results showed 71% agreement (k = 0.445, P = 0.000) between multiplex Real-Time PCR, which is used as a routine diagnostic test and metagenomics approach in the detection of viruses causing gastroenteritis in clinical samples.

CONCLUSION: Despite the difficulties in sample preparation and analysis process, we showed that metagenomics approach is a powerful and promising tool for the detection and characterisation of different viruses in clinical samples.}, } @article {pmid31998300, year = {2019}, author = {Montassier, E and Al-Ghalith, GA and Mathé, C and Le Bastard, Q and Douillard, V and Garnier, A and Guimon, R and Raimondeau, B and Touchefeu, Y and Duchalais, E and Vince, N and Limou, S and Gourraud, PA and Laplaud, DA and Nicot, AB and Soulillou, JP and Berthelot, L}, title = {Distribution of Bacterial α1,3-Galactosyltransferase Genes in the Human Gut Microbiome.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {3000}, pmid = {31998300}, issn = {1664-3224}, mesh = {Bacteria/*classification/*genetics ; Galactosyltransferases/*genetics ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; Microbiota ; Open Reading Frames ; Phylogeny ; }, abstract = {Because of a loss-of-function mutation in the GGTA1 gene, humans are unable to synthetize α1,3-Galactose (Gal) decorated glycans and develop high levels of circulating anti-α1,3-Galactose antibodies (anti-Gal Abs). Anti-Gal Abs have been identified as a major obstacle of organ xenotransplantation and play a role in several host-pathogen relationships including potential susceptibility to infection. Anti-Gal Abs are supposed to stem from immunization against the gut microbiota, an assumption derived from the observation that some pathogens display α1,3-Gal and that antibiotic treatment decreases the level of anti-Gal. However, there is little information to date concerning the microorganisms producing α1,3-Gal in the human gut microbiome. Here, available α1,3-Galactosyltransferase (GT) gene sequences from gut bacteria were selectively quantified for the first time in the gut microbiome shotgun sequences of 163 adult individuals from three published population-based metagenomics analyses. We showed that most of the gut microbiome of adult individuals contained a small set of bacteria bearing α1,3-GT genes. These bacteria belong mainly to the Enterobacteriaceae family, including Escherichia coli, but also to Pasteurellaceae genera, Haemophilus influenza and Lactobacillus species. α1,3-Gal antigens and α1,3-GT activity were detected in healthy stools of individuals exhibiting α1,3-GT bacterial gene sequences in their shotgun data.}, } @article {pmid31997562, year = {2020}, author = {Martinez-Hernandez, F and Luo, E and Tominaga, K and Ogata, H and Yoshida, T and DeLong, EF and Martinez-Garcia, M}, title = {Diel cycling of the cosmopolitan abundant Pelagibacter virus 37-F6: one of the most abundant viruses on earth.}, journal = {Environmental microbiology reports}, volume = {12}, number = {2}, pages = {214-219}, doi = {10.1111/1758-2229.12825}, pmid = {31997562}, issn = {1758-2229}, support = {5334//Gordon and Betty Moore Foundation/International ; RTI2018-094248-B-I00//Secretaría de Estado de Investigación, Desarrollo e Innovación/International ; 329108//Simons Foundation/International ; ACIF/2015/332//Generalitat Valenciana/International ; }, mesh = {Alphaproteobacteria/physiology/*virology ; *Bacteriophages/genetics/physiology ; Circadian Rhythm/*physiology ; Gene Expression Profiling/methods ; Genome, Bacterial ; Genome, Viral ; Metagenomics/methods ; Oceans and Seas ; *Seawater/microbiology/virology ; Transcriptome ; Virome ; }, abstract = {The spatiotemporal dynamics for marine viral populations has only recently been explored. However, nothing is known about temporal activities of the uncultured Pelagibacter virus vSAG 37-F6, which was discovered by single-virus genomics as potentially the most abundant marine virus. Here, we investigate the diel cycling of 37-F6 virus and the putative SAR11 host using coastal and oceanic transcriptomic and viromic time-series data from Osaka Bay and North Pacific Subtropical Gyre. Virus 37-F6 and relatives displayed diel cycling of transcriptional activities synchronized with its putative host. In both virus and host, the lowest transcription rates were observed at 14:00-15:00, coinciding roughly with maximum solar irradiance, while higher transcriptional rates were detected during the night/early morning and afternoon. Diel abundance of free viruses of 37-F6 in seawater roughly mirrored the transcriptional activities of both virus and host. In Osaka Bay, among viral relatives (genus level), virus 37-F6 specifically showed the highest ratio of transcriptional activity to virome abundance, a proxy for viral transcriptional activity relative to free viral particle abundance. This high ratio suggests high infection rate efficiencies in vSAG 37-F6 virus compared to viral relatives. Thus, time-series data revealed temporal transcript activities in one of the most abundant viruses in Earth.}, } @article {pmid31996401, year = {2020}, author = {Ditz, B and Christenson, S and Rossen, J and Brightling, C and Kerstjens, HAM and van den Berge, M and Faiz, A}, title = {Sputum microbiome profiling in COPD: beyond singular pathogen detection.}, journal = {Thorax}, volume = {75}, number = {4}, pages = {338-344}, pmid = {31996401}, issn = {1468-3296}, mesh = {Cross-Sectional Studies ; Female ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Longitudinal Studies ; Male ; Microbiota/*genetics ; Pulmonary Disease, Chronic Obstructive/diagnosis/*microbiology ; RNA, Ribosomal, 16S/*genetics ; Sensitivity and Specificity ; Sequence Analysis, RNA ; Sputum/*microbiology ; }, abstract = {Culture-independent microbial sequencing techniques have revealed that the respiratory tract harbours a complex microbiome not detectable by conventional culturing methods. The contribution of the microbiome to chronic obstructive pulmonary disease (COPD) pathobiology and the potential for microbiome-based clinical biomarkers in COPD are still in the early phases of investigation. Sputum is an easily obtainable sample and has provided a wealth of information on COPD pathobiology, and thus has been a preferred sample type for microbiome studies. Although the sputum microbiome likely reflects the respiratory microbiome only in part, there is increasing evidence that microbial community structure and diversity are associated with disease severity and clinical outcomes, both in stable COPD and during the exacerbations. Current evidence has been limited to mainly cross-sectional studies using 16S rRNA gene sequencing, attempting to answer the question 'who is there?' Longitudinal studies using standardised protocols are needed to answer outstanding questions including differences between sputum sampling techniques. Further, with advancing technologies, microbiome studies are shifting beyond the examination of the 16S rRNA gene, to include whole metagenome and metatranscriptome sequencing, as well as metabolome characterisation. Despite being technically more challenging, whole-genome profiling and metabolomics can address the questions 'what can they do?' and 'what are they doing?' This review provides an overview of the basic principles of high-throughput microbiome sequencing techniques, current literature on sputum microbiome profiling in COPD, and a discussion of the associated limitations and future perspectives.}, } @article {pmid31993987, year = {2020}, author = {Farukh, M}, title = {Comparative genomic analysis of selenium utilization traits in different marine environments.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {58}, number = {2}, pages = {113-122}, pmid = {31993987}, issn = {1976-3794}, mesh = {Ecosystem ; Genes, Bacterial/genetics ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; *Oceans and Seas ; Phosphotransferases/*genetics ; Proteobacteria/metabolism ; Selenium/metabolism ; }, abstract = {Selenium (Se) is an essential trace element for many organisms, which is required in the biosynthesis of proteins with selenocysteine, tRNAs with selenouridine, and certain enzymes with Se as a cofactor. Recent large-scale metagenomics projects provide a unique opportunity for studying the global trends of Se utilization in marine environments. Here, we analyzed samples from different marine microbial communities, revealed by the Tara Oceans project, to characterize the Se utilization traits. We found that the selenophosphate synthetase gene, which defines the overall Se utilization, and Se utilization traits are present in all samples. Regions with samples rich and poor in Se utilization traits were categorized. From the analysis of environmental factors, the mesopelagic zone and high temperature (> 15°C) of water are favorable, while geographical location has little influence on Se utilization. All Se utilization traits showed a relatively independent occurrence. The taxonomic classification of Se traits shows that most of the sequences corresponding to Se utilization traits belong to the phylum Proteobacteria. Overall, our study provides useful insights into the general features of Se utilization in ocean samples and may help to understand the evolutionary dynamics of Se utilization in different marine environments.}, } @article {pmid31992859, year = {2020}, author = {Engelberts, JP and Robbins, SJ and de Goeij, JM and Aranda, M and Bell, SC and Webster, NS}, title = {Characterization of a sponge microbiome using an integrative genome-centric approach.}, journal = {The ISME journal}, volume = {14}, number = {5}, pages = {1100-1110}, pmid = {31992859}, issn = {1751-7370}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; Metagenome ; *Microbiota ; Phylogeny ; Porifera/*microbiology ; Symbiosis ; }, abstract = {Marine sponges often host diverse and species-specific communities of microorganisms that are critical for host health. Previous functional genomic investigations of the sponge microbiome have focused primarily on specific symbiont lineages, which frequently make up only a small fraction of the overall community. Here, we undertook genome-centric analysis of the symbiont community in the model species Ircinia ramosa and analyzed 259 unique, high-quality metagenome-assembled genomes (MAGs) that comprised 74% of the I. ramosa microbiome. Addition of these MAGs to genome trees containing all publicly available microbial sponge symbionts increased phylogenetic diversity by 32% within the archaea and 41% within the bacteria. Metabolic reconstruction of the MAGs showed extensive redundancy across taxa for pathways involved in carbon fixation, B-vitamin synthesis, taurine metabolism, sulfite oxidation, and most steps of nitrogen metabolism. Through the acquisition of all major taxa present within the I. ramosa microbiome, we were able to analyze the functional potential of a sponge-associated microbial community in unprecedented detail. Critical functions, such as carbon fixation, which had previously only been assigned to a restricted set of sponge-associated organisms, were actually spread across diverse symbiont taxa, whereas other essential pathways, such as ammonia oxidation, were confined to specific keystone taxa.}, } @article {pmid31992112, year = {2020}, author = {Huang, Z and Pan, Z and Yang, R and Bi, Y and Xiong, X}, title = {The canine gastrointestinal microbiota: early studies and research frontiers.}, journal = {Gut microbes}, volume = {11}, number = {4}, pages = {635-654}, pmid = {31992112}, issn = {1949-0984}, mesh = {Animal Feed ; Animals ; Bacteria/classification/growth & development/isolation & purification ; Diet/veterinary ; Dog Diseases/diet therapy/microbiology ; Dogs/*microbiology ; Dysbiosis/microbiology/veterinary ; Gastrointestinal Diseases/diet therapy/microbiology/veterinary ; *Gastrointestinal Microbiome ; Humans ; Intestines/microbiology ; Metagenomics ; Probiotics/therapeutic use ; }, abstract = {The canine gut microbiota is a complex microbial population that is potentially related to metabolism, immunologic activity and gastrointestinal (GI) diseases. Early studies revealed that the canine gut microbiota was dynamic, and bacterial populations in the adjacent gut segments were similar, with anaerobes predominating. Metagenomics analysis revealed that nutrient contents in the diet modulated bacterial populations and metabolites in the canine gut. Further research revealed significant correlations between dietary factors and canine gut core microbiomes. Canine GI diseases are closely correlated with gut microbiota dysbiosis and metabolic disorders. Probiotic-related therapies can effectively treat canine GI diseases. Recent studies have revealed that the canine gut microbiota is similar to the human gut microbiota, and dietary factors affect both. Studying canine intestinal microorganisms enables clarifying changes in the canine intestinal bacteria under different conditions, simulating human diseases in dog models, and conducting in-depth studies of the interactions between intestinal bacteria and disease.}, } @article {pmid31991477, year = {2020}, author = {Fitzgibbon, G and Mills, KHG}, title = {The microbiota and immune-mediated diseases: Opportunities for therapeutic intervention.}, journal = {European journal of immunology}, volume = {50}, number = {3}, pages = {326-337}, doi = {10.1002/eji.201948322}, pmid = {31991477}, issn = {1521-4141}, support = {16/IA/4468/SFI_/Science Foundation Ireland/Ireland ; 12/RI/2340/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Animals ; Humans ; Microbiota/*immunology ; }, abstract = {A multitude of diverse microorganisms, termed the microbiota, reside in the gut, respiratory tract, skin, and genital tract of humans and other animals. Recent advances in metagenomic sequencing and bioinformatics have enabled detailed characterization of these vital microbial communities. Studies in animal models have uncovered vital previously unrecognized roles for the microbiota in normal function of the immune responses, and when perturbed, in the pathogenesis of diseases of the gastrointestinal tract and lungs, but also at distant sites in the body including the brain. The composition of gut and respiratory microbiota can influence systemic inflammatory responses that mediate asthma, allergy, inflammatory bowel disease, obesity-related diseases, and neurodevelopmental or neurodegenerative conditions. Experiments in mouse models as well as emerging clinical studies have revealed that therapeutic manipulation of the microbiota, using fecal microbiota transplantation, probiotics, or engineered probiotics represent effective nontoxic approaches for the treatment or prevention of Clostridium difficile infection, allergy, and autoimmune diseases and may enhance the efficacy of certain cancer immunotherapeutics. This review discusses how commensal bacteria can influence immune responses that mediate a range of human diseases and how the microbiota are being targeted to treat these diseases, especially those resistant to pharmacological therapies.}, } @article {pmid31990924, year = {2020}, author = {Ericsson, AC and Personett, AR and Rindt, H and Grobman, ME and Reinero, CR}, title = {Respiratory dysbiosis and population-wide temporal dynamics in canine chronic bronchitis and non-inflammatory respiratory disease.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0228085}, pmid = {31990924}, issn = {1932-6203}, support = {K01 OD019924/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacterial Typing Techniques ; Bronchitis, Chronic/*microbiology/pathology ; Bronchoalveolar Lavage Fluid/microbiology ; Case-Control Studies ; Climate ; Dogs ; Dysbiosis/*microbiology/pathology ; Feces/microbiology ; Female ; Humans ; Lung/*microbiology/pathology ; Male ; Microbiota/*genetics ; Pets ; Principal Component Analysis ; RNA, Ribosomal, 16S/classification/*genetics ; }, abstract = {The lungs of people and companion animals are now recognized to harbor diverse, low biomass bacterial communities. While these communities are difficult to characterize using culture-based approaches, targeted molecular methods such as 16S rRNA amplicon sequencing can do so using DNA extracted from samples such as bronchoalveolar lavage fluid (BALF). Previous studies identified a surprisingly uniform composition of the microbiota in the lungs of healthy research dogs living in a controlled environment, however there are no reports of the lung microbiota of client-owned dogs. Moreover, compositional changes in the lung microbiota depending on disease status have been reported in people, suggesting that similar events may occur in dogs, a species subject to several respiratory disease mechanisms analogous to those seen in people. To address these knowledge gaps, BALF samples from client-owned dogs presenting to the University of Missouri Veterinary Health Center for respiratory signs between 2014 and 2017 were processed for and subjected to 16S rRNA sequencing. Based on specific diagnostic criteria, dogs were categorized as Chronic Bronchitis (CB, n = 53) or non-CB (n = 11). Community structure was compared between groups, as well as to historical data from healthy research dogs (n = 16) of a uniform breed and environment. The lung microbiota detected in all client-owned dogs was markedly different in composition from that previously detected in research dogs and contained increased relative abundance of multiple canine fecal and environmental bacteria, likely due to aspiration associated with their clinical signs. While inter-sample diversity differed significantly between samples from CB and non-CB dogs, the variability within both groups made it difficult to discern reproducible bacterial classifiers of disease. During subsequent analyses to identify other sources of variability within the data however, population-wide temporal dynamics in community structure were observed, with substantial changes occurring in late 2015 and again in early 2017. A review of regional climate data indicated that the first change occurred during a historically warm and wet period, suggesting that changes in environmental conditions may be associated with changes in the respiratory microbiota in the context of respiratory disease. As the lung microbiota in humans and other animals is believed to result from repetitive micro-aspirations during health and in certain disease states associated with dyspnea and laryngeal dysfunction, these data support the increased colonization of the lower airways during compromised airway function, and the potential for temporal effects due to putative factors such as climate.}, } @article {pmid31990909, year = {2020}, author = {Kordy, K and Gaufin, T and Mwangi, M and Li, F and Cerini, C and Lee, DJ and Adisetiyo, H and Woodward, C and Pannaraj, PS and Tobin, NH and Aldrovandi, GM}, title = {Contributions to human breast milk microbiome and enteromammary transfer of Bifidobacterium breve.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0219633}, pmid = {31990909}, issn = {1932-6203}, support = {K12 HD052954/HD/NICHD NIH HHS/United States ; }, mesh = {Acinetobacter/genetics/isolation & purification ; Adolescent ; Adult ; *Bacterial Translocation ; Bifidobacterium breve/genetics/*isolation & purification ; Enterobacter/genetics/isolation & purification ; Female ; Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Infant, Newborn ; Intestines/*microbiology ; Mammary Glands, Human/*microbiology ; Metagenomics/methods ; Milk, Human/*microbiology ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; Staphylococcus/genetics/isolation & purification ; Streptococcus/genetics/isolation & purification ; }, abstract = {Increasing evidence supports the importance of the breast milk microbiome in seeding the infant gut. However, the origin of bacteria in milk and the process of milk microbe-mediated seeding of infant intestine need further elucidation. Presumed sources of bacteria in milk include locations of mother-infant and mother-environment interactions. We investigate the role of mother-infant interaction on breast milk microbes. Shotgun metagenomics and 16S rRNA gene sequencing identified milk microbes of mother-infant pairs in breastfed infants and in infants that have never latched. Although breast milk has low overall biomass, milk microbes play an important role in seeding the infant gut. Breast milk bacteria were largely comprised of Staphylococcus, Streptococcus, Acinetobacter, and Enterobacter primarily derived from maternal areolar skin and infant oral sites in breastfeeding pairs. This suggests that the process of breastfeeding is a potentially important mechanism for propagation of breast milk microbes through retrograde flux via infant oral and areolar skin contact. In one infant delivered via Caesarian section, a distinct strain of Bifidobacteria breve was identified in maternal rectum, breast milk and the infant's stool potentially suggesting direct transmission. This may support the existence of microbial translocation of this anaerobic bacteria via the enteromammary pathway in humans, where maternal bacteria translocate across the maternal gut and are transferred to the mammary glands. Modulating sources of human milk microbiome seeding potentially imply opportunities to ultimately influence the development of the infant microbiome and health.}, } @article {pmid31990790, year = {2020}, author = {Wind, TT and Gacesa, R and Vich Vila, A and de Haan, JJ and Jalving, M and Weersma, RK and Hospers, GAP}, title = {Gut microbial species and metabolic pathways associated with response to treatment with immune checkpoint inhibitors in metastatic melanoma.}, journal = {Melanoma research}, volume = {30}, number = {3}, pages = {235-246}, doi = {10.1097/CMR.0000000000000656}, pmid = {31990790}, issn = {1473-5636}, mesh = {Adult ; Aged ; Aged, 80 and over ; Female ; *Gastrointestinal Microbiome ; Humans ; Immune Checkpoint Inhibitors/*therapeutic use ; Male ; Melanoma/*drug therapy ; Metabolic Networks and Pathways/physiology ; Middle Aged ; Skin Neoplasms/*drug therapy ; Treatment Outcome ; Young Adult ; Melanoma, Cutaneous Malignant ; }, abstract = {In patients with metastatic cancer, gut microbiome composition differs between responder and non-responders to immune checkpoint inhibitors. However, there is little consensus on the microbiome taxa associated with response or lack of response. Additionally, recognized confounders of gut microbiome composition have generally not been taken into account. In this study, metagenomic shotgun sequencing was performed on freshly frozen pre-treatment stool samples from 25 patients (12 responders and 13 non-responders) with unresectable metastatic melanoma treated with immune checkpoint inhibitors. We observed no significant differences in alpha-diversity and bacterial prevalence between responders and non-responders (P > 0.05). In a zero-inflated multivariate analysis, correcting for important confounders such as age, BMI and use of antibiotics, 68 taxa showed differential abundance between responders and non-responders (false-discovery rate < 0.05). Cox-regression analysis showed longer overall survival for carriers of Streptococcus parasanguinis [hazard ratio (HR): 6.9] and longer progression-free survival for carriers of Bacteroides massiliensis (HR: 3.79). In contrast, carriership of Peptostreptococcaceae (unclassified species) was associated with shorter overall survival (HR 0.18) and progression-free survival (HR 0.11). Finally, 17 microbial pathways differentially abundant between responder and non-responders were observed. These results underline the association between gut microbiome composition and response to immune checkpoint inhibitor therapy in a cohort of patients with cutaneous melanoma.}, } @article {pmid31990220, year = {2020}, author = {Dinleyici, M and Pérez-Brocal, V and Arslanoglu, S and Aydemir, O and Ozumut, SS and Tekin, N and Vandenplas, Y and Moya, A and Dinleyici, EC}, title = {Human milk mycobiota composition: relationship with gestational age, delivery mode, and birth weight.}, journal = {Beneficial microbes}, volume = {11}, number = {2}, pages = {151-162}, doi = {10.3920/BM2019.0158}, pmid = {31990220}, issn = {1876-2891}, mesh = {Adult ; *Birth Weight ; Delivery, Obstetric/*methods ; Female ; Fungi/isolation & purification ; *Gestational Age ; Humans ; Male ; Milk, Human/*microbiology ; Mothers ; *Mycobiome ; Weight Gain ; Young Adult ; }, abstract = {Intestinal and human milk microbiota studies during infancy have shown variations according to geographical location, delivery mode, gestational age, and mother-related factors during pregnancy. In this study, we performed metagenomic mycobiota analyses of 44 transient and mature human milk among five different groups: mothers of normal spontaneous delivery-term (NS-T), caesarean delivery-term (CS-T), premature (PT), small for gestational age (SGA), and large for gestational age (LGA) infants. Fungi were detected in 80 out of the 88 samples. Regarding the number of observed fungal species, the NS-T group was more homogeneous (less variable) comparing the other groups (P<0.05). In the transient human milk samples, the most abundant species were Saccharomyces cerevisiae (33.3%) and Aspergillus glaucus (27.4%). While A. glaucus (33.7%) was second most abundant species in mature milk, S. cerevisiae disappeared (P<0.01) and Penicillium rubens became the most abundant species (35.5%) (P<0.05). Among the NS-T group, the most abundant species was Malassezia globosa in both transient and mature milk. In contrast, S. cerevisiae was the most abundant species in transient human milk (45.0%) in the CS-T group, but it disappeared in mature milk (P<0.01). In transient milk, M. globosa was only represented 6.0-9.0% of taxa in the PT, SGA, and LGA groups (P<0.05). In transient and mature milk in the PT, SGA and LGA groups, the most abundant species were A. glaucus and P. rubens. In mature milk samples, P. rubens is more abundant in CS-T group, PT group and LGA group, than the NS-T groups (P<0.05 for all). Although fungi constitute only a very small part of the human milk microbiome, we observed some changes that the human milk mycobiota composition varies in caesarean delivery, premature, SGA and LGA groups, comparing the normal spontaneous delivery, as well as differences between transient and mature human milk.}, } @article {pmid31989644, year = {2020}, author = {Osei Sekyere, J and Maningi, NE and Fourie, PB}, title = {Mycobacterium tuberculosis, antimicrobials, immunity, and lung-gut microbiota crosstalk: current updates and emerging advances.}, journal = {Annals of the New York Academy of Sciences}, volume = {1467}, number = {1}, pages = {21-47}, doi = {10.1111/nyas.14300}, pmid = {31989644}, issn = {1749-6632}, mesh = {Animals ; Anti-Infective Agents/*therapeutic use ; Gastrointestinal Microbiome/*immunology ; Humans ; Lung/*microbiology ; Mice ; *Mycobacterium tuberculosis ; Tuberculosis/*drug therapy/microbiology ; }, abstract = {Increasingly, gut microbiota distortions are being implicated in the pathogenesis of several infectious and noninfectious diseases. Specifically, in the absence of an eubiotic microbiota, mice are more prone to colonization and infection by Mycobacterium tuberculosis (Mtb). In this qualitative analysis, the following were observed: (1) antimicrobials cause long-term gut microbiota perturbations; (2) Mtb causes limited and transient disturbances to the lung-gut microbiota; (3) pathogens (e.g., Helicobacter hepaticus) affect microbiota integrity and reduce resistance to Mtb; (4) dysbiosis depletes bacterial species regulating proper immune functioning, reducing resistance to Mtb; (5) dysregulated immune cells fail to express important pathogen-recognition receptors (e.g., macrophage-inducible C-type lectin; MINCLE) and Mtb-killing cytokines (e.g., IFN-γ, TNF-α, and IL-17), with hampered phagocytic capability; (6) autophagy is central to the immune system's clearance of Mtb, control of inflammation, and immunity-microbiome balance; (7) microbiota-produced short-chain fatty acids, which are reduced by dysbiosis, affect immune cells and increase Mtb proliferation; (8) commensal species (e.g., Lactobacillus plantarum) and microbiota metabolites (e.g., indole propionic acid) reduce tuberculosis progression; and (9) fecal transplants mostly restored eubiosis, increased immune resistance to Mtb, restricted dissemination of Mtb, and reduced tuberculosis-associated organ pathologies. Overuse of antimicrobials, as shown in mice, is a risk factor for reactivating latent or treated tuberculosis.}, } @article {pmid31988585, year = {2020}, author = {Lv, XY and Ding, HG and Zheng, JF and Fan, CL and Li, L}, title = {Rifaximin improves survival in cirrhotic patients with refractory ascites: A real-world study.}, journal = {World journal of gastroenterology}, volume = {26}, number = {2}, pages = {199-218}, pmid = {31988585}, issn = {2219-2840}, mesh = {Aged ; Anti-Bacterial Agents/pharmacology/*therapeutic use ; Ascites/*drug therapy/immunology/microbiology/mortality ; Bacterial Infections/*drug therapy/immunology/microbiology/mortality ; Drug Resistance ; Female ; Gastrointestinal Microbiome/drug effects/immunology ; Humans ; Liver Cirrhosis/complications/*drug therapy/microbiology/mortality ; Male ; Middle Aged ; Peritonitis/*drug therapy/immunology/microbiology/mortality ; Rifaximin/pharmacology/*therapeutic use ; Treatment Outcome ; }, abstract = {BACKGROUND: Rifaximin has been shown to reduce the incidence of hepatic encephalopathy and other complications in patients with cirrhosis. However, few studies have investigated the effect of rifaximin in cirrhotic patients with refractory ascites.

AIM: To evaluate the effects of rifaximin in the treatment of refractory ascites and to preliminarily explore its possible mechanism.

METHODS: A total of 75 cirrhotic patients with refractory ascites were enrolled in the study (50 in a rifaximin and 25 in a control group). Patients in the rifaximin group were divided into two subgroups according to the presence of spontaneous bacterial peritonitis and treatment with or without other antibiotics (19 patients treated with rifaximin and 31 patients treated with rifaximin plus intravenous antibiotics). All patients received conventional treatment for refractory ascites, while patients in the rifaximin group received oral rifaximin-α 200 mg four times daily for at least 2 wk. The ascites grade, fasting weight, liver and kidney function, and inflammatory factors in the plasma were evaluated before and after treatment. In addition, the gut microbiota was determined by metagenomics sequencing to analyse the changes in the characteristics of the gut microbiota before and after rifaximin treatment. The patients were followed for 6 mo.

RESULTS: Compared with the control group, the fasting weight of patients significantly decreased and the ascites significantly subsided after treatment with rifaximin (P = 0.011 and 0.009, respectively). The 6-mo survival rate of patients in the rifaximin group was significantly higher than that in the control group (P = 0.048). The concentration of interferon-inducible protein 10 decreased significantly in the rifaximin group compared with that in the control group (P = 0.024). The abundance of Roseburia, Haemophilus, and Prevotella was significantly reduced after rifaximin treatment, while the abundance of Lachnospiraceae_noname, Subdoligranulum, and Dorea decreased and the abundance of Coprobacillus increased after treatment with rifaximin plus intravenous antibiotics. The gene expression of virulence factors was significantly reduced after treatment in both subgroups treated with rifaximin or rifaximin plus intravenous antibiotics.

CONCLUSION: Rifaximin mitigates ascites and improves survival of cirrhotic patients with refractory ascites. A possible mechanism is that rifaximin regulates the structure and function of intestinal bacteria, thus improving the systemic inflammatory state.}, } @article {pmid31988303, year = {2020}, author = {Bruce-Keller, AJ and Richard, AJ and Fernandez-Kim, SO and Ribnicky, DM and Salbaum, JM and Newman, S and Carmouche, R and Stephens, JM}, title = {Fenugreek Counters the Effects of High Fat Diet on Gut Microbiota in Mice: Links to Metabolic Benefit.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {1245}, pmid = {31988303}, issn = {2045-2322}, support = {P20 GM103528/GM/NIGMS NIH HHS/United States ; P30 DK072476/DK/NIDDK NIH HHS/United States ; P50 AT002776/AT/NCCIH NIH HHS/United States ; R01 AT010279/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; Blood Glucose ; Body Weight/drug effects ; Diet, High-Fat/*adverse effects ; Dietary Supplements ; Disease Models, Animal ; Dyslipidemias/prevention & control ; Gastrointestinal Microbiome/*drug effects ; Glucose/metabolism ; Glucose Intolerance/prevention & control ; Hyperlipidemias/drug therapy ; Male ; Mice ; Mice, Inbred C57BL ; Obesity/drug therapy/microbiology ; Plant Extracts/metabolism/*pharmacology ; RNA, Ribosomal, 16S/genetics ; Trigonella/metabolism ; }, abstract = {Fenugreek (Trigonella foenum-graecum) is an annual herbaceous plant and a staple of traditional health remedies for metabolic conditions including high cholesterol and diabetes. While the mechanisms of the beneficial actions of fenugreek remain unknown, a role for intestinal microbiota in metabolic homeostasis is likely. To determine if fenugreek utilizes intestinal bacteria to offset the adverse effects of high fat diets, C57BL/6J mice were fed control/low fat (CD) or high fat (HFD) diets each supplemented with or without 2% (w/w) fenugreek for 16 weeks. The effects of fenugreek and HFD on gut microbiota were comprehensively mapped and then statistically assessed in relation to effects on metrics of body weight, hyperlipidemia, and glucose tolerance. 16S metagenomic analyses revealed robust and significant effects of fenugreek on gut microbiota, with alterations in both alpha and beta diversity as well as taxonomic redistribution under both CD and HFD conditions. As previously reported, fenugreek attenuated HFD-induced hyperlipidemia and stabilized glucose tolerance without affecting body weight. Finally, fenugreek specifically reversed the dysbiotic effects of HFD on numerous taxa in a manner tightly correlated with overall metabolic function. Collectively, these data reinforce the essential link between gut microbiota and metabolic syndrome and suggest that the preservation of healthy populations of gut microbiota participates in the beneficial properties of fenugreek in the context of modern Western-style diets.}, } @article {pmid31987960, year = {2020}, author = {Mitra, A and Grossman Biegert, GW and Delgado, AY and Karpinets, TV and Solley, TN and Mezzari, MP and Yoshida-Court, K and Petrosino, JF and Mikkelson, MD and Lin, L and Eifel, P and Zhang, J and Ramondetta, LM and Jhingran, A and Sims, TT and Schmeler, K and Okhuysen, P and Colbert, LE and Klopp, AH}, title = {Microbial Diversity and Composition Is Associated with Patient-Reported Toxicity during Chemoradiation Therapy for Cervical Cancer.}, journal = {International journal of radiation oncology, biology, physics}, volume = {107}, number = {1}, pages = {163-171}, pmid = {31987960}, issn = {1879-355X}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; T32 CA101642/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Biodiversity ; Chemoradiotherapy/*adverse effects ; Cohort Studies ; Female ; Gastrointestinal Microbiome/*radiation effects ; Gastrointestinal Tract/*microbiology/*radiation effects ; Humans ; Middle Aged ; Patient Reported Outcome Measures ; *Safety ; Uterine Cervical Neoplasms/drug therapy/*microbiology/radiotherapy/*therapy ; }, abstract = {PURPOSE: Patients receiving pelvic radiation for cervical cancer experience high rates of acute gastrointestinal (GI) toxicity. The association of changes in the gut microbiome with bowel toxicity from radiation is not well characterized.

METHODS AND MATERIALS: Thirty-five patients undergoing definitive chemoradiation therapy (CRT) underwent longitudinal sampling (baseline and weeks 1, 3, and 5) of the gut microbiome and prospective assessment of patient-reported GI toxicity. DNA was isolated from stool obtained at rectal examination and analyzed with 16S rRNA sequencing. GI toxicity was assessed with the Expanded Prostate Cancer Index Composite instrument to evaluate frequency, urgency, and discomfort associated with bowel function. Shannon diversity index was used to characterize alpha (within sample) diversity. Weighted UniFrac principle coordinates analysis was used to compare beta (between sample) diversity between samples using permutational multivariate analysis of variance. Linear discriminant analysis effect size highlighted microbial features that best distinguish categorized patient samples.

RESULTS: Gut microbiome diversity continuously decreased over the course of CRT, with the largest decrease at week 5. Expanded Prostate Cancer Index Composite bowel function scores also declined over the course of treatment, reflecting increased symptom burden. At all individual time points, higher diversity of the gut microbiome was linearly correlated with better patient-reported GI function, but baseline diversity was not predictive of eventual outcome. Patients with high toxicity demonstrated different compositional changes during CRT in addition to compositional differences in Clostridia species.

CONCLUSIONS: Over time, increased radiation toxicity is associated with decreased gut microbiome diversity. Baseline diversity is not predictive of end-of-treatment bowel toxicity, but composition may identify patients at risk for developing high toxicity.}, } @article {pmid31986127, year = {2020}, author = {Wu, Y and Tang, Y and Xiao, NQ and Wang, CH and Tan, ZJ}, title = {Bacterial Lactase Gene Characteristics in Intestinal Contents of Antibiotic-Associated Diarrhea Mice Treated with Debaryomyces hansenii.}, journal = {Medical science monitor : international medical journal of experimental and clinical research}, volume = {26}, number = {}, pages = {e920879}, pmid = {31986127}, issn = {1643-3750}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/*therapeutic use ; Bacteria/drug effects/*genetics ; Base Sequence ; *Biodiversity ; Diarrhea/*drug therapy/*microbiology ; Female ; *Genes, Bacterial ; Intestines/*microbiology ; Lactase/*genetics ; Male ; Mice ; }, abstract = {BACKGROUND Debaryomyces hansenii exhibits a therapeutic effect on antibiotic-associated diarrhea (AAD) by promoting the growth of beneficial intestinal bacteria. Previous research has reported that AAD involves not only dysbacteriosis but also dysfunction of the activity of intestinal enzymes (such as lactase). Enzyme activities can be influenced by many other factors, such as gene expression. The present study showed that D. hansenii has a curative effect on AAD at the lactase gene level. MATERIAL AND METHODS The effect of D. hansenii on the lactase gene from intestinal bacteria in AAD mice was investigated. The diarrhea model was established with a gentamycin sulfate and cefradine capsule mixture. The antibiotic mixture (23.33 mL·kg[-1]·day[-1]) was intragastrically administered for 5 days. Subsequently, half of the diarrhea mice were treated with D. hansenii twice a day for 3 days while the other mice were intragastrically administered with the same volume of distilled water. Next, the intestinal contents were collected, and metagenomic DNA was extracted for high-throughput sequencing analysis. RESULTS The Chao1 and Shannon indices decreased significantly following treatment with D. hansenii (P<0.01 and P<0.05, respectively). Moreover, the clusters in the D. hansenii group mice were quite different from those in the normal group mice and model group mice. Following treatment with D. hansenii, the quantity of lactase genes in Enterobacter sp. 638 and Modestobacter increased markedly, and the richness of intestinal bacterial lactase genes in Fretibacterium recovered. CONCLUSIONS D. hansenii altered the lactase-producing bacterial community structure and promoted the growth of several critical lactase-producing bacteria, such as Enterobacter sp. 638 and Modestobacter.}, } @article {pmid31984532, year = {2020}, author = {Liou, JM and Lee, YC and Wu, MS}, title = {Treatment of Helicobacter pylori infection and its long-term impacts on gut microbiota.}, journal = {Journal of gastroenterology and hepatology}, volume = {35}, number = {7}, pages = {1107-1116}, doi = {10.1111/jgh.14992}, pmid = {31984532}, issn = {1440-1746}, support = {NTU-107L9014-1//Ministry of Education, Taiwan/ ; MOHW107-TDU-B-211-123002//Ministry of Health and Welfare, Taiwan/ ; TCTC 108-2321-B-002-040//Ministry of Science and Technology of Taiwan/ ; MOST 108-2314-B-002-187//Ministry of Science and Technology of Taiwan/ ; MOST 108-2314-B-002-209//Ministry of Science and Technology of Taiwan/ ; NTUH 106-P06//National Taiwan University Hospital/ ; NTUH 107-P05//National Taiwan University Hospital/ ; //Liver Disease Prevention & Treatment Research Foundation, Taiwan/ ; }, mesh = {Anti-Bacterial Agents/*administration & dosage/adverse effects/pharmacology ; Asia ; Bismuth/administration & dosage ; Drug Resistance, Bacterial ; Drug Therapy, Combination ; Gastritis/*drug therapy/*microbiology ; *Gastrointestinal Microbiome/drug effects ; *Helicobacter Infections ; *Helicobacter pylori/drug effects ; Humans ; Levofloxacin/administration & dosage ; }, abstract = {The rising prevalence of antibiotic resistance and the long-term safety following eradication therapy are important issues in the management of Helicobacter pylori infection. The prevalence of clarithromycin, levofloxacin, and metronidazole resistance of H. pylori has increased to 21%, 27%, and 45%, respectively, in the Asia-Pacific region. Personalized treatment guided by susceptibility testing may provide a reliably excellent eradication rate in the first-line treatment but is costly and not widely available. Population-specific empirical therapy according to the local prevalence of antibiotic resistance may be an alternative strategy. Levofloxacin-based therapy and bismuth quadruple therapy are the recommended second-line rescue therapy. Susceptibility testing or genotypic resistance-guided therapy is the preferred treatment for refractory H. pylori infection, but empirical therapy may be an acceptable alternative. Eradication of H. pylori leads to short-term perturbation of gut microbiota. The diversity of gut microbiota can be restored months after eradication therapy, but the speed of recovery varies with regimens. The short-term increases of antibiotic resistance of Escherichia coli and Klebsiella pneumoniae may be restored to basal states months after H. pylori eradication. Future studies that apply in-depth sequencing, such as shotgun metagenomics sequencing, are needed to clarify whether the compositions of gut microbiota at the species level are fully restored.}, } @article {pmid31982498, year = {2020}, author = {Pan, HW and Du, LT and Li, W and Yang, YM and Zhang, Y and Wang, CX}, title = {Biodiversity and richness shifts of mucosa-associated gut microbiota with progression of colorectal cancer.}, journal = {Research in microbiology}, volume = {171}, number = {3-4}, pages = {107-114}, doi = {10.1016/j.resmic.2020.01.001}, pmid = {31982498}, issn = {1769-7123}, mesh = {Aged ; *Biodiversity ; Colorectal Neoplasms/etiology/*pathology ; Computational Biology/methods ; *Dysbiosis ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics ; Middle Aged ; }, abstract = {The host-associated gut microbiota is considered critical for the occurrence and progression of colorectal cancer (CRC); however, systematic evaluations of the changes in the biodiversity and richness of mucosa-associated gut microbiota with the development of CRC have been limited. Twenty-three paired samples from colorectal tumor sites and the surrounding non-tumor tissues were collected from stage I to IV CRC patients. The microbial compositions of the samples were analyzed by Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene. Gut bacterial alterations at the tumor sites and surrounding healthy tissue sites collected from the different stages of CRC patients were analyzed. No significant differences were observed in the overall microbial richness and biodiversity between the CRC tissue and surrounding non-CRC tissue samples, however, composition and community segregation of the gut microbiota with the progression of CRC were observed. A general increasing trend of Bacteroidetes, Firmicutes, and Fusobacteria and decreasing trend of Proteobacteria were observed at the phylum level with the development of CRC. Further analysis revealed that thirty-four taxa differed significantly with the progression of CRC. Conclusively, our findings provide a comprehensive view of the human mucosa-associated gut microbiota, in association with the different stages of CRC.}, } @article {pmid31980025, year = {2020}, author = {Lee, H and Lee, HK and Min, SK and Lee, WH}, title = {16S rDNA microbiome composition pattern analysis as a diagnostic biomarker for biliary tract cancer.}, journal = {World journal of surgical oncology}, volume = {18}, number = {1}, pages = {19}, pmid = {31980025}, issn = {1477-7819}, support = {2017R1C1B5017902//National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT & Future Planning/ ; NRF-2017M3A9F3047497//National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT & Future Planning/ ; }, mesh = {Adult ; Aged ; Bacteria/classification/genetics/isolation & purification ; Biliary Tract Diseases/microbiology ; Biliary Tract Neoplasms/*microbiology ; Biomarkers, Tumor ; DNA, Ribosomal/genetics ; Extracellular Vesicles/microbiology ; Humans ; *Microbiota/genetics ; Middle Aged ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: The aim of this study is to investigate the composition of microbiota in biliary tract cancer patients and healthy adults by metagenome analysis and evaluate its potential values as biomarkers for biliary tract cancer.

METHODS: Patients who were diagnosed with biliary tract cancer or benign inflammation were enrolled in this study. The control group consisted of healthy adults who presented with no history of significant medical issues. We isolated bacteria-derived extracellular vesicles in the plasma. The microbiome composition was investigated with 16S rDNA metagenome analysis. We evaluated each microbiome to ensure suitability for the biliary tract cancer prediction model.

RESULTS: A total of 155 patients were included in this study: 24 patients with diagnosed biliary tract cancers, 43 diagnosed with cholecystitis or cholangitis, and 88 healthy adults. The microbiome composition pattern of the biliary tract cancer differed from the microbiome composition pattern seen in healthy adult group in beta diversity analysis. The percent composition of microbiota was found to be different from the phylum to genus level. Differences in the composition of the Bifidobacteriaceae and Pseudomonaceae families and Corynebacteriaceae Corynebacterium, Oxalobacteraceae Ralstonia and Comamonadaceae Comamonas species may be used to develop predictive models for biliary tract cancer.

CONCLUSION: Biliary tract cancer patients have altered microbiome composition, which represents a promising biomarker to differentiate malignant biliary tract disease from normal control group.}, } @article {pmid31978162, year = {2020}, author = {Chung, YW and Gwak, HJ and Moon, S and Rho, M and Ryu, JH}, title = {Functional dynamics of bacterial species in the mouse gut microbiome revealed by metagenomic and metatranscriptomic analyses.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0227886}, pmid = {31978162}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/*genetics ; Bacteroidetes/genetics ; Feces/microbiology ; Firmicutes/genetics ; Gastrointestinal Microbiome/*genetics ; Metagenome/*genetics ; *Metagenomics ; Mice ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Transcriptome/genetics ; }, abstract = {BACKGROUND: Microbial communities of the mouse gut have been extensively studied; however, their functional roles and regulation are yet to be elucidated. Metagenomic and metatranscriptomic analyses may allow us a comprehensive profiling of bacterial composition and functions of the complex gut microbiota. The present study aimed to investigate the active functions of the microbial communities in the murine cecum by analyzing both metagenomic and metatranscriptomic data on specific bacterial species within the microbial communities, in addition to the whole microbiome.

RESULTS: Bacterial composition of the healthy mouse gut microbiome was profiled using the following three different approaches: 16S rRNA-based profiling based on amplicon and shotgun sequencing data, and genome-based profiling based on shotgun sequencing data. Consistently, Bacteroidetes, Firmicutes, and Deferribacteres emerged as the major phyla. Based on NCBI taxonomy, Muribaculaceae, Lachnospiraceae, and Deferribacteraceae were the predominant families identified in each phylum. The genes for carbohydrate metabolism were upregulated in Muribaculaceae, while genes for cofactors and vitamin metabolism and amino acid metabolism were upregulated in Deferribacteraceae. The genes for translation were commonly enhanced in all three families. Notably, combined analysis of metagenomic and metatranscriptomic sequencing data revealed that the functions of translation and metabolism were largely upregulated in all three families in the mouse gut environment. The ratio of the genes in the metagenome and their expression in the metatranscriptome indicated higher expression of carbohydrate metabolism in Muribaculum, Duncaniella, and Mucispirillum.

CONCLUSIONS: We demonstrated a fundamental methodology for linking genomic and transcriptomic datasets to examine functional activities of specific bacterial species in a complicated microbial environment. We investigated the normal flora of the mouse gut using three different approaches and identified Muribaculaceae, Lachnospiraceae, and Deferribacteraceae as the predominant families. The functional distribution of these families was reflected in the entire microbiome. By comparing the metagenomic and metatranscriptomic data, we found that the expression rates differed for different functional categories in the mouse gut environment. Application of these methods to track microbial transcription in individuals over time, or before and after administration of a specific stimulus will significantly facilitate future development of diagnostics and treatments.}, } @article {pmid31978143, year = {2020}, author = {De Cesare, A and Sala, C and Castellani, G and Astolfi, A and Indio, V and Giardini, A and Manfreda, G}, title = {Effect of Lactobacillus acidophilus D2/CSL (CECT 4529) supplementation in drinking water on chicken crop and caeca microbiome.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0228338}, pmid = {31978143}, issn = {1932-6203}, mesh = {Animals ; Bacteria/*classification/drug effects/genetics ; Cecum/microbiology ; Chickens/*microbiology ; Crop, Avian/microbiology ; Drinking Water/*chemistry ; Lactobacillus acidophilus/*physiology ; Male ; Metagenomics ; Microbiota/drug effects ; Phylogeny ; Probiotics/*administration & dosage/pharmacology ; Sequence Analysis, DNA ; }, abstract = {In this study we gained insights into the effects of the supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) in the chicken drinking water on crop and caeca microbiomes. The probiotic was supplemented at the concentrations of 0.2 g Lactobacillus acidophilus/day/bird and 0.02 g Lactobacillus acidophilus/day/bird and its effect on the crop and caeca microbiomes was assessed at 14 and 35 days of rearing. The results showed that mean relative abundance of Lactobacillus acidophilus in the caeca did not show significative differences in the treated and control birds, although Lactobacillus acidophilus as well as Faecalibacterium prausnitzii, Lactobacillus crispatus and Lactobacillus reuteri significantly increased over time. Moreover, the treatment with the high dose of probiotic significantly increased the abundance of Clostridium asparagiforme, Clostridium hathewayi and Clostridium saccharolyticum producing butyrate and other organic acids supporting the chicken health. Finally, at 35 days, the Cell division protein FtsH (EC 3.4.24.-) and the Site-specific recombinase genes were significantly increased in the caeca of birds treated with the high dose of probiotic in comparison to the control group. The results of this study showed that Lactobacillus acidophilus D2/CSL (CECT 4529) supplementation in the drinking water at the concentrations of 0.2 and 0.02 g Lactobacillus acidophilus/day/bird improved beneficial microbes and functional genes in broiler crops and caeca. Nevertheless, the main site of action of the probiotic is the crop, at least in the early stage of the chicken life. Indeed, at 14 days Lactobacillus acidophilus was significantly higher in the crops of chickens treated with the high dose of LA in comparison to the control (14.094 vs 1.741%, p = 0.036).}, } @article {pmid31977194, year = {2020}, author = {Chevrette, MG and Handelsman, J}, title = {From Metagenomes to Molecules: Innovations in Functional Metagenomics Unlock Hidden Chemistry in the Human Microbiome.}, journal = {Biochemistry}, volume = {59}, number = {6}, pages = {729-730}, doi = {10.1021/acs.biochem.0c00033}, pmid = {31977194}, issn = {1520-4995}, mesh = {Humans ; Metagenome ; *Metagenomics ; *Microbiota ; }, } @article {pmid31974429, year = {2020}, author = {Radjabzadeh, D and Boer, CG and Beth, SA and van der Wal, P and Kiefte-De Jong, JC and Jansen, MAE and Konstantinov, SR and Peppelenbosch, MP and Hays, JP and Jaddoe, VWV and Ikram, MA and Rivadeneira, F and van Meurs, JBJ and Uitterlinden, AG and Medina-Gomez, C and Moll, HA and Kraaij, R}, title = {Diversity, compositional and functional differences between gut microbiota of children and adults.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {1040}, pmid = {31974429}, issn = {2045-2322}, mesh = {Aged ; Aged, 80 and over ; Bacteria/*classification/genetics/*isolation & purification ; Biosynthetic Pathways/genetics ; Child ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metagenome/genetics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Urban Population ; }, abstract = {The gut microbiota has been shown to play diverse roles in human health and disease although the underlying mechanisms have not yet been fully elucidated. Large cohort studies can provide further understanding into inter-individual differences, with more precise characterization of the pathways by which the gut microbiota influences human physiology and disease processes. Here, we aimed to profile the stool microbiome of children and adults from two population-based cohort studies, comprising 2,111 children in the age-range of 9 to 12 years (the Generation R Study) and 1,427 adult individuals in the range of 46 to 88 years of age (the Rotterdam Study). For the two cohorts, 16S rRNA gene profile datasets derived from the Dutch population were generated. The comparison of the two cohorts showed that children had significantly lower gut microbiome diversity. Furthermore, we observed higher relative abundances of genus Bacteroides in children and higher relative abundances of genus Blautia in adults. Predicted functional metagenome analysis showed an overrepresentation of the glycan degradation pathways, riboflavin (vitamin B2), pyridoxine (vitamin B6) and folate (vitamin B9) biosynthesis pathways in children. In contrast, the gut microbiome of adults showed higher abundances of carbohydrate metabolism pathways, beta-lactam resistance, thiamine (vitamin B1) and pantothenic (vitamin B5) biosynthesis pathways. A predominance of catabolic pathways in children (valine, leucine and isoleucine degradation) as compared to biosynthetic pathways in adults (valine, leucine and isoleucine biosynthesis) suggests a functional microbiome switch to the latter in adult individuals. Overall, we identified compositional and functional differences in gut microbiome between children and adults in a population-based setting. These microbiome profiles can serve as reference for future studies on specific human disease susceptibility in childhood, adulthood and specific diseased populations.}, } @article {pmid31972239, year = {2020}, author = {Nguyen, LH and Ma, W and Wang, DD and Cao, Y and Mallick, H and Gerbaba, TK and Lloyd-Price, J and Abu-Ali, G and Hall, AB and Sikavi, D and Drew, DA and Mehta, RS and Arze, C and Joshi, AD and Yan, Y and Branck, T and DuLong, C and Ivey, KL and Ogino, S and Rimm, EB and Song, M and Garrett, WS and Izard, J and Huttenhower, C and Chan, AT}, title = {Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men.}, journal = {Gastroenterology}, volume = {158}, number = {5}, pages = {1313-1325}, pmid = {31972239}, issn = {1528-0012}, support = {C10674/A27140/CRUK_/Cancer Research UK/United Kingdom ; 27140/CRUK_/Cancer Research UK/United Kingdom ; P30 DK043351/DK/NIDDK NIH HHS/United States ; U01 CA152904/CA/NCI NIH HHS/United States ; K24 DK098311/DK/NIDDK NIH HHS/United States ; K07 CA218377/CA/NCI NIH HHS/United States ; R00 CA215314/CA/NCI NIH HHS/United States ; K01 DK120742/DK/NIDDK NIH HHS/United States ; L30 DK118604/DK/NIDDK NIH HHS/United States ; K99 DK119412/DK/NIDDK NIH HHS/United States ; R35 CA197735/CA/NCI NIH HHS/United States ; K01 DK110267/DK/NIDDK NIH HHS/United States ; R01 CA202704/CA/NCI NIH HHS/United States ; P01 CA055075/CA/NCI NIH HHS/United States ; R01 CA151993/CA/NCI NIH HHS/United States ; U01 CA167552/CA/NCI NIH HHS/United States ; L30 CA209764/CA/NCI NIH HHS/United States ; K23 DK125838/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; T32 CA009001/CA/NCI NIH HHS/United States ; UM1 CA167552/CA/NCI NIH HHS/United States ; }, mesh = {Aged ; Bacteria/isolation & purification/*metabolism ; Colorectal Neoplasms/*epidemiology/microbiology/prevention & control ; Diet Surveys/statistics & numerical data ; Feces/*microbiology ; Feeding Behavior/*physiology ; Follow-Up Studies ; Gastrointestinal Microbiome/*physiology ; Health Personnel/statistics & numerical data ; Humans ; Incidence ; Male ; Massachusetts/epidemiology ; Middle Aged ; Prospective Studies ; Risk Factors ; Sulfur/metabolism ; }, abstract = {BACKGROUND & AIMS: Sulfur-metabolizing microbes, which convert dietary sources of sulfur into genotoxic hydrogen sulfide (H2S), have been associated with development of colorectal cancer (CRC). We identified a dietary pattern associated with sulfur-metabolizing bacteria in stool and then investigated its association with risk of incident CRC using data from a large prospective study of men.

METHODS: We collected data from 51,529 men enrolled in the Health Professionals Follow-up Study since 1986 to determine the association between sulfur-metabolizing bacteria in stool and risk of CRC over 26 years of follow-up. First, in a subcohort of 307 healthy men, we profiled serial stool metagenomes and metatranscriptomes and assessed diet using semiquantitative food frequency questionnaires to identify food groups associated with 43 bacterial species involved in sulfur metabolism. We used these data to develop a sulfur microbial dietary score. We then used Cox proportional hazards modeling to evaluate adherence to this pattern among eligible individuals (n = 48,246) from 1986 through 2012 with risk for incident CRC.

RESULTS: Foods associated with higher sulfur microbial diet scores included increased consumption of processed meats and low-calorie drinks and lower consumption of vegetables and legumes. Increased sulfur microbial diet scores were associated with risk of distal colon and rectal cancers, after adjusting for other risk factors (multivariable relative risk, highest vs lowest quartile, 1.43; 95% confidence interval 1.14-1.81; P-trend = .002). In contrast, sulfur microbial diet scores were not associated with risk of proximal colon cancer (multivariable relative risk 0.86; 95% CI 0.65-1.14; P-trend = .31).

CONCLUSIONS: In an analysis of participants in the Health Professionals Follow-up Study, we found that long-term adherence to a dietary pattern associated with sulfur-metabolizing bacteria in stool was associated with an increased risk of distal CRC. Further studies are needed to determine how sulfur-metabolizing bacteria might contribute to CRC pathogenesis.}, } @article {pmid31971995, year = {2020}, author = {Ben Maamar, S and Glawe, AJ and Brown, TK and Hellgeth, N and Hu, J and Wang, JP and Huttenhower, C and Hartmann, EM}, title = {Mobilizable antibiotic resistance genes are present in dust microbial communities.}, journal = {PLoS pathogens}, volume = {16}, number = {1}, pages = {e1008211}, pmid = {31971995}, issn = {1553-7374}, support = {U19 AI135964/AI/NIAID NIH HHS/United States ; }, mesh = {*Air Pollution, Indoor ; Drug Resistance, Microbial/*genetics ; *Dust ; Environmental Microbiology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Metagenomics ; Microbiota/*genetics ; }, abstract = {The decades-long global trend of urbanization has led to a population that spends increasing amounts of time indoors. Exposure to microbes in buildings, and specifically in dust, is thus also increasing, and has been linked to various health outcomes and to antibiotic resistance genes (ARGs). These are most efficiently screened using DNA sequencing, but this method does not determine which microbes are viable, nor does it reveal whether their ARGs can actually disseminate to other microbes. We have thus performed the first study to: 1) examine the potential for ARG dissemination in indoor dust microbial communities, and 2) validate the presence of detected mobile ARGs in viable dust bacteria. Specifically, we integrated 166 dust metagenomes from 43 different buildings. Sequences were assembled, annotated, and screened for potential integrons, transposons, plasmids, and associated ARGs. The same dust samples were further investigated using cultivation and isolate genome and plasmid sequencing. Potential ARGs were detected in dust isolate genomes, and we confirmed their placement on mobile genetic elements using long-read sequencing. We found 183 ARGs, of which 52 were potentially mobile (associated with a putative plasmid, transposon or integron). One dust isolate related to Staphylococcus equorum proved to contain a plasmid carrying an ARG that was detected metagenomically and confirmed through whole genome and plasmid sequencing. This study thus highlights the power of combining cultivation with metagenomics to assess the risk of potentially mobile ARGs for public health.}, } @article {pmid31971861, year = {2020}, author = {Yang, J and Li, D and Yang, Z and Dai, W and Feng, X and Liu, Y and Jiang, Y and Li, P and Li, Y and Tang, B and Zhou, Q and Qiu, C and Zhang, C and Xu, X and Feng, S and Wang, D and Wang, H and Wang, W and Zheng, Y and Zhang, L and Wang, W and Zhou, K and Li, S and Yu, P}, title = {Establishing high-accuracy biomarkers for colorectal cancer by comparing fecal microbiomes in patients with healthy families.}, journal = {Gut microbes}, volume = {11}, number = {4}, pages = {918-929}, pmid = {31971861}, issn = {1949-0984}, mesh = {Adult ; Aged ; Biomarkers ; China ; Cohort Studies ; Colorectal Neoplasms/*diagnosis/*microbiology ; Feces/*microbiology ; Female ; Firmicutes/classification/genetics/*growth & development ; *Gastrointestinal Microbiome ; Genes, Bacterial ; Humans ; Male ; Metagenomics ; Middle Aged ; }, abstract = {Colorectal cancer (CRC) causes high morbidity and mortality worldwide, and noninvasive gut microbiome (GM) biomarkers are promising for early CRC diagnosis. However, the GM varies significantly based on ethnicity, diet and living environment, suggesting varied GM biomarker performance in different regions. We performed a metagenomic association analysis on stools from 52 patients and 55 corresponding healthy family members who lived together to identify GM biomarkers for CRC in Chongqing, China. The GM of patients differed significantly from that of healthy controls. A total of 22 microbial genes were included as screening biomarkers with high accuracy in additional 46 cases and 40 randomly selected healthy adults in Chongqing (area under the receive-operation curve (AUC) = 0.905, 95% CI 0.832-0.977). The classifier based on the identified 22 biomarkers also performed well in the cohort from Hong Kong (AUC = 0.811, 95% CI 0.715-0.907) and French (AUC = 0.859, 95% CI 0.773-0.944) populations. Quantitative PCR was applied for measuring three selected biomarkers in the classification of CRC patients in independent Chongqing population containing 30 cases and 30 controls and the best biomarker from Coprobacillus performed well with high AUC (0.930, 95% CI 0.904-0.955). This study revealed increased sensitivity and applicability of our GM biomarkers compared with previous biomarkers significantly promoting the early diagnosis of CRC.}, } @article {pmid31968354, year = {2020}, author = {Schulz, F and Roux, S and Paez-Espino, D and Jungbluth, S and Walsh, DA and Denef, VJ and McMahon, KD and Konstantinidis, KT and Eloe-Fadrosh, EA and Kyrpides, NC and Woyke, T}, title = {Giant virus diversity and host interactions through global metagenomics.}, journal = {Nature}, volume = {578}, number = {7795}, pages = {432-436}, pmid = {31968354}, issn = {1476-4687}, mesh = {Animals ; *Biodiversity ; Capsid Proteins/genetics ; DNA Viruses/*classification/*genetics ; Eukaryotic Cells/*metabolism/*virology ; Gene Transfer, Horizontal ; Genome, Viral/genetics ; Giant Viruses/classification/genetics ; Host Microbial Interactions/*genetics ; *Metagenomics ; Phylogeny ; }, abstract = {Our current knowledge about nucleocytoplasmic large DNA viruses (NCLDVs) is largely derived from viral isolates that are co-cultivated with protists and algae. Here we reconstructed 2,074 NCLDV genomes from sampling sites across the globe by building on the rapidly increasing amount of publicly available metagenome data. This led to an 11-fold increase in phylogenetic diversity and a parallel 10-fold expansion in functional diversity. Analysis of 58,023 major capsid proteins from large and giant viruses using metagenomic data revealed the global distribution patterns and cosmopolitan nature of these viruses. The discovered viral genomes encoded a wide range of proteins with putative roles in photosynthesis and diverse substrate transport processes, indicating that host reprogramming is probably a common strategy in the NCLDVs. Furthermore, inferences of horizontal gene transfer connected viral lineages to diverse eukaryotic hosts. We anticipate that the global diversity of NCLDVs that we describe here will establish giant viruses-which are associated with most major eukaryotic lineages-as important players in ecosystems across Earth's biomes.}, } @article {pmid31967575, year = {2020}, author = {Probst, AJ and Vaishampayan, P}, title = {Are we There Yet? Understanding Interplanetary Microbial Hitchhikers using Molecular Methods.}, journal = {Current issues in molecular biology}, volume = {38}, number = {}, pages = {33-52}, doi = {10.21775/cimb.038.033}, pmid = {31967575}, issn = {1467-3045}, mesh = {Adenosine Triphosphate/chemistry ; Bacteria/growth & development/*isolation & purification ; Cell Survival ; *Ecological Systems, Closed ; *Environmental Microbiology ; Extraterrestrial Environment/*chemistry ; Genomics ; Metagenomics ; Microbiota ; RNA, Ribosomal/chemistry/isolation & purification ; *Space Flight ; Spacecraft/standards ; Spores/isolation & purification ; Sterilization ; United States ; United States National Aeronautics and Space Administration ; Weightlessness ; }, abstract = {Since the early time of space travel, planetary bodies undergoing chemical or biological evolution have been of particular interest for life detection missions. NASA's and ESA's Planetary Protection offices ensure responsible exploration of the solar system and aim at avoiding inadvertent contamination of celestial bodies with biomolecules or even living organisms. Life forms that have the potential to colonize foreign planetary bodies could be a threat to the integrity of science objectives of life detection missions. While standard requirements for assessing the cleanliness of spacecraft are still based on cultivation approaches, several molecular methods have been applied in the past to elucidate the full breadth of (micro)organisms that can be found on spacecraft and in cleanrooms, where the hardware is assembled. Here, we review molecular assays that have been applied in Planetary Protection research and list their significant advantages and disadvantages. By providing a comprehensive summary of the latest molecular methods yet to be applied in this research area, this article will not only aid in designing technological roadmaps for future Planetary Protection endeavors but also help other disciplines in environmental microbiology that deal with low biomass samples.}, } @article {pmid31965894, year = {2020}, author = {Lee, NY and Yoon, SJ and Han, DH and Gupta, H and Youn, GS and Shin, MJ and Ham, YL and Kwak, MJ and Kim, BY and Yu, JS and Lee, DY and Park, TS and Park, SH and Kim, BK and Joung, HC and Choi, IS and Hong, JT and Kim, DJ and Han, SH and Suk, KT}, title = {Lactobacillus and Pediococcus ameliorate progression of non-alcoholic fatty liver disease through modulation of the gut microbiome.}, journal = {Gut microbes}, volume = {11}, number = {4}, pages = {882-899}, pmid = {31965894}, issn = {1949-0984}, mesh = {Animals ; Bacteroidetes/growth & development ; Cholesterol/blood ; Cytokines/metabolism ; Diet, Western ; Disease Models, Animal ; Disease Progression ; Firmicutes/growth & development ; *Gastrointestinal Microbiome ; Inflammation/physiopathology ; Lactobacillus/*physiology ; Liver/pathology/physiopathology ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/*microbiology/pathology/physiopathology/*therapy ; Pediococcus pentosaceus/*physiology ; *Probiotics ; }, abstract = {Targeting the gut-liver axis by modulating the gut-microbiome can be a promising therapeutic approach in nonalcoholic fatty liver disease (NAFLD). The aim of this study was to evaluate the effects of single species and a combination of Lactobacillus and Pediococcus in NAFLD mice model. Six-week male C57BL/6J mice were divided into 9 groups (n = 10/group; normal, Western diet, and 7 Western diet-strains [10[9] CFU/g, 8 weeks]). The strains used were L. bulgaricus, L. casei, L. helveticus, P. pentosaceus KID7, and three combinations (1: L. casei+L. helveticus, 2: L. casei+L. helveticus+P. pentosaceus KID7, and 3: L. casei+L. helveticus+L. bulgaricus). Liver/Body weight ratio, serum and stool analysis, liver pathology, and metagenomics by 16S rRNA-sequencing were examined. In the liver/body ratio, L. bulgaricus (5.1 ± 0.5), L. helveticus (5.2 ± 0.4), P. pentosaceus KID7 (5.5 ± 0.5), and combination1 and 2 (4.2 ± 0.6 and 4.8 ± 0.7) showed significant reductions compared with Western (6.2 ± 0.6)(p < 0.001). In terms of cholesterol and steatosis/inflammation/NAFLD activity, all groups except for L. casei were associated with an improvement (p < .05). The elevated level of tumor necrosis factor-α/interleukin-1β (pg/ml) in Western (65.8 ± 7.9/163.8 ± 12.2) was found to be significantly reduced in L. bulgaricus (24.2 ± 1.0/58.9 ± 15.3), L. casei (35.6 ± 2.1/62.9 ± 6.0), L. helveticus (43.4 ± 3.2/53.6 ± 7.5), and P. pentosaceus KID7 (22.9 ± 3.4/59.7 ± 12.2)(p < 0.01). Cytokines were improved in the combination groups. In metagenomics, each strains revealed a different composition and elevated Firmicutes/Bacteroidetes ratio in the western (47.1) was decreased in L. bulgaricus (14.5), L. helveticus (3.0), and P. pentosaceus KID7 (13.3). L. bulgaricus, L. casei, L. helveticus, and P. pentosaceus KID7 supplementation can improve NAFLD-progression by modulating gut-microbiome and inflammatory pathway.}, } @article {pmid31965701, year = {2020}, author = {Muñoz-Arenas, LC and Fusaro, C and Hernández-Guzmán, M and Dendooven, L and Estrada-Torres, A and Navarro-Noya, YE}, title = {Soil microbial diversity drops with land-use change in a high mountain temperate forest: a metagenomics survey.}, journal = {Environmental microbiology reports}, volume = {12}, number = {2}, pages = {185-194}, doi = {10.1111/1758-2229.12822}, pmid = {31965701}, issn = {1758-2229}, support = {Ciencia Básica 256096//Consejo Nacional de Ciencia y Tecnología/International ; Cátedras CONACyT 883//Consejo Nacional de Ciencia y Tecnología/International ; Infraestructura 253217//Consejo Nacional de Ciencia y Tecnología/International ; }, mesh = {Agriculture ; *Altitude ; Archaea/genetics ; Bacteria/genetics ; *Biodiversity ; Ecosystem ; *Forests ; Genes, Viral ; *Metagenome ; Metagenomics/methods ; Mexico ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Viruses/genetics ; }, abstract = {Land-use change has been identified as the most severe threat to biodiversity. Soils are important biodiversity reservoirs, but to what extent conversion of high-altitude temperate forest to arable land affects taxonomic and functional soil biodiversity is still largely unknown. Shotgun metagenomics was used to determine the taxonomic and functional diversity of bacteria, archaea and DNA virus in terms of effective number of species in high-altitude temperate oak and pine-oak forest and arable soils from Mexico. Generally, the soil ecosystem maintained its microbial species richness notwithstanding land-use change. Archaea diversity was not affected by land-use change, but the bacterial diversity decreased with 45-55% when the oak forest was converted to arable land and 65-75% when the pine-oak forest was. Loss in bacterial diversity as a result of land-use change was positively correlated (R[2] = 0.41) with the 10-25% loss in functional diversity. The archaeal communities were evener than the bacterial ones, which might explain their different response to land-use change. We expected a decrease in DNA viral communities as the bacterial diversity decreased, i.e. their potential hosts. However, a higher viral diversity was found in the arable than in the forest soils. It was found that converting high altitude oak and pine-oak forests to arable land more than halved the bacterial diversity, but did not affect the archaeal and even increased the viral diversity.}, } @article {pmid31964729, year = {2020}, author = {Flannery, JE and Stagaman, K and Burns, AR and Hickey, RJ and Roos, LE and Giuliano, RJ and Fisher, PA and Sharpton, TJ}, title = {Gut Feelings Begin in Childhood: the Gut Metagenome Correlates with Early Environment, Caregiving, and Behavior.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {31964729}, issn = {2150-7511}, support = {T32 ES007060/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; *Caregivers ; Child ; *Child Behavior ; *Environment ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Models, Theoretical ; Socioeconomic Factors ; }, abstract = {Psychosocial environments impact normative behavioral development in children, increasing the risk of problem behaviors and psychiatric disorders across the life span. Converging evidence demonstrates that early normative development is affected by the gut microbiome, which itself can be altered by early psychosocial environments. However, much of our understanding of the gut microbiome's role in early development stems from nonhuman animal models and predominately focuses on the first years of life, during peri- and postnatal microbial colonization. As a first step to identify if these findings translate to humans and the extent to which these relationships are maintained after initial microbial colonization, we conducted a metagenomic investigation among a cross-sectional sample of early school-aged children with a range of adverse experiences and caregiver stressors and relationships. Our results indicate that the taxonomic and functional composition of the gut microbiome correlates with behavior during a critical period of child development. Furthermore, our analysis reveals that both socioeconomic risk exposure and child behaviors associate with the relative abundances of specific taxa (e.g., Bacteroides and Bifidobacterium species) as well as functional modules encoded in their genomes (e.g., monoamine metabolism) that have been linked to cognition and health. While we cannot infer causality within this study, these findings suggest that caregivers may moderate the gut microbiome's link to environment and behaviors beyond the first few years of life.IMPORTANCE Childhood is a formative period of behavioral and biological development that can be modified, for better or worse, by the psychosocial environment that is in part determined by caregivers. Not only do our own genes and the external environment influence such developmental trajectories, but the community of microbes living in, on, and around our bodies-the microbiome-plays an important role as well. By surveying the gut microbiomes of a cross-sectional cohort of early school-aged children with a range of psychosocial environments and subclinical mental health symptoms, we demonstrated that caregiving behaviors modified the child gut microbiome's association to socioeconomic risk and behavioral dysregulation.}, } @article {pmid31964728, year = {2020}, author = {Carini, P and Delgado-Baquerizo, M and Hinckley, ES and Holland-Moritz, H and Brewer, TE and Rue, G and Vanderburgh, C and McKnight, D and Fierer, N}, title = {Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {31964728}, issn = {2150-7511}, mesh = {*Metagenome ; *Metagenomics/methods ; Microbial Interactions ; *Microbiota ; RNA, Ribosomal, 16S ; Seasons ; Soil/chemistry ; *Soil Microbiology ; Spatio-Temporal Analysis ; }, abstract = {Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes.IMPORTANCE Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.}, } @article {pmid31963239, year = {2020}, author = {Burton, KJ and Krüger, R and Scherz, V and Münger, LH and Picone, G and Vionnet, N and Bertelli, C and Greub, G and Capozzi, F and Vergères, G}, title = {Trimethylamine-N-Oxide Postprandial Response in Plasma and Urine Is Lower After Fermented Compared to Non-Fermented Dairy Consumption in Healthy Adults.}, journal = {Nutrients}, volume = {12}, number = {1}, pages = {}, pmid = {31963239}, issn = {2072-6643}, support = {14/JP-HDHL/B3076//Joint Programming Initiative A healthy diet for a healthy life/ ; 170280//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, mesh = {Adolescent ; Adult ; Bacteria/*metabolism ; Biomarkers/blood/urine ; Cross-Over Studies ; *Cultured Milk Products ; *Dairy Products ; Double-Blind Method ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Methylamines/*blood/*urine ; *Postprandial Period ; Switzerland ; Young Adult ; }, abstract = {Trimethylamine-N-oxide (TMAO) can be produced by the gut microbiota from dietary substrates and is associated with cardiovascular disease. While dairy products contain TMAO precursors, the effect of fermented dairy on TMAO metabolism remains unclear. We used plasma and urine samples collected for two randomised cross-over studies to evaluate the effects of fermented dairy consumption on TMAO metabolism. In Study 1, thirteen healthy young men tested a yogurt and an acidified milk during postprandial tests and a two-week daily intervention. In Study 2, ten healthy adults tested milk and cheese during postprandial tests. TMAO and five related metabolites were measured in plasma and urine by LC-MS/MS and NMR. Faecal microbiota composition was assessed in Study 1 (16S rRNA metagenomics sequencing). Fermented milk products were associated with lower postprandial TMAO responses than non-fermented milks in urine (Study 1, p = 0.01; Study 2, p = 0.02) and in plasma, comparing yogurt and acidified milk (Study 1, p = 0.04). Daily consumption of dairy products did not differentially affect fasting TMAO metabolites. Significant correlations were observed between microbiota taxa and circulating or urinary TMAO concentrations. Fermentation of dairy products appear, at least transiently, to affect associations between dairy products and circulating TMAO levels.}, } @article {pmid31962124, year = {2020}, author = {Niu, J and Li, XL and Wu, YL and Sun, QZ and Zhang, W and Cao, M and Wang, JJ}, title = {RNA virome screening in diverse but ecologically related citrus pests reveals potential virus-host interactions.}, journal = {Journal of invertebrate pathology}, volume = {170}, number = {}, pages = {107329}, doi = {10.1016/j.jip.2020.107329}, pmid = {31962124}, issn = {1096-0805}, mesh = {Animals ; Gene Library ; *Host-Pathogen Interactions ; Insecta/*virology ; Mites/*virology ; RNA, Viral/*analysis ; Snails/*virology ; *Virome ; }, abstract = {As an evergreen ecosystem, citrus orchards have specialized pest species and stable ecological homeostasis; thus, they provide an ideal model for investigating RNA viromes in diverse but ecologically related species. For this purpose, we collected specialized citrus pests from three classes of invertebrates, Insecta, Arachnida, and Gastropoda and we constructed two kinds of libraries (RNA and small RNA) for the pests by deep sequencing. In total, six virus-derived sequences were identified, including four Picornavirales, one Jingchuvirales and one Nidovirales. The picornavirus-derived small RNAs showed significant small RNA peaks and symmetric distribution patterns along the genome, which suggests these viruses infected the hosts and triggered host antiviral immunity RNA interference. Screening of virus-derived sequences in multiple species of citrus pests (n = 10 per species) showed that Eotetranychus kankitus picorna-like virus and Tetranychus urticae mivirus may be present in multiple pests. Our investigation in citrus pests confirmed that RNA viruses revealed by metagenomics could impact host immunity (e.g. RNAi). An approach with parallel deep sequencing of RNAs and small RNAs is useful not only for viral discoveries but also for understanding virus-host interactions of ecologically related but divergent pest species.}, } @article {pmid31961432, year = {2020}, author = {Jones, CMA and Connors, J and Dunn, KA and Bielawski, JP and Comeau, AM and Langille, MGI and Van Limbergen, J}, title = {Bacterial Taxa and Functions Are Predictive of Sustained Remission Following Exclusive Enteral Nutrition in Pediatric Crohn's Disease.}, journal = {Inflammatory bowel diseases}, volume = {26}, number = {7}, pages = {1026-1037}, pmid = {31961432}, issn = {1536-4844}, mesh = {Adolescent ; Bacteria/*classification/genetics ; Bacterial Typing Techniques/methods/*statistics & numerical data ; Child ; Crohn Disease/*microbiology/therapy ; *Enteral Nutrition ; Feces/chemistry/microbiology ; Female ; Follow-Up Studies ; Gastrointestinal Microbiome/*genetics ; Humans ; Leukocyte L1 Antigen Complex/analysis ; Machine Learning ; Male ; Metagenome ; Predictive Value of Tests ; Prospective Studies ; RNA, Ribosomal, 16S ; Recurrence ; Remission Induction ; Severity of Illness Index ; }, abstract = {BACKGROUND: The gut microbiome is extensively involved in induction of remission in pediatric Crohn's disease (CD) patients by exclusive enteral nutrition (EEN). In this follow-up study of pediatric CD patients undergoing treatment with EEN, we employ machine learning models trained on baseline gut microbiome data to distinguish patients who achieved and sustained remission (SR) from those who did not achieve remission nor relapse (non-SR) by 24 weeks.

METHODS: A total of 139 fecal samples were obtained from 22 patients (8-15 years of age) for up to 96 weeks. Gut microbiome taxonomy was assessed by 16S rRNA gene sequencing, and functional capacity was assessed by metagenomic sequencing. We used standard metrics of diversity and taxonomy to quantify differences between SR and non-SR patients and to associate gut microbial shifts with fecal calprotectin (FCP), and disease severity as defined by weighted Pediatric Crohn's Disease Activity Index. We used microbial data sets in addition to clinical metadata in random forests (RFs) models to classify treatment response and predict FCP levels.

RESULTS: Microbial diversity did not change after EEN, but species richness was lower in low-FCP samples (<250 µg/g). An RF model using microbial abundances, species richness, and Paris disease classification was the best at classifying treatment response (area under the curve [AUC] = 0.9). KEGG Pathways also significantly classified treatment response with the addition of the same clinical data (AUC = 0.8). Top features of the RF model are consistent with previously identified IBD taxa, such as Ruminococcaceae and Ruminococcus gnavus.

CONCLUSIONS: Our machine learning approach is able to distinguish SR and non-SR samples using baseline microbiome and clinical data.}, } @article {pmid31961065, year = {2020}, author = {Dunn, CM and Velasco, C and Rivas, A and Andrews, M and Garman, C and Jacob, PB and Jeffries, MA}, title = {Identification of Cartilage Microbial DNA Signatures and Associations With Knee and Hip Osteoarthritis.}, journal = {Arthritis & rheumatology (Hoboken, N.J.)}, volume = {72}, number = {7}, pages = {1111-1122}, pmid = {31961065}, issn = {2326-5205}, support = {K08 AR070891/AR/NIAMS NIH HHS/United States ; P20 GM125528/GM/NIGMS NIH HHS/United States ; U42 OD011158/OD/NIH HHS/United States ; }, mesh = {Aged ; Animals ; Arthroplasty, Replacement, Hip ; Arthroplasty, Replacement, Knee ; Cartilage, Articular/metabolism/*microbiology/pathology ; Classification ; DNA, Bacterial/*analysis ; Disease Susceptibility ; Female ; Genetic Variation ; Humans ; Male ; Metagenome/*genetics ; Mice ; Microbiota/*genetics ; Middle Aged ; Osteoarthritis, Hip/*microbiology/surgery ; Osteoarthritis, Knee/*microbiology/surgery ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {OBJECTIVE: Alterations of the gut microbiota have been implicated in many forms of arthritis, but an examination of cartilage microbial patterns has not been performed. This study was undertaken to characterize the microbial DNA profile of articular cartilage and determine changes associated with osteoarthritis (OA).

METHODS: We performed 16S ribosomal RNA gene deep sequencing on eroded and intact cartilage samples from knee OA patients (n = 21 eroded and 21 intact samples) and hip OA patients (n = 34 eroded and 33 intact samples) and cadaver controls (n = 10 knee samples and 10 hip samples). Microbial DNA diversity was assessed, groups were compared, and metagenomic profiles were reconstructed. Confirmation was performed in an independent cohort by clade-specific quantitative polymerase chain reaction. Findings in human cartilage were compared to those in cartilage from OA-susceptible C57BL/6 (B6) mice and OA-resistant MRL/MpJ (MRL) mice. Germ-free B6 mouse cartilage was analyzed as a methodologic control.

RESULTS: Alpha diversity was reduced in human OA versus control samples (P < 0.0001), and in hip versus knee samples (P < 0.0001). Numerous clades were different in human OA versus control samples, and similar findings were noted in comparisons of murine B6 versus MRL mice. Hip samples were microbiologically distinct from knee samples. OA microbial DNA demonstrated increased gram-negative constituents (P = 0.02). Functional analysis demonstrated increases in lipopolysaccharide production (P = 9.9 × 10[-3]), phosphatidylinositol signaling (P = 4.2 × 10[-4]), and nitrogen metabolism (P = 8 × 10[-3]) and decreases in sphingolipid metabolism (P = 7.7 × 10[-4]) associated with OA.

CONCLUSION: Our study reveals a microbial DNA signature in human and mouse cartilage. Alterations in this signature, including increases in gram-negative constituents, occur during the development and progression of human OA. Furthermore, our findings indicate that strain-specific signatures exist within mouse cartilage that mirror human patterns. Further study of the establishment and potential pathogenic role of these DNA signatures is needed.}, } @article {pmid31960092, year = {2020}, author = {Jongman, M and Carmichael, PC and Bill, M}, title = {Technological Advances in Phytopathogen Detection and Metagenome Profiling Techniques.}, journal = {Current microbiology}, volume = {77}, number = {4}, pages = {675-681}, pmid = {31960092}, issn = {1432-0991}, mesh = {Bacteria/*genetics/pathogenicity ; DNA Barcoding, Taxonomic ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Microbial Viability/genetics ; *Microbiota ; Oligonucleotide Array Sequence Analysis ; Plant Diseases/microbiology ; Plants/*microbiology ; }, abstract = {The use of advanced molecular methods in plant pathology and applied microbiology has necessitated for more accurate, rapid detection and identification of plant pathogens. This is particularly significant given accelerated emergence of virulence that leads to increased prevalence of plant pathogens. Thus, the capacity to contain plant pathogens and ultimately disease progression is key to ensuring crop biosecurity and overall food security. Of recent, research on pathogens utilizes a holistic approach focusing on elucidating growth dynamics within the entire biome rather than studying individual or closely related isolates in unison. This has advanced knowledge and information of microbial ecosystem within natural environments in the twenty first century. Applied technological platforms used for rapid detection and profiling microbial biomes in this regard include digital PCR, pyrosequencing, Illumina, DNA microarray and barcoding, Ion torrent, and nanopore. These technologies have been applied in various fields including human health and medicine, marine and animal biology, crop production and water quality research, to mention but a few. Although much has been done and achieved through the development of several technologies, more accuracy is required to circumvent the shortfalls still experienced. This includes integrating existing methods with new applications such as viability PCRs and microbial viability testing. Hence, this review provides critical analysis of some widely used latest technologies in rapid detection and identification of plant pathogens, and profiling plant associated microbiomes that reveal growth dynamics and population diversity. The advantages and limitations of the technologies are also discussed.}, } @article {pmid31959971, year = {2020}, author = {Fornelos, N and Franzosa, EA and Bishai, J and Annand, JW and Oka, A and Lloyd-Price, J and Arthur, TD and Garner, A and Avila-Pacheco, J and Haiser, HJ and Tolonen, AC and Porter, JA and Clish, CB and Sartor, RB and Huttenhower, C and Vlamakis, H and Xavier, RJ}, title = {Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease.}, journal = {Nature microbiology}, volume = {5}, number = {3}, pages = {486-497}, pmid = {31959971}, issn = {2058-5276}, support = {P40 OD010995/OD/NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; U54DK102557//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/International ; R24DK110499//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/International ; P01DK094779//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/International ; R24 DK110499/DK/NIDDK NIH HHS/United States ; R01 AT009708/AT/NCCIH NIH HHS/United States ; P40OD010995//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/International ; U54 DK102557/DK/NIDDK NIH HHS/United States ; P30 ES010126/ES/NIEHS NIH HHS/United States ; P30 DK040561/DK/NIDDK NIH HHS/United States ; P01 DK094779/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*drug effects/genetics/*growth & development ; Bacteroidetes/drug effects/isolation & purification ; Cohort Studies ; Disease Models, Animal ; Dysbiosis ; Ethanolamines/*pharmacology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/genetics/physiology ; Gene Expression Profiling ; Humans ; Inflammatory Bowel Diseases/*drug therapy/microbiology ; Male ; Metagenome ; Mice ; Mice, Inbred C57BL ; Microbiota/drug effects ; Proteobacteria/drug effects/isolation & purification ; Tandem Mass Spectrometry ; Whole Genome Sequencing ; }, abstract = {Inflammatory bowel diseases (IBD) are associated with alterations in gut microbial abundances and lumenal metabolite concentrations, but the effects of specific metabolites on the gut microbiota in health and disease remain largely unknown. Here, we analysed the influences of metabolites that are differentially abundant in IBD on the growth and physiology of gut bacteria that are also differentially abundant in IBD. We found that N-acylethanolamines (NAEs), a class of endogenously produced signalling lipids elevated in the stool of IBD patients and a T-cell transfer model of colitis, stimulated growth of species over-represented in IBD and inhibited that of species depleted in IBD in vitro. Using metagenomic sequencing, we recapitulated the effects of NAEs in complex microbial communities ex vivo, with Proteobacteria blooming and Bacteroidetes declining in the presence of NAEs. Metatranscriptomic analysis of the same communities identified components of the respiratory chain as important for the metabolism of NAEs, and this was verified using a mutant deficient for respiratory complex I. In this study, we identified NAEs as a class of metabolites that are elevated in IBD and have the potential to shift gut microbiota towards an IBD-like composition.}, } @article {pmid31959969, year = {2020}, author = {Whelan, FJ and Waddell, B and Syed, SA and Shekarriz, S and Rabin, HR and Parkins, MD and Surette, MG}, title = {Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota.}, journal = {Nature microbiology}, volume = {5}, number = {2}, pages = {379-390}, pmid = {31959969}, issn = {2058-5276}, support = {//CIHR/Canada ; }, mesh = {Algorithms ; Cystic Fibrosis/*microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Lung/*microbiology ; Metagenome ; Metagenomics/methods ; Microbiological Techniques ; Microbiota/*genetics ; Sequence Analysis, DNA ; }, abstract = {Amplicon sequencing (for example, of the 16S rRNA gene) identifies the presence and relative abundance of microbial community members. However, metagenomic sequencing is needed to identify the genetic content and functional potential of a community. Metagenomics is challenging in samples dominated by host DNA, such as those from the skin, tissue and respiratory tract. Here, we combine advances in amplicon and metagenomic sequencing with culture-enriched molecular profiling to study the human microbiota. Using the cystic fibrosis lung as an example, we cultured an average of 82.13% of the operational taxonomic units representing 99.3% of the relative abundance identified in direct sequencing of sputum samples; importantly, culture enrichment identified 63.3% more operational taxonomic units than direct sequencing. We developed the PLate Coverage Algorithm (PLCA) to determine a representative subset of culture plates on which to conduct culture-enriched metagenomics, resulting in the recovery of greater taxonomic diversity-including of low-abundance taxa-with better metagenome-assembled genomes, longer contigs and better functional annotations when compared to culture-independent methods. The PLCA is also applied as a proof of principle to a previously published gut microbiota dataset. Culture-enriched molecular profiling can be used to better understand the role of the human microbiota in health and disease.}, } @article {pmid31959912, year = {2020}, author = {Retchless, AC and Kretz, CB and Rodriguez-Rivera, LD and Chen, A and Soeters, HM and Whaley, MJ and Wang, X}, title = {Oropharyngeal microbiome of a college population following a meningococcal disease outbreak.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {632}, pmid = {31959912}, issn = {2045-2322}, mesh = {Adolescent ; Carrier State ; *Disease Outbreaks ; Female ; Humans ; Male ; Meningitis, Meningococcal/*epidemiology/*microbiology ; *Microbial Interactions ; Microbiota/*physiology ; Neisseria meningitidis ; Oropharynx/*microbiology ; Risk Factors ; Sex Factors ; Smoking ; Social Behavior ; Streptococcus ; *Students ; *Universities ; Veillonella ; Young Adult ; }, abstract = {Asymptomatic oropharyngeal carriage of Neisseria meningitidis peaks in adolescence and young adulthood. Following a meningococcal disease outbreak at a U.S. college, we profiled the oropharyngeal microbiomes of 158 students to identify associations between bacterial community composition and meningococcal carriage or risk factors for carriage, including male gender, smoking, and frequent social mixing. Metagenomic shotgun sequencing identified 268 bacterial taxa at the genus or species level, with Streptococcus, Veillonella, and Rothia species being most abundant. Microbiome composition showed weak associations with meningococcal carriage and risk factors for carriage. N. meningitidis abundance was positively correlated with that of Fusobacterium nucleatum, consistent with hypothesized propionic acid cross-feeding. Additional species had positive abundance correlations with N. meningitidis, including Aggregatibacter aphrophilus, Campylobacter rectus, Catonella morbi, Haemophilus haemolyticus, and Parvimonas micra. N. meningitidis abundance was negatively correlated with unidentified Veillonella species. Several of these species are commonly found in dental plaque, while N. meningitidis is primarily found in the pharynx, suggesting that ecological interactions extend throughout the oral cavity. Although risk factors for meningococcal carriage do not strongly impact most bacterial species in the oropharynx, variation in the upper respiratory tract microbiome may create conditions that are more or less favorable for N. meningitidis carriage.}, } @article {pmid31959785, year = {2020}, author = {Moreno-Pino, M and Cristi, A and Gillooly, JF and Trefault, N}, title = {Characterizing the microbiomes of Antarctic sponges: a functional metagenomic approach.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {645}, pmid = {31959785}, issn = {2045-2322}, mesh = {Animals ; Antarctic Regions ; Carbon/metabolism ; Carbon Dioxide/metabolism ; Chemoautotrophic Growth ; Light ; Marine Biology/*methods ; Metagenomics/*methods ; *Microbiota/genetics/physiology ; Nitrogen/metabolism ; Nutrients/metabolism ; Porifera/*genetics/metabolism/*microbiology/physiology ; Seawater/microbiology ; Symbiosis ; }, abstract = {Relatively little is known about the role of sponge microbiomes in the Antarctic marine environment, where sponges may dominate the benthic landscape. Specifically, we understand little about how taxonomic and functional diversity contributes to the symbiotic lifestyle and aids in nutrient cycling. Here we use functional metagenomics to investigate the community composition and metabolic potential of microbiomes from two abundant Antarctic sponges, Leucetta antarctica and Myxilla sp. Genomic and taxonomic analyses show that both sponges harbor a distinct microbial community with high fungal abundance, which differs from the surrounding seawater. Functional analyses reveal both sponge-associated microbial communities are enriched in functions related to the symbiotic lifestyle (e.g., CRISPR system, Eukaryotic-like proteins, and transposases), and in functions important for nutrient cycling. Both sponge microbiomes possessed genes necessary to perform processes important to nitrogen cycling (i.e., ammonia oxidation, nitrite oxidation, and denitrification), and carbon fixation. The latter indicates that Antarctic sponge microorganisms prefer light-independent pathways for CO2 fixation mediated by chemoautotrophic microorganisms. Together, these results show how the unique metabolic potential of two Antarctic sponge microbiomes help these sponge holobionts survive in these inhospitable environments, and contribute to major nutrient cycles of these ecosystems.}, } @article {pmid31959775, year = {2020}, author = {Cooper, RO and Cressler, CE}, title = {Characterization of key bacterial species in the Daphnia magna microbiota using shotgun metagenomics.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {652}, pmid = {31959775}, issn = {2045-2322}, mesh = {Amino Acids ; Animals ; Comamonadaceae ; Daphnia/metabolism/*microbiology ; Flagella/physiology ; High-Throughput Nucleotide Sequencing ; *Host Microbial Interactions ; Metagenomics/*methods ; Microbiota/*genetics/physiology ; Nitrates/metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S ; Sulfur/metabolism ; Vitamins/biosynthesis ; }, abstract = {The keystone zooplankton Daphnia magna has recently been used as a model system for understanding host-microbiota interactions. However, the bacterial species present and functions associated with their genomes are not well understood. In order to understand potential functions of these species, we combined 16S rRNA sequencing and shotgun metagenomics to characterize the whole-organism microbiota of Daphnia magna. We assembled five potentially novel metagenome-assembled genomes (MAGs) of core bacteria in Daphnia magna. Genes involved in host colonization and immune system evasion were detected across the MAGs. Some metabolic pathways were specific to some MAGs, including sulfur oxidation, nitrate reduction, and flagellar assembly. Amino acid exporters were identified in MAGs identified as important for host fitness, and pathways for key vitamin biosynthesis and export were identified across MAGs. In total, our examination of functions in these MAGs shows a diversity of nutrient acquisition and metabolism pathways present that may benefit the host, as well as genomic signatures of host association and immune system evasion.}, } @article {pmid31957879, year = {2020}, author = {Arıkan, M and Mitchell, AL and Finn, RD and Gürel, F}, title = {Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics.}, journal = {Journal of food science}, volume = {85}, number = {2}, pages = {455-464}, pmid = {31957879}, issn = {1750-3841}, support = {215Z672//Türkiye Bilimsel ve Teknolojik Araştirma Kurumu/ ; 20138//Bilimsel Araştirma Projeleri Birimi, Istanbul Üniversitesi/ ; BB/M011755/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R015228/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //European Molecular Biology Laboratory/ ; }, mesh = {Bacteria/classification/genetics/*isolation & purification/metabolism ; Beverages/*microbiology ; Fermentation ; Fermented Foods/*microbiology ; Metagenome ; Metagenomics ; *Microbiota ; Sequence Analysis, DNA ; Yeasts/classification/genetics/*isolation & purification/metabolism ; }, abstract = {Kombucha, a fermented tea generated from the co-culture of yeasts and bacteria, has gained worldwide popularity in recent years due to its potential benefits to human health. As a result, many studies have attempted to characterize both its biochemical properties and microbial composition. Here, we have applied a combination of whole metagenome sequencing (WMS) and amplicon (16S rRNA and Internal Transcribed Spacer 1 [ITS1]) sequencing to investigate the microbial communities of homemade Kombucha fermentations from day 3 to day 15. We identified the dominant bacterial genus as Komagataeibacter and dominant fungal genus as Zygosaccharomyces in all samples at all time points. Furthermore, we recovered three near complete Komagataeibacter genomes and one Zygosaccharomyces bailii genome and then predicted their functional properties. Also, we determined the broad taxonomic and functional profile of plasmids found within the Kombucha microbial communities. Overall, this study provides a detailed description of the taxonomic and functional systems of the Kombucha microbial community. Based on this, we conject that the functional complementarity enables metabolic cross talks between Komagataeibacter species and Z. bailii, which helps establish the sustained a relatively low diversity ecosystem in Kombucha.}, } @article {pmid31956606, year = {2019}, author = {Katagiri, S and Shiba, T and Tohara, H and Yamaguchi, K and Hara, K and Nakagawa, K and Komatsu, K and Watanabe, K and Ohsugi, Y and Maekawa, S and Iwata, T}, title = {Re-initiation of Oral Food Intake Following Enteral Nutrition Alters Oral and Gut Microbiota Communities.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {434}, pmid = {31956606}, issn = {2235-2988}, mesh = {Aged ; Aged, 80 and over ; Bacteria/*classification/genetics/isolation & purification ; Deglutition Disorders/*rehabilitation ; Eating/*physiology ; Enteral Nutrition/*adverse effects/methods ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Metagenome/genetics ; RNA, Ribosomal, 16S/genetics ; Stroke/pathology ; Stroke Rehabilitation/methods ; }, abstract = {Stroke is associated with multiple forms of disability, including dysphagia. Post-stroke dysphagia increases the risks of pneumonia and mortality and often results in cessation of oral feeding. However, appropriate rehabilitation methods can eventually lead to resumption of oral food intake. This study tried to clarify that re-initiating oral food intake could modify the composition of oral/gut microbial communities in patients with dysphagia. From 78 patients with sub-acute stage of stroke, 11 complete tube feeding subjects without taking antibiotics were enrolled and received rehabilitation for re-initiation of oral food intake, and 8 subjects were brought back to complete oral feeding. Oral and gut microbiota community profiles were evaluated using 16S rRNA sequencing of the saliva and feces samples before and after re-initiation of oral food intake in patients recovering from enteral nutrition under the same nutrient condition. Standard nutrition in the hospital was 1,840 kcal, including protein = 75 g, fat = 45 g, and carbohydrates = 280 g both for tube and oral feeding subjects. Oral food intake increased oral and gut microbiome diversity and altered the composition of the microbiome. Oral and gut microbiome compositions were drastically different; however, the abundance of family Carnobacteriaceae and genus Granulicatella was increased in both the oral and gut microbiome after re-initiation of oral food intake. Although oral microbiota showed more significant changes than the gut microbiota, metagenome prediction revealed the presence of more differentially enriched pathways in the gut. In addition, simpler co-occurrence networks of oral and gut microbiomes, indicating improved dysbiosis of the microbiome, were observed during oral feeding as compared to that during tube feeding. Oral food intake affects oral and gut microbiomes in patients recovering from enteral nutrition. Rehabilitation for dysphagia can modify systemic health by increasing the diversity and altering the composition and co-occurrence network structure of oral and gut microbial communities.}, } @article {pmid31956324, year = {2019}, author = {Rinaldi, E and Consonni, A and Cordiglieri, C and Sacco, G and Crasà, C and Fontana, A and Morelli, L and Elli, M and Mantegazza, R and Baggi, F}, title = {Therapeutic Effect of Bifidobacterium Administration on Experimental Autoimmune Myasthenia Gravis in Lewis Rats.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {2949}, pmid = {31956324}, issn = {1664-3224}, mesh = {Animals ; Autoimmunity ; *Bifidobacterium ; Cell Movement ; Dendritic Cells/immunology/metabolism ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Myasthenia Gravis, Autoimmune, Experimental/*etiology ; Probiotics/*administration & dosage ; RNA, Ribosomal, 16S ; Rats ; Rats, Inbred Lew ; }, abstract = {Beneficial effects of probiotics on gut microbiota homeostasis and inflammatory immune responses suggested the investigation of their potential clinical efficacy in experimental models of autoimmune diseases. Indeed, administration of two bifidobacteria and lactobacilli probiotic strains prevented disease manifestations in the Lewis rat model of Myasthenia Gravis (EAMG). Here, we demonstrate the clinical efficacy of therapeutic administration of vital bifidobacteria (i.e., from EAMG onset). The mechanisms involved in immunomodulation were investigated with ex vivo and in vitro experiments. Improvement of EAMG symptoms was associated to decreased anti-rat AChR antibody levels, and differential expression of TGFβ and FoxP3 immunoregulatory transcripts in draining lymph nodes and spleen of treated-EAMG rats. Exposure of rat bone marrow-derived dendritic cells to bifidobacteria or lactobacilli strains upregulated toll-like receptor 2 mRNA expression, a key molecule involved in bacterium recognition via lipotheicoic acid. Live imaging experiments of AChR-specific effector T cells, co-cultured with BMDCs pre-exposed to bifidobacteria, demonstrated increased percentages of motile effector T cells, suggesting a hindered formation of TCR-peptide-MHC complex. Composition of gut microbiota was studied by 16S rRNA gene sequencing, and α and β diversity were determined in probiotic treated EAMG rats, with altered ratios between Tenericutes and Verrucomicrobia (phylum level), and Ruminococcaceae and Lachnospiraceae (family level). Moreover, the relative abundance of Akkermansia genus was found increased compared to healthy and probiotic treated EAMG rats. In conclusion, our findings confirms that the administration of vital bifidobacteria at EAMG onset has beneficial effects on disease progression; this study further supports preclinical research in human MG to evaluate probiotic efficacy as supplementary therapy in MG.}, } @article {pmid31956235, year = {2019}, author = {Benderli, NC and Ogai, K and Lloyd, YM and Arios, JP and Jiyarom, B and Awanakam, AH and Esemu, LF and Hori, A and Megnekou, R and Leke, RGF and Kuraishi, T and Okamoto, S and Ekali, GL}, title = {Feasibility of microbial sample collection on the skin from people in Yaoundé, Cameroon.}, journal = {Drug discoveries & therapeutics}, volume = {13}, number = {6}, pages = {360-364}, doi = {10.5582/ddt.2019.01075}, pmid = {31956235}, issn = {1881-784X}, mesh = {Adult ; Bacteria/*classification/genetics ; Cameroon ; DNA, Bacterial/genetics ; Feasibility Studies ; Female ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Male ; Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Skin/*microbiology ; Specimen Handling/instrumentation/*methods ; Young Adult ; }, abstract = {Characterization of microbial communities in the skin in healthy individuals and diseased patients holds valuable information for understanding pathogenesis of skin diseases and as a source for developing novel therapies. Notably, resources regarding skin microbiome are limited in developing countries where skin disorders from infectious diseases are extremely common. A simple method for sample collection and processing for skin microbiome studies in such countries is crucial. The aim of this study is to confirm the feasibility of collecting skin microbiota from individuals in Yaoundé, a capital city of Cameroon, and subsequent extraction of bacterial DNA in a resource limited setting. Skin swabs from several individuals in Yaoundé were successfully obtained, and sufficient amount of bacterial 16S ribosomal RNA-coding DNA was collected, which was confirmed by quantitative PCR. The median copy number of 16S ribosomal RNA gene varied across participants and collection sites, with significantly more copies in samples collected from the forehead compared to the left and right forearm, or back. This study demonstrated that collecting surface skin microbes using our swabbing method is feasible in a developing country. We further showed that even with limited resources, we could collect sufficient amount of skin microbiota from the inhabitants in Yaoundé where no studies of skin microbiome were reported, which can be passed to further metagenomic analysis such as next generation sequencing.}, } @article {pmid31954373, year = {2020}, author = {Duan, C and Kuang, L and Xiang, X and Zhang, J and Zhu, Y and Wu, Y and Yan, Q and Liu, L and Li, T}, title = {Activated Drp1-mediated mitochondrial ROS influence the gut microbiome and intestinal barrier after hemorrhagic shock.}, journal = {Aging}, volume = {12}, number = {2}, pages = {1397-1416}, pmid = {31954373}, issn = {1945-4589}, mesh = {Animals ; Biomarkers ; Disease Models, Animal ; Dynamins/*genetics/metabolism ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Intestinal Mucosa/*metabolism/*microbiology ; Male ; Metabolomics/methods ; Metagenomics/methods ; Mice ; Mitochondria/*genetics/*metabolism ; Permeability ; RNA, Ribosomal, 16S/genetics ; Reactive Oxygen Species/*metabolism ; Shock, Hemorrhagic/etiology/*metabolism ; }, abstract = {A role of the mitochondrial dynamin-related protein (Drp1) on gut microbiome composition and intestinal barrier function after hemorrhagic shock has not been identified previously and thus addressed in this study. Here, we used a combination of 16S rRNA gene sequencing and mass spectrometry-based metabolomics profiling in WT and Drp1 KO mouse models to examine the functional impact of activated Drp1 on the gut microbiome as well as mitochondrial metabolic regulation after hemorrhagic shock. Our data showed that changes in mitochondrial Drp1 activity participated in the regulation of intestinal barrier function after hemorrhagic shock. Activated Drp1 significantly perturbed gut microbiome composition in the Bacteroidetes phylum. The abundance of short-chain fatty acid (SCFA) producing microbes, such as Bacteroides, Butyricimonas and Odoribacter, was markedly decreased in mice after shock, and was inversely correlated with both the distribution of the tight junction protein ZO1 and intestinal permeability. Together, these data suggest that Drp1 activation perturbs the gut microbiome community and SCFA production in a ROS-specific manner and thereby substantially disturbs tight junctions and intestinal barrier function after hemorrhagic shock. Our findings provide novel insights for targeting Drp1-mediated mitochondrial function as well as the microbiome in the treatment of intestinal barrier dysfunction after shock.}, } @article {pmid31953381, year = {2020}, author = {Vich Vila, A and Collij, V and Sanna, S and Sinha, T and Imhann, F and Bourgonje, AR and Mujagic, Z and Jonkers, DMAE and Masclee, AAM and Fu, J and Kurilshikov, A and Wijmenga, C and Zhernakova, A and Weersma, RK}, title = {Impact of commonly used drugs on the composition and metabolic function of the gut microbiota.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {362}, pmid = {31953381}, issn = {2041-1723}, mesh = {Adult ; Anti-Bacterial Agents/pharmacology ; Antidepressive Agents/pharmacology ; Bacteria/*classification/*drug effects/*metabolism ; Body Mass Index ; Case-Control Studies ; Cohort Studies ; Computational Biology ; Ecosystem ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/*physiology ; Humans ; Irritable Bowel Syndrome/drug therapy/microbiology ; Laxatives/pharmacology ; Male ; *Metagenomics ; Metformin/pharmacology ; Microbial Interactions/drug effects ; Middle Aged ; Proton Pump Inhibitors/pharmacology ; }, abstract = {The human gut microbiota has now been associated with drug responses and efficacy, while chemical compounds present in these drugs can also impact the gut bacteria. However, drug-microbe interactions are still understudied in the clinical context, where polypharmacy and comorbidities co-occur. Here, we report relations between commonly used drugs and the gut microbiome. We performed metagenomics sequencing of faecal samples from a population cohort and two gastrointestinal disease cohorts. Differences between users and non-users were analysed per cohort, followed by a meta-analysis. While 19 of 41 drugs are found to be associated with microbial features, when controlling for the use of multiple medications, proton-pump inhibitors, metformin, antibiotics and laxatives show the strongest associations with the microbiome. We here provide evidence for extensive changes in taxonomy, metabolic potential and resistome in relation to commonly used drugs. This paves the way for future studies and has implications for current microbiome studies by demonstrating the need to correct for multiple drug use.}, } @article {pmid31953342, year = {2020}, author = {Steinke, L and Slysz, GW and Lipton, MS and Klatt, C and Moran, JJ and Romine, MF and Wood, JM and Anderson, G and Bryant, DA and Ward, DM}, title = {Short-Term Stable Isotope Probing of Proteins Reveals Taxa Incorporating Inorganic Carbon in a Hot Spring Microbial Mat.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {7}, pages = {}, pmid = {31953342}, issn = {1098-5336}, mesh = {Carbon Compounds, Inorganic/*metabolism ; Chloroflexi/*metabolism ; Hot Springs/*microbiology ; *Microbiota ; Synechococcus/*metabolism ; }, abstract = {The upper green layer of the chlorophototrophic microbial mats associated with the alkaline siliceous hot springs of Yellowstone National Park consists of oxygenic cyanobacteria (Synechococcus spp.), anoxygenic Roseiflexus spp., and several other anoxygenic chlorophototrophs. Synechococcus spp. are believed to be the main fixers of inorganic carbon (Ci), but some evidence suggests that Roseiflexus spp. also contribute to inorganic carbon fixation during low-light, anoxic morning periods. Contributions of other phototrophic taxa have not been investigated. In order to follow the pathway of Ci incorporation into different taxa, mat samples were incubated with [[13]C]bicarbonate for 3 h during the early-morning, low-light anoxic period. Extracted proteins were treated with trypsin and analyzed by mass spectrometry, leading to peptide identifications and peptide isotopic profile signatures containing evidence of [13]C label incorporation. A total of 25,483 peptides, corresponding to 7,221 proteins, were identified from spectral features and associated with mat taxa by comparison to metagenomic assembly sequences. A total of 1,417 peptides, derived from 720 proteins, were detectably labeled with [13]C. Most [13]C-labeled peptides were derived from proteins of Synechococcus spp. and Roseiflexus spp. Chaperones and proteins of carbohydrate metabolism were most abundantly labeled. Proteins involved in photosynthesis, Ci fixation, and N2 fixation were also labeled in Synechococcus spp. Importantly, most proteins of the 3-hydroxypropionate bi-cycle for Ci fixation in Roseiflexus spp. were labeled, establishing that members of this taxocene contribute to Ci fixation. Other taxa showed much lower [[13]C]bicarbonate incorporation.IMPORTANCE Yellowstone hot spring mats have been studied as natural models for understanding microbial community ecology and as modern analogs of stromatolites, the earliest community fossils on Earth. Stable-isotope probing of proteins (Pro-SIP) permitted short-term interrogation of the taxa that are involved in the important process of light-driven Ci fixation in this highly active community and will be useful in linking other metabolic processes to mat taxa. Here, evidence is presented that Roseiflexus spp., which use the 3-hydroxypropionate bi-cycle, are active in Ci fixation. Because this pathway imparts a lower degree of selection of isotopically heavy Ci than does the Calvin-Benson-Bassham cycle, the results suggest a mechanism to explain why the natural abundance of [13]C in mat biomass is greater than expected if only the latter pathway were involved. Understanding how mat community members influence the [13]C/[12]C ratios of mat biomass will help geochemists interpret the [13]C/[12]C ratios of organic carbon in the fossil record.}, } @article {pmid31953333, year = {2020}, author = {Riiser, ES and Haverkamp, THA and Varadharajan, S and Borgan, Ø and Jakobsen, KS and Jentoft, S and Star, B}, title = {Metagenomic Shotgun Analyses Reveal Complex Patterns of Intra- and Interspecific Variation in the Intestinal Microbiomes of Codfishes.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {6}, pages = {}, pmid = {31953333}, issn = {1098-5336}, mesh = {Animals ; Bacteria/*genetics/isolation & purification ; *Ecotype ; Female ; Gadiformes/*microbiology ; Gadus morhua/microbiology ; Gastrointestinal Microbiome/*genetics ; Male ; *Metagenome ; Norway ; }, abstract = {The relative importance of host-specific selection or environmental factors in determining the composition of the intestinal microbiome in wild vertebrates remains poorly understood. Here, we used metagenomic shotgun sequencing of individual specimens to compare the levels of intra- and interspecific variation of intestinal microbiome communities in two ecotypes (NEAC and NCC) of Atlantic cod (Gadus morhua) that have distinct behavior and habitats and three Gadidae species that occupy a range of ecological niches. Interestingly, we found significantly diverged microbiomes among the two Atlantic cod ecotypes. Interspecific patterns of variation are more variable, with significantly diverged communities for most species' comparisons, apart from the comparison between coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose community compositions are not significantly diverged. The absence of consistent species-specific microbiomes suggests that external environmental factors, such as temperature, diet, or a combination thereof, comprise major drivers of the intestinal community composition of codfishes.IMPORTANCE The composition of the intestinal microbial community associated with teleost fish is influenced by a diversity of factors, ranging from internal factors (such as host-specific selection) to external factors (such as niche occupation). These factors are often difficult to separate, as differences in niche occupation (e.g., diet, temperature, or salinity) may correlate with distinct evolutionary trajectories. Here, we investigate four gadoid species with contrasting levels of evolutionary separation and niche occupation. Using metagenomic shotgun sequencing, we observed distinct microbiomes among two Atlantic cod (Gadus morhua) ecotypes (NEAC and NCC) with distinct behavior and habitats. In contrast, interspecific patterns of variation were more variable. For instance, we did not observe interspecific differentiation between the microbiomes of coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose lineages underwent evolutionary separation over 20 million years ago. The observed pattern of microbiome variation in these gadoid species is therefore most parsimoniously explained by differences in niche occupation.}, } @article {pmid31953253, year = {2020}, author = {Erawijantari, PP and Mizutani, S and Shiroma, H and Shiba, S and Nakajima, T and Sakamoto, T and Saito, Y and Fukuda, S and Yachida, S and Yamada, T}, title = {Influence of gastrectomy for gastric cancer treatment on faecal microbiome and metabolome profiles.}, journal = {Gut}, volume = {69}, number = {8}, pages = {1404-1415}, pmid = {31953253}, issn = {1468-3288}, mesh = {Actinobacteria/isolation & purification/metabolism ; Aged ; Amino Acids, Branched-Chain/metabolism ; Bacillus/isolation & purification/metabolism ; Bacteroidetes/isolation & purification/*metabolism ; Bifidobacterium/isolation & purification/metabolism ; Bile Acids and Salts/*metabolism ; Case-Control Studies ; Clostridiales/isolation & purification/metabolism ; Deoxycholic Acid/metabolism ; Feces/*chemistry/*microbiology ; Female ; Firmicutes/isolation & purification/*metabolism ; *Gastrectomy ; Gastrointestinal Microbiome ; Humans ; Lactobacillus/isolation & purification/metabolism ; Male ; Metabolome ; Metagenomics ; Middle Aged ; Prevotella/isolation & purification/metabolism ; Sequence Analysis, DNA ; Stomach Neoplasms/*surgery ; Streptococcus/isolation & purification/metabolism ; Veillonella/isolation & purification/metabolism ; }, abstract = {OBJECTIVE: Recent evidence points to the gut microbiome's involvement in postoperative outcomes, including after gastrectomy. Here, we investigated the influence of gastrectomy for gastric cancer on the gut microbiome and metabolome, and how it related to postgastrectomy conditions.

DESIGN: We performed shotgun metagenomics sequencing and capillary electrophoresis time-of-flight mass spectrometry-based metabolomics analyses on faecal samples collected from participants with a history of gastrectomy for gastric cancer (n=50) and compared them with control participants (n=56).

RESULTS: The gut microbiota in the gastrectomy group showed higher species diversity and richness (p<0.05), together with greater abundance of aerobes, facultative anaerobes and oral microbes. Moreover, bile acids such as genotoxic deoxycholic acid and branched-chain amino acids were differentially abundant between the two groups (linear discriminant analysis (LDA) effect size (LEfSe): p<0.05, q<0.1, LDA>2.0), as were also Kyoto Encyclopedia of Genes and Genomes modules involved in nutrient transport and organic compounds biosynthesis (LEfSe: p<0.05, q<0.1, LDA>2.0).

CONCLUSION: Our results reveal alterations of gut microbiota after gastrectomy, suggesting its association with postoperative comorbidities. The multi-omic approach applied in this study could complement the follow-up of patients after gastrectomy.}, } @article {pmid31953225, year = {2020}, author = {Xiao, D and Yang, G and Wang, Z and Khalique, A and Zhu, Z and Xiong, L and Li, J and Yuan, X and Ni, X and Zeng, D and Zhang, D and Pan, K}, title = {Efficacy of Bacillus methylotrophicus SY200 strain as feed additive against experimental Salmonella typhimurium infection in mice.}, journal = {Microbial pathogenesis}, volume = {141}, number = {}, pages = {103978}, doi = {10.1016/j.micpath.2020.103978}, pmid = {31953225}, issn = {1096-1208}, mesh = {Animal Feed ; Animals ; *Antibiosis ; Bacillus/*physiology ; Bacterial Load ; Gastrointestinal Microbiome ; Leukocyte Count ; Male ; Metagenomics ; Mice ; Neutrophils ; Phylogeny ; Salmonella Infections, Animal/blood/*microbiology/prevention & control ; Salmonella typhimurium/*physiology ; }, abstract = {To investigate the effects of Bacillus methylotrophicus SY200 on Salmonella typhimurium (STM) infection in mice, a total of 36 three-week-old male mice were selected and randomly divided into 3 equal groups (N = 12). Group A and group B were fed with basal diet while group C was fed the basal diet supplemented with 0.1% (w/w) B. methylotrophicus SY200 during the 21 days experimental period. On the 14th day of the experiment, mice of group A were intragastrically administered with 0.5 ml of normal saline, group B and C were orally administered with 0.5 ml of STM suspension. On the first day and seventh day after STM challenge, the number of total white blood cells (WBCs) and neutrophils, relative weight of visceral organs, the number of Salmonella spp., Escherichia coli, Lactobacillus spp. and Bifidobacterium spp. in ileum and cecum, and diversity of cecal microflora were measured. The results showed that: on the first day and seventh day after STM challenge, the number of WBCs and neutrophils in the blood of the mice was the highest in group B, then followed by group C, and group A. On the first day after STM challenge, the relative weight of spleen in group C was significantly higher than that in group B (p < 0.05), moreover, compared with group B, B. methylotrophicus SY200 significantly reduced the number of Salmonella spp. and E. coli (p < 0.05), and increased the number of Lactobacillus spp. and Bifidobacterium spp. (p < 0.05) in the intestines of mice, and improved the Shannon-Wiener diversity (H), Simpson (E) and richness (S) indices of cecal flora of mice (p < 0.05). The results indicated that B. methylotrophicus SY200 could alleviate the inflammatory reaction after STM infection and resist the adverse effects of STM infection on mice intestinal flora.}, } @article {pmid31950303, year = {2020}, author = {Queiroz, LL and Bendia, AG and Duarte, RTD and das Graças, DA and da Costa da Silva, AL and Nakayama, CR and Sumida, PY and Lima, AOS and Nagano, Y and Fujikura, K and Kitazato, H and Pellizari, VH}, title = {Bacterial diversity in deep-sea sediments under influence of asphalt seep at the São Paulo Plateau.}, journal = {Antonie van Leeuwenhoek}, volume = {113}, number = {5}, pages = {707-717}, doi = {10.1007/s10482-020-01384-8}, pmid = {31950303}, issn = {1572-9699}, support = {2013/09159-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 311010/2015-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Alphaproteobacteria/classification/genetics/isolation & purification ; Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; DNA, Bacterial/genetics ; Deltaproteobacteria/classification/genetics/isolation & purification ; Gammaproteobacteria/classification/genetics/isolation & purification ; Geologic Sediments/*microbiology ; High-Throughput Nucleotide Sequencing/methods ; Hydrocarbons/metabolism ; *Metagenome ; Metagenomics/methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Water Microbiology ; }, abstract = {Here we investigated the diversity of bacterial communities from deep-sea surface sediments under influence of asphalt seeps at the Sao Paulo Plateau using next-generation sequencing method. Sampling was performed at North São Paulo Plateau using the human occupied vehicle Shinkai 6500 and her support vessel Yokosuka. The microbial diversity was studied at two surficial sediment layers (0-1 and 1-4 cm) of five samples collected in cores in water depths ranging from 2456 to 2728 m. Bacterial communities were studied through sequencing of 16S rRNA gene on the Ion Torrent platform and clustered in operational taxonomic units. We observed high diversity of bacterial sediment communities as previously described by other studies. When we considered community composition, the most abundant classes were Alphaproteobacteria (27.7%), Acidimicrobiia (20%), Gammaproteobacteria (11.3%) and Deltaproteobacteria (6.6%). Most abundant OTUs at family level were from two uncultured bacteria from Actinomarinales (5.95%) and Kiloniellaceae (3.17%). The unexpected high abundance of Alphaproteobacteria and Acidimicrobiia in our deep-sea microbial communities may be related to the presence of asphalt seep at North São Paulo Plateau, since these bacterial classes contain bacteria that possess the capability of metabolizing hydrocarbon compounds.}, } @article {pmid31948613, year = {2020}, author = {Knight, SJ and Karon, O and Goddard, MR}, title = {Small scale fungal community differentiation in a vineyard system.}, journal = {Food microbiology}, volume = {87}, number = {}, pages = {103358}, doi = {10.1016/j.fm.2019.103358}, pmid = {31948613}, issn = {1095-9998}, mesh = {Discriminant Analysis ; Fermentation ; Fruit/microbiology ; Fungi/classification/genetics/*isolation & purification ; *Mycobiome ; New Zealand ; Vitis/*microbiology ; Wine/*analysis/microbiology ; }, abstract = {Microbes influence the quality of agricultural commodities and contribute to their distinctive sensorial attributes. Increasingly studies have demonstrated not only differential geographic patterns in microbial communities and populations, but that these contribute to valuable regionally distinct agricultural product identities, the most well-known example being wine. However, little is understood about microbial geographic patterns at scales of less than 100 km. For wine, single vineyards are the smallest (and most valuable) scale at which wine is asserted to differ; however, it is unknown whether microbes play any role in agricultural produce differentiation at this scale. Here we investigate whether vineyard fungal communities and yeast populations driving the spontaneous fermentation of fruit from these same vineyards are differentiated using metagenomics and population genetics. Significant differentiation of fungal communities was revealed between four Central Otago (New Zealand) Pinot Noir vineyard sites. However, there was no vineyard demarcation between fermenting populations of S. cerevisiae. Overall, this provides evidence that vineyard microbiomes potentially contribute to vineyard specific attributes in wine. Understanding the scale at which microbial communities are differentiated, and how these communities influence food product attributes has direct economic implications for industry and could inform sustainable management practices that maintain and enhance microbial diversity.}, } @article {pmid31945519, year = {2020}, author = {Meenatchi, R and Thinesh, T and Brindangnanam, P and Hassan, S and Kiran, GS and Selvin, J}, title = {Revealing the impact of global mass bleaching on coral microbiome through 16S rRNA gene-based metagenomic analysis.}, journal = {Microbiological research}, volume = {233}, number = {}, pages = {126408}, doi = {10.1016/j.micres.2019.126408}, pmid = {31945519}, issn = {1618-0623}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Bacteria/*classification ; Coral Reefs ; *Heat-Shock Response ; High-Throughput Nucleotide Sequencing ; India ; *Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Coral bleaching, a phenomenon by which the expulsion of corals' alveolate endosymbiont (zooxanthellae) occurs when experiencing thermal stress is the major cause for devastation of corals. However, apart from this obligate symbiont of Scleractinian corals, there are different kinds of microbes that exist as stable, transient or sporadic members of the holobiont which reside within various microhabitats in the coral structures. Thus, this study aims to profile the coral bacterial community composition among different coral genera (thermally-sensitive (Acropora digetifera and A. noblis) and thermally resistant (Favites abdita) coral genera analyzed by field monitoring surveys) and also in a particular coral genus (thermally sensitive coral-A. digetifera) at two different sampling times (March 2016 and January 2017). A total of about 608695 paired end reads were obtained through Illumina MiSeq Sequencing platform. The alpha diversity indices (ACE, Chao1 and Shannon) were found to be higher in A. nobilis, followed by A. digetifera and Favites abdita, and the corresponding Simpson values were also found to follow the same trend, indicating that the samples are both rich in species diversity and species evenness. Proteobacteria was found to be the most dominant phylum and Gammaproteobacteria was the predominant class present in all the coral genera studied as also during different sampling time periods. As Vibrionaceae was previously reported to increase its abundance during bleaching stress conditions, bacterial profiling among different coral genera showed the presence of 86 % Vibrionaceae in A. digetifera colonies, and it was 93 % in A. digetifera samples collected during March 2016 whereas, it was found to decrease significantly (7 %) in same tagged colonies collected during January 2017. Thus, profiling of microbiome is of prime importance while studying the holobiont organism like the corals. Stress levels experienced by Palk Bay are even depicted in this microbiome study showing high alpha diversity indices that should alarm reef managers to pay attention to this precious stress tolerant reef community.}, } @article {pmid31944684, year = {2020}, author = {Wang, X and Chen, Z and Mu, Q and Wu, X and Zhang, J and Mao, D and Luo, Y and Alvarez, PJJ}, title = {Ionic Liquid Enriches the Antibiotic Resistome, Especially Efflux Pump Genes, Before Significantly Affecting Microbial Community Structure.}, journal = {Environmental science & technology}, volume = {54}, number = {7}, pages = {4305-4315}, doi = {10.1021/acs.est.9b04116}, pmid = {31944684}, issn = {1520-5851}, mesh = {Anti-Bacterial Agents ; Drug Resistance, Microbial ; Genes, Bacterial ; *Ionic Liquids ; *Microbiota ; }, abstract = {An expanding list of chemicals may permeabilize bacterial cells and facilitate horizontal gene transfer (HGT), which enhances propagation of antibiotic resistance genes (ARGs) in the environment. Previous studies showed that 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]), an ionic liquid, can facilitate HGT of some ARGs among bacteria. However, the dynamic response of a wider range of ARGs and associated mobile genetic elements (MGEs) in different environments is unknown. Here, we used metagenomic tools to study shifts of the resistome and microbiome in both sediments and freshwater microcosms exposed to [BMIm][PF6]. Exposure for 16 h to 0.1 or 1.0 g/L significantly enriched more than 207 ARG subtypes primarily encoding efflux pumps in freshwater microcosms as well as cultivable antibiotic-resistant bacteria. This resistome enrichment was attributed to HGT facilitated by MGEs (428 plasmids, 61 integron-integrase genes, and 45 gene cassettes were enriched) as well as to HGT-related functional genes. Interestingly, resistome enrichment occurred fast (within 16 h) after [BMIm][PF6] exposure, before any significant changes in bacterial community structure. Similar ARG enrichment occurred in sediment microcosms exposed to [BMIm][PF6] for 28 d, and this longer exposure affected the microbial community structure (e.g., Proteobacteria abundance increased significantly). Overall, this study suggests that [BMIm][PF6] releases could rapidly enrich the antibiotic resistome in receiving environments by increasing HGT and fortuitously selecting for efflux pump genes, thus contributing to ARG propagation.}, } @article {pmid31943422, year = {2020}, author = {Li, R and Li, X and Huang, T and Wang, Y and Xue, M and Sun, S and Yan, D and Song, G and Sun, G and Li, M}, title = {Influence of cecotrophy on fat metabolism mediated by caecal microorganisms in New Zealand white rabbits.}, journal = {Journal of animal physiology and animal nutrition}, volume = {104}, number = {2}, pages = {749-757}, doi = {10.1111/jpn.13309}, pmid = {31943422}, issn = {1439-0396}, support = {2018YFD0502203//National Key R&D Program of China/ ; S2013-08-G01//Henan Agriculture Research System/ ; }, mesh = {Animals ; Cecum/*microbiology ; Coprophagia ; Fats/*metabolism ; Female ; Gastrointestinal Microbiome ; Rabbits/microbiology/*physiology ; }, abstract = {Cecotrophy is a special behaviour of rabbits. Eating soft faeces can improve feed efficiency and maintain gut flora in rabbits. In our previous study, we found that fasting from soft faeces significantly reduced growth rate and total cholesterol (TC) in New Zealand white rabbits (NZW rabbits), thereby resulting in lower values for body weight and fat deposition in the soft faeces fasting group than in the control group. However, it has not been demonstrated whether cecotrophy by NZW rabbits can regulate lipid metabolism by changing the diversity of caecal microorganisms. In this study, thirty-six 28-day-old weaned NZW female rabbits were randomly divided into two groups (the soft faeces fasting group and the control group) and fed to 90 days. Rabbits in the experimental group were treated with an Elizabeth circle to prevent them from eating their soft faeces. Then, the caecal contents of three rabbits from the soft faeces fasting group and three rabbits from the control group were collected for metagenomic sequencing. We found that the abundance of Bacteroides increased, while Ruminococcus decreased, compared with the control group after fasting from soft faeces. Relative abundance was depressed for genes related to metabolic pathways such as ascorbate and aldarate metabolism, riboflavin metabolism and bile secretion. Moreover, there was a general correlation between variation in microbial diversity and fat deposition. Bacteroides affects body weight and TC by participating in the riboflavin metabolism pathway. By investigating the effect of cecotrophy on caecal microorganisms of rabbits, we identified the key microorganisms that regulate the rapid growth performance of NZW rabbits, which may provide useful reference for the future research and development of microecological preparations for NZW rabbits.}, } @article {pmid31942082, year = {2020}, author = {Chong, J and Liu, P and Zhou, G and Xia, J}, title = {Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data.}, journal = {Nature protocols}, volume = {15}, number = {3}, pages = {799-821}, pmid = {31942082}, issn = {1750-2799}, mesh = {DNA, Bacterial ; Databases, Genetic ; Meta-Analysis as Topic ; Metagenomics/methods ; Microbiota/*genetics/*physiology ; Models, Statistical ; RNA, Bacterial ; *Software ; }, abstract = {MicrobiomeAnalyst is an easy-to-use, web-based platform for comprehensive analysis of common data outputs generated from current microbiome studies. It enables researchers and clinicians with little or no bioinformatics training to explore a wide variety of well-established methods for microbiome data processing, statistical analysis, functional profiling and comparison with public datasets or known microbial signatures. MicrobiomeAnalyst currently contains four modules: Marker-gene Data Profiling (MDP), Shotgun Data Profiling (SDP), Projection with Public Data (PPD), and Taxon Set Enrichment Analysis (TSEA). This protocol will first introduce the MDP module by providing a step-wise description of how to prepare, process and normalize data; perform community profiling; identify important features; and conduct correlation and classification analysis. We will then demonstrate how to perform predictive functional profiling and introduce several unique features of the SDP module for functional analysis. The last two sections will describe the key steps involved in using the PPD and TSEA modules for meta-analysis and visual exploration of the results. In summary, MicrobiomeAnalyst offers a one-stop shop that enables microbiome researchers to thoroughly explore their preprocessed microbiome data via intuitive web interfaces. The complete protocol can be executed in ~70 min.}, } @article {pmid31941900, year = {2020}, author = {Siranosian, BA and Tamburini, FB and Sherlock, G and Bhatt, AS}, title = {Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {280}, pmid = {31941900}, issn = {2041-1723}, support = {K08 CA184420/CA/NCI NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteriophages/*genetics/physiology ; Bacteroides/virology ; Biodiversity ; Cesarean Section ; Fecal Microbiota Transplantation ; Feces/*virology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Infant ; Metagenome ; Polymorphism, Single Nucleotide ; Tissue Donors ; }, abstract = {CrAss-like phages are double-stranded DNA viruses that are prevalent in human gut microbiomes. Here, we analyze gut metagenomic data from mother-infant pairs and patients undergoing fecal microbiota transplantation to evaluate the patterns of acquisition, transmission and strain diversity of crAss-like phages. We find that crAss-like phages are rarely detected at birth but are increasingly prevalent in the infant microbiome after one month of life. We observe nearly identical genomes in 50% of cases where the same crAss-like clade is detected in both the mother and the infant, suggesting vertical transmission. In cases of putative transmission of prototypical crAssphage (p-crAssphage), we find that a subset of strains present in the mother are detected in the infant, and that strain diversity in infants increases with time. Putative tail fiber proteins are enriched for nonsynonymous strain variation compared to other genes, suggesting a potential evolutionary benefit to maintaining strain diversity in specific genes. Finally, we show that p-crAssphage can be acquired through fecal microbiota transplantation.}, } @article {pmid31940838, year = {2020}, author = {Bastaraud, A and Cecchi, P and Handschumacher, P and Altmann, M and Jambou, R}, title = {Urbanization and Waterborne Pathogen Emergence in Low-Income Countries: Where and How to Conduct Surveys?.}, journal = {International journal of environmental research and public health}, volume = {17}, number = {2}, pages = {}, pmid = {31940838}, issn = {1660-4601}, mesh = {Anti-Bacterial Agents/*analysis ; Bacteria/*isolation & purification ; *Biofilms ; Developing Countries ; Environmental Monitoring/methods ; Humans ; *Microbiota ; Poverty ; Sewage/*microbiology ; Surveys and Questionnaires ; *Urbanization ; *Water Microbiology ; }, abstract = {A major forthcoming sanitary issue concerns the apparition and spreading of drug-resistant microorganisms, potentially threatening millions of humans. In low-income countries, polluted urban runoff and open sewage channels are major sources of microbes. These microbes join natural microbial communities in aquatic ecosystems already impacted by various chemicals, including antibiotics. These composite microbial communities must adapt to survive in such hostile conditions, sometimes promoting the selection of antibiotic-resistant microbial strains by gene transfer. The low probability of exchanges between planktonic microorganisms within the water column may be significantly improved if their contact was facilitated by particular meeting places. This could be specifically the case within biofilms that develop on the surface of the myriads of floating macroplastics increasingly polluting urban tropical surface waters. Moreover, as uncultivable bacterial strains could be involved, analyses of the microbial communities in their whole have to be performed. This means that new-omic technologies must be routinely implemented in low- and middle-income countries to detect the appearance of resistance genes in microbial ecosystems, especially when considering the new 'plastic context.' We summarize the related current knowledge in this short review paper to anticipate new strategies for monitoring and surveying microbial communities.}, } @article {pmid31940381, year = {2020}, author = {Breusing, C and Franke, M and Young, CR}, title = {Intra-host symbiont diversity in eastern Pacific cold seep tubeworms identified by the 16S-V6 region, but undetected by the 16S-V4 region.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0227053}, pmid = {31940381}, issn = {1932-6203}, mesh = {Animals ; Bacteria/*classification/genetics/metabolism ; Biodiversity ; Ecosystem ; Electron Transport Complex IV/genetics ; Geologic Sediments ; Pacific Ocean ; Polychaeta/*classification/genetics/metabolism/*microbiology ; RNA, Ribosomal, 16S/analysis ; Symbiosis ; }, abstract = {Vestimentiferan tubeworms are key taxa in deep-sea chemosynthetic habitats worldwide. As adults they obtain their nutrition through their sulfide-oxidizing bacterial endosymbionts, which are acquired from the environment. Although horizontal transmission should favor infections by various symbiotic microbes, the current paradigm holds that every tubeworm harbors only one endosymbiotic 16S rRNA phylotype. Although previous studies based on traditional Sanger sequencing have questioned these findings, population level high-throughput analyses of the symbiont 16S diversity are still missing. To get further insights into the symbiont genetic variation and uncover hitherto hidden diversity we applied state-of-the-art 16S-V4 amplicon sequencing to populations of the co-occurring tubeworm species Lamellibrachia barhami and Escarpia spicata that were collected during E/V Nautilus and R/V Western Flyer cruises to cold seeps in the eastern Pacific Ocean. In agreement with earlier work our sequence data indicated that L. barhami and E. spicata share one monomorphic symbiont phylotype. However, complementary CARD-FISH analyses targeting the 16S-V6 region implied the existence of an additional phylotype in L. barhami. Our results suggest that the V4 region might not be sufficiently variable to investigate diversity in the intra-host symbiont population at least in the analyzed sample set. This is an important finding given that this region has become the standard molecular marker for high-throughput microbiome analyses. Further metagenomic research will be necessary to solve these issues and to uncover symbiont diversity that is hidden below the 16S rRNA level.}, } @article {pmid31940321, year = {2020}, author = {Honap, TP and Sankaranarayanan, K and Schnorr, SL and Ozga, AT and Warinner, C and Lewis, CM}, title = {Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0226930}, pmid = {31940321}, issn = {1932-6203}, support = {R01 GM089886/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophages/*classification/isolation & purification ; Bacteroides/virology ; *Gastrointestinal Microbiome ; Geography ; Humans ; *Industrial Development ; Life Style ; Metagenome ; Phylogeny ; Population Groups ; }, abstract = {CrAssphage (cross-assembly phage) is a bacteriophage that was first discovered in human gut metagenomic data. CrAssphage belongs to a diverse family of crAss-like bacteriophages thought to infect gut commensal bacteria belonging to Bacteroides species. However, not much is known about the biogeography of crAssphage and whether certain strains are associated with specific human populations. In this study, we screened publicly available human gut metagenomic data from 3,341 samples for the presence of crAssphage sensu stricto (NC_024711.1). We found that crAssphage prevalence is low in traditional, hunter-gatherer populations, such as the Hadza from Tanzania and Matses from Peru, as compared to industrialized, urban populations. Statistical comparisons showed no association of crAssphage prevalence with variables such as age, sex, body mass index, and health status of individuals. Phylogenetic analyses show that crAssphage strains reconstructed from the same individual over multiple time-points, cluster together. CrAssphage strains from individuals from the same study population do not always cluster together. Some evidence of clustering is seen at the level of broadly defined geographic regions, however, the relative positions of these clusters within the crAssphage phylogeny are not well-supported. We hypothesize that this lack of strong biogeographic structuring is suggestive of an expansion event within crAssphage. Using a Bayesian dating approach, we estimate that this expansion has occurred fairly recently. Overall, we determine that crAssphage presence is associated with an industrialized lifestyle and the absence of strong biogeographic structuring within global crAssphage strains is likely due to a recent population expansion within this bacteriophage.}, } @article {pmid31936703, year = {2020}, author = {Kang, S and You, HJ and Lee, YG and Jeong, Y and Johnston, TV and Baek, NI and Ku, S and Ji, GE}, title = {Production, Structural Characterization, and In Vitro Assessment of the Prebiotic Potential of Butyl-Fructooligosaccharides.}, journal = {International journal of molecular sciences}, volume = {21}, number = {2}, pages = {}, pmid = {31936703}, issn = {1422-0067}, support = {2017R1A2B2012390//National Research Foundation of Korea/ ; NRF-2017M3A9F3041747//National Research Foundation of Korea/ ; }, mesh = {Adult ; Ammonia/analysis ; Bacteria/classification/metabolism ; Biodiversity ; Butyrates/*metabolism ; Dietary Fiber ; Fatty Acids, Volatile/metabolism ; Feces/chemistry/microbiology ; Female ; Fermentation ; Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Oligosaccharides/*chemistry/*metabolism ; Prebiotics/*analysis ; Spectroscopy, Fourier Transform Infrared ; Young Adult ; }, abstract = {Short-chain fatty acids (SCFAs), especially butyrate, produced in mammalian intestinal tracts via fermentation of dietary fiber, are known biofunctional compounds in humans. However, the variability of fermentable fiber consumed on a daily basis and the diversity of gut microbiota within individuals often limits the production of short-chain fatty acids in the human gut. In this study, we attempted to enhance the butyrate levels in human fecal samples by utilizing butyl-fructooligosaccharides (B-FOS) as a novel prebiotic substance. Two major types of B-FOS (GF3-1B and GF3-2B), composed of short-chain fructooligosaccharides (FOS) bound to one or two butyric groups by ester bonds, were synthesized. Qualitative analysis of these B-FOS using Fourier transform infrared (FT-IR) spectroscopy, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), nuclear magnetic resonance (NMR) and low-resolution fast-atom bombardment mass spectra (LR-FAB-MS), showed that the chemical structure of GF3-1B and GF3-2B were [O-(1-buty-β-D-fru-(2→1)-O-β-D-fru-(2→1)-O-β-D-fru-O-α-D-glu] and [O-(1-buty)-β-D-fru-(2→1)-O-β-D-fru-(2→1)-O-(4-buty)-β-D-fru-O-α-D-glu], respectively. The ratio of these two compounds was approximately 5:3. To verify their biofunctionality as prebiotic oligosaccharides, proliferation and survival patterns of human fecal microbiota were examined in vitro via 16S rRNA metagenomics analysis compared to a positive FOS control and a negative control without a carbon source. B-FOS treatment showed different enrichment patterns on the fecal microbiota community during fermentation, and especially stimulated the growth of major butyrate producing bacterial consortia and modulated specific butyrate producing pathways with significantly enhanced butyrate levels. Furthermore, the relative abundance of Fusobacterium and ammonia production with related metabolic genes were greatly reduced with B-FOS and FOS treatment compared to the control group. These findings indicate that B-FOS differentially promotes butyrate production through the enhancement of butyrate-producing bacteria and their metabolic genes, and can be applied as a novel prebiotic compound in vivo.}, } @article {pmid31935465, year = {2020}, author = {O' Donovan, CM and Connor, B and Madigan, SM and Cotter, PD and O' Sullivan, O}, title = {Instances of altered gut microbiomes among Irish cricketers over periods of travel in the lead up to the 2016 World Cup: A sequencing analysis.}, journal = {Travel medicine and infectious disease}, volume = {35}, number = {}, pages = {101553}, doi = {10.1016/j.tmaid.2020.101553}, pmid = {31935465}, issn = {1873-0442}, mesh = {*Athletes ; Bacteria/classification/genetics ; Drug Resistance, Microbial ; Feces/microbiology ; Female ; Gastrointestinal Diseases/microbiology ; *Gastrointestinal Microbiome ; Humans ; Ireland ; Male ; RNA, Ribosomal, 16S ; *Travel ; Virulence/genetics ; }, abstract = {BACKGROUND: Changes and stresses experienced during travel have the potential to impact the gut microbiome, with travel implicated in the spread of antibiotic resistance genes across continents. The possibility of gut microbiome-mediated negative impacts arising from travel, and consequences for peak performance, would be of particular concern for elite athletes.

METHODS: Faecal samples were collected from male (N = 14) and female (N = 7) cricket players during the build-up to the 2016 Cricket World Cup. Baseline and post-travel samples were collected from all participants and subjected to 16S rRNA amplicon sequencing. Samples from a subset of participants (N = 4) were also analysed by shotgun metagenomic sequencing.

RESULTS: Analysis revealed a single travel time point as having the potential to have an impact on the gut microbiome. Reductions in alpha diversity following travel were observed, accompanied by shifts in the taxonomic profile of the gut microbiome. Antibiotic resistance and virulence genes were also identified as undergoing changes following travel.

CONCLUSIONS: This study reveals that periods of travel, in particular following gastrointestinal distress, may result in gut microbiome disruption. While this analysis was completed in athletes, the findings are applicable to all travelling individuals and considerations should be made surrounding travel in an attempt to reduce these changes.}, } @article {pmid31933014, year = {2020}, author = {Aguirre-Garrido, JF and Martínez-Abarca, F and Montiel-Lugo, D and Hernández-Soto, LM and Ramírez-Saad, H}, title = {Metagenomic analyses uncover the differential effect of azide treatment on bacterial community structure by enriching a specific Cyanobacteria present in a saline-alkaline environmental sample.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {23}, number = {3}, pages = {467-474}, doi = {10.1007/s10123-020-00119-z}, pmid = {31933014}, issn = {1618-1905}, support = {BIO2017-82244-P//Ministerio de Ciencia, Innovación y Universidades/ ; 710228//Consejo Nacional de Ciencia y Tecnología/ ; 291062//Consejo Nacional de Ciencia y Tecnología/ ; }, mesh = {Bacteria/classification/genetics/isolation & purification ; Cyanobacteria/genetics/*isolation & purification ; DNA, Bacterial ; Environmental Microbiology ; Enzyme Inhibitors/adverse effects ; Genome, Bacterial ; Lakes/microbiology ; Metagenomics/*methods ; *Microbiota/genetics ; Salinity ; Sodium Azide/*adverse effects ; }, abstract = {Treatment of environmental samples under field conditions may require the application of chemical preservatives, although their use sometimes produces changes in the microbial communities. Sodium azide, a commonly used preservative, is known to differentially affect the growth of bacteria. Application of azide and darkness incubation to Isabel soda lake water samples induced changes in the structure of the bacterial community, as assessed by partial 16S rRNA gene pyrosequencing. Untreated water samples (WU) were dominated by gammaproteobacterial sequences accounting for 86%, while in the azide-treated (WA) samples, this group was reduced to 33% abundance, and cyanobacteria-related sequences became dominant with 53%. Shotgun sequencing and genome recruitment analyses pointed to Halomonas campanensis strain LS21 (genome size 4.07 Mbp) and Synechococcus sp. RS9917 (2.58 Mbp) as the higher recruiting genomes from the sequence reads of WA and WU environmental libraries, respectively, covering nearly the complete genomes. Combined treatment of water samples with sodium azide and darkness has proven effective on the selective enrichment of a cyanobacterial group. This approach may allow the complete (or almost-complete) genome sequencing of Cyanobacteria from metagenomic DNA of different origins, and thus increasing the number of the underrepresented cyanobacterial genomes in the databases.}, } @article {pmid31933013, year = {2020}, author = {Xu, Y and Zhang, G and Ding, H and Ci, D and Dai, L and Zhang, Z}, title = {Influence of salt stress on the rhizosphere soil bacterial community structure and growth performance of groundnut (Arachis hypogaea L.).}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {23}, number = {3}, pages = {453-465}, doi = {10.1007/s10123-020-00118-0}, pmid = {31933013}, issn = {1618-1905}, support = {2018YFD1000906//the National Key R&D Program of China/ ; CXGC2018E21//the Agricultural Scientific and the Technological Innovation Project of Shandong Academy of Agricultural Sciences/ ; }, mesh = {Actinobacteria/genetics/isolation & purification ; Arachis/growth & development/*microbiology ; Bacteria/classification/genetics/isolation & purification ; Cyanobacteria/genetics/isolation & purification ; DNA, Bacterial ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S ; *Rhizosphere ; Salinity ; *Salt Stress ; Soil/chemistry ; Soil Microbiology ; Sphingomonas/genetics/isolation & purification ; }, abstract = {Soil salinity is regarded as severe environmental stress that can change the composition of rhizosphere soil bacterial community and import a plethora of harms to crop plants. However, relatively little is known about the relationship between salt stress and root microbial communities in groundnuts. The goal of this study was to assess the effect of salt stress on groundnut growth performance and rhizosphere microbial community structure. Statistical analysis exhibited that salt stress indeed affected groundnut growth and pod yield. Further taxonomic analysis showed that the bacterial community predominantly consisted of phyla Proteobacteria, Actinobacteria, Saccharibacteria, Chloroflexi, Acidobacteria, and Cyanobacteria. Among these bacteria, numbers of Cyanobacteria and Acidobacteria mainly increased, while that of Actinobacteria and Chloroflexi decreased after salt treatment via taxonomic and qPCR analysis. Moreover, Sphingomonas and Microcoleus as the predominant genera in salt-treated rhizosphere soils might enhance salt tolerance as plant growth-promoting rhizobacteria. Metagenomic profiling showed that series of sequences related to signaling transduction, posttranslational modification, and chaperones were enriched in the salt-treated soils, which may have implications for plant survival and salt tolerance. These data will help us better understand the symbiotic relationship between the dominant microbial community and groundnuts and form the foundation for further improvement of salt tolerance of groundnuts via modification of soil microbial community.}, } @article {pmid31931655, year = {2020}, author = {Boling, L and Cuevas, DA and Grasis, JA and Kang, HS and Knowles, B and Levi, K and Maughan, H and McNair, K and Rojas, MI and Sanchez, SE and Smurthwaite, C and Rohwer, F}, title = {Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome.}, journal = {Gut microbes}, volume = {11}, number = {4}, pages = {721-734}, pmid = {31931655}, issn = {1949-0984}, support = {R01 GM095384/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*growth & development ; Diet ; Feces/microbiology ; *Food ; Food Additives/pharmacology ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Plant Extracts/*pharmacology ; *Virus Activation ; }, abstract = {The approximately 10[11] viruses and microbial cells per gram of fecal matter (dry weight) in the large intestine are important to human health. The responses of three common gut bacteria species, and one opportunistic pathogen, to 117 commonly consumed foods, chemical additives, and plant extracts were tested. Many compounds, including Stevia rebaudiana and bee propolis extracts, exhibited species-specific growth inhibition by prophage induction. Overall, these results show that various foods may change the abundances of gut bacteria by modulating temperate phage and suggests a novel path for landscaping the human gut microbiome.}, } @article {pmid31930986, year = {2020}, author = {Casals-Pascual, C and González, A and Vázquez-Baeza, Y and Song, SJ and Jiang, L and Knight, R}, title = {Microbial Diversity in Clinical Microbiome Studies: Sample Size and Statistical Power Considerations.}, journal = {Gastroenterology}, volume = {158}, number = {6}, pages = {1524-1528}, doi = {10.1053/j.gastro.2019.11.305}, pmid = {31930986}, issn = {1528-0012}, mesh = {Bacteria/*genetics/isolation & purification ; Biomarkers/analysis ; Feces/microbiology ; Gastrointestinal Diseases/*diagnosis/microbiology/therapy ; Gastrointestinal Microbiome/*genetics ; Genetic Heterogeneity ; Humans ; Intestinal Mucosa/microbiology ; Metagenomics/*standards ; Observational Studies as Topic/standards ; Phylogeny ; Randomized Controlled Trials as Topic/standards ; Sample Size ; Treatment Outcome ; }, } @article {pmid31928131, year = {2020}, author = {Bowerman, KL and Varelias, A and Lachner, N and Kuns, RD and Hill, GR and Hugenholtz, P}, title = {Continuous pre- and post-transplant exposure to a disease-associated gut microbiome promotes hyper-acute graft-versus-host disease in wild-type mice.}, journal = {Gut microbes}, volume = {11}, number = {4}, pages = {754-770}, pmid = {31928131}, issn = {1949-0984}, mesh = {Acute Disease ; Animals ; Bacteroidetes/growth & development ; Disease Susceptibility ; Dysbiosis ; Enterobacteriaceae/growth & development/pathogenicity ; Feces/microbiology ; *Gastrointestinal Microbiome ; Graft vs Host Disease/*etiology/microbiology ; *Hematopoietic Stem Cell Transplantation ; Housing, Animal ; Metagenome ; Mice ; Mice, Inbred C57BL ; Virulence Factors/metabolism ; }, abstract = {OBJECTIVE: The gut microbiome plays a key role in the development of acute graft-versus-host disease (GVHD) following allogeneic hematopoietic stem cell transplantation. Here we investigate the individual contribution of the pre- and post-transplant gut microbiome to acute GVHD using a well-studied mouse model.

DESIGN: Wild-type mice were cohoused with IL-17RA[-/ -] mice, susceptible to hyperacute GVHD, either pre- or post-transplant alone or continuously (i.e., pre- and post-transplant). Fecal samples were collected from both WT and IL-17RA[-/ -] mice pre- and post-cohousing and post-transplant and the microbiome analyzed using metagenomic sequencing.

RESULTS: Priming wild-type mice via cohousing pre-transplant only is insufficient to accelerate GVHD, however, accelerated disease is observed in WT mice cohoused post-transplant only. When mice are cohoused continuously, the effect of priming and exacerbation is additive, resulting in a greater acceleration of disease in WT mice beyond that seen with cohousing post-transplant only. Metagenomic analysis of the microbiome revealed pre-transplant cohousing is associated with the transfer of specific species within two as-yet-uncultured genera of the bacterial family Muribaculaceae; CAG-485 and CAG-873. Post-transplant, we observed GVHD-associated blooms of Enterobacteriaceae members Escherichia coli and Enterobacter hormaechei subsp. steigerwaltii, and hyperacute GVHD gut microbiome distinct from that associated with delayed-onset disease (>10 days post-transplant).

CONCLUSION: These results clarify the importance of the peri-transplant microbiome in the susceptibility to acute GVHD post-transplant and demonstrate the species-specific nature of this association.}, } @article {pmid31928124, year = {2020}, author = {Ye, Z and Wu, C and Zhang, N and Du, L and Cao, Q and Huang, X and Tang, J and Wang, Q and Li, F and Zhou, C and Xu, Q and Xiong, X and Kijlstra, A and Qin, N and Yang, P}, title = {Altered gut microbiome composition in patients with Vogt-Koyanagi-Harada disease.}, journal = {Gut microbes}, volume = {11}, number = {3}, pages = {539-555}, pmid = {31928124}, issn = {1949-0984}, mesh = {Adrenal Cortex Hormones/therapeutic use ; Adult ; Animals ; Biodiversity ; Butyrates/metabolism ; DNA, Bacterial ; Disease Models, Animal ; Dysbiosis/*microbiology ; Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Genotyping Techniques ; Humans ; Immunosuppressive Agents/therapeutic use ; Lactic Acid/metabolism ; Male ; Mice ; Prognosis ; Uveomeningoencephalitic Syndrome/*microbiology ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Vogt-Koyanagi-Harada (VKH) disease is a multisystemic autoimmune disorder characterized by granulomatous panuveitis. Gut microbiome has been considered to play a role in the pathogenesis of this disease but whether the alternation of gut microbiome was involved is unclear. This study was set up to identify abnormalities of gut microbiome composition in VKH disease.

RESULTS: Depleted butyrate-producing bacteria, lactate-producing bacteria and methanogens as well as enriched Gram-negative bacteria were identified in the active VKH patients, as well as in VKH patients of Mix enterotype and Bacteroides enterotype. Changes of gut microbiome in the VKH patients were partially restored after an immunosuppressive treatment. The disease susceptibility genotype HLA-DRA was associated with Bacteroides sp.2.1.33B, Paraprevotella clara, Alistipes finegoldii and Eubacterium eligens. A microbial marker profile including 40 disease-associated species was established to differentiate patients from controls. Another microbial marker profile including 37 species was found to be associated with the response to treatment. An animal experiment showed that transfer of gut microbiome from VKH patients could significantly exacerbate disease activity clinically and pathologically in the recipient mice.

CONCLUSION: Our results revealed a distinct gut microbiome signature in VKH patients and showed an exacerbating effect of this gut microbiome on experimental autoimmune uveitis (EAU). We also developed two microbial marker profiles in differentiating VKH patients from healthy controls as well as predicting the effectiveness of treatment.}, } @article {pmid31927795, year = {2020}, author = {Zemb, O and Achard, CS and Hamelin, J and De Almeida, ML and Gabinaud, B and Cauquil, L and Verschuren, LMG and Godon, JJ}, title = {Absolute quantitation of microbes using 16S rRNA gene metabarcoding: A rapid normalization of relative abundances by quantitative PCR targeting a 16S rRNA gene spike-in standard.}, journal = {MicrobiologyOpen}, volume = {9}, number = {3}, pages = {e977}, pmid = {31927795}, issn = {2045-8827}, mesh = {Base Sequence ; Biodiversity ; *DNA Barcoding, Taxonomic/methods ; Environmental Microbiology ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/chemistry/*genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Metabarcoding of the 16S rRNA gene is commonly used to characterize microbial communities, by estimating the relative abundance of microbes. Here, we present a method to retrieve the concentrations of the 16S rRNA gene per gram of any environmental sample using a synthetic standard in minuscule amounts (100 ppm to 1% of the 16S rRNA sequences) that is added to the sample before DNA extraction and quantified by two quantitative polymerase chain reaction (qPCR) reactions. This allows normalizing by the initial microbial density, taking into account the DNA recovery yield. We quantified the internal standard and the total load of 16S rRNA genes by qPCR. The qPCR for the latter uses the exact same primers as those used for Illumina sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene to increase accuracy. We are able to calculate the absolute concentration of the species per gram of sample, taking into account the DNA recovery yield. This is crucial for an accurate estimate as the yield varied between 40% and 84%. This method avoids sacrificing a high proportion of the sequencing effort to quantify the internal standard. If sacrificing a part of the sequencing effort to the internal standard is acceptable, we however recommend that the internal standard accounts for 30% of the environmental 16S rRNA genes to avoid the PCR bias associated with rare phylotypes. The method proposed here was tested on a feces sample but can be applied more broadly on any environmental sample. This method offers a real improvement of metabarcoding of microbial communities since it makes the method quantitative with limited efforts.}, } @article {pmid31927673, year = {2020}, author = {Song, Y and Himmel, B and Öhrmalm, L and Gyarmati, P}, title = {The Microbiota in Hematologic Malignancies.}, journal = {Current treatment options in oncology}, volume = {21}, number = {1}, pages = {2}, pmid = {31927673}, issn = {1534-6277}, mesh = {Animals ; Antineoplastic Combined Chemotherapy Protocols/adverse effects/therapeutic use ; Bacteremia/diagnosis/etiology/therapy ; Biodiversity ; Combined Modality Therapy ; Disease Management ; Dysbiosis/diagnosis/*etiology/therapy ; Gastrointestinal Microbiome ; Hematologic Neoplasms/*complications/diagnosis/therapy ; Hematopoietic Stem Cell Transplantation/adverse effects/methods ; Humans ; Immunocompromised Host ; Metagenome ; Metagenomics/methods ; *Microbiota ; }, abstract = {There are approximately 1.2 million new hematologic malignancy cases resulting in ~ 690,000 deaths each year worldwide, and hematologic malignancies remain the most commonly occurring cancer in children. Even though advances in anticancer treatment regimens in recent decades have considerably improved survival rates, their cytotoxic effects and the resulting long-term complications pose a significant burden on the patients and the health care system. Therefore, non-toxic treatment modalities are needed to decrease side effects. The human body is the host to approximately 40 trillion microbes, known as the human microbiota. The large majority of the microbiota is located in the gastrointestinal tract, and is primarily composed of bacteria. The microbiota plays several important physiological roles, ranging from digestive functions to immunological and neural development. Investigating the microbiota in patients with hematologic malignancies has several important implications. The microbiota affects hematopoiesis, and influences the efficacies of chemotherapy and antimicrobial treatments. Determination of the microbiota composition and diversity could be an important part of risk stratification in the future, and may also take part to personalize antimicrobial treatments. Modulation of the microbiota via probiotics or fecal transplant can potentially be involved in reducing side effects of chemotherapy, and eliminating multiple drug resistant strains in patients with hematologic malignancies.}, } @article {pmid31927597, year = {2020}, author = {Sun, F and Wang, C and Chen, H and Zheng, Z}, title = {Metagenomic Analysis of the Effect of Enteromorpha prolifera Bloom on Microbial Community and Function in Aquaculture Environment.}, journal = {Current microbiology}, volume = {77}, number = {5}, pages = {816-825}, pmid = {31927597}, issn = {1432-0991}, support = {2017A020216008//Guangdong Science and Technology Department/ ; 2016I1002//Fujian Provincial Department of Science and Technology/ ; 2017T3010//Fujian Provincial Department of Science and Technology/ ; }, mesh = {Actinomycetales/classification ; *Aquaculture ; *Eutrophication ; Flavobacteriaceae/classification ; *Metagenome ; Metagenomics ; *Microbiota ; Sequence Analysis, DNA ; Ulva/growth & development/*metabolism ; Viruses/classification ; }, abstract = {Enteromorpha prolifera blooms considerably affected coastal environments in recent years. However, the effects of E. prolifera on microbial ecology and function remained unknown. In this study, metagenomic sequencing was used to investigate the effect of E. prolifera bloom on the microbial communities and functional genes in an aquaculture environment. Results showed that E. prolifera bloom could significantly alter the microbial composition and abundance, and heterotrophic bacteria comprised the major groups in the E. prolifera bloom pond, which was dominated by Actinomycetales and Flavobacteriales. The study indicated that viruses played an important role in shaping the microbial community and diversity during E. prolifera bloom. These viruses affected various dominant microbial taxa (such as Rhodobacteraceae, Synechococcus, and Prochlorococcus), which produced an obvious impact on potential nutrient transformation. Functional annotation analysis indicated that E. prolifera bloom would considerably shift the metabolism function by altering the structure and abundance of the microbial community. E. prolifera bloom pond had the low ability of potential metabolic capabilities of nitrogen, sulfur, and phosphate, whereas promoted gene abundance of genetic information processing. These changes in the microbial community and function could produce serious effect on aquaculture ecosystem.}, } @article {pmid31926407, year = {2020}, author = {Edge, TA and Baird, DJ and Bilodeau, G and Gagné, N and Greer, C and Konkin, D and Newton, G and Séguin, A and Beaudette, L and Bilkhu, S and Bush, A and Chen, W and Comte, J and Condie, J and Crevecoeur, S and El-Kayssi, N and Emilson, EJS and Fancy, DL and Kandalaft, I and Khan, IUH and King, I and Kreutzweiser, D and Lapen, D and Lawrence, J and Lowe, C and Lung, O and Martineau, C and Meier, M and Ogden, N and Paré, D and Phillips, L and Porter, TM and Sachs, J and Staley, Z and Steeves, R and Venier, L and Veres, T and Watson, C and Watson, S and Macklin, J}, title = {The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada.}, journal = {The Science of the total environment}, volume = {710}, number = {}, pages = {135906}, doi = {10.1016/j.scitotenv.2019.135906}, pmid = {31926407}, issn = {1879-1026}, mesh = {Animals ; Biodiversity ; Canada ; Fresh Water ; Humans ; *Metagenomics ; *Soil ; }, abstract = {Transformative advances in metagenomics are providing an unprecedented ability to characterize the enormous diversity of microorganisms and invertebrates sustaining soil health and water quality. These advances are enabling a better recognition of the ecological linkages between soil and water, and the biodiversity exchanges between these two reservoirs. They are also providing new perspectives for understanding microorganisms and invertebrates as part of interacting communities (i.e. microbiomes and zoobiomes), and considering plants, animals, and humans as holobionts comprised of their own cells as well as diverse microorganisms and invertebrates often acquired from soil and water. The Government of Canada's Genomics Research and Development Initiative (GRDI) launched the Ecobiomics Project to coordinate metagenomics capacity building across federal departments, and to apply metagenomics to better characterize microbial and invertebrate biodiversity for advancing environmental assessment, monitoring, and remediation activities. The Project has adopted standard methods for soil, water, and invertebrate sampling, collection and provenance of metadata, and nucleic acid extraction. High-throughput sequencing is located at a centralized sequencing facility. A centralized Bioinformatics Platform was established to enable a novel government-wide approach to harmonize metagenomics data collection, storage and bioinformatics analyses. Sixteen research projects were initiated under Soil Microbiome, Aquatic Microbiome, and Invertebrate Zoobiome Themes. Genomic observatories were established at long-term environmental monitoring sites for providing more comprehensive biodiversity reference points to assess environmental change.}, } @article {pmid31925997, year = {2020}, author = {Niu, KM and Lee, BJ and Kothari, D and Lee, WD and Hur, SW and Lim, SG and Kim, KW and Kim, KD and Kim, NN and Kim, SK}, title = {Dietary effect of low fish meal aquafeed on gut microbiota in olive flounder (Paralichthys olivaceus) at different growth stages.}, journal = {MicrobiologyOpen}, volume = {9}, number = {3}, pages = {e992}, pmid = {31925997}, issn = {2045-8827}, mesh = {*Animal Feed ; Animals ; Biodiversity ; Fishes ; Flounder/*growth & development/*microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; RNA, Ribosomal, 16S ; }, abstract = {This study was conducted to investigate the long-term effect of a low fish meal (FM) diet comprising plant-based protein sources (PPS) on changes of gut microbial diversity in olive flounder (Paralichthys olivaceus) over the course of life. Two experimental diets were prepared to contain 74% FM (control) or 52% FM with 22% PPS (30% FM replacement, FM30). Fish were fed one of the two experimental diets for 8 months, and we collected the midgut contents to analyze the gut bacterial community by Illumina MiSeq based on the metagenomic sequences in the V3-V4 regions of 16S rRNA. We found that there were nine dominant phyla, which in turn presented Proteobacteria, Firmicutes, and Actinobacteria as the three major phyla in the gut microbiota of the flounder. At genus level, the dominant genera were Delftia, Prevotella, and Chthoniobacter at the juvenile stage (below 100 g/fish); Chthoniobacter, Bacillus, and Bradyrhizobium at the grower stage (400 g/fish); Chthoniobacter, Bacillus, and Delftia at the subadult stage (800 g/fish); and Lactobacillus and Prevotella at the adult stage (over 1,000 g/fish). The microbial diversity in olive flounders arched from the juvenile and subadult stage and reached a plateau thereafter. The fish fed the FM30 diet significantly had an increased abundance of Lactobacillus and Photobacterium and had less abundance of Prevotella and Paraprevotella than the control. However, the effect of dietary PPS was not significant on total microbial richness, indicating no negative effect as feed sources on the intestinal microbiota in olive flounder. These results indicate that the life stage of olive flounder is more important in modulating intestinal microbiota than is the diet. It could also be concluded that dietary PPS might be used as a potential fish meal alternative without any compromising effects on microbial diversity of olive flounder for long-term feeding.}, } @article {pmid31924616, year = {2020}, author = {Jnana, A and Muthuraman, V and Varghese, VK and Chakrabarty, S and Murali, TS and Ramachandra, L and Shenoy, KR and Rodrigues, GS and Prasad, SS and Dendukuri, D and Morschhauser, A and Nestler, J and Peter, H and Bier, FF and Satyamoorthy, K}, title = {Microbial Community Distribution and Core Microbiome in Successive Wound Grades of Individuals with Diabetic Foot Ulcers.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {6}, pages = {}, pmid = {31924616}, issn = {1098-5336}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/*isolation & purification ; Diabetic Foot/*microbiology ; Female ; Humans ; Male ; *Microbiota ; Middle Aged ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sex Factors ; Young Adult ; }, abstract = {Diabetic foot ulcer (DFU) is a major complication of diabetes with high morbidity and mortality rates. The pathogenesis of DFUs is governed by a complex milieu of environmental and host factors. The empirical treatment is initially based on wound severity since culturing and profiling the antibiotic sensitivity of wound-associated microbes is time-consuming. Hence, a thorough and rapid analysis of the microbial landscape is a major requirement toward devising evidence-based interventions. Toward this, 122 wound (100 diabetic and 22 nondiabetic) samples were sampled for their bacterial community structure using both culture-based and next-generation 16S rRNA-based metagenomics approach. Both the approaches showed that the Gram-negative microbes were more abundant in the wound microbiome. The core microbiome consisted of bacterial genera, including Alcaligenes, Pseudomonas, Burkholderia, and Corynebacterium in decreasing order of average relative abundance. Despite the heterogenous nature and extensive sharing of microbes, an inherent community structure was apparent, as revealed by a cluster analysis based on Euclidean distances. Facultative anaerobes (26.5%) were predominant in Wagner grade 5, while strict anaerobes were abundant in Wagner grade 1 (26%). A nonmetric dimensional scaling analysis could not clearly discriminate samples based on HbA1c levels. Sequencing approach revealed the presence of major culturable species even in samples with no bacterial growth in culture-based approach. Our study indicates that (i) the composition of core microbial community varies with wound severity, (ii) polymicrobial species distribution is individual specific, and (iii) antibiotic susceptibility varies with individuals. Our study suggests the need to evolve better-personalized care for better wound management therapies.IMPORTANCE Chronic nonhealing diabetic foot ulcers (DFUs) are a serious complication of diabetes and are further exacerbated by bacterial colonization. The microbial burden in the wound of each individual displays diverse morphological and physiological characteristics with unique patterns of host-pathogen interactions, antibiotic resistance, and virulence. Treatment involves empirical decisions until definitive results on the causative wound pathogens and their antibiotic susceptibility profiles are available. Hence, there is a need for rapid and accurate detection of these polymicrobial communities for effective wound management. Deciphering microbial communities will aid clinicians to tailor their treatment specifically to the microbes prevalent in the DFU at the time of assessment. This may reduce DFUs associated morbidity and mortality while impeding the rise of multidrug-resistant microbes.}, } @article {pmid31924114, year = {2020}, author = {Liu, Z and Luo, G and Du, R and Sun, W and Li, J and Lan, H and Chen, P and Yuan, X and Cao, D and Li, Y and Liu, C and Liang, S and Jin, X and Yang, R and Bi, Y and Han, Y and Cao, P and Zhao, W and Ling, S and Li, Y}, title = {Effects of spaceflight on the composition and function of the human gut microbiota.}, journal = {Gut microbes}, volume = {11}, number = {4}, pages = {807-819}, pmid = {31924114}, issn = {1949-0984}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/*growth & development ; Bacteroides/genetics/growth & development ; Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Firmicutes/genetics/growth & development ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Genes, Bacterial ; Humans ; Interspersed Repetitive Sequences ; Metagenome ; *Space Flight ; Virulence/genetics ; }, abstract = {Interaction between humans and the gut microbiota is important for human physiology. Here, the gut microbiota was analyzed via metagenomic sequencing, and the fluctuations in the gut microbiota under the conditions of spaceflight were characterized. The composition and function of the gut microbiota were substantially affected by spaceflight; however, individual specificity was uncompromised. We further confirmed the species fluctuations and functional genes from both missions. Resistance and virulence genes in the gut microbiota were affected by spaceflight, but the species attributions remained stable. Spaceflight markedly affected the composition and function of the human gut microbiota, implying that the human gut microbiota is sensitive to spaceflight.}, } @article {pmid31924109, year = {2020}, author = {Triplett, J and Ellis, D and Braddock, A and Roberts, E and Ingram, K and Perez, E and Short, A and Brown, D and Hutzley, V and Webb, C and Soto, A and Chan, V}, title = {Temporal and region-specific effects of sleep fragmentation on gut microbiota and intestinal morphology in Sprague Dawley rats.}, journal = {Gut microbes}, volume = {11}, number = {4}, pages = {706-720}, pmid = {31924109}, issn = {1949-0984}, mesh = {Animals ; Bacterial Adhesion ; Bacterial Physiological Phenomena ; Cecum/microbiology/*pathology ; Colon/microbiology/*pathology ; Cytokines/analysis ; Endotoxins/analysis ; *Gastrointestinal Microbiome ; Hypothalamo-Hypophyseal System/physiology ; Ileum/microbiology/*pathology ; Phylogeny ; Rats ; Rats, Sprague-Dawley ; *Sleep Deprivation/microbiology/pathology/physiopathology ; }, abstract = {Sleep is a fundamental biological process, that when repeatedly disrupted, can result in severe health consequences. Recent studies suggest that both sleep fragmentation (SF) and dysbiosis of the gut microbiome can lead to metabolic disorders, though the underlying mechanisms are largely unclear. To better understand the consequences of SF, we investigated the effects of acute (6 days) and chronic (6 weeks) SF on rats by examining taxonomic profiles of microbiota in the distal ileum, cecum and proximal colon, as well as assessing structural and functional integrity of the gastrointestinal barrier. We further assayed the impact of SF on a host function by evaluating inflammation and immune response. Both acute and chronic SF induced microbial dysbiosis, more dramatically in the distal ileum (compared to other two regions studied), as noted by significant perturbations in alpha- and beta-diversity; though, specific microbial populations were significantly altered throughout each of the three regions. Furthermore, chronic SF resulted in increased crypt depth in the distal ileum and an increase in the number of villi lining both the cecum and proximal colon. Additional changes were noted with chronic SF, including: decreased microbial adhesion and penetration in the distal ileum and cecum, elevation in serum levels of the cytokine KC/GRO, and depressed levels of corticotropin. Importantly, our data show that perturbations to microbial ecology and intestinal morphology intensify in response to prolonged SF and these changes are habitat specific. Together, these results reveal consequences to gut microbiota homeostasis and host response following acute and chronic SF in rats.}, } @article {pmid31922546, year = {2020}, author = {Morris, MM and Frixione, NJ and Burkert, AC and Dinsdale, EA and Vannette, RL}, title = {Microbial abundance, composition, and function in nectar are shaped by flower visitor identity.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {3}, pages = {}, doi = {10.1093/femsec/fiaa003}, pmid = {31922546}, issn = {1574-6941}, mesh = {Animals ; Bees ; Birds ; Flowers ; *Microbiota ; *Plant Nectar ; Pollination ; }, abstract = {Microbial dispersal is essential for establishment in new habitats, but the role of vector identity is poorly understood in community assembly and function. Here, we compared microbial assembly and function in floral nectar visited by legitimate pollinators (hummingbirds) and nectar robbers (carpenter bees). We assessed effects of visitation on the abundance and composition of culturable bacteria and fungi and their taxonomy and function using shotgun metagenomics and nectar chemistry. We also compared metagenome-assembled genomes (MAGs) of Acinetobacter, a common and highly abundant nectar bacterium, among visitor treatments. Visitation increased microbial abundance, but robbing resulted in 10× higher microbial abundance than pollination. Microbial communities differed among visitor treatments: robbed flowers were characterized by predominant nectar specialists within Acetobacteraceae and Metschnikowiaceae, with a concurrent loss of rare taxa, and these resulting communities harbored genes relating to osmotic stress, saccharide metabolism and specialized transporters. Gene differences were mirrored in function: robbed nectar contained a higher percentage of monosaccharides. Draft genomes of Acinetobacter revealed distinct amino acid and saccharide utilization pathways in strains isolated from robbed versus pollinated flowers. Our results suggest an unrecognized cost of nectar robbing for pollination and distinct effects of visitor type on interactions between plants and pollinators. Overall, these results suggest vector identity is an underappreciated factor structuring microbial community assembly and function.}, } @article {pmid31922542, year = {2020}, author = {Kanger, K and Guilford, NGH and Lee, H and Nesbø, CL and Truu, J and Edwards, EA}, title = {Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {2}, pages = {}, doi = {10.1093/femsec/fiaa006}, pmid = {31922542}, issn = {1574-6941}, mesh = {Anaerobiosis ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/*genetics ; Food ; Food Microbiology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Metagenome ; *Microbiota/genetics ; Plasmids ; RNA, Ribosomal, 16S ; *Waste Products ; }, abstract = {Solid organic waste is a significant source of antibiotic resistance genes (ARGs) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here, we studied ARG diversity and abundance as well as the relationship between antibiotic resistome and microbial community structure within a lab-scale solid-state anaerobic digester treating a mixture of food waste, paper and cardboard. A total of 10 samples from digester feed and digestion products were collected for microbial community analysis including small subunit rRNA gene sequencing, total community metagenome sequencing and high-throughput quantitative PCR. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. ARGs were identified in all samples with multidrug resistance being the most abundant ARG type. Thirty-two per cent of ARGs detected in digester feed were located on plasmids indicating potential for horizontal gene transfer. Using metagenomic assembly and binning, we detected potential bacterial hosts of ARGs in digester feed, which included Erwinia, Bifidobacteriaceae, Lactococcus lactis and Lactobacillus. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.}, } @article {pmid31919742, year = {2020}, author = {Zhang, T and Lu, G and Zhao, Z and Liu, Y and Shen, Q and Li, P and Chen, Y and Yin, H and Wang, H and Marcella, C and Cui, B and Cheng, L and Ji, G and Zhang, F}, title = {Washed microbiota transplantation vs. manual fecal microbiota transplantation: clinical findings, animal studies and in vitro screening.}, journal = {Protein & cell}, volume = {11}, number = {4}, pages = {251-266}, pmid = {31919742}, issn = {1674-8018}, mesh = {Animals ; Centrifugation ; Clostridium Infections/*therapy ; *Fecal Microbiota Transplantation/adverse effects ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; High-Throughput Nucleotide Sequencing ; Injections, Intraperitoneal ; Male ; Metabolomics ; Mice ; Mice, Inbred C57BL ; *Microbiota ; Suspensions/administration & dosage/metabolism/*pharmacology ; }, abstract = {Fecal microbiota transplantation (FMT) by manual preparation has been applied to treat diseases for thousands of years. However, this method still endures safety risks and challenges the psychological endurance and acceptance of doctors, patients and donors. Population evidence showed the washed microbiota preparation with microfiltration based on an automatic purification system followed by repeated centrifugation plus suspension for three times significantly reduced FMT-related adverse events. This washing preparation makes delivering a precise dose of the enriched microbiota feasible, instead of using the weight of stool. Intraperitoneal injection in mice with the fecal microbiota supernatant obtained after repeated centrifugation plus suspension for three times induced less toxic reaction than that by the first centrifugation following the microfiltration. The toxic reactions that include death, the change in the level of peripheral white blood cells, and the proliferation of germinal center in secondary lymphoid follicles in spleen were noted. The metagenomic next-generation sequencing (NGS) indicated the increasing types and amount of viruses could be washed out during the washing process. Metabolomics analysis indicated metabolites with pro-inflammatory effects in the fecal microbiota supernatant such as leukotriene B4, corticosterone, and prostaglandin G2 could be removed by repeated washing. Near-infrared absorption spectroscopy could be served as a rapid detection method to control the quality of the washing-process. In conclusion, this study for the first time provides evidence linking clinical findings and animal experiments to support that washed microbiota transplantation (WMT) is safer, more precise and more quality-controllable than the crude FMT by manual.}, } @article {pmid31917273, year = {2020}, author = {Yuan, X and Wang, L and Meng, D and Wu, L and Wang, X and Zhang, D and Luo, Z and Pang, Y and Liu, G}, title = {The impact of NBUVB on microbial community profiling in the lesional skin of vitiligo subjects.}, journal = {Microbial pathogenesis}, volume = {140}, number = {}, pages = {103943}, doi = {10.1016/j.micpath.2019.103943}, pmid = {31917273}, issn = {1096-1208}, mesh = {Actinobacteria/classification/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; Female ; Firmicutes/classification/genetics/isolation & purification ; Humans ; Male ; Metagenomics ; Microbiota/*genetics ; Proteobacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S ; Skin/*microbiology/pathology ; *Ultraviolet Therapy ; Vitiligo/*microbiology ; }, abstract = {BACKGROUND: The impact of NBUVB on the cutaneous microbiota of vitiligo patients remains to be fully elucidated.

METHODS: To characterize the cutaneous microbiota in vitiligo patients, cutaneous samples from 60 patients with vitiligo and after NBUVB irradiation were profiled using the Illumina MiSeq platform. Alpha diversity estimations revealed higher microbiota diversity in samples from patients with lesional skin. Beta diversity (Principal Component Analysis (PCA)) analysis showed that the bacterial community structure segregated differently between different groups.

RESULTS: There was a statistically significant increase in the Sobs, ACE, and Chao indices in the NB group compared with NF group, as determined by t-test. The alpha diversity have no significant difference between NF and DB group. At the phylum level, Firmicutes, Proteobacteria and Actinobacteria were the most predominant phyla. Propionibacterium and Pseudomonas were the most predominant genera in each group. In addition, Staphylococcus, Bacillus and Prevotella were enriched in DF group compared to DB group. Propionibacterium was enriched in DB group compared to DF group.

CONCLUSIONS: Our studies indicate differences in microbial community dynamics of the lesional and non-lesional sites of vitiligo subjects, with greater diversity and higher association between microbial communities of the unaffected site. And NBUVB irradiation might eliminate these differences.}, } @article {pmid31916894, year = {2020}, author = {Kovtun, AS and Averina, OV and Alekseeva, MG and Danilenko, VN}, title = {Antibiotic Resistance Genes in the Gut Microbiota of Children with Autistic Spectrum Disorder as Possible Predictors of the Disease.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {26}, number = {11}, pages = {1307-1320}, doi = {10.1089/mdr.2019.0325}, pmid = {31916894}, issn = {1931-8448}, mesh = {Aminoglycosides/genetics ; Anti-Bacterial Agents/therapeutic use ; Autism Spectrum Disorder/*microbiology ; Bacteria/drug effects/*genetics ; Child ; Child, Preschool ; Drug Resistance, Microbial/drug effects/*genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Genes, Bacterial/*genetics ; Humans ; Male ; Metagenomics/methods ; Moscow ; beta-Lactams/metabolism ; }, abstract = {The gut microbiota (GM), which contains thousands of bacterial species, is a reservoir of antibiotic resistance genes (ARGs) called resistome. Early life exposure to antibiotics alters significantly the composition and function of the gut microbiota of children, which may trigger symptoms of autism spectrum disorder (ASD). This is because the GM plays an important role in the bidirectional communication between the gut and the brain and influences the brain normal functioning through multiple pathways. The goal of this article is to study the distribution of ARGs in the GM of 3- to 5-year-old healthy children and children with ASD living in Moscow, Russia. The metagenomic analysis of samples from both groups revealed differences in the signatures between them. The signatures consisted of the bacterial genera and aminoglycoside, β-lactam, macrolide, and tetracycline resistance genes that they harbored. Our results show an increase in ARGs in the resistome of the GM of children with ASD. These findings emphasize the negative influence of early-life antibiotic therapy. We found three ARGs, aac(6')-aph(2''), cepA-49, and tet(40), which could serve as markers of ASD. The additional functions carried out by the enzymes, encoded by these genes, are being discussed.}, } @article {pmid31915220, year = {2020}, author = {Wang, Z and Tauzin, AS and Laville, E and Tedesco, P and Létisse, F and Terrapon, N and Lepercq, P and Mercade, M and Potocki-Veronese, G}, title = {Harvesting of Prebiotic Fructooligosaccharides by Nonbeneficial Human Gut Bacteria.}, journal = {mSphere}, volume = {5}, number = {1}, pages = {}, pmid = {31915220}, issn = {2379-5042}, mesh = {Bacteria/genetics/*metabolism ; *Carbohydrate Metabolism ; Escherichia coli/genetics/metabolism ; Fermentation ; *Gastrointestinal Microbiome ; Humans ; Metabolomics ; Oligosaccharides/*isolation & purification ; Phosphotransferases/genetics/metabolism ; *Prebiotics ; }, abstract = {Prebiotic oligosaccharides, such as fructooligosaccharides, are increasingly being used to modulate the composition and activity of the gut microbiota. However, carbohydrate utilization analyses and metagenomic studies recently revealed the ability of deleterious and uncultured human gut bacterial species to metabolize these functional foods. Moreover, because of the difficulties of functionally profiling transmembrane proteins, only a few prebiotic transporters have been biochemically characterized to date, while carbohydrate binding and transport are the first and thus crucial steps in their metabolization. Here, we describe the molecular mechanism of a phosphotransferase system, highlighted as a dietary and pathology biomarker in the human gut microbiome. This transporter is encoded by a metagenomic locus that is highly conserved in several human gut Firmicutes, including Dorea species. We developed a generic strategy to deeply analyze, in vitro and in cellulo, the specificity and functionality of recombinant transporters in Escherichia coli, combining carbohydrate utilization locus and host genome engineering and quantification of the binding, transport, and growth rates with analysis of phosphorylated carbohydrates by mass spectrometry. We demonstrated that the Dorea fructooligosaccharide transporter is specific for kestose, whether for binding, transport, or phosphorylation. This constitutes the biochemical proof of effective phosphorylation of glycosides with a degree of polymerization of more than 2, extending the known functional diversity of phosphotransferase systems. Based on these new findings, we revisited the classification of these carbohydrate transporters.IMPORTANCE Prebiotics are increasingly used as food supplements, especially in infant formulas, to modify the functioning and composition of the microbiota. However, little is currently known about the mechanisms of prebiotic recognition and transport by gut bacteria, while these steps are crucial in their metabolism. In this study, we established a new strategy to profile the specificity of oligosaccharide transporters, combining microbiomics, genetic locus and strain engineering, and state-of-the art metabolomics. We revisited the transporter classification database and proposed a new way to classify these membrane proteins based on their structural and mechanistic similarities. Based on these developments, we identified and characterized, at the molecular level, a fructooligosaccharide transporting phosphotransferase system, which constitutes a biomarker of diet and gut pathology. The deciphering of this prebiotic metabolization mechanism by a nonbeneficial bacterium highlights the controversial use of prebiotics, especially in the context of chronic gut diseases.}, } @article {pmid31911661, year = {2020}, author = {Legrand, R and Lucas, N and Dominique, M and Azhar, S and Deroissart, C and Le Solliec, MA and Rondeaux, J and Nobis, S and Guérin, C and Léon, F and do Rego, JC and Pons, N and Le Chatelier, E and Ehrlich, SD and Lambert, G and Déchelotte, P and Fetissov, SO}, title = {Commensal Hafnia alvei strain reduces food intake and fat mass in obese mice-a new potential probiotic for appetite and body weight management.}, journal = {International journal of obesity (2005)}, volume = {44}, number = {5}, pages = {1041-1051}, pmid = {31911661}, issn = {1476-5497}, mesh = {Adipose Tissue/*drug effects ; Animals ; Appetite/drug effects ; Body Weight/drug effects ; Eating/*drug effects ; Gastrointestinal Microbiome/drug effects ; *Hafnia alvei ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Obese ; Probiotics/*pharmacology ; }, abstract = {BACKGROUND/OBJECTIVES: Based on the recent identification of E.coli heat shock protein ClpB as a mimetic of the anorexigenic α-melanocyte stimulating hormone (α-MSH), the objective of this study was to preclinically validate Hafnia alvei, a ClpB-producing commensal bacterium as a potential probiotic for appetite and body weight management in overweight and obesity.

METHODS: The involvement of enterobacterial ClpB in the putative anti-obesity effects was studied using ClpB-deficient E.coli. A food-grade H. alvei HA4597 strain synthetizing the ClpB protein with an α-MSH-like motif was selected as a candidate probiotic to be tested in ob/ob and high-fat diet (HFD)-fed obese and overweight mice. The relevance of the enterobacterial ClpB gene to human obesity was studied by in silico analysis of fecal metagenomes of 569 healthy individuals from the "MetaHIT" database.

RESULTS: Chronic per os administration of native but not ClpB-deficient E.coli strain reduced body weight gain (p < 0.05) and daily meal frequency (p < 0.001) in ob/ob mice. Oral gavage of H.alvei for 18 and 46 days in ob/ob and HFD-fed obese mice, respectively, was well tolerated, reduced body weight gain and fat mass in both obesity models (p < 0.05) and decreased food intake in hyperphagic ob/ob mice (p < 0.001). Elevated fat tissue levels of phosphorylated hormone-sensitive lipase were detected in H.alvei -treated ob/ob mice (p < 0.01). Enterobacterial ClpB gene richness was lower in obese vs. non-obese humans (p < 0.0001) and correlated negatively with BMI in genera of Enterobacter, Klebsiella and Hafnia.

CONCLUSIONS: H.alvei HA4597 strain reduces food intake, body weight and fat mass gain in hyperphagic and obese mice. These data combined with low enterobacterial ClpB gene abundance in the microbiota of obese humans provide the rationale for using H.alvei as a probiotic for appetite and body weight management in overweight and obesity.}, } @article {pmid31911589, year = {2020}, author = {Liu, C and Zhou, N and Du, MX and Sun, YT and Wang, K and Wang, YJ and Li, DH and Yu, HY and Song, Y and Bai, BB and Xin, Y and Wu, L and Jiang, CY and Feng, J and Xiang, H and Zhou, Y and Ma, J and Wang, J and Liu, HW and Liu, SJ}, title = {The Mouse Gut Microbial Biobank expands the coverage of cultured bacteria.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {79}, pmid = {31911589}, issn = {2041-1723}, mesh = {Animals ; Bacteria/classification/genetics/growth & development/*isolation & purification ; Cecum/microbiology ; China ; Databases, Factual ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Male ; Mice/*microbiology ; Mice, Inbred C57BL ; Phylogeny ; }, abstract = {Mice are widely used as experimental models for gut microbiome (GM) studies, yet the majority of mouse GM members remain uncharacterized. Here, we report the construction of a mouse gut microbial biobank (mGMB) that contains 126 species, represented by 244 strains that have been deposited in the China General Microorganism Culture Collection. We sequence and phenotypically characterize 77 potential new species and propose their nomenclatures. The mGMB includes 22 and 17 species that are significantly enriched in ob/ob and wild-type C57BL/6J mouse cecal samples, respectively. The genomes of the 126 species in the mGMB cover 52% of the metagenomic nonredundant gene catalog (sequence identity ≥ 60%) and represent 93-95% of the KEGG-Orthology-annotated functions of the sampled mouse GMs. The microbial and genome data assembled in the mGMB enlarges the taxonomic characterization of mouse GMs and represents a useful resource for studies of host-microbe interactions and of GM functions associated with host health and diseases.}, } @article {pmid31911493, year = {2020}, author = {Saw, JHW and Nunoura, T and Hirai, M and Takaki, Y and Parsons, R and Michelsen, M and Longnecker, K and Kujawinski, EB and Stepanauskas, R and Landry, Z and Carlson, CA and Giovannoni, SJ}, title = {Pangenomics Analysis Reveals Diversification of Enzyme Families and Niche Specialization in Globally Abundant SAR202 Bacteria.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {31911493}, issn = {2150-7511}, mesh = {Biodiversity ; Chloroflexi/*enzymology/*genetics ; Computational Biology/methods ; *Genome, Bacterial ; Metabolic Networks and Pathways ; Metabolomics/methods ; *Metagenome ; *Metagenomics ; *Multigene Family ; Phylogeny ; Phylogeography ; }, abstract = {It has been hypothesized that the abundant heterotrophic ocean bacterioplankton in the SAR202 clade of the phylum Chloroflexi evolved specialized metabolisms for the oxidation of organic compounds that are resistant to microbial degradation via common metabolic pathways. Expansions of paralogous enzymes were reported and implicated in hypothetical metabolism involving monooxygenase and dioxygenase enzymes. In the proposed metabolic schemes, the paralogs serve the purpose of diversifying the range of organic molecules that cells can utilize. To further explore SAR202 evolution and metabolism, we reconstructed single amplified genomes and metagenome-assembled genomes from locations around the world that included the deepest ocean trenches. In an analysis of 122 SAR202 genomes that included seven subclades spanning SAR202 diversity, we observed additional evidence of paralog expansions that correlated with evolutionary history, as well as further evidence of metabolic specialization. Consistent with previous reports, families of flavin-dependent monooxygenases were observed mainly in the group III SAR202 genomes, and expansions of dioxygenase enzymes were prevalent in those of group VII. We found that group I SAR202 genomes encode expansions of racemases in the enolase superfamily, which we propose evolved for the degradation of compounds that resist biological oxidation because of chiral complexity. Supporting the conclusion that the paralog expansions indicate metabolic specialization, fragment recruitment and fluorescent in situ hybridization (FISH) with phylogenetic probes showed that SAR202 subclades are indigenous to different ocean depths and geographical regions. Surprisingly, some of the subclades were abundant in surface waters and contained rhodopsin genes, altering our understanding of the ecological role of SAR202 species in stratified water columns.IMPORTANCE The oceans contain an estimated 662 Pg C in the form of dissolved organic matter (DOM). Information about microbial interactions with this vast resource is limited, despite broad recognition that DOM turnover has a major impact on the global carbon cycle. To explain patterns in the genomes of marine bacteria, we propose hypothetical metabolic pathways for the oxidation of organic molecules that are resistant to oxidation via common pathways. The hypothetical schemes we propose suggest new metabolic pathways and classes of compounds that could be important for understanding the distribution of organic carbon throughout the biosphere. These genome-based schemes will remain hypothetical until evidence from experimental cell biology can be gathered to test them. Our findings also fundamentally change our understanding of the ecology of SAR202 bacteria, showing that metabolically diverse variants of these cells occupy niches spanning all depths and are not relegated to the dark ocean.}, } @article {pmid31911491, year = {2020}, author = {Song, SJ and Sanders, JG and Delsuc, F and Metcalf, J and Amato, K and Taylor, MW and Mazel, F and Lutz, HL and Winker, K and Graves, GR and Humphrey, G and Gilbert, JA and Hackett, SJ and White, KP and Skeen, HR and Kurtis, SM and Withrow, J and Braile, T and Miller, M and McCracken, KG and Maley, JM and Ezenwa, VO and Williams, A and Blanton, JM and McKenzie, VJ and Knight, R}, title = {Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {31911491}, issn = {2150-7511}, mesh = {Animals ; *Biological Evolution ; *Birds ; *Chiroptera ; Computational Biology/methods ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; *Vertebrates ; }, abstract = {Diet and host phylogeny drive the taxonomic and functional contents of the gut microbiome in mammals, yet it is unknown whether these patterns hold across all vertebrate lineages. Here, we assessed gut microbiomes from ∼900 vertebrate species, including 315 mammals and 491 birds, assessing contributions of diet, phylogeny, and physiology to structuring gut microbiomes. In most nonflying mammals, strong correlations exist between microbial community similarity, host diet, and host phylogenetic distance up to the host order level. In birds, by contrast, gut microbiomes are only very weakly correlated to diet or host phylogeny. Furthermore, while most microbes resident in mammalian guts are present in only a restricted taxonomic range of hosts, most microbes recovered from birds show little evidence of host specificity. Notably, among the mammals, bats host especially bird-like gut microbiomes, with little evidence for correlation to host diet or phylogeny. This suggests that host-gut microbiome phylosymbiosis depends on factors convergently absent in birds and bats, potentially associated with physiological adaptations to flight. Our findings expose major variations in the behavior of these important symbioses in endothermic vertebrates and may signal fundamental evolutionary shifts in the cost/benefit framework of the gut microbiome.IMPORTANCE In this comprehensive survey of microbiomes of >900 species, including 315 mammals and 491 birds, we find a striking convergence of the microbiomes of birds and animals that fly. In nonflying mammals, diet and short-term evolutionary relatedness drive the microbiome, and many microbial species are specific to a particular kind of mammal, but flying mammals and birds break this pattern with many microbes shared across different species, with little correlation either with diet or with relatedness of the hosts. This finding suggests that adaptation to flight breaks long-held relationships between hosts and their microbes.}, } @article {pmid31910889, year = {2020}, author = {Lee, K and Kim, DW and Lee, DH and Kim, YS and Bu, JH and Cha, JH and Thawng, CN and Hwang, EM and Seong, HJ and Sul, WJ and Wellington, EMH and Quince, C and Cha, CJ}, title = {Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {2}, pmid = {31910889}, issn = {2049-2618}, support = {MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; MR/S037195/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics/pathogenicity ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; *Genes, MDR ; Humans ; Interspersed Repetitive Sequences ; Metagenome ; Republic of Korea ; Rivers/*microbiology ; Sewage/microbiology ; }, abstract = {BACKGROUND: The impact of human activities on the environmental resistome has been documented in many studies, but there remains the controversial question of whether the increased antibiotic resistance observed in anthropogenically impacted environments is just a result of contamination by resistant fecal microbes or is mediated by indigenous environmental organisms. Here, to determine exactly how anthropogenic influences shape the environmental resistome, we resolved the microbiome, resistome, and mobilome of the planktonic microbial communities along a single river, the Han, which spans a gradient of human activities.

RESULTS: The bloom of antibiotic resistance genes (ARGs) was evident in the downstream regions and distinct successional dynamics of the river resistome occurred across the spatial continuum. We identified a number of widespread ARG sequences shared between the river, human gut, and pathogenic bacteria. These human-related ARGs were largely associated with mobile genetic elements rather than particular gut taxa and mainly responsible for anthropogenically driven bloom of the downstream river resistome. Furthermore, both sequence- and phenotype-based analyses revealed environmental relatives of clinically important proteobacteria as major carriers of these ARGs.

CONCLUSIONS: Our results demonstrate a more nuanced view of the impact of anthropogenic activities on the river resistome: fecal contamination is present and allows the transmission of ARGs to the environmental resistome, but these mobile genes rather than resistant fecal bacteria proliferate in environmental relatives of their original hosts. Video abstract.}, } @article {pmid31910311, year = {2020}, author = {Mizutani, S and Yamada, T and Yachida, S}, title = {Significance of the gut microbiome in multistep colorectal carcinogenesis.}, journal = {Cancer science}, volume = {111}, number = {3}, pages = {766-773}, pmid = {31910311}, issn = {1349-7006}, support = {JPMJCR19U3//Japan Science and Technology Agency/ ; JP18ek0109187//Japan Agency for Medical Research and Development/ ; JP18jk0210009//Japan Agency for Medical Research and Development/ ; JP19cm0106464//Japan Agency for Medical Research and Development/ ; 25-A-4//National Cancer Center Research and Development Fund/ ; 28-A-4//National Cancer Center Research and Development Fund/ ; 29-A-6//National Cancer Center Research and Development Fund/ ; //Joint Research Project of the Institute of Medical Science, the University of Tokyo/ ; JPMJPR1507//Precursory Research for Embryonic Science and Technology/ ; //the Takeda Science Foundation/ ; 142558//Japan Society for the Promotion of Science/ ; 16J10135//Japan Society for the Promotion of Science/ ; 221S0002//Japan Society for the Promotion of Science/ ; //the Yasuda Medical Foundation/ ; //the Yakult Bio-Science Foundation/ ; //the Princess Takamatsu Cancer Research Fund/ ; }, mesh = {Animals ; Carcinogenesis/*pathology ; Colorectal Neoplasms/*microbiology/*pathology ; Gastrointestinal Microbiome/*physiology ; Humans ; Metabolome/physiology ; Metagenome/physiology ; }, abstract = {Colorectal cancer (CRC) is highly prevalent worldwide. In 2018, there were over 1.8 million new cases. Most sporadic CRC develop from polypoid adenomas and are preceded by intramucosal carcinoma (stage 0), which can progress into more malignant forms. This developmental process is known as the adenoma-carcinoma sequence. Early detection and endoscopic removal are crucial for CRC management. Accumulating evidence suggests that the gut microbiota is associated with CRC development in humans. Comprehensive characterization of this microbiota is of great importance to assess its potential as a diagnostic marker in the very early stages of CRC. In this review, we summarized recent studies on CRC-associated bacteria and their carcinogenic mechanisms in animal models, human cell lines and human cohorts. High-throughput technologies have facilitated the identification of CRC-associated bacteria in human samples. We have presented our metagenome and metabolome studies on fecal samples collected from a large Japanese cohort that revealed stage-specific phenotypes of the microbiota in CRC. Furthermore, we have discussed the potential carcinogenic mechanisms of the gut microbiota, from which we can infer whether changes in the gut microbiota are a cause or effect in the multi-step process of CRC carcinogenesis.}, } @article {pmid31907364, year = {2020}, author = {Sausset, R and Petit, MA and Gaboriau-Routhiau, V and De Paepe, M}, title = {New insights into intestinal phages.}, journal = {Mucosal immunology}, volume = {13}, number = {2}, pages = {205-215}, pmid = {31907364}, issn = {1935-3456}, mesh = {Animals ; *Bacteriophages ; Gastrointestinal Microbiome/*immunology ; Humans ; Immune System/*virology ; Immunity ; Intestines/microbiology/*virology ; Metagenome ; }, abstract = {The intestinal microbiota plays important roles in human health. This last decade, the viral fraction of the intestinal microbiota, composed essentially of phages that infect bacteria, received increasing attention. Numerous novel phage families have been discovered in parallel with the development of viral metagenomics. However, since the discovery of intestinal phages by d'Hérelle in 1917, our understanding of the impact of phages on gut microbiota structure remains scarce. Changes in viral community composition have been observed in several diseases. However, whether these changes reflect a direct involvement of phages in diseases etiology or simply result from modifications in bacterial composition is currently unknown. Here we present an overview of the current knowledge in intestinal phages, their identity, lifestyles, and their possible effects on the gut microbiota. We also gather the main data on phage interactions with the immune system, with a particular emphasis on recent findings.}, } @article {pmid31907339, year = {2020}, author = {Wang, QJ and Shen, YE and Wang, X and Fu, S and Zhang, X and Zhang, YN and Wang, RT}, title = {Concomitant memantine and Lactobacillus plantarum treatment attenuates cognitive impairments in APP/PS1 mice.}, journal = {Aging}, volume = {12}, number = {1}, pages = {628-649}, pmid = {31907339}, issn = {1945-4589}, mesh = {Alzheimer Disease/*complications/etiology/metabolism ; Animals ; Animals, Genetically Modified ; Biomarkers ; Choline/administration & dosage ; Cognitive Dysfunction/*etiology/*therapy ; Dietary Supplements ; Disease Models, Animal ; Gastrointestinal Microbiome ; *Lactobacillus plantarum ; Male ; Memantine/*pharmacology ; Metagenomics/methods ; Mice ; Probiotics ; Pyramidal Cells/metabolism ; }, abstract = {Trimethylamine-N-oxide (TMAO) is a gut microbial metabolite that promotes Alzheimer's disease (AD) progression. Given that probiotics can alleviate AD symptoms by inhibiting the synthesis of TMAO, here we investigated the correlation between TMAO and cognitive deterioration by measuring TMAO levels in the plasma of choline-treated APP/PS1 mice (an AD mouse model) with and without probiotic treatments. We found that declines in L.plantarum in the gut were associated with cognitive impairment. Moreover, 12-weeks of treatment with memantine plus L. plantarum ameliorated cognitive deterioration, decreased Αβ levels in the hippocampus, and protected neuronal integrity and plasticity. These effects were accompanied by reductions in TMAO synthesis and neuroinflammation. These experiments demonstrate that L. plantarum augments the beneficial therapeutic effects of memantine treatment in APP/PS1 mice by remodeling the intestinal microbiota, inhibiting the synthesis of TMAO, and reducing clusterin levels. Our results thus highlight intestinal microbiota as a potential therapeutic target to decrease the risk of AD.}, } @article {pmid31907101, year = {2020}, author = {Deblais, L and Kathayat, D and Helmy, YA and Closs, G and Rajashekara, G}, title = {Translating 'big data': better understanding of host-pathogen interactions to control bacterial foodborne pathogens in poultry.}, journal = {Animal health research reviews}, volume = {21}, number = {1}, pages = {15-35}, doi = {10.1017/S1466252319000124}, pmid = {31907101}, issn = {1475-2654}, mesh = {Animals ; *Bacteria/genetics ; *Big Data ; *Food Microbiology ; Foodborne Diseases/*microbiology ; Gastrointestinal Microbiome/physiology ; *Host-Pathogen Interactions ; Humans ; Poultry/*microbiology ; Proteomics ; }, abstract = {Recent technological advances has led to the generation, storage, and sharing of colossal sets of information ('big data'), and the expansion of 'omics' in science. To date, genomics/metagenomics, transcriptomics, proteomics, and metabolomics are arguably the most ground breaking approaches in food and public safety. Here we review some of the recent studies of foodborne pathogens (Campylobacter spp., Salmonella spp., and Escherichia coli) in poultry using big data. Genomic/metagenomic approaches have reveal the importance of the gut microbiota in health and disease. They have also been used to identify, monitor, and understand the epidemiology of antibiotic-resistance mechanisms and provide concrete evidence about the role of poultry in human infections. Transcriptomics studies have increased our understanding of the pathophysiology and immunopathology of foodborne pathogens in poultry and have led to the identification of host-resistance mechanisms. Proteomic/metabolomic approaches have aided in identifying biomarkers and the rapid detection of low levels of foodborne pathogens. Overall, 'omics' approaches complement each other and may provide, at least in part, a solution to our current food-safety issues by facilitating the development of new rapid diagnostics, therapeutic drugs, and vaccines to control foodborne pathogens in poultry. However, at this time most 'omics' approaches still remain underutilized due to their high cost and the high level of technical skills required.}, } @article {pmid31906044, year = {2019}, author = {Tsoleridis, T and Chappell, JG and Monchatre-Leroy, E and Umhang, G and Shi, M and Bennett, M and Tarlinton, RE and McClure, CP and Holmes, EC and Ball, JK}, title = {Discovery and Prevalence of Divergent RNA Viruses in European Field Voles and Rabbits.}, journal = {Viruses}, volume = {12}, number = {1}, pages = {}, pmid = {31906044}, issn = {1999-4915}, support = {BB/J014508/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Animals, Wild/virology ; Arvicolinae/*virology ; Astroviridae/classification/isolation & purification ; Feeding Behavior ; Genome, Viral ; Phylogeny ; Picornaviridae/classification/isolation & purification ; Prevalence ; RNA Viruses/classification/*isolation & purification ; RNA, Viral/genetics ; Rabbits/*virology ; Sequence Analysis, DNA ; United Kingdom ; }, abstract = {The advent of unbiased metagenomic virus discovery has revolutionized studies of virus biodiversity and evolution. Despite this, our knowledge of the virosphere, including in mammalian species, remains limited. We used unbiased metagenomic sequencing to identify RNA viruses in European field voles and rabbits. Accordingly, we identified a number of novel RNA viruses including astrovirus, rotavirus A, picorna-like virus and a morbilli-like paramyxovirus. In addition, we identified a sobemovirus and a novel luteovirus that likely originated from the rabbit diet. These newly discovered viruses were often divergent from those previously described. The novel astrovirus was most closely related to a virus sampled from the rodent-eating European roller bird (Coracias garrulous). PCR screening revealed that the novel morbilli-like paramyxovirus in the UK field vole had a prevalence of approximately 4%, and shared common ancestry with other rodent morbilli-like viruses sampled globally. Two novel rotavirus A sequences were detected in a UK field vole and a French rabbit, the latter with a prevalence of 5%. Finally, a highly divergent picorna-like virus found in the gut of the French rabbit virus was only ~35% similar to an arilivirus at the amino acid level, suggesting the presence of a novel viral genus within the Picornaviridae.}, } @article {pmid31905236, year = {2020}, author = {Dillon, ML and Hawes, I and Jungblut, AD and Mackey, TJ and Eisen, JA and Doran, PT and Sumner, DY}, title = {Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {2}, pages = {}, pmid = {31905236}, issn = {1574-6941}, mesh = {Antarctic Regions ; Archaea/classification/genetics/isolation & purification/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; Biodiversity ; *Energy Metabolism ; Geologic Sediments/chemistry/*microbiology ; Lakes/chemistry/*microbiology ; Microbiota/*genetics ; Oxygen/analysis/metabolism ; Sunlight ; }, abstract = {Ecological communities are regulated by the flow of energy through environments. Energy flow is typically limited by access to photosynthetically active radiation (PAR) and oxygen concentration (O2). The microbial mats growing on the bottom of Lake Fryxell, Antarctica, have well-defined environmental gradients in PAR and (O2). We analyzed the metagenomes of layers from these microbial mats to test the extent to which access to oxygen and light controls community structure. We found variation in the diversity and relative abundances of Archaea, Bacteria and Eukaryotes across three (O2) and PAR conditions: high (O2) and maximum PAR, variable (O2) with lower maximum PAR, and low (O2) and maximum PAR. We found distinct communities structured by the optimization of energy use on a millimeter-scale across these conditions. In mat layers where (O2) was saturated, PAR structured the community. In contrast, (O2) positively correlated with diversity and affected the distribution of dominant populations across the three habitats, suggesting that meter-scale diversity is structured by energy availability. Microbial communities changed across covarying gradients of PAR and (O2). The comprehensive metagenomic analysis suggests that the benthic microbial communities in Lake Fryxell are structured by energy flow across both meter- and millimeter-scales.}, } @article {pmid31905172, year = {2020}, author = {Diling, C and Longkai, Q and Yinrui, G and Yadi, L and Xiaocui, T and Xiangxiang, Z and Miao, Z and Ran, L and Ou, S and Dongdong, W and Yizhen, X and Xujiang, Y and Yang, BB and Qingping, W}, title = {CircNF1-419 improves the gut microbiome structure and function in AD-like mice.}, journal = {Aging}, volume = {12}, number = {1}, pages = {260-287}, pmid = {31905172}, issn = {1945-4589}, mesh = {Alzheimer Disease/etiology ; Animals ; Brain/*metabolism ; Disease Models, Animal ; Disease Susceptibility ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; *Homeostasis ; Male ; Metagenomics/methods ; Mice ; Mice, Transgenic ; RNA, Circular/chemistry ; }, abstract = {Our pre-experiments found that the brain circRNA sequence profiles and gut microbiota in AD-like mice were changed, as circNF1-419 could enhance autophagy to ameliorate senile dementia in AD-like mice, so we conclude that there might some connections between circRNA and gut microbiome. Therefore, we use the over-expressed circNF1-419 adeno-associated virus (AAV) animal system with the aim of identifying possible connections. Our results showed that over-expression of circNF1-419 in brain not only influenced the cholinergic system of brain, but also changed the gut microbiota composition as the Candidatus Arthromitus, Lachnospiraceae FCS020 group, Lachnospiraceae UCG-006, and [Eubacterium] xylanophilum group, and the intestinal homeostasis and physiology, and even the gut microbiota trajectory in new born mice. These findings demonstrate a link between circRNA and gut microbiome, enlarge the 'microbiome- transcriptome' linkage library and provide more information on gut-brain axis.}, } @article {pmid31905103, year = {2020}, author = {Dougas, G and Tsakris, A and Beleri, S and Patsoula, E and Billinis, C and Papaparaskevas, J}, title = {Evidence of Brucella melitensis DNA in the Microbiome of Ctenocephalides felis from Pet Cats in Greece.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {20}, number = {5}, pages = {390-392}, doi = {10.1089/vbz.2019.2510}, pmid = {31905103}, issn = {1557-7759}, mesh = {Animals ; Brucella melitensis/*isolation & purification ; Cats ; Ctenocephalides/*microbiology ; DNA, Bacterial/*isolation & purification ; Flea Infestations/epidemiology/microbiology/*veterinary ; Greece ; Microbiota ; Pets ; }, abstract = {Cat fleas (Ctenocephalides felis) are the most prevalent ectoparasites of pet animals with cosmopolitan distribution, obligatory hematophagous, and may prey on humans to receive bloodmeals. We studied the microbiota of 100 flea-pools, containing C. felis, and collected from equal number of cats and dogs in the region of Attica, Greece, including Athens. The 16S metagenomics technique detected Brucella spp. nucleotide sequence that was identified as Brucella melitensis DNA by a real-time PCR, in five flea-pools, corresponding to five cats, one owned and the remaining four stray, residing in semiurban and urban areas, respectively. No definite conclusions can be drawn as to the pathway that led to the presence of B. melitensis in common fleas parasitizing cats. We suspect flea or cat contact with wild rodents, ubiquitous in various environments, which participate in the B. melitensis biology. The proximity of the cats and their fleas with humans and previous observations of flea potential to transmit B. melitensis in laboratory animals warrant a more elaborate research as to the vectorial dynamics, the ecological pathways resulting in pathogen carriage, and the risk for public health.}, } @article {pmid31904815, year = {2020}, author = {Zhang, X and Yi, N}, title = {Fast zero-inflated negative binomial mixed modeling approach for analyzing longitudinal metagenomics data.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {8}, pages = {2345-2351}, doi = {10.1093/bioinformatics/btz973}, pmid = {31904815}, issn = {1367-4811}, mesh = {Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Models, Statistical ; RNA, Ribosomal, 16S/genetics ; }, abstract = {MOTIVATION: Longitudinal metagenomics data, including both 16S rRNA and whole-metagenome shotgun sequencing data, enhanced our abilities to understand the dynamic associations between the human microbiome and various diseases. However, analytic tools have not been fully developed to simultaneously address the main challenges of longitudinal metagenomics data, i.e. high-dimensionality, dependence among samples and zero-inflation of observed counts.

RESULTS: We propose a fast zero-inflated negative binomial mixed modeling (FZINBMM) approach to analyze high-dimensional longitudinal metagenomic count data. The FZINBMM approach is based on zero-inflated negative binomial mixed models (ZINBMMs) for modeling longitudinal metagenomic count data and a fast EM-IWLS algorithm for fitting ZINBMMs. FZINBMM takes advantage of a commonly used procedure for fitting linear mixed models, which allows us to include various types of fixed and random effects and within-subject correlation structures and quickly analyze many taxa. We found that FZINBMM remarkably outperformed in computational efficiency and was statistically comparable with two R packages, GLMMadaptive and glmmTMB, that use numerical integration to fit ZINBMMs. Extensive simulations and real data applications showed that FZINBMM outperformed other previous methods, including linear mixed models, negative binomial mixed models and zero-inflated Gaussian mixed models.

FZINBMM has been implemented in the R package NBZIMM, available in the public GitHub repository http://github.com//nyiuab//NBZIMM.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid31902141, year = {2020}, author = {Yu, H and Xue, D and Wang, Y and Zheng, W and Zhang, G and Wang, ZL}, title = {Molecular ecological network analysis of the response of soil microbial communities to depth gradients in farmland soils.}, journal = {MicrobiologyOpen}, volume = {9}, number = {3}, pages = {e983}, pmid = {31902141}, issn = {2045-8827}, mesh = {Biodiversity ; Environment ; *Farms ; Geography ; Metagenome ; Metagenomics/methods ; *Microbiota ; *Soil Microbiology ; }, abstract = {Soil microorganisms are considered to be important indicators of soil fertility and soil quality. Most previous studies have focused solely on surface soil, but there were numerous active cells in deeper soil layers. However, studies regarding microbial communities in deeper soil layers were not comprehensive and sufficient. In this study, phylogenetic molecular ecological networks (pMENs) based on the 16S rRNA Miseq sequencing technique were applied to study the response of soil microbial communities to depth gradients and the changes of key genera along 3 meter depth gradients (0-0.2 m, 0.2-0.4 m 0.4-0.6 m, 0.6-0.8 m, 0.8-1.0 m, 1.0-1.3 m, 1.3-1.6 m, 1.6-2.0 m, 2.0-2.5 m, and 2.5-3.0 m). The results showed that the modularity of microbial communities was consistently high in all soil layers and each layer was similar, which indicated that microbial communities were more resistant to depth changes. The pMENs further demonstrated that microbial community interactions were stable as the depth increased and they cooperated well to adapt to changes in different soil gradients. This was evidenced by similar positive links, average degree, and average clustering coefficient. In addition, key genera were obtained by analyzing module hubs in the pMENs. There may be at least one dominant genus in each layer that adapted to and resisted changes in the soil environment. It seems microbial communities demonstrate a stable and strong adaptability to depth gradients in farmland soils.}, } @article {pmid31901868, year = {2020}, author = {Gurung, M and Li, Z and You, H and Rodrigues, R and Jump, DB and Morgun, A and Shulzhenko, N}, title = {Role of gut microbiota in type 2 diabetes pathophysiology.}, journal = {EBioMedicine}, volume = {51}, number = {}, pages = {102590}, pmid = {31901868}, issn = {2352-3964}, support = {R01 DK103761/DK/NIDDK NIH HHS/United States ; R01 DK112360/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/metabolism ; Diabetes Mellitus, Type 2/drug therapy/*microbiology/*physiopathology ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {A substantial body of literature has provided evidence for the role of gut microbiota in metabolic diseases including type 2 diabetes. However, reports vary regarding the association of particular taxonomic groups with disease. In this systematic review, we focused on the potential role of different bacterial taxa affecting diabetes. We have summarized evidence from 42 human studies reporting microbial associations with disease, and have identified supporting preclinical studies or clinical trials using treatments with probiotics. Among the commonly reported findings, the genera of Bifidobacterium, Bacteroides, Faecalibacterium, Akkermansia and Roseburia were negatively associated with T2D, while the genera of Ruminococcus, Fusobacterium, and Blautia were positively associated with T2D. We also discussed potential molecular mechanisms of microbiota effects in the onset and progression of T2D.}, } @article {pmid31901572, year = {2020}, author = {Aagaard, KM}, title = {Mode of delivery and pondering potential sources of the neonatal microbiome.}, journal = {EBioMedicine}, volume = {51}, number = {}, pages = {102554}, pmid = {31901572}, issn = {2352-3964}, mesh = {Bacteria/genetics ; Cesarean Section ; *Delivery, Obstetric ; Humans ; Infant, Newborn ; *Microbiota/genetics ; Odds Ratio ; RNA, Ribosomal, 16S/genetics ; }, } @article {pmid31900552, year = {2020}, author = {Cai, X and Mao, Y and Xu, J and Tian, L and Wang, Y and Iqbal, W and Yang, B and Liu, C and Zhao, X and Wang, Y}, title = {Characterizing community dynamics and exploring bacterial assemblages in two activated sludge systems.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {4}, pages = {1795-1808}, doi = {10.1007/s00253-019-10279-2}, pmid = {31900552}, issn = {1432-0614}, support = {51608329; 51708358//National Natural Science Foundation of China/ ; 41907214//National Natural Science Foundation of China/ ; 2017A030313315//Natural Science Foundation of Guangdong Province/ ; JCYJ20160520165135743, JCYJ20170412171918012//Shenzhen Science and Technology Projects/ ; 2017ZX07202//National Major Science and Technology Program for Water Pollution Control and Treatment (CN)/ ; 827-000223//Natural Science Foundation of Shenzhen University/ ; 2019M653053//Postdoctoral Research Foundation of China/ ; }, mesh = {Animals ; Bacteria/*classification ; Feces/microbiology ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; *Microbiota ; Sewage/*microbiology ; }, abstract = {Bacterial communities in the activated sludge (AS) determine the wastewater treatment performance in the municipal wastewater treatment plants (WWTPs). Aiming at identifying the affecting factors and the variation patterns of the bacterial assemblages in AS, a 2-year time-series AS samples were collected from two separated WWTPs and metagenomic sequencing was conducted. Obvious seasonal shift and succession of the bacterial community were observed in both WWTPs on the genus and species levels, especially for the persistent taxa, implying that temperature was a decisive factor for maintaining bacterial assemblage patterns in long-term period. Taxa abundance distribution (TAD) concerning occurrence frequency and average abundance were found fitting for exponential formulations, and the approximately equal total abundance of persistent taxa suggested that stable and high abundance (~ 90%) of core functional bacterial groups would help to maintain wastewater treatment performance. Drastic changes of environmental factors were found causing temporally significant bacterial structure variation, while the innate correlations between bacterial species could recover the community gradually and maintain relative stability of the AS system. Delayed correlations between environmental factors and abundant (persistent or intermittent) bacterial species were observed widely, while synchronous biotic interactions were identified more frequently. Besides, bacterial species with similar functions were prone to cluster together and shared the same seasonal variation pattern, implicating that the cooperation of functional correlated taxa played the most dominant role in shaping the bacterial assemblages. Furthermore, rare bacterial groups were to be explored for removing emerging pollutants with lower concentrations. The results of this study would assist dealing with operational defect and optimize the treatment system in WWTPs.}, } @article {pmid31898918, year = {2020}, author = {Al Alam, D and Danopoulos, S and Grubbs, B and Ali, NABM and MacAogain, M and Chotirmall, SH and Warburton, D and Gaggar, A and Ambalavanan, N and Lal, CV}, title = {Human Fetal Lungs Harbor a Microbiome Signature.}, journal = {American journal of respiratory and critical care medicine}, volume = {201}, number = {8}, pages = {1002-1006}, pmid = {31898918}, issn = {1535-4970}, support = {P30 DK072482/DK/NIDDK NIH HHS/United States ; R01 HL102371/HL/NHLBI NIH HHS/United States ; P30 CA013148/CA/NCI NIH HHS/United States ; K08 HL141652/HL/NHLBI NIH HHS/United States ; R01 HL141856/HL/NHLBI NIH HHS/United States ; }, mesh = {Female ; Fetus/*microbiology ; *Gestational Age ; Humans ; Lung/*microbiology ; *Metagenome ; Microbiota/*genetics ; Placenta/*microbiology ; Pregnancy ; Pregnancy Trimester, First ; Pregnancy Trimester, Second ; RNA, Ribosomal, 16S/genetics ; }, } @article {pmid31898031, year = {2020}, author = {Pi, S and Sun, J and Feng, L and Zhou, J}, title = {Performance and microbial diversity of denitrifying biofilms on polyurethane foam coupled with various solid carbon sources for nitrate-rich water purification.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {23}, number = {3}, pages = {405-413}, doi = {10.1007/s10123-019-00114-z}, pmid = {31898031}, issn = {1618-1905}, support = {51709236//National Natural Science Foundation of China/ ; }, mesh = {Bacteria/genetics/growth & development/isolation & purification/metabolism ; Biofilms/growth & development ; Carbon/metabolism ; DNA, Bacterial ; *Denitrification ; Environmental Restoration and Remediation ; Metagenomics ; Microbiota/*genetics ; Nitrates/metabolism ; Polyurethanes ; RNA, Ribosomal, 16S/genetics ; Water Purification/*methods ; }, abstract = {This study investigated the performance and microbial communities of denitrifying biofilms on polyurethane foam coupled with various solid carbon sources of acid- and alkali-pretreated rice straw and rice husk. Results showed that acid and alkali-pretreated rice straw both had higher TOC release rates (0.041-0.685 mg g[-1] day[-1]) than those of rice husk (0.019-0.160 mg g[-1] day[-1]) over a month, while acid pretreatment of rice husk and rice straw had a much higher organics release rate than that of alkali pretreatment and non-pretreatment, respectively. Acid-pretreated rice straw achieved the most efficient TN removal performance (82.06 ± 3.65%) with the lower occurrences of NH4[+]-N during denitrification than that of alkali-pretreated rice straw (80.05 ± 4.12%) over more than a month operation. However, alkali pretreatment of rice husk demonstrated much more significantly efficient TN removal efficiency (80.39 ± 2.1%) than did acid pretreatment (69.59 ± 13.43%). MiSeq sequencing analysis showed that the four biofilm samples attached on polyurethane foam with the addition of pretreated rice straw or rice husk had a range of 13-15 differentially abundant phylum and 81-123 differentially abundant genera in comparison with biofilm without extra solid carbon sources, and a higher TN removal efficiency demonstrated more types of differentially abundant genera.}, } @article {pmid31897823, year = {2020}, author = {Najar, IN and Sherpa, MT and Das, S and Thakur, N}, title = {Bacterial diversity and functional metagenomics expounding the diversity of xenobiotics, stress, defense and CRISPR gene ontology providing eco-efficiency to Himalayan Hot Springs.}, journal = {Functional & integrative genomics}, volume = {20}, number = {4}, pages = {479-496}, doi = {10.1007/s10142-019-00723-x}, pmid = {31897823}, issn = {1438-7948}, support = {BCIL/NER-BPMC/2016 & BT/20/NE/2011//Department of Biotechnology, Government of India/ ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Endodeoxyribonucleases/genetics/metabolism ; Hot Springs/*microbiology ; Membrane Transport Proteins/genetics/metabolism ; *Metagenome ; *Microbiota ; Stress, Physiological ; Xenobiotics/metabolism ; beta-Lactamases/genetics/metabolism ; }, abstract = {Sikkim is one of the bio-diverse states of India, which harbors diverse alkaline and sulfur rich hot springs in its vicinity. However, there is a dearth of data present in terms of microbial and its functional diversity as only a few hot springs have been studied in this area. Thus, in this regard, microbial and functional diversity of two hot springs by NGS, PLFA, and culture-independent approaches were carried out. PLFA and culture-dependent analysis was complementary as the Gram-positive bacteria were abundant in both the hot springs with the dominance of phylum Firmicutes with Geobacillus. Metagenomic analysis revealed the abundance of Proteobacteria, Actinobacteria, and Firmicutes in both hot springs. Functional metagenomics suggested that both Yumthang and Reshi hot spring possess a diverse set of genes analogous to stress such as genes allied to osmotic, heat shock, and acid stresses; defense analogies such as multidrug resistance efflux pump, multidrug transport system, and β-lactamase; and CRISPR analogues such as related to Cas1, Cas2, Cas3, cmr1-5 proteins, CT1972, and CT1133 gene families. The xenobiotic analogues were found against benzoate, nitrotolune, xylene, DDT, and chlorocyclohexane/chlorobenzene degradation. Thus, these defensive mechanisms against environmental and anthropogenic hiccups and hindrances provide the eco-efficiency to such thermal habitats. The higher enzymatic, degradation, defense, stress potential and the lower percentage identity (< 95%) of isolates encourage the further exploration and exploitation of these habitats for industrial and biotechnological purposes.}, } @article {pmid31896784, year = {2020}, author = {Hao, L and Michaelsen, TY and Singleton, CM and Dottorini, G and Kirkegaard, RH and Albertsen, M and Nielsen, PH and Dueholm, MS}, title = {Novel syntrophic bacteria in full-scale anaerobic digesters revealed by genome-centric metatranscriptomics.}, journal = {The ISME journal}, volume = {14}, number = {4}, pages = {906-918}, pmid = {31896784}, issn = {1751-7370}, mesh = {Acetates/metabolism ; Anaerobiosis ; Bacteria/*genetics ; Bacteria, Anaerobic/genetics ; Bioreactors/*microbiology ; Butyrates/metabolism ; Environmental Microbiology ; Fatty Acids, Volatile/metabolism ; Metagenome ; Methane/metabolism ; Microbiota ; Oxidation-Reduction ; Propionates/metabolism ; *Transcriptome ; Wastewater ; }, abstract = {Short-chain fatty acid (SCFA) degradation is an important process in methanogenic ecosystems, and is usually catalyzed by SCFA-oxidizing bacteria in syntrophy with methanogens. Current knowledge of this functional guild is mainly based on isolates or enrichment cultures, but these may not reflect the true diversity and in situ activities of the syntrophs predominating in full-scale systems. Here we obtained 182 medium to high quality metagenome-assembled genomes (MAGs) from the microbiome of two full-scale anaerobic digesters. The transcriptomic response of individual MAG was studied after stimulation with low concentrations of acetate, propionate, or butyrate, separately. The most pronounced response to butyrate was observed for two MAGs of the recently described genus Candidatus Phosphitivorax (phylum Desulfobacterota), expressing a butyrate beta-oxidation pathway. For propionate, the largest response was observed for an MAG of a novel genus in the family Pelotomaculaceae, transcribing a methylmalonyl-CoA pathway. All three species were common in anaerobic digesters at Danish wastewater treatment plants as shown by amplicon analysis, and this is the first time their syntrophic features involved in SCFA oxidation were revealed with transcriptomic evidence. Further, they also possessed unique genomic features undescribed in well-characterized syntrophs, including the metabolic pathways for phosphite oxidation, nitrite and sulfate reduction.}, } @article {pmid31896482, year = {2020}, author = {Khan, H and Miao, X and Liu, M and Ahmad, S and Bai, X}, title = {Behavior of last resort antibiotic resistance genes (mcr-1 and blaNDM-1) in a drinking water supply system and their possible acquisition by the mouse gut flora.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {259}, number = {}, pages = {113818}, doi = {10.1016/j.envpol.2019.113818}, pmid = {31896482}, issn = {1873-6424}, mesh = {Animals ; Anti-Bacterial Agents ; Drinking Water/*microbiology ; Drug Resistance, Microbial/*genetics ; Gastrointestinal Microbiome/*physiology ; Genes, Bacterial ; Mice ; Water Supply ; beta-Lactamases ; }, abstract = {Mcr-1 and blaNDM-1 antibiotic resistance genes (ARGs) confer resistance to colistins and carbapenems, which are often antibiotics used as a last resort in tertiary care hospitals. Dissemination of these two ARGs in drinking water supply systems and their effect on healthy gut bacteria are poorly studied. In this study, the dissemination of mcr-1 and blaNDM-1 in a drinking water supply system, and their effect on the antibiotic resistance of mouse gut bacteria are explored. Metagenome analysis revealed that source water (Taipu river and Jinze reservoir) was polluted with ARGs. Mcr-1 and blaNDM-1 can be disseminated through the water distribution system. Even advanced water treatments (ozone and biological activated carbon (BAC)) could not effectively remove mcr-1 and blaNDM-1. Low concentrations of chloramine disinfectants in the water distribution system were not effective at limiting ARG abundance. Mobile genetic elements were also found to play a major role in the dissemination of ARGs via horizontal gene transfer (HGT) throughout the water supply system. Statistical analysis revealed that there was no effect of temperature on the abundance of mcr-1 and blaNDM-1 throughout the water supply system. A last resort ARG, mcr-1 can disseminate from drinking water to the healthy mouse gut. The presence of mcr-1 in a strain belonging to Enterococcus hirae, which is different from the strain belonging to the Bacillus cereus group isolated from drinking water, strongly supports the phenomena of HGT inside the gut. This research provides novel insights into the role of drinking water in disseminating ARGs to the gut and strongly suggests that drinking water may also play a major role apart from other factors known to be involved in the prevalence of last resort ARGs in the gut.}, } @article {pmid31896192, year = {2020}, author = {Li, W and Tan, Q and Zhou, W and Chen, J and Li, Y and Wang, F and Zhang, J}, title = {Impact of substrate material and chlorine/chloramine on the composition and function of a young biofilm microbial community as revealed by high-throughput 16S rRNA sequencing.}, journal = {Chemosphere}, volume = {242}, number = {}, pages = {125310}, doi = {10.1016/j.chemosphere.2019.125310}, pmid = {31896192}, issn = {1879-1298}, mesh = {Biofilms/*drug effects ; Chloramines/*pharmacology ; Chlorine/*pharmacology ; Construction Materials/microbiology ; Disinfectants/*pharmacology ; Disinfection/methods ; Drinking Water/chemistry/*microbiology ; Iron ; Microbiota/*drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; Stainless Steel ; Water Microbiology/standards ; }, abstract = {The bacterial composition of biofilms in drinking water distribution systems is significantly impacted by the disinfection regime and substrate material. However, studies that have addressed the changes in the biofilm community during the early stage of formation (less than 10 weeks) were not yet adequate. Here, we explore the effects of the substrate materials (cast iron, stainless steel, copper, polyvinyl chloride, and high density polyethylene) and different disinfectants (chlorine and chloramine) on the community composition and function of young biofilm by using 16S rDNA sequencing. The results showed that Alphaproteobacteria (39.14%-80.87%) and Actinobacteria (5.90%-40.03%) were the dominant classes in chlorine-disinfection samples, while Alphaproteobacteria (17.46%-74.18%) and Betaproteobacteria (3.79%-68.50%) became dominant in a chloraminated group. The infrequently discussed genus Phreatobacter became predominant in the chlorinated samples, but it was inhibited by chloramine and copper ions. The key driver of the community composition was indicated as different disinfectants according to principle coordination analysis (PCoA) and Permutational multivariate analysis of variance (Adonis test), and the bacterial community changed significantly over time. Communities of biofilms grown on cast iron showed a great distance from the other materials according to Bray-Curtis dissimilarity, and they had a unique dominant genus, Dechloromonas. A metagenomics prediction based on 16S rDNA was used to detect the functional pathways of antibiotic biosynthesis and beta-lactam resistance, and it revealed that several pathways were significantly different in terms of their chlorinated and chloraminated groups.}, } @article {pmid31896132, year = {2020}, author = {Souza, FP and Lima, ECS and Urrea-Rojas, AM and Suphoronski, SA and Facimoto, CT and Bezerra Júnior, JDS and Oliveira, TES and Pereira, UP and Santis, GWD and Oliveira, CAL and Lopera-Barrero, NM}, title = {Effects of dietary supplementation with a microalga (Schizochytrium sp.) on the hemato-immunological, and intestinal histological parameters and gut microbiota of Nile tilapia in net cages.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0226977}, pmid = {31896132}, issn = {1932-6203}, mesh = {Animals ; Blood Cells/drug effects ; Body Weight/drug effects ; Cichlids/blood/immunology/*microbiology ; *Dietary Supplements ; Gastrointestinal Microbiome/drug effects ; Intestines/anatomy & histology/drug effects/immunology ; Male ; *Microalgae ; Microbiota/drug effects ; }, abstract = {Nutritional improvements in intensive aquaculture production systems is necessary for the reduction of stress, maximum utilization of nutritional components, and expression of the genetic potential of fish. The objective of this study was to evaluate the hemato-immunological, and histological parameters and gut microbiota of Nile tilapia fed with the microalga Schizochytrium sp. Males of Nile tilapia were distributed among eight net cages (6 m3), and fed for 105 days with two diets: control (CON), without Schizochytrium sp., and supplemented (SUP), with 1.2% Schizochytrium sp. in the diet. The final weight, mortality, hematocrit, total erythrocyte count (RBC), hemoglobin, hematimetric indices, white blood cell count (WBC), total protein, and serum lysozyme were measured. Alterations in intestinal morphology were evaluated. The gut microbiota was evaluated with next-generation sequencing. No significant differences (p>0.05) were found in the final weight and mortality between diets. Regarding the hematological parameters, a difference (p<0.05) was detected only in RBC, with there being lower values in the SUP, although this group also showed a tendency toward having an increased mean corpuscular hemoglobin level. There were no differences (p>0.05) in total protein and serum lysozyme concentrations or in WBCs between diets, except for lymphocytes, which presented lower values (p<0.05) in the SUP, suggesting immunomodulation by the polyunsaturated fatty acids present in the microalga. There was no difference (p>0.05) in the intestinal morphology between diets. Metagenomic data indicated greater richness (represented by the Chao index) and a higher abundance of the bacterial phylum Firmicutes in the gut microbiota of the tilapia fed with the SUP diet, demonstrating that the digestion and use of the components of the microalga could influence the microbial community. The results indicated that the microalga had modulatory effects on blood cells and the intestinal microbiota, without affecting the structure and integrity of the intestinal villi.}, } @article {pmid31896059, year = {2020}, author = {Vargas, JE and Andrés, S and López-Ferreras, L and López, S}, title = {Effects of supplemental plant oils on rumen bacterial community profile and digesta fatty acid composition in a continuous culture system (RUSITEC).}, journal = {Anaerobe}, volume = {61}, number = {}, pages = {102143}, doi = {10.1016/j.anaerobe.2019.102143}, pmid = {31896059}, issn = {1095-8274}, mesh = {Animal Feed/analysis ; Animals ; Bacteriological Techniques ; *Dietary Supplements ; Fatty Acids/*metabolism ; *Fermentation ; Metagenomics/methods ; *Microbiota ; *Plant Oils ; Rumen/*microbiology ; }, abstract = {Lipid supplementation of ruminant diets may trigger changes in the ruminal microbiota and in anaerobic digestion. Changes in the bacterial community composition and in the fatty acid hydrogenation caused by the addition of different supplemental plant oils to a high concentrate diet were investigated in vitro using RUSITEC (rumen simulation technique) fermenters. The control (CTR) diet was a high-concentrate total mixed ration for dairy sheep, with no supplementary oil. The other experimental diets were supplemented with olive (OLV), sunflower (SFL) or linseed (LNS) oils at 6% (dry matter basis). Four RUSITEC fermenters were used for each experimental diet, all inoculated with rumen digesta of sheep. Extent of dry matter and fat degradation, composition of the bacterial community and long-chain fatty acids in digesta were determined. The addition of plant oils increased (P < 0.001) apparent degradation of fat in the fermenters, whereas fermentation kinetics (gas production and average fermentation rate) were lower (P < 0.05) with the LNS than with the CTR diet. Hydrogenation of C18 unsaturated fatty acids (P < 0.05), in particular that of oleic acid (P < 0.001), and stearic acid proportion (P < 0.001) were reduced, and oleic acid proportion was increased (P < 0.001) with all oil supplements. Addition of OLV decreased linoleic and LNS increased α-linolenic (P < 0.001), whereas conjugated linoleic was increased with SFL oil (P = 0.025) and vaccenic increased with both SFL and LNS oils (P = 0.008). Addition of 6% OLV and LNS reduced (P < 0.05) microbial community diversity and quantity of total bacteria relative to the control. Some specific microbial groups were affected (P < 0.001) by oil addition, with less relative abundance of Clostridiales and Actinobacteria and increased Bacteroidales, Aeromonadales and Lactobacillales species. In conclusion, the supplementation of high-concentrate ruminant diets with plant oils, in particular from sunflower or linseed, causes shifts in the rumen microbiota and fatty acid hydrogenation in the rumen increasing the formation of vaccenic and conjugated linoleic acids.}, } @article {pmid31894501, year = {2020}, author = {Tiew, PY and Mac Aogain, M and Ali, NABM and Thng, KX and Goh, K and Lau, KJX and Chotirmall, SH}, title = {The Mycobiome in Health and Disease: Emerging Concepts, Methodologies and Challenges.}, journal = {Mycopathologia}, volume = {185}, number = {2}, pages = {207-231}, pmid = {31894501}, issn = {1573-0832}, support = {NMRC/Fellowship/0049/2017//National Medical Research Council Singapore/ ; MOH-000141//National Medical Research Council Singapore/ ; 2016-T1-001-050//Singapore Ministry of Education/ ; NIM/03/2018//Nanyang Technological University/ ; ARISE/2017/6//Nanyang Technological University (SG)/ ; }, mesh = {Computational Biology ; *Fungi/genetics/pathogenicity ; High-Throughput Nucleotide Sequencing ; Host Microbial Interactions ; Humans ; Metagenomics ; *Mycobiome ; *Mycoses/epidemiology/etiology/therapy/transmission ; Pathology, Molecular ; }, abstract = {Fungal disease is an increasingly recognised global clinical challenge associated with high mortality. Early diagnosis of fungal infection remains problematic due to the poor sensitivity and specificity of current diagnostic modalities. Advances in sequencing technologies hold promise in addressing these shortcomings and for improved fungal detection and identification. To translate such emerging approaches into mainstream clinical care will require refinement of current sequencing and analytical platforms, ensuring standardisation and consistency through robust clinical benchmarking and its validation across a range of patient populations. In this state-of-the-art review, we discuss current diagnostic and therapeutic challenges associated with fungal disease and provide key examples where the application of sequencing technologies has potential diagnostic application in assessing the human 'mycobiome'. We assess how ready access to fungal sequencing may be exploited in broadening our insight into host-fungal interaction, providing scope for clinical diagnostics and the translation of emerging mycobiome research into clinical practice.}, } @article {pmid31894392, year = {2020}, author = {Huang, J and Zhang, W and Fan, R and Liu, Z and Huang, T and Li, J and Du, T and Xiong, T}, title = {Composition and functional diversity of fecal bacterial community of wild boar, commercial pig and domestic native pig as revealed by 16S rRNA gene sequencing.}, journal = {Archives of microbiology}, volume = {202}, number = {4}, pages = {843-857}, doi = {10.1007/s00203-019-01787-w}, pmid = {31894392}, issn = {1432-072X}, support = {31760457//National Natural Science Foundation of China/ ; 31560449//National Natural Science Foundation of China/ ; 2017YFD0400503-3//National Key Research and Development Program of China/ ; SKLF-ZZA-201610//State Key Laboratory of Food Science and Technology Nanchang University/ ; }, mesh = {Animals ; Bacteria/*classification/*genetics ; *Biodiversity ; Diet ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Genes, Bacterial/genetics ; Metagenome ; RNA, Ribosomal, 16S/*genetics ; Sus scrofa/*microbiology ; }, abstract = {The bacterial community in mammalian gastrointestinal tract is abundant and complex. To date, little is known about the gut microbiota of wild boar. This study aimed to investigate the fecal bacterial diversity of wild boar and compare with commercial pig and domestic native pig. The diet composition showed that the diets of wild boar, commercial pig and domestic native pig were different from each other. More than 1,760,000 quality-filtered sequences were obtained, and the results revealed distinct compositions and diversity of fecal microbiota in three groups. PCoA and NMDS analyses showed that fecal bacterial communities of wild boar, commercial pig and domestic native pig formed distinctly different clusters. Although the three groups shared a large size of OTUs comprising a core microbiota community, a strong distinction existed at family and genus levels. Ruminococcaceae, Prevotellaceae and Christensenellaceae were more abundant in the feces of wild boar than in domestic native pig and commercial pig. At the genus level, the proportion of unidentified Christensenellaceae was remarkably higher in wild boar group, while commercial pig and domestic native pig group had a higher abundance of Streptococcus and Lactobacillus. Tax4Fun predictions of metagenome function showed statistically significant differences in the functions of fecal microbiota in three groups. There were more bacteria genes with amino acid metabolism, cell growth and death, cell motility, energy metabolism, immune system and environmental adaptation observed in wild boar feces, while commercial pig feces contained more bacteria genes with carbohydrate metabolism, drug resistance, aging, infectious diseases, lipid metabolism, endocrine and metabolic diseases. These results indicated that the fecal microbial ecosystem of the wild boar is significantly different from that of domestic native pig and commercial pig, suggesting that diet is an important factor leading to differences in bacterial abundance and diversity in feces.}, } @article {pmid31894373, year = {2020}, author = {Wang, Y and She, M and Liu, K and Zhang, Z and Shuang, Q}, title = {Evaluation of the Bacterial Diversity of Inner Mongolian Acidic Gruel Using Illumina MiSeq and PCR-DGGE.}, journal = {Current microbiology}, volume = {77}, number = {3}, pages = {434-442}, pmid = {31894373}, issn = {1432-0991}, support = {KCBJ2018011//Science and Technology Innovation Guide Reward Projects from Inner Mongolia Autonomous Region/ ; }, mesh = {Acids ; Bacteria/*classification ; China ; DNA, Bacterial/genetics ; Edible Grain/*microbiology ; Fermented Foods/*microbiology ; *Food Microbiology ; High-Throughput Nucleotide Sequencing ; Metagenome ; *Microbiota ; Polymerase Chain Reaction ; }, abstract = {As a traditional fermented cereal, Inner Mongolian acidic gruel has a unique flavor and rich nutrition, but the microbial diversity of acidic gruel and the microbial differences among the products in different regions have not been reported. The bacterial diversity and the lactic acid bacteria species of 27 types of traditional handmade acidic gruel were evaluated using a combination of MiSeq high-throughput sequencing and PCR-DGGE. All 358,205 high-quality 16S rRNA reads were divided into 25,171 OTUs under the similarity of 97%. Firmicutes, Proteobacteria, and Bacteroidetes were the dominant bacterial phyla, and the core dominant genera were Lactobacillus and Acetobacter with average relative abundances of 64.06% and 24.13%, respectively. The primary genera that caused the differences in the bacterial community structure between the Bayan Nur and Ordos acidic gruel samples were Pseudomonas, Leuconostoc, and Acinetobacter as revealed by redundancy analysis (RDA). PCR-DGGE analyses revealed that the lactic acid bacteria in both the Bayan Nur and Ordos samples of acidic gruel were Lactobacillus (L.) amylolyticus, L. alimentarius, L. fermentum, L. hamsteri, L. helveticus, L. panis, L. plantarum, L. pontis, and Leuconostoc lactis. In addition, L. hamsteri was the core strain detected among all the samples. The results deepened the understanding of the microbial community composition and the diversity of acidic gruel to provide a theoretical basis for the preservation and protection of microbial resources in acidic gruel in the Inner Mongolia area.}, } @article {pmid31894129, year = {2019}, author = {Bhat, AH and Prabhu, P and Balakrishnan, K}, title = {A critical analysis of state-of-the-art metagenomics OTU clustering algorithms.}, journal = {Journal of biosciences}, volume = {44}, number = {6}, pages = {}, pmid = {31894129}, issn = {0973-7138}, mesh = {Algorithms ; Cluster Analysis ; *Computational Biology ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*trends ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Software ; }, abstract = {Taxonomic profiling, using hyper-variable regions of 16S rRNA, is one of the important goals in metagenomics analysis. Operational taxonomic unit (OTU) clustering algorithms are the important tools to perform taxonomic profiling by grouping 16S rRNA sequence reads into OTU clusters. Presently various OTU clustering algorithms are available within different pipelines, even some pipelines have implemented more than one clustering algorithms, but there is less literature available for the relative performance and features of these algorithms. This makes the choice of using these methods unclear. In this study five current state-of-the-art OTU clustering algorithms (CDHIT, Mothur's Average Neighbour, SUMACLUST, Swarm, and UCLUST) have been comprehensively evaluated on the metagenomics sequencing data. It was found that in all the datasets, Mothur's average neighbour and Swarm created more number of OTU clusters. Based on normalized mutual information (NMI) and normalized information difference (NID), Swarm and Mothur's average neighbour showed better clustering qualities than others. But in terms of time complexity the greedy algorithms (SUMACLUST, CDHIT, and UCLUST) performed well. So there is a trade-off between quality and time, and it is necessary while analysing large size of 16S rRNA gene sequencing data.}, } @article {pmid31893578, year = {2020}, author = {Zhou, J and Yu, L and Zhang, J and Zhang, X and Xue, Y and Liu, J and Zou, X}, title = {Characterization of the core microbiome in tobacco leaves during aging.}, journal = {MicrobiologyOpen}, volume = {9}, number = {3}, pages = {e984}, pmid = {31893578}, issn = {2045-8827}, mesh = {*Aging ; Bacteria/classification/genetics ; Biodiversity ; Environment ; Humans ; Metagenomics/methods ; Microbiota/genetics ; Plant Leaves/*microbiology ; Nicotiana/growth & development/*microbiology ; }, abstract = {Microbiome plays an important role during the tobacco aging process which was an indispensable link in the production and processing of cigarettes. However, the structure and functions of microbiome have not been clarified during the tobacco aging process. In this study, 16S rDNA and ITS amplicon sequencing techniques were used to analyze the core microbiome of 15 tobacco samples from five different aging stages. The whole bacterial microbiome was classified into 29 microbial phyla and 132 orders. Enterobacteriales (63%), Pseudomonadales (16%), Sphingomonadales (8%), Xanthomonadales (4%), Burkholderiales (4%), Rhizobiales (3%), and Bacillales (2%) comprised the core bacterial microbiome. The whole fungal microbiome was classified into five microbial phyla and 52 orders. Incertae_sedis_Eurotiomycetes (27%), Wallemiales (25%), Sporidiobolales (17%), Capnodiales (5%), Eurotiales (2%), an unclassified Ascomycota (12%), and an unidentified Eurotiomycetes (4%) comprised the core fungal microbiome. FAPROTAX function prediction suggested that the core microbiome has a substantial potential for the carbon cycle, nitrate metabolism, aromatic compound degradation, chitinolysis, cellulolysis, and xylanolysis, but simultaneously, the core microbiome is also a source of human pathogens. The dynamics of the bacterial community were primarily determined by the total nitrogen in tobacco leaves during the aging process, while those of the fungal microbiome were primarily determined by total organic carbon. This study indicated that the core microbiome activities may play an important role in regulating the loss of carbon organic compounds and enhancing the secondary metabolites during tobacco leaves aging process.}, } @article {pmid31892851, year = {2020}, author = {Liang, S and Mao, Y and Liao, M and Xu, Y and Chen, Y and Huang, X and Wei, C and Wu, C and Wang, Q and Pan, X and Tang, W}, title = {Gut microbiome associated with APC gene mutation in patients with intestinal adenomatous polyps.}, journal = {International journal of biological sciences}, volume = {16}, number = {1}, pages = {135-146}, pmid = {31892851}, issn = {1449-2288}, mesh = {Adenomatous Polyps/*genetics ; Aged ; Colorectal Neoplasms/*genetics/*microbiology ; Faecalibacterium prausnitzii/genetics/physiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Genes, APC/physiology ; Humans ; Male ; Metagenomics ; Middle Aged ; Mutation/*genetics ; }, abstract = {Background: The 'adenoma-carcinoma sequence' is a well-recognized model of colorectal cancer (CRC) development. However, the interaction between gut microbiota and genetic variation in the initiation of CRC is not clear. Our study attempts to demonstrate the relationship between gut microbiota and host genetics in patients with intestinal adenomatous polyps. Method: The entire exon region of the APC gene was sequenced in 35 patients with pathologically diagnosed adenomatous polyps. Patients with highly pathogenic APC mutation were classified as the case group, while the others were classified as the control group. The patients'stool and serum samples were respectively collected for metagenomics and metabolomics measurements. Results: In the analysis of gut microbiome, there were three most important species, in which Fusobacterium_mortiferum was significantly increased while Faecalibacterium_prausnitzii and Bifidobacterium_pseudocatenulatum were significantly decreased in the case group. The significantly low abundance of the Photosynthesis pathway in patients with APC mutation was due to the low abundance of species Faecalibacterium_prausnitzii and Bifidobacterium_pseudocatenulatum. Moreover, there were two clusters of KEGG pathways correlated with two clusters of species characterized by Faecalibacterium_prausnitzii and Fusobacterium_mortiferum. As to serum metabolomics, the abundance of (R)-3-Hydroxybutyric acid and 2-Hydroxyphenethylamine were significantly higher in patients with APC mutation, while the abundance of 1-Aminocyclopropanecarboxylic acid,7-Ketocholesterol, DL-lactate, and L-Pyroglutamic acid were significantly higher in controlgroup. After analyzing the metabolome and microbiome data by sparCCmethod, we found that there was a significantly negative correlation between the abundance of Faecalibacterium_prausnitzii and Fusobacterium_mortiferum, and a significantly positive correlation between Faecalibacterium_prausnitzii abundance and the steroid hormone Hydrocortisone (Cortisol) in serum. Conclusions: Host's APC mutation was closely related to the changes of gut microbiota and serum metabolites, and some species of gut microbiome like Faecalibacterium_prausnitzii and Fusobacterium_mortiferum might have the potential to predict the development of CRC from intestinal adenomatous polyps.}, } @article {pmid31892704, year = {2019}, author = {Arif, S and Reitner, J and Hoppert, M}, title = {Composition, Diversity and Functional Analysis of the Modern Microbiome of the Middle Triassic Cava Superiore Beds (Monte San Giorgio, Switzerland).}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {20394}, pmid = {31892704}, issn = {2045-2322}, mesh = {DNA, Bacterial/*genetics ; Firmicutes/*genetics ; *Fossils ; *Microbiota ; Proteobacteria/*genetics ; *Soil Microbiology ; Switzerland ; }, abstract = {Organic-rich laminated shales and limestones from the Monte San Giorgio (Lugano Prealps, Switzerland) are known as famous fossil lagerstätten for excellently preserved fossils from the Middle Triassic Period. The various bituminous shales from Monte San Giorgio are thermally immature and rich in diverse organic compounds, which provide unique substrates for active soil microbial communities. We selected the Cava superior beds of the Acqua del Ghiffo site for this study. To investigate its microbial structure and diversity, contig assembly, Operational Taxonomic Units (OTUs) clustering, and rarefaction analysis were performed for bacterial 16S rDNA preparations from bituminous and non-bituminous limestone strata with the MetaAmp pipeline. Principal coordinates analysis shows that the microbial communities from the bituminous strata differ significantly from limestone samples (P < 0.05 Unifrac weighted). Moreover, metagenomic tools could also be used effectively to analyze the microbial communities shift during enrichment in specific growth media. In the nutrient-rich media, one or few taxa, mainly Proteobacteria and Firmicutes, were enriched which led to the drastic diversity loss while oligotrophic media could enrich many taxa simultaneously and sustain the richness and diversity of the inoculum. Piphillin, METAGENassist and MicrobiomeAnalyst pipeline also predicted that the Monte San Giorgio bituminous shales and oligotrophic enriched microbiomes degrade complex polycyclic aromatic hydrocarbons.}, } @article {pmid31889105, year = {2019}, author = {Oh, TJ and Sul, WJ and Oh, HN and Lee, YK and Lim, HL and Choi, SH and Park, KS and Jang, HC}, title = {Butyrate attenuated fat gain through gut microbiota modulation in db/db mice following dapagliflozin treatment.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {20300}, pmid = {31889105}, issn = {2045-2322}, mesh = {Adipose Tissue/*drug effects ; Animals ; Benzhydryl Compounds/*pharmacology ; Butyric Acid/*pharmacology ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; Glucose/metabolism ; Glucosides/*pharmacology ; Liver/drug effects/metabolism/pathology ; Mice ; Obesity/drug therapy/etiology/metabolism ; Sodium-Glucose Transporter 2 Inhibitors/*pharmacology ; Weight Gain ; }, abstract = {We investigated the effect of a combination treatment with dapagliflozin (Dapa), a sodium-glucose cotransporter-2 inhibitor and butyrate on weight change in db/db mice. Six-week-old male db/db mice were assigned to four groups: vehicle with normal chow diet (NCD), Dapa with NCD, vehicle with 5% sodium butyrate-supplemented NCD (NaB), or Dapa with 5% NaB. After six weeks of treatment, faecal microbiota composition was analysed by sequencing 16S ribosomal RNA genes. In the vehicle with NaB and Dapa + NaB groups, body weight increase was attenuated, and amount of food intake decreased compared with the vehicle with the NCD group. The Dapa + NaB group gained the least total and abdominal fat from baseline. Intestinal microbiota of this group was characterized by a decrease of the Firmicutes to Bacteroidetes ratio, a decrease of Adlercreutzia and Alistipes, as well as an increase of Streptococcus. In addition, the proportion of Adlercreutzia and Alistipes showed a positive correlation with total fat gain, whereas Streptococcus showed a negative correlation. Inferred metagenome function revealed that tryptophan metabolism was upregulated by NaB treatment. We demonstrated a synergistic effect of Dapa and NaB treatment on adiposity reduction, and this phenomenon might be related to intestinal microbiota alteration.}, } @article {pmid31888470, year = {2019}, author = {Goloshchapov, OV and Olekhnovich, EI and Sidorenko, SV and Moiseev, IS and Kucher, MA and Fedorov, DE and Pavlenko, AV and Manolov, AI and Gostev, VV and Veselovsky, VA and Klimina, KM and Kostryukova, ES and Bakin, EA and Shvetcov, AN and Gumbatova, ED and Klementeva, RV and Shcherbakov, AA and Gorchakova, MV and Egozcue, JJ and Pawlowsky-Glahn, V and Suvorova, MA and Chukhlovin, AB and Govorun, VM and Ilina, EN and Afanasyev, BV}, title = {Long-term impact of fecal transplantation in healthy volunteers.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {312}, pmid = {31888470}, issn = {1471-2180}, mesh = {Adult ; *Fecal Microbiota Transplantation ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Time Factors ; }, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) has been recently approved by FDA for the treatment of refractory recurrent clostridial colitis (rCDI). Success of FTM in treatment of rCDI led to a number of studies investigating the effectiveness of its application in the other gastrointestinal diseases. However, in the majority of studies the effects of FMT were evaluated on the patients with initially altered microbiota. The aim of our study was to estimate effects of FMT on the gut microbiota composition in healthy volunteers and to monitor its long-term outcomes.

RESULTS: We have performed a combined analysis of three healthy volunteers before and after capsule FMT by evaluating their general condition, adverse clinical effects, changes of basic laboratory parameters, and several immune markers. Intestinal microbiota samples were evaluated by 16S rRNA gene and shotgun sequencing. The data analysis demonstrated profound shift towards the donor microbiota taxonomic composition in all volunteers. Following FMT, all the volunteers exhibited gut colonization with donor gut bacteria and persistence of this effect for almost ∼1 year of observation. Transient changes of immune parameters were consistent with suppression of T-cell cytotoxicity. FMT was well tolerated with mild gastrointestinal adverse events, however, one volunteer developed a systemic inflammatory response syndrome.

CONCLUSIONS: The FMT leads to significant long-term changes of the gut microbiota in healthy volunteers with the shift towards donor microbiota composition and represents a relatively safe procedure to the recipients without long-term adverse events.}, } @article {pmid31888048, year = {2019}, author = {Sakanaka, M and Gotoh, A and Yoshida, K and Odamaki, T and Koguchi, H and Xiao, JZ and Kitaoka, M and Katayama, T}, title = {Varied Pathways of Infant Gut-Associated Bifidobacterium to Assimilate Human Milk Oligosaccharides: Prevalence of the Gene Set and Its Correlation with Bifidobacteria-Rich Microbiota Formation.}, journal = {Nutrients}, volume = {12}, number = {1}, pages = {}, pmid = {31888048}, issn = {2072-6643}, support = {18K14379; 19K15732; 19K22277; 201860637; 17J08530//Japan Society for the Promotion of Science/ ; }, mesh = {*Bifidobacterium/enzymology/genetics/metabolism ; Breast Feeding ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Genome, Bacterial/genetics ; Humans ; Infant ; Metagenomics ; *Milk, Human/chemistry/metabolism ; Oligosaccharides/*metabolism ; }, abstract = {The infant's gut microbiome is generally rich in the Bifidobacterium genus. The mother's milk contains natural prebiotics, called human milk oligosaccharides (HMOs), as the third most abundant solid component after lactose and lipids, and of the different gut microbes, infant gut-associated bifidobacteria are the most efficient in assimilating HMOs. Indeed, the fecal concentration of HMOs was found to be negatively correlated with the fecal abundance of Bifidobacterium in infants. Given these results, two HMO molecules, 2'-fucosyllactose and lacto-N-neotetraose, have recently been industrialized to fortify formula milk. As of now, however, our knowledge about the HMO consumption pathways in infant gut-associated bifidobacteria is still incomplete. The recent studies indicate that HMO assimilation abilities significantly vary among different Bifidobacterium species and strains. Therefore, to truly maximize the effects of prebiotic and probiotic supplementation in commercialized formula, we need to understand HMO consumption behaviors of bifidobacteria in more detail. In this review, we summarized how different Bifidobacterium species/strains are equipped with varied gene sets required for HMO assimilation. We then examined the correlation between the abundance of the HMO-related genes and bifidobacteria-rich microbiota formation in the infant gut through data mining analysis of a deposited fecal microbiome shotgun sequencing dataset. Finally, we shortly described future perspectives on HMO-related studies.}, } @article {pmid31885873, year = {2019}, author = {Pareek, S and Kurakawa, T and Das, B and Motooka, D and Nakaya, S and Rongsen-Chandola, T and Goyal, N and Kayama, H and Dodd, D and Okumura, R and Maeda, Y and Fujimoto, K and Nii, T and Ogawa, T and Iida, T and Bhandari, N and Kida, T and Nakamura, S and Nair, GB and Takeda, K}, title = {Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi.}, journal = {NPJ biofilms and microbiomes}, volume = {5}, number = {1}, pages = {37}, pmid = {31885873}, issn = {2055-5008}, support = {K08 DK110335/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/*growth & development/*metabolism ; Diet/*methods ; Feces/microbiology ; Fungi/classification/*growth & development/*metabolism ; *Gastrointestinal Microbiome ; Humans ; India ; Japan ; Mice ; *Microbial Interactions ; Models, Animal ; Polysaccharides/metabolism ; }, abstract = {The bacterial species living in the gut mediate many aspects of biological processes such as nutrition and activation of adaptive immunity. In addition, commensal fungi residing in the intestine also influence host health. Although the interaction of bacterium and fungus has been shown, its precise mechanism during colonization of the human intestine remains largely unknown. Here, we show interaction between bacterial and fungal species for utilization of dietary components driving their efficient growth in the intestine. Next generation sequencing of fecal samples from Japanese and Indian adults revealed differential patterns of bacterial and fungal composition. In particular, Indians, who consume more plant polysaccharides than Japanese, harbored increased numbers of Prevotella and Candida. Candida spp. showed strong growth responses to the plant polysaccharide arabinoxylan in vitro. Furthermore, the culture supernatants of Candida spp. grown with arabinoxylan promoted rapid proliferation of Prevotella copri. Arabinose was identified as a potential growth-inducing factor in the Candida culture supernatants. Candida spp. exhibited a growth response to xylose, but not to arabinose, whereas P. copri proliferated in response to both xylose and arabinose. Candida spp., but not P. copri, colonized the intestine of germ-free mice. However, P. copri successfully colonized mouse intestine already harboring Candida. These findings demonstrate a proof of concept that fungal members of gut microbiota can facilitate a colonization of the intestine by their bacterial counterparts, potentially mediated by a dietary metabolite.}, } @article {pmid31884983, year = {2019}, author = {Traoré, SI and Bilen, M and Cadoret, F and Khelaifia, S and Million, M and Raoult, D and Lagier, JC}, title = {Study of Human Gastrointestinal Microbiota by Culturomics in Africa.}, journal = {Medecine et sante tropicales}, volume = {29}, number = {4}, pages = {366-370}, doi = {10.1684/mst.2019.0943}, pmid = {31884983}, issn = {2261-2211}, mesh = {Africa ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/*methods ; }, abstract = {The interest in studying gut microbiota has been rekindled with the advent of molecular techniques, in particular, metagenomics. Culturomics (high throughput microbial culture with identification of the colonies by Maldi-TOF) has demonstrated its complementarity with metagenomics for comprehensive study of the microbiota. The main metagenomic studies have revealed an increase in biodiversity, with in particular an increase of Spirochaetes and Prevotella in subjects of African origin compared with Western subjects. Studies on malnutrition have shown a reduction of all bacteria and in particular of anaerobic bacteria and methanogenic archaea. Of the 1,162 bacteria isolated by culturomics studies, 476 were isolated only from non-African samples, 445 were isolated in African and non-African groups, and 241 bacteria were isolated from samples of African origin including 68 new species. Further studies of African microbiota by culturomics and metagenomics will make it possible to assess whether some bacteria have particular specificities and if these might play a role in certain pathologies such as malnutrition.}, } @article {pmid31884971, year = {2019}, author = {Coutinho, FH and Edwards, RA and Rodríguez-Valera, F}, title = {Charting the diversity of uncultured viruses of Archaea and Bacteria.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {109}, pmid = {31884971}, issn = {1741-7007}, mesh = {Archaea/*virology ; Bacteria/*virology ; Bacteriophages/*genetics ; *Genome, Viral ; *Microbiota ; Phylogeny ; }, abstract = {BACKGROUND: Viruses of Archaea and Bacteria are among the most abundant and diverse biological entities on Earth. Unraveling their biodiversity has been challenging due to methodological limitations. Recent advances in culture-independent techniques, such as metagenomics, shed light on the unknown viral diversity, revealing thousands of new viral nucleotide sequences at an unprecedented scale. However, these novel sequences have not been properly classified and the evolutionary associations between them were not resolved.

RESULTS: Here, we performed phylogenomic analysis of nearly 200,000 viral nucleotide sequences to establish GL-UVAB: Genomic Lineages of Uncultured Viruses of Archaea and Bacteria. The pan-genome content of the identified lineages shed light on some of their infection strategies, potential to modulate host physiology, and mechanisms to escape host resistance systems. Furthermore, using GL-UVAB as a reference database for annotating metagenomes revealed elusive habitat distribution patterns of viral lineages and environmental drivers of community composition.

CONCLUSIONS: These findings provide insights about the genomic diversity and ecology of viruses of prokaryotes. The source code used in these analyses is freely available at https://sourceforge.net/projects/gluvab/.}, } @article {pmid31884727, year = {2020}, author = {Song, Y and Gyarmati, P}, title = {Microbiota changes in a pediatric acute lymphocytic leukemia mouse model.}, journal = {MicrobiologyOpen}, volume = {9}, number = {3}, pages = {e982}, pmid = {31884727}, issn = {2045-8827}, mesh = {Animals ; Biodiversity ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Mice ; *Microbiota ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/*microbiology ; RNA, Ribosomal, 16S ; }, abstract = {Hematological malignancies are the most common type of pediatric cancers, and acute lymphocytic leukemia (ALL) is the most frequently occurring hematological malignancy during childhood. A major cause of mortality in leukemia is bloodstream infection (BSI). The aim of the current study was to explore the gut microbiota in ALL and its potential functional alterations. High-throughput sequencing was used to characterize the bacterial and fungal microbiota in feces and their predicted functional characteristics in a xenotransplant pediatric ALL mouse model. Our work shows that gut microbiota significantly changes in leukemia, which may result in functional alterations. This study may provide potential therapeutic or preventive strategies of BSI in ALL.}, } @article {pmid31884359, year = {2020}, author = {Zhang, L and Li, L and Sha, G and Liu, C and Wang, Z and Wang, L}, title = {Aerobic composting as an effective cow manure management strategy for reducing the dissemination of antibiotic resistance genes: An integrated meta-omics study.}, journal = {Journal of hazardous materials}, volume = {386}, number = {}, pages = {121895}, doi = {10.1016/j.jhazmat.2019.121895}, pmid = {31884359}, issn = {1873-3336}, mesh = {Acinetobacter/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; China ; Composting/*methods ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial/*drug effects ; Manure/*microbiology ; *Metagenomics ; Microbiota/drug effects/*genetics ; Pseudomonas/drug effects/genetics ; Soil/chemistry ; }, abstract = {Livestock manure is considered as an important source for spreading antibiotic resistance genes (ARGs) into the environment, and therefore poses a direct threat to public health. Whereas the effects of reused manure on soil microbial communities and ARGs have been studied extensively, comprehensive characterizations of microbial communities and ARGs of manure produced by different management methods are not well understood. Here, we analyzed the fate of microbial communities and ARGs of cow manure treated by three conventional management strategies: aerobic composting, mechanical drying and precipitation, applying an integrated-omics approach combining metagenomics and metaproteomics. Integrated-omics demonstrated that composted manure contained the lowest diversity of microbial community and ARGs compared with manure treated by other two strategies. Quantitative PCR methods revealed that the abundances of ARGs were reduced by over 83 % after composting for 14 days, regardless of the season. Besides, the potential ARG hosts Acinetobacter and Pseudomonas dominating mechanical drying process were sharply decreased in abundances after composting. The significant co-occurrence networks among bacteria, ARGs and transposase gene tnpA-01 in composting samples indicated the important role of these bacteria in the dissemination of ARGs. These findings offer insight into potential strategies to control the spread of ARGs during livestock manure reuse.}, } @article {pmid31883524, year = {2019}, author = {Manara, S and Asnicar, F and Beghini, F and Bazzani, D and Cumbo, F and Zolfo, M and Nigro, E and Karcher, N and Manghi, P and Metzger, MI and Pasolli, E and Segata, N}, title = {Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {299}, pmid = {31883524}, issn = {1474-760X}, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; Phylogeny ; Primates/*microbiology ; Treponema/genetics ; }, abstract = {BACKGROUND: Humans have coevolved with microbial communities to establish a mutually advantageous relationship that is still poorly characterized and can provide a better understanding of the human microbiome. Comparative metagenomic analysis of human and non-human primate (NHP) microbiomes offers a promising approach to study this symbiosis. Very few microbial species have been characterized in NHP microbiomes due to their poor representation in the available cataloged microbial diversity, thus limiting the potential of such comparative approaches.

RESULTS: We reconstruct over 1000 previously uncharacterized microbial species from 6 available NHP metagenomic cohorts, resulting in an increase of the mappable fraction of metagenomic reads by 600%. These novel species highlight that almost 90% of the microbial diversity associated with NHPs has been overlooked. Comparative analysis of this new catalog of taxa with the collection of over 150,000 genomes from human metagenomes points at a limited species-level overlap, with only 20% of microbial candidate species in NHPs also found in the human microbiome. This overlap occurs mainly between NHPs and non-Westernized human populations and NHPs living in captivity, suggesting that host lifestyle plays a role comparable to host speciation in shaping the primate intestinal microbiome. Several NHP-specific species are phylogenetically related to human-associated microbes, such as Elusimicrobia and Treponema, and could be the consequence of host-dependent evolutionary trajectories.

CONCLUSIONS: The newly reconstructed species greatly expand the microbial diversity associated with NHPs, thus enabling better interrogation of the primate microbiome and empowering in-depth human and non-human comparative and co-diversification studies.}, } @article {pmid31882995, year = {2020}, author = {Anand, S and Kuntal, BK and Mohapatra, A and Bhatt, V and Mande, SS}, title = {FunGeCo: a web-based tool for estimation of functional potential of bacterial genomes and microbiomes using gene context information.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {8}, pages = {2575-2577}, doi = {10.1093/bioinformatics/btz957}, pmid = {31882995}, issn = {1367-4811}, mesh = {Genome, Bacterial/genetics ; Internet ; Metagenome ; *Microbiota/genetics ; *Software ; }, abstract = {MOTIVATION: Functional potential of genomes and metagenomes which are inferred using homology-based methods are often subjected to certain limitations, especially for proteins with homologs which function in multiple pathways. Augmenting the homology information with genomic location of the constituent genes can significantly improve the accuracy of estimated functions. This can help in distinguishing cognate homolog belonging to a candidate pathway from its other homologs functional in different pathways.

RESULTS: In this article, we present a web-based analysis platform 'FunGeCo' to enable gene-context-based functional inference for microbial genomes and metagenomes. It is expected to be a valuable resource and complement the existing tools for understanding the functional potential of microbes which reside in an environment.

https://web.rniapps.net/fungeco [Freely available for academic use].

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid31882580, year = {2019}, author = {Griffen, AL and Thompson, ZA and Beall, CJ and Lilly, EA and Granada, C and Treas, KD and DuBois, KR and Hashmi, SB and Mukherjee, C and Gilliland, AE and Vazquez, JA and Hagensee, ME and Leys, EJ and Fidel, PL}, title = {Significant effect of HIV/HAART on oral microbiota using multivariate analysis.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19946}, pmid = {31882580}, issn = {2045-2322}, support = {R01 DE022815/DE/NIDCR NIH HHS/United States ; U54 GM104940/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Anti-Retroviral Agents/pharmacology ; Antiretroviral Therapy, Highly Active/methods ; CD4 Lymphocyte Count/methods ; Dental Caries/*microbiology ; Female ; HIV Infections/drug therapy/*microbiology ; HIV-1/drug effects/pathogenicity ; Humans ; Male ; Metagenomics/methods ; Microbiota/*drug effects ; Multivariate Analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Persons infected with HIV are particularly vulnerable to a variety of oral microbial diseases. Although various study designs and detection approaches have been used to compare the oral microbiota of HIV-negative and HIV-positive persons, both with and without highly active antiretroviral therapy (HAART), methods have varied, and results have not been consistent or conclusive. The purpose of the present study was to compare the oral bacterial community composition in HIV-positive persons under HAART to an HIV-negative group using 16S rRNA gene sequence analysis. Extensive clinical data was collected, and efforts were made to balance the groups on clinical variables to minimize confounding. Multivariate analysis was used to assess the independent contribution of HIV status. Eighty-nine HIV-negative participants and 252 HIV-positive participants under HAART were sampled. The independent effect of HIV under HAART on the oral microbiome was statistically significant, but smaller than the effect of gingivitis, periodontal disease, smoking, caries, and other clinical variables. In conclusion, a multivariate comparison of a large sample of persons with HIV under HAART to an HIV-negative control group showed a complex set of clinical features that influenced oral bacterial community composition, including the presence of HIV under HAART.}, } @article {pmid31882572, year = {2019}, author = {Wang, Z and Yang, Y and Xia, Y and Wu, T and Zhu, J and Yang, J and Li, Z}, title = {Time-course relationship between environmental factors and microbial diversity in tobacco soil.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19969}, pmid = {31882572}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics ; *Biodiversity ; Chemical Phenomena ; *Environment ; Environmental Microbiology ; Fungi/classification/genetics ; Metagenome ; Metagenomics/methods ; *Microbiota ; Soil/chemistry ; *Soil Microbiology ; Time Factors ; *Nicotiana/growth & development ; }, abstract = {Soil physicochemical properties and microbial diversity both play equally important roles in tobacco cultivation. However, the relationship between these factors remains unclear. In this study, we investigated their correlations through the whole tobacco growth period, including the pretransplanting (YX-p), root extending (R), flourishing (F), and mature (M) stages in the Yuxi region of the Yunnan-Guizhou Plateau by measuring physicochemical properties and conducting 16S/18S rRNA analysis. The analysis demonstrated that the microbial community richness and diversity continuously changed along with the growth course of the tobacco. Multiple environmental factors showed a certain correlation with the diversity of microbial communities. Some bacteria could accumulate nitrogen during the growth stages, and the diversity of the bacterial community also increased when the content of organic matter rose. In addition, the water content and available K also influenced the diversity of the microbial community. The dynamic changes in soil physicochemical properties and enzyme activities gave rise to differences in the microbial community composition and structure, all of which affected the growth of tobacco. This study revealed the time-course relationship between environmental factors and microbial diversity in tobacco soil. An understanding of this relationship provides guidance for research on the interaction system of plants, soil and microbes and on improving plant yield and quality.}, } @article {pmid31880067, year = {2020}, author = {Chen, T and Li, Y and Liang, J and Li, Y and Huang, Z}, title = {Gut microbiota of provisioned and wild rhesus macaques (Macaca mulatta) living in a limestone forest in southwest Guangxi, China.}, journal = {MicrobiologyOpen}, volume = {9}, number = {3}, pages = {e981}, pmid = {31880067}, issn = {2045-8827}, mesh = {Animal Feed ; Animals ; Biodiversity ; *Calcium Carbonate ; China ; *Forests ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; *Macaca mulatta ; Metagenome ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The gut microbiota plays an important role in animal health and is strongly affected by the environment. Captivity and human source food have been shown to influence drastically the gut microbiota composition and function of wild animals. Therefore, in the present study, the gut microbiota of provisioned and wild populations of limestone-living rhesus macaques (Macaca mulatta) were compared using high-throughput 16S rRNA sequencing and bioinformatic analyses. The results indicated that provisioned macaques had a higher microbial richness than wild macaques, but there was no significant difference in the evenness of the gut microbiota between the two populations. Provisioned macaques also showed a higher abundance of Firmicutes and a lower abundance of Bacteroidetes than wild macaques. Functional analysis revealed that wild macaques had enriched microbial pathways involved in glycan biosynthesis and metabolism, transport and catabolism, and the digestive and endocrine systems, while provisioned macaques were richer in pathways associated with signaling molecules and interaction, neurodegenerative diseases. These differences were likely due to modification of the gut microbiota of the provisioned macaques to enable the digestion of new foods.}, } @article {pmid31879084, year = {2020}, author = {Marsh, RL and Aho, C and Beissbarth, J and Bialasiewicz, S and Binks, M and Cervin, A and Kirkham, LS and Lemon, KP and Slack, MPE and Smith-Vaughan, HC}, title = {Panel 4: Recent advances in understanding the natural history of the otitis media microbiome and its response to environmental pressures.}, journal = {International journal of pediatric otorhinolaryngology}, volume = {130 Suppl 1}, number = {Suppl 1}, pages = {109836}, pmid = {31879084}, issn = {1872-8464}, support = {R01 GM117174/GM/NIGMS NIH HHS/United States ; R13 DC017389/DC/NIDCD NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Bacteria ; Disease Models, Animal ; Ear, Middle/*microbiology ; Humans ; *Microbiota/drug effects ; Nasopharynx/microbiology ; Otitis Media/*microbiology ; Smoking ; Vaccines/pharmacology ; }, abstract = {OBJECTIVE: To perform a comprehensive review of otitis media microbiome literature published between 1[st] July 2015 and 30th June 2019.

DATA SOURCES: PubMed database, National Library of Medicine.

REVIEW METHODS: Key topics were assigned to each panel member for detailed review. Draft reviews were collated and circulated for discussion when the panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019. The final draft was prepared with input from all panel members.

CONCLUSIONS: Much has been learned about the different types of bacteria (including commensals) present in the upper respiratory microbiome, but little is known about the virome and mycobiome. A small number of studies have investigated the middle ear microbiome; however, current data are often limited by small sample sizes and methodological heterogeneity between studies. Furthermore, limited reporting of sample collection methods mean that it is often difficult to determine whether bacteria detected in middle ear fluid specimens originated from the middle ear or the external auditory canal. Recent in vitro studies suggest that bacterial interactions in the nasal/nasopharyngeal microbiome may affect otitis media pathogenesis by modifying otopathogen behaviours. Impacts of environmental pressures (e.g. smoke, nutrition) and clinical interventions (e.g. vaccination, antibiotics) on the upper respiratory and middle ear microbiomes remain poorly understood as there are few data.

IMPLICATIONS FOR PRACTICE: Advances in understanding bacterial dynamics in the upper airway microbiome are driving development of microbiota-modifying therapies to prevent or treat disease (e.g. probiotics). Further advances in otitis media microbiomics will likely require technological improvements that overcome the current limitations of OMICs technologies when applied to low volume and low biomass specimens that potentially contain high numbers of host cells. Improved laboratory models are needed to elucidate mechanistic interactions among the upper respiratory and middle ear microbiomes. Minimum reporting standards are critically needed to improve inter-study comparisons and enable future meta-analyses.}, } @article {pmid31877275, year = {2020}, author = {Fuentes-Valencia, MA and Fajer-Ávila, EJ and Chávez-Sánchez, MC and Martínez-Palacios, CA and Martínez-Chávez, CC and Junqueira-Machado, G and Lara, HH and Raggi, L and Gómez-Gil, B and Pestryakov, AA and Bogdanchikova, N}, title = {Silver nanoparticles are lethal to the ciliate model Tetrahymena and safe to the pike silverside Chirostoma estor.}, journal = {Experimental parasitology}, volume = {209}, number = {}, pages = {107825}, doi = {10.1016/j.exppara.2019.107825}, pmid = {31877275}, issn = {1090-2449}, mesh = {Animals ; Aquaculture ; Ectoparasitic Infestations/drug therapy/parasitology/*veterinary ; Fish Diseases/*drug therapy/parasitology ; Fishes ; Fresh Water ; Gastrointestinal Microbiome ; Humans ; Lethal Dose 50 ; Metagenomics ; Metal Nanoparticles/chemistry/*toxicity ; Microscopy, Electron, Scanning/veterinary ; Silver/chemistry/*pharmacology/toxicity ; Tetrahymena/*drug effects/ultrastructure ; }, abstract = {Ciliate ectoparasites are one of the most important groups of pathogens in fish culture, and the traditional treatments are sometimes harmful to the fish and the environment. Thus, the search for novel compounds that are effective at low concentrations and safe for fish are necessary to optimise treatments in aquaculture. The antiprotozoal capacity of silver nanoparticles (AgNPs) against the ciliate Tetrahymena has been documented; however, their toxicity may vary with the synthesis methodology and nanoparticle size. The objectives of this study were a) to evaluate the acute toxicity in vitro of two AgNPs (Argovit™ and UTSA) on Tetrahymena sp., a biological model for ciliated ectoparasites of fish and b) to test the safety of lethal and higher doses of UTSA AgNPs for ciliates on the fish C. estor. Light microscopy and scanning electron microscopy (SEM) were used to determine whether AgNPs affected the structure of the cell surface of Tetrahymena. The mortality, histopathological alterations and metagenomics of the fish were used to determine the major effects of UTSA AgNPs. In Tetrahymena, the median lethal concentration (LC50) for Argovit™ was 2501 ± 1717 ng/L at 15 min and 796 ± 510 ng/L at 60 min, while the LC50 for UTSA AgNPs was 4 ± 2 and 1 ± 0.6 ng/L at 15 min and 60 min, respectively. A concentration of 3300 ng/L Argovit™ and 10.6 ng/L UTSA AgNPs for 15 and 60 min, respectively, was 100% effective against Tetrahymena. After 60 min of exposure to 0.25 and 0.50 ng/L UTSA AgNPs, the number of cilia significantly reduced, there were small holes on the cell surface, and the cellular membrane was ruptured. In fish exposed to lethal (10.6 ng/L) and higher (31.8 and 95.4 ng/L) doses of UTSA, the AgNPs did not affect fish survival after 96 h, and there were no signs of histopathological damage or gut microbial changes. This study is the first report on microscopic and ultrastructural changes in Tetrahymena after exposure to significantly low concentrations of UTSA AgNPs with antiprotozoal efficacy without evidence of harmful effects on fish. These results provide the basis for further studies of both pet aquarium and commercial fish that may validate these findings at a larger experimental scale, taking into account AgNPs bioaccumulation, safety for human consumption and environmental impact.}, } @article {pmid31876912, year = {2020}, author = {Bartolomaeus, TUP and Forslund, SK}, title = {Hitchhiker's guide to microbiome studies.}, journal = {Cardiovascular research}, volume = {116}, number = {3}, pages = {e44-e47}, doi = {10.1093/cvr/cvz316}, pmid = {31876912}, issn = {1755-3245}, mesh = {Bacteria/classification/*genetics/isolation & purification ; DNA, Bacterial/classification/*genetics/isolation & purification ; Feces/microbiology ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Ribotyping ; Skin/*microbiology ; }, } @article {pmid31876614, year = {2020}, author = {Lees, EA and Carrol, ED and Ellaby, NAF and Roberts, P and Corless, CE and Lenzi, L and Darby, A and O'Brien, SJ and Cunliffe, NA and Turner, MA and Miyajima, F and Pirmohamed, M}, title = {Characterization of Circulating Clostridium difficile Strains, Host Response and Intestinal Microbiome in Hospitalized Children With Diarrhea.}, journal = {The Pediatric infectious disease journal}, volume = {39}, number = {3}, pages = {221-228}, doi = {10.1097/INF.0000000000002559}, pmid = {31876614}, issn = {1532-0987}, support = {/DH_/Department of Health/United Kingdom ; MR/K000551/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adolescent ; *Bacteremia ; Bacterial Toxins/genetics ; Biomarkers ; Child ; Child, Preschool ; Clostridioides difficile/classification ; Cytokines/metabolism ; Diarrhea/*epidemiology/*etiology ; Enterocolitis, Pseudomembranous/*epidemiology/*microbiology ; Feces/chemistry/microbiology ; Female ; *Gastrointestinal Microbiome ; Hospitalization ; *Host-Pathogen Interactions ; Humans ; Incidence ; Infant ; Infant, Newborn ; Male ; Metagenomics/methods ; Molecular Typing ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Clostridium difficile is capable of causing severe enterocolitis in adults. The significance of toxin-producing C. difficile in children with diarrhea is unclear and practice differs on whether to institute treatment. We aimed to characterize the microbiome in relation to the presence of C. difficile and co-infection with other pathogens and to describe host response to infection.

METHODS: Participants were children with acute diarrhea, 0-16 years of age, from whom stool samples had been submitted to the hospital laboratory for routine microbiology/virology. Convenience sampling was used for 50 prospective and 150 retrospective samples. No participants were treated for C. difficile. Rates of culture positivity for C. difficile, presence of toxin and PCR-ribotype were compared between age groups. Presence of other potential pathogens, comorbidities and complications were recorded. Microbiotal diversity was measured by 16S profiling.

RESULTS: Nineteen of 77 (25%) children <2 years of age and 13 of 119 (11%) children >2 years of age were C. difficile positive, of whom 10 (53%) and 9 (69%), respectively, carried toxigenic strains. Increased Shannon diversity was seen in children carrying C. difficile, with altered milieu. Presence of C. difficile was not associated with adverse clinical outcomes. In stools containing both Norovirus and C. difficile, there was increased relative abundance of verrucomicrobia.

CONCLUSIONS: Children with diarrhea regularly carried toxigenic and non-toxigenic strains of C. difficile, demonstrating enhanced microbiotal diversity, and change in milieu, without apparent morbidity. This unexpected finding is contrary to that seen in adults with C. difficile disease.}, } @article {pmid31875016, year = {2019}, author = {Passaro, N and Casagrande, A and Chiara, M and Fosso, B and Manzari, C and D'Erchia, AM and Iesari, S and Pisani, F and Famulari, A and Tulissi, P and Mastrosimone, S and Maresca, MC and Mercante, G and Spriano, G and Corrado, G and Vizza, E and Garbuglia, AR and Capobianchi, MR and Mottini, C and Cenci, A and Tartaglia, M and Costa, AN and Pesole, G and Crescenzi, M}, title = {No metagenomic evidence of tumorigenic viruses in cancers from a selected cohort of immunosuppressed subjects.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19815}, pmid = {31875016}, issn = {2045-2322}, mesh = {Computational Biology/methods ; Humans ; *Immunocompromised Host ; Immunosuppression Therapy/adverse effects ; Metagenome ; Metagenomics/*methods ; Microbiota ; Neoplasms/*virology ; Oncogenic Viruses/*genetics ; Probability ; Sequence Analysis, RNA ; Viruses/genetics ; }, abstract = {The possible existence of yet undiscovered human tumorigenic viruses is still under scrutiny. The development of large-scale sequencing technologies, coupled with bioinformatics techniques for the characterization of metagenomic sequences, have provided an invaluable tool for the detection of unknown, infectious, tumorigenic agents, as demonstrated by several recent studies. However, discoveries of novel viruses possibly associated with tumorigenesis are scarce at best. Here, we apply a rigorous bioinformatics workflow to investigate in depth tumor metagenomes from a small but carefully selected cohort of immunosuppressed patients. While a variegated bacterial microbiome was associated with each tumor, no evidence of the presence of putative oncoviruses was found. These results are consistent with the major findings of several recent papers and suggest that new human tumorigenic viruses are not common even in immunosuppressed populations.}, } @article {pmid31874394, year = {2020}, author = {Yan, C and Wang, F and Geng, H and Liu, H and Pu, S and Tian, Z and Chen, H and Zhou, B and Yuan, R and Yao, J}, title = {Integrating high-throughput sequencing and metagenome analysis to reveal the characteristic and resistance mechanism of microbial community in metal contaminated sediments.}, journal = {The Science of the total environment}, volume = {707}, number = {}, pages = {136116}, doi = {10.1016/j.scitotenv.2019.136116}, pmid = {31874394}, issn = {1879-1026}, mesh = {Beijing ; Environmental Monitoring ; Geologic Sediments ; Metagenome ; Metals, Heavy ; *Microbiota ; Rivers ; Water Pollutants, Chemical ; }, abstract = {Some metallic tailings from closed mines were scattered in upstream of the Miyun Reservoir, Beijing, threatening the ecological environment of rivers due to trace metals. The Liuli River, one of the main rivers affected, was investigated as a typical model in this work. In this study, we selected eight sites to assess interactions among the various geochemical factors especially between trace metals and sediment microbiota. Random forest predicted that low concentrations of Cu, Cd, Cr and Ni (lower than 61.8 mg/kg, 3.2 mg/kg, 173.2 mg/kg and 34.1 mg/kg, respectively) were able to enhance community diversity but generally, trace metals contamination impaired microbial diversity. Environmental factor correlation analysis showed that As, pH and available P were the major factors that shifted the distribution of the microbial communities. Metagenome sequencing revealed that Proteobacteria harbored the vast majority of heavy metal resistance genes followed by Actinobacteria and Bacteroidetes. Metal tolerance of Proteobacteria were achieved by exportation of metals by the corresponding transporters, by pumps and ion channels, or by their reduction via redox reactions. In addition, Proteobacteria harbored a greater ability to repair DNA damage via DNA recombination.}, } @article {pmid31873717, year = {2020}, author = {von Martels, JZH and Bourgonje, AR and Klaassen, MAY and Alkhalifah, HAA and Sadaghian Sadabad, M and Vich Vila, A and Gacesa, R and Gabriëls, RY and Steinert, RE and Jansen, BH and Bulthuis, MLC and van Dullemen, HM and Visschedijk, MC and Festen, EAM and Weersma, RK and de Vos, P and van Goor, H and Faber, KN and Harmsen, HJM and Dijkstra, G}, title = {Riboflavin Supplementation in Patients with Crohn's Disease [the RISE-UP study].}, journal = {Journal of Crohn's & colitis}, volume = {14}, number = {5}, pages = {595-607}, pmid = {31873717}, issn = {1876-4479}, mesh = {Adult ; Biomarkers/blood ; Blood Sedimentation ; C-Reactive Protein/metabolism ; Crohn Disease/blood/*drug therapy ; Dietary Supplements ; Enterobacteriaceae/isolation & purification ; Fatty Acids, Volatile/analysis ; Feces/chemistry/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Interleukin-2/blood ; Leukocyte L1 Antigen Complex/analysis ; Male ; Middle Aged ; Oxidative Stress/*drug effects ; Platelet Count ; Prospective Studies ; Quality of Life ; Riboflavin/pharmacology/*therapeutic use ; Severity of Illness Index ; Sulfhydryl Compounds/blood ; Vitamin B Complex/pharmacology/*therapeutic use ; }, abstract = {BACKGROUND AND AIMS: Crohn's disease [CD] is characterised by chronic intestinal inflammation and dysbiosis in the gut. Riboflavin [vitamin B2] has anti-inflammatory, antioxidant and microbiome-modulatory properties. Here, we analysed the effect of riboflavin on oxidative stress, markers of inflammation, clinical symptoms, and faecal microbiome in patients with CD.

METHODS: In this prospective clinical intervention study, patients received 100 mg riboflavin [DSM, Nutritional Products Ltd] daily for 3 weeks. Clinical disease activity [Harvey-Bradshaw Index: HBI], serum biomarkers of inflammation and redox status [plasma free thiols], and faecal microbiome taxonomical composition and functionality [fluorescent in situ hybridisation: FISH; and metagenomic shotgun sequencing: MGS], were analysed before and after riboflavin intervention.

RESULTS: In total, 70 patients with CD with varying disease activity were included. Riboflavin supplementation significantly decreased serum levels of inflammatory markers. In patients with low faecal calprotectin [FC] levels, IL-2 decreased, and in patients with high FC levels, C-reactive protein [CRP] was reduced and free thiols significantly increased after supplementation. Moreover, HBI was significantly decreased by riboflavin supplementation. Riboflavin supplementation led to decreased Enterobacteriaceae in patients with low FC levels as determined by FISH; however, MGS analysis showed no effects on diversity, taxonomy, or metabolic pathways of the faecal microbiome.

CONCLUSIONS: Three weeks of riboflavin supplementation resulted in a reduction in systemic oxidative stress, mixed anti-inflammatory effects, and a reduction in clinical symptoms [HBI]. FISH analysis showed decreased Enterobacteriaceae in patients with CD with low FC levels, though this was not observed in MGS analysis. Our data demonstrate that riboflavin supplementation has a number of anti-inflammatory and anti-oxidant effects in CD.}, } @article {pmid31873203, year = {2020}, author = {Yaffe, E and Relman, DA}, title = {Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation.}, journal = {Nature microbiology}, volume = {5}, number = {2}, pages = {343-353}, pmid = {31873203}, issn = {2058-5276}, support = {R01 AI112401/AI/NIAID NIH HHS/United States ; R01 AI147023/AI/NIAID NIH HHS/United States ; R56 AI147023/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptation, Physiological/genetics ; Adult ; Computer Simulation ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics/*physiology ; Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenome ; Models, Genetic ; Phylogeny ; Time Factors ; }, abstract = {Despite the importance of horizontal gene transfer for rapid bacterial evolution, reliable assignment of mobile genetic elements to their microbial hosts in natural communities such as the human gut microbiota is lacking. We used high-throughput chromosomal conformation capture coupled with probabilistic modelling of experimental noise to resolve 88 strain-level metagenome-assembled genomes of distal gut bacteria from two participants, including 12,251 accessory elements. Comparisons of two samples collected 10 years apart for each of the participants revealed extensive in situ exchange of accessory elements as well as evidence of adaptive evolution in core genomes. Accessory elements were predominantly promiscuous and prevalent in the distal gut metagenomes of 218 adult individuals. This research provides a foundation and approach for studying microbial evolution in natural environments.}, } @article {pmid31873124, year = {2019}, author = {Ottoni, C and Guellil, M and Ozga, AT and Stone, AC and Kersten, O and Bramanti, B and Porcier, S and Van Neer, W}, title = {Metagenomic analysis of dental calculus in ancient Egyptian baboons.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19637}, pmid = {31873124}, issn = {2045-2322}, mesh = {Animals ; DNA, Ancient/*analysis ; Dental Calculus/*microbiology ; Egypt ; Humans ; *Metagenome ; Microbiota/*genetics ; Neanderthals ; Pan troglodytes ; Papio ; }, abstract = {Dental calculus, or mineralized plaque, represents a record of ancient biomolecules and food residues. Recently, ancient metagenomics made it possible to unlock the wealth of microbial and dietary information of dental calculus to reconstruct oral microbiomes and lifestyle of humans from the past. Although most studies have so far focused on ancient humans, dental calculus is known to form in a wide range of animals, potentially informing on how human-animal interactions changed the animals' oral ecology. Here, we characterise the oral microbiome of six ancient Egyptian baboons held in captivity during the late Pharaonic era (9[th]-6[th] centuries BC) and of two historical baboons from a zoo via shotgun metagenomics. We demonstrate that these captive baboons possessed a distinctive oral microbiome when compared to ancient and modern humans, Neanderthals and a wild chimpanzee. These results may reflect the omnivorous dietary behaviour of baboons, even though health, food provisioning and other factors associated with human management, may have changed the baboons' oral microbiome. We anticipate our study to be a starting point for more extensive studies on ancient animal oral microbiomes to examine the extent to which domestication and human management in the past affected the diet, health and lifestyle of target animals.}, } @article {pmid31870316, year = {2019}, author = {Deutscher, AT and Chapman, TA and Shuttleworth, LA and Riegler, M and Reynolds, OL}, title = {Tephritid-microbial interactions to enhance fruit fly performance in sterile insect technique programs.}, journal = {BMC microbiology}, volume = {19}, number = {Suppl 1}, pages = {287}, pmid = {31870316}, issn = {1471-2180}, mesh = {Animals ; *Bacterial Physiological Phenomena ; Domestication ; Female ; Gastrointestinal Microbiome ; Insect Control ; Male ; Pest Control, Biological ; Sexual Behavior, Animal/*physiology ; Tephritidae/microbiology/*physiology ; }, abstract = {BACKGROUND: The Sterile Insect Technique (SIT) is being applied for the management of economically important pest fruit flies (Diptera: Tephritidae) in a number of countries worldwide. The success and cost effectiveness of SIT depends upon the ability of mass-reared sterilized male insects to successfully copulate with conspecific wild fertile females when released in the field.

METHODS: We conducted a critical analysis of the literature about the tephritid gut microbiome including the advancement of methods for the identification and characterization of microbiota, particularly next generation sequencing, the impacts of irradiation (to induce sterility of flies) and fruit fly rearing, and the use of probiotics to manipulate the fruit fly gut microbiota.

RESULTS: Domestication, mass-rearing, irradiation and handling, as required in SIT, may change the structure of the fruit flies' gut microbial community compared to that of wild flies under field conditions. Gut microbiota of tephritids are important in their hosts' development, performance and physiology. Knowledge of how mass-rearing and associated changes of the microbial community impact the functional role of the bacteria and host biology is limited. Probiotics offer potential to encourage a gut microbial community that limits pathogens, and improves the quality of fruit flies.

CONCLUSIONS: Advances in technologies used to identify and characterize the gut microbiota will continue to expand our understanding of tephritid gut microbial diversity and community composition. Knowledge about the functions of gut microbes will increase through the use of gnotobiotic models, genome sequencing, metagenomics, metatranscriptomics, metabolomics and metaproteomics. The use of probiotics, or manipulation of the gut microbiota, offers significant opportunities to enhance the production of high quality, performing fruit flies in operational SIT programs.}, } @article {pmid31870295, year = {2019}, author = {Hadapad, AB and Shettigar, SKG and Hire, RS}, title = {Bacterial communities in the gut of wild and mass-reared Zeugodacus cucurbitae and Bactrocera dorsalis revealed by metagenomic sequencing.}, journal = {BMC microbiology}, volume = {19}, number = {Suppl 1}, pages = {282}, pmid = {31870295}, issn = {1471-2180}, mesh = {Animals ; Bacteria/*classification/genetics/isolation & purification ; Cucurbitaceae/parasitology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/*methods ; Male ; Mangifera/parasitology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA ; Tephritidae/*microbiology ; }, abstract = {BACKGROUND: Insect pests belonging to genus Bactrocera sp. (Diptera: Tephritidae) pose major biotic stress on various fruits and vegetable crops around the world. Zeugodacus and Bactrocera sp. are associated with diverse bacterial communities which play an important role in the fitness of sterile insects. The wild populations of melon fly, Zeugodacus cucurbitae (Coquillett) and Oriental fruit fly, Bactrocera dorsalis (Hendel) were collected from pumpkin and mango fields, respectively. The laboratory populations of Z. cucurbitae and B. dorsalis were mass-reared on bottle gourd and sweet banana, respectively. Bacterial communities present in the gut of wild and mass-reared mature (~ 12 days old) and newly emerged (< 1 h after emergence) male and female adults of Z. cucurbitae and B. dorsalis were assessed. We used Illumina HiSeq next-generation sequencing of 16S rRNA gene to profile the gut bacterial communities of wild and mass-reared mature and newly emerged Z. cucurbitae and B. dorsalis adults.

RESULTS: We found diverse bacterial composition in the gut of wild and mass-reared Z. cucurbitae (ZC) and B. dorsalis (BD) with varied relative abundance. Few taxonomic groups were common to both the species. The most dominant phyla in all samples of Z. cucurbitae and B. dorsalis adults were Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The phylum Proteobacteria occurred more in wild Z. cucurbitae (~ 87.72%) and B. dorsalis (~ 83.87%) as compared to mass-reared Z. cucurbitae (64.15%) and B. dorsalis (~ 80.96%). Higher relative abundance of Phylum Firmicutes was observed in mass-reared fruit fly than wild adults. Cyanobacteria/Chloroplast and Actinobacteria were also present with very low relative abundance in both wild as well as mass-reared melon fly and Oriental fruit fly. Enterobacteriaceae (61.21%) was dominant family in the gut of both wild and mass-reared adults. Providencia and Lactococcus were dominant genera with varied relative abundance in wild as well as in mass-reared mature and newly emerged fruit fly adults of both species. Some of the genera like Morganella and Serratia were only detected in mass-reared mature and newly emerged Z. cucurbitae and B. dorsalis adults. Principal Coordinate Analysis (PCoA) showed that fruit fly adult samples were grouped based on species and age of the adults while no grouping was observed on the basis of sex of the adult fruit fly.

CONCLUSIONS: The gut bacterial communities associated with wild and mass-reared mature and newly emerged adults of Z. cucurbitae and B. dorsalis showed variation that depends on species and age of the insects. Understanding the gut microbiota of wild and mass-reared Z. cucurbitae and B. dorsalis using high throughput technology will help to illustrate microbial diversity and this information could be used to develop efficient mass-rearing protocols for successful implementation of sterile insect technique (SIT).}, } @article {pmid31870202, year = {2020}, author = {Erber, AC and Cetin, H and Berry, D and Schernhammer, ES}, title = {The role of gut microbiota, butyrate and proton pump inhibitors in amyotrophic lateral sclerosis: a systematic review.}, journal = {The International journal of neuroscience}, volume = {130}, number = {7}, pages = {727-735}, doi = {10.1080/00207454.2019.1702549}, pmid = {31870202}, issn = {1563-5279}, mesh = {*Amyotrophic Lateral Sclerosis/drug therapy/metabolism/microbiology ; Animals ; Butyrates/*metabolism ; Disease Progression ; Gastrointestinal Microbiome/*physiology ; Humans ; Proton Pump Inhibitors/*therapeutic use ; }, abstract = {Aim of the study: We conducted a systematic review on existing literature in humans and animals, linking the gut microbiome with amyotrophic lateral sclerosis (ALS). Additionally, we sought to explore the role of the bacterially produced metabolite butyrate as well as of proton pump inhibitors (PPIs) in these associations.Materials and methods: Following PRISMA guidelines for systematic literature reviews, four databases (Medline, Scopus, Embase and Web of Science) were searched and screened by two independent reviewers against defined inclusion criteria. Six studies in humans and six animal studies were identified, summarized and reviewed.Results: Overall, the evidence accrued to date is supportive of changes in the gut microbiome being associated with ALS risk, and potentially progression, though observational studies are small (describing a total of 145 patients with ALS across all published studies), and not entirely conclusive.Conclusions: With emerging studies beginning to apply metagenome sequencing, more clarity regarding the importance and promise of the gut microbiome in ALS can be expected. Future studies may also help establish the therapeutic potential of butyrate, and the role of PPIs in these associations.}, } @article {pmid31868094, year = {2020}, author = {Urban, RJ and Pyles, RB and Stewart, CJ and Ajami, N and Randolph, KM and Durham, WJ and Danesi, CP and Dillon, EL and Summons, JR and Singh, CK and Morrison, M and Kreber, LA and Masel, B and Miller, AL and Wright, TJ and Sheffield-Moore, M}, title = {Altered Fecal Microbiome Years after Traumatic Brain Injury.}, journal = {Journal of neurotrauma}, volume = {37}, number = {8}, pages = {1037-1051}, doi = {10.1089/neu.2019.6688}, pmid = {31868094}, issn = {1557-9042}, mesh = {Adult ; Aged ; Bacteria/genetics/metabolism ; Brain Injuries, Traumatic/*microbiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics/metabolism ; Young Adult ; }, abstract = {Patients with chronic traumatic brain injury (TBI) requiring long-term, permanent care suffer a myriad of clinical symptoms (i.e., impaired cognition, fatigue, and other conditions) that persist for years beyond the acute brain injury. In addition to these comorbid clinical symptoms, chronic TBI patients exhibit altered amino acid and hormonal profiles with distinct cytokine patterns suggesting chronic inflammation. This metabolic link suggests a role of the gut-brain axis in chronic TBI. Thus, we utilized a two-site trial to investigate the role of the gut-brain axis in comorbidities of chronic TBI. The fecal microbiome profile of 22 moderate/severe TBI patients residing in permanent care facilities in Texas and California was compared to 18 healthy age-matched control subjects working within the participating facilities. Each fecal microbiome was characterized by 16S(V4) ribosomal RNA (rRNA) gene sequencing and metagenomic genome sequencing approaches followed by confirmatory full 16S rRNA gene sequencing or focused tuf gene speciation and specific quantitative polymerase chain reaction evaluation of selected genera or species. The average chronic TBI patient fecal microbiome structure was significantly different compared to the control cohort, and these differences persisted after group stratification analysis to identify any unexpected confounders. Notably, the fecal microbiome of the chronic TBI cohort had absent or reduced Prevotella spp. and Bacteroidies spp. Conversely, bacteria in the Ruminococcaceae family were higher in abundance in TBI compared to control profiles. Previously reported hypoaminoacidemia, including significantly reduced levels of l-tryptophan, l-sarcosine, ß-alanine, and alanine, positively correlated with the reduced levels of Prevotella spp. in the TBI cohort samples compared to controls. Although the sequelae of gut-brain axis disruption after TBI is not fully understood, characterizing TBI-related alterations in the fecal microbiome may provide biomarkers and therapeutic targets to address patient morbidity.}, } @article {pmid31866425, year = {2020}, author = {Liu, Q and Liu, Q and Meng, H and Lv, H and Liu, Y and Liu, J and Wang, H and He, L and Qin, J and Wang, Y and Dai, Y and Otto, M and Li, M}, title = {Staphylococcus epidermidis Contributes to Healthy Maturation of the Nasal Microbiome by Stimulating Antimicrobial Peptide Production.}, journal = {Cell host & microbe}, volume = {27}, number = {1}, pages = {68-78.e5}, pmid = {31866425}, issn = {1934-6069}, support = {ZIA AI000904/ImNIH/Intramural NIH HHS/United States ; ZIA AI000904/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Aged, 80 and over ; Antimicrobial Cationic Peptides/*biosynthesis ; Biofilms/growth & development ; Cell Line ; Child ; Child, Preschool ; Epidermal Cells ; Female ; High-Throughput Nucleotide Sequencing ; Host Microbial Interactions ; Humans ; Immunity, Innate ; Male ; Metagenomics ; Microbiota/*immunology ; Nasal Cavity/*microbiology ; RNA, Ribosomal, 16S ; *Staphylococcus epidermidis/isolation & purification/metabolism ; Symbiosis ; Young Adult ; }, abstract = {The composition of the human microbiome profoundly impacts human well-being. However, the mechanisms underlying microbiome maturation are poorly understood. The nasal microbiome is of particular importance as a source of many respiratory infections. Here, we performed a large sequencing and culture-based analysis of the human nasal microbiota from different age groups. We observed a significant decline of pathogenic bacteria before adulthood, with an increase of the commensal Staphylococcus epidermidis. In seniors, this effect was partially reversed. In vitro, many S. epidermidis isolates stimulated nasal epithelia to produce antimicrobial peptides, killing pathogenic competitors, while S. epidermidis itself proved highly resistant owing to its exceptional capacity to form biofilms. Furthermore, S. epidermidis isolates with high antimicrobial peptide-inducing and biofilm-forming capacities outcompeted pathogenic bacteria during nasal colonization in vivo. Our study identifies a pivotal role of S. epidermidis in healthy maturation of the nasal microbiome, which is achieved at least in part by symbiotic cooperation with innate host defense.}, } @article {pmid31863999, year = {2020}, author = {Llorens-Marès, T and Catalan, J and Casamayor, EO}, title = {Taxonomy and functional interactions in upper and bottom waters of an oligotrophic high-mountain deep lake (Redon, Pyrenees) unveiled by microbial metagenomics.}, journal = {The Science of the total environment}, volume = {707}, number = {}, pages = {135929}, doi = {10.1016/j.scitotenv.2019.135929}, pmid = {31863999}, issn = {1879-1026}, mesh = {Bacteria ; Biodiversity ; *Lakes ; *Metagenomics ; Nitrification ; Phylogeny ; }, abstract = {High mountain lakes are, in general, highly sensitive systems to external forcing and good sentinels of global environmental changes. For a better understanding of internal lake processes, we examined microbial biodiversity and potential biogeochemical interactions in the oligotrophic deep high-mountain Lake Redon (Pyrenees, 2240 m altitude) using shotgun metagenomics. We analyzed the two ends of the range of environmental conditions found in Lake Redon, at 2 and 60 m depths. Bacteria were the most abundant component of the metagenomic reads (>90%) and the diversity indices of both taxonomic (16S and 18S rRNA) and functional (carbon-, nitrogen-, sulfur-, and phosphorous-cycling) related genes were higher in the bottom dark layer than in the upper compartment. A marked segregation was observed both in biodiversity and in the dominant energy and biomass generating pathways between the extremes. The aerobic respiration was mainly dominated by heterotrophic Burkholderiales at the top and Actinobacteria and Burkholderiales at the lake bottom. The potential for an active nitrogen cycle (nitrogen fixation, nitrification, nitrite oxidation, and nitrate reduction) was mainly found at 60 m, and potential for methanogenesis, anaerobic ammonia oxidation and dissimilatory sulfur pathways were only observed there. Some unexpected and mostly unseen energy and biomass pathways were found relevant for the biogeochemical cycling in lake Redon, i.e., those related to carbon monoxide oxidation and phosphonates processing. We provide a general scheme of the main biogeochemical processes that may operate in the sentinel deep Lake Redon. This framework may help for a better understanding of the whole lake metabolism.}, } @article {pmid31863791, year = {2020}, author = {Septyaningtrias, DE and Lin, CW and Ouchida, R and Nakai, N and Suda, W and Hattori, M and Morita, H and Honda, K and Tamada, K and Takumi, T}, title = {Altered microbiota composition reflects enhanced communication in 15q11-13 CNV mice.}, journal = {Neuroscience research}, volume = {161}, number = {}, pages = {59-67}, doi = {10.1016/j.neures.2019.12.010}, pmid = {31863791}, issn = {1872-8111}, mesh = {Animals ; *Autism Spectrum Disorder ; Communication ; DNA Copy Number Variations ; Humans ; Mice ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Autism spectrum disorder (ASD) is a complex and heterogeneous neurodevelopmental disorder. In addition to the core symptoms of ASD, many patients with ASD also show comorbid gut dysbiosis, which may lead to various gastrointestinal (GI) problems. Intriguingly, there is evidence that gut microbiota communicate with the central nervous system to modulate behavioral output through the gut-brain axis. To investigate how the microbiota composition is changed in ASD and to identify which microbes are involved in autistic behaviors, we performed a 16S rRNA gene-based metagenomics analysis in an ASD mouse model. Here, we focused on a model with human 15q11-13 duplication (15q dup), the most frequent chromosomal aberration or copy number variation found in ASD. Species diversity of the microbiome was significantly decreased in 15q dup mice. A combination of antibiotics treatment and behavioral analysis showed that neomycin improved social communication in 15q dup mice. Furthermore, comparison of the microbiota composition of mice treated with different antibiotics enabled us to identify beneficial operational taxonomic units (OTUs) for ultrasonic vocalization.}, } @article {pmid31862994, year = {2019}, author = {Chung, AP and Coimbra, C and Farias, P and Francisco, R and Branco, R and Simão, FV and Gomes, E and Pereira, A and Vila, MC and Fiúza, A and Mortensen, MS and Sørensen, SJ and Morais, PV}, title = {Tailings microbial community profile and prediction of its functionality in basins of tungsten mine.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19596}, pmid = {31862994}, issn = {2045-2322}, mesh = {Acinetobacter ; Bacillus ; Cellulomonas ; Environmental Monitoring ; Geography ; Metagenome ; *Microbiota ; *Mining ; Portugal ; Pseudomonas ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Streptococcus ; *Tungsten ; }, abstract = {In a circular economy concept, where more than 300 million tons of mining and quarrying wastes are produced annually, those are valuable resources, supplying metals that are extracted today by other processes, if innovative methods and processes for efficient extraction of these elements are applied. This work aims to assess microbiological and chemical spatial distribution within two tailing basins from a tungsten mine, using a MiSeq approach targeting the 16S rRNA gene, to relate microbial composition and function with chemical variability, thus, providing information to enhance the efficiency of the exploitation of these secondary sources. The tailings sediments core microbiome comprised members of family Anaerolineacea and genera Acinetobacter, Bacillus, Cellulomonas, Pseudomonas, Streptococcus and Rothia, despite marked differences in tailings physicochemical properties. The higher contents of Al and K shaped the community of Basin 1, while As-S-Fe contents were correlated with the microbiome composition of Basin 2. The predicted metabolic functions of the microbiome were rich in genes related to metabolism pathways and environmental information processing pathways. An in-depth understanding of the tailings microbiome and its metabolic capabilities can provide a direction for the management of tailings disposal sites and maximize their potential as secondary resources.}, } @article {pmid31858660, year = {2021}, author = {Suominen, S and Dombrowski, N and Sinninghe Damsté, JS and Villanueva, L}, title = {A diverse uncultivated microbial community is responsible for organic matter degradation in the Black Sea sulphidic zone.}, journal = {Environmental microbiology}, volume = {23}, number = {6}, pages = {2709-2728}, pmid = {31858660}, issn = {1462-2920}, mesh = {Archaea/genetics ; Bacteria/genetics ; Black Sea ; Metagenome ; *Microbiota ; }, abstract = {Organic matter degradation in marine environments is essential for the recycling of nutrients, especially under conditions of anoxia where organic matter tends to accumulate. However, little is known about the diversity of the microbial communities responsible for the mineralization of organic matter in the absence of oxygen, as well as the factors controlling their activities. Here, we determined the active heterotrophic prokaryotic community in the sulphidic water column of the Black Sea, an ideal model system, where a tight coupling between carbon, nitrogen and sulphur cycles is expected. Active microorganisms degrading both dissolved organic matter (DOM) and protein extracts were determined using quantitative DNA stable isotope probing incubation experiments. These results were compared with the metabolic potential of metagenome-assembled genomes obtained from the water column. Organic matter incubations showed that groups like Cloacimonetes and Marinimicrobia are generalists degrading DOM. Based on metagenomic profiles the degradation proceeds in a potential interaction with members of the Deltaproteobacteria and Chloroflexi Dehalococcoidia. On the other hand, microbes with small genomes like the bacterial phyla Parcubacteria, Omnitrophica and of the archaeal phylum Woesearchaeota, were the most active, especially in protein-amended incubations, revealing the potential advantage of streamlined microorganisms in highly reduced conditions.}, } @article {pmid31856723, year = {2019}, author = {Kim, S and Thapa, I and Zhang, L and Ali, H}, title = {A novel graph theoretical approach for modeling microbiomes and inferring microbial ecological relationships.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 11}, pages = {945}, pmid = {31856723}, issn = {1471-2164}, mesh = {Bacteria/classification/genetics/isolation & purification ; Biomarkers ; Computational Biology/*methods ; Crohn Disease/metabolism/microbiology ; Gastrointestinal Microbiome/genetics ; Humans ; Metabolic Networks and Pathways ; Metagenome ; Microbial Interactions/*physiology ; *Microbiota ; *Models, Biological ; Phenotype ; }, abstract = {BACKGROUND: Microbiomes play vital roles in shaping environments and stabilize them based on their compositions and inter-species relationships among its species. Variations in microbial properties have been reported to have significant impact on their host environment. For example, variants in gut microbiomes have been reported to be associated with several chronic conditions, such as inflammatory disease and irritable bowel syndrome. However, how microbial bacteria contribute to pathogenesis still remains unclear and major research questions in this domain remain unanswered.

METHODS: We propose a split graph model to represent the composition and interactions of a given microbiome. We used metagenomes from Korean populations in this study. The dataset consists of three different types of samples, viz. mucosal tissue and stool from Crohn's disease patients and stool from healthy individuals. We use the split graph model to analyze the impact of microbial compositions on various host phenotypes. Utilizing the graph model, we have developed a pipeline that integrates genomic information and pathway analysis to characterize both critical informative components of inter-bacterial correlations and associations between bacterial taxa and various metabolic pathways.

RESULTS: The obtained results highlight the importance of the microbial communities and their inter-relationships and show how these microbial structures are correlated with Crohn's disease. We show that there are significant positive associations between detected taxonomic biomarkers as well as multiple functional modules in the split graph of mucosal tissue samples from CD patients. Bacteria Moraxellaceae and Pseudomonadaceae were detected as taxonomic biomarkers in CD groups. Higher abundance of these bacteria have been reported in previous study and several metabolic pathways associated with these bacteria were characterized in CD samples.

CONCLUSIONS: The proposed pipeline provides a new way to approach the analysis of complex microbiomes. The results obtained from this study show great potential in unraveling mechansims in complex biological systems to understand how various components in such complex environments are associated with critical biological functions.}, } @article {pmid31856722, year = {2019}, author = {Zupančič, J and Turk, M and Črnigoj, M and Ambrožič Avguštin, J and Gunde-Cimerman, N}, title = {The dishwasher rubber seal acts as a reservoir of bacteria in the home environment.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {300}, pmid = {31856722}, issn = {1471-2180}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/*isolation & purification ; Disease Reservoirs/*microbiology ; *Equipment Contamination ; *Housing ; Metagenome ; Microbial Consortia ; Microbial Sensitivity Tests ; *Rubber ; *Water Microbiology ; }, abstract = {BACKGROUND: In modern lifestyles, people make their everyday tasks easier by using household appliances, for example dishwashers. Previous studies showed massive contamination of dishwasher rubber seals with fungi, thus bacterial community, able to survive under harsh conditions, remain undetermined.

METHODS: Bacteria that colonise the extreme environment of household dishwasher rubber seals were investigated using cultivation-dependent and metagenomic approaches. All bacterial isolates were tested for resistance to seven selected antibiotics. Same time bacterial diversity of tap water, connected to the dishwashers was investigated.

RESULTS: All 30 dishwashers investigated were colonised by various bacteria. Cultivation approaches resulted in 632 bacterial isolates in total, belonging to four phyla, eight classes, 40 genera and 74 species. The majority were Gram-positive, as solely Firmicutes (dominated by the Bacillus cereus group) and Actinobacteria. Gammaproteobacteria were primarily represented by Stenotrophomonas maltophilia, Pseudomonas aeruginosa and Escherichia coli. Metagenomic assessment of the bacterial biodiversity of the dishwasher rubber seals confirmed the predominance of Gram-positive bacteria, as primarily Actinobacteria, followed by Proteobacteria dominated by Gammaproteobacteria, and by pathogenic species such as Escherichia sp., Acinetobacter baumannii, Pseudomonas sp., Stenotrophomonas maltophilia, and Enterobacter sp.. Metagenomic assessment of bacterial biodiversity in the tap water connected to dishwashers revealed predominance of Gram-negative bacteria, in particular Proteobacteria, mainly represented by Tepidimonas sp.. Actinobacteria showed low numbers while no Firmicutes were detected in the tap water. The bacterial diversity of tap water was also lower, 23 genera compared to 39 genera on dishwasher rubber seals. Only 13 out of 49 genera identified by metagenomics approach was found in both environments, of those Gordonia was enriched while half of 13 genera were depleted in dishwashers compared to tap water.

CONCLUSIONS: These data indicate that colonisation of dishwasher rubber seals probably depends primarily on the bacterial input from the dirty vessels, and much less on the bacteria in the tap water. Based on the antibiotic resistance data, the dishwasher rubber seal bacterial isolates do not represent a serious threat for the spread of antibiotic resistance into the household environment. Nevertheless dishwashers cannot be ignored as potential sources of human infections, in particular for immuno-compromised individuals.}, } @article {pmid31855786, year = {2020}, author = {Moreno-Mesonero, L and Hortelano, I and Moreno, Y and Ferrús, MA}, title = {Evidence of viable Helicobacter pylori and other bacteria of public health interest associated with free-living amoebae in lettuce samples by next generation sequencing and other molecular techniques.}, journal = {International journal of food microbiology}, volume = {318}, number = {}, pages = {108477}, doi = {10.1016/j.ijfoodmicro.2019.108477}, pmid = {31855786}, issn = {1879-3460}, mesh = {Amoeba/*microbiology ; Bacteria/classification/genetics/isolation & purification ; Food Microbiology ; Food Parasitology ; Helicobacter pylori/genetics/*isolation & purification ; Humans ; Lactuca/*microbiology/*parasitology ; Microbiota/genetics ; Public Health ; Real-Time Polymerase Chain Reaction ; }, abstract = {Vegetables are one of the sources from which Helicobacter pylori can be acquired. This bacterium infects >50% of the global population and is a recognized type I human carcinogen. H. pylori enters into the viable but non-culturable state when it is in the environment, and therefore the use of molecular techniques is much convenient for its detection. Free-living amoebae (FLA) are protozoans found in vegetables. They are transmission vehicles for amoeba-resistant bacteria, among which H. pylori is included. The aim of this study is to study the occurrence and viability of H. pylori from lettuce samples, H. pylori internalized into FLA and the microbiome of FLA isolated from these samples. Special focus was pointed to human pathogenic bacteria. H. pylori was not directly detected in any lettuce sample by means of molecular techniques and neither by culture. However, intra-amoebic H. pylori DNA was detected by means of PMA-qPCR in 55% of the samples and viable intra-amoebic H. pylori cells in 25% of the samples by means of DVC-FISH technique. When FLA microbiome was studied, 21 bacterial genera were part of FLA microbiome in all samples. Helicobacter genus was detected as part of the FLA microbiome in two samples. Other bacteria of public health interest such as Aeromonas sp., Arcobacter sp., Legionella sp., Mycobacterium sp., Pseudomonas sp. and Salmonella sp. were detected as part of FLA microbiome along the analysed samples. This study demonstrates for the first time that H. pylori is internalized as well as alive inside FLA isolated from vegetables. Moreover, this study shows that FLA promote H. pylori detection in environmental samples. In addition, as far as we are aware, this is the first study which studies the microbiome of FLA isolated from vegetables. Among the FLA microbiome, bacteria of public health interest were detected, pointing out that FLA are carriers of these pathogens which can reach humans and cause a public health concern.}, } @article {pmid31855753, year = {2020}, author = {Wang, L and Yin, Z and Jing, C}, title = {Metagenomic insights into microbial arsenic metabolism in shallow groundwater of Datong basin, China.}, journal = {Chemosphere}, volume = {245}, number = {}, pages = {125603}, doi = {10.1016/j.chemosphere.2019.125603}, pmid = {31855753}, issn = {1879-1298}, mesh = {Arsenic/*metabolism ; Carbon/analysis ; China ; Groundwater/*microbiology ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/genetics ; Oxidation-Reduction ; Sulfates/analysis ; Temperature ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Elevated arsenic (As) in groundwater is an urgent environmental problem that has caused serious endemic diseases in Datong basin, China. The fate and toxicity of As are generally regulated by microbial As metabolic processes. However, little is known about the microbial community and As metabolism in Datong basin. Herein, the microbial community structure and As metabolism genes in four wells with different levels of As concentration in Shanyin county were investigated using metagenomics approach. The results showed that the presence of As influenced the microbial communities, and Rhodococcus genus was significantly enriched in elevated As wells. As resistance genes were dominant from low to high As containing wells, and As efflux genes such as arsB and acr3 were positively correlated with As concentrations, suggesting that microbes tend to pump As out of the cell as a strategy for As detoxification. Other environmental factors including oxidation-reduction potential (ORP), total organic carbon (TOC), sulfate, and temperature also played a role in shaping the microbial community structure and As metabolic processes.}, } @article {pmid31855644, year = {2020}, author = {Fajardo, C and Sánchez-Fortún, S and Costa, G and Nande, M and Botías, P and García-Cantalejo, J and Mengs, G and Martín, M}, title = {Evaluation of nanoremediation strategy in a Pb, Zn and Cd contaminated soil.}, journal = {The Science of the total environment}, volume = {706}, number = {}, pages = {136041}, doi = {10.1016/j.scitotenv.2019.136041}, pmid = {31855644}, issn = {1879-1026}, abstract = {We addressed the efficiency of a nanoremediation strategy using zero-valent iron nanoparticles (nZVI), in a case of co-mingled heavy metals (HM) pollution (Pb, Cd and Zn). We applied a combined set of physical-chemical, toxicological and molecular analyses to assess the effectiveness and ecosafety of nZVI (5% w/w) for environmental restoration. After 120 days, nZVI showed immobilization capacity for Pb (20%), it was scarcely effective for Zn (8%) and negligibly effective for Cd. The HMs immobilization in the nZVI treated soils (compared to control soil), reaches its maximum after 15 days (T3) as reflected in the decrease of HM toxicity towards V. fischeri. The overall abundance of the microbial community was similar in both sets of samples during all experiment, although an increase in the number of metabolically active bacteria was recorded 15 days post treatment. We studied the induced impact of nanoremediation on the soil microbial community structure by Next Generation Sequencing (NGS). Even when higher HM immobilization was recorded, no significant recovery of the microbial community structure was found in nZVI-treated soil. The most marked nZVI-induced structural shifts were observed at T3 (increase in the Firmicutes population with a decrease in Gram-negative bacteria). Predictive metagenomic analysis using PICRUSt showed differences among the predicted metagenomes of nZVI-treated and control soils. At T3 we found decrease in detoxification-related proteins or over-representation of germination-related proteins; after 120 days of nZVI exposure, higher abundance of proteins involved in regulation of cellular processes or sporulation-related proteins was detected. This study highlights the partial effectiveness of nanoremediation in multiple-metal contaminated soil in the short term. The apparent lack of recovery of biodiversity after application of nZVI and the decreased effectiveness of nanoremediation over time must be carefully considered to validate this technology when assurance of medium- to long-term immobilization of HMs is required.}, } @article {pmid31854766, year = {2019}, author = {Hu, WC and Zhao, C and Wang, QJ and Liu, RP and Bai, YH}, title = {[Metabolic Functional Analysis of Dominant Microbial Communities in the Rapid Sand Filters for Drinking Water].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {40}, number = {8}, pages = {3604-3611}, doi = {10.13227/j.hjkx.201901167}, pmid = {31854766}, issn = {0250-3301}, mesh = {Denitrification ; *Drinking Water ; *Microbiota ; Nitrogen ; Oxidation-Reduction ; Sand ; Water Microbiology ; *Water Purification ; }, abstract = {Rapid sand filter (RSF) is widely used in drinking water treatment plants. Rapid filtration is always considered a physicochemical process, but the effect of the microorganisms that attach to the filter media remain inadequately investigated. In order to understand the composition and functional characteristics of microbial communities in RSFs, influent water, effluent water, and filter materials from eleven RSFs in eight Chinese cities were sampled and analyzed. After filtration, dissolved organic carbon (DOC) showed a slight but significant removal due to the growth of heterotrophic microbes. The activity of ammonia-oxidizing microbes and nitrite-oxidizing microbes promoted a significant decrease in ammonia nitrogen (NH4[+]-N) and a significant increase in nitrate nitrogen (NO3[-]-N) in water. No significant changes in total nitrogen (TN) were observed, indicating that denitrification and anammox were weak in the RSFs. The composition and function of the microbial communities of RSFs were assessed using metagenomic methods. Genera in the top 10% with respect to relative abundance (14 genera in total) were identified as the dominant genera, including the two ammonia-oxidizing bacteria Nitrospira and Nitrosomonas. Functional gene information for the dominant genera was also extracted for analysis. The dominant genera exhibited higher relative abundances of carbohydrate, nitrogen, sulfur, and xenobiotic metabolic pathways. Aeromonas had the highest relative abundance of carbohydrate metabolic genes, and Bradyrhizobium had the highest relative abundance of nitrogen, sulfur, and xenobiotics metabolic genes, indicating that these two genera play an important role in the transformation of substances in drinking water. Finally, the metabolic potential of the dominant genera on xenobiotics was evaluated, and the results showed that Bradyrhizobium, Sphingomonas, Methyloglobulus, Sphingopyxis, and Klebsiella were the key bacterial genera for the removal of micropollutants in RSFs.}, } @article {pmid31852805, year = {2019}, author = {Engel, K and Ford, SE and Coyotzi, S and McKelvie, J and Diomidis, N and Slater, G and Neufeld, JD}, title = {Stability of Microbial Community Profiles Associated with Compacted Bentonite from the Grimsel Underground Research Laboratory.}, journal = {mSphere}, volume = {4}, number = {6}, pages = {}, pmid = {31852805}, issn = {2379-5042}, mesh = {Bacteria/chemistry/*classification/genetics ; *Bentonite ; Cluster Analysis ; Cytosol/chemistry ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Fatty Acids/analysis ; Metagenomics ; *Microbiota ; Phospholipids/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Switzerland ; }, abstract = {To assess the microbiology and corrosion potential of engineered components of a deep geological repository for long-term storage of high-level nuclear waste, the Materials Corrosion Test is being conducted at the Underground Research Laboratory in Grimsel, Switzerland. Modules containing metal coupons surrounded by highly compacted MX-80 bentonite, at two dry densities (1.25 and 1.50 g/cm[3]), were emplaced within 9-m-deep boreholes, and the first modules were retrieved after 13 months of exposure. Bentonite and associated module materials were sampled, and microbial communities and their distributions were assessed using 16S rRNA gene sequencing and phospholipid fatty acid (PLFA) analysis. Borehole fluid was dominated by amplicon sequence variants (ASVs) affiliated with Desulfosporosinus and Desulfovibrio, which are putatively involved in sulfate reduction. The relative abundance of these ASVs was lower for samples from inside the borehole module, and they were almost undetectable in samples of the inner bentonite layer. The dominant ASV in case and filter sample sequence data was affiliated with Pseudomonas stutzeri, yet its relative abundance decreased in the inner layer samples. Streptomyces sp. ASVs were relatively abundant in all bentonite core sample data both prior to emplacement and after 13 months of exposure, presumably as metabolically inactive spores or extracellular "relic" DNA. PLFA concentrations in outer and inner layer bentonite samples suggested cellular abundances of 1 × 10[6] to 3 × 10[6] cells/g, with similar PLFA distributions within all bentonite samples. Our results demonstrate consistent microbial communities inside the saturated borehole module, providing the first evidence for microbial stability under conditions that mimic a deep geological repository.IMPORTANCE The Materials Corrosion Test in Grimsel Underground Research Laboratory, Switzerland, enables an evaluation of microbiological implications of bentonite clay at densities relevant for a deep geological repository. Our research demonstrates that after 13 months of exposure within a granitic host rock, the microbial 16S rRNA gene signatures of saturated bentonite clay within the modules were consistent with the profiles in the original clay used to pack the modules. Such results provide evidence that densities chosen for this emplacement test are refractory to microbial activity, at least on the relatively short time frame leading to the first time point sampling event, which will help inform in situ engineered barrier system science. This study has important implications for the design of deep geological repository sites under consideration for the Canadian Shield.}, } @article {pmid31852462, year = {2019}, author = {Zhang, X and Browman, G and Siu, W and Basen-Engquist, KM and Hanash, SM and Hoffman, KL and Okhuysen, PC and Scheet, P and Petrosino, JF and Kopetz, S and Daniel, CR}, title = {The BE GONE trial study protocol: a randomized crossover dietary intervention of dry beans targeting the gut microbiome of overweight and obese patients with a history of colorectal polyps or cancer.}, journal = {BMC cancer}, volume = {19}, number = {1}, pages = {1233}, pmid = {31852462}, issn = {1471-2407}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; Institutional Research Grant//University of Texas MD Anderson Cancer Center/ ; 5P30 CA016672-37/CA/NCI NIH HHS/United States ; RSG-17-049-01-NEC//American Cancer Society/ ; RP160097//Cancer Prevention and Research Institute of Texas/ ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Colonic Neoplasms/*diet therapy/microbiology/pathology/prevention & control ; Colonic Polyps/*diet therapy/microbiology/pathology/prevention & control ; Cross-Over Studies ; Female ; *Gastrointestinal Microbiome ; Humans ; Life Style ; Male ; Middle Aged ; Obesity/microbiology/*physiopathology ; Overweight/microbiology/*physiopathology ; Progression-Free Survival ; Risk Factors ; Randomized Controlled Trials as Topic ; }, abstract = {BACKGROUND: Mouse and human studies support the promise of dry beans to improve metabolic health and to lower cancer risk. In overweight/obese patients with a history of colorectal polyps or cancer, the Beans to Enrich the Gut microbiome vs. Obesity's Negative Effects (BE GONE) trial will test whether and how an increase in the consumption of pre-cooked, canned dry beans within the context of usual diet and lifestyle can enhance the gut landscape to improve metabolic health and reduce cancer risk.

METHODS/DESIGN: This randomized crossover trial is designed to characterize changes in (1) host markers spanning lipid metabolism, inflammation, and obesity-related cancer risk; (2) compositional and functional profiles of the fecal microbiome; and (3) host and microbial metabolites. With each subject serving as their own control, the trial will compare the participant's usual diet with (intervention) and without (control) dry beans. Canned, pre-cooked dry beans are provided to participants and the usual diet continually assessed and monitored. Following a 4-week run-in and equilibration period, each participant provides a total of 5 fasting blood and 6 stool samples over a total period of 16 weeks. The intervention consists of a 2-week ramp-up of dry bean intake to 1 cup/d, which is then continued for an additional 6 weeks. Intra- and inter-individual outcomes are assessed across each crossover period with consideration of the joint or modifying effects of the usual diet and baseline microbiome.

DISCUSSION: The BE GONE trial is evaluating a scalable dietary prevention strategy targeting the gut microbiome of high-risk patients to mitigate the metabolic and inflammatory effects of adiposity that influence colorectal cancer risk, recurrence, and survival. The overarching scientific goal is to further elucidate interactions between diet, the gut microbiome, and host metabolism. Improved understanding of the diet-microbiota interplay and effective means to target these relationships will be key to the future of clinical and public health approaches to cancer and other major diet- and obesity-related diseases.

TRIAL REGISTRATION: This protocol is registered with the U.S. National Institutes of Health trial registry, ClinicalTrials.gov, under the identifier NCT02843425. First posted July 25, 2016; last verified January 25, 2019.}, } @article {pmid31850811, year = {2019}, author = {Lo Presti, A and Del Chierico, F and Altomare, A and Zorzi, F and Cella, E and Putignani, L and Guarino, MPL and Monteleone, G and Cicala, M and Angeletti, S and Ciccozzi, M}, title = {Exploring the genetic diversity of the 16S rRNA gene of Akkermansia muciniphila in IBD and IBS.}, journal = {Future microbiology}, volume = {14}, number = {}, pages = {1497-1509}, doi = {10.2217/fmb-2019-0175}, pmid = {31850811}, issn = {1746-0921}, mesh = {Adult ; Akkermansia ; Evolution, Molecular ; Feces/microbiology ; Gastrointestinal Microbiome ; *Genetic Variation ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Irritable Bowel Syndrome/*microbiology ; Middle Aged ; Phylogeny ; Polymorphism, Single Nucleotide ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Verrucomicrobia/*genetics ; }, abstract = {Aim: The human gastrointestinal tract harbors diverse, abundant microbiota and Akkermansia muciniphila is involved in this community. The aim of this study is to characterize 16 new A. muciniphila 16S ribosomal RNA sequences selected from a metagenomic database from stools of patients with irritable bowel syndrome (IBS), inflammatory bowel diseases and control (CTRLs) subjects by a phylogenetic approach. Materials & methods: A phylogenetic approach was used to study the genetic diversity and SNPs in 16 A. muciniphila 16S ribosomal RNA sequences from stools of 107 individuals, 36 of which were patients affected by IBS, 30 by inflammatory bowel disease and 41 were CTRLs. Results: Phylogenetic analysis confirmed the subdivision into different supported clusters. An increase of variability in IBS has been identified. Conclusion: The genetic variation combined to the relative abundance, contribute to the protective role of A. muciniphila. Phylogenesis represent an additional approach to investigate genetic variability.}, } @article {pmid31850241, year = {2019}, author = {Wang, J and Gu, X and Yang, J and Wei, Y and Zhao, Y}, title = {Gut Microbiota Dysbiosis and Increased Plasma LPS and TMAO Levels in Patients With Preeclampsia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {409}, pmid = {31850241}, issn = {2235-2988}, mesh = {Adult ; Biomarkers ; Case-Control Studies ; *Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Lipopolysaccharides/*blood ; Metagenome ; Metagenomics/methods ; Methylamines/*blood ; Pre-Eclampsia/*blood/*etiology ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Objective: To characterize the gut microbiota in patients with preeclampsia (PE) compared with healthy controls. Methods: We analyzed and compared the microbiota communities in the feces of 48 PE patients with 48 age-, gestational weeks-, and pre-pregnancy body mass index-matched healthy controls using 16S rRNA gene sequencing, and also we tested fecal and plasma lipopolysaccharide (LPS) and plasma trimethylamine-N-oxide (TMAO) concentration levels in the two groups. Results: Compared with the control group, microbial alpha diversity was lower in the PE group, but there was no statistically significant difference between the two groups. At the phylum level, Firmicutes (51.64% PE vs. 59.62% Control, P < 0.05), Bacteroidetes (40.51% PE vs. 34.81% Control, P< 0.05), Proteobacteria (4.51% PE vs. 2.56% Control, P < 0.05), and Actinobacteria (2.90% PE vs. 1.77% Control, P < 0.05), exhibited significant differences between the PE group and the control group. LEfSe analysis found 17 differentially abundant taxa between the two groups. PICRUSt analysis found that in the KEGG pathways, the microbial gene functions related to LPS biosynthesis were higher in the fecal microbiome of the PE group. The fecal and plasma LPS concentrations and plasma TMAO concentrations of PE patients were higher than those of the healthy controls. Conclusion: PE patients had gut microbiota dysbiosis and increased plasma LPS and TMAO levels, which will lead to a better understanding of the relationship between the gut microbiota and PE.}, } @article {pmid31849864, year = {2019}, author = {Bains, M and Laney, C and Wolfe, AE and Orr, M and Waschek, JA and Ericsson, AC and Dorsam, GP}, title = {Vasoactive Intestinal Peptide Deficiency Is Associated With Altered Gut Microbiota Communities in Male and Female C57BL/6 Mice.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2689}, pmid = {31849864}, issn = {1664-302X}, support = {K01 OD019924/OD/NIH HHS/United States ; P20 GM109024/GM/NIGMS NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; }, abstract = {Vasoactive intestinal peptide (VIP) is crucial for gastrointestinal tract (GIT) health. VIP sustains GIT homeostasis through maintenance of the intestinal epithelial barrier and acts as a potent anti-inflammatory mediator that contributes to gut bacterial tolerance. Based on these biological functions by VIP, we hypothesized that its deficiency would alter gut microbial ecology. To this end, fecal samples from male and female VIP[+/+], VIP[+/-], and VIP[-/-] littermates (n = 47) were collected and 16S rRNA sequencing was conducted. Our data revealed significant changes in bacterial composition, biodiversity, and weight loss from VIP[-/-] mice compared to VIP[+/+] and VIP[+/-] littermates, irrespective of sex. The gut bacteria compositional changes observed in VIP[-/-] mice was consistent with gut microbial structure changes reported for certain inflammatory and autoimmune disorders. Moreover, predicted functional changes by PICRUSt software suggested an energy surplus within the altered microbiota from VIP[-/-] mice. These data support that VIP plays an important role in maintaining microbiota balance, biodiversity, and GIT function, and its genetic removal results in significant gut microbiota restructuring and weight loss.}, } @article {pmid31848793, year = {2020}, author = {Firmino, FC and Porcellato, D and Cox, M and Suen, G and Broadbent, JR and Steele, JL}, title = {Characterization of microbial communities in ethanol biorefineries.}, journal = {Journal of industrial microbiology & biotechnology}, volume = {47}, number = {2}, pages = {183-195}, pmid = {31848793}, issn = {1476-5535}, mesh = {Bioreactors ; Ethanol/*metabolism ; Fermentation ; Firmicutes/genetics/metabolism ; Lactobacillus/genetics/metabolism ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bacterial contamination of corn-based ethanol biorefineries can reduce their efficiency and hence increase their carbon footprint. To enhance our understanding of these bacterial contaminants, we temporally sampled four biorefineries in the Midwestern USA that suffered from chronic contamination and characterized their microbiomes using both 16S rRNA sequencing and shotgun metagenomics. These microbiotas were determined to be relatively simple, with 13 operational taxonomic units (OTUs) accounting for 90% of the bacterial population. They were dominated by Firmicutes (89%), with Lactobacillus comprising 80% of the OTUs from this phylum. Shotgun metagenomics confirmed our 16S rRNA data and allowed us to characterize bacterial succession at the species level, with the results of this analysis being that Lb. helveticus was the dominant contaminant in this fermentation. Taken together, these results provide insights into the microbiome of ethanol biorefineries and identifies a species likely to be commonly responsible for chronic contamination of these facilities.}, } @article {pmid31848653, year = {2020}, author = {Giwa, AS and Ali, N and Athar, MA and Wang, K}, title = {Dissecting microbial community structure in sewage treatment plant for pathogens' detection using metagenomic sequencing technology.}, journal = {Archives of microbiology}, volume = {202}, number = {4}, pages = {825-833}, doi = {10.1007/s00203-019-01793-y}, pmid = {31848653}, issn = {1432-072X}, support = {21206084//National Natural Science Foundation of China/ ; }, mesh = {Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Microbiota ; Sewage/microbiology ; *Virus Physiological Phenomena ; Viruses/classification/genetics ; Wastewater/*microbiology ; }, abstract = {Continuous observation of wastewater treatment plants is very crucial to keep them safe for proper use and protection from pathogenic contamination. Illumina sequencing technology was used for microbiome structuring from various samples taken from different portions of the wastewater treatment plant, including influent, activated, return sludge and effluent, where different microbial compositions were found. The effluent section was found to have pathogenic microbes such as viruses, Alpha- and deltaproteobacteria, Actinobacteria, Bacteroidetes, clostridia, and bacilli in various concentrations. The presence of viruses, Mycobacterium sp., Mycobacterium fortuitum, bacteroidia, and bacilli was investigated. The species Mycobacterium was found to be higher in quantity in the effluent section. Viruses, including hepatitis A and E, were detected in higher quantity in the effluent part of the sludge in comparison with the influent part of the plant. Our discovery reveals the significance and observation of wastewater treatment plants for the existence of water-borne pathogens in the effluent, principally due to the effect on humans while reusing the water.}, } @article {pmid31848574, year = {2021}, author = {Bharti, R and Grimm, DG}, title = {Current challenges and best-practice protocols for microbiome analysis.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {1}, pages = {178-193}, pmid = {31848574}, issn = {1477-4054}, mesh = {Animals ; DNA Barcoding, Taxonomic/methods/standards ; Humans ; Metagenomics/*methods/standards ; Microbiota/*genetics ; *Practice Guidelines as Topic ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods/standards ; }, abstract = {Analyzing the microbiome of diverse species and environments using next-generation sequencing techniques has significantly enhanced our understanding on metabolic, physiological and ecological roles of environmental microorganisms. However, the analysis of the microbiome is affected by experimental conditions (e.g. sequencing errors and genomic repeats) and computationally intensive and cumbersome downstream analysis (e.g. quality control, assembly, binning and statistical analyses). Moreover, the introduction of new sequencing technologies and protocols led to a flood of new methodologies, which also have an immediate effect on the results of the analyses. The aim of this work is to review the most important workflows for 16S rRNA sequencing and shotgun and long-read metagenomics, as well as to provide best-practice protocols on experimental design, sample processing, sequencing, assembly, binning, annotation and visualization. To simplify and standardize the computational analysis, we provide a set of best-practice workflows for 16S rRNA and metagenomic sequencing data (available at https://github.com/grimmlab/MicrobiomeBestPracticeReview).}, } @article {pmid31845464, year = {2020}, author = {Ganley, JG and D'Ambrosio, HK and Shieh, M and Derbyshire, ER}, title = {Coculturing of Mosquito-Microbiome Bacteria Promotes Heme Degradation in Elizabethkingia anophelis.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {21}, number = {9}, pages = {1279-1284}, doi = {10.1002/cbic.201900675}, pmid = {31845464}, issn = {1439-7633}, mesh = {Animals ; Anopheles/*microbiology ; Bacterial Proteins/*metabolism ; Coculture Techniques ; Flavobacteriaceae/growth & development/*metabolism ; Genome, Bacterial ; Heme/*metabolism ; *Microbiota ; Phylogeny ; Sequence Analysis, DNA ; *Virulence ; }, abstract = {Anopheles mosquito microbiomes are intriguing ecological niches. Within the gut, microbes adapt to oxidative stress due to heme and iron after blood meals. Although metagenomic sequencing has illuminated spatial and temporal fluxes of microbiome populations, limited data exist on microbial growth dynamics. Here, we analyze growth interactions between a dominant microbiome species, Elizabethkingia anophelis, and other Anopheles-associated bacteria. We find E. anophelis inhibits a Pseudomonas sp. via an antimicrobial-independent mechanism and observe biliverdins, heme degradation products, upregulated in cocultures. Purification and characterization of E. anophelis HemS demonstrates heme degradation, and we observe hemS expression is upregulated when cocultured with Pseudomonas sp. This study reveals a competitive microbial interaction between mosquito-associated bacteria and characterizes the stimulation of heme degradation in E. anophelis when grown with Pseudomonas sp.}, } @article {pmid31844663, year = {2019}, author = {Olm, MR and Bhattacharya, N and Crits-Christoph, A and Firek, BA and Baker, R and Song, YS and Morowitz, MJ and Banfield, JF}, title = {Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria.}, journal = {Science advances}, volume = {5}, number = {12}, pages = {eaax5727}, pmid = {31844663}, issn = {2375-2548}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; R01 GM109454/GM/NIGMS NIH HHS/United States ; S10 OD018174/OD/NIH HHS/United States ; }, mesh = {Enterobacteriaceae/genetics ; Enterocolitis, Necrotizing/*genetics/microbiology ; Feces/microbiology ; Fimbriae, Bacterial/*genetics/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Infant, Newborn ; Infant, Premature ; Infant, Premature, Diseases/genetics/microbiology ; Klebsiella/genetics ; *Metagenomics ; Multigene Family/genetics ; }, abstract = {Necrotizing enterocolitis (NEC) is a devastating intestinal disease that occurs primarily in premature infants. We performed genome-resolved metagenomic analysis of 1163 fecal samples from premature infants to identify microbial features predictive of NEC. Features considered include genes, bacterial strain types, eukaryotes, bacteriophages, plasmids, and growth rates. A machine learning classifier found that samples collected before NEC diagnosis harbored significantly more Klebsiella, bacteria encoding fimbriae, and bacteria encoding secondary metabolite gene clusters related to quorum sensing and bacteriocin production. Notably, replication rates of all bacteria, especially Enterobacteriaceae, were significantly higher 2 days before NEC diagnosis. The findings uncover biomarkers that could lead to early detection of NEC and targets for microbiome-based therapeutics.}, } @article {pmid31844297, year = {2020}, author = {Leggett, RM and Alcon-Giner, C and Heavens, D and Caim, S and Brook, TC and Kujawska, M and Martin, S and Peel, N and Acford-Palmer, H and Hoyles, L and Clarke, P and Hall, LJ and Clark, MD}, title = {Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens.}, journal = {Nature microbiology}, volume = {5}, number = {3}, pages = {430-442}, pmid = {31844297}, issn = {2058-5276}, support = {BBS/E/F/00044409/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L01632X/1/MRC_/Medical Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; Computational Biology ; DNA, Bacterial/analysis/genetics ; *Drug Resistance, Bacterial/drug effects/genetics ; Enterobacter cloacae/drug effects/genetics/isolation & purification ; Gastrointestinal Microbiome/drug effects/genetics ; *Infant, Premature ; Klebsiella pneumoniae/drug effects/genetics/isolation & purification ; Metagenome ; Microbial Sensitivity Tests ; *Microbiota/drug effects/genetics ; Nanopores ; Sequence Analysis, DNA ; Software ; Whole Genome Sequencing ; Humans ; Infant, Newborn ; }, abstract = {The MinION sequencing platform offers near real-time analysis of DNA sequence; this makes the tool attractive for deployment in fieldwork or clinical settings. We used the MinION platform coupled to the NanoOK RT software package to perform shotgun metagenomic sequencing and profile mock communities and faecal samples from healthy and ill preterm infants. Using Nanopore data, we reliably classified a 20-species mock community and captured the diversity of the immature gut microbiota over time and in response to interventions such as probiotic supplementation, antibiotic treatment or episodes of suspected sepsis. We also performed rapid real-time runs to assess gut-associated microbial communities in critically ill and healthy infants, facilitated by NanoOK RT software package, which analysed sequences as they were generated. Our pipeline reliably identified pathogenic bacteria (that is, Klebsiella pneumoniae and Enterobacter cloacae) and their corresponding antimicrobial resistance gene profiles within as little as 1 h of sequencing. Results were confirmed using pathogen isolation, whole-genome sequencing and antibiotic susceptibility testing, as well as mock communities and clinical samples with known antimicrobial resistance genes. Our results demonstrate that MinION (including cost-effective Flongle flow cells) with NanoOK RT can process metagenomic samples to a rich dataset in < 5 h, which creates a platform for future studies aimed at developing these tools and approaches in clinical settings with a focus on providing tailored patient antimicrobial treatment options.}, } @article {pmid31843867, year = {2020}, author = {Schlaberg, R}, title = {Microbiome Diagnostics.}, journal = {Clinical chemistry}, volume = {66}, number = {1}, pages = {68-76}, doi = {10.1373/clinchem.2019.303248}, pmid = {31843867}, issn = {1530-8561}, mesh = {Bacteria/genetics/isolation & purification ; Drug Resistance/genetics ; Fungi/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods/standards ; Microbiota/*genetics ; Mitochondria/genetics ; Quality Control ; RNA, Ribosomal, 16S/chemistry/metabolism ; }, abstract = {BACKGROUND: During the past decade, breakthroughs in sequencing technology and computational biology have provided the basis for studies of the myriad ways in which microbial communities ("microbiota") in and on the human body influence human health and disease. In almost every medical specialty, there is now a growing interest in accurate and replicable profiling of the microbiota for use in diagnostic and therapeutic application.

CONTENT: This review provides an overview of approaches, challenges, and considerations for diagnostic applications borrowing from other areas of molecular diagnostics, including clinical metagenomics. Methodological considerations and evolving approaches for microbiota profiling from mitochondrially encoded 16S rRNA-based amplicon sequencing to metagenomics and metatranscriptomics are discussed. To improve replicability, at least the most vulnerable steps in testing workflows will need to be standardized and continuous efforts needed to define QC standards. Challenges such as purity of reagents and consumables, improvement of reference databases, and availability of diagnostic-grade data analysis solutions will require joint efforts across disciplines and with manufacturers.

SUMMARY: The body of literature supporting important links between the microbiota at different anatomic sites with human health and disease is expanding rapidly and therapeutic manipulation of the intestinal microbiota is becoming routine. The next decade will likely see implementation of microbiome diagnostics in diagnostic laboratories to fully capitalize on technological and scientific advances and apply them in routine medical practice.}, } @article {pmid31841891, year = {2020}, author = {Zhang, J and Xu, Y and Liang, S and Ma, X and Lu, Z and Sun, P and Zhang, H and Sun, F}, title = {Synergistic effect of Klebsiella sp. FH-1 and Arthrobacter sp. NJ-1 on the growth of the microbiota in the black soil of Northeast China.}, journal = {Ecotoxicology and environmental safety}, volume = {190}, number = {}, pages = {110079}, doi = {10.1016/j.ecoenv.2019.110079}, pmid = {31841891}, issn = {1090-2414}, mesh = {Agriculture ; Arthrobacter/*metabolism ; Atrazine/*metabolism ; Biodegradation, Environmental ; China ; Fungi/isolation & purification ; Herbicides/*metabolism ; Klebsiella/*metabolism ; Microbiota ; *Soil Microbiology ; }, abstract = {The application of Atrazine in soil has always been a main problem in agriculture because its residuals may maintain in the soil for a long term. In this paper, two strains of Atrazine degrading bacteria (Klebsiella sp. FH-1 and Arthrobacter sp. NJ-1) were used to make biological compound microbial inoculum to repair the Atrazine contaminated typical black soil in Northeast China. Grain chaff was chosen as the optimal carrier material for microbial inoculum. The dynamic changes of Atrazine were detected by gas chromatography. The half-life of Atrazine in soil containing microbial inoculum was shortened from 9.8 d to 4.2 d. The Atrazine sensitive crops grown in the repaired soil showed increased stem length, root length, and emergence rate. The effects of microbial remediation on the original bacterial and fungal biota in the typical black soil in Northeast China were analyzed using the metagenomic approach. Results showed that Atrazine inhibited the original bacteria and fungi populations. The total numbers of bacterial and fungal species in the soil were partially recovered by adding the microbial inoculum. Two genera (Sphingosinicella and Sphingomonas) were the dominant bacteria. The beneficial bacterial biota was recovered and the number of species of the beneficial bacteria was higher than that in the original soil after adding the microbial inoculum. The dominant fungi included genera Guehomyces and Chaetomella. There was a total of 113 unclassified fungal genera (22.6% of 499), indicating the potential utility of the unclassified fungal species in the assessment of the soil contamination by Atrazine.}, } @article {pmid31840403, year = {2020}, author = {Ahlgren, NA and Belisle, BS and Lee, MD}, title = {Genomic mosaicism underlies the adaptation of marine Synechococcus ecotypes to distinct oceanic iron niches.}, journal = {Environmental microbiology}, volume = {22}, number = {5}, pages = {1801-1815}, doi = {10.1111/1462-2920.14893}, pmid = {31840403}, issn = {1462-2920}, mesh = {Acclimatization/genetics ; Adaptation, Physiological/genetics ; Diatoms/genetics ; Ecosystem ; Ecotype ; Genome, Bacterial/*genetics ; Iron/metabolism ; Metagenomics ; *Mosaicism ; Oceans and Seas ; Phytoplankton ; Prochlorococcus/*genetics/*physiology ; Seawater/microbiology ; Synechococcus/*genetics/*physiology ; }, abstract = {Phytoplankton are limited by iron (Fe) in ~40% of the world's oceans including high-nutrient low-chlorophyll (HNLC) regions. While low-Fe adaptation has been well-studied in large eukaryotic diatoms, less is known for small, prokaryotic marine picocyanobacteria. This study reveals key physiological and genomic differences underlying Fe adaptation in marine picocyanobacteria. HNLC ecotype CRD1 strains have greater physiological tolerance to low Fe congruent with their expanded repertoire of Fe transporter, storage and regulatory genes compared to other ecotypes. From metagenomic analysis, genes encoding ferritin, flavodoxin, Fe transporters and siderophore uptake genes were more abundant in low-Fe waters, mirroring paradigms of low-Fe adaptation in diatoms. Distinct Fe-related gene repertories of HNLC ecotypes CRD1 and CRD2 also highlight how coexisting ecotypes have evolved independent approaches to life in low-Fe habitats. Synechococcus and Prochlorococcus HNLC ecotypes likewise exhibit independent, genome-wide reductions of predicted Fe-requiring genes. HNLC ecotype CRD1 interestingly was most similar to coastal ecotype I in Fe physiology and Fe-related gene content, suggesting populations from these different biomes experience similar Fe-selective conditions. This work supports an improved perspective that phytoplankton are shaped by more nuanced Fe niches in the oceans than previously implied from mostly binary comparisons of low- versus high-Fe habitats and populations.}, } @article {pmid31838792, year = {2020}, author = {Chang, DH and Shin, J and Rhee, MS and Park, KR and Cho, BK and Lee, SK and Kim, BC}, title = {Vaginal Microbiota Profiles of Native Korean Women and Associations with High-Risk Pregnancy.}, journal = {Journal of microbiology and biotechnology}, volume = {30}, number = {2}, pages = {248-258}, pmid = {31838792}, issn = {1738-8872}, mesh = {Abortion, Spontaneous/etiology ; Adult ; Bacterial Load ; Biomarkers ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Polymerase Chain Reaction ; Pregnancy ; Pregnancy Outcome ; *Pregnancy, High-Risk ; Premature Birth/etiology ; Prevalence ; Public Health Surveillance ; RNA, Ribosomal, 16S ; Republic of Korea/epidemiology ; Sequence Analysis, DNA ; Vagina/*microbiology ; Young Adult ; }, abstract = {The vaginal microbiota may be important for pregnancy prognosis because vaginal dysbiosis during pregnancy appears to be related to preterm birth (PTB) or pregnancy loss. Previous reports have indicated that a Lactobacillus-poor microbial flora in the vagina and intrauterine infection by diverse anaerobes ascending from the vagina are associated with undesirable delivery outcomes. However, no research has involved the use of pyrosequencing analysis to examine vaginal microbiota profiles or their potential associations with high-risk pregnancy in Korean women. Vaginal swabs were collected from 500 Korean women for the identification of community state types (CSTs). Of these, 137 samples were further analyzed using a Roche/454 GS Junior pyrosequencer. Three distinct CSTs were identified based on the dominant vaginal microbes: CST I (Lactobacillus crispatus dominated), CST III (Lactobacillus iners dominated), and CST IV (with diverse species of anaerobes). Twelve of the 67 pregnant women had undesirable pregnancy outcomes (four miscarriages and eight PTBs). The dominant microbe in the vaginal microbiota of women who gave birth at full-term was L. crispatus. In contrast, L. iners was the dominant vaginal microbe in women who miscarried. Most (n = 6/8) vaginal microbiota profiles of women who experienced PTB could be classified as CST IV, with diverse bacteria, including anaerobic vaginal species. The present study provides valuable information regarding the characteristics of the vaginal microbiota of Korean women related to high-risk pregnancy. Investigation of the vaginal microbiotic structure in pregnant Korean women is necessary to enable better prediction of adverse pregnancy outcomes.}, } @article {pmid31837260, year = {2019}, author = {Duan, J and Yin, B and Li, W and Chai, T and Liang, W and Huang, Y and Tan, X and Zheng, P and Wu, J and Li, Y and Li, Y and Zhou, W and Xie, P}, title = {Age-related changes in microbial composition and function in cynomolgus macaques.}, journal = {Aging}, volume = {11}, number = {24}, pages = {12080-12096}, pmid = {31837260}, issn = {1945-4589}, mesh = {Aging/*physiology ; Amino Acids/metabolism ; Animals ; Bacteria/*classification/enzymology/genetics ; Carbohydrates/chemistry ; Female ; *Gastrointestinal Microbiome ; Macaca fascicularis/*microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Age can significantly affect human physiology and disease risk. Recent studies have shown that age may affect the composition and function of the gut microbiota, but the underlying mechanisms remain largely unknown. Non-human primates are an ideal model for uncovering how age shapes the gut microbiota, as their microbial composition is highly similar to that of humans and is not easily affected by confounding factors. Here, using the 16S rRNA and metagenomic sequencing methods, we characterized the microbial phenotypes of 16 female cynomolgus macaques from three age groups (young, adult and old). Our findings revealed significant differences in microbial composition among the three groups. With increased age, the relative abundances of Veillonellaceae, Coriobacteriaceae and Succinivibrionaceae were significantly increased, Ruminococcaceae and Rikenellaceae were significantly decreased at the family level. Functional enrichment showed that genes that differed among the three groups were mainly involved in arginine biosynthesis, purine metabolism and microbial polysaccharides metabolism. Moreover, CAZymes corresponding to polysaccharide degrading activities were also observed among the three groups. In conclusion, we characterized the composition and function of the gut microbiota at different ages, and our findings provide a new entry point for understanding the effects of age on the human body.}, } @article {pmid31837163, year = {2020}, author = {Li, Q and Zhang, M and Wu, T and Liu, R}, title = {Potential correlation between carbohydrate-active enzyme family 48 expressed by gut microbiota and the expression of intestinal epithelial AMP-activated protein kinase β.}, journal = {Journal of food biochemistry}, volume = {44}, number = {2}, pages = {e13123}, doi = {10.1111/jfbc.13123}, pmid = {31837163}, issn = {1745-4514}, mesh = {AMP-Activated Protein Kinases/genetics ; Animals ; Carbohydrates ; Dietary Fiber ; *Gastrointestinal Microbiome/genetics ; Intestines ; Mice ; }, abstract = {The expression of the carbohydrate-active enzyme family and related genes is known to be influenced by the response of intestinal microbiota to dietary changes. However, it is uncertain whether this is caused by variation in the intestinal microecology. In this study, metabolite analysis, 16S rDNA sequencing, metagenomics, and Western blotting were employed to investigate the effects of dietary intervention on the composition of gut microbiota and microbiota-mediated changes. The results showed that compared with the low fiber-fed group, the fiber diet-fed mice displayed a shift in gut microbiota composition to contain more members of phylum Bacteroidetes, accompanied by higher proportions of Akkermansia and typical probiotic Bifidobacterium. Moreover, correlations were found between microbial genes coding for carbohydrate-binding module family 48 (CBM48) and intestinal epithelial expression levels of AMPK β. This finding provides new insight for elucidating the contribution of dietary intervention through AMPK regulation linked to the microbial carbohydrate-binding family. PRACTICAL APPLICATIONS: The relationship suggested by these data will provide theoretical and applied foundations for the development of potential intervention targeting the interaction between gut microbiota and host health, particularly the use of dietary fiber as a medically relevant food. Additionally, a better understanding of the interactions between gut microbiota and intestinal epithelial will inform the development of gut microbiota intervention as a health-promoting procedure.}, } @article {pmid31836758, year = {2019}, author = {Ting, CH and Pan, CY and Chen, YC and Lin, YC and Chen, TY and Rajanbabu, V and Chen, JY}, title = {Impact of Tilapia hepcidin 2-3 dietary supplementation on the gut microbiota profile and immunomodulation in the grouper (Epinephelus lanceolatus).}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19047}, pmid = {31836758}, issn = {2045-2322}, mesh = {Animal Feed ; Animals ; Anti-Infective Agents/pharmacology ; Bacteria/drug effects ; Bass/genetics/growth & development/*immunology/*microbiology ; *Dietary Supplements ; Feeding Behavior/drug effects ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Regulation/drug effects ; Hepcidins/*pharmacology ; Immunomodulation/*drug effects ; Metagenomics ; Microbial Sensitivity Tests ; Protein Stability/drug effects ; Recombinant Proteins/metabolism ; Spleen/metabolism ; Temperature ; Tilapia/*metabolism ; }, abstract = {Hepcidin regulates iron homeostasis and host-defense mechanisms, while the hepcidin-like protein, Tilapia hepcidin (TH)2-3, functions as an antimicrobial peptide (AMP). Since AMP dietary supplements may be used as alternatives to antibiotics in livestock, we tested the effects of recombinant (r)TH2-3 as a dietary supplement in grouper aquaculture. rTH2-3 was produced by a Pichia pastoris expression system and exhibited thermostability and broad-spectrum antimicrobial activity. The feed conversion ratio and feed efficiency were determined in Epinephelus lanceolatus (grouper) fed with rTH2-3-supplemented diet for 28 days. In addition, grouper showed enhanced superoxide dismutase (SOD) activity after rTH2-3 feeding compared to regular-diet-fed fish. Gut microbiota analysis revealed that microbial diversity was enhanced by feeding grouper with 1% rTH2-3. After challenging grouper with Vibrio alginolyticus, differential regulation of immune-related genes in the liver and spleen was observed between the TH2-3 and regular-diet groups, including for genes associated with antimicrobial and pro-inflammatory functions, complement components, and major histocompatibility complex (Mhc). These findings suggest that overall immunity was improved. Thus, our results suggest long-term supplementation with rTH2-3 may be beneficial for aquacultured grouper. The beneficial effects of the supplement are likely based on changes in the commensal microbial community as well as immunomodulation.}, } @article {pmid31836579, year = {2020}, author = {Ouyang, Y and Norton, JM}, title = {Short-Term Nitrogen Fertilization Affects Microbial Community Composition and Nitrogen Mineralization Functions in an Agricultural Soil.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {5}, pages = {}, pmid = {31836579}, issn = {1098-5336}, mesh = {Agriculture ; *Fertilizers ; *Microbiota ; Nitrogen/administration & dosage/*metabolism ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Soil/*chemistry ; *Soil Microbiology ; Utah ; }, abstract = {Soil extracellular enzymes play a significant role in the N mineralization process. However, few studies have documented the linkage between enzyme activity and the microbial community that performs the function. This study examined the effects of inorganic and organic N fertilization on soil microbial communities and their N mineralization functions over 4 years. Soils were collected from silage corn field plots with four contrasting N treatments: control (no additional N), ammonium sulfate (AS; 100 and 200 kg of N ha[-1]), and compost (200 kg of N ha[-1]). Illumina amplicon sequencing was used to comprehensively assess the overall bacterial community (16S rRNA genes), bacterial ureolytic community (ureC), and bacterial chitinolytic community (chiA). Selected genes involved in N mineralization were also examined using quantitative real-time PCR and metagenomics. Enzymes (and marker genes) included protease (npr and sub), chitinase (chiA), urease (ureC), and arginase (rocF). Compost significantly increased diversity of overall bacterial communities even after one application, while ammonium fertilizers had no influence on the overall bacterial communities over four seasons. Bacterial ureolytic and chitinolytic communities were significantly changed by N fertilization. Compost treatment strongly elevated soil enzyme activities after 4 years of repeated application. Functional gene abundances were not significantly affected by N treatments, and they were not correlated with corresponding enzyme activities. N mineralization genes were recovered from soil metagenomes based on a gene-targeted assembly. Understanding how the structure and function of soil microbial communities involved with N mineralization change in response to fertilization practices may indicate suitable agricultural management practices that improve ecosystem services while reducing negative environmental consequences.IMPORTANCE Agricultural N management practices influence the enzymatic activities involved in N mineralization. However, specific enzyme activities do not identify the microbial species directly involved in the measured process, leaving the link between the composition of the microbial community and the production of key enzymes poorly understood. In this study, the application of high-throughput sequencing, real-time PCR, and metagenomics shed light on how the abundance and diversity of microorganisms involved in N mineralization respond to N management. We suggest that N fertilization has significantly changed bacterial ureolytic and chitinolytic communities.}, } @article {pmid31835740, year = {2019}, author = {Truchado, DA and Diaz-Piqueras, JM and Gomez-Lucia, E and Doménech, A and Milá, B and Pérez-Tris, J and Schmidt-Chanasit, J and Cadar, D and Benítez, L}, title = {A Novel and Divergent Gyrovirus with Unusual Genomic Features Detected in Wild Passerine Birds from a Remote Rainforest in French Guiana.}, journal = {Viruses}, volume = {11}, number = {12}, pages = {}, pmid = {31835740}, issn = {1999-4915}, mesh = {Animals ; Birds/*virology ; Circoviridae Infections/*veterinary ; Computational Biology/methods ; French Guiana ; *Genome, Viral ; *Genomics/methods ; Gyrovirus/*classification/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Phylogeny ; Prevalence ; *Rainforest ; }, abstract = {Sequence-independent amplification techniques have become important tools for virus discovery, metagenomics, and exploration of viral diversity at the global scale, especially in remote areas. Here, we describe the detection and genetic characterization of a novel gyrovirus, named GyV11, present in cloacal, oral, and blood samples from neotropical wild birds in French Guiana. The molecular epidemiology revealed the presence of GyV11 only in passerine birds from three different species at a low prevalence (0.73%). This is the first characterization and prevalence study of a gyrovirus carried out in resident wild bird populations in a remote region, and provides evidence of the fecal-oral route transmission and local circulation of the virus. The molecular phylogeny of gyroviruses reveals the existence of two distinct gyrovirus lineages in which GyV11 is phylogenetically distinct from previously reported gyroviruses. Furthermore, GyV11 is placed basal in the gyrovirus phylogeny, likely owing to its ancestral origin and marked divergence. This study also provides important insights into the ecology, epidemiology, and genomic features of gyroviruses in a remote neotropical rainforest. The pathogenesis of this virus in avian species or whether GyV11 can infect humans and/or chickens needs to be further investigated.}, } @article {pmid31835231, year = {2020}, author = {Zheng, B and Zhong, S and Tang, Y and Chen, L}, title = {Understanding the nutritional functions of thermally-processed whole grain highland barley in vitro and in vivo.}, journal = {Food chemistry}, volume = {310}, number = {}, pages = {125979}, doi = {10.1016/j.foodchem.2019.125979}, pmid = {31835231}, issn = {1873-7072}, mesh = {Animals ; Bifidobacterium ; Diet, High-Fat ; Dietary Fiber/analysis/pharmacology ; Food Handling/*methods ; Gastrointestinal Microbiome/drug effects/*physiology ; Hordeum/*chemistry ; Hot Temperature ; Male ; Nutritional Physiological Phenomena ; Oxidation-Reduction ; Rats, Sprague-Dawley ; Whole Grains/chemistry ; }, abstract = {The objective of this study was to investigate the nutritional functions of highland barley subjected to heat-moisture treatment (HMT) and dry heat treatment (DHT) in vitro and in vivo. In vitro test indicated HMT and DHT play part in the reduced glycemic potency of highland barley. Meanwhile, in vivo results showed that thermally-processed highland barley (THB) supplementation significantly decreased the body weight and serum glucose, improved oxidation resistance and altered the composition of gut microbiota. Bifidobacteria, Fusicatenibacter and Desulfovibrio were identified as types of bacteria that might related to the relatively higher content of dietary fiber in THB. The Spearman's correlation analysis revealed that Fusicatenibacter and Desulfovibrio were positively correlated with T-AOC levels. In addition, the putative metagenomes implicated that THB might regulate the metabolic pathways of gut microbiota. Overall, our findings provide important information for the rational design of highland barley-based health-promoting foods with nutritional functions.}, } @article {pmid31835036, year = {2019}, author = {Pachiadaki, MG and Brown, JM and Brown, J and Bezuidt, O and Berube, PM and Biller, SJ and Poulton, NJ and Burkart, MD and La Clair, JJ and Chisholm, SW and Stepanauskas, R}, title = {Charting the Complexity of the Marine Microbiome through Single-Cell Genomics.}, journal = {Cell}, volume = {179}, number = {7}, pages = {1623-1635.e11}, pmid = {31835036}, issn = {1097-4172}, support = {R21 AI134037/AI/NIAID NIH HHS/United States ; }, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Energy Metabolism ; *Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeography ; Plankton ; Seawater/*microbiology ; Single-Cell Analysis/methods ; Transcriptome ; }, abstract = {Marine bacteria and archaea play key roles in global biogeochemistry. To improve our understanding of this complex microbiome, we employed single-cell genomics and a randomized, hypothesis-agnostic cell selection strategy to recover 12,715 partial genomes from the tropical and subtropical euphotic ocean. A substantial fraction of known prokaryoplankton coding potential was recovered from a single, 0.4 mL ocean sample, which indicates that genomic information disperses effectively across the globe. Yet, we found each genome to be unique, implying limited clonality within prokaryoplankton populations. Light harvesting and secondary metabolite biosynthetic pathways were numerous across lineages, highlighting the value of single-cell genomics to advance the identification of ecological roles and biotechnology potential of uncultured microbial groups. This genome collection enabled functional annotation and genus-level taxonomic assignments for >80% of individual metagenome reads from the tropical and subtropical surface ocean, thus offering a model to improve reference genome databases for complex microbiomes.}, } @article {pmid31833543, year = {2020}, author = {Turner, D and Bishai, J and Reshef, L and Abitbol, G and Focht, G and Marcus, D and Ledder, O and Lev-Tzion, R and Orlanski-Meyer, E and Yerushalmi, B and Aloi, M and Griffiths, AM and Albenberg, L and Kolho, KL and Assa, A and Cohen, S and Gophna, U and Vlamakis, H and Lurz, E and Levine, A}, title = {Antibiotic Cocktail for Pediatric Acute Severe Colitis and the Microbiome: The PRASCO Randomized Controlled Trial.}, journal = {Inflammatory bowel diseases}, volume = {26}, number = {11}, pages = {1733-1742}, doi = {10.1093/ibd/izz298}, pmid = {31833543}, issn = {1536-4844}, mesh = {Acute Disease ; Administration, Intravenous ; Adolescent ; Adrenal Cortex Hormones/*administration & dosage ; Anti-Bacterial Agents/*administration & dosage ; Child ; Colitis, Ulcerative/*drug therapy/*microbiology ; Drug Therapy, Combination ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Pilot Projects ; RNA, Ribosomal, 16S/analysis ; Severity of Illness Index ; Treatment Outcome ; }, abstract = {BACKGROUND: Alterations in the microbiome have been postulated to drive inflammation in IBD. In this pilot randomized controlled trial, we evaluated the effectiveness of quadruple antibiotic cocktail in addition to intravenous-corticosteroids (IVCSs) in acute severe colitis (ASC).

METHODS: Hospitalized children with ASC (pediatric ulcerative colitis activity index [PUCAI] ≥65) were randomized into 2 arms: the first received antibiotics in addition to IVCS (amoxicillin, vancomycin, metronidazole, doxycycline/ciprofloxacin [IVCS+AB]), whereas the other received only IVCS for 14 days. The primary outcome was disease activity (PUCAI) at day 5. Microbiome was analyzed using 16S rRNA gene and metagenome.

RESULTS: Twenty-eight children were included: 16 in the AB + IVCS arm and 12 in the IVCS arm (mean age 13.9 ± 4.1 years and 23 [82%] with extensive colitis). The mean day-5 PUCAI was 25 ± 16.7 vs 40.4 ± 20.4, respectively (P = 0.037). Only 3 and 2 children, respectively, required colectomy during 1-year follow-up (P = 0.89). Microbiome data at time of admission were analyzed for 25 children, of whom 17 (68%) had a predominant bacterial species (>33% abundance); response was not associated with the specific species, whereas decreased microbiome diversity at admission was associated with day-5 response in the IVCS arm.

CONCLUSION: Patients with ASC have alterations in the microbiome characterized by loss of diversity and presence of predominant bacterial species. Quadruple therapy in addition to IVCS improved disease activity on day 5, but larger studies are needed to determine whether this is associated with improved long-term outcomes (clinicaltrials.gov NCT02033408).}, } @article {pmid31832698, year = {2020}, author = {Huang, CL and Sarkar, R and Hsu, TW and Yang, CF and Chien, CH and Chang, WC and Chiang, TY}, title = {Endophytic Microbiome of Biofuel Plant Miscanthus sinensis (Poaceae) Interacts with Environmental Gradients.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {133-144}, doi = {10.1007/s00248-019-01467-8}, pmid = {31832698}, issn = {1432-184X}, support = {106-2621-B-006-001-MY3//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Bacteria/classification/*isolation & purification ; Biofuels ; Ecosystem ; *Ecotype ; *Endophytes ; Metagenomics ; *Microbiota ; Poaceae/*microbiology ; *Rhizosphere ; }, abstract = {Miscanthus in Taiwan occupies a cline along altitude and adapts to diverse environments, e.g., habitats of high salinity and volcanoes. Rhizospheric and endophytic bacteria may help Miscanthus acclimate to those stresses. The relative contributions of rhizosphere vs. endosphere compartments to the adaptation remain unknown. Here, we used targeted metagenomics to compare the microbial communities in the rhizosphere and endosphere among ecotypes of M. sinensis that dwell habitats under different stresses. Proteobacteria and Actinobacteria predominated in the endosphere. Diverse phyla constituted the rhizosphere microbiome, including a core microbiome found consistently across habitats. In endosphere, the predominance of the bacteria colonizing from the surrounding soil suggests that soil recruitment must have subsequently determined the endophytic microbiome in Miscanthus roots. In endosphere, the bacterial diversity decreased with the altitude, likely corresponding to rising limitation to microorganisms according to the species-energy theory. Specific endophytes were associated with different environmental stresses, e.g., Pseudomonas spp. for alpine and Agrobacterium spp. for coastal habitats. This suggests Miscanthus actively recruits an endosphere microbiome from the rhizosphere it influences.}, } @article {pmid31832638, year = {2020}, author = {D'Souza, AW and Moodley-Govender, E and Berla, B and Kelkar, T and Wang, B and Sun, X and Daniels, B and Coutsoudis, A and Trehan, I and Dantas, G}, title = {Cotrimoxazole Prophylaxis Increases Resistance Gene Prevalence and α-Diversity but Decreases β-Diversity in the Gut Microbiome of Human Immunodeficiency Virus-Exposed, Uninfected Infants.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {71}, number = {11}, pages = {2858-2868}, pmid = {31832638}, issn = {1537-6591}, support = {R01 GM099538/GM/NIGMS NIH HHS/United States ; T32 GM007200/GM/NIGMS NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; UM1 AI069422/AI/NIAID NIH HHS/United States ; }, mesh = {Female ; *Gastrointestinal Microbiome/genetics ; HIV ; *HIV Infections/drug therapy ; Humans ; Infant ; Pregnancy ; Prevalence ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; }, abstract = {BACKGROUND: Prophylactic cotrimoxazole treatment is recommended in human immunodeficiency virus (HIV)-exposed, uninfected (HEU) infants, but the effects of this treatment on developing HEU infant gut microbiotas and resistomes are largely undefined.

METHODS: We analyzed whole-metagenome sequencing data from 163 longitudinally collected stool samples from 63 HEU infants randomized to receive (n = 34; CTX-T) or to not receive (n = 29; CTX-N) prophylactic cotrimoxazole treatment. We generated taxonomic, functional pathway, and resistance gene profiles for each sample and compared microbiome signatures between the CTX-T and CTX-N infants.

RESULTS: Metagenomic analysis did not reveal significant differences in taxonomic or functional pathway α-diversity between CTX-T and CTX-N infants. In contrast, resistance gene prevalence (P = .00719) and α-diversity (P = .0045) increased in CTX-T infants. These differences increased over time for both resistance gene prevalence measured by log-normalized abundance (4-month mean, 0.71 [95% confidence interval {CI}, .2-1.2] and 6-month mean, 0.85 [95% CI, .1-1.7]) and α-diversity (P = .0045). Unlike α-diversity, interindividual gut microbiome taxonomic (mean, -0.11 [95% CI, -.15 to -.077]), functional taxonomic (mean, -0.050 [95% CI, -.084 to -.017]), and resistance gene (mean, -0.13 [95% CI, -.17 to -.099]) β-diversity decreased in CTX-T infants compared with CTX-N infants. These results are consistent with persistent antibiotic selection pressure.

CONCLUSIONS: Cotrimoxazole prophylaxis in HEU infants decreased gut microbiome β-diversity and increased antibiotic resistance gene α-diversity and prevalence. Antibiotic resistance is a growing threat, especially in low- and middle-income countries where the higher perinatal HIV exposure rates result in cotrimoxazole prophylaxis. Understanding effects from current HEU infant antibiotic prophylaxis guidelines will inform guideline revisions and efforts to reduce increasing antibiotic resistance.}, } @article {pmid31831655, year = {2019}, author = {Henke, MT and Clardy, J}, title = {Molecular messages in human microbiota.}, journal = {Science (New York, N.Y.)}, volume = {366}, number = {6471}, pages = {1309-1310}, doi = {10.1126/science.aaz4164}, pmid = {31831655}, issn = {1095-9203}, support = {R01 AT009708/AT/NCCIH NIH HHS/United States ; F32 GM126650/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Metagenome ; *Microbiota ; }, } @article {pmid31831198, year = {2020}, author = {Royo-Llonch, M and Sánchez, P and González, JM and Pedrós-Alió, C and Acinas, SG}, title = {Ecological and functional capabilities of an uncultured Kordia sp.}, journal = {Systematic and applied microbiology}, volume = {43}, number = {1}, pages = {126045}, doi = {10.1016/j.syapm.2019.126045}, pmid = {31831198}, issn = {1618-0984}, mesh = {Bacterial Proteins/genetics ; DNA, Bacterial/genetics ; Ecosystem ; Flavobacteriaceae/*classification/*genetics ; Genome, Bacterial/genetics ; Indian Ocean ; Metagenomics ; Microbiota/genetics ; Nucleic Acid Hybridization ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhodopsins, Microbial/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; }, abstract = {Cultivable bacteria represent only a fraction of the diversity in microbial communities. However, the official procedures for classification and characterization of a novel prokaryotic species still rely on isolates. Nevertheless, due to single cell genomics, it is possible to retrieve genomes from environmental samples by sequencing them individually, and to assign specific genes to a specific taxon, regardless of their ability to grow in culture. In this study, a complete description was performed for uncultured Kordia sp. TARA_039_SRF, a proposed novel species within the genus Kordia, using culture-independent techniques. The type material was a high-quality draft genome (94.97% complete, 4.65% gene redundancy) co-assembled using ten nearly identical single amplified genomes (SAGs) from surface seawater in the North Indian Ocean during the Tara Oceans Expedition. The assembly process was optimized to obtain the best possible assembly metrics and a less fragmented genome. The closest relative of the species was Kordia periserrulae, which shared 97.56% similarity of the 16S rRNA gene, 75% orthologs and 89.13% average nucleotide identity. The functional potential of the proposed novel species included proteorhodopsin, the ability to incorporate nitrate, cytochrome oxidases with high affinity for oxygen, and CAZymes that were unique features within the genus. Its abundance at different depths and size fractions was also evaluated together with its functional annotation, revealing that its putative ecological niche could be particles of phytoplanktonic origin. It could putatively attach to these particles and consume them while sinking to the deeper and oxygen depleted layers of the North Indian Ocean.}, } @article {pmid31831130, year = {2019}, author = {Zhou, JC and Zhang, XW}, title = {Akkermansia muciniphila: a promising target for the therapy of metabolic syndrome and related diseases.}, journal = {Chinese journal of natural medicines}, volume = {17}, number = {11}, pages = {835-841}, doi = {10.1016/S1875-5364(19)30101-3}, pmid = {31831130}, issn = {1875-5364}, mesh = {Akkermansia ; Animals ; Gastrointestinal Microbiome ; Humans ; Metabolic Diseases/microbiology/*therapy ; Metabolic Syndrome/microbiology/*therapy ; *Probiotics ; *Verrucomicrobia ; }, abstract = {The probiotic Akkermansia muciniphila (A. muciniphila) is an intestinal bacterium that was first identified in human feces in 2004. Its specialization in mucin degradation makes it a key microorganism that maintains intestinal mucosal barrier function. As an unique representative strain of the phylum Verrucomicrobia that can be cultured in vitro, A. muciniphila is much easier to detect by metagenomic analysis of intestinal flora. In the past few years, A. muciniphila has been getting increasing attention for the positive correlation between its intestinal colonization and host homeostatic metabolism. In this review, we summarize the relationship between A. muciniphila and host health and diseases, especially focusing on metabolic diseases and related mechanisms, as well as the natural food and drug-derived substrates affecting its colonization in the host, expecting to provide evidence and clues for the development of drugs targeting A. muciniphila.}, } @article {pmid31831058, year = {2019}, author = {Halatchev, IG and O'Donnell, D and Hibberd, MC and Gordon, JI}, title = {Applying indirect open-circuit calorimetry to study energy expenditure in gnotobiotic mice harboring different human gut microbial communities.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {158}, pmid = {31831058}, issn = {2049-2618}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; R01 DK030292/DK/NIDDK NIH HHS/United States ; R01 DK070977/DK/NIDDK NIH HHS/United States ; P30 DK056341/DK/NIDDK NIH HHS/United States ; T32 HL007081/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Calorimetry, Indirect/*methods ; Energy Metabolism/*physiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Germ-Free Life/physiology ; Metagenome ; Mice ; Obesity/*microbiology ; }, abstract = {Given the increasing use of gnotobiotic mouse models for deciphering the effects of human microbial communities on host biology, there is a need to develop new methods for characterizing these animals while maintaining their isolation from environmental microbes. We describe a method for performing open-circuit indirect calorimetry on gnotobiotic mice colonized with gut microbial consortia obtained from different human donors. In this illustrative case, cultured collections of gut bacterial strains were obtained from obese and lean co-twins. The approach allows microbial contributions to host energy homeostasis to be characterized.}, } @article {pmid31830598, year = {2020}, author = {Wu, F and Guo, X and Zhang, M and Ou, Z and Wu, D and Deng, L and Lu, Z and Zhang, J and Deng, G and Chen, S and Li, S and Yi, J and Peng, Y}, title = {An Akkermansia muciniphila subtype alleviates high-fat diet-induced metabolic disorders and inhibits the neurodegenerative process in mice.}, journal = {Anaerobe}, volume = {61}, number = {}, pages = {102138}, doi = {10.1016/j.anaerobe.2019.102138}, pmid = {31830598}, issn = {1095-8274}, mesh = {Akkermansia ; Animals ; Blood Glucose ; Body Weight ; *Diet, High-Fat/adverse effects ; Disease Models, Animal ; Disease Susceptibility ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome ; Genome, Bacterial ; Genomics/methods ; Glucose/metabolism ; Gram-Negative Bacterial Infections/*complications/*microbiology ; Metabolic Diseases/*etiology/metabolism/pathology ; Mice ; Neurodegenerative Diseases/*etiology/metabolism/pathology ; Propionates/metabolism ; Pyramidal Cells/metabolism ; Verrucomicrobia/classification/*physiology ; }, abstract = {The prevalence of obesity and diabetes, and their complicating mental disorders, severely affect public health. This study aimed to investigate the long-term effects of an Akkermansia muciniphila subtype (A. muciniphila[sub]) on high-fat diet-induced obesity and diabetes, and to evaluate whether this subtype can alleviate their complicated mental disorders. Whole genome sequencing and short chain fatty acid production analysis in supernatant of pure culture were performed. Female adult C57BL/6 mice were fed a high-fat diet or a normal chow diet and were gavaged with A. muciniphila[sub] or phosphate-buffered saline daily for 10 months. Body weight, food consumption and blood glucose were measured. At the end of the treatment period, all mice were subjected to the Y-maze test, sucrose preference test, analyses of serum, fecal microbiota analysis and histological examination. This A. muciniphila[sub] had 278 unique genes compared to the type strain (A. muciniphila ATCC BAA-835) and produced short chain fatty acids both. A. muciniphila[sub] administration significantly reduced body weight gain and improved the spatial memory of high-fat diet-fed mice. A. muciniphila[sub] increased Nissl bodies in neurons of the hippocampus, and restored the high-fat diet-inhibited tryptophan metabolism. The high-fat diet led to decreased serum 5-hydroxytryptamine and induced depression, which were not alleviated by A. muciniphila[sub]. A. muciniphila[sub] increased the relative fecal abundance of Bifidobacterium, and was negatively correlated with the fecal abundance of Bacteroides. The present study demonstrated the beneficial effects of this A. muciniphila[sub] on body weight, blood glucose control and the alleviation of the memory decay caused by a high-fat diet in mice.}, } @article {pmid31830158, year = {2020}, author = {Ji, X and Hou, C and Gao, Y and Xue, Y and Yan, Y and Guo, X}, title = {Metagenomic analysis of gut microbiota modulatory effects of jujube (Ziziphus jujuba Mill.) polysaccharides in a colorectal cancer mouse model.}, journal = {Food & function}, volume = {11}, number = {1}, pages = {163-173}, doi = {10.1039/c9fo02171j}, pmid = {31830158}, issn = {2042-650X}, mesh = {Animals ; Bacteroidetes ; Colonic Neoplasms/*therapy ; Disease Models, Animal ; Firmicutes ; Fruit/*chemistry ; *Gastrointestinal Microbiome ; Male ; Mice ; Mice, Inbred C57BL ; Polysaccharides/*chemistry ; Prebiotics/*administration & dosage ; Ziziphus/*chemistry ; }, abstract = {Accumulating evidence has reported that the gut microbiota could play important roles in the occurrence and progression of colorectal cancer. The nondigestible plant polysaccharides have always been fermented by the intestinal microbiota. Polysaccharides, the predominant functional composition found in jujube fruit, has been shown to inhibit carcinogenesis in animal models. However, the molecular mechanisms involved in polysaccharides preventing carcinogenesis are still uncharacterized. The aim of this study was to investigate the modulatory effects of jujube polysaccharides (JP) on intestinal microbiota, and the influence of JP on the gut flora structure was then analyzed using an AOM/DSS-induced colitis cancer mouse model, using high-throughput sequencing. Contrasted with control group, the addition of JP could ward off colon cancer by ameliorating colitis cancer-induced gut dysbiosis. In addition, there was a significant decrease in Firmicutes/Bacteroidetes post JP treatment. What's more, KEGG pathways of metabolic pathways, ATP-binding cassette (ABC) transporters and two-component system enriched the most differentially expressed genes after JP intervention for 13 weeks. These results suggested that JP showed prebiotic-like activities by positively modulating intestinal microbiota and affecting certain metabolic pathways contributing to host health. In conclusion, our results demonstrated an appreciable capability of JP to restore the gut microbiota profile altered by AOM/DSS, indicating the potential of jujube polysaccharides as promising prebiotic candidates for the prevention and treatment of colorectal cancer.}, } @article {pmid31830070, year = {2019}, author = {Khilyas, IV and Sorokina, AV and Elistratova, AA and Markelova, MI and Siniagina, MN and Sharipova, MR and Shcherbakova, TA and D'Errico, ME and Cohen, MF}, title = {Microbial diversity and mineral composition of weathered serpentine rock of the Khalilovsky massif.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0225929}, pmid = {31830070}, issn = {1932-6203}, mesh = {Asbestos, Serpentine/*analysis ; Biodiversity ; Computational Biology/methods ; Geologic Sediments/*chemistry/*microbiology ; Metagenome ; Metagenomics/methods ; *Microbiota ; Minerals/*analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Russia ; *Soil Microbiology ; Spectrum Analysis ; }, abstract = {Endolithic microbial communities survive nutrient and energy deficient conditions while contributing to the weathering of their mineral substrate. This study examined the mineral composition and microbial communities of fully serpentinized weathered rock from 0.1 to 6.5 m depth at a site within the Khalilovsky massif, Orenburg Region, Southern Ural Mountains, Russia. The mineral composition includes a major content of serpentinite family (mostly consisting of lizardite and chrysotile), magnesium hydrocarbonates (hydromagnesite with lesser amounts of hydrotalcite and pyroaurite) concentrated in the upper layers, and clay minerals. We found that the deep-seated weathered serpentinites are chrysotile-type minerals, while the middle and surface serpentinites mostly consist of lizardite and chrysotile types. Microbial community analysis, based on 16S rRNA gene sequencing, showed a similar diversity of phyla throughout the depth profile. The dominant bacterial phyla were the Actinobacteria (of which unclassified genera in the orders Acidimicrobiales and Actinomycetales were most numerous), Chloroflexi (dominated by an uncultured P2-11E order) and the Proteobacteria (predominantly class Betaproteobacteria). Densities of several groups of bacteria were negatively correlated with depth. Occurrence of the orders Actinomycetales, Gaiellales, Solirubrobacterales, Rhizobiales and Burkholderiales were positively correlated with depth. Our findings show that endolithic microbial communities of the Khalilovsky massif have similar diversity to those of serpentine soils and rocks, but are substantially different from those of the aqueous environments of actively serpentinizing systems.}, } @article {pmid31830061, year = {2019}, author = {Masha, SC and Owuor, C and Ngoi, JM and Cools, P and Sanders, EJ and Vaneechoutte, M and Crucitti, T and de Villiers, EP}, title = {Comparative analysis of the vaginal microbiome of pregnant women with either Trichomonas vaginalis or Chlamydia trachomatis.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0225545}, pmid = {31830061}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Chlamydia Infections/immunology/*microbiology ; Chlamydia trachomatis/genetics/immunology/isolation & purification ; DNA, Bacterial/isolation & purification ; Female ; Humans ; Microbiota/genetics/*immunology ; Pregnancy ; Pregnancy Complications, Infectious/immunology/*microbiology ; RNA, Ribosomal, 16S/genetics ; Trichomonas Vaginitis/immunology/*microbiology ; Trichomonas vaginalis/genetics/immunology/isolation & purification ; Vagina/*microbiology ; Young Adult ; }, abstract = {BACKGROUND: Although the significance of the human vaginal microbiome for health and disease is increasingly acknowledged, there is paucity of data on the differences in the composition of the vaginal microbiome upon infection with different sexually transmitted pathogens.

METHOD: The composition of the vaginal bacterial community of women with Trichomonas vaginalis (TV, N = 18) was compared to that of women with Chlamydia trachomatis (CT, N = 14), and to that of controls (N = 21) (women negative for TV, CT and bacterial vaginosis). The vaginal bacterial composition was determined using high throughput sequencing with the Ion 16S metagenomics kit of the variable regions 2, 4 and 8 of the bacterial 16S ribosomal RNA gene from the vaginal swab DNA extract of the women. QIIME and R package "Phyloseq" were used to assess the α- and β-diversity and absolute abundance of the 16S rRNA gene per sample in the three groups. Differences in taxa at various levels were determined using the independent T-test.

RESULTS: A total of 545 operational taxonomic units (OTUs) were identified in all the three groups of which 488 occurred in all three groups (core OTUs). Bacterial α-diversity, by both Simpson's and Shannon's indices, was significantly higher, (p = 0.056) and (p = 0.001) respectively, among women with either TV or CT than among controls (mean α-diversity TV-infected > CT-infected > Controls). At the genus level, women infected with TV had a significantly (p < 0.01) higher abundance of Parvimonas and Prevotella species compared to both controls and CT-infected women, whereas women infected with CT had a significantly (p < 0.05) higher abundance of Anaerococcus, Collinsella, Corynebacterium and Dialister.

CONCLUSION: The vaginal microbiomes of TV and CT-infected women were markedly different from each other and from women without TV and CT. Future studies should determine whether the altered microbiomes are merely markers of disease, or whether they actively contribute to the pathology of the two genital infections.}, } @article {pmid31828407, year = {2020}, author = {Paddock, MB and Fernández-Bayo, JD and VanderGheynst, JS}, title = {The effect of the microalgae-bacteria microbiome on wastewater treatment and biomass production.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {2}, pages = {893-905}, doi = {10.1007/s00253-019-10246-x}, pmid = {31828407}, issn = {1432-0614}, support = {1438211//National Science Foundation/ ; ARV-15-008//California Energy Commission/ ; }, mesh = {Ammonium Compounds/analysis ; Bacteria/classification/*growth & development/*metabolism ; Biological Oxygen Demand Analysis ; Bioreactors/microbiology ; Metagenomics ; Microalgae/classification/*growth & development/*metabolism ; *Microbiota ; Nitrogen/analysis ; Wastewater/chemistry/*microbiology ; Water Pollutants/metabolism ; Water Purification/*methods ; }, abstract = {The use of microalgae for wastewater treatment has been proposed as a cost-effective method to produce biofuels while remediating waste streams. This study examined the microalgae biomass production rate, wastewater treatment efficiency, and prokaryotic organism microbiome associated with microalgae Chlorella sorokiniana cultivated on anaerobic digestate effluent. Final microalgae biomass concentrations from nine photobioreactors were highly variable and had values that ranged between 0.14 g/L and 0.90 g/L. Nutrient removal efficiencies for TN (total nitrogen), N-NH4 (ammonium nitrogen), and COD (chemical oxygen demand) ranged from 34% to 67%, 65% to 97%, and-60% to 14%, respectively. Analysis of individual OTUs (operational taxonomic units) from the microbial community revealed that microalgae biomass concentrations were significantly correlated with the relative abundance of OTUs in the genus Pusillimonas. Predictive metagenomic analyses identified additional correlations associated with biomass production and nutrient removal. These results suggest that the microbial community present during microalgae cultivation on wastewater can impact the performance of the system for biomass production and wastewater treatment.}, } @article {pmid31828159, year = {2019}, author = {Nuli, R and Azhati, J and Cai, J and Kadeer, A and Zhang, B and Mohemaiti, P}, title = {Metagenomics and Faecal Metabolomics Integrative Analysis towards the Impaired Glucose Regulation and Type 2 Diabetes in Uyghur-Related Omics.}, journal = {Journal of diabetes research}, volume = {2019}, number = {}, pages = {2893041}, pmid = {31828159}, issn = {2314-6753}, mesh = {Actinobacteria ; Adult ; Bacteroides ; Case-Control Studies ; China/epidemiology ; Diabetes Mellitus, Type 2/epidemiology/metabolism/*microbiology ; Dysbiosis/epidemiology/metabolism/*microbiology ; Feces/chemistry/microbiology ; Female ; Firmicutes ; Gastrointestinal Microbiome/*genetics ; Glucose Intolerance/epidemiology/metabolism/*microbiology ; Humans ; Male ; *Metabolomics ; *Metagenomics ; Middle Aged ; }, abstract = {OBJECTIVE: Gut microbiota and their metabolites play an important role in the development of type 2 diabetes mellitus (T2DM). This research was designed to study the relationship between gut microbiota and faecal metabolites of Uyghur newly onset T2DM and impaired glucose regulation (IGR) patients.

MATERIALS AND METHODS: A total of 60 different glycemic Uyghur subjects were enrolled and divided into T2DM, IGR, and normal glucose tolerance (NGT) groups. Metagenomics and LC-MS-based untargeted faecal metabolomics were employed. Correlations between bacterial composition and faecal metabolomics were evaluated.

RESULTS: We discovered that the composition and diversity of gut microbiota in newly onset T2DM and IGR were different from those in NGT. The α-diversity was higher in NGT than in T2DM and IGR; β-diversity analysis revealed apparent differences in the bacterial community structures between patients with T2DM, IGR, and NGT. LC-MS faecal metabolomics analysis discovered different metabolomics features in the three groups. Alchornoic acid, PE (14 : 0/20 : 3), PI, L-tyrosine, LysoPC (15 : 0), protorifamycin I, pimelic acid, epothilone A, 7-dehydro-desmosterol, L-lysine, LysoPC (14 : 1), and teasterone are the most significant differential enriched metabolites. Most of the differential enriched metabolites were involved in metabolic processes, including carbohydrate metabolism, starch and sucrose metabolism, phenylpropanoid biosynthesis, and biosynthesis of amino acids. Procrustes analysis and correlation analysis identified correlations between gut microbiota and faecal metabolites. Matricin was positively correlated with Bacteroides and negatively correlated with Actinobacteria; protorifamycin I was negatively correlated with Actinobacteria; epothilone A was negatively correlated with Actinobacteria and positively correlated with Firmicutes; PA was positively correlated with Bacteroides and negatively correlated with Firmicutes; and cristacarpin was positively correlated with Actinobacteria; however, this correlation relationship does not imply causality.

CONCLUSIONS: This study used joint metagenomics and metabolomics analyses to elucidate the relationship between gut microbiota and faecal metabolites in different glycemic groups, and the result suggested that metabolic disorders and gut microbiota dysbiosis occurred in Uyghur T2DM and IGR. The results provide a theoretical basis for studying the pathological mechanism for further research.}, } @article {pmid31826972, year = {2019}, author = {Pierce, ML and Ward, JE}, title = {Gut Microbiomes of the Eastern Oyster (Crassostrea virginica) and the Blue Mussel (Mytilus edulis): Temporal Variation and the Influence of Marine Aggregate-Associated Microbial Communities.}, journal = {mSphere}, volume = {4}, number = {6}, pages = {}, pmid = {31826972}, issn = {2379-5042}, mesh = {Animals ; Bacteria/*classification/genetics ; Cluster Analysis ; Connecticut ; Crassostrea/*microbiology ; DNA, Ribosomal/chemistry/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; Mytilus edulis/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Gut microbial community structure was evaluated for two species of bivalve molluscs, the eastern oyster (Crassostrea virginica) and the blue mussel (Mytilus edulis) collected from Long Island Sound, Connecticut, over the course of a year. These bivalves utilize a shared feeding mechanism, which may result in similar gut microbial communities. Their particle diet, marine aggregates, and surrounding environment, aggregate-free seawater (AFSW), were also collected for comparison. Due to the suspension-feeding activities of bivalves, the potential for aggregate- and AFSW-associated microbiota to influence their microbial communities may be significant. Both taxonomic and functional diversity of the samples were assessed. 16S rRNA gene amplicon sequencing indicated that oysters and mussels maintained similar, but not identical, gut microbiomes, with some temporal variation. Throughout the year, bivalve species had gut microbial community compositions that were more similar to one another than to aggregates. Within a month, bivalves shared on average a quarter of their total operational taxonomic units (OTUs) with each other and a 10th of their total OTUs with aggregates. During months with warm water temperatures, individuals within each of the four sample types had similar alpha diversity, but again, temporal variation was observed. On a functional level, bivalve gut microbial communities exhibited variation attributed to host species and season. Unlike oysters, mussel gut bacterial communities maintained high richness and evenness values throughout the year, even when values for the particle diet and AFSW were reduced. Overall, a core gut bivalve microbiome was present, and it was partially influenced by the marine aggregate microbial community.IMPORTANCE This work investigates the influence that extrinsic factors, diet, and the environment can have on the microbiomes of shellfish. Over the course of a year, the gut microbial communities of two species of bivalves, oysters and mussels, held under identical conditions in coastal marine waters were compared. While the mussels and oysters harbored gut microbial communities with similar composition, on a functional level, they exhibited species and temporal variation. These results indicate that intrinsic factors influence the bivalve microbiome, resulting in species variability, even when environmental conditions, feeding mechanism, and particle diet are constant. Seasonal and multispecies comparisons for bivalve-associated microbial communities are rare, and we believe this research represents an important contribution. The results presented here advance our understanding of the symbiotic interactions between marine invertebrates, the microbial communities they harbor, and the environment.}, } @article {pmid31826833, year = {2020}, author = {Tomita, S and Watanabe, J and Nakamura, T and Endo, A and Okada, S}, title = {Characterisation of the bacterial community structures of sunki, a traditional unsalted pickle of fermented turnip leaves.}, journal = {Journal of bioscience and bioengineering}, volume = {129}, number = {5}, pages = {541-551}, doi = {10.1016/j.jbiosc.2019.11.010}, pmid = {31826833}, issn = {1347-4421}, mesh = {Brassica napus/*microbiology ; Fermentation ; Fermented Foods/analysis/microbiology ; Food Microbiology ; Japan ; Lactobacillus/classification/genetics/*isolation & purification/metabolism ; *Microbiota ; Phylogeny ; Plant Leaves/microbiology ; }, abstract = {The bacterial community structure in 29 naturally fermented samples of sunki, an unsalted lactic-fermented pickle in Japan, was determined by 16S rRNA gene-targeted metagenomic analysis. The data revealed that genus Lactobacillus was dominant in all samples and various bacterial species, related to Lactobacillus delbrueckii, Lactobacillus plantarum, Lactobacillus buchneri, Lactobacillus fermentum, Lactobacillus reuteri, Lactobacillus crispatus, Lactobacillus intestinalis, and Lactobacillus gasseri, showed a range of dominance depending on the samples. Comparative analysis of the bacterial composition by principal coordinate analysis and hierarchical clustering classified the varied bacterial composition of the 29 samples into three types of bacterial community structure. These types comprised lactobacilli belonging to different phylogenetic groups: type A had a certain ratio of Lactobacillus fermentum (70.3-22.1%, average 41.2%) in combination with several species belonging to Lactobacillus delbrueckii-phylogenetic group, type B comprised remarkably high levels of species Lactobacillus delbrueckii (average 89.5%), and type C had combinations of species belonging to Lactobacillus plantarum- and Lactobacillus buchneri-phylogenetic groups. Interestingly, these types differed in the compositional profiles of water-soluble and volatile compounds, and statistically significant differences were observed in the levels of acetic acid, succinic acid, ethanol, ethyl acetate, glutamic acid, γ-aminobutyric acid, and isovaleraldehyde. Furthermore, metabolomic analysis revealed a correlation of Lactobacillus fermentum dominance with pH value and lactic and acetic acid levels, with high R values of 0.643, -0.642, and 0.528, respectively. The data reported in this study showed the characteristics of the bacterial composition in the unsalted sunki pickle and its potential relationship with the compositional profile.}, } @article {pmid31825995, year = {2019}, author = {Woloszynek, S and Mell, JC and Zhao, Z and Simpson, G and O'Connor, MP and Rosen, GL}, title = {Exploring thematic structure and predicted functionality of 16S rRNA amplicon data.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0219235}, pmid = {31825995}, issn = {1932-6203}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Crohn Disease/*microbiology ; Humans ; Metagenomics/*methods ; Microbiota ; Mouth Neoplasms/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Software ; Time Factors ; }, abstract = {Analysis of microbiome data involves identifying co-occurring groups of taxa associated with sample features of interest (e.g., disease state). Elucidating such relations is often difficult as microbiome data are compositional, sparse, and have high dimensionality. Also, the configuration of co-occurring taxa may represent overlapping subcommunities that contribute to sample characteristics such as host status. Preserving the configuration of co-occurring microbes rather than detecting specific indicator species is more likely to facilitate biologically meaningful interpretations. Additionally, analyses that use taxonomic relative abundances to predict the abundances of different gene functions aggregate predicted functional profiles across taxa. This precludes straightforward identification of predicted functional components associated with subsets of co-occurring taxa. We provide an approach to explore co-occurring taxa using "topics" generated via a topic model and link these topics to specific sample features (e.g., disease state). Rather than inferring predicted functional content based on overall taxonomic relative abundances, we instead focus on inference of functional content within topics, which we parse by estimating interactions between topics and pathways through a multilevel, fully Bayesian regression model. We apply our methods to three publicly available 16S amplicon sequencing datasets: an inflammatory bowel disease dataset, an oral cancer dataset, and a time-series dataset. Using our topic model approach to uncover latent structure in 16S rRNA amplicon surveys, investigators can (1) capture groups of co-occurring taxa termed topics; (2) uncover within-topic functional potential; (3) link taxa co-occurrence, gene function, and environmental/host features; and (4) explore the way in which sets of co-occurring taxa behave and evolve over time. These methods have been implemented in a freely available R package: https://cran.r-project.org/package=themetagenomics, https://github.com/EESI/themetagenomics.}, } @article {pmid31825977, year = {2019}, author = {Jacobs, L and McMahon, BH and Berendzen, J and Longmire, J and Gleasner, C and Hengartner, NW and Vuyisich, M and Cohn, JR and Jenkins, M and Bartlow, AW and Fair, JM}, title = {California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0225858}, pmid = {31825977}, issn = {1932-6203}, mesh = {Animals ; *Bacteria/classification/genetics/growth & development ; Birds/*microbiology ; *Metagenome ; Microbiota/*physiology ; }, abstract = {Around the world, scavenging birds such as vultures and condors have been experiencing drastic population declines. Scavenging birds have a distinct digestive process to deal with higher amounts of bacteria in their primary diet of carcasses in varying levels of decay. These observations motivate us to present an analysis of captive and healthy California condor (Gymnogyps californianus) microbiomes to characterize a population raised together under similar conditions. Shotgun metagenomic DNA sequences were analyzed from fecal and cloacal samples of captive birds. Classification of shotgun DNA sequence data with peptide signatures using the Sequedex package provided both phylogenetic and functional profiles, as well as individually annotated reads for targeted confirmatory analysis. We observed bacterial species previously associated with birds and gut microbiomes, including both virulent and opportunistic pathogens such as Clostridium perfringens, Propionibacterium acnes, Shigella flexneri, and Fusobacterium mortiferum, common flora such as Lactobacillus johnsonii, Lactobacillus ruminus, and Bacteroides vulgatus, and mucosal microbes such as Delftia acidovorans, Stenotrophomonas maltophilia, and Corynebacterium falsnii. Classification using shotgun metagenomic reads from phylogenetic marker genes was consistent with, and more specific than, analysis based on 16S rDNA data. Classification of samples based on either phylogenetic or functional profiles of genomic fragments differentiated three types of samples: fecal, mature cloacal and immature cloacal, with immature birds having approximately 40% higher diversity of microbes.}, } @article {pmid31824656, year = {2019}, author = {Barton, W and O'Sullivan, O and Cotter, PD}, title = {Metabolic phenotyping of the human microbiome.}, journal = {F1000Research}, volume = {8}, number = {}, pages = {}, pmid = {31824656}, issn = {2046-1402}, mesh = {Humans ; Metabolomics ; *Microbiota ; }, abstract = {The human microbiome has been identified as having a key role in health and numerous diseases. Trillions of microbial cells and viral particles comprise the microbiome, each representing modifiable working elements of an intricate bioactive ecosystem. The significance of the human microbiome as it relates to human biology has progressed through culture-dependent (for example, media-based methods) and, more recently, molecular (for example, genetic sequencing and metabolomic analysis) techniques. The latter have become increasingly popular and evolved from being used for taxonomic identification of microbiota to elucidation of functional capacity (sequencing) and metabolic activity (metabolomics). This review summarises key elements of the human microbiome and its metabolic capabilities within the context of health and disease.}, } @article {pmid31823916, year = {2019}, author = {Singh, S and Verma, N and Taneja, N}, title = {The human gut resistome: Current concepts & future prospects.}, journal = {The Indian journal of medical research}, volume = {150}, number = {4}, pages = {345-358}, pmid = {31823916}, issn = {0971-5916}, mesh = {Databases, Genetic ; Drug Resistance, Microbial/*genetics ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; }, abstract = {The human gut is home to a myriad of organisms. While some are harmless commensals, others are transient, pathogenic flora. The gut microbiome is composed of diverse bacterial flora, and apart from playing a major role in protecting from various infectious and non-infectious diseases, it plays an important role in resistance to antimicrobials. The collection of genes or genetic material that confers antimicrobial resistance constitutes the gut resistome, and it may involve the pathogens or commensals of the intestinal tract. The diversity of this gut resistome is influenced by various environmental factors including the diet and antibiotic exposure. This review highlights the recent concepts pertaining to the human gut resistome, factors affecting it, how it impacts human health and diseases, methods to study the resistome and potential therapeutic approaches.}, } @article {pmid31822775, year = {2019}, author = {Chen, S and Zheng, Y and Zhou, Y and Guo, W and Tang, Q and Rong, G and Hu, W and Tang, J and Luo, H}, title = {Gut Dysbiosis with Minimal Enteritis Induced by High Temperature and Humidity.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {18686}, pmid = {31822775}, issn = {2045-2322}, mesh = {Animals ; Bacterial Translocation ; Body Weight ; Diarrhea/metabolism ; Dysbiosis/*physiopathology ; Enteritis/*microbiology ; Enzyme-Linked Immunosorbent Assay ; *Gastrointestinal Microbiome ; *Hot Temperature ; *Humidity ; Inflammation ; Intestinal Mucosa/metabolism ; Intestines/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Organ Size ; Probiotics/administration & dosage ; RNA, Ribosomal, 16S/metabolism ; Signal Transduction ; }, abstract = {High temperature and humidity (HTH) can cause diarrhea owing to food and drinking water contamination. However, their direct effects on gut microbiota and gastrointestinal inflammation are unknown. This study aimed to investigate the effects of HTH and probiotics on the microbiome. Twenty-one male mice were randomly assigned to normal control (NC), HTH, and broad-spectrum probiotic-treated (PR) groups. HTH and PR groups were regularly housed at 30 ± 0.5 °C with humidity of 85-90% for eight consecutive weeks. A broad-spectrum probiotic was administrated to PR-group mice from day 50 to 56. Clinical signs were observed and gut microbiota were analyzed via 16 S rRNA-based functional metagenomics. Intestinal pathology and the expression of defensins and pro-inflammatory cytokines were also assessed. Mice in the HTH and PR groups gradually developed sticky or loose feces. The HTH group developed a distinct microbiota profile associated with augmented metabolism and human-like pathophysiologies upon suppression of environmental sensing. Pathological assays indicated minimal enteritis, increased bacterial translocation, and elevated intestinal pro-inflammatory cytokine levels. Thus, ambient HTH directly contributes to gut dysbiosis and minimal enteritis, whereas probiotics partially normalized the microbiota and ameliorated gut inflammation. This study provides novel insights into the pathogenesis of environment-associated diseases and offers a potential therapeutic approach.}, } @article {pmid31821372, year = {2019}, author = {Osimani, A and Milanović, V and Roncolini, A and Riolo, P and Ruschioni, S and Isidoro, N and Loreto, N and Franciosi, E and Tuohy, K and Olivotto, I and Zarantoniello, M and Cardinali, F and Garofalo, C and Aquilanti, L and Clementi, F}, title = {Hermetia illucens in diets for zebrafish (Danio rerio): A study of bacterial diversity by using PCR-DGGE and metagenomic sequencing.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0225956}, pmid = {31821372}, issn = {1932-6203}, mesh = {*Animal Feed ; Animals ; Bacteria/classification/genetics ; *Diptera/microbiology ; Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Microbial Viability ; RNA, Ribosomal, 16S ; Zebrafish/*physiology ; }, abstract = {In the present research, bacterial diversity was studied during a 6-month feeding trial utilizing zebrafish (Danio rerio) fed Hermetia illucens reared on different substrates with an emphasis on fish gut bacterial diversity. A polyphasic approach based on viable counting, PCR-DGGE and metagenomic 16S rRNA gene amplicon target sequencing was applied. Two different H. illucens groups were reared on coffee by-products (C) or a mixture of vegetables (S). Viable counts showed a wide variability based on substrate. PCR-DGGE and Illumina sequencing allowed the major and minor bacterial taxa to be detected. Both samples of larvae and their frass reared on the S substrate showed the highest richness and evenness of bacterial communities, whereas zebrafish (ZHC) fed H. illucens reared on substrate C and zebrafish (ZHS) fed H. illucens reared on substrate S had the lowest bacterial richness and evenness. A stimulating effect of bioactive compounds from coffee by-products on the occurrence of Lactobacillaceae and Leuconostoccaceae in H. illucens reared on substrate C has been hypothesized. Zebrafish gut samples originating from the two feeding trials showed complex microbial patterns in which Actinobacteria and Alteromonadales were always detected, irrespective of the diet used. Enterobacteriaceae in fish guts were more abundant in ZHS than in ZHC, thus suggesting an influence of the bioactive compounds (chlorogenic and caffeic acids) in the substrate on Enterobacteriaceae in fish guts. ZHC showed a higher abundance of Clostridia than did ZHS, which was likely explained by stimulating activity on the bacteria in this class by the bioactive compounds contained in H. illucens reared on substrate C. An influence of the microbiota of H. illucens or insect-derived bioactive compounds on the gut microbiota of zebrafish has been suggested. The presence of bacteria consistently associated with zebrafish guts has been found irrespective of the diet, thus attesting to the likely stability of the core fish microbiota.}, } @article {pmid31820171, year = {2019}, author = {Chavira, A and Belda-Ferre, P and Kosciolek, T and Ali, F and Dorrestein, PC and Knight, R}, title = {The Microbiome and Its Potential for Pharmacology.}, journal = {Handbook of experimental pharmacology}, volume = {260}, number = {}, pages = {301-326}, doi = {10.1007/164_2019_317}, pmid = {31820171}, issn = {0171-2004}, mesh = {Humans ; *Microbiota ; Neoplasms ; Nervous System Diseases ; Obesity ; Pharmaceutical Preparations/metabolism ; *Precision Medicine ; }, abstract = {The human microbiota (the microscopic organisms that inhabit us) and microbiome (their genes) hold considerable potential for improving pharmacological practice. Recent advances in multi-"omics" techniques have dramatically improved our understanding of the constituents of the microbiome and their functions. The implications of this research for human health, including microbiome links to obesity, drug metabolism, neurological diseases, cancer, and many other health conditions, have sparked considerable interest in exploiting the microbiome for targeted therapeutics. Links between microbial pathways and disease states further highlight a rich potential for companion diagnostics and precision medicine approaches. For example, the success of fecal microbiota transplantation to treat Clostridium difficile infection has already started to redefine standard of care with a microbiome-directed therapy. In this review we briefly discuss the nature of human microbial ecosystems and with pathologies and biological processes linked to the microbiome. We then review emerging computational metagenomic, metabolomic, and wet lab techniques researchers are using today to learn about the roles host-microbial interactions have with respect to pharmacological purposes and vice versa. Finally, we describe how drugs affect the microbiome, how the microbiome can impact drug response in different people, and the potential of the microbiome itself as a source of new therapeutics.}, } @article {pmid31820107, year = {2020}, author = {Wu, Y and Bible, PW and Long, S and Ming, WK and Ding, W and Long, Y and Wen, X and Li, X and Deng, X and Deng, Y and Guo, S and Doçi, CL and Wei, L and Chen, H and Wang, Z}, title = {Metagenomic analysis reveals gestational diabetes mellitus-related microbial regulators of glucose tolerance.}, journal = {Acta diabetologica}, volume = {57}, number = {5}, pages = {569-581}, doi = {10.1007/s00592-019-01434-2}, pmid = {31820107}, issn = {1432-5233}, support = {2015A030313198//Natural Science of Guangdong Province, China/ ; 17ykpy24//Youth cultivation project of Sun Yat-sen University, China/ ; 2012004//Clinical Medical Project 5010 of Sun Yat-sen University, China/ ; 81771606//National Natural Science Foundation of China/ ; 81571452//National Natural Science Foundation of China/ ; }, mesh = {Adult ; Asian People/ethnology ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Blood Glucose/*metabolism ; China ; Cohort Studies ; Diabetes, Gestational/ethnology/*metabolism/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Glucose Tolerance Test ; Humans ; Metagenome ; Pregnancy ; }, abstract = {AIMS: Recent studies have suggested a possible association between microbiota and gestational diabetes (GDM). However, the results are inconsistent. Our objective was to investigate further the relationship between GDM and microbiota and verify the potential microbial marker.

METHODS: Two complementary approaches were used for the demonstration. First, we compared the gut microbial composition of 23 GDM patients and 26 non-GDM ethnically Chinese Han pregnant women, by using whole-metagenome shotgun sequencing of their stool samples collected at the third trimester. Second, we used Q-PCR (quantitative polymerase chain reaction) to evaluate the gut microbial composition in the stool samples from another cohort of 150 Chinese pregnant women (113 Control and 37 GDM), to further confirm the potential microbial marker.

RESULTS: The gut microbiota of GDM women show lower albeit not statistically significant (p = 0.18) alpha diversity at the species level than non-GDM women. However, the species-level beta-diversity or between-sample diversity measured by Bray-Curtis distance shows significant differences (p < 2.2e-16) between the two groups. The species Bacteroides dorei positively correlated with both OGTT (oral glucose tolerance test) 0-Hour (p = 0.0099) and OGTT 1-Hour (p = 0.0070). There is a similar trend between Bacteroides sp. 3_1_33FAA and both OGTT 0-Hour (p = 0.014) and OGTT 1-Hour (p = 0.0101) response variables. The species Alistipes putredinis negatively correlated with OGTT 1-Hour (p = 0.0172) and OGTT 2-Hour (p = 0.0147). Q-PCR validation further confirmed the association between the glucose tolerance loci of Bacteroides dorei and OGTT response.

CONCLUSIONS: Gut microbiome is related to the diabetic status of Chinese women during pregnancy. Specific species such as Bacteroides dorei associate with glucose response and could be potential monitoring and therapeutic microbial markers for GDM.}, } @article {pmid31820070, year = {2020}, author = {Tyx, RE and Rivera, AJ and Keong, LM and Stanfill, SB}, title = {An exploration of smokeless tobacco product nucleic acids: a combined metagenome and metatranscriptome analysis.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {2}, pages = {751-763}, pmid = {31820070}, issn = {1432-0614}, support = {CC999999/ImCDC/Intramural CDC HHS/United States ; }, mesh = {Bacteria/metabolism ; Biotransformation ; DNA, Bacterial/genetics ; *Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; *Microbiota ; Nitrates/metabolism ; Nitrites/metabolism ; RNA, Bacterial/analysis/genetics ; RNA, Viral/analysis/genetics ; Tobacco, Smokeless/*microbiology ; }, abstract = {Smokeless tobacco (ST) products are used worldwide and are a major public health concern. In addition to harmful chemicals found in these products, microbes found in ST products are believed to be responsible for generating harmful tobacco-specific nitrosamines (TSNAs), the most abundant carcinogens in ST. These microbes also contribute endotoxins and other pro-inflammatory components. A greater understanding of the microbial constituents in these products is sought in order to potentially link select design aspects or manufacturing processes to avoidable increases in harmful constituents. Previous studies looked primarily at bacterial constituents and had not differentiated between viable vs nonviable organisms, so in this study, we sought to use a dual metatranscriptomic and metagenomic analysis to see if differences exist. Using high-throughput sequencing, we observed that there were differences in taxonomic abundances between the metagenome and metatranscriptome, and in the metatranscriptome, we also observed an abundance of plant virus RNA not previously reported in DNA-only studies. We also found in the product tested, that there were no viable bacteria capable of metabolizing nitrate to nitrite. Therefore, the product tested would not be likely to increase TSNAs during shelf storage. We tested only a single product to date using the strategy presented here, but succeeded in demonstrating the value of using of these methods in tobacco products. These results present novel findings from the first combined metagenome and metatranscriptome of a commercial tobacco product.}, } @article {pmid31819214, year = {2020}, author = {Ignacio-Espinoza, JC and Ahlgren, NA and Fuhrman, JA}, title = {Long-term stability and Red Queen-like strain dynamics in marine viruses.}, journal = {Nature microbiology}, volume = {5}, number = {2}, pages = {265-271}, pmid = {31819214}, issn = {2058-5276}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; }, mesh = {Aquatic Organisms/classification/genetics/*virology ; DNA, Viral/genetics ; Ecosystem ; Genome, Viral ; Host Microbial Interactions/genetics ; Metagenome ; Microbiota ; Pacific Ocean ; Polymorphism, Single Nucleotide ; Seawater/*virology ; Species Specificity ; Viruses/*genetics ; *Water Microbiology ; }, abstract = {Viruses that infect microorganisms dominate marine microbial communities numerically, with impacts ranging from host evolution to global biogeochemical cycles[1,2]. However, virus community dynamics, necessary for conceptual and mechanistic model development, remains difficult to assess. Here, we describe the long-term stability of a viral community by analysing the metagenomes of near-surface 0.02-0.2 μm samples from the San Pedro Ocean Time-series[3] that were sampled monthly over 5 years. Of 19,907 assembled viral contigs (>5 kb, mean 15 kb), 97% were found in each sample (by >98% ID metagenomic read recruitment) to have relative abundances that ranged over seven orders of magnitude, with limited temporal reordering of rank abundances along with little change in richness. Seasonal variations in viral community composition were superimposed on the overall stability; maximum community similarity occurred at 12-month intervals. Despite the stability of viral genotypic clusters that had 98% sequence identity, viral sequences showed transient variations in single-nucleotide polymorphisms (SNPs) and constant turnover of minor population variants, each rising and falling over a few months, reminiscent of Red Queen dynamics[4]. The rise and fall of variants within populations, interpreted through the perspective of known virus-host interactions[5], is consistent with the hypothesis that fluctuating selection acts on a microdiverse cloud of strains, and this succession is associated with ever-shifting virus-host defences and counterdefences. This results in long-term virus-host coexistence that is facilitated by perpetually changing minor variants.}, } @article {pmid31819139, year = {2019}, author = {Rosa, UA and Ribeiro, GO and Villanova, F and Luchs, A and Milagres, FAP and Komninakis, SV and Tahmasebi, R and Lobato, MCABS and Brustulin, R and Chagas, RTD and Abrão, MFNDS and Soares, CVDA and Tinker, RJ and Pandey, RP and Raj, VS and Sabino, EC and Deng, X and Delwart, E and Costa, ACD and Leal, É}, title = {First identification of mammalian orthoreovirus type 3 by gut virome analysis in diarrheic child in Brazil.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {18599}, pmid = {31819139}, issn = {2045-2322}, mesh = {Animals ; Brazil/epidemiology ; Cattle ; Child, Preschool ; Chiroptera ; Diarrhea/*virology ; Gastroenteritis/*virology ; Gastrointestinal Microbiome ; Genome, Viral ; Geography ; Humans ; Infant ; Intestines/*virology ; Mammalian orthoreovirus 3/*classification/isolation & purification ; Metagenomics ; Phylogeny ; Rural Population ; Swine ; }, abstract = {Diarrhea remains one of the most common causes of deaths in children. Although many studies have investigated the prevalence of enteric pathogens around the globe some diarrheal episodes remain unexplained. It is possible that some yet-unidentified viral agents could be related to these cases of gastroenteritis. By using viral metagenomics techniques, we screened 251 fecal samples of children between 0.5 to 2.5-year-old with acute diarrhea not associated with common pathogens. These children live in rural areas and have different levels of contact with animals such as pigs, cows and bats. Here we report a complete genome of one mammalian orthoreovirus (MRV) type 3, denoted TO-151/BR, detected in a female child in the state of Tocantins (north of Brazil). Brazilian TO-151/BR strain was classified as MRV-3 based on S1 phylogeny and was closely related to porcine Asian strains. Phylogenetic analyses showed that other segments were more similar to MRV-3s of different geographic locations and hosts, including human and bats, highlighting genome reassortment and lack of host-specific barriers. This is the first report of MRV-3 in South America and a hypothesis of a silent long-term circulation of this virus in Brazil has been raised.}, } @article {pmid31818595, year = {2020}, author = {Brereton, NJB and Gonzalez, E and Desjardins, D and Labrecque, M and Pitre, FE}, title = {Co-cropping with three phytoremediation crops influences rhizosphere microbiome community in contaminated soil.}, journal = {The Science of the total environment}, volume = {711}, number = {}, pages = {135067}, doi = {10.1016/j.scitotenv.2019.135067}, pmid = {31818595}, issn = {1879-1026}, mesh = {Biodegradation, Environmental ; *Microbiota ; Plant Roots ; RNA, Ribosomal, 16S ; Rhizosphere ; Soil ; *Soil Microbiology ; Soil Pollutants ; }, abstract = {Human industrial activities have left millions of hectares of land polluted with trace element metals and persistent organic pollutants (POPs) around the world. Although contaminated sites are environmentally damaging, high economic costs often discourage soil remediation efforts. Phytoremediation is a potential green technology solution but can be challenging due to the diversity of anthropogenic contaminants. Co-cropping could provide improved tolerance to diverse soil challenges by taking advantage of distinct crop capabilities. Co-cropping of three species with potentially complementary functions, Festuca arundinacea, Salix miyabeana and Medicago sativa, perform well on diversely contaminated soils. Here, rhizosphere microbiomes of each crop in monoculture and in all co-cropping combinations were compared using 16S rRNA gene amplification, sequencing and differential abundance analysis. The hyperaccumulating F. arundinacea rhizosphere microbiome included putative plant growth promoting bacteria (PGPB) and metal tolerance species, such as Rhizorhapis suberifaciens, Cellvibrio fibrivorans and Pseudomonas lini. The rhizosphere microbiome of the fast-growing tree S. miyabeana included diverse taxa involved in POP degradation, including the species Phenylobacterium panacis. The well-characterised nitrogen-fixing M. sativa microbiome species, Sinorhizobium meliloti, was identified alongside others involved in nutrient acquisition and putative yet-to-be-cultured Candidatus saccharibacteria (TM7-1 group). The majority of differentially abundant rhizosphere-associated bacterial species were maintained in co-cropping pairs, with pairs having higher numbers of differentially abundant taxa than monocultures in all cases. This was not the case when all three crops were co-cropped, where most host-specific bacterial species were not detected as differentially abundant, indicating the potential for reduced rhizosphere functionality. The crops cultivated in pairs here retained rhizosphere microbiome bacteria involved in these monoculture ecosystem services of plant growth promotion, POP tolerance and degradation, and improved nutrient acquisition. These findings provide a promising outlook of the potential for complementary co-cropping strategies for phytoremediation of the multifaceted anthropogenic pollution which can disastrously affect soils around the world.}, } @article {pmid31818557, year = {2020}, author = {Huang, B and Yan, D and Ouyang, C and Zhang, D and Zhu, J and Liu, J and Li, Y and Wang, Q and Han, Q and Cao, A}, title = {Chloropicrin fumigation alters the soil phosphorus and the composition of the encoding alkaline phosphatase PhoD gene microbial community.}, journal = {The Science of the total environment}, volume = {711}, number = {}, pages = {135080}, doi = {10.1016/j.scitotenv.2019.135080}, pmid = {31818557}, issn = {1879-1026}, mesh = {Alkaline Phosphatase ; Bacteria ; Fumigation ; Hydrocarbons, Chlorinated ; *Microbiota ; Phosphorus ; *Soil ; Soil Microbiology ; }, abstract = {The transformation of phosphorus (P) compounds in soil depends largely on soil microbial communities and is sensitive to agricultural practices. However, the effects of soil fumigation on soil P, and microbes involved in P transformation, are unknown. Our results showed that chloropicrin (CP) fumigation significantly increased the available-P, Leached-P and active-P fractionation (inorganic P extracted from H2O, NaHCO3 and NaOH) in Shangdong and Miyun soils in the early stages of culture, while soil alkaline phosphatase (ALP) activity and phoD gene abundance decreased significantly. Leached-P in fumigated soil was positively correlated with increased active-P fractionation, indicating that it was an important source of soil Leached-P after fumigation. The changes in P-fractionation, Leached-P and ALP after fumigation were also significantly correlated with the composition of the microbial communities. CP fumigation briefly stimulated an increase in the abundance and diversity of phoD-harboring microbial communities and promoted the mineralization process of soil P. PICRUSt metagenomic analysis showed an increase in the relative abundance of microorganisms with involved in carbohydrate/lipid transport and metabolism functions after fumigation. These results suggest CP fumigation altered soil P transformation and phoD-harboring microbes that might lead to an increased risk of P enrichment in waterways.}, } @article {pmid31818556, year = {2020}, author = {Xia, X and Ki Leung, S and Cheung, S and Zhang, S and Liu, H}, title = {Rare bacteria in seawater are dominant in the bacterial assemblage associated with the Bloom-forming dinoflagellate Noctiluca scintillans.}, journal = {The Science of the total environment}, volume = {711}, number = {}, pages = {135107}, doi = {10.1016/j.scitotenv.2019.135107}, pmid = {31818556}, issn = {1879-1026}, mesh = {*Dinoflagellida ; Seawater ; }, abstract = {Noctiluca scintillans is a bloom-forming dinoflagellate, which is widely distributed in the global coastal seas. Associated bacteria have been proven to be essential for the survival and growth of zooplanktons. However, the diversity and function of bacteria associated with Noctiluca scintillans are under studied and largely unknown. Here, we examined the diversity and function of bacteria associated with field-acquired and laboratory-maintained Noctiluca cells. Our results showed that the bacterial communities associated with the laboratory-maintained Noctiluca were dominated by Rhodobacterales, whereas those associated with the field-acquired Noctiluca varied over time. In addition, major Noctiluca-associated bacteria had low relative abundance in the ambient environment. We also observed that when field-acquired Noctiluca were cultivated with a mono-species food source, there was a shift in the associated bacterial communities. Metagenomic analysis showed that genes involved in DNA replication/repair and osmotic regulation were more abundant than other genes in the Noctiluca-associated bacterial community. Furthermore, the associated bacteria were able to degrade various complex carbohydrates and actively participate in the nitrogen cycle in their host cells. In addition, a draft genome of the Rickettsiaceae strain was recovered, and we showed that the genome did not contain genes encoding hexokinase and phosphoglucomutase, two key enzymes involved in glucose utilization. Instead, the primary energy sources of this bacteria were shown to be glutamate, glutamine and pyruvate, which might be obtained from the host. We suggest that in return, the Rickettsiaceae strain is likely to provide cofactors and amino acids to the host. This study highlights the spatial and temporal complexity of bacterial communities associated with Noctiluca, and provides valuable insights into the interaction between a host and its associated bacteria.}, } @article {pmid31818316, year = {2019}, author = {Zeng, Q and Liao, C and Terhune, J and Wang, L}, title = {Impacts of florfenicol on the microbiota landscape and resistome as revealed by metagenomic analysis.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {155}, pmid = {31818316}, issn = {2049-2618}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Aquaculture ; Drug Resistance, Bacterial/*genetics ; Fish Diseases/*microbiology ; Fresh Water ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Ictaluridae/*microbiology ; Microbiota/*drug effects/genetics ; Sepsis/*veterinary ; Thiamphenicol/*analogs & derivatives/pharmacology ; }, abstract = {BACKGROUND: Drug-resistant fish pathogens can cause significant economic loss to fish farmers. Since 2012, florfenicol has become an approved drug for treating both septicemia and columnaris diseases in freshwater fish. Due to the limited drug options available for aquaculture, the impact of the therapeutical florfenicol treatment on the microbiota landscape as well as the resistome present in the aquaculture farm environment needs to be evaluated.

RESULTS: Time-series metagenomic analyses were conducted to the aquatic microbiota present in the tank-based catfish production systems, in which catfish received standard therapeutic 10-day florfenicol treatment following the federal veterinary regulations. Results showed that the florfenicol treatment shifted the structure of the microbiota and reduced the biodiversity of it by acting as a strong stressor. Planctomycetes, Chloroflexi, and 13 other phyla were susceptible to the florfenicol treatment and their abundance was inhibited by the treatment. In contrast, the abundance of several bacteria belonging to the Proteobacteria, Bacteroidetes, Actinobacteria, and Verrucomicrobia phyla increased. These bacteria with increased abundance either harbor florfenicol-resistant genes (FRGs) or had beneficial mutations. The florfenicol treatment promoted the proliferation of florfenicol-resistant genes. The copy number of phenicol-specific resistance genes as well as multiple classes of antibiotic-resistant genes (ARGs) exhibited strong correlations across different genetic exchange communities (p < 0.05), indicating the horizontal transfer of florfenicol-resistant genes among these bacterial species or genera. Florfenicol treatment also induced mutation-driven resistance. Significant changes in single-nucleotide polymorphism (SNP) allele frequencies were observed in membrane transporters, genes involved in recombination, and in genes with primary functions of a resistance phenotype.

CONCLUSIONS: The therapeutical level of florfenicol treatment significantly altered the microbiome and resistome present in catfish tanks. Both intra-population and inter-population horizontal ARG transfer was observed, with the intra-population transfer being more common. The oxazolidinone/phenicol-resistant gene optrA was the most prevalent transferred ARG. In addition to horizontal gene transfer, bacteria could also acquire florfenicol resistance by regulating the innate efflux systems via mutations. The observations made by this study are of great importance for guiding the strategic use of florfenicol, thus preventing the formation, persistence, and spreading of florfenicol-resistant bacteria and resistance genes in aquaculture.}, } @article {pmid31818246, year = {2019}, author = {Shelomi, M and Lin, SS and Liu, LY}, title = {Transcriptome and microbiome of coconut rhinoceros beetle (Oryctes rhinoceros) larvae.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {957}, pmid = {31818246}, issn = {1471-2164}, support = {MOST 106-2311-B-002-002-MY3//Ministry of Science and Technology (TW)/ ; MOST 108-2313-B-002-050//Ministry of Science and Technology, Taiwan/ ; MOST 108-2311-B-002-018-MY3//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification ; Coleoptera/*genetics/*microbiology ; Female ; Gastrointestinal Tract/metabolism/microbiology ; Gene Expression ; Insect Proteins/genetics ; Isoptera/microbiology ; Larva/genetics/microbiology ; Male ; Metagenomics ; *Microbiota/genetics ; Phylogeny ; Transcriptome ; }, abstract = {BACKGROUND: The coconut rhinoceros beetle, Oryctes rhinoceros, is a major pest of palm crops in tropical Asia and the Pacific Islands. Little molecular data exists for this pest, impeding our ability to develop effective countermeasures and deal with the species' growing resistance to viral biocontrols. We present the first molecular biology analyses of this species, including a metagenomic assay to understand the microbiome of different sections of its digestive tract, and a transcriptomics assay to complement the microbiome data and to shed light on genes of interest like plant cell wall degrading enzymes and immunity and xenobiotic resistance genes.

RESULTS: The gut microbiota of Oryctes rhinoceros larvae is quite similar to that of the termite gut, as both species feed on decaying wood. We found the first evidence for endogenous beta-1,4-endoglucanase in the beetle, plus evidence for microbial cellobiase, suggesting the beetle can degrade cellulose together with its gut microfauna. A number of antimicrobial peptides are expressed, particularly by the fat body but also by the midgut and hindgut.

CONCLUSIONS: This transcriptome provides a wealth of data about the species' defense against chemical and biological threats, has uncovered several potentially new species of microbial symbionts, and significantly expands our knowledge about this pest.}, } @article {pmid31816621, year = {2020}, author = {Paul, AA and Hoffman, KL and Hagan, JL and Sampath, V and Petrosino, JF and Pammi, M}, title = {Fungal cutaneous microbiome and host determinants in preterm and term neonates.}, journal = {Pediatric research}, volume = {88}, number = {2}, pages = {225-233}, pmid = {31816621}, issn = {1530-0447}, mesh = {Anti-Bacterial Agents/pharmacology ; CARD Signaling Adaptor Proteins/genetics ; Female ; Fungi/classification ; Genotype ; Humans ; Infant, Premature ; *Intensive Care Units, Neonatal ; Intensive Care, Neonatal ; Longitudinal Studies ; Male ; *Microbiota ; *Mycobiome ; NLR Family, Pyrin Domain-Containing 3 Protein/genetics ; Neoplasm Proteins/genetics ; Nod2 Signaling Adaptor Protein/genetics ; Polymorphism, Single Nucleotide ; Prospective Studies ; Skin/metabolism/*microbiology ; Toll-Like Receptor 4/genetics ; }, abstract = {BACKGROUND: The neonatal cutaneous mycobiome has not been characterized in preterm infants. Invasive fungal infections in preterm neonates are associated with high mortality. The immaturity of the preterm skin predisposes neonates to invasive infection by skin colonizers. We report the clinical and host determinants that influence the skin mycobiome.

METHODS: Skin swabs from the antecubital fossa, forehead, and gluteal region of 15 preterm and 15 term neonates were obtained during the first 5 weeks of life. The mycobiome was sequenced using the conserved pan-fungal ITS2 region. Blood samples were used to genotype immune modulating genes. Clinical metadata was collected to determine the clinical predictors of the abundance and diversity of the skin mycobiome.

RESULTS: The neonatal mycobiome is characterized by few taxa. Alpha diversity of the mycobiome is influenced by antibiotic exposure, the forehead body site, and the neonatal intensive care unit (NICU) environment. Beta diversity varies with mode of delivery, diet, and body site. The host determinants of the cutaneous microbiome include single-nucleotide polymorphisms in TLR4, NLRP3,CARD8, and NOD2.

CONCLUSION: The neonatal cutaneous mycobiome is composed of few genera and is influenced by clinical factors and host genetics, the understanding of which will inform preventive strategies against invasive fungal infections.}, } @article {pmid31815740, year = {2020}, author = {Zhao, L and Yang, W and Chen, Y and Huang, F and Lu, L and Lin, C and Huang, T and Ning, Z and Zhai, L and Zhong, LL and Lam, W and Yang, Z and Zhang, X and Cheng, C and Han, L and Qiu, Q and Shang, X and Huang, R and Xiao, H and Ren, Z and Chen, D and Sun, S and El-Nezami, H and Cai, Z and Lu, A and Fang, X and Jia, W and Bian, Z}, title = {A Clostridia-rich microbiota enhances bile acid excretion in diarrhea-predominant irritable bowel syndrome.}, journal = {The Journal of clinical investigation}, volume = {130}, number = {1}, pages = {438-450}, pmid = {31815740}, issn = {1558-8238}, mesh = {Adolescent ; Adult ; Aged ; Bile Acids and Salts/*metabolism ; Clostridium/*metabolism ; *Diarrhea/metabolism/microbiology/pathology ; Female ; *Gastrointestinal Microbiome ; Humans ; *Irritable Bowel Syndrome/metabolism/microbiology/pathology ; Male ; Middle Aged ; }, abstract = {An excess of fecal bile acids (BAs) is thought to be one of the mechanisms for diarrhea-predominant irritable bowel syndrome (IBS-D). However, the factors causing excessive BA excretion remain incompletely studied. Given the importance of gut microbiota in BA metabolism, we hypothesized that gut dysbiosis might contribute to excessive BA excretion in IBS-D. By performing BA-related metabolic and metagenomic analyses in 290 IBS-D patients and 89 healthy volunteers, we found that 24.5% of IBS-D patients exhibited excessive excretion of total BAs and alteration of BA-transforming bacteria in feces. Notably, the increase in Clostridia bacteria (e.g., C. scindens) was positively associated with the levels of fecal BAs and serum 7α-hydroxy-4-cholesten-3-one (C4), but negatively correlated with serum fibroblast growth factor 19 (FGF19) concentration. Furthermore, colonization with Clostridia-rich IBS-D fecal microbiota or C. scindens individually enhanced serum C4 and hepatic conjugated BAs but reduced ileal FGF19 expression in mice. Inhibition of Clostridium species with vancomycin yielded opposite results. Clostridia-derived BAs suppressed the intestinal FGF19 expression in vitro and in vivo. In conclusion, this study demonstrates that the Clostridia-rich microbiota contributes to excessive BA excretion in IBS-D patients, which provides a mechanistic hypothesis with testable clinical implications.}, } @article {pmid31812384, year = {2020}, author = {Hidalgo, KJ and Teramoto, EH and Soriano, AU and Valoni, E and Baessa, MP and Richnow, HH and Vogt, C and Chang, HK and Oliveira, VM}, title = {Taxonomic and functional diversity of the microbiome in a jet fuel contaminated site as revealed by combined application of in situ microcosms with metagenomic analysis.}, journal = {The Science of the total environment}, volume = {708}, number = {}, pages = {135152}, doi = {10.1016/j.scitotenv.2019.135152}, pmid = {31812384}, issn = {1879-1026}, mesh = {Biodegradation, Environmental ; Hydrocarbons ; *Metagenome ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {Natural attenuation represents all processes that govern contaminant mass removal, which mainly occurs via microbial degradation in the environment. Although this process is intrinsic its rate and efficiency depend on multiple factors. This study aimed to characterize the microbial taxonomic and functional diversity in different aquifer sediments collected in the saturated zone and in situ microcosms (BACTRAP®s) amended with hydrocarbons ([13]C-labeled and non-labeled benzene, toluene and naphthalene) using 16S rRNA gene and "shotgun" Illumina high throughput sequencing at a jet-fuel contaminated site. The BACTRAP®s were installed to assess hydrocarbon metabolism by native bacteria. Results indicated that Proteobacteria, Actinobacteria and Firmicutes were the most dominant phyla (~98%) in the aquifer sediment samples. Meanwhile, in the benzene- and toluene-amended BACTRAP®s the phyla Firmicutes and Proteobacteria accounted for about 90% of total community. In the naphthalene-amended BACTRAP®, members of the SR-FBR-L83 family (Order Ignavibacteriales) accounted for almost 80% of bacterial community. Functional annotation of metagenomes showed that only the sediment sample located at the source zone border and with the lowest BTEX concentration, has metabolic potential to degrade hydrocarbons aerobically. On the other hand, in situ BACTRAP®s allowed enrichment of hydrocarbon-degrading bacteria. Metagenomic data suggest that fumarate addition is the main mechanism for hydrocarbon activation of toluene. Also, indications for methylation, hydroxylation and carboxylation as activation mechanisms for benzene anaerobic conversion were found. After 120 days of exposure in the contaminated groundwater, the isotopic analysis of fatty acids extracted from BACTRAP®s demonstrated the assimilation of isotopic labeled compounds in the cells of microbes expressed by strong isotopic enrichment. We propose that the microbiota in this jet-fuel contaminated site has metabolic potential to degrade benzene and toluene by a syntrophic process, between members of the families Geobacteraceae and Peptococcaceae (genus Pelotomaculum), coupled to nitrate, iron and/or sulfate reduction.}, } @article {pmid31811045, year = {2020}, author = {Chen, J and Wang, Q and Hao, Z and Li, Z and Sahu, SK and Liu, H and Xiao, L}, title = {Relationship between the Gut Microbiome and Energy/Nutrient Intake in a Confined Bioregenerative Life Support System.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {4}, pages = {}, pmid = {31811045}, issn = {1098-5336}, mesh = {Adult ; China ; *Energy Intake ; Female ; *Gastrointestinal Microbiome ; Genome-Wide Association Study ; Humans ; *Life Support Systems ; Male ; *Metagenome ; *Nutritional Status ; Young Adult ; }, abstract = {Recent studies have suggested that the gut microbiome is modified in space analogs and that human health can be affected during actual spaceflight. However, the relationship between the gut microbiome and dietary intake in simulator subjects and astronauts remains unclear. Bioregenerative life support systems (BLSSs) are confined and self-sufficient ecosystems that enable exploration of this issue. Here, we correlate changes in gut microbes to the nutrient types present in controlled diets within subjects cohabitating in a BLSS. A metagenome-wide association study (MWAS) was performed on 55 shotgun-sequenced fecal samples longitudinally obtained from healthy Chinese subjects (n = 4 in total, n = 2 per sex) subjected to a 60-day BLSS stay and a specialized diet. Each food item was categorized based on nutrient type according to the Chinese Food Ingredients List (https://wenku.baidu.com/view/3f2b628488eb172ded630b1c59eef8c75fbf9514.html?from=search). The physical parameters of each subject fluctuated within normal medical ranges. Sex- and individual-specific differences and a trend of individual convergence of the gut microbiome in the BLSS were observed. Depletion of bacterial taxa such as Faecalibacterium prausnitzii, Bifidobacterium longum, and Escherichia coli and functional modules such as short-chain fatty acid (SCFA) production, as well as an increase in an unidentified Lachnospiraceae and glutamate/tryptophan synthesis, were observed in the BLSS. Correlation analysis showed that these compositional and functional changes were associated with energy/nutrient intake during the BLSS stay. Our findings suggest that the gut microbiota is a useful indicator for monitoring health and that individual nutritive diets should be considered according to sex and individual differences in simulations or in spaceflight.IMPORTANCE The gut microbiome shows individual specificity and is affected by sex, environment, and diet; gut microbiome imbalance is related to cancer, cardiovascular diseases, and autoimmune diseases. Astronauts are faced with a challenging environment and limited diet in outer space. Recent studies indicate that the gut microbiome is altered in space simulators and space, but what happens to intestinal microorganisms when astronauts cohabitate in a self-sufficient ecosystem in which they plant and cook food is unclear. Bioregenerative life support systems (BLSSs) are ideal devices to investigate the above issues because they are closed and self-sufficient. Four healthy Chinese subjects cohabitated in a confined BLSS for 60 days, during which their physical parameters and energy/nutrient intake were recorded. We performed a metagenome-wide association study (MWAS) on 55 shotgun-sequenced fecal samples longitudinally obtained from the subjects. Alterations occurred in the gut microbial composition and function, and their relationships with energy/nutrient intake were explored.}, } @article {pmid31810497, year = {2019}, author = {Zhang, X and Li, L and Butcher, J and Stintzi, A and Figeys, D}, title = {Advancing functional and translational microbiome research using meta-omics approaches.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {154}, pmid = {31810497}, issn = {2049-2618}, mesh = {Gastrointestinal Microbiome/*drug effects/*physiology ; Host Microbial Interactions ; Humans ; Metabolomics/*methods ; Metagenomics/*methods ; Precision Medicine/*methods ; Proteomics/*methods ; }, abstract = {The gut microbiome has emerged as an important factor affecting human health and disease. The recent development of -omics approaches, including phylogenetic marker-based microbiome profiling, shotgun metagenomics, metatranscriptomics, metaproteomics, and metabolomics, has enabled efficient characterization of microbial communities. These techniques can provide strain-level taxonomic resolution of the taxa present in microbiomes, assess the potential functions encoded by the microbial community and quantify the metabolic activities occurring within a complex microbiome. The application of these meta-omics approaches to clinical samples has identified microbial species, metabolic pathways, and metabolites that are associated with the development and treatment of human diseases. These findings have further facilitated microbiome-targeted drug discovery and efforts to improve human health management. Recent in vitro and in vivo investigations have uncovered the presence of extensive drug-microbiome interactions. These interactions have also been shown to be important contributors to the disparate patient responses to treatment that are often observed during disease therapy. Therefore, developing techniques or frameworks that enable rapid screening, detailed evaluation, and accurate prediction of drug/host-microbiome interactions is critically important in the modern era of microbiome research and precision medicine. Here we review the current status of meta-omics techniques, including integrative multi-omics approaches, for characterizing the microbiome's functionality in the context of health and disease. We also summarize and discuss new frameworks for applying meta-omics approaches and microbiome assays to study drug-microbiome interactions. Lastly, we discuss and exemplify strategies for implementing microbiome-based precision medicines using these meta-omics approaches and high throughput microbiome assays.}, } @article {pmid31809634, year = {2020}, author = {Mack, A and Bobardt, JS and Haß, A and Nichols, KB and Schmid, RM and Stein-Thoeringer, CK}, title = {Changes in gut microbial metagenomic pathways associated with clinical outcomes after the elimination of malabsorbed sugars in an IBS cohort.}, journal = {Gut microbes}, volume = {11}, number = {3}, pages = {620-631}, pmid = {31809634}, issn = {1949-0984}, support = {P30 CA008748/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Cohort Studies ; DNA, Bacterial ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Irritable Bowel Syndrome/*diet therapy/metabolism/*microbiology ; Malabsorption Syndromes/*diet therapy/metabolism/*microbiology ; Male ; Metabolic Networks and Pathways/*genetics ; Metagenome ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S ; Sugars/metabolism/*therapeutic use ; }, abstract = {Specific diets to manage sugar malabsorption are reported to reduce clinical symptoms of irritable bowel syndrome (IBS). However, the effects of diets for malabsorbed sugars on gut microbiota signatures have not been studied, and associations with clinical outcomes in IBS have not been characterized. 22 IBS patients positively tested for either lactose-, fructose-, sorbitol- or combined malabsorptions were subjected to 2-weeks sugar elimination and subsequent 4-weeks re-introduction. 7 IBS patients tested negative for sugar malabsorption were used as controls. Nutrition and clinical symptoms were recorded throughout the study. Fecal samples were serially collected for 16S rRNA amplicon and shotgun-metagenome sequencing. Dietary intervention supervised by nutrition counseling reduced IBS symptoms during the elimination and tolerance phases. Varying clinical response rates were observed between subjects, and used to dichotomize our cohort into visual analogue scale (VAS) responders and non-responders. Alpha -and beta-diversity analyzes revealed only minor differences regarding 16S rRNA-based fecal microbiota compositions between responder and non-responder patients during baseline or tolerance phase. In shotgun-metagenome analyzes, however, we analyzed microbial metabolic pathways and found significant differences in pathways encoding starch degradation and complex amino acid biosynthesis at baseline between IBS controls and malabsorbers, and notably, between diet responder and non-responders. Faecalibacterium prausnitzii, Ruminococcus spp. and Bifidobacterium longum largely informed these metabolic pathways. Our study demonstrates that diet interventions for specific, malabsorbed carbohydrates reshaped the metagenomic composition of the gut microbiota, with a small community of bacterial taxa contributing to these changes rather than a single species.}, } @article {pmid31808296, year = {2020}, author = {Zhang, Q and Geng, Z and Li, D and Ding, Z}, title = {Characterization and discrimination of microbial community and co-occurrence patterns in fresh and strong flavor style flue-cured tobacco leaves.}, journal = {MicrobiologyOpen}, volume = {9}, number = {2}, pages = {e965}, pmid = {31808296}, issn = {2045-8827}, mesh = {Biodiversity ; Eukaryotic Cells/classification ; *Fermentation ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; *Microbiota ; Neural Networks, Computer ; Phylogeny ; Plant Leaves/*microbiology ; Prokaryotic Cells/classification ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; *Nicotiana ; }, abstract = {Fermentation, also known as aging, is vital for enhancing the quality of flue-cured tobacco leaves (FTLs). Aged FTLs demonstrate high-quality sensory characteristics, while unaged FTLs do not. Microbes play important roles in the FTL fermentation process. However, the eukaryotic microbial community diversity is poorly understood, as are microbial associations within FTLs. We aimed to characterize and compare the microbiota associated with two important categories, fresh and strong flavor style FTLs, and to reveal correlations between the microbial taxa within them. Based on 16S and 18S rRNA Illumina MiSeq sequencing, the community richness and diversity of prokaryotes were almost as high as that of eukaryotes. The dominant microbes of FTLs belonged to seven genera, including Pseudomonas, Bacillus, Methylobacterium, Acinetobacter, Sphingomonas, Neophaeosphaeria, and Cladosporium, of the Proteobacteria, Firmicutes, and Ascomycota phyla. According to partial least square discriminant analysis (PLS-DA), Xanthomonas, Franconibacter, Massilia, Quadrisphaera, Staphylococcus, Cladosporium, Lodderomyces, Symmetrospora, Golovinomyces, and Dioszegia were significantly positively correlated with fresh flavor style FTLs, while Xenophilus, Fusarium, unclassified Ustilaginaceae, Tilletiopsis, Cryphonectria, Colletotrichum, and Cyanodermella were significantly positively correlated with strong flavor style FTLs. Network analysis identified seven hubs, Aureimonas, Kocuria, Massilia, Brachybacterium, Clostridium, Dietzia, and Vishniacozyma, that may play important roles in FTL ecosystem stability, which may be destroyed by Myrmecridium. FTL microbiota was found to be correlated with flavor style. Species present in lower numbers than the dominant microbes might be used as microbial markers to discriminate different flavor style samples and to stabilize FTL microbial communities. This research advances our understanding of FTL microbiota and describes a means of discriminating between fresh and strong flavor FTLs based on their respective stable microbiota.}, } @article {pmid31806458, year = {2020}, author = {Han, L and Liu, Y and Fang, K and Zhang, X and Liu, T and Wang, F and Wang, X}, title = {Azoxystrobin dissipation and its effect on soil microbial community structure and function in the presence of chlorothalonil, chlortetracycline and ciprofloxacin.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {257}, number = {}, pages = {113578}, doi = {10.1016/j.envpol.2019.113578}, pmid = {31806458}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*metabolism ; Chlortetracycline/metabolism/*pharmacology ; Ciprofloxacin/metabolism/*pharmacology ; Manure ; Microbiota/*drug effects ; Nitriles/metabolism/*pharmacology ; Pyrimidines ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/*analysis ; Strobilurins ; }, abstract = {The residual characteristics and the adsorption-desorption behaviors of azoxystrobin (AZO) as well as the soil ecological effects in the individual repeated treatments of AZO and its combination with chlorothalonil (CTL), chlortetracycline (CTC) and ciprofloxacin (CIP) were systematically studied in organic manure (OM)-amended soil under laboratory conditions. The presence of CTL, CTC, and CIP, both individually and combined, decreased the sorption affinity of AZO with the Freundlich adsorption and desorption coefficient decreasing by 0.3-24.2%, and CTC and CIP exhibited greater adverse effects than CTL. AZO dissipated slowly and the residues significantly accumulated during ten repeated treatments. The dissipation of AZO was inhibited to different degrees in the combined treatments. Biolog analysis revealed that the soil microbial functional diversity in the OM-soil + AZO and OM-soil + AZO + CTL treatments was higher than that in the OM-soil treatment during the former three repeated treatments, but which was inhibited during the latter seven repeated treatments. The soil microbial functional diversity in the OM-soil + AZO + CTC, OM-soil + AZO + CIP and OM-soil + AZO + CTL + CTC + CIP treatments was inhibited during the ten repeated treatments compared with OM-soil treatment. Metagenomic results showed that all repeated treatments significantly increased the relative abundance of Actinobacteria, but significantly decreased that of Proteobacteria and Firmicutes during the ten repeated treatments. Furthermore, the relative abundance of soil dominant bacterial genera Rhodococcus, Mycobacterium and Arthrobacter in all the repeated treatments significantly increased by 1.5-1283.9% compared with the OM-soil treatment. It is concluded that coexistence of CTL, CTC and CIP, both individually and combined, with AZO can inhibit the dissipation of AZO, reduce the adsorption affinity of AZO on soil, and alter the soil microbial community structure and functional diversity.}, } @article {pmid31806420, year = {2020}, author = {Zhou, C and Zhao, H and Xiao, XY and Chen, BD and Guo, RJ and Wang, Q and Chen, H and Zhao, LD and Zhang, CC and Jiao, YH and Ju, YM and Yang, HX and Fei, YY and Wang, L and Shen, M and Li, H and Wang, XH and Lu, X and Yang, B and Liu, JJ and Li, J and Peng, LY and Zheng, WJ and Zhang, CY and Zhou, JX and Wu, QJ and Yang, YJ and Su, JM and Shi, Q and Wu, D and Zhang, W and Zhang, FC and Jia, HJ and Liu, DP and Jie, ZY and Zhang, X}, title = {Metagenomic profiling of the pro-inflammatory gut microbiota in ankylosing spondylitis.}, journal = {Journal of autoimmunity}, volume = {107}, number = {}, pages = {102360}, doi = {10.1016/j.jaut.2019.102360}, pmid = {31806420}, issn = {1095-9157}, mesh = {Autoimmunity ; Case-Control Studies ; Disease Susceptibility ; Dysbiosis ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions/immunology ; Humans ; Inflammation Mediators/*metabolism ; *Metagenome ; *Metagenomics/methods ; Spondylitis, Ankylosing/*etiology/*metabolism/pathology ; }, abstract = {OBJECTIVE: Gut dysbiosis has been reported implicated in ankylosing spondylitis (AS), a common chronic inflammatory disease mainly affects sacroiliac joints and spine. Utilizing deep sequencing on the feces of untreated AS patients, our study aimed at providing an in-depth understanding of AS gut microbiota.

METHODS: We analyzed the fecal metagenome of 85 untreated AS patients and 62 healthy controls by metagenomic shotgun sequencing, and 23 post-treatment feces of those AS patients were collected for comparison. Comparative analyses among different cohorts including AS, rheumatoid arthritis and Behcet's disease were performed to uncover some common signatures related to inflammatory arthritis. Molecular mimicry of a microbial peptide was also demonstrated by ELISpot assay.

RESULTS: We identified AS-enriched species including Bacteroides coprophilus, Parabacteroides distasonis, Eubacterium siraeum, Acidaminococcus fermentans and Prevotella copri. Pathway analysis revealed increased oxidative phosphorylation, lipopolysaccharide biosynthesis and glycosaminoglycan degradation in AS gut microbiota. Microbial signatures of AS gut selected by random forest model showed high distinguishing accuracy. Some common signatures related to autoimmunity, such as Bacteroides fragilis and type III secretion system (T3SS), were also found. Finally, in vitro experiments demonstrated an increased amount of IFN-γ producing cells triggered by a bacterial peptide of AS-enriched species, mimicking type II collagen.

CONCLUSIONS: These findings collectively indicate that gut microbiota was perturbed in untreated AS patients with diagnostic potential, and some AS-enriched species might be triggers of autoimmunity by molecular mimicry. Additionally, different inflammatory arthritis shared some common microbial signatures.}, } @article {pmid31806002, year = {2019}, author = {Yeoh, YK and Chan, MH and Chen, Z and Lam, EWH and Wong, PY and Ngai, CM and Chan, PKS and Hui, M}, title = {The human oral cavity microbiota composition during acute tonsillitis: a cross-sectional survey.}, journal = {BMC oral health}, volume = {19}, number = {1}, pages = {275}, pmid = {31806002}, issn = {1472-6831}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Case-Control Studies ; Cross-Sectional Studies ; Female ; Genome, Bacterial/genetics ; Humans ; Male ; Metagenome/*genetics ; *Microbiota ; Mouth/*microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA ; Surveys and Questionnaires ; Tonsillitis/diagnosis/*microbiology ; }, abstract = {BACKGROUND: Microbial culture-based investigations of inflamed tonsil tissues have previously indicated enrichment of several microorganisms such as Streptococcus, Staphylococcus and Prevotella. These taxa were also largely reflected in DNA sequencing studies performed using tissue material. In comparison, less is known about the response of the overall oral cavity microbiota to acute tonsillitis despite their role in human health and evidence showing that their compositions are correlated with diseases such as oral cancers. In addition, the influence of subject-specific circumstances including consumption of prescription antibiotics and smoking habits on the microbiology of acute tonsillitis is unknown.

METHODS: We collected oral rinse samples from 43 individuals admitted into hospital for acute tonsillitis and 165 non-disease volunteers recruited from the public, and compared their microbial community compositions using 16S rRNA gene sequencing. We assessed the impact of tonsillitis, whether subjects were prescribed antibiotics, the presence of oral abscesses and their smoking habits on community composition, and identified specific microbial taxa associated with tonsillitis and smoking.

RESULTS: Oral rinse community composition was primarily associated with disease state (tonsillitis vs non-tonsillitis) although its effect was subtle, followed by smoking habit. Multiple Prevotella taxa were enriched in tonsillitis subjects compared to the non-tonsillitis cohort, whereas the non-tonsillitis cohort primarily showed associations with several Neisseria sequence variants. The presence of oral abscesses did not significantly influence community composition. Antibiotics were prescribed to a subset of individuals in the tonsillitis cohort but we did not observe differences in community composition associated with antibiotics consumption. In both tonsillitis and non-tonsillitis cohorts, smoking habit was associated with enrichment of several Fusobacterium variants.

CONCLUSIONS: These findings show that the oral cavity microbial community is altered during acute tonsillitis, with a consistent enrichment of Prevotella during tonsillitis raising the possibility of targeted interventions. It also supports the possible link between smoking, Fusobacteria and oral cancers.}, } @article {pmid31802337, year = {2020}, author = {Cleary, DFR and Polónia, ARM and Huang, YM and Swierts, T}, title = {Compositional variation between high and low prokaryotic diversity coral reef biotopes translates to different predicted metagenomic gene content.}, journal = {Antonie van Leeuwenhoek}, volume = {113}, number = {4}, pages = {563-587}, doi = {10.1007/s10482-019-01364-7}, pmid = {31802337}, issn = {1572-9699}, support = {PTDC/AAC-AMB/115304/2009//Fundação para a Ciência e a Tecnologia/ ; SFRH/BPD/117563/2016//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {Animals ; Bacteria/*classification/*genetics ; *Coral Reefs ; Invertebrates/*microbiology ; Metagenomics ; Species Specificity ; }, abstract = {In a previous study, we identified host species that housed high and low diversity prokaryotic communities. In the present study, we expand on this and assessed the prokaryotic communities associated with seawater, sediment and 11 host species from 7 different phyla in a Taiwanese coral reef setting. The host taxa sampled included hard, octo- and black corals, molluscs, bryozoans, flatworms, fish and sea urchins. There were highly significant differences in composition among host species and all host species housed distinct communities from those found in seawater and sediment. In a hierarchical clustering analysis, samples from all host species, with the exception of the coral Galaxea astreata, formed significantly supported clusters. In addition to this, the coral G. astreata and the bryozoan Triphyllozoon inornatum on the one hand and the coral Tubastraea coccinea, the hermit crab Calcinus laevimanus and the flatworm Thysanozoon nigropapillosum on the other formed significantly supported clusters. In addition to composition, there were highly pronounced differences in richness and evenness among host species from the most diverse species, the bryozoan T. inornatum at 2518 ± 240 OTUs per 10,000 sequences to the least diverse species, the octocoral Cladiella sp. at 142 ± 14 OTUs per 10,000 sequences. In line with the differences in composition, there were significant differences in predicted metagenomic gene counts among host species. Furthermore, there were pronounced compositional and predicted functional differences between high diversity hosts (Liolophura japonica, G. astreata, T. coccinea, C. laevimanus, T. inornatum) and low diversity hosts (Antipathes sp., Pomacentrus coelestis, Modiolus auriculatus, T. nigropapillosum, Cladiella sp. and Diadema savigny). In particular, we found that all tested low diversity hosts were predicted to be enriched for the phosphotransferase system compared to high diversity hosts.}, } @article {pmid31800638, year = {2019}, author = {Choi, S and Lee, JG and Lee, AR and Eun, CS and Han, DS and Park, CH}, title = {Helicobacter pylori antibody and pepsinogen testing for predicting gastric microbiome abundance.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0225961}, pmid = {31800638}, issn = {1932-6203}, mesh = {Adult ; Antibodies, Bacterial/*immunology ; Bacterial Load ; Comorbidity ; Female ; Helicobacter Infections/diagnosis/*immunology/*metabolism/*microbiology ; Helicobacter pylori/*immunology ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Pepsinogen A/*metabolism ; Prognosis ; Serologic Tests ; Stomach Neoplasms/etiology ; }, abstract = {BACKGROUND: Although the high-throughput sequencing technique is useful for evaluating gastric microbiome, it is difficult to use clinically. We aimed to develop a predictive model for gastric microbiome based on serologic testing.

METHODS: This study was designed to analyze sequencing data obtained from the Hanyang University Gastric Microbiome Cohort, which was established initially to investigate gastric microbial composition according to the intragastric environment. We evaluated the relationship between the relative abundance of potential gastric cancer-associated bacteria (nitrosating/nitrate-reducing bacteria or type IV secretion system [T4SS] protein gene-contributing bacteria) and serologic markers (IgG anti-Helicobacter pylori [HP] antibody or pepsinogen [PG] levels).

RESULTS: We included 57 and 26 participants without and with HP infection, respectively. The relative abundance of nitrosating/nitrate-reducing bacteria was 4.9% and 3.6% in the HP-negative and HP-positive groups, respectively, while that of T4SS protein gene-contributing bacteria was 20.5% and 6.5% in the HP-negative and HP-positive groups, respectively. The relative abundance of both nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria increased exponentially as PG levels decreased. Advanced age (only for nitrosating/nitrate-reducing bacteria), a negative result of IgG anti-HP antibody, low PG levels, and high Charlson comorbidity index were associated with a high relative abundance of nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria. The adjusted coefficient of determination (R2) was 53.7% and 70.0% in the model for nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria, respectively.

CONCLUSION: Not only the negative results of IgG anti-HP antibody but also low PG levels were associated with a high abundance of nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria.}, } @article {pmid31798840, year = {2019}, author = {Bich, VTN and Thanh, LV and Thai, PD and Van Phuong, TT and Oomen, M and Driessen, C and Beuken, E and Hoang, TH and van Doorn, HR and Penders, J and Wertheim, HFL}, title = {An exploration of the gut and environmental resistome in a community in northern Vietnam in relation to antibiotic use.}, journal = {Antimicrobial resistance and infection control}, volume = {8}, number = {}, pages = {194}, pmid = {31798840}, issn = {2047-2994}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Adult ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/genetics ; Child ; Child, Preschool ; Drug Resistance, Multiple, Bacterial/*genetics ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; *Genes, Bacterial ; Humans ; Infant ; Infant, Newborn ; Longitudinal Studies ; Male ; Metagenomics ; Middle Aged ; Pets/microbiology ; Prospective Studies ; Vietnam ; Young Adult ; }, abstract = {BACKGROUND: Antibiotic resistance is a major global public health threat. Antibiotic use can directly impact the antibiotic resistant genes (ARGs) profile of the human intestinal microbiome and consequently the environment through shedding.

METHODS: We determined the resistome of human feces, animal stools, human food and environmental (rain, well, and irrigative water) samples (n = 304) in 40 households within a community cohort and related the data to antibiotic consumption. Metagenomic DNA was isolated and qPCR was used to determine presence of mobile colistin resistance (mcr) genes, genes encoding extended-spectrum β-lactamases (ESBL), carbapenemases and quinolone resistance genes.

RESULTS: Nearly 40 % (39.5%, 120/304) of samples contained ESBL genes (most frequent were CTX-M-9 (23.7% [72/304]), CTX-M-1 (18.8% [57/304]). Quinolone resistance genes (qnrS) were detected in all human and 91% (41/45) of animal stool samples. Mcr-1 and mcr-3 were predominantly detected in human feces at 88% (82/93) and 55% (51/93) and animal feces at 93% (42/45) and 51% (23/45), respectively. Mcr-2, mrc-4 and mcr-5 were not detected in human feces, and only sporadically (< 6%) in other samples. Carbapenemase-encoding genes were most common in water (15% [14/91]) and cooked food (13% [10/75]) samples, while their prevalence in human and animal stools was lower at 4% in both human (4/93) and animal (2/45) samples. We did not find an association between recent antibiotic consumption and ARGs in human stools. Principal component analysis showed that the resistome differs between ecosystems with a strong separation of ARGs profiles of human and animal stools on the one hand versus cooked food and water samples on the other.

CONCLUSIONS: Our study indicated that ARGs were abundant in human and animal stools in a rural Vietnamese community, including ARGs targeting last resort antibiotics. The resistomes of animal and human stools were similar as opposed to the resistomes from water and food sources. No association between antibiotic use and ARG profiles was found in a setting of high background rates of AMR.}, } @article {pmid31797927, year = {2019}, author = {Magruder, M and Sholi, AN and Gong, C and Zhang, L and Edusei, E and Huang, J and Albakry, S and Satlin, MJ and Westblade, LF and Crawford, C and Dadhania, DM and Lubetzky, M and Taur, Y and Littman, E and Ling, L and Burnham, P and De Vlaminck, I and Pamer, E and Suthanthiran, M and Lee, JR}, title = {Gut uropathogen abundance is a risk factor for development of bacteriuria and urinary tract infection.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {5521}, pmid = {31797927}, issn = {2041-1723}, support = {DP2 AI138242/AI/NIAID NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; R21 AI133331/AI/NIAID NIH HHS/United States ; UL1 TR002384/TR/NCATS NIH HHS/United States ; K23 AI124464/AI/NIAID NIH HHS/United States ; R37 AI051652/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics ; Bacterial Infections/*microbiology ; Bacteriuria/etiology/microbiology/urine ; DNA, Bacterial/analysis/*genetics ; Escherichia coli Infections/etiology/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/genetics ; Humans ; Kidney Transplantation/adverse effects/methods ; RNA, Ribosomal, 16S/*genetics ; Risk Factors ; Urinary Tract Infections/etiology/*microbiology/urine ; }, abstract = {The origin of most bacterial infections in the urinary tract is often presumed to be the gut. Herein, we investigate the relationship between the gut microbiota and future development of bacteriuria and urinary tract infection (UTI). We perform gut microbial profiling using 16S rRNA gene deep sequencing on 510 fecal specimens from 168 kidney transplant recipients and metagenomic sequencing on a subset of fecal specimens and urine supernatant specimens. We report that a 1% relative gut abundance of Escherichia is an independent risk factor for Escherichia bacteriuria and UTI and a 1% relative gut abundance of Enterococcus is an independent risk factor for Enterococcus bacteriuria. Strain analysis establishes a close strain level alignment between species found in the gut and in the urine in the same subjects. Our results support a gut microbiota-UTI axis, suggesting that modulating the gut microbiota may be a potential novel strategy to prevent UTIs.}, } @article {pmid31797586, year = {2020}, author = {Khan, S and Kelly, L}, title = {Multiclass Disease Classification from Microbial Whole-Community Metagenomes.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {25}, number = {}, pages = {55-66}, pmid = {31797586}, issn = {2335-6936}, support = {T32 AI070117/AI/NIAID NIH HHS/United States ; T32 GM007288/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology ; Humans ; Machine Learning ; *Metagenome ; *Microbiota/genetics ; Phylogeny ; }, abstract = {The microbiome, the community of microorganisms living within an individual, is a promising avenue for developing non-invasive methods for disease screening and diagnosis. Here, we utilize 5643 aggregated, annotated whole-community metagenomes to implement the first multiclass microbiome disease classifier of this scale, able to discriminate between 18 different diseases and healthy. We compared three different machine learning models: random forests, deep neural nets, and a novel graph convolutional architecture which exploits the graph structure of phylogenetic trees as its input. We show that the graph convolutional model outperforms deep neural nets in terms of accuracy (achieving 75% average test-set accuracy), receiver-operator-characteristics (92.1% average area-under-ROC (AUC)), and precision-recall (50% average area-under-precision-recall (AUPR)). Additionally, the convolutional net's performance complements that of the random forest, showing a lower propensity for Type-I errors (false-positives) while the random forest makes less Type-II errors (false-negatives). Lastly, we are able to achieve over 90% average top-3 accuracy across all of our models. Together, these results indicate that there are predictive, disease-specific signatures across microbiomes that can be used for diagnostic purposes.}, } @article {pmid31795935, year = {2019}, author = {Raj, G and Shadab, M and Deka, S and Das, M and Baruah, J and Bharali, R and Talukdar, NC}, title = {Seed interior microbiome of rice genotypes indigenous to three agroecosystems of Indo-Burma biodiversity hotspot.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {924}, pmid = {31795935}, issn = {1471-2164}, mesh = {Agriculture ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Biodiversity ; Ecosystem ; Genotype ; India ; Metabolic Networks and Pathways ; *Microbiota ; Myanmar ; Oryza/genetics/*microbiology ; Phenotype ; Seeds/microbiology ; }, abstract = {BACKGROUND: Seeds of plants are a confirmation of their next generation and come associated with a unique microbia community. Vertical transmission of this microbiota signifies the importance of these organisms for a healthy seedling and thus a healthier next generation for both symbionts. Seed endophytic bacterial community composition is guided by plant genotype and many environmental factors. In north-east India, within a narrow geographical region, several indigenous rice genotypes are cultivated across broad agroecosystems having standing water in fields ranging from 0-2 m during their peak growth stage. Here we tried to trap the effect of rice genotypes and agroecosystems where they are cultivated on the rice seed microbiota. We used culturable and metagenomics approaches to explore the seed endophytic bacterial diversity of seven rice genotypes (8 replicate hills) grown across three agroecosystems.

RESULTS: From seven growth media, 16 different species of culturable EB were isolated. A predictive metabolic pathway analysis of the EB showed the presence of many plant growth promoting traits such as siroheme synthesis, nitrate reduction, phosphate acquisition, etc. Vitamin B12 biosynthesis restricted to bacteria and archaea; pathways were also detected in the EB of two landraces. Analysis of 522,134 filtered metagenomic sequencing reads obtained from seed samples (n=56) gave 4061 OTUs. Alpha diversity indices showed significant differences in observed OTU richness (P≤0.05) across genotypes. Significant differences were also found between the individual hills of a rice genotype. PCoA analysis exhibited three separate clusters and revealed the clusters separated based on genotype, while agroecosystem showed a minimal effect on the variation of seed microbiota (adonis, R[2]=0.07, P=0.024). Interestingly, animal gut resident bacteria such as Bifidobacterium, Faecalibacterium, Lactobacillus, etc. were found in abundance as members of the seed microbiota.

CONCLUSION: Overall, our study demonstrates, indigenous rice genotypes of north-east India have a unique blend of endophytic bacteria in their mature seeds. While there are notable variations among plants of the same genotype, we found similarities among genotypes cultivated in completely different environmental conditions. The beta diversity variations across the seven rice genotypes were significantly shaped by their genotype rather than their agroecosystems.}, } @article {pmid31793979, year = {2020}, author = {Jing, G and Zhang, Y and Yang, M and Liu, L and Xu, J and Su, X}, title = {Dynamic Meta-Storms enables comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {7}, pages = {2308-2310}, doi = {10.1093/bioinformatics/btz910}, pmid = {31793979}, issn = {1367-4811}, mesh = {Algorithms ; Biological Evolution ; *Metagenome ; *Microbiota ; Phylogeny ; }, abstract = {MOTIVATION: An accurate and reliable distance (or dissimilarity) among shotgun metagenomes is fundamental to deducing the beta-diversity of microbiomes. To compute the distance at the species level, current methods either ignore the evolutionary relationship among species or fail to account for unclassified organisms that cannot be mapped to definite tip nodes in the phylogenic tree, thus can produce erroneous beta-diversity pattern.

RESULTS: To solve these problems, we propose the Dynamic Meta-Storms (DMS) algorithm to enable the comprehensive comparison of metagenomes on the species level with both taxonomy and phylogeny profiles. It compares the identified species of metagenomes with phylogeny, and then dynamically places the unclassified species to the virtual nodes of the phylogeny tree via their higher-level taxonomy information. Its high speed and low memory consumption enable pairwise comparison of 100 000 metagenomes (synthesized from 3688 bacteria) within 6.4 h on a single computing node.

An optimized implementation of DMS is available on GitHub (https://github.com/qibebt-bioinfo/dynamic-meta-storms) under a GNU GPL license. It takes the species-level profiles of metagenomes as input, and generates their pairwise distance matrix. The bacterial species-level phylogeny tree and taxonomy information of MetaPhlAn2 have been integrated into this implementation, while customized tree and taxonomy are also supported.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid31793432, year = {2019}, author = {Silveira, CB and Luque, A and Roach, TN and Villela, H and Barno, A and Green, K and Reyes, B and Rubio-Portillo, E and Le, T and Mead, S and Hatay, M and Vermeij, MJ and Takeshita, Y and Haas, A and Bailey, B and Rohwer, F}, title = {Biophysical and physiological processes causing oxygen loss from coral reefs.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31793432}, issn = {2050-084X}, support = {G00009988//National Science Foundation/International ; MC_UU_00024/1/MRC_/Medical Research Council/United Kingdom ; 3781//Gordon and Betty Moore Foundation/International ; 234702//Conselho Nacional de Desenvolvimento Científico e Tecnológico/International ; MC_U123160651/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Anthozoa/*physiology ; Bacteria/metabolism ; Biomass ; *Biophysics ; Carbon/metabolism ; Coral Reefs ; Ecosystem ; Heterotrophic Processes ; Metagenome ; Microalgae/metabolism ; Oxygen/*metabolism ; Physiological Phenomena/*physiology ; Seawater/microbiology ; Water Microbiology ; }, abstract = {The microbialization of coral reefs predicts that microbial oxygen consumption will cause reef deoxygenation. Here we tested this hypothesis by analyzing reef microbial and primary producer oxygen metabolisms. Metagenomic data and in vitro incubations of bacteria with primary producer exudates showed that fleshy algae stimulate incomplete carbon oxidation metabolisms in heterotrophic bacteria. These metabolisms lead to increased cell sizes and abundances, resulting in bacteria consuming 10 times more oxygen than in coral incubations. Experiments probing the dissolved and gaseous oxygen with primary producers and bacteria together indicated the loss of oxygen through ebullition caused by heterogenous nucleation on algae surfaces. A model incorporating experimental production and loss rates predicted that microbes and ebullition can cause the loss of up to 67% of gross benthic oxygen production. This study indicates that microbial respiration and ebullition are increasingly relevant to reef deoxygenation as reefs become dominated by fleshy algae.}, } @article {pmid31793046, year = {2020}, author = {Liu, G and Chen, F and Cai, Y and Chen, Z and Luan, Q and Yu, X}, title = {Measuring the subgingival microbiota in periodontitis patients: Comparison of the surface layer and the underlying layers.}, journal = {Microbiology and immunology}, volume = {64}, number = {2}, pages = {99-112}, doi = {10.1111/1348-0421.12759}, pmid = {31793046}, issn = {1348-0421}, support = {81470740//National Natural Science Foundation of China/ ; }, mesh = {Actinobacteria/classification/genetics/isolation & purification ; Actinomyces/isolation & purification ; Adult ; Bacteria/classification/genetics/*isolation & purification ; Classification ; Dental Plaque/*microbiology ; Female ; Fusobacteria/classification/genetics/isolation & purification ; Fusobacterium/isolation & purification ; Fusobacterium nucleatum/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Metagenomics ; *Microbiota/genetics ; Periodontitis/*microbiology ; Phylogeny ; Porphyromonas gingivalis/isolation & purification ; Prevotella intermedia/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Spirochaetales/classification/genetics/isolation & purification ; Streptococcus intermedius/isolation & purification ; Treponema/isolation & purification ; Young Adult ; }, abstract = {Periodontitis is a major cause of tooth loss in adults that initially results from dental plaque. Subgingival plaque pathogenesis is affected by both community composition and plaque structures, although limited data are available concerning the latter. To bridge this knowledge gap, subgingival plaques were obtained using filter paper (the fourth layer) and curette (the first-third layers) sequentially and the phylogenetic differences between the first-third layers and the fourth layer were characterized by sequencing the V3-V4 regions of 16S rRNA. A total of 11 phyla, 148 genera, and 308 species were obtained by bioinformatic analysis, and no significant differences between the operational taxonomic unit numbers were observed for these groups. In both groups, the most abundant species were Porphyromonas gingivalis and Fusobacterium nucleatum. Actinomyces naeslundii, Streptococcus intermedius, and Prevotella intermedia possessed relatively high proportions in the first-third layers; while in the fourth layer, both traditional pathogens (Treponema denticola and Campylobacter rectus) and novel pathobionts (Eubacterium saphenum, Filifactor alocis, Treponema sp. HOT238) were prominent. Network analysis showed that either of them exhibited a scale-free property and was constructed by two negatively correlated components (the pathogen component and the nonpathogen component), while the synergy in the nonpathogen component was lower in the first-third layers than that in the fourth layer. After merging these two parts into a whole plaque group, the negative/positive correlation ratio increased. With potential connections, the first-third layers and the fourth layer showed characteristic key nodes in bacterial networks.}, } @article {pmid31792246, year = {2019}, author = {Katani, R and Schilling, MA and Lyimo, B and Tonui, T and Cattadori, IM and Eblate, E and Martin, A and Estes, AB and Buza, T and Rentsch, D and Davenport, KW and Hovde, BT and Lyimo, S and Munuo, L and Stomeo, F and Tiambo, C and Radzio-Basu, J and Mosha, F and Hudson, PJ and Buza, JJ and Kapur, V}, title = {Microbial Diversity in Bushmeat Samples Recovered from the Serengeti Ecosystem in Tanzania.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {18086}, pmid = {31792246}, issn = {2045-2322}, mesh = {Animals ; Animals, Wild/*microbiology ; Bacteria/genetics/isolation & purification ; Ecosystem ; Humans ; Meat/*microbiology/supply & distribution ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Tanzania ; Zoonoses/etiology/microbiology ; }, abstract = {Bushmeat, the meat and organs derived from wildlife species, is a common source of animal protein in the diets of those living in sub-Saharan Africa and is frequently associated with zoonotic spillover of dangerous pathogens. Given the frequent consumption of bushmeat in this region and the lack of knowledge about the microbial communities associated with this meat, the microbiome of 56 fresh and processed bushmeat samples ascertained from three districts in the Western Serengeti ecosystem in Tanzania was characterized using 16S rRNA metagenomic sequencing. The results show that the most abundant phyla present in bushmeat samples include Firmicutes (67.8%), Proteobacteria (18.4%), Cyanobacteria (8.9%), and Bacteroidetes (3.1%). Regardless of wildlife species, sample condition, season, or region, the microbiome is diverse across all samples, with no significant difference in alpha or beta diversity. The findings also suggest the presence of DNA signatures of potentially dangerous zoonotic pathogens, including those from the genus Bacillus, Brucella, Coxiella, and others, in bushmeat. Together, this investigation provides a better understanding of the microbiome associated with this major food source in samples collected from the Western Serengeti in Tanzania and highlights a need for future investigations on the potential health risks associated with the harvesting, trade, and consumption of bushmeat in Sub-Saharan Africa.}, } @article {pmid31787070, year = {2019}, author = {Kang, JB and Siranosian, BA and Moss, EL and Banaei, N and Andermann, TM and Bhatt, AS}, title = {Intestinal microbiota domination under extreme selective pressures characterized by metagenomic read cloud sequencing and assembly.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 16}, pages = {585}, pmid = {31787070}, issn = {1471-2105}, support = {T32 HG000044/HG/NHGRI NIH HHS/United States ; }, mesh = {Base Sequence ; Biodiversity ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics ; *Gastrointestinal Microbiome/genetics ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/genetics ; Principal Component Analysis ; *Selection, Genetic ; Synteny/genetics ; }, abstract = {BACKGROUND: Low diversity of the gut microbiome, often progressing to the point of intestinal domination by a single species, has been linked to poor outcomes in patients undergoing hematopoietic cell transplantation (HCT). Our ability to understand how certain organisms attain intestinal domination over others has been restricted in part by current metagenomic sequencing technologies that are typically unable to reconstruct complete genomes for individual organisms present within a sequenced microbial community. We recently developed a metagenomic read cloud sequencing and assembly approach that generates improved draft genomes for individual organisms compared to conventional short-read sequencing and assembly methods. Herein, we applied metagenomic read cloud sequencing to four stool samples collected longitudinally from an HCT patient preceding treatment and over the course of heavy antibiotic exposure.

RESULTS: Characterization of microbiome composition by taxonomic classification of reads reveals that that upon antibiotic exposure, the subject's gut microbiome experienced a marked decrease in diversity and became dominated by Escherichia coli. While diversity is restored at the final time point, this occurs without recovery of the original species and strain-level composition. Draft genomes for individual organisms within each sample were generated using both read cloud and conventional assembly. Read clouds were found to improve the completeness and contiguity of genome assemblies compared to conventional assembly. Moreover, read clouds enabled the placement of antibiotic resistance genes present in multiple copies both within a single draft genome and across multiple organisms. The occurrence of resistance genes associates with the timing of antibiotics administered to the patient, and comparative genomic analysis of the various intestinal E. coli strains across time points as well as the bloodstream isolate showed that the subject's E. coli bloodstream infection likely originated from the intestine. The E. coli genome from the initial pre-transplant stool sample harbors 46 known antimicrobial resistance genes, while all other species from the pre-transplant sample each contain at most 5 genes, consistent with a model of heavy antibiotic exposure resulting in selective outgrowth of the highly antibiotic-resistant E. coli.

CONCLUSION: This study demonstrates the application and utility of metagenomic read cloud sequencing and assembly to study the underlying strain-level genomic factors influencing gut microbiome dynamics under extreme selective pressures in the clinical context of HCT.}, } @article {pmid31785113, year = {2020}, author = {Hagan, RW and Hofman, CA and Hübner, A and Reinhard, K and Schnorr, S and Lewis, CM and Sankaranarayanan, K and Warinner, CG}, title = {Comparison of extraction methods for recovering ancient microbial DNA from paleofeces.}, journal = {American journal of physical anthropology}, volume = {171}, number = {2}, pages = {275-284}, doi = {10.1002/ajpa.23978}, pmid = {31785113}, issn = {1096-8644}, support = {EXC 2051 #390713860//Deutsche Forschungsgemeinschaft/International ; //Max-Planck-Gesellschaft/International ; R01 GM089886/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anthropology, Physical/*methods ; Archaeology/methods ; DNA, Ancient/*analysis/*isolation & purification ; Dogs ; Feces/*chemistry ; Gastrointestinal Microbiome ; Metagenomics ; Sequence Analysis, DNA/*methods/veterinary ; }, abstract = {OBJECTIVES: Paleofeces are valuable to archeologists and evolutionary biologists for their potential to yield health, dietary, and host information. As a rich source of preserved biomolecules from host-associated microorganisms, they can also provide insights into the recent evolution and changing ecology of the gut microbiome. However, there is currently no standard method for DNA extraction from paleofeces, which combine the dual challenges of complex biological composition and degraded DNA. Due to the scarcity and relatively poor preservation of paleofeces when compared with other archeological remains, it is important to use efficient methods that maximize ancient DNA (aDNA) recovery while also minimizing downstream taxonomic biases.

METHODS: In this study, we use shotgun metagenomics to systematically compare the performance of five DNA extraction methods on a set of well-preserved human and dog paleofeces from Mexico (~1,300 BP).

RESULTS: Our results show that all tested DNA extraction methods yield a consistent microbial taxonomic profile, but that methods optimized for ancient samples recover significantly more DNA.

CONCLUSIONS: These results show promise for future studies that seek to explore the evolution of the human gut microbiome by comparing aDNA data with those generated in modern studies.}, } @article {pmid31784843, year = {2019}, author = {De Mandal, S and Mathipi, V and Muthukumaran, RB and Gurusubramanian, G and Lalnunmawii, E and Kumar, NS}, title = {Amplicon sequencing and imputed metagenomic analysis of waste soil and sediment microbiome reveals unique bacterial communities and their functional attributes.}, journal = {Environmental monitoring and assessment}, volume = {191}, number = {12}, pages = {778}, pmid = {31784843}, issn = {1573-2959}, mesh = {*Bacteria/classification/genetics ; *Environmental Microbiology ; Environmental Monitoring ; Metagenome ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Rivers/chemistry/microbiology ; *Soil Microbiology ; Waste Disposal Facilities ; }, abstract = {The discharge of solid and liquid waste from domestic, municipal, and hospital premises pollutes the soil and river ecosystems. However, the diversity and functions of the microbial communities present in these polluted environments are not well understood and may contain harmful microbial communities with specialized metabolic potential. In this present study, we adapted the Illumina sequencing technology to analyze microbial communities and their metabolic capabilities in polluted environments. A total of 1113884 sequences of v3-v4 hypervariable region of the 16S rRNA were obtained using Illumina sequencing and assigned to the corresponding taxonomical ranks using Greengenes databases. Proteobacteria and Bacteroidetes were dominantly present in all the four studied sites (solid waste dumping site (SWD); Chite river site (CHR), Turial river site (TUR), and Tuikual river site (TUKR)). It was found that the SWD was dominated by Firmicutes, Actinobacteria; CHR by Acidobacteria, Verrucomicrobia, Planctomycetes; TUR by Verrucomicrobia, Acidobacteria; and TUKR by Verrucomicrobia and Firmicutes, respectively. The dominant bacterial genus present in all samples was Acinetobacter, Flavobacterium, Prevotella, Corynebacterium, Comamonas, Bacteroides, Wautersiella, Cloacibacterium, Stenotrophomonas, Sphingobacterium, and Pseudomonas. Twenty-seven putative bacterial pathogens were identified from the contaminated sites belonging to Salmonella enterica, Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus aureus. Functional analysis showed a high representation of genes in the KEGG pathway involved in the metabolism of amino acids and carbohydrates and identified several genes associated with antibiotic resistance and xenobiotic degradation in these environments, which can be a serious problem for human health and environment. The results from this research will provide a new understanding of the possible management practices to minimize the spread of pathogenic microorganisms in the environment.}, } @article {pmid31784184, year = {2020}, author = {Hernández, M and Quijada, NM and Rodríguez-Lázaro, D and Eiros, JM}, title = {[Bioinformatics of next generation sequencing in clinical microbiology diagnosis].}, journal = {Revista Argentina de microbiologia}, volume = {52}, number = {2}, pages = {150-161}, doi = {10.1016/j.ram.2019.06.003}, pmid = {31784184}, issn = {0325-7541}, mesh = {*Computational Biology ; *High-Throughput Nucleotide Sequencing ; Humans ; Infections/*diagnosis/microbiology ; Microbiological Techniques/*methods ; Microbiota ; }, abstract = {Massive parallel sequencing (High-Throughput Sequencing [HTS]) allows to read millions or billions of DNA sequences or fragments (reads) in parallel and is revolutionizing microbiology research, moving from laboratory methods to computed-assisted analyses, with the compelling use of Bioinformatics. The time and cost reduction in studies on the microbiota, microbiome and metagenome, allows to rapidly progress in diagnosis, taxonomy, epidemiology, comparative genomics, virulence, discovery of genes or variants of interest and the association of microorganisms with traditionally considered non-microbial diseases. In this review, the terminology, the sequencing technologies and their applications are described for microbial analysis using open-source bioinformatics software, analysis pipelines, databases and web platforms that allow a user-friendly bioinformatics approach affordable by the clinical microbiologist and infectious disease practitioners.}, } @article {pmid31783517, year = {2019}, author = {Gómez-Silva, B and Vilo-Muñoz, C and Galetović, A and Dong, Q and Castelán-Sánchez, HG and Pérez-Llano, Y and Sánchez-Carbente, MDR and Dávila-Ramos, S and Cortés-López, NG and Martínez-Ávila, L and Dobson, ADW and Batista-García, RA}, title = {Metagenomics of Atacama Lithobiontic Extremophile Life Unveils Highlights on Fungal Communities, Biogeochemical Cycles and Carbohydrate-Active Enzymes.}, journal = {Microorganisms}, volume = {7}, number = {12}, pages = {}, pmid = {31783517}, issn = {2076-2607}, support = {CeBiB FB-0001//Proyecto Basal CONICYT-Chile/ ; SI-5305//Universidad de Antofagasta/ ; Postgraduated fellowships//CONACyT-Mexico/ ; NIH-NCI P30 CA054174//Genome Sequencing Facility, UT Health San Antonio/ ; 1S10OD021805-01//NIH Shared Instrument Grant/ ; Number RP160732//CPRIT Core Facility Award/ ; }, abstract = {Halites, which are typically found in various Atacama locations, are evaporitic rocks that are considered as micro-scaled salterns. Both structural and functional metagenomic analyses of halite nodules were performed. Structural analyses indicated that the halite microbiota is mainly composed of NaCl-adapted microorganisms. In addition, halites appear to harbor a limited diversity of fungal families together with a biodiverse collection of protozoa. Functional analysis indicated that the halite microbiome possesses the capacity to make an extensive contribution to carbon, nitrogen, and sulfur cycles, but possess a limited capacity to fix nitrogen. The halite metagenome also contains a vast repertory of carbohydrate active enzymes (CAZY) with glycosyl transferases being the most abundant class present, followed by glycosyl hydrolases (GH). Amylases were also present in high abundance, with GH also being identified. Thus, the halite microbiota is a potential useful source of novel enzymes that could have biotechnological applicability. This is the first metagenomic report of fungi and protozoa as endolithobionts of halite nodules, as well as the first attempt to describe the repertoire of CAZY in this community. In addition, we present a comprehensive functional metagenomic analysis of the metabolic capacities of the halite microbiota, providing evidence for the first time on the sulfur cycle in Atacama halites.}, } @article {pmid31782201, year = {2020}, author = {Wille, M}, title = {Unravelling virus community ecology in bats through the integration of metagenomics and community ecology.}, journal = {Molecular ecology}, volume = {29}, number = {1}, pages = {23-25}, doi = {10.1111/mec.15306}, pmid = {31782201}, issn = {1365-294X}, mesh = {Animals ; *Biota ; Chiroptera/*virology ; *Ecology ; Humans ; *Metagenomics ; Rabies virus/genetics ; Viruses/*genetics ; }, abstract = {The spillover of viruses from wildlife into agricultural animals or humans has profound socioeconomic and public health impact. Vampire bats, found throughout South America, feed directly on humans and other animals and are an important reservoir for zoonotic viruses, including rabies virus. This has resulted in considerable effort in understanding both the ecology of bat-borne viruses and the composition and associated correlates of the structure of entire virus communities in wildlife, particularly in the context of disease control interventions. In a From the Cover article in this issue of Molecular Ecology, Bergner et al. (2019) set out to reveal virus community dynamics in vampire bats by interrogating factors that affect the structure, diversity and richness of these communities. Due to the linkage of metagenomic sequence data with community ecology, this study represents an important advance in the field of virus ecology.}, } @article {pmid31781816, year = {2020}, author = {Sun, F and Wang, C and Chen, L and Weng, G and Zheng, Z}, title = {The intestinal bacterial community of healthy and diseased animals and its association with the aquaculture environment.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {2}, pages = {775-783}, doi = {10.1007/s00253-019-10236-z}, pmid = {31781816}, issn = {1432-0614}, support = {2017A020216008//Project of Guangdong Science and Technology Department/ ; 2016I1002//Project of Fujian Science and Technology Department/ ; 2017T3010//Project of Fujian Science and Technology Department/ ; }, mesh = {Animals ; Aquaculture ; Bacteria/*classification/*genetics ; Crustacea/*microbiology ; *Gastrointestinal Microbiome ; Geologic Sediments/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Water Microbiology ; }, abstract = {Although increasing levels of attention have been targeted towards aquaculture-associated bacteria, the bacterial community of animal intestines and its relationship with the aquaculture environment need to be further investigated. In this study, we used high-throughput sequencing to analyze the bacterial community of pond water, sediment, and the intestines of diseased and healthy animals. Our data showed that Proteobacteria, Firmicutes, Cyanobacteria, and Bacteroidetes were the dominant taxa of bacteria across all samples and accounted for more than 90% of the total sequence. Difference analysis and Venn diagrams showed that most of the intestinal bacterial OTUs (operational taxonomic units) of diseased and healthy animals were the same as those of sediment and water, indicating that the aquaculture environment was the main source of intestinal bacteria. Compared with healthy animals, a considerable reduction of OTUs was evident in diseased animals. Welch's t test showed that the dominant bacterial taxa in sediment, water, and animal intestine were significantly different (p < 0.05) and each had its own unique dominant microorganisms. In addition, differences between the intestinal bacteria of healthy and diseased animals were represented by potential probiotics and pathogens, such as Bacillus, Vibrio, Oceanobacillus, and Lactococcus. Principal component analysis (PcoA) showed that a similar environment shaped a similar microbial structure. There was a large difference in the spectrum of intestinal bacteria in diseased animals; furthermore, the spectrum of intestinal bacteria in diseased animals was very different from the environment than in healthy animals. This study provides a theoretical basis for a relationship between the intestinal bacteria of healthy and diseased animals and the environment and provides guidance for environmental regulation and disease prevention in aquaculture areas.}, } @article {pmid31781106, year = {2019}, author = {Pessoa, L and Aleti, G and Choudhury, S and Nguyen, D and Yaskell, T and Zhang, Y and Li, W and Nelson, KE and Neto, LLS and Sant'Ana, ACP and Freire, M}, title = {Host-Microbial Interactions in Systemic Lupus Erythematosus and Periodontitis.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {2602}, pmid = {31781106}, issn = {1664-3224}, support = {K99 DE023584/DE/NIDCR NIH HHS/United States ; R00 DE023584/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Autoimmunity ; Computational Biology/methods ; Cytokines/metabolism ; *Disease Susceptibility ; Female ; *Host-Pathogen Interactions ; Humans ; Inflammation Mediators/metabolism ; Lupus Erythematosus, Systemic/*etiology/metabolism ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota/immunology ; Middle Aged ; Periodontitis/*etiology/metabolism ; Phylogeny ; }, abstract = {Background: Systemic lupus erythematosus (SLE) is a potentially fatal complex autoimmune disease, that is characterized by widespread inflammation manifesting tissue damage and comorbidities across the human body including heart, blood vessels, joints, skin, liver, kidneys, and periodontal tissues. The etiology of SLE is partially attributed to a deregulated inflammatory response to microbial dysbiosis and environmental changes. In the mouth, periodontal environment provides an optimal niche for local and systemic inflammation. Our aim was to evaluate the reciprocal impact of periodontal subgingival microbiome on SLE systemic inflammation. Methods: Ninety-one female subjects were recruited, including healthy (n = 31), SLE-inactive (n = 29), and SLE-active (n = 31). Patients were screened for probing depth, bleeding on probing, clinical attachment level, and classified according to CDC/AAP criteria with or without periodontal dysbiosis. Serum inflammatory cytokines were measured by human cytokine panel and a targeted pathogenic subgingival biofilm panel was examined by DNA-DNA checkerboard from subgingival plaque samples. Results: The results showed significant upregulation of serum proinflammatory cytokines in individuals with SLE when compared to controls. Stratification of subject's into SLE-inactive (I) and SLE-active (A) phenotypes or periodontitis and non-periodontitis groups provided new insights into SLE pathophysiology. Ten proinflammatory cytokines were upregulated in serum of SLE-I only and one in SLE-A only. Four molecules overlapped in SLE-A and SLE-I. Anti-inflammatory cytokines included IL-4 IL-10, which were upregulated in SLE-I sera (but not SLE-A), controlling clinical phenotypes. Out of 24 significant differential oral microbial abundances found in SLE, 14 unique subgingival bacteria profiles were found to be elevated in SLE. The most severe oral pathogens (Treponema denticola and Tannerella forsythia) showed increase abundances on SLE-A periodontal sites when compared to SLE-I and healthy controls. Inflammation as measured by cytokine-microbial correlations showed that periodontal pathogens dominating the environment increased proinflammatory cytokines systemically. Conclusions: Altogether, low-grade systemic inflammation that influenced SLE disease activity and severity was correlated to dysbiotic changes of the oral microbiota present in periodontal diseases.}, } @article {pmid31781058, year = {2019}, author = {Oberhofer, M and Hess, J and Leutgeb, M and Gössnitzer, F and Rattei, T and Wawrosch, C and Zotchev, SB}, title = {Exploring Actinobacteria Associated With Rhizosphere and Endosphere of the Native Alpine Medicinal Plant Leontopodium nivale Subspecies alpinum.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2531}, pmid = {31781058}, issn = {1664-302X}, abstract = {The rhizosphere of plants is enriched in nutrients facilitating growth of microorganisms, some of which are recruited as endophytes. Endophytes, especially Actinobacteria, are known to produce a plethora of bioactive compounds. We hypothesized that Leontopodium nivale subsp. alpinum (Edelweiss), a rare alpine medicinal plant, may serve as yet untapped source for uncommon Actinobacteria associated with this plant. Rhizosphere soil of native Alpine plants was used, after physical and chemical pre-treatments, for isolating Actinobacteria. Isolates were selected based on morphology and identified by 16S rRNA gene-based barcoding. Resulting 77 Actinobacteria isolates represented the genera Actinokineospora, Kitasatospora, Asanoa, Microbacterium, Micromonospora, Micrococcus, Mycobacterium, Nocardia, and Streptomyces. In parallel, Edelweiss plants from the same location were surface-sterilized, separated into leaves, roots, rhizomes, and inflorescence and pooled within tissues before genomic DNA extraction. Metagenomic 16S rRNA gene amplicons confirmed large numbers of actinobacterial operational taxonomic units (OTUs) descending in diversity from roots to rhizomes, leaves and inflorescences. These metagenomic data, when queried with isolate sequences, revealed an overlap between the two datasets, suggesting recruitment of soil bacteria by the plant. Moreover, this study uncovered a profound diversity of uncultured Actinobacteria from Rubrobacteridae, Thermoleophilales, Acidimicrobiales and unclassified Actinobacteria specifically in belowground tissues, which may be exploited by a targeted isolation approach in the future.}, } @article {pmid31780826, year = {2019}, author = {Tang, L}, title = {Exploring the chemical space of the human microbiome.}, journal = {Nature methods}, volume = {16}, number = {12}, pages = {1201}, doi = {10.1038/s41592-019-0671-9}, pmid = {31780826}, issn = {1548-7105}, mesh = {Humans ; Metagenome ; *Microbiota ; }, } @article {pmid31780738, year = {2019}, author = {Li, W and Ni, J and Cai, S and Liu, Y and Shen, C and Yang, H and Chen, Y and Tao, J and Yu, Y and Liu, Q}, title = {Variations in microbial community structure and functional gene expression in bio-treatment processes with odorous pollutants.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17870}, pmid = {31780738}, issn = {2045-2322}, mesh = {Acidithiobacillus/genetics/metabolism ; Air Pollutants/*metabolism ; Biodegradation, Environmental ; *Gene Expression Regulation, Bacterial ; *Genes, Bacterial ; Genetic Variation ; Industrial Microbiology/instrumentation/methods ; *Microbiota ; Thiobacillus/genetics/metabolism ; Xenobiotics/metabolism ; }, abstract = {Engineered microbial ecosystems in biofilters have been widely applied to treat odorous gases from industrial emissions. Variations in microbial community structure and function associated with the removal of odorous gases by biofilters are largely unknown. This study performed a metagenomic analysis to discover shifts in microbial community structures in a commercial scale biofilter after treating odorous gas. Our study identified 175,675 functional genes assigned into 43 functional KEGG pathways. Based on the unigene sequences, there were significant changes in microbial community structures in the biofilter after treating odorous gas. The dominant genera were Thiobacillus and Oceanicaulis before the treatment, and were Acidithiobacillus and Ferroplasma after the treatment. A clustering analysis showed that the number of down-regulated microbes exceeded the number of up-regulated microbes, suggesting that odorous gas treatment reduced in microbial community structures. A differential expression analysis identified 29,975 up- and 452,599 down-regulated genes. An enrichment analysis showed 17 classic types of xenobiotic biodegradation pathways. The results identified 16 and 15 genes involved in ammonia and sulfite metabolism, respectively; an analysis of their relative abundance identified several up-regulated genes, which may be efficient genes involved in removing odorous gases. The data provided in this study demonstrate the changes in microbial communities and help identify the dominant microflora and genes that play key roles in treating odorous gases.}, } @article {pmid31780057, year = {2020}, author = {Garud, NR and Pollard, KS}, title = {Population Genetics in the Human Microbiome.}, journal = {Trends in genetics : TIG}, volume = {36}, number = {1}, pages = {53-67}, doi = {10.1016/j.tig.2019.10.010}, pmid = {31780057}, issn = {0168-9525}, mesh = {Bacteria/classification/genetics/metabolism ; Gastrointestinal Microbiome/*genetics ; Genetic Variation/*genetics ; *Genetics, Population ; Humans ; Metagenome/genetics ; Metagenomics/trends ; Microbiota/*genetics ; }, abstract = {While the human microbiome's structure and function have been extensively studied, its within-species genetic diversity is less well understood. However, genetic mutations in the microbiome can confer biomedically relevant traits, such as the ability to extract nutrients from food, metabolize drugs, evade antibiotics, and communicate with the host immune system. The population genetic processes by which these traits evolve are complex, in part due to interacting ecological and evolutionary forces in the microbiome. Advances in metagenomic sequencing, coupled with bioinformatics tools and population genetic models, facilitate quantification of microbiome genetic variation and inferences about how this diversity arises, evolves, and correlates with traits of both microbes and hosts. In this review, we explore the population genetic forces (mutation, recombination, drift, and selection) that shape microbiome genetic diversity within and between hosts, as well as efforts towards predictive models that leverage microbiome genetics.}, } @article {pmid31779234, year = {2019}, author = {Leoni, C and Ceci, O and Manzari, C and Fosso, B and Volpicella, M and Ferrari, A and Fiorella, P and Pesole, G and Cicinelli, E and Ceci, LR}, title = {Human Endometrial Microbiota at Term of Normal Pregnancies.}, journal = {Genes}, volume = {10}, number = {12}, pages = {}, pmid = {31779234}, issn = {2073-4425}, mesh = {Adult ; Bacteria/*classification/genetics ; Cesarean Section ; DNA Barcoding, Taxonomic/*methods ; Endometrium/*microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Microbiota ; Phylogeny ; Pilot Projects ; Pregnancy ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {The endometrium is a challenging site for metagenomic analysis due to difficulties in obtaining uncontaminated samples and the limited abundance of the bacterial population. Indeed, solid correlations between endometrial physio-pathologic conditions and bacteria compositions have not yet been firmly established. Nevertheless, the study of the endometrial microbiota is of great interest due to the close correlations between microbiota profiles, women's health, and successful pregnancies. In this study, we decided to tackle the study of the endometrial microbiota through analysis of bacterial population in women subjected to elective caesarean delivery. As a pilot study, a cohort of 19 Caucasian women at full term of normal pregnancy and with a prospection of elective caesarean delivery was enrolled for endometrium sampling at the time of caesarean section. Sampling was carried out by endometrial biopsy soon after the delivery of the newborn and the discharge of the placenta and fetal membranes from the uterus. Bacterial composition was established by a deep metabarcoding next generation sequencing (NGS) procedure addressing the V5-V6 hypervariable region of the 16S rRNA gene. Amplicon sequences were analysed by bioinformatic procedures for denoising and taxonomic classification. The RDP database was used as 16S rRNA reference collection. Metabarcoding analysis showed the presence of a common bacterial composition, including six genera classifiable within the human microbiota (Cutibacterium, Escherichia, Staphylococcus, Acinetobacter, Streptococcus, Corynebacterium), that could be part of the core endometrial microbiota under the specific conditions examined. These results can provide useful information for future studies on the correlations between bacteria and successful pregnancies.}, } @article {pmid31778179, year = {2019}, author = {Megaw, J and Kelly, SA and Thompson, TP and Skvortsov, T and Gilmore, BF}, title = {Profiling the microbial community of a Triassic halite deposit in Northern Ireland: an environment with significant potential for biodiscovery.}, journal = {FEMS microbiology letters}, volume = {366}, number = {22}, pages = {}, doi = {10.1093/femsle/fnz242}, pmid = {31778179}, issn = {1574-6968}, support = {BB/L017083/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Archaea/*classification/genetics/*isolation & purification ; Bacteria/*classification/genetics/*isolation & purification ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/*microbiology ; Metagenomics ; Microbiological Techniques ; *Microbiota ; Northern Ireland ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Kilroot salt mine, a Triassic halite deposit located in County Antrim, Northern Ireland, is the only permanent hypersaline environment on the island of Ireland. In this study, the microbiome of this unstudied environment was profiled for the first time using conventional and enhanced culturing techniques, and culture independent metagenomic approaches. Using both conventional isolation plates and iChip devices, 89 halophilic archaeal isolates from six known genera, and 55 halophilic or halotolerant bacterial isolates from 18 genera were obtained, based on 16S rRNA gene sequencing. The archaeal isolates were similar to those previously isolated from other ancient halite deposits, and as expected, numerous genera were identified in the metagenome which were not represented among the culturable isolates. Preliminary screening of a selection of isolates from this environment identified antimicrobial activities against a panel of clinically important bacterial pathogens from 15 of the bacterial isolates and one of the archaea. This, alongside previous studies reporting the discovery of novel biocatalysts from the Kilroot mine microbiome, suggests that this environment may be a new, untapped source of of chemical diversity with high biodiscovery potential.}, } @article {pmid31778109, year = {2020}, author = {Huang, R and Li, F and Zhou, Y and Zeng, Z and He, X and Fang, L and Pan, F and Chen, Y and Lin, J and Li, J and Qiu, D and Tian, Y and Tan, X and Song, Y and Xu, Y and Lai, Y and Yi, H and Gao, Q and Fang, X and Shi, M and Zhou, C and Huang, J and He, YT}, title = {Metagenome-wide association study of the alterations in the intestinal microbiome composition of ankylosing spondylitis patients and the effect of traditional and herbal treatment.}, journal = {Journal of medical microbiology}, volume = {69}, number = {6}, pages = {797-805}, pmid = {31778109}, issn = {1473-5644}, mesh = {Adolescent ; Adult ; Drugs, Chinese Herbal/*therapeutic use ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; Middle Aged ; Spondylitis, Ankylosing/drug therapy/metabolism/*microbiology ; Young Adult ; }, abstract = {Introduction. Ankylosing spondylitis (AS) is a systemic progressive disease with an unknown etiology that may be related to the gut microbiome. Therefore, a more thorough understanding of its pathogenesis is necessary for directing future therapy.Aim. We aimed to determine the differences in intestinal microbial composition between healthy individuals and patients with AS who received and who did not receive treatment interventions. In parallel, the pathology of AS in each patient was analysed to better understand the link between AS treatment and the intestinal microbiota of the patients.Methodology. Sixty-six faecal DNA samples, including 37 from healthy controls (HCs), 11 from patients with untreated AS (NM), 7 from patients treated with nonsteroidal anti-inflammatory drugs (e.g. celecoxib; WM) and 11 from patients treated with Chinese herbal medicine (CHM), such as the Bushen-Qiangdu-Zhilv decoction, were collected and used in the drug effect analysis. All samples were sequenced using Illumina HiSeq 4000 and the microbial composition was determined.Results. Four species were enriched in the patients with AS: Flavonifractor plautii, Oscillibacter, Parabacteroides distasonis and Bacteroides nordii (HC vs. NM, P<0.05); only F. plautii was found to be significantly changed in the NM-HC comparison. No additional species were found in the HC vs. CHM analysis, which indicated a beneficial effect of CHM in removing the other three strains. F. plautii was found to be significantly increased in the comparison between the HC and WM groups, along with four other species (Clostridium bolteae, Clostridiales bacterium 1_7_47FAA, C. asparagiforme and C. hathewayi). The patients with AS harboured more bacterial species associated with carbohydrate metabolism and glycan biosynthesis in their faeces. They also had bacterial profiles less able to biodegrade xenobiotics or synthesize and transport vitamins.Conclusion. The gut microbiota of the patients with AS varied from that of the HCs, and the treatment had an impact on this divergence. Our data provide insight that could guide improvements in AS treatment.}, } @article {pmid31776473, year = {2020}, author = {Devkota, S}, title = {Big data and tiny proteins: shining a light on the dark corners of the gut microbiome.}, journal = {Nature reviews. Gastroenterology & hepatology}, volume = {17}, number = {2}, pages = {68-69}, pmid = {31776473}, issn = {1759-5053}, mesh = {*Big Data ; Coculture Techniques ; Culture Techniques ; Datasets as Topic ; Dysbiosis/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Intestinal Mucosa ; Lab-On-A-Chip Devices ; *Metagenome ; *Peptides ; }, } @article {pmid31776248, year = {2019}, author = {Zheng, H and Perreau, J and Powell, JE and Han, B and Zhang, Z and Kwong, WK and Tringe, SG and Moran, NA}, title = {Division of labor in honey bee gut microbiota for plant polysaccharide digestion.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {51}, pages = {25909-25916}, pmid = {31776248}, issn = {1091-6490}, support = {R01 GM108477/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/metabolism ; Bees/*microbiology/*physiology ; Bifidobacterium/genetics/metabolism ; *Digestion ; Gammaproteobacteria/genetics/metabolism ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/microbiology ; Gene Expression Regulation ; Genome, Bacterial ; Lactobacillus/genetics ; Metagenome ; Microbiota ; Neisseriaceae/genetics ; Plants/*chemistry ; Pollen/chemistry ; Polysaccharides/*metabolism ; }, abstract = {Bees acquire carbohydrates from nectar and lipids; and amino acids from pollen, which also contains polysaccharides including cellulose, hemicellulose, and pectin. These potential energy sources could be degraded and fermented through microbial enzymatic activity, resulting in short chain fatty acids available to hosts. However, the contributions of individual microbiota members to polysaccharide digestion have remained unclear. Through analysis of bacterial isolate genomes and a metagenome of the honey bee gut microbiota, we identify that Bifidobacterium and Gilliamella are the principal degraders of hemicellulose and pectin. Both Bifidobacterium and Gilliamella show extensive strain-level diversity in gene repertoires linked to polysaccharide digestion. Strains from honey bees possess more such genes than strains from bumble bees. In Bifidobacterium, genes encoding carbohydrate-active enzymes are colocated within loci devoted to polysaccharide utilization, as in Bacteroides from the human gut. Carbohydrate-active enzyme-encoding gene expressions are up-regulated in response to particular hemicelluloses both in vitro and in vivo. Metabolomic analyses document that bees experimentally colonized by different strains generate distinctive gut metabolomic profiles, with enrichment for specific monosaccharides, corresponding to predictions from genomic data. The other 3 core gut species clusters (Snodgrassella and 2 Lactobacillus clusters) possess few or no genes for polysaccharide digestion. Together, these findings indicate that strain composition within individual hosts determines the metabolic capabilities and potentially affects host nutrition. Furthermore, the niche specialization revealed by our study may promote overall community stability in the gut microbiomes of bees.}, } @article {pmid31775777, year = {2019}, author = {Yang, L and Haidar, G and Zia, H and Nettles, R and Qin, S and Wang, X and Shah, F and Rapport, SF and Charalampous, T and Methé, B and Fitch, A and Morris, A and McVerry, BJ and O'Grady, J and Kitsios, GD}, title = {Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study.}, journal = {Respiratory research}, volume = {20}, number = {1}, pages = {265}, pmid = {31775777}, issn = {1465-993X}, support = {U01 HL098962/HL/NHLBI NIH HHS/United States ; R01 HL097376/HL/NHLBI NIH HHS/United States ; K23 HL139987/HL/NHLBI NIH HHS/United States ; K24 HL123342/HL/NHLBI NIH HHS/United States ; BBS/E/F/000PR10348/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10349/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; K23 GM122069/GM/NIGMS NIH HHS/United States ; P01 HL114453/HL/NHLBI NIH HHS/United States ; MR/N013956/1/MRC_/Medical Research Council/United Kingdom ; BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; RP-PG-0514-20018/DH_/Department of Health/United Kingdom ; }, mesh = {Anti-Bacterial Agents/administration & dosage ; Case-Control Studies ; DNA, Bacterial/*genetics ; Feasibility Studies ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Metagenomics/methods ; Microbiota/*genetics ; *Nanopores ; Pneumonia/diagnosis/*genetics/*therapy ; Reference Values ; Respiration, Artificial/methods ; Respiratory Insufficiency/diagnosis/genetics/therapy ; Risk Factors ; Sensitivity and Specificity ; Severity of Illness Index ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Metagenomic sequencing of respiratory microbial communities for pathogen identification in pneumonia may help overcome the limitations of culture-based methods. We examined the feasibility and clinical validity of rapid-turnaround metagenomics with Nanopore™ sequencing of clinical respiratory specimens.

METHODS: We conducted a case-control study of mechanically-ventilated patients with pneumonia (nine culture-positive and five culture-negative) and without pneumonia (eight controls). We collected endotracheal aspirates and applied a microbial DNA enrichment method prior to metagenomic sequencing with the Oxford Nanopore MinION device. For reference, we compared Nanopore results against clinical microbiologic cultures and bacterial 16S rRNA gene sequencing.

RESULTS: Human DNA depletion enabled in depth sequencing of microbial communities. In culture-positive cases, Nanopore revealed communities with high abundance of the bacterial or fungal species isolated by cultures. In four cases with resistant clinical isolates, Nanopore detected antibiotic resistance genes corresponding to the phenotypic resistance in antibiograms. In culture-negative pneumonia, Nanopore revealed probable bacterial pathogens in 1/5 cases and Candida colonization in 3/5 cases. In controls, Nanopore showed high abundance of oral bacteria in 5/8 subjects, and identified colonizing respiratory pathogens in other subjects. Nanopore and 16S sequencing showed excellent concordance for the most abundant bacterial taxa.

CONCLUSIONS: We demonstrated technical feasibility and proof-of-concept clinical validity of Nanopore metagenomics for severe pneumonia diagnosis, with striking concordance with positive microbiologic cultures, and clinically actionable information obtained from sequencing in culture-negative samples. Prospective studies with real-time metagenomics are warranted to examine the impact on antimicrobial decision-making and clinical outcomes.}, } @article {pmid31775181, year = {2020}, author = {Rambo, IM and Dombrowski, N and Constant, L and Erdner, D and Baker, BJ}, title = {Metabolic relationships of uncultured bacteria associated with the microalgae Gambierdiscus.}, journal = {Environmental microbiology}, volume = {22}, number = {5}, pages = {1764-1783}, doi = {10.1111/1462-2920.14878}, pmid = {31775181}, issn = {1462-2920}, support = {FG-2016-6301//Alfred P. Sloan Foundation/International ; }, mesh = {Biochemical Phenomena ; Dinoflagellida/*microbiology ; Flavobacteriaceae/*genetics ; Genome, Bacterial/*genetics ; Metagenome ; Metagenomics ; Microalgae/*microbiology ; Microbiota/genetics ; Phylogeny ; Phytoplankton/microbiology ; Rhodobacteraceae/*genetics ; }, abstract = {Microbial communities inhabit algae cell surfaces and produce a variety of compounds that can impact the fitness of the host. These interactions have been studied via culturing, single-gene diversity and metagenomic read survey methods that are limited by culturing biases and fragmented genetic characterizations. Higher-resolution frameworks are needed to resolve the physiological interactions within these algal-bacterial communities. Here, we infer the encoded metabolic capabilities of four uncultured bacterial genomes (reconstructed using metagenomic assembly and binning) associated with the marine dinoflagellates Gambierdiscus carolinianus and G. caribaeus. Phylogenetic analyses revealed that two of the genomes belong to the commonly algae-associated families Rhodobacteraceae and Flavobacteriaceae. The other two genomes belong to the Phycisphaeraceae and include the first algae-associated representative within the uncultured SM1A02 group. Analyses of all four genomes suggest these bacteria are facultative aerobes, with some capable of metabolizing phytoplanktonic organosulfur compounds including dimethylsulfoniopropionate and sulfated polysaccharides. These communities may biosynthesize compounds beneficial to both the algal host and other bacteria, including iron chelators, B vitamins, methionine, lycopene, squalene and polyketides. These findings have implications for marine carbon and nutrient cycling and provide a greater depth of understanding regarding the genetic potential for complex physiological interactions between microalgae and their associated bacteria.}, } @article {pmid31773890, year = {2020}, author = {McDermott, TR and Stolz, JF and Oremland, RS}, title = {Arsenic and the gastrointestinal tract microbiome.}, journal = {Environmental microbiology reports}, volume = {12}, number = {2}, pages = {136-159}, doi = {10.1111/1758-2229.12814}, pmid = {31773890}, issn = {1758-2229}, support = {911310//Montana Agricultural Experiment Station/International ; NNX09AW41G/NASA/NASA/United States ; R01 CA215784/CA/NCI NIH HHS/United States ; MCB-1714556//National Science Foundation/International ; /CA/NCI NIH HHS/United States ; NNX09AW41G/NASA/NASA/United States ; /CA/NCI NIH HHS/United States ; }, mesh = {Arsenates/metabolism ; Arsenic/metabolism/*toxicity ; Arsenite Transporting ATPases/*genetics ; Bacteria/classification/genetics/isolation & purification ; Bacteroidetes/classification/genetics/isolation & purification ; Bioaccumulation/physiology ; Drug Resistance/genetics ; Escherichia coli Proteins/genetics ; Firmicutes/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome/drug effects/genetics ; Gastrointestinal Tract/anatomy & histology/microbiology ; Genes, Bacterial/drug effects ; Humans ; Ion Pumps/genetics ; Metagenomics ; Molecular Chaperones/genetics ; Multienzyme Complexes/genetics ; Proteobacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S ; }, abstract = {Arsenic is a toxin, ranking first on the Agency for Toxic Substances and Disease Registry and the Environmental Protection Agency Priority List of Hazardous Substances. Chronic exposure increases the risk of a broad range of human illnesses, most notably cancer; however, there is significant variability in arsenic-induced disease among exposed individuals. Human genetics is a known component, but it alone cannot account for the large inter-individual variability in the presentation of arsenicosis symptoms. Each part of the gastrointestinal tract (GIT) may be considered as a unique environment with characteristic pH, oxygen concentration, and microbiome. Given the well-established arsenic redox transformation activities of microorganisms, it is reasonable to imagine how the GIT microbiome composition variability among individuals could play a significant role in determining the fate, mobility and toxicity of arsenic, whether inhaled or ingested. This is a relatively new field of research that would benefit from early dialogue aimed at summarizing what is known and identifying reasonable research targets and concepts. Herein, we strive to initiate this dialogue by reviewing known aspects of microbe-arsenic interactions and placing it in the context of potential for influencing host exposure and health risks. We finish by considering future experimental approaches that might be of value.}, } @article {pmid31773170, year = {2020}, author = {Sharma, U and Olson, RK and Erhart, FN and Zhang, L and Meng, J and Segura, B and Banerjee, S and Sharma, M and Saluja, AK and Ramakrishnan, S and Abreu, MT and Roy, S}, title = {Prescription Opioids induce Gut Dysbiosis and Exacerbate Colitis in a Murine Model of Inflammatory Bowel Disease.}, journal = {Journal of Crohn's & colitis}, volume = {14}, number = {6}, pages = {801-817}, pmid = {31773170}, issn = {1876-4479}, support = {R01 DA044582/DA/NIDA NIH HHS/United States ; K08 GM113055/GM/NIGMS NIH HHS/United States ; R01 DK117576/DK/NIDDK NIH HHS/United States ; R01 DA050542/DA/NIDA NIH HHS/United States ; R01 DA037843/DA/NIDA NIH HHS/United States ; R01 DA034582/DA/NIDA NIH HHS/United States ; R01 DA043252/DA/NIDA NIH HHS/United States ; R01 DK099076/DK/NIDDK NIH HHS/United States ; T32 DA045734/DA/NIDA NIH HHS/United States ; R01 DA047089/DA/NIDA NIH HHS/United States ; }, mesh = {Analgesics, Opioid/administration & dosage/adverse effects ; Animals ; Azepines/*pharmacology ; Disease Models, Animal ; *Dysbiosis/chemically induced/microbiology/physiopathology/prevention & control ; Enzyme Inhibitors/pharmacology ; *Gastrointestinal Microbiome/drug effects/physiology ; *Hydromorphone/administration & dosage/adverse effects ; *Inflammatory Bowel Diseases/drug therapy/immunology/microbiology ; Interleukin-10/genetics ; Mice ; Mice, Knockout ; Myosin-Light-Chain Kinase/*antagonists & inhibitors ; Naphthalenes/*pharmacology ; Pain Management/adverse effects/methods ; }, abstract = {BACKGROUND AND AIMS: Opioids are the most prescribed analgesics for pain in inflammatory bowel diseases [IBD]; however, the consequences of opioid use on IBD severity are not well defined. This is the first study investigating consequences of hydromorphone in both dextran sodium sulphate [DSS]-induced colitis and spontaneous colitis (IL-10 knockout [IL-10-/-]) mouse models of IBD.

METHODS: To determine the consequences of opioids on IBD pathogenesis, wild-type [WT] mice were treated with clinically relevant doses of hydromorphone and colitis was induced via 3% DSS in drinking water for 5 days. In parallel we also determined the consequences of opioids in a spontaneous colitis model.

RESULTS: Hydromorphone and DSS independently induced barrier dysfunction, bacterial translocation, disruption of tight junction organisation and increased intestinal and systemic inflammation, which were exacerbated in mice receiving hydromorphone in combination with DSS. Hydromorphone + DSS-treated mice exhibited significant microbial dysbiosis. Predictive metagenomic analysis of the gut microbiota revealed high abundance in the bacterial communities associated with virulence, antibiotic resistance, toxin production, and inflammatory properties. Hydromorphone modulates tight junction organisation in a myosin light chain kinase [MLCK]-dependent manner. Treatment with MLCK inhibitor ML-7 ameliorates the detrimental effects of hydromorphone on DSS-induced colitis and thus decreases severity of IBD. Similarly, we demonstrated that hydromorphone treatment in IL-10-/- mice resulted in accelerated clinical manifestations of colitis compared with control mice.

CONCLUSIONS: Opioids used for pain management in IBD accelerate IBD progression by dysregulation of the gut microbiota, leading to expansion of pathogenic bacteria, translocation of bacteria, immune deregulation and sustained inflammation.}, } @article {pmid31772206, year = {2019}, author = {Orellana, LH and Hatt, JK and Iyer, R and Chourey, K and Hettich, RL and Spain, JC and Yang, WH and Chee-Sanford, JC and Sanford, RA and Löffler, FE and Konstantinidis, KT}, title = {Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17630}, pmid = {31772206}, issn = {2045-2322}, mesh = {Ammonium Compounds/*pharmacology ; Archaea/drug effects/genetics/isolation & purification ; Archaeal Proteins/*analysis ; Bacteria/drug effects/genetics/isolation & purification ; Bacterial Proteins/*analysis ; DNA, Archaeal/*analysis ; DNA, Bacterial/*analysis ; *Fertilizers ; Gene Expression Regulation, Archaeal/drug effects ; Gene Expression Regulation, Bacterial/drug effects ; Gene Ontology ; Metagenomics ; Microbiota/*drug effects ; Nitrates/analysis ; *Nitrification/genetics ; Nitrogen Isotopes/analysis ; Oxidation-Reduction ; Phylogeny ; Proteomics ; RNA, Archaeal/*analysis ; RNA, Bacterial/*analysis ; RNA, Ribosomal, 16S/analysis ; Soil/chemistry ; *Soil Microbiology ; Urea/*pharmacology ; }, abstract = {To what extent multi-omic techniques could reflect in situ microbial process rates remains unclear, especially for highly diverse habitats like soils. Here, we performed microcosm incubations using sandy soil from an agricultural site in Midwest USA. Microcosms amended with isotopically labeled ammonium and urea to simulate a fertilization event showed nitrification (up to 4.1 ± 0.87 µg N-NO3[-] g[-1] dry soil d[-1]) and accumulation of N2O after 192 hours of incubation. Nitrification activity (NH4[+] → NH2OH → NO → NO2[-] → NO3[-]) was accompanied by a 6-fold increase in relative expression of the 16S rRNA gene (RNA/DNA) between 10 and 192 hours of incubation for ammonia-oxidizing bacteria Nitrosomonas and Nitrosospira, unlike archaea and comammox bacteria, which showed stable gene expression. A strong relationship between nitrification activity and betaproteobacterial ammonia monooxygenase and nitrite oxidoreductase transcript abundances revealed that mRNA quantitatively reflected measured activity and was generally more sensitive than DNA under these conditions. Although peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that meta-proteomics provided only a qualitative assessment of activity. Altogether, these findings underscore the strengths and limitations of multi-omic approaches for assessing diverse microbial communities in soils and provide new insights into nitrification.}, } @article {pmid31772173, year = {2019}, author = {Sevim, V and Lee, J and Egan, R and Clum, A and Hundley, H and Lee, J and Everroad, RC and Detweiler, AM and Bebout, BM and Pett-Ridge, J and Göker, M and Murray, AE and Lindemann, SR and Klenk, HP and O'Malley, R and Zane, M and Cheng, JF and Copeland, A and Daum, C and Singer, E and Woyke, T}, title = {Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies.}, journal = {Scientific data}, volume = {6}, number = {1}, pages = {285}, pmid = {31772173}, issn = {2052-4463}, support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/International ; }, mesh = {Bacteria/classification ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Microbiota ; Sequence Analysis, DNA/*methods ; }, abstract = {Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2-7.2 Mbp, 40-73% GC content, and 1.5-7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel.}, } @article {pmid31768581, year = {2020}, author = {Kikuchi, T and Mimura, K and Ashizawa, M and Okayama, H and Endo, E and Saito, K and Sakamoto, W and Fujita, S and Endo, H and Saito, M and Momma, T and Saze, Z and Ohki, S and Shimada, K and Yoshimura, K and Tsunoda, T and Kono, K}, title = {Characterization of tumor-infiltrating immune cells in relation to microbiota in colorectal cancers.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {69}, number = {1}, pages = {23-32}, pmid = {31768581}, issn = {1432-0851}, mesh = {Adult ; Aged ; Aged, 80 and over ; Antineoplastic Agents, Immunological/pharmacology/therapeutic use ; Bacteria/immunology/isolation & purification ; Cohort Studies ; Colectomy ; Colon/immunology/microbiology/pathology ; Colorectal Neoplasms/*immunology/microbiology/therapy ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*immunology ; Humans ; Intestinal Mucosa/immunology/microbiology/pathology ; Lymphocytes, Tumor-Infiltrating/drug effects/*immunology/metabolism ; Macrophages/drug effects/*immunology/metabolism ; Male ; Middle Aged ; Tumor Escape/drug effects/*immunology ; Tumor Microenvironment/drug effects/immunology ; }, abstract = {BACKGROUND: Several articles have recently reported that certain colon microbiota can improve the efficacy of cancer immunotherapy. To develop new treatment strategies, including immunotherapy for colorectal cancer (CRC), we evaluated the correlations between subpopulations of tumor-infiltrating immune cells (TIICs) and intestinal microbiota in CRC.

METHODS: Fresh surgically resected specimens, formalin-fixed paraffin-embedded whole tissue samples, and stool samples were collected. TIICs including Tregs, Th17 cells and tumor-associated macrophages (TAMs) in the surgically resected specimens were analyzed using flow cytometry. FOXp3, CD8, CD163, and phosphorylated-STAT1-positive TIICs in the whole tissue samples were analyzed using IHC, and intestinal microbiota in the stool samples was analyzed using 16S metagenome sequencing. TIICs subpopulations in the normal mucosa and tumor samples were evaluated, and the correlations between the TIIC subpopulations and intestinal microbiota were analyzed.

RESULTS: FOXp3[low]CD45RA[+] Tregs were significantly reduced (p = 0.02), FOXp3[low]CD45RA[-] Tregs were significantly increased (p = 0.006), and M1 TAMs were significantly reduced in the tumor samples (p = 0.03). Bacteroides (phylum Bacteroidetes) and Faecalibacterium (phylum Firmicutes) were increased in the patients with high numbers of Tregs and clearly high distribution of FOXp3[high]CD45RA[-] Tregs, which are the effector Tregs. Faecalibacterium, Ruminococcaceae, Eubacterium (phylum Firmicutes), and Bacteroides were increased in patients with a high distribution of M1 TAMs.

CONCLUSIONS: The findings of the present study indicate that immune responses to tumors are suppressed in the tumor microenvironment of CRC depending on the increment of Tregs and the reduction of M1 TAMs and that intestinal microbiota might be involved in immunosuppression.}, } @article {pmid31767028, year = {2019}, author = {Seishima, J and Iida, N and Kitamura, K and Yutani, M and Wang, Z and Seki, A and Yamashita, T and Sakai, Y and Honda, M and Yamashita, T and Kagaya, T and Shirota, Y and Fujinaga, Y and Mizukoshi, E and Kaneko, S}, title = {Gut-derived Enterococcus faecium from ulcerative colitis patients promotes colitis in a genetically susceptible mouse host.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {252}, pmid = {31767028}, issn = {1474-760X}, mesh = {Animals ; Case-Control Studies ; Colitis/etiology/pathology ; Colitis, Ulcerative/drug therapy/*microbiology ; Colon/pathology ; Crohn Disease/microbiology ; Disease Models, Animal ; Drug Therapy, Combination ; Enterococcus faecalis/genetics/*pathogenicity ; Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Interleukin-10/genetics ; Male ; *Metagenome ; Mice ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND: Recent metagenomic analyses have revealed dysbiosis of the gut microbiota of ulcerative colitis (UC) patients. However, the impacts of this dysbiosis are not fully understood, particularly at the strain level.

RESULTS: We perform whole-genome shotgun sequencing of fecal DNA extracts from 13 healthy donors and 16 UC and 8 Crohn's disease (CD) patients. The microbiota of UC and CD patients is taxonomically and functionally divergent from that of healthy donors, with E. faecium being the most differentially abundant species between the two microbial communities. Transplantation of feces from UC or CD patients into Il10[-/-] mice promotes pathological inflammation and cytokine expression in the mouse colon, although distinct cytokine expression profiles are observed between UC and CD. Unlike isolates derived from healthy donors, E. faecium isolates from the feces of UC patients, along with E. faecium strain ATCC 19434, promotes colitis and colonic cytokine expression. Inflammatory E. faecium strains, including ATCC 19434 and a UC-derived strain, cluster separately from commercially available probiotic strains based on whole-genome shotgun sequencing analysis. The presence of E. faecium in fecal samples is associated with large disease extent and the need for multiple medications in UC patients.

CONCLUSIONS: E. faecium strains derived from UC patients display an inflammatory genotype that causes colitis.}, } @article {pmid31766550, year = {2019}, author = {Jonge, PA and Meijenfeldt, FABV and Rooijen, LEV and Brouns, SJJ and Dutilh, BE}, title = {Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages.}, journal = {Viruses}, volume = {11}, number = {12}, pages = {}, pmid = {31766550}, issn = {1999-4915}, support = {639707/ERC_/European Research Council/International ; }, mesh = {Bacteriophages/*genetics ; Bacteroides/*virology ; *Biodiversity ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics ; Genome, Viral/*genetics ; Genomics ; Humans ; Metagenomics ; Phylogeny ; Protein Domains ; Tandem Repeat Sequences/genetics ; Viral Proteins/genetics ; }, abstract = {The human gut contains an expanse of largely unstudied bacteriophages. Among the most common are crAss-like phages, which were predicted to infect Bacteriodetes hosts. CrAssphage, the first crAss-like phage to be discovered, contains a protein encoding a Bacteroides-associated carbohydrate-binding often N-terminal (BACON) domain tandem repeat. Because protein domain tandem repeats are often hotspots of evolution, BACON domains may provide insight into the evolution of crAss-like phages. Here, we studied the biodiversity and evolution of BACON domains in bacteriophages by analysing over 2 million viral contigs. We found a high biodiversity of BACON in seven gut phage lineages, including five known crAss-like phage lineages and two novel gut phage lineages that are distantly related to crAss-like phages. In three BACON-containing phage lineages, we found that BACON domain tandem repeats were associated with phage tail proteins, suggestive of a possible role of these repeats in host binding. In contrast, individual BACON domains that did not occur in tandem were not found in the proximity of tail proteins. In two lineages, tail-associated BACON domain tandem repeats evolved largely through horizontal transfer of separate domains. In the third lineage that includes the prototypical crAssphage, the tandem repeats arose from several sequential domain duplications, resulting in a characteristic tandem array that is distinct from bacterial BACON domains. We conclude that phage tail-associated BACON domain tandem repeats have evolved in at least two independent cases in gut bacteriophages, including in the widespread gut phage crAssphage.}, } @article {pmid31765764, year = {2020}, author = {Zhang, Y and Lou, JW and Kang, A and Zhang, Q and Zhou, SK and Bao, BH and Cao, YD and Yao, WF and Tang, YP and Zhang, L}, title = {Kansuiphorin C and Kansuinin A ameliorate malignant ascites by modulating gut microbiota and related metabolic functions.}, journal = {Journal of ethnopharmacology}, volume = {249}, number = {}, pages = {112423}, doi = {10.1016/j.jep.2019.112423}, pmid = {31765764}, issn = {1872-7573}, mesh = {Animals ; Ascites/*drug therapy/etiology/metabolism ; DNA, Bacterial/isolation & purification ; Disease Models, Animal ; Diterpenes/*pharmacology/therapeutic use ; Drugs, Chinese Herbal/*pharmacology/therapeutic use ; Euphorbia/chemistry ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/physiology ; Helicobacter/genetics/isolation & purification ; Humans ; Lactobacillus/genetics/isolation & purification ; Male ; Metagenome/genetics ; Peritoneal Neoplasms/complications/*drug therapy/metabolism/secondary ; RNA, Ribosomal, 16S/genetics ; Rats ; Toxicity Tests ; }, abstract = {Euphorbia kansui is a toxic Chinese herbal medicine and exhibits promising treatment to the malignant ascites (MA) in its traditional use. Ingenane-type and jastrophane-type diterpenes are demonstrated to be responsible for the toxicity and efficacy of kansui. Two representative compounds, kansuiphorin C (KPC) and kansuinin A (KA) in each type were proved to effectively reduce the ascites. The biological and toxicological effects are closely associated with the gastrointestinal tract, but the possible mechanism and related metabolic functions of KPC and KA treating MA through modulating the gut microbiota remain unclear.

AIM OF THE STUDY: To investigate the possible mechanism and related metabolism of KPC and KA ameliorating malignant ascites through modulating gut microbiota.

MATERIALS AND METHODS: MA rats and normal rats were divided into different groups and administrated with KPC, KA, and positive drug, respectively. 16S rDNA gene sequencing and metagenomes analysis combined with the quantification of short-chain fatty acids of feces were performed to reflect the modulation of gut microbiota. Then, the metabolites of KPC and KA in rat feces under the normal and pathological circumstances were detected by ultra-fast liquid chromatography coupled with MS/MS detector (UFLC-MS/MS) to explore the in-vivo bacterial biotransformation.

RESULTS: KPC and KA were modulatory compounds for gut microbiota. The richness of Lactobacillus and the decreased abundance of Helicobacter involved in the carbohydrate metabolism and amino acid metabolism could be responsible for their prohibitory effects on malignant ascites. KPC exhibited stronger modulation of gut microbiota through making the abundance of Helicobacter about 3.5 times lower than KA. Besides, in-vivo microbial biotransformation of KPC and KA contained oxidation, hydrolysis, dehydration, and methylation to form metabolites of lower polarity. Besides, at the dosage of 10 mg kg[-1], the toxicity of both compounds had weaker influences on the gut microbiota of normal rats.

CONCLUSION: KPC and KA could ameliorate malignant ascites by modulating gut microbiota mainly containing the increase of Lactobacillus and the decrease of Helicobacter and related carbohydrate and amino acid metabolism, providing a basis for their promising clinical usage.}, } @article {pmid31761556, year = {2020}, author = {Sousa, STP and Cabral, L and Lacerda-Júnior, GV and Noronha, MF and Ottoni, JR and Sartoratto, A and Oliveira, VM}, title = {Exploring the genetic potential of a fosmid metagenomic library from an oil-impacted mangrove sediment for metabolism of aromatic compounds.}, journal = {Ecotoxicology and environmental safety}, volume = {189}, number = {}, pages = {109974}, doi = {10.1016/j.ecoenv.2019.109974}, pmid = {31761556}, issn = {1090-2414}, mesh = {Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Dioxygenases/genetics ; Gene Library ; Geologic Sediments/*microbiology ; Hydrocarbons, Aromatic/*metabolism ; *Metagenome ; Metagenomics ; Microbiota ; Mixed Function Oxygenases/genetics ; *Petroleum Pollution ; }, abstract = {Aromatic hydrocarbons (AH) are widely distributed in nature, and many of them have been reported as relevant environmental pollutants and valuable carbon sources for different microorganisms. In this work, high-throughput sequencing of a metagenomic fosmid library was carried out to evaluate the functional and taxonomic diversity of genes involved in aromatic compounds degradation in oil-impacted mangrove sediments. In addition, activity-based approach and gas chromatography were used to assess the degradation potential of fosmid clones. Results indicated that AH degradation genes, such as monooxygenases and dioxygenases, were grouped into the following categories: anaerobic degradation of aromatic compounds (20.34%), metabolism of central aromatic intermediates (35.40%) and peripheral pathways for catabolism of aromatic compounds (22.56%). Taxonomic affiliation of genes related to aromatic compounds metabolism revealed the prevalence of the classes Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria. Aromatic hydrocarbons (phenol, naphthalene, phenanthrene, pyrene and benzopyrene) were used as the only carbon source to screen clones with degradation potential. Of the 2500 clones tested, 48 showed some respiratory activity in at least one of the five carbon sources used. The hydrocarbon degradation ability of the top ten fosmid clones was confirmed by GC-MS. Further, annotation of assembled metagenomic fragments revealed ORFs corresponding to proteins and functional domains directly or indirectly involved in the aromatic compound metabolism, such as catechol 2,3-dioxygenase and ferredoxin oxidoreductase. Finally, these data suggest that the indigenous mangrove sediment microbiota developed essential mechanisms towards ecosystem remediation of petroleum hydrocarbon impact.}, } @article {pmid31759944, year = {2020}, author = {Rapin, A and Chuat, A and Lebon, L and Zaiss, MM and Marsland, BJ and Harris, NL}, title = {Infection with a small intestinal helminth, Heligmosomoides polygyrus bakeri, consistently alters microbial communities throughout the murine small and large intestine.}, journal = {International journal for parasitology}, volume = {50}, number = {1}, pages = {35-46}, doi = {10.1016/j.ijpara.2019.09.005}, pmid = {31759944}, issn = {1879-0135}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Helminthiasis ; Host Microbial Interactions ; Host-Parasite Interactions ; *Intestinal Diseases, Parasitic ; Intestinal Mucosa/microbiology/parasitology ; Intestine, Large/microbiology/parasitology ; Intestines/*microbiology/*parasitology ; Metagenomics ; Mice ; *Nematospiroides dubius/microbiology/parasitology ; Peptostreptococcus/growth & development ; }, abstract = {Increasing evidence suggests that intestinal helminth infection can alter intestinal microbial communities with important impacts on the mammalian host. However, all of the studies to date utilize different techniques to study the microbiome and access different sites of the intestine with little consistency noted between studies. In the present study, we set out to perform a comprehensive analysis of the impact of intestinal helminth infection on the mammalian intestinal bacterial microbiome. For this purpose, we investigated the impact of experimental infection using the natural murine small intestinal helminth, Heligmosomoides polygyrus bakeri and examined possible alterations in both the mucous and luminal bacterial communities along the entire small and large intestine. We also explored the impact of common experimental variables including the parasite batch and pre-infection microbiome, on the outcome of helminth-bacterial interactions. This work provides evidence that helminth infection reproducibly alters intestinal microbial communities, with an impact of infection noted along the entire length of the intestine. Although the exact nature of helminth-induced alterations to the intestinal microbiome differed depending on the microbiome community structure present prior to infection, changes extended well beyond the introduction of new bacterial species by the infecting larvae. Moreover, striking similarities between different experiments were noted, including the consistent outgrowth of a bacterium belonging to the Peptostreptococcaceae family throughout the intestine.}, } @article {pmid31759226, year = {2019}, author = {Cooke, I and Mead, O and Whalen, C and Boote, C and Moya, A and Ying, H and Robbins, S and Strugnell, JM and Darling, A and Miller, D and Voolstra, CR and Adamska, M and , }, title = {Molecular techniques and their limitations shape our view of the holobiont.}, journal = {Zoology (Jena, Germany)}, volume = {137}, number = {}, pages = {125695}, doi = {10.1016/j.zool.2019.125695}, pmid = {31759226}, issn = {1873-2720}, mesh = {*Environmental Microbiology ; *Microbiota ; *Symbiosis ; }, abstract = {It is now recognised that the biology of almost any organism cannot be fully understood without recognising the existence and potential functional importance of associated microbes. Arguably, the emergence of this holistic viewpoint may never have occurred without the development of a crucial molecular technique, 16S rDNA amplicon sequencing, which allowed microbial communities to be easily profiled across a broad range of contexts. A diverse array of molecular techniques are now used to profile microbial communities, infer their evolutionary histories, visualise them in host tissues, and measure their molecular activity. In this review, we examine each of these categories of measurement and inference with a focus on the questions they make tractable, and the degree to which their capabilities and limitations shape our view of the holobiont.}, } @article {pmid31759120, year = {2020}, author = {Kumar, H and Park, W and Lim, D and Srikanth, K and Kim, JM and Jia, XZ and Han, JL and Hanotte, O and Park, JE and Oyola, SO}, title = {Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes.}, journal = {Genomics}, volume = {112}, number = {2}, pages = {1988-1999}, doi = {10.1016/j.ygeno.2019.11.011}, pmid = {31759120}, issn = {1089-8646}, mesh = {Animals ; Bacteroidetes/genetics/pathogenicity ; Cecum/microbiology ; Chickens/*microbiology ; *Drug Resistance, Bacterial ; Ethiopia ; Firmicutes/genetics/pathogenicity ; *Gastrointestinal Microbiome ; *Metagenome ; Metagenomics/methods ; Whole Genome Sequencing/methods ; }, abstract = {We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Through metagenomic analysis we found that microbial populations were mainly dominated by Bacteroidetes and Firmicutes. We identified 2210 common genes in the two groups. LEfSe showed that the distribution of Coprobacter, Geobacter, Cronobacter, Alloprevotella, and Dysgonomonas were more abundant in AF than AM. Analyses using KEGG, eggNOG, and CAZy databases indicated that the pathways of metabolism, genetic information processing, environmental information processing, and cellular process were significantly enriched. Functional abundance was found to be associated with the nutrient absorption and microbial localization of indigenous chickens. We also investigated antibiotic resistant genes and found antibiotics like LSM, cephalosporin, and tetracycline were significantly more abundant in AF than AM.}, } @article {pmid31758610, year = {2019}, author = {Axelrod, CL and Brennan, CJ and Cresci, G and Paul, D and Hull, M and Fealy, CE and Kirwan, JP}, title = {UCC118 supplementation reduces exercise-induced gastrointestinal permeability and remodels the gut microbiome in healthy humans.}, journal = {Physiological reports}, volume = {7}, number = {22}, pages = {e14276}, pmid = {31758610}, issn = {2051-817X}, support = {U54 GM104940/GM/NIGMS NIH HHS/United States ; UL1 TR002548/TR/NCATS NIH HHS/United States ; UL1 RR024989/RR/NCRR NIH HHS/United States ; }, mesh = {Adult ; Cross-Over Studies ; Dietary Supplements ; Double-Blind Method ; Exercise/*physiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/drug effects/*physiology ; Gastrointestinal Tract/drug effects/*metabolism/*microbiology ; Humans ; Intestinal Absorption/drug effects/*physiology ; Ligilactobacillus salivarius ; Male ; Probiotics/*administration & dosage ; }, abstract = {Dysregulation of gut microbiota and intestinal barrier function has emerged as potential mechanisms underlying digestive diseases, yet targeted therapies are lacking The purpose of this investigation was to assess the efficacy of UCC118, a characterized probiotic strain, on exercise-induced GI permeability in healthy humans. In a randomized, double-blind, placebo-controlled crossover study, seven healthy adults received 4 weeks of daily UCC118 or placebo supplementation. GI hyperpermeability was induced by strenuous treadmill running performed before and after each supplementation period. While running, participants ingested 5 g of lactulose, rhamnose, and sucrose. Urine was collected before, immediately after, and every hour for 5 h after exercise to assess GI permeability. Metagenomic sequencing was performed on fecal homogenates collected prior to exercise to identify changes in microbial diversity and taxon abundances. Inflammatory biomarkers were assessed from blood and fecal homogenates collected prior to and immediately following the cessation of exercise. Exercise significantly induced intestinal permeability of lactulose, rhamnose, and sucrose (P < 0.001). UCC118 significantly reduced sucrose (Δ = -0.38 ± 0.13 vs. 1.69 ± 0.79; P < 0.05) recovery, with no substantial change in lactulose (Δ = -0.07 ± 0.23 vs. 0.35 ± 0.15; P = 0.16) or rhamnose (Δ = -0.06 ± 0.22 vs. 0.48 ± 0.28; P = 0.22). Taxonomic sequencing revealed 99 differentially regulated bacteria spanning 6 taxonomic ranks (P < 0.05) after UCC118 supplementation. No differences in plasma IL-6 or fecal zonulin were observed after UCC118 supplementation. The results described herein provide proof of principle that 4 weeks of UCC118 supplementation attenuated exercise-induced intestinal hyperpermeability. Further research is warranted to investigate the as-yet-to-be defined molecular processes of intestinal hyperpermeability and the effects of probiotic supplementation.}, } @article {pmid31758395, year = {2019}, author = {Yang, Z and Zhang, Y and Lv, Y and Yan, W and Xiao, X and Sun, B and Ma, H}, title = {H2 Metabolism revealed by metagenomic analysis of subglacial sediment from East Antarctica.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {57}, number = {12}, pages = {1095-1104}, pmid = {31758395}, issn = {1976-3794}, mesh = {Antarctic Regions ; Archaea/classification/enzymology/genetics/metabolism ; Bacteria/classification/enzymology/genetics/metabolism ; Carbon Cycle ; Chemoautotrophic Growth ; Comamonadaceae/enzymology/metabolism ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Geologic Sediments/*microbiology ; Hydrogen/*metabolism ; Hydrogenase/classification/genetics/isolation & purification ; Metabolic Networks and Pathways ; *Metagenome ; Microbiota/genetics/*physiology ; Nitrates/metabolism ; Oxidative Phosphorylation ; Photosynthesis ; Sequence Analysis, DNA ; }, abstract = {Subglacial ecosystems harbor diverse chemoautotrophic microbial communities in areas with limited organic carbon, and lithological H2 produced during glacial erosion has been considered an important energy source in these ecosystems. To verify the H2-utilizing potential there and to identify the related energy-converting metabolic mechanisms of these communities, we performed metagenomic analysis on subglacial sediment samples from East Antarctica with and without H2 supplementation. Genes coding for several [NiFe]-hydrogenases were identified in raw sediment and were enriched after H2 incubation. All genes in the dissimilatory nitrate reduction and denitrification pathways were detected in the subglacial community, and the genes coding for these pathways became enriched after H2 was supplied. Similarly, genes transcribing key enzymes in the Calvin cycle were detected in raw sediment and were also enriched. Moreover, key genes involved in H2 oxidization, nitrate reduction, oxidative phosphorylation, and the Calvin cycle were identified within one metagenome-assembled genome belonging to a Polaromonas sp. As suggested by our results, the microbial community in the subglacial environment we investigated consisted of chemoautotrophic populations supported by H2 oxidation. These results further confirm the importance of H2 in the cryosphere.}, } @article {pmid31758335, year = {2020}, author = {Malematja, TP and Ijoma, GN and Selvarajan, R and Matambo, T}, title = {Revealing the bacterial community profiles during the degradation of acetone, propionic and hexanoic acids-components of wastewater from the Fischer-Tropsch process.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {23}, number = {2}, pages = {313-324}, doi = {10.1007/s10123-019-00106-z}, pmid = {31758335}, issn = {1618-1905}, support = {Not Applicable//Sasol/ ; }, mesh = {Acetone/metabolism ; Actinobacteria/genetics/isolation & purification/metabolism ; Bacteria/classification/genetics/isolation & purification/*metabolism ; *Biodegradation, Environmental ; Caproates/metabolism ; Firmicutes/genetics/isolation & purification/metabolism ; *Industrial Waste ; Metagenomics ; Microbial Consortia/genetics ; Propionates/metabolism ; Proteobacteria/genetics/isolation & purification/metabolism ; RNA, Ribosomal, 16S ; Wastewater/chemistry/*microbiology ; }, abstract = {The Fischer-Tropsch (F-T) process for production of fuels is entrenched in several countries' approach to meeting energy demands. However, the clean water deficit associated with the down-stream processes has made it necessary to explore bioremediation methods to ameliorate the consequences of its use. In this study, a consortium of bacteria was utilized for determination of biodegradation and removal rates, based on reduction in chemical oxygen demand of a mixture of acetone, propionic acid and hexanoic acid (APH) (all components of F-T wastewater), at an organic loading of 5 and 9.53 g CODL[-1]. The individual degradation efficiencies of the F-T components were determined using a gas chromatograph. Further, the bacterial consortia responsible for the degradation of the mixture of APH were determined using metagenomics data derived from next-generation sequencing. The overall chemical oxygen demand removal was found to be 88.8% and 82.3% at organic loading of 5 and 9.53 g CODL[-1], respectively. The optimal degradation efficiency of acetone, propionic acid and hexanoic acid over a period of 10 days was found to be 100%, 85% and 75.8%, respectively. The primary microbial communities presumed to be responsible for APH degradation by phyla classification across all samples were found to be Proteobacteria (55-92%), Actinobacteria (5-33%) and Firmicutes (0.08-9%). Overall, the study has demonstrated the importance of aerobic consortia interactions in the degradation of components of the F-T wastewater.}, } @article {pmid31758238, year = {2020}, author = {Xiao, S and Liu, C and Chen, M and Zou, J and Zhang, Z and Cui, X and Jiang, S and Shang, E and Qian, D and Duan, J}, title = {Scutellariae radix and coptidis rhizoma ameliorate glycolipid metabolism of type 2 diabetic rats by modulating gut microbiota and its metabolites.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {1}, pages = {303-317}, doi = {10.1007/s00253-019-10174-w}, pmid = {31758238}, issn = {1432-0614}, support = {81673831//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Coptis chinensis ; Diabetes Mellitus, Experimental/physiopathology/*prevention & control ; Drug Combinations ; Drugs, Chinese Herbal/*administration & dosage ; Fatty Acids, Volatile/analysis ; Feces/chemistry ; Gastrointestinal Microbiome/*drug effects ; Glycolipids/*metabolism ; Lipid Metabolism ; Male ; Medicine, Chinese Traditional ; Metabolomics ; RNA, Ribosomal, 16S ; Rats ; Scutellaria baicalensis/*chemistry ; }, abstract = {Scutellariae radix (Scutellaria baicalensis Georgi, SR) and coptidis rhizoma (Coptis chinensis Franch, CR) are both widely used traditional Chinese medicines and have been used together to treat T2DM with synergistic effects in the clinical practices for thousands of years, but their combination mechanism is not clear. Accumulating evidences have implicated gut microbiota as important targets for the therapy of T2DM. Thus, this study aimed to unravel the cooperation mechanism of SR and CR on the amelioration of T2DM based on the systematic analysis of metagenome and metabolome of gut microbiota. Bacterial communities were analyzed based on high-throughput 16S rRNA gene sequencing. Furthermore, ultra high-performance liquid chromatography coupled with quadrupole time of flight mass spectrometry (UPLC-Q-TOF-MS) was used to analyze variations of microbial metabolites in feces and the contents of short chain fatty acids (SCFAs) in the cecum were determined by a gaschromatography-flame ionization detector (GC-FID). 16S rRNA gene sequencing results revealed that T2DM rats treated with SR, CR, and the combination of SR and CR (SC) exhibited changes in the composition of the gut microbiota. The SCFAs-producing bacteria such as Bacteroidales S24-7 group_norank, [Eubacterium] nodatum group, Parasutterella, Prevotellaceae UCG-001, Ruminiclostridium, and Ruminiclostridium 9 in T2DM rats were notably enriched after treatment with SR, CR, and their combination. In contrast, secondary bile acid-producing bacteria such as Escherichia-Shigella strongly decreased in numbers. The perturbance of metabolic profiling in T2DM rats was obviously improved after treatment, exhibiting a lower level of secondary bile acids and a numerical increase of microbially derived SCFAs. Moreover, the correlation analysis illustrated a close relationship among gut microbiota, its metabolites, and T2DM-related indexes. The findings indicated that the crosstalk between microbiota-derived metabolites and the host played an important role in the progress of T2DM and might provide a novel insight regarding gut microbiota and its metabolites as potential new targets of traditional Chinese medicines. Furthermore, this work also suggested that the integration of various omics methods and bioinformatics made a useful template for drug mechanism research.}, } @article {pmid31758176, year = {2020}, author = {Irinyi, L and Hu, Y and Hoang, MTV and Pasic, L and Halliday, C and Jayawardena, M and Basu, I and McKinney, W and Morris, AJ and Rathjen, J and Stone, E and Chen, S and Sorrell, TC and Schwessinger, B and Meyer, W}, title = {Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens: A paradigm shift in mycological diagnostics.}, journal = {Medical mycology}, volume = {58}, number = {5}, pages = {650-660}, doi = {10.1093/mmy/myz109}, pmid = {31758176}, issn = {1460-2709}, mesh = {Bronchoalveolar Lavage Fluid/microbiology ; DNA, Fungal ; Genome, Fungal ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; Mycobiome/genetics ; Nanopores ; Pneumocystis carinii/*classification/*genetics ; Pneumonia, Pneumocystis/*diagnosis/microbiology ; Real-Time Polymerase Chain Reaction ; Respiratory System/microbiology ; Sensitivity and Specificity ; Sputum/microbiology ; }, abstract = {The advent of next generation sequencing technologies has enabled the characterization of the genetic content of entire communities of organisms, including those in clinical specimens, without prior culturing. The MinION from Oxford Nanopore Technologies offers real-time, direct sequencing of long DNA fragments directly from clinical samples. The aim of this study was to assess the ability of unbiased, genome-wide, long-read, shotgun sequencing using MinION to identify Pneumocystis jirovecii directly from respiratory tract specimens and to characterize the associated mycobiome. Pneumocystis pneumonia (PCP) is a life-threatening fungal disease caused by P. jirovecii. Currently, the diagnosis of PCP relies on direct microscopic or real-time quantitative polymerase chain reaction (PCR) examination of respiratory tract specimens, as P. jirovecii cannot be cultured readily in vitro. P. jirovecii DNA was detected in bronchoalveolar lavage (BAL) and induced sputum (IS) samples from three patients with confirmed PCP. Other fungi present in the associated mycobiome included known human pathogens (Aspergillus, Cryptococcus, Pichia) as well as commensal species (Candida, Malassezia, Bipolaris). We have established optimized sample preparation conditions for the generation of high-quality data, curated databases, and data analysis tools, which are key to the application of long-read MinION sequencing leading to a fundamental new approach in fungal diagnostics.}, } @article {pmid31758066, year = {2019}, author = {Wagner Mackenzie, B and Chang, K and Zoing, M and Jain, R and Hoggard, M and Biswas, K and Douglas, RG and Taylor, MW}, title = {Longitudinal study of the bacterial and fungal microbiota in the human sinuses reveals seasonal and annual changes in diversity.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17416}, pmid = {31758066}, issn = {2045-2322}, mesh = {*Bacteria/genetics ; *Biodiversity ; Computational Biology/methods ; DNA, Ribosomal Spacer ; *Fungi/genetics ; Humans ; Metagenomics ; *Microbiota ; Paranasal Sinuses/*microbiology ; RNA, Ribosomal, 16S ; Regression Analysis ; *Seasons ; }, abstract = {There is a pressing need for longitudinal studies which examine the stability of the sinonasal microbiota. In this study, we investigated bacterial and fungal community composition of the sinuses of four healthy individuals every month for one year, then once every three months for an additional year to capture seasonal variation. Sequencing of bacterial 16S rRNA genes and fungal ITS2 revealed communities that were mainly dominated by members of Actinobacteria and Basidiomycota, respectively. We observed overall shifts in both bacterial and fungal community diversity that were attributable to a combination of individual, seasonal and annual changes. The results suggest that each of the subjects possessed a strong bacterial sinonasal signature, but that fungal communities were less subject specific. Differences in fungal and bacterial diversity between subjects, and which OTUs may be correlated with seasonal differences, were investigated. A small core community that persisted throughout the two year sampling period was identified: Corynebacterium, Propionibacterium and Staphylococcus, and one type of fungus, Malassezia restricta. It is likely that bacterial and fungal airway microbiomes are dynamic and experience natural shifts in diversity with time. The underlying reasons for these shifts appear to be a combination of changes in environmental climate and host factors.}, } @article {pmid31758047, year = {2019}, author = {Hallmaier-Wacker, LK and Lüert, S and Roos, C and Knauf, S}, title = {Lactation and menstruation shift the vaginal microbiota in captive rhesus monkeys to be more similar to the male urethral microbiota.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17399}, pmid = {31758047}, issn = {2045-2322}, mesh = {Age Factors ; Animals ; Breeding ; Female ; *Lactation ; Macaca mulatta/*physiology ; Male ; *Menstrual Cycle ; Metagenome ; Metagenomics/methods ; *Microbiota ; Sex Factors ; Sexual Behavior, Animal ; Urethra/*microbiology ; Vagina/*microbiology ; }, abstract = {The vaginal microbiota of nonhuman primates differs substantially from humans in terms of Lactobacillus abundance, overall taxonomic diversity, and vaginal pH. Given these differences, it remains unclear in what way the nonhuman primate genital microbiota protects against pathogens, in particular sexually transmitted infections. Considering the effect that microbiota variations can have on disease acquisition and outcome, we examined endogenous and exogenous factors that influence the urogenital microbiota of male and female captive rhesus monkeys. The male urethral (n = 37) and vaginal (n = 194) microbiota of 11 breeding groups were examined in a cross-sectional study. During lactation and menstruation, the vaginal microbiota becomes significantly more diverse and more similar to the microbes observed in the male urethra. Group association and cage-mate (sexual partners) relationships were additionally associated with significant differences in the urogenital microbiota. Our results demonstrate that microbiota considerations are necessary in order to make informed selection of nonhuman primates as translational animal models.}, } @article {pmid31758037, year = {2019}, author = {Ozga, AT and Gilby, I and Nockerts, RS and Wilson, ML and Pusey, A and Stone, AC}, title = {Oral microbiome diversity in chimpanzees from Gombe National Park.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17354}, pmid = {31758037}, issn = {2045-2322}, mesh = {Animals ; Cluster Analysis ; DNA, Ancient/analysis ; DNA, Bacterial/analysis/genetics ; Dental Plaque/microbiology ; High-Throughput Nucleotide Sequencing ; Metagenome ; *Microbiota/genetics ; Mouth/*microbiology ; Pan troglodytes/*microbiology ; Parks, Recreational ; Phylogeny ; RNA, Ribosomal, 16S/analysis/genetics ; Tanzania ; }, abstract = {Historic calcified dental plaque (dental calculus) can provide a unique perspective into the health status of past human populations but currently no studies have focused on the oral microbial ecosystem of other primates, including our closest relatives, within the hominids. Here we use ancient DNA extraction methods, shotgun library preparation, and next generation Illumina sequencing to examine oral microbiota from 19 dental calculus samples recovered from wild chimpanzees (Pan troglodytes schweinfurthii) who died in Gombe National Park, Tanzania. The resulting sequences were trimmed for quality, analyzed using MALT, MEGAN, and alignment scripts, and integrated with previously published dental calculus microbiome data. We report significant differences in oral microbiome phyla between chimpanzees and anatomically modern humans (AMH), with chimpanzees possessing a greater abundance of Bacteroidetes and Fusobacteria, and AMH showing higher Firmicutes and Proteobacteria. Our results suggest that by using an enterotype clustering method, results cluster largely based on host species. These clusters are driven by Porphyromonas and Fusobacterium genera in chimpanzees and Haemophilus and Streptococcus in AMH. Additionally, we compare a nearly complete Porphyromonas gingivalis genome to previously published genomes recovered from human gingiva to gain perspective on evolutionary relationships across host species. Finally, using shotgun sequence data we assessed indicators of diet from DNA in calculus and suggest exercising caution when making assertions related to host lifestyle. These results showcase core differences between host species and stress the importance of continued sequencing of nonhuman primate microbiomes in order to fully understand the complexity of their oral ecologies.}, } @article {pmid31757825, year = {2020}, author = {Frankel-Bricker, J and Buerki, S and Feris, KP and White, MM}, title = {Influences of a Prolific Gut Fungus (Zancudomyces culisetae) on Larval and Adult Mosquito (Aedes aegypti)-Associated Microbiota.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {3}, pages = {}, pmid = {31757825}, issn = {1098-5336}, support = {P20 GM103408/GM/NIGMS NIH HHS/United States ; P20 GM109095/GM/NIGMS NIH HHS/United States ; P30 GM103324/GM/NIGMS NIH HHS/United States ; }, mesh = {Aedes/growth & development/*microbiology/*physiology ; Animals ; Female ; Fungi/*physiology ; Gastrointestinal Tract/microbiology/physiology ; Larva/growth & development/microbiology/physiology ; Microbiota ; }, abstract = {Adult mosquitoes inherit a bacterial community from larvae via transstadial transmission, an understudied process that may influence host-microbe interactions. Microbes contribute to important host life history traits, and analyzing transmitted microbial communities, the interrelationship between larval and adult-associated microbiota, and factors influencing host-microbe relationships provides targets for research. During its larval stage, the yellow fever mosquito (Aedes aegypti) hosts the trichomycete gut fungus Zancudomyces culisetae, and fungal colonization coincides with environmental perturbations in the digestive tract microecosystem. Natural populations are differentially exposed to fungi, thereby potentially harboring distinct microbiota and experiencing disparate host-microbe interactions. This study's objectives were to characterize larval and initial adult microbiomes, investigate variation in diversity and distribution of microbial communities across individuals, and assess whether larval fungal colonization impacted microbiomes at these developmental stages. Laboratory-based fungal infestation assays, sequencing of 16S rRNA gene amplicons, and bacterial load quantification protocols revealed that initial adult microbiomes varied in diversity and distribution. Larval fungal colonization had downstream effects on initial adult microbiomes, significantly reducing microbial community variation, shifting relative abundances of certain bacterial families, and influencing transstadial transmission outcomes of particular genera. Further, abundances of several families consistently decreased in adults relative to levels in larvae, possibly reflecting impacts of host development on specific bacterial taxa. These findings demonstrated that a prolific gut fungus impacted mosquito-associated microbiota at two developmental stages in an insect connected with global human health.IMPORTANCE Mosquitoes are widespread vectors of numerous human pathogens and harbor microbiota known to affect host phenotypic traits. However, little research has directly investigated how bacterial communities associated with larvae and adults are connected. We characterized whole-body bacterial communities in mosquito larvae preceding pupation and in newly emerged adults, and investigated whether a significant biotic factor, fungal colonization of the larval hindgut, impacted these microbiomes. Results showed that fungal colonization reduced microbial community variation across individuals and differentially impacted the outcomes of transstadial transmission for certain bacterial genera, revealing downstream effects of the fungus on initial adult microbiomes. The importance of our research is in providing a thorough comparative analysis of whole-body microbiota harbored in larvae and adults of the yellow fever mosquito (Aedes aegypti) and in demonstrating the important role a widespread gut fungus played in a host-associated microbiome.}, } @article {pmid31757768, year = {2019}, author = {Clooney, AG and Sutton, TDS and Shkoporov, AN and Holohan, RK and Daly, KM and O'Regan, O and Ryan, FJ and Draper, LA and Plevy, SE and Ross, RP and Hill, C}, title = {Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease.}, journal = {Cell host & microbe}, volume = {26}, number = {6}, pages = {764-778.e5}, doi = {10.1016/j.chom.2019.10.009}, pmid = {31757768}, issn = {1934-6069}, mesh = {Bacteria/classification/genetics ; Bacteriophages/classification/genetics ; Colitis, Ulcerative/microbiology/virology ; Crohn Disease/microbiology/virology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Inflammatory Bowel Diseases/microbiology/*virology ; Male ; *Metagenomics ; Viruses/classification/genetics ; }, abstract = {The human gut virome is thought to significantly impact the microbiome and human health. However, most virome analyses have been performed on a limited fraction of known viruses. Using whole-virome analysis on a published keystone inflammatory bowel disease (IBD) cohort and an in-house ulcerative colitis dataset, we shed light on the composition of the human gut virome in IBD beyond this identifiable minority. We observe IBD-specific changes to the virome and increased numbers of temperate phage sequences in individuals with Crohn's disease. Unlike prior database-dependent methods, no changes in viral richness were observed. Among IBD subjects, the changes in virome composition reflected alterations in bacterial composition. Furthermore, incorporating both bacteriome and virome composition offered greater classification power between health and disease. This approach to analyzing whole virome across cohorts highlights significant IBD signals, which may be crucial for developing future biomarkers and therapeutics.}, } @article {pmid31757632, year = {2019}, author = {Zhang, S and Lin, L and Liu, W and Zou, B and Cai, Y and Liu, D and Xiao, D and Chen, J and Li, P and Zhong, Y and Liao, Q and Xie, Z}, title = {Shen-Ling-Bai-Zhu-San alleviates functional dyspepsia in rats and modulates the composition of the gut microbiota.}, journal = {Nutrition research (New York, N.Y.)}, volume = {71}, number = {}, pages = {89-99}, doi = {10.1016/j.nutres.2019.10.001}, pmid = {31757632}, issn = {1879-0739}, mesh = {Animals ; Disease Models, Animal ; Drugs, Chinese Herbal/*pharmacology ; Dyspepsia/*drug therapy ; Gastrointestinal Microbiome/*drug effects ; Male ; Medicine, Chinese Traditional/*methods ; Rats ; Rats, Sprague-Dawley ; }, abstract = {The pathogenesis of functional dyspepsia (FD) is multifactorial, and the gut microbiota may play a significant role. Shen-Ling-Bai-Zhu-San (SLBZS), a traditional Chinese herbal medicine, has been widely used in the treatment of FD, and appears to influence the gut microbiota. Therefore, we hypothesized that SLBZS would alleviate dyspeptic symptoms by adjusting the composition of the gut microbiota. To test this hypothesis, we aimed to evaluate the effects of SLBZS on FD and elucidate the mechanism that underlies the interactions between gut microbiota and FD during SLBZS treatment. We employed a rat model of FD induced by multiple forms of chronic mild stimulation. 16S rRNA gene sequencing and shotgun metagenomic sequencing were used to analyze the microbial communities in fecal samples from the rats. We found that the SLBZS improved dyspeptic symptoms in FD rats, such as weight loss, decreased intestinal motility, reduced absorptive capacity. Moreover, the SLBZS treatment reversed gut dysbiosis in FD. With SLBZS treatment, FD biomarkers including Prevotella, Mucispirillum and Akkermansia were decreased while SCFA-producing bacteria such as Adlercreutzia and Clostridium, and sulfate-reducing bacteria Desulfovibrio were enriched. Additionally, SLBZS normalized the dysregulated function of the microbiome, upregulating the pathways of energy metabolism and decreasing the oxidative stress as well as bacterial pathogenesis. Our study demonstrated that SLBZS could ameliorate dyspepsia, and amend the dysregulated composition and function of the gut microbial community, providing insight into the mechanism of SLBZS treatment for FD from the perspective of gut microbiota.}, } @article {pmid31757198, year = {2019}, author = {Qian, J and Comin, M}, title = {MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 9}, pages = {367}, pmid = {31757198}, issn = {1471-2105}, mesh = {*Algorithms ; Cluster Analysis ; *Contig Mapping ; Databases, Genetic ; *Metagenome ; *Metagenomics ; Microbiota/genetics ; *Probability ; *Statistics as Topic ; }, abstract = {MOTIVATION: Sequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Because assembly typically produces only genome fragments, also known as contigs, it is crucial to group them into putative species for further taxonomic profiling and down-streaming functional analysis. Taxonomic analysis of microbial communities requires contig clustering, a process referred to as binning, that is still one of the most challenging tasks when analyzing metagenomic data. The major problems are the lack of taxonomically related genomes in existing reference databases, the uneven abundance ratio of species, sequencing errors, and the limitations due to binning contig of different lengths.

RESULTS: In this context we present MetaCon a novel tool for unsupervised metagenomic contig binning based on probabilistic k-mers statistics and coverage. MetaCon uses a signature based on k-mers statistics that accounts for the different probability of appearance of a k-mer in different species, also contigs of different length are clustered in two separate phases. The effectiveness of MetaCon is demonstrated in both simulated and real datasets in comparison with state-of-art binning approaches such as CONCOCT, MaxBin and MetaBAT.}, } @article {pmid31756613, year = {2020}, author = {Makowska, N and Philips, A and Dabert, M and Nowis, K and Trzebny, A and Koczura, R and Mokracka, J}, title = {Metagenomic analysis of β-lactamase and carbapenemase genes in the wastewater resistome.}, journal = {Water research}, volume = {170}, number = {}, pages = {115277}, doi = {10.1016/j.watres.2019.115277}, pmid = {31756613}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; Bacterial Proteins ; *Metagenome ; Poland ; *Wastewater ; beta-Lactamases ; }, abstract = {The emergence and spread of resistance to antibiotics among bacteria is the most serious global threat to public health in recent and coming decades. In this study, we characterized qualitatively and quantitatively β-lactamase and carbapenemase genes in the wastewater resistome of Central Wastewater Treatment Plant in Koziegłowy, Poland. The research concerns determination of the frequency of genes conferring resistance to β-lactam and carbapenem antibiotics in the genomes of culturable bacteria, as well as in the wastewater metagenome at three stages of treatment: raw sewage, aeration tank, and final effluent. In the final effluent we found bacteria with genes that pose the greatest threat to public health, including genes of extended spectrum β-lactamases - blaCTX-M, carbapenemases - blaNDM, blaVIM, blaGES, blaOXA-48, and showed that during the wastewater treatment their frequency increased. Moreover, the wastewater treatment process leads to significant increase in the relative abundance of blaTEM and blaGES genes and tend to increase the relative abundance of blaCTX-M, blaSHV and blaOXA-48 genes in the effluent metagenome. The biodiversity of bacterial populations increased during the wastewater treatment and there was a correlation between the change in the composition of bacterial populations and the variation of relative abundance of β-lactamase and carbapenemase genes. PCR-based quantitative metagenomic analysis combined with analyses based on culture methods provided significant information on the routes of ARBs and ARGs spread through WWTP. The limited effectiveness of wastewater treatment processes in the elimination of antibiotic-resistant bacteria and resistance genes impose the need to develop an effective strategy and implement additional methods of wastewater disinfection, in order to limit the increase and the spread of antibiotic resistance in the environment.}, } @article {pmid31756192, year = {2019}, author = {Watts, GS and Thornton, JE and Youens-Clark, K and Ponsero, AJ and Slepian, MJ and Menashi, E and Hu, C and Deng, W and Armstrong, DG and Reed, S and Cranmer, LD and Hurwitz, BL}, title = {Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity.}, journal = {PLoS computational biology}, volume = {15}, number = {11}, pages = {e1006863}, pmid = {31756192}, issn = {1553-7358}, support = {P30 CA023074/CA/NCI NIH HHS/United States ; P30 ES006694/ES/NIEHS NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/*genetics/*isolation & purification ; DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA/methods ; }, abstract = {Infections are a serious health concern worldwide, particularly in vulnerable populations such as the immunocompromised, elderly, and young. Advances in metagenomic sequencing availability, speed, and decreased cost offer the opportunity to supplement or even replace culture-based identification of pathogens with DNA sequence-based diagnostics. Adopting metagenomic analysis for clinical use requires that all aspects of the workflow are optimized and tested, including data analysis and computational time and resources. We tested the accuracy, sensitivity, and resource requirements of three top metagenomic taxonomic classifiers that use fast k-mer based algorithms: Centrifuge, CLARK, and KrakenUniq. Binary mixtures of bacteria showed all three reliably identified organisms down to 1% relative abundance, while only the relative abundance estimates of Centrifuge and CLARK were accurate. All three classifiers identified the organisms present in their default databases from a mock bacterial community of 20 organisms, but only Centrifuge had no false positives. In addition, Centrifuge required far less computational resources and time for analysis. Centrifuge analysis of metagenomes obtained from samples of VAP, infected DFUs, and FN showed Centrifuge identified pathogenic bacteria and one virus that were corroborated by culture or a clinical PCR assay. Importantly, in both diabetic foot ulcer patients, metagenomic sequencing identified pathogens 4-6 weeks before culture. Finally, we show that Centrifuge results were minimally affected by elimination of time-consuming read quality control and host screening steps.}, } @article {pmid31755272, year = {2020}, author = {Aakko, J and Pietilä, S and Suomi, T and Mahmoudian, M and Toivonen, R and Kouvonen, P and Rokka, A and Hänninen, A and Elo, LL}, title = {Data-Independent Acquisition Mass Spectrometry in Metaproteomics of Gut Microbiota-Implementation and Computational Analysis.}, journal = {Journal of proteome research}, volume = {19}, number = {1}, pages = {432-436}, doi = {10.1021/acs.jproteome.9b00606}, pmid = {31755272}, issn = {1535-3907}, mesh = {Computational Biology/methods ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Mass Spectrometry/*methods ; Proteomics/*methods ; Software ; }, abstract = {Metagenomic approaches focus on taxonomy or gene annotation but lack power in defining functionality of gut microbiota. Therefore, metaproteomics approaches have been introduced to overcome this limitation. However, the common metaproteomics approach uses data-dependent acquisition mass spectrometry, which is known to have limited reproducibility when analyzing samples with complex microbial composition. In this work, we provide a proof of concept for data-independent acquisition (DIA) metaproteomics. To this end, we analyze metaproteomes using DIA mass spectrometry and introduce an open-source data analysis software package, diatools, which enables accurate and consistent quantification of DIA metaproteomics data. We demonstrate the feasibility of our approach in gut microbiota metaproteomics using laboratory-assembled microbial mixtures as well as human fecal samples.}, } @article {pmid31754151, year = {2019}, author = {Mootapally, C and Nathani, NM and Poriya, P and Beleem, I and Dabhi, JC and Gadhvi, IR and Joshi, CG}, title = {Antibiotic Resistome Biomarkers associated to the Pelagic Sediments of the Gulfs of Kathiawar Peninsula and Arabian Sea.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17281}, pmid = {31754151}, issn = {2045-2322}, mesh = {Drug Resistance, Bacterial/*genetics ; Genes, Bacterial/*genetics ; Genetic Markers ; Geologic Sediments/*microbiology ; *Metagenome ; Microbiota/*genetics ; Oceans and Seas ; }, abstract = {Antibiotic resistance has been one of the most persistent global issue. Specifically, marine microbiomes have served as complex reservoirs of antibiotic resistant genes. Molecular advancements have enabled exploration of the uncultured microbial portion from hitherto difficult to sample niches such as deeper oceans. The Gulfs of Kathiawar Peninsula have been known for their unique properties like extreme tidal variations, different sediment textures and physicochemical variations. Pelagic sediment cores across four coordinates each of the Gulf of Kutch, Gulf of Khambhat and an open Arabian Sea were collected, processed for metagenomic sequencing and assessed for antibiotic and metal resistome. The dominant genes were mostly resistant to macrolides, glycopeptides and tetracycline drugs. Studied samples divided into three clusters based on their resistome with carA, macB, bcrA, taeA, srmB, tetA, oleC and sav1866 among the abundant genes. Samples from creek of Gulf of Kutch and mouth of Gulf of Khambhat were most diverse in resistance gene profile. Biomarkers observed include gyrA mutation conferring resistance gene in the Arabian Sea; Proteobacteria species in Gulf of Kutch and Arabian sea; while Aquificae, Acidobacteria and Firmicutes species in the Gulf of Khambhat. Region-wise differentially abundant 23 genes and 3 taxonomic biomarkers were proposed for antibiotic resistance monitoring.}, } @article {pmid31754146, year = {2019}, author = {Bjerre, RD and Hugerth, LW and Boulund, F and Seifert, M and Johansen, JD and Engstrand, L}, title = {Effects of sampling strategy and DNA extraction on human skin microbiome investigations.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17287}, pmid = {31754146}, issn = {2045-2322}, mesh = {Adult ; DNA, Bacterial/isolation & purification ; Female ; Healthy Volunteers ; Humans ; Male ; Metagenomics/*methods ; Microbiota/*genetics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Reagent Kits, Diagnostic ; Sequence Analysis, DNA ; Skin/*microbiology ; Specimen Handling/instrumentation/*methods ; }, abstract = {The human skin is colonized by a wide array of microorganisms playing a role in skin disorders. Studying the skin microbiome provides unique obstacles such as low microbial biomass. The objective of this study was to establish methodology for skin microbiome analyses, focusing on sampling technique and DNA extraction. Skin swabs and scrapes were collected from 9 healthy adult subjects, and DNA extracted using 12 commercial kits. All 165 samples were sequenced using the 16S rRNA gene. Comparing the populations captured by eSwabs and scrapes, 99.3% of sequences overlapped. Using eSwabs yielded higher consistency. The success rate of library preparation applying different DNA extraction kits ranged from 39% to 100%. Some kits had higher Shannon alpha-diversity. Metagenomic shotgun analyses were performed on a subset of samples (N = 12). These data indicate that a reduction of human DNA from 90% to 57% is feasible without lowering the success of 16S rRNA library preparation and without introducing taxonomic bias. Using swabs is a reliable technique to investigate the skin microbiome. DNA extraction methodology is crucial for success of sequencing and adds a substantial amount of variation in microbiome analyses. Reduction of host DNA is recommended for interventional studies applying metagenomics.}, } @article {pmid31753895, year = {2019}, author = {Marißen, J and Haiß, A and Meyer, C and Van Rossum, T and Bünte, LM and Frommhold, D and Gille, C and Goedicke-Fritz, S and Göpel, W and Hudalla, H and Pagel, J and Pirr, S and Siller, B and Viemann, D and Vens, M and König, I and Herting, E and Zemlin, M and Gehring, S and Bork, P and Henneke, P and Härtel, C and , }, title = {Efficacy of Bifidobacterium longum, B. infantis and Lactobacillus acidophilus probiotics to prevent gut dysbiosis in preterm infants of 28+0-32+6 weeks of gestation: a randomised, placebo-controlled, double-blind, multicentre trial: the PRIMAL Clinical Study protocol.}, journal = {BMJ open}, volume = {9}, number = {11}, pages = {e032617}, pmid = {31753895}, issn = {2044-6055}, mesh = {*Bifidobacterium longum ; *Bifidobacterium longum subspecies infantis ; Double-Blind Method ; Dysbiosis/*prevention & control ; Enterocolitis, Necrotizing/prevention & control ; Feces/microbiology ; Gastrointestinal Microbiome ; Gestational Age ; Humans ; Infant, Newborn ; *Infant, Premature ; Intensive Care Units, Neonatal ; *Lactobacillus acidophilus ; Multicenter Studies as Topic ; Probiotics/*administration & dosage ; RNA, Ribosomal, 16S/analysis ; Randomized Controlled Trials as Topic ; Sepsis/prevention & control ; }, abstract = {INTRODUCTION: The healthy 'eubiosis' microbiome in infancy is regarded as the microbiome derived from term, vaginally delivered, antibiotic free, breastfed infants at 4-6 months. Dysbiosis is regarded as a deviation from a healthy state with reduced microbial diversity and deficient capacity to control drug-resistant organisms. Preterm infants are highly sensitive to early gut dysbiosis. Latter has been associated with sepsis and necrotising enterocolitis, but may also contribute to long-term health problems. Probiotics hold promise to reduce the risk for adverse short-term outcomes but the evidence from clinical trials remains inconclusive and none has directly assessed the effects of probiotics on the microbiome at high resolution.

METHODS AND ANALYSIS: A randomised, double blind, placebo-controlled study has been designed to assess the safety and efficacy of the probiotic mix of Bifidobacterium longum and infantis and Lactobacillus acidophilus in the prevention of gut dysbiosis in preterm infants between 28+0 and 32+6 weeks of gestation. The study is conducted in 18 German neonatal intensive care units. Between April 2018 and March 2020, 654 preterm infants of 28+0-32+6 weeks of gestation will be randomised in the first 48 hours of life to 28 days of once daily treatment with either probiotics or placebo. The efficacy endpoint is the prevention of gut dysbiosis at day 30 of life. A compound definition of gut dysbosis is used: (1) colonisation with multidrug-resistant organisms or gram-negative bacteria with high epidemic potential or (2) a significant deviation of the gut microbiota composition as compared with healthy term infants. Dysbiosis is determined by (1) conventional microbiological culture and (2) phylogenetic microbiome analysis by high-throughput 16S rRNA and metagenome sequencing. Persistence of dysbiosis will be assessed at 12-month follow-up visits. Side effects and adverse events related to the intervention will be recorded. Key secondary endpoint(s) are putative consequences of dysbiosis. A subgroup of infants will be thoroughly phenotyped for immune parameters using chipcytometry.

ETHICS AND DISSEMINATION: Ethics approval was obtained in all participating sites. Results of the trial will be published in peer-review journals, at scientific meetings, on the website (www.primal-study.de) and via social media of parent organisations.

TRIAL REGISTRATION NUMBER: DRKS00013197; Pre-results.}, } @article {pmid31752666, year = {2019}, author = {Reis, AC and Kolvenbach, BA and Chami, M and Gales, L and Egas, C and Corvini, PF and Nunes, OC}, title = {Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader 'Candidatus Leucobacter sulfamidivorax' strain GP.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {885}, pmid = {31752666}, issn = {1471-2164}, support = {160332//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; SFRH/BD/95814/2013//Fundação para a Ciência e Tecnologia (FCT)/ ; UID/EQU/00511/2019//FCT/MCTES (PIDDAC)/ ; NORTE-01-0145-FEDER-000005//NORTE 2020/ ; }, mesh = {Actinobacteria/*classification/genetics/metabolism ; Actinomycetales/*classification/genetics ; Genes, Bacterial ; Genome, Bacterial ; Genomics ; Interspersed Repetitive Sequences ; Metagenome ; Microbial Consortia ; Mixed Function Oxygenases/genetics ; Phylogeny ; Sulfonamides/metabolism ; Synteny ; }, abstract = {BACKGROUND: Microbial communities recurrently establish metabolic associations resulting in increased fitness and ability to perform complex tasks, such as xenobiotic degradation. In a previous study, we have described a sulfonamide-degrading consortium consisting of a novel low-abundant actinobacterium, named strain GP, and Achromobacter denitrificans PR1. However, we found that strain GP was unable to grow independently and could not be further purified.

RESULTS: Previous studies suggested that strain GP might represent a new putative species within the Leucobacter genus (16S rRNA gene similarity < 97%). In this study, we found that average nucleotide identity (ANI) with other Leucobacter spp. ranged between 76.8 and 82.1%, further corroborating the affiliation of strain GP to a new provisional species. The average amino acid identity (AAI) and percentage of conserved genes (POCP) values were near the lower edge of the genus delimitation thresholds (65 and 55%, respectively). Phylogenetic analysis of core genes between strain GP and Leucobacter spp. corroborated these findings. Comparative genomic analysis indicates that strain GP may have lost genes related to tetrapyrrole biosynthesis and thiol transporters, both crucial for the correct assembly of cytochromes and aerobic growth. However, supplying exogenous heme and catalase was insufficient to abolish the dependent phenotype. The actinobacterium harbors at least two copies of a novel genetic element containing a sulfonamide monooxygenase (sadA) flanked by a single IS1380 family transposase. Additionally, two homologs of sadB (4-aminophenol monooxygenase) were identified in the metagenome-assembled draft genome of strain GP, but these were not located in the vicinity of sadA nor of mobile or integrative elements.

CONCLUSIONS: Comparative genomics of the genus Leucobacter suggested the absence of some genes encoding for important metabolic traits in strain GP. Nevertheless, although media and culture conditions were tailored to supply its potential metabolic needs, these conditions were insufficient to isolate the PR1-dependent actinobacterium further. This study gives important insights regarding strain GP metabolism; however, gene expression and functional studies are necessary to characterize and further isolate strain GP. Based on our data, we propose to classify strain GP in a provisional new species within the genus Leucobacter, 'Candidatus Leucobacter sulfamidivorax'.}, } @article {pmid31752061, year = {2019}, author = {Yang, SJ and Kim, HW and Choi, SG and Chung, S and Oh, SJ and Borkar, S and Kim, HJ}, title = {Assessment of the Dynamics of Microbial Community Associated with Tetraselmis suecica Culture under Different LED Lights Using Next-Generation Sequencing.}, journal = {Journal of microbiology and biotechnology}, volume = {29}, number = {12}, pages = {1957-1968}, doi = {10.4010/jmb.1910.10046}, pmid = {31752061}, issn = {1738-8872}, mesh = {Aquaculture ; Bacteria/classification/genetics ; Chlorophyta/genetics/*growth & development/*microbiology/*radiation effects ; Color ; *High-Throughput Nucleotide Sequencing ; *Light ; Metagenomics ; Microbiota/genetics/*physiology ; Oxygen/metabolism ; Photosynthesis ; }, abstract = {Tetraselmis is a green algal genus, some of whose species are important in aquaculture as well as biotechnology. In algal culture, fluorescent lamps, traditional light source for culturing algae, are now being replaced by a cost-effective light-emitting diodes (LEDs). In this study, we investigated the effect of LED light of different wavelengths (white, red, yellow, and blue) on the growth of Tetraselmis suecica and its associated microbial community structures using the next-generation sequencing (NGS). The fastest growth rate of T. suecica was shown in the red light, whereas the slowest was in yellow. The highest OTUs (3426) were identified on day 0, whereas the lowest ones (308) were found on day 15 under red light. The top 100 OTUs associated with day 0 and day 5 cultures of T. suecica under the red and yellow LED were compared. Only 26 OTUs were commonly identified among four samples. The highest numbers of unique OTUs were identified at day 0, indicating the high degree of initial microbial diversity of the T. suecica inoculum. The red light-unique OTUs occupied 34.98%, whereas the yellow-specific OTUs accounted for only 2.2%. This result suggested a higher degree of interaction in T. suecica culture under the red light, where stronger photosynthesis occurs. Apparently, the microbial community associated with T. suecica related to the oxygen produced by algal photosynthesis. This result may expand our knowledge about the algaebacteria consortia, which would be useful for various biotechnological applications including wastewater treatment, bioremediation, and sustainable aquaculture.}, } @article {pmid31751342, year = {2019}, author = {Eckstrom, K and Barlow, JW}, title = {Resistome metagenomics from plate to farm: The resistome and microbial composition during food waste feeding and composting on a Vermont poultry farm.}, journal = {PloS one}, volume = {14}, number = {11}, pages = {e0219807}, pmid = {31751342}, issn = {1932-6203}, mesh = {Animal Feed/*microbiology ; Animals ; *Composting ; Drug Resistance, Bacterial/genetics ; Farms ; Food Microbiology ; Humans ; Metagenome ; Metagenomics ; Microbiota/*genetics ; *Poultry ; Refuse Disposal ; Risk Assessment ; Vermont ; }, abstract = {Food waste diversion and composting, either mandated or voluntary, are growing alternatives to traditional waste disposal. An acceptable source of agricultural feed and composting material, methane-emitting food residuals, including post-consumer food scraps, are diverted from landfills allowing recapture of nutrients that would otherwise be lost. However, risk associated with the transfer of antimicrobial resistant bacteria (ARB), antibiotic resistance genes (ARGs), or pathogens from food waste is not well characterized. Using shotgun metagenomic sequencing, ARGs, microbial content, and associated virulence factors were successfully identified across samples from an integrated poultry farm that feeds post-consumer food waste. A total of 495 distinct bacterial species or sub-species, 50 ARGs, and 54 virulence gene sequences were found. ARG sequences related to aminoglycoside, tetracycline, and macrolide resistance were most prominent, while most virulence gene sequences were related to transposon or integron activity. Microbiome content was distinct between on-farm samples and off-farm food waste collection sites, with a reduction in pathogens throughout the composting process. While most samples contained some level of resistance, only 3 resistance gene sequences occurred in both on- and off-farm samples and no multidrug resistance (MDR) gene sequences persisted once on the farm. The risk of incorporating novel or multi-drug resistance from human sources appears to be minimal and the practice of utilizing post-consumer food scraps as feed for poultry and composting material may not present a significant risk for human or animal health. Pearson correlation and co-inertia analysis identified a significant interaction between resistance and virulence genes (P = 0.05, RV = 0.67), indicating that ability to undergo gene transfer may be a better marker for ARG risk than presence of specific bacterial species. This work expands the knowledge of ARG fate during food scrap animal feeding and composting and provides a methodology for reproducible analysis.}, } @article {pmid31750259, year = {2019}, author = {Lin, DM and Koskella, B and Ritz, NL and Lin, D and Carroll-Portillo, A and Lin, HC}, title = {Transplanting Fecal Virus-Like Particles Reduces High-Fat Diet-Induced Small Intestinal Bacterial Overgrowth in Mice.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {348}, pmid = {31750259}, issn = {2235-2988}, mesh = {Animals ; Bacterial Load ; Bacteriophages/isolation & purification/ultrastructure ; Clostridioides difficile ; Diet, High-Fat/*adverse effects ; Disease Models, Animal ; Dysbiosis/*therapy ; Enterocolitis, Pseudomembranous/microbiology/therapy ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Intestine, Small/*microbiology ; Metagenomics/methods ; Mice ; RNA, Ribosomal, 16S ; Treatment Outcome ; }, abstract = {Fecal microbiota transplantation (FMT) is an effective tool for treating Clostridium difficile infection in the setting of dysbiosis of the intestinal microbiome. FMT for other forms of human disorders linked to dysbiosis have been less effective. The fecal microbiota contains a high density of virus-like particles (VLP), up to 90% of which are bacteriophages, thought to have a role in regulating gut bacterial populations. We hypothesized that transplantation of the phage-containing fecal VLP fraction may reduce bacterial density in the dysbiotic setting of small intestinal bacterial overgrowth (SIBO). In an experiment using fecal transplantation, we compared the effect of the fecal VLP fraction (bacteria removed) against "Whole" FMT (bacteria intact) on the ileal microbiome. Recipients were either treated with a 30-day high-fat diet (HFD) as a model of dysbiosis to induce SIBO or were on a standard diet (SD). We observed that transplantation of fecal VLPs from donors on a HFD was sufficient to alter the ileal microbiota, but the effect was dependent on diet of the recipient. In recipients on a HFD, ileal bacterial density was reduced. In recipients on a SD, the ileal microbiome transitioned toward the composition associated with a HFD. In both recipient groups, transplantation of fecal VLP fraction alone produced the same outcome as whole FMT. Neither treatment altered expression of antimicrobial peptides. These findings demonstrated a potential role of VLPs, likely phages, for modifying the gut microbiome during dysbiosis.}, } @article {pmid31744921, year = {2019}, author = {Estrela, AB and Nakashige, TG and Lemetre, C and Woodworth, ID and Weisman, JL and Cohen, LJ and Brady, SF}, title = {Functional Multigenomic Screening of Human-Associated Bacteria for NF-κB-Inducing Bioactive Effectors.}, journal = {mBio}, volume = {10}, number = {6}, pages = {}, pmid = {31744921}, issn = {2150-7511}, support = {R01 AT009562/AT/NCCIH NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Bacterial Infections/*metabolism/*microbiology ; Gene Expression Regulation, Bacterial ; Gene Library ; *Genome, Bacterial ; Humans ; *Metagenomics/methods ; Microbiota ; NF-kappa B/*metabolism ; Operon ; Phylogeny ; }, abstract = {The effect of the microbiota on its human host is driven, at least in part, by small-molecule and protein effectors it produces. Here, we report on the use of functional multigenomic screening to identify microbiota-encoded effectors. In this study, genomic DNA from 116 human-associated bacteria was cloned en masse, and the resulting multigenomic library was screened using a nuclear factor-κB reporter (NF-κB) assay. Functional multigenomics builds on the concept of functional metagenomics but takes advantage of increasing advances in cultivating and sequencing human-associated bacteria. Effector genes found to confer NF-κB-inducing activity to Escherichia coli encode proteins in four general categories: cell wall hydrolases, membrane transporters, lipopolysaccharide biosynthetic enzymes, and proteins of unknown function. The compact nature of multigenomic libraries, which results from the ability to normalize input DNA ratios, should simplify screening of libraries using diverse heterologous hosts and reporter assays, increasing the rate of discovery of novel effector genes.IMPORTANCE Human-associated bacteria are thought to encode bioactive small molecules and proteins that play an intimate role in human health and disease. Here, we report on the creation and functional screening of a multigenomic library constructed using genomic DNA from 116 bacteria found at diverse sites across the human body. Individual clones were screened for genes capable of conferring NF-κB-inducing activity to Escherichia coli NF-κB is a useful reporter for a range of cellular processes related to immunity, pathogenesis, and inflammation. Compared to the screening of metagenomic libraries, the ability to normalize input DNA ratios when constructing a multigenomic library should facilitate the more efficient examination of commensal bacteria for diverse bioactivities. Multigenomic screening takes advantage of the growing available resources in culturing and sequencing the human microbiota and generates starting points for more in-depth studies on the mechanisms by which commensal bacteria interact with their human host.}, } @article {pmid31744665, year = {2020}, author = {French, RK and Holmes, EC}, title = {An Ecosystems Perspective on Virus Evolution and Emergence.}, journal = {Trends in microbiology}, volume = {28}, number = {3}, pages = {165-175}, doi = {10.1016/j.tim.2019.10.010}, pmid = {31744665}, issn = {1878-4380}, mesh = {Biodiversity ; Ecosystem ; Genome, Viral/genetics ; Humans ; Phylogeny ; Virus Diseases/*pathology/*transmission ; Viruses/*genetics/*pathogenicity ; }, abstract = {Understanding the emergence of pathogenic viruses has dominated studies of virus evolution. However, new metagenomic studies imply that relatively few of an immense number of viruses may lead to overt disease. This suggests a change in emphasis, from viruses as habitual pathogens to integral components of ecosystems. Here we show how viruses alter interactions between host individuals, populations, and ecosystems, impacting ecosystem health, resilience, and function, and how host ecology in turn impacts viral abundance and diversity. Moving to an ecosystems perspective will put virus evolution and disease emergence in its true context, and enhance our understanding of ecological processes.}, } @article {pmid31744431, year = {2019}, author = {Scanlan, PD}, title = {Microbial evolution and ecological opportunity in the gut environment.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1915}, pages = {20191964}, pmid = {31744431}, issn = {1471-2954}, mesh = {Animals ; *Biological Evolution ; *Gastrointestinal Microbiome ; Humans ; Life History Traits ; Mice/*microbiology ; Models, Animal ; }, abstract = {Recent genomic and metagenomic studies have highlighted the presence of rapidly evolving microbial populations in the human gut. However, despite the fundamental implications of this intuitive finding for both basic and applied gut microbiome research, very little is known about the mode, tempo and potential functional consequences of microbial evolution in the guts of individual human hosts over a lifetime. Here I assess the potential relevance of ecological opportunity to bacterial adaptation, colonization and persistence in the neonate and germ-free mammalian gut environment as well as over the course of an individual lifetime using data emerging from mouse models as well as human studies to provide examples where possible. I then briefly outline how the continued development and application of experimental evolution approaches coupled to genomic and metagenomic analysis is essential to disentangling drift from selection and identifying specific drivers of evolution in the gut microbiome within and between individual human hosts and populations.}, } @article {pmid31744351, year = {2021}, author = {Bender, JM and Li, F and Purswani, H and Capretz, T and Cerini, C and Zabih, S and Hung, L and Francis, N and Chin, S and Pannaraj, PS and Aldrovandi, G}, title = {Early exposure to antibiotics in the neonatal intensive care unit alters the taxonomic and functional infant gut microbiome.}, journal = {The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians}, volume = {34}, number = {20}, pages = {3335-3343}, pmid = {31744351}, issn = {1476-4954}, support = {K12 HD052954/HD/NICHD NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents ; Dysbiosis ; Feces ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Intensive Care Units, Neonatal ; }, abstract = {INTRODUCTION: The infant gut microbiome is thought to play a key role in developing metabolic and immunologic pathways. Antibiotics have been shown to disrupt the human microbiome, but the impact they have on infants during this key window of development remains poorly understood. Through this study, we further characterize the effect antibiotics have on the gut microbiome of infants by looking at metagenomic sequencing data over time.

MATERIALS AND METHODS: Stool samples were collected on infants from a large tertiary care neonatal intensive care unit. After DNA extraction, metagenomics libraries were generated and sequenced. Taxonomic and functional analyses were then performed. Further directed specimen sequencing for fungal species was also performed.

RESULTS: A total of 51 stool samples from 25 infants were analyzed: seven infants were on antibiotics during at least one of their collection time points. Antibiotics given at birth altered the microbiome (PERMANOVA R[2] = 0.044, p = .002) but later courses did not (R[2] = 0.023, p = .114). Longitudinal samples collected while off antibiotics were more similar than those collected during a transition on or off antibiotics (mean Bray-Curtis distance 0.29 vs. 0.63, Wilcoxon p = .06). Functional analysis revealed four microbial pathways that were disrupted by antibiotics given at-birth (p < .1, folate synthesis, glycerolipid metabolism, fatty acid biosynthesis, and glycolysis). No functional changes associated with current antibiotic use were identified. In a limited sample set, we saw little evidence of fungal involvement in the overall infant microbiome.

CONCLUSION: Through this study, we have further characterized the role antibiotics have in the development of the infant microbiome. Antibiotics given at birth were associated with alterations in the microbiome and had significant impact on the functional pathways involved in folate synthesis and multiple metabolic pathways. Later courses of antibiotics led to stochastic dysbiosis and a significant decrease in Escherichia coli. Further characterization of the infant mycobiome is still needed.}, } @article {pmid31737256, year = {2019}, author = {Thang, MWC and Chua, XY and Price, G and Gorse, D and Field, MA}, title = {MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data.}, journal = {F1000Research}, volume = {8}, number = {}, pages = {726}, pmid = {31737256}, issn = {2046-1402}, mesh = {Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S ; *Software ; *Workflow ; }, abstract = {Metagenomic sequencing is an increasingly common tool in environmental and biomedical sciences. While software for detailing the composition of microbial communities using 16S rRNA marker genes is relatively mature, increasingly researchers are interested in identifying changes exhibited within microbial communities under differing environmental conditions. In order to gain maximum value from metagenomic sequence data we must improve the existing analysis environment by providing accessible and scalable computational workflows able to generate reproducible results. Here we describe a complete end-to-end open-source metagenomics workflow running within Galaxy for 16S differential abundance analysis. The workflow accepts 454 or Illumina sequence data (either overlapping or non-overlapping paired end reads) and outputs lists of the operational taxonomic unit (OTUs) exhibiting the greatest change under differing conditions. A range of analysis steps and graphing options are available giving users a high-level of control over their data and analyses. Additionally, users are able to input complex sample-specific metadata information which can be incorporated into differential analysis and used for grouping / colouring within graphs. Detailed tutorials containing sample data and existing workflows are available for three different input types: overlapping and non-overlapping read pairs as well as for pre-generated Biological Observation Matrix (BIOM) files. Using the Galaxy platform we developed MetaDEGalaxy, a complete metagenomics differential abundance analysis workflow. MetaDEGalaxy is designed for bench scientists working with 16S data who are interested in comparative metagenomics. MetaDEGalaxy builds on momentum within the wider Galaxy metagenomics community with the hope that more tools will be added as existing methods mature.}, } @article {pmid31742865, year = {2020}, author = {Geesink, P and Wegner, CE and Probst, AJ and Herrmann, M and Dam, HT and Kaster, AK and Küsel, K}, title = {Genome-inferred spatio-temporal resolution of an uncultivated Roizmanbacterium reveals its ecological preferences in groundwater.}, journal = {Environmental microbiology}, volume = {22}, number = {2}, pages = {726-737}, doi = {10.1111/1462-2920.14865}, pmid = {31742865}, issn = {1462-2920}, support = {2016 FGI 0024//Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft/International ; CRC 1076//Collaborative Research Centre AquaDiva/International ; ANR-10-INBS-09//France Génomique and French Bioinformatics Institute/International ; ANR-11-INBS-0013//France Génomique and French Bioinformatics Institute/International ; //LABGeM (CEA/Genoscope & CNRS UMR8030)/International ; SAS-2015-HKI-LWC//Leibniz Research Cluster InfectoOptics/International ; //Ministerium für Kultur und Wissenschaft des Landes Nordrhein-Westfalen/International ; 41-5507-2016//Strategy and Innovation Grant from the Free State of Thuringia/International ; //Agence Nationale pour la Recherche/International ; //Deutsche Forschungsgemeinschaft/International ; //Friedrich Schiller University Jena/International ; }, mesh = {Bacteria/genetics/*metabolism ; *Bacterial Physiological Phenomena ; Carbon ; Groundwater/*microbiology ; Lactic Acid/*metabolism ; Metagenomics ; Microbial Interactions/*physiology ; Microbiota/genetics/physiology ; RNA, Ribosomal, 16S/genetics ; Spatio-Temporal Analysis ; Symbiosis ; }, abstract = {Subsurface ecosystems like groundwater harbour diverse microbial communities, including small-sized, putatively symbiotic organisms of the Candidate Phyla Radiation, yet little is known about their ecological preferences and potential microbial partners. Here, we investigated a member of the superphylum Microgenomates (Cand. Roizmanbacterium ADI133) from oligotrophic groundwater using mini-metagenomics and monitored its spatio-temporal distribution using 16S rRNA gene analyses. A Roizmanbacteria-specific quantitative PCR assay allowed us to track its abundance over the course of 1 year within eight groundwater wells along a 5.4 km hillslope transect, where Roizmanbacteria reached maximum relative abundances of 2.3%. In-depth genomic analyses suggested that Cand. Roizmanbacterium ADI133 is a lactic acid fermenter, potentially able to utilize a range of complex carbon substrates, including cellulose. We hypothesize that it attaches to host cells using a trimeric autotransporter adhesin and inhibits their cell wall biosynthesis using a toxin-antitoxin system. Network analyses based on correlating Cand. Roizmanbacterium ADI133 abundances with amplicon sequencing-derived microbial community profiles suggested one potential host organism, classified as a member of the class Thermodesulfovibrionia (Nitrospirae). By providing lactate as an electron donor Cand. Roizmanbacterium ADI133 potentially mediates the transfer of carbon to other microorganisms and thereby is an important connector in the microbial community.}, } @article {pmid31741368, year = {2019}, author = {Fiore, JR and Di Stefano, M and Greco, P and Elnour, MO and Alwazzeh, MJ and Santantonio, T}, title = {The absence of culturable bacteria from at term placentae from HIV-negative and positive women argues against a placental unique microbiota.}, journal = {Minerva ginecologica}, volume = {71}, number = {6}, pages = {476-477}, doi = {10.23736/S0026-4784.19.04474-5}, pmid = {31741368}, issn = {1827-1650}, mesh = {Bacteria ; Female ; *HIV Infections ; Humans ; Metagenomics ; *Microbiota ; Placenta ; Pregnancy ; RNA, Ribosomal, 16S ; Real-Time Polymerase Chain Reaction ; }, } @article {pmid31740752, year = {2020}, author = {Lawson, MAE and O'Neill, IJ and Kujawska, M and Gowrinadh Javvadi, S and Wijeyesekera, A and Flegg, Z and Chalklen, L and Hall, LJ}, title = {Breast milk-derived human milk oligosaccharides promote Bifidobacterium interactions within a single ecosystem.}, journal = {The ISME journal}, volume = {14}, number = {2}, pages = {635-648}, pmid = {31740752}, issn = {1751-7370}, support = {BB/J004529/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 100/974/C/13/Z/WT_/Wellcome Trust/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 100974/WT_/Wellcome Trust/United Kingdom ; BBS/E/F/00044409/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; BB/M011216/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Bifidobacterium/genetics/isolation & purification/physiology ; Breast Feeding ; Carbohydrate Metabolism/*genetics ; Ecosystem ; Female ; Genes, Bacterial ; Genetic Variation ; Genome, Bacterial ; Humans ; Infant ; Metagenome/genetics/physiology ; Microbial Interactions ; Microbiota ; *Milk, Human/chemistry ; Oligosaccharides/*genetics/metabolism ; }, abstract = {Diet-microbe interactions play an important role in modulating the early-life microbiota, with Bifidobacterium strains and species dominating the gut of breast-fed infants. Here, we sought to explore how infant diet drives distinct bifidobacterial community composition and dynamics within individual infant ecosystems. Genomic characterisation of 19 strains isolated from breast-fed infants revealed a diverse genomic architecture enriched in carbohydrate metabolism genes, which was distinct to each strain, but collectively formed a pangenome across infants. Presence of gene clusters implicated in digestion of human milk oligosaccharides (HMOs) varied between species, with growth studies indicating that within single infants there were differences in the ability to utilise 2'FL and LNnT HMOs between strains. Cross-feeding experiments were performed with HMO degraders and non-HMO users (using spent or 'conditioned' media and direct co-culture). Further [1]H-NMR analysis identified fucose, galactose, acetate, and N-acetylglucosamine as key by-products of HMO metabolism; as demonstrated by modest growth of non-HMO users on spend media from HMO metabolism. These experiments indicate how HMO metabolism permits the sharing of resources to maximise nutrient consumption from the diet and highlights the cooperative nature of bifidobacterial strains and their role as 'foundation' species in the infant ecosystem. The intra- and inter-infant bifidobacterial community behaviour may contribute to the diversity and dominance of Bifidobacterium in early life and suggests avenues for future development of new diet and microbiota-based therapies to promote infant health.}, } @article {pmid31740592, year = {2019}, author = {Tanentzap, AJ and Fitch, A and Orland, C and Emilson, EJS and Yakimovich, KM and Osterholz, H and Dittmar, T}, title = {Chemical and microbial diversity covary in fresh water to influence ecosystem functioning.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {49}, pages = {24689-24695}, pmid = {31740592}, issn = {1091-6490}, mesh = {*Biodiversity ; *Carbon Cycle ; DNA, Environmental/genetics/isolation & purification ; Fresh Water/*chemistry/*microbiology ; Geologic Sediments/chemistry/microbiology ; Greenhouse Gases/analysis ; Lakes ; Metagenome/genetics ; Metagenomics/methods ; Tracheophyta/chemistry ; }, abstract = {Invisible to the naked eye lies a tremendous diversity of organic molecules and organisms that make major contributions to important biogeochemical cycles. However, how the diversity and composition of these two communities are interlinked remains poorly characterized in fresh waters, despite the potential for chemical and microbial diversity to promote one another. Here we exploited gradients in chemodiversity within a common microbial pool to test how chemical and biological diversity covary and characterized the implications for ecosystem functioning. We found that both chemodiversity and genes associated with organic matter decomposition increased as more plant litterfall accumulated in experimental lake sediments, consistent with scenarios of future environmental change. Chemical and microbial diversity were also positively correlated, with dissolved organic matter having stronger effects on microbes than vice versa. Under our experimental scenarios that increased sediment organic matter from 5 to 25% or darkened overlying waters by 2.5 times, the resulting increases in chemodiversity could increase greenhouse gas concentrations in lake sediments by an average of 1.5 to 2.7 times, when all of the other effects of litterfall and water color were considered. Our results open a major new avenue for research in aquatic ecosystems by exposing connections between chemical and microbial diversity and their implications for the global carbon cycle in greater detail than ever before.}, } @article {pmid31739640, year = {2019}, author = {Liang, YX and Wen, P and Wang, Y and OuYang, DM and Wang, D and Chen, YZ and Song, Y and Deng, J and Sun, YM and Wang, H}, title = {The Constipation-Relieving Property of d-Tagatose by Modulating the Composition of Gut Microbiota.}, journal = {International journal of molecular sciences}, volume = {20}, number = {22}, pages = {}, pmid = {31739640}, issn = {1422-0067}, support = {2016YFE0106000//National Key R&D Program of China/ ; No. 2019B020211002//Key Area R&D Program of Guangdong Province/ ; 201804020077//Science and Technology Planning Project of Guangzhou City/ ; 2019SCAUGH03//International Cooperation Program of SCAU/ ; 2017//Project Supported by Guangdong Province Universities and Colleges Pearl River Scholar Funded Scheme/ ; }, mesh = {Animals ; Biodiversity ; Constipation/drug therapy ; Defecation/drug effects ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Transit/drug effects ; Hexoses/*pharmacology ; Metagenomics ; Mice ; Neurotransmitter Agents/blood ; Prebiotics ; RNA, Ribosomal, 16S ; }, abstract = {d-tagatose, a monosaccharide as well as a dietary supplement, has been reported as having a wide range of applicability in the food industry, however, the prebiotic activity, anticonstipation effects, and related mechanisms are still unclear. In this study, using the loperamide-induced constipation Kunming mice as the animal model, the effects of d-tagatose for the prevention of constipation were evaluated by gastrointestinal transit experiment and defecation experiment. Furthermore, the underlying mechanism was clarified by evaluating the change of the biochemical indicators and analyzing 16S rRNA amplicon of gut microbiota among the different mice groups. The results showed that the gastrointestinal transit rate, fecal number, and weight in six hours were significantly enhanced after the administration of d-tagatose. In addition, d-tagatose significantly increased the serum levels of acetylcholine (Ach) and substance P (SP), whereas the serum levels of nitric oxide (NO) were significantly decreased. Moreover, the 16S rRNA sequencing analysis revealed that the changes in the gut microbiota caused by constipation were restored by d-tagatose treatment. In conclusion, this study indicated that the administration of d-tagatose as a dietary supplement can effectively prevent and relieve constipation in Kunming mice, and it is a promising prebiotic candidate with constipation-relieving properties.}, } @article {pmid31739261, year = {2020}, author = {Dong, ZX and Li, HY and Chen, YF and Wang, F and Deng, XY and Lin, LB and Zhang, QL and Li, JL and Guo, J}, title = {Colonization of the gut microbiota of honey bee (Apis mellifera) workers at different developmental stages.}, journal = {Microbiological research}, volume = {231}, number = {}, pages = {126370}, doi = {10.1016/j.micres.2019.126370}, pmid = {31739261}, issn = {1618-0623}, mesh = {Animals ; Bees/*microbiology ; Bifidobacterium/genetics ; Gastrointestinal Microbiome/*genetics ; Lactobacillus/genetics ; *Life Cycle Stages ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The role of the gut microbiome in animal health has become increasingly evident. Although the structure of the gut microbiome of A. mellifera is well known, little is known about the dynamic change across different developmental stages. In this study, we explored the dynamic changes of the gut microbiota of A. mellifera at different developmental stages covering the whole life cycle using high-throughput 16S rRNA gene sequencing. The results indicated that the core (shared) gut microbiota changes significantly among different developmental stages. The diversity of the bacterial community in workers among different ages was significantly different. In addition, by comparing the core gut microbiota among different-aged workers, we found that newly emerged workers had fewer core microbiota. Three genera, Gilliamella, Frischella, and Snodgrassella, were significantly colonized at 1 day poste mergence (dpe); Lactobacillus, Bifidobacterium, Commensalibacter were significantly colonized at 3 dpe and significantly reduced with Gilliamella. Lactobacillus kunkeei and Bartonella were significantly colonized at 12 dpe and were significantly decreased with Lactobacillus helsingborgensis. Commensalibacter and Bifidobacterium were significantly decreased at 25 dpe, and Bacteroides, Escherichia-Shigella, and Porphyromonadaceae were significantly decreased between 19 and 25 dpe. Our results reveal the succession of the gut microbiota of workers from birth to senescence, which provides a theoretical basis for further exploring the roles of gut microbiota during different developmental stages.}, } @article {pmid31738795, year = {2019}, author = {Cheong, HC and Yap, PSX and Chong, CW and Cheok, YY and Lee, CYQ and Tan, GMY and Sulaiman, S and Hassan, J and Sabet, NS and Looi, CY and Gupta, R and Arulanandam, B and AbuBakar, S and Teh, CSJ and Chang, LY and Wong, WF}, title = {Diversity of endocervical microbiota associated with genital Chlamydia trachomatis infection and infertility among women visiting obstetrics and gynecology clinics in Malaysia.}, journal = {PloS one}, volume = {14}, number = {11}, pages = {e0224658}, pmid = {31738795}, issn = {1932-6203}, mesh = {Academic Medical Centers ; Adult ; Bacteria, Anaerobic/immunology/isolation & purification ; Cervix Uteri/*microbiology ; Chlamydia Infections/complications/immunology/*microbiology ; Chlamydia trachomatis/*isolation & purification/pathogenicity ; Cohort Studies ; DNA, Bacterial/genetics/isolation & purification ; Female ; Host-Pathogen Interactions/immunology ; Humans ; Infertility/immunology/*microbiology ; Malaysia ; Metagenomics ; Microbiota/genetics/*immunology ; Outpatient Clinics, Hospital ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {The cervical microbiota constitutes an important protective barrier against the invasion of pathogenic microorganisms. A disruption of microbiota within the cervical milieu has been suggested to be a driving factor of sexually transmitted infections. These include Chlamydia trachomatis which frequently causes serious reproductive sequelae such as infertility in women. In this study, we profiled the cervical microbial composition of a population of 70 reproductive-age Malaysian women; among which 40 (57.1%) were diagnosed with genital C. trachomatis infection, and 30 (42.8%) without C. trachomatis infection. Our findings showed a distinct compositional difference between the cervical microbiota of C. trachomatis-infected subjects and subjects without C. trachomatis infection. Specifically, significant elevations of mostly strict and facultative anaerobes such as Streptococcus, Megasphaera, Prevotella, and Veillonella in the cervical microbiota of C. trachomatis-positive women were detected. The results from the current study highlights an interaction of C. trachomatis with the environmental microbiome in the endocervical region.}, } @article {pmid31737577, year = {2019}, author = {Khan, S and Voordouw, MJ and Hill, JE}, title = {Competition Among Gardnerella Subgroups From the Human Vaginal Microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {374}, pmid = {31737577}, issn = {2235-2988}, mesh = {Biofilms ; Female ; Gardnerella/*physiology ; Gram-Positive Bacterial Infections/*microbiology ; Humans ; Metagenome ; Metagenomics/methods ; *Microbial Interactions ; Microbiota ; RNA, Ribosomal, 16S ; Vagina/*microbiology ; Vaginosis, Bacterial/*microbiology ; }, abstract = {Gardnerella spp. are hallmarks of bacterial vaginosis, a clinically significant dysbiosis of the vaginal microbiome. Gardnerella has four subgroups (A, B, C, and D) based on cpn60 sequences. Multiple subgroups are often detected in individual women, and interactions between these subgroups are expected to influence their population dynamics and associated clinical signs and symptoms of bacterial vaginosis. In the present study, contact-independent and contact-dependent interactions between the four Gardnerella subgroups were investigated in vitro. The cell free supernatants of mono- and co-cultures had no effect on growth rates of the Gardnerella subgroups suggesting that there are no contact-independent interactions (and no contest competition). For contact-dependent interactions, mixed communities of 2, 3, or 4 subgroups were created and the initial (0 h) and final population sizes (48 h) were quantified using subgroup-specific PCR. Compared to the null hypothesis of neutral interactions, most (69.3%) of the mixed communities exhibited competition. Competition reduced the growth rates of subgroups A, B, and C. In contrast, the growth rate of subgroup D increased in the presence of the other subgroups. All subgroups were able to form biofilm alone and in mixed communities. Our study suggests that there is scramble competition among Gardnerella subgroups, which likely contributes to the observed distributions of Gardnerella spp. in vaginal microbiomes and the formation of the multispecies biofilms characteristic of bacterial vaginosis.}, } @article {pmid31736262, year = {2020}, author = {Mazón-Suástegui, JM and Salas-Leiva, JS and Medina-Marrero, R and Medina-García, R and García-Bernal, M}, title = {Effect of Streptomyces probiotics on the gut microbiota of Litopenaeus vannamei challenged with Vibrio parahaemolyticus.}, journal = {MicrobiologyOpen}, volume = {9}, number = {2}, pages = {e967}, pmid = {31736262}, issn = {2045-8827}, mesh = {Animals ; Biodiversity ; *Gastrointestinal Microbiome ; Microbial Interactions ; Penaeidae/*microbiology ; Probiotics ; RNA, Ribosomal, 16S/genetics ; *Streptomyces ; Vibrio parahaemolyticus ; }, abstract = {This study assessed the intestinal microbiota of juveniles of the White shrimp Litopenaus vannamei, whose feed was enriched with three probiotic formulations: Streptomyces sp. RL8 (RL8); a mix of Lactobacillus graminis and Streptomyces spp. RL8 and N7 (Lac-Strep); and a mix of Bacillus spp. and Streptomyces spp. RL8 and N7 (Bac-Strep). The analysis was performed by sequencing the V3 region of the 16S rRNA gene of treated animals and the control group before and after Vibrio parahaemolyticus challenge. After challenge, the highest Shannon diversity indexes corresponded to RL8 and Bac-Strep (3.94 ± 0.11 and 3.39 ± 0.3, respectively) and the lowest to the control group (2.58 ± 0.26). The most abundant phyla before and after challenge were Proteobacteria, Actinobacteria, and Bacteroidetes. The principal component analysis and Statistical Analysis of Metagenomic Profiles (STAMP) showed that the gut microbiota of the groups RL8 and Bac-Strep after challenge was different from the other experimental groups, which was characterized by a higher bacterial diversity, as well as a significant stimulation of the Bacteriovorax population and other antimicrobial producing genera that protected shrimp from infection.}, } @article {pmid31734483, year = {2020}, author = {Khan, MS and Koizumi, N and Olds, JL}, title = {Biofixation of atmospheric nitrogen in the context of world staple crop production: Policy perspectives.}, journal = {The Science of the total environment}, volume = {701}, number = {}, pages = {134945}, doi = {10.1016/j.scitotenv.2019.134945}, pmid = {31734483}, issn = {1879-1026}, mesh = {Agriculture ; Air Pollution/*analysis/legislation & jurisprudence/statistics & numerical data ; Biodiversity ; Conservation of Natural Resources ; Crop Production ; *Crops, Agricultural ; Ecosystem ; *Environmental Policy ; Environmental Pollution ; Fertilizers ; Nitrogen/*analysis ; }, abstract = {The extensive use of nitrogen (N) fertilizers implicates a paradox: while fertilizers ensure the supply of a large amount of food, they cause negative environmental externalities, including reduced biodiversity, and eutrophic streams and lakes. Moreover, such fertilizers may also result in a major public health hazard: increased antibiotic resistance. This article discusses the critical implications of perturbations in N cycle caused by excessive use of fertilizers and resulting policy implications as they relate to ecosystem services. While there are solutions such as cover crops, these solutions are expensive and inconvenient for farmers. We advocate the use of biological fixation (BF) for staple crops-microbiome mediated natural supply of fixed N. This would involve engineering a microbiome that can be grown cheaply and at industrial scale. Fertilizers resulting from such innovation are termed as "biofertilizers" in this article. Following a qualitative cost-benefit analysis broken down by key stakeholders and a quick exploration of policy frameworks as they relate to the advancement of biofertilizers, we propose a practical pathway of where and how research investments should be directed to make such a solution feasible. We make five policy recommendations for decision-makers to facilitate a successful trajectory for this solution: (1) Future agricultural science should seek to understand how BF might be employed as a practical and efficient strategy. This effort would require that industry and the government partner to establish a pre-competitive research laboratory equipped with the latest state-of-the-art technologies that conduct metagenomic experiments to reveal signature microbiomes and form novel symbiotic connections. (2) To have a smooth ride in the market, ag-bio companies should: (i) create awareness among farmers; (ii) impart skills to farmers in testing and using biofertilizers, and (iii) conduct extensive field tests and more research in studying the scalability potential of such fertilizers. (3)The United States Department of Agriculture (USDA) and state governments should provide research and development (R&D) tax credits to biotech companies specifically geared towards R&D investments aimed at increasing the viability of BF and microbiome engineering. (4) To control agricultural pollution in the biosphere, federal governments should consider passing a Clean Agriculture Act (CAA), including a specific clause that regulate the use of chemical fertilizers. (5) Governments and the UN Food and Agriculture Organization (FAO) should coordinate Biological Advanced Research in Agriculture (BARA)-a global agricultural innovation initiative for investments and research in biological fixation and ethical, legal, and social implications of such innovation. While biological fixation will be central in BARA, we envision it to conduct research around other agricultural innovations as well, such as increasing photosynthetic efficiency.}, } @article {pmid31734392, year = {2020}, author = {Li, W and Zhuang, JL and Zhou, YY and Meng, FG and Kang, D and Zheng, P and Shapleigh, JP and Liu, YD}, title = {Metagenomics reveals microbial community differences lead to differential nitrate production in anammox reactors with differing nitrogen loading rates.}, journal = {Water research}, volume = {169}, number = {}, pages = {115279}, doi = {10.1016/j.watres.2019.115279}, pmid = {31734392}, issn = {1879-2448}, mesh = {Bioreactors ; Denitrification ; Metagenomics ; *Microbiota ; *Nitrogen ; Oxidation-Reduction ; }, abstract = {Nitrate production during anammox can decrease total nitrogen removal efficiency, which will negatively impact its usefulness for the removal of nitrogen from waste streams. However, neither the performance characteristics nor physiological shifts associated with nitrate accumulation in anammox reactors under different nitrogen loading rates (NLRs) is well understood. Consequently, these parameters were studied in a lower NLR anammox reactor, termed R1, producing higher than expected levels of nitrate and compared with a higher NLR reactor, termed R2, showing no excess nitrate production. While both reactors showed high NH4[+]-N removal efficiencies (>90%), the total nitrogen removal efficiency (<60%) was much lower in R1 due to higher nitrate production. Metagenomic analysis found that the number of reads derived from anammox bacteria were significantly higher in R2. Another notable trend in reads occurrence was the relatively higher levels of reads from genes predicted to be nitrite oxidoreductases (nxr) in R1. Binning yielded 27 high quality draft genomes from the two reactors. Analysis of bin occurrence found that R1 showing both a decrease in anammox bacteria and an unexpected increase in nxr. In-situ assays confirmed that R1 had higher rates of nitrite oxidation to nitrate and suggested that it was not solely due to obligate NOB, but other nxr-containing bacteria are important contributors as well. Our results demonstrate that nitrate accumulation can be a serious operational concern for the application of anammox technology to low-strength wastewater treatment and provide insight into the community changes leading to this outcome.}, } @article {pmid31734341, year = {2020}, author = {Liu, F and Wang, Y and Gao, GF and Zhu, B}, title = {Metagenomic analysis reveals the abundance and diversity of ARGs in children's respiratory tract microbiomes.}, journal = {The Journal of infection}, volume = {80}, number = {2}, pages = {232-254}, doi = {10.1016/j.jinf.2019.11.002}, pmid = {31734341}, issn = {1532-2742}, mesh = {Anti-Bacterial Agents ; Child ; Genes, Bacterial ; Humans ; Metagenome ; *Metagenomics ; *Microbiota ; Respiratory System ; }, } @article {pmid31733968, year = {2020}, author = {Przemieniecki, SW and Kosewska, A and Ciesielski, S and Kosewska, O}, title = {Changes in the gut microbiome and enzymatic profile of Tenebrio molitor larvae biodegrading cellulose, polyethylene and polystyrene waste.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {256}, number = {}, pages = {113265}, doi = {10.1016/j.envpol.2019.113265}, pmid = {31733968}, issn = {1873-6424}, mesh = {Animal Feed ; Animals ; Biodegradation, Environmental ; Cellulose/*metabolism ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/metabolism/microbiology ; Larva/metabolism ; Microbiota/drug effects ; Polyethylene/*metabolism ; Polystyrenes/*metabolism ; Tenebrio/drug effects/*enzymology/microbiology ; beta-Glucosidase/metabolism ; }, abstract = {Recent studies have demonstrated the ability of mealworm (Tenebrio molitor) for plastic degradation. This study is focused on changes in microbiome structure depending on diets. Microbial community obtained from oat and cellulose diet formed similar group, two kinds of polyethylene formed another group, while polystyrene diet showed the highest dissimilarity. The highest relative abundance of bacteria colonizing gut was in PE-oxodegradable feeding, nevertheless all applied diets were higher in comparison to oat. Dominant phyla consisted of Proteobacteria, Bacteroides, Firmicutes and Actinobacteria, however after PS feeding frequency in Planctomycetes and Nitrospirae increased. The unique bacteria characteristic for cellulose diet belonged to Selenomonas, while Pantoea were characteristic for both polyethylene diets, Lactococcus and Elizabethkingia were unique for each plastic diet, and potential diazotropic bacteria were characteristic for polystyrene diet (Agrobacterium, Nitrosomonas, Nitrospira). Enzymatic similarity between oatmeal and cellulose diets, was shown. All three plastics diet resulted in different activity in both, digestive tract and bacteria. The enzymes with the highest activity were included phosphatases, esterases, leucine arylamidase, β-galactosidase, β-glucuronidase, α-glucosidase, β-glucosidase, chitinase, α-mannosidase and α-fucosidase. The activity of digestive tract was stronger than cultured gut bacteria. In addition to known polyethylene degradation methods, larvae may degrade polyethylene with esterase, cellulose and oatmeal waste activity is related with the activity of sugar-degrading enzymes, degradation of polystyrene with anaerobic processes and diazotrophs.}, } @article {pmid31732071, year = {2019}, author = {Jeon, DY and Yum, SJ and Seo, DW and Kim, SM and Jeong, HG}, title = {Leaf-associated microbiota on perilla (Perilla frutescens var. frutescens) cultivated in South Korea to detect the potential risk of food poisoning.}, journal = {Food research international (Ottawa, Ont.)}, volume = {126}, number = {}, pages = {108664}, doi = {10.1016/j.foodres.2019.108664}, pmid = {31732071}, issn = {1873-7145}, mesh = {Foodborne Diseases/microbiology/prevention & control ; Humans ; Metagenome/genetics ; Metagenomics ; Microbiota/*genetics ; Perilla frutescens/*microbiology ; Plant Leaves/*microbiology ; Republic of Korea ; }, abstract = {Perilla (Perilla frutescens) is a commonly consumed herb with various health benefits in Asia. However, the risks of food-borne illness owing to the presence of pathogens on perilla leaves have not been evaluated. In this study, we evaluated the microbiota of perilla leaves harvested in South Korea using Illumina MiSeq sequencing of the 16S rRNA gene. In total, 2,743,003 sequencing reads were obtained, and 92-437 operational taxonomic units were observed in all samples. Bacterial loads were quantified, and the diversity indices were compared. Differences in the microbiota among sampling times and regions were also investigated. Proteobacteria and Firmicutes were predominant phyla at both times. At the class level, the bacterial communities were composed primarily of Alphaproteobacteria, Bacilli, and Gammaproteobacteria. Diverse bacterial taxa, such as Bacillus, uncultured family Enterobacteriaceae, and Sphingomonas were detected, and the representative pathogenic species (i.e., Acinetobacter lwoffii, Klebsiella pneumoniae, and Staphylococcus aureus) were quantified by qRT-PCR. The results of the co-occurrence network analysis showed characteristics of bacterial taxa in the microbiome on perilla leaves and provided insights into the roles of correlations among diverse microbes, including potential pathogens. Based on these results, the potential risk of food-borne illness from consumption of perilla leaves may be higher in July than in April. In summary, the microbial compositions determined in this study can be used as a base data for food-safety management for prediction and prevention of future outbreaks.}, } @article {pmid31731121, year = {2020}, author = {Liu, YR and Delgado-Baquerizo, M and Yang, Z and Feng, J and Zhu, J and Huang, Q}, title = {Microbial taxonomic and functional attributes consistently predict soil CO2 emissions across contrasting croplands.}, journal = {The Science of the total environment}, volume = {702}, number = {}, pages = {134885}, doi = {10.1016/j.scitotenv.2019.134885}, pmid = {31731121}, issn = {1879-1026}, mesh = {Bacteria ; *Biodiversity ; Carbon Dioxide/*metabolism ; Crops, Agricultural ; Fungi ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Despite distinct roles of soil microbes in regulating carbon (C) respiration in diverse environments, it remains unclear whether microbial taxonomic and functional attributes can consistently predict soil C emissions across contrasting ecosystems. Here, we conducted a large-scale sampling event across two contrasting croplands (rice and wheat-corn crop rotation) to identify specific soil microbial phylotypes and functional genes associated with soil respiration rates. The results of structural equation modeling indicated that bacterial community composition had a strong link with C respiration rates in the two contrasting cropland types; however, this link was weaker for fungal communities. More importantly, we found that the relative abundances of bacterial Solirubrobacterales_480-2, Myxococcales_mle1-27 and fungal Westerdykella had consistently negative correlation with respiration rates across paddy and upland soils. We also identified taxa that are significantly correlated to C respiration in the paddy (e.g. Methylocaldum) and upland soils (e.g. Kribbella), respectively. Further, we found multiple associations between functional genes involved in microbial C metabolism and soil respiration rates. Our findings provide novel insights into understanding microbial predictors of soil CO2 emissions in diverse croplands, which have important implications for improving C emission predictions in terrestrial ecosystems.}, } @article {pmid31730850, year = {2019}, author = {Salazar, G and Paoli, L and Alberti, A and Huerta-Cepas, J and Ruscheweyh, HJ and Cuenca, M and Field, CM and Coelho, LP and Cruaud, C and Engelen, S and Gregory, AC and Labadie, K and Marec, C and Pelletier, E and Royo-Llonch, M and Roux, S and Sánchez, P and Uehara, H and Zayed, AA and Zeller, G and Carmichael, M and Dimier, C and Ferland, J and Kandels, S and Picheral, M and Pisarev, S and Poulain, J and , and Acinas, SG and Babin, M and Bork, P and Bowler, C and de Vargas, C and Guidi, L and Hingamp, P and Iudicone, D and Karp-Boss, L and Karsenti, E and Ogata, H and Pesant, S and Speich, S and Sullivan, MB and Wincker, P and Sunagawa, S}, title = {Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome.}, journal = {Cell}, volume = {179}, number = {5}, pages = {1068-1083.e21}, pmid = {31730850}, issn = {1097-4172}, mesh = {*Gene Expression Regulation ; Geography ; *Metagenome ; Microbiota/genetics ; Molecular Sequence Annotation ; *Oceans and Seas ; RNA, Messenger/genetics/metabolism ; Seawater/microbiology ; Temperature ; Transcriptome/*genetics ; }, abstract = {Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. VIDEO ABSTRACT.}, } @article {pmid31730200, year = {2019}, author = {Esposito, A and Borruso, L and Rattray, JE and Brusetti, L and Ahmed, E}, title = {Taxonomic and functional insights into rock varnish microbiome using shotgun metagenomics.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {12}, pages = {}, doi = {10.1093/femsec/fiz180}, pmid = {31730200}, issn = {1574-6941}, mesh = {Acidobacteria/*genetics ; Actinobacteria/*genetics ; Chloroflexi/*genetics ; Genome, Bacterial/genetics ; Iron ; Manganese Compounds ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/physiology ; Oxides ; Paint ; *Soil Microbiology ; }, abstract = {Rock varnish is a microbial habitat, characterised by thin (5-500 μm) and shiny coatings of iron (Fe) and manganese (Mn) oxides associated with clay minerals. This structure is well studied by geologists, and recently there have been reports about the taxonomical composition of its microbiome. In this study, we investigated the rock varnish microbiome using shotgun metagenomics together with analyses of elemental composition, lipid and small molecule biomarkers, and rock surface analyses to explore the biogeography of microbial communities and their functional features. We report taxa and encoded functions represented in metagenomes retrieved from varnish or non-varnish samples, additionally, eight nearly complete genomes have been reconstructed spanning four phyla (Acidobacteria, Actinobacteria, Chloroflexi and TM7). The functional and taxonomic analyses presented in this study provide new insights into the ecosystem dynamics and survival strategies of microbial communities inhabiting varnish and non-varnish rock surfaces.}, } @article {pmid31729407, year = {2019}, author = {Laheij, AMGA and Raber-Durlacher, JE and Koppelmans, RGA and Huysmans, MDNJM and Potting, C and van Leeuwen, SJM and Hazenberg, MD and Brennan, MT and von Bültzingslöwen, I and Johansson, JE and de Soet, JJ and Haverman, TM and Buijs, MJ and Brandt, BW and Rozema, FR and Blijlevens, NMA and Zaura, E}, title = {Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {16929}, pmid = {31729407}, issn = {2045-2322}, mesh = {Aged ; Bacteria/classification/genetics ; Disease Susceptibility ; *Dysbiosis ; Female ; Fungi/classification/genetics ; Hematopoietic Stem Cell Transplantation/*adverse effects ; Humans ; Male ; Metagenome ; Metagenomics ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S ; Stomatitis/diagnosis/drug therapy/*etiology ; Transplant Recipients ; Transplantation, Autologous ; }, abstract = {The aim of this prospective, two center study was to investigate the dynamics of the microbial changes in relation to the development of ulcerative oral mucositis in autologous SCT (autoSCT) recipients. Fifty-one patients were diagnosed with multiple myeloma and treated with high-dose melphalan followed by autoSCT. They were evaluated before, three times weekly during hospitalization, and three months after autoSCT. At each time point an oral rinse was collected and the presence or absence of ulcerative oral mucositis (UOM) was scored (WHO scale). Oral microbiome was determined by using 16S rRNA amplicon sequencing and fungal load by qPCR. Twenty patients (39%) developed UOM. The oral microbiome changed significantly after autoSCT and returned to pre-autoSCT composition after three months. However, changes in microbial diversity and similarity were more pronounced and rapid in patients who developed UOM compared to patients who did not. Already before autoSCT, different taxa discriminated between the 2 groups, suggesting microbially-driven risk factors. Samples with high fungal load (>0.1%) had a significantly different microbial profile from samples without fungi. In conclusion, autoSCT induced significant and reversible changes in the oral microbiome, while patients who did not develop ulcerative oral mucositis had a more resilient microbial ecosystem.}, } @article {pmid31729183, year = {2020}, author = {Manasson, J and Wallach, DS and Guggino, G and Stapylton, M and Badri, MH and Solomon, G and Reddy, SM and Coras, R and Aksenov, AA and Jones, DR and Girija, PV and Neimann, AL and Heguy, A and Segal, LN and Dorrestein, PC and Bonneau, R and Guma, M and Ciccia, F and Ubeda, C and Clemente, JC and Scher, JU}, title = {Interleukin-17 Inhibition in Spondyloarthritis Is Associated With Subclinical Gut Microbiome Perturbations and a Distinctive Interleukin-25-Driven Intestinal Inflammation.}, journal = {Arthritis & rheumatology (Hoboken, N.J.)}, volume = {72}, number = {4}, pages = {645-657}, pmid = {31729183}, issn = {2326-5205}, support = {P30 CA016087/CA/NCI NIH HHS/United States ; R01 AR073324/AR/NIAMS NIH HHS/United States ; R01 DK114038/DK/NIDDK NIH HHS/United States ; T32 AR069515/AR/NIAMS NIH HHS/United States ; K23 AR064318/AR/NIAMS NIH HHS/United States ; R01 AR074500/AR/NIAMS NIH HHS/United States ; T32 AR064194/AR/NIAMS NIH HHS/United States ; R03 AR072182/AR/NIAMS NIH HHS/United States ; }, mesh = {Antibodies, Monoclonal, Humanized/pharmacology/*therapeutic use ; Arthritis, Psoriatic/*drug therapy/metabolism/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Inflammation/*metabolism ; Interleukin-17/*immunology ; Intestinal Mucosa/metabolism ; Intestines/drug effects/microbiology ; Male ; Middle Aged ; Spondylarthritis/*drug therapy/metabolism/microbiology ; Tumor Necrosis Factor Inhibitors/pharmacology/*therapeutic use ; }, abstract = {OBJECTIVE: To characterize the ecological effects of biologic therapies on the gut bacterial and fungal microbiome in psoriatic arthritis (PsA)/spondyloarthritis (SpA) patients.

METHODS: Fecal samples from PsA/SpA patients pre- and posttreatment with tumor necrosis factor inhibitors (TNFi; n = 15) or an anti-interleukin-17A monoclonal antibody inhibitor (IL-17i; n = 14) underwent sequencing (16S ribosomal RNA, internal transcribed spacer and shotgun metagenomics) and computational microbiome analysis. Fecal levels of fatty acid metabolites and cytokines/proteins implicated in PsA/SpA pathogenesis or intestinal inflammation were correlated with sequence data. Additionally, ileal biopsies obtained from SpA patients who developed clinically overt Crohn's disease (CD) after treatment with IL-17i (n = 5) were analyzed for expression of IL-23/Th17-related cytokines, IL-25/IL-17E-producing cells, and type 2 innate lymphoid cells (ILC2s).

RESULTS: There were significant shifts in abundance of specific taxa after treatment with IL-17i compared to TNFi, particularly Clostridiales (P = 0.016) and Candida albicans (P = 0.041). These subclinical alterations correlated with changes in bacterial community co-occurrence, metabolic pathways, IL-23/Th17-related cytokines, and various fatty acids. Ileal biopsies showed that clinically overt CD was associated with expansion of IL-25/IL-17E-producing tuft cells and ILC2s (P < 0.05), compared to pre-IL-17i treatment levels.

CONCLUSION: In a subgroup of SpA patients, the initiation of IL-17A blockade correlated with features of subclinical gut inflammation and intestinal dysbiosis of certain bacterial and fungal taxa, most notably C albicans. Further, IL-17i-related CD was associated with overexpression of IL-25/IL-17E-producing tuft cells and ILC2s. These results may help to explain the potential link between inhibition of a specific IL-17 pathway and the (sub)clinical gut inflammation observed in SpA.}, } @article {pmid31728602, year = {2020}, author = {Quero, GM and Celussi, M and Relitti, F and Kovačević, V and Del Negro, P and Luna, GM}, title = {Inorganic and Organic Carbon Uptake Processes and Their Connection to Microbial Diversity in Meso- and Bathypelagic Arctic Waters (Eastern Fram Strait).}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {823-839}, doi = {10.1007/s00248-019-01451-2}, pmid = {31728602}, issn = {1432-184X}, mesh = {Arctic Regions ; Autotrophic Processes ; Bacteria/metabolism ; Carbon/*metabolism ; *Carbon Cycle ; Heterotrophic Processes ; *Microbiota ; Oceans and Seas ; Seawater/*chemistry ; Svalbard ; }, abstract = {The deep Arctic Ocean is increasingly vulnerable to climate change effects, yet our understanding of its microbial processes is limited. We collected samples from shelf waters, mesopelagic Atlantic Waters (AW) and bathypelagic Norwegian Sea Deep Waters (NSDW) in the eastern Fram Strait, along coast-to-offshore transects off Svalbard during boreal summer. We measured community respiration, heterotrophic carbon production (HCP), and dissolved inorganic carbon utilization (DICu) together with prokaryotic abundance, diversity, and metagenomic predictions. In deep samples, HCP was significantly faster in AW than in NSDW, while we observed no differences in DICu rates. Organic carbon uptake was higher than its inorganic counterpart, suggesting a major reliance of deep microbial Arctic communities on heterotrophic metabolism. Community structure and spatial distribution followed the hydrography of water masses. Distinct from other oceans, the most abundant OTU in our deep samples was represented by the archaeal MG-II. To address the potential biogeochemical role of each water mass-specific microbial community, as well as their link with the measured rates, PICRUSt-based predicted metagenomes were built. The results showed that pathways of auto- and heterotrophic carbon utilization differed between the deep water masses, although this was not reflected in measured DICu rates. Our findings provide new insights to understand microbial processes and diversity in the dark Arctic Ocean and to progress toward a better comprehension of the biogeochemical cycles and their trends in light of climate changes.}, } @article {pmid31727980, year = {2019}, author = {Kim, HJ and Kim, JJ and Myeong, NR and Kim, T and Kim, D and An, S and Kim, H and Park, T and Jang, SI and Yeon, JH and Kwack, I and Sul, WJ}, title = {Segregation of age-related skin microbiome characteristics by functionality.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {16748}, pmid = {31727980}, issn = {2045-2322}, support = {2016R1A6A3A11933991//National Research Foundation of Korea (NRF)/International ; }, mesh = {Adult ; Age Distribution ; Bacteria/*classification/genetics/isolation & purification ; Biodiversity ; Case-Control Studies ; China ; Female ; Humans ; Microbiota ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Skin/*microbiology ; }, abstract = {Although physiological changes are the most evident indicators of skin aging by alteration of the skin's structure and function, we question whether skin aging is also affected by the structure and assembly process of the skin microbiome. We analysed the skin microbiomes of 73 healthy Chinese women in two age groups (25-35 years old and 56-63 years old) using 16S rRNA gene amplicon sequencing; the overall microbiome structure was significantly different between the two age groups. An analysis using ecological theory to evaluate the process of microbial community assembly processes revealed that the microbiomes of the older group were formed under a greater influence of the niche-based process, with the network of microbes being more collapsed than that of the younger group. Inferred metagenomic functional pathways associated with replication and repair were relatively more predominant in the younger group whereas, among the various metabolism-related pathways, those associated with biodegradation were more predominant in the older group. Interestingly, we found two segregated sub-typing patterns in the younger group which were also observed in the skin microbiomes of young Chinese women living in four other cities in China. The results of our study highlights candidate microbes and functional pathways that are important for future research into preventing skin aging and which could lead to a comprehensive understanding of age-related skin microbiome characteristics.}, } @article {pmid31727954, year = {2019}, author = {Liu, HH and Lin, YC and Chung, CS and Liu, K and Chang, YH and Yang, CH and Chen, Y and Ni, YH and Chang, PF}, title = {Integrated Counts of Carbohydrate-Active Protein Domains as Metabolic Readouts to Distinguish Probiotic Biology and Human Fecal Metagenomes.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {16836}, pmid = {31727954}, issn = {2045-2322}, mesh = {Adolescent ; Adult ; Bacteria/*classification/isolation & purification ; Bacterial Proteins/*chemistry/metabolism ; Carbohydrate Metabolism ; Clostridium butyricum/*genetics/physiology ; Feces/chemistry/*microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Male ; Markov Chains ; Metagenomics/*methods ; Middle Aged ; Phylogeny ; Protein Domains ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Bowel microbiota is a "metaorgan" of metabolisms on which quantitative readouts must be performed before interventions can be introduced and evaluated. The study of the effects of probiotic Clostridium butyricum MIYAIRI 588 (CBM588) on intestine transplantees indicated an increased percentage of the "other glycan degradation" pathway in 16S-rRNA-inferred metagenomes. To verify the prediction, a scoring system of carbohydrate metabolisms derived from shotgun metagenomes was developed using hidden Markov models. A significant correlation (R = 0.9, p < 0.015) between both modalities was demonstrated. An independent validation revealed a strong complementarity (R = -0.97, p < 0.002) between the scores and the abundance of "glycogen degradation" in bacteria communities. On applying the system to bacteria genomes, CBM588 had only 1 match and ranked higher than the other 8 bacteria evaluated. The gram-stain properties were significantly correlated to the scores (p < 5 × 10[-4]). The distributions of the scored protein domains indicated that CBM588 had a considerably higher (p < 10[-5]) proportion of carbohydrate-binding modules than other bacteria, which suggested the superior ability of CBM588 to access carbohydrates as a metabolic driver to the bowel microbiome. These results demonstrated the use of integrated counts of protein domains as a feasible readout for metabolic potential within bacteria genomes and human metagenomes.}, } @article {pmid31726738, year = {2019}, author = {Liang, YN and Yu, JG and Zhang, DB and Zhang, Z and Ren, LL and Li, LH and Wang, Z and Tang, ZS}, title = {Indigo Naturalis Ameliorates Dextran Sulfate Sodium-Induced Colitis in Mice by Modulating the Intestinal Microbiota Community.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {22}, pages = {}, pmid = {31726738}, issn = {1420-3049}, support = {81803951//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Biopsy ; Colitis/drug therapy/*etiology/metabolism/*pathology ; Cytokines/metabolism ; Dextran Sulfate/*adverse effects ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; Immunohistochemistry ; Indigo Carmine/chemistry/*pharmacology ; Inflammation Mediators/metabolism ; Intestinal Mucosa/drug effects/metabolism/microbiology/pathology ; Metagenomics ; Mice ; Molecular Structure ; RNA, Ribosomal, 16S ; }, abstract = {Indigo naturalis (IN) is a traditional Chinese medicine, named Qing-Dai, which is extracted from indigo plants and has been used to treat patients with inflammatory bowel disease (IBD) in China and Japan. Though there are notable effects of IN on colitis, the mechanisms remain elusive. Regarding the significance of alterations of intestinal flora related to IBD and the poor water solubility of the blue IN powder, we predicted that the protective action of IN on colitis may occur through modifying gut microbiota. To investigate the relationships of IN, colitis, and gut microbiomes, a dextran sulfate sodium (DSS)-induced mice colitis model was tested to explore the protective effects of IN on macroscopic colitis symptoms, the histopathological structure, inflammation cytokines, and gut microbiota, and their potential functions. Sulfasalazine (SASP) was used as the positive control. Firstly, because it was a mixture, the main chemical compositions of indigo and indirubin in IN were detected by ultra-performance liquid chromatography (UPLC). The clinical activity score (CAS), hematoxylin and eosin (H&E) staining results, and enzyme-linked immunosorbent assay (ELISA) results in this study showed that IN greatly improved the health conditions of the tested colitis mice, ameliorated the histopathological structure of the colon tissue, down-regulated pro-inflammatory cytokines, and up-regulated anti-inflammatory cytokines. The results of 16S rDNA sequences analysis with the Illumina MiSeq platform showed that IN could modulate the balance of gut microbiota, especially by down-regulating the relative quantity of Turicibacter and up-regulating the relative quantity of Peptococcus. The therapeutic effect of IN may be closely related to the anaerobic gram-positive bacteria of Turicibacter and Peptococcus. The inferred metagenomes from 16S data using PICRUSt demonstrated that decreased metabolic genes, such as through biosynthesis of siderophore group nonribosomal peptides, non-homologous end-joining, and glycosphingolipid biosynthesis of lacto and neolacto series, may maintain microbiota homeostasis during inflammation from IN treatment in DSS-induced colitis.}, } @article {pmid31726316, year = {2019}, author = {Fiers, WD and Gao, IH and Iliev, ID}, title = {Gut mycobiota under scrutiny: fungal symbionts or environmental transients?.}, journal = {Current opinion in microbiology}, volume = {50}, number = {}, pages = {79-86}, pmid = {31726316}, issn = {1879-0364}, support = {F32 DK120228/DK/NIDDK NIH HHS/United States ; R01 DK113136/DK/NIDDK NIH HHS/United States ; R21 AI146957/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Fungi/genetics/*physiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenomics ; Mice ; *Mycobiome ; Symbiosis/*genetics/immunology ; }, abstract = {The human gastrointestinal tract is home to a thriving community of microbes including the fungal 'mycobiota'. Although sequencing methodology has enumerated diverse fungal genera within this niche, discerning persistent symbiotic residents from contaminants and purely environmental transients remains a challenge. Recent advances in culturomics and sequencing employing metagenomics, metatranscriptomics and longitudinal studies have begun to reveal a human symbiont 'core mycobiome' that may contribute to human health and disease. Trans-kingdom interactions between the bacterial microbiota and evolution within the niche have defined C. albicans as a true symbiont, setting a bar for defining other fungi. Additionally, elegant investigations of mammalian antifungal immunity have examined mononuclear phagocytes, neutrophils, antigen-specific recognition by T cells and other mechanisms important for local and systemic effects on the host, providing further evidence supporting gut persistence. In this review we discuss current research aimed at investigating the symbiotic mycobiota and propose four criteria aiding in the differentiation of fungal symbionts from environmental transients.}, } @article {pmid31726162, year = {2020}, author = {Guo, WL and Chen, M and Pan, WL and Zhang, Q and Xu, JX and Lin, YC and Li, L and Liu, B and Bai, WD and Zhang, YY and Ni, L and Rao, PF and Lv, XC}, title = {Hypoglycemic and hypolipidemic mechanism of organic chromium derived from chelation of Grifola frondosa polysaccharide-chromium (III) and its modulation of intestinal microflora in high fat-diet and STZ-induced diabetic mice.}, journal = {International journal of biological macromolecules}, volume = {145}, number = {}, pages = {1208-1218}, doi = {10.1016/j.ijbiomac.2019.09.206}, pmid = {31726162}, issn = {1879-0003}, mesh = {Animals ; Blood Glucose/metabolism ; Chelating Agents/*pharmacology ; Cholesterol/blood ; Chromium/*chemistry ; Diabetes Mellitus, Experimental ; Diet, High-Fat/adverse effects ; Dietary Carbohydrates/pharmacology ; Gastrointestinal Microbiome/*drug effects ; Glucose/metabolism ; Grifola/*chemistry ; Hyperglycemia/metabolism ; Hypoglycemic Agents/*pharmacology ; Hypolipidemic Agents/*pharmacology ; Lipid Metabolism/drug effects ; Liver/drug effects/metabolism ; Male ; Metagenomics ; Mice ; Polysaccharides/*pharmacology ; RNA, Messenger/metabolism ; Streptozocin/*pharmacology ; Triglycerides/blood ; }, abstract = {Polysaccharide from Grifola frondosa is an excellent metal-ion chelating agent owing to its distinctive structure and outstanding functional activities. Our previous research has successfully synthesized novel organic chromium derived from the chelation ofG. frondosapolysaccharide-chromium (III) [GFP-Cr(III)]. The purpose of present research was to reveal the hypoglycemic and hypolipidemic mechanism of GFP-Cr(III), and its relationship with the modulation of intestinal microflora. Successful fabrication of GFP-Cr(III) was verified by thermogravimetric analysis (TGA), powder X-ray diffraction (XRD) and [1]H NMR spectrum.The hypoglycemic and hypolipidemic effects were examined using type 2 diabetic mice induced by a high-fat diet (HFD) and streptozocin (STZ). Results indicated that GFP-Cr(III) intervention improved abnormal serum biochemical indicators (triglyceride (TG), cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) and glucose), inhibited lipid accumulation and steatosis in the liver. Metagenomic analysis revealed that GFP-Cr(III) treatment produced obvious changes on the intestinal microflora in T2DM mice. Thecorrelationnetwork analysis further revealed that the serum and hepatic lipid profiles were positively correlated with Streptococcus and Enterococcus, but negatively correlated with Enterorhabdus, Ruminococcaceae-UCG-011, Coriobacteriaceae and Micrococcaceae. Meanwhile, oral administration with GFP-Cr(III) regulated the mRNA expression related to glucose and lipid metabolism. These results of present study suggest that GFP-Cr(III) could be used as potential functional food ingredients for the amelioration of hyperglycemia and hyperlipidemia.}, } @article {pmid31726030, year = {2019}, author = {Fehlner-Peach, H and Magnabosco, C and Raghavan, V and Scher, JU and Tett, A and Cox, LM and Gottsegen, C and Watters, A and Wiltshire-Gordon, JD and Segata, N and Bonneau, R and Littman, DR}, title = {Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates.}, journal = {Cell host & microbe}, volume = {26}, number = {5}, pages = {680-690.e5}, pmid = {31726030}, issn = {1934-6069}, support = {TL1 TR001447/TR/NCATS NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; /ERC_/European Research Council/International ; UL1 RR029893/RR/NCRR NIH HHS/United States ; /HHMI_/Howard Hughes Medical Institute/United States ; R01 AR074500/AR/NIAMS NIH HHS/United States ; UL1 TR001445/TR/NCATS NIH HHS/United States ; T32 CA009161/CA/NCI NIH HHS/United States ; }, mesh = {Diet ; Gastrointestinal Microbiome/*physiology ; Genetic Variation ; Genome, Bacterial/genetics ; Humans ; Intestines/microbiology ; Plants/microbiology ; Polysaccharides/*metabolism ; Prevotella/classification/*isolation & purification/*metabolism ; }, abstract = {Gut-dwelling Prevotella copri (P. copri), the most prevalent Prevotella species in the human gut, have been associated with diet and disease. However, our understanding of their diversity and function remains rudimentary because studies have been limited to 16S and metagenomic surveys and experiments using a single type strain. Here, we describe the genomic diversity of 83 P. copri isolates from 11 human donors. We demonstrate that genomically distinct isolates, which can be categorized into different P. copri complex clades, utilize defined sets of polysaccharides. These differences are exemplified by variations in susC genes involved in polysaccharide transport as well as polysaccharide utilization loci (PULs) that were predicted in part from genomic and metagenomic data. Functional validation of these PULs showed that P. copri isolates utilize distinct sets of polysaccharides from dietary plant, but not animal, sources. These findings reveal both genomic and functional differences in polysaccharide utilization across human intestinal P. copri strains.}, } @article {pmid31723038, year = {2019}, author = {Kundu, P and Lee, HU and Garcia-Perez, I and Tay, EXY and Kim, H and Faylon, LE and Martin, KA and Purbojati, R and Drautz-Moses, DI and Ghosh, S and Nicholson, JK and Schuster, S and Holmes, E and Pettersson, S}, title = {Neurogenesis and prolongevity signaling in young germ-free mice transplanted with the gut microbiota of old mice.}, journal = {Science translational medicine}, volume = {11}, number = {518}, pages = {}, doi = {10.1126/scitranslmed.aau4760}, pmid = {31723038}, issn = {1946-6242}, mesh = {Animals ; Butyrates/metabolism ; Doublecortin Domain Proteins ; *Fecal Microbiota Transplantation ; Fibroblast Growth Factors/metabolism ; Gastrointestinal Microbiome/*physiology ; Germ-Free Life ; Hippocampus/physiology ; Intestines/anatomy & histology/growth & development ; Liver/metabolism ; Longevity/*physiology ; Male ; Metabolome ; Mice, Inbred C57BL ; Microtubule-Associated Proteins/metabolism ; Neurogenesis/*physiology ; Neurons/metabolism ; Neuropeptides/metabolism ; Phenotype ; Proton Magnetic Resonance Spectroscopy ; }, abstract = {The gut microbiota evolves as the host ages, yet the effects of these microbial changes on host physiology and energy homeostasis are poorly understood. To investigate these potential effects, we transplanted the gut microbiota of old or young mice into young germ-free recipient mice. Both groups showed similar weight gain and skeletal muscle mass, but germ-free mice receiving a gut microbiota transplant from old donor mice unexpectedly showed increased neurogenesis in the hippocampus of the brain and increased intestinal growth. Metagenomic analysis revealed age-sensitive enrichment in butyrate-producing microbes in young germ-free mice transplanted with the gut microbiota of old donor mice. The higher concentration of gut microbiota-derived butyrate in these young transplanted mice was associated with an increase in the pleiotropic and prolongevity hormone fibroblast growth factor 21 (FGF21). An increase in FGF21 correlated with increased AMPK and SIRT-1 activation and reduced mTOR signaling. Young germ-free mice treated with exogenous sodium butyrate recapitulated the prolongevity phenotype observed in young germ-free mice receiving a gut microbiota transplant from old donor mice. These results suggest that gut microbiota transplants from aged hosts conferred beneficial effects in responsive young recipients.}, } @article {pmid31722729, year = {2019}, author = {Kawulok, J and Kawulok, M and Deorowicz, S}, title = {Environmental metagenome classification for constructing a microbiome fingerprint.}, journal = {Biology direct}, volume = {14}, number = {1}, pages = {20}, pmid = {31722729}, issn = {1745-6150}, mesh = {*DNA Fingerprinting ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; }, abstract = {BACKGROUND: Nowadays, not only are single genomes commonly analyzed, but also metagenomes, which are sets of, DNA fragments (reads) derived from microbes living in a given environment. Metagenome analysis is aimed at extracting crucial information on the organisms that have left their traces in an investigated environmental sample.In this study we focus on the MetaSUB Forensics Challenge (organized within the CAMDA 2018 conference) which consists in predicting the geographical origin of metagenomic samples. Contrary to the existing methods for environmental classification that are based on taxonomic or functional classification, we rely on the similarity between a sample and the reference database computed at a reads level.

RESULTS: We report the results of our extensive experimental study to investigate the behavior of our method and its sensitivity to different parameters. In our tests, we have followed the protocol of the MetaSUB Challenge, which allowed us to compare the obtained results with the solutions based on taxonomic and functional classification.

CONCLUSIONS: The results reported in the paper indicate that our method is competitive with those based on taxonomic classification. Importantly, by measuring the similarity at the reads level, we avoid the necessity of using large databases with annotated gene sequences. Hence our main finding is that environmental classification of metagenomic data can be proceeded without using large databases required for taxonomic or functional classification.

REVIEWERS: This article was reviewed by Eran Elhaik, Alexandra Bettina Graf, Chengsheng Zhu, and Andre Kahles.}, } @article {pmid31722286, year = {2020}, author = {Hakim, S and Mirza, BS and Imran, A and Zaheer, A and Yasmin, S and Mubeen, F and Mclean, JE and Mirza, MS}, title = {Illumina sequencing of 16S rRNA tag shows disparity in rhizobial and non-rhizobial diversity associated with root nodules of mung bean (Vigna radiata L.) growing in different habitats in Pakistan.}, journal = {Microbiological research}, volume = {231}, number = {}, pages = {126356}, doi = {10.1016/j.micres.2019.126356}, pmid = {31722286}, issn = {1618-0623}, mesh = {Acinetobacter/genetics/isolation & purification ; Bradyrhizobium/genetics/isolation & purification ; DNA, Bacterial/genetics ; Ecosystem ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Microbiota/genetics ; Pakistan ; Phylogeny ; Pseudomonas/genetics/isolation & purification ; RNA, Ribosomal, 16S ; *Rhizobiaceae/classification/genetics ; Root Nodules, Plant/*microbiology ; Sinorhizobium/genetics/isolation & purification ; Vigna/*microbiology ; }, abstract = {In Rhizobium-legume symbiosis, the nodule is the most frequently studied compartment, where the endophytic/symbiotic microbiota demands critical investigation for development of specific inocula. We identified the bacterial diversity within root nodules of mung bean from different growing areas of Pakistan using Illumina sequencing of 16S rRNA gene. We observed specific OTUs related to specific site where Bradyrhizobium was found to be the dominant genus comprising of 82-94% of total rhizobia in nodules with very minor fraction of sequences from other rhizobia at three sites. In contrast, Ensifer (Sinorhizobium) was single dominant genus comprising 99.9% of total rhizobial sequences at site four. Among non-rhizobial sequences, the genus Acinetobacter was abundant (7-18% of total sequences), particularly in Bradyrhizobium-dominated nodule samples. Rhizobia and non-rhizobial PGPR isolated from nodule samples include Ensifer, Bradyrhizobium, Acinetobacter, Microbacterium and Pseudomonas strains. Co-inoculation of multi-trait PGPR Acinetobacter sp. VrB1 with either of the two rhizobia in field exhibited more positive effect on nodulation and plant growth than single-strain inoculation which favors the use of Acinetobacter as an essential component for development of mung bean inoculum. Furthermore, site-specific dominance of rhizobia and non-rhizobia revealed in this study may contribute towards decision making for development and application of specific inocula in different habitats.}, } @article {pmid31722195, year = {2019}, author = {Hertel, J and Harms, AC and Heinken, A and Baldini, F and Thinnes, CC and Glaab, E and Vasco, DA and Pietzner, M and Stewart, ID and Wareham, NJ and Langenberg, C and Trenkwalder, C and Krüger, R and Hankemeier, T and Fleming, RMT and Mollenhauer, B and Thiele, I}, title = {Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson's Disease.}, journal = {Cell reports}, volume = {29}, number = {7}, pages = {1767-1777.e8}, pmid = {31722195}, issn = {2211-1247}, support = {MR/N003284/1/MRC_/Medical Research Council/United Kingdom ; G1000143/MRC_/Medical Research Council/United Kingdom ; MC_UU_12015/1/MRC_/Medical Research Council/United Kingdom ; 14136/CRUK_/Cancer Research UK/United Kingdom ; G0401527/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Aged ; Female ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; Parkinson Disease/*microbiology ; Sulfur/*metabolism ; }, abstract = {Parkinson's disease (PD) exhibits systemic effects on the human metabolism, with emerging roles for the gut microbiome. Here, we integrate longitudinal metabolome data from 30 drug-naive, de novo PD patients and 30 matched controls with constraint-based modeling of gut microbial communities derived from an independent, drug-naive PD cohort, and prospective data from the general population. Our key results are (1) longitudinal trajectory of metabolites associated with the interconversion of methionine and cysteine via cystathionine differed between PD patients and controls; (2) dopaminergic medication showed strong lipidomic signatures; (3) taurine-conjugated bile acids correlated with the severity of motor symptoms, while low levels of sulfated taurolithocholate were associated with PD incidence in the general population; and (4) computational modeling predicted changes in sulfur metabolism, driven by A. muciniphila and B. wadsworthia, which is consistent with the changed metabolome. The multi-omics integration reveals PD-specific patterns in microbial-host sulfur co-metabolism that may contribute to PD severity.}, } @article {pmid31721393, year = {2020}, author = {Beraldi, EJ and Borges, SC and de Almeida, FLA and Dos Santos, A and Saad, MJA and Buttow, NC}, title = {Colonic neuronal loss and delayed motility induced by high-fat diet occur independently of changes in the major groups of microbiota in Swiss mice.}, journal = {Neurogastroenterology and motility}, volume = {32}, number = {2}, pages = {e13745}, doi = {10.1111/nmo.13745}, pmid = {31721393}, issn = {1365-2982}, mesh = {Animals ; Diet, High-Fat/*adverse effects ; *Gastrointestinal Microbiome ; Gastrointestinal Motility/physiology ; Inulin/pharmacology ; Male ; Mice ; Myenteric Plexus/*pathology ; Neurons/*pathology ; Obesity/etiology/*pathology ; Probiotics/pharmacology ; }, abstract = {BACKGROUND: Obesity has been linked to gastrointestinal disorders, and the loss of myenteric neurons in the intestine caused by high-fat diets (HFD) has been attributed to changes in microbiota and lipotoxicity. We investigated whether the prebiotic inulin modulates bacterial populations and alleviates neuronal loss in mice fed HFD.

METHODS: Swiss mice were fed purified rodent diet or HFD (59% kcal fat), or both diets supplemented with inulin for 17 weeks. Intestinal motility was assessed and a metagenome analysis of the colonic microbiota was performed. The gene expression of inflammatory markers was evaluated, and immunofluorescence was performed for different types of myenteric neurons and glial cells in the distal colon.

KEY RESULTS: The HFD caused obesity and delayed colonic motility. The loss of myenteric neurons and glial cells in obese mice affected all of the studied neuronal populations, including neurons positive for myosin-V, neuronal nitric oxide synthase, vasoactive intestinal peptide, and calretinin. Although obese mice supplemented with inulin exhibited improvements in colonic motility, neuronal, and glial cell loss persisted. The HFD did not altered the expression levels of inflammatory cytokines in the intestine or the prevalence of the major groups in microbiota, but inulin increased the proportion of the genus Akkermansia in the obese mice.

CONCLUSIONS AND INFERENCES: In Swiss mice, the HFD-induced neuronal loss but did not change the major groups in microbiota. This suggests that, despite the increase in the beneficial bacteria, other factors that are directly linked to excess dietary lipid intake affect the enteric nervous system.}, } @article {pmid31720799, year = {2020}, author = {Thomas, P and Shaik, SP}, title = {Molecular Profiling on Surface-Disinfected Tomato Seeds Reveals High Diversity of Cultivation-Recalcitrant Endophytic Bacteria with Low Shares of Spore-Forming Firmicutes.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {910-924}, doi = {10.1007/s00248-019-01440-5}, pmid = {31720799}, issn = {1432-184X}, support = {AMAAS Project//National Bureau of Agriculturally Important Microorganisms/ ; }, mesh = {Bacteria/*isolation & purification ; Disinfectants/*administration & dosage ; Endophytes/*isolation & purification ; Firmicutes/isolation & purification ; India ; Solanum lycopersicum/*microbiology ; *Microbiota ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Seeds/microbiology ; }, abstract = {Seeds are known to harbor diverse microorganisms offering protective effects on them with the prospects of quick root colonization at germination, selective recruitment as endophytes, and possible vertical transmission. The study was undertaken to assess the gross seed-internal bacterial community in tomato and to confirm if spore-forming Firmicutes constituted major seed endophytes adopting cultivation versus molecular approach on surface-sterilized seeds. Testing the initial seed wash solutions of "Arka Vikas" and "Arka Abha" cultivars showed > 1000 bacterial cfu per dry seed, largely Bacillus spp. Tissue homogenates from surface-disinfected seeds did not show any cultivable bacteria on enriched media for 1-2 weeks, while 16S rRNA V3-V4 taxonomic profiling revealed a huge bacterial diversity (10-16 phyla per cultivar). Proteobacteria formed the dominant phylum (65.7-69.6% OTUs) followed by Firmicutes, Actinobacteria, Bacteroidetes, and a notable share of Euryarchaeota (1.1-3.1%). Five more phyla appeared common to both cultivars in minor shares (Acidobacteria, Planctomycetes, Chloroflexi, Spirochaetes, Verrucomicrobia) with the ten phyla together constituting 99.6-99.9% OTUs. Class level and family level, the cultivars displayed elevated bacterial diversity, but similar taxonomic profiles. Arka Vikas and Arka Abha showed 114 and 107 genera, respectively, with 63 common genera constituting 96-97% OTUs. Psychrobacter formed the dominant genus. Bacillus and related genera constituted only negligible OTU share (0.16-0.28%). KEGG functional analysis showed metabolism as the major bacterial community role. One-month-old in vitro seedlings showed the activation of some originally uncultivable bacteria uninfluenced by the OTU share. The study reveals a high diversity of cultivation-recalcitrant endophytic bacteria prevailing in tomato seeds with possible vertical transmission and significant roles in plant biology.}, } @article {pmid31719654, year = {2020}, author = {Mann, AE and Mazel, F and Lemay, MA and Morien, E and Billy, V and Kowalewski, M and Di Fiore, A and Link, A and Goldberg, TL and Tecot, S and Baden, AL and Gomez, A and Sauther, ML and Cuozzo, FP and Rice, GAO and Dominy, NJ and Stumpf, R and Lewis, RJ and Swedell, L and Amato, K and Wegener Parfrey, L}, title = {Biodiversity of protists and nematodes in the wild nonhuman primate gut.}, journal = {The ISME journal}, volume = {14}, number = {2}, pages = {609-622}, pmid = {31719654}, issn = {1751-7370}, support = {R01 TW009237/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Animals, Wild/microbiology/parasitology ; *Biodiversity ; Blastocyst/classification ; Cercopithecidae/microbiology/parasitology ; Ciliophora/classification/genetics/isolation & purification ; Diet ; Endolimax/classification/genetics/isolation & purification ; Entamoeba/classification/genetics ; Eukaryota/classification/genetics/isolation & purification ; Feces/microbiology/parasitology ; Fungi/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome ; Hominidae/microbiology/parasitology ; Host Specificity ; Lemur/microbiology/parasitology ; *Metagenomics ; Nematoda/classification/genetics/isolation & purification ; Phylogeny ; Platyrrhini/microbiology/parasitology ; Primates/*microbiology/*parasitology ; }, abstract = {Documenting the natural diversity of eukaryotic organisms in the nonhuman primate (NHP) gut is important for understanding the evolution of the mammalian gut microbiome, its role in digestion, health and disease, and the consequences of anthropogenic change on primate biology and conservation. Despite the ecological significance of gut-associated eukaryotes, little is known about the factors that influence their assembly and diversity in mammals. In this study, we used an 18S rRNA gene fragment metabarcoding approach to assess the eukaryotic assemblage of 62 individuals representing 16 NHP species. We find that cercopithecoids, and especially the cercopithecines, have substantially higher alpha diversity than other NHP groups. Gut-associated protists and nematodes are widespread among NHPs, consistent with their ancient association with NHP hosts. However, we do not find a consistent signal of phylosymbiosis or host-species specificity. Rather, gut eukaryotes are only weakly structured by primate phylogeny with minimal signal from diet, in contrast to previous reports of NHP gut bacteria. The results of this study indicate that gut-associated eukaryotes offer different information than gut-associated bacteria and add to our understanding of the structure of the gut microbiome.}, } @article {pmid31719228, year = {2019}, author = {Kuntal, BK and Mande, SS}, title = {Visual exploration of microbiome data.}, journal = {Journal of biosciences}, volume = {44}, number = {5}, pages = {}, pmid = {31719228}, issn = {0973-7138}, mesh = {Metagenomics ; *Microbiota ; }, abstract = {A dramatic increase in large-scale cross-sectional and temporal-level metagenomic experiments has led to an improved understanding of the microbiome and its role in human well-being. Consequently, a plethora of analytical methods has been developed to decipher microbial biomarkers for various diseases, cluster different ecosystems based on microbial content, and infer functional potential of the microbiome as well as analyze its temporal behavior. Development of user-friendly visualization methods and frameworks is necessary to analyze this data and infer taxonomic and functional patterns corresponding to a phenotype. Thus, new methods as well as application of pre-existing ones has gained importance in recent times pertaining to the huge volume of the generated microbiome data. In this review, we present a brief overview of some useful visualization techniques that have significantly enriched microbiome data analytics.}, } @article {pmid31719223, year = {2019}, author = {Auti, AM and Narwade, NP and Deshpande, NM and Dhotre, DP}, title = {Microbiome and imputed metagenome study of crude and refined petroleum-oil-contaminated soils: Potential for hydrocarbon degradation and plant-growth promotion.}, journal = {Journal of biosciences}, volume = {44}, number = {5}, pages = {}, pmid = {31719223}, issn = {0973-7138}, mesh = {Bacteria/genetics/isolation & purification ; Biodegradation, Environmental ; DNA, Bacterial/genetics/isolation & purification ; *Environmental Pollution ; Hydrocarbons/*metabolism ; *Metagenome ; *Microbiota ; Petroleum/*metabolism ; *Plant Development ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {Microbial community structure of crude petroleum oil (CP)- and refined petroleum oil (RP)-contaminated soil was investigated. The taxonomical and functional diversity of such soils can be a great source of information about microbial community and genes involved in petroleum hydrocarbon (PHC) degradation. In this study, microbial diversity of soils contaminated by RP from urban biome of Pune, India, and CP from agricultural biome of Gujarat, India, were assessed by 16S rRNA amplicon sequencing on Illumina MiSeq platform. Association between the soil microbial community and the physicochemical parameters were investigated for their potential role. In RP- and CP-contaminated soils, the microbiome analysis showed Proteobacteria as most dominant phylum followed by Actinobacteria. Interestingly, Firmicutes were most prevailing in a CP-contaminated sample while they were least prevailing in RP-contaminated soils. Soil moisture content, total organic carbon and organic nitrogen content influenced the taxa diversity in these soils. Species richness was more in RP as compared to CP soils. Further prediction of metagenome using PICRUSt revealed that the RP and CP soils contain microbial communities with excellent metabolic potential for PHC degradation. Microbial community contributing to genes essential for soil health improvement and plant growth promotion was also gauged. Our analysis showed promising results for future bioaugmentation assisted phytoremediation (BAP) strategies for treating such soils.}, } @article {pmid31719221, year = {2019}, author = {Chaudhari, D and Dhotre, D and Agarwal, D and Gondhali, A and Nagarkar, A and Lad, V and Patil, U and Juvekar, S and Sinkar, V and Shouche, Y}, title = {Understanding the association between the human gut, oral and skin microbiome and the Ayurvedic concept of prakriti.}, journal = {Journal of biosciences}, volume = {44}, number = {5}, pages = {}, pmid = {31719221}, issn = {0973-7138}, mesh = {Female ; Humans ; Intestines/*microbiology ; Male ; *Medicine, Ayurvedic ; *Microbiota ; Mouth/*microbiology ; Skin/*microbiology ; }, abstract = {Ayurveda is one of the ancient systems of medicine which is widely practised as a personalized scientific approach towards the general wellness. Ayurvedic prakriti is broadly defined as the phenotypes which are determined on the basis of physical, psychological and physiological traits irrespective of their social, ethnic, dietary and geographical stature. Prakriti is the constitution of a person, which comprises vata, pitta, and kapha and is a key determinant of how one individual is different from the other. Human microbiome is considered the 'latest discovered' human organ and microbiome research reiterates the fundamental principles of Ayurveda for creating a healthy gut environment by maintaining the individual-specific microbiome. Hence, it is important to understand the association of human microbiome with the Ayurvedic prakriti of an individual. Here, we provide a comprehensive analysis of human microbiome from the gut, oral and skin samples of healthy individuals (n=18) by 16S rRNA gene-based metagenomics using standard QIIME pipeline. In the three different prakriti samples differential abundance of Bacteroides, Desulfovibrio, Parabacteroides, Slackia, and Succinivibrio was observed in the gut microbiome. Analysis also revealed prakriti-specific presence of Mogibacterium, Propionibacterium, Pyramidobacter, Rhodococcus in the kapha prakriti individuals Planomicrobium, Hyphomicrobium, Novosphingobium in the pitta prakriti individuals and Carnobacterium, Robiginitalea, Cetobacterium, Psychrobacter in the vata prakriti individuals. Similarly, the oral and skin microbiome also revealed presence of prakriti-specific differential abundance of diverse bacterial genera. Prakriti-specific presence of bacterial taxa was recorded and only 42% microbiome in the oral samples and 52% microbiome in the skin samples were shared. Bacteria known for preventing gut inflammation by digesting the resistant starch were abundant in the pitta prakriti individuals, who are more prone to develop gut-inflammation-related disorders. In summary, human gut, oral and skin microbiome showed presence or high abundance of few bacterial taxa across three prakriti types, suggesting their specific physiological importance.}, } @article {pmid31719220, year = {2019}, author = {Holmes, S}, title = {Successful strategies for human microbiome data generation, storage and analyses.}, journal = {Journal of biosciences}, volume = {44}, number = {5}, pages = {}, pmid = {31719220}, issn = {0973-7138}, mesh = {Humans ; *Microbiota ; Multivariate Analysis ; Probability ; Reproducibility of Results ; }, abstract = {Current interest in the potential for clinical use of new tools for improving human health are now focused on techniques for the study of the human microbiome and its interaction with environmental and clinical covariates. This review outlines the use of statistical strategies that have been developed in past studies and can inform successful design and analyses of controlled perturbation experiments performed in the human microbiome. We carefully outline what the data are, their imperfections and how we need to transform, decontaminate and denoise them. We show how to identify the important unknown parameters and how to can leverage variability we see to produce efficient models for prediction and uncertainty quantification. We encourage a reproducible strategy that builds on best practice principles that can be adapted for effective experimental design and reproducible workflows. Nonparametric, data-driven denoising strategies already provide the best strain identification and decontamination methods. Data driven models can be combined with uncertainty quantification to provide reproducible aids to decision making in the clinical context, as long as careful, separate, registered confirmatory testing are undertaken. Here we provide guidelines for effective longitudinal studies and their analyses. Lessons learned along the way are that visualizations at every step can pinpoint problems and outliers, normalization and filtering improve power in downstream testing. We recommend collecting and binding the metadata and covariates to sample descriptors and recording complete computer scripts into an R markdown supplement that can reduce opportunities for human error and enable collaborators and readers to replicate all the steps of the study. Finally, we note that optimizing the bioinformatic and statistical workflow involves adopting a wait-and-see approach that is particularly effective in cases where the features such as 'mass spectrometry peaks' and metagenomic tables can only be partially annotated.}, } @article {pmid31717498, year = {2019}, author = {Gran-Stadniczeñko, S and Krabberød, AK and Sandaa, RA and Yau, S and Egge, E and Edvardsen, B}, title = {Seasonal Dynamics of Algae-Infecting Viruses and Their Inferred Interactions with Protists.}, journal = {Viruses}, volume = {11}, number = {11}, pages = {}, pmid = {31717498}, issn = {1999-4915}, mesh = {Biodiversity ; Capsid Proteins/genetics ; DNA Viruses/isolation & purification ; Eukaryota/*virology ; Genes, Viral ; Host Microbial Interactions ; Metagenomics ; Microalgae/*virology ; *Mimiviridae/classification/genetics/isolation & purification ; Norway ; *Phycodnaviridae/classification/genetics/isolation & purification ; Phylogeny ; Plankton/virology ; Seasons ; Seawater/virology ; }, abstract = {Viruses are a highly abundant, dynamic, and diverse component of planktonic communities that have key roles in marine ecosystems. We aimed to reveal the diversity and dynamics of marine large dsDNA viruses infecting algae in the Northern Skagerrak, South Norway through the year by metabarcoding, targeting the major capsid protein (MCP) and its correlation to protist diversity and dynamics. Metabarcoding results demonstrated a high diversity of algal viruses compared to previous metabarcoding surveys in Norwegian coastal waters. We obtained 313 putative algal virus operational taxonomic units (vOTUs), all classified by phylogenetic analyses to either the Phycodnaviridae or Mimiviridae families, most of them in clades without any cultured or environmental reference sequences. The viral community showed a clear temporal variation, with some vOTUs persisting for several months. The results indicate co-occurrences between abundant viruses and potential hosts during long periods. This study gives new insights into the virus-algal host dynamics and provides a baseline for future studies of algal virus diversity and temporal dynamics.}, } @article {pmid31717432, year = {2019}, author = {Dalmon, A and Gayral, P and Decante, D and Klopp, C and Bigot, D and Thomasson, M and Herniou, EA and Alaux, C and Le Conte, Y}, title = {Viruses in the Invasive Hornet Vespa velutina.}, journal = {Viruses}, volume = {11}, number = {11}, pages = {}, pmid = {31717432}, issn = {1999-4915}, mesh = {Animals ; Bees ; Biological Control Agents ; Dicistroviridae/genetics/isolation & purification ; Genome, Viral ; *Insect Viruses/genetics/isolation & purification ; Intestines/virology ; Introduced Species ; Metagenome ; RNA Viruses/genetics/isolation & purification ; RNA, Viral ; Wasps/*virology ; }, abstract = {The Asian yellow-legged hornet Vespa velutina nigrithorax, a major predator of honeybees, is spreading in Europe in part due to a lack of efficient control methods. In this study, as a first step to identify biological control agents, we characterized viral RNA sequences present in asymptomatic or symptomatic hornets. Among 19 detected viruses, the honey bee virus Deformed wing virus-B was predominant in all the samples, particularly in muscles from the symptomatic hornet, suggesting a putative cause of the deformed wing symptom. Interestingly, two new viruses closely related to Acyrthosiphon pisumvirus and Himetobi Pvirus and viruses typically associated with honey bees, Acute bee paralysis virus and Black queen cell virus, were detected in the brain and muscles, and may correspond to the circulation and possible replication forms of these viruses in the hornet. Aphid lethal paralysis virus, Bee Macula-like virus, and Moku virus, which are known to infect honey bees, were also identified in the gut virus metagenome of hornets. Therefore, our study underlined the urgent need to study the host range of these newly discovered viruses in hornets to determine whether they represent a new threat for honey bees or a hope for the biocontrol of V. velutina.}, } @article {pmid31713630, year = {2019}, author = {Liu, Y and Liu, S and Zhang, N and Chen, D and Que, P and Liu, N and Höglund, J and Zhang, Z and Wang, B}, title = {Genome Assembly of the Common Pheasant Phasianus colchicus: A Model for Speciation and Ecological Genomics.}, journal = {Genome biology and evolution}, volume = {11}, number = {12}, pages = {3326-3331}, pmid = {31713630}, issn = {1759-6653}, mesh = {Animals ; Base Sequence ; Galliformes/*genetics ; Genetic Speciation ; Genome/*genetics ; Genome Size ; Male ; Metagenomics ; Molecular Sequence Annotation ; Polymorphism, Single Nucleotide ; Proteins/genetics ; Repetitive Sequences, Nucleic Acid ; }, abstract = {The common pheasant (Phasianus colchicus) in the order Galliformes and the family Phasianidae, has 30 subspecies distributed across its native range in the Palearctic realm and has been introduced to Europe, North America, and Australia. It is an important game bird often subjected to wildlife management as well as a model species to study speciation, biogeography, and local adaptation. However, the genomic resources for the common pheasant are generally lacking. We sequenced a male individual of the subspecies torquatus of the common pheasant with the Illumina HiSeq platform. We obtained 94.88 Gb of usable sequences by filtering out low-quality reads of the raw data generated. This resulted in a 1.02 Gb final assembly, which equals the estimated genome size. BUSCO analysis using chicken as a model showed that 93.3% of genes were complete. The contig N50 and scaffold N50 sizes were 178 kb and 10.2 Mb, respectively. All these indicate that we obtained a high-quality genome assembly. We annotated 16,485 protein-coding genes and 123.3 Mb (12.05% of the genome) of repetitive sequences by ab initio and homology-based prediction. Furthermore, we applied a RAD-sequencing approach for another 45 individuals of seven representative subspecies in China and identified 4,376,351 novel single nucleotide polymorphism (SNPs) markers. Using this unprecedented data set, we uncovered the geographic population structure and genetic introgression among common pheasants in China. Our results provide the first high-quality reference genome for the common pheasant and a valuable genome-wide SNP database for studying population genomics and demographic history.}, } @article {pmid31713170, year = {2019}, author = {Astudillo-de la Vega, H and Alonso-Luna, O and Ali-Pérez, J and López-Camarillo, C and Ruiz-Garcia, E}, title = {Oncobiome at the Forefront of a Novel Molecular Mechanism to Understand the Microbiome and Cancer.}, journal = {Advances in experimental medicine and biology}, volume = {1168}, number = {}, pages = {147-156}, doi = {10.1007/978-3-030-24100-1_10}, pmid = {31713170}, issn = {0065-2598}, mesh = {Bacteria/genetics ; Dysbiosis ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; *Microbiota/genetics/physiology ; *Neoplasms/microbiology ; }, abstract = {The microbiome comprises all the genetic material within a microbiota, that represents tenfold higher than that of our cells. The microbiota it includes a wide variety of microorganisms such as bacteria, viruses, protozoans, fungi, and archaea, and this ecosystem is personalized in any body space of every individual. Balanced microbial communities can positively contribute to training the immune system and maintaining immune homeostasis. Dysbiosis is a change in the normal microbiome composition that can initiate chronic inflammation, epithelial barrier breaches, and overgrowth of harmful bacteria. The next-generation sequencing methods have revolutionized the study of the microbiome. Bioinformatic tools to manage large volumes of new information, it became possible to assess species diversity and measure dynamic fluctuations in microbial communities. The burden of infections that are associated to human cancer is increasing but is underappreciated by the cancer research community. The rich content in microbes of normal and tumoral tissue reflect could be defining diverse physiological or pathological states. Genomic research has emerged a new focus on the interplay between the human microbiome and carcinogenesis and has been termed the 'oncobiome'. The interactions among the microbiota in all epithelium, induce changes in the host immune interactions and can be a cause of cancer. Microbes have been shown to have systemic effects on the host that influence the efficacy of anticancer drugs. Metagenomics allows to investigate the composition of microbial community. Metatranscriptome analysis applies RNA sequencing to microbial samples to determine which species are present. Cancer can be caused by changes in the microbiome. The roles of individual microbial species in cancer progression have been identified long ago for various tissue types. The identification of microbiomes of drug resistance in the treatment of cancer patients has been the subject of numerous microbiome studies. The complexity of cancer genetic alterations becomes irrelevant in certain cancers to explain the origin, the cause or the oncogenic maintenance by the oncogene addiction theory.}, } @article {pmid31712738, year = {2020}, author = {De Paepe, K and Verspreet, J and Courtin, CM and Van de Wiele, T}, title = {Microbial succession during wheat bran fermentation and colonisation by human faecal microbiota as a result of niche diversification.}, journal = {The ISME journal}, volume = {14}, number = {2}, pages = {584-596}, pmid = {31712738}, issn = {1751-7370}, mesh = {*Bacteria/classification/genetics/growth & development/metabolism ; Biofilms ; Butyrates/metabolism ; Diet ; Dietary Fiber/metabolism ; Ecosystem ; Fatty Acids, Volatile/metabolism ; Feces/*microbiology ; Fermentation ; *Gastrointestinal Microbiome/genetics/physiology ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The human gut can be viewed as a flow-through system with a short residence time, a high turnover rate and a spatial gradient of physiological conditions. As a consequence, the gut microbiota is exposed to highly fluctuating environmental determinants presented by the host and diet. Here, we assessed the fermentation and colonisation of insoluble wheat bran by faecal microbiota of three individuals at an unprecedented sampling intensity. Time-resolved 16S rRNA gene amplicon sequencing, revealed a dynamic microbial community, characterised by abrupt shifts in composition, delimiting states with a more constant community, giving rise to a succession of bacterial taxa alternately dominating the community over a 72 h timespan. Early stages were dominated by Enterobacteriaceae and Fusobacterium species, growing on the carbohydrate-low, protein rich medium to which wheat bran was supplemented. The onset of wheat bran fermentation, marked by a spike in short chain fatty acid production with an increasing butyrate proportion and an increased endo-1,4-β-xylanase activity, corresponded to donor-dependent proportional increases of Bacteroides ovatus/stercoris, Prevotella copri and Firmicutes species, which were strongly enriched in the bran-attached community. Literature and database searches provided novel insights into the metabolic and growth characteristics underlying the observed succession and colonisation, illustrating the potency of a time-resolved analysis to increase our understanding of gut microbiota dynamics upon dietary modulations.}, } @article {pmid31712737, year = {2020}, author = {Brewer, TE and Albertsen, M and Edwards, A and Kirkegaard, RH and Rocha, EPC and Fierer, N}, title = {Unlinked rRNA genes are widespread among bacteria and archaea.}, journal = {The ISME journal}, volume = {14}, number = {2}, pages = {597-608}, pmid = {31712737}, issn = {1751-7370}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Environmental Microbiology ; Gastrointestinal Microbiome ; Genes, rRNA ; Humans ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S ; rRNA Operon/*genetics ; }, abstract = {Ribosomes are essential to cellular life and the genes for their RNA components are the most conserved and transcribed genes in bacteria and archaea. Ribosomal RNA genes are typically organized into a single operon, an arrangement thought to facilitate gene regulation. In reality, some bacteria and archaea do not share this canonical rRNA arrangement-their 16S and 23S rRNA genes are separated across the genome and referred to as "unlinked". This rearrangement has previously been treated as an anomaly or a byproduct of genome degradation in intracellular bacteria. Here, we leverage complete genome and long-read metagenomic data to show that unlinked 16S and 23S rRNA genes are more common than previously thought. Unlinked rRNA genes occur in many phyla, most significantly within Deinococcus-Thermus, Chloroflexi, and Planctomycetes, and occur in differential frequencies across natural environments. We found that up to 41% of rRNA genes in soil were unlinked, in contrast to the human gut, where all sequenced rRNA genes were linked. The frequency of unlinked rRNA genes may reflect meaningful life history traits, as they tend to be associated with a mix of slow-growing free-living species and intracellular species. We speculate that unlinked rRNA genes may confer selective advantages in some environments, though the specific nature of these advantages remains undetermined and worthy of further investigation. More generally, the prevalence of unlinked rRNA genes in poorly-studied taxa serves as a reminder that paradigms derived from model organisms do not necessarily extend to the broader diversity of bacteria and archaea.}, } @article {pmid31712445, year = {2019}, author = {Sobhani, I and Bergsten, E and Couffin, S and Amiot, A and Nebbad, B and Barau, C and de'Angelis, N and Rabot, S and Canoui-Poitrine, F and Mestivier, D and Pédron, T and Khazaie, K and Sansonetti, PJ}, title = {Colorectal cancer-associated microbiota contributes to oncogenic epigenetic signatures.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {48}, pages = {24285-24295}, pmid = {31712445}, issn = {1091-6490}, support = {R01 AI108682/AI/NIAID NIH HHS/United States ; R01 CA264048/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Cohort Studies ; Colorectal Neoplasms/*genetics/*microbiology ; DNA Methylation ; Dysbiosis/genetics/microbiology/pathology ; *Epigenesis, Genetic ; Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Gene Expression Regulation ; Germ-Free Life ; Humans ; Intestinal Mucosa/metabolism/pathology ; Male ; Mice, Inbred C3H ; Promoter Regions, Genetic ; RNA, Ribosomal, 16S ; }, abstract = {Sporadic colorectal cancer (CRC) is a result of complex interactions between the host and its environment. Environmental stressors act by causing host cell DNA alterations implicated in the onset of cancer. Here we investigate the stressor ability of CRC-associated gut dysbiosis as causal agent of host DNA alterations. The epigenetic nature of these alterations was investigated in humans and in mice. Germ-free mice receiving fecal samples from subjects with normal colonoscopy or from CRC patients were monitored for 7 or 14 wk. Aberrant crypt foci, luminal microbiota, and DNA alterations (colonic exome sequencing and methylation patterns) were monitored following human feces transfer. CRC-associated microbiota induced higher numbers of hypermethylated genes in murine colonic mucosa (vs. healthy controls' microbiota recipients). Several gene promoters including SFRP1,2,3, PENK, NPY, ALX4, SEPT9, and WIF1 promoters were found hypermethylated in CRC but not in normal tissues or effluents from fecal donors. In a pilot study (n = 266), the blood methylation levels of 3 genes (Wif1, PENK, and NPY) were shown closely associated with CRC dysbiosis. In a validation study (n = 1,000), the cumulative methylation index (CMI) of these genes was significantly higher in CRCs than in controls. Further, CMI appeared as an independent risk factor for CRC diagnosis as shown by multivariate analysis that included fecal immunochemical blood test. Consequently, fecal bacterial species in individuals with higher CMI in blood were identified by whole metagenomic analysis. Thus, CRC-related dysbiosis induces methylation of host genes, and corresponding CMIs together with associated bacteria are potential biomarkers for CRC.}, } @article {pmid31711887, year = {2020}, author = {Zhang, L and Jiang, X and Li, A and Waqas, M and Gao, X and Li, K and Xie, G and Zhang, J and Mehmood, K and Zhao, S and Wangdui, B and Li, J}, title = {Characterization of the microbial community structure in intestinal segments of yak (Bos grunniens).}, journal = {Anaerobe}, volume = {61}, number = {}, pages = {102115}, doi = {10.1016/j.anaerobe.2019.102115}, pmid = {31711887}, issn = {1095-8274}, mesh = {Animals ; Biodiversity ; Cattle ; Computational Biology/methods ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Phylogeny ; }, abstract = {Yak (Bos grunniens), a ruminant, has a complex gastrointestinal microbial ecosystem, which is essential for host nutrition and health. However, not much is known about gut microbial communities of yak. This study was conducted to characterize the gut microbial diversity and composition of small intestinal and cecal contents of yaks through high-throughput sequencing targeting V3-V4 hypervariable region of 16S rRNA gene. A total of 916,934 high-quality sequences were obtained and 224 core operational taxonomic units (OTUs) shared all samples. The result showed that the microbial community in the small intestine was different from cecum sample. In all samples, the majority of bacterial phyla were Firmicutes, Bacteroidetes and Proteobacteria. A large proportion of anaerobes in the families Peptostreptococcaceae, Prevotellaceae, Flavobacteriaceae, Lachnospiraceae, and Succinivibrionaceae were present in the various intestinal segments. The relative abundance of Ruminococcaceae, Bacteroidaceae and Muribaculaceae were significantly higher in cecum than in other segments of intestines. At the genus level, Bacteroides was the most predominant genus in cecum. The results indicated that yak have abundant and diverse gut microbial community. In conclusion, this study characterized the profiles of microbial communities across intestinal segments and provide better insight into microbial population structure and diversity of yak.}, } @article {pmid31711703, year = {2020}, author = {Even, G and Mottais, D and Morien, F and Pham, MD and Ostergaard, A and Martel, S and Merlin, S and Audebert, C}, title = {Porcine bacteriospermia examined by high-throughput sequencing.}, journal = {Theriogenology}, volume = {142}, number = {}, pages = {268-275}, doi = {10.1016/j.theriogenology.2019.10.034}, pmid = {31711703}, issn = {1879-3231}, mesh = {Animals ; Bacteria/classification/*isolation & purification ; DNA, Bacterial/chemistry/isolation & purification ; France ; High-Throughput Nucleotide Sequencing/*veterinary ; Insemination, Artificial/methods/*veterinary ; Male ; Metagenomics ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Semen/*microbiology ; *Sus scrofa ; United States ; }, } @article {pmid31709683, year = {2020}, author = {Mayneris-Perxachs, J and Fernández-Real, JM}, title = {Exploration of the microbiota and metabolites within body fluids could pinpoint novel disease mechanisms.}, journal = {The FEBS journal}, volume = {287}, number = {5}, pages = {856-865}, doi = {10.1111/febs.15130}, pmid = {31709683}, issn = {1742-4658}, mesh = {Humans ; Metabolomics/methods ; Metagenomics/methods ; Microbiota/*physiology ; Phenotype ; }, abstract = {Thanks to the emergence and recent advances in high-throughput sequencing technologies, it is becoming more evident every day that changes in the microbiome composition are linked to a myriad of health conditions. Despite this, the mechanisms of host-microbiota signalling remain largely unknown. The microbiome has an extensive metabolic activity that leads to the generation of a large number of compounds that are likely to influence host health. Therefore, the microbiome-host cross-talk is in part mediated by microbial-derived metabolites. Unlike metagenomics, which only provides information about microbial genes and thus the microbiome functional potential, metabolic phenotyping is well suited to capture their actual metabolic activity. Here, we provide an overview of these approaches and propose an integration of metagenomics, as a microbiome compositional readout, with faecal and plasma/urine metabolomics, as a functional readout, to unravel novel mechanisms linking the microbiome to host health and disease.}, } @article {pmid31709198, year = {2019}, author = {Sun, Y and Chen, Q and Lin, P and Xu, R and He, D and Ji, W and Bian, Y and Shen, Y and Li, Q and Liu, C and Dong, K and Tang, YW and Pei, Z and Yang, L and Lu, H and Guo, X and Xiao, L}, title = {Characteristics of Gut Microbiota in Patients With Rheumatoid Arthritis in Shanghai, China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {369}, pmid = {31709198}, issn = {2235-2988}, support = {P30 CA008748/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Arthritis, Rheumatoid/*etiology/metabolism ; Bacteria/classification/genetics ; Biomarkers ; China/epidemiology ; Computational Biology/methods ; *Disease Susceptibility ; Female ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Humans ; Inflammation Mediators/metabolism ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Little is known regarding differences in the gut microbiomes of rheumatoid arthritis (RA) patients and healthy cohorts in China. This study aimed to identify differences in the fecal microbiomes of 66 Chinese patients with RA and 60 healthy Chinese controls. The V3-V4 variable regions of bacterial 16S rRNA genes were sequenced with the Illumina system to define the bacterial composition. The alpha-diversity index of the microbiome of the RA patients was significantly lower than that of the control group. The bacterial genera Bacteroides (p = 0.02202) and Escherichia-Shigella (p = 0.03137) were more abundant in RA patients. In contrast, Lactobacillus (p = 0.000014), Alloprevotella (p = 0.0000008615), Enterobacter (p = 0.000005759), and Odoribacter (p = 0.0000166) were less abundant in the RA group than in the control group. Spearman correlation analysis of blood physiological measures of RA showed that bacterial genera such as Dorea and Ruminococcus were positively correlated with RF-IgA and anti-CCP antibodies. Furthermore, Alloprevotella and Parabacteroides were positively correlated with the erythrocyte sedimentation rate, and Prevotella-2 and Alloprevotella were positively correlated with C-reactive protein, both biomarkers of inflammation. These findings suggest that the gut microbiota may contribute to RA development via interactions with the host immune system.}, } @article {pmid31708159, year = {2020}, author = {Abendroth, C and Latorre-Pérez, A and Porcar, M and Simeonov, C and Luschnig, O and Vilanova, C and Pascual, J}, title = {Shedding light on biogas: Phototrophic biofilms in anaerobic digesters hold potential for improved biogas production.}, journal = {Systematic and applied microbiology}, volume = {43}, number = {1}, pages = {126024}, doi = {10.1016/j.syapm.2019.126024}, pmid = {31708159}, issn = {1618-0984}, mesh = {Anaerobiosis ; Archaea/classification/genetics/isolation & purification/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Biofilms/growth & development ; Biofuels/*microbiology ; Bioreactors/microbiology ; Metagenome ; Microbiota/genetics/*physiology ; *Phototrophic Processes ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/microbiology ; }, abstract = {Conventional anaerobic digesters intended for the production of biogas usually operate in complete darkness. Therefore, little is known about the effect of light on their microbial communities. In the present work, 16S rRNA gene amplicon Nanopore sequencing and shotgun metagenomic sequencing were used to study the taxonomic and functional structure of the microbial community forming a biofilm on the inner wall of a laboratory-scale transparent anaerobic biodigester illuminated with natural sunlight. The biofilm was composed of microorganisms involved in the four metabolic processes needed for biogas production, and it was surprisingly rich in Rhodopseudomonas faecalis, a versatile bacterium able to carry out photoautotrophic metabolism when grown under anaerobic conditions. The results suggested that this bacterium, which is able to fix carbon dioxide, could be considered for use in transparent biogas fermenters in order to contribute to the production of optimized biogas with a higher CH4:CO2 ratio than the biogas produced in regular, opaque digesters. To the best of our knowledge, this is the first study characterising the phototrophic biofilm associated with illuminated bioreactors.}, } @article {pmid31707781, year = {2019}, author = {Li, Q and Chen, H and Zhang, M and Wu, T and Liu, R and Zhang, Z}, title = {Potential Correlation between Dietary Fiber-Suppressed Microbial Conversion of Choline to Trimethylamine and Formation of Methylglyoxal.}, journal = {Journal of agricultural and food chemistry}, volume = {67}, number = {48}, pages = {13247-13257}, doi = {10.1021/acs.jafc.9b04860}, pmid = {31707781}, issn = {1520-5118}, mesh = {Animal Feed/analysis ; Animals ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Choline/*metabolism ; Dietary Fiber/*metabolism ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/metabolism/microbiology ; Glycine/metabolism ; Methylamines/*metabolism ; Mice ; Mice, Inbred C57BL ; Pyruvaldehyde/*metabolism ; Red Meat/analysis ; }, abstract = {Dietary interventions alter the formation of the disease-associated metabolite, trimethylamine (TMA), via intestinal microbial TMA lyase activity. Nevertheless, the mechanisms regulating microbial enzyme production are still unclear. Sequencing of the gut bacteria 16S rDNA demonstrated that dietary intervention changed the composition of the gut microbiota and the functional metagenome involved in the choline utilization pathway. Characterization of the functional profile of the metagenomes and metabonomics analysis revealed that a series of Kyoto Encyclopedia of Genes and Genomes orthologous groups and enzyme groups related to accumulation of methylglyoxal (MG) and glycine were enriched in red meat diet-fed animals, whereas fiber-rich diet suppressed glycine formation via the MG-dependent pathway. Our observations suggest associations between choline-TMA lyase expression and MG formation, which are indicative of a novel role of the gut microbiota in choline metabolism and highlight it as a potential target for inhibiting TMA production.}, } @article {pmid31707285, year = {2020}, author = {Huang, YC and Huang, LT and Sheen, JM and Hou, CY and Yeh, YT and Chiang, CP and Lin, IC and Tiao, MM and Tsai, CC and Lin, YJ and Chen, CC and Tain, YL and Yu, HR}, title = {Resveratrol treatment improves the altered metabolism and related dysbiosis of gut programed by prenatal high-fat diet and postnatal high-fat diet exposure.}, journal = {The Journal of nutritional biochemistry}, volume = {75}, number = {}, pages = {108260}, doi = {10.1016/j.jnutbio.2019.108260}, pmid = {31707285}, issn = {1873-4847}, mesh = {Animals ; Blood Pressure ; Body Weight ; *Diet, High-Fat ; Dysbiosis/*therapy ; Fatty Acids, Volatile/metabolism ; Female ; Gastrointestinal Microbiome ; Gene Expression Regulation ; Glucose Tolerance Test ; Intestines/*drug effects ; Lipid Metabolism ; Maternal Nutritional Physiological Phenomena/genetics ; Metagenome ; Polyphenols/chemistry ; Pregnancy ; Prenatal Exposure Delayed Effects/genetics ; Rats ; Rats, Sprague-Dawley ; Resveratrol/*pharmacology ; }, abstract = {A maternal high-fat (HF) diet sensitizes offspring to the adverse effects of postnatal HF intake and can lead to metabolic dysregulation. Resveratrol, a natural polyphenolic compound found in grapes and red wine, could help to relieve metabolic syndrome dysregulation. Since the gut microbiota is known to be closely related to metabolic homeostasis, this study aimed to investigate the impact of a combination of maternal and postweaning HF diets on the gut microbiota and whether resveratrol could relieve the gut dysbiosis associated with metabolic dysregulation. Sprague-Dawley dams were sustained on either a chow or HF diet before mating, during pregnancy and during lactation. Their offspring were randomly fed chow or a HF diet after weaning. Four experimental groups were generated: CC (maternal/postnatal chow diet), HC (maternal HF/postnatal chow diet), CH (maternal chow/postnatal high-fat diet) and HH (maternal/postnatal HF diet). A fifth group consisted of HH with resveratrol treatment. We found that both maternal and postnatal HF exposure has a distinct effect on the gut microbiota metagenome of offspring. Maternal HF diet exposure decreased plasma acetate, propionate and butyrate level, while postnatal HF diet exposure decreased plasma acetate level in adult life. The metabolic dysregulation programed by the maternal and postnatal HF diets was related to the relevant gut microbiota. Resveratrol treatment ameliorated the altered plasma propionate level related to maternal HF and postnatal HF diet treatment. Resveratrol treatment also improved most of the altered metabolic dysregulation and related dysbiosis programmed by maternal and postnatal HF diet exposure.}, } @article {pmid31706024, year = {2019}, author = {Gui, Q and Hoffman, PS and Lewis, JP}, title = {Amixicile targets anaerobic bacteria within the oral microbiome.}, journal = {Journal of oral biosciences}, volume = {61}, number = {4}, pages = {226-235}, pmid = {31706024}, issn = {1880-3865}, support = {R01 DE023304/DE/NIDCR NIH HHS/United States ; R21 DE023745/DE/NIDCR NIH HHS/United States ; UL1 TR002649/TR/NCATS NIH HHS/United States ; }, mesh = {*Bacteria, Anaerobic ; Benzamides ; *Microbiota ; Thiazoles ; }, abstract = {OBJECTIVES: Anaerobic bacteria are the major causative agents of periodontal disease. However, so far, targeted therapy aimed at reducing those pathogens has not been widely implemented. We have previously reported on a novel antimicrobial, amixicile, that targets anaerobic bacteria through inhibition of the function of the major anaerobic metabolic enzyme pyruvate ferredoxin oxidoreductase (PFOR), while not affecting aerotolerant organisms. It effectively inhibited the growth of oral anaerobes both in monocultures as well as in mixed in vitro mixed cultured however, amixicile's activity in in vivo-like conditions remained to be established.

METHODS: Here, we expand our study using an ex vivo oral microbiome combined with metagenomic sequencing to determine the effect of amixicile treatment on the composition of the microbiome and compare it to that of metronidazole.

RESULTS: Our results show that in the complex microbiomes, anaerobic bacteria are selectively inhibited, while the growth of aerotolerant ones, such as Streptococcus, Klebsiella, Neisseria, and Rothia is unaffected. Veillonella was the most abundant anaerobic genus in our ex vivo microbiome, and we observed complete inhibition of its growth. In addition, growth of other anaerobes, Fusobacterium and Prevotella, was significantly inhibited. It is noteworthy that a change in abundance of bacteriophages, such as Siphoviridae and Myoviridae, associated with the oral microbiome was observed.

CONCLUSIONS: Collectively, our data expand on the so far reported inhibitory spectrum of amixicile and demonstrates that it inhibits anaerobic bacteria, including both clinical isolates and laboratory strains.}, } @article {pmid31705042, year = {2019}, author = {Kundu, P and Manna, B and Majumder, S and Ghosh, A}, title = {Species-wide Metabolic Interaction Network for Understanding Natural Lignocellulose Digestion in Termite Gut Microbiota.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {16329}, pmid = {31705042}, issn = {2045-2322}, mesh = {Animals ; *Gastrointestinal Microbiome ; Isoptera/*metabolism/*microbiology ; Lignin/*metabolism ; *Metabolic Networks and Pathways ; }, abstract = {The structural complexity of lignocellulosic biomass hinders the extraction of cellulose, and it has remained a challenge for decades in the biofuel production process. However, wood-feeding organisms like termite have developed an efficient natural lignocellulolytic system with the help of specialized gut microbial symbionts. Despite having an enormous amount of high-throughput metagenomic data, specific contributions of each individual microbe to achieve this lignocellulolytic functionality remains unclear. The metabolic cross-communication and interdependence that drives the community structure inside the gut microbiota are yet to be explored. We have contrived a species-wide metabolic interaction network of the termite gut-microbiome to have a system-level understanding of metabolic communication. Metagenomic data of Nasutitermes corniger have been analyzed to identify microbial communities in different gut segments. A comprehensive metabolic cross-feeding network of 205 microbes and 265 metabolites was developed using published experimental data. Reconstruction of inter-species influence network elucidated the role of 37 influential microbes to maintain a stable and functional microbiota. Furthermore, in order to understand the natural lignocellulose digestion inside N. corniger gut, the metabolic functionality of each influencer was assessed, which further elucidated 15 crucial hemicellulolytic microbes and their corresponding enzyme machinery.}, } @article {pmid31705027, year = {2019}, author = {Ventura, RE and Iizumi, T and Battaglia, T and Liu, M and Perez-Perez, GI and Herbert, J and Blaser, MJ}, title = {Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {16396}, pmid = {31705027}, issn = {2045-2322}, support = {P30 CA016087/CA/NCI NIH HHS/United States ; R01 DK090989/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Black or African American ; Case-Control Studies ; Clostridium/classification/genetics/isolation & purification ; *Ethnicity ; Female ; *Gastrointestinal Microbiome/genetics ; Hispanic or Latino ; Host Microbial Interactions/immunology ; Humans ; Male ; Metagenome ; Middle Aged ; Multiple Sclerosis/immunology/*microbiology ; RNA, Ribosomal, 16S/genetics ; White People ; Young Adult ; }, abstract = {Although the intestinal microbiome has been increasingly implicated in autoimmune diseases, much is unknown about its roles in Multiple Sclerosis (MS). Our aim was to compare the microbiome between treatment-naïve MS subjects early in their disease course and controls, and between Caucasian (CA), Hispanic (HA), and African American (AA) MS subjects. From fecal samples, we performed 16S rRNA V4 sequencing and analysis from 45 MS subjects (15 CA, 16 HA, 14 AA) and 44 matched healthy controls, and whole metagenomic shotgun sequencing from 24 MS subjects (all newly diagnosed, treatment-naïve, and steroid-free) and 24 controls. In all three ethnic groups, there was an increased relative abundance of the same single genus, Clostridium, compared to ethnicity-matched controls. Analysis of microbiota networks showed significant changes in the network characteristics between combined MS cohorts and controls, suggesting global differences not restricted to individual taxa. Metagenomic analysis revealed significant enrichment of individual species within Clostridia as well as particular functional pathways in the MS subjects. The increased relative abundance of Clostridia in all three early MS cohorts compared to controls provides candidate taxa for further study as biomarkers or as etiologic agents in MS.}, } @article {pmid31704882, year = {2019}, author = {Banskar, S and Detzner, AA and Juarez-Rodriguez, MD and Hozo, I and Gupta, D and Dziarski, R}, title = {The Pglyrp1-Regulated Microbiome Enhances Experimental Allergic Asthma.}, journal = {Journal of immunology (Baltimore, Md. : 1950)}, volume = {203}, number = {12}, pages = {3113-3125}, doi = {10.4049/jimmunol.1900711}, pmid = {31704882}, issn = {1550-6606}, mesh = {Allergens/*immunology ; Animals ; Anti-Bacterial Agents/pharmacology ; Asthma/*etiology/*metabolism/pathology ; Cytokines/*genetics/*metabolism ; Disease Models, Animal ; *Disease Susceptibility ; Immunoglobulin E/immunology ; Immunohistochemistry ; Metagenome ; Metagenomics ; Mice ; Mice, Inbred BALB C ; Mice, Knockout ; *Microbiota/drug effects/immunology ; Pyroglyphidae/immunology ; }, abstract = {Changes in intestinal or respiratory microbiomes in infants correlate with increased incidence of asthma, but the causative role of microbiome in the susceptibility to asthma and the host genes that regulate these changes in microbiome are mostly unknown. In this study, we show that decreased responsiveness to allergic asthma in Pglyrp1 [-/-] mice (lacking bactericidal peptidoglycan recognition protein 1) could be transferred to germ-free wild-type mice by colonization of mothers and newborns with microbiota from Pglyrp1 [-/-] mice. These colonized mice had decreased airway resistance and fewer inflammatory cells, less severe histopathology, and lower levels of IgE and proallergic cytokines and chemokines in the lungs. This microbiome-dependent decreased responsiveness to asthma was most pronounced in colonized germ-free BALB/c mice (genetically predisposed to asthma), only partially evident in outbred germ-free Swiss Webster mice, and marginal in conventional BALB/c mice following depletion of microbiome with antibiotics. Mice with a low asthmatic response colonized with microbiota from Pglyrp1 [-/-] mice had increased abundance of Bacteroidetes and decreased abundance of Firmicutes, Tenericutes, Deferribacteres, and Spirochaetes in the feces and increased abundance of Pasteurella in the oropharynx. These changes in bacterial abundance in the feces and oropharynx correlated with lower asthmatic responses in the lungs. Thus, our results show that Pglyrp1 enhances allergic asthmatic responses primarily through its effect on the host intestinal microbiome and identify several bacteria that may increase or decrease sensitivity to asthma. This effect of microbiome is strong in asthma-prone BALB/c mice and weak in asthma-resistant outbred mice and requires germ-free conditions before colonization with microbiota from Pglyrp1 [-/-] mice.}, } @article {pmid31704413, year = {2020}, author = {Rehman, ZU and Fortunato, L and Cheng, T and Leiknes, T}, title = {Metagenomic analysis of sludge and early-stage biofilm communities of a submerged membrane bioreactor.}, journal = {The Science of the total environment}, volume = {701}, number = {}, pages = {134682}, doi = {10.1016/j.scitotenv.2019.134682}, pmid = {31704413}, issn = {1879-1026}, mesh = {*Biofilms ; Biofouling ; Bioreactors/*microbiology ; Membranes, Artificial ; Metagenome ; *Microbiota ; Sewage/microbiology ; *Waste Disposal, Fluid ; }, abstract = {Biofilm formation on membranes in activated sludge membrane bioreactors (MBR), commonly identified as biofouling, is a significant problem for MBR operations. A better understanding of microbial species involved in the biofilm formation is needed to develop anti-biofilm measures. A read-based and genome-resolved shotgun metagenomic approach was applied to characterize the composition and functional potential of the sludge and early stage biofilm microbial communities in an MBR process. Read-based analysis revealed that the prevalence of different phyla are relatively similar in both the sludge and biofilm samples, with Proteobacteria as the most dominant, followed by Chloroflexi, Bacteroidetes and Planctomycetes. However, the relative abundance of these phyla slightly varies between the sludge and biofilm. Phyla such as Actinobacteria, bacterial candidate phyla, Chlamydiae, Cyanobacteria/Melainabacteria and Firmicutes are 2 to 4 times more abundant in the biofilm than in the sludge. At the genus level, genera belonging to Proteobacteria (Legionella, Caulobacter, Sphingomonas, Acinetobacter and Rhizobium), Cyanobacteria (Hassallia), and Spirochaetes (Turneriella) are at least twice more abundant in the biofilm. These genera, especially those belonging to Phylum Proteobacteria, are known to play an important role in the formation of biofilms on surfaces. The Alpha diversity is found slightly higher in the biofilm, compared with sludge samples. Functional classification of reads through the SEED subsystem shows that functional classes such as those involved in the metabolism of various molecules are significantly different in the biofilm and sludge. A phylogenomic analysis of the six extracted metagenome assembled genomes (MAGs) shows that three MAGs belong to Proteobacteria, and one MAG belong to each of Chloroflexi, Bacteroidetes and Planctomycetes. The relative abundance of the MAG belonging to Alphaproteobacteria is higher in the biofilm. A functional potential analysis of the MAGs reveals their potential to metabolize carbon and nitrogen sources, as well as the prevalence of antibiotic resistance genes.}, } @article {pmid31703871, year = {2020}, author = {Chen, C and Liu, Y and Tian, H and Ai, L and Yu, H}, title = {Metagenomic analysis reveals the impact of JIUYAO microbial diversity on fermentation and the volatile profile of Shaoxing-jiu.}, journal = {Food microbiology}, volume = {86}, number = {}, pages = {103326}, doi = {10.1016/j.fm.2019.103326}, pmid = {31703871}, issn = {1095-9998}, mesh = {Bacteria/classification/genetics/*isolation & purification/metabolism ; *Biodiversity ; Ethanol/metabolism ; Fermentation ; Flavoring Agents/chemistry/metabolism ; Humans ; Metagenome ; Rhizopus/genetics/*isolation & purification/metabolism ; Saccharomyces cerevisiae/genetics/*isolation & purification/metabolism ; Taste ; Volatile Organic Compounds/*chemistry/metabolism ; Wine/*analysis/microbiology ; }, abstract = {This study focused on the microbial communities found in JIUYAO, the fermentation starter traditionally used in Shaoxing-jiu, and elucidated their relationship with the fermentation activities and volatile compounds involved in winemaking. The microbial communities found in all JIUYAO samples tested were dominated by Pediococcus and Weissella bacteria and Saccharomycopsis and Rhizopus fungi. Saccharifying power showed significant positive correlations with the presence of Pedioccoccus, Saccharomycopsis, and Rhizopus, whereas acid production capacity was strongly associated with Pedioccoccus, Weissella, and Rhizopus. Alcohol production capacity positively correlated with the presence of Pedioccoccus and Rhizopus. Fifteen important volatile compounds (odor-activity values ≥ 1) including esters, alcohols, acids, and aldehydes were identified in Huangjiu samples fermented with JIUYAO. Positive correlations were found between Saccharomycopsis and phenylethanol/ethyl butyrate, Rhizopus and ethyl propionate/ethyl laurate/ethyl butyrate, Pedioccoccus and ethyl laurate/acetic acid, and Weissella and decanoic acid/isopentanol. These results imply that these microorganisms significantly contribute to the fermentation activities and flavor of Shaoxing-jiu. Finally, the results showed that a combination of five core microbes with Saccharomyces cerevisiae could be used as a starter in winemaking. To conclude, this study provides a comprehensive overview of the core microbes found in JIUYAO and strategies for the selection of beneficial microorganisms to improve the quality and flavor of Shaoxing-jiu.}, } @article {pmid31703868, year = {2020}, author = {Chen, SH and Fegan, N and Kocharunchitt, C and Bowman, JP and Duffy, LL}, title = {Changes of the bacterial community diversity on chicken carcasses through an Australian poultry processing line.}, journal = {Food microbiology}, volume = {86}, number = {}, pages = {103350}, doi = {10.1016/j.fm.2019.103350}, pmid = {31703868}, issn = {1095-9998}, mesh = {Animals ; Australia ; Bacteria/classification/genetics/*growth & development/isolation & purification ; *Biodiversity ; Chickens/*microbiology ; Colony Count, Microbial ; Food Contamination/analysis ; Food Handling ; Poultry Products/analysis/*microbiology ; }, abstract = {Understanding the bacterial community profile through poultry processing could help the industry to produce better poultry products. In this study, 10 chicken carcasses were randomly sampled from before and after scalding, before and after immersion chilling, and after air chilling each through a modern commercial processing line, along with the contents of 10 caeca. The sampled processing line effectively reduced the bacterial counts by > 4.6 Log10 CFU/ml for each of Total Viable Counts, Escherichia coli and Campylobacter. However, the metagenomics results suggested that Lactobacillus, Staphylococcus and unclassified Lachnospiraceae persisted at all sampling stages. Pseudomonas, Paeniglutamicibacter, Chryseobacterium and Pseudarthrobacter comprised 47.2% in the bacterial community on samples after air chilling compared to 0.3% on samples after immersion chilling, whereas TVCs were the same. Overall, the current interventions of the investigated poultry processing line were unable to eliminate persistence of certain foodborne pathogens, despite a significant reduction of the overall bacterial counts. Chilling is an important controlling point in contamination/cross-contamination, particularly extended air chilling. Lastly, the large presence of Pseudomonas on chickens after air chilling may lead to downstream spoilage related issues, which needs more investigation to explore quantitatively the effect on the shelf life of poultry products.}, } @article {pmid31703372, year = {2019}, author = {Gowers, GF and Vince, O and Charles, JH and Klarenberg, I and Ellis, T and Edwards, A}, title = {Entirely Off-Grid and Solar-Powered DNA Sequencing of Microbial Communities during an Ice Cap Traverse Expedition.}, journal = {Genes}, volume = {10}, number = {11}, pages = {}, pmid = {31703372}, issn = {2073-4425}, support = {BB/K006290/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Electric Power Supplies ; *Expeditions ; Ice Cover/*microbiology ; Iceland ; *Metagenome ; Metagenomics/instrumentation/*methods ; *Microbiota ; Nanopore Sequencing/instrumentation/*methods ; *Solar Energy ; }, abstract = {Microbial communities in remote locations remain under-studied. This is particularly true on glaciers and icecaps, which cover approximately 11% of the Earth's surface. The principal reason for this is the inaccessibility of most of these areas due to their extreme isolation and challenging environmental conditions. While remote research stations have significantly lowered the barrier to studying the microbial communities on icecaps, their use has led to a bias for data collection in the near vicinity of these institutions. Here, miniaturisation of a DNA sequencing lab suitable for off-grid metagenomic studies is demonstrated. Using human power alone, this lab was transported across Europe's largest ice cap (Vatnajökull, Iceland) by ski and sledge. After 11 days of unsupported polar-style travel, a metagenomic study of a geothermal hot spring gorge was conducted on the remote northern edge of the ice cap. This tent-based metagenomic study resulted in over 24 h of Nanopore sequencing, powered by solar power alone. This study demonstrates the ability to conduct DNA sequencing in remote locations, far from civilised resources (mechanised transport, external power supply, internet connection, etc.), whilst greatly reducing the time from sample collection to data acquisition.}, } @article {pmid31703241, year = {2019}, author = {Wang, F and Wan, Y and Yin, K and Wei, Y and Wang, B and Yu, X and Ni, Y and Zheng, J and Huang, T and Song, M and Li, D}, title = {Lower Circulating Branched-Chain Amino Acid Concentrations Among Vegetarians are Associated with Changes in Gut Microbial Composition and Function.}, journal = {Molecular nutrition & food research}, volume = {63}, number = {24}, pages = {e1900612}, doi = {10.1002/mnfr.201900612}, pmid = {31703241}, issn = {1613-4133}, mesh = {Adult ; Amino Acids, Branched-Chain/*blood ; Diet, Vegetarian ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Middle Aged ; RNA, Ribosomal, 16S ; *Vegetarians ; Young Adult ; }, abstract = {SCOPE: Vegetarian diets confer health benefits to many cardiometabolic diseases, although whether and how gut microbiota in vegetarians contributes to host metabolism remains unclear. Thus, the aim is to explore the possible links between the gut microbiota and circulating gut microbiota-host co-metabolites among vegetarians and omnivores.

METHODS AND RESULTS: Fecal and serum samples from 36 adults following a vegan, lacto-ovo vegetarian, or omnivorous diet are collected. A 16S rRNA gene, metagenome, metatranscriptome, and metabolome integrated multi-omics approach is adopted to profile fecal microbial composition and functionality and circulating gut microbiota-host co-metabolites. 16S rRNA gene and metagenomic sequencing suggest a significant difference in gut microbial composition between the two vegetarian groups and the omnivorous group at the family, genus, and species level. Metabolomic analysis reveals that circulating branched-chain amino acids (BCAAs)-valine, leucine, and isoleucine-are significantly lower in the two vegetarian groups than those in the omnivorous group. In line with the lower concentrations of BCAAs, metatranscriptomic analysis shows that the gut microbial pathway for the degradation of BCAAs is significantly upregulated among vegetarians compared with the omnivores.

CONCLUSIONS: The results indicate that gut microbiota plays an important role in the modulation of circulating BCAAs among vegetarians.}, } @article {pmid31703093, year = {2019}, author = {Kato, S and Hirai, M and Ohkuma, M and Suzuki, K}, title = {Microbial metabolisms in an abyssal ferromanganese crust from the Takuyo-Daigo Seamount as revealed by metagenomics.}, journal = {PloS one}, volume = {14}, number = {11}, pages = {e0224888}, pmid = {31703093}, issn = {1932-6203}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Carbon/metabolism ; Metabolic Networks and Pathways ; *Metabolome ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Nitrogen/metabolism ; Phylogeny ; }, abstract = {Rocky outcrops covered with thick Fe and Mn oxide coatings, which are known as ferromanganese (Fe-Mn) crusts, are commonly found on slopes of aged seamounts in bathyal and abyssal zones. Although the presence of diverse microorganisms on these Fe-Mn crusts has been reported, little is known about their metabolism. Here, we report the metabolic potential of the microbial community in an abyssal crust collected in the Takuyo-Daigo Seamount, in the north-western Pacific. We performed shotgun metagenomic sequencing of the Fe-Mn crust, and detected putative genes involved in dissolution and precipitation of Fe and Mn, nitrification, sulfur oxidation, carbon fixation, and decomposition of organics in the metagenome. In addition, four metagenome-assembled genomes (MAGs) of abundant members in the microbial community were recovered from the metagenome. The MAGs were affiliated with Thaumarchaeota, Alphaproteobacteria, and Gammaproteobacteria, and were distantly related to previously reported genomes/MAGs of cultured and uncultured species. Putative genes involved in the above reactions were also found in the crust MAGs. Our results suggest that crust microbial communities play a role in biogeochemical cycling of C, N, S, Fe, and Mn, and imply that they contribute to the growth of Fe-Mn crusts.}, } @article {pmid31701637, year = {2020}, author = {Ren, Q and Si, H and Yan, X and Liu, C and Ding, L and Long, R and Li, Z and Qiu, Q}, title = {Bacterial communities in the solid, liquid, dorsal, and ventral epithelium fractions of yak (Bos grunniens) rumen.}, journal = {MicrobiologyOpen}, volume = {9}, number = {2}, pages = {e963}, pmid = {31701637}, issn = {2045-8827}, mesh = {Animals ; Biodiversity ; Cattle ; Computational Biology/methods ; Gastric Mucosa/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Yak (Bos grunniens) is an important and dominant livestock species in the challenging environment of the Qinghai-Tibetan Plateau. Rumen microbiota of the solid, liquid, and epithelium fractions play key roles in nutrient metabolism and contribute to host adaptation in ruminants. However, there is a little knowledge of the microbiota in these rumen fractions of yak. Therefore, we collected samples of solid, liquid, dorsal, and ventral epithelium fractions from five female yaks, then amplified bacterial 16S rRNA gene V4 regions and sequenced them using an Illumina MiSeq platform. Principal coordinates analysis detected significant differences in bacterial communities between the liquid, solid, and epithelium fractions, and between dorsal and ventral epithelium fractions. Rikenellaceae RC9, the families Lachnospiraceae and Ruminococcaceae, and Fibrobacter spp. were the abundant and enriched bacteria in solid fraction, while the genera Prevotella and Prevotellaceae UCG 003 were higher in the liquid fraction. Campylobacter spp., Comamonas spp., Desulfovibrio spp., and Solobacterium spp. were significantly higher in dorsal epithelium, while Howardella spp., Prevotellaceae UCG 001, Ruminococcaceae UCG 005, and Treponema 2 were enriched in the ventral epithelium. Comparison of predictive functional profiles among the solid, liquid, and dorsal, and ventral epithelium fractions also revealed significant differences. Microbiota in the ventral fraction of yak rumen also significantly differ from reported microbiota of cattle. In conclusion, our results improve our knowledge of the taxonomic composition and roles of yak rumen microbiota.}, } @article {pmid31701197, year = {2019}, author = {Tang, R and Ye, P and Alper, HS and Liu, Z and Zhao, X and Bai, F}, title = {Identification and characterization of novel xylose isomerases from a Bos taurus fecal metagenome.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {23-24}, pages = {9465-9477}, doi = {10.1007/s00253-019-10161-1}, pmid = {31701197}, issn = {1432-0614}, support = {51561145014//National Natural Science Foundation of China/ ; MMLKF19-01//State Key Laboratory of Microbial Metabolism/ ; }, mesh = {Aldose-Ketose Isomerases/*genetics/*metabolism ; Animals ; Bacterial Proteins/*genetics/*metabolism ; Biotechnology ; Cattle ; Codon ; Escherichia coli/genetics ; Feces/microbiology ; Fermentation ; *Gastrointestinal Microbiome ; Metagenome ; Mutation ; Saccharomyces cerevisiae/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {Discovering sugar metabolism genes is of great interest for lignocellulosic biorefinery. Xylose isomerases (XIs) were commonly screened from metagenomes derived from bovine rumen, soil, and other sources. However, so far, XIs and other sugar-utilizing enzymes have not been discovered from fecal metagenomes. In this study, environmental DNA from the fecal samples collected from yellow cattle (Bos taurus) was sequenced and analyzed. In the whole 14.26 Gbp clean data, 92 putative XIs were annotated. After sequence analysis, seven putative XIs were heterologously expressed in Escherichia coli and characterized in vitro. The XIs 58444 and 58960 purified from E. coli exhibited 22% higher enzyme activity when compared with that of the native E. coli XI. The XI 58444, similar to the XI from Lachnospira multipara, exhibited a relatively stable activity profile across different pH conditions. Four XIs were further investigated in budding yeast Saccharomyces cerevisiae after codon optimization. Overexpression of the codon-optimized 58444 enabled S. cerevisiae to utilize 6.4 g/L xylose after 96 h without any other genetic manipulations, which is 56% higher than the control yeast strain overexpressing an optimized XI gene xylA*3 selected by three rounds of mutation. Our results provide evidence that a bovine fecal metagenome is a novel and valuable source of XIs and other industrial enzymes for biotechnology applications.}, } @article {pmid31699813, year = {2020}, author = {Kishikawa, T and Maeda, Y and Nii, T and Motooka, D and Matsumoto, Y and Matsushita, M and Matsuoka, H and Yoshimura, M and Kawada, S and Teshigawara, S and Oguro, E and Okita, Y and Kawamoto, K and Higa, S and Hirano, T and Narazaki, M and Ogata, A and Saeki, Y and Nakamura, S and Inohara, H and Kumanogoh, A and Takeda, K and Okada, Y}, title = {Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population.}, journal = {Annals of the rheumatic diseases}, volume = {79}, number = {1}, pages = {103-111}, pmid = {31699813}, issn = {1468-2060}, mesh = {Arthritis, Rheumatoid/metabolism/*microbiology ; Bacteroides/genetics ; Case-Control Studies ; Fatty Acids/metabolism ; Female ; Gastrointestinal Microbiome/*genetics ; Genome-Wide Association Study ; Humans ; Japan ; Male ; Metabolic Networks and Pathways/genetics ; Metagenome/*genetics ; Metagenomics ; Middle Aged ; Oxidation-Reduction ; Phylogeny ; Prevotella/genetics ; Whole Genome Sequencing ; }, abstract = {OBJECTIVE: The causality and pathogenic mechanism of microbiome composition remain elusive in many diseases, including autoimmune diseases such as rheumatoid arthritis (RA). This study aimed to elucidate gut microbiome's role in RA pathology by a comprehensive metagenome-wide association study (MWAS).

METHODS: We conducted MWAS of the RA gut microbiome in the Japanese population (ncase=82, ncontrol=42) by using whole-genome shotgun sequencing of high depth (average 13 Gb per sample). Our MWAS consisted of three major bioinformatic analytic pipelines (phylogenetic analysis, functional gene analysis and pathway analysis).

RESULTS: Phylogenetic case-control association tests showed high abundance of multiple species belonging to the genus Prevotella (e.g., Prevotella denticola) in the RA case metagenome. The non-linear machine learning method efficiently deconvoluted the case-control phylogenetic discrepancy. Gene functional assessments showed that the abundance of one redox reaction-related gene (R6FCZ7) was significantly decreased in the RA metagenome compared with controls. A variety of biological pathways including those related to metabolism (e.g., fatty acid biosynthesis and glycosaminoglycan degradation) were enriched in the case-control comparison. A population-specific link between the metagenome and host genome was identified by comparing biological pathway enrichment between the RA metagenome and the RA genome-wide association study results. No apparent discrepancy in alpha or beta diversities of metagenome was found between RA cases and controls.

CONCLUSION: Our shotgun sequencing-based MWAS highlights a novel link among the gut microbiome, host genome and pathology of RA, which contributes to our understanding of the microbiome's role in RA aetiology.}, } @article {pmid31698792, year = {2019}, author = {Pettersson, JH and Shi, M and Eden, JS and Holmes, EC and Hesson, JC}, title = {Meta-Transcriptomic Comparison of the RNA Viromes of the Mosquito Vectors Culex pipiens and Culex torrentium in Northern Europe.}, journal = {Viruses}, volume = {11}, number = {11}, pages = {}, pmid = {31698792}, issn = {1999-4915}, mesh = {Animals ; Biological Evolution ; Culex/virology ; Culicidae/virology ; Europe ; Genes, Viral ; Genome, Viral ; Host Microbial Interactions/genetics ; Insect Viruses/genetics ; *Metagenome ; Metagenomics/methods ; Mosquito Vectors/*virology ; Phylogeny ; Phylogeography ; RNA Viruses/*genetics ; RNA-Dependent RNA Polymerase/genetics ; RNA-Seq/methods ; Transcriptome/*genetics ; }, abstract = {Mosquitoes harbor an extensive diversity of 'insect-specific' RNA viruses in addition to those important to human and animal health. However, because most studies of the mosquito virome have been conducted at lower latitudes, little is known about the diversity and evolutionary history of RNA viruses sampled from mosquitoes in northerly regions. Here, we compared the RNA virome of two common northern mosquito species, Culex pipiens and Culex torrentium, collected in south-central Sweden. Following bulk RNA-sequencing (meta-transcriptomics) of 12 libraries, comprising 120 specimens of Cx. pipiens and 150 specimens of Cx. torrentium, we identified 40 viruses (representing 14 virus families) of which 28 were novel based on phylogenetic analysis of the RNA-dependent RNA polymerase (RdRp) protein. Hence, we documented similar levels of virome diversity as in mosquitoes sampled from the more biodiverse lower latitudes. Many viruses were also related to those sampled on other continents, indicative of a widespread global movement and/or long host-virus co-evolution. Although the two mosquito species investigated have overlapping geographical distributions and share many viruses, several viruses were only found at a specific location at this scale of sampling, such that local habitat and geography may play an important role in shaping viral diversity in Culex mosquitoes.}, } @article {pmid31697678, year = {2019}, author = {Srivathsan, A and Nagarajan, N and Meier, R}, title = {Boosting natural history research via metagenomic clean-up of crowdsourced feces.}, journal = {PLoS biology}, volume = {17}, number = {11}, pages = {e3000517}, pmid = {31697678}, issn = {1545-7885}, mesh = {Animals ; Bacteria ; Biodiversity ; Conservation of Natural Resources ; Crowdsourcing ; Feces/chemistry/microbiology/parasitology ; Gastrointestinal Microbiome ; *Mammals ; Metagenome ; *Metagenomics ; Natural History/*methods ; Sequence Analysis, DNA ; }, abstract = {Biodiversity is in crisis due to habitat destruction and climate change. The conservation of many noncharismatic species is hampered by the lack of data. Yet, natural history research-a major source of information on noncharismatic species-is in decline. We here suggest a remedy for many mammal species, i.e., metagenomic clean-up of fecal samples that are "crowdsourced" during routine field surveys. Based on literature data, we estimate that this approach could yield natural history information for circa 1,000 species within a decade. Metagenomic analysis would simultaneously yield natural history data on diet and gut parasites while enhancing our understanding of host genetics, gut microbiome, and the functional interactions between traditional and new natural history data. We document the power of this approach by carrying out a "metagenomic clean-up" on fecal samples collected during a single night of small mammal trapping in one of Alfred Wallace's favorite collecting sites.}, } @article {pmid31696774, year = {2020}, author = {Astbury, S and Atallah, E and Vijay, A and Aithal, GP and Grove, JI and Valdes, AM}, title = {Lower gut microbiome diversity and higher abundance of proinflammatory genus Collinsella are associated with biopsy-proven nonalcoholic steatohepatitis.}, journal = {Gut microbes}, volume = {11}, number = {3}, pages = {569-580}, pmid = {31696774}, issn = {1949-0984}, support = {MR/N005953/1/MRC_/Medical Research Council/United Kingdom ; MR/M016560/1/MRC_/Medical Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; SP/14/8/31352/BHF_/British Heart Foundation/United Kingdom ; BRC-1215-20003/DH_/Department of Health/United Kingdom ; }, mesh = {Actinobacteria/classification/*isolation & purification ; Aged ; Biodiversity ; Body Mass Index ; Clostridiales/classification/*isolation & purification ; Cohort Studies ; DNA, Bacterial/genetics ; *Diet ; Feces/microbiology ; Female ; Host-Pathogen Interactions ; Humans ; Inflammation/microbiology ; Lipids/blood ; Liver Cirrhosis/*microbiology ; Lower Gastrointestinal Tract/*microbiology ; Male ; Metagenome ; Middle Aged ; Non-alcoholic Fatty Liver Disease/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {There is increasing evidence for the role of gut microbial composition in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). Nonalcoholic steatohepatitis (NASH) is the most serious form of NAFLD where inflammation causes liver damage that can progress to cirrhosis. We have characterized the gut microbiome composition in UK patients with biopsy-proven NASH (n = 65) and compared it to that in healthy controls (n = 76). We report a 7% lower Shannon alpha diversity in NASH patients without cirrhosis (n = 40) compared to controls (p = 2.7x 10[-4]) and a 14% drop in NASH patients with cirrhosis (n = 25, p = 5.0x 10[-4]). Beta diversity (Unweighted UniFrac distance) was also significantly reduced in both NASH (p = 5.6x 10[-25]) and NASH-cirrhosis (p = 8.1x 10[-7]) groups. The genus most strongly associated with NASH in this study was Collinsella (0.29% abundance in controls, 3.45% in NASH without cirrhosis (False Discovery Rate (FDR) p = .008), and 4.38% in NASH with cirrhosis (FDR p = .02)). This genus, which has been linked previously to obesity and atherosclerosis, was also positively correlated with fasting levels of triglycerides (p = .01) and total cholesterol (p = 1.2x 10[-4]) and negatively correlated with high-density lipoprotein cholesterol (p = 2.8x 10[-6]) suggesting that some of the pathways present in this microbial genus may influence lipid metabolism in the host. In patients, we also found decreased abundance of some of the Ruminococcaceae which are known to produce high levels of short-chain fatty acids which can lower inflammation. This may thus contribute to pathology associated with NASH.}, } @article {pmid31696235, year = {2020}, author = {Mitchell, AL and Almeida, A and Beracochea, M and Boland, M and Burgin, J and Cochrane, G and Crusoe, MR and Kale, V and Potter, SC and Richardson, LJ and Sakharova, E and Scheremetjew, M and Korobeynikov, A and Shlemov, A and Kunyavskaya, O and Lapidus, A and Finn, RD}, title = {MGnify: the microbiome analysis resource in 2020.}, journal = {Nucleic acids research}, volume = {48}, number = {D1}, pages = {D570-D578}, pmid = {31696235}, issn = {1362-4962}, support = {BB/M011755/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R015228/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N018354/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; DNA, Ribosomal Spacer/genetics ; Databases, Genetic ; *Metagenome ; Metagenomics/methods ; *Microbiota ; *Phylogeny ; *Software ; }, abstract = {MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility. MGnify's new analysis pipelines offer additional approaches for taxonomic assertions based on ribosomal internal transcribed spacer regions (ITS1/2) and expanded protein functional annotations. Biochemical pathways and systems predictions have also been added for assembled contigs. MGnify's growing focus on the assembly of metagenomic data has also seen the number of datasets it has assembled and analysed increase six-fold. The non-redundant protein database constructed from the proteins encoded by these assemblies now exceeds 1 billion sequences. Meanwhile, a newly developed contig viewer provides fine-grained visualisation of the assembled contigs and their enriched annotations.}, } @article {pmid31694288, year = {2019}, author = {Castelán-Sánchez, HG and Elorrieta, P and Romoacca, P and Liñan-Torres, A and Sierra, JL and Vera, I and Batista-García, RA and Tenorio-Salgado, S and Lizama-Uc, G and Pérez-Rueda, E and Quispe-Ricalde, MA and Dávila-Ramos, S}, title = {Intermediate-Salinity Systems at High Altitudes in the Peruvian Andes Unveil a High Diversity and Abundance of Bacteria and Viruses.}, journal = {Genes}, volume = {10}, number = {11}, pages = {}, pmid = {31694288}, issn = {2073-4425}, mesh = {Actinobacteria/genetics ; Altitude ; Archaea/genetics ; Bacteria/genetics ; Bacteroidetes/genetics ; Biodiversity ; Euryarchaeota/genetics ; Metagenomics/*methods ; Microbiota/*genetics/*physiology ; Peru ; Phylogeny ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Salinity ; Salt Tolerance/*genetics ; Viruses/genetics ; }, abstract = {Intermediate-salinity environments are distributed around the world. Here, we present a snapshot characterization of two Peruvian thalassohaline environments at high altitude, Maras and Acos, which provide an excellent opportunity to increase our understanding of these ecosystems. The main goal of this study was to assess the structure and functional diversity of the communities of microorganisms in an intermediate-salinity environment, and we used a metagenomic shotgun approach for this analysis. These Andean hypersaline systems exhibited high bacterial diversity and abundance of the phyla Proteobacteria, Bacteroidetes, Balneolaeota, and Actinobacteria; in contrast, Archaea from the phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota were identified in low abundance. Acos harbored a more diverse prokaryotic community and a higher number of unique species compared with Maras. In addition, we obtained the draft genomes of two bacteria, Halomonas elongata and Idiomarina loihiensis, as well as the viral genomes of Enterobacteria lambda-like phage and Halomonas elongata-like phage and 27 partial novel viral halophilic genomes. The functional metagenome annotation showed a high abundance of sequences associated with detoxification, DNA repair, cell wall and capsule formation, and nucleotide metabolism; sequences for these functions were overexpressed mainly in bacteria and also in some archaea and viruses. Thus, their metabolic profiles afford a decrease in oxidative stress as well as the assimilation of nitrogen, a critical energy source for survival. Our work represents the first microbial characterization of a community structure in samples collected from Peruvian hypersaline systems.}, } @article {pmid31690071, year = {2020}, author = {Firrman, J and Liu, L and Tanes, C and Friedman, ES and Bittinger, K and Daniel, S and van den Abbeele, P and Evans, B}, title = {Metabolic Analysis of Regionally Distinct Gut Microbial Communities Using an In Vitro Platform.}, journal = {Journal of agricultural and food chemistry}, volume = {68}, number = {46}, pages = {13056-13067}, doi = {10.1021/acs.jafc.9b05202}, pmid = {31690071}, issn = {1520-5118}, mesh = {Bacteria/classification/genetics/isolation & purification ; Colon/metabolism/microbiology ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; In Vitro Techniques ; }, abstract = {The colon gut microbiota is responsible for complex chemical conversions of nutrients and subsequent release of metabolites that have diverse biological consequences. However, information on the metabolic dynamics that occur longitudinally through the colon is limited. Here, gas and liquid chromatographies coupled with mass spectrometry were applied to generate metabolic profiles of the region-specific microbial communities cultured using an in vitro platform simulating the ascending (AC), transverse (TC), and descending (DC) colon regions. Comparative analysis revealed a large divergence between metabolic profiles of the AC and the TC and DC regions in terms of short-chain fatty acid production, metabolic spectrum, and conversion of bile acids. Metagenomic evaluation revealed that the regionally derived metabolic profiles had strong correlation to community composition and genetic potential. Together, the results provide key insights regarding the metabolic divergence of the regional communities that are integral to understand the structure-function relationship of the gut microbiota.}, } @article {pmid31689942, year = {2019}, author = {Sommers, P and Fontenele, RS and Kringen, T and Kraberger, S and Porazinska, DL and Darcy, JL and Schmidt, SK and Varsani, A}, title = {Single-Stranded DNA Viruses in Antarctic Cryoconite Holes.}, journal = {Viruses}, volume = {11}, number = {11}, pages = {}, pmid = {31689942}, issn = {1999-4915}, mesh = {Antarctic Regions ; DNA Viruses/classification/*genetics/isolation & purification ; DNA, Circular ; *DNA, Single-Stranded ; DNA, Viral/genetics ; Fresh Water/virology ; Genome, Viral/genetics ; Ice Cover/*virology ; Metagenomics ; Microbiota/genetics ; Microviridae/classification/genetics/isolation & purification ; Open Reading Frames ; Phylogeny ; Viral Proteins/genetics ; }, abstract = {Antarctic cryoconite holes, or small melt-holes in the surfaces of glaciers, create habitable oases for isolated microbial communities with tightly linked microbial population structures. Viruses may influence the dynamics of polar microbial communities, but the viromes of the Antarctic cryoconite holes have yet to be characterized. We characterize single-stranded DNA (ssDNA) viruses from three cryoconite holes in the Taylor Valley, Antarctica, using metagenomics. Half of the assembled metagenomes cluster with those in the viral family Microviridae (n = 7), and the rest with unclassified circular replication associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses (n = 7). An additional 18 virus-like circular molecules encoding either a Rep, a capsid protein gene, or other unidentified but viral-like open reading frames were identified. The samples from which the genomes were identified show a strong gradient in microbial diversity and abundances, and the number of viral genomes detected in each sample mirror that gradient. Additionally, one of the CRESS genomes assembled here shares ~90% genome-wide pairwise identity with a virus identified from a freshwater pond on the McMurdo Ice Shelf (Antarctica). Otherwise, the similarity of these viruses to those previously identified is relatively low. Together, these patterns are consistent with the presence of a unique regional virome present in fresh water host populations of the McMurdo Dry Valley region.}, } @article {pmid31685046, year = {2021}, author = {Lai, WT and Deng, WF and Xu, SX and Zhao, J and Xu, D and Liu, YH and Guo, YY and Wang, MB and He, FS and Ye, SW and Yang, QF and Liu, TB and Zhang, YL and Wang, S and Li, MZ and Yang, YJ and Xie, XH and Rong, H}, title = {Shotgun metagenomics reveals both taxonomic and tryptophan pathway differences of gut microbiota in major depressive disorder patients.}, journal = {Psychological medicine}, volume = {51}, number = {1}, pages = {90-101}, doi = {10.1017/S0033291719003027}, pmid = {31685046}, issn = {1469-8978}, mesh = {Adult ; Aged ; Depressive Disorder, Major/*physiopathology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Middle Aged ; Tryptophan/*metabolism ; }, abstract = {BACKGROUND: The microbiota-gut-brain axis, especially the microbial tryptophan (Trp) biosynthesis and metabolism pathway (MiTBamp), may play a critical role in the pathogenesis of major depressive disorder (MDD). However, studies on the MiTBamp in MDD are lacking. The aim of the present study was to analyze the gut microbiota composition and the MiTBamp in MDD patients.

METHODS: We performed shotgun metagenomic sequencing of stool samples from 26 MDD patients and 29 healthy controls (HCs). In addition to the microbiota community and the MiTBamp analyses, we also built a classification based on the Random Forests (RF) and Boruta algorithm to identify the gut microbiota as biomarkers for MDD.

RESULTS: The Bacteroidetes abundance was strongly reduced whereas that of Actinobacteria was significantly increased in the MDD patients compared with the abundance in the HCs. Most noteworthy, the MDD patients had increased levels of Bifidobacterium, which is commonly used as a probiotic. Four Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologies (KOs) (K01817, K11358, K01626, K01667) abundances in the MiTBamp were significantly lower in the MDD group. Furthermore, we found a negative correlation between the K01626 abundance and the HAMD scores in the MDD group. Finally, RF classification at the genus level can achieve an area under the receiver operating characteristic curve of 0.890.

CONCLUSIONS: The present findings enabled a better understanding of the changes in gut microbiota and the related Trp pathway in MDD. Alterations of the gut microbiota may have the potential as biomarkers for distinguishing MDD patients form HCs.}, } @article {pmid31682994, year = {2020}, author = {Liu, Q and Li, Y and Song, X and Wang, J and He, Z and Zhu, J and Chen, H and Yuan, J and Zhang, X and Jiang, H and Zhang, S and Ruan, B}, title = {Both gut microbiota and cytokines act to atherosclerosis in ApoE-/- mice.}, journal = {Microbial pathogenesis}, volume = {138}, number = {}, pages = {103827}, doi = {10.1016/j.micpath.2019.103827}, pmid = {31682994}, issn = {1096-1208}, mesh = {Animals ; Apolipoproteins E/*deficiency ; Atherosclerosis/*etiology/*metabolism/pathology ; Computational Biology/methods ; Cytokines/genetics/*metabolism ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Gene Ontology ; Lipid Metabolism ; Lipids/blood ; Male ; Metagenomics/methods ; Mice ; Mice, Knockout ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Several studies have suggested a role for the gut microbiome and cytokines in atherosclerosis development, but combined analyses of the changes of the gut microbiota and cytokines have not been explored previously.

METHODS: We treated ApoE-/- and wild-type mice with a high-fat diet for 12 weeks. The gut microbiome and cytokine composition were analyzed using 16S ribosomal DNA sequencing and RayBio Quantibody Arrays, respectively. GO and KEGG analysis were performed to rationalize the potential mechanisms involved in the process of atherosclerosis.

RESULTS: Gut bacterial characteristics in ApoE-/- mice were clearly separated and 21 gut bacterial clades were detected by the LEfSe analysis showing significant differences during the development of atherosclerosis. The relative abundance of Verrucomicrobia, Bacteroidaceae, Bacteroides, and Akkermansia showed significant positive correlations with serum total cholesterol, triglyceride (TG), high-density lipoprotein (HDL) and low-density lipoprotein (LDL). Additionally, the relative abundance of Ruminococcaceae was positive with the level of HDL and the abundance of Rikenellaceae showed a negative relationship with the level of TG and LDL. Thirteen differentially expressed proteins were identified with P-value < 0.05. CXCL5, FGF2, and E-Selectin were significantly negatively associated with Akkermansia and Verrucomicrobia. Additionally, CXCL5 was significantly negatively correlated with Bacteroides and Bacteroidaceae. Three "cellular component" subcategories, 24 ″molecular function" subcategories, 752 ″biological process" subcategories and 29 statistically remarkable KEGG pathway categories were identified.

CONCLUSIONS: Gut microbiota changes of the mice having atherosclerosis and their relationship with the inflammatory status could be one of the major etiological mechanisms underlying atherosclerosis.}, } @article {pmid31682032, year = {2020}, author = {Rosa, CP and Pereira, JA and Cristina de Melo Santos, N and Brancaglion, GA and Silva, EN and Tagliati, CA and Novaes, RD and Corsetti, PP and de Almeida, LA}, title = {Vancomycin-induced gut dysbiosis during Pseudomonas aeruginosa pulmonary infection in a mice model.}, journal = {Journal of leukocyte biology}, volume = {107}, number = {1}, pages = {95-104}, doi = {10.1002/JLB.4AB0919-432R}, pmid = {31682032}, issn = {1938-3673}, mesh = {Animals ; Anti-Bacterial Agents/toxicity ; Disease Models, Animal ; Dysbiosis/*etiology/pathology ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/*immunology ; Intestines/drug effects/immunology/*microbiology ; Lung/drug effects/immunology/*microbiology ; Mice ; Mice, Inbred C57BL ; Pseudomonas Infections/drug therapy/immunology/*microbiology ; Pseudomonas aeruginosa/drug effects/*immunology ; Vancomycin/*toxicity ; }, abstract = {Pseudomonas aeruginosa is one of the most common opportunistic pathogens causing respiratory infections in hospitals. Vancomycin, the antimicrobial agent usually used to treat bacterial nosocomial infections, is associated with gut dysbiosis. As a lung-gut immunologic axis has been described, this study aimed to evaluate both the immunologic and histopathologic effects on the lungs and the large intestine resulting from vancomycin-induced gut dysbiosis in the P. aeruginosa pneumonia murine model. Metagenomic analysis demonstrated that vancomycin-induced gut dysbiosis resulted in higher Proteobacteria and lower Bacteroidetes populations in feces. Given that gut dysbiosis could augment the proinflammatory status of the intestines leading to a variety of acute inflammatory diseases, bone marrow-derived macrophages were stimulated with cecal content from dysbiotic mice showing a higher expression of proinflammatory cytokines and lower expression of IL-10. Dysbiotic mice showed higher levels of viable bacteria in the lungs and spleen when acutely infected with P. aeruginosa, with more lung and cecal damage and increased IL-10 expression in bronchoalveolar lavage. The susceptible and tissue damage phenotype was reversed when dysbiotic mice received fecal microbiota transplantation. In spite of higher recruitment of CD11b+ cells in the lungs, there was no higher CD80+ expression, DC+ cell amounts or proinflammatory cytokine expression. Taken together, our results indicate that the bacterial community found in vancomycin-induced dysbiosis dysregulates the gut inflammatory status, influencing the lung-gut immunologic axis to favor increased opportunistic infections, for example, by P. aeruginosa.}, } @article {pmid31681625, year = {2019}, author = {Acharya, A and Chen, T and Chan, Y and Watt, RM and Jin, L and Mattheos, N}, title = {Species-Level Salivary Microbial Indicators of Well-Resolved Periodontitis: A Preliminary Investigation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {347}, pmid = {31681625}, issn = {2235-2988}, mesh = {Adult ; Aged ; Biodiversity ; Case-Control Studies ; Computational Biology ; DNA, Bacterial ; Female ; High-Throughput Nucleotide Sequencing ; Hong Kong/epidemiology ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Periodontitis/epidemiology/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; }, abstract = {Objective: To profile the salivary microbiomes of a Hong Kong Chinese cohort at a species-level resolution and determine species that discriminated clinically resolved periodontitis from periodontally healthy cases. Methods: Salivary microbiomes of 35 Hong Kong Chinese subjects' under routine supportive dental care were analyzed. All subjects had been treated for any dental caries or periodontal disease with all restorative treatment completed at least 1 year ago and had ≤3 residual pockets. They were categorized based on a past diagnosis of chronic periodontitis into "healthy" (H) or "periodontitis" (P) categories. Unstimulated whole saliva was collected, genomic DNA was isolated, and high throughput Illumina MiSeq sequencing of 16S rRNA (V3-V4) gene amplicons was performed. The sequences were assigned taxonomy at the species level by using a BLASTN based algorithm that used a combined reference database of HOMD RefSeqV14.51, HOMD RefSeqExtended V1.1 and GreenGeneGold. Species-level OTUs were subjected to downstream analysis in QIIME and R. For P and H group comparisons, community diversity measures were compared, differentially abundant species were determined using DESeq2, and disease indicator species were determined using multi-level pattern analysis within the R package "indicspecies." Results: P subjects were significantly older than H subjects (p = 0.003) but not significantly different in their BOP scores (p = 0.82). No significant differences were noted in alpha diversity measures after adjusting for age, gender, and BOP or in the beta diversity estimates. Four species; Treponema sp. oral taxon 237, TM7 sp. Oral Taxon A56, Prevotella sp. oral taxon 314, Prevotella sp. oral taxon 304, and Capnocytophaga leadbetteri were significantly more abundant in P than in the H group. Indicator species analysis showed 7 significant indicators species of P group. Fusobacterium sp oral taxon 370 was the sole positive indicator of P group (positive predictive value = 0.9, p = 0.04). Significant indicators of the H category were Leptotrichia buccalis, Corynebacterium matruchotii, Leptotrichia hofstadii, and Streptococcus intermedius. Conclusion: This exploratory study showed salivary microbial species could discriminate treated, well-maintained chronic periodontitis from healthy controls with similar gingival inflammation levels. The findings suggest that certain salivary microbiome features may identify periodontitis-susceptible individuals despite clinical disease resolution.}, } @article {pmid31681624, year = {2019}, author = {Zhu, S and Liu, S and Li, H and Zhang, Z and Zhang, Q and Chen, L and Zhao, Y and Chen, Y and Gu, J and Min, L and Zhang, S}, title = {Identification of Gut Microbiota and Metabolites Signature in Patients With Irritable Bowel Syndrome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {346}, pmid = {31681624}, issn = {2235-2988}, mesh = {Case-Control Studies ; Computational Biology/methods ; Disease Susceptibility ; Energy Metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Irritable Bowel Syndrome/diagnosis/*etiology/*metabolism ; Male ; *Metabolome ; *Metabolomics/methods ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {Background and Aims: Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder. However, the underlying mechanism of IBS is not fully understood. The aim of this study was to investigate potential mechanism and novel biomarkers of IBS through evaluation of the metabolomic and microbiologic profile. Methods: Fecal samples were collected from 15 irritable bowel syndrome patients and 15 healthy controls. By using gas chromatography coupled to time-of-flight mass spectrometry (GC-TOFMS) and 16S rDNA amplicon sequencing, fecal metabolites and microbiota of healthy controls and the IBS patients were measured. Results: IBS patients had a significantly differential metabolite profile as compared to healthy controls, and 4 clusters with 31 metabolites, including a group of amino acids and fatty acids, were significantly up-regulated as compared to the healthy controls. In addition, 19 microbes were significantly up-regulated, and 12 microbes were down-regulated in the IBS group, when compared with the healthy controls. Some clusters of fecal metabolites or microorganisms were significantly correlated with the severity of IBS symptoms, such as the frequency of abdominal pain/discomfort and the number of bowel movements. Correlation of the metabolite levels with abundances of microbial genera showed some statistically significant metabolite-microbe associations. Four differentially abundant amino acids clustered together were positively correlated with some microbes, including Lachnospira, Clostridium, and so on. Conclusion: The finding of this study puts a global perspective on metabolomics and microbiota profiling in IBS patients and provides a theoretical basis for future research on pathophysiology of IBS.}, } @article {pmid31680682, year = {2019}, author = {Shahi, SK and Zarei, K and Guseva, NV and Mangalam, AK}, title = {Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {152}, pages = {}, pmid = {31680682}, issn = {1940-087X}, support = {P30 ES005605/ES/NIEHS NIH HHS/United States ; R01 AI137075/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Feces/chemistry/microbiology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Microbiota/genetics ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/analysis/*genetics ; Sequence Analysis, RNA/*methods ; }, abstract = {The human gut is colonized by trillions of bacteria that support physiologic functions such as food metabolism, energy harvesting, and regulation of the immune system. Perturbation of the healthy gut microbiome has been suggested to play a role in the development of inflammatory diseases, including multiple sclerosis (MS). Environmental and genetic factors can influence the composition of the microbiome; therefore, identification of microbial communities linked with a disease phenotype has become the first step towards defining the microbiome's role in health and disease. Use of 16S rRNA metagenomic sequencing for profiling bacterial community has helped in advancing microbiome research. Despite its wide use, there is no uniform protocol for 16S rRNA-based taxonomic profiling analysis. Another limitation is the low resolution of taxonomic assignment due to technical difficulties such as smaller sequencing reads, as well as use of only forward (R1) reads in the final analysis due to low quality of reverse (R2) reads. There is need for a simplified method with high resolution to characterize bacterial diversity in a given biospecimen. Advancements in sequencing technology with the ability to sequence longer reads at high resolution have helped to overcome some of these challenges. Present sequencing technology combined with a publicly available metagenomic analysis pipeline such as R-based Divisive Amplicon Denoising Algorithm-2 (DADA2) has helped advance microbial profiling at high resolution, as DADA2 can assign sequence at the genus and species levels. Described here is a guide for performing bacterial profiling using two-step amplification of the V3-V4 region of the 16S rRNA gene, followed by analysis using freely available analysis tools (i.e., DADA2, Phyloseq, and METAGENassist). It is believed that this simple and complete workflow will serve as an excellent tool for researchers interested in performing microbiome profiling studies.}, } @article {pmid31680056, year = {2020}, author = {Heinrichs, L and Aytur, SA and Bucci, JP}, title = {Whole metagenomic sequencing to characterize the sediment microbial community within the Stellwagen Bank National Marine Sanctuary and preliminary biosynthetic gene cluster screening of Streptomyces scabrisporus.}, journal = {Marine genomics}, volume = {50}, number = {}, pages = {100718}, doi = {10.1016/j.margen.2019.100718}, pmid = {31680056}, issn = {1876-7478}, mesh = {Atlantic Ocean ; *Genes, Bacterial ; Geologic Sediments/*microbiology ; Massachusetts ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; *Multigene Family ; Streptomyces/*genetics ; }, abstract = {Understanding the marine sediment microbial community structure is of increasing importance to microbiologists since little is known of the diverse taxonomy that exists within this environment. Quantifying microbial species distribution patterns within marine sanctuaries is necessary to address conservation requirements. The objectives of this study were to characterize the relative abundance and biodiversity of metagenome samples of the sediment microbial community in the Stellwagen Bank National Marine Sanctuary (SBNMS). Related to the need for a comprehensive assessment of the microbial habitat within marine sanctuaries is the increased threat of antibiotic-resistant pathogens, coupled with multi-resistant bacterial strains. This has necessitated a renewed search for bioactive compounds in marine benthic habitat. An additional aim was to initiate quantification of biosynthetic gene clusters in species that have potential for natural product and drug discovery relevant to human health. Surficial sediment from 18 samples was collected in the summer and fall of 2017 from three benthic sites in the SBNMS. Microbial DNA was extracted from samples, and sequencing libraries were prepared for taxonomic analysis. Whole metagenome sequencing (WMGS) in combination with a bioinformatics pipeline was employed to delineate the taxa of bacteria present in each sample. Among all sampling sites, biodiversity was higher for summer compared to fall for class (p = 0.0013; F = 4.5) and genus (p = 0.0219; F = 4.4). Actinobacteria was the fifth most abundant class in both seasons (7.81%). Streptomyces was observed to be the fourth most abundant genus in both seasons with significantly higher prevalence in summer compared to fall samples. In summer, site 3 had the highest percentage of Streptomyces (1.71%) compared to sites 2 (1.62%) and 1 (1.37%). The results enabled preliminary quantification of the sequenced hits from the SBNMS sites with the highest potential for harboring secondary metabolite biosynthetic gene clusters for Streptomyces scabrisporus strain (NF3) genomic regions. This study is one of the first to use a whole metagenomics approach to characterize sediment microbial biodiversity in partnership with the SBNMS and demonstrates the potential for future ecological and biomedical research.}, } @article {pmid31679421, year = {2019}, author = {Marques, FZ and Jama, HA and Tsyganov, K and Gill, PA and Rhys-Jones, D and Muralitharan, RR and Muir, J and Holmes, A and Mackay, CR}, title = {Guidelines for Transparency on Gut Microbiome Studies in Essential and Experimental Hypertension.}, journal = {Hypertension (Dallas, Tex. : 1979)}, volume = {74}, number = {6}, pages = {1279-1293}, doi = {10.1161/HYPERTENSIONAHA.119.13079}, pmid = {31679421}, issn = {1524-4563}, mesh = {Animals ; Blood Pressure Determination/methods ; Diet ; Disease Models, Animal ; *Disease Progression ; Essential Hypertension/drug therapy/epidemiology/*physiopathology ; Evidence-Based Medicine ; Female ; Gastrointestinal Microbiome/*genetics/immunology ; Humans ; Incidence ; Male ; Metagenomics ; Mice ; *Practice Guidelines as Topic ; Prognosis ; Risk Assessment ; }, abstract = {Hypertension is a complex and modifiable condition in which environmental factors contribute to both onset and progression. Recent evidence has accumulated for roles of diet and the gut microbiome as environmental factors in blood pressure regulation. However, this is complex because gut microbiomes are a unique feature of each individual reflecting that individual's developmental and environmental history creating caveats for both experimental models and human studies. Here, we describe guidelines for conducting gut microbiome studies in experimental and clinical hypertension. We provide a complete guide for authors on proper design, analyses, and reporting of gut microbiota/microbiome and metabolite studies and checklists that can be used by reviewers and editors to support robust reporting and interpretation. We discuss factors that modulate the gut microbiota in animal (eg, cohort, controls, diet, developmental age, housing, sex, and models used) and human studies (eg, blood pressure measurement and medication, body mass index, demographic characteristics including age, cultural identification, living structure, sex and socioeconomic environment, and exclusion criteria). We also provide best practice advice on sampling, storage of fecal/cecal samples, DNA extraction, sequencing methods (including metagenomics and 16S rRNA), and computational analyses. Finally, we discuss the measurement of short-chain fatty acids, metabolites produced by the gut microbiota, and interpretation of data. These guidelines should support better transparency, reproducibility, and translation of findings in the field of gut microbiota/microbiome in hypertension and cardiovascular disease.}, } @article {pmid31679002, year = {2020}, author = {Le Bastard, Q and Vangay, P and Batard, E and Knights, D and Montassier, E}, title = {US Immigration Is Associated With Rapid and Persistent Acquisition of Antibiotic Resistance Genes in the Gut.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {71}, number = {2}, pages = {419-421}, doi = {10.1093/cid/ciz1087}, pmid = {31679002}, issn = {1537-6591}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; *Emigration and Immigration ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; Thailand ; }, abstract = {Little is known about the effect of human migration on gut microbiome antibiotic resistance gene (ARG) carriage. Using deep shotgun stool metagenomics analysis, we found a rapid increase in gut microbiome ARG richness and abundance in women from 2 independent ethnic groups relocating from Thailand to the United States.}, } @article {pmid31677518, year = {2020}, author = {Baćmaga, M and Wyszkowska, J and Kucharski, J}, title = {Response of soil microorganisms and enzymes to the foliar application of Helicur 250 EW fungicide on Horderum vulgare L.}, journal = {Chemosphere}, volume = {242}, number = {}, pages = {125163}, doi = {10.1016/j.chemosphere.2019.125163}, pmid = {31677518}, issn = {1879-1298}, mesh = {Bacteria/drug effects/enzymology ; Fungi/drug effects/enzymology ; Fungicides, Industrial/analysis/*toxicity ; Hordeum/*growth & development ; Metagenome/drug effects ; Microbiota/*drug effects/genetics ; Plant Leaves/growth & development ; Soil/chemistry ; Soil Microbiology/*standards ; Soil Pollutants/analysis/*toxicity ; Triazoles/analysis/*toxicity ; }, abstract = {The use of fungicides bears the risk of many undesirable outcomes that are manifested in, among other things, changes in the structure and activity of microorganisms. This study aimed at determining the effect of a Helicur 250 EW preparation, used to protect crops against fungal diseases, on the microbiological and biochemical activity of soil and on the development of Horderum vulgare L. The fungicide was sprayed on leaves of spring barley in the following doses (per active substance, i.e. tebuconazole, TEB): 0.046, 0.093, 0.139, 1.395, and 2.790 mg TEB plant[-1]. The following indices were analyzed in the study: index of microorganisms resistance (RS) to the effects of fungicide, microorganisms colony development index (CD), microorganisms ecophysiological diversity index (EP), genetic diversity of bacteria, enzymatic activity, and effect of the fungicide on spring barley development (IFH). The most susceptible to the effects of the fungicide turned out to be fungi. The metagenomic analysis demonstrated that the bacterial community differed in terms of structure and percentage contribution in the soil exposed to the fungicide from the control soil even at the Phylum level. However, Proteobacteria appeared to be the prevailing taxon in both soils. Bacillus arabhattai, B. soli, and B. simplex occurred exclusively in the control soil, whereas Ramlibacter tataounensis, Azospirillum palatum, and Kaistobacter terrae - exclusively in the soil contaminated with the fungicide. Helicur 250 EW suppressed activities of all soil enzymes except for arylsulfatase. In addition, it proved to be a strong inhibitor of spring barley growth and development.}, } @article {pmid31676992, year = {2020}, author = {Kublanovskaya, A and Solovchenko, A and Fedorenko, T and Chekanov, K and Lobakova, E}, title = {Natural Communities of Carotenogenic Chlorophyte Haematococcus lacustris and Bacteria from the White Sea Coastal Rock Ponds.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {785-800}, doi = {10.1007/s00248-019-01437-0}, pmid = {31676992}, issn = {1432-184X}, support = {18-29-25050//Российский Фонд Фундаментальных Исследований (РФФИ)/ ; }, mesh = {Bacteria/classification/*isolation & purification ; *Bacterial Physiological Phenomena ; Chlorophyta/*microbiology ; *Microbiota ; Oceans and Seas ; Russia ; Seawater/*microbiology ; }, abstract = {Haematococcus lacustris is a biotechnologically important green unicellular alga producing widely used keta-karotenoid astaxanthin. In natural habitats, it exists in the form of algal-bacterial community, and under laboratory conditions, it is also accompanied by bacteria. The issue of the bacterial composition of industrial algal cultures is widely recognized as important. However, there is a dearth of information about bacterial composition of H. lacustris communities. In current work, we analyze the composition of natural H. lacustris communities from the White Sea coastal temporal rock ponds. For the first time, a 16S rRNA gene-based metagenome of natural H. lacustris bacterial communities has been generated. Main results of its analysis are as follow. Bacterial families Comamonadaceae, Cytophagaceae, Xanthomonadaceae, Acetobacteraceae, Rhodobacteraceae, and Rhodocyclaceae were observed in all studied H. lacustris natural communities. They also contained genera Hydrogenophaga and Cytophaga. Bacteria from the Hydrogenophaga genus were present in H. lacustris cultures after their isolation under the conditions of laboratory cultivation. Similar to other planktonic microalgae, H. lacustris forms a phycosphere around the cells. In this zone, bacteria attached to the algal surface. The contact between H. lacustris and bacteria is maintained even after sample drying. The study provides information about possible members of H. lacustris core microbiome, which can be presented in the industrial and laboratory cultures of the microalga.}, } @article {pmid31676854, year = {2020}, author = {Holt, CC and van der Giezen, M and Daniels, CL and Stentiford, GD and Bass, D}, title = {Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster (Homarus gammarus).}, journal = {The ISME journal}, volume = {14}, number = {2}, pages = {531-543}, pmid = {31676854}, issn = {1751-7370}, support = {WT097835MF/WT_/Wellcome Trust/United Kingdom ; BB/N013891/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; WT101650MA/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; BB/K003240/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/M008924/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Bacteria/classification ; Disease Susceptibility/microbiology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Microbial Interactions ; Nephropidae/*microbiology/*virology ; Nudiviridae/*isolation & purification ; Phylogeny ; Seafood/microbiology/virology ; Virus Diseases ; }, abstract = {Microbial communities within the gut can markedly impact host health and fitness. To what extent environmental influences affect the differential distribution of these microbial populations may therefore significantly impact the successful farming of the host. Using a sea-based container culture (SBCC) system for the on-growing of European lobster (Homarus gammarus), we tracked the bacterial gut microbiota over a 1-year period. We compared these communities with lobsters of the same cohort, retained in a land-based culture (LBC) system to assess the effects of the culture environment on gut bacterial assemblage and describe the phylogenetic structure of the microbiota to compare deterministic and stochastic assembly across both environments. Bacterial gut communities from SBCCs were generally more phylogenetically clustered, and therefore deterministically assembled, compared to those reared in land-based systems. Lobsters in SBCCs displayed significantly more species-rich and species-diverse gut microbiota compared to those retained in LBC. A reduction in the bacterial diversity of the gut was also associated with higher infection prevalence of the enteric viral pathogen Homarus gammarus nudivirus (HgNV). SBCCs may therefore benefit the overall health of the host by promoting the assembly of a more diverse gut bacterial community and reducing the susceptibility to disease.}, } @article {pmid31676016, year = {2019}, author = {Wang, Y and Shi, Q and Yang, P and Zhang, C and Mortuza, SM and Xue, Z and Ning, K and Zhang, Y}, title = {Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {229}, pmid = {31676016}, issn = {1474-760X}, support = {R01 GM116960/GM/NIGMS NIH HHS/United States ; GM083107/GM/NIGMS NIH HHS/United States ; GM116960/GM/NIGMS NIH HHS/United States ; R01 AI134678/AI/NIAID NIH HHS/United States ; }, mesh = {Aquatic Organisms ; Deep Learning ; Metagenomics/*methods ; Microbiota ; *Models, Chemical ; Multigene Family ; Proteins/chemistry/*genetics ; *Structure-Activity Relationship ; }, abstract = {INTRODUCTION: The ocean microbiome represents one of the largest microbiomes and produces nearly half of the primary energy on the planet through photosynthesis or chemosynthesis. Using recent advances in marine genomics, we explore new applications of oceanic metagenomes for protein structure and function prediction.

RESULTS: By processing 1.3 TB of high-quality reads from the Tara Oceans data, we obtain 97 million non-redundant genes. Of the 5721 Pfam families that lack experimental structures, 2801 have at least one member associated with the oceanic metagenomics dataset. We apply C-QUARK, a deep-learning contact-guided ab initio structure prediction pipeline, to model 27 families, where 20 are predicted to have a reliable fold with estimated template modeling score (TM-score) at least 0.5. Detailed analyses reveal that the abundance of microbial genera in the ocean is highly correlated to the frequency of occurrence in the modeled Pfam families, suggesting the significant role of the Tara Oceans genomes in the contact-map prediction and subsequent ab initio folding simulations. Of interesting note, PF15461, which has a majority of members coming from ocean-related bacteria, is identified as an important photosynthetic protein by structure-based function annotations. The pipeline is extended to a set of 417 Pfam families, built on the combination of Tara with other metagenomics datasets, which results in 235 families with an estimated TM-score over 0.5.

CONCLUSIONS: These results demonstrate a new avenue to improve the capacity of protein structure and function modeling through marine metagenomics, especially for difficult proteins with few homologous sequences.}, } @article {pmid31673867, year = {2019}, author = {Puri, RR and Adachi, F and Omichi, M and Saeki, Y and Yamamoto, A and Hayashi, S and Ali, MA and Itoh, K}, title = {Metagenomic study of endophytic bacterial community of sweet potato (Ipomoea batatas) cultivated in different soil and climatic conditions.}, journal = {World journal of microbiology & biotechnology}, volume = {35}, number = {11}, pages = {176}, pmid = {31673867}, issn = {1573-0972}, support = {16KT0032//Japan Society for the Promotion of Science/ ; }, mesh = {Bacteria/*classification/genetics/*metabolism ; Base Sequence ; Biodiversity ; *Climate ; DNA, Bacterial/analysis ; DNA, Mitochondrial/analysis ; Endophytes/*classification/genetics ; Ipomoea batatas/*microbiology ; *Metagenome ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {The aim of this study was to clarify effects of soil and climatic conditions on community structure of sweet potato bacterial endophytes by applying locked nucleic acid oligonucleotide-PCR clamping technique and metagenomic analysis. For this purpose, the soil samples in three locations were transferred each other and sweet potato nursery plants from the same farm were cultivated for ca. 3 months. After removal of plastid, mitochondria and undefined sequences, the averaged numbers of retained sequences and operational taxonomic units per sample were 20,891 and 846, respectively. Proteobacteria (85.0%), Bacteroidetes (6.6%) and Actinobacteria (6.3%) were the three most dominant phyla, accounting for 97.9% of the reads, and γ-Proteobacteria (66.3%) being the most abundant. Top 10 genera represented 81.2% of the overall reads in which Pseudomonas (31.9-45.0%) being the most predominant. The overall endophytic bacterial communities were similar among the samples which indicated that the soil and the climatic conditions did not considerably affect the entire endophytic community. The original endophytic bacterial community might be kept during the cultivation period.}, } @article {pmid31673077, year = {2020}, author = {Shi, B and Lux, R and Klokkevold, P and Chang, M and Barnard, E and Haake, S and Li, H}, title = {The subgingival microbiome associated with periodontitis in type 2 diabetes mellitus.}, journal = {The ISME journal}, volume = {14}, number = {2}, pages = {519-530}, pmid = {31673077}, issn = {1751-7370}, support = {R01 DE021574/DE/NIDCR NIH HHS/United States ; RC1 DE020298/DE/NIDCR NIH HHS/United States ; R01DE021574//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/International ; RC1DE020298//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/International ; }, mesh = {Adult ; Bacteria/classification/genetics ; Case-Control Studies ; Coinfection/microbiology ; Diabetes Mellitus, Type 2/*complications ; Dysbiosis/genetics ; Female ; Gingiva/microbiology ; Gingival Diseases/microbiology ; Humans ; Longitudinal Studies ; Male ; *Metagenome ; Microbiota/*genetics ; Middle Aged ; Mouth/microbiology ; Periodontitis/*microbiology ; }, abstract = {Type 2 diabetes mellitus (T2DM) is a systemic disease, predisposing patients to other inflammatory conditions including periodontitis. The subgingival microbiome, a key player in periodontitis pathogenesis, is not well characterized in T2DM population. To better understand whether the subgingival microbiome is different between T2DM and systemically healthy, nondiabetic (ND) subjects, we performed a longitudinal analysis of the subgingival microbiome in T2DM patients (n = 15) compared with ND subjects (n = 16). Using metagenomic shotgun sequencing, we investigated the microbiome in the healthy periodontal state, periodontitis state, and resolved state after treatment. We found that in the periodontitis state, the shift in the subgingival microbiome from the healthy state was less prominent in T2DM compared with ND subjects, yet the clinical signs of disease were similar for both. Furthermore, we revealed highly correlated presence of pathogenic species in relative abundance not only in the periodontitis state, but also in the healthy state in T2DM, suggesting an elevated risk of progression to periodontitis in this cohort. We further investigated the functional potentials of the subgingival microbiome and identified a set of microbial marker genes associated with the clinical states. These genes were significantly enriched in 21 pathways, some of which are associated with periodontitis and some potentially link T2DM and periodontitis. This study identified the longitudinal changes of the subgingival microbiome associated with periodontitis in T2DM and suggests that T2DM patients are more susceptible to shifts in the subgingival microbiome toward dysbiosis, potentially due to impaired host metabolic and immune regulation.}, } @article {pmid31672892, year = {2019}, author = {Carrión, VJ and Perez-Jaramillo, J and Cordovez, V and Tracanna, V and de Hollander, M and Ruiz-Buck, D and Mendes, LW and van Ijcken, WFJ and Gomez-Exposito, R and Elsayed, SS and Mohanraju, P and Arifah, A and van der Oost, J and Paulson, JN and Mendes, R and van Wezel, GP and Medema, MH and Raaijmakers, JM}, title = {Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome.}, journal = {Science (New York, N.Y.)}, volume = {366}, number = {6465}, pages = {606-612}, doi = {10.1126/science.aaw9285}, pmid = {31672892}, issn = {1095-9203}, mesh = {Bacteria/classification ; Bacterial Physiological Phenomena ; Bacteroidetes/physiology ; Beta vulgaris/*microbiology ; Biodiversity ; Chitinases/genetics ; Disease Resistance ; Endophytes/*physiology ; Flavobacterium/physiology ; Genes, Bacterial ; Genome, Bacterial ; Metagenome ; *Microbiota ; Mutagenesis, Site-Directed ; Peptide Synthases/genetics ; Plant Diseases/*microbiology ; Plant Roots/*microbiology ; Polyketide Synthases/genetics ; Rhizoctonia/*pathogenicity ; Soil Microbiology ; }, abstract = {Microorganisms living inside plants can promote plant growth and health, but their genomic and functional diversity remain largely elusive. Here, metagenomics and network inference show that fungal infection of plant roots enriched for Chitinophagaceae and Flavobacteriaceae in the root endosphere and for chitinase genes and various unknown biosynthetic gene clusters encoding the production of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). After strain-level genome reconstruction, a consortium of Chitinophaga and Flavobacterium was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from Flavobacterium was essential for disease suppression by the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.}, } @article {pmid31672156, year = {2019}, author = {Sanders, JG and Nurk, S and Salido, RA and Minich, J and Xu, ZZ and Zhu, Q and Martino, C and Fedarko, M and Arthur, TD and Chen, F and Boland, BS and Humphrey, GC and Brennan, C and Sanders, K and Gaffney, J and Jepsen, K and Khosroheidari, M and Green, C and Liyanage, M and Dang, JW and Phelan, VV and Quinn, RA and Bankevich, A and Chang, JT and Rana, TM and Conrad, DJ and Sandborn, WJ and Smarr, L and Dorrestein, PC and Pevzner, PA and Knight, R}, title = {Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {226}, pmid = {31672156}, issn = {1474-760X}, support = {T32GM8806/NH/NIH HHS/United States ; DA046171/DA/NIDA NIH HHS/United States ; DA039562/DA/NIDA NIH HHS/United States ; }, mesh = {Animals ; Benchmarking ; Gastrointestinal Microbiome ; *Genomic Library ; *High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Mice ; }, abstract = {As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach leaderboard metagenome sequencing. To explore protocol optimization for leaderboard metagenomics in real samples, we introduce a benchmark of library prep and sequencing using internal references generated by synthetic long-read technology, allowing us to evaluate high-throughput library preparation methods against gold-standard reference genomes derived from the samples themselves. We introduce a low-cost protocol for high-throughput library preparation and sequencing.}, } @article {pmid31670799, year = {2020}, author = {Arribas, P and Andújar, C and Moraza, ML and Linard, B and Emerson, BC and Vogler, AP}, title = {Mitochondrial Metagenomics Reveals the Ancient Origin and Phylodiversity of Soil Mites and Provides a Phylogeny of the Acari.}, journal = {Molecular biology and evolution}, volume = {37}, number = {3}, pages = {683-694}, doi = {10.1093/molbev/msz255}, pmid = {31670799}, issn = {1537-1719}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Metagenomics ; Mites/*classification/genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Soil/*parasitology ; }, abstract = {High-throughput DNA methods hold great promise for phylogenetic analysis of lineages that are difficult to study with conventional molecular and morphological approaches. The mites (Acari), and in particular the highly diverse soil-dwelling lineages, are among the least known branches of the metazoan Tree-of-Life. We extracted numerous minute mites from soils in an area of mixed forest and grassland in southern Iberia. Selected specimens representing the full morphological diversity were shotgun sequenced in bulk, followed by genome assembly of short reads from the mixture, which produced >100 mitochondrial genomes representing diverse acarine lineages. Phylogenetic analyses in combination with taxonomically limited mitogenomes available publicly resulted in plausible trees defining basal relationships of the Acari. Several critical nodes were supported by ancestral-state reconstructions of mitochondrial gene rearrangements. Molecular calibration placed the minimum age for the common ancestor of the superorder Acariformes, which includes most soil-dwelling mites, to the Cambrian-Ordovician (likely within 455-552 Ma), whereas the origin of the superorder Parasitiformes was placed later in the Carboniferous-Permian. Most family-level taxa within the Acariformes were dated to the Jurassic and Triassic. The ancient origin of Acariformes and the early diversification of major extant lineages linked to the soil are consistent with a pioneering role for mites in building the earliest terrestrial ecosystems.}, } @article {pmid31670480, year = {2020}, author = {Quigley, KM and Alvarez Roa, C and Torda, G and Bourne, DG and Willis, BL}, title = {Co-dynamics of Symbiodiniaceae and bacterial populations during the first year of symbiosis with Acropora tenuis juveniles.}, journal = {MicrobiologyOpen}, volume = {9}, number = {2}, pages = {e959}, pmid = {31670480}, issn = {2045-8827}, mesh = {Age Factors ; Animals ; Anthozoa/*microbiology ; *Bacterial Physiological Phenomena ; Computational Biology/methods ; DNA, Ribosomal Spacer ; Gene Ontology ; Metagenomics/methods ; *Microbiota ; Molecular Typing ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; }, abstract = {Interactions between corals and their associated microbial communities (Symbiodiniaceae and prokaryotes) are key to understanding corals' potential for and rate of acclimatory and adaptive responses. However, the establishment of microalgal and bacterial communities is poorly understood during coral ontogeny in the wild. We examined the establishment and co-occurrence between multiple microbial communities using 16S rRNA (bacterial) and ITS2 rDNA (Symbiodiniaceae) gene amplicon sequencing in juveniles of the common coral, Acropora tenuis, across the first year of development. Symbiodiniaceae communities in juveniles were dominated by Durusdinium trenchii and glynnii (D1 and D1a), with lower abundances of Cladocopium (C1, C1d, C50, and Cspc). Bacterial communities were more diverse and dominated by taxa within Proteobacteria, Cyanobacteria, and Planctomycetes. Both communities were characterized by significant changes in relative abundance and diversity of taxa throughout the year. D1, D1a, and C1 were significantly correlated with multiple bacterial taxa, including Alpha-, Deltra-, and Gammaproteobacteria, Planctomycetacia, Oxyphotobacteria, Phycisphaerae, and Rhizobiales. Specifically, D1a tended to associate with Oxyphotobacteria and D1 with Alphaproteobacteria, although these associations may represent correlational and not causal relationships. Bioenergetic modeling combined with physiological measurements of coral juveniles (surface area and Symbiodiniaceae cell densities) identified key periods of carbon limitation and nitrogen assimilation, potentially coinciding with shifts in microbial community composition. These results demonstrate that Symbiodiniaceae and bacterial communities are dynamic throughout the first year of ontology and may vary in tandem, with important fitness effects on host juveniles.}, } @article {pmid31670055, year = {2019}, author = {Beraza, N}, title = {Fibrosis and the intestinal microbiome; a focus on chronic liver disease.}, journal = {Current opinion in pharmacology}, volume = {49}, number = {}, pages = {76-81}, doi = {10.1016/j.coph.2019.09.012}, pmid = {31670055}, issn = {1471-4973}, support = {BB/J004529/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/00044509/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG1860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Chronic Disease ; *Gastrointestinal Microbiome ; Humans ; Liver Diseases/*microbiology/therapy ; }, abstract = {The role of the microbiome in progression of liver disease is an exciting area of research that is advancing rapidly supported by the development of next-generation sequencing and bioinformatics tools that simultaneously identify the composition and function of the microbiome. Changes in the microbiome are associated with pathogenesis of chronic liver disease; specifically, changes in microbiome composition predict disease severity and specific microbial signatures can be used to distinguish between mild disease, advanced fibrosis and cirrhosis. Future work combining functional metagenomic analysis with preclinical mechanistic studies will be key to advancing our understanding of how the microbiome affects the pathogenesis of different chronic liver disease aetiologies and to identify personalised therapeutics based on modulation of the microbiome and its function.}, } @article {pmid31668006, year = {2019}, author = {Lugli, GA and Milani, C and Mancabelli, L and Turroni, F and van Sinderen, D and Ventura, M}, title = {A microbiome reality check: limitations of in silico-based metagenomic approaches to study complex bacterial communities.}, journal = {Environmental microbiology reports}, volume = {11}, number = {6}, pages = {840-847}, doi = {10.1111/1758-2229.12805}, pmid = {31668006}, issn = {1758-2229}, support = {15/JP-HDHL/3280//Joint Programming Initiative A healthy diet for a healthy life/International ; //Ministero dell'Istruzione, dell'Università e della Ricerca/International ; SFI/12/RC/2273-P1/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; //University of Parma/International ; }, mesh = {Animals ; Computational Biology/*methods ; Feces/microbiology ; Humans ; Metagenomics/*methods ; *Microbiota ; }, abstract = {In recent years, whole shotgun metagenomics (WSM) of complex microbial communities has become an established technology to perform compositional analyses of complex microbial communities, an approach that is heavily reliant on bioinformatic pipelines to process and interpret the generated raw sequencing data. However, the use of such in silico pipelines for the microbial taxonomic classification of short sequences may lead to significant errors in the compositional outputs deduced from such sequencing data. To investigate the ability of such in silico pipelines, we employed two commonly applied bioinformatic tools, i.e., MetaPhlAn2 and Kraken2 together with two metagenomic data sets originating from human and animal faecal samples. By using these bioinformatic programs that taxonomically classify WSM data based on marker genes, we observed a trend to depict a lower complexity of the microbial communities. Here, we assess the limitations of the most commonly employed bioinformatic pipelines, i.e., MetaPhlAn2 and Kraken2, and based on our findings, we propose that such analyses should ideally be combined with experimentally based microbiological validations.}, } @article {pmid31666597, year = {2019}, author = {Madsen, MSA and Holm, JB and Pallejà, A and Wismann, P and Fabricius, K and Rigbolt, K and Mikkelsen, M and Sommer, M and Jelsing, J and Nielsen, HB and Vrang, N and Hansen, HH}, title = {Metabolic and gut microbiome changes following GLP-1 or dual GLP-1/GLP-2 receptor agonist treatment in diet-induced obese mice.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {15582}, pmid = {31666597}, issn = {2045-2322}, mesh = {Animals ; Diet/*adverse effects ; Gastrointestinal Microbiome/*drug effects ; Glucagon-Like Peptide-1 Receptor/*agonists ; Glucagon-Like Peptide-2 Receptor/*agonists ; Liraglutide/pharmacology ; Male ; Metagenome/drug effects ; Mice ; Mice, Inbred C57BL ; Obesity/chemically induced/drug therapy/*metabolism/*microbiology ; }, abstract = {Enteroendocrine L-cell derived peptide hormones, notably glucagon-like peptide-1 (GLP-1) and glucagon-like peptide-2 (GLP-2), have become important targets in the treatment of type 2 diabetes, obesity and intestinal diseases. As gut microbial imbalances and maladaptive host responses have been implicated in the pathology of obesity and diabetes, this study aimed to determine the effects of pharmacologically stimulated GLP-1 and GLP-2 receptor function on the gut microbiome composition in diet-induced obese (DIO) mice. DIO mice received treatment with a selective GLP-1 receptor agonist (liraglutide, 0.2 mg/kg, BID) or dual GLP-1/GLP-2 receptor agonist (GUB09-145, 0.04 mg/kg, BID) for 4 weeks. Both compounds suppressed caloric intake, promoted a marked weight loss, improved glucose tolerance and reduced plasma cholesterol levels. 16S rDNA sequencing and deep-sequencing shotgun metagenomics was applied for comprehensive within-subject profiling of changes in gut microbiome signatures. Compared to baseline, DIO mice assumed phylogenetically similar gut bacterial compositional changes following liraglutide and GUB09-145 treatment, characterized by discrete shifts in low-abundant species and related bacterial metabolic pathways. The microbiome alterations may potentially associate to the converging biological actions of GLP-1 and GLP-2 receptor signaling on caloric intake, glucose metabolism and lipid handling.}, } @article {pmid31666099, year = {2019}, author = {Zhu, C and Miller, M and Lusskin, N and Mahlich, Y and Wang, Y and Zeng, Z and Bromberg, Y}, title = {Fingerprinting cities: differentiating subway microbiome functionality.}, journal = {Biology direct}, volume = {14}, number = {1}, pages = {19}, pmid = {31666099}, issn = {1745-6150}, support = {U01 GM115486/GM/NIGMS NIH HHS/United States ; U01 GM115486/NH/NIH HHS/United States ; }, mesh = {Cities ; *Metagenome ; *Microbiota ; *Railroads ; }, abstract = {BACKGROUND: Accumulating evidence suggests that the human microbiome impacts individual and public health. City subway systems are human-dense environments, where passengers often exchange microbes. The MetaSUB project participants collected samples from subway surfaces in different cities and performed metagenomic sequencing. Previous studies focused on taxonomic composition of these microbiomes and no explicit functional analysis had been done till now.

RESULTS: As a part of the 2018 CAMDA challenge, we functionally profiled the available ~ 400 subway metagenomes and built predictor for city origin. In cross-validation, our model reached 81% accuracy when only the top-ranked city assignment was considered and 95% accuracy if the second city was taken into account as well. Notably, this performance was only achievable if the similarity of distribution of cities in the training and testing sets was similar. To assure that our methods are applicable without such biased assumptions we balanced our training data to account for all represented cities equally well. After balancing, the performance of our method was slightly lower (76/94%, respectively, for one or two top ranked cities), but still consistently high. Here we attained an added benefit of independence of training set city representation. In testing, our unbalanced model thus reached (an over-estimated) performance of 90/97%, while our balanced model was at a more reliable 63/90% accuracy. While, by definition of our model, we were not able to predict the microbiome origins previously unseen, our balanced model correctly judged them to be NOT-from-training-cities over 80% of the time. Our function-based outlook on microbiomes also allowed us to note similarities between both regionally close and far-away cities. Curiously, we identified the depletion in mycobacterial functions as a signature of cities in New Zealand, while photosynthesis related functions fingerprinted New York, Porto and Tokyo.

CONCLUSIONS: We demonstrated the power of our high-speed function annotation method, mi-faser, by analysing ~ 400 shotgun metagenomes in 2 days, with the results recapitulating functional signals of different city subway microbiomes. We also showed the importance of balanced data in avoiding over-estimated performance. Our results revealed similarities between both geographically close (Ofa and Ilorin) and distant (Boston and Porto, Lisbon and New York) city subway microbiomes. The photosynthesis related functional signatures of NYC were previously unseen in taxonomy studies, highlighting the strength of functional analysis.}, } @article {pmid31665423, year = {2020}, author = {Sanjar, F and Weaver, AJ and Peacock, TJ and Nguyen, JQ and Brandenburg, KS and Leung, KP}, title = {Identification of Metagenomics Structure and Function Associated With Temporal Changes in Rat (Rattus norvegicus) Skin Microbiome During Health and Cutaneous Burn.}, journal = {Journal of burn care & research : official publication of the American Burn Association}, volume = {41}, number = {2}, pages = {347-358}, doi = {10.1093/jbcr/irz165}, pmid = {31665423}, issn = {1559-0488}, mesh = {Animals ; Biopsy ; Burns/*genetics/*microbiology ; Disease Models, Animal ; Male ; *Metagenome ; *Microbiota ; Rats ; Rats, Sprague-Dawley ; Skin/*microbiology ; Time Factors ; }, abstract = {The cutaneous skin microbiome is host to a vast ensemble of resident microbes that provide essential capabilities including protection of skin barrier integrity and modulation of the host immune response. Cutaneous burn-injury promotes alteration of cutaneous and systemic immune response that can affect both commensal and pathogenic microbes. A cross-sectional study of a limited number of burn patients revealed a difference in the bacteriome of burned versus control participants. Temporal changes of the skin microbiome during health and cutaneous burn-injury remains largely unknown. Furthermore, how this microbial shift relates to community function in the collective metagenome remain elusive. Due to cost considerations and reduced healing time, rodents are frequently used in burn research, despite inherent physiological differences between rodents and human skin. Using a rat burn model, a longitudinal study was conducted to characterize the rat skin bacterial residents and associated community functions in states of health (n = 30) (sham-burned) and when compromised by burn-injury (n = 24). To address the knowledge gap, traumatic thermal injury and disruption of cutaneous surface is associated with genus-level changes in the microbiota, reduced bacterial richness, and altered representation of bacterial genes and associated predicted functions across different skin microbial communities. These findings demonstrate that, upon burn-injury, there is a shift in diversity of the skin's organismal assemblages, yielding a core microbiome that is distinct at the genome and functional level. Moreover, deviations from the core community correlate with temporal changes post-injury and community transition from the state of cutaneous health to disease (burn-injury).}, } @article {pmid31662858, year = {2019}, author = {Ungaro, F and Massimino, L and D'Alessio, S and Danese, S}, title = {The gut virome in inflammatory bowel disease pathogenesis: From metagenomics to novel therapeutic approaches.}, journal = {United European gastroenterology journal}, volume = {7}, number = {8}, pages = {999-1007}, pmid = {31662858}, issn = {2050-6406}, mesh = {Animals ; Bacteria/*classification ; Caliciviridae Infections/complications ; Computational Biology/methods ; Dysbiosis/*complications ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Inflammation/virology ; Inflammatory Bowel Diseases/*etiology/therapy/*virology ; Intestines/*virology ; Metagenomics/*methods ; Microbiota/genetics ; Models, Animal ; Molecular Targeted Therapy/methods ; Norovirus/genetics ; Phylogeny ; Viruses/genetics ; }, abstract = {The association of intestinal dysbiosis with the pathogenesis of inflammatory bowel disease has been well established. Besides bacteria, microbiota comprises yeasts, archaea, protists and viruses, neglected actors in inflammatory bowel disease-associated microbiota. In the past, a great limitation in studying microbiota composition was the low sensitivity of sequencing technologies and that few computational approaches were sufficient to thoroughly analyse the whole microbiome. However, new cutting-edge technologies in nucleic acid sequencing, -omics analysis and the innovative statistics and bioinformatics pipelines made possible more sensitive and accurate metagenomics, ultimately identifying novel players in intestinal inflammation, including prokaryotic and eukaryotic viruses, that together form the gut virome. The discovery of peculiar inflammatory bowel disease-associated microbial strains will not only shed new light on inflammatory bowel disease aetiogenesis, they may also support the development of novel therapeutic strategies not merely treating symptoms, but precisely counteracting the primary cause of chronic intestinal inflammation.}, } @article {pmid31662318, year = {2020}, author = {Yin, J and Sternes, PR and Wang, M and Song, J and Morrison, M and Li, T and Zhou, L and Wu, X and He, F and Zhu, J and Brown, MA and Xu, H}, title = {Shotgun metagenomics reveals an enrichment of potentially cross-reactive bacterial epitopes in ankylosing spondylitis patients, as well as the effects of TNFi therapy upon microbiome composition.}, journal = {Annals of the rheumatic diseases}, volume = {79}, number = {1}, pages = {132-140}, doi = {10.1136/annrheumdis-2019-215763}, pmid = {31662318}, issn = {1468-2060}, mesh = {Adult ; Asian People ; Case-Control Studies ; China ; Cross Reactions ; Dysbiosis/immunology/*microbiology ; Epitopes/immunology ; Female ; Gastrointestinal Microbiome/*genetics/immunology ; HLA-B27 Antigen/immunology ; Humans ; Male ; *Metagenome ; Metagenomics ; Middle Aged ; Peptides/immunology ; Spondylitis, Ankylosing/drug therapy/immunology/*microbiology ; Tumor Necrosis Factor Inhibitors/therapeutic use ; Young Adult ; }, abstract = {OBJECTIVES: Diverse evidence including clinical, genetic and microbiome studies support a major role of the gut microbiome in the common immune-mediated arthropathy, ankylosing spondylitis (AS). We set out to (1) further define the key microbial characteristics driving disease, and (2) examine the effects of tumour necrosis factor-inhibitor (TNFi) therapy upon the microbiome.

METHODS: The stools from a case-control cohort of 250 Han-Chinese subjects underwent shotgun metagenomic sequencing. All subjects were genotyped using the Illumina CoreExome SNP microarray.

RESULTS: Previous reports of gut dysbiosis in AS were reconfirmed and several notable bacterial species and functional categories were differentially abundant. TNFi therapy was correlated with a restoration the perturbed microbiome observed in untreated AS cases to that of healthy controls, including several important bacterial species that have been previously associated with AS and other related diseases. Enrichment of bacterial peptides homologous to HLA-B27-presented epitopes was observed in the stools of patients with AS, suggesting that either HLA-B27 fails to clear these or that they are involved in driving HLA-B27-associated immune reactions. TNFi therapy largely restored the perturbed microbiome observed in untreated AS cases to that of healthy controls, including several important bacterial species that have been previously associated with AS and other related diseases. TNFi therapy of patients with AS was also associated with a reduction of potentially arthritogenic bacterial peptides, relative to untreated patients.

CONCLUSION: These findings emphasise the key role that the gut microbiome plays in driving the pathogenesis of AS and highlight potential therapeutic and/or preventative targets.}, } @article {pmid31661299, year = {2020}, author = {Carney, SM and Clemente, JC and Cox, MJ and Dickson, RP and Huang, YJ and Kitsios, GD and Kloepfer, KM and Leung, JM and LeVan, TD and Molyneaux, PL and Moore, BB and O'Dwyer, DN and Segal, LN and Garantziotis, S}, title = {Methods in Lung Microbiome Research.}, journal = {American journal of respiratory cell and molecular biology}, volume = {62}, number = {3}, pages = {283-299}, pmid = {31661299}, issn = {1535-4989}, support = {R01 HL144599/HL/NHLBI NIH HHS/United States ; K23 AI135094/AI/NIAID NIH HHS/United States ; R00 HL139996/HL/NHLBI NIH HHS/United States ; K23 HL130641/HL/NHLBI NIH HHS/United States ; R01 AI117229/AI/NIAID NIH HHS/United States ; R01 AI129958/AI/NIAID NIH HHS/United States ; L40 AI096442/AI/NIAID NIH HHS/United States ; R35 HL144481/HL/NHLBI NIH HHS/United States ; K23 HL139987/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Anti-Infective Agents/pharmacology ; Bacterial Typing Techniques ; Body Fluids/microbiology ; Breath Tests ; Dysbiosis/microbiology ; Environmental Exposure ; *Epidemiologic Methods ; Host Microbial Interactions ; Humans ; Lung/*microbiology ; Metagenomics/methods ; Microbiological Techniques ; *Microbiota/drug effects ; Models, Animal ; Models, Biological ; Reproducibility of Results ; Respiratory System/microbiology ; Specimen Handling/methods ; Sputum/microbiology ; Translational Research, Biomedical ; Whole Genome Sequencing ; }, abstract = {The lung microbiome is associated with host immune response and health outcomes in experimental models and patient cohorts. Lung microbiome research is increasing in volume and scope; however, there are no established guidelines for study design, conduct, and reporting of lung microbiome studies. Standardized approaches to yield reliable and reproducible data that can be synthesized across studies will ultimately improve the scientific rigor and impact of published work and greatly benefit microbiome research. In this review, we identify and address several key elements of microbiome research: conceptual modeling and hypothesis framing; study design; experimental methodology and pitfalls; data analysis; and reporting considerations. Finally, we explore possible future directions and research opportunities. Our goal is to aid investigators who are interested in this burgeoning research area and hopefully provide the foundation for formulating consensus approaches in lung microbiome research.}, } @article {pmid31660953, year = {2019}, author = {Garmaeva, S and Sinha, T and Kurilshikov, A and Fu, J and Wijmenga, C and Zhernakova, A}, title = {Studying the gut virome in the metagenomic era: challenges and perspectives.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {84}, pmid = {31660953}, issn = {1741-7007}, mesh = {Bacteriophages/*physiology ; Gastrointestinal Microbiome/*physiology ; Humans ; *Metagenome ; Metagenomics ; }, abstract = {The human gut harbors a complex ecosystem of microorganisms, including bacteria and viruses. With the rise of next-generation sequencing technologies, we have seen a quantum leap in the study of human-gut-inhabiting bacteria, yet the viruses that infect these bacteria, known as bacteriophages, remain underexplored. In this review, we focus on what is known about the role of bacteriophages in human health and the technical challenges involved in studying the gut virome, of which they are a major component. Lastly, we discuss what can be learned from studies of bacteriophages in other ecosystems.}, } @article {pmid31659200, year = {2019}, author = {Khan, R and Zeb, A and Choi, K and Lee, G and Lee, KW and Lee, SW}, title = {Biochemical and Structural Insights Concerning Triclosan Resistance in a Novel YX7K Type Enoyl-Acyl Carrier Protein Reductase from Soil Metagenome.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {15401}, pmid = {31659200}, issn = {2045-2322}, mesh = {Bacteria/classification/enzymology/genetics ; Bacterial Proteins/chemistry/*genetics/metabolism ; *Drug Resistance, Bacterial ; Enoyl-(Acyl-Carrier-Protein) Reductase (NADH)/chemistry/*genetics/metabolism ; *Metagenome ; Microbiota ; Phylogeny ; *Soil Microbiology ; Triclosan/*toxicity ; }, abstract = {Enoyl-acyl carrier protein reductase (ENR) catalyzes the last reduction step in the bacterial type II fatty acid biosynthesis cycle. ENRs include FabI, FabL, FabL2, FabK, and FabV. Previously, we reported a unique triclosan (TCL) resistant ENR homolog that was predominant in obligate intracellular pathogenic bacteria and Apicomplexa. Herein, we report the biochemical and structural basis of TCL resistance in this novel ENR. The purified protein revealed NADH-dependent ENR activity and shared similarity to prototypic FabI. Thus, this metagenome-derived ENR was designated FabI2. Unlike other prototypic bacterial ENRs with the YX6K type catalytic domain, FabI2 possessed a unique YX7K type catalytic domain. Computational modeling followed by site-directed mutagenesis revealed that mild resistance (20 µg/ml of minimum inhibitory concentration) of FabI2 to TCL was confined to the relatively less bulky side chain of A128. Substitution of A128 in FabI2 with bulky valine (V128) elevated TCL resistance. Phylogenetic analysis further suggested that the novel FabI2 and prototypical FabI evolved from a common short-chain dehydrogenase reductase family. To our best knowledge, FabI2 is the only known ENR shared by intracellular pathogenic prokaryotes, intracellular pathogenic lower eukaryotes, and a few higher eukaryotes. This suggests that the ENRs of prokaryotes and eukaryotes diverged from a common ancestral ENR of FabI2.}, } @article {pmid31659049, year = {2019}, author = {Gusareva, ES and Acerbi, E and Lau, KJX and Luhung, I and Premkrishnan, BNV and Kolundžija, S and Purbojati, RW and Wong, A and Houghton, JNI and Miller, D and Gaultier, NE and Heinle, CE and Clare, ME and Vettath, VK and Kee, C and Lim, SBY and Chénard, C and Phung, WJ and Kushwaha, KK and Nee, AP and Putra, A and Panicker, D and Yanqing, K and Hwee, YZ and Lohar, SR and Kuwata, M and Kim, HL and Yang, L and Uchida, A and Drautz-Moses, DI and Junqueira, ACM and Schuster, SC}, title = {Microbial communities in the tropical air ecosystem follow a precise diel cycle.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {46}, pages = {23299-23308}, pmid = {31659049}, issn = {1091-6490}, mesh = {*Air Microbiology ; Air Pollutants/analysis ; Circadian Rhythm ; Ecosystem ; Metagenome ; *Microbiota ; Models, Biological ; Singapore ; *Tropical Climate ; }, abstract = {The atmosphere is vastly underexplored as a habitable ecosystem for microbial organisms. In this study, we investigated 795 time-resolved metagenomes from tropical air, generating 2.27 terabases of data. Despite only 9 to 17% of the generated sequence data currently being assignable to taxa, the air harbored a microbial diversity that rivals the complexity of other planetary ecosystems. The airborne microbial organisms followed a clear diel cycle, possibly driven by environmental factors. Interday taxonomic diversity exceeded day-to-day and month-to-month variation. Environmental time series revealed the existence of a large core of microbial taxa that remained invariable over 13 mo, thereby underlining the long-term robustness of the airborne community structure. Unlike terrestrial or aquatic environments, where prokaryotes are prevalent, the tropical airborne biomass was dominated by DNA from eukaryotic phyla. Specific fungal and bacterial species were strongly correlated with temperature, humidity, and CO2 concentration, making them suitable biomarkers for studying the bioaerosol dynamics of the atmosphere.}, } @article {pmid31657225, year = {2020}, author = {Albhaisi, SAM and Bajaj, JS and Sanyal, AJ}, title = {Role of gut microbiota in liver disease.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {318}, number = {1}, pages = {G84-G98}, doi = {10.1152/ajpgi.00118.2019}, pmid = {31657225}, issn = {1522-1547}, mesh = {Animals ; Bacteria/metabolism/*pathogenicity ; Disease Progression ; Dysbiosis ; *Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Humans ; Intestines/*microbiology ; Liver/*metabolism/pathology ; Liver Diseases/*metabolism/*microbiology/pathology ; Prognosis ; Risk Factors ; }, abstract = {The gut microbiome is the natural intestinal inhabitant that has been recognized recently as a major player in the maintenance of human health and the pathophysiology of many diseases. Those commensals produce metabolites that have various effects on host biological functions. Therefore, alterations in the normal composition or diversity of microbiome have been implicated in various diseases, including liver cirrhosis and nonalcoholic fatty liver disease. Moreover, accumulating evidence suggests that progression of dysbiosis can be associated with worsening of liver disease. Here, we review the possible roles for gut microbiota in the development, progression, and complication of liver disease.}, } @article {pmid31655999, year = {2019}, author = {Belkova, NL and Nemchenko, UM and Pogodina, AV and Feranchuk, SI and Romanitsa, AI and Novikova, EA and Rychkova, LV}, title = {Composition and Structure of Gut Microbiome in Adolescents with Obesity and Different Breastfeeding Duration.}, journal = {Bulletin of experimental biology and medicine}, volume = {167}, number = {6}, pages = {759-762}, doi = {10.1007/s10517-019-04617-7}, pmid = {31655999}, issn = {1573-8221}, mesh = {Adolescent ; *Biodiversity ; Body Mass Index ; Breast Feeding/*statistics & numerical data ; Case-Control Studies ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant, Newborn ; Male ; Metagenome/genetics ; Pediatric Obesity/epidemiology/*microbiology/pathology ; RNA, Ribosomal, 16S/analysis/genetics ; Time Factors ; }, abstract = {Gut microbiome of adolescents with obesity and different duration of breastfeeding was analyzed by metagenomic analysis of V3-V4 variable domains of the 16S rRNA gene. In subgroup with breastfeeding duration <3 months, intrapopulation structure of gut microbiome by alpha diversity indices was similar in adolescents with obesity and normal body weight. The decrease in phylotype abundance in the structure of communities was associated only with obesity, while dysbiotic state persisted in both lean and overweight adolescents, which confirmed the effect of breastfeeding duration on stability of gut microbiome.}, } @article {pmid31654639, year = {2020}, author = {Kigerl, KA and Zane, K and Adams, K and Sullivan, MB and Popovich, PG}, title = {The spinal cord-gut-immune axis as a master regulator of health and neurological function after spinal cord injury.}, journal = {Experimental neurology}, volume = {323}, number = {}, pages = {113085}, pmid = {31654639}, issn = {1090-2430}, support = {R01 NS083942/NS/NINDS NIH HHS/United States ; R01 NS099532/NS/NINDS NIH HHS/United States ; R35 NS111582/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; *Autonomic Nervous System Diseases/etiology/physiopathology ; *Digestive System Physiological Phenomena ; *Gastrointestinal Microbiome ; Humans ; *Immune System Phenomena ; *Spinal Cord Injuries/complications/physiopathology ; }, abstract = {Most spinal cord injury (SCI) research programs focus only on the injured spinal cord with the goal of restoring locomotor function by overcoming mechanisms of cell death or axon regeneration failure. Given the importance of the spinal cord as a locomotor control center and the public perception that paralysis is the defining feature of SCI, this "spinal-centric" focus is logical. Unfortunately, such a focus likely will not yield new discoveries that reverse other devastating consequences of SCI including cardiovascular and metabolic disease, bladder/bowel dysfunction and infection. The current review considers how SCI changes the physiological interplay between the spinal cord, the gut and the immune system. A suspected culprit in causing many of the pathological manifestations of impaired spinal cord-gut-immune axis homeostasis is the gut microbiota. After SCI, the composition of the gut microbiota changes, creating a chronic state of gut "dysbiosis". To date, much of what we know about gut dysbiosis was learned from 16S-based taxonomic profiling studies that reveal changes in the composition and abundance of various bacteria. However, this approach has limitations and creates taxonomic "blindspots". Notably, only bacteria can be analyzed. Thus, in this review we also discuss how the application of emerging sequencing technologies can improve our understanding of how the broader ecosystem in the gut is affected by SCI. Specifically, metagenomics will provide researchers with a more comprehensive look at post-injury changes in the gut virome (and mycome). Metagenomics also allows changes in microbe population dynamics to be linked to specific microbial functions that can affect the development and progression of metabolic disease, immune dysfunction and affective disorders after SCI. As these new tools become more readily available and used across the research community, the development of an "ecogenomic" toolbox will facilitate an Eco-Systems Biology approach to study the complex interplay along the spinal cord-gut-immune axis after SCI.}, } @article {pmid31653789, year = {2019}, author = {Kleyer, H and Tecon, R and Or, D}, title = {Rapid Shifts in Bacterial Community Assembly under Static and Dynamic Hydration Conditions in Porous Media.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {1}, pages = {}, pmid = {31653789}, issn = {1098-5336}, support = {320499/ERC_/European Research Council/International ; }, mesh = {*Bacteria/classification/genetics/isolation & purification ; Metagenome ; Metagenomics ; Microbial Interactions ; Microbiota/*genetics ; Phylogeny ; Porosity ; RNA, Ribosomal, 16S ; Soil/chemistry ; *Soil Microbiology ; Water ; }, abstract = {The complexity of natural soils presents a challenge to the systematic identification and disentanglement of governing processes that shape natural bacterial communities. Studies have highlighted the critical role of the soil aqueous phase in shaping interactions among soil bacterial communities. To quantify and improve the attributability of soil aqueous-phase effects, we introduced a synthetic and traceable bacterial community to simple porous microcosms and subjected the community to constant or dynamic hydration conditions. The results were expressed in terms of absolute abundance and show species-specific responses to hydration and nutrient conditions. Hydration dynamics exerted a significant influence on the fraction of less-abundant species, especially after extended incubation periods. Phylogenetic relationships did not explain the group of most abundant species. The ability to quantify species-level dynamics in a bacterial community offers an important step toward deciphering the links between community composition and functions in dynamic terrestrial environments.IMPORTANCE The composition and activity of soil bacteria are central to various ecosystem services and soil biogeochemical cycles. A key factor for soil bacterial activity is soil hydration, which is in a constant state of change due to rainfall, drainage, plant water uptake, and evaporation. These dynamic changes in soil hydration state affect the structure and function of soil bacterial communities in complex ways often unobservable in natural soil. We designed an experimental system that retains the salient features of hydrated soil yet enables systematic evaluation of changes in a representative bacterial community in response to cycles of wetting and drying. The study shows that hydration cycles affect community abundance, yet most changes in composition occur with the less-abundant species (while the successful ones remain dominant). This research offers a new path for an improved understanding of bacterial community assembly in natural environments, including bacterial growth, maintenance, and death, with a special focus on the role of hydrological factors.}, } @article {pmid31652964, year = {2019}, author = {Liu, P and Chen, W and Chen, JP}, title = {Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica).}, journal = {Viruses}, volume = {11}, number = {11}, pages = {}, pmid = {31652964}, issn = {1999-4915}, mesh = {Animals ; Coronavirus/classification/genetics/*isolation & purification/physiology ; Coronavirus Infections/*veterinary/virology ; Endangered Species/statistics & numerical data ; Mammals/*virology ; Metagenomics ; Phylogeny ; Respirovirus Infections/*veterinary/virology ; Sendai virus/classification/genetics/*isolation & purification/physiology ; }, abstract = {Pangolins are endangered animals in urgent need of protection. Identifying and cataloguing the viruses carried by pangolins is a logical approach to evaluate the range of potential pathogens and help with conservation. This study provides insight into viral communities of Malayan Pangolins (Manis javanica) as well as the molecular epidemiology of dominant pathogenic viruses between Malayan Pangolin and other hosts. A total of 62,508 de novo assembled contigs were constructed, and a BLAST search revealed 3600 ones (≥300 nt) were related to viral sequences, of which 68 contigs had a high level of sequence similarity to known viruses, while dominant viruses were the Sendai virus and Coronavirus. This is the first report on the viral diversity of pangolins, expanding our understanding of the virome in endangered species, and providing insight into the overall diversity of viruses that may be capable of directly or indirectly crossing over into other mammals.}, } @article {pmid31651219, year = {2019}, author = {Ahmed, N and Mahmoud, NF and Solyman, S and Hanora, A}, title = {Human Nasal Microbiome as Characterized by Metagenomics Differs Markedly Between Rural and Industrial Communities in Egypt.}, journal = {Omics : a journal of integrative biology}, volume = {23}, number = {11}, pages = {573-582}, doi = {10.1089/omi.2019.0144}, pmid = {31651219}, issn = {1557-8100}, mesh = {Bacteria/classification/genetics ; Biodiversity ; DNA Barcoding, Taxonomic ; Egypt ; Humans ; Industry ; *Metagenomics/methods ; *Microbiota ; Nasal Mucosa/*microbiology ; *Occupational Exposure ; Public Health Surveillance ; RNA, Ribosomal, 16S ; *Rural Population ; }, abstract = {Microbial communities residing in the nose play important roles in human health and disease. We report marked differences in nasal microbiota between a rural community and an industrial setting located near a major urban city. Nasal samples were collected from 19 healthy male subjects: 9 samples from persons living in a rural village, and 10 samples from ceramic factory workers in a major industrial Egyptian city. The nasal microbiota in the rural sample had higher and distinct diversity compared with industrial samples from workers exposed to pollution daily. Taxonomic analysis of the sequences revealed five major phyla; among these phyla were Actinobacteria, Proteobacteria, Bacteroidetes, and Fusobacteria, revealing significant abundance variation by geographical location. For example, the rural group had a significant increase in representation of Actinobacteria and Bacteroidetes (p = 0.004, p = 0.01, respectively) compared with the industrial group. However, the industrial group showed a significant increase in relative abundance of phylum Proteobacteria (p = 0.02). The most predominant genera for the rural group were Corynebacterium, Staphylococcus, Alloiococcus, and Peptoniphilus. By contrast, the industrial group was dominated by Staphylococcus, Sphingomonas, and Moraxella. Environmental pollution might alter the nasal microbiome leading to an attendant disturbance in the microbiome community structure. The clinical and public health implications of these nasal microbiome variations by rural and industrialized geography warrant further research. This study contributes to our knowledge of the bacterial composition of nasal microbiome in rural and industrialized geographies, and informs public health, respiratory medicine, and occupational health scholarship.}, } @article {pmid31649656, year = {2019}, author = {Epp Schmidt, DJ and Kotze, DJ and Hornung, E and Setälä, H and Yesilonis, I and Szlavecz, K and Dombos, M and Pouyat, R and Cilliers, S and Tóth, Z and Yarwood, S}, title = {Metagenomics Reveals Bacterial and Archaeal Adaptation to Urban Land-Use: N Catabolism, Methanogenesis, and Nutrient Acquisition.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2330}, pmid = {31649656}, issn = {1664-302X}, abstract = {Urbanization results in the systemic conversion of land-use, driving habitat and biodiversity loss. The "urban convergence hypothesis" posits that urbanization represents a merging of habitat characteristics, in turn driving physiological and functional responses within the biotic community. To test this hypothesis, we sampled five cities (Baltimore, MD, United States; Helsinki and Lahti, Finland; Budapest, Hungary; Potchefstroom, South Africa) across four different biomes. Within each city, we sampled four land-use categories that represented a gradient of increasing disturbance and management (from least intervention to highest disturbance: reference, remnant, turf/lawn, and ruderal). Previously, we used amplicon sequencing that targeted bacteria/archaea (16S rRNA) and fungi (ITS) and reported convergence in the archaeal community. Here, we applied shotgun metagenomic sequencing and QPCR of functional genes to the same soil DNA extracts to test convergence in microbial function. Our results suggest that urban land-use drives changes in gene abundance related to both the soil N and C metabolism. Our updated analysis found taxonomic convergence in both the archaeal and bacterial community (16S amplicon data). Convergence of the archaea was driven by increased abundance of ammonia oxidizing archaea and genes for ammonia oxidation (QPCR and shotgun metagenomics). The proliferation of ammonia-oxidizers under turf and ruderal land-use likely also contributes to the previously documented convergence of soil mineral N pools. We also found a higher relative abundance of methanogens (amplicon sequencing), a higher relative abundance of gene sequences putatively identified as Ni-Fe hydrogenase and nickel uptake (shotgun metagenomics) under urban land-use; and a convergence of gene sequences putatively identified as contributing to the nickel transport function under urban turf sites. High levels of disturbance lead to a higher relative abundance of gene sequences putatively identified as multiple antibiotic resistance protein marA and multidrug efflux pump mexD, but did not lead to an overall convergence in antibiotic resistance gene sequences.}, } @article {pmid31646389, year = {2020}, author = {Komorowski, AS and Pezo, RC}, title = {Untapped "-omics": the microbial metagenome, estrobolome, and their influence on the development of breast cancer and response to treatment.}, journal = {Breast cancer research and treatment}, volume = {179}, number = {2}, pages = {287-300}, doi = {10.1007/s10549-019-05472-w}, pmid = {31646389}, issn = {1573-7217}, mesh = {Animals ; Biomarkers, Tumor ; Breast Neoplasms/diagnosis/*etiology/*metabolism/therapy ; Disease Management ; Disease Models, Animal ; *Disease Susceptibility ; Female ; Gastrointestinal Microbiome ; Genomics/methods ; Host-Pathogen Interactions ; Humans ; Life Style ; Metabolomics/methods ; Metagenomics/methods ; Proteomics/methods ; Treatment Outcome ; }, abstract = {With the advent of next generation sequencing technologies, there is an increasingly complex understanding of the role of gastrointestinal and local breast microbial dysbiosis in breast cancer. In this review, we summarize the current understanding of the microbiome's role in breast carcinogenesis, discussing modifiable risk factors that may affect breast cancer risk by inducing dysbiosis as well as recent sequencing data illustrating breast cancer subtype-specific differences in local breast tissue microbiota. We outline how the 'estrobolome,' the aggregate of estrogen-metabolizing enteric bacterial genes, may affect the risk of developing postmenopausal estrogen receptor-positive breast cancer. We also discuss the microbiome's potent capacity for anticancer therapy activation and deactivation, an important attribute of the gastrointestinal microbiome that has yet to be harnessed clinically.}, } @article {pmid31644955, year = {2020}, author = {Trujillo-Vargas, CM and Schaefer, L and Alam, J and Pflugfelder, SC and Britton, RA and de Paiva, CS}, title = {The gut-eye-lacrimal gland-microbiome axis in Sjögren Syndrome.}, journal = {The ocular surface}, volume = {18}, number = {2}, pages = {335-344}, pmid = {31644955}, issn = {1937-5913}, support = {P30 CA125123/CA/NCI NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; R01 EY026893/EY/NEI NIH HHS/United States ; S10 OD025251/OD/NIH HHS/United States ; P30 EY002520/EY/NEI NIH HHS/United States ; }, mesh = {Animals ; Dry Eye Syndromes ; *Gastrointestinal Microbiome ; *Lacrimal Apparatus ; *Microbiota ; *Sjogren's Syndrome ; }, abstract = {The bacterial communities that collectively inhabit our body are called the microbiome. Virtually all body surface harbors bacteria. Recent advances in next-generation sequencing that have provided insight into the diversity, composition of bacterial communities, and their interaction are discussed in this review, as well as the current knowledge of how the microbiome promotes ocular health. The ocular surface is a site of low bacterial load. Sjögren Syndrome is an autoimmune disease that affects the exocrine glands, causing dry mouth and dry eye. Systemic antibiotic treatment and germ-free mice have demonstrated that commensal bacteria have a protective role for the ocular surface and lacrimal gland. The existence of a gut-eye-lacrimal gland axis-microbiome is discussed.}, } @article {pmid31641523, year = {2019}, author = {Zhang, M and Feng, R and Yang, M and Qian, C and Wang, Z and Liu, W and Ma, J}, title = {Effects of metformin, acarbose, and sitagliptin monotherapy on gut microbiota in Zucker diabetic fatty rats.}, journal = {BMJ open diabetes research & care}, volume = {7}, number = {1}, pages = {e000717}, pmid = {31641523}, issn = {2052-4897}, mesh = {Acarbose/*pharmacology ; Animals ; Bacteria/*drug effects/genetics/isolation & purification ; Biomarkers/analysis ; Blood Glucose/analysis ; Diabetes Mellitus, Experimental/*drug therapy/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/genetics ; Glycoside Hydrolase Inhibitors/pharmacology ; Hypoglycemic Agents/pharmacology ; Male ; Metagenomics ; Metformin/*pharmacology ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Zucker ; Sitagliptin Phosphate/*pharmacology ; }, abstract = {OBJECTIVE: Recent studies have demonstrated that gut microbiota was closely related to metabolic disorders such as type 2 diabetes. Oral antidiabetic medications including metformin, acarbose and sitagliptin lowered blood glucose levels via acting on the gastrointestinal tract. The aim of the study was to observe the comparisons among those medications on gut microbiota composition.

RESEARCH DESIGN AND METHODS: Zucker diabetic fatty rats (n=32) were randomly divided into four groups, and had respectively gastric administration of normal saline (control), metformin (215.15 mg/kg/day), acarbose (32.27 mg/kg/day), or sitagliptin (10.76 mg/kg/day) for 4 weeks. Blood glucose levels were measured during an intragastric starch tolerance test after the treatments. 16S rRNA gene sequencing was used to access the microbiota in the fecal samples.

RESULTS: Metformin, acarbose, and sitagliptin monotherapy effectively decreased fasting and postprandial blood glucose levels (p<0.001). Acarbose group displayed specific cluster and enterotype mainly composed by Ruminococcus 2 while Lactobacillus was the dominant bacterium in the enterotype of the other three groups. The relative abundance of genera Ruminococcus 2 and Bifidobacterium was dramatically higher in acarbose group. Metformin and sitagliptin increased the relative abundance of genus Lactobacillus. Metagenomic prediction showed that the functional profiles of carbohydrate metabolism were enriched in acarbose group.

CONCLUSIONS: Metformin, acarbose and sitagliptin exerted different effects on the composition of gut microbiota and selectively increased the beneficial bacteria. Supplementation with specific probiotics may further improve the hypoglycemic effects of the antidiabetic drugs.}, } @article {pmid31640771, year = {2019}, author = {Wagner, J and Harrison, EM and Martinez Del Pero, M and Blane, B and Mayer, G and Leierer, J and Gopaluni, S and Holmes, MA and Parkhill, J and Peacock, SJ and Jayne, DRW and Kronbichler, A}, title = {The composition and functional protein subsystems of the human nasal microbiome in granulomatosis with polyangiitis: a pilot study.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {137}, pmid = {31640771}, issn = {2049-2618}, support = {G1001787/MRC_/Medical Research Council/United Kingdom ; MR/P007201/1/MRC_/Medical Research Council/United Kingdom ; MR/N002660/1/MRC_/Medical Research Council/United Kingdom ; MR/S00291X/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Case-Control Studies ; Cohort Studies ; Cross-Sectional Studies ; Female ; Granulomatosis with Polyangiitis/*microbiology ; Humans ; Male ; Metagenome/*genetics ; Microbiota/*genetics ; Middle Aged ; Nose/*microbiology ; Pilot Projects ; Staphylococcal Infections/*microbiology ; *Staphylococcus/classification/isolation & purification ; Young Adult ; }, abstract = {BACKGROUND: Ear, nose and throat involvement in granulomatosis with polyangiitis (GPA) is frequently the initial disease manifestation. Previous investigations have observed a higher prevalence of Staphylococcus aureus in patients with GPA, and chronic nasal carriage has been linked with an increased risk of disease relapse. In this cross-sectional study, we investigated changes in the nasal microbiota including a detailed analysis of Staphylococcus spp. by shotgun metagenomics in patients with active and inactive granulomatosis with polyangiitis (GPA). Shotgun metagenomic sequence data were also used to identify protein-encoding genes within the SEED database, and the abundance of proteins then correlated with the presence of bacterial species on an annotated heatmap.

RESULTS: The presence of S. aureus in the nose as assessed by culture was more frequently detected in patients with active GPA (66.7%) compared with inactive GPA (34.1%). Beta diversity analysis of nasal microbiota by bacterial 16S rRNA profiling revealed a different composition between GPA patients and healthy controls (P = 0.039). Beta diversity analysis of shotgun metagenomic sequence data for Staphylococcus spp. revealed a different composition between active GPA patients and healthy controls and disease controls (P = 0.0007 and P = 0.0023, respectively), and between healthy controls and inactive GPA patients and household controls (P = 0.0168 and P = 0.0168, respectively). Patients with active GPA had a higher abundance of S. aureus, mirroring the culture data, while healthy controls had a higher abundance of S. epidermidis. Staphylococcus pseudintermedius, generally assumed to be a pathogen of cats and dogs, showed an abundance of 13% among the Staphylococcus spp. in our cohort. During long-term follow-up of patients with inactive GPA at baseline, a higher S. aureus abundance was not associated with an increased relapse risk. Functional analyses identified ten SEED protein subsystems that differed between the groups. Most significant associations were related to chorismate synthesis and involved in the vitamin B12 pathway.

CONCLUSION: Our data revealed a distinct dysbiosis of the nasal microbiota in GPA patients compared with disease and healthy controls. Metagenomic sequencing demonstrated that this dysbiosis in active GPA patients is manifested by increased abundance of S. aureus and a depletion of S. epidermidis, further demonstrating the antagonist relationships between these species. SEED functional protein subsystem analysis identified an association between the unique bacterial nasal microbiota clusters seen mainly in GPA patients and an elevated abundance of genes associated with chorismate synthesis and vitamin B12 pathways. Further studies are required to further elucidate the relationship between the biosynthesis genes and the associated bacterial species.}, } @article {pmid31639050, year = {2019}, author = {Zhou, G and Jiang, JY and Ju, CJ and Wang, W}, title = {Prediction of microbial communities for urban metagenomics using neural network approach.}, journal = {Human genomics}, volume = {13}, number = {Suppl 1}, pages = {47}, pmid = {31639050}, issn = {1479-7364}, support = {R01 GM115833/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Boston ; Cities ; Databases, Genetic ; Metagenomics/*methods ; Microbiota/*genetics ; Models, Genetic ; *Neural Networks, Computer ; New York ; Reproducibility of Results ; }, abstract = {BACKGROUND: Microbes are greatly associated with human health and disease, especially in densely populated cities. It is essential to understand the microbial ecosystem in an urban environment for cities to monitor the transmission of infectious diseases and detect potentially urgent threats. To achieve this goal, the DNA sample collection and analysis have been conducted at subway stations in major cities. However, city-scale sampling with the fine-grained geo-spatial resolution is expensive and laborious. In this paper, we introduce MetaMLAnn, a neural network based approach to infer microbial communities at unsampled locations given information reflecting different factors, including subway line networks, sampling material types, and microbial composition patterns.

RESULTS: We evaluate the effectiveness of MetaMLAnn based on the public metagenomics dataset collected from multiple locations in the New York and Boston subway systems. The experimental results suggest that MetaMLAnn consistently performs better than other five conventional classifiers under different taxonomic ranks. At genus level, MetaMLAnn can achieve F1 scores of 0.63 and 0.72 on the New York and the Boston datasets, respectively.

CONCLUSIONS: By exploiting heterogeneous features, MetaMLAnn captures the hidden interactions between microbial compositions and the urban environment, which enables precise predictions of microbial communities at unmeasured locations.}, } @article {pmid31637220, year = {2019}, author = {Kolbe, AR and Castro-Nallar, E and Preciado, D and Pérez-Losada, M}, title = {Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {339}, pmid = {31637220}, issn = {2235-2988}, mesh = {Biodiversity ; Child ; Child, Preschool ; Chronic Disease ; Ear, Middle/*microbiology ; Female ; Humans ; Infant ; Male ; Metagenomics ; *Microbiota ; Otitis Media with Effusion/metabolism/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S ; Respiratory Tract Diseases/*etiology/metabolism ; }, abstract = {Chronic otitis media with effusion (COME) is a common childhood disease characterized by an accumulation of fluid behind the eardrum. COME often requires surgical intervention and can also lead to significant hearing loss and subsequent learning disabilities. Recent characterization of the middle ear fluid (MEF) microbiome in pediatric patients has led to an improved understanding of the microbiota present in the middle ear during COME. However, it is not currently known how the MEF microbiome might vary due to other conditions, particularly respiratory disorders. Here, we apply an amplicon sequence variant (ASV) pipeline to MEF 16S rRNA high-throughput sequencing data from 50 children with COME (ages 3-176 months) undergoing tube placement. We achieve a more detailed taxonomic resolution than previously reported, including species and genus level resolution. Additionally, we provide the first report of the functional roles of the MEF microbiome and demonstrate that despite high taxonomic diversity, the functional capacity of the MEF microbiome remains uniform between patients. Furthermore, we analyze microbiome differences between children with COME with and without a history of lower airway disease (i.e., asthma or bronchiolitis). The MEF microbiome was less diverse in participants with lower airway disease than in patients without, and phylogenetic β-diversity (weighted UniFrac) was significantly different based on lower airway disease status. Differential abundance between patients with lower airway disease and those without was observed for the genera Haemophilus, Moraxella, Staphylococcus, Alloiococcus, and Turicella. These findings support previous suggestions of a link between COME and respiratory illnesses and emphasize the need for future study of the middle ear and respiratory tract microbiomes in diseases such as asthma and bronchiolitis.}, } @article {pmid31635933, year = {2019}, author = {Ray, KJ and Cotter, SY and Arzika, AM and Kim, J and Boubacar, N and Zhou, Z and Zhong, L and Porco, TC and Keenan, JD and Lietman, TM and Doan, T}, title = {High-throughput sequencing of pooled samples to determine community-level microbiome diversity.}, journal = {Annals of epidemiology}, volume = {39}, number = {}, pages = {63-68}, pmid = {31635933}, issn = {1873-2585}, support = {K08 EY026986/EY/NEI NIH HHS/United States ; }, mesh = {Administration, Oral ; Anti-Bacterial Agents/*administration & dosage ; Azithromycin/*administration & dosage ; Bacteria/classification/*drug effects/genetics/isolation & purification ; Biodiversity ; Child, Preschool ; Female ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/*microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenomics/*methods ; Microbiota/*genetics ; Niger ; Placebos/administration & dosage ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {PURPOSE: Community-level interventions in cluster randomized controlled trials may alter the gut microbiome of individuals. The current method of estimating community diversities uses microbiome data obtained from multiple individual's specimens. Here we propose randomly pooling a number of microbiome samples from the same community into one sample before sequencing to estimate community-level microbiome diversity.

METHODS: We design and analyze an experiment to compare community microbiome diversity (gamma-diversity) estimates derived from 16S rRNA gene sequencing of 1) individually sequenced specimens vs. 2) pooled specimens collected from a community. Pool sizes of 10, 20, and 40 are considered. We then compare the gamma-estimates using Pearson's correlation as well as using Bland and Altman agreement analysis for three established diversity indices including richness, Simpson's and Shannon's.

RESULTS: The gamma-diversity estimates are highly correlated, with most being statistically significant. All correlations between all three diversity estimates are significant in the 10-pooled data. Pools comprising 40 specimens are closest to the line of agreement, but all pooled samples and individual samples fall within the 95% limits of agreement.

CONCLUSIONS: Pooling microbiome samples before DNA amplification and metagenomics sequencing to estimate community-level diversity is a viable measure to consider in population-level association research studies.}, } @article {pmid31635444, year = {2020}, author = {Wu, M and Li, P and Li, J and An, Y and Wang, M and Zhong, G}, title = {The Differences between Luminal Microbiota and Mucosal Microbiota in Mice.}, journal = {Journal of microbiology and biotechnology}, volume = {30}, number = {2}, pages = {287-295}, pmid = {31635444}, issn = {1738-8872}, mesh = {Animals ; Bacteria/classification/genetics ; Biodiversity ; Colon/microbiology ; Computational Biology/methods ; Duodenum/microbiology ; High-Throughput Nucleotide Sequencing ; Intestinal Mucosa/microbiology ; Metagenome ; Metagenomics/methods ; Mice ; *Microbiota ; Mucous Membrane/*microbiology ; Organ Specificity ; }, abstract = {The differences between luminal microbiota (LM) and mucosal microbiota (MAM) were little known, especially in duodenum. In this study, LM and MAM in colon and duodenum of mice were investigated through 16S rRNA high-throughput sequencing. The lowest bacterial diversity and evenness were observed in duodenal LM (D_LM), followed by duodenal MAM (D_MAM). Meanwhile, the bacterial diversity and evenness were obviously increased in D_MAM than these in D_LM, while no significant difference was observed between colonic MAM (C_MAM) and colonic LM (C_LM). PCoA analysis also showed that bacterial communities of LM and MAM in duodenum were completely separated, while these in colon overlapped partly. The ratio of Firmicutes to Bacteroidetes (F/B) in D_MAM was significantly higher than that in D_LM. Lactobacillus was largely enriched and was the characteristic bacteria in D_LM. The characteristic bacteria in D_MAM were Turicibacter, Parasutterella, Marvinbryantia and Bifidobacterium, while in C_LM they were Ruminiclostridium_6, Ruminiclostridium_9, Ruminococcaceae_UCG_007 and Lachnospiraceae_UCG_010, and in C_MAM they were Lachnospiraceae_NK4A136, Mucispirillum, Alistipes, Ruminiclostridium and Odoribacter. The networks showed that more interactions existed in colonic microbiota (24 nodes and 74 edges) than in duodenal microbiota (17 nodes and 29 edges). The 16S rDNA function prediction results indicated that bigger differences of function exist between LM and MAM in duodenum than these in colon. In conclusion, microbiota from intestinal luminal content and mucosa were different both in colon and in duodenum, and bacteria in colon interacted with each other much more closely than those in duodenum.}, } @article {pmid31635158, year = {2019}, author = {Guo, W and Mishra, S and Wang, C and Zhang, H and Ning, R and Kong, F and Zeng, B and Zhao, J and Li, Y}, title = {Comparative Study of Gut Microbiota in Wild and Captive Giant Pandas (Ailuropoda melanoleuca).}, journal = {Genes}, volume = {10}, number = {10}, pages = {}, pmid = {31635158}, issn = {2073-4425}, mesh = {Amylases/metabolism ; Animals ; Animals, Wild/microbiology/physiology ; Animals, Zoo/*microbiology/physiology ; Diet ; Drug Resistance, Bacterial ; *Gastrointestinal Microbiome ; *Metagenome ; RNA, Ribosomal, 16S ; Ursidae/*microbiology/physiology ; }, abstract = {Captive breeding has been used as an effective approach to protecting endangered animals but its effect on the gut microbiome and the conservation status of these species is largely unknown. The giant panda is a flagship species for the conservation of wildlife. With integrated efforts including captive breeding, this species has been recently upgraded from "endangered" to "vulnerable" (IUCN 2016). Since a large proportion (21.8%) of their global population is still captive, it is critical to understand how captivity changes the gut microbiome of these pandas and how such alterations to the microbiome might affect their future fitness and potential impact on the ecosystem after release into the wild. Here, we use 16S rRNA (ribosomal RNA) marker gene sequencing and shotgun metagenomics sequencing to demonstrate that the fecal microbiomes differ substantially between wild and captive giant pandas. Fecal microbiome diversity was significantly lower in captive pandas, as was the diversity of functional genes. Additionally, captive pandas have reduced functional potential for cellulose degradation but enriched metabolic pathways for starch metabolism, indicating that they may not adapt to a wild diet after being released into the wild since a major component of their diet in the wild will be bamboo. Most significantly, we observed a significantly higher level of amylase activity but a lower level of cellulase activity in captive giant panda feces than those of wild giant pandas, shown by an in vitro experimental assay. Furthermore, antibiotic resistance genes and virulence factors, as well as heavy metal tolerance genes were enriched in the microbiomes of captive pandas, which raises a great concern of spreading these genes to other wild animals and ecosystems when they are released into a wild environment. Our results clearly show that captivity has altered the giant panda microbiome, which could have unintended negative consequences on their adaptability and the ecosystem during the reintroduction of giant pandas into the wild.}, } @article {pmid31634343, year = {2019}, author = {Diakite, A and Dubourg, G and Dione, N and Afouda, P and Bellali, S and Ngom, II and Valles, C and Million, M and Levasseur, A and Cadoret, F and Lagier, JC and Raoult, D}, title = {Extensive culturomics of 8 healthy samples enhances metagenomics efficiency.}, journal = {PloS one}, volume = {14}, number = {10}, pages = {e0223543}, pmid = {31634343}, issn = {1932-6203}, mesh = {Adult ; Bacteria/classification/genetics ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; *Metagenome ; *Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {Molecular approaches have long led to the assumption that the human gut microbiota is dominated by uncultivable bacteria. The recent advent of large-scale culturing methods, and in particular that of culturomics have demonstrated that these prokaryotes can in fact be cultured. This is increasing in a dramatic manner the repertoire of commensal microbes inhabiting the human gut. Following eight years of culturomics approach applied on more than 900 samples, we propose herein a remake of the pioneering study applying a dual approach including culturomics and metagenomics on a cohort of 8 healthy specimen. Here we show that culturomics enable a 20% higher richness when compared to molecular approaches by culturing 1 archaeal species and 494 bacterial species of which 19 were new taxa. Species discovered as a part of previous culturomics studies represent 30% of the cultivated isolates, while sequences derived from these new taxa enabled to increase by 22% the bacterial richness retrieved by metagenomics. Overall, 67% of the total reads generated were covered by cultured isolates, significantly reducing the hidden content of sequencing methods compared to the pioneering study. By redefining culture conditions to recover microbes previously considered fastidious, there are greater opportunities than ever to eradicate metagenomics dark matter.}, } @article {pmid31632686, year = {2019}, author = {Koo, H and Hakim, JA and Crossman, DK and Kumar, R and Lefkowitz, EJ and Morrow, CD}, title = {Individualized recovery of gut microbial strains post antibiotics.}, journal = {NPJ biofilms and microbiomes}, volume = {5}, number = {1}, pages = {30}, pmid = {31632686}, issn = {2055-5008}, mesh = {Anti-Bacterial Agents/*administration & dosage ; *Biological Variation, Individual ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenomics ; }, abstract = {To further understand the impact of antibiotics on the gastrointestinal tract microbial community, the intra-individual recovery pattern of specific microbial strains was determined using metagenomic sequencing coupled with strain-tracking analyses. In a study where 18 individuals were administered a single antibiotic (cefprozil), new microbial genomic variants (herein strains) were transiently detected in 15 individuals, while in a second study that used a cocktail of three antibiotics (meropenem, gentamicin, and vancomycin), all 12 participants had either permanent or transient strain changes. The presence of distinct microbial genomic variants indicates a pattern of strain recovery that is intra-individual specific following disruption of the human gastrointestinal tract with antibiotics.}, } @article {pmid31630520, year = {2020}, author = {Parker, M and Onetto, C and Hixson, J and Bilogrevic, E and Schueth, L and Pisaniello, L and Borneman, A and Herderich, M and de Barros Lopes, M and Francis, L}, title = {Factors Contributing to Interindividual Variation in Retronasal Odor Perception from Aroma Glycosides: The Role of Odorant Sensory Detection Threshold, Oral Microbiota, and Hydrolysis in Saliva.}, journal = {Journal of agricultural and food chemistry}, volume = {68}, number = {38}, pages = {10299-10309}, doi = {10.1021/acs.jafc.9b05450}, pmid = {31630520}, issn = {1520-5118}, mesh = {Adult ; Bacteria/classification/isolation & purification/metabolism ; Flavoring Agents/analysis ; Glycosides/*chemistry ; Humans ; Male ; *Microbiota ; Middle Aged ; Mouth/metabolism/*microbiology ; Odorants/analysis ; *Olfactory Perception ; Saliva/*chemistry/metabolism ; Smell ; Taste ; Young Adult ; }, abstract = {Glycosides are sugar conjugates of aroma compounds that are found in many fruits and vegetables, and while glycosides are non-volatile, they can release flavor during eating, through enzyme hydrolysis from oral microbiota. Recently, a range of sensory phenotypes for glucoside perception have been observed, reflecting interindividual variation in response to precursors of floral and smoky flavors, geranyl glucoside and guaiacyl glucoside. To understand this variation and investigate the role of oral microbiota on in vitro hydrolysis of glucosides in saliva, metagenomic screening was conducted using individuals representing the range of sensory phenotypes for geranyl and guaiacyl glucosides. In parallel, sensory retronasal detection thresholds for geranyl glucoside, guaiacyl glucoside, and the volatile odorants geraniol and guaiacol were determined. Oral microbial communities correlated with hydrolysis of glucosides in saliva, but the relationship did not extend to sensory phenotypes. Overall, the retronasal detection threshold of the volatile odorants studied was the main factor determining sensory phenotype.}, } @article {pmid31629904, year = {2019}, author = {Almeida, AR and Alves, M and Domingues, I and Henriques, I}, title = {The impact of antibiotic exposure in water and zebrafish gut microbiomes: A 16S rRNA gene-based metagenomic analysis.}, journal = {Ecotoxicology and environmental safety}, volume = {186}, number = {}, pages = {109771}, doi = {10.1016/j.ecoenv.2019.109771}, pmid = {31629904}, issn = {1090-2414}, mesh = {Animals ; Anti-Bacterial Agents/*toxicity ; Aquaculture ; Gastrointestinal Microbiome/*drug effects/genetics ; Humans ; Metagenome/*drug effects/genetics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Water Pollutants, Chemical/*toxicity ; Zebrafish/genetics/*microbiology ; }, abstract = {In order to supply human demand for food, the aquaculture industry has been growing fast in the last years, being fish usually cultivated in overcrowded conditions. Hence, to prevent the rapidly disease spreading, antibiotics may be applied to both sick and healthy animals. Due to its broad spectrum, oxytetracycline (OTC) is one of the most used antibiotics in food-production. Yet, although useful to prevent infections, antibiotics may reshape aquatic animals' microbiome, disturbing hosts' welfare. However, the impact of this exposure to the organism microbiome and its surrounding environment is poorly understood. Then, the objective of this study was to analyze in detail the long-term effect of OTC in both zebrafish gut and water microbiomes. Zebrafish adults were exposed, via water, for two months to three concentrations of OTC (0, 10 and 10000 μg/L). Total DNA was extracted from gut and water samples and the V3-V4 region of the bacterial 16 S rRNA gene was sequenced using Illumina technology. Results of alpha and beta-diversity analyses revealed that long-term exposure to OTC impacted both zebrafish gut and water microbiomes. In water samples, effects were observed even at the lowest (10 μg/L) OTC concentration tested resulting in an increase in Deltaproteobacteria, namely the Myxococcales and Bdellovibrionales orders. On the other hand, effects on zebrafish gut were only observed at the highest concentration with the selection of Alphaproteobacteria and Actinobacteria classes. Although these classes are common in fish gut, the increase of Actinobacteria may represent a health problem since some genera like Gordonia are linked to some human infection disease. Nevertheless, in both gut and water, it was observed a decrease in Gamaproteobacteria, probably due to OTC mode of action. In silico functional metagenomic analysis revealed that OTC exposure selected general detoxification mechanisms. In addition, the abundance of functional genes involved in Quorum Sensing (QS) increased under OTC exposure suggesting that QS may help bacteria to survive OTC stress. Thus, future studies should consider post-exposure scenarios for a deeper analysis of the water and zebrafish gut resistome, since bacteria may react differently after exposure ceased.}, } @article {pmid31629686, year = {2019}, author = {Cao, L and Gurevich, A and Alexander, KL and Naman, CB and Leão, T and Glukhov, E and Luzzatto-Knaan, T and Vargas, F and Quinn, R and Bouslimani, A and Nothias, LF and Singh, NK and Sanders, JG and Benitez, RAS and Thompson, LR and Hamid, MN and Morton, JT and Mikheenko, A and Shlemov, A and Korobeynikov, A and Friedberg, I and Knight, R and Venkateswaran, K and Gerwick, WH and Gerwick, L and Dorrestein, PC and Pevzner, PA and Mohimani, H}, title = {MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities.}, journal = {Cell systems}, volume = {9}, number = {6}, pages = {600-608.e4}, pmid = {31629686}, issn = {2405-4720}, support = {R01 GM118815/GM/NIGMS NIH HHS/United States ; R01 GM107550/GM/NIGMS NIH HHS/United States ; P41 GM103484/GM/NIGMS NIH HHS/United States ; R01 GM097509/GM/NIGMS NIH HHS/United States ; T32 CA009523/CA/NCI NIH HHS/United States ; DP2 GM137413/GM/NIGMS NIH HHS/United States ; R01 GM065490/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Genomics/methods ; Humans ; Microbiota/*genetics ; Peptides/chemistry ; Protein Processing, Post-Translational/*genetics ; Ribosomes/genetics ; Software ; }, abstract = {Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that contain antibiotics and a variety of other bioactive compounds. The existing methods for discovery of RiPPs by combining genome mining and computational mass spectrometry are limited to discovering specific classes of RiPPs from small datasets, and these methods fail to handle unknown post-translational modifications. Here, we present MetaMiner, a software tool for addressing these challenges that is compatible with large-scale screening platforms for natural product discovery. After searching millions of spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure against just eight genomic and metagenomic datasets, MetaMiner discovered 31 known and seven unknown RiPPs from diverse microbial communities, including human microbiome and lichen microbiome, and microorganisms isolated from the International Space Station.}, } @article {pmid31629058, year = {2020}, author = {Tilocca, B and Costanzo, N and Morittu, VM and Spina, AA and Soggiu, A and Britti, D and Roncada, P and Piras, C}, title = {Milk microbiota: Characterization methods and role in cheese production.}, journal = {Journal of proteomics}, volume = {210}, number = {}, pages = {103534}, doi = {10.1016/j.jprot.2019.103534}, pmid = {31629058}, issn = {1876-7737}, mesh = {Animals ; Cheese/*microbiology ; Dairying/standards ; Food Microbiology/*standards ; *Genome ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota ; Milk/metabolism/*microbiology ; Proteome/*metabolism ; *Transcriptome ; }, abstract = {Milk is a complex body fluid aimed at addressing the nutritional and defensive needs of the mammal's newborns. Harbored microbiota plays a pivotal role throughout the cheesemaking process and contributes to the development of flavor and texture typical of different type of cheeses. Understanding the dairy microbiota dynamics is of paramount importance for controlling the qualitative, sensorial and biosafety features of the dairy products. Although many studies investigated the contribution of single or few microorganisms, still there is some information lacking about microbial communities. The widespread of the omics platforms and bioinformatic tools enable the investigation of the cheese-associated microbial community in both phylogenetical and functional terms, highlighting the effects of the diverse cheesemaking variables. In this review, the most relevant literature is revised to provide an introduction of the milk- and cheese-associated microbiota, along with their structural and functional dynamics in relation to the diverse cheesemaking technologies and influencing variables. Also, we focus our attention on the latest omics technologies adopted in dairy microbiota investigation. Discussion on the key-steps and major drawbacks of each omics discipline is provided along with a collection of results from the latest research studies performed to unravel the fascinating world of the dairy-associated microbiota. SIGNIFICANCE: Understanding the milk- and cheese- associated microbial community is nowadays considered a key factor in the dairy industry, since it allows a comprehensive knowledge on how all phases of the cheesemaking process impact the harbored microflora; thus, predict the consequences in the finished products in terms of texture, organoleptic characteristics, palatability and biosafety. This review, collect the pioneering and milestones works so far performed in the field of dairy microbiota, and provide the basic guidance to whom approaching the cheese microbiota investigation by means of the latest omics technologies. Also, the review emphasizes the benefits and drawbacks of the omics disciplines, and underline how the integration of diverse omics sciences enhance a comprehensive depiction of the cheese microbiota. In turn, a better consciousness of the dairy microbiota might results in the application of improved starter cultures, cheesemaking practices and technologies; supporting a bio-safe and standardized production of cheese, with a strong economic benefit for both large-scale industries and local traditional dairy farms.}, } @article {pmid31628395, year = {2019}, author = {Althouse, MH and Stewart, C and Jiang, W and Moorthy, B and Lingappan, K}, title = {Impact of Early Life Antibiotic Exposure and Neonatal Hyperoxia on the Murine Microbiome and Lung Injury.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {14992}, pmid = {31628395}, issn = {2045-2322}, support = {R56 ES030221/ES/NIEHS NIH HHS/United States ; R01 HL129794/HL/NHLBI NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; 1R56ES030221//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/International ; K08 HL127103/HL/NHLBI NIH HHS/United States ; R01 HL144775/HL/NHLBI NIH HHS/United States ; 5R01HL129794//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/International ; R03 HL141572/HL/NHLBI NIH HHS/United States ; }, mesh = {Ampicillin/*adverse effects/pharmacology ; Animals ; Animals, Newborn/microbiology ; Anti-Bacterial Agents/*adverse effects/pharmacology ; Bronchopulmonary Dysplasia/*etiology ; Disease Models, Animal ; Dysbiosis/chemically induced ; Female ; Gastrointestinal Microbiome/*drug effects/*genetics ; Hyperoxia/*complications ; Mice ; Mice, Inbred C57BL ; Pregnancy ; Pulmonary Alveoli/pathology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cross talk between the intestinal microbiome and the lung and its role in lung health remains unknown. Perinatal exposure to antibiotics disrupts the neonatal microbiome and may have an impact on the preterm lung. We hypothesized that perinatal antibiotic exposure leads to long-term intestinal dysbiosis and increased alveolar simplification in a murine hyperoxia model. Pregnant C57BL/6 wild type dams and neonatal mice were treated with antibiotics before and/or immediately after delivery. Control mice received phosphate-buffered saline (PBS). Neonatal mice were exposed to 95% oxygen for 4 days or room air. Microbiome analysis was performed using 16S rRNA gene sequencing. Pulmonary alveolarization and vascularization were analyzed at postnatal day (PND) 21. Perinatal antibiotic exposure modified intestinal beta diversity but not alpha diversity in neonatal mice. Neonatal hyperoxia exposure altered intestinal beta diversity and relative abundance of commensal bacteria in antibiotic treated mice. Hyperoxia disrupted pulmonary alveolarization and vascularization at PND 21; however, there were no differences in the degree of lung injury in antibiotic treated mice compared to vehicle treated controls. Our study suggests that exposure to both hyperoxia and antibiotics early in life may cause long-term alterations in the intestinal microbiome, but intestinal dysbiosis may not significantly influence neonatal hyperoxic lung injury.}, } @article {pmid31627129, year = {2019}, author = {Cosetta, CM and Wolfe, BE}, title = {Causes and consequences of biotic interactions within microbiomes.}, journal = {Current opinion in microbiology}, volume = {50}, number = {}, pages = {35-41}, doi = {10.1016/j.mib.2019.09.004}, pmid = {31627129}, issn = {1879-0364}, mesh = {Bacteria/genetics ; Evolution, Molecular ; Host Microbial Interactions ; Humans ; *Metagenome ; *Microbial Interactions ; *Microbiota ; Phylogeny ; }, abstract = {An integrative pattern-process-mechanism approach is revealing the roles of biotic interactions in microbiome assembly. Patterns of microbiome diversity observed in metagenomic studies can be partly explained by interaction processes (e.g. competition, facilitation) and underlying molecular or genetic mechanisms (e.g. antibiotic production, nutrient cross-feeding). Exciting opportunities remain to fully understand the significance and generalizability of biotic interactions within microbiomes. Many microbial interactions have been studied by chasing easily quantifiable phenotypes including changes in growth or pigmentation, but it is likely that diverse cryptic interactions occur without obvious growth changes or macroscopic phenotypes. A narrow phylogenetic breadth of well-studied microbes limits our understanding of whether there are conserved genetic or molecular mechanisms of microbial interactions. Biotic interactions can impose strong selective pressures that could shape rates and modes of microbial evolution, but few studies have examined the evolutionary consequences of interactions within microbiomes. Continued exploration of the chemical and genetic mechanisms underlying biotic interactions may provide novel tools to manipulate and manage microbiomes.}, } @article {pmid31626917, year = {2020}, author = {Khan, KA and Al-Ghamdi, AA and Ghramh, HA and Ansari, MJ and Ali, H and Alamri, SA and Al-Kahtani, SN and Adgaba, N and Qasim, M and Hafeez, M}, title = {Structural diversity and functional variability of gut microbial communities associated with honey bees.}, journal = {Microbial pathogenesis}, volume = {138}, number = {}, pages = {103793}, doi = {10.1016/j.micpath.2019.103793}, pmid = {31626917}, issn = {1096-1208}, mesh = {Animals ; Bees/*physiology ; *Biodiversity ; *Gastrointestinal Microbiome ; Honey/microbiology ; Metagenomics/methods ; Microbiota ; Pollen/microbiology ; Pollination ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Microbial consortia accompanied to all eukaryotes can be inherited from ancestors, environment, and/or from various food source. Gut microbiota study is an emerging discipline of biological sciences that expands our understanding of the ecological and functional dynamics of gut environments. Microorganisms associated with honey bees play an important role in food digestion, colony performance, immunity, pollination, antagonistic effect against different pathogens, amelioration of food and many more. Although, many repots about honey bee gut microbiota are well documented, microbiome with other key components of honey bees such as larvae, adults, their food (pollen, beebread, and honey), honey combs, and floral nectar are poorly understood. Mutual interactions and extent of the roles of microbial communities associated with honey bees are still unclear and demand for more research on the nutritional physiology and health benefits of this ecologically and economically important group. Here in this study, we highlighted all the honey bee microbiome that harbored from different life stages and other relevant components. The anatomical parts of honey bee (larvae, adults), food source (pollen, beebread, and honey), honey combs, and floral nectar were highly flourished by numerous microorganisms like bacteria (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, Actinomycetes, Bacilli, Bacteroidetes, Cocci, Clostridia, Coliforms, Firmicutes, Flavobacteriia, Mollicutes) and fungi (Dothideomycetes, Eurotiomycetes, Mucormycotina, Saccharomycetes, Zygomycetes, Yeasts, Molds). Some distinctive microbial communities of a taxonomically constrained species have coevolved with social bees. This contribution is to enhance the understanding of honey bee gut microbiota, to accelerate bee microbiota and microbiome research in general and to aid design of future experiments in this growing field.}, } @article {pmid31626891, year = {2019}, author = {Wongsurawat, T and Nakagawa, M and Atiq, O and Coleman, HN and Jenjaroenpun, P and Allred, JI and Trammel, A and Puengrang, P and Ussery, DW and Nookaew, I}, title = {An assessment of Oxford Nanopore sequencing for human gut metagenome profiling: A pilot study of head and neck cancer patients.}, journal = {Journal of microbiological methods}, volume = {166}, number = {}, pages = {105739}, pmid = {31626891}, issn = {1872-8359}, support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; }, mesh = {Aged ; Bacteria/*classification ; Female ; Gastrointestinal Microbiome/*genetics ; Head and Neck Neoplasms/*epidemiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Metagenome/*genetics ; Middle Aged ; Nanopore Sequencing/*methods ; Pilot Projects ; Sequence Analysis, DNA/methods ; }, abstract = {Gut metagenome profiling using the Oxford Nanopore Technologies (ONT) sequencer was assessed in a pilot-sized study of 10 subjects. The taxonomic abundance of gut microbiota derived from ONT was comparable with Illumina Technology (IT) for the high-abundance species. IT better detected low-abundance species through amplification, when material was limited.}, } @article {pmid31626280, year = {2020}, author = {Liu, Y and Bible, PW and Zou, B and Liang, Q and Dong, C and Wen, X and Li, Y and Ge, X and Li, X and Deng, X and Ma, R and Guo, S and Liang, J and Chen, T and Pan, W and Liu, L and Chen, W and Wang, X and Wei, L}, title = {CSMD: a computational subtraction-based microbiome discovery pipeline for species-level characterization of clinical metagenomic samples.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {5}, pages = {1577-1583}, doi = {10.1093/bioinformatics/btz790}, pmid = {31626280}, issn = {1367-4811}, mesh = {Computational Biology ; Humans ; *Metagenome ; Metagenomics ; *Microbiota ; Software ; }, abstract = {MOTIVATION: Microbiome analyses of clinical samples with low microbial biomass are challenging because of the very small quantities of microbial DNA relative to the human host, ubiquitous contaminating DNA in sequencing experiments and the large and rapidly growing microbial reference databases.

RESULTS: We present computational subtraction-based microbiome discovery (CSMD), a bioinformatics pipeline specifically developed to generate accurate species-level microbiome profiles for clinical samples with low microbial loads. CSMD applies strategies for the maximal elimination of host sequences with minimal loss of microbial signal and effectively detects microorganisms present in the sample with minimal false positives using a stepwise convergent solution. CSMD was benchmarked in a comparative evaluation with other classic tools on previously published well-characterized datasets. It showed higher sensitivity and specificity in host sequence removal and higher specificity in microbial identification, which led to more accurate abundance estimation. All these features are integrated into a free and easy-to-use tool. Additionally, CSMD applied to cell-free plasma DNA showed that microbial diversity within these samples is substantially broader than previously believed.

CSMD is freely available at https://github.com/liuyu8721/csmd.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid31622928, year = {2019}, author = {Whitfill, T and Oh, J}, title = {Recoding the metagenome: microbiome engineering in situ.}, journal = {Current opinion in microbiology}, volume = {50}, number = {}, pages = {28-34}, doi = {10.1016/j.mib.2019.09.005}, pmid = {31622928}, issn = {1879-0364}, support = {DP2 GM126893/GM/NIGMS NIH HHS/United States ; U54 NS105539/NS/NINDS NIH HHS/United States ; U19 AI142733/AI/NIAID NIH HHS/United States ; R21 AR075174/AR/NIAMS NIH HHS/United States ; R43 AR073562/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/metabolism ; Bacteriophages/genetics/metabolism ; Biosensing Techniques ; *Host Microbial Interactions ; Humans ; *Metabolic Engineering ; *Metagenome ; Mice ; *Microbiota ; Synthetic Biology/methods ; }, abstract = {Synthetic biology has enabled a new generation of tools for engineering the microbiome, including targeted antibiotics, protein delivery, living biosensors and diagnostics, and metabolic factories. Here, we discuss opportunities and limitations in microbiome engineering, focusing on a new generation of tools for in situ genetic modification of a microbiome that hold particular promise in circumventing these limitations.}, } @article {pmid31621728, year = {2019}, author = {Yue, S and Zhao, D and Peng, C and Tan, C and Wang, Q and Gong, J}, title = {Effects of theabrownin on serum metabolites and gut microbiome in rats with a high-sugar diet.}, journal = {Food & function}, volume = {10}, number = {11}, pages = {7063-7080}, doi = {10.1039/c9fo01334b}, pmid = {31621728}, issn = {2042-650X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Body Weight/drug effects ; Catechin/administration & dosage/*analogs & derivatives ; Cecum/metabolism/microbiology ; Cholic Acid/blood ; Dietary Sugars/*metabolism ; Gastrointestinal Microbiome/*drug effects ; Humans ; Indoleacetic Acids/blood ; Male ; Melatonin/blood ; Obesity/blood/*drug therapy/microbiology/physiopathology ; Rats ; }, abstract = {Evidence has proven that the gut microbiota is an important environmental factor contributing to obesity by altering host energy harvest and storage. We performed a high-throughput 16S rDNA sequencing association study and serum metabolomics profiling in rats with a high-sugar diet. Our studies revealed that the high sugar diet reduced the diversity of cecal microorganisms, while the combination of theabrownin and the high sugar diet increased the diversity of cecal microorganisms and promoted reproduction of Alloprevotella, Coprostanoligenes_group, Bacteroides, Prevotellaceae_NK3B31_group, Desulfovibrio, Intestinimonas, Alistipes, Bifidobacterium, Phascolarctobacterium, Ruminococcaceae_UCG-010 and Staphylococcus. The combination also inhibited the growth of Lactobacillus, Prevotellaceae_Ga6A1_group and Tyzzerella. The Firmicutes/Bacteroidetes (F/B) ratio can be significantly reduced after the intervention of theabrownin in high sugar diet rats, and the reproduction of Bacteroides acidifaciens (BA) and Staphylococcus saprophyticus subsp. saprophyticus can be promoted. We found that the obesity-associated gut microbial species were linked to the changes in circulating metabolites. Serum levels of deoxycholic acid, cholic acid, 1H-indole-3-acetic acid, 3-indole acrylic acid and melatonin were negatively correlated with BA and Staphylococcus saprophyticus subsp. saprophyticus, but positively correlated with Lactobacillus murinus, Leptum and Gut_metagenome. 2-Hydroxy-6-methylpyridin-3-carboxylic acid, l-homoserine, and 1,7-dimethylxanthine were positively correlated with BA and Staphylococcus saprophyticus subsp. saprophyticus, but negatively correlated with Lactobacillus murinus, Leptum, and Gut_metagenome. In a high sugar diet mode, theabrownin reduced the body weight and triglycerides and improved insulin resistance mainly by targeting the reproduction of intestinal microorganisms such as BA, Staphylococcus saprophyticus subsp. saprophyticus, Lactobacillus murinus, Leptum, Gut_metagenome and so on. A strong correlation between cecal microorganisms and serum metabolites, obesity and insulin resistance was observed. Theabrownin has high potential in reducing the risk of cardiovascular diseases such as diabetes and obesity.}, } @article {pmid31620923, year = {2019}, author = {Singh, H and Torralba, MG and Moncera, KJ and DiLello, L and Petrini, J and Nelson, KE and Pieper, R}, title = {Gastro-intestinal and oral microbiome signatures associated with healthy aging.}, journal = {GeroScience}, volume = {41}, number = {6}, pages = {907-921}, pmid = {31620923}, issn = {2509-2723}, mesh = {Aged ; Aged, 80 and over ; Biomarkers/metabolism ; Case-Control Studies ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Healthy Aging/*physiology ; Humans ; Male ; Prospective Studies ; Saliva/microbiology ; }, abstract = {The human oral and gut microbiomes influence health via competition for a distinct niche in the body with pathogens, via metabolic capabilities that increase host digestive capacity and generate compounds engaged in signaling pathways and modulation of immune system functions. Old age alters our metabolic and regenerative capacity. Following recruitment of 65 human subjects in the age range of 70 to 82, we discerned healthy aging (HA) and non-healthy aging (NHA) cohorts discordant in the occurrence of one or more major diseases: (1) cancer, (2) acute or chronic cardiovascular diseases, (3) acute or chronic pulmonary diseases, (4) diabetes, and (5) stroke or neurodegenerative disorders. We analyzed these cohorts' oral microbiomes (saliva) and gut microbiomes (stool) to assess diversity and identify microbial biomarkers for HA. In contrast to the gut microbiome where no change was observed, we found that the saliva microbiome had higher α-diversity in the HA compared with the NHA group. We observed the genus Akkermansia to be significantly more abundant in the gut microbiota of the HA group. Akkermansia muciniphila is a colonic mucin-degrading bacterium believed to have beneficial effects on gastrointestinal health, particularly in the context of diabetes and obesity. Erysipelotrichaceae UCG-003 was a taxon increased in abundance in the HA cohort. Streptococcus was the only genus observed to be significantly decreased in abundance in both the gut and oral microbiomes of the HA cohort compared with the NHA cohort. Our data support the notion that these microbes are potential probiotics to decrease the risks of non-healthy aging.}, } @article {pmid31619307, year = {2020}, author = {Elokil, AA and Magdy, M and Melak, S and Ishfaq, H and Bhuiyan, A and Cui, L and Jamil, M and Zhao, S and Li, S}, title = {Faecal microbiome sequences in relation to the egg-laying performance of hens using amplicon-based metagenomic association analysis.}, journal = {Animal : an international journal of animal bioscience}, volume = {14}, number = {4}, pages = {706-715}, doi = {10.1017/S1751731119002428}, pmid = {31619307}, issn = {1751-732X}, mesh = {Actinobacteria/genetics/isolation & purification ; Animals ; Bacteria/*genetics/isolation & purification ; Chickens/*microbiology/physiology ; Cyanobacteria/genetics/isolation & purification ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Genotype ; Metagenome/*genetics ; *Metagenomics ; Ovum ; Proteobacteria/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Exploring the composition and structure of the faecal microbial community improves the understanding of the role of the gut microbiota in the gastrointestinal function and the egg-laying performance of hens. Therefore, detection of hen-microbial interactions can explore a new breeding marker for the selection of egg production due to the important role of the gut microbiome in the host's metabolism and health. Recently, the gut microbiota has been recognised as a regulator of host performance, which has led to investigations of the productive effects of changes in the faecal microbiome in various animals. In the present study, a metagenomics analysis was applied to characterise the composition and structural diversity of faecal microbial communities under two selections of egg-laying performance, high (H, n = 30) and low (L, n = 30), using 16S rRNA-based metagenomic association analysis. The most abundant bacterial compositions were estimated based on the operational classification units among samples and between the groups from metagenomic data sets. The results indicated that Firmicutes phylum has higher significant (P < 0.01) in the H group than in the L group. In addition, higher relative abundance phyla of Bacteroides and Fusobacteria were estimated in the H group than the L group, contrasting the phyla of Actinobacteria, Cyanobacteria and Proteobacteria were more relative abundance in the L group. The families (Lactobacillus, Bifidobacterium, Acinetobacter, Flavobacteriaceae, Lachnoclostridum and Rhodococcus) were more abundant in the H group based on the comparison between the H and L groups. Meanwhile, three types of phyla (Proteobacteria, Actinobacteria and Cyanobacteria) and six families (Acinetobacter, Avibacterium, Clostridium, Corynebacterium, Helicobacter and Peptoclostridium) were more abundant in the L group (P < 0.01). Overall, the selection of genotypes has enriched a relationship between the gut microbiota and the egg-laying performance. These findings suggest that the faecal microbiomes of chickens with high egg-laying performance have more diverse activities than those of chickens with low egg-laying performance, which may be related to the metabolism and health of the host and egg production variation.}, } @article {pmid31617268, year = {2020}, author = {Saborío-Montero, A and Gutiérrez-Rivas, M and García-Rodríguez, A and Atxaerandio, R and Goiri, I and López de Maturana, E and Jiménez-Montero, JA and Alenda, R and González-Recio, O}, title = {Structural equation models to disentangle the biological relationship between microbiota and complex traits: Methane production in dairy cattle as a case of study.}, journal = {Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie}, volume = {137}, number = {1}, pages = {36-48}, doi = {10.1111/jbg.12444}, pmid = {31617268}, issn = {1439-0388}, support = {RTA2015-00022-CO3 (METALGEN) national plan of rese//national plan of research, development and innovation 2013-2020/ ; RTA2015-00022-CO3//National Plan of Research, Development and Innovation 2013-2020/ ; }, mesh = {Animals ; Cattle/*metabolism/*microbiology ; *Dairying ; Markov Chains ; Methane/*biosynthesis ; *Microbiota ; *Models, Statistical ; Monte Carlo Method ; }, abstract = {The advent of metagenomics in animal breeding poses the challenge of statistically modelling the relationship between the microbiome, the host genetics and relevant complex traits. A set of structural equation models (SEMs) of a recursive type within a Markov chain Monte Carlo (MCMC) framework was proposed here to jointly analyse the host-metagenome-phenotype relationship. A non-recursive bivariate model was set as benchmark to compare the recursive model. The relative abundance of rumen microbes (RA), methane concentration (CH4) and the host genetics was used as a case of study. Data were from 337 Holstein cows from 12 herds in the north and north-west of Spain. Microbial composition from each cow was obtained from whole metagenome sequencing of ruminal content samples using a MinION device from Oxford Nanopore Technologies. Methane concentration was measured with Guardian[®] NG infrared gas monitor from Edinburgh Sensors during cow's visits to the milking automated system. A quarterly average from the methane eructation peaks for each cow was computed and used as phenotype for CH4 . Heritability of CH4 was estimated at 0.12 ± 0.01 in both the recursive and bivariate models. Likewise, heritability estimates for the relative abundance of the taxa overlapped between models and ranged between 0.08 and 0.48. Genetic correlations between the microbial composition and CH4 ranged from -0.76 to 0.65 in the non-recursive bivariate model and from -0.68 to 0.69 in the recursive model. Regardless of the statistical model used, positive genetic correlations with methane were estimated consistently for the seven genera pertaining to the Ciliophora phylum, as well as for those genera belonging to the Euryarchaeota (Methanobrevibacter sp.), Chytridiomycota (Neocallimastix sp.) and Fibrobacteres (Fibrobacter sp.) phyla. These results suggest that rumen's whole metagenome recursively regulates methane emissions in dairy cows and that both CH4 and the microbiota compositions are partially controlled by the host genotype.}, } @article {pmid31616028, year = {2019}, author = {Fernández, J and Ledesma, E and Monte, J and Millán, E and Costa, P and de la Fuente, VG and García, MTF and Martínez-Camblor, P and Villar, CJ and Lombó, F}, title = {Traditional Processed Meat Products Re-designed Towards Inulin-rich Functional Foods Reduce Polyps in Two Colorectal Cancer Animal Models.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {14783}, pmid = {31616028}, issn = {2045-2322}, mesh = {Animals ; Azoxymethane/toxicity ; Colon/metabolism/microbiology/pathology ; Colorectal Neoplasms/chemically induced/genetics/microbiology/*prevention & control ; Dextran Sulfate/toxicity ; Dietary Fiber/administration & dosage ; Fatty Acids, Volatile/biosynthesis ; *Functional Food ; Gastrointestinal Microbiome/genetics ; Humans ; Intestinal Mucosa/metabolism/microbiology/pathology ; Intestinal Polyps/chemically induced/genetics/microbiology/*prevention & control ; Inulin/*administration & dosage ; Male ; *Meat Products ; Metagenomics ; Neoplasms, Experimental/chemically induced/genetics/microbiology/*prevention & control ; Prebiotics/administration & dosage ; Rats ; Swine ; }, abstract = {Inulin-rich foods exert a prebiotic effect, as this polysaccharide is able to enhance beneficial colon microbiota populations, giving rise to the in situ production of short-chain fatty acids (SCFAs) such as propionic and butyric acids. These SCFAs are potent preventive agents against colorectal cancer due to their histone deacetylases inhibitory properties, which induce apoptosis in tumor colonocytes. As colorectal cancer is the fourth most common neoplasia in Europe with 28.2 new cases per 100,000 inhabitants, a cost-effective preventive strategy has been tested in this work by redesigning common porcine meat products (chorizo sausages and cooked ham) consumed by a substantial proportion of the population towards potential colorectal cancer preventive functional foods. In order to test the preventive effect of these inulin-rich meat products against colorectal cancer, an animal model (Rattus norvegicus F344) was used, involving two doses of azoxymethane (10 mg/kg) and two treatments with dextran sodium sulfate (DSS) during a 20-week assay period. Control feed, control sausages, functional sausages (15.7% inulin), control cooked ham and functional cooked ham (10% inulin) were used to feed the corresponding animal cohorts. Then, the animals were sacrificed and their digestive tract tissues were analyzed. The results showed a statistically significant 49% reduction in the number of colon polyps in the functional meat products cohorts with respect to the control meat products animals, as well as an increase in the cecum weight (an indicator of a diet rich in prebiotic fiber), a 51.8% increase in colon propionate production, a 39.1% increase in colon butyrate concentrations, and a reduction in the number of hyperplastic Peyer's patches. Metagenomics studies also demonstrated colon microbiota differences, revealing a significant increase in Bacteroidetes populations in the functional meat products (mainly due to an increase in Bacteroidaceae and Prevotellaceae families, which include prominent propionate producers), together with a reduction in Firmicutes (especially due to lower Lachnospiraceae populations). However, functional meat products showed a remarkable increase in the anti-inflammatory and fiber-fermentative Blautia genus, which belongs to this Lachnospiraceae family. The functional meat products cohorts also presented a reduction in important pro-inflammatory bacterial populations, such as those of the genus Desulfovibrio and Bilophila. These results were corroborated in a genetic animal model of CRC (F344/NSlc-Apc[1588/kyo]) that produced similar results. Therefore, processed meat products can be redesigned towards functional prebiotic foods of interest as a cost-effective dietary strategy for preventing colorectal cancer in human populations.}, } @article {pmid31616016, year = {2019}, author = {Polinski, JM and Bucci, JP and Gasser, M and Bodnar, AG}, title = {Metabarcoding assessment of prokaryotic and eukaryotic taxa in sediments from Stellwagen Bank National Marine Sanctuary.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {14820}, pmid = {31616016}, issn = {2045-2322}, mesh = {Archaea/classification/*genetics/isolation & purification ; Atlantic Ocean ; Bacteria/classification/*genetics/isolation & purification ; Conservation of Natural Resources ; DNA Barcoding, Taxonomic ; DNA, Environmental/genetics/isolation & purification ; Ecological Parameter Monitoring ; Eukaryota/classification/*genetics/isolation & purification ; Geologic Sediments/*microbiology ; Maine ; Metagenome ; Microbiota/*genetics ; Phylogeny ; Seawater/microbiology ; }, abstract = {Stellwagen Bank National Marine Sanctuary (SBNMS) in the Gulf of Maine is a historic fishing ground renowned for remarkable productivity. Biodiversity conservation is a key management priority for SBNMS and yet data on the diversity of microorganisms, both prokaryotic and eukaryotic, is lacking. This study utilized next generation sequencing to characterize sedimentary communities within SBNMS at three sites over two seasons. Targeting 16S and 18S small subunit (SSU) rRNA genes and fungal Internal Transcribed Spacer (ITS) rDNA sequences, samples contained high diversity at all taxonomic levels and identified 127 phyla, including 115 not previously represented in the SBNMS Management Plan and Environmental Assessment. A majority of the diversity was bacterial, with 59 phyla, but also represented were nine Archaea, 18 Animalia, 14 Chromista, eight Protozoa, two Plantae, and 17 Fungi phyla. Samples from different sites and seasons were dominated by the same high abundance organisms but displayed considerable variation in rare taxa. The levels of biodiversity seen on this small spatial scale suggest that benthic communities of this area support a diverse array of micro- and macro-organisms, and provide a baseline for future studies to assess changes in community structure in response to rapid warming in the Gulf of Maine.}, } @article {pmid31614751, year = {2019}, author = {Gu, J and Mao, B and Cui, S and Liu, X and Zhang, H and Zhao, J and Chen, W}, title = {Metagenomic Insights into the Effects of Fructooligosaccharides (FOS) on the Composition of Luminal and Mucosal Microbiota in C57BL/6J Mice, Especially the Bifidobacterium Composition.}, journal = {Nutrients}, volume = {11}, number = {10}, pages = {}, pmid = {31614751}, issn = {2072-6643}, support = {31972086//National Natural Science Foundation of China/ ; 31601453//National Natural Science Foundation of China/ ; 31801530//National Natural Science Foundation of China/ ; JUFSTR20180102//National First-Class Discipline Program of Food Science and Technology/ ; }, mesh = {Animal Feed/analysis ; Animals ; Bifidobacterium/classification/*drug effects ; Cecum/*microbiology ; Diet/veterinary ; Dietary Supplements ; Gastrointestinal Contents/microbiology ; Gastrointestinal Microbiome/*drug effects ; Male ; Mice ; Oligosaccharides/*pharmacology ; }, abstract = {Fructooligosaccharides (FOS) are considered prebiotics and have been proven to selectively promote the growth of Bifidobacterium in the gut. This study aimed to clarify the effects of FOS intake on the composition of luminal and mucosal microbiota in mice. Briefly, mice were fed a 0% or 25% FOS (w/w)-supplemented diet for four weeks, and the composition of luminal and mucosal microbiota, especially the Bifidobacterium, was analyzed by sequencing the V3-V4 region of 16S rRNA and groEL gene, respectively. After FOS intervention, there were significant increases in the total and wall weights of the cecum and the amount of total short-chain fatty acids (SCFAs) in the cecal contents of the mice. At the phylum level, the results showed a significant increase in the relative abundance of Actinobacteria in the contents and mucosa from the cecum to the distal colon in the FOS group. Besides Bifidobacterium, a significant increase was observed in the relative abundance of Coprococcus in all samples at the genus level, which may be partially related to the increase in butyric acid levels in the luminal contents. Furthermore, groEL sequencing revealed that Bifidobacterium pseudolongum was almost the sole bifidobacterial species in the luminal contents (>98%) and mucosa (>89%). These results indicated that FOS can selectively promote B. pseudolongum proliferation in the intestine, either in the lumen or the mucosa from the cecum to the distal colon. Further studies are required to reveal the competitive advantage of B. pseudolongum over other FOS-metabolizing bacteria and the response mechanisms of B. pseudolongum to FOS.}, } @article {pmid31614509, year = {2019}, author = {Ambrosino, L and Tangherlini, M and Colantuono, C and Esposito, A and Sangiovanni, M and Miralto, M and Sansone, C and Chiusano, ML}, title = {Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives.}, journal = {Marine drugs}, volume = {17}, number = {10}, pages = {}, pmid = {31614509}, issn = {1660-3397}, mesh = {Animals ; Aquatic Organisms/*genetics/*metabolism ; Biodiversity ; Biotechnology/methods ; Computational Biology/*methods ; Ecosystem ; Humans ; }, abstract = {The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources.}, } @article {pmid31612915, year = {2020}, author = {Kautsar, SA and Blin, K and Shaw, S and Navarro-Muñoz, JC and Terlouw, BR and van der Hooft, JJJ and van Santen, JA and Tracanna, V and Suarez Duran, HG and Pascal Andreu, V and Selem-Mojica, N and Alanjary, M and Robinson, SL and Lund, G and Epstein, SC and Sisto, AC and Charkoudian, LK and Collemare, J and Linington, RG and Weber, T and Medema, MH}, title = {MIBiG 2.0: a repository for biosynthetic gene clusters of known function.}, journal = {Nucleic acids research}, volume = {48}, number = {D1}, pages = {D454-D458}, pmid = {31612915}, issn = {1362-4962}, support = {BB/M008770/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; U41 AT008718/AT/NCCIH NIH HHS/United States ; }, mesh = {Biosynthetic Pathways/genetics ; *Databases, Genetic ; *Genome, Bacterial ; Genomics/*methods ; Molecular Sequence Annotation ; *Multigene Family ; *Software ; }, abstract = {Fueled by the explosion of (meta)genomic data, genome mining of specialized metabolites has become a major technology for drug discovery and studying microbiome ecology. In these efforts, computational tools like antiSMASH have played a central role through the analysis of Biosynthetic Gene Clusters (BGCs). Thousands of candidate BGCs from microbial genomes have been identified and stored in public databases. Interpreting the function and novelty of these predicted BGCs requires comparison with a well-documented set of BGCs of known function. The MIBiG (Minimum Information about a Biosynthetic Gene Cluster) Data Standard and Repository was established in 2015 to enable curation and storage of known BGCs. Here, we present MIBiG 2.0, which encompasses major updates to the schema, the data, and the online repository itself. Over the past five years, 851 new BGCs have been added. Additionally, we performed extensive manual data curation of all entries to improve the annotation quality of our repository. We also redesigned the data schema to ensure the compliance of future annotations. Finally, we improved the user experience by adding new features such as query searches and a statistics page, and enabled direct link-outs to chemical structure databases. The repository is accessible online at https://mibig.secondarymetabolites.org/.}, } @article {pmid31612475, year = {2020}, author = {Andersen, S and Staudacher, H and Weber, N and Kennedy, G and Varelias, A and Banks, M and Bauer, J}, title = {Pilot study investigating the effect of enteral and parenteral nutrition on the gastrointestinal microbiome post-allogeneic transplantation.}, journal = {British journal of haematology}, volume = {188}, number = {4}, pages = {570-581}, doi = {10.1111/bjh.16218}, pmid = {31612475}, issn = {1365-2141}, support = {//Royal Brisbane & Women's Hospital Research Foundation/International ; }, mesh = {Adult ; Allografts ; *Bacteria/classification/growth & development ; *Enteral Nutrition ; Female ; *Gastrointestinal Microbiome ; *Hematologic Neoplasms/microbiology/therapy ; *Hematopoietic Stem Cell Transplantation ; Humans ; Male ; Middle Aged ; *Parenteral Nutrition ; Pilot Projects ; }, abstract = {Nutrition support is frequently required post-allogeneic haematopoietic progenitor cell transplantation (HPCT); however, the impact of mode of feeding on the gastrointestinal microbiome has not been explored. This study aimed to determine if there is a difference in the microbiome between patients receiving enteral nutrition (EN) and parenteral nutrition (PN) post-allogeneic HPCT. Twenty-three patients received either early EN or PN when required. Stool samples were collected at 30 days post-transplant and analysed with shotgun metagenomic sequencing. There was no difference in microbial diversity between patients who received predominantly EN (n = 13) vs. PN (n = 10) however patients who received predominantly EN had greater abundance of Faecalibacterium (P < 0·001) and ruminococcus E bromii (P = 0·026). Patients who had minimal oral intake for a longer duration during provision of nutrition support had a different overall microbial profile (P = 0·044), lower microbial diversity (P = 0·004) and lower abundance of faecalibacterium prausnitzii_C (P = 0·030) and Blautia (P = 0·007) compared to patients with greater oral intake. Lower microbial diversity was found in patients who received additional beta lactam antibiotics (P = 0·042) or had a longer length of hospital stay (P = 0·019). Post-HPCT oral intake should be encouraged to maintain microbiota diversity and, if nutrition support is required, EN may promote a more optimal microbiota profile.}, } @article {pmid31612432, year = {2020}, author = {Rattes de Almeida Couto, C and Catharine de Assis Leite, D and Jurelevicius, D and van Elsas, JD and Seldin, L}, title = {Chemical and biological dispersants differently affect the bacterial communities of uncontaminated and oil-contaminated marine water.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {51}, number = {2}, pages = {691-700}, pmid = {31612432}, issn = {1678-4405}, support = {01//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; -//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; }, mesh = {Bacteria/classification/metabolism ; Biodegradation, Environmental ; Brazil ; Metagenome ; *Microbiota ; Petroleum/metabolism ; Petroleum Pollution ; Seawater/analysis/*microbiology ; Surface-Active Agents/classification/*metabolism ; *Water Microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The use of dispersants in marine environments is a common practice worldwide for oil spill remediation. While the effects of chemical dispersants have been extensively studied, those of biosurfactants, mainly surfactin that is considered one of the most effective surfactants produced by bacteria, have been less considered. We constructed microcosms containing marine water collected from Grumari beach (W_GB, Brazil) and from Schiermonnikoog beach (W_SI, The Netherlands) with the addition of oil (WO), Ultrasperse II plus oil (WOS), surfactin plus oil (WOB), and both dispersants (WS or WB) individually. In these treatments, the composition of bacterial communities and their predictive biodegradation potential were determined over time. High-throughput sequencing of the rrs gene encoding bacterial 16S rRNA revealed that Bacteroidetes (Flavobacteria class) and Proteobacteria (mainly Gammaproteobacteria and Alphaproteobacteria classes) were the most abundant phyla found among the W_GB and W_SI microbiomes, and the relative abundance of the bacterial types in the different microcosms varied based on the treatment applied. Non-metrical multidimensional scaling (NMDS) revealed a clear clustering based on the addition of oil and on the dispersant type added to the GB or SI microcosms, i.e., WB and WOB were separated from WS and WOS in both marine ecosystems studied. The potential presence of diverse enzymes involved in oil degradation was indicated by predictive bacterial metagenome reconstruction. The abundance of predicted genes for degradation of petroleum hydrocarbons increased more in surfactin-treated microcosms than those treated with Ultrasperse II, mainly in the marine water samples from Grumari beach.}, } @article {pmid31611653, year = {2020}, author = {Hoarfrost, A and Nayfach, S and Ladau, J and Yooseph, S and Arnosti, C and Dupont, CL and Pollard, KS}, title = {Global ecotypes in the ubiquitous marine clade SAR86.}, journal = {The ISME journal}, volume = {14}, number = {1}, pages = {178-188}, pmid = {31611653}, issn = {1751-7370}, mesh = {Ecotype ; Gammaproteobacteria/*classification/genetics ; Genes, Bacterial ; Metagenome ; Oceans and Seas ; Phylogeography ; }, abstract = {SAR86 is an abundant and ubiquitous heterotroph in the surface ocean that plays a central role in the function of marine ecosystems. We hypothesized that despite its ubiquity, different SAR86 subgroups may be endemic to specific ocean regions and functionally specialized for unique marine environments. However, the global biogeographical distributions of SAR86 genes, and the manner in which these distributions correlate with marine environments, have not been investigated. We quantified SAR86 gene content across globally distributed metagenomic samples and modeled these gene distributions as a function of 51 environmental variables. We identified five distinct clusters of genes within the SAR86 pangenome, each with a unique geographic distribution associated with specific environmental characteristics. Gene clusters are characterized by the strong taxonomic enrichment of distinct SAR86 genomes and partial assemblies, as well as differential enrichment of certain functional groups, suggesting differing functional and ecological roles of SAR86 ecotypes. We then leveraged our models and high-resolution, remote sensing-derived environmental data to predict the distributions of SAR86 gene clusters across the world's oceans, creating global maps of SAR86 ecotype distributions. Our results reveal that SAR86 exhibits previously unknown, complex biogeography, and provide a framework for exploring geographic distributions of genetic diversity from other microbial clades.}, } @article {pmid31611646, year = {2019}, author = {Ansorge, R and Romano, S and Sayavedra, L and Porras, MÁG and Kupczok, A and Tegetmeyer, HE and Dubilier, N and Petersen, J}, title = {Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels.}, journal = {Nature microbiology}, volume = {4}, number = {12}, pages = {2487-2497}, pmid = {31611646}, issn = {2058-5276}, mesh = {Animals ; Bacteria/classification/*genetics ; Base Sequence ; Biodiversity ; Bivalvia/metabolism/*microbiology ; Ecosystem ; Genetic Heterogeneity ; Hydrogenase/genetics ; Hydrothermal Vents ; Metagenome ; Microbiota/genetics ; Mytilidae/metabolism/microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; *Symbiosis ; Transcriptome ; }, abstract = {Genetic diversity of closely related free-living microorganisms is widespread and underpins ecosystem functioning, but most evolutionary theories predict that it destabilizes intimate mutualisms. Accordingly, strain diversity is assumed to be highly restricted in intracellular bacteria associated with animals. Here, we sequenced metagenomes and metatranscriptomes of 18 Bathymodiolus mussel individuals from four species, covering their known distribution range at deep-sea hydrothermal vents in the Atlantic. We show that as many as 16 strains of intracellular, sulfur-oxidizing symbionts coexist in individual Bathymodiolus mussels. Co-occurring symbiont strains differed extensively in key functions, such as the use of energy and nutrient sources, electron acceptors and viral defence mechanisms. Most strain-specific genes were expressed, highlighting their potential to affect fitness. We show that fine-scale diversity is pervasive in Bathymodiolus sulfur-oxidizing symbionts, and hypothesize that it may be widespread in low-cost symbioses where the environment, rather than the host, feeds the symbionts.}, } @article {pmid31611489, year = {2019}, author = {Nagata, N and Tohya, M and Takeuchi, F and Suda, W and Nishijima, S and Ohsugi, M and Ueki, K and Tsujimoto, T and Nakamura, T and Kawai, T and Miyoshi-Akiyama, T and Uemura, N and Hattori, M}, title = {Effects of storage temperature, storage time, and Cary-Blair transport medium on the stability of the gut microbiota.}, journal = {Drug discoveries & therapeutics}, volume = {13}, number = {5}, pages = {256-260}, doi = {10.5582/ddt.2019.01071}, pmid = {31611489}, issn = {1881-784X}, mesh = {Culture Media/*metabolism ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/metabolism ; Specimen Handling/methods/*statistics & numerical data ; Survival Rate ; Temperature ; Time Factors ; }, abstract = {How long fecal samples can withstand a period of refrigeration or room temperature, and the appropriate preservative, are largely unknown. Cary-Blair transport medium has been used for many years because it is inexpensive and prevents bacterial overgrowth. However, its effectiveness for metagenomic analyses has never been tested. We found that the microbial compositions using a 16S rRNA sequence of samples left at 4°C for 3 or 7 days or at 25°C for 1, 3, or 7 days differed significantly from samples stored at -80°C in no-preservative method. Whereas samples stored in Cary-Blair medium remained unchanged for longer periods. The relative abundances of phylum Bacteroidetes and Actinobacteria, changed significantly at 25°C, whereas Cary-Blair medium inhibited the reduction in Bacteroidetes and the increase in Actinobacteria. The bacterial survival counts were significantly lower in the RNAlater samples than in the Cary-Blair samples under aerobic and anaerobic culture conditions. In conclusion, storage time and storage temperature significantly affect the gut microbial composition in fecal samples. Given the low cost, inhibitory effect on bacterial changes, and potential utility in bacterial isolation, Cary-Blair medium containers are suitable for large-scale or hospital-based microbiome studies, especially if direct freezing at -80°C is unavailable.}, } @article {pmid31611361, year = {2019}, author = {Guitor, AK and Raphenya, AR and Klunk, J and Kuch, M and Alcock, B and Surette, MG and McArthur, AG and Poinar, HN and Wright, GD}, title = {Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes.}, journal = {Antimicrobial agents and chemotherapy}, volume = {64}, number = {1}, pages = {}, pmid = {31611361}, issn = {1098-6596}, support = {MT-14981//CIHR/Canada ; PJT-156214//CIHR/Canada ; }, mesh = {Bacteria/drug effects/genetics/isolation & purification ; DNA Probes/genetics ; Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/genetics ; Genome, Bacterial ; Humans ; *Metagenome ; Metagenomics/methods ; Microbiota/drug effects/genetics ; Whole Genome Sequencing ; }, abstract = {Identification of the nucleotide sequences encoding antibiotic resistance elements and determination of their association with antibiotic resistance are critical to improve surveillance and monitor trends in antibiotic resistance. Current methods to study antibiotic resistance in various environments rely on extensive deep sequencing or laborious culturing of fastidious organisms, both of which are heavily time-consuming operations. An accurate and sensitive method to identify both rare and common resistance elements in complex metagenomic samples is needed. Referencing the sequences in the Comprehensive Antibiotic Resistance Database, we designed a set of 37,826 probes to specifically target over 2,000 nucleotide sequences associated with antibiotic resistance in clinically relevant bacteria. Testing of this probe set on DNA libraries generated from multidrug-resistant bacteria to selectively capture resistance genes reproducibly produced higher numbers of reads on target at a greater length of coverage than shotgun sequencing. We also identified additional resistance gene sequences from human gut microbiome samples that sequencing alone was not able to detect. Our method to capture the resistome enables a sensitive means of gene detection in diverse environments where genes encoding antibiotic resistance represent less than 0.1% of the metagenome.}, } @article {pmid31611016, year = {2020}, author = {Yang, X and Chen, Y and Guo, F and Liu, X and Su, X and He, Q}, title = {Metagenomic analysis of the biotoxicity of titanium dioxide nanoparticles to microbial nitrogen transformation in constructed wetlands.}, journal = {Journal of hazardous materials}, volume = {384}, number = {}, pages = {121376}, doi = {10.1016/j.jhazmat.2019.121376}, pmid = {31611016}, issn = {1873-3336}, mesh = {Metagenome/*drug effects ; Microbiota/*drug effects/genetics ; Models, Theoretical ; Nanoparticles/*toxicity ; Nitrogen/*metabolism ; Titanium/*toxicity ; Waste Disposal, Fluid/methods ; Wastewater/chemistry/microbiology ; Water Pollutants, Chemical/*toxicity ; *Wetlands ; }, abstract = {Extensive use of titanium dioxide nanoparticles (TiO2 NPs) in various products has increased the release of these particles into wastewater, posing potential environmental risks. As an ecological wastewater treatment facility, constructed wetland (CW) is an important sink of NPs. However, little is known about the effects of NPs on microbial nitrogen transformation and related genes in CWs. In this study, short-term (5 days) and long-term (60 days) exposure experiments were conducted to investigate the effect of TiO2 NPs (0, 1, and 50 mg/L) on microbial nitrogen removal in CWs. The results showed that nitrogen removal efficiency was decreased by 35%-51% after long-term exposure to TiO2 NPs. Metagenomic analysis further confirmed that TiO2 NPs declined the relative abundance of functional genes and those enzyme encoding genes involved in the nitrogen metabolism pathway and glycolysis metabolism process. Furthermore, our data proved that the indigent glycolysis metabolism process resulted in the shortage of electron (NADH) and energy sources (ATP), causing inefficient nitrogen removal. Overall, these results revealed that the accumulation of TiO2 NPs altered the genetic expression of biofilm in CWs, which had significant impacts on biological nitrogen transformation.}, } @article {pmid31607556, year = {2019}, author = {Tett, A and Huang, KD and Asnicar, F and Fehlner-Peach, H and Pasolli, E and Karcher, N and Armanini, F and Manghi, P and Bonham, K and Zolfo, M and De Filippis, F and Magnabosco, C and Bonneau, R and Lusingu, J and Amuasi, J and Reinhard, K and Rattei, T and Boulund, F and Engstrand, L and Zink, A and Collado, MC and Littman, DR and Eibach, D and Ercolini, D and Rota-Stabelli, O and Huttenhower, C and Maixner, F and Segata, N}, title = {The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations.}, journal = {Cell host & microbe}, volume = {26}, number = {5}, pages = {666-679.e7}, pmid = {31607556}, issn = {1934-6069}, support = {TL1 TR001447/TR/NCATS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; 716575/ERC_/European Research Council/International ; R24 DK110499/DK/NIDDK NIH HHS/United States ; R01 DK103358/DK/NIDDK NIH HHS/United States ; R01 HG005220/HG/NHGRI NIH HHS/United States ; }, mesh = {Diet ; Ethiopia ; Feces/microbiology ; Fossils/*microbiology ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Genome, Bacterial/*genetics ; Ghana ; Humans ; Prevotella/*classification/*genetics/isolation & purification ; Tanzania ; }, abstract = {Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In a cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes and explored the genetic and population structure of P. copri. P. copri encompasses four distinct clades (>10% inter-clade genetic divergence) that we propose constitute the P. copri complex, and all clades were confirmed by isolate sequencing. These clades are nearly ubiquitous and co-present in non-Westernized populations. Genomic analysis showed substantial functional diversity in the complex with notable differences in carbohydrate metabolism, suggesting that multi-generational dietary modifications may be driving reduced prevalence in Westernized populations. Analysis of ancient metagenomes highlighted patterns of P. copri presence consistent with modern non-Westernized populations and a clade delineation time pre-dating human migratory waves out of Africa. These findings reveal that P. copri exhibits a high diversity that is underrepresented in Western-lifestyle populations.}, } @article {pmid31605831, year = {2020}, author = {Yang, Y and Pan, J and Zhou, Z and Wu, J and Liu, Y and Lin, JG and Hong, Y and Li, X and Li, M and Gu, JD}, title = {Complex microbial nitrogen-cycling networks in three distinct anammox-inoculated wastewater treatment systems.}, journal = {Water research}, volume = {168}, number = {}, pages = {115142}, doi = {10.1016/j.watres.2019.115142}, pmid = {31605831}, issn = {1879-2448}, mesh = {Ammonia ; Bioreactors ; Microbial Consortia ; *Nitrification ; Nitrites ; Nitrogen ; Nitrogen Cycle ; Oxidation-Reduction ; *Wastewater ; }, abstract = {Microbial nitrogen removal mediated by anaerobic ammonium oxidation (anammox) are cost-effective, yet it is time-consuming to accumulate the slow-growing anammox bacteria in conventional wastewater treatment plants (WWTPs). Inoculation of anammox enriched pellets is an effective way to establish anammox and achieve shortcut nitrogen removal in full-scale WWTPs. However, little is known about the complex microbial nitrogen-cycling networks in these anammox-inoculated WWTPs. Here, we applied metagenomic and metatranscriptomic tools to study the microbial nitrogen removal in three conventional WWTPs, which have been inoculated exogenous anammox pellets, representing partial-nitrification anammox (PNA) and nitrification-denitrification nitrogen removal processes. In the PNA system of Bali (BL), ammonia was partially oxidized by ammonia-oxidizing bacteria (AOB) Nitrosomonas and the oxidized nitrite and the remaining ammonium were directly converted to N2 by anammox bacteria Ca. Brocadia and Ca. Kuenenia. In the nitrification-denitrification system of Wenshan (WS), ammonia-oxidizing archaea (AOA) Thaumarchaeota unexpectedly dominated the nitrifying community in the presence of AOB Nitrosomonas. Meanwhile, the biomass yield of Ca. Brocadia was likely inhibited by the high biodegradable organic compound input and limited by substrate competitions from AOA, AOB, complete ammonia oxidizers (comammox) Nitrospira, nitrite-oxidizing bacteria (NOB) Nitrospira, and heterotrophic denitrifiers. Unexpectedly, comammox Nitrospira was the predominant nitrifier in the presence of AOB Nitrosomonas in the organic carbon-rich nitrification-denitrification system of Linkou (LK). These results clearly showed that distinct active groups were working in concert for an effective nitrogen removal in different WWTPs. This study confirmed the feasibility of anammox application in ammonium-rich systems by direct inoculation of the exogenous anammox pellets and improved our understanding of microbial nitrogen cycling in anammox-driven conventional WWTPs from both physiochemical and omics perspectives.}, } @article {pmid31605691, year = {2020}, author = {Dubinsky, V and Reshef, L and Bar, N and Keizer, D and Golan, N and Rabinowitz, K and Godny, L and Yadgar, K and Zonensain, K and Tulchinsky, H and Gophna, U and Dotan, I}, title = {Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy.}, journal = {Gastroenterology}, volume = {158}, number = {3}, pages = {610-624.e13}, doi = {10.1053/j.gastro.2019.10.001}, pmid = {31605691}, issn = {1528-0012}, mesh = {Adult ; Anti-Bacterial Agents/pharmacology/*therapeutic use ; Bacteria/*drug effects/genetics/isolation & purification ; Ciprofloxacin/pharmacology/therapeutic use ; Cytokines/metabolism ; Drug Resistance, Bacterial/*drug effects/genetics ; Feces/chemistry/*microbiology ; Female ; Gastrointestinal Microbiome/drug effects ; HT29 Cells/metabolism ; Humans ; Leukocyte L1 Antigen Complex/analysis ; Male ; Metagenomics ; Metronidazole/therapeutic use ; Middle Aged ; Point Mutation ; Pouchitis/*drug therapy/*microbiology ; Prospective Studies ; Recurrence ; Treatment Outcome ; Virulence Factors/metabolism ; Young Adult ; }, abstract = {BACKGROUND & AIMS: Pouchitis that develops in patients with ulcerative colitis after total proctocolectomy and ileal pouch anal anastomosis is usually treated with antibiotics. Some patients have recurrence of flares, or become antibiotic-dependent, and require repeated courses or prolonged periods of antibiotic therapy. We investigated microbial factors associated with response to antibiotic treatment and development of antibiotic dependence in patients with pouchitis.

METHODS: We performed a prospective study of 49 patients who had undergone pouch surgery at a tertiary center. Disease activity was determined based on clinical, endoscopic, and histologic criteria. Pouch phenotype was defined as recurrent-acute pouchitis (n = 6), chronic pouchitis and Crohn's-like disease of the pouch (n = 27), normal pouch from patient with ulcerative colitis (n = 10), and normal pouch from patient with familial adenomatous polyposis (n = 6). Fecal samples (n = 234) were collected over time during or in the absence of antibiotic treatment (ciprofloxacin and/or metronidazole). Thirty-three patients were treated with antibiotics, for a median of 425 days of cumulative antibiotic therapy, during follow-up. Calprotectin was measured and fecal DNA was sequenced using shotgun metagenomics and analyzed with specifically designed bioinformatic pipelines. Bacterial strains were isolated from fecal samples. We assessed their ciprofloxacin resistance and ability to induce secretion of inflammatory cytokines by HT-29 intestinal epithelial cells.

RESULTS: Most antibiotic-treated patients (79%) had a clinical response to each course of antibiotics; however, 89% of those who completed a 4-week course relapsed within 3 months. Median calprotectin levels decreased by 40% in response to antibiotics. Antibiotic treatment reduced disease-associated bacteria such as Clostridium perfringens, Ruminococcus gnavus, and Klebsiella pneumoniae, but also beneficial species, such as Faecalibacterium prausnitzii. The microbiomes of antibiotic-responsive patients were dominated by facultative anaerobic genera (Escherichia, Enterococcus, and Streptococcus), with multiple ciprofloxacin-resistance mutations in drug target genes and confirmed drug resistance. However, these strains had lower potential for virulence and did not induce secretion of inflammatory cytokines by epithelial cells. After antibiotic cessation, patients had an abrupt shift in microbiome composition, with blooms of oral and disease-associated bacteria. In addition, antibiotic treatment enriched for strains that acquired multidrug resistance loci, encoding enzymes that confer resistance to nonrelated antibiotics, including extended-spectrum beta-lactamases.

CONCLUSIONS: The efficacy of antibiotic treatment of pouchitis might be attributed to the establishment of an antibiotic-resistant microbiome with low inflammatory potential. This microbiome might provide resistance against colonization by bacteria that promote inflammation. To avoid progression to antibiotic-dependent disease and its consequences, strategies such as short-term alternating antibiotics and nutrition- and microbiome-based interventions should be considered.}, } @article {pmid31605240, year = {2019}, author = {Kayser, BD and Prifti, E and Lhomme, M and Belda, E and Dao, MC and Aron-Wisnewsky, J and , and Kontush, A and Zucker, JD and Rizkalla, SW and Dugail, I and Clément, K}, title = {Elevated serum ceramides are linked with obesity-associated gut dysbiosis and impaired glucose metabolism.}, journal = {Metabolomics : Official journal of the Metabolomic Society}, volume = {15}, number = {11}, pages = {140}, pmid = {31605240}, issn = {1573-3890}, support = {T32 HL130357/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Ceramides/*blood/metabolism ; Chromatography, High Pressure Liquid ; Cross-Sectional Studies ; Dysbiosis/*blood/metabolism ; Female ; Gastrointestinal Microbiome ; Glucose/*metabolism ; Humans ; Male ; *Metabolomics ; Middle Aged ; Obesity/*blood/metabolism ; Retrospective Studies ; Sphingolipids/blood/metabolism ; Tandem Mass Spectrometry ; }, abstract = {INTRODUCTION: Low gut microbiome richness is associated with dyslipidemia and insulin resistance, and ceramides and other sphingolipids are implicated in the development of diabetes.

OBJECTIVES: Determine whether circulating sphingolipids, particularly ceramides, are associated with alterations in the gut microbiome among obese patients with increased diabetes risk.

METHODS: This was a cross-sectional and longitudinal retrospective analysis of a dietary/weight loss intervention. Fasted serum was collected from 49 participants (41 women) and analyzed by HPLC-MS/MS to quantify 45 sphingolipids. Shotgun metagenomic sequencing of stool was performed to profile the gut microbiome.

RESULTS: Confirming the link to deteriorated glucose homeostasis, serum ceramides were positively correlated with fasting glucose, but inversely correlated with fasting and OGTT-derived measures of insulin sensitivity and β-cell function. Significant associations with gut dysbiosis were demonstrated, with SM and ceramides being inversely correlated with gene richness. Ceramides with fatty acid chain lengths of 20-24 carbons were the most associated with low richness. Diet-induced weight loss, which improved gene richness, decreased most sphingolipids. Thirty-one MGS, mostly corresponding to unidentified bacteria species, were inversely correlated with ceramides, including a number of Bifidobacterium and Methanobrevibacter smithii. Higher ceramide levels were also associated with increased metagenomic modules for lipopolysaccharide synthesis and flagellan synthesis, two pathogen-associated molecular patterns, and decreased enrichment of genes involved in methanogenesis and bile acid metabolism.

CONCLUSION: This study identifies an association between gut microbiota richness, ceramides, and diabetes risk in overweight/obese humans, and suggests that the gut microbiota may contribute to dysregulation of lipid metabolism in metabolic disorders.}, } @article {pmid31604942, year = {2019}, author = {Kaehler, BD and Bokulich, NA and McDonald, D and Knight, R and Caporaso, JG and Huttley, GA}, title = {Species abundance information improves sequence taxonomy classification accuracy.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4643}, pmid = {31604942}, issn = {2041-1723}, support = {P30 MH062512/MH/NIMH NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Classification/methods ; Computational Biology ; Metagenomics/methods ; Microbiota/*genetics ; *Phylogeny ; Population Density ; Software ; }, abstract = {Popular naive Bayes taxonomic classifiers for amplicon sequences assume that all species in the reference database are equally likely to be observed. We demonstrate that classification accuracy degrades linearly with the degree to which that assumption is violated, and in practice it is always violated. By incorporating environment-specific taxonomic abundance information, we demonstrate a significant increase in the species-level classification accuracy across common sample types. At the species level, overall average error rates decline from 25% to 14%, which is favourably comparable to the error rates that existing classifiers achieve at the genus level (16%). Our findings indicate that for most practical purposes, the assumption that reference species are equally likely to be observed is untenable. q2-clawback provides a straightforward alternative for samples from common environments.}, } @article {pmid31604287, year = {2019}, author = {Cohen, J and Pennisi, E}, title = {DNA pushes back the microbiome frontier.}, journal = {Science (New York, N.Y.)}, volume = {366}, number = {6461}, pages = {23}, doi = {10.1126/science.366.6461.23}, pmid = {31604287}, issn = {1095-9203}, mesh = {Algorithms ; Bacteria/genetics/*growth & development/isolation & purification ; DNA, Bacterial/*genetics ; Humans ; *Metagenome ; *Microbiota ; Mouth/microbiology ; Polyketides/*metabolism ; }, } @article {pmid31602443, year = {2019}, author = {Li, Q and Chen, H and Zhang, M and Wu, T and Liu, R}, title = {Altered short chain fatty acid profiles induced by dietary fiber intervention regulate AMPK levels and intestinal homeostasis.}, journal = {Food & function}, volume = {10}, number = {11}, pages = {7174-7187}, doi = {10.1039/c9fo01465a}, pmid = {31602443}, issn = {2042-650X}, mesh = {AMP-Activated Protein Kinases/genetics/*metabolism ; Animals ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Dietary Fiber/*metabolism ; Fatty Acids, Volatile/chemistry/*metabolism ; Female ; *Gastrointestinal Microbiome ; Homeostasis ; Intestinal Mucosa/enzymology/*metabolism/microbiology ; Male ; Methylamines/blood ; Mice, Inbred C57BL ; Triglycerides/blood ; }, abstract = {The objective of this study was to investigate the effects of dietary intervention on intestinal microbiota-mediated change in short chain fatty acid (SCFA) profile and intestinal homeostasis. Sequencing of the 16S rDNA of gut bacteria, metagenomics, intestinal epithelial transcriptomics, and metabonomics were conducted. Results showed that the dietary interventions altered the microbiota composition of cecal digesta, microbiota-mediated metabolism, and the gene expression profile in intestinal epithelial cells. Compared with red meat-diet-fed mice, fiber-diet-fed mice presented a shift in the gut microbiome toward increased production of butanoate, which was accompanied by up-regulation of microbiota- and AMP-activated protein kinase (AMPK)-dependent gene expression and decrease in serum concentrations of trimethylamine N-oxide (TMAO), triglyceride (TG) and glucose (GLU). The results suggested a new regulatory mechanism via which butanoate and AMPK activation contributed to intestinal integrity and homeostasis by affecting metabolism, intestinal barrier function and transporter expression.}, } @article {pmid31601676, year = {2019}, author = {Moeller, JB and Leonardi, I and Schlosser, A and Flamar, AL and Bessman, NJ and Putzel, GG and Thomsen, T and Hammond, M and Jepsen, CS and Skjødt, K and Füchtbauer, EM and Farber, DL and Sorensen, GL and Iliev, ID and Holmskov, U and Artis, D}, title = {Modulation of the fungal mycobiome is regulated by the chitin-binding receptor FIBCD1.}, journal = {The Journal of experimental medicine}, volume = {216}, number = {12}, pages = {2689-2700}, pmid = {31601676}, issn = {1540-9538}, support = {R01 AI074878/AI/NIAID NIH HHS/United States ; R01 AI095466/AI/NIAID NIH HHS/United States ; U01 AI095608/AI/NIAID NIH HHS/United States ; R56 AI137157/AI/NIAID NIH HHS/United States ; R01 DK113136/DK/NIDDK NIH HHS/United States ; F32 AI124517/AI/NIAID NIH HHS/United States ; R01 AI102942/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Chitin/metabolism ; DNA, Ribosomal Spacer ; Disease Models, Animal ; Enteritis/etiology/metabolism/pathology ; Fungi/*physiology ; Gastrointestinal Microbiome ; Gene Expression ; Humans ; Intestinal Mucosa/metabolism/microbiology/pathology ; Metagenomics ; Mice ; Mice, Transgenic ; *Microbial Interactions ; *Mycobiome ; Protein Binding ; RNA, Ribosomal, 16S ; Receptors, Cell Surface/*metabolism ; }, abstract = {Host-microbiota interactions are critical in regulating mammalian health and disease. In addition to bacteria, parasites, and viruses, beneficial communities of fungi (the mycobiome) are important modulators of immune- and tissue-homeostasis. Chitin is a major component of the fungal cell wall, and fibrinogen C containing domain 1 (FIBCD1) is a chitin-binding protein; however, the role of this molecule in influencing host-mycobiome interactions in vivo has never been examined. Here, we identify direct binding of FIBCD1 to intestinal-derived fungi and demonstrate that epithelial-specific expression of FIBCD1 results in significantly reduced fungal colonization and amelioration of fungal-driven intestinal inflammation. Collectively, these results identify FIBCD1 as a previously unrecognized microbial pattern recognition receptor through which intestinal epithelial cells can recognize and control fungal colonization, limit fungal dysbiosis, and dampen intestinal inflammation.}, } @article {pmid31601060, year = {2019}, author = {Reddy, KE and Kim, HR and Jeong, JY and So, KM and Lee, S and Ji, SY and Kim, M and Lee, HJ and Lee, S and Kim, KH and Kim, M}, title = {Impact of Breed on the Fecal Microbiome of Dogs under the Same Dietary Condition.}, journal = {Journal of microbiology and biotechnology}, volume = {29}, number = {12}, pages = {1947-1956}, doi = {10.4014/jmb.1906.06048}, pmid = {31601060}, issn = {1738-8872}, mesh = {Animal Feed ; Animals ; Bacteria/classification/genetics/isolation & purification ; Body Weight ; DNA, Bacterial/analysis ; *Diet ; Dogs/*microbiology ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Male ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {The gut microbiome influences the health and well-being of dogs. However, little is known about the impact of breed on the fecal microbiome composition in dogs. Therefore, we aimed to investigate the differences in the fecal microbiome in three breeds of dog fed and housed under the same conditions, namely eight Maltese (8.0 ± 0.1 years), eight Miniature Schnauzer (8.0 ± 0.0 years), and nine Poodle dogs (8.0 ± 0.0 years). Fresh fecal samples were collected from the dogs and used to extract metagenomic DNA. The composition of the fecal microbiome was evaluated by 16S rRNA gene amplicon sequencing on the MiSeq platform. A total of 840,501 sequences were obtained from the 25 fecal samples and classified as Firmicutes (32.3-97.3% of the total sequences), Bacteroidetes (0.1-62.6%), Actinobacteria (0.2-14.7%), Fusobacteria (0.0-5.7%), and Proteobacteria (0.0-5.1%). The relative abundance of Firmicutes was significantly lower in the Maltese dog breed than that in the other two breeds, while that of Fusobacteria was significantly higher in the Maltese than in the Miniature Schnauzer breed. At the genus level, the relative abundance of Streptococcus, Fusobacterium, Turicibacter, Succinivibrio, and Anaerobiospirillum differed significantly among the three dog breeds. These genera had no correlation with age, diet, sex, body weight, vaccination history, or parasite protection history. Within a breed, some of these genera had a correlation with at least one blood chemistry value. This study indicates that the composition of the fecal microbiome in dogs is affected by breed.}, } @article {pmid31601001, year = {2019}, author = {Ali, NABM and Mac Aogáin, M and Morales, RF and Tiew, PY and Chotirmall, SH}, title = {Optimisation and Benchmarking of Targeted Amplicon Sequencing for Mycobiome Analysis of Respiratory Specimens.}, journal = {International journal of molecular sciences}, volume = {20}, number = {20}, pages = {}, pmid = {31601001}, issn = {1422-0067}, support = {Clinician-Scientist Individual Research Grant (MOH-000141)//Singapore Ministry of Health's National Medical Research Council/ ; Research Training Fellowship (NMRC/Fellowship/0049/2017)//Singapore Ministry of Health's National Medical Research Council/ ; Singapore Ministry of Education Academic Research Fund Tier 1 (2016-T1-001-050)//Singapore Ministry of Education/ ; NTU Integrated Medical, Biological and Environmental Life Sciences (NIMBELS) [NIM/03/2018]//Nanyang Technological University/ ; }, mesh = {Benchmarking ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fungi/genetics ; Humans ; *Metagenome ; *Metagenomics/methods ; *Mycobiome ; Respiratory Mucosa/*microbiology ; }, abstract = {(1) Background: Firm consensus has yet to be established in relation to taxonomic classification and primer choice in targeted amplicon sequencing of the mycobiome. While the nuclear ribosomal internal transcribed spacer (ITS) region are recognized as the formal fungal taxonomic barcode, appraisal of different ITS sub-regions and the influence of DNA extraction methods have not been comprehensively undertaken using human respiratory specimens. (2) Methods: We performed ITS analysis of respiratory (sputum) samples by assessing (a) the effect of alternate DNA extraction techniques and (b) an evaluation of four different ITS primer pairs (ITS1F and ITS2; ITS1-30F and ITS1-217R; gITS7ngs and ITS4ng; and Fseq and Rseq) on the mycobiome profiles generated for mock fungal communities and their respective clinical (airway) specimens. (3) Results: Primer pairs varied in their resulting ITS mycobiome profiles, suggesting that particular pairs may be more relevant for analysis of respiratory samples compared to others. Assessment of DNA extraction methods highlighted lower final DNA concentrations achieved by mechanical disruption compared to enzymatic lysis. However, despite lower yields, DNA liberated by mechanical lysis more readily yielded ITS bands with highest success in combination with the Fseq and Rseq primers. (4) Conclusion: Choice of extraction method, primers used, and sequencing approach are all important considerations in sequencing the mycobiome and should be tailored to sample type. A standardization of approach to mycobiome studies using respiratory specimens will permit more reliable comparisons between studies and improve our understanding of the role of fungi in the human airway.}, } @article {pmid31600863, year = {2020}, author = {Li, Y and Tremblay, J and Bainard, LD and Cade-Menun, B and Hamel, C}, title = {Long-term effects of nitrogen and phosphorus fertilization on soil microbial community structure and function under continuous wheat production.}, journal = {Environmental microbiology}, volume = {22}, number = {3}, pages = {1066-1088}, doi = {10.1111/1462-2920.14824}, pmid = {31600863}, issn = {1462-2920}, support = {PSS-1555//Agriculture and Agri-Food Canada/International ; //Natural Science and Engineering Research Council of Canada/International ; }, mesh = {Archaea/drug effects/physiology ; Bacterial Physiological Phenomena/drug effects ; Biodiversity ; Fertilizers ; Fungi/drug effects/physiology ; Longitudinal Studies ; Microbiota/*drug effects ; Nitrogen/*pharmacology ; Phosphorus/*pharmacology ; Soil/chemistry ; *Soil Microbiology ; Triticum/growth & development/*microbiology ; }, abstract = {Soil microorganisms play a critical role in the biosphere, and the influence of cropland fertilization on the evolution of soil as a living entity is being actively documented. In this study, we used a shotgun metagenomics approach to globally expose the effects of 50-year N and P fertilization of wheat on soil microbial community structure and function, and their potential involvement in overall N cycling. Nitrogen (N) fertilization increased alpha diversity in archaea and fungi while reducing it in bacteria. Beta diversity of archaea, bacteria and fungi, as well as soil function, were also mainly driven by N fertilization. The abundance of archaea was negatively impacted by N fertilization while bacterial and fungal abundance was increased. The responses of N metabolism-related genes to fertilization differed in archaea, bacteria and fungi. All archaeal N metabolic processes were decreased by N fertilization, while denitrification, assimilatory nitrate reduction and organic-N metabolism were highly increased by N fertilization in bacteria. Nitrate assimilation was the main contribution of fungi to N cycling. Thaumarchaeota and Halobacteria in archaea; Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria in bacteria; and Sordariomycetes in fungi participated dominantly and widely in soil N metabolic processes.}, } @article {pmid31600845, year = {2020}, author = {Zeng, Y and Chen, S and Fu, Y and Wu, W and Chen, T and Chen, J and Yang, B and Ou, Q}, title = {Gut microbiota dysbiosis in patients with hepatitis B virus-induced chronic liver disease covering chronic hepatitis, liver cirrhosis and hepatocellular carcinoma.}, journal = {Journal of viral hepatitis}, volume = {27}, number = {2}, pages = {143-155}, doi = {10.1111/jvh.13216}, pmid = {31600845}, issn = {1365-2893}, mesh = {Adult ; Bacteria/classification ; Carcinoma, Hepatocellular/*virology ; Case-Control Studies ; Dysbiosis/etiology/*genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Hepatitis B virus/pathogenicity ; Hepatitis B, Chronic/*microbiology ; Humans ; Liver Cirrhosis/*virology ; Liver Neoplasms/*virology ; Male ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The information regarding the effect of hepatitis B virus (HBV) infection on gut microbiota and the relationship between gut microbiota dysbiosis and hepatitis B virus-induced chronic liver disease (HBVCLD) is limited. In this study, we aimed at characterizing the gut microbiota composition in the three different stages of hepatitis B virus-induced chronic liver disease patients and healthy individuals. Faecal samples and clinical data were collected from HBVCLD patients and healthy individuals. The 16S rDNA gene amplification products were sequenced. Bioinformatic analysis including alpha diversity and PICRUSt was performed. A total of 19 phyla, 43 classes, 72 orders, 126 families and 225 genera were detected. The beta-diversity showed a separate clustering of healthy controls and HBVCLD patients covering chronic hepatitis (CHB), liver cirrhosis (LC) and hepatocellular carcinoma (HCC); and gut microbiota of healthy controls was more consistent, whereas those of CHB, LC and HCC varied substantially. The abundance of Firmicutes was lower, and Bacteroidetes was higher in patients with CHB, LC and HCC than in healthy controls. Predicted metagenomics of microbial communities showed an increase in glycan biosynthesis and metabolism-related genes and lipid metabolism-related genes in HBVCLD than in healthy individuals. Our study suggested that HBVCLD is associated with gut dysbiosis, with characteristics including, a gain in potential bacteria and a loss in potential beneficial bacteria or genes. Further study of CHB, LC and HCC based on microbiota may provide a novel insight into the pathogenesis of HBVCLD as well as a novel treatment strategy.}, } @article {pmid31600503, year = {2019}, author = {Shkoporov, AN and Clooney, AG and Sutton, TDS and Ryan, FJ and Daly, KM and Nolan, JA and McDonnell, SA and Khokhlova, EV and Draper, LA and Forde, A and Guerin, E and Velayudhan, V and Ross, RP and Hill, C}, title = {The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific.}, journal = {Cell host & microbe}, volume = {26}, number = {4}, pages = {527-541.e5}, doi = {10.1016/j.chom.2019.09.009}, pmid = {31600503}, issn = {1934-6069}, mesh = {Bacteroides/isolation & purification/*virology ; Faecalibacterium/isolation & purification/*virology ; Gastrointestinal Microbiome/*genetics ; Humans ; Longitudinal Studies ; Metagenome/genetics ; Microviridae/classification/*genetics/isolation & purification ; Prevotella/isolation & purification/*virology ; Viral Load ; }, abstract = {The human gut contains a vast array of viruses, mostly bacteriophages. The majority remain uncharacterized, and their roles in shaping the gut microbiome and in impacting on human health remain poorly understood. We performed longitudinal metagenomic analysis of fecal viruses in healthy adults that reveal high temporal stability, individual specificity, and correlation with the bacterial microbiome. Using a database-independent approach that uses most of the sequencing data, we uncovered the existence of a stable, numerically predominant individual-specific persistent personal virome. Clustering of viral genomes and de novo taxonomic annotation identified several groups of crAss-like and Microviridae bacteriophages as the most stable colonizers of the human gut. CRISPR-based host prediction highlighted connections between these stable viral communities and highly predominant gut bacterial taxa such as Bacteroides, Prevotella, and Faecalibacterium. This study provides insights into the structure of the human gut virome and serves as an important baseline for hypothesis-driven research.}, } @article {pmid31597568, year = {2019}, author = {Peters, BA and Wilson, M and Moran, U and Pavlick, A and Izsak, A and Wechter, T and Weber, JS and Osman, I and Ahn, J}, title = {Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients.}, journal = {Genome medicine}, volume = {11}, number = {1}, pages = {61}, pmid = {31597568}, issn = {1756-994X}, support = {R01 CA159036/CA/NCI NIH HHS/United States ; P50 CA225450/CA/NCI NIH HHS/United States ; P30CA016087/CA/NCI NIH HHS/United States ; R01 CA164964/CA/NCI NIH HHS/United States ; P50CA225450/CA/NCI NIH HHS/United States ; R01CA164964/CA/NCI NIH HHS/United States ; }, mesh = {Aged ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Immunotherapy/*methods ; Male ; Melanoma/*genetics/immunology/*pathology/therapy ; *Metagenome ; Microbiota/*genetics ; RNA, Ribosomal, 16S ; *Transcriptome ; }, abstract = {BACKGROUND: Recent evidence suggests that immunotherapy efficacy in melanoma is modulated by gut microbiota. Few studies have examined this phenomenon in humans, and none have incorporated metatranscriptomics, important for determining expression of metagenomic functions in the microbial community.

METHODS: In melanoma patients undergoing immunotherapy, gut microbiome was characterized in pre-treatment stool using 16S rRNA gene and shotgun metagenome sequencing (n = 27). Transcriptional expression of metagenomic pathways was confirmed with metatranscriptome sequencing in a subset of 17. We examined associations of taxa and metagenomic pathways with progression-free survival (PFS) using 500 × 10-fold cross-validated elastic-net penalized Cox regression.

RESULTS: Higher microbial community richness was associated with longer PFS in 16S and shotgun data (p < 0.05). Clustering based on overall microbiome composition divided patients into three groups with differing PFS; the low-risk group had 99% lower risk of progression than the high-risk group at any time during follow-up (p = 0.002). Among the species selected in regression, abundance of Bacteroides ovatus, Bacteroides dorei, Bacteroides massiliensis, Ruminococcus gnavus, and Blautia producta were related to shorter PFS, and Faecalibacterium prausnitzii, Coprococcus eutactus, Prevotella stercorea, Streptococcus sanguinis, Streptococcus anginosus, and Lachnospiraceae bacterium 3 1 46FAA to longer PFS. Metagenomic functions related to PFS that had correlated metatranscriptomic expression included risk-associated pathways of L-rhamnose degradation, guanosine nucleotide biosynthesis, and B vitamin biosynthesis.

CONCLUSIONS: This work adds to the growing evidence that gut microbiota are related to immunotherapy outcomes, and identifies, for the first time, transcriptionally expressed metagenomic pathways related to PFS. Further research is warranted on microbial therapeutic targets to improve immunotherapy outcomes.}, } @article {pmid31597472, year = {2020}, author = {Dreisbach, C and Prescott, S and Alhusen, J}, title = {Influence of Maternal Prepregnancy Obesity and Excessive Gestational Weight Gain on Maternal and Child Gastrointestinal Microbiome Composition: A Systematic Review.}, journal = {Biological research for nursing}, volume = {22}, number = {1}, pages = {114-125}, pmid = {31597472}, issn = {1552-4175}, support = {F31 NR017821/NR/NINR NIH HHS/United States ; }, mesh = {Body Mass Index ; Child ; Female ; *Gastrointestinal Microbiome ; *Gestational Weight Gain ; Humans ; Infant ; Obesity, Maternal/*complications ; Pediatric Obesity/*etiology ; Pregnancy ; }, abstract = {BACKGROUND: Maternal obesity is a well-known risk factor for significant obstetric and neonatal complications. The influence of the gastrointestinal microbiome in the setting of maternal obesity during pregnancy is less understood. The purpose of this systematic review is to synthesize the literature on the relationships between maternal obesity and excessive gestational weight gain (EGWG) and the composition of maternal and child gastrointestinal microbiomes.

METHOD: We searched CINHAL, OVID Medline, Web of Science, and PubMed for relevant literature using medical subject heading terms related to obesity, pregnancy, and the gastrointestinal microbiome. We assessed 249 articles for potential inclusion using the preferred reporting items for systematic review and meta-analyses framework and deemed 11 articles as relevant for this review.

RESULTS: Maternal obesity was associated with significant microbial changes in both maternal and infant fecal microbiome biospecimens including increases in Bacteroidetes, Firmicutes, and the Actinobacteria phyla and decreases in Bifidobacteria. However, inconsistencies in uniform taxonomic results across all studies mean that evidence of specific microbial associations with obesity and EGWG is inconclusive.

CONCLUSION: Our findings suggest that both maternal and child gastrointestinal microbiome composition is altered in the setting of maternal obesity and EGWG during pregnancy. Future microbiome studies should concentrate on the investigation of metagenomic sequencing to elucidate microbial function rather than solely taxonomic composition. More diverse populations of mothers should be sampled to address health disparities and adverse outcomes of underrepresented populations. Finally, analytic pipelines should be standardized across studies to aid in reproducibility.}, } @article {pmid31597208, year = {2020}, author = {Berman, HL and McLaren, MR and Callahan, BJ}, title = {Understanding and interpreting community sequencing measurements of the vaginal microbiome.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {127}, number = {2}, pages = {139-146}, pmid = {31597208}, issn = {1471-0528}, support = {R35 GM133745/GM/NIGMS NIH HHS/United States ; }, mesh = {Female ; Humans ; Microbiota/*genetics ; RNA, Ribosomal, 16S ; Reproducibility of Results ; Sequence Analysis, DNA ; Vagina/*microbiology ; }, abstract = {Community-wide high-throughput sequencing has transformed the study of the vaginal microbiome, and clinical applications are on the horizon. Here we outline the three main community sequencing methods: (1) amplicon sequencing, (2) shotgun metagenomic sequencing, and (3) metatranscriptomic sequencing. We discuss the advantages and limitations of community sequencing generally, and the unique strengths and weaknesses of each method. We briefly review the contributions of community sequencing to vaginal microbiome research and practice. We develop suggestions for critically interpreting research results and potential clinical applications based on community sequencing of the vaginal microbiome. TWEETABLE ABSTRACT: We review the advantages and limitations of amplicon sequencing, metagenomics, and metatranscriptomics methods for the study of the vaginal microbiome.}, } @article {pmid31596877, year = {2019}, author = {Allegrini, M and Gomez, EDV and Smalla, K and Zabaloy, MC}, title = {Suppression treatment differentially influences the microbial community and the occurrence of broad host range plasmids in the rhizosphere of the model cover crop Avena sativa L.}, journal = {PloS one}, volume = {14}, number = {10}, pages = {e0223600}, pmid = {31596877}, issn = {1932-6203}, mesh = {Archaea/genetics ; Avena/drug effects/*microbiology ; DNA Barcoding, Taxonomic ; Glycerol/*analogs & derivatives/pharmacology ; Glycine/*analogs & derivatives/pharmacology ; Herbicides/*pharmacology ; Mesorhizobium/genetics ; *Metagenome ; Metagenomics ; Microbiota/*drug effects/genetics ; *Rhizosphere ; }, abstract = {Cover crop suppression with glyphosate-based herbicides (GBHs) represents a common agricultural practice. The objective of this study was to compare rhizospheric microbial communities of A. sativa plants treated with a GBH relative to the mechanical suppression (mowing) in order to assess their differences and the potential implications for soil processes. Samples were obtained at 4, 10, 17 and 26 days post-suppression. Soil catabolic profiling and DNA-based methods were applied. At 26 days, higher respiration responses and functional diversity indices (Shannon index and catabolic evenness) were observed under glyphosate suppression and a neat separation of catabolic profiles was detected in multivariate analysis. Sarcosine and Tween 20 showed the highest contribution to this separation. Metabarcoding revealed a non-significant effect of suppression method on either alpha-diversity metrics or beta-diversity. Conversely, differences were detected in the relative abundance of specific bacterial taxa. Mesorhizobium sequences were detected in higher relative abundance in glyphosate-treated plants at the end of the experiment while the opposite trend was observed for Gaiella. Quantitative PCR of amoA gene from ammonia-oxidizing archaea showed a lower abundance under GBH suppression again at 26 days, while ammonia-oxidizing bacteria remained lower at all sampling times. Broad host range plasmids IncP-1β and IncP-1ε were exclusively detected in the rhizosphere of glyphosate-treated plants at 10 days and at 26 days, respectively. Overall, our study demonstrates differential effects of suppression methods on the abundance of specific bacterial taxa, on the physiology and mobile genetic elements of microbial communities while no differences were detected in taxonomic diversity.}, } @article {pmid31596250, year = {2020}, author = {Kaufman, JH and Elkins, CA and Davis, M and Weis, AM and Huang, BC and Mammel, MK and Patel, IR and Beck, KL and Edlund, S and Chambliss, D and Douglas, J and Bianco, S and Kunitomi, M and Weimer, BC}, title = {Insular Microbiogeography: Three Pathogens as Exemplars.}, journal = {Current issues in molecular biology}, volume = {36}, number = {}, pages = {89-108}, doi = {10.21775/cimb.036.089}, pmid = {31596250}, issn = {1467-3045}, mesh = {Bacteria/classification/*genetics/pathogenicity ; Databases, Genetic ; Ecology ; Evolution, Molecular ; Genetic Variation ; Genome, Bacterial ; Metagenome ; Microbiota/*genetics ; *Phylogeny ; Phylogeography/methods ; Whole Genome Sequencing ; }, abstract = {Traditional taxonomy in biology assumes that life is organized in a simple tree. Attempts to classify microorganisms in this way in the genomics era led microbiologists to look for finite sets of 'core' genes that uniquely group taxa as clades in the tree. However, the diversity revealed by large-scale whole genome sequencing is calling into question the long-held model of a hierarchical tree of life, which leads to questioning of the definition of a species. Large-scale studies of microbial genome diversity reveal that the cumulative number of new genes discovered increases with the number of genomes studied as a power law and subsequently leads to the lack of evidence for a unique core genome within closely related organisms. Sampling 'enough' new genomes leads to the discovery of a replacement or alternative to any gene. This power law behaviour points to an underlying self-organizing critical process that may be guided by mutation and niche selection. Microbes in any particular niche exist within a local web of organism interdependence known as the microbiome. The same mechanism that underpins the macro-ecological scaling first observed by MacArthur and Wilson also applies to microbial communities. Recent metagenomic studies of a food microbiome demonstrate the diverse distribution of community members, but also genotypes for a single species within a more complex community. Collectively, these results suggest that traditional taxonomic classification of bacteria could be replaced with a quasispecies model. This model is commonly accepted in virology and better describes the diversity and dynamic exchange of genes that also hold true for bacteria. This model will enable microbiologists to conduct population-scale studies to describe microbial behaviour, as opposed to a single isolate as a representative.}, } @article {pmid31595646, year = {2020}, author = {Strazzulli, A and Cobucci-Ponzano, B and Iacono, R and Giglio, R and Maurelli, L and Curci, N and Schiano-di-Cola, C and Santangelo, A and Contursi, P and Lombard, V and Henrissat, B and Lauro, FM and Fontes, CMGA and Moracci, M}, title = {Discovery of hyperstable carbohydrate-active enzymes through metagenomics of extreme environments.}, journal = {The FEBS journal}, volume = {287}, number = {6}, pages = {1116-1137}, doi = {10.1111/febs.15080}, pmid = {31595646}, issn = {1742-4658}, mesh = {Bacterial Proteins/*genetics/metabolism ; Crenarchaeota/enzymology ; *Extreme Environments ; Glucan 1,3-beta-Glucosidase/*genetics/metabolism ; Hydrogen-Ion Concentration ; *Metagenomics ; Temperature ; beta-Mannosidase/*genetics/metabolism ; }, abstract = {The enzymes from hyperthermophilic microorganisms populating volcanic sites represent interesting cases of protein adaptation and biotransformations under conditions where conventional enzymes quickly denature. The difficulties in cultivating extremophiles severely limit access to this class of biocatalysts. To circumvent this problem, we embarked on the exploration of the biodiversity of the solfatara Pisciarelli, Agnano (Naples, Italy), to discover hyperthermophilic carbohydrate-active enzymes (CAZymes) and to characterize the entire set of such enzymes in this environment (CAZome). Here, we report the results of the metagenomic analysis of two mud/water pools that greatly differ in both temperature and pH (T = 85 °C and pH 5.5; T = 92 °C and pH 1.5, for Pool1 and Pool2, respectively). DNA deep sequencing and following in silico analysis led to 14 934 and 17 652 complete ORFs in Pool1 and Pool2, respectively. They exclusively belonged to archaeal cells and viruses with great genera variance within the phylum Crenarchaeota, which reflected the difference in temperature and pH of the two Pools. Surprisingly, 30% and 62% of all of the reads obtained from Pool1 and 2, respectively, had no match in nucleotide databanks. Genes associated with carbohydrate metabolism were 15% and 16% of the total in the two Pools, with 278 and 308 putative CAZymes in Pool1 and 2, corresponding to ~ 2.0% of all ORFs. Biochemical characterization of two CAZymes of a previously unknown archaeon revealed a novel subfamily GH5_19 β-mannanase/β-1,3-glucanase whose hemicellulose specificity correlates with the vegetation surrounding the sampling site, and a novel NAD[+] -dependent GH109 with a previously unreported β-N-acetylglucosaminide/β-glucoside specificity. DATABASES: The sequencing reads are available in the NCBI Sequence Read Archive (SRA) database under the accession numbers SRR7545549 (Pool1) and SRR7545550 (Pool2). The sequences of GH5_Pool2 and GH109_Pool2 are available in GenBank database under the accession numbers MK869723 and MK86972, respectively. The environmental data relative to Pool1 and Pool2 (NCBI BioProject PRJNA481947) are available in the Biosamples database under the accession numbers SAMN09692669 (Pool1) and SAMN09692670 (Pool2).}, } @article {pmid31592756, year = {2019}, author = {Millán-Aguiñaga, N and Soldatou, S and Brozio, S and Munnoch, JT and Howe, J and Hoskisson, PA and Duncan, KR}, title = {Awakening ancient polar Actinobacteria: diversity, evolution and specialized metabolite potential.}, journal = {Microbiology (Reading, England)}, volume = {165}, number = {11}, pages = {1169-1180}, doi = {10.1099/mic.0.000845}, pmid = {31592756}, issn = {1465-2080}, mesh = {Actinobacteria/classification/*genetics/isolation & purification/*metabolism ; Antarctic Regions ; Arctic Regions ; Biodiversity ; Biological Products/classification/metabolism ; DNA, Bacterial/genetics ; Evolution, Molecular ; Geologic Sediments/microbiology ; Metagenomics ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/chemistry ; }, abstract = {Polar and subpolar ecosystems are highly vulnerable to global climate change with consequences for biodiversity and community composition. Bacteria are directly impacted by future environmental change and it is therefore essential to have a better understanding of microbial communities in fluctuating ecosystems. Exploration of Polar environments, specifically sediments, represents an exciting opportunity to uncover bacterial and chemical diversity and link this to ecosystem and evolutionary parameters. In terms of specialized metabolite production, the bacterial order Actinomycetales, within the phylum Actinobacteria are unsurpassed, producing 10 000 specialized metabolites accounting for over 45 % of all bioactive microbial metabolites. A selective isolation approach focused on spore-forming Actinobacteria of 12 sediment cores from the Antarctic and sub-Arctic generated a culture collection of 50 strains. This consisted of 39 strains belonging to rare Actinomycetales genera including Microbacterium, Rhodococcus and Pseudonocardia. This study used a combination of nanopore sequencing and molecular networking to explore the community composition, culturable bacterial diversity, evolutionary relatedness and specialized metabolite potential of these strains. Metagenomic analyses using MinION sequencing was able to detect the phylum Actinobacteria across polar sediment cores at an average of 13 % of the total bacterial reads. The resulting molecular network consisted of 1652 parent ions and the lack of known metabolite identification supports the argument that Polar bacteria are likely to produce previously unreported chemistry.}, } @article {pmid31592688, year = {2019}, author = {Colman, DR and Lindsay, MR and Amenabar, MJ and Boyd, ES}, title = {The Intersection of Geology, Geochemistry, and Microbiology in Continental Hydrothermal Systems.}, journal = {Astrobiology}, volume = {19}, number = {12}, pages = {1505-1522}, doi = {10.1089/ast.2018.2016}, pmid = {31592688}, issn = {1557-8070}, mesh = {Bacterial Proteins/genetics/metabolism ; Biological Evolution ; Extremophiles/*isolation & purification/physiology ; Geologic Sediments/analysis/chemistry/*microbiology ; Hot Springs/chemistry/*microbiology ; Hot Temperature/adverse effects ; Hydrogen-Ion Concentration ; *Metagenome ; Microbiota/*physiology ; Oxidation-Reduction ; Sulfur/metabolism ; Thermodynamics ; Water Microbiology ; }, abstract = {Decompressional boiling of ascending hydrothermal waters and separation into a vapor (gas) and a liquid phase drive extensive variation in the geochemical composition of hot spring waters. Yet little is known of how the process of phase separation influences the distribution of microbial metabolisms in springs. Here, we determined the variation in protein coding genes in 51 metagenomes from chemosynthetic hot spring communities that span geochemical gradients in Yellowstone National Park. The 51 metagenomes could be divided into 5 distinct groups that correspond to low and high temperatures and acidic and circumneutral/alkaline springs. A fifth group primarily comprised metagenomes from springs with moderate acidity and that are influenced by elevated volcanic gas input. Protein homologs putatively involved in the oxidation of sulfur compounds, a process that leads to acidification of spring waters, in addition to those involved in the reduction of sulfur compounds were enriched in metagenomes from acidic springs sourced by vapor phase gases. Metagenomes from springs with evidence for elevated volcanic gas input were enriched in protein homologs putatively involved in oxidation of those gases, including hydrogen and methane. Finally, metagenomes from circumneutral/alkaline springs sourced by liquid phase waters were enriched in protein homologs putatively involved in heterotrophy and respiration of oxidized nitrogen compounds and oxygen. These results indicate that the geological process of phase separation shapes the ecology of thermophilic communities through its influence on the availability of nutrients in the form of gases, solutes, and minerals. Microbial acidification of hot spring waters further influences the kinetic and thermodynamic stabilities of nutrients and their bioavailability. These data therefore provide an important framework to understand how geological processes have shaped the evolutionary history of chemosynthetic thermophiles and how these organisms, in turn, have shaped their geochemical environments.}, } @article {pmid31589561, year = {2019}, author = {Salah, M and Azab, M and Ramadan, A and Hanora, A}, title = {New Insights on Obesity and Diabetes from Gut Microbiome Alterations in Egyptian Adults.}, journal = {Omics : a journal of integrative biology}, volume = {23}, number = {10}, pages = {477-485}, doi = {10.1089/omi.2019.0063}, pmid = {31589561}, issn = {1557-8100}, mesh = {Adult ; Age Factors ; Biomarkers ; DNA Barcoding, Taxonomic ; Diabetes Mellitus/*epidemiology/*etiology ; Egypt ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics/methods ; Middle Aged ; Obesity/*epidemiology/*etiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Obesity and diabetes are reaching epidemic levels globally. Metagenomics and microbiome science have recently emerged as new tools for studying common complex human diseases. We report in this study notable differences in gut microbiome in adult patients with obesity and diabetes in Egypt. The experimental design was based on comparisons of four study groups: (1) Controls (C) with a normal body mass index, without obesity or diabetes, (2) Obese adults (O) without diabetes, (3) adults with diabetes (D) who are not obese, and (4) Adults who are both obese and diabetic (OD). In a total study sample of 60 participants, we sequenced the 16S ribosomal RNA (rRNA) gene using the Illumina MiSeq platform. Alpha diversity analysis revealed greater diversity in bacterial communities of (D) than controls. Phylum-level analysis identified a trend for overrepresentation of Bacteroidetes (p < 0.07) in (O) and (D) than controls. The ratio of Firmicutes/Bacteroidetes (F/B) displayed a remarkable increase in (OD) than controls. At genus level, Faecalibacterium (p < 0.05) and Akkermansia (p < 0.001) distinguished (O) from controls, while Fusobacterium (p < 0.001) and Bacteroides (p < 0.001) was significantly more abundant in (OD) compared with D. Surprisingly, isoquinoline, quinone and ubiquinone alkaloid biosynthesis were overrepresented in controls compared with other three study groups. Presumably, the latter observation might potentially suggest an antihyperglycemic activity of the gut microbiota. In conclusion, the health state of the adults in our study defined the composition of the gut microbiota. Moreover, obesity and diabetes were associated with remarkably enriched populations of Firmicutes and Bacteroidetes. The abundance of Fusobacterium is worth further research and exploration as a candidate biomarker for prediabetes especially in obese individuals. The potential antihyperglycemic activity of the gut microbiota is also noteworthy for future studies in other world populations.}, } @article {pmid31589310, year = {2019}, author = {Ye, L and Das, P and Li, P and Ji, B and Nielsen, J}, title = {Carbohydrate active enzymes are affected by diet transition from milk to solid food in infant gut microbiota.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {11}, pages = {}, doi = {10.1093/femsec/fiz159}, pmid = {31589310}, issn = {1574-6941}, mesh = {Adult ; Animals ; *Carbohydrate Metabolism ; *Diet ; Enzymes/*metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; *Infant Food ; Male ; Metagenomics ; Milk, Human ; Polysaccharides/metabolism ; }, abstract = {Infants experience a dramatic change in their food in the first year after birth when they shift from breast milk to solid food. This results in a large change in presence of indigestible polysaccharides, a primary energy resource of gut microbes. How the gut microbiota adapts to this dietary shift has not been well examined. Here, by using metagenomics data, we studied carbohydrate-active enzymes (CAZymes) of gut microbiota, which are essential enzymes catalyzing the breakdown of polysaccharides, during this dietary shift. We developed a new approach to categorize CAZyme families by food intake and found CAZyme families associated with milk or solid food. We also found CAZymes with most abundance in 12 months infants that are not associated with solid food or milk but may be related to modulating carbohydrates in the mucus. Additionally, the abundance of gut CAZymes were found to be affected by many other factors, including delivery modes and life style in adults. Taken together, our findings provide novel insights into the dynamic change of gut CAZymes in early human life and provide potential markers for food interference or gut microbiota restoration.}, } @article {pmid31588624, year = {2019}, author = {Zhao, F and Zhou, G and Liu, X and Song, S and Xu, X and Hooiveld, G and Müller, M and Liu, L and Kristiansen, K and Li, C}, title = {Dietary Protein Sources Differentially Affect the Growth of Akkermansia muciniphila and Maintenance of the Gut Mucus Barrier in Mice.}, journal = {Molecular nutrition & food research}, volume = {63}, number = {23}, pages = {e1900589}, doi = {10.1002/mnfr.201900589}, pmid = {31588624}, issn = {1613-4133}, mesh = {Akkermansia ; Animals ; Dietary Proteins/*pharmacology ; Energy Metabolism ; *Gastrointestinal Microbiome ; Male ; Mice ; Mice, Inbred C57BL ; Mucus/*metabolism ; Soybean Proteins/pharmacology ; Verrucomicrobia/*growth & development ; }, abstract = {SCOPE: The gut microbiota plays an essential role in linking diet to host health. The specific role of different dietary proteins on the gut microbiota and health is less understood. Here, the impact of proteins derived from chicken and soy on the gut microbiota and host gut barrier in C57BL/6 mice is investigated.

METHODS AND RESULTS: Specific-pathogen-free and germ-free mice are assigned to either a chicken- or a soy protein-based diet for 4 weeks. Compared with a chicken-protein-based diet, intake of a soy-protein-based diet reduces the abundance of A. muciniphila and the number of goblet cells, lowers the level of Muc2 mRNA, and decreases the thickness of the mucus layer in the colon of specific-pathogen-free mice. In germ-free mice, colonization with A. muciniphila combined with intake of a chicken-protein-based diet results in a higher expression of the Muc2 mRNA in colon, and surprisingly, an increased potential for oxidative phosphorylation in A. muciniphila compared with colonized mice fed a soy-protein-based diet.

CONCLUSION: These findings suggest possible mutually beneficial interactions between the growth and function of A. muciniphila and host mucus barrier in response to intake of a chicken-protein-based diet contrasting the intake of a soy-protein-based diet.}, } @article {pmid31587913, year = {2019}, author = {Galvão, KN and Bicalho, RC and Jeon, SJ}, title = {Symposium review: The uterine microbiome associated with the development of uterine disease in dairy cows.}, journal = {Journal of dairy science}, volume = {102}, number = {12}, pages = {11786-11797}, doi = {10.3168/jds.2019-17106}, pmid = {31587913}, issn = {1525-3198}, mesh = {Animals ; Bacteria/genetics/*isolation & purification ; Bacteroidetes/genetics/isolation & purification ; Cattle ; Cattle Diseases/*microbiology/pathology ; Dysbiosis/microbiology/veterinary ; Endometritis/microbiology/*veterinary ; Female ; Fusobacteria/genetics/isolation & purification ; *Microbiota ; Polymerase Chain Reaction ; Postpartum Period ; Uterine Diseases/microbiology/pathology/*veterinary ; Uterus/microbiology ; }, abstract = {Until 2010, our knowledge of the uterine microbiome in cows that developed uterine disease relied almost exclusively on culture-dependent studies and mostly included cows with clinical endometritis (i.e., with purulent uterine discharge). Those studies consistently found a strong positive correlation between Trueperella pyogenes and clinical endometritis, whereas other pathogens such as Escherichia coli, Fusobacterium necrophorum, Prevotella melaninogenica, and Bacteroides spp. were also commonly cocultured. In contrast, Streptococcus spp., Staphylococcus spp., and Bacillus spp. were usually isolated from healthy cows. Starting in 2010, culture-independent studies using PCR explored the microbiome of cows with metritis and clinical endometritis, and observed that E. coli was a pioneer pathogen that predisposed cows to infection with F. necrophorum, which was strongly associated with metritis, and to infection with T. pyogenes, which was strongly associated with clinical endometritis. Starting in 2011, culture-independent studies using metagenomic sequencing expanded our knowledge of the uterine microbiome. It has been shown that cows have bacteria in the uterus even before calving, they have an established uterine microbiome within 20 min of calving, and that the microbiome structure is identical between cows that develop metritis and healthy cows until 2 d postpartum, after which the bacterial structure of cows that developed metritis deviates in favor of greater relative abundance of Bacteroidetes and Fusobacteria and lesser relative abundance of Proteobacteria and Tenericutes. The shift in the uterine microbiome in cows that develop metritis is characterized by a loss of heterogeneity and a decrease in bacterial richness. At the genus level, Bacteroides, Porphyromonas, and Fusobacterium have the strongest association with metritis. At the species level, we observed that Bacteroides pyogenes, Porphyromonas levii, and Helcococcus ovis were potential emerging uterine pathogens. Finally, we have shown that the hematogenous route is a viable route of uterine infection with uterine pathogens. Herein, we propose that metritis is associated with a dysbiosis of the uterine microbiota characterized by decreased richness, and an increase in Bacteroidetes and Fusobacteria, particularly Bacteroides, Porphyromonas, and Fusobacterium.}, } @article {pmid31587490, year = {2020}, author = {O'Callaghan, JL and Turner, R and Dekker Nitert, M and Barrett, HL and Clifton, V and Pelzer, ES}, title = {Re-assessing microbiomes in the low-biomass reproductive niche.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {127}, number = {2}, pages = {147-158}, doi = {10.1111/1471-0528.15974}, pmid = {31587490}, issn = {1471-0528}, support = {//National Health and Medical Research Council Early Career Research fellowship/ ; //Mater Foundation/ ; }, mesh = {*Biomass ; Female ; Gastrointestinal Microbiome/genetics/immunology/*physiology ; Humans ; Metagenomics ; Placenta/immunology/*microbiology ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; *Reproductive Health ; Reproductive Tract Infections/*microbiology ; Sequence Analysis, DNA ; Vagina/immunology/*microbiology ; }, abstract = {The female reproductive tract represents a continuum between the vagina and the upper genital tract. New evidence from cultivation-independent studies suggests that the female upper genital tract is not sterile; however, the significance of this for reproductive health and disease remains to be elucidated fully. Further, diagnosis and treatment of infectious reproductive tract pathologies using cultivation-independent technologies represents a largely unchartered area of modern medical science. The challenge now is to design well-controlled experiments to account for the ease of contamination known to confound molecular-based studies of low-biomass niches, including the uterus and placenta. This will support robust assessment of the potential function of microorganisms, microbial metabolites, and cell-free bacterial DNA on reproductive function in health and disease. TWEETABLE ABSTRACT: Molecular microbial studies of low-biomass niches require stringent experimental controls to reveal causal relations in reproductive health and disease.}, } @article {pmid31586453, year = {2020}, author = {Cox, SR and Lindsay, JO and Fromentin, S and Stagg, AJ and McCarthy, NE and Galleron, N and Ibraim, SB and Roume, H and Levenez, F and Pons, N and Maziers, N and Lomer, MC and Ehrlich, SD and Irving, PM and Whelan, K}, title = {Effects of Low FODMAP Diet on Symptoms, Fecal Microbiome, and Markers of Inflammation in Patients With Quiescent Inflammatory Bowel Disease in a Randomized Trial.}, journal = {Gastroenterology}, volume = {158}, number = {1}, pages = {176-188.e7}, doi = {10.1053/j.gastro.2019.09.024}, pmid = {31586453}, issn = {1528-0012}, mesh = {Adult ; Bacteria/isolation & purification ; Biomarkers/analysis ; Diet, Carbohydrate-Restricted/adverse effects/*methods ; Disaccharides/adverse effects ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*immunology ; Humans ; Inflammatory Bowel Diseases/diagnosis/*diet therapy/microbiology ; Male ; Middle Aged ; Monosaccharides/adverse effects ; Quality of Life ; Severity of Illness Index ; Single-Blind Method ; Treatment Outcome ; United Kingdom ; Young Adult ; }, abstract = {BACKGROUND & AIMS: There is limited evidence that a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) reduces gut symptoms in quiescent inflammatory bowel disease (IBD). We performed a randomized, controlled trial to investigate the effects of a low FODMAP diet on persistent gut symptoms, the intestinal microbiome, and circulating markers of inflammation in patients with quiescent IBD.

METHODS: We performed a single-blind trial of 52 patients with quiescent Crohn's disease or ulcerative colitis and persistent gut symptoms at 2 large gastroenterology clinics in the United Kingdom. Patients were randomly assigned to groups that followed a diet low in FODMAPs (n = 27) or a control diet (n = 25), with dietary advice, for 4 weeks. Gut symptoms and health-related quality of life were measured using validated questionnaires. Stool and blood samples were collected at baseline and end of trial. We assessed fecal microbiome composition and function using shotgun metagenomic sequencing and phenotypes of T cells in blood using flow cytometry.

RESULTS: A higher proportion of patients reported adequate relief of gut symptoms following the low FODMAP diet (14/27, 52%) than the control diet (4/25, 16%, P=.007). Patients had a greater reduction in irritable bowel syndrome severity scores following the low FODMAP diet (mean reduction of 67; standard error, 78) than the control diet (mean reduction of 34; standard error, 50), although this difference was not statistically significant (P = .075). Following the low FODMAP diet, patients had higher health-related quality of life scores (81.9 ± 1.2) than patients on the control diet (78.3 ± 1.2, P = .042). A targeted analysis revealed that in stool samples collected at the end of the study period, patients on the low FODMAP diet had significantly lower abundance of Bifidobacterium adolescentis, Bifidobacterium longum, and Faecalibacterium prausnitzii than patients on control diet. However, microbiome diversity and markers of inflammation did not differ significantly between groups.

CONCLUSIONS: In a trial of the low FODMAP diet vs a control diet in patients with quiescent IBD, we found no significant difference after 4 weeks in change in irritable bowel syndrome severity scores, but significant improvements in specific symptom scores and numbers reporting adequate symptom relief. The low FODMAP diet reduced fecal abundance of microbes believed to regulate the immune response, compared with the control diet, but had no significant effect on markers of inflammation. We conclude that a 4-week diet low in FODMAPs is safe and effective for managing persistent gut symptoms in patients with quiescent IBD. www.isrctn.com no.: ISRCTN17061468.}, } @article {pmid31586158, year = {2020}, author = {Jansson, JK and Hofmockel, KS}, title = {Soil microbiomes and climate change.}, journal = {Nature reviews. Microbiology}, volume = {18}, number = {1}, pages = {35-46}, doi = {10.1038/s41579-019-0265-7}, pmid = {31586158}, issn = {1740-1534}, mesh = {*Climate Change ; Metagenome ; Microbiota/*radiation effects ; *Soil Microbiology ; }, abstract = {The soil microbiome governs biogeochemical cycling of macronutrients, micronutrients and other elements vital for the growth of plants and animal life. Understanding and predicting the impact of climate change on soil microbiomes and the ecosystem services they provide present a grand challenge and major opportunity as we direct our research efforts towards one of the most pressing problems facing our planet. In this Review, we explore the current state of knowledge about the impacts of climate change on soil microorganisms in different climate-sensitive soil ecosystems, as well as potential ways that soil microorganisms can be harnessed to help mitigate the negative consequences of climate change.}, } @article {pmid31585992, year = {2019}, author = {Peña-Gonzalez, A and Soto-Girón, MJ and Smith, S and Sistrunk, J and Montero, L and Páez, M and Ortega, E and Hatt, JK and Cevallos, W and Trueba, G and Levy, K and Konstantinidis, KT}, title = {Metagenomic Signatures of Gut Infections Caused by Different Escherichia coli Pathotypes.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {24}, pages = {}, pmid = {31585992}, issn = {1098-5336}, support = {K01 AI103544/AI/NIAID NIH HHS/United States ; R01 AI137679/AI/NIAID NIH HHS/United States ; }, mesh = {Case-Control Studies ; Child ; Child, Preschool ; Diarrhea/microbiology ; Disease Outbreaks ; Ecuador ; Escherichia coli/genetics/isolation & purification/*metabolism/pathogenicity ; Escherichia coli Infections/*microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Infant ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Escherichia coli is a leading contributor to infectious diarrhea and child mortality worldwide, but it remains unknown how alterations in the gut microbiome vary for distinct E. coli pathotype infections and whether these signatures can be used for diagnostic purposes. Further, the majority of enteric diarrheal infections are not diagnosed with respect to their etiological agent(s) due to technical challenges. To address these issues, we devised a novel approach that combined traditional, isolate-based and molecular-biology techniques with metagenomics analysis of stool samples and epidemiological data. Application of this pipeline to children enrolled in a case-control study of diarrhea in Ecuador showed that, in about half of the cases where an E. coli pathotype was detected by culture and PCR, E. coli was likely not the causative agent based on the metagenome-derived low relative abundance, the level of clonality, and/or the virulence gene content. Our results also showed that diffuse adherent E. coli (DAEC), a pathotype that is generally underrepresented in previous studies of diarrhea and thus, thought not to be highly virulent, caused several small-scale diarrheal outbreaks across a rural to urban gradient in Ecuador. DAEC infections were uniquely accompanied by coelution of large amounts of human DNA and conferred significant shifts in the gut microbiome composition relative to controls or infections caused by other E. coli pathotypes. Our study shows that diarrheal infections can be efficiently diagnosed for their etiological agent and categorized based on their effects on the gut microbiome using metagenomic tools, which opens new possibilities for diagnostics and treatment.IMPORTANCEE. coli infectious diarrhea is an important contributor to child mortality worldwide. However, diagnosing and thus treating E. coli infections remain challenging due to technical and other reasons associated with the limitations of the traditional culture-based techniques and the requirement to apply Koch's postulates. In this study, we integrated traditional microbiology techniques with metagenomics and epidemiological data in order to identify cases of diarrhea where E. coli was most likely the causative disease agent and evaluate specific signatures in the disease-state gut microbiome that distinguish between diffuse adherent, enterotoxigenic, and enteropathogenic E. coli pathotypes. Therefore, our methodology and results should be highly relevant for diagnosing and treating diarrheal infections and have important applications in public health.}, } @article {pmid31585122, year = {2020}, author = {Gu, S and Zaidi, S and Hassan, MI and Mohammad, T and Malta, TM and Noushmehr, H and Nguyen, B and Crandall, KA and Srivastav, J and Obias, V and Lin, P and Nguyen, BN and Yao, M and Yao, R and King, CH and Mazumder, R and Mishra, B and Rao, S and Mishra, L}, title = {Mutated CEACAMs Disrupt Transforming Growth Factor Beta Signaling and Alter the Intestinal Microbiome to Promote Colorectal Carcinogenesis.}, journal = {Gastroenterology}, volume = {158}, number = {1}, pages = {238-252}, pmid = {31585122}, issn = {1528-0012}, support = {I01 BX003732/BX/BLRD VA/United States ; R01 AA023146/AA/NIAAA NIH HHS/United States ; R01 CA236591/CA/NCI NIH HHS/United States ; U01 CA230690/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/isolation & purification ; Carcinoembryonic Antigen/*genetics/metabolism ; Carcinogenesis/*genetics ; Colorectal Neoplasms/*genetics/microbiology/mortality ; Disease Models, Animal ; Feces/microbiology ; GPI-Linked Proteins/genetics/metabolism ; Gain of Function Mutation ; Gastrointestinal Microbiome/*physiology ; Gene Expression Regulation, Neoplastic ; HCT116 Cells ; Humans ; Metagenomics ; Mice ; Mice, Transgenic ; Protein Domains/genetics ; Receptor, Transforming Growth Factor-beta Type I/metabolism ; Signal Transduction/*genetics ; Smad4 Protein/genetics/metabolism ; Spheroids, Cellular ; Survival Analysis ; Transforming Growth Factor beta/metabolism ; }, abstract = {BACKGROUND & AIMS: We studied interactions among proteins of the carcinoembryonic antigen-related cell adhesion molecule (CEACAM) family, which interact with microbes, and transforming growth factor beta (TGFB) signaling pathway, which is often altered in colorectal cancer cells. We investigated mechanisms by which CEACAM proteins inhibit TGFB signaling and alter the intestinal microbiome to promote colorectal carcinogenesis.

METHODS: We collected data on DNA sequences, messenger RNA expression levels, and patient survival times from 456 colorectal adenocarcinoma cases, and a separate set of 594 samples of colorectal adenocarcinomas, in The Cancer Genome Atlas. We performed shotgun metagenomic sequencing analyses of feces from wild-type mice and mice with defects in TGFB signaling (Sptbn1[+/-] and Smad4[+/-]/Sptbn1[+/-]) to identify changes in microbiota composition before development of colon tumors. CEACAM protein and its mutants were overexpressed in SW480 and HCT116 colorectal cancer cell lines, which were analyzed by immunoblotting and proliferation and colony formation assays.

RESULTS: In colorectal adenocarcinomas, high expression levels of genes encoding CEACAM proteins, especially CEACAM5, were associated with reduced survival times of patients. There was an inverse correlation between expression of CEACAM genes and expression of TGFB pathway genes (TGFBR1, TGFBR2, and SMAD3). In colorectal adenocarcinomas, we also found an inverse correlation between expression of genes in the TGFB signaling pathway and genes that regulate stem cell features of cells. We found mutations encoding L640I and A643T in the B3 domain of human CEACAM5 in colorectal adenocarcinomas; structural studies indicated that these mutations would alter the interaction between CEACAM5 and TGFBR1. Overexpression of these mutants in SW480 and HCT116 colorectal cancer cell lines increased their anchorage-independent growth and inhibited TGFB signaling to a greater extent than overexpression of wild-type CEACAM5, indicating that they are gain-of-function mutations. Compared with feces from wild-type mice, feces from mice with defects in TGFB signaling had increased abundance of bacterial species that have been associated with the development of colon tumors, including Clostridium septicum, and decreased amounts of beneficial bacteria, such as Bacteroides vulgatus and Parabacteroides distasonis.

CONCLUSION: We found expression of CEACAMs and genes that regulate stem cell features of cells to be increased in colorectal adenocarcinomas and inversely correlated with expression of TGFB pathway genes. We found colorectal adenocarcinomas to express mutant forms of CEACAM5 that inhibit TGFB signaling and increase proliferation and colony formation. We propose that CEACAM proteins disrupt TGFB signaling, which alters the composition of the intestinal microbiome to promote colorectal carcinogenesis.}, } @article {pmid31584099, year = {2020}, author = {Cheng, L and Qi, C and Zhuang, H and Fu, T and Zhang, X}, title = {gutMDisorder: a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions.}, journal = {Nucleic acids research}, volume = {48}, number = {D1}, pages = {D554-D560}, pmid = {31584099}, issn = {1362-4962}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/drug effects/genetics/pathogenicity ; *Databases, Genetic ; *Databases, Pharmaceutical ; Dysbiosis/drug therapy/genetics/*microbiology ; *Gastrointestinal Microbiome ; Genes, Bacterial ; Humans ; Metagenome ; Mice ; *Software ; }, abstract = {gutMDisorder (http://bio-annotation.cn/gutMDisorder), a manually curated database, aims at providing a comprehensive resource of dysbiosis of the gut microbiota in disorders and interventions. Alterations in the composition of the gut microbial community play crucial roles in the development of chronic disorders. And the beneficial effects of drugs, foods and other intervention measures on disorders could be microbially mediated. The current version of gutMDisorder documents 2263 curated associations between 579 gut microbes and 123 disorders or 77 intervention measures in Human, and 930 curated associations between 273 gut microbes and 33 disorders or 151 intervention measures in Mouse. Each entry in the gutMDisorder contains detailed information on an association, including an intestinal microbe, a disorder name, intervention measures, experimental technology and platform, characteristic of samples, web sites for downloading the sequencing data, a brief description of the association, a literature reference, and so on. gutMDisorder provides a user-friendly interface to browse, retrieve each entry using gut microbes, disorders, and intervention measures. It also offers pages for downloading all the entries and submitting new experimentally validated associations.}, } @article {pmid31582752, year = {2019}, author = {Visconti, A and Le Roy, CI and Rosa, F and Rossi, N and Martin, TC and Mohney, RP and Li, W and de Rinaldis, E and Bell, JT and Venter, JC and Nelson, KE and Spector, TD and Falchi, M}, title = {Interplay between the human gut microbiome and host metabolism.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4505}, pmid = {31582752}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/N01183X/1/MRC_/Medical Research Council/United Kingdom ; MR/N030125/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Age Distribution ; Age Factors ; Aged ; Aged, 80 and over ; Bacteria/isolation & purification/*metabolism ; Biomarkers/blood/metabolism ; Datasets as Topic ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Host Microbial Interactions/*physiology ; Humans ; Male ; Metabolic Networks and Pathways/*physiology ; Metabolome/*physiology ; Metabolomics/methods ; Metagenome ; Middle Aged ; Whole Genome Sequencing ; }, abstract = {The human gut is inhabited by a complex and metabolically active microbial ecosystem. While many studies focused on the effect of individual microbial taxa on human health, their overall metabolic potential has been under-explored. Using whole-metagenome shotgun sequencing data in 1,004 twins, we first observed that unrelated subjects share, on average, almost double the number of metabolic pathways (82%) than species (43%). Then, using 673 blood and 713 faecal metabolites, we found metabolic pathways to be associated with 34% of blood and 95% of faecal metabolites, with over 18,000 significant associations, while species showed less than 3,000 associations. Finally, we estimated that the microbiome was involved in a dialogue between 71% of faecal, and 15% of blood, metabolites. This study underlines the importance of studying the microbial metabolic potential rather than focusing purely on taxonomy to find therapeutic and diagnostic targets, and provides a unique resource describing the interplay between the microbiome and the systemic and faecal metabolic environments.}, } @article {pmid31582724, year = {2019}, author = {Yang, J and McDowell, A and Kim, EK and Seo, H and Lee, WH and Moon, CM and Kym, SM and Lee, DH and Park, YS and Jee, YK and Kim, YK}, title = {Development of a colorectal cancer diagnostic model and dietary risk assessment through gut microbiome analysis.}, journal = {Experimental & molecular medicine}, volume = {51}, number = {10}, pages = {1-15}, pmid = {31582724}, issn = {2092-6413}, support = {NRF-2016M3A9B6901516//National Research Foundation of Korea (NRF)/International ; NRF-2017M3A9F3047497//National Research Foundation of Korea (NRF)/International ; H17C1996//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/International ; }, mesh = {Aged ; Animals ; Bacteria/classification/genetics ; Cholesterol/genetics ; Colorectal Neoplasms/*diagnosis/*genetics/microbiology/pathology ; Diet, High-Fat/adverse effects ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metagenome/*genetics ; Mice ; Microbiota/genetics ; Middle Aged ; Risk Assessment ; }, abstract = {Colorectal cancer (CRC) is the third most common form of cancer and poses a critical public health threat due to the global spread of westernized diets high in meat, cholesterol, and fat. Although the link between diet and colorectal cancer has been well established, the mediating role of the gut microbiota remains elusive. In this study, we sought to elucidate the connection between the gut microbiota, diet, and CRC through metagenomic analysis of bacteria isolated from the stool of CRC (n = 89) and healthy (n = 161) subjects. This analysis yielded a dozen genera that were significantly altered in CRC patients, including increased Bacteroides, Fusobacterium, Dorea, and Porphyromonas prevalence and diminished Pseudomonas, Prevotella, Acinetobacter, and Catenibacterium carriage. Based on these altered genera, we developed two novel CRC diagnostic models through stepwise selection and a simplified model using two increased and two decreased genera. As both models yielded strong AUC values above 0.8, the simplified model was applied to assess diet-based CRC risk in mice. Mice fed a westernized high-fat diet (HFD) showed greater CRC risk than mice fed a regular chow diet. Furthermore, we found that nonglutinous rice, glutinous rice, and sorghum consumption reduced CRC risk in HFD-fed mice. Collectively, these findings support the critical mediating role of the gut microbiota in diet-induced CRC risk as well as the potential of dietary grain intake to reduce microbiota-associated CRC risk. Further study is required to validate the diagnostic prediction models developed in this study as well as the preventive potential of grain consumption to reduce CRC risk.}, } @article {pmid31582523, year = {2019}, author = {Sugimoto, Y and Camacho, FR and Wang, S and Chankhamjon, P and Odabas, A and Biswas, A and Jeffrey, PD and Donia, MS}, title = {A metagenomic strategy for harnessing the chemical repertoire of the human microbiome.}, journal = {Science (New York, N.Y.)}, volume = {366}, number = {6471}, pages = {}, doi = {10.1126/science.aax9176}, pmid = {31582523}, issn = {1095-9203}, support = {DP2 AI124441/AI/NIAID NIH HHS/United States ; }, mesh = {Host Microbial Interactions/*genetics ; Humans ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Multigene Family ; Polyketides/chemistry/*metabolism ; }, abstract = {Extensive progress has been made in determining the effects of the microbiome on human physiology and disease, but the underlying molecules and mechanisms governing these effects remain largely unexplored. Here, we combine a new computational algorithm with synthetic biology to access biologically active small molecules encoded directly in human microbiome-derived metagenomic sequencing data. We discover that members of a clinically used class of molecules are widely encoded in the human microbiome and that they exert potent antibacterial activities against neighboring microbes, implying a possible role in niche competition and host defense. Our approach paves the way toward a systematic unveiling of the chemical repertoire encoded by the human microbiome and provides a generalizable platform for discovering molecular mediators of microbiome-host and microbiome-microbiome interactions.}, } @article {pmid31581017, year = {2020}, author = {Franzetti, A and Gandolfi, I and Bestetti, G and Padoa Schioppa, E and Canedoli, C and Brambilla, D and Cappelletti, D and Sebastiani, B and Federici, E and Papacchini, M and Ambrosini, R}, title = {Plant-microorganisms interaction promotes removal of air pollutants in Milan (Italy) urban area.}, journal = {Journal of hazardous materials}, volume = {384}, number = {}, pages = {121021}, doi = {10.1016/j.jhazmat.2019.121021}, pmid = {31581017}, issn = {1873-3336}, mesh = {Adsorption ; Air Pollutants/analysis/chemistry/*metabolism ; Bacteria/classification/genetics/*metabolism ; Biodegradation, Environmental ; Cedrus/chemistry/*microbiology ; Cities ; Italy ; Magnolia/chemistry/*microbiology ; Microbiota/genetics ; Particulate Matter/analysis/chemistry/*metabolism ; Plant Leaves/chemistry/microbiology ; Polycyclic Aromatic Hydrocarbons/analysis/chemistry/*metabolism ; RNA, Ribosomal, 16S ; }, abstract = {Plants and phyllosphere microorganisms may effectively contribute to reducing air pollution in cities through the adsorption and biodegradation of pollutants onto leaves. In this work, during all seasons, we sampled atmospheric particulate matter (PM10) and leaves of southern magnolia Magnolia grandiflora and deodar cedar Cedrus deodara, two evergreen plant species widespread in the urban area of Milan where the study was carried out. We then quantified Polycyclic Aromatic Hydrocarbons (PAHs) both in PM10 and on leaves and used sequencing of 16S rRNA gene, shotgun metagenomics and qPCR analyses to investigate the microbial communities hosted by the sampled leaves. Taxonomic and functional profiles of epiphytic bacterial communities differed between host plant species and seasons and the microbial communities on leaves harboured genes involved in the degradation of hydrocarbons. Evidence collected in this work also suggested that the abundance of hydrocarbon-degrading microorganisms on evergreen leaves increased with the concentration of hydrocarbons when atmospheric pollutants were deposited at high concentration on leaves, and that the biodegradation on the phyllosphere can contribute to the removal of PAHs from the urban air.}, } @article {pmid31578453, year = {2019}, author = {Wemheuer, F and Wemheuer, B and Daniel, R and Vidal, S}, title = {Deciphering bacterial and fungal endophyte communities in leaves of two maple trees with green islands.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {14183}, pmid = {31578453}, issn = {2045-2322}, mesh = {Acer/*microbiology ; Bacteria/genetics/pathogenicity ; Endophytes/genetics/*pathogenicity ; Fungi/genetics/pathogenicity ; Metagenome ; *Microbiota ; Plant Leaves/*microbiology ; }, abstract = {Green islands (the re-greening of senescent leaf tissues) are particularly evident on leaves infected with fungal pathogens. To date, there is only a limited number of studies investigating foliar endophytic microorganisms in phytopathogen-infected leaves. Here, we analysed bacterial and fungal endophyte communities in leaves without green islands (control leaves; CL), within green island areas (GLA) and the surrounding yellow leaf areas (YLA) of leaves with green islands of Acer campestre and A. platanoides. GLA samples of A. campestre and A. platanoides were dominated by Sawadaea polyfida and S. bicornis, respectively, suggesting that these fungi might be responsible for the green islands. We detected a higher fungal richness and diversity in CL compared to GLA samples of A. campestre. Leaf status (CL, GLA, YLA) significantly altered the composition of fungal communities of A. campestre. This was related to differences in fungal community composition between YLA and GLA samples. Site was the main driver of bacterial communities, suggesting that bacterial and fungal endophytes are shaped by different factors. Overall, we observed Acer species-specific responses of endophyte communities towards the presence of green islands and/or leaf type, which might be attributed to several fungi and bacteria specifically associated with one Acer species.}, } @article {pmid31576454, year = {2019}, author = {Alibrahim, A and Al-Gharabally, D and Mahmoud, H and Dittrich, M}, title = {Proto-dolomite formation in microbial consortia dominated by Halomonas strains.}, journal = {Extremophiles : life under extreme conditions}, volume = {23}, number = {6}, pages = {765-781}, pmid = {31576454}, issn = {1433-4909}, support = {PR17-12SL-10//Kuwait Foundation for the Advancement of Sciences/ ; }, mesh = {Calcium Carbonate ; *Halomonas ; Kuwait ; Magnesium ; *Microbial Consortia ; }, abstract = {Microbes can be found in hypersaline environments forming diverse populations with complex ecological interactions. Microbes in such environments were found to be involved in the formation of minerals including dolomite, a mineral of economic importance and whose origin has been long-debated. Various reports on in vitro experiments using pure cultures provided evidence for the microbial role in dolomite formation. However, culturing experiments have been limited in scope and do not fully address the possible interactions of the naturally occurring microbial communities; consequently, the ability of microbes as a community to form dolomite has been investigated in this study. Our experiments focused on examining the microbial composition by culturing aerobic heterotrophs from the top hypersaline sediments of Al-Khiran sabkha in Kuwait, a modern dolomite-forming environment. The objectives of this study were to assess the ability of two microbial consortia to form dolomite using enrichment culture experiments, mineralogy, and metagenomics. Proto-dolomite was formed by a microbial community dominated by Halomonas strains whereby degradation of the extracellular polymeric substances (EPS) was observed and the pH changed from 7.00 to 8.58. Conversely, proto-dolomite was not observed within a microbial community dominated by Clostridiisalibacter in which EPS continuously accumulated and the pH slightly changed from 7.00 to 7.29.}, } @article {pmid31576426, year = {2019}, author = {Long, Y and Jiang, J and Hu, X and Zhou, J and Hu, J and Zhou, S}, title = {Actinobacterial community in Shuanghe Cave using culture-dependent and -independent approaches.}, journal = {World journal of microbiology & biotechnology}, volume = {35}, number = {10}, pages = {153}, pmid = {31576426}, issn = {1573-0972}, support = {2016YFC0400702//National Key R&D Program of China/ ; }, mesh = {Actinobacteria/classification/genetics/growth & development/*isolation & purification ; Animals ; Asia ; Biodiversity ; Caves/*microbiology ; Chiroptera/microbiology ; DNA, Bacterial/genetics ; Ecosystem ; Geologic Sediments/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {Karst caves, considering to be the "arks" of biodiversity, often contain high levels of endemism. In the present study, the actinobacterial community in Shuanghe Cave, the longest cave in Asia, was analyzed for the first-time using culture-dependent and -independent (16S rRNA amplicon sequencing) approaches. The amplicon sequencing analysis revealed a broad taxonomic diversity in Shuanghe Cave, including 19 phyla (predominantly Actinobacteria) and 264 different genera. While the culture-dependent method got the unrepresentative but supplemental result, a total of 239 actinomycetes were isolated and were identified to seven genera based on culture features and 16S rRNA tests. Among the three habitats (soil, rock soil, and bat guano), the dominant phyla did not differ significantly, while the dominant genus community varied among different habitats, and the richness in soil and rock soil samples was higher than that in bat guano. Furthermore, 16 isolate strains showed antimicrobial activity, especially, the strain S142 (Streptomyces badius) and S761 (Actinoplanes friuliensis) exhibited the most promising activity against various pathogens. Overall, this work showed the abundant bacterial diversity and the antimicrobial potential of the isolates from the Shuanghe Cave.}, } @article {pmid31574349, year = {2019}, author = {Chen, H and Bai, X and Li, Y and Jing, L and Chen, R and Teng, Y}, title = {Source identification of antibiotic resistance genes in a peri-urban river using novel crAssphage marker genes and metagenomic signatures.}, journal = {Water research}, volume = {167}, number = {}, pages = {115098}, doi = {10.1016/j.watres.2019.115098}, pmid = {31574349}, issn = {1879-2448}, mesh = {Animals ; Anti-Bacterial Agents ; Drug Resistance, Microbial ; Genes, Bacterial ; Humans ; Metagenomics ; *Microbiota ; *Rivers ; Swine ; }, abstract = {Antimicrobial resistance is a growing public health concern, and environment is regarded as an important reservoir and dissemination route for antibiotic resistance genes (ARGs). To prevent and control ARG pollution, it is essential to correctly disentangle source-sink relationship of ARGs in the environment. However, accurately apportioning sources of ARGs is still a big challenge due to the complex interaction of multiple sources and contaminants in the environment with changing dynamics. In this study, we addressed this problem and focused on identifying the potential sources of ARGs in a peri-urban river by jointly utilizing two novel microbial source tracking methods. To attain the objective, sediment/water samples were collected from the peri-urban river and four ARG-associated ecotypes including effluents of sewage treatment plants (STPs), STP influent, chicken manures and pig manures. The high-throughput profilings of ARGs and microbial taxa in the river sediments and the four ecotypes were comprehensively characterized in combination of shotgun sequencing and metagenomic assembly analysis. CrAssphage, a recently-discovered DNA bacteriophage, was employed to track the impact of human fecal pollution on ARGs in the river sediments. Further, SourceTracker, a machine-learning classification tool, was used for quantifying the contributions of potential sources to ARGs in the river sediments based on the metagenomic signatures of ARGs and microbial taxa. In total, 888 ARG subtypes belonging to 29 ARG types were detected across all samples, including mcr-1 and a range of carbapenemases types. Statistical analyses suggested different ecotypes generally had distinct profiles of both ARGs and microbial taxa, while the ARG compositions were significantly correlated with the microbial community. Source tracking with crAssphage showed the presence of ARGs in the river sediments might be largely impacted by the extent of human fecal pollution, which was also confirmed by the analyses of SourceTracker that the discharge from STPs was the largest contributor of ARGs (81.6-92.1%) and microbes (49.3-68.1%) in the river sediments. Results of the study can help us to better understand the characterization of ARGs in the peri-urban ecosystem and to design effective prevention and control strategies for reducing ARG dissemination.}, } @article {pmid31573138, year = {2019}, author = {McLean, AHC and Godfray, HCJ and Ellers, J and Henry, LM}, title = {Host relatedness influences the composition of aphid microbiomes.}, journal = {Environmental microbiology reports}, volume = {11}, number = {6}, pages = {808-816}, pmid = {31573138}, issn = {1758-2229}, support = {NBAF708//Natural Environment Research Council/International ; NE/M018016/1//Natural Environment Research Council/International ; VICI 865.12.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/International ; }, mesh = {Animals ; Aphids/classification/*microbiology ; Bacteria/classification/genetics ; *Host Microbial Interactions ; Metagenomics ; *Microbiota ; }, abstract = {Animals are host to a community of microbes, collectively referred to as their microbiome, that can play a key role in their hosts' biology. The bacterial endosymbionts of insects have a particularly strong influence on their hosts, but despite their importance we still know little about the factors that influence the composition of insect microbial communities. Here, we ask: what is the relative importance of host relatedness and host ecology in structuring symbiont communities of diverse aphid species? We used next-generation sequencing to compare the microbiomes of 46 aphid species with known host plant affiliations. We find that relatedness between aphid species is the key factor explaining the microbiome composition, with more closely related aphid species housing more similar bacterial communities. Endosymbionts dominate the microbial communities, and we find a novel bacterium in the genus Sphingopyxis that is associated with numerous aphid species feeding exclusively on trees. The influence of ecology was less pronounced than that of host relatedness. Our results suggest that co-adaptation between insect species and their facultative symbionts is a more important determinant of symbiont species presence in aphids than shared ecology of hosts.}, } @article {pmid31573126, year = {2019}, author = {Galambos, D and Anderson, RE and Reveillaud, J and Huber, JA}, title = {Genome-resolved metagenomics and metatranscriptomics reveal niche differentiation in functionally redundant microbial communities at deep-sea hydrothermal vents.}, journal = {Environmental microbiology}, volume = {21}, number = {11}, pages = {4395-4410}, pmid = {31573126}, issn = {1462-2920}, support = {//Alfred P. Sloan Foundation/International ; ASTEP NNX-327 09AB75G/NASA/NASA/United States ; Exobiology 80NSSC18K1076/NASA/NASA/United States ; OCE-1061863//National Science Foundation/International ; ASTEP NNX-327 09AB75G/NASA/NASA/United States ; Exobiology 80NSSC18K1076/NASA/NASA/United States ; }, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Hydrothermal Vents/*microbiology ; Metagenome ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; Transcriptome ; }, abstract = {The structure and function of microbial communities inhabiting the subseafloor near hydrothermal systems are influenced by fluid geochemistry, geologic setting and fluid flux between vent sites, as well as biological interactions. Here, we used genome-resolved metagenomics and metatranscriptomics to examine patterns of gene abundance and expression and assess potential niche differentiation in microbial communities in venting fluids from hydrothermal vent sites at the Mid-Cayman Rise. We observed similar patterns in gene and transcript abundance between two geochemically distinct vent fields at the community level but found that each vent site harbours a distinct microbial community with differing transcript abundances for individual microbial populations. Through an analysis of metabolic pathways in 64 metagenome-assembled genomes (MAGs), we show that MAG transcript abundance can be tied to differences in metabolic pathways and to potential metabolic interactions between microbial populations, allowing for niche-partitioning and divergence in both population distribution and activity. Our results illustrate that most microbial populations have a restricted distribution within the seafloor, and that the activity of those microbial populations is tied to both genome content and abiotic factors.}, } @article {pmid31572693, year = {2019}, author = {Reid, G}, title = {The Need to Focus on Therapy Instead of Associations.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {327}, pmid = {31572693}, issn = {2235-2988}, mesh = {Dysbiosis/microbiology/*therapy ; Female ; Humans ; Metagenomics ; *Microbial Interactions ; *Microbiota ; Probiotics/*administration & dosage ; Sequence Analysis, DNA ; Vagina/*microbiology ; Vaginosis, Bacterial/microbiology/*therapy ; }, abstract = {Molecular analyses of the vaginal microbiota have uncovered a vast array of organisms in this niche, but not so far changed what has been known for a long time: lactobacilli are dominant in health, and the diagnosis and treatment of symptomatic bacterial vaginosis is sub-optimal, and has not changed for over 40 years. While the lowering cost of DNA sequencing has attracted more researchers to the field, and bioinformatics, and statistical tools have made it possible to produce large datasets, it is functional and actionable studies that are more urgently needed, not more microbial abundance, and health or disease-associative data. The triggers of dysbiosis remain to be identified, but ultimately treatment will require disrupting biofilms of primarily anaerobic bacteria and replacing them with the host's own lactobacilli, or health-promoting organisms. The options of using probiotic strains to displace the biofilms and for prebiotics to encourage resurgence of the indigenous lactobacilli hold great promise, but more researchers need to develop, and test these concepts in humans. The enormity of the problem of vaginal dysbiosis cannot be understated. It should not take another 40 years to offer better management options.}, } @article {pmid31572686, year = {2019}, author = {Genton, L and Mareschal, J and Charretier, Y and Lazarevic, V and Bindels, LB and Schrenzel, J}, title = {Targeting the Gut Microbiota to Treat Cachexia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {305}, pmid = {31572686}, issn = {2235-2988}, mesh = {Adult ; Body Mass Index ; Cachexia/*therapy ; Fecal Microbiota Transplantation/methods ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology ; Humans ; Inflammation ; Malnutrition ; Metagenome ; Obesity/therapy ; Probiotics/therapeutic use ; Weight Loss ; }, abstract = {Cachexia occurs in many chronic diseases and is associated with increased morbidity and mortality. It is treated by nutritional support but often with limited effectiveness, leading to the search of other therapeutic strategies. The modulation of gut microbiota, whether through pro-, pre-, syn- or antibiotics or fecal transplantation, is attracting ever-growing interest in the field of obesity, but could also be an interesting and innovative alternative for treating cachexia. This article reviews the evidence linking the features of malnutrition, as defined by the Global Leadership Initiative on Malnutrition [low body mass index (BMI), unintentional body weight loss, low muscle mass, low appetite, and systemic inflammation] and the gut microbiota in human adults with cachexia-associated diseases, and shows the limitations of the present research in that field with suggestions for future directions.}, } @article {pmid31568677, year = {2019}, author = {Feng, Y and Duan, Y and Xu, Z and Lyu, N and Liu, F and Liang, S and Zhu, B}, title = {An examination of data from the American Gut Project reveals that the dominance of the genus Bifidobacterium is associated with the diversity and robustness of the gut microbiota.}, journal = {MicrobiologyOpen}, volume = {8}, number = {12}, pages = {e939}, pmid = {31568677}, issn = {2045-8827}, mesh = {*Bifidobacterium ; *Biodiversity ; Disease Susceptibility ; *Gastrointestinal Microbiome ; Humans ; Lactobacillus ; Life Style ; Probiotics ; United States ; }, abstract = {Bifidobacterium and Lactobacillus are beneficial for human health, and many strains of these two genera are widely used as probiotics. We used two large datasets published by the American Gut Project (AGP) and a gut metagenomic dataset (NBT) to analyze the relationship between these two genera and the community structure of the gut microbiota. The meta-analysis showed that Bifidobacterium, but not Lactobacillus, is among the dominant genera in the human gut microbiota. The relative abundance of Bifidobacterium was elevated when Lactobacillus was present. Moreover, these two genera showed a positive correlation with some butyrate producers among the dominant genera, and both were associated with alpha diversity, beta diversity, and the robustness of the gut microbiota. Additionally, samples harboring Bifidobacterium present but no Lactobacillus showed higher alpha diversity and were more robust than those only carrying Lactobacillus. Further comparisons with other genera validated the important role of Bifidobacterium in the gut microbiota robustness. Multivariate analysis of 11,744 samples from the AGP dataset suggested Bifidobacterium to be associated with demographic features, lifestyle, and disease. In summary, Bifidobacterium members, which are promoted by dairy and whole-grain consumption, are more important than Lactobacillus in maintaining the diversity and robustness of the gut microbiota.}, } @article {pmid31568480, year = {2019}, author = {Gawande, SJ and Anandhan, S and Ingle, A and Roylawar, P and Khandagale, K and Gawai, T and Jacobson, A and Asokan, R and Singh, M}, title = {Microbiome profiling of the onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae).}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0223281}, pmid = {31568480}, issn = {1932-6203}, mesh = {Actinobacteria/classification/*genetics/isolation & purification ; Animals ; Bacterial Typing Techniques ; Bacteroidetes/classification/*genetics/isolation & purification ; Cyanobacteria/classification/*genetics/isolation & purification ; Firmicutes/classification/*genetics/isolation & purification ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; India ; Phylogeny ; Proteobacteria/classification/*genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Symbiosis/genetics ; Thysanoptera/*microbiology ; Nicotiana/parasitology ; Wolbachia/classification/genetics/isolation & purification ; }, abstract = {The gut microbial community structure of adult Thrips tabaci collected from 10 different agro-climatically diverse locations of India was characterized by using the Illumina MiSeq platform to amplify the V3 region of the 16S rRNA gene of bacteria present in the sampled insects. Analyses were performed to study the bacterial communities associated with Thrips tabaci in India. The complete bacterial metagenome of T. tabaci was comprised of 1662 OTUs of which 62.25% belong to known and 37.7% of unidentified/unknown bacteria. These OTUs constituted 21 bacterial phyla of 276 identified genera. Phylum Proteobacteria was predominant, followed by Actinobacteria, Firmicutes, Bacteroidetes and Cyanobacteria. Additionally, the occurrence of the reproductive endosymbiont, Wolbachia was detected at two locations (0.56%) of the total known OTUs. There is high variation in diversity and species richness among the different locations. Alpha-diversity metrics indicated the higher gut bacterial diversity at Bangalore and lowest at Rahuri whereas higher bacterial species richness at T. tabaci samples from Imphal and lowest at Jhalawar. Beta diversity analyses comparing bacterial communities between the samples showed distinct differences in bacterial community composition of T. tabaci samples from different locations. This paper also constitutes the first record of detailed bacterial communities associated with T. tabaci. The location-wise variation in microbial metagenome profile of T. tabaci suggests that bacterial diversity might be governed by its population genetic structure, environment and habitat.}, } @article {pmid31566729, year = {2020}, author = {Kusakabe, S and Fukushima, K and Maeda, T and Motooka, D and Nakamura, S and Fujita, J and Yokota, T and Shibayama, H and Oritani, K and Kanakura, Y}, title = {Pre- and post-serial metagenomic analysis of gut microbiota as a prognostic factor in patients undergoing haematopoietic stem cell transplantation.}, journal = {British journal of haematology}, volume = {188}, number = {3}, pages = {438-449}, doi = {10.1111/bjh.16205}, pmid = {31566729}, issn = {1365-2141}, mesh = {Adult ; Allografts ; Autografts ; Bacterial Typing Techniques ; Bifidobacterium/isolation & purification ; Case-Control Studies ; DNA, Bacterial/genetics ; Dysbiosis/complications/microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Hematopoietic Stem Cell Transplantation/adverse effects/*methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Intestines/microbiology ; Male ; Metagenomics/methods ; Middle Aged ; Prognosis ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Survival Analysis ; Transplantation Conditioning/methods ; }, abstract = {The human gut harbours diverse microorganisms, and gut dysbiosis has recently attracted attention because of its possible involvement in various diseases. In particular, the lack of diversity in the gut microbiota has been associated with complications of haematopoietic stem cell transplantation (HSCT), such as infections, acute graft-versus-host disease and relapse of primary disease, which lead to a poor prognosis. However, few studies have serially examined the composition of the intestinal microbiota after HSCT. In this study, we demonstrated, using next-generation sequencing of the bacterial 16S ribosomal RNA gene, combined with uniFrac distance analysis, that the intestinal microbiota of patients undergoing allogeneic HSCT substantially differed from that of healthy controls and recipients of autologous transplants. Faecal samples were obtained daily throughout the clinical course, before and after transplantation. Notably, the proportions of Bifidobacterium and genera categorized as butyrate-producing bacteria were significantly lower in patients with allogeneic HSCT than in healthy controls. Furthermore, among allogeneic transplant recipients, a subgroup with a preserved microbiota composition showed a benign course, whereas patients with a skewed microbiota showed a high frequency of complications and mortality after transplantation. Thus, we conclude that the stability of intestinal microbiota is critically involved in outcomes of HSCT.}, } @article {pmid31566105, year = {2019}, author = {Amar, J and Lelouvier, B and Servant, F and Lluch, J and Burcelin, R and Bongard, V and Elbaz, M}, title = {Blood Microbiota Modification After Myocardial Infarction Depends Upon Low-Density Lipoprotein Cholesterol Levels.}, journal = {Journal of the American Heart Association}, volume = {8}, number = {19}, pages = {e011797}, pmid = {31566105}, issn = {2047-9980}, mesh = {Aged ; Bacteria/classification/*genetics/metabolism ; Biomarkers/blood ; Case-Control Studies ; Cholesterol, LDL/*blood ; DNA, Bacterial/blood/*genetics ; Dyslipidemias/*blood/diagnosis ; Female ; Humans ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Myocardial Infarction/*blood/diagnosis/*microbiology ; Pilot Projects ; Ribotyping ; }, abstract = {Background The role of bacteria on the onset of cardiovascular disease has been suggested. Reciprocally, increased intestinal bacterial translocation and bloodstream infection are common comorbidities associated with heart failure and myocardial infarction (MI). In this context, the aim of this study was to analyze the blood microbiome in patients shortly after acute myocardial infarction. Methods and Results We carried out a case control study comparing 103 patients at high cardiovascular risk but free of coronary disease and 99 patients who had an MI. The blood microbiome was analyzed both quantitatively by 16S quantitative polymerase chain reaction and qualitatively by 16S targeted metagenomic sequencing specifically optimized for blood samples. A significant increase in blood bacterial 16S rDNA concentration was observed in patients admitted for MI. This increase in blood bacterial DNA concentration was independent of post-MI left ventricular function and was more marked in patients with low-density lipoprotein cholesterol ≥1 g/L. In addition, differences in the proportion of numerous bacterial taxa in blood were significantly modified with the onset of MI, thus defining a blood microbiota signature of MI. Among the bacterial taxa whose proportions are decreased in patients with MI, at least 6 are known to include species able to metabolize cholesterol. Conclusions These results could provide the basis for the identification of blood microbiome-based biomarkers for the stratification of MI patients. Furthermore, these findings should provide insight into the mechanism underlying the negative correlation reported between low-density lipoprotein cholesterol concentration and the prognosis at the acute onset of MI and mortality. Clinical Trial Registration URL: http://www.clinicaltrials.gov. Unique identifier: NCT02405468.}, } @article {pmid31564708, year = {2019}, author = {Zheng, A and Yi, H and Li, F and Han, L and Yu, J and Cheng, X and Su, H and Hong, K and Li, J}, title = {Changes in Gut Microbiome Structure and Function of Rats with Isoproterenol-Induced Heart Failure.}, journal = {International heart journal}, volume = {60}, number = {5}, pages = {1176-1183}, doi = {10.1536/ihj.18-194}, pmid = {31564708}, issn = {1349-3299}, mesh = {Animals ; Bacteria/*classification/genetics ; Disease Models, Animal ; Echocardiography ; Gastrointestinal Microbiome/*drug effects ; Heart Failure/chemically induced/diagnostic imaging/*microbiology ; High-Throughput Nucleotide Sequencing ; Injections, Intraperitoneal ; Isoproterenol/*adverse effects/pharmacology ; Male ; Metagenomics/*methods ; Phylogeny ; Rats ; Sequence Analysis, DNA ; }, abstract = {Recently, the potential role of gut microbiome (GM) in cardiovascular diseases has been revealed. Heart failure (HF) is one of the most prevalent cardiovascular diseases worldwide; however, whether GM dysbiosis participates in the development of HF remains largely unknown. This study aimed to investigate the specific changes in GM composition and function in isoproterenol (ISO)-induced HF in rats.The rats were divided into C (control), 4w-HF (ISO, 2.5 mg/kg/day for 4 weeks, intraperitoneally), and 2w-HF (ISO, 2.5 mg/kg/day for 2 weeks, intraperitoneally) groups. The cardiac structure and function in rats were assessed, and metagenomic analyses were then performed. Compared with the healthy control group, we found that the Shannon diversity index and microbial gene count in the 4w-HF and 2w-HF groups was drastically decreased. High-throughput sequencing showed that the three groups differed in intestinal bacterial community composition. Overgrowth of bacteria, such as Prevotella, was observed in the 4w-HF group, with reduced growth of bacteria, such as Roseburia, Lactobacillus, and Butyrivibrio, associated with healthy status compared with the C group on the genus level. Concomitant with the alteration of GM composition, underrepresentation of health-linked microbial function was observed in both the 4w-HF and 2w-HF groups compared with the C group.Iso-induced HF rats showed a significant decrease in the diversity and richness of the intestinal microbiome, with a downregulation of the key intestinal bacterial groups and overgrowth of bacteria considered to be involved in inflammatory responses as well as a decrease in health-linked microbial function. Our data indicated that altered GM may be a potential player in the pathogenesis and progression of HF.}, } @article {pmid31563955, year = {2019}, author = {Weinroth, MD and Martin, JN and Doster, E and Geornaras, I and Parker, JK and Carlson, CR and Metcalf, JL and Morley, PS and Belk, KE}, title = {Investigation of tylosin in feed of feedlot cattle and effects on liver abscess prevalence, and fecal and soil microbiomes and resistomes1.}, journal = {Journal of animal science}, volume = {97}, number = {11}, pages = {4567-4578}, pmid = {31563955}, issn = {1525-3163}, support = {T32 OD012201/OD/NIH HHS/United States ; }, mesh = {Animal Feed/analysis ; Animals ; Anti-Bacterial Agents/*administration & dosage ; Cattle ; Cattle Diseases/epidemiology/microbiology/*prevention & control ; Dietary Supplements/*analysis ; Drug Resistance, Bacterial ; Feces/microbiology ; Female ; Geography ; Liver Abscess/epidemiology/microbiology/prevention & control/*veterinary ; Male ; Metagenomics ; Microbiota/*drug effects/genetics ; Models, Statistical ; Prevalence ; Soil Microbiology ; Tylosin/*administration & dosage ; }, abstract = {Liver abscesses in feedlot cattle are detrimental to animal performance and economic return. Tylosin, a macrolide antibiotic, is used to reduce prevalence of liver abscesses, though there is variable efficacy among different groups of cattle. There is an increased importance in better understanding the etiology and pathogenesis of this condition because of growing concern over antibiotic resistance and increased scrutiny regarding use of antibiotics in food animal production. The objective of this study was to compare the microbiomes and antimicrobial resistance genes (resistomes) of feces of feedlot cattle administered or not administered tylosin and in their pen soil in 3 geographical regions with differing liver abscess prevalences. Cattle (total of 2,256) from 3 geographical regions were selected for inclusion based on dietary supplementation with tylosin (yes/no). Feces and pen soil samples were collected before harvest, and liver abscesses were identified at harvest. Shotgun and 16S rRNA amplicon sequencing were used to evaluate the soil and feces. Microbiome and resistome composition of feces (as compared by UniFrac distances and Euclidian distances, respectively) did not differ (P > 0.05) among tylosin or no tylosin-administered cattle. However, feedlot location was associated with differences (P ≤ 0.05) of resistomes and microbiomes. Using LASSO, a statistical model identified both fecal and soil microbial communities as predictive of liver abscess prevalence in pens. This model explained 75% of the variation in liver abscess prevalence, though a larger sample size would be needed to increase robustness of the model. These data suggest that tylosin exposure does not have a large impact on cattle resistomes or microbiomes, but instead, location of cattle production may be a stronger driver of both the resistome and microbiome composition of feces.}, } @article {pmid31563776, year = {2019}, author = {Torres, GG and Figueroa-Galvis, I and Muñoz-García, A and Polanía, J and Vanegas, J}, title = {Potential bacterial bioindicators of urban pollution in mangroves.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {255}, number = {Pt 2}, pages = {113293}, doi = {10.1016/j.envpol.2019.113293}, pmid = {31563776}, issn = {1873-6424}, mesh = {Colombia ; Environmental Biomarkers/*genetics ; Environmental Pollution/*adverse effects ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology/*standards ; *Wetlands ; }, abstract = {Despite their ecological and socioeconomic importance, mangroves are among the most threatened tropical environments in the world. In the past two decades, the world's mangrove degradation and loss were estimated to lie between an 35% and >80%. However, appropriate bioindicators for assessing the impact of external factors, and for differentiating polluted from unpolluted areas are still scarce. Here, we determine the physicochemical profiles of the soils of two mangroves, one exposed to and one not exposed to anthropogenic factors. By metagenomic analysis based on 16S rRNA, we generated the bacterial diversity profiles of the soils and estimated their functional profiles. Our results showed that the two examined mangrove forests differed significantly in the physicochemical properties of the soils, especially regarding organic carbon, phosphorus and metal content, as well as in their microbial communities, which was likely caused by anthropogenic pollution. The physicochemical differences between the soils explained 76% of the differential bacterial composition, and 64% depended solely on gradients of phosphorus, metal ions and potassium. We found two genera JL-ETNP-Z39 and TA06 exclusively in polluted and non-polluted mangroves, respectively. Additionally, the polluted mangrove was enriched in Gemmatimonadetes, Cyanobacteria, Chloroflexi, Firmicutes, Acidobacteria, and Nitrospirae. A total of 77 genera were affected by anthropic contamination, of which we propose 33 as bioindicators; 26 enriched, and 7 depleted upon pollution.}, } @article {pmid31562947, year = {2020}, author = {Hynönen, U and Zoetendal, EG and Virtala, AK and Shetty, S and Hasan, S and Jakava-Viljanen, M and de Vos, WM and Palva, A}, title = {Molecular ecology of the yet uncultured bacterial Ct85-cluster in the mammalian gut.}, journal = {Anaerobe}, volume = {62}, number = {}, pages = {102104}, doi = {10.1016/j.anaerobe.2019.102104}, pmid = {31562947}, issn = {1095-8274}, mesh = {Animals ; Cluster Analysis ; Databases, Genetic ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Mammals ; *Metagenome ; *Metagenomics/methods ; Molecular Typing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In our previous studies on irritable bowel syndrome (IBS) -associated microbiota by molecular methods, we demonstrated that a particular 16S rRNA gene amplicon was more abundant in the feces of healthy subjects or mixed type IBS (IBS-M) -sufferers than in the feces of individuals with diarrhea-type IBS (IBS-D). In the current study, we demonstrated that this, so called Ct85-amplicon, consists of a cluster of very heterogeneous 16S rRNA gene sequences, and defined six 16S rRNA gene types, a to f, within this cluster, each representing a novel species-, genus- or family level taxon. We then designed specific PCR primers for these sequence types, mapped the distribution of the Ct85-cluster sequences and that of the newly defined sequence types in several animal species and compared the sequence types present in the feces of healthy individuals and IBS sufferers using two IBS study cohorts, Finnish and Dutch. Various Ct85-cluster sequence types were detected in the fecal samples of several companion and production animal species with remarkably differing prevalences and abundances. The Ct85 sequence type composition of swine closely resembled that of humans. One of the five types (d) shared between humans and swine was not present in any other animals tested, while one sequence type (b) was found only in human samples. In both IBS study cohorts, one type (e) was more prevalent in healthy individuals than in the IBS-M group. By revealing various sequence types in the widespread Ct85-cluster and their distribution, the results improve our understanding of these uncultured bacteria, which is essential for future efforts to cultivate representatives of the Ct85-cluster and reveal their roles in IBS.}, } @article {pmid31562300, year = {2019}, author = {Liu, J and Taft, DH and Maldonado-Gomez, MX and Johnson, D and Treiber, ML and Lemay, DG and DePeters, EJ and Mills, DA}, title = {The fecal resistome of dairy cattle is associated with diet during nursing.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4406}, pmid = {31562300}, issn = {2041-1723}, support = {R25 GM056765/GM/NIGMS NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; S10 RR027303/RR/NCRR NIH HHS/United States ; R01 AT008759/AT/NCCIH NIH HHS/United States ; R01 AT007079/AT/NCCIH NIH HHS/United States ; }, mesh = {Animal Feed/*analysis ; Animals ; Animals, Newborn ; Anti-Bacterial Agents/pharmacology ; Cattle ; Colostrum/microbiology ; Dairying ; *Diet ; Drug Resistance, Multiple, Bacterial/drug effects/*genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/drug effects/genetics ; *Gene Regulatory Networks ; Genes, Bacterial/*genetics ; Manure/microbiology ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {Antimicrobial resistance is a global public health concern, and livestock play a significant role in selecting for resistance and maintaining such reservoirs. Here we study the succession of dairy cattle resistome during early life using metagenomic sequencing, as well as the relationship between resistome, gut microbiota, and diet. In our dataset, the gut of dairy calves serves as a reservoir of 329 antimicrobial resistance genes (ARGs) presumably conferring resistance to 17 classes of antibiotics, and the abundance of ARGs declines gradually during nursing. ARGs appear to co-occur with antibacterial biocide or metal resistance genes. Colostrum is a potential source of ARGs observed in calves at day 2. The dynamic changes in the resistome are likely a result of gut microbiota assembly, which is closely associated with diet transition in dairy calves. Modifications in the resistome may be possible via early-life dietary interventions to reduce overall antimicrobial resistance.}, } @article {pmid31561965, year = {2019}, author = {Jahn, MT and Arkhipova, K and Markert, SM and Stigloher, C and Lachnit, T and Pita, L and Kupczok, A and Ribes, M and Stengel, ST and Rosenstiel, P and Dutilh, BE and Hentschel, U}, title = {A Phage Protein Aids Bacterial Symbionts in Eukaryote Immune Evasion.}, journal = {Cell host & microbe}, volume = {26}, number = {4}, pages = {542-550.e5}, doi = {10.1016/j.chom.2019.08.019}, pmid = {31561965}, issn = {1934-6069}, mesh = {Animals ; Ankyrins/*metabolism ; Bacteria/genetics/*immunology/virology ; Bacteriophages/classification/*genetics ; Cell Line ; Female ; Immune Evasion/*immunology ; Mice ; Mice, Inbred C57BL ; Microbiota/physiology ; Porifera/*immunology/*virology ; Symbiosis/physiology ; }, abstract = {Phages are increasingly recognized as important members of host-associated microbiomes, with a vast genomic diversity. The new frontier is to understand how phages may affect higher order processes, such as in the context of host-microbe interactions. Here, we use marine sponges as a model to investigate the interplay between phages, bacterial symbionts, and eukaryotic hosts. Using viral metagenomics, we find that sponges, although massively filtering seawater, harbor species-specific and even individually unique viral signatures that are taxonomically distinct from other environments. We further discover a symbiont phage-encoded ankyrin-domain-containing protein, which is widely spread in phages of many host-associated contexts including human. We confirm in macrophage infection assays that the ankyrin protein (ANKp) modulates the eukaryotic host immune response against bacteria. We predict that the role of ANKp in nature is to facilitate coexistence in the tripartite interplay between phages, symbionts, and sponges and possibly many other host-microbe associations.}, } @article {pmid31561379, year = {2019}, author = {Paley, EL}, title = {Discovery of Gut Bacteria Specific to Alzheimer's Associated Diseases is a Clue to Understanding Disease Etiology: Meta-Analysis of Population-Based Data on Human Gut Metagenomics and Metabolomics.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {72}, number = {1}, pages = {319-355}, doi = {10.3233/JAD-190873}, pmid = {31561379}, issn = {1875-8908}, mesh = {Alzheimer Disease/epidemiology/*genetics/*metabolism ; Case-Control Studies ; Gastrointestinal Microbiome/*physiology ; Humans ; Metabolomics/*methods/trends ; Metagenomics/*methods/trends ; Population Surveillance/*methods ; }, abstract = {Alzheimer's disease (AD)-associated sequence (ADAS) of cultured fecal bacteria was discovered in human gut targeted screening. This study provides important information to expand our current understanding of the structure/activity relationship of ADAS and putative inhibitors/activators that are potentially involved in ADAS appearance/disappearance. The NCBI database analysis revealed that ADAS presents at a large proportion in American Indian Oklahoman (C&A) with a high prevalence of obesity/diabetes and in colorectal cancer (CRC) patients from the US and China. An Oklahoman non-native group (NNI) showed no ADAS. Comparison of two large US populations reveals that ADAS is more frequent in individuals aged ≥66 and in females. Prevalence and levels of fecal metabolites are altered in the C&A and CRC groups versus controls. Biogenic amines (histamine, tryptamine, tyramine, phenylethylamine, cadaverine, putrescine, agmatine, spermidine) that present in food and are produced by gut microbiota are significantly higher in C&A (e.g., histamine/histidine 95-fold) versus NNI (histamine/histidine 16-fold). The majority of these bio-amines are cytotoxic at concentrations found in food. Inositol phosphate signaling implicated in AD is altered in C&A and CRC. Tryptamine stimulated accumulation of inositol phosphate. The seizure-eliciting tryptamine induced cytoplasmic vacuolization and vesiculation with cell fragmentation. Present additions of ADAS-carriers at different ages including infants led to an ADAS-comprising human sample size of 2,830 from 27 studies from four continents (North America, Australia, Asia, Europe). Levels of food-derived monoamine oxidase inhibitors and anti-bacterial compounds, the potential modulators of ADAS-bacteria growth and biogenic amine production, were altered in C&A versus NNI. ADAS is attributable to potentially modifiable risk factors of AD associated diseases.}, } @article {pmid31561274, year = {2020}, author = {Bergner, LM and Orton, RJ and Benavides, JA and Becker, DJ and Tello, C and Biek, R and Streicker, DG}, title = {Demographic and environmental drivers of metagenomic viral diversity in vampire bats.}, journal = {Molecular ecology}, volume = {29}, number = {1}, pages = {26-39}, pmid = {31561274}, issn = {1365-294X}, support = {102507/Z/13/A//Wellcome-Beit Prize/International ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; 102507//Wellcome Trust/United Kingdom ; MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Biodiversity ; Chiroptera/*virology ; Communicable Diseases/*virology ; Demography ; *Ecology ; Ecosystem ; Environment ; Humans ; *Metagenome ; Metagenomics ; South America ; Viruses/*genetics ; }, abstract = {Viruses infect all forms of life and play critical roles as agents of disease, drivers of biochemical cycles and sources of genetic diversity for their hosts. Our understanding of viral diversity derives primarily from comparisons among host species, precluding insight into how intraspecific variation in host ecology affects viral communities or how predictable viral communities are across populations. Here we test spatial, demographic and environmental hypotheses explaining viral richness and community composition across populations of common vampire bats, which occur in diverse habitats of North, Central and South America. We demonstrate marked variation in viral communities that was not consistently predicted by a null model of declining community similarity with increasing spatial or genetic distances separating populations. We also find no evidence that larger bat colonies host greater viral diversity. Instead, viral diversity follows an elevational gradient, is enriched by juvenile-biased age structure, and declines with local anthropogenic food resources as measured by livestock density. Our results establish the value of linking the modern influx of metagenomic sequence data with comparative ecology, reveal that snapshot views of viral diversity are unlikely to be representative at the species level, and affirm existing ecological theories that link host ecology not only to single pathogen dynamics but also to viral communities.}, } @article {pmid31561205, year = {2019}, author = {Wu, J and Zhang, PB and Ren, ZQ and Zhou, F and Hu, HH and Zhang, H and Xue, KK and Xu, P and Shao, XQ}, title = {Changes of serum lipopolysaccharide, inflammatory factors, and cecal microbiota in obese rats with type 2 diabetes induced by Roux-en-Y gastric bypass.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {67-68}, number = {}, pages = {110565}, doi = {10.1016/j.nut.2019.110565}, pmid = {31561205}, issn = {1873-1244}, mesh = {Animals ; Cecum/microbiology ; Diabetes Mellitus, Experimental/*blood/etiology/microbiology ; Diabetes Mellitus, Type 2/*blood/etiology/microbiology ; Disease Models, Animal ; Gastric Bypass/adverse effects ; *Gastrointestinal Microbiome ; Hypoglycemic Agents/blood ; Inflammation Mediators/*blood ; Lipopolysaccharides/*blood ; Obesity/surgery ; Postoperative Period ; Rats ; Rats, Sprague-Dawley ; }, abstract = {OBJECTIVES: Previous studies have shown that Roux-en-Y gastric bypass (RYGB) leads to rapid regression of obesity and type 2 diabetes (T2D). However, the underlying mechanism remains unclear. This study aimed to investigate the effect of RYGB on serum lipopolysaccharide (LPS), interleukin (IL)-1, IL-6, tumor necrosis factor alpha (TNF-α), and cecal microbiota in obese rats with T2D.

METHODS: Obese Sprague-Dawley rats with T2D were randomly divided into RYGB diabetes operation (DO; n = 8), diabetes sham operation (DS; n = 8), and diabetic control (DC; n = 8) groups. Healthy Sprague-Dawley rats were grouped as normal control (NC; n = 8). Fasting plasma glucose and body weight were measured. The levels of peripheral serum LPS, IL-1, IL-6, and TNF-α were measured by enzyme-linked immunosorbent assay. The rats were sacrificed 12 wk after operation. Subsequently, a superior mesenteric venous blood sample was taken to measure serum LPS levels by enzyme-linked immunosorbent assay. The cecal contents of the DO and DS groups were taken to extract metagenomic DNA per the genomic DNA standardization procedure. The V4 region of the 16 S rRNA was sequenced with the Illumina Hiseq sequencing platform to compare the structure and relative abundance of cecal microbiota between the DO and DS groups.

RESULTS: Twelve weeks after operation in the DO group, fasting plasma glucose and body weight showed a significant decrease (P < 0.05). Moreover, the levels of peripheral serum LPS, IL-1, IL-6, and TNF-α were obviously decreased (P < 0.05). A change in the LPS level of superior mesenteric venous blood also revealed a dramatic decrease (P < 0.05). Additionally, RYGB resulted in a shift of cecal microbiota in obese rats with T2D.

CONCLUSIONS: Hypoglycemic effects after RYGB may be associated with improved levels of LPS, IL-1, IL-6, and TNF-α. Changes in the structure of cecal microbiota may also play an important role.}, } @article {pmid31558359, year = {2020}, author = {O'Donovan, CM and Madigan, SM and Garcia-Perez, I and Rankin, A and O' Sullivan, O and Cotter, PD}, title = {Distinct microbiome composition and metabolome exists across subgroups of elite Irish athletes.}, journal = {Journal of science and medicine in sport}, volume = {23}, number = {1}, pages = {63-68}, doi = {10.1016/j.jsams.2019.08.290}, pmid = {31558359}, issn = {1878-1861}, support = {PDF-2012-05-456/DH_/Department of Health/United Kingdom ; }, mesh = {*Athletes ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Ireland ; Male ; *Metabolome ; Sports/*classification ; Urine/microbiology ; }, abstract = {OBJECTIVES: The gut microbiome has begun to be characterised in athlete groups, albeit, to date, only across a subset of sports. This study aimed to determine if the gut microbiome and metabolome differed across sports classification groups (SCGs) among elite Irish athletes, many of whom were participating in the 2016 Summer Olympics.

METHODS: Faecal and urine samples were collected from 37 international level athletes. Faecal samples were prepared for shotgun metagenomic sequencing and faecal and urine samples underwent metabolomic profiling.

RESULTS: Differences were observed in the composition and functional capacity of the gut microbiome of athletes across SCGs. The microbiomes of athletes participating in sports with a high dynamic component were the most distinct compositionally (greater differences in proportions of species), while those of athletes participating in sports with high dynamic and static components were the most functionally distinct (greater differences in functional potential). Additionally, both microbial (faecal) and human (urine) derived metabolites were found to vary between SCGs. In particular cis-aconitate, succinic acid and lactate, in urine samples, and creatinine, in faeces, were found to be significantly different between groups. These differences were evident despite the absence of significant differences in diet, as determined using food frequency questionnaires, which were translated into nutrient intake values using FETA.

CONCLUSIONS: Differences in the gut microbiome and metabolome between groups, in the absence of dietary changes, indicates a role for training load or type as a contributory factor. Further exploration of this hypothesis has the potential to benefit athletes, aspiring athletes and the general public.}, } @article {pmid31556231, year = {2019}, author = {Liu, B and Yang, L and Cui, Z and Zheng, J and Huang, J and Zhao, Q and Su, Z and Wang, M and Zhang, W and Liu, J and Wang, T and Li, Q and Lu, H}, title = {Anti-TNF-α therapy alters the gut microbiota in proteoglycan-induced ankylosing spondylitis in mice.}, journal = {MicrobiologyOpen}, volume = {8}, number = {12}, pages = {e927}, pmid = {31556231}, issn = {2045-8827}, mesh = {Animals ; Antirheumatic Agents/pharmacology ; Disease Models, Animal ; Etanercept/*pharmacology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestinal Mucosa/drug effects/metabolism/microbiology/pathology ; Metagenomics/methods ; Mice ; Permeability ; Proteoglycans/*adverse effects ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Spondylitis, Ankylosing/diagnosis/drug therapy/*etiology/*metabolism ; Tight Junction Proteins/metabolism ; Tumor Necrosis Factor-alpha/*antagonists & inhibitors ; }, abstract = {Ankylosing spondylitis is a chronic, progressive disease, and its treatment is relevant to the gut microbiota. Anti-tumor necrosis factor-alpha (anti-TNF-α) therapy alters the gut microbiota in many diseases, including inflammatory bowel disease. However, little is known about the effect of TNF-α blocker treatment on the gut microbiota in ankylosing spondylitis. Herein, the effect of a TNF-α blocker on the gut microbiota in proteoglycan-induced arthritis was investigated. Proteoglycan-induced mice were treated with an rhTNFR:Fc solution of etanercept (5 µg/g) for 4 weeks. rhTNFR:Fc treatment attenuated the arthritis incidence and severity of arthritis in the proteoglycan-induced mice and decreased inflammation in the ankle joints and ameliorated ileal tissue destruction. Moreover, high gut permeability occurred, and zonula occludens-1 and occludin protein levels were reduced in proteoglycan-induced mice. These levels were significantly restored by the administration of rhTNFR:Fc. The serum TNF-α and IL-17 levels were also decreased. In addition, flora analysis via 16S rDNA high-throughput sequencing revealed that rhTNFR:Fc treatment restored the gut microbiota composition to a composition similar to that in control mice. In conclusion, anti-TNF-α therapy attenuated proteoglycan-induced arthritis progression and modulated the gut microbiota and intestinal barrier function. These results provide new insights for anti-TNF-α therapy strategies via regulating the gut microbiota in ankylosing spondylitis.}, } @article {pmid31554820, year = {2019}, author = {Riva, A and Kuzyk, O and Forsberg, E and Siuzdak, G and Pfann, C and Herbold, C and Daims, H and Loy, A and Warth, B and Berry, D}, title = {A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4366}, pmid = {31554820}, issn = {2041-1723}, support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; P 26127/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Colon/*microbiology ; *Diet ; Dietary Fiber/*deficiency ; Gastrointestinal Microbiome/genetics/*physiology ; Intestinal Mucosa/microbiology ; Metagenomics/methods ; Mice, Inbred C57BL ; Microbiota/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Compartmentalization of the gut microbiota is thought to be important to system function, but the extent of spatial organization in the gut ecosystem remains poorly understood. Here, we profile the murine colonic microbiota along longitudinal and lateral axes using laser capture microdissection. We found fine-scale spatial structuring of the microbiota marked by gradients in composition and diversity along the length of the colon. Privation of fiber reduces the diversity of the microbiota and disrupts longitudinal and lateral gradients in microbiota composition. Both mucus-adjacent and luminal communities are influenced by the absence of dietary fiber, with the loss of a characteristic distal colon microbiota and a reduction in the mucosa-adjacent community, concomitant with depletion of the mucus layer. These results indicate that diet has not only global but also local effects on the composition of the gut microbiota, which may affect function and resilience differently depending on location.}, } @article {pmid31553956, year = {2019}, author = {Ye, W and Zhang, Y and He, M and Zhu, C and Feng, XP}, title = {Relationship of tongue coating microbiome on volatile sulfur compounds in healthy and halitosis adults.}, journal = {Journal of breath research}, volume = {14}, number = {1}, pages = {016005}, doi = {10.1088/1752-7163/ab47b4}, pmid = {31553956}, issn = {1752-7163}, mesh = {Adult ; Biodiversity ; Breath Tests ; Case-Control Studies ; Female ; Halitosis/*microbiology ; *Healthy Volunteers ; Humans ; Male ; *Microbiota ; Sulfur Compounds/*analysis ; Tongue/*microbiology ; Volatile Organic Compounds/*analysis ; }, abstract = {AIM: This study aims to assess the microbiome variations related to intraoral halitosis and its relationship with volatile sulfur compounds (VSCs) among periodontally healthy Chinese adults.

MATERIAL AND METHODS: Tongue coating samples were collected from 28 periodontally healthy subjects (16 subjects with halitosis and 12 subjects without halitosis) who fulfilled the selection criteria. The organoleptic score (OS) was used to evaluate the halitosis status. The characterization of associated microbial communities was performed using 16S rRNA gene pyrosequencing and metagenomics methods.

RESULTS: A wide range of microbial communities, including 13 phyla, 23 classes, 37 orders, 134 genera, 266 species and 349 operational taxonomic units (OTUs), were detected. The Shannon index values were significantly higher in the halitosis group. Genera, such as Prevotella, Alloprevotella, Leptotrichia, Peptostreptococcus and Stomatobaculum, exhibited significantly higher relative percentages in halitosis samples, when compared to healthy samples. Peptostreptococcus, Alloprevotella, Eubacterium nodatum and Stomatobaculum exhibited significantly positive correlations with the total number of VSCs. Prevotella, Peptostreptococcus, Eubacterium nodatum and Alloprevotella were correlated with increased H2S and CH3SH concentration values. Bergeyella was correlated with decreased total VSC, H2S and CH3SH concentration values.

CONCLUSION: Microbial diversity was higher in the halitosis group than in the control group, and several bacteria were significantly correlated to halitosis. Furthermore, there were correlations between tongue bacterial composition structure and VSC gases. Tongue coating microbiota can offer important clues in the investigation of the pathogenesis and treatment of halitosis.}, } @article {pmid31553576, year = {2019}, author = {Zallot, R and Oberg, N and Gerlt, JA}, title = {The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways.}, journal = {Biochemistry}, volume = {58}, number = {41}, pages = {4169-4182}, pmid = {31553576}, issn = {1520-4995}, support = {P01 GM118303/GM/NIGMS NIH HHS/United States ; U54 GM093342/GM/NIGMS NIH HHS/United States ; }, mesh = {*Databases, Protein ; Dental Plaque/enzymology ; Feces/enzymology ; Gastrointestinal Microbiome/genetics ; Genomics/*methods ; Healthy Volunteers ; Humans ; Metabolic Networks and Pathways/*genetics ; *Metagenome ; Mouth Mucosa/enzymology ; *Software ; Tongue/enzymology ; }, abstract = {The assignment of functions to uncharacterized proteins discovered in genome projects requires easily accessible tools and computational resources for large-scale, user-friendly leveraging of the protein, genome, and metagenome databases by experimentalists. This article describes the web resource developed by the Enzyme Function Initiative (EFI; accessed at https://efi.igb.illinois.edu/) that provides "genomic enzymology" tools ("web tools") for (1) generating sequence similarity networks (SSNs) for protein families (EFI-EST); (2) analyzing and visualizing genome context of the proteins in clusters in SSNs (in genome neighborhood networks, GNNs, and genome neighborhood diagrams, GNDs) (EFI-GNT); and (3) prioritizing uncharacterized SSN clusters for functional assignment based on metagenome abundance (chemically guided functional profiling, CGFP) (EFI-CGFP). The SSNs generated by EFI-EST are used as the input for EFI-GNT and EFI-CGFP, enabling easy transfer of information among the tools. The networks are visualized and analyzed using Cytoscape, a widely used desktop application; GNDs and CGFP heatmaps summarizing metagenome abundance are viewed within the tools. We provide a detailed example of the integrated use of the tools with an analysis of glycyl radical enzyme superfamily (IPR004184) found in the human gut microbiome. This analysis demonstrates that (1) SwissProt annotations are not always correct, (2) large-scale genome context analyses allow the prediction of novel metabolic pathways, and (3) metagenome abundance can be used to identify/prioritize uncharacterized proteins for functional investigation.}, } @article {pmid31553437, year = {2020}, author = {Breitwieser, FP and Salzberg, SL}, title = {Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {4}, pages = {1303-1304}, pmid = {31553437}, issn = {1367-4811}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; }, mesh = {Data Interpretation, Statistical ; *Metagenomics ; *Microbiota ; Software ; }, abstract = {SUMMARY: Pavian is a web application for exploring classification results from metagenomics experiments. With Pavian, researchers can analyze, visualize and transform results from various classifiers-such as Kraken, Centrifuge and MethaPhlAn-using interactive data tables, heatmaps and Sankey flow diagrams. An interactive alignment coverage viewer can help in the validation of matches to a particular genome, which can be crucial when using metagenomics experiments for pathogen detection.

Pavian is implemented in the R language as a modular Shiny web app and is freely available under GPL-3 from http://github.com/fbreitwieser/pavian.}, } @article {pmid31552140, year = {2019}, author = {Shah, TM and Patel, JG and Gohil, TP and Blake, DP and Joshi, CG}, title = {Host transcriptome and microbiome interaction modulates physiology of full-sibs broilers with divergent feed conversion ratio.}, journal = {NPJ biofilms and microbiomes}, volume = {5}, number = {1}, pages = {24}, pmid = {31552140}, issn = {2055-5008}, mesh = {*Animal Feed ; Animals ; Chickens/*growth & development ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; *Host Microbial Interactions ; Intestines ; Liver ; Siblings ; *Weight Gain ; }, abstract = {Efficient livestock production relies on effective conversion of feed into body weight gain (BWG). High levels of feed conversion are especially important in production of broiler chickens, birds reared for meat, where economic margins are tight. Traits associated with improved broiler growth and feed efficiency have been subjected to intense genetic selection, but measures such as feed conversion ratio (FCR) remain variable, even between full siblings (sibs). Non-genetic factors such as the composition and function of microbial populations within different enteric compartments have been recognized to influence FCR, although the extent of interplay between hosts and their microbiomes is unclear. To examine host-microbiome interactions we investigated variation in the composition and functions of host intestinal-hepatic transcriptomes and the intestinal microbiota of full-sib broilers with divergent FCR. Progeny from 300 broiler families were assessed for divergent FCR set against shared genetic backgrounds and exposure to the same environmental factors. The seven most divergent full-sib pairs were chosen for analysis, exhibiting marked variation in transcription of genes as well as gut microbial diversity. Examination of enteric microbiota in low FCR sibs revealed variation in microbial community structure and function with no difference in feed intake compared to high FCR sibs. Gene transcription in low and high FCR sibs was significantly associated with the abundance of specific microbial taxa. Highly intertwined interactions between host transcriptomes and enteric microbiota are likely to modulate complex traits like FCR and may be amenable to selective modification with relevance to improving intestinal homeostasis and health.}, } @article {pmid31551441, year = {2019}, author = {Aalismail, NA and Ngugi, DK and Díaz-Rúa, R and Alam, I and Cusack, M and Duarte, CM}, title = {Functional metagenomic analysis of dust-associated microbiomes above the Red Sea.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13741}, pmid = {31551441}, issn = {2045-2322}, mesh = {Archaea/genetics ; Bacteria/genetics ; Biodiversity ; DNA Damage/genetics ; Dust ; Eukaryota/genetics ; Indian Ocean ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Viruses/genetics ; }, abstract = {Atmospheric transport is a major vector for the long-range transport of microbial communities, maintaining connectivity among them and delivering functionally important microbes, such as pathogens. Though the taxonomic diversity of aeolian microorganisms is well characterized, the genomic functional traits underpinning their survival during atmospheric transport are poorly characterized. Here we use functional metagenomics of dust samples collected on the Global Dust Belt to initiate a Gene Catalogue of Aeolian Microbiome (GCAM) and explore microbial genetic traits enabling a successful aeolian lifestyle in Aeolian microbial communities. The GCAM reported here, derived from ten aeolian microbial metagenomes, includes a total of 2,370,956 non-redundant coding DNA sequences, corresponding to a yield of ~31 × 10[6] predicted genes per Tera base-pair of DNA sequenced for the aeolian samples sequenced. Two-thirds of the cataloged genes were assigned to bacteria, followed by eukaryotes (5.4%), archaea (1.1%), and viruses (0.69%). Genes encoding proteins involved in repairing UV-induced DNA damage and aerosolization of cells were ubiquitous across samples, and appear as fundamental requirements for the aeolian lifestyle, while genes coding for other important functions supporting the aeolian lifestyle (chemotaxis, aerotaxis, germination, thermal resistance, sporulation, and biofilm formation) varied among the communities sampled.}, } @article {pmid31550982, year = {2020}, author = {Tanaka, M and Sanefuji, M and Morokuma, S and Yoden, M and Momoda, R and Sonomoto, K and Ogawa, M and Kato, K and Nakayama, J}, title = {The association between gut microbiota development and maturation of intestinal bile acid metabolism in the first 3 y of healthy Japanese infants.}, journal = {Gut microbes}, volume = {11}, number = {2}, pages = {205-216}, pmid = {31550982}, issn = {1949-0984}, mesh = {Amidohydrolases/analysis ; Bacteria/classification/genetics/isolation & purification ; Bifidobacterium/genetics/isolation & purification ; Bile/metabolism ; *Bile Acids and Salts/biosynthesis/metabolism ; Child, Preschool ; Clostridiales/genetics/isolation & purification ; Enterobacteriaceae/classification/genetics/isolation & purification ; Feces/enzymology/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant Health ; Infant, Newborn ; Intestines/microbiology ; Japan ; Male ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The gut microbial community greatly changes in early life, influencing infant health and subsequent host physiology, notably through its collective metabolism, including host-microbiota interplay of bile acid (BA) metabolism. However, little is known regarding how the development of the intestinal microbial community is associated with maturation of intestinal BA metabolism. To address this, we monitored the succession of gut bacterial community and its association with fecal BA profile in the first 3 y of ten healthy Japanese infants. The BA profiles were classified into four types, defined by high content of conjugated primary BA (Con type), unconjugated primary BA (chenodeoxycholic acid and cholic acid) (Pri type), ursodeoxycholic acid (Urs type), and deoxycholic and lithocholic acid (Sec type). Most subjects begun with Con type or Pri type profiles during lactation and eventually transited to Sec type through Urs type after the start of solid food intake. Con type and Pri type were associated with Enterobacteriaceae-dominant microbiota corresponding to the neonatal type or Bifidobacterium-dominant microbiota corresponding to lactation type, respectively. Urs type subjects were strongly associated with Ruminococcus gnavus colonization, mostly occurring between Pri type and Sec type. Sec type was associated with adult-type complex microbiota dominated by a variety of Firmicutes and Bacteroidetes species. Addressing the link of the common developmental passage of intestinal BA metabolism with infant's health and subsequent host physiology requires further study.}, } @article {pmid31549683, year = {2019}, author = {Liu, Y and Qin, Y and Guo, XX and Bai, Y}, title = {[Methods and applications for microbiome data analysis].}, journal = {Yi chuan = Hereditas}, volume = {41}, number = {9}, pages = {845-862}, doi = {10.16288/j.yczz.19-222}, pmid = {31549683}, issn = {0253-9772}, mesh = {*Data Analysis ; Databases, Factual ; High-Throughput Nucleotide Sequencing ; Metagenome ; *Microbiota ; Software ; }, abstract = {Development of high-throughput sequencing stimulates a series of microbiome technologies, such as amplicon sequencing, metagenome, metatranscriptome, which have rapidly promoted microbiome research. Microbiome data analysis involves a lot of basic knowledge, software and databases, and it is difficult for peers to learn and select proper methods. This review systematically outlines the basic ideas of microbiome data analysis and the basic knowledge required to conduct analysis. In addition, it summarizes the advantages and disadvantages of commonly used software and databases used in the comparison, visualization, network, evolution, machine learning and association analysis. This review aims to provide a convenient and flexible guide for selecting analytical tools and suitable databases for mining the biological significance of microbiome data.}, } @article {pmid31549239, year = {2019}, author = {Emmanuel, SA and Sul, WJ and Seong, HJ and Rhee, C and Ekpheghere, KI and Kim, IS and Kim, HG and Koh, SC}, title = {Metagenomic analysis of relationships between the denitrification process and carbon metabolism in a bioaugmented full-scale tannery wastewater treatment plant.}, journal = {World journal of microbiology & biotechnology}, volume = {35}, number = {10}, pages = {149}, pmid = {31549239}, issn = {1573-0972}, support = {2017R1D1A3B03036376//National Research Foundation of Korea/ ; }, mesh = {Bacteria/classification/*genetics/isolation & purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Bioreactors/microbiology ; Carbon/*metabolism ; Denitrification ; Ketoglutarate Dehydrogenase Complex/genetics/metabolism ; Metagenomics ; Microbial Consortia ; Nitrates/metabolism ; Sewage/chemistry/microbiology ; Tryptophan Synthase/genetics/metabolism ; Wastewater/*microbiology ; Water Purification/instrumentation/methods ; }, abstract = {The goal of this study was to investigate the relationship between the denitrification process and carbon metabolism in a full-scale tannery wastewater treatment plant bioaugmented with the microbial consortium BM-S-1. The metagenomic analysis of the microbial community showed that Brachymonas denitrificans, a known denitrifier, was present at a high level in the treatment stages of buffering (B), primary aeration (PA), and sludge digestion (SD). The occurrences of the amino acid-degrading enzymes alpha ketoglutarate dehydrogenase (α-KGDH) and tryptophan synthase were highly correlated with the presence of denitrification genes, such as napA, narG, nosZ and norB. The occurrence of glutamate dehydrogenase (GDH) was also highly paralleled with the occurrence of denitrification genes such as napA, narG, and norZ. The denitrification genes (nosZ, narG, napA, norB and nrfA) and amino acid degradation enzymes (tryptophan synthase, α-KGDH and pyridoxal phosphate dependent enzymes) were observed at high levels in B. This indicates that degradation of amino acids and denitrification of nitrate may potentially occur in B. The high concentrations of the fatty acid degradation enzyme groups (enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase and β-ketothiolase) were observed together with the denitrification genes, such as napA, narG and nosZ. Phospholipase/carboxylesterase, enoyl-CoA hydratase/isomerase, acyl-CoA dehydrogenase, phenylacetate degradation enzyme and 3-hydroxyacyl-CoA dehydrogenase 2 were also dominant in B. All these results clearly indicate that the denitrification pathways are potentially linked to the degradation pathways of amino acids and fatty acids whose degradation products go through the TCA cycle, generating the NADH that is used as electron donors for denitrification.}, } @article {pmid31548686, year = {2019}, author = {Zaramela, LS and Martino, C and Alisson-Silva, F and Rees, SD and Diaz, SL and Chuzel, L and Ganatra, MB and Taron, CH and Secrest, P and Zuñiga, C and Huang, J and Siegel, D and Chang, G and Varki, A and Zengler, K}, title = {Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates.}, journal = {Nature microbiology}, volume = {4}, number = {12}, pages = {2082-2089}, pmid = {31548686}, issn = {2058-5276}, support = {R01 GM032373/GM/NIGMS NIH HHS/United States ; T32 GM008806/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/*enzymology ; Bacteroides/enzymology/genetics ; Clostridiales/enzymology/genetics ; Crystallography, X-Ray ; *Diet ; Feces/chemistry/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Neuraminic Acids/*metabolism ; Neuraminidase/*genetics/metabolism ; Polysaccharides/chemistry/*metabolism ; Red Meat/*analysis ; }, abstract = {Dietary habits have been associated with alterations of the human gut resident microorganisms contributing to obesity, diabetes and cancer[1]. In Western diets, red meat is a frequently eaten food[2], but long-term consumption has been associated with increased risk of disease[3,4]. Red meat is enriched in N-glycolylneuraminic acid (Neu5Gc) that cannot be synthesized by humans[5]. However, consumption can cause Neu5Gc incorporation into cell surface glycans[6], especially in carcinomas[4,7]. As a consequence, an inflammatory response is triggered when Neu5Gc-containing glycans encounter circulating anti-Neu5Gc antibodies[8,9]. Although bacteria can use free sialic acids as a nutrient source[10-12], it is currently unknown if gut microorganisms contribute to releasing Neu5Gc from food. We found that a Neu5Gc-rich diet induces changes in the gut microbiota, with Bacteroidales and Clostridiales responding the most. Genome assembling of mouse and human shotgun metagenomic sequencing identified bacterial sialidases with previously unobserved substrate preference for Neu5Gc-containing glycans. X-ray crystallography revealed key amino acids potentially contributing to substrate preference. Additionally, we verified that mouse and human sialidases were able to release Neu5Gc from red meat. The release of Neu5Gc from red meat using bacterial sialidases could reduce the risk of inflammatory diseases associated with red meat consumption, including colorectal cancer[4] and atherosclerosis[13].}, } @article {pmid31548681, year = {2019}, author = {Robbins, SJ and Singleton, CM and Chan, CX and Messer, LF and Geers, AU and Ying, H and Baker, A and Bell, SC and Morrow, KM and Ragan, MA and Miller, DJ and Forêt, S and , and Voolstra, CR and Tyson, GW and Bourne, DG}, title = {A genomic view of the reef-building coral Porites lutea and its microbial symbionts.}, journal = {Nature microbiology}, volume = {4}, number = {12}, pages = {2090-2100}, pmid = {31548681}, issn = {2058-5276}, mesh = {Animals ; Anthozoa/metabolism/*microbiology ; Archaea/*genetics ; Bacteria/*genetics ; Coral Reefs ; Dinoflagellida/genetics ; *Genome ; Metagenomics ; Microbiota ; *Symbiosis ; }, abstract = {Corals and the reef ecosystems that they support are in global decline due to increasing anthropogenic pressures such as climate change[1]. However, effective reef conservation strategies are hampered by a limited mechanistic understanding of coral biology and the functional roles of the diverse microbial communities that underpin coral health[2,3]. Here, we present an integrated genomic characterization of the coral species Porites lutea and its microbial partners. High-quality genomes were recovered from P. lutea, as well as a metagenome-assembled Cladocopium C15 (the dinoflagellate symbiont) and 52 bacterial and archaeal populations. Comparative genomic analysis revealed that many of the bacterial and archaeal genomes encode motifs that may be involved in maintaining association with the coral host and in supplying fixed carbon, B-vitamins and amino acids to their eukaryotic partners. Furthermore, mechanisms for ammonia, urea, nitrate, dimethylsulfoniopropionate and taurine transformation were identified that interlink members of the holobiont and may be important for nutrient acquisition and retention in oligotrophic waters. Our findings demonstrate the critical and diverse roles that microorganisms play within the coral holobiont and underscore the need to consider all of the components of the holobiont if we are to effectively inform reef conservation strategies.}, } @article {pmid31547633, year = {2019}, author = {Ben Mefteh, F and Bouket, AC and Daoud, A and Luptakova, L and Alenezi, FN and Gharsallah, N and Belbahri, L}, title = {Metagenomic Insights and Genomic Analysis of Phosphogypsum and Its Associated Plant Endophytic Microbiomes Reveals Valuable Actors for Waste Bioremediation.}, journal = {Microorganisms}, volume = {7}, number = {10}, pages = {}, pmid = {31547633}, issn = {2076-2607}, abstract = {The phosphogypsum (PG) endogenous bacterial community and endophytic bacterial communities of four plants growing in phosphogypsum-contaminated sites, Suaeda fruticosa (SF), Suaeda mollis (SM), Mesembryanthmum nodiflorum (MN) and Arthrocnemum indicum (AI) were investigated by amplicon sequencing. Results highlight a more diverse community of phosphogypsum than plants associated endophytic communities. Additionally, the bacterial culturable communities of phosphogypsum and associated plant endophytes were isolated and their plant-growth promotion capabilities, bioremediation potential and stress tolerance studied. Most of plant endophytes were endowed with plant growth-promoting (PGP) activities and phosphogypsum communities and associated plants endophytes proved highly resistant to salt, metal and antibiotic stress. They also proved very active in bioremediation of phosphogypsum and other organic and inorganic environmental pollutants. Genome sequencing of five members of the phosphogypsum endogenous community showed that they belong to the recently described species Bacillus albus (BA). Genome mining of BA allowed the description of pollutant degradation and stress tolerance mechanisms. Prevalence of this tool box in the core, accessory and unique genome allowed to conclude that accessory and unique genomes are critical for the dynamics of strain acquisition of bioremediation abilities. Additionally, secondary metabolites (SM) active in bioremediation such as petrobactin have been characterized. Taken together, our results reveal hidden untapped valuable bacterial actors for waste remediation.}, } @article {pmid31546776, year = {2019}, author = {Hickl, O and Heintz-Buschart, A and Trautwein-Schult, A and Hercog, R and Bork, P and Wilmes, P and Becher, D}, title = {Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome.}, journal = {Microorganisms}, volume = {7}, number = {9}, pages = {}, pmid = {31546776}, issn = {2076-2607}, support = {C15/BN/10404093//Fonds National de la Recherche Luxembourg/ ; FZT118//Deutsche Forschungsgemeinschaft/ ; }, abstract = {With the technological advances of the last decade, it is now feasible to analyze microbiome samples, such as human stool specimens, using multi-omic techniques. Given the inherent sample complexity, there exists a need for sample methods which preserve as much information as possible about the biological system at the time of sampling. Here, we analyzed human stool samples preserved and stored using different methods, applying metagenomics as well as metaproteomics. Our results demonstrate that sample preservation and storage have a significant effect on the taxonomic composition of identified proteins. The overall identification rates, as well as the proportion of proteins from Actinobacteria were much higher when samples were flash frozen. Preservation in RNAlater overall led to fewer protein identifications and a considerable increase in the share of Bacteroidetes, as well as Proteobacteria. Additionally, a decrease in the share of metabolism-related proteins and an increase of the relative amount of proteins involved in the processing of genetic information was observed for RNAlater-stored samples. This suggests that great care should be taken in choosing methods for the preservation and storage of microbiome samples, as well as in comparing the results of analyses using different sampling and storage methods. Flash freezing and subsequent storage at -80 °C should be chosen wherever possible.}, } @article {pmid31546774, year = {2019}, author = {Truskewycz, A and Gundry, TD and Khudur, LS and Kolobaric, A and Taha, M and Aburto-Medina, A and Ball, AS and Shahsavari, E}, title = {Petroleum Hydrocarbon Contamination in Terrestrial Ecosystems-Fate and Microbial Responses.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {18}, pages = {}, pmid = {31546774}, issn = {1420-3049}, mesh = {Biodegradation, Environmental ; *Ecosystem ; Hydrocarbons/*analysis/toxicity ; *Microbiota/drug effects ; Petroleum/*analysis ; Petroleum Pollution/*analysis ; }, abstract = {Petroleum hydrocarbons represent the most frequent environmental contaminant. The introduction of petroleum hydrocarbons into a pristine environment immediately changes the nature of that environment, resulting in reduced ecosystem functionality. Natural attenuation represents the single, most important biological process which removes petroleum hydrocarbons from the environment. It is a process where microorganisms present at the site degrade the organic contaminants without the input of external bioremediation enhancers (i.e., electron donors, electron acceptors, other microorganisms or nutrients). So successful is this natural attenuation process that in environmental biotechnology, bioremediation has developed steadily over the past 50 years based on this natural biodegradation process. Bioremediation is recognized as the most environmentally friendly remediation approach for the removal of petroleum hydrocarbons from an environment as it does not require intensive chemical, mechanical, and costly interventions. However, it is under-utilized as a commercial remediation strategy due to incomplete hydrocarbon catabolism and lengthy remediation times when compared with rival technologies. This review aims to describe the fate of petroleum hydrocarbons in the environment and discuss their interactions with abiotic and biotic components of the environment under both aerobic and anaerobic conditions. Furthermore, the mechanisms for dealing with petroleum hydrocarbon contamination in the environment will be examined. When petroleum hydrocarbons contaminate land, they start to interact with its surrounding, including physical (dispersion), physiochemical (evaporation, dissolution, sorption), chemical (photo-oxidation, auto-oxidation), and biological (plant and microbial catabolism of hydrocarbons) interactions. As microorganism (including bacteria and fungi) play an important role in the degradation of petroleum hydrocarbons, investigations into the microbial communities within contaminated soils is essential for any bioremediation project. This review highlights the fate of petroleum hydrocarbons in tertial environments, as well as the contributions of different microbial consortia for optimum petroleum hydrocarbon bioremediation potential. The impact of high-throughput metagenomic sequencing in determining the underlying degradation mechanisms is also discussed. This knowledge will aid the development of more efficient, cost-effective commercial bioremediation technologies.}, } @article {pmid31545807, year = {2019}, author = {Planes, S and Allemand, D and Agostini, S and Banaigs, B and Boissin, E and Boss, E and Bourdin, G and Bowler, C and Douville, E and Flores, JM and Forcioli, D and Furla, P and Galand, PE and Ghiglione, JF and Gilson, E and Lombard, F and Moulin, C and Pesant, S and Poulain, J and Reynaud, S and Romac, S and Sullivan, MB and Sunagawa, S and Thomas, OP and Troublé, R and de Vargas, C and Vega Thurber, R and Voolstra, CR and Wincker, P and Zoccola, D and , }, title = {The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean.}, journal = {PLoS biology}, volume = {17}, number = {9}, pages = {e3000483}, pmid = {31545807}, issn = {1545-7885}, mesh = {Animals ; Anthozoa/*microbiology ; *Coral Reefs ; *Expeditions ; Metabolomics ; Metagenomics ; *Microbiota ; Pacific Ocean ; Symbiosis ; }, abstract = {Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects-in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the "-omics" complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016-2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east-west transect from Panama to Papua New Guinea and a south-north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.}, } @article {pmid31545802, year = {2019}, author = {Guirro, M and Costa, A and Gual-Grau, A and Herrero, P and Torrell, H and Canela, N and Arola, L}, title = {Effects from diet-induced gut microbiota dysbiosis and obesity can be ameliorated by fecal microbiota transplantation: A multiomics approach.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0218143}, pmid = {31545802}, issn = {1932-6203}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Biodiversity ; Body Weight ; *Diet ; Disease Models, Animal ; *Dysbiosis ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/drug effects ; Male ; Metagenome ; Metagenomics ; Obesity/*physiopathology/therapy ; Rats ; }, abstract = {Obesity and its comorbidities are currently considered an epidemic, and the involved pathophysiology is well studied. Hypercaloric diets are tightly related to the obesity etiology and also cause alterations in gut microbiota functionality. Diet and antibiotics are known to play crucial roles in changes in the microbiota ecosystem and the disruption of its balance; therefore, the manipulation of gut microbiota may represent an accurate strategy to understand its relationship with obesity caused by diet. Fecal microbiota transplantation, during which fecal microbiota from a healthy donor is transplanted to an obese subject, has aroused interest as an effective approach for the treatment of obesity. To determine its success, a multiomics approach was used that combined metagenomics and metaproteomics to study microbiota composition and function. To do this, a study was performed in rats that evaluated the effect of a hypercaloric diet on the gut microbiota, and this was combined with antibiotic treatment to deplete the microbiota before fecal microbiota transplantation to verify its effects on gut microbiota-host homeostasis. Our results showed that a high-fat diet induces changes in microbiota biodiversity and alters its function in the host. Moreover, we found that antibiotics depleted the microbiota enough to reduce its bacterial content. Finally, we assessed the use of fecal microbiota transplantation as a complementary obesity therapy, and we found that it reversed the effects of antibiotics and reestablished the microbiota balance, which restored normal functioning and alleviated microbiota disruption. This new approach could be implemented to support the dietary and healthy habits recommended as a first option to maintain the homeostasis of the microbiota.}, } @article {pmid31544365, year = {2019}, author = {Pootakham, W and Mhuantong, W and Yoocha, T and Putchim, L and Jomchai, N and Sonthirod, C and Naktang, C and Kongkachana, W and Tangphatsornruang, S}, title = {Heat-induced shift in coral microbiome reveals several members of the Rhodobacteraceae family as indicator species for thermal stress in Porites lutea.}, journal = {MicrobiologyOpen}, volume = {8}, number = {12}, pages = {e935}, pmid = {31544365}, issn = {2045-8827}, mesh = {Animals ; Anthozoa/*microbiology ; *Biodiversity ; Coral Reefs ; DNA Barcoding, Taxonomic ; Ecosystem ; *Hot Temperature ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Rhodobacteraceae ; *Stress, Physiological ; }, abstract = {The coral holobiont is a complex ecosystem consisting of coral animals and a highly diverse consortium of associated microorganisms including algae, fungi, and bacteria. Several studies have highlighted the importance of coral-associated bacteria and their potential roles in promoting the host fitness and survival. Recently, dynamics of coral-associated microbiomes have been demonstrated to be linked to patterns of coral heat tolerance. Here, we examined the effect of elevated seawater temperature on the structure and diversity of bacterial populations associated with Porites lutea, using full-length 16S rRNA sequences obtained from Pacific Biosciences circular consensus sequencing. We observed a significant increase in alpha diversity indices and a distinct shift in microbiome composition during thermal stress. There was a marked decline in the apparent relative abundance of Gammaproteobacteria family Endozoicomonadaceae after P. lutea had been exposed to elevated seawater temperature. Concomitantly, the bacterial community structure shifted toward the predominance of Alphaproteobacteria family Rhodobacteraceae. Interestingly, we did not observe an increase in relative abundance of Vibrio-related sequences in our heat-stressed samples even though the appearance of Vibrio spp. has often been detected in parallel with the increase in the relative abundance of Rhodobacteraceae during thermal bleaching in other coral species. The ability of full-length 16S rRNA sequences in resolving taxonomic uncertainty of associated bacteria at a species level enabled us to identify 24 robust indicator bacterial species for thermally stressed corals. It is worth noting that the majority of those indicator species were members of the family Rhodobacteraceae. The comparison of bacterial community structure and diversity between corals in ambient water temperature and thermally stressed corals may provide a better understanding on how bacteria symbionts contribute to the resilience of their coral hosts to ocean warming.}, } @article {pmid31543403, year = {2019}, author = {Yuan, J and Chen, C and Cui, J and Lu, J and Yan, C and Wei, X and Zhao, X and Li, N and Li, S and Xue, G and Cheng, W and Li, B and Li, H and Lin, W and Tian, C and Zhao, J and Han, J and An, D and Zhang, Q and Wei, H and Zheng, M and Ma, X and Li, W and Chen, X and Zhang, Z and Zeng, H and Ying, S and Wu, J and Yang, R and Liu, D}, title = {Fatty Liver Disease Caused by High-Alcohol-Producing Klebsiella pneumoniae.}, journal = {Cell metabolism}, volume = {30}, number = {4}, pages = {675-688.e7}, doi = {10.1016/j.cmet.2019.08.018}, pmid = {31543403}, issn = {1932-7420}, mesh = {Animals ; Ethanol/*metabolism ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Hep G2 Cells ; Humans ; Klebsiella pneumoniae/*metabolism/pathogenicity ; Male ; Mice ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/*microbiology ; }, abstract = {The underlying etiology of nonalcoholic fatty liver disease (NAFLD) is believed to be quite varied. Changes in the gut microbiota have been investigated and are believed to contribute to at least some cases of the disease, though a causal relationship remains unclear. Here, we show that high-alcohol-producing Klebsiella pneumoniae (HiAlc Kpn) is associated with up to 60% of individuals with NAFLD in a Chinese cohort. Transfer of clinical isolates of HiAlc Kpn by oral gavage into mice induced NAFLD. Likewise, fecal microbiota transplant (FMT) into mice using a HiAlc-Kpn-strain-containing microbiota isolated from an individual with NASH induced NAFLD. However, selective elimination of the HiAlc Kpn strain before FMT prevented NAFLD in the recipient mice. These results suggest that at least in some cases of NAFLD an alteration in the gut microbiome drives the condition due to excess endogenous alcohol production.}, } @article {pmid31542415, year = {2019}, author = {Tackmann, J and Matias Rodrigues, JF and von Mering, C}, title = {Rapid Inference of Direct Interactions in Large-Scale Ecological Networks from Heterogeneous Microbial Sequencing Data.}, journal = {Cell systems}, volume = {9}, number = {3}, pages = {286-296.e8}, doi = {10.1016/j.cels.2019.08.002}, pmid = {31542415}, issn = {2405-4720}, support = {/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Algorithms ; Biodiversity ; Computational Biology/*methods ; Ecosystem ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics ; *Microbial Interactions ; Microbiota/*physiology ; Models, Statistical ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The availability of large-scale metagenomic sequencing data can facilitate the understanding of microbial ecosystems in unprecedented detail. However, current computational methods for predicting ecological interactions are hampered by insufficient statistical resolution and limited computational scalability. They also do not integrate metadata, which can reduce the interpretability of predicted ecological patterns. Here, we present FlashWeave, a computational approach based on a flexible Probabilistic Graphical Model framework that integrates metadata and predicts direct microbial interactions from heterogeneous microbial abundance data sets with hundreds of thousands of samples. FlashWeave outperforms state-of-the-art methods on diverse benchmarking challenges in terms of runtime and accuracy. We use FlashWeave to analyze a cross-study data set of 69,818 publicly available human gut samples and produce, to the best of our knowledge, the largest and most diverse network of predicted, direct gastrointestinal microbial interactions to date. FlashWeave is freely available for download here: https://github.com/meringlab/FlashWeave.jl.}, } @article {pmid31541154, year = {2019}, author = {Wang, W and Archbold, T and Lam, JS and Kimber, MS and Fan, MZ}, title = {A processive endoglucanase with multi-substrate specificity is characterized from porcine gut microbiota.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13630}, pmid = {31541154}, issn = {2045-2322}, mesh = {Animals ; Bacteria/enzymology/*isolation & purification ; Bacterial Proteins/chemistry/genetics/metabolism ; Catalytic Domain ; Cellobiose/metabolism ; Cellulase/chemistry/genetics/*metabolism ; Cellulose/*metabolism ; Gastrointestinal Microbiome ; Models, Molecular ; Polysaccharides/*metabolism ; Protein Conformation ; Substrate Specificity ; Swine ; Trioses/metabolism ; }, abstract = {Cellulases play important roles in the dietary fibre digestion in pigs, and have multiple industrial applications. The porcine intestinal microbiota display a unique feature in rapid cellulose digestion. Herein, we have expressed a cellulase gene, p4818Cel5_2A, which singly encoded a catalytic domain belonging to glycoside hydrolase family 5 subfamily 2, and was previously identified from a metagenomic expression library constructed from porcine gut microbiome after feeding grower pigs with a cellulose-supplemented diet. The activity of purified p4818Cel5_2A was maximal at pH 6.0 and 50 °C and displayed resistance to trypsin digestion. This enzyme exhibited activities towards a wide variety of plant polysaccharides, including cellulosic substrates of avicel and solka-Floc[®], and the hemicelluloses of β-(1 → 4)/(1 → 3)-glucans, xyloglucan, glucomannan and galactomannan. Viscosity, reducing sugar distribution and hydrolysis product analyses further revealed that this enzyme was a processive endo-β-(1 → 4)-glucanase capable of hydrolyzing cellulose into cellobiose and cellotriose as the primary end products. These catalytic features of p4818Cel5_2A were further explored in the context of a three-dimensional homology model. Altogether, results of this study report a microbial processive endoglucanase identified from the porcine gut microbiome, and it may be tailored as an efficient biocatalyst candidate for potential industrial applications.}, } @article {pmid31541115, year = {2019}, author = {Pinto, PIS and Guerreiro, CC and Costa, RA and Martinez-Blanch, JF and Carballo, C and Codoñer, FM and Manchado, M and Power, DM}, title = {Understanding pseudo-albinism in sole (Solea senegalensis): a transcriptomics and metagenomics approach.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13604}, pmid = {31541115}, issn = {2045-2322}, mesh = {Albinism/*genetics ; Animals ; Computational Biology/methods ; Flatfishes/*genetics/metabolism ; Gastrointestinal Microbiome/genetics ; Gene Expression Profiling/methods ; Intestines/microbiology ; Metagenomics/methods ; Microbiota/genetics ; Skin/microbiology ; Transcriptome/genetics ; }, abstract = {Pseudo-albinism is a pigmentation disorder observed in flatfish aquaculture with a complex, multi-factor aetiology. We tested the hypothesis that pigmentation abnormalities are an overt signal of more generalised modifications in tissue structure and function, using as a model the Senegalese sole and two important innate immune barriers, the skin and intestine, and their microbiomes. Stereological analyses in pseudo-albino sole revealed a significantly increased mucous cell number in skin (P < 0.001) and a significantly thicker muscle layer and lamina propria in gut (P < 0.001). RNA-seq transcriptome analysis of the skin and gut identified 573 differentially expressed transcripts (DETs, FDR < 0.05) between pseudo-albino and pigmented soles (one pool/tissue from 4 individuals/phenotype). DETs were mainly linked to pigment production, skin structure and regeneration and smooth muscle contraction. The microbiome (16 S rRNA analysis) was highly diverse in pigmented and pseudo-albino skin but in gut had low complexity and diverged between the two pigmentation phenotypes. Quantitative PCR revealed significantly lower loads of Mycoplasma (P < 0.05) and Vibrio bacteria (P < 0.01) in pseudo-albino compared to the control. The study revealed that pseudo-albinism in addition to pigmentation changes was associated with generalised changes in the skin and gut structure and a modification in the gut microbiome.}, } @article {pmid31539947, year = {2019}, author = {Yadav, S and Kapley, A}, title = {Exploration of activated sludge resistome using metagenomics.}, journal = {The Science of the total environment}, volume = {692}, number = {}, pages = {1155-1164}, doi = {10.1016/j.scitotenv.2019.07.267}, pmid = {31539947}, issn = {1879-1026}, mesh = {Bacteria ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; India ; *Metagenome ; Metagenomics ; Plasmids ; Sewage/*microbiology ; }, abstract = {Antibiotic resistance is a global problem. In India poor waste management and inadequate sanitary are key factors which encourage the dissemination of antimicrobial resistance. Microbial biodiversity serves as an invaluable source for diverse types of bioactive compounds that encompass most of the pharmaceuticals to date. Therefore, in this study, we used the metagenomic approach for the surveillance of antibiotic resistance genes, drug resistant microbes and mobile-genetic elements in two activated sludge metagenome samples collected from Ankleshwar, Gujarat, India. Proteobacteria were found to be the most abundant bacteria among the metagenome analyzed. Twenty-four genes conferring resistance to antibiotics and heavy metals were found. Multidrug resistant "ESKAPE pathogens" were also abundant in the sludge metagenome. Mobile genetic elements like IncP-1 plasmid pKJK5, IncP-1beta multi resistance plasmid and pB8 were also noticed in the higher abundance. These plasmids play an important role in the spread of antibiotic resistance by the horizontal gene transfer. Statistical analysis of both metagenome using STAMP software confirmed presence of mobile genetic elements such as gene transfer agents, phages, Prophages etc. which also play important role in the dissemination of antibiotic resistant genes.}, } @article {pmid31539022, year = {2020}, author = {McDonnell, K and Waters, N and Howley, E and Abram, F}, title = {Chordomics: a visualization tool for linking function to phylogeny in microbiomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {4}, pages = {1309-1310}, doi = {10.1093/bioinformatics/btz711}, pmid = {31539022}, issn = {1367-4811}, mesh = {Metagenomics ; *Microbiota ; Phylogeny ; *Software ; }, abstract = {SUMMARY: The overarching aim of microbiome analysis is to uncover the links between microbial phylogeny and function in order to access ecosystem functioning. This can be done using several experimental strategies targeting different biomolecules, including DNA (metagenomics), RNA (metatranscriptomics) and proteins (metaproteomics). Despite the importance of linking microbial function to phylogeny there are currently no visualization tools that effectively integrate this information. Chordomics is a Shiny-based application for linked -omics data analysis, allowing users to visualize microbial function and phylogeny on a single plot and compare datasets across time and environments.

Chordomics is available on GitHub: https://github.com/kevinmcdonnell6/chordomics; software is coded in R and JavaScript and a demonstration version is available at https://kmcd.shinyapps.io/ChordomicsDemo/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid31537866, year = {2019}, author = {Park, MS and Oh, SY and Fong, JJ and Houbraken, J and Lim, YW}, title = {The diversity and ecological roles of Penicillium in intertidal zones.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13540}, pmid = {31537866}, issn = {2045-2322}, mesh = {Classification/methods ; DNA, Fungal/chemistry ; Enzyme Activation/physiology ; Geologic Sediments/chemistry ; Penicillium/*genetics/*isolation & purification/*metabolism ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/analysis ; Sequence Analysis, DNA/methods ; Tidal Waves ; }, abstract = {Members of the genus Penicillium are commonly isolated from various terrestrial and marine environments, and play an important ecological role as a decomposer. To gain insight into the ecological role of Penicillium in intertidal zones, we investigated the Penicillium diversity and community structure using a culture-dependent technique and a culture independent metagenomic approach using ITS (ITS-NGS) and partial β-tubulin (BenA-NGS) as targets. The obtained isolates were tested for halotolerance, enzyme activity, and polycyclic aromatic hydrocarbons (PAHs) degradation. A total of 96 Penicillium species were identified from the investigated intertidal zones. Although the BenA-NGS method was efficient for detecting Penicillium, some species were only detected using conventional isolation and/or the ITS-NGS method. The Penicillium community displayed a significant degree of variation relative to season (summer and winter) and seaside (western and southern coast). Many Penicillium species isolated in this study exhibited cellulase and protease activity, and/or degradation of PAHs. These findings support the important role of Penicillium in the intertidal zone for nutrient recycling and pollutant degradation.}, } @article {pmid31537825, year = {2019}, author = {Hoque, MN and Istiaq, A and Clement, RA and Sultana, M and Crandall, KA and Siddiki, AZ and Hossain, MA}, title = {Metagenomic deep sequencing reveals association of microbiome signature with functional biases in bovine mastitis.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13536}, pmid = {31537825}, issn = {2045-2322}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; Biodiversity ; Cattle/microbiology ; Female ; High-Throughput Nucleotide Sequencing/methods ; Mammary Glands, Animal/microbiology ; Mastitis/genetics/microbiology ; Mastitis, Bovine/*genetics/*microbiology ; Metagenome ; Metagenomics/methods ; Microbiota/*genetics/physiology ; Milk/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Milk microbiomes significantly influence the pathophysiology of bovine mastitis. To assess the association between microbiome diversity and bovine mastitis, we compared the microbiome of clinical mastitis (CM, n = 14) and healthy (H, n = 7) milk samples through deep whole metagenome sequencing (WMS). A total of 483.38 million reads generated from both metagenomes were analyzed through PathoScope (PS) and MG-RAST (MR), and mapped to 380 bacterial, 56 archaeal, and 39 viral genomes. We observed distinct shifts and differences in abundance between the microbiome of CM and H milk in phyla Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria with an inclusion of 68.04% previously unreported and/or opportunistic strains in CM milk. PS identified 363 and 146 bacterial strains in CM and H milk samples respectively, and MR detected 356 and 251 bacterial genera respectively. Of the identified taxa, 29.51% of strains and 63.80% of genera were shared between both metagenomes. Additionally, 14 archaeal and 14 viral genera were found to be solely associated with CM. Functional annotation of metagenomic sequences identified several metabolic pathways related to bacterial colonization, proliferation, chemotaxis and invasion, immune-diseases, oxidative stress, regulation and cell signaling, phage and prophases, antibiotic and heavy metal resistance that might be associated with CM. Our WMS study provides conclusive data on milk microbiome diversity associated with bovine CM and its role in udder health.}, } @article {pmid31536813, year = {2020}, author = {Alma, L and Kram, KE and Holtgrieve, GW and Barbarino, A and Fiamengo, CJ and Padilla-Gamiño, JL}, title = {Ocean acidification and warming effects on the physiology, skeletal properties, and microbiome of the purple-hinge rock scallop.}, journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology}, volume = {240}, number = {}, pages = {110579}, doi = {10.1016/j.cbpa.2019.110579}, pmid = {31536813}, issn = {1531-4332}, mesh = {Acclimatization ; Acids/*chemistry ; Animal Shells ; Animals ; Bone and Bones/*metabolism ; Carbon Dioxide/*analysis ; Global Warming ; Homeostasis ; Hydrogen-Ion Concentration ; *Microbiota ; Pectinidae/microbiology/*physiology ; Seawater/*microbiology ; *Temperature ; }, abstract = {Ocean acidification and increased ocean temperature from elevated atmospheric carbon dioxide can significantly influence the physiology, growth and survival of marine organisms. Despite increasing research efforts, there are still many gaps in our knowledge of how these stressors interact to affect economically and ecologically important species. This project is the first to explore the physiological effects of high pCO2 and temperature on the acclimation potential of the purple-hinge rock scallop (Crassadoma gigantea), a widely distributed marine bivalve, important reef builder, and potential aquaculture product. Scallops were exposed to two pCO2 (365 and 1050 μatm) and temperature (14 and 21.5 °C) conditions in a two-factor experimental design. Simultaneous exposure to high temperature and high pCO2 reduced shell strength, decreased outer shell density and increased total lipid content. Despite identical diets, scallops exposed to high pCO2 had higher content of saturated fatty acids, and lower content of polyunsaturated fatty acids suggesting reorganization of fatty acid chains to sustain basic metabolic functions under high pCO2. Metagenomic sequencing of prokaryotes in scallop tissue revealed treatment differences in community composition between treatments and in the presence of genes associated with microbial cell regulation, signaling, and pigmentation. Results from this research highlight the complexity of physiological responses for calcifying species under global change related stress and provide the first insights for understanding the response of a bivalve's microbiome under multiple stressors.}, } @article {pmid31536536, year = {2019}, author = {Kirst, ME and Baker, D and Li, E and Abu-Hasan, M and Wang, GP}, title = {Upper versus lower airway microbiome and metagenome in children with cystic fibrosis and their correlation with lung inflammation.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0222323}, pmid = {31536536}, issn = {1932-6203}, mesh = {Bronchoalveolar Lavage Fluid/microbiology ; Bronchoscopy ; Case-Control Studies ; Child ; Child, Preschool ; Cystic Fibrosis/*microbiology/pathology ; Female ; Humans ; Lung/*microbiology/pathology ; Male ; *Microbiota/genetics ; Oropharynx/*microbiology ; Pharynx/microbiology ; Pneumonia/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVE: Airways of children with cystic fibrosis (CF) harbor complex polymicrobial communities which correlates with pulmonary disease progression and use of antibiotics. Throat swabs are widely used in young CF children as a surrogate to detect potentially pathogenic microorganisms in lower airways. However, the relationship between upper and lower airway microbial communities remains poorly understood. This study aims to determine (1) to what extent oropharyngeal microbiome resembles the lung microbiome in CF children and (2) if lung microbiome composition correlates with airway inflammation.

METHOD: Throat swabs and bronchoalveolar lavage (BAL) were obtained concurrently from 21 CF children and 26 disease controls. Oropharyngeal and lung microbiota were analyzed using 16S rRNA deep sequencing and correlated with neutrophil counts in BAL and antibiotic exposure.

RESULTS: Oropharyngeal microbial communities clustered separately from lung communities and had higher microbial diversity (p < 0.001). CF microbiome differed significantly from non-CF controls, with a higher abundance of Proteobacteria in both upper and lower CF airways. Neutrophil count in the BAL correlated negatively with the diversity but not richness of the lung microbiome. In CF children, microbial genes involved in bacterial motility proteins, two-component system, flagella assembly, and secretion system were enriched in both oropharyngeal and lung microbiome, whereas genes associated with synthesis and metabolism of nucleic acids and protein dominated the non-CF controls.

CONCLUSIONS: This study identified a unique microbial profile with altered microbial diversity and metabolic functions in CF airways which is significantly affected by airway inflammation. These results highlight the limitations of using throat swabs as a surrogate to study lower airway microbiome and metagenome in CF children.}, } @article {pmid31536448, year = {2019}, author = {Chen, Z and Lin, S and Jiang, Y and Liu, L and Jiang, J and Chen, S and Tong, Y and Wang, P}, title = {Effects of Bread Yeast Cell Wall Beta-Glucans on Mice with Loperamide-Induced Constipation.}, journal = {Journal of medicinal food}, volume = {22}, number = {10}, pages = {1009-1021}, doi = {10.1089/jmf.2019.4407}, pmid = {31536448}, issn = {1557-7600}, mesh = {Acetylcholinesterase/metabolism ; Animals ; Constipation/chemically induced/*drug therapy ; Defecation/drug effects ; *Gastrointestinal Microbiome ; Gastrointestinal Transit/drug effects ; Loperamide/*adverse effects ; Male ; Metagenome ; Mice ; Mice, Inbred BALB C ; Mucin-2/metabolism ; Saccharomyces cerevisiae/*chemistry ; Serotonin/metabolism ; Substance P/metabolism ; Zonula Occludens-1 Protein/metabolism ; beta-Glucans/*pharmacology ; }, abstract = {Constipation is a common gastrointestinal disorder characterized by changes in intestinal habits. Increasing evidence indicates that long-term use of irritant laxatives causes serious side effects. Meanwhile, more than 50% of patients are dissatisfied with sense of use of non-prescriptional laxatives. β-glucans are natural polysaccharides widely found in yeast, fungus, and plants, which have been reported to exhibit various pharmacological effects. The aim of this study was to characterize the effect of β-glucans extracted from the bread yeast cell wall on loperamide-induced constipation mice. Forty mice were fed with loperamide (10 mg/kg) to make the constipation model and a diet supplemented with 2.5, 5, and 10 mg/kg β-glucan. We assessed the defecation frequency, intestinal transit function of mice, as well as used high-throughput sequencing to analyze the intestinal microbiota composition and functional biological profiles data. Meanwhile, we detected expression of neurotransmitters including acetylcholinesterase, substance P, and serotonin (5-HT) and expression of tight junction protein (TJP) including zonula occludens-1 and mucin-2 in distal colon to characterize the possible molecular mechanisms. β-glucans significantly enhanced intestinal motility and provided a possibility to regulate the expression of neurotransmitters and TJP in mice. The intestinal microecological portion of the treatment group partially recovered and was closer to the normal group. This study showed that β-glucans can influence the intestinal microbiota and restore microecological balance to regulate the express of neurotransmitters and TJP to recover intestinal epithelial mechanical barrier. We suggested that β-glucans could be used as an active nutritional supplement to protect the damaged intestinal barrier and help patients who have constipation complications and dysbiosis.}, } @article {pmid31534227, year = {2019}, author = {Shao, Y and Forster, SC and Tsaliki, E and Vervier, K and Strang, A and Simpson, N and Kumar, N and Stares, MD and Rodger, A and Brocklehurst, P and Field, N and Lawley, TD}, title = {Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth.}, journal = {Nature}, volume = {574}, number = {7776}, pages = {117-121}, pmid = {31534227}, issn = {1476-4687}, support = {/WT_/Wellcome Trust/United Kingdom ; WT101169MA/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Cesarean Section/*adverse effects ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Infant, Newborn, Diseases/etiology/*microbiology ; Infectious Disease Transmission, Vertical/*prevention & control ; Opportunistic Infections/*congenital/etiology/*microbiology ; Pregnancy ; }, abstract = {Immediately after birth, newborn babies experience rapid colonization by microorganisms from their mothers and the surrounding environment[1]. Diseases in childhood and later in life are potentially mediated by the perturbation of the colonization of the infant gut microbiota[2]. However, the effects of delivery via caesarean section on the earliest stages of the acquisition and development of the gut microbiota, during the neonatal period (≤1 month), remain controversial[3,4]. Here we report the disrupted transmission of maternal Bacteroides strains, and high-level colonization by opportunistic pathogens associated with the hospital environment (including Enterococcus, Enterobacter and Klebsiella species), in babies delivered by caesarean section. These effects were also seen, to a lesser extent, in vaginally delivered babies whose mothers underwent antibiotic prophylaxis and in babies who were not breastfed during the neonatal period. We applied longitudinal sampling and whole-genome shotgun metagenomic analysis to 1,679 gut microbiota samples (taken at several time points during the neonatal period, and in infancy) from 596 full-term babies born in UK hospitals; for a subset of these babies, we collected additional matched samples from mothers (175 mothers paired with 178 babies). This analysis demonstrates that the mode of delivery is a significant factor that affects the composition of the gut microbiota throughout the neonatal period, and into infancy. Matched large-scale culturing and whole-genome sequencing of over 800 bacterial strains from these babies identified virulence factors and clinically relevant antimicrobial resistance in opportunistic pathogens that may predispose individuals to opportunistic infections. Our findings highlight the critical role of the local environment in establishing the gut microbiota in very early life, and identify colonization with antimicrobial-resistance-containing opportunistic pathogens as a previously underappreciated risk factor in hospital births.}, } @article {pmid31533897, year = {2019}, author = {Rawat, N and Joshi, GK}, title = {Bacterial community structure analysis of a hot spring soil by next generation sequencing of ribosomal RNA.}, journal = {Genomics}, volume = {111}, number = {5}, pages = {1053-1058}, doi = {10.1016/j.ygeno.2018.06.008}, pmid = {31533897}, issn = {1089-8646}, mesh = {Bacteria/classification/*genetics ; Hot Springs/*microbiology ; *Metagenome ; *Microbiota ; RNA, Ribosomal/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {In the present study the whole bacterial community structure of Tapovan hot spring soil located in the state of Uttarakhand, India was analysed through next generation sequencing. The hot spring soil is slightly alkaline in nature with abundance of sulphur. The spring soil was rich in various metallic and non-metallic elements required for bacterial survival. The community was found to comprise of 14 bacterial phyla with representation of members belonging to Firmicutes, Proteobacteria, Thermi, Bacteroidetes, Aquificae, Actinobacteria, chloroflexi, TM7, Fusobacteria etc. At the genus level Bacillus, Pseudomonas, Symbiobacterium, Thermus, Geobacillus, Anoxybacillus were found in abundance as compared to other genera like Flavobacterium, Ureibacillus, Clostridium, Meiothermus, Acinetobacter, Desulfotomaculum and Rheinheimera.}, } @article {pmid31533707, year = {2019}, author = {Willmann, M and Vehreschild, MJGT and Biehl, LM and Vogel, W and Dörfel, D and Hamprecht, A and Seifert, H and Autenrieth, IB and Peter, S}, title = {Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {76}, pmid = {31533707}, issn = {1741-7007}, mesh = {Anti-Bacterial Agents/*adverse effects/therapeutic use ; Ciprofloxacin/*adverse effects/therapeutic use ; Cohort Studies ; *Drug Resistance, Microbial/drug effects/genetics ; Gastrointestinal Microbiome/*drug effects ; Genes, Bacterial/drug effects ; Germany ; Humans ; Longitudinal Studies ; Metagenomics/methods ; Plasmids/*drug effects ; Trimethoprim, Sulfamethoxazole Drug Combination/*adverse effects/therapeutic use ; }, abstract = {BACKGROUND: The selection pressure exercised by antibiotic drugs is an important consideration for the wise stewardship of antimicrobial treatment programs. Treatment decisions are currently based on crude assumptions, and there is an urgent need to develop a more quantitative knowledge base that can enable predictions of the impact of individual antibiotics on the human gut microbiome and resistome.

RESULTS: Using shotgun metagenomics, we quantified changes in the gut microbiome in two cohorts of hematological patients receiving prophylactic antibiotics; one cohort was treated with ciprofloxacin in a hospital in Tübingen and the other with cotrimoxazole in a hospital in Cologne. Analyzing this rich longitudinal dataset, we found that gut microbiome diversity was reduced in both treatment cohorts to a similar extent, while effects on the gut resistome differed. We observed a sharp increase in the relative abundance of sulfonamide antibiotic resistance genes (ARGs) by 148.1% per cumulative defined daily dose of cotrimoxazole in the Cologne cohort, but not in the Tübingen cohort treated with ciprofloxacin. Through multivariate modeling, we found that factors such as individual baseline microbiome, resistome, and plasmid diversity; liver/kidney function; and concurrent medication, especially virostatic agents, influence resistome alterations. Strikingly, we observed different effects on the plasmidome in the two treatment groups. There was a substantial increase in the abundance of ARG-carrying plasmids in the cohort treated with cotrimoxazole, but not in the cohort treated with ciprofloxacin, indicating that cotrimoxazole might contribute more efficiently to the spread of resistance.

CONCLUSIONS: Our study represents a step forward in developing the capability to predict the effect of individual antimicrobials on the human microbiome and resistome. Our results indicate that to achieve this, integration of the individual baseline microbiome, resistome, and mobilome status as well as additional individual patient factors will be required. Such personalized predictions may in the future increase patient safety and reduce the spread of resistance.

TRIAL REGISTRATION: ClinicalTrials.gov, NCT02058888 . Registered February 10 2014.}, } @article {pmid31533247, year = {2019}, author = {Modha, S and Hughes, J and Bianco, G and Ferguson, HM and Helm, B and Tong, L and Wilkie, GS and Kohl, A and Schnettler, E}, title = {Metaviromics Reveals Unknown Viral Diversity in the Biting Midge Culicoides impunctatus.}, journal = {Viruses}, volume = {11}, number = {9}, pages = {}, pmid = {31533247}, issn = {1999-4915}, support = {MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/12 and MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Ceratopogonidae/*virology ; Europe ; Genetic Variation ; Genome, Viral/*genetics ; Insect Vectors/*virology ; Metagenomics ; Phylogeny ; RNA Viruses/classification/*genetics ; }, abstract = {Biting midges (Culicoides species) are vectors of arboviruses and were responsible for the emergence and spread of Schmallenberg virus (SBV) in Europe in 2011 and are likely to be involved in the emergence of other arboviruses in Europe. Improved surveillance and better understanding of risks require a better understanding of the circulating viral diversity in these biting insects. In this study, we expand the sequence space of RNA viruses by identifying a number of novel RNA viruses from Culicoides impunctatus (biting midge) using a meta-transcriptomic approach. A novel metaviromic pipeline called MetaViC was developed specifically to identify novel virus sequence signatures from high throughput sequencing (HTS) datasets in the absence of a known host genome. MetaViC is a protein centric pipeline that looks for specific protein signatures in the reads and contigs generated as part of the pipeline. Several novel viruses, including an alphanodavirus with both segments, a novel relative of the Hubei sobemo-like virus 49, two rhabdo-like viruses and a chuvirus, were identified in the Scottish midge samples. The newly identified viruses were found to be phylogenetically distinct to those previous known. These findings expand our current knowledge of viral diversity in arthropods and especially in these understudied disease vectors.}, } @article {pmid31531910, year = {2020}, author = {Verschuren, LMG and Schokker, D and Bergsma, R and Jansman, AJM and Molist, F and Calus, MPL}, title = {Prediction of nutrient digestibility in grower-finisher pigs based on faecal microbiota composition.}, journal = {Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie}, volume = {137}, number = {1}, pages = {23-35}, pmid = {31531910}, issn = {1439-0388}, support = {BO-22.04-010-001//Breed&Feed4Food/ ; }, mesh = {Animals ; *Digestion ; Feces/*microbiology ; Female ; Male ; *Microbiota ; Nutrients/*metabolism ; Phenotype ; Swine/growth & development/metabolism/*microbiology/*physiology ; }, abstract = {Microbiota play an important role in total tract nutrient digestion, especially when fibrous diets are fed to pigs. This study aimed to use metagenomics to predict faecal nutrient digestibility in grower-finisher pigs. The study design consisted of 160 three-way crossbreed grower-finisher pigs (80 female and 80 male) which were either fed a diet based on corn/soybean meal or a more fibrous diet based on wheat/barley/by-products. On the day before slaughter, faecal samples were collected and used to determine faecal digestibility of dry matter, ash, organic matter, crude protein, crude fat, crude fibre and non-starch polysaccharides. The faecal samples were also sequenced for the 16S hypervariable region of bacteria (V3/V4) to profile the faecal microbiome. With these data, we calculated the between-animal variation in faecal nutrient digestibility associated with variation in the faecal microbiome, that is the "microbiability". The microbiability values were significantly greater than zero for dry matter, organic matter, crude protein, crude fibre and non-starch polysaccharides, ranging from 0.58 to 0.93, as well as for crude fat with a value of 0.37, but not significantly different from zero for ash. Using leave-one-out cross-validation, we estimated the accuracy of predicting digestibility values of individual pigs based on their faecal microbiota composition. The accuracies of prediction for crude fat and ash digestibility were virtually 0, and for the other nutrients, the accuracies ranged from 0.42 to 0.63. In conclusion, the faecal microbiota composition gave high microbiability values for faecal digestibility of dry matter, organic matter, crude protein, crude fibre and non-starch polysaccharides. The accuracies of prediction are relatively low if the interest is in precisely predicting faecal nutrient digestibility of individual pigs, but are promising from the perspective of ranking animals in a genetic selection context.}, } @article {pmid31530835, year = {2019}, author = {Vester-Andersen, MK and Mirsepasi-Lauridsen, HC and Prosberg, MV and Mortensen, CO and Träger, C and Skovsen, K and Thorkilgaard, T and Nøjgaard, C and Vind, I and Krogfelt, KA and Sørensen, N and Bendtsen, F and Petersen, AM}, title = {Increased abundance of proteobacteria in aggressive Crohn's disease seven years after diagnosis.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13473}, pmid = {31530835}, issn = {2045-2322}, mesh = {Biodiversity ; Case-Control Studies ; Crohn Disease/diagnosis/*etiology/*pathology ; Disease Progression ; Disease Susceptibility ; *Dysbiosis ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/etiology/pathology ; Metagenomics/methods ; *Proteobacteria ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; }, abstract = {Intestinal dysbiosis in inflammatory bowel disease (IBD) patients depend on disease activity. We aimed to characterize the microbiota after 7 years of follow-up in an unselected cohort of IBD patients according to disease activity and disease severity. Fifty eight Crohn's disease (CD) and 82 ulcerative colitis (UC) patients were included. Disease activity was assessed by the Harvey-Bradshaw Index for CD and Simple Clinical Colitis Activity Index for UC. Microbiota diversity was assessed by 16S rDNA MiSeq sequencing. In UC patients with active disease and in CD patients with aggressive disease the richness (number of OTUs, p = 0.018 and p = 0.013, respectively) and diversity (Shannons index, p = 0.017 and p = 0.023, respectively) were significantly decreased. In the active UC group there was a significant decrease in abundance of the phylum Firmicutes (p = 0.018). The same was found in CD patients with aggressive disease (p = 0.05) while the abundance of Proteobacteria phylum showed a significant increase (p = 0.03) in CD patients. We found a change in the microbial abundance in UC patients with active disease and in CD patients with aggressive disease. These results suggest that dysbiosis of the gut in IBD patients is not only related to current activity but also to the course of the disease.}, } @article {pmid31530813, year = {2019}, author = {Zorz, JK and Sharp, C and Kleiner, M and Gordon, PMK and Pon, RT and Dong, X and Strous, M}, title = {A shared core microbiome in soda lakes separated by large distances.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4230}, pmid = {31530813}, issn = {2041-1723}, mesh = {Alkalies/analysis ; Autotrophic Processes ; Bacteria/classification/genetics/*isolation & purification/radiation effects ; Biodiversity ; Canada ; Carbon Cycle ; Lakes/chemistry/*microbiology ; Light ; *Microbiota ; Phototrophic Processes ; *Phylogeny ; Sulfur/metabolism ; }, abstract = {In alkaline soda lakes, concentrated dissolved carbonates establish productive phototrophic microbial mats. Here we show how microbial phototrophs and autotrophs contribute to this exceptional productivity. Amplicon and shotgun DNA sequencing data of microbial mats from four Canadian soda lakes indicate the presence of > 2,000 species of Bacteria and Eukaryotes. We recover metagenome-assembled-genomes for a core microbiome of < 100 abundant bacteria, present in all four lakes. Most of these are related to microbes previously detected in sediments of Asian alkaline lakes, showing that common selection principles drive community assembly from a globally distributed reservoir of alkaliphile biodiversity. Detection of > 7,000 proteins show how phototrophic populations allocate resources to specific processes and occupy complementary niches. Carbon fixation proceeds by the Calvin-Benson-Bassham cycle, in Cyanobacteria, Gammaproteobacteria, and, surprisingly, Gemmatimonadetes. Our study provides insight into soda lake ecology, as well as a template to guide efforts to engineer biotechnology for carbon dioxide conversion.}, } @article {pmid31530641, year = {2019}, author = {Rahfeld, P and Wardman, JF and Mehr, K and Huff, D and Morgan-Lang, C and Chen, HM and Hallam, SJ and Withers, SG}, title = {Prospecting for microbial α-N-acetylgalactosaminidases yields a new class of GH31 O-glycanase.}, journal = {The Journal of biological chemistry}, volume = {294}, number = {44}, pages = {16400-16415}, pmid = {31530641}, issn = {1083-351X}, mesh = {Gastrointestinal Microbiome/genetics ; Glycoside Hydrolases/*chemical synthesis/chemistry/isolation & purification/metabolism ; Glycosides/metabolism ; Glycosylation ; Hexosaminidases/metabolism ; Humans ; Mucins/metabolism ; Peptides/metabolism ; Polysaccharides/chemistry ; Proteins/metabolism ; Substrate Specificity ; alpha-N-Acetylgalactosaminidase/genetics/*metabolism ; }, abstract = {α-Linked GalNAc (α-GalNAc) is most notably found at the nonreducing terminus of the blood type-determining A-antigen and as the initial point of attachment to the peptide backbone in mucin-type O-glycans. However, despite their ubiquity in saccharolytic microbe-rich environments such as the human gut, relatively few α-N-acetylgalactosaminidases are known. Here, to discover and characterize novel microbial enzymes that hydrolyze α-GalNAc, we screened small-insert libraries containing metagenomic DNA from the human gut microbiome. Using a simple fluorogenic glycoside substrate, we identified and characterized a glycoside hydrolase 109 (GH109) that is active on blood type A-antigen, along with a new subfamily of glycoside hydrolase 31 (GH31) that specifically cleaves the initial α-GalNAc from mucin-type O-glycans. This represents a new activity in this GH family and a potentially useful new enzyme class for analysis or modification of O-glycans on protein or cell surfaces.}, } @article {pmid31529842, year = {2019}, author = {Caguazango, JC and Pazos, ÁJ}, title = {Microbiota according to gastric topography in patients with low or high risk of gastric cancer in Nariño, Colombia.}, journal = {Biomedica : revista del Instituto Nacional de Salud}, volume = {39}, number = {Supl. 2}, pages = {157-171}, doi = {10.7705/biomedica.v39i4.4520}, pmid = {31529842}, issn = {2590-7379}, mesh = {Adult ; Aged ; Colombia/epidemiology ; Female ; Gastric Mucosa/microbiology/pathology ; Gastritis/epidemiology/*microbiology ; Gastritis, Atrophic/epidemiology/microbiology ; *Gastrointestinal Microbiome ; Helicobacter Infections/epidemiology/microbiology ; Helicobacter pylori/genetics/isolation & purification ; Humans ; Male ; Metaplasia ; Middle Aged ; Pyloric Antrum/microbiology ; Ribotyping ; Risk ; Stomach/*microbiology ; Stomach Neoplasms/*epidemiology ; }, abstract = {Introduction: Inflammation in the gastric antrum caused by Helicobacter pylori increases the risk of duodenal ulcer while inflammation in the body generates atrophic gastritis and increased risk of gastric cancer. These inflammatory responses according to gastric topography could be explained by the composition of the gastric microbiota associated with H. pylori. Objective: To identify and compare the microbiota of the gastric antrum and body of individuals from two populations, one with high risk and one with low risk of gastric cancer from Nariño, Colombia. Materials and methods: Biopsies of the gastric antrum and body of patients with non-atrophic gastritis or metaplastic atrophic gastritis were included. The microbiota was defined by sequencing the 16S rRNA gene, V3-V4 region, (illumina-MiSeq™). The operational taxonomic units were classified using the BLASTn and RDPII databases. The differences among microbial populations were evaluated with the PERMANOVA and multivariate analyses. Results: The Epsilonproteobacteria class represented by H. pylori was more abundant in the antrum and body biopsies of individuals with metaplastic atrophic gastritis (>50%) while in individuals with non-atrophic gastritis it was 20 % and had greater metagenomic diversity. Helicobacter pylori infection significantly decreases the metagenomic diversity of the gastric antrum (p=0.005) compared to that of the body. Conclusions: The bacterial groups involved in the dysbiosis can colonize both topographic regions of the stomach, regardless of the sectorized inflammation responses. Helicobacter pylori infection associated with the gastric microbiota is related to its localization in the stomach, the type of lesion, and the population at risk of gastric cancer, which suggests its importance in microbial dysbiosis and gastric disease.}, } @article {pmid31527823, year = {2019}, author = {Ilett, EE and Jørgensen, M and Noguera-Julian, M and Daugaard, G and Murray, DD and Helleberg, M and Paredes, R and Lundgren, J and Sengeløv, H and MacPherson, C}, title = {Gut microbiome comparability of fresh-frozen versus stabilized-frozen samples from hospitalized patients using 16S rRNA gene and shotgun metagenomic sequencing.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13351}, pmid = {31527823}, issn = {2045-2322}, mesh = {Bacteria/*classification/genetics/*isolation & purification ; Cryopreservation/*methods ; DNA, Bacterial/genetics ; Feces/*microbiology ; Freezing ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome/genetics ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Specimen Handling ; }, abstract = {Collection of faecal samples for microbiome analysis in acutely sick patients is logistically difficult, particularly if immediate freezing is required (i.e. fresh-frozen, or FF sampling). Previous studies in healthy/non-hospitalized volunteers have shown that chemical stabilization (i.e. stabilized-frozen, or SF sampling) allows room-temperature storage with comparable results to FF samples. To test this in a hospital setting we compared FF and SF approaches across 17 patients undergoing haematopoietic stem cell transplantation (HSCT) using both 16S rRNA gene and shotgun metagenomic sequencing. A paired (same stool specimen) comparison of FF and SF samples was made, with an overall comparable level in relative taxonomic abundances between the two sampling techniques. Though shotgun metagenomic sequencing found significant differences for certain bacterial genera (P < 0.001), these were considered minor methodological effects. Within-sample diversity of either method was not significantly different (Shannon diversity P16SrRNA = 0.68 and Pshotgun = 0.89) and we could not reject the null hypothesis that between-sample variation in FF and SF were equivalent (P16SrRNA = 0.98 and Pshotgun = 1.0). This indicates that SF samples can be used to reliably study the microbiome in acutely sick patient populations, thus creating and enabling further outcomes-based metagenomic studies on similarly valuable cohorts.}, } @article {pmid31526447, year = {2019}, author = {Ravi, A and Halstead, FD and Bamford, A and Casey, A and Thomson, NM and van Schaik, W and Snelson, C and Goulden, R and Foster-Nyarko, E and Savva, GM and Whitehouse, T and Pallen, MJ and Oppenheim, BA}, title = {Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients.}, journal = {Microbial genomics}, volume = {5}, number = {9}, pages = {}, pmid = {31526447}, issn = {2057-5858}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; BBS/E/F/00044414/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Biodiversity ; Critical Illness ; Enterococcus faecium/isolation & purification/physiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/drug effects ; Humans ; Intensive Care Units ; Male ; Meropenem/pharmacology/therapeutic use ; Metagenomics ; Middle Aged ; Prospective Studies ; }, abstract = {Among long-stay critically ill patients in the adult intensive care unit (ICU), there are often marked changes in the complexity of the gut microbiota. However, it remains unclear whether such patients might benefit from enhanced surveillance or from interventions targeting the gut microbiota or the pathogens therein. We therefore undertook a prospective observational study of 24 ICU patients, in which serial faecal samples were subjected to shotgun metagenomic sequencing, phylogenetic profiling and microbial genome analyses. Two-thirds of the patients experienced a marked drop in gut microbial diversity (to an inverse Simpson's index of <4) at some stage during their stay in the ICU, often accompanied by the absence or loss of potentially beneficial bacteria. Intravenous administration of the broad-spectrum antimicrobial agent meropenem was significantly associated with loss of gut microbial diversity, but the administration of other antibiotics, including piperacillin/tazobactam, failed to trigger statistically detectable changes in microbial diversity. In three-quarters of ICU patients, we documented episodes of gut domination by pathogenic strains, with evidence of cryptic nosocomial transmission of Enterococcus faecium. In some patients, we also saw an increase in the relative abundance of apparent commensal organisms in the gut microbiome, including the archaeal species Methanobrevibacter smithii. In conclusion, we have documented a dramatic absence of microbial diversity and pathogen domination of the gut microbiota in a high proportion of critically ill patients using shotgun metagenomics.}, } @article {pmid31526274, year = {2019}, author = {Schwartz, DJ and Rebeck, ON and Dantas, G}, title = {Complex interactions between the microbiome and cancer immune therapy.}, journal = {Critical reviews in clinical laboratory sciences}, volume = {56}, number = {8}, pages = {567-585}, pmid = {31526274}, issn = {1549-781X}, support = {R01 AT009741/AT/NCCIH NIH HHS/United States ; R25 GM103757/GM/NIGMS NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; U01 AI123394/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Clinical Trials as Topic ; Fecal Microbiota Transplantation ; Humans ; *Immunotherapy ; *Microbiota ; Neoplasms/immunology/*microbiology/*therapy ; Treatment Outcome ; }, abstract = {Immuno-oncology has rapidly grown in the last thirty years, and immunotherapeutic agents are now approved to treat many disparate cancers. Immune checkpoint inhibitors (ICIs) are employed to augment cytotoxic anti-cancer activity by inhibiting negative regulatory elements of the immune system. Modulating the immune system to target neoplasms has improved survivability of numerous cancers in many individuals, but forecasting outcomes post therapy is difficult due to insufficient predictive biomarkers. Recently, the tumor and gastrointestinal microbiome and immune milieu have been investigated as predictors and influencers of cancer immune therapy. In this review, we discuss: (1) ways to measure the microbiome including relevant bioinformatic analyses, (2) recent developments in animal studies and human clinical trials utilizing gut microbial composition and function as biomarkers of cancer immune therapy response and toxicity, and (3) using prebiotics, probiotics, postbiotics, antibiotics, and fecal microbiota transplant (FMT) to modulate immune therapy. We discuss the respective benefits of 16S ribosomal RNA (rRNA) gene and shotgun metagenomic sequencing including important considerations in obtaining samples and in designing and interpreting human and animal microbiome studies. We then focus on studies discussing the differences in response to ICIs in relation to the microbiome and inflammatory mediators. ICIs cause colitis in up to 25% of individuals, and colitis is often refractory to common immunosuppressive medications. Researchers have measured microbiota composition prior to ICI therapy and correlated baseline microbiota composition with efficacy and colitis. Certain bacterial taxa that appear to enhance therapeutic benefit are also implicated in increased susceptibility to colitis, alluding to a delicate balance between pro-inflammatory tumor killing and anti-inflammatory protection from colitis. Pre-clinical and clinical models have trialed probiotic administration, e.g. Bifidobacterium spp. or FMT, to treat colitis when immune suppressive agents fail. We are excited about the future of modulating the microbiome to predict and influence cancer outcomes. Furthermore, novel therapies employed for other illnesses including bacteriophage and genetically-engineered microbes can be adapted in the future to promote increased advancements in cancer treatment and side effect management.}, } @article {pmid31524629, year = {2020}, author = {Lo, KH and Lu, CW and Lin, WH and Chien, CC and Chen, SC and Kao, CM}, title = {Enhanced reductive dechlorination of trichloroethene with immobilized Clostridium butyricum in silica gel.}, journal = {Chemosphere}, volume = {238}, number = {}, pages = {124596}, doi = {10.1016/j.chemosphere.2019.124596}, pmid = {31524629}, issn = {1879-1298}, mesh = {Biodegradation, Environmental ; Chloroflexi/growth & development/*metabolism ; Clostridium butyricum/*metabolism ; Groundwater/*chemistry ; Halogenation ; Metagenomics ; Microbiota/physiology ; Silica Gel ; Trichloroethylene/*metabolism ; }, abstract = {Deteriorated environmental conditions during the bioremediation of trichloroethene (TCE)-polluted groundwater cause decreased treatment efficiencies. This study assessed the effect of applying immobilized Clostridium butyricum (a hydrogen-producing bacterium) in silica gel on enhancing the reductive dechlorination efficiency of TCE with the slow polycolloid-releasing substrate (SPRS) supplement in groundwater. The responses of microbial communities with the immobilized system (immobilized Clostridium butyricum and SPRS amendments) were also characterized by the metagenomics assay. A complete TCE removal in microcosms was obtained within 30 days with the application of this immobilized system via reductive dechlorination processes. An increase in the population of Dehalococcoides spp. was observed using the quantitative polymerase chain reaction (qPCR) analysis. Results of metagenomics assay reveal that the microbial communities in the immobilized system were distinct from those in systems with SPRS only. Bacterial communities associated with TCE biodegradation also increased in microcosms treated with the immobilized system. The immobilized system shows a great potential to promote the TCE dechlorination efficiency, and the metagenomics-based approach provides detailed insights into dechlorinating microbial community dynamics. The results would be helpful in designing an in situ immobilized system to enhance the bioremediation efficiency of TCE-contaminated groundwater.}, } @article {pmid31524291, year = {2020}, author = {Malard, F and Mohty, M}, title = {Gut microbiota alteration during allogeneic haematopoietic cell transplantation: what can we do?.}, journal = {British journal of haematology}, volume = {188}, number = {3}, pages = {351-353}, doi = {10.1111/bjh.16204}, pmid = {31524291}, issn = {1365-2141}, mesh = {*Gastrointestinal Microbiome ; *Hematopoietic Stem Cell Transplantation ; Humans ; Prognosis ; Transplantation, Homologous ; }, } @article {pmid31523007, year = {2019}, author = {Cabral, DJ and Penumutchu, S and Reinhart, EM and Zhang, C and Korry, BJ and Wurster, JI and Nilson, R and Guang, A and Sano, WH and Rowan-Nash, AD and Li, H and Belenky, P}, title = {Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome.}, journal = {Cell metabolism}, volume = {30}, number = {4}, pages = {800-823.e7}, pmid = {31523007}, issn = {1932-7420}, support = {P20 GM109035/GM/NIGMS NIH HHS/United States ; P20 GM121344/GM/NIGMS NIH HHS/United States ; S10 OD023461/OD/NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; }, mesh = {Amoxicillin/*pharmacology ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteroides thetaiotaomicron/*drug effects/*metabolism ; Dietary Fiber/metabolism ; *Drug Resistance, Bacterial ; Female ; Gastrointestinal Microbiome/*drug effects ; Glucose/metabolism ; Mice ; Mice, Inbred C57BL ; Polysaccharides/metabolism ; }, abstract = {Although antibiotics disturb the structure of the gut microbiota, factors that modulate these perturbations are poorly understood. Bacterial metabolism is an important regulator of susceptibility in vitro and likely plays a large role within the host. We applied a metagenomic and metatranscriptomic approach to link antibiotic-induced taxonomic and transcriptional responses within the murine microbiome. We found that antibiotics significantly alter the expression of key metabolic pathways at the whole-community and single-species levels. Notably, Bacteroides thetaiotaomicron, which blooms in response to amoxicillin, upregulated polysaccharide utilization. In vitro, we found that the sensitivity of this bacterium to amoxicillin was elevated by glucose and reduced by polysaccharides. Accordingly, we observed that dietary composition affected the abundance and expansion of B. thetaiotaomicron, as well as the extent of microbiome disruption with amoxicillin. Our work indicates that the metabolic environment of the microbiome plays a role in the response of this community to antibiotics.}, } @article {pmid31521989, year = {2019}, author = {Breton-Deval, L and Sanchez-Flores, A and Juárez, K and Vera-Estrella, R}, title = {Integrative study of microbial community dynamics and water quality along The Apatlaco River.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {255}, number = {Pt 1}, pages = {113158}, doi = {10.1016/j.envpol.2019.113158}, pmid = {31521989}, issn = {1873-6424}, mesh = {Bacteria/classification/*isolation & purification ; Biological Oxygen Demand Analysis ; Environmental Monitoring/*methods ; Humans ; Mexico ; Microbiota ; Nitrogen/analysis ; Oxygen/analysis ; Phosphorus/analysis ; Rivers/chemistry/*microbiology ; Urbanization ; Water Pollutants, Chemical/*analysis ; Water Pollution/*analysis ; Water Quality ; }, abstract = {The increasing demand for clean water resources for human consumption, is raising concerning about the sustainable worldwide provisioning. In Mexico, rivers near to high-density urbanizations are subject to irrational exploitation where polluted water is a risk for human health. Therefore, the aims of this study are to analyze water quality parameters and bacterial community dynamics to understand the relation between them, in the Apatlaco river, which presents a clear environmental perturbance. Parameters such as total coliforms, chemical oxygen demand, harness, ammonium, nitrite, nitrate, total Kjeldahl nitrogen, dissolved oxygen, total phosphorus, total dissolved solids, and temperature were analyzed in 17 sampling points along the river. The high pollution level was registered in the sampling point 10 with 480 mg/L chemical oxygen demand, 7 mg/L nitrite, 34 mg/L nitrate, 2 mg/L dissolved oxygen, and 299 mg/L of total dissolved solids. From these sites, we selected four samples for DNA extraction and performed a metagenomic analysis using a whole metagenome shotgun approach, to compare the microbial communities between polluted and non-polluted sites. In general, Proteobacteria was the most representative phylum in all sites. However, the clean water reference point was enriched with microorganism from the Limnohabitans genus, a planktonic bacterium widespread in freshwater ecosystems. Nevertheless, in the polluted sampled sites, we found a high abundance of potential opportunistic pathogen genera such as Acinetobacter, Arcobacter, and Myroides, among others. This suggests that in addition to water contamination, an imminent human health risk due to pathogenic bacteria can potentially affect a population of ∼1.6 million people dwelling nearby. These results will contribute to the knowledge regarding anthropogenic pollution on the microbial population dynamic and how they affect human health and life quality.}, } @article {pmid31521614, year = {2019}, author = {Yamada, T and Hino, S and Iijima, H and Genda, T and Aoki, R and Nagata, R and Han, KH and Hirota, M and Kinashi, Y and Oguchi, H and Suda, W and Furusawa, Y and Fujimura, Y and Kunisawa, J and Hattori, M and Fukushima, M and Morita, T and Hase, K}, title = {Mucin O-glycans facilitate symbiosynthesis to maintain gut immune homeostasis.}, journal = {EBioMedicine}, volume = {48}, number = {}, pages = {513-525}, pmid = {31521614}, issn = {2352-3964}, mesh = {Adult ; Animals ; Biomarkers ; Butyrates/metabolism ; Case-Control Studies ; Female ; Gastrointestinal Microbiome ; *Homeostasis ; Humans ; *Immunity, Mucosal ; Inflammatory Bowel Diseases/etiology/metabolism/pathology ; Intestinal Mucosa/*immunology/*metabolism ; Male ; Metagenome ; Metagenomics ; Mice ; Middle Aged ; Mucins/*metabolism ; Polysaccharides/*metabolism ; Symbiosis ; }, abstract = {BACKGROUND: The dysbiosis of gut microbiota has been implicated in the pathogenesis of inflammatory bowel diseases; however, the underlying mechanisms have not yet been elucidated. Heavily glycosylated mucin establishes a first-line barrier against pathogens and serves as a niche for microbial growth.

METHODS: To elucidate relationships among dysbiosis, abnormal mucin utilisation, and microbial metabolic dysfunction, we analysed short-chain fatty acids (SCFAs) and mucin components in stool samples of 40 healthy subjects, 49 ulcerative colitis (UC) patients, and 44 Crohn's disease (CD) patients from Japan.

FINDINGS: Levels of n-butyrate were significantly lower in stools of both CD and UC patients than in stools of healthy subjects. Correlation analysis identified seven bacterial species positively correlated with n-butyrate levels; the major n-butyrate producer, Faecalibacterium prausnitzii, was particularly underrepresented in CD patients, but not in UC patients. In UC patients, there were inverse correlations between mucin O-glycan levels and the production of SCFAs, such as n-butyrate, suggesting that mucin O-glycans serve as an endogenous fermentation substrate for n-butyrate production. Indeed, mucin-fed rodents exhibited enhanced n-butyrate production, leading to the expansion of RORgt[+]Treg cells and IgA-producing cells in colonic lamina propria. Microbial utilisation of mucin-associated O-glycans was significantly reduced in n-butyrate-deficient UC patients.

INTERPRETATION: Mucin O-glycans facilitate symbiosynthesis of n-butyrate by gut microbiota. Abnormal mucin utilisation may lead to reduced n-butyrate production in UC patients. FUND: Japan Society for the Promotion of Science, Health Labour Sciences Research Grant, AMED-Crest, AMED, Yakult Foundation, Keio Gijuku Academic Development Funds, The Aashi Grass Foundation, and The Canon Foundation.}, } @article {pmid31521200, year = {2019}, author = {Rausch, P and Rühlemann, M and Hermes, BM and Doms, S and Dagan, T and Dierking, K and Domin, H and Fraune, S and von Frieling, J and Hentschel, U and Heinsen, FA and Höppner, M and Jahn, MT and Jaspers, C and Kissoyan, KAB and Langfeldt, D and Rehman, A and Reusch, TBH and Roeder, T and Schmitz, RA and Schulenburg, H and Soluch, R and Sommer, F and Stukenbrock, E and Weiland-Bräuer, N and Rosenstiel, P and Franke, A and Bosch, T and Baines, JF}, title = {Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {133}, pmid = {31521200}, issn = {2049-2618}, mesh = {Animals ; Bacteria/classification/genetics ; Databases, Genetic ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome/genetics/*physiology ; Microbiota/genetics/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {BACKGROUND: The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution, and development of both players. These interdependencies inspired a new view of multicellular organisms as "metaorganisms." The goal of the Collaborative Research Center "Origin and Function of Metaorganisms" is to understand why and how microbial communities form long-term associations with hosts from diverse taxonomic groups, ranging from sponges to humans in addition to plants.

METHODS: In order to optimize the choice of analysis procedures, which may differ according to the host organism and question at hand, we systematically compared the two main technical approaches for profiling microbial communities, 16S rRNA gene amplicon and metagenomic shotgun sequencing across our panel of ten host taxa. This includes two commonly used 16S rRNA gene regions and two amplification procedures, thus totaling five different microbial profiles per host sample.

CONCLUSION: While 16S rRNA gene-based analyses are subject to much skepticism, we demonstrate that many aspects of bacterial community characterization are consistent across methods. The resulting insight facilitates the selection of appropriate methods across a wide range of host taxa. Overall, we recommend single- over multi-step amplification procedures, and although exceptions and trade-offs exist, the V3 V4 over the V1 V2 region of the 16S rRNA gene. Finally, by contrasting taxonomic and functional profiles and performing phylogenetic analysis, we provide important and novel insight into broad evolutionary patterns among metaorganisms, whereby the transition of animals from an aquatic to a terrestrial habitat marks a major event in the evolution of host-associated microbial composition.}, } @article {pmid31520076, year = {2019}, author = {Koch, L}, title = {Early-life antibiotic use and gut microbiota.}, journal = {Nature reviews. Genetics}, volume = {20}, number = {11}, pages = {630}, doi = {10.1038/s41576-019-0174-7}, pmid = {31520076}, issn = {1471-0064}, mesh = {Anti-Bacterial Agents ; *Gastrointestinal Microbiome ; Hospitalization ; Humans ; Infant ; Metagenome ; }, } @article {pmid31518386, year = {2019}, author = {McCann, A and Jeffery, IB and Ouliass, B and Ferland, G and Fu, X and Booth, SL and Tran, TTT and O'Toole, PW and O'Connor, EM}, title = {Exploratory analysis of covariation of microbiota-derived vitamin K and cognition in older adults.}, journal = {The American journal of clinical nutrition}, volume = {110}, number = {6}, pages = {1404-1415}, pmid = {31518386}, issn = {1938-3207}, mesh = {Aged ; Aged, 80 and over ; Aging/metabolism/*psychology ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Cognition ; Cohort Studies ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; Vitamin K/*metabolism ; Vitamin K 1/metabolism ; }, abstract = {BACKGROUND: Vitamin K has multiple important physiological roles, including blood coagulation and beneficial effects on myelin integrity in the brain. Some intestinal microbes possess the genes to produce vitamin K in the form of menaquinone (MK). MK appears in higher concentration in tissues, such as the brain, particularly MK4, than the dietary form of phylloquinone (PK). Lower PK concentrations have been reported in patients with Alzheimer disease while higher serum PK concentrations have been positively associated with verbal episodic memory. Despite knowledge of the importance of vitamin K for various health parameters, few studies have measured MK concentration and biosynthesis by gut commensals.

OBJECTIVE: The aim of the current study was to investigate the relation between genes involved in gut-microbiota derived MK, concentrations of MK isoforms, and cognitive function.

METHODS: Shotgun metagenomic sequencing of the gut microbiome of 74 elderly individuals with different cognitive ability levels was performed. From this, gene counts for microbial MK biosynthesis were determined. Associations between clusters of individuals, grouped based on a similar presence and prevalence of MK biosynthesis genes, and cognitive ability were investigated. Fecal MK concentrations were quantified by HPLC to investigate correlations with subject clusters.

RESULTS: Separation of subject groups defined by banded quantification of the genetic potential of their microbiome to biosynthesize MK was associated with significant differences in cognitive ability [assessed using the Mini-Mental State Examination (MMSE)]. Three MK isoforms were found to be positively associated with MMSE, along with the identification of key components of the MK pathway that drive this association. Although the causality and direction of these associations remain unknown, these findings justify further studies.

CONCLUSIONS: This study provides evidence that although total concentrations of MK did not covary with cognition, certain MK isoforms synthesized by the gut microbiome, particularly the longer chains, are positively associated with cognition.}, } @article {pmid31515490, year = {2019}, author = {Botté, ES and Nielsen, S and Abdul Wahab, MA and Webster, J and Robbins, S and Thomas, T and Webster, NS}, title = {Changes in the metabolic potential of the sponge microbiome under ocean acidification.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4134}, pmid = {31515490}, issn = {2041-1723}, mesh = {Acids/*chemistry ; Animals ; Carbon/metabolism ; Carbon Cycle ; Carbon Dioxide/metabolism ; Carbonic Anhydrases/metabolism ; Genes, Bacterial ; *Metabolic Networks and Pathways ; *Microbiota ; Nitrogen/metabolism ; *Oceans and Seas ; Porifera/genetics/*microbiology ; Sulfur/metabolism ; }, abstract = {Anthropogenic CO2 emissions are causing ocean acidification, which can affect the physiology of marine organisms. Here we assess the possible effects of ocean acidification on the metabolic potential of sponge symbionts, inferred by metagenomic analyses of the microbiomes of two sponge species sampled at a shallow volcanic CO2 seep and a nearby control reef. When comparing microbial functions between the seep and control sites, the microbiome of the sponge Stylissa flabelliformis (which is more abundant at the control site) exhibits at the seep reduced potential for uptake of exogenous carbohydrates and amino acids, and for degradation of host-derived creatine, creatinine and taurine. The microbiome of Coelocarteria singaporensis (which is more abundant at the seep) exhibits reduced potential for carbohydrate import at the seep, but greater capacity for archaeal carbon fixation via the 3-hydroxypropionate/4-hydroxybutyrate pathway, as well as archaeal and bacterial urea production and ammonia assimilation from arginine and creatine catabolism. Together these metabolic features might contribute to enhanced tolerance of the sponge symbionts, and possibly their host, to ocean acidification.}, } @article {pmid31510682, year = {2019}, author = {Valdes, C and Stebliankin, V and Narasimhan, G}, title = {Large scale microbiome profiling in the cloud.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {14}, pages = {i13-i22}, pmid = {31510682}, issn = {1367-4811}, support = {R15 AI128714/AI/NIAID NIH HHS/United States ; }, mesh = {Algorithms ; *Cloud Computing ; *High-Throughput Nucleotide Sequencing ; Metagenomics ; *Microbiota ; Sequence Analysis, DNA ; Software ; }, abstract = {MOTIVATION: Bacterial metagenomics profiling for metagenomic whole sequencing (mWGS) usually starts by aligning sequencing reads to a collection of reference genomes. Current profiling tools are designed to work against a small representative collection of genomes, and do not scale very well to larger reference genome collections. However, large reference genome collections are capable of providing a more complete and accurate profile of the bacterial population in a metagenomics dataset. In this paper, we discuss a scalable, efficient and affordable approach to this problem, bringing big data solutions within the reach of laboratories with modest resources.

RESULTS: We developed Flint, a metagenomics profiling pipeline that is built on top of the Apache Spark framework, and is designed for fast real-time profiling of metagenomic samples against a large collection of reference genomes. Flint takes advantage of Spark's built-in parallelism and streaming engine architecture to quickly map reads against a large (170 GB) reference collection of 43 552 bacterial genomes from Ensembl. Flint runs on Amazon's Elastic MapReduce service, and is able to profile 1 million Illumina paired-end reads against over 40 K genomes on 64 machines in 67 s-an order of magnitude faster than the state of the art, while using a much larger reference collection. Streaming the sequencing reads allows this approach to sustain mapping rates of 55 million reads per hour, at an hourly cluster cost of $8.00 USD, while avoiding the necessity of storing large quantities of intermediate alignments.

Flint is open source software, available under the MIT License (MIT). Source code is available at https://github.com/camilo-v/flint.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid31509535, year = {2019}, author = {King, CH and Desai, H and Sylvetsky, AC and LoTempio, J and Ayanyan, S and Carrie, J and Crandall, KA and Fochtman, BC and Gasparyan, L and Gulzar, N and Howell, P and Issa, N and Krampis, K and Mishra, L and Morizono, H and Pisegna, JR and Rao, S and Ren, Y and Simonyan, V and Smith, K and VedBrat, S and Yao, MD and Mazumder, R}, title = {Baseline human gut microbiota profile in healthy people and standard reporting template.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0206484}, pmid = {31509535}, issn = {1932-6203}, support = {U01 CA230690/CA/NCI NIH HHS/United States ; R01 CA236591/CA/NCI NIH HHS/United States ; I01 BX003732/BX/BLRD VA/United States ; R01 AA023146/AA/NIAAA NIH HHS/United States ; UL1 TR000075/TR/NCATS NIH HHS/United States ; }, mesh = {Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; }, abstract = {A comprehensive knowledge of the types and ratios of microbes that inhabit the healthy human gut is necessary before any kind of pre-clinical or clinical study can be performed that attempts to alter the microbiome to treat a condition or improve therapy outcome. To address this need we present an innovative scalable comprehensive analysis workflow, a healthy human reference microbiome list and abundance profile (GutFeelingKB), and a novel Fecal Biome Population Report (FecalBiome) with clinical applicability. GutFeelingKB provides a list of 157 organisms (8 phyla, 18 classes, 23 orders, 38 families, 59 genera and 109 species) that forms the baseline biome and therefore can be used as healthy controls for studies related to dysbiosis. This list can be expanded to 863 organisms if closely related proteomes are considered. The incorporation of microbiome science into routine clinical practice necessitates a standard report for comparison of an individual's microbiome to the growing knowledgebase of "normal" microbiome data. The FecalBiome and the underlying technology of GutFeelingKB address this need. The knowledgebase can be useful to regulatory agencies for the assessment of fecal transplant and other microbiome products, as it contains a list of organisms from healthy individuals. In addition to the list of organisms and their abundances, this study also generated a collection of assembled contiguous sequences (contigs) of metagenomics dark matter. In this study, metagenomic dark matter represents sequences that cannot be mapped to any known sequence but can be assembled into contigs of 10,000 nucleotides or higher. These sequences can be used to create primers to study potential novel organisms. All data is freely available from https://hive.biochemistry.gwu.edu/gfkb and NCBI's Short Read Archive.}, } @article {pmid31509433, year = {2019}, author = {Tiffany, CR and Bäumler, AJ}, title = {Dysbiosis: from fiction to function.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {317}, number = {5}, pages = {G602-G608}, pmid = {31509433}, issn = {1522-1547}, support = {R56 AI112949/AI/NIAID NIH HHS/United States ; R01 AI044170/AI/NIAID NIH HHS/United States ; R01 AI096528/AI/NIAID NIH HHS/United States ; R01 AI112949/AI/NIAID NIH HHS/United States ; R01 AI112445/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Dysbiosis/etiology/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; }, abstract = {Advances in data collection technologies reveal that an imbalance (dysbiosis) in the composition of host-associated microbial communities (microbiota) is linked to many human illnesses. This association makes dysbiosis a central concept for understanding how the human microbiota contributes to health and disease. However, it remains problematic to define the term dysbiosis by cataloguing microbial species names. Here, we discuss how incorporating the germ-organ concept, ecological assumptions, and immunological principles into a theoretical framework for microbiota research provides a functional definition for dysbiosis. The generation of such a framework suggests that the next logical step in microbiota research will be to illuminate the mechanistic underpinnings of dysbiosis, which often involves a weakening of immune mechanisms that balance our microbial communities.}, } @article {pmid31509432, year = {2019}, author = {Zhou, F and Paz, HA and Sadri, M and Cui, J and Kachman, SD and Fernando, SC and Zempleni, J}, title = {Dietary bovine milk exosomes elicit changes in bacterial communities in C57BL/6 mice.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {317}, number = {5}, pages = {G618-G624}, pmid = {31509432}, issn = {1522-1547}, support = {P20 GM104320/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Diet ; Exosomes/*metabolism ; Female ; *Gastrointestinal Microbiome ; Male ; Metagenome ; Mice ; Mice, Inbred C57BL ; Milk/*metabolism ; RNA/metabolism ; }, abstract = {Exosomes and exosome-like vesicles participate in cell-to-cell communication in animals, plant, and bacteria. Dietary exosomes in bovine milk are bioavailable in nonbovine species, but a fraction of milk exosomes reaches the large intestine. We hypothesized that milk exosomes alter the composition of the gut microbiome in mice. C57BL/6 mice were fed AIN-93G diets, defined by their content of bovine milk exosomes and RNA cargos: exosome/RNA-depleted (ERD) versus exosome/RNA-sufficient (ERS) diets. Feeding was initiated at age 3 wk, and cecum content was collected at ages 7, 15, and 47 wk. Microbial communities were identified by 16S rRNA gene sequencing. Milk exosomes altered bacterial communities in the murine cecum. The abundance of three phyla, seven families, and 52 operational taxonomic units (OTUs) was different in the ceca from mice fed ERD and ERS (P < 0.05). For example, at the phylum level, Tenericutes had more than threefold abundance in ERS mice at ages 15 and 47 wk compared with ERD mice (P < 0.05). At the family level, Verrucomicrobiaceae were much less abundant in ERS mice compared with ERD mice age 47 wk (P < 0.05). At the OTU level, four OTUs from the family of Lachnospiraceae were more than two times more abundant in ERS mice compared with ERD at age 7 and 47 wk (P < 0.05). We conclude that exosomes in bovine milk alter microbial communities in nonbovine species, suggesting that exosomes and their cargos participate in the crosstalk between bacterial and animal kingdoms.NEW & NOTEWORTHY This is the first report that exosomes from bovine milk alter microbial communities in mice. This report suggests that the gut microbiome facilitates cell-to-cell communication by milk exosomes across species boundaries, and milk exosomes facilitate communication across animal and bacteria kingdoms.}, } @article {pmid31507563, year = {2019}, author = {Liang, Y and Wang, L and Wang, Z and Zhao, J and Yang, Q and Wang, M and Yang, K and Zhang, L and Jiao, N and Zhang, Y}, title = {Metagenomic Analysis of the Diversity of DNA Viruses in the Surface and Deep Sea of the South China Sea.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1951}, pmid = {31507563}, issn = {1664-302X}, abstract = {A metagenomic analysis of the viral community from five surface and five deep sea water (>2000 m below the surface, mbs) samples collected from the central basin of the South China Sea and adjacent Northwest Pacific Ocean during July-August 2017 was conducted herein. We builded up a South China Sea DNA virome (SCSV) dataset of 29,967 viral Operational Taxonomic Units (vOTUs), which is comparable to the viral populations from the original Tara Ocean and Malaspina expeditions. The most abundant and widespread viral populations were from the uncultivated viruses annotated from the viral metagenomics. Only 74 and 37 vOTUs have similarity with the reported genomes from the cultivated viruses and the single-virus genomics, respectively. The community structures of deep sea viromes in the SCSV were generally different from the surface viromes. The carbon flux and nutrients (PO4 and NOx) were related to the surface and deep sea viromes in the SCSV, respectively. In the SCSV, the annotated vOTUs could be affiliated to the cultivated viruses mainly including Pelagibacter (SAR11) phage HTVC010P, Prochlorococcus phages (P-GSP1, P-SSM4, and P-TIM68), Cyanophages (MED4-184 and MED4-117) and Mycobacterium phages (Sparky and Squirty). It indicated that phage infection to the SAR11 cluster may occur ubiquitously and has significant impacts on bathypelagic SAR11 communities in the deep sea. Meanwhile, as Prochlorococcus is prominently distributed in the euphotic ocean, the existence of their potential phages in the deep sea suggested the sedimentation mechanism might contribute to the formation of the deep sea viromes. Intriguingly, the presence of Mycobacterium phages only in the deep sea viromes, suggests inhabitance of endemic viral populations in the deep sea viromes in the SCSV. This study provided an insight of the viral community in the South China Sea and for the first time uncovered the deep sea viral diversity in the central basin of the South China Sea.}, } @article {pmid31506511, year = {2019}, author = {Dong, K and Xin, Y and Cao, F and Huang, Z and Sun, J and Peng, M and Liu, W and Shi, P}, title = {Succession of oral microbiota community as a tool to estimate postmortem interval.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13063}, pmid = {31506511}, issn = {2045-2322}, mesh = {*Autopsy ; Bacteria/classification/genetics ; Biodiversity ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth/*microbiology ; *Postmortem Changes ; }, abstract = {The establishment of postmortem interval is one of the most important aspects of forensic expertise. Microbes may provide a novel way to estimate the postmortem intervals in order to avoid many of these limitations. The oral cavity harbors one of the most diverse microbiomes that play a key role in the decomposition of corpses. In this study, the oral bacterial community showed obvious changes in relative abundance during the process of mice decomposition. Meanwhile, at different taxonomic levels, specific bacteria were found to be significantly correlated with the postmortem interval. Linear regression models between relative abundance and the postmortem interval were constructed. Among these species, Gamma-proteobacteria and Proteus were the best ones that can be used to infer the postmortem interval, especially late postmortem interval. Therefore, we suggest that succession of oral microbial community can be developed as a forensic tool for estimating the postmortem interval.}, } @article {pmid31506464, year = {2019}, author = {Jiang, Z and Li, P and Wang, Y and Liu, H and Wei, D and Yuan, C and Wang, H}, title = {Arsenic mobilization in a high arsenic groundwater revealed by metagenomic and Geochip analyses.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12972}, pmid = {31506464}, issn = {2045-2322}, mesh = {Arsenic/*analysis ; Bacteria/*genetics ; Geologic Sediments/*analysis ; Groundwater/*analysis ; *Metagenome ; Microbiota ; Water Pollutants, Chemical/*analysis ; }, abstract = {Microbial metabolisms of arsenic, iron, sulfur, nitrogen and organic matter play important roles in arsenic mobilization in aquifer. In this study, microbial community composition and functional potentials in a high arsenic groundwater were investigated using integrated techniques of RNA- and DNA-based 16S rRNA gene sequencing, metagenomic sequencing and functional gene arrays. 16S rRNA gene sequencing showed the sample was dominated by members of Proteobacteria (62.3-75.2%), such as genera of Simplicispira (5.7-6.7%), Pseudomonas (3.3-5.7%), Ferribacterium (1.6-4.4%), Solimonas (1.8-3.2%), Geobacter (0.8-2.2%) and Sediminibacterium (0.6-2.4%). Functional potential analyses indicated that organics degradation, assimilatory sulfate reduction, As-resistant pathway, iron reduction, ammonification, nitrogen fixation, denitrification and dissimilatory nitrate reduction to ammonia were prevalent. The composition and function of microbial community and reconstructed genome bins suggest that high level of arsenite in the groundwater may be attributed to arsenate release from iron oxides reductive dissolution by the iron-reducing bacteria, and subsequent arsenate reduction by ammonia-producing bacteria featuring ars operon. This study highlights the relationship between biogeochemical cycling of arsenic and nitrogen in groundwater, which potentially occur in other aquifers with high levels of ammonia and arsenic.}, } @article {pmid31506313, year = {2019}, author = {Manoharan, L and Kozlowski, JA and Murdoch, RW and Löffler, FE and Sousa, FL and Schleper, C}, title = {Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki- and Thorarchaeota.}, journal = {mBio}, volume = {10}, number = {5}, pages = {}, pmid = {31506313}, issn = {2150-7511}, mesh = {Archaea/classification/*genetics/*metabolism ; Biodiversity ; Biosynthetic Pathways/genetics ; *Ecology ; Genome, Archaeal ; Geologic Sediments/*microbiology ; Lipid Metabolism ; Lipids/biosynthesis ; *Metagenome ; Molecular Sequence Annotation ; Phylogeny ; RNA, Ribosomal, 16S/metabolism ; Ribosomal Proteins/classification/genetics ; }, abstract = {The genomes of Asgard Archaea, a novel archaeal proposed superphylum, share an enriched repertoire of eukaryotic signature genes and thus promise to provide insights into early eukaryote evolution. However, the distribution, metabolisms, cellular structures, and ecology of the members within this superphylum are not well understood. Here we provide a meta-analysis of the environmental distribution of the Asgard archaea, based on available 16S rRNA gene sequences. Metagenome sequencing of samples from a salt-crusted lagoon on the Baja California Peninsula of Mexico allowed the assembly of a new Thorarchaeota and three Lokiarchaeota genomes. Comparative analyses of all known Lokiarchaeota and Thorarchaeota genomes revealed overlapping genome content, including central carbon metabolism. Members of both groups contained putative reductive dehalogenase genes, suggesting that these organisms might be able to metabolize halogenated organic compounds. Unlike the first report on Lokiarchaeota, we identified genes encoding glycerol-1-phosphate dehydrogenase in all Loki- and Thorarchaeota genomes, suggesting that these organisms are able to synthesize bona fide archaeal lipids with their characteristic glycerol stereochemistry.IMPORTANCE Microorganisms of the superphylum Asgard Archaea are considered to be the closest living prokaryotic relatives of eukaryotes (including plants and animals) and thus promise to give insights into the early evolution of more complex life forms. However, very little is known about their biology as none of the organisms has yet been cultivated in the laboratory. Here we report on the ecological distribution of Asgard Archaea and on four newly sequenced genomes of the Lokiarchaeota and Thorarchaeota lineages that give insight into possible metabolic features that might eventually help to identify these enigmatic groups of archaea in the environment and to culture them.}, } @article {pmid31504765, year = {2020}, author = {Wu, S and Sun, C and Li, Y and Wang, T and Jia, L and Lai, S and Yang, Y and Luo, P and Dai, D and Yang, YQ and Luo, Q and Gao, NL and Ning, K and He, LJ and Zhao, XM and Chen, WH}, title = {GMrepo: a database of curated and consistently annotated human gut metagenomes.}, journal = {Nucleic acids research}, volume = {48}, number = {D1}, pages = {D545-D553}, pmid = {31504765}, issn = {1362-4962}, mesh = {*Databases, Genetic ; *Gastrointestinal Microbiome ; Genes, Bacterial ; Genome, Human ; Humans ; *Metagenome ; Metagenomics/*methods ; Molecular Sequence Annotation ; *Software ; }, abstract = {GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purpose is to facilitate the reusability and accessibility of the rapidly growing human metagenomic data. This is achieved by consistently annotating the microbial contents of collected samples using state-of-art toolsets and by manual curation of the meta-data of the corresponding human hosts. GMrepo organizes the collected samples according to their associated phenotypes and includes all possible related meta-data such as age, sex, country, body-mass-index (BMI) and recent antibiotics usage. To make relevant information easier to access, GMrepo is equipped with a graphical query builder, enabling users to make customized, complex and biologically relevant queries. For example, to find (1) samples from healthy individuals of 18 to 25 years old with BMIs between 18.5 and 24.9, or (2) projects that are related to colorectal neoplasms, with each containing >100 samples and both patients and healthy controls. Precomputed species/genus relative abundances, prevalence within and across phenotypes, and pairwise co-occurrence information are all available at the website and accessible through programmable interfaces. So far, GMrepo contains 58 903 human gut samples/runs (including 17 618 metagenomes and 41 285 amplicons) from 253 projects concerning 92 phenotypes. GMrepo is freely available at: https://gmrepo.humangut.info.}, } @article {pmid31504457, year = {2019}, author = {Hoyos-Hernandez, C and Courbert, C and Simonucci, C and David, S and Vogel, TM and Larose, C}, title = {Community structure and functional genes in radionuclide contaminated soils in Chernobyl and Fukushima.}, journal = {FEMS microbiology letters}, volume = {366}, number = {21}, pages = {}, doi = {10.1093/femsle/fnz180}, pmid = {31504457}, issn = {1574-6968}, mesh = {*Biota ; Cesium Radioisotopes/*analysis ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Japan ; Metabolic Networks and Pathways/genetics ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants, Radioactive/*analysis ; Strontium Radioisotopes/*analysis ; Ukraine ; }, abstract = {Chernobyl and Fukushima were subjected to radionuclide (RN) contamination that has led to environmental problems. In order to explore the ability of microorganisms to survive in these environments, we used a combined 16S rRNA and metagenomic approach to describe the prokaryotic community structure and metabolic potential over a gradient of RN concentrations (137Cs 1680-0.4 and 90Sr 209.1-1.9 kBq kg-1) in soil samples. The taxonomic results showed that samples with low 137Cs content (37.8-0.4 kBq kg-1) from Fukushima and Chernobyl clustered together. In order to determine the effect of soil chemical parameters such as organic carbon (OC), Cesium-137 (137Cs) and Strontium-90 (90Sr) on the functional potential of microbial communities, multiple predictor model analysis using piecewiseSEM was carried out on Chernobyl soil metagenomes. The model identified 46 genes that were correlated to these parameters of which most have previously been described as mechanisms used by microorganisms under stress conditions. This study provides a baseline taxonomic and metagenomic dataset for Fukushima and Chernobyl, respectively, including physical and chemical characteristics. Our results pave the way for evaluating the possible RN selective pressure that might contribute to shaping microbial community structure and their functions in contaminated soils.}, } @article {pmid31504188, year = {2020}, author = {Kim, KJ and Park, J and Park, SC and Won, S}, title = {Phylogenetic tree-based microbiome association test.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {4}, pages = {1000-1006}, doi = {10.1093/bioinformatics/btz686}, pmid = {31504188}, issn = {1367-4811}, mesh = {Bacteria ; Humans ; Metagenomics ; *Microbiota ; *Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {MOTIVATION: Ecological patterns of the human microbiota exhibit high inter-subject variation, with few operational taxonomic units (OTUs) shared across individuals. To overcome these issues, non-parametric approaches, such as the Mann-Whitney U-test and Wilcoxon rank-sum test, have often been used to identify OTUs associated with host diseases. However, these approaches only use the ranks of observed relative abundances, leading to information loss, and are associated with high false-negative rates. In this study, we propose a phylogenetic tree-based microbiome association test (TMAT) to analyze the associations between microbiome OTU abundances and disease phenotypes. Phylogenetic trees illustrate patterns of similarity among different OTUs, and TMAT provides an efficient method for utilizing such information for association analyses. The proposed TMAT provides test statistics for each node, which are combined to identify mutations associated with host diseases.

RESULTS: Power estimates of TMAT were compared with existing methods using extensive simulations based on real absolute abundances. Simulation studies showed that TMAT preserves the nominal type-1 error rate, and estimates of its statistical power generally outperformed existing methods in the considered scenarios. Furthermore, TMAT can be used to detect phylogenetic mutations associated with host diseases, providing more in-depth insight into bacterial pathology.

The 16S rRNA amplicon sequencing metagenomics datasets for colorectal carcinoma and myalgic encephalomyelitis/chronic fatigue syndrome are available from the European Nucleotide Archive (ENA) database under project accession number PRJEB6070 and PRJEB13092, respectively. TMAT was implemented in the R package. Detailed information is available at http://healthstat.snu.ac.kr/software/tmat.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid31504055, year = {2019}, author = {Scheifler, M and Ruiz-Rodríguez, M and Sanchez-Brosseau, S and Magnanou, E and Suzuki, MT and West, N and Duperron, S and Desdevises, Y}, title = {Characterization of ecto- and endoparasite communities of wild Mediterranean teleosts by a metabarcoding approach.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0221475}, pmid = {31504055}, issn = {1932-6203}, mesh = {Animals ; Apicomplexa/genetics ; Arthropods/genetics ; Ascomycota/genetics ; *Biodiversity ; Ciliophora/genetics ; DNA Barcoding, Taxonomic/methods ; Fishes/microbiology/*parasitology ; Gills/microbiology/parasitology ; Intestines/microbiology/parasitology ; *Metagenome ; Metagenomics/methods ; Nematoda/genetics ; Skin/microbiology/parasitology ; Symbiosis ; }, abstract = {Next-generation sequencing methods are increasingly used to identify eukaryotic, unicellular and multicellular symbiont communities within hosts. In this study, we analyzed the non-specific reads obtained during a metabarcoding survey of the bacterial communities associated to three different tissues collected from 13 wild Mediterranean teleost fish species. In total, 30 eukaryotic genera were identified as putative parasites of teleosts, associated to skin mucus, gills mucus and intestine: 2 ascomycetes, 4 arthropods, 2 cnidarians, 7 nematodes, 10 platyhelminthes, 4 apicomplexans, 1 ciliate as well as one order in dinoflagellates (Syndiniales). These results highlighted that (1) the metabarcoding approach was able to uncover a large spectrum of symbiotic organisms associated to the fish species studied, (2) symbionts not yet identified in several teleost species were putatively present, (3) the parasitic diversity differed markedly across host species and (4) in most cases, the distribution of known parasitic genera within tissues is in accordance with the literature. The current work illustrates the large insights that can be gained by making maximum use of data from a metabarcoding approach.}, } @article {pmid31502536, year = {2019}, author = {McLaren, MR and Willis, AD and Callahan, BJ}, title = {Consistent and correctable bias in metagenomic sequencing experiments.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31502536}, issn = {2050-084X}, support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; R35 GM133745/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics ; *Bias ; Biota ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Metagenomics/*methods ; *Models, Theoretical ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Marker-gene and metagenomic sequencing have profoundly expanded our ability to measure biological communities. But the measurements they provide differ from the truth, often dramatically, because these experiments are biased toward detecting some taxa over others. This experimental bias makes the taxon or gene abundances measured by different protocols quantitatively incomparable and can lead to spurious biological conclusions. We propose a mathematical model for how bias distorts community measurements based on the properties of real experiments. We validate this model with 16S rRNA gene and shotgun metagenomics data from defined bacterial communities. Our model better fits the experimental data despite being simpler than previous models. We illustrate how our model can be used to evaluate protocols, to understand the effect of bias on downstream statistical analyses, and to measure and correct bias given suitable calibration controls. These results illuminate new avenues toward truly quantitative and reproducible metagenomics measurements.}, } @article {pmid31502535, year = {2019}, author = {Forsberg, KJ and Bhatt, IV and Schmidtke, DT and Javanmardi, K and Dillard, KE and Stoddard, BL and Finkelstein, IJ and Kaiser, BK and Malik, HS}, title = {Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31502535}, issn = {2050-084X}, support = {F31 GM125201/GM/NIGMS NIH HHS/United States ; R01 GM105691/GM/NIGMS NIH HHS/United States ; R01 GM124141/GM/NIGMS NIH HHS/United States ; R01 GM124131/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/isolation & purification/*metabolism ; CRISPR-Associated Protein 9/*antagonists & inhibitors ; Enzyme Inhibitors/isolation & purification/*metabolism ; Feces/microbiology/virology ; Humans ; Metagenomics ; *Microbiota ; Mouth/microbiology/virology ; Viral Proteins/genetics/isolation & purification/*metabolism ; }, abstract = {CRISPR-Cas systems protect bacteria and archaea from phages and other mobile genetic elements, which use small anti-CRISPR (Acr) proteins to overcome CRISPR-Cas immunity. Because Acrs are challenging to identify, their natural diversity and impact on microbial ecosystems are underappreciated. To overcome this discovery bottleneck, we developed a high-throughput functional selection to isolate ten DNA fragments from human oral and fecal metagenomes that inhibit Streptococcus pyogenes Cas9 (SpyCas9) in Escherichia coli. The most potent Acr from this set, AcrIIA11, was recovered from a Lachnospiraceae phage. We found that AcrIIA11 inhibits SpyCas9 in bacteria and in human cells. AcrIIA11 homologs are distributed across diverse bacteria; many distantly-related homologs inhibit both SpyCas9 and a divergent Cas9 from Treponema denticola. We find that AcrIIA11 antagonizes SpyCas9 using a different mechanism than other previously characterized Type II-A Acrs. Our study highlights the power of functional selection to uncover widespread Cas9 inhibitors within diverse microbiomes.}, } @article {pmid31502171, year = {2020}, author = {Kumar, M and Singh, P and Murugesan, S and Vetizou, M and McCulloch, J and Badger, JH and Trinchieri, G and Al Khodor, S}, title = {Microbiome as an Immunological Modifier.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2055}, number = {}, pages = {595-638}, pmid = {31502171}, issn = {1940-6029}, support = {ZIA BC011153/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Age Factors ; Aged ; Bacteria/*classification/genetics/isolation & purification ; Bacterial Proteins/*genetics ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Microbiota ; Middle Aged ; Sequence Analysis, DNA ; }, abstract = {Humans are living ecosystems composed of human cells and microbes. The microbiome is the collection of microbes (microbiota) and their genes. Recent breakthroughs in the high-throughput sequencing technologies have made it possible for us to understand the composition of the human microbiome. Launched by the National Institutes of Health in USA, the human microbiome project indicated that our bodies harbor a wide array of microbes, specific to each body site with interpersonal and intrapersonal variabilities. Numerous studies have indicated that several factors influence the development of the microbiome including genetics, diet, use of antibiotics, and lifestyle, among others. The microbiome and its mediators are in a continuous cross talk with the host immune system; hence, any imbalance on one side is reflected on the other. Dysbiosis (microbiota imbalance) was shown in many diseases and pathological conditions such as inflammatory bowel disease, celiac disease, multiple sclerosis, rheumatoid arthritis, asthma, diabetes, and cancer. The microbial composition mirrors inflammation variations in certain disease conditions, within various stages of the same disease; hence, it has the potential to be used as a biomarker.}, } @article {pmid31501537, year = {2019}, author = {Gasparrini, AJ and Wang, B and Sun, X and Kennedy, EA and Hernandez-Leyva, A and Ndao, IM and Tarr, PI and Warner, BB and Dantas, G}, title = {Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome.}, journal = {Nature microbiology}, volume = {4}, number = {12}, pages = {2285-2297}, pmid = {31501537}, issn = {2058-5276}, support = {R01 GM099538/GM/NIGMS NIH HHS/United States ; T32 DK077653/DK/NIDDK NIH HHS/United States ; T32 GM007200/GM/NIGMS NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; U01 AI123394/AI/NIAID NIH HHS/United States ; T32 GM007067/GM/NIGMS NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology/*therapeutic use ; Bacteria/classification/drug effects/genetics ; Biodiversity ; Drug Resistance, Multiple, Bacterial/drug effects ; Enterobacteriaceae/drug effects ; Gastrointestinal Microbiome/*drug effects/genetics ; Gastrointestinal Tract/drug effects/microbiology ; *Hospitalization ; Humans ; Infant, Newborn ; Infant, Newborn, Diseases/drug therapy/microbiology ; Infant, Premature ; *Metagenome ; }, abstract = {Hospitalized preterm infants receive frequent and often prolonged exposures to antibiotics because they are vulnerable to infection. It is not known whether the short-term effects of antibiotics on the preterm infant gut microbiota and resistome persist after discharge from neonatal intensive care units. Here, we use complementary metagenomic, culture-based and machine learning techniques to study the gut microbiota and resistome of antibiotic-exposed preterm infants during and after hospitalization, and we compare these readouts to antibiotic-naive healthy infants sampled synchronously. We find a persistently enriched gastrointestinal antibiotic resistome, prolonged carriage of multidrug-resistant Enterobacteriaceae and distinct antibiotic-driven patterns of microbiota and resistome assembly in extremely preterm infants that received early-life antibiotics. The collateral damage of early-life antibiotic treatment and hospitalization in preterm infants is long lasting. We urge the development of strategies to reduce these consequences in highly vulnerable neonatal populations.}, } @article {pmid31501503, year = {2020}, author = {Kraemer, S and Ramachandran, A and Colatriano, D and Lovejoy, C and Walsh, DA}, title = {Diversity and biogeography of SAR11 bacteria from the Arctic Ocean.}, journal = {The ISME journal}, volume = {14}, number = {1}, pages = {79-90}, pmid = {31501503}, issn = {1751-7370}, mesh = {Arctic Regions ; Bacteria/*classification/genetics/isolation & purification ; Ecotype ; Metagenome ; Oceans and Seas ; Phylogeny ; Phylogeography ; Seawater/*microbiology ; Temperature ; }, abstract = {The Arctic Ocean is relatively isolated from other oceans and consists of strongly stratified water masses with distinct histories, nutrient, temperature, and salinity characteristics, therefore providing an optimal environment to investigate local adaptation. The globally distributed SAR11 bacterial group consists of multiple ecotypes that are associated with particular marine environments, yet relatively little is known about Arctic SAR11 diversity. Here, we examined SAR11 diversity using ITS analysis and metagenome-assembled genomes (MAGs). Arctic SAR11 assemblages were comprised of the S1a, S1b, S2, and S3 clades, and structured by water mass and depth. The fresher surface layer was dominated by an ecotype (S3-derived P3.2) previously associated with Arctic and brackish water. In contrast, deeper waters of Pacific origin were dominated by the P2.3 ecotype of the S2 clade, within which we identified a novel subdivision (P2.3s1) that was rare outside the Arctic Ocean. Arctic S2-derived SAR11 MAGs were restricted to high latitudes and included MAGs related to the recently defined S2b subclade, a finding consistent with bi-polar ecotypes and Arctic endemism. These results place the stratified Arctic Ocean into the SAR11 global biogeography and have identified SAR11 lineages for future investigation of adaptive evolution in the Arctic Ocean.}, } @article {pmid31501492, year = {2019}, author = {Wilkins, LJ and Monga, M and Miller, AW}, title = {Defining Dysbiosis for a Cluster of Chronic Diseases.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12918}, pmid = {31501492}, issn = {2045-2322}, mesh = {Anti-Bacterial Agents/adverse effects/pharmacology ; Bacteria ; Chronic Disease/epidemiology ; Computational Biology ; *Disease Susceptibility ; *Dysbiosis ; Gastrointestinal Microbiome/drug effects ; Humans ; Meta-Analysis as Topic ; Metagenome ; Metagenomics/methods ; *Microbiota/drug effects ; }, abstract = {The prevalence of many chronic diseases has increased over the last decades. It has been postulated that dysbiosis driven by environmental factors such as antibiotic use is shifting the microbiome in ways that increase inflammation and the onset of chronic disease. Dysbiosis can be defined through the loss or gain of bacteria that either promote health or disease, respectively. Here we use multiple independent datasets to determine the nature of dysbiosis for a cluster of chronic diseases that includes urinary stone disease (USD), obesity, diabetes, cardiovascular disease, and kidney disease, which often exist as co-morbidities. For all disease states, individuals exhibited a statistically significant association with antibiotics in the last year compared to healthy counterparts. There was also a statistically significant association between antibiotic use and gut microbiota composition. Furthermore, each disease state was associated with a loss of microbial diversity in the gut. Three genera, Bacteroides, Prevotella, and Ruminococcus, were the most common dysbiotic taxa in terms of being enriched or depleted in disease populations and was driven in part by the diversity of operational taxonomic units (OTUs) within these genera. Results of the cross-sectional analysis suggest that antibiotic-driven loss of microbial diversity may increase the risk for chronic disease. However, longitudinal studies are needed to confirm the causative effect of diversity loss for chronic disease risk.}, } @article {pmid31501472, year = {2019}, author = {Fu, X and Guo, J and Finkelbergs, D and He, J and Zha, L and Guo, Y and Cai, J}, title = {Fungal succession during mammalian cadaver decomposition and potential forensic implications.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12907}, pmid = {31501472}, issn = {2045-2322}, mesh = {Animals ; *Cadaver ; Environmental Microbiology ; *Forensic Sciences ; *Fungi ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Microbiota ; *Postmortem Changes ; Soil Microbiology ; }, abstract = {The necrobiome is the postmortem community that includes bacteria, fungi, arthropods, and other cadaver-associated organisms. It has been suggested as biological evidence for forensic investigation. Fungi form distinctive mildew spots in colonizing decomposing bodies, converting them into moldy cadavers. However, the postmortem fungal community consists of more than these visible species. Characterizing the succession pattern of the fungal community during decomposition is valuable not only for understanding the ecosystem composition of the cadaver decomposition islands but also for contributing to forensic investigations. In the present study, the fungal composition of pig cadavers and succession patterns during decomposition were investigated with high-throughput sequencing. The succession patterns were easier to discern in outdoor cadavers, compared with those that were placed indoors. The metabarcoding approach revealed trends linking particular fungal taxa with specific postmortem intervals (PMIs). Dominant species increased notably in cadavers and soil. Furthermore, the succession of the soil community was driven by the cadaver decomposition. Significant mycoflora differences were observed between environmental and cadaveric soil. The results obtained suggested that postputrefaction mycoflora have considerable potential for PMI estimation, particularly in cases that involve heavily decomposed bodies. In addition, the diversity of fungal communities revealed by the metabarcoding approach allowed us to discriminate the sites of cadaver decomposition, implying that postputrefaction mycoflora may be helpful in identifying the environment in which a cadaver has been placed, or the original location from which a cadaver has been moved. Our results provide an important step towards developing fungal evidence for use in forensic science and add to the growing body of work on postmortem microbial communities.}, } @article {pmid31500892, year = {2019}, author = {Sims, TT and Colbert, LE and Zheng, J and Delgado Medrano, AY and Hoffman, KL and Ramondetta, L and Jazaeri, A and Jhingran, A and Schmeler, KM and Daniel, CR and Klopp, A}, title = {Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls.}, journal = {Gynecologic oncology}, volume = {155}, number = {2}, pages = {237-244}, pmid = {31500892}, issn = {1095-6859}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; T32 CA101642/CA/NCI NIH HHS/United States ; }, mesh = {Aged ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Lymphatic Metastasis ; Middle Aged ; Neoplasm Staging ; Prospective Studies ; Uterine Cervical Neoplasms/genetics/*microbiology/pathology ; }, abstract = {OBJECTIVES: The aim of this study was to characterize variation in the gut microbiome of women with locally advanced cervical cancer and compare it to healthy controls.

METHODS: We characterized the 16S rDNA fecal microbiome in 42 cervical cancer patients and 46 healthy female controls. Shannon diversity index (SDI) was used to evaluate alpha (within sample) diversity. Beta (between sample) diversity was examined using principle coordinate analysis (PCoA) of unweighted Unifrac distances. Relative abundance of microbial taxa was compared between samples using Linear Discriminant Analysis Effect Size (LEfSe).

RESULTS: Within cervical cancer patients, bacterial alpha diversity was positively correlated with age (p = 0.22) but exhibited an inverse relationship in control subjects (p < 0.01). Alpha diversity was significantly higher in cervical cancer patients as compared to controls (p < 0.05), though stratification by age suggested this relationship was restricted to older women (>50 years; p < 0.01). Beta diversity (unweighted Unifrac; p < 0.01) also significantly differed between cervical cancer patients and controls. Based on age- and race-adjusted LEfSe analysis, multiple taxa significantly differed between cervical cancer patients and controls. Prevotella, Porphyromonas, and Dialister were significantly enriched in cervical cancer patients, while Bacteroides, Alistipes and members of the Lachnospiracea family were significantly enriched in healthy subjects.

CONCLUSION: Our study suggests differences in gut microbiota diversity and composition between cervical cancer patients and controls. Associations within the gut microbiome by age may reflect etiologic/clinical differences. These findings provide rationale for further study of the gut microbiome in cervical cancer.}, } @article {pmid31500708, year = {2020}, author = {Menezes, LAA and Sardaro, MLS and Duarte, RTD and Mazzon, RR and Neviani, E and Gatti, M and De Dea Lindner, J}, title = {Sourdough bacterial dynamics revealed by metagenomic analysis in Brazil.}, journal = {Food microbiology}, volume = {85}, number = {}, pages = {103302}, doi = {10.1016/j.fm.2019.103302}, pmid = {31500708}, issn = {1095-9998}, mesh = {Brazil ; Bread/*microbiology ; Colony Count, Microbial ; DNA, Bacterial/genetics ; *Fermentation ; Flour/microbiology ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Microbiota ; Proteobacteria/*classification/growth & development ; RNA, Ribosomal, 16S/genetics ; Temperature ; }, abstract = {This study dealt with the influence of the temperature on the bacterial dynamics of two spontaneously fermented wheat sourdoughs, propagated at 21 ± 1 °C (SD1) and 30 ± 1 °C (SD2), during nine backslopping steps (BS1 to BS9). Proteobacteria was the only phylum found in flour. Escherichia hermannii was predominant, followed by Kosakonia cowanii, besides species belonging to the genera Pantoea and Pseudomonas. After one step of propagation, Clostridium and Bacillus cereus group became predominant. Lactobacillus curvatus was found at low relative abundance. For the second backslopping step, Clostridium was flanked by L. curvatus and Lactobacillus farciminis. From BS4 (6th day) onward, lactic acid bacteria (LAB) became predominant. L. farciminis overcame L. curvatus and remained dominant until the end of propagations for both sourdoughs. At 21 °C, Bacillus, Clostridium, Pseudomonas, and Enterobacteriaceae were gradually inhibited. At the end of propagation, SD1 harbored only LAB. Otherwise, the temperature of 30 °C favored the persistence of atypical bacteria in SD2, as Pseudomonas and Enterobacteriaceae. Therefore, the temperature of 21 °C was more suitable for sourdough propagation in Brazil. This study enhanced the knowledge of temperature's influence on microbial assembly and contributed to the elucidation of sourdough microbial communities in Brazil.}, } @article {pmid31500705, year = {2020}, author = {Dugat-Bony, E and Lossouarn, J and De Paepe, M and Sarthou, AS and Fedala, Y and Petit, MA and Chaillou, S}, title = {Viral metagenomic analysis of the cheese surface: A comparative study of rapid procedures for extracting viral particles.}, journal = {Food microbiology}, volume = {85}, number = {}, pages = {103278}, doi = {10.1016/j.fm.2019.103278}, pmid = {31500705}, issn = {1095-9998}, mesh = {Bacteriophages/genetics ; Cheese/*virology ; *Metagenome ; Metagenomics/*methods ; Microbiota ; Virion/*genetics ; Virology/methods ; }, abstract = {The structure and functioning of microbial communities from fermented foods, including cheese, have been extensively studied during the past decade. However, there is still a lack of information about both the occurrence and the role of viruses in modulating the function of this type of spatially structured and solid ecosystems. Viral metagenomics was recently applied to a wide variety of environmental samples and standardized procedures for recovering viral particles from different type of materials has emerged. In this study, we adapted a procedure originally developed to extract viruses from fecal samples, in order to enable efficient virome analysis of cheese surface. We tested and validated the positive impact of both addition of a filtration step prior to virus concentration and substitution of purification by density gradient ultracentrifugation by a simple chloroform treatment to eliminate membrane vesicles. Viral DNA extracted from the several procedures, as well as a vesicle sample, were sequenced using Illumina paired-end MiSeq technology and the subsequent clusters assembled from the virome were analyzed to assess those belonging to putative phages, plasmid-derived DNA, or even from bacterial chromosomal DNA. The best procedure was then chosen, and used to describe the first cheese surface virome, using Epoisses cheese as example. This study provides the basis of future investigations regarding the ecological importance of viruses in cheese microbial ecosystems.}, } @article {pmid31500701, year = {2020}, author = {Li, Z and Dong, L and Zhao, C and Zhu, Y}, title = {Metagenomic insights into the changes in microbial community and antimicrobial resistance genes associated with different salt content of red pepper (Capsicum annuum L.) sauce.}, journal = {Food microbiology}, volume = {85}, number = {}, pages = {103295}, doi = {10.1016/j.fm.2019.103295}, pmid = {31500701}, issn = {1095-9998}, mesh = {Capsicum/*chemistry ; Drug Resistance, Bacterial/*genetics ; Enterobacteriaceae/*genetics/growth & development ; Fermentation ; Genes, Bacterial ; Lactobacillaceae/*genetics/growth & development ; *Metagenome ; Metagenomics ; *Microbiota ; Osmotic Pressure ; Sodium Chloride/*chemistry ; }, abstract = {Fermented red pepper (FRP) sauce has been eaten in worldwide for many years. The salt content and resident microbial community influences the quality of the FRP sauce and may confer health (e.g., probiotics) or harm (e.g., antibiotic resistance genes) to the consumers in some circumstances; however, the salt-mediated alteration of microbial community and antibiotic resistance genes are little known. In this study, a combination of whole genome sequencing and amplicon analysis was used to investigate the changes in microbial community and antimicrobial resistance genes in response to different salt content during red pepper fermentation. While the family Enterobacteriaceae dominated in high-salt (15-25%) samples, Lactobacillaceae quickly became the dominant population in place of Enterobacteriaceae after 24 days in 10% salt samples. Compared to 0.05 antibiotic resistance genes (ARGs) per cell number on average in 10% salt sample, 16.6 ARGs were present in high-salt samples, wherein the bacterial hosts were major assigned to Enterobacteriaceae including genera Enterobacter, Citrobacter, Escherichia, Salmonella and Klebsiella. Multidrug resistance genes were the predominant ARG type. Functional profiling showed that histidine kinase functions were of much higher abundance in high-salt samples and included several osmotic stress-related two-component systems that simultaneously encoded ARGs. These results give first metagenomic insights into the salt-mediated changes in microbial community composition and a broad view of associated antibiotic resistance genes in the process of food fermentation.}, } @article {pmid31496126, year = {2019}, author = {Yang, Q and Huang, X and Wang, P and Yan, Z and Sun, W and Zhao, S and Gun, S}, title = {Longitudinal development of the gut microbiota in healthy and diarrheic piglets induced by age-related dietary changes.}, journal = {MicrobiologyOpen}, volume = {8}, number = {12}, pages = {e923}, pmid = {31496126}, issn = {2045-8827}, mesh = {Age Factors ; *Animal Feed ; Animals ; Biodiversity ; Biomarkers ; Computational Biology/methods ; Diarrhea/*microbiology ; Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Male ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Swine ; Symbiosis ; Weaning ; }, abstract = {Diarrhea is one of the most common enteric diseases in young piglets. Diverse factors such as an unstable gut microenvironment, immature intestinal immune system, early supplementary feeding, and weaning often induce dysfunction of gut microbiota, thus leading to a continuing high incidence of diarrhea in piglets. However, few studies have characterized the gut microbiota of diarrheic piglets following changes in diet and during the development of intestinal physiology. In this study, we used 16S rRNA gene sequencing to analyze the dynamic establishment of fecal microbiota in six healthy piglets in response to age-related changes in the diet: sow-reared, early supplementary creep-feeding (sow-reared + starter diet), and weaning (solid nursery diet). We compared the gut microbiota of these six healthy piglets with those of diarrheic piglets during each of the three dietary stages (n = 10 sow-reared, n = 10 early supplementary creep-feeding, and n = 5 weaning). We found that weaning (solid nursery feeding) was the primary factor leading to dynamic colonization by microbiota in healthy piglets, and diarrhea primarily affected the microbial communities of piglets before weaning. Healthy piglets showed a continuous decrease in Lactobacillus and Escherichia, as well as a gradual increase in Prevotella with the transition to solid food. An altered relationship between Prevotella and Escherichia may be the main cause of diarrhea in preweaned piglets, whereas reduced numbers of Bacteroides, Ruminococcus, Bulleidia, and Treponema that are responsible for the digestion and utilization of solid feeds may be related to the onset of postweaning piglet diarrhea. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) functional analysis indicated that a reduction in genes involved in carbohydrate metabolism induced by intestinal dysbacteriosis in diarrheic piglets was one of the major causes of diarrhea at the three dietary stages. These findings provide insights into developing an intervention strategy for better management of diarrhea in piglets.}, } @article {pmid31494531, year = {2019}, author = {Jin, J and Gan, Y and Liu, H and Wang, Z and Yuan, J and Deng, T and Zhou, Y and Zhu, Y and Zhu, H and Yang, S and Shen, W and Xie, D and Wu, H and Liu, D and Li, W}, title = {Diminishing microbiome richness and distinction in the lower respiratory tract of lung cancer patients: A multiple comparative study design with independent validation.}, journal = {Lung cancer (Amsterdam, Netherlands)}, volume = {136}, number = {}, pages = {129-135}, doi = {10.1016/j.lungcan.2019.08.022}, pmid = {31494531}, issn = {1872-8332}, mesh = {Adult ; Aged ; Aged, 80 and over ; Area Under Curve ; *Biodiversity ; Biomarkers ; Female ; Gene Expression Profiling ; Humans ; Lung Neoplasms/*complications ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Neoplasm Staging ; Respiratory Tract Infections/diagnosis/*etiology ; }, abstract = {OBJECTIVES: Current evidence suggests that microorganisms are associated with neoplastic diseases; however, the role of the airway microbiome in lung cancer remains unknown. To investigate the taxonomic profiles of the lower respiratory tract (LRT) microbiome in patients with lung cancer.

MATERIALS AND METHODS: BALF samples were collected in a discovery set comprising 150 individuals, including 91 patients with lung cancer, 29 patients with nonmalignant pulmonary diseases and 30 healthy subjects, and an independent validation set including 85 participants. The samples were assessed by metagenomics analysis. Random forest regression analysis was performed to select a diagnostic panel.

RESULTS: In the discovery set, richness was reduced in lung cancer patients compared with that in healthy subjects, and the microbiome of patients with nonmalignant diseases resembled that of patients with lung cancer. Interestingly, Bradyrhizobium japonicum was only found in patients with lung cancer, whereas Acidovorax was found in patients with cancer and nonmalignant pulmonary diseases. A microbiota-related diagnostic model consisting of age, pack year of smoking and eleven types of bacteria was built, and the area under the curve (AUC) for discriminating the patients with cancer was 0.882 (95%CI: 0.807-0.957) in the training set and 0.796 (95%CI: 0.673-0.920) in the independent validation set.

CONCLUSION: Our study demonstrates that the LRT microbiome richness is diminished in lung cancer patients compared with that in healthy subjects and that microbiota-specific biomarkers may be useful for diagnosing patients for whom lung biopsy is not feasible.}, } @article {pmid31494301, year = {2019}, author = {Li, L and Wang, F and Liu, Y and Gu, F}, title = {Intestinal microbiota dysbiosis in children with recurrent respiratory tract infections.}, journal = {Microbial pathogenesis}, volume = {136}, number = {}, pages = {103709}, doi = {10.1016/j.micpath.2019.103709}, pmid = {31494301}, issn = {1096-1208}, mesh = {Bacteria/classification/isolation & purification ; Child ; Dysbiosis/*complications ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; ROC Curve ; Recurrence ; Respiratory Tract Infections/*complications ; }, abstract = {BACKGROUND: The impact of the gut microbiota on recurrent respiratory tract infection (RRTI) remains to be fully elucidated.

METHODS: To characterize the gut microbiota in patients with RRTI, fecal samples from 26 patients with RRTI and 23 healthy volunteers were profiled using the Illumina MiSeq platform. Beta diversity (Principal Component Analysis (PCA), Principal Co-ordinates Analysis (PCoA), Non-metric multidimensional scaling (NMDS)) analysis showed that the bacterial community structure segregated differently between the RRTI and control groups.

RESULTS: Results from alpha diversity analysis revealed lower microbiota diversity in samples from RRTI patients than in normal controls. Taxonomic analysis illustrated that the abundance of six phyla (Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, Tenericutes) and four genera (Enterococcus, Faecalibacterium, Bifidobacterium, Eubacterium were significantly different between these two groups. In addition, Enterococcus (P < 0.001) was more enriched in the RRTI group, whereas the abundances of Eubacterium (P < 0.001), Faecalibacterium (0.01 < P < 0.05) and Bifidobacterium (0.01 < P < 0.05) were reduced in the RRTI group compared to those in the normal control group. The performance of the model was assessed using ROC analysis, and Enterococcus, Eubacterium and Bifidobacterium achieved AUC values of 0.860, 0.820, and 0.689, respectively.

CONCLUSIONS: These results provide fundamental evidence in support of intestinal microbiota dysbiosis in children with RRTI.}, } @article {pmid31492882, year = {2019}, author = {Buettner, C and von Bergen, M and Jehmlich, N and Noll, M}, title = {Pseudomonas spp. are key players in agricultural biogas substrate degradation.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12871}, pmid = {31492882}, issn = {2045-2322}, mesh = {Agriculture/methods ; Anaerobiosis ; Biofuels/*microbiology ; Bioreactors/*microbiology ; Carbohydrate Metabolism ; Conservation of Natural Resources/methods ; *Environmental Microbiology ; Euryarchaeota/classification/genetics/*metabolism ; Hydrolysis ; Metagenome ; Methane/metabolism ; Microbial Interactions ; Microbiota ; Pseudomonas/classification/genetics/*metabolism ; }, abstract = {Anaerobic degradation (AD) of heterogeneous agricultural substrates is a complex process involving a diverse microbial community. While microbial community composition of a variety of biogas plants (BPs) is well described, little is known about metabolic processes and microbial interaction patterns. Here, we analyzed 16 large-scale BPs using metaproteomics. All metabolic steps of AD were observed in the metaproteome, and multivariate analyses indicated that they were shaped by temperature, pH, volatile fatty acid content and substrate types. Biogas plants could be subdivided into hydrogenotrophic, acetoclastic or a mixture of both methanogenic pathways based on their process parameters, taxonomic and functional metaproteome. Network analyses showed large differences in metabolic and microbial interaction patterns. Both, number of interactions and interaction partners were highly dependent on the prevalent methanogenic pathway for most species. Nevertheless, we observed a highly conserved metabolism of different abundant Pseudomonas spp. for all BPs indicating a key role during AD in carbohydrate hydrolysis irrespectively of variabilities in substrate input and process parameters. Thus, Pseudomonas spp. are of high importance for robust and versatile AD food webs, which highlight a large variety of downstream metabolic processes for their respective methanogenic pathways.}, } @article {pmid31492669, year = {2019}, author = {Zhou, K and Zhang, R and Sun, J and Zhang, W and Tian, RM and Chen, C and Kawagucci, S and Xu, Y}, title = {Potential Interactions between Clade SUP05 Sulfur-Oxidizing Bacteria and Phages in Hydrothermal Vent Sponges.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {22}, pages = {}, pmid = {31492669}, issn = {1098-5336}, mesh = {Animals ; Bacteriophages/*classification/metabolism ; Genome, Bacterial ; *Hydrothermal Vents ; Metabolic Networks and Pathways ; Metagenomics ; Microbiota ; Oxidation-Reduction ; Phylogeny ; Porifera/*microbiology/*virology ; RNA, Ribosomal, 16S/genetics ; Sulfur/metabolism ; Sulfur-Reducing Bacteria/*virology ; *Symbiosis ; }, abstract = {In deep-sea hydrothermal vent environments, sulfur-oxidizing bacteria belonging to the clade SUP05 are crucial symbionts of invertebrate animals. Marine viruses, as the most abundant biological entities in the ocean, play essential roles in regulating the sulfur metabolism of the SUP05 bacteria. To date, vent sponge-associated SUP05 and their phages have not been well documented. The current study analyzed microbiomes of Haplosclerida sponges from hydrothermal vents in the Okinawa Trough and recovered the dominant SUP05 genome, designated VS-SUP05. Phylogenetic analysis showed that VS-SUP05 was closely related to endosymbiotic SUP05 strains from mussels living in deep-sea hydrothermal vent fields. Homology and metabolic pathway comparisons against free-living and symbiotic SUP05 strains revealed that the VS-SUP05 genome shared many features with the deep-sea mussel symbionts. Supporting a potentially symbiotic lifestyle, the VS-SUP05 genome contained genes involved in the synthesis of essential amino acids and cofactors that are desired by the host. Analysis of sponge-associated viral sequences revealed putative VS-SUP05 phages, all of which were double-stranded viruses belonging to the families Myoviridae, Siphoviridae, Podoviridae, and Microviridae Among the phage sequences, one contig contained metabolic genes (iscR, iscS, and iscU) involved in iron-sulfur cluster formation. Interestingly, genome sequence comparison revealed horizontal transfer of the iscS gene among phages, VS-SUP05, and other symbiotic SUP05 strains, indicating an interaction between marine phages and SUP05 symbionts. Overall, our findings confirm the presence of SUP05 bacteria and their phages in sponges from deep-sea vents and imply a beneficial interaction that allows adaptation of the host sponge to the hydrothermal vent environment.IMPORTANCE Chemosynthetic SUP05 bacteria dominate the microbial communities of deep-sea hydrothermal vents around the world, SUP05 bacteria utilize reduced chemical compounds in vent fluids and commonly form symbioses with invertebrate organisms. This symbiotic relationship could be key to adapting to such unique and extreme environments. Viruses are the most abundant biological entities on the planet and have been identified in hydrothermal vent environments. However, their interactions with the symbiotic microbes of the SUP05 clade, along with their role in the symbiotic system, remain unclear. Here, using metagenomic sequence-based analyses, we determined that bacteriophages may support metabolism in SUP05 bacteria and play a role in the sponge-associated symbiosis system in hydrothermal vent environments.}, } @article {pmid31492655, year = {2019}, author = {Soto-Perez, P and Bisanz, JE and Berry, JD and Lam, KN and Bondy-Denomy, J and Turnbaugh, PJ}, title = {CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog.}, journal = {Cell host & microbe}, volume = {26}, number = {3}, pages = {325-335.e5}, pmid = {31492655}, issn = {1934-6069}, support = {DP5 OD021344/OD/NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; }, mesh = {Actinobacteria/virology ; Bacteria/genetics/*virology ; Bacteriophages/*genetics ; Base Sequence ; *CRISPR-Cas Systems ; DNA, Bacterial/analysis ; DNA, Viral/analysis ; Databases, Genetic ; Gastrointestinal Tract/*microbiology ; Genome, Bacterial ; Genome, Viral ; Humans ; Metagenomics ; Microbiota/genetics ; Sequence Analysis, DNA ; }, abstract = {Bacteriophages are abundant within the human gastrointestinal tract, yet their interactions with gut bacteria remain poorly understood, particularly with respect to CRISPR-Cas immunity. Here, we show that the type I-C CRISPR-Cas system in the prevalent gut Actinobacterium Eggerthella lenta is transcribed and sufficient for specific targeting of foreign and chromosomal DNA. Comparative analyses of E. lenta CRISPR-Cas systems across (meta)genomes revealed 2 distinct clades according to cas sequence similarity and spacer content. We assembled a human virome database (HuVirDB), encompassing 1,831 samples enriched for viral DNA, to identify protospacers. This revealed matches for a majority of spacers, a marked increase over other databases, and uncovered "hyper-targeted" phage sequences containing multiple protospacers targeted by several E. lenta strains. Finally, we determined the positional mismatch tolerance of observed spacer-protospacer pairs. This work emphasizes the utility of merging computational and experimental approaches for determining the function and targets of CRISPR-Cas systems.}, } @article {pmid31492563, year = {2019}, author = {Zhong, H and Ren, H and Lu, Y and Fang, C and Hou, G and Yang, Z and Chen, B and Yang, F and Zhao, Y and Shi, Z and Zhou, B and Wu, J and Zou, H and Zi, J and Chen, J and Bao, X and Hu, Y and Gao, Y and Zhang, J and Xu, X and Hou, Y and Yang, H and Wang, J and Liu, S and Jia, H and Madsen, L and Brix, S and Kristiansen, K and Liu, F and Li, J}, title = {Distinct gut metagenomics and metaproteomics signatures in prediabetics and treatment-naïve type 2 diabetics.}, journal = {EBioMedicine}, volume = {47}, number = {}, pages = {373-383}, pmid = {31492563}, issn = {2352-3964}, mesh = {Chromatography, Liquid ; Diabetes Mellitus, Type 2/*etiology/*metabolism/therapy ; Feces/virology ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; *Proteomics/methods ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: The gut microbiota plays important roles in modulating host metabolism. Previous studies have demonstrated differences in the gut microbiome of T2D and prediabetic individuals compared to healthy individuals, with distinct disease-related microbial profiles being reported in groups of different age and ethnicity. However, confounding factors such as anti-diabetic medication hamper identification of the gut microbial changes in disease development.

METHOD: We used a combination of in-depth metagenomics and metaproteomics analyses of faecal samples from treatment-naïve type 2 diabetic (TN-T2D, n = 77), pre-diabetic (Pre-DM, n = 80), and normal glucose tolerant (NGT, n = 97) individuals to investigate compositional and functional changes of the gut microbiota and the faecal content of microbial and host proteins in Pre-DM and treatment-naïve T2D individuals to elucidate possible host-microbial interplays characterizing different disease stages.

FINDINGS: We observed distinct differences characterizing the gut microbiota of these three groups and validated several key features in an independent TN-T2D cohort. We also demonstrated that the content of several human antimicrobial peptides and pancreatic enzymes differed in faecal samples between three groups.

INTERPRETATION: Our findings suggest a complex, disease stage-dependent interplay between the gut microbiota and the host and point to the value of metaproteomics to gain further insight into interplays between the gut microbiota and the host. FUND: The study was supported by the National Natural Science Foundation of China (No. 31601073), the National Key Research and Development Program of China (No. 2017YFC0909703) and the Shenzhen Municipal Government of China (No. JCYJ20170817145809215). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.}, } @article {pmid31490939, year = {2019}, author = {Danczak, RE and Johnston, MD and Kenah, C and Slattery, M and Wilkins, MJ}, title = {Capability for arsenic mobilization in groundwater is distributed across broad phylogenetic lineages.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0221694}, pmid = {31490939}, issn = {1932-6203}, mesh = {Arsenic/*metabolism ; Bacteria/classification/genetics/metabolism ; Groundwater/*microbiology ; Iron/metabolism ; Metagenomics ; Microbiota ; *Phylogeny ; Sulfates/metabolism ; }, abstract = {Despite the importance of microbial activity in mobilizing arsenic in groundwater aquifers, the phylogenetic distribution of contributing microbial metabolisms is understudied. Groundwater samples from Ohio aquifers were analyzed using metagenomic sequencing to identify functional potential that could drive arsenic cycling, and revealed mechanisms for direct (i.e., Ars system) and indirect (i.e., iron reduction) arsenic mobilization in all samples, despite differing geochemical conditions. Analyses of 194 metagenome-assembled genomes (MAGs) revealed widespread functionality related to arsenic mobilization throughout the bacterial tree of life. While arsB and arsC genes (components of an arsenic resistance system) were found in diverse lineages with no apparent phylogenetic bias, putative aioA genes (aerobic arsenite oxidase) were predominantly identified in Methylocystaceae MAGs. Both previously described and undescribed respiratory arsenate reduction potential via arrA was detected in Betaproteobacteria, Deltaproteobacteria, and Nitrospirae MAGs, whereas sulfate reduction potential was primarily limited to members of the Deltaproteobacteria and Nitrospirae. Lastly, iron reduction potential was detected in the Ignavibacteria, Deltaproteobacteria, and Nitrospirae. These results expand the phylogenetic distribution of taxa that may play roles in arsenic mobilization in subsurface systems. Specifically, the Nitrospirae are a much more functionally diverse group than previously assumed and may play key biogeochemical roles in arsenic-contaminated ecosystems.}, } @article {pmid31489370, year = {2019}, author = {Sakanaka, M and Hansen, ME and Gotoh, A and Katoh, T and Yoshida, K and Odamaki, T and Yachi, H and Sugiyama, Y and Kurihara, S and Hirose, J and Urashima, T and Xiao, JZ and Kitaoka, M and Fukiya, S and Yokota, A and Lo Leggio, L and Abou Hachem, M and Katayama, T}, title = {Evolutionary adaptation in fucosyllactose uptake systems supports bifidobacteria-infant symbiosis.}, journal = {Science advances}, volume = {5}, number = {8}, pages = {eaaw7696}, pmid = {31489370}, issn = {2375-2548}, mesh = {Adult ; Aged ; Bifidobacterium/metabolism/*physiology ; Biological Evolution ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenome/physiology ; Middle Aged ; Milk, Human/metabolism ; Oligosaccharides/*metabolism ; Symbiosis/*physiology ; Trisaccharides/*metabolism ; Young Adult ; }, abstract = {The human gut microbiota established during infancy has persistent effects on health. In vitro studies have suggested that human milk oligosaccharides (HMOs) in breast milk promote the formation of a bifidobacteria-rich microbiota in infant guts; however, the underlying molecular mechanism remains elusive. Here, we characterized two functionally distinct but overlapping fucosyllactose transporters (FL transporter-1 and -2) from Bifidobacterium longum subspecies infantis. Fecal DNA and HMO consumption analyses, combined with deposited metagenome data mining, revealed that FL transporter-2 is primarily associated with the bifidobacteria-rich microbiota formation in breast-fed infant guts. Structural analyses of the solute-binding protein (SBP) of FL transporter-2 complexed with 2'-fucosyllactose and 3-fucosyllactose, together with phylogenetic analysis of SBP homologs of both FL transporters, highlight a unique adaptation strategy of Bifidobacterium to HMOs, in which the gain-of-function mutations enable FL transporter-2 to efficiently capture major fucosylated HMOs. Our results provide a molecular insight into HMO-mediated symbiosis and coevolution between bifidobacteria and humans.}, } @article {pmid31488869, year = {2019}, author = {Amrane, S and Hocquart, M and Afouda, P and Kuete, E and Pham, TP and Dione, N and Ngom, II and Valles, C and Bachar, D and Raoult, D and Lagier, JC}, title = {Metagenomic and culturomic analysis of gut microbiota dysbiosis during Clostridium difficile infection.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12807}, pmid = {31488869}, issn = {2045-2322}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/growth & development/*isolation & purification/metabolism ; Bacteroides/isolation & purification ; Bifidobacterium/isolation & purification ; Biological Therapy ; Clostridium Infections/*microbiology/therapy ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Middle Aged ; Molecular Typing ; }, abstract = {Recently, cocktail of bacteria were proposed in order to treat Clostridium difficile infection (CDI), but these bacteriotherapies were selected more by chance than experimentation. We propose to comprehensively explore the gut microbiota of patients with CDI compared to healthy donors in order to propose a consortium of bacteria for treating C. difficile. We compared stool samples composition from 11 CDI patients and 8 healthy donors using two techniques: metagenomics, 16S V3-V4 region amplification and sequencing and culturomics, high throughout culture using six culture conditions and MALDI-TOF identification. By culturomics, we detected 170 different species in the CDI group and 275 in the control group. Bacteroidetes were significantly underrepresented in the CDI group (p = 0.007). By metagenomics, 452 different operational taxonomic units assigned to the species level were detected in the CDI group compared to 522 in the control group. By these two techniques, we selected 37 bacteria only found in control group in more than 75% of the samples and/or with high relative abundance, 10 of which have already been tested in published bacteriotherapies against CDI, and 3 of which (Bifidobacterium adolescentis, Bifidobacterium longum and Bacteroides ovatus) have been detected by these two techniques. This controlled number of bacteria could be administrated orally in a non-invasive way in order to treat CDI.}, } @article {pmid31488812, year = {2019}, author = {Mora, M and Wink, L and Kögler, I and Mahnert, A and Rettberg, P and Schwendner, P and Demets, R and Cockell, C and Alekhova, T and Klingl, A and Krause, R and Zolotariof, A and Alexandrova, A and Moissl-Eichinger, C}, title = {Space Station conditions are selective but do not alter microbial characteristics relevant to human health.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {3990}, pmid = {31488812}, issn = {2041-1723}, mesh = {Archaea/*classification/genetics/isolation & purification ; Bacteria/*classification/genetics/isolation & purification ; Biodiversity ; Biofilms/growth & development ; Extremophiles ; Fungi/*classification/genetics/isolation & purification ; *Health ; Host Microbial Interactions ; Humans ; Metagenomics ; Microbiota/genetics/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Space Flight ; }, abstract = {The International Space Station (ISS) is a unique habitat for humans and microorganisms. Here, we report the results of the ISS experiment EXTREMOPHILES, including the analysis of microbial communities from several areas aboard at three time points. We assess microbial diversity, distribution, functional capacity and resistance profile using a combination of cultivation-independent analyses (amplicon and shot-gun sequencing) and cultivation-dependent analyses (physiological and genetic characterization of microbial isolates, antibiotic resistance tests, co-incubation experiments). We show that the ISS microbial communities are highly similar to those present in ground-based confined indoor environments and are subject to fluctuations, although a core microbiome persists over time and locations. The genomic and physiological features selected by ISS conditions do not appear to be directly relevant to human health, although adaptations towards biofilm formation and surface interactions were observed. Our results do not raise direct reason for concern with respect to crew health, but indicate a potential threat towards material integrity in moist areas.}, } @article {pmid31487569, year = {2019}, author = {Wei, ZS and He, YM and Huang, ZS and Xiao, XL and Li, BL and Ming, S and Cheng, XL}, title = {Photocatalytic membrane combined with biodegradation for toluene oxidation.}, journal = {Ecotoxicology and environmental safety}, volume = {184}, number = {}, pages = {109618}, doi = {10.1016/j.ecoenv.2019.109618}, pmid = {31487569}, issn = {1090-2414}, mesh = {Bacteria/classification/genetics/metabolism ; Biodegradation, Environmental ; Biofilms ; Bioreactors/*microbiology ; Membranes ; Microbial Consortia/*physiology ; Oxidation-Reduction ; Photochemical Processes ; Toluene/isolation & purification/*metabolism ; Volatile Organic Compounds/isolation & purification/metabolism ; }, abstract = {Photocatalytic membrane coupled to biodegradation offers potential for degrading volatile organic compounds (VOCs) in photocatalytic membrane biofilm reactor. An intimately coupled photocatalysis and biodegradation reactor was operated in continuous operation for 500 days to treat simulated waste gas containing toluene. Toluene removal efficiency obtained 99%, with the elimination capacity of 550 g m[-3]·h[-1]. Membrane photocatalysis coupled to biodegradation was created to improve toluene removal from 11 to 20%. The dominant genera were Lysinibacillus, Hydrogenophaga, Pseudomonas at 30 d, Rudaea, Dongia, Litorilinea at 230 d xyl, Tod, Tcb, Bed, Tmo, Tbu, Tou, Dmp, Cat were functional genes of toluene metabolism, as shown by16S rDNA and metagenomic sequencing. Photocatalysis destroyed part of the toluene into biodegradable intermediates that were immediately mineralized by microorganisms in biofilm, some toluene was directly degraded by toluene degrading bacterial community into carbon dioxide and water. The novel hybrid photocatalytic membrane biofilm reactor is a cost-effective and robust alternative to VOCs treatment.}, } @article {pmid31485795, year = {2020}, author = {T A, PD and Sahoo, D and Setti, A and Sharma, C and Kalita, MC and S, ID}, title = {Bacterial rhizosphere community profile at different growth stages of Umorok (Capsicum chinense) and its response to the root exudates.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {23}, number = {2}, pages = {241-251}, doi = {10.1007/s10123-019-00097-x}, pmid = {31485795}, issn = {1618-1905}, mesh = {Bacteria/genetics ; Capsicum/growth & development/*microbiology ; Chemotaxis ; DNA, Bacterial ; Metagenomics ; Microbial Consortia/genetics ; Microbial Interactions ; *Microbiota ; Plant Roots/*microbiology ; *Rhizosphere ; Soil Microbiology ; }, abstract = {The role of microflora is an indispensable part of the living organisms. Plants actively recruit specific microbial community to establish favorable habitat with the distinct microbiome, essentially unique for each species, offering new opportunities for plant growth and productivity. Umorok, an indigenous chili variety of northeastern India, production is highly affected by various factors; therefore, rhizosphere bacteria and their relationship with the root exudates released were analyzed to demonstrate rhizosphere bacterial impact on plant growth and health. Culturable and metagenomic bacterial DNA was characterized and the chemical nature of the root exudate was analyzed using chemotaxis assay after its basic analysis in HPLC. Juvenile stage exhibited diverse bacterial species of gammaproteobacteria, alphaproteobacteria, and actinobacteria but lacked the betaproteobacteria while the microbial diversity was reduced in flowering and fruiting stages. However, every growth stage maintained a similar amount of bacterial population regardless of diversity. The population of Pseudomonas, Bacillus, and Burkholderia species was increased several folds in flowering and fruiting stage. Further, the chemotaxis assay unveiled the advantage of root exudate chemical composition for specific microbial recruitment. The chemical composition analysis of root exudates showed substantial variation in the concentration of organic acids, phenolics, and flavonoids that are favoring unique bacterial species. Thus, root exudates confer and limit the related microbial population besides typical plant-bacterial synergetic association. This study emphasized information about the type of microbial load present in each growth stage, which is essential to develop a microbial consortia package for Umorok overall crop improvement.}, } @article {pmid31484222, year = {2019}, author = {Ewart, KM and Johnson, RN and Ogden, R and Joseph, L and Frankham, GJ and Lo, N}, title = {Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species.}, journal = {Molecular ecology resources}, volume = {19}, number = {6}, pages = {1578-1592}, doi = {10.1111/1755-0998.13082}, pmid = {31484222}, issn = {1755-0998}, support = {//Australian Government Research Training Program Scholarship/ ; //Birdlife Australia, Stuart Leslie Bird Research Award/ ; //Australian Museum Foundation/ ; //University of Sydney Merit Award/ ; //University of Sydney Industry and Community Engagement Seed Fund/ ; 16//Australian Museum/ ; 02//Australian Museum/ ; }, mesh = {Animals ; Cockatoos/*genetics ; DNA/genetics ; DNA Fragmentation ; Endangered Species ; Genetic Variation/genetics ; Genome/*genetics ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Museums ; Polymorphism, Single Nucleotide/*genetics ; Sequence Analysis, DNA/methods ; Specimen Handling/methods ; }, abstract = {Natural history museums harbour a plethora of biological specimens which are of potential use in population and conservation genetic studies. Although technical advancements in museum genomics have enabled genome-wide markers to be generated from aged museum specimens, the suitability of these data for robust biological inference is not well characterized. The aim of this study was to test the utility of museum specimens in population and conservation genomics by assessing the biological and technical validity of single nucleotide polymorphism (SNP) data derived from such samples. To achieve this, we generated thousands of SNPs from 47 red-tailed black cockatoo (Calyptorhychus banksii) traditional museum samples (i.e. samples that were not collected with the primary intent of DNA analysis) and 113 fresh tissue samples (cryopreserved liver/muscle) using a restriction site-associated DNA marker approach (DArTseq[™]). Thousands of SNPs were successfully generated from most of the traditional museum samples (with a mean age of 44 years, ranging from 5 to 123 years), although 38% did not provide useful data. These SNPs exhibited higher error rates and contained significantly more missing data compared with SNPs from fresh tissue samples, likely due to considerable DNA fragmentation. However, based on simulation results, the level of genotyping error had a negligible effect on inference of population structure in this species. We did identify a bias towards low diversity SNPs in older samples that appears to compromise temporal inferences of genetic diversity. This study demonstrates the utility of a RADseq-based method to produce reliable genome-wide SNP data from traditional museum specimens.}, } @article {pmid31484218, year = {2019}, author = {Goodman, KR and Prost, S and Bi, K and Brewer, MS and Gillespie, RG}, title = {Host and geography together drive early adaptive radiation of Hawaiian planthoppers.}, journal = {Molecular ecology}, volume = {28}, number = {19}, pages = {4513-4528}, pmid = {31484218}, issn = {1365-294X}, support = {S10 OD018174/OD/NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Animals ; *Computational Biology ; Ecology ; Exons/genetics ; Genetics, Population ; Geography ; Hawaii ; Hemiptera/genetics/*physiology ; Host Specificity ; Islands ; Male ; *Metagenomics ; Phylogeny ; Plants/*parasitology ; Species Specificity ; *Transcriptome ; }, abstract = {The interactions between insects and their plant host have been implicated in driving diversification of both players. Early arguments highlighted the role of ecological opportunity, with the idea that insects "escape and radiate" on new hosts, with subsequent hypotheses focusing on the interplay between host shifting and host tracking, coupled with isolation and fusion, in generating diversity. Because it is rarely possible to capture the initial stages of diversification, it is particularly difficult to ascertain the relative roles of geographic isolation versus host shifts in initiating the process. The current study examines genetic diversity between populations and hosts within a single species of endemic Hawaiian planthopper, Nesosydne umbratica (Hemiptera, Delphacidae). Given that the species was known as a host generalist occupying unrelated hosts, Clermontia (Campanulaceae) and Pipturus (Urticaceae), we set out to determine the relative importance of geography and host in structuring populations in the early stages of differentiation on the youngest islands of the Hawaiian chain. Results from extensive exon capture data showed that N. umbratica is highly structured, both by geography, with discrete populations on each volcano, and by host plant, with parallel radiations on Clermontia and Pipturus leading to extensive co-occurrence. The marked genetic structure suggests that populations can readily become established on novel hosts provided opportunity; subsequent adaptation allows monopolization of the new host. The results support the role of geographic isolation in structuring populations and with host shifts occurring as discrete events that facilitate subsequent parallel geographic range expansion.}, } @article {pmid31482697, year = {2019}, author = {Wang, X and Liu, X and Lu, S and Liu, C and Gu, Z and Zeng, X and Ni, Q}, title = {Culture of attached and suspended Rhodopseudomonas faecalis in the presence of decomposing fish feed.}, journal = {MicrobiologyOpen}, volume = {8}, number = {12}, pages = {e924}, pmid = {31482697}, issn = {2045-8827}, mesh = {Animal Feed/*microbiology ; Animals ; Biomass ; *Fermentation ; *Fishes ; Metagenome ; Metagenomics/methods ; Microbiota ; Photosynthesis ; Rhodopseudomonas/growth & development/*metabolism ; Water Microbiology ; }, abstract = {An approach to culturing attached and suspended forms of Rhodopseudomonas faecalis by using compound fish feed with tap water in transparent containers is reported in this study. The ratio of fish feed to tap water was 14.3-50.8 g/L, and no other inoculum or substances were added during the culture process. When the ratio of fish feed to tap water was 14.3 g/L, the highest total nitrogen, total phosphorus, and total dissolved carbon content recorded in the water in the containers were approximately 730 mg/L, 356 mg/L, and 1,620 mg/L, respectively, during the process of feed decay. Comamonas, Rhodopseudomonas, and Clostridium successively dominated during the culture process. Rhodopseudomonas was the most common dominant genus in both the attached and suspended forms when the water was dark red, and the relative operational taxonomic unit abundance reached 80-89% and 24.8%, respectively. The dominant species was R. faecalis. The maximum thickness of attached bacteria and the biomass of attached Rhodopseudomonas reached up to 0.56 mm and 7.5 mg/cm[2] , respectively. This study provides a method for the mass culture of Rhodopseudomonas by using the fermentation of aquatic compound fish feed.}, } @article {pmid31482204, year = {2019}, author = {Chatterjee, A and Kondabagil, K}, title = {Giant viral genomic signatures in the previously reported gut metagenomes of pre-school children in rural India.}, journal = {Archives of virology}, volume = {164}, number = {11}, pages = {2819-2822}, doi = {10.1007/s00705-019-04387-7}, pmid = {31482204}, issn = {1432-8798}, mesh = {Bacteriophages/*genetics ; Child, Preschool ; Drug Resistance, Microbial/genetics ; Enterobacter/genetics ; Escherichia/virology ; Gastrointestinal Microbiome/*genetics ; Genome, Viral/*genetics ; Giant Viruses/*genetics/isolation & purification ; Humans ; India ; Interspersed Repetitive Sequences/genetics ; Metagenome/*genetics ; Salmonella/virology ; Shigella/virology ; }, abstract = {A recent study by Ghosh et al. compared the gut microbiomes of 20 preschool children from India and found an association between the gut microbiome and the nutritional status of the child. Here, we explored these metagenomes for the presence of genomic signatures of prokaryotic and eukaryotic viruses. Several of the viral signatures found in all 20 metagenomes belonged to giant viruses (GVs). In addition, we found hits for bacteriophages to several major human pathogens, including Shigella, Salmonella, Escherichia, and Enterobacter. Concurrently, we also detected several antibiotic resistance genes (ARGs) in the metagenomes. All of the ARGs detected in this study (beta-lactam, macrolide, metronidazole, and tetracycline) are associated with mobile genetic elements (MGEs) and have been reported to cause high levels of resistance to their respective antibiotics. Despite recent reports of giant viruses and their genomic signatures in gut microbiota, their role in human physiology remains poorly understood. The effect of cooccurrence of ARGs and GVs in the gut needs further investigation.}, } @article {pmid31481728, year = {2019}, author = {Skaltsas, DN and Badotti, F and Vaz, ABM and Silva, FFD and Gazis, R and Wurdack, K and Castlebury, L and Góes-Neto, A and Chaverri, P}, title = {Exploration of stem endophytic communities revealed developmental stage as one of the drivers of fungal endophytic community assemblages in two Amazonian hardwood genera.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12685}, pmid = {31481728}, issn = {2045-2322}, mesh = {Biodiversity ; Brazil ; Comparative Genomic Hybridization ; DNA, Fungal/chemistry/metabolism ; Fungi/genetics/*isolation & purification ; Hevea/growth & development/*microbiology ; *Mycobiome ; Seedlings/microbiology ; Sequence Analysis, DNA ; }, abstract = {Many aspects of the dynamics of tropical fungal endophyte communities are poorly known, including the influence of host taxonomy, host life stage, host defence, and host geographical distance on community assembly and composition. Recent fungal endophyte research has focused on Hevea brasiliensis due to its global importance as the main source of natural rubber. However, almost no data exist on the fungal community harboured within other Hevea species or its sister genus Micrandra. In this study, we expanded sampling to include four additional Hevea spp. and two Micrandra spp., as well as two host developmental stages. Through culture-dependent and -independent (metagenomic) approaches, a total of 381 seedlings and 144 adults distributed across three remote areas within the Peruvian Amazon were sampled. Results from both sampling methodologies indicate that host developmental stage had a greater influence in community assemblage than host taxonomy or locality. Based on FunGuild ecological guild assignments, saprotrophic and mycotrophic endophytes were more frequent in adults, while plant pathogens were dominant in seedlings. Trichoderma was the most abundant genus recovered from adult trees while Diaporthe prevailed in seedlings. Potential explanations for that disparity of abundance are discussed in relation to plant physiological traits and community ecology hypotheses.}, } @article {pmid31480274, year = {2019}, author = {A Duarte, M and F Silva, JM and R Brito, C and S Teixeira, D and L Melo, F and M Ribeiro, B and Nagata, T and S Campos, F}, title = {Faecal Virome Analysis of Wild Animals from Brazil.}, journal = {Viruses}, volume = {11}, number = {9}, pages = {}, pmid = {31480274}, issn = {1999-4915}, mesh = {Animals ; Animals, Wild/*virology ; Birds/virology ; Brazil/epidemiology ; Epidemiological Monitoring ; Feces/*virology ; Genome, Viral/genetics ; Mammals/virology ; Microbiota/*genetics ; Phylogeny ; Viruses/classification/genetics/isolation & purification ; }, abstract = {The Brazilian Cerrado fauna shows very wide diversity and can be a potential viral reservoir. Therefore, the animal's susceptibility to some virus can serve as early warning signs of potential human virus diseases. Moreover, the wild animal virome of this biome is unknown. Based on this scenario, high-throughput sequencing contributes a robust tool for the identification of known and unknown virus species in this environment. In the present study, faeces samples from cerrado birds (Psittacara leucophthalmus, Amazona aestiva, and Sicalis flaveola) and mammals (Didelphis albiventris, Sapajus libidinosus, and Galictis cuja) were collected at the Veterinary Hospital, University of Brasília. Viral nucleic acid was extracted, submitted to random amplification, and sequenced by Illumina HiSeq platform. The reads were de novo assembled, and the identities of the contigs were evaluated by Blastn and tblastx searches. Most viral contigs analyzed were closely related to bacteriophages. Novel archaeal viruses of the Smacoviridae family were detected. Moreover, sequences of members of Adenoviridae, Anelloviridae, Circoviridae, Caliciviridae, and Parvoviridae families were identified. Complete and nearly complete genomes of known anelloviruses, circoviruses, and parvoviruses were obtained, as well as putative novel species. We demonstrate that the metagenomics approach applied in this work was effective for identification of known and putative new viruses in faeces samples from Brazilian Cerrado fauna.}, } @article {pmid31479939, year = {2019}, author = {Li, J and Wang, T and Yu, S and Bai, J and Qin, S}, title = {Community characteristics and ecological roles of bacterial biofilms associated with various algal settlements on coastal reefs.}, journal = {Journal of environmental management}, volume = {250}, number = {}, pages = {109459}, doi = {10.1016/j.jenvman.2019.109459}, pmid = {31479939}, issn = {1095-8630}, mesh = {Animals ; *Anthozoa ; Biofilms ; Coral Reefs ; Ecology ; *Microbiota ; }, abstract = {Bacterial biofilms, which are a group of bacteria attaching to and ultimately forming communities on reefs, perform essential ecological functions in coastal ecosystems. Particularly, they may attract or repulse the settling down of opportunistic algae. However, this phenomenon and the interaction mechanism are not fully understood. This study investigated reefs from the Changdao coastal zone to determine the structures and functions of bacterial biofilms symbiosing with various algae using high-throughput sequencing analysis. The Shannon diversity index of microbiota with algal symbiosis reached 5.34, which was higher than that of microbiota wherein algae were absent (4.80). The beta diversity results for 11 samples revealed that there existed a separation between bacterial communities on reefs with and without attached algae, while communities with similar algae clustered together. The taxa mostly associated with algae-symbiotic microbiota are the Actinobacteria phylum, and the Flavobacteriia and Gammaproteobacteria classes. The Cyanobacteria phylum was not associated with algae-symbiotic microbiota. As revealed by functional analysis, the bacteria mostly involved in the metabolism of sulfur were represented by brown and red algae in the biofilm symbiosis. Bacteria related to the metabolism of certain trace elements were observed only in specific groups. Moreover, phototrophy-related bacteria were less abundant in samples coexisting with algae. This study established the link between bacterial biofilms and algal settlements on costal reefs, and revealed the possible holobiont relationship between them. This may provide new technical directions toward realizing algal cultivation and management during the construction of artificial reef ecosystems.}, } @article {pmid31475121, year = {2019}, author = {Obregón, D and Bard, E and Abrial, D and Estrada-Peña, A and Cabezas-Cruz, A}, title = {Sex-Specific Linkages Between Taxonomic and Functional Profiles of Tick Gut Microbiomes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {298}, pmid = {31475121}, issn = {2235-2988}, mesh = {Amino Acids/metabolism ; Animals ; Bacteria/classification/genetics ; Carbohydrate Metabolism/genetics ; Enzymes/genetics/metabolism ; Female ; *Gastrointestinal Microbiome/genetics ; Host Microbial Interactions/*genetics/*physiology ; Ixodes/microbiology ; Male ; Metabolic Networks and Pathways/genetics ; Metagenomics/methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sex Factors ; Ticks/*genetics/*metabolism/*microbiology ; }, abstract = {Ticks transmit the most diverse array of disease agents and harbor one of the most diverse microbial communities. Major progress has been made in the characterization of the taxonomic profiles of tick microbiota. However, the functional profiles of tick microbiome have been comparatively less studied. In this proof of concept we used state-of-the-art functional metagenomics analytical tools to explore previously reported datasets of bacteria found in male and female Ixodes ovatus, Ixodes persulcatus, and Amblyomma variegatum. Results showed that both taxonomic and functional profiles have differences between sexes of the same species. KEGG pathway analysis revealed that male and female of the same species had major differences in the abundance of genes involved in different metabolic pathways including vitamin B, amino acids, carbohydrates, nucleotides, and antibiotics among others. Partial reconstruction of metabolic pathways using KEGG enzymes suggests that tick microbiome form a complex metabolic network that may increase microbial community resilience and adaptability. Linkage analysis between taxonomic and functional profiles showed that among the KEGG enzymes with differential abundance in male and female ticks only 12% were present in single bacterial genera. The rest of these enzymes were found in more than two bacterial genera, and 27% of them were found in five up to ten bacterial genera. Comparison of bacterial genera contributing to the differences in the taxonomic and functional profiles of males and females revealed that while a small group of bacteria has a dual-role, most of the bacteria contribute only to functional or taxonomic differentiation between sexes. Results suggest that the different life styles of male and female ticks exert sex-specific evolutionary pressures that act independently on the phenomes (set of phenotypes) and genomes of bacteria in tick gut microbiota. We conclude that functional redundancy is a fundamental property of male and female tick microbiota and propose that functional metagenomics should be combined with taxonomic profiling of microbiota because both analyses are complementary.}, } @article {pmid31473511, year = {2019}, author = {Sreng, N and Champion, S and Martin, JC and Khelaifia, S and Christensen, JE and Padmanabhan, R and Azalbert, V and Blasco-Baque, V and Loubieres, P and Pechere, L and Landrier, JF and Burcelin, R and Sérée, E}, title = {Resveratrol-mediated glycemic regulation is blunted by curcumin and is associated to modulation of gut microbiota.}, journal = {The Journal of nutritional biochemistry}, volume = {72}, number = {}, pages = {108218}, doi = {10.1016/j.jnutbio.2019.108218}, pmid = {31473511}, issn = {1873-4847}, mesh = {Amino Acids, Branched-Chain/metabolism ; Animals ; Blood/drug effects/*metabolism ; Curcumin/*pharmacology ; Diet, High-Fat/adverse effects ; Drug Therapy, Combination ; Gastrointestinal Microbiome/*drug effects/physiology ; Hyperglycemia/*diet therapy/etiology/microbiology ; Male ; Mice, Inbred C57BL ; Prediabetic State/diet therapy/metabolism ; Resveratrol/*pharmacology ; }, abstract = {The polyphenols resveratrol (RSV) and curcumin (Cur) are phytoalexines and natural antibiotics with numerous pharmacological functions and metabolic impacts. Recent evidences show a broad control of gut microbiota by polyphenols which could influence glycemic regulation. The aim of this work is to estimate the respective effect of RSV and Cur alone or in association on the control of glycemia and on gut microbiota. A 5-week chronic treatment of hyperglycemic mice with RSV and/or Cur resulted in a differential effect on glucose tolerance test and modified gut microbiome. We precisely identified groups of bacteria representing a specific signature of the glycemic effect of RSV. Inferred metagenomic analysis and metabolic pathway prediction showed that the sulfur and branched-chain amino-acid (BCAA) metabolic activities are tightly correlated with the efficacy of RSV for the control of glycaemia. The impact on BCAA metabolism was further validated by serum metabolomics analysis. Altogether, we show that polyphenols specifically impact gut microbiota and corresponding metabolic functions which could be responsible for their therapeutic role.}, } @article {pmid31473248, year = {2019}, author = {Selvin, J and Lanong, S and Syiem, D and De Mandal, S and Kayang, H and Kumar, NS and Kiran, GS}, title = {Culture-dependent and metagenomic analysis of lesser horseshoe bats' gut microbiome revealing unique bacterial diversity and signatures of potential human pathogens.}, journal = {Microbial pathogenesis}, volume = {137}, number = {}, pages = {103675}, pmid = {31473248}, issn = {1096-1208}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/*classification/drug effects/genetics/*isolation & purification ; *Biodiversity ; Chiroptera/*microbiology ; Chromosome Mapping ; DNA, Bacterial/isolation & purification ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Genetic Variation ; High-Throughput Screening Assays ; Humans ; India ; *Metagenome ; Microbial Sensitivity Tests ; Mycobiome ; RNA, Ribosomal, 16S/genetics ; Zoonoses/microbiology ; }, abstract = {Bats are highly diverse and ecologically important mammals. They harbor various bacteria, viruses, and fungal communities that are either beneficial or potentially pathogenic. Extensive metagenomic studies in bats are limited, particularly for the gut, and to date, there are no reports on the bacterial diversity of Rhinolophus monoceros from Meghalaya, India. There are limited studies on the isolation of potential harmful or beneficial bacteria and their interactions with the environment through culture-dependent approaches. Therefore, high-throughput screening was used to understand the population structure, genetic diversity, and ecological role of the microorganisms. High-throughput sequencing of the 16S rRNA marker for gene mapping showed that the gut samples constitute a diverse group of bacteria that is dominated by Proteobacteria, followed by Firmicutes. The bacterial genera Corynebacterium and Mycobacterium were also observed in the Illumina dataset. Illumina sequencing revealed eight bacterial phyla composed of 112 genera. The metagenomic analysis of the OTUs from the gut revealed diverse bacterial communities as well as zoonotic and human pathogens. There were differences in the bacterial communities between the two methods used in this study, which could be related to host specificity, diet, and habitat. The culture-dependent technique resulted in the isolation of 35 bacterial isolates, of which Bacillus cereus and B. anthracis are well-known bacterial pathogens that show virulent traits including hemolytic and proteolytic activities. Pseudomonas stutzeri is an opportunistic human pathogen that was also isolated and showed similar traits. Antibiotic sensitivity tests were performed on all 35 isolates, and different antibiotics were used for Gram-positive and -negative bacteria. The result showed that some isolates are resistant to antibiotics such as penicillin G and Cefoxitin. This report on gut bacterial communities could attract interest in the possibility of isolating and characterizing bacteria for the production of antibiotics, enzymes, plant growth promoters, and probiotics. However, the presence of potential pathogenic bacteria that may impose health hazards cannot be ignored and needs to be studied further.}, } @article {pmid31472697, year = {2019}, author = {Wang, S and Martins, R and Sullivan, MC and Friedman, ES and Misic, AM and El-Fahmawi, A and De Martinis, ECP and O'Brien, K and Chen, Y and Bradley, C and Zhang, G and Berry, ASF and Hunter, CA and Baldassano, RN and Rondeau, MP and Beiting, DP}, title = {Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {126}, pmid = {31472697}, issn = {2049-2618}, mesh = {Animals ; Bile Acids and Salts/*metabolism ; Child ; Clostridiales/metabolism ; Crohn Disease/*microbiology ; Diet Therapy/*methods ; Dogs ; *Dysbiosis/microbiology/therapy ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; Male ; Mice ; Mice, Inbred C57BL ; Remission Induction ; }, abstract = {BACKGROUND: The microbiome has been implicated in the initiation and persistence of inflammatory bowel disease. Despite the fact that diet is one of the most potent modulators of microbiome composition and function and that dietary intervention is the first-line therapy for treating pediatric Crohn's disease, the relationships between diet-induced remission, enteropathy, and microbiome are poorly understood. Here, we leverage a naturally-occurring canine model of chronic inflammatory enteropathy that exhibits robust remission following nutritional therapy, to perform a longitudinal study that integrates clinical monitoring, 16S rRNA gene amplicon sequencing, metagenomic sequencing, metabolomic profiling, and whole genome sequencing to investigate the relationship between therapeutic diet, microbiome, and disease.

RESULTS: We show that remission induced by a hydrolyzed protein diet is accompanied by alterations in microbial community structure marked by decreased abundance of pathobionts (e.g., Escherichia coli and Clostridium perfringens), reduced severity of dysbiosis, and increased levels of the secondary bile acids, lithocholic and deoxycholic acid. Physiologic levels of these bile acids inhibited the growth of E. coli and C. perfringens isolates, in vitro. Metagenomic analysis and whole genome sequencing identified the bile acid producer Clostridium hiranonis as elevated after dietary therapy and a likely source of secondary bile acids during remission. When C. hiranonis was administered to mice, levels of deoxycholic acid were preserved and pathology associated with DSS colitis was ameliorated. Finally, a closely related bile acid producer, Clostridium scindens, was associated with diet-induced remission in human pediatric Crohn's disease.

CONCLUSIONS: These data highlight that remission induced by a hydrolyzed protein diet is associated with improved microbiota structure, an expansion of bile acid-producing clostridia, and increased levels of secondary bile acids. Our observations from clinical studies of exclusive enteral nutrition in human Crohn's disease, along with our in vitro inhibition assays and in vivo studies in mice, suggest that this may be a conserved response to diet therapy with the potential to ameliorate disease. These findings provide insight into diet-induced remission of gastrointestinal disease and could help guide the rational design of more effective therapeutic diets.}, } @article {pmid31470211, year = {2019}, author = {Salzmann, AP and Russo, G and Aluri, S and Haas, C}, title = {Transcription and microbial profiling of body fluids using a massively parallel sequencing approach.}, journal = {Forensic science international. Genetics}, volume = {43}, number = {}, pages = {102149}, doi = {10.1016/j.fsigen.2019.102149}, pmid = {31470211}, issn = {1878-0326}, mesh = {Blood Chemical Analysis ; Cervix Mucus/chemistry ; Female ; *Gene Expression Profiling ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Male ; Menstruation ; *Metagenome ; Microbiota ; RNA Stability ; RNA, Bacterial/*genetics ; RNA, Messenger ; Saliva/chemistry ; Semen/chemistry ; *Sequence Analysis, RNA ; Transcriptome ; }, abstract = {Analysis of biological evidence typically begins with a preliminary screening for the presence of biological fluids, traditionally with enzymatic or immunologic tests and of late by RNA profiling. The goal of this study was to create a whole transcriptome protocol, to view potential degradation effects in forensically relevant body fluids. Total RNA from fresh and aged blood, menstrual blood, saliva, semen, skin and vaginal secretion was analyzed with a massively parallel sequencing method. Two RNA-Seq library protocols with and without rRNA depletion were tested and compared. The rRNA depletion step had a negative influence on the sequencing quality and on the downstream analyses. From the human and bacterial RNA sequences, source-specific signatures could be identified. Aged samples showed in general a higher level of RNA degradation and decreased bacterial diversity. In summary, we could show that transcriptional profiling and metagenome analysis are powerful tools to provide additional information about the trace evidence.}, } @article {pmid31468349, year = {2019}, author = {Giannattasio-Ferraz, S and Laguardia-Nascimento, M and Gasparini, MR and Leite, LR and Araujo, FMG and de Matos Salim, AC and de Oliveira, AP and Nicoli, JR and de Oliveira, GC and da Fonseca, FG and Barbosa-Stancioli, EF}, title = {A common vaginal microbiota composition among breeds of Bos taurus indicus (Gyr and Nellore).}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {50}, number = {4}, pages = {1115-1124}, pmid = {31468349}, issn = {1678-4405}, support = {473879/2013-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Animals ; Archaea/classification/genetics/*isolation & purification ; Bacteria/classification/genetics/*isolation & purification ; Breeding ; Cattle/genetics/*microbiology ; Female ; Fungi/classification/genetics/*isolation & purification ; Metagenomics ; *Microbiota ; Phylogeny ; Rumen/microbiology ; Vagina/*microbiology ; }, abstract = {Describing the bovine vaginal microbiota is essential to better understand its physiology and its impact on health maintenance. Despite the economic importance of reproduction of these animals, bovine vaginal microbial community is still poorly described in comparison with rumen microbiome. Previous studies of our group described the vaginal microbiota of Nellore, an important Bos taurus indicus breed, using metagenomics. In order to better understand this microbiota, the present work aims to investigate another important breed, Gyr. Results have shown bacterial dominance over Archaea and Fungi was observed, with the most abundant bacterial phylum (Firmicutes) representing 40-50% of bacterial population, followed by Bacteroidetes, Proteobacteria, and Actinobacteria. The Fungi kingdom had the Mycosphaerella genus as its main representative, followed by Cladosporium. Archaea were observed at a very low abundance in all animals, with a high relative abundance of Methanobrevibacter genus. These results demonstrate a high microbial diversity on vaginal tract of Gyr, as demonstrated for Nellore and different from the previously described for other species. Our results indicate a great similarity between vaginal microbiota of Nellore and Gyr despite the differences in animal handling and genetic improvement. As observed for both breeds, individual variation is the largest source of microbial diversity between animals.}, } @article {pmid31467354, year = {2019}, author = {Ichikawa-Seki, M and Motooka, D and Kinami, A and Murakoshi, F and Takahashi, Y and Aita, J and Hayashi, K and Tashibu, A and Nakamura, S and Iida, T and Horii, T and Nishikawa, Y}, title = {Specific increase of Fusobacterium in the faecal microbiota of neonatal calves infected with Cryptosporidium parvum.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12517}, pmid = {31467354}, issn = {2045-2322}, mesh = {Animals ; Cattle ; Cattle Diseases/microbiology/*parasitology ; Cryptosporidiosis/microbiology/*parasitology ; Cryptosporidium parvum/*physiology ; Feces/*microbiology ; Female ; Fusobacterium/genetics/*growth & development/isolation & purification ; *Gastrointestinal Microbiome ; Male ; }, abstract = {The faecal microbiota plays a critical role in host health, with alterations in the human faecal microbial composition associated with various conditions, particularly diarrhoeal diseases. However, little is known about microbial changes during cryptosporidiosis, one of the most important diarrhoeal diseases caused by protozoa in cattle. In this study, alterations in the faecal microbiota of neonatal calves as a result of Cryptosporidium parvum infection were investigated on a C. parvum-positive farm. Comparisons were made among groups of C. parvum-infected, rotavirus-infected, and the pathogen-negative calves. A specific increase in the abundance of Fusobacterium was observed in the faecal microbiota of C. parvum-infected animals. Diarrhoea severity increased in accordance with the abundance of C. parvum and Fusobacterium. Moreover, the specific increase of Fusobacterium appeared to be a universal feature of C. parvum infection, since neonatal calves from geographically separated areas showed the same result. These observations indicated that the growth of Fusobacterium may be an important aggravating factor of cryptosporidiosis.}, } @article {pmid31466255, year = {2019}, author = {Palermo, CN and Fulthorpe, RR and Saati, R and Short, SM}, title = {Metagenomic Analysis of Virus Diversity and Relative Abundance in a Eutrophic Freshwater Harbour.}, journal = {Viruses}, volume = {11}, number = {9}, pages = {}, pmid = {31466255}, issn = {1999-4915}, mesh = {*Biodiversity ; Chlorophyll A/analysis ; Cluster Analysis ; DNA, Viral/genetics ; *Eutrophication ; Fresh Water/chemistry/*virology ; Microbiota/genetics ; Viruses/classification/genetics/*isolation & purification ; Water Microbiology ; }, abstract = {Aquatic viruses have been extensively studied over the past decade, yet fundamental aspects of freshwater virus communities remain poorly described. Our goal was to characterize virus communities captured in the >0.22 µm size-fraction seasonally and spatially in a freshwater harbour. Community DNA was extracted from water samples and sequenced on an Illumina HiSeq platform. Assembled contigs were annotated as belonging to the virus groups (i.e., order or family) Caudovirales, Mimiviridae, Phycodnaviridae, and virophages (Lavidaviridae), or to other groups of undefined viruses. Virophages were often the most abundant group, and discrete virophage taxa were remarkably stable across sites and dates despite fluctuations in Mimiviridae community composition. Diverse Mimiviridae contigs were detected in the samples and the two sites contained distinct Mimiviridae communities, suggesting that Mimiviridae are important algal viruses in this system. Caudovirales and Phycodnaviridae were present at low abundances in most samples. Of the 18 environmental parameters tested, only chlorophyll a explained the variation in the data at the order or family level of classification. Overall, our findings provide insight into freshwater virus community assemblages by expanding the documented diversity of freshwater virus communities, highlighting the potential ecological importance of virophages, and revealing distinct communities over small spatial scales.}, } @article {pmid31465907, year = {2019}, author = {Nnadozie, CF and Odume, ON}, title = {Freshwater environments as reservoirs of antibiotic resistant bacteria and their role in the dissemination of antibiotic resistance genes.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {254}, number = {Pt B}, pages = {113067}, doi = {10.1016/j.envpol.2019.113067}, pmid = {31465907}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents ; Bacteria/genetics ; Drug Resistance, Bacterial/*genetics ; Fresh Water/*microbiology ; *Genes, Bacterial ; Humans ; Lakes ; Metagenomics ; Methicillin-Resistant Staphylococcus aureus/genetics ; Microbiota ; Polymerase Chain Reaction ; Rivers ; Sewage ; Water Microbiology ; }, abstract = {Freshwater environments are susceptible to possible contamination by residual antibiotics that are released through different sources, such as agricultural runoffs, sewage discharges and leaching from nearby farms. Freshwater environment can thus become reservoirs where an antibiotic impact microorganisms, and is an important public health concern. Degradation and dilution processes are fundamental for predicting the actual risk of antibiotic resistance dissemination from freshwater reservoirs. This study reviews major approaches for detecting and quantifying antibiotic resistance bacteria (ARBs) and genes (ARGs) in freshwater and their prevalence in these environments. Finally, the role of dilution, degradation, transmission and the persistence and fate of ARB/ARG in these environments are also reviewed. Culture-based single strain approaches and molecular techniques that include polymerase chain reaction (PCR), quantitative polymerase chain reaction (qPCR) and metagenomics are techniques for quantifying ARB and ARGs in freshwater environments. The level of ARBs is extremely high in most of the river systems (up to 98% of the total detected bacteria), followed by lakes (up to 77% of the total detected bacteria), compared to dam, pond, and spring (<1%). Of most concern is the occurrence of extended-spectrum β-lactamase producing Enterobacteriaceae, methicillin resistant Staphylococcus aureus (MRSA) and vancomycin resistant Enterococcus (VRE), which cause highly epidemic infections. Dilution and natural degradation do not completely eradicate ARBs and ARGs in the freshwater environment. Even if the ARBs in freshwater are effectively inactivated by sunlight, their ARG-containing DNA can still be intact and capable of transferring resistance to non-resistant strains. Antibiotic resistance persists and is preserved in freshwater bodies polluted with high concentrations of antibiotics. Direct transmission of indigenous freshwater ARBs to humans as well as their transitory insertion in the microbiota can occur. These findings are disturbing especially for people that rely on freshwater resources for drinking, crop irrigation, and food in form of fish.}, } @article {pmid31465735, year = {2019}, author = {Guadagnini, D and Rocha, GZ and Santos, A and Assalin, HB and Hirabara, SM and Curi, R and Oliveira, AG and Prada, PO and Saad, MJA}, title = {Microbiota determines insulin sensitivity in TLR2-KO mice.}, journal = {Life sciences}, volume = {234}, number = {}, pages = {116793}, doi = {10.1016/j.lfs.2019.116793}, pmid = {31465735}, issn = {1879-0631}, mesh = {Animals ; Endoplasmic Reticulum Stress ; *Gastrointestinal Microbiome ; Gene Deletion ; Glucose Intolerance/genetics/metabolism/microbiology ; Housing, Animal ; Insulin/*metabolism ; *Insulin Resistance/genetics ; Male ; Mice, Inbred C57BL ; Mice, Knockout ; Toll-Like Receptor 2/*genetics/metabolism ; }, abstract = {INTRODUCTION: Environmental factors have a key role in the control of gut microbiota and obesity. TLR2 knockout (TLR2[-/-]) mice in some housing conditions are protected from diet-induced insulin resistance. However, in our housing conditions these animals are not protected from diet-induced insulin-resistance.

AIM: The aim of the present study was to investigate the influence of our animal housing conditions on the gut microbiota, glucose tolerance and insulin sensitivity in TLR2[-/-] mice.

MATERIAL AND METHODS: The microbiota was investigated by metagenomics, associated with hyperinsulinemic euglycemic clamp and GTT associated with insulin signaling through immunoblotting.

RESULTS: The results showed that TLR2[-/-] mice in our housing conditions presented a phenotype of metabolic syndrome characterized by insulin resistance, glucose intolerance and increase in body weight. This phenotype was associated with differences in microbiota in TLR2[-/-] mice that showed a decrease in the Proteobacteria and Bacteroidetes phyla and an increase in the Firmicutesphylum, associated with and in increase in the Oscillospira and Ruminococcus genera. Furthermore there is also an increase in circulating LPS and subclinical inflammation in TLR2[-/-]. The molecular mechanism that account for insulin resistance was an activation of TLR4, associated with ER stress and JNK activation. The phenotype and metabolic behavior was reversed by antibiotic treatment and reproduced in WT mice by microbiota transplantation.

CONCLUSIONS: Our data show, for the first time, that the intestinal microbiota can induce insulin resistance and obesity in an animal model that is genetically protected from these processes.}, } @article {pmid31465520, year = {2019}, author = {Karmacharya, D and Manandhar, P and Manandhar, S and Sherchan, AM and Sharma, AN and Joshi, J and Bista, M and Bajracharya, S and Awasthi, NP and Sharma, N and Llewellyn, B and Waits, LP and Thapa, K and Kelly, MJ and Vuyisich, M and Starkenburg, SR and Hero, JM and Hughes, J and Wultsch, C and Bertola, L and Fountain-Jones, NM and Sinha, AK}, title = {Gut microbiota and their putative metabolic functions in fragmented Bengal tiger population of Nepal.}, journal = {PloS one}, volume = {14}, number = {8}, pages = {e0221868}, pmid = {31465520}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; *Gastrointestinal Microbiome ; *Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Nepal ; Tigers/*metabolism ; }, abstract = {Bengal tigers (Panthera tigris tigris) serve a pivotal role as an apex predator in forest ecosystems. To increase our knowledge on factors impacting the viability and health of this endangered species, we studied the gut microbiota in 32 individual Bengal tigers from three geographically separated areas (Chitwan National Park (CNP), Bardia National Park (BNP) and Suklaphanta Wildlife Reserve (SWR)) in Nepal, using noninvasive genetic sampling methods. Gut microbiota influence the immune system, impact various physiological functions, and modulates metabolic reactions, that ultimately impact the host health, behavior and development. Across the tiger populations in Nepal, we found significant differences in the composition of microbial communities based on their geographic locations. Specifically, we detected significant differences between CNP and the other two protected areas (CNP vs BNP: pseudo t = 1.944, P = 0.006; CNP vs SWR: pseudo t = 1.9942, P = 0.0071), but no differences between BNP and SWR. This mirrors what has been found for tiger gene flow in the same populations, suggesting gut microbiota composition and host gene flow may be linked. Furthermore, predictive metagenome functional content analysis (PICRUSt) revealed a higher functional enrichment and diversity for significant gut microbiota in the Chitwan tiger population and the lowest enrichment and diversity in Suklaphanta. The CNP tiger population contained higher proportions of microbiota that are associated with predicted functions relevant for metabolism of amino acid, lipid, xenobiotics biodegradation, terpenoides and polyketides than the SWR population. We conclude the tiger population structure, gut microbiota profile and associated functional metabolic categories are correlated, with geographically most separated CNP and SWR tiger population having the most distinct and different host genotype and microbiota profiles. Our work dramatically expands the understanding of tiger microbiota in wild populations and provides a valuable case study on how to investigate genetic diversity at different hierarchical levels, including hosts as well as their microbial communities.}, } @article {pmid31464899, year = {2019}, author = {Liang, W and Yang, Y and Wang, H and Wang, H and Yu, X and Lu, Y and Shen, S and Teng, L}, title = {Gut microbiota shifts in patients with gastric cancer in perioperative period.}, journal = {Medicine}, volume = {98}, number = {35}, pages = {e16626}, pmid = {31464899}, issn = {1536-5964}, mesh = {Adult ; Bacteria/*classification/genetics/isolation & purification ; China ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Gastrectomy ; Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; Perioperative Period ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Stomach Neoplasms/microbiology/*surgery ; }, abstract = {Gastric cancer (GC) is one of the common malignant tumors in China, with a high morbidity and mortality. With the development and application of high-throughput sequencing technologies and metagenomics, a great quantity of studies have shown that gastrointestinal microbiota is closely related to digestive system diseases. Although some studies have reported the effect of long-term follow-up after subtotal gastrectomy on intestinal flora changes in patients with GC. However, the features of gut microbiota and their shifts in patients with GC in perioperative period remain unclear.This study was designed to characterize fecal microbiota shifts of the patients with GC before and after the radical distal gastrectomy (RDG) during their hospital staying periods. Furthermore, fecal microbiota was also compared between the GC patients and healthy individuals.Patients who were diagnosed with advanced gastric adenocarcinoma at distal stomach were enrolled in the study. The bacterial burden within fecal samples was determined using quantitative polymerase chain reaction. To analyze the diversity and composition of gut microbiota from fecal DNA of 20 GC patients and 22 healthy controls, amplicons of the 16S rRNA gene from all subjects were pyrosequenced. To study gut microbiota shifts, the fecal microbiota from 6 GC patients before and after RDG was detected and subsequently analyzed. Short-chain fatty acids were also detected by chromatography spectrometer in these 6 GC patients.RDG had a moderate effect on bacterial richness and evenness, but had pronounced effects on the composition of postoperative gut microbiota compared with preoperative group. The relative abundances of genera Akkermansia, Esherichia/Shigella, Lactobacillus, and Dialister were significant changed in perioperative period. Remarkably, higher abundances of Escherichia/Shigella, Veillonella, and Clostridium XVIII and lower abundances of Bacteroides were observed in gut microbiota of overall GC patients compared to healthy controls.This study is the first study to characterize the altered gut microbiota within fecal samples from GC patients during perioperative period, and provide a new insights on such microbial perturbations as a potential effector of perioperative period phenotype. Further research must validate these discoveries and may evaluate targeted microbiota shifts to improve outcomes in GC patients.}, } @article {pmid31464319, year = {2019}, author = {Qu, W and Liu, S and Zhang, W and Zhu, H and Tao, Q and Wang, H and Yan, H}, title = {Impact of traditional Chinese medicine treatment on chronic unpredictable mild stress-induced depression-like behaviors: intestinal microbiota and gut microbiome function.}, journal = {Food & function}, volume = {10}, number = {9}, pages = {5886-5897}, doi = {10.1039/c9fo00399a}, pmid = {31464319}, issn = {2042-650X}, mesh = {Animals ; Bacteria/classification/drug effects/genetics/isolation & purification ; Behavior, Animal/drug effects ; Depression/*drug therapy/microbiology ; Drugs, Chinese Herbal/*administration & dosage ; Dysbiosis/drug therapy/microbiology/psychology ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Male ; Medicine, Chinese Traditional ; Plants, Medicinal/*chemistry ; Rats ; Stress, Psychological/*drug therapy/microbiology/psychology ; }, abstract = {Gut microbiota dysbiosis is a recognized contributing factor to many noncommunicable diseases, but more evidence is still needed to illustrate its causative impact on mental and brain health disorders and mechanism(s) for targeted mitigation. Traditional Chinese Medicine (TCM) has been used in the management of neuropsychiatric diseases for many years in China. In this study, a randomized, controlled trial was conducted to examine the impact of stress on gut microbiota dysbiosis and depression, and TCM in alleviating the damage using Chronic Unpredictable Mild Stress (CUMS) rats, a well-established rodent model for depression. The behaviors of rats and the profiles of the fecal microbiota were assessed by an array of behavioral tests and 16S rRNA gene sequencing, and the intestinal microbial function was assessed by shotgun sequencing-based metagenomic analysis of microbial DNA from fecal samples. Data on brain targeted metabolites by liquid chromatography-mass spectrometry (LC-MS) were also discussed. Depressive and anxiety-like behaviors and changes in the fecal microbiota profile were observed in CUMS rats, which were then significantly reversed in CUMS rats that received TCM. Specifically, TCM treatment reduced the levels of Firmicutes, and Ruminococcus, and increased the abundance of Bacteroidetes and Roseburia, reportedly being associated with relieving psychiatric disorders. Furthermore, the levels of brain metabolites perturbed by CUMS were reversed by TCM treatment, and Spearman's correlation analysis illustrated strong correlation between brain metabolites and perturbed fecal microbiota genera. Finally, the fecal microbiome of CUMS rats was characterized by alterations in amino acid metabolism and evaluation of bile acid biosynthesis, and TCM-treated rats showed elevation of cysteine and methionine metabolism. Overall, these results indicated that administration of the TCM may mitigate CUMS-induced depression-behaviors, and it is correlated with reversing CUMS-induced intestinal microbiota dysbiosis; evidence also supported related changes in brain metabolites. These findings set up the foundation to further reveal the exact causal relationship among the TCM formula, host responses, gut microbiota dysbiosis and the levels of brain metabolites, and enabled scientific interpretation of the therapeutic function of the TCM.}, } @article {pmid31462412, year = {2019}, author = {Stewart, DB and Wright, JR and Fowler, M and McLimans, CJ and Tokarev, V and Amaniera, I and Baker, O and Wong, HT and Brabec, J and Drucker, R and Lamendella, R}, title = {Integrated Meta-omics Reveals a Fungus-Associated Bacteriome and Distinct Functional Pathways in Clostridioides difficile Infection.}, journal = {mSphere}, volume = {4}, number = {4}, pages = {}, pmid = {31462412}, issn = {2379-5042}, mesh = {Adult ; Aged ; Aged, 80 and over ; Biofilms ; Clostridioides difficile/*genetics ; Clostridium Infections/*microbiology ; Diarrhea/microbiology ; Feces/microbiology ; Fungi/*genetics ; *Gastrointestinal Microbiome ; Humans ; Metabolic Networks and Pathways ; *Metagenomics ; Middle Aged ; Sequence Analysis, DNA ; *Transcriptome ; }, abstract = {There has been no prior application of matched metagenomics and metatranscriptomics in Clostridioides difficile infection (CDI) evaluating the role of fungi in CDI or identifying community functions that contribute to the development of this disease. We collected diarrheal stools from 49 inpatients (18 of whom tested positive for CDI) under stringent inclusion criteria. We utilized a tiered sequencing approach to identify enriched bacterial and fungal taxa, using 16S and internal transcribed spacer (ITS) rRNA gene amplicon sequencing, with matched metagenomics and metatranscriptomics performed on a subset of the population. Distinct bacterial and fungal compositions distinguished CDI-positive and -negative patients, with the greatest differentiation between the cohorts observed based on bacterial metatranscriptomics. Bipartite network analyses demonstrated that Aspergillus and Penicillium taxa shared a strong positive relationship in CDI patients and together formed negative cooccurring relationships with several bacterial taxa, including the Oscillospira, Comamonadaceae, Microbacteriaceae, and Cytophagaceae Metatranscriptomics revealed enriched pathways in CDI patients associated with biofilm production primarily driven by Escherichia coli and Pseudomonas, quorum-sensing proteins, and two-component systems related to functions such as osmotic regulation, linoleic acid metabolism, and flagellar assembly. Differential expression of functional pathways unveiled a mechanism by which the causal dysbiosis of CDI may self-perpetuate, potentially contributing to treatment failures. We propose that CDI has a distinct fungus-associated bacteriome, and this first description of metatranscriptomics in human subjects with CDI demonstrates that inflammation, osmotic changes, and biofilm production are key elements of CDI pathophysiology.IMPORTANCE Our data suggest a potential role for fungi in the most common nosocomial bacterial infection in the United States, introducing the concept of a transkingdom interaction between bacteria and fungi in this disease. We also provide the first direct measure of microbial community function in Clostridioides difficile infection using patient-derived tissue samples, revealing antibiotic-independent mechanisms by which C. difficile infection may resist a return to a healthy gut microbiome.}, } @article {pmid31462278, year = {2019}, author = {Wang, Y and Niu, Q and Zhang, X and Liu, L and Wang, Y and Chen, Y and Negi, M and Figeys, D and Li, YY and Zhang, T}, title = {Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {122}, pmid = {31462278}, issn = {2049-2618}, mesh = {*Bacteria/classification/isolation & purification/metabolism ; Bioreactors/*microbiology ; Metagenome ; Microbial Interactions ; Microbiota/*genetics ; Nitrification ; Nitrogen/*metabolism ; Oxidation-Reduction ; Sewage/*microbiology ; Water Purification/*methods ; }, abstract = {BACKGROUND: The metabolic capacities of anammox bacteria and associated microbial community interactions in partial-nitritation anammox (PNA) reactors have received considerable attention for their crucial roles in energy-efficient nitrogen removal from wastewater. However, a comprehensive understanding of how abiotic and biotic factors shape bacterial community assembly in PNA reactors is not well reported.

RESULTS: Here, we used integrated multi-omics (i.e., high-throughput 16S rRNA gene, metagenomic, metatranscriptomic, and metaproteomic sequencing) to reveal how abiotic and biotic factors shape the bacterial community assembly in a lab-scale one-stage PNA reactor treating synthetic wastewater. Analysis results of amplicon sequences (16S rRNA gene) from a time-series revealed distinct relative abundance patterns of the key autotrophic bacteria, i.e., anammox bacteria and ammonia-oxidizing bacteria (AOB), and the associated heterotrophic populations in the seed sludge and the sludge at the new stable state after deterioration. Using shotgun metagenomic sequences of anammox sludge, we recovered 58 metagenome-assembled genomes (MAGs), including 3 MAGs of anammox bacteria and 3 MAGs of AOB. The integrated metagenomic, metatranscriptomic, and metaproteomic data revealed that nitrogen metabolism is the most active process in the studied PNA reactor. The abundant heterotrophs contribute to the reduction of nitrate to nitrite/ammonium for autotrophic bacteria (anammox bacteria and AOB). Genomic and transcriptomic data revealed that the preference for electron donors of the dominant heterotrophs in different bacterial assemblages (seed and new stable state) varied along with the shift in anammox bacteria that have different metabolic features in terms of EPS composition. Notably, the most abundant heterotrophic bacteria in the reactor were more auxotrophic than the less abundant heterotrophs, regarding the syntheses of amino acids and vitamins. In addition, one of the abundant bacteria observed in the bacterial community exhibited highly transcribed secretion systems (type VI).

CONCLUSIONS: These findings provide the first insight that the bacterial communities in the PNA reactor are defined by not only abiotic factors (operating mode) but also metabolic interactions, such as nitrogen metabolism, exchange of electron donors, and auxotrophies.}, } @article {pmid31461453, year = {2019}, author = {Shin, D and Chang, SY and Bogere, P and Won, K and Choi, JY and Choi, YJ and Lee, HK and Hur, J and Park, BY and Kim, Y and Heo, J}, title = {Beneficial roles of probiotics on the modulation of gut microbiota and immune response in pigs.}, journal = {PloS one}, volume = {14}, number = {8}, pages = {e0220843}, pmid = {31461453}, issn = {1932-6203}, mesh = {Animal Feed/microbiology ; Animals ; Female ; *Gastrointestinal Microbiome ; Immunity ; Lactobacillus plantarum/*immunology ; *Probiotics/pharmacology ; Swine/*immunology/microbiology ; }, abstract = {The importance of probiotics in swine production is widely acknowledged as crucial. However, gaps still remain in the exact roles played by probiotics in modulation of gut microbiota and immune response. This study determined the roles of probiotic Lactobacillus plantarum strain JDFM LP11in gut microbiota modulation and immune response in weaned piglets. L. plantarum JDFM LP11 increased the population of lactic acid bacteria in feces and enhanced the development of villi in the small intestine. Metagenome analysis showed that microbial diversity and richness (Simpson, Shannon, ACE, Chao1) and the relative abundance of the Firmicutes were higher in weaned piglets fed probiotics. Five bacterial families were different in the relative abundance, especially; Prevotellaceae occupied the largest part of microbial community showed the most difference between two groups. Transcriptome analysis identified 25 differentially expressed genes using RNA-sequencing data of the ileum. Further gene ontology and immune DB analysis determined 8 genes associated with innate defense response and cytokine production. BPI, RSAD2, SLPI, LUM, OLFM4, DMBT1 and C6 genes were down-regulated by probiotic supplementation except PLA2G2A. PICRUSt analysis predicting functional profiling of microbial communities indicated branched amino acid biosynthesis and butyrate metabolism promoting gut development and health were increased by probiotics. Altogether, our data suggest that L. plantarum JDFM LP11 increases the diversity and richness in the microbial community, and attenuates the ileal immune gene expression towards gut inflammation, promoting intestinal development in weaned piglets.}, } @article {pmid31461261, year = {2019}, author = {Gilmore, SP and Lankiewicz, TS and Wilken, SE and Brown, JL and Sexton, JA and Henske, JK and Theodorou, MK and Valentine, DL and O'Malley, MA}, title = {Top-Down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation.}, journal = {ACS synthetic biology}, volume = {8}, number = {9}, pages = {2174-2185}, doi = {10.1021/acssynbio.9b00271}, pmid = {31461261}, issn = {2161-5063}, mesh = {Anaerobiosis ; Biofuels ; *Biomass ; Lignin/metabolism ; Methane/metabolism ; Methanobacteriaceae/growth & development/*metabolism ; Microbial Consortia ; Piromyces/growth & development/*metabolism ; Spirochaetaceae/growth & development/*metabolism ; }, abstract = {Consortium-based approaches are a promising avenue toward efficient bioprocessing. However, many complex microbial interactions dictate community dynamics and stability that must be replicated in synthetic systems. The rumen and/or hindguts of large mammalian herbivores harbor complex communities of biomass-degrading fungi and bacteria, as well as archaea and protozoa that work collectively to degrade lignocellulose, yet the microbial interactions responsible for stability, resilience, and activity of the community remain largely uncharacterized. In this work, we demonstrate a "top-down" enrichment-based methodology for selecting a minimal but effective lignocellulose-degrading community that produces methane-rich fermentation gas (biogas). The resulting enrichment consortium produced 0.75-1.9-fold more fermentation gas at 1.4-2.1 times the rate compared to a monoculture of fungi from the enrichment. Metagenomic sequencing of the top-down enriched consortium revealed genomes encoding for functional compartmentalization of the community, spread across an anaerobic fungus (Piromyces), a bacterium (Sphaerochaeta), and two methanogenic archaea (Methanosphaera and Methanocorpusculum). Guided by the composition of the top-down enrichment, several synthetic cocultures were formed from the "bottom-up" using previously isolated fungi, Neocallimastix californiae and Anaeromyces robustus paired with the methanogen Methanobacterium bryantii. While cross-feeding occurred in synthetic co-cultures, removal of fungal metabolites by methanogens did not increase the rate of gas production or the rate of substrate deconstruction by the synthetic community relative to fungal monocultures. Metabolomic characterization verified that syntrophy was established within synthetic co-cultures, which generated methane at similar concentrations compared to the enriched consortium but lacked the temporal stability (resilience) seen in the native system. Taken together, deciphering the membership and metabolic potential of an enriched gut consortium enables the design of methanogenic synthetic co-cultures. However, differences in the growth rate and stability of enriched versus synthetic consortia underscore the difficulties in mimicking naturally occurring syntrophy in synthetic systems.}, } @article {pmid31455406, year = {2019}, author = {Suzuki, Y and Nishijima, S and Furuta, Y and Yoshimura, J and Suda, W and Oshima, K and Hattori, M and Morishita, S}, title = {Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {119}, pmid = {31455406}, issn = {2049-2618}, mesh = {Bacteria/genetics/isolation & purification ; Bacteriophages/*genetics ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Genome, Bacterial ; Humans ; Interspersed Repetitive Sequences/genetics ; Japan ; Metagenome/*genetics ; Plasmids/*genetics ; }, abstract = {BACKGROUND: Elucidating the ecological and biological identity of extrachromosomal mobile genetic elements (eMGEs), such as plasmids and bacteriophages, in the human gut remains challenging due to their high complexity and diversity.

RESULTS: Here, we show efficient identification of eMGEs as complete circular or linear contigs from PacBio long-read metagenomic data. De novo assembly of PacBio long reads from 12 faecal samples generated 82 eMGE contigs (2.5~666.7-kb), which were classified as 71 plasmids and 11 bacteriophages, including 58 novel plasmids and six bacteriophages, and complete genomes of five diverse crAssphages with terminal direct repeats. In a dataset of 413 gut metagenomes from five countries, many of the identified plasmids were highly abundant and prevalent. The ratio of gut plasmids by our plasmid data is more than twice that in the public database. Plasmids outnumbered bacterial chromosomes three to one on average in this metagenomic dataset. Host prediction suggested that Bacteroidetes-associated plasmids predominated, regardless of microbial abundance. The analysis found several plasmid-enriched functions, such as inorganic ion transport, while antibiotic resistance genes were harboured mostly in low-abundance Proteobacteria-associated plasmids.

CONCLUSIONS: Overall, long-read metagenomics provided an efficient approach for unravelling the complete structure of human gut eMGEs, particularly plasmids.}, } @article {pmid31455230, year = {2019}, author = {Zaheer, R and Lakin, SM and Polo, RO and Cook, SR and Larney, FJ and Morley, PS and Booker, CW and Hannon, SJ and Van Domselaar, G and Read, RR and McAllister, TA}, title = {Comparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {197}, pmid = {31455230}, issn = {1471-2180}, support = {T32 OD012201/OD/NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/*drug effects/genetics/*isolation & purification ; Bacterial Proteins/genetics ; Biodiversity ; Canada ; Cattle ; *Drug Resistance, Bacterial ; Feces/*microbiology ; Manure/*microbiology ; *Microbiota ; Sewage/*microbiology ; Soil/chemistry ; Soil Microbiology ; }, abstract = {BACKGROUND: Comparative knowledge of microbiomes and resistomes across environmental interfaces between animal production systems and urban settings is lacking. In this study, we executed a comparative analysis of the microbiota and resistomes of metagenomes from cattle feces, catch basin water, manured agricultural soil and urban sewage.

RESULTS: Metagenomic DNA from composite fecal samples (FC; n = 12) collected from penned cattle at four feedlots in Alberta, Canada, along with water from adjacent catchment basins (CB; n = 13), soil (n = 4) from fields in the vicinity of one of the feedlots and urban sewage influent (SI; n = 6) from two municipalities were subjected to Illumina HiSeq2000 sequencing. Firmicutes exhibited the highest prevalence (40%) in FC, whereas Proteobacteria were most abundant in CB (64%), soil (60%) and SI (83%). Among sample types, SI had the highest diversity of antimicrobial resistance (AMR), and metal and biocide resistance (MBR) classes (13 & 15) followed by FC (10 & 8), CB (8 & 4), and soil (6 & 1). The highest antimicrobial resistant (AMR) gene (ARG) abundance was harboured by FC, whereas soil samples had a very small, but unique resistome which did not overlap with FC & CB resistomes. In the beef production system, tetracycline resistance predominated followed by macrolide resistance. The SI resistome harboured β-lactam, macrolide, tetracycline, aminoglycoside, fluoroquinolone and fosfomycin resistance determinants. Metal and biocide resistance accounted for 26% of the SI resistome with a predominance of mercury resistance.

CONCLUSIONS: This study demonstrates an increasing divergence in the nature of the microbiome and resistome as the distance from the feedlot increases. Consistent with antimicrobial use, tetracycline and macrolide resistance genes were predominant in the beef production system. One of the feedlots contributed both conventional (raised with antibiotics) and natural (raised without antibiotics) pens samples. Although natural pen samples exhibited a microbiota composition that was similar to samples from conventional pens, their resistome was less complex. Similarly, the SI resistome was indicative of drug classes used in humans and the greater abundance of mercury resistance may be associated with contamination of municipal water with household and industrial products.}, } @article {pmid31454888, year = {2019}, author = {Borghi, E and Vignoli, A}, title = {Rett Syndrome and Other Neurodevelopmental Disorders Share Common Changes in Gut Microbial Community: A Descriptive Review.}, journal = {International journal of molecular sciences}, volume = {20}, number = {17}, pages = {}, pmid = {31454888}, issn = {1422-0067}, mesh = {Animals ; Biodiversity ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; Neurodevelopmental Disorders/diagnosis/*etiology ; Phenotype ; Rett Syndrome/diagnosis/*etiology ; }, abstract = {In this narrative review, we summarize recent pieces of evidence of the role of microbiota alterations in Rett syndrome (RTT). Neurological problems are prominent features of the syndrome, but the pathogenic mechanisms modulating its severity are still poorly understood. Gut microbiota was recently demonstrated to be altered both in animal models and humans with different neurodevelopmental disorders and/or epilepsy. By investigating gut microbiota in RTT cohorts, a less rich microbial community was identified which was associated with alterations of fecal microbial short-chain fatty acids. These changes were positively correlated with severe clinical outcomes. Indeed, microbial metabolites can play a crucial role both locally and systemically, having dynamic effects on host metabolism and gene expression in many organs. Similar alterations were found in patients with autism and down syndrome as well, suggesting a potential common pathway of gut microbiota involvement in neurodevelopmental disorders.}, } @article {pmid31452355, year = {2020}, author = {Vilanova, C and Porcar, M}, title = {Art-omics: multi-omics meet archaeology and art conservation.}, journal = {Microbial biotechnology}, volume = {13}, number = {2}, pages = {435-441}, pmid = {31452355}, issn = {1751-7915}, mesh = {*Archaeology ; Humans ; Metabolomics ; Metagenomics ; *Microbiota ; Proteomics ; }, abstract = {Multi-omics can informally be described as the combined use of high-throughput techniques allowing the characterization of complete microbial communities by the sequencing/identification of total pools of biomolecules including DNA, proteins or metabolites. These techniques have allowed an unprecedented level of knowledge on complex microbial ecosystems, which is having key implications in land and marine ecology, industrial biotechnology or biomedicine. Multi-omics have recently been applied to artistic or archaeological objects, with the goal of either contributing to shedding light on the original context of the pieces and/or to inform conservation approaches. In this minireview, we discuss the application of -omic techniques to the study of prehistoric artworks and ancient man-made objects in three main technical blocks: metagenomics, proteomics and metabolomics. In particular, we will focus on how proteomics and metabolomics can provide paradigm-breaking results by unambiguously identifying peptides associated with a given, palaeo-cultural context; and we will discuss how metagenomics can be central for the identification of the microbial keyplayers on artworks surfaces, whose conservation can then be approached by a range of techniques, including using selected microorganisms as 'probiotics' because of their direct or indirect effect in the stabilization and preservation of valuable art objects.}, } @article {pmid31452349, year = {2019}, author = {Xing, R and Gao, QB and Zhang, FQ and Wang, JL and Chen, SL}, title = {Large-scale distribution of bacterial communities in the Qaidam Basin of the Qinghai-Tibet Plateau.}, journal = {MicrobiologyOpen}, volume = {8}, number = {10}, pages = {e909}, pmid = {31452349}, issn = {2045-8827}, mesh = {Bacteria/*classification/*genetics ; Hydrogen-Ion Concentration ; Magnesium/analysis ; Metagenomics ; *Microbiota ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; Spatial Analysis ; Tibet ; }, abstract = {Many studies have investigated patterns of soil microbial communities over large spatial scales. However, these studies mainly focused on a few sites. Here, we studied the near-surface (0-30 cm) soil microbial communities of 35 soil samples collected from most of the areas of the Qaidam Basin, which is the largest basin on the Qinghai-Tibet Plateau. A total of 32 phyla and 838 genera were detected from all the samples, in which Actinobacteria, Proteobacteria, Bacteroidetes, and Acidobacteria were the most dominant and cosmopolitan phyla. The most abundant phyla (relative abundance > 5%) detected in all 35 soil samples were also the most dominant, which could be explained by their great dispersal ability. The microbial community structures correlated strongly with variations in pH and Mg[2+] and were distinct between the high Mg[2+] content (>20 g/kg) samples and other samples (Acidobacteria, Actinobacteria, and Chloroflexi were significantly less abundant in the high Mg[2+] content group, but the abundance of Firmicutes was significantly greater). Finally, the microbial spatial pattern was influenced by both the local environment and spatial distance, but environmental factors were the primary drivers of microbial spatial patterns in the Qaidam Basin.}, } @article {pmid31451725, year = {2019}, author = {Libis, V and Antonovsky, N and Zhang, M and Shang, Z and Montiel, D and Maniko, J and Ternei, MA and Calle, PY and Lemetre, C and Owen, JG and Brady, SF}, title = {Uncovering the biosynthetic potential of rare metagenomic DNA using co-occurrence network analysis of targeted sequences.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {3848}, pmid = {31451725}, issn = {2041-1723}, support = {R35 GM122559/GM/NIGMS NIH HHS/United States ; U01 GM110714/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics/*metabolism ; Biosynthetic Pathways/genetics ; DNA, Bacterial/genetics ; Metagenome/*genetics ; Microbiota/*genetics ; Multigene Family/genetics ; Secondary Metabolism/*genetics ; Sequence Analysis, DNA/methods ; *Soil Microbiology ; }, abstract = {Sequencing of DNA extracted from environmental samples can provide key insights into the biosynthetic potential of uncultured bacteria. However, the high complexity of soil metagenomes, which can contain thousands of bacterial species per gram of soil, imposes significant challenges to explore secondary metabolites potentially produced by rare members of the soil microbiome. Here, we develop a targeted sequencing workflow termed CONKAT-seq (co-occurrence network analysis of targeted sequences) that detects physically clustered biosynthetic domains, a hallmark of bacterial secondary metabolism. Following targeted amplification of conserved biosynthetic domains in a highly partitioned metagenomic library, CONKAT-seq evaluates amplicon co-occurrence patterns across library subpools to identify chromosomally clustered domains. We show that a single soil sample can contain more than a thousand uncharacterized biosynthetic gene clusters, most of which originate from low frequency genomes which are practically inaccessible through untargeted sequencing. CONKAT-seq allows scalable exploration of largely untapped biosynthetic diversity across multiple soils, and can guide the discovery of novel secondary metabolites from rare members of the soil microbiome.}, } @article {pmid31451112, year = {2019}, author = {Ghurye, J and Treangen, T and Fedarko, M and Hervey, WJ and Pop, M}, title = {MetaCarvel: linking assembly graph motifs to biological variants.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {174}, pmid = {31451112}, issn = {1474-760X}, support = {R01 AI100947/AI/NIAID NIH HHS/United States ; R01AI100947//National Institute of Allergy and Infectious Diseases/International ; }, mesh = {Acinetobacter/genetics ; *Algorithms ; Base Sequence ; Databases, Genetic ; Feces/microbiology ; *Genetic Variation ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Mutation/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Analysis, DNA ; }, abstract = {Reconstructing genomic segments from metagenomics data is a highly complex task. In addition to general challenges, such as repeats and sequencing errors, metagenomic assembly needs to tolerate the uneven depth of coverage among organisms in a community and differences between nearly identical strains. Previous methods have addressed these issues by smoothing genomic variants. We present a variant-aware metagenomic scaffolder called MetaCarvel, which combines new strategies for repeat detection with graph analytics for the discovery of variants. We show that MetaCarvel can accurately reconstruct genomic segments from complex microbial mixtures and correctly identify and characterize several classes of common genomic variants.}, } @article {pmid31451108, year = {2019}, author = {Rhoades, N and Barr, T and Hendrickson, S and Prongay, K and Haertel, A and Gill, L and Garzel, L and Whiteson, K and Slifka, M and Messaoudi, I}, title = {Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {173}, pmid = {31451108}, issn = {1474-760X}, support = {P51 OD011092/OD/NIH HHS/United States ; P51 OD011107/OD/NIH HHS/United States ; T32 AI141346/AI/NIAID NIH HHS/United States ; }, mesh = {Aging ; Animals ; Animals, Newborn ; Anti-Bacterial Agents/therapeutic use ; Bacteria/genetics ; Biomarkers/metabolism ; Carrier State/microbiology ; Child ; Child, Preschool ; Developed Countries ; Developing Countries ; Diarrhea/drug therapy/*microbiology ; Disease Susceptibility ; Female ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Infant ; Macaca mulatta ; Male ; Metagenomics ; Phylogeny ; }, abstract = {BACKGROUND: Diarrhea is the second leading cause of death in children under 5 years of age. Enhanced understanding of causal pathways, pathogenesis, and sequelae of diarrhea is urgently needed. Although the gut microbiota is believed to play a role in susceptibility to diarrheal diseases, our understanding of this association remains incomplete. Infant rhesus macaques (Macaca mulatta) are susceptible to diarrhea making them an ideal model to address this question.

RESULTS: The maturation of the infant rhesus macaque gut microbiome throughout the first 8 months of life occurs in a similar pattern as that described for human infants. Moreover, the microbiome of the captive reared infant rhesus macaque more closely resembles that of human infants in the developing world than in the western world. Importantly, prior to disease onset, the gut microbiome of infants that later develop diarrhea is enriched in pathways of immunomodulatory metabolite synthesis, while those of infants that remain asymptomatic are enriched in pathways for short-chain fatty acid production. We identify Prevotella strains that are more abundant at 1 month in infants that later develop diarrhea. At 8 months, the microbiomes of animals that experience diarrhea show increased abundance of Campylobacter and a reduction in Helicobacter macacae.

CONCLUSION: The composition of the microbial community could provide a phenotypic marker of an infant's susceptibility to diarrheal disease. Given the significant physiological and immunological similarities between human and nonhuman primates, these findings provide potential markers of susceptibility to diarrhea that could be modulated to improve infant health, especially in the developing world.}, } @article {pmid31450818, year = {2019}, author = {Enagbonma, BJ and Aremu, BR and Babalola, OO}, title = {Profiling the Functional Diversity of Termite Mound Soil Bacteria as Revealed by Shotgun Sequencing.}, journal = {Genes}, volume = {10}, number = {9}, pages = {}, pmid = {31450818}, issn = {2073-4425}, mesh = {Animals ; Genes, Bacterial ; Isoptera/pathogenicity/*physiology ; *Metagenome ; Metagenomics/methods ; *Microbiota ; Sequence Analysis, DNA/methods ; Soil/chemistry/*parasitology ; *Soil Microbiology ; }, abstract = {Profiling the metabolic processes performed by bacteria is vital both for understanding and for manipulating ecosystems for industrial or research purposes. In this study we aim to assess the bacterial functional diversity in termite mound soils with the assumption that significant differences will be observed in the functional diversity of bacteria between the termite mound soils and their surrounding soils and that each environment has a distinguishing metabolic profile. Here, metagenomic DNA extracted from termite mound soils and their corresponding surrounding soils, which are 10 m apart, were sequenced using a shotgun sequencing approach. Our results revealed that the relative abundances of 16 functional categories differed significantly between both habitats. The α diversity analysis indicated no significant difference in bacterial functional categories within the habitats while the β diversity showed that the bacterial functional categories varied significantly between the termite mound soils and the surrounding soil samples. The variations in soil physical and chemical properties existing between the two environments were held accountable for the differences in bacterial functional structure. With the high relative abundance of functional categories with unknown function reported in this study, this could signify the likelihood of getting novel genes from termite mound soils, which are needed for research and commercial applications.}, } @article {pmid31450659, year = {2019}, author = {Aarnoutse, R and Ziemons, J and Penders, J and Rensen, SS and de Vos-Geelen, J and Smidt, ML}, title = {The Clinical Link between Human Intestinal Microbiota and Systemic Cancer Therapy.}, journal = {International journal of molecular sciences}, volume = {20}, number = {17}, pages = {}, pmid = {31450659}, issn = {1422-0067}, mesh = {Combined Modality Therapy/adverse effects/methods ; Disease Management ; *Gastrointestinal Microbiome/drug effects/radiation effects ; Humans ; Metagenome ; Metagenomics/methods ; Neoplasms/complications/mortality/*therapy ; Prognosis ; Treatment Outcome ; }, abstract = {Clinical interest in the human intestinal microbiota has increased considerably. However, an overview of clinical studies investigating the link between the human intestinal microbiota and systemic cancer therapy is lacking. This systematic review summarizes all clinical studies describing the association between baseline intestinal microbiota and systemic cancer therapy outcome as well as therapy-related changes in intestinal microbiota composition. A systematic literature search was performed and provided 23 articles. There were strong indications for a close association between the intestinal microbiota and outcome of immunotherapy. Furthermore, the development of chemotherapy-induced infectious complications seemed to be associated with the baseline microbiota profile. Both chemotherapy and immunotherapy induced drastic changes in gut microbiota composition with possible consequences for treatment efficacy. Evidence in the field of hormonal therapy was very limited. Large heterogeneity concerning study design, study population, and methods used for analysis limited comparability and generalization of results. For the future, longitudinal studies investigating the predictive ability of baseline intestinal microbiota concerning treatment outcome and complications as well as the potential use of microbiota-modulating strategies in cancer patients are required. More knowledge in this field is likely to be of clinical benefit since modulation of the microbiota might support cancer therapy in the future.}, } @article {pmid31450270, year = {2019}, author = {Sandhu, SS and Pourang, A and Sivamani, RK}, title = {A review of next generation sequencing technologies used in the evaluation of the skin microbiome: what a time to be alive.}, journal = {Dermatology online journal}, volume = {25}, number = {7}, pages = {}, pmid = {31450270}, issn = {1087-2108}, mesh = {*High-Throughput Nucleotide Sequencing ; Humans ; Metabolomics/methods ; Metagenomics/*methods ; *Microbiota ; Proteomics/methods ; Skin/*microbiology ; }, abstract = {The role of the microbiome in healthy and disease states of the human body is progressively being found to extend beyond the gastrointestinal tract and into other organ systems such as the skin. Researching the microbiome thus has become paramount to understanding additional physiological and pathophysiological mechanisms that may be at play between microbes and their hosts. Cell cultures have traditionally been used to study the microbiome, but in our current day and age, advanced metagenomic techniques - such as 16S rRNA amplicon sequencing and whole metagenomic shotgun sequencing - are better able to classify the microorganisms making up the microbiome. Utilizing metagenomics alone, however, does not allow for the study of the more complex effects of the microbiome, such as changes in gene expression and metabolic byproducts. Thus, incorporation of other modalities such as metatranscriptomics, metaproteomics, and metabolomics are needed to further elucidate the extensive intricacies of the skin microbiome.}, } @article {pmid31448249, year = {2019}, author = {Pini Prato, A and Bartow-McKenney, C and Hudspeth, K and Mosconi, M and Rossi, V and Avanzini, S and Faticato, MG and Ceccherini, I and Lantieri, F and Mattioli, G and Larson, D and Pavan, W and De Filippo, C and Di Paola, M and Mavilio, D and Cavalieri, D}, title = {A Metagenomics Study on Hirschsprung's Disease Associated Enterocolitis: Biodiversity and Gut Microbial Homeostasis Depend on Resection Length and Patient's Clinical History.}, journal = {Frontiers in pediatrics}, volume = {7}, number = {}, pages = {326}, pmid = {31448249}, issn = {2296-2360}, support = {T32 AR007465/AR/NIAMS NIH HHS/United States ; }, abstract = {Objectives: Since 2010, several researches demonstrated that microbiota dynamics correlate and can even predispose to Hirschsprung (HSCR) associated enterocolitis (HAEC). This study aims at assessing the structure of the microbiota of HSCR patients in relation to extent of aganglionosis and HAEC status. Methods: All consecutive HSCR patients admitted to Gaslini Institute (Genova, Italy) between May 2012 and November 2014 were enrolled. Institutional review board (IRB) approval was obtained. Stools were sampled and 16S rDNA V3-V4 regions were sequenced using the Illumina-MiSeq. Taxonomy assignments were performed using QIIME RDP. Alpha diversity indexes were analyzed by Shannon and Simpson Indexes, and Phylogenetic Diversity. Results: We enrolled 20 patients. Male to female ratio was 4:1. Six patients suffered from Total Colonic Aganglionosis (TCSA). Considering sample site (i.e., extent of aganglionosis), we confirmed the known relationship between sample site and both biodiversity and composition of intestinal microbiota. Patients with TCSA showed lower biodiversity and increased Proteobacteria/Bacteroidetes relative abundance ratio. When addressing biodiversity, composition and dynamics of TCSA patients we could not find any significant relationship with regard to HAEC occurrences. Conclusions: The composition of HAEC predisposing microbiota is specific to each patient. We could confirm that total colon resections can change the composition of intestinal microbiota and to dramatically reduce microbial diversity. The subsequent reduction of system robustness could expose TCSA patients to environmental microbes that might not be part of the normal microbiota. Future long-term studies should investigate both patients and their family environment, as well as their disease history.}, } @article {pmid31448147, year = {2019}, author = {Wu, B and Hussain, M and Zhang, W and Stadler, M and Liu, X and Xiang, M}, title = {Current insights into fungal species diversity and perspective on naming the environmental DNA sequences of fungi.}, journal = {Mycology}, volume = {10}, number = {3}, pages = {127-140}, pmid = {31448147}, issn = {2150-1203}, abstract = {The global bio-diversity of fungi has been extensively investigated and their species number has been estimated. Notably, the development of molecular phylogeny has revealed an unexpected fungal diversity and utilisation of culture-independent approaches including high-throughput amplicon sequencing has dramatically increased number of fungal operational taxonomic units. A number of novel taxa including new divisions, classes, orders and new families have been established in last decade. Many cryptic species were identified by molecular phylogeny. Based on recently generated data from culture-dependent and -independent survey on same samples, the fungal species on the earth were estimated to be 12 (11.7-13.2) million compared to 2.2-3.8 million species recently estimated by a variety of the estimation techniques. Moreover, it has been speculated that the current use of high-throughput sequencing techniques would reveal an even higher diversity than our current estimation. Recently, the formal classification of environmental sequences and permission of DNA sequence data as fungal names' type were proposed but strongly objected by the mycologist community. Surveys on fungi in unusual niches have indicated that many previously regarded "unculturable fungi" could be cultured on certain substrates under specific conditions. Moreover, the high-throughput amplicon sequencing, shotgun metagenomics and a single-cell genomics could be a powerful means to detect novel taxa. Here, we propose to separate the fungal types into physical type based on specimen, genome DNA (gDNA) type based on complete genome sequence of culturable and uncluturable fungal specimen and digital type based on environmental DNA sequence data. The physical and gDNA type should have priority, while the digital type can be temporal supplementary before the physical type and gDNA type being available. The fungal name based on the "digital type" could be assigned as the "clade" name + species name. The "clade" name could be the name of genus, family or order, etc. which the sequence of digital type affiliates to. Facilitating future cultivation efforts should be encouraged. Also, with the advancement in knowledge of fungi inhabiting various environments mostly because of rapid development of new detection technologies, more information should be expected for fungal diversity on our planet.}, } @article {pmid31446647, year = {2019}, author = {Lemos, LN and Medeiros, JD and Dini-Andreote, F and Fernandes, GR and Varani, AM and Oliveira, G and Pylro, VS}, title = {Genomic signatures and co-occurrence patterns of the ultra-small Saccharimonadia (phylum CPR/Patescibacteria) suggest a symbiotic lifestyle.}, journal = {Molecular ecology}, volume = {28}, number = {18}, pages = {4259-4271}, doi = {10.1111/mec.15208}, pmid = {31446647}, issn = {1365-294X}, support = {BB/P027849/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/*genetics ; Base Sequence ; Gene Regulatory Networks ; *Genome, Bacterial ; *Genomics ; Metabolic Networks and Pathways/genetics ; Metagenome ; Microbiota/genetics ; Mining ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Symbiosis/*genetics ; }, abstract = {The size of bacterial genomes is often associated with organismal metabolic capabilities determining ecological breadth and lifestyle. The recently proposed Candidate Phyla Radiation (CPR)/Patescibacteria encompasses mostly unculturable bacterial taxa with relatively small genome sizes with potential for co-metabolism interdependencies. As yet, little is known about the ecology and evolution of CPR, particularly with respect to how they might interact with other taxa. Here, we reconstructed two novel genomes (namely, Candidatus Saccharibacter sossegus and Candidatus Chaer renensis) of taxa belonging to the class Saccharimonadia within the CPR/Patescibacteria using metagenomes obtained from acid mine drainage (AMD). By testing the hypothesis of genome streamlining or symbiotic lifestyle, our results revealed clear signatures of gene losses in these genomes, such as those associated with de novo biosynthesis of essential amino acids, nucleotides, fatty acids and cofactors. In addition, co-occurrence analysis provided evidence supporting potential symbioses of these organisms with Hydrotalea sp. in the AMD system. Together, our findings provide a better understanding of the ecology and evolution of CPR/Patescibacteria and highlight the importance of genome reconstruction for studying metabolic interdependencies between unculturable Saccharimonadia representatives.}, } @article {pmid31446105, year = {2019}, author = {Wang, M and Chen, G and Chen, D and Ye, H and Sun, Y and Zeng, X and Liu, Z}, title = {Purified fraction of polysaccharides from Fuzhuan brick tea modulates the composition and metabolism of gut microbiota in anaerobic fermentation in vitro.}, journal = {International journal of biological macromolecules}, volume = {140}, number = {}, pages = {858-870}, doi = {10.1016/j.ijbiomac.2019.08.187}, pmid = {31446105}, issn = {1879-0003}, mesh = {*Anaerobiosis ; Chemical Fractionation ; Chemical Phenomena ; Computational Biology ; *Fermentation ; Gastrointestinal Microbiome/*drug effects ; Humans ; Hydrolysis ; Metagenome ; Metagenomics/methods ; Polysaccharides/chemistry/*isolation & purification/*pharmacology ; Tea/*chemistry ; }, abstract = {One purified fraction from crude Fuzhuan brick tea polysaccharides (FBTPS), FBTPS-3, was obtained through column chromatography of DEAE Sepharose Fast Flow. The chemical properties and probiotic effects of FBTPS-3 were evaluated by fermentation in vitro. Moreover, the effects of FBTPS-3 on the function and metabolic pathway of gut microbiota were investigated by metagenomic sequencing. The results showed that FBTPS-3 was an heteropolysaccharide with molecular weight of 741 kDa, which was mainly composed of Man, Rha, GalA, Gal and Ara in molar ratio of 8.7:15.5:42.2:19.7:13.9. The contents of carbohydrates and uronic acid in FBTPS-3 were 44.78 ± 2.85% and 40.4 ± 2.11%, respectively. After fermentation, the molecular weight of FBTPS-3 and content of carbohydrates were significantly decreased, indicating that FBTPS-3 could be utilized by gut microbiota. Furthermore, the relative abundances of Bacteroides, Megasphaera and Prevotella were significantly increased by FBTPS-3. FBTPS-3 also significantly promoted the production of acetic, propionic and n-butyric acids. Based on the metagenomic sequencing, it was found that FBTPS-3 significantly enriched the metabolic pathway of starch and sucrose. All the results suggest that FBTPS-3 is expected to be developed as functional ingredients or foods to improve the host health through regulating the gut microbiota and physiological metabolic functions.}, } @article {pmid31445216, year = {2019}, author = {Guirro, M and Herrero, P and Costa, A and Gual-Grau, A and Ceretó-Massagué, A and Hernández, A and Torrell, H and Arola, L and Canela, N}, title = {Comparison of metaproteomics workflows for deciphering the functions of gut microbiota in an animal model of obesity.}, journal = {Journal of proteomics}, volume = {209}, number = {}, pages = {103489}, doi = {10.1016/j.jprot.2019.103489}, pmid = {31445216}, issn = {1876-7737}, mesh = {Animals ; Buffers ; Disease Models, Animal ; Gastrointestinal Microbiome/*physiology ; Metagenomics ; Obesity/*microbiology ; Proteolysis ; Proteomics/*methods/standards ; Rats ; Specimen Handling/methods ; *Workflow ; }, abstract = {Metaproteomics has emerged as a new, revolutionary approach to study gut microbiota functionality, but the lack of consistent studies in this field due to the great complexity of samples has prompted to search new strategies to achieve better metaproteome characterization. Some steps in sample preparation and data analysis procedures are critical for obtaining accurate results, therefore protein extraction buffers, digestion procedures and fractionation steps were tested here. Initially, two lysis buffers were used to improve protein extraction, two common digestion protocols were compared, and fractionation processes were employed at both the peptide and protein levels. The combination of these procedures resulted in five different methodologies; SDS buffer, in-gel digestion and fractionation at the peptide level provided the best results. Finally, the metaproteomics workflow was tested in a real case study with obese rats, in which a metagenomics study was previously performed. Important differences in protein levels were observed between groups that were potentially related to the taxonomical family, indicating that functional processes are modulated by the microbiota. Therefore, in addition to the necessity of combining different metaomics approaches, an optimized metaproteomics workflow such as the presented in this study is required to obtain a better understanding of the microbiota function. SIGNIFICANCE: Gut microbiota has emerged as an important factor with affects the health balance in host. To study its function new methodologies are necessary and the most appropriate one seems to be metaproteomics. The lack of studies in this field requires a deeply research in the most accurate workflow to better comprehend such complex samples. In this paper, five different methodologies have been compared, mainly in the most critical steps in classical proteomics and the methodology chosen was validated in a real case study in obese animals.}, } @article {pmid31444990, year = {2019}, author = {Viver, T and Orellana, LH and Díaz, S and Urdiain, M and Ramos-Barbero, MD and González-Pastor, JE and Oren, A and Hatt, JK and Amann, R and Antón, J and Konstantinidis, KT and Rosselló-Móra, R}, title = {Predominance of deterministic microbial community dynamics in salterns exposed to different light intensities.}, journal = {Environmental microbiology}, volume = {21}, number = {11}, pages = {4300-4315}, doi = {10.1111/1462-2920.14790}, pmid = {31444990}, issn = {1462-2920}, support = {CGL2012-39627-C03-03//Ministerio de Ciencia e Innovación/International ; CGL2015_66686-C3-2-P//Ministerio de Ciencia e Innovación/International ; CGL2015_66686-C3-3-P//Ministerio de Ciencia e Innovación/International ; CLG2015_66686-C3-1-P//Ministerio de Ciencia e Innovación/International ; PGC2018-096956-B-C41//Ministerio de Ciencia e Innovación/International ; //Ministry of Sciences, Innovation and Universities/International ; PRX18/00048//Georgia Tech/International ; BES-2013-064420//Spanish Government Ministry for Finance and Competition/International ; 1831582//U.S. National Science Foundation/International ; //Max Planck Society/International ; //European Regional Development Fund/International ; }, mesh = {Bacteria/genetics/radiation effects ; *Light ; Metagenome ; Microbiota/*radiation effects ; Photosynthesis ; Salinity ; Stochastic Processes ; }, abstract = {While the dynamics of microbial community assembly driven by environmental perturbations have been extensively studied, our understanding is far from complete, particularly for light-induced perturbations. Extremely halophilic communities thriving in coastal solar salterns are mainly influenced by two environmental factors-salt concentrations and high sunlight irradiation. By experimentally manipulating light intensity through the application of shading, we showed that light acts as a deterministic factor that ultimately drives the establishment of recurrent microbial communities under near-saturation salt concentrations. In particular, the stable and highly change-resistant communities that established under high-light intensities were dominated (>90% of metagenomic reads) by Haloquadratum spp. and Salinibacter spp. On the other hand, under 37-fold lower light intensity, different, less stable and change-resistant communities were established, mainly dominated by yet unclassified haloarchaea and relatively diverse photosynthetic microorganisms. These communities harboured, in general, much lower carotenoid pigment content than their high-irradiation counterparts. Both assemblage types appeared to be highly resilient, re-establishing when favourable conditions returned after perturbation (i.e. high-irradiation for the former communities and low-irradiation for the latter ones). Overall, our results revealed that stochastic processes were of limited significance to explain these patterns.}, } @article {pmid31444782, year = {2019}, author = {Pothmann, A and Illing, T and Wiegand, C and Hartmann, AA and Elsner, P}, title = {The Microbiome and Atopic Dermatitis: A Review.}, journal = {American journal of clinical dermatology}, volume = {20}, number = {6}, pages = {749-761}, doi = {10.1007/s40257-019-00467-1}, pmid = {31444782}, issn = {1179-1888}, mesh = {Animals ; Dermatitis, Atopic/*immunology/microbiology/therapy ; Disease Models, Animal ; Dysbiosis/complications/*immunology/microbiology/therapy ; Humans ; Intestinal Mucosa/immunology/*microbiology ; Microbiota/*immunology ; Probiotics/administration & dosage ; Skin/immunology/*microbiology ; }, abstract = {The microbiome is defined as the sum of microbes, their genomes, and interactions in a given ecological niche. Atopic dermatitis is a multifactorial chronic inflammatory skin disease leading to dryness and itchiness of the skin. It is often associated with comorbidities such as allergic rhinoconjunctivitis and asthma. Today, culture-free techniques have been established to define microbes and their genomes that may be both detrimental and beneficial for their host. There are signs that microbes, both on skin and in the gut, may influence the course of atopic dermatitis. Antiseptic treatment has been used for decades, however now, with the help of traditional culture-based methods and modern metagenomics, we are beginning to understand that targeted treatment of dysbiosis may possibly become part of an integrated therapy plan in the future.}, } @article {pmid31444199, year = {2019}, author = {Loit, K and Adamson, K and Bahram, M and Puusepp, R and Anslan, S and Kiiker, R and Drenkhan, R and Tedersoo, L}, title = {Relative Performance of MinION (Oxford Nanopore Technologies) versus Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {21}, pages = {}, pmid = {31444199}, issn = {1098-5336}, mesh = {Agriculture ; Ascomycota/genetics/isolation & purification/pathogenicity ; Biodiversity ; Computational Biology ; Forests ; Fungi/classification/*genetics/*isolation & purification/pathogenicity ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; *Nanopores ; Oomycetes/genetics/isolation & purification/pathogenicity ; Pathology, Molecular/methods ; Plant Diseases/microbiology ; Sequence Alignment ; Solanum tuberosum ; }, abstract = {Culture-based molecular identification methods have revolutionized detection of pathogens, yet these methods are slow and may yield inconclusive results from environmental materials. The second-generation sequencing tools have much-improved precision and sensitivity of detection, but these analyses are costly and may take several days to months. Of the third-generation sequencing techniques, the portable MinION device (Oxford Nanopore Technologies) has received much attention because of its small size and possibility of rapid analysis at reasonable cost. Here, we compare the relative performances of two third-generation sequencing instruments, MinION and Sequel (Pacific Biosciences), in identification and diagnostics of fungal and oomycete pathogens from conifer (Pinaceae) needles and potato (Solanum tuberosum) leaves and tubers. We demonstrate that the Sequel instrument is efficient for metabarcoding of complex samples, whereas MinION is not suited for this purpose due to a high error rate and multiple biases. However, we find that MinION can be utilized for rapid and accurate identification of dominant pathogenic organisms and other associated organisms from plant tissues following both amplicon-based and PCR-free metagenomics approaches. Using the metagenomics approach with shortened DNA extraction and incubation times, we performed the entire MinION workflow, from sample preparation through DNA extraction, sequencing, bioinformatics, and interpretation, in 2.5 h. We advocate the use of MinION for rapid diagnostics of pathogens and potentially other organisms, but care needs to be taken to control or account for multiple potential technical biases.IMPORTANCE Microbial pathogens cause enormous losses to agriculture and forestry, but current combined culturing- and molecular identification-based detection methods are too slow for rapid identification and application of countermeasures. Here, we develop new and rapid protocols for Oxford Nanopore MinION-based third-generation diagnostics of plant pathogens that greatly improve the speed of diagnostics. However, due to high error rate and technical biases in MinION, the Pacific BioSciences Sequel platform is more useful for in-depth amplicon-based biodiversity monitoring (metabarcoding) from complex environmental samples.}, } @article {pmid31443695, year = {2019}, author = {Malmuthuge, N and Liang, G and Guan, LL}, title = {Regulation of rumen development in neonatal ruminants through microbial metagenomes and host transcriptomes.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {172}, pmid = {31443695}, issn = {1474-760X}, mesh = {Animals ; Animals, Newborn ; Bacteria/*genetics ; Cattle ; Epithelium/growth & development ; Fatty Acids, Volatile/metabolism ; Gene Regulatory Networks ; Metabolome/genetics ; Metagenome/*genetics ; MicroRNAs/genetics/metabolism ; Microbiota/*genetics ; Rumen/*microbiology ; Ruminants/*genetics/*growth & development/microbiology ; Transcriptome/*genetics ; Weaning ; }, abstract = {BACKGROUND: In ruminants, early rumen development is vital for efficient fermentation that converts plant materials to human edible food such as milk and meat. Here, we investigate the extent and functional basis of host-microbial interactions regulating rumen development during the first 6 weeks of life.

RESULTS: The use of microbial metagenomics, together with quantification of volatile fatty acids (VFAs) and qPCR, reveals the colonization of an active bacterial community in the rumen at birth. Colonization of active complex carbohydrate fermenters and archaea with methyl-coenzyme M reductase activity was also observed from the first week of life in the absence of a solid diet. Integrating microbial metagenomics and host transcriptomics reveals only 26.3% of mRNA transcripts, and 46.4% of miRNAs were responsive to VFAs, while others were ontogenic. Among these, one host gene module was positively associated with VFAs, while two other host gene modules and one miRNA module were negatively associated with VFAs. Eight host genes and five miRNAs involved in zinc ion binding-related transcriptional regulation were associated with a rumen bacterial cluster consisting of Prevotella, Bacteroides, and Ruminococcus.

CONCLUSION: This three-way interaction suggests a potential role of bacteria-driven transcriptional regulation in early rumen development via miRNAs. Our results reveal a highly active early microbiome that regulates rumen development of neonatal calves at the cellular level, and miRNAs may coordinate these host-microbial interactions.}, } @article {pmid31443379, year = {2019}, author = {Imanishi, I and Uchiyama, J and Tsukui, T and Hisatsune, J and Ide, K and Matsuzaki, S and Sugai, M and Nishifuji, K}, title = {Therapeutic Potential of an Endolysin Derived from Kayvirus S25-3 for Staphylococcal Impetigo.}, journal = {Viruses}, volume = {11}, number = {9}, pages = {}, pmid = {31443379}, issn = {1999-4915}, mesh = {Administration, Cutaneous ; Animals ; Anti-Bacterial Agents/administration & dosage/pharmacology ; Bacteriolysis ; Caudovirales/*metabolism/pathogenicity ; Endopeptidases/administration & dosage/genetics/*pharmacology ; Genes, Bacterial ; Genes, Viral ; Impetigo/*drug therapy/microbiology ; Metagenomics ; Mice ; Microbiota/genetics ; Pseudomonas aeruginosa/virology ; RNA, Ribosomal, 16S ; Recombinant Proteins/administration & dosage/pharmacology ; Skin/microbiology/pathology ; Staphylococcal Infections/drug therapy ; Staphylococcus Phages/metabolism/pathogenicity ; *Staphylococcus aureus/drug effects/virology ; Staphylococcus epidermidis/virology ; Streptococcus mitis/virology ; }, abstract = {Impetigo is a contagious skin infection predominantly caused by Staphylococcus aureus. Decontamination of S. aureus from the skin is becoming more difficult because of the emergence of antibiotic-resistant strains. Bacteriophage endolysins are less likely to invoke resistance and can eliminate the target bacteria without disturbance of the normal microflora. In this study, we investigated the therapeutic potential of a recombinant endolysin derived from kayvirus S25-3 against staphylococcal impetigo in an experimental setting. First, the recombinant S25-3 endolysin required an incubation period of over 15 minutes to exhibit efficient bactericidal effects against S. aureus. Second, topical application of the recombinant S25-3 endolysin decreased the number of intraepidermal staphylococci and the size of pustules in an experimental mouse model of impetigo. Third, treatment with the recombinant S25-3 endolysin increased the diversity of the skin microbiota in the same mice. Finally, we revealed the genus-specific bacteriolytic effect of recombinant S25-3 endolysin against staphylococci, particularly S. aureus, among human skin commensal bacteria. Therefore, topical treatment with recombinant S25-3 endolysin can be a promising disease management procedure for staphylococcal impetigo by efficient bacteriolysis of S. aureus while improving the cutaneous bacterial microflora.}, } @article {pmid31441243, year = {2019}, author = {Smessaert, J and Van Geel, M and Verreth, C and Crauwels, S and Honnay, O and Keulemans, W and Lievens, B}, title = {Temporal and spatial variation in bacterial communities of "Jonagold" apple (Malus x domestica Borkh.) and "Conference" pear (Pyrus communis L.) floral nectar.}, journal = {MicrobiologyOpen}, volume = {8}, number = {12}, pages = {e918}, pmid = {31441243}, issn = {2045-8827}, mesh = {*Bacteria/classification/genetics ; Biodiversity ; DNA Barcoding, Taxonomic ; Fruit/microbiology ; Malus/*microbiology ; *Microbiota ; *Plant Nectar ; Pyrus/*microbiology ; }, abstract = {Production of many agricultural crops and fruits strongly depends on pollinators. For instance, pome fruits such as apple and pear are highly dependent on pollination for fruit set, fruit quality, and yield. Nectar is often inhabited by microbes, most often yeasts and bacteria, which may change nectar quality and therefore also affect plant-pollinator interactions. Here, we used high-throughput 16S ribosomal RNA gene amplicon sequencing to investigate the temporal and spatial variation in bacterial communities in floral nectar of apple and pear. We sampled 15 apple (Malus x domestica Borkh.) and 15 pear (Pyrus communis L.) orchards distributed over the eastern part of Belgium over a timespan of seven days. Nectar bacterial community composition differed strongly among fruit species. Nectar of pear was dominated by Actinobacteria, followed by Proteobacteria and Firmicutes. Apple nectar was strongly enriched in Bacteroidetes, a phylum which until now has been found to be rarely associated with floral nectar. Nectar was dominated by only a few bacterial species, with Brevibacterium (Actinobacteria) and Undibacterium (Proteobacteria) as the most abundant bacteria in pear and apple nectar, respectively. Bacterial richness and diversity were found to fluctuate during flowering, likely due to changing environmental conditions. Additionally, spatial structure in nectar bacterial community composition was found in apple orchards, while this was not the case for pear. Differences in nectar bacterial communities between apple and pear nectar may differently affect the chemical and nutritional composition of the nectar, influencing pollinator attraction and visitation, and thus pollination efficacy in general.}, } @article {pmid31438955, year = {2019}, author = {Vavourakis, CD and Mehrshad, M and Balkema, C and van Hall, R and Andrei, AŞ and Ghai, R and Sorokin, DY and Muyzer, G}, title = {Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {69}, pmid = {31438955}, issn = {1741-7007}, support = {322551/ERC_/European Research Council/International ; }, mesh = {Archaea/*classification/genetics/*metabolism ; Bacteria/*classification/genetics/*metabolism ; Hydrogen-Ion Concentration ; Lakes/chemistry/*microbiology ; Metagenome ; Oxidation-Reduction ; Phylogeny ; Salinity ; Salts/chemistry ; Siberia ; Sulfur/analysis/*metabolism ; }, abstract = {BACKGROUND: The planetary sulfur cycle is a complex web of chemical reactions that can be microbial-mediated or can occur spontaneously in the environment, depending on the temperature and pH. Inorganic sulfur compounds can serve as energy sources for specialized prokaryotes and are important substrates for microbial growth in general. Here, we investigate dissimilatory sulfur cycling in the brine and sediments of a southwestern Siberian soda lake characterized by an extremely high pH and salinity, combining meta-omics analyses of its uniquely adapted highly diverse prokaryote communities with biogeochemical profiling to identify key microbial players and expand our understanding of sulfur cycling under haloalkaline conditions.

RESULTS: Peak microbial activity was found in the top 4 cm of the sediments, a layer with a steep drop in oxygen concentration and redox potential. The majority of sulfur was present as sulfate or iron sulfide. Thiosulfate was readily oxidized by microbes in the presence of oxygen, but oxidation was partially inhibited by light. We obtained 1032 metagenome-assembled genomes, including novel population genomes of characterized colorless sulfur-oxidizing bacteria (SOB), anoxygenic purple sulfur bacteria, heterotrophic SOB, and highly active lithoautotrophic sulfate reducers. Surprisingly, we discovered the potential for nitrogen fixation in a new genus of colorless SOB, carbon fixation in a new species of phototrophic Gemmatimonadetes, and elemental sulfur/sulfite reduction in the "Candidatus Woesearchaeota." Polysulfide/thiosulfate and tetrathionate reductases were actively transcribed by various (facultative) anaerobes.

CONCLUSIONS: The recovery of over 200 genomes that encoded enzymes capable of catalyzing key reactions in the inorganic sulfur cycle indicates complete cycling between sulfate and sulfide at moderately hypersaline and extreme alkaline conditions. Our results suggest that more taxonomic groups are involved in sulfur dissimilation than previously assumed.}, } @article {pmid31437575, year = {2019}, author = {Li, A and Wang, Y and Pei, L and Mehmood, K and Li, K and Qamar, H and Iqbal, M and Waqas, M and Liu, J and Li, J}, title = {Influence of dietary supplementation with Bacillus velezensis on intestinal microbial diversity of mice.}, journal = {Microbial pathogenesis}, volume = {136}, number = {}, pages = {103671}, doi = {10.1016/j.micpath.2019.103671}, pmid = {31437575}, issn = {1096-1208}, mesh = {Animals ; Bacillus/*growth & development/isolation & purification ; Cattle/microbiology ; Cecum/microbiology ; Diet/*methods ; Duodenum/microbiology ; *Gastrointestinal Microbiome ; Ileum/microbiology ; Jejunum/microbiology ; Metagenomics ; Mice ; Probiotics/*administration & dosage ; Tibet ; }, abstract = {Yaks are an aboriginal breed of the Qinghai-Tibet plateau (3000 m), which are highly adaptable to cold and hypoxic environments. It is noticed that hypoxia and hypothermia can induce changes in intestinal microbial structure in animals. Increasing evidences suggested that probiotics supplementation can improve the balance of gut microbiota of animals. However, so far, very few studies have emphasized on the probiotics isolated from yaks in the Qinghai-Tibet Plateau. Therefore, a potential probiotic strain Bacillus velezensis was isolated from yaks. In the present study, a total of 18 Kunming mice (15-18 g) were equally distributed into two groups; control and probiotic treated groups (1 × 10[9] CFU/day). During the experimental period, all the mice from both groups were given standard normal diet ad libitum. At the end of the experiment, mice were euthanized and the intestines (duodenum, jejunum, ileum, and cecum) were removed for high-throughput sequencing. The results demonstrated that Bacillus velezensis supplementation showed beneficial effects on the gut microbiota of mice. Specifically, Bacillus velezensis supplementation increased the population of Lactobacillus and Ruminococcus in the duodenum, and Candidatus Arthromitus in the jejunum. Additionally, Acinetobacter in the duodenum and Helicobacter in the cecum were decreased after feeding Bacillus velezensis. Altogether, these findings suggested that Bacillus velezensis isolated from Tibetan yaks can improve gut microbiota of mice.}, } @article {pmid31437194, year = {2019}, author = {Pendegraft, AH and Guo, B and Yi, N}, title = {Bayesian hierarchical negative binomial models for multivariable analyses with applications to human microbiome count data.}, journal = {PloS one}, volume = {14}, number = {8}, pages = {e0220961}, pmid = {31437194}, issn = {1932-6203}, mesh = {Bayes Theorem ; DNA, Bacterial/*genetics ; Databases, Factual ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Internet ; Microbial Consortia/*genetics ; Microbiota/*genetics ; Multivariate Analysis ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {The analyses of large volumes of metagenomic data extracted from aggregate populations of microscopic organisms residing on and in the human body are advancing contemporary understandings of the integrated participation of microbes in human health and disease. Next generation sequencing technology facilitates said analyses in terms of diversity, community composition, and differential abundance by filtering and binning microbial 16S rRNA genes extracted from human tissues into operational taxonomic units. However, current statistical tools restrict study designs to investigations of limited numbers of host characteristics mediated by limited numbers of samples potentially yielding a loss of relevant information. This paper presents a Bayesian hierarchical negative binomial model as an efficient technique capable of compensating for multivariable sets including tens or hundreds of host characteristics as covariates further expanding analyses of human microbiome count data. Simulation studies reveal that the Bayesian hierarchical negative binomial model provides a desirable strategy by often outperforming three competing negative binomial model in terms of type I error while simultaneously maintaining consistent power. An application of the Bayesian hierarchical negative binomial model using subsets of the open data published by the American Gut Project demonstrates an ability to identify operational taxonomic units significantly differentiable among persons diagnosed by a medical professional with either inflammatory bowel disease or irritable bowel syndrome that are consistent with contemporary gastrointestinal literature.}, } @article {pmid31437154, year = {2019}, author = {Pichler, V and Kotsakiozi, P and Caputo, B and Serini, P and Caccone, A and Della Torre, A}, title = {Complex interplay of evolutionary forces shaping population genomic structure of invasive Aedes albopictus in southern Europe.}, journal = {PLoS neglected tropical diseases}, volume = {13}, number = {8}, pages = {e0007554}, pmid = {31437154}, issn = {1935-2735}, support = {R01 AI132409/AI/NIAID NIH HHS/United States ; }, mesh = {Aedes/classification/*genetics ; Albania ; Animal Migration ; Animals ; *Biological Evolution ; Europe ; Gene Flow ; Genetic Variation ; Greece ; Insect Vectors/classification/*genetics ; Introduced Species ; Italy ; *Metagenomics ; Phylogeny ; Polymorphism, Single Nucleotide ; }, abstract = {BACKGROUND: In the last four decades, the Asian tiger mosquito, Aedes albopictus, vector of several human arboviruses, has spread from its native range in South-East Asia to all over the world, largely through the transportation of its eggs via the international trade in used tires. Albania was the first country invaded in Europe in 1979, followed by Italy in 1990 and other Mediterranean countries after 2000.

METHODS/PRINCIPAL FINDINGS: We here inferred the invasion history and migration patterns of Ae. albopictus in Italy (today the most heavily-infested country in Europe), Greece and Albania, by analyzing a panel of >100,000 single nucleotide polymorphisms (SNPs) obtained by sequencing of double-digest Restriction site-Associated DNA (ddRADseq). The obtained dataset was combined with samples previously analyzed from both the native and invasive range worldwide to interpret the results using a broader spatial and historical context. The emerging evolutionary scenario complements the results of other studies in showing that the extraordinary worldwide expansion of Ae. albopictus has occurred thanks to multiple independent invasions by large numbers of colonists from multiple geographic locations in both native and previously invaded areas, consistently with the role of used tires shipments to move large numbers of eggs worldwide. By analyzing mosquitoes from nine sites across ~1,000-km transect in Italy, we were able to detect a complex interplay of drift, isolation by distance mediated divergence, and gene flow in shaping the species very recent invasion and range expansion, suggesting overall high connectivity, likely due to passive transportation of adults via ground transportation, as well as specific adaptations to local conditions.

CONCLUSIONS/SIGNIFICANCE: Results contribute to characterize one of the most successful histories of animal invasion, and could be used as a baseline for future studies to track epidemiologically relevant characters (e.g. insecticide resistance).}, } @article {pmid31433440, year = {2019}, author = {Hao, W and He, Z and Zhu, H and Liu, J and Kwek, E and Zhao, Y and Ma, KY and He, WS and Chen, ZY}, title = {Sea buckthorn seed oil reduces blood cholesterol and modulates gut microbiota.}, journal = {Food & function}, volume = {10}, number = {9}, pages = {5669-5681}, doi = {10.1039/c9fo01232j}, pmid = {31433440}, issn = {2042-650X}, mesh = {ATP-Binding Cassette Transporters/genetics/metabolism ; Animals ; Anticholesteremic Agents/chemistry/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; Cholesterol/blood ; Cricetinae ; Fatty Acids/chemistry/metabolism ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Hippophae/*chemistry/metabolism ; Humans ; Hypercholesterolemia/metabolism/*microbiology ; Male ; Mesocricetus ; Phytosterols/chemistry/metabolism ; Plant Oils/chemistry/*metabolism ; Seeds/chemistry/metabolism ; Sterol O-Acyltransferase/genetics/metabolism ; Triglycerides/blood ; }, abstract = {Sea buckthorn seed oil (SBSO) has been used as a functional food in the prevention of heart diseases. The present study investigates the effects of SBSO on blood cholesterol and the gut microbiota in hypercholesterolemia hamsters. Four groups of hamsters (n = 8 each) were given one of four diets, namely a non-cholesterol control diet (NCD), a high-cholesterol control diet (HCD) containing 0.1% cholesterol, and an HCD diet with sea buckthorn seed oil replacing 50% lard (SL) or replacing 100% lard (SH). Feeding SL and SH diets could reduce blood total cholesterol by 20-22%. This was accompanied by the down-regulation of the gene expression of acyl-CoA:cholesterol acyltransferase 2 (ACAT2), microsomal triacylglycerol transport protein (MTP), and ATP-binding cassette transporter8 (ABCG8). SBSO supplementation also increased the production of intestinal short-chain fatty acids and fecal outputs of neutral sterols. Metagenomic analysis demonstrated that feeding SL and SH diets could favorably modulate the relative abundance of Bacteroidales_S24-7_group, Ruminococcaceae, and Eubacteriaceae. It was therefore concluded that SBSO was effective in reducing blood cholesterol in hypercholesterolemic hamsters via increasing intestinal cholesterol excretion and promoting the growth of SCFA-producing bacteria.}, } @article {pmid31432609, year = {2019}, author = {Gao, T and Cui, B and Kong, X and Bai, Z and Zhuang, X and Qian, Z}, title = {Investigation of bacterial diversity and pathogen abundances in gibel carp (Carassius auratus gibelio) ponds during a cyprinid herpesvirus 2 outbreak.}, journal = {MicrobiologyOpen}, volume = {8}, number = {10}, pages = {e907}, pmid = {31432609}, issn = {2045-8827}, mesh = {Animals ; Aquaculture ; Bacteria/*classification/*isolation & purification ; Biological Oxygen Demand Analysis ; *Biota ; China ; Disease Outbreaks ; Fish Diseases/virology ; Goldfish/growth & development/virology ; Herpesviridae/isolation & purification ; Herpesviridae Infections/*veterinary/virology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Nitrogen/analysis ; Ponds/*microbiology ; Real-Time Polymerase Chain Reaction ; Temperature ; Water/analysis ; }, abstract = {Cyprinid herpesvirus 2 (CyHV-2) infection is detrimental to gibel carp health and may result in severe economic loss in freshwater aquaculture. However, information regarding the interaction of this pathogen with the aquatic environment is scarce. In this study, quantitative polymerase chain reaction (qPCR) and high-throughput sequencing were used to determine the abundances of pathogens and bacterial community compositions in two aquaculture ponds in Jiangsu Province, China. The results indicate that the concentrations of six selected pathogens were higher in the water than in the sediment and that these concentrations peaked during disease outbreak. In total, 8,326 and 18,244 operational taxonomic units were identified from water and sediment samples, respectively. The dominant phyla were Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, and Chlorobi in water samples and Proteobacteria, Firmicutes, Actinobacteria, Chloroflexi, and Bacteroidetes in sediment samples. Bacterial communities were similar at the phylum level in different ponds, although significant differences were observed at the genus level. In addition, bacterial diversity was associated with environmental factors (temperature, chemical oxygen demand, NO2[-] -N, NO3[-] -N, and NH4[+] -N) in the pond where the outbreak occurred. Additionally, CyHV-2 abundance was positively correlated with dissolved oxygen levels and Aeromonas spp. abundance in pond water (p < .01). This study provides comprehensive insight into the mechanisms of interaction between potential pathogens and the freshwater environment of aquaculture ponds during CyHV-2 disease outbreaks. Furthermore, the results from this study can contribute to improvement of the aquatic environment and establishment of disease prevention and control measures.}, } @article {pmid31432356, year = {2020}, author = {Rabee, AE and Forster, RJ and Elekwachi, CO and Kewan, KZ and Sabra, E and Mahrous, HA and Khamiss, OA and Shawket, SM}, title = {Composition of bacterial and archaeal communities in the rumen of dromedary camel using cDNA-amplicon sequencing.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {23}, number = {2}, pages = {137-148}, doi = {10.1007/s10123-019-00093-1}, pmid = {31432356}, issn = {1618-1905}, mesh = {Animals ; *Archaea/classification/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; Camelus/*microbiology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; }, abstract = {The camel is known to survive in harsh environmental conditions, due to its higher digestive efficiency of high-fiber diets compared with other ruminants. However, limited data are available on the microbial community in the rumen of a camel. In this study, the Illumina sequencing of V4 region of 16S rRNA genes based on RNA isolation was employed to get insight into the bacterial and archaeal communities associated with liquid and solid rumen fractions in eight camels under different feeding systems. Camels in group C1 were fed Egyptian clover hay plus concentrates mixture and camels of group C2 were fed fresh Egyptian clover. The results showed that liquid fraction has higher operational taxonomic units (OTUs) than solid fraction, and camel group C1 showed a higher microbial diversity than C2. The UniFrac analysis indicated that the microbial communities in camel groups are distinct. Moreover, phylum Firmicutes and Bacteroidetes dominated the bacterial community and Candidatus Methanomethylophilus dominated the archaeal community with a significant difference in the relative abundance between camel groups. Dominant bacterial genera were Prevotella, Fibrobacteres, Ruminococcus, and Butyrivibrio. There were many negative and positive correlations between and within bacterial and archaeal genera. The composition of microbial community in the rumen of a camel is similar to other ruminants with differences in the abundance.}, } @article {pmid31431641, year = {2019}, author = {Kelly, RP and Shelton, AO and Gallego, R}, title = {Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12133}, pmid = {31431641}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Biomass ; Computer Simulation ; DNA Barcoding, Taxonomic/methods ; DNA, Environmental/*analysis ; Metagenomics/methods ; Models, Theoretical ; Polymerase Chain Reaction/*methods ; }, abstract = {As environmental DNA (eDNA) studies have grown in popularity for use in ecological applications, it has become clear that their results differ in significant ways from those of traditional, non-PCR-based surveys. In general, eDNA studies that rely on amplicon sequencing may detect hundreds of species present in a sampled environment, but the resulting species composition can be idiosyncratic, reflecting species' true biomass abundances poorly or not at all. Here, we use a set of simulations to develop a mechanistic understanding of the processes leading to the kinds of results common in mixed-template PCR-based (metabarcoding) studies. In particular, we focus on the effects of PCR cycle number and primer amplification efficiency on the results of diversity metrics in sequencing studies. We then show that proportional indices of amplicon reads capture trends in taxon biomass with high accuracy, particularly where amplification efficiency is high (median correlation up to 0.97). Our results explain much of the observed behavior of PCR-based studies, and lead to recommendations for best practices in the field.}, } @article {pmid31431446, year = {2019}, author = {Keating, JA and Shaughnessy, C and Baubie, K and Kates, AE and Putman-Buehler, N and Watson, L and Dominguez, N and Watson, K and Cook, DB and Rabago, D and Suen, G and Gangnon, R and Safdar, N}, title = {Characterising the gut microbiome in veterans with Gulf War Illness: a protocol for a longitudinal, prospective cohort study.}, journal = {BMJ open}, volume = {9}, number = {8}, pages = {e031114}, pmid = {31431446}, issn = {2044-6055}, support = {I21 CX001574/CX/CSRD VA/United States ; T15 LM007359/LM/NLM NIH HHS/United States ; }, mesh = {Biomarkers/blood ; C-Reactive Protein/analysis ; Case-Control Studies ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; Persian Gulf Syndrome/*microbiology ; Prospective Studies ; Research Design ; *Veterans ; }, abstract = {INTRODUCTION: Approximately 25%-35% of the 1991 Gulf War Veteran population report symptoms consistent with Gulf War Illness (GWI), a chronic, multi-symptom illness characterised by fatigue, pain, irritable bowel syndrome and problems with cognitive function. GWI is a disabling problem for Gulf War Veterans, and there remains a critical need to identify innovative, novel therapies.Gut microbiota perturbation plays a key role in the symptomatology of other chronic multi-symptom illnesses, including myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Given similarities between ME/CFS and GWI and the presence of gastrointestinal disorders in GWI patients, Veterans with GWI may also have gut abnormalities like those seen with ME/CFS. In this longitudinal cohort study, we are comparing the diversity (structure) and the metagenomes (function) of the gut microbiome between Gulf War Veterans with and without GWI. If we find differences in Veterans with GWI, the microbiome could be a target for therapeutic intervention to alleviate GWI symptoms.

METHODS AND ANALYSIS: Participants answer questions about diet, exercise and lifestyle factors. Participants also complete a questionnaire (based on the Kansas case definition of GWI) regarding their medical history and symptoms; we use this questionnaire to group participants into GWI versus healthy control cohorts. We plan to enrol 52 deployed Gulf War Veterans: 26 with GWI and 26 healthy controls. Participants provide stool and saliva samples weekly for an 8-week period for microbiome analyses. Participants also provide blood samples at the beginning and end of this period, which we will use to compare measures of inflammation markers between the groups.

ETHICS AND DISSEMINATION: The protocol was approved by the University of Wisconsin-Madison Health Sciences Institutional Review Board and the William S. Middleton Memorial Veterans Hospital Research and Development Committee. Results of this study will be submitted for publication in a peer-reviewed journal.}, } @article {pmid31429791, year = {2019}, author = {Casimiro-Soriguer, CS and Loucera, C and Perez Florido, J and López-López, D and Dopazo, J}, title = {Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples.}, journal = {Biology direct}, volume = {14}, number = {1}, pages = {15}, pmid = {31429791}, issn = {1745-6150}, mesh = {Biomarkers/*analysis ; Cities ; *Drug Resistance, Microbial ; *Machine Learning ; *Metabolome ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {BACKGROUND: The availability of hundreds of city microbiome profiles allows the development of increasingly accurate predictors of the origin of a sample based on its microbiota composition. Typical microbiome studies involve the analysis of bacterial abundance profiles.

RESULTS: Here we use a transformation of the conventional bacterial strain or gene abundance profiles to functional profiles that account for bacterial metabolism and other cell functionalities. These profiles are used as features for city classification in a machine learning algorithm that allows the extraction of the most relevant features for the classification.

CONCLUSIONS: We demonstrate here that the use of functional profiles not only predict accurately the most likely origin of a sample but also to provide an interesting functional point of view of the biogeography of the microbiota. Interestingly, we show how cities can be classified based on the observed profile of antibiotic resistances.

REVIEWERS: Open peer review: Reviewed by Jin Zhuang Dou, Jing Zhou, Torsten Semmler and Eran Elhaik.}, } @article {pmid31429790, year = {2019}, author = {Yue, S and He, T and Li, B and Qu, Y and Peng, H and Chen, J and Lei, M and Chen, C and Wu, W}, title = {Effectiveness of Yi-Zhi-An-Shen granules on cognition and sleep quality in older adults with amnestic mild cognitive impairment: protocol for a randomized, double-blind, placebo-controlled trial.}, journal = {Trials}, volume = {20}, number = {1}, pages = {518}, pmid = {31429790}, issn = {1745-6215}, support = {JDZX2015298//State Administration of Traditional Chinese Medicine of the People's Republic of China/ ; JDZX2015298//Chengdu Science and Technology Bureau/ ; 2018-504//Cadres Health Care Research Program of Sichuan Province (CN)/ ; 2017-501//Cadres Health Care Research Program of Sichuan Province (CN)/ ; }, mesh = {Aged ; Aged, 80 and over ; Amnesia/diagnosis/*drug therapy/physiopathology/psychology ; Biomarkers/blood ; China ; Cognition/*drug effects ; Cognitive Dysfunction/diagnosis/*drug therapy/physiopathology/psychology ; Double-Blind Method ; Drugs, Chinese Herbal/adverse effects/*therapeutic use ; Female ; Gastrointestinal Microbiome/drug effects ; Humans ; Hypnotics and Sedatives/adverse effects/*therapeutic use ; Inflammation Mediators/blood ; Male ; Memory/*drug effects ; Middle Aged ; Nootropic Agents/adverse effects/*therapeutic use ; Randomized Controlled Trials as Topic ; Sleep/*drug effects ; Time Factors ; Treatment Outcome ; }, abstract = {BACKGROUND: Amnestic mild cognitive impairment (aMCI) is a syndrome characterized by significant forgetfulness that does not meet the criteria of dementia. Individuals with aMCI are at greater risk of progressing to dementia. Current studies suggest that good sleep quality is linked with preserved cognition in the elderly, and sleep complaints are common among the elderly with amnesia. Therefore, improving their sleep may be helpful for maintaining and improving their cognitive capacity. According to the theory of traditional Chinese medicine, Yi-Zhi-An-Shen is an herbal compound which may ameliorate forgetfulness and sleep disorders. As growing evidence indicates that the gut microbiome is associated with major mental symptoms, a hypothesis was proposed that Yi-Zhi-An-Shen granules (YZASG) might work by alternating microbial abundance and diversity. In this study, the investigators intend to assess the efficacy of YZASG on global cognition in the elderly suffering from aMCI and evaluate its safety as well as its potential mechanisms via sleep quality, fecal microbial 16S ribosomal DNA and metagenomics analyses, and serum markers.

METHODS/DESIGN: This study is a randomized, double-blind, placebo-controlled clinical trial. A total of 80 patients (aged 60-85 years) will be recruited and allocated randomly to a treatment group and a placebo group in a 1:1 ratio and will then be administered YZASG or isodose placebo three times a day. The intervention course is 16 weeks, with an 18 months follow-up. The primary outcome is the Alzheimer's Disease Assessment Scale-Cognitive Subscale. Secondary outcome measures are the Mini-Mental State Examination, Montreal Cognitive Assessment, Pittsburgh Sleep Quality Index, serum concentrations of immunological factors and inflammatory cytokines, and fecal microbiota. Fecal microbiota will only be collected at the baseline and endpoint of the intervention.

DISCUSSION: The results of this trial will be conducive to assessing the safety and effectiveness on cognition of YZASG in intervening aMCI among the elderly and determining if it takes effect via the improvement of sleep quality, regulation of gut microbiota, and concentration of certain serum markers.

TRIAL REGISTRATION: ClinicalTrials.gov, NCT03601000 . Registered on 26 July 2018.}, } @article {pmid31427666, year = {2019}, author = {Li, Y and Fang, F and Wei, J and Wu, X and Cui, R and Li, G and Zheng, F and Tan, D}, title = {Humic Acid Fertilizer Improved Soil Properties and Soil Microbial Diversity of Continuous Cropping Peanut: A Three-Year Experiment.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12014}, pmid = {31427666}, issn = {2045-2322}, mesh = {*Arachis ; *Biodiversity ; Crop Production ; *Crops, Agricultural ; Enzyme Activation ; Fertilizers/*analysis ; Food Quality ; *Humic Substances/analysis ; Metagenomics/methods ; Microbiota ; Rhizosphere ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Although humic acid has been demonstrated to improve the quality of some soil types, the long-term effects of humic acid on soil under continuous cropping peanut are not fully understood. This study aimed to investigate the continuous effects of humic acid on the physicochemical properties, microbial diversity, and enzyme activities of soil under continuous cropping peanut. In this study, a three-year consecutive experiment of cropping peanut was conducted in the North China Plain. In addition to the equal nitrogen, phosphorus, and potassium inputs, humic acid treatment was applied with inorganic fertilizers. Compared with control experiments, humic acid increased the yield and quality of continuous cropping peanut. To elucidate the mechanism of humic acid affecting the soil quality, various soil quality indicators were evaluated and compared in this study. It was found that humic acid increased soil nutrient contents, including the total soil nitrogen, total phosphorus, total potassium, available nitrogen, available phosphorus, available potassium, and organic matter contents, which exhibited the maximum effect in the third year. Meanwhile, the urease, sucrase, and phosphatase activities in the soil significantly increased after treated with humic acid, of which the maturity period increased most significantly. The same results were observed for three consecutive years. Microbial diversity varied considerably according to the high throughput sequencing analysis. Specifically, the number of bacteria decreased while that of fungi increased after humic acid treatment. The abundance of Firmicutes in bacteria, Basidiomycota, and Mortierellomycota in fungi all increased, which have been reported as being beneficial to plant growth. In contrast, the abundance of Ascomycota in fungi was reduced, and most of the related genera identified are pathogenic to plants. In conclusion, humic acid improved the yield and quality of continuous cropping peanut because of improved physicochemical properties, enzymatic activities, and microbial diversity of soil, which is beneficial for alleviating the obstacles of continuous cropping peanut.}, } @article {pmid31426820, year = {2019}, author = {Li, H and Li, H and Wang, J and Guo, L and Fan, H and Zheng, H and Yang, Z and Huang, X and Chu, M and Yang, F and He, Z and Li, N and Yang, J and Wu, Q and Shi, H and Liu, L}, title = {The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites.}, journal = {Virology journal}, volume = {16}, number = {1}, pages = {105}, pmid = {31426820}, issn = {1743-422X}, mesh = {Animals ; Anti-Bacterial Agents/administration & dosage ; Bacteria/classification/*isolation & purification ; Feces/microbiology/virology ; Gastrointestinal Microbiome/*drug effects ; Longitudinal Studies ; Macaca mulatta/microbiology/virology ; Metabolic Networks and Pathways ; Metabolome ; Metagenomics ; *Microbial Interactions ; Viruses/classification/*isolation & purification ; }, abstract = {BACKGROUND: The gut microbiome is closely associated with the health of the host; although the interaction between the bacterial microbiome and the whole virome has rarely been studied, it is likely of medical importance. Examination of the interactions between the gut bacterial microbiome and virome of rhesus monkey would significantly contribute to revealing the gut microbiome composition.

METHODS: Here, we conducted a metagenomic analysis of the gut microbiome of rhesus monkeys in a longitudinal cohort treated with an antibiotic cocktail, and we documented the interactions between the bacterial microbiome and virome. The depletion of viral populations was confirmed at the species level by real-time PCR. We also detected changes in the gut metabolome by GC-MS and LC-MS.

RESULTS: A majority of bacteria were depleted after treatment with antibiotics, and the Shannon diversity index decreased from 2.95 to 0.22. Furthermore, the abundance-based coverage estimator (ACE) decreased from 104.47 to 33.84, and the abundance of eukaryotic viruses also changed substantially. In the annotation, 6 families of DNA viruses and 1 bacteriophage family were present in the normal monkeys but absent after gut bacterial microbiome depletion. Intriguingly, we discovered that changes in the gut bacterial microbiome composition may promote changes in the gut virome composition, and tryptophan, arginine, and quinone may play roles in the interaction between the bacterial microbiome and virome.

CONCLUSION: Our results indicated that the clearly altered composition of the virome was correlated with depletion in the bacterial community and that metabolites produced by bacteria possibly play important roles in the interaction.}, } @article {pmid31425594, year = {2019}, author = {Mougeot, JC and Stevens, CB and Morton, DS and Brennan, MT and Mougeot, FB}, title = {Oral Microbiome and Cancer Therapy-Induced Oral Mucositis.}, journal = {Journal of the National Cancer Institute. Monographs}, volume = {2019}, number = {53}, pages = {}, doi = {10.1093/jncimonographs/lgz002}, pmid = {31425594}, issn = {1745-6614}, mesh = {Disease Susceptibility ; Humans ; Intestinal Mucosa/metabolism/microbiology/pathology ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth Mucosa/microbiology/pathology ; Neoplasms/*complications/therapy ; Stomatitis/diagnosis/drug therapy/*etiology/prevention & control ; Systems Biology/methods ; }, abstract = {Characterization of the role of oral microbiome in cancer therapy-induced oral mucositis (CTOM) is critical in preventing the clinically deleterious effects on patients' health that are associated with CTOM. Funding initiatives related to the National Institutes of Health human microbiome project have resulted in groundbreaking advancements in biology and medicine during the last decade. These advancements have shown that a human being is in fact a superorganism made of human cells and associated symbiotic or commensal microbiota. In this review, we describe the state of science as it relates to fundamental knowledge on oral microbiome and its role in CTOM. We also discuss how state-of-the-art technologies and systems biology tools may be used to help tackle the difficult challenges ahead to develop effective treatments or preventive therapies for oral mucositis. We make a clear distinction between disease processes pertaining to the oral microbiome, which includes opportunistic pathogens that may be defined as pathobionts, and those infectious disease processes initiated by exogenous pathogens. We also explored the extent to which knowledge from the gastrointestinal tract in disease and intestinal mucositis could help us better understand CTOM pathobiology. Finally, we propose a model in which the oral microbiome participates in the current five-step CTOM pathobiology model. With the advent of more sophisticated metagenomics technologies and methods of analysis, much hope lies ahead to implement an effective holistic approach to treat cancer patients affected by CTOM.}, } @article {pmid31423298, year = {2019}, author = {Casaburi, G and Duar, RM and Vance, DP and Mitchell, R and Contreras, L and Frese, SA and Smilowitz, JT and Underwood, MA}, title = {Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria.}, journal = {Antimicrobial resistance and infection control}, volume = {8}, number = {}, pages = {131}, pmid = {31423298}, issn = {2047-2994}, support = {S10 OD018174/OD/NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*classification/drug effects/isolation & purification ; Bifidobacterium longum subspecies infantis/physiology ; Breast Feeding ; Case-Control Studies ; *Drug Resistance, Microbial ; Feces/microbiology ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Infant, Newborn ; Metagenomics/*methods ; Microbial Sensitivity Tests ; Probiotics/*administration & dosage ; Whole Genome Sequencing ; beta-Lactamases/genetics ; }, abstract = {BACKGROUND: Antibiotic-resistant (AR) bacteria are a global threat. AR bacteria can be acquired in early life and have long-term sequelae. Limiting the spread of antibiotic resistance without triggering the development of additional resistance mechanisms is of immense clinical value. Here, we show how the infant gut microbiome can be modified, resulting in a significant reduction of AR genes (ARGs) and the potentially pathogenic bacteria that harbor them.

METHODS: The gut microbiome was characterized using shotgun metagenomics of fecal samples from two groups of healthy, term breastfed infants. One group was fed B. infantis EVC001 in addition to receiving lactation support (n = 29, EVC001-fed), while the other received lactation support alone (n = 31, controls). Coliforms were isolated from fecal samples and genome sequenced, as well as tested for minimal inhibitory concentrations against clinically relevant antibiotics.

RESULTS: Infants fed B. infantis EVC001 exhibited a change to the gut microbiome, resulting in a 90% lower level of ARGs compared to controls. ARGs that differed significantly between groups were predicted to confer resistance to beta lactams, fluoroquinolones, or multiple drug classes, the majority of which belonged to Escherichia, Clostridium, and Staphylococcus. Minimal inhibitory concentration assays confirmed the resistance phenotypes among isolates with these genes. Notably, we found extended-spectrum beta lactamases among healthy, vaginally delivered breastfed infants who had never been exposed to antibiotics.

CONCLUSIONS: Colonization of the gut of breastfed infants by a single strain of B. longum subsp. infantis had a profound impact on the fecal metagenome, including a reduction in ARGs. This highlights the importance of developing novel approaches to limit the spread of these genes among clinically relevant bacteria. Future studies are needed to determine whether colonization with B. infantis EVC001 decreases the incidence of AR infections in breastfed infants.

TRIAL REGISTRATION: This clinical trial was registered at ClinicalTrials.gov, NCT02457338.}, } @article {pmid31420693, year = {2019}, author = {Carabeo-Pérez, A and Guerra-Rivera, G and Ramos-Leal, M and Jiménez-Hernández, J}, title = {Metagenomic approaches: effective tools for monitoring the structure and functionality of microbiomes in anaerobic digestion systems.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {23-24}, pages = {9379-9390}, doi = {10.1007/s00253-019-10052-5}, pmid = {31420693}, issn = {1432-0614}, mesh = {Anaerobiosis ; *Metagenome ; Metagenomics/*methods ; Methane/metabolism ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sewage ; }, abstract = {Microbial metagenome analysis has proven its usefulness to investigate the microbiomes present in technical engineered ecosystems such as anaerobic digestion systems. The analysis of the total microbial genomic DNA allows the detailed determination of both the microbial community structure and its functionality. In addition, it enables to study the response of the microbiome to alterations in technical process parameters. Strategies of functional microbial networks to face abiotic stressors, e.g., resistance, resilience, and reorganization, can be evaluated with respect to overall process optimization. The objective of this paper is to review the main metagenomic tools used for effective studies on anaerobic digestion systems in monitoring the dynamic of the microbiomes, as well as the factors that have been identified so far as limiting the metagenomic studies in this ecosystems.}, } @article {pmid31420049, year = {2019}, author = {Ryan, FJ}, title = {Application of machine learning techniques for creating urban microbial fingerprints.}, journal = {Biology direct}, volume = {14}, number = {1}, pages = {13}, pmid = {31420049}, issn = {1745-6150}, mesh = {Cities ; DNA Fingerprinting/*methods ; *Machine Learning ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {BACKGROUND: Research has found that human associated microbial communities play a role in homeostasis and the disruption of these communities may be important in an array of medical conditions. However outside of the human body many of these communities remain poorly studied. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is characterizing the microbiomes of urban environments with the aim to improve design of mass transit systems. As part of the CAMDA 2018 MetaSUB Forensics Challenge 311 city microbiome samples were provided to create urban microbial fingerprints, as well as a further 3 mystery datasets for validation.

RESULTS: MetaSUB samples were clustered using t-SNE in an unsupervised fashion to almost discrete groups, which upon inspection represented city of origin. Based on this clustering, geographically close metropolitan areas appear to display similar microbial profiles such as those of Auckland and Hamilton. Mystery unlabeled samples were provided part of the challenge. A random forest classifier built on the initial dataset of 311 samples was capable of correctly classifying 83.3% of the mystery samples to their city of origin. Random Forest analyses also identified features with the highest discriminatory power, ranking bacterial species such as Campylobacter jejuni and Staphylococcus argenteus as highly predictive of city of origin. The surface from which the sample was collected displayed little detectable impact on the microbial profiles in the data generated here. The proportion of reads classified per sample varied greatly and so de-novo assembly was applied to recover genomic fragments representing organisms not captured in reference databases.

CONCLUSIONS: Current methods can differentiate urban microbiome profiles from each other with relative ease. De-novo assembly indicated that the MetaSUB metagenomic data contains adequate depth to recover metagenomic assembled genomes and that current databases are not sufficient to fully characterize urban microbiomes. Profiles found here indicate there may be a relationship between geographical distance between areas and the urban microbiome composition although this will need further research. The impact of these different profiles on public health is currently unknown but the MetaSUB consortium is uniquely suited to evaluate these and provide a roadmap for the inclusion of urban microbiome information for city planning and public health policy.

REVIEWERS: This article was reviewed by Dimitar Vassilev, Eran Elhaik and Chengsheng Zhu.}, } @article {pmid31419942, year = {2019}, author = {Shami, A and Al-Mijalli, S and Pongchaikul, P and Al-Barrag, A and AbduRahim, S}, title = {The prevalence of the culturable human skin aerobic bacteria in Riyadh, Saudi Arabia.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {189}, pmid = {31419942}, issn = {1471-2180}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacteria, Aerobic/classification/genetics/growth & development/*isolation & purification ; Child ; Female ; Humans ; Male ; Microbiota ; Middle Aged ; Saudi Arabia ; Skin/*microbiology ; Young Adult ; }, abstract = {BACKGROUND: Human skin is an appropriate environment for the growth of different types of microbes that may inhabit the skin as commensal flora. This study aims at identifying the diversity of skin microbiota in healthy Saudi population. In this study, 80 Saudi subjects of both males and females, from different habitat, and different ages (elderly and young), were recruited to determine the aerobic bacterial flora from their three skin sites; hand, scalp and foot. A single colony obtained from aerobic culture was identified using Biomérieux VITEK® 2 system. For those not being identified by VITEK® 2 system, the identification was conducted using 16 s rRNA sequence.

RESULTS: Thirty-three bacterial species were isolated from males, whilst 24 species were isolated from females. Micrococci are the predominant organisms, followed by Staphylococci, Pantoea species, and lastly Enterococcus faecium. Acinetobacter baumannii, Enterococcus faecalis, and Klebsiella pneumoniae were only found in elder subjects, while Pseudomonas aeruginosa was isolated from the young only. The number of bacterial isolates in the elders was higher that of the young. The average number of flora was larger in foot, then hand and lastly scalp.

CONCLUSION: Here we show the difference in the number of cultivable bacteria across age and gender that may result in the variety of local skin infection. This study paves the way to further investigation in the aspect of in-depth metagenomics analysis and host-pathogen interaction.}, } @article {pmid31417554, year = {2019}, author = {Allen, JM and Jaggers, RM and Solden, LM and Loman, BR and Davies, RH and Mackos, AR and Ladaika, CA and Berg, BM and Chichlowski, M and Bailey, MT}, title = {Dietary Oligosaccharides Attenuate Stress-Induced Disruptions in Immune Reactivity and Microbial B-Vitamin Metabolism.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {1774}, pmid = {31417554}, issn = {1664-3224}, mesh = {Agonistic Behavior ; Animals ; Anti-Inflammatory Agents/*therapeutic use ; Bacteria/drug effects/isolation & purification/metabolism ; Colon/metabolism/microbiology ; Dietary Sugars/*therapeutic use ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/immunology ; Glucans/administration & dosage/pharmacology ; Interleukin-6/blood ; Male ; Metagenomics ; Mice, Inbred C57BL ; Oligosaccharides/*therapeutic use ; Prebiotics/*administration & dosage ; Random Allocation ; Ribotyping ; Single-Blind Method ; Social Behavior ; Species Specificity ; Stress, Psychological/*drug therapy/immunology/metabolism ; Tandem Mass Spectrometry ; Vitamin B Complex/*metabolism/therapeutic use ; }, abstract = {Background: Exposure to stressful stimuli dysregulates inflammatory processes and alters the gut microbiota. Prebiotics, including long-chain fermentable fibers and milk oligosaccharides, have the potential to limit inflammation through modulation of the gut microbiota. To determine whether prebiotics attenuate stress-induced inflammation and microbiota perturbations, mice were fed either a control diet or a diet supplemented with galactooligosaccharides, polydextrose and sialyllactose (GOS+PDX+SL) or sialyllactose (SL) for 2 weeks prior to and during a 6-day exposure to a social disruption stressor. Spleens were collected for immunoreactivity assays. Colon contents were examined for stressor- and diet- induced changes in the gut microbiome and metabolome through 16S rRNA gene sequencing, shotgun metagenomic sequencing and UPLC-MS/MS. Results: Stress increased circulating IL-6 and enhanced splenocyte immunoreactivity to an ex vivo LPS challenge. Diets containing GOS+PDX+SL or SL alone attenuated these responses. Stress exposure resulted in large changes to the gut metabolome, including robust shifts in amino acids, peptides, nucleotides/nucleosides, tryptophan metabolites, and B vitamins. Multiple B vitamins were inversely associated with IL-6 and were augmented in mice fed either GOS+PDX+SL or SL diets. Stressed mice exhibited distinct microbial communities with lower abundances of Lactobacillus spp. and higher abundances of Bacteroides spp. Diet supplementation with GOS+PDX+SL, but not SL alone, orthogonally altered the microbiome and enhanced the growth of Bifidobacterium spp. Metagenome-assembled genomes (MAGs) from mice fed the GOS+PDX+SL diet unveiled genes in a Bifidobacterium MAG for de novo B vitamin synthesis. B vitamers directly attenuated the stressor-induced exacerbation of cytokine production in LPS-stimulated splenocytes. Conclusions: Overall, these data indicate that colonic metabolites, including B vitamins, are responsive to psychosocial stress. Dietary prebiotics reestablish colonic B vitamins and limit stress-induced inflammation.}, } @article {pmid31415755, year = {2019}, author = {Tierney, BT and Yang, Z and Luber, JM and Beaudin, M and Wibowo, MC and Baek, C and Mehlenbacher, E and Patel, CJ and Kostic, AD}, title = {The Landscape of Genetic Content in the Gut and Oral Human Microbiome.}, journal = {Cell host & microbe}, volume = {26}, number = {2}, pages = {283-295.e8}, pmid = {31415755}, issn = {1934-6069}, support = {R00 ES023504/ES/NIEHS NIH HHS/United States ; R01 AI127250/AI/NIAID NIH HHS/United States ; T32 HG002295/HG/NHGRI NIH HHS/United States ; T32 DK110919/DK/NIDDK NIH HHS/United States ; K99 ES023504/ES/NIEHS NIH HHS/United States ; R21 ES025052/ES/NIEHS NIH HHS/United States ; P30 DK036836/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics ; Biodiversity ; Cluster Analysis ; DNA Fingerprinting ; Databases, Factual ; Gastrointestinal Tract/microbiology ; Genetic Heterogeneity ; Host Microbial Interactions ; Humans ; Metagenome/*genetics ; Metagenomics ; Microbiota/*genetics/*physiology ; Mouth/microbiology ; Multigene Family ; Phenotype ; }, abstract = {Despite substantial interest in the species diversity of the human microbiome and its role in disease, the scale of its genetic diversity, which is fundamental to deciphering human-microbe interactions, has not been quantified. Here, we conducted a cross-study meta-analysis of metagenomes from two human body niches, the mouth and gut, covering 3,655 samples from 13 studies. We found staggering genetic heterogeneity in the dataset, identifying a total of 45,666,334 non-redundant genes (23,961,508 oral and 22,254,436 gut) at the 95% identity level. Fifty percent of all genes were "singletons," or unique to a single metagenomic sample. Singletons were enriched for different functions (compared with non-singletons) and arose from sub-population-specific microbial strains. Overall, these results provide potential bases for the unexplained heterogeneity observed in microbiome-derived human phenotypes. One the basis of these data, we built a resource, which can be accessed at https://microbial-genes.bio.}, } @article {pmid31413226, year = {2019}, author = {Ward, LM and Idei, A and Nakagawa, M and Ueno, Y and Fischer, WW and McGlynn, SE}, title = {Geochemical and Metagenomic Characterization of Jinata Onsen, a Proterozoic-Analog Hot Spring, Reveals Novel Microbial Diversity including Iron-Tolerant Phototrophs and Thermophilic Lithotrophs.}, journal = {Microbes and environments}, volume = {34}, number = {3}, pages = {278-292}, pmid = {31413226}, issn = {1347-4405}, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; *Biodiversity ; Biomass ; Chemoautotrophic Growth ; Geography ; Hot Springs/*chemistry/*microbiology ; Iron/analysis/*metabolism ; Metagenomics ; Microbiota/genetics ; Oxygen/analysis/metabolism ; Phototrophic Processes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Temperature ; }, abstract = {Hydrothermal systems, including terrestrial hot springs, contain diverse geochemical conditions that vary over short spatial scales due to progressive interactions between reducing hydrothermal fluids, the oxygenated atmosphere, and, in some cases, seawater. At Jinata Onsen on Shikinejima Island, Japan, an intertidal, anoxic, iron-rich hot spring mixes with the oxygenated atmosphere and seawater over short spatial scales, creating diverse chemical potentials and redox pairs over a distance of ~10 m. We characterized geochemical conditions along the outflow of Jinata Onsen as well as the microbial communities present in biofilms, mats, and mineral crusts along its traverse using 16S rRNA gene amplicon and genome-resolved shotgun metagenomic sequencing. Microbial communities significantly changed downstream as temperatures and dissolved iron concentrations decreased and dissolved oxygen increased. Biomass was more limited near the spring source than downstream, and primary productivity appeared to be fueled by the oxidation of ferrous iron and molecular hydrogen by members of Zetaproteobacteria and Aquificae. The microbial community downstream was dominated by oxygenic Cyanobacteria. Cyanobacteria are abundant and active even at ferrous iron concentrations of ~150 μM, which challenges the idea that iron toxicity limited cyanobacterial expansion in Precambrian oceans. Several novel lineages of Bacteria are also present at Jinata Onsen, including previously uncharacterized members of the phyla Chloroflexi and Calditrichaeota, positioning Jinata Onsen as a valuable site for the future characterization of these clades.}, } @article {pmid31411705, year = {2020}, author = {Nanto-Hara, F and Kanemitsu, Y and Fukuda, S and Kikuchi, K and Asaji, K and Saigusa, D and Iwasaki, T and Ho, HJ and Mishima, E and Suzuki, T and Suzuki, C and Tsukimi, T and Matsuhashi, T and Oikawa, Y and Akiyama, Y and Kure, S and Owada, Y and Tomioka, Y and Soga, T and Ito, S and Abe, T}, title = {The guanylate cyclase C agonist linaclotide ameliorates the gut-cardio-renal axis in an adenine-induced mouse model of chronic kidney disease.}, journal = {Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association}, volume = {35}, number = {2}, pages = {250-264}, doi = {10.1093/ndt/gfz126}, pmid = {31411705}, issn = {1460-2385}, mesh = {Adenine/*toxicity ; Animals ; Cardio-Renal Syndrome/chemically induced/*drug therapy/metabolism/pathology ; Disease Models, Animal ; Disease Progression ; Fibrosis/chemically induced/drug therapy/metabolism/pathology ; Gastrointestinal Microbiome/*drug effects ; Guanylate Cyclase/*chemistry ; Guanylyl Cyclase C Agonists/*pharmacology ; Inflammation/chemically induced/drug therapy/metabolism/pathology ; Male ; Mice ; Mice, Inbred C57BL ; Peptides/*pharmacology ; Renal Insufficiency, Chronic/chemically induced/*drug therapy/metabolism/pathology ; }, abstract = {BACKGROUND: Cardiorenal syndrome is a major cause of mortality in patients with chronic kidney disease (CKD). However, the involvement of detrimental humoral mediators in the pathogenesis of cardiorenal syndrome is still controversial. Trimethylamine-N-oxide (TMAO), a hepatic metabolic product of trimethylamine generated from dietary phosphatidylcholine or carnitine derived by the gut microbiota, has been linked directly with progression of cardiovascular disease and renal dysfunction. Thus, targeting TMAO may be a novel strategy for the prevention of cardiovascular disease and chronic kidney disease.

METHODS: Linaclotide, a guanylate cyclase C agonist, was administered to adenine-induced renal failure (RF) mice and changes in renal function and levels of gut-derived uremic toxins, as well as the gut microbiota community, were analyzed using metabolomic and metagenomic methods to reveal its cardiorenal effect.

RESULTS: Linaclotide decreased the plasma levels of TMAO at a clinically used low dose of 10 μg/kg in the adenine-induced RF mouse model. At a high concentration of 100 μg/kg, linaclotide clearly improved renal function and reduced the levels of various uremic toxins. A reduction in TMAO levels following linaclotide treatment was also observed in a choline-fed pro-atherosclerotic model. Linaclotide ameliorated renal inflammation and fibrosis and cardiac fibrosis, as well as decreased the expression of collagen I, transforming growth factor-β, galectin-3 (Gal-3) and ST2 genes. Plasma levels of Gal-3 and ST2 were also reduced. Because exposure of cardiomyocytes to TMAO increased fibronectin expression, these data suggest that linaclotide reduced the levels of TMAO and various uremic toxins and may result in not only renal, but also cardiac, fibrosis. F4/80-positive macrophages were abundant in small intestinal crypts in RF mice, and this increased expression was decreased by linaclotide. Reduced colonic claudin-1 levels were also restored by linaclotide, suggesting that linaclotide ameliorated the 'leaky gut' in RF mice. Metagenomic analysis revealed that the microbial order Clostridiales could be responsible for the change in TMAO levels.

CONCLUSION: Linaclotide reduced TMAO and uremic toxin levels and could be a powerful tool for the prevention and control of the cardiorenal syndrome by modification of the gut-cardio-renal axis.}, } @article {pmid31411526, year = {2020}, author = {Peng, M and Tabashsum, Z and Patel, P and Bernhardt, C and Biswas, C and Meng, J and Biswas, D}, title = {Prevention of enteric bacterial infections and modulation of gut microbiota with conjugated linoleic acids producing Lactobacillus in mice.}, journal = {Gut microbes}, volume = {11}, number = {3}, pages = {433-452}, pmid = {31411526}, issn = {1949-0984}, mesh = {Animals ; Cecum/microbiology ; Cytokines/genetics/metabolism ; DNA, Bacterial/genetics ; Enterohemorrhagic Escherichia coli/growth & development ; Escherichia coli Infections/pathology/*prevention & control ; Female ; *Gastrointestinal Microbiome ; Ileum/microbiology ; Inflammation/genetics/microbiology ; Jejunum/microbiology ; Lacticaseibacillus casei/*physiology ; Linoleic Acids, Conjugated/metabolism/*pharmacology ; Male ; Mice ; Mice, Inbred BALB C ; Probiotics/pharmacology ; RNA, Ribosomal, 16S/genetics ; Salmonella Infections/pathology/*prevention & control ; Salmonella typhimurium/growth & development ; }, abstract = {Probiotics are recognized for outcompeting pathogenic bacteria by competitive receptor-mediated colonization and secretion of functional metabolites which are antimicrobial against certain microbes as well as improving host's gut health and immunity. Recently, we have constructed a bioactive Lactobacillus casei (LC) strain, LC[+mcra] , by inserting mcra (myosin cross-reactive antigen) gene, which stimulates the conversion of conjugated linoleic acids. In this study, we evaluated the modulation of gut microbiome and protective roles of LC[+mcra] against pathogenic Salmonella enterica serovar Typhimurium (ST) and enterohemorrhagic E. coli (EHEC) infections in BALB/cJ mice. We observed that LC[+mcra] colonized efficiently in mice gut intestine and competitively reduced the infection with ST and EHEC in various locations of small and large intestine, specifically cecum, jejunum, and ileum (p < 0.05). Positive modulation of the cecal microbiota, for example, higher relative abundances of Firmicutes, lower relative abundances of Proteobacteria, and increased bacterial species diversity/richness, was detected in ST-challenged mice pretreated with LC[+mcra] based on 16S metagenomic sequencing. Cytokine gene expression analysis indicated that mice pretreated with LC[+mcra] associated with attenuated bacterial pathogen-induced gut inflammation. Furthermore, mice fed daily with LC[+mcra] for one week could protect themselves from the impairments caused by enteric infections with ST or EHEC. These impairments include weight loss, negative hematological changes, intestinal histological alterations, and potential death. This in vivo study suggests that daily consumption of novel conjugated linoleic acids over-producing probiotic effectively improves intestinal microbiota composition and prevents/combats foodborne enteric bacterial infections with pathogenic Salmonella and diarrheagenic E. coli.}, } @article {pmid31409870, year = {2019}, author = {Swe, PM and Zakrzewski, M and Waddell, R and Sriprakash, KS and Fischer, K}, title = {High-throughput metagenome analysis of the Sarcoptes scabiei internal microbiota and in-situ identification of intestinal Streptomyces sp.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11744}, pmid = {31409870}, issn = {2045-2322}, mesh = {Animals ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; In Situ Hybridization, Fluorescence ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Sarcoptes scabiei/*microbiology ; Sodium Hypochlorite/pharmacology ; Streptomyces/*genetics ; }, abstract = {Multiple parasitic arthropods of medical importance depend on symbiotic bacteria. While the link between scabies and secondary bacterial infections causing post infective complications of Group A streptococcal and staphylococcal pyoderma is increasingly recognized, very little is known about the microbiota of Sarcoptes scabiei. Here we analyze adult female mite and egg metagenome datasets. The majority of adult mite bacterial reads matched with Enterobacteriaceae (phylum Proteobacteria), followed by Corynebacteriaceae (phylum Actinobacteria). Klebsiella was the most dominant genus (78%) and Corynebacterium constituted 9% of the assigned sequences. Scabies mite eggs had a more diverse microbial composition with sequences from Proteobacteria being the most dominant (75%), while Actinobacteria, Bacteroidetes and Firmicutes accounted for 23% of the egg microbiome sequences. DNA sequences of a potential endosymbiont, namely Streptomyces, were identified in the metagenome sequence data of both life stages. The presence of Streptomyces was confirmed by conventional PCR. Digital droplet PCR indicated higher Streptomyces numbers in adult mites compared to eggs. Streptomyces were localized histologically in the scabies mite gut and faecal pellets by Fluorescent In Situ Hybridization (FISH). Streptomyces may have essential symbiotic roles in the scabies parasite intestinal system requiring further investigation.}, } @article {pmid31409850, year = {2019}, author = {Posada-Perlaza, CE and Ramírez-Rojas, A and Porras, P and Adu-Oppong, B and Botero-Coy, AM and Hernández, F and Anzola, JM and Díaz, L and Dantas, G and Reyes, A and Zambrano, MM}, title = {Bogotá River anthropogenic contamination alters microbial communities and promotes spread of antibiotic resistance genes.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11764}, pmid = {31409850}, issn = {2045-2322}, mesh = {Colombia ; Drug Resistance, Microbial/*genetics ; Geologic Sediments/microbiology ; *Human Activities ; Humans ; Microbiota/*drug effects ; Rivers ; *Water Microbiology ; Water Pollutants, Chemical/*toxicity ; }, abstract = {The increase in antibiotic resistant bacteria has raised global concern regarding the future effectiveness of antibiotics. Human activities that influence microbial communities and environmental resistomes can generate additional risks to human health. In this work, we characterized aquatic microbial communities and their resistomes in samples collected at three sites along the Bogotá River and from wastewaters at three city hospitals, and investigated community profiles and antibiotic resistance genes (ARGs) as a function of anthropogenic contamination. The presence of antibiotics and other commonly used drugs increased in locations highly impacted by human activities, while the diverse microbial communities varied among sites and sampling times, separating upstream river samples from more contaminated hospital and river samples. Clinically relevant antibiotic resistant pathogens and ARGs were more abundant in contaminated water samples. Tracking of resistant determinants to upstream river waters and city sources suggested that human activities foster the spread of ARGs, some of which were co-localized with mobile genetic elements in assembled metagenomic contigs. Human contamination of this water ecosystem changed both community structure and environmental resistomes that can pose a risk to human health.}, } @article {pmid31408742, year = {2019}, author = {Ari, O and Karabudak, S and Kalcioglu, MT and Gunduz, AY and Durmaz, R}, title = {The bacteriome of otitis media with effusion: Does it originate from the adenoid?.}, journal = {International journal of pediatric otorhinolaryngology}, volume = {126}, number = {}, pages = {109624}, doi = {10.1016/j.ijporl.2019.109624}, pmid = {31408742}, issn = {1872-8464}, mesh = {Adenoids/*microbiology ; Child ; Child, Preschool ; Ear, Middle/*microbiology ; Female ; Humans ; Infant ; Male ; Metagenomics ; *Microbiota ; Otitis Media with Effusion/*microbiology ; RNA, Ribosomal, 16S/analysis ; }, abstract = {OBJECTIVE: The aim of this study was to evaluate the composition and the diversity of bacteriome in middle ear effusion (MEE) and adenoid specimens of pediatric patients having otitis media with effusion (OME).

MATERIALS AND METHODS: Sample collection from children with OME followed by next generation sequencing. Seventeen adenoid and 43 middle ear effusion specimens from 25 children having OME were evaluated. Microbiome analysis was performed via Ion 16S rRNA metagenomics kit.

RESULTS: Twenty-two different bacterial species were identified from all of the samples analyzed. There were variations in the prevalence and relative abundance of the bacteriome observed between adenoid and MEE samples. MEE microbiome was significantly dominated by Alloicoccus otitis (44%), Turicella otitidis (6%), and Staphylococcus auricularis (3%). Whereas, Rothia mucilaginosa (39%), R. dentocariosa (11%), S. aureus (5%), Veillonella rogosae (2%), Granulicatella elegans (2%), Granulicatella adiacens (2%), Eikenella corrodens (1%), and Prevotella nanceiensis (1%) had significantly higher relative abundance in adenoid samples. Overall, there was no statistically significant difference in alpha diversity of MEE and adenoid samples, whereas adenoid samples constituted a cluster in the beta diversity graph.

CONCLUSION: Bacteriome of MEE is mostly dominated by A. otitis yet accompanied by other bacteria with lower relative abundances suggests that OME is likely to be a polymicrobial process. Despite similarities, significant differences in relative abundances of several predominant species between bacteriome in the MEE and adenoid put the theory that OME in children is originated from the adenoids under question.}, } @article {pmid31407448, year = {2019}, author = {Sofyan, A and Uyeno, Y and Shinkai, T and Hirako, M and Kushibiki, S and Kanamori, H and Mori, S and Katayose, Y and Mitsumori, M}, title = {Metagenomic profiles of the rumen microbiota during the transition period in low-yield and high-yield dairy cows.}, journal = {Animal science journal = Nihon chikusan Gakkaiho}, volume = {90}, number = {10}, pages = {1362-1376}, doi = {10.1111/asj.13277}, pmid = {31407448}, issn = {1740-0929}, support = {//Ministry of Agriculture, Forestry and Fisheries (MAFF)/ ; //University of Tsukuba/ ; //National Agriculture and Food Research Organization (NARO)/ ; //RISET-Pro Scholarship Program of the Indonesian Ministry of Research, Technology and Higher Education (Kemenristekdikti)/ ; }, mesh = {Animals ; Cattle ; Female ; Gastrointestinal Microbiome ; Lactation ; Metagenome ; Milk ; Parturition ; Postpartum Period ; Pregnancy ; Rumen/*microbiology ; }, abstract = {We investigated potential relationships between rumen microbiota and milk production in dairy cows during the transition period. Twelve dairy cows were divided into a low-yield (LY) or high-yield (HY) group based on their milk yield. Rumen samples were taken from dairy cows at 3 weeks before parturition, and at 4, 8, and 12 weeks after parturition. 16S rDNA-based metagenomic analysis showed that diversities of rumen microbiota in both groups were similar and the number of operational taxonomic units (OTUs) was lower in the postpartum than prepartum period in both groups. The abundance of Bacteroidetes and ratio of Bacteroidetes:Firmicutes was higher in the HY than the LY group. OTUs assigned to Prevotella bryantii, Fibrobacter succinogenes, Ruminococcus albus, Butyrivibrio fibrisolvens, and Succinivibrio sp. were abundant in the HY group. These OTUs were significantly related to the propionate molar proportion of rumen fluids in the HY group. OTUs assigned to Lachnospiraceae, Bifidobacterium sp. and Saccharofermentans were dominant in the LY group. Predictive functional profiling revealed that abundance of gene families involved in amino acid and vitamin metabolism was higher in the HY than the LY group. These results suggest that the community structure and fermentation products of rumen microbiota could be associated with milk production of dairy cows.}, } @article {pmid31407303, year = {2019}, author = {Kröber, E and Eyice, Ö}, title = {Profiling of Active Microorganisms by Stable Isotope Probing-Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2046}, number = {}, pages = {151-161}, doi = {10.1007/978-1-4939-9721-3_12}, pmid = {31407303}, issn = {1940-6029}, mesh = {Cluster Analysis ; Ecosystem ; Isotope Labeling/methods ; Metabolic Networks and Pathways/genetics ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics/physiology ; Software ; }, abstract = {Stable isotope probing (SIP) provides researchers a culture-independent method to retrieve nucleic acids from active microbial populations performing a specific metabolic activity in complex ecosystems. In recent years, the use of the SIP method in microbial ecology studies has been accelerated. This is partly due to the advances in sequencing and bioinformatics tools, which enable fast and reliable analysis of DNA and RNA from the SIP experiments. One of these sequencing tools, metagenomics, has contributed significantly to the body of knowledge by providing data not only on taxonomy but also on the key functional genes in specific metabolic pathways and their relative abundances. In this chapter, we provide a general background on the application of the SIP-metagenomics approach in microbial ecology and a workflow for the analysis of metagenomic datasets using the most up-to-date bioinformatics tools.}, } @article {pmid31407040, year = {2019}, author = {Evangelista, DE and de Oliveira Arnoldi Pellegrini, V and Santo, ME and McQueen-Mason, S and Bruce, NC and Polikarpov, I}, title = {Biochemical characterization and low-resolution SAXS shape of a novel GH11 exo-1,4-β-xylanase identified in a microbial consortium.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {19}, pages = {8035-8049}, doi = {10.1007/s00253-019-10033-8}, pmid = {31407040}, issn = {1432-0614}, support = {303988/2016-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 11/21608-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 405191/2015-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; BB/I018492/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 11/20505-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 10/52362-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 440977/2016-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 15/13684-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 151963/2018-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Disaccharides/metabolism ; Endo-1,4-beta Xylanases/*chemistry/isolation & purification/*metabolism ; Enzyme Stability ; Gene Expression Profiling ; Hydrogen-Ion Concentration ; Metagenomics ; *Microbial Consortia ; Protein Conformation ; Recombinant Proteins/chemistry/isolation & purification/metabolism ; Scattering, Small Angle ; Temperature ; Xylans/metabolism ; }, abstract = {Biotechnologies that aim to produce renewable fuels, chemicals, and bioproducts from residual ligno(hemi)cellulosic biomass mostly rely on enzymatic depolymerization of plant cell walls (PCW). This process requires an arsenal of diverse enzymes, including xylanases, which synergistically act on the hemicellulose, reducing the long and complex xylan chains to oligomers and simple sugars. Thus, xylanases play a crucial role in PCW depolymerization. Until recently, the largest xylanase family, glycoside hydrolase family 11 (GH11) has been exclusively represented by endo-catalytic β-1,4- and β-1,3-xylanases. Analysis of a metatranscriptome library from a microbial lignocellulose community resulted in the identification of an unusual exo-acting GH11 β-1,4-xylanase (MetXyn11). Detailed characterization has been performed on recombinant MetXyn11 including determination of its low-resolution small-angle X-ray scattering (SAXS) molecular envelope in solution. Our results reveal that MetXyn11 is a monomeric globular enzyme that liberates xylobiose from heteroxylans as the only product. MetXyn11 has an optimal activity in a pH range from 6 to 9 and an optimal temperature of 50 °C. The enzyme maintained above 65% of its original activity in the pH range 5 to 6 after being incubated for 72 h at 50 °C. Addition of the enzyme to a commercial enzymatic cocktail (CelicCtec3) promoted a significant increase of enzymatic hydrolysis yields of hydrothermally pretreated sugarcane bagasse (16% after 24 h of hydrolysis).}, } @article {pmid31406349, year = {2019}, author = {Doan, T and Hinterwirth, A and Worden, L and Arzika, AM and Maliki, R and Abdou, A and Kane, S and Zhong, L and Cummings, ME and Sakar, S and Chen, C and Cook, C and Lebas, E and Chow, ED and Nachamkin, I and Porco, TC and Keenan, JD and Lietman, TM}, title = {Gut microbiome alteration in MORDOR I: a community-randomized trial of mass azithromycin distribution.}, journal = {Nature medicine}, volume = {25}, number = {9}, pages = {1370-1376}, pmid = {31406349}, issn = {1546-170X}, mesh = {Azithromycin/*administration & dosage ; Campylobacter/drug effects/pathogenicity ; Campylobacter Infections/*drug therapy/genetics/mortality ; Child ; Child Mortality ; Child, Preschool ; Drug Resistance, Bacterial/drug effects/genetics ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Regulation, Bacterial/drug effects ; Humans ; Macrolides/administration & dosage ; Male ; *Metagenomics ; Nigeria/epidemiology ; Sequence Analysis, RNA ; }, abstract = {The MORDOR I trial[1], conducted in Niger, Malawi and Tanzania, demonstrated that mass azithromycin distribution to preschool children reduced childhood mortality[1]. However, the large but simple trial design precluded determination of the mechanisms involved. Here we examined the gut microbiome of preschool children from 30 Nigerien communities randomized to either biannual azithromycin or placebo. Gut microbiome γ-diversity was not significantly altered (P = 0.08), but the relative abundances of two Campylobacter species, along with another 33 gut bacteria, were significantly reduced in children treated with azithromycin at the 24-month follow-up. Metagenomic analysis revealed functional differences in gut bacteria between treatment groups. Resistome analysis showed an increase in macrolide resistance gene expression in gut microbiota in communities treated with azithromycin (P = 0.004). These results suggest that prolonged mass azithromycin distribution to reduce childhood mortality reduces certain gut bacteria, including known pathogens, while selecting for antibiotic resistance.}, } @article {pmid31404163, year = {2019}, author = {Beck, BR and Park, GS and Jeong, DY and Lee, YH and Im, S and Song, WH and Kang, J}, title = {Multidisciplinary and Comparative Investigations of Potential Psychobiotic Effects of Lactobacillus Strains Isolated From Newborns and Their Impact on Gut Microbiota and Ileal Transcriptome in a Healthy Murine Model.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {269}, pmid = {31404163}, issn = {2235-2988}, mesh = {Administration, Oral ; Animals ; Circadian Rhythm ; Dopamine/blood ; Feces/microbiology ; *Gastrointestinal Microbiome ; Ileum/immunology/microbiology ; Immunologic Factors/metabolism ; Interleukin-10/metabolism ; Lacticaseibacillus casei/*growth & development/isolation & purification ; Limosilactobacillus reuteri/*growth & development/isolation & purification ; Macrophages/immunology/microbiology ; Mice ; Mice, Inbred C57BL ; *Microbial Interactions ; Probiotics/*administration & dosage ; Psychotropic Drugs/administration & dosage ; RAW 264.7 Cells ; Serotonin/blood ; *Transcriptome ; }, abstract = {Psychobiotics are probiotic microorganisms that may exert positive influence on the psychological status of the host. Studies have revealed immunological and microbiological correlations of gut microbiota and the gut-brain axis, and have investigated psychobiotics based on the findings of the gut-brain axis. Considering their mode of actions, the present study sets anti-inflammatory effect, neurotransmitter modulation, and gut microbiota modulation as three essential criteria to evaluate Lactobacillus casei ATG-F1 (F1), L. reuteri ATG-F3 (F3), and L. reuteri ATG-F4 (F4) isolated from newborns as psychobiotics candidates in a healthy mouse model and compares the results with a non-treated control group and an ampicillin-induced gut dysbiosis (Amp) group as a negative control. The F3 and F4 strains showed anti-inflammatory effects in vitro in RAW264.7 murine macrophages, and the level of anti-inflammatory cytokine interleukin (IL)-10 increased in ileums of mice orally administered with the F4 strain. Serum dopamine level significantly increased only in the F4-treated group as compared with the control group. Serum serotonin level was unaffected in Lactobacillus-treated groups, while a significant decrease in serum serotonin level was observed in the Amp group. Bacteroidetes population increased in fecal samples of the F4-treated group as compared with the control, and Bacteroidales S24-7 and Prevotellaceae population significantly increased at family level in fecal samples from the F4-treated group as compared with the control. In contrast, the Amp group showed an increase in the level of Proteobacteria and a decrease in the level of Bacteroidetes as compared with the control group. Transcriptome analysis revealed a distinctive clustering in ileums from the F4-treated group as compared to other experimental groups. In addition, the circadian rhythm pathway showed maximum enrichment in ileums of Lactobacillus-treated mice, and the F4-treated group showed the highest fold changes in circadian rhythm-related genes (Dbp, Per1, Per2, and Per3). Conclusively, L. reuteri ATG-F4 is suggested as a potential psychobiotics through demonstrations of anti-inflammatory effects, serum dopamine modulation, and gut microbiota modulation in a healthy murine model in the present study. Moreover, we carefully suggest gut circadian rhythm modulation as another important criterion of psychobiotics, which may have an important role in the gut-brain axis.}, } @article {pmid31402174, year = {2019}, author = {Sberro, H and Fremin, BJ and Zlitni, S and Edfors, F and Greenfield, N and Snyder, MP and Pavlopoulos, GA and Kyrpides, NC and Bhatt, AS}, title = {Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes.}, journal = {Cell}, volume = {178}, number = {5}, pages = {1245-1259.e14}, pmid = {31402174}, issn = {1097-4172}, support = {K08 CA184420/CA/NCI NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; S10 OD023452/OD/NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Cell Communication ; Host-Pathogen Interactions ; Humans ; Metagenome ; *Microbiota ; Open Reading Frames/genetics ; Proteins/chemistry/*metabolism ; Ribosomal Proteins/chemistry/metabolism ; Sequence Alignment ; }, abstract = {Small proteins are traditionally overlooked due to computational and experimental difficulties in detecting them. To systematically identify small proteins, we carried out a comparative genomics study on 1,773 human-associated metagenomes from four different body sites. We describe >4,000 conserved protein families, the majority of which are novel; ∼30% of these protein families are predicted to be secreted or transmembrane. Over 90% of the small protein families have no known domain and almost half are not represented in reference genomes. We identify putative housekeeping, mammalian-specific, defense-related, and protein families that are likely to be horizontally transferred. We provide evidence of transcription and translation for a subset of these families. Our study suggests that small proteins are highly abundant and those of the human microbiome, in particular, may perform diverse functions that have not been previously reported.}, } @article {pmid31401774, year = {2020}, author = {Yeruva, T and Vankadara, S and Ramasamy, S and Lingaiah, K}, title = {Identification of Potential Probiotics in the Midgut of Mulberry Silkworm, Bombyx mori Through Metagenomic Approach.}, journal = {Probiotics and antimicrobial proteins}, volume = {12}, number = {2}, pages = {635-640}, doi = {10.1007/s12602-019-09580-3}, pmid = {31401774}, issn = {1867-1314}, mesh = {Animals ; Bacteria/*classification ; Bombyx/*microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; Probiotics/isolation & purification ; }, abstract = {Microorganisms play an important role in the growth and development of numerous insect species. The mulberry silkworm, Bombyx mori (Lepidoptera), harbors several bacteria in its midgut aiding the metabolic processes; however, the variability of bacterial spp. present in the midgut and their role(s) in the growth and development of the silkworm are poorly understood. The present work compares the diversity of midgut bacterial communities in silkworms of variable voltinism (Pure Mysore, PM: multivoltine; CSR2: bivoltine and PM × CSR2: crossbreed) through metagenomics. The predominance of Enterococcus (30.30%) followed by Bacillus (16.96%) was observed in PM, whereas Lactobacillus (56.56%) followed by Enterococcus (10.58%) was seen only in CSR2. Interestingly, crossbreed midgut harbored diverse bacterial communities (36.21% Lactobacillus, 25.94% Bacillus, 8.1% Enterococcus, and 18.37% uncultured bacteria). Metagenomic profiles indicate variability in the gut bacterial population in different kinds of silkworms influencing the physiological activities accordingly. The dominant bacteria, particularly lactobacilli, bacilli, and enterococci could be further explored for identifying the potential probiotic consortia based on a literature survey and potential involvement in nutrient absorption, disease/stress tolerance, and improved economic traits.}, } @article {pmid31401751, year = {2019}, author = {Chen, J and Yu, B and Chen, D and Zheng, P and Luo, Y and Huang, Z and Luo, J and Mao, X and Yu, J and He, J}, title = {Changes of porcine gut microbiota in response to dietary chlorogenic acid supplementation.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {19}, pages = {8157-8168}, doi = {10.1007/s00253-019-10025-8}, pmid = {31401751}, issn = {1432-0614}, support = {2016TD0028//the Youth Innovation teams of animal Feed Biotechnology of Sichuan Province/ ; 2018NZDZX0005//the key Research and Development program of Sichuan Province/ ; }, mesh = {Animals ; Anti-Infective Agents/*administration & dosage ; Bacteria/classification/*drug effects/genetics ; Chlorogenic Acid/*administration & dosage ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gastrointestinal Contents/chemistry ; Gastrointestinal Microbiome/*drug effects ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Swine ; }, abstract = {Chlorogenic acids (CGA), the most abundant natural polyphenol present in human diet and plants, have attracted considerable research interest because of their broad bioactivities including the antimicrobial activity. However, little is known about their influences on intestinal bacterial communities. Here, we described a response in intestinal microbiome to CGA using a porcine model. Twenty-four weaned pigs were allotted to two groups and fed with a basal diet or a basal diet containing 1000 mg/kg CGA. Results showed that CGA significantly increased the length of the small intestine (P < 0.05) and enhanced the activity of diamine oxidase (DAO) and the concentration of MHC-II in the jejunal and ileal mucosa (P < 0.05). Moreover, the acetate concentration in ileum and cecum digesta, and the propionate and butyrate concentrations in the cecum digesta, were significantly elevated by CGA (P < 0.05). Interestingly, CGA significantly increased the total 16S rRNA gene copies and bacterial alpha diversity in the cecum (P < 0.05). The relative abundance of bacteria from phyla Firmicutes and Bacteroidetes was increased in the cecum digesta (P < 0.05), whereas the abundance of bacteria from phylum Protebacteria was decreased by CGA (P < 0.05). Importantly, pigs on CGA-containing diet had higher abundance of Lactobacillus spp., Prevotella spp., Anaerovibrio spp., and Alloprevotella spp. in the cecum (P < 0.05). Not only did our study suggest a synergic response of intestinal barrier function and microbiota to the CGA, but the result will also contribute to understanding of the mechanisms behind the CGA-modulated gut health.}, } @article {pmid31401318, year = {2019}, author = {Chen, R and Wang, J and Zhan, R and Zhang, L and Wang, X}, title = {Fecal metabonomics combined with 16S rRNA gene sequencing to analyze the changes of gut microbiota in rats with kidney-yang deficiency syndrome and the intervention effect of You-gui pill.}, journal = {Journal of ethnopharmacology}, volume = {244}, number = {}, pages = {112139}, doi = {10.1016/j.jep.2019.112139}, pmid = {31401318}, issn = {1872-7573}, mesh = {Animals ; Drugs, Chinese Herbal/therapeutic use ; Dysbiosis/microbiology ; Feces/*chemistry/*microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; Kidney Diseases/drug therapy/*microbiology ; Male ; Metabolome ; RNA, Ribosomal, 16S ; Rats, Sprague-Dawley ; Sequence Analysis, RNA ; Yang Deficiency/drug therapy/*microbiology ; }, abstract = {A myriad of evidence have shown that kidney-yang deficiency syndrome (KYDS) is associated with metabolic disorders of the intestinal microbiota, while TCMs can treat KYDS by regulating gut microbiota metabolism. However, the specific interplay between KYDS and intestinal microbiota, and the intrinsic regulation mechanism of You-gui pill (YGP) on KYDS' gut microbiota remains largely unknown so far.

MATERIALS AND METHODS: In the present study, fecal metabonomics combined with 16S rRNA gene sequencing analysis were used to explore the mutual effect between KYDS and intestinal flora, and the intrinsic regulation mechanism of YGP on KYDS's gut microbiota. Rats' feces from control (CON) group, KYDS group and YGP group were collected, and metabolomic analysis was performed using [1]H NMR technique combined with multivariate statistical analysis to obtain differential metabolites. Simultaneously, 16S rRNA gene sequencing analysis based on the Illumina HiSeq sequencing platform and ANOVA analysis were used to analyze the composition of the intestinal microbiota in the stool samples and to screen for the significant altered microbiota at the genus level. After that, MetaboAnalyst database and PICRUSt software were apply to conduct metabolic pathway analysis and functional prediction analysis of the screened differential metabolites and intestinal microbiota, respectively. What's more, Pearson correlation analysis was performed on these differential metabolites and gut microbiota.

RESULTS: Using fecal metabonomics, KYDS was found to be associated with 21 differential metabolites and seven potential metabolic pathways. These metabolites and metabolic pathways were mainly involved in amino acid metabolism, energy metabolism, methylamine metabolism, bile acid metabolism and urea cycle, and short-chain fatty acid metabolism. Through 16S rRNA gene sequencing analysis, we found that KYDS was related to eleven different intestinal microbiotas. These gut microbiota were mostly involved in amino acid metabolism, energy metabolism, nervous, endocrine, immune and digestive system, lipid metabolism, and carbohydrate metabolism. Combined fecal metabonomics and 16S rRNA gene sequencing analysis, we further discovered that KYDS was primarily linked to three gut microbiotas (i.e. Bacteroides, Desulfovibrio and [Eubacterium]_coprostanoligenes_group) and eleven related metabolites (i.e. deoxycholate, n-butyrate, valine, isoleucine, acetate, taurine, glycine, α-gluconse, β-glucose, glycerol and tryptophan) mediated various metabolic disorders (amino acid metabolism, energy metabolism, especially methylamine metabolism, bile acid metabolism and urea cycle, short-chain fatty acid metabolism. nervous, endocrine, immune and digestive system, lipid metabolism, and carbohydrate metabolism). YGP, however, had the ability to mediate four kinds of microbes (i.e. Ruminiclostridium_9, Ruminococcaceae_UCG-007, Ruminococcaceae_UCG-010, and uncultured_bacterium_f_Bacteroidales_S24-7_group) and ten related metabolites (i.e. deoxycholate, valine, isoleucine, alanine, citrulline, acetate, DMA, TMA, phenylalanine and tryptophan) mediated amino acid metabolism, especially methylamine metabolism, bile acid metabolism and urea cycle, short-chain fatty acid metabolism, endocrine, immune and digestive system, and lipid metabolism, thereby exerting a therapeutic effect on KYDS rats.

CONCLUSION: Overall, our findings have preliminary confirmed that KYDS is closely related to metabolic and microbial dysbiosis, whereas YGP can improve the metabolic disorder of KYDS by acting on intestinal microbiota. Meanwhile, this will lay the foundation for the further KYDS's metagenomic research and the use of intestinal microbiotas as drug targets to treat KYDS.}, } @article {pmid31400683, year = {2019}, author = {Ceccon, DM and Faoro, H and Lana, PDC and Souza, EM and Pedrosa, FO}, title = {Metataxonomic and metagenomic analysis of mangrove microbiomes reveals community patterns driven by salinity and pH gradients in Paranaguá Bay, Brazil.}, journal = {The Science of the total environment}, volume = {694}, number = {}, pages = {133609}, doi = {10.1016/j.scitotenv.2019.133609}, pmid = {31400683}, issn = {1879-1026}, mesh = {Bays/chemistry/*microbiology ; Brazil ; *Environmental Monitoring ; Hydrogen-Ion Concentration ; *Metagenomics ; *Microbiota ; *Salinity ; }, abstract = {While environmental drivers regulate the structure of mangrove microbial communities, their exact nature and the extent of their influence require further elucidation. By means of 16S rRNA gene-based sequencing, we determined the microbial taxonomic profiles of mangroves in the subtropical Paranaguá Bay, Brazil, considering as potential drivers: salinity, as represented by two sectors in the extremes of a salinity gradient (<5 PSU and >30 PSU); proximity to/absence of the prevailing plants, Avicennia schaueriana, Laguncularia racemosa, Rhizophora mangle, and Spartina alterniflora; and the chemical composition of the sediments. Salinity levels within the estuary had the strongest influence on microbial structure, and pH was important to separate two communities within the high salinity environment. About one fourth of the total variation in community structure resulted from covariation of salinity and the overall chemical composition, which might indicate that the chemical profile was also related to salinity. The most prevalent bacterial phyla associated with the mangrove soils analyzed included Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Cyanobacteria. Taxonomic and functional comparisons of our results for whole-genome sequencing with available data from other biomes showed that the studied microbiomes cluster first according to biome type, then to matrix type and salinity status. Metabolic functions were more conserved than organisms within mangroves and across all biomes, indicating that core functions are preserved in any of the given conditions regardless of the specific organisms harboring them.}, } @article {pmid31399606, year = {2019}, author = {Holman, LE and de Bruyn, M and Creer, S and Carvalho, G and Robidart, J and Rius, M}, title = {Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11559}, pmid = {31399606}, issn = {2045-2322}, mesh = {Animals ; Aquatic Organisms/genetics ; Biodiversity ; DNA Barcoding, Taxonomic/methods ; DNA, Environmental/*analysis/genetics ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; Environmental Monitoring/methods ; Geologic Sediments/*analysis ; Metagenomics/methods ; United Kingdom ; Water/*analysis ; }, abstract = {Environmental DNA (eDNA) surveys are increasingly being used for biodiversity monitoring, principally because they are sensitive and can provide high resolution community composition data. Despite considerable progress in recent years, eDNA studies examining how different environmental sample types can affect species detectability remain rare. Comparisons of environmental samples are especially important for providing best practice guidance on early detection and subsequent mitigation of non-indigenous species. Here we used eDNA metabarcoding of COI (cytochrome c oxidase subunit I) and 18S (nuclear small subunit ribosomal DNA) genes to compare community composition between sediment and water samples in artificial coastal sites across the United Kingdom. We first detected markedly different communities and a consistently greater number of distinct operational taxonomic units in sediment compared to water. We then compared our eDNA datasets with previously published rapid assessment biodiversity surveys and found excellent concordance among the different survey techniques. Finally, our eDNA surveys detected many non-indigenous species, including several newly introduced species, highlighting the utility of eDNA metabarcoding for both early detection and temporal / spatial monitoring of non-indigenous species. We conclude that careful consideration on environmental sample type is needed when conducting eDNA surveys, especially for studies assessing community change.}, } @article {pmid31399369, year = {2019}, author = {Thingholm, LB and Rühlemann, MC and Koch, M and Fuqua, B and Laucke, G and Boehm, R and Bang, C and Franzosa, EA and Hübenthal, M and Rahnavard, A and Frost, F and Lloyd-Price, J and Schirmer, M and Lusis, AJ and Vulpe, CD and Lerch, MM and Homuth, G and Kacprowski, T and Schmidt, CO and Nöthlings, U and Karlsen, TH and Lieb, W and Laudes, M and Franke, A and Huttenhower, C}, title = {Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition.}, journal = {Cell host & microbe}, volume = {26}, number = {2}, pages = {252-264.e10}, pmid = {31399369}, issn = {1934-6069}, support = {R01 HL144651/HL/NHLBI NIH HHS/United States ; P01 HL028481/HL/NHLBI NIH HHS/United States ; T32 HL069766/HL/NHLBI NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; R01 GM083198/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Diabetes Mellitus, Type 2/*complications ; Diet ; Dietary Supplements ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Germany ; Humans ; Iron/metabolism ; Magnesium/metabolism ; Male ; Metabolic Diseases/complications ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Multivariate Analysis ; Nutrition Assessment ; Obesity/*complications/*microbiology ; Serum/metabolism ; }, abstract = {Obesity and type 2 diabetes (T2D) are metabolic disorders that are linked to microbiome alterations. However, their co-occurrence poses challenges in disentangling microbial features unique to each condition. We analyzed gut microbiomes of lean non-diabetic (n = 633), obese non-diabetic (n = 494), and obese individuals with T2D (n = 153) from German population and metabolic disease cohorts. Microbial taxonomic and functional profiles were analyzed along with medical histories, serum metabolomics, biometrics, and dietary data. Obesity was associated with alterations in microbiome composition, individual taxa, and functions with notable changes in Akkermansia, Faecalibacterium, Oscillibacter, and Alistipes, as well as in serum metabolites that correlated with gut microbial patterns. However, microbiome associations were modest for T2D, with nominal increases in Escherichia/Shigella. Medications, including antihypertensives and antidiabetics, along with dietary supplements including iron, were significantly associated with microbiome variation. These results differentiate microbial components of these interrelated metabolic diseases and identify dietary and medication exposures to consider in future studies.}, } @article {pmid31397894, year = {2019}, author = {Lendemer, JC and Keepers, KG and Tripp, EA and Pogoda, CS and McCain, CM and Kane, NC}, title = {A taxonomically broad metagenomic survey of 339 species spanning 57 families suggests cystobasidiomycete yeasts are not ubiquitous across all lichens.}, journal = {American journal of botany}, volume = {106}, number = {8}, pages = {1090-1095}, doi = {10.1002/ajb2.1339}, pmid = {31397894}, issn = {1537-2197}, support = {1542639//National Science Foundation's/International ; 1432629//University of Colorado/International ; 1144807//New York Botanical Garden/International ; }, mesh = {Appalachian Region ; *Ascomycota ; *Lichens ; Phylogeny ; Surveys and Questionnaires ; }, abstract = {PREMISE: Lichens are fungi that enter into obligate symbioses with photosynthesizing organisms (algae, cyanobacteria). Traditional narratives of lichens as binary symbiont pairs have given way to their recognition as dynamic metacommunities. Basidiomycete yeasts, particularly of the genus Cyphobasidium, have been inferred to be widespread and important components of lichen metacommunities. Yet, the presence of basidiomycete yeasts across a wide diversity of lichen lineages has not previously been tested.

METHODS: We searched for lichen-associated cystobasidiomycete yeasts in newly generated metagenomic data from 413 samples of 339 lichen species spanning 57 families and 25 orders. The data set was generated as part of a large-scale project to study lichen biodiversity gradients in the southern Appalachian Mountains Biodiversity Hotspot of southeastern North America.

RESULTS: Our efforts detected cystobasidiomycete yeasts in nine taxa (Bryoria nadvornikiana, Heterodermia leucomelos, Lecidea roseotincta, Opegrapha vulgata, Parmotrema hypotropum, P. subsumptum, Usnea cornuta, U. strigosa, and U. subgracilis), representing 2.7% of all species sampled. Seven of these taxa (78%) are foliose (leaf-like) or fruticose (shrubby) lichens that belong to families where basidiomycete yeasts have been previously detected. In several of the nine cases, cystobasidiomycete rDNA coverage was comparable to, or greater than, that of the primary lichen fungus single-copy nuclear genomic rDNA, suggesting sampling artifacts are unlikely to account for our results.

CONCLUSIONS: Studies from diverse areas of the natural sciences have led to the need to reconceptualize lichens as dynamic metacommunities. However, our failure to detect cystobasidiomycetes in 97.3% (330 species) of the sampled species suggests that basidiomycete yeasts are not ubiquitous in lichens.}, } @article {pmid31397876, year = {2019}, author = {Happel, EM and Markussen, T and Teikari, JE and Huchaiah, V and Alneberg, J and Andersson, AF and Sivonen, K and Middelboe, M and Kisand, V and Riemann, L}, title = {Effects of allochthonous dissolved organic matter input on microbial composition and nitrogen-cycling genes at two contrasting estuarine sites.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {9}, pages = {}, doi = {10.1093/femsec/fiz123}, pmid = {31397876}, issn = {1574-6941}, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; Bacterial Proteins/*genetics/metabolism ; Baltic States ; Estuaries ; Heterotrophic Processes ; *Microbiota ; Nitrification ; Nitrogen/analysis/*metabolism ; Rivers/chemistry/*microbiology ; Seawater/chemistry/*microbiology ; }, abstract = {Heterotrophic bacteria are important drivers of nitrogen (N) cycling and the processing of dissolved organic matter (DOM). Projected increases in precipitation will potentially cause increased loads of riverine DOM to the Baltic Sea and likely affect the composition and function of bacterioplankton communities. To investigate this, the effects of riverine DOM from two different catchment areas (agricultural and forest) on natural bacterioplankton assemblages from two contrasting sites in the Baltic Sea were examined. Two microcosm experiments were carried out, where the community composition (16S rRNA gene sequencing), the composition of a suite of N-cycling genes (metagenomics) and the abundance and transcription of ammonia monooxygenase (amoA) genes involved in nitrification (quantitative PCR) were investigated. The river water treatments evoked a significant response in bacterial growth, but the effects on overall community composition and the representation of N-cycling genes were limited. Instead, treatment effects were reflected in the prevalence of specific taxonomic families, specific N-related functions and in the transcription of amoA genes. The study suggests that bacterioplankton responses to changes in the DOM pool are constrained to part of the bacterial community, whereas most taxa remain relatively unaffected.}, } @article {pmid31397240, year = {2019}, author = {Lv, Y and Qin, X and Jia, H and Chen, S and Sun, W and Wang, X}, title = {The association between gut microbiota composition and BMI in Chinese male college students, as analysed by next-generation sequencing.}, journal = {The British journal of nutrition}, volume = {122}, number = {9}, pages = {986-995}, doi = {10.1017/S0007114519001909}, pmid = {31397240}, issn = {1475-2662}, mesh = {Asian People ; Bacteria/*genetics ; Biodiversity ; *Body Mass Index ; China ; Gastrointestinal Microbiome/*genetics ; *High-Throughput Nucleotide Sequencing ; Humans ; Male ; Overweight/*microbiology ; Young Adult ; }, abstract = {Altered gut microbial ecology contributes to the development of metabolic diseases including obesity. However, studies based on different populations have generated conflicting results due to diet, environment, methodologies, etc. The aim of our study was to explore the association between gut microbiota and BMI in Chinese college students. The 16S next-generation sequencing (NGS) was used to test the gut microbiota of nine lean, nine overweight/obesity and ten normal-weight male college students. The differences in gut microbiota distribution among three groups were compared, and the relationship between the richness, diversity, composition of gut microbiota and BMI were analysed. The predominant phyla Bacteroidetes and Firmicutes were further confirmed by real-time PCR. Metagenomic biomarker discovery was conducted by linear discriminant analysis (LDA) effect size (LEfSe). NGS revealed that gut microbiota composition was different among three groups, but there was no difference in the abundance ratio of Firmicutes:Bacteroidetes. Several bacterial taxa were in linear relationship with BMI (positive relationship: uncultured bacterium (Bacteroides genus); negative relationship: Porphyromonadaceae, Acidaminococcaceae, Rikenellaceae, Desulfovibrionaceae, Blautia, Anaerotruncus, Parabacteroides, Alistipes). Moreover, gut microbiota diversity decreased with the increase in BMI. And LEfSe analysis indicated that Blautia, Anaerotruncus and its uncultured species were significantly enriched in the lean group (LDA score ≥ 3), Parasuterella and its uncultured species were significantly enriched in the overweight/obese groups (LDA score ≥ 3). In general, gut microbiota composition and microbial diversity were associated with BMI in Chinese male college students. Our results might enrich the understanding between gut microbiota and obesity.}, } @article {pmid31397054, year = {2019}, author = {Payne, D and Dunham, EC and Mohr, E and Miller, I and Arnold, A and Erickson, R and Fones, EM and Lindsay, MR and Colman, DR and Boyd, ES}, title = {Geologic legacy spanning >90 years explains unique Yellowstone hot spring geochemistry and biodiversity.}, journal = {Environmental microbiology}, volume = {21}, number = {11}, pages = {4180-4195}, doi = {10.1111/1462-2920.14775}, pmid = {31397054}, issn = {1462-2920}, support = {EAR-1820658//National Science Foundation/International ; }, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biodiversity ; Geology ; Hot Springs/*chemistry ; Metagenome ; Microbiota/*physiology ; Oxidation-Reduction ; *Parks, Recreational ; Time ; }, abstract = {Little is known about how the geological history of an environment shapes its physical and chemical properties and how these, in turn, influence the assembly of communities. Evening primrose (EP), a moderately acidic hot spring (pH 5.6, 77.4°C) in Yellowstone National Park (YNP), has undergone dramatic physicochemical change linked to seismic activity. Here, we show that this legacy of geologic change led to the development of an unusual sulphur-rich, anoxic chemical environment that supports a unique archaeal-dominated and anaerobic microbial community. Metagenomic sequencing and informatics analyses reveal that >96% of this community is supported by dissimilatory reduction or disproportionation of inorganic sulphur compounds, including a novel, deeply diverging sulphate-reducing thaumarchaeote. When compared to other YNP metagenomes, the inferred functions of EP populations were like those from sulphur-rich acidic springs, suggesting that sulphur may overprint the predominant influence of pH on the composition of hydrothermal communities. Together, these observations indicate that the dynamic geological history of EP underpins its unique geochemistry and biodiversity, emphasizing the need to consider the legacy of geologic change when describing processes that shape the assembly of communities.}, } @article {pmid31395952, year = {2019}, author = {Romero Picazo, D and Dagan, T and Ansorge, R and Petersen, JM and Dubilier, N and Kupczok, A}, title = {Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated.}, journal = {The ISME journal}, volume = {13}, number = {12}, pages = {2954-2968}, pmid = {31395952}, issn = {1751-7370}, mesh = {Animals ; Bacteria/classification/*genetics/isolation & purification ; Bacterial Physiological Phenomena ; Gills/microbiology ; Microbiota ; Mytilidae/*microbiology ; Phylogeny ; *Symbiosis ; }, abstract = {Eukaryotes are habitats for bacterial organisms where the host colonization and dispersal among individual hosts have consequences for the bacterial ecology and evolution. Vertical symbiont transmission leads to geographic isolation of the microbial population and consequently to genetic isolation of microbiotas from individual hosts. In contrast, the extent of geographic and genetic isolation of horizontally transmitted microbiota is poorly characterized. Here we show that chemosynthetic symbionts of individual Bathymodiolus brooksi mussels constitute genetically isolated subpopulations. The reconstruction of core genome-wide strains from high-resolution metagenomes revealed distinct phylogenetic clades. Nucleotide diversity and strain composition vary along the mussel life span and individual hosts show a high degree of genetic isolation. Our results suggest that the uptake of environmental bacteria is a restricted process in B. brooksi, where self-infection of the gill tissue results in serial founder effects during symbiont evolution. We conclude that bacterial colonization dynamics over the host life cycle is thus an important determinant of population structure and genome evolution of horizontally transmitted symbionts.}, } @article {pmid31393213, year = {2019}, author = {ElRakaiby, MT and Gamal-Eldin, S and Amin, MA and Aziz, RK}, title = {Hospital Microbiome Variations As Analyzed by High-Throughput Sequencing.}, journal = {Omics : a journal of integrative biology}, volume = {23}, number = {9}, pages = {426-438}, doi = {10.1089/omi.2019.0111}, pmid = {31393213}, issn = {1557-8100}, mesh = {Anti-Bacterial Agents/pharmacology ; Computational Biology/methods ; Cross Infection/epidemiology/microbiology ; Drug Resistance, Bacterial ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing ; *Hospitals/standards ; Humans ; *Metagenome ; *Metagenomics/methods ; Microbial Sensitivity Tests ; *Microbiota ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; United States ; }, abstract = {Hospital-acquired infections remain a serious threat to human life and are becoming a top public health issue. As the latest advances in sequencing technologies have allowed the unbiased identification of bacterial communities, we aimed to implement emerging omics technologies to characterize a hospital's microbiome at the center of Cairo, Egypt. To this end, we screened surfaces and inanimate objects in the hospital, focusing on bed sheets and door knobs, with additional screening for resistant microbes and resistance genes. While bacterial load and community composition were not dramatically different between door knobs of hospital units with different hygiene levels, the bacterial communities on door knob samples were richer and more diverse than those detected on bed sheets. Bacteria detected on door knobs were a mix of those associated with dust/particulate matter/debris (e.g., Bacillus, Geobacillus, Aeribacillus) and skin-associated bacteria (e.g., Staphylococcus, Corynebacterium). The latter were among the core genera shared by all analyzed samples. Conversely, bacteria that were more abundant in bed sheets were not associated with a particular source (e.g., Pseudomonas and Nitrobacter). Resistance screening indicated an expansion of a mobile beta-lactamase-encoding gene (blaTEM), reflecting its current global spread. This study is a first step toward more comprehensive screening of hospital surfaces and correlating their microbiome with hospital outbreaks or chronic infections. We conclude that, as hospitals are unique built environments, these findings can inform future infection control strategies in hospitals and health care-related built environments, and attest to the importance of the emerging hospital microbiome research field.}, } @article {pmid31387630, year = {2019}, author = {Zhu, Z and Ren, J and Michail, S and Sun, F}, title = {MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {154}, pmid = {31387630}, issn = {1474-760X}, support = {R01HD081197/NH/NIH HHS/United States ; R01 HD081197/HD/NICHD NIH HHS/United States ; R01 GM120624/GM/NIGMS NIH HHS/United States ; R01 GM131407/GM/NIGMS NIH HHS/United States ; R01GM120624/NH/NIH HHS/United States ; }, mesh = {Colorectal Neoplasms/virology ; Diabetes Mellitus, Type 2/virology ; *Disease ; High-Throughput Nucleotide Sequencing ; Humans ; Liver Cirrhosis/virology ; Metagenomics/*methods ; Microbiota/*genetics ; *Software ; *Virus Physiological Phenomena ; }, abstract = {We develop a metagenomic data analysis pipeline, MicroPro, that takes into account all reads from known and unknown microbial organisms and associates viruses with complex diseases. We utilize MicroPro to analyze four metagenomic datasets relating to colorectal cancer, type 2 diabetes, and liver cirrhosis and show that including reads from unknown organisms significantly increases the prediction accuracy of the disease status for three of the four datasets. We identify new microbial organisms associated with these diseases and show viruses play important prediction roles in colorectal cancer and liver cirrhosis, but not in type 2 diabetes. MicroPro is freely available at https://github.com/zifanzhu/MicroPro .}, } @article {pmid31387544, year = {2019}, author = {Qi, K and Men, X and Wu, J and Xu, Z}, title = {Rearing pattern alters porcine myofiber type, fat deposition, associated microbial communities and functional capacity.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {181}, pmid = {31387544}, issn = {1471-2180}, support = {27304C2054/ES/NIEHS NIH HHS/United States ; }, mesh = {Adipose Tissue/chemistry/metabolism ; Animal Husbandry/*methods ; Animals ; Bacteria/classification/genetics/isolation & purification ; Fats/*metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Meat/analysis ; Microbiota ; Muscles/chemistry/*metabolism ; Myofibrils/chemistry/metabolism ; Swine/*growth & development/*metabolism/microbiology ; Taste ; }, abstract = {BACKGROUND: The Chinese believe that the meat of pigs reared in the past with free range tastes better than that of the pigs reared indoor on a large scale today. Gastrointestinal microflora is closely associated with the main factor of meat flavour, including fibre characteristics and lipid metabolism. Our method in this study involved different raising patterns within the semi free-grazing farm (FF) or indoor feeding farm (DF), the measurement of fat deposition and myofiber type by paraffin section and reverse transcription polymerase chain reaction and the identification of microbiome and functional capacities associated with meat quality through metagenomic sequencing.

RESULTS: Results showed that the fat area in muscle and adipose tissue and the myofiber density significantly increased in the pigs of the FF group. The relative abundance of bacteria associated with lipid metabolism, such as g_Oscillibacter, in the feces of the FF group was higher than that in DF group, and the relative abundance of some bacteria with probiotic function, including g_Lactobacillus and g_Clostridium, was lower than that in DF group. The abundance of g_Clostridium was significantly positively correlated with the intramuscular fat area, whereas health-related bacteria, such as g_Butyricicoccus, g_Eubacterium, g_Phascolarctobacterium and g_Oribacterium, was significantly negatively correlated with abdominal fat area, myofiber density and adipose triglyceride lipase (ATGL) mRNA expression. KEGG analysis showed that pigs raised in semi free-grazing farm can activate the pathway of inosine monophosphate (IMP) biosynthesis, glycolysis/gluconeogenesis and alanine, aspartate and glutamate metabolism.

CONCLUSIONS: Free range feeding improves meat quality by changing the fibre type, myofiber density and metabolic pathways related to flavour amino acids, IMP or glycolysis/gluconeogenesis in muscle. However, prolonged feeding cycle increases fat deposition and associated microbial communities.}, } @article {pmid31384000, year = {2019}, author = {Džunková, M and Low, SJ and Daly, JN and Deng, L and Rinke, C and Hugenholtz, P}, title = {Defining the human gut host-phage network through single-cell viral tagging.}, journal = {Nature microbiology}, volume = {4}, number = {12}, pages = {2192-2203}, pmid = {31384000}, issn = {2058-5276}, mesh = {Bacteria/genetics/virology ; Bacteriophages/genetics/isolation & purification/*physiology ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Gene Transfer, Horizontal ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Host Microbial Interactions/genetics/*physiology ; Humans ; Metagenome ; Microbial Interactions/genetics/*physiology ; Sequence Analysis, DNA ; Species Specificity ; Viruses/genetics ; }, abstract = {Viral discovery is accelerating at an unprecedented rate due to continuing advances in culture-independent sequence-based analyses. One important facet of this discovery is identification of the hosts of these recently characterized uncultured viruses. To this end, we have adapted the viral tagging approach, which bypasses the need for culture-based methods to identify host-phage pairings. Fluorescently labelled anonymous virions adsorb to unlabelled anonymous bacterial host cells, which are then individually sorted as host-phage pairs, followed by genome amplification and high-throughput sequencing to establish the identities of both the host and the attached virus(es). We demonstrate single-cell viral tagging using the faecal microbiome, including cross-tagging of viruses and bacteria between human subjects. A total of 363 unique host-phage pairings were predicted, most of which were subject-specific and involved previously uncharacterized viruses despite the majority of their bacterial hosts having known taxonomy. One-fifth of these pairs were confirmed by multiple individual tagged cells. Viruses targeting more than one bacterial species were conspicuously absent in the host-phage network, suggesting that phages are not major vectors of inter-species horizontal gene transfer in the human gut. A high level of cross-reactivity between phages and bacteria from different subjects was noted despite subject-specific viral profiles, which has implications for faecal microbiota transplant therapy.}, } @article {pmid31383878, year = {2019}, author = {d'Humières, C and Touchon, M and Dion, S and Cury, J and Ghozlane, A and Garcia-Garcera, M and Bouchier, C and Ma, L and Denamur, E and P C Rocha, E}, title = {A simple, reproducible and cost-effective procedure to analyse gut phageome: from phage isolation to bioinformatic approach.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11331}, pmid = {31383878}, issn = {2045-2322}, mesh = {Bacteriophages/*genetics/isolation & purification ; Computational Biology ; Cost-Benefit Analysis ; Feces ; Genome, Viral ; Humans ; Intestines/*virology ; Metagenome/*genetics ; Metagenomics ; Microbiota/genetics ; *Phylogeny ; }, abstract = {The microbiota of the human gut is a complex and rich community where bacteria and their viruses, the bacteriophages, are dominant. There are few studies on the phage community and no clear standard for isolating them, sequencing and analysing their genomes. Since this makes comparisons between studies difficult, we aimed at defining an easy, low-cost, and reproducible methodology. We analysed five different techniques to isolate phages from human adult faeces and developed an approach to analyse their genomes in order to quantify contamination and classify phage contigs in terms of taxonomy and lifestyle. We chose the polyethylene glycol concentration method to isolate phages because of its simplicity, low cost, reproducibility, and of the high number and diversity of phage sequences that we obtained. We also tested the reproducibility of this method with multiple displacement amplification (MDA) and showed that MDA severely decreases the phage genetic diversity of the samples and the reproducibility of the method. Lastly, we studied the influence of sequencing depth on the analysis of phage diversity and observed the beginning of a plateau for phage contigs at 20,000,000 reads. This work contributes to the development of methods for the isolation of phages in faeces and for their comparative analysis.}, } @article {pmid31379808, year = {2019}, author = {Dhakal, S and Wang, L and Antony, L and Rank, J and Bernardo, P and Ghimire, S and Bondra, K and Siems, C and Lakshmanappa, YS and Renu, S and Hogshead, B and Krakowka, S and Kauffman, M and Scaria, J and LeJeune, JT and Yu, Z and Renukaradhya, GJ}, title = {Amish (Rural) vs. non-Amish (Urban) Infant Fecal Microbiotas Are Highly Diverse and Their Transplantation Lead to Differences in Mucosal Immune Maturation in a Humanized Germfree Piglet Model.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {1509}, pmid = {31379808}, issn = {1664-3224}, mesh = {Amish ; Animals ; Fecal Microbiota Transplantation/methods ; Feces/*microbiology ; Firmicutes/immunology ; Gastrointestinal Microbiome/*immunology ; Humans ; Infant ; Metagenome/immunology ; Microbiota/*immunology ; Mucous Membrane/*immunology/*microbiology ; Swine ; }, abstract = {The gut microbiome plays an important role in the immune system development, maintenance of normal health status, and in disease progression. In this study, we comparatively examined the fecal microbiomes of Amish (rural) and non-Amish (urban) infants and investigated how they could affect the mucosal immune maturation in germ-free piglets that were inoculated with the two types of infant fecal microbiota (IFM). Differences in microbiome diversity and structure were noted between the two types of fecal microbiotas. The fecal microbiota of the non-Amish (urban) infants had a greater relative abundance of Actinobacteria and Bacteroidetes phyla, while that of the Amish (rural) counterparts was dominated by Firmicutes. Amish infants had greater species richness compared with the non-Amish infants' microbiota. The fecal microbiotas of the Amish and the non-Amish infants were successfully transplanted into germ-free piglets, and the diversity and structure of the microbiota in the transplanted piglets remained similar at phylum level but not at the genus level. Principal coordinates analysis (PCoA) based on Weighted-UniFrac distance revealed distinct microbiota structure in the intestines of the transplanted piglets. Shotgun metagenomic analysis also revealed clear differences in functional diversity of fecal microbiome between Amish and non-Amish donors as well as microbiota transplanted piglets. Specific functional features were enriched in either of the microbiota transplanted piglet groups directly corresponding to the predominance of certain bacterial populations in their gut environment. Some of the colonized bacterial genera were correlated with the frequency of important lymphoid and myeloid immune cells in the ileal submucosa and mesenteric lymph nodes (MLN), both important for mucosal immune maturation. Overall, this study demonstrated that transplantation of diverse IFM into germ-free piglets largely recapitulates the differences in gut microbiota structure between rural (Amish) and urban (non-Amish) infants. Thus, fecal microbiota transplantation to germ-free piglets could be a useful large animal model system for elucidating the impact of gut microbiota on the mucosal immune system development. Future studies can focus on determining the additional advantages of the pig model over the rodent model.}, } @article {pmid31379089, year = {2019}, author = {Marquina, D and Esparza-Salas, R and Roslin, T and Ronquist, F}, title = {Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches.}, journal = {Molecular ecology resources}, volume = {19}, number = {6}, pages = {1516-1530}, pmid = {31379089}, issn = {1755-0998}, support = {642241//European Union's Horizon 2020/ ; 2014-05901//Swedish Research Council/ ; }, mesh = {Animals ; Arthropods/*genetics ; Biodiversity ; DNA/genetics ; DNA Barcoding, Taxonomic/methods ; DNA Primers/genetics ; Ethanol/chemistry ; Metagenomics/methods ; Soil ; }, abstract = {DNA metabarcoding allows the analysis of insect communities faster and more efficiently than ever before. However, metabarcoding can be conducted through several approaches, and the consistency of results across methods has rarely been studied. We compare the results obtained by DNA metabarcoding of the same communities using two different markers - COI and 16S - and three different sampling methods: (a) homogenized Malaise trap samples (homogenate), (b) preservative ethanol from the same samples, and (c) soil samples. Our results indicate that COI and 16S offer partly complementary information on Malaise trap samples, with each marker detecting a significant number of species not detected by the other. Different sampling methods offer highly divergent estimates of community composition. The community recovered from preservative ethanol of Malaise trap samples is significantly different from that recovered from homogenate. Small and weakly sclerotized insects tend to be overrepresented in ethanol while strong and large taxa are overrepresented in homogenate. For soil samples, highly degenerate COI primers pick up large amounts of nontarget DNA and only 16S provides adequate analyses of insect diversity. However, even with 16S, very little overlap in molecular operational taxonomic unit (MOTU) content was found between the trap and the soil samples. Our results demonstrate that none of the tested sampling approaches is satisfactory on its own. For instance, DNA extraction from preservative ethanol is not a valid replacement for destructive bulk extraction but a complement. In future metabarcoding studies, both should ideally be used together to achieve comprehensive representation of the target community.}, } @article {pmid31376240, year = {2020}, author = {Kuperman, AA and Zimmerman, A and Hamadia, S and Ziv, O and Gurevich, V and Fichtman, B and Gavert, N and Straussman, R and Rechnitzer, H and Barzilay, M and Shvalb, S and Bornstein, J and Ben-Shachar, I and Yagel, S and Haviv, I and Koren, O}, title = {Deep microbial analysis of multiple placentas shows no evidence for a placental microbiome.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {127}, number = {2}, pages = {159-169}, doi = {10.1111/1471-0528.15896}, pmid = {31376240}, issn = {1471-0528}, support = {FP7-PEOPLE-2013-CIG-630956//The Marie Curie International Reintegration Grant/International ; 3-0000-10451//The Israeli Ministry of Health/International ; }, mesh = {Amniotic Fluid/immunology/*microbiology ; Animals ; Female ; Gastrointestinal Microbiome/immunology/*physiology ; Humans ; Immunohistochemistry ; Metagenomics ; Mice ; Microbiota/*genetics ; Placenta/immunology/*microbiology ; Pregnancy ; RNA, Ribosomal, 16S/genetics/*physiology ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: To resolve the controversy regarding the presence of a microbiota in the placenta.

DESIGN: Classical and molecular microbiological study.

SETTING: All samples were collected during caesarean section.

POPULATION: A total of 28 human placentas and six murine placentas.

METHODS: All 28 human placentas were checked for 16S rRNA gene amplification products. Three locations from four selected human placentas and three 'environmental controls' for each placenta were placed in seven culture media. The four selected human placentas were further analysed using Gram stain, immunohistochemistry for bacteria, electron microscopy, and TaqMan RT-qPCR. Six placentas from three SPF mice were cut into four pieces each, and further analysed for 16S rRNA gene amplification.

MAIN OUTCOME MEASURES: Microbiological and molecular evidence of bacteria.

RESULTS: None of the placental cultures used for the full analysis, or their environmental cultures, was positive for bacterial growth. None of the other methods showed any evidence of bacteria. Immunohistochemistry showed negligible bacterial counts. None of the murine placentas showed evidence of 16S rRNA gene amplification.

CONCLUSIONS: Our results support that the fetal environment in the womb is sterile. Based on the immunohistochemistry and the limit of detection of the other methods used, if a placental microbiome exists, it is of extreme low biomass, and thus its effect on clinical phenotypes is probably minor, if it exists at all.

TWEETABLE ABSTRACT: Using several microbiological and molecular methods in parallel, we found no compelling evidence of bacteria in human and mouse placentas.}, } @article {pmid31376000, year = {2020}, author = {Cowan, DA and Hopkins, DW and Jones, BE and Maggs-Kölling, G and Majewska, R and Ramond, JB}, title = {Microbiomics of Namib Desert habitats.}, journal = {Extremophiles : life under extreme conditions}, volume = {24}, number = {1}, pages = {17-29}, pmid = {31376000}, issn = {1433-4909}, mesh = {Bacteria ; Desert Climate ; *Ecosystem ; Soil ; Soil Microbiology ; }, abstract = {The Namib Desert is one of the world's only truly coastal desert ecosystem. Until the end of the 1st decade of the twenty-first century, very little was known of the microbiology of this southwestern African desert, with the few reported studies being based solely on culture-dependent approaches. However, from 2010, an intense research program was undertaken by researchers from the University of the Western Cape Institute for Microbial Biotechnology and Metagenomics, and subsequently the University of Pretoria Centre for Microbial Ecology and Genomics, and their collaborators, led to a more detailed understanding of the ecology of the indigenous microbial communities in many Namib Desert biotopes. Namib Desert soils and the associated specialized niche communities are inhabited by a wide array of prokaryotic, lower eukaryotic and virus/phage taxa. These communities are highly heterogeneous on both small and large spatial scales, with community composition impacted by a range of macro- and micro-environmental factors, from water regime to soil particle size. Community functionality is also surprisingly non-homogeneous, with some taxa retaining functionality even under hyper-arid soil conditions, and with subtle changes in gene expression and phylotype abundances even on diel timescales. Despite the growing understanding of the structure and function of Namib Desert microbiomes, there remain enormous gaps in our knowledge. We have yet to quantify many of the processes in these soil communities, from regional nutrient cycling to community growth rates. Despite the progress that has been made, we still have little knowledge of either the role of phages in microbial community dynamics or inter-species interactions. Furthermore, the intense research efforts of the past decade have highlighted the immense scope for future microbiological research in this dynamic, enigmatic and charismatic region of Africa.}, } @article {pmid31375138, year = {2019}, author = {Bickhart, DM and Watson, M and Koren, S and Panke-Buisse, K and Cersosimo, LM and Press, MO and Van Tassell, CP and Van Kessel, JAS and Haley, BJ and Kim, SW and Heiner, C and Suen, G and Bakshy, K and Liachko, I and Sullivan, ST and Myer, PR and Ghurye, J and Pop, M and Weimer, PJ and Phillippy, AM and Smith, TPL}, title = {Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {153}, pmid = {31375138}, issn = {1474-760X}, support = {R43 AI122654/AI/NIAID NIH HHS/United States ; R44 AI122654/AI/NIAID NIH HHS/United States ; R44 AI150008/AI/NIAID NIH HHS/United States ; R44AI122654-02A1//National Institute of Allergy and Infectious Diseases (US)/International ; }, mesh = {Animals ; Cattle ; Clustered Regularly Interspaced Short Palindromic Repeats ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; Genes, Microbial ; Metagenomics/*methods ; Microbiota/*genetics ; Open Reading Frames ; Prophages/genetics ; Rumen/microbiology/virology ; Sequence Analysis, DNA/*methods ; Viruses/*genetics/isolation & purification ; }, abstract = {We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.}, } @article {pmid31374328, year = {2020}, author = {Nakasaki, K and Nguyen, KK and Ballesteros, FC and Maekawa, T and Koyama, M}, title = {Characterizing the microbial community involved in anaerobic digestion of lipid-rich wastewater to produce methane gas.}, journal = {Anaerobe}, volume = {61}, number = {}, pages = {102082}, doi = {10.1016/j.anaerobe.2019.102082}, pmid = {31374328}, issn = {1095-8274}, mesh = {*Anaerobiosis ; *Biodegradation, Environmental ; *Biotransformation ; Fermentation ; Glycerol/metabolism ; Metagenome ; Metagenomics/methods ; Methane/*biosynthesis ; *Microbiota ; Sewage/microbiology ; Wastewater/*microbiology ; }, abstract = {This study attempted to characterize the microbial community and its role in anaerobic digestion of lipid. Reactors were fed semi-continuously with three related substrates, oil and its degradation intermediates (glycerol and long chain fatty acids (LCFAs)), with a stepwise increase in organic loading rate for 90 days. Microbial community analysis using next-generation sequencing (NGS) with the MiSeq Illumina platform revealed that Anaerolineaceae was the most dominant group of bacteria in all experiments, whereas Clostridium, Desulfovibrio, Rikenellaceae, and Treponema were observed characteristically in glycerol degradation and Leptospirales, Synergistaceae, Thermobaculaceae and Syntrophaceae were seen with high abundance in LCFA and oil mineralization. Furthermore, it was discovered that Methanosaeta was the most dominant archaea. The role of these microorganisms in the methane production from oil was estimated by comparing the microbial groups in the fermentation using three substrates, and a hypothetical pathway of the methane production was proposed.}, } @article {pmid31373933, year = {2019}, author = {Raj, AS and Shanahan, ER and Tran, CD and Bhat, P and Fletcher, LM and Vesey, DA and Morrison, M and Holtmann, G and Macdonald, GA}, title = {Dysbiosis of the Duodenal Mucosal Microbiota Is Associated With Increased Small Intestinal Permeability in Chronic Liver Disease.}, journal = {Clinical and translational gastroenterology}, volume = {10}, number = {8}, pages = {e00068}, pmid = {31373933}, issn = {2155-384X}, mesh = {Adult ; Aged ; Chronic Disease ; DNA, Bacterial/isolation & purification ; Disease Progression ; Duodenum/microbiology/*pathology ; Dysbiosis/diagnosis/microbiology/*pathology ; Female ; Gastrointestinal Microbiome/genetics ; Humans ; Intestinal Mucosa/microbiology/*pathology ; Liver/*pathology ; Liver Diseases/complications/*diagnosis/microbiology/pathology ; Male ; Middle Aged ; Permeability ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVES: Chronic liver disease (CLD) is associated with both alterations of the stool microbiota and increased small intestinal permeability. However, little is known about the role of the small intestinal mucosa-associated microbiota (MAM) in CLD. The aim of this study was to evaluate the relationship between the duodenal MAM and both small intestinal permeability and liver disease severity in CLD.

METHODS: Subjects with CLD and a disease-free control group undergoing routine endoscopy underwent duodenal biopsy to assess duodenal MAM by 16S rRNA gene sequencing. Small intestinal permeability was assessed by a dual sugar (lactulose: rhamnose) assay. Other assessments included transient elastography, endotoxemia, serum markers of hepatic inflammation, dietary intake, and anthropometric measurements.

RESULTS: Forty-six subjects (35 with CLD and 11 controls) were assessed. In subjects with CLD, the composition (P = 0.02) and diversity (P < 0.01) of the duodenal MAM differed to controls. Constrained multivariate analysis and linear discriminate effect size showed this was due to Streptococcus-affiliated lineages. Small intestinal permeability was significantly higher in CLD subjects compared to controls. In CLD, there were inverse correlations between microbial diversity and both increased small intestinal permeability (r = -0.41, P = 0.02) and serum alanine aminotransferase (r = -0.35, P = 0.04). Hepatic stiffness was not associated with the MAM.

DISCUSSION: In CLD, there is dysbiosis of the duodenal MAM and an inverse correlation between microbial diversity and small intestinal permeability.

TRANSLATIONAL IMPACT: Strategies to ameliorate duodenal MAM dysbiosis may ameliorate intestinal barrier dysfunction and liver injury in CLD.}, } @article {pmid31373710, year = {2019}, author = {Koopman, N and Molinaro, A and Nieuwdorp, M and Holleboom, AG}, title = {Review article: can bugs be drugs? The potential of probiotics and prebiotics as treatment for non-alcoholic fatty liver disease.}, journal = {Alimentary pharmacology & therapeutics}, volume = {50}, number = {6}, pages = {628-639}, doi = {10.1111/apt.15416}, pmid = {31373710}, issn = {1365-2036}, support = {016.146.327//ZONMW-VIDI/International ; //Dutch Heart Foundation/International ; //Gilead Research scholarship/International ; //Amsterdam UMC Fellowship/International ; //TKI-PPP/International ; }, mesh = {Animals ; Bariatric Surgery ; Fecal Microbiota Transplantation ; Humans ; Microbiota ; Non-alcoholic Fatty Liver Disease/*therapy ; *Prebiotics ; Probiotics/*therapeutic use ; Synbiotics ; }, abstract = {BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) has become the most common chronic liver condition. A major current research effort is ongoing to find potential strategies to treat NAFLD-non-alcoholic steatohepatitis (NASH), with special attention to the gut microbiota. Multiple animal studies and pilot clinical trials are assessing different gut microbiota modulating strategies such as faecal microbiota transplantation, antibiotics, probiotics, prebiotics and synbiotics.

AIM: To review the role of microbiota in NAFLD-NASH and determine whether pro- and prebiotics have potential as treatment METHODS: Information was obtained from critically reviewing literature on PubMed on targeting the gut microbiota in NAFLD. Search terms included NAFLD, NASH, non-alcoholic fatty liver disease, steatohepatitis; combined with microbiome, microbiota, gut bacteria, probiotics and prebiotics.

RESULTS: Animal studies and the first emerging studies in humans show promising results for both the common probiotics Lactobacillus, Bifidobacterium and Streptococci as for short chain fatty acid (SCFA) butyrate-producing bacteria. Also, prebiotics have positive effects on different mechanisms underlying NAFLD-NASH.

CONCLUSIONS: The most promising strategies thus far developed to alter the microbiome in NAFLD-NASH are probiotics and prebiotics. However, pre- and probiotic treatment of NAFLD-NASH is relatively new and still under development. Actual understanding of the involved mechanisms is lacking and changes in the intestinal microbiota composition after treatment are rarely measured. Furthermore, large clinical trials with comparative endpoints are unavailable. Personalised treatment based on metagenomics gut microbiota analysis will probably be part of the future diagnosis and treatment of NAFLD-NASH.}, } @article {pmid31373310, year = {2019}, author = {Peric, A and Weiss, J and Vulliemoz, N and Baud, D and Stojanov, M}, title = {Bacterial Colonization of the Female Upper Genital Tract.}, journal = {International journal of molecular sciences}, volume = {20}, number = {14}, pages = {}, pmid = {31373310}, issn = {1422-0067}, mesh = {Bacteroidetes/genetics/isolation & purification ; Fallopian Tubes/*microbiology ; Female ; Humans ; Lactobacillus/genetics/*isolation & purification ; Microbiota/physiology ; Ovary/*microbiology ; Placenta/*microbiology ; Pregnancy ; Proteobacteria/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Uterus/*microbiology ; }, abstract = {Bacteria colonize most of the human body, and the female genital tract is not an exception. While the existence of a vaginal microbiota has been well established, the upper genital tract has been considered a sterile environment, with a general assumption that bacterial presence is associated with adverse clinical manifestation. However, recent metagenomic studies identified specific patterns of microbiota colonizing the uterus, fallopian tubes, ovaries, and placenta. These results need confirmation and further investigations since the data are only scarce. Bacterial colonization of these sites appears different from the vaginal one, despite evidence that vaginal bacteria could ascend to the upper genital tract through the cervix. Are these bacteria only commensal or do they play a role in the physiology of the female upper genital tract? Which are the genera that may have a negative and a positive impact on the female reproductive function? The aim of this review is to critically present all available data on upper genital tract microbiota and discuss its role in human reproduction, ranging from the technical aspects of these types of analyses to the description of specific bacterial genera. Although still very limited, research focusing on genital colonization of bacteria other than the vaginal milieu might bring novel insights into physiopathology of human reproduction.}, } @article {pmid31372685, year = {2020}, author = {Cania, B and Vestergaard, G and Kublik, S and Köhne, JM and Fischer, T and Albert, A and Winkler, B and Schloter, M and Schulz, S}, title = {Biological Soil Crusts from Different Soil Substrates Harbor Distinct Bacterial Groups with the Potential to Produce Exopolysaccharides and Lipopolysaccharides.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {326-341}, pmid = {31372685}, issn = {1432-184X}, support = {SCHU 2907/4-1//Deutsche Forschungsgemeinschaft/ ; TRR 38/2 2011 B04//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Bacteria/genetics/*metabolism ; Lipopolysaccharides/metabolism ; Microbiota/*genetics ; Polysaccharides, Bacterial/*metabolism ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Biological soil crusts (biocrusts) play an important role in improving soil stability and resistance to erosion by promoting aggregation of soil particles. During initial development, biocrusts are dominated by bacteria. Some bacterial members of the biocrusts can contribute to the formation of soil aggregates by producing exopolysaccharides and lipopolysaccharides that act as "glue" for soil particles. However, little is known about the dynamics of "soil glue" producers during the initial development of biocrusts. We hypothesized that different types of initial biocrusts harbor distinct producers of adhesive polysaccharides. To investigate this, we performed a microcosm experiment, cultivating biocrusts on two soil substrates. High-throughput shotgun sequencing was used to obtain metagenomic information on microbiomes of bulk soils from the beginning of the experiment, and biocrusts sampled after 4 and 10 months of incubation. We discovered that the relative abundance of genes involved in the biosynthesis of exopolysaccharides and lipopolysaccharides increased in biocrusts compared with bulk soils. At the same time, communities of potential "soil glue" producers that were highly similar in bulk soils underwent differentiation once biocrusts started to develop. In the bulk soils, the investigated genes were harbored mainly by Betaproteobacteria, whereas in the biocrusts, the major potential producers of adhesive polysaccharides were, aside from Alphaproteobacteria, either Cyanobacteria or Chloroflexi and Acidobacteria. Overall, our results indicate that the potential to form exopolysaccharides and lipopolysaccharides is an important bacterial trait for initial biocrusts and is maintained despite the shifts in bacterial community composition during biocrust development.}, } @article {pmid31371784, year = {2019}, author = {Knapik, K and Becerra, M and González-Siso, MI}, title = {Microbial diversity analysis and screening for novel xylanase enzymes from the sediment of the Lobios Hot Spring in Spain.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11195}, pmid = {31371784}, issn = {2045-2322}, mesh = {Archaea/enzymology/genetics ; Archaeal Proteins/chemistry/genetics/isolation & purification/metabolism ; Bacteria/enzymology/genetics ; Bacterial Proteins/chemistry/genetics/isolation & purification/metabolism ; DNA, Environmental/*genetics/isolation & purification ; Disaccharides/metabolism ; Endo-1,4-beta Xylanases/chemistry/genetics/*isolation & purification/metabolism ; Enzyme Assays ; Enzyme Stability ; Extremophiles/*enzymology/genetics ; Geologic Sediments/*microbiology ; Hot Springs/*microbiology ; Industrial Microbiology/methods ; Metagenome ; Microbiota/genetics ; Open Reading Frames/genetics ; Spain ; }, abstract = {Here, we describe the metagenome composition of a microbial community in a hot spring sediment as well as a sequence-based and function-based screening of the metagenome for identification of novel xylanases. The sediment was collected from the Lobios Hot Spring located in the province of Ourense (Spain). Environmental DNA was extracted and sequenced using Illumina technology, and a total of 3.6 Gbp of clean paired reads was produced. A taxonomic classification that was obtained by comparison to the NCBI protein nr database revealed a dominance of Bacteria (93%), followed by Archaea (6%). The most abundant bacterial phylum was Acidobacteria (25%), while Thaumarchaeota (5%) was the main archaeal phylum. Reads were assembled into contigs. Open reading frames (ORFs) predicted on these contigs were searched by BLAST against the CAZy database to retrieve xylanase encoding ORFs. A metagenomic fosmid library of approximately 150,000 clones was constructed to identify functional genes encoding thermostable xylanase enzymes. Function-based screening revealed a novel xylanase-encoding gene (XynA3), which was successfully expressed in E. coli BL21. The resulting protein (41 kDa), a member of glycoside hydrolase family 11 was purified and biochemically characterized. The highest activity was measured at 80 °C and pH 6.5. The protein was extremely thermostable and showed 94% remaining activity after incubation at 60 °C for 24 h and over 70% remaining activity after incubation at 70 °C for 24 h. Xylanolytic activity of the XynA3 enzyme was stimulated in the presence of β-mercaptoethanol, dithiothreitol and Fe[3+] ions. HPLC analysis showed that XynA3 hydrolyzes xylan forming xylobiose with lower proportion of xylotriose and xylose. Specific activity of the enzyme was 9080 U/mg for oat arabinoxylan and 5080 U/mg for beechwood xylan, respectively, without cellulase activity.}, } @article {pmid31371728, year = {2019}, author = {Yang, J and McDowell, A and Kim, EK and Seo, H and Yum, K and Lee, WH and Jee, YK and Kim, YK}, title = {Consumption of a Leuconostoc holzapfelii-enriched synbiotic beverage alters the composition of the microbiota and microbial extracellular vesicles.}, journal = {Experimental & molecular medicine}, volume = {51}, number = {8}, pages = {1-11}, pmid = {31371728}, issn = {2092-6413}, support = {NRF-2016M3A9B6901516//National Research Foundation of Korea (NRF)/International ; NRF-2017M3A9F3047497//National Research Foundation of Korea (NRF)/International ; }, mesh = {Adult ; *Beverages/microbiology ; Blood Chemical Analysis ; Extracellular Vesicles/metabolism/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/drug effects ; Humans ; Leuconostoc/*physiology ; Male ; Metagenome/physiology ; Probiotics/*administration & dosage ; Urinalysis ; Young Adult ; }, abstract = {Synbiotics, the combination of probiotics and prebiotics, are known to confer health benefits via intestinal microbiota modulation. However, significant intestinal microbiota alterations can be difficult to determine in intervention studies based on solely bacterial stool metagenomic analysis. Intestinal microbiota constituents secrete 20-200-nm-sized extracellular vesicles (EVs) containing microbial DNA, proteins, and lipids that are distributed throughout the body, providing an alternative target for microbiota metagenomic analysis. Here, we determined the impact of a synbiotic beverage enriched with the kimchi-derived bacterium Leuconostoc holzapfelii (L. holzapfelii) on the intestinal microbiota and local and circulatory microbiota-derived EV composition of healthy Korean adults. We isolated microbial DNA from stool bacteria, stool EVs, and urinary EVs and conducted next-generation sequencing of the 16S rDNA V3-V4 regions before and after synbiotic consumption. The species diversity of circulating urinary EVs was significantly increased after synbiotic consumption, while stool bacterial and EV diversity remained unchanged. Furthermore, we found that while a single genus was decreased among the stool bacteria constituents, stool EVs and urinary EVs showed significant alterations in four and eight genera, respectively. Blood chemistry assays revealed that synbiotic consumption significantly lowered aspartate aminotransferase (AST) serum levels, particularly in subjects with starting levels above the normal range (>40 UI/L). In conclusion, the L. holzapfelii-enriched synbiotic beverage greatly altered serum AST levels and microbial EV composition in urine and stool, while only minor changes were observed in the gut microbiota composition. Based on these findings, we suggest the potential use of microbiota-derived EVs as surrogate markers in future predictive diagnosis studies.}, } @article {pmid31371723, year = {2019}, author = {Coyne, MJ and Béchon, N and Matano, LM and McEneany, VL and Chatzidaki-Livanis, M and Comstock, LE}, title = {A family of anti-Bacteroidales peptide toxins wide-spread in the human gut microbiota.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {3460}, pmid = {31371723}, issn = {2041-1723}, support = {P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 AI093771/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*biosynthesis/pharmacology ; Bacterial Proteins/biosynthesis/genetics/pharmacology ; Bacterial Toxins/*biosynthesis/genetics/pharmacology ; Bacteriocins/*biosynthesis/*genetics/pharmacology ; Bacteroidetes/drug effects/genetics/*metabolism ; Base Sequence ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal/genetics ; Humans ; Interspersed Repetitive Sequences ; Metagenomics ; Microbial Sensitivity Tests ; Peptides/genetics/*metabolism/pharmacology ; Prevotella/drug effects ; Sequence Analysis, Protein ; Vaginosis, Bacterial ; }, abstract = {Bacteria often produce antimicrobial toxins to compete in microbial communities. Here we identify a family of broad-spectrum peptide toxins, named bacteroidetocins, produced by Bacteroidetes species. We study this toxin family using phenotypic, mutational, bioinformatic, and human metagenomic analyses. Bacteroidetocins are related to class IIa bacteriocins of Gram-positive bacteria and kill members of the Bacteroidetes phylum, including Bacteroides, Parabacteroides, and Prevotella gut species, as well as pathogenic Prevotella species. The bacteroidetocin biosynthesis genes are found in horizontally acquired mobile elements, which likely allow dissemination within the gut microbiota and may explain their wide distribution in human populations. Bacteroidetocins may have potential applications in microbiome engineering and as therapeutics for polymicrobial diseases such as bacterial vaginosis and periodontal disease.}, } @article {pmid31370905, year = {2019}, author = {Harris, ZN and Dhungel, E and Mosior, M and Ahn, TH}, title = {Massive metagenomic data analysis using abundance-based machine learning.}, journal = {Biology direct}, volume = {14}, number = {1}, pages = {12}, pmid = {31370905}, issn = {1745-6150}, mesh = {*Data Analysis ; *Machine Learning ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {BACKGROUND: Metagenomics is the application of modern genomic techniques to investigate the members of a microbial community directly in their natural environments and is widely used in many studies to survey the communities of microbial organisms that live in diverse ecosystems. In order to understand the metagenomic profile of one of the densest interaction spaces for millions of people, the public transit system, the MetaSUB international Consortium has collected and sequenced metagenomes from subways of different cities across the world. In collaboration with CAMDA, MetaSUB has made the metagenomic samples from these cities available for an open challenge of data analysis including, but not limited in scope to, the identification of unknown samples.

RESULTS: To distinguish the metagenomic profiling among different cities and also predict unknown samples precisely based on the profiling, two different approaches are proposed using machine learning techniques; one is a read-based taxonomy profiling of each sample and prediction method, and the other is a reduced representation assembly-based method. Among various machine learning techniques tested, the random forest technique showed promising results as a suitable classifier for both approaches. Random forest models developed from read-based taxonomic profiling could achieve an accuracy of 91% with 95% confidence interval between 80 and 93%. The assembly-based random forest model prediction also reached 90% accuracy. However, both models achieved roughly the same accuracy on the testing test, whereby they both failed to predict the most abundant label.

CONCLUSION: Our results suggest that both read-based and assembly-based approaches are powerful tools for the analysis of metagenomics data. Moreover, our results suggest that reduced representation assembly-based methods are able to simultaneous provide high-accuracy prediction on available data. Overall, we show that metagenomic samples can be traced back to their location with careful generation of features from the composition of microbes and utilizing existing machine learning algorithms. Proposed approaches show high accuracy of prediction, but require careful inspection before making any decisions due to sample noise or complexity.

REVIEWERS: This article was reviewed by Eugene V. Koonin, Jing Zhou and Serghei Mangul.}, } @article {pmid31370880, year = {2019}, author = {Minot, SS and Willis, AD}, title = {Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {110}, pmid = {31370880}, issn = {2049-2618}, support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification ; Cluster Analysis ; Colorectal Neoplasms/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*microbiology ; *Metagenome ; Metagenomics ; Reproducibility of Results ; Sequence Analysis, DNA ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Whole-genome "shotgun" (WGS) metagenomic sequencing is an increasingly widely used tool for analyzing the metagenomic content of microbiome samples. While WGS data contains gene-level information, it can be challenging to analyze the millions of microbial genes which are typically found in microbiome experiments. To mitigate the ultrahigh dimensionality challenge of gene-level metagenomics, it has been proposed to cluster genes by co-abundance to form Co-Abundant Gene groups (CAGs). However, exhaustive co-abundance clustering of millions of microbial genes across thousands of biological samples has previously been intractable purely due to the computational challenge of performing trillions of pairwise comparisons.

RESULTS: Here we present a novel computational approach to the analysis of WGS datasets in which microbial gene groups are the fundamental unit of analysis. We use the Approximate Nearest Neighbor heuristic for near-exhaustive average linkage clustering to group millions of genes by co-abundance. This results in thousands of high-quality CAGs representing complete and partial microbial genomes. We applied this method to publicly available WGS microbiome surveys and found that the resulting microbial CAGs associated with inflammatory bowel disease (IBD) and colorectal cancer (CRC) were highly reproducible and could be validated independently using multiple independent cohorts.

CONCLUSIONS: This powerful approach to gene-level metagenomics provides a powerful path forward for identifying the biological links between the microbiome and human health. By proposing a new computational approach for handling high dimensional metagenomics data, we identified specific microbial gene groups that are associated with disease that can be used to identify strains of interest for further preclinical and mechanistic experimentation.}, } @article {pmid31370775, year = {2019}, author = {Chattopadhyay, I and Verma, M and Panda, M}, title = {Role of Oral Microbiome Signatures in Diagnosis and Prognosis of Oral Cancer.}, journal = {Technology in cancer research & treatment}, volume = {18}, number = {}, pages = {1533033819867354}, pmid = {31370775}, issn = {1533-0338}, mesh = {Carcinogenesis/*genetics/pathology ; Cell Proliferation/genetics ; Fusobacterium nucleatum/pathogenicity ; Humans ; Inflammation/genetics/*microbiology/pathology ; Microbiota/*genetics ; Mouth Neoplasms/diagnosis/genetics/*microbiology/pathology ; Porphyromonas gingivalis/pathogenicity ; Prognosis ; Saliva/microbiology ; }, abstract = {Despite advancement in cancer treatment, oral cancer has a poor prognosis and is often detected at late stage. To overcome these challenges, investigators should search for early diagnostic and prognostic biomarkers. More than 700 bacterial species reside in the oral cavity. The oral microbiome population varies by saliva and different habitats of oral cavity. Tobacco, alcohol, and betel nut, which are causative factors of oral cancer, may alter the oral microbiome composition. Both pathogenic and commensal strains of bacteria have significantly contributed to oral cancer. Numerous bacterial species in the oral cavity are involved in chronic inflammation that lead to development of oral carcinogenesis. Bacterial products and its metabolic by-products may induce permanent genetic alterations in epithelial cells of the host that drive proliferation and/or survival of epithelial cells. Porphyromonas gingivalis and Fusobacterium nucleatum induce production of inflammatory cytokines, cell proliferation, and inhibition of apoptosis, cellular invasion, and migration thorough host cell genomic alterations. Recent advancement in metagenomic technologies may be useful in identifying oral cancer-related microbiome, their genomes, virulence properties, and their interaction with host immunity. It is very important to address which bacterial species is responsible for driving oral carcinogenesis. Alteration in the oral commensal microbial communities have potential application as a diagnostic tool to predict oral squamous cell carcinoma. Clinicians should be aware that the protective properties of the resident microflora are beneficial to define treatment strategies. To develop highly precise and effective therapeutic approaches, identification of specific oral microbiomes may be required. In this review, we narrate the role of microbiome in the progression of oral cancer and its role as an early diagnostic and prognostic biomarker for oral cancer.}, } @article {pmid31368841, year = {2019}, author = {Katsila, T and Balasopoulou, A and Tsagaraki, I and Patrinos, GP}, title = {Pharmacomicrobiomics informs clinical pharmacogenomics.}, journal = {Pharmacogenomics}, volume = {20}, number = {10}, pages = {731-739}, doi = {10.2217/pgs-2019-0027}, pmid = {31368841}, issn = {1744-8042}, mesh = {Databases, Factual ; Drug-Related Side Effects and Adverse Reactions/*genetics ; Host Microbial Interactions/*genetics ; Humans ; Microbiota/*physiology ; Pharmaceutical Preparations/administration & dosage ; Pharmacogenetics/methods ; }, abstract = {Aim: Microbiota-host-xenobiotics interactions in humans become of prime interest when clinical pharmacogenomics is to be implemented. Despite the advent of technology, information still needs to be translated into knowledge for optimum patient stratification and disease management. Material & methods: Herein, we mined metagenomic, pharmacometagenomic and pharmacomicrobiomic datasets to map microbiota-host-drugs networks. Results: Datasets were multifaceted and voluminous. Interoperability, data sparsity and scarcity remain a challenge. Mapping microbiota-host-drugs networks allowed the prediction of drug response/toxicity and modulation of the microbiota-host-drugs interplay. Conclusion: Our approach triangulated microbiota, host and drug networks revealing the need for contextual data and open science via microattribution to accelerate knowledge growth. Our findings may serve as a data storehouse for a user-friendly query system, coupled with databanks and databases.}, } @article {pmid31367746, year = {2019}, author = {Dai, W and Wang, H and Zhou, Q and Li, D and Feng, X and Yang, Z and Wang, W and Qiu, C and Lu, Z and Xu, X and Lyu, M and Xie, G and Li, Y and Bao, Y and Liu, Y and Shen, K and Yao, K and Feng, X and Yang, Y and Zhou, K and Li, S and Zheng, Y}, title = {An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia.}, journal = {GigaScience}, volume = {8}, number = {8}, pages = {}, pmid = {31367746}, issn = {2047-217X}, mesh = {Case-Control Studies ; Child ; Child, Preschool ; Female ; Genes, Microbial ; Humans ; Infant ; Male ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Mycoplasma pneumoniae/*classification/*genetics ; Pneumonia, Mycoplasma/*microbiology ; }, abstract = {BACKGROUND: The imbalanced respiratory microbiota observed in pneumonia causes high morbidity and mortality in childhood. Respiratory metagenomic analysis demands a comprehensive microbial gene catalogue, which will significantly advance our understanding of host-microorganism interactions.

RESULTS: We collected 334 respiratory microbial samples from 171 healthy children and 76 children with pneumonia. The respiratory microbial gene catalogue we established comprised 2.25 million non-redundant microbial genes, covering 90.52% of prevalent genes. The major oropharyngeal microbial species found in healthy children were Prevotella and Streptococcus. In children with Mycoplasma pneumoniae pneumonia (MPP), oropharyngeal microbial diversity and associated gene numbers decreased compared with those of healthy children. The concurrence network of oropharyngeal microorganisms in patients predominantly featured Staphylococcus spp. and M. pneumoniae. Functional orthologues, which are associated with the metabolism of various lipids, membrane transport, and signal transduction, accumulated in the oropharyngeal microbiome of children with pneumonia. Several antibiotic resistance genes and virulence factor genes were identified in the genomes of M. pneumoniae and 13 other microorganisms reconstructed via metagenomic data. Although the common macrolide/β-lactam resistance genes were not identified in the assembled M. pneumoniae genome, a single-nucleotide polymorphism (A2063G) related to macrolide resistance was identified in a 23S ribosomal RNA gene.

CONCLUSIONS: The results of this study will facilitate exploration of unknown microbial components and host-microorganism interactions in studies of the respiratory microbiome. They will also yield further insights into the microbial aetiology of MPP.}, } @article {pmid31367159, year = {2019}, author = {Liu, MT and Huang, YJ and Zhang, TY and Tan, LB and Lu, XF and Qin, J}, title = {Lingguizhugan decoction attenuates diet-induced obesity and hepatosteatosis via gut microbiota.}, journal = {World journal of gastroenterology}, volume = {25}, number = {27}, pages = {3590-3606}, pmid = {31367159}, issn = {2219-2840}, mesh = {Animals ; *Caloric Restriction ; Combined Modality Therapy/methods ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Intestinal Mucosa/drug effects/metabolism/microbiology ; Lipid Metabolism/drug effects ; Lipids/blood ; Liver/drug effects/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/etiology/microbiology/*therapy ; Obesity/etiology/microbiology/*therapy ; Plant Extracts/*administration & dosage ; Treatment Outcome ; }, abstract = {BACKGROUND: Obesity is a major risk factor for a variety of diseases such as diabetes, nonalcoholic fatty liver disease, and cardiovascular diseases. Restricting energy intake, or caloric restriction (CR), can reduce body weight and improve metabolic parameters in overweight or obese patients. We previously found that Lingguizhugan decoction (LZD) in combination with CR can effectively lower plasma lipid levels in patients with metabolic syndrome. However, the mechanism underlying CR and LZD treatment is still unclear.

AIM: To investigate whether CR and LZD improve metabolic parameters by modulating gut microbiota.

METHODS: We extracted the water-soluble components out of raw materials and dried as LZD extracts. Eight-week old male C57BL/6 mice were treated with a 3-d treatment regime that included 24 h-fasting followed by gavage of LZD extracts for 2 consecutive days, followed by a normal diet (ND) ad libitum for 16 wk. To test the effects of gut microbiota on diet-induced obesity, 8-wk old male C57BL/6 mice received fecal microbiota transplantation (FMT) from CR and LZD-treated mice every 3 d and were fed with high-fat diet (HFD) ad libitum for 16 wk. Control mice received either saline gavage or FMT from ND-fed mice receiving saline gavage as mentioned above. Body weight was monitored bi-weekly. Food consumption of each cage hosting five mice was recorded weekly. To monitor blood glucose, total cholesterol, and total triglycerides, blood samples were collected via submandibular bleeding after 6 h fasting. Oxygen consumption rate was monitored with metabolic cages. Feces were collected, and fecal DNA was extracted. Profiles of gut microbiota were mapped by metagenomic sequencing.

RESULTS: We found that CR and LZD treatment significantly reduced the body weight of mice fed with ND (28.71 ± 0.29 vs 28.05 ± 0.15, P < 0.05), but did not affect plasma total cholesterol or total triglyceride levels. We then transplanted the fecal microbiota collected from CR and LZD-treated mice under ND feeding to HFD-fed mice. Intriguingly, transplanting the mice with fecal microbiota from CR and LZD-treated mice potently reduced body weight (44.95 ± 1.02 vs 40.53 ± 0.97, P < 0.001). FMT also reduced HFD-induced hepatosteatosis, in addition to improved glycemic control. Mechanistic studies found that FMT increased OCR of the mice and suppressed the expression and protein abundance of lipogenic genes in the liver. Metagenomic analysis revealed that HFD drastically altered the profile of gut microbiota, and FMT modified the profile of the gut microbiota.

CONCLUSION: Our study suggests that CR and LZD improve metabolic parameters by modulating gut microbiota.}, } @article {pmid31366912, year = {2019}, author = {Camargo, AP and de Souza, RSC and de Britto Costa, P and Gerhardt, IR and Dante, RA and Teodoro, GS and Abrahão, A and Lambers, H and Carazzolle, MF and Huntemann, M and Clum, A and Foster, B and Foster, B and Roux, S and Palaniappan, K and Varghese, N and Mukherjee, S and Reddy, TBK and Daum, C and Copeland, A and Chen, IA and Ivanova, NN and Kyrpides, NC and Pennacchio, C and Eloe-Fadrosh, EA and Arruda, P and Oliveira, RS}, title = {Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot.}, journal = {Scientific data}, volume = {6}, number = {1}, pages = {140}, pmid = {31366912}, issn = {2052-4463}, support = {No. DE-AC02-05CH11231//DOE | Office of Science (SC)/International ; No. DE-AC02-05CH11231//DOE | Office of Science (SC)/International ; No. DE-AC02-05CH11231//DOE | Office of Science (SC)/International ; No. DE-AC02-05CH11231//DOE | Office of Science (SC)/International ; No. DE-AC02-05CH11231//DOE | Office of Science (SC)/International ; No. DE-AC02-05CH11231//DOE | Office of Science (SC)/International ; No. DE-AC02-05CH11231//DOE | Office of Science (SC)/International ; No. DE-AC02-05CH11231//DOE | Office of Science (SC)/International ; No. DE-AC02-05CH11231//DOE | Office of Science (SC)/International ; No. DE-AC02-05CH11231//DOE | Office of Science (SC)/International ; No. DE-AC02-05CH11231//DOE | Office of Science (SC)/International ; No. DE-AC02-05CH11231//DOE | Office of Science (SC)/International ; No. DE-AC02-05CH11231//DOE | Office of Science (SC)/International ; No. DE-AC02-05CH11231//DOE | Office of Science (SC)/International ; No. DE-AC02-05CH11231//DOE | Office of Science (SC)/International ; }, mesh = {Bacteria/classification ; Biodiversity ; Brazil ; Fungi/classification ; Magnoliopsida/*microbiology ; Metagenome ; Methyltransferases/genetics ; *Microbiota ; Phosphorus/*chemistry ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The rocky, seasonally-dry and nutrient-impoverished soils of the Brazilian campos rupestres impose severe growth-limiting conditions on plants. Species of a dominant plant family, Velloziaceae, are highly specialized to low-nutrient conditions and seasonal water availability of this environment, where phosphorus (P) is the key limiting nutrient. Despite plant-microbe associations playing critical roles in stressful ecosystems, the contribution of these interactions in the campos rupestres remains poorly studied. Here we present the first microbiome data of Velloziaceae spp. thriving in contrasting substrates of campos rupestres. We assessed the microbiomes of Vellozia epidendroides, which occupies shallow patches of soil, and Barbacenia macrantha, growing on exposed rocks. The prokaryotic and fungal profiles were assessed by rRNA barcode sequencing of epiphytic and endophytic compartments of roots, stems, leaves and surrounding soil/rocks. We also generated root and substrate (rock/soil)-associated metagenomes of each plant species. We foresee that these data will contribute to decipher how the microbiome contributes to plant functioning in the campos rupestres, and to unravel new strategies for improved crop productivity in stressful environments.}, } @article {pmid31366182, year = {2019}, author = {Deshpande, SV and Reed, TM and Sullivan, RF and Kerkhof, LJ and Beigel, KM and Wade, MM}, title = {Offline Next Generation Metagenomics Sequence Analysis Using MinION Detection Software (MINDS).}, journal = {Genes}, volume = {10}, number = {8}, pages = {}, pmid = {31366182}, issn = {2073-4425}, mesh = {DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome ; Metagenomics/*methods ; Microbiota ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {Field laboratories interested in using the MinION often need the internet to perform sample analysis. Thus, the lack of internet connectivity in resource-limited or remote locations renders downstream analysis problematic, resulting in a lack of sample identification in the field. Due to this dependency, field samples are generally transported back to the lab for analysis where internet availability for downstream analysis is available. These logistics problems and the time lost in sample characterization and identification, pose a significant problem for field scientists. To address this limitation, we have developed a stand-alone data analysis packet using open source tools developed by the Nanopore community that does not depend on internet availability. Like Oxford Nanopore Technologies' (ONT) cloud-based What's In My Pot (WIMP) software, we developed the offline MinION Detection Software (MINDS) based on the Centrifuge classification engine for rapid species identification. Several online bioinformatics applications have been developed surrounding ONT's framework for analysis of long reads. We have developed and evaluated an offline real time classification application pipeline using open source tools developed by the Nanopore community that does not depend on internet availability. Our application has been tested on ATCC's 20 strain even mix whole cell (ATCC MSA-2002) sample. Using the Rapid Sequencing Kit (SQK-RAD004), we were able to identify all 20 organisms at species level. The analysis was performed in 15 min using a Dell Precision 7720 laptop. Our offline downstream bioinformatics application provides a cost-effective option as well as quick turn-around time when analyzing samples in the field, thus enabling researchers to fully utilize ONT's MinION portability, ease-of-use, and identification capability in remote locations.}, } @article {pmid31365065, year = {2019}, author = {Sutela, S and Poimala, A and Vainio, EJ}, title = {Viruses of fungi and oomycetes in the soil environment.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {9}, pages = {}, doi = {10.1093/femsec/fiz119}, pmid = {31365065}, issn = {1574-6941}, mesh = {Fungi/classification/genetics/*isolation & purification ; Oomycetes/classification/genetics/*isolation & purification ; Phylogeny ; Soil/*parasitology ; *Soil Microbiology ; Viruses/classification/genetics/*isolation & purification ; }, abstract = {Soils support a myriad of organisms hosting highly diverse viromes. In this minireview, we focus on viruses hosted by true fungi and oomycetes (members of Stamenopila, Chromalveolata) inhabiting bulk soil, rhizosphere and litter layer, and representing different ecological guilds, including fungal saprotrophs, mycorrhizal fungi, mutualistic endophytes and pathogens. Viruses infecting fungi and oomycetes are characterized by persistent intracellular nonlytic lifestyles and transmission via spores and/or hyphal contacts. Almost all fungal and oomycete viruses have genomes composed of single-stranded or double-stranded RNA, and recent studies have revealed numerous novel viruses representing yet unclassified family-level groups. Depending on the virus-host combination, infections can be asymptomatic, beneficial or detrimental to the host. Thus, mycovirus infections may contribute to the multiplex interactions of hosts, therefore likely affecting the dynamics of fungal communities required for the functioning of soil ecosystems. However, the effects of fungal and oomycete viruses on soil ecological processes are still mostly unknown. Interestingly, new metagenomics data suggest an extensive level of horizontal virus transfer between plants, fungi and insects.}, } @article {pmid31363155, year = {2019}, author = {Li, X and Cao, Z and Yang, Y and Chen, L and Liu, J and Lin, Q and Qiao, Y and Zhao, Z and An, Q and Zhang, C and Li, Q and Ji, Q and Zhang, H and Pan, H}, title = {Correlation between Jejunal Microbial Diversity and Muscle Fatty Acids Deposition in Broilers Reared at Different Ambient Temperatures.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11022}, pmid = {31363155}, issn = {2045-2322}, mesh = {Animals ; Chickens/*microbiology/physiology ; Fatty Acids/*metabolism ; *Gastrointestinal Microbiome ; Jejunum/microbiology ; Metagenome ; Muscle, Skeletal/*metabolism ; *Temperature ; }, abstract = {Temperature, which is an important environmental factor in broiler farming, can significantly influence the deposition of fatty acids in muscle. 300 one-day-old broiler chicks were randomly divided into three groups and reared at high, medium and low temperatures (HJ, MJ and LJ), respectively. Breast muscle and jejunal chyme samples were collected and subjected to analyses of fatty acid composition and 16S rRNA gene sequencing. Through spearman's rank correlation coefficient, the data were used to characterize the correlation between jejunal microbial diversity and muscle fatty acid deposition in the broilers. The results showed that Achromobacter, Stenotrophomonas, Pandoraea, Brevundimonas, Petrobacter and Variovorax were significantly enriched in the MJ group, and all of them were positively correlated with the fatty acid profiling of muscle and multiple lipid metabolism signaling pathways. Lactobacillus was significantly enriched in the HJ group and exhibited a positive correlation with fatty acid deposition. Pyramidobacter, Dialister, Bacteroides and Selenomonas were significantly enriched in the LJ group and displayed negative correlation with fatty acid deposition. Taken together, this study demonstrated that the jejunal microflora manifested considerable changes at high and low ambient temperatures and that jejunal microbiota changes were correlated with fatty acid deposition of muscle in broilers.}, } @article {pmid31361989, year = {2019}, author = {Abbasi, I and Nasereddin, A and Warburg, A}, title = {Development of a next generation DNA sequencing-based multi detection assay for detecting and identifying Leishmania parasites, blood sources, plant meals and intestinal microbiome in phlebotomine sand flies.}, journal = {Acta tropica}, volume = {199}, number = {}, pages = {105101}, doi = {10.1016/j.actatropica.2019.105101}, pmid = {31361989}, issn = {1873-6254}, mesh = {Animals ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Insect Vectors/*parasitology ; Leishmania/genetics/*isolation & purification ; Leishmaniasis/transmission ; Phlebotomus/*parasitology ; }, abstract = {Leishmaniasis is a disease caused by Leishmania parasites transmitted by phlebotomine sand flies (Diptera: Psychodidae). Human infections with different Leishmania species cause characteristic clinical manifestations; cutaneous or visceral leishmaniasis. Here we describe the development and application of a Miseq Next GenerationSequencing (NGS)-based Multi Detection Assay (MDA) designed to characterize metagenomics parameters pertinent to the sand fly vectors which may affect their vectorial capacity for Leishmania. For this purpose, we developed a MDA by which, DNA fragments were amplified through polymerase chain reactions (PCR) and then sequenced by MiSeq/NGS. PCR amplification was achieved using some published and some new primers designed specifically for identifying Leishmania spp. (ITS1), sand fly spp. (cytochrome oxidase I), vertebrate blood (Cytochrome b), plant DNA ribulose-1,5-bisphosphate carboxylase large subunit gene (rbcL), and prokaryotic micobiome (16 s rRNA). This MDA/NGS analysis was performed on two species of wild-caught sand flies that transmit different Leishmania spp. in two ecologically distinct, but geographically neighboring locations. The results were analyzed to identify, quantitate and correlate the measured parameters in order to assess their putative importance in the transmission dynamics of leishmaniasis.}, } @article {pmid31359005, year = {2019}, author = {Bertrand, D and Shaw, J and Kalathiyappan, M and Ng, AHQ and Kumar, MS and Li, C and Dvornicic, M and Soldo, JP and Koh, JY and Tong, C and Ng, OT and Barkham, T and Young, B and Marimuthu, K and Chng, KR and Sikic, M and Nagarajan, N}, title = {Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes.}, journal = {Nature biotechnology}, volume = {37}, number = {8}, pages = {937-944}, doi = {10.1038/s41587-019-0191-2}, pmid = {31359005}, issn = {1546-1696}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*drug effects/*genetics ; Drug Resistance, Bacterial ; Feces/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota/*drug effects ; Nanopores ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {Characterization of microbiomes has been enabled by high-throughput metagenomic sequencing. However, existing methods are not designed to combine reads from short- and long-read technologies. We present a hybrid metagenomic assembler named OPERA-MS that integrates assembly-based metagenome clustering with repeat-aware, exact scaffolding to accurately assemble complex communities. Evaluation using defined in vitro and virtual gut microbiomes revealed that OPERA-MS assembles metagenomes with greater base pair accuracy than long-read (>5×; Canu), higher contiguity than short-read (~10× NGA50; MEGAHIT, IDBA-UD, metaSPAdes) and fewer assembly errors than non-metagenomic hybrid assemblers (2×; hybridSPAdes). OPERA-MS provides strain-resolved assembly in the presence of multiple genomes of the same species, high-quality reference genomes for rare species (<1%) with ~9× long-read coverage and near-complete genomes with higher coverage. We used OPERA-MS to assemble 28 gut metagenomes of antibiotic-treated patients, and showed that the inclusion of long nanopore reads produces more contiguous assemblies (200× improvement over short-read assemblies), including more than 80 closed plasmid or phage sequences and a new 263 kbp jumbo phage. High-quality hybrid assemblies enable an exquisitely detailed view of the gut resistome in human patients.}, } @article {pmid31357928, year = {2019}, author = {Ogier, JC and Pagès, S and Galan, M and Barret, M and Gaudriault, S}, title = {rpoB, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {171}, pmid = {31357928}, issn = {1471-2180}, mesh = {Animals ; Bacteria/classification ; DNA, Bacterial ; DNA-Directed RNA Polymerases/genetics ; Genes, Essential ; *Genetic Markers ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Nematoda/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Microbiome composition is frequently studied by the amplification and high-throughput sequencing of specific molecular markers (metabarcoding). Various hypervariable regions of the 16S rRNA gene are classically used to estimate bacterial diversity, but other universal bacterial markers with a finer taxonomic resolution could be employed. We compared specificity and sensitivity between a portion of the rpoB gene and the V3 V4 hypervariable region of the 16S rRNA gene.

RESULTS: We first designed universal primers for rpoB suitable for use with Illumina sequencing-based technology and constructed a reference rpoB database of 45,000 sequences. The rpoB and V3 V4 markers were amplified and sequenced from (i) a mock community of 19 bacterial strains from both Gram-negative and Gram-positive lineages; (ii) bacterial assemblages associated with entomopathogenic nematodes. In metabarcoding analyses of mock communities with two analytical pipelines (FROGS and DADA2), the estimated diversity captured with the rpoB marker resembled the expected composition of these mock communities more closely than that captured with V3 V4. The rpoB marker had a higher level of taxonomic affiliation, a higher sensitivity (detection of all the species present in the mock communities), and a higher specificity (low rates of spurious OTU detection) than V3 V4. We compared the performance of the rpoB and V3 V4 markers in an animal ecosystem model, the infective juveniles of the entomopathogenic nematode Steinernema glaseri carrying the symbiotic bacteria Xenorhabdus poinarii. Both markers showed the bacterial community associated with this nematode to be of low diversity (< 50 OTUs), but only rpoB reliably detected the symbiotic bacterium X. poinarii.

CONCLUSIONS: Our results confirm that different microbiota composition data may be obtained with different markers. We found that rpoB was a highly appropriate marker for assessing the taxonomic structure of mock communities and the nematode microbiota. Further studies on other ecosystems should be considered to evaluate the universal usefulness of the rpoB marker. Our data highlight two crucial elements that should be taken into account to ensure more reliable and accurate descriptions of microbial diversity in high-throughput amplicon sequencing analyses: i) the need to include mock communities as controls; ii) the advantages of using a multigenic approach including at least one housekeeping gene (rpoB is a good candidate) and one variable region of the 16S rRNA gene. This study will be useful to the growing scientific community describing bacterial communities by metabarcoding in diverse ecosystems.}, } @article {pmid31355459, year = {2019}, author = {Kelly, L}, title = {Harnessing the Microbiome to Improve Drug Therapy.}, journal = {Clinical pharmacology and therapeutics}, volume = {106}, number = {2}, pages = {287-289}, doi = {10.1002/cpt.1510}, pmid = {31355459}, issn = {1532-6535}, mesh = {Drug Therapy ; Drug-Related Side Effects and Adverse Reactions/*microbiology ; *Gastrointestinal Microbiome/drug effects/physiology ; *Gastrointestinal Tract/drug effects/metabolism/microbiology ; Host Microbial Interactions/drug effects/physiology ; Humans ; *Metagenome ; *Microbiota/drug effects/physiology ; Pharmaceutical Preparations/*metabolism ; }, } @article {pmid31354669, year = {2019}, author = {Raimondi, S and Amaretti, A and Gozzoli, C and Simone, M and Righini, L and Candeliere, F and Brun, P and Ardizzoni, A and Colombari, B and Paulone, S and Castagliuolo, I and Cavalieri, D and Blasi, E and Rossi, M and Peppoloni, S}, title = {Longitudinal Survey of Fungi in the Human Gut: ITS Profiling, Phenotyping, and Colonization.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1575}, pmid = {31354669}, issn = {1664-302X}, abstract = {The fungal component of the intestinal microbiota of eight healthy subjects was studied over 12 months using metagenome survey and culture-based approaches. Aspergillus, Candida, Debaryomyces, Malassezia, Penicillium, Pichia, and Saccharomyces were the most recurrent and/or dominant fungal genera, according to metagenomic analysis. The biodiversity of fungal communities was lower and characterized by greater unevenness, when compared to bacterial microbiome. The dissimilarities both among subjects and over the time within the same subject suggested that most of the fungi passed through the gastro-intestinal tract (GIT) without becoming stable colonizers. Certain genera, such as Aspergillus and Penicillium, were isolated in a minority of cases, although they recurred abundantly and frequently in the metagenomics survey, likely being environmental or food-borne fungi that do not inhabit the GIT. Candida genus was recurrently detected. Candida albicans isolates dominated among the cultivable mycobiota and longitudinally persisted, likely as commensals inhabiting the intestine or regularly reaching it from Candida-colonized districts, such as the oral cavity. Other putative colonizers belonged to Candida zeylanoides, Geotrichum candidum, and Rhodotorula mucilaginosa, with persisting biotypes being identified. Phenotyping of fungal isolates indicated that C. albicans adhered to human epithelial cells more efficiently and produced greater amounts of biofilm in vitro than non-albicans Candida (NAC) and non-Candida fungi (NCF). The C. albicans isolates also induced the highest release of HBD-2 by human epithelial cells, further differing from NAC and NCF. Nine representative isolates were administered to mice to evaluate the ability to colonize the intestine. Only two out of three C. albicans strains persisted in stools of animals 2 weeks after the end of the oral administration, whereas NAC and NCF did not. These results confirm the allochthonous nature of most the intestinal fungi, while C. albicans appears to be commonly involved in stable colonization. A combination of specific genetic features in the microbe and in the host likely allow colonization from fungi normally present solely as passengers. It remains to be established if other species identified as potential colonizers, in addition to Candida, are true inhabitants of the GIT or rather reach the intestine spreading from other body districts.}, } @article {pmid31353293, year = {2019}, author = {Powell, EA and Fontanella, S and Boakes, E and Belgrave, D and Shaw, AG and Cornwell, E and Fernandez-Crespo, R and Fink, CG and Custovic, A and Kroll, JS}, title = {Temporal association of the development of oropharyngeal microbiota with early life wheeze in a population-based birth cohort.}, journal = {EBioMedicine}, volume = {46}, number = {}, pages = {486-498}, pmid = {31353293}, issn = {2352-3964}, mesh = {Age Factors ; Biodiversity ; Cohort Studies ; Female ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Oropharynx/*microbiology ; Population Surveillance ; Respiratory Sounds/*etiology ; United Kingdom/epidemiology ; }, abstract = {BACKGROUND: A critical window in infancy has been proposed, during which the microbiota may affect subsequent health. The longitudinal development of the oropharyngeal microbiota is under-studied and may be associated with early-life wheeze. We aimed to investigate the temporal association of the development of the oropharyngeal microbiota with early-life wheeze.

METHODS: A population-based birth cohort based in London, UK was followed for 24 months. We collected oropharyngeal swabs at six time-points. Microbiota was determined using sequencing of the V3-V5 region of the 16S rRNA-encoding gene. Medical records were reviewed for the outcome of doctor diagnosed wheeze. We used a time-varying model to investigate the temporal association between the development of microbiota and doctor-diagnosed wheeze.

FINDINGS: 159 participants completed the study to 24 months and for 98 there was complete sequencing data at all timepoints and outcome data. Of these, 26 had doctor-diagnosed wheeze. We observed significant increase in the abundance of Neisseria between 9 and 24 months in children who developed wheeze (p = 0∙003), while in those without wheezing there was a significant increment in the abundance of Granulicatella (p = 0∙012) between 9 and 12 months, and of Prevotella (p = 0∙018) after 18 months.

INTERPRETATION: A temporal association between the respiratory commensal Granulicatella and also Prevotella with wheeze (negative), and between Neisseria and wheeze (positive) was identified in infants prior to one year of age. This adds to evidence for the proposed role of the microbiota in the development of wheeze. FUND: Research funding from the Winnicott Foundation, Meningitis Now and Micropathology Ltd.}, } @article {pmid31351355, year = {2019}, author = {Zhang, F and Zhang, W and Qian, DK and Dai, K and van Loosdrecht, MCM and Zeng, RJ}, title = {Synergetic alginate conversion by a microbial consortium of hydrolytic bacteria and methanogens.}, journal = {Water research}, volume = {163}, number = {}, pages = {114892}, doi = {10.1016/j.watres.2019.114892}, pmid = {31351355}, issn = {1879-2448}, mesh = {Alginates ; Anaerobiosis ; Bacteria ; Bioreactors ; *Euryarchaeota ; Methane ; *Microbial Consortia ; Sewage ; }, abstract = {Sludge, of which alginate-like biomaterial is a major organic component, is an increasing environmental problem. Thus, efficient anaerobic degradation of alginate provides a new method for sludge utilization. In this study, anaerobic alginate hydrolytic bacteria (AHB) were proposed to enrich with methanogens synergetically to reduce the inhibition of intermediate metabolites. The COD of produced methane reached 80.7 ± 1.9% (n = 4) of initial alginate COD. After considering the microbial growth (8%-18% of COD), a good COD balance indicated that alginate was fully consumed and the main final metabolites were methane and CO2. Methanogenesis could promote alginate conversion by AHB. The enriched bacteria for alginate degradation in this study were different from that of former known AHB. The metabolic pathway of alginate degradation was revealed by metagenomics, in which oligo-alginate lyase was detected in twelve bacteria, and typical carbon metabolic pathways to convert alginate to methane were identified. More studies of bacterial isolation and biofuel production are still needed in the future.}, } @article {pmid31349392, year = {2019}, author = {Seeber, PA and McEwen, GK and Löber, U and Förster, DW and East, ML and Melzheimer, J and Greenwood, AD}, title = {Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes.}, journal = {Molecular ecology resources}, volume = {19}, number = {6}, pages = {1486-1496}, doi = {10.1111/1755-0998.13069}, pmid = {31349392}, issn = {1755-0998}, support = {SAW-2015-IZW-1 440//Leibniz Gemeinschaft/ ; }, mesh = {Animals ; Biodiversity ; DNA, Environmental/*genetics ; DNA, Mitochondrial/genetics ; Ecosystem ; Environmental Monitoring/methods ; Genome, Mitochondrial/genetics ; Hybridization, Genetic/*genetics ; Mammals ; Metagenomics/methods ; Namibia ; Nucleic Acid Hybridization/*genetics ; Tanzania ; Water ; }, abstract = {Determining species distributions can be extremely challenging but is crucial to ecological and conservation research. Environmental DNA (eDNA) approaches have shown particular promise in aquatic systems for several vertebrate and invertebrate species. For terrestrial animals, however, eDNA-based surveys are considerably more difficult due to the lack of or difficulty in obtaining appropriate sampling substrate. In water-limited ecosystem where terrestrial mammals are often forced to congregate at waterholes, water and sediment from shared water sources may be a suitable substrate for noninvasive eDNA approaches. We characterized mitochondrial DNA sequences from a broad range of terrestrial mammal species in two different African ecosystems (in Namibia and Tanzania) using eDNA isolated from native water, sediment and water filtered through glass fibre filters. A hybridization capture enrichment with RNA probes targeting the mitochondrial genomes of 38 mammal species representing the genera/families expected at the respective ecosystems was employed, and 16 species were identified, with a maximum mitogenome coverage of 99.8%. Conventional genus-specific PCRs were tested on environmental samples for two genera producing fewer positive results than hybridization capture enrichment. An experiment with mock samples using DNA from non-African mammals showed that baits covering 30% of nontarget mitogenomes produced 91% mitogenome coverage after capture. In the mock samples, over-representation of DNA of one species still allowed for the detection of DNA of other species that was at a 100-fold lower concentration. Hybridization capture enrichment of eDNA is therefore an effective method for monitoring terrestrial mammal species from shared water sources.}, } @article {pmid31349170, year = {2019}, author = {Basso, L and Rizzo, L and Marzano, M and Intranuovo, M and Fosso, B and Pesole, G and Piraino, S and Stabili, L}, title = {Jellyfish summer outbreaks as bacterial vectors and potential hazards for marine animals and humans health? The case of Rhizostoma pulmo (Scyphozoa, Cnidaria).}, journal = {The Science of the total environment}, volume = {692}, number = {}, pages = {305-318}, doi = {10.1016/j.scitotenv.2019.07.155}, pmid = {31349170}, issn = {1879-1026}, mesh = {Animals ; Aquatic Organisms ; Bacteria/*classification ; *Bacterial Physiological Phenomena ; Humans ; Italy ; Mediterranean Sea ; *Microbiota ; Population Dynamics ; Scyphozoa/*microbiology ; }, abstract = {Jellyfish represent an important component of marine food webs characterized by large fluctuations of population density, with the ability to abruptly form outbreaks, followed by rarity periods. In spite of considerable efforts to investigate how jellyfish populations are responding globally to anthropogenic change, available evidence still remains unclear. In the last 50 years, jellyfish are seemingly on the rise in a number of coastal areas, including the Mediterranean Sea, where jellyfish blooms periodically become an issue to marine and maritime human activities. Their impacts on marine organism welfare have been poorly quantified. The jellyfish, Rhizostoma pulmo, is an outbreak-forming scyphomedusa whose large populations spread across the Mediterranean, with increasing periodicity and variable abundance. Studies on cnidarian jellyfish suggested being important vectors of bacterial pathogens. In the present study, by combination of conventional culture-based methods and a high-throughput amplicon sequencing (HTS) approach, we characterized the diversity of the bacterial community associated with this jellyfish during their summer outbreak. Three distinct jellyfish compartments, namely umbrella, oral arms, and the mucus secretion obtained from whole specimens were screened for specifically associated microbiota. A total of 17 phyla, 30 classes, 73 orders, 146 families and 329 genera of microbial organisms were represented in R. pulmo samples with three major clades (i.e. Spiroplasma, Mycoplasma and Wolinella) representing over 90% of the retrieved total sequences. The taxonomic microbial inventory was then combined with metabolic profiling data obtained from the Biolog Eco-Plate system. Significant differences among the jellyfish compartments were detected in terms of bacterial abundance, diversity and metabolic utilization of 31 different carbon sources with the highest value of abundance and metabolic potential in the mucus secretion compared to the umbrella and oral arms. Results are discussed in the framework of the species ecology as well as the potential health hazard for marine organisms and humans.}, } @article {pmid31347944, year = {2020}, author = {Brown, BP and Jaspan, HB}, title = {Compositional analyses reveal correlations between taxon-level gut bacterial abundance and peripheral T cell marker expression in African infants.}, journal = {Gut microbes}, volume = {11}, number = {2}, pages = {237-244}, pmid = {31347944}, issn = {1949-0984}, support = {K08 HD069201/HD/NICHD NIH HHS/United States ; P30 AI027757/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics/isolation & purification ; Bacteroides/genetics/isolation & purification ; Bifidobacterium/genetics/isolation & purification ; *Breast Feeding ; CD4 Lymphocyte Count ; Cohort Studies ; Escherichia/genetics/isolation & purification ; *Gastrointestinal Microbiome/genetics/immunology ; Genes, Bacterial ; HIV Infections/immunology/transmission ; Humans ; Infant ; Infant, Newborn ; Infectious Disease Transmission, Vertical ; Intraepithelial Lymphocytes/*metabolism ; Longitudinal Studies ; Metagenomics ; Mouth Mucosa/immunology/metabolism/microbiology ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Receptors, Chemokine/metabolism ; South Africa/epidemiology ; T-Lymphocyte Subsets/metabolism ; }, abstract = {Although exclusive breastfeeding has been linked to lower rates of postnatal HIV transmission compared to nonexclusive breastfeeding, mechanisms underlying this are unclear. Across a longitudinally sampled cohort of South African infants, we showed that exclusively breastfed (EBF) infants had altered gut bacterial communities when compared to nonexclusively breastfed (NEBF) infants, as well as reduced peripheral CD4 + T cell activation and lowered chemokine and chemokine receptor expression in the oral mucosa. We further demonstrated that the relative abundance of key taxa was correlated with peripheral CD4 + T cell activation. Here, we supplement those findings by using compositional data analyses to identify shifts in the abundance of several Bifidobacteria strains relative to select strains of Escherichia, Bacteroides, and others that are associated with the transition to NEBF. We illustrate that the abundance ratio of these taxa is tightly correlated with feeding modality and is a strong predictor of peripheral T cell activation. More broadly, we discuss our study in the context of novel developments and explore future directions for the field.}, } @article {pmid31347673, year = {2019}, author = {Kumar, S and Adhikari, P and Oakley, B and Kim, WK}, title = {Changes in cecum microbial community in response to total sulfur amino acid (TSAA: DL-methionine) in antibiotic-free and supplemented poultry birds.}, journal = {Poultry science}, volume = {98}, number = {11}, pages = {5809-5819}, doi = {10.3382/ps/pez380}, pmid = {31347673}, issn = {1525-3171}, mesh = {Amino Acids, Sulfur/administration & dosage/*metabolism ; Animal Feed/analysis ; Animals ; Anti-Bacterial Agents/administration & dosage/*pharmacology ; Bacitracin/administration & dosage/*pharmacology ; Cecum/*microbiology ; Chickens/*microbiology/physiology ; Diet/veterinary ; Dietary Supplements/analysis ; Gastrointestinal Microbiome/*drug effects ; Male ; Racemethionine/administration & dosage/*metabolism ; Random Allocation ; Salicylates/administration & dosage/*pharmacology ; }, abstract = {The effect of essential total sulfur amino acids (TSAA) like methionine and cysteine on the cecal microbiome of broilers was investigated at 2 different time points (days 21 and 42) of broiler rearing. A total of 360-day-old Cobb male broiler chicks were randomly distributed to 6 dietary treatments in a 2 × 3 factorial arrangement, with 2 levels of antibiotic growth promoters (AGP: 0 and 0.05%) and 3 levels of TSAA (DL-methionine) either for starter (0.7, 0.8, and 0.9%) or finisher chicks (0.52, 0.62, and 0.72%), labeled as diets 1 to 6. Cecal digesta from each replicate (n = 10) were sampled on days 21 and 42. DNA was extracted for the amplification of the V4 region of bacterial 16S rRNA genes and subjected to Illumina sequencing. Bioinformatic analyses were performed using QIIME, Mothur, and ad hoc tools and functional profiles of the inferred metagenome were analyzed using PICRUST. Statistical difference was determined by 2-way ANOVA and PERMANOVA. Clustering of cecal communities using PCoA showed clear separation of microbial communities based on age (P < 0.05) of birds and between low and medium/ high levels of TSAA (DL-methionine). At day 21, bacterial richness and diversity were higher than at day 42 where Clostridium cluster XI and Lactobacillus were found most abundant. No variability in taxonomic richness at the genus level was observed with AGP and DL-methionine supplementation. Interbird variation for richness was greater at day 42 compared to day 21. The mean fold difference of richness was greater (1.5 mean fold) with diets 1 and 6, suggesting interactive effects of AGP and TSAA (DL-methionine) in the diet. KEGG function profiles calculated by PICRUST suggest that the cecal microbiome increased glycolysis and energy generation correlated with increased dietary TSAA (DL-methionine) supplementation levels during the late broiler growth period (day 42). This study increases our knowledge of microbial dynamics and functions that are relevant to host nutrition and performance that may help us tailoring alternative strategies for raising poultry birds under antibiotic-free conditions.}, } @article {pmid31345023, year = {2019}, author = {Ahmad, MI and Zou, X and Ijaz, MU and Hussain, M and Liu, C and Xu, X and Zhou, G and Li, C}, title = {Processed Meat Protein Promoted Inflammation and Hepatic Lipogenesis by Upregulating Nrf2/Keap1 Signaling Pathway in Glrx-Deficient Mice.}, journal = {Journal of agricultural and food chemistry}, volume = {67}, number = {32}, pages = {8794-8809}, doi = {10.1021/acs.jafc.9b03136}, pmid = {31345023}, issn = {1520-5118}, mesh = {Animals ; Cholesterol/blood ; Cytokines/metabolism ; Female ; Gastrointestinal Microbiome ; Glutaredoxins/deficiency/*genetics ; Humans ; Inflammation/genetics/immunology/*metabolism/microbiology ; Kelch-Like ECH-Associated Protein 1/genetics/*metabolism ; *Lipogenesis ; Liver/*metabolism ; Male ; Meat Products/*adverse effects ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; NF-E2-Related Factor 2/genetics/*metabolism ; Red Meat ; Signal Transduction ; Triglycerides/blood ; }, abstract = {Oxidative stress may play a critical role in the progression of liver disorders. Increasing interest has been given to the associations among diet, oxidative stress, gut-liver axis, and nonalcoholic fatty liver disease. Here, we investigated the effects of processed meat proteins on biomarkers of lipid homeostasis, hepatic metabolism, antioxidant functions, and gut microbiota composition in glutaredoxin1 deficient (Glrx1[-/-]) mice. The wild-type (WT) and Glrx1[-/-] mice were fed a soy protein diet (SPD), a dry-cured pork protein diet (DPD), a braised pork protein diet (BPD), and a cooked pork protein diet (CPD) at a dose of 20% of protein for 3 months. Serum and hepatic total cholesterol, serum endotoxin, hepatic liver droplet %, and antioxidant capacity were significantly increased in the CPD fed WT mice. In addition, CPD fed Glrx1[-/-] mice significantly increased total cholesterol, triacylglycerol, and pro-inflammatory cytokines which are accompanied by higher steatosis scores, intrahepatic lipid accumulation, and altered gene expression associated with lipid metabolism. Furthermore, hepatic gene expression of Nrf2/keap1 signaling pathway and its downstream signaling targets were determined using RT-qPCR. Glrx1 deficiency increased Nrf2 activity and expression of its target genes (GPx, catalase, SOD1, G6pd, and Bbc3), which was exacerbated by intake of CPD. Metagenomic analyses revealed that Glrx1[-/-] mice fed meat protein diets had higher abundances of Mucispirillum, Oscillibacter, and Mollicutes but lower abundances of Bacteroidales S24-7 group_norank, Blautia, and Anaerotruncus than their wild-type counterparts. In summary, Glrx1 deficiency induced an increase in serum biomarkers for lipid homeostasis, gut microbiota imbalance, and upregulation of Nrf2/Keap1 and antioxidant defense genes, which was aggravated by cooked meat protein diet.}, } @article {pmid31344308, year = {2019}, author = {Gao, ZM and Huang, JM and Cui, GJ and Li, WL and Li, J and Wei, ZF and Chen, J and Xin, YZ and Cai, DS and Zhang, AQ and Wang, Y}, title = {In situ meta-omic insights into the community compositions and ecological roles of hadal microbes in the Mariana Trench.}, journal = {Environmental microbiology}, volume = {21}, number = {11}, pages = {4092-4108}, doi = {10.1111/1462-2920.14759}, pmid = {31344308}, issn = {1462-2920}, mesh = {Alphaproteobacteria/classification/genetics/*metabolism ; Aquatic Organisms/classification/genetics/metabolism ; Archaea/classification/genetics/*metabolism ; Chloroflexi/classification/genetics/*metabolism ; Ecology ; Gammaproteobacteria/classification/genetics/*metabolism ; Heterotrophic Processes ; Metagenome ; Microbiota/genetics ; Nitrification/physiology ; Pacific Ocean ; }, abstract = {The low temperature and elevated hydrostatic pressure in hadal trenches at water depths below 6000 m render sample collection difficult. Here, in situ hadal water microbial samples were collected from the Mariana Trench and analysed. The hadal microbial communities at different depths were revealed to be consistent and were dominated by heterotrophic Marinimicrobia. Thirty high-quality metagenome-assembled genomes (MAGs) were retrieved to represent the major hadal microbes affiliated with 12 prokaryotic phyla. Most of the MAGs were newly reported and probably derived from novel hadal inhabitants as exemplified by a potentially new candidate archaeal phylum in the DPANN superphylum. Metabolic reconstruction indicated that a great number of the MAGs participated in nitrogen and sulfur cycling, in which the nitrification process was driven sequentially by Thaumarchaeota and Nitrospirae and sulfur oxidization by Rhodospirillales in the Alphaproteobacteria class. Moreover, several groups of hadal microbes were revealed to be potential carbon monoxide oxidizers. Metatranscriptomic result highlighted the contribution of Chloroflexi in degrading recalcitrant dissolved organic matter and Marinimicrobia in extracellular protein decomposition. The present work provides an in-depth view on the hadal microbial communities regarding their endemism and element cycles.}, } @article {pmid31344227, year = {2019}, author = {Alessandri, G and Milani, C and Mancabelli, L and Mangifesta, M and Lugli, GA and Viappiani, A and Duranti, S and Turroni, F and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {The impact of human-facilitated selection on the gut microbiota of domesticated mammals.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {9}, pages = {}, doi = {10.1093/femsec/fiz121}, pmid = {31344227}, issn = {1574-6941}, mesh = {Animal Feed/analysis ; Animals ; Bacteria/classification/genetics/*isolation & purification ; Domestication ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Mammals/growth & development/*microbiology ; Metagenomics ; Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Domestication is the process by which anthropogenic forces shape lifestyle and behavior of wild species to accommodate human needs. The impact of domestication on animal physiology and behavior has been extensively studied, whereas its effect on the gut microbiota is still largely unexplored. For this reason, 16S rRNA gene-based and internal transcribed spacer-mediated bifidobacterial profiling, together with shotgun metagenomics, was employed to investigate the taxonomic composition and metabolic repertoire of 146 mammalian fecal samples, corresponding to 12 domesticated-feral dyads. Our results revealed that changes induced by domestication have extensively shaped the taxonomic composition of the mammalian gut microbiota. In this context, the selection of microbial taxa linked to a more efficient feed conversion into body mass and putative horizontal transmission of certain bacterial genera from humans were observed in the fecal microbiota of domesticated animals when compared to their feral relatives and to humans. In addition, profiling of the metabolic arsenal through metagenomics highlighted extensive functional adaptation of the fecal microbial community of domesticated mammals to changes induced by domestication. Remarkably, domesticated animals showed, when compared to their feral relatives, increased abundance of specific glycosyl hydrolases, possibly due to the higher intake of complex plant carbohydrates typical of commercial animal feeds.}, } @article {pmid31344223, year = {2019}, author = {Willis, C and Desai, D and LaRoche, J}, title = {Influence of 16S rRNA variable region on perceived diversity of marine microbial communities of the Northern North Atlantic.}, journal = {FEMS microbiology letters}, volume = {366}, number = {13}, pages = {}, pmid = {31344223}, issn = {1574-6968}, mesh = {Aquatic Organisms/*classification/*genetics ; Archaea/classification/genetics ; Atlantic Ocean ; Bacteria/classification/genetics ; Biodiversity ; Metagenomics/methods ; *Microbiota ; Phylogeny ; *RNA, Ribosomal, 16S ; }, abstract = {Marine microbes play essential roles in global energy and nutrient cycles. A primary method of determining their diversity and distribution is through sequencing of 16S ribosomal RNA genes from environmental samples. However, the perceived community composition may vary significantly based on differences in methodology, including choice of 16S variable region(s). This study investigated the influence of 16S variable region selection (V4-V5 or V6-V8) on perceived community composition and diversity for bacteria, Archaea and chloroplasts by tag-Illumina sequencing. We used 24 samples from the photic zone of the Scotian Shelf, northwest Atlantic, collected during a spring phytoplankton bloom. Taxonomic assignment and community composition varied greatly depending on the choice of variable regions while observed patterns of beta diversity were reproducible between variable regions. V4-V5 was considered the preferred variable region for future studies based on its superior recognition of Archaea, which has received little attention in bloom dynamics. The V6-V8 region captured more of the bacterial diversity, including the abundant SAR11 clades and, to a lesser extent, that of chloroplasts. However, the magnitude of difference between variable regions for bacteria and chloroplast was less than for Archaea.}, } @article {pmid31342640, year = {2019}, author = {Maestre-Carballa, L and Lluesma Gomez, M and Angla Navarro, A and Garcia-Heredia, I and Martinez-Hernandez, F and Martinez-Garcia, M}, title = {Insights into the antibiotic resistance dissemination in a wastewater effluent microbiome: bacteria, viruses and vesicles matter.}, journal = {Environmental microbiology}, volume = {21}, number = {12}, pages = {4582-4596}, doi = {10.1111/1462-2920.14758}, pmid = {31342640}, issn = {1462-2920}, support = {ACIF/2015/332//Generalitat Valenciana/International ; ACOM/2015/133//Generalitat Valenciana/International ; 5334//Gordon and Betty Moore Foundation/International ; RTI2018-094248-B-I00//Ministerio de Ciencia e Innovación/International ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/genetics ; *Drug Resistance, Microbial ; *Extracellular Vesicles ; Genes, Bacterial ; Metagenome ; Microbiota/*drug effects ; Viruses/genetics ; Wastewater/*microbiology ; *Water Microbiology ; }, abstract = {Wastewater treatment plants effluents are considered as hotspots for the dispersion of antibiotic resistance genes (ARGs) into natural ecosystems. The bacterial resistome (ARG collection in a metagenome) analyses have provided clues on antibacterial resistance dynamics. However, viruses and vesicles are frequently ignored. Here, we addressed the bacterial, viral and vesicle resistomes from a representative wastewater effluent in natural conditions and amended with polymyxin, which is used as a last resort antibiotic. Metagenomics showed that the natural prokaryotic resistome was vast (9000 ARG hits/Gb metagenome) and diverse, while viral resistome was two orders of magnitude lower (50 ARG hits/Gb metagenome) suggesting that viruses rarely encoded ARGs. After polymyxin amendment, data showed no ARG enrichment - including to polymyxin - in the microbiome. Remarkably, microbiomes responded to polymyxin with a vast release of putative vesicles (threefold increase compared with the control), which might be used as 'traps' to decrease the antibiotic concentration. Intriguingly, although polymyxin resistance genes (PRGs) were rare in the microbiome (0.018% of total ARG found), in the viral and vesicle fractions, PRGs were more abundant (0.5%-0.8% of total ARG found). Our data suggest that vesicles could have a more active role in the context of transmission of antibiotic resistances.}, } @article {pmid31340852, year = {2019}, author = {Walker, AR and Datta, S}, title = {Identification of city specific important bacterial signature for the MetaSUB CAMDA challenge microbiome data.}, journal = {Biology direct}, volume = {14}, number = {1}, pages = {11}, pmid = {31340852}, issn = {1745-6150}, mesh = {Bacteria/*genetics ; Cities ; High-Throughput Nucleotide Sequencing/*methods ; *Machine Learning ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {BACKGROUND: Metagenomic data of whole genome sequences (WGS) from samples across several cities around the globe may unravel city specific signatures of microbes. Illumina MiSeq sequencing data was provided from 12 cities in 7 different countries as part of the 2018 CAMDA "MetaSUB Forensic Challenge", including also samples from three mystery sets. We used appropriate machine learning techniques on this massive dataset to effectively identify the geographical provenance of "mystery" samples. Additionally, we pursued compositional data analysis to develop accurate inferential techniques for such microbiome data. It is expected that this current data, which is of higher quality and higher sequence depth compared to the CAMDA 2017 MetaSUB challenge data, along with improved analytical techniques would yield many more interesting, robust and useful results that can be beneficial for forensic analysis.

RESULTS: A preliminary quality screening of the data revealed a much better dataset in terms of Phred quality score (hereafter Phred score), and larger paired-end MiSeq reads, and a more balanced experimental design, though still not equal number of samples across cities. PCA (Principal Component Analysis) analysis showed interesting clusters of samples and a large amount of the variability in the data was explained by the first three components (~ 70%). The classification analysis proved to be consistent across both the testing mystery sets with a similar percentage of the samples correctly predicted (up to 90%). The analysis of the relative abundance of bacterial "species" showed that some "species" are specific to some regions and can play important roles for predictions. These results were also corroborated by the variable importance given to the "species" during the internal cross validation (CV) run with Random Forest (RF).

CONCLUSIONS: The unsupervised analysis (PCA and two-way heatmaps) of the log2-cpm normalized data and relative abundance differential analysis seemed to suggest that the bacterial signature of common "species" was distinctive across the cities; which was also supported by the variable importance results. The prediction of the city for mystery sets 1 and 3 showed convincing results with high classification accuracy/consistency. The focus of this work on the current MetaSUB data and the analytical tools utilized here can be of great help in forensic, metagenomics, and other sciences to predict city of provenance of metagenomic samples, as well as in other related fields. Additionally, the pairwise analysis of relative abundance showed that the approach provided consistent and comparable "species" when compared with the classification importance variables.

REVIEWERS: This article was reviewed by Manuela Oliveira, Dimitar Vassilev, and Patrick Lee.}, } @article {pmid31339905, year = {2019}, author = {Sheahan, T and Hakstol, R and Kailasam, S and Glaister, GD and Hudson, AJ and Wieden, HJ}, title = {Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0219961}, pmid = {31339905}, issn = {1932-6203}, mesh = {Ambulances/*standards ; Biological Monitoring/*methods ; Clostridium/genetics/isolation & purification ; Cross Infection/microbiology/prevention & control ; DNA, Bacterial/chemistry/genetics ; Metagenomics/*methods ; *Microbiota ; Nanopore Sequencing/*methods ; Staphylococcus/genetics/isolation & purification ; }, abstract = {Pathogen monitoring, detection and removal are essential to public health and outbreak management. Systems are in place for monitoring the microbial load of hospitals and public health facilities with strategies to mitigate pathogen spread. However, no such strategies are in place for ambulances, which are tasked with transporting at-risk individuals in immunocompromised states. As standard culturing techniques require a laboratory setting, and are time consuming and labour intensive, our approach was designed to be portable, inexpensive and easy to use based on the MinION third-generation sequencing platform from Oxford Nanopore Technologies. We developed a transferable sampling-to-analysis pipeline to characterize the microbial community in emergency medical service vehicles. Our approach identified over sixty-eight organisms in ambulances to the genera level, with a proportion of these being connected with health-care associated infections, such as Clostridium spp. and Staphylococcus spp. We also monitored the microbiome of different locations across three ambulances over time, and examined the dynamic community of microorganisms found in emergency medical service vehicles. Observed differences identified hot spots, which may require heightened monitoring and extensive cleaning. Through metagenomics analysis it is also possible to identify how microorganisms spread between patients and colonize an ambulance over time. The sequencing results aid in the development of practices to mitigate disease spread, while also providing a useful tool for outbreak prediction through ongoing analysis of the ambulance microbiome to identify new and emerging pathogens. Overall, this pipeline allows for the tracking and monitoring of pathogenic microorganisms of epidemiological interest, including those related to health-care associated infections.}, } @article {pmid31338542, year = {2019}, author = {Bohra, V and Dafale, NA and Purohit, HJ}, title = {Understanding the alteration in rumen microbiome and CAZymes profile with diet and host through comparative metagenomic approach.}, journal = {Archives of microbiology}, volume = {201}, number = {10}, pages = {1385-1397}, doi = {10.1007/s00203-019-01706-z}, pmid = {31338542}, issn = {1432-072X}, mesh = {Animals ; Bacteria/*classification/*enzymology/genetics ; Bacteroidetes/genetics ; *Buffaloes/microbiology ; *Cattle/microbiology ; Cellulases/metabolism ; *Diet/veterinary ; Dietary Fiber ; Glycoside Hydrolases/metabolism ; Metagenome ; Metagenomics ; Microbial Consortia/genetics ; Microbiota/*physiology ; Phylogeny ; Rumen/*microbiology ; }, abstract = {Rumen microbial community harbors a distinct genetic reservoir of potent carbohydrate-active enzymes (CAZyme) that functions efficiently for the deconstruction of plant biomass. Based on this premise, metagenomics approach was applied to characterize the rumen microbial community and identify carbohydrate-active genes of Bos taurus (cow) and Bubalus bubalis (buffalo) fed on green or dry roughage. Metadata was generated from the samples: green roughage-fed cow (NDC_GR), buffalo (NDB_GR) and dry roughage-fed cow (NDC_DR), buffalo (NDB_DR). Phylogenetic analysis revealed the dominance of Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria and Fibrobacter in all the four samples, covering 90-96% of the total bacterial population. On finer resolution, higher abundance of bacterial genera Fibrobacter, Bacteroides, Clostridium, Prevotella and Ruminococcus involved in plant biomass hydrolysis was observed in NDB_DR. Functional annotation using dbCAN annotation algorithm identified 28.13%, 8.08% 10.93% and 12.53% of the total contigs as putatively carbohydrate-active against NDC_GR, NDB_GR, NDC_DR and NDB_DR, respectively. Additional profiling of CAZymes revealed an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on dry roughage with substantial enrichments of genes encoding GHs from families GH2, GH3, GH13 and GH43. GHs of families GH45, GH12, GH113, GH128, GH54 and GH27 were observed exclusively in NDB_DR metagenome. A higher abundance of cellulases, hemicellulases, debranching and oligosaccharide hydrolyzing enzymes was revealed in NDB_DR metagenome. Accordingly, it can be concluded that buffalo rumen microbiome are more efficient in plant biomass hydrolysis. The present study provides a deep understanding of the shifts in microbial community and plant polysaccharide deconstructing capabilities of rumen microbiome in response to changes in the feed type and host animal. Activity-specific microbial consortia procured from these animals can be used further for efficient plant biomass hydrolysis. The study also establishes the utility of rumen microbiome as a unique resource for mining diverse lignocellulolytic enzymes.}, } @article {pmid31338073, year = {2019}, author = {Praeg, N and Pauli, H and Illmer, P}, title = {Microbial Diversity in Bulk and Rhizosphere Soil of Ranunculus glacialis Along a High-Alpine Altitudinal Gradient.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1429}, pmid = {31338073}, issn = {1664-302X}, abstract = {Serving as "natural laboratories", altitudinal gradients can be used to study changes in the distribution of microorganisms in response to changing environmental conditions that typically occur over short geographical distances. Besides, rhizosphere zones of plants are known to be hot-spots for microbial diversity and to contain different microbial communities when compared with surrounding bulk soil. To discriminate the effects of altitude and plants, we investigated the microbial communities in the rhizosphere of Ranunculus glacialis and bulk soil along a high-alpine altitudinal gradient (2,600-3,400 m a.s.l.). The research area of this study was Mount (Mt.) "Schrankogel" in the Central Alps of Tyrol (Austria). Our results point to significantly different microbial diversities and community compositions in the different altitudinal belts. In the case of prokaryotes, environmental parameters could explain 41% of the total variation of soil communities, with pH and temperature being the strongest influencing factors. Comparing the effects derived from fraction (bulk vs. rhizosphere soil) and environmental factors, the effects of the roots of R. glacialis accounted for about one third of the explained variation. Fungal communities on the other hand were nearly exclusively influenced by environmental parameters accounting for 37.4% of the total variation. Both, for altitudinal zones as well as for bulk and rhizosphere fractions a couple of very specific biomarker taxa could be identified. Generally, the patterns of abundance of several taxa did not follow a steady increased or decreased trend along the altitudinal gradient but in many cases a maximal or minimal occurrence was established at mid-altitudes (3,000-3,100 m). This mid-altitudinal zone is a transition zone (the so-called alpine-nival ecotone) between the (lower) alpine grassland/tundra zone and the (upper) sparsely vegetated nival zone and was shown to correspond with the summer snow line. Climate change and the associated increase in temperature will shift this transition zone and thus, might also shift the described microbial patterns and biomarkers.}, } @article {pmid31337891, year = {2019}, author = {Kumar, M and Ji, B and Zengler, K and Nielsen, J}, title = {Modelling approaches for studying the microbiome.}, journal = {Nature microbiology}, volume = {4}, number = {8}, pages = {1253-1267}, doi = {10.1038/s41564-019-0491-9}, pmid = {31337891}, issn = {2058-5276}, mesh = {Bacteria/metabolism ; Disease ; Health ; Humans ; Metabolomics ; Metagenome ; Microbial Interactions ; *Microbiota/genetics/physiology ; *Models, Theoretical ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Advances in metagenome sequencing of the human microbiome have provided a plethora of new insights and revealed a close association of this complex ecosystem with a range of human diseases. However, there is little knowledge about how the different members of the microbial community interact with each other and with the host, and we lack basic mechanistic understanding of these interactions related to health and disease. Mathematical modelling has been demonstrated to be highly advantageous for gaining insights into the dynamics and interactions of complex systems and in recent years, several modelling approaches have been proposed to enhance our understanding of the microbiome. Here, we review the latest developments and current approaches, and highlight how different modelling strategies have been applied to unravel the highly dynamic nature of the human microbiome. Furthermore, we discuss present limitations of different modelling strategies and provide a perspective of how modelling can advance understanding and offer new treatment routes to impact human health.}, } @article {pmid31337439, year = {2019}, author = {Zheng, Y and Wang, T and Tu, X and Huang, Y and Zhang, H and Tan, D and Jiang, W and Cai, S and Zhao, P and Song, R and Li, P and Qin, N and Fang, W}, title = {Gut microbiome affects the response to anti-PD-1 immunotherapy in patients with hepatocellular carcinoma.}, journal = {Journal for immunotherapy of cancer}, volume = {7}, number = {1}, pages = {193}, pmid = {31337439}, issn = {2051-1426}, mesh = {Antibodies, Monoclonal, Humanized/*administration & dosage/pharmacology ; Bacteria/*classification/drug effects/genetics/isolation & purification ; Carcinoma, Hepatocellular/*drug therapy/microbiology ; Clinical Decision-Making ; Gastrointestinal Microbiome/drug effects ; Humans ; Immunotherapy ; Liver Neoplasms/*drug therapy/microbiology ; Metabolic Networks and Pathways ; Metagenomics/*methods ; Phylogeny ; Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Sequence Analysis, DNA ; Treatment Outcome ; }, abstract = {BACKGROUND: Checkpoint-blockade immunotherapy targeting programmed cell death protein 1 (PD-1) has recently shown promising efficacy in hepatocellular carcinoma (HCC). However, the factors affecting and predicting the response to anti-PD-1 immunotherapy in HCC are still unclear. Herein, we report the dynamic variation characteristics and specificities of the gut microbiome during anti-PD-1 immunotherapy in HCC using metagenomic sequencing.

RESULTS: Fecal samples from patients responding to immunotherapy showed higher taxa richness and more gene counts than those of non-responders. For dynamic analysis during anti-PD-1 immunotherapy, the dissimilarity of beta diversity became prominent across patients as early as Week 6. In non-responders, Proteobacteria increased from Week 3, and became predominant at Week 12. Twenty responder-enriched species, including Akkermansia muciniphila and Ruminococcaceae spp., were further identified. The related functional genes and metabolic pathway analysis, such as carbohydrate metabolism and methanogenesis, verified the potential bioactivities of responder-enriched species.

CONCLUSIONS: Gut microbiome may have a critical impact on the responses of HCC patients treated with anti-PD-1 immunotherapy. The dynamic variation characteristics of the gut microbiome may provide early predictions of the outcomes of immunotherapy in HCC, which is critical for disease-monitoring and treatment decision-making.}, } @article {pmid31337187, year = {2019}, author = {Zhang, C and Xu, B and Lu, T and Huang, Z}, title = {Metagenomic Analysis of the Fecal Microbiomes of Wild Asian Elephants Reveals Microflora and Enzymes that Mainly Digest Hemicellulose.}, journal = {Journal of microbiology and biotechnology}, volume = {29}, number = {8}, pages = {1255-1265}, doi = {10.4014/jmb.1904.04033}, pmid = {31337187}, issn = {1738-8872}, mesh = {Animals ; Bacteria/classification/enzymology/genetics ; Biodiversity ; Cellulose/metabolism ; China ; Elephants/*microbiology ; Enzymes/*classification ; Feces/*microbiology ; Firmicutes/genetics ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/*microbiology ; Lignin/metabolism ; *Metagenomics ; Phylogeny ; Polysaccharides/*metabolism ; }, abstract = {To investigate the diversity of gastrointestinal microflora and lignocellulose-degrading enzymes in wild Asian elephants, three of these animals living in the same group were selected for study from the Wild Elephant Valley in the Xishuangbanna Nature Reserve of Yunnan Province, China. Fresh fecal samples from the three wild Asian elephants were analyzed by metagenomic sequencing to study the diversity of their gastrointestinal microbes and cellulolytic enzymes. There were a high abundance of Firmicutes and a higher abundance of hemicellulose-degrading hydrolases than cellulose-degrading hydrolases in the wild Asian elephants. Furthermore, there were a high abundance and a rich diversity of carbohydrate active enzymes (CAZymes) obtained from the gene set annotation of the three samples, with the majority of them showing low identity with the CAZy database entry. About half of the CAZymes had no species source at the phylum or genus level. These indicated that the wild Asian elephants might possess greater ability to digest hemicellulose than cellulose to provide energy, and moreover, the gastrointestinal tracts of these pachyderms might be a potential source of novel efficient lignocellulose-degrading enzymes. Therefore, the exploitation and utilization of these enzyme resources could help us to alleviate the current energy crisis and ensure food security.}, } @article {pmid31336253, year = {2019}, author = {Tian, Z and Liu, R and Zhang, H and Yang, M and Zhang, Y}, title = {Developmental dynamics of antibiotic resistome in aerobic biofilm microbiota treating wastewater under stepwise increasing tigecycline concentrations.}, journal = {Environment international}, volume = {131}, number = {}, pages = {105008}, doi = {10.1016/j.envint.2019.105008}, pmid = {31336253}, issn = {1873-6750}, mesh = {Aerobiosis ; Anti-Bacterial Agents/*pharmacology ; Biofilms/*drug effects ; *Drug Resistance, Microbial ; Microbiota/*drug effects ; Tigecycline/*pharmacology ; Wastewater/*chemistry ; }, abstract = {This study aimed to investigate the impact of tigecycline, the third generation tetracycline, on the antibiotic resistance development in environmental microbiota. Two biological contact oxidation reactors containing aerobic biofilm microbiota were constructed, one of which was constantly fed with synthetic wastewater spiked with increasing concentrations of tigecycline (0 to 25 mg/L) under a hydrolytic retention time of 24 h. Over a period of 636 days, chemical oxygen demand removal over 90% and complete nitrification were achieved for both the control and tigecycline-exposed reactors, and effluent tigecycline concentrations in the tigecycline-exposed system were always <0.051 mg/L. Significant increases (p < 0.01) in resistome abundance and resistant bacteria ratio were detected at a tigecycline dose of 10 and 25 mg/L, respectively, revealed by metagenomic sequencing and culture-based method. The increase of resistome in the tigecycline system was mainly attributed to the enrichment of tetX, one cooperative tetracycline degrading gene. Partial canonical correspondence analysis showed that the change of resistome was mainly driven by bacterial community shift (vertical pathway). Network and genome binning analyses further suggested that the proliferation of Flavobacterium harboring tetX contributed to a relatively low community-wide resistance development in the aerobic biofilm microbiota under tigecycline selection by reducing the antibiotic concentration. This work provides scientific bases for the management and evaluation of the resistance risk induced by this novel antibiotic.}, } @article {pmid31336215, year = {2019}, author = {Gual-Grau, A and Guirro, M and Mayneris-Perxachs, J and Arola, L and Boqué, N}, title = {Impact of different hypercaloric diets on obesity features in rats: a metagenomics and metabolomics integrative approach.}, journal = {The Journal of nutritional biochemistry}, volume = {71}, number = {}, pages = {122-131}, doi = {10.1016/j.jnutbio.2019.06.005}, pmid = {31336215}, issn = {1873-4847}, mesh = {Animals ; Bile Acids and Salts/*metabolism ; Cecum/microbiology ; Diet/*adverse effects ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Gastrointestinal Microbiome/genetics/*physiology ; Male ; Metabolome/physiology ; Metabolomics/methods ; Metagenomics/methods ; Obesity/*etiology/genetics/metabolism ; Rats, Wistar ; Sucrose/adverse effects ; Urine/physiology ; }, abstract = {Diet is considered a key influencing agent affecting the gut microbiome. Dysbiosis of microbial communities contributes to the development of metabolic diseases such as obesity. We aimed to characterize the physiological, microbial and metabolic changes induced by different obesogenic diets to understand the diet-specific modulation of the host-microbiota co-metabolism in rodents. For this purpose, Wistar rats were fed standard, cafeteria (CAF), low-fat (LF), high-fat (HF) and high-fat high-sucrose (HFS) diets for 10 weeks. The CAF diet strongly induced an obese phenotype accompanied by dyslipidemia, hyperleptinemia, insulin resistance and hepatic steatosis, whereas both HF and HFS diets promoted overweight. Concerning the microbiome, CAF feeding induced a rise of the Bacteroidetes-to-Firmicutes ratio, while few microbial genera were altered in the HF or HFS group. Changes in microbial activity according to dietary treatment were also reflected in the disruption of short-chain fatty acid production and bile acid metabolism, which were mainly associated with fiber intake. Urinary metabolomics revealed a significant increase in metabolites related to oxidative stress and metabolic inflammation together with an altered excretion of host-microbiota co-metabolites only in the CAF group. Moreover, several associations between metabolic patterns, physiological status and specific microbial communities were described, helping to elucidate the crucial role of the microbiota in host homeostasis. Overall, our study suggests that different hypercaloric dietary models distinctively influence gut microbiota composition and reveals robust and similar clustering patterns concerning both cecal microbiome and urinary metabolome profiles.}, } @article {pmid31335912, year = {2019}, author = {Pragman, AA and Knutson, KA and Gould, TJ and Hodgson, SW and Isaacson, RE and Reilly, CS and Wendt, CH}, title = {Chronic obstructive pulmonary disease upper airway microbiome is associated with select clinical characteristics.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0219962}, pmid = {31335912}, issn = {1932-6203}, support = {UL1 TR002494/TR/NCATS NIH HHS/United States ; T32 AI055433/AI/NIAID NIH HHS/United States ; UL1 TR000114/TR/NCATS NIH HHS/United States ; KL2 TR002492/TR/NCATS NIH HHS/United States ; IK2 CX001095/CX/CSRD VA/United States ; T32 GM108557/GM/NIGMS NIH HHS/United States ; }, mesh = {Aged ; Female ; Humans ; Laryngeal Mucosa/*microbiology ; Male ; Metagenome ; *Microbiota ; Middle Aged ; Nasal Mucosa/*microbiology ; Pulmonary Disease, Chronic Obstructive/epidemiology/*microbiology/pathology ; Smoking/epidemiology ; Sputum/microbiology ; }, abstract = {BACKGROUND: Chronic obstructive pulmonary disease (COPD) is an inflammatory lung disorder associated with lung microbiome dysbiosis. Although the upper airway microbiome is the source of the lung microbiome, the relationships between the oral, nasal, and sputum microbiota are incompletely understood. Our objective was to determine features that differentiate the oral, nasal, and sputum microbiome among subjects with stable COPD.

METHODS: We recruited 15 current or former smokers to provide oral and sputum samples on day 1. On day 2, another oral sample and a nasal sample were obtained. Each sample and control underwent DNA extraction, 16S V4 rRNA amplification, 16S V4 sequencing, and qPCR of 16S rRNA. Data were analyzed using dada2 and R.

RESULTS: Most (14 of 15) subjects were male with a mean age of 65.2. One subject had no pulmonary obstruction, while 5 had mild COPD, 7 had moderate COPD, and 2 had severe COPD. Three subjects (20%) were current tobacco users and 2 subjects (13%) used inhaled corticosteroids (ICS). Subjects had a mean of 49.1 pack-years of tobacco exposure. Bacterial biomass was associated with anatomic site, but no differences in biomass were observed with age, FEV1 percent predicted (FEV1pp), ICS use, smoking status, or edentulous state. Shannon index was associated with site (lower nasal diversity than oral and sputum diversity, p<0.001), but not age, ICS use, FEV1pp, tobacco use, or edentulous state. β-diversity was illustrated by principal coordinate analysis using Bray-Curtis dissimilarity and PERMANOVA analyses, showing sample clustering by anatomic site (p = 0.001) with nasal samples forming a cluster separate from the combined oral wash samples and sputum samples. Clustering was also observed with ICS use (p = 0.029) and edentulous state (p = 0.019), while FEV1pp and current tobacco use were not significant. In an amplicon sequencing variant (ASV)-level analysis of oral samples using a linear regression model with Benjamini-Hochberg correction at an FDR<0.10, 10 ASVs were associated with age while no ASVs were associated with FEV1pp or smoking status. Sputum sample analysis demonstrated that 51 ASVs (25 unique genera) were associated with age, 61 ASVs (32 genera) were associated with FEV1pp, and no ASVs were associated with smoking status. In a combined dataset, the frequent exacerbator phenotype, rather than ICS use, was associated with decreased sputum Shannon diversity.

CONCLUSIONS: Among the upper airway microbiota of COPD subjects, anatomic site was associated with bacterial biomass, Shannon diversity, and β-diversity. ICS use and edentulous state were both associated with β-diversity. Age was associated with taxa relative abundance in oral and sputum samples, while FEV1pp was associated with taxa relative abundance in sputum samples only.}, } @article {pmid31333598, year = {2019}, author = {Thomas, SC and Tamadonfar, KO and Seymour, CO and Lai, D and Dodsworth, JA and Murugapiran, SK and Eloe-Fadrosh, EA and Dijkstra, P and Hedlund, BP}, title = {Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1427}, pmid = {31333598}, issn = {1664-302X}, abstract = {Temperature is a primary driver of microbial community composition and taxonomic diversity; however, it is unclear to what extent temperature affects characteristics of central carbon metabolic pathways (CCMPs) at the community level. In this study, 16S rRNA gene amplicon and metagenome sequencing were combined with [13]C-labeled metabolite probing of the CCMPs to assess community carbon metabolism along a temperature gradient (60-95°C) in Great Boiling Spring, NV. 16S rRNA gene amplicon diversity was inversely proportional to temperature, and Archaea were dominant at higher temperatures. KO richness and diversity were also inversely proportional to temperature, yet CCMP genes were similarly represented across the temperature gradient and many individual metagenome-assembled genomes had complete pathways. In contrast, genes encoding cellulosomes and many genes involved in plant matter degradation and photosynthesis were absent at higher temperatures. In situ [13]C-CO2 production from labeled isotopomer pairs of glucose, pyruvate, and acetate suggested lower relative oxidative pentose phosphate pathway activity and/or fermentation at 60°C, and a stable or decreased maintenance energy demand at higher temperatures. Catabolism of [13]C-labeled citrate, succinate, L-alanine, L-serine, and L-cysteine was observed at 85°C, demonstrating broad heterotrophic activity and confirming functioning of the TCA cycle. Together, these results suggest that temperature-driven losses in biodiversity and gene content in geothermal systems may not alter CCMP function or maintenance energy demands at a community level.}, } @article {pmid31332384, year = {2019}, author = {Levan, SR and Stamnes, KA and Lin, DL and Panzer, AR and Fukui, E and McCauley, K and Fujimura, KE and McKean, M and Ownby, DR and Zoratti, EM and Boushey, HA and Cabana, MD and Johnson, CC and Lynch, SV}, title = {Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance.}, journal = {Nature microbiology}, volume = {4}, number = {11}, pages = {1851-1861}, pmid = {31332384}, issn = {2058-5276}, support = {P01 AI089473/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Asthma/*immunology ; Bacteria/*classification/enzymology/genetics ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics ; Disease Models, Animal ; Epoxide Hydrolases/*genetics ; Feces/*chemistry ; Female ; Gastrointestinal Microbiome ; Humans ; Immune Tolerance ; Infant, Newborn ; Linoleic Acids/*analysis ; Male ; Mice ; T-Lymphocytes, Regulatory/metabolism ; }, abstract = {Neonates at risk of childhood atopy and asthma exhibit perturbation of the gut microbiome, metabolic dysfunction and increased concentrations of 12,13-diHOME in their faeces. However, the mechanism, source and contribution of this lipid to allergic inflammation remain unknown. Here, we show that intra-abdominal treatment of mice with 12,13-diHOME increased pulmonary inflammation and decreased the number of regulatory T (Treg) cells in the lungs. Treatment of human dendritic cells with 12,13-diHOME altered expression of PPARγ-regulated genes and reduced anti-inflammatory cytokine secretion and the number of Treg cells in vitro. Shotgun metagenomic sequencing of neonatal faeces indicated that bacterial epoxide hydrolase (EH) genes are more abundant in the gut microbiome of neonates who develop atopy and/or asthma during childhood. Three of these bacterial EH genes (3EH) specifically produce 12,13-diHOME, and treatment of mice with bacterial strains expressing 3EH caused a decrease in the number of lung Treg cells in an allergen challenge model. In two small birth cohorts, an increase in the copy number of 3EH or the concentration of 12,13-diHOME in the faeces of neonates was found to be associated with an increased probability of developing atopy, eczema or asthma during childhood. Our data indicate that elevated 12,13-diHOME concentrations impede immune tolerance and may be produced by bacterial EHs in the neonatal gut, offering a mechanistic link between perturbation of the gut microbiome during early life and atopy and asthma during childhood.}, } @article {pmid31332325, year = {2019}, author = {Sheth, RU and Li, M and Jiang, W and Sims, PA and Leong, KW and Wang, HH}, title = {Spatial metagenomic characterization of microbial biogeography in the gut.}, journal = {Nature biotechnology}, volume = {37}, number = {8}, pages = {877-883}, pmid = {31332325}, issn = {1546-1696}, support = {K01 EB016071/EB/NIBIB NIH HHS/United States ; R01 GM110494/GM/NIGMS NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; R01 AI132403/AI/NIAID NIH HHS/United States ; T32 GM008224/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; *Gastrointestinal Microbiome ; *Genome, Bacterial ; Metagenome ; Metagenomics/*methods ; Mice ; Microfluidic Analytical Techniques ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA/methods ; }, abstract = {Spatial structuring is important for the maintenance of natural ecological systems[1,2]. Many microbial communities, including the gut microbiome, display intricate spatial organization[3-9]. Mapping the biogeography of bacteria can shed light on interactions that underlie community functions[10-12], but existing methods cannot accommodate the hundreds of species that are found in natural microbiomes[13-17]. Here we describe metagenomic plot sampling by sequencing (MaPS-seq), a culture-independent method to characterize the spatial organization of a microbiome at micrometer-scale resolution. Intact microbiome samples are immobilized in a gel matrix and cryofractured into particles. Neighboring microbial taxa in the particles are then identified by droplet-based encapsulation, barcoded 16S rRNA amplification and deep sequencing. Analysis of three regions of the mouse intestine revealed heterogeneous microbial distributions with positive and negative co-associations between specific taxa. We identified robust associations between Bacteroidales taxa in all gut compartments and showed that phylogenetically clustered local regions of bacteria were associated with a dietary perturbation. Spatial metagenomics could be used to study microbial biogeography in complex habitats.}, } @article {pmid31332169, year = {2019}, author = {Antunes, KH and Fachi, JL and de Paula, R and da Silva, EF and Pral, LP and Dos Santos, AÁ and Dias, GBM and Vargas, JE and Puga, R and Mayer, FQ and Maito, F and Zárate-Bladés, CR and Ajami, NJ and Sant'Ana, MR and Candreva, T and Rodrigues, HG and Schmiele, M and Silva Clerici, MTP and Proença-Modena, JL and Vieira, AT and Mackay, CR and Mansur, D and Caballero, MT and Marzec, J and Li, J and Wang, X and Bell, D and Polack, FP and Kleeberger, SR and Stein, RT and Vinolo, MAR and de Souza, APD}, title = {Microbiota-derived acetate protects against respiratory syncytial virus infection through a GPR43-type 1 interferon response.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {3273}, pmid = {31332169}, issn = {2041-1723}, mesh = {A549 Cells ; Acetates/metabolism/*pharmacology ; Animals ; Cell Line ; Chlorocebus aethiops ; Humans ; Interferon Type I/*metabolism ; Lung/drug effects/metabolism/virology ; Mice, Inbred C57BL ; Mice, Knockout ; *Microbiota ; Polymorphism, Single Nucleotide ; Protective Agents/metabolism/pharmacology ; Receptor, Interferon alpha-beta/genetics ; Receptors, G-Protein-Coupled/genetics/*metabolism ; Respiratory Syncytial Virus Infections/genetics/*prevention & control/virology ; Vero Cells ; Viral Load/drug effects/genetics ; }, abstract = {Severe respiratory syncytial virus (RSV) infection is a major cause of morbidity and mortality in infants <2 years-old. Here we describe that high-fiber diet protects mice from RSV infection. This effect was dependent on intestinal microbiota and production of acetate. Oral administration of acetate mediated interferon-β (IFN-β) response by increasing expression of interferon-stimulated genes in the lung. These effects were associated with reduction of viral load and pulmonary inflammation in RSV-infected mice. Type 1 IFN signaling via the IFN-1 receptor (IFNAR) was essential for acetate antiviral activity in pulmonary epithelial cell lines and for the acetate protective effect in RSV-infected mice. Activation of Gpr43 in pulmonary epithelial cells reduced virus-induced cytotoxicity and promoted antiviral effects through IFN-β response. The effect of acetate on RSV infection was abolished in Gpr43[-/-] mice. Our findings reveal antiviral effects of acetate involving IFN-β in lung epithelial cells and engagement of GPR43 and IFNAR.}, } @article {pmid31331734, year = {2019}, author = {Díaz-Sánchez, S and Estrada-Peña, A and Cabezas-Cruz, A and de la Fuente, J}, title = {Evolutionary Insights into the Tick Hologenome.}, journal = {Trends in parasitology}, volume = {35}, number = {9}, pages = {725-737}, doi = {10.1016/j.pt.2019.06.014}, pmid = {31331734}, issn = {1471-5007}, mesh = {Animals ; *Biological Evolution ; Genome/*genetics ; Host Microbial Interactions/physiology ; Microbiota/physiology ; Symbiosis ; Ticks/classification/*genetics/*microbiology ; }, abstract = {Recently, our knowledge of the composition and complexity of tick microbial communities has increased and supports microbial impact on tick biology. Results support a phylogenetic association between ticks and their microbiota across evolution; this is known as phylosymbiosis. Herein, using published datasets, we confirm the existence of phylosymbiosis between Ixodes ticks and their microbial communities. The strong phylosymbiotic signal and the phylogenetic structure of microbial communities associated with Ixodid ticks revealed that phylosymbiosis may be a widespread phenomenon in tick-microbiota evolution. This finding supports the existence of a species-specific tick hologenome with a largely unexplored influence on tick biology and pathogen transmission. These results may provide potential targets for the construction of paratransgenic ticks to control tick infestations and tick-borne diseases.}, } @article {pmid31330855, year = {2019}, author = {Deng, L and Silins, R and Castro-Mejía, JL and Kot, W and Jessen, L and Thorsen, J and Shah, S and Stokholm, J and Bisgaard, H and Moineau, S and Nielsen, DS}, title = {A Protocol for Extraction of Infective Viromes Suitable for Metagenomics Sequencing from Low Volume Fecal Samples.}, journal = {Viruses}, volume = {11}, number = {7}, pages = {}, pmid = {31330855}, issn = {1999-4915}, support = {//CIHR/Canada ; }, mesh = {Bacteriophages/classification/genetics ; Computational Biology/methods ; Feces/*virology ; *Gastrointestinal Microbiome ; Humans ; Infant ; *Metagenome ; *Metagenomics/methods ; }, abstract = {The human gut microbiome (GM) plays an important role in human health and diseases. However, while substantial progress has been made in understanding the role of bacterial inhabitants of the gut, much less is known regarding the viral component of the GM. Bacteriophages (phages) are viruses attacking specific host bacteria and likely play important roles in shaping the GM. Although metagenomic approaches have led to the discoveries of many new viruses, they remain largely uncultured as their hosts have not been identified, which hampers our understanding of their biological roles. Existing protocols for isolation of viromes generally require relatively high input volumes and are generally more focused on extracting nucleic acids of good quality and purity for down-stream analysis, and less on purifying viruses with infective capacity. In this study, we report the development of an efficient protocol requiring low sample input yielding purified viromes containing phages that are still infective, which also are of sufficient purity for genome sequencing. We validated the method through spiking known phages followed by plaque assays, qPCR, and metagenomic sequencing. The protocol should facilitate the process of culturing novel viruses from the gut as well as large scale studies on gut viromes.}, } @article {pmid31330081, year = {2019}, author = {Reji, L and Tolar, BB and Smith, JM and Chavez, FP and Francis, CA}, title = {Depth distributions of nitrite reductase (nirK) gene variants reveal spatial dynamics of thaumarchaeal ecotype populations in coastal Monterey Bay.}, journal = {Environmental microbiology}, volume = {21}, number = {11}, pages = {4032-4045}, doi = {10.1111/1462-2920.14753}, pmid = {31330081}, issn = {1462-2920}, support = {//NSF Biological Oceanography/International ; //ARCS Foundation Graduate Research Fellowship/International ; //MBARI Postdoctoral Fellowship/International ; //DOE JGI Community Science Project/International ; }, mesh = {Ammonia/metabolism ; Archaea/*classification/*genetics/metabolism ; Bays/*microbiology ; Ecotype ; Energy Metabolism/*genetics ; Genetic Markers/genetics ; Genetic Variation/genetics ; Nitrite Reductases/*genetics/metabolism ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are key players in nutrient cycling, yet large gaps remain in our understanding of their ecology and metabolism. Despite multiple lines of evidence pointing to a central role for copper-containing nitrite reductase (NirK) in AOA metabolism, the thaumarchaeal nirK gene is rarely studied in the environment. In this study, we examine the diversity of nirK in the marine pelagic environment, in light of previously described ecological patterns of pelagic thaumarchaeal populations. Phylogenetic analyses show that nirK better resolves diversification patterns of marine Thaumarchaeota, compared to the conventionally used marker gene amoA. Specifically, we demonstrate that the three major phylogenetic clusters of marine nirK correspond to the three 'ecotype' populations of pelagic Thaumarchaeota. In this context, we further examine the relative distributions of the three variant groups in metagenomes and metatranscriptomes representing two depth profiles in coastal Monterey Bay. Our results reveal that nirK effectively tracks the dynamics of thaumarchaeal ecotype populations, particularly finer-scale diversification patterns within major lineages. We also find evidence for multiple copies of nirK per genome in a fraction of thaumarchaeal cells in the water column, which must be taken into account when using it as a molecular marker.}, } @article {pmid31327695, year = {2019}, author = {Clos-Garcia, M and Andrés-Marin, N and Fernández-Eulate, G and Abecia, L and Lavín, JL and van Liempd, S and Cabrera, D and Royo, F and Valero, A and Errazquin, N and Vega, MCG and Govillard, L and Tackett, MR and Tejada, G and Gónzalez, E and Anguita, J and Bujanda, L and Orcasitas, AMC and Aransay, AM and Maíz, O and López de Munain, A and Falcón-Pérez, JM}, title = {Gut microbiome and serum metabolome analyses identify molecular biomarkers and altered glutamate metabolism in fibromyalgia.}, journal = {EBioMedicine}, volume = {46}, number = {}, pages = {499-511}, pmid = {31327695}, issn = {2352-3964}, mesh = {Adult ; Aged ; Biomarkers ; Chromatography, High Pressure Liquid ; Computational Biology/methods ; Cytokines/metabolism ; Female ; Fibromyalgia/*etiology/*metabolism ; *Gastrointestinal Microbiome ; Glutamates/*metabolism ; Humans ; Male ; *Metabolome ; *Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; ROC Curve ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: Fibromyalgia is a complex, relatively unknown disease characterised by chronic, widespread musculoskeletal pain. The gut-brain axis connects the gut microbiome with the brain through the enteric nervous system (ENS); its disruption has been associated with psychiatric and gastrointestinal disorders. To gain an insight into the pathogenesis of fibromyalgia and identify diagnostic biomarkers, we combined different omics techniques to analyse microbiome and serum composition.

METHODS: We collected faeces and blood samples to study the microbiome, the serum metabolome and circulating cytokines and miRNAs from a cohort of 105 fibromyalgia patients and 54 age- and environment-matched healthy individuals. We sequenced the V3 and V4 regions of the 16S rDNA gene from faeces samples. UPLC-MS metabolomics and custom multiplex cytokine and miRNA analysis (FirePlex™ technology) were used to examine sera samples. Finally, we combined the different data types to search for potential biomarkers.

RESULTS: We found that the diversity of bacteria is reduced in fibromyalgia patients. The abundance of the Bifidobacterium and Eubacterium genera (bacteria participating in the metabolism of neurotransmitters in the host) in these patients was significantly reduced. The serum metabolome analysis revealed altered levels of glutamate and serine, suggesting changes in neurotransmitter metabolism. The combined serum metabolomics and gut microbiome datasets showed a certain degree of correlation, reflecting the effect of the microbiome on metabolic activity. We also examined the microbiome and serum metabolites, cytokines and miRNAs as potential sources of molecular biomarkers of fibromyalgia.

CONCLUSIONS: Our results show that the microbiome analysis provides more significant biomarkers than the other techniques employed in the work. Gut microbiome analysis combined with serum metabolomics can shed new light onto the pathogenesis of fibromyalgia. We provide a list of bacteria whose abundance changes in this disease and propose several molecules as potential biomarkers that can be used to evaluate the current diagnostic criteria.}, } @article {pmid31326442, year = {2020}, author = {Endo, A and Hirano, K and Ose, R and Maeno, S and Tochio, T}, title = {Impact of kestose supplementation on the healthy adult microbiota in in vitro fecal batch cultures.}, journal = {Anaerobe}, volume = {61}, number = {}, pages = {102076}, doi = {10.1016/j.anaerobe.2019.102076}, pmid = {31326442}, issn = {1095-8274}, mesh = {Adult ; Age Factors ; *Dietary Supplements ; Feces/*microbiology ; Female ; Fermentation ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Male ; Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Trisaccharides/*administration & dosage ; Young Adult ; }, abstract = {Prebiotics are widely used to shape a balanced microbiota in humans and animals. 1-Kestose (kestose) is one of the major components in commercialized short-chain fructooligosaccharide and is a promising prebiotic for infants. We herein studied the impact of kestose on the healthy adult microbiota in an in vitro fecal batch culture model. Stool samples obtained from seven healthy adults were diluted, inoculated into broth supplemented with or without 0.5% (w/v) kestose (kestose group and control group, respectively), and cultured under anaerobic conditions. Microbiota in the groups and stool samples were analyzed using 16S rRNA gene sequencing. At the phylum level, the kestose group showed increases in Bacteroidetes, whereas the control group showed increases in Proteobacteria. At the species level, Bifidobacterium longum was the only species showing significantly higher levels in the kestose group than in the control group and stool samples. On the other hand, levels of Escherichia coli were significantly higher in the control group than in stool samples, while the levels were not significantly different between the kestose group and stool samples. Quantitative PCR assays also revealed significantly higher levels of B. longum and lower tendency of E. coli in the kestose group than in the control group. These results suggest that supplementation with kestose increased the levels of beneficial microorganism and prevented the growth of risk-associated microorganisms related to disease development. Further interventional studies are needed to understand the health benefits of kestose in adult humans.}, } @article {pmid31325042, year = {2020}, author = {Liu, Z and Subbaraj, A and Fraser, K and Jia, H and Chen, W and Day, L and Roy, NC and Young, W}, title = {Human milk and infant formula differentially alters the microbiota composition and functional gene relative abundance in the small and large intestines in weanling rats.}, journal = {European journal of nutrition}, volume = {59}, number = {5}, pages = {2131-2143}, pmid = {31325042}, issn = {1436-6215}, mesh = {Animals ; Colon ; Feces ; *Infant Formula ; Intestines ; Male ; *Microbiota ; Milk, Human ; Rats ; Rats, Sprague-Dawley ; }, abstract = {PURPOSE: Human breast milk is the optimal source of nutrients for growing infants. However, many circumstances can arise which preclude breast milk feeding, leading to the use of infant formula, including during the weaning period. Many diet-related effects are modulated by the gut microbiome. Therefore, we investigated the effect of human milk (HM) or infant formula (IF) on the gut microbiota in weanling rats.

METHODS: The gut microbiota of weanling male Sprague-Dawley rats fed HM or IF for 28 days was analysed by shotgun metagenome sequencing. Caecal contents were analysed by liquid chromatography-mass spectrometry metabolomics.

RESULTS: Numerous genera within the Proteobacteria phylum were relatively more abundant in the ileum, caecum, and colon of rats fed HM, including ileal Escherichia (HM = 9.6% ± 4.3 SEM; IF = 0.9% ± 0.3 SEM; P = 0.03). Other taxa that differed between HM- and IF-fed rats included Prevotella and Ruminococcus. Overall, more differences were observed in the ileum than the caecum and colon between rats fed HM and IF. For the rats fed IF, in the ileum, the relative abundance of Bifidobacterium was higher (HM = 1.7% ± 0.7 SEM; IF = 5.0% ± 1.5 SEM; P = 0.04) with gene functions related to carbohydrate and amino acid metabolism also decreased. In the caecum, metabolic features such as bile acids were elevated while amino sugars were also decreased.

CONCLUSION: Our results show that HM and IF composition differences are reflected in the gut microbiome composition and function in both the small and large intestines.}, } @article {pmid31324636, year = {2019}, author = {Steen, AD and Kevorkian, RT and Bird, JT and Dombrowski, N and Baker, BJ and Hagen, SM and Mulligan, KH and Schmidt, JM and Webber, AT and Royalty, TM and Alperin, MJ}, title = {Kinetics and Identities of Extracellular Peptidases in Subsurface Sediments of the White Oak River Estuary, North Carolina.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {19}, pages = {}, pmid = {31324636}, issn = {1098-5336}, mesh = {Carbon/chemistry ; *Estuaries ; Geologic Sediments/*chemistry ; Heterotrophic Processes ; Kinetics ; Metagenome ; *Microbiota ; North Carolina ; Organic Chemicals/chemistry ; Peptide Hydrolases/*isolation & purification/*metabolism ; }, abstract = {Anoxic subsurface sediments contain communities of heterotrophic microorganisms that metabolize organic carbon at extraordinarily low rates. In order to assess the mechanisms by which subsurface microorganisms access detrital sedimentary organic matter, we measured kinetics of a range of extracellular peptidases in anoxic sediments of the White Oak River Estuary, NC. Nine distinct peptidase substrates were enzymatically hydrolyzed at all depths. Potential peptidase activities (Vmax) decreased with increasing sediment depth, although Vmax expressed on a per-cell basis was approximately the same at all depths. Half-saturation constants (Km) decreased with depth, indicating peptidases that functioned more efficiently at low substrate concentrations. Potential activities of extracellular peptidases acting on molecules that are enriched in degraded organic matter (d-phenylalanine and l-ornithine) increased relative to enzymes that act on l-phenylalanine, further suggesting microbial community adaptation to access degraded organic matter. Nineteen classes of predicted, exported peptidases were identified in genomic data from the same site, of which genes for class C25 (gingipain-like) peptidases represented more than 40% at each depth. Methionine aminopeptidases, zinc carboxypeptidases, and class S24-like peptidases, which are involved in single-stranded-DNA repair, were also abundant. These results suggest a subsurface heterotrophic microbial community that primarily accesses low-quality detrital organic matter via a diverse suite of well-adapted extracellular enzymes.IMPORTANCE Burial of organic carbon in marine and estuarine sediments represents a long-term sink for atmospheric carbon dioxide. Globally, ∼40% of organic carbon burial occurs in anoxic estuaries and deltaic systems. However, the ultimate controls on the amount of organic matter that is buried in sediments, versus oxidized into CO2, are poorly constrained. In this study, we used a combination of enzyme assays and metagenomic analysis to identify how subsurface microbial communities catalyze the first step of proteinaceous organic carbon degradation. Our results show that microbial communities in deeper sediments are adapted to access molecules characteristic of degraded organic matter, suggesting that those heterotrophs are adapted to life in the subsurface.}, } @article {pmid31324632, year = {2019}, author = {Danso, D and Chow, J and Streit, WR}, title = {Plastics: Environmental and Biotechnological Perspectives on Microbial Degradation.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {19}, pages = {}, pmid = {31324632}, issn = {1098-5336}, mesh = {*Biodegradation, Environmental ; *Biotechnology ; *Ecosystem ; Environmental Monitoring ; Enzymes ; Metagenome ; *Microbiota ; Plastics/*metabolism ; Recycling ; }, abstract = {Plastics are widely used in the global economy, and each year, at least 350 to 400 million tons are being produced. Due to poor recycling and low circular use, millions of tons accumulate annually in terrestrial or marine environments. Today it has become clear that plastic causes adverse effects in all ecosystems and that microplastics are of particular concern to our health. Therefore, recent microbial research has addressed the question of if and to what extent microorganisms can degrade plastics in the environment. This review summarizes current knowledge on microbial plastic degradation. Enzymes available act mainly on the high-molecular-weight polymers of polyethylene terephthalate (PET) and ester-based polyurethane (PUR). Unfortunately, the best PUR- and PET-active enzymes and microorganisms known still have moderate turnover rates. While many reports describing microbial communities degrading chemical additives have been published, no enzymes acting on the high-molecular-weight polymers polystyrene, polyamide, polyvinylchloride, polypropylene, ether-based polyurethane, and polyethylene are known. Together, these polymers comprise more than 80% of annual plastic production. Thus, further research is needed to significantly increase the diversity of enzymes and microorganisms acting on these polymers. This can be achieved by tapping into the global metagenomes of noncultivated microorganisms and dark matter proteins. Only then can novel biocatalysts and organisms be delivered that allow rapid degradation, recycling, or value-added use of the vast majority of most human-made polymers.}, } @article {pmid31324156, year = {2019}, author = {Yan, F and Yu, X and Duan, Z and Lu, J and Jia, B and Qiao, Y and Sun, C and Wei, C}, title = {Discovery and characterization of the evolution, variation and functions of diversity-generating retroelements using thousands of genomes and metagenomes.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {595}, pmid = {31324156}, issn = {1471-2164}, support = {61472246//National Natural Science Foundation of China/ ; J1210047//National Natural Science Foundation of China/ ; 2013CB956103//National Basic Research Program of China (973 Program)/ ; }, mesh = {Algorithms ; Bacteria/genetics ; *Evolution, Molecular ; *Genetic Variation ; *Genomics ; Humans ; Metagenome/*genetics ; Microbiota/genetics ; Retroelements/*genetics ; }, abstract = {BACKGROUND: Diversity-generating retroelements (DGRs) are a unique family of retroelements that generate sequence diversity of DNA to benefit their hosts by introducing variations and accelerating the evolution of target proteins. They exist widely in bacteria, archaea, phage and plasmid. However, our understanding about DGRs in natural environments was still very limited.

RESULTS: We developed an efficient computational algorithm to identify DGRs, and applied it to characterize DGRs in more than 80,000 sequenced bacterial genomes as well as more than 4,000 human metagenome datasets. In total, we identified 948 non-redundant DGRs, which expanded the number of known DGRs in bacterial genomes and human microbiomes by about 55%, and provided a much more comprehensive reference for the study of DGRs. Phylogenetic analysis was done for identified DGRs. The putative target genes of DGRs were searched, and the functions of these target genes were investigated with a comprehensive alignment against the nr database.

CONCLUSIONS: DGR system is a powerful and universal mechanism to generate diversity. DGR evolution is closely associated with the living environment and their cassette structures. Furthermore, it may impact a wide range of functional processes in addition to receptor-binding. These results significantly improved our understanding about DGRs.}, } @article {pmid31323792, year = {2019}, author = {Santiago-Rodriguez, TM and Hollister, EB}, title = {Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut.}, journal = {Viruses}, volume = {11}, number = {7}, pages = {}, pmid = {31323792}, issn = {1999-4915}, mesh = {Adaptation, Biological ; Animals ; Bacteria/genetics/virology ; Bacteriolysis ; Bacteriophages/physiology ; *Disease Susceptibility ; Dysbiosis ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; *Host-Pathogen Interactions ; Humans ; Metagenomics/methods ; Microbial Interactions ; *Microbiota ; *Viruses/classification/genetics ; }, abstract = {The virome is comprised of endogenous retroviruses, eukaryotic viruses, and bacteriophages and is increasingly being recognized as an essential part of the human microbiome. The human virome is associated with Type-1 diabetes (T1D), Type-2 diabetes (T2D), Inflammatory Bowel Disease (IBD), Human Immunodeficiency Virus (HIV) infection, and cancer. Increasing evidence also supports trans-kingdom interactions of viruses with bacteria, small eukaryotes and host in disease progression. The present review focuses on virus ecology and biology and how this translates mostly to human gut virome research. Current challenges in the field and how the development of bioinformatic tools and controls are aiding to overcome some of these challenges are also discussed. Finally, the present review also focuses on how human gut virome research could result in translational and clinical studies that may facilitate the development of therapeutic approaches.}, } @article {pmid31323117, year = {2019}, author = {McGeoch, MA and Latombe, G and Andrew, NR and Nakagawa, S and Nipperess, DA and Roigé, M and Marzinelli, EM and Campbell, AH and Vergés, A and Thomas, T and Steinberg, PD and Selwood, KE and Henriksen, MV and Hui, C}, title = {Measuring continuous compositional change using decline and decay in zeta diversity.}, journal = {Ecology}, volume = {100}, number = {11}, pages = {e02832}, doi = {10.1002/ecy.2832}, pmid = {31323117}, issn = {1939-9170}, mesh = {*Biodiversity ; *Ecology ; Longitudinal Studies ; }, abstract = {Incidence, or compositional, matrices are generated for a broad range of research applications in biology. Zeta diversity provides a common currency and conceptual framework that links incidence-based metrics with multiple patterns of interest in biology, ecology, and biodiversity science. It quantifies the variation in species (or OTU) composition of multiple assemblages (or cases) in space or time, to capture the contribution of the full suite of narrow, intermediate, and wide-ranging species to biotic heterogeneity. Here we provide a conceptual framework for the application and interpretation of patterns of continuous change in compositional diversity using zeta diversity. This includes consideration of the survey design context, and the multiple ways in which zeta diversity decline and decay can be used to examine and test turnover in the identity of elements across space and time. We introduce the zeta ratio-based retention rate curve to quantify rates of compositional change. We illustrate these applications using 11 empirical data sets from a broad range of taxa, scales, and levels of biological organization-from DNA molecules and microbes to communities and interaction networks-including one of the original data sets used to express compositional change and distance decay in ecology. We show (1) how different sample selection schemes used during the calculation of compositional change are appropriate for different data types and questions, (2) how higher orders of zeta may in some cases better detect shifts and transitions, and (3) the relative roles of rare vs. common species in driving patterns of compositional change. By exploring the application of zeta diversity decline and decay, including the retention rate, across this broad range of contexts, we demonstrate its application for understanding continuous turnover in biological systems.}, } @article {pmid31320306, year = {2019}, author = {Carissimi, C and Laudadio, I and Palone, F and Fulci, V and Cesi, V and Cardona, F and Alfonsi, C and Cucchiara, S and Isoldi, S and Stronati, L}, title = {Functional analysis of gut microbiota and immunoinflammation in children with autism spectrum disorders.}, journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver}, volume = {51}, number = {10}, pages = {1366-1374}, doi = {10.1016/j.dld.2019.06.006}, pmid = {31320306}, issn = {1878-3562}, mesh = {Autism Spectrum Disorder/immunology/*microbiology/physiopathology ; Case-Control Studies ; Child ; Child Development ; Child, Preschool ; Comorbidity ; Cytokines/blood ; Escherichia coli/isolation & purification ; Feces/microbiology ; Female ; Gastrointestinal Diseases/*immunology ; *Gastrointestinal Microbiome ; Humans ; *Inflammation ; Male ; Phenylpropionates/metabolism ; }, abstract = {BACKGROUND AND AIMS: Recent evidence implicates gut microbiota (GM) and immune alterations in autism spectrum disorders (ASD). We assess GM profile and peripheral levels of immunological, neuronal and bacterial molecules in ASD children and controls. Alarmin HMGB1 was explored as a non-invasive biomarker to monitor gastrointestinal (GI) symptoms.

METHODS: Thirty ASD children and 14 controls entered into the study. GM metagenomic analysis was performed for 16 ASD patients and 7 controls. GM functional profile was assessed by GO term analysis. Blood levels of IL-1β, TNFα, TGFβ, IL-10, INFγ, IL-8, lipopolysaccharide, Neurotensin, Sortilin1 and GSSG/GSH ratio were analyzed in all subjects by ELISA. Fecal HMGB1 was analyzed by Western blot.

RESULTS: We observed a significant decrease in bacterial diversity. Furthermore, 82 GO terms underrepresented in ASD. Four of them pointed at 3,3 phenylpropionate catabolism and were imputable to Escherichia coli (E. coli) group. Serum levels of TNFα, TGFβ, NT, and SORT-1 increased in ASD patients. Fecal levels of HMGB1 correlated with GI sign severity in ASD children.

CONCLUSIONS: We suggest that a decrease of E. coli might affect the propionate catabolism in ASD. We report occurrence of peripheral inflammation in ASD children. We propose fecal HMGB1 as a non-invasive biomarker to detect GI symptoms.}, } @article {pmid31319276, year = {2019}, author = {Harvey, E and Rose, K and Eden, JS and Lawrence, A and Doggett, SL and Holmes, EC}, title = {Identification of diverse arthropod associated viruses in native Australian fleas.}, journal = {Virology}, volume = {535}, number = {}, pages = {189-199}, doi = {10.1016/j.virol.2019.07.010}, pmid = {31319276}, issn = {1096-0341}, mesh = {Animals ; Australia ; *Biodiversity ; Gene Expression Profiling ; Insect Vectors/virology ; Metagenomics ; Phylogeny ; RNA Viruses/*classification/genetics/*isolation & purification ; Siphonaptera/*virology ; }, abstract = {Fleas are important vectors of zoonotic disease. However, little is known about the natural diversity and abundance of flea viruses, particularly in the absence of disease associations, nor the evolutionary relationships among those viruses found in different parasitic vector species. Herein, we present the first virome scale study of fleas, based on the meta-transcriptomic analysis of 52 fleas collected along the eastern coast of Australia. Our analysis revealed 18 novel RNA viruses belonging to nine viral families with diverse genome organizations, although the majority (72%) possessed single-stranded positive-sense genomes. Notably, a number of the viruses identified belonged to the same phylogenetic groups as those observed in ticks sampled at the same locations, although none were likely associated with mammalian infection. Overall, we identified high levels of genomic diversity and abundance of viruses in the flea species studied, and established that fleas harbor viruses similar to those seen to other vectors.}, } @article {pmid31318946, year = {2019}, author = {Gaona, O and Gómez-Acata, ES and Cerqueda-García, D and Neri-Barrios, CX and Falcón, LI}, title = {Fecal microbiota of different reproductive stages of the central population of the lesser-long nosed bat, Leptonycteris yerbabuenae.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0219982}, pmid = {31318946}, issn = {1932-6203}, mesh = {Animals ; Chiroptera/*physiology ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Geography ; Male ; Metagenome ; Metagenomics/methods ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; *Reproduction ; }, abstract = {In this study we analyzed the microbiota composition of fecal samples from the lesser-long nosed bat Leptonycteris yerbabuenae in different reproductive stages (juveniles and adult bats of both sexes as well as pregnant and lactating females). The V4 region of the 16s rRNA gene from 33 individuals was analyzed using alpha and beta diversity metrics. We found that microbiota diversity (expressed in Amplicon Sequence Variants) is higher in pregnant and lactating females. The microbiota of the juveniles and non-reproductive adults was dominated by Gammaproteobacteria and Firmicutes. Reproductive females had a much more diverse microbiota, with a significant increase in phyla such as Bacteroidetes and Alphaproteobacteria. There was no difference in fecal microbiota diversity between pregnant and lactating females and juveniles and non-reproductive adults. Results suggest that differences in microbiota diversity are related to reproduction. We infer that males maintain stable microbiota composition because they do not undergo the large physiological changes that females do during reproduction and maintain a more specialized diet throughout all life stages.}, } @article {pmid31316785, year = {2019}, author = {Gutin, L and Piceno, Y and Fadrosh, D and Lynch, K and Zydek, M and Kassam, Z and LaMere, B and Terdiman, J and Ma, A and Somsouk, M and Lynch, S and El-Nachef, N}, title = {Fecal microbiota transplant for Crohn disease: A study evaluating safety, efficacy, and microbiome profile.}, journal = {United European gastroenterology journal}, volume = {7}, number = {6}, pages = {807-814}, pmid = {31316785}, issn = {2050-6406}, mesh = {Adolescent ; Adult ; Aged ; Crohn Disease/etiology/*therapy ; *Fecal Microbiota Transplantation/adverse effects/methods ; Female ; Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics/methods ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; Young Adult ; }, abstract = {BACKGROUND: Emerging trials suggest fecal microbiota transplantation (FMT) is a promising treatment for ulcerative colitis; however, there is a paucity of data in Crohn disease (CD).

OBJECTIVE: The objectives of this article are to determine whether single-dose FMT improves clinical and endoscopic outcomes in CD patients and to identify meaningful changes in the microbiome in response to FMT.

METHODS: We performed a prospective, open-label, single-center study. Ten CD patients underwent FMT and were evaluated for clinical response (defined as decrease in Harvey-Bradshaw Index score ≥3 at one month post-FMT) and microbiome profile (16S ribosomal RNA sequencing) at one month post-FMT.

RESULTS: Three of 10 patients responded to FMT. Two of 10 patients had significant adverse events requiring escalation of therapy. On microbiome analysis, bacterial communities of responders had increased relative abundance of bacteria commonly found in donor gut microbiota.

CONCLUSIONS: Single-dose FMT in this cohort of CD patients showed modest effect and potential for harm. Responders tended to have lower baseline alpha diversity, suggesting baseline perturbation of microbiota may be an indicator of potential responders to FMT in this patient population. Controlled trials are needed to further assess the efficacy and safety of FMT in CD and determine whether FMT is a viable option in this patient population.Clinicaltrials.gov number: NCT02460705.}, } @article {pmid31316056, year = {2019}, author = {Mallick, H and Franzosa, EA and Mclver, LJ and Banerjee, S and Sirota-Madi, A and Kostic, AD and Clish, CB and Vlamakis, H and Xavier, RJ and Huttenhower, C}, title = {Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {3136}, pmid = {31316056}, issn = {2041-1723}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 DK092405/DK/NIDDK NIH HHS/United States ; P30 DK036836/DK/NIDDK NIH HHS/United States ; R01 HG005220/HG/NHGRI NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; P30 DK040561/DK/NIDDK NIH HHS/United States ; }, mesh = {Algorithms ; Colitis, Ulcerative/microbiology ; Crohn Disease/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metabolomics ; Metagenomics ; Microbiota/*genetics ; *Models, Genetic ; }, abstract = {Microbial community metabolomics, particularly in the human gut, are beginning to provide a new route to identify functions and ecology disrupted in disease. However, these data can be costly and difficult to obtain at scale, while amplicon or shotgun metagenomic sequencing data are readily available for populations of many thousands. Here, we describe a computational approach to predict potentially unobserved metabolites in new microbial communities, given a model trained on paired metabolomes and metagenomes from the environment of interest. Focusing on two independent human gut microbiome datasets, we demonstrate that our framework successfully recovers community metabolic trends for more than 50% of associated metabolites. Similar accuracy is maintained using amplicon profiles of coral-associated, murine gut, and human vaginal microbiomes. We also provide an expected performance score to guide application of the model in new samples. Our results thus demonstrate that this 'predictive metabolomic' approach can aid in experimental design and provide useful insights into the thousands of community profiles for which only metagenomes are currently available.}, } @article {pmid31315667, year = {2019}, author = {Pan, H and Guo, R and Ju, Y and Wang, Q and Zhu, J and Xie, Y and Zheng, Y and Li, T and Liu, Z and Lu, L and Li, F and Tong, B and Xiao, L and Xu, X and Leung, EL and Li, R and Yang, H and Wang, J and Zhou, H and Jia, H and Liu, L}, title = {A single bacterium restores the microbiome dysbiosis to protect bones from destruction in a rat model of rheumatoid arthritis.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {107}, pmid = {31315667}, issn = {2049-2618}, mesh = {Animals ; Arthritis, Experimental/*therapy ; Arthritis, Rheumatoid/chemically induced/*therapy ; Bone Diseases/prevention & control/therapy ; Cytokines/genetics/immunology ; Dysbiosis/prevention & control/*therapy ; *Gastrointestinal Microbiome ; Lactobacillales/genetics/*physiology ; Lacticaseibacillus casei/physiology ; Metagenome ; Oxidative Stress ; Probiotics/*therapeutic use ; Rats ; }, abstract = {BACKGROUND: Early treatment is key for optimizing the therapeutic success of drugs, and the current initiating treatment that blocks the progression of bone destruction during the pre-arthritic stages remains unsatisfactory. The microbial disorder in rheumatoid arthritis (RA) patients is significantly reversed with effective treatment. Modulating aberrant gut microbiomes into a healthy state is a potential therapeutic approach for preventing bone damage.

RESULTS: By using metagenomic shotgun sequencing and a metagenome-wide association study, we assessed the effect of Lactobacillus casei (L. casei) on the induction of arthritis as well as on the associated gut microbiota and immune disorders in adjuvant-induced arthritis (AIA) rats. Treatment of AIA rats with L. casei inhibited joint swelling, lowered arthritis scores, and prevented bone destruction. Along with the relief of arthritis symptoms, dysbiosis in the microbiome of arthritic rats was significantly reduced after L. casei intervention. The relative abundance of AIA-decreased Lactobacillus strains, including Lactobacillus hominis, Lactobacillus reuteri, and Lactobacillus vaginalis, were restored to normal and Lactobacillus acidophilus was upregulated by the administration of L. casei to the AIA rats. Moreover, L. casei downregulated the expression of pro-inflammatory cytokines, which are closely linked to the effect of the L. casei treatment-associated microbes. Functionally, the maintenance of the redox balance of oxidative stress was involved in the improvement in the L. casei-treated AIA rats.

CONCLUSION: A single bacterium, L. casei (ATCC334), was able to significantly suppress the induction of AIA and protect bones from destruction in AIA rats by restoring the microbiome dysbiosis in the gut, indicating that using probiotics may be a promising strategy for treating RA, especially in the early stage of the disease.}, } @article {pmid31315377, year = {2019}, author = {Cai, YL and Cao, Y and Fan, XZ and Luo, XR and Meng, JF and Xue, YM and Gao, F and Zou, MC}, title = {[Microbiome analysis of diabetic foot osteomyelitis by metagenome sequencing technology].}, journal = {Zhonghua yi xue za zhi}, volume = {99}, number = {26}, pages = {2057-2061}, doi = {10.3760/cma.j.issn.0376-2491.2019.26.011}, pmid = {31315377}, issn = {0376-2491}, support = {81600648//National Natural Science Foundation of China for Young Scholars/ ; A2017090//Medicine, Science and Technology Research Foundation of Guangdong/ ; 2016ZC0066//Science and Technology Program of Guangdong/ ; }, mesh = {Aged ; *Diabetic Foot ; Female ; Humans ; Male ; Metagenome ; *Microbiota ; Middle Aged ; *Osteomyelitis ; RNA, Ribosomal, 16S ; }, abstract = {Objective: To analyze the microbiome of diabetic foot osteomyelitis (DFO) by means of metagenome sequencing and provide evidence for identification of pathogenic bacteria in DFO. Methods: A total of 5 patients (3 males and 2 females) with DFO hospitalized at the Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University were enrolled and infected bone specimens were obtained between September 2016 and April 2017. The mean age was (55.8±9.5) years. Metagenome sequencing was performed to explore the characteristics of microbiome, and compared with the results of 16S rRNA sequencing. Results: The results of metagenome sequencing showed that DFO contained diverse microorganism. Totally, 22 dominant species were obtained, Klebsiella pneumoniae (69.66%) was the most abundant, followed by Veillonella parvula (36.93%) and Prevotella intermedia (34.19%). Compared with the 16S rRNA sequencing, metagenome sequencing could obtain more species information on the basis of fewer samples. At the genus level, both sequencing techniques suggested the most dominant pathogen in DFO was anaerobe. All bone specimens had polymicrobial communities. Conclusions: More microecological diversity and abundance of DFO can be found by using metagenome sequencing. At the species level, more bacteria, even bacterial strains can be identified by metagenome sequencing. At the genus level, the most abundant bacteria is anaerobe, however, at the species level, it is facultative anaerobe.}, } @article {pmid31314947, year = {2019}, author = {Haas, S and Desai, DK and LaRoche, J and Pawlowicz, R and Wallace, DWR}, title = {Geomicrobiology of the carbon, nitrogen and sulphur cycles in Powell Lake: a permanently stratified water column containing ancient seawater.}, journal = {Environmental microbiology}, volume = {21}, number = {10}, pages = {3927-3952}, doi = {10.1111/1462-2920.14743}, pmid = {31314947}, issn = {1462-2920}, support = {//Canada Excellence Research Chair in Ocean Science and Technology/International ; }, mesh = {Bacteria/genetics/*metabolism ; Canada ; Carbon/*analysis ; Lakes/*microbiology ; Metagenome/genetics ; Microbiota/physiology ; Nitrogen/*analysis ; Nitrogen Fixation/physiology ; Phylogeny ; Seawater/chemistry/microbiology ; Sulfur/*analysis ; Water/analysis ; }, abstract = {We present the first geomicrobiological characterization of the meromictic water column of Powell Lake (British Columbia, Canada), a former fjord, which has been stably stratified since the last glacial period. Its deepest layers (300-350 m) retain isolated, relict seawater from that period. Fine-scale vertical profiling of the water chemistry and microbial communities allowed subdivision of the water column into distinct geomicrobiological zones. These zones were further characterized by phylogenetic and functional marker genes from amplicon and shotgun metagenome sequencing. Binning of metagenomic reads allowed the linkage of function to specific taxonomic groups. Statistical analyses (analysis of similarities, Bray-Curtis similarity) confirmed that the microbial community structure followed closely the geochemical zonation. Yet, our characterization of the genetic potential relevant to carbon, nitrogen and sulphur cycling of each zone revealed unexpected features, including potential for facultative anaerobic methylotrophy, nitrogen fixation despite high ammonium concentrations and potential micro-aerobic nitrifiers within the chemocline. At the oxic-suboxic interface, facultative anaerobic potential was found in the widespread freshwater lineage acI (Actinobacteria), suggesting intriguing ecophysiological similarities to the marine SAR11. Evolutionary divergent lineages among diverse phyla were identified in the ancient seawater zone and may indicate novel adaptations to this unusual environment.}, } @article {pmid31312027, year = {2019}, author = {Macher, JN and Speksnijder, A and Choo, LQ and van der Hoorn, B and Renema, W}, title = {Uncovering bacterial and functional diversity in macroinvertebrate mitochondrial-metagenomic datasets by differential centrifugation.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {10257}, pmid = {31312027}, issn = {2045-2322}, mesh = {Animals ; Bacteria/classification/genetics ; *Biodiversity ; Centrifugation/methods ; Databases, Genetic ; Invertebrates/genetics/*microbiology ; *Metagenome ; Metagenomics/methods ; Mitochondria/genetics ; }, abstract = {PCR-free techniques such as meta-mitogenomics (MMG) can recover taxonomic composition of macroinvertebrate communities, but suffer from low efficiency, as >90% of sequencing data is mostly uninformative due to the great abundance of nuclear DNA that cannot be identified with current reference databases. Current MMG studies do not routinely check data for information on macroinvertebrate-associated bacteria and gene functions. However, this could greatly increase the efficiency of MMG studies by revealing yet overlooked diversity within ecosystems and making currently unused data available for ecological studies. By analysing six 'mock' communities, each containing three macroinvertebrate taxa, we tested whether this additional data on bacterial taxa and functional potential of communities can be extracted from MMG datasets. Further, we tested whether differential centrifugation, which is known to greatly increase efficiency of macroinvertebrate MMG studies by enriching for mitochondria, impacts on the inferred bacterial community composition. Our results show that macroinvertebrate MMG datasets contain a high number of mostly endosymbiont bacterial taxa and associated gene functions. Centrifugation reduced both the absolute and relative abundance of highly abundant Gammaproteobacteria, thereby facilitating detection of rare taxa and functions. When analysing both taxa and gene functions, the number of features obtained from the MMG dataset increased 31-fold ('enriched') respectively 234-fold ('not enriched'). We conclude that analysing MMG datasets for bacteria and gene functions greatly increases the amount of information available and facilitates the use of shotgun metagenomic techniques for future studies on biodiversity.}, } @article {pmid31311477, year = {2019}, author = {Boscaro, V and Husnik, F and Vannini, C and Keeling, PJ}, title = {Symbionts of the ciliate Euplotes: diversity, patterns and potential as models for bacteria-eukaryote endosymbioses.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1907}, pages = {20190693}, pmid = {31311477}, issn = {1471-2954}, mesh = {Burkholderiaceae/classification/genetics/*physiology ; Euplotes/*microbiology ; Microbiota ; Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Symbiosis ; }, abstract = {Endosymbioses between bacteria and eukaryotes are enormously important in ecology and evolution, and as such are intensely studied. Despite this, the range of investigated hosts is narrow in the context of the whole eukaryotic tree of life: most of the information pertains to animal hosts, while most of the diversity is found in unicellular protists. A prominent case study is the ciliate Euplotes, which has repeatedly taken up the bacterium Polynucleobacter from the environment, triggering its transformation into obligate endosymbiont. This multiple origin makes the relationship an excellent model to understand recent symbioses, but Euplotes may host bacteria other than Polynucleobacter, and a more detailed knowledge of these additional interactions is needed in order to correctly interpret the system. Here, we present the first systematic survey of Euplotes endosymbionts, adopting a classical as well as a metagenomic approach, and review the state of knowledge. The emerging picture is indeed quite complex, with some Euplotes harbouring rich, stable prokaryotic communities not unlike those of multicellular animals. We provide insights into the distribution, evolution and diversity of these symbionts (including the establishment of six novel bacterial taxa), and outline differences and similarities with the most well-understood group of eukaryotic hosts: insects.}, } @article {pmid31311405, year = {2020}, author = {Guzmán-Castañeda, SJ and Ortega-Vega, EL and de la Cuesta-Zuluaga, J and Velásquez-Mejía, EP and Rojas, W and Bedoya, G and Escobar, JS}, title = {Gut microbiota composition explains more variance in the host cardiometabolic risk than genetic ancestry.}, journal = {Gut microbes}, volume = {11}, number = {2}, pages = {191-204}, pmid = {31311405}, issn = {1949-0984}, mesh = {Adult ; Black or African American/genetics ; Bacteria/classification/genetics/isolation & purification ; Cardiovascular Diseases/*genetics/metabolism/microbiology ; Cohort Studies ; Cross-Sectional Studies ; Diet ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Genetic Predisposition to Disease/*genetics ; Humans ; Indians, South American/genetics ; Life Style ; Male ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S ; *Risk Factors ; White People/genetics ; Young Adult ; }, abstract = {Cardiometabolic affections greatly contribute to the global burden of disease. The susceptibility to obesity, cardiovascular disease, and type-2 diabetes, conditions that add to the cardiometabolic syndrome (CMS), was associated with the ancestral genetic composition and gut microbiota. Studies explicitly testing associations between genetic ancestry and gut microbes are growing. We here examined whether the host genetic ancestry was associated with gut microbiota composition, and distinguished the effects of genetic ancestry and non-genetic factors on human cardiometabolic health. We performed a cross-sectional study with 441 community-dwelling Colombian mestizos from five cities spanning the Andes, Pacific, and Caribbean coasts. We characterized the host genetic ancestry by genotyping 40 ancestry informative markers; characterized gut microbiota through 16S rRNA gene sequencing; assessed diet intake, physical activity, cigarette, and medicament consumption; and measured cardiometabolic outcomes that allowed calculating a CMS risk scale. On average, each individual of our cohort was 67 ± 6% European, 21 ± 5% Native American and 12 ± 5% African. Multivariable-adjusted generalized linear models showed that individuals with higher Native American and African ancestries had increased fasting insulin, body mass index and CMS risk, as assessed by the CMS risk scale. Furthermore, we identified 21 OTUs associated to the host genetic ancestry and 20 to cardiometabolic health. While we highlight novel associations between genetic ancestry and gut microbiota, we found that the effect of intestinal microbes was more likely to explain the variance in CMS risk scale than the contributions of European, Native American and African genetic backgrounds.}, } @article {pmid31311146, year = {2019}, author = {Vamanu, E and Pelinescu, D and Gatea, F and Sârbu, I}, title = {Altered in Vitro Metabolomic Response of the Human Microbiota to Sweeteners.}, journal = {Genes}, volume = {10}, number = {7}, pages = {}, pmid = {31311146}, issn = {2073-4425}, mesh = {Ammonia/metabolism ; Diterpenes, Kaurane/metabolism ; Dysbiosis ; Fatty Acids/metabolism ; Gastrointestinal Microbiome/drug effects ; Humans ; *Metabolome ; *Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Microbiota/*drug effects ; Sweetening Agents/*pharmacology ; }, abstract = {Non-nutritive sweeteners represent an ingredient class that directly affects human health, via the development of inflammatory processes that promote chronic diseases related to microbiota dysbiosis. Several in vitro tests were conducted in the static GIS1 simulator. The aim of the study was to highlight the effect of sweeteners on the microbiota pattern of healthy individuals, associated with any alteration in the metabolomic response, through the production of organic acids and ammonium. The immediate effect of the in vitro treatment and the influence of the specific sweetener type on the occurrence of dysbiosis were evaluated by determining the biomarkers of the microbiota response. The presence of the steviol reduced the ammonium level (minimum of 410 mg/L), while the addition of cyclamate and saccharin caused a decrease in the number of microorganisms, in addition to lowering the total quantity of synthesized short-chain fatty acids (SCFAs). The bifidobacteria appeared to decrease below 10[2] genomes/mL in all the analyzed samples at the end of the in vitro simulation period. Barring the in vitro treatment of steviol, all the sweeteners tested exerted a negative influence on the fermentative profile, resulting in a decline in the fermentative processes, a rise in the colonic pH, and uniformity of the SCFA ratio.}, } @article {pmid31310864, year = {2019}, author = {Roossinck, MJ}, title = {Viruses in the phytobiome.}, journal = {Current opinion in virology}, volume = {37}, number = {}, pages = {72-76}, doi = {10.1016/j.coviro.2019.06.008}, pmid = {31310864}, issn = {1879-6265}, mesh = {Animals ; Bacteria/virology ; Bacteriophages ; Biological Control Agents ; Cuscuta/virology ; Disease Vectors ; Fungal Viruses/pathogenicity ; Host Microbial Interactions ; Insect Vectors ; Metagenomics ; *Microbial Interactions ; *Microbiota ; Nematoda/virology ; Plant Diseases/microbiology/*virology ; *Plant Viruses/growth & development/pathogenicity ; Plants/*virology ; Symbiosis ; }, abstract = {The phytobiome, defined as plants and all the entities that interact with them, is rich in viruses, but with the exception of plant viruses of crop plants, most of the phytobiome viruses remain very understudied. This review focuses on the neglected portions of the phytobiome, including viruses of other microbes interacting with plants, viruses in the soil, viruses of wild plants, and relationships between viruses and the vectors of plant viruses.}, } @article {pmid31310663, year = {2019}, author = {Feng, S and Liu, Y and Huang, Y and Zhao, J and Zhang, H and Zhai, Q and Chen, W}, title = {Influence of oral administration of Akkermansia muciniphila on the tissue distribution and gut microbiota composition of acute and chronic cadmium exposure mice.}, journal = {FEMS microbiology letters}, volume = {366}, number = {13}, pages = {}, doi = {10.1093/femsle/fnz160}, pmid = {31310663}, issn = {1574-6968}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Administration, Oral ; Akkermansia ; Animals ; Biodiversity ; Cadmium/*administration & dosage/adverse effects ; Dietary Exposure/*adverse effects ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Male ; Metagenomics ; Mice ; *Probiotics/administration & dosage ; RNA, Ribosomal, 16S ; Tissue Distribution ; *Verrucomicrobia ; }, abstract = {Cadmium (Cd) contamination is a serious food safety problem. Acute and chronic Cd exposure changes the gut microbiota composition and damages the gut barrier function. Akkermansia muciniphila (AKK), a promising candidate for the next-generation probiotics, has been reported to protect the mucus layer in the colon and significantly decrease the effects of Cd exposure in mice. Thus, the mice model was adopted to investigate the influence of oral administration of AKK on the toxic distribution and changes of gut microbiota composition caused by acute and chronic Cd exposure. In both acute and chronic Cd exposure experiments, 40 mice were divided into four groups (normal group, AKK group, Cd group and Cd plus AKK group). The Cd contents in feces and tissues were measured by a flame or graphite furnace atomic absorption spectrophotometer and gut microbiota composition was determined through 16S rRNA gene sequencing. The results showed that the gavage of AKK could not reduce the accumulation of Cd in the liver and kidney. The oral administration of AKK showed a certain influence on the gut microbiota composition of acute Cd exposure mice and limited influence on that of chronic Cd exposure mice. These results indicate the failure of AKK, as a potential protective probiotic, to reduce Cd toxicity. However, the gavage of AKK did have an influence on the gut microbiota composition of normal mice, especially on some genera in the Clostridiales order. Besides, when considering AKK's probiotic potential and its effects on host health and disease, we should take into consideration its influence on the gut microbiota composition and micro-environment.}, } @article {pmid31310635, year = {2019}, author = {Tan, Z and Dong, W and Ding, Y and Ding, X and Zhang, Q and Jiang, L}, title = {Changes in cecal microbiota community of suckling piglets infected with porcine epidemic diarrhea virus.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0219868}, pmid = {31310635}, issn = {1932-6203}, mesh = {Animals ; Computational Biology/methods ; Coronavirus Infections/*veterinary ; Feces/*virology ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Molecular Sequence Annotation ; Phylogeny ; *Porcine epidemic diarrhea virus ; RNA, Ribosomal, 16S/genetics ; Swine ; Swine Diseases/*virology ; }, abstract = {Diarrhea, caused by porcine epidemic diarrhea virus (PEDV), is a catastrophic gastrointestinal disease among suckling piglets, with high infectivity, morbidity, and mortality, causing huge economic losses to the pig industry. In the present study, we investigated the different microbiota from the cecal mucosa and cecal contents between healthy and PEDV-infected piglets. High-throughput 16S rRNA gene sequencing was performed to explore differences. The results revealed that microbial dysbiosis by PEDV infection occurred in the cecal mucosa and contents of suckling piglets at each microbial taxonomic level. The abundance of pathogenic bacteria associated with diseases, including diarrhea, was increased. The abundance of Fusobacterium was 26.71% and 33.91% in cecal mucosa and contents of PEDV-infected group, respectively, whereas that in the healthy groups was 17.85% and 9.88%. The proportion of Proteobacteria in the infected groups was relatively high (24.67% and 22.79%, respectively), whereas that in the healthy group was 13.13% and 11.34% in the cecal mucosa and contents, respectively. Additionally, the proportion of Bacteroidetes in the healthy group (29.89%, 37.32%) was approximately twice that of the PEDV-infected group (15.50%, 15.39%). "Nitrate reduction", "Human pathogens diarrhea", "Human pathogens gastroenteritis", "Nitrite respiration", and "Nitrite ammonification" were the enriched functional annotation terms in the PEDV-infected groups. Porcine epidemic diarrhea virus infection increased the proportion of harmful bacteria and decreased the proportion of beneficial bacteria in the cecal mucosa and contents of suckling piglets. Our findings suggest that determining the intestinal microbiota might provide a promising method to prevent PEDV and open a new avenue for future research.}, } @article {pmid31309109, year = {2019}, author = {Wang, S and Li, N and Li, N and Zou, H and Wu, M}, title = {A Comparative Analysis of Biosynthetic Gene Clusters in Lean and Obese Humans.}, journal = {BioMed research international}, volume = {2019}, number = {}, pages = {6361320}, pmid = {31309109}, issn = {2314-6141}, mesh = {Bacteroidetes/*genetics/metabolism ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenome ; Microbial Interactions/*genetics ; *Multigene Family ; *Obesity/genetics/microbiology ; }, abstract = {Obesity is intrinsically linked with the gut microbiome, and studies have identified several obesity-associated microbes. The microbe-microbe interactions can alter the composition of the microbial community and influence host health by producing secondary metabolites (SMs). However, the contribution of these SMs in the prevention and treatment of obesity has been largely ignored. We identified several SM-encoding biosynthetic gene clusters (BGCs) from the metagenomic data of lean and obese individuals and found significant association between some BGCs, including those that produce hitherto unknown SM, and obesity. In addition, the mean abundance of BGCs was positively correlated with obesity, consistent with the lower taxonomic diversity in the gut microbiota of obese individuals. By comparing the BGCs of known SM between obese and nonobese samples, we found that menaquinone produced by Enterobacter cloacae showed the highest correlation with BMI, in agreement with a recent study on human adipose tissue composition. Furthermore, an obesity-related nonribosomal peptide synthetase (NRPS) was negatively associated with Bacteroidetes, indicating that the SMs produced by intestinal microbes in obese individuals can change the microbiome structure. This is the first systemic study of the association between gut microbiome BGCs and obesity and provides new insights into the causes of obesity.}, } @article {pmid31308552, year = {2019}, author = {Ji, BW and Sheth, RU and Dixit, PD and Huang, Y and Kaufman, A and Wang, HH and Vitkup, D}, title = {Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling.}, journal = {Nature methods}, volume = {16}, number = {8}, pages = {731-736}, pmid = {31308552}, issn = {1548-7105}, support = {R01 AI132403/AI/NIAID NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; R01 GM079759/GM/NIGMS NIH HHS/United States ; T32 GM007367/GM/NIGMS NIH HHS/United States ; }, mesh = {*Algorithms ; Bacteria/classification/*genetics ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/*methods ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; *Soil Microbiology ; *Spatio-Temporal Analysis ; Specimen Handling ; }, abstract = {Metagenomic sequencing has enabled detailed investigation of diverse microbial communities, but understanding their spatiotemporal variability remains an important challenge. Here, we present decomposition of variance using replicate sampling (DIVERS), a method based on replicate sampling and spike-in sequencing. The method quantifies the contributions of temporal dynamics, spatial sampling variability, and technical noise to the variances and covariances of absolute bacterial abundances. We applied DIVERS to investigate a high-resolution time series of the human gut microbiome and a spatial survey of a soil bacterial community in Manhattan's Central Park. Our analysis showed that in the gut, technical noise dominated the abundance variability for nearly half of the detected taxa. DIVERS also revealed substantial spatial heterogeneity of gut microbiota, and high temporal covariances of taxa within the Bacteroidetes phylum. In the soil community, spatial variability primarily contributed to abundance fluctuations at short time scales (weeks), while temporal variability dominated at longer time scales (several months).}, } @article {pmid31308384, year = {2019}, author = {Bang, S and Yoo, D and Kim, SJ and Jhang, S and Cho, S and Kim, H}, title = {Establishment and evaluation of prediction model for multiple disease classification based on gut microbial data.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {10189}, pmid = {31308384}, issn = {2045-2322}, mesh = {Algorithms ; Disease/*classification/genetics ; Forecasting/methods ; Gastrointestinal Microbiome/*genetics ; Humans ; Machine Learning ; Metagenomics/*methods ; Support Vector Machine ; }, abstract = {Diseases prediction has been performed by machine learning approaches with various biological data. One of the representative data is the gut microbial community, which interacts with the host's immune system. The abundance of a few microorganisms has been used as markers to predict diverse diseases. In this study, we hypothesized that multi-classification using machine learning approach could distinguish the gut microbiome from following six diseases: multiple sclerosis, juvenile idiopathic arthritis, myalgic encephalomyelitis/chronic fatigue syndrome, acquired immune deficiency syndrome, stroke and colorectal cancer. We used the abundance of microorganisms at five taxonomy levels as features in 696 samples collected from different studies to establish the best prediction model. We built classification models based on four multi-class classifiers and two feature selection methods including a forward selection and a backward elimination. As a result, we found that the performance of classification is improved as we use the lower taxonomy levels of features; the highest performance was observed at the genus level. Among four classifiers, LogitBoost-based prediction model outperformed other classifiers. Also, we suggested the optimal feature subsets at the genus-level obtained by backward elimination. We believe the selected feature subsets could be used as markers to distinguish various diseases simultaneously. The finding in this study suggests the potential use of selected features for the diagnosis of several diseases.}, } @article {pmid31307985, year = {2019}, author = {Burdet, C and Nguyen, TT and Duval, X and Ferreira, S and Andremont, A and Guedj, J and Mentré, F and , }, title = {Impact of Antibiotic Gut Exposure on the Temporal Changes in Microbiome Diversity.}, journal = {Antimicrobial agents and chemotherapy}, volume = {63}, number = {10}, pages = {}, pmid = {31307985}, issn = {1098-6596}, mesh = {Adult ; Anti-Bacterial Agents/*therapeutic use ; Bacteria/drug effects/genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/*genetics ; Healthy Volunteers ; Humans ; Male ; Microbiota/*drug effects/*genetics ; Middle Aged ; Moxifloxacin/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Young Adult ; }, abstract = {Although the global deleterious impact of antibiotics on the intestinal microbiota is well known, temporal changes in microbial diversity during and after an antibiotic treatment are still poorly characterized. We used plasma and fecal samples collected frequently during treatment and up to one month after from 22 healthy volunteers assigned to a 5-day treatment by moxifloxacin (n = 14) or no intervention (n = 8). Moxifloxacin concentrations were measured in both plasma and feces, and bacterial diversity was determined in feces by 16S rRNA gene profiling and quantified using the Shannon index and number of operational taxonomic units (OTUs). Nonlinear mixed effect models were used to relate drug pharmacokinetics and bacterial diversity over time. Moxifloxacin reduced bacterial diversity in a concentration-dependent manner, with a median maximal loss of 27.5% of the Shannon index (minimum [min], 17.5; maximum [max], 27.7) and 47.4% of the number of OTUs (min, 30.4; max, 48.3). As a consequence of both the long fecal half-life of moxifloxacin and the susceptibility of the gut microbiota to moxifloxacin, bacterial diversity indices did not return to their pretreatment levels until days 16 and 21, respectively. Finally, the model characterized the effect of moxifloxacin on bacterial diversity biomarkers and provides a novel framework for analyzing antibiotic effects on the intestinal microbiome.}, } @article {pmid31307536, year = {2019}, author = {Chen, J and McIlroy, SE and Archana, A and Baker, DM and Panagiotou, G}, title = {A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {104}, pmid = {31307536}, issn = {2049-2618}, mesh = {Anti-Infective Agents/pharmacology ; Bacteria/*classification ; China ; Drug Resistance, Microbial/*genetics ; *Environmental Pollution ; Eutrophication ; Geologic Sediments/*microbiology ; *Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {BACKGROUND: Coastal marine environments are one of the most productive ecosystems on Earth. However, anthropogenic impacts exert significant pressure on coastal marine biodiversity, contributing to functional shifts in microbial communities and human health risk factors. However, relatively little is known about the impact of eutrophication-human-derived nutrient pollution-on the marine microbial biosphere.

RESULTS: Here, we tested the hypothesis that benthic microbial diversity and function varies along a pollution gradient, with a focus on human pathogens and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG annotation revealed that zinc, lead, total volatile solids, and ammonia nitrogen were correlated with microbial diversity and function. We propose several microbes, including Planctomycetes and sulfate-reducing microbes as candidates to reflect pollution concentration. Annotation of antibiotic resistance genes showed that the highest abundance of efflux pumps was found at the most polluted site, corroborating the relationship between pollution and human health risk factors. This result suggests that sediments at polluted sites harbor microbes with a higher capacity to reduce intracellular levels of antibiotics, heavy metals, or other environmental contaminants.

CONCLUSIONS: Our findings suggest a correlation between pollution and the marine sediment microbiome and provide insight into the role of high-turnover microbial communities as well as potential pathogenic organisms as real-time indicators of water quality, with implications for human health and demonstrate the inner functional shifts contributed by the microcommunities.}, } @article {pmid31307001, year = {2019}, author = {Wang, J and Khokhar, I and Ren, C and Li, X and Wang, J and Fan, S and Jia, Y and Yan, Y}, title = {Characterization and 16S metagenomic analysis of organophosphorus flame retardants degrading consortia.}, journal = {Journal of hazardous materials}, volume = {380}, number = {}, pages = {120881}, doi = {10.1016/j.jhazmat.2019.120881}, pmid = {31307001}, issn = {1873-3336}, mesh = {Flame Retardants/*metabolism ; *Metagenomics ; *Microbial Consortia ; Organophosphorus Compounds/*metabolism ; Rhodococcus/metabolism ; Sphingomonadaceae/metabolism ; }, abstract = {Three bacterial consortia, named YC-SY1, YC-BJ1 and YC-GZ1, were enriched from different areas of China. Bacterial consortia YC-SY1, YC-BJ1 and YC-GZ1 could efficiently degrade triphenyl phosphate (TPhP) (100 mg/L) by approximately 79.4%, 99.8% and 99.6%, tricresyl phosphate (TCrP) by 90.6%, 91.9% and 96.3%, respectively, within 4 days. And they could retain high degrading efficiency under a broad range of temperature (15-40 ℃), pH (6.0-10.0) and salinity (0-4%). A total of 10 bacterial isolates were selected and investigated their degradation capacity. Among these isolates, two were significantly superior to the others. Strain Rhodococcus sp. YC-JH2 could utilize TPhP (50 mg/L) as sole carbon source for growth with 37.36% degradation within 7 days. Strain Sphingopyxis sp. YC-JH3 could efficiently degrade 96.2% of TPhP (50 mg/L) within 7 days, except that no cell growth was observed. Combined with 16S diversity analysis, our results suggest that the effective components of three bacterial consortia responsible for TPhP and TCrP degradation were almost the same, that is, bacteria capable of degrading TPhP and TCrP are limited, in this study, the most efficient component is Sphingopyxis. This study provides abundant microorganism sources for research on organophosphorus flame retardants (OPFRs) metabolism and bioremediation towards OPFRs-contaminated environments.}, } @article {pmid31306822, year = {2019}, author = {Han, L and Cai, L and Zhang, H and Long, Z and Yu, Y and Fang, H}, title = {Development of antibiotic resistance genes in soils with ten successive treatments of chlortetracycline and ciprofloxacin.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {253}, number = {}, pages = {152-160}, doi = {10.1016/j.envpol.2019.07.031}, pmid = {31306822}, issn = {1873-6424}, mesh = {Agriculture ; Anti-Bacterial Agents/*toxicity ; Chlortetracycline/analysis/*toxicity ; Ciprofloxacin/*toxicity ; Drug Resistance, Microbial/*genetics ; Manure/analysis ; Metagenomics ; Microbiota/drug effects ; Soil ; *Soil Microbiology ; Tetracycline/pharmacology ; Tetracycline Resistance ; }, abstract = {Antibiotic contamination caused by the long-term use of organic manure (OM) in greenhouse agricultural soils poses potential detrimental effects to the soil environment. By applying OM containing chlortetracycline (CTC) and/or ciprofloxacin (CIP) ten times in soil under laboratory conditions, we investigated the dissipation and accumulation characteristics of CTC and CIP in the soil, the changes in the microbial pollution-induced community tolerance (PICT), and the diversity and abundance of antibiotic resistance genes (ARGs) in the soil microbiome. The dissipation of CTC was rapid while CIP was accumulated in repeatedly treated soils; further, CIP could inhibit the dissipation of CTC. Meanwhile, the PICT to CTC and/or CIP significantly increased up to 15.0-fold after ten successive treatments compared to that in the first treatment. As the treatment frequency increased, significant upward trends in the abundances of tetracycline resistance genes tetA(G), tetX2, tetX, tetG, tetA(33), tetA, tetW, and tetA(P), fluoroquinolone resistance gene qnrA6, and multiple resistance gene mexF were revealed by both metagenomic and qPCR analyses. The findings demonstrated that repeated treatments with CTC and/or CIP can alter the dissipation rate, promote an increase in PICT to CTC and/or CIP, and increase the ARGs abundance in steps.}, } @article {pmid31301473, year = {2019}, author = {Bengtsson-Palme, J and Milakovic, M and Švecová, H and Ganjto, M and Jonsson, V and Grabic, R and Udikovic-Kolic, N}, title = {Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities.}, journal = {Water research}, volume = {162}, number = {}, pages = {437-445}, doi = {10.1016/j.watres.2019.06.073}, pmid = {31301473}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; Croatia ; Drug Resistance, Bacterial ; Europe ; Genes, Bacterial ; Macrolides ; *Microbiota ; Sewage ; *Wastewater ; }, abstract = {Antibiotic resistance is an emerging global health crisis, driven largely by overuse and misuse of antibiotics. However, there are examples in which the production of these antimicrobial agents has polluted the environment with active antibiotic residues, selecting for antibiotic resistant bacteria and the genes they carry. In this work, we have used shotgun metagenomics to investigate the taxonomic structure and resistance gene composition of sludge communities in a treatment plant in Croatia receiving wastewater from production of the macrolide antibiotic azithromycin. We found that the total abundance of antibiotic resistance genes was three times higher in sludge from the treatment plant receiving wastewater from pharmaceutical production than in municipal sludge from a sewage treatment plant in Zagreb. Surprisingly, macrolide resistance genes did not have higher abundances in the industrial sludge, but genes associated with mobile genetic elements such as integrons had. We conclude that at high concentrations of antibiotics, selection may favor taxonomic shifts towards intrinsically resistant species or strains harboring chromosomal resistance mutations rather than acquisition of mobile resistance determinants. Our results underscore the need for regulatory action also within Europe to avoid release of antibiotics into the environment.}, } @article {pmid31300992, year = {2019}, author = {Sonthiphand, P and Ruangroengkulrith, S and Mhuantong, W and Charoensawan, V and Chotpantarat, S and Boonkaewwan, S}, title = {Metagenomic insights into microbial diversity in a groundwater basin impacted by a variety of anthropogenic activities.}, journal = {Environmental science and pollution research international}, volume = {26}, number = {26}, pages = {26765-26781}, pmid = {31300992}, issn = {1614-7499}, support = {New Researcher Grant//Mahidol University/ ; MRG6080235//Thailand Research Fund (TRF) Grant/ ; }, mesh = {Anaerobiosis ; Arsenic/metabolism ; Bacteria/genetics ; Biodiversity ; Groundwater/*chemistry/*microbiology ; Metagenomics ; Methane/metabolism ; Microbiota/genetics/*physiology ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Thailand ; Water Pollutants, Chemical/analysis ; }, abstract = {Microbial communities in groundwater are diverse and each may respond differently to environmental change. The goal of this study was to investigate the diversity, abundance, and dynamics of microbial communities in impacted groundwater and correlate them to the corresponding land use and groundwater geochemistry, using an Illumina MiSeq platform targeting the V3 and V4 regions of the 16S rRNA gene. The resulting MiSeq sequencing revealed the co-occurrence patterns of both abundant and rare microbial taxa within an impacted groundwater basin. Proteobacteria were the most common groundwater-associated bacterial phylum, mainly composed of the classes Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria. The phyla detected at less abundances were the Firmicutes, Bacteroidetes, Planctomycetes, Actinobacteria, OD1, and Nitrospirae. The members of detected groundwater microorganisms involved in natural biogeochemical processes such as nitrification, anammox, methane oxidation, sulfate reduction, and arsenic transformation. Some of the detected microorganisms were able to perform anaerobic degradation of organic pollutants. The resulting PCA indicates that major land usage within the sampling area seemed to be significantly linked to the groundwater microbial distributions. The distinct microbial pattern was observed in the groundwater collected from a landfill area. This study suggests that the combinations of anthropogenic and natural effects possibly led to a unique pattern of microbial diversity across different locations at the impacted groundwater basin.}, } @article {pmid31298176, year = {2019}, author = {Michels, N}, title = {Biological underpinnings from psychosocial stress towards appetite and obesity during youth: research implications towards metagenomics, epigenomics and metabolomics.}, journal = {Nutrition research reviews}, volume = {32}, number = {2}, pages = {282-293}, doi = {10.1017/S0954422419000143}, pmid = {31298176}, issn = {1475-2700}, mesh = {Adolescent ; Appetite/*physiology ; Behavior/physiology ; Child ; Child, Preschool ; Diet/psychology ; Eating/physiology/psychology ; *Epigenomics ; Exercise ; Feeding Behavior/physiology ; Gastrointestinal Microbiome/physiology ; Humans ; Hydrocortisone/physiology ; *Metabolomics ; *Metagenomics ; Pediatric Obesity/physiopathology/*psychology ; Stress, Psychological/epidemiology/*physiopathology ; }, abstract = {Psychosocial stress, uncontrolled eating and obesity are three interrelated epidemiological phenomena already present during youth. This broad narrative conceptual review summarises main biological underpinnings of the stress-diet-obesity pathway and how new techniques can further knowledge. Cortisol seems the main biological factor from stress towards central adiposity; and diet, physical activity and sleep are the main behavioural pathways. Within stress-diet, the concepts of comfort food and emotional eating are highlighted, as cortisol affects reward pathways and appetite brain centres with a role for insulin, leptin, neuropeptide Y (NPY), endocannabinoids, orexin and gastrointestinal hormones. More recently researched biological underpinnings are microbiota, epigenetic modifications and metabolites. First, the gut microbiota reaches the stress-regulating and appetite-regulating brain centres via the gut-brain axis. Second, epigenetic analyses are recommended as diet, obesity, stress and gut microbiota can change gene expression which then affects appetite, energy homeostasis and stress reactivity. Finally, metabolomics would be a good technique to disentangle stress-diet-obesity interactions as multiple biological pathways are involved. Saliva might be an ideal biological matrix as it allows metagenomic (oral microbiota), epigenomic and metabolomic analyses. In conclusion, stress and diet/obesity research should be combined in interdisciplinary collaborations with implementation of several -omics analyses.}, } @article {pmid31297792, year = {2019}, author = {Zhang, Y and Zhang, Y and Kuang, Z and Xu, J and Li, C and Li, Y and Jiang, Y and Xie, J}, title = {Comparison of Microbiomes and Resistomes in Two Karst Groundwater Sites in Chongqing, China.}, journal = {Ground water}, volume = {57}, number = {5}, pages = {807-818}, doi = {10.1111/gwat.12924}, pmid = {31297792}, issn = {1745-6584}, mesh = {Bacteria ; China ; Environmental Monitoring ; *Groundwater ; *Microbiota ; }, abstract = {Karst groundwater is an important water resource, as it accounts for about 15% of the total landscape of the earth and supplies 20% of potable water worldwide. The antibiotics resistance is an emerging global concern, and antibiotics residual and increase of antibiotic resistance genes represent serious global concerns and emerging pollutants. There is no report on the antibiotic resistance genes in groundwater. To survey resistome and microbiome in karst groundwater, two karst water samples were chosen for metagenome and metatranscriptome study, namely the 37[th] spring (C) and Dongcao spring (R) in Beibei, Chongqing, China. The two sites differ significantly in sulfur content, geochemical parameters, community structure, antibiotic resistance genes, and mechanisms, and these results may be influenced by anthropogenic activities. Combining with the Antibiotic Resistance Genes Database, three types of resistance genes baca, sul2, sul1 are present in R and C, and ant3ia, ermc, tetpa are also present in R. The number of all resistance genes in R was more than C, and Proteobacteria, Bacteroidetes, Nitrospirae are the main sources of antibiotic resistance genes. In addition, a large number of genes related to antibiotic gene transmission and drug resistance were found in both samples. Karst groundwater is an important source of drinking water and a possible venue for the transmission of microbial antibiotic resistance genes. However, few studies addressed this issue in karst groundwater, despite its widespread and great importance to global ecosystem. Karst groundwater is a reservoir for antibiotic resistant genes, and measures to control these resistant genes are urgently needed.}, } @article {pmid31296857, year = {2019}, author = {Dilthey, AT and Jain, C and Koren, S and Phillippy, AM}, title = {Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {3066}, pmid = {31296857}, issn = {2041-1723}, mesh = {Algorithms ; Computational Biology/*methods ; *Data Analysis ; Datasets as Topic ; High-Throughput Nucleotide Sequencing/methods ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {Metagenomic sequence classification should be fast, accurate and information-rich. Emerging long-read sequencing technologies promise to improve the balance between these factors but most existing methods were designed for short reads. MetaMaps is a new method, specifically developed for long reads, capable of mapping a long-read metagenome to a comprehensive RefSeq database with >12,000 genomes in <16 GB or RAM on a laptop computer. Integrating approximate mapping with probabilistic scoring and EM-based estimation of sample composition, MetaMaps achieves >94% accuracy for species-level read assignment and r[2] > 0.97 for the estimation of sample composition on both simulated and real data when the sample genomes or close relatives are present in the classification database. To address novel species and genera, which are comparatively harder to predict, MetaMaps outputs mapping locations and qualities for all classified reads, enabling functional studies (e.g. gene presence/absence) and detection of incongruities between sample and reference genomes.}, } @article {pmid31296738, year = {2019}, author = {Gehrig, JL and Venkatesh, S and Chang, HW and Hibberd, MC and Kung, VL and Cheng, J and Chen, RY and Subramanian, S and Cowardin, CA and Meier, MF and O'Donnell, D and Talcott, M and Spears, LD and Semenkovich, CF and Henrissat, B and Giannone, RJ and Hettich, RL and Ilkayeva, O and Muehlbauer, M and Newgard, CB and Sawyer, C and Head, RD and Rodionov, DA and Arzamasov, AA and Leyn, SA and Osterman, AL and Hossain, MI and Islam, M and Choudhury, N and Sarker, SA and Huq, S and Mahmud, I and Mostafa, I and Mahfuz, M and Barratt, MJ and Ahmed, T and Gordon, JI}, title = {Effects of microbiota-directed foods in gnotobiotic animals and undernourished children.}, journal = {Science (New York, N.Y.)}, volume = {365}, number = {6449}, pages = {}, pmid = {31296738}, issn = {1095-9203}, support = {P30 AR057235/AR/NIAMS NIH HHS/United States ; P30 AR074992/AR/NIAMS NIH HHS/United States ; P30 DK056341/DK/NIDDK NIH HHS/United States ; P30 DK020579/DK/NIDDK NIH HHS/United States ; T32 GM007200/GM/NIGMS NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; UL1 TR002345/TR/NCATS NIH HHS/United States ; P30 CA091842/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bangladesh ; Blood Proteins/analysis ; Child Nutrition Disorders/*diet therapy/metabolism/*microbiology ; Child, Preschool ; *Gastrointestinal Microbiome ; *Germ-Free Life ; *Host Microbial Interactions ; Humans ; Infant ; *Infant Nutritional Physiological Phenomena ; }, abstract = {To examine the contributions of impaired gut microbial community development to childhood undernutrition, we combined metabolomic and proteomic analyses of plasma samples with metagenomic analyses of fecal samples to characterize the biological state of Bangladeshi children with severe acute malnutrition (SAM) as they transitioned, after standard treatment, to moderate acute malnutrition (MAM) with persistent microbiota immaturity. Host and microbial effects of microbiota-directed complementary food (MDCF) prototypes targeting weaning-phase bacterial taxa underrepresented in SAM and MAM microbiota were characterized in gnotobiotic mice and gnotobiotic piglets colonized with age- and growth-discriminatory bacteria. A randomized, double-blind controlled feeding study identified a lead MDCF that changes the abundances of targeted bacteria and increases plasma biomarkers and mediators of growth, bone formation, neurodevelopment, and immune function in children with MAM.}, } @article {pmid31296445, year = {2019}, author = {Shen, N and Caixàs, A and Ahlers, M and Patel, K and Gao, Z and Dutia, R and Blaser, MJ and Clemente, JC and Laferrère, B}, title = {Longitudinal changes of microbiome composition and microbial metabolomics after surgical weight loss in individuals with obesity.}, journal = {Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery}, volume = {15}, number = {8}, pages = {1367-1373}, pmid = {31296445}, issn = {1878-7533}, support = {R01 DK067561/DK/NIDDK NIH HHS/United States ; UL1 TR000040/TR/NCATS NIH HHS/United States ; R01 MH110418/MH/NIMH NIH HHS/United States ; P30 DK026687/DK/NIDDK NIH HHS/United States ; T32 DK007559/DK/NIDDK NIH HHS/United States ; R01 DK090989/DK/NIDDK NIH HHS/United States ; R01 DK098056/DK/NIDDK NIH HHS/United States ; P30 DK063608/DK/NIDDK NIH HHS/United States ; R01 DK114038/DK/NIDDK NIH HHS/United States ; }, mesh = {*Bariatric Surgery ; Cohort Studies ; DNA, Bacterial/genetics ; Gastrointestinal Microbiome/*genetics ; Humans ; Metabolome/genetics ; Metagenome/genetics ; Obesity/*surgery ; Weight Loss/*physiology ; }, abstract = {BACKGROUND: Some of the metabolic effects of bariatric surgery may be mediated by the gut microbiome.

OBJECTIVES: To study the effect of bariatric surgery on changes to gut microbiota composition and bacterial pathways, and their relation to metabolic parameters after bariatric surgery.

SETTINGS: University hospitals in the United States and Spain.

METHODS: Microbial diversity and composition by 16 S rRNA sequencing, putative bacterial pathways, and targeted circulating metabolites were studied in 26 individuals with severe obesity, with and without type 2 diabetes, before and at 3, 6, and 12 months after either gastric bypass or sleeve gastrectomy.

RESULTS: Bariatric surgery tended to increase alpha diversity, and significantly altered beta diversity, microbiota composition, and function up to 6 months after surgery, but these changes tend to regress to presurgery levels by 12 months. Twelve of 15 bacterial pathways enriched after surgery also regressed to presurgery levels at 12 months. Network analysis identified groups of bacteria significantly correlated with levels of circulating metabolites over time. There were no differences between study sites, surgery type, or diabetes status in terms of microbial diversity and composition at baseline and after surgery.

CONCLUSIONS: The association among changes in microbiome with decreased circulating biomarkers of inflammation, increased bile acids, and products of choline metabolism and other bacterial pathways suggest that the microbiome partially mediates improvement of metabolism during the first year after bariatric surgery.}, } @article {pmid31294712, year = {2019}, author = {Orellana, E and Davies-Sala, C and Guerrero, LD and Vardé, I and Altina, M and Lorenzo, MC and Figuerola, EL and Pontiggia, RM and Erijman, L}, title = {Microbiome network analysis of co-occurrence patterns in anaerobic co-digestion of sewage sludge and food waste.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {79}, number = {10}, pages = {1956-1965}, doi = {10.2166/wst.2019.194}, pmid = {31294712}, issn = {0273-1223}, mesh = {Bioreactors ; Methane ; *Microbiota ; Phylogeny ; *Sewage ; *Waste Disposal, Fluid ; }, abstract = {Addition of food waste (FW) as a co-substrate in anaerobic digesters of wastewater treatment plants is a desirable strategy towards achievement of the potential of wastewater treatment plants to become energy-neutral, diverting at the same time organic waste from landfills. Because substrate type is a driver of variations in phylogenetic structure of digester microbiomes, it is critical to understand how microbial communities respond to changes in substrate composition and concentration. In this work, high throughput sequencing was used to monitor the dynamics of microbiome changes in four parallel laboratory-scale anaerobic digesters treating sewage sludge during acclimation to an increasing amount of food waste. A co-occurrence network was constructed using data from 49 metagenomes sampled over the 161 days of the digesters' operation. More than half of the nodes in the network were clustered in two major modules, i.e. groups of highly interconnected taxa that had much fewer connections with taxa outside the group. The dynamics of co-occurrence networks evidenced shifts that occurred within microbial communities due to the addition of food waste in the co-digestion process. A diverse and reproducible group of hydrolytic and fermentative bacteria, syntrophic bacteria and methanogenic archaea appeared to grow in a concerted fashion to allow stable performance of anaerobic co-digestion at high FW.}, } @article {pmid31293986, year = {2019}, author = {Zhou, P and Li, Z and Xu, D and Wang, Y and Bai, Q and Feng, Y and Su, G and Chen, P and Wang, Y and Liu, H and Wang, X and Zhang, R and Wang, Y}, title = {Cepharanthine Hydrochloride Improves Cisplatin Chemotherapy and Enhances Immunity by Regulating Intestinal Microbes in Mice.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {225}, pmid = {31293986}, issn = {2235-2988}, mesh = {Animals ; Antineoplastic Agents/pharmacology ; Apoptosis/drug effects ; Bacteria/classification/drug effects ; Benzylisoquinolines/*pharmacology ; Cell Line, Tumor ; Cisplatin/*pharmacology ; DNA, Ribosomal/genetics ; Disease Models, Animal ; Drug Synergism ; Drug Therapy/*methods ; Esophageal Neoplasms/drug therapy/pathology ; Esophageal Squamous Cell Carcinoma/drug therapy/pathology ; Female ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Immunity/*drug effects ; Immunity, Innate/drug effects ; Intestinal Mucosa/*drug effects/immunology/microbiology ; Metagenomics ; Mice ; Mice, Inbred BALB C ; Mice, Nude ; Myeloid Differentiation Factor 88/metabolism ; Signal Transduction/drug effects ; Toll-Like Receptor 4/metabolism ; Xenograft Model Antitumor Assays ; }, abstract = {Chemotherapy is one of the major treatment strategies for esophageal squamous cell carcinoma (ESCC). Unfortunately, most chemotherapeutic drugs have significant impacts on the intestinal microbes, resulting in side effects and reduced efficiency. Therefore, new strategies capable of overcoming these disadvantages of current chemotherapies are in urgent need. The natural product, Cepharanthine hydrochloride (CEH), is known for its anticancer and immunoregulatory properties. By sequencing the V4 region of 16S rDNA, we characterized the microbes of tumor-bearing mice treated with different chemotherapy strategies, including with CEH. We found that CEH improved the therapeutic effect of CDDP by manipulating the gut microbiota. Through metagenomic analyses of the microbes community, we identified a severe compositional and functional imbalance in the gut microbes community after CDDP treatment. However, CEH improved the effect of chemotherapy and ameliorated CDDP treatment-induced imbalance in the intestinal microbes. Mechanically, CEH activated TLR4 and MYD88 innate immune signaling, which is advantageous for the activation of the host's innate immunity to exert a balanced intestinal environment as well as to trigger a better chemotherapeutic response to esophageal cancer. In addition, TNFR death receptors were activated to induce apoptosis. In summary, our findings suggest that chemotherapy of CDDP combined with CEH increased the effect of chemotherapy and reduced the side effects on the microbes and intestinal mucosal immunity. We believe that these findings provide a theoretical basis for new clinical treatment strategies.}, } @article {pmid31293117, year = {2019}, author = {Masoodi, I and Alshanqeeti, AS and Ahmad, S and Alyamani, EJ and Al-Lehibi, AA and Qutub, AN and Alsayari, KN and Alomair, AO}, title = {Microbial dysbiosis in inflammatory bowel diseases: results of a metagenomic study in Saudi Arabia.}, journal = {Minerva gastroenterologica e dietologica}, volume = {65}, number = {3}, pages = {177-186}, doi = {10.23736/S1121-421X.19.02576-5}, pmid = {31293117}, issn = {1827-1642}, mesh = {Adolescent ; Adult ; Aged ; Cohort Studies ; Colitis, Ulcerative/*microbiology ; Crohn Disease/*microbiology ; *Dysbiosis ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; *Metagenome ; Middle Aged ; Saudi Arabia ; Young Adult ; }, abstract = {BACKGROUND: The intestinal microbiota plays an essential role in the pathogenesis of ulcerative colitis (UC)and Crohn disease (CD).

METHODS: Metagenomic studies were used to study microbiota in the diagnosed cases of UC and CD at King Fahad Medical City, Riyadh, Saudi Arabia. Each segment of the colon was flushed with distilled water during colonoscopy, and the material was aspirated, immediately frozen for the study. The patients attending for screening colonoscopies were taken as age-matched healthy controls. The UC patients were followed clinically for any signs of exacerbation relapse, and CD patients were followed for any complications.

RESULTS: The metagenomic data on 46 (24 females) patients with CD were analyzed along with a group of age and gender-matched controls. Their age ranged from 14 to 65 years, mean age 25.19±10.67 years. There were 50 UC patient (28 females) mean age of 34.42±12.58, and their age ranged from 13-58 years. This study identified enrichment of 19 genera in the control group (Abiotrophia, Anaerofustis, Butyrivibrio, Campylobacter, Catenibacterium, Coprococcus, Dorea, Eubacterium, Facklamia, Klebsiella, Lactococcus, Oscillibacter, Paenibacillus, Parabacteroides, Parasutterella, Porphyromonas, Prevotella, Ruminococcus, Treponema). There was a significant enrichment of 14 genera in our CD cohort (Beggiatoa, Burkholderia, Cyanothece, Enterococcus, Escherichia, Fusobacterium, Jonquetella, Mitsuokella, Parvimonas, Peptostreptococcus, Shigella, Succinatimonas, ThermoanaerobacterVerrucomicrobiales, Vibrio). There was a significant enrichment of 7 genera in UC cohort (Beggiatoa, Burkholderia, Parascardovia, Parvimonas, Pseudoflavonifractor, Thermoanaerobacter, Verrucomicrobiales).

CONCLUSIONS: A significant dysbiosis was found in UC and CD patients compared to controls.}, } @article {pmid31293086, year = {2020}, author = {Ji, Y and Huotari, T and Roslin, T and Schmidt, NM and Wang, J and Yu, DW and Ovaskainen, O}, title = {SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes.}, journal = {Molecular ecology resources}, volume = {20}, number = {1}, pages = {256-267}, doi = {10.1111/1755-0998.13057}, pmid = {31293086}, issn = {1755-0998}, support = {31400470//National Natural Science Foundation of China/ ; 31500305//National Natural Science Foundation of China/ ; 31670536//National Natural Science Foundation of China/ ; 41661144002//National Natural Science Foundation of China/ ; 276909//Suomen Akatemia/ ; 284601//Suomen Akatemia/ ; 285803//Suomen Akatemia/ ; 309571//Suomen Akatemia/ ; //Jane and Aatos Erkko Foundation Grant/ ; 223257//Research Council of Norway through its Centres of Excellence Funding Scheme/ ; //Danish Environmental Protection Agency/ ; QYZDY-SSW-SMC024//Key Research Program of Frontier Sciences, CAS/ ; GJHZ1754//Bureau of International Cooperation/ ; XDA20050202//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2012FY110800//Ministry of Science and Technology of China/ ; GREKF18-04//State Key Laboratory of Genetic Resources and Evolution/ ; //Kunming Institute of Zoology/ ; //University of East Anglia/ ; //University of Chinese Academy of Sciences/ ; }, mesh = {Animals ; Biodiversity ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; Eukaryota/*classification/*genetics ; Metagenomics/instrumentation/*methods ; }, abstract = {The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community ecology and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (a) a percent-coverage threshold to filter out false positives, (b) an internal-standard DNA spike-in to correct for stochasticity during sequencing, and (c) technical replicates to correct for stochasticity across sequencing runs. The SPIKEPIPE pipeline achieves a strikingly high accuracy of intraspecific abundance estimates (in terms of DNA mass) from samples of known composition (mapping to barcodes R[2] = .93, mitogenomes R[2] = .95) and a high repeatability across environmental-sample replicates (barcodes R[2] = .94, mitogenomes R[2] = .93). As proof of concept, we sequence arthropod samples from the High Arctic, systematically collected over 17 years, detecting changes in species richness, species-specific abundances, and phenology. SPIKEPIPE provides cost-efficient and reliable quantification of eukaryotic communities.}, } @article {pmid31292233, year = {2019}, author = {Moeller, AH and Gomes-Neto, JC and Mantz, S and Kittana, H and Segura Munoz, RR and Schmaltz, RJ and Ramer-Tait, AE and Nachman, MW}, title = {Experimental Evidence for Adaptation to Species-Specific Gut Microbiota in House Mice.}, journal = {mSphere}, volume = {4}, number = {4}, pages = {}, pmid = {31292233}, issn = {2379-5042}, support = {R01 GM074245/GM/NIGMS NIH HHS/United States ; R01 GM127468/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Animals ; Bacteria/*classification ; Female ; *Gastrointestinal Microbiome ; Germ-Free Life ; *Host Microbial Interactions ; *Host Specificity ; Male ; Metagenome ; Mice ; Mice, Inbred C57BL ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {The gut microbial communities of mammals have codiversified with host species, and changes in the gut microbiota can have profound effects on host fitness. Therefore, the gut microbiota may drive adaptation in mammalian species, but this possibility is underexplored. Here, we show that the gut microbiota has codiversified with mice in the genus Mus over the past ∼6 million years, and we present experimental evidence that the gut microbiota has driven adaptive evolution of the house mouse, Mus musculusdomesticus Phylogenetic analyses of metagenome-assembled bacterial genomic sequences revealed that gut bacterial lineages have been retained within and diversified alongside Mus species over evolutionary time. Transplantation of gut microbiotas from various Mus species into germfree M. m. domesticus showed that foreign gut microbiotas slowed growth rate and upregulated macrophage inflammatory protein in hosts. These results suggest adaptation by M. m. domesticus to its gut microbiota since it diverged from other Mus species.IMPORTANCE The communities of bacteria that reside within mammalian guts are deeply integrated with their hosts, but the impact of this gut microbiota on mammalian evolution remains poorly understood. Experimental transplantation of the gut microbiota between mouse species revealed that foreign gut microbiotas lowered the host growth rate and upregulated the expression of an immunomodulating cytokine. In addition, foreign gut microbiotas increased host liver sizes and attenuated sex-specific differences in host muscle and fat content. These results suggest that the house mouse has adapted to its species-specific gut microbiota.}, } @article {pmid31291888, year = {2019}, author = {Chen, L and Wang, YC and Qin, LY and He, HY and Yu, XL and Yang, MZ and Zhang, HB}, title = {Dynamics of fungal communities during Gastrodia elata growth.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {158}, pmid = {31291888}, issn = {1471-2180}, mesh = {Agaricales/genetics/isolation & purification ; Basidiomycota/genetics/isolation & purification ; DNA, Ribosomal Spacer/genetics ; *Gastrodia/growth & development/microbiology ; High-Throughput Nucleotide Sequencing ; *Host Microbial Interactions ; Metagenomics ; Mycobiome/*genetics ; Phylogeny ; Soil Microbiology ; Symbiosis ; }, abstract = {BACKGROUND: Gastrodia elata is a widely distributed achlorophyllous orchid and is highly valued as both medicine and food. Gastrodia elata produces dust-like seeds and relies on mycorrhizal fungi for its germination and growth. In its life cycle, G. elata is considered to switch from a specific single-fungus relationship (Mycena) to another single-fungus relationship (Armillaria). However, no studies have investigated the changes in the plant-fungus relationship during the growth of G. elata in the wild. In this study, high-throughput sequencing was used to characterize the fungal community of tubers in different growth phases as well as the soils surrounding G. elata.

RESULTS: The predominant fungi were Basidiomycota (60.44%) and Ascomycota (26.40%), which exhibited changes in abundance and diversity with the growth phases of G. elata. Diverse basidiomycetes in protocorms (phase P) were Hyphodontia, Sistotrema, Tricholoma, Mingxiaea, Russula, and Mycena, but the community changed from a large proportion of Resinicium bicolor (40%) in rice-like tubers (phase M) to an unidentified Agaricales operational taxonomic unit 1(OTU1,98.45%) in propagation vegetation tubers (phase B). The soil fungi primarily included Simocybe, Psathyrella, Conocybe, and Subulicystidium. Three Mycena OTUs obtained in this study were differentially distributed among the growth phases of G. elata, accounting for less than 1.0% of the total reads, and were phylogenetically close to Mycena epipterygia and M. alexandri.

CONCLUSIONS: Our data indicated that G. elata interacts with a broad range of fungi beyond the Mycena genus. These fungi changed with the growth phases of G. elata. In addition, these data suggested that the development of the fungal community during the growth of G. elata was more complex than previously assumed and that at least two different fungi could be involved in development before the arrival of Armillaria.}, } @article {pmid31291462, year = {2019}, author = {Liu, Y and Ajami, NJ and El-Serag, HB and Hair, C and Graham, DY and White, DL and Chen, L and Wang, Z and Plew, S and Kramer, J and Cole, R and Hernaez, R and Hou, J and Husain, N and Jarbrink-Sehgal, ME and Kanwal, F and Ketwaroo, G and Natarajan, Y and Shah, R and Velez, M and Mallepally, N and Petrosino, JF and Jiao, L}, title = {Dietary quality and the colonic mucosa-associated gut microbiome in humans.}, journal = {The American journal of clinical nutrition}, volume = {110}, number = {3}, pages = {701-712}, pmid = {31291462}, issn = {1938-3207}, support = {I01 CX001430/CX/CSRD VA/United States ; K07 CA181480/CA/NCI NIH HHS/United States ; }, mesh = {Aged ; Bacteria/*classification ; Colon/*microbiology ; Computational Biology ; Cross-Sectional Studies ; DNA, Bacterial/genetics ; Diet/*standards ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/*microbiology ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Despite tremendous interest in modulating the microbiome to improve health, the association between diet and the colonic mucosa-associated gut microbiome in healthy individuals has not been examined.

OBJECTIVE: To investigate the associations between Healthy Eating Index (HEI)-2005 and the colonic mucosa-associated microbiota.

METHODS: In this cross-sectional observational study, we analyzed bacterial community composition and structure using 16S rRNA gene (V4 region) sequencing of 97 colonic mucosal biopsies obtained endoscopically from different colon segments of 34 polyp-free participants. Dietary consumption was ascertained using an FFQ. Differences in α- and β-diversity and taxonomic relative abundances between the higher and lower score of total HEI and its components were compared, followed by multivariable analyses.

RESULTS: The structure of the microbiota significantly differed by the scores for total HEI, total and whole fruits (HEI 1 and HEI 2), whole grains (HEI 6), milk products and soy beverages (HEI 7), and solid fat, alcohol, and added sugar (HEI 12). A lower score for total HEI and HEIs 2, 7, and 12 was associated with significantly lower richness. A lower score for total HEI was associated with significantly reduced relative abundance of Parabacteroides, Roseburia, and Subdoligranulum but higher Fusobacterium. A lower score for HEI 2 was associated with lower Roseburia but higher Bacteroides. A lower score for HEI 7 was associated with lower Faecalibacterium and Fusobacterium but higher Bacteroides. A lower score for HEI 12 was associated with lower Subdoligranulum but higher Escherichia and Fusobacterium (false discovery rate-adjusted P values <0.05). The findings were confirmed by multivariate analysis. Less abundant bacteria such as Alistipes, Odoribacter, Bilophila, and Tyzzerella were also associated with dietary quality.

CONCLUSIONS: A lower score for total HEI-2005 was significantly associated with reduced relative abundance of potentially beneficial bacteria but increased potentially harmful bacteria in the colonic mucosa of endoscopically normal individuals.}, } @article {pmid31290099, year = {2019}, author = {Wang, P and Niu, B}, title = {Plant specialized metabolites modulate root microbiomes.}, journal = {Science China. Life sciences}, volume = {62}, number = {8}, pages = {1111-1113}, doi = {10.1007/s11427-019-9579-6}, pmid = {31290099}, issn = {1869-1889}, mesh = {Biosynthetic Pathways ; Gene Expression Regulation, Bacterial ; Metabolomics ; Metagenomics ; Microbiota/*genetics ; Mutation ; Plant Roots/*metabolism ; Plants/*metabolism ; Soil/chemistry ; Soil Microbiology ; Terpenes/metabolism ; Triterpenes/metabolism ; }, } @article {pmid31289831, year = {2019}, author = {Youens-Clark, K and Bomhoff, M and Ponsero, AJ and Wood-Charlson, EM and Lynch, J and Choi, I and Hartman, JH and Hurwitz, BL}, title = {iMicrobe: Tools and data-dreaiven discovery platform for the microbiome sciences.}, journal = {GigaScience}, volume = {8}, number = {7}, pages = {}, pmid = {31289831}, issn = {2047-217X}, mesh = {Big Data ; Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; *Software ; }, abstract = {BACKGROUND: Scientists have amassed a wealth of microbiome datasets, making it possible to study microbes in biotic and abiotic systems on a population or planetary scale; however, this potential has not been fully realized given that the tools, datasets, and computation are available in diverse repositories and locations. To address this challenge, we developed iMicrobe.us, a community-driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with those from the broader community.

FINDINGS: The iMicrobe platform brings together analysis tools and microbiome datasets by leveraging National Science Foundation-supported cyberinfrastructure and computing resources from CyVerse, Agave, and XSEDE. The primary purpose of iMicrobe is to provide users with a freely available, web-based platform to (1) maintain and share project data, metadata, and analysis products, (2) search for related public datasets, and (3) use and publish bioinformatics tools that run on highly scalable computing resources. Analysis tools are implemented in containers that encapsulate complex software dependencies and run on freely available XSEDE resources via the Agave API, which can retrieve datasets from the CyVerse Data Store or any web-accessible location (e.g., FTP, HTTP).

CONCLUSIONS: iMicrobe promotes data integration, sharing, and community-driven tool development by making open source data and tools accessible to the research community in a web-based platform.}, } @article {pmid31289345, year = {2019}, author = {Maritz, JM and Ten Eyck, TA and Elizabeth Alter, S and Carlton, JM}, title = {Patterns of protist diversity associated with raw sewage in New York City.}, journal = {The ISME journal}, volume = {13}, number = {11}, pages = {2750-2763}, pmid = {31289345}, issn = {1751-7370}, mesh = {Animals ; Biodiversity ; Eukaryota/classification/genetics/*isolation & purification ; Feces/parasitology ; Humans ; Metagenome ; New York City ; RNA, Ribosomal, 18S/genetics ; Sewage/*parasitology ; Soil/parasitology ; }, abstract = {Protists are ubiquitous components of terrestrial and aquatic environments, as well as animal and human microbiomes. Despite this, little is known about protists in urban environments. The ~7400-mile sewer system of New York City (NYC) collects human waste from ~8 million human inhabitants as well as from animals, street runoff, and groundwater, providing an ideal system to study these microbes. We used 18S rRNA amplicon sequencing and shotgun metagenomic sequencing to profile raw sewage microbial communities. Raw sewage samples were collected over a 12-month period from 14 treatment plants of the five NYC boroughs, and compared with samples from other environments including soil, stormwater, and sediment. Sewage contained a diverse protist community dominated by free-living clades, and communities were highly differentiated across environments. Seasonal differences in protist composition were observed; however, network analysis and functional profiling demonstrated that sewage communities were robust and functionally consistent. Protists typically associated with human and animal guts or feces were frequently detected. Abundance of these parasites varied significantly both spatially and temporally, suggesting that spikes could reflect trends in the source population. This underscores sewage as a valuable model system for monitoring patterns in urban microbes and provides a baseline protist metagenome of NYC.}, } @article {pmid31288415, year = {2019}, author = {Wagatsuma, K and Yamada, S and Ao, M and Matsuura, M and Tsuji, H and Iida, T and Miyamoto, K and Oka, K and Takahashi, M and Tanaka, K and Nakase, H}, title = {Diversity of Gut Microbiota Affecting Serum Level of Undercarboxylated Osteocalcin in Patients with Crohn's Disease.}, journal = {Nutrients}, volume = {11}, number = {7}, pages = {}, pmid = {31288415}, issn = {2072-6643}, support = {Investigation and Research for intractable Inflammatory Bowel Disease//Ministry of Health, Labour and Welfare/ ; Grants-in-Aid for Scientific Research (KAKENHI) Grant Number 18H02799//Japan Society for the Promotion of Science/ ; }, mesh = {Adult ; *Crohn Disease/blood/complications/epidemiology/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Middle Aged ; Osteocalcin/*blood ; Vitamin K/blood ; Vitamin K Deficiency/blood/complications/epidemiology/microbiology ; Young Adult ; }, abstract = {Several reports have indicated a possible link between decreasing plasma levels of vitamin K and bone mineral density. It has been suggested that intestinal bacteria contribute to maintenance of vitamin K. Several factors are involved in the reduction of vitamin K in patients with Crohn's disease (CD). We aimed to assess the relationship between gut microbiota and alternative indicators of vitamin K deficiency in patients with CD. We collected the feces of 26 patients with clinically inactive CD. We extracted 16S rRNA from the intestinal bacteria in the feces and amplified it by polymerase chain reaction. The generated polymerase chain reaction product was analyzed using a 16S metagenomic approach by Illumina Miseq platform. Serum undercarboxylated osteocalcin concentration was used as an alternative indicator of vitamin K deficiency. There was a significant negative correlation between serum undercarboxylated osteocalcin and mean Chao1 index in cases of low activity. The diversity of the gut microbiota was significantly lower, and Ruminococcaceae and Lachnospiraceae were significantly decreased in the vitamin K-deficient group in comparison to the vitamin K-normal group. Taken together, these data suggested the significance of investigating the gut microbiota even in patients with clinically inactive CD for improving patients' vitamin K status.}, } @article {pmid31285347, year = {2019}, author = {Johnston, ER and Hatt, JK and He, Z and Wu, L and Guo, X and Luo, Y and Schuur, EAG and Tiedje, JM and Zhou, J and Konstantinidis, KT}, title = {Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {30}, pages = {15096-15105}, pmid = {31285347}, issn = {1091-6490}, mesh = {Alaska ; Arctic Regions ; Carbon/*chemistry/metabolism ; Carbon Cycle ; Carbon Dioxide/*chemistry/metabolism ; Climate Change/statistics & numerical data ; Microbiota/*genetics ; *Models, Statistical ; Permafrost/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Temperature ; *Tundra ; }, abstract = {Northern-latitude tundra soils harbor substantial carbon (C) stocks that are highly susceptible to microbial degradation with rising global temperatures. Understanding the magnitude and direction (e.g., C release or sequestration) of the microbial responses to warming is necessary to accurately model climate change. In this study, Alaskan tundra soils were subjected to experimental in situ warming by ∼1.1 °C above ambient temperature, and the microbial communities were evaluated using metagenomics after 4.5 years, at 2 depths: 15 to 25 cm (active layer at outset of the experiment) and 45 to 55 cm (transition zone at the permafrost/active layer boundary at the outset of the experiment). In contrast to small or insignificant shifts after 1.5 years of warming, 4.5 years of warming resulted in significant changes to the abundances of functional traits and the corresponding taxa relative to control plots (no warming), and microbial shifts differed qualitatively between the two soil depths. At 15 to 25 cm, increased abundances of carbohydrate utilization genes were observed that correlated with (increased) measured ecosystem carbon respiration. At the 45- to 55-cm layer, increased methanogenesis potential was observed, which corresponded with a 3-fold increase in abundance of a single archaeal clade of the Methanosarcinales order, increased annual thaw duration (45.3 vs. 79.3 days), and increased CH4 emissions. Collectively, these data demonstrate that the microbial responses to warming in tundra soil are rapid and markedly different between the 2 critical soil layers evaluated, and identify potential biomarkers for the corresponding microbial processes that could be important in modeling.}, } @article {pmid31285337, year = {2019}, author = {Greenlon, A and Chang, PL and Damtew, ZM and Muleta, A and Carrasquilla-Garcia, N and Kim, D and Nguyen, HP and Suryawanshi, V and Krieg, CP and Yadav, SK and Patel, JS and Mukherjee, A and Udupa, S and Benjelloun, I and Thami-Alami, I and Yasin, M and Patil, B and Singh, S and Sarma, BK and von Wettberg, EJB and Kahraman, A and Bukun, B and Assefa, F and Tesfaye, K and Fikre, A and Cook, DR}, title = {Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {30}, pages = {15200-15209}, pmid = {31285337}, issn = {1091-6490}, mesh = {Biological Evolution ; Cicer/*microbiology ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Mesorhizobium/classification/*genetics ; Metagenomics/methods ; Microbial Consortia/*genetics ; Nitrogen Fixation/physiology ; Phylogeny ; Phylogeography ; Soil/classification ; Soil Microbiology ; Symbiosis/genetics ; }, abstract = {Although microorganisms are known to dominate Earth's biospheres and drive biogeochemical cycling, little is known about the geographic distributions of microbial populations or the environmental factors that pattern those distributions. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea, generating 1,027 draft whole-genome sequences at the level of bacterial populations, including 14 high-quality PacBio genomes from a phylogenetically representative subset. We find that diverse Mesorhizobium taxa perform symbiosis with chickpea and have largely overlapping global distributions. However, sampled locations cluster based on the phylogenetic diversity of Mesorhizobium populations, and diversity clusters correspond to edaphic and environmental factors, primarily soil type and latitude. Despite long-standing evolutionary divergence and geographic isolation, the diverse taxa observed to nodulate chickpea share a set of integrative conjugative elements (ICEs) that encode the major functions of the symbiosis. This symbiosis ICE takes 2 forms in the bacterial chromosome-tripartite and monopartite-with tripartite ICEs confined to a broadly distributed superspecies clade. The pairwise evolutionary relatedness of these elements is controlled as much by geographic distance as by the evolutionary relatedness of the background genome. In contrast, diversity in the broader gene content of Mesorhizobium genomes follows a tight linear relationship with core genome phylogenetic distance, with little detectable effect of geography. These results illustrate how geography and demography can operate differentially on the evolution of bacterial genomes and offer useful insights for the development of improved technologies for sustainable agriculture.}, } @article {pmid31284329, year = {2019}, author = {Aw, W and Fukuda, S}, title = {Protective effects of bifidobacteria against enteropathogens.}, journal = {Microbial biotechnology}, volume = {12}, number = {6}, pages = {1097-1100}, pmid = {31284329}, issn = {1751-7915}, mesh = {Acetates/*metabolism ; Animals ; Anti-Bacterial Agents/*metabolism ; *Antibiosis ; Bifidobacterium/growth & development/*metabolism ; Disease Models, Animal ; Escherichia coli Infections/*prevention & control ; Escherichia coli O157/drug effects/*growth & development ; Gastrointestinal Microbiome ; Metabolome ; Mice ; }, abstract = {Recent major advances in metagenomics and metabolomics technologies have enabled us to collect more data on the gut microbiome and metabolome to evaluate its influence on host health. In this short opinion article, we have chosen to focus on summarizing the protective mechanisms of bifidobacteria, a highly regarded probiotic, and it's metabolite: acetate; against enteropathogens, specifically in the E. coli O157:H7 mice model. We advocate for using a novel approach metabologenomics, which is an integration of metagenomic and metabolomic information on a systems biology-wide approach to better understand this interplay between gut microbiome and host metabolism.}, } @article {pmid31284194, year = {2019}, author = {Li, Y and Gao, Y and Zhang, W and Wang, C and Wang, P and Niu, L and Wu, H}, title = {Homogeneous selection dominates the microbial community assembly in the sediment of the Three Gorges Reservoir.}, journal = {The Science of the total environment}, volume = {690}, number = {}, pages = {50-60}, doi = {10.1016/j.scitotenv.2019.07.014}, pmid = {31284194}, issn = {1879-1026}, mesh = {Biodiversity ; China ; Environmental Monitoring ; Geologic Sediments/*microbiology ; *Microbiota ; *Water Microbiology ; }, abstract = {Deep-water reservoir sediment is a unique habitat sheltering indispensable microorganisms and facilitating their biogeochemical functions; however, the assembly processes of the microbial community therein remain elusive. This study focuses on the assembly processes in the Three Gorges Reservoir Area (TGRA). A total of 42 sediment samples were collected from the TGRA, both in the mainstream and the tributaries, and in different seasons. Metagenomic analyses of 16S rRNA using Exact Sequence Variants revealed the spatiotemporal distribution patterns of the microbial communities. Linear regressions between dissimilarity of microbial communities, geographic and environmental distance showed that environmental, rather than geographic factors, impacted the microbial community. However, the environmental differences explained little variations (14.14%) in community structure, implying the homogeneity of environmental conditions across the TGRA. From the quantification of ecological processes, homogeneous selection was shown to be a dominating factor (51.34%) in the assembly of the microbial communities. The co-occurrence network showed that keystone species were more important than prevalent abundant species in interspecies interactions. Overall, the assembly of microbial community in the deep-water reservoir sediment is mediated by both deterministic and stochastic processes, and homogeneous selection plays a leading role.}, } @article {pmid31281924, year = {2019}, author = {Liang, R and Davidova, I and Hirano, SI and Duncan, KE and Suflita, JM}, title = {Community succession in an anaerobic long-chain paraffin-degrading consortium and impact on chemical and electrical microbially influenced iron corrosion.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {8}, pages = {}, doi = {10.1093/femsec/fiz111}, pmid = {31281924}, issn = {1574-6941}, mesh = {Anaerobiosis/physiology ; Corrosion ; Deltaproteobacteria/*metabolism ; Desulfovibrio/*metabolism ; Iron/*metabolism ; Microbial Consortia/physiology ; Oxidation-Reduction ; Paraffin/*metabolism ; Steel/*chemistry ; Sulfates/metabolism ; }, abstract = {Community compositional changes and the corrosion of carbon steel in the presence of different electron donor and acceptor combinations were examined with a methanogenic consortium enriched for its ability to mineralize paraffins. Despite cultivation in the absence of sulfate, metagenomic analysis revealed the persistence of several sulfate-reducing bacterial taxa. Upon sulfate amendment, the consortium was able to couple C28H58 biodegradation with sulfate reduction. Comparative analysis suggested that Desulforhabdus and/or Desulfovibrio likely supplanted methanogens as syntrophic partners needed for C28H58 mineralization. Further enrichment in the absence of a paraffin revealed that the consortium could also utilize carbon steel as a source of electrons. The severity of both general and localized corrosion increased in the presence of sulfate, regardless of the electron donor utilized. With carbon steel as an electron donor, Desulfobulbus dominated in the consortium and electrons from iron accounted for ∼92% of that required for sulfate reduction. An isolated Desulfovibrio spp. was able to extract electrons from iron and accelerate corrosion. Thus, hydrogenotrophic partner microorganisms required for syntrophic paraffin metabolism can be readily substituted depending on the availability of an external electron acceptor and a single paraffin-degrading consortium harbored microbes capable of both chemical and electrical microbially influenced iron corrosion.}, } @article {pmid31280331, year = {2020}, author = {Chen, H and Li, C and Liu, T and Chen, S and Xiao, H}, title = {A Metagenomic Study of Intestinal Microbial Diversity in Relation to Feeding Habits of Surface and Cave-Dwelling Sinocyclocheilus Species.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {299-311}, pmid = {31280331}, issn = {1432-184X}, support = {31560111//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacteria/genetics/isolation & purification ; *Bacterial Physiological Phenomena ; Caves ; Cyprinidae/*microbiology/*physiology ; *Ecosystem ; *Feeding Behavior ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Species Specificity ; }, abstract = {Light is completely absent in cave habitats, causing a shortage or lack of autochthonous photosynthesis. Thus, understanding the mechanisms underlying the ability of organisms to adapt to the unique cave habitat is of great interest. We used high-throughput sequencing of the 16S ribosomal RNA gene of intestinal microorganisms from 11 Sinocyclocheilus (Cypriniformes: Cyprinidae) species, to explore the characteristics of intestinal microorganisms and the adaptive mechanisms of Sinocyclocheilus cavefish and surface fish. We found that the α-diversity and richness of the intestinal microbiome were much higher in cavefish than in surface fish. Principal coordinate analysis showed that cavefish and surface fish formed three clusters because of different dominant gut microorganisms which are generated by different habitats. Based on PICRUSt-predicted functions, harmful substance degradation pathways were much more common in cavefish intestinal microorganisms than in those from surface fish. The intestinal microbiota of surface fish group 1 had a higher capacity for carbohydrate metabolism, whereas protein and amino acid metabolism and digestive pathways were more abundant in microorganisms from the cavefish group and surface fish group 2. Combined analysis of the intestinal microbial composition and functional predictions further revealed the structures and functions of intestinal microbial communities in Sinocyclocheilus cave and surface species. Moreover, based on their habits and intestinal microbial composition and intestinal microbial functional predictions, we inferred that the three fish groups were all omnivorous; however, surface fish group 1 preferred feeding on plants, while surface fish group 2 and cavefish preferred meat. This study improves our understanding of mechanisms of adaptation in cave habitats and may contribute to the protection of these habitats from water pollution.}, } @article {pmid31279340, year = {2019}, author = {Velsko, IM and Fellows Yates, JA and Aron, F and Hagan, RW and Frantz, LAF and Loe, L and Martinez, JBR and Chaves, E and Gosden, C and Larson, G and Warinner, C}, title = {Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {102}, pmid = {31279340}, issn = {2049-2618}, mesh = {Bacteria/*classification ; *Bacterial Physiological Phenomena ; Bacterial Proteins/genetics ; Biofilms/*growth & development ; Bone and Bones/microbiology ; DNA, Ancient/analysis ; DNA, Bacterial/genetics ; Dental Calculus/history/*microbiology ; Dental Plaque/*microbiology ; Female ; History, Ancient ; Humans ; Male ; Metagenomics ; Microbiota/*physiology ; Periodontal Diseases/microbiology ; Proteomics ; Tooth/*microbiology ; }, abstract = {BACKGROUND: Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm. However, plaque and calculus reflect different conditions of the oral biofilm, and the differences in microbial characteristics between the sample types have not yet been systematically explored. Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates.

RESULTS: Metagenomic data was generated from modern and historic calculus samples, and dental plaque metagenomic data was downloaded from the Human Microbiome Project. Microbial composition and functional profile were assessed. Metaproteomic data was obtained from a subset of historic calculus samples. Comparisons between microbial, protein, and metabolomic profiles revealed distinct taxonomic and metabolic functional profiles between plaque, modern calculus, and historic calculus, but not between calculus collected from healthy teeth and periodontal disease-affected teeth. Species co-exclusion was related to biofilm environment. Proteomic profiling revealed that healthy tooth samples contain low levels of bacterial virulence proteins and a robust innate immune response. Correlations between proteomic and metabolomic profiles suggest co-preservation of bacterial lipid membranes and membrane-associated proteins.

CONCLUSIONS: Overall, we find that there are systematic microbial differences between plaque and calculus related to biofilm physiology, and recognizing these differences is important for accurate data interpretation in studies comparing dental plaque and calculus.}, } @article {pmid31279007, year = {2019}, author = {Cait, A and Cardenas, E and Dimitriu, PA and Amenyogbe, N and Dai, D and Cait, J and Sbihi, H and Stiemsma, L and Subbarao, P and Mandhane, PJ and Becker, AB and Moraes, TJ and Sears, MR and Lefebvre, DL and Azad, MB and Kollmann, T and Turvey, SE and Mohn, WW}, title = {Reduced genetic potential for butyrate fermentation in the gut microbiome of infants who develop allergic sensitization.}, journal = {The Journal of allergy and clinical immunology}, volume = {144}, number = {6}, pages = {1638-1647.e3}, doi = {10.1016/j.jaci.2019.06.029}, pmid = {31279007}, issn = {1097-6825}, support = {148781/CAPMC/CIHR/Canada ; }, mesh = {*Bacteria/classification/genetics/immunology/metabolism ; *Butyric Acid/immunology/metabolism ; Carbohydrate Metabolism/genetics/immunology ; Child, Preschool ; *Dysbiosis/genetics/immunology/metabolism/microbiology ; Female ; *Gastrointestinal Microbiome/genetics/immunology ; Humans ; *Hypersensitivity/genetics/immunology/microbiology/prevention & control ; Infant ; Longitudinal Studies ; Male ; Metagenome ; Prospective Studies ; }, abstract = {BACKGROUND: Allergic disease is the most frequent chronic health issue in children and has been linked to early-life gut microbiome dysbiosis. Many lines of evidence suggest that microbially derived short-chain fatty acids, and particularly butyrate, can promote immune tolerance.

OBJECTIVE: We sought to determine whether bacterial butyrate production in the gut during early infancy is protective against the development of atopic disease in children.

METHODS: We used shotgun metagenomic analysis to determine whether dysbiosis in butyrate fermentation could be identified in human infants, before their developing allergic disease.

RESULTS: We found that the microbiome of infants who went on to develop allergic sensitization later in childhood lacked genes encoding key enzymes for carbohydrate breakdown and butyrate production.

CONCLUSIONS: Our findings support the importance of microbial carbohydrate metabolism during early infancy in protecting against the development of allergies.}, } @article {pmid31278679, year = {2019}, author = {Mitra, S}, title = {Multiple Data Analyses and Statistical Approaches for Analyzing Data from Metagenomic Studies and Clinical Trials.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1910}, number = {}, pages = {605-634}, doi = {10.1007/978-1-4939-9074-0_20}, pmid = {31278679}, issn = {1940-6029}, mesh = {Algorithms ; Biodiversity ; *Computational Biology/methods ; Data Interpretation, Statistical ; *Data Mining/methods ; Evolution, Molecular ; Fatty Acids, Omega-3/pharmacology ; Gastrointestinal Microbiome/drug effects ; Humans ; *Metagenome ; *Metagenomics/methods ; Microbiota ; Molecular Sequence Annotation ; Plaque, Atherosclerotic/etiology ; Workflow ; }, abstract = {Metagenomics, also known as environmental genomics, is the study of the genomic content of a sample of organisms (microbes) obtained from a common habitat. Metagenomics and other "omics" disciplines have captured the attention of researchers for several decades. The effect of microbes in our body is a relevant concern for health studies. There are plenty of studies using metagenomics which examine microorganisms that inhabit niches in the human body, sometimes causing disease, and are often correlated with multiple treatment conditions. No matter from which environment it comes, the analyses are often aimed at determining either the presence or absence of specific species of interest in a given metagenome or comparing the biological diversity and the functional activity of a wider range of microorganisms within their communities. The importance increases for comparison within different environments such as multiple patients with different conditions, multiple drugs, and multiple time points of same treatment or same patient. Thus, no matter how many hypotheses we have, we need a good understanding of genomics, bioinformatics, and statistics to work together to analyze and interpret these datasets in a meaningful way. This chapter provides an overview of different data analyses and statistical approaches (with example scenarios) to analyze metagenomics samples from different medical projects or clinical trials.}, } @article {pmid31278668, year = {2019}, author = {Watson, AK and Lannes, R and Pathmanathan, JS and Méheust, R and Karkar, S and Colson, P and Corel, E and Lopez, P and Bapteste, E}, title = {The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1910}, number = {}, pages = {271-308}, doi = {10.1007/978-1-4939-9074-0_9}, pmid = {31278668}, issn = {1940-6029}, mesh = {Biodiversity ; Biological Evolution ; Computational Biology/methods ; Ecosystem ; Evolution, Molecular ; Gene Ontology ; Gene Regulatory Networks ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; Microbiota ; Molecular Sequence Annotation ; Multigene Family ; }, abstract = {In the post genomic era, large and complex molecular datasets from genome and metagenome sequencing projects expand the limits of what is possible for bioinformatic analyses. Network-based methods are increasingly used to complement phylogenetic analysis in studies in molecular evolution, including comparative genomics, classification, and ecological studies. Using network methods, the vertical and horizontal relationships between all genes or genomes, whether they are from cellular chromosomes or mobile genetic elements, can be explored in a single expandable graph. In recent years, development of new methods for the construction and analysis of networks has helped to broaden the availability of these approaches from programmers to a diversity of users. This chapter introduces the different kinds of networks based on sequence similarity that are already available to tackle a wide range of biological questions, including sequence similarity networks, gene-sharing networks and bipartite graphs, and a guide for their construction and analyses.}, } @article {pmid31278309, year = {2019}, author = {Le Roy, CI and Bowyer, RCE and Castillo-Fernandez, JE and Pallister, T and Menni, C and Steves, CJ and Berry, SE and Spector, TD and Bell, JT}, title = {Dissecting the role of the gut microbiota and diet on visceral fat mass accumulation.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9758}, pmid = {31278309}, issn = {2045-2322}, support = {MR/N01183X/1/MRC_/Medical Research Council/United Kingdom ; SP/14/8/31352/BHF_/British Heart Foundation/United Kingdom ; MR/N030125/1/MRC_/Medical Research Council/United Kingdom ; MR/M016560/1/MRC_/Medical Research Council/United Kingdom ; BB/S020845/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/International ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Aged ; Body Mass Index ; *Diet ; Female ; *Gastrointestinal Microbiome ; Humans ; Intra-Abdominal Fat/*anatomy & histology ; Male ; Metagenomics ; Middle Aged ; Nutrients ; Organ Size ; }, abstract = {Both gut microbiota and diet have been shown to impact visceral fat mass (VFM), a major risk factor for cardiometabolic disease, but their relative contribution has not been well characterised. We aimed to estimate and separate the effect of gut microbiota composition from that of nutrient intake on VFM in 1760 older female twins. Through pairwise association analyses, we identified 93 operational taxonomic units (OTUs) and 10 nutrients independently linked to VFM (FDR < 5%). Conditional analyses revealed that the majority (87%) of the 93 VFM-associated OTUs remained significantly associated with VFM irrespective of nutrient intake correction. In contrast, we observed that the effect of fibre, magnesium, biotin and vitamin E on VFM was partially mediated by OTUs. Moreover, we estimated that OTUs were more accurate predictors of VFM than nutrients and accounted for a larger percentage of its variance. Our results suggest that while the role of certain nutrients on VFM appears to depend on gut microbiota composition, specific gut microbes may affect host adiposity regardless of dietary intake. The findings imply that the gut microbiota may have a greater contribution towards shaping host VFM than diet alone. Thus, microbial-based therapy should be prioritised for VFM reduction in overweight and obese subjects.}, } @article {pmid31278253, year = {2019}, author = {Visnovska, T and Biggs, PJ and Schmeier, S and Frizelle, FA and Purcell, RV}, title = {Metagenomics and transcriptomics data from human colorectal cancer.}, journal = {Scientific data}, volume = {6}, number = {1}, pages = {116}, pmid = {31278253}, issn = {2052-4463}, mesh = {Aged ; Aged, 80 and over ; Bacteria/classification ; Colorectal Neoplasms/*genetics/*microbiology ; DNA Barcoding, Taxonomic ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; *Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; RNA-Seq ; *Transcriptome ; }, abstract = {Colorectal cancer is a heterogenous and mostly sporadic disease, the development of which is associated with microbial dysbiosis. Recent advances in subtype classification have successfully stratified the disease using molecular profiling. To understand potential relationships between molecular mechanisms differentiating the subtypes of colorectal cancer and composition of gut microbial community, we classified a set of 34 tumour samples into molecular subtypes using RNA-sequencing gene expression profiles and determined relative abundances of bacterial taxonomic groups. To identify bacterial community composition, 16S rRNA amplicon metabarcoding was used as well as whole genome metagenomics of the non-human part of RNA-sequencing data. The generated data expands the collection of the data sources related to the disease and connects molecular aspects of the cancer with environmental impact of microbial community.}, } @article {pmid31275319, year = {2019}, author = {Trachsel, J and Briggs, C and Gabler, NK and Allen, HK and Loving, CL}, title = {Dietary Resistant Potato Starch Alters Intestinal Microbial Communities and Their Metabolites, and Markers of Immune Regulation and Barrier Function in Swine.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {1381}, pmid = {31275319}, issn = {1664-3224}, mesh = {Animals ; *Biomarkers ; Computational Biology/methods ; *Diet ; *Gastrointestinal Microbiome/immunology ; Immunoglobulin A/immunology ; Immunohistochemistry ; *Immunomodulation ; Immunophenotyping ; Intestinal Mucosa/immunology/metabolism/microbiology ; *Metabolome ; Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Models, Biological ; Phenotype ; *Solanum tuberosum/chemistry ; *Starch/chemistry ; Swine ; }, abstract = {Interactions between diet, the microbiota, and the host set the ecological conditions in the gut and have broad implications for health. Prebiotics are dietary compounds that may shift conditions toward health by promoting the growth of beneficial microbes that produce metabolites capable of modulating host cells. This study's objective was to assess how a dietary prebiotic could impact host tissues via modulation of the intestinal microbiota. Pigs fed a diet amended with 5% resistant potato starch (RPS) exhibited alterations associated with gut health relative to swine fed an unamended control diet (CON). RPS intake increased abundances of anaerobic Clostridia in feces and several tissues, as well as intestinal concentrations of butyrate. Functional gene amplicons suggested bacteria similar to Anaerostipes hadrus were stimulated by RPS intake. The CON treatment exhibited increased abundances of several genera of Proteobacteria (which utilize respiratory metabolisms) in several intestinal locations. RPS intake increased the abundance of regulatory T cells in the cecum, but not periphery, and cecal immune status alterations were indicative of enhanced mucosal defenses. A network analysis of host and microbial changes in the cecum revealed that regulatory T cells positively correlated with butyrate concentration, luminal IgA concentration, expression of IL-6 and DEF1B, and several mucosa-associated bacterial taxa. Thus, the administration of RPS modulated the microbiota and host immune status, altering markers of cecal barrier function and immunological tolerance, and suggesting a reduced niche for bacterial respiration.}, } @article {pmid31273779, year = {2019}, author = {Zhao, H and Chen, J and Li, X and Sun, Q and Qin, P and Wang, Q}, title = {Compositional and functional features of the female premenopausal and postmenopausal gut microbiota.}, journal = {FEBS letters}, volume = {593}, number = {18}, pages = {2655-2664}, doi = {10.1002/1873-3468.13527}, pmid = {31273779}, issn = {1873-3468}, support = {JCYJ20160229172757249//Science, Technology and Innovation Commission of Shenzhen Municipality/International ; JCYJ20170817145523036//Science, Technology and Innovation Commission of Shenzhen Municipality/International ; }, mesh = {Female ; *Gastrointestinal Microbiome ; Humans ; Middle Aged ; Phenotype ; *Postmenopause ; *Premenopause ; Quality of Life ; }, abstract = {Endogenous estrogen deficiency accelerates many diseases in postmenopausal women, and gut microbes contribute to estrogen level modulation. However, the compositional alterations and influences of the gut microbiota in postmenopausal women remain uncertain. A metagenome-wide association study was performed to compare the gut microbiota of 24 premenopausal and 24 postmenopausal women. Firmicutes and Roseburia spp. are depleted, while Bacteroidetes and the toluene-producing genus Tolumonas are overrepresented in fecal samples from postmenopausal women. The pentose phosphate pathway is enriched in premenopausal women. Homocysteine synthesis-related processes are enriched in postmenopausal women. The gut microbiomes of premenopausal and postmenopausal women differ and produce different metabolites. The gut microbiome may be a therapeutic target to reduce risks and improve the quality of life in postmenopausal women.}, } @article {pmid31273774, year = {2019}, author = {Kirby, TO and Brown, M and Ochoa-Repáraz, J and Roullet, JB and Gibson, KM}, title = {Microbiota Manipulation as a Metagenomic Therapeutic Approach for Rare Inherited Metabolic Disorders.}, journal = {Clinical pharmacology and therapeutics}, volume = {106}, number = {3}, pages = {505-507}, pmid = {31273774}, issn = {1532-6535}, support = {R01 EY027476/EY/NEI NIH HHS/United States ; }, mesh = {4-Aminobutyrate Transaminase/deficiency ; Amino Acid Metabolism, Inborn Errors/physiopathology/therapy ; Animals ; Developmental Disabilities/physiopathology/therapy ; Fecal Microbiota Transplantation/methods ; Gastrointestinal Microbiome/*physiology ; Humans ; Metabolism, Inborn Errors/*physiopathology/therapy ; Mice ; Prebiotics/administration & dosage ; Probiotics/administration & dosage ; RNA, Ribosomal, 16S/metabolism ; Rare Diseases/*physiopathology/therapy ; Severity of Illness Index ; Succinate-Semialdehyde Dehydrogenase/deficiency ; }, } @article {pmid31273405, year = {2020}, author = {Kerfahi, D and Ogwu, MC and Ariunzaya, D and Balt, A and Davaasuren, D and Enkhmandal, O and Purevsuren, T and Batbaatar, A and Tibbett, M and Undrakhbold, S and Boldgiv, B and Adams, JM}, title = {Metal-Tolerant Fungal Communities Are Delineated by High Zinc, Lead, and Copper Concentrations in Metalliferous Gobi Desert Soils.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {420-431}, pmid = {31273405}, issn = {1432-184X}, support = {NRF 2013-031400//National Research Foundation/ ; }, mesh = {Copper/analysis ; Desert Climate ; Fungi/classification/isolation & purification ; Lead/analysis ; Mongolia ; Mycobiome/*drug effects ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants/*analysis ; Zinc/analysis ; }, abstract = {The soil fungal ecology of the southern Gobi region of Mongolia has been little studied. We utilized the ITS1 region from soil DNA to study possible influences soil metal concentrations on soil fungal community variation. In the sample network, a distinctive fungal community was closely associated with high zinc (Zn), lead (Pb), and copper (Cu) concentrations. The pattern of occurrence suggests that high metal concentrations are natural and not a product of mining activities. The metal-associated fungal community differs little from the "normal" community in its major OTUs, and in terms of major fungal guilds and taxa, and its distinctiveness depends on a combination of many less common OTUs. The fungal community in the sites with high metal concentrations is no less diverse than that in areas with normal background levels. Overall, these findings raise interesting questions of the evolutionary origin and functional characteristics of this apparently "metal-tolerant" community, and of the associated soil biota in general. It is possible that rehabilitation of metal-contaminated mined soils from spoil heaps could benefit from the incorporation of fungi derived from these areas.}, } @article {pmid31273300, year = {2019}, author = {Uritskiy, G and Getsin, S and Munn, A and Gomez-Silva, B and Davila, A and Glass, B and Taylor, J and DiRuggiero, J}, title = {Halophilic microbial community compositional shift after a rare rainfall in the Atacama Desert.}, journal = {The ISME journal}, volume = {13}, number = {11}, pages = {2737-2749}, pmid = {31273300}, issn = {1751-7370}, support = {T32 GM007231/GM/NIGMS NIH HHS/United States ; U41 HG006620/HG/NHGRI NIH HHS/United States ; }, mesh = {Adaptation, Biological ; Desert Climate ; Extremophiles/growth & development/metabolism ; Longitudinal Studies ; *Microbiota ; Rain ; *Soil Microbiology ; South America ; }, abstract = {Understanding the mechanisms underlying microbial resistance and resilience to perturbations is essential to predict the impact of climate change on Earth's ecosystems. However, the resilience and adaptation mechanisms of microbial communities to natural perturbations remain relatively unexplored, particularly in extreme environments. The response of an extremophile community inhabiting halite (salt rocks) in the Atacama Desert to a catastrophic rainfall provided the opportunity to characterize and de-convolute the temporal response of a highly specialized community to a major disturbance. With shotgun metagenomic sequencing, we investigated the halite microbiome taxonomic composition and functional potential over a 4-year longitudinal study, uncovering the dynamics of the initial response and of the recovery of the community after a rainfall event. The observed changes can be recapitulated by two general modes of community shifts-a rapid Type 1 shift and a more gradual Type 2 adjustment. In the initial response, the community entered an unstable intermediate state after stochastic niche re-colonization, resulting in broad predicted protein adaptations to increased water availability. In contrast, during recovery, the community returned to its former functional potential by a gradual shift in abundances of the newly acquired taxa. The general characterization and proposed quantitation of these two modes of community response could potentially be applied to other ecosystems, providing a theoretical framework for prediction of taxonomic and functional flux following environmental changes.}, } @article {pmid31272480, year = {2019}, author = {Molinero, N and Ruiz, L and Milani, C and Gutiérrez-Díaz, I and Sánchez, B and Mangifesta, M and Segura, J and Cambero, I and Campelo, AB and García-Bernardo, CM and Cabrera, A and Rodríguez, JI and González, S and Rodríguez, JM and Ventura, M and Delgado, S and Margolles, A}, title = {The human gallbladder microbiome is related to the physiological state and the biliary metabolic profile.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {100}, pmid = {31272480}, issn = {2049-2618}, mesh = {Adult ; Aged ; Bacteria/classification ; Bile/*metabolism/*microbiology ; Female ; Gallbladder/*microbiology/*physiology ; Humans ; Lithiasis/microbiology ; Male ; Metabolomics ; Metagenome ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; }, abstract = {BACKGROUND: The microbial populations of the human intestinal tract and their relationship to specific diseases have been extensively studied during the last decade. However, the characterization of the human bile microbiota as a whole has been hampered by difficulties in accessing biological samples and the lack of adequate methodologies to assess molecular studies. Although a few reports have described the biliary microbiota in some hepatobiliary diseases, the bile microbiota of healthy individuals has not been described. With this in mind, the goal of the present study was to generate fundamental knowledge on the composition and activity of the human bile microbiota, as well as establishing its potential relationship with human bile-related disorders.

RESULTS: Human bile samples from the gallbladder of individuals from a control group, without any record of hepatobiliary disorder, were obtained from liver donors during liver transplantation surgery. A bile DNA extraction method was optimized together with a quantitative PCR (qPCR) assay for determining the bacterial load. This allows the selection of samples to perform functional metagenomic analysis. Bile samples from the gallbladder of individuals suffering from lithiasis were collected during gallbladder resection and the microbial profiles assessed, using a 16S rRNA gene-based sequencing analysis, and compared with those of the control group. Additionally, the metabolic profile of the samples was analyzed by nuclear magnetic resonance (NMR). We detected, for the first time, bacterial communities in gallbladder samples of individuals without any hepatobiliary pathology. In the biliary microecosystem, the main bacterial phyla were represented by Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Significant differences in the relative abundance of different taxa of both groups were found. Sequences belonging to the family Propionibacteriaceae were more abundant in bile samples from control subjects; meanwhile, in patients with cholelithiasis members of the families Bacteroidaceae, Prevotellaceae, Porphyromonadaceae, and Veillonellaceae were more frequently detected. Furthermore, the metabolomics analysis showed that the two study groups have different metabolic profiles.

CONCLUSIONS: Our results indicate that the gallbladder of human individuals, without diagnosed hepatobiliary pathology, harbors a microbial ecosystem that is described for the first time in this study. Its bacterial representatives and metabolites are different from those detected in people suffering from cholelithiasis. In this regard, since liver donors have been subjected to the specific conditions of the hospital's intensive care unit, including an antibiotic treatment, we must be cautious in stating that their bile samples contain a physiologically normal biliary microbiome. In any case, our results open up new possibilities to discover bacterial functions in a microbial ecosystem that has not previously been explored.}, } @article {pmid31271681, year = {2020}, author = {Wang, J and Qian, T and Jiang, J and Yang, Y and Shen, Z and Huang, Y and Chen, G and Zheng, S and Dong, R}, title = {Gut microbial profile in biliary atresia: a case-control study.}, journal = {Journal of gastroenterology and hepatology}, volume = {35}, number = {2}, pages = {334-342}, doi = {10.1111/jgh.14777}, pmid = {31271681}, issn = {1440-1746}, support = {EK112520180301//Children's National Medical Center/ ; EKYY20180204//Children's National Medical Center/ ; EK1125180104//Children's National Medical Center/ ; 14411969800//Natural Science Foundation of Shanghai/ ; 16411952200//Natural Science Foundation of Shanghai/ ; 17411960600//Natural Science Foundation of Shanghai/ ; 18411969100//Natural Science Foundation of Shanghai/ ; 19ZR1406600//Natural Science Foundation of Shanghai/ ; 2017YQ042//The Science Foundation of Shanghai Excellent Youth Scholars/ ; SHDC12018X22//Shanghai Hospital Development Center/ ; 2017ZZ02022//Shanghai Key Disciplines/ ; }, mesh = {Biliary Atresia/complications/diagnosis/*microbiology ; Case-Control Studies ; Dysbiosis/etiology ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {BACKGROUND AND AIM: Biliary atresia (BA) is a progressive fibro-inflammatory cholangiopathy with an unclear etiology. Various liver disorders are associated with an altered microbiome. However, gut microbiome in BA remains unknown. Here, we performed a case-control study to investigate the gut microbiota in BA.

METHODS: A cross-sectional analysis was first conducted for 34 BA patients and 34 healthy controls. Then we investigated the shift in gut microbiota 2 weeks after the Kasai procedure in 16 BA patients. Gut microbiome was initially analyzed using 16S ribosome RNA gene sequencing and further validated by metagenomic sequencing. Fecal bile acids were determined using ultra-high performance liquid chromatography.

RESULTS: Compared with healthy controls, BA showed lower diversity and significant structural segregation in the microbiome. At phylum level, Proteobacteria numbers increased, whereas those of Bacteroidetes decreased in BA. At genus level, several potential pathogens such as Streptococcus and Klebsiella thrived in BA, while numbers for Bifidobacterium and several butyrate-producing bacteria declined. The microbiome was also disturbed after the Kasai procedure. Operational taxonomic units responding to BA showed significant correlation with liver function. Furthermore, the abundance ratio of Streptococcus/Bacteroides showed great promise in distinguishing BA from healthy controls. Intestinal bile acids were dramatically decreased in BA, and Clostridium XIVa positively correlated with the ratio of primary/secondary bile acids.

CONCLUSIONS: Gut microbial dysbiosis, may be caused by decreased bile acids, was associated with liver function and had a good diagnostic potential for BA. Therefore, further exploration of gut microbiota may provide important insights into their potential diagnostic and therapeutic benefits.}, } @article {pmid31271530, year = {2019}, author = {Huang, Q and Lopez, D and Evans, JD}, title = {Shared and unique microbes between Small hive beetles (Aethina tumida) and their honey bee hosts.}, journal = {MicrobiologyOpen}, volume = {8}, number = {10}, pages = {e899}, pmid = {31271530}, issn = {2045-8827}, mesh = {Animals ; Bacteria/classification/genetics ; Bees/*microbiology/*parasitology ; Coleoptera/growth & development/*microbiology ; Insect Vectors/growth & development/*microbiology/*virology ; Metagenomics ; *Microbiota ; RNA Viruses/genetics ; }, abstract = {The small hive beetle (SHB) is an opportunistic parasite that feeds on bee larvae, honey, and pollen. While SHBs can also feed on fruit and other plant products, like its plant-feeding relatives, SHBs prefer to feed on hive resources and only reproduce inside bee colonies. As parasites, SHBs are inevitably exposed to bee-associated microbes, either directly from the bees or from the hive environment. These microbes have unknown impacts on beetles, nor is it known how extensively beetles transfer microbes among their bee hosts. To identify sets of beetle microbes and the transmission of microbes from bees to beetles, a metagenomic analysis was performed. We identified sets of herbivore-associated bacteria, as well as typical bee symbiotic bacteria for pollen digestion, in SHB larvae and adults. Deformed wing virus was highly abundant in beetles, which colonize SHBs as suggested by a controlled feeding trial. Our data suggest SHBs are vectors for pathogen transmission among bees and between colonies. The dispersal of host pathogens by social parasites via floral resources and the hive environment increases the threats of these parasites to honey bees.}, } @article {pmid31271529, year = {2019}, author = {Klemetsen, T and Willassen, NP and Karlsen, CR}, title = {Full-length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis.}, journal = {MicrobiologyOpen}, volume = {8}, number = {10}, pages = {e898}, pmid = {31271529}, issn = {2045-8827}, mesh = {Animals ; Bacteria/*classification/*genetics ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Intestines/microbiology ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Salmo salar/*microbiology ; Sequence Analysis, DNA ; Skin/microbiology ; }, abstract = {Understanding fish-microbial relationships may be of great value for fish producers as fish growth, development and welfare are influenced by the microbial community associated with the rearing systems and fish surfaces. Accurate methods to generate and analyze these microbial communities would be an important tool to help improve understanding of microbial effects in the industry. In this study, we performed taxonomic classification and determination of operational taxonomic units on Atlantic salmon microbiota by taking advantage of full-length 16S rRNA gene sequences. Skin mucus was dominated by the genera Flavobacterium and Psychrobacter. Intestinal samples were dominated by the genera Carnobacterium, Aeromonas, Mycoplasma and by sequences assigned to the order Clostridiales. Applying Sanger sequencing on the full-length bacterial 16S rRNA gene from the pool of 46 isolates obtained in this study showed a clear assignment of the PacBio full-length bacterial 16S rRNA gene sequences down to the genus level. One of the bottlenecks in comparing microbial profiles is that different studies use different 16S rRNA gene regions. Comparisons of sequence assignments between full-length and in silico derived variable 16S rRNA gene regions showed different microbial profiles with variable effects between phylogenetic groups and taxonomic ranks.}, } @article {pmid31271261, year = {2019}, author = {Martoni, CJ and Evans, M and Chow, CT and Chan, LS and Leyer, G}, title = {Impact of a probiotic product on bowel habits and microbial profile in participants with functional constipation: A randomized controlled trial.}, journal = {Journal of digestive diseases}, volume = {20}, number = {9}, pages = {435-446}, pmid = {31271261}, issn = {1751-2980}, mesh = {Adolescent ; Adult ; Aged ; Bacterial Typing Techniques ; Constipation/microbiology/physiopathology/*therapy ; Defecation/physiology ; Double-Blind Method ; Energy Intake/physiology ; Exercise/physiology ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Metagenome/physiology ; Middle Aged ; Probiotics/adverse effects/*therapeutic use ; Prospective Studies ; Psychometrics ; Quality of Life ; Treatment Outcome ; Young Adult ; }, abstract = {OBJECTIVE: To investigate the clinical efficacy of a multi-strain probiotic product on bowel habits and microbial profile in participants with functional constipation.

METHODS: This was a randomized, double-blind, placebo-controlled and parallel-arm study. Altogether 94 otherwise healthy adults aged 18 to 65 years with symptoms of functional constipation were randomized as part of the intention-to-treat population. The participants received a placebo or the probiotic product (1.5 × 10[10] CFU/day), consisting of Lactobacillus acidophilus DDS-1, Bifidobacterium animalis subsp. lactis UABla-12, Bifidobacterium longum UABl-14 and Bifidobacterium bifidum UABb-10 over 4 weeks. Outcomes included the patient assessment of constipation-symptom (PAC-SYM) questionnaire, stool frequency and consistency, and microbial profile.

RESULTS: There were no significant between-group differences in the PAC-SYM score, despite significant within-group differences (P < 0.001) over the study period. The probiotic group showed a faster normalization of stool frequency and consistency, with most participants achieving a normalized profile after 1 week. Fecal samples of the probiotic group exhibited higher relative abundance of Ruminococcaceae (P = 0.0047), including the Ruminococcus genus, and lower relative abundance of Erysipelotrichaceae (P = 0.0172) at end-point compared with baseline. Placebo group samples showed similar abundance profiles over the study, with the exception of Clostridiaceae, which was lower at the study end-point (P = 0.0033). Among treated participants, all four probiotic strains were significantly more abundant after the intervention.

CONCLUSIONS: No significant differences were observed in symptomology, with both groups showing a more than 20% improvement. However, the probiotic helped modulate bowel function earlier than the placebo, with a corresponding shift to a more fibrolytic microbiota.}, } @article {pmid31269412, year = {2019}, author = {Zhang, F and Yang, R}, title = {Life history and functional capacity of the microbiome are altered in beta-cypermethrin-resistant cockroaches.}, journal = {International journal for parasitology}, volume = {49}, number = {9}, pages = {715-723}, doi = {10.1016/j.ijpara.2019.04.006}, pmid = {31269412}, issn = {1879-0135}, mesh = {Animals ; Bacteria/classification/genetics ; Blattellidae/*drug effects/genetics/growth & development/microbiology ; Computational Biology ; DNA, Bacterial/chemistry/isolation & purification ; Female ; Genotype ; Insecticide Resistance/genetics ; Insecticides/*pharmacology ; Male ; Metagenome/genetics ; Microbiota/drug effects/*physiology ; Nymph/growth & development ; Pyrethrins/*pharmacology ; RNA, Ribosomal, 16S/chemistry ; }, abstract = {Cockroaches are widely perceived to evolve resistance to insecticides. Over-expression of a resistance-conferring gene can be costly and may require energy and resource reallocation for metabolic and developmental processes. To evaluate whether changes in the composition of gut microbiota in Blattella germanica affected its resistance evolution to beta-cypermethrin and to determine the role of gut microbiota in host growth and development, we studied the relationship between insecticide resistance and the diversity and genetic content of gut microbiota in cockroaches. Results suggest beta-cypermethrin-resistant cockroaches (R strain) exhibited a delayed development period and reduced adult longevity compared with susceptible cockroaches (S strain). Based on 16S rRNA gene sequencing and community metagenomics, we found that the relative abundance of Lactobacillus and Acetobacteraceae were significantly lower in the R strain compared with the S strain in the foregut and midgut of both strains. Functional annotation of Kyoto Encyclopedia of Genes and Genomes (KEGG) modules of midgut genes in the two strains revealed that 10.6% were involved in metabolism, while the relative abundance in the R strain was 7.4%. Unigenes were also translated into amino acid sequences and assigned to protein families based on hits to the Carbohydrate-Active enzymes (CAZy) database. This process identified the glycoside hydrolases, glycosyl transferases and carbohydrate-binding modules of the S strain as all being significantly higher in diversity than those in the R strain. Overall, we conclude that fitness-related costs increased in the resistant strain of cockroaches compared with the susceptible strain, and the variation in insect gut microbiota, especially those related to growth and development, was an important influencing factor.}, } @article {pmid31267680, year = {2019}, author = {Taubert, M and Grob, C and Crombie, A and Howat, AM and Burns, OJ and Weber, M and Lott, C and Kaster, AK and Vollmers, J and Jehmlich, N and von Bergen, M and Chen, Y and Murrell, JC}, title = {Communal metabolism by Methylococcaceae and Methylophilaceae is driving rapid aerobic methane oxidation in sediments of a shallow seep near Elba, Italy.}, journal = {Environmental microbiology}, volume = {21}, number = {10}, pages = {3780-3795}, doi = {10.1111/1462-2920.14728}, pmid = {31267680}, issn = {1462-2920}, support = {GBMF3303//Gordon and Betty Moore Foundation/International ; ECF2016-626//Leverhulme Trust/International ; }, mesh = {Geologic Sediments/*microbiology ; Italy ; Metagenomics ; Methane/*metabolism ; Methylococcaceae/*metabolism ; Methylophilaceae/*metabolism ; Microbiota/physiology ; Oxidation-Reduction ; Phylogeny ; }, abstract = {The release of abiotic methane from marine seeps into the atmosphere is a major source of this potent greenhouse gas. Methanotrophic microorganisms in methane seeps use methane as carbon and energy source, thus significantly mitigating global methane emissions. Here, we investigated microbial methane oxidation at the sediment-water interface of a shallow marine methane seep. Metagenomics and metaproteomics, combined with [13] C-methane stable isotope probing, demonstrated that various members of the gammaproteobacterial family Methylococcaceae were the key players for methane oxidation, catalysing the first reaction step to methanol. We observed a transfer of carbon to methanol-oxidizing methylotrophs of the betaproteobacterial family Methylophilaceae, suggesting an interaction between methanotrophic and methylotrophic microorganisms that allowed for rapid methane oxidation. From our microcosms, we estimated methane oxidation rates of up to 871 nmol of methane per gram sediment per day. This implies that more than 50% of methane at the seep is removed by microbial oxidation at the sediment-water interface, based on previously reported in situ methane fluxes. The organic carbon produced was further assimilated by different heterotrophic microbes, demonstrating that the methane-oxidizing community supported a complex trophic network. Our results provide valuable eco-physiological insights into this specialized microbial community performing an ecosystem function of global relevance.}, } @article {pmid31267543, year = {2020}, author = {Zhang, L and Li, YY and Tang, X and Zhao, X}, title = {Faecal microbial dysbiosis in children with Wiskott-Aldrich syndrome.}, journal = {Scandinavian journal of immunology}, volume = {91}, number = {1}, pages = {e12805}, doi = {10.1111/sji.12805}, pmid = {31267543}, issn = {1365-3083}, mesh = {Animals ; Biodiversity ; Biomarkers ; Case-Control Studies ; Child, Preschool ; Disease Models, Animal ; *Dysbiosis ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Inflammatory Bowel Diseases/etiology ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Mice, Knockout ; Mutation ; RNA, Ribosomal, 16S/genetics ; Wiskott-Aldrich Syndrome/diagnosis/*etiology ; Wiskott-Aldrich Syndrome Protein/deficiency ; }, abstract = {Wiskott-Aldrich syndrome (WAS) is an X-linked primary immunodeficiency disease caused by a mutation in the WAS gene that encodes the WAS protein (WASp); up to 5-10% of these patients develop inflammatory bowel disease (IBD). The mechanisms by which WASp deficiency causes IBD are unclear. Intestinal microbial dysbiosis and imbalances in host immune responses play important roles in the pathogenesis of polygenetic IBD; however, few studies have conducted detailed examination of the microbial alterations and their relationship with IBD in WAS. Here, we collected faecal samples from 19 children (all less than 2 years old) with WAS and samples from WASp-KO mice with IBD and subjected them to 16S ribosomal RNA sequencing. We found that microbial community richness and structure in WAS children were different from those in controls; WAS children revealed reduced microbial community richness and diversity. Relative abundance of Bacteroidetes and Verrucomicrobiain in WAS children was significantly lower, while that of Proteobacteria was markedly higher. WASp-KO mice revealed a significantly decreased abundance of Firmicutes. Faecal microbial dysbiosis caused by WASp deficiency is similar to that observed for polygenetic IBD, suggesting that WASp may play crucial function in microbial homoeostasis and that microbial dysbiosis may contribute to IBD in WAS. These microbial alterations may be useful targets for monitoring and therapeutically managing intestinal inflammation in WAS.}, } @article {pmid31266971, year = {2019}, author = {Fernández-Correa, I and Truchado, DA and Gomez-Lucia, E and Doménech, A and Pérez-Tris, J and Schmidt-Chanasit, J and Cadar, D and Benítez, L}, title = {A novel group of avian astroviruses from Neotropical passerine birds broaden the diversity and host range of Astroviridae.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9513}, pmid = {31266971}, issn = {2045-2322}, mesh = {Amino Acid Sequence ; Animals ; Astroviridae/classification/*genetics/physiology ; Astroviridae Infections/epidemiology/pathology/virology ; Cloaca/virology ; French Guiana/epidemiology ; Genome, Viral ; *Host Specificity ; Mamastrovirus/genetics ; Open Reading Frames/genetics ; Passeriformes/*virology ; Phylogeny ; Prevalence ; Sequence Alignment ; Viral Proteins/chemistry/classification/metabolism ; }, abstract = {Metagenomics is helping to expand the known diversity of viruses, especially of those with poorly studied hosts in remote areas. The Neotropical region harbors a considerable diversity of avian species that may play a role as both host and short-distance vectors of unknown viruses. Viral metagenomics of cloacal swabs from 50 Neotropical birds collected in French Guiana revealed the presence of four complete astrovirus genomes. They constitute an early diverging novel monophyletic clade within the Avastrovirus phylogeny, representing a putative new astrovirus species (provisionally designated as Avastrovirus 5) according to the International Committee on Taxonomy of Viruses (ICTV) classification criteria. Their genomic organization shares some characteristics with Avastrovirus but also with Mamastrovirus. The pan-astrovirus RT-PCR analysis of the cloacal samples of 406 wild Neotropical birds showed a community-level prevalence of 4.9% (5.1% in passerines, the highest described so far in this order of birds). By screening birds of a remote region, we expanded the known host range of astroviruses to the avian families Cardinalidae, Conopophagidae, Furnariidae, Thamnophilidae, Turdidae and Tyrannidae. Our results provide important first insights into the unexplored viral communities, the ecology, epidemiology and features of host-pathogen interactions that shape the evolution of avastroviruses in a remote Neotropical rainforest.}, } @article {pmid31266879, year = {2019}, author = {Sze, MA and Topçuoğlu, BD and Lesniak, NA and Ruffin, MT and Schloss, PD}, title = {Fecal Short-Chain Fatty Acids Are Not Predictive of Colonic Tumor Status and Cannot Be Predicted Based on Bacterial Community Structure.}, journal = {mBio}, volume = {10}, number = {4}, pages = {}, pmid = {31266879}, issn = {2150-7511}, support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; R01 CA215574/CA/NCI NIH HHS/United States ; UL1 TR002240/TR/NCATS NIH HHS/United States ; }, mesh = {Adenoma/*diagnosis/pathology ; Bacteria/classification/genetics ; Carcinoma/*diagnosis/pathology ; Clinical Decision Rules ; Colonic Neoplasms/*diagnosis/pathology ; Fatty Acids, Volatile/*analysis ; Feces/*chemistry/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; United States ; }, abstract = {Colonic bacterial populations are thought to have a role in the development of colorectal cancer with some protecting against inflammation and others exacerbating inflammation. Short-chain fatty acids (SCFAs) have been shown to have anti-inflammatory properties and are produced in large quantities by colonic bacteria that produce SCFAs by fermenting fiber. We assessed whether there was an association between fecal SCFA concentrations and the presence of colonic adenomas or carcinomas in a cohort of individuals using 16S rRNA gene and metagenomic shotgun sequence data. We measured the fecal concentrations of acetate, propionate, and butyrate within the cohort and found that there were no significant associations between SCFA concentration and tumor status. When we incorporated these concentrations into random forest classification models trained to differentiate between people with healthy colons and those with adenomas or carcinomas, we found that they did not significantly improve the ability of 16S rRNA gene or metagenomic gene sequence-based models to classify individuals. Finally, we generated random forest regression models trained to predict the concentration of each SCFA based on 16S rRNA gene or metagenomic gene sequence data from the same samples. These models performed poorly and were able to explain at most 14% of the observed variation in the SCFA concentrations. These results support the broader epidemiological data that questions the value of fiber consumption for reducing the risks of colorectal cancer. Although other bacterial metabolites may serve as biomarkers to detect adenomas or carcinomas, fecal SCFA concentrations have limited predictive power.IMPORTANCE Considering that colorectal cancer is the third leading cancer-related cause of death within the United States, it is important to detect colorectal tumors early and to prevent the formation of tumors. Short-chain fatty acids (SCFAs) are often used as a surrogate for measuring gut health and for being anticarcinogenic because of their anti-inflammatory properties. We evaluated the fecal SCFA concentrations of a cohort of individuals with different colonic tumor burdens who were previously analyzed to identify microbiome-based biomarkers of tumors. We were unable to find an association between SCFA concentration and tumor burden or use SCFAs to improve our microbiome-based models of classifying people based on their tumor status. Furthermore, we were unable to find an association between the fecal community structure and SCFA concentrations. Our results indicate that the association between fecal SCFAs, the gut microbiome, and tumor burden is weak.}, } @article {pmid31265324, year = {2019}, author = {Dao, MC and Belda, E and Prifti, E and Everard, A and Kayser, BD and Bouillot, JL and Chevallier, JM and Pons, N and Le Chatelier, E and Ehrlich, SD and Doré, J and Aron-Wisnewsky, J and Zucker, JD and Cani, PD and Clément, K}, title = {Akkermansia muciniphila abundance is lower in severe obesity, but its increased level after bariatric surgery is not associated with metabolic health improvement.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {317}, number = {3}, pages = {E446-E459}, doi = {10.1152/ajpendo.00140.2019}, pmid = {31265324}, issn = {1522-1555}, mesh = {Adult ; Akkermansia ; *Bariatric Surgery ; Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Glucose/metabolism ; Glucose Tolerance Test ; Health Status ; Homeostasis ; Humans ; Insulin Resistance ; Longitudinal Studies ; Middle Aged ; Obesity, Morbid/metabolism/*microbiology/*surgery ; Prospective Studies ; Treatment Outcome ; *Verrucomicrobia ; Young Adult ; }, abstract = {The gut bacterial species Akkermansia muciniphila is associated with a healthier clinical profile. The purpose of this study was to determine the association between A. muciniphila and glucose homeostasis in patients undergoing bariatric surgery (BS): gastric banding (GB) or Roux-en-Y gastric bypass (RYGB). This nonrandomized prospective study included 65 women with severe obesity. Longitudinal analysis included subjects for whom A. muciniphila data were available at follow-up [1, 3, and 12 mo; GB (n = 10) or RYGB (n = 11)]. Glucose homeostasis markers were measured under fasting conditions (glucose, insulin, and HbA1c) or during an oral glucose tolerance test. Fecal microbiota was analyzed using shotgun metagenomics, and A. muciniphila relative abundance was assessed with 16S rRNA quantitative PCR. A. muciniphila relative abundance was significantly lower in severe obesity [mean body mass index, 45.7 kg/m[2] (SD 5.4)] than in moderate obesity [33.2 kg/m[2] (SD 3.8)] but not associated with glucose homeostasis markers. A significant increase in A. muciniphila relative abundance after RYGB was not correlated with metabolic improvement. Baseline A. muciniphila abundance was correlated with bacterial gene richness and was highest in the high-richness Ruminococcaceae enterotype. A. muciniphila increased in relative abundance after BS in patients with low baseline A. muciniphila abundance, especially those with a Bacteroides type 2 enterotype classification. Although decreased in severe obesity, relative abundance of A. muciniphila was not associated with glucose homeostasis before or after BS. A certain level of A. muciniphila abundance might be required to observe a beneficial link to health. The severity of obesity and gut dysbiosis may partly explain the discrepancy with previous findings in less obese populations.}, } @article {pmid31264806, year = {2019}, author = {Pereira, O and Hochart, C and Auguet, JC and Debroas, D and Galand, PE}, title = {Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean.}, journal = {MicrobiologyOpen}, volume = {8}, number = {9}, pages = {e00852}, pmid = {31264806}, issn = {2045-8827}, mesh = {Aquatic Organisms/*classification/*genetics ; Euryarchaeota/*classification/*genetics ; Metabolic Networks and Pathways/genetics ; Metagenomics ; *Microbiota ; *Oceans and Seas ; Phylogeny ; Rhodopsins, Microbial/genetics ; Seawater/*microbiology ; }, abstract = {Planktonic Archaea have been detected in all the world's oceans and are found from surface waters to the deep sea. The two most common Archaea phyla are Thaumarchaeota and Euryarchaeota. Euryarchaeota are generally more common in surface waters, but very little is known about their ecology and their potential metabolisms. In this study, we explore the genomic ecology of the Marine Group II (MGII), the main marine planktonic Euryarchaeota, and test if it is composed of different ecologically relevant units. We re-analyzed Tara Oceans metagenomes from the photic layer and the deep ocean by annotating sequences against a custom MGII database and by mapping gene co-occurrences. Our data provide a global view of the distribution of Euryarchaeota, and more specifically of MGII subgroups, and reveal their association to a number of gene-coding sequences. In particular, we show that MGII proteorhodopsins were detected in both the surface and the deep chlorophyll maximum layer and that different clusters of these light harvesting proteins were present. Our approach helped describing the set of genes found together with specific MGII subgroups. We could thus define genomic environments that could theoretically describe ecologically meaningful units and the ecological niche that they occupy.}, } @article {pmid31263569, year = {2019}, author = {Tan, SM and Yung, PYM and Hutchinson, PE and Xie, C and Teo, GH and Ismail, MH and Drautz-Moses, DI and Little, PFR and Williams, RBH and Cohen, Y}, title = {Primer-free FISH probes from metagenomics/metatranscriptomics data permit the study of uncharacterised taxa in complex microbial communities.}, journal = {NPJ biofilms and microbiomes}, volume = {5}, number = {1}, pages = {17}, pmid = {31263569}, issn = {2055-5008}, mesh = {Bacteria/*classification/*genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; In Situ Hybridization, Fluorescence/*methods ; Metagenomics/*methods ; *Microbiota ; Optical Imaging/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; }, abstract = {Methods for the study of member species in complex microbial communities remain a high priority, particularly for rare and/or novel member species that might play an important ecological role. Specifically, methods that link genomic information of member species with its spatial structure are lacking. This study adopts an integrative workflow that permits the characterisation of previously unclassified bacterial taxa from microbiomes through: (1) imaging of the spatial structure; (2) taxonomic classification and (3) genome recovery. Our study attempts to bridge the gaps between metagenomics/metatranscriptomics and high-resolution biomass imaging methods by developing new fluorescence in situ hybridisation (FISH) probes-termed as R-Probes-from shotgun reads that harbour hypervariable regions of the 16S rRNA gene. The sample-centric design of R-Probes means that probes can directly hybridise to OTUs as detected in shotgun sequencing surveys. The primer-free probe design captures larger microbial diversity as compared to canonical probes. R-Probes were designed from deep-sequenced RNA-Seq datasets for both FISH imaging and FISH-Fluorescence activated cell sorting (FISH-FACS). FISH-FACS was used for target enrichment of previously unclassified bacterial taxa prior to downstream multiple displacement amplification (MDA), genomic sequencing and genome recovery. After validation of the workflow on an axenic isolate of Thauera species, the techniques were applied to investigate two previously uncharacterised taxa from a tropical full-scale activated sludge community. In some instances, probe design on the hypervariable region allowed differentiation to the species level. Collectively, the workflow can be readily applied to microbiomes for which shotgun nucleic acid survey data is available.}, } @article {pmid31261372, year = {2020}, author = {Hagbø, M and Ravi, A and Angell, IL and Sunde, M and Ludvigsen, J and Diep, DB and Foley, SL and Vento, M and Collado, MC and Perez-Martinez, G and Rudi, K}, title = {Experimental support for multidrug resistance transfer potential in the preterm infant gut microbiota.}, journal = {Pediatric research}, volume = {88}, number = {1}, pages = {57-65}, pmid = {31261372}, issn = {1530-0447}, mesh = {Animals ; Anti-Bacterial Agents ; Bacteriophages ; Chickens ; Contig Mapping ; DNA Transposable Elements ; DNA, Bacterial/analysis ; Enterococcus/genetics ; Escherichia coli/genetics ; *Gastrointestinal Microbiome ; *Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Humans ; Infant, Newborn ; Infant, Premature ; *Multigene Family ; Plasmids/genetics ; Prevalence ; Prospective Studies ; Sequence Analysis, DNA ; Staphylococcus epidermidis/genetics ; Twins ; }, abstract = {BACKGROUND: There is currently a lack of experimental evidence for horizontal gene transfer (HGT) mechanisms in the human gut microbiota. The aim of this study was therefore to experimentally determine the HGT potential in the microbiota of a healthy preterm infant twin pair and to evaluate the global occurrence of the mobilized elements.

METHODS: Stool samples were collected. Both shotgun metagenome sequencing and bacterial culturing were done for the same samples. A range of experimental conditions were used to test DNA transfer for the cultured isolates. Searches for global distribution of transferable elements were done for the ~120,000 metagenomic samples in the Sequence Read Archive (SRA) database.

RESULTS: DNA transfer experiments demonstrated frequent transmission of an ESBL encoding IncI1 plasmid, a high copy number ColEI plasmid, and bacteriophage P1. Both IncI1 and ColE1 were abundant in the stool samples. In vitro competition experiments showed that transconjugants containing IncI1 plasmids outcompeted the recipient strain in the absence of antibiotic selection. The SRA searches indicated a global distribution of the mobilizable elements, with chicken identified as a possible reservoir for the IncI1 ESBL encoding plasmid.

CONCLUSION: Our results experimentally support a major horizontal transmission and persistence potential of the preterm infant gut microbiota mobilome involving genes encoding ESBL.}, } @article {pmid31261078, year = {2019}, author = {Valentine, G and Prince, A and Aagaard, KM}, title = {The Neonatal Microbiome and Metagenomics: What Do We Know and What Is the Future?.}, journal = {NeoReviews}, volume = {20}, number = {5}, pages = {e258-e271}, doi = {10.1542/neo.20-5-e258}, pmid = {31261078}, issn = {1526-9906}, mesh = {Female ; Forecasting ; Humans ; Infant Health/*trends ; Infant, Newborn ; Metagenome/*physiology ; Metagenomics/methods/*trends ; Microbiota/*physiology ; Pregnancy ; }, abstract = {The human microbiota includes the trillions of microorganisms living in the human body whereas the human microbiome includes the genes and gene products of this microbiota. Bacteria were historically largely considered to be pathogens that inevitably led to human disease. However, because of advances in both cultivation-based methods and the advent of metagenomics, bacteria are now recognized to be largely beneficial commensal organisms and thus, key to normal and healthy human development. This relatively new area of medical research has elucidated insights into diseases such as inflammatory bowel disease and obesity, as well as metabolic and atopic disorders. However, much remains unknown about the complexity of microbe-microbe and microbe-host interactions. Future efforts aimed at answering key questions pertaining to the early establishment of the microbiome, alongside what defines its dysbiosis, will likely lead to long-term health and mitigation of disease. Here, we review the relevant literature pertaining to modulations in the perinatal and neonatal microbiome, the impact of environmental and maternal factors in shaping the neonatal microbiome, and future questions and directions in the exciting emerging arena of metagenomic medicine.}, } @article {pmid31255903, year = {2019}, author = {Beller, L and Matthijnssens, J}, title = {What is (not) known about the dynamics of the human gut virome in health and disease.}, journal = {Current opinion in virology}, volume = {37}, number = {}, pages = {52-57}, doi = {10.1016/j.coviro.2019.05.013}, pmid = {31255903}, issn = {1879-6265}, mesh = {Adult ; Anti-Bacterial Agents/adverse effects ; Autoimmune Diseases/virology ; Bacteria/virology ; Bacteriophages/*immunology ; DNA, Viral ; Diet ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/pathology/*virology ; *Host Microbial Interactions ; Humans ; Infant ; Inflammatory Bowel Diseases/virology ; Intestinal Diseases ; Male ; Microbial Interactions ; Natural Childbirth ; Symbiosis ; Viruses/pathogenicity ; }, abstract = {The human gut virome has an important role in human health but its dynamics remain poorly understood. Few longitudinal studies in healthy adults showed a stable temporal gut virome, with high inter-individual diversity. In contrast, the infant virome shows a high temporal intra-individual diversity. Unfortunately, these virome studies ignore an enormous amount of unknown 'dark matter' sequences, leading to incomplete analyses and possibly incorrect conclusions. Also, the interactions between prokaryotes and bacteriophages in the gut seem to be too complex for currently available models. Therefore, there is a huge need of larger longitudinal cohort studies focusing on both the bacterial and viral component of the microbiome to be able to describe and understand this complex ecosystem.}, } @article {pmid31255682, year = {2020}, author = {Xu, R and Wu, B and Liang, J and He, F and Gu, W and Li, K and Luo, Y and Chen, J and Gao, Y and Wu, Z and Wang, Y and Zhou, W and Wang, M}, title = {Altered gut microbiota and mucosal immunity in patients with schizophrenia.}, journal = {Brain, behavior, and immunity}, volume = {85}, number = {}, pages = {120-127}, doi = {10.1016/j.bbi.2019.06.039}, pmid = {31255682}, issn = {1090-2139}, mesh = {Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Immunity, Mucosal ; RNA, Ribosomal, 16S/genetics ; *Schizophrenia ; }, abstract = {Evidence shows that gut microbiota may play important roles in schizophrenia pathogenesis via the "gut-brain" axis, but the mechanisms remain unclear. Here, eighty-four patients with schizophrenia and 84 sex- and age-matched healthy controls were enrolled. Shotgun metagenomic sequencing and 16S rRNA sequencing were performed, and the gut microbiota-associated epitopes (MEs) were predicted, which, together with IgA content, were used to determine the gut microbiota composition associated with gut immune status. Patients with schizophrenia had significantly reduced gut microbiota richnesses compared with those of the healthy controls, and the gut microbiota compositions clearly distinguished the patients with schizophrenia from the healthy controls. Based on two-stage metagenomic-wide association studies, nineteen gut microbiota taxonomies were associated with schizophrenia, and the microbial dysbiosis (MD) index was calculated based on the abundance of differential taxonomies. We found that MD index was positively correlated with MEs diversity and gut IgA levels, and negatively correlated with gut microbiota richness. Glutamate synthase (GOGAT) was more active in the guts of patients with schizophrenia than in those of healthy controls, and high GOGAT activity was associated with altered gut microbiota taxonomies associated with gut IgA levels. Our results may imply a role of the microbiome in the etiology of schizophrenia and contribute to the development of microbiome targeted interventions for schizophrenia.}, } @article {pmid31255652, year = {2019}, author = {Schwimmer, JB and Johnson, JS and Angeles, JE and Behling, C and Belt, PH and Borecki, I and Bross, C and Durelle, J and Goyal, NP and Hamilton, G and Holtz, ML and Lavine, JE and Mitreva, M and Newton, KP and Pan, A and Simpson, PM and Sirlin, CB and Sodergren, E and Tyagi, R and Yates, KP and Weinstock, GM and Salzman, NH}, title = {Microbiome Signatures Associated With Steatohepatitis and Moderate to Severe Fibrosis in Children With Nonalcoholic Fatty Liver Disease.}, journal = {Gastroenterology}, volume = {157}, number = {4}, pages = {1109-1122}, pmid = {31255652}, issn = {1528-0012}, support = {UL1 TR001442/TR/NCATS NIH HHS/United States ; UL1 TR000100/TR/NCATS NIH HHS/United States ; R01 DK088831/DK/NIDDK NIH HHS/United States ; U01 DK061713/DK/NIDDK NIH HHS/United States ; U01 DK061730/DK/NIDDK NIH HHS/United States ; U24 DK061730/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Bacteria/classification/*genetics/pathogenicity ; Case-Control Studies ; Child ; Cross-Sectional Studies ; DNA, Bacterial/*genetics ; Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Humans ; Intestines/*microbiology ; Liver Cirrhosis/diagnosis/etiology/*microbiology ; Male ; Metagenome ; Non-alcoholic Fatty Liver Disease/complications/diagnosis/*microbiology ; Prospective Studies ; RNA, Ribosomal, 16S/*genetics ; Ribotyping ; Severity of Illness Index ; }, abstract = {BACKGROUND & AIMS: The intestinal microbiome might affect the development and severity of nonalcoholic fatty liver disease (NAFLD). We analyzed microbiomes of children with and without NAFLD.

METHODS: We performed a prospective, observational, cross-sectional study of 87 children (age range, 8-17 years) with biopsy-proven NAFLD and 37 children with obesity without NAFLD (controls). Fecal samples were collected and microbiome composition and functions were assessed using 16S ribosomal RNA amplicon sequencing and metagenomic shotgun sequencing. Microbial taxa were identified using zero-inflated negative binomial modeling. Genes contributing to bacterial pathways were identified using gene set enrichment analysis.

RESULTS: Fecal microbiomes of children with NAFLD had lower α-diversity than those of control children (3.32 vs 3.52, P = .016). Fecal microbiomes from children with nonalcoholic steatohepatitis (NASH) had the lowest α-diversity (control, 3.52; NAFLD, 3.36; borderline NASH, 3.37; NASH, 2.97; P = .001). High abundance of Prevotella copri was associated with more severe fibrosis (P = .036). Genes for lipopolysaccharide biosynthesis were enriched in microbiomes from children with NASH (P < .001). Classification and regression tree model with level of alanine aminotransferase and relative abundance of the lipopolysaccharide pathway gene encoding 3-deoxy-d-manno-octulosonate 8-phosphate-phosphatase identified patients with NASH with an area under the receiver operating characteristic curve value of 0.92. Genes involved in flagellar assembly were enriched in the fecal microbiomes of patients with moderate to severe fibrosis (P < .001). Classification and regression tree models based on level of alanine aminotransferase and abundance of genes encoding flagellar biosynthesis protein had good accuracy for identifying case children with moderate to severe fibrosis (area under the receiver operating characteristic curve, 0.87).

CONCLUSIONS: In an analysis of fecal microbiomes of children with NAFLD, we associated NAFLD and NASH with intestinal dysbiosis. NAFLD and its severity were associated with greater abundance of genes encoding inflammatory bacterial products. Alterations to the intestinal microbiome might contribute to the pathogenesis of NAFLD and be used as markers of disease or severity.}, } @article {pmid31253829, year = {2019}, author = {Alauzet, C and Cunat, L and Wack, M and Lozniewski, A and Busby, H and Agrinier, N and Cailliez-Grimal, C and Frippiat, JP}, title = {Hypergravity disrupts murine intestinal microbiota.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9410}, pmid = {31253829}, issn = {2045-2322}, mesh = {Animals ; Bacteria/classification/genetics ; Biodiversity ; *Gastrointestinal Microbiome ; *Hypergravity ; Metagenomics ; Mice ; Phylogeny ; Space Flight ; }, abstract = {During spaceflight, organisms are subjected to various physical stressors including modification of gravity (G) that, associated with lifestyle, could lead to impaired immunity, intestinal dysbiosis and thus potentially predispose astronauts to illness. Whether space travel affects microbiota homeostasis has not been thoroughly investigated. The aim of this study was to evaluate changes in intestinal microbiota and mucosa in a ground-based murine model consisting in a 21-days confinement of mice in a centrifuge running at 2 or 3G. Results revealed an increased α-diversity and a significant change in intracaecal β-diversity observed only at 3G, with profiles characterized by a decrease of the Firmicutes/Bacteroidetes ratio. Compared to 1G microbiota, 12.1% of the taxa were significantly impacted in 3G microbiota, most of them (78%) being enriched. This study shows a G-level-dependent disruption of intracaecal microbiota, without alteration of mucosal integrity. These first data reinforce those recently obtained with in-flight experimentations or microgravity models, and emphasize the critical need for further studies exploring the impact of spaceflight on intestinal microbiota in order to optimize long-term space travel conditions.}, } @article {pmid31253826, year = {2019}, author = {Gong, B and Cao, H and Peng, C and Perčulija, V and Tong, G and Fang, H and Wei, X and Ouyang, S}, title = {High-throughput sequencing and analysis of microbial communities in the mangrove swamps along the coast of Beibu Gulf in Guangxi, China.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9377}, pmid = {31253826}, issn = {2045-2322}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biodiversity ; China ; Computational Biology/methods ; Ecosystem ; *Environmental Microbiology ; Geography ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Wetlands ; }, abstract = {Mangrove swamp is one of the world's richest and most productive marine ecosystems. This ecosystem also has a great ecological importance, but is highly susceptible to anthropogenic disturbances. The balance of mangrove ecosystem depends largely on the microbial communities in mangrove sediments. Thus, understanding how the mangrove microbial communities respond to spatial differences is essential for more accurate assessment of mangrove ecosystem health. To this end, we performed the first medium-distance (150 km) research on the biogeographic distribution of mangrove microbial communities. The hypervariable regions of 16S rRNA gene was sequenced by Illumina to compare the microbial communities in mangrove sediments collected from six locations (i.e. Zhenzhu harbor, Yuzhouping, Maowei Sea, Qinzhou harbor, Beihai city and Shankou) along the coastline of Beibu Gulf in Guangxi province, China. Collectively, Proteobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, Parvarchaeota, Acidobacteria and Cyanobacteria were the predominant phyla in the mangrove sediments of this area. At genus level, the heat map of microbial communities reflected similarities between study sites and was in agreement with their biogeographic characteristics. Interestingly, the genera Desulfococcus, Arcobacter, Nitrosopumilus and Sulfurimonas showed differences in abundance between study sites. Furthermore, the principal component analysis (PCA) and unweighted UniFrac cluster tree of beta diversity were used to study the biogeographic diversity of the microbial communities. Relatively broader variation of microbial communities was found in Beihai city and Qinzhou harbour, suggesting that environmental condition and historical events may play an important role in shaping the bacterial communities as well. This is the first report on medium-distance range distribution of bacteria in the mangrove swamp ecosystem. Our data is valuable for monitoring and evaluation of the impact of human activity on mangrove habitats from the perspective of microbiome.}, } @article {pmid31252683, year = {2019}, author = {Lawrence, D and Baldridge, MT and Handley, SA}, title = {Phages and Human Health: More Than Idle Hitchhikers.}, journal = {Viruses}, volume = {11}, number = {7}, pages = {}, pmid = {31252683}, issn = {1999-4915}, support = {R01 OD024917/OD/NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Bacteriophages/classification/genetics/*isolation & purification/physiology ; Gastrointestinal Tract/*virology ; Genome, Viral ; Health ; Humans ; *Microbiota ; }, abstract = {Bacteriophages, or phages, are viruses that infect bacteria and archaea. Phages have diverse morphologies and can be coded in DNA or RNA and as single or double strands with a large range of genome sizes. With the increasing use of metagenomic sequencing approaches to analyze complex samples, many studies generate massive amounts of "viral dark matter", or sequences of viral origin unable to be classified either functionally or taxonomically. Metagenomic analysis of phages is still in its infancy, and uncovering novel phages continues to be a challenge. Work over the past two decades has begun to uncover key roles for phages in different environments, including the human gut. Recent studies in humans have identified expanded phage populations in both healthy infants and in inflammatory bowel disease patients, suggesting distinct phage activity during development and in specific disease states. In this review, we examine our current knowledge of phage biology and discuss recent efforts to improve the analysis and discovery of novel phages. We explore the roles phages may play in human health and disease and discuss the future of phage research.}, } @article {pmid31250991, year = {2019}, author = {Kandasamy, S and Liu, EYR and Patterson, G and Saldias, S and Ali, S and Lazarovits, G}, title = {Introducing key microbes from high productive soil transforms native soil microbial community of low productive soil.}, journal = {MicrobiologyOpen}, volume = {8}, number = {10}, pages = {e895}, pmid = {31250991}, issn = {2045-8827}, mesh = {Agriculture/*methods ; Bacteria/*classification/genetics/*growth & development ; Metagenomics ; *Microbiota ; Ontario ; *Soil Microbiology ; Triticum/*growth & development ; Zea mays/*growth & development ; }, abstract = {This study aimed to understand the changes in rhizosphere microbial structure and diversity of an average corn yielding field site soil with the introduced microbial candidates from a high-yielding site. Soils used in this study were from two growers' fields located in Dunnville, Ontario, Canada, where one of the farms has an exceptional high corn yield (G-site soil; ca 20 tons/acre) and the other yields an average crop (H-site soil; 12 tons/acre) (8 years of unpublished A & L data). In growth room experiments using wheat as the indicator crop, calcium alginate beads with microbes composed of Azospirillum lipoferum, Rhizobium leguminosarum, Burkholderia ambifaria, Burkholderia graminis, Burkholderia vietnamiensis, Pseudomonas lurida, Exiguobacterium acetylicum, Kosakonia cowanii, and Paenibacillus polymyxa was introduced into the soil at planting to the average-yielding soil. These bacteria had been isolated from the high-yielding farm soil. Among the nine microbial candidates tested, three (P. polymyxa, E. acetylicum and K. cowanii) significantly impacted the plant health and biometrics in addition to microbial richness and diversity, where the microbial profile became very similar to the high productive G-site soil. One hundred and forty-two bacterial terminal restriction fragments (TRFs) were involved in the community shift and 48 of them showed significant correlation to several interacting soil factors. This study indicates the potential of shifting microbial profiles of average-yielding soils by introducing key candidates from highly productive soils to increase biological soil health.}, } @article {pmid31250988, year = {2019}, author = {Wang, D and Li, Y and Zhong, H and Ding, Q and Lin, Y and Tang, S and Zong, Y and Wang, Q and Zhang, X and Yang, H and Wang, R and Liu, X}, title = {Alterations in the human gut microbiome associated with Helicobacter pylori infection.}, journal = {FEBS open bio}, volume = {9}, number = {9}, pages = {1552-1560}, pmid = {31250988}, issn = {2211-5463}, mesh = {Adult ; Aged ; China ; Female ; Gastrointestinal Microbiome/*genetics ; Helicobacter Infections/*genetics ; Helicobacter pylori/*genetics/isolation & purification ; Humans ; Male ; Middle Aged ; Phenotype ; Vitamin B 12/biosynthesis/blood ; Young Adult ; }, abstract = {Helicobacter pylori infection (HPI) is a prevalent infectious disease associated with gastric ulcer, gastric cancer, and many nongastrointestinal disorders. To identify genes that may serve as microbial markers for HPI, we performed shotgun metagenomic sequencing of fecal samples from 313 Chinese volunteers who had undergone a C14 breath test. Through comparing differences in intestinal microbial community structure between H. pylori-positive and H. pylori-negative individuals, we identified 58 HPI-associated microbial species (P < 0.05, Wilcoxon test). A classifier based on microbial species markers showed high diagnostic ability for HPI (AUC = 0.84). Furthermore, levels of gut microbial vitamin B12 (VB12) biosynthesis and plasma VB12 were significantly lower in H. pylori-positive individuals compared with H. pylori-negative individuals (P < 0.05, Wilcoxon test). This study reveals that certain alterations in gut microbial species and functions are associated with HPI and shows that gut microbial shift in HPI patients may indirectly elevate the risk of VB12 deficiency.}, } @article {pmid31250899, year = {2019}, author = {Aluthge, ND and Van Sambeek, DM and Carney-Hinkle, EE and Li, YS and Fernando, SC and Burkey, TE}, title = {BOARD INVITED REVIEW: The pig microbiota and the potential for harnessing the power of the microbiome to improve growth and health1.}, journal = {Journal of animal science}, volume = {97}, number = {9}, pages = {3741-3757}, pmid = {31250899}, issn = {1525-3163}, mesh = {Animals ; Diet/veterinary ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Metabolomics ; *Prebiotics ; *Probiotics ; Swine/growth & development/*microbiology/physiology ; *Synbiotics ; }, abstract = {A variety of microorganisms inhabit the gastrointestinal tract of animals including bacteria, archaea, fungi, protozoa, and viruses. Pioneers in gut microbiology have stressed the critical importance of diet:microbe interactions and how these interactions may contribute to health status. As scientists have overcome the limitations of culture-based microbiology, the importance of these interactions has become more clear even to the extent that the gut microbiota has emerged as an important immunologic and metabolic organ. Recent advances in metagenomics and metabolomics have helped scientists to demonstrate that interactions among the diet, the gut microbiota, and the host to have profound effects on animal health and disease. However, although scientists have now accumulated a great deal of data with respect to what organisms comprise the gastrointestinal landscape, there is a need to look more closely at causative effects of the microbiome. The objective of this review is intended to provide: 1) a review of what is currently known with respect to the dynamics of microbial colonization of the porcine gastrointestinal tract; 2) a review of the impact of nutrient:microbe effects on growth and health; 3) examples of the therapeutic potential of prebiotics, probiotics, and synbiotics; and 4) a discussion about what the future holds with respect to microbiome research opportunities and challenges. Taken together, by considering what is currently known in the four aforementioned areas, our overarching goal is to set the stage for narrowing the path towards discovering how the porcine gut microbiota (individually and collectively) may affect specific host phenotypes.}, } @article {pmid31250597, year = {2019}, author = {Wang, L and Li, Z and Liu, R and Li, L and Wang, W}, title = {Bacterial Diversity in Soybean Rhizosphere Soil at Seedling and Mature Stages.}, journal = {Polish journal of microbiology}, volume = {68}, number = {2}, pages = {281-284}, pmid = {31250597}, issn = {2544-4646}, mesh = {Bacteria/*classification/genetics/*isolation & purification ; *Biota ; Computational Biology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Rhizosphere ; Seedlings/growth & development/*microbiology ; *Soil Microbiology ; Glycine max/growth & development/*microbiology ; }, abstract = {Changes in the structural diversity of bacterial communities in soybean rhizospheres play important roles in plant growth and crop productivity. However, there are only a few studies on different soybean growth stages. Here, we investigated the changes in the bacterial community of soybean rhizosphere soil at two stages using Illumina high-throughput sequencing. The results showed that the bacterial abundance and diversity in the seeding stage were higher than those in the mature stage and that the diversity changed significantly. Actinobacteria, Acidobacteria, and Proteobacteria were the dominant bacteria in the soybean rhizosphere soil. Additionally, changes in Actinobacteria and Proteobacteria abundances showed opposite trends. Changes in the structural diversity of bacterial communities in soybean rhizospheres play important roles in plant growth and crop productivity. However, there are only a few studies on different soybean growth stages. Here, we investigated the changes in the bacterial community of soybean rhizosphere soil at two stages using Illumina high-throughput sequencing. The results showed that the bacterial abundance and diversity in the seeding stage were higher than those in the mature stage and that the diversity changed significantly. Actinobacteria, Acidobacteria, and Proteobacteria were the dominant bacteria in the soybean rhizosphere soil. Additionally, changes in Actinobacteria and Proteobacteria abundances showed opposite trends.}, } @article {pmid31250091, year = {2019}, author = {Llacsa, LX and Solis-Castro, RL and Mialhe, E and García-Seminario, R}, title = {Metagenomic Analysis of the Bacterial and Fungal Community Associated to the Rhizosphere of Tabebuia chrysantha and T. billbergii.}, journal = {Current microbiology}, volume = {76}, number = {9}, pages = {1073-1080}, pmid = {31250091}, issn = {1432-0991}, support = {Resolución Nº 0543-2014/UNT-R).//Canon Universidad Nacional de Tumbes/ ; }, mesh = {Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; Fungi/classification/genetics/*isolation & purification ; Metagenomics ; Phylogeny ; Rhizosphere ; *Soil Microbiology ; Tabebuia/*microbiology ; }, abstract = {The rhizosphere of plants contains a diversity of microorganisms, some of which play an important role in the growth and development of the host plant. In this work, the diversity of fungi and bacteria associated to the rhizosphere of Tabebuia chrysantha and T. billbergii plants was analyzed. The molecular identification was performed by sequencing the ITS and 16S rDNA for fungi and bacteria, respectively. The analysis of the rDNA sequences of the rhizosphere of T. billergii showed that for domain Eukaria, the most abundant phyla were Glomeromycota (56%) and Ascomycota (39%), and for domain Bacteria, the phylum Firmicutes (19.17%) was the most abundant followed by Actinobacteria (14.90%) and Proteobacteria (8.94%). In the rhizosphere of T. chrysantha the most abundant phylum of Eukaria was Ascomycota (98%), and for Bacteria the most representative phyla were Proteobacteria (18.61%) and Actinobacteria (11.93%). A diversity of genera and species of fungi and bacteria was observed, to be more significant in T. chrysantha than T. billbergii. The taxonomic assignment of metagenomic sequences revealed a homology associated with genomic sequences of 546 bacteria and 147 fungi in T. chrysantha and 154 bacteria and 122 fungi in T. billbergii.}, } @article {pmid31250077, year = {2020}, author = {Goss-Souza, D and Mendes, LW and Rodrigues, JLM and Tsai, SM}, title = {Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {110-122}, pmid = {31250077}, issn = {1432-184X}, support = {2008/58114-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2014/50320-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 140317/2014-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; 311008/2016-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Agriculture ; Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; Forests ; *Microbiota ; Phylogeny ; Rhizosphere ; *Soil Microbiology ; Glycine max/growth & development ; Trees/growth & development ; }, abstract = {Forest-to-agriculture conversion has been identified as a major threat to soil biodiversity and soil processes resilience, although the consequences of long-term land use change to microbial community assembly and ecological processes have been often neglected. Here, we combined metagenomic approach with a large environmental dataset, to (i) identify the microbial assembly patterns and, (ii) to evaluate the ecological processes governing microbial assembly, in bulk soil and soybean rhizosphere, along a long-term forest-to-agriculture conversion chronosequence, in Eastern Amazon. We hypothesized that (i) microbial communities in bulk soil and rhizosphere have different assembly patterns and (ii) the weight of the four ecological processes governing assembly differs between bulk soil and rhizosphere and along the chronosequence in the same fraction. Community assembly in bulk soil fitted most the zero-sum multinomial (ZSM) neutral-based model, regardless of time. Low to intermediate dispersal was observed. Decreasing influence of abiotic factors was counterbalanced by increasing influence of biotic factors, as the chronosequence advanced. Undominated ecological processes of dispersal limitation and variable selection governing community assembly were observed in this soil fraction. For soybean rhizosphere, community assembly fitted most the lognormal niche-based model in all chronosequence areas. High dispersal and an increasing influence of abiotic factors coupled with a decreasing influence of biotic factors were found along the chronosequence. Thus, we found a dominant role of dispersal process governing microbial assembly with a secondary effect of homogeneous selection process, mainly driven by decreasing aluminum and increased cations saturation in soil solution, due to long-term no-till cropping. Together, our results indicate that long-term no-till lead community abundances in bulk soil to be in a transient and conditional state, while for soybean rhizosphere, community abundances reach a periodic and permanent distribution state. Dominant dispersal process in rhizosphere, coupled with homogeneous selection, brings evidences that soybean root system selects microbial taxa via trade-offs in order to keep functional resilience of soil processes.}, } @article {pmid31249397, year = {2019}, author = {Schirmer, M and Garner, A and Vlamakis, H and Xavier, RJ}, title = {Microbial genes and pathways in inflammatory bowel disease.}, journal = {Nature reviews. Microbiology}, volume = {17}, number = {8}, pages = {497-511}, pmid = {31249397}, issn = {1740-1534}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AT009708/AT/NCCIH NIH HHS/United States ; }, mesh = {Bacterial Adhesion ; Biological Factors/metabolism ; Gastrointestinal Microbiome ; *Host-Pathogen Interactions ; Humans ; Immunologic Factors/metabolism ; Inflammatory Bowel Diseases/*pathology/*physiopathology ; *Microbiota ; T-Lymphocytes, Regulatory/*immunology ; Th17 Cells/*immunology ; }, abstract = {Perturbations in the intestinal microbiome are implicated in inflammatory bowel disease (IBD). Studies of treatment-naive patients have identified microbial taxa associated with disease course and treatment efficacy. To gain a mechanistic understanding of how the microbiome affects gastrointestinal health, we need to move from census to function. Bacteria, including those that adhere to epithelial cells as well as several Clostridium species, can alter differentiation of T helper 17 cells and regulatory T cells. Similarly, microbial products such as short-chain fatty acids and sphingolipids also influence immune responses. Metagenomics and culturomics have identified strains of Ruminococcus gnavus and adherent invasive Escherichia coli that are linked to IBD and gut inflammation. Integrated analysis of multiomics data, including metagenomics, metatranscriptomics and metabolomics, with measurements of host response and culturomics, have great potential in understanding the role of the microbiome in IBD. In this Review, we highlight current knowledge of gut microbial factors linked to IBD pathogenesis and discuss how multiomics data from large-scale population studies in health and disease have been used to identify specific microbial strains, transcriptional changes and metabolic alterations associated with IBD.}, } @article {pmid31249384, year = {2019}, author = {Frau, A and Kenny, JG and Lenzi, L and Campbell, BJ and Ijaz, UZ and Duckworth, CA and Burkitt, MD and Hall, N and Anson, J and Darby, AC and Probert, CSJ}, title = {DNA extraction and amplicon production strategies deeply inf luence the outcome of gut mycobiome studies.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9328}, pmid = {31249384}, issn = {2045-2322}, mesh = {DNA Primers/genetics ; DNA, Fungal/genetics/*isolation & purification ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Microbial ecology studies are often performed through extraction of metagenomic DNA followed by amplification and sequencing of a marker. It is known that each step may bias the results. These biases have been explored for the study of bacterial communities, but rarely for fungi. Our aim was therefore to evaluate methods for the study of the gut mycobiome. We first evaluated DNA extraction methods in fungal cultures relevant to the gut. Afterwards, to assess how these methods would behave with an actual sample, stool from a donor was spiked with cells from the same cultures. We found that different extraction kits favour some species and bias against others. In terms of amplicon sequencing, we evaluated five primer sets, two for ITS2 and one for ITS1, 18S and 28S rRNA. Results showed that 18S rRNA outperformed the other markers: it was able to amplify all the species in the mock community and to discriminate among them. ITS primers showed both amplification and sequencing biases, the latter related to the variable length of the product. We identified several biases in the characterisation of the gut mycobiome and showed how crucial it is to be aware of these before drawing conclusions from the results of these studies.}, } @article {pmid31248462, year = {2019}, author = {Marathe, NP and Berglund, F and Razavi, M and Pal, C and Dröge, J and Samant, S and Kristiansson, E and Larsson, DGJ}, title = {Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {97}, pmid = {31248462}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; Bacterial Proteins/*genetics ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; *Hospitals ; Humans ; India ; Integrons/*genetics ; Metagenomics ; Microbial Sensitivity Tests ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; beta-Lactamases/*genetics ; }, abstract = {BACKGROUND: Hospital wastewaters contain fecal material from a large number of individuals, of which many are undergoing antibiotic therapy. It is, thus, plausible that hospital wastewaters could provide opportunities to find novel carbapenemases and other resistance genes not yet described in clinical strains. Our aim was therefore to investigate the microbiota and antibiotic resistome of hospital effluent collected from the city of Mumbai, India, with a special focus on identifying novel carbapenemases.

RESULTS: Shotgun metagenomics revealed a total of 112 different mobile antibiotic resistance gene types, conferring resistance against almost all classes of antibiotics. Beta-lactamase genes, including encoding clinically important carbapenemases, such as NDM, VIM, IMP, KPC, and OXA-48, were abundant. NDM (0.9% relative abundance to 16S rRNA genes) was the most common carbapenemase gene, followed by OXA-58 (0.84% relative abundance to 16S rRNA genes). Among the investigated mobile genetic elements, class 1 integrons (11% relative abundance to 16S rRNA genes) were the most abundant. The genus Acinetobacter accounted for as many as 30% of the total 16S rRNA reads, with A. baumannii accounting for an estimated 2.5%. High throughput sequencing of amplified integron gene cassettes identified a novel functional variant of an IMP-type (proposed IMP-81) carbapenemase gene (eight aa substitutions) along with recently described novel resistance genes like sul4 and blaRSA1. Using a computational hidden Markov model, we detected 27 unique metallo-beta-lactamase (MBL) genes in the shotgun data, of which nine were novel subclass B1 genes, one novel subclass B2, and 10 novel subclass B3 genes. Six of the seven novel MBL genes were functional when expressed in Escherichia coli.

CONCLUSION: By exploring hospital wastewater from India, our understanding of the diversity of carbapenemases has been extended. The study also demonstrates that the microbiota of hospital wastewater can serve as a reservoir of novel resistance genes, including previously uncharacterized carbapenemases with the potential to spread further.}, } @article {pmid31248378, year = {2019}, author = {Wiseschart, A and Mhuantong, W and Tangphatsornruang, S and Chantasingh, D and Pootanakit, K}, title = {Shotgun metagenomic sequencing from Manao-Pee cave, Thailand, reveals insight into the microbial community structure and its metabolic potential.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {144}, pmid = {31248378}, issn = {1471-2180}, mesh = {Bacteria/*classification/*genetics/metabolism ; Biodegradation, Environmental ; Biodiversity ; Biosynthetic Pathways/genetics/physiology ; Carbon Cycle/physiology ; Carbon Dioxide/metabolism ; Ecology ; Energy Metabolism/genetics/physiology ; *Metagenome ; Methane/metabolism ; Microbiota/*genetics/*physiology ; Nitrogen/metabolism ; RNA, Ribosomal, 16S/genetics ; Soil ; *Soil Microbiology ; Sulfur/metabolism ; Thailand ; }, abstract = {BACKGROUND: Due to the cave oligotrophic environment, this habitat presents a challenge for microorganisms to colonize and thrive. However, it has been well documented that microorganisms play important roles in cave development. Survival of microbes in this unique habitat likely involves a broad range of adaptive capabilities. Recently, cave microbiomes all over the world are of great scientific interest. However, the majority of investigations focused mostly on small subunit ribosomal RNA (16S rRNA) gene, leaving the ecological role of the microbial community largely unknown. Here, we are particularly interested in exploring the taxonomic composition and metabolic potential of microorganisms in soil from Manao-Pee cave, a subterranean limestone cave in the western part of Thailand, by using high-throughput shotgun metagenomic sequencing.

RESULTS: From taxonomic composition analysis using ribosomal RNA genes (rRNA), the results confirmed that Actinobacteria (51.2%) and Gammaproteobacteria (24.4%) were the dominant bacterial groups in the cave soil community. Metabolic potential analysis, based on six functional modules of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, revealed that functional genes involved in microbial metabolisms are highly represented in this community (40.6%). To better understand how microbes thrive under unfavorable cave condition, we focused on microbial energy metabolism. The results showed that microbial genes involved in oxidative phosphorylation were the most dominant (28.8%) in Manao-Pee cave, and were followed by methane metabolism (20.5%), carbon fixation (16.0%), nitrogen metabolism (14.7%), and sulfur metabolism (6.3%). In addition, microbial genes involved in xenobiotic biodegradation (26 pathways) and in production of secondary metabolites (27 pathways) were also identified.

CONCLUSION: In addition to providing information on microbial diversity, we also gained insights into microbial adaptations and survival strategies under cave conditions. Based on rRNA genes, the results revealed that bacteria belonging to the Actinobacteria and Gammaproteobacteria were the most abundant in this community. From metabolic potential analysis, energy and nutrient sources that sustain diverse microbial population in this community might be atmospheric gases (methane, carbon dioxide, nitrogen), inorganic sulfur, and xenobiotic compounds. In addition, the presence of biosynthetic pathways of secondary metabolites suggested that they might play important ecological roles in the cave microbiome.}, } @article {pmid31248008, year = {2019}, author = {Steury, RA and Currey, MC and Cresko, WA and Bohannan, BJM}, title = {Population Genetic Divergence and Environment Influence the Gut Microbiome in Oregon Threespine Stickleback.}, journal = {Genes}, volume = {10}, number = {7}, pages = {}, pmid = {31248008}, issn = {2073-4425}, support = {P50GM098911/NH/NIH HHS/United States ; R24RR032670/NH/NIH HHS/United States ; }, mesh = {Animals ; Environment ; Gastrointestinal Microbiome/*genetics ; *Genetic Variation ; Genetics, Population ; Geography ; Host Microbial Interactions ; Metagenomics ; Microbiota ; Oregon ; Smegmamorpha/genetics/*microbiology ; }, abstract = {Much of animal-associated microbiome research has been conducted in&nbsp;species&nbsp;for which little is known of their natural ecology and evolution.&nbsp;Microbiome studies that combine population genetic, environment, and geographic data for wild organisms can be very informative, especially in situations where host genetic variation and the environment both influence microbiome variation.&nbsp;The few studies that have&nbsp;related&nbsp;population genetic&nbsp;and microbiome variation in wild populations&nbsp;have been constrained by observation-based kinship data or&nbsp;incomplete genomic information. Here we&nbsp;integrate population genomic&nbsp;and microbiome analyses&nbsp;in wild threespine stickleback fish distributed throughout western Oregon, USA. We found that gut microbiome diversity and composition partitioned more among than within wild host populations and was better explained by host population genetic divergence than&nbsp;by environment and geography. We also identified gut microbial taxa that were most differentially abundant across environments and across genetically divergent populations. Our findings highlight the benefits of studies that investigate host-associated microbiomes in wild organisms.}, } @article {pmid31247969, year = {2019}, author = {Yu, JC and Hale, VL and Khodadadi, H and Baban, B}, title = {Whole Body Vibration-Induced Omental Macrophage Polarization and Fecal Microbiome Modification in a Murine Model.}, journal = {International journal of molecular sciences}, volume = {20}, number = {13}, pages = {}, pmid = {31247969}, issn = {1422-0067}, mesh = {Animals ; Biodiversity ; Biomarkers ; Diabetes Mellitus, Type 2 ; Disease Models, Animal ; Feces/microbiology ; *Gastrointestinal Microbiome ; Immunophenotyping ; Macrophage Activation/*immunology ; Macrophages/*immunology/metabolism ; Metagenome ; Metagenomics/methods ; Mice ; Omentum/*immunology ; *Vibration ; }, abstract = {Human nutrient metabolism, developed millions of years ago, is anachronistic. Adaptive features that offered survival advantages are now great liabilities. The current dietary pattern, coupled with massively reduced physical activities, causes an epidemic of obesity and chronic metabolic diseases, such as type 2 diabetes mellitus. Chronic inflammation is a major contributing factor to the initiation and progression of most metabolic and cardiovascular diseases. Among all components of an innate immune system, due to their dual roles as phagocytic as well as antigen-presenting cells, macrophages play an important role in the regulation of inflammatory responses, affecting the body's microenvironment and homeostasis. Earlier studies have established the beneficial, anti-inflammatory effects of whole body vibration (WBV) as a partial exercise mimetic, including reversing the effects of glucose intolerance and hepatic steatosis. Here for the first time, we describe potential mechanisms by which WBV may improve metabolic status and ameliorate the adverse consequences through macrophage polarization and altering the fecal microbiome.}, } @article {pmid31247199, year = {2020}, author = {Wang, H and Chan, HH and Ni, MY and Lam, WW and Chan, WMM and Pang, H}, title = {Bacteriophage of the Skin Microbiome in Patients with Psoriasis and Healthy Family Controls.}, journal = {The Journal of investigative dermatology}, volume = {140}, number = {1}, pages = {182-190.e5}, doi = {10.1016/j.jid.2019.05.023}, pmid = {31247199}, issn = {1523-1747}, mesh = {Acinetobacter/*virology ; Adult ; Aged ; Bacteriophages/*physiology ; Female ; Healthy Volunteers ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; Microbiota/*genetics ; Middle Aged ; Pseudomonas/*virology ; Psoriasis/*microbiology/virology ; Skin/*microbiology/virology ; }, abstract = {The bacteriophage (phage) component of the skin microbiome in patients with psoriasis has not been systematically explored. The purpose of this study is to investigate phage and bacterial components of the skin microbiome in patients with psoriasis and in healthy family controls. Lesional skin swabs of four different locations (elbow, forearm, knee, and scalp) were taken from patients with psoriasis. Healthy skin swabs of matched locations were taken from contralateral non-lesional skin and healthy family controls. Skin microbiomes were investigated using next-generation shotgun metagenomics sequencing. 81 skin microbiome samples (27 lesional skin samples and 54 healthy skin samples from contralateral non-lesional skin and family controls) obtained from 16 subjects with psoriasis and 16 matched family controls were sequenced and analyzed. Among phage species with abundant host bacteria, two significantly differential abundant phage species, Acinetobacter phage Presley and Pseudomonas phage O4 (adjusted P < 0.05), between psoriasis lesional skin and healthy skin were identified. Samples with high levels of these phage species had their host bacteria abundance suppressed (P = 0.03 and P < 0.001). Differential phage composition between lesional skin in patients with psoriasis and healthy skin from contralateral non-lesional sites and family controls, as well as the suppression of bacteria host of the respective phage, suggest possible avenues for probiotic phage therapeutics.}, } @article {pmid31245304, year = {2019}, author = {Mattei, V and Murugesan, S and Al Hashmi, M and Mathew, R and James, N and Singh, P and Kumar, M and Lakshmanan, AP and Terranegra, A and Al Khodor, S and Tomei, S}, title = {Evaluation of Methods for the Extraction of Microbial DNA From Vaginal Swabs Used for Microbiome Studies.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {197}, pmid = {31245304}, issn = {2235-2988}, mesh = {Adult ; Biodiversity ; DNA, Bacterial/*isolation & purification ; DNA, Ribosomal/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Vagina/*microbiology ; }, abstract = {Background: The composition of the microbiome in human body sites plays an important role in health. The vaginal environment is colonized by several species of bacteria that have a major influence on reproductive health. The advancement of sequencing technologies has made the assessment of the composition of the microbiota possible through microbial DNA extraction and sequencing. Therefore, it is of a paramount importance to select a sensitive and reproducible DNA extraction method, that facilitates isolation of microbial DNA with a sufficient quantity and purity, from microbial species living in the vaginal environment. Here, we have evaluated four different DNA extraction protocols from self-collected vaginal swabs. Methods: Five healthy female volunteers were enrolled in the study. Each donor was asked to self-collect 4 samples using Copan ESwab. DNA was extracted using Qiagen DNeasy kit and three modified protocols of the MoBio PowerSoil kit ("DNeasy PowerSoil" after acquisition from Qiagen). DNA quantity and integrity was checked through Nanodrop and LabChip GX. DNA was further tested through quantitative real-time PCR (qPCR) and 16S sequencing. Vaginal microbiota diversities were determined using MiSeq-Illumina high-throughput sequencing of bacterial 16S rDNA V1-V3 fingerprint. Sequencing data were analyzed using QIIME pipeline. Results: Qiagen DNeasy protocol resulted in the highest DNA yield as compared to the modified protocols of MoBio Powersoil kit. The size of the DNA extracted using each protocol was ~40 kb. Qiagen DNeasy protocol gave the highest Genomic Quality Score (average ± standard deviation: 4.24 ± 0.36), followed by the different MoBio Powersoil protocols. A substantial variability in microbial DNA abundance was found across the protocols. The vaginal microbiota of the healthy volunteers was dominated by Lactobacillus species. MoBio Powersoil kit provided a significantly higher alpha diversity as compared to the Qiagen DNeasy kit, while beta diversity measures did not reveal any significant cluster changes, except when the Bray-Curtis method was applied. Conclusion: We were able to isolate microbial DNA from the vaginal swabs. Qiagen DNeasy method gave the highest DNA yield and quality but was not optimal in detecting microbial diversity. The modified MoBio PowerSoil protocols showed higher microbial diversities as compared to the standard protocol.}, } @article {pmid31243331, year = {2019}, author = {Evans, MV and Getzinger, G and Luek, JL and Hanson, AJ and McLaughlin, MC and Blotevogel, J and Welch, SA and Nicora, CD and Purvine, SO and Xu, C and Cole, DR and Darrah, TH and Hoyt, DW and Metz, TO and Lee Ferguson, P and Lipton, MS and Wilkins, MJ and Mouser, PJ}, title = {In situ transformation of ethoxylate and glycol surfactants by shale-colonizing microorganisms during hydraulic fracturing.}, journal = {The ISME journal}, volume = {13}, number = {11}, pages = {2690-2700}, pmid = {31243331}, issn = {1751-7370}, mesh = {Bacteria/*classification/genetics ; Biodegradation, Environmental ; Glycols/*metabolism ; *Hydraulic Fracking ; Microbiota ; Minerals/chemistry ; Natural Gas/*analysis ; Ohio ; Oil and Gas Fields/*microbiology ; Proteomics ; Surface-Active Agents/analysis/*metabolism ; Wastewater/microbiology ; }, abstract = {In the last decade, extensive application of hydraulic fracturing technologies to unconventional low-permeability hydrocarbon-rich formations has significantly increased natural-gas production in the United States and abroad. The injection of surface-sourced fluids to generate fractures in the deep subsurface introduces microbial cells and substrates to low-permeability rock. A subset of injected organic additives has been investigated for their ability to support biological growth in shale microbial community members; however, to date, little is known on how complex xenobiotic organic compounds undergo biotransformations in this deep rock ecosystem. Here, high-resolution chemical, metagenomic, and proteomic analyses reveal that widely-used surfactants are degraded by the shale-associated taxa Halanaerobium, both in situ and under laboratory conditions. These halotolerant bacteria exhibit surfactant substrate specificities, preferring polymeric propoxylated glycols (PPGs) and longer alkyl polyethoxylates (AEOs) over polyethylene glycols (PEGs) and shorter AEOs. Enzymatic transformation occurs through repeated terminal-end polyglycol chain shortening during co-metabolic growth through the methylglyoxal bypass. This work provides the first evidence that shale microorganisms can transform xenobiotic surfactants in fracture fluid formulations, potentially affecting the efficiency of hydrocarbon recovery, and demonstrating an important association between injected substrates and microbial growth in an engineered subsurface ecosystem.}, } @article {pmid31243255, year = {2019}, author = {Tamaki, H}, title = {Cultivation Renaissance in the Post-Metagenomics Era: Combining the New and Old.}, journal = {Microbes and environments}, volume = {34}, number = {2}, pages = {117-120}, pmid = {31243255}, issn = {1347-4405}, mesh = {*Archaea/classification/genetics/growth & development ; *Bacteria/classification/genetics/growth & development ; Biodiversity ; Drug Resistance, Microbial ; *Fungi/classification/genetics/growth & development ; Host Microbial Interactions ; Humans ; *Metagenomics ; Microbiological Techniques/*trends ; Microbiota/genetics ; }, } @article {pmid31242612, year = {2019}, author = {Rampelotto, PH and Sereia, AFR and de Oliveira, LFV and Margis, R}, title = {Exploring the Hospital Microbiome by High-Resolution 16S rRNA Profiling.}, journal = {International journal of molecular sciences}, volume = {20}, number = {12}, pages = {}, pmid = {31242612}, issn = {1422-0067}, mesh = {Bacteria/classification/genetics ; Biodiversity ; *Environmental Microbiology ; *Hospitals ; *Metagenomics/methods ; Microbiota/*genetics ; Models, Theoretical ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The aim of this work was to analyze and compare the bacterial communities of 663 samples from a Brazilian hospital by using high-throughput sequencing of the 16S rRNA gene. To increase taxonomic profiling and specificity of 16S-based identification, a strict sequence quality filtering process was applied for the accurate identification of clinically relevant bacterial taxa. Our results indicate that the hospital environment is predominantly inhabited by closely related species. A massive dominance of a few taxa in all taxonomic levels down to the genera was observed, where the ten most abundant genera in each facility represented 64.4% of all observed taxa, with a major predominance of Acinetobacter and Pseudomonas. The presence of several nosocomial pathogens was revealed. Co-occurrence analysis indicated that the present hospital microbial network had low connectedness, forming a clustered topology, but not structured among groups of nodes (i.e., modules). Furthermore, we were able to detect ecologically relevant relationships between specific microbial taxa, in particular, potential competition between pathogens and non-pathogens. Overall, these results provide new insight into different aspects of a hospital microbiome and indicate that 16S rRNA sequencing may serve as a robust one-step tool for microbiological identification and characterization of a wide range of clinically relevant bacterial taxa in hospital settings with a high resolution.}, } @article {pmid31242511, year = {2020}, author = {Faucher, MA and Greathouse, KL and Hastings-Tolsma, M and Padgett, RN and Sakovich, K and Choudhury, A and Sheikh, A and Ajami, NJ and Petrosino, JF}, title = {Exploration of the Vaginal and Gut Microbiome in African American Women by Body Mass Index, Class of Obesity, and Gestational Weight Gain: A Pilot Study.}, journal = {American journal of perinatology}, volume = {37}, number = {11}, pages = {1160-1172}, doi = {10.1055/s-0039-1692715}, pmid = {31242511}, issn = {1098-8785}, support = {Baylor University, Baylor College of Medicine, and Baylor Research Institution-Project//30300146/International ; }, mesh = {Adult ; Black or African American ; Bacteria/classification/genetics/isolation & purification ; Female ; Gastrointestinal Microbiome/*genetics ; Genes, rRNA ; Gestational Weight Gain/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Obesity ; Pilot Projects ; Pregnancy ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Vagina/*microbiology ; *Weight Gain ; Young Adult ; }, abstract = {OBJECTIVE: This study determines the differences in the distal gut and vaginal microbiome in African American (AA) women by prepregnancy body mass index and gestational weight gain (GWG) comparing women with and without obesity and by obesity class.

STUDY DESIGN: We prospectively sampled the vaginal and distal gut microbiome in pregnant AA women at two time points during pregnancy. Samples were analyzed using high-throughput sequencing of the V4 region of the 16S ribosomal ribonucleic acid gene.

RESULTS: Distinct differences in vaginal and distal gut α-diversity were observed at time point 1 between women with and without obesity by total GWG. Significant differences in distal gut β-diversity were also found at time point 1 in obese women by GWG. Within the Bacteroides genus, a significant association was observed by total GWG among obese women which was absent in nonobese women. Women with class III obesity who experienced low GWG had the lowest abundance of distal gut Bacteroides and appreciably higher relative abundance of a consortia of vaginal taxa including Atopobium, Gardnerella, Prevotella, and Sneathia.

CONCLUSION: These results contribute new evidence showing that GWG in combination with obesity and obesity class is associated with an altered distal gut and vaginal composition early in pregnancy among AA women.}, } @article {pmid31241822, year = {2019}, author = {Santillan, E and Seshan, H and Constancias, F and Wuertz, S}, title = {Trait-based life-history strategies explain succession scenario for complex bacterial communities under varying disturbance.}, journal = {Environmental microbiology}, volume = {21}, number = {10}, pages = {3751-3764}, doi = {10.1111/1462-2920.14725}, pmid = {31241822}, issn = {1462-2920}, support = {//Ministry of Education/International ; //Singapore National Research Foundation/International ; }, mesh = {Bacteria/genetics/*growth & development ; Bioreactors ; Ecosystem ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {Trait-based approaches are increasingly gaining importance in community ecology, as a way of finding general rules for the mechanisms driving changes in community structure and function under the influence of perturbations. Frameworks for life-history strategies have been successfully applied to describe changes in plant and animal communities upon disturbance. To evaluate their applicability to complex bacterial communities, we operated replicated wastewater treatment bioreactors for 35 days and subjected them to eight different disturbance frequencies of a toxic pollutant (3-chloroaniline), starting with a mixed inoculum from a full-scale treatment plant. Relevant ecosystem functions were tracked and microbial communities assessed through metagenomics and 16S rRNA gene sequencing. Combining a series of ordination, statistical and network analysis methods, we associated different life-history strategies with microbial communities across the disturbance range. These strategies were evaluated using tradeoffs in community function and genotypic potential, and changes in bacterial genus composition. We further compared our findings with other ecological studies and adopted a semi-quantitative competitors, stress-tolerants, ruderals (CSR) classification. The framework reduces complex data sets of microbial traits, functions and taxa into ecologically meaningful components to help understand the system response to disturbance and hence represents a promising tool for managing microbial communities.}, } @article {pmid31240835, year = {2019}, author = {Weng, YJ and Gan, HY and Li, X and Huang, Y and Li, ZC and Deng, HM and Chen, SZ and Zhou, Y and Wang, LS and Han, YP and Tan, YF and Song, YJ and Du, ZM and Liu, YY and Wang, Y and Qin, N and Bai, Y and Yang, RF and Bi, YJ and Zhi, FC}, title = {Correlation of diet, microbiota and metabolite networks in inflammatory bowel disease.}, journal = {Journal of digestive diseases}, volume = {20}, number = {9}, pages = {447-459}, doi = {10.1111/1751-2980.12795}, pmid = {31240835}, issn = {1751-2980}, support = {81790632//National Natural Science Foundation for Key Programs of China/ ; 2015AA020702//National High Technology Research and Development Program of China (863 Program)/ ; }, mesh = {Adult ; Biopsy ; Body Mass Index ; Case-Control Studies ; *Diet ; Dysbiosis/complications ; Feces/microbiology ; Female ; *Food Preferences ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/metabolism/*microbiology/pathology ; Intestinal Mucosa/microbiology/pathology ; Male ; Metabolic Networks and Pathways/physiology ; Metagenomics ; Middle Aged ; Nutrition Assessment ; Young Adult ; }, abstract = {OBJECTIVES: Microbiota dysbiosis in inflammatory bowel disease (IBD) has been widely reported. The gut microbiota connect diet to the metabolism by producing small molecules via diverse metabolic pathways. In this study we aimed to investigate the dietary preferences of IBD patients, and to explore the interactions among gut microbiota composition, dietary components, and metabolites in relation to IBD.

METHODS: Dietary preferences of IBD patients (including those with ulcerative colitis [UC] and Crohn's disease [CD]) and health controls were investigated, and their gut microbiota were analyzed using 16S rRNA gene sequencing and metagenomic analyses of fecal and biopsy samples. The metabolite profiles of the samples were then analyzed using gas and liquid chromatography-mass spectrometry analyses.

RESULTS: The daily intake of folic acid, niacin, vitamins C and D, calcium, and selenium differed significantly between patients with IBD and healthy controls. A decrease in long-chain (such as arachidic, and oleic acid) and medium-chain fatty acids (sebacic acid and isocaproic acid) as well as bile acid was observed in patients with IBD. Compared with healthy controls, 22 microbial species (including Sulfolobus acidocaldarius, and Clostridium clostridioforme CAG132) in the UC group and 37 microbial species (such as Bacteroides fragilis and Fusobacterium nucleatum) in the CD group were found to be correlated to diet and metabolites. Bacteroides fragilis was enriched in patients with IBD and associated with multi-nutrients, and 21 metabolites including 25-hydroxyvitamin D3 and taurolithocholic acid.

CONCLUSIONS: This study provides an interaction network to identify key micronutrients, microbiota components and metabolites that contribute to IBD.}, } @article {pmid31240754, year = {2019}, author = {Firrman, J and Liu, L and Tanes, C and Bittinger, K and Mahalak, K and Rinaldi, W}, title = {Metagenomic assessment of the Cebus apella gut microbiota.}, journal = {American journal of primatology}, volume = {81}, number = {10-11}, pages = {e23023}, doi = {10.1002/ajp.23023}, pmid = {31240754}, issn = {1098-2345}, support = {//Agricultural Research Service/International ; //US Congress/International ; //US Department of Agriculture and Agricultural Research Service. Project number 8072-41000-102-00-D, In Vitro Human Intestinal Microbial Ecosystem: Effects of Diet/International ; }, mesh = {Animals ; Bacteria/classification/metabolism ; Fatty Acids, Volatile/*metabolism ; Gastrointestinal Microbiome/*genetics/physiology ; Intestines/microbiology ; Male ; *Metagenome ; Phylogeny ; Sapajus apella/*microbiology ; }, abstract = {Cebus Apella (C. apella) is a species of Nonhuman Primate (NHP) used for biomedical research because it is phylogenetically similar and shares anatomical commonalities with humans. Here, the gut microbiota of three C. apella were examined in the different regions of the intestinal tract. Using metagenomics, the gut microbiota associated with the luminal content and mucus layer for each intestinal region was identified, and functionality was investigated by quantifying the levels of short chain fatty acids (SCFAs) produced. The results of this study show a high degree of similarity in the intestinal communities among C. apella subjects, with multiple shared characteristics. First, the communities in the lumen were more phylogenetically diverse and rich compared to the mucus layer communities throughout the entire intestinal tract. The small intestine communities in the lumen displayed a higher Shannon diversity index compared to the colon communities. Second, all the communities were dominated by aero-tolerant taxa such as Streptococcus, Enterococcus, Abiotrophia, and Lactobacillus, although there was preferential colonization of specific taxa observed. Finally, the primary SCFA produced throughout the intestinal tract was acetic acid, with some propionic acid and butyric acid detected in the colon regions. The small intestine microbiota produced significantly less SCFAs compared to the communities in the colon. Collectively, these data provide an in-depth report on the composition, distribution, and SCFA production of the gut microbiota along the intestinal tract of the C. apella NHP animal model.}, } @article {pmid31240449, year = {2019}, author = {Huang, J and Ran, Y and Pradhan, S and Yan, W and Dai, Y}, title = {Investigation on Microecology of Hair Root Fungi in Androgenetic Alopecia Patients.}, journal = {Mycopathologia}, volume = {184}, number = {4}, pages = {505-515}, pmid = {31240449}, issn = {1573-0832}, mesh = {Adult ; Alopecia/*microbiology ; *Dysbiosis ; Female ; Fungi/*classification/genetics/*isolation & purification ; Hair Follicle/*microbiology ; Healthy Volunteers ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; *Microbiota ; Microscopy ; Polymerase Chain Reaction ; }, abstract = {BACKGROUND: This study focused on the differences in hairy root fungal microecology between androgenetic alopecia patients and healthy individuals.

METHODS: Light microscopy was used to observe the morphology of hairy roots. Morphological observations were also performed in the positive specimens using scanning electron microscopy and transmission electron microscopy. The high-throughput sequencing method was used to detect the fungal microecology of hairy roots at different sites. Moreover, the comparison of fungal loads of Malassezia in different group and scalp area were tested by PCR.

RESULTS: The fungi in the hair root observed by optical microscopy are mainly Malassezia yeast. The positive rate of Malassezia in the hair loss group (60%) was higher than that in the control group (40%). The detection efficiency of Malassezia examined by scanning electron microscopy was higher than that by light microscopy. Results acquired from high-throughput molecular sequencing of fungi suggested that Ascomycota was the dominant species, whereas in the occipital hair roots of the control group Basidiomycota was the dominant species in the hair loss group. Malassezia followed by Trichosporon were the most abundant fungal genera. The changes in abundance at the top and occipital region of the control group were more significant than those of the genus Fusarium, followed by Epicoccum and Malassezia. The load of Malassezia located on calvaria in the alopecia group was significantly higher than that in the control group. In the alopecia group, the load of Malassezia on the scalp was higher than that on the occipital region. The load of Malassezia globosa and Malassezia restricta in the hair loss group was higher on calvaria and occipital areas.

CONCLUSION: Malassezia had a positive correlation with the incidence of androgenic alopecia.}, } @article {pmid31240226, year = {2019}, author = {Yu, H and Qin, L and Hu, H and Wang, Z}, title = {Alteration of the Gut Microbiota and Its Effect on AMPK/NADPH Oxidase Signaling Pathway in 2K1C Rats.}, journal = {BioMed research international}, volume = {2019}, number = {}, pages = {8250619}, pmid = {31240226}, issn = {2314-6141}, mesh = {AMP-Activated Protein Kinases/*metabolism ; Acetyl-CoA Carboxylase/metabolism ; Animals ; Bacteria/classification/metabolism ; Fatty Acids, Volatile/blood ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Kidney/*metabolism ; Male ; Metagenomics ; Models, Animal ; NADPH Oxidases/*metabolism ; Nitrates/blood ; Nitrites/blood ; Phosphorylation ; Rats ; Rats, Wistar ; Signal Transduction/*physiology ; Superoxide Dismutase/metabolism ; }, abstract = {BACKGROUND: The purpose of this study was to evaluate the alteration of the gut microbiota and its effect on adenosine monophosphate-activated protein kinase (AMPK)/nicotinamide adenine dinucleotide phosphate oxidase (NADPH oxidase) signaling pathway in two-kidney one-clip (2K1C) rats.

METHODS: The 2K1C rat models were established. The rats were randomly divided into the following 2 groups: 2K1C group and sham group. Alterations of the gut microbiota were analyzed based on the high throughput sequencing method. Plasma concentrations of short chain fatty acids (SCFAs) were measured by chromatography. The protein expression of phosphorylated AMPK and acetyl-CoA carboxylase (ACC) was determined by western blotting. NADPH oxidase activity was measured by a luminometer.

RESULTS: Microbial community analyses revealed that the structure and composition of the gut microbiota were significantly disrupted in 2K1C rats when compared to sham rats. This disruption was associated with the drastic increase in relative abundance of the genera Prevotella and the decrease in SCFA-producing bacterial population. We further confirm that SCFAs produced by the gut microbiota influence NADPH oxidase activity through AMPK.

CONCLUSIONS: Our data implicated the important role of gut microbiota in the regulation of AMPK/NADPH oxidase signaling pathway.}, } @article {pmid31239159, year = {2019}, author = {Costa, M and Weese, JS}, title = {Methods and basic concepts for microbiota assessment.}, journal = {Veterinary journal (London, England : 1997)}, volume = {249}, number = {}, pages = {10-15}, doi = {10.1016/j.tvjl.2019.05.005}, pmid = {31239159}, issn = {1532-2971}, mesh = {Animals ; Bacteria/genetics ; Bacteriological Techniques/*veterinary ; DNA, Bacterial ; Host Microbial Interactions ; *Microbiota ; Sequence Analysis, DNA/veterinary ; }, abstract = {There has been a marked increase in interest regarding complex microbial populations in recent years. The methodology used for microbial assessment has drastically changed over the last two decades and continues to advance at a rapid pace. Culture-based studies have been superseded by those based upon molecular methods, which have been largely used to discover new species and to better characterize complex communities, mainly driven by the advances in DNA sequencing, termed 'next generation sequencing'. These methodologies have allowed for a better understanding of the relationship between hosts and their microbiotas, which have important roles in health maintenance and in the pathophysiology of wide ranging conditions such as obesity, diabetes, allergic diseases and even behavioural changes. While most widely used in humans, these approaches are now commonly used in veterinary research, with increasing interest in direct clinical applications. As these methods provide novel insights that will constitute the basis for the development of new therapeutic and prevention strategies, and as commercial efforts to offer microbiota assessment as a clinical tool expand, it is essential for researchers and clinical veterinarians to understand and have the tools to be able to interpret research performed in this new fascinating field. The objective of this review is to describe some of the most common methods for characterization of microbial communities and to provide an overview of the basic concepts necessary for good interpretation of the research performed in this field.}, } @article {pmid31238873, year = {2019}, author = {Somerville, V and Lutz, S and Schmid, M and Frei, D and Moser, A and Irmler, S and Frey, JE and Ahrens, CH}, title = {Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {143}, pmid = {31238873}, issn = {1471-2180}, mesh = {Bacteria/classification/*virology ; Bacteriophages/*genetics/*physiology ; Biodiversity ; Cheese/microbiology ; Clustered Regularly Interspaced Short Palindromic Repeats ; Genome, Bacterial ; Lactobacillus delbrueckii/genetics ; Lactobacillus helveticus/genetics ; *Metagenome ; Metagenomics ; Microbiota/*genetics/*physiology ; Plasmids ; RNA, Ribosomal, 16S/genetics ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Complete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly of an isolated bacterial strain is in most cases straightforward, more informative data about co-existing bacteria as well as synergistic and antagonistic effects can be obtained from a direct analysis of microbial communities. However, the complexity of metagenomic samples represents a major challenge. While third generation sequencing technologies have been suggested to enable finished metagenome-assembled genomes, to our knowledge, the complete genome assembly of all dominant strains in a microbiome sample has not been demonstrated. Natural whey starter cultures (NWCs) are used in cheese production and represent low-complexity microbiomes. Previous studies of Swiss Gruyère and selected Italian hard cheeses, mostly based on amplicon metagenomics, concurred that three species generally pre-dominate: Streptococcus thermophilus, Lactobacillus helveticus and Lactobacillus delbrueckii.

RESULTS: Two NWCs from Swiss Gruyère producers were subjected to whole metagenome shotgun sequencing using the Pacific Biosciences Sequel and Illumina MiSeq platforms. In addition, longer Oxford Nanopore Technologies MinION reads had to be generated for one to resolve repeat regions. Thereby, we achieved the complete assembly of all dominant bacterial genomes from these low-complexity NWCs, which was corroborated by a 16S rRNA amplicon survey. Moreover, two distinct L. helveticus strains were successfully co-assembled from the same sample. Besides bacterial chromosomes, we could also assemble several bacterial plasmids and phages and a corresponding prophage. Biologically relevant insights were uncovered by linking the plasmids and phages to their respective host genomes using DNA methylation motifs on the plasmids and by matching prokaryotic CRISPR spacers with the corresponding protospacers on the phages. These results could only be achieved by employing long-read sequencing data able to span intragenomic as well as intergenomic repeats.

CONCLUSIONS: Here, we demonstrate the feasibility of complete de novo genome assembly of all dominant strains from low-complexity NWCs based on whole metagenomics shotgun sequencing data. This allowed to gain novel biological insights and is a fundamental basis for subsequent systems-wide omics analyses, functional profiling and phenotype to genotype analysis of specific microbial communities.}, } @article {pmid31236870, year = {2019}, author = {Zheng, T and Zhang, K and Zhu, X and Guan, L and Jiu, S and Li, X and Nasim, M and Jia, H and Fang, J}, title = {Integrated metatranscriptome and transcriptome reveals the microbial community composition and physiological function of xylem sap on grapevine during bleeding period.}, journal = {Genes & genomics}, volume = {41}, number = {9}, pages = {1095-1111}, pmid = {31236870}, issn = {2092-9293}, mesh = {*Metagenome ; *Microbiota ; Stress, Physiological ; *Transcriptome ; Vitis/*genetics/microbiology/physiology ; Xylem/genetics/metabolism/physiology ; }, abstract = {BACKGROUND: The xylem sap of fruit trees ensures the survival during the dormant period, and its flow during the bleeding period is correlated with the start of a new life cycle. Though the simple exploration on ingredients in the sap was carried out in the early years, the specific life activities and physiology functions of the sap during bleeding period have not been reported yet and the bleeding period is still a fruit tree development period worthy of attention.

OBJECTIVES: In this study, the microbial community composition during bleeding period were revealed by metatranscriptome and transcriptomic data. For the first time, the microorganism genome and grape genome in xylem sap were analyzed on transcriptional level, based on which the main physiological functions of the sap were also determined.

METHODS: The genomic RNA in the sap was isolated and sequenced. Kyoto Encyclopedia of Gene and Genome (KEGG), Evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) and Carbohydrate-Active enzymes Database (CAZy) functional annotation were used to analysis the function of micro-organisms in xylem sap. DEGs were analyzed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The genes responsive to biotic and abiotic stresses were finally screened by transcriptome screening, stress data analysis and vitro validation experiments.

RESULTS: The analysis exhibited 36,144,564 micro-related clean reads and 244,213 unigene. KEGG, eggNOG and CAZy functional annotation analysis indicated that signal transduction and material metabolism were the most important function of xylem sap. DEGs analysis were mainly about disease resistance, carbon source metabolism and hormone signal transduction, especially in P3 vs P1, enriched in the plant-pathogen interaction pathway. Analysis on grape genome information revealed xylem sap had little RNA with weak life activity. Metabolic pathways, biosynthesis of secondary metabolites, plant hormone signal transduction and plant-pathogen interaction were the four pathways with the largest number of enriched genes. Moreover, 16 genes responsive to biotic and abiotic stresses were screened out.

CONCLUSION: Promoting plant growth and resisting pathogens were the most important function of xylem sap during the bleeding period, and the function of microbial community were closely related to microorganisms growth and disease resistance. The 16 stress-related genes might be used for the future grape resistance research.}, } @article {pmid31236844, year = {2019}, author = {Kunath, BJ and Minniti, G and Skaugen, M and Hagen, LH and Vaaje-Kolstad, G and Eijsink, VGH and Pope, PB and Arntzen, MØ}, title = {Metaproteomics: Sample Preparation and Methodological Considerations.}, journal = {Advances in experimental medicine and biology}, volume = {1073}, number = {}, pages = {187-215}, doi = {10.1007/978-3-030-12298-0_8}, pmid = {31236844}, issn = {0065-2598}, mesh = {*Metagenomics ; *Microbial Consortia ; Proteins ; *Proteomics ; Specimen Handling/*methods ; }, abstract = {Meta-omic techniques have progressed rapidly in the past decade and are frequently used in microbial ecology to study microorganisms in their natural ecosystems independent from culture restrictions. Metaproteomics, in combination with metagenomics, enables quantitative assessment of expressed proteins and pathways from individual members of the consortium. Together, metaproteomics and metagenomics can provide a detailed understanding of which organisms occupy specific metabolic niches, how they interact, and how they utilize nutrients, and these insights can be obtained directly from environmental samples. Here, we outline key aspects of sample preparation, database generation, and other methodological considerations that are required for successful quantitative metaproteomic analyses and we describe case studies on the integration with metagenomics for enhanced functional output.}, } @article {pmid31236715, year = {2019}, author = {Joishy, TK and Dehingia, M and Khan, MR}, title = {Bacterial diversity and metabolite profiles of curd prepared by natural fermentation of raw milk and back sloping of boiled milk.}, journal = {World journal of microbiology & biotechnology}, volume = {35}, number = {7}, pages = {102}, pmid = {31236715}, issn = {1573-0972}, support = {BT/550/NE/U-Excel/2014//Department of Biotechnology , Ministry of Science and Technology/ ; DST/INSPIRE Fellowship/2015/IF150782//Department of Science and Technology, Ministry of Science and Technology/ ; }, mesh = {Animals ; Bacteria/*isolation & purification/metabolism ; *Biodiversity ; DNA, Bacterial/genetics/isolation & purification ; Enterococcus/isolation & purification/metabolism ; *Fermentation ; Food Handling ; Food Microbiology ; High-Throughput Nucleotide Sequencing ; Lactobacillales ; Lactobacillus/isolation & purification/metabolism ; Lactococcus/isolation & purification/metabolism ; Leuconostoc/isolation & purification/metabolism ; Metagenomics ; Milk/*microbiology ; Multivariate Analysis ; RNA, Ribosomal, 16S/genetics/isolation & purification ; }, abstract = {Preparation of curd vary worldwide due to which its taste, texture and impact on human health also differ. In Assam, curd prepared from raw milk (RMC) is preferred over curd prepared from boiled milk (BMC), a tradition believed to have originated from the Mongoloid customs. Microbial diversity of raw milk (RM), boiled milk (BM), RMC and BMC collected from three farms were investigated by culture dependent and independent techniques. Additionally, metabolite profiles of RMC and BMC were studied by gas chromatography and mass spectroscopy. A total of 59 bacterial isolates were identified from the four different dairy products. In RM, lactic acid bacteria such as Lactococcus, Enterococcus, Lactobacillus and Leuconostoc were obtained along with the environmental bacteria like Bacillus, Staphylococcus, Acetobacter, Chryseobacterium, Streptococcus, Acinetobacter, Kocuria, Klebsiella and Macrococcus. Additionally, Prevotella, Oscillospira, Phascolarctobacterium and Akkermansia were also detected in BM by culture independent technique. In RMC and BMC, Lactococcus, Leuconostoc and Lactobacillus were prevalent. RM and RMC shared Enterococcus, Lactococcus, Streptococcus and Acinetobacter as common bacterial genera. However, no bacterial genus was common in BM and BMC. The correlation analysis revealed that Lactobacillus was negatively correlated to other bacterial genera. Oligotyping analysis revealed that Lactobacillus brevis and L.fermentum were abundant in RMC and BMC, respectively. In metabolomic study, ascorbic acid, dodecanoic acid and hexadecanoic acid were found to be significantly higher in RMC. Presence of different types of probiotics in these curds samples opens a new avenue to understand their effects on human health.}, } @article {pmid31235964, year = {2019}, author = {Scheiman, J and Luber, JM and Chavkin, TA and MacDonald, T and Tung, A and Pham, LD and Wibowo, MC and Wurth, RC and Punthambaker, S and Tierney, BT and Yang, Z and Hattab, MW and Avila-Pacheco, J and Clish, CB and Lessard, S and Church, GM and Kostic, AD}, title = {Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism.}, journal = {Nature medicine}, volume = {25}, number = {7}, pages = {1104-1109}, pmid = {31235964}, issn = {1546-170X}, support = {P30 DK040561/DK/NIDDK NIH HHS/United States ; T15 LM007092/LM/NLM NIH HHS/United States ; T32 HG002295/HG/NHGRI NIH HHS/United States ; T32 DK007260/DK/NIDDK NIH HHS/United States ; P30 DK036836/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Athletes ; Exercise ; *Gastrointestinal Microbiome ; Humans ; Lactic Acid/*metabolism ; *Metagenomics ; Mice ; Mice, Inbred C57BL ; Propionates/metabolism ; *Running ; Veillonella/*metabolism ; }, abstract = {The human gut microbiome is linked to many states of human health and disease[1]. The metabolic repertoire of the gut microbiome is vast, but the health implications of these bacterial pathways are poorly understood. In this study, we identify a link between members of the genus Veillonella and exercise performance. We observed an increase in Veillonella relative abundance in marathon runners postmarathon and isolated a strain of Veillonella atypica from stool samples. Inoculation of this strain into mice significantly increased exhaustive treadmill run time. Veillonella utilize lactate as their sole carbon source, which prompted us to perform a shotgun metagenomic analysis in a cohort of elite athletes, finding that every gene in a major pathway metabolizing lactate to propionate is at higher relative abundance postexercise. Using [13]C3-labeled lactate in mice, we demonstrate that serum lactate crosses the epithelial barrier into the lumen of the gut. We also show that intrarectal instillation of propionate is sufficient to reproduce the increased treadmill run time performance observed with V. atypica gavage. Taken together, these studies reveal that V. atypica improves run time via its metabolic conversion of exercise-induced lactate into propionate, thereby identifying a natural, microbiome-encoded enzymatic process that enhances athletic performance.}, } @article {pmid31235833, year = {2019}, author = {Pham, TP and Tidjani Alou, M and Bachar, D and Levasseur, A and Brah, S and Alhousseini, D and Sokhna, C and Diallo, A and Wieringa, F and Million, M and Raoult, D}, title = {Gut Microbiota Alteration is Characterized by a Proteobacteria and Fusobacteria Bloom in Kwashiorkor and a Bacteroidetes Paucity in Marasmus.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9084}, pmid = {31235833}, issn = {2045-2322}, mesh = {Bacteroidetes/*isolation & purification ; Biodiversity ; Case-Control Studies ; Female ; Fusobacteria/*isolation & purification ; *Gastrointestinal Microbiome ; Humans ; Kwashiorkor/*microbiology ; Male ; Protein-Energy Malnutrition/*microbiology ; Proteobacteria/*isolation & purification ; }, abstract = {Kwashiorkor and marasmus are considered to be two different clinical diseases resulting from severe malnutrition, but this distinction has been questioned. In a previous study comparing children with kwashiorkor and healthy children from Niger and Senegal, we found a dramatic gut microbiota alteration with a predominant depletion of anaerobes and enrichment in Proteobacteria and Fusobacteria in kwashiorkor. However, it remained unknown whether this association was related to malnutrition or was a specific feature of kwashiorkor. In this continuation study, we added 7 new marasmus subjects and 71,162 new colonies from the same countries. Our results showed that, compared to marasmus, the kwashiorkor gut microbiota was characterized by an increased proportion of Proteobacteria (culturomics, Marasmus 5.0%, Kwashiorkor 16.7%, p < 0.0001; metagenomics, Marasmus 14.7%, Kwashiorkor 22.0%, p = 0.001), but there was a decreased proportion of Bacteroidetes in marasmus (culturomics, Marasmus 0.8%, Kwashiorkor 6.5%, p = 0.001; metagenomics, Marasmus 5.4%, Kwashiorkor 7.0%, p = 0.03). Fusobacterium was more frequently cultured from kwashiorkor. All detected potential pathogenic species were enriched in the kwashiorkor gut microbiota. These results provide a biological basis to support the usage of an antibiotic therapy more effective in suppressing the overgrowth of bacterial communities resistant to penicillin, combined with antioxidants and probiotics for nutritional recovery therapies, particularly for kwashiorkor.}, } @article {pmid31234773, year = {2019}, author = {Das, P and Marcišauskas, S and Ji, B and Nielsen, J}, title = {Metagenomic analysis of bile salt biotransformation in the human gut microbiome.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {517}, pmid = {31234773}, issn = {1471-2164}, support = {HEALTH-F4-2012-305312//METACARDIS/ ; }, mesh = {Bacteria/classification/genetics/*metabolism ; Bacterial Proteins/genetics ; Bile Acids and Salts/*metabolism ; Biotransformation/genetics ; Dysbiosis/metabolism/microbiology ; Firmicutes/genetics/metabolism ; Gastrointestinal Microbiome/*genetics ; Humans ; Inflammatory Bowel Diseases/metabolism/microbiology ; Metagenomics ; }, abstract = {BACKGROUND: In the biochemical milieu of human colon, bile acids act as signaling mediators between the host and its gut microbiota. Biotransformation of primary to secondary bile acids have been known to be involved in the immune regulation of human physiology. Several 16S amplicon-based studies with inflammatory bowel disease (IBD) subjects were found to have an association with the level of fecal bile acids. However, a detailed investigation of all the bile salt biotransformation genes in the gut microbiome of healthy and IBD subjects has not been performed.

RESULTS: Here, we report a comprehensive analysis of the bile salt biotransformation genes and their distribution at the phyla level. Based on the analysis of shotgun metagenomes, we found that the IBD subjects harbored a significantly lower abundance of these genes compared to the healthy controls. Majority of these genes originated from Firmicutes in comparison to other phyla. From metabolomics data, we found that the IBD subjects were measured with a significantly low level of secondary bile acids and high levels of primary bile acids compared to that of the healthy controls.

CONCLUSIONS: Our bioinformatics-driven approach of identifying bile salt biotransformation genes predicts the bile salt biotransformation potential in the gut microbiota of IBD subjects. The functional level of dysbiosis likely contributes to the variation in the bile acid pool. This study sets the stage to envisage potential solutions to modulate the gut microbiome with the objective to restore the bile acid pool in the gut.}, } @article {pmid31232514, year = {2019}, author = {Matesanz, S and Pescador, DS and Pías, B and Sánchez, AM and Chacón-Labella, J and Illuminati, A and de la Cruz, M and López-Angulo, J and Marí-Mena, N and Vizcaíno, A and Escudero, A}, title = {Estimating belowground plant abundance with DNA metabarcoding.}, journal = {Molecular ecology resources}, volume = {19}, number = {5}, pages = {1265-1277}, doi = {10.1111/1755-0998.13049}, pmid = {31232514}, issn = {1755-0998}, support = {CGL2015-66809-P//Secretaría de Estado de Investigación, Desarrollo e Innovación/ ; }, mesh = {*Biota ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; Metagenomics/*methods ; Plant Roots/classification/genetics ; Plants/*classification/*genetics ; }, abstract = {Most work on plant community ecology has been performed above ground, neglecting the processes that occur in the soil. DNA metabarcoding, in which multiple species are computationally identified in bulk samples, can help to overcome the logistical limitations involved in sampling plant communities belowground. However, a major limitation of this methodology is the quantification of species' abundances based on the percentage of sequences assigned to each taxon. Using root tissues of five dominant species in a semi-arid Mediterranean shrubland (Bupleurum fruticescens, Helianthemum cinereum, Linum suffruticosum, Stipa pennata and Thymus vulgaris), we built pairwise mixtures of relative abundance (20%, 50% and 80% biomass), and implemented two methods (linear model fits and correction indices) to improve estimates of root biomass. We validated both methods with multispecies mixtures that simulate field-collected samples. For all species, we found a positive and highly significant relationship between the percentage of sequences and biomass in the mixtures (R[2] = .44-.66), but the equations for each species (slope and intercept) differed among them, and two species were consistently over- and under-estimated. The correction indices greatly improved the estimates of biomass percentage for all five species in the multispecies mixtures, and reduced the overall error from 17% to 6%. Our results show that, through the use of post-sequencing quantification methods on mock communities, DNA metabarcoding can be effectively used to determine not only species' presence but also their relative abundance in field samples of root mixtures. Importantly, knowledge of these aspects will allow us to study key, yet poorly understood, belowground processes.}, } @article {pmid31230147, year = {2020}, author = {Kan, J and Cheng, J and Xu, L and Hood, M and Zhong, D and Cheng, M and Liu, Y and Chen, L and Du, J}, title = {The combination of wheat peptides and fucoidan protects against chronic superficial gastritis and alters gut microbiota: a double-blinded, placebo-controlled study.}, journal = {European journal of nutrition}, volume = {59}, number = {4}, pages = {1655-1666}, doi = {10.1007/s00394-019-02020-6}, pmid = {31230147}, issn = {1436-6215}, mesh = {Adult ; Anti-Ulcer Agents/*pharmacology ; China ; Chronic Disease ; Double-Blind Method ; Feces/microbiology ; Female ; Gastric Mucosa/drug effects/microbiology ; Gastritis/*drug therapy ; Gastrointestinal Microbiome/*drug effects ; Humans ; Male ; Peptides/*pharmacology ; Polysaccharides/*pharmacology ; Surveys and Questionnaires ; *Triticum ; }, abstract = {PURPOSE: Chronic gastritis is observed in almost half world population. Traditional medications against chronic gastritis might produce adverse effects, so alternative nutritional strategies are needed to prevent the aggravation of gastric mucosal damage. The aim of this study is to evaluate the protective effect of the combination of wheat peptides and fucoidan (WPF) on adults diagnosed with chronic superficial gastritis in a randomized, double-blind, placebo-controlled clinical trial.

METHODS: Participants were randomized to receive WPF (N = 53) or placebo (N = 53) once daily for 45 days. Pathological grading of gastric mucosal damage was scored using gastroscopy. Fecal samples were collected for the determination of calprotectin, short chain fatty acids (SCFA) levels and metagenomics analysis. Questionnaires for self-reported gastrointestinal discomforts, life quality and food frequency were collected throughout the study.

RESULTS: WPF intervention reduced gastric mucosal damage in 70% subjects (P < 0.001). Significantly less stomach pain (P < 0.001), belching (P = 0.028), bloating (P < 0.001), acid reflux (P < 0.001), loss of appetite (P = 0.021), increased food intake (P = 0.020), and promoted life quality (P = 0.014) were reported in the WPF group. WPF intervention significantly decreased fecal calprotectin level (P = 0.003) while slightly increased fecal SCFAs level (P = 0.092). In addition, we found altered microbiota composition post-intervention with increased Bifidobacterium pseudocatenulatum (P = 0.032), Eubacterium siraeum (P = 0.036), Bacteroides intestinalis (P = 0.024) and decreased Prevotella copri (P = 0.055).

CONCLUSIONS: WPF intervention could be utilized as a nutritional alternative to mitigate the progression of chronic gastritis. Furthermore, WPF played an important role in altering gut microbial profile and SCFA production, which might benefit the lower gastrointestinal tract.}, } @article {pmid31229831, year = {2019}, author = {Souza, FFC and Rissi, DV and Pedrosa, FO and Souza, EM and Baura, VA and Monteiro, RA and Balsanelli, E and Cruz, LM and Souza, RAF and Andreae, MO and Reis, RA and Godoi, RHM and Huergo, LF}, title = {Uncovering prokaryotic biodiversity within aerosols of the pristine Amazon forest.}, journal = {The Science of the total environment}, volume = {688}, number = {}, pages = {83-86}, doi = {10.1016/j.scitotenv.2019.06.218}, pmid = {31229831}, issn = {1879-1026}, mesh = {Aerosols/*analysis ; *Air Microbiology ; Biodiversity ; Brazil ; Environmental Monitoring ; *Forests ; }, abstract = {Biological aerosols (bioaerosol) are atmospheric particles that act as a dispersion unit of living organisms across the globe thereby affecting the biogeographic distribution of organisms. Despite their importance, there is virtually no knowledge about bioaerosols emitted by pristine forests. Here we provide the very first survey of the prokaryotic community of a bioaerosol collected inside pristine Amazon forest at 2 m above ground. Total atmospheric particles were collected at the Amazon Tall Tower Observatory, subjected to metagenomic DNA extraction and the prokaryotic diversity was determined by 16S rRNA gene amplicon sequencing. A total of 271,577 reads of 250 bp of the 16S rRNA gene amplicon were obtained. Only 27% of the reads could be classified using the 16S SILVA database. Most belonged to Proteobacteria, Actinobacteria and Firmicutes which is in good agreement with other bioaerosol studies. Further inspection of the reads using Blast searches and the 18S SILVA database revealed that most of the dataset was composed of Fungi sequences. The identified microbes suggest that the atmosphere may act as an important gateway to interchange bacteria between plants, soil and water ecosystems.}, } @article {pmid31229556, year = {2020}, author = {Parvathi, A and Jasna, V and Aswathy, VK and Aparna, S and Nathan, VK and Jyothibabu, R}, title = {Dominance of Wolbachia sp. in the deep-sea sediment bacterial metataxonomic sequencing analysis in the Bay of Bengal, Indian Ocean.}, journal = {Genomics}, volume = {112}, number = {1}, pages = {1030-1041}, doi = {10.1016/j.ygeno.2019.06.019}, pmid = {31229556}, issn = {1089-8646}, mesh = {Alphaproteobacteria/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Firmicutes/isolation & purification ; Geologic Sediments/chemistry/*microbiology ; High-Throughput Nucleotide Sequencing ; Indian Ocean ; Metagenomics ; Oceans and Seas ; Proteobacteria/isolation & purification ; Sequence Analysis, DNA ; Wolbachia/genetics/*isolation & purification ; }, abstract = {The Bay of Bengal, located in the north-eastern part of the Indian Ocean is world's largest bay occupying an area of ~8,39,000 mile[2]. The variability in bacterial community structure and function in sediment ecosystems of the Bay of Bengal is examined by Illumina high-throughput metagenomic sequencing. Of five metataxonomics data sets presented, two (SD1 and SD2) were from stations close to the shore and three (SD4, SD5, and SD6) were from the deep-sea (~3000 m depth). Phylum Proteobacteria (90.27 to 92.52%) dominated the deep-sea samples, whereas phylum Firmicutes (65.35 to 90.98%) dominated the coastal samples. Comparative analysis showed that coastal and deep-sea sediments showed distinct microbial communities. Wolbachia species, belonging to class Alphaproteobacteria was the most dominant species in the deep-sea sediments. The gene functions of bacterial communities were predicted for deep-sea and coastal sediment ecosystems. The results indicated that deep-sea sediment bacterial communities were involved in metabolic activities like dehalogenation and sulphide oxidation.}, } @article {pmid31229107, year = {2019}, author = {Kim, HE and Lee, JJ and Lee, MJ and Kim, BS}, title = {Analysis of microbiome in raw chicken meat from butcher shops and packaged products in South Korea to detect the potential risk of foodborne illness.}, journal = {Food research international (Ottawa, Ont.)}, volume = {122}, number = {}, pages = {517-527}, doi = {10.1016/j.foodres.2019.05.032}, pmid = {31229107}, issn = {1873-7145}, mesh = {Animals ; Bacterial Load ; Brochothrix/isolation & purification/metabolism ; Carnobacterium/isolation & purification/metabolism ; *Chickens ; DNA, Bacterial/genetics/isolation & purification ; Food Contamination/analysis ; Food Microbiology ; Food Packaging ; Foodborne Diseases/*epidemiology/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Microbiota ; Moraxella/isolation & purification/metabolism ; Poultry/*microbiology ; Pseudomonas/isolation & purification/metabolism ; RNA, Ribosomal, 16S ; Republic of Korea/epidemiology ; Salmonella enterica/isolation & purification/metabolism ; Seasons ; Sequence Analysis, DNA ; Temperature ; }, abstract = {Chicken meat is one of the most widely consumed meats worldwide. The microbiota on the whole body of chicken is a potential source of foodborne pathogens that can be transmitted to humans during the preparation of raw meat. However, to date, there have been no studies comparing the microbiota of packaged chicken products and those of raw chicken carcasses from butcher shops, although such information could be useful for identifying sources of contamination in cases of food poisoning. We addressed this in the present study by analyzing the microbiota of 80 chicken meat samples collected from various butcher shops and processing plants in South Korea with the Illumina MiSeq system based on the 16S rRNA gene sequence. The bacterial amounts in chicken samples were estimated by quantitative real-time PCR. Although different microbial members were present in unpackaged meat from butcher shops as compared to those in packaged products from commercial sources, seasonal differences (sample obtained in January vs. July) in microbiota were more significant even in the packaged products from the same company. We also investigated the influence of contaminated foodborne pathogen on the indigenous microbiota (64 chicken samples) by artificially inoculated with Salmonella enterica serotype Virchow on chicken carcasses under various conditions, and carrying out 16S rRNA gene and whole metagenome sequencing. The amount of contaminated Salmonella in chicken meat samples was the highest and lowest in samples stored at 27 °C and 4 °C after washing, respectively. Additionally, the relative abundance of virulence genes was detected lower in samples stored at 4 °C after washing in both butcher shop and commercial samples. These results could be useful for reducing the risk of foodborne illness caused by cross-contamination during the preparation of chicken meat.}, } @article {pmid31229040, year = {2019}, author = {Ticinesi, A and Nouvenne, A and Meschi, T}, title = {Gut microbiome and kidney stone disease: not just an Oxalobacter story.}, journal = {Kidney international}, volume = {96}, number = {1}, pages = {25-27}, doi = {10.1016/j.kint.2019.03.020}, pmid = {31229040}, issn = {1523-1755}, mesh = {*Gastrointestinal Microbiome ; Homeostasis ; Humans ; *Kidney Calculi ; Oxalates ; Oxalobacter formigenes ; *Urinary Calculi ; }, abstract = {Intestinal regulation of oxalate absorption is a complex mechanism, not exclusively reliant on the oxalate-degrading anaerobe Oxalobacter formigenes. Using metagenomics, Miller et al. were able to describe a network of bacterial taxa co-occurring with Oxalobacter formigenes in fecal samples from non-stone forming controls and less represented in stone formers. These findings may help to illuminate why previous intervention studies with probiotics have failed to reduce the risk of hyperoxaluria, opening new possibilities for future research.}, } @article {pmid31226275, year = {2019}, author = {Assié, A and Samuel, BS}, title = {The Devil Is in the Microbial Genetic Details.}, journal = {Molecular cell}, volume = {74}, number = {6}, pages = {1108-1109}, doi = {10.1016/j.molcel.2019.06.003}, pmid = {31226275}, issn = {1097-4164}, mesh = {*Gastrointestinal Microbiome ; Genetics, Microbial ; Humans ; }, abstract = {The work of Zeevi et al. (2019) in a recent issue of Nature shows that variations in gene content and organization between different strains of the same microbial species are widespread in the human gut microbiota and could be linked to many measures of health.}, } @article {pmid31222023, year = {2019}, author = {Morton, JT and Marotz, C and Washburne, A and Silverman, J and Zaramela, LS and Edlund, A and Zengler, K and Knight, R}, title = {Establishing microbial composition measurement standards with reference frames.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {2719}, pmid = {31222023}, issn = {2041-1723}, support = {GRFP DGE-1144086//National Science Foundation (NSF)/International ; 1F31DE028478//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/International ; 20175015//Janssen Pharmaceuticals (Janssen Pharmaceuticals, Inc.)/International ; G-2017-9838//Alfred P. Sloan Foundation/International ; DBI-1565057//National Science Foundation (NSF)/International ; P30 MH062512/MH/NIMH NIH HHS/United States ; F31 DE028478/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/genetics/*isolation & purification ; Bacterial Load/standards ; Computer Simulation/standards ; *Data Analysis ; Datasets as Topic ; Dermatitis, Atopic/microbiology ; Feasibility Studies ; Healthy Volunteers ; High-Throughput Nucleotide Sequencing/statistics & numerical data ; Humans ; Metagenome/genetics ; Microbiota/*genetics ; *Models, Biological ; RNA, Ribosomal, 16S/isolation & purification ; Reference Standards ; Saliva/microbiology ; Soil Microbiology ; }, abstract = {Differential abundance analysis is controversial throughout microbiome research. Gold standard approaches require laborious measurements of total microbial load, or absolute number of microorganisms, to accurately determine taxonomic shifts. Therefore, most studies rely on relative abundance data. Here, we demonstrate common pitfalls in comparing relative abundance across samples and identify two solutions that reveal microbial changes without the need to estimate total microbial load. We define the notion of "reference frames", which provide deep intuition about the compositional nature of microbiome data. In an oral time series experiment, reference frames alleviate false positives and produce consistent results on both raw and cell-count normalized data. Furthermore, reference frames identify consistent, differentially abundant microbes previously undetected in two independent published datasets from subjects with atopic dermatitis. These methods allow reassessment of published relative abundance data to reveal reproducible microbial changes from standard sequencing output without the need for new assays.}, } @article {pmid31221992, year = {2019}, author = {Villasante, A and Ramírez, C and Rodríguez, H and Catalán, N and Díaz, O and Rojas, R and Opazo, R and Romero, J}, title = {In-depth analysis of swim bladder-associated microbiota in rainbow trout (Oncorhynchus mykiss).}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {8974}, pmid = {31221992}, issn = {2045-2322}, mesh = {Air Sacs/*microbiology ; Animals ; Computational Biology/methods ; Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; *Microbiota ; *Oncorhynchus mykiss ; Symbiosis ; }, abstract = {Our knowledge regarding microbiota associated with the swim bladder of physostomous, fish with the swim bladder connected to the esophagus via the pneumatic duct, remains largely unknown. The goal of this study was to conduct the first in-depth characterization of the swim bladder-associated microbiota using high-throughput sequencing of the V4 region of the 16 S rRNA gene in rainbow trout (Oncorhynchus mykiss). We observed major differences in bacterial communities composition between swim bladder-associated microbiota and distal intestine digesta microbiota in fish. Whilst bacteria genera, such as Cohnella, Lactococcus and Mycoplasma were more abundant in swim bladder-associated microbiota, Citrobacter, Rhodobacter and Clavibacter were more abundant in distal intestine digesta microbiota. The presumptive metabolic function analysis (PICRUSt) revealed several metabolic pathways to be more abundant in the swim bladder-associated microbiota, including metabolism of carbohydrates, nucleotides and lipoic acid as well as oxidative phosphorylation, cell growth, translation, replication and repair. Distal intestine digesta microbiota showed greater abundance of nitrogen metabolism, amino acid metabolism, biosynthesis of unsaturated fatty acids and bacterial secretion system. We demonstrated swim bladder harbors a unique microbiota, which composition and metabolic function differ from microbiota associated with the gut in fish.}, } @article {pmid31221587, year = {2019}, author = {Aho, VTE and Pereira, PAB and Voutilainen, S and Paulin, L and Pekkonen, E and Auvinen, P and Scheperjans, F}, title = {Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression.}, journal = {EBioMedicine}, volume = {44}, number = {}, pages = {691-707}, pmid = {31221587}, issn = {2352-3964}, mesh = {Aged ; Biodiversity ; Case-Control Studies ; Disease Progression ; *Disease Susceptibility ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics/methods ; Middle Aged ; Parkinson Disease/*etiology/*metabolism/pathology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Several publications have described differences in cross-sectional comparisons of gut microbiota between patients with Parkinson's disease and control subjects, with considerable variability of the reported differentially abundant taxa. The temporal stability of such microbiota alterations and their relationship to disease progression have not been previously studied with a high-throughput sequencing based approach.

METHODS: We collected clinical data and stool samples from 64 Parkinson's patients and 64 control subjects twice, on average 2·25 years apart. Disease progression was evaluated based on changes in Unified Parkinson's Disease Rating Scale and Levodopa Equivalent Dose, and microbiota were characterized with 16S rRNA gene amplicon sequencing.

FINDINGS: We compared patients to controls, and patients with stable disease to those with faster progression. There were significant differences between microbial communities of patients and controls when corrected for confounders, but not between timepoints. Specific bacterial taxa that differed between patients and controls at both timepoints included several previously reported ones, such as Roseburia, Prevotella and Bifidobacterium. In progression comparisons, differentially abundant taxa were inconsistent across methods and timepoints, but there was some support for a different distribution of enterotypes and a decreased abundance of Prevotella in faster-progressing patients.

INTERPRETATION: The previously detected gut microbiota differences between Parkinson's patients and controls persisted after 2 years. While we found some evidence for a connection between microbiota and disease progression, a longer follow-up period is required to confirm these findings.}, } @article {pmid31220587, year = {2020}, author = {Trifi, H and Najjari, A and Achouak, W and Barakat, M and Ghedira, K and Mrad, F and Saidi, M and Sghaier, H}, title = {Metataxonomics of Tunisian phosphogypsum based on five bioinformatics pipelines: Insights for bioremediation.}, journal = {Genomics}, volume = {112}, number = {1}, pages = {981-989}, doi = {10.1016/j.ygeno.2019.06.014}, pmid = {31220587}, issn = {1089-8646}, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; Biodegradation, Environmental ; *Calcium Sulfate/chemistry/metabolism ; Computational Biology ; High-Throughput Nucleotide Sequencing ; Microbiota ; *Phosphorus/chemistry/metabolism ; Sequence Analysis, DNA ; Software ; Tunisia ; }, abstract = {Phosphogypsum (PG) is an acidic by-product from the phosphate fertilizer industry and it is characterized by a low nutrient availability and the presence of radionuclides and heavy metals which pose a serious problem in its management. Here, we have applied Illumina MiSeq sequencing technology and five bioinformatics pipelines to explore the phylogenetic communities in Tunisian PG. Taking One Codex as a reference method, we present the results of 16S-rDNA-gene-based metataxonomics abundances with four other alternative bioinformatics pipelines (MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST), mothur, MICrobial Community Analysis (MICCA) and Quantitative Insights into Microbial Ecology (QIIME)), when analyzing the Tunisian PG. Importantly, based on 16S rDNA datasets, the functional capabilities of microbial communities of PG were deciphered. They suggested the presence of PG autochthonous bacteria valorizable into (1) removal of radioactive elements and toxic heavy metals, (2) promotion of plant growth, (3) oxidation and (4) reduction of sulfate. These bacteria can be explored further for applications in the bioremediation of by-products, like PG, by different processes.}, } @article {pmid31219825, year = {2019}, author = {Knudsen, C and Neyrinck, AM and Lanthier, N and Delzenne, NM}, title = {Microbiota and nonalcoholic fatty liver disease: promising prospects for clinical interventions?.}, journal = {Current opinion in clinical nutrition and metabolic care}, volume = {22}, number = {5}, pages = {393-400}, doi = {10.1097/MCO.0000000000000584}, pmid = {31219825}, issn = {1473-6519}, mesh = {Animals ; Biomedical Research ; Disease Progression ; Gastrointestinal Microbiome/*physiology ; Humans ; Metabolomics ; Metagenomics ; Mice ; *Non-alcoholic Fatty Liver Disease/physiopathology/therapy ; Rats ; }, abstract = {PURPOSE OF REVIEW: Nonalcoholic fatty liver disease (NAFLD) is becoming the most important cause of chronic liver disease in Western countries but no pharmacological therapy is currently available. Growing evidence suggests that the microbiota plays a role in the occurrence and evolution of this disease, namely through the production of bioactive metabolites.

RECENT FINDINGS: Omics technologies (metagenomic, metabolomic, and phenomic data) allow providing a robust prediction of steatosis. More than just correlations, causative effects of certain bacterial metabolites have been evidenced in vitro and in rodent models. Butyrate has been shown to be a potent metabolic and inflammatory modulator in the liver. Several aromatic amino-acids such as phenylacetic acid, imidazole propionate, and 3-(4-hydroxyphenyl)lactate have been identified as potential inducers of steatosis and hepatic inflammation, whereas indolic compounds (indole and indole-3-acetate) seem to preserve liver integrity. Current clinical trials aim at evaluating the efficacy of novel approaches (functional foods, prebiotic and probiotics, and fecal microbial transplants).

SUMMARY: The microbiota brings new hopes in the management of nonalcoholic fatty liver diseases, including nonalcoholic steatohepatitis. Adequate intervention studies in targeted patients are needed to unravel the relevance of such approaches in the management of those liver diseases.}, } @article {pmid31216991, year = {2019}, author = {Lo, C and Marculescu, R}, title = {MetaNN: accurate classification of host phenotypes from metagenomic data using neural networks.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 12}, pages = {314}, pmid = {31216991}, issn = {1471-2105}, mesh = {*Algorithms ; Area Under Curve ; Databases, Genetic ; Humans ; Machine Learning ; Metagenomics/*methods ; Microbiota/genetics ; Models, Theoretical ; *Neural Networks, Computer ; Phenotype ; ROC Curve ; Support Vector Machine ; }, abstract = {BACKGROUND: Microbiome profiles in the human body and environment niches have become publicly available due to recent advances in high-throughput sequencing technologies. Indeed, recent studies have already identified different microbiome profiles in healthy and sick individuals for a variety of diseases; this suggests that the microbiome profile can be used as a diagnostic tool in identifying the disease states of an individual. However, the high-dimensional nature of metagenomic data poses a significant challenge to existing machine learning models. Consequently, to enable personalized treatments, an efficient framework that can accurately and robustly differentiate between healthy and sick microbiome profiles is needed.

RESULTS: In this paper, we propose MetaNN (i.e., classification of host phenotypes from Metagenomic data using Neural Networks), a neural network framework which utilizes a new data augmentation technique to mitigate the effects of data over-fitting.

CONCLUSIONS: We show that MetaNN outperforms existing state-of-the-art models in terms of classification accuracy for both synthetic and real metagenomic data. These results pave the way towards developing personalized treatments for microbiome related diseases.}, } @article {pmid31216122, year = {2019}, author = {Gill, T and Brooks, SR and Rosenbaum, JT and Asquith, M and Colbert, RA}, title = {Novel Inter-omic Analysis Reveals Relationships Between Diverse Gut Microbiota and Host Immune Dysregulation in HLA-B27-Induced Experimental Spondyloarthritis.}, journal = {Arthritis & rheumatology (Hoboken, N.J.)}, volume = {71}, number = {11}, pages = {1849-1857}, pmid = {31216122}, issn = {2326-5205}, support = {//Rheumatology Research Foundation/International ; R01 EY029663/EY/NEI NIH HHS/United States ; //Spondylitis Association of America/International ; ZIA AR041184/ImNIH/Intramural NIH HHS/United States ; Z01-AR-041184/AR/NIAMS NIH HHS/United States ; R01 EY029266/EY/NEI NIH HHS/United States ; //Research to Prevent Blindness/International ; Z01 AR041118/AR/NIAMS NIH HHS/United States ; }, mesh = {Akkermansia ; Animals ; Arthritis, Experimental/*immunology/*microbiology ; Clostridiales ; Cytokines/*immunology ; Dysbiosis/immunology/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Gene Expression Profiling ; HLA-B27 Antigen/genetics/*immunology ; Humans ; Interferon-gamma/immunology ; Interleukin-1/immunology ; Interleukin-17/immunology ; Interleukin-23/immunology ; Male ; Prevotella ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Inbred F344 ; Rats, Inbred Lew ; Rats, Transgenic ; Spondylarthropathies/*immunology/*microbiology ; Tumor Necrosis Factor-alpha/immunology ; Verrucomicrobia ; }, abstract = {OBJECTIVE: To define inflammation-related host-microbe interactions in experimental spondyloarthritis (SpA) using novel inter-omic approaches.

METHODS: The relative frequency of gut microbes was determined by 16S ribosomal RNA (rRNA) gene sequencing, and gene expression using RNA-Seq of host tissue. HLA-B27/human β2 -microglobulin-transgenic (HLA-B27-transgenic) and wild-type rats from dark agouti, Lewis, and Fischer backgrounds were used. Inter-omic analyses using Cytoscape were employed to identify relevant relationships. PICRUSt was used to predict microbial functions based on known metagenomic profiles.

RESULTS: Inter-omic analysis revealed several gut microbes that were strongly associated with dysregulated cytokines driving inflammatory response pathways, such as interleukin-17 (IL-17), IL-23, IL-17, IL-1, interferon-γ (IFNγ), and tumor necrosis factor (TNF). Many microbes were uniquely associated with inflammation in Lewis or Fischer rats, and one was relevant on both backgrounds. Several microbes that were strongly correlated with immune dysregulation were not differentially abundant in HLA-B27-transgenic compared to wild-type controls. A multi-omic network analysis revealed non-overlapping clusters of microbes in Lewis and Fischer rats that were strongly linked to overlapping dysregulated immune/inflammatory genes. Prevotella, Clostridiales, and Blautia were important in Lewis rats, while Akkermansia muciniphila and members of the Lachnospiraceae family dominated in Fischer rats. Inflammation-associated metabolic pathway perturbation (e.g., butanoate, propanoate, lipopolysaccharide, and steroid biosynthesis) was also predicted from both backgrounds.

CONCLUSION: Inter-omic and network analysis of gut microbes and the host immune response in experimental SpA provides an unprecedented view of organisms strongly linked to dysregulated IL-23, IL-17, IL-1, IFNγ, and TNF. Functional similarities between these organisms may explain why animals of different genetic backgrounds exhibit common patterns of immune dysregulation, possibly through perturbation of similar metabolic pathways. These results highlight the power of linking analyses of gut microbiota with the host immune response to gain insights into the role of dysbiotic microbes in SpA beyond taxonomic profiling.}, } @article {pmid31215766, year = {2019}, author = {Sheng, Y and Cong, J and Lu, H and Yang, L and Liu, Q and Li, D and Zhang, Y}, title = {Broad-leaved forest types affect soil fungal community structure and soil organic carbon contents.}, journal = {MicrobiologyOpen}, volume = {8}, number = {10}, pages = {e874}, pmid = {31215766}, issn = {2045-8827}, mesh = {China ; Forests ; Fungi/classification/genetics ; Metabolic Networks and Pathways/genetics ; Metagenomics ; *Mycobiome ; Organic Chemicals/*analysis ; Plants/*classification ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Evergreen broad-leaved (EBF) and deciduous broad-leaved (DBF) forests are two important vegetation types in terrestrial ecosystems that play key roles in sustainable biodiversity and global carbon (C) cycling. However, little is known about their associated soil fungal community and the potential metabolic activities involved in biogeochemical processes. In this study, soil samples were collected from EBF and DBF in Shennongjia Mountain, China, and soil fungal community structure and functional gene diversity analyzed based on combined Illumina MiSeq sequencing with GeoChip technologies. The results showed that soil fungal species richness (p = 0.079) and fungal functional gene diversity (p < 0.01) were higher in DBF than EBF. Zygomycota was the most dominant phylum in both broad-leaved forests, and the most dominant genera found in each forest varied (Umbelopsis dominated in DBF, whereas Mortierella dominated in EBF). A total of 4, 439 soil fungi associated functional gene probes involved in C and nitrogen (N) cycling were detected. Interestingly, the relative abundance of functional genes related to labile C degradation (e.g., starch, pectin, hemicellulose, and cellulose) was significantly higher (p < 0.05) in DBF than EBF, and the functional gene relative abundance involved in C cycling was significantly negatively correlated with soil labile organic C (r = -0.720, p = 0.002). In conclusion, the soil fungal community structure and potential metabolic activity showed marked divergence in different broad-leaved forest types, and the higher relative abundance of functional genes involved in C cycling in DBF may be caused by release of loss of organic C in the soil.}, } @article {pmid31213523, year = {2019}, author = {Shi, Z and Yin, H and Van Nostrand, JD and Voordeckers, JW and Tu, Q and Deng, Y and Yuan, M and Zhou, A and Zhang, P and Xiao, N and Ning, D and He, Z and Wu, L and Zhou, J}, title = {Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, pmid = {31213523}, issn = {2379-5077}, abstract = {While functional gene arrays (FGAs) have greatly expanded our understanding of complex microbial systems, specificity, sensitivity, and quantitation challenges remain. We developed a new generation of FGA, GeoChip 5.0, using the Agilent platform. Two formats were created, a smaller format (GeoChip 5.0S), primarily covering carbon-, nitrogen-, sulfur-, and phosphorus-cycling genes and others providing ecological services, and a larger format (GeoChip 5.0M) containing the functional categories involved in biogeochemical cycling of C, N, S, and P and various metals, stress response, microbial defense, electron transport, plant growth promotion, virulence, gyrB, and fungus-, protozoan-, and virus-specific genes. GeoChip 5.0M contains 161,961 oligonucleotide probes covering >365,000 genes of 1,447 gene families from broad, functionally divergent taxonomic groups, including bacteria (2,721 genera), archaea (101 genera), fungi (297 genera), protists (219 genera), and viruses (167 genera), mainly phages. Computational and experimental evaluation indicated that designed probes were highly specific and could detect as little as 0.05 ng of pure culture DNAs within a background of 1 μg community DNA (equivalent to 0.005% of the population). Additionally, strong quantitative linear relationships were observed between signal intensity and amount of pure genomic (∼99% of probes detected; r > 0.9) or soil (∼97%; r > 0.9) DNAs. Application of the GeoChip to a contaminated groundwater microbial community indicated that environmental contaminants (primarily heavy metals) had significant impacts on the biodiversity of the communities. This is the most comprehensive FGA to date, capable of directly linking microbial genes/populations to ecosystem functions.IMPORTANCE The rapid development of metagenomic technologies, including microarrays, over the past decade has greatly expanded our understanding of complex microbial systems. However, because of the ever-expanding number of novel microbial sequences discovered each year, developing a microarray that is representative of real microbial communities, is specific and sensitive, and provides quantitative information remains a challenge. The newly developed GeoChip 5.0 is the most comprehensive microarray available to date for examining the functional capabilities of microbial communities important to biogeochemistry, ecology, environmental sciences, and human health. The GeoChip 5 is highly specific, sensitive, and quantitative based on both computational and experimental assays. Use of the array on a contaminated groundwater sample provided novel insights on the impacts of environmental contaminants on groundwater microbial communities.}, } @article {pmid31212172, year = {2019}, author = {Tapadia-Maheshwari, S and Pore, S and Engineer, A and Shetty, D and Dagar, SS and Dhakephalkar, PK}, title = {Illustration of the microbial community selected by optimized process and nutritional parameters resulting in enhanced biomethanation of rice straw without thermo-chemical pretreatment.}, journal = {Bioresource technology}, volume = {289}, number = {}, pages = {121639}, doi = {10.1016/j.biortech.2019.121639}, pmid = {31212172}, issn = {1873-2976}, mesh = {Anaerobiosis ; Animals ; Biofuels ; Bioreactors ; Cattle ; Methane ; *Microbiota ; *Oryza ; }, abstract = {Effects of different process and nutritional parameters on microbial community structure and function were investigated to enhance the biomethanation of rice straw without any thermochemical pre-treatment. The study was performed in a mesophilic anaerobic digester with cattle dung slurry as inoculum. The highest methane yield of 274 ml g[-1] volatile solids was obtained from particulate rice straw (1 mm size, 7.5% solids loading rate) at 37 °C, pH-7, when supplemented with urea (carbon: nitrogen ratio, 25:1) and zinc as trace element (100 µM) at 21 days hydraulic retention time. The optimization of conditions selected Clostridium, Bacteroides, and Ruminococcus as dominant hydrolytic bacteria and Methanosarcina as the methanogen. Analysis of metagenome and metatranscriptome revealed wide array of bacterial lignocellulolytic enzymes that efficiently hydrolyzed the rice straw. The methane yield was >80% of the theoretical yield, making this green process a sustainable choice for efficient extraction of energy from rice straw.}, } @article {pmid31211676, year = {2019}, author = {Langelier, C and Graves, M and Kalantar, K and Caldera, S and Durrant, R and Fisher, M and Backman, R and Tanner, W and DeRisi, JL and Leung, DT}, title = {Microbiome and Antimicrobial Resistance Gene Dynamics in International Travelers.}, journal = {Emerging infectious diseases}, volume = {25}, number = {7}, pages = {1380-1383}, pmid = {31211676}, issn = {1080-6059}, support = {K23 HL138461/HL/NHLBI NIH HHS/United States ; }, mesh = {Biodiversity ; Communicable Diseases/*epidemiology/*microbiology ; Computational Biology/methods ; Databases, Genetic ; *Drug Resistance, Microbial ; Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Metagenomics/methods ; *Microbiota/drug effects/genetics ; *Travel ; *Travel-Related Illness ; }, abstract = {We used metagenomic next-generation sequencing to longitudinally assess the gut microbiota and antimicrobial resistomes of international travelers to clarify global exchange of resistant organisms. Travel resulted in an increase in antimicrobial resistance genes and a greater proportion of Escherichia species within gut microbial communities without impacting diversity.}, } @article {pmid31207997, year = {2019}, author = {Garrido-Sanz, D and Redondo-Nieto, M and Guirado, M and Pindado Jiménez, O and Millán, R and Martin, M and Rivilla, R}, title = {Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil.}, journal = {Genes}, volume = {10}, number = {6}, pages = {}, pmid = {31207997}, issn = {2073-4425}, mesh = {*Biodegradation, Environmental ; Biodiversity ; Chryseobacterium/classification/genetics ; Metagenome/*genetics ; Microbiota/*genetics ; Petroleum/*metabolism ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/metabolism/toxicity ; Pseudomonas/classification/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Soil Pollutants/metabolism/toxicity ; }, abstract = {Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.}, } @article {pmid31207407, year = {2019}, author = {Parente, E and De Filippis, F and Ercolini, D and Ricciardi, A and Zotta, T}, title = {Advancing integration of data on food microbiome studies: FoodMicrobionet 3.1, a major upgrade of the FoodMicrobionet database.}, journal = {International journal of food microbiology}, volume = {305}, number = {}, pages = {108249}, doi = {10.1016/j.ijfoodmicro.2019.108249}, pmid = {31207407}, issn = {1879-3460}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Databases, Factual ; *Food Microbiology ; Meat/microbiology ; *Microbiota ; Software ; }, abstract = {We present a new version of FoodMicrobionet, a database for the exploration of food bacterial communities. The database, available as an app built with the Shiny package of R, includes data from 44 studies and 2234 samples (food or food environment), covering dairy, meat, fruit and vegetables, cereal based and ready-to-eat foods. The interactive interface allows exploration of data, access to external resources (on line versions of the studies, sequence data on SRA, taxonomic databases), filtering samples on the basis of a number of criteria, aggregation of samples and bacterial taxa and export of data in a variety of formats. FoodMicrobionet is the largest collection of data on food bacterial communities and, due to the structure of sample metadata, largely derived from the European Food Safety Agency FoodEx2 classification, makes comparison and re-analysis of data from published and unpublished studies easy. Data exported from FoodMicrobionet can be readily used for graphical and statistical meta-analyses using open-source software (Gephi, Cytoscape, CoNet, and R packages and apps, such as phyloseq and Shiny-Phyloseq) thus providing scientists, risk assessors and industry with a wealth of information on the structure of food biomes.}, } @article {pmid31207357, year = {2019}, author = {Guss, JD and Taylor, E and Rouse, Z and Roubert, S and Higgins, CH and Thomas, CJ and Baker, SP and Vashishth, D and Donnelly, E and Shea, MK and Booth, SL and Bicalho, RC and Hernandez, CJ}, title = {The microbial metagenome and bone tissue composition in mice with microbiome-induced reductions in bone strength.}, journal = {Bone}, volume = {127}, number = {}, pages = {146-154}, pmid = {31207357}, issn = {1873-2763}, support = {R21 AR068061/AR/NIAMS NIH HHS/United States ; R21 AR071534/AR/NIAMS NIH HHS/United States ; R21 AR073454/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; Bone and Bones/*microbiology/*physiology ; Gastrointestinal Microbiome ; *Metagenome ; Mice, Inbred C57BL ; Microbiota/*genetics ; Spectrum Analysis, Raman ; Vitamin K/metabolism ; }, abstract = {The genetic components of microbial species that inhabit the body are known collectively as the microbiome. Modifications to the microbiome have been implicated in disease processes throughout the body and have recently been shown to influence bone. Prior work has associated changes in the microbial taxonomy (phyla, class, species, etc.) in the gut with bone phenotypes but has provided limited information regarding mechanisms. With the goal of achieving a more mechanistic understanding of the effects of the microbiome on bone, we perform a metagenomic analysis of the gut microbiome that provides information on the functional capacity of the microbes (all microbial genes present) rather than only characterizing the microbial taxa. Male C57Bl/6 mice were subjected to disruption of the gut microbiota (ΔMicrobiome) using oral antibiotics (from 4 to 16 weeks of age) or remained untreated (n = 6-7/group). Disruption of the gut microbiome in this manner has been shown to lead to reductions in tissue mechanical properties and whole bone strength in adulthood with only minor changes in bone geometry and density. ΔMicrobiome led to modifications in the abundance of microbial genes responsible for the synthesis of the bacterial cell wall and capsule; bacterially synthesized carbohydrates; and bacterially synthesized vitamins (B and K) (p < 0.01). Follow up analysis focused on vitamin K, a factor that has previously been associated with bone health. The vitamin K content of the cecum, liver and kidneys was primarily microbe-derived forms of vitamin K (menaquinones) and was decreased by 32-66% in ∆Microbiome mice compared to untreated animals (p < 0.01). Bone mineral crystallinity determined using Raman spectroscopy was decreased in ∆Microbiome mice (p = 0.01). This study illustrates the use of metagenomic analysis to link the microbiome to bone phenotypes and provides preliminary findings implicating microbially synthesized vitamin-K as a regulator of bone matrix quality.}, } @article {pmid31202277, year = {2019}, author = {Soverini, M and Turroni, S and Biagi, E and Brigidi, P and Candela, M and Rampelli, S}, title = {HumanMycobiomeScan: a new bioinformatics tool for the characterization of the fungal fraction in metagenomic samples.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {496}, pmid = {31202277}, issn = {1471-2164}, mesh = {Animals ; Fungi/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Mycobiome/*genetics ; *Software ; }, abstract = {BACKGROUND: Modern metagenomic analysis of complex microbial communities produces large amounts of sequence data containing information on the microbiome in terms of bacterial, archaeal, viral and eukaryotic composition. The bioinformatics tools available are mainly devoted to profiling the bacterial and viral fractions and only a few software packages consider fungi. As the human fungal microbiome (human mycobiome) can play an important role in the onset and progression of diseases, a comprehensive description of host-microbiota interactions cannot ignore this component.

RESULTS: HumanMycobiomeScan is a bioinformatics tool for the taxonomic profiling of the mycobiome directly from raw data of next-generation sequencing. The tool uses hierarchical databases of fungi in order to unambiguously assign reads to fungal species more accurately and > 10,000 times faster than other comparable approaches. HumanMycobiomeScan was validated using in silico generated synthetic communities and then applied to metagenomic data, to characterize the intestinal fungal components in subjects adhering to different subsistence strategies.

CONCLUSIONS: Although blind to unknown species, HumanMycobiomeScan allows the characterization of the fungal fraction of complex microbial ecosystems with good performance in terms of sample denoising from reads belonging to other microorganisms. HumanMycobiomeScan is most appropriate for well-studied microbiomes, for which most of the fungal species have been fully sequenced. This released version is functionally implemented to work with human-associated microbiota samples. In combination with other microbial profiling tools, HumanMycobiomeScan is a frugal and efficient tool for comprehensive characterization of microbial ecosystems through shotgun metagenomics sequencing.}, } @article {pmid31201356, year = {2019}, author = {Szafrański, SP and Kilian, M and Yang, I and Bei der Wieden, G and Winkel, A and Hegermann, J and Stiesch, M}, title = {Diversity patterns of bacteriophages infecting Aggregatibacter and Haemophilus species across clades and niches.}, journal = {The ISME journal}, volume = {13}, number = {10}, pages = {2500-2522}, pmid = {31201356}, issn = {1751-7370}, mesh = {Aggregatibacter/classification/*virology ; Bacteriophages/classification/genetics/isolation & purification/*physiology ; Base Composition ; Biodiversity ; Genome, Viral ; Genomics ; Haemophilus/classification/*virology ; Host Specificity ; Humans ; Lysogeny ; Metagenome ; Phylogeny ; Prophages/classification/genetics/isolation & purification/physiology ; }, abstract = {Aggregatibacter and Haemophilus species are relevant human commensals and opportunistic pathogens. Consequently, their bacteriophages may have significant impact on human microbial ecology and pathologies. Our aim was to reveal the prevalence and diversity of bacteriophages infecting Aggregatibacter and Haemophilus species that colonize the human body. Genome mining with comparative genomics, screening of clinical isolates, and profiling of metagenomes allowed characterization of 346 phages grouped in 52 clusters and 18 superclusters. Less than 10% of the identified phage clusters were represented by previously characterized phages. Prophage diversity patterns varied significantly for different phage types, host clades, and environmental niches. A more diverse phage community lysogenizes Haemophilus influenzae and Haemophilus parainfluenzae strains than Aggregatibacter actinomycetemcomitans and "Haemophilus ducreyi". Co-infections occurred more often in "H. ducreyi". Phages from Aggregatibacter actinomycetemcomitans preferably lysogenized strains of specific serotype. Prophage patterns shared by subspecies clades of different bacterial species suggest similar ecoevolutionary drivers. Changes in frequencies of DNA uptake signal sequences and guanine-cytosine content reflect phage-host long-term coevolution. Aggregatibacter and Haemophilus phages were prevalent at multiple oral sites. Together, these findings should help exploring the ecoevolutionary forces shaping virus-host interactions in the human microbiome. Putative lytic phages, especially phiKZ-like, may provide new therapeutic options.}, } @article {pmid31199864, year = {2019}, author = {Luiken, REC and Van Gompel, L and Munk, P and Sarrazin, S and Joosten, P and Dorado-García, A and Borup Hansen, R and Knudsen, BE and Bossers, A and Wagenaar, JA and Aarestrup, FM and Dewulf, J and Mevius, DJ and Heederik, DJJ and Smit, LAM and Schmitt, H and , }, title = {Associations between antimicrobial use and the faecal resistome on broiler farms from nine European countries.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {9}, pages = {2596-2604}, pmid = {31199864}, issn = {1460-2091}, mesh = {Animals ; Anti-Infective Agents/pharmacology/*therapeutic use ; Bacteria/*drug effects/genetics ; Chickens/*microbiology ; Computational Biology ; Cross-Sectional Studies ; Drug Resistance, Bacterial/*drug effects ; Europe ; Farms ; Feces/microbiology ; *Metagenomics ; Microbiota/*drug effects/genetics ; Risk Factors ; }, abstract = {OBJECTIVES: To determine associations between farm- and flock-level antimicrobial usage (AMU), farm biosecurity status and the abundance of faecal antimicrobial resistance genes (ARGs) on broiler farms.

METHODS: In the cross-sectional pan-European EFFORT study, conventional broiler farms were visited and faeces, AMU information and biosecurity records were collected. The resistomes of pooled faecal samples were determined by metagenomic analysis for 176 farms. A meta-analysis approach was used to relate total and class-specific ARGs (expressed as fragments per kb reference per million bacterial fragments, FPKM) to AMU (treatment incidence per DDD, TIDDDvet) per country and subsequently across all countries. In a similar way, the association between biosecurity status (Biocheck.UGent) and the resistome was explored.

RESULTS: Sixty-six (38%) flocks did not report group treatments but showed a similar resistome composition and roughly similar ARG levels to antimicrobial-treated flocks. Nevertheless, we found significant positive associations between β-lactam, tetracycline, macrolide and lincosamide, trimethoprim and aminoglycoside antimicrobial flock treatments and ARG clusters conferring resistance to the same class. Similar associations were found with purchased products. In gene-level analysis for β-lactams and macrolides, lincosamides and streptogramins, a significant positive association was found with the most abundant gene clusters blaTEM and erm(B). Little evidence was found for associations with biosecurity.

CONCLUSIONS: The faecal microbiome in European broilers contains a high diversity of ARGs, even in the absence of current antimicrobial selection pressure. Despite this, the relative abundance of genes and the composition of the resistome is positively related to AMU in European broiler farms for several antimicrobial classes.}, } @article {pmid31199220, year = {2019}, author = {Karabudak, S and Ari, O and Durmaz, B and Dal, T and Basyigit, T and Kalcioglu, MT and Durmaz, R}, title = {Analysis of the effect of smoking on the buccal microbiome using next-generation sequencing technology.}, journal = {Journal of medical microbiology}, volume = {68}, number = {8}, pages = {1148-1158}, doi = {10.1099/jmm.0.001003}, pmid = {31199220}, issn = {1473-5644}, mesh = {Adult ; Bacteria/classification/genetics ; Female ; Genome, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Microbiota/genetics ; Middle Aged ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Smoking ; Young Adult ; }, abstract = {PURPOSE: This study aimed to investigate the effect of smoking on the buccal microbiome and to analyse the descriptive ability of each of the seven hypervariable regions in their 16S rRNA genes.

METHODOLOGY: Microbiome compositions of 40 buccal swab samples collected from smokers (n =20) and non-smokers (n =20) were determined using 16S rRNA sequencing. Seven different 16S rRNA hypervariable regions (V2, V3, V4, V6-7, V8 and V9) in each sample were amplified using the Ion Torrent 16S Metagenomics kit and were sequenced on the Ion S5 instrument.

RESULTS: Seven hypervariable regions in the 16S rRNA gene were successfully sequenced for all samples tested. The data obtained with the V2 region was found to be informative but the consensus data generated according to a number of operational taxonomic unit reads gathered from all seven hypervariable regions gave the most accurate result. At the phylum level, no statistically significant difference was found between smokers and non-smokers whereas relative abundances of Veillonella atypica, Streptococcus australis, Prevotella melaninogenica, Prevotella salivae and Rothia mucilaginosa showed significant increases in the smoker group (P-adj=0.05). Alpha diversity results did not show a significant difference between the two groups; however, beta diversity analysis indicated that samples of smoker and non-smoker groups had a tendency to be clustered within themselves.

CONCLUSION: The results of the current study indicate that smoking is a factor influencing buccal microbiome composition. In addition, sequencing of all seven hypervariable regions yielded more accurate results than those with any of the single variable regions.}, } @article {pmid31197613, year = {2019}, author = {Debédat, J and Clément, K and Aron-Wisnewsky, J}, title = {Gut Microbiota Dysbiosis in Human Obesity: Impact of Bariatric Surgery.}, journal = {Current obesity reports}, volume = {8}, number = {3}, pages = {229-242}, pmid = {31197613}, issn = {2162-4968}, mesh = {Animals ; Bacteria ; Bariatric Surgery/*methods ; Diabetes Mellitus, Type 2/complications ; Dysbiosis/*complications/*therapy ; Gastrectomy ; Gastrointestinal Microbiome/*physiology ; Humans ; Inflammation ; Obesity/*complications/*surgery ; Obesity, Morbid/complications/surgery ; Postoperative Period ; Treatment Outcome ; Weight Gain ; Weight Loss ; }, abstract = {PURPOSE OF REVIEW: In this review, we summarize what is currently described in terms of gut microbiota (GM) dysbiosis modification post-bariatric surgery (BS) and their link with BS-induced clinical improvement. We also discuss how the major inter-individual variability in terms of GM changes could impact the clinical improvements seen in patients.

RECENT FINDINGS: The persisting increase in severe obesity prevalence has led to the subsequent burst in BS number. Indeed, it is to date the best treatment option to induce major and sustainable weight loss and metabolic improvement in these patients. During obesity, the gut microbiota displays distinctive features such as low microbial gene richness and compositional and functional alterations (termed dysbiosis) which have been associated with low-grade inflammation, increased body weight and fat mass, as well as type-2 diabetes. Interestingly, GM changes post-BS is currently being proposed as one the many mechanism explaining BS beneficial clinical outcomes. BS enables partial rescue of GM dysbiosis observed during obesity. Some of the GM characteristics modified post-BS (composition in terms of bacteria and functions) are linked to BS beneficial outcomes such as weight loss or metabolic improvements. Nevertheless, the changes in GM post-BS display major variability from one patient to the other. As such, further large sample size studies associated with GM transfer studies in animals are still needed to completely decipher the role of GM in the clinical improvements observed post-surgery.}, } @article {pmid31197506, year = {2020}, author = {Chi, C and Xue, Y and Liu, R and Wang, Y and Lv, N and Zeng, H and Buys, N and Zhu, B and Sun, J and Yin, C}, title = {Effects of a formula with a probiotic Bifidobacterium lactis Supplement on the gut microbiota of low birth weight infants.}, journal = {European journal of nutrition}, volume = {59}, number = {4}, pages = {1493-1503}, doi = {10.1007/s00394-019-02006-4}, pmid = {31197506}, issn = {1436-6215}, support = {S160003//Beijing Natural Science Foundation/ ; }, mesh = {Bifidobacterium animalis/*metabolism ; Dietary Supplements ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; *Infant Formula ; Infant, Low Birth Weight ; Infant, Newborn ; Male ; Probiotics/administration & dosage/*pharmacology ; }, abstract = {PURPOSE: Low birth weight (LBW) infants have a less diverse gut microbiota, enriched in potential pathogens, which places them at high risk of systemic inflammation diseases. This study aimed to identify the differences in gut bacterial community structure between LBW infants who received probiotics and LBW infants who did not receive probiotics.

METHODS: Forty-one infants were allocated to the non-probiotic group (N group) and 56 infants to the probiotic group (P group), according to whether the formula they received contained a probiotic Bifidobacterium lactis. Gut bacterial composition was identified with sequencing of the 16S rRNA gene in fecal samples collected at 14 days after birth.

RESULTS: There was no significant difference between the alpha diversity of the two groups, while the beta diversity was significantly different (p < 0.05). Our results showed that Bifidobacterium and Lactobacillus (both p < 0.05) were enriched in the P group, while Veillonella, Dolosigranulum and Clostridium sensu stricto 1 (all p < 0.05) were enriched in the N group. Predicted metagenome function analysis revealed enhancement of fatty acids, peroxisome, starch, alanine, tyrosine and peroxisome pathways in the P group, and enhancement of plant pathogen, Salmonella and Helicobacter pylori infection pathways in the N group.

CONCLUSIONS: Probiotic supplement in formula may affect the composition, stability and function of LBW infants' gut microbiota. LBW infants who receive probiotic intervention may benefit from gut microbiota that contains more beneficial bacteria.}, } @article {pmid31196622, year = {2019}, author = {Ma, Y and Ma, S and Chang, L and Wang, H and Ga, Q and Ma, L and Bai, Z and Shen, Y and Ge, RL}, title = {Gut microbiota adaptation to high altitude in indigenous animals.}, journal = {Biochemical and biophysical research communications}, volume = {516}, number = {1}, pages = {120-126}, doi = {10.1016/j.bbrc.2019.05.085}, pmid = {31196622}, issn = {1090-2104}, mesh = {Acclimatization ; Altitude ; Animals ; Antelopes/*microbiology/physiology ; Equidae/*microbiology/physiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Metagenome ; Sheep/*microbiology/physiology ; Tibet ; }, abstract = {Limited is known about role of gut microbiota in the metabolism of high-altitude-living herbivores, and potential co-evolution between gut microbiome and host genome during high altitude adaptation were not fully understood. Here, DNA from faecal samples was used to investigate the gut microbial compositions and diversity in three host species endemic to the high-altitude Tibetan plateau, the Tibetan antelope (Pantholops hodgsonii, T-antelope, 4300 m) and the Tibetan wild ass (Equus kiang, T-ass, 4300 m), and in the Tibetan sheep (Ovis aries, T-sheep) collected from two different altitudes (T-sheep [k], 4300 m and T-sheep [l] 3000 m). Ordinary sheep (O. aries, sheep) from low altitudes (1800 m) were used for comparison. 16S rRNA gene sequencing revealed that the genera Ruminococcus (22.78%), Oscillospira (20.00%), and Clostridium (10.00%) were common taxa in all high-altitude species (T-antelope, T-ass and T-sheep [k]). Ruminococcaceae, Clostridiales, Clostridia, and Firmicutes showed greater enrichment in the T-antelopes' gut microbiota than in the microbiota of lower-altitude sheep (T-sheep [l] and sheep). The T-antelopes' gut microbiota displayed a higher ratio of Firmicutes to Bacteroidetes than lower-altitude sheep (T-sheep [l] and sheep). A functional capacity analysis of the paired-end metagenomics sequences of the gut metagenomes of high-altitude T-antelopes and T-sheep annotated over 80% of the unique genes to metabolism (especially carbohydrate metabolism pathways) and genetic information processing in the Kyoto Encyclopedia of Genes and Genomes database. The gut metagenome of the T-antelope may have co-evolved with the host genomes (e.g. glycolysis and DNA repair). The higher-altitude herbivores tended to have similar gut microbial compositions, with similar functional capacities, suggesting that their gut microbiota could involved in their high-altitude adaptation.}, } @article {pmid31195972, year = {2019}, author = {Smith, BJ and Miller, RA and Ericsson, AC and Harrison, DC and Strong, R and Schmidt, TM}, title = {Changes in the gut microbiome and fermentation products concurrent with enhanced longevity in acarbose-treated mice.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {130}, pmid = {31195972}, issn = {1471-2180}, support = {U01 AG022307/AG/NIA NIH HHS/United States ; K01 OD019924/OD/NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; U01 AG022308/AG/NIA NIH HHS/United States ; U01 AG022303/AG/NIA NIH HHS/United States ; P30 AG024824/AG/NIA NIH HHS/United States ; }, mesh = {Acarbose/*pharmacology ; Animals ; Bacteria/*classification/drug effects/isolation & purification ; Case-Control Studies ; Fatty Acids, Volatile/metabolism ; Feces/chemistry/microbiology ; Female ; Fermentation/*drug effects ; Gastrointestinal Microbiome/*drug effects ; Longevity/*drug effects ; Male ; Mice ; Phylogeny ; Proportional Hazards Models ; }, abstract = {BACKGROUND: Treatment with the α-glucosidase inhibitor acarbose increases median lifespan by approximately 20% in male mice and 5% in females. This longevity extension differs from dietary restriction based on a number of features, including the relatively small effects on weight and the sex-specificity of the lifespan effect. By inhibiting host digestion, acarbose increases the flux of starch to the lower digestive system, resulting in changes to the gut microbiota and their fermentation products. Given the documented health benefits of short-chain fatty acids (SCFAs), the dominant products of starch fermentation by gut bacteria, this secondary effect of acarbose could contribute to increased longevity in mice. To explore this hypothesis, we compared the fecal microbiome of mice treated with acarbose to control mice at three independent study sites.

RESULTS: Microbial communities and the concentrations of SCFAs in the feces of mice treated with acarbose were notably different from those of control mice. At all three study sites, the bloom of a single bacterial taxon was the most obvious response to acarbose treatment. The blooming populations were classified to the largely uncultured Bacteroidales family Muribaculaceae and were the same taxonomic unit at two of the three sites. Propionate concentrations in feces were consistently elevated in treated mice, while the concentrations of acetate and butyrate reflected a dependence on study site. Across all samples, Muribaculaceae abundance was strongly correlated with propionate and community composition was an important predictor of SCFA concentrations. Cox proportional hazards regression showed that the fecal concentrations of acetate, butyrate, and propionate were, together, predictive of mouse longevity even while controlling for sex, site, and acarbose.

CONCLUSION: We observed a correlation between fecal SCFAs and lifespan in mice, suggesting a role of the gut microbiota in the longevity-enhancing properties of acarbose. Treatment modulated the taxonomic composition and fermentation products of the gut microbiome, while the site-dependence of the responses illustrate the challenges facing reproducibility and interpretation in microbiome studies. These results motivate future studies exploring manipulation of the gut microbial community and its fermentation products for increased longevity, testing causal roles of SCFAs in the observed effects of acarbose.}, } @article {pmid31194939, year = {2019}, author = {Johnson, AJ and Vangay, P and Al-Ghalith, GA and Hillmann, BM and Ward, TL and Shields-Cutler, RR and Kim, AD and Shmagel, AK and Syed, AN and , and Walter, J and Menon, R and Koecher, K and Knights, D}, title = {Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans.}, journal = {Cell host & microbe}, volume = {25}, number = {6}, pages = {789-802.e5}, doi = {10.1016/j.chom.2019.05.005}, pmid = {31194939}, issn = {1934-6069}, mesh = {Adult ; *Diet ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Young Adult ; }, abstract = {Diet is a key determinant of human gut microbiome variation. However, the fine-scale relationships between daily food choices and human gut microbiome composition remain unexplored. Here, we used multivariate methods to integrate 24-h food records and fecal shotgun metagenomes from 34 healthy human subjects collected daily over 17 days. Microbiome composition depended on multiple days of dietary history and was more strongly associated with food choices than with conventional nutrient profiles, and daily microbial responses to diet were highly personalized. Data from two subjects consuming only meal replacement beverages suggest that a monotonous diet does not induce microbiome stability in humans, and instead, overall dietary diversity associates with microbiome stability. Our work provides key methodological insights for future diet-microbiome studies and suggests that food-based interventions seeking to modulate the gut microbiota may need to be tailored to the individual microbiome. Trial Registration: ClinicalTrials.gov: NCT03610477.}, } @article {pmid31194675, year = {2019}, author = {Bernstein, DB and Dewhirst, FE and Segrè, D}, title = {Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31194675}, issn = {2050-084X}, support = {T32GM008764/GM/NIGMS NIH HHS/United States ; T32 GM008764/GM/NIGMS NIH HHS/United States ; R01 DE024468/DE/NIDCR NIH HHS/United States ; R01 GM121950/GM/NIGMS NIH HHS/United States ; DE-SC0012627//Biological and Environmental Research/International ; RGP0020/2016//Human Frontier Science Program/International ; NSFOCE-BSF 1635070//National Science Foundation/International ; HR0011-15-C-0091//Defense Advanced Research Projects Agency/International ; R37DE016937/DE/NIDCR NIH HHS/United States ; R37 DE016937/DE/NIDCR NIH HHS/United States ; R01GM121950/GM/NIGMS NIH HHS/United States ; R01DE024468/DE/NIDCR NIH HHS/United States ; 1457695//National Science Foundation/International ; }, mesh = {Computational Biology ; Humans ; *Metabolic Networks and Pathways ; Metagenomics ; *Microbial Interactions ; *Microbiota ; Mouth/*microbiology ; }, abstract = {The biosynthetic capabilities of microbes underlie their growth and interactions, playing a prominent role in microbial community structure. For large, diverse microbial communities, prediction of these capabilities is limited by uncertainty about metabolic functions and environmental conditions. To address this challenge, we propose a probabilistic method, inspired by percolation theory, to computationally quantify how robustly a genome-derived metabolic network produces a given set of metabolites under an ensemble of variable environments. We used this method to compile an atlas of predicted biosynthetic capabilities for 97 metabolites across 456 human oral microbes. This atlas captures taxonomically-related trends in biomass composition, and makes it possible to estimate inter-microbial metabolic distances that correlate with microbial co-occurrences. We also found a distinct cluster of fastidious/uncultivated taxa, including several Saccharibacteria (TM7) species, characterized by their abundant metabolic deficiencies. By embracing uncertainty, our approach can be broadly applied to understanding metabolic interactions in complex microbial ecosystems.}, } @article {pmid31189707, year = {2019}, author = {Altan, E and Dib, JC and Gulloso, AR and Escribano Juandigua, D and Deng, X and Bruhn, R and Hildebrand, K and Freiden, P and Yamamoto, J and Schultz-Cherry, S and Delwart, E}, title = {Effect of Geographic Isolation on the Nasal Virome of Indigenous Children.}, journal = {Journal of virology}, volume = {93}, number = {17}, pages = {}, pmid = {31189707}, issn = {1098-5514}, support = {HHSN272201400006C/AI/NIAID NIH HHS/United States ; }, mesh = {Biodiversity ; Child ; Child, Preschool ; Colombia ; Female ; Humans ; Indigenous Peoples ; Male ; Metagenomics/*methods ; Nose/*virology ; Phylogeny ; Phylogeography ; Viruses/*classification/isolation & purification ; }, abstract = {The influence of living in small remote villages on the diversity of viruses in the nasal mucosa was investigated in three Colombian villages with very different levels of geographic isolation. Metagenomic analysis was used to characterize viral nucleic acids in nasal swabs from 63 apparently healthy young children. Sequences from human virus members of the families Anelloviridae, Papillomaviridae, Picornaviridae, Herpesviridae, Polyomaviridae, Adenoviridae, and Paramyxoviridae were detected in decreasing proportions of children. The number of papillomavirus infections detected was greater among Hispanic children most exposed to outside contacts, while anellovirus infections were more common in the isolated indigenous villages. The diversity of the other human viruses detected did not differ among the villages. Closely related variants of rhinovirus A or B were identified in 2 to 4 children from each village, reflecting ongoing transmission clusters. Genomes of viruses not currently known to infect humans, including members of the families Parvoviridae, Partitiviridae, Dicistroviridae, and Iflaviridae and circular Rep-encoding single-stranded DNA (CRESS-DNA) virus, were also detected in nasal swabs, possibly reflecting environmental contamination from insect, fungal, or unknown sources. Despite the high levels of geographic and cultural isolation, the overall diversity of human viruses in the nasal passages of children was not reduced in highly isolated indigenous villages, indicating ongoing exposure to globally circulating viruses.IMPORTANCE Extreme geographic and cultural isolation can still be found in some indigenous South American villages. Such isolation may be expected to limit the introduction of otherwise common and widely distributed viruses. Very small population sizes may also result in rapid local viral extinction due to a lack of seronegative subjects to maintain transmission chains for rapidly cleared viruses. We compared the viruses in the nasal passages of young children in three villages with increasing levels of geographic isolation. We found that isolation did not reduce the overall diversity of viral infections. Multiple infections with nearly identical rhinoviruses could be detected within each village, likely reflecting recent viral introductions and transmission clusters among epidemiologically linked members of these very small communities. We conclude that, despite their geographic isolation, remote indigenous villages show evidence of ongoing exposure to globally circulating viruses.}, } @article {pmid31189463, year = {2019}, author = {Thomas, AM and Segata, N}, title = {Multiple levels of the unknown in microbiome research.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {48}, pmid = {31189463}, issn = {1741-7007}, mesh = {Archaea/classification/physiology ; Bacteria/classification ; Bacterial Physiological Phenomena ; *Metagenome ; *Metagenomics ; *Microbiota/genetics ; }, abstract = {Metagenomics allows exploration of aspects of a microbial community that were inaccessible by cultivation-based approaches targeting single microbes. Many new microbial taxa and genes have been discovered using metagenomics, but different kinds of "unknowns" still remain in a microbiome experiment. We discuss here whether and how it is possible to deal with them.}, } @article {pmid31188837, year = {2019}, author = {Williams, GM and Leary, SD and Ajami, NJ and Chipper Keating, S and Petrosin, JF and Hamilton-Shield, JP and Gillespie, KM}, title = {Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a national cohort study.}, journal = {PloS one}, volume = {14}, number = {6}, pages = {e0216557}, pmid = {31188837}, issn = {1932-6203}, support = {/DH_/Department of Health/United Kingdom ; }, mesh = {Bacteria/*classification/genetics ; Cohort Studies ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Parents ; RNA, Ribosomal, 16S/genetics ; Specimen Handling/*methods ; }, abstract = {BACKGROUND: Understanding the role of the gut microbiome is pivotal for the future development of therapies for the prevention and management of autoimmune conditions such as type 1 diabetes when sampling during early life may be particularly important. The current standard methods for collecting gut microbiome samples for research is to extract fresh samples or freeze samples immediately after collection. This is often impractical however for population-based studies. The aim of this study was to determine the optimal method for the stabilization of stool bacterial DNA obtained from nappies and transported by post in ambient conditions to the research centre for a national birth cohort study.

METHODS: Four methods to collect samples were compared to immediate freezing of samples: 1) collecting faeces onto a swab which was immediately frozen, 2) using a commercially available kit with stabilisation solution (OMNIgene•GUT kit) at ambient temperature, 3) collecting onto a swab and 4) collecting into a sterile plain tube. Samples 3) and 4) were returned to the laboratory by post at ambient temperatures. A Bland Altman analysis was used to assess the agreement between the different methods and the frozen standard.

RESULTS: Stool samples were collected by parents. For samples transported in ambient conditions, the limits of agreement showed that the OMNIgene•GUT kit had the narrowest 95% limits of agreement with the frozen standard as measured by the number of operational taxonomic units and the Shannon diversity index.

CONCLUSIONS: All methods assessed for preserving samples collected from nappies at a distance and delivered by post for gut microbiome analysis showed variation / disagreement from the frozen standard. Overall, the OMNIgene•GUT kit preserved the samples with minimal changes compared to other methods and was practical for parents to use.}, } @article {pmid31188063, year = {2019}, author = {Laudadio, I and Fulci, V and Stronati, L and Carissimi, C}, title = {Next-Generation Metagenomics: Methodological Challenges and Opportunities.}, journal = {Omics : a journal of integrative biology}, volume = {23}, number = {7}, pages = {327-333}, doi = {10.1089/omi.2019.0073}, pmid = {31188063}, issn = {1557-8100}, mesh = {Animals ; Big Data ; Biodiversity ; Computational Biology/methods ; Databases, Genetic ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiological Techniques ; Microbiology/trends ; Microbiota ; }, abstract = {Metagenomics is not only one of the newest omics system science technologies but also one that has arguably the broadest set of applications and impacts globally. Metagenomics has found vast utility not only in environmental sciences, ecology, and public health but also in clinical medicine and looking into the future, in planetary health. In line with the One Health concept, metagenomics solicits collaboration between molecular biologists, geneticists, microbiologists, clinicians, computational biologists, plant biologists, veterinarians, and other health care professionals. Almost every ecological niche of our planet hosts an extremely diverse community of organisms that are still poorly characterized. Detailed characterization of the features of such communities is instrumental to our comprehension of ecological, biological, and clinical complexity. This expert review article evaluates how metagenomics is improving our knowledge of microbiota composition from environmental to human samples. Furthermore, we offer an analysis of the common technical and methodological challenges and potential pitfalls arising from metagenomics approaches, such as metagenomics study design, data processing, and interpretation. All in all, at this critical juncture of further growth of the metagenomics field, it is time to critically reflect on the lessons learned and the future prospects of next-generation metagenomics science, technology, and conceivable applications, particularly from the standpoint of a metagenomics methodology perspective.}, } @article {pmid31187895, year = {2019}, author = {Rao, MC}, title = {Physiology of Electrolyte Transport in the Gut: Implications for Disease.}, journal = {Comprehensive Physiology}, volume = {9}, number = {3}, pages = {947-1023}, doi = {10.1002/cphy.c180011}, pmid = {31187895}, issn = {2040-4603}, mesh = {Animals ; Body Water/metabolism ; Electrolytes/*metabolism ; Gastrointestinal Microbiome/physiology ; Intestinal Absorption/physiology ; Intestinal Diseases/*physiopathology ; Intestinal Mucosa/*metabolism ; Ion Transport/*physiology ; Membrane Transport Proteins/physiology ; Neurotransmitter Agents/physiology ; Sodium-Hydrogen Exchangers/physiology ; Sodium-Potassium-Chloride Symporters/physiology ; }, abstract = {We now have an increased understanding of the genetics, cell biology, and physiology of electrolyte transport processes in the mammalian intestine, due to the availability of sophisticated methodologies ranging from genome wide association studies to CRISPR-CAS technology, stem cell-derived organoids, 3D microscopy, electron cryomicroscopy, single cell RNA sequencing, transgenic methodologies, and tools to manipulate cellular processes at a molecular level. This knowledge has simultaneously underscored the complexity of biological systems and the interdependence of multiple regulatory systems. In addition to the plethora of mammalian neurohumoral factors and their cross talk, advances in pyrosequencing and metagenomic analyses have highlighted the relevance of the microbiome to intestinal regulation. This article provides an overview of our current understanding of electrolyte transport processes in the small and large intestine, their regulation in health and how dysregulation at multiple levels can result in disease. Intestinal electrolyte transport is a balance of ion secretory and ion absorptive processes, all exquisitely dependent on the basolateral Na[+] /K[+] ATPase; when this balance goes awry, it can result in diarrhea or in constipation. The key transporters involved in secretion are the apical membrane Cl[-] channels and the basolateral Na[+] -K[+] -2Cl[-] cotransporter, NKCC1 and K[+] channels. Absorption chiefly involves apical membrane Na[+] /H[+] exchangers and Cl[-] /HCO3 [-] exchangers in the small intestine and proximal colon and Na[+] channels in the distal colon. Key examples of our current understanding of infectious, inflammatory, and genetic diarrheal diseases and of constipation are provided. © 2019 American Physiological Society. Compr Physiol 9:947-1023, 2019.}, } @article {pmid31187446, year = {2019}, author = {Gupta, SK and Raza, S and Unno, T}, title = {Comparison of de-novo assembly tools for plasmid metagenome analysis.}, journal = {Genes & genomics}, volume = {41}, number = {9}, pages = {1077-1083}, pmid = {31187446}, issn = {2092-9293}, mesh = {Contig Mapping/*methods ; Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Plasmids/genetics ; Sequence Analysis, DNA/*methods ; *Software ; Water Microbiology ; }, abstract = {BACKGROUND: With the advent of next-generation sequencing techniques, culture-independent metagenome approaches have now made it possible to predict possible presence of genes in the environmental bacteria most of which may be non-cultivable. Short reads obtained from the deep sequencing can be assembled into long contigs some of which include plasmids. Plasmids are the circular double stranded DNA in bacteria and known as one of the major carriers of antibiotic resistance genes.

OBJECTIVE: Metagenomic analyses, especially focused on plasmids, could help us predict dissemination mechanisms of antibiotic resistance genes in the environment. However, with the availability of a myriad of metagenomic assemblers, the selection of the most appropriate metagenome assembler for the plasmid metagenome study might be challenging. Therefore, in this study, we compared five open source assemblers to suggest most effective way of plasmid metagenome analysis.

METHODS: IDBA-UD, MEGAHIT, SPAdes, SOAPdenovo2, and Velvet are compared for conducting plasmid metagenome analyses using two water samples.

RESULTS: Our results clearly showed that abundance and types of antibiotic resistance genes on plasmids varied depending on the selection of assembly tools. IDBA-UD and MEGAHIT demonstrated the overall best assembly statistics with high N50 values with higher portion of longer contigs.

CONCLUSION: These two assemblers also detected more diverse plasmids. Among the two, MEGAHIT showed more memory efficient assembly, therefore we suggest that the use of MEGAHIT for plasmid metagenome analysis may offer more diverse plasmids with less computer resource required. Here, we also summarized a fundamental plasmid metagenome work flow, especially for antibiotic resistance gene investigation.}, } @article {pmid31185914, year = {2019}, author = {Tran, HT and Wang, HC and Hsu, TW and Sarkar, R and Huang, CL and Chiang, TY}, title = {Revegetation on abandoned salt ponds relieves the seasonal fluctuation of soil microbiomes.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {478}, pmid = {31185914}, issn = {1471-2164}, support = {Aim for the Top University Project//National Cheng Kung University/ ; }, mesh = {Ecosystem ; Environmental Restoration and Remediation ; Metabolic Networks and Pathways ; *Microbiota ; *Plant Development ; Ponds/*chemistry/*microbiology ; *Salts ; *Seasons ; *Soil Microbiology ; }, abstract = {BACKGROUND: Salt pond restoration aims to recover the environmental damages that accumulated over the long history of salt production. Of the restoration strategies, phytoremediation that utilizes salt-tolerant plants and soil microorganisms to reduce the salt concentrations is believed to be environmentally-friendly. However, little is known about the change of bacterial community during salt pond restoration in the context of phytoremediation. In the present study, we used 16S metagenomics to compare seasonal changes of bacterial communities between the revegetated and barren salterns at Sicao, Taiwan.

RESULTS: In both saltern types, Proteobacteria, Planctomycetes, Chloroflexi, and Bacteroidetes were predominant at the phylum level. In the revegetated salterns, the soil microbiomes displayed high species diversities and underwent a stepwise transition across seasons. In the barren salterns, the soil microbiomes fluctuated greatly, indicating that mangroves tended to stabilize the soil microorganism communities over the succession. Bacteria in the order Halanaerobiaceae and archaea in the family Halobacteriaceae that were adapted to high salinity exclusively occurred in the barren salterns. Among the 441 persistent operational taxonomic units detected in the revegetated salterns, 387 (87.5%) were present as transient species in the barren salterns. Only 32 persistent bacteria were exclusively detected in the revegetated salterns. Possibly, salt-tolerant plants provided shelters for those new colonizers.

CONCLUSIONS: The collective data indicate that revegetation tended to stabilize the microbiome across seasons and enriched the microbial diversity in the salterns, especially species of Planctomycetes and Acidobacteria.}, } @article {pmid31185897, year = {2019}, author = {Chen, CY and Tang, SL and Chou, ST}, title = {Taxonomy based performance metrics for evaluating taxonomic assignment methods.}, journal = {BMC bioinformatics}, volume = {20}, number = {1}, pages = {310}, pmid = {31185897}, issn = {1471-2105}, support = {105-2410-H-002-101-MY3//The Ministry of Science and Technology of Taiwan/ ; }, mesh = {Bacteria/genetics ; Classification/*methods ; Databases, Genetic ; Metagenomics/*methods ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; }, abstract = {BACKGROUND: Metagenomics experiments often make inferences about microbial communities by sequencing 16S and 18S rRNA, and taxonomic assignment is a fundamental step in such studies. This paper addresses the weaknesses in two types of metrics commonly used by previous studies for measuring the performance of existing taxonomic assignment methods: Sequence count based metrics and Binary error measurement. These metrics made performance evaluation results biased, less informative and mutually incomparable.

RESULTS: We investigated weaknesses in two types of metrics and proposed new performance metrics including Average Taxonomy Distance (ATD) and ATD_by_Taxa, together with the visualized ATD plot.

CONCLUSIONS: By comparing the evaluation results from four popular taxonomic assignment methods across three test data sets, we found the new metrics more robust, informative and comparable.}, } @article {pmid31184575, year = {2019}, author = {Bull, AT and Goodfellow, M}, title = {Dark, rare and inspirational microbial matter in the extremobiosphere: 16 000 m of bioprospecting campaigns.}, journal = {Microbiology (Reading, England)}, volume = {165}, number = {12}, pages = {1252-1264}, doi = {10.1099/mic.0.000822}, pmid = {31184575}, issn = {1465-2080}, mesh = {Actinobacteria/classification/genetics/metabolism ; Biological Products/metabolism ; *Bioprospecting ; Drug Discovery ; Ecosystem ; *Extreme Environments ; Genes, Microbial ; Genome, Bacterial/genetics ; Microbiota/*genetics ; }, abstract = {The rationale of our bioprospecting campaigns is that the extremobiosphere, particularly the deep sea and hyper-arid deserts, harbours undiscovered biodiversity that is likely to express novel chemistry and biocatalysts thereby providing opportunities for therapeutic drug and industrial process development. We have focused on actinobacteria because of their frequent role as keystone species in soil ecosystems and their unrivalled track record as a source of bioactive compounds. Population numbers and diversity of actinobacteria in the extremobiosphere are traditionally considered to be low, although they often comprise the dominant bacterial biota. Recent metagenomic evaluation of 'the uncultured microbial majority' has now revealed enormous taxonomic diversity among 'dark' and 'rare' actinobacteria in samples as diverse as sediments from the depths of the Mariana Trench and soils from the heights of the Central Andes. The application of innovative culture and screening options that emphasize rigorous dereplication at each stage of the analysis, and strain prioritization to identify 'gifted' organisms, have been deployed to detect and characterize bioactive hit compounds and sought-after catalysts from this hitherto untapped resource. The rewards include first-in-a-class chemical entities with novel modes of action, as well as a growing microbial seed bank that represents a potentially enormous source of biotechnological and therapeutic innovation.}, } @article {pmid31184446, year = {2019}, author = {Milyutina, IA and Belevich, TA and Ilyash, LV and Troitsky, AV}, title = {Insight into picophytoplankton diversity of the subarctic White Sea-The first recording of Pedinophyceae in environmental DNA.}, journal = {MicrobiologyOpen}, volume = {8}, number = {10}, pages = {e892}, pmid = {31184446}, issn = {2045-8827}, mesh = {Arctic Regions ; *Biodiversity ; Cluster Analysis ; DNA, Chloroplast/chemistry/genetics ; DNA, Environmental/chemistry/*genetics ; DNA, Plant/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Phylogeny ; Phytoplankton/*classification/*genetics ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 23S/genetics ; RNA, Ribosomal, 28S/genetics ; RNA, Ribosomal, 5.8S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Operational taxonomic units 94%-95% similar to the known Pedinophyceae were found as a result of high-through sequencing of 18S rDNA V4 amplicons of environmental DNA from the summer picophytoplankton samples from the White Sea. Partial sequence of a ribosomal operon (the 5,298 bp includes partial 18S and 28S rDNA, complete 5.8S rDNA, ITS1, and ITS2 sequences) and a partial 2,112 bp chloroplast 23S rDNA sequence White Sea Pedinophyceae was amplified from metagenomic DNA by specific primers and sequenced. A new phylotype was designated as uncultured Pedinophyceae WS. On Chlorophyta phylogenetic trees the discovered phylotype occupies a basal position in the Marsupiomonadales clade. The synapomorphic base substitutions in rRNA hairpins confirm the relationship of Pedinophyceae WS to Marsupiomonadales and its difference from known genera of the order. The obtained results extend knowledge of picophytoplankton diversity in subarctic waters.}, } @article {pmid31183493, year = {2019}, author = {Berhe, T and Ipsen, R and Seifu, E and Kurtu, MY and Fugl, A and Hansen, EB}, title = {Metagenomic analysis of bacterial community composition in Dhanaan: Ethiopian traditional fermented camel milk.}, journal = {FEMS microbiology letters}, volume = {366}, number = {11}, pages = {}, doi = {10.1093/femsle/fnz128}, pmid = {31183493}, issn = {1574-6968}, mesh = {Animals ; Camelus ; Fermentation ; Food Microbiology/*methods ; Lactobacillus/genetics/isolation & purification ; Metagenome/*genetics ; Microbiota/genetics/*physiology ; Milk ; RNA, Ribosomal, 16S/genetics ; Streptococcus/genetics/isolation & purification ; Weissella/genetics/isolation & purification ; }, abstract = {This study was conducted to evaluate the safety and bacterial profile of Dhanaan (Ethiopian traditional fermented camel milk). The composition of the microbial community in Dhanaan samples was analysed by a metagenomic approach of 16S rRNA gene amplicon sequencing. Metagenomic profiling identified 87 different bacterial microorganisms (OTUs) in six samples analysed. Although the Dhanaan samples contained various lactic acid bacteria (LAB), they also all contained undesirable microorganisms in large proportions. The following LAB genera were identified: Streptococcus, Lactococcus and Weissella. One Streptococcus species represented by OTU-1 (operational taxonomic unit) was found in all Dhanaan samples and the dominating species in four out of six samples. This common isolate was found to be closely related to S. lutetiensis and S. infantarius. Undesirable microorganisms from genera such as Escherichia, Klebsiella, Enterobacter, Acinetobacter and Clostridium were, however, also frequent, or even dominant in Dhanaan samples. Thus, this calls for a change in the Dahnaan manufacturing practice to an improved and safer production system. Starter cultures suitable for Dhanaan production might be developed from the Streptococcus, Weissella and Lactococcus microorganisms identified in this study. However, further safety evaluation and technological characterization need to be conducted on strains defined by OTU-1, OTU-2, OTU-3, OTU-8 and OTU-35 before they can be used as food grade starter cultures.}, } @article {pmid31182796, year = {2019}, author = {Gruber-Vodicka, HR and Leisch, N and Kleiner, M and Hinzke, T and Liebeke, M and McFall-Ngai, M and Hadfield, MG and Dubilier, N}, title = {Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2.}, journal = {Nature microbiology}, volume = {4}, number = {9}, pages = {1465-1474}, pmid = {31182796}, issn = {2058-5276}, mesh = {Animals ; Bacteria/classification/genetics/*metabolism ; Biosynthetic Pathways ; Endoplasmic Reticulum, Rough/microbiology ; Genome, Bacterial/genetics ; Microbiota/genetics ; Phylogeny ; Placozoa/cytology/*microbiology ; Species Specificity ; *Symbiosis ; Vacuoles/microbiology ; *Water Microbiology ; }, abstract = {Placozoa is an enigmatic phylum of simple, microscopic, marine metazoans[1,2]. Although intracellular bacteria have been found in all members of this phylum, almost nothing is known about their identity, location and interactions with their host[3-6]. We used metagenomic and metatranscriptomic sequencing of single host individuals, plus metaproteomic and imaging analyses, to show that the placozoan Trichoplax sp. H2 lives in symbiosis with two intracellular bacteria. One symbiont forms an undescribed genus in the Midichloriaceae (Rickettsiales)[7,8] and has a genomic repertoire similar to that of rickettsial parasites[9,10], but does not seem to express key genes for energy parasitism. Correlative image analyses and three-dimensional electron tomography revealed that this symbiont resides in the rough endoplasmic reticulum of its host's internal fibre cells. The second symbiont belongs to the Margulisbacteria, a phylum without cultured representatives and not known to form intracellular associations[11-13]. This symbiont lives in the ventral epithelial cells of Trichoplax, probably metabolizes algal lipids digested by its host and has the capacity to supplement the placozoan's nutrition. Our study shows that one of the simplest animals has evolved highly specific and intimate associations with symbiotic, intracellular bacteria and highlights that symbioses can provide access to otherwise elusive microbial dark matter.}, } @article {pmid31182795, year = {2019}, author = {Rahfeld, P and Sim, L and Moon, H and Constantinescu, I and Morgan-Lang, C and Hallam, SJ and Kizhakkedathu, JN and Withers, SG}, title = {An enzymatic pathway in the human gut microbiome that converts A to universal O type blood.}, journal = {Nature microbiology}, volume = {4}, number = {9}, pages = {1475-1485}, pmid = {31182795}, issn = {2058-5276}, support = {MOP-136940//CIHR/Canada ; R24 GM098791/GM/NIGMS NIH HHS/United States ; }, mesh = {ABO Blood-Group System/*immunology ; Amidohydrolases/chemistry/*metabolism ; Bacterial Proteins/chemistry/*metabolism ; Blood Group Antigens/*metabolism ; Catalytic Domain ; Clostridiales/enzymology/genetics ; Crystallography, X-Ray ; Erythrocytes/immunology/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; Hexosaminidases/chemistry/*metabolism ; Humans ; Male ; Metagenome ; }, abstract = {Access to efficient enzymes that can convert A and B type red blood cells to 'universal' donor O would greatly increase the supply of blood for transfusions. Here we report the functional metagenomic screening of the human gut microbiome for enzymes that can remove the cognate A and B type sugar antigens. Among the genes encoded in our library of 19,500 expressed fosmids bearing gut bacterial DNA, we identify an enzyme pair from the obligate anaerobe Flavonifractor plautii that work in concert to efficiently convert the A antigen to the H antigen of O type blood, via a galactosamine intermediate. The X-ray structure of the N-acetylgalactosamine deacetylase reveals the active site and mechanism of the founding member of an esterase family. The galactosaminidase expands activities within the CAZy family GH36. Their ability to completely convert A to O of the same rhesus type at very low enzyme concentrations in whole blood will simplify their incorporation into blood transfusion practice, broadening blood supply.}, } @article {pmid31182732, year = {2019}, author = {Asao, K and Hashida, N and Ando, S and Motooka, D and Kurakami, H and Nakamura, S and Yamashita, D and Maruyama, K and Kawasaki, S and Yamada, T and Iida, T and Nishida, K}, title = {Conjunctival dysbiosis in mucosa-associated lymphoid tissue lymphoma.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {8424}, pmid = {31182732}, issn = {2045-2322}, mesh = {Aged ; Aged, 80 and over ; Biodiversity ; Case-Control Studies ; Conjunctiva/*microbiology ; Dysbiosis/*complications ; Female ; Humans ; Hydrogen-Ion Concentration ; Immunoglobulin A/metabolism ; Lymphoma, B-Cell, Marginal Zone/*microbiology ; Male ; Middle Aged ; Principal Component Analysis ; Species Specificity ; Tears/metabolism ; }, abstract = {To investigate the conjunctival microbiota and the association between the development of conjunctival mucosa-associated lymphoid tissue (MALT) lymphoma and dysbiosis, DNA samples were collected from 25 conjunctival MALT lymphoma patients and 25 healthy controls. To compare the microbiota, samples were collected from the following four body locations: conjunctiva, meibomian gland, periocular skin and hand. Extracted DNA was analyzed by 16S rRNA sequences, and libraries were sequenced on an Illumina MiSeq sequencer. The differences in bacteria were characterized by using principal coordinate analysis of metagenomics data, and the differences in bacterial compositions were evaluated by linear discriminant analysis effect size. The conjunctival microbiota of MALT lymphoma patients was compositionally different from that of healthy controls. For the conjunctival MALT lymphoma patients, alterations in the microbial composition were detected, and a remarkable change was detected at the conjunctiva. Detailed analysis showed that a specific population of the microbiota, the genus Delftia, was significantly more abundant in conjunctival MALT lymphoma patients, and the genera Bacteroides and Clostridium were less abundant in the MALT lymphoma patients. A specific microbiota on the ocular surface in conjunctival MALT lymphoma patients was detected, and dysbiosis may play an important role in the pathophysiology of conjunctival MALT lymphoma.}, } @article {pmid31181638, year = {2019}, author = {Astó, E and Méndez, I and Rodríguez-Prado, M and Cuñé, J and Espadaler, J and Farran-Codina, A}, title = {Effect of the Degree of Polymerization of Fructans on Ex Vivo Fermented Human Gut Microbiome.}, journal = {Nutrients}, volume = {11}, number = {6}, pages = {}, pmid = {31181638}, issn = {2072-6643}, mesh = {Adult ; Bacteria/*drug effects/growth & development ; Bacterial Typing Techniques/methods ; Colon/microbiology ; Female ; Fermentation ; Fructans/chemistry/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Inulin/chemistry/pharmacology ; Male ; Oligosaccharides/chemistry/*pharmacology ; *Polymerization ; *Prebiotics ; }, abstract = {Prebiotic supplements are used to promote gastrointestinal health by stimulating beneficial bacteria. The aim of this study was to compare the potential prebiotic effects of fructans with increasing degrees of polymerization, namely fructooligosaccharides (FOS) and inulins with a low and high polymerization degree (LPDI and HPDI, respectively), using an ex vivo fermentation system to simulate the colonic environment. The system was inoculated with pooled feces from three healthy donors with the same baseline enterotype. Changes in microbiota composition were measured by 16S metagenomic sequencing after 2, 7, and 14 days of fermentation, and acid production was measured throughout the experiment. Alpha-diversity decreased upon inoculation of the ex vivo fermentation under all treatments. Composition changed significantly across both treatments and time (ANOSIM p < 0.005 for both factors). HPDI and LPDI seemed to be similar to each other regarding composition and acidification activity, but different from the control and FOS. FOS differed from the control in terms of composition but not acidification. HDPI restored alpha-diversity on day 14 as compared to the control (Bonferroni p < 0.05). In conclusion, the prebiotic activity of fructans appears to depend on the degree of polymerization, with LPDI and especially HPDI having a greater effect than FOS.}, } @article {pmid31180804, year = {2019}, author = {Mark Welch, JL and Dewhirst, FE and Borisy, GG}, title = {Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis.}, journal = {Annual review of microbiology}, volume = {73}, number = {}, pages = {335-358}, pmid = {31180804}, issn = {1545-3251}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R37 DE016937/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; Mouth/*microbiology ; Spatial Analysis ; }, abstract = {Microbial communities are complex and dynamic, composed of hundreds of taxa interacting across multiple spatial scales. Advances in sequencing and imaging technology have led to great strides in understanding both the composition and the spatial organization of these complex communities. In the human mouth, sequencing results indicate that distinct sites host microbial communities that not only are distinguishable but to a meaningful degree are composed of entirely different microbes. Imaging suggests that the spatial organization of these communities is also distinct. Together, the literature supports the idea that most oral microbes are site specialists. A clear understanding of microbiota structure at different sites in the mouth enables mechanistic studies, informs the generation of hypotheses, and strengthens the position of oral microbiology as a model system for microbial ecology in general.}, } @article {pmid31178526, year = {2019}, author = {Wang, N and Guo, Y and Li, G and Xia, Y and Ma, M and Zang, J and Ma, Y and Yin, X and Han, W and Lv, J and Cao, H}, title = {Geochemical-Compositional-Functional Changes in Arctic Soil Microbiomes Post Land Submergence Revealed by Metagenomics.}, journal = {Microbes and environments}, volume = {34}, number = {2}, pages = {180-190}, pmid = {31178526}, issn = {1347-4405}, mesh = {Archaea/classification/genetics ; Archaeal Proteins/genetics/metabolism ; Arctic Regions ; Bacteria/classification/genetics ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Geologic Sediments/chemistry/*microbiology ; Lakes ; *Metagenomics ; Methane/metabolism ; *Microbiota/genetics ; Nitrogen/metabolism ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Lakes of meltwater in the Artic have become one of the transforming landscape changes under global warming. We herein compared microbial communities between sediments and bank soils at an arctic lake post land submergence using geochemistry, 16S rRNA amplicons, and metagenomes. The results obtained showed that each sample had approximately 2,609 OTUs on average and shared 1,716 OTUs based on the 16S rRNA gene V3-V4 region. Dominant phyla in sediments and soils included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Nitrospirae; sediments contained a unique phylum, Euryarchaeota, with the phylum Thaumarchaeota being primarily present in bank soils. Among the top 35 genera across all sites, 17 were more abundant in sediments, while the remaining 18 were more abundant in bank soils; seven out of the top ten genera across all sites were only from sediments. A redundancy analysis separated sediment samples from soil samples based on the components of nitrite and ammonium. Metagenome results supported the role of nitrite because most of the genes for denitrification and methane metabolic genes were more abundant in sediments than in soils, while the abundance of phosphorus-utilizing genes was similar and, thus, was not a significant explanatory factor. We identified several modules from the global networks of OTUs that were closely related to some geochemical factors, such as pH and nitrite. Collectively, the present results showing consistent changes in geochemistry, microbiome compositions, and functional genes suggest an ecological mechanism across molecular and community levels that structures microbiomes post land submergence.}, } @article {pmid31174953, year = {2019}, author = {Pietrucci, D and Cerroni, R and Unida, V and Farcomeni, A and Pierantozzi, M and Mercuri, NB and Biocca, S and Stefani, A and Desideri, A}, title = {Dysbiosis of gut microbiota in a selected population of Parkinson's patients.}, journal = {Parkinsonism & related disorders}, volume = {65}, number = {}, pages = {124-130}, doi = {10.1016/j.parkreldis.2019.06.003}, pmid = {31174953}, issn = {1873-5126}, mesh = {Aged ; Dysbiosis/*diagnosis/physiopathology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Middle Aged ; Parkinson Disease/*diagnosis/*microbiology/physiopathology ; }, abstract = {INTRODUCTION: In recent years the hypothesis that gut microbiota associates with Parkinson's disease (PD) has gained importance, although it has not been possible to define a specific microbiota composition as a predictive biomarker of this disease. We have investigated dysbiosis of gut microbiota in a selected population of PD patients from Central Italy, and examined the weight of specific confounders and predictors, in order to identify potential correlations with clinical phenotypes.

METHODS: 152 fecal samples were collected from 80 patients and 72 healthy controls. Patients were enrolled according to tight inclusion criteria. Microbiota composition was studied through 16s ribosomal RNA gene amplicon sequencing analysis in combination with data on dietary/life habits. Age, loss of weight, and sex were recognized as confounding factors, whereas PD-status, age, Body Mass Index, "eat cereals", "gain of weigth" and "physical activity" as predictors. The presence of Lactobacillaceae, Enterobacteriaceae and Enterococcaceae families was significantly higher in feces from PD patients compared to healthy controls, while Lachnospiraceae were significantly reduced. Lower levels of Lachnospiraceae and higher levels of Enterobacteriaceae families also correlated with increased disease severity and motor impairment (Hoehn & Yahr stage, MDS-UPDRS Part III). Predictive metagenomics indicated a significant variation of genes involved in the metabolism of short chain fatty acids and amino acids, and in lipopolysaccharide biosynthesis.

CONCLUSIONS: PD showed a distinctive microbiota composition. Functional predictions suggest changes in pathways favoring a pro-inflammatory environment in the gastrointestinal tract, and a reduction in the biosynthesis of amino acids acting as precursors of physiological transmitters.}, } @article {pmid31174602, year = {2019}, author = {Krummenacker, M and Latendresse, M and Karp, PD}, title = {Metabolic route computation in organism communities.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {89}, pmid = {31174602}, issn = {2049-2618}, support = {R01 GM080746/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Databases, Genetic ; *Gastrointestinal Microbiome ; Humans ; Indican/biosynthesis ; *Metabolic Networks and Pathways ; Metagenome ; Methylamines/metabolism ; *Software ; }, abstract = {BACKGROUND: Microbiomes are complex aggregates of organisms, each of which has its own extensive metabolic network. A variety of metabolites are exchanged between the microbes. The challenge we address is understanding the overall metabolic capabilities of a microbiome: through what series of metabolic transformations can a microbiome convert a starting compound to an ending compound?

RESULTS: We developed an efficient software tool to search for metabolic routes that include metabolic reactions from multiple organisms. The metabolic network for each organism is obtained from BioCyc, where the network was inferred from the annotated genome. The tool searches for optimal metabolic routes that minimize the number of reactions in each route, maximize the number of atoms conserved between the starting and ending compounds, and minimize the number of organism switches. The tool pre-computes the reaction sets found in each organism from BioCyc to facilitate fast computation of the reactions defined in a researcher-specified organism set. The generated routes are depicted graphically, and for each reaction in a route, the tool lists the organisms that can catalyze that reaction. We present solutions for three route-finding problems in the human gut microbiome: (1) production of indoxyl sulfate, (2) production of trimethylamine N-oxide (TMAO), and (3) synthesis and degradation of autoinducers. The optimal routes computed by our multi-organism route-search (MORS) tool for indoxyl sulfate and TMAO were the same as routes reported in the literature.

CONCLUSIONS: Our tool quickly found plausible routes for the discussed multi-organism route-finding problems. The routes shed light on how diverse organisms cooperate to perform multi-step metabolic transformations. Our tool enables scientists to consider multiple alternative routes and identifies the organisms responsible for each reaction.}, } @article {pmid31174412, year = {2019}, author = {Boggs, LM and Scheible, MKR and Machado, G and Meiklejohn, KA}, title = {Single Fragment or Bulk Soil DNA Metabarcoding: Which is Better for Characterizing Biological Taxa Found in Surface Soils for Sample Separation?.}, journal = {Genes}, volume = {10}, number = {6}, pages = {}, pmid = {31174412}, issn = {2073-4425}, mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA Fingerprinting ; Forensic Genetics/*methods ; High-Throughput Nucleotide Sequencing ; Insecta/chemistry/genetics ; Metagenome/*genetics ; Plants/chemistry/genetics ; Soil/*chemistry ; }, abstract = {In forensic geology casework, sample size typically limits routine characterization of material using bulk approaches. To address this, DNA-based characterization of biological taxa has received attention, as the taxa present can be useful for sample-to-sample comparisons and source attribution. In our initial work, low biodiversity was captured when DNA barcodes were Sanger-sequenced from plant and insect fragments isolated from 10 forensic-type surface soils. Considering some forensic laboratories now have access to massively parallel sequencing platforms, we assessed whether biological taxa present in the same surface soils could be better characterized using DNA metabarcoding. To achieve this, plant and animal barcodes were amplified and sequenced on an Illumina MiniSeq for three different DNA sample types (n = 50): individual fragments used in our initial study, and 250 and 100 mg of bulk soil (from the 10 sites used in the initial study). A total of 572 unique target barcode sequences passed quality filtering and were used in downstream statistical analyses: 54, 321, and 285 for individual fragments, 100 mg, and 250 mg bulk soil samples, respectively. Plant barcodes permitted some spatial separation of sample sites in non-metric multidimensional scaling plots; better separation was obtained for samples prepared from bulk soil. This study confirmed that bulk soil DNA metabarcoding is a better approach for characterizing biological taxa present in surface soils, which could supplement traditional geologic examinations.}, } @article {pmid31172250, year = {2019}, author = {Ali, N and Gong, H and Giwa, AS and Yuan, Q and Wang, K}, title = {Metagenomic analysis and characterization of acidogenic microbiome and effect of pH on organic acid production.}, journal = {Archives of microbiology}, volume = {201}, number = {9}, pages = {1163-1171}, doi = {10.1007/s00203-019-01676-2}, pmid = {31172250}, issn = {1432-072X}, support = {21206084//National Natural Science Foundation of China/ ; }, mesh = {Acetates/*metabolism ; Bifidobacterium/classification/*genetics/metabolism ; Bioreactors/*microbiology ; Carbohydrate Metabolism ; Fermentation/genetics ; High-Throughput Nucleotide Sequencing ; Hydrogen-Ion Concentration ; Hydrolysis ; Lactic Acid/*metabolism ; Lactobacillus/classification/*genetics/metabolism ; Metagenomics ; Microbiota/*genetics ; }, abstract = {Organic acid production including lactate and acetate is an economically attractive technology that has gained momentum worldwide over the past years. These series of action need to be performed by an esoteric and complex microbial community, in which different members have distinct roles in the establishment of a collective organization. In this study, we analyzed the bioma from bioreactors with various pH conditions of 4.0, 5.0 and 6.0 (R1, R2 and R3), respectively, involved in acidogenic digestion for stable production of various organic acids by means of high-throughput Illumina sequencing, disclosing thousands of genes and extracting more than 53 microbial genomes. At pH 5.0, the hydrolysis reaction was enhanced and thus the lactic acid fermentation was stably improved to 45.96 mm/L and acetic acid to 73.77 mm/L. R2 was found with the most suitable pH condition for stable organic acids production as Lactobacilli and Bifidobacteria were the major members. Both the members have the key roles in heterofermentation and produce higher transcripts of key encoding enzymes involved in the dominant heterofermentation pathways.}, } @article {pmid31171880, year = {2019}, author = {Yachida, S and Mizutani, S and Shiroma, H and Shiba, S and Nakajima, T and Sakamoto, T and Watanabe, H and Masuda, K and Nishimoto, Y and Kubo, M and Hosoda, F and Rokutan, H and Matsumoto, M and Takamaru, H and Yamada, M and Matsuda, T and Iwasaki, M and Yamaji, T and Yachida, T and Soga, T and Kurokawa, K and Toyoda, A and Ogura, Y and Hayashi, T and Hatakeyama, M and Nakagama, H and Saito, Y and Fukuda, S and Shibata, T and Yamada, T}, title = {Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer.}, journal = {Nature medicine}, volume = {25}, number = {6}, pages = {968-976}, pmid = {31171880}, issn = {1546-170X}, mesh = {Adult ; Aged ; Case-Control Studies ; Colorectal Neoplasms/genetics/*metabolism/*microbiology ; Disease Progression ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Metabolomics ; Metagenomics ; Middle Aged ; Neoplasm Staging ; Young Adult ; }, abstract = {In most cases of sporadic colorectal cancers, tumorigenesis is a multistep process, involving genomic alterations in parallel with morphologic changes. In addition, accumulating evidence suggests that the human gut microbiome is linked to the development of colorectal cancer. Here we performed fecal metagenomic and metabolomic studies on samples from a large cohort of 616 participants who underwent colonoscopy to assess taxonomic and functional characteristics of gut microbiota and metabolites. Microbiome and metabolome shifts were apparent in cases of multiple polypoid adenomas and intramucosal carcinomas, in addition to more advanced lesions. We found two distinct patterns of microbiome elevations. First, the relative abundance of Fusobacterium nucleatum spp. was significantly (P < 0.005) elevated continuously from intramucosal carcinoma to more advanced stages. Second, Atopobium parvulum and Actinomyces odontolyticus, which co-occurred in intramucosal carcinomas, were significantly (P < 0.005) increased only in multiple polypoid adenomas and/or intramucosal carcinomas. Metabolome analyses showed that branched-chain amino acids and phenylalanine were significantly (P < 0.005) increased in intramucosal carcinomas and bile acids, including deoxycholate, were significantly (P < 0.005) elevated in multiple polypoid adenomas and/or intramucosal carcinomas. We identified metagenomic and metabolomic markers to discriminate cases of intramucosal carcinoma from the healthy controls. Our large-cohort multi-omics data indicate that shifts in the microbiome and metabolome occur from the very early stages of the development of colorectal cancer, which is of possible etiological and diagnostic importance.}, } @article {pmid31168933, year = {2019}, author = {Mizutani, Y and Iehata, S and Mori, T and Oh, R and Fukuzaki, S and Tanaka, R}, title = {Diversity, enumeration, and isolation of Arcobacter spp. in the giant abalone, Haliotis gigantea.}, journal = {MicrobiologyOpen}, volume = {8}, number = {10}, pages = {e890}, pmid = {31168933}, issn = {2045-8827}, mesh = {Animals ; Arcobacter/*classification/genetics/*isolation & purification ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gastropoda/*microbiology ; Genotype ; In Situ Hybridization, Fluorescence ; Metagenomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Arcobacter have been frequently detected in and isolated from bivalves, but there is very little information on the genus Arcobacter in the abalone, an important fishery resource. This study aimed to investigate the genetic diversity and abundance of bacteria from the genus Arcobacter in the Japanese giant abalone, Haliotis gigantea, using molecular methods such as Arcobacter-specific clone libraries and fluorescence in situ hybridization (FISH). Furthermore, we attempted to isolate the Arcobacter species detected. Twelve genotypes of clones were obtained from Arcobacter-specific clone libraries. These sequences are not classified with any other known Arcobacter species including pathogenic Arcobacter spp., A. butzleri, A. skirrowii, and A. cryaerophilus, commonly isolated or detected from bivalves. From the FISH analysis, we observed that ARC94F-positive cells, presumed to be Arcobacter, accounted for 6.96 ± 0.72% of all EUB338-positive cells. In the culture method, three genotypes of Arcobacter were isolated from abalones. One genotype had a similarity of 99.2%-100.0% to the 16S rRNA gene of Arcobacter marinus, while the others showed only 93.3%-94.3% similarity to other Arcobacter species. These data indicate that abalones carry Arcobacter as a common bacterial genus which includes uncultured species.}, } @article {pmid31167953, year = {2020}, author = {Bonning, BC}, title = {The Insect Virome: Opportunities and Challenges.}, journal = {Current issues in molecular biology}, volume = {34}, number = {}, pages = {1-12}, doi = {10.21775/cimb.034.001}, pmid = {31167953}, issn = {1467-3045}, mesh = {Animals ; Biodiversity ; Genome, Viral ; Host-Pathogen Interactions/genetics/immunology ; Insect Viruses/*classification/*genetics ; Insecta/genetics/immunology/*virology ; Invertebrates ; Metagenomics ; Microbiota ; }, abstract = {The insect virome is composed of a myriad of viruses. Both field populations and laboratory colonies of insects harbour diverse viruses, including viruses that infect the insect itself, viruses of microbes associated with the insect, and viruses associated with ingested materials. Metagenomics analysis for identification of virus-derived sequences has allowed for new appreciation of the extent and diversity of the insect virome. The complex interactions between insect viruses and host antiviral immune pathways (RNA interference and apoptosis), and between viruses and other members of the microbiome (e.g. Wolbachia) are becoming apparent. In this chapter, an overview of the diversity of viruses in insects and recent virus discovery research for specific insects and insect-derived cell lines is provided. The opportunities and challenges associated with the insect virome, including the potential impacts of viruses on both research and insect management programs are also addressed.}, } @article {pmid31167634, year = {2019}, author = {LaPierre, N and Mangul, S and Alser, M and Mandric, I and Wu, NC and Koslicki, D and Eskin, E}, title = {MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 5}, pages = {423}, pmid = {31167634}, issn = {1471-2164}, support = {R01 ES021801/ES/NIEHS NIH HHS/United States ; R01 MH101782/MH/NIMH NIH HHS/United States ; K25 HL080079/HL/NHLBI NIH HHS/United States ; P01 HL028481/HL/NHLBI NIH HHS/United States ; U01 DA024417/DA/NIDA NIH HHS/United States ; T32 EB016640/EB/NIBIB NIH HHS/United States ; R01 ES022282/ES/NIEHS NIH HHS/United States ; P01 HL030568/HL/NHLBI NIH HHS/United States ; R01 GM083198/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Computational Biology/*methods ; Fungi/classification/*genetics ; *Genetic Markers ; Genome, Fungal ; Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; *Microbiota ; Sequence Analysis, DNA/*methods ; Viruses/classification/*genetics ; }, abstract = {BACKGROUND: High throughput sequencing has spurred the development of metagenomics, which involves the direct analysis of microbial communities in various environments such as soil, ocean water, and the human body. Many existing methods based on marker genes or k-mers have limited sensitivity or are too computationally demanding for many users. Additionally, most work in metagenomics has focused on bacteria and archaea, neglecting to study other key microbes such as viruses and eukaryotes.

RESULTS: Here we present a method, MiCoP (Microbiome Community Profiling), that uses fast-mapping of reads to build a comprehensive reference database of full genomes from viruses and eukaryotes to achieve maximum read usage and enable the analysis of the virome and eukaryome in each sample. We demonstrate that mapping of metagenomic reads is feasible for the smaller viral and eukaryotic reference databases. We show that our method is accurate on simulated and mock community data and identifies many more viral and fungal species than previously-reported results on real data from the Human Microbiome Project.

CONCLUSIONS: MiCoP is a mapping-based method that proves more effective than existing methods at abundance profiling of viruses and eukaryotes in metagenomic samples. MiCoP can be used to detect the full diversity of these communities. The code, data, and documentation are publicly available on GitHub at: https://github.com/smangul1/MiCoP .}, } @article {pmid31167633, year = {2019}, author = {Zhong, C and Yang, Y and Yooseph, S}, title = {GRASP2: fast and memory-efficient gene-centric assembly and homolog search for metagenomic sequencing data.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 11}, pages = {276}, pmid = {31167633}, issn = {1471-2105}, mesh = {Algorithms ; Aquatic Organisms/genetics ; *Genes ; Metagenomics/*methods ; Microbiota/genetics ; ROC Curve ; Sequence Analysis, DNA/*methods ; *Sequence Homology, Nucleic Acid ; *Software ; Time Factors ; }, abstract = {BACKGROUND: A crucial task in metagenomic analysis is to annotate the function and taxonomy of the sequencing reads generated from a microbiome sample. In general, the reads can either be assembled into contigs and searched against reference databases, or individually searched without assembly. The first approach may suffer from fragmentary and incomplete assembly, while the second is hampered by the reduced functional signal contained in the short reads. To tackle these issues, we have previously developed GRASP (Guided Reference-based Assembly of Short Peptides), which accepts a reference protein sequence as input and aims to assemble its homologs from a database containing fragmentary protein sequences. In addition to a gene-centric assembly tool, GRASP also serves as a homolog search tool when using the assembled protein sequences as templates to recruit reads. GRASP has significantly improved recall rate (60-80% vs. 30-40%) compared to other homolog search tools such as BLAST. However, GRASP is both time- and space-consuming. Subsequently, we developed GRASPx, which is 30X faster than GRASP. Here, we present a completely redesigned algorithm, GRASP2, for this computational problem.

RESULTS: GRASP2 utilizes Burrows-Wheeler Transformation (BWT) and FM-index to perform assembly graph generation, and reduces the search space by employing a fast ungapped alignment strategy as a filter. GRASP2 also explicitly generates candidate paths prior to alignment, which effectively uncouples the iterative access of the assembly graph and alignment matrix. This strategy makes the execution of the program more efficient under current computer architecture, and contributes to GRASP2's speedup. GRASP2 is 8-fold faster than GRASPx (and 250-fold faster than GRASP) and uses 8-fold less memory while maintaining the original high recall rate of GRASP. GRASP2 reaches ~ 80% recall rate compared to that of ~ 40% generated by BLAST, both at a high precision level (> 95%). With such a high performance, GRASP2 is only ~3X slower than BLASTP.

CONCLUSION: GRASP2 is a high-performance gene-centric and homolog search tool with significant speedup compared to its predecessors, which makes GRASP2 a useful tool for metagenomics data analysis, GRASP2 is implemented in C++ and is freely available from http://www.sourceforge.net/projects/grasp2 .}, } @article {pmid31166192, year = {2019}, author = {Yu, Z and Zheng, Y and Huang, J and Chistoserdova, L}, title = {Systems Biology Meets Enzymology: Recent Insights into Communal Metabolism of Methane and the Role of Lanthanides.}, journal = {Current issues in molecular biology}, volume = {33}, number = {}, pages = {183-196}, doi = {10.21775/cimb.033.183}, pmid = {31166192}, issn = {1467-3045}, mesh = {Alcohol Oxidoreductases/genetics/metabolism ; Bacteria/enzymology/genetics/metabolism ; Bacterial Proteins/*metabolism ; Energy Metabolism/drug effects/physiology ; Enzymes/classification/*metabolism ; Lanthanoid Series Elements/chemistry/*pharmacology ; Methane/*metabolism ; Methanol/metabolism ; Microbiota/drug effects/*physiology ; Systems Biology/methods ; }, abstract = {In this review article, we cover the recent developments in understanding the principles and the mechanisms by which microbial communities participating in methane consumption in natural environmental niches are assembled, and the physiological and biochemical mechanisms and regulators that allow efficient carbon transfer within the communities. We first give a brief overview of methanotrophy. We then describe the recent evidence on non-random assembly of bacterial communities that utilize carbon from methane, based on stable isotope probing experiments as well as on results from natural community manipulations followed by metagenomic analysis. We follow up by highlighting results from synthetic methanotophic community manipulations identifying the importance of a lanthanide switch that regulates alternative methanol dehydrogenase enzymes in these communities. We further expand on the recently uncovered significance of lanthanides in methylotrophy and review data on the biochemical properties of representatives of two different clades of lanthanide-dependent enzymes. We also provide an overview of the occurrence and the distribution of the lanthanide-dependent alcohol dehydrogenases in the bacterial domain, these data strongly suggesting significance of these metals beyond methylotrophy.}, } @article {pmid31166185, year = {2019}, author = {Smith, GJ and Wrighton, KC}, title = {Metagenomic Approaches Unearth Methanotroph Phylogenetic and Metabolic Diversity.}, journal = {Current issues in molecular biology}, volume = {33}, number = {}, pages = {57-84}, doi = {10.21775/cimb.033.057}, pmid = {31166185}, issn = {1467-3045}, mesh = {Archaea/classification/genetics/metabolism ; *Biodiversity ; Energy Metabolism/*genetics ; *Metagenome/genetics ; Metagenomics/methods ; Methane/*metabolism ; Methanobacteriales/classification/genetics/metabolism ; Microbiota/*genetics ; Phylogeny ; *Soil Microbiology ; }, abstract = {Methanotrophic microorganisms utilize methane as an electron donor and a carbon source. To date, the capacity to oxidize methane is restricted to microorganisms from three bacterial and one archaeal phyla. Most of our knowledge of methanotrophic metabolism has been obtained using highly enriched or pure cultures grown in the laboratory. However, many methanotrophs currently evade cultivation, thus metagenomics provides a complementary approach for gaining insight into currently unisolated microorganisms. Here we synthesize the studies using metagenomics to glean information about methanotrophs. We complement this summary with an analysis of methanotroph marker genes from 235 publically available metagenomic datasets. We analyze the phylogenetic and environmental distribution of methanotrophs sampled by metagenomics. We also highlight metabolic insights that methanotroph genomes assembled from metagenomes are illuminating. In summary, metagenomics has increased methanotrophic foliage within the tree of life, as well as provided new insights into methanotroph metabolism, which collectively can guide new cultivation efforts. Lastly, given the importance of methanotrophs for biotechnological applications and their capacity to filter greenhouse gases from a variety of ecosystems, metagenomics will continue to be an important component in the arsenal of tools needed for understanding methanotroph diversity and metabolism in both engineered and natural systems.}, } @article {pmid31165050, year = {2019}, author = {Tong, X and Su, F and Xu, X and Xu, H and Yang, T and Xu, Q and Dai, H and Huang, K and Zou, L and Zhang, W and Pei, S and Xiao, F and Li, Y and Wang, C}, title = {Alterations to the Lung Microbiome in Idiopathic Pulmonary Fibrosis Patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {149}, pmid = {31165050}, issn = {2235-2988}, mesh = {Biodiversity ; Bronchoalveolar Lavage Fluid/microbiology ; Drug Resistance, Microbial/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Idiopathic Pulmonary Fibrosis/*microbiology ; Lung/*microbiology ; *Microbiota/genetics ; Multivariate Analysis ; Virulence Factors/genetics ; }, abstract = {Lung microbiome ecosystem homeostasis in idiopathic pulmonary fibrosis (IPF) remains uncharacterized. The aims of this study were to identify unique microbial signatures of the lung microbiome and analyze microbial gene function in IPF patients. DNA isolated from BALF samples was obtained for high-throughput gene sequencing. Microbial metagenomic data were used for principal component analysis (PCA) and analyzed at different taxonomic levels. Shotgun metagenomic data were annotated using the KEGG database and were analyzed for functional and metabolic pathways. In this study, 17 IPF patients and 38 healthy subjects (smokers and non-smokers) were recruited. For the PCA, the first and the second principal component explained 16.3 and 13.4% of the overall variability, respectively. The β diversity of microbiome was reduced in the IPF group. Signature of IPF's microbes was enriched of Streptococcus, Pseudobutyrivibrio, and Anaerorhabdus. The translocation of lung microbiome was shown that 32.84% of them were from oral. After analysis of gene function, ABC transporter systems, biofilm formation, and two-component regulatory system were enriched in IPF patients' microbiome. Here we shown the microbiology characteristics in IPF patients. The microbiome may participate in altering internal conditions and involving in generating antibiotic resistance in IPF patients.}, } @article {pmid31164469, year = {2019}, author = {Namasivayam, S and Kauffman, KD and McCulloch, JA and Yuan, W and Thovarai, V and Mittereder, LR and Trinchieri, G and Barber, DL and Sher, A}, title = {Correlation between Disease Severity and the Intestinal Microbiome in Mycobacterium tuberculosis-Infected Rhesus Macaques.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, pmid = {31164469}, issn = {2150-7511}, mesh = {Animals ; Disease Susceptibility/*microbiology ; Dysbiosis/microbiology ; Female ; *Gastrointestinal Microbiome ; Macaca mulatta/microbiology ; Male ; Metagenomics ; Mycobacterium tuberculosis/pathogenicity ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Tuberculosis/*microbiology ; }, abstract = {The factors that determine host susceptibility to tuberculosis (TB) are poorly defined. The microbiota has been identified as a key influence on the nutritional, metabolic, and immunological status of the host, although its role in the pathogenesis of TB is currently unclear. Here, we investigated the influence of Mycobacterium tuberculosis exposure on the microbiome and conversely the impact of the intestinal microbiome on the outcome of M. tuberculosis exposure in a rhesus macaque model of tuberculosis. Animals were infected with different strains and doses of M. tuberculosis in three independent experiments, resulting in a range of disease severities. The compositions of the microbiotas were then assessed using a combination of 16S rRNA and metagenomic sequencing in fecal samples collected pre- and postinfection. Clustering analyses of the microbiota compositions revealed that alterations in the microbiome after M. tuberculosis infection were of much lower magnitude than the variability seen between individual monkeys. However, the microbiomes of macaques that developed severe disease were noticeably distinct from those of the animals with less severe disease as well as from each other. In particular, the bacterial families Lachnospiraceae and Clostridiaceae were enriched in monkeys that were more susceptible to infection, while numbers of Streptococcaceae were decreased. These findings in infected nonhuman primates reveal that certain baseline microbiome communities may strongly associate with the development of severe tuberculosis following infection and can be more important disease correlates than alterations to the microbiota following M. tuberculosis infection itself.IMPORTANCE Why some but not all individuals infected with Mycobacterium tuberculosis develop disease is poorly understood. Previous studies have revealed an important influence of the microbiota on host resistance to infection with a number of different disease agents. Here, we investigated the possible role of the individual's microbiome in impacting the outcome of M. tuberculosis infection in rhesus monkeys experimentally exposed to this important human pathogen. Although M. tuberculosis infection itself caused only minor alterations in the composition of the gut microbiota in these animals, we observed a significant correlation between an individual monkey's microbiome and the severity of pulmonary disease. More importantly, this correlation between microbiota structure and disease outcome was evident even prior to infection. Taken together, our findings suggest that the composition of the microbiome may be a useful predictor of tuberculosis progression in infected individuals either directly because of the microbiome's direct influence on host resistance or indirectly because of its association with other host factors that have this influence. This calls for exploration of the potential of the microbiota composition as a predictive biomarker through carefully designed prospective studies.}, } @article {pmid31164461, year = {2019}, author = {Shaiber, A and Eren, AM}, title = {Composite Metagenome-Assembled Genomes Reduce the Quality of Public Genome Repositories.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, pmid = {31164461}, issn = {2150-7511}, support = {T32 EB009412/EB/NIBIB NIH HHS/United States ; }, mesh = {*Metagenome ; *Microbiota ; }, } @article {pmid31163139, year = {2019}, author = {Mariani, S and Baillie, C and Colosimo, G and Riesgo, A}, title = {Sponges as natural environmental DNA samplers.}, journal = {Current biology : CB}, volume = {29}, number = {11}, pages = {R401-R402}, doi = {10.1016/j.cub.2019.04.031}, pmid = {31163139}, issn = {1879-0445}, mesh = {Animals ; Antarctic Regions ; *Aquatic Organisms/genetics ; *Biodiversity ; DNA Barcoding, Taxonomic/instrumentation/*methods ; DNA, Environmental/*analysis ; Mediterranean Sea ; Metagenomics/instrumentation ; Oceans and Seas ; *Porifera ; }, abstract = {At a time of unprecedented impacts on marine biodiversity, scientists are rapidly becoming persuaded by the potential of screening large swathes of the oceans through the retrieval, amplification and sequencing of trace DNA fragments left behind by marine organisms; an approach known as 'environmental DNA' (eDNA) [1]. In trying to circumvent the many challenges associated with water filtration and DNA isolation from environmental samples, significant investment is being made in high-tech solutions, such as automated underwater vehicles and robots [2]. Here, instead, we explored a simpler, alternative option, based on the recovery of eDNA from sponges (phylum Porifera), the planet's most effective water-filterers. We obtained sponge samples from Mediterranean and Antarctic surveys, extracted total DNA from their tissues, and obtained tens of thousands of fish DNA reads via metabarcoding, which were able to clearly distinguish samples from the two regions. One Antarctic sample yielded hundreds of reads from chinstrap penguin (Pygoscelis antarcticus) and Weddell seal (Leptonychotes weddellii). We argue that this 'natural sampler DNA' (nsDNA) approach is poised to become a powerful, affordable, universal tool for aquatic biodiversity monitoring globally.}, } @article {pmid31161440, year = {2019}, author = {Wu, GL and Lu, HF and Chen, YL and Wang, Q and Cao, H and Li, TY}, title = {Changes of Intestinal Microecology in Patients with Primary Sjogren's Syndrome after Therapy of Yangyin Yiqi Huoxue Recipe ().}, journal = {Chinese journal of integrative medicine}, volume = {25}, number = {9}, pages = {654-662}, pmid = {31161440}, issn = {1993-0402}, mesh = {Adult ; Aged ; Bacteria/chemistry/drug effects ; Biodiversity ; Drugs, Chinese Herbal/pharmacology/*therapeutic use ; Female ; *Gastrointestinal Microbiome/drug effects ; Humans ; Middle Aged ; Phylogeny ; Sjogren's Syndrome/*drug therapy/*microbiology ; }, abstract = {OBJECTIVE: To explore the change of intestinal microecology in patients with primary Sjogren's syndrome (pSS) and correlation with disease activity, and also discuss the therapy effect of Yangyin Yiqi Huoxue Recipe (, YYHD).

METHODS: Sixteen pSS patients were enrolled in the present study, who received 3-month treatment of YYHR, 200 mL orally twice daily. Their pre-and post-test ESSDAI scores, erythrocyte sedimentation rate (ESR) and serum immunoglobulin G (IgG) levels were measured respectively. The 16SrDNA metagenomic sequencing was used to detect and analyze the abundance and diversity of intestinal bacteria flora and the proportion of bacteria at the levels of phylum, family, and genus, in comparision with those of 6 healthy subjects in the control group.

RESULTS: The abundance and diversity of intestinal bacteria flora in pSS patients were lower than those of healthy subjects (P<0.05). After the treatment with YYHD, patients' ESSDAI score and levels of IgG and ESR have decreased significantly (P<0.05). At the phylum level, the proportions of Actinobacteria, Firmicutes, Fusobacteria and Proteobacteria have reduced sharply, while the proportions of Bacteroidetes, Teneriquetes and Candidate-division-TM7 have increased significantly by treatment (all P<0.05). At the classification level, such treatment has caused a significant decrease in the proportions of Bacteroidaceae, Ruminococcaceae, Veillonellaceae, and Enterobacteriacea (all P<0.05), but a significant increase in the proportion of Lachnospiraceae (P<0.05). At the genus level, the treatment has significantly decreased the proportions of Bifidobacterium, Bacteroides, Escherichia-Shigella, Faecalibacterium and Prevotella (all P<0.05), but significantly increased the proportion of Clostridia (P<0.05), close to the levels of healthy subjects (P>0.05).

CONCLUSIONS: There exists an imbalance of intestinal microecology in pSS patients, which can be improved through the treatment with YYHD. Besides, such treatment can also improve the disease activity and adjust the diversity of intestinal bacteria flora, the composition and the abundance of intestinal flora.}, } @article {pmid31161391, year = {2019}, author = {Fujimoto, M and Carey, DE and Zitomer, DH and McNamara, PJ}, title = {Syntroph diversity and abundance in anaerobic digestion revealed through a comparative core microbiome approach.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {15}, pages = {6353-6367}, doi = {10.1007/s00253-019-09862-4}, pmid = {31161391}, issn = {1432-0614}, mesh = {Anaerobiosis ; *Biota ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Fatty Acids, Volatile/metabolism ; Hydrogen-Ion Concentration ; Metagenomics ; Methane/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; *Water Purification ; }, abstract = {Anaerobic digestion is an important biotechnology treatment process for conversion of waste to energy. In this study, a comparative core microbiome approach, i.e., determining taxa that are shared in functioning digesters but not shared in non-functioning digesters, was used to determine microbial taxa that could play key roles for effective anaerobic digestion. Anaerobic digester functions were impaired by adding the broad-spectrum antimicrobial triclosan (TCS) or triclocarban (TCC) at different concentrations, and the core microbiomes in both functioning and non-functioning anaerobic digesters were compared. Digesters treated with high (2500 mg/kg) or medium (450 mg/kg) TCS and high (850 mg/kg) TCC concentrations lost their function, i.e., methane production decreased, effluent volatile fatty acid concentrations increased, and pH decreased. Changes in microbial community diversity and compositions were assessed using 16S rRNA gene amplicon sequencing. Microbial richness decreased significantly in non-functioning digesters (p < 0.001). Microbial community compositions in non-functioning digesters significantly differed from those in functioning digesters (p = 0.001, ANOSIM). Microbes identified as potentially key taxa included previously known fatty acid-degrading syntrophs and amino acid-degrading syntrophs. A diverse group of syntrophs detected in this study had low relative abundance in functioning digesters, suggesting the importance of rare microbes in anaerobic digester operation. The comparative microbiome approach used in this study can be applied to other microbial systems where a community-driven biological phenomena can be observed directly.}, } @article {pmid31160269, year = {2019}, author = {Dahlin, M and Prast-Nielsen, S}, title = {The gut microbiome and epilepsy.}, journal = {EBioMedicine}, volume = {44}, number = {}, pages = {741-746}, pmid = {31160269}, issn = {2352-3964}, mesh = {Animals ; Anticonvulsants/therapeutic use ; Diet Therapy ; Diet, Ketogenic ; Disease Models, Animal ; Dysbiosis ; Epilepsy/*etiology/therapy ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; Nervous System Diseases/etiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recently, evidence from both animal studies and human cases has emerged that a dysbiosis in the gut may be associated with certain forms of epilepsy. The ketogenic diet is an alternative treatment of drug-resistant epilepsy, although its precise mechanism of action has been unclear. It has now been shown that the ketogenic diet changes the composition and function of the gut microbiome in epilepsy patients. Studies in mice have demonstrated that the gut microbiota was necessary for the therapeutic effect of the diet and a mechanism of action has been proposed, providing new potential strategies for treatment. Further studies are needed to confirm the clinical relevance of this discovery. Below, we will discuss the scientific evidence of the role of the microbiome in seizure disorders, the impact of the ketogenic diet on the intestinal microbiota as well as the interactions described between commonly used antiepileptic drugs and intestinal microbial communities. We also discuss the potential of modulators of the gut microbiota as possible future anti-seizure therapeutics.}, } @article {pmid31159860, year = {2019}, author = {Lin, L and Xie, F and Sun, D and Liu, J and Zhu, W and Mao, S}, title = {Ruminal microbiome-host crosstalk stimulates the development of the ruminal epithelium in a lamb model.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {83}, pmid = {31159860}, issn = {2049-2618}, mesh = {Acetates/metabolism ; Animal Feed ; Animals ; Bacteria/classification/metabolism ; Butyrates/metabolism ; Epithelium/microbiology/*physiology ; *Host Microbial Interactions ; Hydrogen-Ion Concentration ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology/physiology ; Sheep/growth & development/microbiology ; *Signal Transduction ; Transcriptome ; }, abstract = {BACKGROUND: The development of the rumen is an important physiological challenge for young ruminants. Previous studies have shown that starter feeding can effectively facilitate the growth and development of the rumen in ruminants. However, the mechanism through which starter feeding stimulates the development of the rumen is not clear. Here, we performed an integrated analysis in ruminal microbiota and a host transcriptomic profile in a lamb model with the intervention of starter feed to understand the ruminal microbiome-host crosstalk in stimulating the development of the ruminal epithelium.

RESULTS: Decreased ruminal pH and increased acetate and butyrate concentrations in the rumen, followed by increasing rumen organ index, were observed in lambs supplemented with starter. Using metagenome sequencing in combination with 16S rRNA and 18S rRNA gene amplicon sequencing, the results showed the abundance of acetate-producing Mitsuokella spp., lactate-producing Sharpea spp., lactate-utilizing Megasphaera spp., and Entodinium spp. was enriched in rumen microbial communities in the starter-feed group. The abundances of genes involved in sugar degradation were decreased in starter-feed lambs, but the GH13 encoding α-amylase was obviously increased. Rumen epithelial transcriptome analysis revealed that seven differentially expressed genes, including MAPK1, PIK3CB, TNFSF10, ITGA6, SNAI2, SAV1, and DLG, related to the cell growth module were upregulated, and BAD's promotion of cell death was downregulated. Correlation analysis revealed that the increase in the concentrations of acetate and butyrate significantly correlated with the expression of these genes, which indicates acetate and butyrate likely acted as important drivers in the ruminal microbiome-host crosstalk.

CONCLUSIONS: The present study comprehensively describes the symbiotic relationship between the rumen microbiota and the host in lambs after starter feeding. Our data demonstrates that the microbiome-driven generation of acetate and butyrate mediated the growth-related genes' regulation of the growth-associated signalling pathway in the ruminal epithelium. These co-development networks regulated many physiological processes in the epithelium, including papillae morphology and rumen epithelial growth.}, } @article {pmid31159288, year = {2019}, author = {Couto-Rodríguez, RL and Montalvo-Rodríguez, R}, title = {Temporal Analysis of the Microbial Community from the Crystallizer Ponds in Cabo Rojo, Puerto Rico, Using Metagenomics.}, journal = {Genes}, volume = {10}, number = {6}, pages = {}, pmid = {31159288}, issn = {2073-4425}, support = {52007566/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Bacteroidetes/genetics ; Euryarchaeota/genetics ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; *Phylogeny ; Ponds/microbiology ; Proteobacteria/genetics ; Puerto Rico ; Tropical Climate ; Water Microbiology ; }, abstract = {The Cabo Rojo solar salterns are a hypersaline environment located in a tropical climate, where conditions remain stable throughout the year. These conditions can favor the establishment of steady microbial communities. Little is known about the microbial composition that thrives in hypersaline environments in the tropics. The main goal of this study was to assess the microbial diversity present in the crystallizer ponds of Cabo Rojo, in terms of structure and metabolic processes across time using metagenomic techniques. Three samplings (December 2014, March and July 2016) were carried out, where water samples (50 L each) were filtered through a Millipore pressurized filtering system. DNA was subsequently extracted using physical-chemical methods and sequenced using paired end Illumina technologies. The sequencing effort produced three paired end libraries with a total of 111,816,040 reads, that were subsequently assembled into three metagenomes. Out of the phyla detected, the microbial diversity was dominated in all three samples by Euryarchaeota, followed by Bacteroidetes and Proteobacteria. However, sample MFF1 (for Muestreo Final Fraternidad) exhibited a higher diversity, with 12 prokaryotic phyla detected at 34% NaCl (w/v), when compared to samples MFF2 and MFF3, which only exhibited three phyla. Precipitation events might be one of the contributing factors to the change in the microbial community composition through time. Diversity at genus level revealed a more stable community structure, with an overwhelming dominance of the square archaeon Haloquadratum in the three metagenomes. Furthermore, functional annotation was carried out in order to detect genes related to metabolic processes, such as carbon, nitrogen, and sulfur cycles. The presence of gene sequences related to nitrogen fixation, ammonia oxidation, sulfate reduction, sulfur oxidation, and phosphate solubilization were detected. Through binning methods, four putative novel genomes were obtained, including a possible novel genus belonging to the Bacteroidetes and possible new species for the genera Natronomonas, Halomicrobium, and Haloquadratum. Using a metagenomic approach, a 3-year study has been performed in a Caribbean hypersaline environment. When compared to other salterns around the world, the Cabo Rojo salterns harbor a similar community composition, which is stable through time. Moreover, an analysis of gene composition highlights the importance of the microbial community in the biogeochemical cycles at hypersaline environments.}, } @article {pmid31158316, year = {2020}, author = {Louati, M and Ennis, NJ and Ghodhbane-Gtari, F and Hezbri, K and Sevigny, JL and Fahnestock, MF and Cherif-Silini, H and Bryce, JG and Tisa, LS and Gtari, M}, title = {Elucidating the ecological networks in stone-dwelling microbiomes.}, journal = {Environmental microbiology}, volume = {22}, number = {4}, pages = {1467-1480}, doi = {10.1111/1462-2920.14700}, pmid = {31158316}, issn = {1462-2920}, support = {//Ministère del'enseignement Supérieur et de la Recherche Scientifique/International ; //University of New Hampshire CoRE program/International ; //University of New Hampshire Summer Teaching Fellowship/International ; DBI-1229361//NSF MRI/International ; }, mesh = {Africa, Northern ; Bacteria/genetics/isolation & purification ; *Extreme Environments ; Metagenome ; *Microbiota/genetics ; Photosynthesis ; Ultraviolet Rays ; }, abstract = {Stone surfaces are extreme environments that support microbial life. This microbial growth occurs despite unfavourable conditions associated with stone including limited sources of nutrients and water, high pH and exposure to extreme variations in temperature, humidity and irradiation. These stone-dwelling microbes are often resistant to extreme environments including exposure to desiccation, heavy metals, UV and Gamma irradiation. Here, we report on the effects of climate and stone geochemistry on microbiomes of Roman stone ruins in North Africa. Stone microbiomes were dominated by Actinobacteria, Cyanobacteria and Proteobacteria but were heavily impacted by climate variables that influenced water availability. Stone geochemistry also influenced community diversity, particularly through biologically available P, Mn and Zn. Functions associated with photosynthesis and UV protection were enriched in the metagenomes, indicating the significance of these functions for community survival on stones. Core members of the stone microbial communities were also identified and included Geodermatophilaceae, Rubrobacter, Sphingomonas and others. Our research has helped to expand the understanding of stone microbial community structure and functional capacity within the context of varying climates, geochemical properties and stone conditions.}, } @article {pmid31154984, year = {2019}, author = {Song, SJ and Sanders, JG and Baldassarre, DT and Chaves, JA and Johnson, NS and Piaggio, AJ and Stuckey, MJ and Nováková, E and Metcalf, JL and Chomel, BB and Aguilar-Setién, A and Knight, R and McKenzie, VJ}, title = {Is there convergence of gut microbes in blood-feeding vertebrates?.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1777}, pages = {20180249}, pmid = {31154984}, issn = {1471-2970}, mesh = {Animals ; Bacteria/classification/*genetics/isolation & purification ; Biological Evolution ; Birds/*genetics/microbiology/physiology ; Chiroptera/*genetics/microbiology/physiology ; DNA, Bacterial/genetics ; Feeding Behavior ; *Gastrointestinal Microbiome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Animal microbiomes play an important role in dietary adaptation, yet the extent to which microbiome changes exhibit parallel evolution is unclear. Of particular interest is an adaptation to extreme diets, such as blood, which poses special challenges in its content of proteins and lack of essential nutrients. In this study, we assessed taxonomic signatures (by 16S rRNA amplicon profiling) and potential functional signatures (inferred by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt)) of haematophagy in birds and bats. Our goal was to test three alternative hypotheses: no convergence of microbiomes, convergence in taxonomy and convergence in function. We find a statistically significant effect of haematophagy in terms of microbial taxonomic convergence across the blood-feeding bats and birds, although this effect is small compared to the differences found between haematophagous and non-haematophagous species within the two host clades. We also find some evidence of convergence at the predicted functional level, although it is possible that the lack of metagenomic data and the poor representation of microbial lineages adapted to haematophagy in genome databases limit the power of this approach. The results provide a paradigm for exploring convergent microbiome evolution replicated with independent contrasts in different host lineages. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.}, } @article {pmid31154531, year = {2019}, author = {Tutuncu, HE and Balci, N and Tuter, M and Karaguler, NG}, title = {Recombinant production and characterization of a novel esterase from a hypersaline lake, Acıgöl, by metagenomic approach.}, journal = {Extremophiles : life under extreme conditions}, volume = {23}, number = {5}, pages = {507-520}, pmid = {31154531}, issn = {1433-4909}, mesh = {Bacterial Proteins/chemistry/*genetics/metabolism ; Enzyme Stability ; Esterases/chemistry/*genetics/metabolism ; Halomonas/enzymology/genetics ; Lakes/microbiology ; *Metagenome ; Microbiota ; Salinity ; *Salt Tolerance ; Substrate Specificity ; }, abstract = {The aim of this study was to isolate a novel esterase from a hypersaline lake by sequence-based metagenomics. The metagenomic DNA was isolated from the enriched hypersaline lake sediment. Degenerate primers targeting the conserved regions of lipolytic enzymes of halophilic microorganisms were used for polymerase chain reaction (PCR) and a whole gene was identified by genome walking. The gene was composed of 783 bp, which corresponds to 260 amino acids with a molecular weight of 28.2 kDa. The deduced amino acid sequence best matched with the esterase from Halomonas gudaonensis with an identity of 91%. Recombinantly expressed enzyme exhibited maximum activity towards pNP-hexanoate with a kcat value of 12.30 s[-1]. The optimum pH and temperature of the enzyme were found as 9 and 30 °C, respectively. The effects of NaCl, solvents, metal ions, detergents and enzyme inhibitors were also studied. In conclusion, a novel enzyme, named as hypersaline lake "Acıgöl" esterase (hAGEst), was identified by sequence-based metagenomics. The high expression level, the ability to maintain activity at cold temperatures and tolerance to DMSO and metal ions are the most outstanding properties of the hAGEst.}, } @article {pmid31153679, year = {2019}, author = {Rettenmaier, R and Duerr, C and Neuhaus, K and Liebl, W and Zverlov, VV}, title = {Comparison of sampling techniques and different media for the enrichment and isolation of cellulolytic organisms from biogas fermenters.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {4}, pages = {481-487}, doi = {10.1016/j.syapm.2019.05.002}, pmid = {31153679}, issn = {1618-0984}, mesh = {Bacteria/classification/genetics/isolation & purification/metabolism ; Biodiversity ; Biofuels/*microbiology ; Biomass ; Bioreactors/microbiology ; Cellulose/*metabolism ; Culture Media ; DNA, Bacterial/genetics ; Industrial Microbiology/*methods ; Metagenome ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Biogas plants achieve its highest yield on plant biomass only with the most efficient hydrolysis of cellulose. This is driven by highly specialized hydrolytic microorganisms, which we have analyzed by investigating enrichment strategies for the isolation of cellulolytic bacteria out of a lab-scale biogas fermenter. We compared three different cultivation media as well as two different inoculation materials: Enrichment on filter paper in nylon bags (in sacco) or raw digestate. Next generation sequencing of the V3/V4 region of the bacterial 16S rRNA of metagenomic DNA from six different enrichment cultures, each in biological triplicates, revealed an average richness of 48 different OTU's with an average evenness of 0.3 in each sample. β-Diversity of the bacterial community revealed significant differences between the two sampling techniques or the different media used. The isolation attempt of single cellulolytic organisms resulted in several clonal pure cultures. Regardless which medium or inoculation material, well-known cellulolytic key players such as Clostridium cellulosi, Herbinix hemicellulosilytica and Hungateiclostridium thermocellum were among the isolates. The inoculation material as well as the cultivation conditions are crucial to cultivate the representative cellulolytic organisms. Taking raw digestate as inoculation material and using the same material, filtered and sterilized, for supplementing media allowed to imitate the natural habitat. Pre-enrichment of cellulolytic organisms directly in their natural habitat led to significant advantages concerning high diversity and high abundance of unknown cellulolytic organisms, which is a key factor for the isolation of hitherto unknown species.}, } @article {pmid31153098, year = {2019}, author = {Farina, R and Severi, M and Carrieri, A and Miotto, E and Sabbioni, S and Trombelli, L and Scapoli, C}, title = {Whole metagenomic shotgun sequencing of the subgingival microbiome of diabetics and non-diabetics with different periodontal conditions.}, journal = {Archives of oral biology}, volume = {104}, number = {}, pages = {13-23}, doi = {10.1016/j.archoralbio.2019.05.025}, pmid = {31153098}, issn = {1879-1506}, mesh = {*Dental Plaque ; *Diabetes Mellitus, Type 2/complications/microbiology ; Gingiva ; Humans ; *Metagenomics ; *Microbiota ; *Mouth/microbiology ; *Periodontitis/complications/microbiology ; }, abstract = {OBJECTIVE: The aim of this study was to use high-resolution whole metagenomic shotgun sequencing to characterize the subgingival microbiome of patients with/without type 2 Diabetes Mellitus and with/without periodontitis.

DESIGN: Twelve subjects, falling into one of the four study groups based on the presence/absence of poorly controlled type 2 Diabetes Mellitus and moderate-severe periodontitis, were selected. For each eligible subject, subgingival plaque samples were collected at 4 sites, all representative of the periodontal condition of the individual (i.e., non-bleeding sulci in subjects without a history of periodontitis, bleeding pockets in patients with moderate-severe periodontitis). The subgingival microbiome was evaluated using high-resolution whole metagenomic shotgun sequencing.

RESULTS: The results showed that: (i) the presence of type 2 Diabetes Mellitus and/or periodontitis were associated with a tendency of the subgingival microbiome to decrease in richness and diversity; (ii) the presence of type 2 Diabetes Mellitus was not associated with significant differences in the relative abundance of one or more species in patients either with or without periodontitis; (iii) the presence of periodontitis was associated with a significantly higher relative abundance of Anaerolineaceae bacterium oral taxon 439 in type 2 Diabetes Mellitus patients.

CONCLUSIONS: Whole metagenomic shotgun sequencing of the subgingival microbiome was extremely effective in the detection of low-abundant taxon. Our results point out a significantly higher relative abundance of Anaerolineaceae bacterium oral taxon 439 in patients with moderate to severe periodontitis vs patients without history of periodontitis, which was maintained when the comparison was restricted to type 2 diabetics.}, } @article {pmid31152950, year = {2019}, author = {Gao, M and Guo, B and Zhang, L and Zhang, Y and Liu, Y}, title = {Microbial community dynamics in anaerobic digesters treating conventional and vacuum toilet flushed blackwater.}, journal = {Water research}, volume = {160}, number = {}, pages = {249-258}, doi = {10.1016/j.watres.2019.05.077}, pmid = {31152950}, issn = {1879-2448}, mesh = {Anaerobiosis ; Archaea ; *Bathroom Equipment ; *Bioreactors ; Methane ; Microbial Consortia ; Sewage ; Vacuum ; Waste Disposal, Fluid ; }, abstract = {Decentralized wastewater treatment represents a promising sustainable option for future wastewater management. Blackwater collected from toilets contains high concentrations of organic matter, ideal for energy recovery using anaerobic digestion. Up-flow anaerobic sludge blanket (UASB) reactors treating conventional toilet (CT, 9 L water per flush) and vacuum toilet (VT, 1 L water per flush) blackwater with increments of loadings were successfully operated to steady state in three phases. The organic loading rates were maintained at comparable levels between the two reactors. The methanisation rates were 0.23-0.29 and 0.41-0.48 gCH4-COD/gfeedCOD in the CT and VT reactors, and the COD removal rates were 72% and 89%, respectively. The enriched microbial consortia and the community dynamics under different loading phases were compared. The rank abundance distributions and alpha-diversity showed that archaeal communities were predominated by mono-enrichments in both CT and VT reactors, while bacterial communities showed lower diversity in the VT reactor. Through principal coordinates analysis (beta-diversity), clear divergences of archaeal and bacterial communities between the CT and VT reactors were revealed, and the archaeal community developed at a slower rate than the bacterial community. The enriched archaea were hydrogenotrophic methanogens, Methanolinea in the CT reactor (56.6%), and Methanogenium in the VT reactor (62.3%). The enriched bacteria were Porphyromonadaceae in both CT (15.9%) and VT (13.4%) reactors, sulfate-reducing bacteria in the CT reactor, and Fibrobacteraceae in the VT reactor (13.8%). Links between enriched consortia and ammonia stress were discussed. Isotope fraction analysis of the biogas showed a slight shift from acetoclastic methanogenesis to hydrogenotrophic methanogenesis. A closer look into the predicted metagenomic functional profiles showed agreeing results, where hydrogenotrophic methanogenesis and fhs gene abundances were higher in the VT reactor. We demonstrated that different blackwater types enriched different microbial consortia, probably due to ammonia concentrations and sulfate loadings, which should be taken into consideration for practical applications.}, } @article {pmid31152018, year = {2019}, author = {Bertucci, M and Calusinska, M and Goux, X and Rouland-Lefèvre, C and Untereiner, B and Ferrer, P and Gerin, PA and Delfosse, P}, title = {Carbohydrate Hydrolytic Potential and Redundancy of an Anaerobic Digestion Microbiome Exposed to Acidosis, as Uncovered by Metagenomics.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {15}, pages = {}, pmid = {31152018}, issn = {1098-5336}, mesh = {Anaerobiosis ; Bacteria/*metabolism ; Bacteroidetes/metabolism ; Biomass ; Bioreactors/*microbiology ; Carbohydrate Metabolism ; Hydrogen-Ion Concentration ; Hydrolysis ; *Metagenome ; *Microbiota ; }, abstract = {Increased hydrolysis of easily digestible biomass may lead to acidosis of anaerobic reactors and decreased methane production. Previously, it was shown that the structure of microbial communities changed during acidosis; however, once the conditions are back to optimal, biogas (initially CO2) production quickly restarts. This suggests the retention of the community functional redundancy during the process failure. In this study, with the use of metagenomics and downstream bioinformatics analyses, we characterize the carbohydrate hydrolytic potential of the microbial community, with a special focus on acidosis. To that purpose, carbohydrate-active enzymes were identified, and to further link the community hydrolytic potential with key microbes, bacterial genomes were reconstructed. In addition, we characterized biochemically the specificity and activity of selected enzymes, thus verifying the accuracy of the in silico predictions. The results confirm the retention of the community hydrolytic potential during acidosis and indicate Bacteroidetes to be largely involved in biomass degradation. Bacteroidetes showed higher diversity and genomic content of carbohydrate hydrolytic enzymes that might favor the dominance of this phylum over other bacteria in some anaerobic reactors. The combination of bioinformatic analyses and activity tests enabled us to propose a model of acetylated glucomannan degradation by BacteroidetesIMPORTANCE The enzymatic hydrolysis of lignocellulosic biomass is mainly driven by the action of carbohydrate-active enzymes. By characterizing the gene profiles at the different stages of the anaerobic digestion experiment, we showed that the microbiome retains its hydrolytic functional redundancy even during severe acidosis, despite significant changes in taxonomic composition. By analyzing reconstructed bacterial genomes, we demonstrate that Bacteroidetes hydrolytic gene diversity likely favors the abundance of this phylum in some anaerobic digestion systems. Further, we observe genetic redundancy within the Bacteroidetes group, which accounts for the preserved hydrolytic potential during acidosis. This work also uncovers new polysaccharide utilization loci involved in the deconstruction of various biomasses and proposes the model of acetylated glucomannan degradation by Bacteroidetes Acetylated glucomannan-enriched biomass is a common substrate for many industries, including pulp and paper production. Using naturally evolved cocktails of enzymes for biomass pretreatment could be an interesting alternative to the commonly used chemical pretreatments.}, } @article {pmid31152014, year = {2019}, author = {Liang, R and Lau, M and Vishnivetskaya, T and Lloyd, KG and Wang, W and Wiggins, J and Miller, J and Pfiffner, S and Rivkina, EM and Onstott, TC}, title = {Predominance of Anaerobic, Spore-Forming Bacteria in Metabolically Active Microbial Communities from Ancient Siberian Permafrost.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {15}, pages = {}, pmid = {31152014}, issn = {1098-5336}, mesh = {Bacteria, Anaerobic/*metabolism ; Geologic Sediments/*microbiology ; *Microbiota ; Permafrost/*microbiology ; Phylogeny ; Siberia ; }, abstract = {The prevalence of microbial life in permafrost up to several million years (Ma) old has been well documented. However, the long-term survivability, evolution, and metabolic activity of the entombed microbes over this time span remain underexplored. We integrated aspartic acid (Asp) racemization assays with metagenomic sequencing to characterize the microbial activity, phylogenetic diversity, and metabolic functions of indigenous microbial communities across a ∼0.01- to 1.1-Ma chronosequence of continuously frozen permafrost from northeastern Siberia. Although Asp in the older bulk sediments (0.8 to 1.1 Ma) underwent severe racemization relative to that in the youngest sediment (∼0.01 Ma), the much lower d-Asp/l-Asp ratio (0.05 to 0.14) in the separated cells from all samples suggested that indigenous microbial communities were viable and metabolically active in ancient permafrost up to 1.1 Ma. The microbial community in the youngest sediment was the most diverse and was dominated by the phyla Actinobacteria and Proteobacteria In contrast, microbial diversity decreased dramatically in the older sediments, and anaerobic, spore-forming bacteria within Firmicutes became overwhelmingly dominant. In addition to the enrichment of sporulation-related genes, functional genes involved in anaerobic metabolic pathways such as fermentation, sulfate reduction, and methanogenesis were more abundant in the older sediments. Taken together, the predominance of spore-forming bacteria and associated anaerobic metabolism in the older sediments suggest that a subset of the original indigenous microbial community entrapped in the permafrost survived burial over geological time.IMPORTANCE Understanding the long-term survivability and associated metabolic traits of microorganisms in ancient permafrost frozen millions of years ago provides a unique window into the burial and preservation processes experienced in general by subsurface microorganisms in sedimentary deposits because of permafrost's hydrological isolation and exceptional DNA preservation. We employed aspartic acid racemization modeling and metagenomics to determine which microbial communities were metabolically active in the 1.1-Ma permafrost from northeastern Siberia. The simultaneous sequencing of extracellular and intracellular genomic DNA provided insight into the metabolic potential distinguishing extinct from extant microorganisms under frozen conditions over this time interval. This in-depth metagenomic sequencing advances our understanding of the microbial diversity and metabolic functions of extant microbiomes from early Pleistocene permafrost. Therefore, these findings extend our knowledge of the survivability of microbes in permafrost from 33,000 years to 1.1 Ma.}, } @article {pmid31150456, year = {2019}, author = {Badiea, EA and Sayed, AA and Maged, M and Fouad, WM and Said, MM and Esmat, AY}, title = {A novel thermostable and halophilic thioredoxin reductase from the Red Sea Atlantis II hot brine pool.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0217565}, pmid = {31150456}, issn = {1932-6203}, mesh = {Aquatic Organisms/*enzymology/genetics ; Enzyme Stability ; Indian Ocean ; Metagenome ; Microbiota/*genetics ; Phylogeny ; Protein Domains ; Seawater/*microbiology ; Sequence Alignment ; Temperature ; Thioredoxin-Disulfide Reductase/chemistry/genetics/*isolation & purification ; Water Microbiology ; }, abstract = {The highly extreme conditions of the lower convective layer in the Atlantis II (ATII) Deep brine pool of the Red Sea make it an ideal environment for the search for novel enzymes that can function under extreme conditions. In the current study, we isolated a novel sequence of a thioredoxin reductase (TrxR) enzyme from the metagenomic dataset established from the microbial community that resides in the lower convective layer of Atlantis II. The gene was cloned, expressed and characterized for redox activity, halophilicity, and thermal stability. The isolated thioredoxin reductase (ATII-TrxR) was found to belong to the high-molecular-weight class of thioredoxin reductases. A search for conserved domains revealed the presence of an extra domain (Crp) in the enzyme sequence. Characterization studies of ATII-TrxR revealed that the enzyme was halophilic (maintained activity at 4 M NaCl), thermophilic (optimum temperature was 65°C) and thermostable (60% of its activity was retained at 70°C). Additionally, the enzyme utilized NADH in addition to NADPH as an electron donor. In conclusion, a novel thermostable and halophilic thioredoxin reductase has been isolated with a unique sequence that adapts to the harsh conditions of the brine pools making this protein a good candidate for biological research and industrial applications.}, } @article {pmid31149718, year = {2019}, author = {Zuo, K and Li, J and Li, K and Hu, C and Gao, Y and Chen, M and Hu, R and Liu, Y and Chi, H and Wang, H and Qin, Y and Liu, X and Li, S and Cai, J and Zhong, J and Yang, X}, title = {Disordered gut microbiota and alterations in metabolic patterns are associated with atrial fibrillation.}, journal = {GigaScience}, volume = {8}, number = {6}, pages = {}, pmid = {31149718}, issn = {2047-217X}, mesh = {Aged ; Asian People ; Atrial Fibrillation/*etiology/microbiology ; Bacteria/*genetics/metabolism ; Feces/chemistry/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metabolomics ; Metagenomics ; Middle Aged ; Serum/chemistry ; }, abstract = {BACKGROUND: With the establishment of the heart-gut axis concept, accumulating studies suggest that the gut microbiome plays an important role in the pathogenesis of cardiovascular diseases. Yet, little evidence has been reported in characterizing the gut microbiota shift in atrial fibrillation.

METHODS: We include the result of the global alterations that occur in the intestinal microbiota in a cohort of 50 patients with atrial fibrillation and 50 matched controls based on a strategy of metagenomic and metabolomic analyses.

RESULTS: The alterations include a dramatic elevation in microbial diversity and a specific perturbation of gut microbiota composition. Overgrowth of Ruminococcus, Streptococcus, and Enterococcus, as well as reduction of Faecalibacterium, Alistipes, Oscillibacter, and Bilophila were detected in patients with atrial fibrillation. A gut microbial function imbalance and correlated metabolic pattern changes were observed with atrial fibrillation in both fecal and serum samples. The differential gut microbiome signatures could be used to identify patients with atrial fibrillation.

CONCLUSIONS: Our findings characterize the disordered gut microbiota and microbial metabolite profiles in atrial fibrillation. Further research could determine whether intervention strategies targeting intestinal microbiome composition might be useful to counteract the progression of atrial fibrillation.}, } @article {pmid31146755, year = {2019}, author = {Dunivin, TK and Yeh, SY and Shade, A}, title = {A global survey of arsenic-related genes in soil microbiomes.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {45}, pmid = {31146755}, issn = {1741-7007}, support = {R25 GM115335/GM/NIGMS NIH HHS/United States ; }, mesh = {Access to Information ; Arsenic/*adverse effects/metabolism ; Bacteria/*drug effects/genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Microbiota/*drug effects/genetics ; *Soil Microbiology ; Soil Pollutants/*adverse effects ; }, abstract = {BACKGROUND: Environmental resistomes include transferable microbial genes. One important resistome component is resistance to arsenic, a ubiquitous and toxic metalloid that can have negative and chronic consequences for human and animal health. The distribution of arsenic resistance and metabolism genes in the environment is not well understood. However, microbial communities and their resistomes mediate key transformations of arsenic that are expected to impact both biogeochemistry and local toxicity.

RESULTS: We examined the phylogenetic diversity, genomic location (chromosome or plasmid), and biogeography of arsenic resistance and metabolism genes in 922 soil genomes and 38 metagenomes. To do so, we developed a bioinformatic toolkit that includes BLAST databases, hidden Markov models and resources for gene-targeted assembly of nine arsenic resistance and metabolism genes: acr3, aioA, arsB, arsC (grx), arsC (trx), arsD, arsM, arrA, and arxA. Though arsenic-related genes were common, they were not universally detected, contradicting the common conjecture that all organisms have them. From major clades of arsenic-related genes, we inferred their potential for horizontal and vertical transfer. Different types and proportions of genes were detected across soils, suggesting microbial community composition will, in part, determine local arsenic toxicity and biogeochemistry. While arsenic-related genes were globally distributed, particular sequence variants were highly endemic (e.g., acr3), suggesting dispersal limitation. The gene encoding arsenic methylase arsM was unexpectedly abundant in soil metagenomes (median 48%), suggesting that it plays a prominent role in global arsenic biogeochemistry.

CONCLUSIONS: Our analysis advances understanding of arsenic resistance, metabolism, and biogeochemistry, and our approach provides a roadmap for the ecological investigation of environmental resistomes.}, } @article {pmid31144773, year = {2019}, author = {Sieow, BF and Nurminen, TJ and Ling, H and Chang, MW}, title = {Meta-Omics- and Metabolic Modeling-Assisted Deciphering of Human Microbiota Metabolism.}, journal = {Biotechnology journal}, volume = {14}, number = {9}, pages = {e1800445}, doi = {10.1002/biot.201800445}, pmid = {31144773}, issn = {1860-7314}, support = {ICP1600012//the Industry Alignment Fund-Industry Collaboration Project/ ; ARO/2019/74459LS//The U.S. Army/ ; NRF-NRFI05-2019-0004//the National Research Foundation Investigatorship/ ; DPRT/943/09/14//the Synthetic Biology Initiative of the National University of Singapore/ ; MOE/2014/T2/2/128//the Ministry of Education, Singapore/ ; RE2016-074//the Ministry of Defence of Singapore/ ; MINDEF//the Ministry of Defence of Singapore/ ; SBP-P2//the Synthetic Biology R&D Programme of the National Research Foundation, Singapore/ ; SBP-P7//the Synthetic Biology R&D Programme of the National Research Foundation, Singapore/ ; NUHSRO/2016/053/SRP/05//Summit Research Program of the National University Health System/ ; DPRT/943/09/14//Synthetic Biology Initiative of the National University of Singapore/ ; RE2016-074//Ministry of Defence of Singapore/ ; MINDEF//Ministry of Defence of Singapore/ ; NRF-NRFI05-2019-0004//National Research Foundation Investigatorship/ ; MOE/2014/T2/2/128//Ministry of Education of Singapore/ ; SBP-P2//Synthetic Biology R&D Programme of the National Research Foundation of Singapore/ ; SBP-P7//Synthetic Biology R&D Programme of the National Research Foundation of Singapore/ ; ICP1600012//Industry Alignment Fund-Industry Collaboration Project/ ; }, mesh = {Animals ; Gastrointestinal Microbiome/genetics ; Humans ; Metabolomics ; Metagenome/*genetics ; Microbiota/*genetics ; }, abstract = {The human microbiota is a complex community of commensal, symbiotic, and pathogenic microbes that play a crucial role in maintaining the homeostasis of human health. Such a homeostasis is maintained through the collective functioning of enzymatic genes responsible for the production of metabolites, enabling the interaction and signaling within microbiota as well as between microbes and the human host. Understanding microbial genes, their associated chemistries and functions would be valuable for engineering systemic metabolic pathways within the microbiota to manage human health and diseases. Given that there are many unknown gene metabolic functions and interactions, increasing efforts have been made to gain insights into the underlying functions of microbiota metabolism. This can be achieved through culture-independent metagenomic approaches and metabolic modeling to simulate the microenvironment of human microbiota. In this article, the recent advances in metagenome mining and functional profiling for the discovery of the genetic and biochemical links in human microbiota metabolism as well as metabolic modeling for simulation and prediction of metabolic fluxes in the human microbiota are reviewed. This review provides useful insights into the understanding, reconstruction, and modulation of the human microbiota guided by the knowledge acquired from the basic understanding of the human microbiota metabolism.}, } @article {pmid31143925, year = {2019}, author = {Hundsdoerfer, AK and Lee, KM and Kitching, IJ and Mutanen, M}, title = {Genome-wide SNP Data Reveal an Overestimation of Species Diversity in a Group of Hawkmoths.}, journal = {Genome biology and evolution}, volume = {11}, number = {8}, pages = {2136-2150}, pmid = {31143925}, issn = {1759-6653}, mesh = {Animals ; *Evolution, Molecular ; *Genome ; Metagenomics/*methods ; Moths/*classification/*genetics ; Phylogeny ; *Polymorphism, Single Nucleotide ; Species Specificity ; }, abstract = {The interface between populations and evolving young species continues to generate much contemporary debate in systematics depending on the species concept(s) applied but which ultimately reduces to the fundamental question of "when do nondiscrete entities become distinct, mutually exclusive evolutionary units"? Species are perceived as critical biological entities, and the discovery and naming of new species is perceived by many authors as a major research aim for assessing current biodiversity before much of it becomes extinct. However, less attention is given to determining whether these names represent valid biological entities because this is perceived as both a laborious chore and an undesirable research outcome. The charismatic spurge hawkmoths (Hyles euphorbiae complex, HEC) offer an opportunity to study this less fashionable aspect of systematics. To elucidate this intriguing systematic challenge, we analyzed over 10,000 ddRAD single nucleotide polymorphisms from 62 individuals using coalescent-based and population genomic methodology. These genome-wide data reveal a clear overestimation of (sub)species-level diversity and demonstrate that the HEC taxonomy has been seriously oversplit. We conclude that only one valid species name should be retained for the entire HEC, namely Hyles euphorbiae, and we do not recognize any formal subspecies or other taxonomic subdivisions within it. Although the adoption of genetic tools has frequently revealed morphologically cryptic diversity, the converse, taxonomic oversplitting of species, is generally (and wrongly in our opinion) accepted as rare. Furthermore, taxonomic oversplitting is most likely to have taken place in intensively studied popular and charismatic organisms such as the HEC.}, } @article {pmid31142849, year = {2019}, author = {Fettweis, JM and Serrano, MG and Brooks, JP and Edwards, DJ and Girerd, PH and Parikh, HI and Huang, B and Arodz, TJ and Edupuganti, L and Glascock, AL and Xu, J and Jimenez, NR and Vivadelli, SC and Fong, SS and Sheth, NU and Jean, S and Lee, V and Bokhari, YA and Lara, AM and Mistry, SD and Duckworth, RA and Bradley, SP and Koparde, VN and Orenda, XV and Milton, SH and Rozycki, SK and Matveyev, AV and Wright, ML and Huzurbazar, SV and Jackson, EM and Smirnova, E and Korlach, J and Tsai, YC and Dickinson, MR and Brooks, JL and Drake, JI and Chaffin, DO and Sexton, AL and Gravett, MG and Rubens, CE and Wijesooriya, NR and Hendricks-Muñoz, KD and Jefferson, KK and Strauss, JF and Buck, GA}, title = {The vaginal microbiome and preterm birth.}, journal = {Nature medicine}, volume = {25}, number = {6}, pages = {1012-1021}, pmid = {31142849}, issn = {1546-170X}, support = {UH2 AI083263/AI/NIAID NIH HHS/United States ; R21 HD092965/HD/NICHD NIH HHS/United States ; U54 HD080784/HD/NICHD NIH HHS/United States ; R25 GM090084/GM/NIGMS NIH HHS/United States ; R01 HD092415/HD/NICHD NIH HHS/United States ; UH3 AI083263/AI/NIAID NIH HHS/United States ; U54 DE023786/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Black or African American ; Biodiversity ; Cohort Studies ; Cytokines/metabolism ; Female ; Host Microbial Interactions/immunology ; Humans ; Infant, Newborn ; Inflammation Mediators/metabolism ; Longitudinal Studies ; Metagenomics ; *Microbiota/genetics/immunology ; Premature Birth/etiology/immunology/*microbiology ; Risk Factors ; United States ; Vagina/immunology/*microbiology ; Young Adult ; }, abstract = {The incidence of preterm birth exceeds 10% worldwide. There are significant disparities in the frequency of preterm birth among populations within countries, and women of African ancestry disproportionately bear the burden of risk in the United States. In the present study, we report a community resource that includes 'omics' data from approximately 12,000 samples as part of the integrative Human Microbiome Project. Longitudinal analyses of 16S ribosomal RNA, metagenomic, metatranscriptomic and cytokine profiles from 45 preterm and 90 term birth controls identified harbingers of preterm birth in this cohort of women predominantly of African ancestry. Women who delivered preterm exhibited significantly lower vaginal levels of Lactobacillus crispatus and higher levels of BVAB1, Sneathia amnii, TM7-H1, a group of Prevotella species and nine additional taxa. The first representative genomes of BVAB1 and TM7-H1 are described. Preterm-birth-associated taxa were correlated with proinflammatory cytokines in vaginal fluid. These findings highlight new opportunities for assessment of the risk of preterm birth.}, } @article {pmid31142780, year = {2019}, author = {Di Salvo, M and Calcagnile, M and Talà, A and Tredici, SM and Maffei, ME and Schönrogge, K and Barbero, F and Alifano, P}, title = {The Microbiome of the Maculinea-Myrmica Host-Parasite Interaction.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {8048}, pmid = {31142780}, issn = {2045-2322}, mesh = {Animal Communication ; Animals ; Ants/microbiology/*parasitology ; Butterflies/*microbiology/physiology ; DNA Barcoding, Taxonomic ; Endangered Species ; Gastrointestinal Microbiome/*physiology ; Host-Parasite Interactions/*physiology ; Larva/*microbiology/physiology ; Metagenome/genetics ; Pheromones/metabolism ; RNA, Ribosomal, 16S/genetics ; Serratia/genetics/isolation & purification/metabolism ; Serratia marcescens/genetics/isolation & purification/metabolism ; Symbiosis/physiology ; }, abstract = {Maculinea (=Phengaris) are endangered butterflies that are characterized by a very complex biological cycle. Maculinea larvae behave as obligate parasites whose survival is strictly dependent on both particular food plants and species-specific Myrmica ants. In this interaction, Maculinea caterpillars induce Myrmica workers to retrieve and rear them in the nest by chemical and acoustic deception. Social insect symbiotic microorganisms play a key role in intraspecific and interspecific communication; therefore, it is possible that the Maculinea caterpillar microbiome might be involved in the chemical cross-talk by producing deceptive semiochemicals for host ants. To address this point, the microbiota of Maculinea alcon at different larval stages (phytophagous early larvae, intermediate larvae, carnivorous late larvae) was analyzed by using 16S rRNA-guided metabarcoding approach and compared to that of the host ant Myrmica scabrinodis. Structural and deduced functional profiles of the microbial communities were recorded, which were used to identify specific groups of microorganisms that may be involved in the chemical cross-talk. One of the most notable features was the presence in all larval stages and in the ants of two bacteria, Serratia marcescens and S. entomophila, which are involved in the chemical cross-talk between the microbes and their hosts.}, } @article {pmid31142575, year = {2019}, author = {Li, S and Tang, H and Ye, Y}, title = {A Meta-proteogenomic Approach to Peptide Identification Incorporating Assembly Uncertainty and Genomic Variation.}, journal = {Molecular & cellular proteomics : MCP}, volume = {18}, number = {8 suppl 1}, pages = {S183-S192}, pmid = {31142575}, issn = {1535-9484}, support = {R01 AI108888/AI/NIAID NIH HHS/United States ; R01 AI143254/AI/NIAID NIH HHS/United States ; }, mesh = {*Algorithms ; Databases, Protein ; Genetic Variation ; Microbiota/*genetics ; Peptides/genetics ; Proteogenomics/*methods ; Seawater/*microbiology ; Tandem Mass Spectrometry ; Wastewater/*microbiology ; }, abstract = {Matching metagenomic and/or metatranscriptomic data, currently often under-used, can be useful reference for metaproteomic tandem mass spectra (MS/MS) data analysis. Here we developed a software pipeline for identification of peptides and proteins from metaproteomic MS/MS data using proteins derived from matching metagenomic (and metatranscriptomic) data as the search database, based on two novel approaches Graph2Pro (published) and Var2Pep (new). Graph2Pro retains and uses uncertainties of metagenome assembly for reference-based MS/MS data analysis. Var2Pep considers the variations found in metagenomic/metatranscriptomic sequencing reads that are not retained in the assemblies (contigs). The new software pipeline provides one stop application of both tools, and it supports the use of metagenome assembly from commonly used assemblers including MegaHit and metaSPAdes. When tested on two collections of multi-omic microbiome data sets, our pipeline significantly improved the identification rate of the metaproteomic MS/MS spectra by about two folds, comparing to conventional contig- or read-based approaches (the Var2Pep alone identified 5.6% to 24.1% more unique peptides, depending on the data set). We also showed that identified variant peptides are important for functional profiling of microbiomes. All results suggested that it is important to take into consideration of the assembly uncertainties and genomic variants to facilitate metaproteomic MS/MS data interpretation.}, } @article {pmid31141902, year = {2019}, author = {Kallies, R and Hölzer, M and Brizola Toscan, R and Nunes da Rocha, U and Anders, J and Marz, M and Chatzinotas, A}, title = {Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters.}, journal = {Viruses}, volume = {11}, number = {6}, pages = {}, pmid = {31141902}, issn = {1999-4915}, mesh = {Caudovirales/genetics ; DNA, Viral/*isolation & purification ; *Gene Library ; *Genome, Viral ; Germany ; Groundwater/*virology ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Myoviridae/genetics ; Nucleic Acid Amplification Techniques ; Phylogeny ; Siphoviridae ; Viruses/*genetics ; }, abstract = {Viral ecology of terrestrial habitats is yet-to be extensively explored, in particular the terrestrial subsurface. One problem in obtaining viral sequences from groundwater aquifer samples is the relatively low amount of virus particles. As a result, the amount of extracted DNA may not be sufficient for direct sequencing of such samples. Here we compared three DNA amplification methods to enrich viral DNA from three pristine limestone aquifer assemblages of the Hainich Critical Zone Exploratory to evaluate potential bias created by the different amplification methods as determined by viral metagenomics. Linker amplification shotgun libraries resulted in lowest redundancy among the sequencing reads and showed the highest diversity, while multiple displacement amplification produced the highest number of contigs with the longest average contig size, suggesting a combination of these two methods is suitable for the successful enrichment of viral DNA from pristine groundwater samples. In total, we identified 27,173, 5,886 and 32,613 viral contigs from the three samples from which 11.92 to 18.65% could be assigned to taxonomy using blast. Among these, members of the Caudovirales order were the most abundant group (52.20 to 69.12%) dominated by Myoviridae and Siphoviridae. Those, and the high number of unknown viral sequences, substantially expand the known virosphere.}, } @article {pmid31141224, year = {2019}, author = {Suzuki, TA and Phifer-Rixey, M and Mack, KL and Sheehan, MJ and Lin, D and Bi, K and Nachman, MW}, title = {Host genetic determinants of the gut microbiota of wild mice.}, journal = {Molecular ecology}, volume = {28}, number = {13}, pages = {3197-3207}, pmid = {31141224}, issn = {1365-294X}, support = {R01 GM074245/GM/NIGMS NIH HHS/United States ; R01 GM127468/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Animals, Wild/microbiology ; Bacteria/*classification ; Biodiversity ; Exome ; *Gastrointestinal Microbiome ; Genetics, Population ; Genome-Wide Association Study ; Host Microbial Interactions/*genetics ; Humans ; Linear Models ; Mice/*microbiology ; Models, Genetic ; Multivariate Analysis ; North America ; Polymorphism, Single Nucleotide ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Identifying a common set of genes that mediate host-microbial interactions across populations and species of mammals has broad relevance for human health and animal biology. However, the genetic basis of the gut microbial composition in natural populations remains largely unknown outside of humans. Here, we used wild house mouse populations as a model system to ask three major questions: (a) Does host genetic relatedness explain interindividual variation in gut microbial composition? (b) Do population differences in the microbiota persist in a common environment? (c) What are the host genes associated with microbial richness and the relative abundance of bacterial genera? We found that host genetic distance is a strong predictor of the gut microbial composition as characterized by 16S amplicon sequencing. Using a common garden approach, we then identified differences in microbial composition between populations that persisted in a shared laboratory environment. Finally, we used exome sequencing to associate host genetic variants with microbial diversity and relative abundance of microbial taxa in wild mice. We identified 20 genes that were associated with microbial diversity or abundance including a macrophage-derived cytokine (IL12a) that contained three nonsynonymous mutations. Surprisingly, we found a significant overrepresentation of candidate genes that were previously associated with microbial measurements in humans. The homologous genes that overlapped between wild mice and humans included genes that have been associated with traits related to host immunity and obesity in humans. Gene-bacteria associations identified in both humans and wild mice suggest some commonality to the host genetic determinants of gut microbial composition across mammals.}, } @article {pmid31140702, year = {2019}, author = {Varoni, EM and Bavarian, R and Robledo-Sierra, J and Porat Ben-Amy, D and Wade, WG and Paster, B and Kerr, R and Peterson, DE and Frandsen Lau, E}, title = {World Workshop on Oral Medicine VII: Targeting the microbiome for oral medicine specialists-Part 1. A methodological guide.}, journal = {Oral diseases}, volume = {25 Suppl 1}, number = {}, pages = {12-27}, doi = {10.1111/odi.13063}, pmid = {31140702}, issn = {1601-0825}, support = {Steering guidance regarding additional text for ac//World Workshop on Oral Medicine VII/ ; }, mesh = {Congresses as Topic ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Microbiota ; *Mouth Diseases ; *Oral Medicine ; Specialization ; }, abstract = {Advances in high-throughput sequencing technologies have allowed for a rapid increase in knowledge about the human microbiome in both healthy and diseased states, which is expected to increase our understanding of multifactorial diseases. The World Workshop on Oral Medicine VII chose the microbiome as one of its topics of focus. Part 1 of this review provides updated knowledge in the field of microbiome research, describes the advantages and disadvantages of currently available sequencing technologies, and proposes a seven-step "recipe" for designing and performing studies that is supported by contemporary evidence. Part 2 of this review in a companion paper discusses the results of high-throughput sequencing studies published to date on the microbiota associated with oral mucosal diseases. The goal of this collective enterprise is to encourage more oral medicine specialists to become engaged in multidisciplinary collaborations to investigate the role of the microbiome in relation to oral diseases, which could potentially lead to enhanced diagnosis, risk assessment and treatment of these patients.}, } @article {pmid31138833, year = {2019}, author = {Gibson, KM and Nguyen, BN and Neumann, LM and Miller, M and Buss, P and Daniels, S and Ahn, MJ and Crandall, KA and Pukazhenthi, B}, title = {Gut microbiome differences between wild and captive black rhinoceros - implications for rhino health.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {7570}, pmid = {31138833}, issn = {2045-2322}, mesh = {Animals ; Animals, Wild/microbiology ; Animals, Zoo/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Mammals/microbiology ; Microbiota/*genetics ; Perissodactyla/*microbiology ; }, abstract = {A number of recent studies have shown the importance of the mammalian gut microbiome in host health. In the context of endangered species, a few studies have examined the relationship between the gut microbiome in wild versus captive populations due to digestive and other health issues. Unfortunately, the results seem to vary across taxa in terms of captive animals having higher, lower, or equivalent microbiome diversity relative to their wild counterparts. Here, we focus on the black rhinoceros as captive animals suffer from a number of potentially dietary related health effects. We compared gut microbiomes of wild and captive black rhinos to test for differences in taxonomic diversity (alpha and beta) and in functional diversity of the microbiome. We incorporated a more powerful metagenomic shotgun sequencing approach rather than a targeted amplification of the 16S gene for taxonomic assignment of the microbiome. Our results showed no significant differences in the alpha diversity levels between wild and captive black rhinos, but significant differences in beta diversity. We found that bacterial taxa traditionally associated with ruminant guts of domesticated animals had higher relative abundances in captive rhinos. Our metagenomic sequencing results suggest that unknown gut microbes of wild rhinos are being replaced by those found in conventional human-domesticated livestock. Wild rhinos have significantly different functional bacterial communities compared to their captive counterparts. Functional profiling results showed greater abundance of glycolysis and amino acid synthesis pathways in captive rhino microbiomes, representing an animal receiving sub-optimal nutrition with a readily available source of glucose but possibly an imbalance of necessary macro and micronutrients. Given the differences observed between wild and captive rhino gut microbiomes, we make a number of recommendations for potentially modifying captive gut microbiome to better reflect their wild counterparts and thereby hopefully improve overall rhino health in captivity.}, } @article {pmid31138751, year = {2019}, author = {Wang, S and El-Fahmawi, A and Christian, DA and Fang, Q and Radaelli, E and Chen, L and Sullivan, MC and Misic, AM and Ellringer, JA and Zhu, XQ and Winter, SE and Hunter, CA and Beiting, DP}, title = {Infection-Induced Intestinal Dysbiosis Is Mediated by Macrophage Activation and Nitrate Production.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, pmid = {31138751}, issn = {2150-7511}, support = {R01 AI125563/AI/NIAID NIH HHS/United States ; R21 AI126042/AI/NIAID NIH HHS/United States ; T32 AI055400/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cytokines/analysis ; Dysbiosis/*immunology ; Enterobacteriaceae/classification ; Female ; *Gastrointestinal Microbiome ; Inflammation ; Interferon-gamma/immunology ; Intestine, Small/*immunology/microbiology/parasitology/*pathology ; *Macrophage Activation ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Nitrates/*metabolism ; Nitric Oxide Synthase Type II/immunology ; Toxoplasma/pathogenicity ; Toxoplasmosis, Animal/*immunology/microbiology ; }, abstract = {Oral infection of C57BL/6J mice with Toxoplasma gondii results in a marked bacterial dysbiosis and the development of severe pathology in the distal small intestine that is dependent on CD4[+] T cells and interferon gamma (IFN-γ). This dysbiosis and bacterial translocation contribute to the development of ileal pathology, but the factors that support the bloom of bacterial pathobionts are unclear. The use of microbial community profiling and shotgun metagenomics revealed that Toxoplasma infection induces a dysbiosis dominated by Enterobacteriaceae and an increased potential for nitrate respiration. In vivo experiments using bacterial metabolic mutants revealed that during this infection, host-derived nitrate supports the expansion of Enterobacteriaceae in the ileum via nitrate respiration. Additional experiments with infected mice indicate that the IFN-γ/STAT1/iNOS axis, while essential for parasite control, also supplies a pool of nitrate that serves as a source for anaerobic respiration and supports overgrowth of Enterobacteriaceae Together, these data reveal a trade-off in intestinal immunity after oral infection of C57BL/6J mice with T. gondii, in which inducible nitric oxide synthase (iNOS) is required for parasite control, while this host enzyme is responsible for specific modification of the composition of the microbiome that contributes to pathology.IMPORTANCEToxoplasma gondii is a protozoan parasite and a leading cause of foodborne illness. Infection is initiated when the parasite invades the intestinal epithelium, and in many host species, this leads to intense inflammation and a dramatic disruption of the normal microbial ecosystem that resides in the healthy gut (the so-called microbiome). One characteristic change in the microbiome during infection with Toxoplasma-as well as numerous other pathogens-is the overgrowth of Escherichia coli or similar bacteria and a breakdown of commensal containment leading to seeding of peripheral organs with gut bacteria and subsequent sepsis. Our findings provide one clear explanation for how this process is regulated, thereby improving our understanding of the relationship between parasite infection, inflammation, and disease. Furthermore, our results could serve as the basis for the development of novel therapeutics to reduce the potential for harmful bacteria to bloom in the gut during infection.}, } @article {pmid31137556, year = {2019}, author = {Kumar, H and Park, W and Srikanth, K and Choi, BH and Cho, ES and Lee, KT and Kim, JM and Kim, K and Park, J and Lim, D and Park, JE}, title = {Comparison of Bacterial Populations in the Ceca of Swine at Two Different Stages and their Functional Annotations.}, journal = {Genes}, volume = {10}, number = {5}, pages = {}, pmid = {31137556}, issn = {2073-4425}, mesh = {Amino Acids/biosynthesis/metabolism ; Animals ; Bacteria/classification ; Bacteroidetes/classification ; Cecum/metabolism/*microbiology/physiology ; Firmicutes/classification ; Gastrointestinal Microbiome/genetics ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, RNA/methods ; Swine/growth & development/*microbiology ; }, abstract = {The microbial composition in the cecum of pig influences host health, immunity, nutrient digestion, and feeding requirements significantly. Advancements in metagenome sequencing technologies such as 16S rRNAs have made it possible to explore cecum microbial population. In this study, we performed a comparative analysis of cecum microbiota of crossbred Korean native pigs at two different growth stages (stage L = 10 weeks, and stage LD = 26 weeks) using 16S rRNA sequencing technology. Our results revealed remarkable differences in microbial composition, α and β diversity, and differential abundance between the two stages. Phylum composition analysis with respect to SILVA132 database showed Firmicutes to be present at 51.87% and 48.76% in stages L and LD, respectively. Similarly, Bacteroidetes were present at 37.28% and 45.98% in L and LD, respectively. The genera Prevotella, Anaerovibrio, Succinivibrio, Megasphaera were differentially enriched in stage L, whereas Clostridium, Terrisporobacter, Rikenellaceae were enriched in stage LD. Functional annotation of microbiome by level-three KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis revealed that glycine, serine, threonine, valine, leucine, isoleucine arginine, proline, and tryptophan metabolism were differentially enriched in stage L, whereas alanine, aspartate, glutamate, cysteine, methionine, phenylalanine, tyrosine, and tryptophan biosynthesis metabolism were differentially enriched in stage LD. Through machine-learning approaches such as LEfSe (linear discriminant analysis effect size), random forest, and Pearson's correlation, we found pathways such as amino acid metabolism, transport systems, and genetic regulation of metabolism are commonly enriched in both stages. Our findings suggest that the bacterial compositions in cecum content of pigs are heavily involved in their nutrient digestion process. This study may help to meet the demand of human food and can play significant roles in medicinal application.}, } @article {pmid31136592, year = {2019}, author = {Czech, L and Stamatakis, A}, title = {Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0217050}, pmid = {31136592}, issn = {1932-6203}, mesh = {Algorithms ; Animals ; Cluster Analysis ; Computational Biology ; Computers ; Databases, Genetic ; Diatoms/classification ; Female ; Gastrointestinal Microbiome/*genetics ; Geography ; Humans ; *Metagenome ; Metagenomics/*methods ; *Oceans and Seas ; *Phylogeny ; Software ; Vaginosis, Bacterial/*microbiology ; }, abstract = {BACKGROUND: The exponential decrease in molecular sequencing cost generates unprecedented amounts of data. Hence, scalable methods to analyze these data are required. Phylogenetic (or Evolutionary) Placement methods identify the evolutionary provenance of anonymous sequences with respect to a given reference phylogeny. This increasingly popular method is deployed for scrutinizing metagenomic samples from environments such as water, soil, or the human gut.

NOVEL METHODS: Here, we present novel and, more importantly, highly scalable methods for analyzing phylogenetic placements of metagenomic samples. More specifically, we introduce methods for (a) visualizing differences between samples and their correlation with associated meta-data on the reference phylogeny, (b) clustering similar samples using a variant of the k-means method, and (c) finding phylogenetic factors using an adaptation of the Phylofactorization method. These methods enable to interpret metagenomic data in a phylogenetic context, to find patterns in the data, and to identify branches of the phylogeny that are driving these patterns.

RESULTS: To demonstrate the scalability and utility of our methods, as well as to provide exemplary interpretations of our methods, we applied them to 3 publicly available datasets comprising 9782 samples with a total of approximately 168 million sequences. The results indicate that new biological insights can be attained via our methods.}, } @article {pmid31134764, year = {2019}, author = {Purahong, W and Pietsch, KA and Bruelheide, H and Wirth, C and Buscot, F and Wubet, T}, title = {Potential links between wood-inhabiting and soil fungal communities: Evidence from high-throughput sequencing.}, journal = {MicrobiologyOpen}, volume = {8}, number = {9}, pages = {e00856}, pmid = {31134764}, issn = {2045-8827}, mesh = {Animals ; China ; Forests ; Fungi/*classification/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Mycobiome ; Pinus ; *Soil Microbiology ; Wood/*microbiology ; }, abstract = {Wood-inhabiting fungi (WIF) are pivotal to wood decomposition, which in turn strongly influences nutrient dynamics in forest soils. However, their dispersal mechanisms remain unclear. We hypothesized that the majority of WIF are soil-borne. For this reason, the presented research aimed to quantify the contribution of soil as a source and medium for the dispersal of WIF to deadwood using high-throughput sequencing. We tested effects of tree species (specifically Schima superba and Pinus massoniana) on the percentage of WIF shared between soil and deadwood in a Chinese subtropical forest ecosystem. We also assessed the taxonomic and ecological functional group affiliations of the fungal community shared between soil and deadwood. Our results indicate that soil is a major route for WIF colonization as 12%-15% (depending on the tree species) of soil fungi were simultaneously detected in deadwood. We also demonstrate that tree species (p < 0.01) significantly shapes the composition of the shared soil and deadwood fungal community. The pH of decomposing wood was shown to significantly correspond (p < 0.01) with the shared community of wood-inhabiting (of both studied tree species) and soil fungi. Furthermore, our data suggest that a wide range of fungal taxonomic (Rozellida, Zygomycota, Ascomycota, and Basidiomycota) and ecological functional groups (saprotrophs, ectomycorrhizal, mycoparasites, and plant pathogens) may use soil as a source and medium for transport to deadwood in subtropical forest ecosystem. While 12%-62% of saprotrophic, ectomycorrhizal, and mycoparasitic WIF may utilize soil to colonize deadwood, only 5% of the detected plant pathogens were detected in both soil and deadwood, implying that these fungi use other dispersal routes. Animal endosymbionts and lichenized WIF were not detected in the soil samples. Future studies should consider assessing the relative contributions of other possible dispersal mechanisms (e.g. wind, water splash, water dispersal, animal dispersal, and mycelial network) in the colonization of deadwood by soil fungi.}, } @article {pmid31134711, year = {2019}, author = {You, YA and Kwon, EJ and Choi, SJ and Hwang, HS and Choi, SK and Lee, SM and Kim, YJ}, title = {Vaginal microbiome profiles of pregnant women in Korea using a 16S metagenomics approach.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {82}, number = {1}, pages = {e13124}, doi = {10.1111/aji.13124}, pmid = {31134711}, issn = {1600-0897}, support = {HI14C0306//Korea Health Industry Development Institute/International ; 1-2016-1388-001-1//Intramural research funds from Ewha womans University/International ; 2016R1A6A3A11932253//The National Research Foundation of Korea/International ; HI18C0378//Ministry of Health & Welfare of the Republic of Korea/International ; }, mesh = {Adult ; Bacteria/classification/genetics ; Female ; Fetal Membranes, Premature Rupture/*microbiology ; Humans ; Metagenomics ; Microbiota/*genetics ; Obstetric Labor, Premature/*microbiology ; Pregnancy ; RNA, Ribosomal, 16S ; Republic of Korea ; Vagina/*microbiology ; }, abstract = {PROBLEM: The stability and dominance of Lactobacillus spp. in vaginal fluid are important for reproductive health. However, the characterization of the vaginal microbiota of women with preterm labor (PTL) or preterm premature rupture of membranes (P-PROM), and its association with preterm birth (PTB) are poorly understood.

METHOD OF STUDY: We collected vaginal fluid from women at risk of PTB (n = 58) in five university hospitals in Korea. We performed a hierarchical clustering analysis and classification according to the Lactobacillus spp. and Lactobacillus abundance using Illumina MiSeq sequencing of 16S rRNA gene amplicons.

RESULTS: Women at risk for PTB caused by P-PROM had greater bacterial richness and diversity at the time of admission than those with PTL (P < 0.05). However, they were not significantly different between term and preterm samples. In the classification by Lactobacillus spp., the community commonly dominated by Bacteroides and Lactobacillus crispatus was found for the first time in pregnant women in Korea, and all women with this community delivered preterm. Intriguingly, women with an abundance of Weissella in a Bacteroides-dominant community delivered at term. Moreover, in the classification by Lactobacillus proportion, the abundances of Weissella and Rickettsiales were associated with term deliveries, but the abundances of Bacteroides and Escherichia-Shigella were associated with PTBs (P < 0.05).

CONCLUSION: This result suggests that Lactobacillus abundance-based classification of vaginal fluid may reveal the microbiome associated with PTB. Further studies are needed to investigate the mechanism underlying the link between the microbiome and PTB.}, } @article {pmid31133738, year = {2019}, author = {Ogwu, MC and Kerfahi, D and Song, H and Dong, K and Seo, H and Lim, S and Srinivasan, S and Kim, MK and Waldman, B and Adams, JM}, title = {Changes in soil taxonomic and functional diversity resulting from gamma irradiation.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {7894}, pmid = {31133738}, issn = {2045-2322}, mesh = {Archaea/classification/genetics/isolation & purification/radiation effects ; Bacteria/classification/genetics/isolation & purification/radiation effects ; DNA, Environmental/genetics/isolation & purification ; Dose-Response Relationship, Radiation ; Fungi/classification/genetics/isolation & purification/radiation effects ; Gamma Rays/*adverse effects ; Metagenome/genetics/radiation effects ; Metagenomics ; Microbiota/genetics/*radiation effects ; Radiation Tolerance/*genetics ; *Soil Microbiology ; }, abstract = {Little is known of the effects of ionizing radiation exposure on soil biota. We exposed soil microcosms to weekly bursts of [60]Co gamma radiation over six weeks, at three levels of exposure (0.1 kGy/hr/wk [low], 1 kGy/hr/wk [medium] and 3 kGy/hr/wk [high]). Soil DNA was extracted, and shotgun metagenomes were sequenced and characterised using MG-RAST. We hypothesized that with increasing radiation exposure there would be a decrease in both taxonomic and functional diversity. While bacterial diversity decreased, diversity of fungi and algae unexpectedly increased, perhaps because of release from competition. Despite the decrease in diversity of bacteria and of biota overall, functional gene diversity of algae, bacteria, fungi and total biota increased. Cycles of radiation exposure may increase the range of gene functional strategies viable in soil, a novel ecological example of the effects of stressors or disturbance events promoting some aspects of diversity. Moreover, repeated density-independent population crashes followed by population expansion may allow lottery effects, promoting coexistence. Radiation exposure produced large overall changes in community composition. Our study suggests several potential novel radiation-tolerant groups: in addition to Deinococcus-Thermus, which reached up to 20% relative abundance in the metagenome, the phyla Chloroflexi (bacteria), Chytridiomycota (fungi) and Nanoarcheota (archaea) may be considered as radiation-tolerant.}, } @article {pmid31129926, year = {2019}, author = {Senés-Guerrero, C and Colón-Contreras, FA and Reynoso-Lobo, JF and Tinoco-Pérez, B and Siller-Cepeda, JH and Pacheco, A}, title = {Biogas-producing microbial composition of an anaerobic digester and associated bovine residues.}, journal = {MicrobiologyOpen}, volume = {8}, number = {9}, pages = {e00854}, pmid = {31129926}, issn = {2045-8827}, mesh = {Anaerobiosis ; Animals ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Biofuels/*microbiology ; *Biota ; Cattle ; Denaturing Gradient Gel Electrophoresis ; Fungi/classification/genetics ; Manure/*microbiology ; Metagenomics ; }, abstract = {Influenced by feedstock type and microbial inoculum, different microbial groups must precisely interact for high-quality biogas yields. As a first approach for optimization, this study aimed to identify through time the biogas-producing microbial community in a 10-ton dry anaerobic digester treating cattle manure by denaturing gradient gel electrophoresis (DGGE) and metagenomics. Moreover, the associated bovine residues or feedstocks (leachate, manure, oxidation lagoon water, rumen) were also characterized to determine their contribution. A diverse and dynamic community characterized by Bacteria (82%-88%) and a considerable amount of Archaea (8%-15%) presented profiles particular to each stage of biogas production. Eukaryotes (2.6%-3.6%), mainly fungi, were a minor but stable component. Proteobacteria represented 47% of the community at the start of the run but only 18% at the end, opposite to the Bacteroidetes/Chlorobi group (8% and 20%, respectively), while Firmicutes (12%-18%) and Actinobacteria (12%-32%) remained relatively constant. Methanogens of the order Methanomicrobiales represented by several species of Methanoculleus were abundant at the end of the run (77%) contrary to Methanosarcinales (11%) and Methanobacteriales (0.7%). Therefore, methanogenesis mainly occurred by the hydrogenotrophic pathway. Manure and oxidation lagoon water seemed to contribute key microorganisms, while rumen dominated by Methanobrevibacter (72%) did not proliferate in the digester. Manure particularly possessed Methanoculleus (24%) and uncultured methanogens identified by DGGE, whereas oxidation lagoon was exclusively abundant in Methanolinea (18%) and Methanosaeta (19%). Leachate, as the microbial inoculum from a previous run, adequately preserved the biogas-producing community. These results could lead to higher biogas yields through bioaugmentation strategies by incorporating higher proportions or an enriched inoculum from the relevant feedstocks.}, } @article {pmid31129882, year = {2019}, author = {Huh, YJ and Seo, JY and Nam, J and Yang, J and McDowell, A and Kim, YK and Lee, JH}, title = {Bariatric/Metabolic Surgery Induces Noticeable Changes of Microbiota and Their Secreting Extracellular Vesicle Composition in the Gut.}, journal = {Obesity surgery}, volume = {29}, number = {8}, pages = {2470-2484}, pmid = {31129882}, issn = {1708-0428}, mesh = {Animals ; Bacteria/classification/isolation & purification ; Bacterial Typing Techniques ; Bariatric Surgery/*methods ; Diabetes Mellitus, Experimental/metabolism/microbiology/*surgery ; Diabetes Mellitus, Type 2/metabolism/microbiology/surgery ; Diet, High-Fat ; Extracellular Vesicles/*metabolism ; Feces/microbiology ; Gastrectomy ; Gastric Bypass ; *Gastrointestinal Microbiome ; Male ; Metagenomics/methods ; Obesity/metabolism/microbiology/*surgery ; Postoperative Period ; Rats ; Rats, Wistar ; }, abstract = {INTRODUCTION: Microbial ecology is reported to be an important regulator of energy homeostasis and glucose metabolism. Microbes secrete extracellular vesicles (EVs) during their proliferation and death to communicate with other cells. To investigate the roles of gut microbiota in glucose metabolism, we analyzed serial changes of gut microbe and microbial EV composition before and after bariatric/metabolic surgery (BMS).

METHODS: Twenty-eight Wistar rats were fed on high-fat diet (HFD) to induce obesity and diabetes. Five of them compared with 5 rats fed on regular chow diet (RCD). Among the remaining 23 rats, Roux-en-Y gastric bypass (RYGB) (n = 10), sleeve gastrectomy (SG) (n = 10), or sham operation (n = 3) was randomly performed. Gut microbiota and EVs from fecal samples were analyzed by 16S rDNA amplicon sequencing.

RESULTS: The present study showed that microbial diversity was decreased in HFD-fed rats versus RCD-fed rats. In addition, BMS reversed glucose intolerance and microbial richness which were induced by HFD. In terms of microbiota and microbial EV composition, both RYGB and SG enhance the composition of phyla Proteobacteria, Verrucomicrobia, and their secreting EVs, but decrease phylum Firmicutes and its EVs. We tried to demonstrate specific genera showed a significant compositional difference in obesity/diabetes-induced rats compared with normal rats and then restored similarly toward normal rats' level after BMS. At the genus level, Lactococcus, Ruminococcus, Dorea in Firmicutes(p), Psychrobacter in Proteobacteria(p), and Akkermansia in Verrucomicrobia(p) fit these conditions after BMS.

CONCLUSION: We suggest that these genera are the candidates contributing to obesity and diabetes improvement mechanism after BMS.}, } @article {pmid31129398, year = {2019}, author = {Qi, M and Huang, H and Zhang, Y and Wang, H and Li, H and Lu, Z}, title = {Novel tetrahydrofuran (THF) degradation-associated genes and cooperation patterns of a THF-degrading microbial community as revealed by metagenomic.}, journal = {Chemosphere}, volume = {231}, number = {}, pages = {173-183}, doi = {10.1016/j.chemosphere.2019.05.137}, pmid = {31129398}, issn = {1879-1298}, mesh = {Actinomycetales ; Furans/analysis/*chemistry/metabolism ; Metagenome/*genetics ; Metagenomics ; Microbiota ; Mixed Function Oxygenases/genetics/metabolism ; Open Reading Frames ; }, abstract = {Our understanding of the tetrahydrofuran (THF) degradation in complex environment is limited. The majority of THF degrading genes reported are group V soluble diiron monooxygenases and share greater than 95% homology with one another. In this study, we used sole-carbon-source incubation combined with high-throughput metagenomic sequencing to investigate this contaminant's degradation in environmental samples. We identified as-yet-uncultivated microbe from the genera Pseudonocardia and fungi Scedosporium sp. (Scedosporium sp. was successfully isolated) as THF degraders as containing THF degradation genes, while microbes from the genera Bordetella, Pandoraea and Rhodanobacter functioned as main cooperators by utilizing acidic intermediates and providing anti-acid mechanisms. Furthermore, a 9387-bp THF degradation cluster designated thmX from the as-yet-uncultivated Pseudonocardia (with 6 main ORFs and with 79-93% amino acid sequence identity with previously reported clusters) was discovered. We also found a THF-degrading related cytochrome P450 monooxygenase from the genus Scedosporium and predicted its cognate reductase for the first time. All the genes and clusters mentioned above were successfully amplified from samples and cloned into the suitable expression vectors. This study will provide novel insights for understanding of THF degradation mechanisms under acid stress conditions and mining new THF degradation genes.}, } @article {pmid31127248, year = {2019}, author = {Woyke, T}, title = {Beyond the census of human gut dwellers.}, journal = {Nature reviews. Microbiology}, volume = {17}, number = {7}, pages = {401}, pmid = {31127248}, issn = {1740-1534}, mesh = {*Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenomics/*methods ; *Microbiota ; }, } @article {pmid31126262, year = {2019}, author = {Ke, S and Fang, S and He, M and Huang, X and Yang, H and Yang, B and Chen, C and Huang, L}, title = {Age-based dynamic changes of phylogenetic composition and interaction networks of health pig gut microbiome feeding in a uniformed condition.}, journal = {BMC veterinary research}, volume = {15}, number = {1}, pages = {172}, pmid = {31126262}, issn = {1746-6148}, support = {31772579//National Natural Science Foundation of China/ ; 31472071//National Natural Science Foundation of China/ ; }, mesh = {*Age Factors ; Animals ; Bacteria/*classification/genetics ; Bacterial Typing Techniques ; Female ; Gastrointestinal Microbiome/*physiology ; Male ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sus scrofa/*microbiology ; }, abstract = {BACKGROUND: The gut microbiota impacts on a range of host biological processes, and the imbalances in its composition are associated with pathology. Though the understanding of contribution of the many factors, e.g. gender, diet and age, in the development of gut microbiota has been well established, the dynamic changes of the phylogenetic composition and the interaction networks along with the age remain unclear in pigs.

RESULTS: Here we applied 16S ribosomal RNA gene sequencing, enterotype-like clustering (Classification of the gut microbiome into distinct types) and phylogenetic co-occurrence network to explore the dynamic changes of pig gut microbiome following the ages with a successive investigation at four ages in a cohort of 953 pigs. We found that Firmicutes and Bacteroidetes are two predominant phyla throughout the experimental period. The richness of gut microbiota was significantly increased from 25 to 240 days of age. Principal coordinates analysis showed a clear difference in the gut microbial community compositions between pre-weaning piglets and the pigs at the other three age groups. The gut microbiota of pre-weaning piglets was clearly classified into two enterotypes, which were dominated by Fusobacterium and p-75-a5, respectively. However, Prevotella and Treponema were the main drivers of the enterotypes for pigs at the age of 80, 120 and 240 days. Besides the piglets, even some adult pigs switched putative enterotypes between ages. We confirmed that the topological features of phylogenetic co-occurrence networks, including scale, stability and complexity were increased along with the age. The biological significance for modules in the network of piglets were mainly associated with the utilization of simple carbohydrate and lactose, whereas the sub-networks identified at the ages of 80, 120 and 240 days may be involved in the digestion of complex dietary polysaccharide. The modules related to the metabolism of protein and amino acids could be identified in the networks at 120 and 240 days. This dynamic change of the functional capacities of gut microbiome was further supported by functional prediction analysis.

CONCLUSIONS: The present study provided meaningful biological insights into the age-based dynamic shifts of ecological community of porcine gut microbiota.}, } @article {pmid31126257, year = {2019}, author = {Plaza-Díaz, J and Álvarez-Mercado, AI and Ruiz-Marín, CM and Reina-Pérez, I and Pérez-Alonso, AJ and Sánchez-Andujar, MB and Torné, P and Gallart-Aragón, T and Sánchez-Barrón, MT and Reyes Lartategui, S and García, F and Chueca, N and Moreno-Delgado, A and Torres-Martínez, K and Sáez-Lara, MJ and Robles-Sánchez, C and Fernández, MF and Fontana, L}, title = {Association of breast and gut microbiota dysbiosis and the risk of breast cancer: a case-control clinical study.}, journal = {BMC cancer}, volume = {19}, number = {1}, pages = {495}, pmid = {31126257}, issn = {1471-2407}, support = {PI-0538-2017//Consejería de Salud, Junta de Andalucía/ ; FIS-PI16/01812//Instituto de Salud Carlos III/ ; }, mesh = {Adult ; Aged ; Biopsy ; Breast/*microbiology/pathology ; Breast Neoplasms/blood/*microbiology/pathology/urine ; Case-Control Studies ; DNA Damage ; Dysbiosis/*microbiology ; Environmental Exposure/adverse effects ; Estrogens/analysis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Metabolome ; Middle Aged ; Surveys and Questionnaires ; }, abstract = {BACKGROUND: Breast cancer ranks first in women, and is the second cause of death in this gender. In addition to genetics, the environment contributes to the development of the disease, although the factors involved are not well known. Among the latter is the influence of microorganisms and, therefore, attention is recently being paid to the mammary microbiota. We hypothesize that the risk of breast cancer could be associated with the composition and functionality of the mammary/gut microbiota, and that exposure to environmental contaminants (endocrine disruptors, EDCs) might contribute to alter these microbiota.

METHODS: We describe a case-control clinical study that will be performed in women between 25 and 70 years of age. Cases will be women diagnosed and surgically intervened of breast cancer (stages I and II). Women with antecedents of cancer or advanced tumor stage (metastasis), or who have received antibiotic treatment within a period of 3 months prior to recruitment, or any neoadjuvant therapy, will be excluded. Controls will be women surgically intervened of breast augmentation or reduction. Women with oncological, gynecological or endocrine history, and those who have received antibiotic treatment within a period of 3 months prior to recruitment will also be excluded. Blood, urine, breast tissue and stool samples will be collected. Data regarding anthropometric, sociodemographic, reproductive history, tumor features and dietary habits will be gathered. Metabolomic studies will be carried out in stool and breast tissue samples. Metagenomic studies will also be performed in stool and breast tissue samples to ascertain the viral, fungal, bacterial and archaea populations of the microbiota. Quantitation of estrogens, estrogen metabolites and EDCs in samples of serum, urine and breast tissue will also be performed.

DISCUSSION: This is the first time that the contribution of bacteria, archaea, viruses and fungi together with their alteration by environmental contaminants to the risk of breast cancer will be evaluated in the same study. Results obtained could contribute to elucidate risk factors, improve the prognosis, as well as to propose novel intervention studies in this disease.

TRIAL REGISTRATION: ClinicalTrials.gov NCT03885648 , 03/25/2019. Retrospectively registered.}, } @article {pmid31124702, year = {2019}, author = {Davis, A and Kohler, C and Alsallaq, R and Hayden, R and Maron, G and Margolis, E}, title = {Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomass.}, journal = {BioTechniques}, volume = {66}, number = {6}, pages = {285-289}, doi = {10.2144/btn-2019-0016}, pmid = {31124702}, issn = {1940-9818}, mesh = {Bacteria/*genetics ; Bacterial Load ; DNA Contamination ; DNA, Bacterial/genetics/*isolation & purification ; Feces/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {A major challenge for microbiome studies is maintaining an even and accurate DNA extraction in the presence of samples with a wide range of bacterial content. Here we compare five DNA extraction methods using replicate stool samples that were diluted to create high and low biomass samples. Our results indicate greater variation in microbiome composition between high and low biomass samples than variation between methods. Many of the extraction methods had reduced yield from low biomass samples; however, our adapted plate column-based extraction method was evenly efficient and captured the largest number of high-quality reads. Based on these results, we have identified a DNA extraction method that ensures adequate yield in metagenomic microbiome studies that have samples with a broad range of bacterial content.}, } @article {pmid31123265, year = {2019}, author = {Li, Y and Fu, X and Ma, J and Zhang, J and Hu, Y and Dong, W and Wan, Z and Li, Q and Kuang, YQ and Lan, K and Jin, X and Wang, JH and Zhang, C}, title = {Altered respiratory virome and serum cytokine profile associated with recurrent respiratory tract infections in children.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {2288}, pmid = {31123265}, issn = {2041-1723}, mesh = {Acute Disease ; Bacteriophages/genetics/*isolation & purification ; Child ; Child, Preschool ; Cytokines/*blood/immunology ; Disease Susceptibility/blood/immunology/microbiology ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Infant ; Longitudinal Studies ; Male ; Metagenomics/methods ; Microbiota/genetics ; Propionibacterium/virology ; Proteomics/methods ; Recurrence ; Respiratory System/immunology/*virology ; Respiratory Tract Infections/*blood/immunology/microbiology ; Retrospective Studies ; }, abstract = {Recurrent acute respiratory tract infections (ARTIs) affect a large population, yet the specific decisive factors are largely unknown. Here we study a population of 4407 children diagnosed with ARTI, comparing respiratory virome and serum cytokine profiles associated with multiple ARTIs and single ARTI during a six-year period. The relative abundance of Propionibacterium phages is significantly elevated in multiple ARTIs compared to single ARTI group. Serum levels of TIMP-1 and PDGF-BB are markedly increased in multiple ARTIs compared to single-ARTI and non-ARTI controls, making these two cytokines potential predictors for multiple ARTIs. The presence of Propionibacterium phages is associated with higher levels of TIMP-1 and PDGF-BB. Receiver operating characteristic (ROC) curve analyses show that the combination of TIMP-1, PDGF-BB and Propionibacterium phages could be a strong predictor for multiple ARTIs. These findings indicate that respiratory microbe homeostasis and specific cytokines are associated with the onset of multiple ARTIs over time.}, } @article {pmid31122082, year = {2019}, author = {McCombe, PA and Henderson, RD and Lee, A and Lee, JD and Woodruff, TM and Restuadi, R and McRae, A and Wray, NR and Ngo, S and Steyn, FJ}, title = {Gut microbiota in ALS: possible role in pathogenesis?.}, journal = {Expert review of neurotherapeutics}, volume = {19}, number = {9}, pages = {785-805}, doi = {10.1080/14737175.2019.1623026}, pmid = {31122082}, issn = {1744-8360}, mesh = {Amyotrophic Lateral Sclerosis/*etiology/*microbiology ; Animals ; Dysbiosis/*complications ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Introduction: The gut microbiota has important roles in maintaining human health. The microbiota and its metabolic byproducts could play a role in the pathogenesis of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Areas covered: The authors evaluate the methods of assessing the gut microbiota, and also review how the gut microbiota affects the various physiological functions of the gut. The authors then consider how gut dysbiosis could theoretically affect the pathogenesis of ALS. They present the current evidence regarding the composition of the gut microbiota in ALS and in rodent models of ALS. Finally, the authors review therapies that could improve gut dysbiosis in the context of ALS. Expert opinion: Currently reported studies suggest some instances of gut dysbiosis in ALS patients and mouse models; however, these studies are limited, and more information with well-controlled larger datasets is required to make a definitive judgment about the role of the gut microbiota in ALS pathogenesis. Overall this is an emerging field that is worthy of further investigation. The authors advocate for larger studies using modern metagenomic techniques to address the current knowledge gaps.}, } @article {pmid31119430, year = {2019}, author = {Klippel, B and Blank, S and Janzer, VA and Piascheck, H and Moccand, C and Bel-Rhlid, R and Antranikian, G}, title = {Characterization of a thermoactive endoglucanase isolated from a biogas plant metagenome.}, journal = {Extremophiles : life under extreme conditions}, volume = {23}, number = {4}, pages = {479-486}, pmid = {31119430}, issn = {1433-4909}, mesh = {Bacterial Proteins/chemistry/genetics/*metabolism ; Biofuels/*microbiology ; Cellulase/chemistry/genetics/*metabolism ; Enzyme Stability ; *Metagenome ; Microbiota ; Power Plants ; Substrate Specificity ; *Thermotolerance ; }, abstract = {A metagenomic library from DNA isolated from a biogas plant was constructed and screened for thermoactive endoglucanases to gain insight into the enzymatic diversity involved in plant biomass breakdown at elevated temperatures. Two cellulase-encoding genes were identified and the corresponding proteins showed sequence similarities of 59% for Cel5A to a putative cellulase from Anaerolinea thermolimosa and 99% for Cel5B to a characterized endoglucanase isolated from a biogas plant reactor. The cellulase Cel5A consists of one catalytical domain showing sequence similarities to glycoside hydrolase family 5 and comprises 358 amino acids with a predicted molecular mass of 41.2 kDa. The gene coding for cel5A was successfully cloned and expressed in Escherichia coli C43(DE3). The recombinant protein was purified to homogeneity using affinity chromatography with a specific activity of 182 U/mg, and a yield of 74%. Enzymatic activity was detectable towards cellulose and mannan containing substrates and over a broad temperature range from 40 °C to 70 °C and a pH range from 4.0 to 7.0 with maximal activity at 55 °C and pH 5.0. Cel5A showed high thermostability at 60 °C without loss of activity after 24 h. Due to the enzymatic characteristics, Cel5A is an attractive candidate for the degradation of lignocellulosic material.}, } @article {pmid31119300, year = {2019}, author = {Kim, H and Worsley, O and Yang, E and Purbojati, RW and Liang, AL and Tan, W and Moses, DID and Hartono, S and Fan, V and Lim, TKH and Schuster, SC and Foo, RS and Chow, PKH and Pettersson, S}, title = {Persistent changes in liver methylation and microbiome composition following reversal of diet-induced non-alcoholic-fatty liver disease.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {76}, number = {21}, pages = {4341-4354}, pmid = {31119300}, issn = {1420-9071}, support = {none//Ministry of Education - Singapore/ ; none//EU grant TORNADO/ ; }, mesh = {Animals ; *DNA Methylation/drug effects ; Diet, High-Fat/*adverse effects ; Dietary Fats/adverse effects/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Liver/drug effects/*metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/*etiology/genetics/metabolism/microbiology ; Obesity/genetics/metabolism/microbiology ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD) is a metabolic liver disease that is thought to be reversible by changing the diet. To examine the impact of dietary changes on progression and cure of NAFLD, we fed mice a high-fat diet (HFD) or high-fructose diet (HFrD) for 9 weeks, followed by an additional 9 weeks, where mice were given normal chow diet. As predicted, the diet-induced NAFLD elicited changes in glucose tolerance, serum cholesterol, and triglyceride levels in both diet groups. Moreover, the diet-induced NAFLD phenotype was reversed, as measured by the recovery of glucose intolerance and high cholesterol levels when mice were given normal chow diet. However, surprisingly, the elevated serum triglyceride levels persisted. Metagenomic analysis revealed dietary-induced changes of microbiome composition, some of which remained altered even after reversing the diet to normal chow, as illustrated by species of the Odoribacter genus. Genome-wide DNA methylation analysis revealed a "priming effect" through changes in DNA methylation in key liver genes. For example, the lipid-regulating gene Apoa4 remained hypomethylated in both groups even after introduction to normal chow diet. Our results support that dietary change, in part, reverses the NAFLD phenotype. However, some diet-induced effects remain, such as changes in microbiome composition, elevated serum triglyceride levels, and hypomethylation of key liver genes. While the results are correlative in nature, it is tempting to speculate that the dietary-induced changes in microbiome composition may in part contribute to the persistent epigenetic modifications in the liver.}, } @article {pmid31119104, year = {2019}, author = {Govender, Y and Gabriel, I and Minassian, V and Fichorova, R}, title = {The Current Evidence on the Association Between the Urinary Microbiome and Urinary Incontinence in Women.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {133}, pmid = {31119104}, issn = {2235-2988}, mesh = {Female ; *Host Microbial Interactions ; Humans ; *Microbiota ; Prevalence ; Risk Factors ; Urinary Incontinence/*epidemiology/*physiopathology ; Urinary Tract/*microbiology ; }, abstract = {Urinary incontinence (UI) is a burdensome condition with high prevalence in middle-aged to older women and an unclear etiology. Advances in our understanding of host-microbe interactions in the urogenital tract have stimulated interest in the urinary microbiome. DNA sequencing and enhanced urine culture suggest that similarly to other mucosal sites, the urinary bladder of healthy individuals harbors resident microbial communities that may play distinct roles in bladder function. This review focused on the urobiome (expanded quantitative urine culture-based or genomic sequencing-based urinary microbiome) associated with different subtypes of UI, including stress, urgency and mixed urinary incontinence, and related syndromes, such as interstitial cystitis and overactive bladder in women, contrasted to urinary tract infections. Furthermore, we examined clinical evidence for the association of the urinary microbiome with responses to pharmacotherapy for amelioration of UI symptoms. Although published studies are still relatively limited in number, study design and sample size, cumulative evidence suggests that certain Lactobacillus species may play a role in maintaining a healthy bladder milieu. Higher bacterial diversity in the absence of Lactobacillus dominance was associated with urgency UI and resistance to anticholinergic treatment for this condition. UI may also facilitate the persistence of uropathogens following antibiotic treatment, which in turn can alter the commensal/potentially beneficial microbial communities. Risk factors of UI, including age, menopausal status, sex steroid hormones, and body mass index may also impact the urinary microbiome. However, it is yet unclear whether the effects of these risks factors on UI are mediated by urinary host-microbe interactions and a mechanistic link with the female urogenital microbiome is still to be established. Strategies for future research are suggested.}, } @article {pmid31118083, year = {2019}, author = {Borsetto, C and Amos, GCA and da Rocha, UN and Mitchell, AL and Finn, RD and Laidi, RF and Vallin, C and Pearce, DA and Newsham, KK and Wellington, EMH}, title = {Microbial community drivers of PK/NRP gene diversity in selected global soils.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {78}, pmid = {31118083}, issn = {2049-2618}, support = {BB/L027801/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Africa ; Antarctic Regions ; Bacteria/*classification/enzymology ; Caribbean Region ; Europe ; *Genetic Variation ; *Microbiota ; Multigene Family ; *Peptide Biosynthesis, Nucleic Acid-Independent ; Phylogeny ; Polyketide Synthases/*genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {BACKGROUND: The emergence of antibiotic-resistant pathogens has created an urgent need for novel antimicrobial treatments. Advances in next-generation sequencing have opened new frontiers for discovery programmes for natural products allowing the exploitation of a larger fraction of the microbial community. Polyketide (PK) and non-ribosomal pepetide (NRP) natural products have been reported to be related to compounds with antimicrobial and anticancer activities. We report here a new culture-independent approach to explore bacterial biosynthetic diversity and determine bacterial phyla in the microbial community associated with PK and NRP diversity in selected soils.

RESULTS: Through amplicon sequencing, we explored the microbial diversity (16S rRNA gene) of 13 soils from Antarctica, Africa, Europe and a Caribbean island and correlated this with the amplicon diversity of the adenylation (A) and ketosynthase (KS) domains within functional genes coding for non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), which are involved in the production of NRP and PK, respectively. Mantel and Procrustes correlation analyses with microbial taxonomic data identified not only the well-studied phyla Actinobacteria and Proteobacteria, but also, interestingly, the less biotechnologically exploited phyla Verrucomicrobia and Bacteroidetes, as potential sources harbouring diverse A and KS domains. Some soils, notably that from Antarctica, provided evidence of endemic diversity, whilst others, such as those from Europe, clustered together. In particular, the majority of the domain reads from Antarctica remained unmatched to known sequences suggesting they could encode enzymes for potentially novel PK and NRP.

CONCLUSIONS: The approach presented here highlights potential sources of metabolic novelty in the environment which will be a useful precursor to metagenomic biosynthetic gene cluster mining for PKs and NRPs which could provide leads for new antimicrobial metabolites.}, } @article {pmid31117952, year = {2019}, author = {Moore, SG and Ericsson, AC and Behura, SK and Lamberson, WR and Evans, TJ and McCabe, MS and Poock, SE and Lucy, MC}, title = {Concurrent and long-term associations between the endometrial microbiota and endometrial transcriptome in postpartum dairy cows.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {405}, pmid = {31117952}, issn = {1471-2164}, mesh = {Animals ; Cattle ; Endometrium/*metabolism/*microbiology ; *Estrous Cycle ; Female ; Lactation ; Metabolome ; *Microbiota ; *Postpartum Period ; RNA, Ribosomal, 16S/genetics ; *Transcriptome ; }, abstract = {BACKGROUND: Fertility in dairy cows depends on ovarian cyclicity and on uterine involution. Ovarian cyclicity and uterine involution are delayed when there is uterine dysbiosis (overgrowth of pathogenic bacteria). Fertility in dairy cows may involve a mechanism through which the uterine microbiota affects ovarian cyclicity as well as the transcriptome of the endometrium within the involuting uterus. The hypothesis was that the transcriptome of the endometrium in postpartum cows would be associated with the cyclicity status of the cow as well as the microbiota during uterine involution. The endometrium of first lactation dairy cows was sampled at 1, 5, and 9 weeks postpartum. All cows were allowed to return to cyclicity without intervention until week 5 and treated with an ovulation synchronization protocol so that sampling at week 9 was on day 13 of the estrous cycle. The endometrial microbiota was measured by 16S rRNA gene sequencing and principal component analysis. The endometrial transcriptome was measured by mRNA sequencing, differential gene expression analysis, and Ingenuity Pathway Analysis.

RESULTS: The endometrial microbiota changed from week 1 to week 5 but the week 5 and week 9 microbiota were similar. The endometrial transcriptome differed for cows that were either cycling or not cycling at week 5 and cyclicity status depended in part on the endometrial microbiota. Compared with cows cycling at week 5, there were large changes in the transcriptome of cows that progressed from non-cycling at week 5 to cycling at week 9. There was evidence for concurrent and longer-term associations between the endometrial microbiota and transcriptome. The week 1 endometrial microbiota had the greatest effect on the subsequent endometrial transcriptome and this effect was greatest at week 5 and diminished by week 9.

CONCLUSIONS: The cumulative response of the endometrial transcriptome to the microbiota represented the combination of past microbial exposure and current microbial exposure. The endometrial transcriptome in postpartum cows, therefore, depended on the immediate and longer-term effects of the uterine microbiota that acted directly on the uterus. There may also be an indirect mechanism through which the microbiome affects the transcriptome through the restoration of ovarian cyclicity postpartum.}, } @article {pmid31116375, year = {2019}, author = {Ma, A and Sun, M and McDermaid, A and Liu, B and Ma, Q}, title = {MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {21}, pages = {4474-4477}, pmid = {31116375}, issn = {1367-4811}, support = {UL1 TR002733/TR/NCATS NIH HHS/United States ; }, mesh = {Feces ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; Metagenomics ; Transcriptome ; }, abstract = {MOTIVATION: Metagenomic and metatranscriptomic analyses can provide an abundance of information related to microbial communities. However, straightforward analysis of this data does not provide optimal results, with a required integration of data types being needed to thoroughly investigate these microbiomes and their environmental interactions.

RESULTS: Here, we present MetaQUBIC, an integrated biclustering-based computational pipeline for gene module detection that integrates both metagenomic and metatranscriptomic data. Additionally, we used this pipeline to investigate 735 paired DNA and RNA human gut microbiome samples, resulting in a comprehensive hybrid gene expression matrix of 2.3 million cross-species genes in the 735 human fecal samples and 155 functional enriched gene modules. We believe both the MetaQUBIC pipeline and the generated comprehensive human gut hybrid expression matrix will facilitate further investigations into multiple levels of microbiome studies.

The package is freely available at https://github.com/OSU-BMBL/metaqubic.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid31114971, year = {2019}, author = {de Assumpção, PP and Araújo, TMT and de Assumpção, PB and Barra, WF and Khayat, AS and Assumpção, CB and Ishak, G and Nunes, DN and Dias-Neto, E and Coelho, LGV}, title = {Suicide journey of H. pylori through gastric carcinogenesis: the role of non-H. pylori microbiome and potential consequences for clinical practice.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {38}, number = {9}, pages = {1591-1597}, pmid = {31114971}, issn = {1435-4373}, mesh = {*Carcinogenesis ; *Dysbiosis ; Gastritis/*microbiology ; Gastritis, Atrophic/microbiology ; *Gastrointestinal Microbiome ; Helicobacter Infections/*microbiology ; Helicobacter pylori/*pathogenicity ; Humans ; Stomach/microbiology ; Stomach Neoplasms/*microbiology ; Tumor Microenvironment ; }, abstract = {Despite being one of the most studied cancer-related infections, the relationship between Helicobacter pylori infection and gastric adenocarcinoma (GC) remains, in some points, obscure. Based on a critical analysis of the available literature regarding stomach microbiota, we aimed to shed light to a possible new interpretation of the current understanding about the Helicobacter pylori-related GC carcinogenesis. We analyzed data from the literature on Helicobacter pylori and other potential carcinogenic pathogens, in both benignant conditions and gastric adenocarcinoma. Helicobacter pylori is the dominant microorganism in benignant conditions as non-complicated gastritis. In atrophic gastritis, metaplasia and, mainly, in gastric adenocarcinoma, a strong reduction in Helicobacter pylori abundance, and increased occurrence of other microorganisms is strongly demonstrated by metagenomic experiments. While causing peptic disease and keeping the stomach's high acidity, Helicobacter pylori infection avoids gastric infection by carcinogenic intestinal microbiota. Nevertheless, Helicobacter pylori persistence may also provoke an atrophic gastritis, a condition that causes its own decline, due to a microenvironment modification, including reduced acidity, resulting in Helicobacter pylori substitution by a cancer-prone microbiota. This new interpretation might result in a dramatic modification on clinical management of Helicobacter pylori-related gastric disease.}, } @article {pmid31114015, year = {2019}, author = {Worrich, A and Musat, N and Harms, H}, title = {Associational effects in the microbial neighborhood.}, journal = {The ISME journal}, volume = {13}, number = {9}, pages = {2143-2149}, pmid = {31114015}, issn = {1751-7370}, mesh = {Ecology ; Metagenome ; *Microbiota ; Plant Development ; Plants/*microbiology ; }, abstract = {Even though "perfect" metagenomes or metatranscriptomes are close at hand, the implicit assumption of spatial homogeneity in the "omic" approaches makes it difficult if not impossible to relate those data to ecological processes occurring in natural and man-made ecosystems. In fact, the distribution of microbes in their habitats is far from being uniform and random. Microbial communities show a high degree of spatial organization that stems from environmental gradients and local interactions. These interactions can be very complex and may involve multiple species. Several studies highlighted the importance of indirect interactions for community stability, but the absence of a theoretical framework for microbial ecology restricts the possibilities to strike a balance between the investigation of simple communities with purely pairwise interactions and the attempts to understand interaction patterns in whole communities based on meta-omics studies. Here we suggest adapting the concept of Associational Effects (AE) from plant ecology, to better understand the link between ecological interactions, spatial arrangement, and stability in microbial communities. By bringing together a conceptual framework developed for plants and observations made for microbes, this perspective article fosters synthesis of related disciplines to yield novel insights into the advancing field of spatial microbial ecology. To promote the integration into microbial ecology, we (i) outline the theoretical background of AE, (ii) collect underlying mechanisms by literature synthesis, (iii) propose a three-point roadmap for the investigation of AE in microbial communities, and (iv) discuss its implications for microbial ecology research.}, } @article {pmid31111267, year = {2019}, author = {Jadeja, NB and Purohit, HJ and Kapley, A}, title = {Decoding microbial community intelligence through metagenomics for efficient wastewater treatment.}, journal = {Functional & integrative genomics}, volume = {19}, number = {6}, pages = {839-851}, pmid = {31111267}, issn = {1438-7948}, mesh = {Biodegradation, Environmental ; Chlorobenzoates/analysis/metabolism ; Cresols/analysis/metabolism ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; Wastewater/chemistry/*microbiology ; }, abstract = {Activated sludge, a microbial ecosystem at industrial wastewater treatment plants, is an active collection of diverse gene pool that creates the intelligence required for coexistence at the cost of pollutants. This study has analyzed one such ecosystem from a site treating wastewater pooled from over 200 different industries. The metagenomics approach used could predict the degradative pathways of more than 30 dominating molecules commonly found in wastewater. Results were extended to design a bioremediation strategy using 4-methylphenol, 2-chlorobenzoate, and 4-chlorobenzoate as target compounds. Catabolic potential required to degrade four aromatic families, namely benzoate family, PAH family, phenol family, and PCB family, was mapped. Results demonstrated a network of diverse genera, where a few phylotypes were seen to contain diverse catabolic capacities and were seen to be present in multiple networks. The study highlights the importance of looking more closely at the microbial community of activated sludge to harness its latent potential. Conventionally treated as a black box, the activated biomass does not perform at its full potential. Metagenomics allows a clearer insight into the complex pathways operating at the site and the detailed documentation of genes allows the activated biomass to be used as a bioresource.}, } @article {pmid31110364, year = {2019}, author = {Diamond, S and Andeer, PF and Li, Z and Crits-Christoph, A and Burstein, D and Anantharaman, K and Lane, KR and Thomas, BC and Pan, C and Northen, TR and Banfield, JF}, title = {Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms.}, journal = {Nature microbiology}, volume = {4}, number = {8}, pages = {1356-1367}, pmid = {31110364}, issn = {2058-5276}, mesh = {Bacteria/classification/*genetics/metabolism ; Biodiversity ; California ; Carbon/*metabolism ; Carbon Cycle ; Ecology ; Ecosystem ; *Genomics ; *Grassland ; Metagenomics ; Nitrogen/*metabolism ; Nitrogen Cycle ; Proteomics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Soil microbial activity drives the carbon and nitrogen cycles and is an important determinant of atmospheric trace gas turnover, yet most soils are dominated by microorganisms with unknown metabolic capacities. Even Acidobacteria, among the most abundant bacteria in soil, remain poorly characterized, and functions across groups such as Verrucomicrobia, Gemmatimonadetes, Chloroflexi and Rokubacteria are understudied. Here, we have resolved 60 metagenomic and 20 proteomic data sets from a Mediterranean grassland soil ecosystem and recovered 793 near-complete microbial genomes from 18 phyla, representing around one-third of all microorganisms detected. Importantly, this enabled extensive genomics-based metabolic predictions for these communities. Acidobacteria from multiple previously unstudied classes have genomes that encode large enzyme complements for complex carbohydrate degradation. Alternatively, most microorganisms encode carbohydrate esterases that strip readily accessible methyl and acetyl groups from polymers like pectin and xylan, forming methanol and acetate, the availability of which could explain the high prevalence of C1 metabolism and acetate utilization in genomes. Microorganism abundances among samples collected at three soil depths and under natural and amended rainfall regimes indicate statistically higher associations of inorganic nitrogen metabolism and carbon degradation in deep and shallow soils, respectively. This partitioning decreased in samples under extended spring rainfall, indicating that long-term climate alteration can affect both carbon and nitrogen cycling. Overall, by leveraging natural and experimental gradients with genome-resolved metabolic profiles, we link microorganisms lacking prior genomic characterization to specific roles in complex carbon, C1, nitrate and ammonia transformations, and constrain factors that impact their distributions in soil.}, } @article {pmid31109865, year = {2019}, author = {Takahashi, Y and Park, J and Hosomi, K and Yamada, T and Kobayashi, A and Yamaguchi, Y and Iketani, S and Kunisawa, J and Mizuguchi, K and Maeda, N and Ohshima, T}, title = {Analysis of oral microbiota in Japanese oral cancer patients using 16S rRNA sequencing.}, journal = {Journal of oral biosciences}, volume = {61}, number = {2}, pages = {120-128}, doi = {10.1016/j.job.2019.03.003}, pmid = {31109865}, issn = {1880-3865}, mesh = {Bacteria ; Humans ; Japan ; *Microbiota ; *Mouth Neoplasms ; RNA, Ribosomal, 16S ; }, abstract = {OBJECTIVES: It is important to determine the cause of increasing oral cancer occurrence and mortality rates in Japan, because the mortality rate has recently decreased in other developed countries. The impact of microbiota in carcinogenesis, especially in the digestive tract has been reported. This study aimed to clarify the relationship between oral cancer and oral microbiota in Japanese patients.

METHODS: DNA was extracted from salivary samples of 60 oral cancer patients and 80 non-cancer individuals as controls. We performed metagenomic analysis using 16S rRNA amplicon sequencing. Statistical analysis in this study was performed using R (version 3.5.0).

RESULTS: Oral cancer patients showed higher α-diversity compared to the control group, and the β-diversity between the two groups differed significantly. Further, there was a significant difference in the abundance ratio of bacterial genera between the two groups. Peptostreptococcus, Fusobacterium, Alloprevotella, and Capnocytophaga were more abundant in the cancer group compared to the control, whereas Rothia and Haemophilus were less abundant (p < 0.01). A negative correlation in the microbiota composition was confirmed between the operational taxonomic units (OTU) of genus Rothia and T-stage progression using the TNM classification method. We performed logistic regression analysis to investigate the impact factor for the oral cancer group, and the result showed that Chao 1 index and sex are statistically significant variables.

CONCLUSIONS: In this study, we observed an increased bacterial diversity in oral cancer patients and found distribution changes for some bacteria.}, } @article {pmid31108361, year = {2019}, author = {Regar, RK and Gaur, VK and Bajaj, A and Tambat, S and Manickam, N}, title = {Comparative microbiome analysis of two different long-term pesticide contaminated soils revealed the anthropogenic influence on functional potential of microbial communities.}, journal = {The Science of the total environment}, volume = {681}, number = {}, pages = {413-423}, doi = {10.1016/j.scitotenv.2019.05.090}, pmid = {31108361}, issn = {1879-1026}, mesh = {*Biodegradation, Environmental ; *Environmental Monitoring ; India ; Microbiota ; Pesticides/*analysis ; *Soil Microbiology ; Soil Pollutants/*analysis ; }, abstract = {Microbial communities play a crucial role in bioremediation of pollutants in contaminated ecosystem. In addition to pure culture isolation and bacterial 16S rRNA based community studies, the focus has now shifted employing the omics technologies enormously for understanding the microbial diversity and functional potential of soil samples. Our previous report on two pesticide-contaminated sites revealed the diversity of both culturable and unculturable bacteria. In the present study, we have observed distinct taxonomic and functional communities in contaminated soil with respect to an uncontaminated soil as control by using shotgun metagenomic sequencing method. Our data demonstrated that Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Acidobacteria significantly dominated the microbial diversity with their cumulative abundance percentage in the range of 98.61, 87.38, and 80.52 for Hindustan Insecticides Limited (HIL), India Pesticides Limited (IPL), and control respectively. Functional gene analysis demonstrated the presence of large number of both substrate specific upper pathway and common lower pathway degradative genes. Relatively lower number of genes was found encoding the degradation of styrene, atrazine, bisphenol, dioxin, and naphthalene. When three bacteria were augumentated with rhamnolipid (20-100 μM) and Triton X-100 (84-417 μM) surfactants in HIL soil, an enhanced degradation to 76%, 70%, and 58% of HCH, Endosulfan, and DDT respectively was achieved. The overall data obtained from two heavily contaminated soil suggest the versatility of the microbial communities for the xenobiotic pollutant degradation which may help in exploiting their potential applications in bioremediation.}, } @article {pmid31106964, year = {2019}, author = {Van der Heyden, C and De Mulder, T and Volcke, EIP and Demeyer, P and Heyndrickx, M and Rasschaert, G}, title = {Long-term microbial community dynamics at two full-scale biotrickling filters treating pig house exhaust air.}, journal = {Microbial biotechnology}, volume = {12}, number = {4}, pages = {775-786}, pmid = {31106964}, issn = {1751-7915}, mesh = {Air Filters/*microbiology ; Animal Husbandry ; Animals ; Bacteria/*classification/genetics ; Cluster Analysis ; DNA Barcoding, Taxonomic ; DNA, Ribosomal/chemistry/genetics ; *Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Swine ; }, abstract = {In this study, the microbial community structure of two full-scale biotrickling filters treating exhaust air from a pig housing facility were evaluated using 16S metabarcoding. The effect of inoculation with activated sludge of a nearby domestic waste water treatment plant was investigated, which is a cheap procedure and easy to apply in practice. The study was performed at a three-stage and a two-stage full-scale biotrickling filter; of which, only the latter was inoculated. Both biotrickling filters evolved towards a rather similar community over time, which differed from the one in the activated sludge used for inoculation. However, the bacterial population at both biotrickling filters showed small differences on the family level. A large population of heterotrophic bacteria, including denitrifying bacteria, was present in both biotrickling filters. In the non-inoculated biotrickling filter, nitrite-oxidizing bacteria (NOB) could not be detected, which corresponded with the incomplete nitrification leading to high nitrite accumulation observed in this system. Inoculation with the wide spectrum inoculum activated sludge had in this study a positive effect on the biotrickling filter performance (higher ammonia removal and lower nitrous oxide production). It could thus be beneficial to inoculate biotrickling filters in order to enrich NOB at the start-up, making it easier to keep the free nitrous acid concentration low enough to not be inhibited by it.}, } @article {pmid31104215, year = {2019}, author = {Li, P and Wu, H and Jin, Y and Huang, X and Chen, Y and Yang, X and Wang, R and Zhang, W}, title = {Exploring the diversity and dynamic of bacterial community vertically distributed in Tongguling National Nature Reserve in Hainan Island, China.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {50}, number = {3}, pages = {729-737}, pmid = {31104215}, issn = {1678-4405}, mesh = {Bacteria/classification/genetics/*isolation & purification ; *Biodiversity ; China ; Conservation of Natural Resources ; DNA, Bacterial/genetics ; Ecosystem ; Human Activities ; Humans ; Islands ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {National nature reserves are important for preserving ecological resources and constructing national ecological security barriers. Tongguling National Nature Reserve (TNNR) is known for its unique tropical island ecosystem and abundant biological resources. This study was conducted to characterize and compare its bacterial community diversity and composition in soils from 10, 20, and 30 cm in depth using high-throughput sequencing of 16S rDNA genes. We found that soils from 20 cm had the highest diversity and might serve as a "middle bridge" to the dynamic distribution between the 10- and 30-cm soil samples. The diversity pattern indicated that the main abundant groups varied distinctly and significantly among soils of different depths. Moreover, Chloroflexi was the most dynamic group in TNNR soils, together with another abundant but rarely reported group, Verrucomicrobia, which greatly enhanced the microbial diversity of TNNR soils. Overall, the results of this study emphasize the urgent need for greater understanding of bacterial community variations in response to human activities and climate change.}, } @article {pmid31102963, year = {2019}, author = {Liu, S and Chen, Q and Zou, H and Yu, Y and Zhou, Z and Mao, J and Zhang, S}, title = {A metagenomic analysis of the relationship between microorganisms and flavor development in Shaoxing mechanized huangjiu fermentation mashes.}, journal = {International journal of food microbiology}, volume = {303}, number = {}, pages = {9-18}, doi = {10.1016/j.ijfoodmicro.2019.05.001}, pmid = {31102963}, issn = {1879-3460}, mesh = {Chromatography, High Pressure Liquid ; *Fermentation ; Fermented Foods/*microbiology ; Gas Chromatography-Mass Spectrometry ; *Metagenomics ; *Microbiota/genetics ; Taste ; }, abstract = {Complex microbial metabolism is responsible for the unique flavor of Shaoxing mechanized huangjiu. However, the relationship between the microorganisms present during fermentation and the formation of specific flavor components is difficult to understand. In this study, gas chromatography-mass spectrometry and high-performance liquid chromatography were used to identify flavor components, and a metagenomic sequencing approach was used to characterize the taxonomic and functional attributes of the Shaoxing mechanized huangjiu fermentation microbiota. The metagenomic sequencing data were used to predict the relationship between microorganisms and flavor formation. The chromatographic analysis identified amino acids, alcohols, acids, phenols and esters as major flavor components, and six microbial genera (Saccharomyces, Aspergillus, Saccharopolyspora, Staphylococcus, Lactobacillus, and Lactococcus) were most closely related to the production of these flavor components. This study helps clarify the different metabolic roles of microorganisms in flavor formation during Shaoxing huangjiu fermentation.}, } @article {pmid31102141, year = {2020}, author = {Sahoo, K and Sahoo, RK and Gaur, M and Subudhi, E}, title = {Cellulolytic thermophilic microorganisms in white biotechnology: a review.}, journal = {Folia microbiologica}, volume = {65}, number = {1}, pages = {25-43}, pmid = {31102141}, issn = {1874-9356}, support = {YSS/2014/000413//Science and Engineering Research Board/ ; }, mesh = {Bacteria/*enzymology/genetics/*metabolism ; Cellulase/*genetics ; Cellulose/metabolism ; Enzymes ; Genetic Engineering ; Industrial Microbiology/*methods ; *Metabolic Engineering ; Metagenomics ; }, abstract = {Enzymes of microbial origin are of immense importance for organic material decomposition leading to bioremediation of organic waste, bioenergy generation, large-scale industrial bioprocesses, etc. The market demand for microbial cellulase enzyme is growing more rapidly which ultimately becomes the driving force towards research on this biocatalyst, widely used in various industrial activities. The use of novel cellulase genes obtained from various thermophiles through metagenomics and genetic engineering as well as following metabolic engineering pathways would be able to enhance the production of thermophilic cellulase at industrial scale. The present review is mainly focused on thermophilic cellulolytic bacteria, discoveries on cellulase gene, genetically modified cellulase, metabolic engineering, and their various industrial applications. A lot of lacunae are yet to overcome for thermophiles such as metagenome analysis, metabolic pathway modification study, search of heterologous hosts in gene expression system, and improved recombinant strain for better cellulase yield as well as value-added product formation.}, } @article {pmid30815250, year = {2018}, author = {Cuscó, A and Catozzi, C and Viñes, J and Sanchez, A and Francino, O}, title = {Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon.}, journal = {F1000Research}, volume = {7}, number = {}, pages = {1755}, pmid = {30815250}, issn = {2046-1402}, mesh = {Animals ; Dogs ; Metagenomics ; *Microbiota ; *Nanopores ; Operon ; RNA, Ribosomal, 16S ; }, abstract = {Background: Profiling the microbiome of low-biomass samples is challenging for metagenomics since these samples are prone to contain DNA from other sources (e.g. host or environment). The usual approach is sequencing short regions of the 16S rRNA gene, which fails to assign taxonomy to genus and species level. To achieve an increased taxonomic resolution, we aim to develop long-amplicon PCR-based approaches using Nanopore sequencing. We assessed two different genetic markers: the full-length 16S rRNA (~1,500 bp) and the 16S-ITS-23S region from the rrn operon (4,300 bp). Methods: We sequenced a clinical isolate of Staphylococcus pseudintermedius, two mock communities and two pools of low-biomass samples (dog skin). Nanopore sequencing was performed on MinION™ using the 1D PCR barcoding kit. Sequences were pre-processed, and data were analyzed using EPI2ME or Minimap2 with rrn database. Consensus sequences of the 16S-ITS-23S genetic marker were obtained using canu. Results: The full-length 16S rRNA and the 16S-ITS-23S region of the rrn operon were used to retrieve the microbiota composition of the samples at the genus and species level. For the Staphylococcus pseudintermedius isolate, the amplicons were assigned to the correct bacterial species in ~98% of the cases with the16S-ITS-23S genetic marker, and in ~68%, with the 16S rRNA gene when using EPI2ME. Using mock communities, we found that the full-length 16S rRNA gene represented better the abundances of a microbial community; whereas, 16S-ITS-23S obtained better resolution at the species level. Finally, we characterized low-biomass skin microbiota samples and detected species with an environmental origin. Conclusions: Both full-length 16S rRNA and the 16S-ITS-23S of the rrn operon retrieved the microbiota composition of simple and complex microbial communities, even from the low-biomass samples such as dog skin. For an increased resolution at the species level, targeting the 16S-ITS-23S of the rrn operon would be the best choice.}, } @article {pmid31101866, year = {2019}, author = {Cho, EJ and Leem, S and Kim, SA and Yang, J and Lee, YB and Kim, SS and Cheong, JY and Cho, SW and Kim, JW and Kim, SM and Yoon, JH and Park, T}, title = {Circulating Microbiota-Based Metagenomic Signature for Detection of Hepatocellular Carcinoma.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {7536}, pmid = {31101866}, issn = {2045-2322}, mesh = {Biomarkers, Tumor/genetics ; Carcinoma, Hepatocellular/*blood/*diagnosis/microbiology ; Cross-Sectional Studies ; DNA, Bacterial/*blood ; DNA, Ribosomal/blood/genetics ; Dysbiosis/*blood/microbiology ; Female ; Humans ; Liver Cirrhosis/blood/microbiology ; Liver Neoplasms/*blood/*diagnosis/microbiology ; Male ; Metagenome/genetics ; Microbiota/genetics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; }, abstract = {Circulating microbial dysbiosis is associated with chronic liver disease including nonalcoholic steatohepatitis and alcoholic liver disease. In this study, we evaluated whether disease-specific alterations of circulating microbiome are present in patients with cirrhosis and hepatocellular carcinoma (HCC), and their potential as diagnostic biomarkers for HCC. We performed cross-sectional metagenomic analyses of serum samples from 79 patients with HCC, 83 with cirrhosis, and 201 matching healthy controls, and validated the results in the same number of subjects. Serum bacterial DNA was analyzed using high-throughput pyrosequencing after amplification of the V3-V4 hypervariable regions of 16S rDNA. Blood microbial diversity was significantly reduced in HCC, compared with cirrhosis and control. There were significant differences in the relative abundances of several bacterial taxa that correlate with the presence of HCC, thus defining a specific blood microbiome-derived metagenomic signature of HCC. We identified 5 microbial gene markers-based model which distinguished HCC from controls with an area under the receiver-operating curve (AUC) of 0.879 and a balanced accuracy of 81.6%. In the validation, this model accurately distinguished HCC with an AUC of 0.875 and an accuracy of 79.8%. In conclusion, circulating microbiome-based signatures may be potential biomarkers for the detection HCC.}, } @article {pmid31101811, year = {2019}, author = {Sande, CJ and Njunge, JM and Mwongeli Ngoi, J and Mutunga, MN and Chege, T and Gicheru, ET and Gardiner, EM and Gwela, A and Green, CA and Drysdale, SB and Berkley, JA and Nokes, DJ and Pollard, AJ}, title = {Airway response to respiratory syncytial virus has incidental antibacterial effects.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {2218}, pmid = {31101811}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Infections/*immunology/microbiology ; Cell Degranulation/immunology ; Child, Preschool ; Humans ; Infant ; Infant, Newborn ; Kenya ; Metagenomics/methods ; Microbiota/immunology ; Neutrophils/*immunology ; Proteomics/methods ; Respiratory Mucosa/cytology/*immunology/microbiology ; Respiratory Syncytial Virus Infections/*immunology/virology ; Respiratory Syncytial Virus, Human/*immunology/isolation & purification ; Streptococcus/immunology/isolation & purification ; }, abstract = {RSV infection is typically associated with secondary bacterial infection. We hypothesise that the local airway immune response to RSV has incidental antibacterial effects. Using coordinated proteomics and metagenomics analysis we simultaneously analysed the microbiota and proteomes of the upper airway and determined direct antibacterial activity in airway secretions of RSV-infected children. Here, we report that the airway abundance of Streptococcus was higher in samples collected at the time of RSV infection compared with samples collected one month later. RSV infection is associated with neutrophil influx into the airway and degranulation and is marked by overexpression of proteins with known antibacterial activity including BPI, EPX, MPO and AZU1. Airway secretions of children infected with RSV, have significantly greater antibacterial activity compared to RSV-negative controls. This RSV-associated, neutrophil-mediated antibacterial response in the airway appears to act as a regulatory mechanism that modulates bacterial growth in the airways of RSV-infected children.}, } @article {pmid31101528, year = {2019}, author = {Hagihara, M and Yamashita, R and Matsumoto, A and Mori, T and Inagaki, T and Nonogaki, T and Kuroki, Y and Higashi, S and Oka, K and Takahashi, M and Mikamo, H}, title = {The impact of probiotic Clostridium butyricum MIYAIRI 588 on murine gut metabolic alterations.}, journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy}, volume = {25}, number = {8}, pages = {571-577}, doi = {10.1016/j.jiac.2019.02.008}, pmid = {31101528}, issn = {1437-7780}, mesh = {Animals ; Clindamycin/adverse effects ; Clostridium butyricum/*growth & development ; Feces/microbiology ; Female ; Firmicutes/drug effects ; Gastrointestinal Microbiome/*drug effects ; Japan ; Metabolic Networks and Pathways/drug effects ; Metagenomics/methods ; Mice ; Mice, Inbred ICR ; Probiotics/*pharmacology ; }, abstract = {INTRODUCTION: Clostridium butyricum MIYAIRI 588 (CBM 588) is a probiotic bacterium used in antidiarrheal medicine in Japan. A few studies analyzed the changes in gut microbiome in patients treated with antimicrobials based on metagenomics sequencing. However, the impact of CBM 588 on gut metabolic alterations has not been fully elucidated. This study was to reveal the impact of CBM 588 on gut metabolic alterations.

MATERIAL AND METHODS: In this in vivo study, mice were divided into four groups and CBM 588, clindamycin (CLDM), and normal saline (control) was orally administered (1. CLDM, 2. CBM 588, 3. CBM 588 + CLDM, 4. water) for 4 days. Fecal samples were collected to extract DNA for metagenomics analysis. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was used to obtain relative Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway abundance information derived from metagenomics data.

RESULTS: CLDM treatment resulted in a dramatic increase in Firmicutes phylum compared to non-CLDM-treated groups (control and CBM 588-treated group). Then, the CBM 588 + CLDM-treated group showed a trend similar in many metabolic pathways to the CLDM-treated group. On the other hand, the CBM 588 + CLDM-treated group showed higher relative abundance compared to the CLDM-treated group especially in starch and sucrose metabolism.

DISCUSSION: We concluded that CBM 588 caused a gut microbiome functional shift toward increased carbohydrate metabolism. These results support the hypothesis that CBM 588 treatment modulates gut microbiome under dysbiosis conditions due to antimicrobials.}, } @article {pmid31098412, year = {2019}, author = {Sato, Y and Hori, T and Koike, H and Navarro, RR and Ogata, A and Habe, H}, title = {Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {179}, pmid = {31098412}, issn = {2399-3642}, mesh = {Biodegradation, Environmental ; Bioreactors/microbiology ; Carbon/*metabolism ; Gene Expression Profiling ; Industrial Oils ; Metagenomics ; Microbiota/genetics/*physiology ; Models, Biological ; Nitrification/genetics/*physiology ; Sewage/*microbiology ; Waste Disposal, Fluid/methods ; Wastewater/microbiology ; }, abstract = {Although metagenomics researches have illuminated microbial diversity in numerous biospheres, understanding individual microbial functions is yet difficult due to the complexity of ecosystems. To address this issue, we applied a metagenome-independent, de novo assembly-based metatranscriptomics to a complex microbiome, activated sludge, which has been used for wastewater treatment for over a century. Even though two bioreactors were operated under the same conditions, their performances differed from each other with unknown causes. Metatranscriptome profiles in high- and low-performance reactors demonstrated that denitrifiers contributed to the anaerobic degradation of heavy oil; however, no marked difference in the gene expression was found. Instead, gene expression-based nitrification activities that fueled the denitrifiers by providing the respiratory substrate were notably high in the high-performance reactor only. Nitrifiers-small minorities with relative abundances of <0.25%-governed the heavy-oil degradation performances of the reactors, unveiling an unexpected linkage of carbon- and nitrogen-metabolisms of the complex microbiome.}, } @article {pmid31097033, year = {2019}, author = {Lugli, GA and Milani, C and Duranti, S and Alessandri, G and Turroni, F and Mancabelli, L and Tatoni, D and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {96}, pmid = {31097033}, issn = {1474-760X}, mesh = {Animals ; Bifidobacterium/genetics/*isolation & purification ; Callimico ; Callithrix ; Cattle ; Gastrointestinal Microbiome ; Metagenomics ; }, abstract = {Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation approach allows the isolation of novel bifidobacteria from animal fecal samples. A combination of in silico analyses based on nucleotide and protein sequences facilitate the identification of genetic material belonging to putative novel species. Consequently, the prediction of metabolic properties by in silico analyses permits the identification of specific substrates that are then employed to isolate these species through a cultivation method.}, } @article {pmid31096909, year = {2019}, author = {Zhang, J and Lacroix, C and Wortmann, E and Ruscheweyh, HJ and Sunagawa, S and Sturla, SJ and Schwab, C}, title = {Gut microbial beta-glucuronidase and glycerol/diol dehydratase activity contribute to dietary heterocyclic amine biotransformation.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {99}, pmid = {31096909}, issn = {1471-2180}, mesh = {Bacteria/*enzymology/genetics ; Bacteroidetes/enzymology/genetics ; Biotransformation ; Carcinogens/metabolism ; Colorectal Neoplasms ; *Diet ; Feces/chemistry/microbiology ; Firmicutes/enzymology/genetics ; *Gastrointestinal Microbiome ; Glucuronidase/*metabolism ; Glucuronides/*metabolism ; Glycerol/chemistry ; Humans ; Imidazoles/metabolism ; Meat/analysis ; Metagenomics ; Propanediol Dehydratase/*metabolism ; Proteobacteria/enzymology/genetics ; }, abstract = {BACKGROUND: Consuming red and processed meat has been associated with an increased risk of colorectal cancer (CRC), which is partly attributed to exposure to carcinogens such as heterocyclic amines (HCA) formed during cooking and preservation processes. The interaction of gut microbes and HCA can result in altered bioactivities and it has been shown previously that human gut microbiota can transform mutagenic HCA to a glycerol conjugate with reduced mutagenic potential. However, the major form of HCA in the colon are glucuronides (HCA-G) and it is not known whether these metabolites, via stepwise microbial hydrolysis and acrolein conjugation, are viable precursors for glycerol conjugated metabolites. We hypothesized that such a process could be concurrently catalyzed by bacterial beta-glucuronidase (B-GUS) and glycerol/diol dehydratase (GDH) activity. We therefore investigated how the HCA-G PhIP-N2-β-D-glucuronide (PhIP-G), a representative liver metabolite of PhIP (2-Amino-1-methyl-6-phenylimidazo [4,5-b] pyridine), which is the most abundant carcinogenic HCA in well-cooked meat, is transformed by enzymatic activity of human gut microbial representatives of the phyla Firmicutes, Bacteroidetes, and Proteobacteria.

RESULTS: We employed a combination of growth and enzymatic assays, and a bioanalysis approach combined with metagenomics. B-GUS of Faecalibacterium prausnitzii converted PhIP-G to PhIP and GDH of Flavonifractor plautii, Blautia obeum, Eubacterium hallii, and Lactobacillus reuteri converted PhIP to PhIP-M1 in the presence of glycerol. In addition, B-GUS- and GDH-positive bacteria cooperatively converted PhIP-G to PhIP-M1. A screen of genes encoding B-GUS and GDH was performed for fecal microbiome data from healthy individuals (n = 103) and from CRC patients (n = 53), which revealed a decrease in abundance of taxa with confirmed GDH and HCA transformation activity in CRC patients.

CONCLUSIONS: This study for the first time demonstrates that gut microbes mediate the stepwise transformation of PhIP-G to PhIP-M1 via the intermediate production of PhIP. Findings from this study suggest that targeted manipulation with gut microbes bearing specific functions, or dietary glycerol supplementation might modify gut microbial activity to reduce HCA-induced CRC risk.}, } @article {pmid31095619, year = {2019}, author = {Motta, V and Luise, D and Bosi, P and Trevisi, P}, title = {Faecal microbiota shift during weaning transition in piglets and evaluation of AO blood types as shaping factor for the bacterial community profile.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0217001}, pmid = {31095619}, issn = {1932-6203}, mesh = {Animal Feed/analysis ; Animals ; Animals, Suckling ; Bacteroidaceae/isolation & purification ; *Blood Group Antigens ; Cluster Analysis ; Enterobacteriaceae/isolation & purification ; Fatty Acids/analysis ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Genotype ; Intestinal Mucosa/microbiology ; Lipid Metabolism ; Milk ; Prevotella/isolation & purification ; Ruminococcus/isolation & purification ; Sus scrofa/*microbiology ; }, abstract = {The host-microbiota interplay is recognized as a key factor for the homeostatic maintenance in animals. In pigs, the weaning transition represents a drastic changes event leading to high risk of gut dysbiosis, which in most cases results in economic losses for swine industry. The blood type antigens expressed on mucosal surfaces can act as receptors for bacterial adhesion and the hypothesis of possible associations between blood groups and intestinal microbial profiles has been tested in human with contrasting results. Nevertheless, no studies testing the blood type as possible shaping factor for gut microbiota are available for pigs. The results of our previous study suggested the porcine AO blood types system as a possible factor influencing the microbiota composition. In the present study, the changes in fecal microbiota of 12 piglets were followed from 7 days after birth to 2 weeks post-weaning, testing the hypothesis that blood types may impact on its structure. No effects attributable to the difference in blood groups were detected, however, the sampling site (faeces) and the low statistical power might have masked the hypothesized impact. The data clearly showed the rearrangement of the bacterial ecosystem triggered by weaning transition; mainly consisting of a shift from a Bacteroidaceae-Enterobacteriaceae dominated community, to a Prevotellaceae-Ruminococcaceae dominated community. The functional analysis by metagenomic predictions suggested a role of the high levels of long-chain fatty acid in swine milk as energy source for Enterobacteriaceae (E. coli), in suckling piglets. This study provides a first insight for further investigations; indicating the need for larger sample size, preferably derived from intestinal mucosa, to test the potential effect of blood groups on gut microbiota profiles, and for analyses aimed at assessing the long-chain fatty acids degradation activity within the intestinal microbiota of suckling piglets, with particular attention to the role of E. coli.}, } @article {pmid31095603, year = {2019}, author = {Khan, MAW and Stephens, WZ and Mohammed, AD and Round, JL and Kubinak, JL}, title = {Does MHC heterozygosity influence microbiota form and function?.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0215946}, pmid = {31095603}, issn = {1932-6203}, support = {DP2 AT008746/AT/NCCIH NIH HHS/United States ; N01AI95375/AI/NIAID NIH HHS/United States ; T32 AI055434/AI/NIAID NIH HHS/United States ; K22 AI123481/AI/NIAID NIH HHS/United States ; R56 AI107090/AI/NIAID NIH HHS/United States ; K22 AI095375/AI/NIAID NIH HHS/United States ; R21 AI109122/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Feces/microbiology ; Female ; Genetic Variation ; Genotype ; *Heterozygote ; Homozygote ; Major Histocompatibility Complex/*genetics ; Mice ; Microbiota/*genetics ; }, abstract = {MHC molecules are essential for the adaptive immune response, and they are the most polymorphic genetic loci in vertebrates. Extreme genetic variation at these loci is paradoxical given their central importance to host health. Classic models of MHC gene evolution center on antagonistic host-pathogen interactions to promote gene diversification and allelic diversity in host populations. However, all multicellular organisms are persistently colonized by their microbiota that perform essential metabolic functions for their host and protect from infection. Here, we provide data to support the hypothesis that MHC heterozygote advantage (a main force of selection thought to drive MHC gene evolution), may operate by enhancing fitness advantages conferred by the host's microbiome. We utilized fecal 16S rRNA gene sequences and their predicted metagenome datasets collected from multiple MHC congenic homozygote and heterozygote mouse strains to describe the influence of MHC heterozygosity on microbiome form and function. We find that in contrast to homozygosity at MHC loci, MHC heterozygosity promotes functional diversification of the microbiome, enhances microbial network connectivity, and results in enrichment for a variety of microbial functions that are positively associated with host fitness. We demonstrate that taxonomic and functional diversity of the microbiome is positively correlated in MHC heterozygote but not homozygote animals, suggesting that heterozygote microbiomes are more functionally adaptive under similar environmental conditions than homozygote microbiomes. Our data complement previous observations on the role of MHC polymorphism in sculpting microbiota composition, but also provide functional insights into how MHC heterozygosity may enhance host health by modulating microbiome form and function. We also provide evidence to support that MHC heterozygosity limits functional redundancy among commensal microbes and may enhance the metabolic versatility of their microbiome. Results from our analyses yield multiple testable predictions regarding the role of MHC heterozygosity on the microbiome that will help guide future research in the area of MHC-microbiome interactions.}, } @article {pmid31095297, year = {2019}, author = {Mhatre, SS and Kaufmann, S and Marshall, IPG and Obrochta, S and Andrèn, T and Jørgensen, BB and Lomstein, BA}, title = {Microbial biomass turnover times and clues to cellular protein repair in energy-limited deep Baltic Sea sediments.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {6}, pages = {}, doi = {10.1093/femsec/fiz068}, pmid = {31095297}, issn = {1574-6941}, support = {294200/ERC_/European Research Council/International ; }, mesh = {Atlantic Ocean ; Bacteria/genetics/*growth & development ; Biomass ; Gene Expression Profiling ; Geologic Sediments/chemistry/*microbiology ; Lakes ; Metagenome ; Microbiota/genetics ; Phylogeny ; Protein D-Aspartate-L-Isoaspartate Methyltransferase/genetics ; *Soil Microbiology ; }, abstract = {The discovery of active microbial life deeply buried beneath the seafloor has opened important questions: how do microorganisms cope with extreme energy limitation, what is their metabolic activity, and how do they repair damages to essential biomolecules? We used a D:L-amino acid model to calculate microbial biomass turnover times. We used a metagenome and metatranscriptome analysis to investigate the distribution of the gene that encodes Protein-L-iso aspartate(D-aspartate) O-methyltransferase (PCMT), an enzyme which recognizes damaged L-isoapartyl and D-aspartyl residues in proteins and catalyzes their repair. Sediment was retrieved during the Integrated Ocean Drilling Program (IODP) Expedition 347 from Landsort Deep and the Little Belt in the Baltic Sea. The study covers the period from the Baltic Ice Lake ca. 13 000 years ago to the present. Our results provide new knowledge on microbial biomass turnover times and protein repair in relation to different regimes of organic matter input. For the first time, we show that the PCMT gene was widely distributed and expressed among phylogenetically diverse groups of microorganisms. Our findings suggest that microbial communities are capable of repairing D-amino acids within proteins using energy obtained from the degradation of a mixture of labile compounds in microbial necromass and more recalcitrant organic matter.}, } @article {pmid31092601, year = {2019}, author = {Hu, H and da Costa, RR and Pilgaard, B and Schiøtt, M and Lange, L and Poulsen, M}, title = {Fungiculture in Termites Is Associated with a Mycolytic Gut Bacterial Community.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, pmid = {31092601}, issn = {2379-5042}, mesh = {Animals ; Bacteria/enzymology/genetics ; *Diet ; Fungi/*growth & development ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/enzymology/microbiology ; Isoptera/*enzymology/*microbiology ; Metagenome ; Phylogeny ; Plant Cells/metabolism ; Sequence Analysis, DNA ; Symbiosis ; Wood/metabolism ; }, abstract = {Termites forage on a range of substrates, and it has been suggested that diet shapes the composition and function of termite gut bacterial communities. Through comparative analyses of gut metagenomes in nine termite species with distinct diets, we characterize bacterial community compositions and use peptide-based functional annotation method to determine biomass-degrading enzymes and the bacterial taxa that encode them. We find that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, while wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Interestingly, wood-feeding termite gut bacterial genes code for abundant chitinolytic enzymes, suggesting that fungal biomass within the decaying wood likely contributes to gut bacterial or termite host nutrition. Across diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community composition, with the most marked difference being the communities coding for the mycolytic capacity of the fungus-growing termite gut.IMPORTANCE Understanding functional capacities of gut microbiomes is important to improve our understanding of symbiotic associations. Here, we use peptide-based functional annotation to show that the gut microbiomes of fungus-farming termites code for a wealth of enzymes that likely target the fungal diet the termites eat. Comparisons to other termites showed that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, whereas wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Across termites with different diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community compositions.}, } @article {pmid31092280, year = {2019}, author = {Heinken, A and Ravcheev, DA and Baldini, F and Heirendt, L and Fleming, RMT and Thiele, I}, title = {Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {75}, pmid = {31092280}, issn = {2049-2618}, mesh = {Bile Acids and Salts/*metabolism ; *Gastrointestinal Microbiome ; Genomics ; Host-Pathogen Interactions ; Humans ; Inflammatory Bowel Diseases/metabolism/*microbiology ; Lipid Metabolism ; Metagenomics ; *Systems Biology ; }, abstract = {BACKGROUND: The human gut microbiome performs important functions in human health and disease. A classic example for host-gut microbial co-metabolism is host biosynthesis of primary bile acids and their subsequent deconjugation and transformation by the gut microbiome. To understand these system-level host-microbe interactions, a mechanistic, multi-scale computational systems biology approach that integrates the different types of omic data is needed. Here, we use a systematic workflow to computationally model bile acid metabolism in gut microbes and microbial communities.

RESULTS: Therefore, we first performed a comparative genomic analysis of bile acid deconjugation and biotransformation pathways in 693 human gut microbial genomes and expanded 232 curated genome-scale microbial metabolic reconstructions with the corresponding reactions (available at https://vmh.life). We then predicted the bile acid biotransformation potential of each microbe and in combination with other microbes. We found that each microbe could produce maximally six of the 13 secondary bile acids in silico, while microbial pairs could produce up to 12 bile acids, suggesting bile acid biotransformation being a microbial community task. To investigate the metabolic potential of a given microbiome, publicly available metagenomics data from healthy Western individuals, as well as inflammatory bowel disease patients and healthy controls, were mapped onto the genomes of the reconstructed strains. We constructed for each individual a large-scale personalized microbial community model that takes into account strain-level abundances. Using flux balance analysis, we found considerable variation in the potential to deconjugate and transform primary bile acids between the gut microbiomes of healthy individuals. Moreover, the microbiomes of pediatric inflammatory bowel disease patients were significantly depleted in their bile acid production potential compared with that of controls. The contributions of each strain to overall bile acid production potential across individuals were found to be distinct between inflammatory bowel disease patients and controls. Finally, bottlenecks limiting secondary bile acid production potential were identified in each microbiome model.

CONCLUSIONS: This large-scale modeling approach provides a novel way of analyzing metagenomics data to accelerate our understanding of the metabolic interactions between the host and gut microbiomes in health and diseases states. Our models and tools are freely available to the scientific community.}, } @article {pmid31091345, year = {2019}, author = {Riiser, ES and Haverkamp, THA and Varadharajan, S and Borgan, Ø and Jakobsen, KS and Jentoft, S and Star, B}, title = {Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod.}, journal = {Environmental microbiology}, volume = {21}, number = {7}, pages = {2576-2594}, doi = {10.1111/1462-2920.14652}, pmid = {31091345}, issn = {1462-2920}, support = {//University of Oslo/International ; 222378//Research Council of Norway/International ; }, mesh = {Animals ; Atlantic Ocean ; Bacteria/classification/genetics/*isolation & purification ; Gadus morhua/*microbiology ; *Gastrointestinal Microbiome ; Intestines/*microbiology ; Metagenome ; Norway ; Photobacterium/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Atlantic cod (Gadus morhua) is an ecologically important species with a wide-spread distribution in the North Atlantic Ocean, yet little is known about the diversity of its intestinal microbiome in its natural habitat. No geographical differentiation in this microbiome was observed based on 16S rRNA amplicon analyses, yet such finding may result from an inherent lack of power of this method to resolve fine-scaled biological complexity. Here, we use metagenomic shotgun sequencing to investigate the intestinal microbiome of 19 adult Atlantic cod individuals from two coastal populations in Norway-located 470 km apart. Resolving the species community to unprecedented resolution, we identify two abundant species, Photobacterium iliopiscarium and Photobacterium kishitanii, which comprise over 50% of the classified reads. Interestingly, the intestinal P. kishitanii strains have functionally intact lux genes, and its high abundance suggests that fish intestines form an important part of its ecological niche. These observations support a hypothesis that bioluminescence plays an ecological role in the marine food web. Despite our improved taxonomical resolution, we identify no geographical differences in bacterial community structure, indicating that the intestinal microbiome of these coastal cod is colonized by a limited number of closely related bacterial species with a broad geographical distribution.}, } @article {pmid31091277, year = {2019}, author = {Ribeiro, H and Martins, A and Gonçalves, M and Guedes, M and Tomasino, MP and Dias, N and Dias, A and Mucha, AP and Carvalho, MF and Almeida, CMR and Ramos, S and Almeida, JM and Silva, E and Magalhães, C}, title = {Development of an autonomous biosampler to capture in situ aquatic microbiomes.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0216882}, pmid = {31091277}, issn = {1932-6203}, mesh = {DNA, Environmental/*analysis ; Microbiota/*physiology ; Plankton/*microbiology ; *Water Microbiology ; }, abstract = {The importance of planktonic microbial communities is well acknowledged, since they are fundamental for several natural processes of aquatic ecosystems. Microorganisms naturally control the flux of nutrients, and also degrade and recycle anthropogenic organic and inorganic contaminants. Nevertheless, climate change effects and/or the runoff of nutrients/pollutants can affect the equilibrium of natural microbial communities influencing the occurrence of microbial pathogens and/or microbial toxin producers, which can compromise ecosystem environmental status. Therefore, improved microbial plankton monitoring is essential to better understand how these communities respond to environmental shifts. The study of marine microbial communities typically involves highly cost and time-consuming sampling procedures, which can limit the frequency of sampling and data availability. In this context, we developed and validated an in situ autonomous biosampler (IS-ABS) able to collect/concentrate in situ planktonic communities of different size fractions (targeting prokaryotes and unicellular eukaryotes) for posterior genomic, metagenomic, and/or transcriptomic analysis at a home laboratory. The IS-ABS field prototype is a small size and compact system able to operate up to 150 m depth. Water is pumped by a micropump (TCS MG2000) through a hydraulic circuit that allows in situ filtration of environmental water in one or more Sterivex filters placed in a filter cartridge. The IS-ABS also includes an application to program sampling definitions, allowing pre-setting configuration of the sampling. The efficiency of the IS-ABS was tested against traditional laboratory filtration standardized protocols. Results showed a good performance in terms of DNA recovery, as well as prokaryotic (16S rDNA) and eukaryotic (18S rDNA) community diversity analysis, using either methodologies. The IS-ABS automates the process of collecting environmental DNA, and is suitable for integration in water observation systems, what will contribute to substantially increase biological surveillances. Also, the use of highly sensitive genomic approaches allows a further study of the diversity and functions of whole or specific microbial communities.}, } @article {pmid31091181, year = {2019}, author = {Joyce, A and McCarthy, CGP and Murphy, S and Walsh, F}, title = {Antibiotic resistomes of healthy pig faecal metagenomes.}, journal = {Microbial genomics}, volume = {5}, number = {5}, pages = {}, pmid = {31091181}, issn = {2057-5858}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/drug effects/genetics/isolation & purification ; Cluster Analysis ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/*genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/drug effects/genetics ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genome, Bacterial ; Humans ; Ireland ; Metagenome/*genetics ; Metagenomics ; Swine ; }, abstract = {Antibiotic resistance reservoirs within food-producing animals are thought to be a risk to animal and human health. This study describes the minimum natural resistome of pig faeces as the bacteria are under no direct antibiotic selective pressure. The faecal resistome of 257 different genes comprised 56 core and 201 accessory resistance genes. The genes present at the highest relative abundances across all samples were tetW, tetQ, tet44, tet37, tet40, mefA, aadE, ant(9)-1, ermB and cfxA2. This study characterized the baseline resistome, the microbiome composition and the metabolic components described by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in healthy pig faeces, without antibiotic selective pressures. The microbiome hierarchical analysis resulted in a cluster tree with a highly similar pattern to that of the accessory resistome cluster tree. Functional capacity profiling identified genes associated with horizontal gene transfer. We identified a statistically significant positive correlation between the total antibiotic resistome and suggested indicator genes, which agree with using these genes as indicators of the total resistomes. The correlation between total resistome and total microbiome in this study was positive and statistically significant. Therefore, the microbiome composition influenced the resistome composition. This study identified a core and accessory resistome present in a cohort of healthy pigs, in the same conditions without antibiotics. It highlights the presence of antibiotic resistance in the absence of antibiotic selective pressure and the variability between animals even under the same housing, food and living conditions. Antibiotic resistance will remain in the healthy pig gut even when antibiotics are not used. Therefore, the risk of antibiotic resistance transfer from animal faeces to human pathogens or the environment will remain in the absence of antibiotics.}, } @article {pmid31089679, year = {2019}, author = {Nicholls, SM and Quick, JC and Tang, S and Loman, NJ}, title = {Ultra-deep, long-read nanopore sequencing of mock microbial community standards.}, journal = {GigaScience}, volume = {8}, number = {5}, pages = {}, pmid = {31089679}, issn = {2047-217X}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/M501621/1/MRC_/Medical Research Council/United Kingdom ; /DH_/Department of Health/United Kingdom ; }, mesh = {*Metagenome ; Metagenomics/*methods/standards ; Microbiota/*genetics ; Nanopore Sequencing/*methods/standards ; Reference Standards ; }, abstract = {BACKGROUND: Long sequencing reads are information-rich: aiding de novo assembly and reference mapping, and consequently have great potential for the study of microbial communities. However, the best approaches for analysis of long-read metagenomic data are unknown. Additionally, rigorous evaluation of bioinformatics tools is hindered by a lack of long-read data from validated samples with known composition.

FINDINGS: We sequenced 2 commercially available mock communities containing 10 microbial species (ZymoBIOMICS Microbial Community Standards) with Oxford Nanopore GridION and PromethION. Both communities and the 10 individual species isolates were also sequenced with Illumina technology. We generated 14 and 16 gigabase pairs from 2 GridION flowcells and 150 and 153 gigabase pairs from 2 PromethION flowcells for the evenly distributed and log-distributed communities, respectively. Read length N50 ranged between 5.3 and 5.4 kilobase pairs over the 4 sequencing runs. Basecalls and corresponding signal data are made available (4.2 TB in total). Alignment to Illumina-sequenced isolates demonstrated the expected microbial species at anticipated abundances, with the limit of detection for the lowest abundance species below 50 cells (GridION). De novo assembly of metagenomes recovered long contiguous sequences without the need for pre-processing techniques such as binning.

CONCLUSIONS: We present ultra-deep, long-read nanopore datasets from a well-defined mock community. These datasets will be useful for those developing bioinformatics methods for long-read metagenomics and for the validation and comparison of current laboratory and software pipelines.}, } @article {pmid31087993, year = {2019}, author = {Liu, ZQ and Zhang, Y and Ma, XS and Zhang, BK and Cao, MJ and Chen, CM}, title = {[Nitrogen Removal Characteristics and Analysis of Microbial Community Structure in an IEM-UF Simultaneous Separation and Denitrification System].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {40}, number = {3}, pages = {1419-1425}, doi = {10.13227/j.hjkx.201808051}, pmid = {31087993}, issn = {0250-3301}, mesh = {Bacteria/classification ; Bioreactors ; *Denitrification ; Ion Exchange ; *Microbiota ; Nitrogen/*isolation & purification ; Ultrafiltration ; Wastewater ; }, abstract = {A system that combines an ion exchange membrane and ultrafiltration membrane (IEM-UF) to form a simultaneous separation and denitrification system was proposed for domestic sewage with a low carbon/nitrogen ratio. The removal of nitrogen and COD in the system was studied under a three phase operating condition. The characteristics of the microbial community in each reactor were analyzed using metagenomics. The results show that, the average rate of ammonia nitrogen enrichment in the separator reached above 116.1% when the current intensity was 0.2 A. When the system was at C/N 2.80 and operating well, the average removal rates of COD and TN reached above 90% and 50%, respectively. The maximum removal rate of TN was above 65.4%. The results of metagenomics showed a genus of phylum Nitrospirae (Nitrospira) and a genus of phylum Proteobacteria (Nitrosomonas), with the proportions of 12.23% and 2.31%, respectively. In the denitrifying reactor, Dechloromonas, Thauera, and Azospira were detected in the proportions 4.57%, 1.76%, and 1.03%, respectively. These proportions were far larger than those of other bacteria in this reactor. Meanwhile, the presence of iron autotrophic denitrifying bacteria increased the denitrification efficiency of the system.}, } @article {pmid31087616, year = {2019}, author = {Martin-Cuadrado, AB and Senel, E and Martínez-García, M and Cifuentes, A and Santos, F and Almansa, C and Moreno-Paz, M and Blanco, Y and García-Villadangos, M and Del Cura, MÁG and Sanz-Montero, ME and Rodríguez-Aranda, JP and Rosselló-Móra, R and Antón, J and Parro, V}, title = {Prokaryotic and viral community of the sulfate-rich crust from Peñahueca ephemeral lake, an astrobiology analogue.}, journal = {Environmental microbiology}, volume = {21}, number = {10}, pages = {3577-3600}, doi = {10.1111/1462-2920.14680}, pmid = {31087616}, issn = {1462-2920}, support = {ESP2015-69540-R//European Regional Development Fund/International ; AYA2011-24803//European Regional Development Fund/International ; CGL2015-66455-R//Spanish Ministry of Economy/International ; CLG2015_66686-C3-3//Spanish Ministry of Economy/International ; CLG2015_66686-C3-1//Spanish Ministry of Economy/International ; }, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Biodiversity ; Exobiology ; Lakes/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sodium Chloride/metabolism ; Spain ; Sulfates/metabolism ; Viruses/classification/*genetics ; }, abstract = {Peñahueca is an athalassohaline hypersaline inland ephemeral lake originated under semiarid conditions in the central Iberian Peninsula (Spain). Its chemical composition makes it extreme for microbial life as well as a terrestrial analogue of other planetary environments. To investigate the persistence of microbial life associated with sulfate-rich crusts, we applied cultivation-independent methods (optical and electron microscopy, 16S rRNA gene profiling and metagenomics) to describe the prokaryotic community and its associated viruses. The diversity for Bacteria was very low and was vastly dominated by endospore formers related to Pontibacillus marinus of the Firmicutes phylum. The archaeal assemblage was more diverse and included taxa related to those normally found in hypersaline environments. Several 'metagenome assembled genomes' were recovered, corresponding to new species of Pontibacillus, several species from the Halobacteria and one new member of the Nanohaloarchaeota. The viral assemblage, although composed of the morphotypes typical of high salt systems, showed little similarity to previously isolated/reconstructed halophages. Several putative prophages of Pontibacillus and haloarchaeal hosts were identified. Remarkably, the Peñahueca sulfate-rich metagenome contained CRISPR-associated proteins and repetitions which were over 10-fold higher than in most hypersaline systems analysed so far.}, } @article {pmid31087436, year = {2019}, author = {Akiyama, K and Nishioka, K and Khan, KN and Tanaka, Y and Mori, T and Nakaya, T and Kitawaki, J}, title = {Molecular detection of microbial colonization in cervical mucus of women with and without endometriosis.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {82}, number = {2}, pages = {e13147}, doi = {10.1111/aji.13147}, pmid = {31087436}, issn = {1600-0897}, support = {18K09295//Japan Society for the Promotion of Science/International ; }, mesh = {Adult ; Bacteria/classification/genetics ; Cervix Mucus/*microbiology ; Corynebacterium/genetics/isolation & purification ; Endometriosis/*microbiology ; Enterobacteriaceae/genetics/isolation & purification ; Female ; Flavobacterium/genetics/isolation & purification ; Gentian Violet ; High-Throughput Nucleotide Sequencing ; Humans ; Lactobacillus/genetics/isolation & purification ; Microbiota/*genetics ; Phenazines ; Pseudomonas/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Streptococcus/genetics/isolation & purification ; Young Adult ; }, abstract = {PROBLEM: Intrauterine microbial colonization and its association with the pathogenesis of endometriosis via an innate immune cascade have been reported. As a potential source of microbial transmission, information on microbial colonization in cervical mucus is unknown. We investigated pattern of microbiota in the cervical mucus collected from women with and without endometriosis using next-generation sequencing (NGS) technology.

METHOD OF STUDY: Cervical mucus samples were collected from women with (n = 30) and without (n = 39) endometriosis. The communities of microbiota in cervical mucus in the endometriosis group and the control group were examined by Gram staining and NGS targeting the V5-V6 region of 16S ribosomal RNA gene. Copy number of some target bacteria was detected by real-time PCR.

RESULTS: We confirmed visual presence of bacteria in cervical mucus by Gram staining. NGS analysis showed that distribution of microbiota was similar in cervical mucus of women with and without endometriosis regardless of the phases of the menstrual cycle. In addition to predominant Lactobacilli spp., the populations of Corynebacterium, Enterobacteriaceae, Flavobacterium, Pseudomonas, and Streptococcus were increased in the endometriosis group. Of them, Enterobacteriaceae and Streptococcus were identified as the more significant candidates in the endometriosis group than in controls by real-time PCR (P < 0.05 for each).

CONCLUSION: Our NGS analysis of cervical mucus indicated that among a variable microbiota, two candidates (Enterobacteriaceae and Streptococcus) were more frequently detected in women with endometriosis. Further investigation is needed to elucidate a mechanistic link of these bacteria in the pathophysiology of endometriosis.}, } @article {pmid31086312, year = {2019}, author = {Wu, L and Ning, D and Zhang, B and Li, Y and Zhang, P and Shan, X and Zhang, Q and Brown, MR and Li, Z and Van Nostrand, JD and Ling, F and Xiao, N and Zhang, Y and Vierheilig, J and Wells, GF and Yang, Y and Deng, Y and Tu, Q and Wang, A and , and Zhang, T and He, Z and Keller, J and Nielsen, PH and Alvarez, PJJ and Criddle, CS and Wagner, M and Tiedje, JM and He, Q and Curtis, TP and Stahl, DA and Alvarez-Cohen, L and Rittmann, BE and Wen, X and Zhou, J}, title = {Global diversity and biogeography of bacterial communities in wastewater treatment plants.}, journal = {Nature microbiology}, volume = {4}, number = {7}, pages = {1183-1195}, pmid = {31086312}, issn = {2058-5276}, mesh = {Bacteria/classification/genetics/isolation & purification ; *Biodiversity ; DNA, Bacterial/genetics ; Geography ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; Water Purification/statistics & numerical data ; }, abstract = {Microorganisms in wastewater treatment plants (WWTPs) are essential for water purification to protect public and environmental health. However, the diversity of microorganisms and the factors that control it are poorly understood. Using a systematic global-sampling effort, we analysed the 16S ribosomal RNA gene sequences from ~1,200 activated sludge samples taken from 269 WWTPs in 23 countries on 6 continents. Our analyses revealed that the global activated sludge bacterial communities contain ~1 billion bacterial phylotypes with a Poisson lognormal diversity distribution. Despite this high diversity, activated sludge has a small, global core bacterial community (n = 28 operational taxonomic units) that is strongly linked to activated sludge performance. Meta-analyses with global datasets associate the activated sludge microbiomes most closely to freshwater populations. In contrast to macroorganism diversity, activated sludge bacterial communities show no latitudinal gradient. Furthermore, their spatial turnover is scale-dependent and appears to be largely driven by stochastic processes (dispersal and drift), although deterministic factors (temperature and organic input) are also important. Our findings enhance our mechanistic understanding of the global diversity and biogeography of activated sludge bacterial communities within a theoretical ecology framework and have important implications for microbial ecology and wastewater treatment processes.}, } @article {pmid31086216, year = {2019}, author = {Agamennone, V and Le, NG and van Straalen, NM and Brouwer, A and Roelofs, D}, title = {Antimicrobial activity and carbohydrate metabolism in the bacterial metagenome of the soil-living invertebrate Folsomia candida.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {7308}, pmid = {31086216}, issn = {2045-2322}, mesh = {Animals ; Carbohydrate Metabolism/*genetics ; DNA, Bacterial/genetics/isolation & purification ; Disease Resistance/*genetics ; Gastrointestinal Microbiome/*genetics ; Gene Transfer, Horizontal ; Host Microbial Interactions/genetics ; Insecta/*genetics/metabolism/microbiology ; Metagenome/*physiology ; Metagenomics ; Polysaccharides/metabolism ; Sequence Analysis, DNA ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The microbiome associated with an animal's gut and other organs is considered an integral part of its ecological functions and adaptive capacity. To better understand how microbial communities influence activities and capacities of the host, we need more information on the functions that are encoded in a microbiome. Until now, the information about soil invertebrate microbiomes is mostly based on taxonomic characterization, achieved through culturing and amplicon sequencing. Using shotgun sequencing and various bioinformatics approaches we explored functions in the bacterial metagenome associated with the soil invertebrate Folsomia candida, an established model organism in soil ecology with a fully sequenced, high-quality genome assembly. Our metagenome analysis revealed a remarkable diversity of genes associated with antimicrobial activity and carbohydrate metabolism. The microbiome also contains several homologs to F. candida genes that were previously identified as candidates for horizontal gene transfer (HGT). We suggest that the carbohydrate- and antimicrobial-related functions encoded by Folsomia's metagenome play a role in the digestion of recalcitrant soil-born polysaccharides and the defense against pathogens, thereby significantly contributing to the adaptation of these animals to life in the soil. Furthermore, the transfer of genes from the microbiome may constitute an important source of new functions for the springtail.}, } @article {pmid31083685, year = {2019}, author = {Grant, ET and Kyes, RC and Kyes, P and Trinh, P and Ramirez, V and Tanee, T and Pinlaor, P and Dangtakot, R and Rabinowitz, PM}, title = {Fecal microbiota dysbiosis in macaques and humans within a shared environment.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0210679}, pmid = {31083685}, issn = {1932-6203}, support = {P51 OD010425/OD/NIH HHS/United States ; T32 ES015459/ES/NIEHS NIH HHS/United States ; T42 OH008433/OH/NIOSH CDC HHS/United States ; T42OH008433/ACL/ACL HHS/United States ; }, mesh = {Animals ; Biodiversity ; Cross-Sectional Studies ; *Environment ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Macaca fascicularis ; Metagenome ; Metagenomics/methods ; Thailand ; }, abstract = {Traditional zoonotic disease research focuses on detection of recognized pathogens and may miss opportunities to understand broader microbial transmission dynamics between humans, animals, and the environment. We studied human-macaque microbiome overlap in Kosum Phisai District, Maha Sarakham Province, Thailand, where a growing population of long-tailed macaques (Macaca fascicularis) in Kosumpee Forest Park interact with humans from an adjacent village. We surveyed workers in or near the park with elevated exposure to macaques to characterize tasks resulting in exposure to macaque feces in addition to dietary and lifestyle factors that influence gut microbiome composition. Fecal samples were collected from 12 exposed workers and 6 controls without macaque exposure, as well as 8 macaques from Kosumpee Forest Park and 4 from an isolated forest patch with minimal human contact. The V4 region of the 16S rRNA gene from fecal sample extracted DNA was amplified and sequenced using Illumina MiSeq to characterize the microbial community. A permuted betadisper test on the weighted UniFrac distances revealed significant differences in the dispersion patterns of gut microbiota from exposed and control macaques (p = 0.03). The high variance in gut microbiota composition of macaques in contact with humans has potential implications for gut microbiome stability and susceptibility to disease, described by the Anna Karenina principle (AKP). Human samples had homogenous variance in beta diversity but different spatial medians between groups (p = 0.02), indicating a shift in microbial composition that may be explained by fundamental lifestyle differences between the groups unrelated to exposure status. SourceTracker was used to estimate the percent of gut taxa in exposed humans that was contributed by macaques. While one worker showed evidence of elevated contribution, the overall trend was not significant. Task observations among workers revealed opportunities to employ protective measures or training to reduce exposure to occupational hazards. These results suggest the potential for hygiene measures to mitigate negative aspects of contact between humans and macaques in order to optimize the health of both populations.}, } @article {pmid31081896, year = {2019}, author = {Rastelli, M and Cani, PD and Knauf, C}, title = {The Gut Microbiome Influences Host Endocrine Functions.}, journal = {Endocrine reviews}, volume = {40}, number = {5}, pages = {1271-1284}, doi = {10.1210/er.2018-00280}, pmid = {31081896}, issn = {1945-7189}, mesh = {Animals ; *Endocrine System ; Energy Metabolism ; *Gastrointestinal Microbiome ; Homeostasis ; Humans ; Inflammation ; }, abstract = {The gut microbiome is considered an organ contributing to the regulation of host metabolism. Since the relationship between the gut microbiome and specific diseases was elucidated, numerous studies have deciphered molecular mechanisms explaining how gut bacteria interact with host cells and eventually shape metabolism. Both metagenomic and metabolomic analyses have contributed to the discovery of bacterial-derived metabolites acting on host cells. In this review, we examine the molecular mechanisms by which bacterial metabolites act as paracrine or endocrine factors, thereby regulating host metabolism. We highlight the impact of specific short-chain fatty acids on the secretion of gut peptides (i.e., glucagon-like peptide-1, peptide YY) and other metabolites produced from different amino acids and regulating inflammation, glucose metabolism, or energy homeostasis. We also discuss the role of gut microbes on the regulation of bioactive lipids that belong to the endocannabinoid system and specific neurotransmitters (e.g., γ-aminobutyric acid, serotonin, nitric oxide). Finally, we review the role of specific bacterial components (i.e., ClpB, Amuc_1100) also acting as endocrine factors and eventually controlling host metabolism. In conclusion, this review summarizes the recent state of the art, aiming at providing evidence that the gut microbiome influences host endocrine functions via several bacteria-derived metabolites.}, } @article {pmid31081685, year = {2019}, author = {Thombre, RS and Shivakarthik, E and Sivaraman, B and Vaishampayan, PA and Seuylemezian, A and Meka, JK and Vijayan, S and Kulkarni, PP and Pataskar, T and Patil, BS}, title = {Survival of Extremotolerant Bacteria from the Mukundpura Meteorite Impact Crater.}, journal = {Astrobiology}, volume = {19}, number = {6}, pages = {785-796}, doi = {10.1089/ast.2018.1928}, pmid = {31081685}, issn = {1557-8070}, mesh = {Acidobacteria/genetics/isolation & purification/radiation effects ; Actinobacteria/genetics/isolation & purification/radiation effects ; Bacillus/genetics/isolation & purification/radiation effects ; DNA, Bacterial/isolation & purification ; High-Energy Shock Waves/*adverse effects ; Metagenomics ; *Meteoroids ; Microbial Viability/*radiation effects ; Microbiota/genetics/*radiation effects ; Origin of Life ; Proteobacteria/genetics/isolation & purification/radiation effects ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Carbonaceous meteorites provide clues with regard to prebiotic chemistry and the origin of life. Geological Survey of India recorded a carbonaceous chondrite meteorite fall in Mukundpura, India, on June 6, 2017. We conducted a study to investigate the microbial community that survived the meteorite impact. 16S rRNA metagenomic sequencing indicates the presence of Actinobacteria, Proteobacteria, and Acidobacteria in meteorite impact soil. Comparative phylogenetic analysis revealed an intriguing abundance of class Bacilli in the impact soil. Bacillus thermocopriae IR-1, a moderately thermotolerant organism, was isolated from a rock, impacted by the Mukundpura meteorite. We investigated the resilience of B. thermocopriae IR-1 to environmental stresses and impact shock in a Reddy shock tube. Bacillus thermocopriae IR-1 survived (28.82% survival) the effect of shock waves at a peak shock pressure of 300 kPa, temperature 400 K, and Mach number of 1.47. This investigation presents the first report on the effect of impact shock on B. thermocopriae IR-1. The study is also the first report on studying the microbial diversity and isolation of bacteria from impact crater soil immediately after meteorite impact event.}, } @article {pmid31081473, year = {2023}, author = {Suryawanshi, PR and Badapanda, C and Singh, KM and Rathore, A}, title = {Exploration of the rumen microbial diversity and carbohydrate active enzyme profile of black Bengal goat using metagenomic approach.}, journal = {Animal biotechnology}, volume = {34}, number = {4}, pages = {761-774}, doi = {10.1080/10495398.2019.1609489}, pmid = {31081473}, issn = {1532-2378}, mesh = {Humans ; Animals ; *Goats/genetics ; Rumen ; Metagenome/genetics ; *Microbiota/genetics ; Ruminants/genetics ; Carbohydrates ; }, abstract = {Black Bengal goats possess a rich source of rumen microbiota that helps them to adapt for the better utilization of plant biomaterial into energy and nutrients, a task largely performed by enzymes encoded by the rumen microbiota. Therefore the study was designed in order to explore the taxonomic profile of rumen microbial communities and potential biomass degradation enzymes present in the rumen of back Bengal goat using Illumina Nextseq-500 platform. A total of 83.18 million high-quality reads were generated and bioinformatics analysis was performed using various tools and subsequently, the predicted ORFs along with the rRNA containing contigs were then uploaded to MG-RAST to analyze taxonomic and functional profiling. The results highlighted that Bacteriodetes (41.38-59.74%) were the most abundant phyla followed by Firmicutes (30.59-39.96%), Proteobacteria (5.07-7.61%), Euryarcheaota (0.71-7.41%), Actinobacteria (2.05-2.75%). Genes that encode glycoside hydrolases (GHs) had the highest number of CAZymes, and accounted for (39.73-37.88%) of all CAZymes in goat rumen. The GT families were the second-most abundant in CAZymes (23.73-23.11%) and followed by Carbohydrate Binding module Domain (17.65-15.61%), Carbohydrate Esterase (12.90-11.95%). This study indicated that goat rumen had complex functional microorganisms produce numerous CAZymes, and that can be further effectively utilised for applied ruminant research and industry based applications.}, } @article {pmid31080075, year = {2019}, author = {Macdonald, SS and Armstrong, Z and Morgan-Lang, C and Osowiecka, M and Robinson, K and Hallam, SJ and Withers, SG}, title = {Development and Application of a High-Throughput Functional Metagenomic Screen for Glycoside Phosphorylases.}, journal = {Cell chemical biology}, volume = {26}, number = {7}, pages = {1001-1012.e5}, doi = {10.1016/j.chembiol.2019.03.017}, pmid = {31080075}, issn = {2451-9448}, mesh = {Carbohydrate Metabolism ; Glucosyltransferases/metabolism ; Glycosides/chemistry/*metabolism ; High-Throughput Screening Assays/methods ; Metagenome/physiology ; Microbiota ; Molybdenum/chemistry ; Phosphorylases/chemistry/*metabolism ; Proof of Concept Study ; Substrate Specificity ; }, abstract = {Glycoside phosphorylases (GPs) catalyze the reversible phosphorolysis of glycosidic bonds, releasing sugar 1-phosphates. To identify a greater range of these under-appreciated enzymes, we have developed a high-throughput functional screening method based on molybdenum blue formation. In a proof-of-principle screen focused on cellulose-degrading GPs we interrogated ∼23,000 large insert (fosmid) clones sourced from microbial communities inhabiting two separate environments and identified seven novel GPs from carbohydrate active enzyme family GH94 and one from GH149. Characterization identified cellobiose phosphorylases, cellodextrin phosphorylases, laminaribiose phosphorylases, and a β-1,3-glucan phosphorylase. To demonstrate the versatility of the screening method, varying substrate combinations were used to identify GP activity from families GH13, GH65, GH112, and GH130 in addition to GH94 and GH149. These pilot screen and substrate versatility results provide a screening paradigm platform for recovering diverse GPs from uncultivated microbial communities acting on different substrates with considerable potential to unravel previously unknown degradative pathways within microbiomes.}, } @article {pmid31078141, year = {2019}, author = {Rocafort, M and Noguera-Julian, M and Rivera, J and Pastor, L and Guillén, Y and Langhorst, J and Parera, M and Mandomando, I and Carrillo, J and Urrea, V and Rodríguez, C and Casadellà, M and Calle, ML and Clotet, B and Blanco, J and Naniche, D and Paredes, R}, title = {Evolution of the gut microbiome following acute HIV-1 infection.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {73}, pmid = {31078141}, issn = {2049-2618}, mesh = {Acute Disease ; Adult ; Bacteria/*classification/isolation & purification ; CD4-Positive T-Lymphocytes ; CD8-Positive T-Lymphocytes ; Chronic Disease ; Feces/virology ; Female ; *Gastrointestinal Microbiome ; HIV Infections/drug therapy/*microbiology ; HIV-1/isolation & purification ; Humans ; Male ; Metagenomics ; Middle Aged ; Mozambique ; Prospective Studies ; *Transcriptome ; Viral Load ; Virus Shedding ; Young Adult ; }, abstract = {BACKGROUND: In rhesus macaques, simian immunodeficiency virus infection is followed by expansion of enteric viruses but has a limited impact on the gut bacteriome. To understand the longitudinal effects of HIV-1 infection on the human gut microbiota, we prospectively followed 49 Mozambican subjects diagnosed with recent HIV-1 infection (RHI) and 54 HIV-1-negative controls for 9-18 months and compared them with 98 chronically HIV-1-infected subjects treated with antiretrovirals (n = 27) or not (n = 71).

RESULTS: We show that RHI is followed by increased fecal adenovirus shedding, which persists during chronic HIV-1 infection and does not resolve with ART. Recent HIV-1 infection is also followed by transient non-HIV-specific changes in the gut bacterial richness and composition. Despite early resilience to change, an HIV-1-specific signature in the gut bacteriome-featuring depletion of Akkermansia, Anaerovibrio, Bifidobacterium, and Clostridium-previously associated with chronic inflammation, CD8+ T cell anergy, and metabolic disorders, can be eventually identified in chronically HIV-1-infected subjects.

CONCLUSIONS: Recent HIV-1 infection is associated with increased fecal shedding of eukaryotic viruses, transient loss of bacterial taxonomic richness, and long-term reductions in microbial gene richness. An HIV-1-associated microbiome signature only becomes evident in chronically HIV-1-infected subjects.}, } @article {pmid31076501, year = {2019}, author = {Toivonen, L and Hasegawa, K and Waris, M and Ajami, NJ and Petrosino, JF and Camargo, CA and Peltola, V}, title = {Early nasal microbiota and acute respiratory infections during the first years of life.}, journal = {Thorax}, volume = {74}, number = {6}, pages = {592-599}, doi = {10.1136/thoraxjnl-2018-212629}, pmid = {31076501}, issn = {1468-3296}, mesh = {Acute Disease ; Corynebacterium/isolation & purification ; Disease Susceptibility ; Female ; Finland/epidemiology ; Gram-Positive Bacteria/isolation & purification ; Humans ; Incidence ; Infant ; Infant, Newborn ; Male ; *Microbiota ; Moraxella/isolation & purification ; Nasal Cavity/*microbiology ; Prospective Studies ; Respiratory Tract Infections/epidemiology/*microbiology ; Staphylococcus/isolation & purification ; Streptococcus/isolation & purification ; }, abstract = {BACKGROUND: Emerging evidence shows that airway microbiota may modulate local immune responses, thereby contributing to the susceptibility and severity of acute respiratory infections (ARIs). However, there are little data on the longitudinal relationships between airway microbiota and susceptibility to ARIs in children.

OBJECTIVE: We aimed to investigate the association of early nasal microbiota and the subsequent risk of ARIs during the first years of life.

METHODS: In this prospective population-based birth-cohort study in Finland, we followed 839 healthy infants for ARIs from birth to age 24 months. Nasal microbiota was tested using 16S rRNA gene sequencing at age 2 months. We applied an unsupervised clustering approach to identify early nasal microbiota profiles, and examined the association of profiles with the rate of ARIs during age 2-24 months.

RESULTS: We identified five nasal microbiota profiles dominated by Moraxella, Streptococcus, Dolosigranulum, Staphylococcus and Corynebacteriaceae, respectively. Incidence rate of ARIs was highest in children with an early Moraxella-dominant profile and lowest in those with a Corynebacteriaceae-dominant profile (738 vs 552/100 children years; unadjusted incidence rate ratio (IRR), 1.34; 95% CI 1.16 to 1.54; p < 0.001). After adjusting for nine potential confounders, the Moraxella-dominant profile-ARI association persisted (adjusted IRR (aIRR), 1.19; 95% CI 1.04 to 1.37; p = 0.01). Similarly, the incidence rate of lower respiratory tract infections (a subset of all ARIs) was significantly higher in children with an early Moraxella-dominant profile (aIRR, 2.79; 95% CI 1.04 to 8.09; p = 0.04).

CONCLUSION: Moraxella-dominant nasal microbiota profile in early infancy was associated with an increased rate of ARIs during the first 2 years of life.}, } @article {pmid31074596, year = {2019}, author = {Feng, M and Tripathi, BM and Shi, Y and Adams, JM and Zhu, YG and Chu, H}, title = {Interpreting distance-decay pattern of soil bacteria via quantifying the assembly processes at multiple spatial scales.}, journal = {MicrobiologyOpen}, volume = {8}, number = {9}, pages = {e00851}, pmid = {31074596}, issn = {2045-8827}, mesh = {Bacteria/*classification/*genetics ; China ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; *Microbiota ; *Soil Microbiology ; *Spatial Analysis ; Zea mays/*growth & development ; }, abstract = {It has been widely accepted that there is a distance-decay pattern in the soil microbiome. However, few studies have attempted to interpret the microbial distance-decay pattern from the perspective of quantifying underlying processes. In this study, we examined the processes governing bacterial community assembly at multiple spatial scales in maize fields of Northeast China using Illumina MiSeq sequencing. Results showed that the processes governing spatial turnover in bacterial community composition shifted regularly with spatial scale, with homogenizing dispersal dominating at small spatial scales and variable selection dominating at larger scales, which in turn explained the distance-decay pattern that closer located sites tended to have higher community similarity. Together, homogenizing dispersal and dispersal limitation resulting from geographic factors governed about 33% of spatial turnover in bacterial community composition. Deterministic selection processes had the strongest influence, at 57%, with biotic factors and abiotic environmental filtering (mainly imposed by soil pH) respectively contributing about 37% and 63% of variation. Our results provided a novel and comprehensive way to explain the distance-decay pattern of soil microbiome via quantifying the assembly processes at multiple spatial scales, as well as the method to quantify the influence of abiotic, biotic, and geographic factors in shaping microbial community structure, thus enabling understanding of widely acknowledged microbial biogeographic patterns and microbial ecology.}, } @article {pmid31073898, year = {2019}, author = {Zhao, H and Yan, B and Mo, S and Nie, S and Li, Q and Ou, Q and Wu, B and Jiang, G and Tang, J and Li, N and Jiang, C}, title = {Carbohydrate metabolism genes dominant in a subtropical marine mangrove ecosystem revealed by metagenomics analysis.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {57}, number = {7}, pages = {575-586}, pmid = {31073898}, issn = {1976-3794}, mesh = {*Archaea/classification/genetics/metabolism ; *Bacteria/classification/genetics/metabolism ; Carbohydrate Metabolism/genetics ; China ; Geologic Sediments/*microbiology ; Metagenomics/methods ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Wetlands ; }, abstract = {Mangrove sediment microorganisms play a vital role in the energy transformation and element cycling in marine wetland ecosystems. Using metagenomics analysis strategy, we compared the taxonomic structure and gene profile of the mangrove and non-mangrove sediment samples at the subtropical estuary in Beibu Gulf, South China Sea. Proteobacteria, Bacteroidetes, and Firmicutes were the most abundant bacterial phyla. Archaeal family Methanosarcinaceae and bacterial genera Vibrio and Dehalococcoides were significantly higher in the mangrove sediments than in the nonmangrove sediments. Functional analysis showed that "Carbohydrate metabolism" was the most abundant metabolic category. The feature of carbohydrate-active enzymes (CZs) was analyzed using the Carbohydrate-Active EnZymes Database. The significant differences of CZs between mangrove and non-mangrove sediments, were attributed to the amounts of polyphenol oxidase (EC 1.10.3.-), hexosyltransferase (EC 2.4.1.-), and β-N-acetylhexosaminidase (EC 3.2.1.52), which were higher in the mangrove sediment samples. Principal component analysis indicated that the microbial community and gene profile between mangrove and non-mangrove sediments were distinct. Redundancy analysis showed that total organic carbon is a significant factor that affects the microbial community and gene distribution. The results indicated that the mangrove ecosystem with massive amounts of organic carbon may promote the richness of carbohydrate metabolism genes and enhance the degradation and utilization of carbohydrates in the mangrove sediments.}, } @article {pmid31073691, year = {2019}, author = {Bersanelli, M and Santoni, M and Ticinesi, A and Buti, S}, title = {The Urinary Microbiome and Anticancer Immunotherapy: The Potentially Hidden Role of Unculturable Microbes.}, journal = {Targeted oncology}, volume = {14}, number = {3}, pages = {247-252}, pmid = {31073691}, issn = {1776-260X}, mesh = {Antineoplastic Agents, Immunological/*therapeutic use ; Bacteriuria/drug therapy/immunology/*microbiology ; Biomarkers/*urine ; Cell Cycle Checkpoints/*drug effects ; Humans ; Immunotherapy ; Microbiota/*drug effects ; Neoplasms/drug therapy/immunology/*microbiology ; Urinary Tract/drug effects/*microbiology ; }, abstract = {Several urinary disorders, including overactive bladder, urinary incontinence, and interstitial cystitis, are often characterized by negative urine cultures. The application of metagenomics (i.e., 16S rRNA microbial profiling or whole-genome shotgun sequencing) to urine samples has enabled the identification of previously undetected bacteria, contributing to the discovery and characterization of the urinary microbiome. The most frequent species isolated are Lactobacillus (15%), Corynebacterium (14.2%), Streptococcus (11.9%), Actinomyces (6.9%), and Staphylococcus (6.9%). Although several studies are emerging in this context, the role of urinary microbiota in the pathogenesis of infections and in tumor carcinogenesis remains unclear. Furthermore, data on the activity of gut microbiota in modulating sensitivity to immune checkpoint inhibitors in advanced cancer patients suggest that the influence of urinary microbiota on tumor response to anticancer therapy should also be investigated. Moreover, its possible relationship with tumor mutational burden, which is in turn correlated with response to immunotherapy, should be the focus of future studies. Of note, the effect of antibiotics on this complex scenario seems to deserve careful consideration.}, } @article {pmid31072660, year = {2019}, author = {Ramírez, AS and Vega-Orellana, OM and Viver, T and Poveda, JB and Rosales, RS and Poveda, CG and Spergser, J and Szostak, MP and Caballero, MJ and Ressel, L and Bradbury, JM and Mar Tavío, M and Karthikeyan, S and Amann, R and Konstantinidis, KT and Rossello-Mora, R}, title = {First description of two moderately halophilic and psychrotolerant Mycoplasma species isolated from cephalopods and proposal of Mycoplasma marinum sp. nov. and Mycoplasma todarodis sp. nov.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {4}, pages = {457-467}, doi = {10.1016/j.syapm.2019.04.003}, pmid = {31072660}, issn = {1618-0984}, mesh = {Animals ; Cephalopoda/classification/*microbiology ; DNA, Bacterial/genetics ; Genome, Bacterial/genetics ; Marine Biology ; Mycoplasma/*classification/cytology/*physiology ; Phenotype ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sequence Analysis, DNA ; Species Specificity ; Temperature ; }, abstract = {Two moderately halophilic and psychrotolerant new Mycoplasma species were isolated from common cephalopods. Three strains were isolated in pure culture from two individual European flying squid (Todarodes sagittatus), and two individual octopuses (Octopus vulgaris). The strains showed optimal growth at 25 °C and a salinity of 3% (w/v) NaCl. Molecular analyses revealed that the isolates belonged to two new, but phylogenetically related species, divergent from all previously described Mollicutes, representing the first marine isolates of the class, and also the first Mycoplasma strains for which NaCl requirement has been demonstrated. A genome search against all available marine metagenomes and 16S rRNA gene databases indicated that these two species represent a novel non-free-living marine lineage of Mollicutes, specifically associated with marine animals. Morphology and physiology were compatible with other members of this group, and genomic and phenotypic analyses demonstrated that these organisms represent two novel species of the genus Mycoplasma, for which the names Mycoplasma marinum sp. nov. and Mycoplasma todarodis sp. nov. are proposed; the type strains are PE[T] (DSM 105487[T], CIP 111404[T]) and 5H[T] (DSM 105,488[T], CIP 111405[T]), respectively.}, } @article {pmid31072384, year = {2019}, author = {Zhang, X and Nieuwdorp, M and Groen, AK and Zwinderman, AH}, title = {Statistical evaluation of diet-microbe associations.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {90}, pmid = {31072384}, issn = {1471-2180}, mesh = {*Computer Simulation ; Diet/*statistics & numerical data ; Humans ; Metagenome/genetics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; *Software ; }, abstract = {BACKGROUND: Statistical evaluation of the association between microbial abundance and dietary variables can be done in various ways. Currently, there is no consensus on which methods are to be preferred in which circumstances. Application of particular methods seems to be based on the tradition of a particular research group, availability of experience with particular software, or depending on the outcomes of the analysis.

RESULTS: We applied four popular methods including edgeR, limma, metagenomeSeq and shotgunFunctionalizeR, to evaluate the association between dietary variables and abundance of microbes. We found large difference in results between the methods. Our simulation studies revealed that no single method was optimal.

CONCLUSIONS: We advise researchers to run multiple analyses and focus on the significant findings identified by multiple methods in order to achieve a better control of false discovery rate, although the false discovery rate can still be substantial.}, } @article {pmid31071918, year = {2019}, author = {Dai, L and Zhang, G and Yu, Z and Ding, H and Xu, Y and Zhang, Z}, title = {Effect of Drought Stress and Developmental Stages on Microbial Community Structure and Diversity in Peanut Rhizosphere Soil.}, journal = {International journal of molecular sciences}, volume = {20}, number = {9}, pages = {}, pmid = {31071918}, issn = {1422-0067}, support = {2018YFD0201007//National Key Research and Development Program of China/ ; SDAIT-04-06//Modern Agricultural Industry Technical System of Shandong Province/ ; }, mesh = {Acidobacteria/classification/genetics ; Actinobacteria/classification/genetics ; Arachis/genetics/*microbiology ; Chloroflexi/classification/genetics ; Cyanobacteria/classification/genetics ; *Droughts ; High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; Phylogeny ; Plant Roots/microbiology ; Proteobacteria/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Seedlings/genetics ; Soil Microbiology ; Stress, Physiological/*genetics ; Tropical Climate ; }, abstract = {BACKGROUND: Peanut (Arachis hypogaea L.), an important oilseed and food legume, is widely cultivated in the semi-arid tropics. Drought is the major stress in this region which limits productivity. Microbial communities in the rhizosphere are of special importance to stress tolerance. However, relatively little is known about the relationship between drought and microbial communities in peanuts.

METHOD: In this study, deep sequencing of the V3-V4 region of the 16S rRNA gene was performed to characterize the microbial community structure of drought-treated and untreated peanuts.

RESULTS: Taxonomic analysis showed that Actinobacteria, Proteobacteria, Saccharibacteria, Chloroflexi, Acidobacteria and Cyanobacteria were the dominant phyla in the peanut rhizosphere. Comparisons of microbial community structure of peanuts revealed that the relative abundance of Actinobacteria and Acidobacteria dramatically increased in the seedling and podding stages in drought-treated soil, while that of Cyanobacteria and Gemmatimonadetes increased in the flowering stage in drought-treated rhizospheres. Metagenomic profiling indicated that sequences related to metabolism, signaling transduction, defense mechanism and basic vital activity were enriched in the drought-treated rhizosphere, which may have implications for plant survival and drought tolerance.

CONCLUSION: This microbial communities study will form the foundation for future improvement of drought tolerance of peanuts via modification of the soil microbes.}, } @article {pmid31071293, year = {2019}, author = {MacLeod, AS}, title = {Bad "Staph" in the Wound Environment of Diabetic Foot Ulcers.}, journal = {Cell host & microbe}, volume = {25}, number = {5}, pages = {638-640}, doi = {10.1016/j.chom.2019.04.006}, pmid = {31071293}, issn = {1934-6069}, mesh = {Biofilms ; *Diabetic Foot ; Humans ; *Microbiota ; *Staphylococcal Infections ; Wound Healing ; }, abstract = {Diabetic foot ulcers (DFUs) are a leading cause of high morbidity among diabetic patients. In this issue of Cell Host & Microbe, Kalan et al. (2019) examine the microbial bio-burden of DFUs and reveal biofilm and virulence pathways in the microbial metagenome that are linked to clinical healing outcomes.}, } @article {pmid31069173, year = {2019}, author = {Sun, L and Zhang, X and Zhang, Y and Zheng, K and Xiang, Q and Chen, N and Chen, Z and Zhang, N and Zhu, J and He, Q}, title = {Antibiotic-Induced Disruption of Gut Microbiota Alters Local Metabolomes and Immune Responses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {99}, pmid = {31069173}, issn = {2235-2988}, mesh = {Animals ; Anti-Bacterial Agents/*administration & dosage ; Bacteria/classification/genetics ; Colon/*chemistry/*immunology/microbiology ; Cytokines/analysis ; Gastrointestinal Microbiome/*drug effects ; *Immunity, Innate ; Intestinal Mucosa/immunology ; *Metabolome ; *Metagenome ; Mice ; }, abstract = {Gut microbiome plays an essential role in modulating host immune responses. However, little is known about the interaction of microbiota, their metabolites and relevant inflammatory responses in the gut. By treating the mice with three different antibiotics (enrofloxacin, vancomycin, and polymixin B sulfate), we aimed to investigate the effects of different antibiotics exposure on gut microbiota, microbial metabolism, inflammation responses in the gut, and most importantly, pinpoint the underlying interactions between them. Although the administration of different antibiotics can lead to different effects on mouse models, the treatment did not affect the average body weight of the mice. A heavier caecum was observed in vancomycin treated mice. Treatment by these three antibiotics significantly up-regulated gene expression of various cytokines in the colon. Enrofloxacin treated mice seemed to have an increased Th1 response in the colon. However, such a difference was not found in mice treated by vancomycin or polymixin B sulfate. Vancomycin treatment induced significant changes in bacterial composition at phylum and family level and decreased richness and diversity at species level. Enrofloxacin treatment only induced changes in composition at family presenting as an increase in Prevotellaceae and Rikenellaceae and a decrease in Bacteroidaceae. However, no significant difference was observed after polymixin B sulfate treatment. When compared with the control group, significant metabolic shift was found in the enrofloxacin and vancomycin treated group. The metabolic changes mainly occurred in Valine, leucine, and isoleucine biosynthesis pathway and beta-Alanine metabolism in enrofloxacin treated group. For vancomycin treatment metabolic changes were mainly found in beta-Alanine metabolism and Alanine, aspartate and glutamate metabolism pathway. Moreover, modifications observed in the microbiota compositions were correlated with the metabolite concentrations. For example, concentration of pentadecanoic acid was positively correlated with richness of Rikenellaceae and Prevotellaceae and negatively correlated with Enterobacteriaceae. This study suggests that the antibiotic-induced changes in gut microbiota might contribute to the inflammation responses through the alternation of metabolic status, providing a novel insight regarding a complex network that integrates the different interactions between gut microbiota, metabolic functions, and immune responses in host.}, } @article {pmid31068624, year = {2019}, author = {Catron, TR and Swank, A and Wehmas, LC and Phelps, D and Keely, SP and Brinkman, NE and McCord, J and Singh, R and Sobus, J and Wood, CE and Strynar, M and Wheaton, E and Tal, T}, title = {Microbiota alter metabolism and mediate neurodevelopmental toxicity of 17β-estradiol.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {7064}, pmid = {31068624}, issn = {2045-2322}, support = {EP-C-15-010/EPA/EPA/United States ; }, mesh = {Animals ; Embryonic Development/drug effects ; Estradiol/metabolism/*pharmacology ; Estrogens/metabolism/pharmacology ; Germ-Free Life/*drug effects ; Larva/drug effects/metabolism ; Locomotion/drug effects ; Microbiota/drug effects/*genetics ; Neurogenesis/drug effects ; RNA, Ribosomal, 16S/genetics ; Zebrafish/*embryology/metabolism/*microbiology ; }, abstract = {Estrogenic chemicals are widespread environmental contaminants associated with diverse health and ecological effects. During early vertebrate development, estrogen receptor signaling is critical for many different physiologic responses, including nervous system function. Recently, host-associated microbiota have been shown to influence neurodevelopment. Here, we hypothesized that microbiota may biotransform exogenous 17-βestradiol (E2) and modify E2 effects on swimming behavior. Colonized zebrafish were continuously exposed to non-teratogenic E2 concentrations from 1 to 10 days post-fertilization (dpf). Changes in microbial composition and predicted metagenomic function were evaluated. Locomotor activity was assessed in colonized and axenic (microbe-free) zebrafish exposed to E2 using a standard light/dark behavioral assay. Zebrafish tissue was collected for chemistry analyses. While E2 exposure did not alter microbial composition or putative function, colonized E2-exposed larvae showed reduced locomotor activity in the light, in contrast to axenic E2-exposed larvae, which exhibited normal behavior. Measured E2 concentrations were significantly higher in axenic relative to colonized zebrafish. Integrated peak area for putative sulfonated and glucuronidated E2 metabolites showed a similar trend. These data demonstrate that E2 locomotor effects in the light phase are dependent on the presence of microbiota and suggest that microbiota influence chemical E2 toxicokinetics. More broadly, this work supports the concept that microbial colonization status may influence chemical toxicity.}, } @article {pmid31068435, year = {2019}, author = {Guron, GKP and Arango-Argoty, G and Zhang, L and Pruden, A and Ponder, MA}, title = {Effects of Dairy Manure-Based Amendments and Soil Texture on Lettuce- and Radish-Associated Microbiota and Resistomes.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, pmid = {31068435}, issn = {2379-5042}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/drug effects/isolation & purification ; Cattle ; Dairying ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial ; Farms ; Female ; Lactuca/*microbiology ; Manure/*analysis ; Metagenome ; *Microbiota ; Raphanus/*microbiology ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {Dairy cattle are routinely treated with antibiotics, and the resulting manure or composted manure is commonly used as a soil amendment for crop production, raising questions regarding the potential for antibiotic resistance to propagate from "farm to fork." The objective of this study was to compare the microbiota and "resistomes" (i.e., carriage of antibiotic resistance genes [ARGs]) associated with lettuce leaf and radish taproot surfaces grown in different soils amended with dairy manure, compost, or chemical fertilizer only (control). Manure was collected from antibiotic-free dairy cattle (DC) or antibiotic-treated dairy cattle (DA), with a portion composted for parallel comparison. Amendments were applied to loamy sand or silty clay loam, and lettuce and radishes were cultivated to maturity in a greenhouse. Metagenomes were profiled via shotgun Illumina sequencing. Radishes carried a distinct ARG composition compared to that of lettuce, with greater relative abundance of total ARGs. Taxonomic species richness was also greater for radishes by 1.5-fold. The resistomes of lettuce grown with DC compost were distinct from those grown with DA compost, DC manure, or fertilizer only. Further, compost applied to loamy sand resulted in twofold-greater relative abundance of total ARGs on lettuce than when applied to silty clay loam. The resistomes of radishes grown with biological amendments were distinct from the corresponding fertilizer controls, but effects of composting or antibiotic use were not measureable. Cultivation in loamy sand resulted in higher species richness for both lettuce and radishes than when grown in silty clay loam by 2.2-fold and 1.2-fold, respectively, when amended with compost.IMPORTANCE A controlled, integrated, and replicated greenhouse study, along with comprehensive metagenomic analysis, revealed that multiple preharvest factors, including antibiotic use during manure collection, composting, biological soil amendment, and soil type, influence vegetable-borne resistomes. Here, radishes, a root vegetable, carried a greater load of ARGs and species richness than lettuce, a leafy vegetable. However, the lettuce resistome was more noticeably influenced by upstream antibiotic use and composting. Network analysis indicated that cooccurring ARGs and mobile genetic elements were almost exclusively associated with conditions receiving raw manure amendments, suggesting that composting could alleviate the mobility of manure-derived resistance traits. Effects of preharvest factors on associated microbiota and resistomes of vegetables eaten raw are worthy of further examination in terms of potential influence on human microbiomes and spread of antibiotic resistance. This research takes a step toward identifying on-farm management practices that can help mitigate the spread of agricultural sources of antibiotic resistance.}, } @article {pmid31067837, year = {2019}, author = {Sarmiento, MRA and de Paula, TO and Borges, FM and Ferreira-Machado, AB and Resende, JA and Moreira, APB and Dutra Luquetti, SCP and Cesar, DE and da Silva, VL and Diniz, CG}, title = {Obesity, Xenobiotic Intake and Antimicrobial-Resistance Genes in the Human Gastrointestinal Tract: A Comparative Study of Eutrophic, Overweight and Obese Individuals.}, journal = {Genes}, volume = {10}, number = {5}, pages = {}, pmid = {31067837}, issn = {2073-4425}, mesh = {Adult ; Antacids/therapeutic use ; Anti-Inflammatory Agents, Non-Steroidal/therapeutic use ; Antihypertensive Agents/therapeutic use ; Dietary Supplements ; Drug Resistance, Microbial/*genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/*microbiology ; Humans ; In Situ Hybridization, Fluorescence ; Male ; Middle Aged ; Overweight/*microbiology ; Sweetening Agents/administration & dosage ; Xenobiotics/administration & dosage ; Young Adult ; }, abstract = {Although lifestyle and physiology in obese individuals are accepted to lead to changes in the intestinal microbiota, uncertainty remains about microbiota dysbiosis, and xenobiotics intake, as a source of selective pressure, independent of antimicrobial chemotherapy. The aim of this study was to compare the occurrence of antimicrobial resistance genetic markers (ARG) in faecal specimens of eutrophic, overweight and obese individuals, and their correlation with xenobiotic intake and gut bacteria density. Methods: This was a cross-sectional case-controlled study including 72 adult participants with no record of intestinal or systemic diseases, or recent use of antimicrobials, grouped as eutrophic, overweight, or obese. Anthropometric profile, eating habits and oral xenobiotics intake were recorded. Faecal metagenomic DNA was used to screen for ARG by PCR, and to measure bacterial groups by fluorescence in situ hybridization (FISH). Student's t and Wilcoxon tests were used to compare means and differences in ARG detection (95% confidence intervals). Correlation analyses (odds ratio) and relationships between bacteria density and ARG were determined. Results: Increase in abdominal circumference, waist circumference, hip, waist-hip ratio, BMI, carbohydrate, fibres, and total calorie intakes were different from eutrophic to obese participants. Habitual use of antihypertensive and anti-inflammatory drugs, antacids, and artificial sweeteners were associated mainly with obesity and overweight. Nutritional supplements were associated to the eutrophic group. ARG screening showed differences being more frequent among obese, and positive for 27 genetic markers related to β-lactams, tetracyclines, the macrolide lincosamide and streptogramin group, quinolones, sulfonamides, aminoglycosides, and efflux pump. Positive correlation between ARG and BMI, caloric intake, and intake of xenobiotics, was observed for obese individuals. Relationships among ARG detection and bacteria densities were also different. Conclusions: This study reinforces the hypothesis that obese individuals may harbour an altered gut microbiota, if compared to eutrophic. The overweight individuals display a transitional gut microbiota which seems to be between eutrophic and obese. Furthermore, the increased xenobiotic intake associated to obesity may play an important role in the antimicrobial resistance phenomenon.}, } @article {pmid31066440, year = {2019}, author = {Klaassen, MAY and Imhann, F and Collij, V and Fu, J and Wijmenga, C and Zhernakova, A and Dijkstra, G and Festen, EAM and Gacesa, R and Vich Vila, A and Weersma, RK}, title = {Anti-inflammatory Gut Microbial Pathways Are Decreased During Crohn's Disease Exacerbations.}, journal = {Journal of Crohn's & colitis}, volume = {13}, number = {11}, pages = {1439-1449}, pmid = {31066440}, issn = {1876-4479}, mesh = {Adult ; Bacteria/genetics/metabolism ; Cohort Studies ; Crohn Disease/*microbiology ; DNA, Bacterial ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Female ; Folic Acid/metabolism ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Principal Component Analysis ; Riboflavin/metabolism ; Thiamine/metabolism ; Whole Genome Sequencing ; }, abstract = {BACKGROUND AND AIMS: Crohn's disease [CD] is a chronic inflammatory disorder of the gastrointestinal tract characterised by alternating periods of exacerbation and remission. We hypothesised that changes in the gut microbiome are associated with CD exacerbations, and therefore aimed to correlate multiple gut microbiome features to CD disease activity.

METHODS: Faecal microbiome data generated using whole-genome metagenomic shotgun sequencing of 196 CD patients were of obtained from the 1000IBD cohort [one sample per patient]. Patient disease activity status at time of sampling was determined by re-assessing clinical records 3 years after faecal sample production. Faecal samples were designated as taken 'in an exacerbation' or 'in remission'. Samples taken 'in remission' were further categorised as 'before the next exacerbation' or 'after the last exacerbation', based on the exacerbation closest in time to the faecal production date. CD activity was correlated with gut microbial composition and predicted functional pathways via logistic regressions using MaAsLin software.

RESULTS: In total, 105 bacterial pathways were decreased during CD exacerbation (false-discovery rate [FDR] <0.1) in comparison with the gut microbiome of patients both before and after an exacerbation. Most of these decreased pathways exert anti-inflammatory properties facilitating the biosynthesis and fermentation of various amino acids [tryptophan, methionine, and arginine], vitamins [riboflavin and thiamine], and short-chain fatty acids [SCFAs].

CONCLUSIONS: CD exacerbations are associated with a decrease in microbial genes involved in the biosynthesis of the anti-inflammatory mediators riboflavin, thiamine, and folate, and SCFAs, suggesting that increasing the intestinal abundances of these mediators might provide new treatment opportunities. These results were generated using bioinformatic analyses of cross-sectional data and need to be replicated using time-series and wet lab experiments.}, } @article {pmid31066111, year = {2019}, author = {Prince, AL and Pace, RM and Dean, T and Takahashi, D and Kievit, P and Friedman, JE and Aagaard, KM}, title = {The development and ecology of the Japanese macaque gut microbiome from weaning to early adolescence in association with diet.}, journal = {American journal of primatology}, volume = {81}, number = {10-11}, pages = {e22980}, pmid = {31066111}, issn = {1098-2345}, support = {P51 OD011092/OD/NIH HHS/United States ; K12 GM084897/GM/NIGMS NIH HHS/United States ; R56 DK114711/DK/NIDDK NIH HHS/United States ; R01 HD091731/HD/NICHD NIH HHS/United States ; //Eunice Kennedy Shriver National Institute of Child Health and Human Development/International ; P30 DK020593/DK/NIDDK NIH HHS/United States ; R01 DK089201/DK/NIDDK NIH HHS/United States ; R24 DK090964/DK/NIDDK NIH HHS/United States ; P30 DK048520/DK/NIDDK NIH HHS/United States ; F32 HD082969/HD/NICHD NIH HHS/United States ; }, mesh = {Age Factors ; Animals ; Bacteria/classification ; Diet/*veterinary ; Diet, High-Fat/veterinary ; Female ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Longitudinal Studies ; Macaca fuscata/growth & development/*microbiology ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; Treponema ; Weaning ; }, abstract = {Previously we have shown that the Japanese macaque gut microbiome differs not by obesity per se, but rather in association with high-fat diet (HFD) feeding. This held true for both pregnant dams, as well as their 1-year-old offspring, even when weaned onto a control diet. Here we aimed to examine the stability of the gut microbiome over time and in response to maternal and postweaning HFD feeding from 6 months of age, and at 1 and 3 years of age. In both cross-sectional and longitudinal specimens, we performed analysis of the V4 hypervariable region of the 16S rRNA gene on anus swabs collected from pregnant dams and their juveniles at age 6 months to 3 years (n = 55). Extracted microbial DNA was subjected to 16S-amplicon-based metagenomic sequencing on the Illumina MiSeq platform. We initially identified 272 unique bacterial genera, and multidimensional scaling revealed samples to cluster by age and diet exposures. Dirichlet multinomial mixture modeling of microbiota abundances enabled identification of two predominant enterotypes to which samples sorted, characterized primarily by Treponema abundance, or lack thereof. Approximating the time of initial weaning (6 months), the Japanese macaque offspring microbiome underwent a significant state type transition which stabilized from 1 to 3 years of age. However, we also found the low abundance Treponema enterotype to be strongly associated with HFD exposure, be it during gestation/lactation or in the postweaning interval. Examination of taxonomic co-occurrences revealed samples within the low Treponema cluster were relatively permissive (allowing for increased interactions between microbiota) whereas samples within the high Treponema cluster were relatively exclusionary (suggesting decreased interactions amongst microbiota). Taken together, these findings suggest that Treponemes are keystone species in the developing gut microbiome of the gut, and susceptible to HFD feeding in their relative abundance.}, } @article {pmid31065734, year = {2019}, author = {Mikolajczyk, R and Roesner, LM}, title = {[General aspects regarding the skin microbiome].}, journal = {Der Hautarzt; Zeitschrift fur Dermatologie, Venerologie, und verwandte Gebiete}, volume = {70}, number = {6}, pages = {400-406}, pmid = {31065734}, issn = {1432-1173}, mesh = {Bacteria/classification/*genetics ; DNA, Bacterial/*genetics ; DNA, Fungal/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota ; Sequence Analysis, DNA/*methods ; Skin/*microbiology ; Skin Diseases, Bacterial/microbiology ; }, abstract = {The human body is densely populated by trillions of microorganisms, which are collectively known as the human microbiota. On the outermost barrier, the skin, a plethora of different bacteria and fungi as well as viruses and mites reside. The skin of different body sites shows a high degree of heterogeneity, generating multiple ecological niches. For example, moisture, sebum and sweat promote the growth of different microorganisms. This diversity has hampered a global and objective analysis of the composition of the microbiota in the past. Today, approximately 10 years after the development of metagenome analysis by next generation high-throughput DNA sequencing, these techniques are now established and affordable in research fields. These techniques enable investigations on the microorganisms living in and on body surfaces and represent an important tool in diverse clinical questions. This review addresses new developments in the (physiological) composition of the skin microbiota and briefly summarizes the research techniques applied.}, } @article {pmid31065547, year = {2019}, author = {Zhuang, H and Cheng, L and Wang, Y and Zhang, YK and Zhao, MF and Liang, GD and Zhang, MC and Li, YG and Zhao, JB and Gao, YN and Zhou, YJ and Liu, SL}, title = {Dysbiosis of the Gut Microbiome in Lung Cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {112}, pmid = {31065547}, issn = {2235-2988}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Lung Neoplasms/*complications ; Male ; Metagenomics ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Lung cancer (LC) is one of the most serious malignant tumors, which has the fastest growing morbidity and mortality worldwide. A role of the lung microbiota in LC pathogenesis has been analyzed, but a comparable role of the gut microbiota has not yet been investigated. In this study, the gut microbiota of 30 LC patients and 30 healthy controls were examined via next-generation sequencing of 16S rRNA and analyzed for diversity and biomarkers. We found that there was no decrease in significant microbial diversity (alpha diversity) in LC patients compared to controls (P observed = 0.1422), while the composition (beta diversity) differed significantly between patients and controls (phylum [stress = 0.153], class [stress = 0.16], order [stress = 0.146], family [stress = 0.153]). Controls had a higher abundance of the bacterial phylum Actinobacteria and genus Bifidobacterium, while patients with LC showed elevated levels of Enterococcus. These bacteria were found as possible biomarkers for LC. A decline of normal function of the gut microbiome in LC patients was also observed. These results provide the basic guidance for a systematic, multilayered assessment of the role of the gut microbiome in LC, which has a promising potential for early prevention and targeted intervention.}, } @article {pmid31064831, year = {2019}, author = {Haran, JP and Bhattarai, SK and Foley, SE and Dutta, P and Ward, DV and Bucci, V and McCormick, BA}, title = {Alzheimer's Disease Microbiome Is Associated with Dysregulation of the Anti-Inflammatory P-Glycoprotein Pathway.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, pmid = {31064831}, issn = {2150-7511}, support = {R01 DK056754/DK/NIDDK NIH HHS/United States ; R03 AG056356/AG/NIA NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; T32 AI007349/AI/NIAID NIH HHS/United States ; K23 AG057790/AG/NIA NIH HHS/United States ; R15 AI112985/AI/NIAID NIH HHS/United States ; }, mesh = {ATP Binding Cassette Transporter, Subfamily B/*metabolism ; Aged ; Aged, 80 and over ; Alzheimer Disease/metabolism/*microbiology ; Bacteria/classification/isolation & purification ; Dementia/microbiology ; *Dysbiosis ; Epithelial Cells/metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Homeostasis ; Humans ; Inflammation/complications ; Intestines/microbiology ; Machine Learning ; Male ; Metabolic Networks and Pathways/immunology ; Metagenomics ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The microbiota-gut-brain axis is a bidirectional communication system that is poorly understood. Alzheimer's disease (AD), the most common cause of dementia, has long been associated with bacterial infections and inflammation-causing immunosenescence. Recent studies examining the intestinal microbiota of AD patients revealed that their microbiome differs from that of subjects without dementia. In this work, we prospectively enrolled 108 nursing home elders and followed each for up to 5 months, collecting longitudinal stool samples from which we performed metagenomic sequencing and in vitro T84 intestinal epithelial cell functional assays for P-glycoprotein (P-gp) expression, a critical mediator of intestinal homeostasis. Our analysis identified clinical parameters as well as numerous microbial taxa and functional genes that act as predictors of AD dementia in comparison to elders without dementia or with other dementia types. We further demonstrate that stool samples from elders with AD can induce lower P-gp expression levels in vitro those samples from elders without dementia or with other dementia types. We also paired functional studies with machine learning approaches to identify bacterial species differentiating the microbiome of AD elders from that of elders without dementia, which in turn are accurate predictors of the loss of dysregulation of the P-gp pathway. We observed that the microbiome of AD elders shows a lower proportion and prevalence of bacteria with the potential to synthesize butyrate, as well as higher abundances of taxa that are known to cause proinflammatory states. Therefore, a potential nexus between the intestinal microbiome and AD is the modulation of intestinal homeostasis by increases in inflammatory, and decreases in anti-inflammatory, microbial metabolism.IMPORTANCE Studies of the intestinal microbiome and AD have demonstrated associations with microbiome composition at the genus level among matched cohorts. We move this body of literature forward by more deeply investigating microbiome composition via metagenomics and by comparing AD patients against those without dementia and with other dementia types. We also exploit machine learning approaches that combine both metagenomic and clinical data. Finally, our functional studies using stool samples from elders demonstrate how the c microbiome of AD elders can affect intestinal health via dysregulation of the P-glycoprotein pathway. P-glycoprotein dysregulation contributes directly to inflammatory disorders of the intestine. Since AD has been long thought to be linked to chronic bacterial infections as a possible etiology, our findings therefore fill a gap in knowledge in the field of AD research by identifying a nexus between the microbiome, loss of intestinal homeostasis, and inflammation that may underlie this neurodegenerative disorder.}, } @article {pmid31062778, year = {2019}, author = {Liu, J and Hao, W and He, Z and Kwek, E and Zhao, Y and Zhu, H and Liang, N and Ma, KY and Lei, L and He, WS and Chen, ZY}, title = {Beneficial effects of tea water extracts on the body weight and gut microbiota in C57BL/6J mice fed with a high-fat diet.}, journal = {Food & function}, volume = {10}, number = {5}, pages = {2847-2860}, doi = {10.1039/c8fo02051e}, pmid = {31062778}, issn = {2042-650X}, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification/metabolism ; Body Weight ; Camellia sinensis/chemistry/*metabolism ; Diet, High-Fat/adverse effects ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Obesity/*diet therapy/microbiology/physiopathology ; Tea/*metabolism ; }, abstract = {Accumulative evidence has suggested that tea consumption has benefits in reducing body fat and alleviating metabolic syndrome. We hypothesize that benefits of tea consumption can be partially mediated by modulating intestinal microbiota via inhibiting the formation of lipopolysaccharides (LPS) and promoting the production of short chain fatty acids (SCFAs). C57BL/6J mice were fed a high fat diet with the addition of 1% water extracts of green tea, oolong tea and black tea. Results showed that the dietary supplementation of three tea water extracts equally improved the glucose tolerance and reduced a high fat diet-induced gain in weight, hepatic lipids, and white adipose tissue weights. This was accompanied by a significant reduction in plasma LPS and a significant increase in the production of SCFAs. The metagenomic analyses showed that the tea extracts changed the overall composition of gut microbiota and decreased the relative abundance of family Rikenellaceae and Desulfovibrionaceae. In addition, tea water extracts could also change the abundance of key operational taxonomic units (OTUs) including OTU473 (Alistipes), OTU229 (Rikenella), OTU179 (Ruminiclostridium) and OTU264 (Acetatifactor). In conclusion, three tea extracts could improve the glucose tolerance, induce the production of SCFAs and inhibit the production of endotoxin LPS, most likely mediated by modulating gut microbiota.}, } @article {pmid31062682, year = {2019}, author = {Gruninger, RJ and Ribeiro, GO and Cameron, A and McAllister, TA}, title = {Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants.}, journal = {Animal : an international journal of animal bioscience}, volume = {13}, number = {9}, pages = {1843-1854}, doi = {10.1017/S1751731119000752}, pmid = {31062682}, issn = {1751-732X}, mesh = {Anaerobiosis ; Animals ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; *Computational Biology ; Diet/veterinary ; Fungi/genetics/*metabolism ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/veterinary ; Rumen/metabolism ; Ruminants/*microbiology/physiology ; Sequence Analysis, DNA/veterinary ; }, abstract = {Ruminants are unique among livestock due to their ability to efficiently convert plant cell wall carbohydrates into meat and milk. This ability is a result of the evolution of an essential symbiotic association with a complex microbial community in the rumen that includes vast numbers of bacteria, methanogenic archaea, anaerobic fungi and protozoa. These microbes produce a diverse array of enzymes that convert ingested feedstuffs into volatile fatty acids and microbial protein which are used by the animal for growth. Recent advances in high-throughput sequencing and bioinformatic analyses have helped to reveal how the composition of the rumen microbiome varies significantly during the development of the ruminant host, and with changes in diet. These sequencing efforts are also beginning to explain how shifts in the microbiome affect feed efficiency. In this review, we provide an overview of how meta-omics technologies have been applied to understanding the rumen microbiome, and the impact that diet has on the rumen microbial community.}, } @article {pmid31062073, year = {2019}, author = {Tamura, K and Foley, MH and Gardill, BR and Dejean, G and Schnizlein, M and Bahr, CME and Louise Creagh, A and van Petegem, F and Koropatkin, NM and Brumer, H}, title = {Surface glycan-binding proteins are essential for cereal beta-glucan utilization by the human gut symbiont Bacteroides ovatus.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {76}, number = {21}, pages = {4319-4340}, pmid = {31062073}, issn = {1420-9071}, support = {R01 GM118475/GM/NIGMS NIH HHS/United States ; T32 GM145304/GM/NIGMS NIH HHS/United States ; MOP-119404/CAPMC/CIHR/Canada ; MOP-137134/CAPMC/CIHR/Canada ; P41 GM103393/GM/NIGMS NIH HHS/United States ; MOP-142472/CAPMC/CIHR/Canada ; T32 GM008353/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteroides/genetics/metabolism/*physiology ; Carbohydrate Metabolism/physiology ; Carbohydrate Sequence ; Dietary Fiber/metabolism ; Edible Grain/*metabolism ; Gastrointestinal Microbiome/physiology ; Gastrointestinal Tract/*metabolism/*microbiology ; Gene Expression Regulation, Bacterial ; Genetic Loci ; Glycoside Hydrolases/genetics/metabolism ; Humans ; Membrane Proteins/metabolism/*physiology ; Polysaccharides/*metabolism ; beta-Glucans/*metabolism ; }, abstract = {The human gut microbiota, which underpins nutrition and systemic health, is compositionally sensitive to the availability of complex carbohydrates in the diet. The Bacteroidetes comprise a dominant phylum in the human gut microbiota whose members thrive on dietary and endogenous glycans by employing a diversity of highly specific, multi-gene polysaccharide utilization loci (PUL), which encode a variety of carbohydrases, transporters, and sensor/regulators. PULs invariably also encode surface glycan-binding proteins (SGBPs) that play a central role in saccharide capture at the outer membrane. Here, we present combined biophysical, structural, and in vivo characterization of the two SGBPs encoded by the Bacteroides ovatus mixed-linkage β-glucan utilization locus (MLGUL), thereby elucidating their key roles in the metabolism of this ubiquitous dietary cereal polysaccharide. In particular, molecular insight gained through several crystallographic complexes of SGBP-A and SGBP-B with oligosaccharides reveals that unique shape complementarity of binding platforms underpins specificity for the kinked MLG backbone vis-à-vis linear β-glucans. Reverse-genetic analysis revealed that both the presence and binding ability of the SusD homolog BoSGBPMLG-A are essential for growth on MLG, whereas the divergent, multi-domain BoSGBPMLG-B is dispensable but may assist in oligosaccharide scavenging from the environment. The synthesis of these data illuminates the critical role SGBPs play in concert with other MLGUL components, reveals new structure-function relationships among SGBPs, and provides fundamental knowledge to inform future (meta)genomic, biochemical, and microbiological analyses of the human gut microbiota.}, } @article {pmid31061496, year = {2019}, author = {Gandy, KAO and Zhang, J and Nagarkatti, P and Nagarkatti, M}, title = {The role of gut microbiota in shaping the relapse-remitting and chronic-progressive forms of multiple sclerosis in mouse models.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6923}, pmid = {31061496}, issn = {2045-2322}, support = {F32 AT008539/AT/NCCIH NIH HHS/United States ; R01 AI129788/AI/NIAID NIH HHS/United States ; R01 MH094755/MH/NIMH NIH HHS/United States ; P20 GM103641/GM/NIGMS NIH HHS/United States ; P01 AT003961/AT/NCCIH NIH HHS/United States ; R01 AT006888/AT/NCCIH NIH HHS/United States ; R01 AI123947/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Chronic Disease ; Disease Models, Animal ; *Disease Progression ; Dysbiosis/complications ; Feces/microbiology ; Female ; Firmicutes/physiology ; *Gastrointestinal Microbiome ; Immunization ; Mice ; Multiple Sclerosis/complications/*microbiology/pathology ; Recurrence ; }, abstract = {Using a mouse model of multiple sclerosis (MS), experimental autoimmune encephalitis (EAE), we evaluated the role of gut microbiota in modulating chronic-progressive (CP) versus relapse-remitting (RR) forms of the disease. We hypothesized that clinical courses of EAE may be shaped by differential gut microbiota. Metagenomic sequencing of prokaryotic 16S rRNA present in feces from naïve mice and those exhibiting CP-EAE or RR-EAE revealed significantly diverse microbial populations. Microbiota composition was considerably different between naïve strains of mice, suggesting microbial components present in homeostatic conditions may prime mice for divergent courses of disease. Additionally, there were differentially abundant bacteria in CP and RR forms of EAE, indicating a potential role for gut microbiota in shaping tolerant or remittance-favoring, and pathogenic or pro-inflammatory-promoting conditions. Furthermore, immunization to induce EAE led to significant alterations in gut microbiota, some were shared between disease courses and others were course-specific, supporting a role for gut microbial composition in EAE pathogenesis. Moreover, using Linear Discriminant Analysis (LDA) coupled with effect size measurement (LEfSe) to analyze microbial content, biomarkers of each naïve and disease states were identified. Our findings demonstrate for the first time that gut microbiota may determine the susceptibility to CP or RR forms of EAE.}, } @article {pmid31059117, year = {2019}, author = {Jagodzinski, A and Zielinska, E and Laczmanski, L and Hirnle, L}, title = {The early years of life. Are they influenced by our microbiome?.}, journal = {Ginekologia polska}, volume = {90}, number = {4}, pages = {228-232}, doi = {10.5603/GP.2019.0041}, pmid = {31059117}, issn = {2543-6767}, mesh = {Child ; *Child Development ; Child, Preschool ; Gastrointestinal Microbiome ; Humans ; Hypersensitivity ; Infant ; Infant, Newborn ; *Microbiota ; Milk, Human ; Parturition ; }, abstract = {Human microbiome contains the genetic pool of bacteria and other microbes such as Achaea, fungi and viruses inhabiting the human body. It holds an immense potential to affect both physiological and pathological processes. The microbiome's composition can be defined in detail by analyzing ribosomal 16S rRNA and metagenomic tests. Recent increases in cesar- ean sections, the use of antibiotics during pregnancy, the increasing amount of prematurely born children and changes in infant nutrition have an impact on the microbiome forming process. A correlation between the bowel microbiome's com- position and the occurrence of certain diseases, especially inflammatory bowel diseases (IBD), asthma and type 1 diabetes has been demonstrated. The influence on the development of cognitive functions and behaviour has also been displayed. This correlation justifies attempts to restore the beneficial the composition of the microbiome through the use of probiotics, vaginal microflora transfer in case of cesarean section and encouraging breastfeeding. Development of multiple studies on the topic of the human microbiome and its impact on the human body is necessary in order to reach final conclusions. The aim of this article is to summarize recent findings regarding the development of the human microbiome from the first days of life and the influence of changes in its composition on human health.}, } @article {pmid31058468, year = {2019}, author = {Shurigin, V and Hakobyan, A and Panosyan, H and Egamberdieva, D and Davranov, K and Birkeland, NK}, title = {A glimpse of the prokaryotic diversity of the Large Aral Sea reveals novel extremophilic bacterial and archaeal groups.}, journal = {MicrobiologyOpen}, volume = {8}, number = {9}, pages = {e00850}, pmid = {31058468}, issn = {2045-8827}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Environmental/genetics/isolation & purification ; DNA, Ribosomal/chemistry/genetics ; Lakes/*microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Uzbekistan ; }, abstract = {During the last five decades, the Aral Sea has gradually changed from a saline water body to a hypersaline lake. Microbial community inhabiting the Aral Sea has been through a succession and continuous adaptation during the last 50 years of increasing salinization, but so far, the microbial diversity has not been explored. Prokaryotic diversity of the Large Aral Sea using cultivation-independent methods based on determination of environmental 16S rRNA gene sequences revealed a microbial community related to typical marine or (hyper) saline-adapted Bacteria and Archaea. The archaeal sequences were phylogenetically affiliated with the order Halobacteriales, with a large number of operational taxonomic units constituting a novel cluster in the Haloferacaceae family. Bacterial community analysis indicated a higher diversity with representatives belonging to Proteobacteria, Actinobacteria and Bacteroidetes. Many members of Alphaproteobacteria and Gammaproteobacteria were affiliated with genera like Roseovarius, Idiomarina and Spiribacter which have previously been found in marine or hypersaline waters. The majority of the phylotypes was most closely related to uncultivated organisms and shared less than 97% identity with their closest match in GenBank, indicating a unique community structure in the Large Aral Sea with mostly novel species or genera.}, } @article {pmid31055095, year = {2019}, author = {Hassan, M and Essam, T and Mira, A and Megahed, S}, title = {Biomonitoring detoxification efficiency of an algal-bacterial microcosm system for treatment of coking wastewater: Harmonization between Chlorella vulgaris microalgae and wastewater microbiome.}, journal = {The Science of the total environment}, volume = {677}, number = {}, pages = {120-130}, doi = {10.1016/j.scitotenv.2019.04.304}, pmid = {31055095}, issn = {1879-1026}, mesh = {Bacteria/*metabolism ; Chlorella vulgaris/*metabolism ; Coke ; Egypt ; Environmental Monitoring/*methods ; Environmental Restoration and Remediation/*methods ; Microalgae/metabolism ; Microbiota ; Wastewater/*analysis/*microbiology ; Water Pollutants, Chemical/analysis ; Water Pollution, Chemical/prevention & control ; }, abstract = {Nowadays, due to worldwide water shortage, water utilities are forced to re-evaluate treated wastewater. Consequently, wastewater treatment plants need to conduct biomonitoring. Coking wastewater (CWW) has toxic, mutative and carcinogenic components with threatening effect on the environment. CWW was selected as a model for complex highly toxic industrial wastewater that should be treated. CWW from Egypt was treated in a nine-liter photobioreactor using an algal-bacterial system. The photobioreactor was operated for 154 days changing different parameters (toxic load and light duration) for optimization. Optimized conditions achieved significant reduction (45%) in the operation cost. The algal-bacterial system was monitored using chemical assays (chemical oxygen demand and phenol analysis), bioassays (phytotoxicity, Artemia-toxicity, cytotoxicity, algal-bacterial ratio and settleability) and Illumina-MiSeq sequencing of 16S rRNA gene. The algal-bacterial system detoxified (in terms of phytotoxicity, cytotoxicity and Artemia-toxicity) CWW introduced as influent through all phases. A significant difference was recorded in the microbial diversity between influent and effluent samples. Four phyla dominated influent samples; Proteobacteria (77%), Firmicutes (11%), Bacteroidetes (5%) and Deferribacteres (3%) compared to only two in effluent samples; Proteobacteria (66%) and Bacteroidetes (26%). The significant relative-abundance of versatile aromatic degraders (Comamonadaceae and Pseudomonadaceae families) in influent samples conformed to the nature of CWW. Microbial community shifted and promoted the activity of catabolically versatile and xenobiotics degrading families (Chitinophagaceae and Xanthomonadaceae). Co-culture of microalgae had a positive effect on the biodegrading bacteria that was reflected by enhanced treatment efficiency, significant increase in relative abundance of bacterial genera with cyanide-decomposing potential and negative effect on waterborne pathogens.}, } @article {pmid31055031, year = {2019}, author = {Seferovic, MD and Pace, RM and Carroll, M and Belfort, B and Major, AM and Chu, DM and Racusin, DA and Castro, ECC and Muldrew, KL and Versalovic, J and Aagaard, KM}, title = {Visualization of microbes by 16S in situ hybridization in term and preterm placentas without intraamniotic infection.}, journal = {American journal of obstetrics and gynecology}, volume = {221}, number = {2}, pages = {146.e1-146.e23}, pmid = {31055031}, issn = {1097-6868}, support = {R01 DK089201/DK/NIDDK NIH HHS/United States ; R01 HD091731/HD/NICHD NIH HHS/United States ; R01 NR014792/NR/NINR NIH HHS/United States ; }, mesh = {Adult ; DNA Barcoding, Taxonomic ; Female ; Humans ; In Situ Hybridization ; Metagenomics ; Microbiota ; Placenta/*microbiology ; Pregnancy ; Premature Birth ; RNA, Bacterial/analysis ; *RNA, Ribosomal, 16S ; Sequence Analysis, RNA ; Term Birth ; }, abstract = {BACKGROUND: Numerous reports have documented bacteria in the placental membranes and basal plate decidua in the absence of immunopathology using histologic techniques. Similarly, independent metagenomic characterizations have identified an altered taxonomic makeup in association with spontaneous preterm birth. Here we sought to corroborate these findings by localizing presumptive intact bacteria using molecular histology within the placental microanatomy.

OBJECTIVE: Here we examined for microbes in term and preterm gestations using a signal-amplified 16S universal in situ hybridization probe set for bacterial rRNA, alongside traditional histologic methods of Warthin-Starry and Gram stains, as well as clinical culture methodologies. We further sought to differentiate accompanying 16S gene sequencing taxonomic profiles from germ-free (gnotobiotic) mouse and extraction and amplicon contamination controls.

STUDY DESIGN: Placentas were collected from a total of 53 subjects, composed of term labored (n = 4) and unlabored cesarean deliveries (n = 22) and preterm vaginal (n = 18) and cesarean deliveries (n = 8); a placenta from a single subject with clinical and histologic evident choriomanionitis was employed as a positive control (n = 1). The preterm cohort included spontaneous preterm birth with (n = 6) and without (n = 10) preterm premature rupture of membranes, as well as medically indicated preterm births (n = 10). Placental microbes were visualized using an in situ hybridization probe set designed against highly conserved regions of the bacterial 16S ribosome, which produces an amplified stable signal using branched DNA probes. Extracted bacterial nucleic acids from these same samples were subjected to 16S rRNA metagenomic sequencing (Illumina, V4) for course taxonomic analysis, alongside environmental and kit contaminant controls. A subset of unlabored, cesarean-delivered term pregnancies were also assessed with clinical culture for readily cultivatable pathogenic microbes.

RESULTS: Molecular in situ hybridization of bacterial rRNA enabled visualization and localization of low-abundance microbes after systematic high-power scanning. Despite the absence of clinical or histologic chorioamnionitis in 52 of 53 subjects, instances of 16S rRNA signal were confidently observed in 13 of 16 spontaneous preterm birth placentas, which was not significantly different from term unlabored cesarean specimens (18 of 22; P > .05). 16S rRNA signal was largely localized to the villous parenchyma and/or syncytiotrophoblast, and less commonly the chorion and the maternal intervillous space. In all term and unlabored cesarean deliveries, visualization of evident placental microbes by in situ hybridization occurred in the absence of clinical or histologic detection using conventional clinical cultivation, hematoxylin-eosin, and Gram staining. In 1 subject, appreciable villous bacteria localized to an infarction, where 16S microbial detection was confirmed by Warthin-Starry stain. In all instances, parallel sample principle coordinate analysis using Bray-Cutis distances of 16S rRNA gene sequencing data demonstrated consistent taxonomic distinction from all negative or potential contamination controls (P = .024, PERMANOVA). Classification from contaminant filtered data identified a distinct taxonomic makeup among term and preterm cohorts when compared with contaminant controls (false discovery rate <0.05).

CONCLUSION: Presumptively intact placental microbes are visualized as low-abundance, low-biomass and sparse populations within the placenta regardless of gestational age and mode of delivery. Their taxonomic makeup is distinct from contamination controls. These findings further support several previously published findings, including our own, which have used metagenomics to characterize low-abundance and low-biomass microbial communities in the placenta.}, } @article {pmid31055020, year = {2019}, author = {Xiao Joe, JT and Chiou, PP and Kuo, CY and Jia Lin, JH and Wu, JL and Lu, MW}, title = {The microbiota profile and transcriptome analysis of immune response during metamorphosis stages in orange spotted grouper (Epinephelus coioides).}, journal = {Fish & shellfish immunology}, volume = {90}, number = {}, pages = {141-149}, doi = {10.1016/j.fsi.2019.03.063}, pmid = {31055020}, issn = {1095-9947}, mesh = {Animals ; Bass/*genetics/growth & development/immunology/*microbiology ; Gastrointestinal Microbiome/*physiology ; Gene Expression Profiling ; Gene Expression Regulation/immunology ; Immunity, Innate/*genetics ; Metagenomics ; Metamorphosis, Biological/genetics/immunology ; Transcriptome/*immunology ; }, abstract = {Metamorphosis is a transformation process in larval development associated with changes in morphological and physiological features, including the immune system. The gastrointestinal tract harbors a plethora of bacteria, which might affect the digestion and absorption of nutrients, immunity, and gut-brain crosstalk in the host. In this study, we have performed metagenomic and transcriptomic analyses on the intestines of grouper at the pre-, mid- and post-metamorphosis stages. The sequencing data of 16S rRNA gene showed drastic changes in the microbial communities at different developmental stages. The transcriptomic data revealed that the leukocyte transendothelial migration and the phagosome pathways might play important roles in mediating immunity in grouper at the three developmental stages. This information will increase our understanding of the metamorphosis process in grouper larvae, and shed light on the development of antimicrobial strategy during larval development.}, } @article {pmid31054103, year = {2019}, author = {Han, Y and Jiang, X and Ling, Q and Wu, L and Wu, P and Tang, R and Xu, X and Yang, M and Zhang, L and Zhu, W and Wang, B and Li, L}, title = {Antibiotics-mediated intestinal microbiome perturbation aggravates tacrolimus-induced glucose disorders in mice.}, journal = {Frontiers of medicine}, volume = {13}, number = {4}, pages = {471-481}, pmid = {31054103}, issn = {2095-0225}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/isolation & purification ; Blood Glucose/metabolism ; Diabetes Mellitus, Experimental/chemically induced/microbiology ; Gastrointestinal Microbiome/*drug effects ; Glucose Tolerance Test ; Immunosuppressive Agents/*adverse effects ; Insulin/metabolism ; Insulin Resistance ; Lipid Metabolism/drug effects ; Male ; Mice ; Mice, Inbred C57BL ; Tacrolimus/*adverse effects ; }, abstract = {Both immunosuppressants and antibiotics (ABX) are indispensable for transplant patients. However, the former increases the risk of new-onset diabetes, whereas the latter impacts intestinal microbiota (IM). It is still unclear whether and how the interaction between immunosuppressants and ABX alters the IM and thus leads to glucose metabolism disorders. This study examined the alterations of glucose and lipid metabolism and IM in mice exposed to tacrolimus (TAC) with or without ABX. We found that ABX further aggravated TAC-induced glucose tolerance and increased insulin secretion. Combined treatment resulted in exacerbated lipid accumulation in the liver. TAC-altered microbial community was further amplified by ABX administration, as characterized by reductions in phylum Firmicutes, family Lachnospiraceae, and genus Coprococcus. Analyses based on the metagenomic profiles revealed that ABX augmented the effect of TAC on microbial metabolic function mostly related to lipid metabolism. The altered components of gut microbiome and predicted microbial functional profiles showed significant correlation with hepatic lipid accumulation and glucose disorders. In conclusion, ABX aggravated the effect of TAC on the microbiome and its metabolic capacities, which might contribute to hepatic lipid accumulation and glucose disorders. These findings suggest that the ABX-altered microbiome can amplify the diabetogenic effect of TAC and could be a novel therapeutic target for patients.}, } @article {pmid31053982, year = {2019}, author = {Van Dexter, S and Oubre, C and Boopathy, R}, title = {Carbon ecology of termite gut and phenol degradation by a bacterium isolated from the gut of termite.}, journal = {Journal of industrial microbiology & biotechnology}, volume = {46}, number = {9-10}, pages = {1265-1271}, pmid = {31053982}, issn = {1476-5535}, mesh = {Animals ; Bacteria/isolation & purification/*metabolism ; Carbon/*metabolism ; Cellobiose/metabolism ; Ecosystem ; Gastrointestinal Microbiome ; Isoptera/*microbiology ; Metagenomics ; Phenols/*metabolism ; }, abstract = {Metagenomics and transcriptomics have had some success analyzing community and functional ecology of the termite gut, but carbon utilization ecology and the effect of diet on the gut community are not well understood. This study was done to determine the effect of three hardwood tree types, oak (Quercus spp.), red maple (Acer rubrum), and tupelo (Nyssa aquatica) on the termite species, Reticulitermes flavipes in the family Rhinotermitidae. Termite abdomen homogenates were incubated on agar plates containing three common carbon sources in the termite gut, namely, acetate, cellobiose, and phenol under aerobic and anaerobic conditions. Bacterial growth was higher on cellobiose than any other carbon source. Higher bacterial growth on cellobiose was observed from termite colonies feeding on oak than on phenol from the other two wood types. The difference between aerobic and anaerobic conditions was not significant. A bacterium, Acinetobacter tandoii isolated and identified from our previous study was subjected to high concentrations of phenol as the sole carbon source and this bacterium was able to degrade phenol concentration up to 600 mg/L.}, } @article {pmid31053582, year = {2019}, author = {Comeau, AM and Lagunas, MG and Scarcella, K and Varela, DE and Lovejoy, C}, title = {Nitrate Consumers in Arctic Marine Eukaryotic Communities: Comparative Diversities of 18S rRNA, 18S rRNA Genes, and Nitrate Reductase Genes.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {14}, pages = {}, pmid = {31053582}, issn = {1098-5336}, mesh = {Aquatic Organisms/metabolism ; Arctic Regions ; *Biodiversity ; Canada ; DNA, Ribosomal/analysis ; Eukaryota/*metabolism ; High-Throughput Nucleotide Sequencing ; Microbiota ; Plankton/*metabolism ; RNA, Ribosomal, 18S/analysis ; *Seawater/microbiology/parasitology ; }, abstract = {For photosynthetic microbial eukaryotes, the rate-limiting step in NO3[-] assimilation is its reduction to nitrite (NO2[-]), which is catalyzed by assimilatory nitrate reductase (NR). Oceanic productivity is primarily limited by available nitrogen and, although nitrate is the most abundant form of available nitrogen in oceanic waters, little is known about the identity of microbial eukaryotes that take up nitrate. This lack of knowledge is especially severe for ice-covered seas that are being profoundly affected by climate change. To address this, we examined the distribution and diversity of NR genes in the Arctic region by way of clone libraries and data mining of available metagenomes (total of 4.24 billion reads). We directly compared NR clone phylogenies with the V4 region of the 18S rRNA gene (DNA pool) and 18S rRNA (RNA pool) at two ice-influenced stations in the Canada Basin (Beaufort Sea). The communities from the two nucleic acid templates were similar at the level of major groups, and species identified by way of NR gene phylogeny and microscopy were a subset of the 18S results. Most NR genes from arctic clone libraries matched diatoms and chromist nanoflagellates, including novel clades, while the NR genes in arctic eukaryote metagenomes were dominated by chlorophyte NR, in keeping with the ubiquitous occurrence of Mamiellophyceae in the Arctic Ocean. Overall, these data suggest that a dynamic and mixed eukaryotic community utilizes nitrate across the Arctic region, and they show the potential utility of NR as a tool to identify ongoing changes in arctic photosynthetic communities.IMPORTANCE To better understand the diversity of primary producers in the Arctic Ocean, we targeted a nitrogen cycle gene, NR, which is required for phytoplankton to assimilate nitrate into organic forms of nitrogen macromolecules. We compared this to the more detailed taxonomy from ice-influenced stations using a general taxonomic gene (18S rRNA). NR genes were ubiquitous and could be classified as belonging to diatoms, dinoflagellates, other flagellates, chlorophytes, and unknown microbial eukaryotes, suggesting novel diversity of both species and metabolism in arctic phytoplankton.}, } @article {pmid31053581, year = {2019}, author = {Mandhania, MH and Paul, D and Suryavanshi, MV and Sharma, L and Chowdhury, S and Diwanay, SS and Diwanay, SS and Shouche, YS and Patole, MS}, title = {Diversity and Succession of Microbiota during Fermentation of the Traditional Indian Food Idli.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {13}, pages = {}, pmid = {31053581}, issn = {1098-5336}, mesh = {Bacteria/classification/*isolation & purification ; Breakfast ; *Fermentation ; *Food Microbiology ; India ; *Microbiota ; Oryza/metabolism/*microbiology ; }, abstract = {Idli, a naturally fermented Indian food, is prepared from a mixture of rice and black gram (lentil). To understand its microbial community during fermentation, detailed analysis of the structural and functional dynamics of the idli microbiome was performed by culture-dependent and -independent approaches. The bacterial diversity and microbial succession were assessed at different times of fermentation by 16S rRNA amplicon sequencing. Results highlighted that most microbiota belonged to phylum Firmicutes (70%) and Proteobacteria (22%). Denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) analysis confirmed the diversity and succession involved therein. A culture-dependent approach revealed that the microbially diverse populations were conserved across different geographical locations. The fermentation was primarily driven by lactic acid bacteria as they constitute 86% of the total bacterial population, and genus Weissella emerged as the most important organism in fermentation. The natural microbiota of the grains mainly drives the fermentation, as surface sterilized grains did not show any fermentation. Growth kinetics of idli microbiota and physicochemical parameters corroborated the changes in microbial dynamics, acid production, and leavening occurring during fermentation. Using a metagenomic prediction tool, we found that the major metabolic activities of these microbial fermenters were augmented during the important phase of fermentation. The involvement of the heterofermentative hexose monophosphate (HMP) pathway in batter leavening was substantiated by radiolabeled carbon dioxide generated from d-[1-[14]C]-glucose. Hydrolases degrading starch and phytins and the production of B vitamins were reported. Moreover, culturable isolates showing beneficial attributes, such as acid and bile tolerance, hydrophobicity, antibiotic sensitivity, and antimicrobial activity, suggest idli to be a potential dietary supplement.IMPORTANCE This is a comprehensive analysis of idli fermentation employing modern molecular tools which provided valuable information about the bacterial diversity enabling its fermentation. The study has demonstrated the relationship between the bacterial population and its functional role in the process. The nature of idli fermentation was found to be more complex than other food fermentations due to the succession of the bacterial population. Further studies using metatranscriptomics and metabolomics may enhance the understanding of this complex fermentation process. Moreover, the presence of microorganisms with beneficial properties plausibly makes idli a suitable functional food.}, } @article {pmid31053425, year = {2019}, author = {Keohane, DM and Woods, T and O'Connor, P and Underwood, S and Cronin, O and Whiston, R and O'Sullivan, O and Cotter, P and Shanahan, F and Molloy, MGM}, title = {Four men in a boat: Ultra-endurance exercise alters the gut microbiome.}, journal = {Journal of science and medicine in sport}, volume = {22}, number = {9}, pages = {1059-1064}, doi = {10.1016/j.jsams.2019.04.004}, pmid = {31053425}, issn = {1878-1861}, mesh = {Adult ; Athletes ; Bacteria/*classification ; Biodiversity ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Male ; *Physical Endurance ; Prospective Studies ; Water Sports/*physiology ; }, abstract = {OBJECTIVES: Compositional and functional adaptions occur in the gut microbiome in response to habitual physical activity. The response of the gut microbiome to sustained, intense exercise in previously active individuals, however, is unknown. This study aimed to prospectively explore the gut microbiome response of four well-trained male athletes to prolonged, high intensity trans-oceanic rowing, describing changes in microbial diversity, abundance and metabolic capacity.

DESIGN: A prospective, repeated-measures, within-subject report.

METHODS: Serial stool samples were obtained from four male athletes for metagenomic whole-genome shotgun sequencing to record microbial community structure and relevant functional gene profiles before, during and after a continuous, unsupported 33-day, 5000 km transoceanic rowing race. Calorific intake and macronutrient composition were recorded by validated food frequency questionnaire and anthropometry was determined by body composition analysis and cardiorespiratory testing.

RESULTS: Microbial diversity increased throughout the ultra-endurance event. Variations in taxonomic composition included increased abundance of butyrate producing species and species associated with improved metabolic health, including improved insulin sensitivity. The functional potential of bacterial species involved in specific amino and fatty acid biosynthesis also increased. Many of the adaptions in microbial community structure and metaproteomics persisted at three months follow up.

CONCLUSIONS: These findings demonstrate that prolonged, intense exercise positively influences gut microbial diversity, increases the relative abundance of some bacterial species and up-regulates the metabolic potential of specific pathways expressing microbial gene products. These adaptions may play a compensatory role in controlling the physiological stress associated with sustained exertion as well as negating the deleterious consequences accompanying endurance exercise.}, } @article {pmid31051396, year = {2019}, author = {Cabral, L and Noronha, MF and de Sousa, STP and Lacerda-Júnior, GV and Richter, L and Fostier, AH and Andreote, FD and Hess, M and Oliveira, VM}, title = {The metagenomic landscape of xenobiotics biodegradation in mangrove sediments.}, journal = {Ecotoxicology and environmental safety}, volume = {179}, number = {}, pages = {232-240}, doi = {10.1016/j.ecoenv.2019.04.044}, pmid = {31051396}, issn = {1090-2414}, mesh = {Biodegradation, Environmental ; Drug Resistance, Microbial/genetics ; Gene Library ; *Geologic Sediments/chemistry/microbiology ; Hydrolases/genetics ; Metagenomics/*methods ; Metals, Heavy/*analysis/toxicity ; Microbiota/drug effects/*genetics ; Petroleum/analysis/toxicity ; *Wetlands ; Xenobiotics/*analysis/toxicity ; }, abstract = {Metagenomics is a powerful approach to study microorganisms present in any given environment and their potential to maintain and improve ecosystem health without the need of cultivating these microorganisms in the laboratory. In this study, we combined a cultivation-independent metagenomics approach with functional assays to identify the detoxification potential of microbial genes evaluating their potential to contribute to xenobiotics resistance in oil-impacted mangrove sediments. A metagenomic fosmid library containing 12,960 clones from highly contaminated mangrove sediment was used in this study. For assessment of metal resistance, clones were grown in culture medium with increasing concentrations of mercury. The analyses metagenomic library sequences revealed the presence of genes related to heavy metals and antibiotics resistance in the oil-impacted mangrove microbiome. The taxonomic profiling of these sequences suggests that at the genus level, Geobacter was the most abundant genus in our dataset. A functional screening assessment of the metagenomic library successfully detected 24 potential heavy metal tolerant clones, six of which were capable of growing with increased concentrations of mercury. The genetic characterization of selected clones allowed the detection of genes related to detoxification processes, such as chromate transport protein ChrA, haloacid dehalogenase-like hydrolase, lipopolysaccharide transport system, and 3-oxoacyl-[acyl-carrier-protein] reductase. Clones were capable of growing in medium containing increased concentrations of metals and antibiotics, but none manifested strong mercury removal from culture medium characteristic of mercuric reductase activity. These results suggest that resistance to xenobiotic stress varies greatly and that additional studies to elucidate the potential of metal biotransformation need to be carried out with the goal of improving bioremediation application.}, } @article {pmid31049708, year = {2019}, author = {Dutta, A and Peoples, LM and Gupta, A and Bartlett, DH and Sar, P}, title = {Exploring the piezotolerant/piezophilic microbial community and genomic basis of piezotolerance within the deep subsurface Deccan traps.}, journal = {Extremophiles : life under extreme conditions}, volume = {23}, number = {4}, pages = {421-433}, pmid = {31049708}, issn = {1433-4909}, support = {MoES/P.O.(Seismo)/1(181)/2013 dated April 7//Ministry of Earth Sciences, India/ ; 2014//Ministry of Earth Sciences, India/ ; IIT/SRIC/BT/ODM/2015-16/141//IIT Kharagpur SGBSI challenge grant 2015/ ; }, mesh = {Comamonadaceae/isolation & purification ; Genes, Archaeal ; Genes, Bacterial ; Groundwater/*microbiology ; *Hydrostatic Pressure ; *Metagenome ; *Microbiota ; *Salt Tolerance ; }, abstract = {The deep biosphere is often characterized by multiple extreme physical-chemical conditions, of which pressure is an important parameter that influences life but remains less studied. This geomicrobiology study was designed to understand the response of a subterranean microbial community of the Deccan traps to high-pressure conditions and to elucidate their genomic properties. Groundwater from a deep basaltic aquifer of the Deccan traps was used to ascertain the community response to 25 MPa and 50 MPa pressure following enrichment in high-salt and low-salt organic media. Quantitative PCR data indicated a decrease in bacterial and archaeal cell numbers with increasing pressure. 16S rRNA gene sequencing displayed substantial changes in the microbial community in which Acidovorax appeared to be the most dominant genus in the low-salt medium and Microbacteriaceae emerged as the major family in the high-salt medium under both pressure conditions. Genes present in metagenome-associated genomes which have previously been associated with piezotolerance include those related to nutrient uptake and extracytoplasmic stress (omp, rseC), protein folding and unfolding (dnaK, groEL and others), and DNA repair mechanisms (mutT, uvr and others). We hypothesize that these genes facilitate tolerance to high pressure by certain groups of microbes residing in subsurface Deccan traps.}, } @article {pmid31049590, year = {2019}, author = {Butina, TV and Bukin, YS and Krasnopeev, AS and Belykh, OI and Tupikin, AE and Kabilov, MR and Sakirko, МV and Belikov, SI}, title = {Estimate of the diversity of viral and bacterial assemblage in the coastal water of Lake Baikal.}, journal = {FEMS microbiology letters}, volume = {366}, number = {9}, pages = {}, doi = {10.1093/femsle/fnz094}, pmid = {31049590}, issn = {1574-6968}, mesh = {Bacteria/*classification ; *Biodiversity ; DNA, Bacterial/isolation & purification ; DNA, Viral/isolation & purification ; High-Throughput Nucleotide Sequencing ; Lakes/*microbiology/*virology ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Russia ; Viruses/*classification ; }, abstract = {In this study, we analysed the diversity and composition of double-stranded DNA viral and bacterial communities within the sample of surface coastal water of Southern Baikal through metagenomics and deep sequencing of the 16S ribosomal RNA gene, respectively. The 16S rRNA gene analysis has revealed 14 phyla and dominance of the 'Actinobacteria' (43.6%), 'Proteobacteria' (25.2%) and 'Bacteroidetes' (11.5%). The bacterial composition was similar to that obtained previously in Lake Baikal littoral zone. Out of 1 030 169 processed virome reads, 37.4% of sequences (385 421) were identified as viral; 15.1% were identified as nonviral and related to the domains Eukarya, Bacteria and Archaea; and 47.5% had no matches in the databases. The identified virotypes belonged to different families and were predicted to infect a wide range of organisms, from bacteria to mammals. Six families (Myoviridae, Poxviridae, Mimiviridae, Siphoviridae, Phycodnaviridae and Podoviridae) were dominant accounting for more than 90% of the identified sequences (48.3%, 17.4%, 8.3%, 6.8%, 5.8% and 4.1%, respectively). In contrast to other freshwater systems, high percentage of the Poxviridae and Mimiviridae was recorded in the water sample of Lake Baikal.}, } @article {pmid31048728, year = {2019}, author = {Lee, S and La, TM and Lee, HJ and Choi, IS and Song, CS and Park, SY and Lee, JB and Lee, SW}, title = {Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6838}, pmid = {31048728}, issn = {2045-2322}, mesh = {Animals ; Chick Embryo ; Female ; Gastrointestinal Microbiome/*physiology ; Lactobacillus/physiology ; Microbiota/genetics/*physiology ; Oviducts/*microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {The transferred microbiota from mother to baby constitutes the initial infant gastrointestinal microbiota and has an important influence on the development and health of infants in human. However, the reproductive tract microbiota of avian species and its inheritance have rarely been studied. We aimed to characterize the microbial community in the chicken reproductive tract and determine the origin of the chicken embryo gut microbiota. Microbiota in four different portions of chicken oviduct were determined using 16S rRNA metagenomic approach with the IonTorrent platform. Additionally, we analyzed the mother hen's magnum and cloaca, descendent egg, and embryo gut microbiota. The microbial composition and relative abundance of bacterial genera were stable throughout the entire chicken reproductive tract, without significant differences between the different parts of the oviduct. The chicken reproductive tract showed a relatively high abundance of Lactobacillus species. The number of bacterial species in the chicken reproductive tract significantly increased following sexual maturation. Core genera analysis detected 21 of common genera in the maternal magnum and cloaca, descendent egg shell, egg white, and embryo gut. Some elements of the maternal oviduct microbiota appear to be transferred to the embryo through the egg white and constitute most of the embryo gut bacterial population.}, } @article {pmid31046662, year = {2019}, author = {Metzler-Zebeli, BU and Newman, MA and Grüll, D and Zebeli, Q}, title = {Functional adaptations in the cecal and colonic metagenomes associated with the consumption of transglycosylated starch in a pig model.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {87}, pmid = {31046662}, issn = {1471-2180}, mesh = {*Animal Feed ; Animals ; Bacteria/classification/isolation & purification ; Cecum/*microbiology ; Colon/*microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Glycosylation ; Male ; Metagenome/*drug effects ; Sequence Analysis, DNA ; Starch/administration & dosage/*chemistry ; Swine ; }, abstract = {BACKGROUND: Both phylogeny and functional capabilities within the gut microbiota populations are of great importance for influencing host health. As a novel type of resistant starch, transglycosylated starch (TGS) modifies the microbial community and metabolite profiles along the porcine gut, but little is known about the related functional adaptations in key metabolic pathways and their taxonomic identity.

RESULTS: Metagenomic sequencing was used to characterize the functional alterations in the cecal and colonic microbiomes of growing pigs fed TGS or control starch (CON) diets for 10 days (n = 8/diet). Bacterial communities were clearly distinguishable at taxonomic and functional level based on the dietary starch, with effects being similar at both gut sites. Cecal and colonic samples from TGS-fed pigs were enriched in Prevotella, Bacteroides, Acidaminoccus and Veillonella, whereas Treponema, Ruminococcus, and Aeromonas declined at both gut sites compared to CON-fed pigs (log2 fold change > ±1; p < 0.001 (q < 0.05)). This was associated with increased enzymatic capacities for amino acid metabolism, galactose, fructose and mannose metabolism, pentose and glucuronate interconversions, citrate cycle and vitamin metabolism for samples from TGS-fed pigs. However, TGS-fed pigs comprised fewer reads for starch and sucrose metabolism and genetic information processing. Changes in key catabolic steps were found to be the result of changes in taxa associated with each type of starch. Functional analysis indicated steps in the breakdown of TGS by the action of α- and β-galactosidases, which mainly belonged to Bacteroides and Prevotella. Reads mapped to alpha-amylase were less frequent in TGS- compared to CON-fed pigs, with the major source of this gene pool being Bacillus, Aeromonas and Streptococcus. Due to the taxonomic shifts, gene abundances of potent stimulants of the mucosal innate immune response were altered by the starches. The cecal and colonic metagenomes of TGS-fed pigs comprised more reads annotated in lipopolysaccharides biosynthesis, whereas they became depleted of genes for flagellar assembly compared to CON-fed pigs.

CONCLUSIONS: Metagenomic sequencing revealed distinct cecal and colonic bacterial communities in CON- and TGS-fed pigs, with strong discrimination among samples by functional capacities related to the respective starch in each pig's diet.}, } @article {pmid31043514, year = {2019}, author = {Escudeiro, P and Pothier, J and Dionisio, F and Nogueira, T}, title = {Antibiotic Resistance Gene Diversity and Virulence Gene Diversity Are Correlated in Human Gut and Environmental Microbiomes.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, pmid = {31043514}, issn = {2379-5042}, mesh = {Adolescent ; Adult ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; Child ; Child, Preschool ; Drug Resistance, Microbial/*genetics ; *Environmental Microbiology ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/microbiology ; *Genetic Variation ; Humans ; Infant ; Metagenome ; Metagenomics ; Microbiota/*drug effects ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Virulence ; Virulence Factors/genetics ; Young Adult ; }, abstract = {Human beings have used large amounts of antibiotics, not only in medical contexts but also, for example, as growth factors in agriculture and livestock, resulting in the contamination of the environment. Even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are affected as well. Therefore, both pathogenic and nonpathogenic bacteria have gradually become resistant to antibiotics. We tested whether there is still cooccurrence of resistance and virulence determinants. We performed a comparative study of environmental and human gut metagenomes from different individuals and from distinct human populations across the world. We found a great diversity of antibiotic resistance determinants (AR diversity [ARd]) and virulence factors (VF diversity [VFd]) in metagenomes. Importantly there is a correlation between ARd and VFd, even after correcting for protein family richness. In the human gut, there are less ARd and VFd than in more diversified environments, and yet correlations between the ARd and VFd are stronger. They can vary from very high in Malawi, where antibiotic consumption is unattended, to nonexistent in the uncontacted Amerindian population. We conclude that there is cooccurrence of resistance and virulence determinants in human gut microbiomes, suggesting a possible coselective mechanism.IMPORTANCE Every year, thousands of tons of antibiotics are used, not only in human and animal health but also as growth promoters in livestock. Consequently, during the last 75 years, antibiotic-resistant bacterial strains have been selected in human and environmental microbial communities. This implies that, even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are also affected. Here, we performed a comparative study of environmental and human gut microbial communities issuing from different individuals and from distinct human populations across the world. We found that antibiotic resistance and pathogenicity are correlated and speculate that, by selecting for resistant bacteria, we may be selecting for more virulent strains as a side effect of antimicrobial therapy.}, } @article {pmid31040301, year = {2019}, author = {Torres-Cortés, G and Garcia, BJ and Compant, S and Rezki, S and Jones, P and Préveaux, A and Briand, M and Roulet, A and Bouchez, O and Jacobson, D and Barret, M}, title = {Differences in resource use lead to coexistence of seed-transmitted microbial populations.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6648}, pmid = {31040301}, issn = {2045-2322}, mesh = {*Environmental Microbiology ; Genome, Bacterial ; Germination ; Metagenome ; Metagenomics/methods ; Microbial Interactions ; *Microbiota ; Plant Diseases/microbiology ; Popular Culture ; Seeds/*microbiology ; Xanthomonas ; }, abstract = {Seeds are involved in the vertical transmission of microorganisms in plants and act as reservoirs for the plant microbiome. They could serve as carriers of pathogens, making the study of microbial interactions on seeds important in the emergence of plant diseases. We studied the influence of biological disturbances caused by seed transmission of two phytopathogenic agents, Alternaria brassicicola Abra43 (Abra43) and Xanthomonas campestris pv. campestris 8004 (Xcc8004), on the structure and function of radish seed microbial assemblages, as well as the nutritional overlap between Xcc8004 and the seed microbiome, to find seed microbial residents capable of outcompeting this pathogen. According to taxonomic and functional inference performed on metagenomics reads, no shift in structure and function of the seed microbiome was observed following Abra43 and Xcc8004 transmission. This lack of impact derives from a limited overlap in nutritional resources between Xcc8004 and the major bacterial populations of radish seeds. However, two native seed-associated bacterial strains belonging to Stenotrophomonas rhizophila displayed a high overlap with Xcc8004 regarding the use of resources; they might therefore limit its transmission. The strategy we used may serve as a foundation for the selection of seed indigenous bacterial strains that could limit seed transmission of pathogens.}, } @article {pmid31039168, year = {2019}, author = {De La Torre, U and Henderson, JD and Furtado, KL and Pedroja, M and Elenamarie, O and Mora, A and Pechanec, MY and Maga, EA and Mienaltowski, MJ}, title = {Utilizing the fecal microbiota to understand foal gut transitions from birth to weaning.}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0216211}, pmid = {31039168}, issn = {1932-6203}, mesh = {Animals ; Animals, Newborn ; Bacteria/growth & development ; Biodiversity ; Feces/*microbiology ; Gastrointestinal Tract/*microbiology ; Horses/*microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; Principal Component Analysis ; *Weaning ; }, abstract = {A healthy gastrointestinal (GI) tract with a properly established microbiota is necessary for a foal to develop into a healthy weanling. A foal's health can be critically impacted by aberrations in the microbiome such as with diarrhea which can cause great morbidity and mortality in foals. In this study, we hypothesized that gut establishment in the foal transitioning from a diet of milk to a diet of grain, forage, and pasture would be detectable through analyses of the fecal microbiotas. Fecal samples from 37 sets of foals and mares were collected at multiple time points ranging from birth to weaning. Bacterial DNA was isolated from the samples, and the V4 domain of bacterial 16S rRNA genes were amplified via polymerase chain reaction. Next generation sequencing was then performed on the resulting amplicons, and analyses were performed to characterize the microbiome as well as the relative abundance of microbiota present. We found that bacterial population compositions followed a pattern throughout the early life of the foal in an age-dependent manner. As foals transitioned from milk consumption to a forage and grain diet, there were recognizable changes in fecal microbial compositions from initial populations predominant in the ability to metabolize milk to populations capable of utilizing fibrous plant material. We were also able to recognize differences in microbial populations amongst diarrheic foals as well as microbial population differences associated with differences in management styles between facilities. Future efforts will gauge the effects of lesser abundant bacterial populations that could also be essential to GI health, as well as to determine how associations between microbial population profiles and animal management practices can be used to inform strategies for improving upon the health and growth of horses overall.}, } @article {pmid31036935, year = {2019}, author = {Lee, SM and Kim, N and Nam, RH and Park, JH and Choi, SI and Park, YT and Kim, YR and Seok, YJ and Shin, CM and Lee, DH}, title = {Gut microbiota and butyrate level changes associated with the long-term administration of proton pump inhibitors to old rats.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6626}, pmid = {31036935}, issn = {2045-2322}, mesh = {Animals ; Butyrates/*pharmacology ; Firmicutes/drug effects/genetics ; Gastrointestinal Microbiome/*drug effects/genetics ; Lactobacillus/drug effects/genetics ; Male ; Proton Pump Inhibitors/*pharmacology ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Inbred F344 ; }, abstract = {The association between adverse effects of PPI and gut microbiota in old age has yet to be elucidated. We assessed changes in the gut microbiota and butyrate levels following the long-term administration of PPIs to old rats and investigated their associations. F344 aged male rats were fed a PPI-supplemented diet for 50 weeks. The ileal microbiota was analysed by metagenomic sequencing of the 16S rRNA, while the butyrate concentration was measured by high-performance liquid chromatography. We observed a significant decrease in microbial diversity following PPI administration in the 2-year-old rats but not in the 74-week-old rats. PPI treatment reduced both commensal bacteria and opportunistic pathogens, particularly in the 2-year-old rats. Enterotypes comprising the majority of the control samples were enriched in Lactobacillus, while other enterotypes in the PPI group were dominated by Turicibacter or Romboutsia. The PPI treatment reduced the butyrate concentrations in the intestines and colons of 74-week-old rats compared to the control group. The abundance of Lactobacillus significantly correlated with butyrate concentrations in 74-week-old rats. In conclusion, long-term administration of PPIs alters the gut microbiota and butyrate concentrations in rats, particularly in old age, which may be an underlying mechanism of PPI-induced adverse effects such as pseudomembranous colitis.}, } @article {pmid31036930, year = {2019}, author = {Zhang, J and Liu, YX and Zhang, N and Hu, B and Jin, T and Xu, H and Qin, Y and Yan, P and Zhang, X and Guo, X and Hui, J and Cao, S and Wang, X and Wang, C and Wang, H and Qu, B and Fan, G and Yuan, L and Garrido-Oter, R and Chu, C and Bai, Y}, title = {NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice.}, journal = {Nature biotechnology}, volume = {37}, number = {6}, pages = {676-684}, doi = {10.1038/s41587-019-0104-4}, pmid = {31036930}, issn = {1546-1696}, mesh = {Alleles ; Anion Transport Proteins/chemistry/*genetics ; Bacteria/classification/*genetics ; Genotype ; Metagenomics ; Microbiota/*genetics ; Nitrate Transporters ; Nitrogen/metabolism ; Oryza/*genetics/growth & development/metabolism/microbiology ; Phylogeny ; Plant Breeding ; Plant Roots/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Nitrogen-use efficiency of indica varieties of rice is superior to that of japonica varieties. We apply 16S ribosomal RNA gene profiling to characterize root microbiota of 68 indica and 27 japonica varieties grown in the field. We find that indica and japonica recruit distinct root microbiota. Notably, indica-enriched bacterial taxa are more diverse, and contain more genera with nitrogen metabolism functions, than japonica-enriched taxa. Using genetic approaches, we provide evidence that NRT1.1B, a rice nitrate transporter and sensor, is associated with the recruitment of a large proportion of indica-enriched bacteria. Metagenomic sequencing reveals that the ammonification process is less abundant in the root microbiome of the nrt1.1b mutant. We isolated 1,079 pure bacterial isolates from indica and japonica roots and derived synthetic communities (SynComs). Inoculation of IR24, an indica variety, with an indica-enriched SynCom improved rice growth in organic nitrogen conditions compared with a japonica-enriched SynCom. The links between plant genotype and root microbiota membership established in this study will inform breeding strategies to improve nitrogen use in crops.}, } @article {pmid31036790, year = {2019}, author = {Ghani, MI and Ali, A and Atif, MJ and Ali, M and Amin, B and Anees, M and Khurshid, H and Cheng, Z}, title = {Changes in the Soil Microbiome in Eggplant Monoculture Revealed by High-Throughput Illumina MiSeq Sequencing as Influenced by Raw Garlic Stalk Amendment.}, journal = {International journal of molecular sciences}, volume = {20}, number = {9}, pages = {}, pmid = {31036790}, issn = {1422-0067}, support = {2016KTCL02-01//Shaanxi Provincial Sci Tech Innovation Plan/ ; 2016NY-048//Shaanxi provincial Agricultural Sci Tech Innovation and Development Plan/ ; NCI 1501//Xian City Agricultural Sci Tech Innovation Plan P.R China/ ; }, mesh = {Biodiversity ; *Garlic ; *High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; *Microbiota ; Soil/chemistry ; *Soil Microbiology ; *Solanum melongena ; }, abstract = {The incorporation of plant residues into soil can be considered a keystone sustainability factor in improving soil structure function. However, the effects of plant residue addition on the soil microbial communities involved in biochemical cycles and abiotic stress phenomena are poorly understood. In this study, experiments were conducted to evaluate the role of raw garlic stalk (RGS) amendment in avoiding monoculture-related production constraints by studying the changes in soil chemical properties and microbial community structures. RGS was applied in four different doses, namely the control (RGS0), 1% (RGS1), 3% (RGS2), and 5% (RGS3) per 100 g of soil. The RGS amendment significantly increased soil electrical conductivity (EC), N, P, K, and enzyme activity. The soil pH significantly decreased with RGS application. High-throughput Illumina MiSeq sequencing revealed significant alterations in bacterial community structures in response to RGS application. Among the 23 major taxa detected, Anaerolineaceae, Acidobacteria, and Cyanobacteria exhibited an increased abundance level. RGS2 increased some bacteria reported to be beneficial including Acidobacteria, Bacillus, and Planctomyces (by 42%, 64%, and 1% respectively). Furthermore, internal transcribed spacer (ITS) fungal regions revealed significant diversity among the different treatments, with taxa such as Chaetomium (56.2%), Acremonium (4.3%), Fusarium (4%), Aspergillus (3.4%), Sordariomycetes (3%), and Plectosphaerellaceae (2%) showing much abundance. Interestingly, Coprinellus (14%) was observed only in RGS-amended soil. RGS treatments effectively altered soil fungal community structures and reduced certain known pathogenic fungal genera, i.e., Fusarium and Acremonium. The results of the present study suggest that RGS amendment potentially affects the microbial community structures that probably affect the physiological and morphological attributes of eggplant under a plastic greenhouse vegetable cultivation system (PGVC) in monoculture.}, } @article {pmid31035521, year = {2019}, author = {Agarbati, A and Canonico, L and Mancabelli, L and Milani, C and Ventura, M and Ciani, M and Comitini, F}, title = {The Influence of Fungicide Treatments on Mycobiota of Grapes and Its Evolution during Fermentation Evaluated by Metagenomic and Culture-Dependent Methods.}, journal = {Microorganisms}, volume = {7}, number = {5}, pages = {}, pmid = {31035521}, issn = {2076-2607}, abstract = {The present study evaluated the impact of organic and conventional fungicide treatments compared with untreated samples (no fungicides were used) on the grape berry yeast community of the Montepulciano variety. The yeast dynamics during the spontaneous fermentation using culture-dependent and -independent methods was also evaluated. Results showed a reduction of yeast biodiversity by conventional treatments determining a negative influence on fermenting yeasts in favor of oxidative yeasts such as Aerobasidium pullulans. Starmerella bacillaris was significantly more present in organic samples (detected by next generation sequencing (NGS)), while Hanseniaspopa uvarum was significantly less present in untreated samples (detected by the culture-dependent method). The fermenting yeasts, developed during the spontaneous fermentation, were differently present depending on the fungicide treatments used. Culture-dependent and -independent methods exhibited the same most abundant yeast species during the spontaneous fermentation but a different relative abundance. Differently, the NGS method was able to detect a greater biodiversity (lower abundant species) in comparison with the culture-dependent method. In this regard, the methodologies used gave a different picture of yeast dynamics during the fermentation process. The results indicated that the fungal treatments can influence the yeast community of grapes leading must fermentation and the final composition of wine.}, } @article {pmid31035394, year = {2019}, author = {Jaswal, R and Pathak, A and Edwards, B and Lewis, R and Seaman, JC and Stothard, P and Krivushin, K and Blom, J and Rupp, O and Chauhan, A}, title = {Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA.}, journal = {Genes}, volume = {10}, number = {5}, pages = {}, pmid = {31035394}, issn = {2073-4425}, mesh = {Ascomycota/genetics/radiation effects ; Biodegradation, Environmental ; Burkholderia/genetics/radiation effects ; Ecosystem ; Grassland ; Humans ; Metagenomics ; Microbiota/*genetics/radiation effects ; Penicillium/genetics/radiation effects ; Rivers ; *Soil Microbiology ; United States ; Uranium/*toxicity ; }, abstract = {Despite the recent advancements in culturomics, isolation of the majority of environmental microbiota performing critical ecosystem services, such as bioremediation of contaminants, remains elusive. Towards this end, we conducted a metagenomics-guided comparative assessment of soil microbial diversity and functions present in uraniferous soils relative to those that grew in diffusion chambers (DC) or microbial traps (MT), followed by isolation of uranium (U) resistant microbiota. Shotgun metagenomic analysis performed on the soils used to establish the DC/MT chambers revealed Proteobacterial phyla and Burkholderia genus to be the most abundant among bacteria. The chamber-associated growth conditions further increased their abundances relative to the soils. Ascomycota was the most abundant fungal phylum in the chambers relative to the soils, with Penicillium as the most dominant genus. Metagenomics-based taxonomic findings completely mirrored the taxonomic composition of the retrieved isolates such that the U-resistant bacteria and fungi mainly belonged to Burkholderia and Penicillium species, thus confirming that the chambers facilitated proliferation and subsequent isolation of specific microbiota with environmentally relevant functions. Furthermore, shotgun metagenomic analysis also revealed that the gene classes for carbohydrate metabolism, virulence, and respiration predominated with functions related to stress response, membrane transport, and metabolism of aromatic compounds were also identified, albeit at lower levels. Of major note was the successful isolation of a potentially novel Penicillium species using the MT approach, as evidenced by whole genome sequence analysis and comparative genomic analysis, thus enhancing our overall understanding on the uranium cycling microbiota within the tested uraniferous soils.}, } @article {pmid31034867, year = {2019}, author = {Tsiaoussis, J and Antoniou, MN and Koliarakis, I and Mesnage, R and Vardavas, CI and Izotov, BN and Psaroulaki, A and Tsatsakis, A}, title = {Effects of single and combined toxic exposures on the gut microbiome: Current knowledge and future directions.}, journal = {Toxicology letters}, volume = {312}, number = {}, pages = {72-97}, doi = {10.1016/j.toxlet.2019.04.014}, pmid = {31034867}, issn = {1879-3169}, mesh = {Environmental Pollutants/*toxicity ; Gastrointestinal Microbiome/*drug effects ; Hazardous Substances/*toxicity ; Humans ; }, abstract = {Human populations are chronically exposed to mixtures of toxic chemicals. Predicting the health effects of these mixtures require a large amount of information on the mode of action of their components. Xenobiotic metabolism by bacteria inhabiting the gastrointestinal tract has a major influence on human health. Our review aims to explore the literature for studies looking to characterize the different modes of action and outcomes of major chemical pollutants, and some components of cosmetics and food additives, on gut microbial communities in order to facilitate an estimation of their potential mixture effects. We identified good evidence that exposure to heavy metals, pesticides, nanoparticles, polycyclic aromatic hydrocarbons, dioxins, furans, polychlorinated biphenyls, and non-caloric artificial sweeteners affect the gut microbiome and which is associated with the development of metabolic, malignant, inflammatory, or immune diseases. Answering the question 'Who is there?' is not sufficient to define the mode of action of a toxicant in predictive modeling of mixture effects. Therefore, we recommend that new studies focus to simulate real-life exposure to diverse chemicals (toxicants, cosmetic/food additives), including as mixtures, and which combine metagenomics, metatranscriptomics and metabolomic analytical methods achieving in that way a comprehensive evaluation of effects on human health.}, } @article {pmid31034054, year = {2019}, author = {Li, S and Chen, M and Chen, Y and Tong, J and Wang, L and Xu, Y and Hu, Z and Chen, H}, title = {Epibiotic bacterial community composition in red-tide dinoflagellate Akashiwo sanguinea culture under various growth conditions.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {5}, pages = {}, doi = {10.1093/femsec/fiz057}, pmid = {31034054}, issn = {1574-6941}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Dinoflagellida/*growth & development/*microbiology ; Harmful Algal Bloom ; High-Throughput Nucleotide Sequencing ; In Situ Hybridization, Fluorescence ; Microbiota ; Phylogeny ; Phytoplankton/microbiology ; }, abstract = {The phycosphere of phytoplankton harbors a diversity of microbes that can potentially interact with the host phytoplankton cells. In spite of increasing reports regarding the interactions between some model phytoplankton and bacteria, there remain many unknowns regarding interactions between the dinoflagellate Akashiwo sanguinea and its phycosphere bacteria. Here we used both cultivation and metagenomic sequencing methods to investigate the microbial community composition in A. sanguinea batch cultures under various growth conditions. The microbial community dynamics under different growth stages and nutrient (nitrogen and iron) depletion scenarios were determined by Illumina MiSeq sequencing of 16S rRNA gene amplicons. Rhodobacteraceae, Alteromonadaceae and Flavobacteriaceae were the main bacterial families and varied significantly under different states of the host A. sanguinea. Selective fluorescence in situ hybridization was also performed to label Rhodobacterales and Alteromonas clade bacteria to confirm their attachment to A. sanguinea cells under confocal laser scanning microscopy. Plate streaking protocol isolated 19 bacterial strains from A. sanguinea cultures, identified through 16S rRNA analysis. Most culturable strains (11 of 19) belonged to Rhodobacteraceae consistent with Illumina MiSeq sequencing data. The possible interaction pathway between these epibiotic bacteria and A. sanguinea in the phycosphere is also discussed.}, } @article {pmid31032975, year = {2020}, author = {Budinska, E and Gojda, J and Heczkova, M and Bratova, M and Dankova, H and Wohl, P and Bastova, H and Lanska, V and Kostovcik, M and Dastych, M and Senkyrik, M and Krizova, J and Mraz, M and Hradecky, J and Hajslova, J and Lenicek, M and Podzimkova, K and Chalupsky, K and Sedlacek, R and Cahova, M}, title = {Microbiome and Metabolome Profiles Associated With Different Types of Short Bowel Syndrome: Implications for Treatment.}, journal = {JPEN. Journal of parenteral and enteral nutrition}, volume = {44}, number = {1}, pages = {105-118}, doi = {10.1002/jpen.1595}, pmid = {31032975}, issn = {1941-2444}, mesh = {Bacteria/*classification ; Bile Acids and Salts/analysis ; Dysbiosis ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Metabolome ; Parenteral Nutrition ; Short Bowel Syndrome/*microbiology ; Volatile Organic Compounds/analysis ; }, abstract = {BACKGROUND: The gut microbiome and metabolome may significantly influence clinical outcomes in patients with short bowel syndrome (SBS). The study aimed to describe specific metagenomic/metabolomics profiles of different SBS types and to identify possible therapeutic targets.

METHODS: Fecal microbiome (FM), volatile organic compounds (VOCs), and bile acid (BA) spectrum were analyzed in parenteral nutrition (PN)-dependent SBS I, SBS II, and PN-independent (non-PN) SBS patients.

RESULTS: FM in SBS I, SBS II, and non-PN SBS shared characteristic features (depletion of beneficial anaerobes, high abundance of Lactobacilaceae and Enterobacteriaceae). SBS I patients were characterized by the abundance of oxygen-tolerant microrganisms and depletion of strict anaerobes. Non-PN SBS subjects showed markers of partial FM normalization. FM dysbiosis was translated into VOC and BA profiles characteristic for each SBS cohort. A typical signature of all SBS patients comprised high saturated aldehydes and medium-chain fatty acids and reduced short-chain fatty acid (SCFA) content. Particularly, SBS I and II exhibited low protein metabolism intermediate (indole, p-cresol) content despite the hypothetical presence of relevant metabolism pathways. Distinctive non-PN SBS marker was high phenol content. SBS patients' BA fecal spectrum was enriched by chenodeoxycholic and deoxycholic acids and depleted of lithocholic acid.

CONCLUSIONS: Environmental conditions in SBS gut significantly affect FM composition and metabolic activity. The common feature of diverse SBS subjects is the altered VOC/BA profile and the lack of important products of microbial metabolism. Strategies oriented on the microbiome/metabolome reconstitution and targeted delivery of key compounds may represent a promising therapeutic strategy in SBS patients.}, } @article {pmid31031001, year = {2019}, author = {Gregory, AC and Zayed, AA and Conceição-Neto, N and Temperton, B and Bolduc, B and Alberti, A and Ardyna, M and Arkhipova, K and Carmichael, M and Cruaud, C and Dimier, C and Domínguez-Huerta, G and Ferland, J and Kandels, S and Liu, Y and Marec, C and Pesant, S and Picheral, M and Pisarev, S and Poulain, J and Tremblay, JÉ and Vik, D and , and Babin, M and Bowler, C and Culley, AI and de Vargas, C and Dutilh, BE and Iudicone, D and Karp-Boss, L and Roux, S and Sunagawa, S and Wincker, P and Sullivan, MB}, title = {Marine DNA Viral Macro- and Microdiversity from Pole to Pole.}, journal = {Cell}, volume = {177}, number = {5}, pages = {1109-1123.e14}, pmid = {31031001}, issn = {1097-4172}, support = {T32 AI112542/AI/NIAID NIH HHS/United States ; }, mesh = {Aquatic Organisms/*genetics ; *Biodiversity ; DNA Viruses/*genetics ; DNA, Viral/*genetics ; *Metagenome ; *Water Microbiology ; }, abstract = {Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.}, } @article {pmid31030156, year = {2019}, author = {Darlison, J and Mogren, L and Rosberg, AK and Grudén, M and Minet, A and Liné, C and Mieli, M and Bengtsson, T and Håkansson, Å and Uhlig, E and Becher, PG and Karlsson, M and Alsanius, BW}, title = {Leaf mineral content govern microbial community structure in the phyllosphere of spinach (Spinacia oleracea) and rocket (Diplotaxis tenuifolia).}, journal = {The Science of the total environment}, volume = {675}, number = {}, pages = {501-512}, doi = {10.1016/j.scitotenv.2019.04.254}, pmid = {31030156}, issn = {1879-1026}, mesh = {Biodiversity ; Brassicaceae/chemistry/*microbiology ; *Environmental Monitoring ; Microbiota ; Minerals/*analysis ; Plant Leaves/chemistry/*microbiology ; Spinacia oleracea/chemistry/*microbiology ; }, abstract = {The plant microbiome is an important factor for plant health and productivity. While the impact of nitrogen (N) availability for plant growth and development is well established, its influence on the microbial phyllosphere community structure is unknown. We hypothesize that nitrogen impacts the growth and abundance of several microorganisms on the leaf surface. The bacterial and fungal communities of baby leaf spinach (Spinacia oleracea), and rocket (Diplotaxis tenuifolia) were investigated in a field trial for two years in a commercial setting. Nitrogen fertilizer was tested in four doses (basic nitrogen, basic + suboptimal, basic + commercial, basic + excess) with six replicates in each. Culture-independent (Illumina sequencing) and culture-dependent (viable count and identification of bacterial isolates) community studies were combined with monitoring of plant physiology and site weather conditions. This study found that alpha diversity of bacterial communities decreased in response to increasing nitrogen fertilizer dose, whereas viable counts showed no differences. Correspondingly, fungal communities of the spinach phyllosphere showed a decreasing pattern, whereas the decreasing diversity of fungal communities of rocket was not significant. Plant species and effects of annual variations on microbiome structure were observed for bacterial and fungal communities on both spinach and rocket. This study provides novel insights on the impact of nitrogen fertilizer regime on a nutrient scarce habitat, the phyllosphere.}, } @article {pmid31028005, year = {2019}, author = {Zhao, S and Lieberman, TD and Poyet, M and Kauffman, KM and Gibbons, SM and Groussin, M and Xavier, RJ and Alm, EJ}, title = {Adaptive Evolution within Gut Microbiomes of Healthy People.}, journal = {Cell host & microbe}, volume = {25}, number = {5}, pages = {656-667.e8}, pmid = {31028005}, issn = {1934-6069}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {*Adaptation, Biological ; Adult ; Bacteroides fragilis/*genetics/*growth & development ; Female ; *Gastrointestinal Microbiome ; Genetics, Population ; Healthy Volunteers ; Humans ; Male ; Metagenomics ; *Microbiota ; Mutation ; Selection, Genetic ; Young Adult ; }, abstract = {Natural selection shapes bacterial evolution in all environments. However, the extent to which commensal bacteria diversify and adapt within the human gut remains unclear. Here, we combine culture-based population genomics and metagenomics to investigate the within-microbiome evolution of Bacteroides fragilis. We find that intra-individual B. fragilis populations contain substantial de novo nucleotide and mobile element diversity, preserving years of within-person history. This history reveals multiple signatures of within-person adaptation, including parallel evolution in sixteen genes. Many of these genes are implicated in cell-envelope biosynthesis and polysaccharide utilization. Tracking evolutionary trajectories using near-daily metagenomic sampling, we find evidence for years-long coexistence in one subject despite adaptive dynamics. We used public metagenomes to investigate one adaptive mutation common in our cohort and found that it emerges frequently in Western, but not Chinese, microbiomes. Collectively, these results demonstrate that B. fragilis adapts within individual microbiomes, pointing to factors that promote long-term gut colonization.}, } @article {pmid31027801, year = {2019}, author = {Pangallo, D and Kraková, L and Puškárová, A and Šoltys, K and Bučková, M and Koreňová, J and Budiš, J and Kuchta, T}, title = {Transcription activity of lactic acid bacterial proteolysis-related genes during cheese maturation.}, journal = {Food microbiology}, volume = {82}, number = {}, pages = {416-425}, doi = {10.1016/j.fm.2019.03.015}, pmid = {31027801}, issn = {1095-9998}, mesh = {Animals ; Bacterial Proteins/*genetics/metabolism ; Cheese/*microbiology ; Female ; *Food Microbiology ; Gene Expression Profiling ; Lactobacillales/classification/genetics/isolation & purification/*metabolism ; Metagenomics ; Microbiota/genetics ; Milk/microbiology ; Proteolysis ; RNA, Ribosomal, 16S/genetics ; Sheep ; Transcription, Genetic ; }, abstract = {The catabolism of milk protein in cheese is one way how the microorganisms influence the sensorial characteristics of the final product. In this investigation, we paid attention to four genes [prtP (cell-envelope proteinase gene), pepX (X-prolyl dipeptidyl aminopeptidase gene), pepN (aminopeptidase gene) and bcaT (branched chain aminotransferase gene)] responsible for the production of volatile aroma-active compounds from milk proteins by lactic acid bacteria (LAB). We studied the dynamics of these genes and their corresponding LAB host, during the maturation of a raw ewes' milk-based cheese, using metagenomics and metatranscriptomics approaches. The transcriptome-oriented experiments included the analysis of total RNA (at three stages of cheese maturation) and also the construction of specific cDNA sub-libraries of the abovementioned genes. The proteolytic transcriptome analysis was supported by following the transcription activity of 16S rRNA gene and by metagenomic investigation. The combination of the described methods permitted to screen the dynamics of targeted genes throughout the cheese production. Lactococci were the major players in the LAB group, but the analysis provided also information on the role and properties of members of the genus Lactobacillus, such as Lb. rhamnosus, Lb. helveticus, Lb. pentosus, Lb. curvatus, Lb. parabuchneri, Lb. plantarum, Lb. brevis, Lb. delbrueckii, Lb. paracasei, Lb. fermentum and Lb. heilongjiangensis, proteolysis-related genes of which were active during cheese ripening.}, } @article {pmid31027515, year = {2019}, author = {Kim, J and Guk, JH and Mun, SH and An, JU and Song, H and Kim, J and Ryu, S and Jeon, B and Cho, S}, title = {Metagenomic analysis of isolation methods of a targeted microbe, Campylobacter jejuni, from chicken feces with high microbial contamination.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {67}, pmid = {31027515}, issn = {2049-2618}, mesh = {Animals ; Bacteriological Techniques ; Campylobacter jejuni/*genetics/*isolation & purification ; Chickens/*microbiology ; Culture Media/chemistry ; Feces/*microbiology ; Metagenomics ; *Microbiota ; }, abstract = {BACKGROUND: Originating from poultry, particularly chickens, Campylobacter jejuni is the leading foodborne pathogen worldwide and a major cause of campylobacteriosis. Isolating C. jejuni is difficult due to its specific growth requirements, the presence of viable but non-culturable bacteria, and because it is often masked by competing flora. Currently, there is no optimized method for isolating C. jejuni from chicken feces. Here, we evaluated the method for isolating C. jejuni from chicken feces using culture-independent sequence-based metagenomics and culture-dependent tools. Further, we assessed changes in microbial communities during microbe isolation to determine how the process can be improved.

RESULTS: Fourteen different variations of C. jejuni isolation procedures were applied to all 35 chicken fecal samples. These variations included using different enrichment broths (without enrichment or enrichment in Bolton or Preston broth), different ratios of sample-to-enrichment broth (1:10[1], 1:10[2], and 1:10[3]), and different selective agars (modified charcoal-cefoperazone-deoxycholate agar (mCCDA) or Preston agar). Enrichment during isolation of C. jejuni was evaluated on the basis of microbial diversity and taxonomic composition using metagenomics tools. The effect of selective media was evaluated using a combination of metagenomics and culture-dependent tools. Microbial diversity significantly decreased during the enrichment process, regardless of the type of enrichment broth, with the most significant decrease observed at a feces-to-broth ratio of 1:10[3]. Particularly, in 10[3]-Preston broth, the relative abundance of Campylobacter increased, while extended-spectrum beta-lactamase-producing Escherichia coli, which interfere with Campylobacter isolation, decreased. Metagenomics results were validated by quantitative PCR and culture-dependent analysis. Additionally, selective media affected the isolation results, although microbes with high relative abundance during enrichment were also frequently isolated using culture-dependent methods. Significantly more C. jejuni was isolated from mCCDA than from Preston agar enriched in 10[3] Preston broth.

CONCLUSIONS: Enrichment in Preston broth at a ratio of 1:10[3] followed by spreading onto mCCDA was the most effective method for isolating C. jejuni. This is the first study to apply metagenomics to evaluate a method for isolating a targeted microbe, C. jejuni, from chicken feces, a source with high microbial contamination. Thus, metagenomics can be applied to improve methods for isolating bacteria that are difficult to separate.}, } @article {pmid31027194, year = {2019}, author = {Teigen, LM and Geng, Z and Sadowsky, MJ and Vaughn, BP and Hamilton, MJ and Khoruts, A}, title = {Dietary Factors in Sulfur Metabolism and Pathogenesis of Ulcerative Colitis.}, journal = {Nutrients}, volume = {11}, number = {4}, pages = {}, pmid = {31027194}, issn = {2072-6643}, support = {2017-2019//Allen Foundation/ ; 2017-2019//Healthy Foods, Healthy Lives Institute, University of Minnesota/ ; }, mesh = {Bacteria/metabolism ; Colitis, Ulcerative/*metabolism/*microbiology/pathology ; *Diet ; Gastrointestinal Microbiome ; Humans ; Sulfur/*metabolism ; }, abstract = {The biogeography of inflammation in ulcerative colitis (UC) suggests a proximal to distal concentration gradient of a toxin. Hydrogen sulfide (H2S) has long been considered one such toxin candidate, and dietary sulfur along with the abundance of sulfate reducing bacteria (SRB) were considered the primary determinants of H2S production and clinical course of UC. The metabolic milieu in the lumen of the colon, however, is the result of a multitude of factors beyond dietary sulfur intake and SRB abundance. Here we present an updated formulation of the H2S toxin hypothesis for UC pathogenesis, which strives to incorporate the interdependency of diet composition and the metabolic activity of the entire colon microbial community. Specifically, we suggest that the increasing severity of inflammation along the proximal-to-distal axis in UC is due to the dilution of beneficial factors, concentration of toxic factors, and changing detoxification capacity of the host, all of which are intimately linked to the nutrient flow from the diet.}, } @article {pmid31026582, year = {2019}, author = {Li, J and Rettedal, EA and van der Helm, E and Ellabaan, M and Panagiotou, G and Sommer, MOA}, title = {Antibiotic Treatment Drives the Diversification of the Human Gut Resistome.}, journal = {Genomics, proteomics & bioinformatics}, volume = {17}, number = {1}, pages = {39-51}, pmid = {31026582}, issn = {2210-3244}, mesh = {Adult ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/isolation & purification ; Drug Resistance, Bacterial/*genetics ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Metagenomics ; Prospective Studies ; }, abstract = {Despite the documented antibiotic-induced disruption of the gut microbiota, the impact of antibiotic intake on strain-level dynamics, evolution of resistance genes, and factors influencing resistance dissemination potential remains poorly understood. To address this gap we analyzed public metagenomic datasets from 24 antibiotic treated subjects and controls, combined with an in-depth prospective functional study with two subjects investigating the bacterial community dynamics based on cultivation-dependent and independent methods. We observed that short-term antibiotic treatment shifted and diversified the resistome composition, increased the average copy number of antibiotic resistance genes, and altered the dominant strain genotypes in an individual-specific manner. More than 30% of the resistance genes underwent strong differentiation at the single nucleotide level during antibiotic treatment. We found that the increased potential for horizontal gene transfer, due to antibiotic administration, was ∼3-fold stronger in the differentiated resistance genes than the non-differentiated ones. This study highlights how antibiotic treatment has individualized impacts on the resistome and strain level composition, and drives the adaptive evolution of the gut microbiota.}, } @article {pmid31026577, year = {2019}, author = {Jiang, X and Li, X and Yang, L and Liu, C and Wang, Q and Chi, W and Zhu, H}, title = {How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes.}, journal = {Genomics, proteomics & bioinformatics}, volume = {17}, number = {1}, pages = {91-105}, pmid = {31026577}, issn = {2210-3244}, mesh = {Gastrointestinal Microbiome/genetics ; *Genes, Microbial ; Humans ; Microbiota/*genetics ; Mining ; Models, Genetic ; Water Pollution ; }, abstract = {Exploring the mechanisms of maintaining microbial community structure is important to understand biofilm development or microbiota dysbiosis. In this paper, we propose a functional gene-based composition prediction (FCP) model to predict the population structure composition within a microbial community. The model predicts the community composition well in both a low-complexity community as acid mine drainage (AMD) microbiota, and a complex community as human gut microbiota. Furthermore, we define community structure shaping (CSS) genes as functional genes crucial for shaping the microbial community. We have identified CSS genes in AMD and human gut microbiota samples with FCP model and find that CSS genes change with the conditions. Compared to essential genes for microbes, CSS genes are significantly enriched in the genes involved in mobile genetic elements, cell motility, and defense mechanisms, indicating that the functions of CSS genes are focused on communication and strategies in response to the environment factors. We further find that it is the minority, rather than the majority, which contributes to maintaining community structure. Compared to health control samples, we find that some functional genes associated with metabolism of amino acids, nucleotides, and lipopolysaccharide are more likely to be CSS genes in the disease group. CSS genes may help us to understand critical cellular processes and be useful in seeking addable gene circuitries to maintain artificial self-sustainable communities. Our study suggests that functional genes are important to the assembly of microbial communities.}, } @article {pmid31025063, year = {2019}, author = {Negi, A and Sarethy, IP}, title = {Microbial Biodeterioration of Cultural Heritage: Events, Colonization, and Analyses.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {1014-1029}, pmid = {31025063}, issn = {1432-184X}, mesh = {Architecture ; *Bacterial Physiological Phenomena ; Biofilms/*growth & development ; Construction Materials/*microbiology ; Microbiota/*physiology ; }, abstract = {Geochemical cycles result in the chemical, physical, and mineralogical modification of rocks, eventually leading to formation of soil. However, when the stones and rocks are a part of historic buildings and monuments, the effects are deleterious. In addition, microorganisms also colonize these monuments over a period of time, resulting in formation of biofilms; their metabolites lead to physical weakening and discoloration of stone eventually. This process, known as biodeterioration, leads to a significant loss of cultural heritage. For formulating effective conservation strategies to prevent biodeterioration and restore monuments, it is important to know which microorganisms are colonizing the substrate and the different energy sources they consume to sustain themselves. With this view in scope, this review focuses on studies that have attempted to understand the process of biodeterioration, the mechanisms by which they colonize and affect the monuments, the techniques used for assessment of biodeterioration, and conservation strategies that aim to preserve the original integrity of the monuments. This review also includes the "omics" technologies that have started playing a large role in elucidating the nature of microorganisms, and how they can play a role in hastening the formulation of effective conservation strategies.}, } @article {pmid31024861, year = {2019}, author = {Meriwether, KV and Lei, Z and Singh, R and Gaskins, J and Hobson, DTG and Jala, V}, title = {The Vaginal and Urinary Microbiomes in Premenopausal Women With Interstitial Cystitis/Bladder Pain Syndrome as Compared to Unaffected Controls: A Pilot Cross-Sectional Study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {92}, pmid = {31024861}, issn = {2235-2988}, mesh = {Adult ; Cross-Sectional Studies ; Cystitis, Interstitial/*microbiology ; Female ; Humans ; Metagenomics ; *Microbiota ; *Premenopause ; Surveys and Questionnaires ; Urine/*microbiology ; Vagina/*microbiology ; Young Adult ; }, abstract = {Interstitial cystitis/bladder pain syndrome (ICBPS) may be related to an altered genitourinary microbiome. Our aim was to compare the vaginal and urinary microbiomes between premenopausal women with ICBPS and unaffected controls. This cross-sectional study screened premenopausal women with an O'Leary-Sant questionnaire (ICBPS if score ≥6 on either index; controls <6 on both). Women completed questionnaires on health characteristics, pelvic floor symptoms (OABq, PFDI-20), body image (mBIS), and sexual function (PISQ-IR). Bacterial genomic DNA was isolated from vaginal and clean-catch urinary specimens; the bacterial 16 rRNA gene was sequenced and analyzed using the QIIME pipeline. We performed UniFrac analysis (β-diversity) and generated Chao1 estimator (richness) and Simpson index (richness and evenness) values. We analyzed 23 ICBPS and 18 non-ICBPS patients. ICBPS patients had increased vaginal deliveries, BMI, and public insurance as well as worsened OAB-q, PFDI-20, mBIS, and PISQ-IR domain scores. Lactobacilli was the most abundant genus in both cohorts, and anaerobic or fastidious predominance was similar between groups (p = 0.99). For both the urine and vagina specimens, Chao1 and Simpson indices were similar between ICBPS and unaffected women. Weighted and unweighted UniFrac analyses showed no differences between groups. A significant correlation existed between the urinary and vaginal Simpson indices in ICBPS women, but not in unaffected women. Premenopausal women with ICBPS, despite worsened socioeconomic indicators and pelvic floor function, were not found to have significantly different urinary and vaginal microbiomes compared to women without ICBPS.}, } @article {pmid31024486, year = {2019}, author = {Sirén, K and Mak, SST and Melkonian, C and Carøe, C and Swiegers, JH and Molenaar, D and Fischer, U and Gilbert, MTP}, title = {Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {697}, pmid = {31024486}, issn = {1664-302X}, abstract = {Although there is an extensive tradition of research into the microbes that underlie the winemaking process, much remains to be learnt. We combined the high-throughput sequencing (HTS) tools of metabarcoding and metagenomics, to characterize how microbial communities of Riesling musts sampled at four different vineyards, and their subsequent spontaneously fermented derivatives, vary. We specifically explored community variation relating to three points: (i) how microbial communities vary by vineyard; (ii) how community biodiversity changes during alcoholic fermentation; and (iii) how microbial community varies between musts that successfully complete alcoholic fermentation and those that become 'stuck' in the process. Our metabarcoding data showed a general influence of microbial composition at the vineyard level. Two of the vineyards (4 and 5) had strikingly a change in the differential abundance of Metschnikowia. We therefore additionally performed shotgun metagenomic sequencing on a subset of the samples to provide preliminary insights into the potential relevance of this observation, and used the data to both investigate functional potential and reconstruct draft genomes (bins). At these two vineyards, we also observed an increase in non-Saccharomycetaceae fungal functions, and a decrease in bacterial functions during the early fermentation stage. The binning results yielded 11 coherent bins, with both vineyards sharing the yeast bins Hanseniaspora and Saccharomyces. Read recruitment and functional analysis of this data revealed that during fermentation, a high abundance of Metschnikowia might serve as a biocontrol agent against bacteria, via a putative iron depletion pathway, and this in turn could help Saccharomyces dominate the fermentation. During alcoholic fermentation, we observed a general decrease in biodiversity in both the metabarcoding and metagenomic data. Unexpected Micrococcus behavior was observed in vineyard 4 according to metagenomic analyses based on reference-based read mapping. Analysis of open reading frames using these data showed an increase of functions assigned to class Actinobacteria in the end of fermentation. Therefore, we hypothesize that bacteria might sit-and-wait until Saccharomyces activity slows down. Complementary approaches to annotation instead of relying a single database provide more coherent information true species. Lastly, our metabarcoding data enabled us to identify a relationship between stuck fermentations and Starmerella abundance. Given that robust chemical analysis indicated that although the stuck samples contained residual glucose, all fructose had been consumed, we hypothesize that this was because fructophilic Starmerella, rather than Saccharomyces, dominated these fermentations. Overall, our results showcase the different ways in which metagenomic analyses can improve our understanding of the wine alcoholic fermentation process.}, } @article {pmid31023629, year = {2019}, author = {Tokarz, R and Tagliafierro, T and Sameroff, S and Cucura, DM and Oleynik, A and Che, X and Jain, K and Lipkin, WI}, title = {Microbiome analysis of Ixodes scapularis ticks from New York and Connecticut.}, journal = {Ticks and tick-borne diseases}, volume = {10}, number = {4}, pages = {894-900}, doi = {10.1016/j.ttbdis.2019.04.011}, pmid = {31023629}, issn = {1877-9603}, mesh = {Anaplasma phagocytophilum/genetics/isolation & purification ; Animals ; Babesia microti/genetics/isolation & purification ; Bacteria/*genetics/isolation & purification ; Borrelia/genetics/isolation & purification ; Connecticut ; Encephalitis Viruses, Tick-Borne/genetics/isolation & purification ; Female ; High-Throughput Nucleotide Sequencing ; Ixodes/*microbiology/parasitology/virology ; Male ; Metagenomics ; *Microbiota ; Nematoda/genetics/isolation & purification ; New York ; Nymph/microbiology/parasitology/virology ; Rickettsia/genetics/isolation & purification ; Viruses/*genetics/isolation & purification ; }, abstract = {We employed high throughput sequencing to survey the microbiomes of Ixodes scapularis collected in New York and Connecticut. We examined 197 individual I. scapularis adults and pools from 132 adults and 197 nymphs. We detected Borrelia burgdorferi sensu stricto in 56.3% of individual ticks, Anaplasma phagocytophilum in 10.6%, Borrelia miyamotoi in 5%, Babesia microti in 7.6%, and Powassan virus in 3.6%. We did not detect Borrelia mayonii, Ehrlichia muris eauclairensis, Bartonella spp. or pathogenic Babesia species other than B. microti. The most abundant bacterium (65%), and only rickettsial species identified, was the endosymbiont Rickettsia buchneri. A filarial nematode was found in 13.7% of adult ticks. Fourteen viruses were detected including South Bay virus (22%) and blacklegged tick phlebovirus 1 and 2 (73%). This study provides insight into the microbial diversity of I. scapularis in New York State and Connecticut.}, } @article {pmid31022704, year = {2019}, author = {Benic, GZ and Farella, M and Morgan, XC and Viswam, J and Heng, NC and Cannon, RD and Mei, L}, title = {Oral probiotics reduce halitosis in patients wearing orthodontic braces: a randomized, triple-blind, placebo-controlled trial.}, journal = {Journal of breath research}, volume = {13}, number = {3}, pages = {036010}, doi = {10.1088/1752-7163/ab1c81}, pmid = {31022704}, issn = {1752-7163}, mesh = {Administration, Oral ; Adolescent ; Adult ; Breath Tests ; Child ; Dental Plaque Index ; Double-Blind Method ; Female ; Halitosis/*microbiology/*therapy ; Humans ; Male ; Metagenomics ; Microbiota/genetics ; *Orthodontic Brackets ; Periodontal Index ; Placebos ; Probiotics/*administration & dosage/*therapeutic use ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Sulfur Compounds/analysis ; Young Adult ; }, abstract = {Orthodontic braces can impede oral hygiene and promote halitosis. The aim of the study was to investigate the effect of the oral probiotic Streptococcus salivarius M18 on oral hygiene indices and halitosis in patients wearing orthodontic braces. The study was a prospective, randomized, triple-blind, placebo-controlled trial. Patients undergoing fixed orthodontic treatment were randomly allocated to a probiotic group (n = 32) and a placebo group (n = 32). Patients consumed 2 lozenges d[-1] for one month. Assessments were taken at baseline, at the end of the intervention, and at a 3 month follow-up. The outcome measures were plaque index (PI), gingival index (GI) and halitosis-causing volatile sulfur compound (VSC) levels. The dental biofilms before and after the intervention were analyzed utilizing next-generation sequencing of bacterial 16S rRNA genes. PI and GI scores were not significantly influenced by the probiotic intervention (intervention × time: p > 0.05). The level of VSCs decreased significantly in both the probiotic group (VSC reduction = -8.5%, 95%CI = -7.4% to -9.1%, p = 0.015) and the placebo group (-6.5%, 95%CI = -6.0% to -7.4%, p = 0.039) after 1 month intervention. However, at the 3 month follow-up, the VSC levels in the placebo group returned to baseline levels whereas those in the probiotic group decreased further (-10.8%, 95%CI = -10.5% to -12.9%, p = 0.005). Time, but not treatment, was associated with the decrease in microbial community alpha diversity and a modest effect on beta diversity. Oral probiotic S. salivarius M18 reduced the level of halitosis in patients with orthodontic braces, but had minimal effects on PI, GI and dental biofilm microflora.}, } @article {pmid31022528, year = {2019}, author = {Watts, MP and Spurr, LP and Lê Cao, KA and Wick, R and Banfield, JF and Moreau, JW}, title = {Genome-resolved metagenomics of an autotrophic thiocyanate-remediating microbial bioreactor consortium.}, journal = {Water research}, volume = {158}, number = {}, pages = {106-117}, doi = {10.1016/j.watres.2019.02.058}, pmid = {31022528}, issn = {1879-2448}, mesh = {Autotrophic Processes ; Bioreactors ; *Metagenomics ; Microbial Consortia ; *Thiocyanates ; }, abstract = {Industrial thiocyanate (SCN[-]) waste streams from gold mining and coal coking have polluted environments worldwide. Modern SCN[-] bioremediation involves use of complex engineered heterotrophic microbiomes; little attention has been given to the ability of a simple environmental autotrophic microbiome to biodegrade SCN[-]. Here we present results from a bioreactor experiment inoculated with SCN[-] -loaded mine tailings, incubated autotrophically, and subjected to a range of environmentally relevant conditions. Genome-resolved metagenomics revealed that SCN[-] hydrolase-encoding, sulphur-oxidizing autotrophic bacteria mediated SCN[-] degradation. These microbes supported metabolically-dependent non-SCN[-]-degrading sulphur-oxidizing autotrophs and non-sulphur oxidizing heterotrophs, and "niche" microbiomes developed spatially (planktonic versus sessile) and temporally (across changing environmental parameters). Bioreactor microbiome structures changed significantly with increasing temperature, shifting from Thiobacilli to a novel SCN[-] hydrolase-encoding gammaproteobacteria. Transformation of carbonyl sulphide (COS), a key intermediate in global biogeochemical sulphur cycling, was mediated by plasmid-hosted CS2 and COS hydrolase genes associated with Thiobacillus, revealing a potential for horizontal transfer of this function. Our work shows that simple native autotrophic microbiomes from mine tailings can be employed for SCN[-] bioremediation, thus improving the recycling of ore processing waters and reducing the hydrological footprint of mining.}, } @article {pmid31021803, year = {2019}, author = {Wassan, JT and Wang, H and Browne, F and Zheng, H}, title = {Phy-PMRFI: Phylogeny-Aware Prediction of Metagenomic Functions Using Random Forest Feature Importance.}, journal = {IEEE transactions on nanobioscience}, volume = {18}, number = {3}, pages = {273-282}, doi = {10.1109/TNB.2019.2912824}, pmid = {31021803}, issn = {1558-2639}, mesh = {Algorithms ; Databases, Genetic ; *Decision Trees ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/*genetics ; *Metagenomics/classification/methods ; Microbiota/genetics ; Pharynx/microbiology ; Phylogeny ; *Support Vector Machine ; }, abstract = {High-throughput sequencing techniques have accelerated functional metagenomics studies through the generation of large volumes of omics data. The integration of these data using computational approaches is potentially useful for predicting metagenomic functions. Machine learning (ML) models can be trained using microbial features which are then used to classify microbial data into different functional classes. For example, ML analyses over the human microbiome data has been linked to the prediction of important biological states. For analysing omics data, integrating abundance count of taxonomical features with their biological relationships is important. These relationships can potentially be uncovered from the phylogenetic tree of microbial taxa. In this paper, we propose a novel integrative framework Phy-PMRFI. This framework is driven by the phylogeny-based modeling of omics data to predict metagenomic functions using important features selected by a random forest importance (RFI) strategy. The proposed framework integrates the underlying phylogenetic tree information with abundance measures of microbial species (features) by creating a novel phylogeny and abundance aware matrix structure (PAAM). Phy-PMRFI progresses by ranking the microbial features using an RFI measure. This is then used as input for microbiome classification. The resultant feature set enhances the performance of the state-of-art methods such as support vector machines. Our proposed integrative framework also outperforms the state-of-the-art pipeline of phylogenetic isometric log-ratio transform (PhILR) and MetaPhyl. Prediction accuracy of 90 % is obtained with Phy-PMRFI over human throat microbiome in comparison to other approaches of PhILR with 53% and MetaPhyl with 71% accuracy.}, } @article {pmid31021335, year = {2019}, author = {Zhang, Y and Ying, H and Xu, Y}, title = {Comparative genomics and metagenomics of the metallomes.}, journal = {Metallomics : integrated biometal science}, volume = {11}, number = {6}, pages = {1026-1043}, doi = {10.1039/c9mt00023b}, pmid = {31021335}, issn = {1756-591X}, mesh = {Animals ; Biological Evolution ; Genomics/*methods ; Humans ; Metagenomics/methods ; Metalloproteins/genetics/metabolism ; Metals/*metabolism ; Microbiota ; Trace Elements/metabolism ; }, abstract = {Biological trace metals are needed by all living organisms in very small quantities. They play important roles in a variety of key cellular processes, resulting in a varying degree of dependence on metals for different organisms. While most effort has been placed on identifying metal metabolic pathways and characterizing metalloproteins and their functions, computational and systematical analyses of the metallomes (or metalloproteomes) have been limited. In the past several years, comparative genomics of the metallomes has arisen, which provides significant insights into the metabolism and function of metals as well as their evolution. This review focuses on recent progress in comparative genomic analysis of trace metals (such as copper, molybdenum, nickel, cobalt, selenium, iron and zinc) in both prokaryotes and eukaryotes. These studies reveal distinct and dynamic evolutionary patterns of the utilization of different metals and metalloproteins. We also discuss advances in comparative metagenomic analysis of metals in microbial communities in diverse environments such as the global marine ecosystem, which offer new clues to the relationship between metal utilization and different types of environmental factors. Overall, comparative genomic and metagenomic analyses of the metallomes provide a foundation for systematic understanding of metal utilization, function and related evolutionary trends in the three domains of life.}, } @article {pmid31021333, year = {2019}, author = {Xu, H and Zhao, F and Hou, Q and Huang, W and Liu, Y and Zhang, H and Sun, Z}, title = {Metagenomic analysis revealed beneficial effects of probiotics in improving the composition and function of the gut microbiota in dogs with diarrhoea.}, journal = {Food & function}, volume = {10}, number = {5}, pages = {2618-2629}, doi = {10.1039/c9fo00087a}, pmid = {31021333}, issn = {2042-650X}, mesh = {Animals ; Bacteria/classification/drug effects/*genetics/isolation & purification ; Diarrhea/drug therapy/microbiology/*veterinary ; Dog Diseases/*drug therapy/microbiology ; Dogs ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Metagenomics ; Phylogeny ; Probiotics/*administration & dosage ; }, abstract = {The aim of the present study was to evaluate the effects of probiotics on the composition and function of the gut microbiota in dogs with diarrhoea. Forty dogs with diarrhoea were randomly allocated to the treatment group or control group. Probiotics, containing Lactobacillus casei Zhang, Lactobacillus plantarum P-8, and Bifidobacterium animalis subsp. lactis V9, were only fed to 20 treated dogs for 60 days. The faecal samples of all dogs at day 0 and day 60 were analyzed using a metagenomic approach. The results showed a significantly higher microbial diversity and an obvious change in the structure of the gut microbiota in the treatment group. There was also an increase in the abundance of some beneficial bacteria in differently aged dogs, such as Lactobacillus johnsonii (P < 0.05), Lactobacillus reuteri (P < 0.01), Lactobacillus acidophilus (P < 0.05) and Butyricicoccus pullicaecorum (P < 0.05), and a reduction in the abundance of many opportunistic pathogenic bacteria such as Clostridium perfringens (P < 0.05) and Stenotrophomonas maltophilia (P < 0.05) with the supplementation of probiotics. Intriguingly, the correlated networks among some pathogenic bacteria decreased following the administration of probiotics. Additionally, metagenomic analysis revealed the upregulation of pathways involved in the metabolism of amino acids and biosynthesis of secondary metabolites, accompanied by the downregulation of pathways associated with virulence of pathogenic bacteria and cell signaling, suggesting that probiotics could improve the health of dogs with diarrhoea through regulation of the gut microbiota. Our research provides new information relevant to the treatment of diarrhoea in animals and humans.}, } @article {pmid31015324, year = {2019}, author = {Easton, AV and Quiñones, M and Vujkovic-Cvijin, I and Oliveira, RG and Kepha, S and Odiere, MR and Anderson, RM and Belkaid, Y and Nutman, TB}, title = {The Impact of Anthelmintic Treatment on Human Gut Microbiota Based on Cross-Sectional and Pre- and Postdeworming Comparisons in Western Kenya.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, pmid = {31015324}, issn = {2150-7511}, support = {MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anthelmintics/*administration & dosage ; Ascariasis/*drug therapy ; Bacteria/*classification/genetics ; Child ; Child, Preschool ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Kenya ; Metagenomics ; Microbiota/*drug effects ; Middle Aged ; Necatoriasis/*drug therapy ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Rural Population ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Murine studies suggest that the presence of some species of intestinal helminths is associated with changes in host microbiota composition and diversity. However, studies in humans have produced varied conclusions, and the impact appears to vary widely depending on the helminth species present. To demonstrate how molecular approaches to the human gut microbiome can provide insights into the complex interplay among disparate organisms, DNA was extracted from cryopreserved stools collected from residents of 5 rural Kenyan villages prior to and 3 weeks and 3 months following albendazole (ALB) therapy. Samples were analyzed by quantitative PCR (qPCR) for the presence of 8 species of intestinal parasites and by MiSeq 16S rRNA gene sequencing. Based on pretreatment results, the presence of neither Ascaris lumbricoides nor Necator americanus infection significantly altered the overall diversity of the microbiota in comparison with age-matched controls. Following ALB therapy and clearance of soil-transmitted helminths (STH), there were significant increases in the proportion of the microbiota made up by Clostridiales (P = 0.0002; average fold change, 0.57) and reductions in the proportion made up by Enterobacteriales (P = 0.0004; average fold change, -0.58). There was a significant posttreatment decrease in Chao1 richness, even among individuals who were uninfected pretreatment, suggesting that antimicrobial effects must be considered in any posttreatment setting. Nevertheless, the helminth-associated changes in Clostridiales and Enterobacteriales suggest that clearance of STH, and of N. americanus in particular, alters the gut microbiota.IMPORTANCE The gut microbiome is an important factor in human health. It is affected by what we eat, what medicines we take, and what infections we acquire. In turn, it affects the way we absorb nutrients and whether we have excessive intestinal inflammation. Intestinal worms may have an important impact on the composition of the gut microbiome. Without a complete understanding of the impact of mass deworming programs on the microbiome, it is impossible to accurately calculate the cost-effectiveness of such public health interventions and to guard against any possible deleterious side effects. Our research examines this question in a "real-world" setting, using a longitudinal cohort, in which individuals with and without worm infections are treated with deworming medication and followed up at both three weeks and three months posttreatment. We quantify the impact of roundworms and hookworms on gut microbial composition, suggesting that the impact is small, but that treatment of hookworm infection results in significant changes. This work points to the need for follow-up studies to further examine the impact of hookworm on the gut microbiota and determine the health consequences of the observed changes.}, } @article {pmid31013927, year = {2019}, author = {Laitinen, K and Mokkala, K}, title = {Overall Dietary Quality Relates to Gut Microbiota Diversity and Abundance.}, journal = {International journal of molecular sciences}, volume = {20}, number = {8}, pages = {}, pmid = {31013927}, issn = {1422-0067}, support = {#258606//Academy of Finland/ ; -//State research funding for university level health research of the Turku University Hospital Expert Responsibility Area/ ; -//Diabetes Research Foundation/ ; -//Juho Vainio Foundation/ ; }, mesh = {Biodiversity ; *Diet ; Disease Susceptibility ; Female ; *Food Quality ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/methods ; Obesity ; Overweight ; Pregnancy ; Public Health Surveillance ; RNA, Ribosomal, 16S ; }, abstract = {Disturbances in gut microbiota homeostasis may have metabolic consequences with potentially serious clinical manifestations. Diet influences the host's metabolic health in several ways, either directly or indirectly by modulating the composition and function of gut microbiota. This study investigated the extent to which dietary quality is reflected in gut microbiota diversity in overweight and obese pregnant women at risk for metabolic complications. Dietary quality was measured by a validated index of diet quality (IDQ) and microbiota composition was analyzed using 16SrRNA gene sequencing from 84 women pregnant less than 18 weeks. The alpha diversity, measured as Chao1, observed operational taxonomic units (OTUs), phylogenetic diversity, and the Shannon index were calculated. The IDQ score correlated positively with the Shannon index (rho = 0.319, p = 0.003), but not with the other indexes. The women who had the highest dietary quality (highest IDQ quartile) had higher gut microbiota diversity in all the investigated indexes, when compared to the women with the lowest dietary quality (lowest IDQ quartile; p < 0.032). Consequently, a higher dietary quality was reflected in a higher gut microbiota diversity. The presented approach may aid in devising new tools for dietary counseling aiming at holistic health, as well as in microbiome studies, to control for dietary variance.}, } @article {pmid31012060, year = {2019}, author = {Lorenzi, AS and Chia, MA and Lopes, FAC and Silva, GGZ and Edwards, RA and Bittencourt-Oliveira, MDC}, title = {Cyanobacterial biodiversity of semiarid public drinking water supply reservoirs assessed via next-generation DNA sequencing technology.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {57}, number = {6}, pages = {450-460}, pmid = {31012060}, issn = {1976-3794}, mesh = {Alkaloids ; Bacterial Toxins/analysis/genetics/isolation & purification ; *Biodiversity ; Brazil ; Cyanobacteria/*classification/genetics/*isolation & purification ; Cyanobacteria Toxins ; DNA, Bacterial/analysis ; Drinking Water/*microbiology ; Environmental Monitoring/methods ; Genes, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Microcystis/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Saxitoxin/genetics ; Seasons ; Sequence Analysis, DNA/*methods ; Uracil/analogs & derivatives ; *Water Microbiology ; *Water Supply ; }, abstract = {Next-generation DNA sequencing technology was applied to generate molecular data from semiarid reservoirs during well-defined seasons. Target sequences of 16S-23S rRNA ITS and cpcBA-IGS were used to reveal the taxonomic groups of cyanobacteria present in the samples, and genes coding for cyanotoxins such as microcystins (mcyE), saxitoxins (sxtA), and cylindrospermopsins (cyrJ) were investigated. The presence of saxitoxins in the environmental samples was evaluated using ELISA kit. Taxonomic analyses of high-throughput DNA sequencing data showed the dominance of the genus Microcystis in Mundaú reservoir. Furthermore, it was the most abundant genus in the dry season in Ingazeira reservoir. In the rainy season, 16S-23S rRNA ITS analysis revealed that Cylindrospermopsis raciborskii comprised 46.8% of the cyanobacterial community in Ingazeira reservoir, while the cpcBAIGS region revealed that C. raciborskii (31.8%) was the most abundant taxon followed by Sphaerospermopsis aphanizomenoides (17.3%) and Planktothrix zahidii (16.6%). Despite the presence of other potential toxin-producing genera, the detected sxtA gene belonged to C. raciborskii, while the mcyE gene belonged to Microcystis in both reservoirs. The detected mcyE gene had good correlation with MC content, while the amplification of the sxtA gene was related to the presence of STX. The cyrJ gene was not detected in these samples. Using DNA analyses, our results showed that the cyanobacterial composition of Mundaú reservoir was similar in successive dry seasons, and it varied between seasons in Ingazeira reservoir. In addition, our data suggest that some biases of analysis influenced the cyanobacterial communities seen in the NGS output of Ingazeira reservoir.}, } @article {pmid31009573, year = {2019}, author = {Zhang, X and Figeys, D}, title = {Perspective and Guidelines for Metaproteomics in Microbiome Studies.}, journal = {Journal of proteome research}, volume = {18}, number = {6}, pages = {2370-2380}, doi = {10.1021/acs.jproteome.9b00054}, pmid = {31009573}, issn = {1535-3907}, support = {MOP-114872//CIHR/Canada ; }, mesh = {Computational Biology/methods ; Dysbiosis/genetics/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Proteomics/*methods ; }, abstract = {The microbiome is emerging as a prominent factor affecting human health, and its dysbiosis is associated with various diseases. Compositional profiling of microbiome is increasingly being supplemented with functional characterization. Metaproteomics is intrinsically focused on functional changes and therefore will be an important tool in those studies of the human microbiome. In the past decade, development of new experimental and bioinformatic approaches for metaproteomics has enabled large-scale human metaproteomic studies. However, challenges still exist, and there remains a lack of standardizations and guidelines for properly performing metaproteomic studies on human microbiome. Herein, we provide a perspective of recent developments, the challenges faced, and the future directions of metaproteomics and its applications. In addition, we propose a set of guidelines/recommendations for performing and reporting the results from metaproteomic experiments for the study of human microbiomes. We anticipate that these guidelines will be optimized further as more metaproteomic questions are raised and addressed, and metaproteomic applications are published, so that they are eventually recognized and applied in the field.}, } @article {pmid31009062, year = {2019}, author = {Zhang, J and Lin, W}, title = {Scalable estimation and regularization for the logistic normal multinomial model.}, journal = {Biometrics}, volume = {75}, number = {4}, pages = {1098-1108}, doi = {10.1111/biom.13071}, pmid = {31009062}, issn = {1541-0420}, mesh = {Algorithms ; Computer Simulation ; Gastrointestinal Microbiome/genetics ; Humans ; *Logistic Models ; Metagenomics/*methods ; Methods ; Sequence Analysis ; Stochastic Processes ; }, abstract = {Clustered multinomial data are prevalent in a variety of applications such as microbiome studies, where metagenomic sequencing data are summarized as multinomial counts for a large number of bacterial taxa per subject. Count normalization with ad hoc zero adjustment tends to result in poor estimates of abundances for taxa with zero or small counts. To account for heterogeneity and overdispersion in such data, we suggest using the logistic normal multinomial (LNM) model with an arbitrary correlation structure to simultaneously estimate the taxa compositions by borrowing information across subjects. We overcome the computational difficulties in high dimensions by developing a stochastic approximation EM algorithm with Hamiltonian Monte Carlo sampling for scalable parameter estimation in the LNM model. The ill-conditioning problem due to unstructured covariance is further mitigated by a covariance-regularized estimator with a condition number constraint. The advantages of the proposed methods are illustrated through simulations and an application to human gut microbiome data.}, } @article {pmid31006638, year = {2019}, author = {Kalan, LR and Meisel, JS and Loesche, MA and Horwinski, J and Soaita, I and Chen, X and Uberoi, A and Gardner, SE and Grice, EA}, title = {Strain- and Species-Level Variation in the Microbiome of Diabetic Wounds Is Associated with Clinical Outcomes and Therapeutic Efficacy.}, journal = {Cell host & microbe}, volume = {25}, number = {5}, pages = {641-655.e5}, pmid = {31006638}, issn = {1934-6069}, support = {R01 NR009448/NR/NINR NIH HHS/United States ; R01 AR066663/AR/NIAMS NIH HHS/United States ; P30 AR069589/AR/NIAMS NIH HHS/United States ; T32 GM007229/GM/NIGMS NIH HHS/United States ; P20 NR018081/NR/NINR NIH HHS/United States ; R01 NR015639/NR/NINR NIH HHS/United States ; T32 AR007465/AR/NIAMS NIH HHS/United States ; R00 AR060873/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; Anti-Infective Agents/*therapeutic use ; Coinfection/*microbiology/therapy ; *Debridement ; Diabetic Foot/*microbiology/therapy ; Disease Models, Animal ; Longitudinal Studies ; Mice ; *Microbiota ; Prospective Studies ; Treatment Outcome ; Wound Healing ; Wound Infection/*microbiology/therapy ; }, abstract = {Chronic wounds are a major complication of diabetes associated with high morbidity and health care expenditures. To investigate the role of colonizing microbiota in diabetic wound healing, clinical outcomes, and response to interventions, we conducted a longitudinal, prospective study of patients with neuropathic diabetic foot ulcers (DFU). Metagenomic shotgun sequencing revealed that strain-level variation of Staphylococcus aureus and genetic signatures of biofilm formation were associated with poor outcomes. Cultured wound isolates of S. aureus elicited differential phenotypes in mouse models that corresponded with patient outcomes, while wound "bystanders" such as Corynebacterium striatum and Alcaligenes faecalis, typically considered commensals or contaminants, also significantly impacted wound severity and healing. Antibiotic resistance genes were widespread, and debridement, rather than antibiotic treatment, significantly shifted the DFU microbiota in patients with more favorable outcomes. These findings suggest that the DFU microbiota may be a marker for clinical outcomes and response to therapeutic interventions.}, } @article {pmid31006170, year = {2020}, author = {Coker, MO and Hoen, AG and Dade, E and Lundgren, S and Li, Z and Wong, AD and Zens, MS and Palys, TJ and Morrison, HG and Sogin, ML and Baker, ER and Karagas, MR and Madan, JC}, title = {Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {127}, number = {2}, pages = {217-227}, pmid = {31006170}, issn = {1471-0528}, support = {NIGMS P20GM104416/NH/NIH HHS/United States ; RD83544201//U.S. Environmental Protection Agency/International ; 1P20ES018175-02/NH/NIH HHS/United States ; UH3 OD023275/OD/NIH HHS/United States ; R01 GM123014/GM/NIGMS NIH HHS/United States ; RD83459901//U.S. Environmental Protection Agency/International ; R01 LM012723/LM/NLM NIH HHS/United States ; K01 LM011985/LM/NLM NIH HHS/United States ; NIEHS P01ES022832/NH/NIH HHS/United States ; P20 ES018175/ES/NIEHS NIH HHS/United States ; NIEHS P20ES018175/NH/NIH HHS/United States ; P01 ES022832/ES/NIEHS NIH HHS/United States ; NLM K01LM011985/NH/NIH HHS/United States ; P20 GM104416/GM/NIGMS NIH HHS/United States ; }, mesh = {*Antibiotic Prophylaxis ; Bacteroides/growth & development ; Bacteroidetes ; Bifidobacterium ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant, Newborn ; Lactobacillus ; Maternal Exposure ; Mothers ; Pregnancy ; Prospective Studies ; RNA, Ribosomal, 16S ; Sequence Analysis, RNA ; Term Birth ; Vagina/*microbiology ; beta-Lactamases ; }, abstract = {OBJECTIVE: To evaluate the potential impact of intrapartum antibiotics, and their specific classes, on the infant gut microbiota in the first year of life.

DESIGN: Prospective study of infants in the New Hampshire Birth Cohort Study (NHBCS).

SETTINGS: Rural New Hampshire, USA.

POPULATION OR SAMPLE: Two hundred and sixty-six full-term infants from the NHBCS.

METHODS: Intrapartum antibiotic use during labour and delivery was abstracted from medical records. Faecal samples collected at 6 weeks and 1 year of age were characterised by 16S rRNA sequencing, and metagenomics analysis in a subset of samples.

EXPOSURES: Maternal exposure to antibiotics during labour and delivery.

MAIN OUTCOME MEASURE: Taxonomic and functional profiles of faecal samples.

RESULTS: Infant exposure to intrapartum antibiotics, particularly to two or more antibiotic classes, was independently associated with lower microbial diversity scores as well as a unique bacterial community at 6 weeks (GUnifrac, P = 0.02). At 1 year, infants in the penicillin-only group had significantly lower α diversity scores than infants not exposed to intrapartum antibiotics. Within the first year of life, intrapartum exposure to penicillins was related to a significantly lower increase in several taxa including Bacteroides, use of cephalosporins was associated with a significantly lower rise over time in Bifidobacterium and infants in the multi-class group experienced a significantly higher increase in Veillonella dispar.

CONCLUSIONS: Our findings suggest that intrapartum antibiotics alter the developmental trajectory of the infant gut microbiome, and specific antibiotic types may impact community composition, diversity and keystone immune training taxa.

TWEETABLE ABSTRACT: Class of intrapartum antibiotics administered during delivery relates to maturation of infant gut microbiota.}, } @article {pmid31005411, year = {2019}, author = {Hollister, EB and Oezguen, N and Chumpitazi, BP and Luna, RA and Weidler, EM and Rubio-Gonzales, M and Dahdouli, M and Cope, JL and Mistretta, TA and Raza, S and Metcalf, GA and Muzny, DM and Gibbs, RA and Petrosino, JF and Heitkemper, M and Savidge, TC and Shulman, RJ and Versalovic, J}, title = {Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome.}, journal = {The Journal of molecular diagnostics : JMD}, volume = {21}, number = {3}, pages = {449-461}, pmid = {31005411}, issn = {1943-7811}, support = {U01 AI124290/AI/NIAID NIH HHS/United States ; K23 DK101688/DK/NIDDK NIH HHS/United States ; R01 NR013497/NR/NINR NIH HHS/United States ; UH3 DK083990/DK/NIDDK NIH HHS/United States ; R03 DK117219/DK/NIDDK NIH HHS/United States ; R01 NR005337/NR/NINR NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; RC2 NR011959/NR/NINR NIH HHS/United States ; U01 CA170930/CA/NCI NIH HHS/United States ; U54 HG004973/HG/NHGRI NIH HHS/United States ; R01 AT004326/AT/NCCIH NIH HHS/United States ; R21 DK096323/DK/NIDDK NIH HHS/United States ; }, mesh = {Abdominal Pain/etiology/microbiology ; Bacteria/genetics ; Case-Control Studies ; Child ; Feces/microbiology ; Female ; Gastrointestinal Tract/microbiology ; Genomics ; Humans ; Irritable Bowel Syndrome/complications/*microbiology ; Male ; Metabolome ; *Microbiota ; Multivariate Analysis ; Principal Component Analysis ; Statistics, Nonparametric ; }, abstract = {Accurate diagnosis and stratification of children with irritable bowel syndrome (IBS) remain challenging. Given the central role of recurrent abdominal pain in IBS, we evaluated the relationships of pediatric IBS and abdominal pain with intestinal microbes and fecal metabolites using a comprehensive clinical characterization and multiomics strategy. Using rigorous clinical phenotyping, we identified preadolescent children (aged 7 to 12 years) with Rome III IBS (n = 23) and healthy controls (n = 22) and characterized their fecal microbial communities using whole-genome shotgun metagenomics and global unbiased fecal metabolomic profiling. Correlation-based approaches and machine learning algorithms identified associations between microbes, metabolites, and abdominal pain. IBS cases differed from controls with respect to key bacterial taxa (eg, Flavonifractor plautii and Lachnospiraceae bacterium 7_1_58FAA), metagenomic functions (eg, carbohydrate metabolism and amino acid metabolism), and higher-order metabolites (eg, secondary bile acids, sterols, and steroid-like compounds). Significant associations between abdominal pain frequency and severity and intestinal microbial features were identified. A random forest classifier built on metagenomic and metabolic markers successfully distinguished IBS cases from controls (area under the curve, 0.93). Leveraging multiple lines of evidence, intestinal microbes, genes/pathways, and metabolites were associated with IBS, and these features were capable of distinguishing children with IBS from healthy children. These multi-omics features, and their links to childhood IBS coupled with nutritional interventions, may lead to new microbiome-guided diagnostic and therapeutic strategies.}, } @article {pmid31004827, year = {2019}, author = {Sung, CM and Lin, YF and Chen, KF and Ke, HM and Huang, HY and Gong, YN and Tsai, WS and You, JF and Lu, MJ and Cheng, HT and Lin, CY and Kuo, CJ and Tsai, IJ and Hsieh, SY}, title = {Predicting Clinical Outcomes of Cirrhosis Patients With Hepatic Encephalopathy From the Fecal Microbiome.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {8}, number = {2}, pages = {301-318.e2}, pmid = {31004827}, issn = {2352-345X}, mesh = {Adult ; Aged ; Bacteria/*isolation & purification ; *Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Hepatic Encephalopathy/*diagnosis/microbiology ; Humans ; *Liver Cirrhosis ; Male ; Middle Aged ; Prognosis ; }, abstract = {BACKGROUND & AIMS: Gut dysbiosis plays a role in hepatic encephalopathy (HE), while its relationship at the acute episode of overt HE (AHE), the disease progression and clinical outcomes remains unclear. We aimed to identify AHE-specific microbiome and its association to patients' outcomes.

METHODS: We profiled fecal microbiome changes for a cohort of 62 patients with cirrhosis and AHE i) before treatment, ii) 2-3 days after medication and iii) 2-3 months after recovery, and three control cohorts i) healthy individuals, patients with ii) compensated or iii) decompensated cirrhosis.

RESULTS: Comparison of the microbiome shift from compensated, decompensated cirrhosis, AHE to recovery revealed the AHE-specific gut-dysbiosis. The gut microbiome diversity was decreased during AHE, further reduced after medication, and only partially reversed during the recovery. The relative abundance of Bacteroidetes phylum in the microbiome decreased, whereas that of Firmicute, Proteobacteria and Actinobacteria increased in patients during AHE compared with those with compensated cirrhosis. A total of 70 operational taxonomic units (OTUs) were significantly different between AHE and decompensated cirrhosis abundances. Of them, the abundance of Veillonella parvula increased the most during AHE via a metagenomics recovery of the genomes. Moreover, the relative abundances of three (Alistipes, Bacteroides, Phascolarctobacterium) and five OTUs (Clostridium-XI, Bacteroides, Bacteroides, Lactobacillus, Clostridium-sedis) at AHE were respectively associated with HE recurrence and overall survival during the subsequent one-year follow-up.

CONCLUSIONS: AHE-specific gut OTUs were identified that may be involved in HE development and able to predict clinical outcomes, providing new strategies for the prevention and treatment of HE recurrence in patients with cirrhosis.}, } @article {pmid31001490, year = {2019}, author = {Hu, Y and Feng, Y and Wu, J and Liu, F and Zhang, Z and Hao, Y and Liang, S and Li, B and Li, J and Lv, N and Xu, Y and Zhu, B and Sun, Z}, title = {The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {90}, pmid = {31001490}, issn = {2235-2988}, mesh = {Bacteria/classification/genetics/metabolism ; *Dysbiosis ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Microbiota ; Tuberculosis, Pulmonary/*complications ; }, abstract = {Cross talk occurs between the human gut and the lung through a gut-lung axis involving the gut microbiota. However, the signatures of the human gut microbiota after active Mycobacterium tuberculosis infection have not been fully understood. Here, we investigated changes in the gut microbiota in tuberculosis (TB) patients by shotgun sequencing the gut microbiomes of 31 healthy controls and 46 patients. We observed a dramatic changes in gut microbiota in tuberculosis patients as reflected by significant decreases in species number and microbial diversity. The gut microbiota of TB patients were mostly featured by the striking decrease of short-chain fatty acids (SCFAs)-producingbacteria as well as associated metabolic pathways. A classification model based on the abundance of three species, Haemophilus parainfluenzae, Roseburia inulinivorans, and Roseburia hominis, performed well for discriminating between healthy and diseased patients. Additionally, the healthy and diseased states can be distinguished by SNPs in the species of B. vulgatus. We present a comprehensive profile of changes in the microbiota in clinical TB patients. Our findings will shed light on the design of future diagnoses and treatments for M. tuberculosis infections.}, } @article {pmid31000700, year = {2019}, author = {Dong, X and Greening, C and Rattray, JE and Chakraborty, A and Chuvochina, M and Mayumi, D and Dolfing, J and Li, C and Brooks, JM and Bernard, BB and Groves, RA and Lewis, IA and Hubert, CRJ}, title = {Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1816}, pmid = {31000700}, issn = {2041-1723}, mesh = {Acetates/metabolism ; Archaea/genetics/isolation & purification/*metabolism ; Bacteria/genetics/isolation & purification/*metabolism ; Geologic Sediments/chemistry/*microbiology ; Hydrocarbons/metabolism ; Hydrogen/metabolism ; Metagenome ; Metagenomics/methods ; Mexico ; Microbial Interactions/physiology ; Microbiota/*physiology ; Petroleum/*metabolism ; }, abstract = {The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism.}, } @article {pmid31000244, year = {2019}, author = {Rocchetti, G and Senizza, A and Gallo, A and Lucini, L and Giuberti, G and Patrone, V}, title = {In vitro large intestine fermentation of gluten-free rice cookies containing alfalfa seed (Medicago sativa L.) flour: A combined metagenomic/metabolomic approach.}, journal = {Food research international (Ottawa, Ont.)}, volume = {120}, number = {}, pages = {312-321}, doi = {10.1016/j.foodres.2019.03.003}, pmid = {31000244}, issn = {1873-7145}, mesh = {Cooking ; DNA, Bacterial/genetics/isolation & purification ; Edible Grain/chemistry ; Fatty Acids, Volatile/analysis ; Fermentation ; Flour/*analysis ; Gastrointestinal Microbiome ; Glutens/analysis ; Intestine, Large/*metabolism ; Lignans/analysis ; Medicago sativa/*chemistry ; *Metabolomics ; *Metagenomics ; Oryza/*chemistry ; Phenols/analysis ; Polyphenols/analysis ; RNA, Ribosomal, 16S/genetics/isolation & purification ; Seeds/*chemistry ; Sequence Analysis, DNA ; }, abstract = {Alfalfa seed flour (ASF) at different inclusion levels (0% as control, 30% and 45% w/w) was used to prepare rice flour-based gluten-free (GF) cookies (CK). Samples underwent a simulated in vitro digestion and fermentation process. The comprehensive changes in the phenolic profiles were evaluated during 48 h of fermentation by means of untargeted UHPLC-QTOF mass spectrometry followed by multivariate statistics. Furthermore, the modifications in microbial profile and the production of short chain fatty acids (SCFA) were investigated. Cookies presenting 30% (30-CK) and 45% (45-CK) ASF possessed the greater total phenolic content when compared to the control, being 0.42 and 0.56 mg/g versus 0.15 mg/g, respectively. The orthogonal projection to latent structure discriminant analysis, applied to untargeted metabolomics-based data, showed a clear modulation of the profile in phenolic metabolites over time (from 8 up to 48 h of in vitro fermentation). In this regard, the in vitro fermentation of 30-CK and 45-CK resulted in the maximum increase in lignans and phenolic acids, whose bioaccessibility at 24 h of in vitro fermentation was 16.2% and 12.2%, respectively. In addition, the metagenomic sequencing approach allowed to identify in Clostridiaceae, Ruminococcaceae, Lachnospiraceae and Streptococcaceae the most represented bacterial populations during the in vitro fermentation. A greater total SCFA production (p < .05) was recorded overtime for all ASF-enriched cookies when compared to the control. Therefore, ASF proved to be an excellent alternative to common non-wheat cereal flours (such as pseudocereals or legumes) for improving possible health-promoting properties in GF cookie formulation.}, } @article {pmid30997495, year = {2019}, author = {Hornung, BVH and Zwittink, RD and Kuijper, EJ}, title = {Issues and current standards of controls in microbiome research.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {5}, pages = {}, pmid = {30997495}, issn = {1574-6941}, mesh = {Humans ; *Microbiota ; Reproducibility of Results ; Research/*standards ; }, abstract = {Good scientific practice is important in all areas of science. In recent years this has gained more and more attention, especially considering the 'scientific reproducibility crisis'. While most researchers are aware of the issues with good scientific practice, not all of these issues are necessarily clear, and the details can be very complicated. For many years it has been accepted to perform and publish sequencing based microbiome studies without including proper controls. Although in recent years more scientists realize the necessity of implementing controls, this poses a problem due to the complexity of the field. Another concern is the inability to properly interpret the information gained from controls in microbiome studies. Here, we will discuss these issues and provide a comprehensive overview of problematic points regarding controls in microbiome research, and of the current standards in this area.}, } @article {pmid30995949, year = {2019}, author = {Fessler, J and Matson, V and Gajewski, TF}, title = {Exploring the emerging role of the microbiome in cancer immunotherapy.}, journal = {Journal for immunotherapy of cancer}, volume = {7}, number = {1}, pages = {108}, pmid = {30995949}, issn = {2051-1426}, support = {F32 CA236296/CA/NCI NIH HHS/United States ; F99 CA234946/CA/NCI NIH HHS/United States ; R35 CA210098/CA/NCI NIH HHS/United States ; T32 CA009594/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*adverse effects ; Antineoplastic Agents, Immunological/*pharmacology/therapeutic use ; Disease Models, Animal ; Drug Resistance, Neoplasm/immunology ; Gastrointestinal Microbiome/drug effects/*immunology ; Humans ; Immunotherapy/*methods ; Mice ; Neoplasms/immunology/microbiology/mortality/*therapy ; Progression-Free Survival ; }, abstract = {The activity of the commensal microbiota significantly impacts human health and has been linked to the development of many diseases, including cancer. Gnotobiotic animal models have shown that the microbiota has many effects on host physiology, including on the development and regulation of immune responses. More recently, evidence has indicated that the microbiota can more specifically influence the outcome of cancer immunotherapy. Therapeutic interventions to optimize microbiota composition to improve immunotherapy outcomes have shown promise in mouse studies. Ongoing endeavors are translating these pre-clinical findings to early stage clinical testing. In this review we summarize 1) basic methodologies and considerations for studies of host-microbiota interactions; 2) experimental evidence towards a causal link between gut microbiota composition and immunotherapeutic efficacy; 3) possible mechanisms governing the microbiota-mediated impact on immunotherapy efficacy. Moving forward, there is need for a deeper understanding of the underlying biological mechanisms that link specific bacterial strains to host immunity. Integrating microbiome effects with other tumor and host factors regulating immunotherapy responsiveness versus resistance could facilitate optimization of therapeutic outcomes.}, } @article {pmid30995938, year = {2019}, author = {Le Doujet, T and De Santi, C and Klemetsen, T and Hjerde, E and Willassen, NP and Haugen, P}, title = {Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua).}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {64}, pmid = {30995938}, issn = {2049-2618}, mesh = {*Animal Migration ; Animals ; DNA, Bacterial/genetics ; Female ; Gadus morhua/*microbiology ; *Gastrointestinal Microbiome ; Genetic Variation ; Genome, Bacterial ; Male ; *Metagenomics ; Norway ; Photobacterium/*classification ; Proteomics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The population of Atlantic cod (Gadus morhua), also known as Northeast Arctic cod, migrating Atlantic cod, or simply "skrei," lives mainly in the Barents Sea and Svalbard waters and migrates in annual cycles to the Norwegian coast in order to spawn eggs during late winter. It is the world's largest population of Atlantic cod, and the population is distinct from the Norwegian coastal cod (or "fjord" cod). Despite the biological, economic, and cultural importance of migrating Atlantic cod, current knowledge on the associated microbiota is very limited. Using shotgun metagenomics and metaproteomics approaches, we present here the gut microbiota, metagenome-assembled genomes (MAGs) of the most abundant bacterial species, DNA-based functional profile, and the metaproteome of Atlantic cod specimens caught at a spawning area in an open ocean outside of Tromsø, Norway.

RESULTS: Our analyses identified 268 bacterial families in DNA isolated from feces of 6 individual migrating Atlantic cod. The most abundant family was Vibrionaceae (52%; 83% if unclassified reads are excluded), with Photobacterium (genus) representing the vast majority. The recovery of metagenome-assembled genomes provided further details and suggests that several closely related Photobacterium strains from the Photobacterium phosphoreum clade are the most abundant. A genomic-based functional profiling showed that the most abundant functional subsystems are "Carbohydrates"; "Amino Acids and Derivatives"; "Protein Metabolism"; "Cofactors, Vitamins, Prosthetic, Groups, and Pigments"; and "DNA Metabolism," which is in agreement with other studies of gut microbiomes of marine organisms. Finally, the MS-based metaproteomic dataset revealed that the functional category "Protein Metabolism" is highly overrepresented (3×) when compared to the genome-based functional profile, which shows that ribosomal proteins are rich in the bacterial cytosol.

CONCLUSION: We present here the first study of bacterial diversity of the gut of migrating Atlantic cod using shotgun sequencing and metagenome-assembled genomes (MAGs). The most abundant bacteria belong to the Photobacterium genus (Vibrionaceae family). We also constructed functional profiles of the gut microbiome. These may be used in future studies as a platform for mining of commercially interesting cold-active enzymes.}, } @article {pmid30995692, year = {2019}, author = {Langer, SG and Gabris, C and Einfalt, D and Wemheuer, B and Kazda, M and Bengelsdorf, FR}, title = {Different response of bacteria, archaea and fungi to process parameters in nine full-scale anaerobic digesters.}, journal = {Microbial biotechnology}, volume = {12}, number = {6}, pages = {1210-1225}, pmid = {30995692}, issn = {1751-7915}, mesh = {Anaerobiosis ; Archaea/classification/genetics/*growth & development ; Bacteria, Anaerobic/classification/genetics/*growth & development ; Biofuels ; Bioreactors/*microbiology ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fungi/classification/genetics/*growth & development ; Manure/*microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; }, abstract = {Biogas production is a biotechnological process realized by complex bacterial, archaeal and likely fungal communities. Their composition was assessed in nine full-scale biogas plants with distinctly differing feedstock input and process parameters. This study investigated the actually active microbial community members by using a comprehensive sequencing approach based on ribosomal 16S and 28S rRNA fragments. The prevailing taxonomical units of each respective community were subsequently linked to process parameters. Ribosomal rRNA of bacteria, archaea and fungi, respectively, showed different compositions with respect to process parameters and supplied feedstocks: (i) bacterial communities were affected by the key factors temperature and ammonium concentration; (ii) composition of archaea was mainly related to process temperature; and (iii) relative abundance of fungi was linked to feedstocks supplied to the digesters. Anaerobic digesters with a high methane yield showed remarkably similar bacterial communities regarding identified taxonomic families. Although archaeal communities differed strongly on genus level from each other, the respective digesters still showed high methane yields. Functional redundancy of the archaeal communities may explain this effect. 28S rRNA sequences of fungi in all nine full-scale anaerobic digesters were primarily classified as facultative anaerobic Ascomycota and Basidiomycota. Since the presence of ribosomal 28S rRNA indicates that fungi may be active in the biogas digesters, further research should be carried out to examine to which extent they are important players in anaerobic digestion processes.}, } @article {pmid30994668, year = {2019}, author = {Li, L and Guo, WL and Zhang, W and Xu, JX and Qian, M and Bai, WD and Zhang, YY and Rao, PF and Ni, L and Lv, XC}, title = {Grifola frondosa polysaccharides ameliorate lipid metabolic disorders and gut microbiota dysbiosis in high-fat diet fed rats.}, journal = {Food & function}, volume = {10}, number = {5}, pages = {2560-2572}, doi = {10.1039/c9fo00075e}, pmid = {30994668}, issn = {2042-650X}, mesh = {Animals ; Bacteria/classification/drug effects/genetics/isolation & purification ; Cholesterol/blood ; Cholesterol 7-alpha-Hydroxylase/genetics/metabolism ; Diet, High-Fat/adverse effects ; Dysbiosis/*drug therapy/metabolism/microbiology ; Fatty Acids, Nonesterified/blood ; Gastrointestinal Microbiome/*drug effects ; Grifola/*chemistry ; Humans ; Lipid Metabolism/drug effects ; Lipid Metabolism Disorders/*drug therapy/genetics/metabolism/microbiology ; Liver/drug effects/metabolism ; Male ; Plant Extracts/*administration & dosage ; Polysaccharides/*administration & dosage ; Rats ; Rats, Wistar ; Triglycerides/blood ; }, abstract = {The purpose of this study was to assess the potential effects of polysaccharides from edible mushroom Grifola frondosa (GFP) on lipid metabolic disorders and gut microbiota dysbiosis, and elucidate their possible regulatory mechanisms on lipid and cholesterol metabolism in high-fat diet (HFD)-exacerbated hyperlipidemic and hypercholesterolemic rats. Results showed that oral administration of GFP markedly alleviated dyslipidaemia through decreasing the serum levels of total triglycerides, total cholesterol, and free fatty acids, and significantly suppressing hepatic lipid accumulation and steatosis. Besides, the excretion of fecal bile acids was also promoted by oral administration of GFP. Metagenomic analysis revealed that GFP supplementation (400 mg kg-1 day-1) resulted in significant structure changes on gut microbiota in HFD-fed rats, in particular modulating the relative abundance of functionally relevant microbial phylotypes compared with the HFD group. Key microbial phylotypes responding to GFP intervention were identified to strongly correlate with the lipid metabolism disorder associated parameters using the correlation network based on Spearman's correlation coefficient. Serum and hepatic lipid profiles were found positively correlated with Clostridium-XVIII, Butyricicoccus and Turicibacter, but negatively correlated with Helicobater, Intestinimonas, Barnesiella, Parasutterella, Ruminococcus and Flavonifracter. Moreover, GFP treatment (400 mg kg-1 day-1) regulated the mRNA expression levels of the genes responsible for hepatic lipid and cholesterol metabolism. Oral supplementation of GFP markedly increased the mRNA expression of cholesterol 7α-hydroxylase (CYP7A1) and bile salt export pump (BSEP), suggesting an enhancement of bile acid (BA) synthesis and excretion from the liver. These findings illustrated that GFP could ameliorate lipid metabolic disorders through modulating specific gut microbial phylotypes and regulating hepatic lipid and cholesterol metabolism related genes, and therefore could be used as a potential functional food ingredient for the prevention or treatment of hyperlipidemia.}, } @article {pmid30994437, year = {2019}, author = {Carrasco, J and Tello, ML and de Toro, M and Tkacz, A and Poole, P and Pérez-Clavijo, M and Preston, G}, title = {Casing microbiome dynamics during button mushroom cultivation: implications for dry and wet bubble diseases.}, journal = {Microbiology (Reading, England)}, volume = {165}, number = {6}, pages = {611-624}, doi = {10.1099/mic.0.000792}, pmid = {30994437}, issn = {1465-2080}, mesh = {Agaricus/*growth & development ; Bacteria/classification/genetics/growth & development/isolation & purification ; Culture Media/chemistry ; Hypocreales/growth & development/isolation & purification ; Microbial Interactions ; Microbiota/*physiology ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {The casing material required in mushroom cultivation presents a very rich ecological niche, which is inhabited by a diverse population of bacteria and fungi. In this work three different casing materials, blonde peat, black peat and a 50 : 50 mixture of both, were compared for their capacity to show a natural suppressive response against dry bubble, Lecanicillium fungicola (Preuss) Zare and Gams, and wet bubble, Mycogone perniciosa (Magnus) Delacroix. The highest mushroom production was collected from crops cultivated using the mixed casing and black peat, which were not significantly different in yield. However, artificial infection with mycoparasites resulted in similar yield losses irrespective of the material used, indicating that the casing materials do not confer advantages in disease suppression. The composition of the microbiome of the 50 : 50 casing mixture along the crop cycle and the compost and basidiomes was evaluated through next-generation sequencing (NGS) of the V3-V4 region of the bacterial 16S rRNA gene and the fungal ITS2 region. Once colonized by Agaricus bisporus, the bacterial diversity of the casing microbiome increased and the fungal diversity drastically decreased. From then on, the composition of the casing microbiome remained relatively stable. Analysis of the composition of the bacterial microbiome in basidiomes indicated that it is highly influenced by the casing microbiota. Notably, L. fungicola was consistently detected in uninoculated control samples of compost and casing using NGS, even in asymptomatic crops. This suggests that the naturally established casing microbiota was able to help to suppress disease development when inoculum levels were low, but was not effective in suppressing high pressure from artificially introduced fungal inoculum. Determination of the composition of the casing microbiome paves the way for the development of synthetic casing communities that can be used to investigate the role of specific components of the casing microbiota in mushroom production and disease control.}, } @article {pmid30994187, year = {2019}, author = {Wang, T and Yang, C and Zhao, H}, title = {Prediction analysis for microbiome sequencing data.}, journal = {Biometrics}, volume = {75}, number = {3}, pages = {875-884}, doi = {10.1111/biom.13061}, pmid = {30994187}, issn = {1541-0420}, mesh = {Algorithms ; Bacteria/genetics ; Humans ; Likelihood Functions ; Microbiota/*genetics ; Monte Carlo Method ; Regression Analysis ; *Sequence Analysis ; }, abstract = {One goal of human microbiome studies is to relate host traits with human microbiome compositions. The analysis of microbial community sequencing data presents great statistical challenges, especially when the samples have different library sizes and the data are overdispersed with many zeros. To address these challenges, we introduce a new statistical framework, called predictive analysis in metagenomics via inverse regression (PAMIR), to analyze microbiome sequencing data. Within this framework, an inverse regression model is developed for overdispersed microbiota counts given the trait, and then a prediction rule is constructed by taking advantage of the dimension-reduction structure in the model. An efficient Monte Carlo expectation-maximization algorithm is proposed for maximum likelihood estimation. The method is further generalized to accommodate other types of covariates. We demonstrate the advantages of PAMIR through simulations and two real data examples.}, } @article {pmid30992508, year = {2019}, author = {Yang, Y and Zhang, S and Li, N and Chen, H and Jia, H and Song, X and Liu, G and Ni, C and Wang, Z and Shao, H and Zhang, S}, title = {Metagenomic insights into effects of wheat straw compost fertiliser application on microbial community composition and function in tobacco rhizosphere soil.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6168}, pmid = {30992508}, issn = {2045-2322}, mesh = {Bacteria/genetics/isolation & purification ; Basidiomycota/genetics/isolation & purification ; *Composting ; *Fertilizers/analysis ; Metagenome ; Microbiota ; Soil/*chemistry ; *Soil Microbiology ; Nicotiana/growth & development ; Triticum/*chemistry ; }, abstract = {The application of fertilisers incorporated with plant residues improves nutrient availability in soils, which shifts the microbial community structure and favours plant growth. To understand the impact of wheat straw compost fertiliser on soil properties and microbial community structure, tobacco planting soils were treated with four different fertilisers using varied amounts of straw compost fertiliser and a no fertiliser control (CK). Results showed that different fertilisers affected available soil nutrient contents differently. Treatment of tobacco soil with application of combined chemical fertiliser/wheat straw compost led to improved soil chemical properties, and increased soil organic matter and available phosphorus and potassium content. Treatment with FT1 200 kg/mu straw was found to be superior in improving soil fertility. Metagenomic DNA sequencing revealed that different fertiliser treatments resulted in changes in the microbial community composition. In soil treated with FT2 300 kg/mu straw for 60 days, the predominant bacterial phyla were Proteobacteria, Actinobacteria, and Verrucomicrobia, whereas Cyanobacteria, Basidiomycota, and Chlorophyta were found in high abundance in soil samples treated with FT1 200 kg/mu straw for 30 days. Functional annotation of metagenomic sequences revealed that genes involved in metabolic pathways were among the most abundant type. PCoA analysis clearly separated the samples containing straw compost fertiliser and chemical fertiliser. A significant correlation between soil properties and the dominant phyla was identified.}, } @article {pmid30992350, year = {2019}, author = {Cobián Güemes, AG and Lim, YW and Quinn, RA and Conrad, DJ and Benler, S and Maughan, H and Edwards, R and Brettin, T and Cantú, VA and Cuevas, D and Hamidi, R and Dorrestein, P and Rohwer, F}, title = {Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, pmid = {30992350}, issn = {2150-7511}, mesh = {Adult ; Case-Control Studies ; Coinfection/complications ; Cystic Fibrosis/*complications/microbiology ; Disease Management ; *Disease Progression ; Escherichia coli Infections/*diagnosis ; Fatal Outcome ; Gene Expression Profiling ; *Genomics ; Humans ; Lung/*microbiology/physiopathology ; Male ; Metabolome ; *Metabolomics ; Metagenome ; Microbiota ; Shiga Toxin/genetics ; Shiga-Toxigenic Escherichia coli/genetics/pathogenicity ; }, abstract = {Pulmonary exacerbations are the leading cause of death in cystic fibrosis (CF) patients. To track microbial dynamics during acute exacerbations, a CF rapid response (CFRR) strategy was developed. The CFRR relies on viromics, metagenomics, metatranscriptomics, and metabolomics data to rapidly monitor active members of the viral and microbial community during acute CF exacerbations. To highlight CFRR, a case study of a CF patient is presented, in which an abrupt decline in lung function characterized a fatal exacerbation. The microbial community in the patient's lungs was closely monitored through the multi-omics strategy, which led to the identification of pathogenic shigatoxigenic Escherichia coli (STEC) expressing Shiga toxin. This case study illustrates the potential for the CFRR to deconstruct complicated disease dynamics and provide clinicians with alternative treatments to improve the outcomes of pulmonary exacerbations and expand the life spans of individuals with CF.IMPORTANCE Proper management of polymicrobial infections in patients with cystic fibrosis (CF) has extended their life span. Information about the composition and dynamics of each patient's microbial community aids in the selection of appropriate treatment of pulmonary exacerbations. We propose the cystic fibrosis rapid response (CFRR) as a fast approach to determine viral and microbial community composition and activity during CF pulmonary exacerbations. The CFRR potential is illustrated with a case study in which a cystic fibrosis fatal exacerbation was characterized by the presence of shigatoxigenic Escherichia coli The incorporation of the CFRR within the CF clinic could increase the life span and quality of life of CF patients.}, } @article {pmid30992349, year = {2019}, author = {Aleti, G and Baker, JL and Tang, X and Alvarez, R and Dinis, M and Tran, NC and Melnik, AV and Zhong, C and Ernst, M and Dorrestein, PC and Edlund, A}, title = {Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, pmid = {30992349}, issn = {2150-7511}, support = {F32 DE026947/DE/NIDCR NIH HHS/United States ; K99 DE024543/DE/NIDCR NIH HHS/United States ; R00 DE024543/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/genetics/isolation & purification ; Biosynthetic Pathways/*genetics ; Child ; Child, Preschool ; Computational Biology ; Dental Caries/microbiology ; Dysbiosis ; Humans ; Mass Spectrometry ; Metagenome ; *Microbial Interactions ; Microbiota/*genetics ; Mouth/*microbiology ; *Multigene Family ; Periodontitis/microbiology ; Saliva/microbiology ; }, abstract = {Small molecules are the primary communication media of the microbial world. Recent bioinformatic studies, exploring the biosynthetic gene clusters (BGCs) which produce many small molecules, have highlighted the incredible biochemical potential of the signaling molecules encoded by the human microbiome. Thus far, most research efforts have focused on understanding the social language of the gut microbiome, leaving crucial signaling molecules produced by oral bacteria and their connection to health versus disease in need of investigation. In this study, a total of 4,915 BGCs were identified across 461 genomes representing a broad taxonomic diversity of oral bacteria. Sequence similarity networking provided a putative product class for more than 100 unclassified novel BGCs. The newly identified BGCs were cross-referenced against 254 metagenomes and metatranscriptomes derived from individuals either with good oral health or with dental caries or periodontitis. This analysis revealed 2,473 BGCs, which were differentially represented across the oral microbiomes associated with health versus disease. Coabundance network analysis identified numerous inverse correlations between BGCs and specific oral taxa. These correlations were present in healthy individuals but greatly reduced in individuals with dental caries, which may suggest a defect in colonization resistance. Finally, corroborating mass spectrometry identified several compounds with homology to products of the predicted BGC classes. Together, these findings greatly expand the number of known biosynthetic pathways present in the oral microbiome and provide an atlas for experimental characterization of these abundant, yet poorly understood, molecules and socio-chemical relationships, which impact the development of caries and periodontitis, two of the world's most common chronic diseases.IMPORTANCE The healthy oral microbiome is symbiotic with the human host, importantly providing colonization resistance against potential pathogens. Dental caries and periodontitis are two of the world's most common and costly chronic infectious diseases and are caused by a localized dysbiosis of the oral microbiome. Bacterially produced small molecules, often encoded by BGCs, are the primary communication media of bacterial communities and play a crucial, yet largely unknown, role in the transition from health to dysbiosis. This study provides a comprehensive mapping of the BGC repertoire of the human oral microbiome and identifies major differences in health compared to disease. Furthermore, BGC representation and expression is linked to the abundance of particular oral bacterial taxa in health versus dental caries and periodontitis. Overall, this study provides a significant insight into the chemical communication network of the healthy oral microbiome and how it devolves in the case of two prominent diseases.}, } @article {pmid30989804, year = {2019}, author = {Mediavilla, O and Geml, J and Olaizola, J and Oria-de-Rueda, JA and Baldrian, P and Martín-Pinto, P}, title = {Effect of forest fire prevention treatments on bacterial communities associated with productive Boletus edulis sites.}, journal = {Microbial biotechnology}, volume = {12}, number = {6}, pages = {1188-1198}, pmid = {30989804}, issn = {1751-7915}, mesh = {Bacteria/*classification/*genetics ; Basidiomycota/*growth & development ; Cistus/growth & development/*microbiology ; DNA Barcoding, Taxonomic ; Metagenomics ; Microbial Interactions ; *Microbiota ; *Soil Microbiology ; Wildfires/*prevention & control ; }, abstract = {Cistus ladanifer scrublands, traditionally considered as unproductive, have nonetheless been observed to produce large quantities of king bolete (Boletus edulis) fruitbodies. These pyrophytic scrublands are prone to wildfires, which severely affect fungi, hence the need for fire prevention in producing C. ladanifer scrublands. In addition, B. edulis productions have severely decreased in the last years. A deeper understanding of the B. edulis life cycle and of biotic and abiotic factors influencing sporocarp formation is needed to implement management practices that facilitate B. edulis production. For example, some bacteria likely are involved in sporocarp production, representing a key part in the triple symbiosis (plant-fungus-bacteria). In this study, we used soil DNA metabarcoding in C. ladanifer scrublands to (i) assess the effect of site history and fire prevention treatment on bacterial richness and community composition; (ii) test if there was any correlation between various taxonomic groups of bacteria and mycelial biomass and sporocarp production of B. edulis; and to (iii) identify indicator bacteria associated with the most productive B. edulis sites. Our results show that site history drives bacterial richness and community composition, while fire prevention treatments have a weaker, but still detectable effect, particularly in the senescent plots. Sporocarp production correlated positively with genera in Verrucomicrobia. Several genera, e.g. Azospirillum and Gemmatimonas, were identified as indicators of the most productive sites, suggesting a potential biological role in B. edulis fructification. This study provides a better understanding of the triple symbiosis (plant-fungus-bacteria) involved in C. ladanifer-B. edulis systems.}, } @article {pmid30989782, year = {2019}, author = {Guo, MY and Hou, CJ and Bian, MH and Shen, CH and Zhang, SY and Huo, DQ and Ma, Y}, title = {Characterization of microbial community profiles associated with quality of Chinese strong-aromatic liquor through metagenomics.}, journal = {Journal of applied microbiology}, volume = {127}, number = {3}, pages = {750-762}, doi = {10.1111/jam.14279}, pmid = {30989782}, issn = {1365-2672}, support = {31171684//National Natural Science Foundation of China (NSFC)/ ; 2010NZ0093//Science and Technology Support Program of Sichuan Province (STSP-SC)/ ; 2013FZ0043//Science and Technology Support Program of Sichuan Province (STSP-SC)/ ; GY2015-01//Workstation in Sichuan Province/ ; }, mesh = {Alcoholic Beverages/*microbiology ; Bacteria/*classification/genetics ; China ; *Fermentation ; Metagenomics ; Microbiota/*genetics ; Sequence Analysis, DNA ; }, abstract = {AIMS: Microorganisms in fermentation pits (FPs) play key roles for Chinese-strong-aromatic-liquor (CSAL) production. However, the microbial community in the FPs is still poorly understood. Here, the aim of this study was to reveal the diversity and potential functions of microbiota in FPs.

METHODS AND RESULTS: Sequencing-by-synthesis-based metagenomic sequencing and annotation results revealed that the microbiota of FPs was primarily composed of Firmicutes (54·6%), Euryarchaeota (15·3%), Bacteroidetes (10·1%), Gammaproteobacteria (5·8%), Opisthokonta (5·7%) and Unclassified_Bacteria (2·3%). And 133 genera were identified as the dominant genera of this fermentative food. Lactobacillus, Sedimentibacter, Syntrophomonas, Methanoculleus, Methanobacterium, Bacillus, Clostridium, Galactomyces, Candida, Pichia, Penicillium and Aspergillus were defined as active populations for biosynthesizing the characteristic volatile compounds of CSAL. The study also revealed that the microbial community structures changed significantly with different cellar ages and over different geographical regions. (i) The presence of Bacteroidetes was the most distinctive feature that characterized the different FPs ages. (ii) Distinct contents of Gammaproteobacteria and Euryarchaeota were observed at different positions in the FPs. (iii) Euryarchaeota markedly contributed to the generation of the character of the liquors with distinct geographical associations.

CONCLUSIONS: This study demonstrated that the changes of microbial communities determined the different quality characteristics of CSAL.

This research contributes to a deeper understanding of the FPs microbial composition and shows a new microbial resource for biotechnological applications.}, } @article {pmid30989200, year = {2019}, author = {Ye, L and Chan, EWC and Chen, S}, title = {Selective and suppressive effects of antibiotics on donor and recipient bacterial strains in gut microbiota determine transmission efficiency of blaNDM-1-bearing plasmids.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {7}, pages = {1867-1875}, doi = {10.1093/jac/dkz137}, pmid = {30989200}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/*administration & dosage ; Escherichia coli/*drug effects/genetics ; Gastrointestinal Microbiome/*drug effects ; Gene Transfer, Horizontal/*drug effects ; Klebsiella pneumoniae/*drug effects/genetics ; Male ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Rats, Sprague-Dawley ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: To test whether antibiotics of different functional categories exhibit differential potential in promoting transmission of MDR-encoding plasmids among members of the gut microbiome.

METHODS: Rats inoculated with blaNDM-1-bearing Klebsiella pneumoniae were subjected to treatment with different types of antibiotics. The structural changes in the gastrointestinal (GI) tract microbiome were determined by 16S rRNA sequencing and analysis. In addition, the efficiency of transmission of blaNDM-1-bearing plasmids to different subtypes of GI tract Escherichia coli was also confirmed in vitro.

RESULTS: We showed that drugs that are commonly used to treat Gram-negative bacterial infections, such as ampicillin and amoxicillin, could enrich both carbapenem-resistant Enterobacteriaceae (CRE) and antibiotic-susceptible E. coli in the GI tract, thereby promoting transmission of the blaNDM-1-bearing plasmid in the gut microbiome. In contrast, meropenem was found to minimize the population of CRE in the gut microbiome, hence treatment with this drug exhibited drastically lower potential to promote transmission of the blaNDM-1-bearing plasmid to the recipient strains. We further showed that an increased population size of Proteobacteria due to a suppressive effect on Firmicutes is a key factor in enhancing the efficiency of transmission of the blaNDM-1-bearing plasmid and hence dissemination of carbapenem-resistant strains.

CONCLUSIONS: This study depicted for the first time the effect of different antibiotics on the structure of the rat GI tract microbiome, which in turn determined the pattern and rate of transmission of the blaNDM-1-bearing plasmid. Such findings can help establish new guidelines for prudent antibiotic usage to minimize the chance of dissemination of mobile resistance elements among members of the GI tract microbiome.}, } @article {pmid30985920, year = {2019}, author = {Langan, EA and Künstner, A and Miodovnik, M and Zillikens, D and Thaçi, D and Baines, JF and Ibrahim, SM and Solbach, W and Knobloch, JK}, title = {Combined culture and metagenomic analyses reveal significant shifts in the composition of the cutaneous microbiome in psoriasis.}, journal = {The British journal of dermatology}, volume = {181}, number = {6}, pages = {1254-1264}, doi = {10.1111/bjd.17989}, pmid = {30985920}, issn = {1365-2133}, support = {//German Institute for Infection Research/International ; }, mesh = {Adult ; Bacteria/genetics/immunology/*isolation & purification ; Bacteriological Techniques ; DNA, Bacterial/genetics/isolation & purification ; Female ; Humans ; Male ; Metagenomics ; Microbiota/genetics/*immunology ; Middle Aged ; Prospective Studies ; Psoriasis/immunology/*microbiology ; RNA, Ribosomal, 16S/genetics ; Skin/immunology/*microbiology ; }, abstract = {BACKGROUND: The treatment of psoriasis has been revolutionized by the development of biologic therapies. However, the pathogenesis of psoriasis, in particular the role of the cutaneous microbiome, remains incompletely understood. Moreover, skin microbiome studies have relied heavily on 16S rRNA sequencing data in the absence of bacterial culture.

OBJECTIVES: To characterize and compare the cutaneous microbiome in 20 healthy controls and 23 patients with psoriasis using metagenomic analyses and to determine changes in the microbiome during treatment.

METHODS: Swabs from lesional and nonlesional skin from patients with psoriasis, and from controls matched for site and skin microenvironment, were analysed using both 16S rRNA sequencing and traditional culture combined with mass spectrometry (MALDI-TOF) in a prospective study.

RESULTS: Psoriasis was associated with an increased abundance of Firmicutes and a corresponding reduction in Actinobacteria, most marked in lesional skin, and at least partially reversed during systemic treatment. Shifts in bacterial community composition in lesional sites were reflected in similar changes in culturable bacteria, although changes in the microbiota over repeated swabbing were detectable only with sequencing. The composition of the microbial communities varied by skin site and microenvironment. Prevotella and Staphylococcus were significantly associated with lesional skin, and Anaerococcus and Propionibacterium with nonlesional skin. There were no significant differences in the amount of bacteria cultured from the skin of healthy controls and patients with psoriasis.

CONCLUSIONS: Shifts in the cutaneous microbiome in psoriasis, particularly during treatment, may shed new light on the pathogenesis of the disease and may be clinically exploited to predict treatment response. What's already known about this topic? Alterations in the composition of the cutaneous microbiome have been described in psoriasis, although methodological differences in study design prevent direct comparison of results. To date, most cutaneous microbiome studies have focused on 16S rRNA sequencing data, including both living and dead bacteria. What does this study add? This prospective observational study confirms that changes in the composition of the cutaneous microbiome, detected by 16S rRNA sequencing, are consistent with those identified by bacterial culture and mass spectrometry. The changes in the microbiome during antipsoriasis therapy should be further investigated to determine whether these represent potential novel biomarkers of treatment response. What is the translational message? Characterization of cutaneous microbiota may ultimately move into the clinic to help facilitate treatment selection, not only by optimizing currently available treatments, but also by identifying new therapeutic targets.}, } @article {pmid30985198, year = {2019}, author = {Aagaard, K}, title = {Feeding Babies and Bugs.}, journal = {Breastfeeding medicine : the official journal of the Academy of Breastfeeding Medicine}, volume = {14}, number = {S1}, pages = {S7-S8}, doi = {10.1089/bfm.2019.0028}, pmid = {30985198}, issn = {1556-8342}, mesh = {*Breast Feeding ; Cesarean Section/adverse effects ; Diet ; Epigenesis, Genetic ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Maternal Behavior ; Metagenome ; Milk, Human/chemistry/microbiology ; Pregnancy ; Prenatal Exposure Delayed Effects/genetics/microbiology ; Uterus/microbiology ; }, } @article {pmid30983011, year = {2019}, author = {Ovadia, C and Perdones-Montero, A and Spagou, K and Smith, A and Sarafian, MH and Gomez-Romero, M and Bellafante, E and Clarke, LCD and Sadiq, F and Nikolova, V and Mitchell, A and Dixon, PH and Santa-Pinter, N and Wahlström, A and Abu-Hayyeh, S and Walters, JRF and Marschall, HU and Holmes, E and Marchesi, JR and Williamson, C}, title = {Enhanced Microbial Bile Acid Deconjugation and Impaired Ileal Uptake in Pregnancy Repress Intestinal Regulation of Bile Acid Synthesis.}, journal = {Hepatology (Baltimore, Md.)}, volume = {70}, number = {1}, pages = {276-293}, pmid = {30983011}, issn = {1527-3350}, support = {//Tommy's Baby Charity/International ; //Imperial College Healthcare NHS Trust/International ; P30874/WT_/Wellcome Trust/United Kingdom ; //King's College London/International ; //NIHR Imperial Biomedical Research Centre/International ; //Genesis Research Trust/International ; /WT_/Wellcome Trust/United Kingdom ; //NIHR Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust and King's College London/International ; //National Institute for Health Research Biomedical Research Centres at Guy's and St Thomas' NHS Foundation Trust/International ; //ICP Support/International ; //Tommy's/International ; }, mesh = {Amidohydrolases/genetics ; Animals ; Bacteroides/isolation & purification ; Cecum/drug effects/microbiology ; Cholic Acids/*blood/pharmacology ; Enterocytes/drug effects ; Female ; *Gastrointestinal Microbiome ; Humans ; *Intestinal Reabsorption ; Mice, Inbred C57BL ; Pregnancy/*blood ; Receptors, Cytoplasmic and Nuclear/agonists/*metabolism ; }, abstract = {Pregnancy is associated with progressive hypercholanemia, hypercholesterolemia, and hypertriglyceridemia, which can result in metabolic disease in susceptible women. Gut signals modify hepatic homeostatic pathways, linking intestinal content to metabolic activity. We sought to identify whether enteric endocrine signals contribute to raised serum bile acids observed in human and murine pregnancies, by measuring fibroblast growth factor (FGF) 19/15 protein and mRNA levels, and 7α-hydroxy-4-cholesten-3-one. Terminal ileal farnesoid X receptor (FXR)-mediated gene expression and apical sodium bile acid transporter (ASBT) protein concentration were measured by qPCR and western blotting. Shotgun whole-genome sequencing and ultra-performance liquid chromatography tandem mass spectrometry were used to determine the cecal microbiome and metabonome. Targeted and untargeted pathway analyses were performed to predict the systemic effects of the altered metagenome and metabolite profiles. Dietary CA supplementation was used to determine whether the observed alterations could be overcome by intestinal bile acids functioning as FXR agonists. Human and murine pregnancy were associated with reduced intestinal FXR signaling, with lower FGF19/15 and resultant increased hepatic bile acid synthesis. Terminal ileal ASBT protein was reduced in murine pregnancy. Cecal bile acid conjugation was reduced in pregnancy because of elevated bile salt hydrolase-producing Bacteroidetes. CA supplementation induced intestinal FXR signaling, which was not abrogated by pregnancy, with strikingly similar changes to the microbiota and metabonome as identified in pregnancy. Conclusion: The altered intestinal microbiota of pregnancy enhance bile acid deconjugation, reducing ileal bile acid uptake and lowering FXR induction in enterocytes. This exacerbates the effects mediated by reduced bile acid uptake transporters in pregnancy. Thus, in pregnant women and mice, there is reduced FGF19/15-mediated hepatic repression of hepatic bile acid synthesis, resulting in hypercholanemia.}, } @article {pmid30981666, year = {2019}, author = {Wang, JJ and Zhang, RQ and Zhai, QY and Liu, JC and Li, N and Liu, WX and Li, L and Shen, W}, title = {Metagenomic analysis of gut microbiota alteration in a mouse model exposed to mycotoxin deoxynivalenol.}, journal = {Toxicology and applied pharmacology}, volume = {372}, number = {}, pages = {47-56}, doi = {10.1016/j.taap.2019.04.009}, pmid = {30981666}, issn = {1096-0333}, mesh = {Animals ; Bacteria/*drug effects/genetics/metabolism ; Cecum/*drug effects/microbiology ; DNA, Bacterial/*genetics ; Dysbiosis ; Feces/microbiology ; *Food Microbiology ; Gastrointestinal Microbiome/*drug effects ; *Genome, Bacterial ; Metagenomics/*methods ; Mice ; Trichothecenes/*toxicity ; }, abstract = {As one of the most prevalent contaminants in animal and human food, the deleterious effects of trichothecene mycotoxin deoxynivalenol (DON) warrant extensive investigation. Here, to assess the effects of DON exposure to the populations of gut microbiota, four-weeks-old mice were exposed to different doses (1.0 and 5.0 mg/kg) of DON every two days for 14 days. The contents of the cecum were then collected for DNA extraction and metagenomic shotgun sequencing, in order to detect alterations of the gut microbiota. We found that the average body weight and daily gain in the high dose DON treated group decreased. Metagenomic analysis demonstrated that the relative abundance of Firmicutes in the low and Bacteroidetes in the high dose groups increased compared to that in the untreated control group. Moreover, using gene calling and functional annotation, we found that large numbers of biosynthesis and degradation dependent populations were altered. As a result, metabolism pathways including sphingolipid, protein digestion/absorption, and lipoic acid pathways in the high dose DON exposed group dramatically fluctuated in comparison to the control and low dose groups. In addition, metagenomic binning identified ten microbiota genome drafts, with high levels of completeness, that further explain the DON-induced intestinal toxicity. Our findings suggested that DON exposure significantly impacted the microbiota community in the mouse, causing biosynthesis and degradation damage and metabolism pathway disorders.}, } @article {pmid30980731, year = {2019}, author = {Tang, H and Xiao, X and Xu, Y and Li, C and Cheng, K and Pan, X and Li, W}, title = {Utilization of carbon sources in the rice rhizosphere and nonrhizosphere soils with different long-term fertilization management.}, journal = {Journal of basic microbiology}, volume = {59}, number = {6}, pages = {621-631}, doi = {10.1002/jobm.201800736}, pmid = {30980731}, issn = {1521-4028}, support = {31872851//National Natural Science Foundation of China/ ; 2017JJ1018//Hunan Provincial Natural Science Foundation of China/ ; }, mesh = {Agriculture/methods ; Bacteria/classification/genetics/isolation & purification/metabolism ; Bacterial Proteins/metabolism ; Carbon/*metabolism ; China ; Fertilizers/*analysis ; *Microbial Consortia ; Oryza/*microbiology ; *Rhizosphere ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {Carbon (C) plays an important role in the interaction between plant and rhizosphere microbial communities, but there is still limited information about how C source utilization soil microbial structure responds to soil fertility changes under the double-cropping rice (Oryza sativa L.) system in Southern China paddy fields. Therefore, the effects of long-term (33 years) fertilizer regimes on the characteristics of C utilization in both rhizosphere and nonrhizosphere soils under double-cropping rice fields in Southern China were investigated by using the metagenome sequencing technology. The experiment began in 1986, and included five fertilizer treatments: without fertilizer input (CK), chemical fertilizer alone (MF), rice straw residue and chemical fertilizer (RF), 30% organic matter, and 70% chemical fertilizer (LOM), and 60% organic matter and 40% chemical fertilizer (HOM). The results showed that the relative abundance of Gemmatimonadetes and Planctomycetia in both the rhizosphere and nonrhizosphere soils was increased by application of rice straw residue and organic manure, whereas the relative abundance of Gammaproteobacteria and Nitrospira was promoted by application of inorganic fertilizers. The largest group of clusters of orthologous groups of proteins categories was "amino acid transport and metabolism" with 16.46% unigenes, followed by "general function prediction only" (12.23%). Regarding the gene ontology categories, biological process were the largest category (174 949, 46.40%), followed by cellular component (126 766, 33.62%), and molecular function (110 353, 29.26%). The principal coordinate analysis indicated that different parts of the root zone were the most important factors affecting the variation of C source utilization bacteria community, and the different fertilizer treatments were the second important factor affecting the variation of C source utilization bacteria community. As a result, the application of fertilization practices had significant effects on the abundance and community composition of C source utilization microbes in paddy soils. The results showed that the combined application of rice straw residue or organic manure with chemical fertilizer practices significantly increases the C source utilization of soil microorganisms in double-cropping rice fields.}, } @article {pmid30979963, year = {2019}, author = {Singer, GAC and Fahner, NA and Barnes, JG and McCarthy, A and Hajibabaei, M}, title = {Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5991}, pmid = {30979963}, issn = {2045-2322}, mesh = {*Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Environmental/*genetics ; *Seawater ; Sequence Analysis, DNA ; }, abstract = {The characterization of biodiversity is a crucial element of ecological investigations as well as environmental assessment and monitoring activities. Increasingly, amplicon-based environmental DNA metabarcoding (alternatively, marker gene metagenomics) is used for such studies given its ability to provide biodiversity data from various groups of organisms simply from analysis of bulk environmental samples such as water, soil or sediments. The Illumina MiSeq is currently the most popular tool for carrying out this work, but we set out to determine whether typical studies were reading enough DNA to detect rare organisms (i.e., those that may be of greatest interest such as endangered or invasive species) present in the environment. We collected sea water samples along two transects in Conception Bay, Newfoundland and analyzed them on the MiSeq with a sequencing depth of 100,000 reads per sample (exceeding the 60,000 per sample that is typical of similar studies). We then analyzed these same samples on Illumina's newest high-capacity platform, the NovaSeq, at a depth of 7 million reads per sample. Not surprisingly, the NovaSeq detected many more taxa than the MiSeq thanks to its much greater sequencing depth. However, contrary to our expectations this pattern was true even in depth-for-depth comparisons. In other words, the NovaSeq can detect more DNA sequence diversity within samples than the MiSeq, even at the exact same sequencing depth. Even when samples were reanalyzed on the MiSeq with a sequencing depth of 1 million reads each, the MiSeq's ability to detect new sequences plateaued while the NovaSeq continued to detect new sequence variants. These results have important biological implications. The NovaSeq found 40% more metazoan families in this environment than the MiSeq, including some of interest such as marine mammals and bony fish so the real-world implications of these findings are significant. These results are most likely associated to the advances incorporated in the NovaSeq, especially a patterned flow cell, which prevents similar sequences that are neighbours on the flow cell (common in metabarcoding studies) from being erroneously merged into single spots by the sequencing instrument. This study sets the stage for incorporating eDNA metabarcoding in comprehensive analysis of oceanic samples in a wide range of ecological and environmental investigations.}, } @article {pmid30979882, year = {2019}, author = {Kelly, LW and Nelson, CE and Haas, AF and Naliboff, DS and Calhoun, S and Carlson, CA and Edwards, RA and Fox, MD and Hatay, M and Johnson, MD and Kelly, ELA and Lim, YW and Macherla, S and Quinlan, ZA and Silva, GGZ and Vermeij, MJA and Zgliczynski, B and Sandin, SA and Smith, JE and Rohwer, F}, title = {Diel population and functional synchrony of microbial communities on coral reefs.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1691}, pmid = {30979882}, issn = {2041-1723}, mesh = {Alteromonas ; *Coral Reefs ; Ecosystem ; Environmental Monitoring ; Halomonas ; *Microbiota ; Organic Chemicals/chemistry ; Pacific Ocean ; *Photoperiod ; Psychrobacter ; RNA, Ribosomal/chemistry ; Roseobacter ; }, abstract = {On coral reefs, microorganisms are essential for recycling nutrients to primary producers through the remineralization of benthic-derived organic matter. Diel investigations of reef processes are required to holistically understand the functional roles of microbial players in these ecosystems. Here we report a metagenomic analysis characterizing microbial communities in the water column overlying 16 remote forereef sites over a diel cycle. Our results show that microbial community composition is more dissimilar between day and night samples collected from the same site than between day or night samples collected across geographically distant reefs. Diel community differentiation is largely driven by the flux of Psychrobacter sp., which is two-orders of magnitude more abundant during the day. Nighttime communities are enriched with species of Roseobacter, Halomonas, and Alteromonas encoding a greater variety of pathways for carbohydrate catabolism, further illustrating temporal patterns of energetic provisioning between different marine microbes. Dynamic diel fluctuations of microbial populations could also support the efficient trophic transfer of energy posited in coral reef food webs.}, } @article {pmid30979841, year = {2019}, author = {Dalcin Martins, P and Frank, J and Mitchell, H and Markillie, LM and Wilkins, MJ}, title = {Wetland Sediments Host Diverse Microbial Taxa Capable of Cycling Alcohols.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {12}, pages = {}, pmid = {30979841}, issn = {1098-5336}, mesh = {Alcohols/*metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; Geologic Sediments/*microbiology ; Metagenome ; Microbiota ; North Dakota ; Sequence Analysis, DNA ; Wetlands ; }, abstract = {Alcohols are commonly derived from the degradation of organic matter and yet are rarely measured in environmental samples. Wetlands in the Prairie Pothole Region (PPR) support extremely high methane emissions and the highest sulfate reduction rates reported to date, likely contributing to a significant proportion of organic matter mineralization in this system. While ethanol and isopropanol concentrations up to 4 to 5 mM in PPR wetland pore fluids have been implicated in sustaining these high rates of microbial activity, the mechanisms that support alcohol cycling in this ecosystem are poorly understood. We leveraged metagenomic and transcriptomic tools to identify genes, pathways, and microorganisms potentially accounting for alcohol cycling in PPR wetlands. Phylogenetic analyses revealed diverse alcohol dehydrogenases and putative substrates. Alcohol dehydrogenase and aldehyde dehydrogenase genes were included in 62 metagenome-assembled genomes (MAGs) affiliated with 16 phyla. The most frequently encoded pathway (in 30 MAGs) potentially accounting for alcohol production was a Pyrococcus furiosus-like fermentation which can involve pyruvate:ferredoxin oxidoreductase (PFOR). Transcripts for 93 of 137 PFOR genes in these MAGs were detected, as well as for 158 of 243 alcohol dehydrogenase genes retrieved from these same MAGs. Mixed acid fermentation and heterofermentative lactate fermentation were also frequently encoded. Finally, we identified 19 novel putative isopropanol dehydrogenases in 15 MAGs affiliated with Proteobacteria, Acidobacteria, Chloroflexi, Planctomycetes, Ignavibacteriae, Thaumarchaeota, and the candidate divisions KSB1 and Rokubacteria We conclude that diverse microorganisms may use uncommon and potentially novel pathways to produce ethanol and isopropanol in PPR wetland sediments.IMPORTANCE Understanding patterns of organic matter degradation in wetlands is essential for identifying the substrates and mechanisms supporting greenhouse gas production and emissions from wetlands, the main natural source of methane in the atmosphere. Alcohols are common fermentation products but are poorly studied as key intermediates in organic matter degradation in wetlands. By investigating genes, pathways, and microorganisms potentially accounting for the high concentrations of ethanol and isopropanol measured in Prairie Pothole wetland sediments, this work advanced our understanding of alcohol fermentations in wetlands linked to extremely high greenhouse gas emissions. Moreover, the novel alcohol dehydrogenases and microbial taxa potentially involved in alcohol metabolism may serve biotechnological efforts in bioengineering commercially valuable alcohol production and in the discovery of novel isopropanol producers or isopropanol fermentation pathways.}, } @article {pmid30978480, year = {2019}, author = {Reddy, B and Pandey, J and Dubey, SK}, title = {Assessment of environmental gene tags linked with carbohydrate metabolism and chemolithotrophy associated microbial community in River Ganga.}, journal = {Gene}, volume = {704}, number = {}, pages = {31-41}, doi = {10.1016/j.gene.2019.04.004}, pmid = {30978480}, issn = {1879-0038}, mesh = {Animals ; Bacteria/classification/genetics/growth & development ; Carbohydrate Metabolism/*genetics ; Chemoautotrophic Growth/*genetics ; DNA Barcoding, Taxonomic ; Environment ; Geologic Sediments/*microbiology ; Humans ; India ; Metabolic Networks and Pathways/genetics ; Metagenome ; *Metagenomics/methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; }, abstract = {The microbial community mediated biogeochemical cycles play important role in global C-cycle and display a sensitive response to environmental changes. Limited information is available on microbial composition and functional diversity controlling biogeochemical cycles in the riverine environment. The Ganga River water and sediment samples were studied for environmental gene tags with reference to carbohydrate metabolism, photoheterotrophy and chemolithotrophy using high throughput shotgun metagenomic sequencing and functional annotation. The diversity of environmental gene tags specific microbial community was annotated against reference sequence database using Kaiju taxonomic classifier. The metagenomic analyses revealed that the river harbored a broad range of carbohydrate and energy metabolism genes. The in-depth investigation of metagenomic data revealed that the enzymes associated with reverse TCA cycle, Calvin-Benson cycle enzyme RuBisCO, starch and sucrose metabolism genes were highly abundant. The enzymes associated with sulfur metabolism such as EC:2.7.7.4 (sulfate to ammonium per sulfate), EC:1.8.1.2, EC:1.8.7.1 (sulfite to H2S) were prevalent in both the class of samples. The principal component analysis of the functional profiles revealed that the water and sediment samples were clustered distinctly suggesting that both the sites had variable abundance of functional genes and associated microbiota. The taxonomic classification showed abundance of Proteobacteria, Actinobacteria and Bacteroidetes phyla. Also, the metagenomic study showed the presence of purple sulfur bacteria viz. Thiodictyon, Nitrosococcus and purple non-sulfur bacteria viz. Bradyrhozobium and Rhodobacter. The study demonstrates that the Ganga River microbiome has prevalence of functional genes involved in carbohydrate anabolism and catabolism, and CO2 fixation with great prospects in cellulose and sulfide degrading enzyme production and characterization.}, } @article {pmid30974142, year = {2019}, author = {Cheng, Y and Sibusiso, L and Hou, L and Jiang, H and Chen, P and Zhang, X and Wu, M and Tong, H}, title = {Sargassum fusiforme fucoidan modifies the gut microbiota during alleviation of streptozotocin-induced hyperglycemia in mice.}, journal = {International journal of biological macromolecules}, volume = {131}, number = {}, pages = {1162-1170}, doi = {10.1016/j.ijbiomac.2019.04.040}, pmid = {30974142}, issn = {1879-0003}, mesh = {Animals ; Blood Glucose/*drug effects ; Chemical Phenomena ; Diabetes Mellitus, Experimental ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Profiling ; Hyperglycemia/*blood/drug therapy/*etiology ; Liver/drug effects/metabolism/pathology ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Oxidative Stress/drug effects ; Polysaccharides/*chemistry/*pharmacology ; Sargassum/*chemistry ; Spectrum Analysis ; Streptozocin/adverse effects ; Transcriptome ; }, abstract = {Diabetes is a complicated endocrine and metabolic disorder, which has become an epidemic health issue worldwide. Fucoidan is extensively distributed in the brown algae and several marine invertebrates exhibiting diverse biological activities. In the present study, the physicochemical property of Sargassum fusiforme fucoidan (SFF) and its effects on streptozotocin (STZ)-induced diabetic mice and gut microbiota were investigated. Diabetes mice not only showed abnormal blood glucose, but also accompanied by multiple symptoms, such as gradual emaciation, decreased body weight, increased food and water intake. Compared with diabetic mice after 6-week treatment, administration of SFF significantly decreased the fasting blood glucose, diet and water intake. Furthermore, SFF attenuated the pathological change in the heart and liver, improved the liver function, and suppressed oxidative stress in STZ-induced diabetic mice. Simultaneously, SFF significantly altered the gut microbiota in the faeces of diabetic mice, decreased the relative abundances of the diabetes-related intestinal bacteria, which is a potential mechanism for relieving the symptoms of diabetes. Therefore, SFF might be considered as one of the promising complementary and alternative medicines for the management of diabetes mellitus in future.}, } @article {pmid30971183, year = {2019}, author = {Kurilshikov, A and van den Munckhof, ICL and Chen, L and Bonder, MJ and Schraa, K and Rutten, JHW and Riksen, NP and de Graaf, J and Oosting, M and Sanna, S and Joosten, LAB and van der Graaf, M and Brand, T and Koonen, DPY and van Faassen, M and , and Slagboom, PE and Xavier, RJ and Kuipers, F and Hofker, MH and Wijmenga, C and Netea, MG and Zhernakova, A and Fu, J}, title = {Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk.}, journal = {Circulation research}, volume = {124}, number = {12}, pages = {1808-1820}, doi = {10.1161/CIRCRESAHA.118.314642}, pmid = {30971183}, issn = {1524-4571}, mesh = {Adult ; Aged ; Cardiovascular Diseases/*epidemiology/genetics/*metabolism ; Cohort Studies ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Metabolome/*physiology ; Middle Aged ; Netherlands/epidemiology ; Obesity/*epidemiology/genetics/*metabolism ; Phenotype ; Prospective Studies ; Risk Factors ; }, abstract = {RATIONALE: Altered gut microbial composition has been linked to cardiovascular diseases (CVDs), but its functional links to host metabolism and immunity in relation to CVD development remain unclear.

OBJECTIVES: To systematically assess functional links between the microbiome and the plasma metabolome, cardiometabolic phenotypes, and CVD risk and to identify diet-microbe-metabolism-immune interactions in well-documented cohorts.

METHODS AND RESULTS: We assessed metagenomics-based microbial associations between 231 plasma metabolites and microbial species and pathways in the population-based LLD (Lifelines DEEP) cohort (n=978) and a clinical obesity cohort (n=297). After correcting for age, sex, and body mass index, the gut microbiome could explain ≤11.1% and 16.4% of the variation in plasma metabolites in the population-based and obesity cohorts, respectively. Obese-specific microbial associations were found for lipid compositions in the VLDL, IDL, and LDL lipoprotein subclasses. Bacterial L-methionine biosynthesis and a Ruminococcus species were associated to cardiovascular phenotypes in obese individuals, namely atherosclerosis and liver fat content, respectively. Integration of microbiome-diet-inflammation analysis in relation to metabolic risk score of CVD in the population cohort revealed 48 microbial pathways associated to CVD risk that were largely independent of diet and inflammation. Our data also showed that plasma levels rather than fecal levels of short-chain fatty acids were relevant to inflammation and CVD risk.

CONCLUSIONS: This study presents the largest metagenome-based association study on plasma metabolism and microbiome relevance to diet, inflammation, CVD risk, and cardiometabolic phenotypes in both population-based and clinical obesity cohorts. Our findings identified novel bacterial species and pathways that associated to specific lipoprotein subclasses and revealed functional links between the gut microbiome and host health that provide a basis for developing microbiome-targeted therapy for disease prevention and treatment.}, } @article {pmid30968165, year = {2019}, author = {Rossmassler, K and Snow, CD and Taggart, D and Brown, C and De Long, SK}, title = {Advancing biomarkers for anaerobic o-xylene biodegradation via metagenomic analysis of a methanogenic consortium.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {10}, pages = {4177-4192}, doi = {10.1007/s00253-019-09762-7}, pmid = {30968165}, issn = {1432-0614}, support = {CBET 1438660//National Science Foundation/ ; }, mesh = {Anaerobiosis ; *Biotransformation ; Enzymes/*genetics ; *Genetic Markers ; Metagenomics ; Microbial Consortia/*genetics ; Xylenes/*metabolism ; }, abstract = {Quantifying functional biomarker genes and their transcripts provides critical lines of evidence for contaminant biodegradation; however, accurate quantification depends on qPCR primers that contain no, or minimal, mismatches with the target gene. Developing accurate assays has been particularly challenging for genes encoding fumarate-adding enzymes (FAE) due to the high level of genetic diversity in this gene family. In this study, metagenomics applied to a field-derived, o-xylene-degrading methanogenic consortium revealed genes encoding FAE that would not be accurately quantifiable by any previously available PCR assays. Sequencing indicated that a gene similar to the napthylmethylsuccinate synthase gene (nmsA) was most abundant, although benzylsuccinate synthase genes (bssA) also were present along with genes encoding alkylsuccinate synthase (assA). Upregulation of the nmsA-like gene was observed during o-xylene degradation. Protein homology modeling indicated that mutations in the active site, relative to a BssA that acts on toluene, increase binding site volume and accessibility, potentially to accommodate the relatively larger o-xylene. The new nmsA-like gene was also detected at substantial concentrations at field sites with a history of xylene contamination.}, } @article {pmid30967122, year = {2019}, author = {Ai, D and Li, X and Pan, H and Chen, J and Cram, JA and Xia, LC}, title = {Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 2}, pages = {185}, pmid = {30967122}, issn = {1471-2164}, support = {R01 HG006137/HG/NHGRI NIH HHS/United States ; }, mesh = {*Algorithms ; Bacteria/*classification/genetics ; Biodiversity ; Computational Biology/*methods ; *Metagenome ; *Microbial Interactions ; *Microbiota ; *Software ; }, abstract = {BACKGROUND: Discovering the key microbial species and environmental factors of microbial community and characterizing their relationships with other members are critical to ecosystem studies. The microbial co-occurrence patterns across a variety of environmental settings have been extensively characterized. However, previous studies were limited by their restriction toward pairwise relationships, while there was ample evidence of third-party mediated co-occurrence in microbial communities.

METHODS: We implemented and applied the triplet-based liquid association analysis in combination with the local similarity analysis procedure to microbial ecology data. We developed an intuitive scheme to visualize those complex triplet associations along with pairwise correlations. Using a time series from the marine microbial ecosystem as example, we identified pairs of operational taxonomic units (OTUs) where the strength of their associations appeared to relate to the values of a third "mediator" variable. These "mediator" variables appear to modulate the associations between pairs of bacteria.

RESULTS: Using this analysis, we were able to assess the OTUs' ability to regulate its functional partners in the community, typically not manifested in the pairwise correlation patterns. For example, we identified Flavobacteria as a multifaceted player in the marine microbial ecosystem, and its clades were involved in mediating other OTU pairs. By contrast, SAR11 clades were not active mediators of the community, despite being abundant and highly correlated with other OTUs. Our results suggested that Flavobacteria are more likely to respond to situations where particles and unusual sources of dissolved organic material are prevalent, such as after a plankton bloom. On the other hand, SAR11s are oligotrophic chemoheterotrophs with inflexible metabolisms, and their relationships with other organisms may be less governed by environmental or biological factors.

CONCLUSIONS: By integrating liquid association with local similarity analysis to explore the mediated co-varying dynamics, we presented a novel perspective and a useful toolkit to analyze and interpret time series data from microbial community. Our augmented association network analysis is thus more representative of the true underlying dynamic structure of the microbial community. The analytic software in this study was implemented as new functionalities of the ELSA (Extended local similarity analysis) tool, which is available for free download (http://bitbucket.org/charade/elsa).}, } @article {pmid30967118, year = {2019}, author = {Yang, P and Yu, S and Cheng, L and Ning, K}, title = {Meta-network: optimized species-species network analysis for microbial communities.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 2}, pages = {187}, pmid = {30967118}, issn = {1471-2164}, mesh = {Algorithms ; Bacteria/classification/*genetics/*isolation & purification ; Cohort Studies ; Data Mining/*methods ; *Gastrointestinal Microbiome ; *Gene Regulatory Networks ; Humans ; *Metagenome ; *Microbial Interactions ; Species Specificity ; Young Adult ; }, abstract = {BACKGROUND: The explosive growth of microbiome data provides ample opportunities to gain a better understanding of the microbes and their interactions in microbial communities. Given these massive data, optimized data mining methods become important and necessary to perform deep and comprehensive analysis. Among the various priorities for microbiome data mining, the examination of species-species co-occurrence patterns becomes one of the key themes in urgent need.

RESULTS: Hence, in this work, we propose the Meta-Network framework to lucubrate the microbial communities. Rooted in loose definitions of network (two species co-exist in a certain samples rather than all samples) as well as association rule mining (mining more complex forms of correlations like indirect correlation and mutual information), this framework outperforms other methods in restoring the microbial communities, based on two cohorts of microbial communities: (a) the loose definition strategy is capable to generate more reasonable relationships among species in the species-species co-occurrence network; (b) important species-species co-occurrence patterns could not be identified by other existing approaches, but could successfully generated by association rule mining.

CONCLUSIONS: Results have shown that the species-species co-occurrence network we generated are much more informative than those based on traditional methods. Meta-Network has consistently constructed more meaningful networks with biologically important clusters, hubs, and provides a general approach towards deciphering the species-species co-occurrence networks.}, } @article {pmid30967110, year = {2019}, author = {Hua, K and Zhang, X}, title = {Estimating the total genome length of a metagenomic sample using k-mers.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 2}, pages = {183}, pmid = {30967110}, issn = {1471-2164}, mesh = {Algorithms ; Datasets as Topic ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA ; *Software ; }, abstract = {BACKGROUND: Metagenomic sequencing is a powerful technology for studying the mixture of microbes or the microbiomes on human and in the environment. One basic task of analyzing metagenomic data is to identify the component genomes in the community. This task is challenging due to the complexity of microbiome composition, limited availability of known reference genomes, and usually insufficient sequencing coverage.

RESULTS: As an initial step toward understanding the complete composition of a metagenomic sample, we studied the problem of estimating the total length of all distinct component genomes in a metagenomic sample. We showed that this problem can be solved by estimating the total number of distinct k-mers in all the metagenomic sequencing data. We proposed a method for this estimation based on the sequencing coverage distribution of observed k-mers, and introduced a k-mer redundancy index (KRI) to fill in the gap between the count of distinct k-mers and the total genome length. We showed the effectiveness of the proposed method on a set of carefully designed simulation data corresponding to multiple situations of true metagenomic data. Results on real data indicate that the uncaptured genomic information can vary dramatically across metagenomic samples, with the potential to mislead downstream analyses.

CONCLUSIONS: We proposed the question of how long the total genome length of all different species in a microbial community is and introduced a method to answer it.}, } @article {pmid30967109, year = {2019}, author = {Abe, K and Hirayama, M and Ohno, K and Shimamura, T}, title = {ENIGMA: an enterotype-like unigram mixture model for microbial association analysis.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 2}, pages = {191}, pmid = {30967109}, issn = {1471-2164}, mesh = {Bacteria/*classification/genetics/isolation & purification ; Case-Control Studies ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Microbial Interactions ; Microbiota ; *Models, Biological ; Parkinson Disease/genetics/*microbiology ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: One of the major challenges in microbial studies is detecting associations between microbial communities and a specific disease. A specialized feature of microbiome count data is that intestinal bacterial communities form clusters called as "enterotype", which are characterized by differences in specific bacterial taxa, making it difficult to analyze these data under health and disease conditions. Traditional probabilistic modeling cannot distinguish between the bacterial differences derived from enterotype and those related to a specific disease.

RESULTS: We propose a new probabilistic model, named as ENIGMA (Enterotype-like uNIGram mixture model for Microbial Association analysis), which can be used to address these problems. ENIGMA enabled simultaneous estimation of enterotype-like clusters characterized by the abundances of signature bacterial genera and the parameters of environmental effects associated with the disease.

CONCLUSION: In the simulation study, we evaluated the accuracy of parameter estimation. Furthermore, by analyzing the real-world data, we detected the bacteria related to Parkinson's disease. ENIGMA is implemented in R and is available from GitHub (https://github.com/abikoushi/enigma).}, } @article {pmid30964393, year = {2019}, author = {Navarro-Barrón, E and Hernández, C and Llera-Herrera, R and García-Gasca, A and Gómez-Gil, B}, title = {Overfeeding a High-Fat Diet Promotes Sex-Specific Alterations on the Gut Microbiota of the Zebrafish (Danio rerio).}, journal = {Zebrafish}, volume = {16}, number = {3}, pages = {268-279}, doi = {10.1089/zeb.2018.1648}, pmid = {30964393}, issn = {1557-8542}, mesh = {Animals ; *Diet, High-Fat ; Eating/*physiology ; Female ; *Gastrointestinal Microbiome ; Male ; Random Allocation ; Sex Factors ; Zebrafish/*microbiology ; }, abstract = {Diet modulates the gut microbiota and is one of the main factors promoting obesity and overweight. In the present study, we investigated the effect of a high-fat diet (HFD) on the gut microbiota of the zebrafish (Danio rerio). Fish were separated into three groups and fed in different regimes: low fat, high fat, and high fat overfed; the experiments were performed on males and females separately. We analyzed more than 2.6 million sequences of variable region V3 of the 16S rRNA gene generated by the Illumina Miniseq platform, clustered to 97% similarity with vsearch and classified with the EzBioCloud database. The weight gain, condition factor (K), and body mass index were calculated as indicators of obesity. Multivariate analysis (PERMANOVA and ANOSIM) and diversity indices (Shannon and Dominance) revealed that overfeeding a HFD disturbs the gut microbiota differently in males and females suggesting that sex is a significant factor (p < 0.05) for the composition of the gut microbiota of zebrafish. The results also indicate that a HFD provided in a basal caloric regime does not promote obesity or alterations in the gut microbiota.}, } @article {pmid30962514, year = {2019}, author = {Tan, S and Liu, J and Fang, Y and Hedlund, BP and Lian, ZH and Huang, LY and Li, JT and Huang, LN and Li, WJ and Jiang, HC and Dong, HL and Shu, WS}, title = {Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics.}, journal = {The ISME journal}, volume = {13}, number = {8}, pages = {2044-2057}, pmid = {30962514}, issn = {1751-7370}, mesh = {Adaptation, Physiological ; *Biodiversity ; China ; Deltaproteobacteria/*genetics/physiology ; Ecology ; Gene Expression Profiling ; Iron/metabolism ; Metagenome/*genetics ; Metagenomics ; Mining ; Nitrogen Fixation ; Oxidation-Reduction ; Oxygen/metabolism ; Stress, Physiological ; Sulfides/chemistry ; Sulfur/*chemistry ; *Transcriptome ; }, abstract = {Several abundant but yet uncultivated bacterial groups exist in extreme iron- and sulfur-rich environments, and the physiology, biodiversity, and ecological roles of these bacteria remain a mystery. Here we retrieved four metagenome-assembled genomes (MAGs) from an artificial acid mine drainage (AMD) system, and propose they belong to a new deltaproteobacterial order, Candidatus Acidulodesulfobacterales. The distribution pattern of Ca. Acidulodesulfobacterales in AMDs across Southeast China correlated strongly with ferrous iron. Reconstructed metabolic pathways and gene expression profiles showed that they were likely facultatively anaerobic autotrophs capable of nitrogen fixation. In addition to dissimilatory sulfate reduction, encoded by dsrAB, dsrD, dsrL, and dsrEFH genes, these microorganisms might also oxidize sulfide, depending on oxygen concentration and/or oxidation reduction potential. Several genes with homology to those involved in iron metabolism were also identified, suggesting their potential role in iron cycling. In addition, the expression of abundant resistance genes revealed the mechanisms of adaptation and response to the extreme environmental stresses endured by these organisms in the AMD environment. These findings shed light on the distribution, diversity, and potential ecological role of the new order Ca. Acidulodesulfobacterales in nature.}, } @article {pmid30962186, year = {2019}, author = {Shah, NB and Allegretti, AS and Nigwekar, SU and Kalim, S and Zhao, S and Lelouvier, B and Servant, F and Serena, G and Thadhani, RI and Raj, DS and Fasano, A}, title = {Blood Microbiome Profile in CKD : A Pilot Study.}, journal = {Clinical journal of the American Society of Nephrology : CJASN}, volume = {14}, number = {5}, pages = {692-701}, pmid = {30962186}, issn = {1555-905X}, support = {K23 DK106479/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Aged ; Cross-Sectional Studies ; DNA, Bacterial/*blood ; Female ; *Gastrointestinal Microbiome ; Glomerular Filtration Rate ; Humans ; Male ; Metagenomics ; Middle Aged ; Pilot Projects ; RNA, Ribosomal, 16S/analysis ; Renal Insufficiency, Chronic/blood/*microbiology/physiopathology ; }, abstract = {BACKGROUND AND OBJECTIVES: The association between gut dysbiosis, high intestinal permeability, and endotoxemia-mediated inflammation is well established in CKD. However, changes in the circulating microbiome in patients with CKD have not been studied. In this pilot study, we compare the blood microbiome profile between patients with CKD and healthy controls using 16S ribosomal DNA sequencing.

Blood bacterial DNA was studied in buffy coat samples quantitatively by 16S PCR and qualitatively by 16S targeted metagenomic sequencing using a molecular pipeline specifically optimized for blood samples in a cross-sectional study comparing 20 nondiabetic patients with CKD and 20 healthy controls.

RESULTS: There were 22 operational taxonomic units significantly different between the two groups. 16S metagenomic sequencing revealed a significant reduction in α diversity (Chao1 index) in the CKD group compared with healthy controls (127±18 versus 145±31; P=0.04). Proteobacteria phylum, Gammaproteobacteria class, and Enterobacteriaceae and Pseudomonadaceae families were more abundant in the CKD group compared with healthy controls. Median 16S ribosomal DNA levels did not significantly differ between CKD and healthy groups (117 versus 122 copies/ng DNA; P=0.38). GFR correlated inversely with the proportion of Proteobacteria (r=-0.54; P≤0.01).

CONCLUSIONS: Our pilot study demonstrates qualitative differences in the circulating microbiome profile with lower α diversity and significant taxonomic variations in the blood microbiome in patients with CKD compared with healthy controls.}, } @article {pmid30962029, year = {2019}, author = {Brink, M and Rhode, C and Macey, BM and Christison, KW and Roodt-Wilding, R}, title = {Metagenomic assessment of body surface bacterial communities of the sea urchin, Tripneustes gratilla.}, journal = {Marine genomics}, volume = {47}, number = {}, pages = {100675}, doi = {10.1016/j.margen.2019.03.010}, pmid = {30962029}, issn = {1876-7478}, mesh = {Animals ; Aquaculture ; Bacteria/classification/*genetics ; *Metagenome ; Microbiota/*genetics ; Sea Urchins/*microbiology ; South Africa ; }, abstract = {Sea urchins, including Tripneustes gratilla, are susceptible to a disease known as bald sea urchin disease, which has the potential to lead to economic losses in this emerging aquaculture industry in South Africa. This disease is characterized by lesions that form on sea urchin exoskeletal surfaces. This study aimed to characterize the body surface bacterial communities associated with T. gratilla, using a 16S rDNA gene metagenomics approach, to provide insight into the bacterial agents associated with this aquaculture species, as well as with this balding disease. Bacterial samples were collected from non-lesioned healthy animals obtained from natural locations along the eastern coast of South Africa, as well as from different cultured cohorts: non-lesioned healthy-, lesioned diseased- and non-lesioned stressed animals. A total of 1,067,515 individual bacterial operational taxonomic units (OTUs) were identified, belonging to 133 family-, 123 genus- and 113 species level OTU groups. Alpha diversity analyses, based on Chao1, Shannon and Simpson indices, showed that there were no statistically significant differences (ANOVA; P > 0.05) between the respective cohorts, as all cohorts displayed a high degree of bacterial diversity. Similarly, beta diversity analyses (Non-metric multidimensional scaling) showed a large degree of overlapping OTUs across the four cohorts. Within each cohort, various OTUs commonly associated with marine environments were found, predominantly belonging to the families Vibrionaceae, Saprospiraceae, Flavobacteriaceae and Sphingomonadaceae. Differential abundance analysis (DESeq2) revealed that OTUs that are differentially abundant across cohorts were likely not responsible for this balding disease, suggesting that complex bacterial agents, rather than a specific pathogenic agent, are likely causing this disease. Furthermore, the putative metabolic functions assigned to the bacterial communities showed that heterotrophic bacteria appear to be responsible for tissue lysis of degrading animal matter. The results from this study, obtained through univariate and multivariate-based approaches, contributes to future management strategies of this emerging aquaculture species by providing insight into the bacterial communities associated with both natural and cultured environments.}, } @article {pmid30961521, year = {2019}, author = {Dos Santos, HRM and Argolo, CS and Argôlo-Filho, RC and Loguercio, LL}, title = {A 16S rDNA PCR-based theoretical to actual delta approach on culturable mock communities revealed severe losses of diversity information.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {74}, pmid = {30961521}, issn = {1471-2180}, mesh = {Bacteria/classification/growth & development ; Cacao/microbiology ; DNA Fingerprinting ; DNA Primers ; DNA, Bacterial/genetics ; DNA, Ribosomal/*genetics ; Endophytes/*classification ; *Genetic Variation ; *Microbiota ; *Models, Theoretical ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Stem Cells ; }, abstract = {BACKGROUND: Subunits of ribosomal RNA genes (rDNAs) characterized by PCR-based protocols have been the proxy for studies in microbial taxonomy, phylogenetics, evolution and ecology. However, relevant factors have shown to interfere in the experimental outputs in a variety of systems. In this work, a 'theoretical' to 'actual' delta approach was applied to data on culturable mock bacterial communities (MBCs) to study the levels of losses in operational taxonomic units (OTUs) detectability. Computational and lab-bench strategies based on 16S rDNA amplification by 799F and U1492R primers were employed, using a fingerprinting method with highly improved detectability of fragments as a case-study tool. MBCs were of two major types: in silico MBCs, assembled with database-retrieved sequences, and in vitro MBCs, with AluI digestions of PCR data generated from culturable endophytes isolated from cacao trees.

RESULTS: Interfering factors for the 16 s rDNA amplifications, such as the type of template, direct and nested PCR, proportion of chloroplast DNA from a tropical plant source (Virola officinalis), and biased-amplification by the primers resulted in altered bacterial 16S rDNA amplification, both on MBCs and V. officinalis leaf-extracted DNA. For the theoretical data, the maximum number of fragments for in silico and in vitro cuts were not significantly different from each other. Primers' preferences for certain sequences were detected, depending on the MBCs' composition prior to PCR. The results indicated overall losses from 2.3 up to 8.2 times in the number of OTUs detected from actual AluI digestions of MBCs when compared to in silico and in vitro theoretical data.

CONCLUSIONS: Due to all those effects, the final amplification profile of the bacterial community assembled was remarkably simplified when compared to the expected number of detectable fragments known to be present in the MBC. From these findings, the scope of hypotheses generation and conclusions from experiments based on PCR amplifications of bacterial communities was discussed.}, } @article {pmid30959166, year = {2019}, author = {Marón, CF and Kohl, KD and Chirife, A and Di Martino, M and Fons, MP and Navarro, MA and Beingesser, J and McAloose, D and Uzal, FA and Dearing, MD and Rowntree, VJ and Uhart, M}, title = {Symbiotic microbes and potential pathogens in the intestine of dead southern right whale (Eubalaena australis) calves.}, journal = {Anaerobe}, volume = {57}, number = {}, pages = {107-114}, doi = {10.1016/j.anaerobe.2019.04.003}, pmid = {30959166}, issn = {1095-8274}, mesh = {Animals ; Animals, Newborn ; Argentina ; Bacteria/*classification/*isolation & purification ; Bacteriological Techniques ; *Cadaver ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Metagenomics ; Whales/*microbiology ; }, abstract = {Between 2003 and 2017, at least 706 southern right whale (Eubalaena australis) calves died at the Península Valdés calving ground in Argentina. Pathogenic microbes are often suggested to be the cause of stranding events in cetaceans; however, to date there is no evidence supporting bacterial infections as a leading cause of right whale calf deaths in Argentina. We used high-throughput sequencing and culture methods to characterize the bacterial communities and to detect potential pathogens from the intestine of stranded calves. We analyzed small and large intestinal contents from 44 dead calves that stranded at Península Valdés from 2005 to 2010 and found 108 bacterial genera, most identified as Firmicutes or Bacteroidetes, and 9 genera that have been previously implicated in diseases of marine mammals. Only one operational taxonomic unit was present in all samples and identified as Clostridium perfringens type A. PCR results showed that all C. perfringens isolates (n = 38) were positive for alpha, 50% for beta 2 (n = 19) and 47% for enterotoxin (CPE) genes (n = 18). The latter is associated with food-poisoning and gastrointestinal diseases in humans and possibly other animals. The prevalence of the cpe gene found in the Valdés' calves is unusually high compared with other mammals. However, insufficient histologic evidence of gastrointestinal inflammation or necrosis (the latter possibly masked by autolysis) in the gut of stranded calves, and absence of enterotoxin detection precludes conclusions about the role of C. perfringens in calf deaths. Further work is required to determine whether C. perfringens or other pathogens detected in this study are causative agents of calf deaths at Península Valdés.}, } @article {pmid30958827, year = {2019}, author = {Martí, JM}, title = {Recentrifuge: Robust comparative analysis and contamination removal for metagenomics.}, journal = {PLoS computational biology}, volume = {15}, number = {4}, pages = {e1006967}, pmid = {30958827}, issn = {1553-7358}, mesh = {Algorithms ; Big Data ; Computational Biology/methods ; DNA Contamination ; High-Throughput Nucleotide Sequencing ; Humans ; Internet ; Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; Software ; Whole Genome Sequencing/methods ; }, abstract = {Metagenomic sequencing is becoming widespread in biomedical and environmental research, and the pace is increasing even more thanks to nanopore sequencing. With a rising number of samples and data per sample, the challenge of efficiently comparing results within a specimen and between specimens arises. Reagents, laboratory, and host related contaminants complicate such analysis. Contamination is particularly critical in low microbial biomass body sites and environments, where it can comprise most of a sample if not all. Recentrifuge implements a robust method for the removal of negative-control and crossover taxa from the rest of samples. With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications. In addition to contamination-subtracted samples, Recentrifuge provides shared and exclusive taxa per sample, thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics. Regarding the first area, Recentrifuge's novel approach has already demonstrated its benefits showing that microbiomes of Arctic and Antarctic solar panels display similar taxonomic profiles. In the clinical field, to confirm Recentrifuge's ability to analyze complex metagenomes, we challenged it with data coming from a metagenomic investigation of RNA in plasma that suffered from critical contamination to the point of preventing any positive conclusion. Recentrifuge provided results that yielded new biological insight into the problem, supporting the growing evidence of a blood microbiota even in healthy individuals, mostly translocated from the gut, the oral cavity, and the genitourinary tract. We also developed a synthetic dataset carefully designed to rate the robust contamination removal algorithm, which demonstrated a significant improvement in specificity while retaining a high sensitivity even in the presence of cross-contaminants. Recentrifuge's official website is www.recentrifuge.org. The data and source code are anonymously and freely available on GitHub and PyPI. The computing code is licensed under the AGPLv3. The Recentrifuge Wiki is the most extensive and continually-updated source of documentation for Recentrifuge, covering installation, use cases, testing, and other useful topics.}, } @article {pmid30957268, year = {2019}, author = {Tian, M and Chen, M and Bao, Y and Xu, C and Qin, Q and Zhang, W and He, Y and Shao, Q}, title = {Microbial contributions to bronchial asthma occurrence in children: A metagenomic study.}, journal = {Journal of cellular biochemistry}, volume = {120}, number = {8}, pages = {13853-13860}, doi = {10.1002/jcb.28658}, pmid = {30957268}, issn = {1097-4644}, mesh = {Adolescent ; Asthma/*epidemiology/*microbiology ; Bacteria/*genetics ; Biodiversity ; Case-Control Studies ; Child ; Child, Preschool ; Female ; Humans ; Male ; *Metagenomics ; }, abstract = {Bronchial asthma, a common chronic respiratory disease in children, is traditionally regarded as a noninfectious disease. Current hypotheses, however, argue that asthma can be caused by microbial infection. We, therefore, hypothesize that a variety of microbes are more commonly found in the sputum of children with asthma, and these microbes may contribute to the occurrence and development of asthma. The present study proposes to use metagenomic approach to explore microbial diversity and to identify the microbial community characteristics of sputum from children with asthma. We found that microbial communities in the sputum of children differed significantly between asthmatics and controls. Kruskal-Wallis testing showed that 16 phyla, 104 genera, and 159 species were significantly downregulated, whereas two phyla including Platyhelminthes phylum and Chordata phylum, two genera including Spirometra genus and Homo sapiens, and the Spirometra erinaceieuropaei species were significantly upregulated in asthma patients compared with controls (P < 0.05). Among them, H. sapiens and S. erinaceieuropaei exhibited 2.3- and 2.0-fold overabundance in asthmatics vs controls, respectively. Meanwhile, metastats assay demonstrated that 31 phyla, 400 genera, and 813 species were significantly downregulated, whereas two phyla, 10 genera, and 16 species were significantly upregulated in asthma patients compared with controls (P < 0.05). Among them, Tetrahymena thermophila and Candidatus Zinderia insecticola exhibited 4.7-fold overabundance in asthmatics vs controls. Our study establishes a link between microbial infection and the mechanisms leading to asthma development, which will be useful for developing novel diagnostic biomarkers and aiding in the prevention and control of asthma.}, } @article {pmid30956802, year = {2019}, author = {Keravec, M and Mounier, J and Guilloux, CA and Fangous, MS and Mondot, S and Vallet, S and Gouriou, S and Le Berre, R and Rault, G and Férec, C and Barbier, G and Lepage, P and Héry-Arnaud, G}, title = {Porphyromonas, a potential predictive biomarker of Pseudomonas aeruginosa pulmonary infection in cystic fibrosis.}, journal = {BMJ open respiratory research}, volume = {6}, number = {1}, pages = {e000374}, pmid = {30956802}, issn = {2052-4439}, mesh = {Adolescent ; Adult ; Biomarkers ; Child ; Cystic Fibrosis/*complications/immunology ; DNA, Bacterial/isolation & purification ; Female ; Follow-Up Studies ; France ; Humans ; Male ; Metagenomics ; Microbiota/genetics/immunology ; Porphyromonas/genetics/immunology/*isolation & purification ; Predictive Value of Tests ; Prognosis ; Prospective Studies ; Pseudomonas Infections/*diagnosis/etiology/microbiology ; Pseudomonas aeruginosa/immunology/*isolation & purification ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Respiratory Mucosa/*microbiology ; Sputum/microbiology ; Symbiosis/immunology ; Young Adult ; }, abstract = {INTRODUCTION: Pseudomonas aeruginosa pulmonary infections are the primary cause of morbi-mortality in patients with cystic fibrosis (CF). In this cohort study, the objective was to identify candidate biomarkers of P. aeruginosa infection within the airway microbiota.

METHODS: A 3-year prospective multicentre study (PYOMUCO study) was conducted in Western France and included patients initially P. aeruginosa free for at least 1 year. A 16S-targeted metagenomics approach was applied on iterative sputum samples of a first set of patients (n=33). The composition of airway microbiota was compared according to their P. aeruginosa status at the end of the follow-up (colonised vs non-colonised), and biomarkers associated with P. aeruginosa were screened. In a second step, the distribution of a candidate biomarker according to the two groups of patients was verified by qPCR on a second set of patients (n=52) coming from the same cohort and its load quantified throughout the follow-up.

RESULTS: Porphyromonas (mainly P. catoniae) was found to be an enriched phylotype in patients uninfected by P. aeruginosa (p<0.001). This result was confirmed by quantitative PCR. Conversely, in patients who became P. aeruginosa-positive, P. catoniae significantly decreased before P. aeruginosa acquisition (p=0.014).

DISCUSSION: Further studies on replication cohorts are needed to validate this potential predictive biomarker, which may be relevant for the follow-up in the early years of patients with CF. The identification of infection candidate biomarkers may offer new strategies for CF precision medicine.}, } @article {pmid30955771, year = {2019}, author = {Cotta, SR and Cadete, LL and van Elsas, JD and Andreote, FD and Dias, ACF}, title = {Exploring bacterial functionality in mangrove sediments and its capability to overcome anthropogenic activity.}, journal = {Marine pollution bulletin}, volume = {141}, number = {}, pages = {586-594}, doi = {10.1016/j.marpolbul.2019.03.001}, pmid = {30955771}, issn = {1879-3363}, mesh = {Bacteria/genetics/metabolism ; Biodiversity ; Brazil ; Carbon/metabolism ; Ecosystem ; Gene Transfer, Horizontal ; Geologic Sediments/*microbiology ; Metagenomics ; *Microbiota/genetics ; Sulfur/metabolism ; *Wetlands ; }, abstract = {Mangrove forests are highly productive yet vulnerable ecosystems that act as important carbon sinks ("blue carbon"). The objective of this work was to analyze the impact of anthropogenic activities on microbiome structure and functioning. The metagenomic analysis revealed that the taxonomic compositions were grossly similar across all mangrove microbiomes. Remarkably, these microbiomes, along the gradient of anthropogenic impact, showed fluctuations in the relative abundances of bacterial taxa predicted to be involved in sulfur cycling processes. Functions involved in sulfur metabolism, such as APS pathways (associated with sulfate reduction and sulfur oxidation processes) were prevalent across the microbiomes, being sox and dsrAB genes highly expressed on anthropogenically-impacted areas. Apparently, the oil-impacted microbiomes were more affected in taxonomic than in functional terms, as high functional redundancies were noted across them. The microbial gene diversity found was typical for a functional system, even following the previous disturbance.}, } @article {pmid30955749, year = {2019}, author = {Fernandes, C and Kankonkar, H and Meena, RM and Menezes, G and Shenoy, BD and Khandeparker, R}, title = {Metagenomic analysis of tarball-associated bacteria from Goa, India.}, journal = {Marine pollution bulletin}, volume = {141}, number = {}, pages = {398-403}, doi = {10.1016/j.marpolbul.2019.02.040}, pmid = {30955749}, issn = {1879-3363}, mesh = {Biodegradation, Environmental ; Environmental Monitoring/*methods ; Humans ; India ; Marinobacter/genetics/isolation & purification ; Metagenome/*genetics ; Metagenomics ; Microbiota/*genetics ; Petroleum/*analysis ; Polycyclic Aromatic Hydrocarbons/*analysis ; Proteobacteria/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Water Pollutants, Chemical/*analysis ; }, abstract = {The beaches of Goa state in India are frequently polluted with tarballs, specifically during pre-monsoon and monsoon seasons. Tarballs contain hydrocarbons, including polycyclic aromatic hydrocarbons, which pose significant environmental risks. Microbes associated with tarballs reportedly possess capabilities to degrade toxic hydrocarbons present in tarballs. In this study, bacterial diversity associated with tarballs from Vagator and Morjim beaches of north Goa was analysed based on V3-V4 regions of 16S rRNA gene sequenced using Illumina Miseq Platform. The Proteobacterial members were dominant in both Vagator (≥85.5%) and Morjim (≥94.0%) samples. Many of the identified taxa have been previously reported as hydrocarbon degraders (e.g. Halomonas, Marinobacter) or possible human pathogens (e.g. Acinetobacter, Klebsiella, Rhodococcus, Staphylococcus, Vibrio). This is the first study reported on a metagenomic analysis of bacteria associated with tarballs from Goa.}, } @article {pmid30953747, year = {2019}, author = {Wei, T and Bao, JY and Yang, HH and Lin, JF and Zheng, QW and Ye, ZW and Zou, Y and Li, X and Jiang, ZL and Guo, LQ}, title = {Musa basjoo regulates the gut microbiota in mice by rebalancing the abundance of probiotic and pathogen.}, journal = {Microbial pathogenesis}, volume = {131}, number = {}, pages = {205-211}, doi = {10.1016/j.micpath.2019.04.003}, pmid = {30953747}, issn = {1096-1208}, mesh = {Animal Feed ; Animals ; Bacteroides/physiology ; Cell Wall/metabolism ; China ; DNA, Ribosomal ; Disease Models, Animal ; Feces/microbiology ; Food Safety ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Lacticaseibacillus casei/physiology ; Lactobacillus plantarum/physiology ; Metagenomics ; Mice/*microbiology ; Mice, Inbred BALB C ; Musa/*chemistry ; *Probiotics/classification/pharmacology ; Specific Pathogen-Free Organisms ; }, abstract = {Musa basjoo is a kind of popular slimming fruit in southern China. However, even though the trophic component and physiological effect are well studied, its internal mechanism in reconstructing gut microbiota remains unclear. In this study, maturity of M. basjoo were divided into four levels. Results indicated that M. basjoo in level Ⅱ (with 35% maturity) represented the greatest increase in the growth in vitro of probiotics, Lactobacillus plantarum FMNP01 and Lactobacillus casei FMNP02. After feeding M. basjoo with the middle dose (2.67 g/kg·BW) to mice for 21 days, gut microbiota from mice feces was isolated and sequenced. Results of 16SrDNA sequencing showed that the scattered genera of gut microbiota were significantly gathered. The amounts of different pathogens were decreased, while probiotics such as genera Bacteroides and Roseburia were significantly increased (p < 0.05). Results of function prediction indicated that the reconstruction of gut microbiota may due to the change in carbohydrate transportation, biosynthesis of cell wall, cell membrane, and cell envelope. This study has drawn a basic mechanism in reconstructing gut microbiota by feeding M. basjoo and lay out a foundation for further reach on the interaction between human as diner and M. basjoo as food.}, } @article {pmid30953542, year = {2019}, author = {Raymond, F and Boissinot, M and Ouameur, AA and Déraspe, M and Plante, PL and Kpanou, SR and Bérubé, È and Huletsky, A and Roy, PH and Ouellette, M and Bergeron, MG and Corbeil, J}, title = {Culture-enriched human gut microbiomes reveal core and accessory resistance genes.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {56}, pmid = {30953542}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*classification/drug effects/genetics/growth & development ; Bacterial Proteins/genetics ; Bacteriological Techniques/*methods ; *Drug Resistance, Microbial ; Escherichia coli/genetics/growth & development/isolation & purification ; Feces/cytology/microbiology ; Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; Humans ; Metagenomics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing. In addition, it is a challenge to associate the presence of resistance genes with their risk of acquisition by pathogens. In this study, we used liquid culture enrichment of stools to assemble the genome of lower-abundance bacteria from fecal samples. We then investigated the gene content recovered from these culture-enriched and culture-independent metagenomes in relation with their taxonomic origin, specifically antibiotic resistance genes. We finally used a pangenome approach to associate resistance genes with the core or accessory genome of Enterobacteriaceae and inferred their propensity to horizontal gene transfer.

RESULTS: Using culture-enrichment approaches with stools allowed assembly of 187 bacterial species with an assembly size greater than 1 million nucleotides. Of these, 67 were found only in culture-enriched conditions, and 22 only in culture-independent microbiomes. These assembled metagenomes allowed the evaluation of the gene content of specific subcommunities of the gut microbiome. We observed that differentially distributed metabolic enzymes were associated with specific culture conditions and, for the most part, with specific taxa. Gene content differences between microbiomes, for example, antibiotic resistance, were for the most part not associated with metabolic enzymes, but with other functions. We used a pangenome approach to determine if the resistance genes found in Enterobacteriaceae, specifically E. cloacae or E. coli, were part of the core genome or of the accessory genome of this species. In our healthy volunteer cohort, we found that E. cloacae contigs harbored resistance genes that were part of the core genome of the species, while E. coli had a large accessory resistome proximal to mobile elements.

CONCLUSION: Liquid culture of stools contributed to an improved functional and comparative genomics study of less-abundant gut bacteria, specifically those associated with antibiotic resistance. Defining whether a gene is part of the core genome of a species helped in interpreting the genomes recovered from culture-independent or culture-enriched microbiomes.}, } @article {pmid30953134, year = {2019}, author = {Grieco, MB and Lopes, FAC and Oliveira, LS and Tschoeke, DA and Popov, CC and Thompson, CC and Gonçalves, LC and Constantino, R and Martins, OB and Kruger, RH and de Souza, W and Thompson, FL}, title = {Metagenomic Analysis of the Whole Gut Microbiota in Brazilian Termitidae Termites Cornitermes cumulans, Cyrilliotermes strictinasus, Syntermes dirus, Nasutitermes jaraguae, Nasutitermes aquilinus, Grigiotermes bequaerti, and Orthognathotermes mirim.}, journal = {Current microbiology}, volume = {76}, number = {6}, pages = {687-697}, pmid = {30953134}, issn = {1432-0991}, support = {563055/2010-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; E-26/ 110.634/2014//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; }, mesh = {Animals ; Bacteria/*classification/*genetics ; Biodiversity ; Brazil ; Feeding Behavior ; *Gastrointestinal Microbiome ; Isoptera/*microbiology/physiology ; Metagenomics ; }, abstract = {Although some previous studies have described the microbial diversity of termite in Brazil, the lack of studies about this subject is still evident. In the present study, we described by whole genome sequencing, the gut microbiota of seven species of termites (Termitidae) with different feeding habits from four Brazilian locations. For the litter species, the most abundant bacterial phylum was Firmicutes, where Cornitermes cumulans and Syntermes dirus (Syntermitinae) were identified. For the humus species, the most abundant bacterial phylum was Proteobacteria where three species were studied: Cyrilliotermes strictinasus (Syntermitinae), Grigiotermes bequaerti (Apicotermitinae), and Orthognathotermes mirim (Termitinae). For the wood termites, Firmicutes and Spirochaetes were the most abundant phyla, respectively, where two species were identified: Nasutitermes aquilinus and Nasutitermes jaraguae (Nasutitermitinae). The gut microbiota of all four examined subfamilies shared a conserved functional and carbohydrate-active enzyme profile and specialized in cellulose and chitin degradation. Taken together, these results provide insight into the partnerships between termite and microbes that permit the use of refractory energy sources.}, } @article {pmid30953119, year = {2019}, author = {Deng, Y and Xu, X and Yin, X and Lu, H and Chen, G and Yu, J and Ruan, Y}, title = {Effect of stock density on the microbial community in biofloc water and Pacific white shrimp (Litopenaeus vannamei) gut microbiota.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {10}, pages = {4241-4252}, doi = {10.1007/s00253-019-09773-4}, pmid = {30953119}, issn = {1432-0614}, mesh = {Animals ; Aquaculture/*methods ; Bacteria/*classification/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; Penaeidae/*microbiology ; *Water Microbiology ; }, abstract = {Biofloc technology is an efficient approach for intensive shrimp culture. However, the extent to which this process can influence the composition of intestinal microbial community is still unknown. Here, we surveyed the shrimp intestinal bacteria as well as the floc water from three biofloc systems with different stock densities. Our study revealed a similar variation trend in phylum taxonomy level between floc bacteria and gut microbiota. Microbial community varied notably in floc water from different stock densities, while a core genus with dominating relative abundance was detected in gut samples. Extensive variation was discovered in gut microbiota, but still clustered into groups according to stock density. Our results indicated that shrimp intestinal microbiota as well as bacteria aggregated in flocs assembled into distinct communities from different stock densities, and the intestinal communities were more similar with the surrounding environment as the increase of stock density and resulting high floc biomass. The high stock density changed the core gut microbiota by reducing the relative abundance of Paracoccus and increasing that of Nocardioides, which may negatively influence shrimp performance. Therefore, this study helps us to understand further bacteria and host interactions in biofloc system.}, } @article {pmid30953072, year = {2019}, author = {De Cesare, A and Faria do Valle, Ì and Sala, C and Sirri, F and Astolfi, A and Castellani, G and Manfreda, G}, title = {Effect of a low protein diet on chicken ceca microbiome and productive performances.}, journal = {Poultry science}, volume = {98}, number = {9}, pages = {3963-3976}, doi = {10.3382/ps/pez132}, pmid = {30953072}, issn = {1525-3171}, mesh = {Animal Feed/analysis ; Animals ; Bacteria/classification/*genetics ; Bacterial Physiological Phenomena ; Cecum/microbiology ; Chickens/*microbiology ; Diet/veterinary ; Diet, Protein-Restricted/*veterinary ; Gastrointestinal Microbiome/drug effects/genetics/*physiology ; Male ; *Metagenome ; Time Factors ; }, abstract = {The aim of this study was to investigate the impact of supplementation of a low protein diet on ceca microbiome and productive performances of broiler chickens. A total of 1,170 one-day-old male chicks (Ross 308) were divided in 2 diet groups and reared in the same conditions up to 42 D. Birds belonging to the control group were fed a basal diet. Birds belonging to the low protein group the basal diet with a reduced level of crude protein (-7%). Cecum contents from randomly selected birds were collected at 14 and 42 D within each diet group, submitted to DNA extraction and then tested by shotgun metagenomic sequencing. Abundances of species belonging to Actinobacteria and Proteobacteria were mainly affected by the diet as well as interaction between diet and time, while species belonging to Firmicutes and Cyanobacteria changed mainly according to the age of the birds. At family level, Lactobacillaceae significantly decreased in the low protein group up to 14 D. However, at the end of the rearing period the same family was significantly higher in the low protein group. The most abundant functional genes, represented by cystine desulfurase, alpha-galactosidase, and serine hydroxymethyltransferase, displayed comparable abundances in both diet groups, although significative differences were identified for less abundant functional genes at both sampling times. Birds fed control and low protein diets showed similar productive performances. However, in the finisher phase, feed conversion rate was significantly better in chickens fed the low protein diet. Overall, this study showed that a reduced intake of crude protein in broilers increases the abundance of Lactobacillaceae in the ceca over time and this seems to be linked to a better feed conversion rate between 36 and 42 D. A reduced intake of crude protein in chicken production can help to improve exploitation of edible resources, while reducing the emission of nitrogen pollutants in the environment.}, } @article {pmid30952929, year = {2019}, author = {Li, Y and Zheng, L and Zhang, Y and Liu, H and Jing, H}, title = {Comparative metagenomics study reveals pollution induced changes of microbial genes in mangrove sediments.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5739}, pmid = {30952929}, issn = {2045-2322}, mesh = {*Environmental Monitoring ; *Metagenomics ; Metals, Heavy/*analysis ; *Microbiota ; Water Pollutants, Chemical/*analysis ; Wetlands ; }, abstract = {Mangrove forests are widespread along the subtropical and tropical coasts. They provide a habitat for a wide variety of plants, animals and microorganisms, and act as a buffer zone between the ocean and land. Along with other coastal environments, mangrove ecosystems are under increasing pressure from human activities, such as excessive input of nutrients and toxic pollutants. Despite efforts to understand the diversity of microbes in mangrove sediments, their metabolic capability in pristine and contaminated mangrove sediments remains largely unknown. By using metagenomic approach, we investigated the metabolic capacity of microorganisms in contaminated (CMS) and pristine (PMS) mangrove sediments at subtropical and tropical coastal sites. When comparing the CMS with PMS, we found that the former had a reduced diazotroph abundance and nitrogen fixing capability, but an enhanced metabolism that is related to the generation of microbial greenhouse gases via increased methanogenesis and sulfate reduction. In addition, a high concentration of heavy metals (mainly Zn, Cd, and Pb) and abundance of metal/antibiotic resistance encoding genes were found in CMS. Together, these data provide evidence that contamination in mangrove sediment can markedly change microbial community and metabolism; however, no significant differences in gene distribution were found between the subtropical and tropical mangrove sediments. In summary, contamination in mangrove sediments might weaken the microbial metabolisms that enable the mangrove ecosystems to act as a buffer zone for terrestrial nutrients deposition, and induce bioremediation processes accompanied with an increase in greenhouse gas emission.}, } @article {pmid30952693, year = {2019}, author = {Hay, ID and Lithgow, T}, title = {Filamentous phages: masters of a microbial sharing economy.}, journal = {EMBO reports}, volume = {20}, number = {6}, pages = {}, pmid = {30952693}, issn = {1469-3178}, mesh = {Bacteria/virology ; Bacterial Physiological Phenomena ; *Bacteriophages/classification/physiology ; Biodiversity ; Biofilms ; *Biotechnology/economics ; Genome, Viral ; *Host-Pathogen Interactions ; Life Cycle Stages ; }, abstract = {Bacteriophage ("bacteria eaters") or phage is the collective term for viruses that infect bacteria. While most phages are pathogens that kill their bacterial hosts, the filamentous phages of the sub-class Inoviridae live in cooperative relationships with their bacterial hosts, akin to the principal behaviours found in the modern-day sharing economy: peer-to-peer support, to offset any burden. Filamentous phages impose very little burden on bacteria and offset this by providing service to help build better biofilms, or provision of toxins and other factors that increase virulence, or modified behaviours that provide novel motile activity to their bacterial hosts. Past, present and future biotechnology applications have been built on this phage-host cooperativity, including DNA sequencing technology, tools for genetic engineering and molecular analysis of gene expression and protein production, and phage-display technologies for screening protein-ligand and protein-protein interactions. With the explosion of genome and metagenome sequencing surveys around the world, we are coming to realize that our knowledge of filamentous phage diversity remains at a tip-of-the-iceberg stage, promising that new biology and biotechnology are soon to come.}, } @article {pmid30952661, year = {2019}, author = {Yu, J and Deem, LM and Crow, SE and Deenik, J and Penton, CR}, title = {Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential after 2 Years of Biochar Amendment in a Tropical Oxisol.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {11}, pages = {}, pmid = {30952661}, issn = {1098-5336}, mesh = {Agriculture ; Biodiversity ; Carbon ; Carbon Dioxide ; Charcoal/*metabolism/pharmacology ; Denitrification ; Metabolic Networks and Pathways ; *Metagenomics ; Microbiota/drug effects/*physiology ; Nitrous Oxide ; Nutrients/*metabolism ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The complex structural and functional responses of agricultural soil microbial communities to the addition of carbonaceous compounds such as biochar remain poorly understood. This severely limits the predictive ability for both the potential enhancement of soil fertility and greenhouse gas mitigation. In this study, we utilized shotgun metagenomics in order to decipher changes in the microbial community in soil microcosms after 14 days of incubation at 23°C, which contained soils from biochar-amended and control plots cultivated with Napier grass. Our analyses revealed that biochar-amended soil microbiomes exhibited significant shifts in both community composition and predicted metabolism. Key metabolic pathways related to carbon turnover, such as the utilization of plant-derived carbohydrates as well as denitrification, were enriched under biochar amendment. These community shifts were in part associated with increased soil carbon, such as labile and aromatic carbon compounds, which was likely stimulated by the increased available nutrients associated with biochar amendment. These findings indicate that the soil microbiome response to the combination of biochar addition and to incubation conditions confers enhanced nutrient cycling and a small decrease in CO2 emissions and potentially mitigates nitrous oxide emissions.IMPORTANCE The incorporation of biochar into soil is a promising management strategy for sustainable agriculture owing to its potential to sequester carbon and improve soil fertility. Expanding the addition of biochar to large-scale agriculture hinges on its lasting beneficial effects on the microbial community. However, there exists a significant knowledge gap regarding the specific role that biochar plays in altering the key biological soil processes that influence plant growth and carbon storage in soil. Previous studies that examined the soil microbiome under biochar amendment principally characterized only how the composition alters in response to biochar amendment. In the present study, we shed light on the functional alterations of the microbial community response 2 years after biochar amendment. Our results show that biochar increased the abundance of genes involved in denitrification and carbon turnover and that biochar-amended soil microcosms had a reduction in cumulative CO2 production.}, } @article {pmid30951921, year = {2019}, author = {De Jode, A and David, R and Haguenauer, A and Cahill, AE and Erga, Z and Guillemain, D and Sartoretto, S and Rocher, C and Selva, M and Le Gall, L and Féral, JP and Chenuil, A}, title = {From seascape ecology to population genomics and back. Spatial and ecological differentiation among cryptic species of the red algae Lithophyllum stictiforme/L. cabiochiae, main bioconstructors of coralligenous habitats.}, journal = {Molecular phylogenetics and evolution}, volume = {137}, number = {}, pages = {104-113}, doi = {10.1016/j.ympev.2019.04.005}, pmid = {30951921}, issn = {1095-9513}, mesh = {Animals ; Anthozoa/*physiology ; Biodiversity ; *Ecosystem ; Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Mediterranean Sea ; *Metagenomics ; Phylogeny ; Principal Component Analysis ; Rhodophyta/*genetics ; Species Specificity ; }, abstract = {Ecosystem engineering species alter the physical structure of their environment and can create or modify habitats, having a massive impact on local biodiversity. Coralligenous reefs are highly diverse habitats endemic to the Mediterranean Sea built by calcareous benthic organisms among which Crustose Coralline Algae are the main engineering species. We analyzed the diversity of Lithophyllum stictiforme or L. cabiochiae in coralligenous habitats combining a multiple barcode and a population genomics approach with seascape features. Population genomics allowed disentangling pure spatial effects from environmental effects. We found that these taxa form a complex of eight highly divergent cryptic species that are easily identifiable using classic barcode markers (psbA, LSU, COI). Three factors have a significant effect on the relative abundances of these cryptic species: the location along the French Mediterranean coast, depth and Photosynthetic Active Radiation (PAR). The analysis of around 5000 SNPs for the most abundant species revealed genetic differentiation among localities in the Bay of Marseille but no differentiation between depths within locality. Thus, the effect of depth and PAR on cryptic species communities is not a consequence of restricted connectivity but rather due to differential settlement or survival among cryptic species. This differential is more likely driven by irradiance levels rather than by pressure or temperature. Both the genetic and species diversity patterns are congruent with the main patterns of currents in the Bay. Ecological differentiation among these engineering cryptic species, sensitive to ocean warming and acidification, could have important consequences on the diversity and structure of the coralligenous communities.}, } @article {pmid30951391, year = {2020}, author = {Suez, J and Zmora, N and Elinav, E}, title = {Probiotics in the next-generation sequencing era.}, journal = {Gut microbes}, volume = {11}, number = {1}, pages = {77-93}, pmid = {30951391}, issn = {1949-0984}, mesh = {Anti-Bacterial Agents/*adverse effects ; *Gastrointestinal Microbiome/drug effects/genetics/physiology ; Humans ; Metagenomics ; Probiotics/*therapeutic use ; }, abstract = {Technological developments, including massively parallel DNA sequencing, gnotobiotics, metabolomics, RNA sequencing and culturomics, have markedly propelled the field of microbiome research in recent years. These methodologies can be harnessed to improve our in-depth mechanistic understanding of basic concepts related to consumption of probiotics, including their rules of engagement with the indigenous microbiome and impacts on the human host. We have recently demonstrated that even during probiotic supplementation, resident gut bacteria in a subset of individuals resist the mucosal presence of probiotic strains, limiting their modulatory effect on the microbiome and on the host gut transcriptional landscape. Resistance is partly alleviated by antibiotics treatment, which enables probiotics to interact with the host at the gut mucosal interface, although rather than promoting reconstitution of the indigenous microbiome and of the host transcriptional profile, they inhibit these components from returning to their naïve pre-antibiotic configurations. In this commentary, we discuss our findings in the context of previous and recent works, and suggest that incorporating the state-of-the-art methods currently utilized in microbiome research into the field of probiotics may lead to improved understanding of their mechanisms of activity, as well as their efficacy and long-term safety.}, } @article {pmid30948795, year = {2019}, author = {D'Amico, F and Soverini, M and Zama, D and Consolandi, C and Severgnini, M and Prete, A and Pession, A and Barone, M and Turroni, S and Biagi, E and Brigidi, P and Masetti, R and Rampelli, S and Candela, M}, title = {Gut resistome plasticity in pediatric patients undergoing hematopoietic stem cell transplantation.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5649}, pmid = {30948795}, issn = {2045-2322}, mesh = {Adolescent ; Anti-Bacterial Agents/adverse effects ; Child ; Drug Resistance, Microbial/*genetics ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Graft vs Host Disease/etiology ; Hematopoietic Stem Cell Transplantation/methods ; Hematopoietic Stem Cells/*metabolism ; Humans ; Male ; Metagenomics/methods ; Transplantation, Homologous/adverse effects ; }, abstract = {The gut microbiome of pediatric patients undergoing allo-hematopoietic stem cell transplantation (HSCT) has recently been considered as a potential reservoir of antimicrobial resistance, with important implications in terms of patient mortality rate. By means of shotgun metagenomics, here we explored the dynamics of the gut resistome - i.e. the pattern of antibiotic resistance genes provided by the gut microbiome - in eight pediatric patients undergoing HSCT, half of whom developed acute Graft-versus-Host Disease (aGvHD). According to our findings, the patients developing aGvHD are characterized by post-HSCT expansion of their gut resistome, involving the acquisition of new resistances, as well as the consolidation of those already present before HSCT. Interestingly, the aGvHD-associated bloom in resistome diversity is not limited to genes coding for resistance to the antibiotics administered along the therapeutic course, but rather involves a broad pattern of different resistance classes, including multidrug resistance, as well as resistance to macrolides, aminoglycosides, tetracyclines and beta-lactams. Our data stress the relevance of mapping the gut resistome in HSCT pediatric patients to define the most appropriate anti-infective treatment post HSCT.}, } @article {pmid30947688, year = {2019}, author = {Sevigny, JL and Rothenheber, D and Diaz, KS and Zhang, Y and Agustsson, K and Bergeron, RD and Thomas, WK}, title = {Marker genes as predictors of shared genomic function.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {268}, pmid = {30947688}, issn = {1471-2164}, support = {P20 GM103506/GM/NIGMS NIH HHS/United States ; 16-052: SA 16-18//Gulf of Mexico Research Initiative/ ; 5 P20 GM 10350605//National Institutes of Health: New Hampshire Idea Network of Biological Research Excellence/ ; }, mesh = {Bacteria/*classification/*genetics ; DNA, Bacterial/genetics ; Evolution, Molecular ; Genes, Bacterial/genetics/*physiology ; *Genetic Markers ; *Genome, Bacterial ; *Metagenome ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Although high-throughput marker gene studies provide valuable insight into the diversity and relative abundance of taxa in microbial communities, they do not provide direct measures of their functional capacity. Recently, scientists have shown a general desire to predict functional profiles of microbial communities based on phylogenetic identification inferred from marker genes, and recent tools have been developed to link the two. However, to date, no large-scale examination has quantified the correlation between the marker gene based taxonomic identity and protein coding gene conservation. Here we utilize 4872 representative prokaryotic genomes from NCBI to investigate the relationship between marker gene identity and shared protein coding gene content.

RESULTS: Even at 99-100% marker gene identity, genomes share on average less than 75% of their protein coding gene content. This occurs regardless of the marker gene(s) used: V4 region of the 16S rRNA, complete 16S rRNA, or single copy orthologs through a multi-locus sequence analysis. An important aspect related to this observation is the intra-organism variation of 16S copies from a single genome. Although the majority of 16S copies were found to have high sequence similarity (> 99%), several genomes contained copies that were highly diverged (< 97% identity).

CONCLUSIONS: This is the largest comparison between marker gene similarity and shared protein coding gene content to date. The study highlights the limitations of inferring a microbial community's functions based on marker gene phylogeny. The data presented expands upon the results of previous studies that examined one or few bacterial species and supports the hypothesis that 16S rRNA and other marker genes cannot be directly used to fully predict the functional potential of a bacterial community.}, } @article {pmid30946154, year = {2019}, author = {Sessa, L and Reddel, S and Manno, E and Quagliariello, A and Cotugno, N and Del Chierico, F and Amodio, D and Capponi, C and Leone, F and Bernardi, S and Rossi, P and Putignani, L and Palma, P}, title = {Distinct gut microbiota profile in antiretroviral therapy-treated perinatally HIV-infected patients associated with cardiac and inflammatory biomarkers.}, journal = {AIDS (London, England)}, volume = {33}, number = {6}, pages = {1001-1011}, doi = {10.1097/QAD.0000000000002131}, pmid = {30946154}, issn = {1473-5571}, mesh = {Adolescent ; Adult ; Anti-Retroviral Agents/therapeutic use ; Bacteria/classification/genetics ; Bacterial Translocation ; Cardiovascular Diseases/*pathology ; Child ; Child, Preschool ; Cross-Sectional Studies ; Dysbiosis/*complications ; Female ; *Gastrointestinal Microbiome ; HIV Infections/*complications/*drug therapy ; Humans ; Inflammation/*pathology ; Male ; Metagenomics ; *Microbiota ; Young Adult ; }, abstract = {OBJECTIVE: Persistent inflammation and higher risk to develop cardiovascular diseases still represent a major complication for HIV-infected patients despite effective antiretroviral therapy (ART). We investigated the correlation between the gut microbiota profile, markers of inflammation, vascular endothelial activation (VEA) and microbial translocation (MT) in perinatally HIV-infected patients (PHIV) under ART.

DESIGN: Cross-sectional study including 61 ART-treated PHIV (age range 3-30 years old) and 71 age-matched healthy controls. Blood and stool sample were collected at the same time and analyzed for gut microbiota composition and plasma biomarkers.

METHODS: Gut microbiota composition was determined by 16S rRNA targeted-metagenomics. Soluble markers of MT, inflammation and VEA were quantified by ELISA or Luminex assay. Markers of immune activation were analyzed by flow cytometry on CD4 and CD8T cells.

RESULTS: We identified two distinct gut microbiota profiles (groups A and B) among PHIV. No different clinical parameters (age, sex, ethnicity, clinical class), dietary and sexual habits were found between the groups. The group A showed a relative dominance of Akkermansia muciniphila, whereas gut microbiota of group B was characterized by a higher biodiversity. The analysis of soluble markers revealed a significantly higher level of soluble E-selectine (P = 0.0296), intercellular adhesion molecule-1 (P = 0.0028), vascular adhesion molecule-1 (P = 0.0230), IL-6 (P = 0.0247) and soluble CD14 (P = 0.0142) in group A compared with group B.

CONCLUSION: Distinctive gut microbiota profiles are differently associated with inflammation, microbial translocation and VEA. Future studies are needed to understand the role of A. muciniphila and risk to develop cardiovascular diseases in PHIV.}, } @article {pmid30942867, year = {2019}, author = {Brown, SM and Chen, H and Hao, Y and Laungani, BP and Ali, TA and Dong, C and Lijeron, C and Kim, B and Wultsch, C and Pei, Z and Krampis, K}, title = {MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs.}, journal = {GigaScience}, volume = {8}, number = {4}, pages = {}, pmid = {30942867}, issn = {2047-217X}, support = {UH3 CA140233/CA/NCI NIH HHS/United States ; UL1 TR000457/TR/NCATS NIH HHS/United States ; G12 MD007599/MD/NIMHD NIH HHS/United States ; R01 AI110372/AI/NIAID NIH HHS/United States ; U54 CA221705/CA/NCI NIH HHS/United States ; UL1 TR002384/TR/NCATS NIH HHS/United States ; R01 CA159036/CA/NCI NIH HHS/United States ; R21 DE025352/DE/NIDCR NIH HHS/United States ; U01 CA182370/CA/NCI NIH HHS/United States ; }, mesh = {Algorithms ; Cloud Computing ; Computational Biology/*methods ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiology ; Microbiota ; Molecular Sequence Annotation ; Reproducibility of Results ; *Software ; Workflow ; }, abstract = {BACKGROUND: Current methods used for annotating metagenomics shotgun sequencing (MGS) data rely on a computationally intensive and low-stringency approach of mapping each read to a generic database of proteins or reference microbial genomes.

RESULTS: We developed MGS-Fast, an analysis approach for shotgun whole-genome metagenomic data utilizing Bowtie2 DNA-DNA alignment of reads that is an alternative to using the integrated catalog of reference genes database of well-annotated genes compiled from human microbiome data. This method is rapid and provides high-stringency matches (>90% DNA sequence identity) of the metagenomics reads to genes with annotated functions. We demonstrate the use of this method with data from a study of liver disease and synthetic reads, and Human Microbiome Project shotgun data, to detect differentially abundant Kyoto Encyclopedia of Genes and Genomes gene functions in these experiments. This rapid annotation method is freely available as a Galaxy workflow within a Docker image.

CONCLUSIONS: MGS-Fast can confidently transfer functional annotations from gene databases to metagenomic reads, with speed and accuracy.}, } @article {pmid30942859, year = {2019}, author = {Paul, VJ and Freeman, CJ and Agarwal, V}, title = {Chemical Ecology of Marine Sponges: New Opportunities through "-Omics".}, journal = {Integrative and comparative biology}, volume = {59}, number = {4}, pages = {765-776}, pmid = {30942859}, issn = {1557-7023}, support = {R00 ES026620/ES/NIEHS NIH HHS/United States ; R01 CA172310/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Aquatic Organisms/genetics/physiology ; Genome/*physiology ; *Host Microbial Interactions ; Microbiota ; Porifera/genetics/microbiology/*physiology ; Transcriptome/*physiology ; }, abstract = {The chemical ecology and chemical defenses of sponges have been investigated for decades; consequently, sponges are among the best understood marine organisms in terms of their chemical ecology, from the level of molecules to ecosystems. Thousands of natural products have been isolated and characterized from sponges, and although relatively few of these compounds have been studied for their ecological functions, some are known to serve as chemical defenses against predators, microorganisms, fouling organisms, and other competitors. Sponges are hosts to an exceptional diversity of microorganisms, with almost 40 microbial phyla found in these associations to date. Microbial community composition and abundance are highly variable across host taxa, with a continuum from diverse assemblages of many microbial taxa to those that are dominated by a single microbial group. Microbial communities expand the nutritional repertoire of their hosts by providing access to inorganic and dissolved sources of nutrients. Not only does this continuum of microorganism-sponge associations lead to divergent nutritional characteristics in sponges, these associated microorganisms and symbionts have long been suspected, and are now known, to biosynthesize some of the natural products found in sponges. Modern "omics" tools provide ways to study these sponge-microbe associations that would have been difficult even a decade ago. Metabolomics facilitate comparisons of sponge compounds produced within and among taxa, and metagenomics and metatranscriptomics provide tools to understand the biology of host-microbe associations and the biosynthesis of ecologically relevant natural products. These combinations of ecological, microbiological, metabolomic and genomics tools, and techniques provide unprecedented opportunities to advance sponge biology and chemical ecology across many marine ecosystems.}, } @article {pmid30942434, year = {2019}, author = {Liu, Z and Kong, Y and Gao, Y and Ren, Y and Zheng, C and Deng, X and Chen, T}, title = {Revealing the interaction between intrauterine adhesion and vaginal microbiota using high‑throughput sequencing.}, journal = {Molecular medicine reports}, volume = {19}, number = {5}, pages = {4167-4174}, pmid = {30942434}, issn = {1791-3004}, mesh = {Adolescent ; Adult ; Biodiversity ; Computational Biology/methods ; *Disease Susceptibility ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Public Health Surveillance ; Tissue Adhesions/diagnosis/epidemiology/*etiology ; Uterine Diseases/diagnosis/epidemiology/*etiology ; Vagina/*microbiology ; Young Adult ; }, abstract = {Intrauterine adhesion (IUA) is one of the most common diseases of the reproductive system. Due to the high postoperative recurrence rate of IUA, it is crucial to identify the possible causes of pathogenesis and recurrence of this disease. In the present study, a high‑throughput sequencing approach was applied to compare the vaginal microbiota between healthy women [healthy vaginal secretion (HVS) group] and patients with IUA [intrauterine adhesion patients' vaginal secretion (IAVS) group]. The results indicated that IUA had little effect on the number of vaginal bacterial species. However, at the phylum level, patients with IUA had a significantly lower percentage of Firmicutes and a higher percentage of Actinobacteria than the HVS group (P<0.05). At the genus level, ~50% of patients with IUA were found to have a marked reduction in probiotic Lactobacillus accompanied by an overgrowth of pathogenic Gardnerella and Prevotella (P<0.05), and the Principal Coordinates Analysis confirmed that 10/20 samples in the IAVS group were scattered far away from the HVS group. Therefore, it was concluded that the interaction between IUA and vaginal microbiota greatly influenced the vaginal diversity of patients with IUA. In order to increase the recovery rate and lower the recurrence rate of IUA, increasing the vaginal Lactobacillus population should be considered.}, } @article {pmid30941531, year = {2019}, author = {Qian, W and Ao, W and Jia, C and Li, Z}, title = {Bacterial colonisation of reeds and cottonseed hulls in the rumen of Tarim red deer (Cervus elaphus yarkandensis).}, journal = {Antonie van Leeuwenhoek}, volume = {112}, number = {9}, pages = {1283-1296}, doi = {10.1007/s10482-019-01260-0}, pmid = {30941531}, issn = {1572-9699}, support = {HS201702//Opening Project of Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production & Construction Group/ ; 31460610//National Natural Science Foundation of China/ ; 31660671//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacteria/*classification/*genetics/metabolism ; *Biota ; Cellulose/metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Deer/*microbiology ; Gossypium/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Phylogeny ; Poaceae/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The rumen microbiome contributes greatly to the degradation of plant fibres to volatile fatty acids and microbial products, affecting the health and productivity of ruminants. In this study, we investigated the dynamics of colonisation by bacterial communities attached to reeds and cottonseed hulls in the rumen of Tarim red deer, a native species distributed in the desert of the Tarim Basin. The reed and cottonseed hull samples incubated in nylon bags for 1, 6, 12, and 48 h were collected and used to examine the bacterial communities by next-generation sequencing of the bacterial 16S rRNA gene. Prevotella1 and Rikenellaceae RC9 were the most abundant taxa in both the reed and cottonseed hull groups at various times, indicating a key role of these organisms in rumen fermentation in Tarim red deer. The relative abundances of cellulolytic bacteria, such as members of Fibrobacter, Treponema 2, Ruminococcaceae NK4A214 and Succiniclasticum increased, while that of the genus Prevotella 1 decreased, with increasing incubation time in both reeds and cottonseed hulls. Moreover, the temporal changes in bacterial diversity between reeds and cottonseed hulls were different, as demonstrated by the variations in the taxa Ruminococcaceae UCG 010 and Papillibacter in the reed group and Sphaerochaeta and Erysipelotrichaceae UCG 004 in the cottonseed hull group; the abundances of these bacteria first decreased and then increased. In conclusion, our results reveal the dynamics of bacterial colonisation of reeds and cottonseed hulls in the rumen of Tarim red deer.}, } @article {pmid30938752, year = {2019}, author = {Koedooder, R and Mackens, S and Budding, A and Fares, D and Blockeel, C and Laven, J and Schoenmakers, S}, title = {Identification and evaluation of the microbiome in the female and male reproductive tracts.}, journal = {Human reproduction update}, volume = {25}, number = {3}, pages = {298-325}, doi = {10.1093/humupd/dmy048}, pmid = {30938752}, issn = {1460-2369}, mesh = {Female ; Fertilization ; Genitalia, Female/*microbiology/*parasitology ; Genitalia, Male/*microbiology/*parasitology ; Humans ; Male ; Microbiota/*genetics ; Pregnancy ; Pregnancy Outcome ; Pregnancy, Multiple ; }, abstract = {BACKGROUND: The existence of an extensive microbiome in and on the human body has increasingly dominated the scientific literature during the last decade. A shift from culture-dependent to culture-independent identification of microbes has occurred since the emergence of next-generation sequencing (NGS) techniques, whole genome shotgun and metagenomic sequencing. These sequencing analyses have revealed the presence of a rich diversity of microbes in most exposed surfaces of the human body, such as throughout the reproductive tract. The results of microbiota analyses are influenced by the technical specifications of the applied methods of analyses. Therefore, it is difficult to correctly compare and interpret the results of different studies of the same anatomical niche.

OBJECTIVES AND RATIONALE: The aim of this narrative review is to provide an overview of the currently used techniques and the reported microbiota compositions in the different anatomical parts of the female and male reproductive tracts since the introduction of NGS in 2005. This is crucial to understand and determine the interactions and roles of the different microbes necessary for successful reproduction.

SEARCH METHODS: A search in Embase, Medline Ovid, Web of science, Cochrane and Google scholar was conducted. The search was limited to English language and studies published between January 2005 and April 2018. Included articles needed to be original microbiome research related to the reproductive tracts.

OUTCOMES: The review provides an extensive up-to-date overview of current microbiome research in the field of human reproductive medicine. The possibility of drawing general conclusions is limited due to diversity in the execution of analytical steps in microbiome research, such as local protocols, sampling methods, primers used, sequencing techniques and bioinformatic pipelines, making it difficult to compare and interpret results of the available studies. Although some microbiota are associated with reproductive success and a good pregnancy outcome, it is still unknown whether a causal link exists. More research is needed to further explore the possible clinical implications and therapeutic interventions.

WIDER IMPLICATIONS: For the field of reproductive medicine, determination of what is a favourable reproductive tract microbiome will provide insight into the mechanisms of both unsuccessful and successful human reproduction. To increase pregnancy chances with live birth and to reduce reproduction-related health costs, future research could focus on postponing treatment or conception in case of the presence of unfavourable microbiota and on the development of therapeutic interventions, such as microbial therapeutics and lifestyle adaptations.}, } @article {pmid30937653, year = {2019}, author = {Parvathi, A and Jasna, V and Aswathy, VK and Nathan, VK and Aparna, S and Balachandran, KK}, title = {Microbial diversity in a coastal environment with co-existing upwelling and mud-banks along the south west coast of India.}, journal = {Molecular biology reports}, volume = {46}, number = {3}, pages = {3113-3127}, pmid = {30937653}, issn = {1573-4978}, support = {OLP1709//National Institute of Oceanography, India/ ; }, mesh = {*Biodiversity ; Computational Biology/methods ; *Environmental Microbiology ; Geography ; India ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; Seawater/*microbiology ; *Soil Microbiology ; *Water Microbiology ; }, abstract = {Upwelling and mud banks are two prominent oceanographic features in the coastal waters along the south west coast of India during the southwest monsoon (MON) season. The present study investigates the microbial diversity in the coastal environments of Alappuzha, India, where upwelling and mud banks co-exist. Water samples were collected from three stations, M1, M2, and M3, on a weekly basis to estimate the physico-chemical parameters and microbial abundance (MA). Presence of cold waters (< 26 °C) with high nitrate (6-8 µM) and low dissolved oxygen (5 µM) in the sub surface waters during monsoon (M) confirmed the presence of upwelling at all the three stations. Simultaneously, presence of unusually calm waters was seen at M2 alone during M indicating the formation of mud banks. The microbial diversity was determined from three stations, with distinct oceanographic conditions (M1: coastal reference station with only upwelling, M2: mud banks + upwelling, and M3: offshore reference station with only upwelling). The water samples were collected during two seasons, pre-monsoon (April) and M (July) and analysed using 16S rRNA-based Illumina high-throughput metagenomic sequencing. Proteobacteria was the most dominant phyla, followed by Bacteroidetes, Firmicutes, Cyanobacteria, Actinobacteria, and Verrucomicrobia in order, with variations in their relative abundance spatially and seasonally. Though the MA increased during M at all the stations, the relative abundance of most of the bacterial phyla except Proteobacteria decreased during M season. Interestingly, most of the sequences at M2 during mud banks were unclassified at the class level indicating the presence of unique microbial populations in this station. Prediction of metabolic activity revealed ammonia oxidation, nitrite reduction, sulphate reduction, xylan degradation, dehalogenation, chitin degradation, etc. as important functions. The metabolic activity throws light on the role of microbes in this environment thereby providing a system-scale perspective of microbial community interactions.}, } @article {pmid30936548, year = {2019}, author = {Thomas, AM and Manghi, P and Asnicar, F and Pasolli, E and Armanini, F and Zolfo, M and Beghini, F and Manara, S and Karcher, N and Pozzi, C and Gandini, S and Serrano, D and Tarallo, S and Francavilla, A and Gallo, G and Trompetto, M and Ferrero, G and Mizutani, S and Shiroma, H and Shiba, S and Shibata, T and Yachida, S and Yamada, T and Wirbel, J and Schrotz-King, P and Ulrich, CM and Brenner, H and Arumugam, M and Bork, P and Zeller, G and Cordero, F and Dias-Neto, E and Setubal, JC and Tett, A and Pardini, B and Rescigno, M and Waldron, L and Naccarati, A and Segata, N}, title = {Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.}, journal = {Nature medicine}, volume = {25}, number = {4}, pages = {667-678}, pmid = {30936548}, issn = {1546-170X}, support = {R01 CA189184/CA/NCI NIH HHS/United States ; R01 CA207371/CA/NCI NIH HHS/United States ; R01 CA230551/CA/NCI NIH HHS/United States ; R21 AI121784/AI/NIAID NIH HHS/United States ; P30 CA042014/CA/NCI NIH HHS/United States ; U01 CA206110/CA/NCI NIH HHS/United States ; U24 CA180996/CA/NCI NIH HHS/United States ; }, mesh = {Biomarkers, Tumor/metabolism ; Choline/*metabolism ; Cohort Studies ; Colorectal Neoplasms/diagnosis/*metabolism/*microbiology ; Databases, Genetic ; Gastrointestinal Microbiome ; Humans ; Lyases/genetics/metabolism ; *Metagenomics ; Species Specificity ; }, abstract = {Several studies have investigated links between the gut microbiome and colorectal cancer (CRC), but questions remain about the replicability of biomarkers across cohorts and populations. We performed a meta-analysis of five publicly available datasets and two new cohorts and validated the findings on two additional cohorts, considering in total 969 fecal metagenomes. Unlike microbiome shifts associated with gastrointestinal syndromes, the gut microbiome in CRC showed reproducibly higher richness than controls (P < 0.01), partially due to expansions of species typically derived from the oral cavity. Meta-analysis of the microbiome functional potential identified gluconeogenesis and the putrefaction and fermentation pathways as being associated with CRC, whereas the stachyose and starch degradation pathways were associated with controls. Predictive microbiome signatures for CRC trained on multiple datasets showed consistently high accuracy in datasets not considered for model training and independent validation cohorts (average area under the curve, 0.84). Pooled analysis of raw metagenomes showed that the choline trimethylamine-lyase gene was overabundant in CRC (P = 0.001), identifying a relationship between microbiome choline metabolism and CRC. The combined analysis of heterogeneous CRC cohorts thus identified reproducible microbiome biomarkers and accurate disease-predictive models that can form the basis for clinical prognostic tests and hypothesis-driven mechanistic studies.}, } @article {pmid30936547, year = {2019}, author = {Wirbel, J and Pyl, PT and Kartal, E and Zych, K and Kashani, A and Milanese, A and Fleck, JS and Voigt, AY and Palleja, A and Ponnudurai, R and Sunagawa, S and Coelho, LP and Schrotz-King, P and Vogtmann, E and Habermann, N and Niméus, E and Thomas, AM and Manghi, P and Gandini, S and Serrano, D and Mizutani, S and Shiroma, H and Shiba, S and Shibata, T and Yachida, S and Yamada, T and Waldron, L and Naccarati, A and Segata, N and Sinha, R and Ulrich, CM and Brenner, H and Arumugam, M and Bork, P and Zeller, G}, title = {Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.}, journal = {Nature medicine}, volume = {25}, number = {4}, pages = {679-689}, pmid = {30936547}, issn = {1546-170X}, support = {716575/ERC_/European Research Council/International ; P30 CA042014/NH/NIH HHS/United States ; R01 CA189184/NH/NIH HHS/United States ; R01 CA189184/CA/NCI NIH HHS/United States ; U01 CA206110/CA/NCI NIH HHS/United States ; R01 CA207371/NH/NIH HHS/United States ; ZIA CP010198/ImNIH/Intramural NIH HHS/United States ; P30 CA042014/CA/NCI NIH HHS/United States ; U01 CA206110/NH/NIH HHS/United States ; 669830/ERC_/European Research Council/International ; R01 CA207371/CA/NCI NIH HHS/United States ; 268985/ERC_/European Research Council/International ; }, mesh = {Adenoma/genetics/microbiology ; Aged ; Biomarkers, Tumor/metabolism ; Cohort Studies ; Colorectal Neoplasms/*genetics/*microbiology ; Databases, Genetic ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; *Metagenome ; Middle Aged ; Models, Biological ; Reproducibility of Results ; Species Specificity ; }, abstract = {Association studies have linked microbiome alterations with many human diseases. However, they have not always reported consistent results, thereby necessitating cross-study comparisons. Here, a meta-analysis of eight geographically and technically diverse fecal shotgun metagenomic studies of colorectal cancer (CRC, n = 768), which was controlled for several confounders, identified a core set of 29 species significantly enriched in CRC metagenomes (false discovery rate (FDR) < 1 × 10[-5]). CRC signatures derived from single studies maintained their accuracy in other studies. By training on multiple studies, we improved detection accuracy and disease specificity for CRC. Functional analysis of CRC metagenomes revealed enriched protein and mucin catabolism genes and depleted carbohydrate degradation genes. Moreover, we inferred elevated production of secondary bile acids from CRC metagenomes, suggesting a metabolic link between cancer-associated gut microbes and a fat- and meat-rich diet. Through extensive validations, this meta-analysis firmly establishes globally generalizable, predictive taxonomic and functional microbiome CRC signatures as a basis for future diagnostics.}, } @article {pmid30936104, year = {2019}, author = {Burdet, C and Grall, N and Linard, M and Bridier-Nahmias, A and Benhayoun, M and Bourabha, K and Magnan, M and Clermont, O and d'Humières, C and Tenaillon, O and Denamur, E and Massias, L and Tubiana, S and Alavoine, L and Andremont, A and Mentré, F and Duval, X and , }, title = {Ceftriaxone and Cefotaxime Have Similar Effects on the Intestinal Microbiota in Human Volunteers Treated by Standard-Dose Regimens.}, journal = {Antimicrobial agents and chemotherapy}, volume = {63}, number = {6}, pages = {}, pmid = {30936104}, issn = {1098-6596}, mesh = {Adolescent ; Adult ; Anti-Bacterial Agents/*therapeutic use ; Cefotaxime/*pharmacology ; Ceftriaxone/*therapeutic use ; Cephalosporins/therapeutic use ; Feces ; Female ; Gastrointestinal Microbiome/*drug effects ; Gram-Negative Bacteria/*drug effects ; Gram-Negative Bacterial Infections/drug therapy ; Healthy Volunteers ; Humans ; Male ; Middle Aged ; RNA, Ribosomal, 16S/drug effects ; Young Adult ; }, abstract = {Ceftriaxone has a higher biliary elimination than cefotaxime (40% versus 10%), which may result in a more pronounced impact on the intestinal microbiota. We performed a monocenter, randomized open-label clinical trial in 22 healthy volunteers treated by intravenous ceftriaxone (1 g/24 h) or cefotaxime (1 g/8 h) for 3 days. We collected fecal samples for phenotypic analyses, 16S rRNA gene profiling, and measurement of the antibiotic concentration and compared the groups for the evolution of microbial counts and indices of bacterial diversity over time. Plasma samples were drawn at day 3 for pharmacokinetic analysis. The emergence of 3rd-generation-cephalosporin-resistant Gram-negative enteric bacilli (Enterobacterales), Enterococcus spp., or noncommensal microorganisms was not significantly different between the groups. Both antibiotics reduced the counts of total Gram-negative enteric bacilli and decreased the bacterial diversity, but the differences between the groups were not significant. All but one volunteer from each group exhibited undetectable levels of antibiotic in feces. Plasma pharmacokinetic endpoints were not correlated to alteration of the bacterial diversity of the gut. Both antibiotics markedly impacted the intestinal microbiota, but no significant differences were detected when standard clinical doses were administered for 3 days. This might be related to the similar daily amounts of antibiotics excreted through the bile using a clinical regimen. (This study has been registered at ClinicalTrials.gov under identifier NCT02659033.).}, } @article {pmid30935879, year = {2019}, author = {Wang, Y and Hu, Y and Cao, J and Bi, Y and Lv, N and Liu, F and Liang, S and Shi, Y and Jiao, X and Gao, GF and Zhu, B}, title = {Antibiotic resistance gene reservoir in live poultry markets.}, journal = {The Journal of infection}, volume = {78}, number = {6}, pages = {445-453}, doi = {10.1016/j.jinf.2019.03.012}, pmid = {30935879}, issn = {1532-2742}, mesh = {Animals ; Anti-Bacterial Agents/administration & dosage ; Chickens ; Disease Reservoirs/*veterinary ; Drug Resistance, Microbial/*genetics ; Feces/microbiology/virology ; Gastrointestinal Microbiome/*genetics ; *Genes, MDR ; Genetic Variation ; Humans ; *Metagenome ; Poultry ; Swine ; }, abstract = {OBJECTIVES: The heavy use of antibiotics in farm animals contributes to the enrichment and spread of antibiotic resistance genes (ARGs) in "one-health" settings. Numerous ARGs have been identified in livestock-associated environments but not in Chinese live poultry markets (LPMs).

METHODS: We collected 753 poultry fecal samples from LPMs of 18 provinces and municipalities in China and sequenced the metagenomes of 130 samples. Bioinformatic tools were used to construct the gene catalog and analyze the ARG content. PCR amplification and Sanger sequencing were used to survey the distribution of mcr-1 gene in all 753 fecal samples.

RESULTS: We found that a low number of genes but a high percentage of gene functions were shared among the poultry, human and pig gut gene catalogs. The poultry gut possessed 539 ARGs which were classified into 235 types. Both the ARG number and abundance were significantly higher in poultry than that in either pigs or humans. Fourteen ARG types were found present in all 130 samples, and tetracycline resistance (TcR) genes were the most abundant ARGs in both animals and humans. Moreover, 59.63% LPM samples harbored the colistin resistance gene mcr-1, and other mcr gene variants were also found.

CONCLUSIONS: We demonstrated that the Chinese LPMs is a repository for ARGs, posing a high risk for ARG dissemination from food animals to humans under such a trade system, which has not been addressed before.}, } @article {pmid30935838, year = {2019}, author = {Lin, BY and Lin, WD and Huang, CK and Hsin, MC and Lin, WY and Pryor, AD}, title = {Changes of gut microbiota between different weight reduction programs.}, journal = {Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery}, volume = {15}, number = {5}, pages = {749-758}, doi = {10.1016/j.soard.2019.01.026}, pmid = {30935838}, issn = {1878-7533}, mesh = {China ; Counseling ; Diet, Reducing ; Female ; Gastrectomy ; *Gastrointestinal Microbiome ; Hospitals, University ; Humans ; Male ; Middle Aged ; Obesity/*therapy ; *Weight Reduction Programs ; }, abstract = {BACKGROUND: Gut microbiota may induce obesity, diabetes, and metabolic syndrome. Different weight reduction programs may induce different changes in gut microbiota.

OBJECTIVES: To assess the changes in gut microbiota between obese adults who participated in 2 different weight reduction programs, the dietary counseling (DC) group and sleeve gastrectomy (SG) group, for 3 months.

SETTING: A University Hospital.

METHODS: Ten obese participants from each group were matched according to sex, age, and body mass index. Gut microbiota compositions were determined by metagenomics using next-generation sequencing before and after treatment. Anthropometric indices, metabolic factors, and gut microbiota were compared between and within groups.

RESULTS: After 3 months of treatment, compared with subjects in DC group, subjects in SG group experienced a greater reduction in body weight, body mass index, body fat, waist and hip circumference, diastolic blood pressure, hemoglobin, insulin, insulin resistance, glutamate pyruvate transaminase, blood urine nitrogen, and glycated hemoglobin (HbA1C). A total of 8, 17, and 46 species experienced significant abundance changes in DC, in SG, and between the 2 groups, respectively. Diversity of the gut flora increased in SG and between the 2 groups after treatment. The weight change over the course of the weight loss program was further adjusted and only 4 species, including Peptoniphilus lacrimalis 315 B, Selenomonas 4 sp., Prevotella 2 sp., and Pseudobutyrivibrio sp., were found to be significantly different between the 2 weight loss programs. These 4 species may be the different gut microbiota change between internal and surgical weight reduction programs.

CONCLUSIONS: There are significant differences not only in anthropometric indices and metabolic factors but also in gut microbiota change between the 2 programs.}, } @article {pmid30929665, year = {2019}, author = {Caesar, R}, title = {Pharmacologic and Nonpharmacologic Therapies for the Gut Microbiota in Type 2 Diabetes.}, journal = {Canadian journal of diabetes}, volume = {43}, number = {3}, pages = {224-231}, doi = {10.1016/j.jcjd.2019.01.007}, pmid = {30929665}, issn = {2352-3840}, mesh = {Diabetes Mellitus, Type 2/immunology/metabolism/*microbiology ; Diet Therapy ; Dietary Fiber/therapeutic use ; Dysbiosis/*therapy ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/drug effects ; Glucose/*metabolism ; Humans ; Immunity, Innate ; Metformin/adverse effects/therapeutic use ; Probiotics/therapeutic use ; }, abstract = {The gut microbiota is an important regulator of host metabolism. Metagenome analyses have demonstrated that the gut microbiota differs between patients with type 2 diabetes and healthy subjects, and several studies have shown that impaired glucose metabolism is associated with decreased levels of butyrate-producing bacteria. Gut microbiota-produced metabolites, such as short-chain fatty acids, amino acid derivatives and secondary bile acids, participate in metabolic and immunologic processes and, hence, pose putative links between the gut microbiota and glucose homeostasis. Strategies to prevent and treat type 2 diabetes through manipulation of the gut microbiota are being developed. These include replacement of the gut microbiota by fecal transplantation, consumption of fibres to promote the function and growth of beneficial bacteria and treatment with probiotic bacterial strains. Furthermore, it has been shown that many drugs, including drugs used for treatment of diabetes, have major impacts on gut microbiota and, thereby, potentially on glucose metabolism. In particular, the commonly used drug metformin has been shown to influence the functional capacity of the gut microbiota, and recent evidence indicates that this may contribute to the antidiabetes effect of metformin.}, } @article {pmid30928605, year = {2019}, author = {Kraberger, S and Cook, CN and Schmidlin, K and Fontenele, RS and Bautista, J and Smith, B and Varsani, A}, title = {Diverse single-stranded DNA viruses associated with honey bees (Apis mellifera).}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {71}, number = {}, pages = {179-188}, doi = {10.1016/j.meegid.2019.03.024}, pmid = {30928605}, issn = {1567-7257}, mesh = {Animals ; Bees/*virology ; DNA Viruses/*genetics ; Metagenomics ; Microbiota/genetics ; Microviridae/genetics ; }, abstract = {Honey bees (Apis mellifera) research has increased in light of their progressive global decline over the last decade and the important role they play in pollination. One expanding area of honey bee research is analysis of their microbial community including viruses. Several RNA viruses have been characterized but little is known about DNA viruses associated with bees. Here, using a metagenomics based approach, we reveal the presence of a broad range of novel single-stranded DNA viruses from the hemolymph and brain of nurse and forager (worker divisions of labour) bees belonging to two honey bees subspecies, Italian (Apis mellifera linguistica) and New World Carniolan (Apis mellifera carnica). Genomes of 100 diverse viruses were identified, designated into three groupings; genomoviruses (family Genomoviridae) (n = 4), unclassified replication associated protein encoding single-stranded DNA viruses (n = 28), and microviruses (family Microviridae; subfamily Gokushovirinae) (n = 70). Amongst the viruses identified, it appears that nurses harbour a higher diversity of these viruses comparative to the foragers. Between subspecies, the most striking outcome was the extremely high number of diverse microviruses identified in the Italian bees comparative to the New World Carniolan, likely indicating an association to the diversity of the bacterial community associated with these subspecies.}, } @article {pmid30927646, year = {2019}, author = {Rong, H and Xie, XH and Zhao, J and Lai, WT and Wang, MB and Xu, D and Liu, YH and Guo, YY and Xu, SX and Deng, WF and Yang, QF and Xiao, L and Zhang, YL and He, FS and Wang, S and Liu, TB}, title = {Similarly in depression, nuances of gut microbiota: Evidences from a shotgun metagenomics sequencing study on major depressive disorder versus bipolar disorder with current major depressive episode patients.}, journal = {Journal of psychiatric research}, volume = {113}, number = {}, pages = {90-99}, doi = {10.1016/j.jpsychires.2019.03.017}, pmid = {30927646}, issn = {1879-1379}, mesh = {Adult ; Bipolar Disorder/*microbiology ; Depressive Disorder, Major/*microbiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Metagenomics/*methods/statistics & numerical data ; }, abstract = {BACKGROUND: To probe the differences of gut microbiota among major depressive disorder (MDD), bipolar disorder with current major depressive episode (BPD) and health participants.

METHODS: Thirty one MDD patients, thirty BPD patients, and thirty healthy controls (HCs) were recruited. All the faecal samples were analyzed by shotgun metagenomics sequencing. Except for routine analyses of alpha diversity, we specially designed a new indicator, the Gm coefficient, to evaluate the inequality of relative abundances of microbiota for each participant.

RESULTS: The Gm coefficients are significant decreased in both MDD and BPD groups. The relative abundances of increased phyla Firmicutes and Actinobacteria and decreased Bacteroidetes were significantly in the MDD and BPD groups. At genus level, four of top five enriched genera (Bacteroides, Clostridium, Bifidobacterium, Oscillibacter and Streptococcus) were found increased significantly in the MDD and BPD groups compared with HCs. The genera Escherichia and Klebsiella showed significant changes in abundances only between the BPD and HC groups. At the species level, compared with BPD patients, MDD patients had a higher abundance of Prevotellaceae including Prevotella denticola F0289, Prevotella intermedia 17, Prevotella ruminicola, and Prevotella intermedia. Furthermore, the abundance of Fusobacteriaceae, Escherichia blattae DSM 4481 and Klebsiella oxytoca were significantly increased, whereas the Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 was significantly reduced in BPD group compared with MDD group.

CONCLUSIONS: Our study suggested that gut microbiota may be involved in the pathogenesis of both MDD and BPD patients, and the nuances of bacteria may have the potentiality of being the biomarkers of MDD and BPD.}, } @article {pmid30927638, year = {2019}, author = {Wei, Z and Yu, S and Huang, Z and Xiao, X and Tang, M and Li, B and Zhang, X}, title = {Simultaneous removal of elemental mercury and NO by mercury induced thermophilic community in membrane biofilm reactor.}, journal = {Ecotoxicology and environmental safety}, volume = {176}, number = {}, pages = {170-177}, doi = {10.1016/j.ecoenv.2019.03.082}, pmid = {30927638}, issn = {1090-2414}, mesh = {Biofilms/*growth & development ; Bioreactors/*microbiology ; Denitrification ; Mercury/*analysis ; Metagenomics ; Microbiota/drug effects/genetics ; Nitric Oxide/*analysis ; Nitrification ; Oxidation-Reduction ; }, abstract = {Thermophilic membrane biofilm reactor (TMBR) for elemental mercury (Hg[0]) and NO removal in simulated flue gas was investigated at oxygen content of 6% and 60 °C. The performance, the microbial community structures, gene function and the mechanism for Hg[0] and NO removal in the TMBR were evaluated. TMBR achieved effective simultaneous Hg[0] and NO removal in 210 days of operation, Hg[0] and NO removal efficiency were up to 88.9% and 85.3%, respectively. Mercury induced thermophilic community had been formed significantly. Comamonas, Pseudomonas, Desulfomicrobium, Burkholderia and Halomonas were thermophilic mercury resistant bacteria. Brucella, Paracoccus, Tepidiphilus, Proteobacteria, Pseudomonas and Symbiobacterium were nitrifying/denitrifying genera, and had functional genes of mercury and nitrogen metabolism, as shown by16S rDNA and metagenomic sequencing. The biofilm in TMBR was characterized by XPS, HPLC. XPS and HPLC spectra indicate the formation of a mercuric species (Hg[2+]) from mercury oxidation. TMBR used oxygen as electron acceptor, NO and Hg[0] as electron donor in nitrification; O2, NO and NO3[-] could be used as electron acceptor and Hg[0] as electron donor in denitrification.}, } @article {pmid30927421, year = {2019}, author = {Ding, GC and Bai, M and Han, H and Li, H and Ding, X and Yang, H and Xu, T and Li, J}, title = {Microbial taxonomic, nitrogen cycling and phosphorus recycling community composition during long-term organic greenhouse farming.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {5}, pages = {}, doi = {10.1093/femsec/fiz042}, pmid = {30927421}, issn = {1574-6941}, mesh = {Acidobacteria/genetics ; Ammonia/*metabolism ; Archaea/classification/genetics/*isolation & purification/*metabolism ; Bacteria/classification/genetics/*isolation & purification/*metabolism ; Denitrification ; Metagenome ; Nitrogen Cycle ; Organic Agriculture ; Phosphorus/*metabolism ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; Time Factors ; }, abstract = {Understanding the interplay between the farming system and soil microbiomes could aid the design of a sustainable and efficient farming system. A comparative greenhouse experiment consisting of organic (ORG), integrated (INT) and conventional (CON) farming systems was established in northern China in 2002. The effects of 12 years of organic farming on soil microbiomes were explored by metagenomic and 16S rRNA gene amplicon sequencing analyses. Long-term ORG shifted the community composition of dominant phyla, especially Acidobacteria, increased the relative abundance of Ignavibacteria and Acidobacteria Gp6 and decreased the relative abundance of Nitrosomonas, Bacillus and Paenibacillus. Metagenomic analysis further revealed that relative abundance of ammonia oxidizing microorganisms (Bacteria and Archaea) and anaerobic ammonium oxidation bacteria decreased during ORG. Conversely, the relative abundance of bacteria-carrying periplasmic nitrate reductases (napA) was slightly higher for ORG. Long-term organic farming also caused significant alterations to the community composition of functional groups associated with ammonia oxidation, denitrification and phosphorus recycling. In summary, this study provides key insights into the composition of soil microbiomes and long-term organic farming under greenhouse conditions.}, } @article {pmid30927344, year = {2019}, author = {Bergsveinson, J and Perry, BJ and Simpson, GL and Yost, CK and Schutzman, RJ and Hall, BD and Cameron, ADS}, title = {Spatial analysis of a hydrocarbon waste-remediating landfarm demonstrates influence of management practices on bacterial and fungal community structure.}, journal = {Microbial biotechnology}, volume = {12}, number = {6}, pages = {1199-1209}, pmid = {30927344}, issn = {1751-7915}, mesh = {Bacteria/*classification/genetics/metabolism ; *Biodegradation, Environmental ; Biotransformation ; Fungi/*classification/genetics/metabolism ; High-Throughput Nucleotide Sequencing ; Hydrocarbons/*metabolism ; Metagenomics ; *Microbiota ; Saskatchewan ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/*metabolism ; Spatial Analysis ; }, abstract = {Cultivation of dedicated soil plots called 'landfarms' is an effective technology for bioremediation of hydrocarbon waste generated by various industrial practices. To understand the influence of soil conditions on landfarm microbial communities, analysis of bacterial and fungal community structure using next-generation sequencing at different sections and depths was performed across a hydrocarbon-waste landfarm in Regina, Saskatchewan, Canada. While a core set of hydrocarbon-associated bacterial and fungal taxa are present throughout the landfarm, unique bacterial and fungal operational taxonomic units are differentially abundant at sections within the landfarm, which correlate with differences in soil physiochemical properties and management practices. Increased frequency of waste application resulted in strong positive correlations between bacterial community assemblages and elevated amounts of oil, grease and F3 - F4 hydrocarbon fractions. In areas of standing water and lower application of hydrocarbon, microbial community structure correlated with soil pH, trace nutrients and metals. Overall, diversity and structure of bacterial communities remain relatively stable across the landfarm, while in contrast, fungal community structure appears more responsive to soil oxygen conditions. Results are consistent with the hypothesis that years of bioremediation activity have shaped microbial communities; however, several management practices can be undertaken to increase efficiency of remediation, including the removal of standing water and soil tilling across the landfarm.}, } @article {pmid30926487, year = {2019}, author = {Ji, X and Hou, C and Zhang, X and Han, L and Yin, S and Peng, Q and Wang, M}, title = {Microbiome-metabolomic analysis of the impact of Zizyphus jujuba cv. Muzao polysaccharides consumption on colorectal cancer mice fecal microbiota and metabolites.}, journal = {International journal of biological macromolecules}, volume = {131}, number = {}, pages = {1067-1076}, doi = {10.1016/j.ijbiomac.2019.03.175}, pmid = {30926487}, issn = {1879-0003}, mesh = {Animal Feed ; Animals ; Biomarkers ; Colorectal Neoplasms/etiology/*metabolism/pathology ; Cytokines/metabolism ; Disease Models, Animal ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; Inflammation Mediators/metabolism ; Male ; Metabolic Networks and Pathways ; *Metabolome ; *Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Mice ; *Polysaccharides ; RNA, Ribosomal, 16S/genetics ; Ziziphus/*chemistry ; }, abstract = {It is still uncertain whether the consumption of Zizyphus jujuba cv. Muzao polysaccharides (ZMP) alleviates colorectal cancer (CRC) through the gut microbiota. In this study, we investigated the mortality, colon length, inflammatory factors and cecal microbiota, metabolites of healthy and azoxymethane (AOM) and dextran sodium sulfate (DSS) in induced CRC mice, consuming ZMP. Fecal-microbiota composition was examined using 16S rDNA sequencing and fecal-metabolome profiles were evaluated by ultra-high performance liquid chromatograph mass spectrometry (UHPLC-MS). The results showed ZMP consumption prevented CRC mouse colon shortening, decreased their mortality, reduced pro-inflammatory cytokines, increased the concentration of total short-chain fatty acids (SCFAs) and modulated gut microbiota in their feces. ZMP also increased the richness of Bifidobacterium, Bacteroides and Lactobacillus. In addition, among 39 perturbed metabolites, carbohydrate and amino acid production were noticeably altered. Moreover, higher correlations were found between fluctuant gut microbiota and metabolites. These findings provide mechanistic insights into the impact of dietary Zizyphus jujuba cv. Muzao polysaccharides on host health.}, } @article {pmid30924428, year = {2019}, author = {Precup, G and Vodnar, DC}, title = {Gut Prevotella as a possible biomarker of diet and its eubiotic versus dysbiotic roles: a comprehensive literature review.}, journal = {The British journal of nutrition}, volume = {122}, number = {2}, pages = {131-140}, doi = {10.1017/S0007114519000680}, pmid = {30924428}, issn = {1475-2662}, mesh = {*Biomarkers ; *Diet ; Dietary Fiber/administration & dosage ; Dysbiosis/*microbiology ; Feeding Behavior/physiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Humans ; Metabolic Syndrome/microbiology ; Obesity/microbiology ; Plants, Edible ; Polysaccharides/metabolism ; Prevotella/*physiology ; }, abstract = {The gut microbiota has a profound impact on human health. Emerging data show that dietary patterns are associated with different communities of bacterial species within the gut. Prevotella species have been correlated with plant-rich diets, abundant in carbohydrates and fibres. Dysbiosis within the gut ecosystem has been associated with the development of non-communicable diseases such as obesity, the metabolic syndrome, inflammatory bowel disease, irritable bowel syndrome, colorectal cancer, type 1 diabetes, allergies and other diseases. The purpose of this comprehensive literature review was to evaluate the available data on the impact of diet on the Prevotella genus, as a dietary fibre fermenter in the gut as well as its implications as a potential biomarker for homeostasis or disease state through its metabolite signature. Studies were identified by conducting PubMed, Web of Science Core Collection and Google Scholar electronic searches. We found eighty-five publications reporting the impact of dietary patterns on gut microbial communities, including Prevotella or Prevotella/Bacteroides ratio in particular. Moreover, the role of Prevotella species on health status was also evaluated. Prevotella possess a high genetic diversity, representing one of the important groups found in the oral cavity and large intestine of man. The gut commensal Prevotella bacteria contribute to polysaccharide breakdown, being dominant colonisers of agrarian societies. However, studies also suggested a potential role of Prevotella species as intestinal pathobionts. Further metagenomic studies are needed in order to reveal health- or disease-modulating properties of Prevotella species in the gut.}, } @article {pmid30922964, year = {2019}, author = {Liao, X and Song, L and Zeng, B and Liu, B and Qiu, Y and Qu, H and Zheng, Y and Long, M and Zhou, H and Wang, Y and Du, Y and Xu, J and Shen, R and Tong, Q and Cai, L and Li, X and Guo, S and Yang, G and Zhu, Z and Pu, X and Wei, H and Zheng, H}, title = {Alteration of gut microbiota induced by DPP-4i treatment improves glucose homeostasis.}, journal = {EBioMedicine}, volume = {44}, number = {}, pages = {665-674}, pmid = {30922964}, issn = {2352-3964}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Blood Glucose ; Diabetes Mellitus, Type 2/metabolism ; Diet, High-Fat ; Dipeptidyl-Peptidase IV Inhibitors/*pharmacology ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; Glucose/*metabolism ; Glucose Tolerance Test ; Homeostasis/*drug effects ; Humans ; Insulin/metabolism ; Male ; Metagenome ; Metagenomics/methods ; Mice ; }, abstract = {BACKGROUND: Increasing evidence indicates that the gut microbiota contributes to the occurrence and development of metabolic diseases. However, little is known about the effects of commonly used antidiabetic agents on the gut microbiota. In this study, we investigated the roles of dipeptidyl peptidase-4 inhibitors (DPP-4i) and α-glucosidase inhibitor in modulating the gut microbiota.

METHODS: 16S-rDNA sequencing was performed to analyse the effects of DPP-4i and acarbose on the gut microbiota in mice fed a high-fat diet (HFD). Fecal microbiota transplantation (FMT) from type 2 diabetes patients to germ-free mice was performed to investigate the contribution of the altered microbiome to antidiabetic effects of the drugs. Fecal metabolomics was also analysed by untargeted and targeted GC-MS systems.

FINDINGS: Although DPP-4i and α-glucosidase inhibitor both altered the gut microbial composition, only the microbiome modulation of DPP-4i contributed to its hypoglycemic effect. Specifically, the changes of 68.6% genera induced by HFD were rescued by DPP-4i. FMT showed that the DPP-4i-altered microbiome improved glucose tolerance in colonized mice, while acarbose did not. Moreover, DPP-4i increased the abundance of Bacteroidetes, and also promoted a functional shift in the gut microbiome, especially increasing the production of succinate.

INTERPRETATION: Our findings demonstrate an important effect of DPP-4i on the gut microbiota, revealing a new hypoglycemic mechanism and an additional benefit of it. Furthermore, modulating the microbial composition, and the functional shift arising from changes in the microbiome, might be a potential strategy for improving glucose homeostasis. FUND: This work was supported by grants from the National Natural Science Foundation of China (No. 81700757, No. 81471039, No. 81700714 and No. 81770434), the National Key R&D Program of China (No. 2017YFC1309602, No. 2016YFC1101100, No. 2017YFD0500503 and No. 2017YFD0501001), and the Natural Science Foundation of Chongqing (No. cstc2014jcyjjq10006, No. cstc2016jcyjA0093 and No. cstc2016jcyjA0518).}, } @article {pmid30920634, year = {2019}, author = {De Grandi, R and Bottagisio, M and Di Girolamo, S and Bidossi, A and De Vecchi, E and Drago, L}, title = {Modulation of opportunistic species Corynebacterium diphtheriae, Haemophilus parainfluenzae, Moraxella catarrhalis, Prevotella denticola, Prevotella melaninogenica, Rothia dentocariosa, Staphylococcus aureus and Streptococcus pseudopneumoniae by intranasal administration of Streptococcus salivarius 24SMBc and Streptococcus oralis 89a combination in healthy subjects.}, journal = {European review for medical and pharmacological sciences}, volume = {23}, number = {1 Suppl}, pages = {60-66}, doi = {10.26355/eurrev_201903_17351}, pmid = {30920634}, issn = {2284-0729}, mesh = {Administration, Intranasal ; Adult ; Female ; Healthy Volunteers ; Humans ; Male ; Microbiota/*drug effects ; Middle Aged ; Nose/*microbiology ; Probiotics/administration & dosage/*pharmacology ; *Streptococcus oralis ; *Streptococcus salivarius ; Time Factors ; Young Adult ; }, abstract = {OBJECTIVE: Probiotics S. salivarius 24SMBc and S. oralis 89a comprised in the nasal spray Rinogermina are known to exert inhibition of harmful pathogens and ameliorate the outcome of patients with chronic upper airways infections. In this study, for the first time, the effect of this formulation on the modulation of the microflora of healthy subjects was evaluated, with particular interest on pathobionts and pathogens present.

PATIENTS AND METHODS: Metagenomic identification and quantification of bacterial abundances in healthy subjects were carried out by means of Ion Torrent Personal Machine. In particular, nasal swabs were sampled one, two and four weeks after seven days of treatment with Rinogermina.

RESULTS: The modulation of the abundance of pathobionts and pathogenic species (i.e., Corynebacterium diphtheriae, Haemophilus parainfluenzae, Moraxella catarrhalis, Prevotella denticola, Prevotella melaninogenica, Rothia dentocariosa, Staphylococcus aureus and Streptococcus pseudopneumoniae) was characterized and a significant temporary decrease in their presence was identified.

CONCLUSIONS: The beneficial effects of S. salivarius 24SMBc and S. oralis 89a nasal intake was assessed but seemed to be restricted in specific temporal windows. Thus it would be interesting to evaluate also this positive impact of longer administration of this probiotic formulation.}, } @article {pmid30918994, year = {2019}, author = {Klima, CL and Holman, DB and Ralston, BJ and Stanford, K and Zaheer, R and Alexander, TW and McAllister, TA}, title = {Lower Respiratory Tract Microbiome and Resistome of Bovine Respiratory Disease Mortalities.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {446-456}, pmid = {30918994}, issn = {1432-184X}, support = {2015R025R//Alberta Livestock and Meat Agency/ ; 001//Growing Forward II/ ; 001//Genomics Research Initiative/ ; }, mesh = {Alberta ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/*isolation & purification ; Bacterial Infections/microbiology/mortality/*veterinary ; Cattle ; Cattle Diseases/*microbiology/mortality ; *Drug Resistance, Bacterial ; *Microbiota ; Respiratory System/*microbiology ; Respiratory Tract Diseases/microbiology/mortality/*veterinary ; }, abstract = {Bovine respiratory disease (BRD) continues to be a serious health problem in beef cattle production. A multifactorial condition, BRD encompasses several types of pneumonia that are associated with multiple viral and bacterial agents. Comprehensive identification of microbes associated with BRD fatalities could enhance our understanding of the range of pathogens that contribute to the disease and identify new therapeutic targets. This study used metagenomic analysis to describe the lower respiratory tract microbiome and resistome of 15 feedlot cattle BRD and 3 non-BRD mortalities along with any affiliated integrative and conjugative elements (ICEs). Known bacterial pathogens associated with BRD, including Histophilus somni, Mannheimia haemolytica, and Mycoplasma bovis, were relatively abundant (> 5%) in most, but not all samples. Other relatively abundant genera (> 1%) included Acinetobacter, Bacillus, Bacteroides, Clostridium, Enterococcus, and Pseudomonas. Antimicrobial resistance genes (ARGs) comprised up to 0.5% of sequences and many of these genes were associated with ICEs previously described within the Pasteurellaceae family. A total of 20 putative ICEs were detected among 16 samples. These results document the wide diversity of microorganisms in the lower respiratory tract of cattle that have succumbed to BRD. The data also strongly suggest that antimicrobial-resistant Pasteurellaceae strains are prevalent in BRD cases in Alberta and that the resistance observed is associated with ICEs. The presence of ICEs harboring a wide array of ARGs holds significant consequence for the effectiveness of drug therapies for the control of BRD in beef cattle.}, } @article {pmid30918406, year = {2019}, author = {Zeevi, D and Korem, T and Godneva, A and Bar, N and Kurilshikov, A and Lotan-Pompan, M and Weinberger, A and Fu, J and Wijmenga, C and Zhernakova, A and Segal, E}, title = {Structural variation in the gut microbiome associates with host health.}, journal = {Nature}, volume = {568}, number = {7750}, pages = {43-48}, pmid = {30918406}, issn = {1476-4687}, mesh = {Adaptation, Physiological/genetics ; Bacteria/classification/*genetics/growth & development/metabolism ; Butyrates/metabolism ; Cohort Studies ; Disease Susceptibility/*microbiology ; Ecosystem ; Eubacterium/genetics/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics/physiology ; Genes, Bacterial/*genetics ; *Genetic Variation ; *Health ; Host Microbial Interactions/*genetics/physiology ; Humans ; Inositol/metabolism ; Metagenomics ; Microbial Viability/genetics ; Risk Factors ; }, abstract = {Differences in the presence of even a few genes between otherwise identical bacterial strains may result in critical phenotypic differences. Here we systematically identify microbial genomic structural variants (SVs) and find them to be prevalent in the human gut microbiome across phyla and to replicate in different cohorts. SVs are enriched for CRISPR-associated and antibiotic-producing functions and depleted from housekeeping genes, suggesting that they have a role in microbial adaptation. We find multiple associations between SVs and host disease risk factors, many of which replicate in an independent cohort. Exploring genes that are clustered in the same SV, we uncover several possible mechanistic links between the microbiome and its host, including a region in Anaerostipes hadrus that encodes a composite inositol catabolism-butyrate biosynthesis pathway, the presence of which is associated with lower host metabolic disease risk. Overall, our results uncover a nascent layer of variability in the microbiome that is associated with microbial adaptation and host health.}, } @article {pmid30918057, year = {2019}, author = {Thomas, M and Wongkuna, S and Ghimire, S and Kumar, R and Antony, L and Doerner, KC and Singery, A and Nelson, E and Woyengo, T and Chankhamhaengdecha, S and Janvilisri, T and Scaria, J}, title = {Gut Microbial Dynamics during Conventionalization of Germfree Chicken.}, journal = {mSphere}, volume = {4}, number = {2}, pages = {}, pmid = {30918057}, issn = {2379-5042}, mesh = {Animals ; Bacteria/*classification/isolation & purification ; Bacteroidetes/classification/isolation & purification ; Chickens/growth & development ; DNA, Bacterial/genetics ; Firmicutes/classification/isolation & purification ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; *Germ-Free Life ; *Host Microbial Interactions ; Metagenomics ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A gnotobiotic Gallus gallus (chicken) model was developed to study the dynamics of intestinal microflora from hatching to 18 days of age employing metagenomics. Intestinal samples were collected from a local population of feral chickens and administered orally to germfree 3-day-old chicks. Animals were euthanized on days 9 and 18 postinoculation, and intestinal samples were collected and subjected to metagenomic analysis. On day 18, the five most prevalent phyla were Bacteroidetes (43.03 ± 3.19%), Firmicutes (38.51 ± 2.67%), Actinobacteria (6.77 ± 0.7%), Proteobacteria (6.38 ± 0.7%), and Spirochaetes (2.71 ± 0.55%). Principal-coordinate analysis showed that the day 18 variables clustered more closely than the day 9 variables, suggesting that the microbial communities had changed temporally. The Morista-Horn index values ranged from 0.7 to 1, indicating that the communities in the inoculum and in the day 9 and day 18 samples were more similar than dissimilar. The predicted functional profiles of the microbiomes of the inoculum and the day 9 and day 18 samples were also similar (values of 0.98 to 1). These results indicate that the gnotobiotic chicks stably maintained the phylogenetic diversity and predicted metabolic functionality of the inoculum community.IMPORTANCE The domestic chicken is the cornerstone of animal agriculture worldwide, with a flock population exceeding 40 billion birds/year. It serves as an economically valuable source of protein globally. The microbiome of poultry has important effects on chicken growth, feed conversion, immune status, and pathogen resistance. The aim of our research was to develop a gnotobiotic chicken model appropriate for the study chicken gut microbiota function. Our experimental model shows that young germfree chicks are able to colonize diverse sets of gut bacteria. Therefore, besides the use of this model to study mechanisms of gut microbiota interactions in the chicken gut, it could be also used for applied aspects such as determining the safety and efficacy of new probiotic strains derived from chicken gut microbiota.}, } @article {pmid30916575, year = {2019}, author = {Khandelwal, P and Andersen, H and Romick-Rosendale, L and Taggart, CB and Watanabe, M and Lane, A and Dandoy, CE and Lake, KE and Litts, BA and Morrow, AL and Lee, ML and Haslam, DB and Davies, SM}, title = {A Pilot Study of Human Milk to Reduce Intestinal Inflammation After Bone Marrow Transplant.}, journal = {Breastfeeding medicine : the official journal of the Academy of Breastfeeding Medicine}, volume = {14}, number = {3}, pages = {193-202}, doi = {10.1089/bfm.2018.0199}, pmid = {30916575}, issn = {1556-8342}, mesh = {Animals ; Bacteremia/epidemiology/prevention & control ; Bone Marrow Transplantation/*adverse effects ; Child, Preschool ; Cytokines/metabolism ; *Enteral Nutrition ; Female ; Gastrointestinal Microbiome ; Graft vs Host Disease/epidemiology/prevention & control ; Humans ; Infant ; Inflammation/*prevention & control ; Intestines/microbiology/*pathology ; Male ; *Milk, Human ; Ohio ; Pilot Projects ; Wound Healing ; }, abstract = {OBJECTIVE: Human milk administration in the early peritransplant period would lower intestinal inflammation after bone marrow transplant (BMT).

MATERIALS AND METHODS: Children 0-5 years undergoing BMT received either a ready-to-feed human milk preparation designed for these children (Prolacta Bioscience, Duarte, CA) or standard formula. Babies breastfeeding at the time of BMT were also enrolled on the human milk arm. Human milk was administered from day -3 until day +14 after BMT. Metagenomic shotgun sequencing and metabolomics of stool, plasma cytokines, and regenerating islet-derived 3α (REG3α) levels were measured at enrollment and day +14. Human leukocyte antigen-DR isotype (HLA-DR), CD38, and CD69 expression on T cells were evaluated at day +21.

RESULTS: Forty-six children were enrolled, 32 received human milk (donor milk n = 23, breastfeeding babies n = 9), and 14 were controls who received standard feeds supervised by a BMT dietician. Twenty-four patients received at least 60% of goal human milk and were evaluable. Plasma interleukin (IL)-8 (p = 0.04), IL-10 (p = 0.02), and REG3α (p = 0.03) were decreased in the human milk cohort. Peripheral blood CD69[+] CD8[+] T cells were higher in controls (p = 0.01). Species abundance of Adenovirus (p = 0.00034), Escherichia coli (p = 0.0017), Cryptosporidium parvum (p = 0.0006), Dialister invisus (p = 0.01), and Pseudomonas aeruginosa (p = 0.05) from stool was higher in controls. Stool alanine, tyrosine, methionine, and the ratio of fecal alanine to choline and phosphocholine were higher in controls (p < 0.05). No difference was observed in stool propionate and butyrate levels as measures of short-chain fatty acids between the two cohorts.

CONCLUSIONS: Administration of human milk resulted in decreased markers of intestinal inflammation and could be a valuable adjunct for patients after BMT.}, } @article {pmid30915691, year = {2019}, author = {Akyol, Ç and Ozbayram, EG and Demirel, B and Onay, TT and Ince, O and Ince, B}, title = {Linking nano-ZnO contamination to microbial community profiling in sanitary landfill simulations.}, journal = {Environmental science and pollution research international}, volume = {26}, number = {13}, pages = {13580-13591}, pmid = {30915691}, issn = {1614-7499}, support = {112Y322//TUBITAK/ ; 13081//Boğaziçi University Research Fund Project/ ; }, mesh = {Archaea ; Bacteria ; Biofuels ; Bioreactors/*microbiology ; Microbiota ; RNA, Ribosomal, 16S/*chemistry ; Refuse Disposal/methods ; Solid Waste/*analysis ; Waste Disposal Facilities ; Zinc Oxide/*analysis/chemistry ; }, abstract = {Nanomaterials (NMs) commercially used for various activities mostly end up in landfills. Reduced biogas productions reported in landfill reactors create a need for more comprehensive research on these greatly-diverse microbial pools. In order to evaluate the impact of one of the most widely-used NMs, namely nano-zinc oxide (nano-ZnO), simulated bioreactor and conventional landfills were operated using real municipal solid waste (MSW) for 300 days with addition nano-ZnO. Leachate samples were taken at different phases and analyzed by 16S rRNA gene amplicon sequencing. The bacterial communities were distinctly characterized by Cloacamonaceae (phylum WWE1), Rhodocyclaceae (phylum Proteobacteria), Porphyromonadaceae (phylum Bacteroidetes), and Synergistaceae (phylum Synergistetes). The bacterial community in the bioreactors shifted at the end of the operation and was dominated by Rhodocyclaceae. There was not a major change in the bacterial community in the conventional reactors. The methanogenic archaeal diversity highly differed between the bioreactors and conventional reactors. The dominance of Methanomicrobiaceae was observed in the bioreactors during the peak methane-production period; however, their prominence shifted to WSA2 in the nano-ZnO-added bioreactor and to Methanocorpusculaceae in the control bioreactor towards the end. Methanocorpusculaceae was the most abundant family in both conventional control and nano-ZnO-containing reactors.}, } @article {pmid30915455, year = {2019}, author = {Taft, DH and Salinero, LK and Vongbhavit, K and Kalanetra, KM and Masarweh, C and Yu, A and Underwood, MA and Mills, DA}, title = {Bacterial colonization and antimicrobial resistance genes in neonatal enteral feeding tubes.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {4}, pages = {}, pmid = {30915455}, issn = {1574-6941}, support = {F32 HD093185/HD/NICHD NIH HHS/United States ; R01 AT008759/AT/NCCIH NIH HHS/United States ; S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics/*isolation & purification ; Drug Resistance, Bacterial/*genetics ; Enteral Nutrition/*instrumentation ; Feces/microbiology ; Genome, Bacterial/genetics ; Humans ; Infant Formula ; Infant, Newborn ; Intensive Care Units, Neonatal ; Microbiota/genetics ; Milk, Human ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Enteral feeding is a key component of care in neonatal intensive care units (NICUs); however, feeding tubes harbor microbes. These microbes have the potential to cause disease, yet their source remains controversial and clinical recommendations to reduce feeding tube colonization are lacking. This study aims to improve our understanding of the bacteria in neonatal feeding tubes and to evaluate factors that may affect these bacteria. 16S rRNA gene sequencing was used to characterize the bacteria present in pharyngeal, esophageal, and gastric portions of feeding tubes, residual fluid of the tubes, and infant stool using samples from 47 infants. Similar distributions of taxa were observed in all samples, although beta diversity differed by sample type. Feeding tube samples had lower alpha diversity than stool samples, and alpha diversity increased with gestational age, day of life, and tube dwell time. In a subset of samples from 6 infants analyzed by whole metagenome sequencing, there was greater overlap in transferable antimicrobial resistance genes between tube and fecal samples in breast milk fed infants than in formula fed infants. These findings develop our understanding of neonatal feeding tube colonization, laying a foundation for research into methods for minimizing NICU patients' exposure to antimicrobial resistant microbes.}, } @article {pmid30915280, year = {2019}, author = {Wei, Y and Shi, M and Zhen, M and Wang, C and Hu, W and Nie, Y and Wu, X}, title = {Comparison of Subgingival and Buccal Mucosa Microbiome in Chronic and Aggressive Periodontitis: A Pilot Study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {53}, pmid = {30915280}, issn = {2235-2988}, mesh = {Adult ; Aggressive Periodontitis/*microbiology ; Chronic Disease ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Gingiva/*microbiology ; Humans ; Male ; Metagenomics ; *Microbiota ; Mouth Mucosa/*microbiology ; Phylogeny ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Periodontal microorganisms not only colonize subgingival pockets, but also are detected on various mucous membranes in patients with periodontitis. The object of this pilot study was, using the next-generation sequencing of 16S RNA gene, to characterize the microbiota in two oral habitats (buccal mucosas and subgingival pockets) in patients with different forms of periodontitis. Thirty-two buccal swab samples and 113 subgingival samples were obtained from eleven subjects with chronic periodontitis (ChP), twelve subjects with aggressive periodontitis (AgP), and nine periodontally healthy individuals (HP). Using Miseq Sequencing of 16S rRNA gene, we found that the subgingival and buccal mucosa microbiome of ChP and AgP patients both differed from HP. Meanwhile, Veillonella, Treponema, Filifactor, Fretibacterium, Peptostreptococcaceae_[XI][G-6], Peptostreptococcaceae_[XI][G-5], Bacteroidetes_[G-5], Bacteroidetes_[G-3], Peptostreptococcaceae_[XI][G-4], Peptostreptococcaceae_[XI][G-2] significantly increased both in buccal and subgingival plaque samples in periodontitis subjects (ChP and AgP) compared with HP. Moreover, the results based on the Unweighted UniFrac distance showed that buccal and subgingival plaque samples from the same individuals show higher community divergence than same habitats from different subject samples. This study demonstrated that the microbiome of buccal mucosa can be influenced by periodontitis. However, subgingival and buccal mucosa microbiome seem to be characterized by species-specific colonization patterns. This pilot study provides a glimpse at the changes of subgingival and buccal mucosa associated with periodontitis from a holistic view. Further studies should be taken to illuminate the interplay between these detected changes and periodontitis development.}, } @article {pmid30914730, year = {2019}, author = {Tragin, M and Vaulot, D}, title = {Novel diversity within marine Mamiellophyceae (Chlorophyta) unveiled by metabarcoding.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5190}, pmid = {30914730}, issn = {2045-2322}, mesh = {Aquatic Organisms/*classification/*genetics ; Base Sequence ; *Biodiversity ; Chlorophyta/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Geography ; *Metagenomics ; Phylogeny ; }, abstract = {Mamiellophyceae (unicellular green algae) are a key phytoplankton group in coastal waters. Although extensively studied over the last 20 years, the overall oceanic distribution of the major species/clades is still poorly known. To address this problem, we analyzed the 2014 Ocean Sampling Day (OSD) metabarcoding dataset providing sequences from the V4 hypervariable region of the 18S rRNA gene for 157 samples collected at 143 mostly coastal stations. Mamiellophyceae were found at nearly all OSD stations and represented 55% of the green microalgae (Chlorophyta) reads. We performed phylogenetic analyses of unique OSD metabarcodes (amplicon single variants, ASVs) and GenBank reference sequences from cultures and from the environment, focusing on the four most represented genera: Ostreococcus (45% of the Mamiellophyceae reads), Micromonas (34%), Bathycoccus (10%) and Mantoniella (8.7%). These analyses uncovered novel diversity within each genus except Bathycoccus. In Ostreococcus, a new clade (E) was the second most represented clade after Ostreococcus "lucimarinus". Micromonas could be separated into nine clades, exceeding the six species and candidate species already described. Finally, we found two new environmental clades within Mantoniella. Each Mamiellophyceae clade had a specific distribution in the OSD dataset suggesting that they are adapted to different ecological niches.}, } @article {pmid30914068, year = {2019}, author = {Wang, W and Hu, H and Zijlstra, RT and Zheng, J and Gänzle, MG}, title = {Metagenomic reconstructions of gut microbial metabolism in weanling pigs.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {48}, pmid = {30914068}, issn = {2049-2618}, mesh = {Animals ; Bacteria/*classification/genetics/isolation & purification ; Bacteroidetes/genetics/isolation & purification/metabolism ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Dietary Carbohydrates/*metabolism ; Firmicutes/genetics/isolation & purification/metabolism ; Gastrointestinal Microbiome ; Lactobacillus/genetics/isolation & purification/metabolism ; Male ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Swine ; }, abstract = {BACKGROUND: The piglets' transition from milk to solid feed induces a succession of bacterial communities, enhancing the hosts' ability to harvest energy from dietary carbohydrates. To reconstruct microbial carbohydrate metabolism in weanling pigs, this study combined 16S rRNA gene sequencing (n = 191) and shotgun metagenomics (n = 72).

RESULTS: Time and wheat content in feed explained most of the variation of the microbiota as assessed by 16S rRNA gene sequencing in weanling pigs. De novo metagenomic binning reconstructed 360 high-quality genomes that represented 11 prokaryotic and 1 archaeal phylum. Analysis of carbohydrate metabolism in these genomes revealed that starch fermentation is carried out by a consortium of Firmicutes expressing extracellular α-(1 → 4)-glucan branching enzyme (GH13) and Bacteroidetes expressing periplasmic neopullulanase (GH13) and α-glucosidase (GH97). Fructans were degraded by extracellular GH32 enzymes from Bacteriodetes and Lactobacillus. Lactose fermentation by β-galactosidases (GH2 and GH42) was identified in Firmicutes. In conclusion, the assembly of 360 high-quality genomes as the first metagenomic reference for swine intestinal microbiota allowed identification of key microbial contributors to degradation of starch, fructans, and lactose.

CONCLUSIONS: Microbial consortia that are responsible for degradation of these glycans differ substantially from the microbial consortia that degrade the same glycans in humans. Our study thus enables improvement of feeding models with higher feed efficiency and better pathogen control for weanling pigs.}, } @article {pmid30913025, year = {2019}, author = {Tauzin, AS and Bruel, L and Laville, E and Nicoletti, C and Navarro, D and Henrissat, B and Perrier, J and Potocki-Veronese, G and Giardina, T and Lafond, M}, title = {Sucrose 6[F]-phosphate phosphorylase: a novel insight in the human gut microbiome.}, journal = {Microbial genomics}, volume = {5}, number = {4}, pages = {}, pmid = {30913025}, issn = {2057-5858}, mesh = {Animals ; Clostridiales/*enzymology ; *Gastrointestinal Microbiome ; *Glycoside Hydrolases/chemistry/classification/genetics ; Humans ; Intestines/microbiology ; Mice ; Mice, Inbred C57BL ; Substrate Specificity ; Sucrose/*analogs & derivatives/metabolism ; Sugar Phosphates/*metabolism ; }, abstract = {The human gut microbiome plays an essential role in maintaining human health including in degradation of dietary fibres and carbohydrates further used as nutrients by both the host and the gut bacteria. Previously, we identified a polysaccharide utilization loci (PUL) involved in sucrose and raffinose family oligosaccharide (RFO) metabolism from one of the most common Firmicutes present in individuals, Ruminococcus gnavus E1. One of the enzymes encoded by this PUL was annotated as a putative sucrose phosphate phosphorylase (RgSPP). In the present study, we have in-depth characterized the heterologously expressed RgSPP as sucrose 6[F]-phosphate phosphorylase (SPP), expanding our knowledge of the glycoside hydrolase GH13_18 subfamily. Specifically, the enzymatic characterization showed a selective activity on sucrose 6[F]-phosphate (S6[F]P) acting both in phosphorolysis releasing alpha-d-glucose-1-phosphate (G1P) and alpha-d-fructose-6-phosphate (F6P), and in reverse phosphorolysis from G1P and F6P to S6[F]P. Interestingly, such a SPP activity had never been observed in gut bacteria before. In addition, a phylogenetic and synteny analysis showed a clustering and a strictly conserved PUL organization specific to gut bacteria. However, a wide prevalence and abundance study with a human metagenomic library showed a correlation between SPP activity and the geographical origin of the individuals and, thus, most likely linked to diet. Rgspp gene overexpression has been observed in mice fed with a high-fat diet suggesting, as observed for humans, that intestine lipid and carbohydrate microbial metabolisms are intertwined. Finally, based on the genomic environment analysis, in vitro and in vivo studies, results provide new insights into the gut microbiota catabolism of sucrose, RFOs and S6[F]P.}, } @article {pmid30906284, year = {2019}, author = {Cycoń, M and Mrozik, A and Piotrowska-Seget, Z}, title = {Antibiotics in the Soil Environment-Degradation and Their Impact on Microbial Activity and Diversity.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {338}, pmid = {30906284}, issn = {1664-302X}, abstract = {Antibiotics play a key role in the management of infectious diseases in humans, animals, livestock, and aquacultures all over the world. The release of increasing amount of antibiotics into waters and soils creates a potential threat to all microorganisms in these environments. This review addresses issues related to the fate and degradation of antibiotics in soils and the impact of antibiotics on the structural, genetic and functional diversity of microbial communities. Due to the emergence of bacterial resistance to antibiotics, which is considered a worldwide public health problem, the abundance and diversity of antibiotic resistance genes (ARGs) in soils are also discussed. When antibiotic residues enter the soil, the main processes determining their persistence are sorption to organic particles and degradation/transformation. The wide range of DT50 values for antibiotic residues in soils shows that the processes governing persistence depend on a number of different factors, e.g., physico-chemical properties of the residue, characteristics of the soil, and climatic factors (temperature, rainfall, and humidity). The results presented in this review show that antibiotics affect soil microorganisms by changing their enzyme activity and ability to metabolize different carbon sources, as well as by altering the overall microbial biomass and the relative abundance of different groups (i.e., Gram-negative bacteria, Gram-positive bacteria, and fungi) in microbial communities. Studies using methods based on analyses of nucleic acids prove that antibiotics alter the biodiversity of microbial communities and the presence of many types of ARGs in soil are affected by agricultural and human activities. It is worth emphasizing that studies on ARGs in soil have resulted in the discovery of new genes and enzymes responsible for bacterial resistance to antibiotics. However, many ambiguous results indicate that precise estimation of the impact of antibiotics on the activity and diversity of soil microbial communities is a great challenge.}, } @article {pmid30904192, year = {2019}, author = {Dubois, H and van Loo, G and Wullaert, A}, title = {Nucleic Acid Induced Interferon and Inflammasome Responses in Regulating Host Defense to Gastrointestinal Viruses.}, journal = {International review of cell and molecular biology}, volume = {345}, number = {}, pages = {137-171}, pmid = {30904192}, issn = {1937-6448}, mesh = {Animals ; Gastrointestinal Microbiome ; Gastrointestinal Tract/*virology ; Humans ; Inflammasomes/*metabolism ; Interferons/*metabolism ; Nucleic Acids/*pharmacology ; Viruses/*immunology ; }, abstract = {The gut bacterial and fungal communities residing in the gastrointestinal tract have undisputed far-reaching effects in regulating host health. In the meantime, however, metagenomic sequencing efforts are revealing enteric viruses as the most abundant dimension of the intestinal gut ecosystem, and the first gut virome-wide association studies showed that inflammatory bowel disease as well as type 1 diabetes could be linked to the presence or absence of particular viral inhabitants in the intestine. In line with the genetic component of these human diseases, mouse model studies demonstrated how beneficial functions of a resident virus can switch to detrimental inflammatory effects in a genetically predisposed host. Such viral-induced intestinal immune disturbances are also recapitulated by several gastrointestinal infectious viruses such as rotavirus and human norovirus. This wide range of viral effects on intestinal immunity emphasizes the need for understanding the innate immune responses to gastrointestinal viruses. Numerous nucleic acid sensors such as DexD/H helicases and AIM2 serve as cytosolic viral guardians to induce antiviral interferon and/or pro-inflammatory inflammasome responses. In both cases, pioneering examples are emerging in which RNA helicases cooperate with particular Nod-like receptors to trigger these cellular responses to enteric viruses. Here we summarize the reported beneficial versus detrimental effects of enteric viruses in the intestinal immune system, and we zoom in on the mechanisms through which sensing of nucleic acids from these enteric viruses trigger interferon and inflammasome responses.}, } @article {pmid30904077, year = {2019}, author = {Grogan, MD and Bartow-McKenney, C and Flowers, L and Knight, SAB and Uberoi, A and Grice, EA}, title = {Research Techniques Made Simple: Profiling the Skin Microbiota.}, journal = {The Journal of investigative dermatology}, volume = {139}, number = {4}, pages = {747-752.e1}, pmid = {30904077}, issn = {1523-1747}, support = {R01 AR066663/AR/NIAMS NIH HHS/United States ; P30 AR069589/AR/NIAMS NIH HHS/United States ; R01 NR015639/NR/NINR NIH HHS/United States ; T32 AR007465/AR/NIAMS NIH HHS/United States ; R00 AR060873/AR/NIAMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics/isolation & purification ; Biomedical Research/*methods ; Dermatitis/*genetics/microbiology/pathology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome/*genetics ; Microbiota/*genetics ; Sequence Analysis, DNA ; Skin/*microbiology/pathology ; }, abstract = {Skin is colonized by microbial communities (microbiota) that participate in immune homeostasis, development and maintenance of barrier function, and protection from pathogens. The past decade has been marked by an increased interest in the skin microbiota and its role in cutaneous health and disease, in part due to advances in next-generation sequencing platforms that enable high-throughput, culture-independent detection of bacteria, fungi, and viruses. Various approaches, including bacterial 16S ribosomal RNA gene sequencing and metagenomic shotgun sequencing, have been applied to profile microbial communities colonizing healthy skin and diseased skin including atopic dermatitis, psoriasis, and acne, among others. Here, we provide an overview of culture-dependent and -independent approaches to profiling the skin microbiota and the types of questions that may be answered by each approach. We additionally highlight important study design considerations, selection of controls, interpretation of results, and limitations and challenges.}, } @article {pmid30902785, year = {2019}, author = {Kumar, R and Mishra, A and Jha, B}, title = {Bacterial community structure and functional diversity in subsurface seawater from the western coastal ecosystem of the Arabian Sea, India.}, journal = {Gene}, volume = {701}, number = {}, pages = {55-64}, doi = {10.1016/j.gene.2019.02.099}, pmid = {30902785}, issn = {1879-0038}, mesh = {*Bacteria/classification/genetics/growth & development ; *Biodiversity ; India ; Microbial Consortia/*physiology ; Oceans and Seas ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {The present study revealed the spatial variability of bacteria in relation to physicochemical variations at four different locations (Diu - DIU, Veraval - VER, Porbandar - POR and Okha - OKH) along the Gujarat coast (Arabian Sea, India). The natural habitat was analyzed for temperature, salinity, pH, total dissolved solids, total organic content, total inorganic content, biological oxygen demand, conductivity and total dissolved oxygen. The lowest salinity and conductivity were observed at the VER site, whereas the highest salinity and conductivity were measured with OKH samples. In contrast, the pH was slightly alkaline at all of the sites. The VER site contained the maximum total dissolved solids (TDS), total carbon (TC), total organic carbon (TOC), and total inorganic carbon (TIC), while OKH showed the maximum dissolve oxygen (DO), biological oxygen demand (BOD), pH, temperature, conductivity, and salinity. The physicochemical characteristics showed that the Gujarat coast is alkaline and has a nutrient heterogeneous nature. Average well color development (AWCD) values, calculated using Biolog EcoPlates, showed that the microbial community from VER contained the highest metabolic activities and could metabolize all 31 substrates, followed by DIU > OKH > POR samples. In contrast, the abundance of the bacterial community, determined by qRT-PCR, was maximum in VER samples, followed by OKH > POR > DIU samples. The Shannon and Simpson indices showed that DIU, POR and OKH seawater clone libraries were more diverse. Furthermore, Chao estimator revealed the high diversity of POR and DIU clone libraries. Interestingly, DIU and OKH did not share any common operational taxonomic units (OTUs), and overall, the maximum bacterial diversity was observed with the POR seawater sample. Moreover, these observations were supported by statistical analysis, such as canonical correspondence analysis (CCA) and principal component analysis (PCA). The molecular phylogeny revealed the dominance of Proteobacteria followed by Firmicutes. Within the Proteobacteria phylum, most of the sequences were affiliated with the Gammaproteobacteria class. In total, about 726 OTUs were observed from all four sites which covers 59.79% DIU, 87.5% VER, 50% POR and 98.83% OKH of samples. This study is the first report to describe physicochemical attributes and the bacterial diversity of the coastal area of Gujarat. The study will provide useful insights about bacterial diversity, distribution, and abundance, as well as their relationships with the habitat.}, } @article {pmid30901843, year = {2019}, author = {Cortes, L and Wopereis, H and Tartiere, A and Piquenot, J and Gouw, JW and Tims, S and Knol, J and Chelsky, D}, title = {Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome.}, journal = {International journal of molecular sciences}, volume = {20}, number = {6}, pages = {}, pmid = {30901843}, issn = {1422-0067}, mesh = {Anti-Bacterial Agents/pharmacology ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome/drug effects ; Humans ; Infant ; Informatics/methods ; Male ; Metagenome ; *Metagenomics/methods ; Proteome ; *Proteomics/methods ; *RNA, Ribosomal, 16S ; }, abstract = {A metaproteomic analysis was conducted on the fecal microbiome of eight infants to characterize global protein and pathway expression. Although mass spectrometry-based proteomics is now a routine tool, analysis of the microbiome presents specific technical challenges, including the complexity and dynamic range of member taxa, the need for well-annotated metagenomic databases, and high inter-protein sequence redundancy and similarity. In this study, an approach was developed for assessment of biological phenotype and metabolic status, as a functional complement to DNA sequence analysis. Fecal samples were prepared and analysed by tandem mass spectrometry and a homology-based meta-clustering strategy was used to combine peptides from multiple species into representative proteins. In total, 15,250 unique peptides were sequenced and assigned to 2154 metaclusters, which were then assigned to pathways and functional groups. Differences were noted in several pathways, consistent with the dominant genera observed in different subjects. Although this study was not powered to draw conclusions from the comparisons, the results obtained demonstrate the applicability of this approach and provide the methods needed for performing semi-quantitative comparisons of human fecal microbiome composition, physiology and metabolism, as well as a more detailed assessment of microbial composition in comparison to 16S rRNA gene sequencing.}, } @article {pmid30901505, year = {2019}, author = {Yamashita, M and Okubo, H and Kobuke, K and Ohno, H and Oki, K and Yoneda, M and Tanaka, J and Hattori, N}, title = {Alteration of gut microbiota by a Westernized lifestyle and its correlation with insulin resistance in non-diabetic Japanese men.}, journal = {Journal of diabetes investigation}, volume = {10}, number = {6}, pages = {1463-1470}, pmid = {30901505}, issn = {2040-1124}, support = {JP16K19538//Japan Society for the Promotion of Science KAKENHI/ ; //Japan Association for Diabetes Education and Care/ ; }, mesh = {Asian/*statistics & numerical data ; Asian People/*statistics & numerical data ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Glucose Intolerance/*etiology/pathology ; Humans ; *Insulin Resistance ; *Life Style ; Male ; Middle Aged ; Prognosis ; }, abstract = {AIMS/INTRODUCTION: The severity of insulin resistance is higher in Japanese-American people with American lifestyles than in native Japanese people with Japanese lifestyles. Recently, the role of gut microbiota in the control of host metabolic homeostasis and organ physiology has been recognized. In addition, gut microbiota alterations have been suggested to contribute to pathogenesis of insulin resistance. The principle aim of the present study was to evaluate the impact of a Westernized lifestyle on the gut microbiota of Japanese-Americans versus native Japanese, and its correlation with insulin resistance.

MATERIALS AND METHODS: A total of 14 native Japanese men living in Hiroshima, Japan, and 14 Japanese-American men living in Los Angeles, USA, were included. A 75-g oral glucose tolerance test was carried out for all participants to assess their glucose tolerance, and normal glucose tolerance was observed. We compared the insulin response with oral glucose load, the Matsuda Index, and the composition of the gut microbiota between the native Japanese and Japanese-American men.

RESULTS: Japanese-American men showed higher area under the curve values for serum insulin concentrations during the oral glucose tolerance test and lower Matsuda Index than native Japanese men. Gut microbiota composition of the Japanese-American men was different; in particular, they showed a relatively lower abundance of Odoribacter than native Japanese men. The ratio between relative abundance of Odoribacter and Matsuda Index was positively correlated between the two groups.

CONCLUSIONS: Our findings suggest that Westernized lifestyles alter gut microbiota, and its alteration might induce insulin resistance in non-diabetic Japanese men.}, } @article {pmid30901128, year = {2019}, author = {Martins, FMS and Galhardo, M and Filipe, AF and Teixeira, A and Pinheiro, P and Paupério, J and Alves, PC and Beja, P}, title = {Have the cake and eat it: Optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring.}, journal = {Molecular ecology resources}, volume = {19}, number = {4}, pages = {863-876}, pmid = {30901128}, issn = {1755-0998}, support = {PTDC/AAGMAA/2261/2014-POCI-1-145-FEDER-356016824//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/104703/2014//Fundação para a Ciência e a Tecnologia/ ; 668981//Horizon 2020 Framework Programme/ ; //EDP-Biodiversity Chair/ ; }, mesh = {Animals ; DNA/*genetics/isolation & purification ; DNA Barcoding, Taxonomic/*methods ; Ecological Parameter Monitoring/*methods ; Fresh Water/*chemistry ; Invertebrates/classification/genetics ; Metagenomics/*methods ; }, abstract = {DNA metabarcoding can contribute to improving cost-effectiveness and accuracy of biological assessments of aquatic ecosystems, but significant optimization and standardization efforts are still required to mainstream its application into biomonitoring programmes. In assessments based on freshwater macroinvertebrates, a key challenge is that DNA is often extracted from cleaned, sorted and homogenized bulk samples, which is time-consuming and may be incompatible with sample preservation requirements of regulatory agencies. Here, we optimize and evaluate metabarcoding procedures based on DNA recovered from 96% ethanol used to preserve field samples and thus including potential PCR inhibitors and nontarget organisms. We sampled macroinvertebrates at five sites and subsampled the preservative ethanol at 1 to 14 days thereafter. DNA was extracted using column-based enzymatic (TISSUE) or mechanic (SOIL) protocols, or with a new magnetic-based enzymatic protocol (BEAD), and a 313-bp COI fragment was amplified. Metabarcoding detected at least 200 macroinvertebrate taxa, including most taxa detected through morphology and for which there was a reference barcode. Better results were obtained with BEAD than SOIL or TISSUE, and with subsamples taken 7-14 than 1-7 days after sampling, in terms of DNA concentration and integrity, taxa diversity and matching between metabarcoding and morphology. Most variation in community composition was explained by differences among sites, with small but significant contributions of subsampling day and extraction method, and negligible contributions of extraction and PCR replication. Our methods enhance reliability of preservative ethanol as a potential source of DNA for macroinvertebrate metabarcoding, with a strong potential application in freshwater biomonitoring.}, } @article {pmid30900136, year = {2020}, author = {Chen, W and Wei, Y and Xiong, A and Li, Y and Guan, H and Wang, Q and Miao, Q and Bian, Z and Xiao, X and Lian, M and Zhang, J and Li, B and Cao, Q and Fan, Z and Zhang, W and Qiu, D and Fang, J and Gershwin, ME and Yang, L and Tang, R and Ma, X}, title = {Comprehensive Analysis of Serum and Fecal Bile Acid Profiles and Interaction with Gut Microbiota in Primary Biliary Cholangitis.}, journal = {Clinical reviews in allergy & immunology}, volume = {58}, number = {1}, pages = {25-38}, pmid = {30900136}, issn = {1559-0267}, support = {81620108002//National Natural Science Foundation of China/ ; 81771732//National Natural Science Foundation of China/ ; 81830016//National Natural Science Foundation of China/ ; 81570469//National Natural Science Foundation of China/ ; 81873561//National Natural Science Foundation of China/ ; 81573581//National Natural Science Foundation of China/ ; 81421001//National Natural Science Foundation of China/ ; 81500435//National Natural Science Foundation of China/ ; 20161311//Shanghai Municipal Education Commission-Gaofeng Clinical Medicine Grant/ ; }, mesh = {Adult ; Aged ; Bile Acids and Salts/blood/chemistry/*metabolism ; Biomarkers ; Case-Control Studies ; Cluster Analysis ; Computational Biology/methods ; Cross-Sectional Studies ; *Disease Susceptibility ; *Feces/chemistry ; Female ; Fibroblast Growth Factors/blood ; *Gastrointestinal Microbiome ; Humans ; Hydrophobic and Hydrophilic Interactions ; Liver Cirrhosis, Biliary/blood/diagnosis/*etiology/*metabolism ; Liver Function Tests ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Models, Biological ; Severity of Illness Index ; }, abstract = {Accumulation of bile acids (BAs) contributes significantly to the pathogenesis of primary biliary cholangitis (PBC). Here, we sought to systematically characterize the serum and fecal BA profiles and the linkage between BAs and gut microbiota in PBC. The serum and fecal BAs were compared between 65 UDCA treatment-naive PBC and 109 healthy controls using UPLC-MS in cross-sectional study. In a prospective study, a subgroup of patients was enrolled for BA and microbiota analysis before and after UDCA therapy. BA compositions in serum and feces significantly differed between treatment-naive PBC and controls. Particularly, PBC was associated with decreased conversions of conjugated to unconjugated, and primary to secondary BAs, indicating impaired microbial metabolism of BAs. PBC patients at advanced stage exhibited a more abnormal BA profile compared with early-stage patients. UDCA treatment led to a decreased level of taurine-conjugated BAs, thereby reversing the conjugated/unconjugated ratio in PBC. Moreover, the level of secondary BAs such as DCA and conjugated DCA inversely correlated with PBC-enriched gut microbes (e.g., Veillonella, Klebsiella), while positively correlated with control-enriched microbes (e.g., Faecalibacterium, Oscillospira). Microbiota analysis also revealed a significant increase of taurine-metabolizing bacteria Bilophila spp. in patients after UDCA, which was strongly correlated with decreased taurine-conjugated BAs. In addition, serum FGF19 was remarkably increased in treatment-naïve PBC and decreased after UDCA. Our study established specific alterations of BA compositions in serum and feces of PBC, suggesting the potential for using BAs for diagnosis, and highlighting the possibility of modulating BA profile by altering gut microbiota. Graphical Abstract.}, } @article {pmid30900006, year = {2019}, author = {Horne, R and St Pierre, J and Odeh, S and Surette, M and Foster, JA}, title = {Microbe and host interaction in gastrointestinal homeostasis.}, journal = {Psychopharmacology}, volume = {236}, number = {5}, pages = {1623-1640}, pmid = {30900006}, issn = {1432-2072}, mesh = {Animals ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*metabolism/microbiology ; Homeostasis/*physiology ; Host Microbial Interactions/*physiology ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S/genetics/metabolism ; Species Specificity ; }, abstract = {RATIONALE: Researchers in psychiatry and neuroscience are increasingly recognizing the importance of gut-brain communication in mental health. Both genetics and environmental factors influence gut microbiota composition and function. This study examines host-microbe signaling at the gastrointestinal barrier to identify bottom-up mechanisms of microbiota-brain communication.

OBJECTIVES: We examined differences in gut microbiota composition and fecal miRNA profiles in BALB/c and C57BL/6 mice, in relation to gastrointestinal homeostasis and evaluated the response to perturbation of the gut microbiota by broad-spectrum antibiotic treatment.

METHODS AND RESULTS: Differences in the gut microbiota composition between BALB/c and C57BL/6 mice, evaluated by fecal 16S rRNA gene sequencing, included significant differences in genera Prevotella, Alistipes, Akkermansia, and Ruminococcus. Significant differences in fecal miRNA profiles were determined using the nCounter NanoString platform. A BLASTn analysis identified conserved fecal miRNA target regions in bacterial metagenomes with 14 significant correlations found between fecal miRNA and predicted taxa relative abundance in our dataset. Treatment with broad-spectrum antibiotics for 2 weeks resulted in a host-specific physiological response at the gastrointestinal barrier including a decrease in barrier permeability in BALB/c mice and alterations in the expression of barrier regulating genes in both strains. Genera Parabacteroides and Bacteroides were associated with changes in barrier function.

CONCLUSIONS: The results of this study provide insight into how specific taxa influence gut barrier integrity and function. More generally, these data in the context of recent published studies makes a significant contribution to our understanding of host-microbe interactions providing new knowledge that can be harnessed by us and others in future mechanistic studies.}, } @article {pmid30899033, year = {2019}, author = {Reddel, S and Del Chierico, F and Quagliariello, A and Giancristoforo, S and Vernocchi, P and Russo, A and Fiocchi, A and Rossi, P and Putignani, L and El Hachem, M}, title = {Gut microbiota profile in children affected by atopic dermatitis and evaluation of intestinal persistence of a probiotic mixture.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4996}, pmid = {30899033}, issn = {2045-2322}, mesh = {Bacteroides/genetics ; Child ; Child, Preschool ; Dermatitis, Atopic/*genetics/microbiology/pathology ; Dysbiosis/*genetics/microbiology/pathology ; Faecalibacterium/genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Infant ; Infant, Newborn ; Intestines/microbiology ; Male ; *Metagenomics ; Probiotics/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Atopic dermatitis (AD) has been hypothesised to be associated with gut microbiota (GM) composition. We performed a comparative study of the GM profile of 19 AD children and 18 healthy individuals aimed at identifying bacterial biomarkers associated with the disease. The effect of probiotic intake (Bifidobacterium breve plus Lactobacillus salivarius) on the modulation of GM and the probiotic persistence in the GM were also evaluated. Faecal samples were analysed by real-time PCR and 16S rRNA targeted metagenomics. Although the probiotics, chosen for this study, did not shape the entire GM profile, we observed the ability of these species to pass through the gastrointestinal tract and to persist (only B. breve) in the GM. Moreover, the GM of patients compared to CTRLs showed a dysbiotic status characterised by an increase of Faecalibacterium, Oscillospira, Bacteroides, Parabacteroides and Sutterella and a reduction of short-chain fatty acid (SCFA)-producing bacteria (i.e., Bifidobacterium, Blautia, Coprococcus, Eubacterium and Propionibacterium). Taken togheter these results show an alteration in AD microbiota composition with the depletion or absence of some species, opening the way to future probiotic intervention studies.}, } @article {pmid30898652, year = {2019}, author = {O'Connor, KM and Lucking, EF and Golubeva, AV and Strain, CR and Fouhy, F and Cenit, MC and Dhaliwal, P and Bastiaanssen, TFS and Burns, DP and Stanton, C and Clarke, G and Cryan, JF and O'Halloran, KD}, title = {Manipulation of gut microbiota blunts the ventilatory response to hypercapnia in adult rats.}, journal = {EBioMedicine}, volume = {44}, number = {}, pages = {618-638}, pmid = {30898652}, issn = {2352-3964}, mesh = {Animals ; Anti-Bacterial Agents/administration & dosage/adverse effects ; Biomarkers ; Blood Gas Analysis ; Brain Stem/metabolism/physiopathology ; Breath Tests ; Cell Membrane Permeability ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Heart Function Tests ; Heart Rate ; Hypercapnia/blood/*etiology/*physiopathology ; Hypoxia/metabolism ; Intestinal Mucosa/metabolism ; Male ; Metagenome ; Metagenomics/methods ; Rats ; Receptors, Serotonin, 5-HT3/metabolism ; *Respiration ; }, abstract = {BACKGROUND: It is increasingly evident that perturbations to the diversity and composition of the gut microbiota have significant consequences for the regulation of integrative physiological systems. There is growing interest in the potential contribution of microbiota-gut-brain signalling to cardiorespiratory control in health and disease.

METHODS: In adult male rats, we sought to determine the cardiorespiratory effects of manipulation of the gut microbiota following a 4-week administration of a cocktail of antibiotics. We subsequently explored the effects of administration of faecal microbiota from pooled control (vehicle) rat faeces, given by gavage to vehicle- and antibiotic-treated rats.

FINDINGS: Antibiotic intervention depressed the ventilatory response to hypercapnic stress in conscious animals, owing to a reduction in the respiratory frequency response to carbon dioxide. Baseline frequency, respiratory timing variability, and the expression of apnoeas and sighs were normal. Microbiota-depleted rats had decreased systolic blood pressure. Faecal microbiota transfer to vehicle- and antibiotic-treated animals also disrupted the gut microbiota composition, associated with depressed ventilatory responsiveness to hypercapnia. Chronic antibiotic intervention or faecal microbiota transfer both caused significant disruptions to brainstem monoamine neurochemistry, with increased homovanillic acid:dopamine ratio indicative of increased dopamine turnover, which correlated with the abundance of several bacteria of six different phyla.

INTERPRETATION: Chronic antibiotic administration and faecal microbiota transfer disrupt gut microbiota, brainstem monoamine concentrations and the ventilatory response to hypercapnia. We suggest that aberrant microbiota-gut-brain axis signalling has a modulatory influence on respiratory behaviour during hypercapnic stress. FUND: Department of Physiology and APC Microbiome Ireland, University College Cork, Ireland.}, } @article {pmid30897248, year = {2019}, author = {Alrafas, HR and Busbee, PB and Nagarkatti, M and Nagarkatti, PS}, title = {Resveratrol modulates the gut microbiota to prevent murine colitis development through induction of Tregs and suppression of Th17 cells.}, journal = {Journal of leukocyte biology}, volume = {106}, number = {2}, pages = {467-480}, pmid = {30897248}, issn = {1938-3673}, support = {R01 AI129788/AI/NIAID NIH HHS/United States ; R01 MH094755/MH/NIMH NIH HHS/United States ; P20 GM103641/GM/NIGMS NIH HHS/United States ; P01 AT003961/AT/NCCIH NIH HHS/United States ; R01 AT006888/AT/NCCIH NIH HHS/United States ; R01 AI123947/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Inflammatory Agents, Non-Steroidal/*pharmacology ; Biomarkers ; Colitis/*etiology/metabolism/pathology/prevention & control ; Colonoscopy ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Female ; Gastrointestinal Microbiome/*drug effects/*immunology ; Humans ; Immunomodulation/*drug effects ; Metagenomics/methods ; Mice ; Resveratrol/*pharmacology ; T-Lymphocyte Subsets/immunology/metabolism ; T-Lymphocytes, Regulatory/drug effects/*immunology/metabolism ; Th17 Cells/drug effects/*immunology/metabolism ; }, abstract = {Inflammatory diseases of the gastrointestinal tract are often associated with microbial dysbiosis. Thus, dietary interactions with intestinal microbiota, to maintain homeostasis, play a crucial role in regulation of clinical disorders such as colitis. In the current study, we investigated if resveratrol, a polyphenol found in a variety of foods and beverages, would reverse microbial dysbiosis induced during colitis. Administration of resveratrol attenuated colonic inflammation and clinical symptoms in the murine model of 2,4,6-trinitrobenzenesulfonic acid (TNBS)-induced colitis. Resveratrol treatment in mice with colitis led to an increase in CD4[+] FOXP3[+] and CD4[+] IL-10[+] T cells, and a decrease in CD4[+] IFN-γ[+] and CD4[+] IL-17[+] T cells. 16S rRNA gene sequencing to investigate alterations in the gut microbiota revealed that TNBS caused significant dysbiosis, which was reversed following resveratrol treatment. Analysis of cecal flush revealed that TNBS administration led to an increase in species such as Bacteroides acidifaciens, but decrease in species such as Ruminococcus gnavus and Akkermansia mucinphilia, as well as a decrease in SCFA i-butyric acid. However, resveratrol treatment restored the gut bacteria back to homeostatic levels, and increased production of i-butyric acid. Fecal transfer experiments confirmed the protective role of resveratrol-induced microbiota against colitis inasmuch as such recipient mice were more resistant to TNBS-colitis and exhibited polarization toward CD4[+] FOXP3[+] T cells and decreases in CD4[+] IFN-γ[+] and CD4[+] IL-17[+] T cells. Collectively, these data demonstrate that resveratrol-mediated attenuation of colitis results from reversal of microbial dysbiosis induced during colitis and such microbiota protect the host from colonic inflammation by inducing Tregs while suppressing inflammatory Th1/Th17 cells.}, } @article {pmid30895406, year = {2019}, author = {Nguyen, VD and Nguyen, TT and Pham, TT and Packianather, M and Le, CH}, title = {Molecular screening and genetic diversity analysis of anticancer Azurin-encoding and Azurin-like genes in human gut microbiome deduced through cultivation-dependent and cultivation-independent studies.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {22}, number = {4}, pages = {437-449}, doi = {10.1007/s10123-019-00070-8}, pmid = {30895406}, issn = {1618-1905}, support = {106-YS.04-2014.40//National Foundation for Science and Technology Development/ ; }, mesh = {Adolescent ; Adult ; Azurin/*genetics/metabolism ; Child ; Culture Media/metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Genetic Variation ; Humans ; Male ; Phylogeny ; Pseudomonas aeruginosa/*genetics/growth & development/*isolation & purification/metabolism ; Young Adult ; }, abstract = {Azurin, a bacteriocin produced by a human gut bacterium Pseudomonas aeruginosa, can reveal selectively cytotoxic and induce apoptosis in cancer cells. After overcoming two phase I trials, a functional region of Azurin called p28 has been approved as a drug for the treatment of brain tumor glioma by FDA. The present study aims to improve a screening procedure and assess genetic diversity of Azurin genes in P. aeruginosa and Azurin-like genes in the gut microbiome of a specific population in Vietnam and global populations. Firstly, both cultivation-dependent and cultivation-independent techniques based on genomic and metagenomic DNAs extracted from fecal samples of the healthy specific population were performed and optimized to detect Azurin genes. Secondly, the Azurin gene sequences were analyzed and compared with global populations by using bioinformatics tools. Finally, the screening procedure improved from the first step was applied for screening Azurin-like genes, followed by the protein synthesis and NCI in vitro screening for anticancer activity. As a result, this study has successfully optimized the annealing temperatures to amplify DNAs for screening Azurin genes and applying to Azurin-like genes from human gut microbiota. The novelty of this study is the first of its kind to classify Azurin genes into five different genotypes at a global scale and confirm the potential anticancer activity of three Azurin-like synthetic proteins (Cnazu1, Dlazu11, and Ruazu12). The results contribute to the procedure development applied for screening anticancer proteins from human microbiome and a comprehensive understanding of their therapeutic response at a genetic level.}, } @article {pmid30894435, year = {2019}, author = {Majta, J and Odrzywolek, K and Milanovic, B and Hubar, V and Wrobel, S and Strycharz-Angrecka, E and Wojciechowski, S and Milanowska, K}, title = {Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population.}, journal = {mSphere}, volume = {4}, number = {2}, pages = {}, pmid = {30894435}, issn = {2379-5042}, mesh = {*Adaptation, Physiological ; Bacteroides/genetics/*metabolism ; Bifidobacterium/genetics/*metabolism ; Feces/microbiology ; Finland ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Genome, Bacterial ; Humans ; Infant ; *Metabolic Networks and Pathways ; Metagenomics ; Milk, Human/*chemistry ; Oligosaccharides/metabolism ; }, abstract = {A variety of autoimmune and allergy events are becoming increasingly common, especially in Western countries. Some pieces of research link such conditions with the composition of microbiota during infancy. In this period, the predominant form of nutrition for gut microbiota is oligosaccharides from human milk (HMO). A number of gut-colonizing strains, such as Bifidobacterium and Bacteroides, are able to utilize HMO, but only some Bifidobacterium strains have evolved to digest the specific composition of human oligosaccharides. Differences in the proportions of the two genera that are able to utilize HMO have already been associated with the frequency of allergies and autoimmune diseases in the Finnish and the Russian populations. Our results show that differences in terms of the taxonomic annotation do not explain the reason for the differences in the Bifidobacterium/Bacteroides ratio between the Finnish and the Russian populations. In this paper, we present the results of function-level analysis. Unlike the typical workflow for gene abundance analysis, BiomeScout technology explains the differences in the Bifidobacterium/Bacteroides ratio. Our research shows the differences in the abundances of the two enzymes that are crucial for the utilization of short type 1 oligosaccharides.IMPORTANCE Knowing the limitations of taxonomy-based research, there is an emerging need for the development of higher-resolution techniques. The significance of this research is demonstrated by the novel method used for the analysis of function-level metagenomes. BiomeScout-the presented technology-utilizes proprietary algorithms for the detection of differences between functionalities present in metagenomic samples.}, } @article {pmid30894059, year = {2019}, author = {Bjørkhaug, ST and Aanes, H and Neupane, SP and Bramness, JG and Malvik, S and Henriksen, C and Skar, V and Medhus, AW and Valeur, J}, title = {Characterization of gut microbiota composition and functions in patients with chronic alcohol overconsumption.}, journal = {Gut microbes}, volume = {10}, number = {6}, pages = {663-675}, pmid = {30894059}, issn = {1949-0984}, mesh = {Adult ; Aged ; Aged, 80 and over ; Alcoholism/blood/*microbiology/physiopathology ; Ascorbic Acid/blood ; Bacteria/classification/genetics/isolation & purification ; Bacterial Proteins/genetics ; Fatty Acids, Volatile/analysis ; Feces/chemistry/microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Hand Strength ; Humans ; Male ; Metagenomics ; Middle Aged ; Nutrition Assessment ; RNA, Ribosomal, 16S/genetics ; Vitamins/blood ; }, abstract = {Excessive alcohol intake can alter the gut microbiota, which may underlie the pathophysiology of alcohol-related diseases. We examined gut microbiota composition and functions in patients with alcohol overconsumption for >10 years, compared to a control group of patients with a history of no or low alcohol intake. Faecal microbiota composition was assessed by 16S rRNA sequencing. Gut microbiota functions were evaluated by quantification of short-chain fatty acids (SCFAs) and predictive metagenome profiling (PICRUSt). Twenty-four patients, mean age 64.8 years (19 males), with alcohol overconsumption, and 18 control patients, mean age 58.2 years (14 males) were included. The two groups were comparable regarding basic clinical variables. Nutritional assessment revealed lower total score on the screening tool Mini Nutritional Assessment, lower muscle mass as assessed by handgrip strength, and lower plasma vitamin C levels in the alcohol overconsumption group. Bacteria from phylum Proteobacteria were found in higher relative abundance, while bacteria from genus Faecalibacterium were found in lower relative abundance in the group of alcohol overconsumers. The group also had higher levels of the genera Sutterella, Holdemania and Clostridium, and lower concentration and percentage of butyric acid. When applying PICRUSt to predict the metagenomic composition, we found that genes related to invasion of epithelial cells were more common in the group of alcohol overconsumers. We conclude that gut microbiota composition and functions in patients with alcohol overconsumption differ from patients with low consumption of alcohol, and seem to be skewed into a putative pro-inflammatory direction.}, } @article {pmid30891034, year = {2019}, author = {Bello-Gil, D and Audebert, C and Olivera-Ardid, S and Pérez-Cruz, M and Even, G and Khasbiullina, N and Gantois, N and Shilova, N and Merlin, S and Costa, C and Bovin, N and Mañez, R}, title = {The Formation of Glycan-Specific Natural Antibodies Repertoire in GalT-KO Mice Is Determined by Gut Microbiota.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {342}, pmid = {30891034}, issn = {1664-3224}, mesh = {Animals ; Antibodies/*immunology ; Antigens/immunology ; Bacteria/immunology ; Female ; Gastrointestinal Microbiome/*immunology ; Intestines/immunology/microbiology ; Male ; Metagenome/immunology ; Mice ; Mice, Knockout ; Microbiota/*immunology ; Polysaccharides/*immunology ; RNA, Ribosomal, 16S/immunology ; }, abstract = {Gut commensal bacteria are known to have a significant role in regulating the innate and adaptive immune homeostasis. Alterations in the intestinal microbial composition have been associated with several disease states, including autoimmune and inflammatory conditions. However, it is not entirely clear how commensal gut microbiota modulate and contribute to the systemic immunity, and whether circulating elements of the host immune system could regulate the microbiome. Thus, we have studied the diversity and abundance of specific taxons in the gut microbiota of inbred GalT-KO mice during 7 months of animal life by metagenetic high-throughput sequencing (16S rRNA gene, variable regions V3-V5). The repertoire of glycan-specific natural antibodies, obtained by printed glycan array technology, was then associated with the microbial diversity for each animal by metagenome-wide association studies (MWAS). Our data show that the orders clostridiales (most abundant), bacteriodales, lactobacillales, and deferribacterales may be associated with the development of the final repertoire of natural anti-glycan antibodies in GalT-KO mice. The main changes in microbiota diversity (month-2 and month-3) were related to important changes in levels and repertoire of natural anti-glycan antibodies in these mice. Additionally, significant positive and negative associations were found between the gut microbiota and the pattern of specific anti-glycan antibodies. Regarding individual features, the gut microbiota and the corresponding repertoire of natural anti-glycan antibodies showed differences among the examined animals. We also found redundancy in different taxa associated with the development of specific anti-glycan antibodies. Differences in microbial diversity did not, therefore, necessarily influence the overall functional output of the gut microbiome of GalT-KO mice. In summary, the repertoire of natural anti-carbohydrate antibodies may be partially determined by the continuous antigenic stimulation produced by the gut bacterial population of each GalT-KO mouse. Small differences in gut microbiota diversity could determine different repertoire and levels of natural anti-glycan antibodies and consequently might induce different immune responses to pathogens or other potential threats.}, } @article {pmid30890181, year = {2019}, author = {Zheng, T and Li, J and Ni, Y and Kang, K and Misiakou, MA and Imamovic, L and Chow, BKC and Rode, AA and Bytzer, P and Sommer, M and Panagiotou, G}, title = {Mining, analyzing, and integrating viral signals from metagenomic data.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {42}, pmid = {30890181}, issn = {2049-2618}, mesh = {Algorithms ; Anti-Bacterial Agents/*administration & dosage ; Bacteria/*classification/isolation & purification/virology ; Bacteriophages/*genetics ; CRISPR-Cas Systems ; Data Mining/*methods ; Feces/microbiology ; Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Metagenomics/*methods ; Random Allocation ; }, abstract = {BACKGROUND: Viruses are important components of microbial communities modulating community structure and function; however, only a couple of tools are currently available for phage identification and analysis from metagenomic sequencing data. Here we employed the random forest algorithm to develop VirMiner, a web-based phage contig prediction tool especially sensitive for high-abundances phage contigs, trained and validated by paired metagenomic and phagenomic sequencing data from the human gut flora.

RESULTS: VirMiner achieved 41.06% ± 17.51% sensitivity and 81.91% ± 4.04% specificity in the prediction of phage contigs. In particular, for the high-abundance phage contigs, VirMiner outperformed other tools (VirFinder and VirSorter) with much higher sensitivity (65.23% ± 16.94%) than VirFinder (34.63% ± 17.96%) and VirSorter (18.75% ± 15.23%) at almost the same specificity. Moreover, VirMiner provides the most comprehensive phage analysis pipeline which is comprised of metagenomic raw reads processing, functional annotation, phage contig identification, and phage-host relationship prediction (CRISPR-spacer recognition) and supports two-group comparison when the input (metagenomic sequence data) includes different conditions (e.g., case and control). Application of VirMiner to an independent cohort of human gut metagenomes obtained from individuals treated with antibiotics revealed that 122 KEGG orthology and 118 Pfam groups had significantly differential abundance in the pre-treatment samples compared to samples at the end of antibiotic administration, including clustered regularly interspaced short palindromic repeats (CRISPR), multidrug resistance, and protein transport. The VirMiner webserver is available at http://sbb.hku.hk/VirMiner/ .

CONCLUSIONS: We developed a comprehensive tool for phage prediction and analysis for metagenomic samples. Compared to VirSorter and VirFinder-the most widely used tools-VirMiner is able to capture more high-abundance phage contigs which could play key roles in infecting bacteria and modulating microbial community dynamics.

TRIAL REGISTRATION: The European Union Clinical Trials Register, EudraCT Number: 2013-003378-28 . Registered on 9 April 2014.}, } @article {pmid30887686, year = {2019}, author = {Weyrich, LS and Farrer, AG and Eisenhofer, R and Arriola, LA and Young, J and Selway, CA and Handsley-Davis, M and Adler, CJ and Breen, J and Cooper, A}, title = {Laboratory contamination over time during low-biomass sample analysis.}, journal = {Molecular ecology resources}, volume = {19}, number = {4}, pages = {982-996}, pmid = {30887686}, issn = {1755-0998}, support = {DECRA 150101574//Australian Research Council/ ; }, mesh = {*DNA Contamination ; *Diagnostic Errors ; Metagenomics/*methods ; Molecular Biology/*methods ; }, abstract = {Bacteria are not only ubiquitous on earth but can also be incredibly diverse within clean laboratories and reagents. The presence of both living and dead bacteria in laboratory environments and reagents is especially problematic when examining samples with low endogenous content (e.g., skin swabs, tissue biopsies, ice, water, degraded forensic samples or ancient material), where contaminants can outnumber endogenous microorganisms within samples. The contribution of contaminants within high-throughput studies remains poorly understood because of the relatively low number of contaminant surveys. Here, we examined 144 negative control samples (extraction blank and no-template amplification controls) collected in both typical molecular laboratories and an ultraclean ancient DNA laboratory over 5 years to characterize long-term contaminant diversity. We additionally compared the contaminant content within a home-made silica-based extraction method, commonly used to analyse low endogenous content samples, with a widely used commercial DNA extraction kit. The contaminant taxonomic profile of the ultraclean ancient DNA laboratory was unique compared to modern molecular biology laboratories, and changed over time according to researcher, month and season. The commercial kit also contained higher microbial diversity and several human-associated taxa in comparison to the home-made silica extraction protocol. We recommend a minimum of two strategies to reduce the impacts of laboratory contaminants within low-biomass metagenomic studies: (a) extraction blank controls should be included and sequenced with every batch of extractions and (b) the contributions of laboratory contamination should be assessed and reported in each high-throughput metagenomic study.}, } @article {pmid30887528, year = {2019}, author = {Mauras, A and Wopereis, H and Yeop, I and Esber, N and Delannoy, J and Labellie, C and Reygner, J and Kapel, N and Slump, R and van Eijndthoven, T and Rutten, L and Knol, J and Garssen, J and Harthoorn, LF and Butel, MJ and Bajaj-Elliott, M and Hartog, A and Waligora-Dupriet, AJ}, title = {Gut microbiota from infant with cow's milk allergy promotes clinical and immune features of atopy in a murine model.}, journal = {Allergy}, volume = {74}, number = {9}, pages = {1790-1793}, pmid = {30887528}, issn = {1398-9995}, support = {//Danone Nutricia Research/International ; }, mesh = {Animals ; Cattle ; Disease Models, Animal ; *Disease Susceptibility ; *Gastrointestinal Microbiome/immunology ; Humans ; Hypersensitivity, Immediate/*etiology ; Infant ; Metagenomics/methods ; Mice ; Milk Hypersensitivity/*etiology ; }, } @article {pmid30886779, year = {2019}, author = {Eisenhofer, R and Weyrich, LS}, title = {Assessing alignment-based taxonomic classification of ancient microbial DNA.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6594}, pmid = {30886779}, issn = {2167-8359}, abstract = {The field of palaeomicrobiology-the study of ancient microorganisms-is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.}, } @article {pmid30885807, year = {2019}, author = {Murray, AK and Zhang, L and Snape, J and Gaze, WH}, title = {Comparing the selective and co-selective effects of different antimicrobials in bacterial communities.}, journal = {International journal of antimicrobial agents}, volume = {53}, number = {6}, pages = {767-773}, pmid = {30885807}, issn = {1872-7913}, mesh = {Anti-Infective Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics ; Benzalkonium Compounds/pharmacology ; Biota/*drug effects ; Ciprofloxacin/pharmacology ; *Drug Resistance, Bacterial ; Evolution, Molecular ; Genes, Bacterial ; Metagenomics ; *Selection, Genetic ; Trimethoprim/pharmacology ; Wastewater/*microbiology ; }, abstract = {Bacterial communities are exposed to a cocktail of antimicrobial agents, including antibiotics, heavy metals and biocidal antimicrobials such as quaternary ammonium compounds (QACs). The extent to which these compounds may select or co-select for antimicrobial resistance (AMR) is not fully understood. In this study, human-associated, wastewater-derived bacterial communities were exposed to either benzalkonium chloride (BAC), ciprofloxacin or trimethoprim at sub-point-of-use concentrations for one week to determine selective and co-selective potential. Metagenome analyses were performed to determine effects on bacterial community structure and prevalence of antibiotic resistance genes (ARGs) and metal or biocide resistance genes (MBRGS). Ciprofloxacin had the greatest co-selective potential, significantly enriching for resistance mechanisms to multiple antibiotic classes. Conversely, BAC exposure significantly reduced relative abundance of ARGs and MBRGS, including the well characterised qac efflux genes. However, BAC exposure significantly impacted bacterial community structure. Therefore BAC, and potentially other QACs, did not play as significant a role in co-selection for AMR as antibiotics such as ciprofloxacin at sub-point-of-use concentrations in this study. This approach can be used to identify priority compounds for further study, to better understand evolution of AMR in bacterial communities exposed to sub-point-of-use concentrations of antimicrobials.}, } @article {pmid30885780, year = {2019}, author = {Zuo, X and Deguchi, Y and Xu, W and Liu, Y and Li, HS and Wei, D and Tian, R and Chen, W and Xu, M and Yang, Y and Gao, S and Jaoude, JC and Liu, F and Chrieki, SP and Moussalli, MJ and Gagea, M and Sebastian, MM and Zheng, X and Tan, D and Broaddus, R and Wang, J and Ajami, NJ and Swennes, AG and Watowich, SS and Shureiqi, I}, title = {PPARD and Interferon Gamma Promote Transformation of Gastric Progenitor Cells and Tumorigenesis in Mice.}, journal = {Gastroenterology}, volume = {157}, number = {1}, pages = {163-178}, pmid = {30885780}, issn = {1528-0012}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; R01 CA206539/CA/NCI NIH HHS/United States ; R01 CA195686/CA/NCI NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 CA142969/CA/NCI NIH HHS/United States ; }, mesh = {Adenocarcinoma/genetics/immunology ; Animals ; Carcinogenesis/*genetics/immunology ; Cell Lineage ; Cell Transformation, Neoplastic/*genetics/immunology ; Chemokine CCL20/metabolism ; Chemokine CXCL1/metabolism ; Chemokines ; Cytokines/*immunology ; Feedback, Physiological ; Gastric Mucosa/*metabolism ; Gene Expression Profiling ; Inflammation ; Interferon-gamma/*immunology ; Mice ; Microbiota/immunology ; Microfilament Proteins/genetics ; Receptors, Cytoplasmic and Nuclear/*genetics ; Stem Cells/immunology/*metabolism ; Stomach/*immunology/microbiology ; Stomach Neoplasms/genetics/immunology ; }, abstract = {BACKGROUND & AIMS: The peroxisome proliferator-activated receptor delta (PPARD) regulates cell metabolism, proliferation, and inflammation and has been associated with gastric and other cancers. Villin-positive epithelial cells are a small population of quiescent gastric progenitor cells. We expressed PPARD from a villin promoter to investigate the role of these cells and PPARD in development of gastric cancer.

METHODS: We analyzed gastric tissues from mice that express the Ppard (PPARD1 and PPARD2 mice) from a villin promoter, and mice that did not carry this transgene (controls), by histology and immunohistochemistry. We performed cell lineage-tracing experiments and analyzed the microbiomes, chemokine and cytokine production, and immune cells and transcriptomes of stomachs of these mice. We also performed immunohistochemical analysis of PPARD levels in 2 sets of human gastric tissue microarrays.

RESULTS: Thirty-eight percent of PPARD mice developed spontaneous, invasive gastric adenocarcinomas, with severe chronic inflammation. Levels of PPARD were increased in human gastric cancer tissues, compared with nontumor tissues, and associated with gastric cancer stage and grade. We found an inverse correlation between level of PPARD in tumor tissue and patient survival time. Gastric microbiomes from PPARD and control mice did not differ significantly. Lineage-tracing experiments identified villin-expressing gastric progenitor cells (VGPCs) as the origin of gastric tumors in PPARD mice. In these mice, PPARD up-regulated CCL20 and CXCL1, which increased infiltration of the gastric mucosa by immune cells. Immune cell production of inflammatory cytokines promoted chronic gastric inflammation and expansion and transformation of VGPCs, leading to tumorigenesis. We identified a positive-feedback loop between PPARD and interferon gamma signaling that sustained gastric inflammation to induce VGPC transformation and gastric carcinogenesis.

CONCLUSIONS: We found PPARD overexpression in VPGCs to result in inflammation, dysplasia, and tumor formation. PPARD and VGPCs might be therapeutic targets for stomach cancer.}, } @article {pmid30885720, year = {2019}, author = {LaPierre, N and Ju, CJ and Zhou, G and Wang, W}, title = {MetaPheno: A critical evaluation of deep learning and machine learning in metagenome-based disease prediction.}, journal = {Methods (San Diego, Calif.)}, volume = {166}, number = {}, pages = {74-82}, pmid = {30885720}, issn = {1095-9130}, support = {R01 GM115833/GM/NIGMS NIH HHS/United States ; T32 EB016640/EB/NIBIB NIH HHS/United States ; }, mesh = {Algorithms ; *Deep Learning ; Diabetes Mellitus, Type 2/*genetics/microbiology ; Humans ; Machine Learning/statistics & numerical data ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/genetics ; Obesity/*genetics/microbiology ; }, abstract = {The human microbiome plays a number of critical roles, impacting almost every aspect of human health and well-being. Conditions in the microbiome have been linked to a number of significant diseases. Additionally, revolutions in sequencing technology have led to a rapid increase in publicly-available sequencing data. Consequently, there have been growing efforts to predict disease status from metagenomic sequencing data, with a proliferation of new approaches in the last few years. Some of these efforts have explored utilizing a powerful form of machine learning called deep learning, which has been applied successfully in several biological domains. Here, we review some of these methods and the algorithms that they are based on, with a particular focus on deep learning methods. We also perform a deeper analysis of Type 2 Diabetes and obesity datasets that have eluded improved results, using a variety of machine learning and feature extraction methods. We conclude by offering perspectives on study design considerations that may impact results and future directions the field can take to improve results and offer more valuable conclusions. The scripts and extracted features for the analyses conducted in this paper are available via GitHub:https://github.com/nlapier2/metapheno.}, } @article {pmid30885689, year = {2019}, author = {Hildonen, M and Kodama, M and Puetz, LC and Gilbert, MTP and Limborg, MT}, title = {A comparison of storage methods for gut microbiome studies in teleosts: Insights from rainbow trout (Oncorhynchus mykiss).}, journal = {Journal of microbiological methods}, volume = {160}, number = {}, pages = {42-48}, doi = {10.1016/j.mimet.2019.03.010}, pmid = {30885689}, issn = {1872-8359}, mesh = {Animals ; Freezing ; Gastrointestinal Microbiome/*genetics ; Oncorhynchus mykiss/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Specimen Handling/*methods ; }, abstract = {Immediate freezing is perhaps the most preferred method used for preserving gut microbial samples, but research on sample preservation has been principally based around samples from mammalian species, and little is known about the advantages or disadvantages relating to different storage methods for fish guts. Fish gut samples may pose additional challenges due to the different chemical and enzymatic profile, as well as the higher water content, which might affect the yield and purity of DNA recovered. To explore this, we took gut content and mucosal scrape samples from 10 rainbow trout (Oncorhynchus mykiss), and tested whether different preservation methods have any effect on the ability to construct high quality genomic libraries for shotgun and 16S rRNA gene sequencing. Four different storage methods were compared for the gut content samples (immediate freezing on dry ice, 96% ethanol, RNAlater and DNA/RNA shield), while two different methods were compared for mucosal scrape samples (96% ethanol and RNAlater). The samples were thereafter stored at -80 °C. Our findings concluded that 96% ethanol outperforms the other storage methods when considering DNA quantity, quality, cost and labor. Ethanol works consistently well for both gut content and mucosal scrape samples, and enables construction of DNA sequencing libraries of sufficient quantity and with a fragment length distribution suitable for shotgun sequencing. Two main conclusions from our study are i) sample storage optimisation is an important part of establishing a microbiome research program in a new species or sample type system, and ii) 96% ethanol is the preferred method for storing rainbow trout gut content and mucosal scrape samples.}, } @article {pmid30885294, year = {2019}, author = {Prodan, A and Levin, E and Nieuwdorp, M}, title = {Does disease start in the mouth, the gut or both?.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {30885294}, issn = {2050-084X}, mesh = {Bacteria ; *Gastrointestinal Microbiome ; *Gastrointestinal Tract ; Metagenomics ; *Microbiota ; Mouth ; }, abstract = {Oral bacteria colonize the gut more frequently than previously thought.}, } @article {pmid30885266, year = {2019}, author = {Westreich, ST and Ardeshir, A and Alkan, Z and Kable, ME and Korf, I and Lemay, DG}, title = {Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {41}, pmid = {30885266}, issn = {2049-2618}, support = {P51 OD011107/OD/NIH HHS/United States ; S10 OD010786/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics ; Diarrhea/*genetics/metabolism/microbiology/parasitology ; Feces/microbiology ; Fucose/*metabolism ; Gastrointestinal Microbiome ; Gene Expression Profiling/*veterinary ; Gene Expression Regulation ; Macaca mulatta ; Metagenomics/*methods ; Mucins/*metabolism ; Proteolysis ; Sequence Analysis, RNA/veterinary ; Trichomonas/classification/genetics ; }, abstract = {BACKGROUND: Idiopathic chronic diarrhea (ICD) is a common cause of morbidity and mortality among juvenile rhesus macaques. Characterized by chronic inflammation of the colon and repeated bouts of diarrhea, ICD is largely unresponsive to medical interventions, including corticosteroid, antiparasitic, and antibiotic treatments. Although ICD is accompanied by large disruptions in the composition of the commensal gut microbiome, no single pathogen has been concretely identified as responsible for the onset and continuation of the disease.

RESULTS: Fecal samples were collected from 12 ICD-diagnosed macaques and 12 age- and sex-matched controls. RNA was extracted for metatranscriptomic analysis of organisms and functional annotations associated with the gut microbiome. Bacterial, fungal, archaeal, protozoan, and macaque (host) transcripts were simultaneously assessed. ICD-afflicted animals were characterized by increased expression of host-derived genes involved in inflammation and increased transcripts from bacterial pathogens such as Campylobacter and Helicobacter and the protozoan Trichomonas. Transcripts associated with known mucin-degrading organisms and mucin-degrading enzymes were elevated in the fecal microbiomes of ICD-afflicted animals. Assessment of colon sections using immunohistochemistry and of the host transcriptome suggests differential fucosylation of mucins between control and ICD-afflicted animals. Interrogation of the metatranscriptome for fucose utilization genes reveals possible mechanisms by which opportunists persist in ICD. Bacteroides sp. potentially cross-fed fucose to Haemophilus whereas Campylobacter expressed a mucosa-associated transcriptome with increased expression of adherence genes.

CONCLUSIONS: The simultaneous profiling of bacterial, fungal, archaeal, protozoan, and macaque transcripts from stool samples reveals that ICD of rhesus macaques is associated with increased gene expression by pathogens, increased mucin degradation, and altered fucose utilization. The data suggest that the ICD-afflicted host produces fucosylated mucins that are leveraged by potentially pathogenic microbes as a carbon source or as adhesion sites.}, } @article {pmid30885206, year = {2019}, author = {Ziko, L and Saqr, AA and Ouf, A and Gimpel, M and Aziz, RK and Neubauer, P and Siam, R}, title = {Antibacterial and anticancer activities of orphan biosynthetic gene clusters from Atlantis II Red Sea brine pool.}, journal = {Microbial cell factories}, volume = {18}, number = {1}, pages = {56}, pmid = {30885206}, issn = {1475-2859}, mesh = {Anti-Bacterial Agents ; Antineoplastic Agents ; Biodiversity ; Cloning, Molecular/methods ; Metagenome/*genetics ; Multigene Family/*genetics ; Seawater/*microbiology ; }, abstract = {BACKGROUND: Cancer and infectious diseases are problematic because of continuous emergence of drug resistance. One way to address this enormous global health threat is bioprospecting the unlikeliest environments, such as extreme marine niches, which have tremendous biodiversity that is barely explored. One such environment is the Red Sea brine pool, Atlantis II Deep (ATII). Here, we functionally screened a fosmid library of metagenomic DNA isolated from the ATII lower convective layer (LCL) for antibacterial and anticancer activities.

RESULTS: Selected clones, 14-7E and 10-2G, displayed antibacterial effects on the marine strain Bacillus sp. Cc6. Moreover, whole cell lysates from 14-7E and 10-2G exhibited decreased cell viability against MCF-7 (39.1% ± 6.6, 42% ± 8.1 at 50% v/v) and U2OS cells (35.7% ± 1.9, 79.9% ± 5.9 at 50% v/v), respectively. By sequencing the insert DNA from 14-7E and 10-2G, we identified two putative orphan biosynthetic gene clusters. Both clusters harbored putative ATP-binding cassette (ABC) transporter permeases and S-adenosylmethionine-related genes. Interestingly, the biosynthetic gene cluster identified on 14-7E is of archaeal origin and harbors a putative transcription factor. Several identified genes may be responsible for the observed antibacterial and anticancer activities. The 14-7E biosynthetic gene cluster may be encoding enzymes producing a specialized metabolite (effect of detected genes involved in C-C bond formation and glycosylation). The bioactivity may also be due to predicted subtilases encoded by this cluster. The 10-2G cluster harbored putative glycosyltransferase and non-ribosomal peptide synthase genes; thus the observed activity of this clone could be caused by a bioactive peptide.

CONCLUSIONS: The ATII LCL prokaryotic metagenome hosts putative orphan biosynthetic gene clusters that confer antibiotic and anticancer effects. Further biochemical studies should characterize the detected bioactive components, and the potential use of 14-7E metabolite for antibiosis and 10-2G metabolite as a selective anti-breast cancer drug.}, } @article {pmid30884638, year = {2019}, author = {Santiyanont, P and Chantarasakha, K and Tepkasikul, P and Srimarut, Y and Mhuantong, W and Tangphatsornruang, S and Zo, YG and Chokesajjawatee, N}, title = {Dynamics of biogenic amines and bacterial communities in a Thai fermented pork product Nham.}, journal = {Food research international (Ottawa, Ont.)}, volume = {119}, number = {}, pages = {110-118}, doi = {10.1016/j.foodres.2019.01.060}, pmid = {30884638}, issn = {1873-7145}, mesh = {Animals ; Bacteria/*classification/genetics/isolation & purification ; Batch Cell Culture Techniques ; Biogenic Amines/*biosynthesis ; Bioreactors ; Fermentation ; Fermented Foods/*microbiology ; Food Microbiology ; Food Safety ; High-Throughput Nucleotide Sequencing ; Humans ; Hydrogen-Ion Concentration ; Meat Products/*microbiology ; Metagenome ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Red Meat/*microbiology ; Swine ; Thailand ; Tyramine/metabolism ; Weissella/isolation & purification/metabolism ; }, abstract = {A traditional Thai fermented pork, nham, is a product popularly consumed in Thailand. Fermentation of the protein-rich product by uncontrolled bacterial community can result in high amounts of hazardous biogenic amines (BA). This study aimed to unveil dynamics of microbial community and its relation to BA accumulation in nham. Three batches of nham were analyzed for pH, lactic acid bacteria population, concentrations of organic acids and BA. Bacterial communities were analyzed by pyrosequencing of 16S rRNA gene amplicons. In all batches, pH dropped to the quality standard of nham (≤4.6) within 3-5 days by production of lactic acid and acetic acid. Initial BA levels varied batch-by-batch and increased with fermentation time. In the highest quality batch, levels of histamine, tyramine, and total BA were within the recommended safety limits (200, 100 and 1000 mg/kg, respectively) throughout the 10-days study. However, in other batches, unsafe levels of tyramine and total BA were found after 5 days of fermentation. The results indicated that over-fermentation and inferior conditions of ingredients increased risk due to high levels of BA. Lactobacillus, Lactococcus, Pediococcus and Weissella were prevalent and comprised >90% of total bacteria during fermentation. Weissella was predominant in the batch with low BA while Lactobacillus and Pediococcus were predominant in the higher BA batches. A negative correlation between Weissella dominance and total BA was observed (r = -0.90, p = .003). A 10% increase in dominance of Weissella was associated with 75-170 mg/kg decrease in total BA. W. hellenica was the species prevalent only in low BA batch. Therefore, W. hellenica isolates were suggested as subjects for future study to develop efficient starter culture securing safety of nham.}, } @article {pmid30881924, year = {2019}, author = {Tribble, GD and Angelov, N and Weltman, R and Wang, BY and Eswaran, SV and Gay, IC and Parthasarathy, K and Dao, DV and Richardson, KN and Ismail, NM and Sharina, IG and Hyde, ER and Ajami, NJ and Petrosino, JF and Bryan, NS}, title = {Frequency of Tongue Cleaning Impacts the Human Tongue Microbiome Composition and Enterosalivary Circulation of Nitrate.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {39}, pmid = {30881924}, issn = {2235-2988}, mesh = {Anti-Bacterial Agents/*administration & dosage ; Blood Pressure/drug effects ; Chlorhexidine/*administration & dosage ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Healthy Volunteers ; Humans ; Microbiota/*drug effects ; Mouthwashes/administration & dosage ; Nitrates/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tongue/*microbiology ; }, abstract = {The oral microbiome has the potential to provide an important symbiotic function in human blood pressure physiology by contributing to the generation of nitric oxide (NO), an essential cardiovascular signaling molecule. NO is produced by the human body via conversion of arginine to NO by endogenous nitric oxide synthase (eNOS) but eNOS activity varies by subject. Oral microbial communities are proposed to supplement host NO production by reducing dietary nitrate to nitrite via bacterial nitrate reductases. Unreduced dietary nitrate is delivered to the oral cavity in saliva, a physiological process termed the enterosalivary circulation of nitrate. Previous studies demonstrated that disruption of enterosalivary circulation via use of oral antiseptics resulted in increases in systolic blood pressure. These previous studies did not include detailed information on the oral health of enrolled subjects. Using 16S rRNA gene sequencing and analysis, we determined whether introduction of chlorhexidine antiseptic mouthwash for 1 week was associated with changes in tongue bacterial communities and resting systolic blood pressure in healthy normotensive individuals with documented oral hygiene behaviors and free of oral disease. Tongue cleaning frequency was a predictor of chlorhexidine-induced changes in systolic blood pressure and tongue microbiome composition. Twice-daily chlorhexidine usage was associated with a significant increase in systolic blood pressure after 1 week of use and recovery from use resulted in an enrichment in nitrate-reducing bacteria on the tongue. Individuals with relatively high levels of bacterial nitrite reductases had lower resting systolic blood pressure. These results further support the concept of a symbiotic oral microbiome contributing to human health via the enterosalivary nitrate-nitrite-NO pathway. These data suggest that management of the tongue microbiome by regular cleaning together with adequate dietary intake of nitrate provide an opportunity for the improvement of resting systolic blood pressure.}, } @article {pmid30878035, year = {2019}, author = {Rowe, WP and Carrieri, AP and Alcon-Giner, C and Caim, S and Shaw, A and Sim, K and Kroll, JS and Hall, LJ and Pyzer-Knapp, EO and Winn, MD}, title = {Streaming histogram sketching for rapid microbiome analytics.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {40}, pmid = {30878035}, issn = {2049-2618}, support = {BBS/E/F/00044409/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M011216/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 100/974/C/13/Z/WT_/Wellcome Trust/United Kingdom ; BB/J004529/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacteria/*classification ; Bacterial Infections/drug therapy ; Cohort Studies ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Infant, Premature ; Machine Learning ; Metagenomics/*methods ; Sequence Analysis, DNA ; Software ; }, abstract = {BACKGROUND: The growth in publically available microbiome data in recent years has yielded an invaluable resource for genomic research, allowing for the design of new studies, augmentation of novel datasets and reanalysis of published works. This vast amount of microbiome data, as well as the widespread proliferation of microbiome research and the looming era of clinical metagenomics, means there is an urgent need to develop analytics that can process huge amounts of data in a short amount of time. To address this need, we propose a new method for tyrhe compact representation of microbiome sequencing data using similarity-preserving sketches of streaming k-mer spectra. These sketches allow for dissimilarity estimation, rapid microbiome catalogue searching and classification of microbiome samples in near real time.

RESULTS: We apply streaming histogram sketching to microbiome samples as a form of dimensionality reduction, creating a compressed 'histosketch' that can efficiently represent microbiome k-mer spectra. Using public microbiome datasets, we show that histosketches can be clustered by sample type using the pairwise Jaccard similarity estimation, consequently allowing for rapid microbiome similarity searches via a locality sensitive hashing indexing scheme. Furthermore, we use a 'real life' example to show that histosketches can train machine learning classifiers to accurately label microbiome samples. Specifically, using a collection of 108 novel microbiome samples from a cohort of premature neonates, we trained and tested a random forest classifier that could accurately predict whether the neonate had received antibiotic treatment (97% accuracy, 96% precision) and could subsequently be used to classify microbiome data streams in less than 3 s.

CONCLUSIONS: Our method offers a new approach to rapidly process microbiome data streams, allowing samples to be rapidly clustered, indexed and classified. We also provide our implementation, Histosketching Using Little K-mers (HULK), which can histosketch a typical 2 GB microbiome in 50 s on a standard laptop using four cores, with the sketch occupying 3000 bytes of disk space. (https://github.com/will-rowe/hulk).}, } @article {pmid30877015, year = {2019}, author = {Gómez-Acata, ES and Centeno, CM and Falcón, LI}, title = {Methods for extracting 'omes from microbialites.}, journal = {Journal of microbiological methods}, volume = {160}, number = {}, pages = {1-10}, doi = {10.1016/j.mimet.2019.02.014}, pmid = {30877015}, issn = {1872-8359}, mesh = {DNA, Bacterial/*isolation & purification ; Geologic Sediments/*microbiology ; Metagenome ; *Microbiota/genetics/physiology ; RNA, Bacterial/*isolation & purification ; Viruses/*isolation & purification ; }, abstract = {Microbialites are organo-sedimentary structures formed by complex microbial communities that interact with abiotic factors to form carbonate rich fabrics. Extraction of DNA or total RNA from microbialites can be difficult because of the high carbonate mineral concentration and exopolymeric substances. The methods employed until now include substances such as cetyltrimethylammonium bromide, sodium dodecyl sulfate, xanthogenate, lysozyme and proteinase K, as well as mechanical disruption. Additionally, several commercial kits have been used to improve DNA and total RNA extraction. This minireview presents different methods applied for DNA and RNA extraction from microbialites and discusses their advantages and disadvantages. Moreover, extraction of all 'omes (DNA, RNA, Protein, Lipids, polar metabolites) using multiomic extraction methods (MPlex), as well as the state of art for extraction of viruses from microbialites, are also discussed.}, } @article {pmid30876405, year = {2019}, author = {Doyle, SR and Illingworth, CJR and Laing, R and Bartley, DJ and Redman, E and Martinelli, A and Holroyd, N and Morrison, AA and Rezansoff, A and Tracey, A and Devaney, E and Berriman, M and Sargison, N and Cotton, JA and Gilleard, JS}, title = {Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {218}, pmid = {30876405}, issn = {1471-2164}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/M003949/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; DNA, Helminth ; *Drug Resistance ; *Evolution, Molecular ; Genetic Variation ; Haemonchus/*drug effects/*genetics ; Insecticides/pharmacology ; Ivermectin/*pharmacology ; *Metagenomics ; *Quantitative Trait Loci ; }, abstract = {BACKGROUND: Infections with helminths cause an enormous disease burden in billions of animals and plants worldwide. Large scale use of anthelmintics has driven the evolution of resistance in a number of species that infect livestock and companion animals, and there are growing concerns regarding the reduced efficacy in some human-infective helminths. Understanding the mechanisms by which resistance evolves is the focus of increasing interest; robust genetic analysis of helminths is challenging, and although many candidate genes have been proposed, the genetic basis of resistance remains poorly resolved.

RESULTS: Here, we present a genome-wide analysis of two genetic crosses between ivermectin resistant and sensitive isolates of the parasitic nematode Haemonchus contortus, an economically important gastrointestinal parasite of small ruminants and a model for anthelmintic research. Whole genome sequencing of parental populations, and key stages throughout the crosses, identified extensive genomic diversity that differentiates populations, but after backcrossing and selection, a single genomic quantitative trait locus (QTL) localised on chromosome V was revealed to be associated with ivermectin resistance. This QTL was common between the two geographically and genetically divergent resistant populations and did not include any leading candidate genes, suggestive of a previously uncharacterised mechanism and/or driver of resistance. Despite limited resolution due to low recombination in this region, population genetic analyses and novel evolutionary models supported strong selection at this QTL, driven by at least partial dominance of the resistant allele, and that large resistance-associated haplotype blocks were enriched in response to selection.

CONCLUSIONS: We have described the genetic architecture and mode of ivermectin selection, revealing a major genomic locus associated with ivermectin resistance, the most conclusive evidence to date in any parasitic nematode. This study highlights a novel genome-wide approach to the analysis of a genetic cross in non-model organisms with extreme genetic diversity, and the importance of a high-quality reference genome in interpreting the signals of selection so identified.}, } @article {pmid30875404, year = {2019}, author = {Kumar, S and Suyal, DC and Yadav, A and Shouche, Y and Goel, R}, title = {Microbial diversity and soil physiochemical characteristic of higher altitude.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0213844}, pmid = {30875404}, issn = {1932-6203}, mesh = {*Altitude ; Bacteria/*classification/genetics/*isolation & purification ; *Biodiversity ; DNA, Bacterial/*genetics ; Phylogeny ; RNA, Ribosomal, 16S ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Altitude is the major factor affecting both biodiversity and soil physiochemical properties of soil ecosystems. In order to understand the effect of altitude on soil physiochemical properties and bacterial diversity across the Himalayan cold desert, high altitude Gangotri soil ecosystem was studied and compared with the moderate altitude Kandakhal soil. Soil physiochemical analysis showed that altitude was positively correlated with soil pH, organic matter and total nitrogen content. However soil mineral nutrients and soil phosphorus were negatively correlated to the altitude. RT-PCR based analysis revealed the decreased bacterial and diazotrophic abundance at high altitude. Metagenomic study showed that Proteobacteria, Acidobacteria and Actinobacteria were dominant bacteria phyla at high altitude soil while Bacteroidetes and Fermicutes were found dominant at low altitude. High ratio of Gram-negative to Gram positive bacteria at Gangotri suggests the selective proliferation of Gram negative bacteria at high altitude with decrease in Gram positive bacteria. Moreover, Alphaproteobacteria was found more abundant at high altitude while the opposite was true for Betaproteobacteria. Abundance of Cytophaga, Flavobacterium and Bacteroides (CFB) were also found comparatively high at high altitude. Presence of many taxonomically unclassified sequences in Gangotri soil indicates the presence of novel bacterial diversity at high altitude. Further, isolation of bacteria through indigenously designed diffusion chamber revealed the existence of bacteria which has been documented in unculturable study of WIH (Western Indian Himalaya) but never been cultivated from WIH. Nevertheless, diverse functional free-living psychrotrophic diazotrophs were isolated only from the high altitude Gangotri soil. Molecular characterization revealed them as Arthrobacter humicola, Brevibacillus invocatus, Pseudomonas mandelii and Pseudomonas helmanticensis. Thus, this study documented the bacterial and psychrophilic diazotrophic diversity at high altitude and is an effort for exploration of low temperature bacteria in agricultural productivity with the target for sustainable hill agriculture.}, } @article {pmid30875036, year = {2019}, author = {Al-Masaudi, S and El Kaoutari, A and Drula, E and Redwan, EM and Lombard, V and Henrissat, B}, title = {A metagenomics investigation of carbohydrate-active enzymes along the goat and camel intestinal tract.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {22}, number = {4}, pages = {429-435}, doi = {10.1007/s10123-019-00068-2}, pmid = {30875036}, issn = {1618-1905}, support = {67/130/35-HiCi//Deanship of Scientific Research, King Abdulaziz University, Jeddah/ ; }, mesh = {Animals ; Bacteria/classification/*enzymology/genetics/isolation & purification ; Bacterial Proteins/*genetics/metabolism ; Camelus/metabolism/*microbiology ; *Carbohydrate Metabolism ; *Gastrointestinal Microbiome ; Goats/metabolism/*microbiology ; Intestines/microbiology ; Metagenomics ; Rumen/metabolism/microbiology ; Sheep ; }, abstract = {Studies of the digestive microbiota of ruminant animals most often focus on the bacterial diversity in the rumen or the feces of the animals, but little is known about the diversity and functions of their distal intestine. Here, the bacterial microbiota of the distal intestinal tract of two goats and two camels was investigated by metagenomics techniques. The bacterial taxonomic diversity and carbohydrate-active enzyme profile were estimated for samples taken from the small intestine, the large intestine, and the rectum of each animal. The bacterial diversity and abundance in the small intestine were lower than in the rectal and large intestinal samples. Analysis of the carbohydrate-active enzyme profiles at each site revealed a comparatively low abundance of enzymes targeting xylan and cellulose in all animals examined, similar to what has been reported earlier for sheep and therefore suggesting that plant cell wall digestion probably takes place elsewhere, such as in the rumen.}, } @article {pmid30872807, year = {2019}, author = {Thomas, F and Corre, E and Cébron, A}, title = {Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil.}, journal = {The ISME journal}, volume = {13}, number = {7}, pages = {1814-1830}, pmid = {30872807}, issn = {1751-7370}, mesh = {Bacteria/genetics/*isolation & purification/metabolism ; Biodegradation, Environmental ; Carbon Isotopes/analysis ; Lolium/*microbiology ; *Metagenomics ; *Microbial Consortia ; Phenanthrenes/*analysis ; Plant Roots/metabolism ; Polycyclic Aromatic Hydrocarbons/*analysis ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/*analysis ; Sphingomonadaceae/genetics/isolation & purification/metabolism ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil pollutants. The discovery that plants can stimulate microbial degradation of PAHs has promoted research on rhizoremediation strategies. We combined DNA-SIP with metagenomics to assess the influence of plants on the identity and metabolic functions of active PAH-degrading bacteria in contaminated soil, using phenanthrene (PHE) as a model hydrocarbon. [13]C-PHE dissipation was 2.5-fold lower in ryegrass-planted conditions than in bare soil. Metabarcoding of 16S rDNA revealed significantly enriched OTUs in [13]C-SIP incubations compared to [12]C-controls, namely 130 OTUs from bare soil and 73 OTUs from planted soil. Active PHE-degraders were taxonomically diverse (Proteobacteria, Actinobacteria and Firmicutes), with Sphingomonas and Sphingobium dominating in bare and planted soil, respectively. Plant root exudates favored the development of PHE-degraders having specific functional traits at the genome level. Indeed, metagenomes of [13]C-enriched DNA fractions contained more genes involved in aromatic compound metabolism in bare soil, whereas carbohydrate catabolism genes were more abundant in planted soil. Functional gene annotation allowed reconstruction of complete pathways with several routes for PHE catabolism. Sphingomonadales were the major taxa performing the first steps of PHE degradation in both conditions, suggesting their critical role to initiate in situ PAH remediation. Active PHE-degraders act in a consortium, whereby complete PHE mineralization is achieved through the combined activity of taxonomically diverse co-occurring bacteria performing successive metabolic steps. Our study reveals hitherto underestimated functional interactions for full microbial detoxification in contaminated soils.}, } @article {pmid30872712, year = {2019}, author = {Oh, S and Choi, D and Cha, CJ}, title = {Ecological processes underpinning microbial community structure during exposure to subinhibitory level of triclosan.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4598}, pmid = {30872712}, issn = {2045-2322}, mesh = {Biodiversity ; Ecology ; Metagenome ; Metagenomics/methods ; Microbiota/*drug effects ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; Triclosan/*pharmacology ; }, abstract = {Ecological processes shaping the structure and diversity of microbial communities are of practical importance for managing the function and resilience of engineered biological ecosystems such as activated sludge processes. This study systematically evaluated the ecological processes acting during continuous exposure to a subinhibitory level of antimicrobial triclosan (TCS) as an environmental stressor. 16S rRNA gene-based community profiling revealed significant perturbations on the community structure and dramatic reduction (by 20-30%) in species diversity/richness compared to those under the control conditions. In addition, community profiling determined the prevalence of the deterministic processes overwhelming the ecological stochasticity. Analysis of both community composition and phenotypes in the TCS-exposed communities suggested the detailed deterministic mechanism: selection of TCS degrading (Sphingopyxis) and resistant (Pseudoxanthomonas) bacterial populations. The analysis also revealed a significant reduction of core activated sludge members, Chitinophagaceae (e.g., Ferruginibacter) and Comamonadaceae (e.g., Acidovorax), potentially affecting ecosystem functions (e.g., floc formation and nutrient removal) directly associated with system performance (i.e., wastewater treatment efficiency and effluent quality). Overall, our study provides new findings that inform the mechanisms underlying the community structure and diversity of activated sludge, which not only advances the current understanding of microbial ecology in activated sludge, but also has practical implications for the design and operation of environmental bioprocesses for treatment of antimicrobial-bearing waste streams.}, } @article {pmid30872659, year = {2019}, author = {Johnston, J and LaPara, T and Behrens, S}, title = {Composition and Dynamics of the Activated Sludge Microbiome during Seasonal Nitrification Failure.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4565}, pmid = {30872659}, issn = {2045-2322}, mesh = {Metagenome ; Metagenomics/methods ; *Microbiota ; Minnesota ; *Nitrification ; RNA, Ribosomal, 16S/genetics ; *Seasons ; Sewage/*microbiology ; Waste Management ; }, abstract = {Wastewater treatment plants in temperate climate zones frequently undergo seasonal nitrification failure in the winter month yet maintain removal efficiency for other contaminants. We tested the hypothesis that nitrification failure can be correlated to shifts in the nitrifying microbial community. We monitored three parallel, full-scale sequencing batch reactors over the course of a year with respect to reactor performance, microbial community composition via 16S rRNA gene amplicon sequencing, and functional gene abundance using qPCR. All reactors demonstrated similar changes to their core microbiome, and only subtle variations among seasonal and transient taxa. We observed a decrease in species richness during the winter, with a slow recovery of the activated sludge community during spring. Despite the change in nitrification performance, ammonia monooxygenase gene abundances remained constant throughout the year, as did the relative sequence abundance of Nitrosomonadacae. This suggests that nitrification failure at colder temperatures might result from different reaction kinetics of nitrifying taxa, or that other organisms with strong seasonal shifts in population abundance, e.g. an uncultured lineage of Saprospiraceae, affect plant performance in the winter. This research is a comprehensive analysis of the seasonal microbial community dynamics in triplicate full-scale sequencing batch reactors and ultimately strengthens our basic understanding of the microbial ecology of activated sludge communities by revealing seasonal succession patterns of individual taxa that correlate with nutrient removal efficiency.}, } @article {pmid30871856, year = {2019}, author = {Minot, SS}, title = {De novo Assembly Vastly Expands the Known Microbial Universe.}, journal = {Trends in microbiology}, volume = {27}, number = {5}, pages = {385-386}, doi = {10.1016/j.tim.2019.02.007}, pmid = {30871856}, issn = {1878-4380}, mesh = {Geography ; Humans ; Life Style ; *Metagenome ; *Microbiota ; }, abstract = {The study of the human microbiome relies heavily on the genomes of bacterial isolates that can be grown in culture. A recent study (Pasolli et al. Cell 2019;176:649-662) of stool microbiome samples generated over 150 000 microbial genomes without any culture, vastly expanding our knowledge of the biases in existing reference databases.}, } @article {pmid30871675, year = {2019}, author = {Ni, YH}, title = {Bugs to debug? The exploration of gut microbiome in human health and diseases.}, journal = {Journal of the Formosan Medical Association = Taiwan yi zhi}, volume = {118 Suppl 1}, number = {}, pages = {S1-S2}, doi = {10.1016/j.jfma.2019.01.017}, pmid = {30871675}, issn = {0929-6646}, mesh = {*Disease ; Environment ; Gastrointestinal Microbiome/*physiology ; *Health ; Host Microbial Interactions/*physiology ; Humans ; Metagenomics ; }, } @article {pmid30871469, year = {2019}, author = {Perz, AI and Giles, CB and Brown, CA and Porter, H and Roopnarinesingh, X and Wren, JD}, title = {MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 2}, pages = {96}, pmid = {30871469}, issn = {1471-2105}, support = {P20 GM103636/GM/NIGMS NIH HHS/United States ; P30 AG050911/AG/NIA NIH HHS/United States ; T32 AG052363/AG/NIA NIH HHS/United States ; U54 GM104938/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {BACKGROUND: The number of publicly available metagenomic experiments in various environments has been rapidly growing, empowering the potential to identify similar shifts in species abundance between different experiments. This could be a potentially powerful way to interpret new experiments, by identifying common themes and causes behind changes in species abundance.

RESULTS: We propose a novel framework for comparing microbial shifts between conditions. Using data from one of the largest human metagenome projects to date, the American Gut Project (AGP), we obtain differential abundance vectors for microbes using experimental condition information provided with the AGP metadata, such as patient age, dietary habits, or health status. We show it can be used to identify similar and opposing shifts in microbial species, and infer putative interactions between microbes. Our results show that groups of shifts with similar effects on microbiome can be identified and that similar dietary interventions display similar microbial abundance shifts.

CONCLUSIONS: Without comparison to prior data, it is difficult for experimentalists to know if their observed changes in species abundance have been observed by others, both in their conditions and in others they would never consider comparable. Yet, this can be a very important contextual factor in interpreting the significance of a shift. We've proposed and tested an algorithmic solution to this problem, which also allows for comparing the metagenomic signature shifts between conditions in the existing body of data.}, } @article {pmid30871459, year = {2019}, author = {Thrash, A and Arick, M and Barbato, RA and Jones, RM and Douglas, TA and Esdale, J and Perkins, EJ and Garcia-Reyero, N}, title = {Keanu: a novel visualization tool to explore biodiversity in metagenomes.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 2}, pages = {103}, pmid = {30871459}, issn = {1471-2105}, support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; }, mesh = {Biodiversity ; Metagenomics/*methods ; }, abstract = {BACKGROUND: One of the main challenges when analyzing complex metagenomics data is the fact that large amounts of information need to be presented in a comprehensive and easy-to-navigate way. In the process of analyzing FASTQ sequencing data, visualizing which organisms are present in the data can be useful, especially with metagenomics data or data suspected to be contaminated. Here, we describe the development and application of a command-line tool, Keanu, for visualizing and exploring sample content in metagenomics data. We developed Keanu as an interactive tool to make viewing complex data easier.

RESULTS: Keanu, a tool for exploring sequence content, helps a user to understand the presence and abundance of organisms in a sample by analyzing alignments against a database that contains taxonomy data and displaying them in an interactive web page. The content of a sample can be presented either as a collapsible tree, with node size indicating abundance, or as a bilevel partition graph, with arc size indicating abundance. Here, we illustrate how Keanu works by exploring shotgun metagenomics data from a sample collected from a bluff that contained paleosols and a krotovina in an alpine site in Ft. Greely, Alaska.

CONCLUSIONS: Keanu provides a simple means by which researchers can explore and visualize species present in sequence data generated from complex communities and environments. Keanu is written in Python and is freely available at https://github.com/IGBB/keanu .}, } @article {pmid30871224, year = {2019}, author = {Gurwara, S and Ajami, NJ and Jang, A and Hessel, FC and Chen, L and Plew, S and Wang, Z and Graham, DY and Hair, C and White, DL and Kramer, J and Kourkoumpetis, T and Hoffman, K and Cole, R and Hou, J and Husain, N and Jarbrink-Sehgal, M and Hernaez, R and Kanwal, F and Ketwaroo, G and Shah, R and Velez, M and Natarajan, Y and El-Serag, HB and Petrosino, JF and Jiao, L}, title = {Dietary Nutrients Involved in One-Carbon Metabolism and Colonic Mucosa-Associated Gut Microbiome in Individuals with an Endoscopically Normal Colon.}, journal = {Nutrients}, volume = {11}, number = {3}, pages = {}, pmid = {30871224}, issn = {2072-6643}, support = {I01 CX001430/CX/CSRD VA/United States ; RP#140767//Cancer Prevention and Research Institute of Texas/ ; 1000//Gillson Longenbaugh Foundation/ ; 0000//Golfers Against Cancer/ ; }, mesh = {Aged ; Bacteria/*metabolism ; Colon/*microbiology ; Cross-Sectional Studies ; *Diet ; Food Analysis ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Intestinal Mucosa/*microbiology ; Male ; Middle Aged ; Prospective Studies ; }, abstract = {One carbon (1C) metabolism nutrients influence epigenetic regulation and they are supplied by diet and synthesized by gut microbiota. We examined the association between dietary consumption of methyl donors (methionine, betaine and choline) and B vitamins (folate, B2, B6, and B12) and the community composition and structure of the colonic mucosa-associated gut microbiota determined by 16S rRNA gene sequencing in 97 colonic biopsies of 35 men. We used the food frequency questionnaire to assess daily consumption of nutrients, and the UPARSE and SILVA databases for operational taxonomic unit classification. The difference in bacterial diversity and taxonomic relative abundance were compared between low versus high consumption of these nutrients. False discover rate (FDR) adjusted p value < 0.05 indicated statistical significance. The bacterial richness and composition differed significantly by the consumption of folate and B vitamins (p < 0.001). Compared with higher consumption, a lower consumption of these nutrients was associated with a lower abundance of Akkermansia (folate), Roseburia (vitamin B2), and Faecalibacterium (vitamins B2, B6, and B12) but a higher abundance of Erysipelatoclostridium (vitamin B2) (FDR p values < 0.05). The community composition and structure of the colonic bacteria differed significantly by dietary consumption of folate and B vitamins.}, } @article {pmid30870464, year = {2019}, author = {Burcham, ZM and Schmidt, CJ and Pechal, JL and Brooks, CP and Rosch, JW and Benbow, ME and Jordan, HR}, title = {Detection of critical antibiotic resistance genes through routine microbiome surveillance.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0213280}, pmid = {30870464}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics ; Bacterial Infections/*diagnosis/epidemiology/genetics/microbiology ; Cadaver ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; Humans ; *Metagenome ; Microbiota ; *Population Surveillance ; United States/epidemiology ; }, abstract = {Population-based public health data on antibiotic resistance gene carriage is poorly surveyed. Research of the human microbiome as an antibiotic resistance reservoir has primarily focused on gut associated microbial communities, but data have shown more widespread microbial colonization across organs than originally believed, with organs previously considered as sterile being colonized. Our study demonstrates the utility of postmortem microbiome sampling during routine autopsy as a method to survey antibiotic resistance carriage in a general population. Postmortem microbial sampling detected pathogens of public health concern including genes for multidrug efflux pumps, carbapenem, methicillin, vancomycin, and polymixin resistances. Results suggest that postmortem assessments of host-associated microbial communities are useful in acquiring community specific data while reducing selective-participant biases.}, } @article {pmid30868805, year = {2019}, author = {Liu, ZX and Xu, J and Sun, W and Shi, YH and Chen, SL}, title = {[Application of DNA metabarcoding in species identification of Chinese herbal medicines].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {44}, number = {1}, pages = {1-8}, doi = {10.19540/j.cnki.cjcmm.2019.0001}, pmid = {30868805}, issn = {1001-5302}, mesh = {Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Drugs, Chinese Herbal/*analysis ; High-Throughput Nucleotide Sequencing ; Plants, Medicinal/*classification ; }, abstract = {DNA metabarcoding,one rapid and robust method using specific standard DNA fragments,has been widely used for rapid species identification of a bulk sample through high-throughput sequencing technologies.While it has been widely used in the studies of metagenomics,animal and plant biodiversity,it has gradually come to be used as a profitable method in species identification of mixed Chinese herbal medicines.In this paper,we mainly summarize the current studies of the application of DNA metabarcoding in species identification of mixed Chinese herbal medicines.Moreover,high-throughput sequencing technologies adopted in those studies,such as Sanger,the next-generation,and third-generation sequencing technologies,are discussed.It is conducted to provide a theoretical guidance for the application of DNA metabarcoding in species identification of mixed Chinese herbal medicines and in more other biodiversity studies.}, } @article {pmid30867587, year = {2019}, author = {Nayfach, S and Shi, ZJ and Seshadri, R and Pollard, KS and Kyrpides, NC}, title = {New insights from uncultivated genomes of the global human gut microbiome.}, journal = {Nature}, volume = {568}, number = {7753}, pages = {505-510}, pmid = {30867587}, issn = {1476-4687}, mesh = {Bacteria/*classification/*genetics/growth & development/isolation & purification ; Bacterial Physiological Phenomena/genetics ; Biosynthetic Pathways/genetics ; Disease ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics/physiology ; Genome, Bacterial/*genetics ; Genomics ; Geographic Mapping ; Humans ; Metagenome/*genetics ; Phylogeny ; Rural Population ; Species Specificity ; }, abstract = {The genome sequences of many species of the human gut microbiome remain unknown, largely owing to challenges in cultivating microorganisms under laboratory conditions. Here we address this problem by reconstructing 60,664 draft prokaryotic genomes from 3,810 faecal metagenomes, from geographically and phenotypically diverse humans. These genomes provide reference points for 2,058 newly identified species-level operational taxonomic units (OTUs), which represents a 50% increase over the previously known phylogenetic diversity of sequenced gut bacteria. On average, the newly identified OTUs comprise 33% of richness and 28% of species abundance per individual, and are enriched in humans from rural populations. A meta-analysis of clinical gut-microbiome studies pinpointed numerous disease associations for the newly identified OTUs, which have the potential to improve predictive models. Finally, our analysis revealed that uncultured gut species have undergone genome reduction that has resulted in the loss of certain biosynthetic pathways, which may offer clues for improving cultivation strategies in the future.}, } @article {pmid30867497, year = {2019}, author = {Tu, P and Gao, B and Chi, L and Lai, Y and Bian, X and Ru, H and Lu, K}, title = {Subchronic low-dose 2,4-D exposure changed plasma acylcarnitine levels and induced gut microbiome perturbations in mice.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4363}, pmid = {30867497}, issn = {2045-2322}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 ES024950/ES/NIEHS NIH HHS/United States ; }, mesh = {2,4-Dichlorophenoxyacetic Acid/*administration & dosage/adverse effects ; Animals ; Carnitine/*analogs & derivatives/blood ; Computational Biology ; Environmental Exposure ; Gastrointestinal Microbiome/*drug effects ; Herbicides/*administration & dosage/adverse effects ; Metabolome/drug effects ; Metabolomics/methods ; Metagenome ; Mice ; }, abstract = {The gut microbiota critically confers various health benefits, whereas environmental chemicals can affect its constitution and functionality thereby increasing disease risk. In the present study, we aim to evaluate the toxic effects of a wildly-used herbicide 2,4-D (2,4-dichlorophenoxyacetic acid) on the gut microbiome and host using an occupationally relevant dose. A mouse model was used combined with metagenomic sequencing and metabolomic profiling to examine the alterations induced by subchronic low-dose 2,4-D exposure in fecal and plasma samples. The metagenomics results revealed a distinct gut microbial community with profound changes in diverse microbial pathways including urea degradation, amino acid and carbohydrate metabolism in 2,4-D-treated mice. Moreover, the metabolomics results revealed that the metabolic profiles in treatment group were differentiated from control group in both fecal and plasma samples. Toxic effects on the host of 2,4-D at an occupationally relevant dose were observed indicated by decreased acylcarnitine levels in plasma. These findings indicated that 2,4-D can cause toxicity and substantially impact the gut microbiome in mice at occupationally relevant doses, inferring that the relationship between environmental contaminants and microbiota is largely underestimated calling for more comprehensive consideration of the toxicity of occupational exposures.}, } @article {pmid30867308, year = {2019}, author = {Chong, R and Shi, M and Grueber, CE and Holmes, EC and Hogg, CJ and Belov, K and Barrs, VR}, title = {Fecal Viral Diversity of Captive and Wild Tasmanian Devils Characterized Using Virion-Enriched Metagenomics and Metatranscriptomics.}, journal = {Journal of virology}, volume = {93}, number = {11}, pages = {}, pmid = {30867308}, issn = {1098-5514}, mesh = {Animals ; Animals, Wild ; Animals, Zoo ; Australia ; Endangered Species ; Feces/*virology ; Gene Expression Profiling/methods ; Marsupialia/*virology ; Metagenomics/methods ; Transcriptome/genetics ; Virion ; }, abstract = {The Tasmanian devil is an endangered carnivorous marsupial threatened by devil facial tumor disease (DFTD). While research on DFTD has been extensive, little is known about viruses in devils and whether any are of potential conservation relevance for this endangered species. Using both metagenomics based on virion enrichment and sequence-independent amplification (virion-enriched metagenomics) and metatranscriptomics based on bulk RNA sequencing, we characterized and compared the fecal viromes of captive and wild devils. A total of 54 fecal samples collected from two captive and four wild populations were processed for virome characterization using both approaches. In total, 24 novel marsupial-related viruses, comprising a sapelovirus, astroviruses, rotaviruses, picobirnaviruses, parvoviruses, papillomaviruses, polyomaviruses, and a gammaherpesvirus, were identified, as well as known mammalian pathogens such as rabbit hemorrhagic disease virus 2. Captive devils showed significantly lower viral diversity than wild devils. Comparison of the two virus discovery approaches revealed substantial differences in the number and types of viruses detected, with metatranscriptomics better suited for RNA viruses and virion-enriched metagenomics largely identifying more DNA viruses. Thus, the viral communities revealed by virion-enriched metagenomics and metatranscriptomics were not interchangeable and neither approach was able to detect all viruses present. An integrated approach using both virion-enriched metagenomics and metatranscriptomics constitutes a powerful tool for obtaining a complete overview of both the taxonomic and functional profiles of viral communities within a sample.IMPORTANCE The Tasmanian devil is an iconic Australian marsupial that has suffered an 80% population decline due to a contagious cancer, devil facial tumor disease, along with other threats. Until now, viral discovery in this species has been confined to one gammaherpesvirus (dasyurid herpesvirus 2 [DaHV-2]), for which captivity was identified as a significant risk factor. Our discovery of 24 novel marsupial-associated RNA and DNA viruses, and that viral diversity is lower in captive than in wild devils, has greatly expanded our knowledge of gut-associated viruses in devils and provides important baseline information that will contribute to the conservation and captive management of this endangered species. Our results also revealed that a combination of virion-enriched metagenomics and metatranscriptomics may be a more comprehensive approach for virome characterization than either method alone. Our results thus provide a springboard for continuous improvements in the way we study complex viral communities.}, } @article {pmid30866822, year = {2019}, author = {Lee, Y and Schmidt, H and Collier, TC and Conner, WR and Hanemaaijer, MJ and Slatkin, M and Marshall, JM and Chiu, JC and Smartt, CT and Lanzaro, GC and Mulligan, FS and Cornel, AJ}, title = {Genome-wide divergence among invasive populations of Aedes aegypti in California.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {204}, pmid = {30866822}, issn = {1471-2164}, support = {U01CK000516//ACL HHS/United States ; HR0011-17-2-0047//Defense Sciences Office, DARPA/ ; 1U01CK000516//Centers for Disease Control and Prevention/ ; }, mesh = {Aedes/*classification/genetics ; Animals ; California ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Genome Size ; *Genome, Insect ; Introduced Species ; Metagenomics ; Mosquito Vectors/classification/genetics ; Phylogeny ; Phylogeography ; Whole Genome Sequencing/*veterinary ; }, abstract = {BACKGROUND: In the summer of 2013, Aedes aegypti Linnaeus was first detected in three cities in central California (Clovis, Madera and Menlo Park). It has now been detected in multiple locations in central and southern CA as far south as San Diego and Imperial Counties. A number of published reports suggest that CA populations have been established from multiple independent introductions.

RESULTS: Here we report the first population genomics analyses of Ae. aegypti based on individual, field collected whole genome sequences. We analyzed 46 Ae. aegypti genomes to establish genetic relationships among populations from sites in California, Florida and South Africa. Based on 4.65 million high quality biallelic SNPs, we identified 3 major genetic clusters within California; one that includes all sample sites in the southern part of the state (South of Tehachapi mountain range) plus the town of Exeter in central California and two additional clusters in central California.

CONCLUSIONS: A lack of concordance between mitochondrial and nuclear genealogies suggests that the three founding populations were polymorphic for two main mitochondrial haplotypes prior to being introduced to California. One of these has been lost in the Clovis populations, possibly by a founder effect. Genome-wide comparisons indicate extensive differentiation between genetic clusters. Our observations support recent introductions of Ae. aegypti into California from multiple, genetically diverged source populations. Our data reveal signs of hybridization among diverged populations within CA. Genetic markers identified in this study will be of great value in pursuing classical population genetic studies which require larger sample sizes.}, } @article {pmid30866812, year = {2019}, author = {Das, P and Babaei, P and Nielsen, J}, title = {Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {208}, pmid = {30866812}, issn = {1471-2164}, support = {HEALTH-F4-2012-305312//METACARDIS/ ; }, mesh = {Bacteria/*classification/genetics/isolation & purification/metabolism ; Bacterial Proteins/*genetics ; China ; Feces/microbiology ; Gastrointestinal Microbiome ; Gene Expression Profiling ; Humans ; Metagenomics/*methods ; Phylogeny ; Phylogeography ; United States ; Vitamins/*metabolism ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Human gut microbial communities have been known to produce vitamins, which are subsequently absorbed by the host in the large intestine. However, the relationship between species with vitamin pathway associated functional features or their gene abundance in different states of health and disease is lacking. Here, we analyzed shotgun fecal metagenomes of individuals from four different countries for genes that are involved in vitamin biosynthetic pathways and transport mechanisms and corresponding species' abundance.

RESULTS: We found that the prevalence of these genes were found to be distributed across the dominant phyla of gut species. The number of positive correlations were high between species harboring genes related to vitamin biosynthetic pathways and transporter mechanisms than that with either alone. Although, the range of total gene abundances remained constant across healthy populations at the global level, species composition and their presence for metabolic pathway related genes determine the abundance and functional genetic content of vitamin metabolism. Based on metatranscriptomics data, the equation between abundance of vitamin-biosynthetic enzymes and vitamin-dependent enzymes suggests that the production and utilization potential of these enzymes seems way more complex usage allocations than just mere direct linear associations.

CONCLUSIONS: Our findings provide a rationale to examine and disentangle the interrelationship between B-vitamin dosage (dietary or microbe-mediated) on gut microbial members and the host, in the gut microbiota of individuals with under- or overnutrition.}, } @article {pmid30866714, year = {2019}, author = {Park, H and Laffin, MR and Jovel, J and Millan, B and Hyun, JE and Hotte, N and Kao, D and Madsen, KL}, title = {The success of fecal microbial transplantation in Clostridium difficile infection correlates with bacteriophage relative abundance in the donor: a retrospective cohort study.}, journal = {Gut microbes}, volume = {10}, number = {6}, pages = {676-687}, pmid = {30866714}, issn = {1949-0984}, support = {//CIHR/Canada ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/genetics/isolation & purification ; Bacteriophages/*classification/genetics ; Clostridioides difficile/physiology ; Clostridium Infections/microbiology/*therapy/*virology ; Cohort Studies ; *Fecal Microbiota Transplantation ; Feces/microbiology/virology ; Female ; Gastrointestinal Microbiome/genetics ; Humans ; Male ; Middle Aged ; Recurrence ; Retrospective Studies ; *Tissue Donors ; Treatment Outcome ; }, abstract = {Background: Fecal microbial transplantation (FMT) is used in the treatment of relapsing Clostridium difficile infection (rCDI). Failure rate for FMT is as high as 10% but the mechanisms contributing to a failed FMT are not understood. We utilized metagenomic data to identify the role of bacteria and bacteriophages on FMT success.Results: Subjects with rCDI (n = 19) received FMT from volunteer donors (n = 7) via colonoscopy. Twelve patients fully recovered after a single FMT, while seven patients required a subsequent FMT. DNA was extracted from patient and donor stool samples for shotgun metagenomic analysis. Metagenomics libraries were analyzed focusing on bacterial taxonomy and bacteriophage sequences. Gammaproteobacteria were dominant in rCDI patients prior to FMT largely due to elevated levels of Klebsiella and Escherichia. A successful FMT led to increased levels of Clostridia and Bacteroidia and a reduction in Gammaproteobacteria. In contrast, a failed FMT led to no significant changes in bacterial composition. Bacteriophages were classified during whole metagenomic analysis of each sample and were markedly different between rCDI patients, donors, and a healthy control cohort (n = 96). Bacteriophage sequence reads were increased in CDI patients compared with donors and healthy controls. Successful FMT donors had higher bacteriophage α-diversity and lower relative abundance compared to the donors of a failed initial FMT.Conclusions: In this retrospective analysis, FMTs with increased bacteriophage α-diversity were more likely to successfully treat rCDI. In addition, the relative number of bacteriophage reads was lower in donations leading to a successful FMT. These results suggest that bacteriophage abundance may have some role in determining the relative success of FMT.}, } @article {pmid30866521, year = {2019}, author = {François, S and Mutuel, D and Duncan, AB and Rodrigues, LR and Danzelle, C and Lefevre, S and Santos, I and Frayssinet, M and Fernandez, E and Filloux, D and Roumagnac, P and Froissart, R and Ogliastro, M}, title = {A New Prevalent Densovirus Discovered in Acari. Insight from Metagenomics in Viral Communities Associated with Two-Spotted Mite (Tetranychus urticae) Populations.}, journal = {Viruses}, volume = {11}, number = {3}, pages = {}, pmid = {30866521}, issn = {1999-4915}, mesh = {Animals ; Capsid Proteins/genetics ; Densovirus/*genetics/*isolation & purification ; Female ; *Genetic Variation ; Genome, Viral ; Metagenomics ; *Microbiota ; Phylogeny ; Plants/virology ; Prevalence ; Tetranychidae/*virology ; Viral Nonstructural Proteins/genetics ; }, abstract = {Viral metagenomics and high throughput sequence mining have revealed unexpected diversity, and the potential presence, of parvoviruses in animals from all phyla. Among arthropods, this diversity highlights the poor knowledge that we have regarding the evolutionary history of densoviruses. The aim of this study was to explore densovirus diversity in a small arthropod pest belonging to Acari, the two-spotted spider mite Tetranychus urticae, while using viral metagenomics based on virus-enrichment. Here, we present the viromes obtained from T. urticae laboratory populations made of contigs that are attributed to nine new potential viral species, including the complete sequence of a novel densovirus. The genome of this densovirus has an ambisens genomic organization and an unusually compact size with particularly small non-structural proteins and a predicted major capsid protein that lacks the typical PLA2 motif that is common to all ambidensoviruses described so far. In addition, we showed that this new densovirus had a wide prevalence across populations of mite species tested and a genomic diversity that likely correlates with the host phylogeny. In particular, we observed a low densovirus genomic diversity between the laboratory and natural populations, which suggests that virus within-species evolution is probably slower than initially thought. Lastly, we showed that this novel densovirus can be inoculated to the host plant following feeding by infected mites, and circulate through the plant vascular system. These findings offer new insights into densovirus prevalence, evolution, and ecology.}, } @article {pmid30864326, year = {2019}, author = {Han, W and Ye, Y}, title = {A repository of microbial marker genes related to human health and diseases for host phenotype prediction using microbiome data.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {24}, number = {}, pages = {236-247}, pmid = {30864326}, issn = {2335-6936}, support = {R01 AI108888/AI/NIAID NIH HHS/United States ; R01 AI143254/AI/NIAID NIH HHS/United States ; }, mesh = {Carcinoma, Non-Small-Cell Lung/genetics/microbiology/therapy ; Carcinoma, Renal Cell/genetics/microbiology/therapy ; Computational Biology/methods ; Databases, Genetic ; Diabetes Mellitus, Type 2/genetics/microbiology ; *Genes, Microbial ; Genetic Markers ; Host Microbial Interactions/*genetics ; Humans ; Immunotherapy ; Kidney Neoplasms/genetics/microbiology/therapy ; Liver Cirrhosis/genetics/microbiology ; Lung Neoplasms/genetics/microbiology/therapy ; Machine Learning ; Metagenomics/methods/statistics & numerical data ; Microbiota/*genetics ; Phenotype ; Translational Research, Biomedical ; }, abstract = {The microbiome research is going through an evolutionary transition from focusing on the characterization of reference microbiomes associated with different environments/hosts to the translational applications, including using microbiome for disease diagnosis, improving the effcacy of cancer treatments, and prevention of diseases (e.g., using probiotics). Microbial markers have been identified from microbiome data derived from cohorts of patients with different diseases, treatment responsiveness, etc, and often predictors based on these markers were built for predicting host phenotype given a microbiome dataset (e.g., to predict if a person has type 2 diabetes given his or her microbiome data). Unfortunately, these microbial markers and predictors are often not published so are not reusable by others. In this paper, we report the curation of a repository of microbial marker genes and predictors built from these markers for microbiome-based prediction of host phenotype, and a computational pipeline called Mi2P (from Microbiome to Phenotype) for using the repository. As an initial effort, we focus on microbial marker genes related to two diseases, type 2 diabetes and liver cirrhosis, and immunotherapy efficacy for two types of cancer, non-small-cell lung cancer (NSCLC) and renal cell carcinoma (RCC). We characterized the marker genes from metagenomic data using our recently developed subtractive assembly approach. We showed that predictors built from these microbial marker genes can provide fast and reasonably accurate prediction of host phenotype given microbiome data. As understanding and making use of microbiome data (our second genome) is becoming vital as we move forward in this age of precision health and precision medicine, we believe that such a repository will be useful for enabling translational applications of microbiome data.}, } @article {pmid30864226, year = {2019}, author = {Zhang, Y and Zhao, R and Shi, D and Sun, S and Ren, H and Zhao, H and Wu, W and Jin, L and Sheng, J and Shi, Y}, title = {Characterization of the circulating microbiome in acute-on-chronic liver failure associated with hepatitis B.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {39}, number = {7}, pages = {1207-1216}, doi = {10.1111/liv.14097}, pmid = {30864226}, issn = {1478-3231}, mesh = {Acute-On-Chronic Liver Failure/*blood/microbiology/mortality ; Adult ; Biomarkers/blood ; Case-Control Studies ; Cytokines/blood ; DNA, Bacterial/blood ; Female ; Hepatitis B, Chronic/*blood/microbiology ; Humans ; Inflammation Mediators/blood ; Liver Cirrhosis/*blood/microbiology ; Male ; *Microbiota ; Middle Aged ; Predictive Value of Tests ; }, abstract = {BACKGROUND: Patients with hepatitis B-related acute-on-chronic liver failure (HB-ACLF) may have an increased circulating microbial burden. This study aimed to assess circulating microbial load and composition and to explore the association between the circulating microbiome and both systemic inflammation (SI) and clinical outcome in HB-ACLF.

METHODS: Plasma from 50 HB-ACLF patients, 23 healthy controls and 25 patients with compensated liver cirrhosis (C-LC) was analysed for chemokines/cytokines and bacterial DNA and further analysed by 16S rDNApyrosequencing. Linear discriminant analysis effect size (LEfSe) and inferred metagenomics analyses were performed.

RESULTS: The circulating bacterial DNA was significantly increased in HB-ACLF patients compared to that in the control groups. The overall microbial diversity was significantly decreased in HB-ACLF patients. HB-ACLF patients were enriched with Moraxellaceae, Sulfurovum, Comamonas and Burkholderiaceae but were depleted in Actinobacteria, Deinococcus-Thermus, Alphaproteobacteria, Xanthomonadaceae and Enterobacteriaceae compared to controls. Network analysis revealed a direct positive correlation between Burkholderiaceae and chemokine IP-10 in HB-ACLF patients. The relative abundance of Prevotellaceae independently predicted 28-day mortality. Inferred functional metagenomics predicted an enrichment of bacteria with genes related to methane, alanine, aspartate, glutamate, pyrimidine, purine and energy metabolism.

CONCLUSIONS: HB-ACLF patients display increased circulating microbial burden, altered microbiome composition and a shift in microbiome functionality. The alteration in circulating microbiota is associated with SI and clinical outcome in HB-ACLF.}, } @article {pmid30862830, year = {2019}, author = {Sieradzki, ET and Ignacio-Espinoza, JC and Needham, DM and Fichot, EB and Fuhrman, JA}, title = {Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1169}, pmid = {30862830}, issn = {2041-1723}, mesh = {Bacteriophages/*genetics/metabolism ; Cyanobacteria/*physiology/virology ; Genome, Viral/genetics ; Host Microbial Interactions/physiology ; Metagenome/genetics ; Microbiota/*physiology ; Photosynthesis/*physiology ; Photosystem II Protein Complex/metabolism ; Phylogeny ; Phytoplankton/*physiology/virology ; Seawater/microbiology/virology ; Sequence Analysis, DNA ; }, abstract = {Viruses provide top-down control on microbial communities, yet their direct study in natural environments was hindered by culture limitations. The advance of bioinformatics enables cultivation-independent study of viruses. Many studies assemble new viral genomes and study viral diversity using marker genes from free viruses. Here we use cellular metatranscriptomics to study active community-wide viral infections. Recruitment to viral contigs allows tracking infection dynamics over time and space. Our assemblies represent viral populations, but appear biased towards low diversity viral taxa. Tracking relatives of published T4-like cyanophages and pelagiphages reveals high genomic continuity. We determine potential hosts by matching dynamics of infection with abundance of particular microbial taxa. Finally, we quantify the relative contribution of cyanobacteria and viruses to photosystem-II psbA (reaction center) expression in our study sites. We show sometimes >50% of all cyanobacterial+viral psbA expression is of viral origin, highlighting the contribution of viruses to photosynthesis and oxygen production.}, } @article {pmid30860572, year = {2020}, author = {Wang, Z and Wang, Y and Fuhrman, JA and Sun, F and Zhu, S}, title = {Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences.}, journal = {Briefings in bioinformatics}, volume = {21}, number = {3}, pages = {777-790}, pmid = {30860572}, issn = {1477-4054}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Computational Biology/*methods ; Datasets as Topic ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics ; Microbiota/genetics ; }, abstract = {In metagenomic studies of microbial communities, the short reads come from mixtures of genomes. Read assembly is usually an essential first step for the follow-up studies in metagenomic research. Understanding the power and limitations of various read assembly programs in practice is important for researchers to choose which programs to use in their investigations. Many studies evaluating different assembly programs used either simulated metagenomes or real metagenomes with unknown genome compositions. However, the simulated datasets may not reflect the real complexities of metagenomic samples and the estimated assembly accuracy could be misleading due to the unknown genomes in real metagenomes. Therefore, hybrid strategies are required to evaluate the various read assemblers for metagenomic studies. In this paper, we benchmark the metagenomic read assemblers by mixing reads from real metagenomic datasets with reads from known genomes and evaluating the integrity, contiguity and accuracy of the assembly using the reads from the known genomes. We selected four advanced metagenome assemblers, MEGAHIT, MetaSPAdes, IDBA-UD and Faucet, for evaluation. We showed the strengths and weaknesses of these assemblers in terms of integrity, contiguity and accuracy for different variables, including the genetic difference of the real genomes with the genome sequences in the real metagenomic datasets and the sequencing depth of the simulated datasets. Overall, MetaSPAdes performs best in terms of integrity and continuity at the species-level, followed by MEGAHIT. Faucet performs best in terms of accuracy at the cost of worst integrity and continuity, especially at low sequencing depth. MEGAHIT has the highest genome fractions at the strain-level and MetaSPAdes has the overall best performance at the strain-level. MEGAHIT is the most efficient in our experiments. Availability: The source code is available at https://github.com/ziyewang/MetaAssemblyEval.}, } @article {pmid30858573, year = {2019}, author = {Kessler, AJ and Chen, YJ and Waite, DW and Hutchinson, T and Koh, S and Popa, ME and Beardall, J and Hugenholtz, P and Cook, PLM and Greening, C}, title = {Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments.}, journal = {Nature microbiology}, volume = {4}, number = {6}, pages = {1014-1023}, pmid = {30858573}, issn = {2058-5276}, mesh = {Bacteria/*genetics/*metabolism ; Bacteria, Anaerobic/metabolism ; Carbon Cycle ; *Fermentation ; Gammaproteobacteria/metabolism ; Geologic Sediments/*microbiology ; Hydrogen/metabolism ; Hydrogenase/classification/genetics ; *Hypoxia ; Metagenomics ; Microbiota ; Nitrates/metabolism ; Nitrites/metabolism ; Oceans and Seas ; Oxidation-Reduction ; RNA, Ribosomal, 16S ; Sulfates/metabolism ; }, abstract = {Permeable (sandy) sediments cover half of the continental margin and are major regulators of oceanic carbon cycling. The microbial communities within these highly dynamic sediments frequently shift between oxic and anoxic states, and hence are less stratified than those in cohesive (muddy) sediments. A major question is, therefore, how these communities maintain metabolism during oxic-anoxic transitions. Here, we show that molecular hydrogen (H2) accumulates in silicate sand sediments due to decoupling of bacterial fermentation and respiration processes following anoxia. In situ measurements show that H2 is 250-fold supersaturated in the water column overlying these sediments and has an isotopic composition consistent with fermentative production. Genome-resolved shotgun metagenomic profiling suggests that the sands harbour diverse and specialized microbial communities with a high abundance of [NiFe]-hydrogenase genes. Hydrogenase profiles predict that H2 is primarily produced by facultatively fermentative bacteria, including the dominant gammaproteobacterial family Woeseiaceae, and can be consumed by aerobic respiratory bacteria. Flow-through reactor and slurry experiments consistently demonstrate that H2 is rapidly produced by fermentation following anoxia, immediately consumed by aerobic respiration following reaeration and consumed by sulfate reduction only during prolonged anoxia. Hydrogenotrophic sulfur, nitrate and nitrite reducers were also detected, although contrary to previous hypotheses there was limited capacity for microalgal fermentation. In combination, these experiments confirm that fermentation dominates anoxic carbon mineralization in these permeable sediments and, in contrast to the case in cohesive sediments, is largely uncoupled from anaerobic respiration. Frequent changes in oxygen availability in these sediments may have selected for metabolically flexible bacteria while excluding strict anaerobes.}, } @article {pmid30858509, year = {2019}, author = {Ghanbari, M and Klose, V and Crispie, F and Cotter, PD}, title = {The dynamics of the antibiotic resistome in the feces of freshly weaned pigs following therapeutic administration of oxytetracycline.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4062}, pmid = {30858509}, issn = {2045-2322}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria ; Bacteroidetes/drug effects/genetics ; Dietary Supplements ; Drug Resistance, Microbial/drug effects/genetics ; Escherichia/drug effects/genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/drug effects/*genetics ; Humans ; *Metagenomics ; Oxytetracycline/*pharmacology ; Proteobacteria/drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; Swine/genetics ; Weaning ; }, abstract = {In this study, shotgun metagenomics was employed to monitor the effect of oxytetracycline, administered at a therapeutic dose, on the dynamics of the microbiota and resistome in the feces of weaned pigs. Sixteen weaning pigs were assigned to one of two treatments including standard starter diet for 21 days or antibiotic-supplemented diet (10 g oxytetracycline/100 kg body weight/day) for 7 days, followed by 14 days of standard starter diet. Feces were collected from the pigs on days 0, 8, and 21 for microbiota and resistome profiling. Pigs receiving oxytetracycline exhibited a significantly greater richness (ANOVA, P = 0.034) and diversity (ANOVA, P = 0.048) of antibiotic resistance genes (ARGs) than the control pigs. Antibiotic administration significantly enriched the abundances of 41 ARGs, mainly from the tetracycline, betalactam and multidrug resistance classes. Compositional shifts in the bacterial communities were observed following 7 days of antibiotic adminstration, with the medicated pigs showing an increase in Escherichia (Proteobacteria) and Prevotella (Bacteroidetes) populations compared with the nonmedicated pigs. This might be explained by the potential of these taxa to carry ARGs that may be transferred to other susceptible bacteria in the densely populated gut environment. These findings will help in the optimization of therapeutic schemes involving antibiotic usage in swine production.}, } @article {pmid30856229, year = {2019}, author = {Salgado-Flores, A and Tveit, AT and Wright, AD and Pope, PB and Sundset, MA}, title = {Characterization of the cecum microbiome from wild and captive rock ptarmigans indigenous to Arctic Norway.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0213503}, pmid = {30856229}, issn = {1932-6203}, mesh = {Animals ; Animals, Wild/metabolism/microbiology ; Archaea/genetics/isolation & purification/metabolism ; Arctic Regions ; Bacteria/genetics/isolation & purification/metabolism ; Cecum/metabolism/*microbiology ; Galliformes/metabolism/*microbiology ; Metagenome ; Methane/metabolism ; Microbiota ; Norway ; Svalbard ; }, abstract = {Rock ptarmigans (Lagopus muta) are gallinaceous birds inhabiting arctic and sub-arctic environments. Their diet varies by season, including plants or plant parts of high nutritional value, but also toxic plant secondary metabolites (PSMs). Little is known about the microbes driving organic matter decomposition in the cecum of ptarmigans, especially the last steps leading to methanogenesis. The cecum microbiome in wild rock ptarmigans from Arctic Norway was characterized to unveil their functional potential for PSM detoxification, methanogenesis and polysaccharides degradation. Cecal samples were collected from wild ptarmigans from Svalbard (L. m. hyperborea) and northern Norway (L. m. muta) during autumn/winter (Sept-Dec). Samples from captive Svalbard ptarmigans fed commercial pelleted feed were included to investigate the effect of diet on microbial composition and function. Abundances of methanogens and bacteria were determined by qRT-PCR, while microbial community composition and functional potential were studied using 16S rRNA gene sequencing and shotgun metagenomics. Abundances of bacteria and methanogenic Archaea were higher in wild ptarmigans compared to captive birds. The ceca of wild ptarmigans housed bacterial groups involved in PSM-degradation, and genes mediating the conversion of phenol compounds to pyruvate. Methanomassiliicoccaceae was the major archaeal family in wild ptarmigans, carrying the genes for methanogenesis from methanol. It might be related to increased methanol production from pectin degradation in wild birds due to a diet consisting of primarily fresh pectin-rich plants. Both wild and captive ptarmigans possessed a broad suite of genes for the depolymerization of hemicellulose and non-cellulosic polysaccharides (e.g. starch). In conclusion, there were no physiological and phenotypical dissimilarities in the microbiota found in the cecum of wild ptarmigans on mainland Norway and Svalbard. While substantial differences in the functional potential for PSM degradation and methanogenesis in wild and captive birds seem to be a direct consequence of their dissimilar diets.}, } @article {pmid30853704, year = {2019}, author = {Watahiki, S and Kimura, N and Yamazoe, A and Miura, T and Sekiguchi, Y and Noda, N and Matsukura, S and Kasai, D and Takahata, Y and Nojiri, H and Fukuda, M}, title = {Ecological impact assessment of a bioaugmentation site on remediation of chlorinated ethylenes by multi-omics analysis.}, journal = {The Journal of general and applied microbiology}, volume = {65}, number = {5}, pages = {225-233}, doi = {10.2323/jgam.2018.10.003}, pmid = {30853704}, issn = {1349-8037}, mesh = {Bacteria/classification/genetics/growth & development/metabolism ; Biodegradation, Environmental ; Gene Expression Profiling ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; Hydrocarbons, Chlorinated/*metabolism ; Metagenomics ; *Microbial Consortia/genetics ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; Rhodococcus/classification/genetics/growth & development/metabolism ; Sequence Analysis, DNA ; Time Factors ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Bioremediation may affect the ecological system around bioremediation sites. However, little is known about how microbial community structures change over time after the initial injection of degraders. In this study, we have assessed the ecological impact of bioaugmentation using metagenomic and metatranscriptomic approaches to remove trichlorinated ethylene/cis-dichloroethylene (TCE/cDCE) by Rhodococcus jostii strain RHA1 as an aerobic chemical compound degrader. Metagenomic analysis showed that the number of organisms belonging to the genus Rhodococcus, including strain RHA1, increased from 0.1% to 76.6% of the total microbial community on day 0 at the injection site. Subsequently, the populations of strain RHA1 and other TCE/cDCE-degrading bacteria gradually decreased over time, whereas the populations of the anaerobic dechlorinators Geobacter and Dehalococcoides increased at later stages. Metatranscriptomic analysis revealed a high expression of aromatic compound-degrading genes (bphA1-A4) in strain RHA1 after RHA1 injection. From these results, we concluded that the key dechlorinators of TCE/cDCE were mainly aerobic bacteria, such as RHA1, until day 1, after which the key dechlorinators changed to anaerobic bacteria, such as Geobacter and Dehalococcocides, after day 6 at the injection well. Based on the α-diversity, the richness levels of the microbial community were increased after injection of strain RHA1, and the microbial community composition had not been restored to that of the original composition during the 19 days after treatment. These results provide insights into the assessment of the ecological impact and bioaugmentation process of RHA1 at bioremediation sites.}, } @article {pmid30853028, year = {2019}, author = {Yason, JA and Liang, YR and Png, CW and Zhang, Y and Tan, KSW}, title = {Interactions between a pathogenic Blastocystis subtype and gut microbiota: in vitro and in vivo studies.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {30}, pmid = {30853028}, issn = {2049-2618}, mesh = {Animals ; Bacterial Proteins/genetics ; Bifidobacterium longum/genetics/growth & development ; Blastocystis/classification/*growth & development/isolation & purification/pathogenicity ; Blastocystis Infections/*microbiology ; Coculture Techniques ; Disease Models, Animal ; Feces/microbiology ; Gastrointestinal Diseases/*microbiology ; *Gastrointestinal Microbiome ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Bacterial ; HT29 Cells ; Humans ; Lactobacillus/genetics/growth & development ; Metagenomics ; Mice ; }, abstract = {BACKGROUND: Blastocystis is a common gut eukaryote detected in humans and animals. It has been associated with gastrointestinal disease in the past although recent metagenomic studies also suggest that it is a member of normal microbiota. This study investigates interactions between pathogenic human isolates belonging to Blastocystis subtype 7 (ST7) and bacterial representatives of the gut microbiota.

RESULTS: Generally, Blastocystis ST7 exerts a positive effect on the viability of representative gut bacteria except on Bifidobacterium longum. Gene expression analysis and flow cytometry indicate that the bacterium may be undergoing oxidative stress in the presence of Blastocystis. In vitro assays demonstrate that Blastocystis-induced host responses are able to decrease Bifidobacterium counts. Mice infected with Blastocystis also reveal a decrease in beneficial bacteria Bifidobacterium and Lactobacillus.

CONCLUSIONS: This study shows that particular isolates of Blastocystis ST7 cause changes in microbiota populations and potentially lead to an imbalance of the gut microbiota. This study suggests that certain isolates of Blastocystis exert their pathogenic effects through disruption of the gut microbiota and provides a counterpoint to the increasing reports indicating the commensal nature of this ubiquitous parasite.}, } @article {pmid30852309, year = {2019}, author = {Garau, G and Porceddu, A and Sanna, M and Silvetti, M and Castaldi, P}, title = {Municipal solid wastes as a resource for environmental recovery: Impact of water treatment residuals and compost on the microbial and biochemical features of As and trace metal-polluted soils.}, journal = {Ecotoxicology and environmental safety}, volume = {174}, number = {}, pages = {445-454}, doi = {10.1016/j.ecoenv.2019.03.007}, pmid = {30852309}, issn = {1090-2414}, mesh = {Adsorption ; Arsenic/*analysis ; Composting/*methods ; Italy ; Metals, Heavy/*analysis ; Microbiota/*drug effects ; RNA, Ribosomal, 16S ; Soil/chemistry ; Soil Microbiology/standards ; Soil Pollutants/*analysis ; Solid Waste/*analysis ; Trace Elements/*analysis ; Water Purification/*methods ; }, abstract = {In this study we evaluated the microbiological and biochemical impact of iron-based water treatment residuals (Fe-WTRs) and municipal solid waste compost (MSWC), alone and combined, on three different soils co-contaminated with arsenic (As) and trace-metals (TM), i.e. Pb, Cu and Zn. Overall, all the amendments considered significantly increased the abundance of culturable heterotrophic bacteria, with MSWC showing the greatest impact across all soils (up to a 24% increase). In most of treated soils this was accompanied by a significant reduction of both the (culturable) fungal/bacterial ratio, and the proportion of culturable As(V)- and As(III)-resistant bacteria with respect to total bacterial population. The catabolic potential and versatility of the resident microbial communities (assessed by community level physiological profile) was highly soil-dependent and substantial increases of both parameters were observed in the amended soils with the higher total As concentration (from approx. 749 to 22,600 mg kg[-1]). Moreover, both carbon source utilisation profile and 16S rRNA soil metagenome sequencing indicated a significant impact of MSWC and Fe-WTRs on the structure and diversity of soil microbial communities, with Proteobacteria, Actinobacteria and Firmicutes being the most affected taxa. The assessment of selected soil enzyme activities (dehydrogenase, urease and β-glucosidase) indicated an increase of metabolic functioning especially in soils treated with MSWC (e.g. dehydrogenase activity increased up to 19.5-fold in the most contaminated soil treated with MSWC). Finally, the microbial and biochemical features of treated (and untreated) contaminated soils (i.e. total bacterial counts, catabolic potential and versatility and soil enzyme activities) were highly correlated with the concentrations of labile As and TM in these latter soils and supported a clear role of the tested amendments (especially MSWC) as As- and TM-immobilising agents.}, } @article {pmid30851368, year = {2019}, author = {Yu, J and Liu, Y and Guo, J and Tao, W and Chen, Y and Fan, X and Shen, J and Duan, JA}, title = {Health risk of Licorice-Yuanhua combination through induction of colonic H2S metabolism.}, journal = {Journal of ethnopharmacology}, volume = {236}, number = {}, pages = {136-146}, doi = {10.1016/j.jep.2019.01.042}, pmid = {30851368}, issn = {1872-7573}, mesh = {Animals ; Colon/*drug effects/metabolism/microbiology ; Daphne/*chemistry ; Desulfovibrio/drug effects/genetics ; Drug Synergism ; Drugs, Chinese Herbal/isolation & purification/*toxicity ; Feces/chemistry ; Flowers/chemistry ; Gastrointestinal Microbiome/*drug effects/genetics ; Glycyrrhiza/*chemistry ; Hydrogen Sulfide/analysis/*metabolism ; Male ; Medicine, Chinese Traditional ; Metagenome/genetics ; Mice, Inbred ICR ; Plant Roots/chemistry ; }, abstract = {Licorice and Yuanhua are both famous herbs in Traditional Chinese Medicine (TCM), and their combination is used by some TCM doctors to treat renal and gastrointestinal diseases as well as tumors. On the other hand, the compatibility theory of TCM warns that toxic effects might be triggered by Licorice-Yuanhua combination. The usability of Licorice-Yuanhua combination has long been controversial due to lack of evidence and mechanism illustration. Colonic hydrogen sulfide (H2S) metabolism imbalance is closely related with colonic inflammation, tumor promotion and many other diseases.

AIM OF THE STUDY: This study was carried out to investigate if licorice-Yuanhua combination could induce potential toxic effects in the aspect of colonic H2S metabolism.

MATERIALS AND METHODS: Normal mice were treated with high or low doses of Licorice, Yuanhua and Licorice-Yuanhua combination. Fecal H2S concentration was measured by colorimetric method, colon sulfomucin production was compared through tissue staining, fecal microbiota and microbial metagenomes were analyzed by 16S rDNA sequencing and data mining.

RESULTS: Data shows that although licorice cannot change colonic H2S concentration, it can exacerbate Yuanhua induced H2S rising. Licorice or Yuanhua increases colon sulfomucin production, and their combination further enhances this effect. 16S rDNA sequencing analysis revealed that licorice or Yuanhua has little influence on gut microbiota, however, licorice-Yuanhua combination can impact gut microbiota structural balance and increase the abundance of Desulfovibrio genus and other related genera. Moreover, the combination extensively changes microbial metagenomes, influencing 1172 genes that cannot be changed by individual licorice or Yuanhua. By searching in KEGG database, ten genes are annotated with H2S producing gene, and these genes are remarkably increased by licorice-Yuanhua combination, more significantly than licorice or Yuanhua.

CONCLUSIONS: This study provides evidences and mechanisms for licorice induced risks, which is related with colonic H2S metabolism disturbance, gut microbiota and microbial metagenomes. More risk assessment should be evaluated when licorice was used in combination with foods, herbs or drugs. The study provides an example where healthy risks can be induced by combination of food additive, herbs or drugs, through regulating gut microbiota and its metagenomes.}, } @article {pmid30851141, year = {2019}, author = {Nadeau, SA and Roco, CA and Debenport, SJ and Anderson, TR and Hofmeister, KL and Walter, MT and Shapleigh, JP}, title = {Metagenomic analysis reveals distinct patterns of denitrification gene abundance across soil moisture, nitrate gradients.}, journal = {Environmental microbiology}, volume = {21}, number = {4}, pages = {1255-1266}, doi = {10.1111/1462-2920.14587}, pmid = {30851141}, issn = {1462-2920}, support = {DGE-1650441//Division of Graduate Education/International ; 2014-67019-21636//National Institute of Food and Agriculture/International ; NYC-123425//National Institute of Food and Agriculture/International ; Grant No. 1069193//National Science Foundation/International ; DGE-1650441//National Science Foundation/International ; //Department of Agriculture/International ; //Cornell University/International ; 2014-67019-21636//United States Department of Agriculture/International ; NYC-123425//National Institute of Food and Agriculture/International ; }, mesh = {Bacteria/genetics ; Denitrification/*genetics ; Genes, Bacterial/*genetics ; *Metagenome ; Microbiota/*genetics ; Nitrates/metabolism ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {This study coupled a landscape-scale metagenomic survey of denitrification gene abundance in soils with in situ denitrification measurements to show how environmental factors shape distinct denitrification communities that exhibit varying denitrification activity. Across a hydrologic gradient, the distribution of total denitrification genes (nap/nar + nirK/nirS + cNor/qNor + nosZ) inferred from metagenomic read abundance exhibited no consistent patterns. However, when genes were considered independently, nirS, cNor and nosZ read abundance was positively associated with areas of higher soil moisture, higher nitrate and higher annual denitrification rates, whereas nirK and qNor read abundance was negatively associated with these factors. These results suggest that environmental conditions, in particular soil moisture and nitrate, select for distinct denitrification communities that are characterized by differential abundance of genes encoding apparently functionally redundant proteins. In contrast, taxonomic analysis did not identify notable variability in denitrifying community composition across sites. While the capacity to denitrify was ubiquitous across sites, denitrification genes with higher energetic costs, such as nirS and cNor, appear to confer a selective advantage in microbial communities experiencing more frequent soil saturation and greater nitrate inputs. This study suggests metagenomics can help identify denitrification hotspots that could be protected or enhanced to treat non-point source nitrogen pollution.}, } @article {pmid30850636, year = {2019}, author = {Hendriksen, RS and Munk, P and Njage, P and van Bunnik, B and McNally, L and Lukjancenko, O and Röder, T and Nieuwenhuijse, D and Pedersen, SK and Kjeldgaard, J and Kaas, RS and Clausen, PTLC and Vogt, JK and Leekitcharoenphon, P and van de Schans, MGM and Zuidema, T and de Roda Husman, AM and Rasmussen, S and Petersen, B and , and Amid, C and Cochrane, G and Sicheritz-Ponten, T and Schmitt, H and Alvarez, JRM and Aidara-Kane, A and Pamp, SJ and Lund, O and Hald, T and Woolhouse, M and Koopmans, MP and Vigre, H and Petersen, TN and Aarestrup, FM}, title = {Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1124}, pmid = {30850636}, issn = {2041-1723}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Africa ; Asia ; Bacteria/classification/*drug effects/genetics/isolation & purification ; Drug Resistance, Multiple, Bacterial/*genetics ; Epidemiological Monitoring ; Europe ; *Genes, Bacterial ; Humans ; *Metagenome ; Metagenomics/methods ; Microbial Consortia/drug effects/genetics ; North America ; Oceania ; Population Health ; Sewage/*microbiology ; Socioeconomic Factors ; South America ; }, abstract = {Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.}, } @article {pmid30848090, year = {2019}, author = {Liao, B and Yan, X and Zhang, J and Chen, M and Li, Y and Huang, J and Lei, M and He, H and Wang, J}, title = {Microbial community composition in alpine lake sediments from the Hengduan Mountains.}, journal = {MicrobiologyOpen}, volume = {8}, number = {9}, pages = {e00832}, pmid = {30848090}, issn = {2045-8827}, mesh = {Bacteria/*classification/*genetics ; China ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/*microbiology ; High-Throughput Nucleotide Sequencing ; Lakes/*microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Microbial communities in sediments play an important role in alpine lake ecosystems. However, the microbial diversity and community composition of alpine lake sediments from the Hengduan Mountains remain largely unknown. Therefore, based on the Illumina MiSeq platform, high-throughput sequencing analysis of the 16S rRNA gene was performed on 15 alpine lake sediments collected at different locations in the Hengduan Mountains. The abundance-based coverage estimate (ACE), Chao1, and Shannon indices indicated that the microbial abundance and diversity of these sediments were high. There are some differences in the composition of microbial communities among sediments. However, in general, Proteobacteria accounted for the largest proportion of all sediments (22.3%-67.6%) and was the dominant phylum. Followed by Bacteroidetes, Acidobacteria, Chloroflexi, and Planctomycetes. In addition, the operational taxonomic unit (OTU) interactions network had modular structures and suggested more cooperation than competition in the microbial community. Besides, we also found that temperature has a significant contribution to the sample-environment relationship. This study revealed the diversity and composition of microbial communities in alpine lake sediments from the Hengduan Mountains, and describe the correlation between microbial community structure and different environmental variables.}, } @article {pmid30844814, year = {2019}, author = {Yun, Y and Kim, HN and Chang, Y and Lee, Y and Ryu, S and Shin, H and Kim, WS and Kim, HL and Nam, JH}, title = {Characterization of the Blood Microbiota in Korean Females with Rosacea.}, journal = {Dermatology (Basel, Switzerland)}, volume = {235}, number = {3}, pages = {255-259}, doi = {10.1159/000496968}, pmid = {30844814}, issn = {1421-9832}, mesh = {Blood/*microbiology ; Dysbiosis/*blood/ethnology ; Female ; Humans ; Microbiota/*physiology ; Republic of Korea/ethnology ; Rosacea/*blood/ethnology ; }, } @article {pmid30844070, year = {2019}, author = {Fritz, B and Stavnsbjerg, C and Markvart, M and Damgaard, PB and Nielsen, SH and Bjørndal, L and Qvortrup, K and Bjarnsholt, T}, title = {Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition.}, journal = {Pathogens and disease}, volume = {77}, number = {1}, pages = {}, doi = {10.1093/femspd/ftz013}, pmid = {30844070}, issn = {2049-632X}, mesh = {Bacteria/*classification/*genetics/ultrastructure ; Biodiversity ; *Biofilms ; Humans ; *Metagenome ; *Metagenomics ; }, abstract = {Bacterial biofilm infections often involve aggregates of bacteria heterogeneously distributed throughout a tissue or on a surface (such as an implanted medical device). Identification of a biofilm infection requires direct visualization via microscopy, followed by characterization of the microbial community by culturing or sequencing-based approaches. A sample, therefore, must be divided prior to analysis, often leading to inconsistent results. We demonstrate a combined approach, using scanning electron microscopy and next-generation shotgun sequencing, to visually identify a biofilm and characterize the microbial community, without dividing the sample. A clinical sample recovered from a patient following a dental root-filling procedure was prepared and visualized by scanning electron microscopy. DNA was then extracted from the sample several years later and analyzed by shotgun sequencing. The method was subsequently validated on in vitro cultures of Pseudomonas aeruginosa biofilm. Between 19 and 21 different genera and species were identified in the clinical sample with an estimated relative abundance greater than 1% by two different estimation approaches. Only eight genera identified were not associated with endodontic infections. This provides a proof-of-concept for a dual, microscopy and sequencing-based approach to identify and characterize bacterial biofilms, which could also easily be implemented in other scientific fields.}, } @article {pmid30843322, year = {2019}, author = {More, KD and Giosan, L and Grice, K and Coolen, MJL}, title = {Holocene paleodepositional changes reflected in the sedimentary microbiome of the Black Sea.}, journal = {Geobiology}, volume = {17}, number = {4}, pages = {436-448}, doi = {10.1111/gbi.12338}, pmid = {30843322}, issn = {1472-4669}, mesh = {Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; Black Sea ; Bulgaria ; Fossils ; Geologic Sediments/*microbiology ; *Metagenome ; *Microbiota ; }, abstract = {Subsurface microbial communities are generally thought to be structured through in situ environmental conditions such as the availability of electron acceptors and donors and porosity, but recent studies suggest that the vertical distribution of a subset of subseafloor microbial taxa, which were present at the time of deposition, were selected by the paleodepositional environment. However, additional highly resolved temporal records of subsurface microbiomes and paired paleoenvironmental reconstructions are needed to justify this claim. Here, we performed a highly resolved shotgun metagenomics survey to study the taxonomic and functional diversity of the subsurface microbiome in Holocene sediments underlying the permanently stratified and anoxic Black Sea. Obligate aerobic bacteria made the largest contribution to the observed shifts in microbial communities associated with known Holocene climate stages and transitions. This suggests that the aerobic fraction of the subseafloor microbiome was seeded from the water column and did not undergo post-depositional selection. In contrast, obligate and facultative anaerobic bacteria showed the most significant response to the establishment of modern-day environmental conditions 5.2 ka ago that led to a major shift in planktonic communities and in the type of sequestered organic matter available for microbial degradation. No significant shift in the subseafloor microbiome was observed as a result of environmental changes that occurred shortly after the marine reconnection, 9 ka ago. This supports the general view that the marine reconnection was a gradual process. We conclude that a high-resolution analysis of downcore changes in the subseafloor microbiome can provide detailed insights into paleoenvironmental conditions and biogeochemical processes that occurred at the time of deposition.}, } @article {pmid30842565, year = {2019}, author = {Stewart, LC and Algar, CK and Fortunato, CS and Larson, BI and Vallino, JJ and Huber, JA and Butterfield, DA and Holden, JF}, title = {Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents.}, journal = {The ISME journal}, volume = {13}, number = {7}, pages = {1711-1721}, pmid = {30842565}, issn = {1751-7370}, mesh = {Archaea/classification/genetics/*isolation & purification/*metabolism ; Chemoautotrophic Growth ; Hydrogen/metabolism ; Hydrology ; Hydrothermal Vents/chemistry/*microbiology ; Methane/*metabolism ; Microbiota ; Oceans and Seas ; }, abstract = {The size and biogeochemical impact of the subseafloor biosphere in oceanic crust remain largely unknown due to sampling limitations. We used reactive transport modeling to estimate the size of the subseafloor methanogen population, volume of crust occupied, fluid residence time, and nature of the subsurface mixing zone for two low-temperature hydrothermal vents at Axial Seamount. Monod CH4 production kinetics based on chemostat H2 availability and batch-culture Arrhenius growth kinetics for the hyperthermophile Methanocaldococcus jannaschii and thermophile Methanothermococcus thermolithotrophicus were used to develop and parameterize a reactive transport model, which was constrained by field measurements of H2, CH4, and metagenome methanogen concentration estimates in 20-40 °C hydrothermal fluids. Model results showed that hyperthermophilic methanogens dominate in systems where a narrow flow path geometry is maintained, while thermophilic methanogens dominate in systems where the flow geometry expands. At Axial Seamount, the residence time of fluid below the surface was 29-33 h. Only 10[11] methanogenic cells occupying 1.8-18 m[3] of ocean crust per m[2] of vent seafloor area were needed to produce the observed CH4 anomalies. We show that variations in local geology at diffuse vents can create fluid flow paths that are stable over space and time, harboring persistent and distinct microbial communities.}, } @article {pmid30842211, year = {2019}, author = {Zuo, T and Lu, XJ and Zhang, Y and Cheung, CP and Lam, S and Zhang, F and Tang, W and Ching, JYL and Zhao, R and Chan, PKS and Sung, JJY and Yu, J and Chan, FKL and Cao, Q and Sheng, JQ and Ng, SC}, title = {Gut mucosal virome alterations in ulcerative colitis.}, journal = {Gut}, volume = {68}, number = {7}, pages = {1169-1179}, pmid = {30842211}, issn = {1468-3288}, mesh = {Adult ; Case-Control Studies ; China ; Colitis, Ulcerative/pathology/*virology ; Dysbiosis/pathology/*virology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/*virology ; Male ; Rectum/pathology/*virology ; }, abstract = {OBJECTIVE: The pathogenesis of UC relates to gut microbiota dysbiosis. We postulate that alterations in the viral community populating the intestinal mucosa play an important role in UC pathogenesis. This study aims to characterise the mucosal virome and their functions in health and UC.

DESIGN: Deep metagenomics sequencing of virus-like particle preparations and bacterial 16S rRNA sequencing were performed on the rectal mucosa of 167 subjects from three different geographical regions in China (UC=91; healthy controls=76). Virome and bacteriome alterations in UC mucosa were assessed and correlated with patient metadata. We applied partition around medoids clustering algorithm and classified mucosa viral communities into two clusters, referred to as mucosal virome metacommunities 1 and 2.

RESULTS: In UC, there was an expansion of mucosa viruses, particularly Caudovirales bacteriophages, and a decrease in mucosa Caudovirales diversity, richness and evenness compared with healthy controls. Altered mucosal virome correlated with intestinal inflammation. Interindividual dissimilarity between mucosal viromes was higher in UC than controls. Escherichia phage and Enterobacteria phage were more abundant in the mucosa of UC than controls. Compared with metacommunity 1, metacommunity 2 was predominated by UC subjects and displayed a significant loss of various viral species. Patients with UC showed substantial abrogation of diverse viral functions, whereas multiple viral functions, particularly functions of bacteriophages associated with host bacteria fitness and pathogenicity, were markedly enriched in UC mucosa. Intensive transkingdom correlations between mucosa viruses and bacteria were significantly depleted in UC.

CONCLUSION: We demonstrated for the first time that UC is characterised by substantial alterations of the mucosa virobiota with functional distortion. Enrichment of Caudovirales bacteriophages, increased phage/bacteria virulence functions and loss of viral-bacterial correlations in the UC mucosa highlight that mucosal virome may play an important role in UC pathogenesis.}, } @article {pmid30841395, year = {2019}, author = {Cordeiro, MC and Garcia, GD and Rocha, AM and Tschoeke, DA and Campeão, ME and Appolinario, LR and Soares, AC and Leomil, L and Froes, A and Bahiense, L and Rezende, CE and de Almeida, MG and Rangel, TP and De Oliveira, BCV and de Almeida, DQR and Thompson, MC and Thompson, CC and Thompson, FL}, title = {Insights on the freshwater microbiomes metabolic changes associated with the world's largest mining disaster.}, journal = {The Science of the total environment}, volume = {654}, number = {}, pages = {1209-1217}, doi = {10.1016/j.scitotenv.2018.11.112}, pmid = {30841395}, issn = {1879-1026}, mesh = {*Chemical Hazard Release ; Disasters ; *Environmental Monitoring ; Fresh Water/*microbiology ; Microbiota ; Mining ; *Water Microbiology ; Water Pollutants, Chemical/*analysis ; }, abstract = {To evaluate the impacts of the Fundão tailings dam failure (Minas Gerais, Brazil) on water quality of the Doce River, we analyzed metagenomics and physicochemical parameters during the month of the disaster and again 6 and 10 months after the disaster. To compare dam conditions before and after the failure, we performed a meta-analysis of physicochemical data from a public database. Immediately after the failure, suspended particulate matter (SPM) in the Doce River was 225-1877 mg L[-1]. Turbidity and dissolved aluminum and iron concentrations were extremely high, whereas dissolved oxygen was below Brazilian legislation norm (<5 mg L[-1]) in several locations. Six months later, physicochemical values were below thresholds set by Brazilian guidelines (e.g., SPM = 8-166 mg L[-1]). Short-term impacts on microbial communities included an increase in Actinobacteria and Bacteroidetes and gene sequences related to microbial virulence, motility, respiration, membrane transport, iron and nitrogen metabolism, suggesting changes in microbial metabolic profiles. The 11 recovered partial genomes from metagenomes (MAGs) had genes related to Fe cycle and metal resistance.}, } @article {pmid30838598, year = {2019}, author = {Divaris, K and Shungin, D and Rodríguez-Cortés, A and Basta, PV and Roach, J and Cho, H and Wu, D and Ferreira Zandoná, AG and Ginnis, J and Ramamoorthy, S and Kinchen, JM and Kwintkiewicz, J and Butz, N and Ribeiro, AA and Azcarate-Peril, MA}, title = {The Supragingival Biofilm in Early Childhood Caries: Clinical and Laboratory Protocols and Bioinformatics Pipelines Supporting Metagenomics, Metatranscriptomics, and Metabolomics Studies of the Oral Microbiome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1922}, number = {}, pages = {525-548}, pmid = {30838598}, issn = {1940-6029}, support = {P30 DK034987/DK/NIDDK NIH HHS/United States ; U01 DE025046/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/*genetics/isolation & purification/metabolism ; *Biofilms ; Child, Preschool ; DNA, Bacterial/genetics ; Dental Caries/etiology/*microbiology ; Gene Expression Profiling/methods ; Gingiva/microbiology ; Humans ; Metabolomics/*methods ; Metagenomics/*methods ; Microbiota ; RNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA/methods ; Software ; Specimen Handling/methods ; Tooth, Deciduous/*microbiology ; Transcriptome ; }, abstract = {Early childhood caries (ECC) is a biofilm-mediated disease. Social, environmental, and behavioral determinants as well as innate susceptibility are major influences on its incidence; however, from a pathogenetic standpoint, the disease is defined and driven by oral dysbiosis. In other words, the disease occurs when the natural equilibrium between the host and its oral microbiome shifts toward states that promote demineralization at the biofilm-tooth surface interface. Thus, a comprehensive understanding of dental caries as a disease requires the characterization of both the composition and the function or metabolic activity of the supragingival biofilm according to well-defined clinical statuses. However, taxonomic and functional information of the supragingival biofilm is rarely available in clinical cohorts, and its collection presents unique challenges among very young children. This paper presents a protocol and pipelines available for the conduct of supragingival biofilm microbiome studies among children in the primary dentition, that has been designed in the context of a large-scale population-based genetic epidemiologic study of ECC. The protocol is being developed for the collection of two supragingival biofilm samples from the maxillary primary dentition, enabling downstream taxonomic (e.g., metagenomics) and functional (e.g., transcriptomics and metabolomics) analyses. The protocol is being implemented in the assembly of a pediatric precision medicine cohort comprising over 6000 participants to date, contributing social, environmental, behavioral, clinical, and biological data informing ECC and other oral health outcomes.}, } @article {pmid30838178, year = {2019}, author = {Nearing, JT and Connors, J and Whitehouse, S and Van Limbergen, J and Macdonald, T and Kulkarni, K and Langille, MGI}, title = {Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {28}, pmid = {30838178}, issn = {2235-2988}, mesh = {Child ; Child, Preschool ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Dysbiosis/*complications ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Metagenomics ; *Microbiota ; Opportunistic Infections/*microbiology ; Phylogeny ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/*complications ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Acute lymphoblastic leukemia is the most common pediatric cancer. Fortunately, survival rates exceed 90%, however, infectious complications remain a significant issue that can cause reductions in the quality of life and prognosis of patients. Recently, numerous studies have linked shifts in the gut microbiome composition to infection events in various hematological malignances including acute lymphoblastic leukemia (ALL). These studies have been limited to observing broad taxonomic changes using 16S rRNA gene profiling, while missing possible differences within microbial functions encoded by individual species. In this study we present the first combined 16S rRNA gene and metagenomic shotgun sequencing study on the gut microbiome of an independent pediatric ALL cohort during treatment. In this study we found distinctive differences in alpha diversity and beta diversity in samples from patients with infectious complications in the first 6 months of therapy. We were also able to find specific species and functional pathways that were significantly different in relative abundance between samples that came from patients with infectious complications. Finally, machine learning models based on patient metadata and bacterial species were able to classify samples with high accuracy (84.09%), with bacterial species being the most important classifying features. This study strengthens our understanding of the association between infection and pediatric acute lymphoblastic leukemia treatment and warrants further investigation in the future.}, } @article {pmid30837612, year = {2019}, author = {Liu, Y and Zheng, Z and Yu, L and Wu, S and Sun, L and Wu, S and Xu, Q and Cai, S and Qin, N and Bao, W}, title = {Examination of the temporal and spatial dynamics of the gut microbiome in newborn piglets reveals distinct microbial communities in six intestinal segments.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {3453}, pmid = {30837612}, issn = {2045-2322}, mesh = {Age Factors ; Animals ; Animals, Newborn ; *Biodiversity ; Feces/microbiology ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; RNA, Ribosomal, 16S ; Swine ; }, abstract = {Intestinal microbiota plays a crucial role in immune development and disease progression in mammals from birth onwards. The gastrointestinal tract of newborn mammals is rapidly colonized by microbes with tremendous biomass and diversity. Understanding how this complex of segmental communities evolves in different gastrointestinal sites over time has great biological significance and medical implications. However, most previous reports examining intestinal microbiota have focused on fecal samples, a strategy that overlooks the spatial microbial dynamics in different intestinal segments. Using intestinal digesta from six intestinal segments (duodenum, jejunum, ileum, cecum, colon and rectum) of newborn piglets, we herein conducted a large-scale 16S rRNA gene sequencing-based study to characterize the segmental dynamics of porcine gut microbiota at eight postnatal intervals (days 1, 7, 14, 21, 28, 35, 120 and 180). A total of 4,465 OTUs were obtained and showed that the six intestinal segments could be divided into three parts; in the duodenum-jejunum section, the most abundant genera included Lactobacillus and Bacteroides; in the ileum, Fusobacterium and Escherichia; and in the cecum-rectum section, Prevotella. Although the microbial communities of the piglets were similar among the six intestinal segments on postnatal day 1, they evolved and quickly differentiated at later intervals. An examination of time-dependent alterations in the dominant microbes revealed that the microbiome in the large intestine was very different from and much more stable than that in the small intestine. The gut microbiota in newborn piglets exhibited apparent temporal and spatial variations in different intestinal segments. The database of gut microbes in piglets could be a referable resource for future studies on mammalian gut microbiome development in early host growth phases.}, } @article {pmid30836173, year = {2019}, author = {Ruppé, E and Schrenzel, J}, title = {Messages from the third International Conference on Clinical Metagenomics (ICCMg3).}, journal = {Microbes and infection}, volume = {21}, number = {7}, pages = {273-277}, doi = {10.1016/j.micinf.2019.02.004}, pmid = {30836173}, issn = {1769-714X}, mesh = {*Clinical Laboratory Techniques/standards/trends ; Communicable Diseases/*diagnosis/microbiology ; Computational Biology/standards/trends ; High-Throughput Nucleotide Sequencing/standards/trends ; Humans ; Metagenome/genetics ; *Metagenomics/standards/statistics & numerical data ; Microbiota/genetics ; }, abstract = {Clinical metagenomics (CMg), referring to as the application of metagenomic sequencing of clinical samples in order to recover clinically-relevant information, has been rapidly evolving these last years. Following this trend, we held the third International Conference on Clinical Metagenomics (ICCMg3) in Geneva in October 2018. During the two days of the conference, several aspects of CMg were addressed, which we propose to summarize in the present manuscript. During this ICCMg3, we kept on following the progresses achieved worldwide on clinical metagenomics, but also this year in clinical genomics. Besides, the use of metagenomics in cancer diagnostic and management was addressed. Some new challenges have also been raised such as the way to report clinical (meta)genomics output to clinicians and the pivotal place of ethics in this expanding field.}, } @article {pmid30834996, year = {2019}, author = {Boers, SA and Jansen, R and Hays, JP}, title = {Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic laboratory.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {38}, number = {6}, pages = {1059-1070}, pmid = {30834996}, issn = {1435-4373}, support = {602860//FP7 Health/ ; }, mesh = {DNA, Bacterial/genetics/standards ; Diagnostic Tests, Routine/*standards ; High-Throughput Nucleotide Sequencing/*standards ; Humans ; Infections/*diagnosis/epidemiology/microbiology ; Metagenomics/standards ; Microbiological Techniques/standards ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics/standards ; Sequence Analysis, DNA/standards ; }, abstract = {Recent advancements in next-generation sequencing (NGS) have provided the foundation for modern studies into the composition of microbial communities. The use of these NGS methods allows for the detection and identification of ('difficult-to-culture') microorganisms using a culture-independent strategy. In the field of routine clinical diagnostics however, the application of NGS is currently limited to microbial strain typing for epidemiological purposes only, even though the implementation of NGS for microbial community analysis may yield clinically important information. This lack of NGS implementation is due to many different factors, including issues relating to NGS method standardization and result reproducibility. In this review article, the authors provide a general introduction to the most widely used NGS methods currently available (i.e., targeted amplicon sequencing and shotgun metagenomics) and the strengths and weaknesses of each method is discussed. The focus of the publication then shifts toward 16S rRNA gene NGS methods, which are currently the most cost-effective and widely used NGS methods for research purposes, and are therefore more likely to be successfully implemented into routine clinical diagnostics in the short term. In this respect, the experimental pitfalls and biases created at each step of the 16S rRNA gene NGS workflow are explained, as well as their potential solutions. Finally, a novel diagnostic microbiota profiling platform ('MYcrobiota') is introduced, which was developed by the authors by taking into consideration the pitfalls, biases, and solutions explained in this article. The development of the MYcrobiota, and future NGS methodologies, will help pave the way toward the successful implementation of NGS methodologies into routine clinical diagnostics.}, } @article {pmid30834068, year = {2019}, author = {Bhushan, B and Yadav, AP and Singh, SB and Ganju, L}, title = {Diversity and functional analysis of salivary microflora of Indian Antarctic expeditionaries.}, journal = {Journal of oral microbiology}, volume = {11}, number = {1}, pages = {1581513}, pmid = {30834068}, issn = {2000-2297}, abstract = {Introduction: The human oral microbiota continues to change phenotype by many factors (environment, diet, genetics, stress, etc.), throughout life with a major impact on human physiology, psychology, metabolism and immune system. Amongst one such factor with unique and extreme environmental conditions is Antarctica. The sea voyage to Antarctica has many risks than at station for expedition members. In this study, we investigated the influence of Antarctic sea voyage and stay at the Indian Antarctic station Maitri, on the health of Indian expedition members by using a metagenomic approach to explore oral biodiversity. Methods: Saliva samples were collected from 12 expedition members, at 3 different time points viz. before the start of the ship voyage, after the completion of the voyage and at the end of the stay at Antarctica. Samples were analyzed for whole genome and 16S rRNA sequencing. Result: The oral microbial diversity of the expedition members was significantly changed, during the days of sailing and after the stay at Antarctica. The oral microbiota comprised mainly of the phyla Firmicutes (46%, 29% & 36%); Proteobacteria (40%, 48%, & 44%), Bacteroidetes (10%, 22%, &14%), Fusobacterium and Actinobacteria (5%-1%) and Unclassified (17%, 25% & 23%), at three time points, respectively. Further, the differential analysis of microbes across all the phyla revealed 89, 157 and 157 OTUs genera. The altered microbiota indicated changes in amino acid, lipid and carbohydrate metabolism. Conclusion: Study suggests that understanding the compositional and functional differences in the oral microbiota of Antarctic expedition members, can lay the foundation to relate these differences to their health status. It will further demonstrate the need for providing improved management during ship voyage and stay in Antarctica.}, } @article {pmid30833729, year = {2019}, author = {Borrel, G and Adam, PS and McKay, LJ and Chen, LX and Sierra-García, IN and Sieber, CMK and Letourneur, Q and Ghozlane, A and Andersen, GL and Li, WJ and Hallam, SJ and Muyzer, G and de Oliveira, VM and Inskeep, WP and Banfield, JF and Gribaldo, S}, title = {Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea.}, journal = {Nature microbiology}, volume = {4}, number = {4}, pages = {603-613}, pmid = {30833729}, issn = {2058-5276}, mesh = {Alkanes/*chemistry/metabolism ; Archaea/classification/genetics/growth & development/*metabolism ; *Biodiversity ; DNA, Archaeal ; Metagenome ; Methane/chemistry/*metabolism ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Methanogenesis is an ancient metabolism of key ecological relevance, with direct impact on the evolution of Earth's climate. Recent results suggest that the diversity of methane metabolisms and their derivations have probably been vastly underestimated. Here, by probing thousands of publicly available metagenomes for homologues of methyl-coenzyme M reductase complex (MCR), we have obtained ten metagenome-assembled genomes (MAGs) belonging to potential methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea. Five of these MAGs represent under-sampled (Verstraetearchaeota, Methanonatronarchaeia, ANME-1 and GoM-Arc1) or previously genomically undescribed (ANME-2c) archaeal lineages. The remaining five MAGs correspond to lineages that are only distantly related to previously known methanogens and span the entire archaeal phylogeny. Comprehensive comparative annotation substantially expands the metabolic diversity and energy conservation systems of MCR-bearing archaea. It also suggests the potential existence of a yet uncharacterized type of methanogenesis linked to short-chain alkane/fatty acid oxidation in a previously undescribed class of archaea ('Candidatus Methanoliparia'). We redefine a common core of marker genes specific to methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea, and propose a possible scenario for the evolutionary and functional transitions that led to the emergence of such metabolic diversity.}, } @article {pmid30833676, year = {2020}, author = {Pearson-Leary, J and Zhao, C and Bittinger, K and Eacret, D and Luz, S and Vigderman, AS and Dayanim, G and Bhatnagar, S}, title = {The gut microbiome regulates the increases in depressive-type behaviors and in inflammatory processes in the ventral hippocampus of stress vulnerable rats.}, journal = {Molecular psychiatry}, volume = {25}, number = {5}, pages = {1068-1079}, pmid = {30833676}, issn = {1476-5578}, mesh = {Animals ; Anxiety ; Behavior, Animal ; Depression ; *Gastrointestinal Microbiome ; Hippocampus ; Rats ; Stress, Psychological ; }, abstract = {Chronic exposure to stress is associated with increased incidence of depression, generalized anxiety, and PTSD. However, stress induces vulnerability to such disorders only in a sub-population of individuals, as others remain resilient. Inflammation has emerged as a putative mechanism for promoting stress vulnerability. Using a rodent model of social defeat, we have previously shown that rats with short-defeat latencies (SL/vulnerable rats) show increased anxiety- and depression-like behaviors, and these behaviors are mediated by inflammation in the ventral hippocampus. The other half of socially defeated rats show long-latencies to defeat (LL/resilient) and are similar to controls. Because gut microbiota are important activators of inflammatory substances, we assessed the role of the gut microbiome in mediating vulnerability to repeated social defeat stress. We analyzed the fecal microbiome of control, SL/vulnerable, and LL/resilient rats using shotgun metagenome sequencing and observed increased expression of immune-modulating microbiota, such as Clostridia, in SL/vulnerable rats. We then tested the importance of gut microbiota to the SL/vulnerable phenotype. In otherwise naive rats treated with microbiota from SL/vulnerable rats, there was higher microglial density and IL-1β expression in the vHPC, and higher depression-like behaviors relative to rats that received microbiota from LL/resilient rats, non-stressed control rats, or vehicle-treated rats. However, anxiety-like behavior during social interaction was not altered by transplant of the microbiome of SL/vulnerable rats into non-stressed rats. Taken together, the results suggest the gut microbiome contributes to the depression-like behavior and inflammatory processes in the vHPC of stress vulnerable individuals.}, } @article {pmid30833550, year = {2019}, author = {Milanese, A and Mende, DR and Paoli, L and Salazar, G and Ruscheweyh, HJ and Cuenca, M and Hingamp, P and Alves, R and Costea, PI and Coelho, LP and Schmidt, TSB and Almeida, A and Mitchell, AL and Finn, RD and Huerta-Cepas, J and Bork, P and Zeller, G and Sunagawa, S}, title = {Microbial abundance, activity and population genomic profiling with mOTUs2.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1014}, pmid = {30833550}, issn = {2041-1723}, mesh = {Algorithms ; Cluster Analysis ; Computational Biology/methods ; Gene Expression Profiling ; Genes, Essential ; Genetic Markers ; Genome ; Host Microbial Interactions ; Humans ; *Metagenomics ; Microbiota/*genetics ; Molecular Sequence Annotation ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Metagenomic sequencing has greatly improved our ability to profile the composition of environmental and host-associated microbial communities. However, the dependency of most methods on reference genomes, which are currently unavailable for a substantial fraction of microbial species, introduces estimation biases. We present an updated and functionally extended tool based on universal (i.e., reference-independent), phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) enabling the profiling of >7700 microbial species. As more than 30% of them could not previously be quantified at this taxonomic resolution, relative abundance estimates based on mOTUs are more accurate compared to other methods. As a new feature, we show that mOTUs, which are based on essential housekeeping genes, are demonstrably well-suited for quantification of basal transcriptional activity of community members. Furthermore, single nucleotide variation profiles estimated using mOTUs reflect those from whole genomes, which allows for comparing microbial strain populations (e.g., across different human body sites).}, } @article {pmid30832984, year = {2019}, author = {Theis, KR and Romero, R and Winters, AD and Greenberg, JM and Gomez-Lopez, N and Alhousseini, A and Bieda, J and Maymon, E and Pacora, P and Fettweis, JM and Buck, GA and Jefferson, KK and Strauss, JF and Erez, O and Hassan, SS}, title = {Does the human placenta delivered at term have a microbiota? Results of cultivation, quantitative real-time PCR, 16S rRNA gene sequencing, and metagenomics.}, journal = {American journal of obstetrics and gynecology}, volume = {220}, number = {3}, pages = {267.e1-267.e39}, pmid = {30832984}, issn = {1097-6868}, support = {HHSN275201300006C/HD/NICHD NIH HHS/United States ; U54 DE023786/DE/NIDCR NIH HHS/United States ; U54 HD080784/HD/NICHD NIH HHS/United States ; ZIA HD002400-27/ImNIH/Intramural NIH HHS/United States ; R01 HD092415/HD/NICHD NIH HHS/United States ; }, mesh = {Adult ; Cesarean Section ; Cross-Sectional Studies ; DNA Contamination ; DNA, Bacterial/analysis ; Female ; Genetic Markers ; Humans ; Metagenomics ; *Microbiota/genetics ; Placenta/*microbiology ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Term Birth ; }, abstract = {BACKGROUND: The human placenta has been traditionally viewed as sterile, and microbial invasion of this organ has been associated with adverse pregnancy outcomes. Yet, recent studies that utilized sequencing techniques reported that the human placenta at term contains a unique microbiota. These conclusions are largely based on the results derived from the sequencing of placental samples. However, such an approach carries the risk of capturing background-contaminating DNA (from DNA extraction kits, polymerase chain reaction reagents, and laboratory environments) when low microbial biomass samples are studied.

OBJECTIVE: To determine whether the human placenta delivered at term in patients without labor who undergo cesarean delivery harbors a resident microbiota ("the assemblage of microorganisms present in a defined niche or environment").

STUDY DESIGN: This cross-sectional study included placentas from 29 women who had a cesarean delivery without labor at term. The study also included technical controls to account for potential background-contaminating DNA, inclusive in DNA extraction kits, polymerase chain reaction reagents, and laboratory environments. Bacterial profiles of placental tissues and background technical controls were characterized and compared with the use of bacterial culture, quantitative real-time polymerase chain reaction, 16S ribosomal RNA gene sequencing, and metagenomic surveys.

RESULTS: (1) Twenty-eight of 29 placental tissues had a negative culture for microorganisms. The microorganisms retrieved by culture from the remaining sample were likely contaminants because corresponding 16S ribosomal RNA genes were not detected in the same sample. (2) Quantitative real-time polymerase chain reaction did not indicate greater abundances of bacterial 16S ribosomal RNA genes in placental tissues than in technical controls. Therefore, there was no evidence of the presence of microorganisms above background contamination from reagents in the placentas. (3) 16S ribosomal RNA gene sequencing did not reveal consistent differences in the composition or structure of bacterial profiles between placental samples and background technical controls. (4) Most of the bacterial sequences obtained from metagenomic surveys of placental tissues were from cyanobacteria, aquatic bacteria, or plant pathogens, which are microbes unlikely to populate the human placenta. Coprobacillus, which constituted 30.5% of the bacterial sequences obtained through metagenomic sequencing of placental samples, was not identified in any of the 16S ribosomal RNA gene surveys of these samples. These observations cast doubt as to whether this organism is really present in the placenta of patients at term not in labor.

CONCLUSION: With the use of multiple modes of microbiologic inquiry, a resident microbiota could not be identified in human placentas delivered at term from women without labor. A consistently significant difference in the abundance and/or presence of a microbiota between placental tissue and background technical controls could not be found. All cultures of placental tissue, except 1, did not yield bacteria. Incorporating technical controls for potential sources of background-contaminating DNA for studies of low microbial biomass samples, such as the placenta, is necessary to derive reliable conclusions.}, } @article {pmid30832983, year = {2019}, author = {Bushman, FD}, title = {De-Discovery of the Placenta Microbiome.}, journal = {American journal of obstetrics and gynecology}, volume = {220}, number = {3}, pages = {213-214}, doi = {10.1016/j.ajog.2018.11.1093}, pmid = {30832983}, issn = {1097-6868}, mesh = {Female ; Humans ; *Metagenomics ; *Microbiota ; Placenta ; Pregnancy ; RNA, Ribosomal, 16S ; Real-Time Polymerase Chain Reaction ; }, } @article {pmid30832576, year = {2019}, author = {Stewart, CJ and Fatemizadeh, R and Parsons, P and Lamb, CA and Shady, DA and Petrosino, JF and Hair, AB}, title = {Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {52}, pmid = {30832576}, issn = {1471-2180}, mesh = {Bacteroidetes/classification ; DNA, Bacterial/isolation & purification ; Enterocolitis, Necrotizing/*microbiology ; Female ; *Formaldehyde ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Infant, Premature ; *Intestinal Perforation ; Intestines/microbiology ; Male ; *Paraffin Embedding ; Proteobacteria/classification ; RNA, Ribosomal, 16S/genetics ; Rupture, Spontaneous ; }, abstract = {BACKGROUND: Necrotising enterocolitis (NEC) is a common cause of death in preterm infants and is closely linked to the gut microbiota. Spontaneous intestinal perforation (SIP) also occurs in preterm neonates, but results in lower mortality and less adverse neonatal outcomes than NEC. Existing studies are largely limited to non-invasive stool samples, which may not be reflective of the anatomical site of disease. Therefore, we analysed historical formalin-fixed paraffin-embedded (FFPE) tissue from NEC and SIP preterm infants. A total of 13 NEC and 16 SIP infants were included. Extracted DNA from FFPE tissue blocks underwent 16S rRNA gene sequencing. For a subset of infants, diseased tissue and marginal healthy tissue from the same infant were compared.

RESULTS: Xylene provided a cost and time effective means of deparaffinization. Tissue from the site of disease was highly comparable to adjacent healthier tissue. Comparing only diseased tissue from all infants showed significantly lower Shannon diversity in NEC (P = 0.026). The overall bacterial communities were also significantly different in NEC samples compared to SIP (P = 0.038), and large variability within NEC infants was observed. While no single OTU or genus was significantly associated with NEC or SIP, at the phylum level Proteobacteria (P = 0.045) and Bacteroidetes (P = 0.024) were significantly higher in NEC and SIP infants, respectively.

CONCLUSIONS: Existing banks of intestinal FFPE blocks provide a robust and specific sample for profiling the microbiota at the site of disease. We showed preterm infants with NEC have lower diversity and different bacterial communities when compared to SIP controls.}, } @article {pmid30832245, year = {2019}, author = {Cortes-Rodriguez, N and Campana, MG and Berry, L and Faegre, S and Derrickson, SR and Ha, RR and Dikow, RB and Rutz, C and Fleischer, RC}, title = {Population Genomics and Structure of the Critically Endangered Mariana Crow (Corvus kubaryi).}, journal = {Genes}, volume = {10}, number = {3}, pages = {}, pmid = {30832245}, issn = {2073-4425}, support = {BB/G023913/2//Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship/International ; }, mesh = {Animals ; Conservation of Natural Resources ; Crows/*classification/genetics ; Endangered Species ; Evolution, Molecular ; Female ; Guam ; High-Throughput Nucleotide Sequencing ; Male ; Metagenomics/*methods ; Phylogeography ; Polymorphism, Single Nucleotide ; Whole Genome Sequencing/*methods ; }, abstract = {The Mariana Crow, or Åga (Corvus kubaryi), is a critically endangered species (IUCN -International Union for Conservation of Nature), endemic to the islands of Guam and Rota in the Mariana Archipelago. It is locally extinct on Guam, and numbers have declined dramatically on Rota to a historical low of less than 55 breeding pairs throughout the island in 2013. Because of its extirpation on Guam and population decline on Rota, it is of critical importance to assess the genetic variation among individuals to assist ongoing recovery efforts. We conducted a population genomics analysis comparing the Guam and Rota populations and studied the genetic structure of the Rota population. We used blood samples from five birds from Guam and 78 birds from Rota. We identified 145,552 candidate single nucleotide variants (SNVs) from a genome sequence of an individual from Rota and selected a subset of these to develop an oligonucleotide in-solution capture assay. The Guam and Rota populations were genetically differentiated from each other. Crow populations sampled broadly across their range on Rota showed significant genetic structuring [-] a surprising result given the small size of this island and the good flight capabilities of the species. Knowledge of its genetic structure will help improve management strategies to help with its recovery.}, } @article {pmid30830220, year = {2019}, author = {Helber, SB and Steinert, G and Wu, YC and Rohde, S and Hentschel, U and Muhando, CA and Schupp, PJ}, title = {Sponges from Zanzibar host diverse prokaryotic communities with potential for natural product synthesis.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {4}, pages = {}, doi = {10.1093/femsec/fiz026}, pmid = {30830220}, issn = {1574-6941}, mesh = {Animals ; Biological Products/metabolism ; Coral Reefs ; Indian Ocean ; *Microbiota/genetics ; Porifera/chemistry/classification/*microbiology ; Prokaryotic Cells/*classification/metabolism ; Seawater/chemistry/microbiology ; Species Specificity ; Tanzania ; }, abstract = {Sponges are one of the most dominant organisms in marine ecosystems. One reason for their success is their association with microorganisms that are besides the host itself responsible for the chemical defence. Sponge abundances have been increasing on coral reefs in the Western Indian Ocean (WIO) and are predicted to increase further with rising anthropogenic impacts on coral reefs. However, there is a paucity of information on chemical ecology of sponges from the WIO and their prokaryotic community composition. We used a combination of Illumina sequencing and a predictive metagenomic analysis to (i) assess the prokaryotic community composition of sponges from Zanzibar, (ii) predict the presence of KEGG metabolic pathways responsible for bioactive compound production and (iii) relate their presence to the degree of observed chemical defence in their respective sponge host. We found that sponges from Zanzibar host diverse prokaryotic communities that are host species-specific. Sponge-species and respective specimens that showed strong chemical defences in previous studies were also predicted to be highly enriched in various pathways responsible for secondary metabolite production. Hence, the combined sequencing and predictive metagenomic approach proved to be a useful indicator for the metabolic potential of sponge holobionts.}, } @article {pmid30826613, year = {2019}, author = {Zeng, J and Pan, Y and Yang, J and Hou, M and Zeng, Z and Xiong, W}, title = {Metagenomic insights into the distribution of antibiotic resistome between the gut-associated environments and the pristine environments.}, journal = {Environment international}, volume = {126}, number = {}, pages = {346-354}, doi = {10.1016/j.envint.2019.02.052}, pmid = {30826613}, issn = {1873-6750}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; Chickens ; Drug Resistance, Microbial/*genetics ; Environmental Monitoring ; Environmental Pollutants/*analysis ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; *Genes, Bacterial ; Humans ; Metagenomics ; Seawater/*microbiology ; *Soil Microbiology ; Swine ; }, abstract = {Antibiotic resistance genes (ARGs) in the environment are promoted by anthropogenic activities, which cause potential risks to human health. However, large-scale quantitative data on antibiotic resistome from the pristine and anthropogenic environments remains largely unexplored. Here, we used metagenome-wide analysis to investigate the share and divergence in ARG profiles and their potential bacterial hosts between the pristine and gut-associated environments. We found that the abundance of total ARGs in gut-associated environments was significantly higher than the pristine environments (P < 0.001). The mcr-1 and tetX, the genes resistant to the last resort antibiotics (colistin and tigecycline, respectively), were in high abundance (4.57 copies/Gb and 3.39 copies/Gb, respectively) in gut-associated environments, suggesting the ARG pollution caused by anthropogenic antibiotics. Metagenomic assembly-based host-tracking analysis identified Escherichia, Bacteroides, and Clostridium as the predominant bacterial hosts of ARGs in gut-associated environments, while Alteromonas, Vibrio, and Proteobacteria as the predominant bacterial hosts of ARGs in pristine environments. We first described the broad diversity of ARG hosts in different environments using metagenome-wide analysis. Our results revealed the heterogeneous distribution of ARGs and their hosts among different microbial niches in gut-associated environments and the pristine environments.}, } @article {pmid30826606, year = {2019}, author = {Bai, Y and Ruan, X and Xie, X and Yan, Z}, title = {Antibiotic resistome profile based on metagenomics in raw surface drinking water source and the influence of environmental factor: A case study in Huaihe River Basin, China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {248}, number = {}, pages = {438-447}, doi = {10.1016/j.envpol.2019.02.057}, pmid = {30826606}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacitracin/pharmacology ; Burkholderiaceae/drug effects/*genetics ; China ; Drinking Water/*microbiology ; Drug Resistance, Microbial/*genetics ; Flavobacterium/drug effects/*genetics ; Genes, Bacterial/genetics ; Humans ; Metagenomics ; Microbiota/drug effects ; Rivers/*microbiology ; Tetracyclines/pharmacology ; Verrucomicrobia/drug effects/*genetics ; beta-Lactams/pharmacology ; }, abstract = {The contamination with antibiotic resistance genes (ARGs) in raw drinking water source may pose a direct threat to human health. In this study, metagenomics sequencing and analysis were applied to investigate the ARG pattern in 12 drinking water sources in upper and middle reach of Huaihe River Basin, China. Based on the redundant analysis and multi-linear regression model, location, specific microbial taxa, number of livestock and health facilities significantly influenced the ARG profile in drinking water sources. Besides the cluster effect of ARG in samples from plain and bedrock mountain areas, the samples from fracture aquifer areas also showed a distinctive biogeographic pattern with that from porous aquifer areas. Putative ARGs host Opitutus and Flavobacterium were the enriched biomarkers in plain and fracture aquifer area respectively, which mainly carried bacitracin, multidrug, beta-lactam and tetracycline ARGs. This result illuminated that both natural background and anthropogenic activities in the watershed influenced the ARG profile in natural freshwater system significantly. The low MGEs abundance and absence of pathogen revealed a low ARG dissemination risk in sampled drinking water sources, while Polynucleobacter was an abundant ARGs host and was significantly related to the ARG profile, which indicated that specific bacteria was responsible for ARGs propagation and accumulation in surface freshwater system. Further researches are needed to assess human exposure to raw drinking water source and the potential risk, as well as the species interaction in microbial community and its impact on ARG propagation under oligotrophic condition.}, } @article {pmid30824791, year = {2019}, author = {McGaughey, KD and Yilmaz-Swenson, T and Elsayed, NM and Cruz, DA and Rodriguiz, RM and Kritzer, MD and Peterchev, AV and Roach, J and Wetsel, WC and Williamson, DE}, title = {Relative abundance of Akkermansia spp. and other bacterial phylotypes correlates with anxiety- and depressive-like behavior following social defeat in mice.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {3281}, pmid = {30824791}, issn = {2045-2322}, support = {R01 MH091083/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Anxiety Disorders/*microbiology ; *Behavior, Animal ; Depression/genetics/*microbiology ; *Gastrointestinal Microbiome ; Male ; Metagenome ; Mice ; RNA, Ribosomal, 16S ; Stress, Psychological/genetics/*microbiology ; *Verrucomicrobia/classification/genetics/growth & development ; }, abstract = {As discussion of stress and stress-related disorders rapidly extends beyond the brain, gut microbiota have emerged as a promising contributor to individual differences in the risk of illness, disease course, and treatment response. Here, we employed chronic mild social defeat stress and 16S rRNA gene metagenomic sequencing to investigate the role of microbial composition in mediating anxiety- and depressive-like behavior. In socially defeated animals, we found significant reductions in the overall diversity and relative abundances of numerous bacterial genera, including Akkermansia spp., that positively correlated with behavioral metrics of both anxiety and depression. Functional analyses predicted a reduced frequency of signaling molecule pathways, including G-protein-coupled receptors, in defeated animals. Collectively, our data suggest that shifts in microbial composition may play a role in the pathogenesis of anxiety and depression.}, } @article {pmid30824335, year = {2019}, author = {Davies, NK and O'Sullivan, JM and Plank, LD and Murphy, R}, title = {Altered gut microbiome after bariatric surgery and its association with metabolic benefits: A systematic review.}, journal = {Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery}, volume = {15}, number = {4}, pages = {656-665}, doi = {10.1016/j.soard.2019.01.033}, pmid = {30824335}, issn = {1878-7533}, mesh = {*Bariatric Surgery ; *Gastrointestinal Microbiome ; Humans ; *Obesity/physiopathology/surgery ; Treatment Outcome ; }, abstract = {Bariatric surgery is currently the recommended therapy for significant weight reduction and remission of type 2 diabetes. Different types of bariatric surgery result in dramatic changes to gut bacteria but the contribution of such changes to the metabolic benefits achieved is still unclear. This systematic review of 14 clinical studies, incorporating 222 participants (146 patients with Roux-en-Y gastric bypass, 25 with sleeve gastrectomy, 30 with biliointestinal bypass, 7 with vertical banded gastroplasty, and 14 with an adjustable gastric band) reveals generally increased microbial diversity and gene richness after surgery. Major species-level changes include a decrease in the relative abundance of Faecalibacterium prausnitzii and increase in Escherichia coli. Decreases in the relative abundance of Firmicutes after sleeve gastrectomy and increases in Bacteroidetes and Proteobacteria after Roux-en-Y gastric bypass were seen. Microbial changes after surgery are discussed in the context of potential confounding effects of baseline diet, medications, and type 2 diabetes, with recommendations to consider these factors in future studies, to identify potentially causal associations with observed metabolic benefits.}, } @article {pmid30820491, year = {2019}, author = {Lam, TJ and Ye, Y}, title = {CRISPRs for Strain Tracking and Their Application to Microbiota Transplantation Data Analysis.}, journal = {The CRISPR journal}, volume = {2}, number = {1}, pages = {41-50}, pmid = {30820491}, issn = {2573-1599}, support = {R01 AI108888/AI/NIAID NIH HHS/United States ; R01 AI143254/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Typing Techniques/*methods ; CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Computational Biology/methods ; DNA, Intergenic/classification/*genetics/metabolism ; Datasets as Topic ; Dysbiosis/microbiology/*therapy ; Fecal Microbiota Transplantation/*methods ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenome ; }, abstract = {CRISPR-Cas systems are adaptive immune systems naturally found in bacteria and archaea. Prokaryotes use these immune systems to defend against invaders, which include phages, plasmids, and other mobile genetic elements. Relying on the integration of spacers derived from invader sequences (protospacers) into CRISPR loci (forming spacers flanked by repeats), CRISPR-Cas systems are able to store the memory of past immunological encounters. While CRISPR-Cas systems have evolved in response to invading mobile genetic elements, invaders have also developed mechanisms to avoid detection. As a result of an arms race between CRISPR-Cas systems and their targets, CRISPR arrays typically undergo rapid turnover of spacers through the acquisition and loss events. Additionally, microbiomes of different individuals rarely share spacers. Here, we present a computational pipeline, CRISPRtrack, for strain tracking based on CRISPR spacer content, and we applied it to fecal transplantation microbiome data to study the retention of donor strains in recipients. Our results demonstrate the potential use of CRISPRs as a simple yet effective tool for donor-strain tracking in fecal transplantation and as a general purpose tool for quantifying microbiome similarity.}, } @article {pmid30820034, year = {2019}, author = {Du Toit, A}, title = {Gut phages at the centre.}, journal = {Nature reviews. Microbiology}, volume = {17}, number = {4}, pages = {195}, doi = {10.1038/s41579-019-0174-9}, pmid = {30820034}, issn = {1740-1534}, mesh = {Adult ; Bacteriophages/*genetics ; *Gastrointestinal Microbiome ; *Gastrointestinal Tract ; Humans ; Metagenome ; Twins, Monozygotic ; }, } @article {pmid30817265, year = {2019}, author = {Touyz, RM and Camargo, LL}, title = {Microglia, the Missing Link in the Brain-Gut-Hypertension Axis.}, journal = {Circulation research}, volume = {124}, number = {5}, pages = {671-673}, pmid = {30817265}, issn = {1524-4571}, support = {CH/12/4/29762/BHF_/British Heart Foundation/United Kingdom ; CH/4/29762/BHF_/British Heart Foundation/United Kingdom ; }, mesh = {Angiotensin II ; Brain ; *Gastrointestinal Microbiome ; Humans ; *Hypertension ; Microglia ; }, } @article {pmid30816927, year = {2019}, author = {Dai, Z and Wong, SH and Yu, J and Wei, Y}, title = {Batch effects correction for microbiome data with Dirichlet-multinomial regression.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {5}, pages = {807-814}, doi = {10.1093/bioinformatics/bty729}, pmid = {30816927}, issn = {1367-4811}, mesh = {Bayes Theorem ; *Microbiota ; Regression Analysis ; Research Design ; }, abstract = {MOTIVATION: Metagenomic sequencing techniques enable quantitative analyses of the microbiome. However, combining the microbial data from these experiments is challenging due to the variations between experiments. The existing methods for correcting batch effects do not consider the interactions between variables-microbial taxa in microbial studies-and the overdispersion of the microbiome data. Therefore, they are not applicable to microbiome data.

RESULTS: We develop a new method, Bayesian Dirichlet-multinomial regression meta-analysis (BDMMA), to simultaneously model the batch effects and detect the microbial taxa associated with phenotypes. BDMMA automatically models the dependence among microbial taxa and is robust to the high dimensionality of the microbiome and their association sparsity. Simulation studies and real data analysis show that BDMMA can successfully adjust batch effects and substantially reduce false discoveries in microbial meta-analyses.

An R package" BDMMA" for Windows and Linux is available at https://github.com/DAIZHENWEI/BDMMA/BDMMA, and a version for MacOS is provided at https://github.com/DAIZHENWEI/BDMMA/BDMMA_MacOS.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid30816674, year = {2019}, author = {Philley, JV and Kannan, A and Olusola, P and McGaha, P and Singh, KP and Samten, B and Griffith, DE and Dasgupta, S}, title = {Microbiome Diversity in Sputum of Nontuberculous Mycobacteria Infected Women with a History of Breast Cancer.}, journal = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology}, volume = {52}, number = {2}, pages = {263-279}, doi = {10.33594/000000020}, pmid = {30816674}, issn = {1421-9778}, support = {Startup Fund//The University of Texas Health Science Center at Tyler/International ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; *Bacteria/classification/genetics/growth & development ; Breast Neoplasms/*microbiology ; Female ; Humans ; Lung Diseases/*microbiology ; *Microbiota ; Middle Aged ; Mycobacterium Infections, Nontuberculous/*microbiology ; Sputum/*microbiology ; }, abstract = {BACKGROUND/AIMS: The nontuberculous mycobacterial lung disease (NTM), caused by Mycobacterium avium complex (MAC) is an increasing health problem in the USA and worldwide. The NTM disease is prevalent in Caucasian women with a current diagnosis or history of breast cancer (BCa), posing a significant challenge towards treatment. We hypothesize that NTM affected women with considerable therapeutic resistance may harbor pathogenic microbes other than nontuberculous mycobacterium, aiding in disease progression and therapeutic resistance.

METHODS: We assessed microbiome diversity in sputa from healthy women, women with nontuberculous mycobacterial lung disease (NTM) and women with both nontuberculous mycobacterial lung disease and breast cancer (NTM-BCa). First, we collected sputa and isolated DNA from sputa of these healthy women and women with NTM and NTM-BCa. We also isolated DNA from sera derived extracellular vesicles from women with NTM-BCa. To identify diverse pathogenic microbes in various groups of subjects, we then performed 16S rDNA sequencing. Data analysis was performed utilizing the analytical pipelines at the Center for Metagenomic and Microbiome Research (CMMR), Baylor College of Medicine.

RESULTS: A large community of resident microbes, including bacteria, virus, Archeas and Fungi live in the human body are being increasingly recognized as the key components of human health and disease. We identified a diverse microbiome community in the sputa and the extracellular vesicles dominated by Streptococcus, Haemophillus, Veillonella, Neisseria, Prevotella, Fusobacterium, Bacteroides, Allistipes, Faecalibacterium and Staphylococcus in women with nontuberculous mycobacterial lung disease as well as women with both nontuberculous mycobacterial lung disease and breast cancer. Some of these genera, including Fusobacterium, Bacteroides, and Allistipes have estrobolome activity and associated with breast and other neoplasms.

CONCLUSION: This work confirms the presence of a distinct pathogenic microbiome other than nontuberculous mycobacteria in the sputa and the circulating extracellular vesicles of these patients. This information could be useful for better therapeutic design to treat the NTM patients.}, } @article {pmid30816592, year = {2019}, author = {Subramaniyan, V and Gurumurthy, K}, title = {Diversity of probiotic adhesion genes in the gastrointestinal tract of goats.}, journal = {Journal of cellular biochemistry}, volume = {120}, number = {8}, pages = {12422-12428}, doi = {10.1002/jcb.28508}, pmid = {30816592}, issn = {1097-4644}, mesh = {Animals ; *Bacterial Adhesion ; Bacterial Proteins/*genetics/metabolism ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; *Genetic Variation ; Goats/*genetics/microbiology ; Phylogeny ; Probiotics/*metabolism ; }, abstract = {Gastrointestinal (GI) microflora is an important system in the host, as it has both pathogenic and probiotic bacteria. Most of the studies were focused on the human gut microflora and the available information on the intestinal microflora of goats was limited. This urged the need to inspect the impacts of the goat's gut microflora. Metagenomic investigation of probiotic bacteria in the GI tract of goat is one of the challenging streams because of the less available data of the uncultivable bacteria. In our report, comparative analysis of metagenomic and enrichment samples of goat intestinal content was done and this approach will be helpful in analyzing the identification of uncultivable and cultivable probiotic bacteria. This study mainly focused on three key probiotic adhesion genes, such as EF-Tu, mapA, and mub. The GI of four different goats were investigated for these genes. The data from this study showed that there is a wide diversity of these genes among goat intestinal samples.}, } @article {pmid30816235, year = {2019}, author = {Wilkins, LGE and Ettinger, CL and Jospin, G and Eisen, JA}, title = {Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {3059}, pmid = {30816235}, issn = {2045-2322}, mesh = {Archaea/genetics/isolation & purification ; Bacteria/genetics/isolation & purification ; DNA, Environmental/*genetics/isolation & purification ; *Genome, Archaeal ; *Genome, Bacterial ; Geography ; Hot Springs/*microbiology ; Metagenome ; Microbiota/*genetics ; Molecular Sequence Annotation ; Phylogeny ; Russia ; Whole Genome Sequencing ; }, abstract = {Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. We assembled genomes of bacteria and archaea using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and inferred their placement in a phylogenetic tree consisting of 3,240 publicly available microbial genomes. We highlight MAGs that were taxonomically assigned to groups previously underrepresented in available genome data. This includes several archaea (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study adds comprehensive information about phylogenetic diversity and functional potential within two hot springs in the caldera of Kamchatka.}, } @article {pmid30815668, year = {2020}, author = {Ayling, M and Clark, MD and Leggett, RM}, title = {New approaches for metagenome assembly with short reads.}, journal = {Briefings in bioinformatics}, volume = {21}, number = {2}, pages = {584-594}, pmid = {30815668}, issn = {1477-4054}, support = {BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M004805/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CSP17270/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Algorithms ; Animals ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Metagenome ; Microbiota/genetics ; Plants/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {In recent years, the use of longer range read data combined with advances in assembly algorithms has stimulated big improvements in the contiguity and quality of genome assemblies. However, these advances have not directly transferred to metagenomic data sets, as assumptions made by the single genome assembly algorithms do not apply when assembling multiple genomes at varying levels of abundance. The development of dedicated assemblers for metagenomic data was a relatively late innovation and for many years, researchers had to make do using tools designed for single genomes. This has changed in the last few years and we have seen the emergence of a new type of tool built using different principles. In this review, we describe the challenges inherent in metagenomic assemblies and compare the different approaches taken by these novel assembly tools.}, } @article {pmid30814504, year = {2019}, author = {Mahnert, A and Moissl-Eichinger, C and Zojer, M and Bogumil, D and Mizrahi, I and Rattei, T and Martinez, JL and Berg, G}, title = {Man-made microbial resistances in built environments.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {968}, pmid = {30814504}, issn = {2041-1723}, mesh = {Biodiversity ; *Built Environment ; *Drug Resistance, Microbial/genetics ; *Environmental Microbiology ; Gram-Negative Bacteria/drug effects/genetics/isolation & purification ; Gram-Positive Bacteria/drug effects/genetics/isolation & purification ; Humans ; Metagenome ; *Microbiota/drug effects/genetics ; }, abstract = {Antimicrobial resistance is a serious threat to global public health, but little is known about the effects of microbial control on the microbiota and its associated resistome. Here we compare the microbiota present on surfaces of clinical settings with other built environments. Using state-of-the-art metagenomics approaches and genome and plasmid reconstruction, we show that increased confinement and cleaning is associated with a loss of microbial diversity and a shift from Gram-positive bacteria, such as Actinobacteria and Firmicutes, to Gram-negative such as Proteobacteria. Moreover, the microbiome of highly maintained built environments has a different resistome when compared to other built environments, as well as a higher diversity in resistance genes. Our results highlight that the loss of microbial diversity correlates with an increase in resistance, and the need for implementing strategies to restore bacterial diversity in certain built environments.}, } @article {pmid30813950, year = {2019}, author = {Iszatt, N and Janssen, S and Lenters, V and Dahl, C and Stigum, H and Knight, R and Mandal, S and Peddada, S and González, A and Midtvedt, T and Eggesbø, M}, title = {Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {34}, pmid = {30813950}, issn = {2049-2618}, mesh = {Adult ; Humans ; Infant, Newborn ; *Bacteria/classification/drug effects/genetics ; Biodiversity ; Cohort Studies ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; *Environmental Pollutants/adverse effects/analysis ; *Fatty Acids, Volatile/analysis ; Feces/chemistry/microbiology ; Flame Retardants/adverse effects/analysis ; *Gastrointestinal Microbiome/drug effects ; Hydrocarbons, Chlorinated/adverse effects/analysis ; Maternal Age ; Metabolomics ; *Milk, Human/chemistry ; Norway ; Pesticides/adverse effects/analysis ; Polychlorinated Biphenyls/adverse effects/analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Female ; }, abstract = {BACKGROUND: Early disruption of the microbial community may influence life-long health. Environmental toxicants can contaminate breast milk and the developing infant gut microbiome is directly exposed. We investigated whether environmental toxicants in breastmilk affect the composition and function of the infant gut microbiome at 1 month. We measured environmental toxicants in breastmilk, fecal short-chain fatty acids (SCFAs), and gut microbial composition from 16S rRNA gene amplicon sequencing using samples from 267 mother-child pairs in the Norwegian Microbiota Cohort (NoMIC). We tested 28 chemical exposures: polychlorinated biphenyls (PCBs), polybrominated flame retardants (PBDEs), per- and polyfluoroalkyl substances (PFASs), and organochlorine pesticides. We assessed chemical exposure and alpha diversity/SCFAs using elastic net regression modeling and generalized linear models, adjusting for confounders, and variation in beta diversity (UniFrac), taxa abundance (ANCOM), and predicted metagenomes (PiCRUSt) in low, medium, and high exposed groups.

RESULTS: PBDE-28 and the surfactant perfluorooctanesulfonic acid (PFOS) were associated with less microbiome diversity. Some sub-OTUs of Lactobacillus, an important genus in early life, were lower in abundance in samples from infants with relative "high" (> 80th percentile) vs. "low" (< 20th percentile) toxicant exposure in this cohort. Moreover, breast milk toxicants were associated with microbiome functionality, explaining up to 34% of variance in acetic and propionic SCFAs, essential signaling molecules. Per one standard deviation of exposure, PBDE-28 was associated with less propionic acid (- 24% [95% CI - 35% to - 14%] relative to the mean), and PCB-209 with less acetic acid (- 15% [95% CI - 29% to - 0.4%]). Conversely, PFOA and dioxin-like PCB-167 were associated with 61% (95% CI 35% to 87%) and 22% (95% CI 8% to 35%) more propionic and acetic acid, respectively.

CONCLUSIONS: Environmental toxicant exposure may influence infant gut microbial function during a critical developmental window. Future studies are needed to replicate these novel findings and investigate whether this has any impact on child health.}, } @article {pmid30810996, year = {2019}, author = {Pérez-Fernández, CA and Iriarte, M and Rivera-Pérez, J and Tremblay, RL and Toranzos, GA}, title = {Microbiota dispersion in the Uyuni salt flat (Bolivia) as determined by community structure analyses.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {22}, number = {3}, pages = {325-336}, doi = {10.1007/s10123-018-00052-2}, pmid = {30810996}, issn = {1618-1905}, support = {5R25GM061151-12, -13//Research Initiative for Scientific Enhancement Program/ ; }, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biota ; Bolivia ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Soil microbial communities are an important component of biological diversity and terrestrial ecosystems which is responsible for processes such as decomposition, mineralization of nutrients, and accumulation of organic matter. One of the factors that provide information on the mechanisms regulating biodiversity is spatial scaling. We characterized the microbial communities using 16S rRNA gene sequences from DNA isolated from halite at various locations and correlated these to geographic distance in the Uyuni salt flat (Bolivia). Sequences from each site were analyzed to determine any spatial patterns of diversity, as well as to describe the microbial communities. Results suggest that different taxa are able to disperse over Uyuni's surface crust regardless of distance. As expected, ubiquitous taxa included members of Halobacteriaceae such as Haloarcula, Halorubrum, Halorhabdus, Halolamina, and halophilic bacteria Salinibacter, Halorhodospira, and unclassified members of the Gammaproteobacteria. Archaeal communities were homogeneous across the salt flat. In contrast, bacterial communities present strong local variations which could be attributed to external factors. Likely sources for these variations are the Rio Grande river influent in the south shore and the Tunupa volcano influencing the northern area.}, } @article {pmid30809304, year = {2019}, author = {Sun, L and Ma, L and Zhang, H and Cao, Y and Wang, C and Hou, N and Huang, N and von Deneen, KM and Zhao, C and Shi, Y and Pan, Y and Wang, M and Ji, G and Nie, Y}, title = {Fto Deficiency Reduces Anxiety- and Depression-Like Behaviors in Mice via Alterations in Gut Microbiota.}, journal = {Theranostics}, volume = {9}, number = {3}, pages = {721-733}, pmid = {30809304}, issn = {1838-7640}, mesh = {Alpha-Ketoglutarate-Dependent Dioxygenase FTO/*deficiency/genetics ; Animals ; Anxiety/*genetics/microbiology ; Depression/*genetics/microbiology ; *Gastrointestinal Microbiome ; Inflammation/psychology ; Lactobacillus/physiology ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Obesity/genetics/microbiology/psychology ; }, abstract = {Depression and obesity have high concurrence within individuals, which may be explained by sharing the same risk factors, including disruption of the intestinal microbiota. However, evidence that delineated the causal connections is extremely scarce. Methods: Mice lacking fat mass- and obesity-associated gene (Fto) were generated. Fto-deficient and wild-type control mice were subjected to novel conditions with or without chronic unpredictable mild stress (CUMS) for 6 weeks. Some mice were treated with antibiotics via their drinking water for 6 weeks in order to deplete their microbiota. Behavioral tests were performed to evaluate anxiety- and depression-like behaviors. 16S rRNA amplicon and metagenomic sequencing were employed to analyse fecal microbiota. Plasma levels of inflammatory cytokines and lipopolysaccharides (LPS) were also compared. Results: Deletion of Fto led to lower body weight and decreased anxiety- and depression-like behaviors, Fto+/- mice were also less susceptible to stress stimulation, highlighting the essential role of Fto in pathogenesis of depression. With regard to gut microbiota, Fto deficiency mice harbored specific bacterial signature of suppressing inflammation, characterized with higher abundance of Lactobacillus, lower Porphyromonadaceae and Helicobacter. Critically, behavioral alterations of Fto[+/-] mice are mediated by shift in gut microbiota, as such changes can be partially attenuated using antibiotics. Exposure to CUMS increased serum IL-6 level while Fto deficiency reduced its level, which may be explained by a lower LPS concentration. Conclusion: Together, our findings uncover the roles of Fto on depression and provide insights into microbiota-related biological mechanisms underlying the association between obesity and depression.}, } @article {pmid30809227, year = {2019}, author = {Schwarzer, M and Hermanova, P and Srutkova, D and Golias, J and Hudcovic, T and Zwicker, C and Sinkora, M and Akgün, J and Wiedermann, U and Tuckova, L and Kozakova, H and Schabussova, I}, title = {Germ-Free Mice Exhibit Mast Cells With Impaired Functionality and Gut Homing and Do Not Develop Food Allergy.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {205}, pmid = {30809227}, issn = {1664-3224}, mesh = {Animals ; Biomarkers ; Cell Degranulation/genetics/immunology ; Cell Differentiation/genetics/immunology ; Cytokines/metabolism ; Disease Models, Animal ; Disease Susceptibility ; Female ; Food Hypersensitivity/*etiology/*metabolism/pathology ; Gastrointestinal Microbiome ; Germ-Free Life ; Mast Cells/*immunology/*metabolism ; Metagenome ; Metagenomics/methods ; Mice ; *Microbiota/immunology ; RNA, Ribosomal, 16S ; }, abstract = {Background: Mucosal mast cells (MC) are key players in IgE-mediated food allergy (FA). The evidence on the interaction between gut microbiota, MC and susceptibility to FA is contradictory. Objective: We tested the hypothesis that commensal bacteria are essential for MC migration to the gut and their maturation impacting the susceptibility to FA. Methods: The development and severity of FA symptoms was studied in sensitized germ-free (GF), conventional (CV), and mice mono-colonized with L. plantarum WCFS1 or co-housed with CV mice. MC were phenotypically and functionally characterized. Results: Systemic sensitization and oral challenge of GF mice with ovalbumin led to increased levels of specific IgE in serum compared to CV mice. Remarkably, despite the high levels of sensitization, GF mice did not develop diarrhea or anaphylactic hypothermia, common symptoms of FA. In the gut, GF mice expressed low levels of the MC tissue-homing markers CXCL1 and CXCL2, and harbored fewer MC which exhibited lower levels of MC protease-1 after challenge. Additionally, MC in GF mice were less mature as confirmed by flow-cytometry and their functionality was impaired as shown by reduced edema formation after injection of degranulation-provoking compound 48/80. Co-housing of GF mice with CV mice fully restored their susceptibility to develop FA. However, this did not occur when mice were mono-colonized with L. plantarum. Conclusion: Our results demonstrate that microbiota-induced maturation and gut-homing of MC is a critical step for the development of symptoms of experimental FA. This new mechanistic insight into microbiota-MC-FA axis can be exploited in the prevention and treatment of FA in humans.}, } @article {pmid30809010, year = {2019}, author = {Jones, DS and Walker, GM and Johnson, NW and Mitchell, CPJ and Coleman Wasik, JK and Bailey, JV}, title = {Molecular evidence for novel mercury methylating microorganisms in sulfate-impacted lakes.}, journal = {The ISME journal}, volume = {13}, number = {7}, pages = {1659-1675}, pmid = {30809010}, issn = {1751-7370}, mesh = {Bacteria/classification/*genetics/isolation & purification/metabolism ; Bacterial Proteins/genetics/metabolism ; Lakes/analysis/*microbiology ; Mercury/analysis/*metabolism ; Methylation ; Methylmercury Compounds/analysis/metabolism ; Microbiota ; Sulfates/analysis/*metabolism ; Sulfides/analysis/metabolism ; }, abstract = {Methylmercury (MeHg) is a bioaccumulative neurotoxin that is produced by certain anaerobic microorganisms, but the abundance and importance of different methylating populations in the environment is not well understood. We combined mercury geochemistry, hgcA gene cloning, rRNA methods, and metagenomics to compare microbial communities associated with MeHg production in two sulfate-impacted lakes on Minnesota's Mesabi Iron Range. The two lakes represent regional endmembers among sulfate-impacted sites in terms of their dissolved sulfide concentrations and MeHg production potential. rRNA amplicon sequencing indicates that sediments and anoxic bottom waters from both lakes contained diverse communities with multiple clades of sulfate reducing Deltaproteobacteria and Clostridia. In hgcA gene clone libraries, however, hgcA sequences were from taxa associated with methanogenesis and iron reduction in addition to sulfate reduction, and the most abundant clones were from unknown groups. We therefore applied metagenomics to identify the unknown populations in the lakes with the capability to methylate mercury, and reconstructed 27 genomic bins with hgcA. Some of the most abundant potential methylating populations were from phyla that are not typically associated with MeHg production, including a relative of the Aminicenantes (formerly candidate phylum OP8) and members of the Kiritimatiellaeota (PVC superphylum) and Spirochaetes that, together, were more than 50% of the potential methylators in some samples. These populations do not have genes for sulfate reduction, and likely degrade organic compounds by fermentation or other anaerobic processes. Our results indicate that previously unrecognized populations with hgcAB are abundant and may be important for MeHg production in some freshwater ecosystems.}, } @article {pmid30808753, year = {2019}, author = {Ramírez-Flandes, S and González, B and Ulloa, O}, title = {Redox traits characterize the organization of global microbial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {9}, pages = {3630-3635}, pmid = {30808753}, issn = {1091-6490}, mesh = {Ecology ; *Ecosystem ; Humans ; *Metagenomics ; Microbiota/*genetics ; *Oxidation-Reduction ; Soil Microbiology ; }, abstract = {The structure of biological communities is conventionally described as profiles of taxonomic units, whose ecological functions are assumed to be known or, at least, predictable. In environmental microbiology, however, the functions of a majority of microorganisms are unknown and expected to be highly dynamic and collectively redundant, obscuring the link between taxonomic structure and ecosystem functioning. Although genetic trait-based approaches at the community level might overcome this problem, no obvious choice of gene categories can be identified as appropriate descriptive units in a general ecological context. We used 247 microbial metagenomes from 18 biomes to determine which set of genes better characterizes the differences among biomes on the global scale. We show that profiles of oxidoreductase genes support the highest biome differentiation compared with profiles of other categories of enzymes, general protein-coding genes, transporter genes, and taxonomic gene markers. Based on oxidoreductases' description of microbial communities, the role of energetics in differentiation and particular ecosystem function of different biomes become readily apparent. We also show that taxonomic diversity is decoupled from functional diversity, e.g., grasslands and rhizospheres were the most diverse biomes in oxidoreductases but not in taxonomy. Considering that microbes underpin biogeochemical processes and nutrient recycling through oxidoreductases, this functional diversity should be relevant for a better understanding of the stability and conservation of biomes. Consequently, this approach might help to quantify the impact of environmental stressors on microbial ecosystems in the context of the global-scale biome crisis that our planet currently faces.}, } @article {pmid30808694, year = {2019}, author = {Feng, J and Penton, CR and He, Z and Van Nostrand, JD and Yuan, MM and Wu, L and Wang, C and Qin, Y and Shi, ZJ and Guo, X and Schuur, EAG and Luo, Y and Bracho, R and Konstantinidis, KT and Cole, JR and Tiedje, JM and Yang, Y and Zhou, J}, title = {Long-Term Warming in Alaska Enlarges the Diazotrophic Community in Deep Soils.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, pmid = {30808694}, issn = {2150-7511}, mesh = {Alaska ; *Biota ; *Global Warming ; Metagenomics ; Microarray Analysis ; *Nitrogen Fixation ; Oxidoreductases/genetics ; Plant Development ; *Soil Microbiology ; Tundra ; }, abstract = {Tundra ecosystems are typically carbon (C) rich but nitrogen (N) limited. Since biological N2 fixation is the major source of biologically available N, the soil N2-fixing (i.e., diazotrophic) community serves as an essential N supplier to the tundra ecosystem. Recent climate warming has induced deeper permafrost thaw and adversely affected C sequestration, which is modulated by N availability. Therefore, it is crucial to examine the responses of diazotrophic communities to warming across the depths of tundra soils. Herein, we carried out one of the deepest sequencing efforts of nitrogenase gene (nifH) to investigate how 5 years of experimental winter warming affects Alaskan soil diazotrophic community composition and abundance spanning both the organic and mineral layers. Although soil depth had a stronger influence on diazotrophic community composition than warming, warming significantly (P < 0.05) enhanced diazotrophic abundance by 86.3% and aboveground plant biomass by 25.2%. Diazotrophic composition in the middle and lower organic layers, detected by nifH sequencing and a microarray-based tool (GeoChip), was markedly altered, with an increase of α-diversity. Changes in diazotrophic abundance and composition significantly correlated with soil moisture, soil thaw duration, and plant biomass, as shown by structural equation modeling analyses. Therefore, more abundant diazotrophic communities induced by warming may potentially serve as an important mechanism for supplementing biologically available N in this tundra ecosystem.IMPORTANCE With the likelihood that changes in global climate will adversely affect the soil C reservoir in the northern circumpolar permafrost zone, an understanding of the potential role of diazotrophic communities in enhancing biological N2 fixation, which constrains both plant production and microbial decomposition in tundra soils, is important in elucidating the responses of soil microbial communities to global climate change. A recent study showed that the composition of the diazotrophic community in a tundra soil exhibited no change under a short-term (1.5-year) winter warming experiment. However, it remains crucial to examine whether the lack of diazotrophic community responses to warming is persistent over a longer time period as a possibly important mechanism in stabilizing tundra soil C. Through a detailed characterization of the effects of winter warming on diazotrophic communities, we showed that a long-term (5-year) winter warming substantially enhanced diazotrophic abundance and altered community composition, though soil depth had a stronger influence on diazotrophic community composition than warming. These changes were best explained by changes in soil moisture, soil thaw duration, and plant biomass. These results provide crucial insights into the potential factors that may impact future C and N availability in tundra regions.}, } @article {pmid30808411, year = {2019}, author = {, }, title = {A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {31}, pmid = {30808411}, issn = {2049-2618}, mesh = {Biomedical Research/*economics/*organization & administration ; Humans ; Metagenomics/economics/organization & administration ; Microbiota ; National Institutes of Health (U.S.) ; United States ; }, abstract = {The National Institutes of Health (NIH) is the primary federal government agency for biomedical research in the USA. NIH provides extensive support for human microbiome research with 21 of 27 NIH Institutes and Centers (ICs) currently funding this area through their extramural research programs. This analysis of the NIH extramural portfolio in human microbiome research briefly reviews the early history of this field at NIH, summarizes the program objectives and the resources developed in the recently completed 10-year (fiscal years 2007-2016) $215 M Human Microbiome Project (HMP) program, evaluates the scope and range of the $728 M NIH investment in extramural human microbiome research activities outside of the HMP over fiscal years 2012-2016, and highlights some specific areas of research which emerged from this investment. This analysis closes with a few comments on the technical needs and knowledge gaps which remain for this field to be able to advance over the next decade and for the outcomes of this research to be able to progress to microbiome-based interventions for treating disease and supporting health.}, } @article {pmid30808380, year = {2019}, author = {DeMaere, MZ and Darling, AE}, title = {bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {46}, pmid = {30808380}, issn = {1474-760X}, mesh = {Computer Simulation ; Feces/microbiology ; *Genome, Bacterial ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA ; *Software ; }, abstract = {Most microbes cannot be easily cultured, and metagenomics provides a means to study them. Current techniques aim to resolve individual genomes from metagenomes, so-called metagenome-assembled genomes (MAGs). Leading approaches depend upon time series or transect studies, the efficacy of which is a function of community complexity, target abundance, and sequencing depth. We describe an unsupervised method that exploits the hierarchical nature of Hi-C interaction rates to resolve MAGs using a single time point. We validate the method and directly compare against a recently announced proprietary service, ProxiMeta. bin3C is an open-source pipeline and makes use of the Infomap clustering algorithm (https://github.com/cerebis/bin3C).}, } @article {pmid30805695, year = {2020}, author = {Strain, CR and Collins, KC and Naughton, V and McSorley, EM and Stanton, C and Smyth, TJ and Soler-Vila, A and Rea, MC and Ross, PR and Cherry, P and Allsopp, PJ}, title = {Effects of a polysaccharide-rich extract derived from Irish-sourced Laminaria digitata on the composition and metabolic activity of the human gut microbiota using an in vitro colonic model.}, journal = {European journal of nutrition}, volume = {59}, number = {1}, pages = {309-325}, pmid = {30805695}, issn = {1436-6215}, support = {MFFRI/07/01//Sea Change Strategy, Department of Agriculture, Food and the Marine (IE)/ ; }, mesh = {Colon/*metabolism/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; In Vitro Techniques ; Laminaria/*metabolism/*microbiology ; Models, Biological ; Plant Extracts/metabolism/*pharmacology ; Polysaccharides/metabolism/*pharmacology ; }, abstract = {BACKGROUND: Brown seaweeds are known to be a rich source of fiber with the presence of several non-digestible polysaccharides including laminarin, fucoidan and alginate. These individual polysaccharides have previously been shown to favorably alter the gut microbiota composition and activity albeit the effect of the collective brown seaweed fiber component on the microbiota remains to be determined.

METHODS: This study investigated the effect of a crude polysaccharide-rich extract obtained from Laminaria digitata (CE) and a depolymerized CE extract (DE) on the gut microbiota composition and metabolism using an in vitro fecal batch culture model though metagenomic compositional analysis using 16S rRNA FLX amplicon pyrosequencing and short-chain fatty acid (SCFA) analysis using GC-FID.

RESULTS: Selective culture analysis showed no significant changes in cultured lactobacilli or bifidobacteria between the CE or DE and the cellulose-negative control at any time point measured (0, 5, 10, 24, 36, 48 h). Following metagenomic analysis, the CE and DE significantly altered the relative abundance of several families including Lachnospiraceae and genera including Streptococcus, Ruminococcus and Parabacteroides of human fecal bacterial populations in comparison to cellulose after 24 h. The concentrations of acetic acid, propionic acid, butyric acid and total SCFA were significantly higher for both the CE and DE compared to cellulose after 10, 24, 36 and 48 h fermentation (p < 0.05). Furthermore, the acetate:propionate ratio was significantly reduced (p < 0.05) for both CD and DE following 24, 36 and 48 h fermentation.

CONCLUSION: The microbiota-associated metabolic and compositional changes noted provide initial indication of putative beneficial health benefits of L. digitata in vitro; however, research is needed to clarify if L. digitata-derived fiber can favorably alter the gut microbiota and confer health benefits in vivo.}, } @article {pmid30804923, year = {2018}, author = {Ma, ZS and Li, L}, title = {Semen Microbiome Biogeography: An Analysis Based on a Chinese Population Study.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3333}, pmid = {30804923}, issn = {1664-302X}, abstract = {Investigating inter-subject heterogeneity (or spatial distribution) of human semen microbiome diversity is of important significance. Theoretically, the spatial distribution of biodiversity constitutes the core of microbiome biogeography. Practically, the inter-subject heterogeneity is crucial for understanding the normal (healthy) flora of semen microbiotas as well as their possible changes associated with abnormal fertility. In this article, we analyze the scaling (changes) of semen microbiome diversity across individuals with DAR (diversity-area relationship) analysis, a recent extension to classic SAR (species-area relationship) law in biogeography and ecology. Specifically, the unit of "area" is individual subject, and the microbial diversity in seminal fluid of an individual (area) is assessed via metagenomic DNA sequencing technique and measured in the Hill numbers. The DAR models were then fitted to the accrued diversity across different number of individuals (area size). We further tested the difference in DAR parameters among the healthy, subnormal, and abnormal microbiome samples in terms of their fertility status based on a cross-sectional study of a Chinese cohort. Given that no statistically significant differences in the DAR parameters were detected among the three groups, we built unified DAR models for semen microbiome by combining the healthy, subnormal, and abnormal groups. The model parameters were used to (i) estimate the microbiome diversity scaling in a population (cohort), and construct the so-termed DAR profile; (ii) predict/construct the maximal accrual diversity (MAD) profile in a population; (iii) estimate the pair-wise diversity overlap (PDO) between two individuals and construct the PDO profile; (iv) assess the ratio of individual diversity to population (RIP) accrual diversity. The last item (RIP) is a new concept we propose in this study, which is essentially a ratio of local diversity to regional or global diversity (LRD/LGD), applicable to general biodiversity investigation beyond human microbiome.}, } @article {pmid30804518, year = {2019}, author = {Monnahan, P and Kolář, F and Baduel, P and Sailer, C and Koch, J and Horvath, R and Laenen, B and Schmickl, R and Paajanen, P and Šrámková, G and Bohutínská, M and Arnold, B and Weisman, CM and Marhold, K and Slotte, T and Bomblies, K and Yant, L}, title = {Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa.}, journal = {Nature ecology & evolution}, volume = {3}, number = {3}, pages = {457-468}, doi = {10.1038/s41559-019-0807-4}, pmid = {30804518}, issn = {2397-334X}, support = {BBS/E/J/000PR9773/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/J/000PR9788/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; T32 GM008313/GM/NIGMS NIH HHS/United States ; }, mesh = {Arabidopsis/*genetics ; Evolution, Molecular ; *Gene Duplication ; *Gene Flow ; *Genome, Plant ; Metagenomics ; }, abstract = {Ploidy-variable species allow direct inference of the effects of chromosome copy number on fundamental evolutionary processes. While an abundance of theoretical work suggests polyploidy should leave distinct population genomic signatures, empirical data remains sparse. We sequenced ~300 individuals from 39 populations of Arabidopsis arenosa, a naturally diploid-autotetraploid species. We find that the impacts of polyploidy on population genomic processes are subtle yet pervasive, such as reduced efficiency of purifying selection, differences in linked selection and rampant gene flow from diploids. Initial masking of deleterious mutations, faster rates of nucleotide substitution and interploidy introgression likely conspire to shape the evolutionary potential of polyploids.}, } @article {pmid30802772, year = {2019}, author = {Liu, P and Hou, J and Zou, Y and Stephenson, SL and Huo, X and Hu, X and Li, Y}, title = {Developmental features and associated symbiont bacterial diversity in essential life cycle stages of Heterostelium colligatum.}, journal = {European journal of protistology}, volume = {68}, number = {}, pages = {99-107}, doi = {10.1016/j.ejop.2019.02.003}, pmid = {30802772}, issn = {1618-0429}, mesh = {Bacteria/classification ; *Bacterial Physiological Phenomena ; *Biodiversity ; Dictyostelium/*growth & development/*microbiology ; Life Cycle Stages/*physiology ; Symbiosis/*physiology ; }, abstract = {Dictyostelium discoideum is a specialized amoebozoan protist that can feed on, carry and disperse bacteria. However, the symbiont bacterial diversity in other species of dictyostelids and the diversity associated with essential life cycle stages are still unknown until now. Here, another species of dictyostelids, Heterostelium colligatum, a new record for tropical China, was isolated from the soil collected in Xishuangbanna Tropical Botanical Garden, Yunnan Province, China. We describe the complete life cycle of this species and illustrate details of spore-to-spore development. The symbiont bacterial diversity and relative abundance associated with life cycle stages of H. colligatum, including the aggregation, pseudoplasmodium, and sorocarp stages, were investigated by high throughput metagenomic techniques. H. colligatum appears to be capable of carrying different types of bacteria during its life history in addition to those used as a food resource. The dominant groups of those three stages in its life cycle were the Proteobacteria, Actinobacteria and Firmicutes. The relative abundance of the dominant phyla and shared OTUs were different for the aggregation, pseudoplasmodium, and sorocarp stages. A comparison of the symbiont bacterial assemblages associated with D. discoideum and H. colligatum indicated that different dictyostelid species carried different species of symbiont associated bacteria.}, } @article {pmid30799264, year = {2019}, author = {De Filippis, F and Pasolli, E and Tett, A and Tarallo, S and Naccarati, A and De Angelis, M and Neviani, E and Cocolin, L and Gobbetti, M and Segata, N and Ercolini, D}, title = {Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets.}, journal = {Cell host & microbe}, volume = {25}, number = {3}, pages = {444-453.e3}, doi = {10.1016/j.chom.2019.01.004}, pmid = {30799264}, issn = {1934-6069}, mesh = {Diet/*methods ; *Feeding Behavior ; Female ; Gastrointestinal Microbiome ; Genome, Bacterial ; Genotype ; Healthy Volunteers ; Humans ; Italy ; Male ; *Microbiota ; Phenotype ; Prevalence ; Prevotella/*classification/genetics/*isolation & purification/physiology ; }, abstract = {The role of intestinal Prevotella species in human health is controversial, with both positive and negative associations. Strain-level diversity may contribute to discrepancies in genus and species associations with health and disease. We dissected the gut metagenomes of Italians with varying dietary habits, investigating the presence of distinct Prevotella copri strains. Fiber-rich diets were linked to P. copri types with enhanced potential for carbohydrate catabolism. P. copri strains associated with an omnivore diet had a higher prevalence of the leuB gene-involved in branched-chain amino acid biosynthesis-a risk factor for glucose intolerance and type 2 diabetes. These P. copri pangenomes were compared to existing cohorts, providing evidence of distinct gene repertoires characterizing different P. copri populations, with drug metabolism and complex carbohydrate degradation significantly associated with Western and non-Western individuals, respectively. Strain-level P. copri diversity in gut microbiomes is affected by diet and should be considered when examining host-microbe associations.}, } @article {pmid30796503, year = {2020}, author = {Lebre, PH and Cowan, DA}, title = {Genomics of Alkaliphiles.}, journal = {Advances in biochemical engineering/biotechnology}, volume = {172}, number = {}, pages = {135-155}, doi = {10.1007/10_2018_83}, pmid = {30796503}, issn = {0724-6145}, mesh = {Archaea ; Bacteria ; *Extremophiles/genetics ; *Genomics ; *Microbiota ; }, abstract = {Alkalinicity presents a challenge for life due to a "reversed" proton gradient that is unfavourable to many bioenergetic processes across the membranes of microorganisms. Despite this, many bacteria, archaea, and eukaryotes, collectively termed alkaliphiles, are adapted to life in alkaline ecosystems and are of great scientific and biotechnological interest due to their niche specialization and ability to produce highly stable enzymes. Advances in next-generation sequencing technologies have propelled not only the genomic characterization of many alkaliphilic microorganisms that have been isolated from nature alkaline sources but also our understanding of the functional relationships between different taxa in microbial communities living in these ecosystems. In this review, we discuss the genetics and molecular biology of alkaliphiles from an "omics" point of view, focusing on how metagenomics and transcriptomics have contributed to our understanding of these extremophiles. Graphical Abstract.}, } @article {pmid30794590, year = {2019}, author = {Saito, K and Koido, S and Odamaki, T and Kajihara, M and Kato, K and Horiuchi, S and Adachi, S and Arakawa, H and Yoshida, S and Akasu, T and Ito, Z and Uchiyama, K and Saruta, M and Xiao, JZ and Sato, N and Ohkusa, T}, title = {Metagenomic analyses of the gut microbiota associated with colorectal adenoma.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0212406}, pmid = {30794590}, issn = {1932-6203}, mesh = {Adenoma/genetics/*microbiology ; Aged ; Bacteria/*classification/genetics/isolation & purification ; Case-Control Studies ; Colorectal Neoplasms/genetics/*microbiology ; Disease Progression ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; *Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Recent studies have suggested an association between certain members of the Fusobacterium genus, especially F. nucleatum, and the progression of advanced colorectal carcinoma (CRC). We assessed such an association of the gut microbiota in Japanese patients with colorectal adenoma (CRA) or intramucosal CRC using colonoscopy aspirates. We analyzed samples from 81 Japanese patients, including 47 CRA and 24 intramucosal CRC patients, and 10 healthy subjects. Metagenomic analysis of the V3-V4 region of the 16S ribosomal RNA gene was performed. The linear discriminant analysis (LDA) effect size (LEfSe) method was used to examine microbial dysbiosis, revealing significant differences in bacterial abundances between the healthy controls and CRA or intramucosal CRC patients. In particular, F. varium was statistically more abundant in patients with CRA and intramucosal CRC than in healthy subjects. Here, we present the metagenomic profile of CRA and intramucosal CRC and demonstrate that F. varium is at least partially involved in the pathogenesis of CRA and intramucosal CRC.}, } @article {pmid30794288, year = {2019}, author = {Banerjee, S and Alwine, JC and Wei, Z and Tian, T and Shih, N and Sperling, C and Guzzo, T and Feldman, MD and Robertson, ES}, title = {Microbiome signatures in prostate cancer.}, journal = {Carcinogenesis}, volume = {40}, number = {6}, pages = {749-764}, doi = {10.1093/carcin/bgz008}, pmid = {30794288}, issn = {1460-2180}, mesh = {Chromosomes, Human ; Cluster Analysis ; Helicobacter/isolation & purification ; Herpesvirus 8, Human/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; *Microbiota ; Nucleic Acid Hybridization ; Papillomaviridae/genetics ; Polymerase Chain Reaction/methods ; Prostatic Neoplasms/*microbiology/virology ; Reproducibility of Results ; Virus Integration ; }, abstract = {We have established a microbiome signature for prostate cancer using an array-based metagenomic and capture-sequencing approach. A diverse microbiome signature (viral, bacterial, fungal and parasitic) was observed in the prostate cancer samples compared with benign prostate hyperplasia controls. Hierarchical clustering analysis identified three distinct prostate cancer-specific microbiome signatures. The three signatures correlated with different grades, stages and scores of the cancer. Thus, microbiome signature analysis potentially provides clinical diagnosis and outcome predictions. The array data were validated by PCR and targeted next-generation sequencing (NGS). Specific NGS data suggested that certain viral genomic sequences were inserted into the host somatic chromosomes of the prostate cancer samples. A randomly selected group of these was validated by direct PCR and sequencing. In addition, PCR validation of Helicobacter showed that Helicobacter cagA sequences integrated within specific chromosomes of prostate tumor cells. The viral and Helicobacter integrations are predicted to affect the expression of several cellular genes associated with oncogenic processes.}, } @article {pmid30793504, year = {2019}, author = {Kwon, YM and Patra, AK and Chiura, HX and Kim, SJ}, title = {Production of extracellular vesicles with light-induced proton pump activity by proteorhodopsin-containing marine bacteria.}, journal = {MicrobiologyOpen}, volume = {8}, number = {8}, pages = {e00808}, pmid = {30793504}, issn = {2045-8827}, mesh = {Aquatic Organisms/*metabolism/radiation effects ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Extracellular Vesicles/*metabolism/ultrastructure ; Flavobacteriaceae/*metabolism/radiation effects ; Gene Expression Regulation, Bacterial/*radiation effects ; *Light ; Metabolic Networks and Pathways/genetics ; Microscopy, Electron, Transmission ; Phylogeny ; Proton Pumps/*metabolism ; RNA, Ribosomal, 16S/genetics ; Rhodopsins, Microbial/*metabolism ; Sequence Analysis, DNA ; }, abstract = {The production and release of extracellular vesicles (EVs) is a common process occurring in various types of bacteria. However, little is known regarding the functions of EVs derived from marine bacteria. We observed that during cell growth, Sediminicola sp. YIK13, a proteorhodopsin (PR)-containing marine flavobacterium, produces EVs (S13EVs). Transmission electron microscopy showed that Sediminicola sp. YIK13 released two spherical vesicle types, with mono- and/or bi-layered membranes, in the culture. Interestingly, the S13EVs have an orange pigment, indicating the presence of putative carotenoid and PR pigments ascribed to the parental cells. The S13EVs demonstrated the same PR-derived absorption peak spectrum and light-induced proton pump activity as the parental cells. Western blot (immunoblot) analysis of the S13EVs revealed the presence of PR. We confirmed the 16S rRNA gene, pro gene, and genes required for chromophore retinal synthesis, namely blh and crtI, in the DNA packaged into these vesicles. In addition, by metagenomic sequencing, we found microbial rhodopsin-related genes in vesicles derived from natural aquatic environments. Our results suggest that EVs as well potentially pursue horizontal gene transfer of diverse microbial rhodopsin genes in marine ecosystems.}, } @article {pmid30791436, year = {2019}, author = {Jaimes, JD and Jarosova, V and Vesely, O and Mekadim, C and Mrazek, J and Marsik, P and Killer, J and Smejkal, K and Kloucek, P and Havlik, J}, title = {Effect of Selected Stilbenoids on Human Fecal Microbiota.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {4}, pages = {}, pmid = {30791436}, issn = {1420-3049}, support = {16-07193S//Grantová Agentura České Republiky/ ; CIGA 20172031//Česká Zemědělská Univerzita v Praze/ ; }, mesh = {Feces/*microbiology ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; Humans ; Metagenome ; Metagenomics/methods ; Molecular Structure ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Stilbenes/*pharmacology ; }, abstract = {Dietary phenolics or polyphenols are mostly metabolized by the human gut microbiota. These metabolites appear to confer the beneficial health effects attributed to phenolics. Microbial composition affects the type of metabolites produced. Reciprocally, phenolics modulate microbial composition. Understanding this relationship could be used to positively impact health by phenolic supplementation and thus create favorable colonic conditions. This study explored the effect of six stilbenoids (batatasin III, oxyresveratrol, piceatannol, pinostilbene, resveratrol, thunalbene) on the gut microbiota composition. Stilbenoids were anaerobically fermented with fecal bacteria from four donors, samples were collected at 0 and 24 h, and effects on the microbiota were assessed by 16S rRNA gene sequencing. Statistical tests identified affected microbes at three taxonomic levels. Observed microbial composition modulation by stilbenoids included a decrease in the Firmicutes to Bacteroidetes ratio, a decrease in the relative abundance of strains from the genus Clostridium, and effects on the family Lachnospiraceae. A frequently observed effect was a further decrease of the relative abundance when compared to the control. An opposite effect to the control was observed for Faecalibacterium prausnitzii, whose relative abundance increased. Observed effects were more frequently attributed to resveratrol and piceatannol, followed by thunalbene and batatasin III.}, } @article {pmid30788772, year = {2019}, author = {Federici, M}, title = {Gut microbiome and microbial metabolites: a new system affecting metabolic disorders.}, journal = {Journal of endocrinological investigation}, volume = {42}, number = {9}, pages = {1011-1018}, pmid = {30788772}, issn = {1720-8386}, mesh = {*Gastrointestinal Microbiome ; Humans ; Metabolic Diseases/*etiology/metabolism/pathology ; *Metabolome ; }, abstract = {INTRODUCTION: The gut microbiome is emerging as an important player in the field of metabolic disorders.

MATERIALS AND METHODS: Currently, several studies are ongoing to determine whether the effect of gut microbiome on obesity, type 2 diabetes, non-alcoholic fatty liver disease, and other metabolic diseases is determined by singular species or rather by a functional role of bacterial metabolism at higher taxonomical level. Deciphering if a single or more species are responsible for metabolic traits or rather microbial metabolic pathways are responsible for effects on host metabolism may help to identify appropriate dietary interventions to support microbial functions according to the prevalent host disease. Furthermore, the combination of metagenomics and metabolomics-based signature might be applied in the future to improve the risk prediction in healthy subjects.

CONCLUSION: In this review, I will summarize the current findings regarding the role of gut microbiome and metabolites in metabolic disorders to argue whether the current achievements may be translated into clinical practice.}, } @article {pmid30787410, year = {2019}, author = {Shaw, LM and Blanchard, A and Chen, Q and An, X and Davies, P and Tötemeyer, S and Zhu, YG and Stekel, DJ}, title = {DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {2373}, pmid = {30787410}, issn = {2045-2322}, mesh = {Animals ; *Bacteria/classification/genetics ; Biostatistics/*methods ; China ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Genes, Bacterial/genetics ; Hoof and Claw/*microbiology ; Metagenome/genetics ; Microbiota/*genetics ; Oryza/*microbiology ; Rhizosphere ; Sewage/*microbiology ; Sheep/microbiology ; Soil Microbiology ; United Kingdom ; United States ; }, abstract = {High throughput genomics technologies are applied widely to microbiomes in humans, animals, soil and water, to detect changes in bacterial communities or the genes they carry, between different environments or treatments. We describe a method to test the statistical significance of differences in bacterial population or gene composition, applicable to metagenomic or quantitative polymerase chain reaction data. Our method goes beyond previous published work in being universally most powerful, thus better able to detect statistically significant differences, and through being more reliable for smaller sample sizes. It can also be used for experimental design, to estimate how many samples to use in future experiments, again with the advantage of being universally most powerful. We present three example analyses in the area of antimicrobial resistance. The first is to published data on bacterial communities and antimicrobial resistance genes (ARGs) in the environment; we show that there are significant changes in both ARG and community composition. The second is to new data on seasonality in bacterial communities and ARGs in hooves from four sheep. While the observed differences are not significant, we show that a minimum group size of eight sheep would provide sufficient power to observe significance of similar changes in further experiments. The third is to published data on bacterial communities surrounding rice crops. This is a much larger data set and is used to verify the new method. Our method has broad uses for statistical testing and experimental design in research on changing microbiomes, including studies on antimicrobial resistance.}, } @article {pmid30787169, year = {2019}, author = {Leung, DYM and Calatroni, A and Zaramela, LS and LeBeau, PK and Dyjack, N and Brar, K and David, G and Johnson, K and Leung, S and Ramirez-Gama, M and Liang, B and Rios, C and Montgomery, MT and Richers, BN and Hall, CF and Norquest, KA and Jung, J and Bronova, I and Kreimer, S and Talbot, CC and Crumrine, D and Cole, RN and Elias, P and Zengler, K and Seibold, MA and Berdyshev, E and Goleva, E}, title = {The nonlesional skin surface distinguishes atopic dermatitis with food allergy as a unique endotype.}, journal = {Science translational medicine}, volume = {11}, number = {480}, pages = {}, pmid = {30787169}, issn = {1946-6242}, support = {R01 AR041256/AR/NIAMS NIH HHS/United States ; U01 AI147462/AI/NIAID NIH HHS/United States ; R01 HL135156/HL/NHLBI NIH HHS/United States ; U19 AI117673/AI/NIAID NIH HHS/United States ; R01 HL128439/HL/NHLBI NIH HHS/United States ; U01 AI178756/AI/NIAID NIH HHS/United States ; UL1 TR002535/TR/NCATS NIH HHS/United States ; UM2 AI117870/AI/NIAID NIH HHS/United States ; P01 HL132821/HL/NHLBI NIH HHS/United States ; R01 MD010443/MD/NIMHD NIH HHS/United States ; }, mesh = {Adolescent ; Area Under Curve ; Child ; Child, Preschool ; Dendritic Cells/metabolism ; Dermatitis, Atopic/*diagnosis/pathology ; Epidermis/metabolism ; Filaggrin Proteins ; Food Hypersensitivity/*diagnosis/pathology ; Humans ; Intermediate Filament Proteins/metabolism ; Keratins/metabolism ; Lipids/analysis ; Microbiota ; Skin/microbiology/*pathology ; Surgical Tape ; Transcriptome/genetics ; Water Loss, Insensible ; }, abstract = {Skin barrier dysfunction has been reported in both atopic dermatitis (AD) and food allergy (FA). However, only one-third of patients with AD have FA. The purpose of this study was to use a minimally invasive skin tape strip sampling method and a multiomics approach to determine whether children with AD and FA (AD FA+) have stratum corneum (SC) abnormalities that distinguish them from AD without FA (AD FA-) and nonatopic (NA) controls. Transepidermal water loss was found to be increased in AD FA+. Filaggrin and the proportion of ω-hydroxy fatty acid sphingosine ceramide content in nonlesional skin of children with AD FA+ were substantially lower than in AD FA- and NA skin. These abnormalities correlated with morphologic changes in epidermal lamellar bilayer architecture responsible for barrier homeostasis. Shotgun metagenomic studies revealed that the nonlesional skin of AD FA+ had increased abundance of Staphylococcus aureus compared to NA. Increased expression of keratins 5, 14, and 16 indicative of hyperproliferative keratinocytes was observed in the SC of AD FA+. The skin transcriptome of AD FA+ had increased gene expression for dendritic cells and type 2 immune pathways. A network analysis revealed keratins 5, 14, and 16 were positively correlated with AD FA+, whereas filaggrin breakdown products were negatively correlated with AD FA+. These data suggest that the most superficial compartment of nonlesional skin in AD FA+ has unique properties associated with an immature skin barrier and type 2 immune activation.}, } @article {pmid30784601, year = {2019}, author = {Nelson, MT and Pope, CE and Marsh, RL and Wolter, DJ and Weiss, EJ and Hager, KR and Vo, AT and Brittnacher, MJ and Radey, MC and Hayden, HS and Eng, A and Miller, SI and Borenstein, E and Hoffman, LR}, title = {Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles.}, journal = {Cell reports}, volume = {26}, number = {8}, pages = {2227-2240.e5}, pmid = {30784601}, issn = {2211-1247}, support = {K24 HL141669/HL/NHLBI NIH HHS/United States ; P30 DK089507/DK/NIDDK NIH HHS/United States ; T32 AI055396/AI/NIAID NIH HHS/United States ; T32 GM007266/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Infections/diagnosis/*microbiology ; DNA Barcoding, Taxonomic/*methods ; Humans ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; Molecular Diagnostic Techniques/methods ; Respiratory Mucosa/metabolism/microbiology ; Sputum/*microbiology ; }, abstract = {Metagenomic sequencing is a promising approach for identifying and characterizing organisms and their functional characteristics in complex, polymicrobial infections, such as airway infections in people with cystic fibrosis. These analyses are often hampered, however, by overwhelming quantities of human DNA, yielding only a small proportion of microbial reads for analysis. In addition, many abundant microbes in respiratory samples can produce large quantities of extracellular bacterial DNA originating either from biofilms or dead cells. We describe a method for simultaneously depleting DNA from intact human cells and extracellular DNA (human and bacterial) in sputum, using selective lysis of eukaryotic cells and endonuclease digestion. We show that this method increases microbial sequencing depth and, consequently, both the number of taxa detected and coverage of individual genes such as those involved in antibiotic resistance. This finding underscores the substantial impact of DNA from sources other than live bacteria in microbiological analyses of complex, chronic infection specimens.}, } @article {pmid30784035, year = {2019}, author = {Leavitt, J and Saleh, N}, title = {The Microbiome and Colorectal Cancer: Current Clinical Trials.}, journal = {Oncology (Williston Park, N.Y.)}, volume = {33}, number = {2}, pages = {78}, pmid = {30784035}, issn = {0890-9091}, mesh = {Bile Acids and Salts/metabolism ; Colorectal Neoplasms/*microbiology/mortality/therapy ; Colorectal Neoplasms, Hereditary Nonpolyposis/microbiology ; Dietary Fiber/administration & dosage ; Fatty Acids, Omega-3/administration & dosage ; Gastrointestinal Microbiome/*physiology ; Humans ; Metagenomics ; Sulfur/metabolism ; }, } @article {pmid30783153, year = {2019}, author = {Maccario, L and Carpenter, SD and Deming, JW and Vogel, TM and Larose, C}, title = {Sources and selection of snow-specific microbial communities in a Greenlandic sea ice snow cover.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {2290}, pmid = {30783153}, issn = {2045-2322}, mesh = {Alteromonadaceae/physiology ; Arctic Regions ; Climate ; Ecosystem ; Greenland ; *Ice Cover ; Microbiota/physiology ; *Snow ; }, abstract = {Sea ice and its snow cover are critical for global processes including climate regulation and biogeochemical cycles. Despite an increase in studies focused on snow microorganisms, the ecology of snow inhabitants remains unclear. In this study, we investigated sources and selection of a snowpack-specific microbial community by comparing metagenomes from samples collected in a Greenlandic fjord within a vertical profile including atmosphere, snowpack with four distinct layers of snow, sea ice brine and seawater. Microbial communities in all snow layers derived from mixed sources, both marine and terrestrial, and were more similar to atmospheric communities than to sea ice or seawater communities. The surface snow metagenomes were characterized by the occurrence of genes involved in photochemical stress resistance, primary production and metabolism of diverse carbon sources. The basal saline snow layer that was in direct contact with the sea ice surface harbored a higher abundance of cells than the overlying snow layers, with a predominance of Alteromonadales and a higher relative abundance of marine representatives. However, the overall taxonomic structure of the saline layer was more similar to that of other snow layers and the atmosphere than to underlying sea ice and seawater. The expulsion of relatively nutrient-rich sea ice brine into basal snow might have stimulated the growth of copiotrophic psychro- and halotolerant snow members. Our study indicates that the size, composition and function of snowpack microbial communities over sea ice were influenced primarily by atmospheric deposition and inflow of sea ice brine and that they form a snow-specific assemblage reflecting the particular environmental conditions of the snowpack habitat.}, } @article {pmid30782660, year = {2019}, author = {López-Pérez, M and Jayakumar, JM and Haro-Moreno, JM and Zaragoza-Solas, A and Reddi, G and Rodriguez-Valera, F and Shapiro, OH and Alam, M and Almagro-Moreno, S}, title = {Evolutionary Model of Cluster Divergence of the Emergent Marine Pathogen Vibrio vulnificus: From Genotype to Ecotype.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, pmid = {30782660}, issn = {2150-7511}, mesh = {Aquaculture ; Aquatic Organisms/microbiology ; Cluster Analysis ; Computational Biology ; *Ecotype ; Evolution, Molecular ; Gene Flow ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial ; *Genotype ; Phenotype ; Recombination, Genetic ; Vibrio vulnificus/*classification/*genetics/isolation & purification/physiology ; }, abstract = {Vibrio vulnificus, an opportunistic pathogen, is the causative agent of a life-threatening septicemia and a rising problem for aquaculture worldwide. The genetic factors that differentiate its clinical and environmental strains remain enigmatic. Furthermore, clinical strains have emerged from every clade of V. vulnificus In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species from an evolutionary and ecological point of view. Genome comparisons and bioinformatic analyses of 113 V. vulnificus isolates indicate that the population of V. vulnificus is made up of four different clusters. We found evidence that recombination and gene flow between the two largest clusters (cluster 1 [C1] and C2) have drastically decreased to the point where they are diverging independently. Pangenome and phenotypic analyses showed two markedly different lifestyles for these two clusters, indicating commensal (C2) and bloomer (C1) ecotypes, with differences in carbohydrate utilization, defense systems, and chemotaxis, among other characteristics. Nonetheless, we identified frequent intra- and interspecies exchange of mobile genetic elements (e.g., antibiotic resistance plasmids, novel "chromids," or two different and concurrent type VI secretion systems) that provide high levels of genetic diversity in the population. Surprisingly, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together. We propose an evolutionary model of V. vulnificus that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections and emergence.IMPORTANCEVibrio vulnificus is an emergent marine pathogen and is the cause of a deadly septicemia. However, the genetic factors that differentiate its clinical and environmental strains and its several biotypes remain mostly enigmatic. In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species to elucidate the traits that make these strains emerge as a human pathogen. The acquisition of different ecological determinants could have allowed the development of highly divergent clusters with different lifestyles within the same environment. However, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together, posing a potential risk of recombination and of emergence of novel variants. We propose a new evolutionary model that provides a perspective that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections.}, } @article {pmid30782659, year = {2019}, author = {Klein, C and Gonzalez, D and Samwel, K and Kahesa, C and Mwaiselage, J and Aluthge, N and Fernando, S and West, JT and Wood, C and Angeletti, PC}, title = {Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, pmid = {30782659}, issn = {2150-7511}, support = {U54 CA190155/CA/NCI NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics ; Cervix Uteri/*microbiology/*pathology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; HIV Infections/*complications ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; *Microbiota ; Phylogeny ; Precancerous Conditions/*epidemiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tanzania/epidemiology ; Uterine Cervical Neoplasms/*epidemiology ; }, abstract = {Nearly all cervical cancers are causally associated with human papillomavirus (HPV). The burden of HPV-associated dysplasias in sub-Saharan Africa is influenced by HIV. To investigate the role of the bacterial microbiome in cervical dysplasia, cytobrush samples were collected directly from cervical lesions of 144 Tanzanian women. The V4 hypervariable region of the 16S rRNA gene was amplified and deep sequenced. Alpha diversity metrics (Chao1, PD whole tree, and operational taxonomic unit [OTU] estimates) displayed significantly higher bacterial richness in HIV-positive patients (P = 0.01) than in HIV-negative patients. In HIV-positive patients, there was higher bacterial richness in patients with high-grade squamous intraepithelial lesions (HSIL) (P = 0.13) than those without lesions. The most abundant OTUs associated with high-grade squamous intraepithelial lesions were Mycoplasmatales, Pseudomonadales, and Staphylococcus We suggest that a chronic mycoplasma infection of the cervix may contribute to HPV-dependent dysplasia by sustained inflammatory signals.IMPORTANCE HPV is known to be the causal agent in the majority of cervical cancers. However, the role of the cervical bacterial microbiome in cervical cancer is not clear. To investigate that possibility, we collected cervical cytobrush samples from 144 Tanzanian women and performed deep sequencing of bacterial 16S rRNA genes. We found that HIV-positive patients had greater bacterial richness (P = 0.01) than HIV-negative patients. We also observed that women with high-grade squamous intraepithelial lesions (HSIL) had greater cervical bacterial diversity than women with cytologically normal cervices. Data from our precise sampling of cervical lesions leads us to propose that Mycoplasma contributes to a cervical microbiome status that promotes HPV-related cervical lesions. These results suggest a greater influence of the bacterial microbiota on the outcome of HPV infection than previously thought.}, } @article {pmid30782206, year = {2019}, author = {Lagkouvardos, I and Lesker, TR and Hitch, TCA and Gálvez, EJC and Smit, N and Neuhaus, K and Wang, J and Baines, JF and Abt, B and Stecher, B and Overmann, J and Strowig, T and Clavel, T}, title = {Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {28}, pmid = {30782206}, issn = {2049-2618}, mesh = {Animals ; Bacteriological Techniques/*methods ; Bacteroides/*classification/genetics/growth & development ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Gastrointestinal Microbiome ; Metagenomics/*methods ; Mice ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: Bacteria within family S24-7 (phylum Bacteroidetes) are dominant in the mouse gut microbiota and detected in the intestine of other animals. Because they had not been cultured until recently and the family classification is still ambiguous, interaction with their host was difficult to study and confusion still exists regarding sequence data annotation.

METHODS: We investigated family S24-7 by combining data from large-scale 16S rRNA gene analysis and from functional and taxonomic studies of metagenomic and cultured species.

RESULTS: A total of 685 species was inferred by full-length 16S rRNA gene sequence clustering. While many species could not be assigned ecological habitats (93,045 samples analyzed), the mouse was the most commonly identified host (average of 20% relative abundance and nine co-occurring species). Shotgun metagenomics allowed reconstruction of 59 molecular species, of which 34 were representative of the 16S rRNA gene-derived species clusters. In addition, cultivation efforts allowed isolating five strains representing three species, including two novel taxa. Genome analysis revealed that S24-7 spp. are functionally distinct from neighboring families and versatile with respect to complex carbohydrate degradation.

CONCLUSIONS: We provide novel data on the diversity, ecology, and description of bacterial family S24-7, for which the name Muribaculaceae is proposed.}, } @article {pmid30779309, year = {2019}, author = {Braukmann, TWA and Ivanova, NV and Prosser, SWJ and Elbrecht, V and Steinke, D and Ratnasingham, S and de Waard, JR and Sones, JE and Zakharov, EV and Hebert, PDN}, title = {Metabarcoding a diverse arthropod mock community.}, journal = {Molecular ecology resources}, volume = {19}, number = {3}, pages = {711-727}, pmid = {30779309}, issn = {1755-0998}, support = {//Ministry of Research, Innovation and Science/ ; }, mesh = {Animals ; Arthropods/*classification/*genetics ; DNA/chemistry/genetics/*isolation & purification ; DNA Barcoding, Taxonomic/*methods ; *Metagenome ; Models, Theoretical ; Sequence Analysis, DNA ; }, abstract = {Although DNA metabarcoding is an attractive approach for monitoring biodiversity, it is often difficult to detect all the species present in a bulk sample. In particular, sequence recovery for a given species depends on its biomass and mitome copy number as well as the primer set employed for PCR. To examine these variables, we constructed a mock community of terrestrial arthropods comprised of 374 species. We used this community to examine how species recovery was impacted when amplicon pools were constructed in four ways. The first two protocols involved the construction of bulk DNA extracts from different body segments (Bulk Abdomen, Bulk Leg). The other protocols involved the production of DNA extracts from single legs which were then merged prior to PCR (Composite Leg) or PCR-amplified separately (Single Leg) and then pooled. The amplicons generated by these four treatments were then sequenced on three platforms (Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5). The choice of sequencing platform did not substantially influence species recovery, although the Miseq delivered the highest sequence quality. As expected, species recovery was most efficient from the Single Leg treatment because amplicon abundance varied little among taxa. Among the three treatments where PCR occurred after pooling, the Bulk Abdomen treatment produced a more uniform read abundance than the Bulk Leg or Composite Leg treatment. Primer choice also influenced species recovery and evenness. Our results reveal how variation in protocols can have substantial impacts on perceived diversity unless sequencing coverage is sufficient to reach an asymptote.}, } @article {pmid30779273, year = {2019}, author = {Chekanov, K and Kublanovskaya, A and Lobakova, E}, title = {Eukaryotic Sequences in the 16SrRNA Metagenomic Dataset of Algal-bacterial Consortia of the White Sea Coastal Zone.}, journal = {The Journal of eukaryotic microbiology}, volume = {66}, number = {5}, pages = {853-856}, doi = {10.1111/jeu.12722}, pmid = {30779273}, issn = {1550-7408}, mesh = {Bacteria/classification/*genetics/isolation & purification ; DNA, Ribosomal/genetics ; Databases, Genetic ; Eukaryota/classification/genetics/*isolation & purification ; Metagenome ; Microalgae/microbiology/parasitology ; Microbial Consortia ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The libraries of bacterial 16SrRNA gene fragment from algal-bacterial consortia of the White Sea coastal zone are analyzed. Up to 3% of the reads have revealed to correspond to eukaryotic rRNA. They related to following main eukaryotic clades: Discoba, Stramenopiles, Ciliata, Amoebozoa, and Nucletmycea. Amoebae, especially Vermamoeba, were present in all samples. In one sample, heterolobose amoeba Paravahlkampfia was detected. These microorganisms are parasites of microalgae, which can induce significant damage to industrial cultures. However, the data on their physiology and distribution are scarce. This study provides new evidence about the diversity of herbivorous eukaryotic microorganisms in natural algal-containing consortia.}, } @article {pmid30778224, year = {2019}, author = {Sanna, S and van Zuydam, NR and Mahajan, A and Kurilshikov, A and Vich Vila, A and Võsa, U and Mujagic, Z and Masclee, AAM and Jonkers, DMAE and Oosting, M and Joosten, LAB and Netea, MG and Franke, L and Zhernakova, A and Fu, J and Wijmenga, C and McCarthy, MI}, title = {Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases.}, journal = {Nature genetics}, volume = {51}, number = {4}, pages = {600-605}, pmid = {30778224}, issn = {1546-1718}, support = {/WT_/Wellcome Trust/United Kingdom ; U01 DK105535/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Diabetes Mellitus, Type 2/genetics ; Fatty Acids, Volatile/*genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Genotype ; Glucose Tolerance Test/methods ; Humans ; Male ; Metabolic Diseases/*genetics ; Middle Aged ; Netherlands ; Young Adult ; }, abstract = {Microbiome-wide association studies on large population cohorts have highlighted associations between the gut microbiome and complex traits, including type 2 diabetes (T2D) and obesity[1]. However, the causal relationships remain largely unresolved. We leveraged information from 952 normoglycemic individuals for whom genome-wide genotyping, gut metagenomic sequence and fecal short-chain fatty acid (SCFA) levels were available[2], then combined this information with genome-wide-association summary statistics for 17 metabolic and anthropometric traits. Using bidirectional Mendelian randomization (MR) analyses to assess causality[3], we found that the host-genetic-driven increase in gut production of the SCFA butyrate was associated with improved insulin response after an oral glucose-tolerance test (P = 9.8 × 10[-5]), whereas abnormalities in the production or absorption of another SCFA, propionate, were causally related to an increased risk of T2D (P = 0.004). These data provide evidence of a causal effect of the gut microbiome on metabolic traits and support the use of MR as a means to elucidate causal relationships from microbiome-wide association findings.}, } @article {pmid30778155, year = {2019}, author = {Ata, B and Yildiz, S and Turkgeldi, E and Brocal, VP and Dinleyici, EC and Moya, A and Urman, B}, title = {The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {2204}, pmid = {30778155}, issn = {2045-2322}, mesh = {Adult ; Case-Control Studies ; Cervix Uteri/*microbiology ; Endometriosis/*diagnosis/etiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Severity of Illness Index ; Vagina/*microbiology ; Young Adult ; }, abstract = {Dysbiosis in the genital tract or gut microbiome can be associated with endometriosis. We sampled vaginal, cervical and gut microbiota from 14 women with histology proven stage 3/4 endometriosis and 14 healthy controls. The V3 and V4 regions of the 16S rRNA gene were amplified following the 16S Metagenomic Sequencing Library Preparation. Despite overall similar vaginal, cervical and intestinal microbiota composition between stage 3/4 endometriosis group and controls, we observed differences at genus level. The complete absence of Atopobium in the vaginal and cervical microbiota of the stage 3/4 endometriosis group was noteworthy. In the cervical microbiota, Gardnerella, Streptococcus, Escherichia, Shigella, and Ureoplasma, all of which contain potentially pathogenic species, were increased in stage 3/4 endometriosis. More women in the stage 3/4 endometriosis group had Shigella/Escherichia dominant stool microbiome. Further studies can clarify whether the association is causal, and whether dysbiosis leads to endometriosis or endometriosis leads to dysbiosis.}, } @article {pmid30777011, year = {2019}, author = {Feng, Y and Ramnarine, VR and Bell, R and Volik, S and Davicioni, E and Hayes, VM and Ren, S and Collins, CC}, title = {Metagenomic and metatranscriptomic analysis of human prostate microbiota from patients with prostate cancer.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {146}, pmid = {30777011}, issn = {1471-2164}, support = {CSC201606325044//China Scholarship Council/ ; 201012TFF//Terry Fox Foundation/ ; T2013-01//Prostate Cancer Canada/ ; 81472397//National Natural Science Foundation of China/ ; }, mesh = {Aged ; Biodiversity ; Computational Biology/methods ; Humans ; Kaplan-Meier Estimate ; Male ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; Prostate/*microbiology/pathology ; Prostatic Neoplasms/*etiology/metabolism/mortality/pathology ; }, abstract = {BACKGROUND: Prostate cancer (PCa) is the most common malignant neoplasm among men in many countries. Since most precancerous and cancerous tissues show signs of inflammation, chronic bacterial prostatitis has been hypothesized to be a possible etiology. However, establishing a causal relationship between microbial inflammation and PCa requires a comprehensive analysis of the prostate microbiome. The aim of this study was to characterize the microbiome in prostate tissue of PCa patients and investigate its association with tumour clinical characteristics as well as host expression profiles.

RESULTS: The metagenome and metatranscriptome of tumour and the adjacent benign tissues were assessed in 65 Chinese radical prostatectomy specimens. Escherichia, Propionibacterium, Acinetobacter and Pseudomonas were abundant in both metagenome and metatranscriptome, thus constituting the core of the prostate microbiome. The biodiversity of the microbiomes could not be differentiated between the matched tumour/benign specimens or between the tumour specimens of low and high Gleason Scores. The expression profile of ten Pseudomonas genes was strongly correlated with that of eight host small RNA genes; three of the RNA genes may negatively associate with metastasis. Few viruses could be identified from the prostate microbiomes.

CONCLUSIONS: This is the first study of the human prostate microbiome employing an integrated metagenomics and metatranscriptomics approach. In this Chinese cohort, both metagenome and metatranscriptome analyses showed a non-sterile microenvironment in the prostate of PCa patients, but we did not find links between the microbiome and local progression of PCa. However, the correlated expression of Pseudomonas genes and human small RNA genes may provide tantalizing preliminary evidence that Pseudomonas infection may impede metastasis.}, } @article {pmid30774969, year = {2019}, author = {Santillan, E and Seshan, H and Constancias, F and Drautz-Moses, DI and Wuertz, S}, title = {Frequency of disturbance alters diversity, function, and underlying assembly mechanisms of complex bacterial communities.}, journal = {NPJ biofilms and microbiomes}, volume = {5}, number = {1}, pages = {8}, pmid = {30774969}, issn = {2055-5008}, mesh = {Bioreactors/*microbiology ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; *Environmental Exposure ; Environmental Pollutants/*toxicity ; Metagenome ; Microbiota/*drug effects ; Models, Theoretical ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; }, abstract = {Disturbance is known to affect the ecosystem structure, but predicting its outcomes remains elusive. Similarly, community diversity is believed to relate to ecosystem functions, yet the underlying mechanisms are poorly understood. Here, we tested the effect of disturbance on the structure, assembly, and ecosystem function of complex microbial communities within an engineered system. We carried out a microcosm experiment where activated sludge bioreactors operated in daily cycles were subjected to eight different frequency levels of augmentation with a toxic pollutant, from never (undisturbed) to every day (press-disturbed), for 35 days. Microbial communities were assessed by combining distance-based methods, general linear multivariate models, α-diversity indices, and null model analyses on metagenomics and 16S rRNA gene amplicon data. A stronger temporal decrease in α-diversity at the extreme, undisturbed and press-disturbed, ends of the disturbance range led to a hump-backed pattern, with the highest diversity found at intermediate levels of disturbance. Undisturbed and press-disturbed levels displayed the highest community and functional similarity across replicates, suggesting deterministic processes were dominating. The opposite was observed amongst intermediately disturbed levels, indicating stronger stochastic assembly mechanisms. Trade-offs were observed in the ecosystem function between organic carbon removal and both nitrification and biomass productivity, as well as between diversity and these functions. Hence, not every ecosystem function was favoured by higher community diversity. Our results show that the assessment of changes in diversity, along with the underlying stochastic-deterministic assembly processes, is essential to understanding the impact of disturbance in complex microbial communities.}, } @article {pmid30774010, year = {2019}, author = {Umiker, B and Lee, HH and Cope, J and Ajami, NJ and Laine, JP and Fregeau, C and Ferguson, H and Alves, SE and Sciammetta, N and Kleinschek, M and Salmon, M}, title = {The NLRP3 inflammasome mediates DSS-induced intestinal inflammation in Nod2 knockout mice.}, journal = {Innate immunity}, volume = {25}, number = {2}, pages = {132-143}, pmid = {30774010}, issn = {1753-4267}, mesh = {Animals ; Colitis/chemically induced/*immunology ; Crohn Disease/*immunology ; Dextran Sulfate ; Disease Models, Animal ; Furans/administration & dosage/pharmacology ; Gastrointestinal Microbiome/*immunology ; Heterocyclic Compounds, 4 or More Rings ; Humans ; Indenes ; Inflammasomes/*metabolism ; Interleukin-1beta/metabolism ; Intestinal Mucosa/*immunology ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; NLR Family, Pyrin Domain-Containing 3 Protein/antagonists & inhibitors/*metabolism ; Nod2 Signaling Adaptor Protein/*genetics ; Signal Transduction ; Sulfonamides/administration & dosage/pharmacology ; Sulfones ; }, abstract = {Crohn's disease (CD) is a chronic disorder of the gastrointestinal tract characterized by inflammation and intestinal epithelial injury. Loss of function mutations in the intracellular bacterial sensor NOD2 are major risk factors for the development of CD. In the absence of robust bacterial recognition by NOD2 an inflammatory cascade is initiated through alternative PRRs leading to CD. In the present study, MCC950, a specific small molecule inhibitor of NLR pyrin domain-containing protein 3 (NLRP3), abrogated dextran sodium sulfate (DSS)-induced intestinal inflammation in Nod2[-/-] mice. NLRP3 inflammasome formation was observed at a higher rate in NOD2-deficient small intestinal lamina propria cells after insult by DSS. NLRP3 complex formation led to an increase in IL-1β secretion in both the small intestine and colon of Nod2ko mice. This increase in IL-1β secretion in the intestine was attenuated by MCC950 leading to decreased disease severity in Nod2ko mice. Our work suggests that NLRP3 inflammasome activation may be a key driver of intestinal inflammation in the absence of functional NOD2. NLRP3 pathway inhibition can prevent intestinal inflammation in the absence of robust NOD2 signaling.}, } @article {pmid30773302, year = {2019}, author = {Sasaki, H and Kawamura, K and Kawamura, T and Odamaki, T and Katsumata, N and Xiao, JZ and Suzuki, N and Tanaka, M}, title = {Distinctive subpopulations of the intestinal microbiota are present in women with unexplained chronic anovulation.}, journal = {Reproductive biomedicine online}, volume = {38}, number = {4}, pages = {570-578}, doi = {10.1016/j.rbmo.2018.12.026}, pmid = {30773302}, issn = {1472-6491}, mesh = {Adolescent ; Adult ; Anovulation/*microbiology/*physiopathology ; Clostridiales ; Dysbiosis/physiopathology ; Feces ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Menstrual Cycle ; Ovary/microbiology/physiology ; Ovulation ; Prevotella ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Ruminococcus ; Young Adult ; }, abstract = {RESEARCH QUESTION: Do gut microbiota associate with the ovulatory cycle in women showing normogonadotrophic anovulation? In humans, the gut microbiota affects diverse physiological functions and dysbiosis (microbial imbalance) may lead to pathological syndromes. However, there is comparatively little information on the relevance of gut microbiota to reproductive functions in women. Here, a group of women with idiopathic chronic anovulation were examined, who do not exhibit any apparent endocrinological disorder, as they are suitable for investigating the relationship between intestinal bacteria and ovulatory disorders.

DESIGN: A prospective observational cohort study was performed on two groups of women who did not exhibit apparent endocrinological disorders but showed either irregular menstrual cycles (IMC group) or normal menstrual cycles (controls). The bacterial composition of faeces from rectal swabs from the women was analysed using next-generation sequencing based on bacterial 16SrRNA genes.

RESULTS: A metagenomic analysis indicated that the two groups of women had significant differences in 28 bacterial taxa in their faeces. Prevotella-enriched microbiomes were more abundant in the IMC group, whereas Clostridiales, Ruminococcus and Lachnospiraceae (butyrate-producing bacteria) were present at lower levels in the IMC group.

CONCLUSIONS: Distinctive subpopulations of intestinal microbiota were identified in women with unexplained chronic anovulation. The results indicate that gut microbiota could be associated with ovarian functions.}, } @article {pmid30773139, year = {2019}, author = {Sáenz, JS and Marques, TV and Barone, RSC and Cyrino, JEP and Kublik, S and Nesme, J and Schloter, M and Rath, S and Vestergaard, G}, title = {Oral administration of antibiotics increased the potential mobility of bacterial resistance genes in the gut of the fish Piaractus mesopotamicus.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {24}, pmid = {30773139}, issn = {2049-2618}, mesh = {Administration, Oral ; Animals ; Anti-Bacterial Agents/*administration & dosage/adverse effects ; Aquaculture ; Bacteria/*classification/drug effects/genetics ; Bacterial Proteins/genetics ; Biodiversity ; Characiformes/*microbiology ; *Drug Resistance, Bacterial ; Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Phylogeny ; Thiamphenicol/administration & dosage/adverse effects/*analogs & derivatives ; }, abstract = {BACKGROUND: Aquaculture is on the rise worldwide, and the use of antibiotics is fostering higher production intensity. However, recent findings suggest that the use of antibiotics comes at the price of increased antibiotic resistance. Yet, the effect of the oral administration of antibiotics on the mobility of microbial resistance genes in the fish gut is not well understood. In the present study, Piaractus mesopotamicus was used as a model to evaluate the effect of the antimicrobial florfenicol on the diversity of the gut microbiome as well as antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) using a metagenomic approach.

RESULTS: The total relative abundance of ARGs and MGEs significantly increased during the antibiotic exposure. Additionally, phage integrases, transposases, and transposons flanking ARGs accumulated in the gut microbiome of P. mesopotamicus because of the antibiotic exposure. MGEs co-occurring with ARGs showed a significant positive correlation with the total ARGs found. Furthermore, shifts in the gut microbiome towards well-known putative pathogens such as Salmonella, Plesiomonas, and Citrobacter were observed following florfenicol treatment. Mainly Plesiomonas and Citrobacter harbored genes that code for multidrug and phenicol efflux pumps. Moreover, several genes related to RNA processing and modification, cell motility, SOS response, and extracellular structure were enriched due to the antibiotic application. The observed effects were visible during the complete application phase and disappeared at the post-exposure phase.

CONCLUSIONS: Our findings suggest that the oral administration of antibiotics increases the potential for MGE-mediated exchange of ARGs in the gut of fish and could contribute to the enrichment and dispersion of ARGs in aquaculture systems. Importantly, this increase in the potential for ARGs exchange could be an effect of changes in community structure and/or ARG mobilization.}, } @article {pmid30771735, year = {2019}, author = {Petersen, C and Wankhade, UD and Bharat, D and Wong, K and Mueller, JE and Chintapalli, SV and Piccolo, BD and Jalili, T and Jia, Z and Symons, JD and Shankar, K and Anandh Babu, PV}, title = {Dietary supplementation with strawberry induces marked changes in the composition and functional potential of the gut microbiome in diabetic mice.}, journal = {The Journal of nutritional biochemistry}, volume = {66}, number = {}, pages = {63-69}, pmid = {30771735}, issn = {1873-4847}, support = {R01 HL141540/HL/NHLBI NIH HHS/United States ; R03 AG052848/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Diabetes Mellitus, Experimental/diet therapy/*microbiology ; Dietary Supplements ; *Fragaria ; Gastrointestinal Microbiome/*physiology ; Male ; Metabolic Networks and Pathways ; Mice, Inbred C57BL ; Mice, Mutant Strains ; Receptors, Leptin/genetics ; }, abstract = {Gut microbiota contributes to the biological activities of berry anthocyanins by transforming them into bioactive metabolites, and anthocyanins support the growth of specific bacteria, indicating a two-way relationship between anthocyanins and microbiota. In the present study, we tested the hypothesis that strawberry supplementation alters gut microbial ecology in diabetic db/db mice. Control (db/+) and diabetic (db/db) mice (7 weeks old) consumed standard diet or diet supplemented with 2.35% freeze-dried strawberry (db/db + SB) for 10 weeks. Colon contents were used to isolate bacterial DNA. V4 variable region of 16S rRNA gene was amplified. Data analyses were performed using standardized pipelines (QIIME 1.9 and R packages). Differences in predictive metagenomics function were identified by PICRUSt. Principal coordinate analyses confirmed that the microbial composition was significantly influenced by both host genotype and strawberry consumption. Further, α-diversity indices and β-diversity were different at the phylum and genus levels, and genus and operational taxonomical units levels, respectively (P<.05). At the phylum level, strawberry supplementation decreased the abundance of Verrucomicrobia in db/db + SB vs. db/db mice (P<.05). At the genus level, db/db mice exhibited a decrease in the abundance of Bifidobacterium, and strawberry supplementation increased Bifidobacterium in db/db + SB vs. db/db mice (P<.05). PICRUSt revealed significant differences in 45 predicted metabolic functions among the 3 groups. Our study provides evidence for marked changes in the composition and functional potential of the gut microbiome with strawberry supplementation in diabetic mice. Importantly, strawberry supplementation increased the abundance of beneficial bacteria Bifidobacterium which play a pivotal role in the metabolism of anthocyanins.}, } @article {pmid30770850, year = {2019}, author = {Kouchaki, S and Tapinos, A and Robertson, DL}, title = {A signal processing method for alignment-free metagenomic binning: multi-resolution genomic binary patterns.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {2159}, pmid = {30770850}, issn = {2045-2322}, support = {MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; BB/M001121/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 555 (MC_UU_1201412)//RCUK | Medical Research Council (MRC)/International ; }, mesh = {Algorithms ; Bacteria/*classification/*genetics ; Computational Biology/*methods ; Gastrointestinal Microbiome ; Metagenomics/*methods ; Microbiota ; *Sequence Homology, Nucleic Acid ; }, abstract = {Algorithms in bioinformatics use textual representations of genetic information, sequences of the characters A, T, G and C represented computationally as strings or sub-strings. Signal and related image processing methods offer a rich source of alternative descriptors as they are designed to work in the presence of noisy data without the need for exact matching. Here we introduce a method, multi-resolution local binary patterns (MLBP) adapted from image processing to extract local 'texture' changes from nucleotide sequence data. We apply this feature space to the alignment-free binning of metagenomic data. The effectiveness of MLBP is demonstrated using both simulated and real human gut microbial communities. Sequence reads or contigs can be represented as vectors and their 'texture' compared efficiently using machine learning algorithms to perform dimensionality reduction to capture eigengenome information and perform clustering (here using randomized singular value decomposition and BH-tSNE). The intuition behind our method is the MLBP feature vectors permit sequence comparisons without the need for explicit pairwise matching. We demonstrate this approach outperforms existing methods based on k-mer frequencies. The signal processing method, MLBP, thus offers a viable alternative feature space to textual representations of sequence data. The source code for our Multi-resolution Genomic Binary Patterns method can be found at https://github.com/skouchaki/MrGBP .}, } @article {pmid30765765, year = {2019}, author = {Singhal, M and Turturice, BA and Manzella, CR and Ranjan, R and Metwally, AA and Theorell, J and Huang, Y and Alrefai, WA and Dudeja, PK and Finn, PW and Perkins, DL and Gill, RK}, title = {Serotonin Transporter Deficiency is Associated with Dysbiosis and Changes in Metabolic Function of the Mouse Intestinal Microbiome.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {2138}, pmid = {30765765}, issn = {2045-2322}, support = {R01 DK109709/DK/NIDDK NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; IK6 BX005243/BX/BLRD VA/United States ; R01 DK092441/DK/NIDDK NIH HHS/United States ; F30 DK113703/DK/NIDDK NIH HHS/United States ; I01 BX000152/BX/BLRD VA/United States ; I01 BX002011/BX/BLRD VA/United States ; U01 AI132898/AI/NIAID NIH HHS/United States ; R01 HL138628/HL/NHLBI NIH HHS/United States ; R01 DK081858/DK/NIDDK NIH HHS/United States ; F30 HL136001/HL/NHLBI NIH HHS/United States ; R01 DK071596/DK/NIDDK NIH HHS/United States ; R01 DK054016/DK/NIDDK NIH HHS/United States ; R01 DK098170/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/*metabolism ; Dysbiosis/etiology/*metabolism/pathology ; Feces/*microbiology ; *Gastrointestinal Microbiome ; *Gene Expression Regulation ; Metagenomics/*methods ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; RNA, Ribosomal, 16S/analysis/genetics ; Serotonin Plasma Membrane Transport Proteins/*physiology ; }, abstract = {Serotonin transporter (SERT) plays a critical role in regulating extracellular availability of serotonin (5-HT) in the gut and brain. Mice with deletion of SERT develop metabolic syndrome as they age. Changes in the gut microbiota are being increasingly implicated in Metabolic Syndrome and Diabetes. To investigate the relationship between the gut microbiome and SERT, this study assessed the fecal and cecal microbiome profile of 11 to 12 week-old SERT[+/+] and SERT[-/-] mice. Microbial DNA was isolated, processed for metagenomics shotgun sequencing, and taxonomic and functional profiles were assessed. 34 differentially abundant bacterial species were identified between SERT[+/+] and SERT[-/-]. SERT[-/-] mice displayed higher abundances of Bacilli species including genera Lactobacillus, Streptococcus, Enterococcus, and Listeria. Furthermore, SERT[-/-] mice exhibited significantly lower abundances of Bifidobacterium species and Akkermansia muciniphilia. Bacterial community structure was altered in SERT[-/-] mice. Differential abundance of bacteria was correlated with changes in host gene expression. Bifidobacterium and Bacilli species exhibited significant associations with host genes involved in lipid metabolism pathways. Our results show that SERT deletion is associated with dysbiosis similar to that observed in obesity. This study contributes to the understanding as to how changes in gut microbiota are associated with metabolic phenotype seen in SERT deficiency.}, } @article {pmid30764497, year = {2019}, author = {Plaza-Díaz, J and Gómez-Fernández, A and Chueca, N and Torre-Aguilar, MJ and Gil, Á and Perez-Navero, JL and Flores-Rojas, K and Martín-Borreguero, P and Solis-Urra, P and Ruiz-Ojeda, FJ and Garcia, F and Gil-Campos, M}, title = {Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota.}, journal = {Nutrients}, volume = {11}, number = {2}, pages = {}, pmid = {30764497}, issn = {2072-6643}, support = {404 Research Grant INVEST from the Spanish Society of Pediatrics and Red de Salud Materno Infantil (RED SAMID)//FUNDACIÓ AGRUPACIÓ Àmbit de la Infància/ ; }, mesh = {Autism Spectrum Disorder/*microbiology ; Bacteria/*classification/genetics ; Child, Preschool ; DNA, Bacterial/genetics ; Diet ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; }, abstract = {New microbiome sequencing technologies provide novel information about the potential interactions among intestinal microorganisms and the host in some neuropathologies as autism spectrum disorders (ASD). The microbiota[-]gut[-]brain axis is an emerging aspect in the generation of autistic behaviors; evidence from animal models suggests that intestinal microbial shifts may produce changes fitting the clinical picture of autism. The aim of the present study was to evaluate the fecal metagenomic profiles in children with ASD and compare them with healthy participants. This comparison allows us to ascertain how mental regression (an important variable in ASD) could influence the intestinal microbiota profile. For this reason, a subclassification in children with ASD by mental regression (AMR) and no mental regression (ANMR) phenotype was performed. The present report was a descriptive observational study. Forty-eight children aged 2[-]6 years with ASD were included: 30 with ANMR and 18 with AMR. In addition, a control group of 57 normally developing children was selected and matched to the ASD group by sex and age. Fecal samples were analyzed with a metagenomic approach using a next-generation sequencing platform. Several differences between children with ASD, compared with the healthy group, were detected. Namely, Actinobacteria and Proteobacteria at phylum level, as well as, Actinobacteria, Bacilli, Erysipelotrichi, and Gammaproteobacteria at class level were found at higher proportions in children with ASD. Additionally, Proteobacteria levels showed to be augmented exclusively in AMR children. Preliminary results, using a principal component analysis, showed differential patterns in children with ASD, ANMR and AMR, compared to healthy group, both for intestinal microbiota and food patterns. In this study, we report, higher levels of Actinobacteria, Proteobacteria and Bacilli, aside from Erysipelotrichi, and Gammaproteobacteria in children with ASD compared to healthy group. Furthermore, AMR children exhibited higher levels of Proteobacteria. Further analysis using these preliminary results and mixing metagenomic and other "omic" technologies are needed in larger cohorts of children with ASD to confirm these intestinal microbiota changes.}, } @article {pmid30763538, year = {2019}, author = {Gogokhia, L and Buhrke, K and Bell, R and Hoffman, B and Brown, DG and Hanke-Gogokhia, C and Ajami, NJ and Wong, MC and Ghazaryan, A and Valentine, JF and Porter, N and Martens, E and O'Connell, R and Jacob, V and Scherl, E and Crawford, C and Stephens, WZ and Casjens, SR and Longman, RS and Round, JL}, title = {Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis.}, journal = {Cell host & microbe}, volume = {25}, number = {2}, pages = {285-299.e8}, pmid = {30763538}, issn = {1934-6069}, support = {DP2 AT008746/AT/NCCIH NIH HHS/United States ; P40 OD010995/OD/NIH HHS/United States ; R00 HL102228/HL/NHLBI NIH HHS/United States ; T32 HG008962/HG/NHGRI NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R01 DK114252/DK/NIDDK NIH HHS/United States ; DP2 GM111099/GM/NIGMS NIH HHS/United States ; N01AI95375/AI/NIAID NIH HHS/United States ; T32 GM145304/GM/NIGMS NIH HHS/United States ; R01 GM114817/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*virology ; *Bacteriophages ; CD4-Positive T-Lymphocytes/metabolism ; Colitis, Ulcerative/*immunology/*microbiology/pathology ; Colorectal Neoplasms/*immunology/*microbiology/pathology ; Disease Models, Animal ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Humans ; Interferon-gamma/metabolism ; Intestinal Mucosa/*immunology/*microbiology/pathology ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Pilot Projects ; Prospective Studies ; Specific Pathogen-Free Organisms ; }, abstract = {Bacteriophages are the most abundant members of the microbiota and have the potential to shape gut bacterial communities. Changes to bacteriophage composition are associated with disease, but how phages impact mammalian health remains unclear. We noted an induction of host immunity when experimentally treating bacterially driven cancer, leading us to test whether bacteriophages alter immune responses. Treating germ-free mice with bacteriophages leads to immune cell expansion in the gut. Lactobacillus, Escherichia, and Bacteroides bacteriophages and phage DNA stimulated IFN-γ via the nucleotide-sensing receptor TLR9. The resultant immune responses were both phage and bacteria specific. Additionally, increasing bacteriophage levels exacerbated colitis via TLR9 and IFN-γ. Similarly, ulcerative colitis (UC) patients responsive to fecal microbiota transplantation (FMT) have reduced phages compared to non-responders, and mucosal IFN-γ positively correlates with bacteriophage levels. Bacteriophages from active UC patients induced more IFN-γ compared to healthy individuals. Collectively, these results indicate that bacteriophages can alter mucosal immunity to impact mammalian health.}, } @article {pmid30762914, year = {2019}, author = {Yu, H and Yu, Z and Huang, H and Li, P and Tang, Q and Wang, X and Shen, S}, title = {Gut microbiota signatures and lipids metabolism profiles by exposure to polyene phosphatidylcholine.}, journal = {BioFactors (Oxford, England)}, volume = {45}, number = {3}, pages = {439-449}, doi = {10.1002/biof.1495}, pmid = {30762914}, issn = {1872-8081}, mesh = {Animals ; Fatty Acids, Nonesterified/*metabolism ; Female ; Gastrointestinal Microbiome/*drug effects ; Lipid Metabolism/*drug effects ; Lipopolysaccharides/blood ; Liver/drug effects/*metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Phosphatidylcholines/*pharmacology ; }, abstract = {The aim of the study was to address the causality links and identify specific features of the gut microbiota signatures contributing to host lipids metabolism in the presence or absence of polyene phosphatidylcholine (PPC) administration, and evaluate potential risk of PPC consumption. About 20 C57BL/6J mice were randomly allocated into two groups, normal diet group (CK) and PPC administration group (205.2 mg/kg). Compared with CK group, the contents of unsaturated fatty acids were increased and the saturated fatty acids were decreased in PPC group. The content of free fatty acids (FFA) and lipopolysaccharides (LPS) were significantly decreased (P < 0.05), and expression of carnitine palmitoyltransferase 1A (CPT1A), cluster of differentiation 36 (CD36), liver fatty acid binding protein (L-FABP), fatty acid transport protein 5 (FATP5), and fatty acid synthase (FASN) were significantly decreased in the mRNA and protein levels after treated by PPC (P < 0.05, P < 0.01). Also, we found that acetic acid in feces was significantly increased after consumption of PPC (P < 0.05). After PPC administration the relative abundances of Firmicutes and Clostridia were increased within the phylum level and the class level, respectively. Microbial abundances in genus level were dominated by Lachnospiraceae and Lachnospiraceae_NK4A136_group, whereas the proportion of sequences assigned to Bacteroidetes within the phylum level, class Bacteroidias and Mollicutes, order Anaeroplasmatalesl, genus Bacteroidales_S24-7_group were decreased in metagenomes of treated group with PPC and did not significantly influence on the accumulation of trimethylamine-N-oxide (TMAO). This study revealed that intake of PPC could regulate the gut microbiota signatures and lipids metabolism in mice without TMAO accumulations. © 2019 BioFactors, 45(3):439-449, 2019.}, } @article {pmid30761108, year = {2019}, author = {Ulloa, R and Moya-Beltrán, A and Rojas-Villalobos, C and Nuñez, H and Chiacchiarini, P and Donati, E and Giaveno, A and Quatrini, R}, title = {Domestication of Local Microbial Consortia for Efficient Recovery of Gold Through Top-Down Selection in Airlift Bioreactors.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {60}, pmid = {30761108}, issn = {1664-302X}, abstract = {Extreme acidophiles play central roles in the geochemical cycling of diverse elements in low pH environments. This has been harnessed in biotechnologies such as biomining, where microorganisms facilitate the recovery of economically important metals such as gold. By generating both extreme acidity and a chemical oxidant (ferric iron) many species of prokaryotes that thrive in low pH environments not only catalyze mineral dissolution but also trigger both community and individual level adaptive changes. These changes vary in extent and direction depending on the ore mineralogy, water availability and local climate. The use of indigenous versus introduced microbial consortia in biomining practices is still a matter of debate. Yet, indigenous microbial consortia colonizing sulfidic ores that have been domesticated, i.e., selected for their ability to survive under specific polyextreme conditions, are claimed to outperform un-adapted foreign consortia. Despite this, little is known on the domestication of acidic microbial communities and the changes elicited in their members. In this study, high resolution targeted metagenomic techniques were used to analyze the changes occurring in the community structure of local microbial consortia acclimated to growing under extreme acidic conditions and adapted to endure the conditions imposed by the target mineral during biooxidation of a gold concentrate in an airlift reactor over a period of 2 years. The results indicated that operative conditions evolving through biooxidation of the mineral concentrate exerted strong selective pressures that, early on, purge biodiversity in favor of a few Acidithiobacillus spp. over other iron oxidizing acidophiles. Metagenomic analysis of the domesticated consortium present at the end of the adaptation experiment enabled reconstruction of the RVS1-MAG, a novel representative of Acidithiobacillus ferrooxidans from the Andacollo gold mineral district. Comparative genomic analysis performed with this genome draft revealed a net enrichment of gene functions related to heavy metal transport and stress management that are likely to play a significant role in adaptation and survival to adverse conditions experienced by these acidophiles during growth in presence of gold concentrates.}, } @article {pmid30760820, year = {2019}, author = {Karimi, E and Keller-Costa, T and Slaby, BM and Cox, CJ and da Rocha, UN and Hentschel, U and Costa, R}, title = {Genomic blueprints of sponge-prokaryote symbiosis are shared by low abundant and cultivatable Alphaproteobacteria.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {1999}, pmid = {30760820}, issn = {2045-2322}, mesh = {Alphaproteobacteria/classification/*genetics/*growth & development/isolation & purification ; Animals ; Biodegradation, Environmental ; Drug Resistance, Bacterial/genetics ; Genome, Bacterial/*genetics ; Microbiota/genetics ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Symbiosis/*genetics ; }, abstract = {Marine sponges are early-branching, filter-feeding metazoans that usually host complex microbiomes comprised of several, currently uncultivatable symbiotic lineages. Here, we use a low-carbon based strategy to cultivate low-abundance bacteria from Spongia officinalis. This approach favoured the growth of Alphaproteobacteria strains in the genera Anderseniella, Erythrobacter, Labrenzia, Loktanella, Ruegeria, Sphingorhabdus, Tateyamaria and Pseudovibrio, besides two likely new genera in the Rhodobacteraceae family. Mapping of complete genomes against the metagenomes of S. officinalis, seawater, and sediments confirmed the rare status of all the above-mentioned lineages in the marine realm. Remarkably, this community of low-abundance Alphaproteobacteria possesses several genomic attributes common to dominant, presently uncultivatable sponge symbionts, potentially contributing to host fitness through detoxification mechanisms (e.g. heavy metal and metabolic waste removal, degradation of aromatic compounds), provision of essential vitamins (e.g. B6 and B12 biosynthesis), nutritional exchange (especially regarding the processing of organic sulphur and nitrogen) and chemical defence (e.g. polyketide and terpenoid biosynthesis). None of the studied taxa displayed signs of genome reduction, indicative of obligate mutualism. Instead, versatile nutrient metabolisms along with motility, chemotaxis, and tight-adherence capacities - also known to confer environmental hardiness - were inferred, underlying dual host-associated and free-living life strategies adopted by these diverse sponge-associated Alphaproteobacteria.}, } @article {pmid30759800, year = {2019}, author = {Tremblay, ÉD and Kimoto, T and Bérubé, JA and Bilodeau, GJ}, title = {High-Throughput Sequencing to Investigate Phytopathogenic Fungal Propagules Caught in Baited Insect Traps.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {5}, number = {1}, pages = {}, pmid = {30759800}, issn = {2309-608X}, support = {OLF-P-1304, GRDI, QIS and CFIA OFL-P-1411, Genome Canada, and Genome BC (LSARP2112), CFIA-RPS and CFIA-TD and GRDI-CFIA mandated//Canadian Food Inspection Agency/ ; }, abstract = {Studying the means of dispersal of plant pathogens is crucial to better understand the dynamic interactions involved in plant infections. On one hand, entomologists rely mostly on both traditional molecular methods and morphological characteristics, to identify pests. On the other hand, high-throughput sequencing (HTS) is becoming the go-to avenue for scientists studying phytopathogens. These organisms sometimes infect plants, together with insects. Considering the growing number of exotic insect introductions in Canada, forest pest-management efforts would benefit from the development of a high-throughput strategy to investigate the phytopathogenic fungal and oomycete species interacting with wood-boring insects. We recycled formerly discarded preservative fluids from the Canadian Food Inspection Agency annual survey using insect traps and analysed more than one hundred samples originating from across Canada. Using the Ion Torrent Personal Genome Machine (PGM) HTS technology and fusion primers, we performed metabarcoding to screen unwanted fungi and oomycetes species, including Phytophthora spp. Community profiling was conducted on the four different wood-boring, insect-attracting semiochemicals; although the preservative (contained ethanol) also attracted other insects. Phytopathogenic fungi (e.g., Leptographium spp. and Meria laricis in the pine sawyer semiochemical) and oomycetes (mainly Peronospora spp. and Pythium aff. hypogynum in the General Longhorn semiochemical), solely associated with one of the four types of semiochemicals, were detected. This project demonstrated that the insect traps' semiochemical microbiome represents a new and powerful matrix for screening phytopathogens. Compared to traditional diagnostic techniques, the fluids allowed for a faster and higher throughput assessment of the biodiversity contained within. Additionally, minimal modifications to this approach would allow it to be used in other phytopathology fields.}, } @article {pmid30759613, year = {2019}, author = {Wang, X and Li, X and Yu, L and Huang, L and Xiu, J and Lin, W and Zhang, Y}, title = {Characterizing the microbiome in petroleum reservoir flooded by different water sources.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {872-885}, doi = {10.1016/j.scitotenv.2018.10.410}, pmid = {30759613}, issn = {1879-1026}, mesh = {Betaproteobacteria/genetics/*metabolism ; China ; Environmental Monitoring ; Gammaproteobacteria/genetics/*metabolism ; Metagenomics ; *Microbiota/genetics ; Oil and Gas Fields/*microbiology ; Petroleum/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S ; Water Microbiology ; *Water Resources/supply & distribution ; }, abstract = {Petroleum reservoir is an unusual subsurface biosphere, where indigenous microbes lived and evolved for million years. However, continual water injection changed the situation by introduction of new electron acceptors, donors and exogenous microbes. In this study, 16S-rRNA gene sequencing, comparative metagenomics and genomic bins reconstruction were employed to investigate the microbial community and metabolic potential in three typical water-flooded blocks of the Shen84 oil reservoir in Liaohe oil field, China. The results showed significant difference of microbial community compositions and metabolic characteristics existed between the injected water and the produced water/oil mixtures; however, there was considerable uniformity between the produced samples in different blocks. Microbial communities in the produced fluids were dominated by exogenous facultative microbes such as Pseudomonas and Thauera members from Proteobacteria phylum. Metabolic potentials for O2-dependent hydrocarbon degradation, dissimilarly nitrate reduction, and thiosulfate‑sulfur oxidation were much more abundant, whereas genes involved in dissimilatory sulfate reduction, anaerobic hydrocarbon degradation and methanogenesis were less abundant in the oil reservoir. Statistical analysis indicated the water composition had an obvious influence on microbial community composition and metabolic potential. The water-flooding process accompanied with introduction of nitrate or nitrite, and dissolved oxygen promoted the alteration of microbiome in oil reservoir from slow-growing anaerobic indigenous microbes (such as Thermotoga, Clostridia, and Syntrophobacter) to fast-growing opportunists as Beta- and Gama- Proteobacteria. The findings of this study shed light on the microbial ecology change in water flooded petroleum reservoir.}, } @article {pmid30759596, year = {2019}, author = {Miao, L and Wang, P and Hou, J and Yao, Y and Liu, Z and Liu, S}, title = {Low concentrations of copper oxide nanoparticles alter microbial community structure and function of sediment biofilms.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {705-713}, doi = {10.1016/j.scitotenv.2018.10.354}, pmid = {30759596}, issn = {1879-1026}, mesh = {Biofilms/*drug effects/growth & development ; Copper/analysis/*toxicity ; Dose-Response Relationship, Drug ; Fresh Water/chemistry/microbiology ; Geologic Sediments/chemistry/*microbiology ; Humic Substances/analysis ; Microbiota/*drug effects ; Models, Theoretical ; Nanoparticles/analysis/*toxicity ; Water Pollutants, Chemical/analysis/*toxicity ; }, abstract = {In this study, we investigated the effects of copper oxide (CuO) NPs on freshwater sediment biofilms in terms of the functional properties and microbial community structure. Biofilms were incubated in microcosms and CuO NPs (1 mg/L uncoated and humic-acid-coated) were exposed with Cu[2+] (Cu(NO3)2) as the positive control. As determined from DO (dissolved oxygen) microelectrodes measurements, a high-DO region emerged inside the biofilms after 5-day exposure to CuO NPs compared with those before NP additions, which suggested CuO NPs inhibit the oxygen respiration activity. These results were consistent with the decreased heterotrophic respiration. CuO NPs significantly altered the bacterial community composition and decreased the abundances of Anaerolineaceae, Acidobacteria, Aminicenantes, and Anaerolinea. Functional analysis from PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States)-predicted metagenomes indicated that bacterial genera depleted by CuO NP treatments were related to carbohydrate and glycan biosynthesis and metabolism, and biosynthesis of other secondary metabolites. These functional profiles combined with the decreased activities of extracellular enzymes, β-glucosidase (GLU) and l-leucine aminopeptidase (LAP), suggested that the introduction of CuO NPs exhibit negative effects on the biogeochemical processes and the cycling of carbon and nitrogen in biofilm systems. Whereas these toxic effects of CuO NPs could be mitigated when the aquatic environment is enriched with natural organic matters such as humic acid.}, } @article {pmid30755506, year = {2019}, author = {Hausmann, B and Pelikan, C and Rattei, T and Loy, A and Pester, M}, title = {Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, pmid = {30755506}, issn = {2150-7511}, support = {P 23117/FWF_/Austrian Science Fund FWF/Austria ; P 25111/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacterial Load ; Biomass ; Gene Expression Profiling ; Genome, Bacterial ; Metagenomics ; Peptococcaceae/*genetics/*growth & development ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Soil Microbiology ; *Transcription, Genetic ; }, abstract = {Microbial diversity in the environment is mainly concealed within the rare biosphere (all species with <0.1% relative abundance). While dormancy explains a low-abundance state very well, the mechanisms leading to rare but active microorganisms remain elusive. We used environmental systems biology to genomically and transcriptionally characterize "Candidatus Desulfosporosinus infrequens," a low-abundance sulfate-reducing microorganism cosmopolitan to freshwater wetlands, where it contributes to cryptic sulfur cycling. We obtained its near-complete genome by metagenomics of acidic peat soil. In addition, we analyzed anoxic peat soil incubated under in situ-like conditions for 50 days by Desulfosporosinus-targeted qPCR and metatranscriptomics. The Desulfosporosinus population stayed at a constant low abundance under all incubation conditions, averaging 1.2 × 10[6] 16S rRNA gene copies per cm[3] soil. In contrast, transcriptional activity of "Ca. Desulfosporosinus infrequens" increased at day 36 by 56- to 188-fold when minor amendments of acetate, propionate, lactate, or butyrate were provided with sulfate, compared to the no-substrate-control. Overall transcriptional activity was driven by expression of genes encoding ribosomal proteins, energy metabolism, and stress response but not by expression of genes encoding cell growth-associated processes. Since our results did not support growth of these highly active microorganisms in terms of biomass increase or cell division, they had to invest their sole energy for maintenance, most likely counterbalancing acidic pH conditions. This finding explains how a rare biosphere member can contribute to a biogeochemically relevant process while remaining in a zero-growth state over a period of 50 days.IMPORTANCE The microbial rare biosphere represents the largest pool of biodiversity on Earth and constitutes, in sum of all its members, a considerable part of a habitat's biomass. Dormancy or starvation is typically used to explain the persistence of low-abundance microorganisms in the environment. We show that a low-abundance microorganism can be highly transcriptionally active while remaining in a zero-growth state for at least 7 weeks. Our results provide evidence that this zero growth at a high cellular activity state is driven by maintenance requirements. We show that this is true for a microbial keystone species, in particular a cosmopolitan but permanently low-abundance sulfate-reducing microorganism in wetlands that is involved in counterbalancing greenhouse gas emissions. In summary, our results provide an important step forward in understanding time-resolved activities of rare biosphere members relevant for ecosystem functions.}, } @article {pmid30755154, year = {2019}, author = {Cronin, O and Barton, W and Moran, C and Sheehan, D and Whiston, R and Nugent, H and McCarthy, Y and Molloy, CB and O'Sullivan, O and Cotter, PD and Molloy, MG and Shanahan, F}, title = {Moderate-intensity aerobic and resistance exercise is safe and favorably influences body composition in patients with quiescent Inflammatory Bowel Disease: a randomized controlled cross-over trial.}, journal = {BMC gastroenterology}, volume = {19}, number = {1}, pages = {29}, pmid = {30755154}, issn = {1471-230X}, support = {N/a//Irish Centre for Arthritis Research and Education/ ; SFI/12/RC/2273//Science Foundation Ireland/Ireland ; 11/PI/1137//Science Foundation Ireland/Ireland ; 13/SIRG/2160//Science Foundation Ireland/Ireland ; 13/SIRG/2160//Science Foundation Ireland/Ireland ; }, mesh = {Adult ; Affect ; *Body Composition ; Body Mass Index ; Cross-Over Studies ; Cytokines/blood ; *Exercise ; Female ; Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*complications/immunology/microbiology/psychology ; Male ; Overweight/*complications/*therapy ; Prospective Studies ; Quality of Life ; *Resistance Training/adverse effects ; Young Adult ; }, abstract = {BACKGROUND: Overweight and metabolic problems now add to the burden of illness in patients with Inflammatory Bowel Disease. We aimed to determine if a program of aerobic and resistance exercise could safely achieve body composition changes in patients with Inflammatory Bowel Disease.

METHODS: A randomized, cross-over trial of eight weeks combined aerobic and resistance training on body composition assessed by Dual Energy X-ray Absorptiometry was performed. Patients in clinical remission and physically inactive with a mean age of 25 ± 6.5 years and Body Mass Index of 28.9 ± 3.8 were recruited from a dedicated Inflammatory Bowel Disease clinic. Serum cytokines were quantified, and microbiota assessed using metagenomic sequencing.

RESULTS: Improved physical fitness was demonstrated in the exercise group by increases in median estimated VO2max (Baseline: 43.41mls/kg/min; post-intervention: 46.01mls/kg/min; p = 0.03). Improvement in body composition was achieved by the intervention group (n = 13) with a median decrease of 2.1% body fat compared with a non-exercising group (n = 7) (0.1% increase; p = 0.022). Lean tissue mass increased by a median of 1.59 kg and fat mass decreased by a median of 1.52 kg in the exercising group. No patients experienced a deterioration in disease activity scores during the exercise intervention. No clinically significant alterations in the α- and β-diversity of gut microbiota and associated metabolic pathways were evident.

CONCLUSIONS: Moderate-intensity combined aerobic and resistance training is safe in physically unfit patients with quiescent Inflammatory Bowel Disease and can quickly achieve favourable body compositional changes without adverse effects.

TRIAL REGISTRATION: The study was registered at ClinicalTrials.gov; Trial number: NCT02463916 .}, } @article {pmid30748086, year = {2021}, author = {Cahn, JKB and Piel, J}, title = {Opening up the Single-Cell Toolbox for Microbial Natural Products Research.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {60}, number = {34}, pages = {18412-18428}, doi = {10.1002/anie.201900532}, pmid = {30748086}, issn = {1521-3773}, mesh = {Biological Products/*analysis ; *Microbiota ; *Single-Cell Analysis ; }, abstract = {The diverse microbes that produce natural products represent an important source of novel therapeutics, drug leads, and scientific tools. However, the vast majority have not been grown in axenic culture and are members of complex communities. While meta-'omic methods such as metagenomics, -transcriptomics, and -proteomics reveal collective molecular features of this "microbial dark matter", the study of individual microbiome members can be challenging. To address these limits, a number of techniques with single-bacterial resolution have been developed in the last decade and a half. While several of these are embraced by microbial ecologists, there has been less use by researchers interested in mining microbes for natural products. In this review, we discuss the available and emerging techniques for targeted single-cell analysis with a particular focus on applications to the discovery and study of natural products.}, } @article {pmid30747914, year = {2019}, author = {Gastauer, M and Vera, MPO and de Souza, KP and Pires, ES and Alves, R and Caldeira, CF and Ramos, SJ and Oliveira, G}, title = {A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining.}, journal = {Scientific data}, volume = {6}, number = {}, pages = {190008}, pmid = {30747914}, issn = {2052-4463}, mesh = {Archaea/genetics ; Bacteria/genetics ; Brazil ; Environmental Monitoring/*methods ; High-Throughput Nucleotide Sequencing ; Iron ; Metagenomics/*methods ; *Microbiota/genetics ; Mining ; *Soil Microbiology ; Viruses/genetics ; }, abstract = {Microorganisms are useful environmental indicators, able to deliver essential insights to processes regarding mine land rehabilitation. To compare microbial communities from a chronosequence of mine land rehabilitation to pre-disturbance levels from references sites covered by native vegetation, we sampled non-rehabilitated, rehabilitating and reference study sites from the Urucum Massif, Southwestern Brazil. From each study site, three composed soil samples were collected for chemical, physical, and metagenomics analysis. We used a paired-end library sequencing technology (NextSeq 500 Illumina); the reads were assembled using MEGAHIT. Coding DNA sequences (CDS) were identified using Kaiju in combination with non-redundant NCBI BLAST reference sequences containing archaea, bacteria, and viruses. Additionally, a functional classification was performed by EMG v2.3.2. Here, we provide the raw data and assembly (reads and contigs), followed by initial functional and taxonomic analysis, as a base-line for further studies of this kind. Further investigation is needed to fully understand the mechanisms of environmental rehabilitation in tropical regions, inspiring further researchers to explore this collection for hypothesis testing.}, } @article {pmid30747106, year = {2019}, author = {Schmidt, TS and Hayward, MR and Coelho, LP and Li, SS and Costea, PI and Voigt, AY and Wirbel, J and Maistrenko, OM and Alves, RJ and Bergsten, E and de Beaufort, C and Sobhani, I and Heintz-Buschart, A and Sunagawa, S and Zeller, G and Wilmes, P and Bork, P}, title = {Extensive transmission of microbes along the gastrointestinal tract.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {30747106}, issn = {2050-084X}, support = {ERC-AdG-669830//H2020 European Research Council/International ; 669830/ERC_/European Research Council/International ; 661019//H2020 Marie Skłodowska-Curie Actions/International ; de.NBI #031A537B//German Network for Bioinformatics Infrastructure/International ; CORE/15/BM/10404093//Fonds National de la Recherche Luxembourg/International ; de.NBI #031A537B//German Network Bioinformatics/International ; }, mesh = {Bacteria/*classification/*genetics ; Cluster Analysis ; Feces/microbiology ; Humans ; Intestine, Large/*microbiology ; Metagenomics ; *Microbiota ; Mouth/*microbiology ; Saliva/microbiology ; }, abstract = {The gastrointestinal tract is abundantly colonized by microbes, yet the translocation of oral species to the intestine is considered a rare aberrant event, and a hallmark of disease. By studying salivary and fecal microbial strain populations of 310 species in 470 individuals from five countries, we found that transmission to, and subsequent colonization of, the large intestine by oral microbes is common and extensive among healthy individuals. We found evidence for a vast majority of oral species to be transferable, with increased levels of transmission in colorectal cancer and rheumatoid arthritis patients and, more generally, for species described as opportunistic pathogens. This establishes the oral cavity as an endogenous reservoir for gut microbial strains, and oral-fecal transmission as an important process that shapes the gastrointestinal microbiome in health and disease.}, } @article {pmid30745586, year = {2019}, author = {Almeida, A and Mitchell, AL and Boland, M and Forster, SC and Gloor, GB and Tarkowska, A and Lawley, TD and Finn, RD}, title = {A new genomic blueprint of the human gut microbiota.}, journal = {Nature}, volume = {568}, number = {7753}, pages = {499-504}, pmid = {30745586}, issn = {1476-4687}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*classification/*genetics/isolation & purification/metabolism ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/*genetics ; *Genomics ; Humans ; Metagenome/*genetics ; Multigene Family ; Phylogeny ; Species Specificity ; }, abstract = {The composition of the human gut microbiota is linked to health and disease, but knowledge of individual microbial species is needed to decipher their biological roles. Despite extensive culturing and sequencing efforts, the complete bacterial repertoire of the human gut microbiota remains undefined. Here we identify 1,952 uncultured candidate bacterial species by reconstructing 92,143 metagenome-assembled genomes from 11,850 human gut microbiomes. These uncultured genomes substantially expand the known species repertoire of the collective human gut microbiota, with a 281% increase in phylogenetic diversity. Although the newly identified species are less prevalent in well-studied populations compared to reference isolate genomes, they improve classification of understudied African and South American samples by more than 200%. These candidate species encode hundreds of newly identified biosynthetic gene clusters and possess a distinctive functional capacity that might explain their elusive nature. Our work expands the known diversity of uncultured gut bacteria, which provides unprecedented resolution for taxonomic and functional characterization of the intestinal microbiota.}, } @article {pmid30744870, year = {2019}, author = {Lin, S and Han, Y and Jiangyuan, C and Luo, Y and Xu, W and Luo, H and Pang, G}, title = {Revealing the biodiversity and the response of pathogen to a combined use of procymidone and thiamethoxam in tomatoes.}, journal = {Food chemistry}, volume = {284}, number = {}, pages = {73-79}, doi = {10.1016/j.foodchem.2019.01.094}, pmid = {30744870}, issn = {1873-7072}, mesh = {Bacteria/isolation & purification ; *Biodiversity ; Bridged Bicyclo Compounds/*administration & dosage ; Fungicides, Industrial/*administration & dosage ; Insecticides/*administration & dosage ; Solanum lycopersicum/chemistry/*microbiology ; Pesticide Residues/analysis ; Plant Diseases/microbiology/prevention & control ; Thiamethoxam/*administration & dosage ; }, abstract = {The dissipation kinetics of a combined use of procymidone and thiamethoxam, and their impact on the biodiversity and pathogen on surface of tomatoes were studied. The half-lives of procymidone and thiamethoxam, used either on their own or in combination with each other, were 2.94 or 3.26 days and 2.41 or 2.67 days, respectively. The residues dropped below the maximum residue limit (MRL) after 7 or 10 days (MRL 2 mg·kg[-1] for procymidone), and 10 or 14 days (MRL 0.2 mg·kg[-1] for thiamethoxam), respectively. The phylum Bacteroidetes, Cyanobacteria, and Proteobacteria, were dominantly present in all studied samples. The genus Escherichia-Shigella was found and exposed to the dissipation of procymidone (r = -0.9209 for procymidone on its own, and r = -0.8611 for procymidone in combination with thiamethoxam). These results will contribute to establish adequate monitoring of pesticides residues and their incorporation in surface ecology and pathogen management strategies in tomatoes.}, } @article {pmid30743822, year = {2018}, author = {Liu, T and Cui, C and He, J and Tang, J}, title = {Insights into the succession of the bacterial microbiota during biodrying of storage sludge mixed with beer lees: Studies on its biodiversity, structure, associations, and functionality.}, journal = {The Science of the total environment}, volume = {644}, number = {}, pages = {1088-1100}, doi = {10.1016/j.scitotenv.2018.06.298}, pmid = {30743822}, issn = {1879-1026}, mesh = {Beer ; *Biodiversity ; *Microbiota ; Phylogeny ; Waste Disposal, Fluid/*methods ; }, abstract = {Biodrying was first used for post-treatment of storage sludge mixed with beer lees. In this study, dynamic changes in dissolved organic matter (DOM), bacterial community structure, bacterial associations as well as metabolic functions were investigated using Excitation-Emission Matrix (EEM) spectra, high-throughput sequencing, network and correlation matrix analyses, and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Furthermore, a hypothetical model was proposed to better understand the biodrying process. The results showed that desired performance was obtained and DOM variations revealed that biodrying can increase biostability of the matrix. The bacterial communities differed among different stages of the biodrying. At the phylum level, the dominant phyla were Proteobacteria and Bacteroidetes in the mesophilic and cooling phases, whereas Firmicutes became the most dominant phylum in the thermophilic phase. At the genus level, the dominant bacteria in the mesophilic and cooling phases were not obvious, while Ureibacillus and Bacillus were the dominant genera in the thermophilic phase. Network and correlation matrix analyses were useful tools for insights into the bacterial interactions. PICRUSt metagenome inference indicated that metabolism, genetic information processing, and environmental information processing were the primary metabolic pathways. These results allowed us to advance a hypothetical model explaining how succession in bacterial associations regulates the dynamics of a biodrying system.}, } @article {pmid30741985, year = {2019}, author = {Vera-Gargallo, B and Chowdhury, TR and Brown, J and Fansler, SJ and Durán-Viseras, A and Sánchez-Porro, C and Bailey, VL and Jansson, JK and Ventosa, A}, title = {Spatial distribution of prokaryotic communities in hypersaline soils.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {1769}, pmid = {30741985}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Chemical Phenomena ; Geologic Sediments/microbiology ; Metagenome ; Metagenomics/methods ; Mice ; *Microbiota ; *Prokaryotic Cells ; *Salinity ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Increasing salinization in wetland systems is a major threat to ecosystem services carried out by microbial communities. Thus, it is paramount to understand how salinity drives both microbial community structures and their diversity. Here we evaluated the structure and diversity of the prokaryotic communities from a range of highly saline soils (EC1:5 from 5.96 to 61.02 dS/m) from the Odiel Saltmarshes and determined their association with salinity and other soil physicochemical features by analyzing 16S rRNA gene amplicon data through minimum entropy decomposition (MED). We found that these soils harbored unique communities mainly composed of halophilic and halotolerant taxa from the phyla Euryarchaeota, Proteobacteria, Balneolaeota, Bacteroidetes and Rhodothermaeota. In the studied soils, several site-specific properties were correlated with community structure and individual abundances of particular sequence variants. Salinity had a secondary role in shaping prokaryotic communities in these highly saline samples since the dominant organisms residing in them were already well-adapted to a wide range of salinities. We also compared ESV-based results with OTU-clustering derived ones, showing that, in this dataset, no major differences in ecological outcomes were obtained by the employment of one or the other method.}, } @article {pmid30741334, year = {2019}, author = {Suleiman, M and Klippel, B and Busch, P and Schäfers, C and Moccand, C and Bel-Rhlid, R and Palzer, S and Antranikian, G}, title = {Enrichment of anaerobic heterotrophic thermophiles from four Azorean hot springs revealed different community composition and genera abundances using recalcitrant substrates.}, journal = {Extremophiles : life under extreme conditions}, volume = {23}, number = {3}, pages = {277-281}, pmid = {30741334}, issn = {1433-4909}, mesh = {*Archaea/classification/genetics/growth & development/isolation & purification ; *Bacteria/classification/genetics/growth & development/isolation & purification ; *Biodiversity ; Hot Springs/*microbiology ; *Metagenome ; Metagenomics ; Portugal ; *Water Microbiology ; }, abstract = {DGGE analysis combined with a metagenomic approach was used to get insights into heterotrophic anoxic enrichment cultures of four hot springs of Vale das Furnas, Portugal, using the recalcitrant substrate spent coffee ground (SCG). Parallel enrichment cultures were performed using the major components of spent coffee ground, namely arabinogalactan, galactomannan, cellulose, and proteins. DGGE revealed that heterotrophic thermophilic bacteria are highly abundant in the hydrothermal springs and significant differences in community composition depending on the substrate were observed. DNA, isolated from enrichment cultures of different locations that were grown on the same substrate were pooled, and the respective metagenomes were analyzed. Results indicated that cultures grown on recalcitrant substrate SCG consists of a totally different thermophilic community, dominated by Dictyoglomus. Enrichments with galactomannan and arabinogalactan were dominated by Thermodesulfovibrio, while cultures with casein and cellulose were dominated by Thermus. This study indicates the high potential of thermophilic bacteria degrading recalcitrant substrate such as SCG and furthermore how the accessibility to complex polymers shapes the bacterial community.}, } @article {pmid30740092, year = {2019}, author = {Grządziel, J and Gałązka, A}, title = {Fungal Biodiversity of the Most Common Types of Polish Soil in a Long-Term Microplot Experiment.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {6}, pmid = {30740092}, issn = {1664-302X}, abstract = {The aim of the study was to investigate fungal genetic diversity in eight different types of soil in a long-term microplot experiment founded in 1881 in Puławy, Poland. The experiment consists of eight plots (14 m[2]), each 1 m deep with concrete walls, filled with profiles of different soils. The soils represent the most common Polish soil types (Cambic Leptosol, Fluvic Cambisol, Gleyic Chernozem, Cambisol and Haplic Cambisol, two Brunic Arenosols and Haplic Luvisol). Each soil was characterized by different pH (from 4.0 to 7.5) and organic carbon content (4.5-21.3 g kg[-1]). The soil structure was not destroyed by compaction because the soils had always been cultivated by hand. The same plant species were always grown in all plots at the same time and the soils received the same fertilization. Moreover, the soils were always under the same weather conditions. Ascomycota was the most abundant phylum in all samples, ranging from 70 to 90% of total fungi. Some genera (Mortierella, Solicoccozyma, and Mycosphaerella) were found to be adapted to a wide range of pH. Acidic soils were dominated by Talaromyces, Cladophialophora, Devriesia, and Saitozyma, while good quality soils primarily consisted of Plectosphaerella, Tetracladium, and Mortierella. The study confirmed previous reports that pH has a decisive influence on soil fungal diversity, but also indicated the strong impact of soil type itself. These studies have launched a new cycle of research in these historical soil profiles.}, } @article {pmid30738924, year = {2019}, author = {Wang, Y and Liu, F and Urban, JF and Paerewijck, O and Geldhof, P and Li, RW}, title = {Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome.}, journal = {International journal for parasitology}, volume = {49}, number = {3-4}, pages = {247-256}, doi = {10.1016/j.ijpara.2018.10.007}, pmid = {30738924}, issn = {1879-0135}, mesh = {Animals ; Ascariasis/complications/epidemiology/*veterinary ; Ascaris suum/*isolation & purification ; Cluster Analysis ; Colon/microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Dysbiosis/epidemiology/*veterinary ; Fatty Acids, Volatile/analysis ; Feces/chemistry/microbiology ; *Gastrointestinal Microbiome ; Metabolomics ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Swine ; Swine Diseases/*epidemiology ; }, abstract = {The effect of infection of pigs with Ascaris suum on the microbial composition in the proximal colon and fecal matter was investigated using 16S rRNA gene sequencing. The infection significantly decreased various microbial diversity indices including Chao1 richness, but the effect on Chao1 in the colon luminal contents was worm burden-independent. The abundance of 49 genera present in colon contents, such as Prevotella and Faecalibacterium, and 179 operational taxonomic units was significantly changed as a result of infection. Notably, infection was also associated with a significant shift in the metabolic potential of the proximal colon microbiome, where the relative abundance of at least 30 metabolic pathways including carbohydrate metabolism and amino acid metabolism was reduced, while the abundance of 28 pathways was increased by infection. Furthermore, the microbial co-occurrence network in infected pigs was highly modular. Two of 52 modules or subnetworks were negatively correlated with fecal butyrate concentrations (r < -0.7; P < 0.05) while one module with 18 members was negatively correlated with fecal acetate, propionate and total short-chain fatty acids. A partial Mantel test identified a strong positive correlation between node connectivity of the operational taxonomic units assigned to β-Proteobacteria (especially the family Alcaligenaceae) and fecal acetate and propionate levels (r = 0.82 and 0.74, respectively), while that of the family Porphyromonadaceae was positively correlated with fecal egg counts. Overall, Ascaris infection was associated with a profound change in the gut microbiome, especially in the proximity of the initial site of larval infection, and should facilitate our understanding of the pathophysiological consequence of gastrointestinal nematode infections.}, } @article {pmid30737678, year = {2019}, author = {Yamamoto, K and Ishigami, M and Honda, T and Takeyama, T and Ito, T and Ishizu, Y and Kuzuya, T and Hayashi, K and Goto, H and Hirooka, Y}, title = {Influence of proton pump inhibitors on microbiota in chronic liver disease patients.}, journal = {Hepatology international}, volume = {13}, number = {2}, pages = {234-244}, pmid = {30737678}, issn = {1936-0541}, mesh = {Aged ; Chronic Disease ; Esophageal and Gastric Varices/etiology ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/physiology ; Hepatic Encephalopathy/*etiology ; Humans ; Liver Diseases/*complications/metabolism ; Male ; Metagenome/drug effects ; Middle Aged ; Peritonitis/*microbiology ; Proton Pump Inhibitors/*pharmacology/therapeutic use ; Signal Transduction ; }, abstract = {BACKGROUND: Current knowledge suggests that proton pump inhibitors (PPIs) are associated with an increased risk of hepatic encephalopathy (HE) and spontaneous bacterial peritonitis (SBP). These conditions and PPI use are related to gut microbiota. The aim of this study is to research the changes in gut microbiota caused by PPI in patients with chronic liver disease.

METHODS: From 198 Japanese patients, 31 patients in the PPI and non-PPI groups were matched using propensity score matching (PSM) based on age, sex, and Child-Turcotte-Pugh class. We investigated the gut microbial composition of stool samples using the Illumina MiSeq sequencing platform and compared them using linear discriminant analysis effect size and phylogenetic investigation of communities by reconstruction of unobserved states.

RESULTS: Before PSM, Child-Turcotte-Pugh score (p = 0.038), ascites (p = 0.049), encephalopathy (p = 0.023), and esophageal varices (p < 0.01) were significantly higher in the PPI group than in the non-PPI group. After PSM, six genera, consisting of Lactobacillus, Streptococcus, Selenomonas, Veillonella, Campylobacter, and Haemophilus were enriched in the PPI group. Eggerthella, Paraprevotella, Turicibacter, Dorea, Anaerotruncus, and Ruminococcus were less abundant in the PPI group. We identified five types of level 3 KEGG pathways predicted to be significantly different.

CONCLUSIONS: Part of microbial changes caused by PPI use was common to the changes by progression of liver cirrhosis. Increases in oral bacterial flora and decreases in autochthonous flora may produce the intestinal environment which tends to make the risk factor for HE or SBP.}, } @article {pmid30737379, year = {2019}, author = {Colman, DR and Lindsay, MR and Boyd, ES}, title = {Mixing of meteoric and geothermal fluids supports hyperdiverse chemosynthetic hydrothermal communities.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {681}, pmid = {30737379}, issn = {2041-1723}, abstract = {Little is known of how mixing of meteoric and geothermal fluids supports biodiversity in non-photosynthetic ecosystems. Here, we use metagenomic sequencing to investigate a chemosynthetic microbial community in a hot spring (SJ3) of Yellowstone National Park that exhibits geochemistry consistent with mixing of a reduced volcanic gas-influenced end member with an oxidized near-surface meteoric end member. SJ3 hosts an exceptionally diverse community with representatives from ~50% of known higher-order archaeal and bacterial lineages, including several divergent deep-branching lineages. A comparison of functional potential with other available chemosynthetic community metagenomes reveals similarly high diversity and functional potentials (i.e., incorporation of electron donors supplied by volcanic gases) in springs sourced by mixed fluids. Further, numerous closely related SJ3 populations harbor differentiated metabolisms that may function to minimize niche overlap, further increasing endemic diversity. We suggest that dynamic mixing of waters generated by subsurface and near-surface geological processes may play a key role in the generation and maintenance of chemosynthetic biodiversity in hydrothermal and other similar environments.}, } @article {pmid30737349, year = {2019}, author = {Tuttle, RN and Demko, AM and Patin, NV and Kapono, CA and Donia, MS and Dorrestein, P and Jensen, PR}, title = {Detection of Natural Products and Their Producers in Ocean Sediments.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {8}, pages = {}, pmid = {30737349}, issn = {1098-5336}, mesh = {Bacteria/genetics/*metabolism ; Biological Products/chemistry/*isolation & purification ; Drug Discovery ; Geologic Sediments/microbiology ; High-Throughput Nucleotide Sequencing ; Metabolome ; Metabolomics ; Metagenome ; Microbiota/physiology ; Micromonosporaceae/metabolism ; Multigene Family ; *Oceans and Seas ; Seawater/microbiology ; }, abstract = {Thousands of natural products have been identified from cultured microorganisms, yet evidence of their production in the environment has proven elusive. Technological advances in mass spectrometry, combined with public databases, now make it possible to address this disparity by detecting compounds directly from environmental samples. Here, we used adsorbent resins, tandem mass spectrometry, and next-generation sequencing to assess the metabolome of marine sediments and its relationship to bacterial community structure. We identified natural products previously reported from cultured bacteria, providing evidence they are produced in situ, and compounds of anthropogenic origin, suggesting this approach can be used as an indicator of environmental impact. The bacterial metabolite staurosporine was quantified and shown to reach physiologically relevant concentrations, indicating that it may influence sediment community structure. Staurosporine concentrations were correlated with the relative abundance of the staurosporine-producing bacterial genus Salinispora and production confirmed in strains cultured from the same location, providing a link between compound and candidate producer. Metagenomic analyses revealed numerous biosynthetic gene clusters related to indolocarbazole biosynthesis, providing evidence for noncanonical sources of staurosporine and a path forward to assess the relationships between natural products and the organisms that produce them. Untargeted environmental metabolomics circumvents the need for laboratory cultivation and represents a promising approach to understanding the functional roles of natural products in shaping microbial community structure in marine sediments.IMPORTANCE Natural products are readily isolated from cultured bacteria and exploited for useful purposes, including drug discovery. However, these compounds are rarely detected in the environments from which the bacteria are obtained, thus limiting our understanding of their ecological significance. Here, we used environmental metabolomics to directly assess chemical diversity in marine sediments. We identified numerous metabolites and, in one case, isolated strains of bacteria capable of producing one of the compounds detected. Coupling environmental metabolomics with community and metagenomic analyses provides opportunities to link compounds and producers and begin to assess the complex interactions mediated by specialized metabolites in marine sediments.}, } @article {pmid30736849, year = {2019}, author = {Fritz, A and Hofmann, P and Majda, S and Dahms, E and Dröge, J and Fiedler, J and Lesker, TR and Belmann, P and DeMaere, MZ and Darling, AE and Sczyrba, A and Bremges, A and McHardy, AC}, title = {CAMISIM: simulating metagenomes and microbial communities.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {17}, pmid = {30736849}, issn = {2049-2618}, mesh = {Algorithms ; Animals ; *Computer Simulation ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Mice ; Models, Biological ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {BACKGROUND: Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, to effectively assess the performance of metagenomic analysis software, a wide range of benchmark data sets are required.

RESULTS: We describe the CAMISIM microbial community and metagenome simulator. The software can model different microbial abundance profiles, multi-sample time series, and differential abundance studies, includes real and simulated strain-level diversity, and generates second- and third-generation sequencing data from taxonomic profiles or de novo. Gold standards are created for sequence assembly, genome binning, taxonomic binning, and taxonomic profiling. CAMSIM generated the benchmark data sets of the first CAMI challenge. For two simulated multi-sample data sets of the human and mouse gut microbiomes, we observed high functional congruence to the real data. As further applications, we investigated the effect of varying evolutionary genome divergence, sequencing depth, and read error profiles on two popular metagenome assemblers, MEGAHIT, and metaSPAdes, on several thousand small data sets generated with CAMISIM.

CONCLUSIONS: CAMISIM can simulate a wide variety of microbial communities and metagenome data sets together with standards of truth for method evaluation. All data sets and the software are freely available at https://github.com/CAMI-challenge/CAMISIM.}, } @article {pmid30734843, year = {2019}, author = {Phetcharat, T and Dawkrajai, P and Chitov, T and Mhuantong, W and Champreda, V and Bovonsombut, S}, title = {Biosurfactant-Producing Capability and Prediction of Functional Genes Potentially Beneficial to Microbial Enhanced Oil Recovery in Indigenous Bacterial Communities of an Onshore Oil Reservoir.}, journal = {Current microbiology}, volume = {76}, number = {3}, pages = {382-391}, pmid = {30734843}, issn = {1432-0991}, mesh = {Bacillus licheniformis/classification/enzymology/genetics/*metabolism ; Conservation of Natural Resources ; Genes, Bacterial ; *Industrial Microbiology ; *Microbial Consortia ; Nitrates/metabolism ; Oil and Gas Fields/*microbiology ; Petroleum/microbiology ; Phosphates/metabolism ; Potassium Compounds/metabolism ; RNA, Ribosomal, 16S/genetics ; Surface-Active Agents/*metabolism ; }, abstract = {Microbial enhanced oil recovery (MEOR) is a bio-based technology with economic and environmental benefits. The success of MEOR depends greatly on the types and characteristics of indigenous microbes. The aim of this study was to evaluate the feasibility of applying MEOR at Mae Soon Reservoir, an onshore oil reservoir experiencing a decline in its production rate. We investigated the capability of the reservoir's bacteria to produce biosurfactants, and evaluated the potentials of uncultured indigenous bacteria to support MEOR by means of prediction of MEOR-related functional genes, based on a set of metagenomic 16s rRNA gene data. The biosurfactant-producing bacteria isolated from the oil-bearing sandstones from the reservoir belonged to one species: Bacillus licheniformis, with one having the ability to decrease surface tension from 72 to 32 mN/m. Gene sequences responsible for biosurfactant (licA3), lipase (lipP1) and catechol 2,3-dioxygenase (C23O) were detected in these isolates. The latter two, and other genes encoding MEOR-related functional proteins such as enoyl-CoA hydratase and alkane 1-monooxygenase, were predicted in the bacterial communities residing the reservoir's sandstones. Exposure of these sandstones to nutrients, consisting of KNO3 and NaH2PO4, resulted in an increase in the proportions of some predicted functional genes. These results indicated the potentials of MEOR application at Mae Soon site. Using the approaches demonstrated in this study would also assist evaluation of the feasibility of applying MEOR in oil reservoirs, which may be enhanced by an appropriate nutrient treatment.}, } @article {pmid30733472, year = {2019}, author = {Zhang, W and Li, J and Lu, S and Han, N and Miao, J and Zhang, T and Qiang, Y and Kong, Y and Wang, H and Gao, T and Liu, Y and Li, X and Peng, X and Chen, X and Zhao, X and Che, J and Zhang, L and Chen, X and Zhang, Q and Hu, M and Li, Q and Kan, B}, title = {Gut microbiota community characteristics and disease-related microorganism pattern in a population of healthy Chinese people.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {1594}, pmid = {30733472}, issn = {2045-2322}, mesh = {Adolescent ; China ; *Disease ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; *Healthy Volunteers ; Humans ; Male ; Middle Aged ; Young Adult ; }, abstract = {China's population accounts for about 1/5[th] of the world's total population. Owing to differences in environment, race, living habits, and other factors, the structure of the intestinal flora of Chinese individuals is expected to have unique features; however, this has not been thoroughly examined. Here, we collected faecal samples from healthy adults living in three cities of China and investigated their gut microbiome using metagenomics and bioinformatics technology. We found that 11 core bacterial genera were present in all of the Chinese faecal samples; moreover, several patient characteristics (age, region, body mass index, physical exercise, smoking habits, and alcoholic drink, and yogurt consumption) were found to have different effects on the gut microbiome of healthy Chinese people. We also examined the distribution patterns of disease-related microorganisms (DRMs), revealing which DRMs can potentially be used as markers for assessment of health risk. We also developed a program called "Guthealthy" for evaluating the health status associated with the microbiome and DRM pattern in the faecal samples. The microbiota data obtained in this study will provide a basis for a healthy gut microbiome composition in the Chinese population.}, } @article {pmid30729757, year = {2019}, author = {Staniszewska, A and Kunicka-Styczyńska, A and Otlewska, A and Gawor, J and Gromadka, R and Żuchniewicz, K and Ziemiński, K}, title = {High-throughput sequencing approach in analysis of microbial communities colonizing natural gas pipelines.}, journal = {MicrobiologyOpen}, volume = {8}, number = {8}, pages = {e00806}, pmid = {30729757}, issn = {2045-8827}, mesh = {Bacteria/*classification/genetics ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; *Microbiota ; Natural Gas/*microbiology ; *Phylogeny ; Poland ; }, abstract = {This study provides a deep modern insight into the phylogenetic diversity among bacterial consortia found in working and nonworking high-methane natural gas pipelines located in Poland. The working pipeline was characterized by lower biodiversity (140-154 bacterial genera from 22 to 23 classes, depending on the source of the debris) in comparison to the off-gas pipeline (169 bacterial genera from 23 classes). The sediment recovered from the working pipeline contained mostly DNA identified as belonging to the phylum Firmicutes (66.4%-45.9% operational taxonomic units [OTUs]), predominantly Bacillus (41.4%-31.1% OTUs) followed by Lysinibacillus (2.6%-1.5% OTUs) and Clostridium (2.4%-1.8% OTUs). In the nonworking pipeline, Proteobacteria (46.8% OTUs) and Cyanobacteria (27.8% OTUs) were dominant. Over 30% of the Proteobacteria sequences showed homologies to Gammaproteobacteria, with Pseudomonas (7.1%), Enhydrobacter (2.1%), Stenotrophomonas (0.5%), and Haempohilus (0.4%) among the others. Differences were noted in terms of the chemical compositions of deposits originating from the working and nonworking gas pipelines. The deposits from the nonworking gas pipeline contained iron, as well as carbon (42.58%), sulphur (15.27%), and oxygen (15.32%). This composition can be linked to both the quantity and type of the resident microorganisms. The presence of a considerable amount of silicon (17.42%), and of aluminum, potassium, calcium, and magnesium at detectable levels, may likewise affect the metabolic activity of the resident consortia in the working gas pipeline. All the analyzed sediments included both bacteria known for causing and intensifying corrosion (e.g., Pseudomonas, Desulfovibrio, Shewanella, Serratia) and bacteria that can protect the surface of pipelines against deterioration (e.g., Bacillus). Biocorrosion is not related to a single mechanism or one species of microorganism, but results from the multidirectional activity of multiple microbial communities. The analysis presented here of the state of the microbiome in a gas pipeline during the real gas transport is a particularly valuable element of this work.}, } @article {pmid30729265, year = {2019}, author = {Bernard, C and Escalas, A and Villeriot, N and Agogué, H and Hugoni, M and Duval, C and Carré, C and Got, P and Sarazin, G and Jézéquel, D and Leboulanger, C and Grossi, V and Ader, M and Troussellier, M}, title = {Very Low Phytoplankton Diversity in a Tropical Saline-Alkaline Lake, with Co-dominance of Arthrospira fusiformis (Cyanobacteria) and Picocystis salinarum (Chlorophyta).}, journal = {Microbial ecology}, volume = {78}, number = {3}, pages = {603-617}, pmid = {30729265}, issn = {1432-184X}, support = {ANR-13-BS06-0001//Agence Nationale de la Recherche/ ; }, mesh = {Biodiversity ; Biomass ; Chlorophyll A/metabolism ; Chlorophyta/*growth & development/metabolism ; Ecosystem ; Indian Ocean ; Islands ; Lakes/*microbiology ; Phytoplankton/genetics/*growth & development ; Seasons ; Spirulina/*growth & development/metabolism ; }, abstract = {Lake Dziani Dzaha (Mayotte Island, Indian Ocean) is a tropical thalassohaline lake which geochemical and biological conditions make it a unique aquatic ecosystem considered as a modern analogue of Precambrian environments. In the present study, we focused on the diversity of phytoplanktonic communities, which produce very high and stable biomass (mean2014-2015 = 652 ± 179 μg chlorophyll a L[-1]). As predicted by classical community ecology paradigms, and as observed in similar environments, a single species is expected to dominate the phytoplanktonic communities. To test this hypothesis, we sampled water column in the deepest part of the lake (18 m) during rainy and dry seasons for two consecutive years. Phytoplanktonic communities were characterized using a combination of metagenomic, microscopy-based and flow cytometry approaches, and we used statistical modeling to identify the environmental factors determining the abundance of dominant organisms. As hypothesized, the overall diversity of the phytoplanktonic communities was very low (15 OTUs), but we observed a co-dominance of two, and not only one, OTUs, viz., Arthrospira fusiformis (Cyanobacteria) and Picocystis salinarum (Chlorophyta). We observed a decrease in the abundance of these co-dominant taxa along the depth profile and identified the adverse environmental factors driving this decline. The functional traits measured on isolated strains of these two taxa (i.e., size, pigment composition, and concentration) are then compared and discussed to explain their capacity to cope with the extreme environmental conditions encountered in the aphotic, anoxic, and sulfidic layers of the water column of Lake Dziani Dzaha.}, } @article {pmid30728080, year = {2019}, author = {Yu, K and Yi, S and Li, B and Guo, F and Peng, X and Wang, Z and Wu, Y and Alvarez-Cohen, L and Zhang, T}, title = {An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {16}, pmid = {30728080}, issn = {2049-2618}, mesh = {Alcaligenaceae/genetics/isolation & purification/*metabolism ; Benzhydryl Compounds/*metabolism ; *Biodegradation, Environmental ; Metagenomics ; Microbial Interactions/physiology ; Microbiota/physiology ; Phenols/*metabolism ; Pseudomonas/genetics/isolation & purification/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sphingomonas/genetics/isolation & purification/*metabolism ; }, abstract = {BACKGROUND: Understanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. However, unraveling microbial interactions as well as substrates involved in complex microbial communities is a challenging task. Here, we demonstrate an integrated approach of metagenomics, metatranscriptomics, and targeted metabolite analysis to identify the substrates involved in interspecies interactions from a potential cross-feeding model community-bisphenol A (BPA)-biodegrading community, aiming to establish an identification method of microbial interactions in engineering or environmental bioprocesses.

RESULTS: The community-level BPA-metabolic pathway was constructed using integrated metagenomics and targeted metabolite analyses. The dynamics of active functions and metabolism of major community members were identified using metagenomic and metatranscriptomic analyses in concert. Correlating the community BPA biodegradation performance to the individual bacterial activities enabled the discovery of substrates involved in a synergistic interaction of cross-feeding between BPA-degrading Sphingonomas species and intermediate users, Pseudomonas sp. and Pusillimonas sp. This proposed synergistic interaction was confirmed by the co-culture of a Sphingonomas sp. and Pseudomonas sp. isolates, which demonstrated enhanced BPA biodegradation compared to the isolate of Sphingonomas sp. alone.

CONCLUSION: The three types of integrated meta-omics analyses effectively revealed the metabolic capability at both community-wide and individual bacterial levels. The correlation between these two levels revealed the hidden connection between apparent overall community performance and the contributions of individual community members and their interactions in a BPA-degrading microbial community. In addition, we demonstrated that using integrated multi-omics in conjunction with culture-based confirmation approach is effective to elucidate the microbial interactions affecting the performance outcome. We foresee this approach would contribute the future application and operation of environmental bioprocesses on a knowledge-based control.}, } @article {pmid30728065, year = {2019}, author = {Johnson, ME and Franks, JM and Cai, G and Mehta, BK and Wood, TA and Archambault, K and Pioli, PA and Simms, RW and Orzechowski, N and Arron, S and Whitfield, ML}, title = {Microbiome dysbiosis is associated with disease duration and increased inflammatory gene expression in systemic sclerosis skin.}, journal = {Arthritis research & therapy}, volume = {21}, number = {1}, pages = {49}, pmid = {30728065}, issn = {1478-6362}, support = {T32 AI007363/AI/NIAID NIH HHS/United States ; T32 LM012204/LM/NLM NIH HHS/United States ; W81XWH-14-1-0224//U.S. Department of Defense/International ; }, mesh = {Adult ; Aged ; Bacteria/classification/genetics ; Biopsy ; Cohort Studies ; Dysbiosis/*genetics ; Female ; Gene Expression Profiling ; Humans ; Inflammation/*genetics/microbiology/pathology ; Male ; Metagenomics/methods ; Microbiota/*genetics ; Middle Aged ; Population Dynamics ; Scleroderma, Systemic/*genetics/microbiology/pathology ; Skin/*metabolism/microbiology/pathology ; Time Factors ; }, abstract = {BACKGROUND: Infectious agents have long been postulated to be disease triggers for systemic sclerosis (SSc), but a definitive link has not been found. Metagenomic analyses of high-throughput data allows for the unbiased identification of potential microbiome pathogens in skin biopsies of SSc patients and allows insight into the relationship with host gene expression.

METHODS: We examined skin biopsies from a diverse cohort of 23 SSc patients (including lesional forearm and non-lesional back samples) by RNA-seq. Metagenomic filtering and annotation was performed using the Integrated Metagenomic Sequencing Analysis (IMSA). Associations between microbiome composition and gene expression were analyzed using single-sample gene set enrichment analysis (ssGSEA).

RESULTS: We find the skin of SSc patients exhibits substantial changes in microbial composition relative to controls, characterized by sharp decreases in lipophilic taxa, such as Propionibacterium, combined with increases in a wide range of gram-negative taxa, including Burkholderia, Citrobacter, and Vibrio.

CONCLUSIONS: Microbiome dysbiosis is associated with disease duration and increased inflammatory gene expression. These data provide a comprehensive portrait of the SSc skin microbiome and its association with local gene expression, which mirrors the molecular changes in lesional skin.}, } @article {pmid30725462, year = {2019}, author = {Morales, E and Chen, J and Greathouse, KL}, title = {Compositional Analysis of the Human Microbiome in Cancer Research.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1928}, number = {}, pages = {299-335}, doi = {10.1007/978-1-4939-9027-6_16}, pmid = {30725462}, issn = {1940-6029}, mesh = {Biological Evolution ; Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; *Research ; }, abstract = {Gut microbial composition has shown to be associated with obesity, diabetes mellitus, inflammatory bowel disease, colitis, autoimmune disorders, and cancer, among other diseases. Microbiome research has significantly evolved through the years and continues to advance as we develop new and better strategies to more accurately measure its composition and function. Careful selection of study design, inclusion and exclusion criteria of participants, and methodology are paramount to accurately analyze microbial structure. Here we present the most up-to-date available information on methods for gut microbial collection and analysis.}, } @article {pmid30724441, year = {2019}, author = {Ghaly, TM and Geoghegan, JL and Alroy, J and Gillings, MR}, title = {High diversity and rapid spatial turnover of integron gene cassettes in soil.}, journal = {Environmental microbiology}, volume = {21}, number = {5}, pages = {1567-1574}, doi = {10.1111/1462-2920.14551}, pmid = {30724441}, issn = {1462-2920}, support = {DP130103839//Australian Research Council/International ; }, mesh = {Antarctic Regions ; Anti-Bacterial Agents/pharmacology ; Australia ; Bacteria/classification/drug effects/*genetics/isolation & purification ; *Biodiversity ; Drug Resistance, Bacterial ; *Integrons ; Metagenome ; Phylogeny ; *Soil Microbiology ; }, abstract = {Integrons are genetic elements that promote rapid adaptation in bacteria by capturing exogenous, mobile gene cassettes. Recently, a subset of gene cassettes has facilitated the global spread of antibiotic resistance. However, outside clinical settings, very little is known about their diversity and spatial ecology. To address this question, we sequenced integron gene cassettes from soils sampled across Australia and Antarctica. We recovered 44 970 open reading frames that encoded 27 215 unique proteins, representing an order of magnitude more cassettes than previous sequencing efforts. We found that cassettes have extremely high local richness, significantly greater than previously predicted, with estimates ranging from 4000 to 18 000 unique cassettes per 0.3 g of soil. We show that cassettes have a heterogeneous distribution across space, and that they exhibit rapid turnover with distance. Similarity between samples drops to between 0.1% and 10% at distances of as little as 100 m. Together, these data provide key insights into the ecology and size of the gene cassette metagenome.}, } @article {pmid30724439, year = {2019}, author = {Ramos-Barbero, MD and Martínez, JM and Almansa, C and Rodríguez, N and Villamor, J and Gomariz, M and Escudero, C and Rubin, SD and Antón, J and Martínez-García, M and Amils, R}, title = {Prokaryotic and viral community structure in the singular chaotropic salt lake Salar de Uyuni.}, journal = {Environmental microbiology}, volume = {21}, number = {6}, pages = {2029-2042}, doi = {10.1111/1462-2920.14549}, pmid = {30724439}, issn = {1462-2920}, support = {CGL2015-66242-R//MINECO/International ; CLG2015_66686-C3-3//MINECO/International ; //European Regional Development Fund (FEDER)/International ; }, mesh = {Archaea/classification/genetics/*isolation & purification ; Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; Lakes/analysis/*microbiology/*virology ; Metagenome ; Phylogeny ; Salinity ; Viruses/classification/genetics/*isolation & purification ; }, abstract = {Salar de Uyuni (SdU) is the largest hypersaline salt flat and the highest lithium reservoir on Earth. In addition to extreme temperatures and high UV irradiance, SdU has high concentrations of chaotropic salts which can be important factors in controlling microbial diversity. Here, for the first time we characterize the viral diversity of this hypersaline environment during the two seasons, as well as the physicochemical characteristics and the prokaryotic communities of the analysed samples. Most of the selected samples showed a peculiar physicochemical composition and prokaryotic diversity, mostly different from each other even for samples from locations in close proximity or the same season. In contrast to most hypersaline systems Bacteria frequently outnumbered Archaea. Furthermore, an outstanding percentage of members of Salinibacter sp., likely a species different from the cosmopolitan Salinibacter ruber, was obtained in most of the samples. Viral communities displayed the morphologies normally found in hypersaline environments. Two seasonal samples were chosen for a detailed metagenomic analysis of the viral assemblage. Both viral communities shared common sequences but were dominated by sample-specific viruses, mirroring the differences also observed in physicochemical and prokaryotic community composition. These metaviromes were distinct from those detected in other hypersaline systems analysed to date.}, } @article {pmid30724437, year = {2019}, author = {Ma, Y and Zilles, JL and Kent, AD}, title = {An evaluation of primers for detecting denitrifiers via their functional genes.}, journal = {Environmental microbiology}, volume = {21}, number = {4}, pages = {1196-1210}, doi = {10.1111/1462-2920.14555}, pmid = {30724437}, issn = {1462-2920}, support = {//U.S. Department of Agriculture/International ; 2015-67019-23584//National Institute of Food and Agriculture/International ; }, mesh = {Base Sequence ; DNA Primers/genetics/*standards ; Denitrification/*genetics ; Ecosystem ; Metagenome ; Microbiota/*genetics ; Nitrogen ; Soil ; *Soil Microbiology ; }, abstract = {Microbial populations provide nitrogen cycling ecosystem services at the nexus of agriculture, environmental quality and climate change. Denitrification, in particular, impacts socio-environmental systems in both positive and negative ways, through reduction of aquatic and atmospheric nitrogen pollution, but also reduction of soil fertility and production of greenhouse gases. However, denitrification rates are quite variable in time and space, and therefore difficult to model. Microbial ecology is working to improve the predictive ecology of denitrifiers by quantifying and describing the diversity of microbial functional groups. However, metagenomic sequencing has revealed previously undescribed diversity within these functional groups, and highlighted a need to reevaluate coverage of existing DNA primers for denitrification functional genes. We provide here a comprehensive in silico evaluation of primer sets that target diagnostic genes in the denitrification pathway. This analysis makes use of current DNA sequence data available for each functional gene. It contributes a comparative analysis of the strengths and limitations of each primer set for describing denitrifier functional groups. This analysis identifies genes for which development of new tools is needed, and aids in interpretation of existing datasets, both of which will facilitate application of molecular methods to further develop the predictive ecology of denitrifiers.}, } @article {pmid30720800, year = {2019}, author = {Bukin, YS and Galachyants, YP and Morozov, IV and Bukin, SV and Zakharenko, AS and Zemskaya, TI}, title = {The effect of 16S rRNA region choice on bacterial community metabarcoding results.}, journal = {Scientific data}, volume = {6}, number = {}, pages = {190007}, pmid = {30720800}, issn = {2052-4463}, mesh = {Bacteria/genetics ; Computational Biology/methods ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing ; Lakes ; Metagenomics/*methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; Russia ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {In this work, we compare the resolution of V2-V3 and V3-V4 16S rRNA regions for the purposes of estimating microbial community diversity using paired-end Illumina MiSeq reads, and show that the fragment, including V2 and V3 regions, has higher resolution for lower-rank taxa (genera and species). It allows for a more precise distance-based clustering of reads into species-level OTUs. Statistically convergent estimates of the diversity of major species (defined as those that together are covered by 95% of reads) can be achieved at the sample sizes of 10000 to 15000 reads. The relative error of the Shannon index estimate for this condition is lower than 4%.}, } @article {pmid30719705, year = {2019}, author = {Cheng, L and Chen, Y and Zhang, X and Zheng, X and Cao, J and Wu, Z and Qin, W and Cheng, K}, title = {A metagenomic analysis of the modulatory effect of Cyclocarya paliurus flavonoids on the intestinal microbiome in a high-fat diet-induced obesity mouse model.}, journal = {Journal of the science of food and agriculture}, volume = {99}, number = {8}, pages = {3967-3975}, doi = {10.1002/jsfa.9622}, pmid = {30719705}, issn = {1097-0010}, support = {//K. C. Wong Magna Fund of Ningbo University/ ; 2017C02039//Key Research and Development Project of Zhejiang Province/ ; 2018C02047//Key Research and Development Project of Zhejiang Province/ ; LY19C200006//Zhejiang Provincial Natural Science Foundation of China/ ; }, mesh = {Adult ; Animals ; Bacteria/classification/drug effects/*genetics/isolation & purification ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Dysbiosis/drug therapy/metabolism/microbiology ; Female ; Flavonoids/*administration & dosage/analysis ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestines/*microbiology ; Juglandaceae/*chemistry ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Obesity/*drug therapy/microbiology ; Plant Extracts/*administration & dosage/analysis ; }, abstract = {BACKGROUND: As a result of a low bioavailability, the majority of Cyclocarya paliurus flavonoids (CPF) remain in the large intestine where they accumulate to exert a modulatory effect on the intestinal micro-ecology. Therefore, the present study investigated the modulatory effect of CPF on intestinal microbiota.

RESULTS: CPF dramatically ameliorated the obesity-induced gut dysbiosis. A significant decrease (P < 0.05) was observed in the ratio of Firmicutes/Bacteroidetes after CPF treatment for 8 weeks. Moreover, Kyoto Encyclopedia of Genes and Genomes pathways of biosynthesis of amino acids, the two-component system and ATP-binding cassette transporters enriched the most differentially expressed genes after CPF intervention.

CONCLUSION: The results of the present study indicate that CPF might have prebiotic-like activity and could be used as a functional food component with potential therapeutic utility to prevent obesity-related metabolic disorders by manipulating the gut flora and affecting certain metabolic pathways, thus contributing to the improvement of human health. © 2019 Society of Chemical Industry.}, } @article {pmid30718869, year = {2019}, author = {Forster, SC and Kumar, N and Anonye, BO and Almeida, A and Viciani, E and Stares, MD and Dunn, M and Mkandawire, TT and Zhu, A and Shao, Y and Pike, LJ and Louie, T and Browne, HP and Mitchell, AL and Neville, BA and Finn, RD and Lawley, TD}, title = {A human gut bacterial genome and culture collection for improved metagenomic analyses.}, journal = {Nature biotechnology}, volume = {37}, number = {2}, pages = {186-192}, pmid = {30718869}, issn = {1546-1696}, support = {/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/classification ; Computational Biology/methods ; Contig Mapping ; Gastrointestinal Microbiome ; *Genome, Bacterial ; Genome, Human ; Humans ; *Metagenome ; *Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/metabolism ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Understanding gut microbiome functions requires cultivated bacteria for experimental validation and reference bacterial genome sequences to interpret metagenome datasets and guide functional analyses. We present the Human Gastrointestinal Bacteria Culture Collection (HBC), a comprehensive set of 737 whole-genome-sequenced bacterial isolates, representing 273 species (105 novel species) from 31 families found in the human gastrointestinal microbiota. The HBC increases the number of bacterial genomes derived from human gastrointestinal microbiota by 37%. The resulting global Human Gastrointestinal Bacteria Genome Collection (HGG) classifies 83% of genera by abundance across 13,490 shotgun-sequenced metagenomic samples, improves taxonomic classification by 61% compared to the Human Microbiome Project (HMP) genome collection and achieves subspecies-level classification for almost 50% of sequences. The improved resource of gastrointestinal bacterial reference sequences circumvents dependence on de novo assembly of metagenomes and enables accurate and cost-effective shotgun metagenomic analyses of human gastrointestinal microbiota.}, } @article {pmid30718868, year = {2019}, author = {Zou, Y and Xue, W and Luo, G and Deng, Z and Qin, P and Guo, R and Sun, H and Xia, Y and Liang, S and Dai, Y and Wan, D and Jiang, R and Su, L and Feng, Q and Jie, Z and Guo, T and Xia, Z and Liu, C and Yu, J and Lin, Y and Tang, S and Huo, G and Xu, X and Hou, Y and Liu, X and Wang, J and Yang, H and Kristiansen, K and Li, J and Jia, H and Xiao, L}, title = {1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses.}, journal = {Nature biotechnology}, volume = {37}, number = {2}, pages = {179-185}, pmid = {30718868}, issn = {1546-1696}, mesh = {Bacteria/classification ; Cluster Analysis ; Computational Biology/*methods ; Conserved Sequence ; Feces ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Genomics ; Humans ; *Metagenome ; Metagenomics ; Phylogeny ; Polymorphism, Single Nucleotide ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Reference genomes are essential for metagenomic analyses and functional characterization of the human gut microbiota. We present the Culturable Genome Reference (CGR), a collection of 1,520 nonredundant, high-quality draft genomes generated from >6,000 bacteria cultivated from fecal samples of healthy humans. Of the 1,520 genomes, which were chosen to cover all major bacterial phyla and genera in the human gut, 264 are not represented in existing reference genome catalogs. We show that this increase in the number of reference bacterial genomes improves the rate of mapping metagenomic sequencing reads from 50% to >70%, enabling higher-resolution descriptions of the human gut microbiome. We use the CGR genomes to annotate functions of 338 bacterial species, showing the utility of this resource for functional studies. We also carry out a pan-genome analysis of 38 important human gut species, which reveals the diversity and specificity of functional enrichment between their core and dispensable genomes.}, } @article {pmid30718848, year = {2019}, author = {Valles-Colomer, M and Falony, G and Darzi, Y and Tigchelaar, EF and Wang, J and Tito, RY and Schiweck, C and Kurilshikov, A and Joossens, M and Wijmenga, C and Claes, S and Van Oudenhove, L and Zhernakova, A and Vieira-Silva, S and Raes, J}, title = {The neuroactive potential of the human gut microbiota in quality of life and depression.}, journal = {Nature microbiology}, volume = {4}, number = {4}, pages = {623-632}, pmid = {30718848}, issn = {2058-5276}, mesh = {3,4-Dihydroxyphenylacetic Acid/metabolism ; Adult ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Cohort Studies ; Depression/metabolism/*microbiology/psychology ; Dopamine/metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestines/microbiology ; Male ; Middle Aged ; Quality of Life ; }, abstract = {The relationship between gut microbial metabolism and mental health is one of the most intriguing and controversial topics in microbiome research. Bidirectional microbiota-gut-brain communication has mostly been explored in animal models, with human research lagging behind. Large-scale metagenomics studies could facilitate the translational process, but their interpretation is hampered by a lack of dedicated reference databases and tools to study the microbial neuroactive potential. Surveying a large microbiome population cohort (Flemish Gut Flora Project, n = 1,054) with validation in independent data sets (ntotal = 1,070), we studied how microbiome features correlate with host quality of life and depression. Butyrate-producing Faecalibacterium and Coprococcus bacteria were consistently associated with higher quality of life indicators. Together with Dialister, Coprococcus spp. were also depleted in depression, even after correcting for the confounding effects of antidepressants. Using a module-based analytical framework, we assembled a catalogue of neuroactive potential of sequenced gut prokaryotes. Gut-brain module analysis of faecal metagenomes identified the microbial synthesis potential of the dopamine metabolite 3,4-dihydroxyphenylacetic acid as correlating positively with mental quality of life and indicated a potential role of microbial γ-aminobutyric acid production in depression. Our results provide population-scale evidence for microbiome links to mental health, while emphasizing confounder importance.}, } @article {pmid30718047, year = {2019}, author = {Zegarra-Ruiz, DF and Diehl, GE}, title = {Skin IL-17-Producing T Cells Support Repair 2!.}, journal = {Trends in immunology}, volume = {40}, number = {3}, pages = {177-179}, doi = {10.1016/j.it.2019.01.004}, pmid = {30718047}, issn = {1471-4981}, mesh = {Animals ; Cytokines/metabolism ; Humans ; Immunity, Cellular ; Mice ; Microbiota/*immunology ; Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism ; Receptors, Antigen, T-Cell/metabolism ; Th2 Cells/*immunology ; *Wound Healing ; }, abstract = {In a recent study, Harrison et al. (Science 2019;363;eaat6280) report that RORγt-expressing skin commensal-specific T cells rapidly respond to tissue wounding by producing type 2 T helper cell (Th2) cytokines in mice. The cells constitutively coexpress GATA-3 and type 2 cytokine mRNAs that are translated after injury. These T cells act as sentinels, linking T cell receptor (TCR) recognition of commensals, tissue damage, and wound repair.}, } @article {pmid30717674, year = {2019}, author = {Lei, Z and Zhang, K and Li, C and Jiao, T and Wu, J and Wei, Y and Tian, K and Li, C and Tang, D and Davis, DI and Casper, DP and Jiang, H and Wang, X and Wang, J}, title = {Ruminal metagenomic analyses of goat data reveals potential functional microbiota by supplementation with essential oil-cobalt complexes.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {30}, pmid = {30717674}, issn = {1471-2180}, mesh = {Animal Feed/analysis ; Animals ; Cobalt/*administration & dosage ; *Dietary Supplements ; Digestion ; Fatty Acids, Volatile/metabolism ; Fermentation ; Goats ; Male ; *Metagenomics ; Methane/metabolism ; Microbiota/*drug effects ; Oils, Volatile/*administration & dosage ; Rumen/*microbiology ; }, abstract = {BACKGROUND: Essential Oils (EO) are complex mixtures of plant secondary metabolites that have been proposed as promising feed additives for mitigating methane and ammonia emissions. We have previously demonstrated that Essential Oil-Cobalt (EOC) supplementation resulted in increased average daily gain and improved phenotypes (cashmere fiber traits, carcass weight, and meat quality) when cashmere goats received supplementation at approximately 2 mg/kg of body weight. However, the ruminal microbiological effects of EO remain poorly understood with regard to the extent to which ruminal populations can adapt to EO presence as feed ingredients. The effects of varying levels of EO require additional study.

RESULTS: In this study, we conducted metagenomic analyses using ruminal fluid samples from three groups (addition of 0, 52, and 91 mg) to evaluate the influence of dietary EOC supplementation on goat rumen bacterial community dynamics. EOC addition resulted in changes of ruminal fermentation types and the EOC dose strongly impacted the stability of ruminal microbiota. The Bacteroides sp. and Succinivibrio sp. type bacterial community was positively associated with improved volatile fatty acid production when the diet was supplemented with EOC.

CONCLUSIONS: A clear pattern was found that reflected rapid fermentative improvement in the rumen, subsequent to butyrate metabolism and EOC based feed additives may affect rumen microbes to further improve feed conversion. This observation indicates that EOC can be safely used to enhance animal productivity and to reduce ammonia and waste gas emissions, thus positively impacting the environment.}, } @article {pmid30717665, year = {2019}, author = {Jayasundara, D and Herath, D and Senanayake, D and Saeed, I and Yang, CY and Sun, Y and Chang, BC and Tang, SL and Halgamuge, SK}, title = {ENVirT: inference of ecological characteristics of viruses from metagenomic data.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 13}, pages = {377}, pmid = {30717665}, issn = {1471-2105}, support = {LP140100670//Australian Research Council/ ; DP150103512//Australian Research Council/ ; }, mesh = {*Algorithms ; Computer Simulation ; *Ecological and Environmental Phenomena ; Fermented Foods ; Gastrointestinal Microbiome ; Genome, Viral ; Humans ; Lakes/virology ; *Metagenomics ; Time Factors ; Viruses/genetics ; }, abstract = {BACKGROUND: Estimating the parameters that describe the ecology of viruses,particularly those that are novel, can be made possible using metagenomic approaches. However, the best-performing existing methods require databases to first estimate an average genome length of a viral community before being able to estimate other parameters, such as viral richness. Although this approach has been widely used, it can adversely skew results since the majority of viruses are yet to be catalogued in databases.

RESULTS: In this paper, we present ENVirT, a method for estimating the richness of novel viral mixtures, and for the first time we also show that it is possible to simultaneously estimate the average genome length without a priori information. This is shown to be a significant improvement over database-dependent methods, since we can now robustly analyze samples that may include novel viral types under-represented in current databases. We demonstrate that the viral richness estimates produced by ENVirT are several orders of magnitude higher in accuracy than the estimates produced by existing methods named PHACCS and CatchAll when benchmarked against simulated data. We repeated the analysis of 20 metavirome samples using ENVirT, which produced results in close agreement with complementary in virto analyses.

CONCLUSIONS: These insights were previously not captured by existing computational methods. As such, ENVirT is shown to be an essential tool for enhancing our understanding of novel viral populations.}, } @article {pmid30717284, year = {2019}, author = {Ai, D and Pan, H and Han, R and Li, X and Liu, G and Xia, LC}, title = {Using Decision Tree Aggregation with Random Forest Model to Identify Gut Microbes Associated with Colorectal Cancer.}, journal = {Genes}, volume = {10}, number = {2}, pages = {}, pmid = {30717284}, issn = {2073-4425}, support = {HG006137-07//Foundation for the National Institutes of Health/International ; }, mesh = {*Algorithms ; Colorectal Neoplasms/*microbiology ; Firmicutes/genetics/isolation & purification ; Fusobacterium/genetics/isolation & purification ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; Porphyromonas/genetics/isolation & purification ; Sequence Analysis, DNA/methods ; }, abstract = {The imbalance of human gut microbiota has been associated with colorectal cancer. In recent years, metagenomics research has provided a large amount of scientific data enabling us to study the dedicated roles of gut microbes in the onset and progression of cancer. We removed unrelated and redundant features during feature selection by mutual information. We then trained a random forest classifier on a large metagenomics dataset of colorectal cancer patients and healthy people assembled from published reports and extracted and analysed the information from the learned decision trees. We identified key microbial species associated with colorectal cancers. These microbes included Porphyromonasasaccharolytica, Peptostreptococcusstomatis, Fusobacterium,Parvimonas sp., Streptococcusvestibularis and Flavonifractorplautii. We obtained the optimal splitting abundance thresholds for these species to distinguish between healthy and colorectal cancer samples. This extracted consensus decision tree may be applied to the diagnosis of colorectal cancers.}, } @article {pmid30716065, year = {2019}, author = {Louca, S and Mazel, F and Doebeli, M and Parfrey, LW}, title = {A census-based estimate of Earth's bacterial and archaeal diversity.}, journal = {PLoS biology}, volume = {17}, number = {2}, pages = {e3000106}, pmid = {30716065}, issn = {1545-7885}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biodiversity ; Databases, Genetic ; *Earth, Planet ; Phylogeny ; Prokaryotic Cells/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The global diversity of Bacteria and Archaea, the most ancient and most widespread forms of life on Earth, is a subject of intense controversy. This controversy stems largely from the fact that existing estimates are entirely based on theoretical models or extrapolations from small and biased data sets. Here, in an attempt to census the bulk of Earth's bacterial and archaeal ("prokaryotic") clades and to estimate their overall global richness, we analyzed over 1.7 billion 16S ribosomal RNA amplicon sequences in the V4 hypervariable region obtained from 492 studies worldwide, covering a multitude of environments and using multiple alternative primers. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs, 16S-V4 gene clusters at 97% similarity), a commonly used measure of microbial richness. Using several statistical approaches, we estimate that there exist globally about 0.8-1.6 million prokaryotic OTUs, of which we recovered somewhere between 47%-96%, representing >99.98% of prokaryotic cells. Consistent with this conclusion, our data set independently "recaptured" 91%-93% of 16S sequences from multiple previous global surveys, including PCR-independent metagenomic surveys. The distribution of relative OTU abundances is consistent with a log-normal model commonly observed in larger organisms; the total number of OTUs predicted by this model is also consistent with our global richness estimates. By combining our estimates with the ratio of full-length versus partial-length (V4) sequence diversity in the SILVA sequence database, we further estimate that there exist about 2.2-4.3 million full-length OTUs worldwide. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar richness estimates as for the global data set, suggesting that most OTUs are globally distributed. Qualitatively similar results are also obtained for other 16S similarity thresholds (90%, 95%, and 99%). Our estimates constrain the extent of a poorly quantified rare microbial biosphere and refute recent predictions that there exist trillions of prokaryotic OTUs.}, } @article {pmid30715365, year = {2019}, author = {Goss-Souza, D and Mendes, LW and Borges, CD and Rodrigues, JLM and Tsai, SM}, title = {Amazon forest-to-agriculture conversion alters rhizosphere microbiome composition while functions are kept.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {3}, pages = {}, doi = {10.1093/femsec/fiz009}, pmid = {30715365}, issn = {1574-6941}, mesh = {Agriculture/methods ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Conservation of Natural Resources ; Forests ; Metagenomics ; *Microbiota/genetics ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; Glycine max/microbiology ; }, abstract = {The conversion of native forest to agriculture is the main cause of microbial biodiversity loss in Amazon soils. In order to better understand this effect, we used metagenomics to investigate microbial patterns and functions in bulk soil and rhizosphere of soybean, in a long-term forest-to-agriculture conversion. Long-term forest-to-agriculture led to microbial homogenization and loss of diversity in both bulk soil and rhizosphere, mainly driven by decreasing aluminum concentration and increased cations saturation in soil, due to liming and fertilization in long-term no-till cropping. Data revealed that long-term no-till cropping culminated in a decrease in Acidobacteria, Actinobacteria and Proteobacteria abundances. However, α- and β-Proteobacteria abundances were higher in the rhizosphere than in bulk soil, regardless of the time after forest-to-agriculture conversion. Changes in functional potential occurred predominantly in bulk soil, with decreases in functions related to potassium metabolism and virulence, disease and defense, while functions related to nucleic acids metabolism increased. Functions in the soybean rhizosphere remained stable, except for those related to potassium metabolism, which decreased after 20-year no-till cropping. Together, our results show that the soybean root system selects microbial taxa via trade-offs, to maintain functional resilience in the rhizosphere microbiome over time.}, } @article {pmid30712189, year = {2019}, author = {Brito, EMS and Romero-Núñez, VM and Caretta, CA and Bertin, P and Valerdi-Negreros, JC and Guyoneaud, R and Goñi-Urriza, M}, title = {The bacterial diversity on steam vents from Paricutín and Sapichu volcanoes.}, journal = {Extremophiles : life under extreme conditions}, volume = {23}, number = {2}, pages = {249-263}, pmid = {30712189}, issn = {1433-4909}, support = {0627/15//Convocatoria de Apoyo a la Investigacion de la UG (DAIP)/ ; ANR-CONACyT-188775//Biometal Project/ ; }, mesh = {Bacteria/*classification/genetics/isolation & purification ; Hydrothermal Vents/*microbiology ; *Microbiota ; Phylogeny ; *Volcanic Eruptions ; }, abstract = {Vapor steam vents are prevailing structures on geothermal sites in which local geochemical conditions allow the development of extremophilic microorganisms. We describe the structure of the prokaryotic community able to grow on the walls and rocks of such microecosystems in two terrestrial Mexican volcanoes: Paricutín (PI and PII samples) and its satellite Sapichu (S sample). The investigated samples showed similar diversity indices, with few dominant OTUs (abundance > 1%): 21, 16 and 23, respectively for PI, PII and S. However, each steam vent showed a particular community profile: PI was dominated by photosynthetic bacteria (Cyanobacteria and Chloroflexia class), PII by Actinobacteria and Proteobacteria, and S by Ktedonobacteria class, Acidobacteria and Cyanobacteria phyla. Concerning the predicted metabolic potential, we found a dominance of cellular pathways, especially the ones for energy generation with metabolisms for sulfur respiration, nitrogen fixation, methanogenesis, carbon fixation, photosynthesis, and metals, among others. We suggest a different maturity stage for the three studied fumaroles, from the youngest (PI) to the oldest (S and PII), also influenced by the temperature and other geochemical parameters. Furthermore, four anaerobic strains were isolated, belonging to Clostridia class (Clostridium sphenoides, C. swellfunanium and Anaerocolumna cellulosilytica) and to Bacilli class (Paenibacillus azoreducens).}, } @article {pmid30710817, year = {2019}, author = {Pore, SD and Engineer, A and Dagar, SS and Dhakephalkar, PK}, title = {Meta-omics based analyses of microbiome involved in biomethanation of rice straw in a thermophilic anaerobic bioreactor under optimized conditions.}, journal = {Bioresource technology}, volume = {279}, number = {}, pages = {25-33}, doi = {10.1016/j.biortech.2019.01.099}, pmid = {30710817}, issn = {1873-2976}, mesh = {Anaerobiosis ; Animals ; *Bioreactors ; Carbon/metabolism ; Cattle ; Euryarchaeota/metabolism ; Hydrolysis ; Methane/*biosynthesis ; Methanobacteriaceae/metabolism ; *Microbiota ; Nitrogen/metabolism ; Oryza/*metabolism ; }, abstract = {Biomethanation of rice straw was performed at 55 °C without thermochemical pretreatment using cattle dung supplemented with Methanothermobacter thermautotrophicus strains. Methane yield of 323 ml g[-1] VS obtained under optimized conditions such as particle size (1 mm), carbon to nitrogen ratio (15:1), substrate to inoculum ratio (1:1), organic loading rate (7.5% w/v) and hydraulic retention time (20 days), was one of the highest ever reported from rice straw. Metagenome analysis revealed several putative novel taxa among resident microbes. The genomes of Clostridium, Hungateiclostridium, Alkaliphilus, Anaerocolumna, Olsenella, Paenibacillus, Pseudoclostridium, Tepidanaerobacter and Turicibacter were recovered as metagenome assisted genomes. Clostridium spp. and M. thermautotrophicus were the dominant hydrolytic and methanogenic microbes, respectively. Syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis was found to be the major pathway for methane production. Efficient thermophilic biomethanation of rice straw without thermochemical pretreatment using cattle dung supplemented with M. thermautotrophicus is reported for the first time.}, } @article {pmid30710781, year = {2019}, author = {Sun, FL and Fan, LL and Wang, YS and Huang, LY}, title = {Metagenomic analysis of the inhibitory effect of chromium on microbial communities and removal efficiency in A2O sludge.}, journal = {Journal of hazardous materials}, volume = {368}, number = {}, pages = {523-529}, doi = {10.1016/j.jhazmat.2019.01.076}, pmid = {30710781}, issn = {1873-3336}, mesh = {Bacteria/classification/drug effects/genetics ; Bioreactors ; Chromium/*toxicity ; High-Throughput Nucleotide Sequencing ; Microbiota/*drug effects/genetics ; RNA, Ribosomal, 16S ; Sewage/microbiology ; Water Pollutants, Chemical/*toxicity ; }, abstract = {This is the first study exploring the effects of persistent Cr(VI) treatment on microbial communities and function as well as the process efficiency of an A2O system. The inhibitory effect was clearly higher at a high Cr(VI) concentration than a low Cr(VI) concentration, and different Cr(VI) concentrations had distinct effects on the microbial communities as well as on the performance efficiency of the system. Functional annotation analysis indicated that Cr(VI) stress inhibited most of the metabolic pathway and functional genes of the microbial communities, especially those involved in the denitrification pathway. Network analysis was used to investigate the co-occurrence patterns between denitrification genes and microbial taxa; the results indicated that microorganisms with functional genes had high diversity and were adversely affected by Cr(VI) exposure. This study is the first to establish a relationship between Cr(VI) stress and microbial communities and function as well as to determine the underlying mechanisms and roles of Cr(VI) in A2O sludge.}, } @article {pmid30709420, year = {2019}, author = {Shi, W and Li, M and Wei, G and Tian, R and Li, C and Wang, B and Lin, R and Shi, C and Chi, X and Zhou, B and Gao, Z}, title = {The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {14}, pmid = {30709420}, issn = {2049-2618}, mesh = {Geologic Sediments/microbiology ; Microbiota/*genetics ; Plant Diseases/*microbiology ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil Microbiology ; Solanum tuberosum/*microbiology ; Streptomyces/*classification/genetics/*isolation & purification ; }, abstract = {BACKGROUND: Soil microorganisms can mediate the occurrence of plant diseases. Potato common scab (CS) is a refractory disease caused by pathogenic Streptomyces that occurs worldwide, but little is known about the interactions between CS and the soil microbiome. In this study, four soil-root system compartments (geocaulosphere soil (GS), rhizosphere soil (RS), root-zone soil (ZS), and furrow soil (FS)) were analyzed for potato plants with naturally high (H) and low (L) scab severity levels. We aimed to determine the composition and putative function of the soil microbiome associated with potato CS.

RESULTS: The copy numbers of the scab phytotoxin biosynthetic gene txtAB and the bacterial 16S rRNA gene as well as the diversity and composition of each of the four soil-root system compartments were examined; GS was the only compartment that exhibited significant differences between the H and L groups. Compared to the H group, the L group exhibited a lower txtAB gene copy number, lower bacterial 16S copy number, higher diversity, higher co-occurrence network complexity, and higher community function similarity within the GS microbiome. The community composition and function of the GS samples were further revealed by shotgun metagenomic sequencing. Variovorax, Stenotrophomonas, and Agrobacterium were the most abundant genera that were significantly and positively correlated with the scab severity level, estimated absolute abundance (EAA) of pathogenic Streptomyces, and txtAB gene copy number. In contrast, Geobacillus, Curtobacterium, and unclassified Geodermatophilaceae were significantly negatively correlated with these three parameters. Compared to the function profiles in the L group, several genes involved in "ABC transporters," the "bacterial secretion system," "quorum sensing (QS)," "nitrogen metabolism," and some metabolism by cytochrome P450 were enriched in the H group. In contrast, some antibiotic biosynthesis pathways were enriched in the L group. Based on the differences in community composition and function, a simple model was proposed to explain the putative relationships between the soil microbiome and CS occurrence.

CONCLUSIONS: The GS microbiome was closely associated with CS severity in the soil-root system, and the occurrence of CS was accompanied by changes in community composition and function. The differential functions provide new clues to elucidate the mechanism underlying the interaction between CS occurrence and the soil microbiome, and varying community compositions provide novel insights into CS occurrence.}, } @article {pmid30709012, year = {2019}, author = {Dang, Z and McLenachan, PA and Lockhart, PJ and Waipara, N and Er, O and Reynolds, C and Blanchon, D}, title = {Metagenome Profiling Identifies Potential Biocontrol Agents for Selaginella kraussiana in New Zealand.}, journal = {Genes}, volume = {10}, number = {2}, pages = {}, pmid = {30709012}, issn = {2073-4425}, mesh = {Introduced Species ; *Metagenome ; Pseudomonas syringae/pathogenicity ; Selaginellaceae/*genetics/microbiology ; Weed Control/methods ; Xanthomonas/pathogenicity ; }, abstract = {Metagenomics can be used to identify potential biocontrol agents for invasive species and was used here to identify candidate species for biocontrol of an invasive club moss in New Zealand. Profiles were obtained for Selaginella kraussiana collected from nine geographically disjunct locations in Northern New Zealand. These profiles were distinct from those obtained for the exotic club moss Selaginella moellendorffii and the native club mosses Lycopodium deuterodensum and Lycopodium volubile also collected in Northern New Zealand. Fungi and bacteria implicated elsewhere in causing plant disease were identified on plants of Selaginella that exhibited signs of necrosis. Most notably, high densities of sequence reads from Xanthomonas translucens and Pseudomonas syringae were associated with some populations of Selaginella but not Lycopodium. Since these bacteria are already in use as biocontrol agents elsewhere, further investigation into their potential as biocontrol of Selaginella in New Zealand is suggested.}, } @article {pmid30706916, year = {2019}, author = {Li, Y and Han, H and Yin, J and He, X and Tang, Z and Li, T and Yao, K and Yin, Y}, title = {d- and l-Aspartate regulates growth performance, inflammation and intestinal microbial community in young pigs.}, journal = {Food & function}, volume = {10}, number = {2}, pages = {1028-1037}, doi = {10.1039/c8fo01410h}, pmid = {30706916}, issn = {2042-650X}, mesh = {Animal Feed ; Animal Nutritional Physiological Phenomena ; Animals ; Aspartic Acid/administration & dosage/*pharmacology ; Bacteria/classification/genetics ; Diet/veterinary ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Regulation/drug effects/immunology ; Inflammation/*prevention & control ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Random Allocation ; Swine/*growth & development ; }, abstract = {d-aspartate (d-Asp), an endogenous amino acid, occurs widely in animals and humans with d-enantiomers and plays an important role in the endocrine and nervous systems. However, very few studies are available on growth performance, microbial community, and the intestinal immune and inflammatory status in response to d- and l-aspartate (l-Asp). Thus, in this study, we mainly investigated the effects of dietary 1% d- and l-Asp on growth performance, inflammation, and microbial community in young pigs. Twenty-eight young pigs were randomly divided into four groups (n = 7): a control group, in which piglets were fed a basal diet, and other three groups, in which piglets received 1% d-Asp, 1% l-Asp, and 1% dl-aspartate (dl-Asp) for 35 days. The results showed that dietary 1% d-Asp significantly inhibited average daily feed intake and average daily weight gain. Gut microbes were tested and the results showed that l-Asp enhanced bacterial diversity (Shannon and Simpson). At the phylum level, l-Asp enhanced intestinal Actinobacteria and Bacteroidetes abundance but decreased Firmicutes abundance. In contrast, dl-Asp decreased intestinal Actinobacteria and Bacteroidetes abundance and increased Firmicutes abundance. At the genus level, d-Asp enhanced Clostridium sensu stricto 1 and Intestinibacter abundance. Metagenomic predictions by PICRUSt suggested that the altered microbiota were mainly involved in membrane transport, carbohydrate metabolism, amino acid metabolism, replication and repair, translation, and nucleotide metabolism. In addition, dl-Asp markedly increased the activities of serum alanine aminotransferase, aspartate transaminase and alkaline phosphatase. Also, dietary d- and dl-Asp down-regulated TLR 4, NOD1, and MyD88 in the jejunum to mediate the inflammatory response. Collectively, these results indicated that dietary d-Asp and l-Asp affect the growth performance and inflammation in piglets, which might be associated with gut microbiota.}, } @article {pmid30705275, year = {2019}, author = {Zhang, W and Ding, W and Li, YX and Tam, C and Bougouffa, S and Wang, R and Pei, B and Chiang, H and Leung, P and Lu, Y and Sun, J and Fu, H and Bajic, VB and Liu, H and Webster, NS and Qian, PY}, title = {Marine biofilms constitute a bank of hidden microbial diversity and functional potential.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {517}, pmid = {30705275}, issn = {2041-1723}, mesh = {Biodiversity ; *Biofilms ; CRISPR-Cas Systems/genetics/physiology ; Metagenome/genetics ; Seawater/microbiology ; }, abstract = {Recent big data analyses have illuminated marine microbial diversity from a global perspective, focusing on planktonic microorganisms. Here, we analyze 2.5 terabases of newly sequenced datasets and the Tara Oceans metagenomes to study the diversity of biofilm-forming marine microorganisms. We identify more than 7,300 biofilm-forming 'species' that are undetected in seawater analyses, increasing the known microbial diversity in the oceans by more than 20%, and provide evidence for differentiation across oceanic niches. Generation of a gene distribution profile reveals a functional core across the biofilms, comprised of genes from a variety of microbial phyla that may play roles in stress responses and microbe-microbe interactions. Analysis of 479 genomes reconstructed from the biofilm metagenomes reveals novel biosynthetic gene clusters and CRISPR-Cas systems. Our data highlight the previously underestimated ocean microbial diversity, and allow mining novel microbial lineages and gene resources.}, } @article {pmid30704595, year = {2019}, author = {Kamimura, BA and De Filippis, F and Sant'Ana, AS and Ercolini, D}, title = {Large-scale mapping of microbial diversity in artisanal Brazilian cheeses.}, journal = {Food microbiology}, volume = {80}, number = {}, pages = {40-49}, doi = {10.1016/j.fm.2018.12.014}, pmid = {30704595}, issn = {1095-9998}, mesh = {Animals ; *Biodiversity ; Brazil ; Cheese/*microbiology ; Cluster Analysis ; DNA, Bacterial/genetics ; *Food Microbiology ; Geography ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Brazilian artisanal cheeses are characterized by the use of raw milk and in some cases, natural starter cultures, known as "pingo", as well as following simple and traditional manufacturing technology. In this study, a large-scale screening of the microbial ecology of 11 different types of artisanal cheeses produced in five geographical areas of Brazil was performed. Besides, the specific origin-related microbial signatures were identified. Clear geography- and technology-based differences in the microbiota were observed. Lactic acid bacteria dominated in all cheeses although Enterobacteriaceae and Staphylococcus also occurred in North, Northeast and Central cheeses. Differences in the lactic acid bacteria patterns were also highlighted: Streptococcus, Leuconostoc, Lactococcus and Lactobacillus were differently combined in terms of relative abundance according to product type and region of production. This study provides a comprehensive, unprecedented microbiological mapping of Brazilian cheeses, highlighting the impact of geographical origin and mode of production on microbial diversity. The results obtained will help to plan an evaluation of microbial contamination sources that will need to be studied for the improvement of cheese quality and safety.}, } @article {pmid30701707, year = {2019}, author = {Jerde, CL and Wilson, EA and Dressler, TL}, title = {Measuring global fish species richness with eDNA metabarcoding.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {19-22}, doi = {10.1111/1755-0998.12929}, pmid = {30701707}, issn = {1755-0998}, support = {AID-OAA-A-16-00057//United States Agency for International Development/ ; }, mesh = {Animals ; *Biodiversity ; Computational Biology ; DNA/chemistry/genetics/isolation & purification ; DNA Barcoding, Taxonomic/*methods ; Fishes/*classification/*genetics ; French Guiana ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Water/chemistry ; }, abstract = {Despite mounting threats to global freshwater and marine biodiversity, including climate change, habitat alteration, overharvesting and pollution, we struggle to know which species are present below the water's surface that are suffering from these stressors. However, the idea that a water sample containing environmental DNA (eDNA) can be screened using high-throughput sequencing and bioinformatics to reveal the identity of aquatic species is a revolutionary advance for studying the patterns of species extirpation, invasive species establishment and the dynamics of species richness. To date, many of the critical tests of fisheries diversity using this metabarcoding approach have been conducted in lower diversity systems (<40 fish species), but in this issue of Molecular Ecology Resources, Cilleros et al. (2018) described their eDNA application in the species-rich French Guiana fishery (>200 fish species) and showed the greater potential and some limitations of using eDNA in species-rich environments.}, } @article {pmid30701077, year = {2019}, author = {Lindefeldt, M and Eng, A and Darban, H and Bjerkner, A and Zetterström, CK and Allander, T and Andersson, B and Borenstein, E and Dahlin, M and Prast-Nielsen, S}, title = {The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy.}, journal = {NPJ biofilms and microbiomes}, volume = {5}, number = {1}, pages = {5}, pmid = {30701077}, issn = {2055-5008}, support = {R01 GM124312/GM/NIGMS NIH HHS/United States ; }, mesh = {Adolescent ; Bacteria/*classification/genetics ; Child ; Child, Preschool ; *Diet, Ketogenic ; Epilepsy/*therapy ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant ; Male ; Metagenomics ; Microbiota/*drug effects ; }, abstract = {The gut microbiota has been linked to various neurological disorders via the gut-brain axis. Diet influences the composition of the gut microbiota. The ketogenic diet (KD) is a high-fat, adequate-protein, low-carbohydrate diet established for treatment of therapy-resistant epilepsy in children. Its efficacy in reducing seizures has been confirmed, but the mechanisms remain elusive. The diet has also shown positive effects in a wide range of other diseases, including Alzheimer's, depression, autism, cancer, and type 2 diabetes. We collected fecal samples from 12 children with therapy-resistant epilepsy before starting KD and after 3 months on the diet. Parents did not start KD and served as diet controls. Applying shotgun metagenomic DNA sequencing, both taxonomic and functional profiles were established. Here we report that alpha diversity is not changed significantly during the diet, but differences in both taxonomic and functional composition are detected. Relative abundance of bifidobacteria as well as E. rectale and Dialister is significantly diminished during the intervention. An increase in relative abundance of E. coli is observed on KD. Functional analysis revealed changes in 29 SEED subsystems including the reduction of seven pathways involved in carbohydrate metabolism. Decomposition of these shifts indicates that bifidobacteria and Escherichia are important contributors to the observed functional shifts. As relative abundance of health-promoting, fiber-consuming bacteria becomes less abundant during KD, we raise concern about the effects of the diet on the gut microbiota and overall health. Further studies need to investigate whether these changes are necessary for the therapeutic effect of KD.}, } @article {pmid30700713, year = {2019}, author = {Coutinho, FH and Silveira, CB and Gregoracci, GB and Thompson, CC and Edwards, RA and Brussaard, CPD and Dutilh, BE and Thompson, FL}, title = {Reply to: Caution in inferring viral strategies from abundance correlations in marine metagenomes.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {502}, pmid = {30700713}, issn = {2041-1723}, mesh = {*Metagenome ; Phylogeny ; }, } @article {pmid30700057, year = {2019}, author = {Castillo Villamizar, GA and Nacke, H and Griese, L and Tabernero, L and Funkner, K and Daniel, R}, title = {Characteristics of the First Protein Tyrosine Phosphatase with Phytase Activity from a Soil Metagenome.}, journal = {Genes}, volume = {10}, number = {2}, pages = {}, pmid = {30700057}, issn = {2073-4425}, mesh = {6-Phytase/chemistry/*genetics/metabolism ; Amino Acid Motifs ; Bacterial Proteins/chemistry/*genetics/metabolism ; Cloning, Molecular ; *Metagenome ; Microbiota ; Mycobacterium tuberculosis/enzymology ; Phytic Acid/metabolism ; Protein Tyrosine Phosphatases/chemistry/*genetics/metabolism ; *Soil Microbiology ; }, abstract = {Protein tyrosine phosphatases (PTPs) fulfil multiple key regulatory functions. Within the group of PTPs, the atypical lipid phosphatases (ALPs) are known for their role as virulence factors associated with human pathogens. Another group of PTPs, which is capable of using inositol-hexakisphosphate (InsP6) as substrate, are known as phytases. Phytases play major roles in the environmental phosphorus cycle, biotechnology, and pathogenesis. So far, all functionally characterized PTPs, including ALPs and PTP-phytases, have been derived exclusively from isolated microorganisms. In this study, screening of a soil-derived metagenomic library resulted in identification of a gene (pho16B), encoding a PTP, which shares structural characteristics with the ALPs. In addition, the characterization of the gene product (Pho16B) revealed the capability of the protein to use InsP6 as substrate, and the potential of soil as a source of phytases with so far unknown characteristics. Thus, Pho16B represents the first functional environmentally derived PTP-phytase. The enzyme has a molecular mass of 38 kDa. The enzyme is promiscuous, showing highest activity and affinity toward naphthyl phosphate (Km 0.966 mM). Pho16B contains the HCXXGKDR[TA]G submotif of PTP-ALPs, and it is structurally related to PtpB of Mycobacterium tuberculosis. This study demonstrates the presence and functionality of an environmental gene codifying a PTP-phytase homologous to enzymes closely associated to bacterial pathogenicity.}, } @article {pmid30698687, year = {2019}, author = {Dhakan, DB and Maji, A and Sharma, AK and Saxena, R and Pulikkan, J and Grace, T and Gomez, A and Scaria, J and Amato, KR and Sharma, VK}, title = {The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches.}, journal = {GigaScience}, volume = {8}, number = {3}, pages = {}, pmid = {30698687}, issn = {2047-217X}, mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; Cluster Analysis ; Discriminant Analysis ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; *Genes ; Humans ; India ; Infant ; Least-Squares Analysis ; Membrane Transport Proteins/metabolism ; *Metabolome ; Metabolomics/*methods ; Metagenome ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Statistics, Nonparametric ; Young Adult ; }, abstract = {BACKGROUND: Metagenomic studies carried out in the past decade have led to an enhanced understanding of the gut microbiome in human health; however, the Indian gut microbiome has not been well explored. We analyzed the gut microbiome of 110 healthy individuals from two distinct locations (North-Central and Southern) in India using multi-omics approaches, including 16S rRNA gene amplicon sequencing, whole-genome shotgun metagenomic sequencing, and metabolomic profiling of fecal and serum samples.

RESULTS: The gene catalogue established in this study emphasizes the uniqueness of the Indian gut microbiome in comparison to other populations. The gut microbiome of the cohort from North-Central India, which was primarily consuming a plant-based diet, was found to be associated with Prevotella and also showed an enrichment of branched chain amino acid (BCAA) and lipopolysaccharide biosynthesis pathways. In contrast, the gut microbiome of the cohort from Southern India, which was consuming an omnivorous diet, showed associations with Bacteroides, Ruminococcus, and Faecalibacterium and had an enrichment of short chain fatty acid biosynthesis pathway and BCAA transporters. This corroborated well with the metabolomics results, which showed higher concentration of BCAAs in the serum metabolome of the North-Central cohort and an association with Prevotella. In contrast, the concentration of BCAAs was found to be higher in the fecal metabolome of the Southern-India cohort and showed a positive correlation with the higher abundance of BCAA transporters.

CONCLUSIONS: The study reveals the unique composition of the Indian gut microbiome, establishes the Indian gut microbial gene catalogue, and compares it with the gut microbiome of other populations. The functional associations revealed using metagenomic and metabolomic approaches provide novel insights on the gut-microbe-metabolic axis, which will be useful for future epidemiological and translational researches.}, } @article {pmid30696918, year = {2019}, author = {Song, HK and Shi, Y and Yang, T and Chu, H and He, JS and Kim, H and Jablonski, P and Adams, JM}, title = {Environmental filtering of bacterial functional diversity along an aridity gradient.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {866}, pmid = {30696918}, issn = {2045-2322}, mesh = {Animals ; Bacteria/*genetics ; Biodiversity ; Biota ; Climate ; Ecosystem ; Humans ; Metagenome ; *Microbial Interactions ; Oxidative Stress ; Soil Microbiology ; Water ; }, abstract = {Studying how metagenome composition and diversity varies along environmental gradients may improve understanding of the general principles of community and ecosystem structuring. We studied soil bacterial metagenomes along a precipitation gradient on the eastern Tibetan Plateau, varying between 500 mm and 60 mm mean annual precipitation (MAP). We found that lower MAP was strongly associated with reduced functional diversity of bacterial genes. It appears that extreme environmental conditions associated with aridity constrain the diversity of functional strategies present in soil biota - analogous to broad scale patterns found in plant functional diversity along environmental gradients. In terms of specific functions, more extreme arid conditions were also associated with increased relative abundance of genes related to dormancy and osmoprotectants. Decreased relative abundance of genes related to antibiotic resistance and virulence in more arid conditions suggests reduced intensity of biotic interaction under extreme physiological conditions. These trends parallel those seen in earlier, more preliminary comparisons of metagenomes across biomes.}, } @article {pmid30696861, year = {2019}, author = {Okazaki, F and Zang, L and Nakayama, H and Chen, Z and Gao, ZJ and Chiba, H and Hui, SP and Aoki, T and Nishimura, N and Shimada, Y}, title = {Microbiome Alteration in Type 2 Diabetes Mellitus Model of Zebrafish.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {867}, pmid = {30696861}, issn = {2045-2322}, mesh = {Animals ; Bacteria/genetics ; Diabetes Mellitus/*genetics/metabolism/*microbiology ; Disease Models, Animal ; Gastrointestinal Microbiome/*genetics ; Glucose Intolerance/genetics ; Male ; Metagenome/genetics ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Zebrafish/microbiology ; }, abstract = {Understanding the gut microbiota in metabolic disorders, including type 2 diabetes mellitus (T2DM), is now gaining importance due to its potential role in disease risk and progression. We previously established a zebrafish model of T2DM, which shows glucose intolerance with insulin resistance and responds to anti-diabetic drugs. In this study, we analysed the gut microbiota of T2DM zebrafish by deep sequencing the 16S rRNA V3-V4 hypervariable regions, and imputed a functional profile using predictive metagenomic tools. While control and T2DM zebrafish were fed with the same kind of feed, the gut microbiota in T2DM group was less diverse than that of the control. Predictive metagenomics profiling using PICRUSt revealed functional alternation of the KEGG pathways in T2DM zebrafish. Several amino acid metabolism pathways (arginine, proline, and phenylalanine) were downregulated in the T2DM group, similar to what has been previously reported in humans. In summary, we profiled the gut microbiome in T2DM zebrafish, which revealed functional similarities in gut bacterial environments between these zebrafish and T2DM affected humans. T2DM zebrafish can become an alternative model organism to study host-bacterial interactions in human obesity and related diseases.}, } @article {pmid30696735, year = {2019}, author = {Baxter, NT and Schmidt, AW and Venkataraman, A and Kim, KS and Waldron, C and Schmidt, TM}, title = {Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, pmid = {30696735}, issn = {2150-7511}, support = {52008119/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Adolescent ; Adult ; Biostatistics ; Chemistry Techniques, Analytical ; Cichorium intybus ; Dietary Fiber/*administration & dosage ; Fatty Acids, Volatile/*metabolism ; Feces/*chemistry/*microbiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Inulin/administration & dosage ; Metagenomics ; Solanum tuberosum ; Starch/administration & dosage ; Young Adult ; Zea mays ; }, abstract = {Production of short-chain fatty acids (SCFAs), especially butyrate, in the gut microbiome is required for optimal health but is frequently limited by the lack of fermentable fiber in the diet. We attempted to increase butyrate production by supplementing the diets of 174 healthy young adults for 2 weeks with resistant starch from potatoes (RPS), resistant starch from maize (RMS), inulin from chicory root, or an accessible corn starch control. RPS resulted in the greatest increase in total SCFAs, including butyrate. Although the majority of microbiomes responded to RPS with increases in the relative abundance of bifidobacteria, those that responded with an increase in Ruminococcus bromii or Clostridium chartatabidum were more likely to yield higher butyrate concentrations, especially when their microbiota were replete with populations of the butyrate-producing species Eubacterium rectale RMS and inulin induced different changes in fecal communities, but they did not generate significant increases in fecal butyrate levels.IMPORTANCE These results reveal that not all fermentable fibers are equally capable of stimulating SCFA production, and they highlight the importance of the composition of an individual's microbiota in determining whether or not they respond to a specific dietary supplement. In particular, R. bromii or C. chartatabidum may be required for enhanced butyrate production in response to RS. Bifidobacteria, though proficient at degrading RS and inulin, may not contribute to the butyrogenic effect of those fermentable fibers in the short term.}, } @article {pmid30696492, year = {2019}, author = {Cernava, T and Erlacher, A and Soh, J and Sensen, CW and Grube, M and Berg, G}, title = {Enterobacteriaceae dominate the core microbiome and contribute to the resistome of arugula (Eruca sativa Mill.).}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {13}, pmid = {30696492}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/pharmacology ; Base Sequence ; Brassicaceae/*microbiology ; Drug Resistance, Bacterial/genetics ; Enterobacteriaceae/*classification/genetics/*isolation & purification ; Foodborne Diseases/microbiology ; Metagenome/*genetics ; Microbial Sensitivity Tests ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Arugula is a traditional medicinal plant and popular leafy green today. It is mainly consumed raw in the Western cuisine and known to contain various bioactive secondary metabolites. However, arugula has been also associated with high-profile outbreaks causing severe food-borne human diseases. A multiphasic approach integrating data from metagenomics, amplicon sequencing, and arugula-derived bacterial cultures was employed to understand the specificity of the indigenous microbiome and resistome of the edible plant parts.

RESULTS: Our results indicate that arugula is colonized by a diverse, plant habitat-specific microbiota. The indigenous phyllosphere bacterial community was shown to be dominated by Enterobacteriaceae, which are well-equipped with various antibiotic resistances. Unexpectedly, the prevalence of specific resistance mechanisms targeting therapeutic antibiotics (fluoroquinolone, chloramphenicol, phenicol, macrolide, aminocoumarin) was only surpassed by efflux pump assignments.

CONCLUSIONS: Enterobacteria, being core microbiome members of arugula, have a substantial implication in the overall resistome. Detailed insights into the natural occurrence of antibiotic resistances in arugula-associated microorganisms showed that the plant is a hotspot for distinctive defense mechanisms. The specific functioning of microorganisms in this unusual ecosystem provides a unique model to study antibiotic resistances in an ecological context.}, } @article {pmid30694507, year = {2019}, author = {Delafont, V and Perrin, Y and Bouchon, D and Moulin, L and Héchard, Y}, title = {Targeted Metagenomics of Microbial Diversity in Free-Living Amoebae and Water Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1921}, number = {}, pages = {421-428}, doi = {10.1007/978-1-4939-9048-1_26}, pmid = {30694507}, issn = {1940-6029}, mesh = {Amoeba/*microbiology ; Biodiversity ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S ; *Water Microbiology ; }, abstract = {The presence of Legionella spp. in natural and man-made water systems is a great public health concern and heavily depends on the presence of free-living amoebae. Taking advantage of the development and affordability of next-generation sequencing technology, we present here a method to characterize the whole bacterial community directly from water samples, as well as from isolated free-living amoebae.}, } @article {pmid30692672, year = {2019}, author = {Devoto, AE and Santini, JM and Olm, MR and Anantharaman, K and Munk, P and Tung, J and Archie, EA and Turnbaugh, PJ and Seed, KD and Blekhman, R and Aarestrup, FM and Thomas, BC and Banfield, JF}, title = {Megaphages infect Prevotella and variants are widespread in gut microbiomes.}, journal = {Nature microbiology}, volume = {4}, number = {4}, pages = {693-700}, pmid = {30692672}, issn = {2058-5276}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; R21 AG055777/AG/NIA NIH HHS/United States ; }, mesh = {Adult ; Animals ; Bacteria/*virology ; Bacteriophages/classification/genetics/*isolation & purification ; Female ; *Gastrointestinal Microbiome ; Genome, Viral ; Humans ; Male ; Metagenome ; *Microbiota ; Middle Aged ; Papio/*microbiology ; Phylogeny ; Prevotella/classification/genetics/*virology ; Swine/*microbiology ; }, abstract = {Bacteriophages (phages) dramatically shape microbial community composition, redistribute nutrients via host lysis and drive evolution through horizontal gene transfer. Despite their importance, much remains to be learned about phages in the human microbiome. We investigated the gut microbiomes of humans from Bangladesh and Tanzania, two African baboon social groups and Danish pigs; many of these microbiomes contain phages belonging to a clade with genomes >540 kilobases in length, the largest yet reported in the human microbiome and close to the maximum size ever reported for phages. We refer to these as Lak phages. CRISPR spacer targeting indicates that Lak phages infect bacteria of the genus Prevotella. We manually curated to completion 15 distinct Lak phage genomes recovered from metagenomes. The genomes display several interesting features, including use of an alternative genetic code, large intergenic regions that are highly expressed and up to 35 putative transfer RNAs, some of which contain enigmatic introns. Different individuals have distinct phage genotypes, and shifts in variant frequencies over consecutive sampling days reflect changes in the relative abundance of phage subpopulations. Recent homologous recombination has resulted in extensive genome admixture of nine baboon Lak phage populations. We infer that Lak phages are widespread in gut communities that contain the Prevotella species, and conclude that megaphages, with fascinating and underexplored biology, may be common but largely overlooked components of human and animal gut microbiomes.}, } @article {pmid30691532, year = {2019}, author = {Korzhenkov, AA and Toshchakov, SV and Bargiela, R and Gibbard, H and Ferrer, M and Teplyuk, AV and Jones, DL and Kublanov, IV and Golyshin, PN and Golyshina, OV}, title = {Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {11}, pmid = {30691532}, issn = {2049-2618}, support = {BB/M029085/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Acids/metabolism ; Archaea/*classification/genetics/*isolation & purification ; Bacteria/classification/genetics/*isolation & purification ; Cold Temperature ; Ecosystem ; Geologic Sediments/*microbiology ; Metagenome/genetics ; Microbiota/physiology ; RNA, Ribosomal, 16S/genetics ; Wales ; }, abstract = {BACKGROUND: The current view suggests that in low-temperature acidic environments, archaea are significantly less abundant than bacteria. Thus, this study of the microbiome of Parys Mountain (Anglesey, UK) sheds light on the generality of this current assumption. Parys Mountain is a historically important copper mine and its acid mine drainage (AMD) water streams are characterised by constant moderate temperatures (8-18 °C), extremely low pH (1.7) and high concentrations of soluble iron and other metal cations.

RESULTS: Metagenomic and SSU rRNA amplicon sequencing of DNA from Parys Mountain revealed a significant proportion of archaea affiliated with Euryarchaeota, which accounted for ca. 67% of the community. Within this phylum, potentially new clades of Thermoplasmata were overrepresented (58%), with the most predominant group being "E-plasma", alongside low-abundant Cuniculiplasmataceae, 'Ca. Micrarchaeota' and 'Terrestrial Miscellaneous Euryarchaeal Group' (TMEG) archaea, which were phylogenetically close to Methanomassilicoccales and clustered with counterparts from acidic/moderately acidic settings. In the sediment, archaea and Thermoplasmata contributed the highest numbers in V3-V4 amplicon reads, in contrast with the water body community, where Proteobacteria, Nitrospirae, Acidobacteria and Actinobacteria outnumbered archaea. Cultivation efforts revealed the abundance of archaeal sequences closely related to Cuniculiplasma divulgatum in an enrichment culture established from the filterable fraction of the water sample. Enrichment cultures with unfiltered samples showed the presence of Ferrimicrobium acidiphilum, C. divulgatum, 'Ca. Mancarchaeum acidiphilum Mia14', 'Ca. Micrarchaeota'-related and diverse minor (< 2%) bacterial metagenomic reads.

CONCLUSION: Contrary to expectation, our study showed a high abundance of archaea in this extremely acidic mine-impacted environment. Further, archaeal populations were dominated by one particular group, suggesting that they are functionally important. The prevalence of archaea over bacteria in these microbiomes and their spatial distribution patterns represents a novel and important advance in our understanding of acidophile ecology. We also demonstrated a procedure for the specific enrichment of cell wall-deficient members of the archaeal component of this community, although the large fraction of archaeal taxa remained unculturable. Lastly, we identified a separate clustering of globally occurring acidophilic members of TMEG that collectively belong to a distinct order within Thermoplasmata with yet unclear functional roles in the ecosystem.}, } @article {pmid30691529, year = {2019}, author = {Sutton, TDS and Clooney, AG and Ryan, FJ and Ross, RP and Hill, C}, title = {Choice of assembly software has a critical impact on virome characterisation.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {12}, pmid = {30691529}, issn = {2049-2618}, mesh = {Bacteriophages/*classification/genetics/*isolation & purification ; Databases, Factual ; Gastrointestinal Microbiome/*genetics ; Gene Library ; Genome, Viral/*genetics ; Humans ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The viral component of microbial communities plays a vital role in driving bacterial diversity, facilitating nutrient turnover and shaping community composition. Despite their importance, the vast majority of viral sequences are poorly annotated and share little or no homology to reference databases. As a result, investigation of the viral metagenome (virome) relies heavily on de novo assembly of short sequencing reads to recover compositional and functional information. Metagenomic assembly is particularly challenging for virome data, often resulting in fragmented assemblies and poor recovery of viral community members. Despite the essential role of assembly in virome analysis and difficulties posed by these data, current assembly comparisons have been limited to subsections of virome studies or bacterial datasets.

DESIGN: This study presents the most comprehensive virome assembly comparison to date, featuring 16 metagenomic assembly approaches which have featured in human virome studies. Assemblers were assessed using four independent virome datasets, namely, simulated reads, two mock communities, viromes spiked with a known phage and human gut viromes.

RESULTS: Assembly performance varied significantly across all test datasets, with SPAdes (meta) performing consistently well. Performance of MIRA and VICUNA varied, highlighting the importance of using a range of datasets when comparing assembly programs. It was also found that while some assemblers addressed the challenges of virome data better than others, all assemblers had limitations. Low read coverage and genomic repeats resulted in assemblies with poor genome recovery, high degrees of fragmentation and low-accuracy contigs across all assemblers. These limitations must be considered when setting thresholds for downstream analysis and when drawing conclusions from virome data.}, } @article {pmid30690359, year = {2019}, author = {Qiao, R and Sheng, C and Lu, Y and Zhang, Y and Ren, H and Lemos, B}, title = {Microplastics induce intestinal inflammation, oxidative stress, and disorders of metabolome and microbiome in zebrafish.}, journal = {The Science of the total environment}, volume = {662}, number = {}, pages = {246-253}, doi = {10.1016/j.scitotenv.2019.01.245}, pmid = {30690359}, issn = {1879-1026}, mesh = {Animals ; Dose-Response Relationship, Drug ; Dysbiosis/chemically induced/immunology/*physiopathology ; Fish Diseases/chemically induced/*immunology/physiopathology ; Gastrointestinal Microbiome/drug effects ; Inflammation/chemically induced/*immunology ; Intestines/immunology/physiology ; Metabolome/drug effects ; Metagenomics ; Oxidative Stress/drug effects ; Polystyrenes/*adverse effects/metabolism ; Random Allocation ; Toxicity Tests, Chronic ; Water Pollutants, Chemical/*adverse effects/metabolism ; *Zebrafish/metabolism/microbiology ; }, abstract = {Microplastics (MPs) can be ingested by a variety of species and mainly accumulate in the gut. However, the consequences of MPs exposure in the gut are largely unknown. Here we evaluated the impacts of MPs exposure in zebrafish gut. Animals were experimentally exposed to polystyrene MPs (5-μm beads; 50 μg/L and 500 μg/L) for 21 days and monitored for alterations in tissue histology, enzymatic biomarkers, gut microbiome and metabolomic responses. Inflammation and oxidative stress were observed in the zebrafish gut after exposed to MPs. Furthermore, significant alterations in the gut microbiome and tissue metabolic profiles were observed, with most of these were associated with oxidative stress, inflammation and lipid metabolism. This study provides evidence that MPs exposure causes gut damage as well as alterations in gut metabolome and microbiome, yielding novel insights into the consequences of MPs exposure.}, } @article {pmid30689834, year = {2019}, author = {Zheng, Q and Lu, J and Wang, Y and Jiao, N}, title = {Genomic reconstructions and potential metabolic strategies of generalist and specialist heterotrophic bacteria associated with an estuary Synechococcus culture.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {3}, pages = {}, doi = {10.1093/femsec/fiz017}, pmid = {30689834}, issn = {1574-6941}, mesh = {*Estuaries ; Flavobacteriaceae/classification/genetics/metabolism/physiology ; Genomics ; Heterotrophic Processes/genetics/*physiology ; Metabolic Networks and Pathways/genetics ; Microbial Interactions ; Microbiota/genetics ; Roseobacter/classification/genetics/metabolism/physiology ; Seawater/*microbiology ; Synechococcus/genetics/*physiology ; }, abstract = {Interactions between photoautotrophs and heterotrophs are central to marine microbial ecosystems. Synechococcus are dominant marine phototrophs, and they are frequently associated with heterotrophic bacteria. These co-cultures provide a useful research system to investigate photoautotroph-heterotroph interactions in marine systems. Bacteria within the Roseobacter clade and Flavobacteria are two of the main bacterial lineages that exhibit intimate associations with Synechococcus populations. We conducted metagenomic analyses of a Synechococcus culture, followed by genomic binning of metagenomic contigs, and recovered five nearly complete genomes, including members of the Roseobacter clade (i.e. Marivita sp. XM-24) and Flavobacteria (i.e. Fluviicola sp. XM-24). Marivita sp. XM-24 is an ecological generalist of the Roseobacter clade and displays diverse metabolic capacities for the acquisition of nutrients and energy sources. Specifically, the genome contained numerous gene complements involved in the uptake and metabolism of nitrogen- and phosphorus-containing inorganic and organic compounds, in addition to the potential for aerobic anoxygenic photosynthesis, oxidation of carbon monoxide, inorganic sulfur oxidation, DMSP demethylation and PHA metabolism. The genome of the Flavobacteria representative, Fluviicola sp. XM-24, contained numerous peptidases, glycoside hydrolases, adhesion-related proteins and genes involved in gliding motility. Fluviicola sp. XM-24 likely specialize in the degradation of high molecular weight compound exudates from Synechococcus cells, including polysaccharides and polypeptides via attachment to particles, surfaces or cells. The distinct metabolic strategies identified within several heterotrophic bacteria that are associated with Syneochococcus cells provide insights into their lifestyles and nutrient utilization patterns, in addition to their interactions with photoautotrophs. Biological interactions, including mutualism, competition and antagonism, shape the microbial community structure of marine environments and are critical for understanding biogeochemical cycling in the ocean. These results provide valuable insights into the nature of interactions between dominant marine photoautotrophs and associated bacterial heterotrophs.}, } @article {pmid30685386, year = {2019}, author = {Liu, J and Johnson, R and Dillon, S and Kroehl, M and Frank, DN and Tuncil, YE and Zhang, X and Ir, D and Robertson, CE and Seifert, S and Higgins, J and Hamaker, B and Wilson, CC and Erlandson, KM}, title = {Among older adults, age-related changes in the stool microbiome differ by HIV-1 serostatus.}, journal = {EBioMedicine}, volume = {40}, number = {}, pages = {583-594}, pmid = {30685386}, issn = {2352-3964}, support = {K23 AG050260/AG/NIA NIH HHS/United States ; T32 AG000279/AG/NIA NIH HHS/United States ; UL1 TR002535/TR/NCATS NIH HHS/United States ; }, mesh = {Age Factors ; Aged ; Aged, 80 and over ; Biomarkers ; Case-Control Studies ; Computational Biology/methods ; Diet ; Dysbiosis ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; HIV Infections/*epidemiology/*virology ; HIV Seropositivity ; *HIV-1 ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; }, abstract = {BACKGROUND: HIV-1 infection and physiological aging are independently linked to elevated systemic inflammation and changes in enteric microbial communities (dysbiosis). However, knowledge of the direct effect of HIV infection on the aging microbiome and potential links to systemic inflammation is lacking.

METHODS: In a cross-sectional study of older people living with HIV (PLWH) (median age 61.5 years, N = 14) and uninfected controls (median 58 years, n = 22) we compared stool microbiota, levels of microbial metabolites (short-chain fatty acid levels, SCFA) and systemic inflammatory biomarkers by HIV serostatus and age.

FINDINGS: HIV and age were independently associated with distinct changes in the stool microbiome. For example, abundances of Enterobacter and Paraprevotella were higher and Eggerthella and Roseburia lower among PLWH compared to uninfected controls. Age-related microbiome changes also differed by HIV serostatus. Some bacteria with inflammatory potential (e.g. Escherichia) increased with age among PLWH, but not controls. Stool SCFA levels were similar between the two groups yet patterns of associations between individual microbial taxa and SCFA levels differed. Abundance of various genera including Escherichia and Bifidobacterium positively associated with inflammatory biomarkers (e.g. soluble Tumor Necrosis Factor Receptors) among PLWH, but not among controls.

INTERPRETATION: The age effect on the gut microbiome and associations between microbiota and microbial metabolites or systemic inflammation differed based on HIV serostatus, raising important implications for the impact of therapeutic interventions, dependent on HIV serostatus or age.}, } @article {pmid30683956, year = {2019}, author = {Mahato, NK and Sharma, A and Singh, Y and Lal, R}, title = {Comparative metagenomic analyses of a high-altitude Himalayan geothermal spring revealed temperature-constrained habitat-specific microbial community and metabolic dynamics.}, journal = {Archives of microbiology}, volume = {201}, number = {3}, pages = {377-388}, doi = {10.1007/s00203-018-01616-6}, pmid = {30683956}, issn = {1432-072X}, support = {BT/PR15118/BCE/8/1141/2015//Department of Biotechnology, Ministry of Science and Technology/ ; }, mesh = {Altitude ; Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Flagella/genetics ; Geologic Sediments/*microbiology ; Hot Springs/*microbiology ; Hot Temperature ; India ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Phylogeny ; Temperature ; Type IV Secretion Systems/genetics ; }, abstract = {Metagenomic surveys across microbial mat (~ 55 °C) samples of high-altitude (1760 m above sea level) Himalayan geothermal springs have revealed specialized community enriched with niche-specific functions. In this study, we have performed metagenomic sequence-based analyses to get insights into taxonomic composition and functional potential of hyperthermophiles in water (~ 95 °C) and sediment samples (78-98 °C). Community analyses revealed predominance of thermophilic bacterial and archeal genera dwelling in water in contrast to microbial mats (55 °C), namely Methylophilus, Methyloversatilis, Emticicia, Caulobacter, Thermus, Enhydrobacter and Pyrobaculum. Sediment samples having surface temperature (~ 78 °C) were colonized by Pyrobaculum and Chloroflexus while genus Massilia was found to be inhabited in high-temperature sediments (~ 98 °C). Functional analyses of metagenomic sequences revealed genetic enrichment of genes such as type IV secretion system, flagellar assembly and two-component system in contrast to mats. Furthermore, inter-sample comparison of enriched microbial diversity among water, sediment and microbial mats revealed habitat-specific clustering of the samples within same environment highlighting the role of temperature dynamics in modulating community structure across different habitats in same niche. However, function-based analysis demonstrated site-specific clustering among sediment, microbial mat and water samples. Furthermore, a novel thermophilic genotype of the genus Emticicia (designated as strain MM) was reconstructed from metagenome data. This is a correlative study between three major habitats present in geothermal spring environment, i.e., water, sediment and microbial mats revealing greater phylogenetic and functional dispersion emphasizing changing habitat-specific dynamics with temperature.}, } @article {pmid30683920, year = {2019}, author = {Vacheron, J and Péchy-Tarr, M and Brochet, S and Heiman, CM and Stojiljkovic, M and Maurhofer, M and Keel, C}, title = {T6SS contributes to gut microbiome invasion and killing of an herbivorous pest insect by plant-beneficial Pseudomonas protegens.}, journal = {The ISME journal}, volume = {13}, number = {5}, pages = {1318-1329}, pmid = {30683920}, issn = {1751-7370}, mesh = {Animals ; Bacterial Proteins/genetics/*metabolism ; Feeding Behavior ; *Gastrointestinal Microbiome ; Insecta/*microbiology/physiology ; Larva/microbiology/physiology ; Pseudomonas/genetics/*physiology ; Symbiosis ; Type VI Secretion Systems/genetics/*metabolism ; }, abstract = {Pseudomonas protegens are multi-talented plant-colonizing bacteria that suppress plant pathogens and stimulate plant defenses. In addition, they are capable of invading and killing agriculturally important plant pest insects that makes them promising candidates for biocontrol applications. Here we assessed the role of type VI secretion system (T6SS) components of type strain CHA0 during interaction with larvae of the cabbage pest Pieris brassicae. We show that the T6SS core apparatus and two VgrG modules, encompassing the respective T6SS spikes (VgrG1a and VgrG1b) and associated effectors (RhsA and Ghh1), contribute significantly to insect pathogenicity of P. protegens in oral infection assays but not when bacteria are injected directly into the hemolymph. Monitoring of the colonization levels of P. protegens in the gut, hemolymph, and excrements of the insect larvae revealed that the invader relies on T6SS and VgrG1a module function to promote hemocoel invasion. A 16S metagenomic analysis demonstrated that T6SS-supported invasion by P. protegens induces significant changes in the insect gut microbiome affecting notably Enterobacteriaceae, a dominant group of the commensal gut bacteria. Our study supports the concept that pathogens deploy T6SS-based strategies to disrupt the commensal microbiota in order to promote host colonization and pathogenesis.}, } @article {pmid30683856, year = {2019}, author = {Ellegaard, KM and Engel, P}, title = {Genomic diversity landscape of the honey bee gut microbiota.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {446}, pmid = {30683856}, issn = {2041-1723}, mesh = {Age Factors ; Animals ; Bees/*microbiology ; Bifidobacterium/classification/*genetics/isolation & purification ; *Biological Variation, Individual ; DNA, Bacterial/genetics ; Firmicutes/classification/*genetics/isolation & purification ; Gammaproteobacteria/classification/*genetics/isolation & purification ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Metagenomics ; Microbial Consortia/genetics ; Phylogeny ; Symbiosis/physiology ; }, abstract = {The structure and distribution of genomic diversity in natural microbial communities is largely unexplored. Here, we used shotgun metagenomics to assess the diversity of the honey bee gut microbiota, a community consisting of few bacterial phylotypes. Our results show that most phylotypes are composed of sequence-discrete populations, which co-exist in individual bees and show age-specific abundance profiles. In contrast, strains present within these sequence-discrete populations were found to segregate into individual bees. Consequently, despite a conserved phylotype composition, each honey bee harbors a distinct community at the functional level. While ecological differentiation seems to facilitate coexistence at higher taxonomic levels, our findings suggest that, at the level of strains, priority effects during community assembly result in individualized profiles, despite the social lifestyle of the host. Our study underscores the need to move beyond phylotype-level characterizations to understand the function of this community, and illustrates its potential for strain-level analysis.}, } @article {pmid30683748, year = {2019}, author = {Burkert, A and Douglas, TA and Waldrop, MP and Mackelprang, R}, title = {Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {7}, pages = {}, pmid = {30683748}, issn = {1098-5336}, mesh = {Actinobacteria/genetics/isolation & purification ; Alaska ; Bacillaceae/genetics/isolation & purification ; Carbon/metabolism ; Clostridiaceae/genetics/isolation & purification ; DNA, Bacterial/genetics/isolation & purification ; Ecology ; Freezing ; Metagenomics ; Microbiota/genetics/*physiology ; Permafrost/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; Spores, Bacterial/physiology ; Temperature ; }, abstract = {Permafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the class Bacilli were more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of the Clostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous "relic" DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.IMPORTANCE Permafrost soils store more than half of Earth's soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171-179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.}, } @article {pmid30681281, year = {2019}, author = {Wang, J}, title = {A parsimony estimator of the number of populations from a STRUCTURE-like analysis.}, journal = {Molecular ecology resources}, volume = {19}, number = {4}, pages = {970-981}, doi = {10.1111/1755-0998.13000}, pmid = {30681281}, issn = {1755-0998}, mesh = {*Biodiversity ; Biostatistics/*methods ; Genetics, Population/*methods ; Metagenomics/*methods ; }, abstract = {Population genetics model based Bayesian methods have been proposed and widely applied to making unsupervised inference of population structure from a sample of multilocus genotypes. Usually they provide good estimates of the ancestry (or population membership) of sampled individuals by clustering them probabilistically or proportionally into (anonymous) populations. However, they have difficulties in accurately estimating the number of populations (K) represented by the sampled individuals. This study proposed a new ad hoc estimator of K, calculable from the output of a population clustering program such as STRUCTURE or ADMIXTURE. The new criterion, called parsimony index (PI), aims to identify the number of populations (K) which yields consistently the minimal admixture estimates of sampled individuals. Extensive simulated and empirical data were used to compare the accuracy of PI and two popular K estimators based on Pr[X|K] (i.e., the probability of genotype data X given K) and ΔK (i.e., the rate of change of the probability of data as a function of K) calculated from STRUCTURE outputs, and the accuracy of PI and the cross-validation method calculated from ADMIXTURE outputs. It was shown that PI was more accurate than the other methods consistently in various population structure (e.g., hierarchical island model, different extents of differentiation) and sampling (e.g., unbalanced sample sizes, different marker information contents) scenarios. The ΔK method was more accurate than the Pr[X|K] method only for hierarchically structured or highly inbred populations, and the opposite was true in the other scenarios. The PI method was implemented in a computer program, KFinder, which can be run on all major computer platforms.}, } @article {pmid30680877, year = {2019}, author = {Alessandri, G and Milani, C and Mancabelli, L and Mangifesta, M and Lugli, GA and Viappiani, A and Duranti, S and Turroni, F and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {Metagenomic dissection of the canine gut microbiota: insights into taxonomic, metabolic and nutritional features.}, journal = {Environmental microbiology}, volume = {21}, number = {4}, pages = {1331-1343}, doi = {10.1111/1462-2920.14540}, pmid = {30680877}, issn = {1462-2920}, support = {//EU Joint Programming Initiative - A Healthy Diet for a Healthy Life/International ; //Fondazione Cariparma/International ; //Ministero dell'Istruzione, dell'Università e della Ricerca/International ; 15/JP-HDHL/3280/SFI_/Science Foundation Ireland/Ireland ; //JPI HDHL/International ; }, mesh = {Animals ; Bacteria/*classification/*genetics ; Bifidobacterium/genetics ; *Biodiversity ; Dogs/*microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Metagenome/*genetics ; Metagenomics ; *Nutritional Physiological Phenomena ; RNA, Ribosomal, 16S/genetics ; Wolves/microbiology ; }, abstract = {Domestication of dogs from wolves is the oldest known example of ongoing animal selection, responsible for generating more than 300 dog breeds worldwide. In order to investigate the taxonomic and functional evolution of the canine gut microbiota, a multi-omics approach was applied to six wild wolves and 169 dog faecal samples, the latter encompassing 51 breeds, which fully covers currently known canine genetic biodiversity. Specifically, 16S rRNA gene and bifidobacterial Internally Transcribed Spacer (ITS) profiling were employed to reconstruct and then compare the canine core gut microbiota to those of wolves and humans, revealing that artificial selection and subsequent cohabitation of dogs with their owners influenced the microbial population of canine gut through loss and acquisition of specific bacterial taxa. Moreover, comparative analysis of the intestinal bacterial population of dogs fed on Bones and Raw Food (BARF) or commercial food (CF) diet, coupled with shotgun metagenomics, highlighted that both bacterial composition and metabolic repertoire of the canine gut microbiota have evolved to adapt to high-protein or high-carbohydrates intake. Altogether, these data indicate that artificial selection and domestication not only affected the canine genome, but also shaped extensively the bacterial population harboured by the canine gut.}, } @article {pmid30680143, year = {2019}, author = {Rytkönen, S and Vesterinen, EJ and Westerduin, C and Leviäkangas, T and Vatka, E and Mutanen, M and Välimäki, P and Hukkanen, M and Suokas, M and Orell, M}, title = {From feces to data: A metabarcoding method for analyzing consumed and available prey in a bird-insect food web.}, journal = {Ecology and evolution}, volume = {9}, number = {1}, pages = {631-639}, pmid = {30680143}, issn = {2045-7758}, abstract = {Diets play a key role in understanding trophic interactions. Knowing the actual structure of food webs contributes greatly to our understanding of biodiversity and ecosystem functioning. The research of prey preferences of different predators requires knowledge not only of the prey consumed, but also of what is available. In this study, we applied DNA metabarcoding to analyze the diet of 4 bird species (willow tits Poecile montanus, Siberian tits Poecile cinctus, great tits Parus major and blue tits Cyanistes caeruleus) by using the feces of nestlings. The availability of their assumed prey (Lepidoptera) was determined from feces of larvae (frass) collected from the main foraging habitat, birch (Betula spp.) canopy. We identified 53 prey species from the nestling feces, of which 11 (21%) were also detected from the frass samples (eight lepidopterans). Approximately 80% of identified prey species in the nestling feces represented lepidopterans, which is in line with the earlier studies on the parids' diet. A subsequent laboratory experiment showed a threshold for fecal sample size and the barcoding success, suggesting that the smallest frass samples do not contain enough larval DNA to be detected by high-throughput sequencing. To summarize, we apply metabarcoding for the first time in a combined approach to identify available prey (through frass) and consumed prey (via nestling feces), expanding the scope and precision for future dietary studies on insectivorous birds.}, } @article {pmid30678352, year = {2019}, author = {Yang, Q and Gao, C and Jiang, Y and Wang, M and Zhou, X and Shao, H and Gong, Z and McMinn, A}, title = {Metagenomic Characterization of the Viral Community of the South Scotia Ridge.}, journal = {Viruses}, volume = {11}, number = {2}, pages = {}, pmid = {30678352}, issn = {1999-4915}, mesh = {Antarctic Regions ; Bacteriophages/genetics ; *Genetic Variation ; *Genome, Viral ; *Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; Podoviridae/genetics/isolation & purification ; Seawater/virology ; Viruses/*classification ; Water Microbiology ; }, abstract = {Viruses are the most abundant biological entities in aquatic ecosystems and harbor an enormous amount of genetic diversity. Whereas their influence on marine ecosystems is widely acknowledged, current information about their diversity remains limited. We conducted a viral metagenomic analysis of water samples collected during the austral summer of 2016 from the South Scotia Ridge (SSR), near the Antarctic Peninsula. The taxonomic composition and diversity of the viral communities were investigated, and a functional assessment of the sequences was performed. Phylotypic analysis showed that most viruses belonged to the order Caudovirales, especially the family Podoviridae (41.92[-]48.7%), which is similar to the situation in the Pacific Ocean. Functional analysis revealed a relatively high frequency of phage-associated and metabolism genes. Phylogenetic analyses of phage TerL and Capsid_NCLDV (nucleocytoplasmic large DNA viruses) marker genes indicated that many sequences associated with Caudovirales and NCLDV were novel and distinct from known phage genomes. High Phaeocystis globosa virus virophage (Pgvv) signatures were found and complete and partial Pgvv-like were obtained, which influence host[-]virus interactions. Our study expands existing knowledge of viral communities and their diversities from the Antarctic region and provides basic data for further exploring polar microbiomes.}, } @article {pmid30675371, year = {2019}, author = {Layeghifard, M and Li, H and Wang, PW and Donaldson, SL and Coburn, B and Clark, ST and Caballero, JD and Zhang, Y and Tullis, DE and Yau, YCW and Waters, V and Hwang, DM and Guttman, DS}, title = {Microbiome networks and change-point analysis reveal key community changes associated with cystic fibrosis pulmonary exacerbations.}, journal = {NPJ biofilms and microbiomes}, volume = {5}, number = {1}, pages = {4}, pmid = {30675371}, issn = {2055-5008}, support = {//CIHR/Canada ; }, mesh = {Bacteria/*classification/genetics ; Canada ; Child ; Cystic Fibrosis/*complications ; Humans ; Longitudinal Studies ; Metagenomics ; *Microbiota ; Pneumonia/*microbiology ; Sputum/*microbiology ; }, abstract = {Over 90% of cystic fibrosis (CF) patients die due to chronic lung infections leading to respiratory failure. The decline in CF lung function is greatly accelerated by intermittent and progressively severe acute pulmonary exacerbations (PEs). Despite their clinical impact, surprisingly few microbiological signals associated with PEs have been identified. Here we introduce an unsupervised, systems-oriented approach to identify key members of the microbiota. We used two CF sputum microbiome data sets that were longitudinally collected through periods spanning baseline health and PEs. Key taxa were defined based on three strategies: overall relative abundance, prevalence, and co-occurrence network interconnectedness. We measured the association between changes in the abundance of the key taxa and changes in patient clinical status over time via change-point detection, and found that taxa with the highest level of network interconnectedness tracked changes in patient health significantly better than taxa with the highest abundance or prevalence. We also cross-sectionally stratified all samples into the clinical states and identified key taxa associated with each state. We found that network interconnectedness most strongly delineated the taxa among clinical states, and that anaerobic bacteria were over-represented during PEs. Many of these anaerobes are oropharyngeal bacteria that have been previously isolated from the respiratory tract, and/or have been studied for their role in CF. The observed shift in community structure, and the association of anaerobic taxa and PEs lends further support to the growing consensus that anoxic conditions and the subsequent growth of anaerobic microbes are important predictors of PEs.}, } @article {pmid30673701, year = {2019}, author = {Garud, NR and Good, BH and Hallatschek, O and Pollard, KS}, title = {Evolutionary dynamics of bacteria in the gut microbiome within and across hosts.}, journal = {PLoS biology}, volume = {17}, number = {1}, pages = {e3000102}, pmid = {30673701}, issn = {1545-7885}, support = {R01 GM115851/GM/NIGMS NIH HHS/United States ; R25 GM067110/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics/metabolism ; Biological Evolution ; Computer Simulation ; Ecology ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics/*physiology ; Genetic Variation ; Humans ; Microbiota/*genetics ; }, abstract = {Gut microbiota are shaped by a combination of ecological and evolutionary forces. While the ecological dynamics have been extensively studied, much less is known about how species of gut bacteria evolve over time. Here, we introduce a model-based framework for quantifying evolutionary dynamics within and across hosts using a panel of metagenomic samples. We use this approach to study evolution in approximately 40 prevalent species in the human gut. Although the patterns of between-host diversity are consistent with quasi-sexual evolution and purifying selection on long timescales, we identify new genealogical signatures that challenge standard population genetic models of these processes. Within hosts, we find that genetic differences that accumulate over 6-month timescales are only rarely attributable to replacement by distantly related strains. Instead, the resident strains more commonly acquire a smaller number of putative evolutionary changes, in which nucleotide variants or gene gains or losses rapidly sweep to high frequency. By comparing these mutations with the typical between-host differences, we find evidence that some sweeps may be seeded by recombination, in addition to new mutations. However, comparisons of adult twins suggest that replacement eventually overwhelms evolution over multi-decade timescales, hinting at fundamental limits to the extent of local adaptation. Together, our results suggest that gut bacteria can evolve on human-relevant timescales, and they highlight the connections between these short-term evolutionary dynamics and longer-term evolution across hosts.}, } @article {pmid30669548, year = {2019}, author = {Chávez-Carbajal, A and Nirmalkar, K and Pérez-Lizaur, A and Hernández-Quiroz, F and Ramírez-Del-Alto, S and García-Mena, J and Hernández-Guerrero, C}, title = {Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome.}, journal = {International journal of molecular sciences}, volume = {20}, number = {2}, pages = {}, pmid = {30669548}, issn = {1422-0067}, support = {11a Convocatoria Para Proyectos de Investigación Básica.//Universidad Iberoamericana Ciudad de México/ ; CONACyT-163235 INFR-2011-01//Consejo Nacional de Ciencia y Tecnología/ ; FONSEC SS/IMSS/ISSSTE-CONACYT-233361.//Consejo Nacional de Ciencia y Tecnología/ ; }, mesh = {Adult ; Biodiversity ; Female ; *Gastrointestinal Microbiome ; Humans ; *Metabolic Networks and Pathways ; Metabolic Syndrome/complications/*etiology/*metabolism ; Metagenome ; Metagenomics/methods ; Mexico ; Middle Aged ; Obesity/complications/*etiology/*metabolism ; RNA, Ribosomal, 16S ; Sex Factors ; Young Adult ; }, abstract = {Obesity is an excessive fat accumulation that could lead to complications like metabolic syndrome. There are reports on gut microbiota and metabolic syndrome in relation to dietary, host genetics, and other environmental factors; however, it is necessary to explore the role of the gut microbiota metabolic pathways in populations like Mexicans, where the prevalence of obesity and metabolic syndrome is high. This study identify alterations of the gut microbiota in a sample of healthy Mexican women (CO), women with obesity (OB), and women with obesity plus metabolic syndrome (OMS). We studied 67 women, characterizing their anthropometric and biochemical parameters along with their gut bacterial diversity by high-throughput DNA sequencing. Our results indicate that in OB or OMS women, Firmicutes was the most abundant bacterial phylum. We observed significant changes in abundances of bacteria belonging to the Ruminococcaceae, Lachnospiraceae, and Erysipelotrichaceae families and significant enrichment of gut bacteria from 16 different taxa that might explain the observed metabolic alterations between the groups. Finally, the predicted functional metagenome of the gut microbiota found in each category shows differences in metabolic pathways related to lipid metabolism. We demonstrate that Mexican women have a particular bacterial gut microbiota characteristic of each phenotype. There are bacteria that potentially explain the observed metabolic differences between the groups, and gut bacteria in OMS and OB conditions carry more genes of metabolic pathways implicated in lipid metabolism.}, } @article {pmid30669085, year = {2019}, author = {Liu, JL and Yao, J and Wang, F and Min, N and Gu, JH and Li, ZF and Sunahara, G and Duran, R and Solevic-Knudsen, T and Hudson-Edwards, KA and Alakangas, L}, title = {Bacterial diversity in typical abandoned multi-contaminated nonferrous metal(loid) tailings during natural attenuation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {247}, number = {}, pages = {98-107}, doi = {10.1016/j.envpol.2018.12.045}, pmid = {30669085}, issn = {1873-6424}, mesh = {Bacteria/*genetics ; *Biodegradation, Environmental ; China ; *Genetic Variation ; Iron/analysis ; Metals/*analysis ; Microbiota ; Oxidation-Reduction ; Plants ; Sulfides/analysis ; }, abstract = {Abandoned nonferrous metal(loid) tailings sites are anthropogenic, and represent unique and extreme ecological niches for microbial communities. Tailings contain elevated and toxic content of metal(loid)s that had negative effects on local human health and regional ecosystems. Microbial communities in these typical tailings undergoing natural attenuation are often very poorly examined. The diversity and inferred functions of bacterial communities were examined at seven nonferrous metal(loid) tailings sites in Guangxi (China), which were abandoned between 3 and 31 years ago. The acidity of the tailings sites rose over 31 years of site inactivity. Desulfurivibrio, which were always coupled with sulfur/sulfide oxidation to dissimilate the reduction of nitrate/nitrite, were specific in tailings with 3 years abandonment. However, genus beneficial to plant growth (Rhizobium), and iron/sulfur-oxidizing bacteria and metal(loid)-related genera (Acidiferrobacter and Acidithiobacillus) were specific within tailings abandoned for 23 years or more. The increased abundance of acid-generating iron/sulfur-oxidizing and metal(loid)-related bacteria and specific bacterial communities during the natural attenuation could provide new insights for understanding microbial ecosystem functioning in mine tailings. OTUs related to Sulfuriferula, Bacillus, Sulfurifustis, Gaiella, and Thiobacillus genera were the main contributors differentiating the bacterial communities between the different tailing sites. Multiple correlation analyses between bacterial communities and geochemical parameters indicated that pH, TOC, TN, As, Pb, and Cu were the main drivers influencing the bacterial community structures. PICRUSt functional exploration revealed that the main functions were related to DNA repair and recombination, important functions for bacterial adaptation to cope with the multi-contamination of tailings. Such information provides new insights to guide future metagenomic studies for the identification of key functions beyond metal-transformation/resistance. As well, our results offers novel outlooks for the management of bacterial communities during natural attenuation of multi-contaminated nonferrous metal(loid) tailings sites.}, } @article {pmid30669029, year = {2019}, author = {Zeng, D and Yin, Q and Du, Q and Wu, G}, title = {System performance and microbial community in ethanol-fed anaerobic reactors acclimated with different organic carbon to sulfate ratios.}, journal = {Bioresource technology}, volume = {278}, number = {}, pages = {34-42}, doi = {10.1016/j.biortech.2019.01.047}, pmid = {30669029}, issn = {1873-2976}, mesh = {Bioreactors/microbiology ; Carbon/*metabolism ; Desulfovibrio/metabolism ; Ethanol/*metabolism ; *Microbiota ; Sulfates/*metabolism ; Sulfur Oxides/*metabolism ; Sulfur-Reducing Bacteria/metabolism ; }, abstract = {Sulfate influences the organics removal and methanogenic performance during anaerobic wastewater treatment. System performance, microbial community and metabolic pathways in ethanol-fed anaerobic reactors were investigated under different COD/SO4[2-] ratios (2, 1 and 0.67) and control without sulfate addition. The sulfate removal percentages declined (99%, 60% and 49%) with decreasing COD/SO4[2-] ratios, and methanogenesis was completely inhibited. Acetate accumulated to 903-734 mg/L, though propionate was constantly lower than 30 mg/L. Without sulfate, acetate and propionate did not accumulate, despite the extended time for propionate degradation. Incomplete oxidizing sulfate reducing bacteria (Desulfobulbus and Desulfomicrobium) and hydrolysis-acidification genera (Treponema and Bacteroidales) predominated but could not degrade acetate. Desulfobulbus was the key genus for propionate degradation through the pyruvate & propanoate metabolism pathway. Pseudomonas and Desulfobulbus, possessing genes encoding Type IV pili and cytochrome c6 OmcF, respectively, potentially participated in the direct interspecies electron transfer in sulfate-rich conditions.}, } @article {pmid30667580, year = {2019}, author = {Chen, T and Liu, AB and Sun, S and Ajami, NJ and Ross, MC and Wang, H and Zhang, L and Reuhl, K and Kobayashi, K and Onishi, JC and Zhao, L and Yang, CS}, title = {Green Tea Polyphenols Modify the Gut Microbiome in db/db Mice as Co-Abundance Groups Correlating with the Blood Glucose Lowering Effect.}, journal = {Molecular nutrition & food research}, volume = {63}, number = {8}, pages = {e1801064}, pmid = {30667580}, issn = {1613-4133}, support = {P30 ES005022/ES/NIEHS NIH HHS/United States ; P30 ES023512/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Biflavonoids/pharmacology ; Blood Glucose/*metabolism ; Body Weight/drug effects ; Catechin/analogs & derivatives/pharmacology ; Female ; Gastrointestinal Microbiome/*drug effects/genetics/physiology ; Hypoglycemic Agents/pharmacology ; Insulin/blood ; Insulin-Secreting Cells/drug effects/pathology ; Mice, Mutant Strains ; Organ Size/drug effects ; Polyphenols/*pharmacology ; RNA, Ribosomal, 16S ; Tea/*chemistry ; }, abstract = {SCOPE: The effects of green tea polyphenols, Polyphenon E (PPE), and black tea polyphenols, theaflavins (TFs), on gut microbiota and development of diabetes in db/db mice are investigated and compared.

METHODS AND RESULTS: Supplementation of PPE (0.1%) in the diet of female db/db mice for 7 weeks decreases fasting blood glucose levels and mesenteric fat while increasing the serum level of insulin, possibly through protection against β-cell damage. However, TFs are less or not effective. Microbiome analysis through 16S rRNA gene sequencing shows that PPE and TFs treatments significantly alter the bacterial community structure in the cecum and colon, but not in the ileum. The key bacterial phylotypes responding to the treatments are then clustered into 11 co-abundance groups (CAGs). CAGs 6 and 7, significantly increased by PPE but not by TFs, are negatively associated with blood glucose levels. The operational taxonomic units in these CAGs are from two different phyla, Firmicutes and Bacteroidetes. CAG 10, decreased by PPE and TFs, is positively associated with blood glucose levels.

CONCLUSION: Gut microbiota respond to tea polyphenol treatments as CAGs instead of taxa. Some of the CAGs associated with the blood glucose lowering effect are enriched by PPE, but not TFs.}, } @article {pmid30666248, year = {2018}, author = {Malla, MA and Dubey, A and Kumar, A and Yadav, S and Hashem, A and Abd Allah, EF}, title = {Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment.}, journal = {Frontiers in immunology}, volume = {9}, number = {}, pages = {2868}, pmid = {30666248}, issn = {1664-3224}, mesh = {Communicable Diseases/etiology/*microbiology ; Computational Biology/trends ; Dysbiosis/complications ; Forecasting ; High-Throughput Nucleotide Sequencing/instrumentation/*trends ; Host Microbial Interactions/*genetics ; Host-Pathogen Interactions/*genetics ; Humans ; Metagenomics/*trends ; Microbiota/*physiology ; Nanotechnology/methods ; }, abstract = {The interaction between the human microbiome and immune system has an effect on several human metabolic functions and impacts our well-being. Additionally, the interaction between humans and microbes can also play a key role in determining the wellness or disease status of the human body. Dysbiosis is related to a plethora of diseases, including skin, inflammatory, metabolic, and neurological disorders. A better understanding of the host-microbe interaction is essential for determining the diagnosis and appropriate treatment of these ailments. The significance of the microbiome on host health has led to the emergence of new therapeutic approaches focused on the prescribed manipulation of the host microbiome, either by removing harmful taxa or reinstating missing beneficial taxa and the functional roles they perform. Culturing large numbers of microbial taxa in the laboratory is problematic at best, if not impossible. Consequently, this makes it very difficult to comprehensively catalog the individual members comprising a specific microbiome, as well as understanding how microbial communities function and influence host-pathogen interactions. Recent advances in sequencing technologies and computational tools have allowed an increasing number of metagenomic studies to be performed. These studies have provided key insights into the human microbiome and a host of other microbial communities in other environments. In the present review, the role of the microbiome as a therapeutic agent and its significance in human health and disease is discussed. Advances in high-throughput sequencing technologies for surveying host-microbe interactions are also discussed. Additionally, the correlation between the composition of the microbiome and infectious diseases as described in previously reported studies is covered as well. Lastly, recent advances in state-of-the-art bioinformatics software, workflows, and applications for analysing metagenomic data are summarized.}, } @article {pmid30665461, year = {2019}, author = {Hansen, MEB and Rubel, MA and Bailey, AG and Ranciaro, A and Thompson, SR and Campbell, MC and Beggs, W and Dave, JR and Mokone, GG and Mpoloka, SW and Nyambo, T and Abnet, C and Chanock, SJ and Bushman, FD and Tishkoff, SA}, title = {Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {16}, pmid = {30665461}, issn = {1474-760X}, support = {1R01GM113657-01/NH/NIH HHS/United States ; 5T32AI007532-18/NH/NIH HHS/United States ; T32 ES019851/ES/NIEHS NIH HHS/United States ; R01 GM113657/GM/NIGMS NIH HHS/United States ; T32ES019851-02/NH/NIH HHS/United States ; T32 AI007532/AI/NIAID NIH HHS/United States ; R01 DK104339/DK/NIDDK NIH HHS/United States ; DP1 ES022577-04/NH/NIH HHS/United States ; R35 GM134957/GM/NIGMS NIH HHS/United States ; 1R01DK104339-01/NH/NIH HHS/United States ; DP1 ES022577/ES/NIEHS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Agriculture ; Animals ; Bacteroidaceae/isolation & purification ; Botswana ; Cattle ; Clostridiales/isolation & purification ; Cohort Studies ; Diet, Paleolithic ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Middle Aged ; Philadelphia ; Population Groups ; Rural Population ; Tanzania ; Young Adult ; }, abstract = {BACKGROUND: Gut microbiota from individuals in rural, non-industrialized societies differ from those in individuals from industrialized societies. Here, we use 16S rRNA sequencing to survey the gut bacteria of seven non-industrialized populations from Tanzania and Botswana. These include populations practicing traditional hunter-gatherer, pastoralist, and agropastoralist subsistence lifestyles and a comparative urban cohort from the greater Philadelphia region.

RESULTS: We find that bacterial diversity per individual and within-population phylogenetic dissimilarity differs between Botswanan and Tanzanian populations, with Tanzania generally having higher diversity per individual and lower dissimilarity between individuals. Among subsistence groups, the gut bacteria of hunter-gatherers are phylogenetically distinct from both agropastoralists and pastoralists, but that of agropastoralists and pastoralists were not significantly different from each other. Nearly half of the Bantu-speaking agropastoralists from Botswana have gut bacteria that are very similar to the Philadelphian cohort. Based on imputed metagenomic content, US samples have a relative enrichment of genes found in pathways for degradation of several common industrial pollutants. Within two African populations, we find evidence that bacterial composition correlates with the genetic relatedness between individuals.

CONCLUSIONS: Across the cohort, similarity in bacterial presence/absence compositions between people increases with both geographic proximity and genetic relatedness, while abundance weighted bacterial composition varies more significantly with geographic proximity than with genetic relatedness.}, } @article {pmid30664775, year = {2019}, author = {Lin, M and Kussell, E}, title = {Inferring bacterial recombination rates from large-scale sequencing datasets.}, journal = {Nature methods}, volume = {16}, number = {2}, pages = {199-204}, doi = {10.1038/s41592-018-0293-7}, pmid = {30664775}, issn = {1548-7105}, mesh = {Computational Biology/*methods ; Computer Simulation ; *DNA, Ancient ; DNA, Bacterial ; Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/genetics ; Gastrointestinal Microbiome ; Genetic Techniques ; Genetic Variation ; Helicobacter pylori/genetics ; History, Medieval ; Humans ; Metagenomics/*methods ; Models, Genetic ; Mutation ; Plague/history/microbiology ; *Recombination, Genetic ; *Sequence Analysis, DNA ; Yersinia pestis/genetics ; }, abstract = {We present a robust, computationally efficient method (https://github.com/kussell-lab/mcorr) for inferring the parameters of homologous recombination in bacteria, which can be applied in diverse datasets, from whole-genome sequencing to metagenomic shotgun sequencing data. Using correlation profiles of synonymous substitutions, we determine recombination rates and diversity levels of the shared gene pool that has contributed to a given sample. We validated the recombination parameters using data from laboratory experiments. We determined the recombination parameters for a wide range of bacterial species, and inferred the distribution of shared gene pools for global Helicobacter pylori isolates. Using metagenomics data of the infant gut microbiome, we measured the recombination parameters of multidrug-resistant Escherichia coli ST131. Lastly, we analyzed ancient samples of bacterial DNA from the Copper Age 'Iceman' mummy and from 14th century victims of the Black Death, obtaining measurements of bacterial recombination rates and gene pool diversity of earlier eras.}, } @article {pmid30664014, year = {2019}, author = {Joris, BR and Gloor, GB}, title = {Unaccounted risk of cardiovascular disease: the role of the microbiome in lipid metabolism.}, journal = {Current opinion in lipidology}, volume = {30}, number = {2}, pages = {125-133}, doi = {10.1097/MOL.0000000000000582}, pmid = {30664014}, issn = {1473-6535}, mesh = {Animals ; Atherosclerosis/genetics/immunology/*microbiology/pathology ; Bile Acids and Salts/immunology/metabolism ; Carnitine/immunology/metabolism ; Choline/immunology/metabolism ; Energy Metabolism/genetics/immunology ; Fatty Acids, Volatile/immunology/*metabolism ; Gastrointestinal Microbiome/genetics/*immunology ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Lipid Metabolism/genetics/*immunology ; Metabolic Syndrome/genetics/immunology/*microbiology/pathology ; Methylamines/immunology/*metabolism/pharmacology ; Phosphatidylcholines/immunology/metabolism ; RNA, Ribosomal, 16S/genetics ; T-Lymphocytes, Helper-Inducer/drug effects/immunology/microbiology ; Triglycerides/immunology/metabolism ; }, abstract = {PURPOSE OF REVIEW: Not all of the risk of cardiovascular disease can be explained by diet and genetics, and the human microbiome, which lies at the interface of these two factors, may help explain some of the unaccounted risk. This review examines some of the well established links between the microbiome and cardiovascular health, and proposes relatively unexplored associations.

RECENT FINDINGS: Byproducts of microbial metabolism are associated with health and disease: Trimethylamine N oxide is associated with atherosclerosis; whereas short-chain fatty acids are associated with decreased inflammation and increased energy expenditure. More broadly, a large number of association studies have been conducted to explore the connections between bacterial taxa and metabolic syndrome. In contrast, the relationship between the microbiome and triglycerides levels remains poorly understood.

SUMMARY: We suggest that deeper understanding of the molecular mechanisms that drive linkages between the microbiome and disease can be determined by replacing 16S rRNA gene sequencing with shotgun metagenomic sequencing or other functional approaches. Furthermore, to ensure translatability and reproducibility of research findings, a combination of multiple different complementary '-omic' approaches should be employed.}, } @article {pmid30661755, year = {2019}, author = {Pasolli, E and Asnicar, F and Manara, S and Zolfo, M and Karcher, N and Armanini, F and Beghini, F and Manghi, P and Tett, A and Ghensi, P and Collado, MC and Rice, BL and DuLong, C and Morgan, XC and Golden, CD and Quince, C and Huttenhower, C and Segata, N}, title = {Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.}, journal = {Cell}, volume = {176}, number = {3}, pages = {649-662.e20}, pmid = {30661755}, issn = {1097-4172}, support = {BB/L027801/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; U54 DE023798/DE/NIDCR NIH HHS/United States ; R01 HG005220/HG/NHGRI NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; }, mesh = {Big Data ; Genetic Variation/genetics ; Geography ; Humans ; Life Style ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and in international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% of high quality) spanning body sites, ages, countries, and lifestyles. We recapitulated 4,930 species-level genome bins (SGBs), 77% without genomes in public repositories (unknown SGBs [uSGBs]). uSGBs are prevalent (in 93% of well-assembled samples), expand underrepresented phyla, and are enriched in non-Westernized populations (40% of the total SGBs). We annotated 2.85 M genes in SGBs, many associated with conditions including infant development (94,000) or Westernization (106,000). SGBs and uSGBs permit deeper microbiome analyses and increase the average mappability of metagenomic reads from 67.76% to 87.51% in the gut (median 94.26%) and 65.14% to 82.34% in the mouth. We thus identify thousands of microbial genomes from yet-to-be-named species, expand the pangenomes of human-associated microbes, and allow better exploitation of metagenomic technologies.}, } @article {pmid30660184, year = {2019}, author = {Keijser, BJF and Agamennone, V and van den Broek, TJ and Caspers, M and van de Braak, A and Bomers, R and Havekes, M and Schoen, E and van Baak, M and Mioch, D and Bomers, L and Montijn, RC}, title = {Dose-dependent impact of oxytetracycline on the veal calf microbiome and resistome.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {65}, pmid = {30660184}, issn = {1471-2164}, support = {060.24960//Agentschap NL/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; Dose-Response Relationship, Drug ; Drug Resistance, Microbial/*drug effects/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/genetics ; Genes, Bacterial/genetics ; Metagenomics/*methods ; Microbial Sensitivity Tests/methods ; Oxytetracycline/*pharmacology ; RNA, Ribosomal, 16S/chemistry/genetics ; Random Allocation ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Antibiotic therapy is commonly used in animal agriculture. Antibiotics excreted by the animals can contaminate farming environments, resulting in long term exposure of animals to sub-inhibitory levels of antibiotics. Little is known on the effect of this exposure on antibiotic resistance. In this study, we aimed to investigate the long term effects of sub-inhibitory levels of antibiotics on the gut microbiota composition and resistome of veal calves in vivo. Forty-two veal calves were randomly assigned to three groups. The first group (OTC-high) received therapeutic oral dosages of 1 g oxytetracycline (OTC), twice per day, during 5 days. The second group (OTC-low) received an oral dose of OTC of 100-200 μg per day during 7 weeks, mimicking animal exposure to environmental contamination. The third group (CTR) did not receive OTC, serving as unexposed control. Antibiotic residue levels were determined over time. The temporal effects on the gut microbiota and antibiotic resistance gene abundance was analysed by metagenomic sequencing.

RESULTS: In the therapeutic group, OTC levels exceeded MIC values. The low group remained at sub-inhibitory levels. The control group did not reach any significant OTC levels. 16S rRNA gene-based analysis revealed significant changes in the calf gut microbiota. Time-related changes accounted for most of the variation in the sequence data. Therapeutic application of OTC had transient effect, significantly impacting gut microbiota composition between day 0 and day 2. By metagenomic sequence analysis we identified six antibiotic resistance genes representing three gene classes (tetM, floR and mel) that differed in relative abundance between any of the intervention groups and the control. qPCR was used to validate observations made by metagenomic sequencing, revealing a peak of tetM abundance at day 28-35 in the OTC-high group. No increase in resistance genes abundance was seen in the OTC-low group.

CONCLUSIONS: Under the conditions tested, sub-therapeutic administration of OTC did not result in increased tetM resistance levels as observed in the therapeutic group.}, } @article {pmid30659724, year = {2019}, author = {Turgay, E and Steinum, TM and Colquhoun, D and Karataş, S}, title = {Environmental biofilm communities associated with early-stage common dentex (Dentex dentex) culture.}, journal = {Journal of applied microbiology}, volume = {126}, number = {4}, pages = {1032-1043}, doi = {10.1111/jam.14205}, pmid = {30659724}, issn = {1365-2672}, support = {20950//Scientific Research Project Coordination Unit of Istanbul University/ ; }, mesh = {Animal Feed/analysis ; Animals ; Bacteria/classification/genetics/isolation & purification ; Biofilms/classification/*growth & development ; *Life Cycle Stages ; Metagenomics ; Microbiota/*genetics ; Perciformes/*growth & development/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {AIMS: To describe the biofilm microbiota associated with various feeding phases during larval common dentex (Dentex dentex) culture.

METHODS AND RESULTS: A targeted metagenomic (metagenetic) study was performed by means of 16S rRNA gene-based PCR and NextGen pyrosequencing. The resulting dataset was scrutinized with microbial community analysis software (r packages) using r/Rstudio. While median observed and estimated alpha-diversities were 171 ± 38 and 207 ± 27 taxa, respectively, 72·1-85·8% of individual biofilm communities comprised only 27-46 taxa. Members of the genus Methylobacterium and family Rhodobacteraceae dominated biofilms formed during all feeding phases while genera Nannochloropsis and Tetraselmis microalgae were major constituents of biofilms during rotifer live feeding. Both potential fish pathogenic genera, for example, Vibrio and putatively probiotic taxa, for example, Phaeobacter gallaeciensis were identified.

CONCLUSIONS: Relatively stable biofilm communities were identified during each feeding phase but varied significantly between feeding phases, most likely in response to the introduction of live feed/microalgae-associated bacteria into rearing tanks.

The structure of the bacterial communities identified represents a 'template' for successful larval dentex culture and provides a foundation for future investigations into failed production cycles.}, } @article {pmid30658995, year = {2019}, author = {Hildebrand, F and Moitinho-Silva, L and Blasche, S and Jahn, MT and Gossmann, TI and Huerta-Cepas, J and Hercog, R and Luetge, M and Bahram, M and Pryszlak, A and Alves, RJ and Waszak, SM and Zhu, A and Ye, L and Costea, PI and Aalvink, S and Belzer, C and Forslund, SK and Sunagawa, S and Hentschel, U and Merten, C and Patil, KR and Benes, V and Bork, P}, title = {Antibiotics-induced monodominance of a novel gut bacterial order.}, journal = {Gut}, volume = {68}, number = {10}, pages = {1781-1790}, pmid = {30658995}, issn = {1468-3288}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics ; Gastrointestinal Microbiome/*drug effects ; Humans ; Metagenomics/*methods ; Microbiota/drug effects/*genetics ; }, abstract = {OBJECTIVE: The composition of the healthy human adult gut microbiome is relatively stable over prolonged periods, and representatives of the most highly abundant and prevalent species have been cultured and described. However, microbial abundances can change on perturbations, such as antibiotics intake, enabling the identification and characterisation of otherwise low abundant species.

DESIGN: Analysing gut microbial time-series data, we used shotgun metagenomics to create strain level taxonomic and functional profiles. Community dynamics were modelled postintervention with a focus on conditionally rare taxa and previously unknown bacteria.

RESULTS: In response to a commonly prescribed cephalosporin (ceftriaxone), we observe a strong compositional shift in one subject, in which a previously unknown species, [U]Borkfalki ceftriaxensis, was identified, blooming to 92% relative abundance. The genome assembly reveals that this species (1) belongs to a so far undescribed order of Firmicutes, (2) is ubiquitously present at low abundances in at least one third of adults, (3) is opportunistically growing, being ecologically similar to typical probiotic species and (4) is stably associated to healthy hosts as determined by single nucleotide variation analysis. It was the first coloniser after the antibiotic intervention that led to a long-lasting microbial community shift and likely permanent loss of nine commensals.

CONCLUSION: The bloom of [U]B. ceftriaxensis and a subsequent one of Parabacteroides distasonis demonstrate the existence of monodominance community states in the gut. Our study points to an undiscovered wealth of low abundant but common taxa in the human gut and calls for more highly resolved longitudinal studies, in particular on ecosystem perturbations.}, } @article {pmid30658982, year = {2019}, author = {Jiao, S and Chen, W and Wei, G}, title = {Resilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant Growth.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {6}, pages = {}, pmid = {30658982}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/*isolation & purification/metabolism ; Biodiversity ; Fabaceae/*growth & development/*microbiology ; Metagenomics ; Metals/analysis/metabolism ; *Microbiota ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/analysis/*metabolism ; }, abstract = {A lack of knowledge of the microbial responses to environmental change at the species and functional levels hinders our ability to understand the intrinsic mechanisms underlying the maintenance of microbial ecosystems. Here, we present results from temporal microcosms that introduced inorganic and organic contaminants into agro-soils for 90 days, with three common legume plants. Temporal dynamics and assemblage of soil microbial communities and functions in response to contamination under the influence of growth of different plants were explored via sequencing of the 16S rRNA amplicon and by shotgun metagenomics. Soil microbial alpha diversity and structure at the taxonomic and functional levels exhibited resilience patterns. Functional profiles showed greater resilience than did taxonomic ones. Different legume plants imposed stronger selection on taxonomic profiles than on functional ones. Network and random forest analyses revealed that the functional potential of soil microbial communities was fostered by various taxonomic groups. Betaproteobacteria were important predictors of key functional traits such as amino acid metabolism, nucleic acid metabolism, and hydrocarbon degradation. Our study reveals the strong resilience of the soil microbiome to chemical contamination and sensitive responses of taxonomic rather than functional profiles to selection processes induced by different legume plants. This is pivotal to develop approaches and policies for the protection of soil microbial diversity and functions in agro-ecosystems with different response strategies from global environmental drivers, such as soil contamination and plant invasion.IMPORTANCE Exploring the microbial responses to environmental disturbances is a central issue in microbial ecology. Understanding the dynamic responses of soil microbial communities to chemical contamination and the microbe-soil-plant interactions is essential for forecasting the long-term changes in soil ecosystems. Nevertheless, few studies have applied multi-omics approaches to assess the microbial responses to soil contamination and the microbe-soil-plant interactions at the taxonomic and functional levels simultaneously. Our study reveals clear succession and resilience patterns of soil microbial diversity and structure in response to chemical contamination. Different legume plants exerted stronger selection processes on taxonomic than on functional profiles in contaminated soils, which could benefit plant growth and fitness as well as foster the potential abilities of hydrocarbon degradation and metal tolerance. These results provide new insight into the resilience and assemblage of soil microbiome in response to environmental disturbances in agro-ecosystems at the species and functional levels.}, } @article {pmid30658977, year = {2019}, author = {Li, Y and Pinto-Tomás, AA and Rong, X and Cheng, K and Liu, M and Huang, Y}, title = {Population Genomics Insights into Adaptive Evolution and Ecological Differentiation in Streptomycetes.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {7}, pages = {}, pmid = {30658977}, issn = {1098-5336}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Biodiversity ; *Ecology ; Ecosystem ; *Evolution, Molecular ; Gene Flow ; Genes, Bacterial ; Genetic Variation ; Genome-Wide Association Study ; Genotype ; Homologous Recombination ; Insecta/microbiology ; *Metagenomics ; Multigene Family/genetics ; N-Acetylneuraminic Acid/metabolism ; Organic Chemicals/metabolism ; Phylogeny ; Polymorphism, Single Nucleotide ; Soil Microbiology ; Streptomyces/classification/*genetics/isolation & purification/*physiology ; Water Microbiology ; }, abstract = {Deciphering the genomic variation that represents microevolutionary processes toward species divergence is key to understanding microbial speciation, which has long been under debate. Streptomycetes are filamentous bacteria that are ubiquitous in nature and the richest source of antibiotics; however, their speciation processes remain unknown. To tackle this issue, we performed a comprehensive population genomics analysis on Streptomyces albidoflavus residing in different habitats and with a worldwide distribution and identified and characterized the foundational changes within the species. We detected three well-defined phylogenomic clades, of which clades I and III mainly contained free-living (soil/marine) and insect-associated strains, respectively, and clade II had a mixed origin. By performing genome-wide association studies (GWAS), we identified a number of genetic variants associated with free-living or entomic (denoting or relating to insects) habitats in both the accessory and core genomes. These variants contributed collectively to the population structure and had annotated or confirmed functions that likely facilitate differential adaptation of the species. In addition, we detected higher levels of homologous recombination within each clade and in the free-living group than within the whole species and in the entomic group. A subset of the insect-associated strains (clade III) showed a relatively independent evolutionary trajectory with more symbiosis-favorable genes but little genetic interchange with the other lineages. Our results demonstrate that ecological adaptation promotes genetic differentiation in S. albidoflavus, suggesting a model of ecological speciation with gene flow in streptomycetes.IMPORTANCE Species are the fundamental units of ecology and evolution, and speciation leads to the astounding diversity of life on Earth. Studying speciation is thus of great significance to understand, protect, and exploit biodiversity, but it is a challenge in the microbial world. In this study, using population genomics, we placed Streptomyces albidoflavus strains in a spectrum of speciation and showed that the genetic differences between phylogenomic clusters evolved mainly by environmental selection and gene-specific sweeps. These findings highlight the role of ecology in structuring recombining bacterial species, making a step toward a deeper understanding of microbial speciation. Our results also raise concerns of an underrated microbial diversity at the intraspecies level, which can be utilized for mining of ecologically relevant natural products.}, } @article {pmid30658973, year = {2019}, author = {Malmuthuge, N and Liang, G and Griebel, PJ and Guan, LL}, title = {Taxonomic and Functional Compositions of the Small Intestinal Microbiome in Neonatal Calves Provide a Framework for Understanding Early Life Gut Health.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {6}, pages = {}, pmid = {30658973}, issn = {1098-5336}, support = {//Canadian Institute for Health Research/International ; }, mesh = {Animals ; Animals, Newborn/*microbiology ; Bacteria/*classification/genetics/*isolation & purification ; Cattle ; DNA, Bacterial/genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Intestine, Small/*microbiology ; Male ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A lack of information on the intestinal microbiome of neonatal calves prevents the use of microbial intervention strategies to improve calf gut health. This study profiled the taxonomic and functional composition of the small intestinal luminal microbiome of neonatal calves using whole-genome sequencing of the metagenome, aiming to understand the dynamics of microbial establishment during early life. Despite highly individualized microbial communities, we identified two distinct taxonomy-based clusters from the collective luminal microbiomes comprising a high level of either Lactobacillus or Bacteroides Among the clustered microbiomes, Lactobacillus-dominant ileal microbiomes had significantly lower abundances of Bacteroides, Prevotella, Roseburia, Ruminococcus, and Veillonella compared to the Bacteroides-dominated ileal microbiomes. In addition, the upregulated ileal genes of the Lactobacillus-dominant calves were related to leukocyte and lymphocyte chemotaxis, the cytokine/chemokine-mediated signaling pathway, and inflammatory responses, while the upregulated ileal genes of the Bacteroides-dominant calves were related to cell adhesion, response to stimulus, cell communication and regulation of mitogen-activated protein kinase cascades. The functional profiles of the luminal microbiomes also revealed two distinct clusters consisting of functions related to either high protein metabolism or sulfur metabolism. A lower abundance of Bifidobacterium and a higher abundance of sulfur-reducing bacteria (SRB) were observed in the sulfur metabolism-dominant cluster (0.2% ± 0.1%) compared to the protein metabolism-dominant cluster (12.6% ± 5.7%), suggesting an antagonistic relationship between SRB and Bifidobacterium, which both compete for cysteine. These distinct taxonomic and functional clusters may provide a framework to further analyze interactions between the intestinal microbiome and the immune function and health of neonatal calves.IMPORTANCE Dietary interventions to manipulate neonatal gut microbiota have been proposed to generate long-term impacts on hosts. Currently, our understanding of the early gut microbiome of neonatal calves is limited to 16S rRNA gene amplicon based microbial profiling, which is a barrier to developing dietary interventions to improve calf gut health. The use of a metagenome sequencing-based approach in the present study revealed high individual animal variation in taxonomic and functional abundance of intestinal microbiome and potential impacts of early microbiome on mucosal immune responses during the preweaning period. During this developmental period, age- and diet-related changes in microbial diversity, richness, density, and the abundance of taxa and functions were observed. A correlation-based approach to further explore the individual animal variation revealed potential enterotypes that can be linked to calf gut health, which may pave the way to developing strategies to manipulate the microbiome and improve calf health.}, } @article {pmid30658727, year = {2019}, author = {Sarin, SK and Pande, A and Schnabl, B}, title = {Microbiome as a therapeutic target in alcohol-related liver disease.}, journal = {Journal of hepatology}, volume = {70}, number = {2}, pages = {260-272}, doi = {10.1016/j.jhep.2018.10.019}, pmid = {30658727}, issn = {1600-0641}, support = {R01 AA020703/AA/NIAAA NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; U01 AA021856/AA/NIAAA NIH HHS/United States ; U01 AA026939/AA/NIAAA NIH HHS/United States ; }, mesh = {Adrenal Cortex Hormones/therapeutic use ; Animals ; Anti-Bacterial Agents/therapeutic use ; Dysbiosis/chemically induced/microbiology ; Ethanol/*pharmacology ; Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/*drug effects ; Humans ; Liver Diseases, Alcoholic/*diet therapy/*drug therapy/metabolism/microbiology ; Metabolome/drug effects ; Probiotics/therapeutic use ; }, abstract = {Alcohol-related liver disease is associated with significant changes in gut microbial composition. The transmissibility of ethanol-induced liver disease has been demonstrated using faecal microbiota transfer in preclinical models. This technique has also led to improved survival in patients with severe alcoholic hepatitis, suggesting that changes in the composition and function of the gut microbiota are causatively linked to alcohol-related liver disease. A major mechanism by which gut microbiota influence the development of alcohol-related liver disease is through a leaky intestinal barrier. This permits translocation of viable bacteria and microbial products to the liver, where they induce and promote inflammation, as well as contribute to hepatocyte death and the fibrotic response. In addition, gut dysbiosis is associated with changes in the metabolic function of the intestinal microbiota, bile acid composition and circulation, immune dysregulation during onset and progression of alcohol-related liver disease. Findings from preclinical and human studies will be used to demonstrate how alcohol causes intestinal pathology and contributes to alcohol-related liver disease and how the latter is self-perpetuating. Additionally, we summarise the effects of untargeted treatment approaches on the gut microbiota, such as diet, probiotics, antibiotics and faecal microbial transplantation in alcohol-related liver disease. We further discuss how targeted approaches can restore intestinal homeostasis and improve alcohol-related liver disease. These approaches are likely to add to the therapeutic options for alcohol-related liver disease independently or in conjunction with steroids.}, } @article {pmid30658700, year = {2019}, author = {Las Heras, V and Clooney, AG and Ryan, FJ and Cabrera-Rubio, R and Casey, PG and Hueston, CM and Pinheiro, J and Rudkin, JK and Melgar, S and Cotter, PD and Hill, C and Gahan, CGM}, title = {Short-term consumption of a high-fat diet increases host susceptibility to Listeria monocytogenes infection.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {7}, pmid = {30658700}, issn = {2049-2618}, mesh = {Animals ; Diet, High-Fat/*adverse effects ; Diet, Western/adverse effects ; Disease Models, Animal ; Feces/microbiology ; Female ; Firmicutes/drug effects/genetics/isolation & purification ; Gene Expression Regulation/drug effects ; Goblet Cells/cytology/drug effects ; Listeria monocytogenes/*pathogenicity ; Listeriosis/*etiology/genetics/immunology ; Metagenome/drug effects ; Mice ; Microbiota/*drug effects ; Obesity/complications/etiology/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: A westernized diet comprising a high caloric intake from animal fats is known to influence the development of pathological inflammatory conditions. However, there has been relatively little focus upon the implications of such diets for the progression of infectious disease. Here, we investigated the influence of a high-fat (HF) diet upon parameters that influence Listeria monocytogenes infection in mice.

RESULTS: We determined that short-term administration of a HF diet increases the number of goblet cells, a known binding site for the pathogen, in the gut and also induces profound changes to the microbiota and promotes a pro-inflammatory gene expression profile in the host. Host physiological changes were concordant with significantly increased susceptibility to oral L. monocytogenes infection in mice fed a HF diet relative to low fat (LF)- or chow-fed animals. Prior to Listeria infection, short-term consumption of HF diet elevated levels of Firmicutes including Coprococcus, Butyricicoccus, Turicibacter and Clostridium XIVa species. During active infection with L. monocytogenes, microbiota changes were further exaggerated but host inflammatory responses were significantly downregulated relative to Listeria-infected LF- or chow-fed groups, suggestive of a profound tempering of the host response influenced by infection in the context of a HF diet. The effects of diet were seen beyond the gut, as a HF diet also increased the sensitivity of mice to systemic infection and altered gene expression profiles in the liver.

CONCLUSIONS: We adopted a systems approach to identify the effects of HF diet upon L. monocytogenes infection through analysis of host responses and microbiota changes (both pre- and post-infection). Overall, the results indicate that short-term consumption of a westernized diet has the capacity to significantly alter host susceptibility to L. monocytogenes infection concomitant with changes to the host physiological landscape. The findings suggest that diet should be a consideration when developing models that reflect human infectious disease.}, } @article {pmid30658400, year = {2019}, author = {Liew, WP and Mohd-Redzwan, S and Than, LTL}, title = {Gut Microbiota Profiling of Aflatoxin B1-Induced Rats Treated with Lactobacillus casei Shirota.}, journal = {Toxins}, volume = {11}, number = {1}, pages = {}, pmid = {30658400}, issn = {2072-6651}, mesh = {Aflatoxin B1/*toxicity ; Animals ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/genetics ; *Lacticaseibacillus casei ; Male ; RNA, Ribosomal, 16S ; Rats, Sprague-Dawley ; }, abstract = {Aflatoxin B1 (AFB1) is a ubiquitous carcinogenic food contaminant. Gut microbiota is of vital importance for the host's health, regrettably, limited studies have reported the effects of xenobiotic toxins towards gut microbiota. Thus, the present study aims to investigate the interactions between AFB1 and the gut microbiota. Besides, an AFB1-binding microorganism, Lactobacillus casei Shirota (Lcs) was tested on its ability to ameliorate the changes on gut microbiota induced by AFB1. The fecal contents of three groups of rats included an untreated control group, an AFB1 group, as well as an Lcs + AFB1 group, were analyzed. Using the MiSeq platform, the PCR products of 16S rDNA gene extracted from the feces were subjected to next-generation sequencing. The alpha diversity index (Shannon) showed that the richness of communities increased significantly in the Lcs + AFB1 group compared to the control and AFB1 groups. Meanwhile, beta diversity indices demonstrated that AFB1 group significantly deviated from the control and Lcs + AFB1 groups. AFB1-exposed rats were especially high in Alloprevotella spp. abundance. Such alteration in the bacterial composition might give an insight on the interactions of AFB1 towards gut microbiota and how Lcs plays its role in detoxification of AFB1.}, } @article {pmid30658055, year = {2019}, author = {Pellock, SJ and Walton, WG and Ervin, SM and Torres-Rivera, D and Creekmore, BC and Bergan, G and Dunn, ZD and Li, B and Tripathy, A and Redinbo, MR}, title = {Discovery and Characterization of FMN-Binding β-Glucuronidases in the Human Gut Microbiome.}, journal = {Journal of molecular biology}, volume = {431}, number = {5}, pages = {970-980}, pmid = {30658055}, issn = {1089-8638}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; T32 GM008570/GM/NIGMS NIH HHS/United States ; R01 CA161879/CA/NCI NIH HHS/United States ; R01 CA207416/CA/NCI NIH HHS/United States ; R01 CA098468/CA/NCI NIH HHS/United States ; }, mesh = {Catalytic Domain/physiology ; Clostridiales/metabolism ; Flavin Mononucleotide/*metabolism ; Gastrointestinal Microbiome/*physiology ; Glucuronidase/*metabolism ; Humans ; Kinetics ; Metagenome/physiology ; Microbiota/physiology ; Ruminococcus/metabolism ; }, abstract = {The human gut microbiota encodes β-glucuronidases (GUSs) that play key roles in health and disease via the metabolism of glucuronate-containing carbohydrates and drugs. Hundreds of putative bacterial GUS enzymes have been identified by metagenomic analysis of the human gut microbiome, but less than 10% have characterized structures and functions. Here we describe a set of unique gut microbial GUS enzymes that bind flavin mononucleotide (FMN). First, we show using mass spectrometry, isothermal titration calorimetry, and x-ray crystallography that a purified GUS from the gut commensal microbe Faecalibacterium prausnitzii binds to FMN on a surface groove located 30 Å away from the active site. Second, utilizing structural and functional data from this FMN-binding GUS, we analyzed the 279 unique GUS sequences from the Human Microbiome Project database and identified 14 putative FMN-binding GUSs. We characterized four of these hits and solved the structure of two, the GUSs from Ruminococcus gnavus and Roseburia hominis, which confirmed that these are FMN binders. Third, binding and kinetic analysis of the FMN-binding site mutants of these five GUSs show that they utilize a conserved site to bind FMN that is not essential for GUS activity, but can affect KM. Lastly, a comprehensive structural review of the PDB reveals that the FMN-binding site employed by these enzymes is unlike any structurally characterized FMN binders to date. These findings reveal the first instance of an FMN-binding glycoside hydrolase and suggest a potential link between FMN and carbohydrate metabolism in the human gut microbiota.}, } @article {pmid30657979, year = {2019}, author = {Liu, J and Lian, Q and Chen, Y and Qi, J}, title = {Amino acid based de Bruijn graph algorithm for identifying complete coding genes from metagenomic and metatranscriptomic short reads.}, journal = {Nucleic acids research}, volume = {47}, number = {5}, pages = {e30}, pmid = {30657979}, issn = {1362-4962}, mesh = {*Algorithms ; Amino Acids/*genetics ; Datasets as Topic ; Feces/microbiology ; Gastrointestinal Microbiome/genetics ; Genes/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Transcriptome/*genetics ; }, abstract = {Metagenomic studies, greatly promoted by the fast development of next-generation sequencing (NGS) technologies, uncover complex structures of microbial communities and their interactions with environment. As the majority of microbes lack information of genome sequences, it is essential to assemble prokaryotic genomes ab initio aiming to retrieve complete coding genes from various metabolic pathways. The complex nature of microbial composition and the burden of handling a vast amount of metagenomic data, bring great challenges to the development of effective and efficient bioinformatic tools. Here we present a protein assembler (MetaPA), based on de Bruijn graph searching on oligopeptide spaces and can be applied on both metagenomic and metatranscriptomic sequencing data. When public homologous protein sequences are involved to guide the assembling procedures, MetaPA assembles 85% of total proteins in complete sequences with high precision of 83% on real high-throughput sequencing datasets. Application of MetaPA on metatranscriptomic data successfully identifies the majority of actively transcribed genes validated in related studies. The results suggest that MetaPA has a good potential in both metagenomic and metatranscriptomic studies to characterize the composition and abundance of microbiota.}, } @article {pmid30657007, year = {2019}, author = {Machiavelli, A and Duarte, RTD and Pires, MMS and Zárate-Bladés, CR and Pinto, AR}, title = {The impact of in utero HIV exposure on gut microbiota, inflammation, and microbial translocation.}, journal = {Gut microbes}, volume = {10}, number = {5}, pages = {599-614}, pmid = {30657007}, issn = {1949-0984}, mesh = {Adult ; Bacteria/classification/genetics/growth & development/isolation & purification ; Child ; Female ; *Gastrointestinal Microbiome/genetics ; *HIV Infections/microbiology ; Humans ; Metagenome ; Mothers ; Pregnancy ; *Pregnancy Complications, Infectious/microbiology ; Prenatal Exposure Delayed Effects/*microbiology ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {HIV-exposed but uninfected (HEU) children represent a growing population and show a significantly higher number of infectious diseases, several immune alterations, compromised growth, and increased mortality rates when compared to HIV-unexposed children. Considering the impact that the gut microbiota has on general host homeostasis and immune system development and modulation, we hypothesized that HEU children present altered gut microbiota that is linked to the increased morbidity and the immune system disorders faced by them. Our experiments revealed no differences in beta and alpha diversity of the gut microbiota between HEU and unexposed children or between HIV-infected and uninfected mothers. However, there were differences in the abundance of several taxa from the gut microbiota between HEU and unexposed children and between HIV-infected and uninfected mothers. Functional prediction based on 16S rRNA sequences also indicated differences between HEU and unexposed children and between infected and uninfected mothers. In addition, we detected no differences between HEU and unexposed children in relation to weight, weight-for-age z scores, albumin serum levels, or microbial translocation and inflammation markers. In summary, HIV-infected mothers and their HIV-exposed children present alterations in the abundance of several taxa in the gut microbiome and the predicted functional metagenome when compared to uninfected mothers and unexposed children. Knowledge about the gut microbiome of HEU children in different settings is essential in order to determine better treatments for this susceptible population.}, } @article {pmid30655087, year = {2019}, author = {Markowski, MC and Boorjian, SA and Burton, JP and Hahn, NM and Ingersoll, MA and Maleki Vareki, S and Pal, SK and Sfanos, KS}, title = {The Microbiome and Genitourinary Cancer: A Collaborative Review.}, journal = {European urology}, volume = {75}, number = {4}, pages = {637-646}, pmid = {30655087}, issn = {1873-7560}, support = {P30 CA006973/CA/NCI NIH HHS/United States ; }, mesh = {Female ; Genitalia/*microbiology/pathology ; Host-Pathogen Interactions ; Humans ; Kidney Neoplasms/*microbiology/pathology/therapy/urine ; Male ; *Microbiota ; Prognosis ; Prostatic Neoplasms/*microbiology/pathology/therapy/urine ; Risk Factors ; Testicular Neoplasms/*microbiology/pathology/therapy/urine ; Urinary Bladder Neoplasms/*microbiology/pathology/therapy/urine ; Urinary Tract/*microbiology/pathology ; Urine/microbiology ; }, abstract = {CONTEXT: The recent discovery of the existence of a human genitourinary microbiome has led to the investigation of its role in mediating the pathogenesis of genitourinary malignancies, including bladder, kidney, and prostate cancers. Furthermore, although it is largely recognized that members of the gastrointestinal microbiota are actively involved in drug metabolism, new studies demonstrate additional roles and the potential necessity of the gastrointestinal microbiota in dictating cancer treatment response.

OBJECTIVE: To summarize the current evidence of a mechanistic role for the genitourinary and gastrointestinal microbiome in genitourinary cancer initiation and treatment response.

EVIDENCE ACQUISITION: We conducted a literature search up to October 2018. Search terms included microbiome, microbiota, urinary microbiome, bladder cancer, urothelial carcinoma, renal cell carcinoma, kidney cancer, testicular cancer, and prostate cancer.

EVIDENCE SYNTHESIS: There is preliminary evidence to implicate the members of the genitourinary microbiota as causative factors or cofactors in genitourinary malignancy. Likewise, the current evidence for gastrointestinal microbes in dictating cancer treatment response is mainly correlative; however, we provide examples where therapeutic agents used for the treatment of genitourinary cancers are affected by the human-associated microbiota, or vice versa. Clinical trials, such as fecal microbiota transplant to increase the efficacy of immunotherapy, are currently underway.

CONCLUSIONS: The role of the microbiome in genitourinary cancer is an emerging field that merits further studies. Translating microbiome research into clinical action will require incorporation of microbiome surveillance into ongoing and future clinical trials as well as expansion of studies to include metagenomic sequencing and metabolomics.

PATIENT SUMMARY: This review covers recent evidence that microbial populations that reside in the genitourinary tract-and were previously not known to exist-may influence the development of genitourinary malignancies including bladder, kidney, and prostate cancers. Furthermore, microbial populations that exist at sites outside of the genitourinary tract, such as those that reside in our gut, may influence cancer development and/or treatment response.}, } @article {pmid30652494, year = {2019}, author = {Kalantar, KL and Moazed, F and Christenson, SC and Wilson, J and Deiss, T and Belzer, A and Vessel, K and Caldera, S and Jauregui, A and Bolourchi, S and DeRisi, JL and Calfee, CS and Langelier, C}, title = {Metagenomic comparison of tracheal aspirate and mini-bronchial alveolar lavage for assessment of respiratory microbiota.}, journal = {American journal of physiology. Lung cellular and molecular physiology}, volume = {316}, number = {3}, pages = {L578-L584}, pmid = {30652494}, issn = {1522-1504}, support = {K23 HL136844/HL/NHLBI NIH HHS/United States ; K23 HL138461/HL/NHLBI NIH HHS/United States ; R35 HL140026/HL/NHLBI NIH HHS/United States ; K23 HL123778/HL/NHLBI NIH HHS/United States ; R01 HL110969/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Aged ; *Bronchoalveolar Lavage/methods ; Bronchoalveolar Lavage Fluid/*microbiology ; Female ; Humans ; Male ; Microbiota ; Middle Aged ; Pneumonia, Bacterial/diagnosis/*microbiology ; *Specimen Handling ; Therapeutic Irrigation/methods ; }, abstract = {Accurate and informative microbiological testing is essential for guiding diagnosis and management of pneumonia in patients who are critically ill. Sampling of tracheal aspirate (TA) is less invasive compared with mini-bronchoalveolar lavage (mBAL) and is now recommended as a frontline diagnostic approach in patients who are mechanically ventilated, despite the historical belief that TA was suboptimal due to contamination from oral microbes. Advancements in metagenomic next-generation sequencing (mNGS) now permit assessment of airway microbiota without a need for culture and, as such, provide an opportunity to examine differences between mBAL and TA at a resolution previously unachievable. Here, we engaged shotgun mNGS to assess quantitatively the airway microbiome in matched mBAL and TA specimens from a prospective cohort of critically ill adults. We observed moderate differences between sample types across all subjects; however, we found significant compositional similarity in subjects with bacterial pneumonia, whose microbial communities were characterized by dominant pathogens. In contrast, in patients with noninfectious acute respiratory illnesses, significant differences were observed between sample types. Our findings suggest that TA sampling provides a similar assessment of airway microbiota as more invasive testing by mBAL in patients with pneumonia.}, } @article {pmid30649386, year = {2019}, author = {Van Gompel, L and Luiken, REC and Sarrazin, S and Munk, P and Knudsen, BE and Hansen, RB and Bossers, A and Aarestrup, FM and Dewulf, J and Wagenaar, JA and Mevius, DJ and Schmitt, H and Heederik, DJJ and Dorado-García, A and Smit, LAM and , }, title = {The antimicrobial resistome in relation to antimicrobial use and biosecurity in pig farming, a metagenome-wide association study in nine European countries.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {4}, pages = {865-876}, doi = {10.1093/jac/dky518}, pmid = {30649386}, issn = {1460-2091}, mesh = {Animal Husbandry/*methods ; Animals ; Anti-Infective Agents/*therapeutic use ; Biota/*drug effects ; Computational Biology ; Cross-Sectional Studies ; *Drug Resistance, Bacterial ; Drug Utilization/*statistics & numerical data ; Europe ; Feces/*microbiology ; *Genes, Bacterial ; Metagenomics ; Swine ; }, abstract = {OBJECTIVES: Previous studies in food-producing animals have shown associations between antimicrobial use (AMU) and resistance (AMR) in specifically isolated bacterial species. Multi-country data are scarce and only describe between-country differences. Here we investigate associations between the pig faecal mobile resistome and characteristics at the farm-level across Europe.

METHODS: A cross-sectional study was conducted among 176 conventional pig farms from nine European countries. Twenty-five faecal samples from fattening pigs were pooled per farm and acquired resistomes were determined using shotgun metagenomics and the Resfinder reference database, i.e. the full collection of horizontally acquired AMR genes (ARGs). Normalized fragments resistance genes per kilobase reference per million bacterial fragments (FPKM) were calculated. Specific farm-level data (AMU, biosecurity) were collected. Random-effects meta-analyses were performed by country, relating farm-level data to relative ARG abundances (FPKM).

RESULTS: Total AMU during fattening was positively associated with total ARG (total FPKM). Positive associations were particularly observed between widely used macrolides and tetracyclines, and ARGs corresponding to the respective antimicrobial classes. Significant AMU-ARG associations were not found for β-lactams and only few colistin ARGs were found, despite high use of these antimicrobial classes in younger pigs. Increased internal biosecurity was directly related to higher abundances of ARGs mainly encoding macrolide resistance. These effects of biosecurity were independent of AMU in mutually adjusted models.

CONCLUSIONS: Using resistome data in association studies is unprecedented and adds accuracy and new insights to previously observed AMU-AMR associations. Major components of the pig resistome are positively and independently associated with on-farm AMU and biosecurity conditions.}, } @article {pmid30649283, year = {2019}, author = {Sickel, W and Van de Weyer, AL and Bemm, F and Schultz, J and Keller, A}, title = {Venus flytrap microbiotas withstand harsh conditions during prey digestion.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {3}, pages = {}, doi = {10.1093/femsec/fiz010}, pmid = {30649283}, issn = {1574-6941}, mesh = {Amino Acids/pharmacology ; Animals ; Droseraceae/*microbiology ; Host Microbial Interactions ; Indenes/pharmacology ; Metagenomics ; *Microbiota/drug effects/genetics ; Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The carnivorous Venus flytrap (Dionaea muscipula) overcomes environmental nutrient limitation by capturing small animals. Such prey is digested with an acidic enzyme-containing mucilage that is secreted into the closed trap. However, surprisingly little is known about associations with microorganisms. Therefore, we assessed microbiotas of traps and petioles for the Venus flytrap by 16S amplicon meta-barcoding. We also performed time-series assessments of dynamics during digestion in traps and experimental acidification of petioles. We found that the traps hosted distinct microbiotas that differed from adjacent petioles. Further, they showed a significant taxonomic turnover during digestion. Following successful catches, prey-associated bacteria had strong effects on overall composition. With proceeding digestion, however, microbiotas were restored to compositions resembling pre-digestion stages. A comparable, yet less extensive shift was found when stimulating digestion with coronatine. Artificial acidification of petioles did not induce changes towards trap-like communities. Our results show that trap microbiota were maintained during digestion despite harsh conditions and recovered after short-term disturbances through prey microbiota. This indicates trap-specific and resilient associations. By mapping to known genomes, we predicted putative adaptations and functional implications for the system, yet direct mechanisms and quantification of host benefits, like the involvement in digestion, remain to be addressed.}, } @article {pmid30649168, year = {2019}, author = {Griffith, JC and Morgan, XC}, title = {Invited Commentary: Improving the Accessibility of Human Microbiome Project Data Through Integration With R/Bioconductor.}, journal = {American journal of epidemiology}, volume = {188}, number = {6}, pages = {1027-1030}, doi = {10.1093/aje/kwz007}, pmid = {30649168}, issn = {1476-6256}, mesh = {Computational Biology ; Humans ; Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Alterations in the composition of the microbiota have been implicated in many diseases. The Human Microbiome Project (HMP) provides a comprehensive reference data set of the "normal" human microbiome of 242 healthy adults at 5 major body sites. The HMP used both 16S ribosomal RNA gene sequencing and whole-genome metagenomic sequencing to profile the subjects' microbial communities. However, accessing and analyzing the HMP data set still presents technical and bioinformatic challenges, given that researchers must import the microbiome data, integrate phylogenetic trees, and access and merge public and restricted metadata. The HMP16SData R/Bioconductor package developed by Schiffer et al. (Am J Epidemiol. 2019;188(6):1023-1026) greatly simplifies access to the HMP data by combining 16S taxonomic abundance data, public patient metadata, and phylogenetic trees as a single data object. The authors also provide an interface for users with approved Database of Genotypes and Phenotypes (dbGaP) projects to easily retrieve and merge the controlled-access HMP metadata. This package has a broad range of appeal to researchers across disciplines and with various levels of expertise in using R and/or other statistical tools, which translates to improved data accessibility for public health research, with data from healthy individuals serving as a reference for disease-associated studies.}, } @article {pmid30649166, year = {2019}, author = {Schiffer, L and Azhar, R and Shepherd, L and Ramos, M and Geistlinger, L and Huttenhower, C and Dowd, JB and Segata, N and Waldron, L}, title = {HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor.}, journal = {American journal of epidemiology}, volume = {188}, number = {6}, pages = {1023-1026}, pmid = {30649166}, issn = {1476-6256}, support = {R01 HG005220/HG/NHGRI NIH HHS/United States ; R21 AI121784/AI/NIAID NIH HHS/United States ; U24 CA180996/CA/NCI NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Computational Biology ; Databases, Genetic/*statistics & numerical data ; Female ; Humans ; Male ; Microbiota/*physiology ; RNA, Ribosomal, 16S/*metabolism ; Young Adult ; }, abstract = {Phase 1 of the Human Microbiome Project (HMP) investigated 18 body subsites of 242 healthy American adults to produce the first comprehensive reference for the composition and variation of the "healthy" human microbiome. Publicly available data sets from amplicon sequencing of two 16S ribosomal RNA variable regions, with extensive controlled-access participant data, provide a reference for ongoing microbiome studies. However, utilization of these data sets can be hindered by the complex bioinformatic steps required to access, import, decrypt, and merge the various components in formats suitable for ecological and statistical analysis. The HMP16SData package provides count data for both 16S ribosomal RNA variable regions, integrated with phylogeny, taxonomy, public participant data, and controlled participant data for authorized researchers, using standard integrative Bioconductor data objects. By removing bioinformatic hurdles of data access and management, HMP16SData enables epidemiologists with only basic R skills to quickly analyze HMP data.}, } @article {pmid30648011, year = {2019}, author = {Susi, H and Filloux, D and Frilander, MJ and Roumagnac, P and Laine, AL}, title = {Diverse and variable virus communities in wild plant populations revealed by metagenomic tools.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6140}, pmid = {30648011}, issn = {2167-8359}, abstract = {Wild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in Plantago lanceolata populations, and to understand the variation in their prevalence and distribution across the Åland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of P. lanceolata plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species Plantago lanceolata latent virus (PlLV), we found four potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus community with newly developed tools and protocols that offer exciting opportunities for future studies on the eco-evolutionary dynamics of viruses infecting plants in the wild.}, } @article {pmid30645723, year = {2019}, author = {}, title = {Profile of Dr. Fuwen Wei.}, journal = {Science China. Life sciences}, volume = {62}, number = {2}, pages = {165-167}, doi = {10.1007/s11427-019-9468-8}, pmid = {30645723}, issn = {1869-1889}, mesh = {Adaptation, Physiological ; Animals ; *Conservation of Natural Resources ; History, 20th Century ; History, 21st Century ; Humans ; Metagenomics ; Microbiota/genetics ; Ursidae/microbiology/physiology ; Zoology/*education ; }, } @article {pmid30643240, year = {2019}, author = {Nakamoto, N and Sasaki, N and Aoki, R and Miyamoto, K and Suda, W and Teratani, T and Suzuki, T and Koda, Y and Chu, PS and Taniki, N and Yamaguchi, A and Kanamori, M and Kamada, N and Hattori, M and Ashida, H and Sakamoto, M and Atarashi, K and Narushima, S and Yoshimura, A and Honda, K and Sato, T and Kanai, T}, title = {Gut pathobionts underlie intestinal barrier dysfunction and liver T helper 17 cell immune response in primary sclerosing cholangitis.}, journal = {Nature microbiology}, volume = {4}, number = {3}, pages = {492-503}, doi = {10.1038/s41564-018-0333-1}, pmid = {30643240}, issn = {2058-5276}, mesh = {Adult ; Aged ; Animals ; Bacterial Translocation ; Cholangitis, Sclerosing/*immunology/microbiology ; Colitis, Ulcerative/complications ; Enterococcus/isolation & purification ; Epithelial Cells/microbiology/pathology ; Female ; *Gastrointestinal Microbiome ; Germ-Free Life ; Humans ; Intestines/immunology/*pathology ; Klebsiella pneumoniae/isolation & purification/*pathogenicity ; Liver/*immunology/pathology ; Lymph Nodes/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Middle Aged ; Organoids/microbiology ; Proteus mirabilis/isolation & purification ; Th17 Cells/*immunology ; }, abstract = {Primary sclerosing cholangitis (PSC) is a chronic inflammatory liver disease and its frequent complication with ulcerative colitis highlights the pathogenic role of epithelial barrier dysfunction. Intestinal barrier dysfunction has been implicated in the pathogenesis of PSC, yet its underlying mechanism remains unknown. Here, we identify Klebsiella pneumonia in the microbiota of patients with PSC and demonstrate that K. pneumoniae disrupts the epithelial barrier to initiate bacterial translocation and liver inflammatory responses. Gnotobiotic mice inoculated with PSC-derived microbiota exhibited T helper 17 (TH17) cell responses in the liver and increased susceptibility to hepatobiliary injuries. Bacterial culture of mesenteric lymph nodes in these mice isolated K. pneumoniae, Proteus mirabilis and Enterococcus gallinarum, which were prevalently detected in patients with PSC. A bacterial-organoid co-culture system visualized the epithelial-damaging effect of PSC-derived K. pneumoniae that was associated with bacterial translocation and susceptibility to TH17-mediated hepatobiliary injuries. We also show that antibiotic treatment ameliorated the TH17 immune response induced by PSC-derived microbiota. These results highlight the role of pathobionts in intestinal barrier dysfunction and liver inflammation, providing insights into therapeutic strategies for PSC.}, } @article {pmid30643213, year = {2019}, author = {Ronda, C and Chen, SP and Cabral, V and Yaung, SJ and Wang, HH}, title = {Metagenomic engineering of the mammalian gut microbiome in situ.}, journal = {Nature methods}, volume = {16}, number = {2}, pages = {167-170}, pmid = {30643213}, issn = {1548-7105}, support = {DP5 OD009172/OD/NIH HHS/United States ; T32 GM007367/GM/NIGMS NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; R01 AI132403/AI/NIAID NIH HHS/United States ; F30 DK111145/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Cell Separation ; Escherichia coli/genetics ; Female ; Flow Cytometry ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/physiology ; Gene Transfer Techniques ; Genome ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Mice ; Mice, Inbred C57BL ; Microbiota/*genetics ; Plasmids/genetics ; Protein Engineering/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Engineering of microbial communities in open environments remains challenging. Here we describe a platform used to identify and modify genetically tractable mammalian microbiota by engineering community-wide horizontal gene transfer events in situ. With this approach, we demonstrate that diverse taxa in the mouse gut microbiome can be modified directly with a desired genetic payload. In situ microbiome engineering in living animals allows novel capabilities to be introduced into established communities in their native milieu.}, } @article {pmid30642268, year = {2019}, author = {Aiemjoy, K and Altan, E and Aragie, S and Fry, DM and Phan, TG and Deng, X and Chanyalew, M and Tadesse, Z and Callahan, EK and Delwart, E and Keenan, JD}, title = {Viral species richness and composition in young children with loose or watery stool in Ethiopia.}, journal = {BMC infectious diseases}, volume = {19}, number = {1}, pages = {53}, pmid = {30642268}, issn = {1471-2334}, support = {F31 HD088070/HD/NICHD NIH HHS/United States ; R01 HL105770/HL/NHLBI NIH HHS/United States ; U10 EY016214/EY/NEI NIH HHS/United States ; }, mesh = {Biodiversity ; Caliciviridae Infections/virology ; Child, Preschool ; Diarrhea/epidemiology/*virology ; Ethiopia/epidemiology ; Feces/*virology ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenomics ; Norovirus/genetics/isolation & purification ; Picornaviridae/genetics/isolation & purification ; Picornaviridae Infections/virology ; Prevalence ; Viruses/genetics/*isolation & purification ; }, abstract = {BACKGROUND: Stool consistency is an important diagnostic criterion in both research and clinical medicine and is often used to define diarrheal disease.

METHODS: We examine the pediatric enteric virome across stool consistencies to evaluate differences in richness and community composition using fecal samples collected from children aged 0 to 5 years participating in a clinical trial in the Amhara region of Ethiopia. The consistency of each sample was graded according to the modified Bristol Stool Form Scale for children (mBSFS-C) before a portion of stool was preserved for viral metagenomic analysis. Stool samples were grouped into 29 pools according to stool consistency type. Differential abundance was determined using negative-binomial modeling.

RESULTS: Of 446 censused children who were eligible to participate, 317 presented for the study visit examination and 269 provided stool samples. The median age of children with stool samples was 36 months. Species richness was highest in watery-consistency stool and decreased as stool consistency became firmer (Spearman's r = - 0.45, p = 0.013). The greatest differential abundance comparing loose or watery to formed stool was for norovirus GII (7.64, 95% CI 5.8, 9.5) followed by aichivirus A (5.93, 95% CI 4.0, 7.89) and adeno-associated virus 2 (5.81, 95%CI 3.9, 7.7).

CONCLUSIONS: In conclusion, we documented a difference in pediatric enteric viromes according to mBSFS-C stool consistency category, both in species richness and composition.}, } @article {pmid30640553, year = {2019}, author = {Ozkan, J and Willcox, MD}, title = {The Ocular Microbiome: Molecular Characterisation of a Unique and Low Microbial Environment.}, journal = {Current eye research}, volume = {44}, number = {7}, pages = {685-694}, doi = {10.1080/02713683.2019.1570526}, pmid = {30640553}, issn = {1460-2202}, mesh = {Bacteria/*isolation & purification ; Conjunctiva/*microbiology ; Eyelids/*microbiology ; Genome, Bacterial/*genetics ; Humans ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Aim: The ocular surface is continually exposed to bacteria from the environment and traditional culture-based microbiological studies have isolated a low diversity of microorganisms from this region. The use of culture-independent methods to define the ocular microbiome, primarily involving 16S ribosomal RNA gene sequencing studies, have shown that the microbial communities present on the ocular surface have a greater diversity than previously reported. Method: A review of the literature on ocular microbiome research in health and disease. Results: Molecular techniques have been used to investigate the effect of contact lens wear and disease on the microbiota of the ocular surface and eyelids and the immunoregulatory role of the ocular surface microbiota. Studies have shown that compositional changes in the microbiota occur in ocular surface disorders such as blepharitis, trachoma and dry eye and also suggest a role of the ocular and non-ocular microbiome in retinal disease including age-related macular degeneration, glaucoma, uveitis and diabetic retinopathy. However, ocular microbiome studies need to recognise the potential for contamination to impact findings and carefully control each stage of the experimental procedure and to utilise statistical methods to identify contamination signals. Conclusion: The healthy ocular surface is characterised by a relatively stable, comparatively low diversity microbiome with recent findings that the bacteria of the ocular surface appear to have a role in maintaining homeostasis by modulating immune function.}, } @article {pmid30637962, year = {2019}, author = {Asante, J and Osei Sekyere, J}, title = {Understanding antimicrobial discovery and resistance from a metagenomic and metatranscriptomic perspective: advances and applications.}, journal = {Environmental microbiology reports}, volume = {11}, number = {2}, pages = {62-86}, doi = {10.1111/1758-2229.12735}, pmid = {30637962}, issn = {1758-2229}, mesh = {Animals ; Anti-Bacterial Agents/isolation & purification/*pharmacology ; Bacteria/drug effects/genetics ; Bacterial Proteins/genetics/metabolism ; *Drug Discovery ; Drug Resistance, Bacterial/*genetics ; Environmental Microbiology ; Humans ; *Metagenomics ; Microbiota/*genetics ; }, abstract = {Our inability to cultivate most microorganisms, specifically bacteria, in the laboratory has for many years restricted our view and understanding of the bacterial meta-resistome in all living and nonliving environments. As a result, reservoirs, sources and distribution of antibiotic resistance genes (ARGS) and antibiotic-producers, as well as the effects of human activity and antibiotics on the selection and dissemination of ARGs were not well comprehended. With the advances made in the fields of metagenomics and metatranscriptomics, many of the hitherto little-understood concepts are becoming clearer. Further, the discovery of antibiotics such as lugdinin and lactocillin from the human microbiota, buttressed the importance of these new fields. Metagenomics and metatranscriptomics are becoming important clinical diagnostic tools for screening and detecting pathogens and ARGs, assessing the effects of antibiotics, other xenobiotics and human activity on the environment, characterizing the microbiome and the environmental resistome with lesser turnaround time and decreasing cost, as well as discovering antibiotic-producers. However, challenges with accurate binning, skewed ARGs databases, detection of less abundant and allelic variants of ARGs and efficient mobilome characterization remain. Ongoing efforts in long-read, phased- and single-cell sequencing, strain-resolved binning, chromosomal-conformation capture, DNA-methylation binning and deep-learning bioinformatic approaches offer promising prospects in reconstructing complete strain-level genomes and mobilomes from metagenomes.}, } @article {pmid30636326, year = {2019}, author = {Lucek, K and Gompert, Z and Nosil, P}, title = {The role of structural genomic variants in population differentiation and ecotype formation in Timema cristinae walking sticks.}, journal = {Molecular ecology}, volume = {28}, number = {6}, pages = {1224-1237}, doi = {10.1111/mec.15016}, pmid = {30636326}, issn = {1365-294X}, support = {R/129639//H2020 European Research Council/International ; P2BEP3_152103//Swiss National Science Foundation/Switzerland ; }, mesh = {Adaptation, Biological/genetics ; Animals ; *Ecotype ; Genetic Drift ; Genetics, Population ; Genome/*genetics ; Genomic Structural Variation/*genetics ; Genomics ; Metagenomics/methods ; Neoptera/*genetics ; Selection, Genetic ; }, abstract = {Theory predicts that structural genomic variants such as inversions can promote adaptive diversification and speciation. Despite increasing empirical evidence that adaptive divergence can be triggered by one or a few large inversions, the degree to which widespread genomic regions under divergent selection are associated with structural variants remains unclear. Here we test for an association between structural variants and genomic regions that underlie parallel host-plant-associated ecotype formation in Timema cristinae stick insects. Using mate-pair resequencing of 20 new whole genomes we find that moderately sized structural variants such as inversions, deletions and duplications are widespread across the genome, being retained as standing variation within and among populations. Using 160 previously published, standard-orientation whole genome sequences we find little to no evidence that the DNA sequences within inversions exhibit accentuated differentiation between ecotypes. In contrast, a formerly described large region of reduced recombination that harbours genes controlling colour-pattern exhibits evidence for accentuated differentiation between ecotypes, which is consistent with differences in the frequency of colour-pattern morphs between host-associated ecotypes. Our results suggest that some types of structural variants (e.g., large inversions) are more likely to underlie adaptive divergence than others, and that structural variants are not required for subtle yet genome-wide genetic differentiation with gene flow.}, } @article {pmid30635385, year = {2019}, author = {Fredriksen, L and Stokke, R and Jensen, MS and Westereng, B and Jameson, JK and Steen, IH and Eijsink, VGH}, title = {Discovery of a Thermostable GH10 Xylanase with Broad Substrate Specificity from the Arctic Mid-Ocean Ridge Vent System.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {6}, pages = {}, pmid = {30635385}, issn = {1098-5336}, mesh = {Arctic Regions ; Bacteria/classification/*enzymology/genetics/isolation & purification ; Bacterial Proteins/*chemistry/genetics/metabolism ; Cellulose/metabolism ; Endo-1,4-beta Xylanases/*chemistry/genetics/metabolism ; Enzyme Stability ; Geologic Sediments/microbiology ; Glucans/metabolism ; Hot Temperature ; Hydrothermal Vents/*microbiology ; Kinetics ; Oceans and Seas ; Substrate Specificity ; Xylans/metabolism ; }, abstract = {A two-domain GH10 xylanase-encoding gene (amor_gh10a) was discovered from a metagenomic data set, generated after in situ incubation of a lignocellulosic substrate in hot sediments on the sea floor of the Arctic Mid-Ocean Ridge (AMOR). AMOR_GH10A comprises a signal peptide, a carbohydrate-binding module belonging to a previously uncharacterized family, and a catalytic glycosyl hydrolase (GH10) domain. The enzyme shares the highest sequence identity (42%) with a hypothetical protein from a Verrucomicrobia bacterium, and its GH10 domain shares low identity (24 to 28%) with functionally characterized xylanases. Purified AMOR_GH10A showed thermophilic and halophilic properties and was active toward various xylans. Uniquely, the enzyme showed high activity toward amorphous cellulose, glucomannan, and xyloglucan and was more active toward cellopentaose than toward xylopentaose. Binding assays showed that the N-terminal domain of this broad-specificity GH10 binds strongly to amorphous cellulose, as well as to microcrystalline cellulose, birchwood glucuronoxylan, barley β-glucan, and konjac glucomannan, confirming its classification as a novel CBM (CBM85).IMPORTANCE Hot springs at the sea bottom harbor unique biodiversity and are a promising source of enzymes with interesting properties. We describe the functional characterization of a thermophilic and halophilic multidomain xylanase originating from the Arctic Mid-Ocean Ridge vent system, belonging to the well-studied family 10 of glycosyl hydrolases (GH10). This xylanase, AMOR_GH10A, has a surprisingly wide substrate range and is more active toward cellopentaose than toward xylopentaose. This substrate promiscuity is unique for the GH10 family and could prove useful in industrial applications. Emphasizing the versatility of AMOR_GH10A, its N-terminal domain binds to both xylans and glycans, while not showing significant sequence similarities to any known carbohydrate-binding module (CBM) in the CAZy database. Thus, this N-terminal domain lays the foundation for the new CBM85 family.}, } @article {pmid30635058, year = {2019}, author = {Simon, JC and Marchesi, JR and Mougel, C and Selosse, MA}, title = {Host-microbiota interactions: from holobiont theory to analysis.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {5}, pmid = {30635058}, issn = {2049-2618}, mesh = {Animals ; Food Microbiology ; *Host Microbial Interactions ; Humans ; *Microbiota ; Plants/microbiology ; Symbiosis ; }, abstract = {In the recent years, the holobiont concept has emerged as a theoretical and experimental framework to study the interactions between hosts and their associated microbial communities in all types of ecosystems. The spread of this concept in many branches of biology results from the fairly recent realization of the ubiquitous nature of host-associated microbes and their central role in host biology, ecology, and evolution. Through this special series "Host-microbiota interactions: from holobiont theory to analysis," we wanted to promote this field of research which has considerable implications for human health, food production, and ecosystem protection. In this preface, we highlight a collection of articles selected for this special issue that show, use, or debate the concept of holobiont to approach taxonomically and ecologically diverse organisms, from humans and plants to sponges and insects. We also identify some theoretical and methodological challenges and propose directions for future research on holobionts.}, } @article {pmid30635018, year = {2019}, author = {Akorli, J and Namaali, PA and Ametsi, GW and Egyirifa, RK and Pels, NAP}, title = {Generational conservation of composition and diversity of field-acquired midgut microbiota in Anopheles gambiae (sensu lato) during colonization in the laboratory.}, journal = {Parasites & vectors}, volume = {12}, number = {1}, pages = {27}, pmid = {30635018}, issn = {1756-3305}, support = {DEL-15-007: Awandare//DELTAS Africa/ ; }, mesh = {Animals ; Anopheles/*microbiology ; Bacteria/*classification/genetics ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Larva ; Pupa ; }, abstract = {BACKGROUND: The gut microbiota is known to play a role in a mosquito vector's life history, a subject of increasing research. Laboratory experiments are essential for such studies and require laboratory colonies. In this study, the conservation of field-obtained midgut microbiota was evaluated in laboratory-reared Anopheles gambiae (s.l.) mosquitoes continuously hatched in water from field breeding habitats.

METHODS: Pupae and late instars were obtained from the field and reared, and the emerged adults were blood-fed. The eggs obtained from them were hatched in either water from the field or in dechlorinated tap water. The mosquito colonies were maintained for 10 generations. Midguts of female adults from unfed F0 (emerging from field-caught pupae and larvae), F5 and F10 were dissected out and genomic DNA was extracted for 16S metagenomic sequencing. The sequences were compared to investigate the diversity and bacterial compositional differences using ANCOM and correlation clustering methods.

RESULTS: Less than 10% of the bacterial families identified had differential relative abundances between generational groups and accounted for 46% of the variation observed. Although diversity reduced in F10 mosquitoes during laboratory colonization (Shannon-Weaver; P-value < 0.05), 50% of bacterial genera were conserved in those bred continuously in field-water compared to 38% in those bred in dechlorinated tap water.

CONCLUSIONS: To our knowledge, this study is the first report on the assessment of gut bacterial community of mosquitoes during laboratory colonization and recommends the use of water from the natural breeding habitats if they are intended for microbiota research.}, } @article {pmid30632609, year = {2019}, author = {Hamada, T and Nowak, JA and Milner, DA and Song, M and Ogino, S}, title = {Integration of microbiology, molecular pathology, and epidemiology: a new paradigm to explore the pathogenesis of microbiome-driven neoplasms.}, journal = {The Journal of pathology}, volume = {247}, number = {5}, pages = {615-628}, pmid = {30632609}, issn = {1096-9896}, support = {R35 CA197735/CA/NCI NIH HHS/United States ; K99 CA215314/CA/NCI NIH HHS/United States ; R00 CA215314/CA/NCI NIH HHS/United States ; }, mesh = {Carcinogenesis/pathology ; Forecasting ; Humans ; Microbiota/*physiology ; Neoplasms/epidemiology/*microbiology/therapy ; Precision Medicine/methods ; }, abstract = {Molecular pathological epidemiology (MPE) is an integrative transdisciplinary field that addresses heterogeneous effects of exogenous and endogenous factors (collectively termed 'exposures'), including microorganisms, on disease occurrence and consequences, utilising molecular pathological signatures of the disease. In parallel with the paradigm of precision medicine, findings from MPE research can provide aetiological insights into tailored strategies of disease prevention and treatment. Due to the availability of molecular pathological tests on tumours, the MPE approach has been utilised predominantly in research on cancers including breast, lung, prostate, and colorectal carcinomas. Mounting evidence indicates that the microbiome (inclusive of viruses, bacteria, fungi, and parasites) plays an important role in a variety of human diseases including neoplasms. An alteration of the microbiome may be not only a cause of neoplasia but also an informative biomarker that indicates or mediates the association of an epidemiological exposure with health conditions and outcomes. To adequately educate and train investigators in this emerging area, we herein propose the integration of microbiology into the MPE model (termed 'microbiology-MPE'), which could improve our understanding of the complex interactions of environment, tumour cells, the immune system, and microbes in the tumour microenvironment during the carcinogenic process. Using this approach, we can examine how lifestyle factors, dietary patterns, medications, environmental exposures, and germline genetics influence cancer development and progression through impacting the microbial communities in the human body. Further integration of other disciplines (e.g. pharmacology, immunology, nutrition) into microbiology-MPE would expand this developing research frontier. With the advent of high-throughput next-generation sequencing technologies, researchers now have increasing access to large-scale metagenomics as well as other omics data (e.g. genomics, epigenomics, proteomics, and metabolomics) in population-based research. The integrative field of microbiology-MPE will open new opportunities for personalised medicine and public health. Copyright © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.}, } @article {pmid30630933, year = {2019}, author = {Jiang, X and Hall, AB and Arthur, TD and Plichta, DR and Covington, CT and Poyet, M and Crothers, J and Moses, PL and Tolonen, AC and Vlamakis, H and Alm, EJ and Xavier, RJ}, title = {Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut.}, journal = {Science (New York, N.Y.)}, volume = {363}, number = {6423}, pages = {181-187}, pmid = {30630933}, issn = {1095-9203}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AT009708/AT/NCCIH NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/*genetics ; DNA, Bacterial/genetics ; DNA, Intergenic/*genetics ; Drug Resistance, Bacterial/*genetics ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; *Promoter Regions, Genetic ; }, abstract = {Phase variation, the reversible alternation between genetic states, enables infection by pathogens and colonization by commensals. However, the diversity of phase variation remains underexplored. We developed the PhaseFinder algorithm to quantify DNA inversion-mediated phase variation. A systematic search of 54,875 bacterial genomes identified 4686 intergenic invertible DNA regions (invertons), revealing an enrichment in host-associated bacteria. Invertons containing promoters often regulate extracellular products, underscoring the importance of surface diversity for gut colonization. We found invertons containing promoters regulating antibiotic resistance genes that shift to the ON orientation after antibiotic treatment in human metagenomic data and in vitro, thereby mitigating the cost of antibiotic resistance. We observed that the orientations of some invertons diverge after fecal microbiota transplant, potentially as a result of individual-specific selective forces.}, } @article {pmid30628657, year = {2019}, author = {Chen, L and Li, H and Li, J and Chen, Y and Yang, Y}, title = {Lactobacillus rhamnosus GG treatment improves intestinal permeability and modulates microbiota dysbiosis in an experimental model of sepsis.}, journal = {International journal of molecular medicine}, volume = {43}, number = {3}, pages = {1139-1148}, pmid = {30628657}, issn = {1791-244X}, mesh = {Animals ; Apoptosis ; Biomarkers ; Cell Proliferation ; Colon/metabolism/microbiology/pathology ; Disease Models, Animal ; *Dysbiosis ; *Gastrointestinal Microbiome ; Lacticaseibacillus rhamnosus/*physiology ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Mortality ; Permeability ; Phylogeny ; Probiotics/*administration & dosage ; RNA, Ribosomal, 16S/genetics ; Sepsis/diagnosis/*metabolism/*microbiology/therapy ; }, abstract = {Decrease of 'health‑benefiting' microbes and increase of pathogenic bacteria (a condition termed dysbiosis) in intensive care unit patients is considered to induce or aggravate sepsis (gut‑origin sepsis). Orally administered probiotics have been effective in the prevention of nosocomial infections. However, the mechanisms of probiotic‑induced anti‑infection and anti‑sepsis remain to be explored. In the present study, 4‑week‑old C57BL6 mice were orally administrated with Lactobacillus rhamnosus GG (LGG) or normal saline (control) 4 weeks prior to cecal ligation and puncture (CLP). A subset of the mice were sacrificed at 24 h post‑CLP, and the others were used for survival studies. Ileum tissues, blood and fecal samples were collected. The survival rate of septic mice pretreated with LGG was significantly improved compared with untreated mice. The levels of inflammatory cytokines were reduced in LGG‑pretreated septic mice. A decrease of colonic proliferation and epithelial tight junctions and an increase of colonic apoptosis were observed in control septic CLP+saline mice. LGG pretreatment reversed the colonic proliferation, apoptosis and expression of tight junction proteins to the levels of the sham group. LGG pretreatment improved the richness and diversity of intestinal microbiota in septic mice. The principal coordinates analysis clustering plots revealed a significant separate clustering in microbiota structure between three groups. Bacteria associated with energy consumption, including Bacteroidetes, with opportunistic infection, including Proteobacteria, Staphylococcaceae and Enterococcaceae, lipopolysaccharide producers, including Enterobacteriaceae, and facultative anaerobes, such as Bacteroidaceae and Erysipelotrichaceae, increased in septic mice. By contrast, bacteria associated with energy harvest, including Firmicutes, intestinal barrier function regulators, including Akkermansia, hepatic function regulators, including Coprococcus and Oscillospira, and obligate anaerobes, including Prevotellaceae, decreased in septic mice. With LGG pretreatment, the sepsis‑induced microbiota dysbiosis was reversed. The present results elucidated the potential mechanism of LGG treatment in sepsis, by improving intestinal permeability and modulating microbiota dysbiosis.}, } @article {pmid30626904, year = {2019}, author = {Delgado, B and Bach, A and Guasch, I and González, C and Elcoso, G and Pryce, JE and Gonzalez-Recio, O}, title = {Whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11}, pmid = {30626904}, issn = {2045-2322}, mesh = {*Animal Feed ; Animals ; Cattle ; Euryarchaeota/growth & development ; Firmicutes/growth & development ; *Gastrointestinal Microbiome/genetics/physiology ; Metagenome ; Methanobrevibacter/growth & development ; Prevotella/growth & development ; Rumen/*microbiology ; }, abstract = {The current research was carried out to determine the associations between the rumen microbiota and traits related with feed efficiency in a Holstein cattle population (n = 30) using whole metagenome sequencing. Improving feed efficiency (FE) is important for a more sustainable livestock production. The variability for the efficiency of feed utilization in ruminants is partially controlled by the gastrointestinal microbiota. Modulating the microbiota composition can promote a more sustainable and efficient livestock. This study revealed that most efficient cows had larger relative abundance of Bacteroidetes (P = 0.041) and Prevotella (P = 0.003), while lower, but non-significant (P = 0.119), relative abundance of Firmicutes. Methanobacteria (P = 0.004) and Methanobrevibacter (P = 0.003) were also less abundant in the high-efficiency cows. A de novo metagenome assembly was carried out using de Bruijn graphs in MEGAHIT resulting in 496,375 contigs. An agnostic pre-selection of microbial contigs allowed high classification accuracy for FE and intake levels using hierarchical classification. These microbial contigs were also able to predict FE and intake levels with accuracy of 0.19 and 0.39, respectively, in an independent population (n = 31). Nonetheless, a larger potential accuracy up to 0.69 was foreseen in this study for datasets that allowed a larger statistical power. Enrichment analyses showed that genes within these contigs were mainly involved in fatty acids and cellulose degradation pathways. The findings indicated that there are differences between the microbiota compositions of high and low-efficiency animals both at the taxonomical and gene levels. These differences are even more evident in terms of intake levels. Some of these differences remain even between populations under different diets and environments, and can provide information on the feed utilization performance without information on the individual intake level.}, } @article {pmid30625669, year = {2019}, author = {Costeira, R and Doherty, R and Allen, CCR and Larkin, MJ and Kulakov, LA}, title = {Analysis of viral and bacterial communities in groundwater associated with contaminated land.}, journal = {The Science of the total environment}, volume = {656}, number = {}, pages = {1413-1426}, doi = {10.1016/j.scitotenv.2018.11.429}, pmid = {30625669}, issn = {1879-1026}, mesh = {Bacteria/classification/*genetics ; Groundwater/*microbiology/virology ; *Metagenome ; *Microbiota ; Northern Ireland ; Soil Pollutants/*analysis ; Viruses/classification/*genetics ; }, abstract = {This work aimed at the comprehensive analysis of total microbial communities inhabiting a typical hydrocarbon-polluted site, where chemical characteristics of the groundwater were readily available. To achieve this, a joint metagenomic characterization of bacteria and viruses surrounding a contaminant plume was performed over a one-year period. The results presented demonstrated that both potential hydrocarbon degraders and their bacteriophages were dominant around the plume, and that the viral and bacterial diversities found at the site were probably influenced by the pH of the groundwater. Niche-specific and dispersed associations between phages and bacteria were identified. The niche phage-host associations were found at the edge of the site and at the core of the plume where pH was the highest (9.52). The identified host populations included several classes of bacteria (e.g. Clostridia and Proteobacteria). Thirty-six viral generalists were also discovered, with BGW-G9 having the broadest host range across 23 taxa, including Pseudomonas, Polycyclovorans, Methylocaldum and Candidatus Magnetobacterium species. The phages with broad host ranges are presumed to have significant effects on prokaryotic production and horizontal gene transfer, and therefore impact the biodegradation processes conducted by various bacteria of the environment studied. This study for the first time characterized the phages and their bacterial hosts associated with a contaminant plume.}, } @article {pmid30624643, year = {2019}, author = {Baldrian, P}, title = {The known and the unknown in soil microbial ecology.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {2}, pages = {}, doi = {10.1093/femsec/fiz005}, pmid = {30624643}, issn = {1574-6941}, mesh = {Bacteria/*classification/enzymology/genetics ; Ecology ; Ecosystem ; Fungi/*classification/enzymology/genetics ; Metabolomics ; Metagenomics ; Microbiota/*genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The methodical developments in the fields of molecular biology and analytical chemistry significantly increased the level of detail that we achieve when exploring soils and their microbial inhabitants. High-resolution description of microbial communities, detection of taxa with minor abundances, screening of gene expression or the detailed characterization of metabolomes are nowadays technically feasible. Despite all of this, our understanding of soil is limited in many ways. The imperfect tools to describe microbial communities and limited possibilities to assign traits to community members make it difficult to link microbes to functions. Also the analysis of processes exemplified by enzyme activity measurements is still imperfect. In the future, it is important to look at soil at a finer detail to obtain a better picture on the properties of individual microbes, their in situ interactions, metabolic rates and activity at a scale relevant to individual microbes. Scaling up is needed as well to get answers at ecosystem or biome levels and to enable global modelling. The recent development of novel tools including metabolomics, identification of genomes in metagenomics sequencing datasets or collection of trait data have the potential to bring soil ecology further. It will, however, always remain a highly demanding scientific discipline.}, } @article {pmid30624596, year = {2019}, author = {Yadav, D and Dutta, A and Mande, SS}, title = {OTUX: V-region specific OTU database for improved 16S rRNA OTU picking and efficient cross-study taxonomic comparison of microbiomes.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {26}, number = {2}, pages = {147-156}, pmid = {30624596}, issn = {1756-1663}, mesh = {Bacteria/*classification/genetics ; Computational Biology/*methods ; *Databases, Genetic ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; Microbiota/*genetics ; RNA, Bacterial ; *RNA, Ribosomal, 16S ; Sequence Analysis, DNA/methods ; }, abstract = {Many microbiome studies employ reference-based operational taxonomic unit (OTU)-picking methods, which in general, rely on databases cataloguing reference OTUs identified through clustering full-length 16S rRNA genes. Given that the rate of accumulation of mutations are not uniform throughout the length of a 16S rRNA gene across different taxonomic clades, results of OTU identification or taxonomic classification obtained using 'short-read' sequence queries (as generated by next-generation sequencing platforms) can be inconsistent and of suboptimal accuracy. De novo OTU clustering results too can significantly vary depending upon the hypervariable region (V-region) targeted for sequencing. As a consequence, comparison of microbiomes profiled in different scientific studies becomes difficult and often poses a challenge in analysing new findings in context of prior knowledge. The OTUX approach of reference-based OTU-picking proposes to overcome these limitations by using 'customized' OTU reference databases, which can cater to different sets of short-read sequences corresponding to different 16S V-regions. The results obtained with OTUX-approach (which are in terms of OTUX-OTU identifiers) can also be 'mapped back' or represented in terms of other OTU database identifiers/taxonomy, e.g. Greengenes, thus allowing for easy cross-study comparisons. Validation with simulated datasets indicates more efficient, accurate, and consistent taxonomic classifications obtained using OTUX-approach, as compared with conventional methods.}, } @article {pmid30623484, year = {2019}, author = {Zhai, J and Knox, K and Twigg, HL and Zhou, H and Zhou, JJ}, title = {Exact variance component tests for longitudinal microbiome studies.}, journal = {Genetic epidemiology}, volume = {43}, number = {3}, pages = {250-262}, pmid = {30623484}, issn = {1098-2272}, support = {R01 GM105785/GM/NIGMS NIH HHS/United States ; P30 ES006694/ES/NIEHS NIH HHS/United States ; R01 HG006139/HG/NHGRI NIH HHS/United States ; U01 HL098960/HL/NHLBI NIH HHS/United States ; HG006139/HG/NHGRI NIH HHS/United States ; K01DK106116/DK/NIDDK NIH HHS/United States ; GM053275/GM/NIGMS NIH HHS/United States ; GM105785/GM/NIGMS NIH HHS/United States ; K01 DK106116/DK/NIDDK NIH HHS/United States ; R01 GM053275/GM/NIGMS NIH HHS/United States ; U01 HL121831/HL/NHLBI NIH HHS/United States ; }, mesh = {Computer Simulation ; Humans ; Longitudinal Studies ; Lung/microbiology ; *Microbiota ; *Models, Genetic ; }, abstract = {In metagenomic studies, testing the association between microbiome composition and clinical outcomes translates to testing the nullity of variance components. Motivated by a lung human immunodeficiency virus (HIV) microbiome project, we study longitudinal microbiome data by using variance component models with more than two variance components. Current testing strategies only apply to models with exactly two variance components and when sample sizes are large. Therefore, they are not applicable to longitudinal microbiome studies. In this paper, we propose exact tests (score test, likelihood ratio test, and restricted likelihood ratio test) to (a) test the association of the overall microbiome composition in a longitudinal design and (b) detect the association of one specific microbiome cluster while adjusting for the effects from related clusters. Our approach combines the exact tests for null hypothesis with a single variance component with a strategy of reducing multiple variance components to a single one. Simulation studies demonstrate that our method has a correct type I error rate and superior power compared to existing methods at small sample sizes and weak signals. Finally, we apply our method to a longitudinal pulmonary microbiome study of HIV-infected patients and reveal two interesting genera Prevotella and Veillonella associated with forced vital capacity. Our findings shed light on the impact of the lung microbiome on HIV complexities. The method is implemented in the open-source, high-performance computing language Julia and is freely available at https://github.com/JingZhai63/VCmicrobiome.}, } @article {pmid30623233, year = {2019}, author = {Kim, JY and Kim, EM and Yi, MH and Lee, J and Lee, S and Hwang, Y and Yong, D and Sohn, WM and Yong, TS}, title = {Chinese liver fluke Clonorchis sinensis infection changes the gut microbiome and increases probiotic Lactobacillus in mice.}, journal = {Parasitology research}, volume = {118}, number = {2}, pages = {693-699}, pmid = {30623233}, issn = {1432-1955}, support = {NRF-2016R1A2B4016194//National Research Foundation of Korea/ ; 2011-0012166//National Research Foundation of Korea/ ; }, mesh = {Animals ; Clonorchiasis/*immunology/parasitology ; Clonorchis sinensis/growth & development/*immunology ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; High-Throughput Nucleotide Sequencing ; Lactobacillus/classification/cytology/*growth & development ; Metacercariae/cytology ; Mice ; Mice, Inbred C57BL ; Probiotics/*analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Chinese liver fluke Clonorchis sinensis changes the host's immune system. Recently, it has been reported that helminths including C. sinensis can ameliorate immune-related diseases such as allergy. In addition, recent studies showed that helminth infection can alleviate immune-mediated disorders by altering the gut microbiome. However, changes in the gut microbiome due to C. sinensis have not been reported yet. In this study, changes in the gut microbiome of C57BL/6 mice infected with C. sinensis metacercariae were evaluated over time. Stool was analyzed by 16S rRNA amplicon analysis using high-throughput sequencing technology. There was no apparent difference in species richness and diversity between the infected and control groups. However, the composition of the microbiome was different between the infected and control groups at 20 days and 30 days post-infection, and the difference disappeared at 50 days post-infection. In particular, this microbiome alteration was associated with a change in the relative abundance of genus Lactobacillus and the probiotic Lactobacillus species that are known to have an immune-modulation role in immune-mediated diseases.}, } @article {pmid30623212, year = {2019}, author = {de Sousa, AGG and Tomasino, MP and Duarte, P and Fernández-Méndez, M and Assmy, P and Ribeiro, H and Surkont, J and Leite, RB and Pereira-Leal, JB and Torgo, L and Magalhães, C}, title = {Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {388-408}, pmid = {30623212}, issn = {1432-184X}, support = {244646//Research Council of Norway/ ; NORTE-01-0145-FEDER-000031//Structured Program of R&D&I MarInfo/ ; Arktis 2030//Norwegian Ministries of Foreign Affairs and Climate and Environment/ ; NITROLIMIT - PTDC 2017 - PTDC/CTA-AMB/30997/2017//Funda??o para a Ci?ncia e a Tecnologia/ ; }, mesh = {Arctic Regions ; Bacteria/classification/genetics/*isolation & purification ; *Biodiversity ; Eukaryota/classification/genetics/*isolation & purification ; Ice Cover/chemistry/*microbiology/*parasitology ; Phylogeny ; Seasons ; Seawater/chemistry/microbiology/parasitology ; Svalbard ; }, abstract = {One of the most prominent manifestations of climate change is the changing Arctic sea-ice regime with a reduction in the summer sea-ice extent and a shift from thicker, perennial multiyear ice towards thinner, first-year ice. These changes in the physical environment are likely to impact microbial communities, a key component of Arctic marine food webs and biogeochemical cycles. During the Norwegian young sea ICE expedition (N-ICE2015) north of Svalbard, seawater samples were collected at the surface (5 m), subsurface (20 or 50 m), and mesopelagic (250 m) depths on 9 March, 27 April, and 16 June 2015. In addition, several physical and biogeochemical data were recorded to contextualize the collected microbial communities. Through the massively parallel sequencing of the small subunit ribosomal RNA amplicon and metagenomic data, this work allows studying the Arctic's microbial community structure during the late winter to early summer transition. Results showed that, at compositional level, Alpha- (30.7%) and Gammaproteobacteria (28.6%) are the most frequent taxa across the prokaryotic N-ICE2015 collection, and also the most phylogenetically diverse. Winter to early summer trends were quite evident since there was a high relative abundance of thaumarchaeotes in the under-ice water column in late winter while this group was nearly absent during early summer. Moreover, the emergence of Flavobacteria and the SAR92 clade in early summer might be associated with the degradation of a spring bloom of Phaeocystis. High relative abundance of hydrocarbonoclastic bacteria, particularly Alcanivorax (54.3%) and Marinobacter (6.3%), was also found. Richness showed different patterns along the depth gradient for prokaryotic (highest at mesopelagic depth) and protistan communities (higher at subsurface depths). The microbial N-ICE2015 collection analyzed in the present study provides comprehensive new knowledge about the pelagic microbiota below drifting Arctic sea-ice. The higher microbial diversity found in late winter/early spring communities reinforces the need to continue with further studies to properly characterize the winter microbial communities under the pack-ice.}, } @article {pmid30622080, year = {2019}, author = {Cota-Ruiz, K and López de Los Santos, Y and Hernández-Viezcas, JA and Delgado-Rios, M and Peralta-Videa, JR and Gardea-Torresdey, JL}, title = {A comparative metagenomic and spectroscopic analysis of soils from an international point of entry between the US and Mexico.}, journal = {Environment international}, volume = {123}, number = {}, pages = {558-566}, doi = {10.1016/j.envint.2018.12.055}, pmid = {30622080}, issn = {1873-6750}, support = {G12 MD007592/MD/NIMHD NIH HHS/United States ; }, mesh = {Agriculture ; Bacteria/classification ; Environmental Pollution ; Hydrocarbons/toxicity ; Metagenomics ; Metals, Heavy/toxicity ; Mexico ; *Microbiota ; Nitrogen/analysis ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants/*toxicity ; Spectrum Analysis ; }, abstract = {The Paso del Norte region is characterized by its dynamic industries and active agriculture. Throughout the years, urban and agricultural soils from this region have been exposed to xenobiotics, heavy metals, and excess of hydrocarbons. In this study, samples of urban [domestic workshops (DW)] and agricultural-intended (AI) soils from different sites of Ciudad Juárez, Mexico were evaluated for their fertility, element content, and microbial diversity. Chemical analyses showed that nitrites, nitrates, P, K, Mg, and Mn were predominantly higher in AI soils, compared to DW soils (p ≤ 0.05). The composition of soil microbial communities showed that Proteobacteria phylum was the most abundant in both soils (67%, p ≤ 0.05). In AI soils, Paracoccus denitrificans was reduced (p ≤ 0.05), concurring with an increment in nitrates, while the content of nitrogen was negatively correlated with the rhizobium group (r[2] = -0.65, p ≤ 0.05). In DW soils, the Firmicutes phylum represented up to ~25%, and the relative abundance of Proteobacteria strongly correlated with a higher Cu content (r[2] = 0.99, p ≤ 0.0001). The monotypic genus Sulfuricurvum was found only in oil-contaminated soil samples. Finally, all samples showed the presence of the recently created phylum Candidatus saccharibacteria. These results describe the productivity parameters of AI soils and its correlation to the microbial diversity, which are very important to understand and potentiate the productivity of soils. The data also suggest that soils impacted with hydrocarbons and metal(oid)s allow the reproduction of microorganisms with the potential to alleviate contaminated sites.}, } @article {pmid30621868, year = {2019}, author = {Ottesen, A and Ramachandran, P and Reed, E and Gu, G and Gorham, S and Ducharme, D and Newell, M and Rideout, S and Turini, T and Hill, T and Strain, E and Brown, E}, title = {Metagenome tracking biogeographic agroecology: Phytobiota of tomatoes from Virginia, Maryland, North Carolina and California.}, journal = {Food microbiology}, volume = {79}, number = {}, pages = {132-136}, doi = {10.1016/j.fm.2018.12.001}, pmid = {30621868}, issn = {1095-9998}, mesh = {Bacteria/classification/genetics/*isolation & purification ; California ; *Food Microbiology ; Food Safety ; Solanum lycopersicum/*microbiology ; Maryland ; Metagenomics ; Microbiota/*genetics ; North Carolina ; RNA, Ribosomal, 16S/genetics ; Salmonella/classification/genetics/isolation & purification ; Virginia ; }, abstract = {Describing baseline microbiota associated with agricultural commodities in the field is an important step towards improving our understanding of a wide range of important objectives from plant pathology and horticultural sustainability, to food safety. Environmental pressures on plants (wind, dust, drought, water, temperature) vary by geography and characterizing the impact of these variable pressures on phyllosphere microbiota will contribute to improved stewardship of fresh produce for both plant and human health. A higher resolution understanding of the incidence of human pathogens on food plants and co-occurring phytobiota using metagenomic approaches (metagenome tracking) may contribute to improved source attribution and risk assessment in cases where human pathogens become introduced to agro-ecologies. Between 1990 and 2007, as many as 1990 culture-confirmed Salmonella illnesses were linked to tomatoes from as many as 12 multistate outbreaks (Bell et al., 2012; Bell et al., 2015; Bennett et al., 2014; CDC, 2004; CDC, 2007; Greene et al., 2005a; Gruszynski et al., 2014). When possible, source attribution for these incidents revealed a biogeographic trend, most events were associated with eastern growing regions. To improve our understanding of potential biogeographically linked trends in contamination of tomatoes by Salmonella, we profiled microbiota from the surfaces of tomatoes from Virginia, Maryland, North Carolina and California. Bacterial profiles from California tomatoes were completely different than those of Maryland, Virginia and North Carolina (which were highly similar to each other). A statistically significant enrichment of Firmicutes taxa was observed in California phytobiota compared to the three eastern states. Rhizobiaceae, Sphingobacteriaceae and Xanthobacteraceae were the most abundant bacterial families associated with tomatoes grown in eastern states. These baseline metagenomic profiles of phyllosphere microbiota may contribute to improved understanding of how certain ecologies provide supportive resources for human pathogens on plants and how components of certain agro-ecologies may play a role in the introduction of human pathogens to plants.}, } @article {pmid30621867, year = {2019}, author = {Marino, M and Dubsky de Wittenau, G and Saccà, E and Cattonaro, F and Spadotto, A and Innocente, N and Radovic, S and Piasentier, E and Marroni, F}, title = {Metagenomic profiles of different types of Italian high-moisture Mozzarella cheese.}, journal = {Food microbiology}, volume = {79}, number = {}, pages = {123-131}, doi = {10.1016/j.fm.2018.12.007}, pmid = {30621867}, issn = {1095-9998}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; Buffaloes ; Cattle ; Cheese/analysis/*microbiology ; Cluster Analysis ; DNA, Bacterial/genetics ; *Food Microbiology ; Metagenomics ; Microbiota/*genetics ; Milk/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The microbiota of different types of Italian high-moisture Mozzarella cheese produced using cow or buffalo milk, acidified with natural or selected cultures, and sampled at the dairy or at the mass market, was evaluated using a Next Generation Sequencing approach, in order to identify possible drivers of the bacterial diversity. Cow Mozzarella and buffalo Mozzarella acidified with commercial cultures were dominated by Streptococcus thermophilus, while buffalo samples acidified with natural whey cultures showed similar prevalence of L. delbrueckii subsp. bulgaricus, L. helveticus and S. thermophilus. Moreover, several species of non-starter lactic acid bacteria were frequently detected. The diversity in cow Mozzarella microbiota was much higher than that of water buffalo samples. Cluster analysis clearly separated cow's cheeses from buffalo's ones, the former having a higher prevalence of psychrophilic taxa, and the latter of Lactobacillus and Streptococcus. A higher prevalence of psychrophilic species and potential spoilers was observed in samples collected at the mass retail, suggesting that longer exposures to cooling temperatures and longer production-to-consumption times could significantly affect microbiota diversity. Our results could help in detecting some kind of thermal abuse during the production or storage of mozzarella cheese.}, } @article {pmid30621760, year = {2018}, author = {Gerner, SM and Rattei, T and Graf, AB}, title = {Assessment of urban microbiome assemblies with the help of targeted in silico gold standards.}, journal = {Biology direct}, volume = {13}, number = {1}, pages = {22}, pmid = {30621760}, issn = {1745-6150}, mesh = {Bacteria/*genetics ; Cities ; Computer Simulation ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Microbiota ; Software ; }, abstract = {BACKGROUND: Microbial communities play a crucial role in our environment and may influence human health tremendously. Despite being the place where human interaction is most abundant we still know little about the urban microbiome. This is highlighted by the large amount of unclassified DNA reads found in urban metagenome samples. The only in silico approach that allows us to find unknown species, is the assembly and classification of draft genomes from a metagenomic dataset. In this study we (1) investigate the applicability of an assembly and binning approach for urban metagenome datasets, and (2) develop a new method for the generation of in silico gold standards to better understand the specific challenges of such datasets and provide a guide in the selection of available software.

RESULTS: We applied combinations of three assembly (Megahit, SPAdes and MetaSPAdes) and three binning tools (MaxBin, MetaBAT and CONCOCT) to whole genome shotgun datasets from the CAMDA 2017 Challenge. Complex in silico gold standards with a simulated bacterial fraction were generated for representative samples of each surface type and city. Using these gold standards, we found the combination of SPAdes and MetaBAT to be optimal for urban metagenome datasets by providing the best trade-off between the number of high-quality genome draft bins (MIMAG standards) retrieved, the least amount of misassemblies and contamination. The assembled draft genomes included known species like Propionibacterium acnes but also novel species according to respective ANI values.

CONCLUSIONS: In our work, we showed that, even for datasets with high diversity and low sequencing depth from urban environments, assembly and binning-based methods can provide high-quality genome drafts. Of vital importance to retrieve high-quality genome drafts is sequence depth but even more so a high proportion of the bacterial sequence fraction too achieve high coverage for bacterial genomes. In contrast to read-based methods relying on database knowledge, genome-centric methods as applied in this study can provide valuable information about unknown species and strains as well as functional contributions of single community members within a sample. Furthermore, we present a method for the generation of sample-specific highly complex in silico gold standards.

REVIEWERS: This article was reviewed by Craig Herbold, Serghei Mangul and Yana Bromberg.}, } @article {pmid30621600, year = {2019}, author = {Imhann, F and Van der Velde, KJ and Barbieri, R and Alberts, R and Voskuil, MD and Vich Vila, A and Collij, V and Spekhorst, LM and Van der Sloot, KWJ and Peters, V and Van Dullemen, HM and Visschedijk, MC and Festen, EAM and Swertz, MA and Dijkstra, G and Weersma, RK}, title = {The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1.}, journal = {BMC gastroenterology}, volume = {19}, number = {1}, pages = {5}, pmid = {30621600}, issn = {1471-230X}, support = {016.136.308//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 92.003.577//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; MLDS D16-14//Maag Lever Darm Stichting/ ; CD14-04//Maag Lever Darm Stichting (NL)/ ; }, mesh = {Adolescent ; Adult ; Aged ; Biomarkers ; Biopsy ; Diet ; Environment ; Female ; Gastrointestinal Microbiome ; Genotype ; Humans ; Inflammatory Bowel Diseases/*classification/drug therapy/*genetics/pathology ; Male ; Middle Aged ; Netherlands ; Phenotype ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Transcriptome ; Exome Sequencing ; Young Adult ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic complex disease of the gastrointestinal tract. Patients with IBD can experience a wide range of symptoms, but the pathophysiological mechanisms that cause these individual differences in clinical presentation remain largely unknown. In consequence, IBD is currently classified into subtypes using clinical characteristics. If we are to develop a more targeted treatment approach, molecular subtypes of IBD need to be discovered that can be used as new drug targets. To achieve this, we need multiple layers of molecular data generated from the same IBD patients.

CONSTRUCTION AND CONTENT: We initiated the 1000IBD project (https://1000ibd.org) to prospectively follow more than 1000 IBD patients from the Northern provinces of the Netherlands. For these patients, we have collected a uniquely large number of phenotypes and generated multi-omics profiles. To date, 1215 participants have been enrolled in the project and enrolment is on-going. Phenotype data collected for these participants includes information on dietary and environmental factors, drug responses and adverse drug events. Genome information has been generated using genotyping (ImmunoChip, Global Screening Array and HumanExomeChip) and sequencing (whole exome sequencing and targeted resequencing of IBD susceptibility loci), transcriptome information generated using RNA-sequencing of intestinal biopsies and microbiome information generated using both sequencing of the 16S rRNA gene and whole genome shotgun metagenomic sequencing.

UTILITY AND DISCUSSION: All molecular data generated within the 1000IBD project will be shared on the European Genome-Phenome Archive (https://ega-archive.org , accession no: EGAS00001002702). The first data release, detailed in this announcement and released simultaneously with this publication, will contain basic phenotypes for 1215 participants, genotypes of 314 participants and gut microbiome data from stool samples (315 participants) and biopsies (107 participants) generated by tag sequencing the 16S gene. Future releases will comprise many more additional phenotypes and -omics data layers. 1000IBD data can be used by other researchers as a replication cohort, a dataset to test new software tools, or a dataset for applying new statistical models.

CONCLUSIONS: We report on the establishment and future development of the 1000IBD project: the first comprehensive multi-omics dataset aimed at discovering IBD biomarker profiles and treatment targets.}, } @article {pmid30619779, year = {2018}, author = {Hu, YL and Pang, W and Huang, Y and Zhang, Y and Zhang, CJ}, title = {The Gastric Microbiome Is Perturbed in Advanced Gastric Adenocarcinoma Identified Through Shotgun Metagenomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {433}, pmid = {30619779}, issn = {2235-2988}, mesh = {Adenocarcinoma/*complications/pathology ; Aged ; Bacteria/*classification/*genetics ; China ; Dysbiosis/*complications ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Middle Aged ; Stomach Neoplasms/*complications/pathology ; }, abstract = {Objective: Dysbiosis of gastric microbiota such as Helicobacter pylori plays a significant role in pathogenesis and progression of gastric cancer. Our aim was to evaluate the composition and functional effects of gastric microbiota in superficial gastritis (SG) and advanced gastric adenocarcinoma (GC). Methods: We carried out shotgun metagenomic sequencing on gastric wash samples from 6 patients with GC and 5 patients with SG. The taxonomic composition was profiled using MetaPhlAn2 and functional gene pathway was profiled using HUMAnN2. Differences in microbial composition and pathways between the two patient groups were assessed via LEfSe. Results: The gastric microbiota in GC patients was characterized by reduced species richness, enrichment of 13 bacterial taxa and depletion of 31 taxa (q < 0.05). The most representative taxa which were abundant in GC corresponded to the commensals or opportunistic pathogens that usually colonize the oral cavity, including genera Neisseria, Alloprevotella, and Aggregatibacter, species Streptococcus_mitis_oralis_pneumoniae and strain Porphyromonas_endodontalis.t_GCF_000174815. Each of the three GC-associated genera could separate GC from SG completely. In particular, Sphingobium yanoikuyae, a bacterium capable of degrading carcinogenic compounds, was depleted in GC. Functionally, pathways associated with the biosynthesis of lipopolysaccharide (LPS) and L-arginine were enriched in GC, whereas pathways involved in the fermentation of short chain fatty acids (SCFAs) and branched amino acid metabolism were more abundant in SG. Conclusions: Our results present new alterations in the gastric microbiome in patients with GC from a whole-genome perspective, suggesting that microbiome composition and function can be used for prognosis and diagnosis of GC.}, } @article {pmid30619130, year = {2018}, author = {Timmers, PHA and Vavourakis, CD and Kleerebezem, R and Damsté, JSS and Muyzer, G and Stams, AJM and Sorokin, DY and Plugge, CM}, title = {Metabolism and Occurrence of Methanogenic and Sulfate-Reducing Syntrophic Acetate Oxidizing Communities in Haloalkaline Environments.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3039}, pmid = {30619130}, issn = {1664-302X}, support = {322551/ERC_/European Research Council/International ; 323009/ERC_/European Research Council/International ; }, abstract = {Anaerobic syntrophic acetate oxidation (SAO) is a thermodynamically unfavorable process involving a syntrophic acetate oxidizing bacterium (SAOB) that forms interspecies electron carriers (IECs). These IECs are consumed by syntrophic partners, typically hydrogenotrophic methanogenic archaea or sulfate reducing bacteria. In this work, the metabolism and occurrence of SAOB at extremely haloalkaline conditions were investigated, using highly enriched methanogenic (M-SAO) and sulfate-reducing (S-SAO) cultures from south-western Siberian hypersaline soda lakes. Activity tests with the M-SAO and S-SAO cultures and thermodynamic calculations indicated that H2 and formate are important IECs in both SAO cultures. Metagenomic analysis of the M-SAO cultures showed that the dominant SAOB was 'Candidatus Syntrophonatronum acetioxidans,' and a near-complete draft genome of this SAOB was reconstructed. 'Ca. S. acetioxidans' has all genes necessary for operating the Wood-Ljungdahl pathway, which is likely employed for acetate oxidation. It also encodes several genes essential to thrive at haloalkaline conditions; including a Na[+]-dependent ATP synthase and marker genes for 'salt-out' strategies for osmotic homeostasis at high soda conditions. Membrane lipid analysis of the M-SAO culture showed the presence of unusual bacterial diether membrane lipids which are presumably beneficial at extreme haloalkaline conditions. To determine the importance of SAO in haloalkaline environments, previously obtained 16S rRNA gene sequencing data and metagenomic data of five different hypersaline soda lake sediment samples were investigated, including the soda lakes where the enrichment cultures originated from. The draft genome of 'Ca. S. acetioxidans' showed highest identity with two metagenome-assembled genomes (MAGs) of putative SAOBs that belonged to the highly abundant and diverse Syntrophomonadaceae family present in the soda lake sediments. The 16S rRNA gene amplicon datasets of the soda lake sediments showed a high similarity of reads to 'Ca. S. acetioxidans' with abundance as high as 1.3% of all reads, whereas aceticlastic methanogens and acetate oxidizing sulfate-reducers were not abundant (≤0.1%) or could not be detected. These combined results indicate that SAO is the primary anaerobic acetate oxidizing pathway at extreme haloalkaline conditions performed by haloalkaliphilic syntrophic consortia.}, } @article {pmid30616051, year = {2019}, author = {Zhao, R and Feng, J and Liu, J and Fu, W and Li, X and Li, B}, title = {Deciphering of microbial community and antibiotic resistance genes in activated sludge reactors under high selective pressure of different antibiotics.}, journal = {Water research}, volume = {151}, number = {}, pages = {388-402}, doi = {10.1016/j.watres.2018.12.034}, pmid = {30616051}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; Drug Resistance, Microbial ; Genes, Bacterial ; *Microbiota ; RNA, Ribosomal, 16S ; *Sewage ; }, abstract = {Currently, the effects of high antibiotic concentrations on the performance of microbiota and antibiotic resistance genes (ARGs) in activated sludge (AS) process are not well characterized. Lab-scale batch reactors were performed to evaluate the dynamics of microbial community and ARGs in response to six antibiotics at different concentrations using high-throughput sequencing-based 16S rRNA gene and metagenomic analyses. The presence of antibiotics remarkably decreased the microbial diversity, caused a great change of the microbiota structure, and exerted a selective pressure on the enrichment of potential antibiotic resistant bacteria (ARB), such as Arthrobacter, Thauera, Geothrix, Rudaea, Aridibacter, Conexibacter, Terrimonas, etc. High antibiotic selective pressures increased ARG abundance but simultaneously reduced ARG number. In total, 491 ARG subtypes belonging to 20 ARG types were detected and kanamycin treatment showed the highest ARG abundances. A core set of 54 ARG subtypes that accounted for 66.7%-99.6% of the total ARG abundances were shared by all samples. The increase of the abundances of both corresponding and non-corresponding ARGs under a specific antibiotic treatment revealed the collateral effects of antibiotic selective pressure. Microbial community may play an important role in the composition of ARGs. Network analysis indicated that both internal-type and external-type of ARGs exhibited higher non-random co-occurrence incidences and 18 genera were speculated as the possible hosts for multiple ARGs. This study deciphered the profiles and relationships between microbial community and ARGs in AS process treating wastewater with high antibiotic concentrations and could provide helpful guidance for controlling the development and dissemination of ARB and ARGs.}, } @article {pmid30612183, year = {2019}, author = {Ding, W and Zhang, W and Alikunhi, NM and Batang, Z and Pei, B and Wang, R and Chen, L and Al-Suwailem, A and Qian, PY}, title = {Metagenomic Analysis of Zinc Surface-Associated Marine Biofilms.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {406-416}, pmid = {30612183}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Bacterial Physiological Phenomena ; Biodiversity ; *Biofilms ; Indian Ocean ; Metagenomics ; Phylogeny ; Seawater/analysis/*microbiology ; Zinc/analysis/*metabolism ; }, abstract = {Biofilms are a significant source of marine biofouling. Marine biofilm communities are established when microorganisms adhere to immersed surfaces. Despite the microbe-inhibiting effect of zinc surfaces, microbes can still attach to the surface and form biofilms. However, the diversity of biofilm-forming microbes that can attach to zinc surfaces and their common functional features remain elusive. Here, by analyzing 9,000,000 16S rRNA gene amplicon sequences and 270 Gb of metagenomic data, we comprehensively explored the taxa and functions related to biofilm formation in subtidal zones of the Red Sea. A clear difference was observed between the biofilm and adjacent seawater microbial communities in terms of the taxonomic structure at phylum and genus levels, and a huge number of genera were only present in the biofilms. Saturated alpha-diversity curves suggested the existence of more than 14,000 operational taxonomic units in one biofilm sample, which is much higher than previous estimates. Remarkably, the biofilms contained abundant and diverse transposase genes, which were localized along microbial chromosomal segments and co-existed with genes related to metal ion transport and resistance. Genomic analyses of two cyanobacterial strains that were abundant in the biofilms revealed a variety of metal ion transporters and transposases. Our analyses revealed the high diversity of biofilm-forming microbes that can attach to zinc surfaces and the ubiquitous role of transposase genes in microbial adaptation to toxic metal surfaces.}, } @article {pmid30612083, year = {2019}, author = {Zhu, X and Campanaro, S and Treu, L and Kougias, PG and Angelidaki, I}, title = {Novel ecological insights and functional roles during anaerobic digestion of saccharides unveiled by genome-centric metagenomics.}, journal = {Water research}, volume = {151}, number = {}, pages = {271-279}, doi = {10.1016/j.watres.2018.12.041}, pmid = {30612083}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Bioreactors ; Metagenome ; *Metagenomics ; Microbial Consortia ; }, abstract = {In typical anaerobic digestion (AD) systems, the microbial functional assertion is hampered by synchronised versatile metabolism required for heterogeneous substrates degradation. Thus, the intricate methanogenic process from organic compounds remains an enigma after decades of empirical operation. In this study, simplified AD microbial communities were obtained with substrate specifications and continuous reactor operation. Genome-centric metagenomic approach was followed to holistically investigate the metabolic pathways of the AD and the microbial synergistic networks. In total, 63 metagenome assembled genomes (MAGs) were assembled from 8 metagenomes acquired in specific methanogenic niches. The metabolic pathways were reconstructed from the annotated genes and their dynamicity under experimental conditions. The results show that the methanogenic niches nourish unique metabolism beyond current knowledge acquired from cultivation-based methods. A novel glucose mineralization model without acetate formation was proposed and asserted in a pair of syntrophs: Clostridiaceae sp. and Methanoculleus thermophilus. Moreover, the catabolic pathway was elucidated in uncharacterized syntrophic acetate oxidizers, Synergistaceae spp. A remarkable evolutionary insight is the discovery that electron transport and energy conservation mechanisms impose selective pressure on syntrophic partners. Overall, the functional roles of the individual microbes tightly rely on the catabolic pathways and cannot always be physiologically defined in accordance with conventional four-step AD concept. The substrate-specific systems provided a traceable microbial community to dissecting the AD process. The genome-centric metagenomics successfully constructed genomes of microbes that have not been previously isolated and illustrated metabolic pathways that beyond the current knowledge of AD process. This study provides new perspectives to unravel the AD microbial ecology and suggests more attention should be paid on uncharacterized metabolism specifically harboured by AD microbial communities.}, } @article {pmid30610284, year = {2019}, author = {Xia, Y and Tan, D and Akbary, R and Kong, J and Seviour, R and Kong, Y}, title = {Aqueous raw and ripe Pu-erh tea extracts alleviate obesity and alter cecal microbiota composition and function in diet-induced obese rats.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {4}, pages = {1823-1835}, doi = {10.1007/s00253-018-09581-2}, pmid = {30610284}, issn = {1432-0614}, support = {ZD2015015//Yunnan Provincial Department of Education/ ; 2016FA052//Yunnan Provincial Science and Technology Department/ ; 31860029//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacteria/*classification/genetics/*isolation & purification ; Cecum/*microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gastrointestinal Microbiome/*drug effects ; Obesity/*drug therapy ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rats ; Sequence Analysis, DNA ; *Teas, Medicinal ; }, abstract = {Pu-erh tea is attracting increased attention worldwide because of its unique flavor and health effects, but its impact on the composition and function of the gut microbiota remains unclear. The aim of this study was to investigate the effects of aqueous extracts of fermented (ripe) and non-fermented (raw) Pu-erh teas on the composition and function of the intestinal microbiota of rats with diet-induced obesity. We conducted a comparative metagenomic and meta-proteomic investigation of the microbial communities in cecal samples taken from obese rats treated with or without extracts of raw or ripe Pu-erh teas. By analyzing the composition and diversity of 16S rRNA amplicons and expression profiles of 814 distinct proteins, we found that despite differences in the chemical compositions of raw and ripe Pu-erh teas, administration of either tea at two doses (0.15- and 0.40-g/kg body weight) significantly (P < 0.05) increased microbial diversity and changed the composition of cecal microbiota by increasing the relative abundances of Firmicutes and decreasing those of Bacteroidetes. Community metabolic processes, including sucrose metabolism, glycolysis, and syntheses of proteins, rRNAs, and antibiotics were significantly (P < 0.05) promoted or had a tendency (0.10 < P < 0.05) to be promoted due to the enrichment of relevant enzymes. Furthermore, evidence at population, molecular, and metabolic levels indicated that polyphenols of raw Pu-erh tea and their metabolites potentially promote Akkermansia muciniphila growth by stimulating a type II and III secretion system protein, the elongation factor Tu, and a glyceraldehyde-3-phosphate dehydrogenase. This study provides new evidence for the prebiotic effects of Pu-erh tea.}, } @article {pmid30609942, year = {2019}, author = {Yang, SH and Tandon, K and Lu, CY and Wada, N and Shih, CJ and Hsiao, SS and Jane, WN and Lee, TC and Yang, CM and Liu, CT and Denis, V and Wu, YT and Wang, LT and Huang, L and Lee, DC and Wu, YW and Yamashiro, H and Tang, SL}, title = {Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {3}, pmid = {30609942}, issn = {2049-2618}, mesh = {Animals ; Anthozoa/*microbiology ; Chlorobi/*classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Endolithic microbes in coral skeletons are known to be a nutrient source for the coral host. In addition to aerobic endolithic algae and Cyanobacteria, which are usually described in the various corals and form a green layer beneath coral tissues, the anaerobic photoautotrophic green sulfur bacteria (GSB) Prosthecochloris is dominant in the skeleton of Isopora palifera. However, due to inherent challenges in studying anaerobic microbes in coral skeleton, the reason for its niche preference and function are largely unknown.

RESULTS: This study characterized a diverse and dynamic community of endolithic microbes shaped by the availability of light and oxygen. In addition, anaerobic bacteria isolated from the coral skeleton were cultured for the first time to experimentally clarify the role of these GSB. This characterization includes GSB's abundance, genetic and genomic profiles, organelle structure, and specific metabolic functions and activity. Our results explain the advantages endolithic GSB receive from living in coral skeletons, the potential metabolic role of a clade of coral-associated Prosthecochloris (CAP) in the skeleton, and the nitrogen fixation ability of CAP.

CONCLUSION: We suggest that the endolithic microbial community in coral skeletons is diverse and dynamic and that light and oxygen are two crucial factors for shaping it. This study is the first to demonstrate the ability of nitrogen uptake by specific coral-associated endolithic bacteria and shed light on the role of endolithic bacteria in coral skeletons.}, } @article {pmid30609875, year = {2019}, author = {Waseem, H and Jameel, S and Ali, J and Saleem Ur Rehman, H and Tauseef, I and Farooq, U and Jamal, A and Ali, MI}, title = {Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {1}, pages = {}, pmid = {30609875}, issn = {1420-3049}, mesh = {Anti-Infective Agents/*pharmacology ; Computational Biology/methods ; Data Analysis ; *Drug Resistance, Microbial ; *Environmental Microbiology ; Gastrointestinal Microbiome ; Genes, Bacterial ; *High-Throughput Screening Assays ; Humans ; Metagenome ; Metagenomics/methods ; Quality Control ; *Real-Time Polymerase Chain Reaction ; }, abstract = {Expansion in whole genome sequencing and subsequent increase in antibiotic resistance targets have paved the way of high throughput qPCR (HT-qPCR) for analyzing hundreds of antimicrobial resistance genes (ARGs) in a single run. A meta-analysis of 51 selected studies is performed to evaluate ARGs abundance trends over the last 7 years. WaferGen[TM] SmartChip is found to be the most widely used HT-qPCR platform among others for evaluating ARGs. Up till now around 1000 environmental samples (excluding biological replicates) from different parts of the world have been analyzed on HT-qPCR. Calculated detection frequency and normalized ARGs abundance (ARGs/16S rRNA gene) reported in gut microbiome studies have shown a trend of low ARGs as compared to other environmental matrices. Disparities in the HT-qPCR data analysis which are causing difficulties to researchers in precise interpretation of results have been highlighted and a possible way forward for resolving them is also suggested. The potential of other amplification technologies and point of care or field deployable devices for analyzing ARGs have also been discussed in the review. Our review has focused on updated information regarding the role, current status and future perspectives of HT-qPCR in the field of antimicrobial resistance.}, } @article {pmid30607855, year = {2019}, author = {Li, H and Chi, Z and Yan, B}, title = {Successful start-up of the anammox process in constructed wetland microcosms: influence of the electron acceptors on performance, microbial community, and functional genes.}, journal = {Environmental science and pollution research international}, volume = {26}, number = {5}, pages = {5202-5209}, pmid = {30607855}, issn = {1614-7499}, support = {NO. 2017YFC0505901//National Key R&D Program of China/ ; NO.41401548//National Natural Science Foundation of China/ ; NOs.201804910339//China Scholarship Council/ ; }, mesh = {Ammonia/*analysis/metabolism ; Anaerobiosis ; Bioreactors/*microbiology ; Genes, Bacterial ; Metagenome ; Microbiota/*genetics ; Nitrogen/*analysis/metabolism ; Oxidation-Reduction ; Water Pollutants, Chemical/*analysis/metabolism ; Water Purification/*methods ; *Wetlands ; }, abstract = {Nitrogen removal by anammox process has been recognized as efficient, cost-effective, and low-energy alternative removal. The longer start-up periods of anammox process hindered the widespread application of anammox-based technology. In this study, four identical unplanted subsurface-flow constructed wetlands (USFCWs) were built up to investigate the effects of electron acceptors (Fe[3+], Mn[4+], SO4[2-]) on the start-up of anammox process. Results indicated that the start-up time of anammox process was shortened to 105 days in R1 (with Fe[3+] addition) and 110 days in R2 (with Mn[4+] addition) with nitrogen removal efficiencies of above 75%, compared with 148 days in R0 (control). The addition of SO4[2-] had no significant effect on start-up process. High-throughput sequencing results demonstrated that Shannon index increased significantly from 2.87 (R0) to 5.08 (R1) and 5.00 (R2), and the relative abundance of Candidatus Anammoxoglobus rose from 3.6 to 5.3% in R1. Denitratisoma increased significantly in R2 under addition of Mn[4+], which was beneficial for the occurrence of anammox process. The functional genes that related to signal transduction mechanisms and secondary metabolite biosynthesis, transport, and catabolism were upregulated after addition of electron acceptors. These results demonstrated that adding electron acceptors Fe[3+] or Mn[4+] could be an effective way to accelerate the start-up of anammox process. Graphical abstract ᅟ.}, } @article {pmid30606403, year = {2019}, author = {Gong, J and Noel, S and Pluznick, JL and Hamad, ARA and Rabb, H}, title = {Gut Microbiota-Kidney Cross-Talk in Acute Kidney Injury.}, journal = {Seminars in nephrology}, volume = {39}, number = {1}, pages = {107-116}, pmid = {30606403}, issn = {1558-4488}, support = {R01 DK111209/DK/NIDDK NIH HHS/United States ; }, mesh = {Acute Kidney Injury/immunology/*microbiology ; Animals ; Blood Pressure ; Dysbiosis/*complications ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*immunology ; Humans ; Methylamines/metabolism ; Prebiotics ; Probiotics/therapeutic use ; Uremia/microbiology ; }, abstract = {The recent surge in research on the intestinal microbiota has greatly changed our understanding of human biology. Significant technical advances in DNA sequencing analysis and its application to metagenomics and metatranscriptomics has profoundly enhanced our ability to quantify and track complex microbial communities and to begin understanding their impact on human health and disease. This has led to a better understanding of the relationships between the intestinal microbiome and renal physiology/pathophysiology. In this review, we discuss the interactions between intestinal microbiota and kidney. We focus on select aspects including the intestinal barrier, immunologic and soluble mediators of microbiome effects, and effects of dysbiosis on acute kidney injury. Relevant studies on microbiome changes in other renal diseases are highlighted. We also introduce potential mechanisms of intervention with regard to gut microbiota in renal diseases.}, } @article {pmid30606162, year = {2019}, author = {Xue, F and Nan, X and Li, Y and Pan, X and Guo, Y and Jiang, L and Xiong, B}, title = {Metagenomic insights into effects of thiamine supplementation on ruminal non-methanogen archaea in high-concentrate diets feeding dairy cows.}, journal = {BMC veterinary research}, volume = {15}, number = {1}, pages = {7}, pmid = {30606162}, issn = {1746-6148}, support = {Grant No. 31572435//Project of National Nature Science Foundation of China/ ; 2016YFD0700205//National Key Research and Development Plan/ ; }, mesh = {Animal Feed ; Animals ; Archaea/*drug effects/genetics ; Cattle ; Diet/*veterinary ; *Dietary Supplements ; Eating/drug effects ; Female ; Gastrointestinal Microbiome/drug effects ; Hydrogen-Ion Concentration ; Lactation/drug effects ; Metagenomics ; Rumen/chemistry/*microbiology ; Thiamine/analysis/*pharmacology ; }, abstract = {BACKGROUND: Overfeeding of high-concentrate diet (HC) frequently leads to subacute ruminal acidosis (SARA) in modern dairy cows' production. Thiamine supplementation has been confirmed to attenuate HC induced SARA by increasing ruminal pH and ratio of acetate to propionate, and decreasing rumen lactate, biogenic amines and lipopolysaccharide (LPS). The effects of thiamine supplementation in HC on rumen bacteria and fungi profile had been detected in our previous studies, however, effects of thiamine supplementation in HC on rumen non-methanogen archaea is still unclear. The objective of the present study was therefore to investigate the effects of thiamine supplementation on ruminal archaea, especially non-methanogens in HC induced SARA cows.

RESULTS: HC feeding significantly decreased dry matter intake, milk production, milk fat content, ruminal pH and the concentrations of thiamine and acetate in rumen fluid compared with control diet (CON) (P < 0.05), while the concentrations of propionate and ammonia-nitrogen (NH3-N) were significantly increased compared with CON (P < 0.05). These changes caused by HC were inversed by thiamine supplementation (P < 0.05). The taxonomy results showed that ruminal archaea ranged from 0.37 to 0.47% of the whole microbiota. Four characterized phyla, a number of Candidatus archaea and almost 660 species were identified in the present study. In which Euryarchaeota occupied the largest proportion of the whole archaea. Furthermore, thiamine supplementation treatment significantly increased the relative abundance of non-methanogens compared with CON and HC treatments. Thaumarchaeota was increased in HC compared with CON. Thiamine supplementation significantly increased Crenarchaeota, Nanoarchaeota and the Candidatus phyla, however decreased Thaumarchaeota compared with HC treatment.

CONCLUSIONS: HC feeding significantly decreased ruminal pH and increased the content of NH3-N which led to N loss and the increase of the relative abundance of Thaumarchaeota. Thiamine supplementation increased ruminal pH, improved the activity of ammonia utilizing bacteria, and decreased Thaumarchaeota abundance to reduce the ruminal NH3 content and finally reduced N loss. Overall, these findings contributed to the understanding of thiamine's function in dairy cows and provided new strategies to improve dairy cows' health under high-concentrate feeding regime.}, } @article {pmid30605809, year = {2019}, author = {Bai, Y and Ruan, X and Wang, F and Antoine, G and van der Hoek, JP}, title = {Sulfonamides removal under different redox conditions and microbial response to sulfonamides stress during riverbank filtration: A laboratory column study.}, journal = {Chemosphere}, volume = {220}, number = {}, pages = {668-677}, doi = {10.1016/j.chemosphere.2018.12.167}, pmid = {30605809}, issn = {1879-1298}, mesh = {Biodegradation, Environmental ; Filtration ; Microbiota/*drug effects/physiology ; Oxidation-Reduction ; Phylogeny ; Rivers ; Sulfonamides/*isolation & purification/pharmacology ; }, abstract = {Riverbank filtration (RBF) as a barrier of pathogenic microorganisms and organic micropollutants recently has been proven capable of removing sulfonamides. However, the study about the effect of redox conditions on biodegradation of common and persistent sulfonamides in RBF is limited and the response of microbial communities to sulfonamides stress during RBF is unknown. In this study, two column set-ups (with residence time 5 days and 11 days respectively), simulating different redox conditions of riverbank filtration systems, were operated for seven months to investigate 1) the long-term effect of redox conditions on ng∙L[-1] level sulfonamides (sulfapyridine, sulfadiazine, sulfamethoxazole, sulfamethazine, sulfaquinoxaline) removal, and 2) the microbial community evolution represented by the phylogenetic and metabolic function shift under non-lethal selective pressures of sulfonamides. The results showed that sulfonamides were more degradable under anoxic conditions than oxic and suboxic conditions. In the sulfonamides stressed community, the phylogenetic diversity increased slightly. Relative abundance of an intrinsic sulfonamides resistant bacteria Bacillus spp. increased, suggesting that sulfonamide resistance developed in specific bacteria under sulfonamides contamination pressure in RBF systems. At the same time, an activated transport function in the stressed microbial community was noticed. The predicted relative abundance of gene folP, which encodes dihydropteroate synthase, also increased significantly, indicating a detoxification mechanism and sulfonamides resistance potential under non-lethal selective pressures of sulfonamides in RBF systems.}, } @article {pmid30604012, year = {2019}, author = {Tyagi, A and Singh, B and Billekallu Thammegowda, NK and Singh, NK}, title = {Shotgun metagenomics offers novel insights into taxonomic compositions, metabolic pathways and antibiotic resistance genes in fish gut microbiome.}, journal = {Archives of microbiology}, volume = {201}, number = {3}, pages = {295-303}, doi = {10.1007/s00203-018-1615-y}, pmid = {30604012}, issn = {1432-072X}, support = {YSS/2014/000269//Science and Engineering Research Board/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Aquaculture ; *Bacteria/classification/drug effects/genetics ; Carps/*microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Fishes ; Gastrointestinal Microbiome/*genetics ; Gene Transfer, Horizontal ; Metabolic Networks and Pathways ; Metagenomics/methods ; Probiotics ; }, abstract = {Gut microbiota of freshwater carp (Labeo rohita) was investigated by shotgun metagenomics to understand its taxonomic composition and functional capabilities. With the presence of 36 phyla, 326 families and 985 genera, the fish gut microbiota was found to be quite diverse in nature. However, at the phylum level, more than three-fourths of gut microbes belonged to Proteobacteria. Very low prevalence of commonly used probiotic bacteria (Bacillus, Lactobacillus, Streptococcus, and Lactococcus) in fish gut suggested the need to search for alternative probiotics for aquaculture use. Biosynthesis pathways were found to be the most dominant (51%) followed by degradation (39%), energy metabolism (4%) and fermentation (2%). In conformity with herbivorous feeding habit of L. rohita, gut microbiome also had pathways for the degradation of cellulose, hemicellulose, chitin, pectin, starch, and other complex carbohydrates. High prevalence of Actinobacteria and antibiotic biosynthesis pathways in the fish gut microbiome indicated its potential for bioprospecting of potentially novel natural antibiotics. Fifty-one different types of antibiotic resistance genes (ARGs) belonging to 15 antimicrobial resistance (AMR) gene families and conferring resistance against 24 antibiotic types were detected in fish gut. Some of the ARGs for multi-drug resistance were also found to be located on sequences of plasmid origin. The presence of pathogenic bacteria and ARGs on plasmid sequences suggested the potential risk due to horizontal gene transfer in the confined gut environment. The role of ARGs in fish gut microbiome needs further investigations.}, } @article {pmid30602367, year = {2019}, author = {Chen, YY and Chen, DQ and Chen, L and Liu, JR and Vaziri, ND and Guo, Y and Zhao, YY}, title = {Microbiome-metabolome reveals the contribution of gut-kidney axis on kidney disease.}, journal = {Journal of translational medicine}, volume = {17}, number = {1}, pages = {5}, pmid = {30602367}, issn = {1479-5876}, support = {81673578//National Natural Science Foundation of China/International ; 81603271//National Natural Science Foundation of China/International ; 81872985//National Natural Science Foundation of China/International ; }, mesh = {Animals ; Dysbiosis/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Kidney/*microbiology ; Kidney Diseases/*microbiology ; *Metabolome ; *Microbiota ; }, abstract = {Dysbiosis represents changes in composition and structure of the gut microbiome community (microbiome), which may dictate the physiological phenotype (health or disease). Recent technological advances and efforts in metagenomic and metabolomic analyses have led to a dramatical growth in our understanding of microbiome, but still, the mechanisms underlying gut microbiome-host interactions in healthy or diseased state remain elusive and their elucidation is in infancy. Disruption of the normal gut microbiota may lead to intestinal dysbiosis, intestinal barrier dysfunction, and bacterial translocation. Excessive uremic toxins are produced as a result of gut microbiota alteration, including indoxyl sulphate, p-cresyl sulphate, and trimethylamine-N-oxide, all implicated in the variant processes of kidney diseases development. This review focuses on the pathogenic association between gut microbiota and kidney diseases (the gut-kidney axis), covering CKD, IgA nephropathy, nephrolithiasis, hypertension, acute kidney injury, hemodialysis and peritoneal dialysis in clinic. Targeted interventions including probiotic, prebiotic and symbiotic measures are discussed for their potential of re-establishing symbiosis, and more effective strategies for the treatment of kidney diseases patients are suggested. The novel insights into the dysbiosis of the gut microbiota in kidney diseases are helpful to develop novel therapeutic strategies for preventing or attenuating kidney diseases and complications.}, } @article {pmid30601862, year = {2019}, author = {Thornbury, M and Sicheri, J and Slaine, P and Getz, LJ and Finlayson-Trick, E and Cook, J and Guinard, C and Boudreau, N and Jakeman, D and Rohde, J and McCormick, C}, title = {Characterization of novel lignocellulose-degrading enzymes from the porcupine microbiome using synthetic metagenomics.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0209221}, pmid = {30601862}, issn = {1932-6203}, mesh = {Animals ; Endo-1,4-beta Xylanases/genetics/metabolism ; Escherichia coli/genetics/metabolism ; Fermentation ; Glycoside Hydrolases/genetics/metabolism ; Kinetics ; Lignin/*metabolism ; Metagenomics ; Microbiota/*genetics/*physiology ; Phylogeny ; Porcupines/metabolism/*microbiology ; Recombinant Proteins/genetics/metabolism ; Synthetic Biology ; Xylosidases/genetics/metabolism ; beta-Glucosidase/genetics/metabolism ; }, abstract = {Plant cell walls are composed of cellulose, hemicellulose, and lignin, collectively known as lignocellulose. Microorganisms degrade lignocellulose to liberate sugars to meet metabolic demands. Using a metagenomic sequencing approach, we previously demonstrated that the microbiome of the North American porcupine (Erethizon dorsatum) is replete with genes that could encode lignocellulose-degrading enzymes. Here, we report the identification, synthesis and partial characterization of four novel genes from the porcupine microbiome encoding putative lignocellulose-degrading enzymes: β-glucosidase, α-L-arabinofuranosidase, β-xylosidase, and endo-1,4-β-xylanase. These genes were identified via conserved catalytic domains associated with cellulose- and hemicellulose-degradation. Phylogenetic trees were created for each of these putative enzymes to depict genetic relatedness to known enzymes. Candidate genes were synthesized and cloned into plasmid expression vectors for inducible protein expression and secretion. The putative β-glucosidase fusion protein was efficiently secreted but did not permit Escherichia coli (E. coli) to use cellobiose as a sole carbon source, nor did the affinity purified enzyme cleave p-Nitrophenyl β-D-glucopyranoside (p-NPG) substrate in vitro over a range of physiological pH levels (pH 5-7). The putative hemicellulose-degrading β-xylosidase and α-L-arabinofuranosidase enzymes also lacked in vitro enzyme activity, but the affinity purified endo-1,4-β-xylanase protein cleaved a 6-chloro-4-methylumbelliferyl xylobioside substrate in acidic and neutral conditions, with maximal activity at pH 7. At this optimal pH, KM, Vmax, and kcat were determined to be 32.005 ± 4.72 μM, 1.16x10-5 ± 3.55x10-7 M/s, and 94.72 s-1, respectively. Thus, our pipeline enabled successful identification and characterization of a novel hemicellulose-degrading enzyme from the porcupine microbiome. Progress towards the goal of introducing a complete lignocellulose-degradation pathway into E. coli will be accelerated by combining synthetic metagenomic approaches with functional metagenomic library screening, which can identify novel enzymes unrelated to those found in available databases.}, } @article {pmid30599960, year = {2019}, author = {Xie, M and Wu, J and An, F and Yue, X and Tao, D and Wu, R and Lee, Y}, title = {An integrated metagenomic/metaproteomic investigation of microbiota in dajiang-meju, a traditional fermented soybean product in Northeast China.}, journal = {Food research international (Ottawa, Ont.)}, volume = {115}, number = {}, pages = {414-424}, doi = {10.1016/j.foodres.2018.10.076}, pmid = {30599960}, issn = {1873-7145}, mesh = {Bacteria/metabolism ; China ; Chromatography, Liquid ; Fermentation ; Fermented Foods/*microbiology ; Fungi/metabolism ; *Metagenome ; Microbiota/*physiology ; Penicillium/metabolism ; Proteins/metabolism ; Rhizopus/metabolism ; Glycine max/*chemistry ; Tandem Mass Spectrometry ; }, abstract = {Dajiang-meju have been used as major ingredients for the preparation of traditional spontaneously fermented soybean paste in Northeast China. In this work, we sequenced and analyzed the metagenome of 12 dajiang-meju samples. To complement the metagenome analysis, we analyzed the taxonomic and functional diversity of the microbiota by metaproteomics (LC-MS/MS). The analysis of metagenomic data revealed that the communities were primarily dominated by Enterobacter, Enterococcus, Leuconostoc, Lactobacillus, Citrobacter and Leclercia. Moreover, changes in the functional levels were monitored, and metaproteomic analysis revealed that most of the proteins were mainly expressed by members of Rhizopus, Penicillium and Geotrichum. The number of sequences allocated to fungi in the fermentation process decreased, whereas the number of sequences assigned to bacteria increased with time of fermentation. In addition, functional metagenomic profiling indicated that a series of sequences related to carbohydrates and amino acids metabolism were enriched. Additionally, enzymes associated with glycolysis metabolic pathways were presumed to contribute to the generation of flavor in dajiang-meju. Proteins from different dajiang-meju samples involved in global and overview maps, carbohydrate metabolism, nucleic acid metabolism and energy metabolism were differentially expressed. This information improves the understanding of microbial metabolic patterns with respect to the metaproteomes of dajiang-meju and provides a powerful tool for studying the fermentation process of soybean products.}, } @article {pmid30599936, year = {2019}, author = {Danneskiold-Samsøe, NB and Dias de Freitas Queiroz Barros, H and Santos, R and Bicas, JL and Cazarin, CBB and Madsen, L and Kristiansen, K and Pastore, GM and Brix, S and Maróstica Júnior, MR}, title = {Interplay between food and gut microbiota in health and disease.}, journal = {Food research international (Ottawa, Ont.)}, volume = {115}, number = {}, pages = {23-31}, doi = {10.1016/j.foodres.2018.07.043}, pmid = {30599936}, issn = {1873-7145}, mesh = {*Diet ; Dietary Fiber/metabolism ; Dietary Proteins/metabolism ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Lipid Metabolism ; Polyphenols/metabolism ; Prebiotics/analysis ; }, abstract = {Numerous microorganisms colonize the human gastrointestinal tract playing pivotal roles in relation to digestion and absorption of dietary components. They biotransform food components and produce metabolites, which in combination with food components shape and modulate the host immune system and metabolic responses. Reciprocally, the diet modulates the composition and functional capacity of the gut microbiota, which subsequently influence host biochemical processes establishing a system of mutual interaction and inter-dependency. Macronutrients, fibers, as well as polyphenols and prebiotics are strong drivers shaping the composition of the gut microbiota. Especially, short-chain fatty acids produced from ingested fibers and tryptophan metabolites are key in modulating host immune responses. Since reciprocal interactions between diet, host, and microbiota are personal, understanding this complex network of interactions calls for novel use of large datasets and the implementation of machine learning algorithms and artificial intelligence. In this review, we aim to provide a base for future investigations of how interactions between food components and gut microbiota may influence or even determine human health and disease.}, } @article {pmid30598099, year = {2018}, author = {Abe, K and Hirayama, M and Ohno, K and Shimamura, T}, title = {A latent allocation model for the analysis of microbial composition and disease.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 19}, pages = {519}, pmid = {30598099}, issn = {1471-2105}, mesh = {*Algorithms ; Bacteria/*classification ; Case-Control Studies ; Colorectal Neoplasms/*microbiology ; Computer Simulation ; Humans ; *Microbiota ; *Models, Statistical ; Parkinson Disease/*microbiology ; }, abstract = {BACKGROUND: Establishing the relationship between microbiota and specific diseases is important but requires appropriate statistical methodology. A specialized feature of microbiome count data is the presence of a large number of zeros, which makes it difficult to analyze in case-control studies. Most existing approaches either add a small number called a pseudo-count or use probability models such as the multinomial and Dirichlet-multinomial distributions to explain the excess zero counts, which may produce unnecessary biases and impose a correlation structure taht is unsuitable for microbiome data.

RESULTS: The purpose of this article is to develop a new probabilistic model, called BERnoulli and MUltinomial Distribution-based latent Allocation (BERMUDA), to address these problems. BERMUDA enables us to describe the differences in bacteria composition and a certain disease among samples. We also provide a simple and efficient learning procedure for the proposed model using an annealing EM algorithm.

CONCLUSION: We illustrate the performance of the proposed method both through both the simulation and real data analysis. BERMUDA is implemented with R and is available from GitHub (https://github.com/abikoushi/Bermuda).}, } @article {pmid30598080, year = {2018}, author = {Chen, HM and Chang, TH and Lin, FM and Liang, C and Chiu, CM and Yang, TL and Yang, T and Huang, CY and Cheng, YN and Chang, YA and Chang, PY and Weng, SL}, title = {Vaginal microbiome variances in sample groups categorized by clinical criteria of bacterial vaginosis.}, journal = {BMC genomics}, volume = {19}, number = {Suppl 10}, pages = {876}, pmid = {30598080}, issn = {1471-2164}, mesh = {Adult ; DNA, Bacterial/genetics ; Female ; *Genetic Variation ; Humans ; Microbiota/*genetics ; Vagina/*microbiology ; Vaginosis, Bacterial/microbiology ; }, abstract = {BACKGROUND: One of the most common and recurrent vaginal infections is bacterial vaginosis (BV). The diagnosis is based on changes to the "normal" vaginal microbiome; however, the normal microbiome appears to differ according to reproductive status and ethnicity, and even among individuals within these groups. The Amsel criteria and Nugent score test are widely used for diagnosing BV; however, these tests are based on different criteria, and so may indicate distinct changes in the vaginal microbial community. Nevertheless, few studies have compared the results of these test against metagenomics analysis.

METHODS: Vaginal flora samples from 77 participants were classified according to the Amsel criteria and Nugent score test. The microbiota composition was analyzed using 16S ribosome RNA gene amplicon sequencing. Bioinformatics analysis and multivariate statistical analysis were used to evaluate the microbial diversity and function.

RESULTS: Only 3 % of the participants diagnosed BV negative using the Amsel criteria (A-) were BV-positive according to the Nugent score test (N+), while over half of the BV-positive patients using the Amsel criteria (A+) were BV-negative according to the Nugent score test (N-). Thirteen genera showed significant differences in distribution among BV status defined by BV tests (e.g., A - N-, A + N- and A + N+). Variations in the four most abundant taxa, Lactobacillus, Gardnerella, Prevotella, and Escherichia, were responsible for most of this dissimilarity. Furthermore, vaginal microbial diversity differed significantly among the three groups classified by the Nugent score test (N-, N+, and intermediate flora), but not between the Amsel criteria groups. Numerous predictive microbial functions, such as bacterial chemotaxis and bacterial invasion of epithelial cells, differed significantly among multiple BV test, but not between the A- and A+ groups.

CONCLUSIONS: Metagenomics analysis can greatly expand our current understanding of vaginal microbial diversity in health and disease. Metagenomics profiling may also provide more reliable diagnostic criteria for BV testing.}, } @article {pmid30597002, year = {2019}, author = {Choi, I and Ponsero, AJ and Bomhoff, M and Youens-Clark, K and Hartman, JH and Hurwitz, BL}, title = {Libra: scalable k-mer-based tool for massive all-vs-all metagenome comparisons.}, journal = {GigaScience}, volume = {8}, number = {2}, pages = {}, pmid = {30597002}, issn = {2047-217X}, mesh = {Algorithms ; Cluster Analysis ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; *Software ; }, abstract = {BACKGROUND: Shotgun metagenomics provides powerful insights into microbial community biodiversity and function. Yet, inferences from metagenomic studies are often limited by dataset size and complexity and are restricted by the availability and completeness of existing databases. De novo comparative metagenomics enables the comparison of metagenomes based on their total genetic content.

RESULTS: We developed a tool called Libra that performs an all-vs-all comparison of metagenomes for precise clustering based on their k-mer content. Libra uses a scalable Hadoop framework for massive metagenome comparisons, Cosine Similarity for calculating the distance using sequence composition and abundance while normalizing for sequencing depth, and a web-based implementation in iMicrobe (http://imicrobe.us) that uses the CyVerse advanced cyberinfrastructure to promote broad use of the tool by the scientific community.

CONCLUSIONS: A comparison of Libra to equivalent tools using both simulated and real metagenomic datasets, ranging from 80 million to 4.2 billion reads, reveals that methods commonly implemented to reduce compute time for large datasets, such as data reduction, read count normalization, and presence/absence distance metrics, greatly diminish the resolution of large-scale comparative analyses. In contrast, Libra uses all of the reads to calculate k-mer abundance in a Hadoop architecture that can scale to any size dataset to enable global-scale analyses and link microbial signatures to biological processes.}, } @article {pmid30596703, year = {2018}, author = {Quinn, O and Gruber, MAM and Brown, RL and Baty, JW and Bulgarella, M and Lester, PJ}, title = {A metatranscriptomic analysis of diseased social wasps (Vespula vulgaris) for pathogens, with an experimental infection of larvae and nests.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0209589}, pmid = {30596703}, issn = {1932-6203}, mesh = {Animals ; Gene Expression Profiling/methods ; *Host-Pathogen Interactions ; Larva/microbiology ; *Metagenome ; *Metagenomics ; *Microbiota ; Phylogeny ; Wasps/*microbiology/ultrastructure ; }, abstract = {Social wasps are a major pest in many countries around the world. Pathogens may influence wasp populations and could provide an option for population management via biological control. We investigated the pathology of nests of apparently healthy common wasps, Vespula vulgaris, with nests apparently suffering disease. First, next-generation sequencing and metatranscriptomic analysis were used to examine pathogen presence. The transcriptome of healthy and diseased V. vulgaris showed 27 known microbial phylotypes. Four of these were observed in diseased larvae alone (Aspergillus fumigatus, Moellerella wisconsensis, Moku virus, and the microsporidian Vavraia culicis). Kashmir Bee Virus (KBV) was found to be present in both healthy and diseased larvae. Moellerella wisconsensis is a human pathogen that was potentially misidentified in our wasps by the MEGAN analysis: it is more likely to be the related bacteria Hafnia alvei that is known to infect social insects. The closest identification to the putative pathogen identified as Vavraia culicis was likely to be another microsporidian Nosema vulgaris. PCR and subsequent Sanger sequencing using published or our own designed primers, confirmed the identity of Moellerella sp. (which may be Hafnia alvei), Aspergillus sp., KBV, Moku virus and Nosema. Secondly, we used an infection study by homogenising diseased wasp larvae and feeding them to entire nests of larvae in the laboratory. Three nests transinfected with diseased larvae all died within 19 days. No pathogen that we monitored, however, had a significantly higher prevalence in diseased than in healthy larvae. RT-qPCR analysis indicated that pathogen infections were significantly correlated, such as between KBV and Aspergillus sp. Social wasps clearly suffer from an array of pathogens, which may lead to the collapse of nests and larval death.}, } @article {pmid30594064, year = {2019}, author = {Procopio, N and Ghignone, S and Williams, A and Chamberlain, A and Mello, A and Buckley, M}, title = {Metabarcoding to investigate changes in soil microbial communities within forensic burial contexts.}, journal = {Forensic science international. Genetics}, volume = {39}, number = {}, pages = {73-85}, doi = {10.1016/j.fsigen.2018.12.002}, pmid = {30594064}, issn = {1878-0326}, mesh = {Animals ; Burial ; DNA Barcoding, Taxonomic/*methods ; Forensic Sciences ; Metagenomics/methods ; Microbiota/*genetics ; Models, Animal ; Polymerase Chain Reaction ; *Postmortem Changes ; RNA, Ribosomal, 16S ; *Soil Microbiology ; Swine ; }, abstract = {The estimation of the time elapsed since death (post-mortem interval, or PMI) is one of the key themes that forensic scientists have to address frequently. However, the estimation of PMI still suffers from poor accuracy and biases especially when decomposition stages are prolonged, so further improvements in methods for PMI estimation are desirable. Soil microbial communities associated with decomposing bodies have been shown to be good candidates for the estimation of the PMI of exposed bodies. Nevertheless, further research is required to better understand the bacterial succession associated with decomposition of buried carcasses in order to test its reliability and applicability for the estimation of PMI and to better understand the dynamics involved with decomposition within this particular scenario. Therefore we explored the succession of soil microbial communities associated with four decomposing pig carcasses (from one to six months PMI) using a metabarcoding approach. The sequencing of the bacterial 16S rRNA variable region 4 (V4) revealed trends linking particular microbial taxa with specific PMIs, and notably an increase in Proteobacteria, Firmicutes and Bacteroidetes at specific PMIs as well as a decrease in Acidobacteria. Our results, in accordance with previous studies conducted on exposed bodies of different mammalian species (including humans), also showed a general reduction of the taxonomic richness from two months PMI onwards, as well as an incomplete re-establishment of the starting soil microbial conditions after six months PMI. We also found specific mammal-derived taxa, such as Bacteroides spp., being still present in the soil after six months PMI. As such, this study serves as a baseline for additional research to allow the characterisation of biomarkers associated with specific PMIs. Due to the similarity between the results presented here and those reported in other types of decomposition studies we believe that the metabarcoding approach has considerable potential in the estimation of the PMI, particularly to clarify cases involving heavily skeletonised bodies or for the investigation of clandestine graves in which the carcass has been moved from its original place of deposition.}, } @article {pmid30592383, year = {2019}, author = {van Dijkhuizen, EHP and Del Chierico, F and Malattia, C and Russo, A and Pires Marafon, D and Ter Haar, NM and Magni-Manzoni, S and Vastert, SJ and Dallapiccola, B and Prakken, B and Martini, A and De Benedetti, F and Putignani, L and , }, title = {Microbiome Analytics of the Gut Microbiota in Patients With Juvenile Idiopathic Arthritis: A Longitudinal Observational Cohort Study.}, journal = {Arthritis & rheumatology (Hoboken, N.J.)}, volume = {71}, number = {6}, pages = {1000-1010}, pmid = {30592383}, issn = {2326-5205}, mesh = {Arthritis, Juvenile/epidemiology/*microbiology ; Case-Control Studies ; Child ; Child, Preschool ; Cohort Studies ; Comorbidity ; Dysbiosis/*epidemiology ; Faecalibacterium prausnitzii ; Female ; Firmicutes ; Gastrointestinal Microbiome/*genetics ; Humans ; Italy/epidemiology ; Logistic Models ; Longitudinal Studies ; Male ; Metagenomics ; Netherlands/epidemiology ; RNA, Ribosomal, 16S ; Severity of Illness Index ; }, abstract = {OBJECTIVE: To assess the composition of gut microbiota in Italian and Dutch patients with juvenile idiopathic arthritis (JIA) at baseline, with inactive disease, and with persistent activity compared to healthy controls.

METHODS: In a multicenter, prospective, observational cohort study, fecal samples were collected at baseline from 78 Italian and 21 Dutch treatment-naive JIA patients with <6 months of disease duration and compared to 107 geographically matched samples from healthy children. Forty-four follow-up samples from patients with inactive disease and 25 follow-up samples from patients with persistent activity were analyzed. Gut microbiota composition was determined by 16S ribosomal RNA-based metagenomics. Alpha- and β-diversity were computed, and log ratios of relative abundance were compared between patients and healthy controls using random forest models and logistic regression.

RESULTS: Baseline samples from Italian patients showed reduced richness compared to healthy controls (P < 0.001). Random forest models distinguished between Italian patient baseline samples and healthy controls and suggested differences between Dutch patient samples and healthy controls (areas under the curve >0.99 and 0.71, respectively). The operational taxonomic units (OTUs) of Erysipelotrichaceae (increased in patients), Allobaculum (decreased in patients), and Faecalibacterium prausnitzii (increased in patients) showed different relative abundance in Italian patient baseline samples compared to controls after controlling for multiple comparisons. Some OTUs differed between Dutch patient samples and healthy controls, but no evidence remained after controlling for multiple comparisons. No differences were found in paired analysis between Italian patient baseline and inactive disease samples.

CONCLUSION: Our findings show evidence for dysbiosis in JIA patients. Only patient/control status, age, and geographic origin appear to be drivers of the microbiota profiles, regardless of disease activity stage, inflammation, and markers of autoimmunity.}, } @article {pmid30590681, year = {2019}, author = {Mandal, RK and Crane, RJ and Berkley, JA and Gumbi, W and Wambua, J and Ngoi, JM and Ndungu, FM and Schmidt, NW}, title = {Longitudinal Analysis of Infant Stool Bacteria Communities Before and After Acute Febrile Malaria and Artemether-Lumefantrine Treatment.}, journal = {The Journal of infectious diseases}, volume = {220}, number = {4}, pages = {687-698}, pmid = {30590681}, issn = {1537-6613}, support = {R01 AI123486/AI/NIAID NIH HHS/United States ; 103376/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Antimalarials/*administration & dosage ; Artemether, Lumefantrine Drug Combination/*administration & dosage ; Computational Biology ; Dysbiosis ; Feces/microbiology ; Female ; Fever ; *Gastrointestinal Microbiome ; Humans ; Infant ; Kenya ; Longitudinal Studies ; Malaria/*drug therapy/pathology ; Male ; Plasmodium/*drug effects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Gut microbiota were recently shown to impact malaria disease progression and outcome, and prior studies have shown that Plasmodium infections increase the likelihood of enteric bacteria causing systemic infections. Currently, it is not known whether Plasmodium infection impacts human gut microbiota as a prelude to bacteremia or whether antimalarials affect gut microbiota. Our goal was to determine to what degree Plasmodium infections and antimalarial treatment affect human gut microbiota.

METHODS: One hundred Kenyan infants underwent active surveillance for malaria from birth to 10 months of age. Each malaria episode was treated with artemether-lumefantrine (AL). Any other treatments, including antibiotics, were recorded. Stool samples were collected on an approximately biweekly basis. Ten children were selected on the basis of stool samples having been collected before (n = 27) or after (n = 17) a malaria episode and without antibiotics having been administered between collections. These samples were subjected to 16S ribosomal ribonucleic acid gene (V3-V4 region) sequencing.

RESULTS: Bacterial community network analysis revealed no obvious differences in the before and after malaria/AL samples, which was consistent with no difference in alpha and beta diversity and taxonomic analysis at the family and genus level with one exception. At the sequence variant (SV) level, akin to bacterial species, only 1 of the top 100 SVs was significantly different. In addition, predicted metagenome analysis revealed no significant difference in metagenomic capacity between before and after malaria/AL samples. The number of malaria episodes, 1 versus 2, explained significant variation in gut microbiota composition of the infants.

CONCLUSIONS: In-depth bioinformatics analysis of stool bacteria has revealed for the first time that human malaria episode/AL treatment have minimal effects on gut microbiota in Kenyan infants.}, } @article {pmid30590603, year = {2019}, author = {Mansbach, JM and Hasegawa, K and Piedra, PA and Avadhanula, V and Petrosino, JF and Sullivan, AF and Espinola, JA and Camargo, CA}, title = {Haemophilus-Dominant Nasopharyngeal Microbiota Is Associated With Delayed Clearance of Respiratory Syncytial Virus in Infants Hospitalized for Bronchiolitis.}, journal = {The Journal of infectious diseases}, volume = {219}, number = {11}, pages = {1804-1808}, pmid = {30590603}, issn = {1537-6613}, support = {R01 AI127507/AI/NIAID NIH HHS/United States ; R21 HL129909/HL/NHLBI NIH HHS/United States ; R01 AI134940/AI/NIAID NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; UH3 OD023253/OD/NIH HHS/United States ; R01 AI137091/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; R01 AI114552/AI/NIAID NIH HHS/United States ; R01 AI108588/AI/NIAID NIH HHS/United States ; }, mesh = {Bronchiolitis/*microbiology ; Female ; Haemophilus/*growth & development ; Hospitalization ; Humans ; Infant ; Male ; *Microbiota ; Nasopharynx/microbiology/virology ; Respiratory Syncytial Virus Infections/virology ; Respiratory Syncytial Virus, Human/*immunology ; Viral Load ; }, abstract = {The relation of nasopharyngeal microbiota to the clearance of respiratory syncytial virus (RSV) in infants hospitalized for bronchiolitis is not known. In a multicenter cohort, we found that 106 of 557 infants (19%) hospitalized with RSV bronchiolitis had the same RSV subtype 3 weeks later (ie, delayed clearance of RSV). Using 16S ribosomal RNA gene sequencing and a clustering approach, infants with a Haemophilus-dominant microbiota profile at hospitalization were more likely than those with a mixed profile to have delayed clearance, after adjustment for 11 factors, including viral load. Nasopharyngeal microbiota composition is associated with delayed RSV clearance.}, } @article {pmid30589606, year = {2019}, author = {Yasir, M and Qureshi, AK and Khan, I and Bibi, F and Rehan, M and Khan, SB and Azhar, EI}, title = {Culturomics-Based Taxonomic Diversity of Bacterial Communities in the Hot Springs of Saudi Arabia.}, journal = {Omics : a journal of integrative biology}, volume = {23}, number = {1}, pages = {17-27}, doi = {10.1089/omi.2018.0176}, pmid = {30589606}, issn = {1557-8100}, mesh = {Bacteria/*genetics ; Biodiversity ; Hot Springs/*microbiology ; Hot Temperature ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Saudi Arabia ; Sequence Analysis, DNA/methods ; }, abstract = {Hot springs are natural habitats for thermophilic microorganisms and provide a significant opportunity for bioprospecting thermostable biomolecules. However, the scientific community has only a fragmented understanding of the microbial diversity and composition in these biotopes. In this study, bacterial diversity in sediment samples from six hot springs of Saudi Arabia was investigated using an improved culture-dependent approach. High-throughput MALDI-TOF MS (matrix assisted laser desorption/ionization mass spectrometry) and 16S rRNA genes sequencing were used for the identification of purified isolates. Most of the hot springs had a neutral pH and a temperature range of 45-89°C. Relatively higher colony-forming units (1.9 ± 0.45 × 10[4]) were observed with 60°C incubation of an 89°C sediment sample from the hot spring at Ain al Harra1. Among the 536 purified isolates, 6 novel candidate species were found, and the remaining isolates represented 139 distinct species. Several species, such as Bacillus cereus, Bacillus subtilis, and Bacillus schlegelii, were ubiquitous in the hot springs sampled, but 102 of the identified species were uniquely distributed among the hot springs. Sixteen of the isolated thermophilic bacteria, including Geobacillus kaustophilus, Thermus oshimai, and Brevibacillus thermoruber, grew at ≥60°C. In addition, 21 species exhibited hydrolytic enzymatic activity. Most of these species belonged to Bacillus and Brevibacillus. Overall, this study contributes to global knowledgebase on bacterial communities by comprehensively profiling culture-based bacterial diversity in the hot springs of Saudi Arabia. Further studies are required for investigating bacteria from hot springs by a metagenomic approach.}, } @article {pmid30588856, year = {2019}, author = {Fajardo, C and García-Cantalejo, J and Botías, P and Costa, G and Nande, M and Martin, M}, title = {New insights into the impact of nZVI on soil microbial biodiversity and functionality.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering}, volume = {54}, number = {3}, pages = {157-167}, doi = {10.1080/10934529.2018.1535159}, pmid = {30588856}, issn = {1532-4117}, mesh = {Actinobacteria/isolation & purification ; Biodiversity ; Firmicutes/isolation & purification ; Iron/chemistry/*toxicity ; Metagenome/drug effects ; Microbiota/*drug effects/genetics ; Nanoparticles/*chemistry ; Phylogeny ; Proteobacteria/isolation & purification ; Soil/*chemistry ; Soil Microbiology/*standards ; Soil Pollutants/chemistry/*toxicity ; }, abstract = {Nanoscale zero-valent iron (nZVI) is a strong reducing agent used for in situ remediation of soil. The impacts of nZVI (5-10% w/w) on the soil microbial biodiversity and functionality of two soils (Lufa 2.2 and 2.4) were assessed. Illumina MiSeq technology was used to evaluate the structure of soil microbiomes after 21 days of exposure. Proteobacteria, Verrucomicrobia, Firmicutes and Actinobacteria were the most abundant phyla in both soils. However, the dynamics of bacterial community composition following nZVI addition differed. nZVI exposure induced pronounced shifts in the microbial composition of soil 2.4, but not in soil 2.2; an increase in Verrucomicrobia abundance was the unique common taxonomic pattern observed in both soils. The PICRUSt approach was applied to predict the functional composition of each metagenome. Environmental information processing function (membrane transport) was decreased in both nZVI-spiked soils, although soil 2.4 samples were enriched in functions involved in cellular processes and metabolism. The effects of nZVI on autochthonous bacterial communities clearly varied with the soil type assessed; changes at the phylogenetic level appeared to be more abundant than those observed at the functional level, and thus, the overall effort of the soil ecosystem might involve the maintenance of functionality following nZVI exposure.}, } @article {pmid30588764, year = {2019}, author = {Woyke, T and Schulz, F}, title = {Entities inside one another - a matryoshka doll in biology?.}, journal = {Environmental microbiology reports}, volume = {11}, number = {1}, pages = {26-28}, pmid = {30588764}, issn = {1758-2229}, mesh = {*Biological Evolution ; Eukaryota/physiology ; Giant Viruses/physiology ; Metagenomics ; Microbial Consortia ; Organelles/physiology ; *Symbiosis ; Thiothrix/physiology ; }, } @article {pmid30588567, year = {2019}, author = {Wei, F and Wu, Q and Hu, Y and Huang, G and Nie, Y and Yan, L}, title = {Conservation metagenomics: a new branch of conservation biology.}, journal = {Science China. Life sciences}, volume = {62}, number = {2}, pages = {168-178}, doi = {10.1007/s11427-018-9423-3}, pmid = {30588567}, issn = {1869-1889}, mesh = {Animals ; Animals, Wild/*microbiology/physiology ; Biological Coevolution ; Conservation of Natural Resources/*trends ; Humans ; *Metagenomics ; Microbiota/genetics/*physiology ; }, abstract = {Multifaceted approaches are required to monitor wildlife populations and improve conservation efforts. In the last decade, increasing evidence suggests that metagenomic analysis offers valuable perspectives and tools for identifying microbial communities and functions. It has become clear that gut microbiome plays a critical role in health, nutrition, and physiology of wildlife, including numerous endangered animals in the wild and in captivity. In this review, we first introduce the human microbiome and metagenomics, highlighting the importance of microbiome for host fitness. Then, for the first time, we propose the concept of conservation metagenomics, an emerging subdiscipline of conservation biology, which aims to understand the roles of the microbiota in evolution and conservation of endangered animals. We define what conservation metagenomics is along with current approaches, main scientific issues and significant implications in the study of host evolution, physiology, nutrition, ecology and conservation. We also discuss future research directions of conservation metagenomics. Although there is still a long way to go, conservation metagenomics has already shown a significant potential for improving the conservation and management of wildlife.}, } @article {pmid30587114, year = {2018}, author = {Tyakht, AV and Manolov, AI and Kanygina, AV and Ischenko, DS and Kovarsky, BA and Popenko, AS and Pavlenko, AV and Elizarova, AV and Rakitina, DV and Baikova, JP and Ladygina, VG and Kostryukova, ES and Karpova, IY and Semashko, TA and Larin, AK and Grigoryeva, TV and Sinyagina, MN and Malanin, SY and Shcherbakov, PL and Kharitonova, AY and Khalif, IL and Shapina, MV and Maev, IV and Andreev, DN and Belousova, EA and Buzunova, YM and Alexeev, DG and Govorun, VM}, title = {Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn's disease discovered using metagenomic and genomic analyses.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {968}, pmid = {30587114}, issn = {1471-2164}, support = {16-15-00258//Russian Science Foundation/ ; }, mesh = {Cluster Analysis ; Crohn Disease/microbiology/*pathology ; Escherichia coli/*genetics/isolation & purification ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Genetic Variation ; Genome, Bacterial ; Humans ; Intestinal Mucosa/microbiology ; Metagenomics/*methods ; }, abstract = {BACKGROUND: Crohn's disease is associated with gut dysbiosis. Independent studies have shown an increase in the abundance of certain bacterial species, particularly Escherichia coli with the adherent-invasive pathotype, in the gut. The role of these species in this disease needs to be elucidated.

METHODS: We performed a metagenomic study investigating the gut microbiota of patients with Crohn's disease. A metagenomic reconstruction of the consensus genome content of the species was used to assess the genetic variability.

RESULTS: The abnormal shifts in the microbial community structures in Crohn's disease were heterogeneous among the patients. The metagenomic data suggested the existence of multiple E. coli strains within individual patients. We discovered that the genetic diversity of the species was high and that only a few samples manifested similarity to the adherent-invasive varieties. The other species demonstrated genetic diversity comparable to that observed in the healthy subjects. Our results were supported by a comparison of the sequenced genomes of isolates from the same microbiota samples and a meta-analysis of published gut metagenomes.

CONCLUSIONS: The genomic diversity of Crohn's disease-associated E. coli within and among the patients paves the way towards an understanding of the microbial mechanisms underlying the onset and progression of the Crohn's disease and the development of new strategies for the prevention and treatment of this disease.}, } @article {pmid30584534, year = {2018}, author = {Ranjan, R and Rani, A and Finn, PW and Perkins, DL}, title = {Multiomic Strategies Reveal Diversity and Important Functional Aspects of Human Gut Microbiome.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {6074918}, pmid = {30584534}, issn = {2314-6141}, support = {R01 AI053878/AI/NIAID NIH HHS/United States ; R01 HL081663/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Bacteria/genetics ; Biodiversity ; Dysbiosis/genetics/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; Transcriptome/genetics ; }, abstract = {It is well accepted that dysbiosis of microbiota is associated with disease; however, the biological mechanisms that promote susceptibility or resilience to disease remain elusive. One of the major limitations of previous microbiome studies has been the lack of complementary metatranscriptomic (functional) data to complement the interpretation of metagenomics (bacterial abundance). The purpose of this study was twofold, first to evaluate the bacterial diversity and differential gene expression of gut microbiota using complementary shotgun metagenomics (MG) and metatranscriptomics (MT) from same fecal sample. Second, to compare sequence data using different Illumina platforms and with different sequencing parameters as new sequencers are introduced, and to determine if the data are comparable on different platforms. In this study, we perform ultradeep metatranscriptomic shotgun sequencing for a sample that we previously analyzed with metagenomics shotgun sequencing. We performed sequencing analysis using different Illumina platforms, with different sequencing and analysis parameters. Our results suggest that use of different Illumina platform did not lead to detectable bias in the sequencing data. The analysis of the sample using MG and MT approach shows that some species genes are highly represented in the MT than in the MG, indicating that some species are highly metabolically active. Our analysis also shows that ~52% of the genes in the metagenome are in the metatranscriptome and therefore are robustly expressed. The functions of the low and rare abundance bacterial species remain poorly understood. Our observations indicate that among the low abundant species analyzed in this study some were found to be more metabolically active compared to others, and can contribute distinct profiles of biological functions that may modulate the host-microbiota and bacteria-bacteria interactions.}, } @article {pmid30584255, year = {2018}, author = {Li, Y and Guo, Y and Wen, Z and Jiang, X and Ma, X and Han, X}, title = {Weaning Stress Perturbs Gut Microbiome and Its Metabolic Profile in Piglets.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {18068}, pmid = {30584255}, issn = {2045-2322}, mesh = {Animals ; *Gastrointestinal Microbiome ; Metabolome ; Metagenome ; Stress, Psychological/*microbiology ; Swine ; *Weaning ; }, abstract = {Weaned piglets are vulnerable to nutritional, physiological, and psychological stressors, leading to abrupt taxonomic and functional shifts in the intestinal microbiome. In this study, an integrated approach combination of 16S rDNA gene sequencing and the mass spectrometry-based metabolomics techniques was used to investigate the effects of weaning stress on intestinal microbial composition and its metabolic profiles of piglets. Three litters of suckling piglets with same parity were chosen. The samples of colonic contents were collected from each selected piglets (weaned day, 3 days after weaned) for microbial and metabolomics analysis. The results showed that Lachnospiraceae, Negativicutes, Selenomonadales, Campylobacterales and other 15 species increased after weaning, while Porphyromonadaceace, Alloprevotella, Barnesiella and Oscillibacter decreased. Based on the function profiles prediction and metabolomic analysis, five key metabolic pathways including Phenylalanine metabolism, Citrate cycle (TCA cycle), Glycolysis or Gluconeogenesis, Propanoate metabolism, Nicotinate and nicotinamide metabolism might be the relevant pathways involved in weaning stress-induced gut microbiota dysbiosis. Taken together, these results indicated that weaning stress not only changed microbial composition and function but altered the microbial metabolic profiles in the intestine, which might provide a new insight in alleviating weaning stress and facilitating disease prevention during the period of weaning in piglets.}, } @article {pmid30584235, year = {2018}, author = {Piredda, R and Claverie, JM and Decelle, J and de Vargas, C and Dunthorn, M and Edvardsen, B and Eikrem, W and Forster, D and Kooistra, WHCF and Logares, R and Massana, R and Montresor, M and Not, F and Ogata, H and Pawlowski, J and Romac, S and Sarno, D and Stoeck, T and Zingone, A}, title = {Diatom diversity through HTS-metabarcoding in coastal European seas.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {18059}, pmid = {30584235}, issn = {2045-2322}, mesh = {*Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Protozoan/chemistry/*genetics ; Diatoms/classification/*genetics ; Metagenome ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal/genetics ; }, abstract = {Diatoms constitute a diverse lineage of unicellular organisms abundant and ecologically important in aquatic ecosystems. Compared to other protists, their biology and taxonomy are well-studied, offering the opportunity to combine traditional approaches and new technologies. We examined a dataset of diatom 18S rRNA- and rDNA- (V4 region) reads from different plankton size-fractions and sediments from six European coastal marine sites, with the aim of identifying peculiarities and commonalities with respect to the whole protistan community. Almost all metabarcodes (99.6%) were assigned to known genera (121) and species (236), the most abundant of which were those already known from classic studies and coincided with those seen in light microscopy. rDNA and rRNA showed comparable patterns for the dominant taxa, but rRNA revealed a much higher diversity particularly in the sediment communities. Peculiar to diatoms is a tight bentho-pelagic coupling, with many benthic or planktonic species colonizing both water column and sediments and the dominance of planktonic species in both habitats. Overall metabarcoding results reflected the marked specificity of diatoms compared to other protistan groups in terms of morphological and ecological characteristics, at the same time confirming their great potential in the description of protist communities.}, } @article {pmid30584008, year = {2019}, author = {Liu, X and Shao, L and Liu, X and Ji, F and Mei, Y and Cheng, Y and Liu, F and Yan, C and Li, L and Ling, Z}, title = {Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer.}, journal = {EBioMedicine}, volume = {40}, number = {}, pages = {336-348}, pmid = {30584008}, issn = {2352-3964}, mesh = {Aged ; Biodiversity ; Cohort Studies ; Combined Modality Therapy ; Computational Biology/methods ; Dysbiosis ; Female ; Gastric Mucosa/*microbiology/pathology ; Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Neoplasm Grading ; Neoplasm Staging ; RNA, Ribosomal, 16S ; Stomach Neoplasms/*etiology/pathology/therapy ; }, abstract = {BACKGROUND: As part of the tumor microenvironment, the gastric microbiota play vital roles in tumor initiation, progression and metastasis, but stomach microhabitats are not always uniform. We aimed to characterize differences of gastric microbiota in stomach microhabitats associated with gastric cancer (GC) development.

METHODS: A cohort of 276 GC patients without preoperative chemotherapy was enrolled retrospectively, and 230 normal, 247 peritumoral and 229 tumoral tissues were obtained for gastric microbiota analysis targeting the 16S rRNA gene by MiSeq sequencing. The microbial diversity and composition, bacterial co-occurrence correlations and predictive functional profiles were compared across different microhabitats.

FINDINGS: GC-specific stomach microhabitats, not GC stages or types, determine the composition and diversity of the gastric microbiota. Most notably, bacterial richness was decreased in peritumoral and tumoral microhabitats, and the correlation network of abundant gastric bacteria was simplified in tumoral microhabitat. Helicobacter pylori (HP), Prevotella copri and Bacteroides uniformis were significantly decreased, whereas Prevotella melaninogenica, Streptococcus anginosus and Propionibacterium acnes were increased in tumoral microhabitat. Higher HP colonisation influenced the overall structure of the gastric microbiota in normal and peritumoral microhabitats. PiCRUSt analysis revealed that genes associated with nucleotide transport and metabolism and amino acid transport and metabolism were significantly enriched in tumoral microbiota, while gastric acid secretion was significantly higher in HP positive group of the tumoral microbiota.

INTERPRETATION: Our present study provided new insights into the roles of gastric microbiota in different stomach microhabitats in gastric carcinogenesis, especially the pathogenesis of HP. FUND: National Natural Science Foundation of China.}, } @article {pmid30582999, year = {2019}, author = {Snowdon, RJ and Schiessl, S}, title = {Illuminating Crop Adaptation Using Population Genomics.}, journal = {Molecular plant}, volume = {12}, number = {1}, pages = {27-29}, doi = {10.1016/j.molp.2018.12.014}, pmid = {30582999}, issn = {1752-9867}, mesh = {Adaptation, Physiological/genetics ; Brassica rapa/*genetics ; Ecotype ; Genome ; Genomics ; Metagenomics ; }, } @article {pmid30582346, year = {2020}, author = {Rizo, J and Guillén, D and Farrés, A and Díaz-Ruiz, G and Sánchez, S and Wacher, C and Rodríguez-Sanoja, R}, title = {Omics in traditional vegetable fermented foods and beverages.}, journal = {Critical reviews in food science and nutrition}, volume = {60}, number = {5}, pages = {791-809}, doi = {10.1080/10408398.2018.1551189}, pmid = {30582346}, issn = {1549-7852}, mesh = {Beverages/*microbiology ; Fermentation ; Fermented Foods/*microbiology ; *Food Analysis ; *Microbiota ; Vegetables/*microbiology ; }, abstract = {For a long time, food microbiota has been studied using traditional microbiological techniques. With the arrival of molecular or culture-independent techniques, a strong understanding of microbiota dynamics has been achieved. However, analyzing the functional role of microbial communities is not an easy task. The application of omics sciences to the study of fermented foods would provide the metabolic and functional understanding of the microbial communities and their impact on the fermented product, including the molecules that define its aroma and flavor, as well as its nutritional properties. Until now, most omics studies have focused on commercial fermented products, such as cheese, wine, bread and beer, but traditional fermented foods have been neglected. Therefore, the information that allows to relate the present microbiota in the food and its properties remains limited. In this review, reports on the applications of omics in the study of traditional fermented foods and beverages are reviewed to propose new ways to analyze the fermentation phenomena.}, } @article {pmid30581850, year = {2018}, author = {Chen, WP and Chang, SH and Tang, CY and Liou, ML and Tsai, SJ and Lin, YL}, title = {Composition Analysis and Feature Selection of the Oral Microbiota Associated with Periodontal Disease.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {3130607}, pmid = {30581850}, issn = {2314-6141}, mesh = {Bacteria/*genetics ; Chronic Periodontitis/*microbiology ; Gingiva/*microbiology ; Humans ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Tooth/microbiology ; }, abstract = {Periodontitis is an inflammatory disease involving complex interactions between oral microorganisms and the host immune response. Understanding the structure of the microbiota community associated with periodontitis is essential for improving classifications and diagnoses of various types of periodontal diseases and will facilitate clinical decision-making. In this study, we used a 16S rRNA metagenomics approach to investigate and compare the compositions of the microbiota communities from 76 subgingival plagues samples, including 26 from healthy individuals and 50 from patients with periodontitis. Furthermore, we propose a novel feature selection algorithm for selecting features with more information from many variables with a combination of these features and machine learning methods were used to construct prediction models for predicting the health status of patients with periodontal disease. We identified a total of 12 phyla, 124 genera, and 355 species and observed differences between health- and periodontitis-associated bacterial communities at all phylogenetic levels. We discovered that the genera Porphyromonas, Treponema, Tannerella, Filifactor, and Aggregatibacter were more abundant in patients with periodontal disease, whereas Streptococcus, Haemophilus, Capnocytophaga, Gemella, Campylobacter, and Granulicatella were found at higher levels in healthy controls. Using our feature selection algorithm, random forests performed better in terms of predictive power than other methods and consumed the least amount of computational time.}, } @article {pmid30581574, year = {2019}, author = {Angelakis, E and Bachar, D and Yasir, M and Musso, D and Djossou, F and Melenotte, C and Robert, C and Davoust, B and Gaborit, B and Azhar, EI and Bibi, F and Dutour, A and Raoult, D}, title = {Comparison of the gut microbiota of obese individuals from different geographic origins.}, journal = {New microbes and new infections}, volume = {27}, number = {}, pages = {40-47}, pmid = {30581574}, issn = {2052-2975}, abstract = {Few studies have examined the interaction of human geography, microbial community structure and obesity. We tested obese adult volunteers from France, Saudi Arabia, French Polynesia and from a traditional population in the village of Trois-Sauts in French Guiana by sequencing the V3-V4 region. We also sequenced homemade fermented cachiri beers that were obtained from the traditional Amazonian population and are highly consumed by this population. We found that French and Saudis had significantly less richness and biodiversity in their gut microbiota than Amazonians and Polynesians (p <0.05). Principle coordinate analysis of the overall composition of the genera communities revealed that the microbiomes of Amazonians clustered independently from the other obese individuals. Moreover, we found that Amazonians presented significantly stricter anaerobic genera than the Saudis, French and Polynesians (p < 0.001). Polynesians presented significantly lower relative abundance of Lactobacillus sp. than French (p 0.01) and Saudis (p 0.05). Treponema berlinense and Treponema succinifaciens were only present in the gut microbiome of Amazonians. The cachiri beers presented significantly more bacterial species in common with the gut microbiome of Amazonians (p < 0.005). Obese individuals with different origins present modifications in their gut microbiota, and we provide evidence that the cachiri beers influenced the gut microbiome of Amazonians.}, } @article {pmid30581271, year = {2018}, author = {Rojas-Feria, M and Romero-García, T and Fernández Caballero-Rico, JÁ and Pastor Ramírez, H and Avilés-Recio, M and Castro-Fernandez, M and Chueca Porcuna, N and Romero-Gόmez, M and García, F and Grande, L and Del Campo, JA}, title = {Modulation of faecal metagenome in Crohn's disease: Role of microRNAs as biomarkers.}, journal = {World journal of gastroenterology}, volume = {24}, number = {46}, pages = {5223-5233}, pmid = {30581271}, issn = {2219-2840}, mesh = {Adolescent ; Adult ; Bacteroidetes/*genetics/isolation & purification ; Biomarkers/analysis ; Colonoscopy ; Crohn Disease/diagnosis/*microbiology/pathology ; Feces/*microbiology ; Female ; Firmicutes/*genetics/isolation & purification ; Gastrointestinal Microbiome/*genetics ; Gene Expression Profiling ; Humans ; Intestinal Mucosa/diagnostic imaging/microbiology/pathology ; Male ; Metagenome ; MicroRNAs/genetics/*isolation & purification ; Middle Aged ; RNA, Ribosomal, 16S/genetics/isolation & purification ; Young Adult ; }, abstract = {BACKGROUND: The gut microbiota plays a key role in the maintenance of intestinal homeostasis and the development and activation of the host immune system. It has been shown that commensal bacterial species can regulate the expression of host genes. 16S rRNA gene sequencing has shown that the microbiota in inflammatory bowel disease (IBD) is abnormal and characterized by reduced diversity. MicroRNAs (miRNAs) have been explored as biomarkers and therapeutic targets, since they are able to regulate specific genes associated with Crohn's disease (CD). In this work, we aim to investigate the composition of gut microbiota of active treatment-naïve adult CD patients, with miRNA profile from gut microbiota.

AIM: To investigate the composition of gut microbiota of active treatment-naïve adult CD patients, with miRNA profile from gut microbiota.

METHODS: Patients attending the outpatient clinics at Valme University Hospital without relevant co-morbidities were matched according to age and gender. Faecal samples of new-onset CD patients, free of treatment, and healthy controls were collected. Faecal samples were homogenized, and DNA was amplified by PCR using primers directed to the 16S bacterial rRNA gene. Pyrosequencing was performed using GS-Junior platform. For sequence analysis, MG-RAST server with the database Ribosomal Project was used. MiRNA profile and their relative abundance were analyzed by quantitative PCR.

RESULTS: Microbial community was characterized using 16S rRNA gene sequencing in 29 samples (n = 13 CD patients, and n = 16 healthy controls). The mean Shannon diversity was higher in the healthy control population compared to CD group (5.5 vs 3.7). A reduction in Firmicutes and an increase in Bacteroidetes were found. Clostridia class was also significantly reduced in CD. Principal components analysis showed a grouping pattern, identified in most of the subjects in both groups, showing a marked difference between control and CD groups. A functional metabolic study showed that a lower metabolism of carbohydrates (P = 0.000) was found in CD group, while the metabolism of lipids was increased. In CD patients, three miRNAs were induced in affected mucosa: mir-144 (6.2 ± 1.3 fold), mir-519 (21.8 ± 3.1) and mir-211 (2.3 ± 0.4).

CONCLUSION: Changes in microbial function in active non-treated CD subjects and three miRNAs in affected vs non-affected mucosa have been found. miRNAs profile may serve as a biomarker.}, } @article {pmid30580413, year = {2019}, author = {Bridier, A}, title = {Exploring Foodborne Pathogen Ecology and Antimicrobial Resistance in the Light of Shotgun Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1918}, number = {}, pages = {229-245}, doi = {10.1007/978-1-4939-9000-9_19}, pmid = {30580413}, issn = {1940-6029}, mesh = {Anti-Infective Agents/pharmacology ; Bacteria/classification/genetics ; Biodiversity ; *Drug Resistance, Microbial ; Food Microbiology ; Food Safety ; Foodborne Diseases/diagnosis/*microbiology ; Genome ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Metagenomics/methods ; Whole Genome Sequencing ; }, abstract = {In this chapter, applications of shotgun metagenomics for taxonomic profiling and functional investigation of food microbial communities with a focus on antimicrobial resistance (AMR) were overviewed in the light of last data in the field. Potentialities of metagenomic approach, along with the challenges encountered for a wider and routinely use in food safety was discussed.}, } @article {pmid30580412, year = {2019}, author = {Feye, KM and Ricke, SC}, title = {Establishment of a Standardized 16S rDNA Library Preparation to Enable Analysis of Microbiome in Poultry Processing Using Illumina MiSeq Platform.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1918}, number = {}, pages = {213-227}, doi = {10.1007/978-1-4939-9000-9_18}, pmid = {30580412}, issn = {1940-6029}, mesh = {Animals ; Data Analysis ; *Gene Library ; High-Throughput Nucleotide Sequencing ; Metagenome ; *Metagenomics/methods ; *Microbiota ; Polymerase Chain Reaction ; Poultry/*microbiology ; Quality Control ; *RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; }, abstract = {The standardization of the microbiome sequencing of poultry rinsates is essential for generating comparable microbial composition data among poultry processing facilities if this technology is to be adopted by the industry. Samples must first be acquired, DNA must be extracted, and libraries must be constructed. In order to proceed to library sequencing, the samples should meet quality control standards. Finally, data must be analyzed using computer bioinformatics pipelines. This data can subsequently be incorporated into more advanced computer algorithms for risk assessment. Ultimately, a uniform sequencing pipeline will enable both the government regulatory agencies and the poultry industry to identify potential weaknesses in food safety. This chapter presents the different steps for monitoring the population dynamics of the microbiome in poultry processing using 16S rDNA sequencing.}, } @article {pmid30579332, year = {2018}, author = {Getachew, B and Aubee, JI and Schottenfeld, RS and Csoka, AB and Thompson, KM and Tizabi, Y}, title = {Ketamine interactions with gut-microbiota in rats: relevance to its antidepressant and anti-inflammatory properties.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {222}, pmid = {30579332}, issn = {1471-2180}, support = {R03 AA022479/AA/NIAAA NIH HHS/United States ; R21 AG047474/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Anti-Inflammatory Agents/*pharmacology ; Antidepressive Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics/isolation & purification ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestines/microbiology ; Ketamine/*pharmacology ; Male ; Rats ; Rats, Wistar ; }, abstract = {BACKGROUND: Appreciable evidence suggest that dysbiosis in microbiota, reflected in gut microbial imbalance plays a key role in the pathogenesis of neuropsychiatric disorders including depression and inflammatory diseases. Recently, the antidepressant properties of ketamine have gained prominence due to its fast and long lasting effects. Additional uses for ketamine in inflammatory disorders such as irritable bowel syndrome have been suggested. However, ketamine's exact mechanism of action and potential effects on microbiome is not known. Here, we examined the effects of low dose ketamine, known to induce antidepressant effects, on stool microbiome profile in adult male Wistar rats. Animals (5/group) were injected intraperitoneally with ketamine (2.5 mg/kg) or saline, daily for 7 days and sacrificed on day 8 when intestinal stools were collected and stored at - 80 °C. DNA was extracted from the samples and the 16 S rRNA gene-based microbiota analysis was performed using 16S Metagenomics application.

RESULTS: At genus-level, ketamine strikingly amplified Lactobacillus, Turicibacter and Sarcina by 3.3, 26 and 42 fold, respectively. Conversely, opportunistic pathogens Mucispirillum and Ruminococcus were reduced by approximately 2.6 and 26 fold, respectively, in ketamine group. Low levels of Lactobacillus and Turicibacter are associated with various disorders including depression and administration of certain species of Lactobacillus ameliorates depressive-like behavior in animal models. Hence, some of the antidepressant effects of ketamine might be mediated through its interaction with these gut bacteria. Additionally, high level of Ruminococcus is positively associated with the severity of irritable bowel syndrome (IBS), and some species of Mucispirillum have been associated with intestinal inflammation. Indirect evidence of anti-inflammatory role of Sarcina has been documented. Hence, some of the anti-inflammatory effects of ketamine and its usefulness in specific inflammatory diseases including IBS may be mediated through its interaction with these latter bacteria.

CONCLUSION: Our data suggest that at least some of the antidepressant and anti-inflammatory effects of daily ketamine treatment for 7 days may be mediated via its interaction with specific gut bacteria. These findings further validate the usefulness of microbiome as a target for therapeutic intervention and call for more detailed investigation of microbiome interaction with central mediators of mood and/or inflammatory disorders.}, } @article {pmid30579193, year = {2019}, author = {Deng, Y and Wang, Y and Xia, Y and Zhang, AN and Zhao, Y and Zhang, T}, title = {Genomic resolution of bacterial populations in saccharin and cyclamate degradation.}, journal = {The Science of the total environment}, volume = {658}, number = {}, pages = {357-366}, doi = {10.1016/j.scitotenv.2018.12.162}, pmid = {30579193}, issn = {1879-1026}, mesh = {Alphaproteobacteria/genetics/isolation & purification/metabolism ; *Biodegradation, Environmental ; Biodiversity ; Cyclamates/*metabolism ; *Genome, Bacterial ; Metagenomics/methods ; Methylobacteriaceae/genetics/isolation & purification/metabolism ; Rhodocyclaceae/genetics/isolation & purification/metabolism ; Saccharin/*metabolism ; Sphingomonadaceae/genetics/isolation & purification/metabolism ; Water Microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The benefits of extensive artificial sweeteners use come at a cost of their ubiquitous occurrence in the aquatic environment. Biodegradation is crucial for the removal of artificial sweeteners in the environment, yet comprehensive characterizations of the degradation consortia that degrade these compounds have not been initiated. Here, we performed metagenomic analysis of microbial communities fulfilling complete mineralization of two typical artificial sweeteners, i.e. saccharin and cyclamate. Genome-resolved metagenomics enabled the recovery and metabolic characterization of total 23 population genomes from 8 phyla in the two consortia, most of which represented novel species. The saccharin-degrading consortia was notably dominated by a betaproteobacterial genome from the family Rhodocyclaceae, accounting for 15.5% of total sequences. For the cyclamate enrichment, 28.1% of the total sequences were assigned to three similarly abundant Alphaproteobacteria population genomes belonging to the family Sphingomonadaceae and Methylobacteriaceae. The metabolic potential of these population genomes were examined to potentially identify the roles of these populations in biodegradation of artificial sweeteners, and focusing on the energy and nutrient metabolisms.}, } @article {pmid30578963, year = {2019}, author = {Piewngam, P and Quiñones, M and Thirakittiwatthana, W and Yungyuen, T and Otto, M and Kiratisin, P}, title = {Composition of the intestinal microbiota in extended-spectrum β-lactamase-producing Enterobacteriaceae carriers and non-carriers in Thailand.}, journal = {International journal of antimicrobial agents}, volume = {53}, number = {4}, pages = {435-441}, pmid = {30578963}, issn = {1872-7913}, support = {Z01 AI000904-07//Intramural NIH HHS/United States ; ZIA AI000904//Intramural NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacteroides/isolation & purification ; Carrier State/microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacteriaceae/*classification/genetics/metabolism ; Enterobacteriaceae Infections/*drug therapy/microbiology ; Farmers/statistics & numerical data ; Gastrointestinal Microbiome/*genetics ; Healthy Volunteers/statistics & numerical data ; Humans ; Intestines/*microbiology ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/genetics ; Thailand ; beta-Lactamases/metabolism ; }, abstract = {There is increasing recognition that the intestinal microbiota govern human well-being and prevent diseases. Intestinal colonization by antibiotic-resistant pathogens, however, can lead to the spread of resistance as well as serious infections. Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) represent particularly dangerous pathogens, which are known to asymptomatically colonize the intestinal tract in the community. Here, we performed a 16S rRNA metagenomics sequence analysis to analyse differences in the microbiota composition between ESBL-E carriers and non-carriers in Thailand, where ESBL-E carriage rates are notoriously high. The most notable difference detected was that the phylum Bacteroidetes, and in particular, the species Bacteroides uniformis, were significantly more abundant in ESBL-E non-carriers than carriers. The Shannon diversity index in non-carriers (5.10 ± 0.69) was also lower than that in ESBL-E carriers (5.39 ± 0.48) without statistical significance (P=0.13). The overall beta diversity difference of the intestinal microbiota of ESBL-E carriers as compared to non-carriers was statistically significant (Adonis on weighted unifrac: R[2]=0.14, P=0.005). Furthermore, ESBL-E carriage was significantly lower in farmers than in those with other occupations. Our findings suggest that a dynamic interaction exists between microbiota diversity and ESBL-E carriage, which is possibly driven by dietary composition and may be exploited using probiotic approaches to control the spread of ESBL-E.}, } @article {pmid30578263, year = {2019}, author = {Wegner, CE and Gaspar, M and Geesink, P and Herrmann, M and Marz, M and Küsel, K}, title = {Biogeochemical Regimes in Shallow Aquifers Reflect the Metabolic Coupling of the Elements Nitrogen, Sulfur, and Carbon.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {5}, pages = {}, pmid = {30578263}, issn = {1098-5336}, mesh = {Ammonium Compounds/metabolism ; Archaea/classification/metabolism ; Bacteria/classification/metabolism ; Bacteroidetes ; Carbon/*metabolism ; Denitrification ; Ecosystem ; Groundwater/*chemistry/*microbiology ; Metagenomics ; Microbiota ; Nitrification ; Nitrogen/*metabolism ; Phylogeny ; Proteobacteria ; Sulfur/*metabolism ; Water Microbiology ; }, abstract = {Near-surface groundwaters are prone to receive (in)organic matter input from their recharge areas and are known to harbor autotrophic microbial communities linked to nitrogen and sulfur metabolism. Here, we use multi-omic profiling to gain holistic insights into the turnover of inorganic nitrogen compounds, carbon fixation processes, and organic matter processing in groundwater. We sampled microbial biomass from two superimposed aquifers via monitoring wells that follow groundwater flow from its recharge area through differences in hydrogeochemical settings and land use. Functional profiling revealed that groundwater microbiomes are mainly driven by nitrogen (nitrification, denitrification, and ammonium oxidation [anammox]) and to a lesser extent sulfur cycling (sulfur oxidation and sulfate reduction), depending on local hydrochemical differences. Surprisingly, the differentiation potential of the groundwater microbiome surpasses that of hydrochemistry for individual monitoring wells. Being dominated by a few phyla (Bacteroidetes, Proteobacteria, Planctomycetes, and Thaumarchaeota), the taxonomic profiling of groundwater metagenomes and metatranscriptomes revealed pronounced differences between merely present microbiome members and those actively participating in community gene expression and biogeochemical cycling. Unexpectedly, we observed a constitutive expression of carbohydrate-active enzymes encoded by different microbiome members, along with the groundwater flow path. The turnover of organic carbon apparently complements for lithoautotrophic carbon assimilation pathways mainly used by the groundwater microbiome depending on the availability of oxygen and inorganic electron donors, like ammonium.IMPORTANCE Groundwater is a key resource for drinking water production and irrigation. The interplay between geological setting, hydrochemistry, carbon storage, and groundwater microbiome ecosystem functioning is crucial for our understanding of these important ecosystem services. We targeted the encoded and expressed metabolic potential of groundwater microbiomes along an aquifer transect that diversifies in terms of hydrochemistry and land use. Our results showed that the groundwater microbiome has a higher spatial differentiation potential than does hydrochemistry.}, } @article {pmid30577803, year = {2018}, author = {Chappell, T and Geva, S and Hogan, JM and Huygens, F and Rathnayake, IU and Rudd, S and Kelly, W and Perrin, D}, title = {Rapid analysis of metagenomic data using signature-based clustering.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 20}, pages = {509}, pmid = {30577803}, issn = {1471-2105}, mesh = {Algorithms ; Cluster Analysis ; *Data Analysis ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; }, abstract = {BACKGROUND: Sequencing highly-variable 16S regions is a common and often effective approach to the study of microbial communities, and next-generation sequencing (NGS) technologies provide abundant quantities of data for analysis. However, the speed of existing analysis pipelines may limit our ability to work with these quantities of data. Furthermore, the limited coverage of existing 16S databases may hamper our ability to characterise these communities, particularly in the context of complex or poorly studied environments.

RESULTS: In this article we present the SigClust algorithm, a novel clustering method involving the transformation of sequence reads into binary signatures. When compared to other published methods, SigClust yields superior cluster coherence and separation of metagenomic read data, while operating within substantially reduced timeframes. We demonstrate its utility on published Illumina datasets and on a large collection of labelled wound reads sourced from patients in a wound clinic. The temporal analysis is based on tracking the dominant clusters of wound samples over time. The analysis can identify markers of both healing and non-healing wounds in response to treatment. Prominent clusters are found, corresponding to bacterial species known to be associated with unfavourable healing outcomes, including a number of strains of Staphylococcus aureus.

CONCLUSIONS: SigClust identifies clusters rapidly and supports an improved understanding of the wound microbiome without reliance on a reference database. The results indicate a promising use for a SigClust-based pipeline in wound analysis and prediction, and a possible novel method for wound management and treatment.}, } @article {pmid30576077, year = {2019}, author = {Jeunen, GJ and Knapp, M and Spencer, HG and Lamare, MD and Taylor, HR and Stat, M and Bunce, M and Gemmell, NJ}, title = {Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement.}, journal = {Molecular ecology resources}, volume = {19}, number = {2}, pages = {426-438}, doi = {10.1111/1755-0998.12982}, pmid = {30576077}, issn = {1755-0998}, mesh = {Aquatic Organisms/*classification/genetics/growth & development ; *Biota ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; DNA, Ribosomal/chemistry/genetics ; *Ecosystem ; Electron Transport Complex IV/genetics ; Eukaryota/*classification/genetics/growth & development ; *Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Movements ; }, abstract = {While in recent years environmental DNA (eDNA) metabarcoding surveys have shown great promise as an alternative monitoring method, the integration into existing marine monitoring programs may be confounded by the dispersal of the eDNA signal. Currents and tidal influences could transport eDNA over great distances, inducing false-positive species detection, leading to inaccurate biodiversity assessments and, ultimately, mismanagement of marine environments. In this study, we determined the ability of eDNA metabarcoding surveys to distinguish localized signals obtained from four marine habitats within a small spatial scale (<5 km) subject to significant tidal and along-shore water flow. Our eDNA metabarcoding survey detected 86 genera, within 77 families and across 11 phyla using three established metabarcoding assays targeting fish (16S rRNA gene), crustacean (16S rRNA gene) and eukaryotic (cytochrome oxidase subunit 1) diversity. Ordination and cluster analyses for both taxonomic and OTU data sets show distinct eDNA signals between the sampled habitats, suggesting dispersal of eDNA among habitats was limited. Individual taxa with strong habitat preferences displayed localized eDNA signals in accordance with their respective habitat, whereas taxa known to be less habitat-specific generated more ubiquitous signals. Our data add to evidence that eDNA metabarcoding surveys in marine environments detect a broad range of taxa that are spatially discrete. Our work also highlights that refinement of assay choice is essential to realize the full potential of eDNA metabarcoding surveys in marine biodiversity monitoring programs.}, } @article {pmid30574802, year = {2019}, author = {Murphy, R and Morgan, XC and Wang, XY and Wickens, K and Purdie, G and Fitzharris, P and Otal, A and Lawley, B and Stanley, T and Barthow, C and Crane, J and Mitchell, EA and Tannock, GW}, title = {Eczema-protective probiotic alters infant gut microbiome functional capacity but not composition: sub-sample analysis from a RCT.}, journal = {Beneficial microbes}, volume = {10}, number = {1}, pages = {5-17}, doi = {10.3920/BM2017.0191}, pmid = {30574802}, issn = {1876-2891}, mesh = {Adult ; Age Factors ; Biological Transport ; Breast Feeding ; Child, Preschool ; Dermatitis, Atopic/microbiology/*prevention & control ; Dietary Supplements ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Glycerophosphates/metabolism ; Humans ; Infant ; Infant, Newborn ; Lacticaseibacillus rhamnosus/*physiology ; Metagenomics ; Mothers ; Postpartum Period ; *Probiotics ; }, abstract = {Probiotic Lactobacillus rhamnosus HN001 given in early life has been shown to reduce infant eczema risk, but its effect on gut microbiota development has not been quantitatively and functionally examined. The aim of this study was to investigate the impact of early life probiotic exposure on the composition and functional capacity of infant gut microbiota from birth to 2 years considering the effects of age, delivery mode, antibiotics, pets and eczema. We performed shotgun metagenomic sequencing analysis of 650 infant faecal samples, collected at birth, 3, 12, and 24 months, as part of a randomised, controlled, 3-arm trial assessing the effect of L. rhamnosus HN001, Bifidobacterium animalis subsp. lactis HN019 supplementation on eczema development in 474 infants. There was a 50% reduced eczema risk in the HN001 probiotic group compared to placebo. Both mothers (from 35 weeks gestation until 6 months post-partum if breastfeeding) and infants (from birth to 2 years) received either a placebo or one of two probiotics, L. rhamnosus HN001 (6×10[9] cfu), or B. animalis subsp. lactis HN019 (9×10[9] cfu). L. rhamnosus HN001 probiotic supplementation was associated with increased overall glycerol-3 phosphate transport capacity and enrichment of L. rhamnosus. There were no other significant changes in infant gut microbiota composition or diversity. Increased capacity to transport glycerol-3-phosphate was positively correlated with relative abundance of L. rhamnosus. Children who developed eczema had gut microbiota with increased capacity for glycosaminoglycan degradation and flagellum assembly but had no significant differences in microbiota composition or diversity. Early life HN001 probiotic use is associated with both increased L. rhamnosus and increased infant gut microbiota functional capacity to transport glycerol-3 phosphate. The mechanistic relationship of such functional alteration in gut microbiota with reduced eczema risk and long-term health merits further investigation.}, } @article {pmid30572101, year = {2019}, author = {Wang, S and Li, N and Zou, H and Wu, M}, title = {Gut microbiome-based secondary metabolite biosynthetic gene clusters detection in Parkinson's disease.}, journal = {Neuroscience letters}, volume = {696}, number = {}, pages = {93-98}, doi = {10.1016/j.neulet.2018.12.021}, pmid = {30572101}, issn = {1872-7972}, mesh = {Brain/pathology ; Case-Control Studies ; Feces ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/metabolism/*microbiology ; Humans ; Multigene Family/*genetics ; Parkinson Disease/*genetics ; }, abstract = {The microbiota of individuals with Parkinson's disease (PD) has been the focus of research in recent years. However, the mechanisms underlying the interactions between the gut microbiome and the brain, as well as its role in PD pathogenesis, remain to be elucidated. In this study, we used a systematic approach to predict putative biosynthetic gene clusters (BGCs) from the raw metagenomic data of the gut microbiome, and identified 43 BGCs that were significantly enriched in the PD patients. Fourteen of these clusters originated from microbes that were not increased in the patients, and the most significantly enriched one encoded a putative efflux protein and a radical SAM protein, indicating a potential role in PD. Based on a random forest classifier, these BGCs can be used to correctly discriminate between PD patients and healthy controls, with a cross-validated AUC of 0.91 from the 31 early stage PD patients and 28 healthy controls. Our study provides an alternative method to analyze the microbiota of PD patients, and further increase our understanding of this disease.}, } @article {pmid30567928, year = {2018}, author = {Vich Vila, A and Imhann, F and Collij, V and Jankipersadsing, SA and Gurry, T and Mujagic, Z and Kurilshikov, A and Bonder, MJ and Jiang, X and Tigchelaar, EF and Dekens, J and Peters, V and Voskuil, MD and Visschedijk, MC and van Dullemen, HM and Keszthelyi, D and Swertz, MA and Franke, L and Alberts, R and Festen, EAM and Dijkstra, G and Masclee, AAM and Hofker, MH and Xavier, RJ and Alm, EJ and Fu, J and Wijmenga, C and Jonkers, DMAE and Zhernakova, A and Weersma, RK}, title = {Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome.}, journal = {Science translational medicine}, volume = {10}, number = {472}, pages = {}, doi = {10.1126/scitranslmed.aap8914}, pmid = {30567928}, issn = {1946-6242}, mesh = {Bacteria/growth & development/pathogenicity ; Biodiversity ; Case-Control Studies ; Drug Resistance, Microbial ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Irritable Bowel Syndrome/*microbiology ; Metagenome ; Models, Biological ; Phenotype ; Principal Component Analysis ; ROC Curve ; Species Specificity ; Virulence ; }, abstract = {Changes in the gut microbiota have been associated with two of the most common gastrointestinal diseases, inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). Here, we performed a case-control analysis using shotgun metagenomic sequencing of stool samples from 1792 individuals with IBD and IBS compared with control individuals in the general population. Despite substantial overlap between the gut microbiome of patients with IBD and IBS compared with control individuals, we were able to use gut microbiota composition differences to distinguish patients with IBD from those with IBS. By combining species-level profiles and strain-level profiles with bacterial growth rates, metabolic functions, antibiotic resistance, and virulence factor analyses, we identified key bacterial species that may be involved in two common gastrointestinal diseases.}, } @article {pmid30565880, year = {2019}, author = {Thorn, CE and Bergesch, C and Joyce, A and Sambrano, G and McDonnell, K and Brennan, F and Heyer, R and Benndorf, D and Abram, F}, title = {A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes and pure cultures.}, journal = {Molecular ecology resources}, volume = {19}, number = {2}, pages = {439-455}, doi = {10.1111/1755-0998.12979}, pmid = {30565880}, issn = {1755-0998}, support = {//NUI Galway/ ; }, mesh = {Cost-Benefit Analysis ; DNA/genetics/*isolation & purification ; Metagenomics/economics/*methods ; *Microbiota ; Proteins/analysis/*isolation & purification ; Proteomics/economics/*methods ; RNA/genetics/*isolation & purification ; *Soil Microbiology ; }, abstract = {The soil microbiome is inherently complex with high biological diversity, and spatial heterogeneity typically occurring on the submillimetre scale. To study the microbial ecology of soils, and other microbiomes, biomolecules, that is, nucleic acids and proteins, must be efficiently and reliably co-recovered from the same biological samples. Commercial kits are currently available for the co-extraction of DNA, RNA and proteins but none has been developed for soil samples. We present a new protocol drawing on existing phenol-chloroform-based methods for nucleic acids co-extraction but incorporating targeted precipitation of proteins from the phenol phase. The protocol is cost-effective and robust, and easily implemented using reagents commonly available in laboratories. The method is estimated to be eight times cheaper than using disparate commercial kits for the isolation of DNA and/or RNA, and proteins, from soil. The method is effective, providing good quality biomolecules from a diverse range of soil types, with clay contents varying from 9.5% to 35.1%, which we successfully used for downstream, high-throughput gene sequencing and metaproteomics. Additionally, we demonstrate that the protocol can also be easily implemented for biomolecule co-extraction from other complex microbiome samples, including cattle slurry and microbial communities recovered from anaerobic bioreactors, as well as from Gram-positive and Gram-negative pure cultures.}, } @article {pmid30565165, year = {2019}, author = {Serena, G and Fasano, A}, title = {Use of Probiotics to Prevent Celiac Disease and IBD in Pediatrics.}, journal = {Advances in experimental medicine and biology}, volume = {1125}, number = {}, pages = {69-81}, doi = {10.1007/5584_2018_317}, pmid = {30565165}, issn = {0065-2598}, support = {R01 DK104344/DK/NIDDK NIH HHS/United States ; }, mesh = {Celiac Disease/*prevention & control ; Child ; Dysbiosis/complications ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*prevention & control ; Pediatrics ; Probiotics/*therapeutic use ; }, abstract = {The incidence of chronic inflammatory diseases (CIDs) is increasing worldwide. Their dramatic rise associated with limited effective strategies to slow down these epidemics calls for a better understanding of their pathophysiology in order to decrease the burdens on childhood. Several cross-sectional studies have demonstrated the association between intestinal dysbiosis and active diseases. Although informative, these studies do not mechanistically link alterations of the microflora with disease pathogenesis and, therefore, with potential therapeutic targets. More prospective studies are needed to determine whether intestinal dysbiosis plays a causative role in the onset and development of CIDs. Furthermore, given the complexity of the microflora interaction with the host, it is necessary to design a systems-level model of interactions between the host and the development of disease by integrating microbiome, metagenomics, metatranscriptomics, and metabolomics with either clinical either environmental data.In this chapter we will discuss the current knowledge regarding the microbiome's contribution to celiac disease and inflammatory bowel disease with a particular focus on how probiotics may be used as potential preventive therapy for CIDs.}, } @article {pmid30562947, year = {2018}, author = {Ishii, C and Nakanishi, Y and Murakami, S and Nozu, R and Ueno, M and Hioki, K and Aw, W and Hirayama, A and Soga, T and Ito, M and Tomita, M and Fukuda, S}, title = {A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet.}, journal = {International journal of molecular sciences}, volume = {19}, number = {12}, pages = {}, pmid = {30562947}, issn = {1422-0067}, support = {15H01522//Japan Society for the Promotion of Science/ ; 16H04901//Japan Society for the Promotion of Science/ ; 17H05654//Japan Society for the Promotion of Science/ ; 18H04805//Japan Society for the Promotion of Science/ ; JPMJPR1537//Japan Science and Technology Agency/ ; }, mesh = {Animals ; *Diet ; *Gastrointestinal Microbiome ; Humans ; Male ; *Metabolome ; *Metagenomics ; Mice ; *Ruminococcus/genetics/growth & development ; }, abstract = {Intestinal microbiota and their metabolites are strongly associated with host physiology. Developments in DNA sequencing and mass spectrometry technologies have allowed us to obtain additional data that enhance our understanding of the interactions among microbiota, metabolites, and the host. However, the strategies used to analyze these datasets are not yet well developed. Here, we describe an original analytical strategy, metabologenomics, consisting of an integrated analysis of mass spectrometry-based metabolome data and high-throughput-sequencing-based microbiome data. Using this approach, we compared data obtained from C57BL/6J mice fed an American diet (AD), which contained higher amounts of fat and fiber, to those from mice fed control rodent diet. The feces of the AD mice contained higher amounts of butyrate and propionate, and higher relative abundances of Oscillospira and Ruminococcus. The amount of butyrate positively correlated with the abundance of these bacterial genera. Furthermore, integrated analysis of the metabolome data and the predicted metagenomic data from Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) indicated that the abundance of genes associated with butyrate metabolism positively correlated with butyrate amounts. Thus, our metabologenomic approach is expected to provide new insights and understanding of intestinal metabolic dynamics in complex microbial ecosystems.}, } @article {pmid30562162, year = {2018}, author = {Peng, W and Yi, P and Yang, J and Xu, P and Wang, Y and Zhang, Z and Huang, S and Wang, Z and Zhang, C}, title = {Association of gut microbiota composition and function with a senescence-accelerated mouse model of Alzheimer's Disease using 16S rRNA gene and metagenomic sequencing analysis.}, journal = {Aging}, volume = {10}, number = {12}, pages = {4054-4065}, pmid = {30562162}, issn = {1945-4589}, mesh = {Aging ; Alzheimer Disease ; Animals ; *Disease Models, Animal ; Gastrointestinal Microbiome/*genetics ; Male ; Metagenomics ; Mice ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Although an intriguing potential association of the gut microbiome with Alzheimer's disease (AD) has attracted recent interest, few studies have directly assessed this relationship or underlying mechanism. Here, we compared the gut microbiota composition and functional differentiation of senescence-accelerated mouse prone 8 (SAMP8) mice with control senescence-accelerated mouse resistant 1 (SAMR1) mice using 16S rRNA gene and metagenomic sequencing analysis, respectively. Specifically, 16S sequencing results showed that the SAMP8 mice displayed a characteristic composition of the gut microbiome that clearly differed from that of the SAMR1 mice. Moreover, network analysis revealed that the gut microbiota of SAMP8 mice had decreased correlation density and clustering of operational taxonomic units. Metagenomic results revealed that the predominant Cluster of Orthologous Groups functional category related to these changes was the metabolism cluster in SAMP8 mice. The Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation further demonstrated enrichment of the relative abundance of some dominant metabolism-related KEGG pathways in the SAMP8 mice, consistent with the suggested pathogenic mechanisms of AD. In conclusion, this study suggests that perturbations of the gut microbiota composition and the functional metagenome may be associated with AD. Further studies are warranted to elucidate the potential new mechanism contributing to AD progression.}, } @article {pmid30561396, year = {2018}, author = {Ticinesi, A and Nouvenne, A and Tana, C and Prati, B and Cerundolo, N and Miraglia, C and De' Angelis, GL and Di Mario, F and Meschi, T}, title = {The impact of intestinal microbiota on bio-medical research: definitions, techniques and physiology of a "new frontier".}, journal = {Acta bio-medica : Atenei Parmensis}, volume = {89}, number = {9-S}, pages = {52-59}, pmid = {30561396}, issn = {2531-6745}, mesh = {Adult ; Aged ; Aging ; Bacteria/genetics/isolation & purification ; DNA, Bacterial/genetics ; Diet ; Exercise ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics/physiology ; High-Throughput Nucleotide Sequencing ; Homeostasis ; Humans ; *Metagenomics/trends ; Research ; Ribotyping ; }, abstract = {In recent years the metagenomics techniques have allowed to study composition and function of the intestinal microbiota. The microbiota is a new frontier of biomedical research to be explored and there is growing evidence of its fundamental health-promoting activity. The present review gives a synthetic overview on the characteristics and the role of the microbiota in the adult with particular reference to physiology, pathophysiology and relationships with the host and the environment.}, } @article {pmid30561093, year = {2019}, author = {Cherkasov, SV and Popova, LY and Vivtanenko, TV and Demina, RR and Khlopko, YA and Balkin, AS and Plotnikov, AO}, title = {Oral microbiomes in children with asthma and dental caries.}, journal = {Oral diseases}, volume = {25}, number = {3}, pages = {898-910}, doi = {10.1111/odi.13020}, pmid = {30561093}, issn = {1601-0825}, support = {18-7-8-26//Basic Research Program from the Ural Branch of the Russian Academy of Sciences/ ; }, mesh = {Asthma/*complications/microbiology ; Case-Control Studies ; Child, Preschool ; Computational Biology ; Dental Caries/*complications/microbiology ; Dental Plaque/*microbiology ; Female ; Humans ; Male ; *Microbiota ; Neisseria/isolation & purification ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, RNA ; Veillonella/isolation & purification ; }, abstract = {OBJECTIVE: Recently, a significant association between dental caries and the severity of bronchial asthma in children has been revealed. This finding indicates a possible relationship between the oral microbiome and the pathogenesis of asthma. The purpose of our study was to estimate differences in the dental plaque microbiota of asthmatic children with and without dental caries by 16S rDNA sequencing.

MATERIAL AND METHODS: Dental plaque samples were obtained with a spoon excavator from the occlusal surface of one deciduous tooth (the second mandibular left molar in caries-free children and the most affected tooth in caries-affected children). Total DNA was extracted from dental plaque. DNA libraries were analysed by 16S rRNA gene sequencing on the MiSeq (Illumina) platform.

RESULTS: There were no significant differences in the composition of bacterial communities from both caries-affected and caries-free children with asthma. The "caries-enriched" genus was Veillonella (Veillonellaceae, Selenomonadales, Negativicutes). Relative abundance of Neisseria was significantly higher in caries-free children with asthma (p < 0.05).

CONCLUSIONS: The most significant difference in compared bacterial communities was a higher relative abundance of Veillonella in caries-affected plaques that suggests its involvement in pathogenesis of caries. Potential respiratory pathogens are present in oral cavity of both caries-affected and caries-free asthmatic children.}, } @article {pmid30559737, year = {2018}, author = {Gong, Z and Liang, Y and Wang, M and Jiang, Y and Yang, Q and Xia, J and Zhou, X and You, S and Gao, C and Wang, J and He, J and Shao, H and McMinn, A}, title = {Viral Diversity and Its Relationship With Environmental Factors at the Surface and Deep Sea of Prydz Bay, Antarctica.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2981}, pmid = {30559737}, issn = {1664-302X}, abstract = {A viral metagenomic analysis of five surface and two bottom water (878 meters below surface, mbs, and 3,357 mbs) samples from Prydz Bay, was conducted during February-March 2015. The results demonstrated that most of the DNA viruses were dsDNA viruses (79.73-94.06%, except at PBI1, 37.51%). Of these, Caudovirales (Siphoviridae, Myoviridae, and Podoviridae) phages were most abundant in surface seawater (67.67-71.99%), while nucleocytoplasmic large DNA viruses (NCLDVs) (Phycodnaviridae, Mimiviridae, and Pandoraviridae accounted for >30% of dsDNA viruses) were most abundant in the bottom water (3,357 mbs). Of the ssDNA viruses, Microviridae was the dominant family in PBI2, PBI3, PBOs, and PBI4b (57.09-87.55%), while Inoviridae (58.16%) was the dominant family in PBI1. Cellulophaga phages (phi38:1 and phi10:1) and Flavobacterium phage 11b, infecting the possible host strains affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes, were abundant in surface water dsDNA viromes. The long contig (PBI2_1_C) from the viral metagenomes were most similar to the genome architectures of Cellulophaga phage phi10:1 and Flavobacterium phage 11b from the Arctic Ocean. Comparative analysis showed that the surface viral community of Prydz Bay could be clearly separated from other marine and freshwater environments. The deep sea viral community was similar to the deep sea viral metagenome at A Long-term Oligotrophic Habitat Assessment Station (ALOHA, at 22°45'N, 158°00'W). The multivariable analysis indicated that nutrients probably played an important role in shaping the local viral community structure. This study revealed the preliminary characteristics of the viral community in Prydz Bay, from both the surface and the deep sea. It provided evidence of the relationships between the virome and the environment in Prydz Bay and provided the first data from the deep sea viral community of the Southern Ocean.}, } @article {pmid30559407, year = {2019}, author = {Vatanen, T and Plichta, DR and Somani, J and Münch, PC and Arthur, TD and Hall, AB and Rudolf, S and Oakeley, EJ and Ke, X and Young, RA and Haiser, HJ and Kolde, R and Yassour, M and Luopajärvi, K and Siljander, H and Virtanen, SM and Ilonen, J and Uibo, R and Tillmann, V and Mokurov, S and Dorshakova, N and Porter, JA and McHardy, AC and Lähdesmäki, H and Vlamakis, H and Huttenhower, C and Knip, M and Xavier, RJ}, title = {Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.}, journal = {Nature microbiology}, volume = {4}, number = {3}, pages = {470-479}, pmid = {30559407}, issn = {2058-5276}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; UM1 AI110498/AI/NIAID NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Age Factors ; Bacteriophages/genetics ; Bacteroides/genetics/virology ; Bifidobacterium bifidum/genetics ; Bifidobacterium longum/genetics ; Child Development ; Child, Preschool ; Estonia ; Feces/microbiology ; Female ; Finland ; Gastrointestinal Microbiome/*genetics ; *Genetic Variation ; *Genome, Bacterial ; Humans ; Infant ; Longitudinal Studies ; Male ; Metabolic Networks and Pathways ; Metagenomics ; Polymorphism, Single Nucleotide ; Probiotics ; Russia ; }, abstract = {The human gut microbiome matures towards the adult composition during the first years of life and is implicated in early immune development. Here, we investigate the effects of microbial genomic diversity on gut microbiome development using integrated early childhood data sets collected in the DIABIMMUNE study in Finland, Estonia and Russian Karelia. We show that gut microbial diversity is associated with household location and linear growth of children. Single nucleotide polymorphism- and metagenomic assembly-based strain tracking revealed large and highly dynamic microbial pangenomes, especially in the genus Bacteroides, in which we identified evidence of variability deriving from Bacteroides-targeting bacteriophages. Our analyses revealed functional consequences of strain diversity; only 10% of Finnish infants harboured Bifidobacterium longum subsp. infantis, a subspecies specialized in human milk metabolism, whereas Russian infants commonly maintained a probiotic Bifidobacterium bifidum strain in infancy. Groups of bacteria contributing to diverse, characterized metabolic pathways converged to highly subject-specific configurations over the first two years of life. This longitudinal study extends the current view of early gut microbial community assembly based on strain-level genomic variation.}, } @article {pmid30559406, year = {2019}, author = {Kintses, B and Méhi, O and Ari, E and Számel, M and Györkei, Á and Jangir, PK and Nagy, I and Pál, F and Fekete, G and Tengölics, R and Nyerges, Á and Likó, I and Bálint, A and Molnár, T and Bálint, B and Vásárhelyi, BM and Bustamante, M and Papp, B and Pál, C}, title = {Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota.}, journal = {Nature microbiology}, volume = {4}, number = {3}, pages = {447-458}, pmid = {30559406}, issn = {2058-5276}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Antimicrobial Cationic Peptides/*genetics ; Bacteria/*genetics ; Escherichia coli/genetics ; Gastrointestinal Microbiome/*genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Humans ; Metagenomics ; *Phylogeny ; }, abstract = {The human gut microbiota has adapted to the presence of antimicrobial peptides (AMPs), which are ancient components of immune defence. Despite its medical importance, it has remained unclear whether AMP resistance genes in the gut microbiome are available for genetic exchange between bacterial species. Here, we show that AMP resistance and antibiotic resistance genes differ in their mobilization patterns and functional compatibilities with new bacterial hosts. First, whereas AMP resistance genes are widespread in the gut microbiome, their rate of horizontal transfer is lower than that of antibiotic resistance genes. Second, gut microbiota culturing and functional metagenomics have revealed that AMP resistance genes originating from phylogenetically distant bacteria have only a limited potential to confer resistance in Escherichia coli, an intrinsically susceptible species. Taken together, functional compatibility with the new bacterial host emerges as a key factor limiting the genetic exchange of AMP resistance genes. Finally, our results suggest that AMPs induce highly specific changes in the composition of the human microbiota, with implications for disease risks.}, } @article {pmid30559036, year = {2019}, author = {Freitas, RC and Marques, HIF and Silva, MACD and Cavalett, A and Odisi, EJ and Silva, BLD and Montemor, JE and Toyofuku, T and Kato, C and Fujikura, K and Kitazato, H and Lima, AOS}, title = {Evidence of selective pressure in whale fall microbiome proteins and its potential application to industry.}, journal = {Marine genomics}, volume = {45}, number = {}, pages = {21-27}, doi = {10.1016/j.margen.2018.11.004}, pmid = {30559036}, issn = {1876-7478}, mesh = {Animals ; Atlantic Ocean ; Bacterial Proteins/*genetics/metabolism ; *Metagenome ; *Microbiota ; *Selection, Genetic ; Whales/*microbiology ; }, abstract = {The present study addresses the microbiome of the first whale fall (YOKO 16) that has been described in the deep sea in the southern Atlantic Ocean (São Paulo Plateau; 4204 m depth), in terms of its metabolic uniqueness. Sets of ten thousand protein sequences from YOKO 16 and 29 public domain metagenomes (SRA and GenBank databases) that represent various marine, terrestrial and gut-associated microbial communities were analyzed. The determination of protein functionality, based on the KAAS server, indicated that the YOKO 16 microbiome has industrially-relevant proteins, such as proteases and lipases, that have low similarity (~50%) with previously-described enzymes. The amino acid usage in the YOKO 16 protein sequences (based on blastp and Clustal analysis) revealed a pattern of preference similar to that of extremophiles, with an increased usage of polar, charged and acidic amino acids and a decreased usage of nonpolar residues. We concluded that the targeted microbiome is of potential biotechnological use, which justifies the allocation of resources for the discovery of enzymes in deep-sea whale fall communities.}, } @article {pmid30558682, year = {2018}, author = {Sirová, D and Bárta, J and Šimek, K and Posch, T and Pech, J and Stone, J and Borovec, J and Adamec, L and Vrba, J}, title = {Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {225}, pmid = {30558682}, issn = {2049-2618}, mesh = {Aquatic Organisms/microbiology/physiology ; Bacteria/*classification/genetics/isolation & purification ; DNA, Algal/genetics ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; Fungi/*classification/genetics/isolation & purification ; Gene Expression Profiling/methods ; Lamiales/*microbiology/physiology ; Metagenomics/*methods ; Microbial Consortia ; Phylogeny ; }, abstract = {BACKGROUND: Utricularia are rootless aquatic carnivorous plants which have recently attracted the attention of researchers due to the peculiarities of their miniaturized genomes. Here, we focus on a novel aspect of Utricularia ecophysiology-the interactions with and within the complex communities of microorganisms colonizing their traps and external surfaces.

RESULTS: Bacteria, fungi, algae, and protozoa inhabit the miniature ecosystem of the Utricularia trap lumen and are involved in the regeneration of nutrients from complex organic matter. By combining molecular methods, microscopy, and other approaches to assess the trap-associated microbial community structure, diversity, function, as well as the nutrient turn-over potential of bacterivory, we gained insight into the nutrient acquisition strategies of the Utricularia hosts.

CONCLUSIONS: We conclude that Utricularia traps can, in terms of their ecophysiological function, be compared to microbial cultivators or farms, which center around complex microbial consortia acting synergistically to convert complex organic matter, often of algal origin, into a source of utilizable nutrients for the plants.}, } @article {pmid30554770, year = {2019}, author = {Cordier, T and Lanzén, A and Apothéloz-Perret-Gentil, L and Stoeck, T and Pawlowski, J}, title = {Embracing Environmental Genomics and Machine Learning for Routine Biomonitoring.}, journal = {Trends in microbiology}, volume = {27}, number = {5}, pages = {387-397}, doi = {10.1016/j.tim.2018.10.012}, pmid = {30554770}, issn = {1878-4380}, mesh = {Bacteria/*classification ; DNA Barcoding, Taxonomic ; Ecosystem ; Environmental Microbiology ; Environmental Monitoring/*methods ; Genetic Variation ; *Machine Learning ; *Metagenomics ; Microbiota ; }, abstract = {Genomics is fast becoming a routine tool in medical diagnostics and cutting-edge biotechnologies. Yet, its use for environmental biomonitoring is still considered a futuristic ideal. Until now, environmental genomics was mainly used as a replacement of the burdensome morphological identification, to screen known morphologically distinguishable bioindicator taxa. While prokaryotic and eukaryotic microbial diversity is of key importance in ecosystem functioning, its implementation in biomonitoring programs is still largely unappreciated, mainly because of difficulties in identifying microbes and limited knowledge of their ecological functions. Here, we argue that the combination of massive environmental genomics microbial data with machine learning algorithms can be extremely powerful for biomonitoring programs and pave the way to fill important gaps in our understanding of microbial ecology.}, } @article {pmid30554441, year = {2019}, author = {Curtis, K and Stewart, CJ and Robinson, M and Molfese, DL and Gosnell, SN and Kosten, TR and Petrosino, JF and De La Garza, R and Salas, R}, title = {Insular resting state functional connectivity is associated with gut microbiota diversity.}, journal = {The European journal of neuroscience}, volume = {50}, number = {3}, pages = {2446-2452}, pmid = {30554441}, issn = {1460-9568}, support = {//McNair Medical Institute/International ; //Toomim Family Fund/International ; //Pilot Award from the Core for Advanced MR Imaging at Baylor College of Medicine/International ; P30 CA125123/CA/NCI NIH HHS/United States ; 19295//NARSAD/International ; I01 CX000994/CX/CSRD VA/United States ; VHA5I01CX000994//the Veteran Health Administration/International ; R03 DA029167/DA/NIDA NIH HHS/United States ; K01 DA026539/DA/NIDA NIH HHS/United States ; DA09167//National Institute of Health/International ; DA026539//National Institute of Health/International ; 5P30CA0125123/BC/NCI NIH HHS/United States ; }, mesh = {Adult ; Cerebral Cortex/*diagnostic imaging/*physiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Magnetic Resonance Imaging/methods ; Male ; Nerve Net/*diagnostic imaging/*physiology ; Rest/*physiology ; Young Adult ; }, abstract = {The gut microbiota has recently gained attention as a possible modulator of brain activity. A number of reports suggest that the microbiota may be associated with neuropsychiatric conditions such as major depressive disorder, autism and anxiety. The gut microbiota is thought to influence the brain via vagus nerve signalling, among other possible mechanisms. The insula processes and integrates these vagal signals. To determine if microbiota diversity and structure modulate brain activity, we collected faecal samples and examined insular function using resting state functional connectivity (RSFC). Thirty healthy participants (non-smokers, tobacco smokers and electronic cigarette users, n = 10 each) were studied. We found that the RSFC between the insula and several regions (frontal pole left, lateral occipital cortex right, lingual gyrus right and cerebellum 4, 5 and vermis 9) were associated with bacterial microbiota diversity and structure. In addition, two specific bacteria genera, Prevotella and Bacteroides, were specifically different in tobacco smokers and also associated with insular connectivity. In conclusion, we show that insular connectivity is associated with microbiome diversity, structure and at least two specific bateria genera. Furthemore, this association is potentially modulated by tobacco smoking, although the sample sizes for the different smoking groups were small and this result needs validation in a larger cohort. While replication is necessary, the microbiota is a readily accessible therapeutic target for modulating insular connectivity, which has previously been shown to be abnormal in anxiety and tobacco use disorders.}, } @article {pmid30552020, year = {2018}, author = {Castellanos, JG and Woo, V and Viladomiu, M and Putzel, G and Lima, S and Diehl, GE and Marderstein, AR and Gandara, J and Perez, AR and Withers, DR and Targan, SR and Shih, DQ and Scherl, EJ and Longman, RS}, title = {Microbiota-Induced TNF-like Ligand 1A Drives Group 3 Innate Lymphoid Cell-Mediated Barrier Protection and Intestinal T Cell Activation during Colitis.}, journal = {Immunity}, volume = {49}, number = {6}, pages = {1077-1089.e5}, pmid = {30552020}, issn = {1097-4180}, support = {110199/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; R03 DK111852/DK/NIDDK NIH HHS/United States ; K08 DK099381/DK/NIDDK NIH HHS/United States ; UL1 TR002384/TR/NCATS NIH HHS/United States ; R01 AI125264/AI/NIAID NIH HHS/United States ; T32 GM007739/GM/NIGMS NIH HHS/United States ; K08 DK093578/DK/NIDDK NIH HHS/United States ; R01 DK114252/DK/NIDDK NIH HHS/United States ; R01 DK056328/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Aged ; Animals ; Colitis/genetics/*immunology/metabolism ; Female ; Humans ; Immunity, Innate/genetics/*immunology ; Interleukins/genetics/immunology/metabolism ; Intestinal Mucosa/immunology/metabolism/microbiology ; Lymphocyte Activation/genetics/immunology ; Lymphocytes/*immunology/metabolism ; Male ; Mice, Inbred C57BL ; Mice, Knockout ; Mice, Transgenic ; Microbiota/*immunology/physiology ; Middle Aged ; Phagocytes/cytology/immunology/metabolism ; T-Lymphocytes/immunology/metabolism ; Tumor Necrosis Factor Ligand Superfamily Member 15/genetics/*immunology/metabolism ; Young Adult ; Interleukin-22 ; }, abstract = {Inflammatory bowel disease (IBD) results from a dysregulated interaction between the microbiota and a genetically susceptible host. Genetic studies have linked TNFSF15 polymorphisms and its protein TNF-like ligand 1A (TL1A) with IBD, but the functional role of TL1A is not known. Here, we found that adherent IBD-associated microbiota induced TL1A release from CX3CR1[+] mononuclear phagocytes (MNPs). Using cell-specific genetic deletion models, we identified an essential role for CX3CR1[+]MNP-derived TL1A in driving group 3 innate lymphoid cell (ILC3) production of interleukin-22 and mucosal healing during acute colitis. In contrast to this protective role in acute colitis, TL1A-dependent expression of co-stimulatory molecule OX40L in MHCII[+] ILC3s during colitis led to co-stimulation of antigen-specific T cells that was required for chronic T cell colitis. These results identify a role for ILC3s in activating intestinal T cells and reveal a central role for TL1A in promoting ILC3 barrier immunity during colitis.}, } @article {pmid30551574, year = {2018}, author = {Dias, DM and Kolba, N and Binyamin, D and Ziv, O and Regini Nutti, M and Martino, HSD and Glahn, RP and Koren, O and Tako, E}, title = {Iron Biofortified Carioca Bean (Phaseolus vulgaris L.)-Based Brazilian Diet Delivers More Absorbable Iron and Affects the Gut Microbiota In Vivo (Gallus gallus).}, journal = {Nutrients}, volume = {10}, number = {12}, pages = {}, pmid = {30551574}, issn = {2072-6643}, mesh = {Animal Feed/*analysis ; Animal Nutritional Physiological Phenomena ; Animals ; *Biofortification ; Brazil ; Caco-2 Cells ; Chickens ; *Diet ; Dietary Fiber/analysis ; Dietary Proteins/analysis ; Female ; Ferritins/metabolism ; *Food, Fortified ; Gastrointestinal Microbiome/drug effects ; Humans ; Iron/*administration & dosage/chemistry ; Male ; Phaseolus/*chemistry ; Phytic Acid/analysis ; Polyphenols/analysis ; }, abstract = {Biofortification aims to improve the micronutrient concentration and bioavailability in staple food crops. Unlike other strategies utilized to alleviate Fe deficiency, studies of the gut microbiota in the context of Fe biofortification are scarce. In this study, we performed a 6-week feeding trial in Gallus gallus (n = 15), aimed to investigate the Fe status and the alterations in the gut microbiome following the administration of Fe-biofortified carioca bean based diet (BC) versus a Fe-standard carioca bean based diet (SC). The tested diets were designed based on the Brazilian food consumption survey. Two primary outcomes were observed: (1) a significant increase in total body Hb-Fe values in the group receiving the Fe-biofortified carioca bean based diet; and (2) changes in the gut microbiome composition and function were observed, specifically, significant changes in phylogenetic diversity between treatment groups, as there was increased abundance of bacteria linked to phenolic catabolism, and increased abundance of beneficial SCFA-producing bacteria in the BC group. The BC group also presented a higher intestinal villi height compared to the SC group. Our results demonstrate that the Fe-biofortified carioca bean variety was able to moderately improve Fe status and to positively affect the intestinal functionality and bacterial populations.}, } @article {pmid30546094, year = {2019}, author = {Libertucci, J and Young, VB}, title = {The role of the microbiota in infectious diseases.}, journal = {Nature microbiology}, volume = {4}, number = {1}, pages = {35-45}, doi = {10.1038/s41564-018-0278-4}, pmid = {30546094}, issn = {2058-5276}, support = {U01 AI124255/AI/NIAID NIH HHS/United States ; }, mesh = {Communicable Disease Control/*methods ; Communicable Diseases/microbiology/transmission ; Disease Susceptibility/*microbiology ; Fecal Microbiota Transplantation ; Gastrointestinal Tract/microbiology ; Humans ; Metagenome/genetics ; Microbiota/*genetics ; Prebiotics/*microbiology ; Probiotics/*therapeutic use ; Respiratory Mucosa/microbiology ; }, abstract = {The human body is colonized by a diverse community of microorganisms collectively referred to as the microbiota. Here, we describe how the human microbiota influences susceptibility to infectious diseases using examples from the respiratory, gastrointestinal and female reproductive tract. We will discuss how interactions between the host, the indigenous microbiota and non-native microorganisms, including bacteria, viruses and fungi, can alter the outcome of infections. This Review Article will highlight the complex mechanisms by which the microbiota mediates colonization resistance, both directly and indirectly, against infectious agents. Strategies for the therapeutic modulation of the microbiota to prevent or treat infectious diseases will be discussed, and we will review potential therapies that directly target the microbiota, including prebiotics, probiotics, synbiotics and faecal microbiota transplantation.}, } @article {pmid30545401, year = {2018}, author = {Forbes, JD and Chen, CY and Knox, NC and Marrie, RA and El-Gabalawy, H and de Kievit, T and Alfa, M and Bernstein, CN and Van Domselaar, G}, title = {A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {221}, pmid = {30545401}, issn = {2049-2618}, mesh = {Adult ; Arthritis, Rheumatoid/microbiology ; Bacteria/*classification/genetics/isolation & purification ; Case-Control Studies ; Colitis, Ulcerative/microbiology ; Crohn Disease/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Dysbiosis/*diagnosis ; Female ; Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Machine Learning ; Male ; Metagenomics/*methods ; Middle Aged ; Multiple Sclerosis/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Immune-mediated inflammatory disease (IMID) represents a substantial health concern. It is widely recognized that IMID patients are at a higher risk for developing secondary inflammation-related conditions. While an ambiguous etiology is common to all IMIDs, in recent years, considerable knowledge has emerged regarding the plausible role of the gut microbiome in IMIDs. This study used 16S rRNA gene amplicon sequencing to compare the gut microbiota of patients with Crohn's disease (CD; N = 20), ulcerative colitis (UC; N = 19), multiple sclerosis (MS; N = 19), and rheumatoid arthritis (RA; N = 21) versus healthy controls (HC; N = 23). Biological replicates were collected from participants within a 2-month interval. This study aimed to identify common (or unique) taxonomic biomarkers of IMIDs using both differential abundance testing and a machine learning approach.

RESULTS: Significant microbial community differences between cohorts were observed (pseudo F = 4.56; p = 0.01). Richness and diversity were significantly different between cohorts (pFDR < 0.001) and were lowest in CD while highest in HC. Abundances of Actinomyces, Eggerthella, Clostridium III, Faecalicoccus, and Streptococcus (pFDR < 0.001) were significantly higher in all disease cohorts relative to HC, whereas significantly lower abundances were observed for Gemmiger, Lachnospira, and Sporobacter (pFDR < 0.001). Several taxa were found to be differentially abundant in IMIDs versus HC including significantly higher abundances of Intestinibacter in CD, Bifidobacterium in UC, and unclassified Erysipelotrichaceae in MS and significantly lower abundances of Coprococcus in CD, Dialister in MS, and Roseburia in RA. A machine learning approach to classify disease versus HC was highest for CD (AUC = 0.93 and AUC = 0.95 for OTU and genus features, respectively) followed by MS, RA, and UC. Gemmiger and Faecalicoccus were identified as important features for classification of subjects to CD and HC. In general, features identified by differential abundance testing were consistent with machine learning feature importance.

CONCLUSIONS: This study identified several gut microbial taxa with differential abundance patterns common to IMIDs. We also found differentially abundant taxa between IMIDs. These taxa may serve as biomarkers for the detection and diagnosis of IMIDs and suggest there may be a common component to IMID etiology.}, } @article {pmid30545218, year = {2019}, author = {Liu, CW and Chi, L and Tu, P and Xue, J and Ru, H and Lu, K}, title = {Isobaric Labeling Quantitative Metaproteomics for the Study of Gut Microbiome Response to Arsenic.}, journal = {Journal of proteome research}, volume = {18}, number = {3}, pages = {970-981}, doi = {10.1021/acs.jproteome.8b00666}, pmid = {30545218}, issn = {1535-3907}, support = {R01 ES024950/ES/NIEHS NIH HHS/United States ; P30 ES010126/ES/NIEHS NIH HHS/United States ; }, mesh = {Arsenic/*pharmacology ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/genetics ; Humans ; Proteome/analysis/drug effects ; Proteomics/*methods/standards ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Quantitative metaproteomics is a relatively new research field that applies proteomics techniques to study microbial proteins of the microbiome and holds great potential in truly quantifying the functional proteins actually expressed by microbes in the biological environment, such as the gastrointestinal tract. The significant association between arsenic exposure and gut microbiome perturbations has been reported; however, metaproteomics has not yet been applied to study arsenic-induced proteome changes of the microbiome. Most importantly, to our knowledge, isobaric-labeling-based large-scale metaproteomics has not been reported using the advanced database-search approaches such as MetaPro-IQ and matched metagenome database-search strategies to provide high quantification accuracy and fewer missing quantification values. In the present study, a new experimental workflow coupled to isobaric labeling and MetaPro-IQ was demonstrated for the metaproteomics study of arsenic-induced gut microbiome perturbations. The advantages of this workflow were also discussed. For all 18 fecal samples analyzed, 7611 protein groups were quantified without any missing values. The consistent results of expression profiles were observed between 16S rRNA gene sequencing and metaproteomics. This isobaric-labeling-based workflow demonstrated the significant improvement of quantitative metaproteomics for gut microbiome study.}, } @article {pmid30544159, year = {2019}, author = {Pedrinho, A and Mendes, LW and Merloti, LF and da Fonseca, MC and Cannavan, FS and Tsai, SM}, title = {Forest-to-pasture conversion and recovery based on assessment of microbial communities in Eastern Amazon rainforest.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {3}, pages = {}, doi = {10.1093/femsec/fiy236}, pmid = {30544159}, issn = {1574-6941}, mesh = {Agriculture ; Biodiversity ; *Conservation of Natural Resources ; Ecosystem ; *Environmental Restoration and Remediation ; Metagenome ; Microbiota/*genetics ; *Rainforest ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Amazon rainforest has been subjected to particularly high rates of deforestation caused mainly by the expansion of cattle pasture and agriculture. A commonly observed response to land-use change is a negative impact on biodiversity of plant and animal species. However, its effect on the soil microbial community and ecosystem functioning is still poorly understood. Here, we used a DNA metagenomic sequencing approach to investigate the impact of land-use change on soil microbial community composition and its potential functions in three land-use systems (primary forest, pasture and secondary forest) in the Amazon region. In general, the microbial community structure was influenced by changes in soil physicochemical properties. Aluminum and water-holding capacity significantly correlated to overall community structure and most of microbial phyla. Taxonomic changes were followed by potential functional changes in the soil microbial community, with pasture presenting the most distinct profile in comparison with other sites. Although taxonomic structure was very distinct among sites, we observed a recovery of the potential functions in secondary forest after pasture abandonment. Our findings elucidate a significant shift in belowground microbial taxonomic and potential functional diversity following natural forest re-establishment and have implications for ecological restoration programs in tropical and sub-tropical ecosystems.}, } @article {pmid30543873, year = {2019}, author = {Lima, DA and Cibulski, SP and Tochetto, C and Varela, APM and Finkler, F and Teixeira, TF and Loiko, MR and Cerva, C and Junqueira, DM and Mayer, FQ and Roehe, PM}, title = {The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics.}, journal = {Virus research}, volume = {261}, number = {}, pages = {9-20}, doi = {10.1016/j.virusres.2018.12.005}, pmid = {30543873}, issn = {1872-7492}, mesh = {Animals ; Chickens ; Feces/*virology ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Malabsorption Syndromes/*veterinary/virology ; Metagenomics ; Poultry Diseases/*virology ; Viruses/*classification/*genetics ; }, abstract = {Malabsorption syndrome (MAS) is an economically important disease of young, commercially reared broilers, characterized by growth retardation, defective feather development and diarrheic faeces. Several viruses have been tentatively associated to such syndrome. Here, in order to examine potential associations between enteric viruses and MAS, the faecal viromes of 70 stool samples collected from diseased (n = 35) and healthy (n = 35) chickens from seven flocks were characterized and compared. Following high-throughput sequencing, a total of 8,347,319 paired end reads, with an average of 231 nt, were generated. Through analysis of de novo assembled contigs, 144 contigs > 1000 nt were identified with hits to eukaryotic viral sequences, as determined by GenBank database. A number of known and unknown representatives of Adenoviridae, Anelloviridae, Astroviridae, Caliciviridae, Circoviridae, Parvoviridae, Picobirnaviridae, Picornaviridae and Reoviridae, as well as novel uncharacterized CRESS-DNA viruses, were identified. However, the distribution of sequence reads of viral genomes identified in diseased or healthy birds revealed no statistically significant differences. These findings indicate no association between the occurrence of MAS and enteric viruses. The viral genomes reported in the present study, including a variety of novel viruses, seem part of the normal intestinal microbiota of chickens.}, } @article {pmid30522530, year = {2018}, author = {Edlund, A and Yang, Y and Yooseph, S and He, X and Shi, W and McLean, JS}, title = {Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {217}, pmid = {30522530}, issn = {2049-2618}, support = {R01 DE026186/DE/NIDCR NIH HHS/United States ; R01 DE020102/DE/NIDCR NIH HHS/United States ; R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 GM095373/GM/NIGMS NIH HHS/United States ; K99 DE024543/DE/NIDCR NIH HHS/United States ; R00 DE024543/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Bacteria/*classification/genetics/growth & development ; Bacterial Proteins/genetics ; Biofilms ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Dental Plaque/*microbiology ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Bacterial ; Humans ; Hydrogen-Ion Concentration ; Metabolic Networks and Pathways ; Metagenomics/*methods ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Dental plaque is composed of hundreds of bacterial taxonomic units and represents one of the most diverse and stable microbial ecosystems associated with the human body. Taxonomic composition and functional capacity of mature plaque is gradually shaped during several stages of community assembly via processes such as co-aggregation, competition for space and resources, and by bacterially produced reactive agents. Knowledge on the dynamics of assembly within complex communities is very limited and derives mainly from studies composed of a limited number of bacterial species. To fill current knowledge gaps, we applied parallel metagenomic and metatranscriptomic analyses during assembly and maturation of an in vitro oral biofilm. This model system has previously demonstrated remarkable reproducibility in taxonomic composition across replicate samples during maturation.

RESULTS: Time course analysis of the biofilm maturation was performed by parallel sampling every 2-3 h for 24 h for both DNA and RNA. Metagenomic analyses revealed that community taxonomy changed most dramatically between three and six hours of growth when pH dropped from 6.5 to 5.5. By applying comparative metatranscriptome analysis we could identify major shifts in overall community activities between six and nine hours of growth when pH dropped below 5.5, as 29,015 genes were significantly up- or down- expressed. Several of the differentially expressed genes showed unique activities for individual bacterial genomes and were associated with pyruvate and lactate metabolism, two-component signaling pathways, production of antibacterial molecules, iron sequestration, pH neutralization, protein hydrolysis, and surface attachment. Our analysis also revealed several mechanisms responsible for the niche expansion of the cariogenic pathogen Lactobacillus fermentum.

CONCLUSION: It is highly regarded that acidic conditions in dental plaque cause a net loss of enamel from teeth. Here, as pH drops below 5.5 pH to 4.7, we observe blooms of cariogenic lactobacilli, and a transition point of many bacterial gene expression activities within the community. To our knowledge, this represents the first study of the assembly and maturation of a complex oral bacterial biofilm community that addresses gene level functional responses over time.}, } @article {pmid30540709, year = {2019}, author = {Chen, LA and Hourigan, SK and Grigoryan, Z and Gao, Z and Clemente, JC and Rideout, JR and Chirumamilla, S and Rabidazeh, S and Saeed, S and Elson, CO and Oliva-Hemker, M and Blaser, MJ and Sears, CL}, title = {Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {68}, number = {4}, pages = {502-508}, doi = {10.1097/MPG.0000000000002210}, pmid = {30540709}, issn = {1536-4801}, support = {U01 AI122285/AI/NIAID NIH HHS/United States ; UL1 TR000038/TR/NCATS NIH HHS/United States ; R01 DK090989/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Alabama ; Baltimore ; Child ; Child, Preschool ; *Clostridioides difficile ; Clostridium Infections/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*complications ; Male ; Prospective Studies ; Young Adult ; }, abstract = {OBJECTIVES: The gut microbiome is believed to play a role in the susceptibility to and treatment of Clostridium difficile infections (CDIs). It is, however, unknown whether the gut microbiome is also affected by asymptomatic C difficile colonization. Our study aimed to evaluate the fecal microbiome of children based on C difficile colonization, and CDI risk factors, including antibiotic use and comorbid inflammatory bowel disease (IBD).

METHODS: Subjects with IBD and non-IBD controls were prospectively enrolled from pediatric clinics for a biobanking project (n = 113). A fecal sample was collected from each subject for research purposes only and was evaluated for asymptomatic toxigenic C difficile colonization. Fecal microbiome composition was determined by 16S rRNA sequencing.

RESULTS: We found reduced bacterial diversity and altered microbiome composition in subjects with C difficile colonization, concurrent antibiotic use, and/or concomitant IBD (all P < 0.05). Accounting for antibiotic use and IBD status, children colonized with C difficile had significant enrichment in taxa from the genera Ruminococcus, Eggerthella, and Clostridium. Children without C difficile had increased relative abundances of Faecalibacterium and Rikenellaceae. Imputed metagenomic functions of those colonized were enriched for genes in oxidative phosphorylation and beta-lactam resistance, whereas in the subjects without C difficile, several functions in translation and metabolism were over-represented.

CONCLUSIONS: In children, C difficile colonization, or factors that predispose to colonization such as antibiotic use and IBD status were associated with decreased gut bacterial diversity and altered microbiome composition. Averting such microbiome alterations may be a method to prevent or treat CDI.}, } @article {pmid30537931, year = {2018}, author = {Benavides, A and Isaza, JP and Niño-García, JP and Alzate, JF and Cabarcas, F}, title = {CLAME: a new alignment-based binning algorithm allows the genomic description of a novel Xanthomonadaceae from the Colombian Andes.}, journal = {BMC genomics}, volume = {19}, number = {Suppl 8}, pages = {858}, pmid = {30537931}, issn = {1471-2164}, mesh = {*Algorithms ; Colombia ; Genes, Bacterial ; Genetic Markers ; *Genome, Bacterial ; *Metagenomics ; Microbiota ; Phylogeny ; Sequence Analysis, DNA/*methods ; Xanthomonadaceae/*classification/*genetics ; }, abstract = {BACKGROUND: Hot spring bacteria have unique biological adaptations to survive the extreme conditions of these environments; these bacteria produce thermostable enzymes that can be used in biotechnological and industrial applications. However, sequencing these bacteria is complex, since it is not possible to culture them. As an alternative, genome shotgun sequencing of whole microbial communities can be used. The problem is that the classification of sequences within a metagenomic dataset is very challenging particularly when they include unknown microorganisms since they lack genomic reference. We failed to recover a bacterium genome from a hot spring metagenome using the available software tools, so we develop a new tool that allowed us to recover most of this genome.

RESULTS: We present a proteobacteria draft genome reconstructed from a Colombian's Andes hot spring metagenome. The genome seems to be from a new lineage within the family Rhodanobacteraceae of the class Gammaproteobacteria, closely related to the genus Dokdonella. We were able to generate this genome thanks to CLAME. CLAME, from Spanish "CLAsificador MEtagenomico", is a tool to group reads in bins. We show that most reads from each bin belong to a single chromosome. CLAME is very effective recovering most of the reads belonging to the predominant species within a metagenome.

CONCLUSIONS: We developed a tool that can be used to extract genomes (or parts of them) from a complex metagenome.}, } @article {pmid30537922, year = {2018}, author = {Noreña-P, A and González Muñoz, A and Mosquera-Rendón, J and Botero, K and Cristancho, MA}, title = {Colombia, an unknown genetic diversity in the era of Big Data.}, journal = {BMC genomics}, volume = {19}, number = {Suppl 8}, pages = {859}, pmid = {30537922}, issn = {1471-2164}, mesh = {Animals ; Bacteria/*genetics ; Base Sequence ; *Big Data ; *Biodiversity ; Colombia ; *Genomics ; Metagenome ; Plants/*genetics ; }, abstract = {BACKGROUND: Latin America harbors some of the most biodiverse countries in the world, including Colombia. Despite the increasing use of cutting-edge technologies in genomics and bioinformatics in several biological science fields around the world, the region has fallen behind in the inclusion of these approaches in biodiversity studies. In this study, we used data mining methods to search in four main public databases of genetic sequences such as: NCBI Nucleotide and BioProject, Pathosystems Resource Integration Center, and Barcode of Life Data Systems databases. We aimed to determine how much of the Colombian biodiversity is contained in genetic data stored in these public databases and how much of this information has been generated by national institutions. Additionally, we compared this data for Colombia with other countries of high biodiversity in Latin America, such as Brazil, Argentina, Costa Rica, Mexico, and Peru.

RESULTS: In Nucleotide, we found that 66.84% of total records for Colombia have been published at the national level, and this data represents less than 5% of the total number of species reported for the country. In BioProject, 70.46% of records were generated by national institutions and the great majority of them is represented by microorganisms. In BOLD Systems, 26% of records have been submitted by national institutions, representing 258 species for Colombia. This number of species reported for Colombia span approximately 0.46% of the total biodiversity reported for the country (56,343 species). Finally, in PATRIC database, 13.25% of the reported sequences were contributed by national institutions. Colombia has a better biodiversity representation in public databases in comparison to other Latin American countries, like Costa Rica and Peru. Mexico and Argentina have the highest representation of species at the national level, despite Brazil and Colombia, which actually hold the first and second places in biodiversity worldwide.

CONCLUSIONS: Our findings show gaps in the representation of the Colombian biodiversity at the molecular and genetic levels in widely consulted public databases. National funding for high-throughput molecular research, NGS technologies costs, and access to genetic resources are limiting factors. This fact should be taken as an opportunity to foster the development of collaborative projects between research groups in the Latin American region to study the vast biodiversity of these countries using 'omics' technologies.}, } @article {pmid30536648, year = {2018}, author = {Taniguchi, H and Tanisawa, K and Sun, X and Kubo, T and Hoshino, Y and Hosokawa, M and Takeyama, H and Higuchi, M}, title = {Effects of short-term endurance exercise on gut microbiota in elderly men.}, journal = {Physiological reports}, volume = {6}, number = {23}, pages = {e13935}, pmid = {30536648}, issn = {2051-817X}, mesh = {Aged ; Blood Pressure ; Clostridioides difficile ; Endurance Training/adverse effects/*methods ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; }, abstract = {Regular exercise reduces the risks for cardiovascular diseases. Although the gut microbiota has been associated with fitness level and cardiometabolic risk factors, the effects of exercise-induced gut microbiota changes in elderly individuals are unclear. This study evaluated whether endurance exercise modulates the gut microbiota in elderly subjects, and whether these changes are associated with host cardiometabolic phenotypes. In a randomized crossover trial, 33 elderly Japanese men participated in a 5-week endurance exercise program. 16S rRNA gene-based metagenomic analyses revealed that the effect of endurance exercise on gut microbiota diversity was not greater than interindividual differences, whereas changes in α-diversity indices during intervention were negatively correlated with changes in systolic and diastolic blood pressure, especially during exercise. Microbial composition analyses showed that the relative abundance of Clostridium difficile significantly decreased, whereas that of Oscillospira significantly increased during exercise as compared to the control period. The changes in these taxa were correlated with the changes in several cardiometabolic risk factors. The findings indicate that short-term endurance exercise has little effect on gut microbiota in elderly individuals, and that the changes in gut microbiota were associated with cardiometabolic risk factors, such as systolic and diastolic blood pressure, providing preliminary insight into the associations between the gut microbiota and cardiometabolic phenotypes.}, } @article {pmid30535578, year = {2019}, author = {Zhang, F and Zheng, W and Xue, Y and Yao, W}, title = {Suhuai suckling piglet hindgut microbiome-metabolome responses to different dietary copper levels.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {2}, pages = {853-868}, pmid = {30535578}, issn = {1432-0614}, support = {JATS[2018]287//The earmarked fund for Jiangsu Agricultural Industry Technology System/ ; 31372321//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Animals, Newborn ; Blood Chemical Analysis ; Copper/*administration & dosage ; Diet/*methods ; Feces/chemistry ; Gas Chromatography-Mass Spectrometry ; Gastrointestinal Microbiome/*drug effects ; High-Throughput Nucleotide Sequencing ; Metabolome/*drug effects ; Metabolomics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Swine ; Trace Elements/*administration & dosage ; }, abstract = {Unabsorbed copper accumulates in the hindgut of pigs that consume high levels of dietary copper, which enhances the coselection of antibiotic-resistant bacteria and is considered detrimental to the environment and to porcine health. In our study, a combination of 16S rRNA pyrosequencing and nontargeted metabolomics was used to investigate the microbiome-metabolome responses to dietary copper levels in the hindgut of suckling piglets. The results showed that the dietary copper level affected the abundance of several Clostridia genera and that the relative abundance of butyrate-producing bacteria, such as Coprococcus, Roseburia, and Acidaminococcus, was reduced in the 300 mg kg[-1] (high) Cu group. Metabolomic analysis revealed that dietary copper levels affected protein and carbohydrate metabolites, protein biosynthesis, the urea cycle, galactose metabolism, gluconeogenesis, and amino acid metabolism (including the metabolism of arginine, proline, β-alanine, phenylalanine, tyrosine, and methionine). Furthermore, Pearson's correlation analysis showed that the abundance levels of Coprococcus (family Lachnospiraceae) and operational taxonomic unit (OTU) 18 (family Ruminococcaceae) were positively correlated with energy metabolism pathways (gluconeogenesis, glycolysis, and the pentose phosphate pathway). The abundance of Streptococcus was negatively correlated with amino acid metabolism pathways (protein biosynthesis, glycine, serine, threonine, methionine, phenylalanine, and tyrosine metabolism), and OTU583 and OTU1067 (family Rikenellaceae) were positively correlated with amino acid metabolism pathways. These results suggest that the copper levels consumed by LC (low-copper group) versus HC (high-copper group) animals alter the composition of the gut microbiota and modulate microbial metabolic pathways, which may further affect the health of suckling piglets.}, } @article {pmid30532085, year = {2018}, author = {Chen, B and Yu, T and Xie, S and Du, K and Liang, X and Lan, Y and Sun, C and Lu, X and Shao, Y}, title = {Comparative shotgun metagenomic data of the silkworm Bombyx mori gut microbiome.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180285}, pmid = {30532085}, issn = {2052-4463}, mesh = {Acinetobacter/genetics ; Animals ; Bombyx/*microbiology ; Enterobacter/genetics ; Enterococcus/genetics ; *Gastrointestinal Microbiome ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; }, abstract = {Lepidoptera (butterflies and moths) is a major insect order including important pollinators and agricultural pests, however their microbiomes are little studied. Here, using next-generation sequencing (NGS)-based shotgun metagenomics, we characterize both the biodiversity and functional potential of gut microbiota of a lepidopteran model insect, the silkworm Bombyx mori. Two metagenomes, including the standard inbred strain Dazao (P50) and an improved hybrid strain Qiufeng × Baiyu (QB) widely used in commercial silk production, were generated, containing 45,505,084 and 69,127,002 raw reads, respectively. Taxonomic analysis revealed that a total of 663 bacterial species were identified in P50 silkworms, while 322 unique species in QB silkworms. Notably, Enterobacter, Acinetobacter and Enterococcus were dominated in both strains. The further functional annotation was performed by both BlastP and MG-RAST against various databases including Nr, COG, KEGG, CAZy and SignalP, which revealed >5 × 10[6] protein-coding genes. These datasets not only provide first insights into all bacterial genes in silkworm guts, but also help to generate hypotheses for subsequently testing functional traits of gut microbiota in an important insect group.}, } @article {pmid30531976, year = {2019}, author = {Franzosa, EA and Sirota-Madi, A and Avila-Pacheco, J and Fornelos, N and Haiser, HJ and Reinker, S and Vatanen, T and Hall, AB and Mallick, H and McIver, LJ and Sauk, JS and Wilson, RG and Stevens, BW and Scott, JM and Pierce, K and Deik, AA and Bullock, K and Imhann, F and Porter, JA and Zhernakova, A and Fu, J and Weersma, RK and Wijmenga, C and Clish, CB and Vlamakis, H and Huttenhower, C and Xavier, RJ}, title = {Gut microbiome structure and metabolic activity in inflammatory bowel disease.}, journal = {Nature microbiology}, volume = {4}, number = {2}, pages = {293-305}, pmid = {30531976}, issn = {2058-5276}, support = {U01 DK097430/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 DK092405/DK/NIDDK NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; P30 DK040561/DK/NIDDK NIH HHS/United States ; }, mesh = {Biodiversity ; Biomarkers/metabolism ; Colitis, Ulcerative/immunology/metabolism/microbiology ; Crohn Disease/immunology/metabolism/microbiology ; Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/genetics/immunology ; Humans ; Inflammation/metabolism/microbiology ; Inflammatory Bowel Diseases/immunology/*metabolism/*microbiology ; Leukocyte L1 Antigen Complex/analysis ; Metabolome ; Metagenome ; }, abstract = {The inflammatory bowel diseases (IBDs), which include Crohn's disease (CD) and ulcerative colitis (UC), are multifactorial chronic conditions of the gastrointestinal tract. While IBD has been associated with dramatic changes in the gut microbiota, changes in the gut metabolome-the molecular interface between host and microbiota-are less well understood. To address this gap, we performed untargeted metabolomic and shotgun metagenomic profiling of cross-sectional stool samples from discovery (n = 155) and validation (n = 65) cohorts of CD, UC and non-IBD control patients. Metabolomic and metagenomic profiles were broadly correlated with faecal calprotectin levels (a measure of gut inflammation). Across >8,000 measured metabolite features, we identified chemicals and chemical classes that were differentially abundant in IBD, including enrichments for sphingolipids and bile acids, and depletions for triacylglycerols and tetrapyrroles. While > 50% of differentially abundant metabolite features were uncharacterized, many could be assigned putative roles through metabolomic 'guilt by association' (covariation with known metabolites). Differentially abundant species and functions from the metagenomic profiles reflected adaptation to oxidative stress in the IBD gut, and were individually consistent with previous findings. Integrating these data, however, we identified 122 robust associations between differentially abundant species and well-characterized differentially abundant metabolites, indicating possible mechanistic relationships that are perturbed in IBD. Finally, we found that metabolome- and metagenome-based classifiers of IBD status were highly accurate and, like the vast majority of individual trends, generalized well to the independent validation cohort. Our findings thus provide an improved understanding of perturbations of the microbiome-metabolome interface in IBD, including identification of many potential diagnostic and therapeutic targets.}, } @article {pmid30530851, year = {2019}, author = {Gharaibeh, RZ and Jobin, C}, title = {Microbiota and cancer immunotherapy: in search of microbial signals.}, journal = {Gut}, volume = {68}, number = {3}, pages = {385-388}, pmid = {30530851}, issn = {1468-3288}, support = {R01 DK073338/DK/NIDDK NIH HHS/United States ; }, mesh = {Gastrointestinal Microbiome/*immunology ; Host Microbial Interactions ; Humans ; Immunotherapy/*methods ; Intestines/microbiology ; Metagenome/immunology ; Neoplasms/*microbiology/*therapy ; Programmed Cell Death 1 Receptor/antagonists & inhibitors ; }, } @article {pmid30529583, year = {2019}, author = {Paramsothy, S and Nielsen, S and Kamm, MA and Deshpande, NP and Faith, JJ and Clemente, JC and Paramsothy, R and Walsh, AJ and van den Bogaerde, J and Samuel, D and Leong, RWL and Connor, S and Ng, W and Lin, E and Borody, TJ and Wilkins, MR and Colombel, JF and Mitchell, HM and Kaakoush, NO}, title = {Specific Bacteria and Metabolites Associated With Response to Fecal Microbiota Transplantation in Patients With Ulcerative Colitis.}, journal = {Gastroenterology}, volume = {156}, number = {5}, pages = {1440-1454.e2}, doi = {10.1053/j.gastro.2018.12.001}, pmid = {30529583}, issn = {1528-0012}, mesh = {Bacteria/classification/genetics/growth & development/*metabolism ; Biomarkers/metabolism ; Colitis, Ulcerative/diagnosis/microbiology/*therapy ; Double-Blind Method ; Fecal Microbiota Transplantation/adverse effects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metabolomics ; New South Wales ; Remission Induction ; Ribotyping ; Time Factors ; Treatment Outcome ; }, abstract = {BACKGROUND & AIMS: Fecal microbiota transplantation (FMT) can induce remission in patients with ulcerative colitis (UC). In a randomized controlled trial of FMT in patients with active UC, we aimed to identify bacterial taxonomic and functional factors associated with response to therapy.

METHODS: We performed a double-blind trial of 81 patients with active UC randomly assigned to groups that received an initial colonoscopic infusion and then intensive multidonor FMT or placebo enemas, 5 d/wk for 8 weeks. Patients in the FMT group received blended homogenized stool from 3-7 unrelated donors. Patients in the placebo group were eligible to receive open-label FMT after the double-blind study period. We collected 314 fecal samples from the patients at screening, every 4 weeks during treatment, and 8 weeks after the blinded or open-label FMT therapy. We also collected 160 large-bowel biopsy samples from the patients at study entry, at completion of 8 weeks of blinded therapy, and at the end of open-label FMT, if applicable. We analyzed 105 fecal samples from the 14 individual donors (n = 55), who in turn contributed to 21 multidonor batches (n = 50). Bacteria in colonic and fecal samples were analyzed by both 16S ribosomal RNA gene and transcript amplicon sequencing; 285 fecal samples were analyzed by shotgun metagenomics, and 60 fecal samples were analyzed for metabolome features.

RESULTS: FMT increased microbial diversity and altered composition, based on analyses of colon and fecal samples collected before vs after FMT. Diversity was greater in fecal and colon samples collected before and after FMT treatment from patients who achieved remission compared with patients who did not. Patients in remission after FMT had enrichment of Eubacterium hallii and Roseburia inulivorans compared with patients who did not achieve remission after FMT and had increased levels of short-chain fatty acid biosynthesis and secondary bile acids. Patients who did not achieve remission had enrichment of Fusobacterium gonidiaformans, Sutterella wadsworthensis, and Escherichia species and increased levels of heme and lipopolysaccharide biosynthesis. Bacteroides in donor stool were associated with remission in patients receiving FMT, and Streptococcus species in donor stool was associated with no response to FMT.

CONCLUSIONS: In an analysis of fecal and colonic mucosa samples from patients receiving FMT for active UC and stool samples from donors, we associated specific bacteria and metabolic pathways with induction of remission. These findings may be of value in the design of microbe-based therapies for UC. ClinicalTrials.gov, Number NCT01896635.}, } @article {pmid30528276, year = {2019}, author = {Ramos-Barbero, MD and Martin-Cuadrado, AB and Viver, T and Santos, F and Martinez-Garcia, M and Antón, J}, title = {Recovering microbial genomes from metagenomes in hypersaline environments: The Good, the Bad and the Ugly.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {1}, pages = {30-40}, doi = {10.1016/j.syapm.2018.11.001}, pmid = {30528276}, issn = {1618-0984}, mesh = {Archaea/genetics/isolation & purification ; Bacteria/genetics/isolation & purification ; *Genome, Microbial ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; *Salinity ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Current metagenomic tools allow the recovery of microbial genomes directly from the environment. This can be accomplished by binning metagenomic contigs according to their coverage and tetranucleotide frequency, followed by an estimation of the bin quality. The public availability of bioinformatics tools, together with the decreasing cost of next generation sequencing, are democratizing this powerful approach that is spreading from specialized research groups to the general public. Using metagenomes from hypersaline environments, as well as mock metagenomes composed of Archaea and Bacteria frequently found in these systems, we have analyzed the advantages and difficulties of the binning process in these extreme environments to tackle microbial population diversity. These extreme systems harbor relatively low species diversity but high intraspecific diversity, which can compromise metagenome assembly and therefore the whole binning process. The main goal is to compare the output of the binning process with what is previously known from the analyzed samples, based on years of study using different approaches. Several scenarios have been analyzed in detail: (i) a good quality bin from a species highly abundant in the environment; (ii) an intermediate quality bin with incongruences that can be solved by further analyses and manual curation, and (iii) a low-quality bin to investigate the failure to recover a very abundant microbial genome as well as some possible solutions. The latter can be considered the "great metagenomics anomaly" and is mainly due to assembly problems derived from the microdiversity of naturally co-existing populations in nature.}, } @article {pmid30526624, year = {2018}, author = {Wu, G and Niu, M and Tang, W and Hu, J and Wei, G and He, Z and Chen, Y and Jiang, Y and Chen, P}, title = {L-Fucose ameliorates high-fat diet-induced obesity and hepatic steatosis in mice.}, journal = {Journal of translational medicine}, volume = {16}, number = {1}, pages = {344}, pmid = {30526624}, issn = {1479-5876}, support = {2016A030306043//Natural Science Foundation of Guangdong Province/International ; 2017B030314034//Natural Science Foundation of Guangdong Province/International ; 2016A020216015//China Association for Science and Technology/International ; }, mesh = {Adiposity/drug effects ; Animals ; Cecum/drug effects/microbiology ; *Diet, High-Fat ; Dysbiosis/complications/microbiology/pathology ; Feeding Behavior ; Fucose/pharmacology/*therapeutic use ; Gastrointestinal Microbiome/drug effects ; Glucose Tolerance Test ; Insulin ; Metagenomics ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/*complications/*drug therapy/microbiology ; Obesity/*complications/*drug therapy/microbiology ; Weight Gain/drug effects ; }, abstract = {BACKGROUND: L-Fucose (Fuc), a six-deoxy hexose monosaccharide, is present endogenously in humans and animals and has a wide range of biological functions. In the present study, we aimed to examine the effect of Fuc on obesity and hepatic steatosis in mice fed a high-fat diet (HFD).

METHODS: C57BL/6 mice were fed a normal chow (NC) or HFD for 18 weeks to induce obesity and fatty liver. Fuc was administered intragastrically from the 8th week to the end of the experiment (18 weeks).

RESULTS: Metagenomic analysis showed that HFD altered the genomic profile of gut microbiota in the mice; specifically, expression of alpha-L-fucosidase, the gene responsible for Fuc generation, was markedly reduced in the HFD group compared with that in the NC group. Fuc treatment decreased body weight gain, fat accumulation, and hepatic triglyceride elevation in HFD-fed mice. In addition, Fuc decreased the levels of endotoxin-producing bacteria of the Desulfovibrionaceae family and restored HFD-induced enteric dysbiosis at both compositional and functional levels.

CONCLUSION: Our findings suggest that Fuc might be a novel strategy to treat HFD-induced obesity and fatty liver.}, } @article {pmid30525954, year = {2019}, author = {Kleinjans, L and Veening-Griffioen, DH and Wehkamp, T and van Bergenhenegouwen, J and Knol, J and Garssen, J and Knippels, LMJ and Belzer, C and Jeurink, PV}, title = {Mice co-administrated with partially hydrolysed whey proteins and prebiotic fibre mixtures show allergen-specific tolerance and a modulated gut microbiota.}, journal = {Beneficial microbes}, volume = {10}, number = {2}, pages = {165-178}, doi = {10.3920/BM2018.0001}, pmid = {30525954}, issn = {1876-2891}, mesh = {Allergens/*immunology ; Animals ; Antibodies/blood ; Bacteria/classification ; Dietary Fiber/*administration & dosage ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/*drug effects ; Hypersensitivity/*prevention & control ; Immune Tolerance/*drug effects ; Metagenome ; Mice, Inbred C3H ; Prebiotics/*administration & dosage ; Treatment Outcome ; Whey Proteins/*administration & dosage ; }, abstract = {Non-breastfed infants at-risk of allergy are recommended to use a hydrolysed formula before the age of 6 months. The addition of prebiotics to this formula may reduce the allergy development in these infants, but clinical evidence is still inconclusive. This study evaluates (1) whether the exposure duration to different prebiotics alongside a partially hydrolysed whey protein (pHP) influences its' effectiveness to prevent allergy development and (2) whether the gut microbiota plays a role in this process. Mice orally sensitised with whey and/or cholera toxin were orally treated for six days before sensitization with phosphate buffered saline, whey or pHP to potentially induce tolerance. Two groups received an oligosaccharide diet only from day -7 until -2 (GFshort and GFAshort) whereas two other groups received their diets from day -15 until 37 (GFlong and GFAlong). On day 35, mice underwent an intradermal whey challenge, and the acute allergic skin response, shock score, and body temperatures were measured. At day 37, mice received whey orally and serum mouse mast cell protease-1, SLPI and whey-specific antibodies were assessed. Faecal samples were taken at day -15, -8 and 34. Feeding mice pHP alone during tolerance induction did not reduce ear swelling. The tolerance inducing mechanisms seem to vary according to the oligosaccharide-composition. GFshort, GFlong, and GFAlong reduced the allergic skin response, whereas GFAshort was not potent enough. However, in the treatment groups, the dominant Lactobacillus species decreased, being replaced by Bacteroidales family S24-7 members. In addition, the relative abundance of Prevotella was significantly higher in the GFlong, GFAshort and GFAlong groups. Co-administration of oligosaccharides and pHP can induce immunological tolerance in mice, although tolerance induction was strongest in the animals that were fed oligosaccharides during the entire protocol. Some microbial changes coincided with tolerance induction, however, a specific mechanism could not be determined based on these data.}, } @article {pmid30525951, year = {2019}, author = {Ma, ZF and Yusof, N and Hamid, N and Lawenko, RM and Mohammad, WMZW and Liong, MT and Sugahara, H and Odamaki, T and Xiao, J and Lee, YY}, title = {Bifidobacterium infantis M-63 improves mental health in victims with irritable bowel syndrome developed after a major flood disaster.}, journal = {Beneficial microbes}, volume = {10}, number = {2}, pages = {111-120}, doi = {10.3920/BM2018.0008}, pmid = {30525951}, issn = {1876-2891}, mesh = {Bifidobacterium longum subspecies infantis/*growth & development ; Cluster Analysis ; Controlled Before-After Studies ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; *Floods ; Gastrointestinal Microbiome ; Humans ; Irritable Bowel Syndrome/*complications ; Male ; Mental Disorders/*therapy ; Mental Health ; Middle Aged ; Phylogeny ; Probiotics/*administration & dosage ; Prospective Studies ; Quality of Life ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Treatment Outcome ; }, abstract = {Individuals in a community who developed irritable bowel syndrome (IBS) after major floods have significant mental health impairment. We aimed to determine if Bifidobacterium infantis M-63 was effective in improving symptoms, psychology and quality of life measures in flood-affected individuals with IBS and if the improvement was mediated by gut microbiota changes. Design was non-randomised, open-label, controlled before-and-after. Of 53 participants, 20 with IBS were given B. infantis M-63 (1×10[9] cfu/sachet/day) for three months and 33 were controls. IBS symptom severity scale, hospital anxiety and depression scale, SF-36 Questionnaire, hydrogen breath testing for small intestinal bacterial overgrowth and stools for 16S rRNA metagenomic analysis were performed before and after intervention. 11 of 20 who were given probiotics (M-63) and 20 of 33 controls completed study as per-protocol. Mental well-being was improved with M-63 vs controls for full analysis (P=0.03) and per-protocol (P=0.01) populations. Within-group differences were observed for anxiety and bodily pain (both P=0.04) in the M-63 per-protocol population. Lower ratio of Firmicutes/Bacteroidetes was observed with M-63 vs controls (P=0.01) and the lower ratio was correlated with higher post-intervention mental score (P=0.04). B. infantis M-63 is probably effective in improving mental health of victims who developed IBS after floods and this is maybe due to restoration of microbial balance and the gut-brain axis. However, our conclusion must be interpreted within the context of limited sample size. The study was retrospectively registered on 12 October 2017 and the Trial Registration Number (TRN) was NCT03318614.}, } @article {pmid30525950, year = {2019}, author = {Hibberd, AA and Yde, CC and Ziegler, ML and Honoré, AH and Saarinen, MT and Lahtinen, S and Stahl, B and Jensen, HM and Stenman, LK}, title = {Probiotic or synbiotic alters the gut microbiota and metabolism in a randomised controlled trial of weight management in overweight adults.}, journal = {Beneficial microbes}, volume = {10}, number = {2}, pages = {121-135}, doi = {10.3920/BM2018.0028}, pmid = {30525950}, issn = {1876-2891}, mesh = {Adult ; Aged ; Bacteria/classification/metabolism ; Body Fat Distribution ; Double-Blind Method ; Feces/chemistry/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolomics ; Metagenomics ; *Microbiota ; Middle Aged ; Obesity/*therapy ; Overweight/*therapy ; Placebos/administration & dosage ; Probiotics/*administration & dosage ; Synbiotics/*administration & dosage ; Treatment Outcome ; }, abstract = {The gut microbiota contributes to host energy metabolism, and altered gut microbiota has been associated with obesity-related metabolic disorders. We previously reported that a probiotic alone or together with a prebiotic controls body fat mass in healthy overweight or obese individuals in a randomised, double-blind, placebo controlled clinical study (ClinicalTrials.gov NCT01978691). We now aimed to investigate whether changes in the gut microbiota may be associated with the observed clinical benefits. Faecal and plasma samples were obtained from a protocol compliant subset (n=134) of participants from a larger clinical study where participants were randomised (1:1:1:1) into four groups: (1) placebo, 12 g/d microcrystalline cellulose; (2) Litesse® Ultra™ polydextrose (LU), 12 g/day; (3) Bifidobacterium animalis subsp. lactis 420™ (B420), 10[10] cfu/d in 12 g microcrystalline cellulose; (4) LU+B420, 1010 cfu/d of B420 in 12 g/d LU for 6 months of intervention. The faecal microbiota composition and metabolites were assessed as exploratory outcomes at baseline, 2, 4, 6 months, and +1 month post-intervention and correlated to obesity-related clinical outcomes. Lactobacillus and Akkermansia were more abundant with B420 at the end of the intervention. LU+B420 increased Akkermansia, Christensenellaceae and Methanobrevibacter, while Paraprevotella was reduced. Christensenellaceae was consistently increased in the LU and LU+B420 groups across the intervention time points, and correlated negatively to waist-hip ratio and energy intake at baseline, and waist-area body fat mass after 6 months treatment with LU+B420. Functional metagenome predictions indicated alterations in pathways related to cellular processes and metabolism. Plasma bile acids glycocholic acid, glycoursodeoxycholic acid, and taurohyodeoxycholic acid and tauroursodeoxycholic acid were reduced in LU+B420 compared to Placebo. Consumption of B420 and its combination with LU resulted in alterations of the gut microbiota and its metabolism, and may support improved gut barrier function and obesity-related markers.}, } @article {pmid30521551, year = {2018}, author = {Vernocchi, P and Del Chierico, F and Russo, A and Majo, F and Rossitto, M and Valerio, M and Casadei, L and La Storia, A and De Filippis, F and Rizzo, C and Manetti, C and Paci, P and Ercolini, D and Marini, F and Fiscarelli, EV and Dallapiccola, B and Lucidi, V and Miccheli, A and Putignani, L}, title = {Gut microbiota signatures in cystic fibrosis: Loss of host CFTR function drives the microbiota enterophenotype.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0208171}, pmid = {30521551}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/adverse effects ; Bacteria/*isolation & purification ; Child, Preschool ; Cohort Studies ; Cystic Fibrosis/drug therapy/genetics/*physiopathology ; Cystic Fibrosis Transmembrane Conductance Regulator/*genetics ; Dysbiosis/microbiology/physiopathology ; Exocrine Pancreatic Insufficiency/genetics/physiopathology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/drug effects/*physiology ; Host Microbial Interactions/physiology ; Humans ; Intestinal Mucosa/microbiology/*physiopathology ; Male ; Metabolomics ; Metagenomics ; Phenotype ; }, abstract = {BACKGROUND: Cystic fibrosis (CF) is a disorder affecting the respiratory, digestive, reproductive systems and sweat glands. This lethal hereditary disease has known or suspected links to the dysbiosis gut microbiota. High-throughput meta-omics-based approaches may assist in unveiling this complex network of symbiosis modifications.

OBJECTIVES: The aim of this study was to provide a predictive and functional model of the gut microbiota enterophenotype of pediatric patients affected by CF under clinical stability.

METHODS: Thirty-one fecal samples were collected from CF patients and healthy children (HC) (age range, 1-6 years) and analysed using targeted-metagenomics and metabolomics to characterize the ecology and metabolism of CF-linked gut microbiota. The multidimensional data were low fused and processed by chemometric classification analysis.

RESULTS: The fused metagenomics and metabolomics based gut microbiota profile was characterized by a high abundance of Propionibacterium, Staphylococcus and Clostridiaceae, including Clostridium difficile, and a low abundance of Eggerthella, Eubacterium, Ruminococcus, Dorea, Faecalibacterium prausnitzii, and Lachnospiraceae, associated with overexpression of 4-aminobutyrate (GABA), choline, ethanol, propylbutyrate, and pyridine and low levels of sarcosine, 4-methylphenol, uracil, glucose, acetate, phenol, benzaldehyde, and methylacetate. The CF gut microbiota pattern revealed an enterophenotype intrinsically linked to disease, regardless of age, and with dysbiosis uninduced by reduced pancreatic function and only partially related to oral antibiotic administration or lung colonization/infection.

CONCLUSIONS: All together, the results obtained suggest that the gut microbiota enterophenotypes of CF, together with endogenous and bacterial CF biomarkers, are direct expression of functional alterations at the intestinal level. Hence, it's possible to infer that CFTR impairment causes the gut ecosystem imbalance.This new understanding of CF host-gut microbiota interactions may be helpful to rationalize novel clinical interventions to improve the affected children's nutritional status and intestinal function.}, } @article {pmid30520232, year = {2019}, author = {Yu, Y and Gao, F and Chen, X and Zheng, S and Zhang, J}, title = {Changes in the distal esophageal microbiota in Chinese patients with reflux esophagitis.}, journal = {Journal of digestive diseases}, volume = {20}, number = {1}, pages = {18-24}, doi = {10.1111/1751-2980.12692}, pmid = {30520232}, issn = {1751-2980}, support = {2018-2-1053//Capital's Funds for Health Improvement and Research/ ; QML20170606//Beijing Municipal Administration of Hospitals' Youth Programme/ ; }, mesh = {Adult ; Asian People ; Esophagitis, Peptic/*microbiology ; Esophagus/*microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Healthy Volunteers ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Middle Aged ; }, abstract = {OBJECTIVE: Changes in microbiota composition in the distal esophagus may be associated with the pathogenesis of gastroesophageal reflux disease. We aimed to compare the composition of distal esophageal microbiota between Chinese patients with reflux esophagitis (RE) and healthy volunteers using metagenomic high-throughput DNA sequencing and bioinformatic analyses.

METHODS: Healthy volunteers (controls) and patients with reflux esophagitis (RE) were enrolled. Distal esophageal (2 cm above the gastroesophageal junction) biopsy specimens were obtained under endoscopy. Microbial DNA was extracted from the specimens, followed by 16S rDNA gene amplification and Illumina sequencing. Bioinformatic tools were applied to dissect the community structure.

RESULTS: No dramatic differences in microbiota were found in RE patients compared with the controls. At the phylum level, only Bacteroidetes differed between the groups, being less abundant in the RE group. The overall number and diversity of species tended to be lower in RE patients, but there were no significant differences between the groups. Three genera, Prevotella, Helicobacter, and Moraxella, were obviously depleted in RE patients, as revealed by linear discriminant analysis.

CONCLUSIONS: The composition of distal esophageal microbiota in Chinese patients with RE showed moderate changes compared with healthy controls. To what extent these changes are associated with the pathogenesis of RE needs further investigation.}, } @article {pmid30518415, year = {2018}, author = {Alonso, L and Creuzé-des-Châtelliers, C and Trabac, T and Dubost, A and Moënne-Loccoz, Y and Pommier, T}, title = {Rock substrate rather than black stain alterations drives microbial community structure in the passage of Lascaux Cave.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {216}, pmid = {30518415}, issn = {2049-2618}, mesh = {Bacteria/*classification/genetics/isolation & purification ; Carbon Dioxide/analysis ; Caves/*microbiology ; DNA, Fungal/genetics ; France ; Fungi/*classification/genetics/isolation & purification ; Geologic Sediments/microbiology ; High-Throughput Nucleotide Sequencing ; Human Activities ; Humans ; Metagenomics ; Microbiota ; Phylogeny ; Seasons ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: The World-famous UNESCO heritage from the Paleolithic human society, Lascaux Cave (France), has endeavored intense microclimatic perturbations, in part due to high touristic pressure. These perturbations have resulted in numerous disturbances of the cave ecosystem, including on its microbial compartment, which resulted in the formation of black stains especially on the rock faces of the passage. We investigated the cave microbiome in this part of Lascaux by sampling three mineral substrates (soil, banks, and inclined planes) on and outside stains to assess current cave microbial assemblage and explore the possibility that pigmented microorganisms involved in stain development occur as microbial consortia.

METHODS: Microbial abundance and diversity were assessed by means of quantitative PCR and high-throughput sequencing (Illumina MiSeq) of several DNA and cDNA taxonomic markers. Five sampling campaigns were carried out during winter and summer to embrace potential seasonal effect in this somewhat stable environment (based on measurements of temperature and CO2 concentration).

RESULTS: While the season or type of mineral substrate did not affect the abundances of bacteria and micro-eukaryotes on or outside stains, mineral substrate rather than stain presence appears to be the most significant factor determining microbial diversity and structuring microbial community, regardless of whether DNA or cDNA markers were considered. A phylogenetic signal was also detected in relation to substrate types, presence of stains but not with season among the OTUs common to the three substrates. Co-occurrence network analyses showed that most bacterial and fungal interactions were positive regardless of the factor tested (season, substrate, or stain), but these networks varied according to ecological conditions and time. Microorganisms known to harbor pigmentation ability were well established inside but also outside black stains, which may be prerequisite for subsequent stain formation.

CONCLUSIONS: This first high throughput sequencing performed in Lascaux Cave showed that black stains were secondary to mineral substrate in determining microbiome community structure, regardless of whether total or transcriptionally active bacterial and micro-eukaryotic communities were considered. These results revealed the potential for new stain formation and highlight the need for careful microbiome management to avoid further cave wall degradation.}, } @article {pmid30518356, year = {2018}, author = {Bin, P and Tang, Z and Liu, S and Chen, S and Xia, Y and Liu, J and Wu, H and Zhu, G}, title = {Intestinal microbiota mediates Enterotoxigenic Escherichia coli-induced diarrhea in piglets.}, journal = {BMC veterinary research}, volume = {14}, number = {1}, pages = {385}, pmid = {30518356}, issn = {1746-6148}, mesh = {Animals ; Bacteria/classification/genetics ; Diarrhea/microbiology/*veterinary ; Dysbiosis/immunology/microbiology/*veterinary ; Enterotoxigenic Escherichia coli/immunology/physiology ; Escherichia coli Infections/veterinary ; Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/*genetics/*immunology ; Intestinal Diseases/immunology/microbiology/*veterinary ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Swine ; Swine Diseases/immunology/*microbiology ; }, abstract = {BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) causes diarrhea in humans, cows, and pigs. The gut microbiota underlies pathology of several infectious diseases yet the role of the gut microbiota in the pathogenesis of ETEC-induced diarrhea is unknown.

RESULTS: By using an ETEC induced diarrheal model in piglet, we profiled the jejunal and fecal microbiota using metagenomics and 16S rRNA sequencing. A jejunal microbiota transplantation experiment was conducted to determine the role of the gut microbiota in ETEC-induced diarrhea. ETEC-induced diarrhea influenced the structure and function of gut microbiota. Diarrheal piglets had lower Bacteroidetes: Firmicutes ratio and microbiota diversity in the jejunum and feces, and lower percentage of Prevotella in the feces, but higher Lactococcus in the jejunum and higher Escherichia-Shigella in the feces. The transplantation of the jejunal microbiota from diarrheal piglets to uninfected piglets leaded to diarrhea after transplantation. Microbiota transplantation experiments also supported the notion that dysbiosis of gut microbiota is involved in the immune responses in ETEC-induced diarrhea.

CONCLUSION: We conclude that ETEC infection influences the gut microbiota and the dysbiosis of gut microbiota after ETEC infection mediates the immune responses in ETEC infection.}, } @article {pmid30518125, year = {2018}, author = {Raimundo, I and Silva, SG and Costa, R and Keller-Costa, T}, title = {Bioactive Secondary Metabolites from Octocoral-Associated Microbes-New Chances for Blue Growth.}, journal = {Marine drugs}, volume = {16}, number = {12}, pages = {}, pmid = {30518125}, issn = {1660-3397}, support = {EXPL/MAR-EST/1664/2013//Fundação para a Ciência e a Tecnologia/ ; PTDC/MAR-BIO/1547/2014//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/genetics/*metabolism ; Biological Products/isolation & purification/metabolism/*pharmacology ; Biosynthetic Pathways/*genetics ; Fungi/genetics/*metabolism ; Industrial Microbiology/methods ; Microbiota/physiology ; Multigene Family ; Symbiosis ; Technology, Pharmaceutical/methods ; }, abstract = {Octocorals (Cnidaria, Anthozoa Octocorallia) are magnificent repositories of natural products with fascinating and unusual chemical structures and bioactivities of interest to medicine and biotechnology. However, mechanistic understanding of the contribution of microbial symbionts to the chemical diversity of octocorals is yet to be achieved. This review inventories the natural products so-far described for octocoral-derived bacteria and fungi, uncovering a true chemical arsenal of terpenes, steroids, alkaloids, and polyketides with antibacterial, antifungal, antiviral, antifouling, anticancer, anti-inflammatory, and antimalarial activities of enormous potential for blue growth. Genome mining of 15 bacterial associates (spanning 12 genera) cultivated from Eunicella spp. resulted in the identification of 440 putative and classifiable secondary metabolite biosynthetic gene clusters (BGCs), encompassing varied terpene-, polyketide-, bacteriocin-, and nonribosomal peptide-synthase BGCs. This points towards a widespread yet uncharted capacity of octocoral-associated bacteria to synthetize a broad range of natural products. However, to extend our knowledge and foster the near-future laboratory production of bioactive compounds from (cultivatable and currently uncultivatable) octocoral symbionts, optimal blending between targeted metagenomics, DNA recombinant technologies, improved symbiont cultivation, functional genomics, and analytical chemistry are required. Such a multidisciplinary undertaking is key to achieving a sustainable response to the urgent industrial demand for novel drugs and enzyme varieties.}, } @article {pmid30507071, year = {2019}, author = {Alsammar, HF and Naseeb, S and Brancia, LB and Gilman, RT and Wang, P and Delneri, D}, title = {Targeted metagenomics approach to capture the biodiversity of Saccharomyces genus in wild environments.}, journal = {Environmental microbiology reports}, volume = {11}, number = {2}, pages = {206-214}, pmid = {30507071}, issn = {1758-2229}, support = {BB/L021471/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biodiversity ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Genome, Fungal/genetics ; Italy ; Metagenomics/*methods ; Saccharomyces/classification/*genetics/isolation & purification ; Saccharomyces cerevisiae/classification/genetics/isolation & purification ; Sequence Analysis, DNA ; *Soil Microbiology ; Trees ; }, abstract = {The species of the genus Saccharomyces are commonly inhabiting tree bark and the surrounding soil, but their abundance have likely been underestimated due to biases in culturing methods. Metagenomic studies have so far been unable to detect Saccharomyces species in wild environments. Here, we sequenced the mycobiome of soils surrounding different trees at various altitudes in the Italian Alps. To survey for yeasts species belonging to Saccharomyces genus rather than other fungal species, we performed a selectivity step involving the isolation of the internal transcribed spacer (ITS) region that is specific to this yeast group. Reads mapping to Saccharomyces species were detected in all soil samples, including reads for S. mikatae and for S. eubayanus. ITS1 alignment of the S. cerevisiae, S. paradoxus and S. kudriavzevii sequences showed up to three base pair polymorphisms with other known strains, indicating possible new lineages. Basidiomycetous fungi were still the dominant species, compared to the Ascomycota, but the selectivity step allowed for the first time the detection and study of the biodiversity of the Saccharomyces species in their natural environment.}, } @article {pmid30506399, year = {2019}, author = {Ren, F and Dong, W and Yan, DH}, title = {Endophytic bacterial communities of Jingbai Pear trees in north China analyzed with Illumina sequencing of 16S rDNA.}, journal = {Archives of microbiology}, volume = {201}, number = {2}, pages = {199-208}, doi = {10.1007/s00203-018-1597-9}, pmid = {30506399}, issn = {1432-072X}, support = {CAFYBB2017MA019//The Fundamental Research Funds for the Central Non-profit Research Institution of CAF/ ; }, mesh = {Actinobacteria/isolation & purification ; Bacteria/genetics/*isolation & purification ; China ; Cyanobacteria/isolation & purification ; DNA, Ribosomal/chemistry ; Endophytes ; Microbiota ; Proteobacteria/isolation & purification ; Pyrus/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; Soil Microbiology ; Trees/microbiology ; }, abstract = {Plant endophytes play a crucial role in plant growth, health and ecological function. Jingbai pear (the best quality cultivar of Pyrus ussuriensi Maxim. ex Rupr.) has important ecological and economic value in north China. Conversation of its genetics has great meanings to pear genus (Pyrus L.). However, the bacterial community associated with the cultivar remains unknown. In this study, the structure of endophytic bacterial communities associated with different tissues and soil of Jingbai Pear trees was analyzed with Illumina Miseq sequencing of bacterial 16S rDNA. This is the first report on bacterial microbiome associated with Jingbai pear. Our results demonstrated that different tissues harbored a unique bacterial assemblage. Interestingly, Cyanobacteria was the most abundant phylum, followed by Proteobacteria and Actinobacteria. Samples from three different sites (soils) had significant differences in microbial communities structure. Redundancy analysis (RDA) showed that the bacterial community structure correlated significantly with soil properties-temperature, pH, nitrogen and carbon contents. The conclusion could facilitate to understand the interaction and ecological function of endophytic bacteria with host Jingbai pear trees, so as to benefit the pear variety genetic resource conservation and protection.}, } @article {pmid30504906, year = {2018}, author = {Wampach, L and Heintz-Buschart, A and Fritz, JV and Ramiro-Garcia, J and Habier, J and Herold, M and Narayanasamy, S and Kaysen, A and Hogan, AH and Bindl, L and Bottu, J and Halder, R and Sjöqvist, C and May, P and Andersson, AF and de Beaufort, C and Wilmes, P}, title = {Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5091}, pmid = {30504906}, issn = {2041-1723}, mesh = {Cesarean Section ; Delivery, Obstetric ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; In Vitro Techniques ; Infant, Newborn ; Infectious Disease Transmission, Vertical ; Interleukin-18/metabolism ; Lipopolysaccharides/metabolism ; Metagenomics/methods ; Pregnancy ; Tumor Necrosis Factor-alpha/metabolism ; }, abstract = {The rate of caesarean section delivery (CSD) is increasing worldwide. It remains unclear whether disruption of mother-to-neonate transmission of microbiota through CSD occurs and whether it affects human physiology. Here we perform metagenomic analysis of earliest gut microbial community structures and functions. We identify differences in encoded functions between microbiomes of vaginally delivered (VD) and CSD neonates. Several functional pathways are over-represented in VD neonates, including lipopolysaccharide (LPS) biosynthesis. We link these enriched functions to individual-specific strains, which are transmitted from mothers to neonates in case of VD. The stimulation of primary human immune cells with LPS isolated from early stool samples of VD neonates results in higher levels of tumour necrosis factor (TNF-α) and interleukin 18 (IL-18). Accordingly, the observed levels of TNF-α and IL-18 in neonatal blood plasma are higher after VD. Taken together, our results support that CSD disrupts mother-to-neonate transmission of specific microbial strains, linked functional repertoires and immune-stimulatory potential during a critical window for neonatal immune system priming.}, } @article {pmid30504850, year = {2018}, author = {Letuma, P and Arafat, Y and Waqas, M and Lin, F and Lin, W and Zhang, Y and Masita, M and Fan, K and Li, Z and Lin, W}, title = {Gene mutation associated with esl mediates shifts on fungal community composition in rhizosphere soil of rice at grain-filling stage.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {17521}, pmid = {30504850}, issn = {2045-2322}, support = {31701329//National Natural Science Foundation of China (National Science Foundation of China)/International ; 2015M580560//China Postdoctoral Science Foundation/International ; 2016J01100//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/International ; }, mesh = {Biomass ; *Edible Grain ; Fungi/classification/genetics/*isolation & purification ; *Genes, Fungal ; Metagenomics ; *Mutation ; *Mycobiome ; Oryza/*genetics ; Plant Leaves/metabolism ; RNA, Ribosomal, 18S/genetics ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Generally, plant roots shape the rhizosphere fungal community but how individual plant genes involved in senescence affect this shaping is less studied. We used an early senescence leaf (esl) mutant rice and compared it with its isogenic wild type variety to evaluate the effect of the vacuolar H[+]-ATPase (VHA-A1) gene mutation on the rhizosphere fungal community structure and composition using a metagenomic pyrosequencing approach. The most predominate fungal phyla identified for both isogenic lines belonged to Ascomycota, Basidiomycota and Glomeromycota, where Ascomycota were more prevalent in the esl mutant than the wild type variety. Real-time quantitative PCR analysis confirmed a significant rise in the richness of Cladosporium cladosporioides in esl mutant rice than the wild type variety. Correlation analysis revealed four most abundant genera identified for the esl mutant and their close association with yield and biomass decline, lipid peroxidation, lower root vitality, chlorophyll degradation and limited VHA activity. Higher K[+] efflux, H[+] and a lower Ca[2+] influx was also observed in the esl mutant which could be the reason for abnormal functioning of mutant plants. These results illustrate that besides the well-known effect of senescence on plant physiology and yield decline, it can further shape the rhizosphere fungal community.}, } @article {pmid30504642, year = {2019}, author = {Nakagawa, T and Tsuchiya, Y and Ueda, S and Fukui, M and Takahashi, R}, title = {Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan.}, journal = {Microbes and environments}, volume = {34}, number = {1}, pages = {13-22}, pmid = {30504642}, issn = {1347-4405}, mesh = {Ammonia/metabolism ; Archaea/classification/genetics/isolation & purification/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; Geologic Sediments/*microbiology ; Japan ; Lakes/*microbiology ; Metagenomics ; *Microbiota/genetics ; Nitrous Oxide/*metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics ; *Saline Waters ; *Water Microbiology ; Zosteraceae/*microbiology ; }, abstract = {Nitrous oxide (N2O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N2O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N2O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N2O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N2O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N2O-reducing microbiome in the in situ sediments of eelgrass zones. Sulfur-oxidizing Gammaproteobacteria within nosZ gene clade II dominated in the lineage Dechloromonas-Magnetospirillum-Thiocapsa. Alphaproteobacteria within nosZ gene clade I were predominant in both zones. The proportions of Epsilonproteobacteria within nosZ gene clade II increased after incubations in the eelgrass zone microcosm supplemented with N2O only. Collectively, these results suggest that the N2O-reducing microbiome in eelgrass meadows is largely responsible for coastal N2O mitigation.}, } @article {pmid30504213, year = {2019}, author = {Zinke, LA and Glombitza, C and Bird, JT and Røy, H and Jørgensen, BB and Lloyd, KG and Amend, JP and Reese, BK}, title = {Microbial Organic Matter Degradation Potential in Baltic Sea Sediments Is Influenced by Depositional Conditions and In Situ Geochemistry.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {4}, pages = {}, pmid = {30504213}, issn = {1098-5336}, mesh = {Biodegradation, Environmental ; Carbohydrate Metabolism ; Carbon/metabolism ; *Carbon Cycle ; Ecology ; Fatty Acids, Volatile/analysis ; Fermentation ; Food Chain ; Geologic Sediments/*chemistry/*microbiology ; Heterotrophic Processes ; Metabolic Networks and Pathways/genetics ; Metagenome ; Microbiota/genetics/*physiology ; Multivariate Analysis ; Open Reading Frames/genetics ; Seawater/*chemistry/*microbiology ; }, abstract = {Globally, marine sediments are a vast repository of organic matter, which is degraded through various microbial pathways, including polymer hydrolysis and monomer fermentation. The sources, abundances, and quality (i.e., labile or recalcitrant) of the organic matter and the composition of the microbial assemblages vary between sediments. Here, we examine new and previously published sediment metagenomes from the Baltic Sea and the nearby Kattegat region to determine connections between geochemistry and the community potential to degrade organic carbon. Diverse organic matter hydrolysis encoding genes were present in sediments between 0.25 and 67 meters below seafloor and were in higher relative abundances in those sediments that contained more organic matter. New analysis of previously published metatranscriptomes demonstrated that many of these genes were transcribed in two organic-rich Holocene sediments. Some of the variation in deduced pathways in the metagenomes correlated with carbon content and depositional conditions. Fermentation-related genes were found in all samples and encoded multiple fermentation pathways. Notably, genes involved in alcohol metabolism were amongst the most abundant of these genes, indicating that this is an important but underappreciated aspect of sediment carbon cycling. This study is a step towards a more complete understanding of microbial food webs and the impacts of depositional facies on present sedimentary microbial communities.IMPORTANCE Sediments sequester organic matter over geologic time scales and impact global climate regulation. Microbial communities in marine sediments drive organic matter degradation, but the factors controlling their assemblages and activities, which in turn impact their role in organic matter degradation, are not well understood. Hence, determining the role of microbial communities in carbon cycling in various sediment types is necessary for predicting future sediment carbon cycling. We examined microbial communities in Baltic Sea sediments, which were deposited across various climatic and geographical regimes to determine the relationship between microbial potential for breakdown of organic matter and abiotic factors, including geochemistry and sediment lithology. The findings from this study will contribute to our understanding of carbon cycling in the deep biosphere and how microbial communities live in deeply buried environments.}, } @article {pmid30504145, year = {2018}, author = {Tokuda, G and Mikaelyan, A and Fukui, C and Matsuura, Y and Watanabe, H and Fujishima, M and Brune, A}, title = {Fiber-associated spirochetes are major agents of hemicellulose degradation in the hindgut of wood-feeding higher termites.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {51}, pages = {E11996-E12004}, pmid = {30504145}, issn = {1091-6490}, mesh = {Animals ; Cellulases/genetics/metabolism ; Cellulose/metabolism ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Gene Expression Regulation, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Glycoside Hydrolases/genetics/metabolism ; Isoptera/*microbiology ; Metagenome/genetics ; Metagenomics ; Phylogeny ; Polysaccharides/*metabolism ; Sequence Analysis, DNA ; Spirochaetales/*enzymology/*genetics/*metabolism ; Symbiosis ; Wood/*metabolism ; Xylans/metabolism ; Xylosidases/classification/genetics/metabolism ; }, abstract = {Symbiotic digestion of lignocellulose in wood-feeding higher termites (family Termitidae) is a two-step process that involves endogenous host cellulases secreted in the midgut and a dense bacterial community in the hindgut compartment. The genomes of the bacterial gut microbiota encode diverse cellulolytic and hemicellulolytic enzymes, but the contributions of host and bacterial symbionts to lignocellulose degradation remain ambiguous. Our previous studies of Nasutitermes spp. documented that the wood fibers in the hindgut paunch are consistently colonized not only by uncultured members of Fibrobacteres, which have been implicated in cellulose degradation, but also by unique lineages of Spirochaetes. Here, we demonstrate that the degradation of xylan, the major component of hemicellulose, is restricted to the hindgut compartment, where it is preferentially hydrolyzed over cellulose. Metatranscriptomic analysis documented that the majority of glycoside hydrolase (GH) transcripts expressed by the fiber-associated bacterial community belong to family GH11, which consists exclusively of xylanases. The substrate specificity was further confirmed by heterologous expression of the gene encoding the predominant homolog. Although the most abundant transcripts of GH11 in Nasutitermes takasagoensis were phylogenetically placed among their homologs of Firmicutes, immunofluorescence microscopy, compositional binning of metagenomics contigs, and the genomic context of the homologs indicated that they are encoded by Spirochaetes and were most likely obtained by horizontal gene transfer among the intestinal microbiota. The major role of spirochetes in xylan degradation is unprecedented and assigns the fiber-associated Treponema clades in the hindgut of wood-feeding higher termites a prominent part in the breakdown of hemicelluloses.}, } @article {pmid30503454, year = {2018}, author = {Hwang, J and Park, SY and Lee, S and Lee, TK}, title = {High diversity and potential translocation of DNA viruses in ballast water.}, journal = {Marine pollution bulletin}, volume = {137}, number = {}, pages = {449-455}, doi = {10.1016/j.marpolbul.2018.10.053}, pmid = {30503454}, issn = {1879-3363}, mesh = {Animals ; DNA Viruses/*genetics/*isolation & purification ; Introduced Species ; Metagenomics ; Mexico ; New York ; Panama ; Republic of Korea ; Saudi Arabia ; *Ships ; Water/*analysis/chemistry ; Water Microbiology ; }, abstract = {Ballast water is a common vector for the transport of invasive species to new marine and aquatic environments. We used a metagenomics approach to examine the composition and diversity of viral communities in ballast water from ships originating in Mexico, Saudi Arabia, New York, and Panama, and in water from the port of their destination in Busan, Korea. Myoviridae was the most abundant virus family in ballast water, followed Podoviridae and Siphoviridae. We also identified viruses that infect invertebrates, amoebas, and algae in ballast water and in the Busan port water. Interestingly, there were several viruses that infect humans or other animals (Swinepox virus, Raccoonpox virus, Suid herpesvirus, and Human endogenous retrovirus) in the samples from New York and Panama. In addition, there were giant viruses in all the ballast water samples, especially, identified Megavirus chilensis in New York and Panama, and Pandoravirus salinus in Mexico and Saudi Arabia. These results provide detailed descriptions of the characteristics of the viruses present in ballast water, document significant viral diversity, and indicate the potential translocation of viruses via ballast water.}, } @article {pmid30502941, year = {2018}, author = {Foutel-Rodier, T and Thierry, A and Koszul, R and Marbouty, M}, title = {Generation of a Metagenomics Proximity Ligation 3C Library of a Mammalian Gut Microbiota.}, journal = {Methods in enzymology}, volume = {612}, number = {}, pages = {183-195}, doi = {10.1016/bs.mie.2018.08.001}, pmid = {30502941}, issn = {1557-7988}, mesh = {Animals ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenome/*genetics ; Metagenomics/*methods ; Sequence Analysis, DNA/methods ; }, abstract = {Microbial species thrive in very diverse environments and play fundamental roles in their equilibrium and dynamics. Metagenomics consists in extracting, sequencing, and studying the DNA present in ecosystems to better understand their regulation. Ideally, the maximal amount of information would be gathered from the full sequences of the genomes, episomes, and phages present in the microbial communities. Current high-throughput DNA sequencing produces reads ranging in size from a few dozen base pairs for the most commonly used technologies to several kb for emerging single-molecule real-time sequencing techniques. Although valuable information can be extracted from processing these DNA sequences into contigs, reconstructing full genomes remains a difficult task. Clustering contigs according to their similarities or read coverage covariations gives some insights on these genomes, but remains limited as viral sequences, or recent horizontal gene transfers, often differ from their host genomes. We recently developed meta3C, a proximity ligation approach that bins contigs in a sequence-independent way by quantifying and exploiting their tridimensional collisions frequencies in vivo. This technique has demonstrated a great potential to reconstruct genomes as well as to assign plasmids and phages to their hosts. It nevertheless requires a specific processing of the microbial samples before sequencing, which has to be carefully planned.}, } @article {pmid30517025, year = {2019}, author = {Bazin, A and Debroas, D and Mephu Nguifo, E}, title = {A De Novo Robust Clustering Approach for Amplicon-Based Sequence Data.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {26}, number = {6}, pages = {618-624}, doi = {10.1089/cmb.2018.0170}, pmid = {30517025}, issn = {1557-8666}, mesh = {Algorithms ; Cluster Analysis ; Computational Biology/methods ; Metagenomics/methods ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {When analyzing microbial communities, an active and computational challenge concerns the categorization of 16S rRNA gene sequences into operational taxonomic units (OTUs). Established clustering tools use a one pass algorithm to tackle high number of gene sequences and produce OTUs in reasonable time. However, all of the current tools are based on a crisp clustering approach, where a gene sequence is assigned to one cluster. The weak quality of the output compared with more complex clustering algorithms forces the user to postprocess the obtained OTUs. Providing a membership degree when assigning a gene sequence to an OTU will help the user during the postprocessing task. Moreover it is possible to use this membership degree to automatically evaluate the quality of the obtained OTUs. So the goal of this study is to propose a new clustering approach that takes into account uncertainty when producing OTUs, and improves both the quality and the presentation of the OTU results.}, } @article {pmid30514364, year = {2018}, author = {Vray, M and Hedible, BG and Adam, P and Tondeur, L and Manirazika, A and Randremanana, R and Mainassara, H and Briend, A and Artaud, C and von Platen, C and Altmann, M and Jambou, R}, title = {A multicenter, randomized controlled comparison of three renutrition strategies for the management of moderate acute malnutrition among children aged from 6 to 24 months (the MALINEA project).}, journal = {Trials}, volume = {19}, number = {1}, pages = {666}, pmid = {30514364}, issn = {1745-6215}, support = {2101375618//MEAE/ ; }, mesh = {Acute Disease ; Africa ; Age Factors ; Albendazole/administration & dosage ; Anti-Bacterial Agents/*administration & dosage/adverse effects ; Antiparasitic Agents/administration & dosage ; Azithromycin/*administration & dosage/adverse effects ; Child Development ; Child, Preschool ; Female ; *Flour/adverse effects ; *Food, Fortified/adverse effects ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant ; Infant Nutrition Disorders/diagnosis/microbiology/physiopathology/*therapy ; *Infant Nutritional Physiological Phenomena ; Male ; Malnutrition/diagnosis/microbiology/physiopathology/*therapy ; Multicenter Studies as Topic ; *Nutritional Status ; Prebiotics/*administration & dosage/adverse effects ; Randomized Controlled Trials as Topic ; Time Factors ; Treatment Outcome ; }, abstract = {BACKGROUND: The aim of this open-label, randomized controlled trial conducted in four African countries (Madagascar, Niger, Central African Republic, and Senegal) is to compare three strategies of renutrition for moderate acute malnutrition (MAM) in children based on modulation of the gut microbiota with enriched flours alone, enriched flours with prebiotics or enriched flours coupled with antibiotic treatment.

METHODS: To be included, children aged between 6 months and 2 years are preselected based on mid-upper-arm circumference (MUAC) and are included based on a weight-for-height Z-score (WHZ) between - 3 and - 2 standard deviations (SD). As per current protocols, children receive renutrition treatment for 12 weeks and are assessed weekly to determine improvement. The primary endpoint is recovery, defined by a WHZ ≥ - 1.5 SD after 12 weeks of treatment. Data collected include clinical and socioeconomic characteristics, side effects, compliance and tolerance to interventions. Metagenomic analysis of gut microbiota is conducted at inclusion, 3 months, and 6 months. The cognitive development of children is evaluated in Senegal using only the Developmental Milestones Checklist II (DMC II) questionnaire at inclusion and at 3, 6, and 9 months. The data will be correlated with renutrition efficacy and metagenomic data.

DISCUSSION: This study will provide new insights for the treatment of MAM, as well as original data on the modulation of gut microbiota during the renutrition process to support (or not) the microbiota hypothesis of malnutrition.

TRIAL REGISTRATION: ClinicalTrials.gov, ID: NCT03474276 Last update 28 May 2018.}, } @article {pmid30513942, year = {2018}, author = {Pinho, CJ and Santos, B and Mata, VA and Seguro, M and Romeiras, MM and Lopes, RJ and Vasconcelos, R}, title = {What Is the Giant Wall Gecko Having for Dinner? Conservation Genetics for Guiding Reserve Management in Cabo Verde.}, journal = {Genes}, volume = {9}, number = {12}, pages = {}, pmid = {30513942}, issn = {2073-4425}, support = {MP/EAM/2016/06//Fondation Ensemble/ ; NA//Club 300 Foundation for Bird Protection/ ; NA//Monaco Explorations/ ; Fellowships PD/BD/106055/2015 (to BS), PD/BD/113462/2015 (to VAM), SFRH/BPD/84141/2012 (to RJL), and SFRH/BPD/79913/2011 (to RV) were funded by FCT/MEC and POPH/QREN/FSE//Fundação para a Ciência e a Tecnologia/ ; (NORTE-01-0145-FEDER-AGRIGEN)//NORTE2020/PORTUGAL/ ; VAM by ERA Chair in Environmental Metagenomics (EU Horizon 2020 Research and Innovation Programme Grant agreement No 668981)//Horizon 2020/ ; MACDIV-FCT-PTDC/BIABIC/0054/2014, and CVAgrobiodiversity/333111699 (to MMR)//Aga Khan Development Network (AKDN) and FCT/ ; }, abstract = {Knowledge on diet composition of a species is an important step to unveil its ecology and guide conservation actions. This is especially important for species that inhabit remote areas within biodiversity hotspots, with little information about their ecological roles. The emblematic giant wall gecko of Cabo Verde, Tarentola gigas, is restricted to the uninhabited Branco and Raso islets, and presents two subspecies. It is classified as Endangered, and locally Extinct on Santa Luzia Island; however, little information is known about its diet and behaviour. In this study, we identified the main plant, arthropods, and vertebrates consumed by both gecko subspecies using next generation sequencing (NGS) (metabarcoding of faecal pellets), and compared them with the species known to occur on Santa Luzia. Results showed that plants have a significant role as diet items and identified vertebrate and invertebrate taxa with higher taxonomic resolution than traditional methods. With this study, we now have data on the diet of both subspecies for evaluating the reintroduction of this threatened gecko on Santa Luzia as potentially successful, considering the generalist character of both populations. The information revealed by these ecological networks is important for the development of conservation plans by governmental authorities, and reinforces the essential and commonly neglected role of reptiles on island systems.}, } @article {pmid30510171, year = {2019}, author = {Daly, RA and Roux, S and Borton, MA and Morgan, DM and Johnston, MD and Booker, AE and Hoyt, DW and Meulia, T and Wolfe, RA and Hanson, AJ and Mouser, PJ and Moore, JD and Wunch, K and Sullivan, MB and Wrighton, KC and Wilkins, MJ}, title = {Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing.}, journal = {Nature microbiology}, volume = {4}, number = {2}, pages = {352-361}, doi = {10.1038/s41564-018-0312-6}, pmid = {30510171}, issn = {2058-5276}, mesh = {Bacteriophages/classification/genetics/*physiology ; Biodiversity ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Firmicutes/classification/genetics/*growth & development/*virology ; Hydraulic Fracking ; Metagenome ; *Microbial Consortia/genetics ; Oil and Gas Fields/*microbiology/*virology ; Virus Activation ; }, abstract = {The deep terrestrial biosphere harbours a substantial fraction of Earth's biomass and remains understudied compared with other ecosystems. Deep biosphere life primarily consists of bacteria and archaea, yet knowledge of their co-occurring viruses is poor. Here, we temporally catalogued viral diversity from five deep terrestrial subsurface locations (hydraulically fractured wells), examined virus-host interaction dynamics and experimentally assessed metabolites from cell lysis to better understand viral roles in this ecosystem. We uncovered high viral diversity, rivalling that of peatland soil ecosystems, despite low host diversity. Many viral operational taxonomic units were predicted to infect Halanaerobium, the dominant microorganism in these ecosystems. Examination of clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins (CRISPR-Cas) spacers elucidated lineage-specific virus-host dynamics suggesting active in situ viral predation of Halanaerobium. These dynamics indicate repeated viral encounters and changing viral host range across temporally and geographically distinct shale formations. Laboratory experiments showed that prophage-induced Halanaerobium lysis releases intracellular metabolites that can sustain key fermentative metabolisms, supporting the persistence of microorganisms in this ecosystem. Together, these findings suggest that diverse and active viral populations play critical roles in driving strain-level microbial community development and resource turnover within this deep terrestrial subsurface ecosystem.}, } @article {pmid30509871, year = {2019}, author = {Kozyrskyj, AL and Bourque, SL and Ospina, MB}, title = {Microbiota be nimble.}, journal = {EBioMedicine}, volume = {39}, number = {}, pages = {21-22}, pmid = {30509871}, issn = {2352-3964}, mesh = {Dietary Carbohydrates/metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Metagenome ; Metagenomics/methods ; Pregnancy ; }, } @article {pmid30509257, year = {2018}, author = {He, F and Liu, D and Zhang, L and Zhai, J and Ma, Y and Xu, Y and Jiang, G and Rong, K and Ma, J}, title = {Metagenomic analysis of captive Amur tiger faecal microbiome.}, journal = {BMC veterinary research}, volume = {14}, number = {1}, pages = {379}, pmid = {30509257}, issn = {1746-6148}, support = {31372209//National Natural Science Foundation of China/ ; 2572017AA20//The Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; Animals, Zoo/*microbiology ; Bacteria/*classification/genetics/metabolism ; Endangered Species ; Feces/*microbiology ; *Gastrointestinal Microbiome ; *Metagenome ; Tigers/*microbiology ; }, abstract = {BACKGROUND: The gastrointestinal tracts of animals are home to large, complex communities of microbes. The compositions of these communities ultimately reflect the coevolution of microorganisms with their animal host and are influenced by the living environment, diet and immune status of the host. Gut microbes have been shown to be important for human disease and health, but little research exists in the gut microbiome of the Amur tiger, which is one of the most endangered species in the world.

RESULTS: In this study, we present the use of whole-metagenome shotgun sequencing to analyze the composition and functional structures of the gut microbiota in captive Amur tigers. Our results showed a high abundance of four major phyla in captive Amur tigers, including Proteobacteria, Firmicutes, Actinobacteria and Fusobacteria. Moreover, at the genus level, Escherichia, Collinsella and Fusobacterium were most abundant in the captive Amur tiger fecal metagenome. At the species level, Escherichia coli, Fusobacterium ulcerans and Fusobacterium varium were the species with highest abundances in the captive Amur tiger gut microbiota. The primary functional categories of the Amur tiger faecal metagenome were associated mainly with Carbohydrate metabolism, Membrane transport and Amino acid metabolism based on the KEGG pathway database. The comparative metagenomic analyses showed that the captive Amur tiger fecal metagenome had a lower abundance of Spirochaetes, Cyanobacteria and Ascomycota than other animals, and the primary functional categories were primarily associated with carbohydrate metabolism subsystems, clustering-based subsystems and protein metabolism.

CONCLUSIONS: We presented here for the first time the use of the shotgun metagenomic sequencing approach to study the composition and functional structures of the gut microbiota in captive Amur tiger.}, } @article {pmid30502597, year = {2019}, author = {Yang, Y and Liu, G and Song, W and Ye, C and Lin, H and Li, Z and Liu, W}, title = {Plastics in the marine environment are reservoirs for antibiotic and metal resistance genes.}, journal = {Environment international}, volume = {123}, number = {}, pages = {79-86}, doi = {10.1016/j.envint.2018.11.061}, pmid = {30502597}, issn = {1873-6750}, mesh = {Anti-Bacterial Agents ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Microbial ; *Genes, Bacterial ; Metagenomics ; Metals ; *Microbiota ; Pacific Ocean ; *Plastics ; RNA, Ribosomal, 16S ; Seawater/microbiology ; Water Pollution/*analysis ; }, abstract = {Plastics have been accumulated offshore and in the deep oceans at an unprecedented scale. Microbial communities have colonized the plastisphere, which has become a reservoir for both antibiotic and metal resistance genes (ARGs and MRGs). This is the first analysis of the diversity, abundance, and co-occurrence of ARGs and MRGs, and their relationships within the microbial community, using metagenomic data of plastic particles observed in the North Pacific Gyre obtained from the National Centre for Biotechnology Information Sequence Read Archive database. The abundance of ARGs and MRGs in microbial communities on the plastics were in the ranges 7.07 × 10[-4]-1.21 × 10[-2] and 5.51 × 10[-3]-4.82 × 10[-2] copies per 16S rRNA, respectively. Both the Shannon-Wiener indices and richness of ARGs and MRGs in plastics microbiota were significantly greater than those of ARGs and MRGs in seawater microbiota in the North Pacific Gyre via one-way analysis of variance. Multidrug resistance genes and multi-metal resistance genes were the main classes of genes detected in plastic microbiota. There were no significant differences in the abundance or diversity of ARGs and MRGs between macroplastics biota and microplastics biota, indicating that particle size had no effect on resistance genes. Procrustes analysis suggested that microbial community composition was the determining factor of the ARG profile but not for MRG. Some ARGs and MRGs had a higher incidence of non-random co-occurrence, suggesting that the co-effects of selection for antibiotic or metal resistance are important factors influencing the resistome of the microbiota on the plastic particles.}, } @article {pmid30500759, year = {2019}, author = {Huang, Z and Wei, Z and Xiao, X and Tang, M and Li, B and Zhang, X}, title = {Nitrification/denitrification shaped the mercury-oxidizing microbial community for simultaneous Hg[0] and NO removal.}, journal = {Bioresource technology}, volume = {274}, number = {}, pages = {18-24}, doi = {10.1016/j.biortech.2018.11.069}, pmid = {30500759}, issn = {1873-2976}, mesh = {Biofilms ; Bioreactors/microbiology ; Denitrification ; Mercury/*isolation & purification ; *Microbiota ; Nitrification ; Nitrosomonas/metabolism ; Oxidation-Reduction ; Xanthomonadaceae/metabolism ; }, abstract = {A denitrifying/nitrifying membrane biofilm reactor for simultaneous removal of Hg[0] and NO was investigated. Hg[0] and NO removal efficiency attained 94.5% and 86%, respectively. The mercury-oxidizing microbial community was significantly shaped by nitrification/denitrification after the supply of gaseous Hg[0]and NO continuously. Dominant genera Rhodanobacter and Nitrosomonas participated in Hg[0] oxidation, nitrification and denitrification simultaneously. Hg[0] oxidizing bacteria (Gallionella, Rhodanobacter, Ottowia, Nitrosomonas and etc.), nitrifying bacteria (Nitrosomonas, Rhodanobacter, Diaphorobacte and etc.) and denitrifying bacteria (Nitrosomonas, Rhodanobacter, Castellaniella and etc.) co-existed in the MBfR, as shown by metagenomic sequencing. X-ray photoelectron spectroscopy (XPS) and high performance liquid chromatography-inductively coupled plasma mass spectrometry (HPLC-ICP-MS) confirmed the formation of a mercuric species (Hg[2+]) from mercury bio-oxidation. Mechanism of mercury oxidation can be described as the bacterial oxidation of Hg[0] in which Hg[0] serves as electron donor, NO serves as electron donor in nitrification and electron acceptor in denitrification, oxygen serves as electron acceptor.}, } @article {pmid30500755, year = {2019}, author = {Cattò, C and Garuglieri, E and Borruso, L and Erba, D and Casiraghi, MC and Cappitelli, F and Villa, F and Zecchin, S and Zanchi, R}, title = {Impacts of dietary silver nanoparticles and probiotic administration on the microbiota of an in-vitro gut model.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {245}, number = {}, pages = {754-763}, doi = {10.1016/j.envpol.2018.11.019}, pmid = {30500755}, issn = {1873-6424}, mesh = {Bacillus subtilis/drug effects/growth & development ; Bacteroidetes ; Caco-2 Cells ; Clostridium ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; Humans ; In Situ Hybridization, Fluorescence ; *Metal Nanoparticles ; Probiotics/*pharmacology ; Silver/*pharmacology ; }, abstract = {Ingestion of silver nanoparticles (AgNPs) is inevitable linked to their widespread use in food, medicines and other consumer products. However, their effects on human microbiota at non-lethal concentrations remain poorly understood. In this study, the interactions among 1 μg mL[-1] AgNPs, the intestinal microbiota, and the probiotic Bacillus subtilis (BS) were tested using in-vitro batch fermentation models inoculated with human fecal matter. Results from metagenomic investigations revealed that the core bacterial community was not affected by the exposure of AgNPs and BS at the later stage of fermentation, while the proportions of rare species changed drastically with the treatments. Furthermore, shifts in the Firmicutes/Bacteriodetes (F/B) ratios were observed after 24 h with an increase in the relative abundance of Firmicutes species and a decrease in Bacteroidetes in all fermentation cultures. The co-exposure to AgNPs and BS led to the lowest F/B ratio. Fluorescent in-situ hybridization analyses indicated that non-lethal concentration of AgNPs negatively affected the relative percentage of Faecalibacterium prausnitzii and Clostridium coccoides/Eubacterium rectales taxa in the fermentation cultures after 24 h. However, exposure to single and combined treatments of AgNPs and BS did not change the overall diversity of the fecal microflora. Functional differences in cell motility, translation, transport, and xenobiotics degradation occurred in AgNPs-treated fermentation cultures but not in AgNPs+BS-treated samples. Compared to the control samples, treated fecal cultures showed no significant statistical differences in terms of short-chain fatty acids profiles, cytotoxic and genotoxic effects on Caco-2 cell monolayers. Overall, AgNPs did not affect the composition and diversity of the core fecal microflora and its metabolic and toxic profiles. This work indicated a chemopreventive role of probiotic on fecal microflora against AgNPs, which were shown by the decrease of F/B ratio and the unaltered state of some key metabolic pathways.}, } @article {pmid30499334, year = {2019}, author = {Robino, P and Ferrocino, I and Rossi, G and Dogliero, A and Alessandria, V and Grosso, L and Galosi, L and Tramuta, C and Cocolin, L and Nebbia, P}, title = {Changes in gut bacterial communities in canaries infected by Macrorhabdus ornithogaster.}, journal = {Avian pathology : journal of the W.V.P.A}, volume = {48}, number = {2}, pages = {111-120}, doi = {10.1080/03079457.2018.1553294}, pmid = {30499334}, issn = {1465-3338}, mesh = {Animals ; Bacteria/genetics/*isolation & purification ; Bird Diseases/*microbiology ; Canaries/*microbiology ; Computational Biology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/veterinary ; Italy ; Male ; Polymerase Chain Reaction/veterinary ; Saccharomycetales/*physiology ; }, abstract = {Macrorhabdus ornithogaster is an opportunistic yeast that colonizes the gastric mucosa of many avian species. Until now, no studies have focused on the influence of a gastric infection on the balance of the intestinal microbiota of birds. In this study, 44 faecal samples from individual canaries, with and without M. ornithogaster infection, were analysed. The detection of the yeast was evaluated by 18S rRNA PCR. In order to evaluate the impact of the Macrorhabdus infection on the bacterial communities, culture-independent methods, by the use of amplicon-based sequencing as well as 16S rRNA-DGGE, were adopted. The different health status of animals affected the relative abundance of the main OTUs, with a greater diversification of the gut microbiota in healthy animals compared to the infected. In particular, Lactococcus, Pseudomonas, Acinetobacter, Lachnospiraceae, Propionibacterium and Weissella were found to be characteristic of uninfected animals (FDR < 0.05), while Lactobacillus and Candidatus Arthromitus were characteristic of infected animals (FDR < 0.05). Both these taxa have been reported as immunostimulatory, involved in immunological disorders. In infected animals the inferred metagenome assessed by PICRUST clearly showed a positive correlation between the presence of M. ornithogaster and KEGG genes related to ether lipid metabolism, already reported to be immunostimulatory by activation of macrophages and to play a pathophysiological role in several immunological disorders. Finally, our results show an interaction between infection of the digestive tract and intestinal microbiota of pet birds and provide insight into the changing of the complex enteric bacterial community. HIGHLIGHTS Macrorabdus ornithogaster is a gastric yeast that colonizes a wide range of birds. Differences were found between infected and healthy animals in gut microbiota. Candidatus Arthromitus was closely associated with infected birds. M. ornithogaster can affect intestinal microbiota composition of canaries.}, } @article {pmid30498254, year = {2018}, author = {Dutta, A and Dutta Gupta, S and Gupta, A and Sarkar, J and Roy, S and Mukherjee, A and Sar, P}, title = {Exploration of deep terrestrial subsurface microbiome in Late Cretaceous Deccan traps and underlying Archean basement, India.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {17459}, pmid = {30498254}, issn = {2045-2322}, support = {MoES/P.O.(Seismo)/1(181)/2013//Ministry of Earth Sciences (MoES)/International ; }, mesh = {Biodiversity ; Computational Biology/methods ; *Environmental Microbiology ; Geologic Sediments/*microbiology ; India ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Scientific deep drilling at Koyna, western India provides a unique opportunity to explore microbial life within deep biosphere hosted by ~65 Myr old Deccan basalt and Archaean granitic basement. Characteristic low organic carbon content, mafic/felsic nature but distinct trend in sulfate and nitrate concentrations demarcates the basaltic and granitic zones as distinct ecological habitats. Quantitative PCR indicates a depth independent distribution of microorganisms predominated by bacteria. Abundance of dsrB and mcrA genes are relatively higher (at least one order of magnitude) in basalt compared to granite. Bacterial communities are dominated by Alpha-, Beta-, Gammaproteobacteria, Actinobacteria and Firmicutes, whereas Euryarchaeota is the major archaeal group. Strong correlation among the abundance of autotrophic and heterotrophic taxa is noted. Bacteria known for nitrite, sulfur and hydrogen oxidation represent the autotrophs. Fermentative, nitrate/sulfate reducing and methane metabolising microorganisms represent the heterotrophs. Lack of shared operational taxonomic units and distinct clustering of major taxa indicate possible community isolation. Shotgun metagenomics corroborate that chemolithoautotrophic assimilation of carbon coupled with fermentation and anaerobic respiration drive this deep biosphere. This first report on the geomicrobiology of the subsurface of Deccan traps provides an unprecedented opportunity to understand microbial composition and function in the terrestrial, igneous rock-hosted, deep biosphere.}, } @article {pmid30497919, year = {2019}, author = {Eisenhofer, R and Minich, JJ and Marotz, C and Cooper, A and Knight, R and Weyrich, LS}, title = {Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations.}, journal = {Trends in microbiology}, volume = {27}, number = {2}, pages = {105-117}, doi = {10.1016/j.tim.2018.11.003}, pmid = {30497919}, issn = {1878-4380}, mesh = {*Biomass ; *DNA Contamination ; DNA, Bacterial/analysis/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; Microbiological Techniques/methods/standards ; Microbiota/*genetics ; Reproducibility of Results ; Specimen Handling ; }, abstract = {Next-generation sequencing approaches in microbiome research have allowed surveys of microbial communities, their genomes, and their functions with higher sensitivity than ever before. However, this sensitivity is a double-edged sword because these tools also efficiently detect contaminant DNA and cross-contamination, which can confound the interpretation of microbiome data. Therefore, there is an urgent need to integrate key controls into microbiome research to improve the integrity of microbiome studies. Here, we review how contaminant DNA and cross-contamination arise within microbiome studies and discuss their negative impacts, especially during the analysis of low microbial biomass samples. We then identify several key measures that researchers can implement to reduce the impact of contaminant DNA and cross-contamination during microbiome research. We put forward a set of minimal experimental criteria, the 'RIDE' checklist, to improve the validity of future low microbial biomass research.}, } @article {pmid30496201, year = {2018}, author = {Biscarini, F and Palazzo, F and Castellani, F and Masetti, G and Grotta, L and Cichelli, A and Martino, G}, title = {Rumen microbiome in dairy calves fed copper and grape-pomace dietary supplementations: Composition and predicted functional profile.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0205670}, pmid = {30496201}, issn = {1932-6203}, mesh = {*Animal Feed ; Animals ; Cattle ; Copper/*administration & dosage ; *Dietary Supplements ; Microbiota/*drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; Rumen/drug effects/microbiology ; Vitis/chemistry ; }, abstract = {The rumen microbiome is fundamental for the productivity and health of dairy cattle and diet is known to influence the rumen microbiota composition. In this study, grape-pomace, a natural source of polyphenols, and copper sulfate were provided as feed supplementation in 15 Holstein-Friesian calves, including 5 controls. After 75 days of supplementation, genomic DNA was extracted from the rumen liquor and prepared for 16S rRNA-gene sequencing to characterize the composition of the rumen microbiota. From this, the rumen metagenome was predicted to obtain the associated gene functions and metabolic pathways in a cost-effective manner. Results showed that feed supplementations did alter the rumen microbiome of calves. Copper and grape-pomace increased the diversity of the rumen microbiota: the Shannon's and Fisher's alpha indices were significantly different across groups (p-values 0.045 and 0.039), and Bray-Curtis distances could separate grape-pomace calves from the other two groups. Differentially abundant taxa were identified: in particular, an uncultured Bacteroidales UCG-001 genus and OTUs from genus Sarcina were the most differentially abundant in pomace-supplemented calves compared to controls (p-values 0.003 and 0.0002, respectively). Enriched taxonomies such as Ruminiclostridium and Eubacterium sp., whose functions are related to degradation of the grape- pomace constituents (e.g. flavonoids or xyloglucan) have been described (p-values 0.027/0.028 and 0.040/0.022 in Pomace vs Copper and Controls, respectively). The most abundant predicted metagenomic genes belonged to the arginine and proline metabolism and the two- component (sensor/responder) regulatory system, which were increased in the supplemented groups. Interestingly, the lipopolysaccharide biosynthetic pathway was decreased in the two supplemented groups, possibly as a result of antimicrobial effects. Methanogenic taxa also responded to the feed supplementation, and methane metabolism in the rumen was the second most different pathway (up-regulated by feed supplementations) between experimental groups.}, } @article {pmid30489678, year = {2019}, author = {Vieira, FR and Pecchia, JA and Segato, F and Polikarpov, I}, title = {Exploring oyster mushroom (Pleurotus ostreatus) substrate preparation by varying phase I composting time: changes in bacterial communities and physicochemical composition of biomass impacting mushroom yields.}, journal = {Journal of applied microbiology}, volume = {126}, number = {3}, pages = {931-944}, doi = {10.1111/jam.14168}, pmid = {30489678}, issn = {1365-2672}, support = {005707/2012-05//Coordination for the Improvement of Higher Education Personnel/ ; 403090/2012-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 490022/2009-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 443916/2014-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; //University of São Paulo (USP) via NAP/ ; 2009/52840-7//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2013/21545-5//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2014/18714-2//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2015/13684-0//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; }, mesh = {*Bacteria/chemistry/metabolism ; Biodegradation, Environmental ; *Biomass ; *Composting ; *Microbial Consortia ; *Pleurotus/chemistry/metabolism ; }, abstract = {AIMS: To investigate characterization of the bacterial community composition and functionality and their impact on substrate biodegradation as well as mushroom yield.

METHODS AND RESULTS: Bacterial diversity, composition and functionality were accessed by DNA-derived analysis for a sugarcane straw-based substrate composted for either 5, 10 or 15 days. In addition, carbon and nitrogen losses, carbohydrate conversion and mushroom yields were measured for the different treatments. Changes were observed in the bacterial community diversity and composition after the process started, but not during the composting process itself. Following phase I, Acinetobacter sequences were recovered in high numbers, and selected genes associated with nitrogen metabolism and lignocellulose deconstruction were mapped. Substrate physicochemical composition showed elevated carbon and nitrogen losses after 10 and 15 days of phase I with reductions in mushroom yield.

CONCLUSIONS: Acinetobacter species appear to play an important role in substrate degradation processes, and a 5-day phase I period showed a significant higher mushroom yield compared to composting for either 10 or 15 days.

This study confers a better understanding of the bacterial community manipulation during the substrate preparation and their influence in substrate selectivity for the Pleurotus ostreatus cultivation.}, } @article {pmid30489677, year = {2019}, author = {Sánchez-González, M and Álvarez-Uribe, H and Rivera-Solís, R and González-Burgos, A and Escalante-Réndiz, D and Rojas-Herrera, R}, title = {Analysis of a phenol-adapted microbial community: degradation capacity, taxonomy and metabolic description.}, journal = {Journal of applied microbiology}, volume = {126}, number = {3}, pages = {771-779}, doi = {10.1111/jam.14166}, pmid = {30489677}, issn = {1365-2672}, mesh = {Bacteria/classification/enzymology/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Metagenomics ; *Microbiota ; Mixed Function Oxygenases/genetics/metabolism ; Phenol/*metabolism ; Phylogeny ; }, abstract = {AIMS: In this study, the ability of the consortium MR-01 to degrade phenol was determined. The effects of this chemical on the taxonomy and the metabolic behaviour were analysed through metagenomics.

METHODS AND RESULTS: Consortium MR-01 was acclimated in a sublethal concentration of phenol. After this process, the capacity to degrade this molecule was analysed. Results showed that degradation increased with the increment of the initial phenol concentration. Metagenomic analysis indicates that the consortium metabolized phenol under aerobic conditions using phenol 2-monooxygenase and the meta-cleavage pathway. Sequence of the enzymes involved in the phenol degradation was ascribed to the Actinomycetales and Chloroflexales orders, with relative abundances <1%. The most abundant genera were part of the Sphingomonadales order; however, the role of these species in the consortium is not clear.

CONCLUSIONS: Consortium MR-01 degrades efficiently high concentrations of phenol. The participation of extremophiles in the degradation process and the emergence of beneficial metabolic dependencies between the community members are some of the strategies used by the consortium to survive and develop under harsh environmental conditions.

This is one of the few studies describing the taxonomy and metabolic profile of a phenol degrading consortium.}, } @article {pmid30487175, year = {2019}, author = {Kriaa, A and Bourgin, M and Potiron, A and Mkaouar, H and Jablaoui, A and Gérard, P and Maguin, E and Rhimi, M}, title = {Microbial impact on cholesterol and bile acid metabolism: current status and future prospects.}, journal = {Journal of lipid research}, volume = {60}, number = {2}, pages = {323-332}, pmid = {30487175}, issn = {1539-7262}, mesh = {Animals ; Bile Acids and Salts/*metabolism ; Cholesterol/*metabolism ; Dysbiosis/metabolism/microbiology ; Dyslipidemias/metabolism/microbiology ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Recently, the gut microbiota has emerged as a crucial factor that influences cholesterol metabolism. Ever since, significant interest has been shown in investigating these host-microbiome interactions to uncover microbiome-mediated functions on cholesterol and bile acid (BA) metabolism. Indeed, changes in gut microbiota composition and, hence, its derived metabolites have been previously reported to subsequently impact the metabolic processes and have been linked to several diseases. In this context, associations between a disrupted gut microbiome, impaired BA metabolism, and cholesterol dysregulation have been highlighted. Extensive advances in metagenomic and metabolomic studies in this field have allowed us to further our understanding of the role of intestinal bacteria in metabolic health and disease. However, only a few have provided mechanistic insights into their impact on cholesterol metabolism. Identifying the myriad functions and interactions of these bacteria to maintain cholesterol homeostasis remain an important challenge in such a field of research. In this review, we discuss the impact of gut microbiota on cholesterol metabolism, its association with disease settings, and the potential of modulating gut microbiota as a promising therapeutic target to lower hypercholesterolemia.}, } @article {pmid30486439, year = {2018}, author = {Yi, X and Yuan, J and Zhu, Y and Yi, X and Zhao, Q and Fang, K and Cao, L}, title = {Comparison of the Abundance and Community Structure of N-Cycling Bacteria in Paddy Rhizosphere Soil under Different Rice Cultivation Patterns.}, journal = {International journal of molecular sciences}, volume = {19}, number = {12}, pages = {}, pmid = {30486439}, issn = {1422-0067}, mesh = {Bacteria/*classification/genetics/metabolism ; *Biodiversity ; Enzymes/genetics/metabolism ; Metagenome ; Metagenomics/methods ; Nitrogen ; Oryza/*microbiology ; Phylogeny ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Eco-agricultural systems aim to reduce the use of chemical fertilizers in order to improve sustainable production and maintain a healthy ecosystem. The aim of this study was to explore the effects of rice-frog farming on the bacterial community and N-cycling microbes in paddy rhizosphere soil. This experiment involved three rice cultivation patterns: Conventionally cultivated rice (CR), green rice-frog farming (GR), and organic rice-frog farming (OR). The rice yield, paddy soil enzyme activities, physicochemical variables and bacterial and N-cycling bacterial abundances were quantitatively analyzed. Rice-frog cultivations significantly increased soil protease, nitrate and reductase activity. Additionally, the nirS gene copy number and the relative abundance of denitrifying bacteria also increased, however urease activity and the relative abundance of nitrifying bacteria significantly decreased. The bacterial community richness and diversity of OR soil was significantly higher than that of the GR or CR soil. Nitrogen use efficiency (NUE) of GR was highest. The N-cycling bacterial community was positively correlated with the total carbon (TC), total nitrogren (TN) and carbon to nitrogen (C:N) ratio. The present work strengthens our current understanding of the soil bacterial community structure and its functions under rice-frog farming. The present work also provides certain theoretical support for the selection of rational rice cultivation patterns.}, } @article {pmid30486388, year = {2018}, author = {Labbé, M and Raymond, F and Lévesque, A and Thaler, M and Mohit, V and Audet, M and Corbeil, J and Culley, A}, title = {Communities of Phytoplankton Viruses across the Transition Zone of the St. Lawrence Estuary.}, journal = {Viruses}, volume = {10}, number = {12}, pages = {}, pmid = {30486388}, issn = {1999-4915}, mesh = {Biodiversity ; Ecosystem ; Environment ; *Estuaries ; Evolution, Molecular ; Geography ; Metagenome ; Metagenomics/methods ; Phycodnaviridae/classification/genetics ; Phylogeny ; Phytoplankton/*virology ; RNA, Ribosomal, 18S ; *Water Microbiology ; }, abstract = {The St. Lawrence hydrographic system includes freshwater, brackish, and marine habitats, and is the largest waterway in North America by volume. The food-webs in these habitats are ultimately dependent on phytoplankton. Viral lysis is believed to be responsible for a major part of phytoplankton mortality. To better understand their role, we characterized the diversity and distribution of two viral taxa infecting phytoplankton: the picornaviruses and phycodnaviruses. Our study focused on the estuary transition zone, which is an important nursery for invertebrates and fishes. Both viral taxa were investigated by PCR amplification of conserved molecular markers and next-generation sequencing at six sites, ranging from freshwater to marine. Our results revealed few shared viral phylotypes between saltwater and freshwater sites. Salinity appeared to be the primary determinant of viral community composition. Moreover, our analysis indicated that the viruses identified in this region of the St. Lawrence diverge from classified viruses and homologous published environmental virotypes. These results suggest that DNA and RNA viruses infecting phytoplankton are likely active in the estuary transition zone, and that this region harbors its own unique viral assemblages.}, } @article {pmid30486338, year = {2018}, author = {Amedei, A and Boem, F}, title = {I've Gut A Feeling: Microbiota Impacting the Conceptual and Experimental Perspectives of Personalized Medicine.}, journal = {International journal of molecular sciences}, volume = {19}, number = {12}, pages = {}, pmid = {30486338}, issn = {1422-0067}, support = {FAS SALUTE 2014//Regione Toscana/ ; P2016.0808//Ente Cassa di Risparmio di Firenze/ ; }, mesh = {Animals ; Biodiversity ; Biological Therapy ; Disease Susceptibility ; Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genomics/methods ; Humans ; Metagenomics/methods ; Microbiota ; Organ Specificity ; *Precision Medicine/methods ; Research ; Symbiosis ; }, abstract = {In recent years, the human microbiota has gained increasing relevance both in research and clinical fields. Increasing studies seem to suggest the centrality of the microbiota and its composition both in the development and maintenance of what we call "health" and in generating and/or favoring (those cases in which the microbiota's complex relational architecture is dysregulated) the onset of pathological conditions. The complex relationships between the microbiota and human beings, which invest core notions of biomedicine such as "health" and "individual," do concern not only problems of an empirical nature but seem to require the need to adopt new concepts and new perspectives in order to be properly analysed and utilized, especially for their therapeutic implementation. In this contribution we report and discuss some of the theoretical proposals and innovations (from the ecological component to the notion of polygenomic organism) aimed at producing this change of perspective. In conclusion, we summarily analyze what impact and what new challenges these new approaches might have on personalized/person centred/precision medicine.}, } @article {pmid30485662, year = {2019}, author = {Koziol, A and Stat, M and Simpson, T and Jarman, S and DiBattista, JD and Harvey, ES and Marnane, M and McDonald, J and Bunce, M}, title = {Environmental DNA metabarcoding studies are critically affected by substrate selection.}, journal = {Molecular ecology resources}, volume = {19}, number = {2}, pages = {366-376}, doi = {10.1111/1755-0998.12971}, pmid = {30485662}, issn = {1755-0998}, support = {LP160100839//Australian Research Council/ ; }, mesh = {Aquatic Organisms/*classification/*genetics ; Australia ; *Biodiversity ; DNA/chemistry/genetics/*isolation & purification ; DNA Barcoding, Taxonomic/*methods ; Kazakhstan ; Metagenomics/*methods ; Seawater ; }, abstract = {Effective biomonitoring is critical for driving management outcomes that ensure long-term sustainability of the marine environment. In recent years, environmental DNA (eDNA), coupled with metabarcoding methodologies, has emerged as a promising tool for generating biotic surveys of marine ecosystems, including those under anthropogenic pressure. However, more empirical data are needed on how to best implement eDNA field sampling approaches to maximize their utility for each specific application. The effect of the substrate chosen for eDNA sampling on the diversity of marine taxa detected by DNA metabarcoding has not yet been systematically analysed, despite aquatic systems being those most commonly targeted for eDNA studies. We investigated the effect of four commonly used eDNA substrates to explore taxonomic diversity: (a) surface water, (b) marine sediment, (c) settlement plates and (d) planktonic tows. With a focus on coastal ports, 332 eDNA samples from Australia (Indian and Southern oceans) and Kazakhstan (Caspian Sea) were collected and analysed by multi-assay DNA metabarcoding. Across study locations, between 30% and 52% of eukaryotic families detected were unique to a particular substrate and <6% of families were found in all four substrates. Taxonomic composition varied significantly depending on the substrate sampled implying that the suitability (and bias) of an eDNA substrate will depend on the focal taxa. These findings demonstrate that single substrate eDNA metabarcoding likely underestimates the total eukaryotic diversity. Future eDNA experimental design should consider incorporating multiple substrates or select substrate(s) best suited to the specific detection of target taxa.}, } @article {pmid30485448, year = {2019}, author = {Chang, Y and Desirò, A and Na, H and Sandor, L and Lipzen, A and Clum, A and Barry, K and Grigoriev, IV and Martin, FM and Stajich, JE and Smith, ME and Bonito, G and Spatafora, JW}, title = {Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota.}, journal = {The New phytologist}, volume = {222}, number = {1}, pages = {511-525}, doi = {10.1111/nph.15613}, pmid = {30485448}, issn = {1469-8137}, support = {DEB-1441604//National Science Foundation/International ; DEB-1441715//National Science Foundation/International ; DEB-1441677//National Science Foundation/International ; DEB 1737898//National Science Foundation/International ; MICL02416//United States Department of Agriculture NIFA/International ; ANR-11-LABX-0002-01//French National Research Agency through the Laboratory of Excellence ARBRE/International ; DE-AC02-05CH11231//Office of Science of the US Department of Energy/International ; }, mesh = {*Biological Evolution ; Genome, Fungal ; Metagenomics ; Microbiota/genetics ; Molecular Sequence Annotation ; Mucorales/*genetics ; Mycoplasma/genetics ; Mycorrhizae/*physiology ; *Phylogeny ; Repetitive Sequences, Nucleic Acid/genetics ; }, abstract = {Endogonales (Mucoromycotina), composed of Endogonaceae and Densosporaceae, is the only known non-Dikarya order with ectomycorrhizal members. They also form mycorrhizal-like association with some nonspermatophyte plants. It has been recently proposed that Endogonales were among the earliest mycorrhizal partners with land plants. It remains unknown whether Endogonales possess genomes with mycorrhizal-lifestyle signatures and whether Endogonales originated around the same time as land plants did. We sampled sporocarp tissue from four Endogonaceae collections and performed shotgun genome sequencing. After binning the metagenome data, we assembled and annotated the Endogonaceae genomes. We performed comparative analysis on plant-cell-wall-degrading enzymes (PCWDEs) and small secreted proteins (SSPs). We inferred phylogenetic placement of Endogonaceae and estimated the ages of Endogonaceae and Endogonales with expanded taxon sampling. Endogonaceae have large genomes with high repeat content, low diversity of PCWDEs, but without elevated SSP/secretome ratios. Dating analysis estimated that Endogonaceae originated in the Permian-Triassic boundary and Endogonales originated in the mid-late Silurian. Mycoplasma-related endobacterium sequences were identified in three Endogonaceae genomes. Endogonaceae genomes possess typical signatures of mycorrhizal lifestyle. The early origin of Endogonales suggests that the mycorrhizal association between Endogonales and plants might have played an important role during the colonization of land by plants.}, } @article {pmid30482864, year = {2018}, author = {Langelier, C and Kalantar, KL and Moazed, F and Wilson, MR and Crawford, ED and Deiss, T and Belzer, A and Bolourchi, S and Caldera, S and Fung, M and Jauregui, A and Malcolm, K and Lyden, A and Khan, L and Vessel, K and Quan, J and Zinter, M and Chiu, CY and Chow, ED and Wilson, J and Miller, S and Matthay, MA and Pollard, KS and Christenson, S and Calfee, CS and DeRisi, JL}, title = {Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {52}, pages = {E12353-E12362}, pmid = {30482864}, issn = {1091-6490}, support = {K23 HL136844/HL/NHLBI NIH HHS/United States ; R35 HL140026/HL/NHLBI NIH HHS/United States ; K23 HL123778/HL/NHLBI NIH HHS/United States ; K23 HL138461/HL/NHLBI NIH HHS/United States ; P01 AI091575/AI/NIAID NIH HHS/United States ; K24 HL133390/HL/NHLBI NIH HHS/United States ; R01 HL110969/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Area Under Curve ; Case-Control Studies ; Cohort Studies ; Critical Illness ; Female ; Humans ; Male ; Microbiota/genetics ; Middle Aged ; Predictive Value of Tests ; Respiratory Tract Infections/*diagnosis/*immunology/microbiology ; Sequence Analysis, DNA/*methods ; Transcriptome/genetics ; Whole Genome Sequencing/methods ; }, abstract = {Lower respiratory tract infections (LRTIs) lead to more deaths each year than any other infectious disease category. Despite this, etiologic LRTI pathogens are infrequently identified due to limitations of existing microbiologic tests. In critically ill patients, noninfectious inflammatory syndromes resembling LRTIs further complicate diagnosis. To address the need for improved LRTI diagnostics, we performed metagenomic next-generation sequencing (mNGS) on tracheal aspirates from 92 adults with acute respiratory failure and simultaneously assessed pathogens, the airway microbiome, and the host transcriptome. To differentiate pathogens from respiratory commensals, we developed a rules-based model (RBM) and logistic regression model (LRM) in a derivation cohort of 20 patients with LRTIs or noninfectious acute respiratory illnesses. When tested in an independent validation cohort of 24 patients, both models achieved accuracies of 95.5%. We next developed pathogen, microbiome diversity, and host gene expression metrics to identify LRTI-positive patients and differentiate them from critically ill controls with noninfectious acute respiratory illnesses. When tested in the validation cohort, the pathogen metric performed with an area under the receiver-operating curve (AUC) of 0.96 (95% CI, 0.86-1.00), the diversity metric with an AUC of 0.80 (95% CI, 0.63-0.98), and the host transcriptional classifier with an AUC of 0.88 (95% CI, 0.75-1.00). Combining these achieved a negative predictive value of 100%. This study suggests that a single streamlined protocol offering an integrated genomic portrait of pathogen, microbiome, and host transcriptome may hold promise as a tool for LRTI diagnosis.}, } @article {pmid30482830, year = {2018}, author = {Espinoza, JL and Harkins, DM and Torralba, M and Gomez, A and Highlander, SK and Jones, MB and Leong, P and Saffery, R and Bockmann, M and Kuelbs, C and Inman, JM and Hughes, T and Craig, JM and Nelson, KE and Dupont, CL}, title = {Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, pmid = {30482830}, issn = {2150-7511}, support = {R01 DE019665/DE/NIDCR NIH HHS/United States ; R01 GM120624/GM/NIGMS NIH HHS/United States ; }, mesh = {Australia ; Bacteria/*classification/*genetics ; Child ; Child, Preschool ; Dental Caries/*microbiology ; Dental Plaque/*microbiology ; Humans ; Metabolic Networks and Pathways/genetics ; Metagenomics ; *Microbiota ; Sequence Analysis, DNA ; }, abstract = {To address the question of how microbial diversity and function in the oral cavities of children relates to caries diagnosis, we surveyed the supragingival plaque biofilm microbiome in 44 juvenile twin pairs. Using shotgun sequencing, we constructed a genome encyclopedia describing the core supragingival plaque microbiome. Caries phenotypes contained statistically significant enrichments in specific genome abundances and distinct community composition profiles, including strain-level changes. Metabolic pathways that are statistically associated with caries include several sugar-associated phosphotransferase systems, antimicrobial resistance, and metal transport. Numerous closely related previously uncharacterized microbes had substantial variation in central metabolism, including the loss of biosynthetic pathways resulting in auxotrophy, changing the ecological role. We also describe the first complete Gracilibacteria genomes from the human microbiome. Caries is a microbial community metabolic disorder that cannot be described by a single etiology, and our results provide the information needed for next-generation diagnostic tools and therapeutics for caries.IMPORTANCE Oral health has substantial economic importance, with over $100 billion spent on dental care in the United States annually. The microbiome plays a critical role in oral health, yet remains poorly classified. To address the question of how microbial diversity and function in the oral cavities of children relate to caries diagnosis, we surveyed the supragingival plaque biofilm microbiome in 44 juvenile twin pairs. Using shotgun sequencing, we constructed a genome encyclopedia describing the core supragingival plaque microbiome. This unveiled several new previously uncharacterized but ubiquitous microbial lineages in the oral microbiome. Caries is a microbial community metabolic disorder that cannot be described by a single etiology, and our results provide the information needed for next-generation diagnostic tools and therapeutics for caries.}, } @article {pmid30482513, year = {2019}, author = {Díaz-Sánchez, S and Hernández-Jarguín, A and Torina, A and de Mera, IGF and Blanda, V and Caracappa, S and Gortazar, C and de la Fuente, J}, title = {Characterization of the bacterial microbiota in wild-caught Ixodes ventalloi.}, journal = {Ticks and tick-borne diseases}, volume = {10}, number = {2}, pages = {336-343}, doi = {10.1016/j.ttbdis.2018.11.014}, pmid = {30482513}, issn = {1877-9603}, mesh = {Anaplasma/genetics ; Animals ; Borrelia/genetics ; DNA, Bacterial/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Ixodes/*microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sicily ; Symbiosis ; }, abstract = {Exploring the microbial diversity of ticks is crucial to understand geographical dispersion and pathogen transmission. Tick microbes participate in many biological processes implicated in the acquisition, maintenance, and transmission of pathogens, and actively promote host phenotypic changes, and adaptation to new environments. The microbial community of Ixodes ventalloi still remains unexplored. In this study, the bacterial microbiota of wild-caught I. ventalloi was characterized using shotgun-metagenomic sequencing in samples from unfed adults collected during December 2013-January 2014 in two locations from Sicily, Italy. The microbiota identified in I. ventalloi was mainly composed of symbiotic, commensal, and environmental bacteria. Interestingly, we identified the genera Anaplasma and Borrelia as members of the microbiota of I. ventalloi. These results advance our information on I. ventalloi microbiota composition, with potential implications in tick-host adaptation, geographic expansion, and vector competence.}, } @article {pmid30482240, year = {2018}, author = {Huang, P and Zhang, Y and Xiao, K and Jiang, F and Wang, H and Tang, D and Liu, D and Liu, B and Liu, Y and He, X and Liu, H and Liu, X and Qing, Z and Liu, C and Huang, J and Ren, Y and Yun, L and Yin, L and Lin, Q and Zeng, C and Su, X and Yuan, J and Lin, L and Hu, N and Cao, H and Huang, S and Guo, Y and Fan, W and Zeng, J}, title = {The chicken gut metagenome and the modulatory effects of plant-derived benzylisoquinoline alkaloids.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {211}, pmid = {30482240}, issn = {2049-2618}, mesh = {Animals ; Benzylisoquinolines/*pharmacology ; Chickens/*growth & development/*microbiology ; Gastrointestinal Microbiome/genetics ; Growth Substances/*pharmacology ; Lactobacillus/*growth & development ; Plant Extracts/*pharmacology ; Probiotics/pharmacology ; Ranunculales/chemistry ; }, abstract = {BACKGROUND: Sub-therapeutic antibiotics are widely used as growth promoters in the poultry industry; however, the resulting antibiotic resistance threatens public health. A plant-derived growth promoter, Macleaya cordata extract (MCE), with effective ingredients of benzylisoquinoline alkaloids, is a potential alternative to antibiotic growth promoters. Altered intestinal microbiota play important roles in growth promotion, but the underlying mechanism remains unknown.

RESULTS: We generated 1.64 terabases of metagenomic data from 495 chicken intestinal digesta samples and constructed a comprehensive chicken gut microbial gene catalog (9.04 million genes), which is also the first gene catalog of an animal's gut microbiome that covers all intestinal compartments. Then, we identified the distinctive characteristics and temporal changes in the foregut and hindgut microbiota. Next, we assessed the impact of MCE on chickens and gut microbiota. Chickens fed with MCE had improved growth performance, and major microbial changes were confined to the foregut, with the predominant role of Lactobacillus being enhanced, and the amino acids, vitamins, and secondary bile acids biosynthesis pathways being upregulated, but lacked the accumulation of antibiotic-resistance genes. In comparison, treatment with chlortetracycline similarly enriched some biosynthesis pathways of nutrients in the foregut microbiota, but elicited an increase in antibiotic-producing bacteria and antibiotic-resistance genes.

CONCLUSION: The reference gene catalog of the chicken gut microbiome is an important supplement to animal gut metagenomes. Metagenomic analysis provides insights into the growth-promoting mechanism of MCE, and underscored the importance of utilizing safe and effective growth promoters.}, } @article {pmid30481710, year = {2019}, author = {Abia, ALK and Alisoltani, A and Ubomba-Jaswa, E and Dippenaar, MA}, title = {Microbial life beyond the grave: 16S rRNA gene-based metagenomic analysis of bacteria diversity and their functional profiles in cemetery environments.}, journal = {The Science of the total environment}, volume = {655}, number = {}, pages = {831-841}, doi = {10.1016/j.scitotenv.2018.11.302}, pmid = {30481710}, issn = {1879-1026}, mesh = {Biodiversity ; *Cemeteries ; Cities ; *Environmental Monitoring ; Humans ; *Metagenomics ; Microbiota/genetics ; Molecular Sequence Annotation ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; South Africa ; }, abstract = {Recent studies have identified cemeteries as potential environmental reservoirs of multi-drug resistant pathogenic bacteria that could contaminate groundwater sources posing public health threats. However, these findings were based on the identification of culturable bacteria and at times not below burial grounds. Investigation on the bacterial diversity and functional profiles of bacterial communities above and below burial grounds in human cemeteries are few. The current study used high-throughput sequencing techniques to determine the bacterial composition and their associated functional profiles in cemetery soil samples collected at the surface and below burial ground in two South African cemeteries (Maitland Cemetery in Cape Town and Fontein Street Cemetery in Middelburg) to evaluate the potential health threat to surrounding populations through contamination of groundwater. Significant differences were observed between sample depths with the clustering of the surface (0 m) and the 2 m samples into separate groups. Pseudomonas and Corynebacterium were the most abundant genera across all samples. Pseudomonas and Rhodococcus were the dominant genera in the 2 m samples while Prauserella and Staphylococcus were dominant in the surface samples. The 2 m samples showed a lower alpha diversity but recorded higher proportions of human diseases functional classes compared to the surface samples. Human disease functional profiles revealed involvement, in infectious (cholera), neurodegenerative (Alzheimer's disease) cardiovascular (hypertrophic cardiomyopathy) immune system (Systemic lupus erythematosus) metabolic (Type I & II diabetes) diseases and cancer. Antibiotic resistance and antibiotics synthesis signatures were also identified. Thus, cemeteries could be potential sources of microbial and antibiotic pollution in groundwater, especially in areas with shallow water tables such as Maitland. Selection of sites for use as cemeteries should, therefore, require a proper understanding of the hydrogeological characteristics of the selected site. However, further studies are required to trace the actual movement of these pollutants into groundwater resources.}, } @article {pmid30481069, year = {2019}, author = {Edwards, CE and Swift, JF and Lance, RF and Minckley, TA and Lindsay, DL}, title = {Evaluating the efficacy of sample collection approaches and DNA metabarcoding for identifying the diversity of plants utilized by nectivorous bats.}, journal = {Genome}, volume = {62}, number = {1}, pages = {19-29}, doi = {10.1139/gen-2018-0102}, pmid = {30481069}, issn = {1480-3321}, mesh = {Agave/*genetics ; Animals ; *Biodiversity ; Chiroptera/*physiology ; DNA Barcoding, Taxonomic/*methods/standards ; DNA, Plant/*genetics ; Feces/chemistry ; Food Chain ; Herbivory ; *Metagenome ; Pollen/genetics ; }, abstract = {In this study, we evaluated the efficacy of sample collection approaches and DNA metabarcoding to identify plants utilized by nectivorous bats. Samples included guano collected from beneath bat roosts and pollen-swabs from bat fur, both of which were subjected to DNA metabarcoding and visual identification of pollen (microscopy) to measure plant diversity. Our objectives were to determine whether DNA metabarcoding could detect likely food plants of nectivorous bats, whether sample types would produce different estimates of plant diversity, and to compare results of DNA metabarcoding to visual identification. Visual identification found that 99% of pollen was from Agave, which is thought to be the bats' main food source. The dominant taxon found by metabarcoding was also Agavoideae, but a broader diversity of plant species was also detected, many of which are likely "by-catch" from the broader environment. Metabarcoding outcomes differed between sample types, likely because pollen-swabs measured the plant species visited by bats and guano samples measured all items consumed in the bat's diet, even those that were not pollen or nectar. Overall, metabarcoding is a powerful, high-throughput tool to understand bat ecology and species interactions, but careful analysis of results is necessary to derive accurate ecological conclusions.}, } @article {pmid30479342, year = {2018}, author = {Ramani, S and Stewart, CJ and Laucirica, DR and Ajami, NJ and Robertson, B and Autran, CA and Shinge, D and Rani, S and Anandan, S and Hu, L and Ferreon, JC and Kuruvilla, KA and Petrosino, JF and Venkataram Prasad, BV and Bode, L and Kang, G and Estes, MK}, title = {Human milk oligosaccharides, milk microbiome and infant gut microbiome modulate neonatal rotavirus infection.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5010}, pmid = {30479342}, issn = {2041-1723}, support = {R01 AI036040/AI/NIAID NIH HHS/United States ; R01 AI080656/AI/NIAID NIH HHS/United States ; R01 AI105101/AI/NIAID NIH HHS/United States ; R37 AI036040/AI/NIAID NIH HHS/United States ; }, mesh = {Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Milk, Human/*chemistry/*microbiology ; Oligosaccharides/*metabolism ; Rotavirus/pathogenicity ; Rotavirus Infections/immunology/*microbiology ; Rotavirus Vaccines/immunology ; }, abstract = {Neonatal rotavirus infections are predominantly asymptomatic. While an association with gastrointestinal symptoms has been described in some settings, factors influencing differences in clinical presentation are not well understood. Using multidisciplinary approaches, we show that a complex interplay between human milk oligosaccharides (HMOs), milk microbiome, and infant gut microbiome impacts neonatal rotavirus infections. Validating in vitro studies where HMOs are not decoy receptors for neonatal strain G10P[11], population studies show significantly higher levels of Lacto-N-tetraose (LNT), 2'-fucosyllactose (2'FL), and 6'-siallylactose (6'SL) in milk from mothers of rotavirus-positive neonates with gastrointestinal symptoms. Further, these HMOs correlate with abundance of Enterobacter/Klebsiella in maternal milk and infant stool. Specific HMOs also improve the infectivity of a neonatal strain-derived rotavirus vaccine. This study provides molecular and translational insight into host factors influencing neonatal rotavirus infections and identifies maternal components that could promote the performance of live, attenuated rotavirus vaccines.}, } @article {pmid30479272, year = {2018}, author = {Glover, AG and Wiklund, H and Chen, C and Dahlgren, TG}, title = {Managing a sustainable deep-sea 'blue economy' requires knowledge of what actually lives there.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {30479272}, issn = {2050-084X}, mesh = {*Biodiversity ; Conservation of Energy Resources/*methods ; *Ecosystem ; Metagenomics/*methods ; *Oceans and Seas ; }, abstract = {Ensuring that the wealth of resources contained in our oceans are managed and developed in a sustainable manner is a priority for the emerging 'blue economy'. However, modern ecosystem-based management approaches do not translate well to regions where we know almost nothing about the individual species found in the ecosystem. Here, we propose a new taxon-focused approach to deep-sea conservation that includes regulatory oversight to set targets for the delivery of taxonomic data. For example, a five-year plan to deliver taxonomic and genomic knowledge on a thousand species in regions of the ocean earmarked for industrial activity is an achievable target. High-throughput, integrative taxonomy can, therefore, provide the data that is needed to monitor various ecosystem services (such as the natural history, connectivity, value and function of species) and to help break the regulatory deadlock of high-seas conservation.}, } @article {pmid30478535, year = {2019}, author = {Cui, J and Cui, H and Yang, M and Du, S and Li, J and Li, Y and Liu, L and Zhang, X and Li, S}, title = {Tongue coating microbiome as a potential biomarker for gastritis including precancerous cascade.}, journal = {Protein & cell}, volume = {10}, number = {7}, pages = {496-509}, pmid = {30478535}, issn = {1674-8018}, mesh = {Adult ; Biomarkers/analysis ; Case-Control Studies ; Female ; Gastritis/*microbiology ; Humans ; Male ; *Microbiota ; Middle Aged ; Precancerous Conditions/*microbiology ; Tongue/*microbiology ; }, abstract = {The development of gastritis is associated with an increased risk of gastric cancer. Current invasive gastritis diagnostic methods are not suitable for monitoring progress. In this work based on 78 gastritis patients and 50 healthy individuals, we observed that the variation of tongue-coating microbiota was associated with the occurrence and development of gastritis. Twenty-one microbial species were identified for differentiating tongue-coating microbiomes of gastritis and healthy individuals. Pathways such as microbial metabolism in diverse environments, biosynthesis of antibiotics and bacterial chemotaxis were up-regulated in gastritis patients. The abundance of Campylobacter concisus was found associated with the gastric precancerous cascade. Furthermore, Campylobacter concisus could be detected in tongue coating and gastric fluid in a validation cohort containing 38 gastritis patients. These observations provided biological evidence of tongue diagnosis in traditional Chinese medicine, and indicated that tongue-coating microbiome could be a potential non-invasive biomarker, which might be suitable for long-term monitoring of gastritis.}, } @article {pmid30478343, year = {2018}, author = {Regan, T and Barnett, MW and Laetsch, DR and Bush, SJ and Wragg, D and Budge, GE and Highet, F and Dainat, B and de Miranda, JR and Watson, M and Blaxter, M and Freeman, TC}, title = {Characterisation of the British honey bee metagenome.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4995}, pmid = {30478343}, issn = {2041-1723}, support = {BBS/E/D/20211550/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/D/20211551/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/D/20211552/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/D/20211554/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/I001107/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bees/*genetics/microbiology ; Contig Mapping ; Genetic Variation ; *Metagenome ; Metagenomics ; Microbiota/genetics ; Sequence Analysis, DNA ; Symbiosis/genetics ; United Kingdom ; }, abstract = {The European honey bee (Apis mellifera) plays a major role in pollination and food production. Honey bee health is a complex product of the environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of these factors will help manage modern challenges to bee health. Here we used DNA sequencing to characterise the genomes and metagenomes of 19 honey bee colonies from across Britain. Low heterozygosity was observed in many Scottish colonies which had high similarity to the native dark bee. Colonies exhibited high diversity in composition and relative abundance of individual microbiome taxa. Most non-bee sequences were derived from known honey bee commensal bacteria or pathogens. However, DNA was also detected from additional fungal, protozoan and metazoan species. To classify cobionts lacking genomic information, we developed a novel network analysis approach for clustering orphan DNA contigs. Our analyses shed light on microbial communities associated with honey bees and demonstrate the power of high-throughput, directed metagenomics for identifying novel biological threats in agroecosystems.}, } @article {pmid30478001, year = {2018}, author = {Wei, S and Mortensen, MS and Stokholm, J and Brejnrod, AD and Thorsen, J and Rasmussen, MA and Trivedi, U and Bisgaard, H and Sørensen, SJ}, title = {Short- and long-term impacts of azithromycin treatment on the gut microbiota in children: A double-blind, randomized, placebo-controlled trial.}, journal = {EBioMedicine}, volume = {38}, number = {}, pages = {265-272}, pmid = {30478001}, issn = {2352-3964}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; Azithromycin/*pharmacology/therapeutic use ; Biodiversity ; Child, Preschool ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant ; Male ; Metagenome ; Metagenomics ; Time Factors ; }, abstract = {BACKGROUND: Macrolides are commonly prescribed for respiratory infections and asthma-like episodes in children. While their clinical benefits have been proved, concerns regarding the side-effects of their therapeutic use have been raised. Here we assess the short- and long-term impacts of azithromycin on the gut microbiota of young children.

METHODS: We performed a randomized, double-blind, placebo-controlled trial in a group of children aged 12-36 months, diagnosed with recurrent asthma-like symptoms from the COPSAC2010 cohort. Each acute asthma-like episode was randomized to a 3-day course of azithromycin oral solution of 10 mg/kg per day or placebo. Azithromycin reduced episode duration by half, which was the primary end-point and reported previously. The assessment of gut microbiota after treatment was the secondary end-point and reported in this study. Fecal samples were collected 14 days after randomization (N = 59, short-term) and again at age 4 years (N = 49, long-term, of whom N = 18 were placebo treated) and investigated by 16S rRNA gene amplicon sequencing.

FINDINGS: Short-term, azithromycin caused a 23% reduction in observed richness and 13% reduction in Shannon diversity. Microbiota composition was shifted primarily in the Actinobacteria phylum, especially a reduction of abundance in the genus Bifidobacterium. Long-term (13-39 months after treatment), we did not observe any differences between the azithromycin and placebo recipients in their gut microbiota composition.

INTERPRETATION: Azithromycin treatment induced a perturbation in the gut microbiota 14 days after randomization but did not have long-lasting effects on the gut microbiota composition. However, it should be noted that our analyses included a limited number of fecal samples for the placebo treated group at age 4 years. FUND: Lundbeck Foundation, Danish Ministry of Health, Danish Council for Strategic Research, Capital Region Research Foundation, China Scholarship Council.}, } @article {pmid30477563, year = {2018}, author = {Sinha, R and Ahsan, H and Blaser, M and Caporaso, JG and Carmical, JR and Chan, AT and Fodor, A and Gail, MH and Harris, CC and Helzlsouer, K and Huttenhower, C and Knight, R and Kong, HH and Lai, GY and Hutchinson, DLS and Le Marchand, L and Li, H and Orlich, MJ and Shi, J and Truelove, A and Verma, M and Vogtmann, E and White, O and Willett, W and Zheng, W and Mahabir, S and Abnet, C}, title = {Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16-17, 2017.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {210}, pmid = {30477563}, issn = {2049-2618}, support = {P30 CA016520/CA/NCI NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Humans ; Microbiota/*physiology ; Neoplasms/*etiology ; Prospective Studies ; Reproducibility of Results ; *Research Design ; }, abstract = {The National Cancer Institute (NCI) sponsored a 2-day workshop, "Next Steps in Studying the Human Microbiome and Health in Prospective Studies," in Bethesda, Maryland, May 16-17, 2017. The workshop brought together researchers in the field to discuss the challenges of conducting microbiome studies, including study design, collection and processing of samples, bioinformatics and statistical methods, publishing results, and ensuring reproducibility of published results. The presenters emphasized the great potential of microbiome research in understanding the etiology of cancer. This report summarizes the workshop and presents practical suggestions for conducting microbiome studies, from workshop presenters, moderators, and participants.}, } @article {pmid30474920, year = {2019}, author = {Bell, T}, title = {Next-generation experiments linking community structure and ecosystem functioning.}, journal = {Environmental microbiology reports}, volume = {11}, number = {1}, pages = {20-22}, doi = {10.1111/1758-2229.12711}, pmid = {30474920}, issn = {1758-2229}, mesh = {Bacteria/classification/genetics/metabolism ; Biodiversity ; *Ecosystem ; Metagenomics ; Microbiota ; Population Dynamics ; Reproducibility of Results ; }, } @article {pmid30474727, year = {2019}, author = {Meng, H and Zhou, Z and Wu, R and Wang, Y and Gu, JD}, title = {Diazotrophic microbial community and abundance in acidic subtropical natural and re-vegetated forest soils revealed by high-throughput sequencing of nifH gene.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {2}, pages = {995-1005}, doi = {10.1007/s00253-018-9466-7}, pmid = {30474727}, issn = {1432-0614}, support = {31470562//National Natural Science Foundation of China/ ; 701913//Hong Kong RGC GRF grant/ ; }, mesh = {Acids/analysis ; Archaea/*classification/enzymology/genetics/metabolism ; Bacteria/*classification/enzymology/genetics/metabolism ; Chemical Phenomena ; Forests ; *Genetic Variation ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Microbiota ; *Nitrogen Fixation ; Oxidoreductases/*genetics ; Seasons ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Biological nitrogen fixation (BNF) is an important natural biochemical process converting the inert dinitrogen gas (N2) in the atmosphere to ammonia (NH3) in the N cycle. In this study, the nifH gene was chosen to detect the diazotrophic microorganisms with high-throughput sequencing from five acidic forest soils, including three natural forests and two re-vegetated forests. Soil samples were taken in two seasons (summer and winter) at two depth layers (surface and lower depths). A dataset of 179,600 reads obtained from 20 samples were analyzed to provide the microbial community structure, diversity, abundance, and relationship with physiochemical parameters. Both archaea and bacteria were detected in these samples and diazotrophic bacteria were the dominant members contributing to the biological dinitrogen fixation in the acidic forest soils. Cyanobacteria, Firmicutes, Proteobacteria, Spirocheates, and Verrucomicrobia were observed, especially the Proteobacteria as the most abundant phylum. The core genera were Bradyrhizobium and Methylobacterium from α-Proteobacteia, and Desulfovibrio from δ-Proteobacteia in the phylum of Proteobacteia of these samples. The diversity indices and the gene abundances of all samples were higher in the surface layer than the lower layer. Diversity was apparently higher in re-vegetated forests than the natural forests. Significant positive correlation to the organic matter and nitrogen-related parameters was observed, but there was no significant seasonal variation on the community structure and diversity in these samples between the summer and winter. The application of high-throughput sequencing method provides a better understanding and more comprehensive information of diazotrophs in acidic forest soils than conventional and PCR-based ones.}, } @article {pmid30472682, year = {2019}, author = {Coker, OO and Nakatsu, G and Dai, RZ and Wu, WKK and Wong, SH and Ng, SC and Chan, FKL and Sung, JJY and Yu, J}, title = {Enteric fungal microbiota dysbiosis and ecological alterations in colorectal cancer.}, journal = {Gut}, volume = {68}, number = {4}, pages = {654-662}, pmid = {30472682}, issn = {1468-3288}, mesh = {Aged ; Biomarkers, Tumor/*analysis ; Case-Control Studies ; Colorectal Neoplasms/*microbiology ; Dysbiosis/*microbiology ; Female ; *Gastrointestinal Microbiome ; Hong Kong ; Humans ; Male ; Middle Aged ; *Mycobiome ; Principal Component Analysis ; }, abstract = {OBJECTIVES: Bacteriome and virome alterations are associated with colorectal cancer (CRC). Nevertheless, the gut fungal microbiota in CRC remains largely unexplored. We aimed to characterise enteric mycobiome in CRC.

DESIGN: Faecal shotgun metagenomic sequences of 184 patients with CRC, 197 patients with adenoma and 204 control subjects from Hong Kong were analysed (discovery cohort: 73 patients with CRC and 92 control subjects; validation cohort: 111 patients with CRC, 197 patients with adenoma and 112 controls from Hong Kong). CRC-associated fungal markers and ecological changes were also validated in additional independent cohorts of 90 patients with CRC, 42 patients with adenoma and 66 control subjects of published repository sequences from Germany and France. Assignment of taxonomies was performed by exact k-mer alignment against an integrated microbial reference genome database.

RESULTS: Principal component analysis revealed separate clusters for CRC and control (p<0.0001), with distinct mycobiomes in early-stage and late-stage CRC (p=0.0048). Basidiomycota:Ascomycota ratio was higher in CRC (p=0.0042), with increase in Malasseziomycetes (p<0.0001) and decrease in Saccharomycetes (p<0.0001) and Pneumocystidomycetes (p=0.0017). Abundances of 14 fungal biomarkers distinguished CRC from controls with an area under the receiver-operating characteristic curve (AUC) of 0.93 and validated AUCs of 0.82 and 0.74 in independent Chinese cohort V1 and European cohort V2, respectively. Further ecological analysis revealed higher numbers of co-occurring fungal intrakingdom and co-exclusive bacterial-fungal correlations in CRC (p<0.0001). Moreover, co-occurrence interactions between fungi and bacteria, mostly contributed by fungal Ascomycota and bacterial Proteobacteria in control, were reverted to co-exclusive interplay in CRC (p=0.00045).

CONCLUSIONS: This study revealed CRC-associated mycobiome dysbiosis characterised by altered fungal composition and ecology, signifying that the gut mycobiome might play a role in CRC.}, } @article {pmid30470770, year = {2018}, author = {Sang, S and Zhang, X and Dai, H and Hu, BX and Ou, H and Sun, L}, title = {Diversity and predictive metabolic pathways of the prokaryotic microbial community along a groundwater salinity gradient of the Pearl River Delta, China.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {17317}, pmid = {30470770}, issn = {2045-2322}, support = {2016YFC0402805//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/International ; 2016YFC0402805//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/International ; }, mesh = {Bacteria/*classification/drug effects/*genetics ; China ; Environmental Monitoring ; Groundwater/*microbiology ; *Metabolic Networks and Pathways ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; *Salinity ; Sequence Analysis, DNA ; }, abstract = {Almost half of the groundwater in the Pearl River Delta (PRD) contains salt water originally derived from paleo-seawater due to the Holocene transgression, which then generates intense physicochemical gradients in the mixing zone between freshwater and saltwater. Although some studies have been conducted on the hydrological and geochemical characteristics of groundwater in the PRD to monitor the intrusion of seawater, little attention has been paid to the microbial community of this particular region. In this study, we implemented a high-throughput sequencing analysis to characterize the microbial communities along a salinity gradient in the PRD aquifer, China. Our results indicated that the microbial community composition varied significantly depending on the salinity of the aquifer. The presence of abundant anaerobic microorganisms of the genera Desulfovibrio and Methanococcus in certain saltwater samples may be responsible for the gas generation of H2S and CH4 in the stratum. In saline water samples (TDS > 10 g/L), the linear discriminant analysis effect size (LEfSe) analysis found two biomarkers that usually live in marine environments, and the aquifers of the PRD still contained large quantity of saltwater, indicating that the impact of the paleo-seawater has lasted to this day. The predictive metagenomic analysis revealed that the metabolic pathways present in the groundwater samples studied, included the degradation of pesticides and refractory organics (dichlorodiphenyltrichloroethane (DDT), atrazine and polycyclic aromatic hydrocarbons), matter cycling (methane, nitrogen and sulfur), and inorganic ion and mineral metabolites. This study can help enhance our understanding of the composition of the microbial assemblages and its implications as an environmental indicator in an aquifer affected by saltwater intrusion.}, } @article {pmid30470178, year = {2018}, author = {Griffith, BC and Weiss, BL and Aksoy, E and Mireji, PO and Auma, JE and Wamwiri, FN and Echodu, R and Murilla, G and Aksoy, S}, title = {Analysis of the gut-specific microbiome from field-captured tsetse flies, and its potential relevance to host trypanosome vector competence.}, journal = {BMC microbiology}, volume = {18}, number = {Suppl 1}, pages = {146}, pmid = {30470178}, issn = {1471-2180}, support = {D43 TW007391/TW/FIC NIH HHS/United States ; R01 AI051584/AI/NIAID NIH HHS/United States ; R01 AI068932/AI/NIAID NIH HHS/United States ; U01 AI115648/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification ; *Gastrointestinal Microbiome ; Geography ; High-Throughput Nucleotide Sequencing ; Insect Vectors/*microbiology/parasitology ; Kenya ; Symbiosis ; Trypanosoma/*physiology ; Tsetse Flies/*microbiology/parasitology ; Uganda ; }, abstract = {BACKGROUND: The tsetse fly (Glossina sp.) midgut is colonized by maternally transmitted and environmentally acquired bacteria. Additionally, the midgut serves as a niche in which pathogenic African trypanosomes reside within infected flies. Tsetse's bacterial microbiota impacts many aspects of the fly's physiology. However, little is known about the structure of tsetse's midgut-associated bacterial communities as they relate to geographically distinct fly habitats in east Africa and their contributions to parasite infection outcomes. We utilized culture dependent and independent methods to characterize the taxonomic structure and density of bacterial communities that reside within the midgut of tsetse flies collected at geographically distinct locations in Kenya and Uganda.

RESULTS: Using culture dependent methods, we isolated 34 strains of bacteria from four different tsetse species (G. pallidipes, G. brevipalpis, G. fuscipes and G. fuscipleuris) captured at three distinct locations in Kenya. To increase the depth of this study, we deep sequenced midguts from individual uninfected and trypanosome infected G. pallidipes captured at two distinct locations in Kenya and one in Uganda. We found that tsetse's obligate endosymbiont, Wigglesworthia, was the most abundant bacterium present in the midgut of G. pallidipes, and the density of this bacterium remained largely consistent regardless of whether or not its tsetse host was infected with trypanosomes. These fly populations also housed the commensal symbiont Sodalis, which was found at significantly higher densities in trypanosome infected compared to uninfected flies. Finally, midguts of field-captured G. pallidipes were colonized with distinct, low density communities of environmentally acquired microbes that differed in taxonomic structure depending on parasite infection status and the geographic location from which the flies were collected.

CONCLUSIONS: The results of this study will enhance our understanding of the tripartite relationship between tsetse, its microbiota and trypanosome vector competence. This information may be useful for developing novel disease control strategies or enhancing the efficacy of those already in use.}, } @article {pmid30468938, year = {2019}, author = {Zhao, G and Droit, L and Gilbert, MH and Schiro, FR and Didier, PJ and Si, X and Paredes, A and Handley, SA and Virgin, HW and Bohm, RP and Wang, D}, title = {Virome biogeography in the lower gastrointestinal tract of rhesus macaques with chronic diarrhea.}, journal = {Virology}, volume = {527}, number = {}, pages = {77-88}, pmid = {30468938}, issn = {1096-0341}, support = {P30 DK052574/DK/NIDDK NIH HHS/United States ; P51 OD011104/OD/NIH HHS/United States ; R24 OD019793/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteriophages/classification/genetics/*physiology ; *Biodiversity ; Chronic Disease ; Colon/pathology/virology ; Contig Mapping ; Diarrhea/*veterinary/virology ; Feces/virology ; Ileum/pathology/virology ; Lower Gastrointestinal Tract/pathology/*virology ; *Macaca mulatta ; Metagenome ; Primate Diseases/*virology ; Rectum/virology ; }, abstract = {The composition of gastrointestinal tract viromes has been associated with multiple diseases. Our understanding of virus communities in the GI tract is still very limited due to challenges in sampling from different GI sites. Here we defined the GI viromes of 15 rhesus macaques with chronic diarrhea. Luminal content samples from terminal ileum, proximal and distal colon were collected at necropsy while samples from the rectum were collected antemortem using a fecal loop. The composition of and ecological parameters associated with the terminal ileum virome were distinct from the colon and rectum samples; these differences were driven by bacteriophages rather than eukaryotic viruses. The six contigs that were most discriminative of the viromes were distantly related to bacteriophages from three different families. Our analysis provides support for using fecal loop sampling of the rectum as a proxy of the colonic virome in humans.}, } @article {pmid30465678, year = {2018}, author = {Shao, Y and Wang, Z}, title = {Changes in the nutrients of camels' milk alter the functional features of the intestine microbiota.}, journal = {Food & function}, volume = {9}, number = {12}, pages = {6484-6494}, doi = {10.1039/c8fo00812d}, pmid = {30465678}, issn = {2042-650X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Camelus ; Food Handling ; *Gastrointestinal Microbiome ; Hot Temperature ; Intestines/*microbiology ; Male ; Mice, Inbred C57BL ; Milk/*chemistry ; Nutrients/analysis/metabolism ; Phylogeny ; }, abstract = {Heat treatment alters the nutritive quality of camels' milk and thus the intestine microbiota, but the effect of heat treatment-induced nutrient loss on the functional features of the intestine microbiota is unknown. In this study, the influence of two heat treatments of camels' milk on the intestine microbiota was investigated to establish the correlations between milk nutrients and the functional features of the intestine microbiota. Camels' milk, heat treated at low (65 °C) or high (100 °C) temperatures, was administered to mice (LM = low; HM = high); control mice received sterile distilled water (CW = control). Intestine microbiota were compared in the three groups using metagenomic-based 16S rRNA gene high throughput sequencing. The results showed that the relative abundance of probiotic genera (Akkermansia, Bifidobacterium and Lactobacillus) was significantly higher in the LM group mice than in the HM group mice, due to the high-temperature degradation of the nutrients of camels' milk. The diversity of the intestine microbiota in mice receiving milk was lower than in the control group because of the intrinsically high antimicrobial components (lactoferrin and lysozyme) detected in camels' milk. Carbohydrate digestion/absorption, and cysteine and methionine metabolism were significantly higher in the intestine microbiota of the LM group mice than in the HM group mice owing to the corresponding degradation of lactose, cysteine and methionine in camels' milk at high temperatures. Changes in the nutrients of camels' milk affected the changes in the functional features of the intestine microbiota. This research suggests that low temperature heat treatment achieves nutrient preservation, but also encourages probiotic genera.}, } @article {pmid30464766, year = {2018}, author = {Purahong, W and Orrù, L and Donati, I and Perpetuini, G and Cellini, A and Lamontanara, A and Michelotti, V and Tacconi, G and Spinelli, F}, title = {Plant Microbiome and Its Link to Plant Health: Host Species, Organs and Pseudomonas syringae pv. actinidiae Infection Shaping Bacterial Phyllosphere Communities of Kiwifruit Plants.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1563}, pmid = {30464766}, issn = {1664-462X}, abstract = {Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of the bacterial canker, the most devastating disease of kiwifruit vines. Before entering the host tissues, this pathogen has an epiphytic growth phase on kiwifruit flowers and leaves, thus the ecological interactions within epiphytic bacterial community may greatly influence the onset of the infection process. The bacterial community associated to the two most important cultivated kiwifruit species, Actinidia chinensis and Actinidia deliciosa, was described both on flowers and leaves using Illumina massive parallel sequencing of the V3 and V4 variable regions of the 16S rRNA gene. In addition, the effect of plant infection by Psa on the epiphytic bacterial community structure and biodiversity was investigated. Psa infection affected the phyllosphere microbiome structures in both species, however, its impact was more pronounced on A. deliciosa leaves, where a drastic drop in microbial biodiversity was observed. Furthermore, we also showed that Psa was always present in syndemic association with Pseudomonas syringae pv. syringae and Pseudomonas viridiflava, two other kiwifruit pathogens, suggesting the establishment of a pathogenic consortium leading to a higher pathogenesis capacity. Finally, the analyses of the dynamics of bacterial populations provided useful information for the screening and selection of potential biocontrol agents against Psa.}, } @article {pmid30464240, year = {2018}, author = {Wood, JR and Díaz, FP and Latorre, C and Wilmshurst, JM and Burge, OR and Gutiérrez, RA}, title = {Plant pathogen responses to Late Pleistocene and Holocene climate change in the central Atacama Desert, Chile.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {17208}, pmid = {30464240}, issn = {2045-2322}, support = {Core funding for Crown Research Institutes//Ministry of Business, Innovation and Employment (MBIE)/International ; Core funding to Crown Research Institutes//Ministry for Business Innovation and Employment (MBIE)/International ; }, mesh = {Animals ; Chile ; *Climate Change ; DNA, Ancient/*isolation & purification ; DNA, Fungal/*isolation & purification ; Desert Climate ; Feces/chemistry ; *Fossils ; Fungi/*classification/*genetics ; Metagenomics/methods ; Plant Diseases/*microbiology ; RNA, Ribosomal, 18S/genetics ; Rodentia ; }, abstract = {Future climate change has the potential to alter the distribution and prevalence of plant pathogens, which may have significant implications for both agricultural crops and natural plant communities. However, there are few long-term datasets against which modelled predictions of pathogen responses to climate change can be tested. Here, we use 18S metabarcoding of 28 rodent middens (solidified deposits of rodent coprolites and nesting material) from the Central Atacama, spanning the last ca. 49 ka, to provide the first long-term late Quaternary record of change in plant pathogen communities in response to changing climate. Plant pathogen richness was significantly greater in middens deposited during the Central Andean Pluvial Event (CAPE); a period of increased precipitation between 17.5-8.5 ka. Moreover, the occurrence frequency of Pucciniaceae (rust fungi) was significantly greater during the CAPE, and the highest relative abundances for five additional potentially pathogenic taxa also occurred during this period. The results demonstrate the promising potential for ancient DNA analysis of late Quaternary samples to reveal insights into how plant pathogens responded to past climatic and environmental change, which could help predict how pathogens may responded to future change.}, } @article {pmid30463925, year = {2018}, author = {Bulow, C and Langdon, A and Hink, T and Wallace, M and Reske, KA and Patel, S and Sun, X and Seiler, S and Jones, S and Kwon, JH and Burnham, CA and Dantas, G and Dubberke, ER}, title = {Impact of Amoxicillin-Clavulanate followed by Autologous Fecal Microbiota Transplantation on Fecal Microbiome Structure and Metabolic Potential.}, journal = {mSphere}, volume = {3}, number = {6}, pages = {}, pmid = {30463925}, issn = {2379-5042}, support = {TL1 TR002344/TR/NCATS NIH HHS/United States ; U54 CK000609/CK/NCEZID CDC HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; KL2 TR002346/TR/NCATS NIH HHS/United States ; TL1 TR000449/TR/NCATS NIH HHS/United States ; UL1 TR002345/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Amoxicillin-Potassium Clavulanate Combination/*administration & dosage ; Anti-Bacterial Agents/*administration & dosage ; Enema ; Fecal Microbiota Transplantation/*methods ; Female ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Male ; *Metabolism ; *Microbiota ; Middle Aged ; Treatment Outcome ; Young Adult ; beta-Lactamase Inhibitors/*administration & dosage ; }, abstract = {Strategies to prevent multidrug-resistant organism (MDRO) infections are scarce, but autologous fecal microbiota transplantation (autoFMT) may limit gastrointestinal MDRO expansion. AutoFMT involves banking one's feces during a healthy state for later use in restoring gut microbiota following perturbation. This pilot study evaluated the effect of autoFMT on gastrointestinal microbiome taxonomic composition, resistance gene content, and metabolic capacity after exposure to amoxicillin-clavulanic acid (Amox-Clav). Ten healthy participants were enrolled. All received 5 days of Amox-Clav. Half were randomized to autoFMT, derived from stool collected pre-antimicrobial exposure, by enema, and half to saline enema. Participants submitted stool samples pre- and post-Amox-Clav and enema and during a 90-day follow-up period. Shotgun metagenomic sequencing revealed taxonomic composition, resistance gene content, and metabolic capacity. Amox-Clav significantly altered gut taxonomic composition in all participants (n = 10, P < 0.01); however, only three participants exhibited major changes at the phylum level following exposure. In the cohort as a whole, beta-lactamase genes were enriched following Amox-Clav (P < 0.05), and predicted metabolic capacity was significantly altered (P < 0.01). Species composition, metabolic capacity, and beta-lactamase abundance returned to pre-antimicrobial exposure state 7 days after either autoFMT or saline enema (P > 0.05, compared to enrollment). Alterations to microbial metabolic capacity occurred following antimicrobial exposure even in participants without substantial taxonomic disruption, potentially creating open niches for pathogen colonization. Our findings suggest that metabolic potential is an important consideration for complete assessment of antimicrobial impact on the microbiome. AutoFMT was well tolerated and may have contributed to phylogenetic recovery. (This study has been registered at ClinicalTrials.gov under identifier NCT02046525.)IMPORTANCE The spread of multidrug resistance among pathogenic organisms threatens the efficacy of antimicrobial treatment options. The human gut serves as a reservoir for many drug-resistant organisms and their resistance genes, and perturbation of the gut microbiome by antimicrobial exposure can open metabolic niches to resistant pathogens. Once established in the gut, antimicrobial-resistant bacteria can persist even after antimicrobial exposure ceases. Strategies to prevent multidrug-resistant organism (MDRO) infections are scarce, but autologous fecal microbiota transplantation (autoFMT) may limit gastrointestinal MDRO expansion. AutoFMT involves banking one's feces during a healthy state for later use in restoring gut microbiota following perturbation. This pilot study evaluated the effect of amoxicillin-clavulanic acid (Amox-Clav) exposure and autoFMT on gastrointestinal microbiome taxonomic composition, resistance gene content, and metabolic capacity. Importantly, we found that metabolic capacity was perturbed even in cases where gross phylogeny remained unchanged and that autoFMT was safe and well tolerated.}, } @article {pmid30462578, year = {2020}, author = {Miao, J and Shi, Y and Zeng, D and Wu, G}, title = {Enhanced shortcut nitrogen removal and metagenomic analysis of functional microbial communities in a double sludge system treating ammonium-rich wastewater.}, journal = {Environmental technology}, volume = {41}, number = {14}, pages = {1877-1887}, doi = {10.1080/09593330.2018.1551432}, pmid = {30462578}, issn = {1479-487X}, mesh = {Ammonia ; *Ammonium Compounds ; Bioreactors ; Denitrification ; *Microbiota ; Nitrification ; Nitrogen ; Sewage ; Wastewater ; }, abstract = {Biological nitrogen removal processes based on partial nitrification are promising for ammonium-rich wastewater treatment. In this study, a partial nitrification-denitrification double sludge system was applied to treat synthetic ammonium-rich wastewater. Metagenomic analysis of functional genes and metabolic pathways was conducted, also with the evaluation of system performance and nitrous oxide (N2O) emission. In the nitrifying sequencing batch reactor (SBRPN), the removal percentage of ammonium nitrogen reached to 99.98% with a high nitritation efficiency of 93.24%, and the N2O emission factor was 0.88%. In the denitrifying sequencing batch reactor (SBRDN), there was almost no nitrate nitrogen and nitrite nitrogen in the effluent, and the maximum N2O emission was 0.078 mg N/L. The dominant ammonia oxidizing bacteria was Nitrosomonas in SBRPN (13.6%), and the main potential denitrifiers in SBRDN were Thauera (14.6%), an uncultured genus in the Comamonadaceae family (4.0%), an uncultured genus in Rhodocyclaceae family (2.4%) and Comamonas (1.1%). Metagenomic analysis revealed that amo mainly distributed in Nitrosomonas eutropha (38.3%), Nitrosomonas europaea (27.1%), Nitrosomonas sp. GH22 (20.5%) and Nitrosomonas sp. TK794 (15.0%), and Bacteroidetes had the N2O reduction potential in SBRPN.}, } @article {pmid30462522, year = {2019}, author = {Shi, Z and Fultz, RS and Engevik, MA and Gao, C and Hall, A and Major, A and Mori-Akiyama, Y and Versalovic, J}, title = {Distinct roles of histamine H1- and H2-receptor signaling pathways in inflammation-associated colonic tumorigenesis.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {316}, number = {1}, pages = {G205-G216}, pmid = {30462522}, issn = {1522-1547}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; U01 CA170930/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Carcinogenesis/drug effects/*metabolism ; Colon/drug effects/metabolism ; Disease Models, Animal ; Gastrointestinal Microbiome/drug effects ; Histamine/metabolism ; Histamine H1 Antagonists/pharmacology ; Inflammation/*metabolism ; Intestinal Mucosa/drug effects/metabolism ; Lipopolysaccharides/pharmacology ; Mice, Transgenic ; Receptors, Histamine H1/drug effects/*metabolism ; Receptors, Histamine H2/drug effects/*metabolism ; Signal Transduction/drug effects ; }, abstract = {Inflammatory bowel disease (IBD) is a well-known risk factor for the development of colorectal cancer. Prior studies have demonstrated that microbial histamine can ameliorate intestinal inflammation in mice. We tested the hypothesis whether microbe-derived luminal histamine suppresses inflammation-associated colon cancer in Apc[min/+] mice. Mice were colonized with the human-derived Lactobacillus reuteri. Chronic inflammation was induced by repeated cycles of low-dose dextran sulfate sodium (DSS). Mice that were given histamine-producing L. reuteri via oral gavage developed fewer colonic tumors, despite the presence of a complex mouse gut microbiome. We further demonstrated that administration of a histamine H1-receptor (H1R) antagonist suppressed tumorigenesis, while administration of histamine H2-receptor (H2R) antagonist significantly increased both tumor number and size. The bimodal functions of histamine include protumorigenic effects through H1R and antitumorigenic effects via H2R, and these results were supported by gene expression profiling studies on tumor specimens of patients with colorectal cancer. Greater ratios of gene expression of H2R (HRH2) vs. H1R (HRH1) were correlated with improved overall survival outcomes in patients with colorectal cancer. Additionally, activation of H2R suppressed phosphorylation of mitogen-activated protein kinases (MAPKs) and inhibited chemokine gene expression induced by H1R activation in colorectal cancer cells. Moreover, the combination of a H1R antagonist and a H2R agonist yielded potent suppression of lipopolysaccharide-induced MAPK signaling in macrophages. Given the impact on intestinal epithelial and immune cells, simultaneous modulation of H1R and H2R signaling pathways may be a promising therapeutic target for the prevention and treatment of inflammation-associated colorectal cancer. NEW & NOTEWORTHY Histamine-producing Lactobacillus reuteri can suppress development of inflammation-associated colon cancer in an established mouse model. The net effects of histamine may depend on the relative activity of H1R and H2R signaling pathways in the intestinal mucosa. Our findings suggest that treatment with H1R or H2R antagonists could yield opposite effects. However, by harnessing the ability to block H1R signaling while stimulating H2R signaling, novel strategies for suppression of intestinal inflammation and colorectal neoplasia could be developed.}, } @article {pmid30462168, year = {2019}, author = {Baldini, F and Heinken, A and Heirendt, L and Magnusdottir, S and Fleming, RMT and Thiele, I}, title = {The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {13}, pages = {2332-2334}, pmid = {30462168}, issn = {1367-4811}, mesh = {Microbial Interactions ; *Microbiota ; }, abstract = {MOTIVATION: The application of constraint-based modeling to functionally analyze metagenomic data has been limited so far, partially due to the absence of suitable toolboxes.

RESULTS: To address this gap, we created a comprehensive toolbox to model (i) microbe-microbe and host-microbe metabolic interactions, and (ii) microbial communities using microbial genome-scale metabolic reconstructions and metagenomic data. The Microbiome Modeling Toolbox extends the functionality of the constraint-based reconstruction and analysis toolbox.

The Microbiome Modeling Toolbox and the tutorials at https://git.io/microbiomeModelingToolbox.}, } @article {pmid30459421, year = {2018}, author = {Xu, J and Zhang, Y and Zhang, P and Trivedi, P and Riera, N and Wang, Y and Liu, X and Fan, G and Tang, J and Coletta-Filho, HD and Cubero, J and Deng, X and Ancona, V and Lu, Z and Zhong, B and Roper, MC and Capote, N and Catara, V and Pietersen, G and Vernière, C and Al-Sadi, AM and Li, L and Yang, F and Xu, X and Wang, J and Yang, H and Jin, T and Wang, N}, title = {The structure and function of the global citrus rhizosphere microbiome.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4894}, pmid = {30459421}, issn = {2041-1723}, mesh = {Bacteria/classification/genetics ; Citrus/*microbiology ; DNA, Ribosomal Spacer/genetics ; Fungi/classification/genetics ; Metagenome/genetics ; Metagenomics/classification/methods ; Microbiota/*genetics ; Phylogeny ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes. The core citrus rhizosphere microbiome comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax and Paraburkholderia, some of which are potential plant beneficial microbes. We also identify over-represented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition and plant growth promotion in citrus rhizosphere. The results provide valuable information to guide microbial isolation and culturing and, potentially, to harness the power of the microbiome to improve plant production and health.}, } @article {pmid30459334, year = {2018}, author = {Jersie-Christensen, RR and Lanigan, LT and Lyon, D and Mackie, M and Belstrøm, D and Kelstrup, CD and Fotakis, AK and Willerslev, E and Lynnerup, N and Jensen, LJ and Cappellini, E and Olsen, JV}, title = {Quantitative metaproteomics of medieval dental calculus reveals individual oral health status.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4744}, pmid = {30459334}, issn = {2041-1723}, mesh = {Adult ; Archaeology/methods ; Bacteria/classification ; Bacterial Proteins/analysis ; DNA, Ancient/analysis ; DNA, Bacterial/analysis ; Denmark ; Dental Calculus/*microbiology ; Dental Plaque/microbiology ; Dietary Proteins ; Female ; *Health Status ; Humans ; Male ; Metagenomics/methods ; Microbiota/genetics ; Middle Aged ; *Oral Health ; Proteomics/*methods ; }, abstract = {The composition of ancient oral microbiomes has recently become accessible owing to advanced biomolecular methods such as metagenomics and metaproteomics, but the utility of metaproteomics for such analyses is less explored. Here, we use quantitative metaproteomics to characterize the dental calculus associated with the remains of 21 humans retrieved during the archeological excavation of the medieval (ca. 1100-1450 CE) cemetery of Tjærby, Denmark. We identify 3671 protein groups, covering 220 bacterial species and 81 genera across all medieval samples. The metaproteome profiles of bacterial and human proteins suggest two distinct groups of archeological remains corresponding to health-predisposed and oral disease-susceptible individuals, which is supported by comparison to the calculus metaproteomes of healthy living individuals. Notably, the groupings identified by metaproteomics are not apparent from the bioarchaeological analysis, illustrating that quantitative metaproteomics has the potential to provide additional levels of molecular information about the oral health status of individuals from archeological contexts.}, } @article {pmid30459201, year = {2018}, author = {Hannigan, GD and Duhaime, MB and Ruffin, MT and Koumpouras, CC and Schloss, PD}, title = {Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, pmid = {30459201}, issn = {2150-7511}, support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; T32 AI007528/AI/NIAID NIH HHS/United States ; U01 CA086400/CA/NCI NIH HHS/United States ; }, mesh = {Bacteria/genetics/virology ; Bacteriophages/*genetics/isolation & purification ; Cohort Studies ; Colorectal Neoplasms/*diagnosis/microbiology/*virology ; Feces/microbiology/virology ; Humans ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Viruses/*genetics ; }, abstract = {Human viruses (those that infect human cells) have been associated with many cancers, largely due to their mutagenic and functionally manipulative abilities. Despite this, cancer microbiome studies have focused almost exclusively on bacteria instead of viruses. We began evaluating the cancer virome by focusing on colorectal cancer, a primary cause of morbidity and mortality throughout the world and a cancer linked to altered colonic bacterial community compositions but with an unknown association with the gut virome. We used 16S rRNA gene, whole shotgun metagenomic, and purified virus metagenomic sequencing of stool to evaluate the differences in human colorectal cancer virus and bacterial community composition. Through random forest modeling, we identified differences in the healthy and colorectal cancer viromes. The cancer-associated virome consisted primarily of temperate bacteriophages that were also predicted to be bacterium-virus community network hubs. These results provide foundational evidence that bacteriophage communities are associated with colorectal cancer and potentially impact cancer progression by altering the bacterial host communities.IMPORTANCE Colorectal cancer is a leading cause of cancer-related death in the United States and worldwide. Its risk and severity have been linked to colonic bacterial community composition. Although human-specific viruses have been linked to other cancers and diseases, little is known about colorectal cancer virus communities. We addressed this knowledge gap by identifying differences in colonic virus communities in the stool of colorectal cancer patients and how they compared to bacterial community differences. The results suggested an indirect role for the virome in impacting colorectal cancer by modulating the associated bacterial community. These findings both support the idea of a biological role for viruses in colorectal cancer and provide a new understanding of basic colorectal cancer etiology.}, } @article {pmid30458701, year = {2018}, author = {Banos, S and Lentendu, G and Kopf, A and Wubet, T and Glöckner, FO and Reich, M}, title = {A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {190}, pmid = {30458701}, issn = {1471-2180}, mesh = {Biodiversity ; DNA Primers/*genetics ; DNA, Fungal/*genetics ; Fungi/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/*genetics ; Species Specificity ; }, abstract = {BACKGROUND: Several fungi-specific primers target the 18S rRNA gene sequence, one of the prominent markers for fungal classification. The design of most primers goes back to the last decades. Since then, the number of sequences in public databases increased leading to the discovery of new fungal groups and changes in fungal taxonomy. However, no reevaluation of primers was carried out and relevant information on most primers is missing. With this study, we aimed to develop an 18S rRNA gene sequence primer toolkit allowing an easy selection of the best primer pair appropriate for different sequencing platforms, research aims (biodiversity assessment versus isolate classification) and target groups.

RESULTS: We performed an intensive literature research, reshuffled existing primers into new pairs, designed new Illumina-primers, and annealing blocking oligonucleotides. A final number of 439 primer pairs were subjected to in silico PCRs. Best primer pairs were selected and experimentally tested. The most promising primer pair with a small amplicon size, nu-SSU-1333-5'/nu-SSU-1647-3' (FF390/FR-1), was successful in describing fungal communities by Illumina sequencing. Results were confirmed by a simultaneous metagenomics and eukaryote-specific primer approach. Co-amplification occurred in all sample types but was effectively reduced by blocking oligonucleotides.

CONCLUSIONS: The compiled data revealed the presence of an enormous diversity of fungal 18S rRNA gene primer pairs in terms of fungal coverage, phylum spectrum and co-amplification. Therefore, the primer pair has to be carefully selected to fulfill the requirements of the individual research projects. The presented primer toolkit offers comprehensive lists of 164 primers, 439 primer combinations, 4 blocking oligonucleotides, and top primer pairs holding all relevant information including primer's characteristics and performance to facilitate primer pair selection.}, } @article {pmid30452938, year = {2018}, author = {Bilal, T and Malik, B and Hakeem, KR}, title = {Metagenomic analysis of uncultured microorganisms and their enzymatic attributes.}, journal = {Journal of microbiological methods}, volume = {155}, number = {}, pages = {65-69}, doi = {10.1016/j.mimet.2018.11.014}, pmid = {30452938}, issn = {1872-8359}, mesh = {Bioengineering/methods ; Biofuels ; Biotechnology ; Enzyme Activation ; *Enzymes/genetics/metabolism ; Extremophiles/*enzymology/*genetics ; Genome, Microbial/*genetics ; Genomics ; Metagenomics/*methods ; Microbiological Techniques/methods ; Microbiota/genetics ; }, abstract = {Although second generation biofuel technology is a sustainable route for bioethanol production it is not currently a robust technology because of certain hindrances viz., unavailability of potential enzyme resources, low efficiency of enzymes and restricted availability of potent enzymes that work under harsh conditions in industrial processes. Therefore, bioprospecting of extremophilic microorganisms using metagenomics is a promising alternative to discover novel microbes and enzymes with efficient tolerance to unfavourable conditions and thus could revolutionize the energy sector. Metagenomics a recent field in "omics" technology enables the genomic study of uncultured microorganisms with the goal of better understanding microbial dynamics. Metagenomics in conjunction with NextGen Sequencing technology facilitates the sequencing of microbial DNA directly from environmental samples and has expanded, and transformed our knowledge of the microbial world. However, filtering the meaningful information from the millions of genomic sequences offers a serious challenge to bioinformaticians. The current review holds the opinion tool 'know- how' to unravel the secrets of nature while expediting the bio-industrial world. We also discuss the novel biocatalytic agents discovered through metagenomics and how bioengineering plays a pivotal role to enhance their efficiency.}, } @article {pmid30449316, year = {2018}, author = {Guerin, E and Shkoporov, A and Stockdale, SR and Clooney, AG and Ryan, FJ and Sutton, TDS and Draper, LA and Gonzalez-Tortuero, E and Ross, RP and Hill, C}, title = {Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut.}, journal = {Cell host & microbe}, volume = {24}, number = {5}, pages = {653-664.e6}, doi = {10.1016/j.chom.2018.10.002}, pmid = {30449316}, issn = {1934-6069}, mesh = {Bacteriophages/*classification/*genetics/*physiology/ultrastructure ; Base Sequence ; Capsid Proteins/genetics ; DNA Viruses ; Feces/virology ; Fermentation ; *Gastrointestinal Microbiome ; Genome, Viral/genetics ; Genomics ; Humans ; Metagenomics/methods ; *Phylogeny ; Sequence Analysis ; Viral Proteins/genetics ; }, abstract = {CrAssphages represent the most abundant virus in the human gut microbiota, but the lack of available genome sequences for comparison has kept them enigmatic. Recently, sequence-based classification of distantly related crAss-like phages from multiple environments was reported, leading to a proposed familial-level taxonomic group. Here, we assembled the metagenomic sequencing reads from 702 human fecal virome/phageome samples and analyzed 99 complete circular crAss-like phage genomes and 150 contigs ≥70 kb. In silico comparative genomics and taxonomic analysis enabled a classification scheme of crAss-like phages from human fecal microbiomes into four candidate subfamilies composed of ten candidate genera. Laboratory analysis was performed on fecal samples from an individual harboring seven distinct crAss-like phages. We achieved crAss-like phage propagation in ex vivo human fecal fermentations and visualized short-tailed podoviruses by electron microscopy. Mass spectrometry of a crAss-like phage capsid protein could be linked to metagenomic sequencing data, confirming crAss-like phage structural annotations.}, } @article {pmid30449244, year = {2019}, author = {Sterlin, D and Fieschi, C and Malphettes, M and Larsen, M and Gorochov, G and Fadlallah, J}, title = {Immune/microbial interface perturbation in human IgA deficiency.}, journal = {Gut microbes}, volume = {10}, number = {3}, pages = {429-433}, pmid = {30449244}, issn = {1949-0984}, mesh = {Bacteria/classification/genetics/immunology ; Biodiversity ; Common Variable Immunodeficiency/immunology/microbiology ; Gastrointestinal Microbiome/genetics/*immunology ; Humans ; IgA Deficiency/*immunology/*microbiology ; Immunoglobulin A/*immunology/metabolism ; Immunoglobulin M/immunology/metabolism ; }, abstract = {In a recently published article we report the metagenomic analysis of human gut microbiomes evolved in the absence of immunoglobulin A (IgA). We show that human IgA deficiency is not associated with massive quantitative perturbations of gut microbial ecology. While our study underlines a rather expected pathobiont expansion, we at the same time highlight a less expected depletion in some typically beneficial symbionts. We also show that IgM partially supply IgA deficiency, explaining the relatively mild clinical phenotype associated with the early steps of this condition. Microbiome studies in patients should consider potential issues such as cohort size, human genetic polymorphism and treatments. In this commentary, we discuss how such issues were taken into account in our own study.}, } @article {pmid30448738, year = {2019}, author = {Rehman, ZU and Ali, M and Iftikhar, H and Leiknes, T}, title = {Genome-resolved metagenomic analysis reveals roles of microbial community members in full-scale seawater reverse osmosis plant.}, journal = {Water research}, volume = {149}, number = {}, pages = {263-271}, doi = {10.1016/j.watres.2018.11.012}, pmid = {30448738}, issn = {1879-2448}, mesh = {Biofilms ; *Biofouling ; Membranes, Artificial ; *Microbiota ; Osmosis ; Seawater ; *Water Purification ; }, abstract = {Biofouling of Reverse Osmosis (RO) membrane is a significant issue for the water treatment industry. In this study, we apply the metagenomic shot-gun sequencing technology to characterise the composition and functional potential of the microbial community in a full-scale RO plant, at different stages of seawater treatment. We find Proteobacteria, Bacteroidetes and Planctomycetes to be the most abundant bacterial phyla. The genetic potential of the RO membrane microbial community shows the enrichment of genes involved in biofilm formation, representing the selective pressure of the biofilm formation process. We recover 31 metagenome-assembled genomes (MAGs) from intake (raw seawater), fouled RO membranes (leading and middle RO module) and brine reject water. A total of 25 MAGs are recovered from the biofilm samples (leading and middle RO modules), with 9 of them (36%) belonging to Planctomycetes. We investigate all 25 MAGs for genes (pili, flagella, quorum sensing, quorum quenching and nitrate reduction) that play an important role in biofilm formation and sustenance of cells. We show that Planctomycetes contain genes for the formation of flagella and pili, and the reduction of nitrate. Although genes for quorum sensing are not detected, quorum quenching genes are identified in the biofilm MAGs. Our results show that Planctomycetes, along with other microbes, play an important role in the formation and sustenance of biofilms on seawater RO membranes.}, } @article {pmid30447983, year = {2019}, author = {Vasquez, AK and Ganda, EK and Capel, MB and Eicker, S and Virkler, PD and Bicalho, RC and Nydam, DV}, title = {The microbiome of Escherichia coli and culture-negative nonsevere clinical mastitis: Characterization and associations with linear score and milk production.}, journal = {Journal of dairy science}, volume = {102}, number = {1}, pages = {578-594}, doi = {10.3168/jds.2018-15062}, pmid = {30447983}, issn = {1525-3198}, mesh = {Animals ; Anti-Infective Agents/therapeutic use ; Bacteria/classification/genetics ; Biodiversity ; Cattle ; Escherichia coli/*isolation & purification ; Female ; Lactation/*physiology ; Mastitis, Bovine/*microbiology ; Metagenomics ; Microbiota/*physiology ; Milk/microbiology ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Culture-negative and Escherichia coli cases are uncommonly treated in pathogen-based protocols for nonsevere mastitis. High-throughput 16S rRNA sequencing might reveal the presence of other pathogens and can provide information on microbial diversity. The objective was to explore the milk microbiome at the time of the mastitis event (enrollment) and its association with survival in the herd, milk production, and postevent linear score (LS) for cows with clinical mastitis characterized as negative or E. coli by culture. Fifty E. coli-positive and 35 culture-negative samples from cases were enrolled. No cases were treated with antimicrobials. All E. coli-positive quarters were characterized as transient; microbiological culture of samples taken 15 d postmastitis were negative for this organism. However, a difference in α-diversity (Shannon index) was present between enrollment and follow-up samples (3.8 vs. 5.1). When α-diversity was explored for enrollment E. coli samples, no relationship was observed between the Shannon indices of these samples and postmastitis LS. Alpha-diversity of the enrollment samples was lower for E. coli-positive cows that subsequently had greater losses in milk production. This difference was explained by a greater relative abundance of the family Enterobacteriaceae (67.8 vs. 38.4%) for cows that dropped in production. Analysis of composition of the microbiome identified one phylum, Proteobacteria, that differed between E. coli-positive cows that dropped in production and those that did not. Evaluation of β -diversity found no statistical relationship between postmastitis LS and the microbiome. When evaluating α- and β-diversities and composition of the microbiomes for culture-negative quarters, no associations were found for milk production changes and postmastitis LS. Three cows did not remain in the herd, limiting the ability to analyze survival. The findings suggest that a contributing factor to negative outcomes in E. coli-positive cows is relative abundance of this pathogen, and that no single or collective group of bacterial families is associated with milk production changes or postmastitis LS in culture-negative quarters. Although additional studies should be performed, the absence of associations between outcomes explored and microbial profiles in this study suggests that we are not missing opportunities by not treating nonsevere E. coli or culture-negative mastitis cases.}, } @article {pmid30446434, year = {2018}, author = {Lucking, EF and O'Connor, KM and Strain, CR and Fouhy, F and Bastiaanssen, TFS and Burns, DP and Golubeva, AV and Stanton, C and Clarke, G and Cryan, JF and O'Halloran, KD}, title = {Chronic intermittent hypoxia disrupts cardiorespiratory homeostasis and gut microbiota composition in adult male guinea-pigs.}, journal = {EBioMedicine}, volume = {38}, number = {}, pages = {191-205}, pmid = {30446434}, issn = {2352-3964}, mesh = {Age Factors ; Animals ; Apnea/metabolism/physiopathology ; Basal Metabolism ; Biomarkers ; Brain Stem/metabolism ; Carotid Body ; *Gastrointestinal Microbiome ; Guinea Pigs ; Heart/*physiology/*physiopathology ; Homeostasis ; Hypoxia/*metabolism ; Male ; Metagenome ; Metagenomics ; Models, Animal ; Morbidity ; *Respiratory Physiological Phenomena ; Respiratory System/*physiopathology ; Sex Factors ; }, abstract = {BACKGROUND: Carotid body (peripheral oxygen sensor) sensitisation is pivotal in the development of chronic intermittent hypoxia (CIH)-induced hypertension. We sought to determine if exposure to CIH, modelling human sleep apnoea, adversely affects cardiorespiratory control in guinea-pigs, a species with hypoxia-insensitive carotid bodies. We reasoned that CIH-induced disruption of gut microbiota would evoke cardiorespiratory morbidity.

METHODS: Adult male guinea-pigs were exposed to CIH (6.5% O2 at nadir, 6 cycles.hour[-1]) for 8 h.day[-1] for 12 consecutive days.

FINDINGS: CIH-exposed animals established reduced faecal microbiota species richness, with increased relative abundance of Bacteroidetes and reduced relative abundance of Firmicutes bacteria. Urinary corticosterone and noradrenaline levels were unchanged in CIH-exposed animals, but brainstem noradrenaline concentrations were lower compared with sham. Baseline ventilation was equivalent in CIH-exposed and sham animals; however, respiratory timing variability, sigh frequency and ventilation during hypoxic breathing were all lower in CIH-exposed animals. Baseline arterial blood pressure was unaffected by exposure to CIH, but β-adrenoceptor-dependent tachycardia and blunted bradycardia during phenylephrine-induced pressor responses was evident compared with sham controls.

INTERPRETATION: Increased carotid body chemo-afferent signalling appears obligatory for the development of CIH-induced hypertension and elevated chemoreflex control of breathing commonly reported in mammals, with hypoxia-sensitive carotid bodies. However, we reveal that exposure to modest CIH alters gut microbiota richness and composition, brainstem neurochemistry, and autonomic control of heart rate, independent of carotid body sensitisation, suggesting modulation of breathing and autonomic homeostasis via the microbiota-gut-brainstem axis. The findings have relevance to human sleep-disordered breathing.

FUNDING: The Department of Physiology, and APC Microbiome Ireland, UCC.}, } @article {pmid30446169, year = {2019}, author = {Kosek, K and Kozioł, K and Luczkiewicz, A and Jankowska, K and Chmiel, S and Polkowska, Ż}, title = {Environmental characteristics of a tundra river system in Svalbard. Part 2: Chemical stress factors.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {1585-1596}, doi = {10.1016/j.scitotenv.2018.11.012}, pmid = {30446169}, issn = {1879-1026}, mesh = {Bacteria/classification/*drug effects ; *Environmental Monitoring ; Formaldehyde/analysis ; Metagenomics ; Metals/analysis ; Microbiota/*drug effects ; Phenols/analysis ; Polycyclic Aromatic Hydrocarbons/analysis ; Rivers/*chemistry/*microbiology ; Svalbard ; Tundra ; Water Pollutants, Chemical/*analysis ; }, abstract = {Bacterial communities in the Arctic environment are subject to multiple stress factors, including contaminants, although typically their concentrations are small. The Arctic contamination research has focused on persistent organic pollutants (POPs) because they are bioaccumulative, resistant to degradation and toxic for all organisms. Pollutants have entered the Arctic predominantly by atmospheric and oceanic long-range transport, and this was facilitated by their volatile or semi-volatile properties, while their chemical stability extended their lifetimes following emission. Chemicals present in the Arctic at detectable and quantifiable concentrations testify to their global impact. Chemical contamination may induce serious disorders in the integrity of polar ecosystems influencing the growth of bacterial communities. In this study, the abundance and the types of bacteria in the Arctic freshwater were examined and the microbial characteristics were compared to the amount of potentially harmful chemical compounds in particular elements of the Arctic catchment. The highest concentrations of all determined PAHs were observed in two samples in the vicinity of the estuary both in June and September 2016 and were 1964 ng L[-1] (R12) and 3901 ng L[-1] (R13) in June, and 2179 ng L[-1] (R12) and 1349 ng L[-1] (R13) in September. Remarkable concentrations of the sum of phenols and formaldehyde were detected also at the outflow of the Revelva river into the sea (R12) and were 0.24 mg L[-1] in June and 0.35 mg L[-1] in September 2016. The elevated concentrations of chemical compounds near the estuary suggest a potential impact of the water from the lower tributaries (including the glacier-fed stream measured at R13) or the sea currents and the sea aerosol as pollutant sources. The POPs' degradation at low temperature is not well understood but bacteria capable to degrading such compounds were noted in each sampling point.}, } @article {pmid30445563, year = {2019}, author = {Ramos-Sevillano, E and Wade, WG and Mann, A and Gilbert, A and Lambkin-Williams, R and Killingley, B and Nguyen-Van-Tam, JS and Tang, CM}, title = {The Effect of Influenza Virus on the Human Oropharyngeal Microbiome.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {68}, number = {12}, pages = {1993-2002}, pmid = {30445563}, issn = {1537-6591}, support = {102908/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Biodiversity ; Case-Control Studies ; Humans ; Influenza, Human/etiology ; Metagenome ; Metagenomics/methods ; *Microbial Interactions ; *Microbiota ; Oropharynx/*microbiology ; *Orthomyxoviridae ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Secondary bacterial infections are an important cause of morbidity and mortality associated with influenza infections. As bacterial disease can be caused by a disturbance of the host microbiome, we examined the impact of influenza on the upper respiratory tract microbiome in a human challenge study.

METHODS: The dynamics and ecology of the throat microbiome were examined following an experimental influenza challenge of 52 previously-healthy adult volunteers with influenza A/Wisconsin/67/2005 (H3N2) by intranasal inoculation; 35 healthy control subjects were not subjected to the viral challenge. Serial oropharyngeal samples were taken over a 30-day period, and the V1-V3 region of the bacterial 16S ribosomal RNA sequences were amplified and sequenced to determine the composition of the microbiome. The carriage of pathogens was also detected.

RESULTS: Of the 52 challenged individuals, 43 developed proven influenza infections, 33 of whom became symptomatic. None of the controls developed influenza, although 22% reported symptoms. The diversity of bacterial communities remained remarkably stable following the acquisition of influenza, with no significant differences over time between individuals with influenza and those in the control group. Influenza infection was not associated with perturbation of the microbiome at the level of phylum or genus. There was no change in colonization rates with Streptococcus pneumoniae or Neisseria meningitidis.

CONCLUSIONS: The throat microbiota is resilient to influenza infection, indicating the robustness of the upper-airway microbiome.}, } @article {pmid30445325, year = {2019}, author = {Lopez, S and Goux, X and Echevarria, G and Calusinska, M and Morel, JL and Benizri, E}, title = {Community diversity and potential functions of rhizosphere-associated bacteria of nickel hyperaccumulators found in Albania.}, journal = {The Science of the total environment}, volume = {654}, number = {}, pages = {237-249}, doi = {10.1016/j.scitotenv.2018.11.056}, pmid = {30445325}, issn = {1879-1026}, mesh = {Albania ; Biodegradation, Environmental ; Biodiversity ; Brassicaceae/*growth & development/metabolism ; Environmental Monitoring/*methods ; Nickel/*analysis/metabolism ; Proteobacteria/classification/genetics/*isolation & purification ; *Rhizosphere ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/*analysis/metabolism ; }, abstract = {Ultramafic (i.e. serpentine) soils are widespread in the Balkans and particularly in Albania. They account for a large part of plant endemism in that region and host several hyperaccumulator species, which are characterized by leaf nickel concentrations frequently above 1%. This rich nickel hyperaccumulating flora could serve as candidate to be used in phytoextraction and agromining. Despite recent interest in metal hyperaccumulating plants and agromining, very few studies have investigated the bacterial diversity and the influence of environmental factors on microbial gene profiles in the rhizosphere of hyperaccumulator plants growing on ultramafic soils. Because rhizospheric bacteria could be crucial to the success of phytoremediation, we studied a total of 48 nickel-hyperaccumulating plants which were sampled from four species that are widespread in Albania: Noccaea ochroleuca, Odontarrhena smolikana, O. rigida and O. chalcidica. All samples were taken from the ultramafic regions of Librazhd and Pogradec in eastern Albania in October 2015. Our study shows that Proteobacteria, Actinobacteria and Acidobacteria dominated the soil bacterial communities. Of these three phyla, only Proteobacteria was relatively abundant. This study underlines the influence of soil Cation Exchange Capacity on the bacterial community's diversity and structure. Based on the predicted metagenomes, the genes belonging to amino acid, lipid and carbohydrate metabolisms were identified as major gene families. Our study sheds some light on our understanding of how bacterial communities are structured within and affect the rhizosphere of hyperaccumulator plants from ultramafic soils in Albania.}, } @article {pmid30442907, year = {2019}, author = {Zhou, W and Chow, KH and Fleming, E and Oh, J}, title = {Selective colonization ability of human fecal microbes in different mouse gut environments.}, journal = {The ISME journal}, volume = {13}, number = {3}, pages = {805-823}, pmid = {30442907}, issn = {1751-7370}, support = {DP2 GM126893/GM/NIGMS NIH HHS/United States ; K22 AI119231/AI/NIAID NIH HHS/United States ; 1 DP2 GM126893-01//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/International ; }, mesh = {Animals ; Bacteroides/growth & development/*physiology ; Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Genotype ; Humans ; *Metagenomics ; Mice ; Mice, Inbred C57BL ; }, abstract = {Mammalian hosts constantly interact with diverse exogenous microbes, but only a subset of the microbes manage to colonize due to selective colonization resistance exerted by host genetic factors as well as the native microbiota of the host. An important question in microbial ecology and medical science is if such colonization resistance can discriminate closely related microbial species, or even closely related strains of the same species. Using human-mouse fecal microbiota transplantation and metagenomic shotgun sequencing, we reconstructed colonization patterns of human fecal microbes in mice with different genotypes (C57BL6/J vs. NSG) and with or without an intact gut microbiota. We found that mouse genotypes and the native mouse gut microbiota both exerted different selective pressures on exogenous colonizers: human fecal Bacteroides successfully established in the mice gut, however, different species of Bacteroides selectively enriched under different gut conditions, potentially due to a multitude of functional differences, ranging from versatility in nutrient acquisition to stress responses. Additionally, different clades of Bacteroides cellulosilyticus strains were selectively enriched in different gut conditions, suggesting that the fitness of conspecific microbial strains in a novel host environment could differ.}, } @article {pmid30440884, year = {2018}, author = {Gao, Z and Chen, KY and Mueller, O and Zhang, H and Rakhilin, N and Chen, J and Shen, X}, title = {Microbiota of Inflammatory Bowel Disease Models.}, journal = {Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference}, volume = {2018}, number = {}, pages = {2374-2377}, pmid = {30440884}, issn = {2694-0604}, support = {R01 GM114254/GM/NIGMS NIH HHS/United States ; R35 GM122465/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Disease Models, Animal ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Intestines/microbiology ; Male ; Rats ; }, abstract = {Gut microbiome plays an important role in inflammatory bowel disease (IBD), a group of intestinal chronic inflammation conditions that affect a large population. The animal models of IBD have long been established on basis of pathological features, but their ability to recapitulate patient gut microbiota is unknown. We investigated and compared the composition and biodiversity of bacterial population in the fecal samples from rat models of the two IBD subtypes, and compared them with patient samples. Our analyses revealed that inflammation reduces overall microbiome diversity and increased variation between individuals. We identified specific microbial signatures associated with the two IBD subtypes that were consistent between the animal models and human IBD patients, suggesting that the animal models can partially recapitulate the microbiota in human diseases. Furthermore, metagenome prediction analysis suggested microbial functions that were likely altered by host-microbiota interactions in IBD models.}, } @article {pmid30440093, year = {2019}, author = {Park, CH and Lee, AR and Lee, YR and Eun, CS and Lee, SK and Han, DS}, title = {Evaluation of gastric microbiome and metagenomic function in patients with intestinal metaplasia using 16S rRNA gene sequencing.}, journal = {Helicobacter}, volume = {24}, number = {1}, pages = {e12547}, pmid = {30440093}, issn = {1523-5378}, support = {//National Research Foundation of Korea (NRF)/ ; NRF-2017R1C1B5015928//Korea government (MSIP; Ministry of Science, ICT & Future Planning)/ ; }, mesh = {Adult ; Aged ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/classification/genetics/isolation & purification ; Disease Progression ; Female ; Gastritis/microbiology/pathology ; Gastritis, Atrophic/drug therapy/microbiology/pathology ; Gastrointestinal Microbiome/drug effects/*genetics ; Helicobacter Infections/drug therapy/*microbiology/*pathology ; Helicobacter pylori/drug effects/genetics/isolation & purification ; Humans ; Intestines/*microbiology/*pathology ; Male ; Metagenomics ; Metaplasia/*microbiology ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Stomach Neoplasms/microbiology/pathology ; Type IV Secretion Systems/genetics ; Young Adult ; }, abstract = {BACKGROUND: Despite recent advances in studies on the gastric microbiome, the role of the non-Helicobacter pylori gastric microbiome in gastric carcinogenesis remains unclear. We evaluated the characteristics of the gastric microbiome and metagenomic functions in patients with IM.

METHODS: Participants were classified into six groups according to disease status (chronic superficial gastritis [CSG], intestinal metaplasia [IM], and cancer) and H. pylori- infection status (H. pylori-positive and H. pylori-negative). The gastric microbiome was analyzed in mucosal tissues at the gastric antrum by 16S rRNA gene sequencing. Moreover, we assessed the metagenome including the type IV secretion system (T4SS) gene, as T4SS proteins are essential for transferring CagA from H. pylori- into the human gastric epithelium.

RESULTS: Among the 138 included patients, 48, 9, 23, 14, 12, and 32 were classified into the H. pylori-negative CSG, H. pylori-negative IM, H. pylori-negative cancer, H. pylori-positive CSG, H. pylori-positive IM, and H. pylori-positive cancer groups, respectively. Cyanobacteria were predominant in the H. pylori-negative CSG group compared to in the H. pylori-negative IM and H. pylori-negative cancer groups (H. pylori-negative CSG vs H. pylori-negative IM vs H. pylori-negative cancer: 14.0% vs 4.2% vs 0.04%, P < 0.001). In contrast, Rhizobiales were commonly observed in the H. pylori-negative IM group (H. pylori-negative CSG vs H. pylori-negative IM vs H. pylori-negative cancer: 1.9% vs 15.4% vs 2.8%, P < 0.001). The relative abundance of Rhizobiales increased as H. pylori-infected stomachs progressed from gastritis to IM. In the H. pylori-negative IM group, genes encoding T4SS were prevalent among the metagenome. Additionally, after H. pylori- eradication therapy, the gastric microbiome was similar to the microbiome observed after spontaneous clearance of H. pylori-.

CONCLUSIONS: The relative abundance of Rhizobiales was higher in patients with H. pylori-negative IM than in those with H. pylori-negative CSG or cancer. Additionally, T4SS genes were highly observed in the metagenome of patients with IM. Highly abundant T4SS proteins in these patients may promote gastric carcinogenesis.}, } @article {pmid30431224, year = {2019}, author = {Koskella, B}, title = {New approaches to characterizing bacteria-phage interactions in microbial communities and microbiomes.}, journal = {Environmental microbiology reports}, volume = {11}, number = {1}, pages = {15-16}, doi = {10.1111/1758-2229.12706}, pmid = {30431224}, issn = {1758-2229}, mesh = {Bacteria/classification/*virology ; Bacteriophages/classification/genetics/*physiology ; Biodiversity ; Genetic Variation ; Genome, Viral/genetics ; Metagenomics ; *Microbiota ; Single-Cell Analysis ; }, } @article {pmid30427852, year = {2018}, author = {Brito, TL and Campos, AB and Bastiaan von Meijenfeldt, FA and Daniel, JP and Ribeiro, GB and Silva, GGZ and Wilke, DV and de Moraes, DT and Dutilh, BE and Meirelles, PM and Trindade-Silva, AE}, title = {The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0200437}, pmid = {30427852}, issn = {1932-6203}, mesh = {Animals ; Bivalvia/*microbiology/physiology ; Gammaproteobacteria/*enzymology/genetics/*physiology ; Genomics ; Gills/microbiology ; Glycoside Hydrolases/genetics/*metabolism ; Metagenome ; Microbiota ; Multigene Family ; Phylogeny ; Polysaccharides/*metabolism ; Secondary Metabolism ; *Symbiosis ; Wood/metabolism/parasitology ; }, abstract = {Teredinidae are a family of highly adapted wood-feeding and wood-boring bivalves, commonly known as shipworms, whose evolution is linked to the acquisition of cellulolytic gammaproteobacterial symbionts harbored in bacteriocytes within the gills. In the present work we applied metagenomics to characterize microbiomes of the gills and digestive tract of Neoteredo reynei, a mangrove-adapted shipworm species found over a large range of the Brazilian coast. Comparative metagenomics grouped the gill symbiont community of different N. reynei specimens, indicating closely related bacterial types are shared. Similarly, the intestine and digestive gland communities were related, yet were more diverse than and showed no overlap with the gill community. Annotation of assembled metagenomic contigs revealed that the gill symbiotic community of N. reynei encodes a plethora of plant cell wall polysaccharides degrading glycoside hydrolase encoding genes, and Biosynthetic Gene Clusters (BGCs). In contrast, the digestive tract microbiomes seem to play little role in wood digestion and secondary metabolites biosynthesis. Metagenome binning recovered the nearly complete genome sequences of two symbiotic Teredinibacter strains from the gills, a representative of Teredinibacter turnerae "clade I" strain, and a yet to be cultivated Teredinibacter sp. type. These Teredinibacter genomes, as well as un-binned gill-derived gammaproteobacteria contigs, also include an endo-β-1,4-xylanase/acetylxylan esterase multi-catalytic carbohydrate-active enzyme, and a trans-acyltransferase polyketide synthase (trans-AT PKS) gene cluster with the gene cassette for generating β-branching on complex polyketides. Finally, we use multivariate analyses to show that the secondary metabolome from the genomes of Teredinibacter representatives, including genomes binned from N. reynei gills' metagenomes presented herein, stands out within the Cellvibrionaceae family by size, and enrichments for polyketide, nonribosomal peptide and hybrid BGCs. Results presented here add to the growing characterization of shipworm symbiotic microbiomes and indicate that the N. reynei gill gammaproteobacterial community is a prolific source of biotechnologically relevant enzymes for wood-digestion and bioactive compounds production.}, } @article {pmid30427574, year = {2019}, author = {Barnes, RC and Kim, H and Fang, C and Bennett, W and Nemec, M and Sirven, MA and Suchodolski, JS and Deutz, N and Britton, RA and Mertens-Talcott, SU and Talcott, ST}, title = {Body Mass Index as a Determinant of Systemic Exposure to Gallotannin Metabolites during 6-Week Consumption of Mango (Mangifera indica L.) and Modulation of Intestinal Microbiota in Lean and Obese Individuals.}, journal = {Molecular nutrition & food research}, volume = {63}, number = {2}, pages = {e1800512}, doi = {10.1002/mnfr.201800512}, pmid = {30427574}, issn = {1613-4133}, mesh = {Adult ; *Body Mass Index ; Fatty Acids, Volatile/biosynthesis ; Feces/chemistry ; Female ; *Gastrointestinal Microbiome ; Humans ; Hydrolyzable Tannins/*metabolism ; Male ; *Mangifera/chemistry ; Obesity/*metabolism/microbiology ; Phenols/analysis ; Polymerase Chain Reaction ; }, abstract = {SCOPE: This human clinical pilot trial investigated pharmacokinetics of gallotannin-metabolites and modulation of intestinal microbiota in healthy lean and obese individuals after 6 weeks of daily mango consumption.

METHODS AND RESULTS: Participants are divided into three groups: Lean Mango (LM: n = 12; BMI = 22.9 kg m[-2]), Obese Mango (OM: n = 9; BMI = 34.6 kg m[-2]), and Lean Control (LC: n = 11; BMI = 22.1 kg m[-2]). LM and OM consumed 400 g of mango per day for 6 weeks. LC consumed mango only on Days 0 and 42. After 6 weeks, LM experienced increased systemic exposure (AUC0-8h) to gallotannin-metabolites, 1.4-fold (p = 0.043). The greatest increase is 4-O-methyl-gallic acid, 3.3-fold (p = 0.0026). Cumulative urinary excretion of gallotannin-metabolites significantly increased in LM and OM, but not LC. For OM, qPCR data show increased levels of tannase-producing Lactococcus lactis and decreased levels of Clostridium leptum and Bacteroides thetaiotaomicron, bacteria associated with obesity. LM experienced an increased trend of fecal levels of butyric (1.3-fold; p = 0.09) and valeric acids (1.5-fold; p = 0.056). Plasma endotoxins showed a decreased trend in LM and OM.

CONCLUSION: Continuous mango intake significantly increased systemic exposure to gallotannin- metabolites and induced an increased trend for fecal short-chain fatty acids in lean but not obese individuals. This pharmacokinetic discrepancy may result in BMI-associated reduced gallotannin-derived health benefits.}, } @article {pmid30425247, year = {2018}, author = {Hansen, LBS and Roager, HM and Søndertoft, NB and Gøbel, RJ and Kristensen, M and Vallès-Colomer, M and Vieira-Silva, S and Ibrügger, S and Lind, MV and Mærkedahl, RB and Bahl, MI and Madsen, ML and Havelund, J and Falony, G and Tetens, I and Nielsen, T and Allin, KH and Frandsen, HL and Hartmann, B and Holst, JJ and Sparholt, MH and Holck, J and Blennow, A and Moll, JM and Meyer, AS and Hoppe, C and Poulsen, JH and Carvalho, V and Sagnelli, D and Dalgaard, MD and Christensen, AF and Lydolph, MC and Ross, AB and Villas-Bôas, S and Brix, S and Sicheritz-Pontén, T and Buschard, K and Linneberg, A and Rumessen, JJ and Ekstrøm, CT and Ritz, C and Kristiansen, K and Nielsen, HB and Vestergaard, H and Færgeman, NJ and Raes, J and Frøkiær, H and Hansen, T and Lauritzen, L and Gupta, R and Licht, TR and Pedersen, O}, title = {A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4630}, pmid = {30425247}, issn = {2041-1723}, mesh = {Adult ; Aged ; Body Mass Index ; Creatinine/urine ; Cross-Over Studies ; Cytokines/blood ; DNA, Bacterial/analysis ; Denmark ; *Diet ; Fasting ; Feces/microbiology ; Female ; Fermentation ; *Gastrointestinal Microbiome/genetics ; Glutens/*administration & dosage/*adverse effects ; Humans ; Hydrogen ; Intestines/microbiology ; Male ; Metabolomics ; Metagenomics ; Middle Aged ; Postprandial Period ; Self Report ; Young Adult ; }, abstract = {Adherence to a low-gluten diet has become increasingly common in parts of the general population. However, the effects of reducing gluten-rich food items including wheat, barley and rye cereals in healthy adults are unclear. Here, we undertook a randomised, controlled, cross-over trial involving 60 middle-aged Danish adults without known disorders with two 8-week interventions comparing a low-gluten diet (2 g gluten per day) and a high-gluten diet (18 g gluten per day), separated by a washout period of at least six weeks with habitual diet (12 g gluten per day). We find that, in comparison with a high-gluten diet, a low-gluten diet induces moderate changes in the intestinal microbiome, reduces fasting and postprandial hydrogen exhalation, and leads to improvements in self-reported bloating. These observations suggest that most of the effects of a low-gluten diet in non-coeliac adults may be driven by qualitative changes in dietary fibres.}, } @article {pmid30424933, year = {2019}, author = {Castillo-Álvarez, F and Marzo-Sola, ME}, title = {Disease of the holobiont, the example of multiple sclerosis.}, journal = {Medicina clinica}, volume = {152}, number = {4}, pages = {147-153}, doi = {10.1016/j.medcli.2018.08.019}, pmid = {30424933}, issn = {1578-8989}, mesh = {Animals ; Disease Models, Animal ; Encephalomyelitis, Autoimmune, Experimental/immunology/*microbiology/prevention & control ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Immunity, Cellular ; Male ; Multiple Sclerosis/*microbiology ; Sex Factors ; Symbiosis ; }, abstract = {In recent years there has been a revolution regarding the role of the microbiota in different diseases, most of them within the spectrum of inflammatory and autoimmune diseases, associated with the development of metagenomics and the concept of holobiont, a large organism together with its microbiota. Specifically, in Multiple Sclerosis, multiple evidence points to the role of the microbiota in experimental autoimmune encephalomyelitis, animal model of the disease, and several articles have been published in recent years about differences in intestinal microbiota among patients with multiple sclerosis and control subjects. We review in this article the concept of holobiont and the gut microbiota functions, as well as the evidence accumulated about the role of the microbiota in experimental autoimmune encephalomyelitis and multiple sclerosis. Nowadays, there is a lot of evidence showing the role of the microbiota in the genesis, prevention and treatment of experimental autoimmune encephalomyelitis based mainly on three immunological pillars, the Th1-Th17 / Th2 balance, the Treg cells and the humoral immunity. It is also well documented that there are differences in the microbiota of patients with MS that are associated with a different expression of genes related to inflammation.}, } @article {pmid30424824, year = {2018}, author = {Haney, MM and Ericsson, AC and Lever, TE}, title = {Effects of Intraoperative Vagal Nerve Stimulation on the Gastrointestinal Microbiome in a Mouse Model of Amyotrophic Lateral Sclerosis.}, journal = {Comparative medicine}, volume = {68}, number = {6}, pages = {452-460}, pmid = {30424824}, issn = {2769-819X}, support = {K01 OD019924/OD/NIH HHS/United States ; T32 OD011126/OD/NIH HHS/United States ; }, mesh = {Amyotrophic Lateral Sclerosis/*microbiology ; Analysis of Variance ; Animals ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Mice ; Multivariate Analysis ; Signal Transduction ; Vagus Nerve Stimulation/*adverse effects ; }, abstract = {The gastrointestinal microbiota (GM) plays a fundamental role in health and disease and contributes to the bidirectional signaling between the gastrointestinal system and brain. The direct line of communication between these organ systems is through the vagus nerve. Therefore, vagal nerve stimulation (VNS), a commonly used technique for multiple disorders, has potential to modulate the enteric microbiota, enabling investigation and possibly treatment of numerous neurologic disorders in which the microbiota has been linked with disease. Here we investigate the effect of VNS in a mouse model of amyotrophic lateral sclerosis (ALS). B6SJL-Tg(SOD1*G93A)[dl]1Gur (SOD1[dl]) and wildtype mice underwent ventral neck surgery to access the vagus nerve. During surgery, the experimental group received 1 h of VNS, whereas the sham group underwent 1 h of sham treatment. The third (control) group did not undergo any surgical manipulation. Fecal samples were collected before surgery and at 8 d after the initial collection. Microbial DNA was sequenced to determine the GM profiles at both time points. GM profiles did not differ between genotypes at either the initial or end point. In addition, VNS did not alter GM populations, according to the parameters chosen in this study, indicating that this short intraoperative treatment is safe and has no lasting effects on the GM. Future studies are warranted to determine whether different stimulation parameters or chronic use of VNS affect GM profiles.}, } @article {pmid30424821, year = {2018}, author = {Singh, NK and Wood, JM and Karouia, F and Venkateswaran, K}, title = {Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {204}, pmid = {30424821}, issn = {2049-2618}, mesh = {Archaea/drug effects/genetics/*isolation & purification ; Azides/pharmacology ; Bacteria/drug effects/genetics/*isolation & purification ; Drug Resistance, Bacterial/*genetics ; Fungi/drug effects/genetics/*isolation & purification ; Humans ; Metagenome/genetics ; Microbiota/drug effects/genetics ; Propidium/analogs & derivatives/pharmacology ; *Space Flight ; *Spacecraft ; Virulence/genetics ; }, abstract = {BACKGROUND: The International Space Station (ISS) is an ideal test bed for studying the effects of microbial persistence and succession on a closed system during long space flight. Culture-based analyses, targeted gene-based amplicon sequencing (bacteriome, mycobiome, and resistome), and shotgun metagenomics approaches have previously been performed on ISS environmental sample sets using whole genome amplification (WGA). However, this is the first study reporting on the metagenomes sampled from ISS environmental surfaces without the use of WGA. Metagenome sequences generated from eight defined ISS environmental locations in three consecutive flights were analyzed to assess the succession and persistence of microbial communities, their antimicrobial resistance (AMR) profiles, and virulence properties. Metagenomic sequences were produced from the samples treated with propidium monoazide (PMA) to measure intact microorganisms.

RESULTS: The intact microbial communities detected in Flight 1 and Flight 2 samples were significantly more similar to each other than to Flight 3 samples. Among 318 microbial species detected, 46 species constituting 18 genera were common in all flight samples. Risk group or biosafety level 2 microorganisms that persisted among all three flights were Acinetobacter baumannii, Haemophilus influenzae, Klebsiella pneumoniae, Salmonella enterica, Shigella sonnei, Staphylococcus aureus, Yersinia frederiksenii, and Aspergillus lentulus. Even though Rhodotorula and Pantoea dominated the ISS microbiome, Pantoea exhibited succession and persistence. K. pneumoniae persisted in one location (US Node 1) of all three flights and might have spread to six out of the eight locations sampled on Flight 3. The AMR signatures associated with β-lactam, cationic antimicrobial peptide, and vancomycin were detected. Prominent virulence factors were cobalt-zinc-cadmium resistance and multidrug-resistance efflux pumps.

CONCLUSIONS: There was an increase in AMR and virulence gene factors detected over the period sampled, and metagenome sequences of human pathogens persisted over time. Comparative analysis of the microbial compositions of ISS with Earth analogs revealed that the ISS environmental surfaces were different in microbial composition. Metagenomics coupled with PMA treatment would help future space missions to estimate problematic risk group microbial pathogens. Cataloging AMR/virulence characteristics, succession, accumulation, and persistence of microorganisms would facilitate the development of suitable countermeasures to reduce their presence in the closed built environment.}, } @article {pmid30423107, year = {2018}, author = {García-Jiménez, B and de la Rosa, T and Wilkinson, MD}, title = {MDPbiome: microbiome engineering through prescriptive perturbations.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {17}, pages = {i838-i847}, pmid = {30423107}, issn = {1367-4811}, mesh = {Algorithms ; Markov Chains ; Metagenomics ; *Microbiota ; Molecular Conformation ; Software ; }, abstract = {MOTIVATION: Recent microbiome dynamics studies highlight the current inability to predict the effects of external perturbations on complex microbial populations. To do so would be particularly advantageous in fields such as medicine, bioremediation or industrial scenarios.

RESULTS: MDPbiome statistically models longitudinal metagenomics samples undergoing perturbations as a Markov Decision Process (MDP). Given a starting microbial composition, our MDPbiome system suggests the sequence of external perturbation(s) that will engineer that microbiome to a goal state, for example, a healthier or more performant composition. It also estimates intermediate microbiome states along the path, thus making it possible to avoid particularly undesirable/unhealthy states. We demonstrate MDPbiome performance over three real and distinct datasets, proving its flexibility, and the reliability and universality of its output 'optimal perturbation policy'. For example, an MDP created using a vaginal microbiome time series, with a goal of recovering from bacterial vaginosis, suggested avoidance of perturbations such as lubricants or sex toys; while another MDP provided a quantitative explanation for why salmonella vaccine accelerates gut microbiome maturation in chicks. This novel analytical approach has clear applications in medicine, where it could suggest low-impact clinical interventions that will lead to achievement or maintenance of a healthy microbial population, or alternately, the sequence of interventions necessary to avoid strongly negative microbiome states.

Code (https://github.com/beatrizgj/MDPbiome) and result files (https://tomdelarosa.shinyapps.io/MDPbiome/) are available online.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid30422704, year = {2019}, author = {Yue, SJ and Liu, J and Wang, AT and Meng, XT and Yang, ZR and Peng, C and Guan, HS and Wang, CY and Yan, D}, title = {Berberine alleviates insulin resistance by reducing peripheral branched-chain amino acids.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {316}, number = {1}, pages = {E73-E85}, doi = {10.1152/ajpendo.00256.2018}, pmid = {30422704}, issn = {1522-1555}, mesh = {3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)/metabolism ; 3T3-L1 Cells ; Adipocytes/drug effects/metabolism ; Adipose Tissue, White/*drug effects/metabolism ; Adult ; Amino Acids, Branched-Chain/*drug effects/metabolism ; Animals ; Berberine/*pharmacology ; Diabetes Mellitus/metabolism ; Diet, High-Fat ; Dysbiosis/*metabolism ; Fatty Liver ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Glucose Intolerance ; Hepatocytes/drug effects/metabolism ; Humans ; *Insulin Resistance ; Liver/*drug effects/metabolism ; Male ; Metagenomics ; Mice ; Middle Aged ; Obesity/*metabolism ; Protein Kinases ; }, abstract = {Increased circulating branched-chain amino acids (BCAAs) have been involved in the pathogenesis of obesity and insulin resistance (IR). However, evidence relating berberine (BBR), gut microbiota, BCAAs, and IR is limited. Here, we showed that BBR could effectively rectify steatohepatitis and glucose intolerance in high-fat diet (HFD)-fed mice. BBR reorganized gut microbiota populations under both the normal chow diet (NCD) and HFD. Particularly, BBR noticeably decreased the relative abundance of BCAA-producing bacteria, including order Clostridiales; families Streptococcaceae, Clostridiaceae, and Prevotellaceae; and genera Streptococcus and Prevotella. Compared with the HFD group, predictive metagenomics indicated a reduction in the proportion of gut microbiota genes involved in BCAA biosynthesis but the enrichment genes for BCAA degradation and transport by BBR treatment. Accordingly, the elevated serum BCAAs of HFD group were significantly decreased by BBR. Furthermore, the Western blotting results implied that BBR could promote the BCAA catabolism in the liver and epididymal white adipose tissues of HFD-fed mice by activation of the multienzyme branched-chain α-ketoacid dehydrogenase complex (BCKDC), whereas by inhibition of the phosphorylation state of BCKDHA (E1α subunit) and branched-chain α-ketoacid dehydrogenase kinase (BCKDK). The ex vivo assay further confirmed that BBR could increase BCAA catabolism in both AML12 hepatocytes and 3T3-L1 adipocytes. Finally, data from healthy subjects and diabetics confirmed that BBR could improve glycemic control and modulate circulating BCAAs. Together, our findings clarified BBR improving IR associated not only with gut microbiota alteration in BCAA biosynthesis but also with BCAA catabolism in liver and adipose tissues.}, } @article {pmid30420843, year = {2018}, author = {Alves, LF and Meleiro, LP and Silva, RN and Westmann, CA and Guazzaroni, ME}, title = {Novel Ethanol- and 5-Hydroxymethyl Furfural-Stimulated β-Glucosidase Retrieved From a Brazilian Secondary Atlantic Forest Soil Metagenome.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2556}, pmid = {30420843}, issn = {1664-302X}, abstract = {Beta-glucosidases are key enzymes involved in lignocellulosic biomass degradation for bioethanol production, which complete the final step during cellulose hydrolysis by converting cellobiose into glucose. Currently, industry requires enzymes with improved catalytic performance or tolerance to process-specific parameters. In this sense, metagenomics has become a powerful tool for accessing and exploring the biochemical biodiversity present in different natural environments. Here, we report the identification of a novel β-glucosidase from metagenomic DNA isolated from soil samples enriched with decaying plant matter from a Secondary Atlantic Forest region. For this, we employed a functional screening approach using an optimized and synthetic broad host-range vector for library production. The novel β-glucosidase - named Lfa2 - displays three GH3-family conserved domains and conserved catalytic amino acids D283 and E487. The purified enzyme was most active in pH 5.5 and at 50°C, and showed hydrolytic activity toward several pNP synthetic substrates containing β-glucose, β-galactose, β-xylose, β-fucose, and α-arabinopyranose, as well as toward cellobiose. Lfa2 showed considerable glucose tolerance, exhibiting an IC50 of 300 mM glucose and 30% of remaining activity in 600 mM glucose. In addition, Lfa2 retained full or slightly enhanced activity in the presence of several metal ions. Further, β-glucosidase activity was increased by 1.7-fold in the presence of 10% (v/v) ethanol, a concentration that can be reached in conventional fermentation processes. Similarly, Lfa2 showed 1.7-fold enhanced activity at high concentrations of 5-hydroxymethyl furfural, one of the most important cellulase inhibitors in pretreated sugarcane bagasse hydrolysates. Moreover, the synergistic effect of Lfa2 on Bacillus subtilis GH5-CBM3 endoglucanase activity was demonstrated by the increased production of glucose (1.6-fold). Together, these results indicate that β-glucosidase Lfa2 is a promissory enzyme candidate for utilization in diverse industrial applications, such as cellulosic biomass degradation or flavor enhancement in winemaking and grape processing.}, } @article {pmid30420838, year = {2018}, author = {Li, W and Yuan, Y and Xia, Y and Sun, Y and Miao, Y and Ma, S}, title = {A Cross-Scale Neutral Theory Approach to the Influence of Obesity on Community Assembly of Human Gut Microbiome.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2320}, pmid = {30420838}, issn = {1664-302X}, abstract = {Background: The implications of gut microbiome to obesity have been extensively investigated in recent years although the exact mechanism is still unclear. The question whether or not obesity influences gut microbiome assembly has not been addressed. The question is significant because it is fundamental for investigating the diversity maintenance and stability of gut microbiome, and the latter should hold a key for understanding the etiological implications of gut microbiome to obesity. Methods: In this study, we adopt a dual neutral theory modeling strategy to address this question from both species and community perspectives, with both discrete and continuous neutral theory models. The first neutral theory model we apply is Hubbell's neutral theory of biodiversity that has been extensively tested in macro-ecology of plants and animals, and the second we apply is Sloan's neutral theory model that was developed particularly for microbial communities based on metagenomic sequencing data. Both the neutral models are complementary to each other and integrated together offering a comprehensive approach to more accurately revealing the possible influence of obesity on gut microbiome assembly. This is not only because the focus of both neutral theory models is different (community vs. species), but also because they adopted two different modeling strategies (discrete vs. continuous). Results: We test both the neutral theory models with datasets from Turnbaugh et al. (2009). Our tests showed that the species abundance distributions of more than ½ species (59-69%) in gut microbiome satisfied the prediction of Sloan's neutral theory, although at the community level, the number of communities satisfied the Hubbell's neutral theory was negligible (2 out of 278). Conclusion: The apparently contradictory findings above suggest that both stochastic neutral effects and deterministic environmental (host) factors play important roles in shaping the assembly and diversity of gut microbiome. Furthermore, obesity may just be one of the host factors, but its influence may not be strong enough to tip the balance between stochastic and deterministic forces that shape the community assembly. Finally, the apparent contradiction from both the neutral theories should not be surprising given that there are still near 30-40% species that do not obey the neutral law.}, } @article {pmid30420594, year = {2018}, author = {Yost, S and Stashenko, P and Choi, Y and Kukuruzinska, M and Genco, CA and Salama, A and Weinberg, EO and Kramer, CD and Frias-Lopez, J}, title = {Increased virulence of the oral microbiome in oral squamous cell carcinoma revealed by metatranscriptome analyses.}, journal = {International journal of oral science}, volume = {10}, number = {4}, pages = {32}, pmid = {30420594}, issn = {2049-3169}, support = {R01 DE021553/DE/NIDCR NIH HHS/United States ; }, mesh = {Carcinoma, Squamous Cell/*microbiology ; Humans ; *Metagenome ; *Microbiota ; Mouth Neoplasms/*microbiology ; Phylogeny ; Pilot Projects ; RNA, Messenger/metabolism ; *Transcriptome ; Virulence ; Virulence Factors/*metabolism ; }, abstract = {Oral squamous cell carcinoma (OSCC) is the most prevalent and most commonly studied oral cancer. However, there is a void regarding the role that the oral microbiome may play in OSCC. Although the relationship between microbial community composition and OSCC has been thoroughly investigated, microbial profiles of the human microbiome in cancer are understudied. Here we performed a small pilot study of community-wide metatranscriptome analysis to profile mRNA expression in the entire oral microbiome in OSCC to reveal molecular functions associated with this disease. Fusobacteria showed a statistically significantly higher number of transcripts at tumour sites and tumour-adjacent sites of cancer patients compared to the healthy controls analysed. Regardless of the community composition, specific metabolic signatures were consistently found in disease. Activities such as iron ion transport, tryptophanase activity, peptidase activities and superoxide dismutase were over-represented in tumour and tumour-adjacent samples when compared to the healthy controls. The expression of putative virulence factors in the oral communities associated with OSCC showed that activities related to capsule biosynthesis, flagellum synthesis and assembly, chemotaxis, iron transport, haemolysins and adhesins were upregulated at tumour sites. Moreover, activities associated with protection against reactive nitrogen intermediates, chemotaxis, flagellar and capsule biosynthesis were also upregulated in non-tumour sites of cancer patients. Although they are preliminary, our results further suggest that Fusobacteria may be the leading phylogenetic group responsible for the increase in expression of virulence factors in the oral microbiome of OSCC patients.}, } @article {pmid30420263, year = {2019}, author = {Lamprecht, P and Fischer, N and Huang, J and Burkhardt, L and Lütgehetmann, M and Arndt, F and Rolfs, I and Kerstein, A and Iking-Konert, C and Laudien, M}, title = {Changes in the composition of the upper respiratory tract microbial community in granulomatosis with polyangiitis.}, journal = {Journal of autoimmunity}, volume = {97}, number = {}, pages = {29-39}, doi = {10.1016/j.jaut.2018.10.005}, pmid = {30420263}, issn = {1095-9157}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Arthritis, Rheumatoid/immunology ; Biodiversity ; Case-Control Studies ; Computational Biology/methods ; Disease Susceptibility ; *Dysbiosis ; Female ; Granulomatosis with Polyangiitis/*etiology ; Humans ; Male ; Metagenomics/methods ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S ; Respiratory Mucosa/*microbiology ; Young Adult ; }, abstract = {Dysbiosis¸ i.e. changes in microbial composition at a mucosal interface, is implicated in the pathogenesis of many chronic inflammatory and autoimmune diseases. To assess the composition of the microbial upper respiratory tract (URT) community in patients with granulomatosis with polyangiitis (GPA), we used culture-independent high-throughput methods. In this prospective clinical study, nasal swabs were collected from patients with GPA, patients with rheumatoid arthritis (RA, disease control), and healthy controls. Nasal bacterial taxa were assessed using V3-V4 region 16S rRNA amplicon sequencing. Staphylococcus aureus, Haemophilus influenza, and entero- and rhinoviruses were detected using qPCR. Unbiased metagenomic RNA sequencing (UMERS) was performed in a subset of samples to determine the relative abundance of bacterial, fungal, and viral species. A trend toward reduced microbiome diversity was detected in GPA samples compared with healthy controls. The abundance of bacterial taxa and microbial richness were significantly decreased in GPA samples compared with RA samples. The relative abundance of bacterial families shifted, with increased Planococcaceae and decreased Moraxellaceae, Tissierellaceae, Staphylococcaceae, and Propionibacteriaceae in GPA and RA. Further, decreased abundance of Corynebacteriaceae, and Aerococcaceae was observed in GPA samples. Significantly more colonization of S. aureus was seen in the nasal microbiome of GPA compared with RA and healthy control samples. H. influenzae colonization was also observed in GPA samples. UMERS detected the presence of rhinoviral sequences in some GPA samples. Thus, our study uncovered changes in the URT microbial composition in patients with GPA and RA, suggesting that both immunosuppression and disease background affect the URT microbiome. Complex alterations of host-microbiome interactions in the URT could influence chronic endonasal inflammation in GPA.}, } @article {pmid30419949, year = {2018}, author = {Silverman, JD and Durand, HK and Bloom, RJ and Mukherjee, S and David, LA}, title = {Dynamic linear models guide design and analysis of microbiota studies within artificial human guts.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {202}, pmid = {30419949}, issn = {2049-2618}, support = {R01 DK116187/DK/NIDDK NIH HHS/United States ; T32 GM007171/GM/NIGMS NIH HHS/United States ; }, mesh = {Artificial Organs/*microbiology ; Bacteroides/*growth & development ; Enterobacteriaceae/*growth & development ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Linear Models ; *Models, Anatomic ; }, abstract = {BACKGROUND: Artificial gut models provide unique opportunities to study human-associated microbiota. Outstanding questions for these models' fundamental biology include the timescales on which microbiota vary and the factors that drive such change. Answering these questions though requires overcoming analytical obstacles like estimating the effects of technical variation on observed microbiota dynamics, as well as the lack of appropriate benchmark datasets.

RESULTS: To address these obstacles, we created a modeling framework based on multinomial logistic-normal dynamic linear models (MALLARDs) and performed dense longitudinal sampling of four replicate artificial human guts over the course of 1 month. The resulting analyses revealed how the ratio of biological variation to technical variation from sample processing depends on sampling frequency. In particular, we find that at hourly sampling frequencies, 76% of observed variation could be ascribed to technical sources, which could also skew the observed covariation between taxa. We also found that the artificial guts demonstrated replicable trajectories even after a recovery from a transient feed disruption. Additionally, we observed irregular sub-daily oscillatory dynamics associated with the bacterial family Enterobacteriaceae within all four replicate vessels.

CONCLUSIONS: Our analyses suggest that, beyond variation due to sequence counting, technical variation from sample processing can obscure temporal variation from biological sources in artificial gut studies. Our analyses also supported hypotheses that human gut microbiota fluctuates on sub-daily timescales in the absence of a host and that microbiota can follow replicable trajectories in the presence of environmental driving forces. Finally, multiple aspects of our approach are generalizable and could ultimately be used to facilitate the design and analysis of longitudinal microbiota studies in vivo.}, } @article {pmid30418043, year = {2018}, author = {Muleviciene, A and D'Amico, F and Turroni, S and Candela, M and Jankauskiene, A}, title = {Iron deficiency anemia-related gut microbiota dysbiosis in infants and young children: A pilot study.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {65}, number = {4}, pages = {551-564}, doi = {10.1556/030.65.2018.045}, pmid = {30418043}, issn = {1217-8950}, mesh = {Anemia, Iron-Deficiency/*complications ; Bacteria/classification/genetics ; Child ; Child, Preschool ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Metagenomics ; *Microbiota ; Phylogeny ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Nutritional iron deficiency (ID) causes not only anemia but also malfunction of the entire human organism. Recently, a role of the gut microbiota has been hypothesized, but limited data are available especially in infants. Here, we performed a pilot study to explore the gut microbiota in 10 patients with iron deficiency anemia (IDA) and 10 healthy controls aged 6-34 months. Fresh stool samples were collected from diapers, and the fecal microbiota was profiled by next-generation sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Except for diet diversity, the breastfeeding status at the enrollment, the exclusive breastfeeding duration, and the introduction of complementary foods did not differ between groups. Distinct microbial signatures were found in IDA patients, with increased relative abundance of Enterobacteriaceae (mean relative abundance, patients vs. controls, 4.4% vs. 3.0%) and Veillonellaceae (13.7% vs. 3.6%), and reduced abundance of Coriobacteriaceae (3.5% vs. 8.8%) compared to healthy controls. A decreased Bifidobacteriaceae/Enterobacteriaceae ratio was observed in IDA patients. Notwithstanding the low sample size, our data highlight microbiota dysbalance in IDA worth for further investigations, aimed at unraveling the ID impact on the microbiome trajectory in early life, and the possible long-term consequences.}, } @article {pmid30417889, year = {2018}, author = {Hyeon, JY and Mann, DA and Townsend, AM and Deng, X}, title = {Quasi-metagenomic Analysis of Salmonella from Food and Environmental Samples.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {140}, pages = {}, pmid = {30417889}, issn = {1940-087X}, mesh = {Animals ; Cattle ; Environmental Monitoring ; Food Microbiology/*methods ; High-Throughput Nucleotide Sequencing ; Immunomagnetic Separation/*methods ; Metagenomics/*methods ; Microbiota ; Polymerase Chain Reaction ; *Salmonella enterica ; }, abstract = {Quasi-metagenomics sequencing refers to the sequencing-based analysis of modified microbiomes of food and environmental samples. In this protocol, microbiome modification is designed to concentrate genomic DNA of a target foodborne pathogen contaminant to facilitate the detection and subtyping of the pathogen in a single workflow. Here, we explain and demonstrate the sample preparation steps for the quasi-metagenomics analysis of Salmonella enterica from representative food and environmental samples including alfalfa sprouts, ground black pepper, ground beef, chicken breast and environmental swabs. Samples are first subjected to the culture enrichment of Salmonella for a shortened and adjustable duration (4-24 h). Salmonella cells are then selectively captured from the enrichment culture by immunomagnetic separation (IMS). Finally, multiple displacement amplification (MDA) is performed to amplify DNA from IMS-captured cells. The DNA output of this protocol can be sequenced by high throughput sequencing platforms. An optional quantitative PCR analysis can be performed to replace sequencing for Salmonella detection or assess the concentration of Salmonella DNA before sequencing.}, } @article {pmid30417110, year = {2018}, author = {Wei, ST and Wu, YW and Lee, TH and Huang, YS and Yang, CY and Chen, YL and Chiang, YR}, title = {Microbial Functional Responses to Cholesterol Catabolism in Denitrifying Sludge.}, journal = {mSystems}, volume = {3}, number = {5}, pages = {}, pmid = {30417110}, issn = {2379-5077}, abstract = {The 2,3-seco pathway, the pathway for anaerobic cholesterol degradation, has been established in the denitrifying betaproteobacterium Sterolibacterium denitrificans. However, knowledge of how microorganisms respond to cholesterol at the community level is elusive. Here, we applied mesocosm incubation and 16S rRNA sequencing to reveal that, in denitrifying sludge communities, three betaproteobacterial operational taxonomic units (OTUs) with low (94% to 95%) 16S rRNA sequence similarity to Stl. denitrificans are cholesterol degraders and members of the rare biosphere. Metatranscriptomic and metabolite analyses show that these degraders adopt the 2,3-seco pathway to sequentially catalyze the side chain and sterane of cholesterol and that two molybdoenzymes-steroid C25 dehydrogenase and 1-testosterone dehydrogenase/hydratase-are crucial for these bioprocesses, respectively. The metatranscriptome further suggests that these betaproteobacterial degraders display chemotaxis and motility toward cholesterol and that FadL-like transporters may be the key components for substrate uptake. Also, these betaproteobacteria are capable of transporting micronutrients and synthesizing cofactors essential for cellular metabolism and cholesterol degradation; however, the required cobalamin is possibly provided by cobalamin-de novo-synthesizing gamma-, delta-, and betaproteobacteria via the salvage pathway. Overall, our results indicate that the ability to degrade cholesterol in sludge communities is reserved for certain rare biosphere members and that C25 dehydrogenase can serve as a biomarker for sterol degradation in anoxic environments. IMPORTANCE Steroids are ubiquitous and abundant natural compounds that display recalcitrance. Biodegradation via sludge communities in wastewater treatment plants is the primary removal process for steroids. To date, compared to studies for aerobic steroid degradation, the knowledge of anaerobic degradation of steroids has been based on only a few model organisms. Due to the increase of anthropogenic impacts, steroid inputs may affect microbial diversity and functioning in ecosystems. Here, we first investigated microbial functional responses to cholesterol, the most abundant steroid in sludge, at the community level. Our metagenomic and metatranscriptomic analyses revealed that the capacities for cholesterol approach, uptake, and degradation are unique traits of certain low-abundance betaproteobacteria, indicating the importance of the rare biosphere in bioremediation. Apparent expression of genes involved in cofactor de novo synthesis and salvage pathways suggests that these micronutrients play important roles for cholesterol degradation in sludge communities.}, } @article {pmid30416033, year = {2019}, author = {van der Meulen, TA and Harmsen, HJM and Vila, AV and Kurilshikov, A and Liefers, SC and Zhernakova, A and Fu, J and Wijmenga, C and Weersma, RK and de Leeuw, K and Bootsma, H and Spijkervet, FKL and Vissink, A and Kroese, FGM}, title = {Shared gut, but distinct oral microbiota composition in primary Sjögren's syndrome and systemic lupus erythematosus.}, journal = {Journal of autoimmunity}, volume = {97}, number = {}, pages = {77-87}, doi = {10.1016/j.jaut.2018.10.009}, pmid = {30416033}, issn = {1095-9157}, mesh = {Adult ; Biodiversity ; Case-Control Studies ; Disease Susceptibility ; Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Lupus Erythematosus, Systemic/diagnosis/*etiology/metabolism ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Mouth Mucosa/*microbiology ; Phenotype ; RNA, Ribosomal, 16S/genetics ; Sjogren's Syndrome/diagnosis/*etiology/metabolism ; }, abstract = {OBJECTIVE: Alterations in the microbiota composition of the gastro-intestinal tract are suspected to be involved in the etiopathogenesis of two closely related systemic inflammatory autoimmune diseases: primary Sjögren's syndrome (pSS) and systemic lupus erythematosus (SLE). Our objective was to assess whether alterations in gut and oral microbiota compositions are specific for pSS and SLE.

METHODS: 16S ribosomal RNA gene sequencing was performed on fecal samples from 39 pSS patients, 30 SLE patients and 965 individuals from the general population, as well as on buccal swab and oral washing samples from the same pSS and SLE patients. Alpha-diversity, beta-diversity and relative abundance of individual bacteria were used as outcome measures. Multivariate analyses were performed to test associations between individual bacteria and disease phenotype, taking age, sex, body-mass index, proton-pump inhibitor use and sequencing-depth into account as possible confounding factors.

RESULTS: Fecal microbiota composition from pSS and SLE patients differed significantly from population controls, but not between pSS and SLE. pSS and SLE patients were characterized by lower bacterial richness, lower Firmicutes/Bacteroidetes ratio and higher relative abundance of Bacteroides species in fecal samples compared with population controls. Oral microbiota composition differed significantly between pSS patients and SLE patients, which could partially be explained by oral dryness in pSS patients.

CONCLUSIONS: pSS and SLE patients share similar alterations in gut microbiota composition, distinguishing patients from individuals in the general population, while oral microbiota composition shows disease-specific differences between pSS and SLE patients.}, } @article {pmid30414158, year = {2019}, author = {Bosch, TCG}, title = {Hydra as Model to Determine the Role of FOXO in Longevity.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1890}, number = {}, pages = {231-238}, doi = {10.1007/978-1-4939-8900-3_19}, pmid = {30414158}, issn = {1940-6029}, mesh = {Aging/genetics/metabolism ; Animals ; Animals, Genetically Modified ; Forkhead Transcription Factors/*genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; Genes, Reporter ; Genetic Vectors/genetics ; Hydra/classification/*genetics/metabolism ; Longevity/*genetics ; Metagenome ; Metagenomics/methods ; Microbiota ; Molecular Imaging ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Recombinant Fusion Proteins ; Stem Cells/metabolism ; }, abstract = {In non-senescent Hydra, continuously high activity of transcription factor FOXO contributes to continuous stem cell proliferation. Here, we describe how genetic manipulation of Hydra polyps using embryo-microinjection allows uncovering the role of FOXO in coordinating both stem cell proliferation and antimicrobial peptide0073 , effector molecules of the innate immune system, and regulators of the microbiome.}, } @article {pmid30413731, year = {2018}, author = {Suryavanshi, MV and Bhute, SS and Gune, RP and Shouche, YS}, title = {Functional eubacteria species along with trans-domain gut inhabitants favour dysgenic diversity in oxalate stone disease.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16598}, pmid = {30413731}, issn = {2045-2322}, mesh = {Bacteria/classification/*genetics ; Calcium Oxalate/*adverse effects/chemistry ; Case-Control Studies ; Dysbiosis/*classification/etiology/*pathology ; Gastrointestinal Microbiome/*physiology ; Humans ; Kidney Calculi/*complications ; *Metagenomics ; }, abstract = {Analyses across all three domains of life are necessary to advance our understanding of taxonomic dysbiosis in human diseases. In the present study, we assessed gut microbiota (eubacteria, archaea, and eukaryotes) of recurrent oxalate kidney stone suffers to explore the extent of trans-domain and functional species dysbiosis inside the gut. Trans-domain taxonomic composition, active oxalate metabolizer and butyrate-producing diversity were explored by utilizing frc-, but-, and buk- functional gene amplicon analysis. Operational taxonomic units (OTUs) level analyses confound with the observation that dysbiosis in gut microbiota is not just limited to eubacteria species, but also to other domains like archaea and eukaryotes. We found that some of healthy eubacterial population retained together with Oxalobacter formigenes and Lactobacillus plantarum colonization in disease condition (p < 0.001 & FDR = 0.05). Interestingly, trans-domain species diversity has been less shared and dysgenic taxa augmentation was found to be higher. Oxalate metabolizing bacterial species (OMBS) and butyrate-producing eubacteria species were found to be decreased in Oxalobacter non-colonizers; and Prevotella and Ruminococcus species which may contribute to oxalate metabolism and butyrate synthesis as well. Our study underscores fact that microbial dysbiosis is not limited to eubacteria only hence suggest the necessity of the trans-domain surveillance in metabolic diseases for intervention studies.}, } @article {pmid30413473, year = {2019}, author = {Coscolín, C and Katzke, N and García-Moyano, A and Navarro-Fernández, J and Almendral, D and Martínez-Martínez, M and Bollinger, A and Bargiela, R and Gertler, C and Chernikova, TN and Rojo, D and Barbas, C and Tran, H and Golyshina, OV and Koch, R and Yakimov, MM and Bjerga, GEK and Golyshin, PN and Jaeger, KE and Ferrer, M}, title = {Bioprospecting Reveals Class III ω-Transaminases Converting Bulky Ketones and Environmentally Relevant Polyamines.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {2}, pages = {}, pmid = {30413473}, issn = {1098-5336}, support = {BB/M029085/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; *Bioprospecting ; *Genes, Bacterial ; Ketones/*metabolism ; Polyamines/*metabolism ; Pseudomonas oleovorans/enzymology/*genetics/metabolism ; Sequence Alignment ; Transaminases/*genetics/metabolism ; }, abstract = {Amination of bulky ketones, particularly in (R) configuration, is an attractive chemical conversion; however, known ω-transaminases (ω-TAs) show insufficient levels of performance. By applying two screening methods, we discovered 10 amine transaminases from the class III ω-TA family that were 38% to 76% identical to homologues. We present examples of such enzymes preferring bulky ketones over keto acids and aldehydes with stringent (S) selectivity. We also report representatives from the class III ω-TAs capable of converting (R) and (S) amines and bulky ketones and one that can convert amines with longer alkyl substituents. The preference for bulky ketones was associated with the presence of a hairpin region proximal to the conserved Arg414 and residues conforming and close to it. The outward orientation of Arg414 additionally favored the conversion of (R) amines. This configuration was also found to favor the utilization of putrescine as an amine donor, so that class III ω-TAs with Arg414 in outward orientation may participate in vivo in the catabolism of putrescine. The positioning of the conserved Ser231 also contributes to the preference for amines with longer alkyl substituents. Optimal temperatures for activity ranged from 45 to 65°C, and a few enzymes retained ≥50% of their activity in water-soluble solvents (up to 50% [vol/vol]). Hence, our results will pave the way to design, in the future, new class III ω-TAs converting bulky ketones and (R) amines for the production of high-value products and to screen for those converting putrescine.IMPORTANCE Amine transaminases of the class III ω-TAs are key enzymes for modification of chemical building blocks, but finding those capable of converting bulky ketones and (R) amines is still challenging. Here, by an extensive analysis of the substrate spectra of 10 class III ω-TAs, we identified a number of residues playing a role in determining the access and positioning of bulky ketones, bulky amines, and (R)- and (S) amines, as well as of environmentally relevant polyamines, particularly putrescine. The results presented can significantly expand future opportunities for designing (R)-specific class III ω-TAs to convert valuable bulky ketones and amines, as well as for deepening the knowledge into the polyamine catabolic pathways.}, } @article {pmid30412889, year = {2019}, author = {Nathani, NM and Mootapally, C and Dave, BP}, title = {Antibiotic resistance genes allied to the pelagic sediment microbiome in the Gulf of Khambhat and Arabian Sea.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {446-454}, doi = {10.1016/j.scitotenv.2018.10.409}, pmid = {30412889}, issn = {1879-1026}, mesh = {Bacteria/classification/drug effects/*genetics/*isolation & purification ; *Drug Resistance, Microbial ; Genes, Bacterial/*drug effects ; Geologic Sediments/*microbiology ; Indian Ocean ; *Microbiota ; }, abstract = {Antibiotics have been widely spread in the environments, imposing profound stress on the resistome of the residing microbes. Marine microbiomes are well established large reservoirs of novel antibiotics and corresponding resistance genes. The Gulf of Khambhat is known for its extreme tides and complex sedimentation process. We performed high throughput sequencing and applied bioinformatics techniques on pelagic sediment microbiome across four coordinates of the Gulf of Khambhat to assess the marine resistome, its corresponding bacterial community and compared with the open Arabian Sea sample. We identified a total of 2354 unique types of resistance genes, with most abundant and diverse gene profile in the area that had anthropogenic activities being carried out on-shore. The genes with >1% abundance in all samples included carA, macB, sav1866, tlrC, srmB, taeA, tetA, oleC and bcrA which belonged to the macrolides, glycopeptides and peptide drug classes. ARG enriched phyla distribution was quite varying between all the sites, with Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes among the dominant phyla. Based on the outcomes, we also propose potential biomarker candidates Desulfovibrio, Thermotaga and Pelobacter for antibiotic monitoring in the two of the Gulf samples probable contamination prone environments, and genera Nitrosocccus, Marinobacter and Streptomyces in the rest of the three studied samples. Outcomes support the concept that ARGs naturally originate in environments and human activities contribute to the dissemination of antibiotic resistance.}, } @article {pmid30412047, year = {2018}, author = {Charles, J and Tangudu, CS and Hurt, SL and Tumescheit, C and Firth, AE and Garcia-Rejon, JE and Machain-Williams, C and Blitvich, BJ}, title = {Detection of novel and recognized RNA viruses in mosquitoes from the Yucatan Peninsula of Mexico using metagenomics and characterization of their in vitro host ranges.}, journal = {The Journal of general virology}, volume = {99}, number = {12}, pages = {1729-1738}, pmid = {30412047}, issn = {1465-2099}, support = {//Wellcome Trust/United Kingdom ; R01 AI114720/AI/NIAID NIH HHS/United States ; R21 AI067281/AI/NIAID NIH HHS/United States ; 106207/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Biodiversity ; Cell Line ; Culicidae/*virology ; *Host Specificity ; Humans ; Metagenomics ; Mexico ; Phylogeny ; RNA Viruses/classification/genetics/*growth & development/*isolation & purification ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; Virus Cultivation ; }, abstract = {A metagenomics approach was used to detect novel and recognized RNA viruses in mosquitoes from the Yucatan Peninsula of Mexico. A total of 1359 mosquitoes of 7 species and 5 genera (Aedes, Anopheles, Culex, Mansonia and Psorophora) were sorted into 37 pools, homogenized and inoculated onto monolayers of Aedes albopictus (C6/36) cells. A second blind passage was performed and then total RNA was extracted and analysed by RNA-seq. Two novel viruses, designated Uxmal virus and Mayapan virus, were identified. Uxmal virus was isolated from three pools of Aedes (Ochlerotatus) taeniorhynchus and phylogenetic data indicate that it should be classified within the recently proposed taxon Negevirus. Mayapan virus was recovered from two pools of Psorophora ferox and is most closely related to unclassified Nodaviridae-like viruses. Two recognized viruses were also detected: Culex flavivirus (family Flaviviridae) and Houston virus (family Mesoniviridae), with one and two isolates being recovered, respectively. The in vitro host ranges of all four viruses were determined by assessing their replicative abilities in cell lines of avian, human, monkey, hamster, murine, lepidopteran and mosquito (Aedes, Anopheles and Culex) origin, revealing that all viruses possess vertebrate replication-incompetent phenotypes. In conclusion, we report the isolation of both novel and recognized RNA viruses from mosquitoes collected in Mexico, and add to the growing plethora of viruses discovered recently through the use of metagenomics.}, } @article {pmid30411190, year = {2019}, author = {Rossi, A and Bellone, A and Fokin, SI and Boscaro, V and Vannini, C}, title = {Detecting Associations Between Ciliated Protists and Prokaryotes with Culture-Independent Single-Cell Microbiomics: a Proof-of-Concept Study.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {232-242}, pmid = {30411190}, issn = {1432-184X}, support = {565-60%2016//University of Pisa/ ; 565-60%2017//University of Pisa/ ; 565-FFABR 2017//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; }, mesh = {Bacteria/classification/genetics/*isolation & purification ; Bacterial Physiological Phenomena ; Biological Evolution ; Ciliophora/genetics/isolation & purification/*microbiology/physiology ; Ecosystem ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; Pilot Projects ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Symbioses between prokaryotes and microbial eukaryotes, particularly ciliated protists, have been studied for a long time. Nevertheless, researchers have focused only on a few host genera and species, mainly due to difficulties in cultivating the hosts, and usually have considered a single symbiont at a time. Here, we present a pilot study using a single-cell microbiomic approach to circumvent these issues. Unicellular ciliate isolation followed by simultaneous amplification of eukaryotic and prokaryotic markers was used. Our preliminary test gave reliable and satisfactory results both on samples collected from different habitats (marine and freshwater) and on ciliates belonging to different taxonomic groups. Results suggest that, as already assessed for many macro-organisms like plants and metazoans, ciliated protists harbor distinct microbiomes. The applied approach detected new potential symbionts as well as new hosts for previously described ones, with relatively low time and cost effort and without culturing. When further developed, single-cell microbiomics for ciliates could be applied to a large number of studies aiming to unravel the evolutionary and ecological meaning of these symbiotic systems.}, } @article {pmid30406643, year = {2019}, author = {Gao, B and Chi, L and Tu, P and Gao, N and Lu, K}, title = {The Carbamate Aldicarb Altered the Gut Microbiome, Metabolome, and Lipidome of C57BL/6J Mice.}, journal = {Chemical research in toxicology}, volume = {32}, number = {1}, pages = {67-79}, doi = {10.1021/acs.chemrestox.8b00179}, pmid = {30406643}, issn = {1520-5010}, support = {R01 ES024950/ES/NIEHS NIH HHS/United States ; }, mesh = {Administration, Oral ; Aldicarb/administration & dosage/*pharmacology ; Animals ; DNA Damage ; Gastrointestinal Microbiome/*drug effects ; Insecticides/administration & dosage/*pharmacology ; Lipidomics ; *Lipids ; Male ; Metabolome/*drug effects ; Mice ; Mice, Inbred C57BL ; Molecular Structure ; Oxidative Stress/drug effects ; }, abstract = {The gut microbiome is highly involved in numerous aspects of host physiology, from energy harvest to stress response, and can confer many benefits to the host. The gut microbiome development could be affected by genetic and environmental factors, including pesticides. The carbamate insecticide aldicarb has been extensively used in agriculture, which raises serious public health concerns. However, the impact of aldicarb on the gut microbiome, host metabolome, and lipidome has not been well studied yet. Herein, we use multiomics approaches, including16S rRNA sequencing, shotgun metagenomics sequencing, metabolomics, and lipidomics, to elucidate aldicarb-induced toxicity in the gut microbiome and the host metabolic homeostasis. We demonstrated that aldicarb perturbed the gut microbiome development trajectory, enhanced gut bacterial pathogenicity, altered complex lipid profile, and induced oxidative stress, protein degradation, and DNA damage. The brain metabolism was also disturbed by the aldicarb exposure. These findings may provide a novel understanding of the toxicity of carbamate insecticides.}, } @article {pmid30406041, year = {2018}, author = {Xiao, P and Li, C and Zhang, Y and Han, J and Guo, X and Xie, L and Tian, M and Li, Y and Wang, M and Liu, H and Ren, J and Zhou, H and Lu, H and Jin, N}, title = {Metagenomic Sequencing From Mosquitoes in China Reveals a Variety of Insect and Human Viruses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {364}, pmid = {30406041}, issn = {2235-2988}, mesh = {Animals ; *Biodiversity ; China ; Chlorocebus aethiops ; Computational Biology ; *Metagenomics ; Mosquito Vectors/*virology ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Viruses/*classification/*genetics ; }, abstract = {We collected 8,700 mosquitoes in three sites in China, which belonged to seven species. Their viromes were tested using metagenomic sequencing and bioinformatic analysis. The abundant viral sequences were detected and annotated belonging to more than 50 viral taxonomic families. The results were verified by PCR, followed by phylogenetic analysis. In the present study, we identified partial viral genes of dengue virus (DENV), a novel circovirus (CCV), densovirus (DNV), Japanese encephalitis virus (JEV), and Wuhan mosquito virus (WMV) in mosquitoes. Metagenomic analysis and PCR amplification revealed three DENV sequences, which were as homologous to the NS3 gene of DENV from Singapore isolated in 2005, with at least 91% nucleotide (nt) identity. Seven fragments of JEV encoding structural proteins were identified belonging to genotype I. They all shared high homology with structural protein genes of JEV isolated from Laos in 2009. The production of infectious virus particles of the newly isolated virus YunnanJEV2017-4 increased after passage from the BHK-21 cell line to the Vero cell line. Novel circovirus-related genes were identified and as being related to an unnamed gene of a mosquito circovirus (MCCV) sequence from the USA isolated in 2011, with at least 41% nt identity: this distant relationship suggests that the parent virus might belong to a novel circovirus genus. Additionally, numerous known viruses and some unknown viruses were also detected in mosquitoes from Yunnan province, China, which will be tested for propagation.}, } @article {pmid30405577, year = {2018}, author = {Bertelli, C and Courtois, S and Rosikiewicz, M and Piriou, P and Aeby, S and Robert, S and Loret, JF and Greub, G}, title = {Reduced Chlorine in Drinking Water Distribution Systems Impacts Bacterial Biodiversity in Biofilms.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2520}, pmid = {30405577}, issn = {1664-302X}, abstract = {In drinking water distribution systems (DWDS), a disinfectant residual is usually applied to limit bacterial regrowth. However, delivering water with no or reduced chlorine residual could potentially decrease the selection for antimicrobial resistant microorganisms, favor bacterial regrowth and result in changes in bacterial populations. To evaluate the feasibility of water reduction in local DWDS while ensuring water safety, water quality was measured over 2 months in two different networks, each of them harboring sub-areas with normal and reduced chlorine. Water quality remained good in chlorine reduced samples, with limited development of total flora and absence of coliforms. Furthermore, 16S rRNA amplicon-based metagenomics was used to investigate the diversity and the composition of microbial communities in the sub-networks. Taxonomic classification of sequence reads showed a reduced bacterial diversity in sampling points with higher chlorine residuals. Chlorine disinfection created more homogeneous bacterial population, dominated by Pseudomonas, a genus that contains some major opportunistic pathogens such as P. aeruginosa. In the absence of chlorine, a larger and unknown biodiversity was unveiled, also highlighted by a decreased rate of taxonomic classification to the genus and species level. Overall, this experiment in a functional DWDS will facilitate the move toward potable water delivery systems without residual disinfectants and will improve water taste for consumers.}, } @article {pmid30405201, year = {2018}, author = {Wankhade, UD and Zhong, Y and Kang, P and Alfaro, M and Chintapalli, SV and Piccolo, BD and Mercer, KE and Andres, A and Thakali, KM and Shankar, K}, title = {Maternal High-Fat Diet Programs Offspring Liver Steatosis in a Sexually Dimorphic Manner in Association with Changes in Gut Microbial Ecology in Mice.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16502}, pmid = {30405201}, issn = {2045-2322}, mesh = {Animals ; Bile Acids and Salts/metabolism ; Biodiversity ; Biomarkers ; Diet, High-Fat/*adverse effects ; Fatty Liver/*etiology/*metabolism/pathology ; Female ; *Gastrointestinal Microbiome ; Lipid Metabolism ; Male ; Maternal Exposure/*adverse effects ; Metabolic Networks and Pathways ; Metagenome ; Metagenomics/methods ; Mice ; Phylogeny ; Sex Characteristics ; Weight Gain ; }, abstract = {The contributions of maternal diet and obesity in shaping offspring microbiome remain unclear. Here we employed a mouse model of maternal diet-induced obesity via high-fat diet feeding (HFD, 45% fat calories) for 12 wk prior to conception on offspring gut microbial ecology. Male and female offspring were provided access to control or HFD from weaning until 17 wk of age. Maternal HFD-associated programming was sexually dimorphic, with male offspring from HFD dams showing hyper-responsive weight gain to postnatal HFD. Likewise, microbiome analysis of offspring cecal contents showed differences in α-diversity, β-diversity and higher Firmicutes in male compared to female mice. Weight gain in offspring was significantly associated with abundance of Lachnospiraceae and Clostridiaceae families and Adlercreutzia, Coprococcus and Lactococcus genera. Sex differences in metagenomic pathways relating to lipid metabolism, bile acid biosynthesis and immune response were also observed. HFD-fed male offspring from HFD dams also showed worse hepatic pathology, increased pro-inflammatory cytokines, altered expression of bile acid regulators (Cyp7a1, Cyp8b1 and Cyp39a1) and serum bile acid concentrations. These findings suggest that maternal HFD alters gut microbiota composition and weight gain of offspring in a sexually dimorphic manner, coincident with fatty liver and a pro-inflammatory state in male offspring.}, } @article {pmid30405146, year = {2018}, author = {Lloyd, MM and Pespeni, MH}, title = {Microbiome shifts with onset and progression of Sea Star Wasting Disease revealed through time course sampling.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16476}, pmid = {30405146}, issn = {2045-2322}, mesh = {Animal Diseases/*microbiology ; Animals ; Disease Progression ; Metagenomics/methods ; *Microbiota ; Starfish/*microbiology ; Time Factors ; }, abstract = {The recent outbreak of Sea Star Wasting Disease (SSWD) is one of the largest marine epizootics in history, but the host-associated microbial community changes specific to disease progression have not been characterized. Here, we sampled the microbiomes of ochre sea stars, Pisaster ochraceus, through time as animals stayed healthy or became sick and died with SSWD. We found community-wide differences in the microbiomes of sick and healthy sea stars, changes in microbial community composition through disease progression, and a decrease in species richness of the microbiome in late stages of SSWD. Known beneficial taxa (Pseudoalteromonas spp.) decreased in abundance at symptom onset and through disease progression, while known pathogenic (Tenacibaculum spp.) and putatively opportunistic bacteria (Polaribacter spp. and Phaeobacter spp.) increased in abundance in early and late disease stages. Functional profiling revealed microbes more abundant in healthy animals performed functions that inhibit growth of other microbes, including pathogen detection, biosynthesis of secondary metabolites, and degradation of xenobiotics. Changes in microbial composition with disease onset and progression suggest that a microbial imbalance of the host could lead to SSWD or be a consequence of infection by another pathogen. This work highlights the importance of the microbiome in SSWD and also suggests that a healthy microbiome may help confer resistance to SSWD.}, } @article {pmid30404941, year = {2019}, author = {Morand, A and Cornu, F and Dufour, JC and Tsimaratos, M and Lagier, JC and Raoult, D}, title = {Human Bacterial Repertoire of the Urinary Tract: a Potential Paradigm Shift.}, journal = {Journal of clinical microbiology}, volume = {57}, number = {3}, pages = {}, pmid = {30404941}, issn = {1098-660X}, mesh = {Bacteria/classification/genetics/growth & development/pathogenicity ; Bacterial Physiological Phenomena ; *Biodiversity ; Dysbiosis ; Gastrointestinal Microbiome ; Humans ; Microbiota ; Urinary Tract/*microbiology ; Urinary Tract Infections/microbiology ; Urine/*microbiology ; }, abstract = {The aim of this article is to review the human repertoire of bacteria in urine already described by culture and metagenomic techniques and published in the literature. Our study led us to compare this repertoire with other available human repertoires. We followed automatic and manual bibliographical methods and found 562 bacterial species reported in the literature as part of the human urinary microbiota. Of the 562 species, 322 were described only by culture, 101 by both culture and metagenomics, and 139 only by metagenomics. A total of 352 species (62.6%) have been associated with at least one case report of human infection, of which 225 (40.0%) have been described as causative agents of urinary tract infection. The urinary tract bacterial repertoire contains 21.4% of the known prokaryotic diversity associated with human beings (464 species in common), and it shares 23.6% species with the human gut microbiota (350 species in common, 62.3% of the urine species). The urinary repertoire shares a significant difference in aerointolerant species compared with those of the gut microbiota (100/562 [17.8%] and 505/1,484 [34.0%], respectively; P < 0.001; odds ratio [OR] = 9.0 [7.0 to 11.4]). Studies using high-throughput sequencing show a higher proportion of aerointolerant bacteria in urine (74/240 [30.8%]) than studies using culture techniques (40/423 [9.5%]). Most pathogenic bacteria are part of the commensal human urinary tract bacteria, and their pathogenicity may occur following any imbalance of this microbiota. The restoration of urinary tract health can occur following a fecal transplantation. The potential gut origin of the human bacterial microbiota has to be explored.}, } @article {pmid30404694, year = {2018}, author = {Ma, LK and Xue, Y and He, TC and Zhang, YM}, title = {[Associations of Socioeconomic Factors,Nutrients Intake,and Gut Microbiota of Healthy Pregnant Women in the Third Trimester with Gestational Weight Gain].}, journal = {Zhongguo yi xue ke xue yuan xue bao. Acta Academiae Medicinae Sinicae}, volume = {40}, number = {5}, pages = {630-636}, doi = {10.3881/j.issn.1000-503X.10505}, pmid = {30404694}, issn = {1000-503X}, mesh = {Body Mass Index ; *Diet ; Female ; *Gastrointestinal Microbiome ; *Gestational Weight Gain ; Humans ; Nutrients ; Pregnancy ; Pregnancy Trimester, Third ; *Socioeconomic Factors ; }, abstract = {Objective To investigate the associations of socioeconomic factors,nutrients intake,and gut microbiota of healthy pregnant women in the third trimester with gestational weight gain (GWG).Methods We recruited 98 pregnant women in the third trimester who had received antenatal care in the Department of Obstetrics Gynecology,Peking Union Medical College Hospital from October,2015 to May,2016. We collected socioeconomic information through a structured questionnaire covering age,ethnicity,height,pre-pregnancy weight,and education. Nutritional status of these pregnant women was assessed by a 24-hour dietary intake recall. The participants were provided with collective tubes for faecal sample collection at home;their weight before the delivery was recorded. The pre-pregnancy weight and GWG were classified according to World Health Organization body mass index (BMI) standard for adults and the Institute of Medicine GWG guidelines (2009),respectively. The gut microbiota of the participants were analyzed using a whole-metagenome shotgun sequencing method.Results Insufficient and excessive GWG accounted for 15.3% and 50.0% of the cohort,respectively. Appropriate GWG level was associated with intakes of fat (F=3.113,P=0.049),carbohydrates (F=3.750,P=0.027),and dietary fiber (F=4.499,P=0.014) but not with age (F=2.495,P=0.088),ethnicity (Χ [2]=0.065,P=0.968),education (Χ [2]=0.827,P=0.661),or pre-pregnancy BMI (F=0.121,P=0.887). Compared with the participants with appropriate GWG,those with excessive GWG had significantly higher abundance of Akkermansia muciniphila,Atopobium parvulum,and Alistipes indistinctus as well as lower abundance of Lactobacillus rhamnosus,Weissella unclassified,Eubacterium ventriosum,Ruminococcus torques,and Bacteroides uniformis. Compared with the participants with appropriate GWG,those with insufficient GWG had significantly higher abundance of Dialister invisus,Alistipes unclassified,Peptoniphilus harei,Escherichia unclassified,Parvimonas unclassified,Campylobacter ureolyticus,Lactobacillus crispatus,and Fusobacterium nucleatum and lower abundance of Eubacterium ventriosum.Conclusions Abnormal GWG is common in pregnant women. GWG is significantly associated with gut microbiota as well as with nutritional factors including fat,carbohydrate,and dietary fiber intake.}, } @article {pmid30403636, year = {2020}, author = {Sokolovska, N and Permiakova, O and Forslund, SK and Zucker, JD}, title = {Using Unlabeled Data to Discover Bivariate Causality with Deep Restricted Boltzmann Machines.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {17}, number = {1}, pages = {358-364}, doi = {10.1109/TCBB.2018.2879504}, pmid = {30403636}, issn = {1557-9964}, mesh = {Causality ; Computational Biology/*methods ; Databases, Genetic ; Gastrointestinal Microbiome/drug effects ; Humans ; Metagenome/genetics ; Metformin/pharmacology ; *Models, Statistical ; *Neural Networks, Computer ; Supervised Machine Learning ; }, abstract = {An important question in microbiology is whether treatment causes changes in gut flora, and whether it also affects metabolism. The reconstruction of causal relations purely from non-temporal observational data is challenging. We address the problem of causal inference in a bivariate case, where the joint distribution of two variables is observed. We consider, in particular, data on discrete domains. The state-of-the-art causal inference methods for continuous data suffer from high computational complexity. Some modern approaches are not suitable for categorical data, and others need to estimate and fix multiple hyper-parameters. In this contribution, we introduce a novel method of causal inference which is based on the widely used assumption that if X causes Y, then P(X) and P(Y|X) are independent. We propose to explore a semi-supervised approach where P(Y|X) and P(X) are estimated from labeled and unlabeled data respectively, whereas the marginal probability is estimated potentially from much more (cheap unlabeled) data than the conditional distribution. We validate the proposed method on the standard cause-effect pairs. We illustrate by experiments on several benchmarks of biological network reconstruction that the proposed approach is very competitive in terms of computational time and accuracy compared to the state-of-the-art methods. Finally, we apply the proposed method to an original medical task where we study whether drugs confound human metagenome.}, } @article {pmid30403635, year = {2020}, author = {Zheng, H and Wang, H and Dewhurst, RJ and Roehe, R}, title = {Improving the Inference of Co-Occurrence Networks in the Bovine Rumen Microbiome.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {17}, number = {3}, pages = {858-867}, doi = {10.1109/TCBB.2018.2879342}, pmid = {30403635}, issn = {1557-9964}, mesh = {Animal Feed ; Animals ; Cattle ; Diet ; *Gastrointestinal Microbiome/genetics/physiology ; Metagenome/genetics ; Metagenomics/*methods ; Methane/metabolism ; Rumen/*microbiology ; }, abstract = {The importance of the composition and signature of rumen microbial communities has gained increasing attention. One of the key techniques was to infer co-abundance networks through correlation analysis based on relative abundances. While substantial insights and progress have been made, it has been found that due to the compositional nature of data, correlation analysis derived from relative abundance could produce misleading results and spurious associations. In this study, we proposed the use of a framework including a compendium of two correlation measures and three dissimilarity metrics in an attempt to mitigate the compositional effect in the inference of significant associations in the bovine rumen microbiome. We tested the framework on rumen microbiome data including both 16S rRNA and KEGG genes associated with methane production in cattle. Based on the identification of significant positive and negative associations supported by multiple metrics, two co-occurrence networks, e.g., co-presence and mutual-exclusion networks, were constructed. Significant modules associated with methane emissions were identified. In comparison to previous studies, our analysis demonstrates that deriving microbial associations based on the correlations between relative abundances may not only lead to missing information but also produce spurious associations. To bridge together different co-presence and mutual-exclusion relations, a multiplex network model has been proposed for integrative analysis of co-occurrence networks which has great potential to support the prediction of animal phytotypes and to provide additional insights into biological mechanisms of the microbiome associated with the traits.}, } @article {pmid30401779, year = {2018}, author = {Bratburd, JR and Keller, C and Vivas, E and Gemperline, E and Li, L and Rey, FE and Currie, CR}, title = {Gut Microbial and Metabolic Responses to Salmonella enterica Serovar Typhimurium and Candida albicans.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, pmid = {30401779}, issn = {2150-7511}, support = {U19 AI109673/AI/NIAID NIH HHS/United States ; R56 DK071801/DK/NIDDK NIH HHS/United States ; R01 DK108259/DK/NIDDK NIH HHS/United States ; S10 RR029531/RR/NCRR NIH HHS/United States ; T32 AI055397/AI/NIAID NIH HHS/United States ; R01 DK071801/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Biosynthetic Pathways ; Candida albicans/pathogenicity ; Candidiasis/*microbiology ; Cecum/microbiology ; Disease Models, Animal ; Enterobacteriaceae/isolation & purification ; *Gastrointestinal Microbiome ; Germ-Free Life ; Humans ; Male ; Metabolomics ; Metagenomics ; Mice ; Mice, Inbred C57BL ; *Microbiota ; Oxidative Stress ; Salmonella Infections, Animal/*microbiology ; Salmonella typhimurium/pathogenicity ; }, abstract = {The gut microbiota confers resistance to pathogens of the intestinal ecosystem, yet the dynamics of pathogen-microbiome interactions and the metabolites involved in this process remain largely unknown. Here, we use gnotobiotic mice infected with the virulent pathogen Salmonella enterica serovar Typhimurium or the opportunistic pathogen Candida albicans in combination with metagenomics and discovery metabolomics to identify changes in the community and metabolome during infection. To isolate the role of the microbiota in response to pathogens, we compared mice monocolonized with the pathogen, uninfected mice "humanized" with a synthetic human microbiome, or infected humanized mice. In Salmonella-infected mice, by 3 days into infection, microbiome community structure and function changed substantially, with a rise in Enterobacteriaceae strains and a reduction in biosynthetic gene cluster potential. In contrast, Candida-infected mice had few microbiome changes. The LC-MS metabolomic fingerprint of the cecum differed between mice monocolonized with either pathogen and humanized infected mice. Specifically, we identified an increase in glutathione disulfide, glutathione cysteine disulfide, inosine 5'-monophosphate, and hydroxybutyrylcarnitine in mice infected with Salmonella in contrast to uninfected mice and mice monocolonized with Salmonella These metabolites potentially play a role in pathogen-induced oxidative stress. These results provide insight into how the microbiota community members interact with each other and with pathogens on a metabolic level.IMPORTANCE The gut microbiota is increasingly recognized for playing a critical role in human health and disease, especially in conferring resistance to both virulent pathogens such as Salmonella, which infects 1.2 million people in the United States every year (E. Scallan, R. M. Hoekstra, F. J. Angulo, R. V. Tauxe, et al., Emerg Infect Dis 17:7-15, 2011, https://doi.org/10.3201/eid1701.P11101), and opportunistic pathogens like Candida, which causes an estimated 46,000 cases of invasive candidiasis each year in the United States (Centers for Disease Control and Prevention, Antibiotic Resistance Threats in the United States, 2013, 2013). Using a gnotobiotic mouse model, we investigate potential changes in gut microbial community structure and function during infection using metagenomics and metabolomics. We observe that changes in the community and in biosynthetic gene cluster potential occur within 3 days for the virulent Salmonella enterica serovar Typhimurium, but there are minimal changes with a poorly colonizing Candida albicans In addition, the metabolome shifts depending on infection status, including changes in glutathione metabolites in response to Salmonella infection, potentially in response to host oxidative stress.}, } @article {pmid30400812, year = {2018}, author = {Kumar, MS and Slud, EV and Okrah, K and Hicks, SC and Hannenhalli, S and Corrada Bravo, H}, title = {Analysis and correction of compositional bias in sparse sequencing count data.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {799}, pmid = {30400812}, issn = {1471-2164}, support = {K99 HG009007/HG/NHGRI NIH HHS/United States ; R01 RR021967/RR/NCRR NIH HHS/United States ; GM114267/NH/NIH HHS/United States ; R01 GM083084/GM/NIGMS NIH HHS/United States ; HG005220/NH/NIH HHS/United States ; R00 HG009007/HG/NHGRI NIH HHS/United States ; R01 HG005220/HG/NHGRI NIH HHS/United States ; R21 GM107683/GM/NIGMS NIH HHS/United States ; 1564785//National Science Foundation (US)/ ; R01 GM114267/GM/NIGMS NIH HHS/United States ; GM083084/NH/NIH HHS/United States ; R01 GM103552/GM/NIGMS NIH HHS/United States ; }, mesh = {*Algorithms ; Bayes Theorem ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; *Microbiota ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {BACKGROUND: Count data derived from high-throughput deoxy-ribonucliec acid (DNA) sequencing is frequently used in quantitative molecular assays. Due to properties inherent to the sequencing process, unnormalized count data is compositional, measuring relative and not absolute abundances of the assayed features. This compositional bias confounds inference of absolute abundances. Commonly used count data normalization approaches like library size scaling/rarefaction/subsampling cannot correct for compositional or any other relevant technical bias that is uncorrelated with library size.

RESULTS: We demonstrate that existing techniques for estimating compositional bias fail with sparse metagenomic 16S count data and propose an empirical Bayes normalization approach to overcome this problem. In addition, we clarify the assumptions underlying frequently used scaling normalization methods in light of compositional bias, including scaling methods that were not designed directly to address it.

CONCLUSIONS: Compositional bias, induced by the sequencing machine, confounds inferences of absolute abundances. We present a normalization technique for compositional bias correction in sparse sequencing count data, and demonstrate its improved performance in metagenomic 16s survey data. Based on the distribution of technical bias estimates arising from several publicly available large scale 16s count datasets, we argue that detailed experiments specifically addressing the influence of compositional bias in metagenomics are needed.}, } @article {pmid30397794, year = {2019}, author = {Lau, NS and Zarkasi, KZ and Md Sah, ASR and Shu-Chien, AC}, title = {Diversity and Coding Potential of the Microbiota in the Photic and Aphotic Zones of Tropical Man-Made Lake with Intensive Aquaculture Activities: a Case Study on Temengor Lake, Malaysia.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {20-32}, pmid = {30397794}, issn = {1432-184X}, mesh = {Aquaculture ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Biodiversity ; DNA, Bacterial/genetics ; Ecosystem ; Lakes/chemistry/*microbiology ; Malaysia ; Metagenomics ; *Microbiota ; Nitrogen/analysis/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfur/analysis/metabolism ; }, abstract = {Although freshwater biomes cover less than 1% of the Earth's surface, they have disproportionate ecological significances. Attempts to study the taxonomy and function of freshwater microbiota are currently limited to samples collected from temperate lakes. In this study, we investigated samples from the photic and aphotic of an aquaculture site (disturbed) of Temengor Lake, a tropical lake in comparison with the undisturbed site of the lake using 16S rRNA amplicon and shotgun metagenomic approaches. Vertical changes in bacterial community composition and function of the Temengor Lake metagenomes were observed. The photic water layer of Temengor Lake was dominated by typical freshwater assemblages consisting of Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, and Cyanobacteria lineages. On the other hand, the aphotic water featured in addition to Proteobacteria, Bacteroidetes, Verrucomicrobia, and two more abundant bacterial phyla that are typically ubiquitous in anoxic habitats (Chloroflexi and Firmicutes). The aphotic zone of Temengor Lake exhibited genetic potential for nitrogen and sulfur metabolisms for which terminal electron acceptors other than oxygen are used in the reactions. The aphotic water of the disturbed site also showed an overrepresentation of genes associated with the metabolism of carbohydrates, likely driven by the enrichment of nutrient resulting from aquaculture activities at the site. The results presented in this study can serve as a basis for understanding the structure and functional capacity of the microbial communities in the photic and aphotic zones/water layers of tropical man-made lakes.}, } @article {pmid30397357, year = {2018}, author = {Tirosh, O and Conlan, S and Deming, C and Lee-Lin, SQ and Huang, X and , and Su, HC and Freeman, AF and Segre, JA and Kong, HH}, title = {Expanded skin virome in DOCK8-deficient patients.}, journal = {Nature medicine}, volume = {24}, number = {12}, pages = {1815-1821}, pmid = {30397357}, issn = {1546-170X}, support = {Z01 HG000180-08//Intramural NIH HHS/United States ; ZIA AI001193-04//Intramural NIH HHS/United States ; ZIA BC010938-10//Intramural NIH HHS/United States ; }, mesh = {Adolescent ; Bacteriophages/genetics ; Child ; Female ; Genome, Viral/genetics ; Guanine Nucleotide Exchange Factors/deficiency/*genetics ; Healthy Volunteers ; Host Microbial Interactions/genetics/immunology ; Humans ; Immunity/genetics ; Immunologic Deficiency Syndromes/microbiology/pathology/*virology ; Lymphocytes/virology ; Male ; Metagenome/genetics/immunology ; Microbiota/genetics ; Papillomaviridae/isolation & purification/pathogenicity ; Skin/microbiology/*virology ; Skin Diseases/genetics/microbiology/pathology/*virology ; }, abstract = {Human microbiome studies have revealed the intricate interplay of host immunity and bacterial communities to achieve homeostatic balance. Healthy skin microbial communities are dominated by bacteria with low viral representation[1-3], mainly bacteriophage. Specific eukaryotic viruses have been implicated in both common and rare skin diseases, but cataloging skin viral communities has been limited. Alterations in host immunity provide an opportunity to expand our understanding of microbial-host interactions. Primary immunodeficient patients manifest with various viral, bacterial, fungal, and parasitic infections, including skin infections[4]. Dedicator of cytokinesis 8 (DOCK8) deficiency is a rare primary human immunodeficiency characterized by recurrent cutaneous and systemic infections, as well as atopy and cancer susceptibility[5]. DOCK8, encoding a guanine nucleotide exchange factor highly expressed in lymphocytes, regulates actin cytoskeleton, which is critical for migration through collagen-dense tissues such as skin[6]. Analyzing deep metagenomic sequencing data from DOCK8-deficient skin samples demonstrated a notable increase in eukaryotic viral representation and diversity compared with healthy volunteers. De novo assembly approaches identified hundreds of novel human papillomavirus genomes, illuminating microbial dark matter. Expansion of the skin virome in DOCK8-deficient patients underscores the importance of immune surveillance in controlling eukaryotic viral colonization and infection.}, } @article {pmid30397356, year = {2018}, author = {Sun, L and Xie, C and Wang, G and Wu, Y and Wu, Q and Wang, X and Liu, J and Deng, Y and Xia, J and Chen, B and Zhang, S and Yun, C and Lian, G and Zhang, X and Zhang, H and Bisson, WH and Shi, J and Gao, X and Ge, P and Liu, C and Krausz, KW and Nichols, RG and Cai, J and Rimal, B and Patterson, AD and Wang, X and Gonzalez, FJ and Jiang, C}, title = {Gut microbiota and intestinal FXR mediate the clinical benefits of metformin.}, journal = {Nature medicine}, volume = {24}, number = {12}, pages = {1919-1929}, pmid = {30397356}, issn = {1546-170X}, support = {T32 GM102057/GM/NIGMS NIH HHS/United States ; T32 LM012415/LM/NLM NIH HHS/United States ; Z01 BC005561-20/ImNIH/Intramural NIH HHS/United States ; Z01 BC005561-21/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Bacteroides/drug effects/pathogenicity ; Bile Acids and Salts/metabolism ; Diabetes Mellitus, Type 2/*drug therapy/genetics/microbiology/pathology ; Diet, High-Fat/adverse effects ; Gastrointestinal Microbiome/*drug effects/genetics ; Gene Expression Regulation, Bacterial/drug effects ; Glucose Intolerance/drug therapy/genetics/microbiology ; Humans ; Hyperglycemia/drug therapy/genetics/microbiology/pathology ; Metabolome/drug effects/genetics ; Metagenomics/methods ; Metformin/*administration & dosage ; Obesity/*drug therapy/genetics/microbiology/pathology ; Receptors, Cytoplasmic and Nuclear/*genetics ; Ursodeoxycholic Acid/analogs & derivatives ; }, abstract = {The anti-hyperglycemic effect of metformin is believed to be caused by its direct action on signaling processes in hepatocytes, leading to lower hepatic gluconeogenesis. Recently, metformin was reported to alter the gut microbiota community in humans, suggesting that the hyperglycemia-lowering action of the drug could be the result of modulating the population of gut microbiota. However, the critical microbial signaling metabolites and the host targets associated with the metabolic benefits of metformin remained elusive. Here, we performed metagenomic and metabolomic analysis of samples from individuals with newly diagnosed type 2 diabetes (T2D) naively treated with metformin for 3 d, which revealed that Bacteroides fragilis was decreased and the bile acid glycoursodeoxycholic acid (GUDCA) was increased in the gut. These changes were accompanied by inhibition of intestinal farnesoid X receptor (FXR) signaling. We further found that high-fat-diet (HFD)-fed mice colonized with B. fragilis were predisposed to more severe glucose intolerance, and the metabolic benefits of metformin treatment on glucose intolerance were abrogated. GUDCA was further identified as an intestinal FXR antagonist that improved various metabolic endpoints in mice with established obesity. Thus, we conclude that metformin acts in part through a B. fragilis-GUDCA-intestinal FXR axis to improve metabolic dysfunction, including hyperglycemia.}, } @article {pmid30396371, year = {2018}, author = {Meisel, JS and Nasko, DJ and Brubach, B and Cepeda-Espinoza, V and Chopyk, J and Corrada-Bravo, H and Fedarko, M and Ghurye, J and Javkar, K and Olson, ND and Shah, N and Allard, SM and Bazinet, AL and Bergman, NH and Brown, A and Caporaso, JG and Conlan, S and DiRuggiero, J and Forry, SP and Hasan, NA and Kralj, J and Luethy, PM and Milton, DK and Ondov, BD and Preheim, S and Ratnayake, S and Rogers, SM and Rosovitz, MJ and Sakowski, EG and Schliebs, NO and Sommer, DD and Ternus, KL and Uritskiy, G and Zhang, SX and Pop, M and Treangen, TJ}, title = {Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {197}, pmid = {30396371}, issn = {2049-2618}, support = {R01 AI100947/AI/NIAID NIH HHS/United States ; R01 GM114267/GM/NIGMS NIH HHS/United States ; U54 CA143924/CA/NCI NIH HHS/United States ; U54 CA143925/CA/NCI NIH HHS/United States ; }, mesh = {*Biological Warfare Agents ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/physiology ; Sequence Analysis, DNA/methods ; }, abstract = {The Mid-Atlantic Microbiome Meet-up (M[3]) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M[3] held its fourth meeting, which focused on recent advances in biodefense, specifically those relating to infectious disease, and the use of metagenomic methods for pathogen detection. Presentations highlighted the utility of next-generation sequencing technologies for identifying and tracking microbial community members across space and time. However, they also stressed the current limitations of genomic approaches for biodefense, including insufficient sensitivity to detect low-abundance pathogens and the inability to quantify viable organisms. Participants discussed ways in which the community can improve software usability and shared new computational tools for metagenomic processing, assembly, annotation, and visualization. Looking to the future, they identified the need for better bioinformatics toolkits for longitudinal analyses, improved sample processing approaches for characterizing viruses and fungi, and more consistent maintenance of database resources. Finally, they addressed the necessity of improving data standards to incentivize data sharing. Here, we summarize the presentations and discussions from the meeting, identifying the areas where microbiome analyses have improved our ability to detect and manage biological threats and infectious disease, as well as gaps of knowledge in the field that require future funding and focus.}, } @article {pmid30396006, year = {2019}, author = {Velikonja, A and Lipoglavšek, L and Zorec, M and Orel, R and Avguštin, G}, title = {Alterations in gut microbiota composition and metabolic parameters after dietary intervention with barley beta glucans in patients with high risk for metabolic syndrome development.}, journal = {Anaerobe}, volume = {55}, number = {}, pages = {67-77}, doi = {10.1016/j.anaerobe.2018.11.002}, pmid = {30396006}, issn = {1095-8274}, mesh = {Adult ; Aged ; Cholesterol/blood ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Diet Therapy/*methods ; Dietary Fiber/*administration & dosage ; Double-Blind Method ; Fatty Acids, Volatile/analysis ; Feces/chemistry ; Female ; Gastrointestinal Microbiome/*drug effects ; Healthy Volunteers ; Hordeum/*chemistry ; Humans ; Male ; Metabolic Syndrome/*therapy ; Middle Aged ; Phylogeny ; Placebos/administration & dosage ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Treatment Outcome ; beta-Glucans/*administration & dosage ; }, abstract = {Metabolic syndrome is a complex disease that is exponentially increasing in the western world, and diet is one of the possible ways to improve the metabolic status of patients. Barley beta glucans are dietary fibres that show promise for improvement cholesterol levels and postprandial glucose response, but they have been rarely investigated in human trials with concurrent focus on gut microbiota. A double-blind, placebo-controlled, randomised clinical trial was conducted with 43 volunteers with high risk for metabolic syndrome development or with diagnosed metabolic syndrome. During a four-week intervention study, participants consumed experimental bread containing 6 g of barley beta glucans or equal bread but without beta glucans. After dietary intervention, total plasma cholesterol decreased in the test group (-0.26 ± 0.54, p = 0.019), but not in the control group. Short chain fatty acids (SCFA) composition in faeces significantly changed with increase of propionic acid in test group (43.2%, p = 0.045) and with decrease of acetic acid in control group (41.8%, p = 0.011). The microbiome analysis based on Illumina paired end sequencing of 16S rRNA genes showed a decrease in microbial diversity and richness in the test group. The pre-intervention gut microbiota composition showed higher abundance of health associated Bifidobacterium spp. and Akkermansia municiphila within cholesterol-responsive group, showing that diet-induced metabolic response is possibly dependent on individual gut microbiota composition.}, } @article {pmid30394664, year = {2019}, author = {Spang, A and Offre, P}, title = {Towards a systematic understanding of differences between archaeal and bacterial diversity.}, journal = {Environmental microbiology reports}, volume = {11}, number = {1}, pages = {9-12}, pmid = {30394664}, issn = {1758-2229}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; *Biodiversity ; Biological Evolution ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Single-Cell Analysis ; }, abstract = {In this crystal ball, we discuss emerging methodologies that can help reaching a synthesis on the biodiversity of Archaea and Bacteria and thereby inform a central enigma in microbiology, i.e. the fundamental split between these primary domains of life and the apparent lower diversity of the Archaea.}, } @article {pmid30394652, year = {2018}, author = {Borton, MA and Daly, RA and O'Banion, B and Hoyt, DW and Marcus, DN and Welch, S and Hastings, SS and Meulia, T and Wolfe, RA and Booker, AE and Sharma, S and Cole, DR and Wunch, K and Moore, JD and Darrah, TH and Wilkins, MJ and Wrighton, KC}, title = {Comparative genomics and physiology of the genus Methanohalophilus, a prevalent methanogen in hydraulically fractured shale.}, journal = {Environmental microbiology}, volume = {20}, number = {12}, pages = {4596-4611}, doi = {10.1111/1462-2920.14467}, pmid = {30394652}, issn = {1462-2920}, support = {1342701//National Science Foundation Dimensions of Biodiversity/International ; FE0024297//Department of Energy's National Energy Technology Laboratory/International ; //U.S. Department of Energy Joint Genome Institute/International ; DE-AC02-05CH11231//Office of Science of the U.S. Department of Energy/International ; }, mesh = {Ecosystem ; Genome, Bacterial ; *Hydraulic Fracking ; Metagenome ; Methanosarcinaceae/genetics/*physiology ; Natural Gas ; Oil and Gas Fields ; }, abstract = {About 60% of natural gas production in the United States comes from hydraulic fracturing of unconventional reservoirs, such as shales or organic-rich micrites. This process inoculates and enriches for halotolerant microorganisms in these reservoirs over time, resulting in a saline ecosystem that includes methane producing archaea. Here, we survey the biogeography of methanogens across unconventional reservoirs, and report that members of genus Methanohalophilus are recovered from every hydraulically fractured unconventional reservoir sampled by metagenomics. We provide the first genomic sequencing of three isolate genomes, as well as two metagenome assembled genomes (MAGs). Utilizing six other previously sequenced isolate genomes and MAGs, we perform comparative analysis of the 11 genomes representing this genus. This genomic investigation revealed distinctions between surface and subsurface derived genomes that are consistent with constraints encountered in each environment. Genotypic differences were also uncovered between isolate genomes recovered from the same well, suggesting niche partitioning among closely related strains. These genomic substrate utilization predictions were then confirmed by physiological investigation. Fine-scale microdiversity was observed in CRISPR-Cas systems of Methanohalophilus, with genomes from geographically distinct unconventional reservoirs sharing spacers targeting the same viral population. These findings have implications for augmentation strategies resulting in enhanced biogenic methane production in hydraulically fractured unconventional reservoirs.}, } @article {pmid30394313, year = {2019}, author = {Wang, M and Zhou, J and He, F and Cai, C and Wang, H and Wang, Y and Lin, Y and Rong, H and Cheng, G and Xu, R and Zhou, W}, title = {Alteration of gut microbiota-associated epitopes in children with autism spectrum disorders.}, journal = {Brain, behavior, and immunity}, volume = {75}, number = {}, pages = {192-199}, doi = {10.1016/j.bbi.2018.10.006}, pmid = {30394313}, issn = {1090-2139}, mesh = {Autism Spectrum Disorder/*microbiology/physiopathology ; Child ; Child Development ; Child, Preschool ; Connexin 43/immunology ; Epitopes/immunology ; Feces/microbiology ; Female ; Gastrointestinal Diseases/*immunology ; Gastrointestinal Microbiome/*immunology/physiology ; Humans ; Immunity ; Intracellular Signaling Peptides and Proteins/immunology ; Male ; Nuclear Proteins/immunology ; PAX3 Transcription Factor/immunology ; Protein Tyrosine Phosphatases/immunology ; }, abstract = {BACKGROUND: Autism spectrum disorder (ASD) affects 1% of children and has no cure. Gastrointestinal (GI) problems are common in children with ASD, and although gut microbiota is known to play an important role in ASD through the gut-brain axis, the specific mechanism is unknown. Recent evidence suggests that gut microbiota may participate in the pathogenesis of ASD through immune- and inflammation-mediated pathways. Here, we identified potentially immunogenic epitopes derived from gut microbiota in stool samples from ASD children with and without GI problems and typically developing (TD) children.

METHODS: Candidate gut microbiota-associated epitopes (MEs) were identified by blast shotgun metagenomic sequencing of fecal samples from 43 ASD children (19 with and 24 without GI involvement) and 31 sex- and age-matched typically developing (TD) children. Potentially immunogenic epitopes were screened against a predictive human Immune Epitope Database. The composition and abundance of candidate MEs were compared between the three groups of children.

RESULTS: MEs identified in ASD children with GI problems were significantly more diverse than those in TD children. ME composition could discriminate between the three groups of children. We identified 34 MEs that were significantly more or less abundant in ASD children than TD children, most (29/34) of the differences in MEs were reduced in ASD and associated with abnormal gut IgA level and altered gut microbiota composition, these MEs were limited effected by clinical factors such as age, gender, and GI problems, of which eleven MEs were pathogenic microorganisms peptides with strong T or B cell response, nine MEs showed high homology to peptides from human self proteins associated with autoimmune disease occurrence, eliciting immune attack against hematopoietic stem cells and inhibition antigen binding. We also found that the abundance of five MEs were increased in ASD, including three human self proteins, gap junction alpha-1 (GJA1), paired box protein Pax-3 (PAX3) and eyes absent homolog 1 isoform 4 (EYA1) which associated with cancer, and a ME with homology to a Listeriolysin O peptide from the pathogenic bacterium Listeria monocytogenes was significantly increased in ASD children compared with TD children.

CONCLUSIONS: Our findings demonstrate the abnormal of MEs composition in the gut of children with ASD, moreover, the abnormality in MEs composition was associated with abnormal gut IgA levels and altered gut microbiota composition, this abnormality also suggests that there may be abnormalities in intestinal immunity in children with ASD; In all, thirty-four MEs identified were potential biomarker of ASD, and alterations in MEs may contribute to abnormalities in gut immunity and/or homeostasis in ASD children. Further study of the MEs identified here may advance our understanding of the pathogenesis of ASD.}, } @article {pmid30392727, year = {2019}, author = {Wang, L and Ravichandran, V and Yin, Y and Yin, J and Zhang, Y}, title = {Natural Products from Mammalian Gut Microbiota.}, journal = {Trends in biotechnology}, volume = {37}, number = {5}, pages = {492-504}, doi = {10.1016/j.tibtech.2018.10.003}, pmid = {30392727}, issn = {1879-3096}, mesh = {Animals ; *Bacteria/chemistry/genetics/metabolism ; *Biological Products ; Drug Discovery ; *Gastrointestinal Microbiome ; Genomics ; Humans ; Mammals/*microbiology ; }, abstract = {The mammalian gut has a remarkable abundance of microbes. These microbes have strong potential to biosynthesize distinct metabolites that are promising drugs, and many more bioactive compounds have yet to be explored as potential drug candidates. These small bioactive molecules often mediate important host-microbe and microbe-microbe interactions. In this review, we provide perspectives on and challenges associated with three mining strategies - culture-based, (meta)genomics-based, and metabolomics-based mining approaches - for discovering natural products derived from biosynthetic gene clusters (BGCs) in mammalian gut microbiota. In addition, we comprehensively summarize the structures, biological functions, and BGCs of these compounds. Improving these techniques, including by using combinatorial approaches, may accelerate drug discovery from gut microbes.}, } @article {pmid30390805, year = {2018}, author = {Wang, Q and Yang, F and Jia, H}, title = {Mining the Microbiome for Drug Targets.}, journal = {Methods in enzymology}, volume = {610}, number = {}, pages = {59-72}, doi = {10.1016/bs.mie.2018.09.014}, pmid = {30390805}, issn = {1557-7988}, mesh = {Drug Discovery/*methods ; Humans ; Metagenome/drug effects ; Metagenomics/*methods ; Microbiota/*drug effects ; Molecular Targeted Therapy/methods ; }, abstract = {The human microbiome is our "other genome." Implicated in a growing list of complex diseases, for which genomic studies typically explain a portion of the disease susceptibility, the human gut microbiome has been at the spotlight for our understanding of human diseases. As the microbiome is intrinsically more variable than the human genome, it is important to take careful considerations at each step of a study. Here, we put forward our recommendations, which we envision would facilitate identification of true drug targets in the human microbiome in the colon as well as at other body sites.}, } @article {pmid30390509, year = {2019}, author = {Leng, L and Nobu, MK and Narihiro, T and Yang, P and Amy Tan, GY and Lee, PH}, title = {Shaping microbial consortia in coupling glycerol fermentation and carboxylate chain elongation for Co-production of 1,3-propanediol and caproate: Pathways and mechanisms.}, journal = {Water research}, volume = {148}, number = {}, pages = {281-291}, doi = {10.1016/j.watres.2018.10.063}, pmid = {30390509}, issn = {1879-2448}, mesh = {Caproates ; Fermentation ; *Glycerol ; *Microbial Consortia ; Propylene Glycols ; }, abstract = {Glycerol is presently being generated in surplus with the rapid growth of the biodiesel industry and seeks ways to be upcycled, rather than to be treated with costs. Glycerol for the co-production of 1,3-propanediol (1,3-PDO) and caproate has a great prospect. Yet, its technical difficulty lies in the enhancement of caproate productivity, which requires the presence of ethanol as a co-substrate and necessitates the co-existence of functional microbes for glycerol fermentation and chain elongation. This study successfully achieved 6.38 mM C 1,3-PDO d[-1] and 2.95 mM C caproate d[-1] in a 2-L mixed-cultured semi-continuous fermenter with a glycerol-ethanol-acetate stoichiometric ratio of 4:3:1. Such conversions were mainly facilitated by a microbial community of Eubacterium limosum, Clostridium kluyveri and Massilibacterium senegalense. With such a synergistic microbiome, the co-production of 1,3-PDO and caproate was achieved from glycerol without ethanol addition. Based on metagenomics, E. limosum is capable of converting glycerol to 1,3-PDO, ethanol and H2, and also redirecting the electron potential of H2 into acetate via the Wood-Ljungdahl pathway, which is then used for chain elongation. C. kluyveri worked synergistically with E. limosum by consuming ethanol and acetate for caproate production. M. senegalense encodes for ethanol oxidation to acetate and butyrate, facilitating the generation of these intermediates for C. kluyveri elongation to caproate. During the transition between fermentation and elongation, an unexpected observation of poly-β-hydroxybutyrate (PHB) formation and reutilization by M. senegalense may be associated with butyrate formation for further caproate generation. The knowledge gleaned from the substrate constitute, microbial consortium and their synergetic metabolism demonstrates a resource upgrade potential for crude glycerol or glycerol-containing wastewater generated from the biodiesel industry.}, } @article {pmid30389965, year = {2018}, author = {Ammon, UV and Wood, SA and Laroche, O and Zaiko, A and Tait, L and Lavery, S and Inglis, GJ and Pochon, X}, title = {Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16290}, pmid = {30389965}, issn = {2045-2322}, mesh = {Animals ; Aquatic Organisms/genetics/*isolation & purification ; Biodiversity ; *Biofouling ; DNA Barcoding, Taxonomic/methods ; Databases, Genetic/statistics & numerical data ; *Introduced Species ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/*genetics ; New Zealand ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Marine infrastructure can favor the spread of non-indigenous marine biofouling species by providing a suitable habitat for them to proliferate. Cryptic organisms or those in early life stages can be difficult to distinguish by conventional morphological taxonomy. Molecular tools, such as metabarcoding, may improve their detection. In this study, the ability of morpho-taxonomy and metabarcoding (18S rRNA and COI) using three reference databases (PR2, BOLD and NCBI) to characterize biodiversity and detect non-indigenous species (NIS) in biofouling was compared on 60 passive samplers deployed over summer and winter in a New Zealand marina. Highest resolution of metazoan taxa was identified using 18S rRNA assigned to PR2. There were higher assignment rates to NCBI reference sequences, but poorer taxonomic identification. Using all methods, 48 potential NIS were identified. Metabarcoding detected the largest proportion of those NIS: 77% via 18S rRNA/PR2 and NCBI and 35% via COI/BOLD and NCBI. Morpho-taxonomy detected an additional 14% of all identified NIS comprising mainly of bryozoan taxa. The data highlight several on-going challenges, including: differential marker resolution, primer biases, incomplete sequence reference databases, and variations in bioinformatic pipelines. Combining morpho-taxonomy and molecular analysis methods will likely enhance the detection of NIS from complex biofouling.}, } @article {pmid30388453, year = {2018}, author = {Vangay, P and Johnson, AJ and Ward, TL and Al-Ghalith, GA and Shields-Cutler, RR and Hillmann, BM and Lucas, SK and Beura, LK and Thompson, EA and Till, LM and Batres, R and Paw, B and Pergament, SL and Saenyakul, P and Xiong, M and Kim, AD and Kim, G and Masopust, D and Martens, EC and Angkurawaranon, C and McGready, R and Kashyap, PC and Culhane-Pera, KA and Knights, D}, title = {US Immigration Westernizes the Human Gut Microbiome.}, journal = {Cell}, volume = {175}, number = {4}, pages = {962-972.e10}, pmid = {30388453}, issn = {1097-4172}, support = {R01 DK114007/DK/NIDDK NIH HHS/United States ; UL1 TR002494/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; *Asian People ; Bacteroides/isolation & purification ; Dietary Fiber/metabolism ; Emigrants and Immigrants ; *Emigration and Immigration ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Obesity/epidemiology/microbiology ; Prevotella/isolation & purification ; United States ; }, abstract = {Many US immigrant populations develop metabolic diseases post immigration, but the causes are not well understood. Although the microbiome plays a role in metabolic disease, there have been no studies measuring the effects of US immigration on the gut microbiome. We collected stool, dietary recalls, and anthropometrics from 514 Hmong and Karen individuals living in Thailand and the United States, including first- and second-generation immigrants and 19 Karen individuals sampled before and after immigration, as well as from 36 US-born European American individuals. Using 16S and deep shotgun metagenomic DNA sequencing, we found that migration from a non-Western country to the United States is associated with immediate loss of gut microbiome diversity and function in which US-associated strains and functions displace native strains and functions. These effects increase with duration of US residence and are compounded by obesity and across generations.}, } @article {pmid30384903, year = {2018}, author = {Huang, X and Zhu, J and Cai, Z and Lao, Y and Jin, H and Yu, K and Zhang, B and Zhou, J}, title = {Profiles of quorum sensing (QS)-related sequences in phycospheric microorganisms during a marine dinoflagellate bloom, as determined by a metagenomic approach.}, journal = {Microbiological research}, volume = {217}, number = {}, pages = {1-13}, doi = {10.1016/j.micres.2018.08.015}, pmid = {30384903}, issn = {1618-0623}, mesh = {Acyltransferases/genetics/metabolism ; Bacteria/classification/*genetics/*metabolism ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/metabolism ; Carbon-Sulfur Lyases/genetics/metabolism ; China ; Dinoflagellida/growth & development/*microbiology ; Eutrophication/physiology ; Marine Biology ; Metagenomics/*methods ; Microbiota/*genetics/*physiology ; Phylogeny ; Proteobacteria/genetics/metabolism ; Quorum Sensing/*genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis ; Sequence Analysis, Protein ; Sequence Homology ; Symbiosis ; Transcription Factors/genetics/metabolism ; }, abstract = {The complicated relationships among environmental microorganisms are regulated by quorum sensing (QS). Understanding QS-based signals could shed light on the interactions between microbial communities in certain environments. Although QS characteristics have been widely discussed, few studies have been conducted on the role of QS in phycospheric microorganisms. Here, we used metagenomics to examine the profile of AI-1 (AinS, HdtS, LuxI) and AI-2 (LuxS) autoinducers from a deeply sequenced microbial database, obtained from a complete dinoflagellate bloom. A total of 3001 putative AI-1 homologs and 130 AI-2 homologs were identified. The predominant member among the AI groups was HdtS. The abundance of HdtS, AinS, and LuxS increased as the bloom developed, whereas the abundance of LuxI showed the opposite trend. Phylogenetic analysis suggested that HdtS and LuxI synthase originated mainly from alpha-, beta-, and gamma-Proteobacteria, whereas AinS synthase originated solely from Vibrionales. In comparison to AI-1, the sequences related to AI-2 (LuxS) demonstrated a much wider taxonomic coverage. Some significant correlations were found between dominant species and QS signals. In addition to the QS, we also performed parallel analysis of the quorum quenching (QQ) sequences. In comparison to QS, the relative abundance of QQ signals was lower; however, an obvious frequency correlation was observed. These results suggested that QS and QQ signals co-participate in regulating microbial communities during an algal bloom. These data helped to reveal the characteristic behavior of algal symbiotic bacteria, and facilitated a better understanding of microbial dynamics during an algal bloom event from a chemical ecological perspective.}, } @article {pmid30384205, year = {2019}, author = {Duan, Y and Awasthi, SK and Chen, H and Liu, T and Zhang, Z and Zhang, L and Awasthi, MK and Taherzadeh, MJ}, title = {Evaluating the impact of bamboo biochar on the fungal community succession during chicken manure composting.}, journal = {Bioresource technology}, volume = {272}, number = {}, pages = {308-314}, doi = {10.1016/j.biortech.2018.10.045}, pmid = {30384205}, issn = {1873-2976}, mesh = {Animals ; Charcoal/*metabolism ; Chickens ; *Composting ; Manure/*microbiology ; *Mycobiome ; Sasa/*metabolism ; }, abstract = {The objective of this study was to investigate the fungal community succession and variations in chicken manure (CM) compost with different concentration of bamboo biochar (BB) as additive via the using of metagenomics method. The consequent obviously revealed that Chytridiomycota, Mucoromycota, Ascomycota and Basidiomycota were the dominant phylum, while Batrachochytrium, Funneliformis, Mucor, Phizophagus and Pyronema were the pre-dominant genera in each treatment. Redundancy analyses indicated that higher dosage of biochar applied treatments has significant correlation between fungal communities and environmental factors. The diversity of fungal community was analogous but the relative abundance (RA) was inconsistent among the all treatments. In addition, the principal component analysis was also confirmed that T5 and T6 treatments have considerably correlation than other treatments. However, the mean value of RA remained maximum in higher dosage of biochar blended treatments. Ultimately, the RA of different fungal genus and species were influenced in CM compost by the BB amendment.}, } @article {pmid30382616, year = {2019}, author = {Ganuza, M and Pastor, N and Boccolini, M and Erazo, J and Palacios, S and Oddino, C and Reynoso, MM and Rovera, M and Torres, AM}, title = {Evaluating the impact of the biocontrol agent Trichoderma harzianum ITEM 3636 on indigenous microbial communities from field soils.}, journal = {Journal of applied microbiology}, volume = {126}, number = {2}, pages = {608-623}, doi = {10.1111/jam.14147}, pmid = {30382616}, issn = {1365-2672}, support = {//Agencia Nacional de Promoción Científica y Tecnológica (MINCyT)/ ; }, mesh = {Agriculture ; Arachis ; Argentina ; Bacteria/genetics/isolation & purification ; *Biological Control Agents ; Denaturing Gradient Gel Electrophoresis ; Fungi/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Microbiota ; Polymerase Chain Reaction ; Seeds ; Soil/chemistry ; *Soil Microbiology ; *Trichoderma ; }, abstract = {AIM: To investigate the impact of inoculating peanut seeds with the biocontrol agent Trichoderma harzianum ITEM 3636 on the structure of bacterial and fungal communities from agricultural soils.

METHODS AND RESULTS: Polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (PCR-DGGE) and next-generation sequencing (NGS) of amplicons (or marker gene amplification metagenomics) were performed to investigate potential changes in the structure of microbial communities from fields located in a peanut-producing area in the province of Córdoba, Argentina. Fields had history of peanut smut (caused by Thecaphora frezii) incidence. The Shannon indexes (H'), which estimate diversity, obtained from the PCR-DGGE assays did not show significant differences neither for bacterial nor for fungal communities between control and inoculation treatments. On the other hand, the number of operational taxonomic units obtained after NGS was similar between all the analysed samples. Moreover, results of alpha and beta diversity showed that there were no significant variations between the relative abundances of the most representative bacterial and fungal phyla and genera, in both fields.

CONCLUSIONS: Trichoderma harzianum ITEM 3636 decreases the incidence and severity of agriculturally relevant diseases without causing significant changes in the microbial communities of agricultural soils.

Our investigations provide information on the structure of bacterial and fungal communities in peanut-producing fields after inoculation of seeds with a biocontrol agent.}, } @article {pmid30382244, year = {2018}, author = {Pedersen, HK and Forslund, SK and Gudmundsdottir, V and Petersen, AØ and Hildebrand, F and Hyötyläinen, T and Nielsen, T and Hansen, T and Bork, P and Ehrlich, SD and Brunak, S and Oresic, M and Pedersen, O and Nielsen, HB}, title = {A computational framework to integrate high-throughput '-omics' datasets for the identification of potential mechanistic links.}, journal = {Nature protocols}, volume = {13}, number = {12}, pages = {2781-2800}, doi = {10.1038/s41596-018-0064-z}, pmid = {30382244}, issn = {1750-2799}, mesh = {Computational Biology/*methods ; *Gastrointestinal Microbiome ; Humans ; *Metabolome ; Metabolomics/methods ; Phenotype ; Serum/*metabolism ; Software ; Workflow ; }, abstract = {We recently presented a three-pronged association study that integrated human intestinal microbiome data derived from shotgun-based sequencing with untargeted serum metabolome data and measures of host physiology. Metabolome and microbiome data are high dimensional, posing a major challenge for data integration. Here, we present a step-by-step computational protocol that details and discusses the dimensionality-reduction techniques used and methods for subsequent integration and interpretation of such heterogeneous types of data. Dimensionality reduction was achieved through a combination of data normalization approaches, binning of co-abundant genes and metabolites, and integration of prior biological knowledge. The use of prior knowledge to overcome functional redundancy across microbiome species is one central advance of our method over available alternative approaches. Applying this framework, other investigators can integrate various '-omics' readouts with variables of host physiology or any other phenotype of interest (e.g., connecting host and microbiome readouts to disease severity or treatment outcome in a clinical cohort) in a three-pronged association analysis to identify potential mechanistic links to be tested in experimental settings. Although we originally developed the framework for a human metabolome-microbiome study, it is generalizable to other organisms and environmental metagenomes, as well as to studies including other -omics domains such as transcriptomics and proteomics. The provided R code runs in ~1 h on a standard PC.}, } @article {pmid30377376, year = {2018}, author = {Franzosa, EA and McIver, LJ and Rahnavard, G and Thompson, LR and Schirmer, M and Weingart, G and Lipson, KS and Knight, R and Caporaso, JG and Segata, N and Huttenhower, C}, title = {Species-level functional profiling of metagenomes and metatranscriptomes.}, journal = {Nature methods}, volume = {15}, number = {11}, pages = {962-968}, pmid = {30377376}, issn = {1548-7105}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/*classification/*genetics/isolation & purification ; Bacterial Proteins/*genetics/metabolism ; *Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; Microbiota ; *Software ; Species Specificity ; *Transcriptome ; }, abstract = {Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types.}, } @article {pmid30377368, year = {2018}, author = {McDonald, D and Vázquez-Baeza, Y and Koslicki, D and McClelland, J and Reeve, N and Xu, Z and Gonzalez, A and Knight, R}, title = {Striped UniFrac: enabling microbiome analysis at unprecedented scale.}, journal = {Nature methods}, volume = {15}, number = {11}, pages = {847-848}, pmid = {30377368}, issn = {1548-7105}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; }, mesh = {*Algorithms ; Bacteria/*classification/*genetics ; Computational Biology/*methods ; Computer Simulation ; Humans ; *Metagenome ; *Microbiota ; Models, Statistical ; Phylogeny ; }, } @article {pmid30376898, year = {2018}, author = {Leiby, JS and McCormick, K and Sherrill-Mix, S and Clarke, EL and Kessler, LR and Taylor, LJ and Hofstaedter, CE and Roche, AM and Mattei, LM and Bittinger, K and Elovitz, MA and Leite, R and Parry, S and Bushman, FD}, title = {Lack of detection of a human placenta microbiome in samples from preterm and term deliveries.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {196}, pmid = {30376898}, issn = {2049-2618}, support = {P30 AI045008/AI/NIAID NIH HHS/United States ; T32 AI007324/AI/NIAID NIH HHS/United States ; T32 AI007632/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Bacteria/genetics/*isolation & purification ; DNA, Bacterial/genetics ; Female ; Humans ; Microbiota/*genetics ; Placenta/*microbiology ; Pregnancy ; Premature Birth ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Term Birth ; Uterus/*microbiology ; }, abstract = {BACKGROUND: Historically, the human womb has been thought to be sterile in healthy pregnancies, but this idea has been challenged by recent studies using DNA sequence-based methods, which have suggested that the womb is colonized with bacteria. For example, analysis of DNA from placenta samples yielded small proportions of microbial sequences which were proposed to represent normal bacterial colonization. However, an analysis by our group showed no distinction between background negative controls and placenta samples. Also supporting the idea that the womb is sterile is the observation that germ-free mammals can be generated by sterile delivery of neonates into a sterile isolator, after which neonates remain germ-free, which would seem to provide strong data in support of sterility of the womb.

RESULTS: To probe this further and to investigate possible placental colonization associated with spontaneous preterm birth, we carried out another study comparing microbiota in placenta samples from 20 term and 20 spontaneous preterm deliveries. Both 16S rRNA marker gene sequencing and shotgun metagenomic sequencing were used to characterize placenta and control samples. We first quantified absolute amounts of bacterial 16S rRNA gene sequences using 16S rRNA gene quantitative PCR (qPCR). As in our previous study, levels were found to be low in the placenta samples and indistinguishable from negative controls. Analysis by DNA sequencing did not yield a placenta microbiome distinct from negative controls, either using marker gene sequencing as in our previous work, or with shotgun metagenomic sequencing. Several types of artifacts, including erroneous read classifications and barcode misattribution, needed to be identified and removed from the data to clarify this point.

CONCLUSIONS: Our findings do not support the existence of a consistent placental microbiome, in either placenta from term deliveries or spontaneous preterm births.}, } @article {pmid30375431, year = {2018}, author = {Jasna, V and Parvathi, A and Dash, A}, title = {Genetic and functional diversity of double-stranded DNA viruses in a tropical monsoonal estuary, India.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16036}, pmid = {30375431}, issn = {2045-2322}, support = {SIP1302//CSIR | National Institute of Oceanography, India (CSIR, National Institute of Oceanography)/International ; }, mesh = {*Biodiversity ; DNA Barcoding, Taxonomic ; DNA Viruses/classification/*genetics ; DNA, Viral ; *Environmental Microbiology ; Environmental Monitoring ; India ; Metagenomics/methods ; Seasons ; *Tropical Climate ; }, abstract = {The present study illustrates the genetic diversity of four uncultured viral communities from the surface waters of Cochin Estuary (CE), India. Viral diversity inferred using Illumina HiSeq paired-end sequencing using a linker-amplified shotgun library (LASL) revealed different double-stranded DNA (dsDNA) viral communities. The water samples were collected from four stations PR1, PR2, PR3, and PR4, during the pre-monsoon (PRM) season. Analysis of virus families indicated that the Myoviridae was the most common viral community in the CE followed by Siphoviridae and Podoviridae. There were significant (p < 0.05) spatial variations in the relative abundance of dominant families in response to the salinity regimes. The relative abundance of Myoviridae and Podoviridae were high in the euryhaline region and Siphoviridae in the mesohaline region of the estuary. The predominant phage type in CE was phages that infected Synechococcus. The viral proteins were found to be involved in major functional activities such as ATP binding, DNA binding, and DNA replication. The study highlights the genetic diversity of dsDNA viral communities and their functional protein predictions from a highly productive estuarine system. Further, the metavirome data generated in this study will enhance the repertoire of publicly available dataset and advance our understanding of estuarine viral ecology.}, } @article {pmid30374198, year = {2018}, author = {Baumann-Dudenhoeffer, AM and D'Souza, AW and Tarr, PI and Warner, BB and Dantas, G}, title = {Infant diet and maternal gestational weight gain predict early metabolic maturation of gut microbiomes.}, journal = {Nature medicine}, volume = {24}, number = {12}, pages = {1822-1829}, pmid = {30374198}, issn = {1546-170X}, support = {R01 GM099538/GM/NIGMS NIH HHS/United States ; P30 DK056341/DK/NIDDK NIH HHS/United States ; T32 GM007200/GM/NIGMS NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; K08 DK102673/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/pathogenicity ; Breast Feeding ; *Diet ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/physiology ; Gestational Weight Gain/*physiology ; Humans ; Infant ; Infant, Newborn ; Metabolic Networks and Pathways/genetics ; Obesity/*diet therapy/microbiology/physiopathology ; }, abstract = {Commensal gut bacterial communities (microbiomes) are predicted to influence human health and disease[1,2]. Neonatal gut microbiomes are colonized with maternal and environmental flora and mature toward a stable composition over 2-3 years[3,4]. To study pre- and postnatal determinants of infant microbiome development, we analyzed 402 fecal metagenomes from 60 infants aged 0-8 months, using longitudinal generalized linear mixed models (GLMMs). Distinct microbiome signatures correlated with breastfeeding, formula ingredients, and maternal gestational weight gain (GWG). Amino acid synthesis pathway accretion in breastfed microbiomes complemented normative breastmilk composition. Prebiotic oligosaccharides, designed to promote breastfed-like microflora[5], predicted functional pathways distinct from breastfed infant microbiomes. Soy formula in six infants was positively associated with Lachnospiraceae and pathways suggesting a short-chain fatty acid (SCFA)-rich environment, including glycerol to 1-butanol fermentation, which is potentially dysbiotic. GWG correlated with altered carbohydrate degradation and enriched vitamin synthesis pathways. Maternal and postnatal antibiotics predicted microbiome alterations, while delivery route had no persistent effects. Domestic water source correlates suggest water may be an underappreciated determinant of microbiome acquisition. Clinically important microbial pathways with statistically significant dietary correlates included dysbiotic markers[6,7], core enterotype features[8], and synthesis pathways for enteroprotective[9] and immunomodulatory[10,11] metabolites, epigenetic mediators[1], and developmentally critical vitamins[12], warranting further investigation.}, } @article {pmid30373533, year = {2018}, author = {Yao, Y and Jin, Z and Lee, JH}, title = {An improved statistical model for taxonomic assignment of metagenomics.}, journal = {BMC genetics}, volume = {19}, number = {1}, pages = {98}, pmid = {30373533}, issn = {1471-2156}, support = {R03 AG054186/AG/NIA NIH HHS/United States ; R56 AG051876/AG/NIA NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/classification/genetics ; Gastrointestinal Microbiome ; Humans ; Likelihood Functions ; Logistic Models ; Metagenomics/*methods ; *Models, Statistical ; Mouth/microbiology ; }, abstract = {BACKGROUND: With the advances in the next-generation sequencing technologies, researchers can now rapidly examine the composition of samples from humans and their surroundings. To enhance the accuracy of taxonomy assignments in metagenomic samples, we developed a method that allows multiple mismatch probabilities from different genomes.

RESULTS: We extended the algorithm of taxonomic assignment of metagenomic sequence reads (TAMER) by developing an improved method that can set a different mismatch probability for each genome rather than imposing a single parameter for all genomes, thereby obtaining a greater degree of accuracy. This method, which we call TADIP (Taxonomic Assignment of metagenomics based on DIfferent Probabilities), was comprehensively tested in simulated and real datasets. The results support that TADIP improved the performance of TAMER especially in large sample size datasets with high complexity.

CONCLUSIONS: TADIP was developed as a statistical model to improve the estimate accuracy of taxonomy assignments. Based on its varying mismatch probability setting and correlated variance matrix setting, its performance was enhanced for high complexity samples when compared with TAMER.}, } @article {pmid30373468, year = {2019}, author = {Sinha, T and Vich Vila, A and Garmaeva, S and Jankipersadsing, SA and Imhann, F and Collij, V and Bonder, MJ and Jiang, X and Gurry, T and Alm, EJ and D'Amato, M and Weersma, RK and Scherjon, S and Wijmenga, C and Fu, J and Kurilshikov, A and Zhernakova, A}, title = {Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles.}, journal = {Gut microbes}, volume = {10}, number = {3}, pages = {358-366}, pmid = {30373468}, issn = {1949-0984}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/*pharmacology ; *Biodiversity ; Drug Resistance, Microbial/*genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Genes, Bacterial/genetics ; Humans ; Irritable Bowel Syndrome/microbiology ; Lincosamides/pharmacology ; Male ; Metagenome/*genetics ; Middle Aged ; Prospective Studies ; Sex Factors ; Young Adult ; }, abstract = {Several gastrointestinal diseases show a sex imbalance, although the underlying (patho)physiological mechanisms behind this are not well understood. The gut microbiome may be involved in this process, forming a complex interaction with host immune system, sex hormones, medication and other environmental factors. Here we performed sex-specific analyses of fecal microbiota composition in 1135 individuals from a population-based cohort. The overall gut microbiome composition of females and males was significantly different (p = 0.001), with females showing a greater microbial diversity (p = 0.009). After correcting for the effects of intrinsic factors, smoking, diet and medications, female hormonal factors such as the use of oral contraceptives and undergoing an ovariectomy were associated with microbial species and pathways. Females had a higher richness of antibiotic-resistance genes, with the most notable being resistance to the lincosamide nucleotidyltransferase (LNU) gene family. The higher abundance of resistance genes is consistent with the greater prescription of the Macrolide-Lincosamide-Streptogramin classes of antibiotics to females. Furthermore, we observed an increased resistance to aminoglycosides in females with self-reported irritable bowel syndrome. These results throw light upon the effects of common medications that are differentially prescribed between sexes and highlight the importance of sex-specific analysis when studying the gut microbiome and resistome.}, } @article {pmid30373071, year = {2019}, author = {Bondarczuk, K and Piotrowska-Seget, Z}, title = {Microbial diversity and antibiotic resistance in a final effluent-receiving lake.}, journal = {The Science of the total environment}, volume = {650}, number = {Pt 2}, pages = {2951-2961}, doi = {10.1016/j.scitotenv.2018.10.050}, pmid = {30373071}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Physiological Phenomena/*drug effects ; *Drug Resistance, Bacterial ; Lakes/*microbiology ; Microbiota/drug effects ; Poland ; Waste Disposal, Fluid ; Wastewater/*microbiology ; beta-Lactams/pharmacology ; }, abstract = {Wastewater treatment plants have been recognised as hotspots for antibiotic resistance genes and antibiotic-resistant bacteria which enter the environment. However, the persistence of these genes and bacteria in receiving ecosystems remains poorly understood. The aim of the study was to evaluate the effect of final effluent release on microbial diversity and the antibiotic resistance gene pool in a final effluent-receiving lake. The numbers of total culturable heterotrophs and unculturable bacteria (represented as the 16S rRNA gene copy number) were significantly reduced during the treatment process. The number of ampicillin-resistant bacteria was higher in the sediment than in water samples, suggesting accumulation of ampicillin-resistant bacteria in freshwater sediments. Using an exogenous method, we captured 56 resistance plasmids which were further characterised. Next-generation sequencing revealed that the microbial phyla represented in the studied metagenomes were typical of corresponding environments. The highest relative abundance of antibiotic resistance genes was observed in the final effluent, suggesting that a considerable number of genes were released from the wastewater treatment plant. However, the lowest relative abundance and lowest diversity of the genes in the lake water, compared to the other studied metagenomes, suggest a negligible effect of treated sewage release on antibiotic resistance within water microbial communities of the lake. Furthermore, uncontrolled sewage dumping into this reservoir in the past as well as lower quality of the water upstream of the lake indicated that the wastewater treatment plant protected the studied ecosystem.}, } @article {pmid30372979, year = {2019}, author = {Park, SE and Seo, SH and Kim, EJ and Byun, S and Na, CS and Son, HS}, title = {Changes of microbial community and metabolite in kimchi inoculated with different microbial community starters.}, journal = {Food chemistry}, volume = {274}, number = {}, pages = {558-565}, doi = {10.1016/j.foodchem.2018.09.032}, pmid = {30372979}, issn = {1873-7072}, mesh = {Bacteria/metabolism ; Brassica/metabolism/*microbiology ; *Fermentation ; Fermented Foods/*microbiology ; *Food Microbiology ; *Microbiota ; }, abstract = {Gas chromatography mass spectrometry-based metabolomics and next generation sequencing-based metagenomics were applied to investigate the effect of different microbial community starters (MCSs) on kimchi fermentation. Profiles of metabolites and microbial community in kimchi were remarkably different from those on the first day of fermentation according to MCS used. Kimchi inoculated with MCS5 or MCS10 had relatively higher levels of lactic acid, leucine, propanedioic acid, serine, glycerol, erythritol, and sorbitol but lower levels of butanedioic acid, glyceric acid, myo-inositol, xylose, fructose, and talose compared to control kimchi or kimchi inoculated with MCS1. Microbial communities of kimchi inoculated with MCS1, MCS5, and MCS10 were characterized by high ratios of Leuconostoc, Lactobacillus plantarum, and Lactobacillus brevis, respectively. The microbial community of kimchi formed on the first day of fermentation was stable for 50 days, suggesting that microbial communities containing multiple microorganisms can be used as starters to obtain desired quality of kimchi.}, } @article {pmid30370682, year = {2019}, author = {Nogueira, T and David, PHC and Pothier, J}, title = {Antibiotics as both friends and foes of the human gut microbiome: The microbial community approach.}, journal = {Drug development research}, volume = {80}, number = {1}, pages = {86-97}, doi = {10.1002/ddr.21466}, pmid = {30370682}, issn = {1098-2299}, mesh = {Animals ; Anti-Bacterial Agents/adverse effects/*therapeutic use ; Bacterial Infections/drug therapy/genetics/metabolism ; Databases, Genetic/trends ; Dysbiosis/drug therapy/genetics/metabolism ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Metagenomics/*methods/trends ; Microbiota/*drug effects ; }, abstract = {The exposure of the human gut to antibiotics can have a great impact on human health. Antibiotics pertain to the preservation of human health and are useful tools for fighting bacterial infections. They can be used for curing infections and can play a critical role in immunocompromised or chronic patients, or in fighting childhood severe malnutrition. Yet, the genomic and phylogenetic diversity of the human gut changes under antibiotic exposure. Antibiotics can also have severe side effects on human gut health, due to the spreading of potential antibiotic resistance genetic traits and to their correlation with virulence of some bacterial pathogens. They can shape, and even disrupt, the composition and functioning diversity of the human gut microbiome. Traditionally bacterial antibiotic resistances have been evaluated at clone or population level. However, the understanding of these two apparently disparate perspectives as both friends and foes may come from the study of microbiomes as a whole and from the evaluation of both positive and negative effects of antibiotics on microbial community dynamics and diversity. In this review we present some metagenomic tools and databases that enable the studying of antibiotic resistance in human gut metagenomes, promoting the development of personalized medicine strategies, new antimicrobial therapy protocols and patient follow-up.}, } @article {pmid30369115, year = {2018}, author = {Sivakala, KK and Jose, PA and Anandham, R and Thinesh, T and Jebakumar, SRD and Samaddar, S and Chatterjee, P and Sivakumar, N and Sa, T}, title = {Spatial Physiochemical and Metagenomic Analysis of Desert Environment.}, journal = {Journal of microbiology and biotechnology}, volume = {28}, number = {9}, pages = {1517-1526}, doi = {10.4014/jmb.1804.04005}, pmid = {30369115}, issn = {1738-8872}, mesh = {Bacteria/*chemistry/classification/*genetics/metabolism ; Biodiversity ; *Desert Climate ; India ; Metabolic Networks and Pathways ; *Metagenomics ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Spatial Analysis ; }, abstract = {Investigating the bacterial diversity and their metabolic capabilities are crucial for interpreting ecological patterns in desert environment, and assessing the presence of exploitable microbial resources. In this study, we evaluated the spatial heterogeneity of physico-chemical parameters, soil bacterial diversity and metabolic adaptation at meter scale. Soil samples were collected from two quadrates a desert environment (Thar Desert, India) which face hot arid climate with very little rainfall and extreme temperatures. Analysis of physico-chemical parameters and subsequent variance analysis (p-values < 0.05) revealed that sulfate, potassium and magnesium ions were the most variable between the quadrates. Microbial diversity of the two quadrates was studied using Illumina bar coded sequencing by targeting V3-V4 regions of 16S rDNA. As the results, 702504 high-quality sequence reads, assigned to 173 operationaltaxonomic units (OTUs) at species level. The most abundant phyla in both quadrates were Actinobacteria (38.72%), Proteobacteria (32.94%), and Acidobacteria (9.24%). At genus level, Gaiellarepresented highest prevalence, followed by Streptomyces, Solirubrobacter, Aciditerrimonas, Geminicoccus, Geodermatophilus, Microvirga, and Rubrobacter. Between the quadrates, significant difference (p-values < 0.05) was found in the abundance of Aciditerrimonas, Geodermatophilus Geminicoccus, Ilumatobacter, Marmoricola, Nakamurella and Solirubrobacter. Metabolic functional mapping revealed diverse biological activities, and was significantly correlated with physico-chemical parameters. The results revealed spatial variation of ions, microbial abundance and functional attributes in the studied quadrates, and patchy nature in local scale. Interestingly, abundance ofthe biotechnologically important phylum Actinobacteria, with large proposition of unclassified speciesin the desert suggested that this arid environment is the promising site for bioprospection.}, } @article {pmid30368579, year = {2019}, author = {Zhu, L and Liao, R and Wu, N and Zhu, G and Yang, C}, title = {Heat stress mediates changes in fecal microbiome and functional pathways of laying hens.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {1}, pages = {461-472}, doi = {10.1007/s00253-018-9465-8}, pmid = {30368579}, issn = {1432-0614}, support = {CARS-40-K03//Agriculture Research System of China/ ; }, mesh = {Animals ; Chickens/*microbiology ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Heat-Shock Response/*physiology ; Lipids/blood ; Metabolic Networks and Pathways ; }, abstract = {Chicken gastrointestinal microbiota plays important roles in health, productivity, and disease. However, knowledge of the relationship between heat stress and the gut microbial ecosystem of poultry, especially laying hens, is still limited. Here, we aimed to provide important knowledge for heat stress intervention in the egg industry. We performed high-throughput sequencing metagenomics on fecal contents to unravel the microbial taxa and functional capacity of the gut microbiome of caged laying hens under heat stress. Results showed that the fecal microbial communities of laying hens were dominated by Firmicutes, Bacteroidetes, and Proteobacteria phyla. The Firmicutes were significantly decreased, and Bacteroidetes were increased in the fecal microbiota under heat stress. Functional prediction of these changes in microbiota revealed that metabolism-related pathways, including cysteine and methionine metabolism and benzoate degradation, were more abundant. Conversely, retinol metabolism and phenylpropanoid biosynthesis were decreased by heat stress, suggesting differences in metabolism between layers in different temperature environments. Clear contributions were identified between active taxa (genus level) and metabolic pathways, which were associated with the liver and intestinal dysfunction in layers. These data revealed that heat stress induced a significant taxonomic perturbation in the gut microbiome of caged laying hens. This was related to the negative effects of heat stress in poultry and provided important basic knowledge for heat stress intervention.}, } @article {pmid30368524, year = {2019}, author = {Li, X and Jousset, A and de Boer, W and Carrión, VJ and Zhang, T and Wang, X and Kuramae, EE}, title = {Legacy of land use history determines reprogramming of plant physiology by soil microbiome.}, journal = {The ISME journal}, volume = {13}, number = {3}, pages = {738-751}, pmid = {30368524}, issn = {1751-7370}, mesh = {Agriculture ; Arachis/*microbiology/physiology ; Crops, Agricultural ; *Metagenome ; Microbiota/genetics/*physiology ; Plant Roots/microbiology/physiology ; Rhizosphere ; *Soil Microbiology ; }, abstract = {Microorganisms associated with roots are thought to be part of the so-called extended plant phenotypes with roles in the acquisition of nutrients, production of growth hormones, and defense against diseases. Since the crops selectively enrich most rhizosphere microbes out of the bulk soil, we hypothesized that changes in the composition of bulk soil communities caused by agricultural management affect the extended plant phenotype. In the current study, we performed shotgun metagenome sequencing of the rhizosphere microbiome of the peanut (Arachis hypogaea) and metatranscriptome analysis of the roots of peanut plants grown in the soil with different management histories, peanut monocropping and crop rotation. We found that the past planting record had a significant effect on the assembly of the microbial community in the peanut rhizosphere, indicating a soil memory effect. Monocropping resulted in a reduction of the rhizosphere microbial diversity, an enrichment of several rare species, and a reduced representation of traits related to plant performance, such as nutrients metabolism and phytohormone biosynthesis. Furthermore, peanut plants in monocropped soil exhibited a significant reduction in growth coinciding with a down-regulation of genes related to hormone production, mainly auxin and cytokinin, and up-regulation of genes related to the abscisic acid, salicylic acid, jasmonic acid, and ethylene pathways. These findings suggest that land use history affects crop rhizosphere microbiomes and plant physiology.}, } @article {pmid30367805, year = {2018}, author = {Şener, DD and Santoni, D and Felici, G and Oğul, H}, title = {A Content-Based Retrieval Framework for Whole Metagenome Sequencing Samples.}, journal = {Journal of integrative bioinformatics}, volume = {15}, number = {4}, pages = {}, pmid = {30367805}, issn = {1613-4516}, mesh = {Algorithms ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Metagenome ; *Microbiota ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {Finding similarities and differences between metagenomic samples within large repositories has been rather a significant issue for researchers. Over the recent years, content-based retrieval has been suggested by various studies from different perspectives. In this study, a content-based retrieval framework for identifying relevant metagenomic samples is developed. The framework consists of feature extraction, selection methods and similarity measures for whole metagenome sequencing samples. Performance of the developed framework was evaluated on given samples. A ground truth was used to evaluate the system performance such that if the system retrieves patients with the same disease, -called positive samples-, they are labeled as relevant samples otherwise irrelevant. The experimental results show that relevant experiments can be detected by using different fingerprinting approaches. We observed that Latent Semantic Analysis (LSA) Method is a promising fingerprinting approach for representing metagenomic samples and finding relevance among them. Source codes and executable files are available at www.baskent.edu.tr/∼hogul/WMS_retrieval.rar.}, } @article {pmid30366990, year = {2019}, author = {Zhang, W and Watanabe, HK and Ding, W and Lan, Y and Tian, RM and Sun, J and Chen, C and Cai, L and Li, Y and Oguri, K and Toyofuku, T and Kitazato, H and Drazen, JC and Bartlett, D and Qian, PY}, title = {Gut Microbial Divergence between Two Populations of the Hadal Amphipod Hirondellea gigas.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {1}, pages = {}, pmid = {30366990}, issn = {1098-5336}, mesh = {Amphipoda/*microbiology ; Animals ; Archaea/classification/*physiology ; Bacteria/classification ; *Bacterial Physiological Phenomena ; Gastrointestinal Microbiome/*physiology ; Hydrothermal Vents ; }, abstract = {Hadal environments sustain diverse microorganisms. A few studies have investigated hadal microbial communities consisting of free-living or particle-associated bacteria and archaea. However, animal-associated microbial communities in hadal environments remain largely unexplored, and comparative analyses of animal gut microbiota between two isolated hadal environments have never been done so far. In the present study, 228 Gb of gut metagenomes of the giant amphipod Hirondellea gigas from two hadal trenches, the Mariana Trench and Japan Trench, were sequenced and analyzed. Taxonomic analysis identified 49 microbial genera commonly shared by the gut microbiota of the two H. gigas populations. However, the results of statistical analysis, in congruency with the alpha and beta diversity analyses, revealed significant differences in gut microbial composition across the two trenches. Abundance variation of Psychromonas, Propionibacterium, and Pseudoalteromonas species was observed. Microbial cooccurrence was demonstrated for microbes that were overrepresented in the Mariana trench. Comparison of functional potential showed that the percentage of carbohydrate metabolic genes among the total microbial genes was significantly higher in the guts of H. gigas specimens from the Mariana Trench. Integrating carbon input information and geological characters of the two hadal trenches, we propose that the differences in the community structure might be due to several selective factors, such as environmental variations and microbial interactions.IMPORTANCE The taxonomic composition and functional potential of animal gut microbiota in deep-sea environments remain largely unknown. Here, by performing comparative metagenomics, we suggest that the gut microbial compositions of two Hirondellea gigas populations from the Mariana Trench and the Japan Trench have undergone significant divergence. Through analyses of functional potentials and microbe-microbe correlations, our findings shed light on the contributions of animal gut microbiota to host adaptation to hadal environments.}, } @article {pmid30366118, year = {2019}, author = {Maya-Lucas, O and Murugesan, S and Nirmalkar, K and Alcaraz, LD and Hoyo-Vadillo, C and Pizano-Zárate, ML and García-Mena, J}, title = {The gut microbiome of Mexican children affected by obesity.}, journal = {Anaerobe}, volume = {55}, number = {}, pages = {11-23}, doi = {10.1016/j.anaerobe.2018.10.009}, pmid = {30366118}, issn = {1095-8274}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Child ; Dysbiosis/*complications ; Fatty Acids, Volatile/analysis ; Feces/chemistry/microbiology ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metabolome ; Mexico ; Obesity/*complications ; Sequence Analysis, DNA ; Viruses/*classification/genetics ; }, abstract = {Obesity is a metabolic disorder and global health issue. In Mexico 34.4% of children between 5 and 11 years-old are overweight or obese. Here we address this issue studying the gut microbiome in a sample of Mexican children affected by obesity. We performed metagenomic shotgun-sequencing of DNA isolated from fecal samples from a cohort of normal weight and obese Mexican children using Illumina platform with HiSeq 2500. We also examined their metabolic factors and fecal short-chain fatty acids concentration. The results show that a remarkable dysbiosis of bacteria, archaea and viruses was not observed in the obese children group compared to the normal weight group; however, the archaeal community exhibited an increase of unclassified Methanobrevibacter spp. in obese children. The bacterial communities of all participants were clustered into three different enterotypes. Most normal weight children have a gut bacterial community dominated by Ruminococcus spp. (Enterotype 3), while most obese children had a community dominated by Prevotella spp. (Enterotype 2). On the other hand, changes in the gut microbiome were correlated with clinical metadata and could be used to stratify individuals based on their phenotype. The species Megamonas spp. were over-represented in obese children, whereas members of the family Oscillospiraceae were depleted in the same individuals and negatively correlated with levels of serum cholesterol. A microbiome comparative metabolic pathway analysis showed that two KEGG pathway modules of glycolysis, Glycolysis I (from Glucose 6-Phosphate), and Glycolysis II (from Fructose 6-Phosphate) were significantly overrepresented in normal weight children. Our results establish specific alterations in the gut microbiome of Mexican children affected of obesity, along with clinical alterations, providing information on the microbiome composition that may be useful for prognosis, diagnosis, and treatment.}, } @article {pmid30365027, year = {2019}, author = {Shi, W and Qi, H and Sun, Q and Fan, G and Liu, S and Wang, J and Zhu, B and Liu, H and Zhao, F and Wang, X and Hu, X and Li, W and Liu, J and Tian, Y and Wu, L and Ma, J}, title = {gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data.}, journal = {Nucleic acids research}, volume = {47}, number = {D1}, pages = {D637-D648}, pmid = {30365027}, issn = {1362-4962}, mesh = {*Databases, Genetic ; *Metagenome ; Metagenomics/*methods/standards ; *Microbiota ; Reference Standards ; *Software ; }, abstract = {Meta-omics approaches have been increasingly used to study the structure and function of the microbial communities. A variety of large-scale collaborative projects are being conducted to encompass samples from diverse environments and habitats. This change has resulted in enormous demands for long-term data maintenance and capacity for data analysis. The Global Catalogue of Metagenomics (gcMeta) is a part of the 'Chinese Academy of Sciences Initiative of Microbiome (CAS-CMI)', which focuses on studying the human and environmental microbiome, establishing depositories of samples, strains and data, as well as promoting international collaboration. To accommodate and rationally organize massive datasets derived from several thousands of human and environmental microbiome samples, gcMeta features a database management system for archiving and publishing data in a standardized way. Another main feature is the integration of more than ninety web-based data analysis tools and workflows through a Docker platform which enables data analysis by using various operating systems. This platform has been rapidly expanding, and now hosts data from the CAS-CMI and a number of other ongoing research projects. In conclusion, this platform presents a powerful and user-friendly service to support worldwide collaborative efforts in the field of meta-omics research. This platform is freely accessible at https://gcmeta.wdcm.org/.}, } @article {pmid30362648, year = {2019}, author = {Larivière-Gauthier, G and Thibodeau, A and Letellier, A and Yergeau, É and Fravalo, P}, title = {Salmonella shedding status of the sow affects the microbiota of their piglets at weaning.}, journal = {Journal of applied microbiology}, volume = {126}, number = {2}, pages = {411-423}, doi = {10.1111/jam.14139}, pmid = {30362648}, issn = {1365-2672}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; *Bacterial Shedding ; Female ; *Microbiota ; Pregnancy ; Salmonella/*isolation & purification ; Swine/growth & development/*microbiology ; Weaning ; }, abstract = {AIM: To observe the transfer of the digestive microbiota from sow to piglet, describe the impact of the sow's Salmonella shedding on this transfer and identify transferred populations that could be associated with the future Salmonella status of the piglets.

METHODS AND RESULTS: Salmonella shedding status of 19 sows was determined at the beginning and end of gestation. Four piglets were randomly selected from each sow. Using MiSeq, the microbiotas of the sows at the end of gestation and of their piglets 1 day before weaning were described. Results showed that the Salmonella shedding of the sows, the birth mother, the lairage room, the parity and the contamination of the lairage environment were associated to the microbiota of the piglets (permanova P < 0·05). Several genera were associated with piglets born from negative or positive sows.

CONCLUSION: There is a link between the microbiota of the sows at the end of gestation and the microbiota of their piglets at weaning, and the Salmonella shedding of the sow is associated with the microbiota of the piglets.

Salmonella status of the sows affects the microbiota of their piglets and could affect the long-term Salmonella colonization resistance of these animals and their health.}, } @article {pmid30362076, year = {2019}, author = {Almeida, OGG and De Martinis, ECP}, title = {Bioinformatics tools to assess metagenomic data for applied microbiology.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {1}, pages = {69-82}, doi = {10.1007/s00253-018-9464-9}, pmid = {30362076}, issn = {1432-0614}, support = {17/13759-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 6762/2006-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; }, mesh = {Biodiversity ; Computational Biology/*methods ; Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Industrial Microbiology/*methods ; Metagenomics/*methods/statistics & numerical data ; Phylogeny ; Quality Control ; }, abstract = {The reduction of the price of DNA sequencing has resulted in the emergence of large data sets to handle and analyze, especially in microbial ecosystems, which are characterized by high taxonomic and functional diversities. To assess the properties of these complex ecosystems, a conceptual background of the application of NGS technology and bioinformatics analysis to metagenomics is required. Accordingly, this article presents an overview of the evolution of knowledge of microbial ecology from traditional culture-dependent methods to culture-independent methods and the last frontier in knowledge, metagenomics. Topics that will be covered include sample preparation for NGS, starting with total DNA extraction and library preparation, followed by a brief discussion of the chemistry of NGS to help provide an understanding of which bioinformatics pipeline approach may be helpful for achieving a researcher's goals. The importance of selecting appropriate sequencing coverage and depth parameters to obtain a suitable measure of microbial diversity is discussed. As all DNA sequencing processes produce base-calling errors that compromise data analysis, including genome assembly and microbial functional analysis, dedicated software is presented and conceptually discussed with regard to potential applications in the general microbial ecology field.}, } @article {pmid30359379, year = {2018}, author = {Bidot, WA and Ericsson, AC and Franklin, CL}, title = {Effects of water decontamination methods and bedding material on the gut microbiota.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0198305}, pmid = {30359379}, issn = {1932-6203}, support = {K01 OD019924/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/isolation & purification ; Cecum/microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Housing, Animal ; Mice, Inbred ICR ; *Water Microbiology ; Water Purification/*methods ; }, abstract = {Rodent models are invaluable to understanding health and disease in many areas of biomedical research. Unfortunately, many models suffer from lack of phenotype reproducibility. Our laboratory has shown that differences in gut microbiota (GM) can modulate phenotypes of models of colon cancer and inflammatory bowel disease. We and others have also shown that a number of factors associated with rodent research, including vendor, cage system, and bedding can alter GM. The objective of this study was to expand these studies to examine the effect of additional bedding materials and methods of water decontamination on GM diversity and composition. To this end, Crl:CD1 (ICR) mice were housed on corn cob or compressed paper chip bedding and provided water that was decontaminated by four different methods: autoclaving with reverse osmosis, autoclaving with hydrochloric acid, autoclaving with sulfuric acid, and autoclaving alone. Feces was collected at day 0, and at day 28 (endpoint), fecal and cecal samples were collected. DNA was extracted from samples, amplified by PCR using conserved bacterial primer sets and subjected to next generation sequencing. Sequence data were analyzed using Qiime and groups were compared using principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA). Two factor PERMANOVA of cecal GM data revealed significant changes when comparing bedding and water decontamination methods, while no significant effects were noted in the fecal GM data. Subsequent PERMANOVA and PCoA of cecal data revealed that several combinations of bedding and water decontamination methods resulted in differing GM, highlighting the complexity by which environmental factors interact to modulate GM.}, } @article {pmid30359203, year = {2019}, author = {Wang, Y and Leong, LEX and Keating, RL and Kanno, T and Abell, GCJ and Mobegi, FM and Choo, JM and Wesselingh, SL and Mason, AJ and Burr, LD and Rogers, GB}, title = {Opportunistic bacteria confer the ability to ferment prebiotic starch in the adult cystic fibrosis gut.}, journal = {Gut microbes}, volume = {10}, number = {3}, pages = {367-381}, pmid = {30359203}, issn = {1949-0984}, support = {/WT_/Wellcome Trust/United Kingdom ; /BHF_/British Heart Foundation/United Kingdom ; }, mesh = {Adult ; Amylose/analysis/metabolism ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Biodiversity ; Cystic Fibrosis/*microbiology ; Fatty Acids, Volatile/metabolism ; Feces/chemistry/microbiology ; Female ; *Fermentation ; Gastrointestinal Microbiome/genetics ; Humans ; Male ; Metabolome ; Metagenome ; Middle Aged ; *Prebiotics/analysis ; RNA, Ribosomal, 16S/genetics ; Starch/*chemistry/*metabolism ; Young Adult ; }, abstract = {Chronic disruption of the intestinal microbiota in adult cystic fibrosis (CF) patients is associated with local and systemic inflammation, and has been linked to the risk of serious comorbidities. Supplementation with high amylose maize starch (HAMS) might provide clinical benefit by promoting commensal bacteria and the biosynthesis of immunomodulatory metabolites. However, whether the disrupted CF gut microbiota has the capacity to utilise these substrates is not known. We combined metagenomic sequencing, in vitro fermentation, amplicon sequencing, and metabolomics to define the characteristics of the faecal microbiota in adult CF patients and assess HAMS fermentation capacity. Compared to healthy controls, the faecal metagenome of adult CF patients had reduced bacterial diversity and prevalence of commensal fermentative clades. In vitro fermentation models seeded with CF faecal slurries exhibited reduced acetate levels compared to healthy control reactions, but comparable levels of butyrate and propionate. While the commensal genus Faecalibacterium was strongly associated with short chain fatty acid (SCFA) production by healthy microbiota, it was displaced in this role by Clostridium sensu stricto 1 in the microbiota of CF patients. A subset of CF reactions exhibited enterococcal overgrowth, resulting in lactate accumulation and reduced SCFA biosynthesis. The addition of healthy microbiota to CF faecal slurries failed to displace predominant CF taxa, or substantially influence metabolite biosynthesis. Despite significant microbiota disruption, the adult CF gut microbiota retains the capacity to exploit HAMS. Our findings highlight the potential for taxa associated with the altered CF gut microbiotato mediate prebiotic effects in microbial systems subject to ongoing perturbation, irrespective of the depletion of common commensal clades.}, } @article {pmid30358106, year = {2019}, author = {Siegenthaler, A and Wangensteen, OS and Soto, AZ and Benvenuto, C and Corrigan, L and Mariani, S}, title = {Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {206-220}, pmid = {30358106}, issn = {1755-0998}, support = {//Santander Advantage Fund/ ; //University of Salford Manchester/ ; NE/N005759/1//Natural Environment Research Council/ ; //Mersey Gateway Environmental Trust/ ; }, mesh = {Animals ; *Biodiversity ; Crangonidae/*physiology ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV ; Estuaries ; Europe ; Feeding Behavior ; Fishes/*classification/*genetics ; *Gastrointestinal Contents ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; RNA, Ribosomal/genetics ; }, abstract = {Given their positioning and biological productivity, estuaries have long represented key providers of ecosystem services and consequently remain under remarkable pressure from numerous forms of anthropogenic impact. The monitoring of fish communities in space and time is one of the most widespread and established approaches to assess the ecological status of estuaries and other coastal habitats, but traditional fish surveys are invasive, costly, labour intensive and highly selective. Recently, the application of metabarcoding techniques, on either sediment or aqueous environmental DNA, has rapidly gained popularity. Here, we evaluate the application of a novel, high-throughput DNA-based monitoring tool to assess fish diversity, based on the analysis of the gut contents of a generalist predator/scavenger, the European brown shrimp, Crangon crangon. Sediment and shrimp samples were collected from eight European estuaries, and DNA metabarcoding (using both 12S and COI markers) was carried out to infer fish assemblage composition. We detected 32 teleost species (16 and 20, for 12S and COI, respectively). Twice as many species were recovered using metabarcoding than by traditional net surveys. By comparing and interweaving trophic, environmental DNA and traditional survey-based techniques, we show that the DNA-assisted gut content analysis of a ubiquitous, easily accessible, generalist species may serve as a powerful, rapid and cost-effective tool for large-scale, routine estuarine biodiversity monitoring.}, } @article {pmid30357583, year = {2019}, author = {Koringa, PG and Thakkar, JR and Pandit, RJ and Hinsu, AT and Parekh, MJ and Shah, RK and Jakhesara, SJ and Joshi, CG}, title = {Metagenomic characterisation of ruminal bacterial diversity in buffaloes from birth to adulthood using 16S rRNA gene amplicon sequencing.}, journal = {Functional & integrative genomics}, volume = {19}, number = {2}, pages = {237-247}, pmid = {30357583}, issn = {1438-7948}, support = {NO. ICAR letter No. 10(2)/2011-EPD dated 15-07-2014//Indian Council of Agricultural Research/ ; }, mesh = {Animals ; Buffaloes/*microbiology ; *Gastrointestinal Microbiome ; Male ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Rumen/growth & development/*microbiology ; }, abstract = {Microbial colonisation in the forestomach of a ruminant is one of the most crucial factors in determining many of its physiological developments and digestive capabilities. The present study attempts to identify establishment pattern of microbes in relation to food, age and rumen development in the buffalo calves at every fortnight interval from birth to 6 months of age, followed by every month till animals became 1 year of age. Diversity study based on 16S rRNA gene sequencing identified rapidly changing bacterial population during initial 60 days of life, which got assemblage as rumen became physiologically mature with increasing age of animals. A lactate fermenting aerobic to facultative anaerobic genera found during initial 30 days of life were expeditiously replaced by strict anaerobic cellulolytic bacterial population with increasing age. The study confirms that initial colonisation mainly depends on the oral cavity and skin of the mother, followed by the surrounding environment and feed offered, which is reversed in order once animal gets older. Some of the well-described genera based on culture-dependent studies like Ruminococcus spp. were found to be in lesser proportion suggesting an additional role of other microbes or niche in cellulose degradation. We report the presence of Porphyromonas spp. and Mannheimia glucosidal for the first time in bovine infants.}, } @article {pmid30356699, year = {2018}, author = {Weißbecker, C and Wubet, T and Lentendu, G and Kühn, P and Scholten, T and Bruelheide, H and Buscot, F}, title = {Experimental Evidence of Functional Group-Dependent Effects of Tree Diversity on Soil Fungi in Subtropical Forests.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2312}, pmid = {30356699}, issn = {1664-302X}, abstract = {Deconvoluting the relative contributions made by specific biotic and abiotic drivers to soil fungal community compositions facilitates predictions about the functional responses of ecosystems to environmental changes, such as losses of plant diversity, but it is hindered by the complex interactions involved. Experimental assembly of tree species allows separation of the respective effects of plant community composition (biotic components) and soil properties (abiotic components), enabling much greater statistical power than can be achieved in observational studies. We therefore analyzed these contributions by assessing, via pyrotag sequencing of the internal transcribed spacer (ITS2) rDNA region, fungal communities in young subtropical forest plots included in a large experiment on the effects of tree species richness. Spatial variables and soil properties were the main drivers of soil fungal alpha and beta-diversity, implying strong early-stage environmental filtering and dispersal limitation. Tree related variables, such as tree community composition, significantly affected arbuscular mycorrhizal and pathogen fungal community structure, while differences in tree host species and host abundance affected ectomycorrhizal fungal community composition. At this early stage of the experiment, only a limited amount of carbon inputs (rhizodeposits and leaf litter) was being provided to the ecosystem due to the size of the tree saplings, and persisting legacy effects were observed. We thus expect to find increasing tree related effects on fungal community composition as forest development proceeds.}, } @article {pmid30356187, year = {2018}, author = {Stewart, CJ and Ajami, NJ and O'Brien, JL and Hutchinson, DS and Smith, DP and Wong, MC and Ross, MC and Lloyd, RE and Doddapaneni, H and Metcalf, GA and Muzny, D and Gibbs, RA and Vatanen, T and Huttenhower, C and Xavier, RJ and Rewers, M and Hagopian, W and Toppari, J and Ziegler, AG and She, JX and Akolkar, B and Lernmark, A and Hyoty, H and Vehik, K and Krischer, JP and Petrosino, JF}, title = {Temporal development of the gut microbiome in early childhood from the TEDDY study.}, journal = {Nature}, volume = {562}, number = {7728}, pages = {583-588}, pmid = {30356187}, issn = {1476-4687}, support = {U01 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK063863/DK/NIDDK NIH HHS/United States ; HHSN267200700014C/DK/NIDDK NIH HHS/United States ; U01 DK063861/DK/NIDDK NIH HHS/United States ; UL1 TR001427/TR/NCATS NIH HHS/United States ; U01 DK063790/DK/NIDDK NIH HHS/United States ; UL1 TR001082/TR/NCATS NIH HHS/United States ; UL1 TR000064/TR/NCATS NIH HHS/United States ; U01 DK063836/DK/NIDDK NIH HHS/United States ; U01 DK063829/DK/NIDDK NIH HHS/United States ; U01 DK063865/DK/NIDDK NIH HHS/United States ; UC4 DK095300/DK/NIDDK NIH HHS/United States ; UC4 DK063861/DK/NIDDK NIH HHS/United States ; UC4 DK063829/DK/NIDDK NIH HHS/United States ; UC4 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK117483/DK/NIDDK NIH HHS/United States ; UC4 DK063836/DK/NIDDK NIH HHS/United States ; UC4 DK112243/DK/NIDDK NIH HHS/United States ; UC4 DK063865/DK/NIDDK NIH HHS/United States ; U01 DK063863/DK/NIDDK NIH HHS/United States ; UC4 DK106955/DK/NIDDK NIH HHS/United States ; UC4 DK100238/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Animals ; Bifidobacterium/classification/genetics/isolation & purification ; Breast Feeding/statistics & numerical data ; Case-Control Studies ; Child ; Child, Preschool ; Cluster Analysis ; Datasets as Topic ; Diabetes Mellitus, Type 1/immunology/microbiology ; Female ; Firmicutes/classification/genetics/isolation & purification ; Gastrointestinal Microbiome/genetics/*immunology/*physiology ; Humans ; Infant ; Male ; Milk, Human/immunology/microbiology ; Pets ; RNA, Ribosomal, 16S/genetics ; Siblings ; *Surveys and Questionnaires ; Time Factors ; }, abstract = {The development of the microbiome from infancy to childhood is dependent on a range of factors, with microbial-immune crosstalk during this time thought to be involved in the pathobiology of later life diseases[1-9] such as persistent islet autoimmunity and type 1 diabetes[10-12]. However, to our knowledge, no studies have performed extensive characterization of the microbiome in early life in a large, multi-centre population. Here we analyse longitudinal stool samples from 903 children between 3 and 46 months of age by 16S rRNA gene sequencing (n = 12,005) and metagenomic sequencing (n = 10,867), as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We show that the developing gut microbiome undergoes three distinct phases of microbiome progression: a developmental phase (months 3-14), a transitional phase (months 15-30), and a stable phase (months 31-46). Receipt of breast milk, either exclusive or partial, was the most significant factor associated with the microbiome structure. Breastfeeding was associated with higher levels of Bifidobacterium species (B. breve and B. bifidum), and the cessation of breast milk resulted in faster maturation of the gut microbiome, as marked by the phylum Firmicutes. Birth mode was also significantly associated with the microbiome during the developmental phase, driven by higher levels of Bacteroides species (particularly B. fragilis) in infants delivered vaginally. Bacteroides was also associated with increased gut diversity and faster maturation, regardless of the birth mode. Environmental factors including geographical location and household exposures (such as siblings and furry pets) also represented important covariates. A nested case-control analysis revealed subtle associations between microbial taxonomy and the development of islet autoimmunity or type 1 diabetes. These data determine the structural and functional assembly of the microbiome in early life and provide a foundation for targeted mechanistic investigation into the consequences of microbial-immune crosstalk for long-term health.}, } @article {pmid30356183, year = {2018}, author = {Vatanen, T and Franzosa, EA and Schwager, R and Tripathi, S and Arthur, TD and Vehik, K and Lernmark, Å and Hagopian, WA and Rewers, MJ and She, JX and Toppari, J and Ziegler, AG and Akolkar, B and Krischer, JP and Stewart, CJ and Ajami, NJ and Petrosino, JF and Gevers, D and Lähdesmäki, H and Vlamakis, H and Huttenhower, C and Xavier, RJ}, title = {The human gut microbiome in early-onset type 1 diabetes from the TEDDY study.}, journal = {Nature}, volume = {562}, number = {7728}, pages = {589-594}, pmid = {30356183}, issn = {1476-4687}, support = {U01 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK063863/DK/NIDDK NIH HHS/United States ; UL1 TR002535/TR/NCATS NIH HHS/United States ; UL1 TR001427/TR/NCATS NIH HHS/United States ; U01 DK063790/DK/NIDDK NIH HHS/United States ; UL1 TR001082/TR/NCATS NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; UL1 TR000064/TR/NCATS NIH HHS/United States ; HHSN267200700014C/LM/NLM NIH HHS/United States ; U01 DK063836/DK/NIDDK NIH HHS/United States ; U01 DK063829/DK/NIDDK NIH HHS/United States ; U01 DK063865/DK/NIDDK NIH HHS/United States ; UC4 DK095300/DK/NIDDK NIH HHS/United States ; UC4 DK063861/DK/NIDDK NIH HHS/United States ; UC4 DK063829/DK/NIDDK NIH HHS/United States ; UC4 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK117483/DK/NIDDK NIH HHS/United States ; UC4 DK063836/DK/NIDDK NIH HHS/United States ; UC4 DK112243/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; U01 DK063861/DK/NIDDK NIH HHS/United States ; UC4 DK063865/DK/NIDDK NIH HHS/United States ; U01 DK063863/DK/NIDDK NIH HHS/United States ; UC4 DK106955/DK/NIDDK NIH HHS/United States ; UC4 DK100238/DK/NIDDK NIH HHS/United States ; }, mesh = {Age of Onset ; Animals ; Bifidobacterium/enzymology/genetics/isolation & purification ; Breast Feeding ; Child, Preschool ; Diabetes Mellitus, Type 1/*epidemiology/genetics/*microbiology/prevention & control ; Disease Models, Animal ; Fatty Acids, Volatile/pharmacology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/immunology/*physiology ; *Health Surveys ; Humans ; Infant ; Islets of Langerhans/immunology ; Longitudinal Studies ; Male ; Mice ; Milk, Human/immunology/microbiology ; Proteobacteria/enzymology/genetics/isolation & purification ; White People ; }, abstract = {Type 1 diabetes (T1D) is an autoimmune disease that targets pancreatic islet beta cells and incorporates genetic and environmental factors[1], including complex genetic elements[2], patient exposures[3] and the gut microbiome[4]. Viral infections[5] and broader gut dysbioses[6] have been identified as potential causes or contributing factors; however, human studies have not yet identified microbial compositional or functional triggers that are predictive of islet autoimmunity or T1D. Here we analyse 10,913 metagenomes in stool samples from 783 mostly white, non-Hispanic children. The samples were collected monthly from three months of age until the clinical end point (islet autoimmunity or T1D) in the The Environmental Determinants of Diabetes in the Young (TEDDY) study, to characterize the natural history of the early gut microbiome in connection to islet autoimmunity, T1D diagnosis, and other common early life events such as antibiotic treatments and probiotics. The microbiomes of control children contained more genes that were related to fermentation and the biosynthesis of short-chain fatty acids, but these were not consistently associated with particular taxa across geographically diverse clinical centres, suggesting that microbial factors associated with T1D are taxonomically diffuse but functionally more coherent. When we investigated the broader establishment and development of the infant microbiome, both taxonomic and functional profiles were dynamic and highly individualized, and dominated in the first year of life by one of three largely exclusive Bifidobacterium species (B. bifidum, B. breve or B. longum) or by the phylum Proteobacteria. In particular, the strain-specific carriage of genes for the utilization of human milk oligosaccharide within a subset of B. longum was present specifically in breast-fed infants. These analyses of TEDDY gut metagenomes provide, to our knowledge, the largest and most detailed longitudinal functional profile of the developing gut microbiome in relation to islet autoimmunity, T1D and other early childhood events. Together with existing evidence from human cohorts[7,8] and a T1D mouse model[9], these data support the protective effects of short-chain fatty acids in early-onset human T1D.}, } @article {pmid30356154, year = {2018}, author = {Solden, LM and Naas, AE and Roux, S and Daly, RA and Collins, WB and Nicora, CD and Purvine, SO and Hoyt, DW and Schückel, J and Jørgensen, B and Willats, W and Spalinger, DE and Firkins, JL and Lipton, MS and Sullivan, MB and Pope, PB and Wrighton, KC}, title = {Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem.}, journal = {Nature microbiology}, volume = {3}, number = {11}, pages = {1274-1284}, pmid = {30356154}, issn = {2058-5276}, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification/metabolism ; Carbon/*metabolism ; Host Microbial Interactions ; Metabolic Networks and Pathways ; Metagenomics ; *Microbial Consortia ; Phylogeny ; Proteomics ; *Rumen/metabolism/microbiology/virology ; Ruminants ; Viruses/classification/genetics/isolation & purification/metabolism ; Wood/metabolism ; }, abstract = {Because of their agricultural value, there is a great body of research dedicated to understanding the microorganisms responsible for rumen carbon degradation. However, we lack a holistic view of the microbial food web responsible for carbon processing in this ecosystem. Here, we sampled rumen-fistulated moose, allowing access to rumen microbial communities actively degrading woody plant biomass in real time. We resolved 1,193 viral contigs and 77 unique, near-complete microbial metagenome-assembled genomes, many of which lacked previous metabolic insights. Plant-derived metabolites were measured with NMR and carbohydrate microarrays to quantify the carbon nutrient landscape. Network analyses directly linked measured metabolites to expressed proteins from these unique metagenome-assembled genomes, revealing a genome-resolved three-tiered carbohydrate-fuelled trophic system. This provided a glimpse into microbial specialization into functional guilds defined by specific metabolites. To validate our proteomic inferences, the catalytic activity of a polysaccharide utilization locus from a highly connected metabolic hub genome was confirmed using heterologous gene expression. Viral detected proteins and linkages to microbial hosts demonstrated that phage are active controllers of rumen ecosystem function. Our findings elucidate the microbial and viral members, as well as their metabolic interdependencies, that support in situ carbon degradation in the rumen ecosystem.}, } @article {pmid30355340, year = {2018}, author = {Mailhe, M and Ricaboni, D and Vitton, V and Gonzalez, JM and Bachar, D and Dubourg, G and Cadoret, F and Robert, C and Delerce, J and Levasseur, A and Fournier, PE and Angelakis, E and Lagier, JC and Raoult, D}, title = {Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {157}, pmid = {30355340}, issn = {1471-2180}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/*classification/isolation & purification ; Colon/*microbiology ; Colonoscopy ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Endoscopy, Digestive System ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Hydrogen-Ion Concentration ; Male ; *Metagenomics ; Middle Aged ; Proton Pump Inhibitors/administration & dosage ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Stomach/*microbiology ; Young Adult ; }, abstract = {BACKGROUND: Most studies on the human microbiota have analyzed stool samples, although a large proportion of the absorption of nutrients takes place in upper gut tract. We collected samples from different locations along the entire gastrointestinal tract from six patients who had simultaneously undergone upper endoscopy and colonoscopy, to perform a comprehensive analysis using culturomics with matrix assisted laser desorption ionisation - time of flight (MALDI-TOF) identification and by metagenomics targeting the 16S ribosomal ribonucleic acid (rRNA) gene.

RESULTS: Using culturomics, we isolated 368 different bacterial species, including 37 new species. Fewer species were isolated in the upper gut: 110 in the stomach and 106 in the duodenum, while 235 were isolated from the left colon (p < 0.02). We isolated fewer aero-intolerant species in the upper gut: 37 from the stomach and 150 from the left colon (p < 0.004). Using metagenomics, 1,021 species were identified. The upper gut microbiota was revealed to be less rich than the lower gut microbiota, with 37,622 reads from the stomach, 28,390 from the duodenum, and 79,047 from the left colon (p < 0.009). There were fewer reads for aero-intolerant species in the upper gut (8,656 in the stomach, 5,188 in the duodenum and 72,262 in the left colon, p < 0.02). Patients taking proton pump inhibitors (PPI) were then revealed to have a higher stomach pH and a greater diversity of species in the upper digestive tract than patients not receiving treatment (p < 0.001).

CONCLUSION: Significant modifications in bacterial composition and diversity exist throughout the gastrointestinal tract. We suggest that the upper gut may be key to understanding the relationship between the gut microbiota and health.}, } @article {pmid30354816, year = {2018}, author = {Ganesh, BP and Nelson, JW and Eskew, JR and Ganesan, A and Ajami, NJ and Petrosino, JF and Bryan, RM and Durgan, DJ}, title = {Prebiotics, Probiotics, and Acetate Supplementation Prevent Hypertension in a Model of Obstructive Sleep Apnea.}, journal = {Hypertension (Dallas, Tex. : 1979)}, volume = {72}, number = {5}, pages = {1141-1150}, pmid = {30354816}, issn = {1524-4563}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 HL134838/HL/NHLBI NIH HHS/United States ; R01 NS080531/NS/NINDS NIH HHS/United States ; }, mesh = {Acetates/*therapeutic use ; Animals ; Blood Pressure/physiology ; Disease Models, Animal ; Gastrointestinal Microbiome/physiology ; Hypertension/complications/*prevention & control ; Male ; *Prebiotics ; *Probiotics ; Rats ; Rats, Long-Evans ; Sleep Apnea, Obstructive/*complications ; }, abstract = {Disruption of the gut microbiota, termed gut dysbiosis, has been described in animal models of hypertension and hypertensive patients. We have shown that gut dysbiosis plays a causal role in the development of hypertension in a rat model of obstructive sleep apnea (OSA). Functional analysis of the dysbiotic microbiota in OSA demonstrates a loss of short chain fatty acid-producing bacteria. However, measurements of short chain fatty acid concentrations and testing of their role in blood pressure regulation are lacking. We hypothesized that reduced short chain fatty acids in the gut are responsible for OSA-induced hypertension. OSA significantly increased systolic blood pressure at 7 and 14 days (P<0.05), an effect that was abolished by the probiotic Clostridium butyricum or the prebiotic Hylon VII. The 16S rRNA analysis identified several short chain fatty acid-producing bacteria that were significantly increased by Cbutyricum and Hylon treatment. Acetate concentration in the cecum was decreased by 48% after OSA (P<0.05), an effect that was prevented by Cbutyricum and Hylon. Cbutyricum and Hylon reduced OSA-induced dysbiosis, epithelial goblet cell loss, mucus barrier thinning, and activation of brain microglia (P<0.05 for each). To examine the role of acetate in OSA-induced hypertension, we chronically infused acetate into the cecum during 2 weeks of sham or OSA. Restoring cecal acetate concentration prevented OSA-induced gut inflammation and hypertension (P<0.05). These studies identify acetate as a key player in OSA-induced hypertension. We demonstrate that various methods to increase cecal acetate concentrations are protective from the adverse effects of OSA on the microbiota, gut, brain, and blood pressure.}, } @article {pmid30353943, year = {2018}, author = {Sonoda, A and Kamiyama, N and Ozaka, S and Gendo, Y and Ozaki, T and Hirose, H and Noguchi, K and Saechue, B and Sachi, N and Sakai, K and Mizukami, K and Hidano, S and Murakami, K and Kobayashi, T}, title = {Oral administration of antibiotics results in fecal occult bleeding due to metabolic disorders and defective proliferation of the gut epithelial cell in mice.}, journal = {Genes to cells : devoted to molecular & cellular mechanisms}, volume = {23}, number = {12}, pages = {1043-1055}, doi = {10.1111/gtc.12649}, pmid = {30353943}, issn = {1365-2443}, support = {//Suzuken Memorial Foundation/ ; 15K08953//Japan Society for the Promotion of Science/ ; 15K19577//Japan Society for the Promotion of Science/ ; 16K01872//Japan Society for the Promotion of Science/ ; 17H04649//Japan Society for the Promotion of Science/ ; 17H17104//Japan Society for the Promotion of Science/ ; 17K08695//Japan Society for the Promotion of Science/ ; 17K08889//Japan Society for the Promotion of Science/ ; 17K15954//Japan Society for the Promotion of Science/ ; 17K16346//Japan Society for the Promotion of Science/ ; //GlaxoSmithKline/ ; }, mesh = {Administration, Oral ; Ampicillin/administration & dosage/pharmacology ; Animals ; Anti-Bacterial Agents/*administration & dosage/*adverse effects ; Antimicrobial Cationic Peptides/metabolism ; Butyric Acid/pharmacology ; Carbohydrate Metabolism/drug effects ; Cecum/microbiology ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Colon/*pathology ; Colonic Neoplasms/pathology ; Cytokines/metabolism ; Epithelial Cells/*pathology ; Glutamine/administration & dosage ; Lipid Metabolism/drug effects ; Macrophages/drug effects/metabolism ; Metabolic Diseases/*complications ; Metabolome/drug effects ; Metagenomics ; Mice ; Microbiota/drug effects/genetics ; *Occult Blood ; RAW 264.7 Cells ; Regeneration/drug effects ; Sodium Glutamate/administration & dosage ; Species Specificity ; Vancomycin/administration & dosage/pharmacology ; }, abstract = {Antibiotics sometimes exert adverse effects on the pathogenesis of colitis due to the dysbiosis resulting from the disruption of gut homeostasis. However, the precise mechanisms underlying colitogenic effects of antibiotic-induced colitis are largely unknown. Here, we show a novel murine fecal occult bleeding model induced by the combinatorial treatment of ampicillin and vancomycin, which is accompanied by an enlarged cecum, upregulation of pro-inflammatory cytokines IL-6 and IL-12, a reduction in Ki-67-positive epithelial cell number and an increase in the apoptotic cell number in the colon. Moreover, gas chromatography-tandem mass analysis showed that various kinds of metabolites, including glutamic acid and butyric acid, were significantly decreased in the cecal contents. In addition, abundance of butyric acid producer Clostridiales was dramatically reduced in the enlarged cecum. Interestingly, supplementation of monosodium glutamate or its precursor glutamine suppressed colonic IL-6 and IL-12, protected from cell apoptosis and prevented fecal occult blood indicating that the reduced level of glutamic acid is a possible mechanism of antibiotic-induced fecal occult bleeding. Our data showed a novel mechanism of antibiotic-induced fecal occult bleeding providing a new insight into the clinical application of glutamic acid for the treatment of antibiotic-induced colitis.}, } @article {pmid30352611, year = {2018}, author = {Earl, JP and Adappa, ND and Krol, J and Bhat, AS and Balashov, S and Ehrlich, RL and Palmer, JN and Workman, AD and Blasetti, M and Sen, B and Hammond, J and Cohen, NA and Ehrlich, GD and Mell, JC}, title = {Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {190}, pmid = {30352611}, issn = {2049-2618}, support = {U01 DK082316/DK/NIDDK NIH HHS/United States ; R01 DC013588/DC/NIDCD NIH HHS/United States ; R01 DC002148/DC/NIDCD NIH HHS/United States ; }, mesh = {Bacteria/*classification/*genetics/isolation & purification ; Base Sequence ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Hypophysectomy ; Metagenome/genetics ; Microbiota/*genetics ; Molecular Typing/methods ; Paranasal Sinuses/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Pan-bacterial 16S rRNA microbiome surveys performed with massively parallel DNA sequencing technologies have transformed community microbiological studies. Current 16S profiling methods, however, fail to provide sufficient taxonomic resolution and accuracy to adequately perform species-level associative studies for specific conditions. This is due to the amplification and sequencing of only short 16S rRNA gene regions, typically providing for only family- or genus-level taxonomy. Moreover, sequencing errors often inflate the number of taxa present. Pacific Biosciences' (PacBio's) long-read technology in particular suffers from high error rates per base. Herein, we present a microbiome analysis pipeline that takes advantage of PacBio circular consensus sequencing (CCS) technology to sequence and error correct full-length bacterial 16S rRNA genes, which provides high-fidelity species-level microbiome data.

RESULTS: Analysis of a mock community with 20 bacterial species demonstrated 100% specificity and sensitivity with regard to taxonomic classification. Examination of a 250-plus species mock community demonstrated correct species-level classification of > 90% of taxa, and relative abundances were accurately captured. The majority of the remaining taxa were demonstrated to be multiply, incorrectly, or incompletely classified. Using this methodology, we examined the microgeographic variation present among the microbiomes of six sinonasal sites, by both swab and biopsy, from the anterior nasal cavity to the sphenoid sinus from 12 subjects undergoing trans-sphenoidal hypophysectomy. We found greater variation among subjects than among sites within a subject, although significant within-individual differences were also observed. Propiniobacterium acnes (recently renamed Cutibacterium acnes) was the predominant species throughout, but was found at distinct relative abundances by site.

CONCLUSIONS: Our microbial composition analysis pipeline for single-molecule real-time 16S rRNA gene sequencing (MCSMRT, https://github.com/jpearl01/mcsmrt) overcomes deficits of standard marker gene-based microbiome analyses by using CCS of entire 16S rRNA genes to provide increased taxonomic and phylogenetic resolution. Extensions of this approach to other marker genes could help refine taxonomic assignments of microbial species and improve reference databases, as well as strengthen the specificity of associations between microbial communities and dysbiotic states.}, } @article {pmid30350766, year = {2018}, author = {Bassene, H and Niang, EHA and Fenollar, F and Dipankar, B and Doucouré, S and Ali, E and Michelle, C and Raoult, D and Sokhna, C and Mediannikov, O}, title = {16S Metagenomic Comparison of Plasmodium falciparum-Infected and Noninfected Anopheles gambiae and Anopheles funestus Microbiota from Senegal.}, journal = {The American journal of tropical medicine and hygiene}, volume = {99}, number = {6}, pages = {1489-1498}, pmid = {30350766}, issn = {1476-1645}, mesh = {Actinobacteria/classification/*genetics/isolation & purification ; Animals ; Anopheles/*microbiology ; Disease Eradication/methods ; Firmicutes/classification/*genetics/isolation & purification ; Humans ; Malaria, Falciparum/epidemiology/parasitology/prevention & control/*transmission ; Metagenomics/methods ; Microbiota/genetics ; Mosquito Control/methods ; Mosquito Vectors/*microbiology ; Phylogeny ; Plasmodium falciparum/pathogenicity/physiology ; Principal Component Analysis ; Proteobacteria/classification/*genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics/isolation & purification ; Senegal/epidemiology ; }, abstract = {In the context of the pre-elimination of malaria, biological control may provide an alternative or additional tool to current malaria control strategies. During their various stages of development, mosquitoes undergo subsequent changes in their associated microbiota, depending on their environment and nutritional status. Although Anopheles gambiae s.l. and Anopheles funestus are the two major malaria vectors in Senegal, the composition of their microbiota is not yet well known. In this study, we explored the microbiota of mosquitoes naturally infected or not by Plasmodium falciparum (Pf) using the 16S ribosomal RNA gene-based bacterial metagenomic approach. In both vector species, the microbiota was more diverse in Pf-infected samples than in the noninfected ones, although the total number of reads appeared to be higher in noninfected mosquitoes. Overall, the microbiota was different between the two vector species. Noteworthy, the bacterial microbiota was significantly different between Pf-positive and Pf-negative groups whatever the species, but was similar between individuals of the same infection status within a species. Overall, the phylum of Proteobacteria was the most predominant in both species, with bacteria of the genus Burkholderia outweighing the others in noninfected vectors. The presence of some specific bacterial species such as Asaia bogorensis, Enterobacter cloacae, Burkholderia fungorum, and Burkholderia cepacia was also observed in Pf-free samples only. These preliminary observations pave the way for further characterization of the mosquito microbiota to select promising bacterial candidates for potential use in an innovative approach to controlling malaria and overcoming the challenges to achieving a malaria-free world.}, } @article {pmid30349083, year = {2018}, author = {Palleja, A and Mikkelsen, KH and Forslund, SK and Kashani, A and Allin, KH and Nielsen, T and Hansen, TH and Liang, S and Feng, Q and Zhang, C and Pyl, PT and Coelho, LP and Yang, H and Wang, J and Typas, A and Nielsen, MF and Nielsen, HB and Bork, P and Wang, J and Vilsbøll, T and Hansen, T and Knop, FK and Arumugam, M and Pedersen, O}, title = {Recovery of gut microbiota of healthy adults following antibiotic exposure.}, journal = {Nature microbiology}, volume = {3}, number = {11}, pages = {1255-1265}, doi = {10.1038/s41564-018-0257-9}, pmid = {30349083}, issn = {2058-5276}, mesh = {Adolescent ; Adult ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/drug effects/genetics/isolation & purification ; *Bacterial Physiological Phenomena ; Biodiversity ; Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/*physiology ; Genes, Bacterial ; Healthy Volunteers ; Humans ; Male ; Metagenomics ; Virulence Factors/genetics ; Young Adult ; }, abstract = {To minimize the impact of antibiotics, gut microorganisms harbour and exchange antibiotics resistance genes, collectively called their resistome. Using shotgun sequencing-based metagenomics, we analysed the partial eradication and subsequent regrowth of the gut microbiota in 12 healthy men over a 6-month period following a 4-day intervention with a cocktail of 3 last-resort antibiotics: meropenem, gentamicin and vancomycin. Initial changes included blooms of enterobacteria and other pathobionts, such as Enterococcus faecalis and Fusobacterium nucleatum, and the depletion of Bifidobacterium species and butyrate producers. The gut microbiota of the subjects recovered to near-baseline composition within 1.5 months, although 9 common species, which were present in all subjects before the treatment, remained undetectable in most of the subjects after 180 days. Species that harbour β-lactam resistance genes were positively selected for during and after the intervention. Harbouring glycopeptide or aminoglycoside resistance genes increased the odds of de novo colonization, however, the former also decreased the odds of survival. Compositional changes under antibiotic intervention in vivo matched results from in vitro susceptibility tests. Despite a mild yet long-lasting imprint following antibiotics exposure, the gut microbiota of healthy young adults are resilient to a short-term broad-spectrum antibiotics intervention and their antibiotics resistance gene carriage modulates their recovery processes.}, } @article {pmid30348104, year = {2018}, author = {Roy, A and Sar, P and Sarkar, J and Dutta, A and Sarkar, P and Gupta, A and Mohapatra, B and Pal, S and Kazy, SK}, title = {Petroleum hydrocarbon rich oil refinery sludge of North-East India harbours anaerobic, fermentative, sulfate-reducing, syntrophic and methanogenic microbial populations.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {151}, pmid = {30348104}, issn = {1471-2180}, mesh = {Archaea/classification/isolation & purification ; Bacteria, Anaerobic/*classification/isolation & purification ; Biodegradation, Environmental ; Fermentation ; Hydrocarbons/*metabolism ; India ; Methane/*biosynthesis ; Microbial Consortia ; Petroleum/*metabolism/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Sulfur-Reducing Bacteria/*classification/isolation & purification ; }, abstract = {BACKGROUND: Sustainable management of voluminous and hazardous oily sludge produced by petroleum refineries remains a challenging problem worldwide. Characterization of microbial communities of petroleum contaminated sites has been considered as the essential prerequisite for implementation of suitable bioremediation strategies. Three petroleum refinery sludge samples from North Eastern India were analyzed using next-generation sequencing technology to explore the diversity and functional potential of inhabitant microorganisms and scope for their on-site bioremediation.

RESULTS: All sludge samples were hydrocarbon rich, anaerobic and reduced with sulfate as major anion and several heavy metals. High throughput sequencing of V3-16S rRNA genes from sludge metagenomes revealed dominance of strictly anaerobic, fermentative, thermophilic, sulfate-reducing bacteria affiliated to Coprothermobacter, Fervidobacterium, Treponema, Syntrophus, Thermodesulfovibrio, Anaerolinea, Syntrophobacter, Anaerostipes, Anaerobaculum, etc., which have been well known for hydrocarbon degradation. Relatively higher proportions of archaea were detected by qPCR. Archaeal 16S rRNA gene sequences showed presence of methanogenic Methanobacterium, Methanosaeta, Thermoplasmatales, etc. Detection of known hydrocarbon utilizing aerobic/facultative anaerobic (Mycobacterium, Pseudomonas, Longilinea, Geobacter, etc.), nitrate reducing (Gordonia, Novosphigobium, etc.) and nitrogen fixing (Azovibrio, Rhodobacter, etc.) bacteria suggested niche specific guilds with aerobic, facultative anaerobic and strict anaerobic populations. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predicted putative genetic repertoire of sludge microbiomes and their potential for hydrocarbon degradation; lipid-, nitrogen-, sulfur- and methane- metabolism. Methyl coenzyme M reductase A (mcrA) and dissimilatory sulfite reductase beta-subunit (dsrB) genes phylogeny confirmed methanogenic and sulfate-reducing activities within sludge environment endowed by hydrogenotrophic methanogens and sulfate-reducing Deltaproteobacteria and Firmicutes members.

CONCLUSION: Refinery sludge microbiomes were comprised of hydrocarbon degrading, fermentative, sulfate-reducing, syntrophic, nitrogen fixing and methanogenic microorganisms, which were in accordance with the prevailing physicochemical nature of the samples. Analysis of functional biomarker genes ascertained the activities of methanogenic and sulfate-reducing organisms within sludge environment. Overall data provided better insights on microbial diversity and activity in oil contaminated environment, which could be exploited suitably for in situ bioremediation of refinery sludge.}, } @article {pmid30346157, year = {2018}, author = {Sun, W and Xiao, E and Häggblom, M and Krumins, V and Dong, Y and Sun, X and Li, F and Wang, Q and Li, B and Yan, B}, title = {Bacterial Survival Strategies in an Alkaline Tailing Site and the Physiological Mechanisms of Dominant Phylotypes As Revealed by Metagenomic Analyses.}, journal = {Environmental science & technology}, volume = {52}, number = {22}, pages = {13370-13380}, doi = {10.1021/acs.est.8b03853}, pmid = {30346157}, issn = {1520-5851}, mesh = {*Bacteria ; Biodegradation, Environmental ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {Microorganisms inhabiting mine tailings require specific metabolic strategies to survive, which may hold potential for pollution clean up. Effective in situ bioremediation will rely on an in-depth understanding of the function of the bacterial communities, especially the abundant and metabolically active phylotypes. In this study, the bacterial communities collected from an alkaline tailing site were profiled by 16S rRNA gene amplicon sequencing as well as shotgun metagenomic analysis. Our results indicated that potentials for carbon and nitrogen fixation as well as metal resistance and transformation were widespread among the bacterial community members, especially in highly enriched phylotypes, such as members of Thiobacillus and Meiothermus. Important functional microbial guilds including carbon and nitrogen fixers may contribute to phytoremediation by providing nutrients for hyperaccumulator plants. In addition, metal-metabolizing bacteria may influence metal speciation and solubility. This discovery provides an understanding for microbial survival strategies in the tailings and lays the foundation for future potential manipulation of the tailing microbiome for in situ bioremediation.}, } @article {pmid30346155, year = {2018}, author = {Pérez-Burillo, S and Pastoriza, S and Jiménez-Hernández, N and D'Auria, G and Francino, MP and Rufián-Henares, JA}, title = {Effect of Food Thermal Processing on the Composition of the Gut Microbiota.}, journal = {Journal of agricultural and food chemistry}, volume = {66}, number = {43}, pages = {11500-11509}, doi = {10.1021/acs.jafc.8b04077}, pmid = {30346155}, issn = {1520-5118}, mesh = {Bacteria/classification ; *Cooking ; Edible Grain ; Fabaceae ; Fatty Acids, Volatile/analysis ; Fermentation ; Fruit ; Furaldehyde/analogs & derivatives/analysis ; *Gastrointestinal Microbiome ; *Hot Temperature ; Humans ; Lysine/analogs & derivatives/analysis ; Maillard Reaction ; Meat ; RNA, Ribosomal, 16S/genetics ; Vegetables ; }, abstract = {Cooking modifies food composition due to chemical reactions. Additionally, food composition shapes the human gut microbiota. Thus, the objective of this research was to unravel the effect of different food cooking methods on the structure and functionality of the gut microbiota. Common culinary techniques were applied to five foods, which were submitted to in vitro digestion-fermentation. Furosine, 5-(hydroxymethyl)furfural, and furfural were used as Maillard reaction indicators to control the heat treatment. Short-chain fatty acids production was quantified as indicator of healthy metabolic output. Gut microbial community structure was analyzed through 16S rRNA. Both food composition and cooking methods modified the microbiota composition and released short-chain fatty acids. In general, intense cooking technologies (roasting and grilling) increased the abundance of beneficial bacteria like Ruminococcus spp. or Bifidobacterium spp. compared to milder treatments (boiling). However, for some foods (banana or bread), intense cooking decreased the levels of healthy bacteria.}, } @article {pmid30346069, year = {2019}, author = {Suzuki, TA and Martins, FM and Nachman, MW}, title = {Altitudinal variation of the gut microbiota in wild house mice.}, journal = {Molecular ecology}, volume = {28}, number = {9}, pages = {2378-2390}, pmid = {30346069}, issn = {1365-294X}, support = {R01 GM074245/GM/NIGMS NIH HHS/United States ; R01 GM127468/GM/NIGMS NIH HHS/United States ; }, mesh = {Altitude ; Animals ; Blood Pressure ; Body Mass Index ; Bolivia ; Ecuador ; Gastrointestinal Microbiome/genetics/*physiology ; Metagenome ; Mice/*microbiology ; Oxygen ; Prevotella ; RNA, Ribosomal, 16S ; }, abstract = {The maintenance of oxygen homeostasis in the gut is critical for the maintenance of a healthy gut microbiota. However, few studies have explored how the concentration of atmospheric oxygen affects the gut microbiota in natural populations. High-altitude environments provide an opportunity to study the potential effects of atmospheric oxygen on the composition and function of the gut microbiota. Here, we characterized the caecal microbial communities of wild house mice (Mus musculus domesticus) in two independent altitudinal transects, one in Ecuador and one in Bolivia, from sea level to nearly 4,000 m. First, we found that differences in altitude were associated with differences in the gut microbial community after controlling for the effects of body mass, diet, reproductive status and population of origin. Second, obligate anaerobes tended to show a positive correlation with altitude, while all other microbes tended to show a negative correlation with altitude. These patterns were seen independently in both transects, consistent with the expected effects of atmospheric oxygen on gut microbes. Prevotella was the most-enriched genus at high elevations in both transects, consistent with observations in high-altitude populations of pikas, ruminants and humans, and also consistent with observations of laboratory mice exposed to hypoxic conditions. Lastly, the renin-angiotensin system, a recently proposed microbiota-mediated pathway of blood pressure regulation, was the top predicted metagenomic pathway enriched in high altitudes in both transects. These results suggest that high-altitude environments affect the composition and function of the gut microbiota in wild mammals.}, } @article {pmid30342721, year = {2018}, author = {Free, A and McDonald, MA and Pagaling, E}, title = {Diversity-Function Relationships in Natural, Applied, and Engineered Microbial Ecosystems.}, journal = {Advances in applied microbiology}, volume = {105}, number = {}, pages = {131-189}, doi = {10.1016/bs.aambs.2018.07.002}, pmid = {30342721}, issn = {0065-2164}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Ecosystem ; Industrial Microbiology/*methods/trends ; *Metabolism ; *Microbial Consortia ; }, abstract = {The connection between ecosystem function and taxonomic diversity has been of interest and relevance to macroecologists for decades. After many years of lagging behind due to the difficulty of assigning both taxonomy and function to poorly distinguishable microscopic cells, microbial ecology now has access to a suite of powerful molecular tools which allow its practitioners to generate data relating to diversity and function of a microbial community on an unprecedented scale. Instead, the problem facing today's microbial ecologists is coupling the ease of generation of these datasets with the formulation and testing of workable hypotheses relating the diversity and function of environmental, host-associated, and engineered microbial communities. Here, we review the current state of knowledge regarding the links between taxonomic alpha- and beta-diversity and ecosystem function, comparing our knowledge in this area to that obtained by macroecologists who use more traditional techniques. We consider the methodologies that can be applied to study these properties and how successful they are at linking function to diversity, using examples from the study of model microbial ecosystems, methanogenic bioreactors (anaerobic digesters), and host-associated microbiota. Finally, we assess ways in which our newly acquired understanding might be used to manipulate diversity in ecosystems of interest in order to improve function for the benefit of us or the environment in general through the provision of ecosystem services.}, } @article {pmid30342317, year = {2019}, author = {Zhou, S and Wang, Z and He, F and Qiu, H and Wang, Y and Wang, H and Zhou, J and Zhou, J and Cheng, G and Zhou, W and Xu, R and Wang, M}, title = {Association of serum bilirubin in newborns affected by jaundice with gut microbiota dysbiosis.}, journal = {The Journal of nutritional biochemistry}, volume = {63}, number = {}, pages = {54-61}, doi = {10.1016/j.jnutbio.2018.09.016}, pmid = {30342317}, issn = {1873-4847}, mesh = {Bifidobacterium/genetics ; Bilirubin/*blood ; Breast Feeding ; Case-Control Studies ; Child, Preschool ; Cholestasis/blood/microbiology ; Dysbiosis/*blood/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Infant, Newborn ; Jaundice, Neonatal/*blood/microbiology ; Male ; }, abstract = {BACKGROUND AND AIMS: Breast milk jaundice (BMJ) is common and benign, but neonatal cholestasis (NC) is rare and not benign, so early differentiation between NC and non-NC jaundice is important and may facilitate diagnosis and treatment. Gut microbiota plays an important role in enterohepatic circulation, which in turn plays an important role in the secretion of bilirubin. We aimed to determine the composition of gut microbiota in patients with NC and BMJ, and to identify the gut microbiota composition associated with NC and BMJ.

METHODS: Data on age, gender, delivery, feeding mode, serum total bilirubin, direct bilirubin, and liver function were collected for NC patients, BMJ patients and healthy controls, respectively. Shotgun metagenomic sequencing and metagenome-wide association were performed.

RESULTS: Forty NC patients, 16 patients affected by BMJ, and 14 healthy controls (CON) without jaundice were enrolled. A significant increase in species richness, especially Bacteroides, was found in NC patients. The abundances of potentially pathogenic species and KEGG orthologies (KOs) of virulence factor genes were positively correlated with serum bilirubin level. The abundances of nine species of Bifidobacterium and three KOs of galactose metabolism were significantly decreased in the jaundice group (NC and BMJ) and were negatively correlated with serum bilirubin level.

CONCLUSIONS: The gut microbiota in NC patients is characterized by a significant increase in species richness, possibly due to the proliferation of potentially pathogenic species. Additionally, the gut microbiota in jaundice patients is characterized by a decreased abundance of Bifidobacterium. Decreased Bifidobacterium has been associated with elevated bilirubin and abnormal gut microbiota galactose metabolic pathway. Further, ten bacteria species were identified as potential biomarker of jaundice.

KEY POINTS: Question Is there any alteration of gut microbiotain neonatal cholestasis patients? Does gut microbiota have any involvement in the occurrence of neonatal cholestasis or breast milk jaundice? Findings The alteration of gut microbiota in neonatal cholestasis patients mainly manifested as a significant increase in species richness and an increased abundance of potentially pathogenic species, while the main manifestation in jaundice patients was a significant decrease in Bifidobacterium which may be involved in the metabolism of bilirubin through the galactose metabolic pathway. Meaning The results suggest that an imbalance of gut microbiota exist in neonatal cholestasis and breast milk jaundice patients, primarily in the form of a substantial reduction in the abundance of Bifidobacterium, suggesting the possibility of intervention treatment for neonatal cholestasis and breast milk jaundice by supplementing probiotics.}, } @article {pmid30342083, year = {2018}, author = {De Mol, ML and Snoeck, N and De Maeseneire, SL and Soetaert, WK}, title = {Hidden antibiotics: Where to uncover?.}, journal = {Biotechnology advances}, volume = {36}, number = {8}, pages = {2201-2218}, doi = {10.1016/j.biotechadv.2018.10.008}, pmid = {30342083}, issn = {1873-1899}, mesh = {Animals ; *Anti-Bacterial Agents/isolation & purification/pharmacology ; Bacteria/chemistry/drug effects/genetics ; *Drug Discovery ; Gastrointestinal Microbiome/genetics ; Humans ; *Metagenomics ; Mice ; *Synthetic Biology ; }, abstract = {The struggle of humans versus pathogens is a never ending battle. Since the discovery of antibiotics humans have tipped the scales in their favour, but today bacteria are nullifying this advantage by developing resistance mechanisms against these molecules. The plethora of different antibiotics active against pathogens is shrinking while the discovery of new molecules is arduous. Especially the development of drugs active against Gram[-] pathogens continues slowly. New strategies to discover novel, potent antibiotics are hence needed. Adopting the optimistic view of technological singularity, innovative and disruptive approaches are required and hence proposed to lift the current conundrum. In this review, questions are answered on where and how to look for new natural product hit molecules with antibacterial activity, on how the field of synthetic biology can aid the contemporary pharmaceutical challenge and whether we are ready to make the transition towards other approaches, such as narrow-spectrum antibiotics and phage therapy.}, } @article {pmid30342053, year = {2018}, author = {Vallianou, NG and Stratigou, T and Tsagarakis, S}, title = {Microbiome and diabetes: Where are we now?.}, journal = {Diabetes research and clinical practice}, volume = {146}, number = {}, pages = {111-118}, doi = {10.1016/j.diabres.2018.10.008}, pmid = {30342053}, issn = {1872-8227}, mesh = {Animals ; Diabetes Mellitus, Type 2/*microbiology ; Dysbiosis/*microbiology ; Fecal Microbiota Transplantation/*methods ; Gastrointestinal Microbiome/*genetics ; Humans ; Mice ; Prebiotics/*microbiology ; Probiotics/*metabolism ; }, abstract = {Alterations in the diversity or structure of gut microbiota known as dysbiosis, may affect metabolic activities, resulting in metabolic disorders, such as obesity and diabetes. The development of more sophisticated methods, such as metagenomics sequencing, PCR-denaturing gradient gel electrophoresis, microarrays and fluorescence in situ hybridization, has expanded our knowledge on gut microbiome. Dysbiosis has been related to increased plasma concentrations of gut microbiota-derived lipopolysaccharide (LPS), which triggers the production of a variety of cytokines and the recruitment of inflammatory cells. Metabolomics have demonstrated that butyrate and propionate suppress weight gain in mice with high fat diet-induced obesity, and acetate has been proven to reduce food intake in healthy mice. The role of prebiotics, probiotics, genetically modified bacteria and fecal microbiota transplantation, as potential therapeutic challenges for type 2 diabetes will be discussed in this review.}, } @article {pmid30340631, year = {2018}, author = {Li, HY and Wang, H and Wang, HT and Xin, PY and Xu, XH and Ma, Y and Liu, WP and Teng, CY and Jiang, CL and Lou, LP and Arnold, W and Cralle, L and Zhu, YG and Chu, JF and Gilbert, JA and Zhang, ZJ}, title = {The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {187}, pmid = {30340631}, issn = {2049-2618}, mesh = {Bacteria/*classification/genetics/isolation & purification/*metabolism ; Carbon Cycle ; Fresh Water/*chemistry/*microbiology ; Geography ; Mass Spectrometry ; Metagenome/genetics ; Microbiota/*genetics ; Organic Chemicals/*analysis ; Oryza/*microbiology ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {BACKGROUND: Paddy soil dissolved organic matter (DOM) represents a major hotspot for soil biogeochemistry, yet we know little about its chemodiversity let alone the microbial community that shapes it. Here, we leveraged ultrahigh-resolution mass spectrometry, amplicon, and metagenomic sequencing to characterize the molecular distribution of DOM and the taxonomic and functional microbial diversity in paddy soils across China. We hypothesized that variances in microbial community significantly associate with changes in soil DOM molecular composition.

RESULTS: We report that both microbial and DOM profiles revealed geographic patterns that were associated with variation in mean monthly precipitation, mean annual temperature, and pH. DOM molecular diversity was significantly correlated with microbial taxonomic diversity. An increase in DOM molecules categorized as peptides, carbohydrates, and unsaturated aliphatics, and a decrease in those belonging to polyphenolics and polycyclic aromatics, significantly correlated with proportional changes in some of the microbial taxa, such as Syntrophobacterales, Thermoleophilia, Geobacter, Spirochaeta, Gaiella, and Defluviicoccus. DOM composition was also associated with the relative abundances of the microbial metabolic pathways, such as anaerobic carbon fixation, glycolysis, lignolysis, fermentation, and methanogenesis.

CONCLUSIONS: Our study demonstrates the continental-scale distribution of DOM is significantly correlated with the taxonomic profile and metabolic potential of the rice paddy microbiome. Abiotic factors that have a distinct effect on community structure can also influence the chemodiversity of DOM and vice versa. Deciphering these associations and the underlying mechanisms can precipitate understanding of the complex ecology of paddy soils, as well as help assess the effects of human activities on biogeochemistry and greenhouse gas emissions in paddy soils.}, } @article {pmid30338752, year = {2018}, author = {Abranches, J and Zeng, L and Kajfasz, JK and Palmer, SR and Chakraborty, B and Wen, ZT and Richards, VP and Brady, LJ and Lemos, JA}, title = {Biology of Oral Streptococci.}, journal = {Microbiology spectrum}, volume = {6}, number = {5}, pages = {}, pmid = {30338752}, issn = {2165-0497}, support = {R56 DE021789/DE/NIDCR NIH HHS/United States ; R01 DE012236/DE/NIDCR NIH HHS/United States ; R01 DE021789/DE/NIDCR NIH HHS/United States ; HHSN272200900007C/AI/NIAID NIH HHS/United States ; R01 DE019783/DE/NIDCR NIH HHS/United States ; R01 DE019452/DE/NIDCR NIH HHS/United States ; R21 DE025348/DE/NIDCR NIH HHS/United States ; R01 DE022559/DE/NIDCR NIH HHS/United States ; R01 DE008007/DE/NIDCR NIH HHS/United States ; }, mesh = {Carbohydrate Metabolism ; Dental Caries/microbiology ; Endocarditis/microbiology ; Fermentation ; Humans ; Hydrogen Peroxide/metabolism ; Metagenomics ; Microbiota/physiology ; Mouth/*microbiology ; Phylogeny ; Streptococcus/classification/genetics/pathogenicity/*physiology ; Streptococcus gordonii/metabolism ; Streptococcus mutans ; Streptococcus salivarius/metabolism ; }, abstract = {Bacteria belonging to the genus Streptococcus are the first inhabitants of the oral cavity, which can be acquired right after birth and thus play an important role in the assembly of the oral microbiota. In this article, we discuss the different oral environments inhabited by streptococci and the species that occupy each niche. Special attention is given to the taxonomy of Streptococcus, because this genus is now divided into eight distinct groups, and oral species are found in six of them. Oral streptococci produce an arsenal of adhesive molecules that allow them to efficiently colonize different tissues in the mouth. Also, they have a remarkable ability to metabolize carbohydrates via fermentation, thereby generating acids as byproducts. Excessive acidification of the oral environment by aciduric species such as Streptococcus mutans is directly associated with the development of dental caries. However, less acid-tolerant species such as Streptococcus salivarius and Streptococcus gordonii produce large amounts of alkali, displaying an important role in the acid-base physiology of the oral cavity. Another important characteristic of certain oral streptococci is their ability to generate hydrogen peroxide that can inhibit the growth of S. mutans. Thus, oral streptococci can also be beneficial to the host by producing molecules that are inhibitory to pathogenic species. Lastly, commensal and pathogenic streptococci residing in the oral cavity can eventually gain access to the bloodstream and cause systemic infections such as infective endocarditis.}, } @article {pmid30338244, year = {2018}, author = {Saxena, R and Mittal, P and Clavaud, C and Dhakan, DB and Hegde, P and Veeranagaiah, MM and Saha, S and Souverain, L and Roy, N and Breton, L and Misra, N and Sharma, VK}, title = {Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {346}, pmid = {30338244}, issn = {2235-2988}, mesh = {Adult ; Bacteria/classification/*isolation & purification ; Dandruff/*microbiology ; Female ; Fungi/classification/*isolation & purification ; Humans ; India ; Metabolic Networks and Pathways/genetics ; Metagenomics ; *Microbiota ; Scalp/*microbiology ; *Symbiosis ; Young Adult ; }, abstract = {Several scalp microbiome studies from different populations have revealed the association of dandruff with bacterial and fungal dysbiosis. However, the functional role of scalp microbiota in scalp disorders and health remains scarcely explored. Here, we examined the bacterial and fungal diversity of the scalp microbiome and their potential functional role in the healthy and dandruff scalp of 140 Indian women. Propionibacterium acnes and Staphylococcus epidermidis emerged as the core bacterial species, where the former was associated with a healthy scalp and the latter with dandruff scalp. Along with the commonly occurring Malassezia species (M. restricta and M. globosa) on the scalp, a strikingly high association of dandruff with yet uncharacterized Malassezia species was observed in the core mycobiome. Functional analysis showed that the fungal microbiome was enriched in pathways majorly implicated in cell-host adhesion in the dandruff scalp, while the bacterial microbiome showed a conspicuous enrichment of pathways related to the synthesis and metabolism of amino acids, biotin, and other B-vitamins, which are reported as essential nutrients for hair growth. A systematic measurement of scalp clinical and physiological parameters was also carried out, which showed significant correlations with the microbiome and their associated functional pathways. The results point toward a new potential role of bacterial commensals in maintaining the scalp nutrient homoeostasis and highlights an important and yet unknown role of the scalp microbiome, similar to the gut microbiome. This study, therefore, provides new perspectives on the better understanding of the pathophysiology of dandruff.}, } @article {pmid30337568, year = {2018}, author = {Ma, Y and Wang, W and Zhang, H and Wang, J and Zhang, W and Gao, J and Wu, S and Qi, G}, title = {Supplemental Bacillus subtilis DSM 32315 manipulates intestinal structure and microbial composition in broiler chickens.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {15358}, pmid = {30337568}, issn = {2045-2322}, mesh = {Animal Feed ; Animals ; Bacillus subtilis/*physiology ; Body Weight ; Cecum/*microbiology ; Chickens/*growth & development/microbiology/physiology ; Dietary Supplements/analysis ; Gastrointestinal Microbiome/*drug effects ; Intestines/*chemistry/*microbiology ; Male ; Probiotics/*administration & dosage ; }, abstract = {Knowledge about the modulation of gut microbiota improves our understanding of the underlying mechanism by which probiotic treatment benefits the chickens. This study examined the effects of Bacillus subtilis DSM 32315 on intestinal structure and microbial composition in broilers. Broiler chicks were fed basal diets without or with B. subtilis supplementation (1.0 × 10[9] spores/kg of diet). Supplemental B. subtilis increased average body weight and average daily gain, as well as elevated villus height and villus height to crypt depth ratio of ileum in broilers. Multi-dimension analysis showed a certain degree of separation between the cecal microbiota from treatment and control groups. Increased Firmicutes abundance and reduced Bacteroidetes abundance in cecum were observed responded to B. subtilis addition, which also increased the abundances of Christensenellaceae and Caulobacteraceae, and simultaneously decreased the abundances of potentially harmful bacteria such as Vampirovibrio, Escherichia/Shigella and Parabacteroides. Network analysis signified that B. subtilis addition improved the interaction pattern within cecal microbiota of broilers, however, it exerted little influence on the metabolic pathways of cecal microbiota by comparison of the functional prediction of metagenomes. In conclusion, supplemental B. subtilis DSM 32315 improved growth performance and intestinal structure of broilers, which could be at least partially responsible by the manipulation of cecal microbial composition.}, } @article {pmid30336790, year = {2018}, author = {Liu, YR and Delgado-Baquerizo, M and Bi, L and Zhu, J and He, JZ}, title = {Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {183}, pmid = {30336790}, issn = {2049-2618}, mesh = {Bacteroidetes/classification/genetics/*growth & development ; Biodiversity ; China ; Environmental Monitoring ; Environmental Pollution/*analysis ; Firmicutes/classification/genetics/*growth & development ; Mercury/*analysis ; Metagenome/genetics ; Methylmercury Compounds/*analysis ; Microbiota/genetics ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/*analysis ; }, abstract = {BACKGROUND: The ecological consequences of mercury (Hg) pollution-one of the major pollutants worldwide-on microbial taxonomic and functional attributes remain poorly understood and largely unexplored. Using soils from two typical Hg-impacted regions across China, here, we evaluated the role of Hg pollution in regulating bacterial abundance, diversity, and co-occurrence network. We also investigated the associations between Hg contents and the relative abundance of microbial functional genes by analyzing the soil metagenomes from a subset of those sites.

RESULTS: We found that soil Hg largely influenced the taxonomic and functional attributes of microbial communities in the two studied regions. In general, Hg pollution was negatively related to bacterial abundance, but positively related to the diversity of bacteria in two separate regions. We also found some consistent associations between soil Hg contents and the community composition of bacteria. For example, soil total Hg content was positively related to the relative abundance of Firmicutes and Bacteroidetes in both paddy and upland soils. In contrast, the methylmercury (MeHg) concentration was negatively correlated to the relative abundance of Nitrospirae in the two types of soils. Increases in soil Hg pollution correlated with drastic changes in the relative abundance of ecological clusters within the co-occurrence network of bacterial communities for the two regions. Using metagenomic data, we were also able to detect the effect of Hg pollution on multiple functional genes relevant to key soil processes such as element cycles and Hg transformations (e.g., methylation and reduction).

CONCLUSIONS: Together, our study provides solid evidence that Hg pollution has predictable and significant effects on multiple taxonomic and functional attributes including bacterial abundance, diversity, and the relative abundance of ecological clusters and functional genes. Our results suggest an increase in soil Hg pollution linked to human activities will lead to predictable shifts in the taxonomic and functional attributes in the Hg-impacted areas, with potential implications for sustainable management of agricultural ecosystems and elsewhere.}, } @article {pmid30336176, year = {2019}, author = {Brusaferro, A and Cavalli, E and Farinelli, E and Cozzali, R and Principi, N and Esposito, S}, title = {Gut dysbiosis and paediatric Crohn's disease.}, journal = {The Journal of infection}, volume = {78}, number = {1}, pages = {1-7}, doi = {10.1016/j.jinf.2018.10.005}, pmid = {30336176}, issn = {1532-2742}, mesh = {Autophagy ; Child ; Crohn Disease/*microbiology/physiopathology/therapy ; *Dysbiosis ; Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenomics ; Probiotics/therapeutic use ; }, abstract = {OBJECTIVES: The main objective of this manuscript is to discuss our present knowledge of the relationships between dysbiosis and paediatric Crohn's disease (CD). The therapeutic role of the methods currently used to re-establish normal gut microbiota composition is also analysed.

METHODS: PubMed was used to search for all of the studies published from January 2008 to June 2018 using the key words: "Crohn's disease" and "gut dysbiosis" or "microbiota" or "microbioma" or "probiotic" and "children" or "paediatric". More than 100 articles were found, but only those published in English or providing evidence-based data were included in the evaluation.

RESULTS: Gut microbiota are primary actors in CD's pathogenesis. The new techniques developed in metagenomics allow us to reveal new details of microbiota composition in healthy subjects and CD patients, and to elucidate the link between microbiota and numerous pathologies, such as obesity, allergies and type 1 diabetes mellitus.

CONCLUSION: Discoveries on the role of gut microbiota could potentially disclose new therapeutic options for CD treatment and improve the existing therapies. Further studies are needed to facilitate the diagnosis and tailor the therapy of a pathology that is an increasing burden on public health.}, } @article {pmid30335986, year = {2018}, author = {Liu, YR and Johs, A and Bi, L and Lu, X and Hu, HW and Sun, D and He, JZ and Gu, B}, title = {Unraveling Microbial Communities Associated with Methylmercury Production in Paddy Soils.}, journal = {Environmental science & technology}, volume = {52}, number = {22}, pages = {13110-13118}, doi = {10.1021/acs.est.8b03052}, pmid = {30335986}, issn = {1520-5851}, mesh = {China ; Humans ; *Mercury ; *Methylmercury Compounds ; *Microbiota ; Phylogeny ; Soil ; }, abstract = {Rice consumption is now recognized as an important pathway of human exposure to the neurotoxin methylmercury (MeHg), particularly in countries where rice is a staple food. Although the discovery of a two-gene cluster hgcAB has linked Hg methylation to several phylogenetically diverse groups of anaerobic microorganisms converting inorganic mercury (Hg) to MeHg, the prevalence and diversity of Hg methylators in microbial communities of rice paddy soils remain unclear. We characterized the abundance and distribution of hgcAB genes using third-generation PacBio long-read sequencing and Illumina short-read metagenomic sequencing, in combination with quantitative PCR analyses in several mine-impacted paddy soils from southwest China. Both Illumina and PacBio sequencing analyses revealed that Hg methylating communities were dominated by iron-reducing bacteria (i.e., Geobacter) and methanogens, with a relatively low abundance of hgcA [+] sulfate-reducing bacteria in the soil. A positive correlation was observed between the MeHg content in soil and the relative abundance of Geobacter carrying the hgcA gene. Phylogenetic analysis also uncovered some hgcAB sequences closely related to three novel Hg methylators, Geobacter anodireducens, Desulfuromonas sp. DDH964, and Desulfovibrio sp. J2, among which G. anodireducens was validated for its ability to methylate Hg. These findings shed new light on microbial community composition and major clades likely driving Hg methylation in rice paddy soils.}, } @article {pmid30333180, year = {2018}, author = {Kato, T and Yamazaki, K and Nakajima, M and Date, Y and Kikuchi, J and Hase, K and Ohno, H and Yamazaki, K}, title = {Oral Administration of Porphyromonas gingivalis Alters the Gut Microbiome and Serum Metabolome.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, pmid = {30333180}, issn = {2379-5042}, mesh = {Administration, Oral ; Animals ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Intestines/*microbiology ; Male ; Metabolic Diseases/*microbiology ; Metabolome ; Mice ; Mice, Inbred C57BL ; Periodontal Diseases/*complications/*microbiology ; Porphyromonas gingivalis/*pathogenicity ; RNA, Ribosomal, 16S/genetics ; Serum/metabolism ; Statistics, Nonparametric ; }, abstract = {Periodontal disease induced by periodontopathic bacteria like Porphyromonas gingivalis is demonstrated to increase the risk of metabolic, inflammatory, and autoimmune disorders. Although precise mechanisms for this connection have not been elucidated, we have proposed mechanisms by which orally administered periodontopathic bacteria might induce changes in gut microbiota composition, barrier function, and immune system, resulting in an increased risk of diseases characterized by low-grade systemic inflammation. Accumulating evidence suggests a profound effect of altered gut metabolite profiles on overall host health. Therefore, it is possible that P. gingivalis can affect these metabolites. To test this, C57BL/6 mice were administered with P. gingivalis W83 orally twice a week for 5 weeks and compared with sham-inoculated mice. The gut microbial communities were analyzed by pyrosequencing the 16S rRNA genes. Inferred metagenomic analysis was used to determine the relative abundance of KEGG pathways encoded in the gut microbiota. Serum metabolites were analyzed using nuclear magnetic resonance (NMR)-based metabolomics coupled with multivariate statistical analyses. Oral administration of P. gingivalis induced a change in gut microbiota composition. The distributions of metabolic pathways differed between the two groups, including those related to amino acid metabolism and, in particular, the genes for phenylalanine, tyrosine, and tryptophan biosynthesis. Also, alanine, glutamine, histidine, tyrosine, and phenylalanine were significantly increased in the serum of P. gingivalis-administered mice. In addition to altering immune modulation and gut barrier function, oral administration of P. gingivalis affects the host's metabolic profile. This supports our hypothesis regarding a gut-mediated systemic pathology resulting from periodontal disease.IMPORTANCE Increasing evidence suggest that alterations of the gut microbiome underlie metabolic disease pathology by modulating gut metabolite profiles. We have shown that orally administered Porphyromonas gingivalis, a representative periodontopathic bacterium, alters the gut microbiome; that may be a novel mechanism by which periodontitis increases the risk of various diseases. Given the association between periodontal disease and metabolic diseases, it is possible that P. gingivalis can affect the metabolites. Metabolite profiling analysis demonstrated that several amino acids related to a risk of developing diabetes and obesity were elevated in P. gingivalis-administered mice. Our results revealed that the increased risk of various diseases by P. gingivalis might be mediated at least in part by alteration of metabolic profiles. The findings should add new insights into potential links between periodontal disease and systemic disease for investigators in periodontal disease and also for investigators in the field of other diseases, such as metabolic diseases.}, } @article {pmid30332487, year = {2018}, author = {Wyman, SK and Avila-Herrera, A and Nayfach, S and Pollard, KS}, title = {A most wanted list of conserved microbial protein families with no known domains.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0205749}, pmid = {30332487}, issn = {1932-6203}, mesh = {Bacterial Proteins/*chemistry/genetics ; Computational Biology ; *Databases, Nucleic Acid ; Humans ; Metagenome/*genetics ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; Protein Domains/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {The number and proportion of genes with no known function are growing rapidly. To quantify this phenomenon and provide criteria for prioritizing genes for functional characterization, we developed a bioinformatics pipeline that identifies robustly defined protein families with no annotated domains, ranks these with respect to phylogenetic breadth, and identifies them in metagenomics data. We applied this approach to 271 965 protein families from the SFams database and discovered many with no functional annotation, including >118 000 families lacking any known protein domain. From these, we prioritized 6 668 conserved protein families with at least three sequences from organisms in at least two distinct classes. These Function Unknown Families (FUnkFams) are present in Tara Oceans Expedition and Human Microbiome Project metagenomes, with distributions associated with sampling environment. Our findings highlight the extent of functional novelty in sequence databases and establish an approach for creating a "most wanted" list of genes to prioritize for further characterization.}, } @article {pmid30329017, year = {2019}, author = {Graspeuntner, S and Waschina, S and Künzel, S and Twisselmann, N and Rausch, TK and Cloppenborg-Schmidt, K and Zimmermann, J and Viemann, D and Herting, E and Göpel, W and Baines, JF and Kaleta, C and Rupp, J and Härtel, C and Pagel, J}, title = {Gut Dysbiosis With Bacilli Dominance and Accumulation of Fermentation Products Precedes Late-onset Sepsis in Preterm Infants.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {69}, number = {2}, pages = {268-277}, doi = {10.1093/cid/ciy882}, pmid = {30329017}, issn = {1537-6591}, mesh = {Anaerobiosis ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Dysbiosis/*complications ; Feces/chemistry/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; *Infant, Premature ; Male ; *Metabolome ; Metabolomics ; Metagenomics ; Neonatal Sepsis/*pathology ; Phylogeny ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Gut dysbiosis has been suggested as a major risk factor for the development of late-onset sepsis (LOS), a main cause of mortality and morbidity in preterm infants. We aimed to assess specific signatures of the gut microbiome, including metabolic profiles, in preterm infants <34 weeks of gestation preceding LOS.

METHODS: In a single-center cohort, fecal samples from preterm infants were prospectively collected during the period of highest vulnerability for LOS (days 7, 14, and 21 of life). Following 16S rRNA gene profiling, we assessed microbial community function using microbial metabolic network modeling. Data were adjusted for gestational age and use of probiotics.

RESULTS: We studied stool samples from 71 preterm infants with LOS and 164 unaffected controls (no LOS/necrotizing enterocolitis). In most cases, the bacteria isolated in diagnostic blood culture corresponded to the genera in the gut microbiome. LOS cases had a decelerated development of microbial diversity. Before onset of disease, LOS cases had specific gut microbiome signatures with higher abundance of Bacilli (specifically coagulase-negative Staphylococci) and a lack of anaerobic bacteria. In silico modeling of bacterial community metabolism suggested accumulation of the fermentation products ethanol and formic acid in LOS cases before the onset of disease.

CONCLUSIONS: Intestinal dysbiosis preceding LOS is characterized by an accumulation of Bacilli and their fermentation products and a paucity of anaerobic bacteria. Early microbiome and metabolic patterns may become a valuable biomarker to guide individualized prevention strategies of LOS in highly vulnerable populations.}, } @article {pmid30326954, year = {2018}, author = {Korpela, K and Salonen, A and Vepsäläinen, O and Suomalainen, M and Kolmeder, C and Varjosalo, M and Miettinen, S and Kukkonen, K and Savilahti, E and Kuitunen, M and de Vos, WM}, title = {Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {182}, pmid = {30326954}, issn = {2049-2618}, support = {250172/ERC_/European Research Council/International ; }, mesh = {Anti-Bacterial Agents/*administration & dosage ; Bifidobacterium/*classification ; Breast Feeding ; Cesarean Section ; Clostridium/isolation & purification ; Dietary Supplements ; Double-Blind Method ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Infant ; Lacticaseibacillus rhamnosus/*classification ; Male ; Pregnancy ; Probiotics/*administration & dosage ; Propionibacterium/*classification ; Proteobacteria/isolation & purification ; }, abstract = {BACKGROUND: Infants born by caesarean section or receiving antibiotics are at increased risk of developing metabolic, inflammatory and immunological diseases, potentially due to disruption of normal gut microbiota at a critical developmental time window. We investigated whether probiotic supplementation could ameliorate the effects of antibiotic use or caesarean birth on infant microbiota in a double blind, placebo-controlled randomized clinical trial. Mothers were given a multispecies probiotic, consisting of Bifidobacterium breve Bb99 (Bp99 2 × 10[8] cfu) Propionibacterium freundenreichii subsp. shermanii JS (2 × 10[9]cfu), Lactobacillus rhamnosus Lc705 (5 × 10[9] cfu) and Lactobacillus rhamnosus GG (5 × 10[9] cfu) (N = 168 breastfed and 31 formula-fed), or placebo supplement (N = 201 breastfed and 22 formula-fed) during pregnancy, and the infants were given the same supplement. Faecal samples of the infants were collected at 3 months and analyzed using taxonomic, metagenomic and metaproteomic approaches.

RESULTS: The probiotic supplement had a strong overall impact on the microbiota composition, but the effect depended on the infant's diet. Only breastfed infants showed the expected increase in bifidobacteria and reduction in Proteobacteria and Clostridia. In the placebo group, both birth mode and antibiotic use were significantly associated with altered microbiota composition and function, particularly reduced Bifidobacterium abundance. In the probiotic group, the effects of antibiotics and birth mode were either completely eliminated or reduced.

CONCLUSIONS: The results indicate that it is possible to correct undesired changes in microbiota composition and function caused by antibiotic treatments or caesarean birth by supplementing infants with a probiotic mixture together with at least partial breastfeeding.

TRIAL REGISTRATION: clinicaltrials.gov NCT00298337 . Registered March 2, 2006.}, } @article {pmid30326458, year = {2019}, author = {Zhou, H and Zhang, D and Jiang, Z and Sun, P and Xiao, H and Yuxin, W and Chen, J}, title = {Changes in the soil microbial communities of alpine steppe at Qinghai-Tibetan Plateau under different degradation levels.}, journal = {The Science of the total environment}, volume = {651}, number = {Pt 2}, pages = {2281-2291}, doi = {10.1016/j.scitotenv.2018.09.336}, pmid = {30326458}, issn = {1879-1026}, mesh = {Bacteria/*isolation & purification ; China ; *Grassland ; *Metagenome ; *Microbiota ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Soil Microbiology ; }, abstract = {The alpine steppe at Qinghai-Tibetan Plateau is an important area for conserving water source and grassland productivity; however, knowledge about the microbial community structure and function and the risk to human health due to alpine plant-soil ecosystems is limited. Thus, we used prediction methods, such as Tax4Fun, and performed a metagenome pre-study using 16S rRNA sequencing reads for a small scale survey of the microbial communities at degraded alpine steppes (i.e., non-degraded (ND), lightly degraded (LD), moderately degraded (MD), heavily degraded (HD), and extremely degraded (ED) steppes) by Illumina high-throughput sequencing technology. Although there were no significant differences in the microbial alpha diversity among the different degraded alpine steppes and the dominant phyla at the different degraded alpine steppes, including Actinobacteria, Proteobacterial, Acidobacteria and Chloroflexi, were similar, the beta-diversity significantly differed, indicating that alpine steppe degradation might result in variation in microbial community compositions. The linear discriminate analysis (LDA) effect size (LEfSe) analysis found twenty-one biomarkers, most of which belonged to Actinobacteria, suggesting that microbes with a special function (such as the decomposition soil organic matter) might survive in alpine steppes. In addition, the functional profiles of the bacterial populations revealed an association with many human diseases, including infectious diseases. In addition, the microbial communities were mainly correlated with the populations of Gramineae and soil total phosphorous. These results suggested that alpine steppe degradation could result in variations in the microbial community composition, structure and function at Qinghai-Tibetan Plateau. Further studies investigating the degraded alpine steppe environment are needed to isolate these potential pathogenic microbes and help protect livestock using these alpine steppes.}, } @article {pmid30326425, year = {2018}, author = {Luis, AS and Martens, EC}, title = {Interrogating gut bacterial genomes for discovery of novel carbohydrate degrading enzymes.}, journal = {Current opinion in chemical biology}, volume = {47}, number = {}, pages = {126-133}, doi = {10.1016/j.cbpa.2018.09.012}, pmid = {30326425}, issn = {1879-0402}, support = {R21 AI128120/AI/NIAID NIH HHS/United States ; }, mesh = {Carbohydrate Metabolism ; Carbohydrate Sequence ; Catalysis ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial ; Glycoside Hydrolases/*genetics/*metabolism ; Humans ; Metagenome ; Polysaccharide-Lyases/*genetics/*metabolism ; Polysaccharides/*metabolism ; }, abstract = {Individual human gut bacteria often encode hundreds of enzymes for degrading different polysaccharides. Identification of co-localized and co-regulated genes in these bacteria has been a successful approach to identify enzymes that participate in full or partial saccharification of complex carbohydrates, often unmasking novel catalytic activities. Here, we review recent studies that have led to the discovery of new activities from gut bacteria and summarize a general scheme for identifying gut bacteria with novel catalytic abilities, locating the enzymes involved and investigating their activities in detail. The strength of this approach is amplified by the availability of abundant genomic and metagenomic data for the human gut microbiome, which facilitates comparative approaches to mine existing data for new or orthologous enzymes.}, } @article {pmid30325092, year = {2019}, author = {Zhang, SY and Tsementzi, D and Hatt, JK and Bivins, A and Khelurkar, N and Brown, J and Tripathi, SN and Konstantinidis, KT}, title = {Intensive allochthonous inputs along the Ganges River and their effect on microbial community composition and dynamics.}, journal = {Environmental microbiology}, volume = {21}, number = {1}, pages = {182-196}, doi = {10.1111/1462-2920.14439}, pmid = {30325092}, issn = {1462-2920}, support = {//Georgia Institute of Technology/International ; DEB 1241046//National Science Foundation/International ; }, mesh = {*Biodiversity ; Cities ; Drug Resistance, Microbial/genetics ; *Environmental Monitoring ; Humans ; India ; Metagenome ; Metagenomics ; Microbiota/genetics/*physiology ; Plankton/microbiology ; Rivers/*microbiology ; *Seasons ; *Sewage ; }, abstract = {Little is known about microbial communities in the Ganges River, India and how they respond to intensive anthropogenic inputs. Here we applied shotgun metagenomics sequencing to study microbial community dynamics and function in planktonic samples collected along an approximately 700 km river transect, including urban cities and rural settings in upstream waters, before and after the monsoon rainy season. Our results showed that 11%-32% of the microbes represented terrestrial, sewage and human inputs (allochthonous). Sewage inputs significantly contributed to the higher abundance, by 13-fold of human gut microbiome (HG) associated sequences and 2-fold of antibiotic resistance genes (ARGs) in the Ganges relative to other riverine ecosystems in Europe, North and South America. Metagenome-assembled genome sequences (MAGs) representing allochthonous populations were detectable and tractable across the river after 1-2 days of (downstream) transport (> 200 km apart). Only approximately 8% of these MAGs were abundant in U.S. freshwater ecosystems, revealing distinct biodiversity for the Ganges. Microbial communities in the rainy season exhibited increased alpha-diversity and spatial heterogeneity and showed significantly weaker distance-decay patterns compared with the dry season. These results advance our understanding of the Ganges microbial communities and how they respond to anthropogenic pollution.}, } @article {pmid30315079, year = {2018}, author = {Xia, F and Wang, JG and Zhu, T and Zou, B and Rhee, SK and Quan, ZX}, title = {Ubiquity and Diversity of Complete Ammonia Oxidizers (Comammox).}, journal = {Applied and environmental microbiology}, volume = {84}, number = {24}, pages = {}, pmid = {30315079}, issn = {1098-5336}, mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Geologic Sediments/chemistry ; Metagenomics ; Nitrates/metabolism ; Nitrification ; Nitrites/metabolism ; Nitrogen Cycle ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Sewage/chemistry ; Soil/chemistry ; Soil Microbiology ; Water/chemistry ; }, abstract = {The discovery of complete ammonia oxidizers (comammox) refutes the century-old paradigm that nitrification requires the activity of two types of microbes. Determining the distribution and abundance of comammox in various environments is important for revealing the ecology of microbial nitrification within the global nitrogen cycle. In this study, the ubiquity and diversity of comammox were analyzed for samples from different types of environments, including soil, sediment, sludge, and water. The results of a two-step PCR using highly degenerate primers (THDP-PCR) and quantitative real-time PCR (qPCR) supported the relatively high abundance of comammox in nearly half of all samples tested, sometimes even outnumbering canonical ammonia-oxidizing bacteria (AOB). In addition, a relatively high proportion of comammox in tap and coastal water samples was confirmed via analysis of metagenomic data sets in public databases. The diversity of comammox was estimated by comammox-specific partial nested PCR amplification of the ammonia monooxygenase subunit A (amoA) gene, and phylogenetic analysis of comammox AmoA clearly showed a split of clade A into clades A.1 and A.2, with the proportions of clades A.1, A.2, and B differing among the various environmental samples. Moreover, compared to the amoA genes of AOB and ammonia-oxidizing archaea (AOA), the comammox amoA gene exhibited higher diversity indices. The ubiquitous distribution and high diversity of comammox indicate that they are likely overlooked contributors to nitrification in various ecosystems.IMPORTANCE The discovery of complete ammonia oxidizers (comammox), which oxidize ammonia to nitrate via nitrite, refutes the century-old paradigm that nitrification requires the activity of two types of microbes and redefines a key process in the biogeochemical nitrogen cycle. Understanding the functional relationships between comammox and other nitrifiers is important for ecological studies on the nitrogen cycle. Therefore, the diversity and contribution of comammox should be considered during ecological analyses of nitrifying microorganisms. In this study, a ubiquitous and highly diverse distribution of comammox was observed in various environmental samples, similar to the distribution of canonical ammonia-oxidizing bacteria. The proportion of comammox was relatively high in coastal water and sediment samples, whereas it was nearly undetectable in open-ocean samples. The ubiquitous distribution and high diversity of comammox indicate that these microorganisms might be important contributors to nitrification.}, } @article {pmid30311571, year = {2018}, author = {Shillitoe, EJ}, title = {The Microbiome of Oral Cancer.}, journal = {Critical reviews in oncogenesis}, volume = {23}, number = {3-4}, pages = {153-160}, doi = {10.1615/CritRevOncog.2018027422}, pmid = {30311571}, issn = {0893-9675}, mesh = {Animals ; Bacterial Infections/complications/microbiology ; Cell Transformation, Neoplastic ; Disease Susceptibility ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth Neoplasms/*etiology ; Mycoses/complications/microbiology ; Virus Diseases/complications/virology ; }, abstract = {The pathogenesis of oral cancer is complex, and not all relevant factors involved in it have been determined. In particular, the role of the microbiota is not well understood because of difficulties in isolating and culturing its organisms. However, the recent development of metagenomic sequencing allows the discovery of all the DNA sequences in a specimen, and thus, the microbiome is now under intensive investigation. Studies of the bacteriome, the mycobiome, and the virome have revealed new organisms and have uncovered various differences between healthy persons and patients with oral cancer. In addition, sequencing of human samples shows the existence of DNA sequences that may be from novel microbes but are actually of unknown origin and so are referred to as the dark matter. The large volumes of data that are being produced by sequencing projects must be studied further to reveal novel pathogens and new pathways in the development of oral cancer.}, } @article {pmid30311422, year = {2019}, author = {Shu, Y and Hong, P and Tang, D and Qing, H and Omondi Donde, O and Wang, H and Xiao, B and Wu, H}, title = {Comparison of intestinal microbes in female and male Chinese concave-eared frogs (Odorrana tormota) and effect of nematode infection on gut bacterial communities.}, journal = {MicrobiologyOpen}, volume = {8}, number = {6}, pages = {e00749}, pmid = {30311422}, issn = {2045-8827}, mesh = {Animals ; Anura/*microbiology/parasitology ; Bacteria/classification/genetics/isolation & purification ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Male ; Nematoda/*physiology ; Nematode Infections/parasitology/*veterinary ; Phylogeny ; }, abstract = {The Chinese concave-eared frog (Odorrana tormota) is a rare and threatened species with remarkable sexual dimorphism. Intestinal microbes are understood to play important roles in animal physiology, growth, ecology, and evolution. However, little is known about the intestinal microbes in female and male frogs, as well as the contributing effect by gut infesting nematodes to the co-habiting bacteria and their function in degradation food rich in chitin. Here, this study analyzed the microbiota of the intestinal tract of both female and male, healthy as well as nematode-infested concave-eared frogs using high throughput 16S rRNA sequencing and metagenomic techniques. The results showed that the bacterial composition of the microbiota at the phylum level was dominated by Firmicutes, Verrucomicrobia, Bacteroidetes, and Proteobacteria. The study also revealed that the community composition below the class level could be represent sex differences, particularly with regard to Enterobacteriales, Enterobacteriaceae, Peptostreptococcaceae, and Rikenellaceae, among others. Carbohydrate-active enzyme-encoding genes and modules were identified in related gut bacteria by metagenomic analysis, with Bacteroidia, Clostridia, and gammaproteobacteria predicted to be the main classes of chitin-decomposing bacteria in the frog intestine. In addition, the abundance of some bacteria significantly increased or decreased in nematode-infected hosts compared with healthy individuals, including Verrucomicrobia, Verrucomicrobiae, Negativicutes, Actinobacteria, and Bacilli, among others. This indicates that nematode infection may affect the richness and composition of some gut bacteria.}, } @article {pmid30310127, year = {2018}, author = {Cuer, CA and Rodrigues, RAR and Balieiro, FC and Jesus, J and Silva, EP and Alves, BJR and Rachid, CTCC}, title = {Short-term effect of Eucalyptus plantations on soil microbial communities and soil-atmosphere methane and nitrous oxide exchange.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {15133}, pmid = {30310127}, issn = {2045-2322}, mesh = {Atmosphere/*chemistry ; Brazil ; Environmental Monitoring ; *Eucalyptus ; Forests ; Metagenomics/methods ; Methane/*analysis ; Microbiota ; Nitrous Oxide/*analysis ; RNA, Ribosomal, 16S ; Soil/*chemistry ; *Soil Microbiology ; Time Factors ; }, abstract = {Soil greenhouse gas (GHG) emissions are a significant environmental problem resulting from microbially-mediated nitrogen (N) and carbon (C) cycling. This study aimed to investigate the impact of Eucalyptus plantations on the structure and function of a soil microbial community, and how resulting alterations may be linked to GHG fluxes. We sampled and monitored two adjacent Eucalyptus plantations-a recently logged site that harbored new seedlings and an adult plantation-and compared them to a site hosting native vegetation. We used 16S rRNA gene sequencing and qPCR amplifications of key nitrogen and methane cycle genes to characterize microbial structure and functional gene abundance and compared our data with soil parameters and GHG fluxes. Both microbial community attributes were significantly affected by land use and logging of Eucalyptus plantations. The genes nosZ and archaeal amoA were significantly more abundant in native forest than in either young or old Eucalyptus plantations. Statistical analyses suggest that land use type has a greater impact on microbial community structure and functional gene abundance than Eucalyptus rotation. There was no correlation between GHG fluxes and shifts in microbial community, suggesting that microbial community structure and functional gene abundance are not the main drivers of GHG fluxes in this system.}, } @article {pmid30309375, year = {2018}, author = {Zepeda Mendoza, ML and Roggenbuck, M and Manzano Vargas, K and Hansen, LH and Brunak, S and Gilbert, MTP and Sicheritz-Pontén, T}, title = {Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging.}, journal = {Acta veterinaria Scandinavica}, volume = {60}, number = {1}, pages = {61}, pmid = {30309375}, issn = {1751-0147}, support = {R52-A5062//Lundbeckfonden/ ; }, mesh = {Adaptation, Biological ; Animals ; Animals, Wild/microbiology ; Bacteria/classification/genetics/*isolation & purification ; Falconiformes/*microbiology/physiology ; *Feeding Behavior ; Gastrointestinal Tract/*microbiology ; *Microbiota ; Skin/*microbiology ; }, abstract = {BACKGROUND: Vultures have adapted the remarkable ability to feed on carcasses that may contain microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that the genetic basis of such adaptation may not only lie within their genomes, but additionally in their associated microbes. To explore this, we generated shotgun DNA sequencing datasets of the facial skin and large intestine microbiomes of the black vulture (Coragyps atratus) and the turkey vulture (Cathartes aura). We characterized the functional potential and taxonomic diversity of their microbiomes, the potential pathogenic challenges confronted by vultures, and the microbial taxa and genes that could play a protective role on the facial skin and in the gut.

RESULTS: We found microbial taxa and genes involved in diseases, such as dermatitis and pneumonia (more abundant on the facial skin), and gas gangrene and food poisoning (more abundant in the gut). Interestingly, we found taxa and functions with potential for playing beneficial roles, such as antilisterial bacteria in the gut, and genes for the production of antiparasitics and insecticides on the facial skin. Based on the identified phages, we suggest that phages aid in the control and possibly elimination, as in phage therapy, of microbes reported as pathogenic to a variety of species. Interestingly, we identified Adineta vaga in the gut, an invertebrate that feeds on dead bacteria and protozoans, suggesting a defensive predatory mechanism. Finally, we suggest a colonization resistance role through biofilm formation played by Fusobacteria and Clostridia in the gut.

CONCLUSIONS: Our results highlight the importance of complementing genomic analyses with metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the importance of microbiome-mediated health protection for adaptation to extreme diets, such as scavenging.}, } @article {pmid30308944, year = {2018}, author = {Fehlbaum, S and Prudence, K and Kieboom, J and Heerikhuisen, M and van den Broek, T and Schuren, FHJ and Steinert, RE and Raederstorff, D}, title = {In Vitro Fermentation of Selected Prebiotics and Their Effects on the Composition and Activity of the Adult Gut Microbiota.}, journal = {International journal of molecular sciences}, volume = {19}, number = {10}, pages = {}, pmid = {30308944}, issn = {1422-0067}, mesh = {*Biodiversity ; Dietary Fiber ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Fermentation ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; *Prebiotics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recently, the concept of prebiotics has been revisited to expand beyond non-digestible oligosaccharides, and the requirements for selective stimulation were extended to include microbial groups other than, and additional to, bifidobacteria and lactobacilli. Here, the gut microbiota-modulating effects of well-known and novel prebiotics were studied. An in vitro fermentation screening platform (i-screen) was inoculated with adult fecal microbiota, exposed to different dietary fibers that had a range of concentrations (inulin, alpha-linked galacto-oligosaccharides (alpha-GOS), beta-linked GOS, xylo-oligosaccharides (XOS) from corn cobs and high-fiber sugar cane, and beta-glucan from oats), and compared to a positive fructo-oligosaccharide (FOS) control and a negative control (no fiber addition). All dietary fibers displayed prebiotic activity, with beta-glucan showing more distinct effects on the microbial composition and metabolism compared to the other fibers. Beta-glucan induced the growth of Prevotella and Roseburia with a concomitant increase in propionate production. Inulin and both forms of GOS and XOS had a strong bifidogenic effect on the microbial composition. A dose-response effect was observed for butyrate when exposed to beta-glucan and inulin. The findings of this study support the potential for alpha-GOS, XOS, and oat beta-glucan to serve as novel prebiotics, due to their association with the positive shifts in microbiome composition and short-chain fatty acid production that point to potential health benefits.}, } @article {pmid30308887, year = {2019}, author = {Coble, AA and Flinders, CA and Homyack, JA and Penaluna, BE and Cronn, RC and Weitemier, K}, title = {eDNA as a tool for identifying freshwater species in sustainable forestry: A critical review and potential future applications.}, journal = {The Science of the total environment}, volume = {649}, number = {}, pages = {1157-1170}, doi = {10.1016/j.scitotenv.2018.08.370}, pmid = {30308887}, issn = {1879-1026}, mesh = {Aquatic Organisms/*chemistry ; DNA/*analysis ; *Environment ; Environmental Monitoring/*methods ; *Forestry ; Fresh Water ; Hydrobiology/*methods ; }, abstract = {Environmental DNA (eDNA) is an emerging biological monitoring tool that can aid in assessing the effects of forestry and forest manufacturing activities on biota. Monitoring taxa across broad spatial and temporal scales is necessary to ensure forest management and forest manufacturing activities meet their environmental goals of maintaining biodiversity. Our objectives are to describe potential applications of eDNA across the wood products supply chain extending from regenerating forests, harvesting, and wood transport, to manufacturing facilities, and to review the current state of the science in this context. To meet our second objective, we summarize the taxa examined with targeted (PCR, qPCR or ddPCR) or metagenomic eDNA methods (eDNA metabarcoding), evaluate how estimated species richness compares between traditional field sampling and eDNA metabarcoding approaches, and compare the geographical representation of prior eDNA studies in freshwater ecosystems to global wood baskets. Potential applications of eDNA include evaluating the effects of forestry and forest manufacturing activities on aquatic biota, delineating fish-bearing versus non fish-bearing reaches, evaluating effectiveness of constructed road crossings for freshwater organism passage, and determining the presence of at-risk species. Studies using targeted eDNA approaches focused on fish, amphibians, and invertebrates, while metagenomic studies focused on fish, invertebrates, and microorganisms. Rare, threatened, or endangered species received the least attention in targeted eDNA research, but are arguably of greatest interest to sustainable forestry and forest manufacturing that seek to preserve freshwater biodiversity. Ultimately, using eDNA methods will enable forestry and forest manufacturing managers to have data-driven prioritization for conservation actions for all freshwater species.}, } @article {pmid30308248, year = {2018}, author = {Hessler, T and Harrison, STL and Huddy, RJ}, title = {Stratification of microbial communities throughout a biological sulphate reducing up-flow anaerobic packed bed reactor, revealed through 16S metagenomics.}, journal = {Research in microbiology}, volume = {169}, number = {10}, pages = {543-551}, doi = {10.1016/j.resmic.2018.09.003}, pmid = {30308248}, issn = {1769-7123}, mesh = {Anaerobiosis ; Bacteria/classification/*genetics/isolation & purification/*metabolism ; Biodegradation, Environmental ; Biodiversity ; Bioreactors/*microbiology ; DNA, Bacterial/genetics ; Genome, Bacterial ; Metagenomics ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sulfur Compounds/*metabolism ; }, abstract = {Biological sulphate reduction (BSR) is a promising low-cost treatment of acid rock drainage effluents. In this paper, the system performance and microbial ecology of a lactate supplemented BSR up-flow anaerobic packed bed reactor (UAPBR) are evaluated across reactor height and compared to a continuous stirred tank reactor (CSTR). The biomass concentrations of planktonic and biofilm communities were quantified and subsequently characterised by 16S rRNA gene amplicon sequencing. The defined microbial communities were shown to correlate with differing availability of lactate, volatile fatty acids produced from lactate degradation and sulphate concentration. The UAPBR was able to achieve near complete sulphate conversion at a 4-day hydraulic residence time (HRT) at a sulphate feed concentration of 10.41 mM (1 g/L). The high volumetric sulphate reduction rate of 0.184 mM/L.h achieved in the first third of the reactor was attributed to OTUs present in the planktonic and biofilm communities. While the scavenging of sulphate within the final third of the UAPBR was attributed to an acetate oxidising genus of SRB which was not detected in the lactate-fed CSTR. The detailed analyses of the microbial communities throughout the UAPBR and CSTR contribute to the growing understanding of the impact of the microbial communities of BSR reactors on system performance.}, } @article {pmid30308038, year = {2018}, author = {Nam, BH and Jang, J and Caetano-Anolles, K and Kim, YO and Park, JY and Sohn, H and Yoon, SH and Kim, H and Kwak, W}, title = {Microbial community and functions associated with digestion of algal polysaccharides in the visceral tract of Haliotis discus hannai: Insights from metagenome and metatranscriptome analysis.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0205594}, pmid = {30308038}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Enzymes/metabolism ; Gastrointestinal Microbiome/*physiology ; Metagenome ; Phaeophyceae ; Phylogeny ; Polysaccharides/*metabolism ; RNA, Ribosomal, 16S ; Snails/*metabolism/*microbiology ; Transcriptome ; }, abstract = {Haliotis discus hannai, a species of Pacific abalone, is a highly valuable food source throughout Northeast Asia. As H. discus hannai primarily feed on brown algae and largely extract their energy from algal polysaccharides, understanding the mechanisms by which they digest algal polysaccharides is essential for elucidating their energy metabolism. Gut microbes, as well as the host animal, are involved in the process of polysaccharide degradation. To identify algal polysaccharide-digestion mechanisms and their origin, we analyzed the metagenome and metatranscriptome of abalone visceral extracts. Microbial communities were characterized using the 16S rRNA gene sequences in the metagenome and our results differed significantly from those of previous studies using traditional microbiological methods such as bacterial cultivation and cloning. A greater diversity of bacterial taxa was identified here than was previously identified using cultivation methods. Furthermore, the most abundant bacterial taxa also differed from previous studies, which is not common when comparing the results of bacterial culturing with those of molecular methodologies. Based on the metatranscriptome, overall functions were identified and additional analyses were performed on the coding sequences of algal polysaccharide-digestive enzymes, including alginate lyase. Results of the transcriptomic analyses suggest that alginate lyase in the visceral extracts of H. discus hannai was produced by the host itself, not by visceral bacteria. This is the first next-generation sequencing study performed on abalone to characterize the visceral microbiota and the source of the ability to digest algal polysaccharides by analyzing the metagenome and metatranscriptome together.}, } @article {pmid30305667, year = {2018}, author = {Carvalho, R and Vaz, A and Pereira, FL and Dorella, F and Aguiar, E and Chatel, JM and Bermudez, L and Langella, P and Fernandes, G and Figueiredo, H and Goes-Neto, A and Azevedo, V}, title = {Gut microbiome modulation during treatment of mucositis with the dairy bacterium Lactococcus lactis and recombinant strain secreting human antimicrobial PAP.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {15072}, pmid = {30305667}, issn = {2045-2322}, mesh = {Animals ; Anti-Infective Agents/*pharmacology ; Biodiversity ; Feces/microbiology ; Female ; Fluorouracil/pharmacology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Inflammation/microbiology/pathology ; Lactococcus lactis/*physiology ; Mice, Inbred BALB C ; Mucositis/*microbiology/*therapy ; Pancreatitis-Associated Proteins/*pharmacology ; Phylogeny ; Recombination, Genetic/*genetics ; }, abstract = {Mucositis is an inflammatory condition of the gut, caused by an adverse effect of chemotherapy drugs, such as 5-fluorouracil (5-FU). In an attempt to develop alternative treatments for the disease, several research groups have proposed the use of probiotics, in particular, Lactic Acid Bacteria (LAB). In this context, the use of recombinant LAB, for delivering anti-inflammatory compounds has also been explored. In previous work, we demonstrated that either Lactococcus lactis NZ9000 or a recombinant strain expressing an antimicrobial peptide involved in human gut homeostasis, the Pancreatitis-associated Protein (PAP), could ameliorate 5-FU-induced mucositis in mice. However, the impact of these strains on the gut microbiota still needs to be elucidated. Therefore, in the present study, we aimed to characterize the effects of both Lactococci strains in the gut microbiome of mice through a 16 S rRNA gene sequencing metagenomic approach. Our data show 5-FU caused a significant decrease in protective bacteria and increase of several bacteria associated with pro-inflammatory traits. The Lactococci strains were shown to reduce several potential opportunistic microbes, while PAP delivery was able to suppress the growth of Enterobacteriaceae during inflammation. We conclude the strain secreting antimicrobial PAP was more effective in the control of 5-FU-dysbiosis.}, } @article {pmid30305166, year = {2018}, author = {Guyomar, C and Legeai, F and Jousselin, E and Mougel, C and Lemaitre, C and Simon, JC}, title = {Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {181}, pmid = {30305166}, issn = {2049-2618}, mesh = {Animals ; Aphids/*microbiology ; Buchnera/classification/genetics/*isolation & purification ; Genome, Bacterial/genetics ; Metagenome/genetics ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rickettsia/classification/genetics/*isolation & purification ; Symbiosis/*physiology ; }, abstract = {BACKGROUND: Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunities to shed light on the diversity of microbial communities and to give some insights into the functions they perform in a broad array of hosts. The pea aphid is a model system for the study of insect-bacteria symbiosis. It is organized in a complex of biotypes, each adapted to specific host plants. It harbors both an obligatory symbiont supplying key nutrients and several facultative symbionts bringing additional functions to the host, such as protection against biotic and abiotic stresses. However, little is known on how the symbiont genomic diversity is structured at different scales: across host biotypes, among individuals of the same biotype, or within individual aphids, which limits our understanding on how these multi-partner symbioses evolve and interact.

RESULTS: We present a framework well adapted to the study of genomic diversity and evolutionary dynamics of the pea aphid holobiont from metagenomic read sets, based on mapping to reference genomes and whole genome variant calling. Our results revealed that the pea aphid microbiota is dominated by a few heritable bacterial symbionts reported in earlier works, with no discovery of new microbial associates. However, we detected a large and heterogeneous genotypic diversity associated with the different symbionts of the pea aphid. Partitioning analysis showed that this fine resolution diversity is distributed across the three considered scales. Phylogenetic analyses highlighted frequent horizontal transfers of facultative symbionts between host lineages, indicative of flexible associations between the pea aphid and its microbiota. However, the evolutionary dynamics of symbiotic associations strongly varied depending on the symbiont, reflecting different histories and possible constraints. In addition, at the intra-host scale, we showed that different symbiont strains may coexist inside the same aphid host.

CONCLUSIONS: We present a methodological framework for the detailed analysis of NGS data from microbial communities of moderate complexity and gave major insights into the extent of diversity in pea aphid-symbiont associations and the range of evolutionary trajectories they could take.}, } @article {pmid30301312, year = {2018}, author = {Yu, YC and Yum, SJ and Jeon, DY and Jeong, HG}, title = {Analysis of the Microbiota on Lettuce (Lactuca sativa L.) Cultivated in South Korea to Identify Foodborne Pathogens.}, journal = {Journal of microbiology and biotechnology}, volume = {28}, number = {8}, pages = {1318-1331}, doi = {10.4014/jmb.1803.03007}, pmid = {30301312}, issn = {1738-8872}, mesh = {Bacteria/classification/genetics/isolation & purification ; Biodiversity ; DNA, Bacterial/genetics ; *Food Microbiology ; Foodborne Diseases/*microbiology ; Geography ; Lactuca/*microbiology ; Metagenomics ; Microbial Interactions ; Microbiota/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; }, abstract = {Lettuce (Lactuca sativa L.) is a major ingredient used in many food recipes in South Korea. Lettuce samples were collected during their maximum production period between April and July in order to investigate the microbiota of lettuce during different seasons. 16S rRNA gene-based sequencing was conducted using Illumina MiSeq, and real-time PCR was performed for quantification. The number of total bacterial was greater in lettuce collected in July than in that collected in April, albeit with reduced diversity. The bacterial compositions varied according to the site and season of sample collection. Potential pathogenic species such as Bacillus spp., Enterococcus casseliflavus, Klebsiella pneumoniae, and Pseudomonas aeruginosa showed season-specific differences. Results of the network co-occurrence analysis with core genera correlations showed characteristics of bacterial species in lettuce, and provided clues regarding the role of different microbes, including potential pathogens, in this microbiota. Although further studies are needed to determine the specific effects of regional and seasonal characteristics on the lettuce microbiota, our results imply that the 16S rRNA gene-based sequencing approach can be used to detect pathogenic bacteria in lettuce.}, } @article {pmid30298261, year = {2018}, author = {Adeolu, M and Parkinson, J and Xiong, X}, title = {Analyzing Metabolic Pathways in Microbiomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {291-307}, doi = {10.1007/978-1-4939-8728-3_18}, pmid = {30298261}, issn = {1940-6029}, mesh = {High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Metabolic Networks and Pathways ; Metagenomics ; *Microbiota ; *Transcriptome ; }, abstract = {Understanding the metabolic activity of a microbial community, at both the level of the individual microbe and the whole microbiome, provides fundamental biological, biochemical, and clinical insights into the nature of the microbial community and interactions with their hosts in health and disease. Here, we discuss a method to examine the expression of metabolic pathways in microbial communities using data from metatranscriptomic next-generation sequencing data. The methodology described here encompasses enzyme function annotation, differential enzyme expression and pathway enrichment analyses, and visualization of metabolic networks with differential enzyme expression levels.}, } @article {pmid30298260, year = {2018}, author = {Dunn, KA and Andrews, K and Bashwih, RO and Bielawski, JP}, title = {Bayesian Inference of Microbial Community Structure from Metagenomic Data Using BioMiCo.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {267-289}, doi = {10.1007/978-1-4939-8728-3_17}, pmid = {30298260}, issn = {1940-6029}, mesh = {*Algorithms ; *Bayes Theorem ; Computational Biology/*methods ; Metagenomics/*methods ; *Microbiota ; }, abstract = {Microbial samples taken from an environment often represent mixtures of communities, where each community is composed of overlapping assemblages of species. Such data represent a serious analytical challenge, as the community structures will be present as complex mixtures, there will be very large numbers of component species, and the species abundance will often be sparse over samples. The structure and complexity of these samples will vary according to both biotic and abiotic factors, and classical methods of data analysis will have a limited value in this setting. A novel Bayesian modeling framework, called BioMiCo, was developed to meet this challenge. BioMiCo takes abundance data derived from environmental DNA, and models each sample by a two-level mixture, where environmental OTUs contribute community structures, and those structures are related to the known biotic and abiotic features of each sample. The model is constrained by Dirichlet priors, which induces compact structures, minimizes variance, and maximizes model interpretability. BioMiCo is trained on a portion of the data, and once trained a BioMiCo model can be employed to make predictions about the features of new samples. This chapter provides a set of protocols that illustrate the application of BioMiCo to real inference problems. Each protocol is designed around the analysis of a real dataset, which was carefully chosen to illustrate specific aspects of real data analysis. With these protocols, users of BioMiCo will be able to undertake basic research into the properties of complex microbial systems, as well as develop predictive models for applied microbiomics.}, } @article {pmid30298257, year = {2018}, author = {Hug, LA}, title = {Subsampled Assemblies and Hybrid Nucleotide Composition/Differential Coverage Binning for Genome-Resolved Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {215-225}, doi = {10.1007/978-1-4939-8728-3_14}, pmid = {30298257}, issn = {1940-6029}, mesh = {Algorithms ; *Genome, Microbial ; Metagenomics/*methods ; *Microbiota ; Nucleotides/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Metagenomic analyses for reconstruction of genomes from mixed microbial community datasets now routinely allow rapid, accurate genome recovery for tens to hundreds of organisms from environmental samples. This chapter provides a step-by-step protocol for reconstructing genomes from metagenomic datasets, with a focus on the most abundant community members. Subsampling assembly approaches are implemented to improve assembly of abundant genome sequences, an iterative process that targets progressively less abundant populations and improves total community representation in the final merged assembly. A hybrid approach to genome binning is described, combining differential coverage information from a series of metagenomic samples with nucleotide composition information. This approach strengthens binning through application of multiple independent variables for contig clustering. Genome curation through error correction and gap closure leads to high-quality draft genomes, and, for some community members, closed and complete genome sequences reconstructed directly from environmental samples.}, } @article {pmid30298256, year = {2018}, author = {Macklaim, JM and Gloor, GB}, title = {From RNA-seq to Biological Inference: Using Compositional Data Analysis in Meta-Transcriptomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {193-213}, doi = {10.1007/978-1-4939-8728-3_13}, pmid = {30298256}, issn = {1940-6029}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Computational Biology/*methods ; Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Metagenome ; *Microbiota ; *Transcriptome ; }, abstract = {The proper analysis of high-throughput sequencing datasets of mixed microbial communities (meta-transcriptomics) is substantially more complex than for datasets composed of single organisms. Adapting commonly used RNA-seq methods to the analysis of meta-transcriptome datasets can be misleading and not use all the available information in a consistent manner. However, meta-transcriptomic experiments can be investigated in a principled manner using Bayesian probabilistic modeling of the data at a functional level coupled with analysis under a compositional data analysis paradigm. We present a worked example for the differential functional evaluation of mixed-species microbial communities obtained from human clinical samples that were sequenced on an Illumina platform. We demonstrate methods to functionally map reads directly, conduct a compositionally appropriate exploratory data analysis, evaluate differential relative abundance, and finally identify compositionally associated (constant ratio) functions. Using these approaches we have found that meta-transcriptomic functional analyses are highly reproducible and convey significant information regarding the ecosystem.}, } @article {pmid30298255, year = {2018}, author = {Zhang, Q}, title = {Metagenome Assembly and Contig Assignment.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {179-192}, doi = {10.1007/978-1-4939-8728-3_12}, pmid = {30298255}, issn = {1940-6029}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Computational Biology/methods ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing/*methods ; *Metagenome ; Microbiota ; Molecular Sequence Annotation ; *Software ; }, abstract = {The recent development of metagenomic assembly has revolutionized metagenomic data analysis, thanks to the improvement of sequencing techniques, more powerful computational infrastructure and the development of novel algorithms and methods. Using longer assembled contigs rather than raw reads improves the process of metagenomic binning and annotation significantly, ultimately resulting in a deeper understanding of the microbial dynamics of the metagenomic samples being analyzed. In this chapter, we demonstrate a typical metagenomic analysis pipeline including raw read quality evaluation and trimming, assembly and contig binning. Alternative tools that can be used for each step are also discussed.}, } @article {pmid30298254, year = {2018}, author = {Douglas, GM and Beiko, RG and Langille, MGI}, title = {Predicting the Functional Potential of the Microbiome from Marker Genes Using PICRUSt.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {169-177}, doi = {10.1007/978-1-4939-8728-3_11}, pmid = {30298254}, issn = {1940-6029}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Biodiversity ; Computational Biology/*methods ; *Genetic Markers ; High-Throughput Nucleotide Sequencing/*methods ; *Metagenome ; *Microbiota ; Phylogeny ; *Software ; }, abstract = {Marker-gene sequencing is a cost-effective method of taxonomically profiling microbial communities. Unlike metagenomic approaches, marker-gene sequencing does not provide direct information about the functional genes that are present in the genomes of community members. However, by capitalizing on the rapid growth in the number of sequenced genomes, it is possible to infer which functions are likely associated with a marker gene based on its sequence similarity with a reference genome. The PICRUSt tool is based on this idea and can predict functional category abundances based on an input marker gene. In brief, this method requires a reference phylogeny with tips corresponding to taxa with reference genomes as well as taxa lacking sequenced genomes. A modified ancestral state reconstruction (ASR) method is then used to infer counts of functional categories for taxa without reference genomes. The predictions are written to pre-calculated files, which can be cross-referenced with other datasets to quickly generate predictions of functional potential for a community. This chapter will give an in-depth description of these methods and describe how PICRUSt should be used.}, } @article {pmid30298253, year = {2018}, author = {McMurdie, PJ}, title = {Normalization of Microbiome Profiling Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {143-168}, doi = {10.1007/978-1-4939-8728-3_10}, pmid = {30298253}, issn = {1940-6029}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Computational Biology/*methods ; Data Analysis ; High-Throughput Nucleotide Sequencing/*methods ; *Metagenome ; *Microbiota ; Phylogeny ; *Software ; }, abstract = {Normalization is a term that is often used but rarely defined and poorly understood. The number of choices of normalization procedure is large-some are inappropriate or inadmissible-and all are narrowly relevant to a specific analysis that depends on both the nature of the data and the question being asked. This chapter describes key definitions of normalization as they apply in metagenomics, mainly for taxonomic profiling data; while also demonstrating specific, reproducible examples of normalization procedures in the context of analysis techniques for which they were intended. The analysis and graphics code is distributed as a supplemental companion to this chapter so that the motivated reader can re-use it on new data.}, } @article {pmid30298252, year = {2018}, author = {Douglas, GM and Comeau, AM and Langille, MGI}, title = {Processing a 16S rRNA Sequencing Dataset with the Microbiome Helper Workflow.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {131-141}, doi = {10.1007/978-1-4939-8728-3_9}, pmid = {30298252}, issn = {1940-6029}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; *Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; *Software ; Workflow ; }, abstract = {Sequencing microbiome samples has recently become a fast and cost-effective method to taxonomically profile communities. The growing interest in analyzing microbial sequencing data has attracted many new researchers to the field. Here, we present a straightforward bioinformatic pipeline that aims to streamline the processing of 16S rRNA sequencing data. This workflow is part of the larger project called Microbiome Helper (Comeau et al. mSyst 2:e00127-16, 2017), which includes other bioinformatic workflows, tutorials, and scripts available here: https://github.com/mlangill/microbiome_helper/wiki .}, } @article {pmid30298244, year = {2018}, author = {Daly, RA and Wrighton, KC and Wilkins, MJ}, title = {Characterizing the Deep Terrestrial Subsurface Microbiome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {1-15}, doi = {10.1007/978-1-4939-8728-3_1}, pmid = {30298244}, issn = {1940-6029}, mesh = {Bacteria/*classification/*genetics ; Biomass ; DNA, Bacterial/*analysis ; Gene Library ; Geologic Sediments/*microbiology ; Metagenomics ; *Microbiota ; Soil Microbiology ; Water Microbiology ; }, abstract = {A large portion of the earth's biomass resides in the subsurface and recent studies have expanded our knowledge of indigenous microbial life. Advances in the field of metagenomics now allow analysis of microbial communities from low-biomass samples such as deep (>2.5 km) shale core samples. Here we present protocols for the best practices in contamination control, handling core material, extraction of nucleic acids, and low-input library preparation for subsequent metagenomic sequencing.}, } @article {pmid30296008, year = {2019}, author = {Wang, W and Zheng, S and Li, L and Yang, Y and Liu, Y and Wang, A and Sharshov, K and Li, Y}, title = {Comparative metagenomics of the gut microbiota in wild greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea).}, journal = {MicrobiologyOpen}, volume = {8}, number = {5}, pages = {e00725}, pmid = {30296008}, issn = {2045-8827}, mesh = {Animals ; Bacteria/*classification/*genetics ; China ; Ducks/*microbiology ; *Gastrointestinal Microbiome ; Geese/*microbiology ; *Metagenome ; Metagenomics ; }, abstract = {Gut microbiome contributes to host health by maintaining homeostasis, increasing digestive efficiency, and facilitating the development of immune system. Wild greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea), migrating along the central Asian flyway, appear to be one of the most popular species in the rare birds rearing industries of China. However, the structure and function of the gut microbial communities associated with these two bird species remain poorly understood. Here, for the first time, we compared gut metagenomes from greylag geese to ruddy shelducks and investigated the similarities and differences between these two bird species in detail. Taxonomic classifications revealed the top three bacterial phyla, Firmicutes, Proteobacteria, and Fusobacteria, in both greylag geese and ruddy shelducks. Furthermore, between the two species, 12 bacterial genera were found to be more abundant in ruddy shelducks and 41 genera were significantly higher in greylag geese. A total of 613 genera (approximately 70%) were found to be present in both groups. Metabolic categories related to carbohydrate metabolism, metabolism of cofactors and vitamins, lipid metabolism, amino acid metabolism, and glycan biosynthesis and metabolism were significantly more abundant in ruddy shelducks, while greylag geese were enriched in nucleotide metabolism and energy metabolism. The herbivorous greylag geese gut microbiota harbored more carbohydrate-active enzymes than omnivorous ruddy shelducks. In our study, a range of antibiotic resistance categories were also identified in the gut microbiota of greylag geese and ruddy shelducks. In addition to providing a better understanding of the composition and function of wild birds gut microbiome, this comparative study provides reference values of the artificial domestication of these birds.}, } @article {pmid30292975, year = {2019}, author = {Uddin, M and Chen, J and Qiao, X and Tian, R and Arafat, Y and Yang, X}, title = {Bacterial community variations in paddy soils induced by application of veterinary antibiotics in plant-soil systems.}, journal = {Ecotoxicology and environmental safety}, volume = {167}, number = {}, pages = {44-53}, doi = {10.1016/j.ecoenv.2018.09.101}, pmid = {30292975}, issn = {1090-2414}, mesh = {Acidobacteria/drug effects/isolation & purification ; Actinobacteria/drug effects/isolation & purification ; Anti-Bacterial Agents/*analysis ; Bacteroidetes/drug effects/isolation & purification ; Biodiversity ; Carbon/analysis ; Firmicutes/drug effects/isolation & purification ; Nitrogen/analysis ; Oryza/microbiology ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Veterinary Drugs/*analysis ; }, abstract = {Soil bacterial communities have complex regulatory networks, which are mainly associated with soil fertility and ecological functions, and are likely to be disturbed due to antibiotics applications. The impact of antibiotics, particularly in mixtures form, on bacterial communities in different paddy soils is poorly understood. Using pyrosequencing techniques of 16 S rRNA genes, this study investigated the synergistic effects of veterinary antibiotics (sulfadiazine, sulfamethoxazole, trimethoprim, florfenicol, and clarithromycin) on bacterial communities in a soil-bacteria-plant system. Rice was grown under controlled greenhouse conditions where unplanted and planted treatments were doped with 200 µg kg[-1] of combined antibiotics over a period of 3 months. Bacterial richness remained unaltered, while a significant decline was observed in bacterial diversity due to antibiotics in the four paddy soils. Bacteroidetes and Acidobacteria were increased, while Actinobacteria and Firmicutes decreased under antibiotics exposure. Despite antibiotics perturbation, compositional variations were mainly attributed to the different paddy soils which harbor distinct bacterial communities. Haliangium and Gaiella were among the sensitive genera that were negatively correlated to antibiotics perturbation. Additionally, electrical conductivity, total organic carbon, and total nitrogen of soil solution were the key physiochemical indices which significantly influenced the structure of bacterial communities in the paddy soils. These findings expanded our knowledge of effects from synergistic antibiotics application and variations in bacterial communities among different paddy soils.}, } @article {pmid30292825, year = {2018}, author = {Minty, M and Canceill, T and Lê, S and Dubois, P and Amestoy, O and Loubieres, P and Christensen, JE and Champion, C and Azalbert, V and Grasset, E and Hardy, S and Loubes, JM and Mallet, JP and Tercé, F and Vergnes, JN and Burcelin, R and Serino, M and Diemer, F and Blasco-Baque, V}, title = {Oral health and microbiota status in professional rugby players: A case-control study.}, journal = {Journal of dentistry}, volume = {79}, number = {}, pages = {53-60}, doi = {10.1016/j.jdent.2018.10.001}, pmid = {30292825}, issn = {1879-176X}, mesh = {*Athletes ; Case-Control Studies ; Football ; Humans ; *Microbiota ; *Oral Health ; Sports ; }, abstract = {OBJECTIVE: Elite athletes are prone to develop oral diseases, which could increase the risk for injuries. The aim of this study was to evaluate the oral health and the composition of oral microbiota of elite rugby players compared to the general population.

METHODS: We set up a case-control study by screening 24 professional rugby players (PRG) and 22 control patients (CG) for dental and gingival examinations and performed a taxonomic analysis and a predicted functional analysis of oral microbiota.

RESULTS: The Decay, Missing and Filled (DMF) teeth index (5.54 ± 6.18 versus 2.14 ± 3.01; p = 0.01) and the frequency of gingivitis (58,33% versus 13.63%) were significantly increased in PRG compared to CG. PRG were characterized by a dysbiotic oral microbiota (Shannon Index: 3.32 ± 0.62 in PRG versus 3.79 ± 0.68 in CG; p = 0.03) with an increase of Streptococcus (58.43 ± 16.84 versus 42.60 ± 17.45; p = 0.005), the main genus implicated in caries. Predicted metagenomics of oral microbiota in rugby players was suggestive of a cariogenic metagenome favourable to the development of caries.

CONCLUSIONS: Our study shows that the oral health of PRG was poorer than the general population. PRG are characterized by a dysbiotic oral microbiota with an increase of the relative abundance of Streptococcus genus, positively correlated to the weight and negatively correlated to the diversity of oral microbiota.

CLINICAL SIGNIFICANCE: Dental screening should be included in the medical follow-up of professional rugby players as a part of their health management. New strategies such as using probiotics like Lactobacillus could help to control the dysbiosis of oral microbiota.}, } @article {pmid30292553, year = {2018}, author = {Derakhshani, H and Fehr, KB and Sepehri, S and Francoz, D and De Buck, J and Barkema, HW and Plaizier, JC and Khafipour, E}, title = {Invited review: Microbiota of the bovine udder: Contributing factors and potential implications for udder health and mastitis susceptibility.}, journal = {Journal of dairy science}, volume = {101}, number = {12}, pages = {10605-10625}, doi = {10.3168/jds.2018-14860}, pmid = {30292553}, issn = {1525-3198}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Cattle ; Female ; Mammary Glands, Animal/*microbiology ; Mastitis, Bovine/*microbiology ; *Microbiota ; }, abstract = {Various body sites of vertebrates provide stable and nutrient-rich ecosystems for a diverse range of commensal, opportunistic, and pathogenic microorganisms to thrive. The collective genomes of these microbial symbionts (the microbiome) provide host animals with several advantages, including metabolism of indigestible carbohydrates, biosynthesis of vitamins, and modulation of innate and adaptive immune systems. In the context of the bovine udder, however, the relationship between cow and microbes has been traditionally viewed strictly from the perspective of host-pathogen interactions, with intramammary infections by mastitis pathogens triggering inflammatory responses (i.e., mastitis) that are often detrimental to mammary tissues and cow physiology. This traditional view has been challenged by recent metagenomic studies indicating that mammary secretions of clinically healthy quarters can harbor genomic markers of diverse bacterial groups, the vast majority of which have not been associated with mastitis. These observations have given rise to the concept of "commensal mammary microbiota," the ecological properties of which can have important implications for understanding the pathogenesis of mastitis and offer opportunities for development of novel prophylactic or therapeutic products (or both) as alternatives to antimicrobials. Studies conducted to date have suggested that an optimum diversity of mammary microbiota is associated with immune homeostasis, whereas the microbiota of mastitic quarters, or those with a history of mastitis, are considerably less diverse. Whether disruption of the diversity of udder microbiota (dysbiosis) has a role in determining mastitis susceptibility remains unknown. Moreover, little is known about contributions of various biotic and abiotic factors in shaping overall diversity of udder microbiota. This review summarizes current understanding of the microbiota within various niches of the udder and highlights the need to view the microbiota of the teat apex, teat canal, and mammary secretions as interconnected niches of a highly dynamic microbial ecosystem. In addition, host-associated factors, including physiological and anatomical parameters, as well as genetic traits that may affect the udder microbiota are briefly discussed. Finally, current understanding of the effect of antimicrobials on the composition of intramammary microbiota is discussed, highlighting the resilience of udder microbiota to exogenous perturbants.}, } @article {pmid30291903, year = {2018}, author = {Matsumoto, A and Yamagishi, Y and Miyamoto, K and Oka, K and Takahashi, M and Mikamo, H}, title = {Characterization of the vaginal microbiota of Japanese women.}, journal = {Anaerobe}, volume = {54}, number = {}, pages = {172-177}, doi = {10.1016/j.anaerobe.2018.10.001}, pmid = {30291903}, issn = {1095-8274}, mesh = {Adult ; Bacteria/classification/genetics/*isolation & purification ; Female ; Humans ; Japan ; Lactobacillus/classification/genetics/isolation & purification ; *Microbiota ; Phylogeny ; Pregnancy ; Sex Work/statistics & numerical data ; Vagina/*microbiology ; Young Adult ; }, abstract = {The composition of vaginal microbiota changes throughout life in response to health status, sexual activity, and pregnancy. Here the constitution of the vaginal microbiota among non-pregnant women, pregnant woman, and commercial sex workers (CSWs) in Japan were compared. Vaginal samples were obtained from 54 women between January 2014 and February 2015 and the microbiota of each was analyzed by 16S metagenomics as well as cluster and diversity analyses to identify differences. In addition, vaginal Lactobacillus spp. were isolated for comparison. Furthermore, data regarding the use of ritodrine hydrochloride by pregnant women was collected from medical charts. The vaginal microbiota were clustered into three groups. Group 1 was most often dominated by Lactobacillus spp., whereas groups 2 and 3 included not only Lactobacillus spp. but also Bifidobacterium, Atopobium, Prevotella, and Gardnerella spp., in addition to a few other taxa. In non-pregnant women, the proportions of microbes in groups 1, 2, and 3 were 31.8%, 36.4%, and 31.8%, respectively. In pregnant women, the abundance of group 1 microbes was notably greater than that of groups 2 and 3 (66.7% vs. 12.5% and 20.8%, respectively). In CSWs, the prevalence of group 3 microbes was far greater than that of group 1 (87.5% vs. 12.5%, respectively). The alpha diversity of non-pregnant women was significantly greater than that of pregnant women. The detection rate of live Lactobacillus spp. in CSWs was lower than in pregnant and non-pregnant women (25% vs. 50% and 68.2%, respectively). The vaginal microbiota of most pregnant women (60%) who received ritodrine hydrochloride was not dominated by Lactobacillus spp. These results suggest that there were clear differences in the colonization rate of Lactobacillus spp. among non-pregnant, pregnant, and CSW women groups. In addition, the dominance of Lactobacillus may influence the risk of preterm birth among women who received ritodrine hydrochloride during pregnancy.}, } @article {pmid30289528, year = {2019}, author = {Chen, IA and Chu, K and Palaniappan, K and Pillay, M and Ratner, A and Huang, J and Huntemann, M and Varghese, N and White, JR and Seshadri, R and Smirnova, T and Kirton, E and Jungbluth, SP and Woyke, T and Eloe-Fadrosh, EA and Ivanova, NN and Kyrpides, NC}, title = {IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes.}, journal = {Nucleic acids research}, volume = {47}, number = {D1}, pages = {D666-D677}, pmid = {30289528}, issn = {1362-4962}, mesh = {Data Management/*methods ; *Databases, Genetic ; Genomics/*methods ; *Metagenome ; *Microbiota ; Molecular Sequence Annotation/methods ; Sequence Alignment/methods ; *Software ; }, abstract = {The Integrated Microbial Genomes & Microbiomes system v.5.0 (IMG/M: https://img.jgi.doe.gov/m/) contains annotated datasets categorized into: archaea, bacteria, eukarya, plasmids, viruses, genome fragments, metagenomes, cell enrichments, single particle sorts, and metatranscriptomes. Source datasets include those generated by the DOE's Joint Genome Institute (JGI), submitted by external scientists, or collected from public sequence data archives such as NCBI. All submissions are typically processed through the IMG annotation pipeline and then loaded into the IMG data warehouse. IMG's web user interface provides a variety of analytical and visualization tools for comparative analysis of isolate genomes and metagenomes in IMG. IMG/M allows open access to all public genomes in the IMG data warehouse, while its expert review (ER) system (IMG/MER: https://img.jgi.doe.gov/mer/) allows registered users to access their private genomes and to store their private datasets in workspace for sharing and for further analysis. IMG/M data content has grown by 60% since the last report published in the 2017 NAR Database Issue. IMG/M v.5.0 has a new and more powerful genome search feature, new statistical tools, and supports metagenome binning.}, } @article {pmid30287908, year = {2018}, author = {Günther, B and Knebelsberger, T and Neumann, H and Laakmann, S and Martínez Arbizu, P}, title = {Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14822}, pmid = {30287908}, issn = {2045-2322}, mesh = {Aquatic Organisms/classification/genetics ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics/*isolation & purification ; DNA, Ribosomal/*genetics/*isolation & purification ; Electron Transport Complex IV/genetics ; Metagenomics/*methods ; North Sea ; RNA, Ribosomal, 18S/genetics ; Seawater/*chemistry ; }, abstract = {We establish the new approach of environmental DNA (eDNA) analyses for the North Sea. Our study uses a multigene approach, including the mitochondrial cytochrome-c-oxidase subunit I (COI) gene for analyzing species composition and the nuclear hypervariable region V8 of 18S rDNA for analyzing supraspecific biodiversity. A new minibarcode primer (124 bp) was created on the basis of a metazoan COI barcode library with 506 species and tested in silico, in vitro, and in situ. We applied high throughput sequencing to filtrates of 23 near-bottom water samples taken at three seasons from 14 stations. The set of COI primers allowed amplification of mitochondrial minibarcodes for diverse metazoan phyla and the differentiation at the species level for more than 99% of the specimens in the dataset. Our results revealed that the number of sequences is not consistent with proportions in the given DNA mixture. Altogether, environmental sequences could be assigned to 114 species and to 12 metazoan phyla. A spatial distribution of taxa recovered by eDNA was congruent with known distributions. Finally, the successful detection of species and biodiversity depends on a comprehensive sequence reference database. Our study offers a powerful tool for future biodiversity research, including the detection of nonnative species.}, } @article {pmid30287886, year = {2019}, author = {Kuntal, BK and Chandrakar, P and Sadhu, S and Mande, SS}, title = {'NetShift': a methodology for understanding 'driver microbes' from healthy and disease microbiome datasets.}, journal = {The ISME journal}, volume = {13}, number = {2}, pages = {442-454}, pmid = {30287886}, issn = {1751-7370}, mesh = {Databases, Factual ; Humans ; Metagenomics/*methods ; *Microbial Consortia ; *Microbiota ; Models, Biological ; }, abstract = {The combined effect of mutual association within the co-inhabiting microbes in human body is known to play a major role in determining health status of individuals. The differential taxonomic abundance between healthy and disease are often used to identify microbial markers. However, in order to make a microbial community based inference, it is important not only to consider microbial abundances, but also to quantify the changes observed among inter microbial associations. In the present study, we introduce a method called 'NetShift' to quantify rewiring and community changes in microbial association networks between healthy and disease. Additionally, we devise a score to identify important microbial taxa which serve as 'drivers' from the healthy to disease. We demonstrate the validity of our score on a number of scenarios and apply our methodology on two real world metagenomic datasets. The 'NetShift' methodology is also implemented as a web-based application available at https://web.rniapps.net/netshift.}, } @article {pmid30287354, year = {2018}, author = {Staley, C and Sadowsky, MJ}, title = {Practical considerations for sampling and data analysis in contemporary metagenomics-based environmental studies.}, journal = {Journal of microbiological methods}, volume = {154}, number = {}, pages = {14-18}, doi = {10.1016/j.mimet.2018.09.020}, pmid = {30287354}, issn = {1872-8359}, mesh = {Algorithms ; Biodiversity ; Biostatistics/methods ; Computational Biology/methods ; DNA/analysis/isolation & purification ; *Data Analysis ; Ecology ; Ecosystem ; Environment ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeography ; Sequence Analysis, DNA/methods ; Specimen Handling/*methods ; }, abstract = {Recent advancements in metagenomic-based studies, especially analyses of amplicon-based DNA sequencing targeting taxonomic marker genes, has led to an unprecedented characterization of microbial communities from diverse ecosystems around the world. While originally constrained by a lack of appropriate analytical tools and sequencing depth, new technologies and computational and statistical algorithms have been developed to handle highly dimensional, next-generation sequencing datasets. Both these tools allow for the robust analysis of structural and distributional patterns of microbiota essential for the understanding of microbial ecology and biogeography. Furthermore, consortia of individual laboratories working on large interdisciplinary research programs, like the Human and Earth Microbiome Projects, have developed standardized protocols for DNA extraction, sequencing pipelines, and bioinformatics. These approaches provide large repositories of publicly available data to serve as references for on-going and future, hypothesis-driven studies to better characterize the roles of microbial communities in diverse ecosystems. In this review, we outline the currently available statistical approaches and tools to aid in statistically powered study designs and analyses. Given what is now known about the enormous diversity and variability of the microbial communities in aquatic and terrestrial habitats, we also discuss practical considerations for sample collection. Due to the extensive advances made in the field of metagenomics over the last decade, rigorous, well replicated, hypothesis-driven studies are: 1) needed, 2) now possible, and 3) essential to make best use of sequencing-based technologies to characterize the roles of microbial communities in the structure and function of diverse ecosystems.}, } @article {pmid30286722, year = {2018}, author = {Mancini, MV and Damiani, C and Accoti, A and Tallarita, M and Nunzi, E and Cappelli, A and Bozic, J and Catanzani, R and Rossi, P and Valzano, M and Serrao, A and Ricci, I and Spaccapelo, R and Favia, G}, title = {Estimating bacteria diversity in different organs of nine species of mosquito by next generation sequencing.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {126}, pmid = {30286722}, issn = {1471-2180}, mesh = {Animal Structures/*microbiology ; Animals ; Bacteria/classification/genetics/*isolation & purification ; *Biodiversity ; Culicidae/classification/*microbiology ; DNA, Bacterial/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Male ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Symbiosis in insects is accumulating significant amount of studies: the description of a wide array of mutualistic associations across the evolutionary history of insects suggests that resident microbiota acts as a driving force by affecting several aspects of hosts biology. Among arthropods, mosquito midgut microbiota has been largely investigated, providing crucial insights on the role and implications of host-symbiont relationships. However, limited amount of studies addressed their efforts on the investigation of microbiota colonizing salivary glands and reproductive tracts, crucial organs for pathogen invasion and vertical transmission of symbiotic microorganisms. Using 16S rRNA gene sequencing-based approach, we analysed the microbiota of gut, salivary glands and reproductive tracts of several mosquito species, representing some of the main vectors of diseases, aiming at describing the dynamics of bacterial communities within the individual.

RESULTS: We identified a shared core microbiota between different mosquito species, although interesting inter- and intra-species differences were detected. Additionally, our results showed deep divergences between genera, underlining microbiota specificity and adaptation to their host.

CONCLUSIONS: The comprehensive landscape of the bacterial microbiota components may ultimately provide crucial insights and novel targets for possible application of symbionts in innovative strategies for the control of vector borne diseases, globally named Symbiotic Control (SC), and suggesting that the holobiont of different mosquito species may significantly vary. Moreover, mosquito species are characterized by distinctive microbiota in different organs, likely reflecting different functions and/or adaptation processes.}, } @article {pmid30285861, year = {2018}, author = {O'Neill, AM and Gallo, RL}, title = {Host-microbiome interactions and recent progress into understanding the biology of acne vulgaris.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {177}, pmid = {30285861}, issn = {2049-2618}, support = {R01 AI116576/AI/NIAID NIH HHS/United States ; R01 AR064781/AR/NIAMS NIH HHS/United States ; R01 AR069653/AR/NIAMS NIH HHS/United States ; U19 AI117673/AI/NIAID NIH HHS/United States ; }, mesh = {Acne Vulgaris/drug therapy/*microbiology ; Dysbiosis/microbiology ; Hair Follicle/*microbiology ; Humans ; Metagenome/genetics ; Microbiota/genetics ; Propionibacterium acnes/*genetics/isolation & purification ; Sebaceous Glands/*microbiology ; Staphylococcus epidermidis/*genetics/isolation & purification ; }, abstract = {Acne is one of the most common skin diseases worldwide and results in major health care costs and significant morbidity to severely affected individuals. However, the pathophysiology of this disorder is not well understood. Host-microbiome interactions that affect both innate and adaptive immune homeostasis appear to be a central factor in this disease, with recent observations suggesting that the composition and activities of the microbiota in acne is perturbed. Staphylococcus epidermidis and Cutibacterium acnes (C. acnes; formerly Propionibacterium acnes) are two major inhabitants of the skin that are thought to contribute to the disease but are also known to promote health by inhibiting the growth and invasion of pathogens. Because C. acnes is ubiquitous in sebaceous-rich skin, it is typically labeled as the etiological agent of acne yet it fails to fulfill all of Koch's postulates. The outdated model of acne progression proposes that increased sebum production promotes over-proliferation of C. acnes in a plugged hair follicle, thereby driving inflammation. In contrast, growing evidence indicates that C. acnes is equally abundant in both unaffected and acne-affected follicles. Moreover, recent advances in metagenomic sequencing of the acne microbiome have revealed a diverse population structure distinct from healthy individuals, uncovering new lineage-specific virulence determinants. In this article, we review recent developments in the interactions of skin microbes with host immunity, discussing the contribution of dysbiosis to the immunobiology of acne and newly emerging skin microbiome-based therapeutics to treat acne.}, } @article {pmid30285625, year = {2018}, author = {Pacchioni, F and Esposito, A and Giacobazzi, E and Bettua, C and Struffi, P and Jousson, O}, title = {Air and waterborne microbiome of a pharmaceutical plant provide insights on spatiotemporal variations and community resilience after disturbance.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {124}, pmid = {30285625}, issn = {1471-2180}, mesh = {Air Microbiology ; Bacteria/classification/genetics/*isolation & purification ; DNA, Bacterial/genetics ; Fresh Water/*microbiology ; Groundwater/*microbiology ; *Microbiota ; Phylogeny ; Plants, Medicinal/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The presence of microrganisms in pharmaceutical production plant environments is typically monitored by cultural methods, however these cannot detect the unculturable fraction of the microbial community. To get more accurate information on the composition of these indoor microbial communities, both water and air microbiome from a pharmaceutical production plant were profiled by 16S amplicon sequencing.

RESULTS: In the water system, we found taxa which typically characterize surface freshwater, groundwater and oligotrophic environments. The airborne microbiome resulted dominated by taxa usually found in outdoor air in combination with human-associated taxa. The alpha- and beta- diversity values showed that the heat-based sanitization process of the water plant affects the composition of the water microbiome by transiently increasing both diversity and evenness. Taxonomic compositional shifts were also detected in response to sanitization, consisting in an increase of Firmicutes and α-Proteobacteria. On the other hand, seasonality seems to be the main driver of bacterial community composition in air of this work environment.

CONCLUSIONS: This approach resulted useful to describe the taxonomy of these indoor microbiomes and could be further applied to other built environments, in which the knowledge of the microbiome composition is of relevance. In addition, this study could assist in the design of new guidelines to improve microbiological quality control in indoor work environments.}, } @article {pmid30285475, year = {2020}, author = {Afshari, R and Pillidge, CJ and Dias, DA and Osborn, AM and Gill, H}, title = {Cheesomics: the future pathway to understanding cheese flavour and quality.}, journal = {Critical reviews in food science and nutrition}, volume = {60}, number = {1}, pages = {33-47}, doi = {10.1080/10408398.2018.1512471}, pmid = {30285475}, issn = {1549-7852}, mesh = {Cheese/*analysis/microbiology ; Computational Biology ; *Food Microbiology ; Metagenomics ; *Microbiota ; Taste ; }, abstract = {Cheese is a fermented dairy product, harboring diverse microbial communities (microbiota) that change over time and vary depending on the type of cheese and their respective starter and adjunct cultures. These microorganisms play a crucial role in determining the flavor, quality and safety of the final product. Exploring the composition of cheese microbiota and the underlying molecular mechanisms involved in cheese ripening has been the subject of many studies. Recent advances in next generation sequencing (NGS) methods and the development of sophisticated bioinformatics tools have provided deeper insights into the composition and potential functionality of cheese microbiota far beyond the information provided by culture-dependent methods. These advances, which include rRNA gene amplicon sequencing and metagenomics, have been complemented and expanded in recent years by the application of metatranscriptomics, metaproteomics and metabolomics. This paper reviews studies in which application of these meta-omics technologies has led to a better understanding of the microbial composition and functionality of cheese and highlights opportunities by which the integration of outputs from diverse multi-omics analytical platforms (cheesomics) could be used in the future to advance our knowledge of the cheese ripening process and identify biomarkers for predicting cheese flavor, quality, texture and safety, and bioactive metabolites with potential to influence human health.}, } @article {pmid30284602, year = {2019}, author = {Lin, X and Hetharua, B and Lin, L and Xu, H and Zheng, T and He, Z and Tian, Y}, title = {Mangrove Sediment Microbiome: Adaptive Microbial Assemblages and Their Routed Biogeochemical Processes in Yunxiao Mangrove National Nature Reserve, China.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {57-69}, pmid = {30284602}, issn = {1432-184X}, support = {2017YFC05061001//National Key Research and Development Program of China/ ; }, mesh = {Ammonium Compounds/metabolism ; Bacteria/*classification/genetics/*isolation & purification/metabolism ; Biodiversity ; China ; Conservation of Natural Resources ; DNA, Bacterial/genetics ; Geologic Sediments/chemistry/*microbiology ; *Microbiota ; Nitrates/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfur/metabolism ; Wetlands ; }, abstract = {Microorganisms play important roles in mangrove ecosystems. However, we know little about the ecological implications of mangrove microbiomes for high productivity and the efficient circulation of elements in mangrove ecosystems. Here, we focused on mangrove sediments located at the Yunxiao National Mangrove Reserve in southeast China, uncovering the mangrove microbiome using the 16S rRNA gene and shotgun metagenome sequencing approaches. Physicochemical assays characterized the Yunxiao mangrove sediments as carbon (C)-rich, sulfur (S)-rich, and nitrogen (N)-limited environment. Then phylogenetic analysis profiling a distinctive microbiome with an unexpected high frequency of Chloroflexi and Nitrospirae appeared to be an adaptive characteristic of microbial structure in S-rich habitat. Metagenome sequencing analysis revealed that the metabolic pathways of N and S cycling at the community-level were routed through ammonification and dissimilatory nitrate reduction to ammonium for N conservation in this N-limited habitat, and dissimilatory sulfate reduction along with polysulfide formation for generating bioavailable S resource avoiding the biotoxicity of sulfide in mangrove sediments. In addition, methane metabolism acted as a bridge to connect C cycling to N and S cycling. Further identification of possible biogeochemical linkers suggested Syntrophobacter, Sulfurovum, Nitrospira, and Anaerolinea potentially drive the coupling of C, N, and S cycling. These results highlighting the adaptive routed metabolism flow, a previously undescribed property of mangrove sediment microbiome, appears to be a defining characteristic of this habitat and may significantly contribute to the high productivity of mangrove ecosystems, which could be used as indicators for the health and biodiversity of mangrove ecosystems.}, } @article {pmid30282116, year = {2019}, author = {Taylor, SL and O'Farrell, HE and Simpson, JL and Yang, IA and Rogers, GB}, title = {The contribution of respiratory microbiome analysis to a treatable traits model of care.}, journal = {Respirology (Carlton, Vic.)}, volume = {24}, number = {1}, pages = {19-28}, doi = {10.1111/resp.13411}, pmid = {30282116}, issn = {1440-1843}, mesh = {Airway Management/*methods ; Humans ; Metagenomics/methods ; Microbiological Phenomena ; *Microbiota/drug effects/physiology ; Models, Organizational ; Patient Care Management/*organization & administration ; *Pulmonary Disease, Chronic Obstructive/immunology/microbiology/physiopathology/therapy ; Respiratory System/*microbiology ; }, abstract = {The composition of the airway microbiome in patients with chronic airway diseases, such as severe asthma, chronic obstructive pulmonary disease (COPD), bronchiectasis and cystic fibrosis (CF), has the potential to inform a precision model of clinical care. Patients with these conditions share overlapping disease characteristics, including airway inflammation and airflow limitation. The clinical management of chronic respiratory conditions is increasingly moving away from a one-size-fits-all model based on primary diagnosis, towards care targeting individual disease traits, and is particularly useful for subgroups of patients who respond poorly to conventional therapies. Respiratory microbiome analysis is an important potential contributor to such a 'treatable traits' approach, providing insight into both microbial drivers of airways disease, and the selective characteristics of the changing lower airway environment. We explore the potential to integrate respiratory microbiome analysis into a treatable traits model of clinical care and provide a practical guide to the application and clinical interpretation of respiratory microbiome analysis.}, } @article {pmid30281913, year = {2019}, author = {Jusino, MA and Banik, MT and Palmer, JM and Wray, AK and Xiao, L and Pelton, E and Barber, JR and Kawahara, AY and Gratton, C and Peery, MZ and Lindner, DL}, title = {An improved method for utilizing high-throughput amplicon sequencing to determine the diets of insectivorous animals.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {176-190}, doi = {10.1111/1755-0998.12951}, pmid = {30281913}, issn = {1755-0998}, support = {//United States Forest Service, Northern Research Station/ ; Hatch Formula Funds//University of Wisconsin-Madison, Wisconsin Agricultural Experiment Station/ ; IOS-1121739//National Science Foundation/ ; IOS-1121807//National Science Foundation/ ; }, mesh = {Animals ; *Chiroptera ; Computational Biology/*methods ; DNA/chemistry/genetics/isolation & purification ; Electron Transport Complex IV/genetics ; Feces/chemistry ; *Feeding Behavior ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; }, abstract = {DNA analysis of predator faeces using high-throughput amplicon sequencing (HTS) enhances our understanding of predator-prey interactions. However, conclusions drawn from this technique are constrained by biases that occur in multiple steps of the HTS workflow. To better characterize insectivorous animal diets, we used DNA from a diverse set of arthropods to assess PCR biases of commonly used and novel primer pairs for the mitochondrial gene, cytochrome oxidase C subunit 1 (COI). We compared diversity recovered from HTS of bat guano samples using a commonly used primer pair "ZBJ" to results using the novel primer pair "ANML." To parameterize our bioinformatics pipeline, we created an arthropod mock community consisting of single-copy (cloned) COI sequences. To examine biases associated with both PCR and HTS, mock community members were combined in equimolar amounts both pre- and post-PCR. We validated our system using guano from bats fed known diets and using composite samples of morphologically identified insects collected in pitfall traps. In PCR tests, the ANML primer pair amplified 58 of 59 arthropod taxa (98%), whereas ZBJ amplified 24-40 of 59 taxa (41%-68%). Furthermore, in an HTS comparison of field-collected samples, the ANML primers detected nearly fourfold more arthropod taxa than the ZBJ primers. The additional arthropods detected include medically and economically relevant insect groups such as mosquitoes. Results revealed biases at both the PCR and sequencing levels, demonstrating the pitfalls associated with using HTS read numbers as proxies for abundance. The use of an arthropod mock community allowed for improved bioinformatics pipeline parameterization.}, } @article {pmid30280756, year = {2018}, author = {Patini, R and Staderini, E and Lajolo, C and Lopetuso, L and Mohammed, H and Rimondini, L and Rocchetti, V and Franceschi, F and Cordaro, M and Gallenzi, P}, title = {Relationship between oral microbiota and periodontal disease: a systematic review.}, journal = {European review for medical and pharmacological sciences}, volume = {22}, number = {18}, pages = {5775-5788}, doi = {10.26355/eurrev_201809_15903}, pmid = {30280756}, issn = {2284-0729}, mesh = {Humans ; *Microbiota ; Mouth/*microbiology ; Periodontal Diseases/*microbiology ; }, abstract = {OBJECTIVE: In recent years metagenomic analysis has become more accessible for the characterization of biological specimens. There has been an important increase of studies using this technique for subgingival human samples. To date, there are no updated systematic reviews on the relationship between oral microbiota and periodontal disease. The aim of the present systematic review was to update data about studies concerning the influences of changes in oral microbiota composition on the periodontal status in human subjects.

MATERIALS AND METHODS: An electronic search was conducted in four databases (MEDLINE, Scopus, CENTRAL and Web of Science) for articles published in English from January 2014 to April 2018. In vitro or animal studies, case reports, case series, retrospective studies, review articles, abstracts and discussions were excluded. Also, studies that evaluated less than 5 microbial species, only viruses or already known periodontal pathogens were excluded. Two independent researches selected the studies and extracted the data. The quality of evidence was assessed as high, moderate or low for each microorganism.

RESULTS: Eight studies and three additional publications recovered from the bibliography search of the selected articles were included in the review. The Bacteria domain was the main detected among the others and it included 53 species. The review confirmed the presence of recognized periodontal pathogens such as the members of the red complex but also identified, with high weight of evidence, the presence of new pathogens.

CONCLUSIONS: The results of this systematic review support high evidence for the association of 3 new species/genera with the etiology of periodontitis. Future investigations on the actual role of these new pathogens in the onset and progression of the disease are needed.}, } @article {pmid30278220, year = {2019}, author = {Wang, J and Huang, Y and Xu, K and Zhang, X and Sun, H and Fan, L and Yan, M}, title = {White spot syndrome virus (WSSV) infection impacts intestinal microbiota composition and function in Litopenaeus vannamei.}, journal = {Fish & shellfish immunology}, volume = {84}, number = {}, pages = {130-137}, doi = {10.1016/j.fsi.2018.09.076}, pmid = {30278220}, issn = {1095-9947}, mesh = {Animals ; Bacteria/genetics/isolation & purification ; DNA Virus Infections/*microbiology/veterinary ; DNA, Bacterial/genetics ; *Gastrointestinal Microbiome ; Penaeidae/*microbiology ; RNA, Ribosomal, 16S/genetics ; *White spot syndrome virus 1 ; }, abstract = {Intestinal microbiota homeostasis is crucial to the health of host. Pathogen invasion results in dynamics of microbiota composition and structure, disrupting their function in maintaining host health. WSSV is the most prevalent viral pathogen and is able to cause extremely high mortality in Litopenaeus vannamei. However, the changes of intestinal microbiota induced by WSSV are yet to be elucidated. In this study, we analyzed and compared the microbiota of healthy and WSSV-challenged shrimp intestines. Though the richness and diversity of microbiota was barely affected by WSSV, the abundance of predominant phyla like Proteobacteria and Fusobacteria were upregulated significantly, while Bacteroidetes and Tenericutes were significantly decreased in WSSV-infected shrimps. At the genus level, significant increase was observed in Photobacterium, Propionigenium and Arcobacter, as well as significant decrease in Candidatus Bacilloplasma and Flavobacterium in WSSV-infected shrimps. Additionally, metagenomic predictions by PICRUSt suggested that the altered microbiota was mainly related to metabolism, human diseases, genetic information processing, environmental information processing and cellular processes. These results suggested that the invasion of WSSV could impact intestinal microbiota composition and function in L. vannamei.}, } @article {pmid30277147, year = {2018}, author = {Vamanu, E}, title = {Complementary Functional Strategy for Modulation of Human Gut Microbiota.}, journal = {Current pharmaceutical design}, volume = {24}, number = {35}, pages = {4144-4149}, doi = {10.2174/1381612824666181001154242}, pmid = {30277147}, issn = {1873-4286}, mesh = {Agaricales/*chemistry ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Polyphenols/chemistry/*pharmacology ; }, abstract = {Two pathologies commonly associated with gut microbiota dysbiosis are type 2 diabetes and cardiovascular diseases. Since diet and medication are two important causes of microbiome fingerprint modifications, new complementary and alternative methods can include wild edible mushrooms, which serve as functional products, given their properties in modulating the microbial pattern at the colon level. A disturbance in microbial balance translates into the occurrence of degenerative dysfunctions that are also associated with other pathologies, such as obesity, colon cancer. The metagenomic study has enabled the identification of some competitive microbiological and biochemical biomarkers which allow the development of innovative strategies in controling microbial disbalance from human gut. Thus, the aim of this review was to present the significant findings related to human microbiome modulation via the prebiotic effects of wild edible mushrooms as a complementary strategy to modern treatment. Certain mushroom species have been approached and their effects on the microbiota fingerprint of two major target groups are highlighted.}, } @article {pmid30275573, year = {2018}, author = {Gonzalez, A and Navas-Molina, JA and Kosciolek, T and McDonald, D and Vázquez-Baeza, Y and Ackermann, G and DeReus, J and Janssen, S and Swafford, AD and Orchanian, SB and Sanders, JG and Shorenstein, J and Holste, H and Petrus, S and Robbins-Pianka, A and Brislawn, CJ and Wang, M and Rideout, JR and Bolyen, E and Dillon, M and Caporaso, JG and Dorrestein, PC and Knight, R}, title = {Qiita: rapid, web-enabled microbiome meta-analysis.}, journal = {Nature methods}, volume = {15}, number = {10}, pages = {796-798}, pmid = {30275573}, issn = {1548-7105}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; P30 MH062512/MH/NIMH NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Humans ; *Internet ; *Metagenomics ; *Microbiota ; *Software ; User-Computer Interface ; }, abstract = {Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be fully understood, data must be aggregated into meta-analyses. This makes it possible to generate new hypotheses by finding features that are reproducible across biospecimens and data layers. Qiita dramatically accelerates such integration tasks in a web-based microbiome-comparison platform, which we demonstrate with Human Microbiome Project and Integrative Human Microbiome Project (iHMP) data.}, } @article {pmid30274716, year = {2018}, author = {Batista, D and Costa, R and Carvalho, AP and Batista, WR and Rua, CPJ and de Oliveira, L and Leomil, L and Fróes, AM and Thompson, FL and Coutinho, R and Dobretsov, S}, title = {Environmental conditions affect activity and associated microorganisms of marine sponges.}, journal = {Marine environmental research}, volume = {142}, number = {}, pages = {59-68}, doi = {10.1016/j.marenvres.2018.09.020}, pmid = {30274716}, issn = {1879-0291}, mesh = {Animals ; Aquatic Organisms/chemistry/drug effects/microbiology ; *Environment ; Microbiota/*drug effects ; Porifera/chemistry/drug effects/*microbiology ; Water Pollutants/*toxicity ; }, abstract = {Changes in environmental conditions can influence sponges and their holobionts. The present study investigated the effect of upwelling and anthropogenic pollution on the bioactivity of marine sponges, microbial communities and functional genes, and composition of their chemical compounds. The species Dysidea etheria, Darwinella sp., Hymeniacidon heliophila and Tedania ignis were collected from areas with distinct influence of upwelling and low anthropogenic impact and from areas without influence of upwelling but affected by sewage and the port. In most cases, the same sponge species collected from areas with distinct environmental conditions had a different chemical composition, antifouling activity, composition and diversity of associated microorganisms. Antimicrobial, quorum sensing inhibitory and anti-larval activities of sponge extracts were more pronounced in the area without upwelling showing higher level of anthropogenic pollution. This study suggests that upwelling and anthropogenic pollution affect the chemical activity and holobiome composition of sponges.}, } @article {pmid30273610, year = {2018}, author = {Schriefer, AE and Cliften, PF and Hibberd, MC and Sawyer, C and Brown-Kennerly, V and Burcea, L and Klotz, E and Crosby, SD and Gordon, JI and Head, RD}, title = {A multi-amplicon 16S rRNA sequencing and analysis method for improved taxonomic profiling of bacterial communities.}, journal = {Journal of microbiological methods}, volume = {154}, number = {}, pages = {6-13}, pmid = {30273610}, issn = {1872-8359}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; R01 DK030292/DK/NIDDK NIH HHS/United States ; R01 DK070977/DK/NIDDK NIH HHS/United States ; P30 CA091842/CA/NCI NIH HHS/United States ; UL1 TR000448/TR/NCATS NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; UL1 TR002345/TR/NCATS NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/*classification/*genetics ; Base Sequence ; Biodiversity ; DNA, Bacterial/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {Metagenomic sequencing of bacterial samples has become the gold standard for profiling microbial populations, but 16S rRNA profiling remains widely used due to advantages in sample throughput, cost, and sensitivity even though the approach is hampered by primer bias and lack of specificity. We hypothesized that a hybrid approach, that combined targeted PCR amplification with high-throughput sequencing of multiple regions of the genome, would capture many of the advantages of both approaches. We developed a method that identifies and quantifies members of bacterial communities through simultaneous analysis of multiple variable regions of the bacterial 16S rRNA gene. The method combines high-throughput microfluidics for PCR amplification, short read DNA sequencing, and a custom algorithm named MVRSION (Multiple 16S Variable Region Species-Level IdentificatiON) for optimizing taxonomic assignment. MVRSION performance was compared to single variable region analyses (V3 or V4) of five synthetic mixtures of human gut bacterial strains using existing software (QIIME), and the results of community profiling by shotgun sequencing (COPRO-Seq) of fecal DNA samples collected from gnotobiotic mice colonized with a defined, phylogenetically diverse consortium of human gut bacterial strains. Positive predictive values for MVRSION ranged from 65%-91% versus 44%-61% for single region QIIME analyses (p < .01, p < .001), while the abundance estimate r[2] for MVRSION compared to COPRO-Seq was 0.77 vs. 0.46 and 0.45 for V3-QIIME and V4-QIIME, respectively. MVRSION represents a generally applicable tool for taxonomic classification that is superior to single-region 16S rRNA methods, resource efficient, highly scalable for assessing the microbial composition of up to thousands of samples concurrently, with multiple applications ranging from whole community profiling to targeted tracking of organisms of interest in diverse habitats as a function of specified variables/perturbations.}, } @article {pmid30272305, year = {2018}, author = {Zhou, S and Cai, Y and Wang, M and Yang, WD and Duan, N}, title = {Oral microbial flora of patients with Sicca syndrome.}, journal = {Molecular medicine reports}, volume = {18}, number = {6}, pages = {4895-4903}, pmid = {30272305}, issn = {1791-3004}, mesh = {Biodiversity ; Case-Control Studies ; Computational Biology/methods ; Female ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth/*microbiology ; Sjogren's Syndrome/*etiology ; }, abstract = {Primary sicca syndrome (pSS) is a systemic autoimmune disease. However, its exact etiology and pathogenesis remain elusive. Various infectious factors have been identified to be closely associated with the occurrence and development of PSS. The present study aimed to assess the composition of the oral microbial flora of patients with pSS in China in order to provide guidance for treatment. The microbial flora of nine patients with pSS and five healthy controls from East China was evaluated in saliva samples using high‑throughput sequencing. A high microbial diversity was detected in the pSS and control groups, with bacteroidetes, firmicutes and proteobacteria constituting the largest phyla in the two groups. Compared with the control group, bacteroidetes and actinobacteria were significantly more abundant in the pSS group, whereas proteobacteria were significantly less abundant. However, no significant differences in bacterial richness and diversity were observed between the two groups. According to a Kyoto Encyclopedia of Genes and Genomes linear discriminant analysis, genes regulating cell apoptosis and the immune and digestive systems were significantly upregulated in the pSS group compared with those in the control group. In conclusion, the present study provided basic data on the flora of the oral cavity in patients with pSS from East China and may serve as a reference for the treatment of this condition.}, } @article {pmid30272228, year = {2018}, author = {Hu, F and Xue, Y and Guo, C and Liu, J and Mao, S}, title = {The response of ruminal fermentation, epithelium-associated microbiota, and epithelial barrier function to severe feed restriction in pregnant ewes.}, journal = {Journal of animal science}, volume = {96}, number = {10}, pages = {4293-4305}, pmid = {30272228}, issn = {1525-3163}, mesh = {Animal Feed/*analysis ; Animals ; Butyrates/analysis ; Diet/veterinary ; Epithelium/microbiology/physiology ; Fatty Acids, Volatile/analysis ; Female ; Fermentation ; *Food Deprivation ; *Microbiota ; Pregnancy ; Propionates/analysis ; Random Allocation ; Rumen/microbiology/physiology ; Sheep/microbiology/*physiology ; }, abstract = {The objective of this study was to evaluate the changes in the ruminal fermentation, epithelium-associated microbiota, and ruminal epithelial barrier function in response to severe feed restriction (SFR) in pregnant ewes. Sixteen pregnant ewes (108 d of gestation) were randomly blocked and assigned to 1 of 2 treatments: control (CON, n = 8) and SFR (n = 8). Ewes were fed a common diet with a 60:40 forage to concentrate ratio for 7-d baseline period followed by a SFR challenge period. Ewes on the SFR treatment were restricted to 30% of the base for 15 d. At the end of the experimental period, all animals were slaughtered and then ruminal contents and ruminal epithelial tissue were collected. Results showed that ruminal pH was greater in SFR group (P = 0.040) compared with CON group, while SFR decreased (P < 0.05) the concentrations of ruminal acetate, propionate, butyrate, and total volatile fatty acid. A plot of principal coordinate analysis and analysis of molecular variance revealed that the composition of ruminal epithelial bacterial communities in the CON group was distinct from that of the ruminal epithelial microbiome in the SFR animals. At the genus level, SFR increased the abundance of unclassified Neisseriaceae, Comamonas, and Papillibacter, and decreased the proportion of Howardella, Desulfobulbus, and Suttonella (P < 0.05) compared with CON group. The metagenome of ruminal epithelium-associated microbiota predicted by PICRUSt revealed that the SFR significantly affected 14 metabolic pathways, and 9 were significantly enriched in the SFR group. In particular, SFR markedly increased relative abundances of dominant gene families involved in amino acid metabolism (P = 0.003), cellular processes and signaling (P = 0.021), and lipid metabolism (P = 0.001). The real-time PCR results showed SFR decreased the mRNA expression of IL-10 (P = 0.003) and upregulated the mRNA expression of IL-6 (P = 0.003) and TLR4 (P = 0.021). The mRNA expression of Claudin-1 (P = 0.001) and ZO-1 (P = 0.009) were lower in the SFR group compared with the CON group. Generally, our data suggest that SFR decreased most ruminal fermentation parameters, altered the composition of rumen epithelium-associated microbiota, and compromised the barrier function of rumen epithelium. These findings are of great importance for understanding the alteration in the rumen function following SFR in pregnant ewes.}, } @article {pmid30271256, year = {2018}, author = {Anslan, S and Nilsson, RH and Wurzbacher, C and Baldrian, P and Leho Tedersoo, and Bahram, M}, title = {Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding.}, journal = {MycoKeys}, volume = {}, number = {39}, pages = {29-40}, pmid = {30271256}, issn = {1314-4049}, abstract = {Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.}, } @article {pmid30270610, year = {2018}, author = {Fan, Y and Ya-E, Z and Ji-Dong, W and Yu-Fan, L and Ying, Z and Ya-Lun, S and Meng-Yu, M and Rui-Ling, Z}, title = {Comparison of Microbial Diversity and Composition in Jejunum and Colon of the Alcohol-dependent Rats.}, journal = {Journal of microbiology and biotechnology}, volume = {28}, number = {11}, pages = {1883-1895}, doi = {10.4014/jmb.1806.06050}, pmid = {30270610}, issn = {1738-8872}, mesh = {Alcoholism/*microbiology ; Animals ; Bacteria/classification/genetics ; *Biodiversity ; Colon/*microbiology ; Disease Models, Animal ; Dysbiosis/*microbiology ; Ethanol/adverse effects ; Gastrointestinal Microbiome/genetics ; Jejunum/*microbiology ; Male ; Metabolic Networks and Pathways/genetics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Wistar ; }, abstract = {Alcohol dependence is a global public health problem, yet the mechanisms of alcohol dependence are incompletely understood. The traditional view has been that ethanol alters various neurotransmitters and their receptors in the brain and causes the addiction. However, an increasing amount of experimental evidence suggests that gut microbiota also influence brain functions via gut-to-brain interactions, and may therefore induce the development of alcohol use disorders. In this study, a rat model of alcohol dependence and withdrawal was employed, the gut microbiota composition was analyzed by high-throughput 16S rRNA gene sequencing, and the metagenome function was predicted by PICRUSt software. The results suggested that chronic alcohol consumption did not significantly alter the diversity and richness of gut microbiota in the jejunum and colon, but rather markedly changed the microbiota composition structure in the colon. The phyla Bacteroidetes and eight genera including Bacteroidales S24-7, Ruminococcaceae, Parabacteroides, Butyricimonas, et al were drastically increased, however the genus Lactobacillus and gauvreauii in the colon were significantly decreased in the alcohol dependence group compared with the withdrawal and control groups. The microbial functional prediction analysis revealed that the proportions of amino acid metabolism, polyketide sugar unit biosynthesis and peroxisome were significantly increased in the AD group. This study demonstrated that chronic alcohol consumption has a dramatic effect on the microbiota composition structure in the colon but few effects on the jejunum. Inducement of colonic microbiota dysbiosis due to alcohol abuse seems to be a factor of alcohol dependence, which suggests that modulating colonic microbiota composition might be a potentially new target for treating alcohol addiction.}, } @article {pmid30270525, year = {2019}, author = {Black, EM and Chimenti, MS and Just, CL}, title = {Metagenomic analysis of nitrogen-cycling genes in upper Mississippi river sediment with mussel assemblages.}, journal = {MicrobiologyOpen}, volume = {8}, number = {5}, pages = {e00739}, pmid = {30270525}, issn = {2045-8827}, support = {P30 ES005605/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Bivalvia/*growth & development ; Geologic Sediments/*microbiology ; Metabolic Networks and Pathways/*genetics ; Microbiota ; *Nitrogen Cycle ; Nitrogen Fixation ; Rivers/*microbiology ; }, abstract = {We investigated the impact of native freshwater mussel assemblages (order Unionoida) on the abundance and composition of nitrogen-cycling genes in sediment of an upper Mississippi river habitat. We hypothesized that the genomic potential for ammonia and nitrite oxidation would be greater in the sediment with mussel assemblages, presumably due to mussel biodeposition products, namely ammonia and organic carbon. Regardless of the presence of mussels, upper Mississippi river sediment microbial communities had the largest genomic potential for nitrogen fixation followed by urea catabolism, nitrate metabolism, and nitrate assimilation, as evidenced by analysis of nitrogen cycling pathway abundances. However, genes encoding nitrate and nitrite redox reactions, narGHI and nxrAB, were the most abundant functional genes of the nitrogen cycling gene families. Using linear discriminant analysis (LDA), we found nitrification genes were the most important biomarkers for nitrogen cycling genomic potential when mussels were present, and this presented an opposing effect on the abundance of genes encoding nitric oxide reduction. The genes involved in nitrification that increased the most were amoA associated with comammox Nitrospira and nxr homologs associated with Nitrospira. On the other hand, the most distinctive biomarkers of microbial communities without mussels were norB and nrfA, as part of denitrification and dissimilatory nitrate reduction to ammonium pathways, respectively. Ultimately, this research demonstrates the impact of native mollusks on microbial nitrogen cycling in an aquatic agroecosystem.}, } @article {pmid30270128, year = {2020}, author = {Antunes-Lopes, T and Vale, L and Coelho, AM and Silva, C and Rieken, M and Geavlete, B and Rashid, T and Rahnama'i, SM and Cornu, JN and Marcelissen, T and , }, title = {The Role of Urinary Microbiota in Lower Urinary Tract Dysfunction: A Systematic Review.}, journal = {European urology focus}, volume = {6}, number = {2}, pages = {361-369}, doi = {10.1016/j.euf.2018.09.011}, pmid = {30270128}, issn = {2405-4569}, mesh = {Humans ; Lower Urinary Tract Symptoms/*microbiology ; *Microbiota ; Urinary Tract/*microbiology ; }, abstract = {CONTEXT: Until 2012, the urinary tract of healthy individuals was considered to be sterile. The advent of metagenomic sequencing revealed a unique urinary microbiota (UM). This paradigm shift appears to have prolific implications in the etiology of several functional lower urinary tract (LUT) disorders.

OBJECTIVE: To systematically summarize recent data on the role of UM in LUT dysfunction.

EVIDENCE ACQUISITION: We performed a critical review according to the Preferred Reporting Items for Systematic Review and Meta-analysis (PRISMA) statement. We conducted a search on PubMed/MEDLINE and SCOPUS with the following MESH terms/keywords: "Microbiome OR Microbiota AND (urinary disorder OR urinary tract symptom OR overactive bladder OR urinary incontinence OR interstitial cystitis OR chronic prostatitis)." The range of search was placed between January 2010 and April 2018, and articles with no full text available or those not written in English were excluded. All retrieved papers were first reviewed by title and abstract, yielding a total of 303 papers. Additional manuscripts, such as those referenced by reviews, were further included. Thirty-six publications were included.

EVIDENCE SYNTHESIS: Analysis by 16S rRNA sequence and expanded quantitative urine culture provided evidence for the presence of live bacteria in urine, nondetectable by standard culture protocols. Moreover, differences in the UM between healthy individuals and patients with LUT dysfunction were demonstrated.

CONCLUSIONS: In the near future, urologists must consider urinary dysbiosis as a possible cause of different functional LUT disorders, with potential clinical implications in their diagnosis and treatment.

PATIENT SUMMARY: Development of metagenomic sequencing revealed a unique urinary microbiota nondetectable by standard culture protocols. This systematic review summarizing recent data on the role of urinary microbiota in lower urinary tract (LUT) dysfunction supports urinary dysbiosis as a possible cause of different functional LUT disorders.}, } @article {pmid30269412, year = {2018}, author = {Tarnecki, AM and Rhody, NR and Walsh, CJ}, title = {Health Characteristics and Blood Bacterial Assemblages of Healthy Captive Red Drum: Implications for Aquaculture and Fish Health Management.}, journal = {Journal of aquatic animal health}, volume = {30}, number = {4}, pages = {339-353}, doi = {10.1002/aah.10047}, pmid = {30269412}, issn = {1548-8667}, mesh = {Animals ; Aquaculture/methods ; Bacteremia/immunology/*veterinary ; Bacteria/classification/genetics ; Fish Diseases/immunology/microbiology ; Immunity, Innate ; *Microbiota ; Perciformes/blood/immunology/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The newly emerging tissue microbiota hypothesis suggests that bacteria found in blood and tissues play a role in host health, as these bacterial communities have been associated with various noncommunicable diseases such as obesity, liver disease, and cardiovascular disease. Numerous reports have identified bacteria in the blood of healthy finfish, indicating bacteremia may not always indicate disease. Current research priorities in aquaculture include the development of technologies and practices that will allow for an effective reduction in antibiotic use for the prevention and treatment of disease. Overall, a better understanding of fish health is needed, particularly among species selected for commercial-scale production. This study investigated blood characteristics of cultured Red Drum Sciaenops ocellatus with the tissue microbiota hypothesis in mind. Bacterial assemblages within the blood were characterized using next-generation sequencing and compared with other various blood characteristics, including innate immune function enzymes, between two fish cohorts reared in aquaculture. A total of 137 prokaryotic operational taxonomic units (OTUs) were identified from the blood of Red Drum. Microbiota diversity and structure varied greatly among individuals, for which the number of OTUs ranged from 4 to 58; however, predicted metagenomic function was highly similar between individuals and was dominated by the metabolism of carbohydrates and amino acids and membrane transport. Communities were dominated by Proteobacteria, followed by Bacteroidetes, Firmicutes, and Actinobacteria. The most commonly identified genera included Acinetobacter, Bacillus, Corynebacterium, and Pseudomonas. Three genera previously identified as containing marine fish pathogens were detected: Corynebacterium, Pantoea, and Chryseobacterium. A subset of bacterial OTUs were positively correlated with superoxide dismutase activity and negatively correlated with lysozyme activity, indicating a relationship between blood microbiota and the innate immune system. The results of this study provide further evidence for the tissue microbiota hypothesis and demonstrate the potential for these bacterial communities to be linked to immunological characteristics often used as biomarkers for fish health.}, } @article {pmid30269123, year = {2018}, author = {Hattori, M}, title = {[Ecology and function of human microbiomes.].}, journal = {Clinical calcium}, volume = {28}, number = {10}, pages = {1398-1405}, pmid = {30269123}, issn = {0917-5857}, mesh = {Bacteria ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; }, abstract = {Hundreds of trillions of bacteria consisting of ~1,000 species reside in various human body sites to form bacterial communities(microbiomes)specific for the sites. In the past decade, the human microbiome research in the world incredibly advanced by development of a culture-independent metagenomic analysis based on next-generation sequencing technologies. Particularly, current studies have revealed that the human gut microbiome is profoundly associated with the host's health and disease.}, } @article {pmid30268905, year = {2018}, author = {Levin, BJ and Balskus, EP}, title = {Discovering radical-dependent enzymes in the human gut microbiota.}, journal = {Current opinion in chemical biology}, volume = {47}, number = {}, pages = {86-93}, doi = {10.1016/j.cbpa.2018.09.011}, pmid = {30268905}, issn = {1879-0402}, mesh = {Choline/metabolism ; Enzymes/*analysis/genetics/metabolism ; *Gastrointestinal Microbiome ; Humans ; Lyases/analysis/genetics/metabolism ; Metagenome/physiology ; Methylamines/metabolism ; Propanediol Dehydratase/analysis/genetics/metabolism ; Proteome/genetics/metabolism ; }, abstract = {Human gut microbes have a tremendous impact on human health, in part due to their unique chemical capabilities. In the anoxic environment of the healthy human gut, many important microbial metabolic transformations are performed by radical-dependent enzymes. Although identifying and characterizing these enzymes has been challenging, recent advances in genome and metagenome sequencing have enabled studies of their chemistry and biology. Focusing on the glycyl radical enzyme family, one of the most enriched protein families in the human gut microbiota, we highlight different approaches for discovering radical-dependent enzymes that influence host health and disease.}, } @article {pmid30268435, year = {2018}, author = {Beyter, D and Lin, MS and Yu, Y and Pieper, R and Bafna, V}, title = {ProteoStorm: An Ultrafast Metaproteomics Database Search Framework.}, journal = {Cell systems}, volume = {7}, number = {4}, pages = {463-467.e6}, pmid = {30268435}, issn = {2405-4712}, support = {P41 GM103484/GM/NIGMS NIH HHS/United States ; P41 RR024851/RR/NCRR NIH HHS/United States ; R01 GM114362/GM/NIGMS NIH HHS/United States ; T32 GM008806/GM/NIGMS NIH HHS/United States ; }, mesh = {Databases, Genetic ; Humans ; *Metagenome ; Microbiota/genetics ; Proteomics/*methods/standards ; *Software ; Urinary Tract Infections/microbiology ; }, abstract = {Shotgun metaproteomics has the potential to reveal the functional landscape of microbial communities but lacks appropriate methods for complex samples with unknown compositions. In the absence of prior taxonomic information, tandem mass spectra would be searched against large pan-microbial databases, which requires heavy computational workload and reduces sensitivity. We present ProteoStorm, an efficient database search framework for large-scale metaproteomics studies, which identifies high-confidence peptide-spectrum matches (PSMs) while achieving a two-to-three orders-of-magnitude speedup over popular tools. A reanalysis of a urinary tract infection (UTI) dataset of 110 individuals revealed a complex pattern of polymicrobial expression, including sub-types of UTIs, cases of bacterial vaginosis, and evidence of no underlying disease. Importantly, compared to the initial UTI study that restricted the search database to a manually curated list of 20 genera, ProteoStorm identified additional genera that were previously unreported, including a case of infection with the rare pathogen Propionimicrobium.}, } @article {pmid30267472, year = {2019}, author = {Suchan, T and Talavera, G and Sáez, L and Ronikier, M and Vila, R}, title = {Pollen metabarcoding as a tool for tracking long-distance insect migrations.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {149-162}, doi = {10.1111/1755-0998.12948}, pmid = {30267472}, issn = {1755-0998}, support = {CGL2016-76322//AEI/FEDER, UE/ ; IJCI-2016-29083//MINECO programme Juan de la Cierva Incorporación/ ; LRB16/1015//British Ecological Society/ ; //Polish Academy of Sciences statutory fund/ ; 622716//FP7/ ; WW1-300R-18//National Geographic Society/ ; }, mesh = {Africa ; *Animal Migration ; Animals ; Arabia ; Butterflies/*physiology ; DNA Barcoding, Taxonomic/*methods ; Entomology/*methods ; Mediterranean Region ; Metagenomics/*methods ; Pollen/*genetics ; Spain ; }, abstract = {Insects account for a large portion of Earth's biodiversity and are key players for ecosystems, notably as pollinators. While insect migration is suspected to represent a natural phenomenon of major importance, remarkably little is known about it, except for a few flagship species. The reason for this situation is mainly due to technical limitations in the study of insect movement. Here, we propose using metabarcoding of pollen carried by insects as a method for tracking their migrations. We developed a flexible and simple protocol allowing efficient multiplexing and not requiring DNA extraction, one of the most time-consuming part of metabarcoding protocols, and apply this method to the study of the long-distance migration of the butterfly Vanessa cardui, an emerging model for insect migration. We collected 47 butterfly samples along the Mediterranean coast of Spain in spring and performed metabarcoding of pollen collected from their bodies to test for potential arrivals from the African continent. In total, we detected 157 plant species from 23 orders, most of which (82.8%) were insect-pollinated. Taxa present in Africa-Arabia represented 73.2% of our data set, and 19.1% were endemic to this region, strongly supporting the hypothesis that migratory butterflies colonize southern Europe from Africa in spring. Moreover, our data suggest that a northwards trans-Saharan migration in spring is plausible for early arrivals (February) into Europe, as shown by the presence of Saharan floristic elements. Our results demonstrate the possibility of regular insect-mediated transcontinental pollination, with potential implications for ecosystem functioning, agriculture and plant phylogeography.}, } @article {pmid30267313, year = {2018}, author = {Song, EJ and Lee, ES and Nam, YD}, title = {Progress of analytical tools and techniques for human gut microbiome research.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {56}, number = {10}, pages = {693-705}, pmid = {30267313}, issn = {1976-3794}, mesh = {Computational Biology/*trends ; Data Analysis ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/*trends ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Massive DNA sequencing studies have expanded our insights and understanding of the ecological and functional characteristics of the gut microbiome. Advanced sequencing technologies allow us to understand the close association of the gut microbiome with human health and critical illnesses. In the future, analyses of the gut microbiome will provide key information associating with human individual health, which will help provide personalized health care for diseases. Numerous molecular biological analysis tools have been rapidly developed and employed for the gut microbiome researches; however, methodological differences among researchers lead to inconsistent data, limiting extensive share of data. It is therefore very essential to standardize the current methodologies and establish appropriate pipelines for human gut microbiome research. Herein, we review the methods and procedures currently available for studying the human gut microbiome, including fecal sample collection, metagenomic DNA extraction, massive DNA sequencing, and data analyses with bioinformatics. We believe that this review will contribute to the progress of gut microbiome research in the clinical and practical aspects of human health.}, } @article {pmid30266729, year = {2018}, author = {Vital, M and Howe, A and Bergeron, N and Krauss, RM and Jansson, JK and Tiedje, JM}, title = {Metagenomic Insights into the Degradation of Resistant Starch by Human Gut Microbiota.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {23}, pages = {}, pmid = {30266729}, issn = {1098-5336}, support = {RC1 DK086472/DK/NIDDK NIH HHS/United States ; UH3 DK083993/DK/NIDDK NIH HHS/United States ; UL1 TR000004/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Bacteria/classification/*genetics/*isolation & purification/metabolism ; Diabetes Mellitus, Type 2/diet therapy/metabolism/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Phylogeny ; Starch/analysis/*metabolism ; }, abstract = {Several studies monitoring alterations in the community structure upon resistant starch (RS) interventions are available, although comprehensive function-based analyses are lacking. Recently, a multiomics approach based on 16S rRNA gene sequencing, metaproteomics, and metabolomics on fecal samples from individuals subjected to high and low doses of type 2 RS (RS2; 48 g and 3 g/2,500 kcal, respectively, daily for 2 weeks) in a crossover intervention experiment was performed. In the present study, we did pathway-based metagenomic analyses on samples from a subset of individuals (n = 12) from that study to obtain additional detailed insights into the functional structure at high resolution during RS2 intervention. A mechanistic framework based on obtained results is proposed where primary degradation was governed by Firmicutes, with Ruminococcus bromii as a major taxon involved, providing fermentation substrates and increased acetate concentrations for the growth of various major butyrate producers exhibiting the enzyme butyryl-coenzyme A (CoA):acetate CoA-transferase. H2-scavenging sulfite reducers and acetogens concurrently increased. Individual responses of gut microbiota were noted, where seven of the 12 participants displayed all features of the outlined pattern, whereas four individuals showed mixed behavior and one subject was unresponsive. Intervention order did not affect the outcome, emphasizing a constant substrate supply for maintaining specific functional communities.IMPORTANCE Manipulation of gut microbiota is increasingly recognized as a promising approach to reduce various noncommunicable diseases, such as obesity and type 2 diabetes. Specific dietary supplements, including resistant starches (RS), are often a focus, yet comprehensive insights into functional responses of microbiota are largely lacking. Furthermore, unresponsiveness in certain individuals is poorly understood. Our data indicate that distinct parts of microbiota work jointly to degrade RS and successively form health-promoting fermentation end products. It highlights the need to consider both primary degraders and specific more-downstream-acting bacterial groups in order to achieve desired intervention outcomes. The gained insights will assist the design of personalized treatment strategies based on an individual's microbiota.}, } @article {pmid30266101, year = {2018}, author = {Alneberg, J and Karlsson, CMG and Divne, AM and Bergin, C and Homa, F and Lindh, MV and Hugerth, LW and Ettema, TJG and Bertilsson, S and Andersson, AF and Pinhassi, J}, title = {Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {173}, pmid = {30266101}, issn = {2049-2618}, support = {310039/ERC_/European Research Council/International ; }, mesh = {Bacteria/classification/*genetics ; Genome, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenome/*genetics ; Microbiota/*genetics ; *Nucleic Acid Amplification Techniques ; Oceans and Seas ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sweden ; Whole Genome Sequencing/*methods ; }, abstract = {BACKGROUND: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.

RESULTS: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs.

CONCLUSIONS: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.}, } @article {pmid30266099, year = {2018}, author = {Rath, S and Rud, T and Karch, A and Pieper, DH and Vital, M}, title = {Pathogenic functions of host microbiota.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {174}, pmid = {30266099}, issn = {2049-2618}, mesh = {Bacteria/*genetics/*metabolism ; Bacterial Infections/microbiology/*pathology ; Bacterial Physiological Phenomena/genetics ; Bile Acids and Salts/biosynthesis ; Gastrointestinal Microbiome/*genetics ; Humans ; Hydrogen Sulfide/metabolism ; Methylamines/metabolism ; }, abstract = {BACKGROUND: It is becoming evident that certain features of human microbiota, encoded by distinct autochthonous taxa, promote disease. As a result, borders between the so-called opportunistic pathogens, pathobionts, and commensals are increasingly blurred, and specific targets for manipulating microbiota to improve host health are becoming elusive.

RESULTS: In this study, we focus on the functions of host bacterial communities that have the potential to cause disease, proposing the term "pathogenic function (pathofunction)". The concept is presented via three distinct examples, namely, the formation of (i) trimethylamine, (ii) secondary bile acids, and (iii) hydrogen sulfide, which represent metabolites of the gut microbiota linked to the development of non-communicable diseases. Using publicly available metagenomic and metatranscriptomic data (n = 2975), we quantified those pathofunctions in health and disease and exposed the key players. Pathofunctions were ubiquitously present with increased abundances in patient groups. Overall, the three pathofunctions were detected at low mean concentrations (< 1% of total bacteria carried respective genes) and encompassed various taxa, including uncultured members.

CONCLUSIONS: We outline how this function-centric approach, where all members of a community exhibiting a particular pathofunction are redundant, can contribute to risk assessment and the development of precision treatment directing gut microbiota to increase host health.}, } @article {pmid30261940, year = {2018}, author = {Denman, SE and Morgavi, DP and McSweeney, CS}, title = {Review: The application of omics to rumen microbiota function.}, journal = {Animal : an international journal of animal bioscience}, volume = {12}, number = {s2}, pages = {s233-s245}, doi = {10.1017/S175173111800229X}, pmid = {30261940}, issn = {1751-732X}, mesh = {Animals ; Bacteria/*classification/genetics ; Gastrointestinal Microbiome/*genetics ; Gene Expression Profiling/veterinary ; *Genomics ; Livestock ; *Metagenome ; Metagenomics ; Methane/*metabolism ; RNA, Ribosomal, 16S/genetics ; Rumen/metabolism ; }, abstract = {Rumen microbiome profiling uses 16S rRNA (18S rRNA, internal transcribed spacer) gene sequencing, a method that usually sequences a small portion of a single gene and is often biased and varies between different laboratories. Functional information can be inferred from this data, but only for those that are closely related to known annotated species, and even then may not truly reflect the function performed within the environment being studied. Genome sequencing of isolates and metagenome-assembled genomes has now reached a stage where representation of the majority of rumen bacterial genera are covered, but this still only represents a portion of rumen microbial species. The creation of a microbial genome (bins) database with associated functional annotations will provide a consistent reference to allow mapping of RNA-Seq reads for functional gene analysis from within the rumen microbiome. The integration of multiple omic analytics is linking functional gene activity, metabolic pathways and rumen metabolites with the responsible microbiota, supporting our biological understanding of the rumen system. The application of these techniques has advanced our understanding of the major microbial populations and functional pathways that are used in relation to lower methane emissions, higher feed efficiencies and responses to different feeding regimes. Continued and more precise use of these tools will lead to a detailed and comprehensive understanding of compositional and functional capacity and design of techniques for the directed intervention and manipulation of the rumen microbiota towards a desired state.}, } @article {pmid30261899, year = {2018}, author = {Clarke, EL and Connell, AJ and Six, E and Kadry, NA and Abbas, AA and Hwang, Y and Everett, JK and Hofstaedter, CE and Marsh, R and Armant, M and Kelsen, J and Notarangelo, LD and Collman, RG and Hacein-Bey-Abina, S and Kohn, DB and Cavazzana, M and Fischer, A and Williams, DA and Pai, SY and Bushman, FD}, title = {T cell dynamics and response of the microbiota after gene therapy to treat X-linked severe combined immunodeficiency.}, journal = {Genome medicine}, volume = {10}, number = {1}, pages = {70}, pmid = {30261899}, issn = {1756-994X}, support = {UM1 AI126620/AI/NIAID NIH HHS/United States ; R01 AI082020/AI/NIAID NIH HHS/United States ; U19 AI117950/AI/NIAID NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; 269037/ERC_/European Research Council/International ; U01 AI087628/AI/NIAID NIH HHS/United States ; R01 AI052845/AI/NIAID NIH HHS/United States ; }, mesh = {Cell Division ; Child, Preschool ; Complementarity Determining Regions/genetics ; *Genetic Therapy ; Humans ; *Microbiota ; Receptors, Antigen, T-Cell, alpha-beta/metabolism ; T-Lymphocytes/*immunology ; X-Linked Combined Immunodeficiency Diseases/*immunology/microbiology/*therapy/virology ; }, abstract = {BACKGROUND: Mutation of the IL2RG gene results in a form of severe combined immune deficiency (SCID-X1), which has been treated successfully with hematopoietic stem cell gene therapy. SCID-X1 gene therapy results in reconstitution of the previously lacking T cell compartment, allowing analysis of the roles of T cell immunity in humans by comparing before and after gene correction.

METHODS: Here we interrogate T cell reconstitution using four forms of high throughput analysis. (1) Estimation of the numbers of transduced progenitor cells by monitoring unique positions of integration of the therapeutic gene transfer vector. (2) Estimation of T cell population structure by sequencing of the recombined T cell receptor (TCR) beta locus. (3) Metagenomic analysis of microbial populations in oropharyngeal, nasopharyngeal, and gut samples. (4) Metagenomic analysis of viral populations in gut samples.

RESULTS: Comparison of progenitor and mature T cell populations allowed estimation of a minimum number of cell divisions needed to generate the observed populations. Analysis of microbial populations showed the effects of immune reconstitution, including normalization of gut microbiota and clearance of viral infections. Metagenomic analysis revealed enrichment of genes for antibiotic resistance in gene-corrected subjects relative to healthy controls, likely a result of higher healthcare exposure.

CONCLUSIONS: This multi-omic approach enables the characterization of multiple effects of SCID-X1 gene therapy, including T cell repertoire reconstitution, estimation of numbers of cell divisions between progenitors and daughter T cells, normalization of the microbiome, clearance of microbial pathogens, and modulations in antibiotic resistance gene levels. Together, these results quantify several aspects of the long-term efficacy of gene therapy for SCID-X1. This study includes data from ClinicalTrials.gov numbers NCT01410019, NCT01175239, and NCT01129544.}, } @article {pmid30260956, year = {2018}, author = {Hunt, KA and Jennings, RM and Inskeep, WP and Carlson, RP}, title = {Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community.}, journal = {PLoS computational biology}, volume = {14}, number = {9}, pages = {e1006431}, pmid = {30260956}, issn = {1553-7358}, support = {U01 EB019416/EB/NIBIB NIH HHS/United States ; }, mesh = {Autotrophic Processes ; Biomass ; Carbon/chemistry ; Computer Simulation ; Electron Transport ; Electrons ; Ferric Compounds/*chemistry ; Genome, Archaeal ; Heterotrophic Processes ; Hot Temperature ; Iron/chemistry ; Metagenomics ; *Microbiota ; Oxygen/chemistry ; Phylogeny ; Sulfides/chemistry ; Sulfolobaceae/*metabolism ; Transcriptome ; }, abstract = {Interactions among microbial community members can lead to emergent properties, such as enhanced productivity, stability, and robustness. Iron-oxide mats in acidic (pH 2-4), high-temperature (> 65 °C) springs of Yellowstone National Park contain relatively simple microbial communities and are well-characterized geochemically. Consequently, these communities are excellent model systems for studying the metabolic activity of individual populations and key microbial interactions. The primary goals of the current study were to integrate data collected in situ with in silico calculations across process-scales encompassing enzymatic activity, cellular metabolism, community interactions, and ecosystem biogeochemistry, as well as to predict and quantify the functional limits of autotroph-heterotroph interactions. Metagenomic and transcriptomic data were used to reconstruct carbon and energy metabolisms of an important autotroph (Metallosphaera yellowstonensis) and heterotroph (Geoarchaeum sp. OSPB) from the studied Fe(III)-oxide mat communities. Standard and hybrid elementary flux mode and flux balance analyses of metabolic models predicted cellular- and community-level metabolic acclimations to simulated environmental stresses, respectively. In situ geochemical analyses, including oxygen depth-profiles, Fe(III)-oxide deposition rates, stable carbon isotopes and mat biomass concentrations, were combined with cellular models to explore autotroph-heterotroph interactions important to community structure-function. Integration of metabolic modeling with in situ measurements, including the relative population abundance of autotrophs to heterotrophs, demonstrated that Fe(III)-oxide mat communities operate at their maximum total community growth rate (i.e. sum of autotroph and heterotroph growth rates), as opposed to net community growth rate (i.e. total community growth rate subtracting autotroph consumed by heterotroph), as predicted from the maximum power principle. Integration of multiscale data with ecological theory provides a basis for predicting autotroph-heterotroph interactions and community-level cellular organization.}, } @article {pmid30260954, year = {2018}, author = {Becker, DJ and Bergner, LM and Bentz, AB and Orton, RJ and Altizer, S and Streicker, DG}, title = {Genetic diversity, infection prevalence, and possible transmission routes of Bartonella spp. in vampire bats.}, journal = {PLoS neglected tropical diseases}, volume = {12}, number = {9}, pages = {e0006786}, pmid = {30260954}, issn = {1935-2735}, support = {/WT_/Wellcome Trust/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; 102507/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Bacterial Proteins/genetics ; Bartonella/*classification/*genetics/isolation & purification ; Bartonella Infections/epidemiology/transmission/*veterinary ; Belize ; Blood/microbiology ; Chiroptera/*microbiology ; Cluster Analysis ; *Disease Transmission, Infectious ; Feces/microbiology ; *Genetic Variation ; Glutamate Synthase/genetics ; Peru ; Phylogeny ; Polymerase Chain Reaction ; Prevalence ; Risk Factors ; Saliva/microbiology ; Seasons ; Sequence Analysis, DNA ; }, abstract = {Bartonella spp. are globally distributed bacteria that cause endocarditis in humans and domestic animals. Recent work has suggested bats as zoonotic reservoirs of some human Bartonella infections; however, the ecological and spatiotemporal patterns of infection in bats remain largely unknown. Here we studied the genetic diversity, prevalence of infection across seasons and years, individual risk factors, and possible transmission routes of Bartonella in populations of common vampire bats (Desmodus rotundus) in Peru and Belize, for which high infection prevalence has previously been reported. Phylogenetic analysis of the gltA gene for a subset of PCR-positive blood samples revealed sequences that were related to Bartonella described from vampire bats from Mexico, other Neotropical bat species, and streblid bat flies. Sequences associated with vampire bats clustered significantly by country but commonly spanned Central and South America, implying limited spatial structure. Stable and nonzero Bartonella prevalence between years supported endemic transmission in all sites. The odds of Bartonella infection for individual bats was unrelated to the intensity of bat flies ectoparasitism, but nearly all infected bats were infested, which precluded conclusive assessment of support for vector-borne transmission. While metagenomic sequencing found no strong evidence of Bartonella DNA in pooled bat saliva and fecal samples, we detected PCR positivity in individual saliva and feces, suggesting the potential for bacterial transmission through both direct contact (i.e., biting) and environmental (i.e., fecal) exposures. Further investigating the relative contributions of direct contact, environmental, and vector-borne transmission for bat Bartonella is an important next step to predict infection dynamics within bats and the risks of human and livestock exposures.}, } @article {pmid30258172, year = {2019}, author = {Wilhelm, RC and Singh, R and Eltis, LD and Mohn, WW}, title = {Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing.}, journal = {The ISME journal}, volume = {13}, number = {2}, pages = {413-429}, pmid = {30258172}, issn = {1751-7370}, mesh = {Bacteria/genetics/*metabolism ; Biomass ; Forests ; Fungi/genetics/metabolism ; Isotopes ; Lignin/*metabolism ; *Metagenomics ; Microbiota ; North America ; Soil/*chemistry ; *Soil Microbiology ; Wood/metabolism ; }, abstract = {Delignification, or lignin-modification, facilitates the decomposition of lignocellulose in woody plant biomass. The extant diversity of lignin-degrading bacteria and fungi is underestimated by culture-dependent methods, limiting our understanding of the functional and ecological traits of decomposers populations. Here, we describe the use of stable isotope probing (SIP) coupled with amplicon and shotgun metagenomics to identify and characterize the functional attributes of lignin, cellulose and hemicellulose-degrading fungi and bacteria in coniferous forest soils from across North America. We tested the extent to which catabolic genes partitioned among different decomposer taxa; the relative roles of bacteria and fungi, and whether taxa or catabolic genes correlated with variation in lignocellulolytic activity, measured as the total assimilation of [13]C-label into DNA and phospholipid fatty acids. We found high overall bacterial degradation of our model lignin substrate, particularly by gram-negative bacteria (Comamonadaceae and Caulobacteraceae), while fungi were more prominent in cellulose-degradation. Very few taxa incorporated [13]C-label from more than one lignocellulosic polymer, suggesting specialization among decomposers. Collectively, members of Caulobacteraceae could degrade all three lignocellulosic polymers, providing new evidence for their importance in lignocellulose degradation. Variation in lignin-degrading activity was better explained by microbial community properties, such as catabolic gene content and community structure, than cellulose-degrading activity. SIP significantly improved shotgun metagenome assembly resulting in the recovery of several high-quality draft metagenome-assembled genomes and over 7500 contigs containing unique clusters of carbohydrate-active genes. These results improve understanding of which organisms, conditions and corresponding functional genes contribute to lignocellulose decomposition.}, } @article {pmid30258040, year = {2018}, author = {Taft, DH and Liu, J and Maldonado-Gomez, MX and Akre, S and Huda, MN and Ahmad, SM and Stephensen, CB and Mills, DA}, title = {Bifidobacterial Dominance of the Gut in Early Life and Acquisition of Antimicrobial Resistance.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, pmid = {30258040}, issn = {2379-5042}, support = {S10 RR029668/RR/NCRR NIH HHS/United States ; S10 RR027303/RR/NCRR NIH HHS/United States ; F32 HD093185/HD/NICHD NIH HHS/United States ; R01 AT008759/AT/NCCIH NIH HHS/United States ; R01 AT007079/AT/NCCIH NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bangladesh ; Bifidobacterium/genetics/*physiology ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Metagenomics ; Probiotics/therapeutic use ; Regression Analysis ; }, abstract = {Bifidobacterium species are important commensals capable of dominating the infant gut microbiome, in part by producing acids that suppress growth of other taxa. Bifidobacterium species are less prone to possessing antimicrobial resistance (AMR) genes (ARGs) than other taxa that may colonize infants. Given that AMR is a growing public health crisis and ARGs are present in the gut microbiome of humans from early life, this study examines the correlation between a Bifidobacterium-dominated infant gut microbiome and AMR levels, measured by a culture-independent metagenomic approach both in early life and as infants become toddlers. In general, Bifidobacterium dominance is associated with a significant reduction in AMR in a Bangladeshi cohort, both in the number of acquired AMR genes present and in the abundance of AMR genes. However, by year 2, Bangladeshi infants had no significant differences in AMR related to their early-life Bifidobacterium levels. A generalized linear model including all infants in a previously published Swedish cohort found a significant negative association between log-transformed total AMR and Bifidobacterium levels, thus confirming the relationship between Bifidobacterium levels and AMR. In both cohorts, there was no change between early-life and later-life AMR abundance in high-Bifidobacterium infants but a significant reduction in AMR abundance in low-Bifidobacterium infants. These results support the hypothesis that early Bifidobacterium dominance of the infant gut microbiome may help reduce colonization by taxa containing ARGs.IMPORTANCE Infants are vulnerable to an array of infectious diseases, and as the gut microbiome may serve as a reservoir of AMR for pathogens, reducing the levels of AMR in infants is important to infant health. This study demonstrates that high levels of Bifidobacterium are associated with reduced levels of AMR in early life and suggests that probiotic interventions to increase infant Bifidobacterium levels have the potential to reduce AMR in infants. However, this effect is not sustained at year 2 of age in Bangladeshi infants, underscoring the need for more detailed studies of the biogeography and timing of infant AMR acquisition.}, } @article {pmid30257633, year = {2018}, author = {White, LS and Van den Bogaerde, J and Kamm, M}, title = {The gut microbiota: cause and cure of gut diseases.}, journal = {The Medical journal of Australia}, volume = {209}, number = {7}, pages = {312-317}, doi = {10.5694/mja17.01067}, pmid = {30257633}, issn = {1326-5377}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Diseases/microbiology/physiopathology/therapy ; *Gastrointestinal Microbiome/drug effects/genetics/physiology ; Humans ; Inflammatory Bowel Diseases/microbiology/physiopathology/therapy ; Liver Diseases/microbiology/physiopathology/therapy ; Metabolic Syndrome/microbiology/physiopathology/therapy ; Metagenomics ; Mice ; *Obesity/microbiology/physiopathology/therapy ; }, abstract = {The gastrointestinal microbiota is emerging as a central factor in the pathogenesis of a range of gastrointestinal and hepatic disorders. Epidemiological studies, and experimental studies in animals and humans, have highlighted a likely causative role of this microbial community in the modern global epidemics of inflammatory bowel disease, non-alcoholic fatty liver disease, non-alcoholic steato-hepatitis, obesity and metabolic syndrome. New techniques for microbial culture and gene sequencing are enabling the identification of specific pathogens and protective organisms in these conditions. Factors that change the microbiota are being defined: dietary pattern, specific foods, food additives in processed food and drinks, such as emulsifiers and non-sugar sweeteners, and antibiotics. Microbiota changes in early life appear critical to the later development of a range of inflammatory disorders. For many of these conditions, the treatment paradigm will change, at least in part, from immune suppression and drug therapy to treatments that reshape the microbiota or restore its integrity. These treatments include dietary changes, specific microbial manipulation and faecal microbiota transplantation. A dialogue is needed regarding population strategies that target disease prevention. This will include how food is produced, what additives it contains, and how it is processed. Widespread use of antibiotics, from agricultural and veterinary to medicinal settings, needs more attention. At the individual level, microbial profiles may be able to predict who is at risk of disease when subjected to particular environmental influences, and what microbial restoration is needed to minimise risk.}, } @article {pmid30256843, year = {2018}, author = {Pozzo, T and Higdon, SM and Pattathil, S and Hahn, MG and Bennett, AB}, title = {Characterization of novel glycosyl hydrolases discovered by cell wall glycan directed monoclonal antibody screening and metagenome analysis of maize aerial root mucilage.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0204525}, pmid = {30256843}, issn = {1932-6203}, mesh = {Antibodies, Monoclonal ; Bacterial Proteins/chemistry/genetics/metabolism ; Cell Wall/metabolism ; Glycoside Hydrolases/chemistry/*genetics/*metabolism ; Metagenome ; Microbiota/genetics ; Phylogeny ; Plant Components, Aerial/enzymology/microbiology ; Plant Mucilage/chemistry/metabolism ; Polysaccharides/immunology/metabolism ; Recombinant Proteins/chemistry/genetics/metabolism ; Zea mays/*enzymology/*microbiology ; }, abstract = {An indigenous maize landrace from the Sierra Mixe region of Oaxaca, Mexico exhibits extensive formation of aerial roots which exude large volumes of a polysaccharide-rich gel matrix or "mucilage" that harbors diazotrophic microbiota. We hypothesize that the mucilage associated microbial community carries out multiple functions, including disassembly of the mucilage polysaccharide. In situ, hydrolytic assay of the mucilage revealed endogenous arabinofuranosidase, galactosidase, fucosidase, mannosidase and xylanase activities. Screening the mucilage against plant cell wall glycan-specific monoclonal antibodies recognized the presence of carbohydrate epitopes of hemicellulosic polysaccharides like xyloglucan (both non-fucosylated and fucosylated), xylan (both substituted and unsubstituted xylan domains) and pectic-arabinogalactans, all of which are potential carbon sources for mucilage microbial residents. Mucilage metagenome annotation using MG-RAST identified the members forming the microbial community, and gene fragments with predicted functions associated with carbohydrate disassembly. Data from the in situ hydrolytic activity and monoclonal antibody screening assays were used to guide the selection of five full length genes with predicted glycosyl hydrolase function from the GenBank database that were similar to gene fragments of high relative abundance in the mucilage metagenomes. These five genes were then synthesized for recombinant production in Escherichia coli. Here we report the characterization of an α-N-arabinofuranosidase (GH51) and an oligosaccharide reducing-end xylanase (GH8) from Flavobacterium johnsoniae; an α-L-fucosidase (GH29) and a xylan β-1,4 xylosidase (GH39) from Spirosoma linguale, and a β-mannosidase (GH2) from Agrobacterium fabrum. Biochemical characterization of these enzymes revealed a β-Mannosidase that also exhibits a secondary activity towards the cleavage of galactosyl residues. We also describe two xylanases (GH8 and GH39) from underexplored glycosyl hydrolase families, one thermostable α-L-Fucosidase (GH29) and a thermostable α-N-Arabinofuranosidase (GH51).}, } @article {pmid30252901, year = {2018}, author = {Poirier, S and Rué, O and Peguilhan, R and Coeuret, G and Zagorec, M and Champomier-Vergès, MC and Loux, V and Chaillou, S}, title = {Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0204629}, pmid = {30252901}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/*genetics/isolation & purification ; DNA Gyrase/*genetics ; DNA Topoisomerase IV/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Food Microbiology/*methods ; Genes, Bacterial ; Genetic Markers ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Humans ; Meat/*microbiology ; Metagenome ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seafood/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Meat and seafood spoilage ecosystems harbor extensive bacterial genomic diversity that is mainly found within a small number of species but within a large number of strains with different spoilage metabolic potential. To decipher the intraspecies diversity of such microbiota, traditional metagenetic analysis using the 16S rRNA gene is inadequate. We therefore assessed the potential benefit of an alternative genetic marker, gyrB, which encodes the subunit B of DNA gyrase, a type II DNA topoisomerase. A comparison between 16S rDNA-based (V3-V4) amplicon sequencing and gyrB-based amplicon sequencing was carried out in five types of meat and seafood products, with five mock communities serving as quality controls. Our results revealed that bacterial richness in these mock communities and food samples was estimated with higher accuracy using gyrB than using16S rDNA. However, for Firmicutes species, 35% of putative gyrB reads were actually identified as sequences of a gyrB paralog, parE, which encodes subunit B of topoisomerase IV; we therefore constructed a reference database of published sequences of both gyrB and pare for use in all subsequent analyses. Despite this co-amplification, the deviation between relative sequencing quantification and absolute qPCR quantification was comparable to that observed for 16S rDNA for all the tested species. This confirms that gyrB can be used successfully alongside 16S rDNA to determine the species composition (richness and evenness) of food microbiota. The major benefit of gyrB sequencing is its potential for improving taxonomic assignment and for further investigating OTU richness at the subspecies level, thus allowing more accurate discrimination of samples. Indeed, 80% of the reads of the 16S rDNA dataset were represented by thirteen 16S rDNA-based OTUs that could not be assigned at the species-level. Instead, these same clades corresponded to 44 gyrB-based OTUs, which differentiated various lineages down to the subspecies level. The increased ability of gyrB-based analyses to track and trace phylogenetically different groups of strains will generate improved resolution and more reliable results for studies of the strains implicated in food processes.}, } @article {pmid30252582, year = {2019}, author = {Ungaro, F and Massimino, L and Furfaro, F and Rimoldi, V and Peyrin-Biroulet, L and D'Alessio, S and Danese, S}, title = {Metagenomic analysis of intestinal mucosa revealed a specific eukaryotic gut virome signature in early-diagnosed inflammatory bowel disease.}, journal = {Gut microbes}, volume = {10}, number = {2}, pages = {149-158}, pmid = {30252582}, issn = {1949-0984}, mesh = {Adolescent ; Child ; Colitis, Ulcerative/diagnosis/pathology/virology ; Crohn Disease/diagnosis/pathology/virology ; Databases, Factual ; Feces/virology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Inflammation/pathology/virology ; Inflammatory Bowel Diseases/diagnosis/pathology/*virology ; Intestinal Mucosa/pathology/*virology ; Male ; Metagenomics ; Viruses/classification/genetics/isolation & purification ; }, abstract = {Intestinal dysbiosis is one of the causes underlying the pathogenesis of inflammatory bowel disease (IBD), encompassing ulcerative colitis (UC) and Crohn's disease (CD). Besides bacteria, microbiota comprises both prokaryotic and eukaryotic viruses, that together compose the gut virome. Few works have defined the viral composition of stools, while the virome populating intestinal mucosae from early-diagnosed IBD patients has never been studied. Here we show that, by in-depth metagenomic analysis of RNA-Seq data obtained from gut mucosae of young treatment-naïve patients, early-diagnosed for CD and UC, and from healthy subjects (Ctrl), UC patients display significantly higher levels of eukaryotic Hepadnaviridae transcripts by comparison with both Ctrl and CD patients, whereas CD patients show increased abundance of Hepeviridae versus Ctrl. Moreover, we found that UC gut mucosa is characterized by lower levels of Polydnaviridae and Tymoviridae, whereas the mucosa of patients with CD showed a reduced abundance of Virgaviridae. Our findings support the idea that certain eukaryotic viruses might trigger intestinal inflammation and contribute to IBD pathogenesis and pave the way not only for the discovery of novel diagnostic biomarkers but also for the development of anti-viral drugs for the treatment of IBD.}, } @article {pmid30252023, year = {2019}, author = {Plaza Oñate, F and Le Chatelier, E and Almeida, M and Cervino, ACL and Gauthier, F and Magoulès, F and Ehrlich, SD and Pichaud, M}, title = {MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {9}, pages = {1544-1552}, pmid = {30252023}, issn = {1367-4811}, mesh = {Genome, Bacterial ; Genome, Microbial ; Humans ; Metagenome ; *Metagenomics ; *Microbiota ; Software ; }, abstract = {MOTIVATION: Analysis toolkits for shotgun metagenomic data achieve strain-level characterization of complex microbial communities by capturing intra-species gene content variation. Yet, these tools are hampered by the extent of reference genomes that are far from covering all microbial variability, as many species are still not sequenced or have only few strains available. Binning co-abundant genes obtained from de novo assembly is a powerful reference-free technique to discover and reconstitute gene repertoire of microbial species. While current methods accurately identify species core parts, they miss many accessory genes or split them into small gene groups that remain unassociated to core clusters.

RESULTS: We introduce MSPminer, a computationally efficient software tool that reconstitutes Metagenomic Species Pan-genomes (MSPs) by binning co-abundant genes across metagenomic samples. MSPminer relies on a new robust measure of proportionality coupled with an empirical classifier to group and distinguish not only species core genes but accessory genes also. Applied to a large scale metagenomic dataset, MSPminer successfully delineates in a few hours the gene repertoires of 1661 microbial species with similar specificity and higher sensitivity than existing tools. The taxonomic annotation of MSPs reveals microorganisms hitherto unknown and brings coherence in the nomenclature of the species of the human gut microbiota. The provided MSPs can be readily used for taxonomic profiling and biomarkers discovery in human gut metagenomic samples. In addition, MSPminer can be applied on gene count tables from other ecosystems to perform similar analyses.

The binary is freely available for non-commercial users at www.enterome.com/downloads.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid30250246, year = {2018}, author = {Leventhal, GE and Boix, C and Kuechler, U and Enke, TN and Sliwerska, E and Holliger, C and Cordero, OX}, title = {Strain-level diversity drives alternative community types in millimetre-scale granular biofilms.}, journal = {Nature microbiology}, volume = {3}, number = {11}, pages = {1295-1303}, doi = {10.1038/s41564-018-0242-3}, pmid = {30250246}, issn = {2058-5276}, support = {T32 GM087237/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biofilms ; *Genetic Variation ; Genome, Bacterial/genetics ; Genotype ; Metagenome/genetics ; Microbiota/*genetics ; Phylogeny ; Sewage/microbiology ; }, abstract = {Microbial communities are often highly diverse in their composition, both at a coarse-grained taxonomic level, such as genus, and at a highly resolved level, such as strains, within species. This variability can be driven by either extrinsic factors such as temperature and or by intrinsic ones, for example demographic fluctuations or ecological interactions. The relative contributions of these factors and the taxonomic level at which they influence community composition remain poorly understood, in part because of the difficulty in identifying true community replicates assembled under the same environmental parameters. Here, we address this problem using an activated granular sludge reactor in which millimetre-scale biofilm granules represent true community replicates. Differences in composition are then expected to be driven primarily by biotic factors. Using 142 shotgun metagenomes of single biofilm granules we found that, at the commonly used genus-level resolution, community replicates varied much more in their composition than would be expected from neutral assembly processes. This variation did not translate into any clear partitioning into discrete community types, that is, distinct compositional states, such as enterotypes in the human gut. However, a strong partition into community types did emerge at the strain level for the dominant organism: genotypes of Candidatus Accumulibacter that coexisted in the metacommunity (the reactor) excluded each other within community replicates (granules). Individual granule communities maintained a significant lineage structure, whereby the strain phylogeny of Accumulibacter correlated with the overall composition of the community, indicating a high potential for co-diversification among species and communities. Our results suggest that due to the high functional redundancy and competition between close relatives, alternative community types are most probably observed at the level of recently differentiated genotypes but not at higher orders of genetic resolution.}, } @article {pmid30250208, year = {2018}, author = {Pärnänen, K and Karkman, A and Hultman, J and Lyra, C and Bengtsson-Palme, J and Larsson, DGJ and Rautava, S and Isolauri, E and Salminen, S and Kumar, H and Satokari, R and Virta, M}, title = {Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {3891}, pmid = {30250208}, issn = {2041-1723}, mesh = {Anti-Bacterial Agents/*adverse effects ; Antibiotic Prophylaxis/adverse effects ; Breast Feeding ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/drug effects/*genetics ; Humans ; Infant ; Interspersed Repetitive Sequences/*genetics ; Maternal Inheritance ; Metagenomics ; Milk, Human/*microbiology ; Phylogeny ; Time Factors ; }, abstract = {The infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) compared to adults, even in the absence of antibiotic exposure. Here we study potential sources of infant gut ARGs by performing metagenomic sequencing of breast milk, as well as infant and maternal gut microbiomes. We find that fecal ARG and mobile genetic element (MGE) profiles of infants are more similar to those of their own mothers than to those of unrelated mothers. MGEs in mothers' breast milk are also shared with their own infants. Termination of breastfeeding and intrapartum antibiotic prophylaxis of mothers, which have the potential to affect microbial community composition, are associated with higher abundances of specific ARGs, the composition of which is largely shaped by bacterial phylogeny in the infant gut. Our results suggest that infants inherit the legacy of past antibiotic consumption of their mothers via transmission of genes, but microbiota composition still strongly impacts the overall resistance load.}, } @article {pmid30250126, year = {2018}, author = {Zhernakova, DV and Le, TH and Kurilshikov, A and Atanasovska, B and Bonder, MJ and Sanna, S and Claringbould, A and Võsa, U and Deelen, P and Franke, L and de Boer, RA and Kuipers, F and Netea, MG and Hofker, MH and Wijmenga, C and Zhernakova, A and Fu, J and , and , }, title = {Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome.}, journal = {Nature genetics}, volume = {50}, number = {11}, pages = {1524-1532}, pmid = {30250126}, issn = {1546-1718}, support = {310372/ERC_/European Research Council/International ; 322698/ERC_/European Research Council/International ; 637640/ERC_/European Research Council/International ; }, mesh = {Adult ; Biological Variation, Individual ; Blood Proteins/*genetics/metabolism ; Brain/physiology ; Cardiovascular Diseases/*blood/*genetics/*microbiology ; Cohort Studies ; Female ; Gastrointestinal Microbiome/*physiology ; Genome-Wide Association Study ; Host Microbial Interactions/genetics ; Humans ; Intestines/innervation/microbiology ; Lipid Metabolism/genetics ; Male ; Metagenome/genetics ; Middle Aged ; Netherlands ; Oxidation-Reduction ; Quantitative Trait Loci/genetics ; }, abstract = {Despite a growing body of evidence, the role of the gut microbiome in cardiovascular diseases is still unclear. Here, we present a systems-genome-wide and metagenome-wide association study on plasma concentrations of 92 cardiovascular-disease-related proteins in the population cohort LifeLines-DEEP. We identified genetic components for 73 proteins and microbial associations for 41 proteins, of which 31 were associated to both. The genetic and microbial factors identified mostly exert additive effects and collectively explain up to 76.6% of inter-individual variation (17.5% on average). Genetics contribute most to concentrations of immune-related proteins, while the gut microbiome contributes most to proteins involved in metabolism and intestinal health. We found several host-microbe interactions that impact proteins involved in epithelial function, lipid metabolism, and central nervous system function. This study provides important evidence for a joint genetic and microbial effect in cardiovascular disease and provides directions for future applications in personalized medicine.}, } @article {pmid30250051, year = {2019}, author = {Ju, F and Beck, K and Yin, X and Maccagnan, A and McArdell, CS and Singer, HP and Johnson, DR and Zhang, T and Bürgmann, H}, title = {Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes.}, journal = {The ISME journal}, volume = {13}, number = {2}, pages = {346-360}, pmid = {30250051}, issn = {1751-7370}, mesh = {Anti-Bacterial Agents/analysis ; Bacteria/drug effects/genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Metagenome ; Metagenomics ; *Microbiota ; Transcriptome ; Up-Regulation ; Waste Disposal, Fluid ; Wastewater/chemistry/*microbiology ; }, abstract = {Wastewater treatment plants (WWTPs) are implicated as hotspots for the dissemination of antibacterial resistance into the environment. However, the in situ processes governing removal, persistence, and evolution of resistance genes during wastewater treatment remain poorly understood. Here, we used quantitative metagenomic and metatranscriptomic approaches to achieve a broad-spectrum view of the flow and expression of genes related to antibacterial resistance to over 20 classes of antibiotics, 65 biocides, and 22 metals. All compartments of 12 WWTPs share persistent resistance genes with detectable transcriptional activities that were comparatively higher in the secondary effluent, where mobility genes also show higher relative abundance and expression ratios. The richness and abundance of resistance genes vary greatly across metagenomes from different treatment compartments, and their relative and absolute abundances correlate with bacterial community composition and biomass concentration. No strong drivers of resistome composition could be identified among the chemical stressors analyzed, although the sub-inhibitory concentration (hundreds of ng/L) of macrolide antibiotics in wastewater correlates with macrolide and vancomycin resistance genes. Contig-based analysis shows considerable co-localization between resistance and mobility genes and implies a history of substantial horizontal resistance transfer involving human bacterial pathogens. Based on these findings, we propose future inclusion of mobility incidence (M%) and host pathogenicity of antibiotic resistance genes in their quantitative health risk ranking models with an ultimate goal to assess the biological significance of wastewater resistomes with regard to disease control in humans or domestic livestock.}, } @article {pmid30249182, year = {2018}, author = {Cavalcanti, GS and Shukla, P and Morris, M and Ribeiro, B and Foley, M and Doane, MP and Thompson, CC and Edwards, MS and Dinsdale, EA and Thompson, FL}, title = {Rhodoliths holobionts in a changing ocean: host-microbes interactions mediate coralline algae resilience under ocean acidification.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {701}, pmid = {30249182}, issn = {1471-2164}, mesh = {Biodiversity ; Hydrogen-Ion Concentration ; Metagenome ; *Microbiota/genetics ; Oceans and Seas ; Photosynthesis ; Rhodophyta/metabolism/*microbiology/physiology ; Seawater/chemistry/microbiology ; Stress, Physiological ; }, abstract = {BACKGROUND: Life in the ocean will increasingly have to contend with a complex matrix of concurrent shifts in environmental properties that impact their physiology and control their life histories. Rhodoliths are coralline red algae (Corallinales, Rhodophyta) that are photosynthesizers, calcifiers, and ecosystem engineers and therefore represent important targets for ocean acidification (OA) research. Here, we exposed live rhodoliths to near-future OA conditions to investigate responses in their photosynthetic capacity, calcium carbonate production, and associated microbiome using carbon uptake, decalcification assays, and whole genome shotgun sequencing metagenomic analysis, respectively. The results from our live rhodolith assays were compared to similar manipulations on dead rhodolith (calcareous skeleton) biofilms and water column microbial communities, thereby enabling the assessment of host-microbiome interaction under climate-driven environmental perturbations.

RESULTS: Under high pCO2 conditions, live rhodoliths exhibited positive physiological responses, i.e. increased photosynthetic activity, and no calcium carbonate biomass loss over time. Further, whereas the microbiome associated with live rhodoliths remained stable and resembled a healthy holobiont, the microbial community associated with the water column changed after exposure to elevated pCO2.

CONCLUSIONS: Our results suggest that a tightly regulated microbial-host interaction, as evidenced by the stability of the rhodolith microbiome recorded here under OA-like conditions, is important for host resilience to environmental stress. This study extends the scarce comprehension of microbes associated with rhodolith beds and their reaction to increased pCO2, providing a more comprehensive approach to OA studies by assessing the host holobiont.}, } @article {pmid30248115, year = {2018}, author = {Kurobe, T and Lehman, PW and Hammock, BG and Bolotaolo, MB and Lesmeister, S and Teh, SJ}, title = {Biodiversity of cyanobacteria and other aquatic microorganisms across a freshwater to brackish water gradient determined by shotgun metagenomic sequencing analysis in the San Francisco Estuary, USA.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0203953}, pmid = {30248115}, issn = {1932-6203}, support = {S10 OD010786/OD/NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Chlorophyta/classification/genetics ; Cyanobacteria/classification/*genetics/*isolation & purification ; DNA, Bacterial/genetics ; Diatoms/classification/genetics/isolation & purification ; Estuaries ; Fresh Water/microbiology ; Genotype ; Harmful Algal Bloom ; Metagenomics ; Microcystis/genetics/isolation & purification ; Phylogeny ; Polymerase Chain Reaction ; Saline Waters ; Salinity ; San Francisco ; Spatio-Temporal Analysis ; *Water Microbiology ; }, abstract = {Blooms of Microcystis and other harmful cyanobacteria can degrade water quality by producing cyanotoxins or other toxic compounds. The goals of this study were (1) to facilitate understanding of community structure for various aquatic microorganisms in brackish water and freshwater regions with emphasis on cyanobacteria, and (2) to test a hypothesis that Microcystis genotypes that tolerate higher salinity were blooming in brackish water environments during the severe drought, 2014. Shotgun metagenomic analysis revealed that cyanobacteria dominated the brackish water region while bacteria dominated the freshwater region. A group of cyanobacteria (e.g., Aphanizomenon, Microcystis, Planktothrix, Pseudanabaena), bacteria (e.g., Bacillus, Porphyrobacter), and diatoms (Phaeodactylum and Thalassiosira) were abundant in the brackish water region. In contrast, Hassallia (cyanobacteria) and green algae (Nannochloropsis, Chlamydomonas, and Volvox) were abundant in the landward freshwater region. Station variation was also apparent. One landward sampling station located downstream of an urbanized area differed substantially from the other stations in terms of both water chemistry and community structure, with a higher percentage of arthropods, green algae, and eukaryotes. Screening of the Microcystis internal transcribed spacer region revealed six representative genotypes, and two of which were successfully quantified using qPCR (Genotypes I and VI). Both genotypes occurred predominantly in the freshwater region, so the data from this study did not support the hypothesis that salinity tolerant Microcystis genotypes bloomed in the brackish water region in 2014.}, } @article {pmid30246365, year = {2018}, author = {Murakami, T and Segawa, T and Takeuchi, N and Barcaza Sepúlveda, G and Labarca, P and Kohshima, S and Hongoh, Y}, title = {Metagenomic analyses highlight the symbiotic association between the glacier stonefly Andiperla willinki and its bacterial gut community.}, journal = {Environmental microbiology}, volume = {20}, number = {11}, pages = {4170-4183}, doi = {10.1111/1462-2920.14420}, pmid = {30246365}, issn = {1462-2920}, support = {16H04840//Japan Society for the Promotion of Science/International ; 17K19423//Japan Society for the Promotion of Science/International ; 22241005//Japan Society for the Promotion of Science/International ; 23117003//Japan Society for the Promotion of Science/International ; 26241020//Japan Society for the Promotion of Science/International ; GS009//NEXT/International ; }, mesh = {Animals ; Bacteria/classification/*genetics/*isolation & purification ; Bacterial Physiological Phenomena ; Ecosystem ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Ice Cover/*parasitology ; In Situ Hybridization, Fluorescence ; Insecta/*microbiology/physiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; }, abstract = {The glacier stonefly Andiperla willinki is the largest metazoan inhabiting the Patagonian glaciers. In this study, we analysed the gut microbiome of the aquatic nymphs by 16S rRNA gene amplicon and metagenomic sequencing. The bacterial gut community was consistently dominated by taxa typical of animal digestive tracts, such as Dysgonomonadaceae and Lachnospiraceae, as well as those generally indigenous to glacier environments, such as Polaromonas. Interestingly, the dominant Polaromonas phylotypes detected in the stonefly gut were almost never detected in the glacier surface habitat. Fluorescence in situ hybridization analysis revealed that the bacterial lineages typical of animal guts colonized the gut wall in a co-aggregated form, while Polaromonas cells were not included in the aggregates. Draft genomes of several dominant bacterial lineages were reconstructed from metagenomic datasets and indicated that the predominant Dysgonomonadaceae bacterium is capable of degrading various polysaccharides derived from host-ingested food, such as algae, and that other dominant bacterial lineages ferment saccharides liberated by the polysaccharide degradation. Our results suggest that the gut bacteria-host association in the glacier stonefly contributes to host nutrition as well as material cycles in the glacier environment.}, } @article {pmid30242844, year = {2019}, author = {Lee, JJ and Kim, SH and Lee, MJ and Kim, BK and Song, WJ and Park, HW and Cho, SH and Hong, SJ and Chang, YS and Kim, BS}, title = {Different upper airway microbiome and their functional genes associated with asthma in young adults and elderly individuals.}, journal = {Allergy}, volume = {74}, number = {4}, pages = {709-719}, doi = {10.1111/all.13608}, pmid = {30242844}, issn = {1398-9995}, support = {2017R1D1A1B03029282//Ministry of Education/International ; 2015-ER6604-00//Research of Korea Centers for Disease Control and Prevention/International ; }, mesh = {Age Factors ; Aged ; Asthma/*microbiology ; Bacteria/genetics/isolation & purification ; Female ; Humans ; Male ; Microbiota/*genetics/immunology ; Nasopharyngeal Diseases/microbiology ; Respiratory System/*microbiology ; Young Adult ; }, abstract = {BACKGROUND: Microbes in the airway have been shown to be associated with the pathogenesis of asthma. The upper airway microbiome influences the dysbiosis of the lower airway microbiome. However, to date, the influence of upper airway microbiome for adult and elderly asthma has not been fully elucidated. Here, the metagenome of upper airway microbiome of young adults and elderly was analyzed to identify their association with adult asthma.

METHODS: Nasopharyngeal swabs were collected from young adult and elderly asthma patients and non-asthmatic subjects. The compositions and functional genes of airway microbiome were analyzed by high-throughput sequencing.

RESULTS: The composition of microbiota differed between young adult and elderly, and it was different between asthmatics and non-asthmatics in each age group. Different bacteria were related to FEV1% predicted in each age group. Genes related to lysine degradation, N-glycan biosynthesis, caprolactam degradation, and PPAR signaling pathway, which could be related to the reduction in inflammation and degradation of air pollutants, were higher in non-asthmatics. Genes related to pentose phosphate pathway, lipopolysaccharide biosynthesis, flagella assembly, and bacterial chemotaxis-which may all be related to increased inflammation and colonization of pathogenic bacteria-were higher in young adult asthmatic patients. However, the functional genes of airway microbiome in elderly patients were not significantly different according to asthma morbidity.

CONCLUSIONS: These results suggest that the composition and function of upper airway microbiome could influence asthma pathogenesis, and the microbiome could play various roles depending on the age group.}, } @article {pmid30242595, year = {2018}, author = {Hemmat-Jou, MH and Safari-Sinegani, AA and Mirzaie-Asl, A and Tahmourespour, A}, title = {Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach.}, journal = {Ecotoxicology (London, England)}, volume = {27}, number = {9}, pages = {1281-1291}, pmid = {30242595}, issn = {1573-3017}, mesh = {Environmental Monitoring/*methods ; Metagenome ; *Metagenomics ; Metals, Heavy/*toxicity ; Soil ; *Soil Microbiology ; Soil Pollutants/*toxicity ; }, abstract = {Soil pollution occurring at mining sites has adverse impacts on soil microbial diversity. New approaches, such as metagenomics approach, have become a powerful tool to investigate biodiversity of soil microbial communities. In the current study, metagenomics approach was used to investigate the microbial diversity of soils contaminated with different concentrations of lead (Pb) and zinc (Zn). The contaminated soils were collected from a Pb and Zn mine. The soil total DNA was extracted and 16S rDNA genes were amplified using universal primers. The PCR amplicons were sequenced and bioinformatic analysis of metagenomes was conducted to identify prokaryotic diversity in the Pb- and Zn-contaminated soils. The results indicated that the ten most abundant bacteria in all samples were Solirubrobacter (Actinobacteria), Geobacter (Proteobacteria), Edaphobacter (Acidobacteria), Pseudomonas (Proteobacteria), Gemmatiomonas (Gemmatimonadetes), Nitrosomonas, Xanthobacter, and Sphingomonas (Proteobacteria), Pedobacter (Bacterioidetes), and Ktedonobacter (Chloroflexi), descendingly. Archaea were also numerous, and Nitrososphaerales which are important in the nitrogen cycle had the highest abundance in the samples. Although, alpha and beta diversity showed negative effects of Pb and Zn contamination on soil microbial communities, microbial diversity of the contaminated soils was not subjected to a significant change. This study provided valuable insights into microbial composition in heavy metals-contaminated soils.}, } @article {pmid30240894, year = {2019}, author = {Allaband, C and McDonald, D and Vázquez-Baeza, Y and Minich, JJ and Tripathi, A and Brenner, DA and Loomba, R and Smarr, L and Sandborn, WJ and Schnabl, B and Dorrestein, P and Zarrinpar, A and Knight, R}, title = {Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians.}, journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association}, volume = {17}, number = {2}, pages = {218-230}, pmid = {30240894}, issn = {1542-7714}, support = {K08 DK102902/DK/NIDDK NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Individuality ; Metabolomics/*methods ; Metagenomics/*methods ; *Microbiota ; }, abstract = {Advances in technical capabilities for reading complex human microbiomes are leading to an explosion of microbiome research, leading in turn to intense interest among clinicians in applying these techniques to their patients. In this review, we discuss the content of the human microbiome, including intersubject and intrasubject variability, considerations of study design including important confounding factors, and different methods in the laboratory and on the computer to read the microbiome and its resulting gene products and metabolites. We highlight several common pitfalls for clinicians, including the expectation that an individual's microbiome will be stable, that diet can induce rapid changes that are large compared with the differences among subjects, that everyone has essentially the same core stool microbiome, and that different laboratory and computational methods will yield essentially the same results. We also highlight the current limitations and future promise of these techniques, with the expectation that an understanding of these considerations will help accelerate the path toward routine clinical application of these techniques developed in research settings.}, } @article {pmid30240699, year = {2018}, author = {Harris, L and van Zyl, LJ and Kirby-McCullough, BM and Damelin, LH and Tiemessen, CT and Trindade, M}, title = {Identification and sequence analysis of two novel cryptic plasmids isolated from the vaginal mucosa of South African women.}, journal = {Plasmid}, volume = {98}, number = {}, pages = {56-62}, doi = {10.1016/j.plasmid.2018.09.008}, pmid = {30240699}, issn = {1095-9890}, mesh = {DNA, Bacterial/*genetics ; Female ; Humans ; Lactobacillus/classification/*genetics/*isolation & purification/metabolism ; Microbiota ; Mucous Membrane/*microbiology ; Phylogeny ; Plasmids/chemistry/*genetics ; Sequence Analysis, DNA ; South Africa/epidemiology ; Vagina/*microbiology ; Vaginosis, Bacterial/epidemiology/*microbiology ; }, abstract = {The vaginal mucosa is dominated by Gram positive, rod shaped lactobacilli which serve as a natural barrier against infection. In both healthy- and bacterial vaginosis (BV)-infected women Lactobacillus crispatus and Lactobacillus jensenii have been found to be the predominant Lactobacillus species. Many studies have been conducted to assess factors influencing lactobacilli dominance in the vaginal microbiome. In the present study two plasmids, pLc4 and pLc17, isolated from vaginal Lactobacillus strains of both healthy and BV-infected women were characterized. The smaller plasmid, pLc4 (4224 bp), was detected in both L. crispatus and L. jensenii strains, while pLc17 was only detected in L. crispatus. Based on its nucleotide sequence pLc4 appears highly novel, with its replication protein having 44% identity to the replication initiation protein of pSMQ173b_03. Phylogenetic analysis with other Rolling Circle Replication plasmids confirmed that pLc4 shows a low degree of similarity to these plasmids. Plasmid pLc17 (16,663 bp) appears to carry both a RCR replicon and a theta replicon, which is rare in naturally occurring plasmids. pLc4 was maintained at a high copy number of 29, while pLc17 appears to be a medium copy number plasmid maintained at 11 copies per chromosome. While sequence analysis is a valuable tool to study cryptic plasmids, further function-based analysis will be required in order to fully elucidate the role of these plasmids within the vaginal milieu.}, } @article {pmid30240114, year = {2019}, author = {Bergner, LM and Orton, RJ and da Silva Filipe, A and Shaw, AE and Becker, DJ and Tello, C and Biek, R and Streicker, DG}, title = {Using noninvasive metagenomics to characterize viral communities from wildlife.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {128-143}, pmid = {30240114}, issn = {1755-0998}, support = {102507/Z/13/A//Wellcome-Beit Prize/ ; MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; 102507/Z/13/Z//Sir Henry Dale Fellowship, jointly funded by the Wellcome Trust and Royal Society/ ; }, mesh = {Animals ; Biodiversity ; Chiroptera/*virology ; Feces/virology ; Metagenomics/*methods ; Oropharynx/virology ; Peru ; Sequence Analysis, DNA/*methods ; Specimen Handling/*methods ; Virus Diseases/*veterinary/virology ; Viruses/*classification/*genetics ; }, abstract = {Microbial communities play an important role in organismal and ecosystem health. While high-throughput metabarcoding has revolutionized the study of bacterial communities, generating comparable viral communities has proven elusive, particularly in wildlife samples where the diversity of viruses and limited quantities of viral nucleic acid present distinctive challenges. Metagenomic sequencing is a promising solution for studying viral communities, but the lack of standardized methods currently precludes comparisons across host taxa or localities. Here, we developed an untargeted shotgun metagenomic sequencing protocol to generate comparable viral communities from noninvasively collected faecal and oropharyngeal swabs. Using samples from common vampire bats (Desmodus rotundus), a key species for virus transmission to humans and domestic animals, we tested how different storage media, nucleic acid extraction procedures and enrichment steps affect viral community detection. Based on finding viral contamination in foetal bovine serum, we recommend storing swabs in RNAlater or another nonbiological medium. We recommend extracting nucleic acid directly from swabs rather than from supernatant or pelleted material, which had undetectable levels of viral RNA. Results from a low-input RNA library preparation protocol suggest that ribosomal RNA depletion and light DNase treatment reduce host and bacterial nucleic acid, and improve virus detection. Finally, applying our approach to twelve pooled samples from seven localities in Peru, we showed that detected viral communities saturated at the attained sequencing depth, allowing unbiased comparisons of viral community composition. Future studies using the methods outlined here will elucidate the determinants of viral communities across host species, environments and time.}, } @article {pmid30239621, year = {2019}, author = {Zinter, MS and Dvorak, CC and Mayday, MY and Iwanaga, K and Ly, NP and McGarry, ME and Church, GD and Faricy, LE and Rowan, CM and Hume, JR and Steiner, ME and Crawford, ED and Langelier, C and Kalantar, K and Chow, ED and Miller, S and Shimano, K and Melton, A and Yanik, GA and Sapru, A and DeRisi, JL}, title = {Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {68}, number = {11}, pages = {1847-1855}, pmid = {30239621}, issn = {1537-6591}, support = {K23 HL133437/HL/NHLBI NIH HHS/United States ; K23 HL138461/HL/NHLBI NIH HHS/United States ; K12 HD068371/HD/NICHD NIH HHS/United States ; K12 HD000850/HD/NICHD NIH HHS/United States ; L60 MD010865/MD/NIMHD NIH HHS/United States ; }, mesh = {Adolescent ; Bacteria/genetics ; Child ; Child, Preschool ; Female ; Fungi/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Immunocompromised Host ; Lung/*microbiology/*virology ; Lung Diseases/diagnosis/*microbiology/*virology ; Male ; *Metagenome ; Metagenomics ; Microbiota ; Missed Diagnosis ; Pilot Projects ; Retrospective Studies ; Viruses/genetics ; }, abstract = {BACKGROUND: Despite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant mortality. Therefore, we aimed to develop a highly sensitive metagenomic next-generation sequencing (mNGS) assay capable of evaluating the pulmonary microbiome and identifying diverse pathogens in the lungs of immunocompromised children.

METHODS: We collected 41 lower respiratory specimens from 34 immunocompromised children undergoing evaluation for pulmonary disease at 3 children's hospitals from 2014-2016. Samples underwent mechanical homogenization, parallel RNA/DNA extraction, and metagenomic sequencing. Sequencing reads were aligned to the National Center for Biotechnology Information nucleotide reference database to determine taxonomic identities. Statistical outliers were determined based on abundance within each sample and relative to other samples in the cohort.

RESULTS: We identified a rich cross-domain pulmonary microbiome that contained bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Samples with bacterial outliers had significantly depressed alpha-diversity (median, 0.61; interquartile range [IQR], 0.33-0.72 vs median, 0.96; IQR, 0.94-0.96; P < .001). Potential pathogens were detected in half of samples previously negative by clinical diagnostics, demonstrating increased sensitivity for missed pulmonary pathogens (P < .001).

CONCLUSIONS: An optimized mNGS assay for pulmonary microbes demonstrates significant inoculation of the lower airways of immunocompromised children with diverse bacteria, fungi, and viruses. Potential pathogens can be identified based on absolute and relative abundance. Ongoing investigation is needed to determine the pathogenic significance of outlier microbes in the lungs of immunocompromised children with pulmonary disease.}, } @article {pmid30234027, year = {2018}, author = {Wang, Z and Zolnik, CP and Qiu, Y and Usyk, M and Wang, T and Strickler, HD and Isasi, CR and Kaplan, RC and Kurland, IJ and Qi, Q and Burk, RD}, title = {Comparison of Fecal Collection Methods for Microbiome and Metabolomics Studies.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {301}, pmid = {30234027}, issn = {2235-2988}, support = {R01 MD011389/MD/NIMHD NIH HHS/United States ; R01 HL095140/HL/NHLBI NIH HHS/United States ; R01 HL126543/HL/NHLBI NIH HHS/United States ; K12 GM102779/GM/NIGMS NIH HHS/United States ; K01 HL129892/HL/NHLBI NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; P30 AI124414/AI/NIAID NIH HHS/United States ; P30 CA013330/CA/NCI NIH HHS/United States ; U01 AI035004/AI/NIAID NIH HHS/United States ; P30 DK041296/DK/NIDDK NIH HHS/United States ; R01 HL083760/HL/NHLBI NIH HHS/United States ; R01 HL132794/HL/NHLBI NIH HHS/United States ; }, mesh = {Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fatty Acids/analysis ; Feces/*chemistry/*microbiology ; Healthy Volunteers ; Humans ; Metabolomics/*methods ; Metagenomics/*methods ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Specimen Handling/*methods ; Temperature ; }, abstract = {Background: Integrated microbiome and metabolomics analyses hold the potential to reveal interactions between host and microbiota in relation to disease risks. However, there are few studies evaluating how field methods influence fecal microbiome characterization and metabolomics profiling. Methods: Five fecal collection methods [immediate freezing at -20°C without preservative, OMNIgene GUT, 95% ethanol, RNAlater, and Flinders Technology Associates (FTA) cards] were used to collect 40 fecal samples from eight healthy volunteers. We performed gut microbiota 16S rRNA sequencing, untargeted metabolomics profiling, and targeted metabolomics focusing on short chained fatty acids (SCFAs). Metrics included α-diversity and β-diversity as well as distributions of predominant phyla. To evaluate the concordance with the "gold standard" immediate freezing, the intraclass correlation coefficients (ICCs) for alternate fecal collection systems were calculated. Correlations between SCFAs and gut microbiota were also examined. Results: The FTA cards had the highest ICCs compared to the immediate freezing method for α-diversity indices (ICCs = 0.96, 0.96, 0.76 for Shannon index, Simpson's Index, Chao-1 Index, respectively), followed by OMNIgene GUT, RNAlater, and 95% ethanol. High ICCs (all >0.88) were observed for all methods for the β-diversity metric. For untargeted metabolomics, in comparison to immediate freezing which detected 621 metabolites at ≥75% detectability level, 95% ethanol showed the largest overlapping set of metabolites (n = 430; 69.2%), followed by FTA cards (n = 330; 53.1%) and OMNIgene GUT (n = 213; 34.3%). Both OMNIgene GUT (ICCs = 0.82, 0.93, 0.64) and FTA cards (ICCs = 0.87, 0.85, 0.54) had acceptable ICCs for the top three predominant SCFAs (butyric acid, propionic acid and acetic acid). Nominally significant correlations between bacterial genera and SCFAs (P < 0.05) were observed in fecal samples collected by different methods. Of note, a high correlation between the genus Blautia (known butyrate producer) and butyric acid was observed for both immediate freezing (r = 0.83) and FTA cards (r = 0.74). Conclusions: Four alternative fecal collection methods are generally comparable with immediate freezing, but there are differences in certain measures of the gut microbiome and fecal metabolome across methods. Choice of method depends on the research interests, simplicity of fecal collection procedures and ease of transportation to the lab, especially for large epidemiological studies.}, } @article {pmid30232678, year = {2019}, author = {Osman, JR and Regeard, C and Badel, C and Fernandes, G and DuBow, MS}, title = {Variation of bacterial biodiversity from saline soils and estuary sediments present near the Mediterranean Sea coast of Camargue (France).}, journal = {Antonie van Leeuwenhoek}, volume = {112}, number = {3}, pages = {351-365}, doi = {10.1007/s10482-018-1164-z}, pmid = {30232678}, issn = {1572-9699}, mesh = {Bacteria/*classification/genetics/*isolation & purification ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Estuaries ; France ; Geologic Sediments/*microbiology ; Mediterranean Sea ; Metagenomics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Salinity is an important environmental factor influencing microbial community composition. To better understand this influence, we determined the bacterial communities present in 17 different sites of brackish sediment (underwater) and soil (surface) samples from the Camargue region (Rhône river delta) in southern France during the fall of 2013 and 2014 using pyrosequencing of the V3-V4 regions of the 16S rRNA genes amplified by PCR. This region is known for abundant flora and fauna and, though saline, 30% of rice consumed in France is grown here. We found that bacterial abundance in 1 g of soil or sediment, calculated by qPCR, was higher in sediments than in surface soil samples. Members belonging to the Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes phyla dominated the bacterial communities of sediment samples, while members belonging to the Proteobacteria, Bacteroidetes, Gemmatimonadetes, Actinobacteria, Firmicutes and Acidobacteria phyla dominated the bacterial communities of the soil samples. The most abundant bacterial genera present in the saline sediments and soils from the Camargue belonged mostly to halophilic and sulphate reducing bacteria, suggesting that the Camargue may be a valuable system to investigate saline, yet agriculturally productive, sediment and soil microbial ecosystem.}, } @article {pmid30232167, year = {2018}, author = {Ingala, MR and Simmons, NB and Perkins, SL}, title = {Bats Are an Untapped System for Understanding Microbiome Evolution in Mammals.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, pmid = {30232167}, issn = {2379-5042}, mesh = {Animals ; Chiroptera/*microbiology ; *Diet ; Ecology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; *Metagenomics ; Phylogeny ; }, abstract = {Mammals evolved in a microbial world, and consequently, microbial symbionts have played a role in their evolution. An exciting new subdiscipline of metagenomics considers the ways in which microbes, particularly those found in the gut, have facilitated the ecological and phylogenetic radiation of mammals. However, the vast majority of such studies focus on domestic animals, laboratory models, or charismatic megafauna (e.g., pandas and chimpanzees). The result is a plethora of studies covering few taxa across the mammal tree of life, leaving broad patterns of microbiome function and evolution unclear. Wildlife microbiome research urgently needs a model system in which to test hypotheses about metagenomic involvement in host ecology and evolution. We propose that bats (Order: Chiroptera) represent a model system ideal for comparative microbiome research, affording opportunities to examine host phylogeny, diet, and other natural history characteristics in relation to the evolution of the gut microbiome.}, } @article {pmid30231921, year = {2018}, author = {Vavourakis, CD and Andrei, AS and Mehrshad, M and Ghai, R and Sorokin, DY and Muyzer, G}, title = {A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {168}, pmid = {30231921}, issn = {2049-2618}, support = {322551/ERC_/European Research Council/International ; }, mesh = {Bacteria/classification/*genetics/isolation & purification/metabolism ; Carbon Cycle ; Genetic Variation ; Genome, Bacterial ; Geologic Sediments/analysis/*microbiology ; Lakes/analysis/*microbiology ; Metagenome ; Metagenomics ; Microbiota ; Nitrogen Cycle ; Phylogeny ; Sodium Chloride/analysis ; }, abstract = {BACKGROUND: Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages.

RESULTS: We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L[-1]. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria.

CONCLUSIONS: Our first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments.}, } @article {pmid30230652, year = {2018}, author = {Little, MS and Ervin, SM and Walton, WG and Tripathy, A and Xu, Y and Liu, J and Redinbo, MR}, title = {Active site flexibility revealed in crystal structures of Parabacteroides merdae β-glucuronidase from the human gut microbiome.}, journal = {Protein science : a publication of the Protein Society}, volume = {27}, number = {12}, pages = {2010-2022}, pmid = {30230652}, issn = {1469-896X}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 CA207416/CA/NCI NIH HHS/United States ; }, mesh = {Bacteroidaceae/*enzymology ; Catalytic Domain ; Crystallography, X-Ray ; *Gastrointestinal Microbiome ; Glucuronidase/*metabolism ; Humans ; Models, Molecular ; Protein Conformation ; }, abstract = {β-Glucuronidase (GUS) enzymes in the gastrointestinal tract are involved in maintaining mammalian-microbial symbiosis and can play key roles in drug efficacy and toxicity. Parabacteroides merdae GUS was identified as an abundant mini-Loop 2 (mL2) type GUS enzyme in the Human Microbiome Project gut metagenomic database. Here, we report the crystal structure of P. merdae GUS and highlight the differences between this enzyme and extant structures of gut microbial GUS proteins. We find that P. merdae GUS exhibits a distinct tetrameric quaternary structure and that the mL2 motif traces a unique path within the active site, which also includes two arginines distinctive to this GUS. We observe two states of the P. merdae GUS active site; a loop repositions itself by more than 50 Å to place a functionally-relevant residue into the enzyme's catalytic site. Finally, we find that P. merdae GUS is able to bind to homo and heteropolymers of the polysaccharide alginic acid. Together, these data broaden our understanding of the structural and functional diversity in the GUS family of enzymes present in the human gut microbiome and point to specialization as an important feature of microbial GUS orthologs.}, } @article {pmid30228802, year = {2018}, author = {Gacesa, R and Baranasic, D and Starcevic, A and Diminic, J and Korlević, M and Najdek, M and Blažina, M and Oršolić, D and Kolesarić, D and Long, PF and Cullum, J and Hranueli, D and Orlic, S and Zucko, J}, title = {Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from Northern Adriatic Sea Sediments.}, journal = {Food technology and biotechnology}, volume = {56}, number = {2}, pages = {270-277}, pmid = {30228802}, issn = {1330-9862}, support = {MC_EX_MR/S300007/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Three metagenomic libraries were constructed using surface sediment samples from the northern Adriatic Sea. Two of the samples were taken from a highly polluted and an unpolluted site respectively. The third sample from a polluted site had been enriched using crude oil. The results of the metagenome analyses were incorporated in the REDPET relational database (http://redpet.bioinfo.pbf.hr/REDPET), which was generated using the previously developed MEGGASENSE platform. The database includes taxonomic data to allow the assessment of the biodiversity of metagenomic libraries and a general functional analysis of genes using hidden Markov model (HMM) profiles based on the KEGG database. A set of 22 specialised HMM profiles was developed to detect putative genes for hydrocarbon-degrading enzymes. Use of these profiles showed that the metagenomic library generated after selection on crude oil had enriched genes for aerobic n-alkane degradation. The use of this system for bioprospecting was exemplified using potential alkB and almA genes from this library.}, } @article {pmid30228361, year = {2018}, author = {Mangifesta, M and Mancabelli, L and Milani, C and Gaiani, F and de'Angelis, N and de'Angelis, GL and van Sinderen, D and Ventura, M and Turroni, F}, title = {Mucosal microbiota of intestinal polyps reveals putative biomarkers of colorectal cancer.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {13974}, pmid = {30228361}, issn = {2045-2322}, mesh = {Adenomatous Polyps/*diagnosis/genetics/microbiology ; Aged ; Bacteria/*classification/genetics/isolation & purification ; Biomarkers/*analysis ; Colorectal Neoplasms/*diagnosis/genetics/microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Intestinal Polyps/*diagnosis/genetics/microbiology ; Male ; Metagenomics ; Microbiota/*genetics ; Mucous Membrane/*metabolism/microbiology ; Pilot Projects ; Prognosis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The human intestine retains a complex microbial ecosystem, which performs crucial functions that impact on host health. Several studies have indicated that intestinal dysbiosis may impact on the establishment of life-threatening intestinal diseases such as colorectal cancer. An adenomatous polyp is the result of abnormal tissue growth, which is benign but is considered to be associated with a high risk of developing colorectal cancer, based on its grade of dysplasia. Development of diagnostic tools that are based on surveying the gut microbiota and are aimed at early detection of colorectal cancer represent highly desirable target. For this purpose, we performed a pilot study in which we applied a metataxonomic analysis based on 16S rRNA gene sequencing approach to unveil the composition of microbial communities of intestinal polyps. Moreover, we performed a meta-analysis involving the reconstructed microbiota composition of adenomatous polyps and publicly available metagenomics datasets of colorectal cancer. These analyses allowed the identification of microbial taxa such as Faecalibacterium, Bacteroides and Romboutsia, which appear to be depleted in cancerogenic mucosa as well as in adenomatous polyps, thus representing novel microbial biomarkers associated with early tumor formation. Furthermore, an absolute quantification of Fusubacterium nucleatum in polyps further compounded the important role of this microorganism as a valuable putative microbial biomarker for early diagnosis of colorectal cancer.}, } @article {pmid30227897, year = {2018}, author = {Arora-Williams, K and Olesen, SW and Scandella, BP and Delwiche, K and Spencer, SJ and Myers, EM and Abraham, S and Sooklal, A and Preheim, SP}, title = {Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {165}, pmid = {30227897}, issn = {2049-2618}, mesh = {Bacteria/classification/isolation & purification/metabolism ; Carbon/chemistry/metabolism ; Ecosystem ; Lakes/*chemistry/*microbiology ; Metagenome ; Metagenomics ; Methane/chemistry/metabolism ; *Microbiota ; Oxidation-Reduction ; Oxygen/chemistry/metabolism ; }, abstract = {BACKGROUND: Microbial processes are intricately linked to the depletion of oxygen in in-land and coastal water bodies, with devastating economic and ecological consequences. Microorganisms deplete oxygen during biomass decomposition, degrading the habitat of many economically important aquatic animals. Microbes then turn to alternative electron acceptors, which alter nutrient cycling and generate potent greenhouse gases. As oxygen depletion is expected to worsen with altered land use and climate change, understanding how chemical and microbial dynamics impact dead zones will aid modeling efforts to guide remediation strategies. More work is needed to understand the complex interplay between microbial genes, populations, and biogeochemistry during oxygen depletion.

RESULTS: Here, we used 16S rRNA gene surveys, shotgun metagenomic sequencing, and a previously developed biogeochemical model to identify genes and microbial populations implicated in major biogeochemical transformations in a model lake ecosystem. Shotgun metagenomic sequencing was done for one time point in Aug., 2013, and 16S rRNA gene sequencing was done for a 5-month time series (Mar.-Aug., 2013) to capture the spatiotemporal dynamics of genes and microorganisms mediating the modeled processes. Metagenomic binning analysis resulted in many metagenome-assembled genomes (MAGs) that are implicated in the modeled processes through gene content similarity to cultured organism and the presence of key genes involved in these pathways. The MAGs suggested some populations are capable of methane and sulfide oxidation coupled to nitrate reduction. Using the model, we observe that modulating these processes has a substantial impact on overall lake biogeochemistry. Additionally, 16S rRNA gene sequences from the metagenomic and amplicon libraries were linked to processes through the MAGs. We compared the dynamics of microbial populations in the water column to the model predictions. Many microbial populations involved in primary carbon oxidation had dynamics similar to the model, while those associated with secondary oxidation processes deviated substantially.

CONCLUSIONS: This work demonstrates that the unique capabilities of resident microbial populations will substantially impact the concentration and speciation of chemicals in the water column, unless other microbial processes adjust to compensate for these differences. It further highlights the importance of the biological aspects of biogeochemical processes, such as fluctuations in microbial population dynamics. Integrating gene and population dynamics into biogeochemical models has the potential to improve predictions of the community response under altered scenarios to guide remediation efforts.}, } @article {pmid30225935, year = {2019}, author = {Drinkwater, R and Schnell, IB and Bohmann, K and Bernard, H and Veron, G and Clare, E and Gilbert, MTP and Rossiter, SJ}, title = {Using metabarcoding to compare the suitability of two blood-feeding leech species for sampling mammalian diversity in North Borneo.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {105-117}, pmid = {30225935}, issn = {1755-0998}, support = {SAS-2016-100//The Leverhulme Trust/ ; NE/K016148/1//Natural Environment Research Council/ ; DFF 5051-00140//The Danish Council for Independent Research/ ; }, mesh = {Animals ; Borneo ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal/chemistry/genetics ; *Feeding Behavior ; High-Throughput Nucleotide Sequencing ; *Host Specificity ; Leeches/*physiology ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The application of high-throughput sequencing (HTS) for metabarcoding of mixed samples offers new opportunities in conservation biology. Recently, the successful detection of prey DNA from the guts of leeches has raised the possibility that these, and other blood-feeding invertebrates, might serve as useful samplers of mammals. Yet little is known about whether sympatric leech species differ in their feeding preferences, and whether this has a bearing on their relative suitability for monitoring local mammalian diversity. To address these questions, we collected spatially matched samples of two congeneric leech species Haemadipsa picta and Haemadipsa sumatrana from lowland rainforest in Borneo. For each species, we pooled ~500 leeches into batches of 10 individuals, performed PCR to target a section of the mammalian 16S rRNA locus and undertook sequencing of amplicon libraries using an Illumina MiSeq. In total, we identified sequences from 14 mammalian genera, spanning nine families and five orders. We found greater numbers of detections, and higher diversity of OTUs, in H. picta compared with H. sumatrana, with rodents only present in the former leech species. However, comparison of samples from across the landscape revealed no significant difference in mammal community composition between the leech species. We therefore suggest that H. picta is the more suitable iDNA sampler in this degraded Bornean forest. We conclude that the choice of invertebrate sampler can influence the detectability of different mammal groups and that this should be accounted for when designing iDNA studies.}, } @article {pmid30223906, year = {2018}, author = {Bredon, M and Dittmer, J and Noël, C and Moumen, B and Bouchon, D}, title = {Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {162}, pmid = {30223906}, issn = {2049-2618}, mesh = {Animals ; Bacteria/enzymology/genetics/isolation & purification ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/metabolism ; Gastrointestinal Microbiome ; Isopoda/*metabolism/*microbiology/physiology ; Lignin/*metabolism ; Phylogeny ; Soil/parasitology ; *Symbiosis ; }, abstract = {BACKGROUND: Woodlice are recognized as keystone species in terrestrial ecosystems due to their role in the decomposition of organic matter. Thus, they contribute to lignocellulose degradation and nutrient cycling in the environment together with other macroarthropods. Lignocellulose is the main component of plants and is composed of cellulose, lignin and hemicellulose. Its digestion requires the action of multiple Carbohydrate-Active enZymes (called CAZymes), typically acting together as a cocktail with complementary, synergistic activities and modes of action. Some invertebrates express a few endogenous lignocellulose-degrading enzymes but in most species, an efficient degradation and digestion of lignocellulose can only be achieved through mutualistic associations with endosymbionts. Similar to termites, it has been suspected that several bacterial symbionts may be involved in lignocellulose degradation in terrestrial isopods, by completing the CAZyme repertoire of their hosts.

RESULTS: To test this hypothesis, host transcriptomic and microbiome shotgun metagenomic datasets were obtained and investigated from the pill bug Armadillidium vulgare. Many genes of bacterial and archaeal origin coding for CAZymes were identified in the metagenomes of several host tissues and the gut content of specimens from both laboratory lineages and a natural population of A. vulgare. Some of them may be involved in the degradation of cellulose, hemicellulose, and lignin. Reconstructing a lignocellulose-degrading microbial community based on the prokaryotic taxa contributing relevant CAZymes revealed two taxonomically distinct but functionally redundant microbial communities depending on host origin. In parallel, endogenous CAZymes were identified from the transcriptome of the host and their expression in digestive tissues was demonstrated by RT-qPCR, demonstrating a complementary enzyme repertoire for lignocellulose degradation from both the host and the microbiome in A. vulgare.

CONCLUSIONS: Our results provide new insights into the role of the microbiome in the evolution of terrestrial isopods and their adaptive radiation in terrestrial habitats.}, } @article {pmid30223687, year = {2019}, author = {Lin, H and He, QY and Shi, L and Sleeman, M and Baker, MS and Nice, EC}, title = {Proteomics and the microbiome: pitfalls and potential.}, journal = {Expert review of proteomics}, volume = {16}, number = {6}, pages = {501-511}, doi = {10.1080/14789450.2018.1523724}, pmid = {30223687}, issn = {1744-8387}, mesh = {Animals ; Biomarkers/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/physiology ; Humans ; Microbiota/*physiology ; Precision Medicine ; Proteomics/*methods ; }, abstract = {Introduction: Human symbiotic microbiota are now known to play important roles in human health and disease. Significant progress in our understanding of the human microbiome has been driven by recent technological advances in the fields of genomics, transcriptomics, and proteomics. As a complementary method to metagenomics, proteomics is enabling detailed protein profiling of the microbiome to decipher its structure and function and to analyze its relationship with the human body. Fecal proteomics is being increasingly applied to discover and validate potential health and disease biomarkers, and Therapeutic Goods Administration (TGA)-approved instrumentation and a range of clinical assays are being developed that will collectively play key roles in advancing personalized medicine. Areas covered: This review will introduce the complexity of the microbiome and its role in health and disease (in particular the gastrointestinal tract or gut microbiome), discuss current genomic and proteomic methods for studying this system, including the discovery of potential biomarkers, and outline the development of clinically accepted protocols leading to personalized medicine. Expert commentary: Recognition of the important role the microbiome plays in both health and disease is driving current research in this key area. A proteogenomics approach will be essential to unravel the biologies underlying this complex network.}, } @article {pmid30222584, year = {2020}, author = {Arabameri, A and Asemani, D and Teymourpour, P}, title = {Detection of Colorectal Carcinoma Based on Microbiota Analysis Using Generalized Regression Neural Networks and Nonlinear Feature Selection.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {17}, number = {2}, pages = {547-557}, doi = {10.1109/TCBB.2018.2870124}, pmid = {30222584}, issn = {1557-9964}, mesh = {Aged ; Algorithms ; Bacteria/classification/genetics ; *Colorectal Neoplasms/diagnosis/microbiology ; Diagnosis, Computer-Assisted ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Machine Learning ; Male ; Metagenome/genetics ; Middle Aged ; *Neural Networks, Computer ; }, abstract = {To obtain a screening tool for colorectal cancer (CRC) based on gut microbiota, we seek here to identify an optimal classifier for CRC detection as well as a novel nonlinear feature selection method for determining the most discriminative microbial species. In this study, the intestinal microflora in feces of 141 patients were modeled using general regression neural networks (GRNNs) combined with the proposed feature selection method. The proposed model led to slightly higher accuracy (AUC = 0.911) than previous studies . The results show that the Clostridium scindens and Bifidobacterium angulatum are indicators of healthy gut flora and CRC happens to reduce these bacterial species. In addition, Fusobacterium gonidiaformans was found to be closely correlated with the CRC. The occurrence of colorectal adenoma was not sufficiently discriminatory based on fecal microbiota implicating that the change of colonic flora happens in the advanced phase of CRC development rather than initial adenoma. Integrating the proposed model with fecal occult blood test (FOBT), the CRC detection accuracy remained nearly unchanged (AUC = 0.915). The performance of the proposed method is validated using independent cohorts from America and Austria. Our results suggest that the proposed feature selection method combined with GRNN is potentially an accurate method for CRC detection.}, } @article {pmid30221538, year = {2018}, author = {Venkataraman, A and Parlov, M and Hu, P and Schnell, D and Wei, X and Tiesman, JP}, title = {Spike-in genomic DNA for validating performance of metagenomics workflows.}, journal = {BioTechniques}, volume = {65}, number = {6}, pages = {315-321}, doi = {10.2144/btn-2018-0089}, pmid = {30221538}, issn = {1940-9818}, mesh = {Bacteria/*genetics/isolation & purification ; DNA, Bacterial/*genetics/isolation & purification ; Gene Library ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; *Microbiota ; Rhodopseudomonas/genetics/isolation & purification ; *Workflow ; }, abstract = {Shotgun metagenomics is a powerful platform to characterize human microbiomes. However, to translate such survey data into consumer-relevant products or services, it is critical to have a robust metagenomics workflow. We present a tool - spike-in DNA - to assess performance of metagenomics workflows. The spike-in is DNA from two organisms - Alivibrio fischeri and Rhodopseudomonas palustris, in a ratio of 4:1 added to samples before DNA extraction. With a valid workflow, the output ratio of relative abundances of these organisms should be close to 4. This expectation was tested in samples of varying diversities (n = 110), and the mean ratio was 4.73 (99% CI [4.0, 5.24]). We anticipate this tool to be a relevant community resource for assessing the quality of shotgun metagenomics workflows and thereby enable robust characterization of microbiomes.}, } @article {pmid30219103, year = {2018}, author = {Uritskiy, GV and DiRuggiero, J and Taylor, J}, title = {MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {158}, pmid = {30219103}, issn = {2049-2618}, support = {R01 AI134384/AI/NIAID NIH HHS/United States ; T32 GM007231/GM/NIGMS NIH HHS/United States ; U24 HG006620/HG/NHGRI NIH HHS/United States ; U41 HG006620/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/classification/genetics/isolation & purification ; Data Analysis ; Data Mining ; Gastrointestinal Microbiome ; *Genome, Bacterial ; Humans ; Metagenome ; Metagenomics/*methods ; *Software ; }, abstract = {BACKGROUND: The study of microbiomes using whole-metagenome shotgun sequencing enables the analysis of uncultivated microbial populations that may have important roles in their environments. Extracting individual draft genomes (bins) facilitates metagenomic analysis at the single genome level. Software and pipelines for such analysis have become diverse and sophisticated, resulting in a significant burden for biologists to access and use them. Furthermore, while bin extraction algorithms are rapidly improving, there is still a lack of tools for their evaluation and visualization.

RESULTS: To address these challenges, we present metaWRAP, a modular pipeline software for shotgun metagenomic data analysis. MetaWRAP deploys state-of-the-art software to handle metagenomic data processing starting from raw sequencing reads and ending in metagenomic bins and their analysis. MetaWRAP is flexible enough to give investigators control over the analysis, while still being easy-to-install and easy-to-use. It includes hybrid algorithms that leverage the strengths of a variety of software to extract and refine high-quality bins from metagenomic data through bin consolidation and reassembly. MetaWRAP's hybrid bin extraction algorithm outperforms individual binning approaches and other bin consolidation programs in both synthetic and real data sets. Finally, metaWRAP comes with numerous modules for the analysis of metagenomic bins, including taxonomy assignment, abundance estimation, functional annotation, and visualization.

CONCLUSIONS: MetaWRAP is an easy-to-use modular pipeline that automates the core tasks in metagenomic analysis, while contributing significant improvements to the extraction and interpretation of high-quality metagenomic bins. The bin refinement and reassembly modules of metaWRAP consistently outperform other binning approaches. Each module of metaWRAP is also a standalone component, making it a flexible and versatile tool for tackling metagenomic shotgun sequencing data. MetaWRAP is open-source software available at https://github.com/bxlab/metaWRAP .}, } @article {pmid30217839, year = {2018}, author = {Han, W and He, P and Shao, L and Lü, F}, title = {Metabolic Interactions of a Chain Elongation Microbiome.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {22}, pages = {}, pmid = {30217839}, issn = {1098-5336}, mesh = {Adenosine Triphosphate/metabolism ; Bacteria/classification/*genetics/isolation & purification/*metabolism ; Biofuels/analysis ; Bioreactors/microbiology ; Carbon/*metabolism ; Genome, Bacterial ; Metagenome ; *Microbiota ; }, abstract = {Carbon chain elongation (CCE), a reaction within the carboxylate platform that elongates short-chain to medium-chain carboxylates by mixed culture, has attracted worldwide interest. The present study provides insights into the microbial diversity and predictive microbial metabolic pathways of a mixed-culture CCE microbiome on the basis of a comparative analysis of the metagenome and metatranscriptome. We found that the microbial structure of an acclimated chain elongation microbiome was a highly similar to that of the original inoculating biogas reactor culture; however, the metabolic activities were completely different, demonstrating the high stability of the microbial structure and flexibility of its functions. Additionally, the fatty acid biosynthesis (FAB) pathway, rather than the well-known reverse β-oxidation (RBO) pathway for CCE, was more active and pivotal, though the FAB pathway had more steps and consumed more ATP, a phenomenon that has rarely been observed in previous CCE studies. A total of 91 draft genomes were reconstructed from the metagenomic reads, of which three were near completion (completeness, >97%) and were assigned to unknown strains of Methanolinea tarda, Bordetella avium, and Planctomycetaceae The last two strains are likely new-found active participators of CCE in the mixed culture. Finally, a conceptual framework of CCE, including both pathways and the potential participators, was proposed.IMPORTANCE Carbon chain elongation means the conversion of short-chain volatile fatty acids to medium-chain carboxylates, such as n-caproate and n-caprylate with electron donors under anaerobic condition. This bio-reaction can both expand the resource of valuable biochemicals and broaden the utilization of low-grade organic residues in a sustainable biorefinery context. Clostridium kluyveri is conventionally considered model microbe for carbon chain elongation which uses the reverse β-oxidation pathway. However, little is known about the detailed microbial structure and function of other abundant microorganism in a mixed culture (or open culture) of chain elongation. We conducted the comparative metagenomic and metatranscriptomic analysis of a chain elongation microbiome to throw light on the underlying functional microbes and alternative pathways.}, } @article {pmid30217078, year = {2018}, author = {Li, Y and Hingamp, P and Watai, H and Endo, H and Yoshida, T and Ogata, H}, title = {Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters.}, journal = {Viruses}, volume = {10}, number = {9}, pages = {}, pmid = {30217078}, issn = {1999-4915}, support = {203143100025//Canon Foundation for Scientific Research/International ; 16KT0020//Japan Society for the Promotion of Science/International ; 17H03850//Japan Society for the Promotion of Science/International ; 26430184//Japan Society for the Promotion of Science/International ; 2016-28//Institute for Chemical Research, Kyoto University/International ; 2017-25//Institute for Chemical Research, Kyoto University/International ; ANR-11-BTBR-0008//French Investments for the Future program/International ; }, mesh = {*Biodiversity ; Computational Biology/methods ; Genome, Viral ; Giant Viruses/*classification/*genetics ; Metagenome ; Metagenomics/methods ; Phylogeny ; *Polymerase Chain Reaction/methods ; Seawater/*virology ; *Water Microbiology ; }, abstract = {"Megaviridae" is a proposed family of giant viruses infecting unicellular eukaryotes. These viruses are ubiquitous in the sea and have impact on marine microbial community structure and dynamics through their lytic infection cycle. However, their diversity and biogeography have been poorly characterized due to the scarce detection of Megaviridae sequences in metagenomes, as well as the limitation of reference sequences used to design specific primers for this viral group. Here, we propose a set of 82 degenerated primers (referred to as MEGAPRIMER), targeting DNA polymerase genes (polBs) of Megaviridae. MEGAPRIMER was designed based on 921 Megaviridae polBs from sequenced genomes and metagenomes. By applying this primer set to environmental DNA meta-barcoding of a coastal seawater sample, we report 5595 non-singleton operational taxonomic units (OTUs) of Megaviridae at 97% nucleotide sequence identity. The majority of the OTUs were found to form diverse clades, which were phylogenetically distantly phylogenetically related to known viruses such as Mimivirus. The Megaviridae OTUs detected in this study outnumber the giant virus OTUs identified in previous individual studies by more than an order of magnitude. Hence, MEGAPRIMER represents a useful tool to study the diversity of Megaviridae at the population level in natural environments.}, } @article {pmid30217037, year = {2018}, author = {Liu, H and Liu, M and Fu, X and Zhang, Z and Zhu, L and Zheng, X and Liu, J}, title = {Astaxanthin Prevents Alcoholic Fatty Liver Disease by Modulating Mouse Gut Microbiota.}, journal = {Nutrients}, volume = {10}, number = {9}, pages = {}, pmid = {30217037}, issn = {2072-6643}, support = {31672511//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Anti-Inflammatory Agents/*pharmacology ; Biomarkers/blood ; Disease Models, Animal ; Dysbiosis ; Fatty Liver, Alcoholic/metabolism/microbiology/pathology/*prevention & control ; Gastrointestinal Microbiome/*drug effects/genetics ; Gastrointestinal Tract/*drug effects/microbiology ; Inflammation Mediators/metabolism ; Lipid Metabolism/drug effects ; Liver/*drug effects/metabolism/pathology ; Male ; Metagenome/drug effects ; Mice, Inbred C57BL ; Xanthophylls/pharmacology ; }, abstract = {The development and progression of alcoholic fatty liver disease (AFLD) is influenced by the intestinal microbiota. Astaxanthin, a type of oxygenated carotenoid with strong antioxidant and anti-inflammatory properties, has been proven to relieve liver injury. However, the relationship between the gut microbiota regulation effect of astaxanthin and AFLD improvement remains unclear. The effects of astaxanthin on the AFLD phenotype, overall structure, and composition of gut microbiota were assessed in ethanol-fed C57BL/6J mice. The results showed that astaxanthin treatment significantly relieves inflammation and decreases excessive lipid accumulation and serum markers of liver injury. Furthermore, astaxanthin was shown to significantly decrease species from the phyla Bacteroidetes and Proteobacteria and the genera Butyricimonas, Bilophila, and Parabacteroides, as well as increase species from Verrucomicrobia and Akkermansia compared with the Et (ethanol)group. Thirteen phylotypes related to inflammation as well as correlated with metabolic parameters were significantly altered by ethanol, and then notably reversed by astaxanthin. Additionally, astaxanthin altered 18 and 128 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways involved in lipid metabolism and xenobiotic biodegradation and metabolism at levels 2 and 3, respectively. These findings suggest that Aakkermansia may be a potential target for the astaxanthin-induced alleviation of AFLD and may be a potential treatment for bacterial disorders induced by AFLD.}, } @article {pmid30213145, year = {2018}, author = {Gómez-Villegas, P and Vigara, J and León, R}, title = {Characterization of the Microbial Population Inhabiting a Solar Saltern Pond of the Odiel Marshlands (SW Spain).}, journal = {Marine drugs}, volume = {16}, number = {9}, pages = {}, pmid = {30213145}, issn = {1660-3397}, support = {0055_ALGARED_PLUS_5_E//INTERREG VA España-Portugal (POCTEP) 2014-2020 Cooperation Program/ ; }, mesh = {Bacteroidetes/*genetics/isolation & purification ; Biodiversity ; Biotechnology/methods ; DNA, Bacterial/isolation & purification ; Genetic Variation ; Halobacteriales/*genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Sequence Analysis, DNA ; Spain ; *Water Microbiology ; Wetlands ; }, abstract = {The solar salterns located in the Odiel marshlands, in southwest Spain, are an excellent example of a hypersaline environment inhabited by microbial populations specialized in thriving under conditions of high salinity, which remains poorly explored. Traditional culture-dependent taxonomic studies have usually under-estimated the biodiversity in saline environments due to the difficulties that many of these species have to grow at laboratory conditions. Here we compare two molecular methods to profile the microbial population present in the Odiel saltern hypersaline water ponds (33% salinity). On the one hand, the construction and characterization of two clone PCR amplified-16S rRNA libraries, and on the other, a high throughput 16S rRNA sequencing approach based on the Illumina MiSeq platform. The results reveal that both methods are comparable for the estimation of major genera, although massive sequencing provides more information about the less abundant ones. The obtained data indicate that Salinibacter ruber is the most abundant genus, followed by the archaea genera, Halorubrum and Haloquadratum. However, more than 100 additional species can be detected by Next Generation Sequencing (NGS). In addition, a preliminary study to test the biotechnological applications of this microbial population, based on its ability to produce and excrete haloenzymes, is shown.}, } @article {pmid30209883, year = {2018}, author = {Chase, AB and Gomez-Lunar, Z and Lopez, AE and Li, J and Allison, SD and Martiny, AC and Martiny, JBH}, title = {Emergence of soil bacterial ecotypes along a climate gradient.}, journal = {Environmental microbiology}, volume = {20}, number = {11}, pages = {4112-4126}, doi = {10.1111/1462-2920.14405}, pmid = {30209883}, issn = {1462-2920}, support = {DE-PS02-09ER09-25//US Department of Energy Office of Science, Biological and Environmental Research/International ; GM-69337//National Institutes of Health Maximizing Access to Research Careers (MARC)/International ; DE-SC0016410//US Department of Energy Office of Science, Biological and Environmental Research/International ; DEB-1457160//Division of Environmental Biology/International ; //University of California Institute for Mexico and the United States/International ; GM-69337/GM/NIGMS NIH HHS/United States ; Graduate Assistance of National Need (GAANN)//Office of Postsecondary Education/International ; DEB-1457160//National Science Foundation/International ; //US Department of Education Graduate Assistance of National Need (GAANN)/International ; DE-PS02-09ER09-25 DE-SC0016410//Biological and Environmental Research/International ; //UC MEXUS-CONACYT/International ; }, mesh = {Bacteria/classification/*genetics/isolation & purification ; Climate ; Ecosystem ; *Ecotype ; Plant Leaves ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The high diversity of soil bacteria is attributed to the spatial complexity of soil systems, where habitat heterogeneity promotes niche partitioning among bacterial taxa. This premise remains challenging to test, however, as it requires quantifying the traits of closely related soil bacteria and relating these traits to bacterial abundances and geographic distributions. Here, we sought to investigate whether the widespread soil taxon Curtobacterium consists of multiple coexisting ecotypes with differential geographic distributions. We isolated Curtobacterium strains from six sites along a climate gradient and assayed four functional traits that may contribute to niche partitioning in leaf litter, the top layer of soil. Our results revealed that cultured isolates separated into fine-scale genetic clusters that reflected distinct suites of phenotypic traits, denoting the existence of multiple ecotypes. We then quantified the distribution of Curtobacterium by analysing metagenomic data collected across the gradient over 18 months. Six abundant ecotypes were observed with differential abundances along the gradient, suggesting fine-scale niche partitioning. However, we could not clearly explain observed geographic distributions of ecotypes by relating their traits to environmental variables. Thus, while we can resolve soil bacterial ecotypes, the traits delineating their distinct niches in the environment remain unclear.}, } @article {pmid30209587, year = {2019}, author = {Hernández-Gómez, O and Briggler, JT and Williams, RN}, title = {Captivity-Induced Changes in the Skin Microbial Communities of Hellbenders (Cryptobranchus alleganiensis).}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {782-793}, pmid = {30209587}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Female ; Male ; *Microbiota ; Missouri ; Phylogeny ; Skin/*microbiology ; Urodela/growth & development/*microbiology ; }, abstract = {Variation in environmental conditions can result in disparate associations between hosts and microbial symbionts. As such, it is imperative to evaluate how environmental variables (e.g., habitat quality) can influence host-associated microbiome composition. Within wildlife conservation programs, captive conditions can negatively influence the establishment and maintenance of "wild-type" microbiotas within a host. Alternative microbial communities can result in the proliferation of disease among captive stock or upon reintroduction. Hellbenders (Cryptobranchus alleganiensis) are a threatened salamander for which extensive captive management is currently employed. Using metabarcoding, we characterized the skin microbiota of wild and captive hellbenders from two subspecies in the state of Missouri, the eastern (C. a. alleganiensis) and the Ozark hellbender (C. a. bishopi). Both subspecies in our study included wild adults and captive juveniles that were collected from the wild as eggs. Our objectives were to investigate differences in the skin microbial communities' richness/diversity, composition, and functional profiles of microbes between wild and captive individuals. Captive eastern hellbenders possessed richer communities than wild cohorts, whereas the opposite pattern was observed within the Ozark subspecies. We found significant microbial community structure between wild and captive populations of both subspecies. Microbiota structure translated into differences in the predicted metagenome of wild and captive individuals as well. As such, we can expect captive hellbenders to experience alternative microbial structure and function upon reintroduction into the wild. Our study provides a baseline for the effect of captivity on the skin microbial communities of hellbenders, and highlights the need to incorporate microbiota management in current captive-rearing programs.}, } @article {pmid30209011, year = {2018}, author = {Shade, A and Dunn, RR and Blowes, SA and Keil, P and Bohannan, BJM and Herrmann, M and Küsel, K and Lennon, JT and Sanders, NJ and Storch, D and Chase, J}, title = {Macroecology to Unite All Life, Large and Small.}, journal = {Trends in ecology & evolution}, volume = {33}, number = {10}, pages = {731-744}, doi = {10.1016/j.tree.2018.08.005}, pmid = {30209011}, issn = {1872-8383}, mesh = {*Biodiversity ; Ecology/classification/*methods ; }, abstract = {Macroecology is the study of the mechanisms underlying general patterns of ecology across scales. Research in microbial ecology and macroecology have long been detached. Here, we argue that it is time to bridge the gap, as they share a common currency of species and individuals, and a common goal of understanding the causes and consequences of changes in biodiversity. Microbial ecology and macroecology will mutually benefit from a unified research agenda and shared datasets that span the entirety of the biodiversity of life and the geographic expanse of the Earth.}, } @article {pmid30208875, year = {2018}, author = {Wang, Q and Li, F and Liang, B and Liang, Y and Chen, S and Mo, X and Ju, Y and Zhao, H and Jia, H and Spector, TD and Xie, H and Guo, R}, title = {A metagenome-wide association study of gut microbiota in asthma in UK adults.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {114}, pmid = {30208875}, issn = {1471-2180}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/N01183X/1/MRC_/Medical Research Council/United Kingdom ; 105022/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adult ; Asthma/*microbiology ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestines/microbiology ; Male ; Metagenome ; United Kingdom ; }, abstract = {BACKGROUND: Asthma, one of the most common chronic respiratory disorders, is associated with the hyper-activation of the T-cell subset of adaptive immunity. The gut microbiota may be involved in the development of asthma through the production of short-chain fatty acids (SCFAs), exhibiting modulatory effects on Th. So, we performed a metagenome-wide association study (MWAS) of the fecal microbiota from individuals with asthma and healthy controls. And that was the first case to resolve the relationship between asthma and microbiome among UK adults.

RESULTS: The microbiota of the individuals with asthma consisted of fewer microbial entities than the microbiota of healthy individuals. Faecalibacterium prausnitzii, Sutterella wadsworthensis and Bacteroides stercoris were depleted in cases, whereas Clostridiums with Eggerthella lenta were over-represented in individuals with asthma. Functional analysis shows that the SCFAs might be altered in the microbiota of asthma patients.

CONCLUSION: In all, the adult human gut microbiome of asthma patients is clearly different from healthy controls. The functional and taxa results showed that the change of asthma patients might related to SCFAs.}, } @article {pmid30208728, year = {2018}, author = {Myint, H and Kishi, H and Iwahashi, Y and Saburi, W and Koike, S and Kobayashi, Y}, title = {Functional modulation of caecal fermentation and microbiota in rat by feeding bean husk as a dietary fibre supplement.}, journal = {Beneficial microbes}, volume = {9}, number = {6}, pages = {963-974}, doi = {10.3920/BM2017.0174}, pmid = {30208728}, issn = {1876-2891}, mesh = {*Animal Feed ; Animals ; Cecum/*metabolism/*microbiology ; Dietary Fiber/*administration & dosage ; Fermentation/*drug effects ; Gastrointestinal Contents/chemistry ; Gastrointestinal Microbiome/*drug effects ; Metagenomics ; Organic Chemicals/analysis ; Phaseolus ; Prebiotics/*administration & dosage ; Rats, Sprague-Dawley ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Glycine max ; }, abstract = {A feeding study using rats was conducted to evaluate the utility of lablab bean husk and soya bean husk as sources of potential prebiotic fibre. Twenty 5-week-old Sprague Dawley rats were divided into 4 groups and fed one of the following diets for 3 weeks: purified diet (AIN93 G) containing 5% cellulose (CEL), or the same diet in which cellulose was replaced by corn starch (STA), lablab bean husk (LBH), or soya bean husk (SBH). Rats were sacrificed at 8 weeks of age and caecal digesta were collected. Feed intake, body weight, anatomical parameters, and caecal ammonia level did not differ significantly among diets. Rats on LBH and SBH showed higher concentrations of caecal short-chain fatty acid and lactate than those on CEL. Rats on CEL, SBH, and LBH exhibited lower caecal indole and skatole levels. LBH yielded increased caecal abundance of Akkermansia muciniphila and Oscillibacter relatives, as demonstrated by either qPCR, MiSeq, or clone library analysis. SBH favoured the growth of lactobacilli as assessed by both qPCR and MiSeq, and favoured the growth of bifidobacteria as assessed by MiSeq. In comparison with STA, LBH and SBH yielded lower caecal abundance of bacteria related to Dorea massiliensis, as demonstrated by qPCR, MiSeq, and clone library analysis. Both types of bean husk were found to contain oligosaccharides that might selectively stimulate the growth of beneficial bacteria. Based on these results, the two species of bean husk tested are considered potentially functional for promoting the gut health of monogastric animals.}, } @article {pmid30207838, year = {2019}, author = {Matthews, C and Crispie, F and Lewis, E and Reid, M and O'Toole, PW and Cotter, PD}, title = {The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency.}, journal = {Gut microbes}, volume = {10}, number = {2}, pages = {115-132}, pmid = {30207838}, issn = {1949-0984}, mesh = {Animals ; Cattle ; Diet/*veterinary ; Dietary Proteins/metabolism ; *Food Industry ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Methane/metabolism ; Nitrogen/*metabolism ; Rumen/anatomy & histology/*microbiology/physiology ; }, abstract = {Methane is generated in the foregut of all ruminant animals by the microorganisms present. Dietary manipulation is regarded as the most effective and most convenient way to reduce methane emissions (and in turn energy loss in the animal) and increase nitrogen utilization efficiency. This review examines the impact of diet on bovine rumen function and outlines what is known about the rumen microbiome. Our understanding of this area has increased significantly in recent years due to the application of omics technologies to determine microbial composition and functionality patterns in the rumen. This information can be combined with data on nutrition, rumen physiology, nitrogen excretion and/or methane emission to provide comprehensive insights into the relationship between rumen microbial activity, nitrogen utilisation efficiency and methane emission, with an ultimate view to the development of new and improved intervention strategies.}, } @article {pmid30206336, year = {2019}, author = {Seck, EH and Senghor, B and Merhej, V and Bachar, D and Cadoret, F and Robert, C and Azhar, EI and Yasir, M and Bibi, F and Jiman-Fatani, AA and Konate, DS and Musso, D and Doumbo, O and Sokhna, C and Levasseur, A and Lagier, JC and Khelaifia, S and Million, M and Raoult, D}, title = {Salt in stools is associated with obesity, gut halophilic microbiota and Akkermansia muciniphila depletion in humans.}, journal = {International journal of obesity (2005)}, volume = {43}, number = {4}, pages = {862-871}, doi = {10.1038/s41366-018-0201-3}, pmid = {30206336}, issn = {1476-5497}, mesh = {Adult ; Case-Control Studies ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Global Health ; Humans ; Inflammation/etiology/*microbiology/physiopathology ; Male ; Obesity/etiology/*microbiology/physiopathology ; RNA, Ribosomal, 16S/genetics ; Refractometry ; Sodium Chloride, Dietary/*adverse effects ; }, abstract = {BACKGROUND/OBJECTIVES: High salt intake has been linked to several diseases including obesity and an increased risk of death; however, fecal salinity and the ability of salt to alter the gut microbiota, which was recently identified as an instrumental factor for health and disease, remains poorly explored.

METHODS/SUBJECTS: We analyzed the fecal samples of 1326 human individuals for salinity by refractometry, 572 for gut microbiota by culturomics, and 164 by 16S rRNA-targeted metagenomics. Geographical origin, age, gender, and obesity were tested as predictors of fecal salinity and halophilic diversity. All halophilic isolates were characterized by taxonogenomics and their genome sequenced.

RESULTS: Fecal salinity was associated with obesity independently of geographical origin, gender, and age. The first 2 human-associated halophilic archaeal members were isolated along with 64 distinct halophilic species, including 21 new species and 41 known in the environment but not in humans. No halophiles grow in less than 1.5% salinity. Above this threshold, the richness of the halophilic microbiota was correlated with fecal salinity (r = 0.58, p < 0.0001). 16S metagenomics linked high fecal salinity to decreased diversity (linear regression, p < .035) and a depletion in anti-obesity Akkermansia muciniphila and Bifidobacterium, specifically B. longum and B. adolescentis. Genomics analysis suggested that halophilic microbes are not only transient passengers but may be residents of the human gut.

CONCLUSIONS: High salt levels are associated with alteration of the gut microbial ecosystem and halophilic microbiota, as discovered during this study. Further studies should clarify if the gut microbiota alterations associated with high salt levels and the human halophilic microbiota could be causally related to human disease, such as obesity.}, } @article {pmid30205462, year = {2018}, author = {Hidalgo-Cantabrana, C and Sanozky-Dawes, R and Barrangou, R}, title = {Insights into the Human Virome Using CRISPR Spacers from Microbiomes.}, journal = {Viruses}, volume = {10}, number = {9}, pages = {}, pmid = {30205462}, issn = {1999-4915}, support = {support//North Carolina Agricultural Foundation/International ; internal support//North Carolina State University/International ; }, mesh = {*Biodiversity ; Clustered Regularly Interspaced Short Palindromic Repeats ; Humans ; Metagenomics ; *Microbiota ; Viruses/*classification/genetics/*isolation & purification ; }, abstract = {Due to recent advances in next-generation sequencing over the past decade, our understanding of the human microbiome and its relationship to health and disease has increased dramatically. Yet, our insights into the human virome, and its interplay with important microbes that impact human health, is relatively limited. Prokaryotic and eukaryotic viruses are present throughout the human body, comprising a large and diverse population which influences several niches and impacts our health at various body sites. The presence of prokaryotic viruses like phages, has been documented at many different body sites, with the human gut being the richest ecological niche. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and associated proteins constitute the adaptive immune system of bacteria, which prevents attack by invasive nucleic acid. CRISPR-Cas systems function by uptake and integration of foreign genetic element sequences into the CRISPR array, which constitutes a genomic archive of iterative vaccination events. Consequently, CRISPR spacers can be investigated to reconstruct interplay between viruses and bacteria, and metagenomic sequencing data can be exploited to provide insights into host-phage interactions within a niche. Here, we show how the CRISPR spacer content of commensal and pathogenic bacteria can be used to determine the evidence of their phage exposure. This framework opens new opportunities for investigating host-virus dynamics in metagenomic data, and highlights the need to dedicate more efforts for virome sampling and sequencing.}, } @article {pmid30204780, year = {2018}, author = {Wang, T and Yu, L and Xu, C and Pan, K and Mo, M and Duan, M and Zhang, Y and Xiong, H}, title = {Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0203503}, pmid = {30204780}, issn = {1932-6203}, mesh = {Adult ; Asian People ; China ; Fatigue Syndrome, Chronic/*microbiology ; *Fusobacteria/classification/genetics ; Humans ; *Metagenome ; *Microbiota ; Mouth/*microbiology ; }, abstract = {Host-microbe interactions have been implicated in the pathogenesis of chronic fatigue syndrome (CFS), but whether the oral microbiome is altered in CFS patients is unknown. We explored alterations of the oral microbiome in Chinese Han CFS patients using 16S rRNA gene sequencing and alterations in the functional potential of the oral microbiome using PICRUSt. We found that Shannon and Simpson diversity indices were not different in CFS patients compared to healthy controls, but the overall oral microbiome composition was different (MANOVA, p < 0.01). CFS patients had a higher relative abundance of Fusobacteria compared with healthy controls. Further, the genera Leptotrichia, Prevotella, and Fusobacterium were enriched and Haemophilus, Veillonella, and Porphyromonas were depleted in CFS patients compared to healthy controls. Functional analysis from inferred metagenomes showed that bacterial genera altered in CFS patients were primarily associated with amino acid and energy metabolism. Our findings demonstrate that the oral microbiome in CFS patients is different from healthy controls, and these differences lead to shifts in functional pathways with implications for CFS pathogenesis. These findings increase our understanding of the relationship between the oral microbiota and CFS, which will advance our understanding of CFS pathogenesis and may contribute to future improvements in treatment and diagnosis.}, } @article {pmid30203066, year = {2019}, author = {Biderre-Petit, C and Taib, N and Gardon, H and Hochart, C and Debroas, D}, title = {New insights into the pelagic microorganisms involved in the methane cycle in the meromictic Lake Pavin through metagenomics.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {3}, pages = {}, doi = {10.1093/femsec/fiy183}, pmid = {30203066}, issn = {1574-6941}, mesh = {Hydrogen/metabolism ; Lakes/chemistry/*microbiology ; Metabolic Networks and Pathways/genetics ; Metagenome ; Metagenomics ; Methane/*metabolism ; Microbiota/*genetics ; Nitrogen/metabolism ; Plankton/classification/genetics/isolation & purification/metabolism ; *Water Microbiology ; }, abstract = {Advances in metagenomics have given rise to the possibility of obtaining genome sequences from uncultured microorganisms, even for those poorly represented in the microbial community, thereby providing an important means to study their ecology and evolution. In this study, metagenomic sequencing was carried out at four sampling depths having different oxygen concentrations or environmental conditions in the water column of Lake Pavin. By analyzing the sequenced reads and matching the contigs to the proxy genomes of the closest cultivated relatives, we evaluated the metabolic potential of the dominant planktonic species involved in the methane cycle. We demonstrated that methane-producing communities were dominated by the genus Methanoregula while methane-consuming communities were dominated by the genus Methylobacter, thus confirming prior observations. Our work allowed the reconstruction of a draft of their core metabolic pathways. Hydrogenotrophs, the genes required for acetate activation in the methanogen genome, were also detected. Regarding methanotrophy, Methylobacter was present in the same areas as the non-methanotrophic, methylotrophic Methylotenera, which could suggest a relationship between these two groups. Furthermore, the presence of a large gene inventory for nitrogen metabolism (nitrate transport, denitrification, nitrite assimilation and nitrogen fixation, for instance) was detected in the Methylobacter genome.}, } @article {pmid30202961, year = {2018}, author = {Kohl, KD and Oakeson, KF and Orr, TJ and Miller, AW and Forbey, JS and Phillips, CD and Dale, C and Weiss, RB and Dearing, MD}, title = {Metagenomic sequencing provides insights into microbial detoxification in the guts of small mammalian herbivores (Neotoma spp.).}, journal = {FEMS microbiology ecology}, volume = {94}, number = {12}, pages = {}, pmid = {30202961}, issn = {1574-6941}, support = {F32 DK102277/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Cactaceae/*chemistry ; Cecum/metabolism ; Herbivory/physiology ; Inactivation, Metabolic/*genetics/physiology ; Juniperus/*chemistry ; Metagenomics ; Microbiota/genetics ; Oxalates/analysis ; Phenols/analysis ; Sigmodontinae/classification/*metabolism/*microbiology ; Terpenes/analysis ; }, abstract = {Microbial detoxification of plant toxins influences the use of plants as food sources by herbivores. Stephen's woodrats (Neotoma stephensi) specialize on juniper, which is defended by oxalate, phenolics and monoterpenes, while closely related N. albigula specialize on cactus, which only contains oxalate. Woodrats maintain two gut chambers harboring dense microbial communities: a foregut chamber proximal to the major site of toxin absorption, and a cecal chamber in their hindgut. We performed several experiments to investigate the location and nature of microbial detoxification in the woodrat gut. First, we measured toxin concentrations across gut chambers of N. stephensi. Compared to food material, oxalate concentrations were immediately lower in the foregut, while concentrations of terpenes remained high in the foregut, and were lowest in the cecal chamber. We conducted metagenomic sequencing of the foregut chambers of both woodrat species and cecal chambers of N. stephensi to compare microbial functions. We found that most genes associated with detoxification were more abundant in the cecal chambers of N. stephensi. However, some genes associated with degradation of oxalate and phenolic compounds were more abundant in the foregut chambers. Thus, microbial detoxification may take place in various chambers depending on the class of chemical compound.}, } @article {pmid30202918, year = {2020}, author = {Zhang, Y and Bernau, C and Parmigiani, G and Waldron, L}, title = {The impact of different sources of heterogeneity on loss of accuracy from genomic prediction models.}, journal = {Biostatistics (Oxford, England)}, volume = {21}, number = {2}, pages = {253-268}, pmid = {30202918}, issn = {1468-4357}, support = {R01 CA142832/CA/NCI NIH HHS/United States ; R03 CA191447/CA/NCI NIH HHS/United States ; U24 CA180996/CA/NCI NIH HHS/United States ; RC4 CA156551/CA/NCI NIH HHS/United States ; R01 CA174206/CA/NCI NIH HHS/United States ; }, mesh = {Biostatistics/*methods ; *Genetic Research ; Genomics/*methods/standards ; Humans ; Metagenome/genetics ; Microarray Analysis/methods/standards ; Microbiota/genetics ; *Models, Biological ; *Models, Statistical ; Sequence Analysis, RNA/methods ; }, abstract = {Cross-study validation (CSV) of prediction models is an alternative to traditional cross-validation (CV) in domains where multiple comparable datasets are available. Although many studies have noted potential sources of heterogeneity in genomic studies, to our knowledge none have systematically investigated their intertwined impacts on prediction accuracy across studies. We employ a hybrid parametric/non-parametric bootstrap method to realistically simulate publicly available compendia of microarray, RNA-seq, and whole metagenome shotgun microbiome studies of health outcomes. Three types of heterogeneity between studies are manipulated and studied: (i) imbalances in the prevalence of clinical and pathological covariates, (ii) differences in gene covariance that could be caused by batch, platform, or tumor purity effects, and (iii) differences in the "true" model that associates gene expression and clinical factors to outcome. We assess model accuracy, while altering these factors. Lower accuracy is seen in CSV than in CV. Surprisingly, heterogeneity in known clinical covariates and differences in gene covariance structure have very limited contributions in the loss of accuracy when validating in new studies. However, forcing identical generative models greatly reduces the within/across study difference. These results, observed consistently for multiple disease outcomes and omics platforms, suggest that the most easily identifiable sources of study heterogeneity are not necessarily the primary ones that undermine the ability to accurately replicate the accuracy of omics prediction models in new studies. Unidentified heterogeneity, such as could arise from unmeasured confounding, may be more important.}, } @article {pmid30197411, year = {2018}, author = {Mise, K and Fujita, K and Kunito, T and Senoo, K and Otsuka, S}, title = {Phosphorus-mineralizing Communities Reflect Nutrient-Rich Characteristics in Japanese Arable Andisols.}, journal = {Microbes and environments}, volume = {33}, number = {3}, pages = {282-289}, pmid = {30197411}, issn = {1347-4405}, mesh = {Alkaline Phosphatase/*genetics/metabolism ; Bacteria/classification/enzymology/genetics/*metabolism ; Bacterial Proteins/*genetics/metabolism ; Biodiversity ; Computational Biology ; DNA, Bacterial/genetics ; Genes, Bacterial/genetics ; Geography ; Japan ; Metagenome/genetics ; Phosphorus/analysis/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Elucidating the soil phosphorus cycle driven by soil microbes is a vital question in soil microbial ecology. The Japanese arable Andisols, occupying half of the Japanese cropland, are known for their high phosphorus sorption capacity. However, limited information is currently available on microbially driven phosphorus mineralization in arable Andisols. We herein report that the phosphorus-mineralizing community in the Japanese arable Andisols showed characteristic distribution and composition patterns, from those in other types of soils. We performed a chemical analysis and microbial community analysis of 43 arable Andisols along the Japanese archipelago. Soil phosphomonoesterase activities measured at pH 11 were approximately 70% of those at pH 6.5, which indicates that alkaline phosphatase contributes to phosphorus cycling, although most soil samples were acidic. Functional gene predictions based on 16S rRNA gene sequencing indicated that the alkaline phosphatase gene phoD was more abundant than other alkaline phosphatase genes and, thus, plays major roles. Hence, amplicon sequencing targeting phoD was performed and the results obtained showed that alphaproteobacterial phoD was dominant. This is in contrast to previously reported phoD compositions in other soils and may be attributed to the nutrient conditions in arable Andisols, which favor copiotrophic Alphaproteobacteria. Furthermore, the composition of phoD correlated with soil pH and bioavailable phosphorus concentrations rather than carbon or nitrogen concentrations. These results were partly different from previous findings, varying in the soil types and geographic ranges of sampling sites. Collectively, the present results indicate that the phosphorus-mineralizing community in the Japanese arable Andisols is regulated differently from those in other soil types.}, } @article {pmid30197212, year = {2019}, author = {Overmann, J and Huang, S and Nübel, U and Hahnke, RL and Tindall, BJ}, title = {Relevance of phenotypic information for the taxonomy of not-yet-cultured microorganisms.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {1}, pages = {22-29}, doi = {10.1016/j.syapm.2018.08.009}, pmid = {30197212}, issn = {1618-0984}, mesh = {Archaea/*classification ; Bacteria/*classification ; Classification/*methods ; Phenotype ; *Terminology as Topic ; }, abstract = {To date, far less than 1% of the estimated global species of Bacteria and Archaea have been described and their names validly published. Aside from these quantitative limitations, our understanding of phenotypic and functional diversity of prokaryotes is also highly biased as not a single species has been described for 85 of the 118 phyla that are currently recognized. Due to recent advances in sequencing technology and capacity, metagenomic datasets accumulate at an increasing speed and new bacterial and archaeal genome sequences become available at a faster rate than newly described species. The growing gap between the diversity of Bacteria and Archaea held in pure culture and that detected by molecular methods has led to the proposal to establish a formal nomenclature for not-yet-cultured taxa primarily based on sequence information. According to this proposal, the concept of Candidatus species would be extended to groups of closely related genome sequences and their names validly published following established rules of bacterial nomenclature. The corresponding sequences would be deposited in public databases as the type. The suggested alterations of the International Code of Nomenclature of Prokaryotes raise concerns regarding (1) the reliability and stability of nomenclature, (2) the technological and conceptual limitations as well as availability of reference genomes, (3) the information content of in silico functional predictions, and (4) the recognition of evolutionary units of microbial diversity. These challenges need to be overcome to arrive at a meaningful taxonomy of not-yet-cultured prokaryotes with so far poorly understood phenotypes.}, } @article {pmid30193112, year = {2018}, author = {Zmora, N and Zilberman-Schapira, G and Suez, J and Mor, U and Dori-Bachash, M and Bashiardes, S and Kotler, E and Zur, M and Regev-Lehavi, D and Brik, RB and Federici, S and Cohen, Y and Linevsky, R and Rothschild, D and Moor, AE and Ben-Moshe, S and Harmelin, A and Itzkovitz, S and Maharshak, N and Shibolet, O and Shapiro, H and Pevsner-Fischer, M and Sharon, I and Halpern, Z and Segal, E and Elinav, E}, title = {Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features.}, journal = {Cell}, volume = {174}, number = {6}, pages = {1388-1405.e21}, doi = {10.1016/j.cell.2018.08.041}, pmid = {30193112}, issn = {1097-4172}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Animals ; Bacteria/genetics/isolation & purification ; Feces/microbiology ; Female ; Gastric Mucosa/microbiology ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/microbiology ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Middle Aged ; Placebo Effect ; Principal Component Analysis ; Probiotics/*administration & dosage ; RNA, Ribosomal, 16S/genetics/metabolism ; Transcriptome ; Young Adult ; }, abstract = {Empiric probiotics are commonly consumed by healthy individuals as means of life quality improvement and disease prevention. However, evidence of probiotic gut mucosal colonization efficacy remains sparse and controversial. We metagenomically characterized the murine and human mucosal-associated gastrointestinal microbiome and found it to only partially correlate with stool microbiome. A sequential invasive multi-omics measurement at baseline and during consumption of an 11-strain probiotic combination or placebo demonstrated that probiotics remain viable upon gastrointestinal passage. In colonized, but not germ-free mice, probiotics encountered a marked mucosal colonization resistance. In contrast, humans featured person-, region- and strain-specific mucosal colonization patterns, hallmarked by predictive baseline host and microbiome features, but indistinguishable by probiotics presence in stool. Consequently, probiotics induced a transient, individualized impact on mucosal community structure and gut transcriptome. Collectively, empiric probiotics supplementation may be limited in universally and persistently impacting the gut mucosa, meriting development of new personalized probiotic approaches.}, } @article {pmid30192933, year = {2018}, author = {Li, F and Chen, C and Wei, W and Wang, Z and Dai, J and Hao, L and Song, L and Zhang, X and Zeng, L and Du, H and Tang, H and Liu, N and Yang, H and Wang, J and Madsen, L and Brix, S and Kristiansen, K and Xu, X and Li, J and Wu, R and Jia, H}, title = {The metagenome of the female upper reproductive tract.}, journal = {GigaScience}, volume = {7}, number = {10}, pages = {}, pmid = {30192933}, issn = {2047-217X}, mesh = {Biodiversity ; Computational Biology/methods ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Reproductive Tract Infections/*microbiology ; Vagina/microbiology ; }, abstract = {BACKGROUND: The human uterus is traditionally believed to be sterile, while the vaginal microbiota plays an important role in fending off pathogens. Emerging evidence demonstrates the presence of bacteria beyond the vagina. However, a microbiome-wide metagenomic analysis characterizing the diverse microbial communities has been lacking.

RESULTS: We performed shotgun-sequencing of 52 samples from the cervical canal and the peritoneal fluid of Chinese women of reproductive age using the Illumina platform. Direct annotation of sequencing reads identified the taxonomy of bacteria, archaea, fungi and viruses, confirming and extending the results from our previous study. We replicated our previous findings in another 24 samples from the vagina, the cervical canal, the uterus and the peritoneal fluid using the BGISEQ-500 platform revealing that microorganisms in the samples from the same individuals were largely shared in the entire reproductive tract. Human sequences made up more than 99% of the 20GB raw data. After filtering, vaginal microorganisms were well covered in the generated reproductive tract gene catalogue, while the more diverse upper reproductive tract microbiota would require greater depth of sequencing and more samples to meet the full coverage scale.

CONCLUSIONS: We provide novel detailed data on the microbial composition of a largely unchartered body site, the female reproductive tract. Our results indicated the presence of an intra-individual continuum of microorganisms that gradually changed from the vagina to the peritoneal fluid. This study also provides a framework for understanding the implications of the composition and functional potential of the distinct microbial ecosystems of the female reproductive tract in relation to health and disease.}, } @article {pmid30189365, year = {2018}, author = {Zhou, J and Tang, L and Shen, CL and Wang, JS}, title = {Green tea polyphenols modify gut-microbiota dependent metabolisms of energy, bile constituents and micronutrients in female Sprague-Dawley rats.}, journal = {The Journal of nutritional biochemistry}, volume = {61}, number = {}, pages = {68-81}, doi = {10.1016/j.jnutbio.2018.07.018}, pmid = {30189365}, issn = {1873-4847}, support = {R24 TW009489/TW/FIC NIH HHS/United States ; U01 AT006691/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; Bile/drug effects/metabolism ; Dose-Response Relationship, Drug ; Energy Metabolism/*drug effects ; Female ; Gastrointestinal Contents/chemistry ; Gastrointestinal Microbiome/*drug effects/genetics/physiology ; Micronutrients/metabolism ; Polyphenols/administration & dosage/*pharmacology ; Rats, Sprague-Dawley ; Tea/*chemistry ; }, abstract = {Our recent metagenomics analysis has uncovered remarkable modifying effects of green tea polyphenols (GTP) on gut-microbiota community structure and energy conversion related gene orthologs in rats. How these genomic changes could further influence host health is still unclear. In this work, the alterations of gut-microbiota dependent metabolites were studied in the GTP-treated rats. Six groups of female SD rats (n=12/group) were administered drinking water containing 0%, 0.5%, and 1.5% GTP (wt/vol). Their gut contents were collected at 3 and 6 months and were analyzed via high performance liquid chromatography (HPLC) and gas chromatography (GC)-mass spectrometry (MS). GC-MS based metabolomics analysis captured 2668 feature, and 57 metabolites were imputatively from top 200 differential features identified via NIST fragmentation database. A group of key metabolites were quantitated using standard calibration methods. Compared with control, the elevated components in the GTP-treated groups include niacin (8.61-fold), 3-phenyllactic acid (2.20-fold), galactose (3.13-fold), mannose (2.05-fold), pentadecanoic acid (2.15-fold), lactic acid (2.70-fold), and proline (2.15-fold); the reduced components include cholesterol (0.29-fold), cholic acid (0.62-fold), deoxycholic acid (0.41-fold), trehalose (0.14-fold), glucose (0.46-fold), fructose (0.12-fold), and alanine (0.61-fold). These results were in line with the genomic alterations of gut-microbiome previously discovered by metagenomics analysis. The alterations of these metabolites suggested the reduction of calorific carbohydrates, elevation of vitamin production, decreases of bile constituents, and modified metabolic pattern of amino acids in the GTP-treated animals. Changes in gut-microbiota associated metabolism may be a major contributor to the anti-obesity function of GTP.}, } @article {pmid30187987, year = {2019}, author = {Hooper, R and Brealey, JC and van der Valk, T and Alberdi, A and Durban, JW and Fearnbach, H and Robertson, KM and Baird, RW and Bradley Hanson, M and Wade, P and Gilbert, MTP and Morin, PA and Wolf, JBW and Foote, AD and Guschanski, K}, title = {Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin.}, journal = {Molecular ecology}, volume = {28}, number = {2}, pages = {484-502}, pmid = {30187987}, issn = {1365-294X}, support = {//Lindblad Expeditions/National Geographic Conservation Fund/International ; ERCStG-336536//European Research Council/International ; DNRF94//Danish National Research Foundation/International ; //Antarctic Science Bursary/International ; //Welsh Government and Higher Education Funding Council for Wales through the Sêr Cymru National Research Network for Low Carbon, Energy and Environment/International ; 663830//European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie/International ; SR17/1227//British Ecological Society/International ; 2016-00835//FORMAS/International ; 5051-00033//Danish Council for Independent Research-DFF/International ; R250-2017-1351//Lundbeckfonden/International ; }, mesh = {Animals ; Antarctic Regions ; Diatoms/genetics ; Geography ; *Metagenomics ; Microbiota/*genetics ; Skin/*microbiology ; Whale, Killer/*microbiology/parasitology ; }, abstract = {Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.}, } @article {pmid30185512, year = {2018}, author = {Rohwer, RR and Hamilton, JJ and Newton, RJ and McMahon, KD}, title = {TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, pmid = {30185512}, issn = {2379-5042}, mesh = {Algorithms ; Animals ; Bacteria/*classification ; DNA, Bacterial/genetics ; Databases as Topic ; *Databases, Genetic ; Ecosystem ; Fresh Water/*microbiology ; *Metagenomics ; Mice ; *Microbial Consortia ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Taxonomy assignment of freshwater microbial communities is limited by the minimally curated phylogenies used for large taxonomy databases. Here we introduce TaxAss, a taxonomy assignment workflow that classifies 16S rRNA gene amplicon data using two taxonomy reference databases: a large comprehensive database and a small ecosystem-specific database rigorously curated by scientists within a field. We applied TaxAss to five different freshwater data sets using the comprehensive SILVA database and the freshwater-specific FreshTrain database. TaxAss increased the percentage of the data set classified compared to using only SILVA, especially at fine-resolution family to species taxon levels, while across the freshwater test data sets classifications increased by as much as 11 to 40% of total reads. A similar increase in classifications was not observed in a control mouse gut data set, which was not expected to contain freshwater bacteria. TaxAss also maintained taxonomic richness compared to using only the FreshTrain across all taxon levels from phylum to species. Without TaxAss, most organisms not represented in the FreshTrain were unclassified, but at fine taxon levels, incorrect classifications became significant. We validated TaxAss using simulated amplicon data derived from full-length clone libraries and found that 96 to 99% of test sequences were correctly classified at fine resolution. TaxAss splits a data set's sequences into two groups based on their percent identity to reference sequences in the ecosystem-specific database. Sequences with high similarity to sequences in the ecosystem-specific database are classified using that database, and the others are classified using the comprehensive database. TaxAss is free and open source and is available at https://www.github.com/McMahonLab/TaxAssIMPORTANCE Microbial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon data sets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at the phylum, class, and order levels lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or unique sequences. These fine-resolution groupings are more ecologically relevant, but OTU definitions are data set dependent and cannot be compared between data sets. Microbial ecologists studying freshwater have curated a small, ecosystem-specific taxonomy database to provide consistent and up-to-date terminology. We created TaxAss, a workflow that leverages this database to assign taxonomy. We found that TaxAss improves fine-resolution taxonomic classifications (family, genus, and species). Fine taxonomic groupings are more ecologically relevant, so they provide an alternative to OTU-based analyses that is consistent and comparable between data sets.}, } @article {pmid30185233, year = {2018}, author = {Mukherjee, C and Beall, CJ and Griffen, AL and Leys, EJ}, title = {High-resolution ISR amplicon sequencing reveals personalized oral microbiome.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {153}, pmid = {30185233}, issn = {2049-2618}, support = {R01 DE024327/DE/NIDCR NIH HHS/United States ; R01 DE024463/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Bacteria/classification/genetics/*isolation & purification ; DNA, Bacterial/genetics ; DNA, Intergenic/*genetics ; Female ; Genetic Variation ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Male ; *Microbiota ; Middle Aged ; Mouth/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {BACKGROUND: Sequencing of the 16S rRNA gene has been the standard for studying the composition of microbial communities. While it allows identification of bacteria at the level of species, this method does not usually provide sufficient information to resolve communities at the sub-species level. Species-level resolution is not adequate for studies of transmission or stability or for exploring subspecies variation in disease association. Strain level analysis using whole metagenome shotgun sequencing has significant limitations that can make it unsuitable for large-scale studies. Achieving sufficient depth of sequencing can be cost-prohibitive, and even with adequate coverage, deconvoluting complex communities such as the oral microbiota is computationally very challenging. Thus, there is a need for high-resolution, yet cost-effective, high-throughput methods for characterizing microbial communities.

RESULTS: Significant improvement in resolution for amplicon-based bacterial community analysis was achieved by combining amplicon sequencing of a high-diversity marker gene, the ribosomal 16-23S intergenic spacer region (ISR), with a probabilistic error modeling based denoising algorithm, DADA2. The resolving power of this new approach was compared to that of both standard and high-resolution 16S-based approaches using a set of longitudinal subgingival plaque samples. The ISR strategy resulted in a 5.2-fold increase in community resolution compared to reference-based 16S rRNA gene analysis and showed 100% accuracy in predicting the correct source of a clinical sample. Individuals' microbial communities were highly personalized, and although they exhibited some drift in membership and levels over time, that difference was always smaller than the differences between any two subjects, even after 1 year. The construction of an ISR database from publicly available genomic sequences allowed us to explore genomic variation within species, resulting in the identification of multiple variants of the ISR for most species.

CONCLUSIONS: The ISR approach resulted in significantly improved resolution of communities and revealed a highly personalized human oral microbiota that was stable over 1 year. Multiple ISR types were observed for all species examined, demonstrating a high level of subspecies variation in the oral microbiota. The approach is high-throughput, high-resolution yet cost-effective, allowing subspecies-level community fingerprinting at a cost comparable to that of 16S rRNA gene amplicon sequencing. It will be useful for a range of applications that require high-resolution identification of organisms, including microbial tracking, community fingerprinting, and potentially for identification of virulence-associated strains.}, } @article {pmid30179232, year = {2018}, author = {Biller, SJ and Berube, PM and Dooley, K and Williams, M and Satinsky, BM and Hackl, T and Hogle, SL and Coe, A and Bergauer, K and Bouman, HA and Browning, TJ and De Corte, D and Hassler, C and Hulston, D and Jacquot, JE and Maas, EW and Reinthaler, T and Sintes, E and Yokokawa, T and Chisholm, SW}, title = {Marine microbial metagenomes sampled across space and time.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180176}, pmid = {30179232}, issn = {2052-4463}, mesh = {Archaea/*genetics ; Atlantic Ocean ; Bacteria/*genetics ; Biodiversity ; Ecosystem ; Eukaryota/*genetics ; *Metagenome ; Metagenomics ; Pacific Ocean ; Viruses/*genetics ; Water Microbiology ; }, abstract = {Recent advances in understanding the ecology of marine systems have been greatly facilitated by the growing availability of metagenomic data, which provide information on the identity, diversity and functional potential of the microbial community in a particular place and time. Here we present a dataset comprising over 5 terabases of metagenomic data from 610 samples spanning diverse regions of the Atlantic and Pacific Oceans. One set of metagenomes, collected on GEOTRACES cruises, captures large geographic transects at multiple depths per station. The second set represents two years of time-series data, collected at roughly monthly intervals from 3 depths at two long-term ocean sampling sites, Station ALOHA and BATS. These metagenomes contain genomic information from a diverse range of bacteria, archaea, eukaryotes and viruses. The data's utility is strengthened by the availability of extensive physical, chemical, and biological measurements associated with each sample. We expect that these metagenomes will facilitate a wide range of comparative studies that seek to illuminate new aspects of marine microbial ecosystems.}, } @article {pmid30177919, year = {2018}, author = {Lin, JD and Lemay, MA and Parfrey, LW}, title = {Diverse Bacteria Utilize Alginate Within the Microbiome of the Giant Kelp Macrocystis pyrifera.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1914}, pmid = {30177919}, issn = {1664-302X}, abstract = {Bacteria are integral to marine carbon cycling. They transfer organic carbon to higher trophic levels and remineralise it into inorganic forms. Kelp forests are among the most productive ecosystems within the global oceans, yet the diversity and metabolic capacity of bacteria that transform kelp carbon is poorly understood. Here, we use 16S amplicon and metagenomic shotgun sequencing to survey bacterial communities associated with the surfaces of the giant kelp Macrocystis pyrifera and assess the capacity of these bacteria for carbohydrate metabolism. We find that Macrocystis-associated communities are distinct from the water column, and that they become more diverse and shift in composition with blade depth, which is a proxy for tissue age. These patterns are also observed in metagenomic functional profiles, though the broader functional groups-carbohydrate active enzyme families-are largely consistent across samples and depths. Additionally, we assayed more than 250 isolates cultured from Macrocystis blades and the surrounding water column for the ability to utilize alginate, the primary polysaccharide in Macrocystis tissue. The majority of cultured bacteria (66%) demonstrated this capacity; we find that alginate utilization is patchily distributed across diverse genera in the Bacteroidetes and Proteobacteria, yet can also vary between isolates with identical 16S rRNA sequences. The genes encoding enzymes involved in alginate metabolism were detected in metagenomic data across taxonomically diverse bacterial communities, further indicating this capacity is likely widespread amongst bacteria in kelp forests. Overall, the M. pyrifera epibiota shifts across a depth gradient, demonstrating a connection between bacterial assemblage and host tissue state.}, } @article {pmid30177915, year = {2018}, author = {Wu, YT and Yang, CY and Chiang, PW and Tseng, CH and Chiu, HH and Saeed, I and Baatar, B and Rogozin, D and Halgamuge, S and Degermendzhi, A and Tang, SL}, title = {Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1763}, pmid = {30177915}, issn = {1664-302X}, abstract = {Microorganisms are critical to maintaining stratified biogeochemical characteristics in meromictic lakes; however, their community composition and potential roles in nutrient cycling are not thoroughly described. Both metagenomics and metaviromics were used to determine the composition and capacity of archaea, bacteria, and viruses along the water column in the landlocked meromictic Lake Shunet in Siberia. Deep sequencing of 265 Gb and high-quality assembly revealed a near-complete genome corresponding to Nonlabens sp. sh3vir. in a viral sample and 38 bacterial bins (0.2-5.3 Mb each). The mixolimnion (3.0 m) had the most diverse archaeal, bacterial, and viral communities, followed by the monimolimnion (5.5 m) and chemocline (5.0 m). The bacterial and archaeal communities were dominated by Thiocapsa and Methanococcoides, respectively, whereas the viral community was dominated by Siphoviridae. The archaeal and bacterial assemblages and the associated energy metabolism were significantly related to the various depths, in accordance with the stratification of physicochemical parameters. Reconstructed elemental nutrient cycles of the three layers were interconnected, including co-occurrence of denitrification and nitrogen fixation in each layer and involved unique processes due to specific biogeochemical properties at the respective depths. According to the gene annotation, several pre-dominant yet unknown and uncultured bacteria also play potentially important roles in nutrient cycling. Reciprocal BLAST analysis revealed that the viruses were specific to the host archaea and bacteria in the mixolimnion. This study provides insights into the bacterial, archaeal, and viral assemblages and the corresponding capacity potentials in Lake Shunet, one of the three meromictic lakes in central Asia. Lake Shunet was determined to harbor specific and diverse viral, bacterial, and archaeal communities that intimately interacted, revealing patterns shaped by indigenous physicochemical parameters.}, } @article {pmid30177353, year = {2018}, author = {Rhoads, JM and Collins, J and Fatheree, NY and Hashmi, SS and Taylor, CM and Luo, M and Hoang, TK and Gleason, WA and Van Arsdall, MR and Navarro, F and Liu, Y}, title = {Infant Colic Represents Gut Inflammation and Dysbiosis.}, journal = {The Journal of pediatrics}, volume = {203}, number = {}, pages = {55-61.e3}, pmid = {30177353}, issn = {1097-6833}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; R34 AT006727/AT/NCCIH NIH HHS/United States ; }, mesh = {Acinetobacter/isolation & purification ; Breast Feeding ; Case-Control Studies ; Colic/*complications ; Dysbiosis/*diagnosis ; Feces/*chemistry/microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Infant ; Infant Formula ; Infant, Newborn ; Inflammation/*diagnosis ; Lactobacillus/isolation & purification ; Leukocyte L1 Antigen Complex/*analysis ; Male ; }, abstract = {OBJECTIVE: To dissect potential confounding effects of breast milk and formula feeding on crying + fussing, fecal calprotectin, and gut microbiota in babies with colic. We hypothesized that infant colic is associated with gut inflammation linked to intestinal dysbiosis.

STUDY DESIGN: A nested case-control design of 3 of our studies was used to analyze clinical and laboratory data at presentation, comparing babies with colic with controls. All investigators other than the biostatistician were blinded during data analysis. Subjects were recruited based on their age and crying + fussy time. We screened 65 infants, 37 with colic, as defined by Barr diary (crying + fussing time >3 hours daily), who were compared with 28 noncolicky infants.

RESULTS: Fecal calprotectin was elevated in babies with colic. For each mode of infant feeding (breast milk, formula, or breast + formula), infants' fecal calprotectin was higher in babies with colic. Infants with colic had similar levels of fecal alpha diversity (richness) when compared with controls, and alpha diversity was lower in breast-fed babies. Beta diversity at the phylum level revealed significant differences in microbial population. A phylum difference resulted from reduced Actinobacteria (95% of which are Bifidobacilli) in babies with colic. Species significantly associated with colic were Acinetobacter and Lactobacillus iners.

CONCLUSIONS: Colic is linked with gut inflammation (as determined by fecal calprotectin) and dysbiosis, independent of mode of feeding, with fewer Bifidobacilli.

TRIAL REGISTRATION: Clinicaltrials.gov: NCT01279265 and NCT01849991.}, } @article {pmid30176961, year = {2018}, author = {Xu, H and Li, X and Zheng, X and Xia, Y and Fu, Y and Li, X and Qian, Y and Zou, J and Zhao, A and Guan, J and Gu, M and Yi, H and Jia, W and Yin, S}, title = {Pediatric Obstructive Sleep Apnea is Associated With Changes in the Oral Microbiome and Urinary Metabolomics Profile: A Pilot Study.}, journal = {Journal of clinical sleep medicine : JCSM : official publication of the American Academy of Sleep Medicine}, volume = {14}, number = {9}, pages = {1559-1567}, pmid = {30176961}, issn = {1550-9397}, mesh = {Child ; Child, Preschool ; China ; Chromatography, Liquid ; Female ; Humans ; Male ; Mass Spectrometry ; Metabolome/*physiology ; Metabolomics/*methods ; Microbiota/*physiology ; Mouth/*microbiology ; Pilot Projects ; Sleep Apnea, Obstructive/*microbiology/*urine ; }, abstract = {STUDY OBJECTIVES: Several cross-sectional studies have reported associations between oral diseases and obstructive sleep apnea (OSA). However, there have been no reports regarding the structure and composition of the oral microbiota with simultaneous evaluation of potential associations with perturbed metabolic profiles in pediatric OSA.

METHODS: An integrated approach, combining metagenomics based on high-throughput 16S rRNA gene sequencing, and metabolomics based on ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry and gas chromatography coupled with time-of-flight mass spectrometry, was used to evaluate the oral microbiome and the urinary metabolome.

RESULTS: 16S rRNA gene sequencing indicated that the oral microbiome composition was significantly perturbed in pediatric OSA compared with normal controls, especially with regard to Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, and Actinobacteria. Moreover, metabolomics profiling indicated that 57 metabolites, 5 of which were metabolites related to the microflora of the digestive tract, were differentially present in the urine of pediatric patients with OSA and controls. Co-inertia and correlation analyses revealed that several oral microbiome changes were correlated with urinary metabolite perturbations in pediatric OSA. However, this correlation relationship does not imply causality.

CONCLUSIONS: High-throughput sequencing revealed that the oral microbiome composition and function were significantly altered in pediatric OSA. Further studies are needed to confirm and determine the mechanisms underlying these findings.}, } @article {pmid30176453, year = {2019}, author = {Hu, M and Sun, W and Krumins, V and Li, F}, title = {Arsenic contamination influences microbial community structure and putative arsenic metabolism gene abundance in iron plaque on paddy rice root.}, journal = {The Science of the total environment}, volume = {649}, number = {}, pages = {405-412}, doi = {10.1016/j.scitotenv.2018.08.388}, pmid = {30176453}, issn = {1879-1026}, mesh = {Arsenic/*adverse effects ; Iron/metabolism ; Metagenome/drug effects ; Microbiota/*drug effects/genetics ; Oryza/*drug effects/metabolism/microbiology ; Plant Roots/drug effects/metabolism/microbiology ; Soil Pollutants/*adverse effects ; }, abstract = {Iron (Fe) plaque on rice roots contains a unique microbiota that connects the root and rhizosphere environments. However, the factors controlling the microbial community structure and function in Fe plaque are unknown. We performed Illumina sequencing of 16S rRNA gene amplicons and of total community DNA to compare the microbial community structure and metabolic potential of Fe plaques derived from arsenic (As)- and non-contaminated sites. Geobacter and Hydrogenophaga were identified as the genera that differed significantly in abundance between As-contaminated and control samples (P < 0.05). Significant differences were found between contaminated and control samples in the relative abundances of predicted As functional genes of the microbial community in Fe plaque, in which the relative abundances of the arsC (encoding As(V) reductase) and arsB genes (encoding As(III) efflux membrane protein) in Fe plaque from contaminated sites (YH and TP samples) were significantly higher than those from the control samples (P < 0.05). In addition, the As concentration in Fe plaque contributed significantly to the relative abundance of genes related to As metabolism and correlated most strongly with the abundance of arrB genes (encoding respiratory arsenate reductase, FeS subunit). These results suggest that As contamination influences the community structure and metabolic potential of Fe plaque-associated microorganisms and may help in understanding the environmental behavior of As at the interface of Fe plaque.}, } @article {pmid30173823, year = {2018}, author = {Flannigan, KL and Taylor, MR and Pereira, SK and Rodriguez-Arguello, J and Moffat, AW and Alston, L and Wang, X and Poon, KK and Beck, PL and Rioux, KP and Jonnalagadda, M and Chelikani, PK and Galipeau, HJ and Lewis, IA and Workentine, ML and Greenway, SC and Hirota, SA}, title = {An intact microbiota is required for the gastrointestinal toxicity of the immunosuppressant mycophenolate mofetil.}, journal = {The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation}, volume = {37}, number = {9}, pages = {1047-1059}, doi = {10.1016/j.healun.2018.05.002}, pmid = {30173823}, issn = {1557-3117}, support = {//CIHR/Canada ; }, mesh = {Animals ; Colon/drug effects/microbiology ; *Disease Models, Animal ; Gastrointestinal Tract/*drug effects/*microbiology ; Germ-Free Life ; High-Throughput Nucleotide Sequencing ; Humans ; Immunosuppressive Agents/therapeutic use/*toxicity ; Male ; Mice ; Mice, Inbred Strains ; Microbiota/*drug effects/immunology ; Mycophenolic Acid/therapeutic use/*toxicity ; Proteobacteria ; RNA, Ribosomal, 16S ; Sequence Analysis, RNA ; Weight Loss/drug effects ; }, abstract = {BACKGROUND: Mycophenolate mofetil (MMF) is commonly prescribed after transplantation and has major advantages over other immunosuppressive drugs, but frequent gastrointestinal (GI) side-effects limit its use. The mechanism(s) underlying MMF-related GI toxicity have yet to be elucidated.

METHODS: To investigate MMF-related GI toxicity, experimental mice were fed chow containing MMF (0.563%) and multiple indices of toxicity, including weight loss and colonic inflammation, were measured. Changes in intestinal microbial composition were detected using 16S rRNA Illumina sequencing, and downstream PICRUSt analysis was used to predict metagenomic pathways involved. Germ-free (GF) mice and mice treated with orally administered broad-spectrum antibiotics (ABX) were utilized to interrogate the importance of the microbiota in MMF-induced GI toxicity.

RESULTS: Mice treated with MMF exhibited significant weight loss, related to loss of body fat and muscle, and marked colonic inflammation. MMF exposure was associated with changes in gut microbial composition, as demonstrated by a loss of overall diversity, expansion of Proteobacteria (specifically Escherichia/Shigella), and enrichment of genes involved in lipopolysaccharide (LPS) biosynthesis, which paralleled increased levels of LPS in the feces and serum. MMF-related GI toxicity was dependent on the intestinal microbiota, as MMF did not induce weight loss or colonic inflammation in GF mice. Furthermore, ABX prevented and reversed MMF-induced weight loss and colonic inflammation.

CONCLUSIONS: An intact intestinal microbiota is required to initiate and sustain the GI toxicity of MMF. MMF treatment causes dynamic changes in the composition of the intestinal microbiota that may be a targetable driver of the GI side-effects of MMF.}, } @article {pmid30173738, year = {2018}, author = {Stroebel, C and Alexander, T and Workentine, ML and Timsit, E}, title = {Effects of transportation to and co-mingling at an auction market on nasopharyngeal and tracheal bacterial communities of recently weaned beef cattle.}, journal = {Veterinary microbiology}, volume = {223}, number = {}, pages = {126-133}, doi = {10.1016/j.vetmic.2018.08.007}, pmid = {30173738}, issn = {1873-2542}, mesh = {Animals ; Bacteria/genetics/*isolation & purification ; Bovine Respiratory Disease Complex/*microbiology ; Cattle ; DNA, Bacterial/chemistry/genetics ; Female ; *Metagenomics ; *Microbiota ; Moraxella/genetics/isolation & purification ; Mycoplasma/genetics/isolation & purification ; Nasopharynx/microbiology ; RNA, Ribosomal, 16S/chemistry/genetics ; Trachea/microbiology ; Transportation ; Weaning ; }, abstract = {The objective was to study effects of transportation to and co-mingling at an auction market on nasopharyngeal and tracheal bacterial communities of feedlot cattle. Two groups of 30 Angus-cross heifers were studied from weaning to 28 d after arrival at a feedlot. For each group, half the heifers were either transported directly to a feedlot after weaning (RANC) or transported to and co-mingled at an auction market for 24 h before being placed in a feedlot (AUCT). Deep nasal swabs (DNS) and trans-tracheal aspirates (TTA) were collected at weaning (d0) and at on-arrival processing at the feedlot (d2). At 7 (d9) and 28 d (d30) after arrival, DNS were repeated. The DNA was extracted from DNS and TTA and the V4 region of the 16S rRNA gene sequenced (MiSeq). Alpha diversity analysis did not reveal differences between AUCT and RANC. However, bacterial diversity decreased over time in the nasopharynx, especially at d9. Although beta-diversity was not different between AUCT and RANC, interval after arrival and feedlot where heifers were placed affected composition of the nasopharyngeal bacterial communities. In both groups, a large increase in Mycoplasma was observed after arrival; in one group, Mycoplasma bovis was dominant at d9 and remained dominant until d30. However, in the other group, Mycoplasma dispar dominated at d9 and was replaced by Moraxella at d30. We concluded that transportation to and co-mingling at an auction market for 24 h did not significantly influence diversity or composition of nasopharyngeal or tracheal bacterial communities.}, } @article {pmid30171304, year = {2019}, author = {Bedarf, JR and Hildebrand, F and Goeser, F and Bork, P and Wüllner, U}, title = {[The gut microbiome in Parkinson's disease].}, journal = {Der Nervenarzt}, volume = {90}, number = {2}, pages = {160-166}, pmid = {30171304}, issn = {1433-0407}, mesh = {Case-Control Studies ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; *Parkinson Disease/diagnosis/microbiology ; REM Sleep Behavior Disorder/microbiology ; }, abstract = {The vast majority of Parkinson's disease (PD) cases are of sporadic origin and despite extensive research in recent years, the etiology still remains unclear. Several current case control studies are aiming to characterize a putative PD-specific composition of the gut microbiome, reflecting the potential relevance of microbiota in the pathogenesis of PD. Although methodologies and cohort sizes differed, the currently available studies showed reproducible or consistent results in terms of PD-specific alterations to the intestinal bacteria. By applying metagenomic sequencing procedures, it is even possible to distinguish PD cases from healthy individuals at a very early disease stage by means of individually modified microbiota. Among others, microbiota that are associated with an altered intestinal barrier or immune function, such as Akkermansia, Lactobacillus, Faecalibacterium and Prevotella were significantly over-represented or under-represented. There may even be a prodromal microbiome, as a comparable microbial shift is also found in patients with rapid eye movement (REM) sleep behavior disorder (RBD), a risk factor for the later development of synucleinopathies, such as PD.}, } @article {pmid30171206, year = {2019}, author = {Guillén, Y and Noguera-Julian, M and Rivera, J and Casadellà, M and Zevin, AS and Rocafort, M and Parera, M and Rodríguez, C and Arumí, M and Carrillo, J and Mothe, B and Estany, C and Coll, J and Bravo, I and Herrero, C and Saz, J and Sirera, G and Torrella, A and Navarro, J and Crespo, M and Negredo, E and Brander, C and Blanco, J and Calle, ML and Klatt, NR and Clotet, B and Paredes, R}, title = {Low nadir CD4+ T-cell counts predict gut dysbiosis in HIV-1 infection.}, journal = {Mucosal immunology}, volume = {12}, number = {1}, pages = {232-246}, pmid = {30171206}, issn = {1935-3456}, mesh = {Adult ; Archaea ; Bacteroides ; Butyrates/metabolism ; CD4 Lymphocyte Count/*methods ; CD4-Positive T-Lymphocytes/*immunology ; Cross-Sectional Studies ; Dysbiosis/complications/diagnosis/*immunology ; Feces/chemistry/microbiology ; Female ; Gastrointestinal Microbiome/immunology ; HIV Infections/complications/diagnosis/*immunology ; HIV-1/*physiology ; Humans ; Intestinal Mucosa/*immunology/microbiology ; Male ; Middle Aged ; Prognosis ; }, abstract = {Human immunodeficiency virus (HIV)-1 infection causes severe gut and systemic immune damage, but its effects on the gut microbiome remain unclear. Previous shotgun metagenomic studies in HIV-negative subjects linked low-microbial gene counts (LGC) to gut dysbiosis in diseases featuring intestinal inflammation. Using a similar approach in 156 subjects with different HIV-1 phenotypes, we found a strong, independent, dose-effect association between nadir CD4+ T-cell counts and LGC. As in other diseases involving intestinal inflammation, the gut microbiomes of subjects with LGC were enriched in gram-negative Bacteroides, acetogenic bacteria and Proteobacteria, which are able to metabolize reactive oxygen and nitrogen species; and were depleted in oxygen-sensitive methanogenic archaea and sulfate-reducing bacteria. Interestingly, subjects with LGC also showed increased butyrate levels in direct fecal measurements, consistent with enrichment in Roseburia intestinalis despite reductions in other butyrate producers. The microbiomes of subjects with LGC were also enriched in bacterial virulence factors, as well as in genes associated with beta-lactam, lincosamide, tetracycline, and macrolide resistance. Thus, low nadir CD4+ T-cell counts, rather than HIV-1 serostatus per se, predict the presence of gut dysbiosis in HIV-1 infected subjects. Such dysbiosis does not display obvious HIV-specific features; instead, it shares many similarities with other diseases featuring gut inflammation.}, } @article {pmid30168288, year = {2018}, author = {Minich, JJ and Zhu, Q and Xu, ZZ and Amir, A and Ngochera, M and Simwaka, M and Allen, EE and Zidana, H and Knight, R}, title = {Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus).}, journal = {MicrobiologyOpen}, volume = {7}, number = {6}, pages = {e00716}, pmid = {30168288}, issn = {2045-8827}, mesh = {Animal Feed/analysis/microbiology ; Animals ; Aquaculture ; Bacteria/classification/genetics/*isolation & purification ; Catfishes/*growth & development/metabolism ; Cattle ; Livestock ; Manure/analysis/*microbiology ; Microbiota ; Ponds/analysis/*microbiology ; Poultry ; Swine ; Tilapia/*growth & development/metabolism ; }, abstract = {The majority of seafood is farmed, with most finfish coming from freshwater ponds. Ponds are often fertilized to promote microbial productivity as a natural feed source to fish. To understand if pond fertilization with livestock manure induces a probiotic or prebiotic effect, we communally reared tilapia (Oreochromis shiranus), and North African catfish (Clarias gariepinus), for 4 weeks under seven manure treatments including layer chicken, broiler chicken, guinea fowl, quail, pig, cow, vs. commercial feed to evaluate microbial community dynamics of the manure, pond water, and fish feces using 16S and 18S rRNA marker genes along with metagenome sequencing. Catfish growth, but not tilapia, was positively associated with plankton abundance (p = 0.0006, R[2] = 0.4887) and greatest in ponds fertilized with quail manure (ANOVA, p < 0.05). Manure was unique and influenced the 16S microbiome in pond water, tilapia gut, and catfish gut and 18S community in pond water and catfish guts (PERMANOVA, p = 0.001). On average, 18.5%, 18.6%, and 45.3% of manure bacteria sOTUs, (sub-operational taxonomic units), were present in the water column, catfish feces, and tilapia feces which comprised 3.7%, 12.8%, and 10.9% of the total microbial richness of the communities, respectively. Antibiotic resistance genes were highest in the manure and water samples followed by tilapia feces and lowest in catfish feces (p < 0.0001). In this study, we demonstrate how the bacterial and eukaryotic microbial composition of fish ponds are influenced by specific livestock manure inputs and that the gut microbiome of tilapia is more sensitive and responsive than catfish to these changes. We conclude that animal manure used as fertilizer induces a primarily prebiotic effect on the pond ecosystem rather than a direct probiotic effect on fish.}, } @article {pmid30166176, year = {2018}, author = {Müller, A and Rösch, N and Cho, GS and Meinhardt, AK and Kabisch, J and Habermann, D and Böhnlein, C and Brinks, E and Greiner, R and Franz, CMAP}, title = {Influence of iodized table salt on fermentation characteristics and bacterial diversity during sauerkraut fermentation.}, journal = {Food microbiology}, volume = {76}, number = {}, pages = {473-480}, doi = {10.1016/j.fm.2018.07.009}, pmid = {30166176}, issn = {1095-9998}, mesh = {Bacteria/classification/genetics/*isolation & purification/*metabolism ; *Biodiversity ; Brassica/chemistry/*microbiology ; Fermentation ; Fermented Foods/analysis/*microbiology ; Food Microbiology ; Hydrogen-Ion Concentration ; Iodine/*metabolism ; Lactobacillus plantarum/genetics/isolation & purification/metabolism ; Leuconostoc/genetics/isolation & purification/metabolism ; Sodium Chloride, Dietary/*metabolism ; }, abstract = {The effect of iodine present in 1.0% table salt in combination with the use of starter cultures in sauerkraut fermentations were investigated in order to determine whether iodine interferes with lactic acid bacteria responsible for the fermentation. The effect of iodine was tested in fermentations performed using selected starter cultures or without starters (spontaneous fermentation). Lactobacillus plantarum and Leuconostoc mesenteroides used as starters at levels of ca. 1 × 10[7] cfu ml[-1] led to a quick establishment of lactic acid bacteria (LAB) as predominant microorganisms, reaching 1 × 10[9] cfu ml[-1] after 24 h decreasing the pH to below 4.0. In contrast, LAB counts in control fermentations without starters increased slower from 1 × 10[5] cfu ml[-1] to 1 × 10[9] cfu ml[-1] and a pH reduction below 4.0 was achieved only after 3 days fermentation. A metagenomic investigation showed a more diverse bacterial community in fermentations without starters, consisting of enterobacteria and pseudomonads in the first days of fermentation, and of LAB such as lactococci in the later stages. In fermentations with starters, lactobacilli predominated. Leuconostocs also occurred, but at much lower sequence abundance than lactobacilli, and thus were not able to predominate. Determination of iodine in the fermentation with starter bacteria and with iodized salt showed that the fermentation did not affect iodine concentration. The use of iodized salt did not statistically significantly influence microbial populations in the fermentation. Thus, there is no basis for the popular held belief that the use of iodized salt inhibits the growth of the bacteria important for the sauerkraut fermentation. A statistically near significant effect (p = 0.06), however, was noted for the effect of iodine on yeasts and mould populations in the fermentations performed without starter cultures. As sauerkraut is usually produced without starters, this should be further investigated.}, } @article {pmid30166168, year = {2018}, author = {Li, Z and Feng, C and Luo, X and Yao, H and Zhang, D and Zhang, T}, title = {Revealing the influence of microbiota on the quality of Pu-erh tea during fermentation process by shotgun metagenomic and metabolomic analysis.}, journal = {Food microbiology}, volume = {76}, number = {}, pages = {405-415}, doi = {10.1016/j.fm.2018.07.001}, pmid = {30166168}, issn = {1095-9998}, mesh = {Aspergillus/classification/genetics/isolation & purification/metabolism ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Camellia sinensis/chemistry/*microbiology ; Fermentation ; Flavoring Agents/chemistry/metabolism ; Metabolomics ; Metagenomics ; *Microbiota ; Phenols/chemistry/metabolism ; Quality Control ; Tea/*chemistry/microbiology ; }, abstract = {Multispecies microbial community in natural solid-state fermentation (SSF) is crucial for the formation of Chinese Pu-erh tea's unique quality. However, the association between microbiota and tea quality are still poorly understood. Herein, shotgun metagenomic and metabolomic analysis showed that significant variations in composition of microbiota, collective functional genes, and flavour compounds occurred during SSF process. Furthermore, the formation pathways of the dominant flavours including theabrownin, methoxy-phenolic compound, alcohol and carvone were proposed. Moreover, biological interaction networks analysis among functional core microbiota, functional genes, and dominant flavours indicated Aspergillus was the main flavour-producing microorganism in the early SSF, while many other genera including Bacillus, Rasamsonia, Lichtheimia, Debaryomyces were determined as the functional core microorganism for flavours production in the late SSF. This study provides a perspective for bridging the gap between the microbiota and quality in Pu-erh tea, and benefited for further optimizing production efficiency and product quality.}, } @article {pmid30166158, year = {2018}, author = {Bouju-Albert, A and Pilet, MF and Guillou, S}, title = {Influence of lactate and acetate removal on the microbiota of French fresh pork sausages.}, journal = {Food microbiology}, volume = {76}, number = {}, pages = {328-336}, doi = {10.1016/j.fm.2018.06.011}, pmid = {30166158}, issn = {1095-9998}, mesh = {Acetates/*pharmacology ; Animals ; Brochothrix/drug effects/genetics/isolation & purification ; Colony Count, Microbial ; Food Microbiology/methods ; Food Packaging/methods ; Food Preservation/methods ; Food Preservatives/chemistry/*pharmacology ; Hydrogen-Ion Concentration ; Lactic Acid/*pharmacology ; Lactobacillus/drug effects/genetics/isolation & purification ; Leuconostoc/drug effects/genetics/isolation & purification ; Meat Products/analysis/*microbiology ; Metagenomics ; Microbiota/*drug effects/genetics ; RNA, Ribosomal, 16S ; Red Meat/*microbiology ; Swine ; Vacuum ; }, abstract = {The microbiota of fresh French pork sausages were characterised in five batches of comminuted pork meat that were equally divided into two formulations either containing the acid-based preservatives lactate and acetate, or no preservatives. Conventional microbiological analysis and high-throughput 16S rDNA amplicon sequencing methods were performed on meat batches packed under modified atmosphere (70% oxygen and 30% carbon dioxide) during chilled storage. In addition, meat pH and colour, and gas composition of the packages were monitored until the end of the shelf-life. During storage, the population of mesophilic and lactic acid bacteria increased from 4 log CFU/g to 8 log CFU/g after 15 days of chilled storage, both with and without preservatives. Despite similar changes of the physical and chemical parameters, such as pH and package gas composition, spoilage was delayed in the meat containing the preservatives, suggesting that lactate and acetate are effective against spoilage. Metagenetic analysis showed that at the end of the shelf-life, the species distribution differed between both the formulations and the batches. Lactic acid bacteria were shown to dominate both with and without preservatives; however, samples containing no preservatives were characterised by the presence of an increased population of Brochothrix spp. and Pseudomonas spp. whereas, Leuconostoc mesenteroides/pseudomesenteroides and Lactobacillus curvatus/graminis were more abundant in the meat with preservatives.}, } @article {pmid30166157, year = {2018}, author = {Jung, MJ and Kim, MS and Yun, JH and Lee, JY and Kim, PS and Lee, HW and Ha, JH and Roh, SW and Bae, JW}, title = {Viral community predicts the geographical origin of fermented vegetable foods more precisely than bacterial community.}, journal = {Food microbiology}, volume = {76}, number = {}, pages = {319-327}, doi = {10.1016/j.fm.2018.06.010}, pmid = {30166157}, issn = {1095-9998}, mesh = {Bacteria/genetics/isolation & purification/virology ; Bacteriophages/genetics/isolation & purification ; Brassica/microbiology ; DNA, Bacterial/genetics ; DNA, Viral/genetics ; Fermented Foods/*microbiology/*virology ; Food Microbiology ; Geography ; High-Throughput Nucleotide Sequencing ; Humans ; Lactobacillales/genetics/isolation & purification/virology ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vegetables/*microbiology/*virology ; }, abstract = {Fermented foods are considered as an integral part of the global human diet. Fermented foods also have unique microbial communities such as bacteria, archaea, fungi, and viruses that are essential to the fermentation process and affect final product characteristics. Despite the ecological importance of virus, little is known about the diversity and ecological role of virus in the food ecosystem. In this study, the viral and host bacterial communities from 10 representative samples of Korean and Chinese kimchi were analyzed in triplicate using next-generation sequencing technology. The overall structures of bacterial and viral communities were dominated by lactic acid bacteria in phylum Firmicutes and bacteriophages in order Caudovirales, respectively. For the single-stranded DNA (ssDNA) viruses, bacteriophage in family Microviridae were dominant in Korean kimchi. After correction for multiple comparisons using false discovery rate (FDR, P < 0.05), the relative abundances of 6 bacterial taxa and 33 viral host taxa at the genus level were significantly different between Korean and Chinese kimchi. Notably, in beta-diversity analysis, viral communities were much more clearly separated according to their geographical origin (PERMANOVA pseudo-F = 11.57, P < 0.001 in Bray-Curtis PCoA) than bacterial communities (pseudo-F = 4.75, P < 0.001 in unweighted UniFrac PCoA). Thus, viral metagenomics represents a potentially useful in-depth analytical method for determining the geographical origins of fermented foods.}, } @article {pmid30166151, year = {2018}, author = {Mataragas, M and Alessandria, V and Ferrocino, I and Rantsiou, K and Cocolin, L}, title = {A bioinformatics pipeline integrating predictive metagenomics profiling for the analysis of 16S rDNA/rRNA sequencing data originated from foods.}, journal = {Food microbiology}, volume = {76}, number = {}, pages = {279-286}, doi = {10.1016/j.fm.2018.05.009}, pmid = {30166151}, issn = {1095-9998}, mesh = {Algorithms ; Cheese/microbiology ; *Computational Biology ; DNA, Ribosomal ; Food Microbiology/methods ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways ; Metagenomics/*methods ; Microbial Consortia/*genetics ; RNA, Ribosomal, 16S/*genetics ; *Sequence Analysis, DNA ; Software ; }, abstract = {The recent advances in molecular biology, such as the advent of next-generation sequencing (NGS) platforms, have paved the way to new exciting tools which rapidly transform food microbiology. Nowadays, NGS methods such as 16S rDNA/rRNA metagenomics or amplicon sequencing are used for the taxonomic profiling of the food microbial communities. Although 16S rDNA/rRNA NGS-based microbial data are not suited for the investigation of the functional potential of the identified operational taxonomic units as compared to shotgun metagenomics, advances in the bioinformatics discipline allow now the performance of such studies. In this paper, a bioinformatics workflow is described integrating predictive metagenomics profiling with specific application to food microbiology data. Bioinformatics tools pertinent to each sub-module of the pipeline are suggested as well. The published 16S rDNA/rRNA amplicon data originated from an Italian Grana-type cheese, using an NGS platform, was employed to demonstrate the predictive metagenomics profiling approach. The pipeline identified the microbial community and the changes that occurred in the microbial profile during manufacture of the food product studied (taxonomic profiling). The workflow also indicated significant changes in the functional profiling of the community. The tool may help to investigate the functional potential, alterations, and interactions of a microbial community. The proposed workflow may also find an application in the investigation of the ecology of foodborne pathogens encountered in various food products.}, } @article {pmid30165813, year = {2018}, author = {Rotimi, AM and Pierneef, R and Reva, ON}, title = {Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {309}, pmid = {30165813}, issn = {1471-2105}, support = {93664//National Research Foundation/ ; }, mesh = {Algorithms ; Bacteria/*genetics ; Base Sequence ; DNA Barcoding, Taxonomic/*methods ; *Genes, Bacterial ; Genetic Markers ; Humans ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; ROC Curve ; Reproducibility of Results ; Sample Size ; *Software ; Species Specificity ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Metagenomic approaches have revealed the complexity of environmental microbiomes with the advancement in whole genome sequencing displaying a significant level of genetic heterogeneity on the species level. It has become apparent that patterns of superior bioactivity of bacteria applicable in biotechnology as well as the enhanced virulence of pathogens often requires distinguishing between closely related species or sub-species. Current methods for binning of metagenomic reads usually do not allow for identification below the genus level and generally stops at the family level.

RESULTS: In this work, an attempt was made to improve metagenomic binning resolution by creating genome specific barcodes based on the core and accessory genomes. This protocol was implemented in novel software tools available for use and download from http://bargene.bi.up.ac.za /. The most abundant barcode genes from the core genomes were found to encode for ribosomal proteins, certain central metabolic genes and ABC transporters. Performance of metabarcode sequences created by this package was evaluated using artificially generated and publically available metagenomic datasets. Furthermore, a program (Barcoding 2.0) was developed to align reads against barcode sequences and thereafter calculate various parameters to score the alignments and the individual barcodes. Taxonomic units were identified in metagenomic samples by comparison of the calculated barcode scores to set cut-off values. In this study, it was found that varying sample sizes, i.e. number of reads in a metagenome and metabarcode lengths, had no significant effect on the sensitivity and specificity of the algorithm. Receiver operating characteristics (ROC) curves were calculated for different taxonomic groups based on the results of identification of the corresponding genomes in artificial metagenomic datasets. The reliability of distinguishing between species of the same genus or family by the program was nearly perfect.

CONCLUSIONS: The results showed that the novel online tool BarcodeGenerator (http://bargene.bi.up.ac.za /) is an efficient approach for generating barcode sequences from a set of complete genomes provided by users. Another program, Barcoder 2.0 is available from the same resource to enable an efficient and practical use of metabarcodes for visualization of the distribution of organisms of interest in environmental and clinical samples.}, } @article {pmid30158571, year = {2018}, author = {Caussy, C and Loomba, R}, title = {Gut microbiome, microbial metabolites and the development of NAFLD.}, journal = {Nature reviews. Gastroenterology & hepatology}, volume = {15}, number = {12}, pages = {719-720}, doi = {10.1038/s41575-018-0058-x}, pmid = {30158571}, issn = {1759-5053}, support = {MR/L01632X/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Female ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Non-alcoholic Fatty Liver Disease ; Obesity ; }, } @article {pmid30158489, year = {2018}, author = {Garcia, R and La Clair, JJ and Müller, R}, title = {Future Directions of Marine Myxobacterial Natural Product Discovery Inferred from Metagenomics.}, journal = {Marine drugs}, volume = {16}, number = {9}, pages = {}, pmid = {30158489}, issn = {1660-3397}, support = {German Center for Infection Research//Deutsches Zentrum für Infektionsforschung/ ; X//Xenobe Research Institute/ ; }, mesh = {Aquatic Organisms/*genetics/metabolism ; Biodiversity ; Biological Products/metabolism/*pharmacology ; DNA, Bacterial/genetics ; *Metagenomics ; Myxococcales/*genetics/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Salt Tolerance/genetics ; Sequence Analysis, DNA ; }, abstract = {Over the last two decades, halophilic (organisms that thrive at high salt concentrations) and halotolerant (organisms that have adapted to high salt concentrations) myxobacteria emerged as an important source of structurally diverse secondary metabolites from the marine environment. This review explores the advance of metagenomics analysis and 16S rRNA gene phylogeny of the cultured and uncultured myxobacteria from marine and other salt-environments up to July 2018. The diversity of novel groups of myxobacteria in these environments appears unprecedented, especially in the Sorangiineae and Nannocystineae suborders. The Sandaracinaceae related clade in the Sorangiineae suborder seems more widely distributed compared to the exclusively marine myxobacterial cluster. Some of the previously identified clones from metagenomic studies were found to be related to the Nannocystineae suborder. This understanding provides the foundation for a vital, unexplored resource. Understanding the conditions required to cultivate these yet "uncultured" myxobacteria in the laboratory, while a key next step, offers a significant potential to further expand access to diverse secondary metabolites.}, } @article {pmid30155977, year = {2018}, author = {Bálint, M and Nowak, C and Márton, O and Pauls, SU and Wittwer, C and Aramayo, JL and Schulze, A and Chambert, T and Cocchiararo, B and Jansen, M}, title = {Accuracy, limitations and cost efficiency of eDNA-based community survey in tropical frogs.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1415-1426}, doi = {10.1111/1755-0998.12934}, pmid = {30155977}, issn = {1755-0998}, support = {//USGS Amphibian Research and Monitoring Initiative/ ; //Globetrotter/ ; //Erika and Walter Datz-Stiftung/ ; LOEWE - Landes-Offensive zur Entwicklung Wissens//Hessisches Ministerium für Wissenschaft und Kunst/ ; //Ministry of Higher Education/ ; }, mesh = {Amphibians/*classification/*genetics ; Animals ; *Biota ; Bolivia ; Costs and Cost Analysis ; DNA Barcoding, Taxonomic/economics/*methods ; Metagenomics/economics/*methods ; Tropical Climate ; }, abstract = {Rapid environmental change in highly biodiverse tropical regions demands efficient biomonitoring programmes. While existing metrics of species diversity and community composition rely on encounter-based survey data, eDNA recently emerged as alternative approach. Costs and ecological value of eDNA-based methods have rarely been evaluated in tropical regions, where high species richness is accompanied by high functional diversity (e.g., the use of different microhabitats by different species and life stages). We first tested whether estimation of tropical frogs' community structure derived from eDNA data is compatible with expert field assessments. Next, we evaluated whether eDNA is a financially viable solution for biodiversity monitoring in tropical regions. We applied eDNA metabarcoding to investigate frog species occurrence in five ponds in the Chiquitano dry forest region in Bolivia and compared our data with a simultaneous visual and audio encounter survey (VAES). We found that taxon lists and community structure generated with eDNA and VAES correspond closely, and most deviations are attributable to different species' life histories. Cost efficiency of eDNA surveys was mostly influenced by the richness of local fauna and the number of surveyed sites: VAES may be less costly in low-diversity regions, but eDNA quickly becomes more cost-efficient in high-diversity regions with many sites sampled. The results highlight that eDNA is suitable for large-scale biodiversity surveys in high-diversity areas if life history is considered, and certain precautions in sampling, genetic analyses and data interpretation are taken. We anticipate that spatially extensive, standardized eDNA biodiversity surveys will quickly emerge in the future.}, } @article {pmid30155556, year = {2019}, author = {Ma, ZS}, title = {Sketching the Human Microbiome Biogeography with DAR (Diversity-Area Relationship) Profiles.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {821-838}, pmid = {30155556}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation & purification ; *Biodiversity ; Humans ; Metagenomics ; *Microbiota ; Models, Biological ; }, abstract = {SAR (species area relationship) is a classic ecological theory that has been extensively investigated and applied in the studies of global biogeography and biodiversity conservation in macro-ecology. It has also found important applications in microbial ecology in recent years thanks to the breakthroughs in metagenomic sequencing technology. Nevertheless, SAR has a serious limitation for practical applications-ignoring the species abundance and treating all species as equally abundant. This study aims to explore the biogeography discoveries of human microbiome over 18 sites of 5 major microbiome habitats, establish the baseline DAR (diversity-area scaling relationship) parameters, and perform comparisons with the classic SAR. The extension from SAR to DAR by adopting the Hill numbers as diversity measures not only overcomes the previously mentioned flaw of SAR but also allows for obtaining a series of important findings on the human microbiome biodiversity and biogeography. Specifically, two types of DAR models were built, the traditional power law (PL) and power law with exponential cutoff (PLEC), using comprehensive datasets from the HMP (human microbiome project). Furthermore, the biogeography "maps" for 18 human microbiome sites using their DAR profiles for assessing and predicting the diversity scaling across individuals, PDO profiles (pair-wise diversity overlap) for measuring diversity overlap (similarity), and MAD profile (for predicting the maximal accrual diversity in a population) were sketched out. The baseline biogeography maps for the healthy human microbiome diversity can offer guidelines for conserving human microbiome diversity and investigating the health implications of the human microbiome diversity and heterogeneity.}, } @article {pmid30154496, year = {2019}, author = {Ruff, SE and Felden, J and Gruber-Vodicka, HR and Marcon, Y and Knittel, K and Ramette, A and Boetius, A}, title = {In situ development of a methanotrophic microbiome in deep-sea sediments.}, journal = {The ISME journal}, volume = {13}, number = {1}, pages = {197-213}, pmid = {30154496}, issn = {1751-7370}, mesh = {Archaea/genetics/*isolation & purification/metabolism ; Bacteria/genetics/*isolation & purification/metabolism ; Geologic Sediments/*microbiology ; Metagenome ; Methane/*metabolism ; Microbiota/*physiology ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Emission of the greenhouse gas methane from the seabed is globally controlled by marine aerobic and anaerobic methanotrophs gaining energy via methane oxidation. However, the processes involved in the assembly and dynamics of methanotrophic populations in complex natural microbial communities remain unclear. Here we investigated the development of a methanotrophic microbiome following subsurface mud eruptions at Håkon Mosby mud volcano (1250 m water depth). Freshly erupted muds hosted deep-subsurface communities that were dominated by Bathyarchaeota, Atribacteria and Chloroflexi. Methanotrophy was initially limited to a thin surface layer of Methylococcales populations consuming methane aerobically. With increasing distance to the eruptive center, anaerobic methanotrophic archaea, sulfate-reducing Desulfobacterales and thiotrophic Beggiatoaceae developed, and their respective metabolic capabilities dominated the biogeochemical functions of the community. Microbial richness, evenness, and cell numbers of the entire microbial community increased up to tenfold within a few years downstream of the mud flow from the eruptive center. The increasing diversity was accompanied by an up to fourfold increase in sequence abundance of relevant metabolic genes of the anaerobic methanotrophic and thiotrophic guilds. The communities fundamentally changed in their structure and functions as reflected in the metagenome turnover with distance from the eruptive center, and this was reflected in the biogeochemical zonation across the mud volcano caldera. The observed functional succession provides a framework for the response time and recovery of complex methanotrophic communities after disturbances of the deep-sea bed.}, } @article {pmid30153857, year = {2018}, author = {Ugarte, A and Vicedomini, R and Bernardes, J and Carbone, A}, title = {A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {149}, pmid = {30153857}, issn = {2049-2618}, mesh = {Algorithms ; Bacteria/classification/*genetics/isolation & purification ; Bacterial Proteins/*chemistry/*genetics/metabolism ; Databases, Genetic ; Environmental Microbiology ; Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/*methods ; Molecular Sequence Annotation/*methods ; Protein Domains ; }, abstract = {BACKGROUND: Biochemical and regulatory pathways have until recently been thought and modelled within one cell type, one organism and one species. This vision is being dramatically changed by the advent of whole microbiome sequencing studies, revealing the role of symbiotic microbial populations in fundamental biochemical functions. The new landscape we face requires the reconstruction of biochemical and regulatory pathways at the community level in a given environment. In order to understand how environmental factors affect the genetic material and the dynamics of the expression from one environment to another, we want to evaluate the quantity of gene protein sequences or transcripts associated to a given pathway by precisely estimating the abundance of protein domains, their weak presence or absence in environmental samples.

RESULTS: MetaCLADE is a novel profile-based domain annotation pipeline based on a multi-source domain annotation strategy. It applies directly to reads and improves identification of the catalog of functions in microbiomes. MetaCLADE is applied to simulated data and to more than ten metagenomic and metatranscriptomic datasets from different environments where it outperforms InterProScan in the number of annotated domains. It is compared to the state-of-the-art non-profile-based and profile-based methods, UProC and HMM-GRASPx, showing complementary predictions to UProC. A combination of MetaCLADE and UProC improves even further the functional annotation of environmental samples.

CONCLUSIONS: Learning about the functional activity of environmental microbial communities is a crucial step to understand microbial interactions and large-scale environmental impact. MetaCLADE has been explicitly designed for metagenomic and metatranscriptomic data and allows for the discovery of patterns in divergent sequences, thanks to its multi-source strategy. MetaCLADE highly improves current domain annotation methods and reaches a fine degree of accuracy in annotation of very different environments such as soil and marine ecosystems, ancient metagenomes and human tissues.}, } @article {pmid30152883, year = {2018}, author = {Toivonen, L and Hasegawa, K and Ajami, NJ and Celedón, JC and Mansbach, JM and Petrosino, JF and Camargo, CA}, title = {Circulating 25-hydroxyvitamin D, nasopharyngeal microbiota, and bronchiolitis severity.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {29}, number = {8}, pages = {877-880}, pmid = {30152883}, issn = {1399-3038}, support = {R01 AI127507/AI/NIAID NIH HHS/United States ; //Päivikki ja Sakari Sohlbergin Säätiö/International ; R01 AI134940/AI/NIAID NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; UH3 OD023253/OD/NIH HHS/United States ; R01 AI137091/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; //Suomen Lääketieteen Säätiö/International ; }, mesh = {Bronchiolitis/*etiology ; Cohort Studies ; Female ; Humans ; Infant ; Male ; Microbiota/genetics/*immunology ; Nasopharynx/*microbiology ; Prospective Studies ; Risk Factors ; United States ; Vitamin D/*analogs & derivatives/blood ; }, } @article {pmid30149004, year = {2018}, author = {Kim, JY and Kim, EM and Yi, MH and Lee, J and Lee, S and Hwang, Y and Yong, D and Sohn, WM and Yong, TS}, title = {Intestinal fluke Metagonimus yokogawai infection increases probiotic Lactobacillus in mouse cecum.}, journal = {Experimental parasitology}, volume = {193}, number = {}, pages = {45-50}, doi = {10.1016/j.exppara.2018.08.002}, pmid = {30149004}, issn = {1090-2449}, mesh = {Animals ; Bacteria/classification/growth & development ; Cecum/*microbiology ; Fish Diseases/parasitology ; Gastrointestinal Microbiome ; Heterophyidae/*physiology ; *Lactobacillus ; Mice ; Mice, Inbred ICR ; Osmeriformes/parasitology ; *Probiotics ; Trematode Infections/*microbiology ; }, abstract = {Helminth infection can alleviate immune-mediated disorders such as allergies and autoimmune diseases, by altering the gut microbiome. However, changes in gut microbiome due to intestinal trematodes remain unelucidated. Here, we evaluated the changes in the gut microbiome of ICR mice infected with Metagonimus yokogawai, a hypo-virulent intestinal trematode. Four weeks after infection, mouse cecal content was analyzed by 16S rRNA amplicon analysis. Although there was no apparent difference in species richness and diversity, the microbiome composition was different in the infected and control groups. Furthermore, several Lactobacillus species with known immunomodulatory role in immune-mediated diseases were increased in the infected group.}, } @article {pmid30146515, year = {2018}, author = {Suda, W and Ogata, Y and Nishijima, S}, title = {[Analysis of human microbiome using NGS.].}, journal = {Clinical calcium}, volume = {28}, number = {9}, pages = {1274-1281}, pmid = {30146515}, issn = {0917-5857}, mesh = {DNA ; *High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {Recently, next generation sequencers(NGS)became prevalent and enable us possible to comprehensively analyze the entire human microbiome community structures including difficult-to-culture microbes. In this review, we introduce the NGS-based analytical methods of human microbiome, called "meta-16S analysis" and "metagenomic analysis", then show several fundamental data basing these analyses. Furthermore, we also introduce the importance of database improvement used for analysis and the DNA preparation method from human samples.}, } @article {pmid30146296, year = {2018}, author = {Metzler-Zebeli, BU and Haselmann, A and Klevenhusen, F and Knaus, W and Zebeli, Q}, title = {Lactic acid treatment of by-products and phosphorus level in the diet modulate bacterial microbiome and the predicted metagenome functions using the rumen simulation technique.}, journal = {Journal of dairy science}, volume = {101}, number = {11}, pages = {9800-9814}, doi = {10.3168/jds.2018-14821}, pmid = {30146296}, issn = {1525-3198}, mesh = {Animals ; Bacteria/drug effects/genetics ; Butyrates/analysis ; Diet/veterinary ; *Dietary Supplements ; Fatty Acids, Volatile/analysis ; Female ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; Lactic Acid/*pharmacology ; Metagenome/*drug effects ; Methane/analysis ; Phosphorus/*analysis ; Phosphorus, Dietary/*analysis ; RNA, Ribosomal, 16S/genetics ; Rumen/drug effects/microbiology ; Waste Products ; }, abstract = {This study used a rumen simulation technique to evaluate the effects of soaking of by-product-rich concentrate (BPC) in 5% lactic acid (LAC; vol/vol) on the rumen microbiota, predicted metagenome, fermentation characteristics, and nutrient degradation without or with supplemented P. The diet was supplemented with 1.6 g of P in the form of monocalcium phosphate per kilogram of dry matter in addition to 284 mg of inorganic P/d per fermentor via artificial saliva. Fermentor fluid was collected for analyses of short-chain fatty acids, fermentation gases, redox potential, and microbiota and feed residues for calculation of nutrient degradation. The microbiota composition was assessed using paired-end Illumina (Illumina Inc., San Diego, CA) MiSeq sequencing of the V3 to V5 region of the 16S rRNA gene. Soaking in LAC reduced the contents of crude protein, neutral and acid detergent fibers, and organic matter fractions as well as ash and P content of the BPC. Both the LAC treatment of BPC and the inorganic P modified the relative bacterial abundances mainly within the predominant orders Bacteroidales and Clostridiales. Supervised DIABLO N-integration networking supported that operational taxonomic units related to BS11, Ruminococcaceae, Christensenellaceae, Eubacterium, and Selenomonas were the most discriminant for the LAC-treated BPC, whereas other operational taxonomic units related to BS11, RFN20, Ruminococcus, and Succiniclasticum were best correlated with the inorganic P supplementation. Integration networking also showed that carbohydrate and pyruvate metabolism, biosynthesis of unsaturated fatty acids, and degradation of several xenobiotics were stimulated by the LAC treatment of BPC. Those data supported the enhanced fermentation activity as indicated by increased total short-chain fatty acid concentration, especially propionate and butyrate, and methane, but decreased ruminal crude protein degradation, with the LAC-treated compared with control-treated BPC. In contrast, despite an increased abundance of imputed functions, such as inositol phosphate metabolism, phosphatidylinositol signaling, and fructose and mannose metabolism, the reduced abundance of the imputed Kyoto Encyclopedia of Genes and Genomes pathway "transcription machinery" as well as the decrease in total short-chain fatty acids and nutrient degradation indicated reduced bacterial metabolic activity with the inorganic P supplementation. In conclusion, soaking of BPC in LAC may favor the proliferation of certain fibrolytic bacterial taxa and stimulate their metabolic activity, whereas the supplemented P to a diet already meeting ruminal P needs may impair ruminal nutrient utilization.}, } @article {pmid30144516, year = {2018}, author = {Nguyen, D and Khanal, SK}, title = {A little breath of fresh air into an anaerobic system: How microaeration facilitates anaerobic digestion process.}, journal = {Biotechnology advances}, volume = {36}, number = {7}, pages = {1971-1983}, doi = {10.1016/j.biotechadv.2018.08.007}, pmid = {30144516}, issn = {1873-1899}, mesh = {Anaerobiosis ; Bacteria/*metabolism ; Bioreactors ; Fermentation ; Gene Expression Profiling ; Hydrogen Sulfide/*metabolism ; Hydrolysis ; Metabolic Networks and Pathways ; Metagenomics ; Methane/*metabolism ; Methanomicrobiales/*metabolism ; Microbial Consortia/*physiology ; Oxidation-Reduction ; Oxygen/*metabolism ; Proteomics ; }, abstract = {Exposure of a small amount of oxygen/air (microaeration) has been reported to benefit the anaerobic digestion (AD) process in enhancing hydrolysis, improving methane yield, stabilizing the process and scavenging hydrogen sulfide among others. The underlying mechanism of enhancing AD process via microaeration is the augmentation of activity and diversity of the microbial consortia that promotes syntrophic interactions among different microbial groups, thereby creating a more stable process. To design and implement a microaeration-based AD process, fundamental insights about the mechanism of the AD system at process, microbial and molecular levels must be fully explored. This review critically examines microaeration-based AD processes through our recent understandings of the effect of oxygen on microbial community structure, enzymatic, energetic, physiological, and biochemical aspects of the microbial-mediated process. Syntrophic interactions between hydrolytic, fermentative, sulfate reducing, syntrophic bacteria and methanogens under microaerobic conditions are examined to reveal putative mechanism and factors that need to be considered when implementing microaeration in AD process. Further studies are needed to better understand the microbial pathways and bioenergetics of the microaerobic AD process by adopting advanced molecular techniques such as metagenomics, transcriptomics, and proteomics.}, } @article {pmid30144429, year = {2018}, author = {Friedman, ES and Li, Y and Shen, TD and Jiang, J and Chau, L and Adorini, L and Babakhani, F and Edwards, J and Shapiro, D and Zhao, C and Carr, RM and Bittinger, K and Li, H and Wu, GD}, title = {FXR-Dependent Modulation of the Human Small Intestinal Microbiome by the Bile Acid Derivative Obeticholic Acid.}, journal = {Gastroenterology}, volume = {155}, number = {6}, pages = {1741-1752.e5}, pmid = {30144429}, issn = {1528-0012}, support = {R01 AA026302/AA/NIAAA NIH HHS/United States ; K08 DK106457/DK/NIDDK NIH HHS/United States ; R01 GM123056/GM/NIGMS NIH HHS/United States ; K08 AA021424/AA/NIAAA NIH HHS/United States ; P30 DK050306/DK/NIDDK NIH HHS/United States ; P30 DK019525/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Animals ; Bile Acids and Salts/*physiology ; Chenodeoxycholic Acid/*analogs & derivatives/pharmacokinetics ; Female ; Gastrointestinal Microbiome/*drug effects ; Healthy Volunteers ; Humans ; Intestine, Small/*microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Receptors, Cytoplasmic and Nuclear/*physiology ; }, abstract = {BACKGROUND & AIMS: Intestinal bacteria can modify the composition of bile acids and bile acids, which are regulated by the farnesoid X receptor, affect the survival and growth of gut bacteria. We studied the effects of obeticholic acid (OCA), a bile acid analogue and farnesoid X receptor agonist, on the intestinal microbiomes of humans and mice.

METHODS: We performed a phase I study in 24 healthy volunteers given OCA (5, 10, or 25 mg/d for 17 days). Fecal and plasma specimens were collected at baseline (day 0) and on days 17 (end of dosing) and 37 (end of study). The fecal specimens were analyzed by shotgun meta-genomic sequencing. A Uniref90 high-stringency genomic analysis was used to assign specific genes to the taxonomic signature of bacteria whose abundance was associated with OCA. Male C57BL/6 mice were gavage fed daily with water, vehicle, or OCA (10 mg/kg) for 2 weeks. Small intestine luminal contents were collected by flushing with saline and fecal pellets were collected at baseline and day 14. Mouse samples were analyzed by 16S-tagged sequencing. Culture experiments were performed to determine the taxonomic-specific effects of bile acids and OCA on bacterial growth.

RESULTS: Suppression of endogenous bile acid synthesis by OCA in subjects led to a reversible induction of gram-positive bacteria that are found in the small intestine and are components of the diet and oral microbiota. We found that bile acids decreased proliferation of these bacteria in minimum inhibitory concentration assays. In these organisms, there was an increase in the representation of microbial genomic pathways involved in DNA synthesis and amino acid metabolism with OCA treatment of subjects. Consistent with these findings, mice fed OCA had lower endogenous bile acid levels and an increased proportion of Firmicutes, specifically in the small intestine, compared with mice fed water or vehicle.

CONCLUSIONS: In studying the effects of OCA in humans and mice, we found evidence for interactions between bile acids and features of the small intestinal microbiome. These findings indicate that farnesoid X receptor activation alters the intestinal microbiota and could provide opportunities for microbiome biomarker discovery or new approaches to engineering the human microbiome. ClinicalTrials.gov, NCT01933503.}, } @article {pmid30143657, year = {2018}, author = {Crespo-Piazuelo, D and Estellé, J and Revilla, M and Criado-Mesas, L and Ramayo-Caldas, Y and Óvilo, C and Fernández, AI and Ballester, M and Folch, JM}, title = {Characterization of bacterial microbiota compositions along the intestinal tract in pigs and their interactions and functions.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12727}, pmid = {30143657}, issn = {2045-2322}, mesh = {Animals ; Bacteria/classification ; Intestines/*microbiology ; Male ; Metagenome ; *Microbiota/genetics ; Phylogeny ; Swine/*microbiology ; }, abstract = {In addition to its value in meat production, the pig is an interesting animal model for human digestive tract studies due to its physiological similarities. The aim of this study was to describe the microbiome composition, distribution and interaction along the Iberian pig intestinal tract and its role in whole-body energy homeostasis. The V3-V4 region of the 16S rRNA gene was amplified and sequenced from the microbiomes of five gut sections (duodenum, jejunum, ileum, and proximal and distal colon) in thirteen castrated male pigs. A total of 1,669 operational taxonomic units distributed in 179 genera were found among all samples. The two most abundant genera in the small intestine were Lactobacillus and Clostridium, while Prevotella was predominant in the colon. The colon samples were more similar among the pigs and richer in species than the small intestine samples were. In the small intestine, the metagenome prediction pointed to rapid internalization and conversion of the available simple carbohydrates for microbial proliferation and maintenance. In the colon, a competition among anaerobic bacteria for plant polysaccharide degradation to produce short chain fatty acids was found. This study confirms that the energy pathways of the gut microbiome differ along its sections and provides a description of the correlations between genera.}, } @article {pmid30143202, year = {2018}, author = {Shikata, A and Sermsathanaswadi, J and Thianheng, P and Baramee, S and Tachaapaikoon, C and Waeonukul, R and Pason, P and Ratanakhanokchai, K and Kosugi, A}, title = {Characterization of an Anaerobic, Thermophilic, Alkaliphilic, High Lignocellulosic Biomass-Degrading Bacterial Community, ISHI-3, Isolated from Biocompost.}, journal = {Enzyme and microbial technology}, volume = {118}, number = {}, pages = {66-75}, doi = {10.1016/j.enzmictec.2018.07.001}, pmid = {30143202}, issn = {1879-0909}, mesh = {Alkalies/chemistry ; Animals ; Bacteria, Anaerobic/growth & development ; *Biomass ; Cattle ; *Composting ; Lignin/*metabolism ; Metagenome ; *Microbial Consortia ; Oryza/*metabolism/microbiology ; Phylogeny ; Temperature ; Zea mays/*metabolism/microbiology ; }, abstract = {The generation of a complex microbial consortium is a promising approach for efficient biomass decomposition. An anaerobic thermophilic alkaliphilic microbial consortium with efficient degradation ability was screened from bovine manure compost using non-pretreated milling corn stover (CS) and rice straw (RS). A stable microbial consortium ISHI-3 with high degradation ability for CS and RS was isolated by the roll tube technique. ISHI-3 comprised Herbivorax saccincola and bacteria belonging to the classes Pelotomaculum, Tepidanaerobacter, and Tepidimicrobium, as determined by DGGE of the PCR-generated 16S rRNA genes. Furthermore, metagenomics analysis using a 16S rRNA library was carried out to determine the bacterial distribution during degradation of CS and RS. H. saccincola and bacteria belonging to Pelotomaculum were relatively abundant in the beginning to middle periods of culture with CS and RS whereas bacteria belonging to Tepidanaerobacter and Tepidimicrobium gradually increased in the population during the later stages. To understand the role of non-cellulolytic bacteria in the consortium, novel strains ET1 and GL4, which were most closely related to Tepidimicrobium ferriphilum and Tepidanaerobacter acetatoxydans, were isolated from ISHI-3. Based on their carbon source usage, morphology, and phylogenetic analysis, we propose that strains ET1 and GL4 should be classified as a novel genus or species. Bacteria ET1 and GL4 can utilize different organic compounds as carbon and energy sources such as organic acids, alcohols, sugars, and amino acids, showing a preference for organic acids and alcohols rather than sugars such as glucose and cellobiose. These results indicated that ET1 and GL4 help to accelerate efficient lignocellulose degradation of H. saccincola.}, } @article {pmid30143055, year = {2018}, author = {Chiarello, M and Auguet, JC and Bettarel, Y and Bouvier, C and Claverie, T and Graham, NAJ and Rieuvilleneuve, F and Sucré, E and Bouvier, T and Villéger, S}, title = {Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {147}, pmid = {30143055}, issn = {2049-2618}, mesh = {Animal Feed ; Animals ; Bacteria/*classification/genetics ; Biodiversity ; Coral Reefs ; Fishes/classification/*microbiology ; Humans ; Metagenomics/*methods ; Microbiota ; Phylogeny ; Plankton/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Skin/microbiology ; Species Specificity ; }, abstract = {BACKGROUND: The surface of marine animals is covered by abundant and diversified microbial communities, which have major roles for the health of their host. While such microbiomes have been deeply examined in marine invertebrates such as corals and sponges, the microbiomes living on marine vertebrates have received less attention. Specifically, the diversity of these microbiomes, their variability among species, and their drivers are still mostly unknown, especially among the fish species living on coral reefs that contribute to key ecosystem services while they are increasingly affected by human activities. Here, we investigated these knowledge gaps analyzing the skin microbiome of 138 fish individuals belonging to 44 coral reef fish species living in the same area.

RESULTS: Prokaryotic communities living on the skin of coral reef fishes are highly diverse, with on average more than 600 OTUs per fish, and differ from planktonic microbes. Skin microbiomes varied between fish individual and species, and interspecific differences were slightly coupled to the phylogenetic affiliation of the host and its ecological traits.

CONCLUSIONS: These results highlight that coral reef biodiversity is greater than previously appreciated, since the high diversity of macro-organisms supports a highly diversified microbial community. This suggest that beyond the loss of coral reefs-associated macroscopic species, anthropic activities on coral reefs could also lead to a loss of still unexplored host-associated microbial diversity, which urgently needs to be assessed.}, } @article {pmid30141128, year = {2019}, author = {Li, H and Mishra, M and Ding, S and Miyamoto, MM}, title = {Diversity and Dynamics of "Candidatus Endobugula" and Other Symbiotic Bacteria in Chinese Populations of the Bryozoan, Bugula neritina.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {243-256}, pmid = {30141128}, issn = {1432-184X}, support = {201205024-2//Public Welfare Project of the State Oceanic Administration/ ; 2013FY110700//National Basic Research Foundation of China/ ; }, mesh = {Animals ; Biodiversity ; Bryostatins/metabolism ; Bryozoa/growth & development/*microbiology ; China ; DNA, Bacterial/isolation & purification ; Ecology ; Gammaproteobacteria/*classification/genetics/*isolation & purification/*metabolism ; Geography ; Larva/microbiology ; Life Cycle Stages ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; }, abstract = {Bugula neritina is a common invasive cosmopolitan bryozoan that harbors (like many sessile marine invertebrates) a symbiotic bacterial (SB) community. Among the SB of B. neritina, "Candidatus Endobugula sertula" continues to receive the greatest attention, because it is the source of bryostatins. The bryostatins are potent bioactive polyketides, which have been investigated for their therapeutic potential to treat various cancers, Alzheimer's disease, and AIDS. In this study, we compare the metagenomics sequences for the 16S ribosomal RNA gene of the SB communities from different geographic and life cycle samples of Chinese B. neritina. Using a variety of approaches for estimating alpha/beta diversity and taxonomic abundance, we find that the SB communities vary geographically with invertebrate and fish mariculture and with latitude and environmental temperature. During the B. neritina life cycle, we find that the diversity and taxonomic abundances of the SB communities change with the onset of host metamorphosis, filter feeding, colony formation, reproduction, and increased bryostatin production. "Ca. Endobugula sertula" is confirmed as the symbiont of the Chinese "Ca. Endobugula"/B. neritina symbiosis. Our study extends our knowledge about B. neritina symbiosis from the New to the Old World and offers new insights into the environmental and life cycle factors that can influence its SB communities, "Ca. Endobugula," and bryostatins more globally.}, } @article {pmid30138419, year = {2018}, author = {Oliveira, JL and Cury, JC and Gurgel-Gonçalves, R and Bahia, AC and Monteiro, FA}, title = {Field-collected Triatoma sordida from central Brazil display high microbiota diversity that varies with regard to developmental stage and intestinal segmentation.}, journal = {PLoS neglected tropical diseases}, volume = {12}, number = {8}, pages = {e0006709}, pmid = {30138419}, issn = {1935-2735}, mesh = {Animals ; Bacteria/*classification ; Brazil ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Male ; Nymph ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Triatoma/growth & development/*microbiology ; }, abstract = {BACKGROUND/METHODOLOGY: Triatomine bugs are the vectors of Trypanosoma cruzi, the agent of Chagas disease. Vector control has for decades relied upon insecticide spraying, but insecticide resistance has recently emerged in several triatomine populations. One alternative strategy to reduce T. cruzi transmission is paratransgenesis, whereby symbiotic bacteria are genetically engineered to produce T. cruzi-killing proteins in the vector's gut. This approach requires in-depth knowledge of the vectors' natural gut microbiota. Here, we use metagenomics (16S rRNA 454 pyrosequencing) to describe the gut microbiota of field-caught Triatoma sordida-likely the most common peridomestic triatomine in Brazil. For large nymphs (4th and 5th stage) and adults, we also studied separately the three main digestive-tract segments-anterior midgut, posterior midgut, and hindgut.

PRINCIPAL FINDINGS: Bacteria of four phyla (12 genera) were present in both nymphs (all five stages) and adults, thus defining T. sordida's 'bacterial core': Actinobacteria (Brevibacterium, Corynebacterium, Dietzia, Gordonia, Nitriliruptor, Nocardia, Nocardiopsis, Rhodococcus, and Williamsia), Proteobacteria (Pseudomonas and Sphingobium), and Firmicutes (Staphylococcus). We found some clear differences in bacterial composition and relative abundance among development stages; overall, Firmicutes and Proteobacteria increased, but Actinobacteria decreased, through development. Finally, the bacterial microbiotas of the bugs' anterior midgut, posterior midgut, and hindgut were sharply distinct.

CONCLUSIONS/SIGNIFICANCE: Our results identify the 'bacterial core set' of T. sordida and reveal important gut microbiota differences among development stages-particularly between 1st-3rd stage nymphs and adults. Further, we show that, within any given development stage, the vectors' gut cannot be regarded as a single homogeneous environment. Cultivable, non-pathogenic 'core' bacterial species may now be tested as candidates for paratransgenic control of T. cruzi transmission by T. sordida.}, } @article {pmid30138339, year = {2018}, author = {Whitfield-Cargile, CM and Chamoun-Emanuelli, AM and Cohen, ND and Richardson, LM and Ajami, NJ and Dockery, HJ}, title = {Differential effects of selective and non-selective cyclooxygenase inhibitors on fecal microbiota in adult horses.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0202527}, pmid = {30138339}, issn = {1932-6203}, mesh = {4-Butyrolactone/administration & dosage/adverse effects/analogs & derivatives ; Adult ; Animals ; Anti-Inflammatory Agents, Non-Steroidal/*administration & dosage/adverse effects ; Cyclooxygenase 2/genetics ; Cyclooxygenase 2 Inhibitors/*administration & dosage/adverse effects ; Feces/microbiology ; Horses/microbiology ; Humans ; Metagenome/drug effects ; Microbiota/*drug effects ; Phenylbutazone/administration & dosage/adverse effects ; RNA, Ribosomal, 16S/*genetics ; Sulfones/administration & dosage/adverse effects ; }, abstract = {Non-steroidal anti-inflammatory drugs (NSAIDs) are routinely used in both veterinary and human medicine. Gastrointestinal injury is a frequent adverse event associated with NSAID use and evidence suggests that NSAIDs induce gastrointestinal microbial imbalance (i.e., dysbiosis) in both animals and people. It is unknown, however, whether cyclooxygenase (COX)-2-selective NSAIDs induce dysbiosis, or if this phenomenon occurs in horses administered any class of NSAIDs. Therefore, our objectives were to determine whether the composition and diversity of the fecal microbiota of adult horses were altered by NSAID use, and whether these effects differed between non-selective and COX-2-selective NSAIDs. Twenty-five adult horses were randomly assigned to 1 of 3 groups: control (n = 5); phenylbutazone (n = 10); or, firocoxib (n = 10). Treatments were administered for 10 days. Fecal samples were collected every 5 days for 25 days. DNA was extracted from feces and the 16S rRNA gene amplified and sequenced to determine the composition of the microbiota and the inferred metagenome. While the fecal microbiota profile of the control group remained stable over time, the phenylbutazone and firocoxib groups had decreased diversity, and alteration of their microbiota profiles was most pronounced at day 10. Similarly, there were clear alterations of the inferred metagenome at day 10 compared to all other days, indicating that use of both non-selective and selective COX inhibitors resulted in temporary alterations of the fecal microbiota and inferred metagenome. Dysbiosis associated with NSAID administration is clinically relevant because dysbiosis has been associated with several important diseases of horses including abdominal pain (colic), colitis, enteric infections, and laminitis.}, } @article {pmid30137571, year = {2019}, author = {Chen, WL and Tang, SGH and Jahromi, MF and Candyrine, SCL and Idrus, Z and Abdullah, N and Liang, JB}, title = {Metagenomics analysis reveals significant modulation of cecal microbiota of broilers fed palm kernel expeller diets.}, journal = {Poultry science}, volume = {98}, number = {1}, pages = {56-68}, doi = {10.3382/ps/pey366}, pmid = {30137571}, issn = {1525-3171}, mesh = {Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Arecaceae/chemistry ; Cecum/*microbiology ; Chickens/*microbiology ; Diet/veterinary ; Firmicutes/isolation & purification ; Gastrointestinal Microbiome/*drug effects/genetics ; Lactobacillus/isolation & purification ; Male ; *Metagenome ; Oligosaccharides/pharmacology ; RNA, Ribosomal, 16S ; }, abstract = {The potential use of palm kernel expeller (PKE) as an alternative energy source in broiler diets is limited by the high fiber content. Although enzymatic treatment could alleviate the fiber component and increase the nutritive value of PKE, this apparent improvement is not reflected in the growth response of birds fed with the treated-PKE. As chicken's ceca are the most heavily populated with microflora within their gastrointestinal tract, it was hypothesized that any modulation of the intestinal environment by dietary treatments should be reflected by the composition and activities of the cecal microflora. There is a correlation between cecal microbiota composition and the efficiency of the host to extract energy from the diet and to deposit that energy into improved feed conversion ratio. At present, little is known about the changes on cecal microflora of broilers fed with PKE diets. Hence, this study was designed to assess the effects of feeding different forms of PKE; namely untreated PKE (UPKE), enzyme-treated PKE (EPKE), and oligosaccharides extracted from PKE (OligoPKE), on the cecal microbiota of broiler chickens at 14 d old (day 14) and 28 d old (day 28) using 16S rRNA gene high-throughput next-generation sequencing method. The results showed that temporal changes in cecal microbiota of broiler chickens were evident on day 14 and day 28. The relative abundance of phylum Firmicutes, known to be involved in nutrient uptake and absorption in both age groups was higher in the UPKE as compared to EPKE group. In addition, supplementation of OligoPKE increased (P < 0.05) the relative abundance of Lactobacillus on both D14 and D28, signifying its effect as prebiotics in enhancing growth of indigenous Lactobacillus. Our results showed that cecal microbiota was significantly modulated by dietary treatments and that the lower relative abundance of phylum Firmicutes in chickens fed with EPKE could be a reason why broiler chickens fed with EPKE of higher metabolizable energy (ME) content did not show improvement in their growth performance.}, } @article {pmid30137359, year = {2018}, author = {Li, X and Liang, S and Xia, Z and Qu, J and Liu, H and Liu, C and Yang, H and Wang, J and Madsen, L and Hou, Y and Li, J and Jia, H and Kristiansen, K and Xiao, L}, title = {Establishment of a Macaca fascicularis gut microbiome gene catalog and comparison with the human, pig, and mouse gut microbiomes.}, journal = {GigaScience}, volume = {7}, number = {9}, pages = {}, pmid = {30137359}, issn = {2047-217X}, mesh = {Animals ; Bacteria/*classification/*genetics ; Gastrointestinal Microbiome/*genetics ; *Genes, Bacterial ; Humans ; Macaca fascicularis ; Mice ; Swine ; }, abstract = {Macaca fascicularis, the cynomolgus macaque, is a widely used model in biomedical research and drug development as its genetics and physiology are close to those of humans. Detailed information on the cynomolgus macaque gut microbiota, the functional interplay between the gut microbiota and host physiology, and possible similarities to humans and other mammalians is very limited. The aim of this study was to construct the first cynomolgus macaque gut microbial gene catalog and compare this catalog to the human, pig, and mouse gut microbial gene catalogs. We performed metagenomic sequencing on fecal samples from 20 cynomolgus macaques and identified 1.9 million non-redundant bacterial genes of which 39.49% and 25.45% are present in the human and pig gut bacterial gene catalogs, respectively, whereas only 0.6% of the genes are present in the mouse gut bacterial gene catalog. By contrast, at the functional levels, more than 76% Kyoto Encyclopedia of Genes and Genomes orthologies are shared between the gut microbiota of all four mammalians. Thirty-two highly abundant bacterial genera could be defined as core genera of these mammalians. We demonstrated significant differences in the composition and functional potential of the gut microbiota as well as in the distribution of predicted bacterial phage sequences in cynomolgus macaques fed either a low-fat/high-fiber diet or a high-fat/low-fiber diet. Interestingly, the gut microbiota of cynomolgus macaques fed the high-fat/low-fiber diet became more similar to the gut microbiota of humans.}, } @article {pmid30136922, year = {2018}, author = {Cornet, L and Bertrand, AR and Hanikenne, M and Javaux, EJ and Wilmotte, A and Baurain, D}, title = {Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures.}, journal = {Microbial genomics}, volume = {4}, number = {9}, pages = {}, pmid = {30136922}, issn = {2057-5858}, mesh = {Antarctic Regions ; Arctic Regions ; Cyanobacteria/*classification/*genetics/isolation & purification ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cyanobacteria form one of the most diversified phyla of Bacteria. They are important ecologically as primary producers, for Earth evolution and biotechnological applications. Yet, Cyanobacteria are notably difficult to purify and grow axenically, and most strains in culture collections contain heterotrophic bacteria that were probably associated with Cyanobacteria in the environment. Obtaining cyanobacterial DNA without contaminant sequences is thus a challenging and time-consuming task. Here, we describe a metagenomic pipeline that enables the easy recovery of genomes from non-axenic cultures. We tested this pipeline on 17 cyanobacterial cultures from the BCCM/ULC public collection and generated novel genome sequences for 12 polar or subpolar strains and three temperate ones, including three early-branching organisms that will be useful for phylogenomics. In parallel, we assembled 31 co-cultivated bacteria (12 nearly complete) from the same cultures and showed that they mostly belong to Bacteroidetes and Proteobacteria, some of them being very closely related in spite of geographically distant sampling sites.}, } @article {pmid30135468, year = {2019}, author = {Orkin, JD and Campos, FA and Myers, MS and Cheves Hernandez, SE and Guadamuz, A and Melin, AD}, title = {Seasonality of the gut microbiota of free-ranging white-faced capuchins in a tropical dry forest.}, journal = {The ISME journal}, volume = {13}, number = {1}, pages = {183-196}, pmid = {30135468}, issn = {1751-7370}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Cebus/*microbiology ; Costa Rica ; Diet ; Feces/*microbiology ; *Forests ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Metagenomics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S ; *Seasons ; Tropical Climate ; }, abstract = {Research on the gut microbiota of free-ranging mammals is offering new insights into dietary ecology. However, for free-ranging primates, little information is available for how microbiomes are influenced by ecological variation through time. Primates inhabiting seasonal tropical dry forests undergo seasonally specific decreases in food abundance and water availability, which have been linked to adverse health effects. Throughout the course of a seasonal transition in 2014, we collected fecal samples from three social groups of free-ranging white-faced capuchin monkeys (Cebus capucinus imitator) in Sector Santa Rosa, Área de Conservación Guanacaste, Costa Rica. 16S rRNA sequencing data reveal that unlike other primates, the white-faced capuchin monkey gut is dominated by Bifidobacterium and Streptococcus. Linear mixed effects models indicate that abundances of these genera are associated with fluctuating availability and consumption of fruit and arthropods, whereas beta diversity clusters by rainfall season. Whole shotgun metagenomics revealed that the capuchin gut is dominated by carbohydrate-binding modules associated with digestion of plant polysaccharides and chitin, matching seasonal dietary patterns. We conclude that rainfall and diet are associated with the diversity, composition, and function of the capuchin gut microbiome. Additionally, microbial fluctuations are likely contributing to nutrient uptake and the health of wild primate populations.}, } @article {pmid30134786, year = {2018}, author = {Denning, NL and Prince, JM}, title = {Neonatal intestinal dysbiosis in necrotizing enterocolitis.}, journal = {Molecular medicine (Cambridge, Mass.)}, volume = {24}, number = {1}, pages = {4}, pmid = {30134786}, issn = {1528-3658}, mesh = {Animals ; Anti-Bacterial Agents/therapeutic use ; *Dysbiosis/chemically induced ; *Enterocolitis, Necrotizing/immunology/microbiology ; *Gastrointestinal Microbiome ; Histamine H2 Antagonists/therapeutic use ; Humans ; Infant, Newborn ; Toll-Like Receptors/immunology ; }, abstract = {Necrotizing Enterocolitis (NEC) is one of the most devastating gastrointestinal diseases in neonates, particularly among preterm infants in whom surgical NEC is the leading cause of morbidity. NEC pathophysiology occurs in the hyper-reactive milieu of the premature gut after bacterial colonization. The resultant activation of the TLR4 pathway appears to be a strongly contributing factor. Advancements in metagenomics may yield new clarity to the relationship between the neonatal intestinal microbiome and the development of NEC. After a century without effective directed treatments, microbiome manipulation offers a promising therapeutic target for the prevention and treatment of this devastating disease.}, } @article {pmid30133062, year = {2018}, author = {Bracewell-Milnes, T and Saso, S and Nikolaou, D and Norman-Taylor, J and Johnson, M and Thum, MY}, title = {Investigating the effect of an abnormal cervico-vaginal and endometrial microbiome on assisted reproductive technologies: A systematic review.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {80}, number = {5}, pages = {e13037}, doi = {10.1111/aji.13037}, pmid = {30133062}, issn = {1600-0897}, mesh = {Animals ; Cervix Uteri/*microbiology ; Endometrium/*microbiology ; Female ; Humans ; Infertility/*microbiology/therapy ; Metagenomics ; Microbiota/*physiology ; Reproductive Techniques, Assisted ; Vagina/*microbiology ; }, abstract = {The female reproductive tract has an active microbiome, and it is suggested that these microbes could influence the outcome of assisted reproductive technologies (ART). This systematic review aimed to assess the vaginal/uterine microbiome, specifically with regard to improving the outcome of ART. English peer-reviewed journals were searched for studies investigating the vaginal/uterine micriobiome and female reproductive tract, using PRISMA guidelines. Twenty-six studies were included, 19 studying the vaginal and seven investigating the uterine microbiome. Studies using culture-based technologies found an abnormal vaginal microbiome AVM was not associated with ART outcome. However, studies using sequence-based technologies found an abnormal vaginal microbiome had a negative effect on ART. An abnormal uterine microbiome impacted ART outcome in all of the studies which used culture-based methods and the most extensive of the two studies using metagenomic sequencing. This review has revealed a lack of translational data relating an abnormal vaginal/uterine microbiome to ART outcomes, with inconsistencies between the results of the different studies. Therefore the nature of the relationship between the vaginal/uterine microbiome and fertility remains unknown. As we better characterize this relationship using modern metagenomic techniques, the potential to manipulate the female reproductive tract microbiome to improve ART could be a reality.}, } @article {pmid30131068, year = {2018}, author = {Jiao, S and Chen, W and Wang, J and Du, N and Li, Q and Wei, G}, title = {Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {146}, pmid = {30131068}, issn = {2049-2618}, mesh = {Archaea/*classification/genetics/isolation & purification/metabolism ; Bacteria/*classification/genetics/isolation & purification/metabolism ; Biodiversity ; Fungi/*classification/genetics/isolation & purification/metabolism ; Metagenomics ; Nutrients/metabolism ; Phylogeny ; Plant Roots/microbiology ; Sequence Analysis, DNA ; Soil/chemistry ; Soil Microbiology ; Trees/*growth & development/microbiology ; }, abstract = {BACKGROUND: Soil microbiomes play an important role in the services and functioning of terrestrial ecosystems. However, little is known of their vertical responses to restoration process and their contributions to soil nutrient cycling in the subsurface profiles. Here, we investigated the community assembly of soil bacteria, archaea, and fungi along vertical (i.e., soil depths of 0-300 cm) and horizontal (i.e., distance from trees of 30-90 cm) profiles in a chronosequence of reforestation sites that represent over 30 years of restoration.

RESULTS: In the superficial layers (0-80 cm), bacterial and fungal diversity decreased, whereas archaeal diversity increased with increasing soil depth. As reforestation proceeded over time, the vertical spatial variation in bacterial communities decreased, while that in archaeal and fungal communities increased. Vertical distributions of the soil microbiomes were more related to the variation in soil properties, while their horizontal distributions may be driven by a gradient effect of roots extending from the tree. Bacterial and archaeal beta-diversity were strongly related to multi-nutrient cycling in the soil, respectively, playing major roles in deep and superficial layers.

CONCLUSIONS: Taken together, these results reveal a new perspective on the vertical and horizontal spatial variation in soil microbiomes at the fine scale of single trees. Distinct response patterns underpinned the contributions of soil bacteria, archaea, and fungi as a function of subsurface nutrient cycling during the reforestation of ex-arable land.}, } @article {pmid30129704, year = {2018}, author = {Macher, JN and Vivancos, A and Piggott, JJ and Centeno, FC and Matthaei, CD and Leese, F}, title = {Comparison of environmental DNA and bulk-sample metabarcoding using highly degenerate cytochrome c oxidase I primers.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1456-1468}, doi = {10.1111/1755-0998.12940}, pmid = {30129704}, issn = {1755-0998}, mesh = {Aquatic Organisms/classification/*genetics ; DNA/chemistry/*genetics/isolation & purification ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*genetics ; Electron Transport Complex IV/*genetics ; *Fresh Water ; Metagenomics/*methods ; New Zealand ; Rivers ; }, abstract = {Freshwater biodiversity provides important ecosystem services and is at the core of water quality monitoring worldwide. To assess freshwater biodiversity, genetic methods such as metabarcoding are increasingly used as they are faster and allow better taxonomic resolution than manual identification methods. Either sampled organisms are used directly for "bulk metabarcoding," or water is filtered and the extracted environmental DNA serves as a proxy for biodiversity via "eDNA metabarcoding." Despite the advantages of both methods, questions remain regarding their comparability and applicability for routine biomonitoring and stressor impact assessment. Therefore, we compared metabarcoding results from bulk and eDNA samples taken from 19 streams spanning a wide gradient of farming intensities in New Zealand. We performed PCR with highly degenerate cytochrome c oxidase I primers and sequenced libraries on an Illumina MiSeq. The inferred community composition differed strongly between the two methods. More taxa were captured by eDNA than bulk-sample metabarcoding (5,819 vs. 1,483), but more of the commonly used invertebrate bioindicator taxa (mayflies, stoneflies and caddisflies) were found in bulk (47) than eDNA samples (37). Catchment-wide and local land use impacts on communities were detected better by eDNA metabarcoding, especially for non-metazoan taxa. Our findings imply that bulk-sample metabarcoding resembles classical freshwater biomonitoring approaches better, as more indicator macroinvertebrate taxa are captured. However, eDNA metabarcoding might be better suited to infer the impact of stressors on stream ecosystems at larger scales, as many new and potentially more informative taxa are registered. We therefore suggest exploring both methods in future assessments of stream biodiversity.}, } @article {pmid30128993, year = {2018}, author = {Mitchell, AB and Glanville, AR}, title = {Introduction to Techniques and Methodologies for Characterizing the Human Respiratory Virome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1838}, number = {}, pages = {111-123}, doi = {10.1007/978-1-4939-8682-8_9}, pmid = {30128993}, issn = {1940-6029}, mesh = {Animals ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Metagenomics ; *Microbiota ; Polymerase Chain Reaction ; Respiratory Tract Infections/*virology ; Sequence Analysis, DNA ; Viruses/*genetics ; }, abstract = {There have been great advances in the methodologies available for the detection of respiratory viruses. Accompanying this, our knowledge surrounding the impact of these viruses has also made a great leap forward. We have come a long way from the once commonly accepted belief that the lower respiratory tract was sterile and that the detection of any microbial species must represent a breach in host defence and likely be associated with symptomatic infection. With the advent of molecular detection techniques and improvements in sequencing-based methodologies to make these tools more accessible and cost effective, we now know that there is an abundant and diverse ecosystem within the lower-respiratory tract. This chapter will outline the clinical impact of the human respiratory virome, techniques for sampling the lower respiratory tract, the evolution of the diagnostic tools available, and the current limitations in our instruments and knowledge in this area. The human respiratory virome is an exciting new area of research that will continue to grow with the aid of the methodologies outlined in the following chapters and the advent of even more efficient tools in the future.}, } @article {pmid30128992, year = {2018}, author = {Mayo-Muñoz, D}, title = {Viral Genome Isolation from Human Faeces for Succession Assessment of the Human Gut Virome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1838}, number = {}, pages = {97-108}, doi = {10.1007/978-1-4939-8682-8_8}, pmid = {30128992}, issn = {1940-6029}, mesh = {Feces/*virology ; *Gastrointestinal Microbiome ; *Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Metagenomics/methods ; Whole Genome Sequencing ; }, abstract = {Despite the important role of the microbiota in the human gastrointestinal tract (GIT) and its impact on life-long health, the successional process through which this microbial community develops during infancy is still poorly understood. Specially, little is known about how the amount and type of viruses present in the GIT, i.e., the virome, varies throughout this period and about the role this collection of viruses may play in the assembly of the GIT microbiota.The patterns of taxonomic change of the GIT viral community can be analyzed in a birth cohort of infants during the first year of life. The present chapter presents a detailed protocol for the isolation and extraction of viral nucleic acids from collected human faecal samples, whole genome amplification (WGA) using phi29 DNA polymerase and preparation for sequencing through high-throughput 454 pyrosequencing. The sequencing data can be posteriorly used for taxonomic classification in order to establish the composition of the virome present in each sample and to assess the process of viral dynamics through time.}, } @article {pmid30128990, year = {2018}, author = {Kramná, L and Cinek, O}, title = {Virome Sequencing of Stool Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1838}, number = {}, pages = {59-83}, doi = {10.1007/978-1-4939-8682-8_6}, pmid = {30128990}, issn = {1940-6029}, mesh = {Bacteriophages/*classification/*genetics/isolation & purification ; DNA, Viral/genetics/isolation & purification ; Feces/*virology ; *Gastrointestinal Microbiome ; Gene Library ; *Metagenome ; *Metagenomics/methods ; Polymerase Chain Reaction ; RNA, Viral/genetics/isolation & purification ; Ultracentrifugation ; }, abstract = {Next-generation sequencing has opened avenues to studying complex populations such as the bacteriome (all bacteria), mycobiome (all fungi), and virome (all viruses in a given sample). Viromes are less often investigated as compared to bacteriomes. The reasons are mostly methodological: because no common pan-viral sequence signature exists, metagenomic sequencing remains the only option. This brings about the need of laborious virus enrichment, multiple signal amplification steps with virtually no possibility of interim quality control, and complicated bioinformatic analysis of the ensuing sequence data. Nevertheless, over the past decade virome sequencing has been enormously successful in identifying new agents in human and animal diseases, and in characterizing viruses in various ecological niches. Recently, virome sequencing has been also employed in studies of non-infectious diseases, which has brought about new challenges of sensitivity, costs, and reproducibility in testing of large sets of samples. Here, we present a detailed protocol that has been utilized in virome studies where hundreds of samples had to be reliably tested in order to assess the association of the stool virome with susceptibility to type 1 diabetes, a non-infectious autoimmune disease.}, } @article {pmid30128989, year = {2018}, author = {Castro-Mejía, JL and Deng, L and Vogensen, FK and Reyes, A and Nielsen, DS}, title = {Extraction and Purification of Viruses from Fecal Samples for Metagenome and Morphology Analyses.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1838}, number = {}, pages = {49-57}, doi = {10.1007/978-1-4939-8682-8_5}, pmid = {30128989}, issn = {1940-6029}, mesh = {Feces/*virology ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; Microscopy, Fluorescence ; Ultracentrifugation ; Viruses/*genetics/*isolation & purification/ultrastructure ; }, abstract = {The human enteric virome consists of endogenous retro elements and viruses that infect the host and members of the gut microbiome (GM). Mounting evidence suggests that the gut virome plays a central role in maintaining homeostasis and via the GM influences immunology of the host. To thoroughly characterize the gut virome, it is often very useful to first separate and concentrate extracellular viral-like particles (eVLPs) enabling an integrative characterization of them. Here, we describe a detailed protocol for extraction and concentration of the viral fraction from fecal samples based on a polyethylene glycol precipitation (PEG) approach. These procedures maximize the yields of eVLPs (and their DNA) with high purity well suited for down-stream analysis such as quantification and morphological assessment, determination of phage-host pairs as well as virome sequencing.}, } @article {pmid30128756, year = {2018}, author = {Mukhtar, S and Mirza, BS and Mehnaz, S and Mirza, MS and Mclean, J and Malik, KA}, title = {Impact of soil salinity on the microbial structure of halophyte rhizosphere microbiome.}, journal = {World journal of microbiology & biotechnology}, volume = {34}, number = {9}, pages = {136}, pmid = {30128756}, issn = {1573-0972}, support = {Project # HEC (FD/2012/1843)//Higher Education Commission, Pakistan/ ; Project # 5-9/PAS/2012/969//Pakistan Academy of Sciences/ ; }, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; DNA, Bacterial ; Ecosystem ; Metagenomics ; Microbiota/genetics/*physiology ; Pakistan ; Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; *Salinity ; Salt-Tolerant Plants/classification/*microbiology ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The rhizosphere microbiome plays a significant role in the life of plants in promoting plant survival under adverse conditions. However, limited information is available about microbial diversity in saline environments. In the current study, we compared the composition of the rhizosphere microbiomes of the halophytes Urochloa, Kochia, Salsola, and Atriplex living in moderate and high salinity environments (Khewra salt mines; Pakistan) with that of the non-halophyte Triticum. Soil microbiomes analysis using pyrosequencing of 16S rRNA gene indicated that Actinobacteria were dominant in saline soil samples whereas Proteobacteria predominated in non-saline soil samples. Firmicutes, Acidobacteria, Bacteriodetes and Thaumarchaeota were predominant phyla in saline and non-saline soils, whereas Cyanobacteria, Verrucomicrobia, Gemmatimonadetes and the unclassified WPS-2 were less abundant. Sequences from Euryarchaeota, Ignavibacteriae, and Nanohaloarchaeota were identified only from the rhizosphere of halophytes. Dominant halophilic bacteria and archaea identified in this study included Agrococcus, Armatimonadetes gp4, Halalkalicoccus, Haloferula and Halobacterium. Our analysis showed that increases in soil salinity correlated with significant differences in the alpha and beta diversity of the microbial communities across saline and non-saline soil samples. Having a complete inventory of the soil bacteria from different saline environments in Pakistan will help in the discovery of potential inoculants for crops growing on salt-affected land.}, } @article {pmid30127329, year = {2019}, author = {Cui, YF and Wang, FJ and Yu, L and Ye, HH and Yang, GB}, title = {Metagenomic comparison of the rectal microbiota between rhesus macaques (Macaca mulatta) and cynomolgus macaques (Macaca fascicularis).}, journal = {Zoological research}, volume = {40}, number = {2}, pages = {89-93}, pmid = {30127329}, issn = {2095-8137}, mesh = {Animals ; Bacteria/classification/*genetics ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Genomics ; Macaca fascicularis/*microbiology ; Macaca mulatta/*microbiology ; Rectum/*microbiology ; Species Specificity ; }, abstract = {Rhesus macaques (Macaca mulatta) and cynomolgus macaques (Macaca fascicularis) are frequently used in establishing animal models for human diseases. To determine the differences in gut microbiota between these species, rectal swabs from 20 rhesus macaques and 21 cynomolgus macaques were collected, and the microbial composition was examined by deep sequencing of the 16S rRNA gene. We found that the rectal microbiota of cynomolgus macaques exhibited significantly higher alpha diversity than that of rhesus macaques, although the observed number of operational taxonomic units (OTUs) was almost the same. The dominant taxa at both the phylum and genus levels were similar between the two species, although the relative abundances of these dominant taxa were significantly different between them. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed significant differences in the functional components between the microbiota of the two species, in particular the lipopolysaccharide (LPS) synthesis proteins. The above data indicated significant differences in microbial composition and function between these two closely related macaque species, which should be taken into consideration in the future selection of these animals for disease models.}, } @article {pmid30126689, year = {2019}, author = {Schiattarella, GG and Sannino, A and Esposito, G and Perrino, C}, title = {Diagnostics and therapeutic implications of gut microbiota alterations in cardiometabolic diseases.}, journal = {Trends in cardiovascular medicine}, volume = {29}, number = {3}, pages = {141-147}, doi = {10.1016/j.tcm.2018.08.003}, pmid = {30126689}, issn = {1873-2615}, mesh = {Animals ; Anti-Bacterial Agents/administration & dosage ; Bacteria/drug effects/enzymology/*metabolism ; Cardiovascular Diseases/diagnosis/*microbiology/therapy ; Diet, Healthy ; Dysbiosis ; Enzyme Inhibitors/therapeutic use ; Exercise ; *Gastrointestinal Microbiome/drug effects ; Host-Pathogen Interactions ; Humans ; Metabolic Diseases/diagnosis/*microbiology/therapy ; Prebiotics/administration & dosage ; Probiotics/administration & dosage ; Risk Reduction Behavior ; }, abstract = {Alterations in gut microbiota composition and its metabolic activity are emerging as one of the most powerful determinants of cardiovascular disease. Although our knowledge of the precise molecular mechanisms by which gut microbiota influences cardiometabolic homeostasis is still limited, a growing body of knowledge has recently been uncovered about the potential modulation of microbiome for cardiovascular diagnostic and therapeutic aspects. The multitude of interactions between the microorganisms inhabiting the digestive tract and the host has been recognized crucial in the development and progression of atherosclerosis, obesity, diabetes and hypertension. Here, we summarize the role of gut microbiota in host physiology as well as in the pathophysiology of the most common cardio-metabolic disorders, discussing the potential therapeutic opportunities offered by interventions aimed at modifying microbiome composition and activity.}, } @article {pmid30126456, year = {2018}, author = {Milani, C and Casey, E and Lugli, GA and Moore, R and Kaczorowska, J and Feehily, C and Mangifesta, M and Mancabelli, L and Duranti, S and Turroni, F and Bottacini, F and Mahony, J and Cotter, PD and McAuliffe, FM and van Sinderen, D and Ventura, M}, title = {Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {145}, pmid = {30126456}, issn = {2049-2618}, mesh = {Bacteriophages/*classification/genetics/isolation & purification ; Computational Biology/*methods/standards ; Feces/*virology ; Female ; Gastrointestinal Microbiome ; Genotype ; Humans ; Infant, Newborn ; Male ; Metagenomics/*methods/standards ; Mothers ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {BACKGROUND: Despite the relevance of viral populations, our knowledge of (bacterio) phage populations, i.e., the phageome, suffers from the absence of a "gold standard" protocol for viral DNA extraction with associated in silico sequence processing analyses. To overcome this apparent hiatus, we present here a comprehensive performance evaluation of various protocols and propose an optimized pipeline that covers DNA extraction, sequencing, and bioinformatic analysis of phageome data.

RESULTS: Five widely used protocols for viral DNA extraction from fecal samples were tested for their performance in removal of non-viral DNA. Moreover, we developed a novel bioinformatic platform, METAnnotatorX, for metagenomic dataset analysis. This in silico tool facilitates a range of read- and assembly-based analyses, including taxonomic profiling using an iterative multi-database pipeline, classification of contigs at genus and species level, as well as functional characterizations of reads and assembled data. Performances of METAnnotatorX were assessed through investigation of seven mother-newborn pairs, leading to the identification of shared phage genotypes, of which two were genomically decoded and characterized. METAnnotatorX was furthermore employed to evaluate a protocol for the identification of contaminant non-viral DNA in sequenced datasets and was exploited to determine the amount of metagenomic data needed for robust evaluation of human adult-derived (fecal) phageomes.

CONCLUSIONS: Results obtained in this study demonstrate that a comprehensive pipeline for analysis of phageomes will be pivotal for future explorations of the ecology of phages in the gut environment as well as for understanding their impact on the physiology and bacterial community kinetics as players of dysbiosis and homeostasis in the gut microbiota.}, } @article {pmid30126153, year = {2018}, author = {Dix, C and Wright, O}, title = {Bioavailability of a Novel Form of Microencapsulated Bovine Lactoferrin and Its Effect on Inflammatory Markers and the Gut Microbiome: A Pilot Study.}, journal = {Nutrients}, volume = {10}, number = {8}, pages = {}, pmid = {30126153}, issn = {2072-6643}, mesh = {Adolescent ; Adult ; Aged ; Animals ; Biological Availability ; Biomarkers/blood ; Cattle ; Cross-Over Studies ; Dietary Supplements ; Dose-Response Relationship, Drug ; Double-Blind Method ; Feces/chemistry/microbiology ; *Gastrointestinal Microbiome ; Humans ; Intestinal Absorption ; Lactoferrin/administration & dosage/*pharmacokinetics ; Male ; Middle Aged ; Pilot Projects ; T-Lymphocytes/classification ; Young Adult ; }, abstract = {Bovine lactoferrin, extracted from milk or whey, is used in a range of products to enhance immunity and support digestive health, iron absorption, and homeostasis. This study examined the absorption and effect of Progel (Brisbane, Queensland, Australia) microencapsulated bovine lactoferrin (Inferrin[TM], Bega Bionutrients, Victoria, Australia) on immune markers and the microbiome. A double-blind randomised, cross-over trial was conducted with 12 healthy males randomised to one of two doses, equivalent to 200 mg or 600 mg lactoferrin, for two four-week supplementation arms, with a two-week washout period. Subjects received either standard bovine lactoferrin or Inferrin[TM] for each arm. Baseline and post each trial arm, CD69+ activation on CD4+ and CD8+ cells was analysed, bovine and human lactoferrin contents of faecal and serum samples were reported, and the gut microbiome was analysed using 16S sequencing and metagenomic sequencing. The mean level of CD69+ activation on the CD4+ cells was lower after supplementation regardless of the form or dose of lactoferrin. This was statistically significant for the 200 mg dose. A higher level of bovine lactoferrin was found post-supplementation in those taking Inferrin[TM], although this was not statistically significant. Changes in phylum-level microbial community profiling were detected post-supplementation in the second trial arm, particularly in those receiving Inferrin[TM]. Metagenomic sequencing showed changes in the volumes of the top 100 species of bacteria present before and after all treatment arms. Results suggest that lactoferrin supplementation may have beneficial effects on the microbiome and immune system, and that the use of Inferrin[TM] improves absorption. Larger detailed studies are needed to ascertain the potential positive effects of bovine lactoferrin supplementation.}, } @article {pmid30124863, year = {2018}, author = {McGrath, C}, title = {Up in the Air: The Emerging Science of Dust and Sandstorm Microbes.}, journal = {Genome biology and evolution}, volume = {10}, number = {8}, pages = {2008-2009}, pmid = {30124863}, issn = {1759-6653}, mesh = {*Dust ; Health ; Humans ; Metagenomics ; *Microbiota ; Soil Microbiology ; }, } @article {pmid30124822, year = {2018}, author = {Tas, N and Brandt, BW and Braster, M and van Breukelen, BM and Röling, WFM}, title = {Subsurface landfill leachate contamination affects microbial metabolic potential and gene expression in the Banisveld aquifer.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {10}, pages = {}, doi = {10.1093/femsec/fiy156}, pmid = {30124822}, issn = {1574-6941}, mesh = {Carbon-Carbon Lyases/genetics ; Ecosystem ; Environmental Monitoring ; Gene Expression/*drug effects ; Groundwater/chemistry/*microbiology ; Hydrocarbons, Aromatic/analysis/metabolism/*pharmacology ; Microbial Consortia/*drug effects ; Netherlands ; Phosphates/analysis ; Water Pollutants, Chemical/analysis/metabolism/*pharmacology ; }, abstract = {Microbial communities in groundwater ecosystems can develop the capacity to degrade complex mixtures of chemicals resulting from pollution by landfill leachate. Monitoring this natural attenuation requires insight into the metabolic potential and activity of microbial communities. We contrasted the metagenomes and metatranscriptomes from a leachate-polluted aquifer downstream of the Banisveld (the Netherlands) landfill with uncontaminated groundwater, which revealed changes in microbial genomic content and activity. Banisveld landfill leachate contains mono-aromatic hydrocarbons and the assessment of natural attenuation of these compounds in the aquifer had been a focal point of research. In the contaminated groundwater, active microbial functions were the ones involved in degradation of complex carbon substrates and organic pollutants. We found that benzylsuccinate synthase genes-involved in the catabolism of toluene-were highly expressed close to the source of contamination, confirming the ongoing natural attenuation of organic mono-aromatic hydrocarbon pollution in this aquifer. Additionally, metatranscriptomes were indicative of phosphorus limitation that can constrain total microbial activity and agree with the low phosphate concentrations (<0.4 μmol/L) in this aquifer. Through the application of metagenomics and metatranscriptomics, we were able to determine functional potential and expression patterns to assess the natural attenuation processes and constraints on microbial communities.}, } @article {pmid30123190, year = {2018}, author = {Roscini, L and Tristezza, M and Corte, L and Colabella, C and Perrotta, C and Rampino, P and Robert, V and Vu, D and Cardinali, G and Grieco, F}, title = {Early Ongoing Speciation of Ogataea uvarum Sp. Nov. Within the Grape Ecosystem Revealed by the Internal Variability Among the rDNA Operon Repeats.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1687}, pmid = {30123190}, issn = {1664-302X}, abstract = {A yeast strain was isolated during a study on vineyard-associated yeast strains from Apulia in Southern Italy. ITS and LSU D1/D2 rDNA sequences showed this strain not to belong to any known species and was described as the type strain of Ogataea uvarum sp. nov., a close relative of O. philodendri. Several secondary peaks appeared in the sequences, suggesting internal heterogeneity among the copies of the rDNA. This hypothesis was tested by sequencing single clones of the marker region. The analyses showed different levels of variability throughout the operon with differences between the rRNA encoding genes and the internally transcribed regions. O. uvarum and O. philodendri share high frequency variants, i.e., variants frequently found in many clones, whereas there is a large variability of the low frequency polymorphisms, suggesting that the mechanism of homogenization is more active with the former than with the latter type of variation. These findings indicate that low frequency variants are detected in Sanger sequencing as secondary peaks whereas in Next Generation Sequencing (NGS) of metagenomics DNA would lead to an overestimate of the alpha diversity. For the first time in our knowledge, this investigation shed light on the variation of the copy number of the rDNA cistron during the yeast speciation process. These polymorphisms can be used to investigate on the processes occurring in these taxonomic markers during the separation of fungal species, it being a genetic process highly frequent in the complex microbial ecosystem existing in grape, must and wine.}, } @article {pmid30122883, year = {2018}, author = {Zhao, Y and Mao, YF and Tang, YS and Ni, MZ and Liu, QH and Wang, Y and Feng, Q and Peng, JH and Hu, YY}, title = {Altered oral microbiota in chronic hepatitis B patients with different tongue coatings.}, journal = {World journal of gastroenterology}, volume = {24}, number = {30}, pages = {3448-3461}, pmid = {30122883}, issn = {2219-2840}, mesh = {Adult ; Bacteria/genetics/*isolation & purification/metabolism ; Case-Control Studies ; DNA, Viral/isolation & purification ; Female ; Gastrointestinal Microbiome/*physiology ; Healthy Volunteers ; Hepatitis B virus/genetics/*isolation & purification ; Hepatitis B, Chronic/diagnosis/metabolism/*microbiology ; Humans ; Male ; Medicine, Chinese Traditional/methods ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Tongue/*microbiology ; }, abstract = {AIM: To elucidate tongue coating microbiota and metabolic differences in chronic hepatitis B (CHB) patients with yellow or white tongue coatings.

METHODS: Tongue coating samples were collected from 53 CHB patients (28 CHB yellow tongue coating patients and 25 CHB white tongue coating patients) and 22 healthy controls. Microbial DNA was extracted from the tongue samples, and the bacterial 16S ribosomal RNA gene V3 region was amplified from all samples and sequenced with the Ion Torrent PGM™ sequencing platform according to the standard protocols. The metabolites in the tongue coatings were evaluated using a liquid chromatography-mass spectrometry (LC-MS) platform. Statistical analyses were then performed.

RESULTS: The relative compositions of the tongue coating microbiotas and metabolites in the CHB patients were significantly different from those of the healthy controls, but the tongue coating microbiota abundances and diversity levels were not significantly different. Compared with the CHB white tongue coating patients, the CHB yellow tongue coating patients had higher hepatitis B viral DNA (HBV-DNA) titers (median 21210 vs 500, respectively, P = 0.03) and a significantly lower level of Bacteroidetes (20.14% vs 27.93%, respectively, P = 0.013) and higher level of Proteobacteria (25.99% vs 18.17%, respectively, P = 0.045) in the microbial compositions at the phylum level. The inferred metagenomic pathways enriched in the CHB yellow tongue coating patients were mainly those involved in amino acid metabolism, which was consistent with the metabolic disorder. The abundances of bacteria from Bacteroidales at the order level were higher in the CHB white tongue coating patients (19.2% vs 27.22%, respectively, P = 0.011), whereas Neisseriales were enriched in the yellow tongue coating patients (21.85% vs 13.83%, respectively, P = 0.029). At the family level, the abundance of Neisseriaceae in the yellow tongue patients was positively correlated with the HBV-DNA level but negatively correlated with the S-adenosyl-L-methionine level.

CONCLUSION: This research illustrates specific clinical features and bacterial structures in CHB patients with different tongue coatings, which facilitates understanding of the traditional tongue diagnosis.}, } @article {pmid30121535, year = {2019}, author = {Bedoya, K and Coltell, O and Cabarcas, F and Alzate, JF}, title = {Metagenomic assessment of the microbial community and methanogenic pathways in biosolids from a municipal wastewater treatment plant in Medellín, Colombia.}, journal = {The Science of the total environment}, volume = {648}, number = {}, pages = {572-581}, doi = {10.1016/j.scitotenv.2018.08.119}, pmid = {30121535}, issn = {1879-1026}, mesh = {Colombia ; *Metagenome ; Methane/*biosynthesis ; *Microbiota/genetics ; Solid Waste/*analysis ; *Waste Disposal, Fluid ; Wastewater/*microbiology ; }, abstract = {Abundance and diversity of microbial communities in biosolids are variable and poorly studied in the tropics, and it is known that rainfall is one of the events that could affect the phylogenetic and functional microbial structure. In the present study, using NGS technics, we studied the microbial diversity as well as the methanogenesis pathway in one of the largest WWTP in Colombia. Besides, we sampled and analyzed biosolids from rainy season and dry season. Phylogenetic classification showed a predominance of bacteria in both samples and difference in the dominant groups depending on the rainfall season. Whereas Pseudomonas was the dominant bacteria in the dry season, Coprothermobacter was in the rainy season. Archaea abundance was higher in the rainy season (11.5%) doubling dry season proportion. The bioreactor biogas production and total solids content showed similar results between rainy and dry season at the sampling dates. The most abundant Archaea related with methanogenesis was Methanosaeta, which is a methanogenic microorganism that exclusively uses acetate to produce methane. Moreover, annotation of the methanogenic pathway in the metagenome showed abundance in genes encoding Acetyl-CoA synthetases (ACSS), an enzyme that catalyzes acetate activation. Our results suggest that the microbial diversity was stable among the two time points tested, rainy season and dry season; and, although there were changes in the microbial abundance of dominant bacterial species, anaerobic digester performance is not affected.}, } @article {pmid30120375, year = {2018}, author = {Goldsmith, DB and Kellogg, CA and Morrison, CL and Gray, MA and Stone, RP and Waller, RG and Brooke, SD and Ross, SW}, title = {Comparison of microbiomes of cold-water corals Primnoa pacifica and Primnoa resedaeformis, with possible link between microbiome composition and host genotype.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12383}, pmid = {30120375}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*genetics/*microbiology ; Bacteria/classification/genetics ; *Biodiversity ; Computational Biology/methods ; *Genotype ; Metagenome ; Metagenomics/methods ; *Microbiota ; Microsatellite Repeats ; }, abstract = {Cold-water corals provide critical habitats for a multitude of marine species, but are understudied relative to tropical corals. Primnoa pacifica is a cold-water coral prevalent throughout Alaskan waters, while another species in the genus, Primnoa resedaeformis, is widely distributed in the Atlantic Ocean. This study examined the V4-V5 region of the 16S rRNA gene after amplifying and pyrosequencing bacterial DNA from samples of these species. Key differences between the two species' microbiomes included a robust presence of bacteria belonging to the Chlamydiales order in most of the P. pacifica samples, whereas no more than 2% of any microbial community from P. resedaeformis comprised these bacteria. Microbiomes of P. resedaeformis exhibited higher diversity than those of P. pacifica, and the two species largely clustered separately in a principal coordinate analysis. Comparison of P. resedaeformis microbiomes from samples collected in two submarine canyons revealed a significant difference between locations. This finding mirrored significant genetic differences among the P. resedaeformis from the two canyons based upon population genetic analysis of microsatellite loci. This study presents the first report of microbiomes associated with these two coral species.}, } @article {pmid30119090, year = {2018}, author = {Koch, M}, title = {Probiotics and Evidence-based Medicine: To All Involved: We have a Problem.}, journal = {Journal of clinical gastroenterology}, volume = {52 Suppl 1, Proceedings from the 9th Probiotics, Prebiotics and New Foods, Nutraceuticals and Botanicals for Nutrition & Human and Microbiota Health Meeting, held in Rome, Italy from September 10 to 12, 2017}, number = {}, pages = {S4-S6}, doi = {10.1097/MCG.0000000000001106}, pmid = {30119090}, issn = {1539-2031}, mesh = {*Evidence-Based Medicine ; Humans ; Metagenome ; *Microbiota ; *Probiotics ; }, abstract = {The methods used to discern the structure (anatomy) and function (physiology) of the indigenous microbiota can be divided according to which aspect of the microbiota they can interrogate and are positioned accordingly. At the most basic level, methods can simply describe the community structure of the microbiota, that is, which taxa are present and in what relative amounts. Methods that investigate functional potential generally catalog the coding potential of individual members of the microbiota or the entire community (the metagenome). To measure function directly a catalog of the expressed microbial genes (the metatranscriptome) or the proteins or metabolites present in the microbiome environment must be generated. So, complexity in understanding the role of microbiota is quite rejecting the interested clinician. Evidence-based medicine can offer an answer suggesting strict definition of populations, measurement techniques, and external validity.}, } @article {pmid30118379, year = {2019}, author = {Ito, T and Sekizuka, T and Kishi, N and Yamashita, A and Kuroda, M}, title = {Conventional culture methods with commercially available media unveil the presence of novel culturable bacteria.}, journal = {Gut microbes}, volume = {10}, number = {1}, pages = {77-91}, pmid = {30118379}, issn = {1949-0984}, mesh = {Bacteria/classification/genetics/*growth & development/*isolation & purification ; *Bacteriological Techniques ; Culture Media ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Genome, Bacterial/genetics ; Humans ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Recent metagenomic analysis has revealed that our gut microbiota plays an important role in not only the maintenance of our health but also various diseases such as obesity, diabetes, inflammatory bowel disease, and allergy. However, most intestinal bacteria are considered 'unculturable' bacteria, and their functions remain unknown. Although culture-independent genomic approaches have enabled us to gain insight into their potential roles, culture-based approaches are still required to understand their characteristic features and phenotypes. To date, various culturing methods have been attempted to obtain these 'unculturable' bacteria, but most such methods require advanced techniques. Here, we have tried to isolate possible unculturable bacteria from a healthy Japanese individual by using commercially available media. A 16S rRNA (ribosomal RNA) gene metagenomic analysis revealed that each culture medium showed bacterial growth depending on its selective features and a possibility of the presence of novel bacterial species. Whole genome sequencing of these candidate strains suggested the isolation of 8 novel bacterial species classified in the Actinobacteria and Firmicutes phyla. Our approach indicates that a number of intestinal bacteria hitherto considered unculturable are potentially culturable and can be cultured on commercially available media. We have obtained novel gut bacteria from a healthy Japanese individual using a combination of comprehensive genomics and conventional culturing methods. We would expect that the discovery of such novel bacteria could illuminate pivotal roles for the gut microbiota in association with human health.}, } @article {pmid30117250, year = {2018}, author = {Cabello-Yeves, PJ and Picazo, A and Camacho, A and Callieri, C and Rosselli, R and Roda-Garcia, JJ and Coutinho, FH and Rodriguez-Valera, F}, title = {Ecological and genomic features of two widespread freshwater picocyanobacteria.}, journal = {Environmental microbiology}, volume = {20}, number = {10}, pages = {3757-3771}, doi = {10.1111/1462-2920.14377}, pmid = {30117250}, issn = {1462-2920}, support = {//FEDER funds/International ; //Generalitat Valenciana/International ; CGL2015-69557-R'//CLIMAWET/International ; //Spanish Ministry of Economy and Competitiveness/International ; //European Fund for Regional Development/International ; }, mesh = {Cyanobacteria/classification/*genetics/isolation & purification ; Ecology ; Ecosystem ; Genome, Bacterial ; Genomics ; Ice Cover/microbiology ; Lakes/chemistry/*microbiology ; Metagenome ; Phylogeny ; Synechococcus/classification/*genetics/isolation & purification ; }, abstract = {We present two genomes of widespread freshwater picocyanobacteria isolated by extinction dilution from a Spanish oligotrophic reservoir. Based on microscopy and genomic properties, both picocyanobacteria were tentatively designated Synechococcus lacustris Tous, formerly described as a metagenome assembled genome (MAG) from the same habitat, and Cyanobium usitatum Tous, described here for the first time. Both strains were purified in unicyanobacterial cultures, and their genomes were sequenced. They are broadly distributed in freshwater systems; the first seems to be a specialist on temperate reservoirs (Tous, Amadorio, Dexter, Lake Lanier, Sparkling), and the second appears to also be abundant in cold environments including ice-covered lakes such as Lake Baikal, Lake Erie or the brackish Baltic Sea. Having complete genomes provided access to the flexible genome that does not assemble in MAGs. We found several genomic islands in both genomes, within which there were genes for nitrogen acquisition, transporters for a wide set of compounds and biosynthesis of phycobilisomes in both strains. Some of these regions of low coverage in metagenomes also included antimicrobial compounds, transposases and phage defence systems, including a novel type III CRISPR-Cas phage defence system that was only detected in Synechococcus lacustris Tous.}, } @article {pmid30116044, year = {2019}, author = {Liu, N and Li, H and Chevrette, MG and Zhang, L and Cao, L and Zhou, H and Zhou, X and Zhou, Z and Pope, PB and Currie, CR and Huang, Y and Wang, Q}, title = {Functional metagenomics reveals abundant polysaccharide-degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood-feeding higher termite.}, journal = {The ISME journal}, volume = {13}, number = {1}, pages = {104-117}, pmid = {30116044}, issn = {1751-7370}, support = {T32 GM008505/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Carbohydrate Metabolism ; Cellobiose/*metabolism ; Cellulose/*metabolism ; Enzymes/genetics/metabolism ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/microbiology ; Gene Expression Regulation, Enzymologic ; Isoptera/*microbiology ; Metagenomics ; Multigene Family ; Polysaccharides/metabolism ; Wood/metabolism ; }, abstract = {Plant cell-wall polysaccharides constitute the most abundant but recalcitrant organic carbon source in nature. Microbes residing in the digestive tract of herbivorous bilaterians are particularly efficient at depolymerizing polysaccharides into fermentable sugars and play a significant support role towards their host's lifestyle. Here, we combine large-scale functional screening of fosmid libraries, shotgun sequencing, and biochemical assays to interrogate the gut microbiota of the wood-feeding "higher" termite Globitermes brachycerastes. A number of putative polysaccharide utilization gene clusters were identified with multiple fibrolytic genes. Our large-scale functional screening of 50,000 fosmid clones resulted in 464 clones demonstrating plant polysaccharide-degrading activities, including 267 endoglucanase-, 24 exoglucanase-, 72 β-glucosidase-, and 101 endoxylanase-positive clones. We sequenced 173 functionally active clones and identified ~219 genes encoding putative carbohydrate-active enzymes (CAZymes) targeting cellulose, hemicellulose and pectin. Further analyses revealed that 68 of 154 contigs encode one or more CAZyme, which includes 35 examples of putative saccharolytic operons, suggesting that clustering of CAZymes is common in termite gut microbial inhabitants. Biochemical characterization of a representative xylanase cluster demonstrated that constituent enzymes exhibited complementary physicochemical properties and saccharolytic capabilities. Furthermore, diverse cellobiose-metabolizing enzymes include β-glucosidases, cellobiose phosphorylases, and phopho-6-β-glucosidases were identified and functionally verified, indicating that the termite gut micro-ecosystem utilizes diverse metabolic pathways to interconnect hydrolysis and central metabolism. Collectively, these results provide an in-depth view of the adaptation and digestive strategies employed by gut microbiota within this tiny-yet-efficient host-associated ecosystem.}, } @article {pmid30114593, year = {2018}, author = {Zhang, YZ and Wu, WC and Shi, M and Holmes, EC}, title = {The diversity, evolution and origins of vertebrate RNA viruses.}, journal = {Current opinion in virology}, volume = {31}, number = {}, pages = {9-16}, pmid = {30114593}, issn = {1879-6265}, mesh = {Animals ; Biodiversity ; *Biological Evolution ; Birds/virology ; Fishes/virology ; *Genetic Variation ; Genome, Viral ; *Host Microbial Interactions ; Humans ; Phylogeny ; RNA Viruses/*genetics ; Vertebrates/*virology ; }, abstract = {Despite a substantial increase in our knowledge of the biodiversity and evolution of vertebrate RNA viruses, far less is known about the diversity, evolution and origin of RNA viruses across the diverse phylogenetic range of viruses, and particularly in healthy animals that are often only rarely utilized for virological sampling. Fortunately, recent advances in virus discovery using metagenomic approaches are beginning to reveal a multitude of RNA viruses in vertebrates other than birds and mammals. In particular, fish harbor a remarkable array of RNA viruses, including the relatives of important pathogens. In addition, despite frequent cross-species transmission, the RNA viruses in vertebrates generally follow the evolutionary history of their hosts, which began in the oceans and then moved to terrestrial habitats over timescales covering hundreds of millions of years.}, } @article {pmid30113227, year = {2018}, author = {Lal, CV and Kandasamy, J and Dolma, K and Ramani, M and Kumar, R and Wilson, L and Aghai, Z and Barnes, S and Blalock, JE and Gaggar, A and Bhandari, V and Ambalavanan, N}, title = {Early airway microbial metagenomic and metabolomic signatures are associated with development of severe bronchopulmonary dysplasia.}, journal = {American journal of physiology. Lung cellular and molecular physiology}, volume = {315}, number = {5}, pages = {L810-L815}, pmid = {30113227}, issn = {1522-1504}, support = {K08 HL141652/HL/NHLBI NIH HHS/United States ; P30 CA013148/CA/NCI NIH HHS/United States ; R01 HL129907/HL/NHLBI NIH HHS/United States ; }, mesh = {Biomarkers/metabolism ; Bronchopulmonary Dysplasia/*metabolism/*microbiology ; Gestational Age ; Humans ; Infant, Newborn ; Infant, Premature ; Metabolic Networks and Pathways/*physiology ; Metabolome/*physiology ; Metabolomics/methods ; Metagenome/*physiology ; Microbiota/*physiology ; RNA, Ribosomal, 16S/metabolism ; Trachea/metabolism/*microbiology ; }, abstract = {The pathogenesis of bronchopulmonary dysplasia (BPD) is not well understood. We previously identified differences in the airway microbiome at birth between preterm infants who were BPD predisposed versus those who were BPD resistant. In this study, we attempted to identify mechanisms by which the airway microbiome could modify the risk for BPD. We used a software-based method to predict the metagenome of the tracheal aspirate (TA) microbiome from 16S rRNA sequencing data in preterm infants and to identify functional ortholog genes that were differentially abundant in BPD-predisposed and BPD-resistant infants. We also identified metabolites that were differentially enriched in these samples by use of untargeted mass spectrometry and mummichog to identify the metabolic pathways involved. Microbial metagenome analysis identified specific pathways that were less abundant in the functional metagenome of the microbiota of BPD-predisposed infants compared with BPD-resistant infants. The airway metabolome of BPD-predisposed infants was enriched for metabolites involved in fatty acid activation and androgen and estrogen biosynthesis compared with BPD-resistant infants. These findings suggest that in extremely preterm infants the early airway microbiome may alter the metabolome, thereby modifying the risk of BPD. The differential enrichment of sex steroid metabolic pathways supports previous studies suggesting a role for sexual dimorphism in BPD risk. This study also suggests a role for metabolomic and metagenomic profiles to serve as early biomarkers of BPD risk.}, } @article {pmid30111822, year = {2018}, author = {Ferrocino, I and Ponzo, V and Gambino, R and Zarovska, A and Leone, F and Monzeglio, C and Goitre, I and Rosato, R and Romano, A and Grassi, G and Broglio, F and Cassader, M and Cocolin, L and Bo, S}, title = {Changes in the gut microbiota composition during pregnancy in patients with gestational diabetes mellitus (GDM).}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12216}, pmid = {30111822}, issn = {2045-2322}, mesh = {Adult ; Blood Glucose/metabolism ; Body Mass Index ; Diabetes, Gestational/*microbiology ; Diet ; Fasting ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics/physiology ; Humans ; Insulin Resistance ; Microbiota/genetics ; Pregnancy ; Pregnancy Complications ; Prospective Studies ; RNA, Ribosomal, 16S/analysis/genetics ; }, abstract = {Gestational diabetes mellitus (GDM), a common pregnancy complication, is associated with an increased risk of maternal/perinatal outcomes. We performed a prospective observational explorative study in 41 GDM patients to evaluate their microbiota changes during pregnancy and the associations between the gut microbiota and variations in nutrient intakes, anthropometric and laboratory variables. GDM patients routinely received nutritional recommendations according to guidelines. The fecal microbiota (by 16S amplicon-based sequencing), was assessed at enrolment (24-28 weeks) and at 38 weeks of gestational age. At the study end, the microbiota α-diversity significantly increased (P < 0.001), with increase of Firmicutes and reduction of Bacteroidetes and Actinobacteria. Patients who were adherent to the dietary recommendations showed a better metabolic and inflammatory pattern at the study-end and a significant decrease in Bacteroides. In multiple regression models, Faecalibacterium was significantly associated with fasting glucose; Collinsella (directly) and Blautia (inversely) with insulin, and with Homeostasis-Model Assessment Insulin-Resistance, while Sutterella with C-reactive protein levels. Consistent with this latter association, the predicted metagenomes showed a correlation between those taxa and inferred KEGG genes associated with lipopolysaccharide biosynthesis. A higher bacterial richness and strong correlations between pro-inflammatory taxa and metabolic/inflammatory variables were detected in GDM patients across pregnancy. Collectively these findings suggest that the development of strategies to modulate the gut microbiota might be a potentially useful tool to impact on maternal metabolic health.}, } @article {pmid30110928, year = {2018}, author = {Wu, L and Wang, J and Wu, H and Chen, J and Xiao, Z and Qin, X and Zhang, Z and Lin, W}, title = {Comparative Metagenomic Analysis of Rhizosphere Microbial Community Composition and Functional Potentials under Rehmannia glutinosa Consecutive Monoculture.}, journal = {International journal of molecular sciences}, volume = {19}, number = {8}, pages = {}, pmid = {30110928}, issn = {1422-0067}, mesh = {*Bacteria/classification/genetics/growth & development ; *Metagenome ; Microbial Consortia/*physiology ; Rehmannia/*microbiology ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Consecutive monoculture of Rehmannia glutinosa, highly valued in traditional Chinese medicine, leads to a severe decline in both quality and yield. Rhizosphere microbiome was reported to be closely associated with the soil health and plant performance. In this study, comparative metagenomics was applied to investigate the shifts in rhizosphere microbial structures and functional potentials under consecutive monoculture. The results showed R. glutinosa monoculture significantly decreased the relative abundances of Pseudomonadaceae and Burkholderiaceae, but significantly increased the relative abundances of Sphingomonadaceae and Streptomycetaceae. Moreover, the abundances of genera Pseudomonas, Azotobacter, Burkholderia, and Lysobacter, among others, were significantly lower in two-year monocultured soil than in one-year cultured soil. For potentially harmful/indicator microorganisms, the percentages of reads categorized to defense mechanisms (i.e., ATP-binding cassette (ABC) transporters, efflux transporter, antibiotic resistance) and biological metabolism (i.e., lipid transport and metabolism, secondary metabolites biosynthesis, transport and catabolism, nucleotide transport and metabolism, transcription) were significantly higher in two-year monocultured soil than in one-year cultured soil, but the opposite was true for potentially beneficial microorganisms, which might disrupt the equilibrium between beneficial and harmful microbes. Collectively, our results provide important insights into the shifts in genomic diversity and functional potentials of rhizosphere microbiome in response to R. glutinosa consecutive monoculture.}, } @article {pmid30108275, year = {2018}, author = {Shin, JH and Eom, H and Song, WJ and Rho, M}, title = {Integrative metagenomic and biochemical studies on rifamycin ADP-ribosyltransferases discovered in the sediment microbiome.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12143}, pmid = {30108275}, issn = {2045-2322}, mesh = {ADP Ribose Transferases/chemistry/*genetics ; Amino Acid Sequence/genetics ; Bacterial Proteins/chemistry/*genetics ; Drug Resistance, Microbial/*genetics ; Enzyme Assays ; Escherichia coli/drug effects/genetics ; Genes, Bacterial/genetics ; Geologic Sediments/microbiology ; Metagenomics ; Microbial Sensitivity Tests ; Microbiota/*genetics ; Mutation ; Phylogeny ; Recombinant Proteins/chemistry/genetics ; Rifampin/*pharmacology ; Sequence Alignment ; Soil Microbiology ; Transformation, Bacterial ; }, abstract = {Antibiotic resistance is a serious and growing threat to human health. The environmental microbiome is a rich reservoir of resistomes, offering opportunities to discover new antibiotic resistance genes. Here we demonstrate an integrative approach of utilizing gene sequence and protein structural information to characterize unidentified genes that are responsible for the resistance to the action of rifamycin antibiotic rifampin, a first-line antimicrobial agent to treat tuberculosis. Biochemical characterization of four environmental metagenomic proteins indicates that they are adenosine diphosphate (ADP)-ribosyltransferases and effective in the development of resistance to FDA-approved rifamycins. Our analysis suggests that even a single residue with low sequence conservation plays an important role in regulating the degrees of antibiotic resistance. In addition to advancing our understanding of antibiotic resistomes, this work demonstrates the importance of an integrative approach to discover new metagenomic genes and decipher their biochemical functions.}, } @article {pmid30108256, year = {2018}, author = {Stefanni, S and Stanković, D and Borme, D and de Olazabal, A and Juretić, T and Pallavicini, A and Tirelli, V}, title = {Multi-marker metabarcoding approach to study mesozooplankton at basin scale.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12085}, pmid = {30108256}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Ecological Parameter Monitoring/*methods ; High-Throughput Nucleotide Sequencing/methods ; Introduced Species ; Marine Biology/methods ; Metagenome/genetics ; Metagenomics/*methods ; Oceans and Seas ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA/methods ; Zooplankton/classification/*genetics ; }, abstract = {Zooplankton plays a pivotal role in marine ecosystems and the characterisation of its biodiversity still represents a challenge for marine ecologists. In this study, mesozooplankton composition from 46 samples collected in summer along the western Adriatic Sea, was retrieved by DNA metabarcoding analysis. For the first time, the highly variable fragments of the mtDNA COI and the V9 region of 18S rRNA genes were used in a combined matrix to compile an inventory of mesozooplankton at basin scale. The number of sequences retrieved after quality filtering were 824,148 and 223,273 for COI and 18S (V9), respectively. The taxonomical assignment against reference sequences, using 95% (for COI) and 97% (for 18S) similarity thresholds, recovered 234 taxa. NMDS plots and cluster analysis divided coastal from offshore samples and the most representative species of these clusters were distributed according to the dominant surface current pattern of the Adriatic for the summer period. For selected sampling sites, mesozooplankton species were also identified under a stereo microscope providing insights on the strength and weakness of the two approaches. In addition, DNA metabarcoding was shown to be helpful for the monitoring of non-indigenous marine metazoans and spawning areas of commercial fish species. We defined pros and cons of applying this approach at basin scale and the benefits of combining the datasets from two genetic markers.}, } @article {pmid30108167, year = {2018}, author = {Peura, S and Buck, M and Aalto, SL and Morales, SE and Nykänen, H and Eiler, A}, title = {Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake.}, journal = {mBio}, volume = {9}, number = {4}, pages = {}, pmid = {30108167}, issn = {2150-7511}, mesh = {Anaerobiosis ; *Autotrophic Processes ; *Biota ; Carbon/*metabolism ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Finland ; Lakes/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Oxygen-stratified lakes are typical for the boreal zone and also a major source of greenhouse gas emissions in the region. Due to shallow light penetration, restricting the growth of phototrophic organisms, and large allochthonous organic carbon inputs from the catchment area, the lake metabolism is expected to be dominated by heterotrophic organisms. In this study, we test this assumption and show that the potential for autotrophic carbon fixation and internal carbon cycling is high throughout the water column. Further, we show that during the summer stratification carbon fixation can exceed respiration in a boreal lake even below the euphotic zone. Metagenome-assembled genomes and 16S profiling of a vertical transect of the lake revealed multiple organisms in an oxygen-depleted compartment belonging to novel or poorly characterized phyla. Many of these organisms were chemolithotrophic, potentially deriving their energy from reactions related to sulfur, iron, and nitrogen transformations. The community, as well as the functions, was stratified along the redox gradient. The autotrophic potential in the lake metagenome below the oxygenic zone was high, pointing toward a need for revising our concepts of internal carbon cycling in boreal lakes. Further, the importance of chemolithoautotrophy for the internal carbon cycling suggests that many predicted climate change-associated fluctuations in the physical properties of the lake, such as altered mixing patterns, likely have consequences for the whole-lake metabolism even beyond the impact to the phototrophic community.IMPORTANCE Autotrophic organisms at the base of the food web are the only life form capable of turning inorganic carbon into the organic form, facilitating the survival of all other organisms. In certain environments, the autotrophic production is limited by environmental conditions and the food web is supported by external carbon inputs. One such environment is stratified boreal lakes, which are one of the biggest natural sources of greenhouse gas emissions in the boreal region. Thus, carbon cycling in these habitats is of utmost importance for the future climate. Here, we demonstrate a high potential for internal carbon cycling via phototrophic and novel chemolithotrophic organisms in the anoxic, poorly illuminated layers of a boreal lake. Our results significantly increase our knowledge on the microbial communities and their metabolic potential in oxygen-depleted freshwaters and help to understand and predict how climate change-induced alterations could impact the lake carbon dynamics.}, } @article {pmid30107526, year = {2018}, author = {Liu, C and Zhang, Y and Ren, Y and Wang, H and Li, S and Jiang, F and Yin, L and Qiao, X and Zhang, G and Qian, W and Liu, B and Fan, W}, title = {The genome of the golden apple snail Pomacea canaliculata provides insight into stress tolerance and invasive adaptation.}, journal = {GigaScience}, volume = {7}, number = {9}, pages = {}, pmid = {30107526}, issn = {2047-217X}, mesh = {Acclimatization/*genetics ; Animals ; *Genome ; *Introduced Species ; Snails/*genetics ; Stress, Physiological/*genetics ; }, abstract = {BACKGROUND: The golden apple snail (Pomacea canaliculata) is a freshwater snail listed among the top 100 worst invasive species worldwide and a noted agricultural and quarantine pest that causes great economic losses. It is characterized by fast growth, strong stress tolerance, a high reproduction rate, and adaptation to a broad range of environments.

RESULTS: Here, we used long-read sequencing to produce a 440-Mb high-quality, chromosome-level assembly of the P. canaliculata genome. In total, 50 Mb (11.4%) repeat sequences and 21,533 gene models were identified in the genome. The major findings of this study include the recent explosion of DNA/hAT-Charlie transposable elements, the expansion of the P450 gene family, and the constitution of the cellular homeostasis system, which contributes to ecological plasticity in stress adaptation. In addition, the high transcriptional levels of perivitelline genes in the ovary and albumen gland promote the function of nutrient supply and defense ability in eggs. Furthermore, the gut metagenome also contains diverse genes for food digestion and xenobiotic degradation.

CONCLUSIONS: These findings collectively provide novel insights into the molecular mechanisms of the ecological plasticity and high invasiveness.}, } @article {pmid30106226, year = {2018}, author = {Heeger, F and Bourne, EC and Baschien, C and Yurkov, A and Bunk, B and Spröer, C and Overmann, J and Mazzoni, CJ and Monaghan, MT}, title = {Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1500-1514}, doi = {10.1111/1755-0998.12937}, pmid = {30106226}, issn = {1755-0998}, support = {SAW-2014-IGB-1//Leibniz Association/ ; }, mesh = {Aquatic Organisms/classification/genetics ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Fungi/*classification/*genetics ; Metagenomics/*methods ; Phylogeny ; RNA, Fungal/*genetics ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {DNA metabarcoding is widely used to study prokaryotic and eukaryotic microbial diversity. Technological constraints limit most studies to marker lengths below 600 base pairs (bp). Longer sequencing reads of several thousand bp are now possible with third-generation sequencing. Increased marker lengths provide greater taxonomic resolution and allow for phylogenetic methods of classification, but longer reads may be subject to higher rates of sequencing error and chimera formation. In addition, most bioinformatics tools for DNA metabarcoding were designed for short reads and are therefore unsuitable. Here, we used Pacific Biosciences circular consensus sequencing (CCS) to DNA-metabarcode environmental samples using a ca. 4,500 bp marker that included most of the eukaryote SSU and LSU rRNA genes and the complete ITS region. We developed an analysis pipeline that reduced error rates to levels comparable to short-read platforms. Validation using a mock community indicated that our pipeline detected 98% of chimeras de novo. We recovered 947 OTUs from water and sediment samples from a natural lake, 848 of which could be classified to phylum, 397 to genus and 330 to species. By allowing for the simultaneous use of three databases (Unite, SILVA and RDP LSU), long-read DNA metabarcoding provided better taxonomic resolution than any single marker. We foresee the use of long reads enabling the cross-validation of reference sequences and the synthesis of ribosomal rRNA gene databases. The universal nature of the rRNA operon and our recovery of >100 nonfungal OTUs indicate that long-read DNA metabarcoding holds promise for studies of eukaryotic diversity more broadly.}, } @article {pmid30106217, year = {2019}, author = {Rubin, BER and Kautz, S and Wray, BD and Moreau, CS}, title = {Dietary specialization in mutualistic acacia-ants affects relative abundance but not identity of host-associated bacteria.}, journal = {Molecular ecology}, volume = {28}, number = {4}, pages = {900-916}, doi = {10.1111/mec.14834}, pmid = {30106217}, issn = {1365-294X}, support = {DEB-1311417//National Science Foundation/International ; DEB-1050243//National Science Foundation/International ; DEB-1442316//National Science Foundation/International ; }, mesh = {Acacia/*physiology ; Acetobacteraceae/physiology ; Animals ; Ants/*physiology ; Bartonella/physiology ; Herbivory/physiology ; Metagenomics ; Microbiota/physiology ; Nocardiaceae/physiology ; Symbiosis/genetics/physiology ; }, abstract = {Acacia-ant mutualists in the genus Pseudomyrmex nest obligately in acacia plants and, as we show through stable isotope analysis, feed at a remarkably low trophic level. Insects with diets such as these sometimes depend on bacterial symbionts for nutritional enrichment. We, therefore, examine the bacterial communities associated with acacia-ants in order to determine whether they host bacterial partners likely to contribute to their nutrition. Despite large differences in trophic position, acacia-ants and related species with generalized diets do not host distinct bacterial taxa. However, we find that a small number of previously undescribed bacterial taxa do differ in relative abundance between acacia-ants and generalists, including several Acetobacteraceae and Nocardiaceae lineages related to common insect associates. Comparisons with an herbivorous generalist, a parasite that feeds on acacias and a mutualistic species with a generalized diet show that trophic level is likely responsible for these small differences in bacterial community structure. While we did not experimentally test for a nutritional benefit to hosts of these bacterial lineages, metagenomic analysis reveals a Bartonella relative with an intact nitrogen-recycling pathway widespread across Pseudomyrmex mutualists and generalists. This taxon may be contributing to nitrogen enrichment of its ant hosts through urease activity and, concordant with an obligately host-associated lifestyle, appears to be experiencing genomewide relaxed selection. The lack of distinctiveness in bacterial communities across trophic level in this group of ants shows a remarkable ability to adjust to varied diets, possibly with assistance from these diverse ant-specific bacterial lineages.}, } @article {pmid30104612, year = {2018}, author = {Jenkins, TP and Peachey, LE and Ajami, NJ and MacDonald, AS and Hsieh, MH and Brindley, PJ and Cantacessi, C and Rinaldi, G}, title = {Schistosoma mansoni infection is associated with quantitative and qualitative modifications of the mammalian intestinal microbiota.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12072}, pmid = {30104612}, issn = {2045-2322}, support = {R01 AI072773/AI/NIAID NIH HHS/United States ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //HHSN272201000005I/International ; HHSN272201000005C/AI/NIAID NIH HHS/United States ; HHSN272201000005I/AI/NIAID NIH HHS/United States ; R21 AI109532/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteroides/genetics/immunology/isolation & purification ; DNA, Bacterial/isolation & purification ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/genetics/*immunology ; Humans ; Intestines/*microbiology/pathology ; Lactobacillus/genetics/immunology/isolation & purification ; Mice ; RNA, Ribosomal, 16S/genetics ; Schistosoma mansoni/immunology/*pathogenicity ; Schistosomiasis mansoni/*immunology/microbiology/parasitology/pathology ; Verrucomicrobia/genetics/immunology/isolation & purification ; }, abstract = {In spite of the extensive contribution of intestinal pathology to the pathophysiology of schistosomiasis, little is known of the impact of schistosome infection on the composition of the gut microbiota of its mammalian host. Here, we characterised the fluctuations in the composition of the gut microbial flora of the small and large intestine, as well as the changes in abundance of individual microbial species, of mice experimentally infected with Schistosoma mansoni with the goal of identifying microbial taxa with potential roles in the pathophysiology of infection and disease. Bioinformatic analyses of bacterial 16S rRNA gene data revealed an overall reduction in gut microbial alpha diversity, alongside a significant increase in microbial beta diversity characterised by expanded populations of Akkermansia muciniphila (phylum Verrucomicrobia) and lactobacilli, in the gut microbiota of S. mansoni-infected mice when compared to uninfected control animals. These data support a role of the mammalian gut microbiota in the pathogenesis of hepato-intestinal schistosomiasis and serves as a foundation for the design of mechanistic studies to unravel the complex relationships amongst parasitic helminths, gut microbiota, pathophysiology of infection and host immunity.}, } @article {pmid30102711, year = {2018}, author = {Watanabe, K and Igarashi, M and Li, X and Nakatani, A and Miyamoto, J and Inaba, Y and Sutou, A and Saito, T and Sato, T and Tachibana, N and Inoue, H and Kimura, I}, title = {Dietary soybean protein ameliorates high-fat diet-induced obesity by modifying the gut microbiota-dependent biotransformation of bile acids.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0202083}, pmid = {30102711}, issn = {1932-6203}, mesh = {Animals ; Bile Acids and Salts/*metabolism ; Biodiversity ; Diet, High-Fat/adverse effects ; Dietary Supplements ; Gastrointestinal Microbiome/*drug effects ; Glucagon-Like Peptide 1/metabolism ; Intestinal Mucosa/drug effects/metabolism/microbiology ; Male ; Metabolic Networks and Pathways/*drug effects ; Metagenome ; Metagenomics/methods ; Mice ; Obesity/*etiology/*metabolism ; Soybean Proteins/*pharmacology ; }, abstract = {The consumption of soybean protein has well-known favorable metabolic effects (e.g., reduced body weight, body fat, hyperglycemia, insulin resistance, hepatic steatosis, and lipogenesis). These effects of soy protein have been linked to modulation by the gut microbiota; however, the dynamic interplay among these factors remains unclear. Accordingly, we examined the metabolic phenotype, intestinal BA pool, and the gut microbiome of male C57BL/6 mice that were randomized to receive either a regular high-fat diet (HFD) or HFD that contained soybean protein isolate (SPI) in place of dairy protein. The intake of SPI significantly reduced the HFD-induced weight gain and adipose tissue mass accumulation and attenuated hepatic steatosis. Along with an enhancement in the secretion of intestinal Glucagon-like peptide-1 (GLP-1), an enlarged cecal BA pool with an elevated secondary/primary BA ratio was observed in the mice that consumed SPI, while fecal BA excretion remained unaltered. SPI also elicited dramatic changes in the gut microbiome, characterized by an expansion of taxa that may be involved in the biotransformation of BAs. The observed effects were abolished in germ-free (GF) mice, indicating that they were dependent on the microbiota. These findings collectively indicate that the metabolic benefits of SPI under the HFD regime may arise from a microbiota-driven increase in BA transformation and increase in GLP-1 secretion.}, } @article {pmid30101334, year = {2018}, author = {Kadnikov, VV and Mardanov, AV and Beletsky, AV and Banks, D and Pimenov, NV and Frank, YA and Karnachuk, OV and Ravin, NV}, title = {A metagenomic window into the 2-km-deep terrestrial subsurface aquifer revealed multiple pathways of organic matter decomposition.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {10}, pages = {}, doi = {10.1093/femsec/fiy152}, pmid = {30101334}, issn = {1574-6941}, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; Carbohydrate Metabolism/*genetics ; Fermentation ; Genome, Bacterial/genetics ; Groundwater/chemistry/*microbiology ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfates/metabolism ; }, abstract = {We have sequenced metagenome of the microbial community of a deep subsurface thermal aquifer in the Tomsk Region of the Western Siberia, Russia. Our goal was the recovery of near-complete genomes of the community members to enable accurate reconstruction of metabolism and ecological roles of the microbial majority, including previously unstudied lineages. The water, obtained via a 2.6 km deep borehole 1-R, was anoxic, with a slightly alkaline pH, and a temperature around 45°C. Microbial community, as revealed by 16S rRNA gene profiling over 2 years, mostly consisted of sulfate-reducing Firmicutes and Deltaproteobacteria, and uncultured lineages of the phyla Chlorofexi, Ignavibacteriae and Aminicenantes (OP8). 25 composite genomes with more than 90% completeness were recovered from metagenome and used for metabolic reconstruction. Members of uncultured lineages of Chlorofexi and Ignavibacteriae are likely involved in degradation of carbohydrates by fermentation, and are also capable of aerobic and anaerobic respiration. The Chlorofexi bacterium has the Wood-Ljungdahl pathway of CO2 fixation. The recently identified candidate phylum Riflebacteria accounted for 5%-10% of microbial community. Metabolic reconstruction of a member of Riflebacteria predicted that it is an anaerobe capable to grow on carbohydrates by fermentation or dissimilatory Fe(III) reduction.}, } @article {pmid30099499, year = {2018}, author = {Schlub, TE and Buchmann, JP and Holmes, EC}, title = {A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences.}, journal = {Molecular biology and evolution}, volume = {35}, number = {10}, pages = {2572-2581}, pmid = {30099499}, issn = {1537-1719}, mesh = {*Genes, Overlapping ; *Genetic Techniques ; *Genome, Viral ; *Open Reading Frames ; RNA Viruses/*genetics ; }, abstract = {Overlapping genes in viruses maximize the coding capacity of their genomes and allow the generation of new genes without major increases in genome size. Despite their importance, the evolution and function of overlapping genes are often not well understood, in part due to difficulties in their detection. In addition, most bioinformatic approaches for the detection of overlapping genes require the comparison of multiple genome sequences that may not be available in metagenomic surveys of virus biodiversity. We introduce a simple new method for identifying candidate functional overlapping genes using single virus genome sequences. Our method uses randomization tests to estimate the expected length of open reading frames and then identifies overlapping open reading frames that significantly exceed this length and are thus predicted to be functional. We applied this method to 2548 reference RNA virus genomes and find that it has both high sensitivity and low false discovery for genes that overlap by at least 50 nucleotides. Notably, this analysis provided evidence for 29 previously undiscovered functional overlapping genes, some of which are coded in the antisense direction suggesting there are limitations in our current understanding of RNA virus replication.}, } @article {pmid30097447, year = {2018}, author = {Burns, AS and Padilla, CC and Pratte, ZA and Gilde, K and Regensburger, M and Hall, E and Dove, ADM and Stewart, FJ}, title = {Broad Phylogenetic Diversity Associated with Nitrogen Loss through Sulfur Oxidation in a Large Public Marine Aquarium.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {20}, pages = {}, pmid = {30097447}, issn = {1098-5336}, mesh = {Bacteria/*classification/metabolism ; Biodiversity ; Bioreactors/microbiology ; *Denitrification ; *Genetic Variation ; Georgia ; Metagenomics ; Microbiota ; Nitrogen/*metabolism ; Oxidation-Reduction ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sulfur/*metabolism ; Wastewater ; }, abstract = {Denitrification by sulfur-oxidizing bacteria is an effective nitrate removal strategy in engineered aquatic systems. However, the community taxonomic and metabolic diversity of sulfur-driven denitrification (SDN) systems, as well as the relationship between nitrate removal and SDN community structure, remains underexplored. This is particularly true for SDN reactors applied to marine aquaria, despite the increasing use of this technology to supplement filtration. We applied 16S rRNA gene, metagenomic, and metatranscriptomic analyses to explore the microbial basis of SDN reactors operating on Georgia Aquarium's Ocean Voyager, the largest indoor closed-system seawater exhibit in the United States. The exhibit's two SDN systems vary in water retention time and nitrate removal efficiency. The systems also support significantly different microbial communities. These communities contain canonical SDN bacteria, including a strain related to Thiobacillus thioparus that dominates the system with the higher water retention time and nitrate removal but is effectively absent from the other system. Both systems contain a wide diversity of other microbes whose metagenome-assembled genomes contain genes of SDN metabolism. These include hundreds of strains of the epsilonproteobacterium Sulfurimonas, as well as gammaproteobacterial sulfur oxidizers of the Thiotrichales and Chromatiales, and a relative of Sedimenticolathiotaurini with complete denitrification potential. The SDN genes are transcribed and the taxonomic richness of the transcript pool varies markedly among the enzymatic steps, with some steps dominated by transcripts from noncanonical SDN taxa. These results indicate complex and variable SDN communities that may involve chemical dependencies among taxa as well as the potential for altering community structure to optimize nitrate removal.IMPORTANCE Engineered aquatic systems such as aquaria and aquaculture facilities have large societal value. Ensuring the health of animals in these systems requires understanding how microorganisms contribute to chemical cycling and waste removal. Focusing on the largest seawater aquarium in the United States, we explore the microbial communities in specialized reactors designed to remove excess nitrogen through the metabolic activity of sulfur-consuming microbes. We show that the diversity of microbes in these reactors is both high and highly variable, with distinct community types associated with significant differences in nitrogen removal rate. We also show that the genes encoding the metabolic steps of nitrogen removal are distributed broadly throughout community members, suggesting that the chemical transformations in this system are likely a result of microbes relying on other microbes. These results provide a framework for future studies exploring the contributions of different community members, both in waste removal and in structuring microbial biodiversity.}, } @article {pmid30095376, year = {2018}, author = {Galla, S and Chakraborty, S and Cheng, X and Yeo, J and Mell, B and Zhang, H and Mathew, AV and Vijay-Kumar, M and Joe, B}, title = {Disparate effects of antibiotics on hypertension.}, journal = {Physiological genomics}, volume = {50}, number = {10}, pages = {837-845}, pmid = {30095376}, issn = {1531-2267}, support = {K08 HL130944/HL/NHLBI NIH HHS/United States ; P30 DK081943/DK/NIDDK NIH HHS/United States ; R01 CA219144/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Blood Pressure/*drug effects/physiology ; Gastrointestinal Microbiome/*drug effects/genetics/physiology ; Hypertension/genetics/*physiopathology ; Minocycline/pharmacology ; Neomycin/pharmacology ; Rats, Inbred Dahl ; Rats, Inbred SHR ; Sodium Chloride, Dietary/administration & dosage ; Species Specificity ; Vancomycin/pharmacology ; }, abstract = {Gut microbiota are associated with a variety of complex polygenic diseases. The usage of broad-spectrum antibiotics by patients affected by such diseases is an important environmental factor to consider, because antibiotics, which are widely prescribed to curb pathological bacterial infections, also indiscriminately eliminate gut commensal microbiota. However, the extent to which antibiotics reshape gut microbiota and per se contribute to these complex diseases is understudied. Because genetics play an important role in predisposing individuals to these modern diseases, we hypothesize that the extent to which antibiotics influence complex diseases depends on the host genome and metagenome. The current study tests this hypothesis in the context of hypertension, which is a serious risk factor for cardiovascular diseases. A 3 × 2 factorial design was used to test the blood pressure (BP) and microbiotal effects of three different antibiotics, neomycin, minocycline, and vancomycin, on two well-known, preclinical, genetic models of hypertension, the Dahl salt-sensitive (S) rat and the spontaneously hypertensive rat (SHR), both of which develop hypertension, but for different genetic reasons. Regardless of the class, oral administration of antibiotics increased systolic blood pressure of the S rat, while minocycline and vancomycin, but not neomycin, lowered systolic blood pressure in the SHR. These disparate BP effects were accompanied by significant alterations in gut microbiota. Our study highlights the need to consider an individualized approach for the usage of antibiotics among hypertensives, as their BP could be affected differentially based on their individual genetic and microbiotal communities.}, } @article {pmid30095241, year = {2019}, author = {Leis, ML and Costa, MO}, title = {Initial description of the core ocular surface microbiome in dogs: Bacterial community diversity and composition in a defined canine population.}, journal = {Veterinary ophthalmology}, volume = {22}, number = {3}, pages = {337-344}, doi = {10.1111/vop.12599}, pmid = {30095241}, issn = {1463-5224}, support = {419248//U of S Faculty Recruitment and Retention Program/ ; 100008920//U of S Faculty Recruitment and Retention Program/ ; }, mesh = {Animals ; Bacteria/*isolation & purification ; Conjunctiva/*microbiology ; DNA, Bacterial/analysis ; Dogs/*microbiology ; Female ; High-Throughput Nucleotide Sequencing/veterinary ; Male ; Microbiota ; }, abstract = {OBJECTIVE: To characterize the bacterial community residing on the conjunctiva of clinically healthy dogs.

METHODS: Bacterial DNA from conjunctival swabs of 10 dogs with normal ocular examinations (both OD and OS, n = 20) was extracted, and 16S rRNA amplicons were sequenced using Illumina MiSeq 600. Resulting data were subjected to quality control steps, and analyzed for bacterial community richness and diversity, within- and between-group dissimilarity, and relative taxonomic composition.

RESULTS: High-quality reads (2.22 million bp) resulted in a mean of 159 068 sequences per sample. Bacterial community evenness and diversity was high when compared to other species, and did not significantly differ when samples were grouped by dogs or eyes. As expected, within-dog samples were more similar than between-dog samples. Taxonomic classification revealed that >95% of the community consisted of Firmicutes (34.9 ± 8.8%), Actinobacteria (26.3 ± 7.1%), Proteobacteria (26.2 ± 6.6%), and Bacteroidetes (9.4 ± 2.4%). Key members of the dog ocular surface microbiome, found in all dogs and corresponding to >25% of all identified OTUs (operational taxonomic units), were part of the Bifidobacteriaceae, Lachnospiraceae, Moraxellaceae, Corynebacteriaceae families. Genera previously thought to account for the majority of the core ocular surface microbiome in the dog (Staphylococcus sp., Streptococcus sp., and Bacillus sp.) were associated with only 2.63% of overall reads.

CONCLUSIONS: This study shows the feasibility of conjunctival swabs and high-throughput sequencing to profile the bacterial community structure of the canine ocular surface. A core ocular surface microbiome was identified for this canine population.}, } @article {pmid30094589, year = {2018}, author = {Yu, C and Hou, L and Zheng, Y and Liu, M and Yin, G and Gao, J and Liu, C and Chang, Y and Han, P}, title = {Evidence for complete nitrification in enrichment culture of tidal sediments and diversity analysis of clade a comammox Nitrospira in natural environments.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {21}, pages = {9363-9377}, doi = {10.1007/s00253-018-9274-0}, pmid = {30094589}, issn = {1432-0614}, support = {2016YFA0600904//Chinese National Key Programs for Fundamental Research and Development/ ; 41725002//National Natural Science Foundations of China/ ; }, mesh = {Ammonia/metabolism ; Archaea/genetics ; Bacteria/genetics ; Betaproteobacteria/genetics ; Biodiversity ; Ecosystem ; Geologic Sediments/*microbiology ; Nitrification/*genetics ; Nitrogen Cycle/genetics ; Oxidation-Reduction ; Transcriptome/genetics ; }, abstract = {Complete ammonia oxidizers (comammox), as novel microbial communities, are predicted to play an important role in the nitrogen cycle. Here we reported the presence of complete nitrification in tidal sediments and examined the diversity and abundance of comammox in natural ecosystems. Metagenome and metatranscriptome of the enrichment culture from tidal sediments harbored the genes of comammox. Near-complete comammox AmoA/B/C- and Hao-like sequences showed close relationships to the known comammox (with sequence identity from 79 to 99%) rather than classical betaproteobacterial ammonia-oxidizing bacteria (β-AOB) (57 to 66%) and ammonia-oxidizing archaea (AOA) (24 to 38%). To analyze the diversity of comammox in natural environments, a new primer set targeting clade A comammox Nitrospira (COM-A) amoA genes was designed based on sequences obtained in this study and sequences from published database. In silico evaluation of the primers showed the high coverage of 89 and 100% in the COM-A amoA database. Application of the primers in six different ecosystems proved their strong availability. Community composition of COM-A suggested a relatively higher diversity than β-AOB in similar environments. Quantification results showed that COM-A amoA genes accounted for about 0.4-5.6% in total amoA genes. These results provide novel insight into our perception of the enigmatic comammox and have significant implications for profound understanding of complex nitrification process.}, } @article {pmid30092815, year = {2018}, author = {Murali, A and Bhargava, A and Wright, ES}, title = {IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {140}, pmid = {30092815}, issn = {2049-2618}, mesh = {Bacteria/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Machine Learning ; Metagenomics/*methods ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Software ; }, abstract = {BACKGROUND: Microbiome studies often involve sequencing a marker gene to identify the microorganisms in samples of interest. Sequence classification is a critical component of this process, whereby sequences are assigned to a reference taxonomy containing known sequence representatives of many microbial groups. Previous studies have shown that existing classification programs often assign sequences to reference groups even if they belong to novel taxonomic groups that are absent from the reference taxonomy. This high rate of "over classification" is particularly detrimental in microbiome studies because reference taxonomies are far from comprehensive.

RESULTS: Here, we introduce IDTAXA, a novel approach to taxonomic classification that employs principles from machine learning to reduce over classification errors. Using multiple reference taxonomies, we demonstrate that IDTAXA has higher accuracy than popular classifiers such as BLAST, MAPSeq, QIIME, SINTAX, SPINGO, and the RDP Classifier. Similarly, IDTAXA yields far fewer over classifications on Illumina mock microbial community data when the expected taxa are absent from the training set. Furthermore, IDTAXA offers many practical advantages over other classifiers, such as maintaining low error rates across varying input sequence lengths and withholding classifications from input sequences composed of random nucleotides or repeats.

CONCLUSIONS: IDTAXA's classifications may lead to different conclusions in microbiome studies because of the substantially reduced number of taxa that are incorrectly identified through over classification. Although misclassification error is relatively minor, we believe that many remaining misclassifications are likely caused by errors in the reference taxonomy. We describe how IDTAXA is able to identify many putative mislabeling errors in reference taxonomies, enabling training sets to be automatically corrected by eliminating spurious sequences. IDTAXA is part of the DECIPHER package for the R programming language, available through the Bioconductor repository or accessible online (http://DECIPHER.codes).}, } @article {pmid30092513, year = {2019}, author = {Peng, Z and Zhang, J and Fanning, S and Wang, L and Li, M and Maheshwari, N and Sun, J and Li, F}, title = {Effects of metal and metalloid pollutants on the microbiota composition of feces obtained from twelve commercial pig farms across China.}, journal = {The Science of the total environment}, volume = {647}, number = {}, pages = {577-586}, doi = {10.1016/j.scitotenv.2018.08.026}, pmid = {30092513}, issn = {1879-1026}, mesh = {*Animal Husbandry ; Animals ; China ; Farms ; Feces/*microbiology ; Metalloids/analysis/*toxicity ; Metals/analysis/*toxicity ; Metals, Heavy ; Microbiota/*drug effects ; Swine ; }, abstract = {Understanding the metal and metalloid contamination and microbiota composition of pig feces is an important step required to support the design and implementation of effective pollution control and prevention strategies. A survey was implemented in 12 locations across China to investigate the content of metals and metalloids, and the main composition of the microbial communities of commercially reared pigs during two growth periods, defined as the early (Q group) and the later fattening growth phases (H group). These data showed widespread Al, Mn, Cu, Zn, and Fe pollution in pig feces. The concentration of Zn in the Q group feces was nearly two times higher than the levels measured in the H group. The microbial composition of the Q group exhibited greater richness of operational taxonomic units (OTUs) and fewer bacteria associated with zoonotic diseases compared with the microbial composition of the H group. Spearman rank correlation analysis showed that Cu and northern latitudes had a significant positive effect on the richness of bacterial communities in pig feces. Zn and Cd exhibited the biggest impact on microbial community composition based on canonical correspondence analysis. Functional metagenomic prediction indicated that about 0.8% genes present in the pig feces bacteria community are related to human diseases, and significantly more predicted pathogenic genes were detected in the H group than in the Q group. These results support the need to monitor heavy metal contamination and to control for zoonotic pathogens disseminated from pig feces in Chinese pig farms.}, } @article {pmid30091981, year = {2018}, author = {Bradley, PH and Nayfach, S and Pollard, KS}, title = {Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.}, journal = {PLoS computational biology}, volume = {14}, number = {8}, pages = {e1006242}, pmid = {30091981}, issn = {1553-7358}, support = {T32 GM067547/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Gastrointestinal Microbiome/*genetics/physiology ; Gene Expression Regulation, Bacterial/genetics ; Genes, Microbial/genetics ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; }, abstract = {The mechanisms by which different microbes colonize the healthy human gut versus other body sites, the gut in disease states, or other environments remain largely unknown. Identifying microbial genes influencing fitness in the gut could lead to new ways to engineer probiotics or disrupt pathogenesis. We approach this problem by measuring the statistical association between a species having a gene and the probability that the species is present in the gut microbiome. The challenge is that closely related species tend to be jointly present or absent in the microbiome and also share many genes, only a subset of which are involved in gut adaptation. We show that this phylogenetic correlation indeed leads to many false discoveries and propose phylogenetic linear regression as a powerful solution. To apply this method across the bacterial tree of life, where most species have not been experimentally phenotyped, we use metagenomes from hundreds of people to quantify each species' prevalence in and specificity for the gut microbiome. This analysis reveals thousands of genes potentially involved in adaptation to the gut across species, including many novel candidates as well as processes known to contribute to fitness of gut bacteria, such as acid tolerance in Bacteroidetes and sporulation in Firmicutes. We also find microbial genes associated with a preference for the gut over other body sites, which are significantly enriched for genes linked to fitness in an in vivo competition experiment. Finally, we identify gene families associated with higher prevalence in patients with Crohn's disease, including Proteobacterial genes involved in conjugation and fimbria regulation, processes previously linked to inflammation. These gene targets may represent new avenues for modulating host colonization and disease. Our strategy of combining metagenomics with phylogenetic modeling is general and can be used to identify genes associated with adaptation to any environment.}, } @article {pmid30089798, year = {2018}, author = {Kim, DJ and Yoon, S and Ji, SC and Yang, J and Kim, YK and Lee, S and Yu, KS and Jang, IJ and Chung, JY and Cho, JY}, title = {Ursodeoxycholic acid improves liver function via phenylalanine/tyrosine pathway and microbiome remodelling in patients with liver dysfunction.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {11874}, pmid = {30089798}, issn = {2045-2322}, support = {HI14C2770//Korea Health Industry Development Institute (KHIDI)/International ; HI14C2770//Korea Health Industry Development Institute (KHIDI)/International ; HI14C2770//Korea Health Industry Development Institute (KHIDI)/International ; HI14C2770//Korea Health Industry Development Institute (KHIDI)/International ; HI14C2770//Korea Health Industry Development Institute (KHIDI)/International ; HI14C2770//Korea Health Industry Development Institute (KHIDI)/International ; HI14C2770//Korea Health Industry Development Institute (KHIDI)/International ; HI14C2770//Korea Health Industry Development Institute (KHIDI)/International ; HI14C2770//Korea Health Industry Development Institute (KHIDI)/International ; HI14C2770//Korea Health Industry Development Institute (KHIDI)/International ; }, mesh = {Adult ; Antioxidants/metabolism ; Humans ; Liver/*drug effects/microbiology ; Liver Diseases/metabolism/microbiology ; Male ; MicroRNAs/*metabolism ; Microbiota/*drug effects ; Phenylalanine/*metabolism ; Tyrosine/*metabolism ; Ursodeoxycholic Acid/*pharmacology ; Vitamin E/metabolism ; Young Adult ; }, abstract = {Ursodeoxycholic acid (UDCA) is a metabolic by-product of intestinal bacteria, showing hepatoprotective effects. However, its underlying molecular mechanisms remain unclear. The purpose of this study was to elucidate the action mechanisms underlying the protective effects of UDCA and vitamin E against liver dysfunction using metabolomics and metagenomic analysis. In this study, we analysed blood and urine samples from patients with obesity and liver dysfunction. Nine patients were randomly assigned to receive UDCA (300 mg twice daily), and 10 subjects received vitamin E (400 IU twice daily) for 8 weeks. UDCA significantly improved the liver function scores after 4 weeks of treatment and effectively reduced hepatic deoxycholic acid and serum microRNA-122 levels. To better understand its protective mechanism, a global metabolomics study was conducted, and we found that UDCA regulated uremic toxins (hippuric acid, p-cresol sulphate, and indole-derived metabolites), antioxidants (ascorbate sulphate and N-acetyl-L-cysteine), and the phenylalanine/tyrosine pathway. Furthermore, microbiome involvement, particularly of Lactobacillus and Bifidobacterium, was demonstrated through metagenomic analysis of bacteria-derived extracellular vesicles. Meanwhile, vitamin E treatment did not result in such alterations, except that it reduced uremic toxins and liver dysfunction. Our findings suggested that both treatments were effective in improving liver function, albeit via different mechanisms.}, } @article {pmid30086520, year = {2018}, author = {Crampon, M and Bodilis, J and Portet-Koltalo, F}, title = {Linking initial soil bacterial diversity and polycyclic aromatic hydrocarbons (PAHs) degradation potential.}, journal = {Journal of hazardous materials}, volume = {359}, number = {}, pages = {500-509}, doi = {10.1016/j.jhazmat.2018.07.088}, pmid = {30086520}, issn = {1873-3336}, mesh = {Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Microbiota ; Polycyclic Aromatic Hydrocarbons/*metabolism ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {The aim of this study was to understand the role of indigenous soil microbial communities on the biodegradation of polycyclic aromatic hydrocarbons (PAHs) and to determine whether PAHs degradation potential in soils may be evaluated by analysis of bacterial diversity and potential metabolisms using a metagenomics approach. Five different soils were artificially contaminated with seven selected PAHs and the most abundant bacterial taxa were assessed by sequencing the 16S rRNA gene, and linking them to PAH biodegradation efficiencies. A PICRUSt approach was then led to estimate the degradation potentials by metagenomics inference. Although the role of bacteria in PAHs degradation is not directly established here, the presence of a large number of bacteria belonging to the Betaproteobacteria class correlated to a higher degradation of LMW PAHs. A link with specific bacterial taxa was more difficult to establish concerning HMW PAHs, which seemed to require more complex mechanisms as shown by PICRUSt.}, } @article {pmid30086347, year = {2018}, author = {Miró-Abella, E and Torrell, H and Herrero, P and Canela, N and Arola, L and Borrull, F and Ras, R and Fontanals, N}, title = {Monitoring and evaluation of the interaction between deoxynivalenol and gut microbiota in Wistar rats by mass spectrometry-based metabolomics and next-generation sequencing.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {121}, number = {}, pages = {124-130}, doi = {10.1016/j.fct.2018.08.006}, pmid = {30086347}, issn = {1873-6351}, mesh = {Animals ; Chromatography, High Pressure Liquid/methods ; Feces/chemistry ; Gastrointestinal Microbiome/*drug effects ; High-Throughput Nucleotide Sequencing/*methods ; Metabolomics/*methods ; Metagenomics ; Mycotoxins/analysis/*toxicity ; No-Observed-Adverse-Effect Level ; RNA, Ribosomal, 16S/metabolism ; Rats ; Rats, Wistar ; Tandem Mass Spectrometry/*methods ; Trichothecenes/analysis/*toxicity ; }, abstract = {Published evidence has demonstrated the several toxic characteristics of mycotoxins and their considerable risk to human and animal health. One of the most common uncertainties regards whether if very low concentrations of the mycotoxin deoxynivalenol (DON), easily consumed within the Mediterranean Diet, can cause metabolic alterations; some of them produced by the interaction between DON and gut microbiota. Accordingly, faecal samples were collected from Wistar rats that had consumed the mycotoxin DON at low levels (60 and 120 μg kg[-1] body weight of DON per day), and were analysed by ultra-high performance liquid chromatography coupled with tandem mass spectrometry detection, in order to monitor the mycotoxin DON and its metabolite de-epoxy deoxynivalenol (DOM-1). The obtained results showed an evolution in DON excretion and the metabolite DOM-1 which has less toxic properties, over the course of the days of the study. To elucidate whether intestinal microbiota had a role in the observed detoxification process, the changes in microbial gut biodiversity were explored through 16s rRNA high throughput sequencing. No main changes were detected but significant increase in Coprococcus genus relative abundance was found. Further studies are needed to confirm if intestinal microbiota composition and function are affected by low mycotoxin concentrations.}, } @article {pmid30084235, year = {2018}, author = {Markussen, T and Happel, EM and Teikari, JE and Huchaiah, V and Alneberg, J and Andersson, AF and Sivonen, K and Riemann, L and Middelboe, M and Kisand, V}, title = {Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change.}, journal = {Environmental microbiology}, volume = {20}, number = {8}, pages = {3083-3099}, doi = {10.1111/1462-2920.14371}, pmid = {30084235}, issn = {1462-2920}, support = {//Estonian Research Council/International ; //Academy of Finland/International ; //Swedish Research Council FORMAS/International ; //Danish Council for Independent Research/International ; }, mesh = {Bacteria/*classification/*genetics/isolation & purification/metabolism ; Climate Change ; Ecosystem ; Fresh Water/analysis/microbiology ; Metagenome ; Metagenomics ; Microbiota ; Organic Chemicals/analysis/metabolism ; Oxygen/analysis/metabolism ; Seawater/analysis/microbiology ; }, abstract = {Bacteria are major drivers of biogeochemical nutrient cycles and energy fluxes in marine environments, yet how bacterial communities respond to environmental change is not well known. Metagenomes allow examination of genetic responses of the entire microbial community to environmental change. However, it is challenging to link metagenomes directly to biogeochemical process rates. Here, we investigate metagenomic responses in natural bacterioplankton communities to simulated environmental stressors in the Baltic Sea, including increased river water input, increased nutrient concentration, and reduced oxygen level. This allowed us to identify informative prokaryotic gene markers, responding to environmental perturbation. Our results demonstrate that metagenomic and metabolic changes in bacterial communities in response to environmental stressors are influenced both by the initial community composition and by the biogeochemical factors shaping the functional response. Furthermore, the different sources of dissolved organic matter (DOM) had the largest impact on metagenomic blueprint. Most prominently, changes in DOM loads influenced specific transporter types reflecting the substrate availability and DOC assimilation and consumption pathways. The results provide new knowledge for developing models of ecosystem structure and biogeochemical cycling in future climate change scenarios and advance our exploration of the potential use of marine microorganisms as markers for environmental conditions.}, } @article {pmid30082592, year = {2018}, author = {Xu, Z and Te, SH and Xu, C and He, Y and Gin, KY}, title = {Variations of Bacterial Community Composition and Functions in an Estuary Reservoir during Spring and Summer Alternation.}, journal = {Toxins}, volume = {10}, number = {8}, pages = {}, pmid = {30082592}, issn = {2072-6651}, mesh = {Bacteria/classification/genetics ; China ; Chlorophyll A/analysis ; DNA, Bacterial/genetics ; Environmental Monitoring ; *Estuaries ; Microbiota ; RNA, Ribosomal, 16S/genetics ; *Seasons ; *Water Microbiology ; }, abstract = {In this study, we focused on the dynamics of bacterial community composition in a large reservoir in the Yangtze estuary during spring and summer seasons, especially the variations of functional mechanisms of microbial community during the seasonal alternation between spring and summer. Both 16S rRNA gene sequencing and shotgun metagenomic sequencing technology were used for these purposes. The results indicated that obvious variations of bacterial community structures were found at different sites. Particle-associated bacterial taxa exhibited higher abundance at the inlet site, which was closer to the Yangtze River with a high level of turbidity. In other sites, Synechococcus, as the most dominant cyanobacterial species, revealed high abundance driven by increased temperature. Moreover, some heterotrophic bacterial taxa revealed high abundance following the increased Synechococcus in summer, which indicated potential correlations about carbon source utilization between these microorganisms. In addition, the shotgun metagenomic data indicated during the period of seasonal alternation between spring and summer, the carbohydrate transport and metabolism, energy production and conversion, translation/ribosomal biogenesis, and cell wall/membrane/envelope biogenesis were significantly enhanced at the exit site. However, the course of cell cycle control/division was more active at the internal site.}, } @article {pmid30081953, year = {2018}, author = {Zhu, J and Liao, M and Yao, Z and Liang, W and Li, Q and Liu, J and Yang, H and Ji, Y and Wei, W and Tan, A and Liang, S and Chen, Y and Lin, H and Zhu, X and Huang, S and Tian, J and Tang, R and Wang, Q and Mo, Z}, title = {Breast cancer in postmenopausal women is associated with an altered gut metagenome.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {136}, pmid = {30081953}, issn = {2049-2618}, mesh = {Adult ; Bacteria/*classification/genetics ; Bacterial Proteins/genetics ; Breast Neoplasms/metabolism/*microbiology ; C-Reactive Protein/metabolism ; Case-Control Studies ; Estradiol/metabolism ; Female ; *Gastrointestinal Microbiome ; Gene Regulatory Networks ; Humans ; Metagenomics/*methods ; Middle Aged ; Phylogeny ; Postmenopause/metabolism ; Premenopause/metabolism ; }, abstract = {BACKGROUND: Increasing evidence suggests that gut microbiota play a role in the pathogenesis of breast cancer. The composition and functional capacity of gut microbiota associated with breast cancer have not been studied systematically.

METHODS: We performed a comprehensive shotgun metagenomic analysis of 18 premenopausal breast cancer patients, 25 premenopausal healthy controls, 44 postmenopausal breast cancer patients, and 46 postmenopausal healthy controls.

RESULTS: Microbial diversity was higher in breast cancer patients than in controls. Relative species abundance in gut microbiota did not differ significantly between premenopausal breast cancer patients and premenopausal controls. In contrast, relative abundance of 45 species differed significantly between postmenopausal patients and postmenopausal controls: 38 species were enriched in postmenopausal patients, including Escherichia coli, Klebsiella sp_1_1_55, Prevotella amnii, Enterococcus gallinarum, Actinomyces sp. HPA0247, Shewanella putrefaciens, and Erwinia amylovora, and 7 species were less abundant in postmenopausal patients, including Eubacterium eligens and Lactobacillus vaginalis. Acinetobacter radioresistens and Enterococcus gallinarum were positively but weakly associated with expression of high-sensitivity C-reactive protein; Shewanella putrefaciens and Erwinia amylovora were positively but weakly associated with estradiol levels. Actinomyces sp. HPA0247 negatively but weakly correlated with CD3[+]CD8[+] T cell numbers. Further characterization of metagenome functional capacity indicated that the gut metagenomes of postmenopausal breast cancer patients were enriched in genes encoding lipopolysaccharide biosynthesis, iron complex transport system, PTS system, secretion system, and beta-oxidation.

CONCLUSION: The composition and functions of the gut microbial community differ between postmenopausal breast cancer patients and healthy controls. The gut microbiota may regulate or respond to host immunity and metabolic balance. Thus, while cause and effect cannot be determined, there is a reproducible change in the microbiota of treatment-naive patients relative to matched controls.}, } @article {pmid30078113, year = {2018}, author = {Song, J and Kim, SY and Kim, DH and Lee, YS and Sim, JS and Hahn, BS and Lee, CM}, title = {Characterization of an inhibitor-resistant endo-1,4-β-mannanase from the gut microflora metagenome of Hermetia illucens.}, journal = {Biotechnology letters}, volume = {40}, number = {9-10}, pages = {1377-1387}, doi = {10.1007/s10529-018-2596-2}, pmid = {30078113}, issn = {1573-6776}, support = {PJ01045703//Rural Development Administration/ ; PJ01086901//Rural Development Administration/ ; }, mesh = {Animals ; Cloning, Molecular ; Diptera/genetics/*microbiology ; Enzyme Inhibitors/pharmacology ; Escherichia coli/genetics ; Galactose/analogs & derivatives ; Gastrointestinal Microbiome/*genetics ; Insect Proteins/antagonists & inhibitors/genetics/metabolism ; Mannans/metabolism ; *Metagenome ; Phylogeny ; Recombinant Proteins/genetics/metabolism ; Substrate Specificity ; beta-Mannosidase/*antagonists & inhibitors/genetics/*metabolism ; }, abstract = {OBJECTIVE: Hermetia illucens is a voracious insect scavenger that efficiently decomposes food waste. To exploit novel hydrolytic enzymes from this insect, we constructed a fosmid metagenome library using unculturable H. illucens intestinal microorganisms.

RESULTS: Functional screening of the library on carboxymethyl cellulose plates identified a fosmid clone with a product displaying hydrolytic activity. Fosmid sequence analysis revealed a novel mannan-degrading gene (ManEM17) composed of 1371 base pairs, encoding 456 amino acids with a deduced 54 amino acid N-terminal signal peptide sequence. Conceptual translation and domain analysis revealed that sequence homology was highest (46%) with endo-1,4-β-mannosidase of Anaerophaga thermohalophila. Phylogenetic and domain analysis indicated that ManEM17 belongs to a novel β-mannanase containing a glycoside hydrolase family 26 domain. The recombinant protein (rManEM17) was expressed in Escherichia coli, exhibiting the highest activity at 55 °C and pH 6.5. The protein hydrolyzed substrates with β-1,4-glycosidic mannoses; maximum specific activity (5467 U mg[-1]) occurred toward locust bean gum galactomannan. However, rManEM17 did not hydrolyze p-Nitrophenyl-β-pyranosides, demonstrating endo-form mannanase activity. Furthermore, rManEM17 was highly stable under stringent conditions, including polar organic solvents as well as chemical reducing and denaturing reagents.

CONCLUSIONS: ManEM17 is an attractive candidate for mannan degradation under the high-organic-solvent and protein-denaturing processes in food and feed industries.}, } @article {pmid30077182, year = {2018}, author = {Ye, Z and Zhang, N and Wu, C and Zhang, X and Wang, Q and Huang, X and Du, L and Cao, Q and Tang, J and Zhou, C and Hou, S and He, Y and Xu, Q and Xiong, X and Kijlstra, A and Qin, N and Yang, P}, title = {A metagenomic study of the gut microbiome in Behcet's disease.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {135}, pmid = {30077182}, issn = {2049-2618}, mesh = {Animals ; Bacteria/*classification/genetics/isolation & purification ; Bacterial Capsules/genetics ; Behcet Syndrome/*microbiology ; Case-Control Studies ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gene Expression Regulation, Bacterial ; Humans ; Male ; Metagenomics/*methods ; Mice ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Saliva/microbiology ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Behcet's disease (BD) is a recalcitrant, multisystemic inflammatory disease that can lead to irreversible blindness. Microbial agents have been considered to contribute to the pathogenesis of this disease, but the underlying mechanisms remain unclear. In this study, we investigated the association of gut microbiome composition with BD as well as its possible roles in the development of this disease.

METHODS: Fecal and saliva samples were collected from 32 active BD patients and 74 healthy controls. DNA extracted from fecal samples was subjected to metagenomic analysis, whereas DNA extracted from saliva samples was subjected to 16S rRNA gene sequencing analysis. The results were used to compare the composition and biological function of the microbiome between patients and healthy controls. Lastly, transplantation of pooled fecal samples from active BD patients into B10RIII mice undergoing experimental autoimmune uveitis (EAU) was performed to determine the causal relationship between the gut microbiome and BD.

RESULTS: Fecal samples from active BD patients were shown to be enriched in Bilophila spp., a sulfate-reducing bacteria (SRB) and several opportunistic pathogens (e.g., Parabacteroides spp. and Paraprevotella spp.) along with a lower level of butyrate-producing bacteria (BPB) Clostridium spp. and methanogens (Methanoculleus spp. Methanomethylophilus spp.). Analysis of microbial functions revealed that capsular polysaccharide transport system, oxidation-reduction process, type III, and type IV secretion systems were also increased in active BD patients. Network analysis showed that the BD-enriched SRB and opportunistic pathogens were positively correlated with each other, but they were negatively associated with the BPB and methanogens. Animal experiments revealed that fecal microbiota transplantation with feces from BD patients significantly exacerbated EAU activity and increased the production of inflammatory cytokines including IL-17 and IFN-γ.

CONCLUSIONS: Our findings revealed that BD is associated with considerable gut microbiome changes, which is corroborated by a mouse study of fecal microbiota transplants. A model explaining the association of the gut microbiome composition with BD pathogenesis is proposed.}, } @article {pmid30076897, year = {2018}, author = {Hagihara, M and Yamashita, R and Matsumoto, A and Mori, T and Kuroki, Y and Kudo, H and Oka, K and Takahashi, M and Nonogaki, T and Yamagishi, Y and Mikamo, H}, title = {The impact of Clostridium butyricum MIYAIRI 588 on the murine gut microbiome and colonic tissue.}, journal = {Anaerobe}, volume = {54}, number = {}, pages = {8-18}, doi = {10.1016/j.anaerobe.2018.07.012}, pmid = {30076897}, issn = {1095-8274}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Clostridium butyricum/genetics/isolation & purification/metabolism/*physiology ; Colon/*microbiology/pathology ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred ICR ; Phylogeny ; Probiotics/pharmacology ; }, abstract = {BACKGROUND: Clostridium butyricum MIYAIRI 588 (CBM 588) is a probiotic bacterium that is used as an anti-diarrheal medicine in Japan. However, the impact of this probiotic on the gut microbiome has not been fully elucidated, especially, when used with antimicrobials.

MATERIAL AND METHODS: In an in vivo study, CBM 588 monotherapy, clindamycin monotherapy, CBM 588 and clindamycin (combination therapy), or normal saline (control) was orally administered to mice for 4 days, and fecal samples were collected for 18 days to enumerate C. butyricum. We also extracted DNA from these fecal samples for metagenomics analysis by amplification of the V3-V4 region of the bacterial 16S rRNA gene and MiSeq Illumina sequencing. In addition, the concentrations of some short chain fatty acids were assessed in the fecal samples. A histological analysis was also conducted.

RESULTS: On day 4 (the last treatment day), there was no difference in the total counts of C. butyricum between the CBM 588 monotherapy and combination therapy groups (5.21 ± 0.78 vs. 5.13 ± 0.45 log10 cfu/g, p = 0.86). Clindamycin treatment resulted in dramatic increases in the phylum Firmicutes, especially Enterobacteriaceae, Clostridiaceae, Lactobacillus, and Enterococcus, compared with the other groups during the treatment period. CBM 588 treatment modified the bacterial community composition at lower phylogenetic levels. Some bacterial taxa, such as Bifidobacterium, Coprococcus, and Bacteroides, were significantly increased in the combination therapy group when compared with the other groups. In the metabolic analysis, CBM 588 enhanced lactic acid production. It also enhanced the efficiency of lactic acid use for the production of butyric acid. Only the clindamycin monotherapy group showed abnormal colon tissue, with superficial epithelial necrosis and the presence of inflammatory cells.

CONCLUSION: CBM 588 treatment modulated the gut microbiota composition under dysbiosis due to the use of an antimicrobial with strong activity against anaerobes and significantly reduced epithelial damage.}, } @article {pmid30075203, year = {2018}, author = {Kumar, M and Ji, B and Babaei, P and Das, P and Lappa, D and Ramakrishnan, G and Fox, TE and Haque, R and Petri, WA and Bäckhed, F and Nielsen, J}, title = {Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: Lessons from genome-scale metabolic modeling.}, journal = {Metabolic engineering}, volume = {49}, number = {}, pages = {128-142}, pmid = {30075203}, issn = {1096-7184}, support = {R01 AI043596/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acids/*blood ; Child ; *Child Nutrition Disorders/blood/genetics/microbiology ; Child, Preschool ; *Dysbiosis/blood/genetics/microbiology ; Female ; *Gastrointestinal Microbiome ; *Genome, Bacterial ; Humans ; Male ; }, abstract = {Malnutrition is a severe non-communicable disease, which is prevalent in children from low-income countries. Recently, a number of metagenomics studies have illustrated associations between the altered gut microbiota and child malnutrition. However, these studies did not examine metabolic functions and interactions between individual species in the gut microbiota during health and malnutrition. Here, we applied genome-scale metabolic modeling to model the gut microbial species, which were selected from healthy and malnourished children from three countries. Our analysis showed reduced metabolite production capabilities in children from two low-income countries compared with a high-income country. Additionally, the models were also used to predict the community-level metabolic potentials of gut microbes and the patterns of pairwise interactions among species. Hereby we found that due to bacterial interactions there may be reduced production of certain amino acids in malnourished children compared with healthy children from the same communities. To gain insight into alterations in the metabolism of malnourished (stunted) children, we also performed targeted plasma metabolic profiling in the first 2 years of life of 25 healthy and 25 stunted children. Plasma metabolic profiling further revealed that stunted children had reduced plasma levels of essential amino acids compared to healthy controls. Our analyses provide a framework for future efforts towards further characterization of gut microbial metabolic capabilities and their contribution to malnutrition.}, } @article {pmid30072968, year = {2018}, author = {Dittberner, H and Ohlmann, N and Acquisti, C}, title = {Stoichio-Metagenomics of Ocean Waters: A Molecular Evolution Approach to Trace the Dynamics of Nitrogen Conservation in Natural Communities.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1590}, pmid = {30072968}, issn = {1664-302X}, abstract = {Nitrogen is crucially limiting in ocean surface waters, and its availability varies substantially with coastal regions typically richer in nutrients than open oceans. In a biological stoichiometry framework, a parsimonious strategy of nitrogen allocation predicts nitrogen content of proteins to be lower in communities adapted to open ocean than to coastal regions. To test this hypothesis we have directly interrogated marine microbial communities, using a series of metagenomics datasets with a broad geographical distribution from the Global Ocean Sampling Expedition. Analyzing over 20 million proteins, we document a ubiquitous signal of nitrogen conservation in open ocean communities, both in membrane and non-membrane proteins. Efficient nitrogen allocation is expected to specifically target proteins that are expressed at high rate in response to nitrogen starvation. Furthermore, in order to preserve protein functional efficiency, economic nitrogen allocation is predicted to target primarily the least functionally constrained regions of proteins. Contrasting the NtcA-induced pathway, typically up-regulated in response to nitrogen starvation, with the arginine anabolic pathway, which is instead up-regulated in response to nitrogen abundance, we show how both these predictions are fulfilled. Using evolutionary rates as an informative proxy of functional constraints, we show that variation in nitrogen allocation between open ocean and coastal communities is primarily localized in the least functionally constrained regions of the genes triggered by NtcA. As expected, such a pattern is not detectable in the genes involved in the arginine anabolic pathway. These results directly link environmental nitrogen availability to different adaptive strategies of genome evolution, and emphasize the relevance of the material costs of evolutionary change in natural ecosystems.}, } @article {pmid30069051, year = {2018}, author = {Bahram, M and Hildebrand, F and Forslund, SK and Anderson, JL and Soudzilovskaia, NA and Bodegom, PM and Bengtsson-Palme, J and Anslan, S and Coelho, LP and Harend, H and Huerta-Cepas, J and Medema, MH and Maltz, MR and Mundra, S and Olsson, PA and Pent, M and Põlme, S and Sunagawa, S and Ryberg, M and Tedersoo, L and Bork, P}, title = {Structure and function of the global topsoil microbiome.}, journal = {Nature}, volume = {560}, number = {7717}, pages = {233-237}, doi = {10.1038/s41586-018-0386-6}, pmid = {30069051}, issn = {1476-4687}, mesh = {Bacteria/genetics/*isolation & purification ; *Biodiversity ; DNA Barcoding, Taxonomic ; Drug Resistance, Microbial/genetics ; *Earth, Planet ; Fungi/genetics/*isolation & purification ; Hydrogen-Ion Concentration ; Metagenomics ; Microbiota/genetics/*physiology ; Oceans and Seas ; Rain ; Seawater/microbiology ; *Soil Microbiology ; }, abstract = {Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities[1-4]. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial-fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.}, } @article {pmid30069039, year = {2018}, author = {Shelyakin, PV and Garushyants, SK and Nikitin, MA and Mudrova, SV and Berumen, M and Speksnijder, AGCL and Hoeksema, BW and Fontaneto, D and Gelfand, MS and Ivanenko, VN}, title = {Microbiomes of gall-inducing copepod crustaceans from the corals Stylophora pistillata (Scleractinia) and Gorgonia ventalina (Alcyonacea).}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {11563}, pmid = {30069039}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*microbiology/*parasitology ; Caribbean Region ; Cluster Analysis ; Copepoda/*growth & development ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saudi Arabia ; Sequence Analysis, DNA ; }, abstract = {Corals harbor complex and diverse microbial communities that strongly impact host fitness and resistance to diseases, but these microbes themselves can be influenced by stresses, like those caused by the presence of macroscopic symbionts. In addition to directly influencing the host, symbionts may transmit pathogenic microbial communities. We analyzed two coral gall-forming copepod systems by using 16S rRNA gene metagenomic sequencing: (1) the sea fan Gorgonia ventalina with copepods of the genus Sphaerippe from the Caribbean and (2) the scleractinian coral Stylophora pistillata with copepods of the genus Spaniomolgus from the Saudi Arabian part of the Red Sea. We show that bacterial communities in these two systems were substantially different with Actinobacteria, Alphaproteobacteria, and Betaproteobacteria more prevalent in samples from Gorgonia ventalina, and Gammaproteobacteria in Stylophora pistillata. In Stylophora pistillata, normal coral microbiomes were enriched with the common coral symbiont Endozoicomonas and some unclassified bacteria, while copepod and gall-tissue microbiomes were highly enriched with the family ME2 (Oceanospirillales) or Rhodobacteraceae. In Gorgonia ventalina, no bacterial group had significantly different prevalence in the normal coral tissues, copepods, and injured tissues. The total microbiome composition of polyps injured by copepods was different. Contrary to our expectations, the microbial community composition of the injured gall tissues was not directly affected by the microbiome of the gall-forming symbiont copepods.}, } @article {pmid30068938, year = {2018}, author = {Hoedt, EC and Parks, DH and Volmer, JG and Rosewarne, CP and Denman, SE and McSweeney, CS and Muir, JG and Gibson, PR and Cuív, PÓ and Hugenholtz, P and Tyson, GW and Morrison, M}, title = {Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size.}, journal = {The ISME journal}, volume = {12}, number = {12}, pages = {2942-2953}, pmid = {30068938}, issn = {1751-7370}, mesh = {Animals ; Cattle ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genome Size/*genetics ; Humans ; *Metagenomics ; Methanobacteriaceae/*genetics/physiology ; Methanobrevibacter/genetics/physiology ; Phylogeny ; Rumen/microbiology ; }, abstract = {The genus Methanosphaera is a well-recognized but poorly characterized member of the mammalian gut microbiome, and distinctive from Methanobrevibacter smithii for its ability to induce a pro-inflammatory response in humans. Here we have used a combination of culture- and metagenomics-based approaches to expand the representation and information for the genus, which has supported the examination of their phylogeny and physiological capacity. Novel isolates of the genus Methanosphaera were recovered from bovine rumen digesta and human stool, with the bovine isolate remarkable for its large genome size relative to other Methanosphaera isolates from monogastric hosts. To substantiate this observation, we then recovered seven high-quality Methanosphaera-affiliated population genomes from ruminant and human gut metagenomic datasets. Our analyses confirm a monophyletic origin of Methanosphaera spp. and that the colonization of monogastric and ruminant hosts favors representatives of the genus with different genome sizes, reflecting differences in the genome content needed to persist in these different habitats.}, } @article {pmid30067975, year = {2018}, author = {Kang, K and Ni, Y and Li, J and Imamovic, L and Sarkar, C and Kobler, MD and Heshiki, Y and Zheng, T and Kumari, S and Wong, JCY and Archna, A and Wong, CWM and Dingle, C and Denizen, S and Baker, DM and Sommer, MOA and Webster, CJ and Panagiotou, G}, title = {The Environmental Exposures and Inner- and Intercity Traffic Flows of the Metro System May Contribute to the Skin Microbiome and Resistome.}, journal = {Cell reports}, volume = {24}, number = {5}, pages = {1190-1202.e5}, doi = {10.1016/j.celrep.2018.06.109}, pmid = {30067975}, issn = {2211-1247}, mesh = {Drug Resistance, Bacterial/genetics ; *Environmental Exposure ; Hong Kong ; Humans ; Metagenome ; *Microbiota ; *Railroads ; Skin/*microbiology ; }, abstract = {The skin functions as the primary interface between the human body and the external environment. To understand how the microbiome varies within urban mass transit and influences the skin microbiota, we profiled the human palm microbiome after contact with handrails within the Hong Kong Mass Transit Railway (MTR) system. Intraday sampling time was identified as the primary determinant of the variation and recurrence of the community composition, whereas human-associated species and clinically important antibiotic resistance genes (ARGs) were captured as p.m. signatures. Line-specific signatures were notably correlated with line-specific environmental exposures and city characteristics. The sole cross-border line appeared as an outlier in most analyses and showed high relative abundance and a significant intraday increment of clinically important ARGs (24.1%), suggesting potential cross-border ARG transmission, especially for tetracycline and vancomycin resistance. Our study provides an important reference for future public health strategies to mitigate intracity and cross-border pathogen and ARG transmission.}, } @article {pmid30066173, year = {2019}, author = {Scorza, C and Piccini, C and Martínez Busi, M and Abin Carriquiry, JA and Zunino, P}, title = {Alterations in the Gut Microbiota of Rats Chronically Exposed to Volatilized Cocaine and Its Active Adulterants Caffeine and Phenacetin.}, journal = {Neurotoxicity research}, volume = {35}, number = {1}, pages = {111-121}, pmid = {30066173}, issn = {1476-3524}, mesh = {Animals ; Biodiversity ; Caffeine/*administration & dosage ; Central Nervous System Agents/*administration & dosage ; Cocaine/*administration & dosage ; Cocaine-Related Disorders/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/genetics ; Illicit Drugs/pharmacology ; Male ; Phenacetin/*administration & dosage ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Random Allocation ; Rats, Wistar ; Volatilization ; }, abstract = {A role of the gut microbiota in influencing brain function and emotional disorders has been suggested. However, only a few studies have investigated the gut microbiota in the context of drug addiction.Cocaine can be smoked (i.e., crack or coca paste) and its consumption is associated with a very high abuse liability and toxicity. We have recently reported that cocaine base seized samples contained caffeine and phenacetin as main active adulterants, which may potentiate its motivational, reinforcing, and toxic effects. However, the effect of volatilized cocaine and adulterants on the gut microbiota remained unknown. In the present study, we evaluated the effect of volatilized cocaine and two adulterants on the structure, diversity, and functionality of the gut microbiota in rats. Animals were chronically exposed to the fume of cocaine, caffeine, and phenacetin during 14 days. At the end of the treatment, feces were collected and the structure, composition, and functional predictions of the gut microbiota were analyzed. Cocaine significantly decreased the community richness and diversity of the gut microbiota while both cocaine and phenacetin drastically changed its composition. Phenacetin significantly increased the Firmicutes-Bacteroidetes ratio compared to the control group. When the predicted metagenome functional content of the bacterial communities was analyzed, all the treatments induced a dramatic decrease of the aromatic amino acid decarboxylase gene. Our findings suggest that repeated exposure to volatilized cocaine, as well as to the adulterants caffeine and phenacetin, leads to changes in the gut microbiota. Future studies are needed to understand the mechanisms underlying these changes and how this information may support the development of novel treatments in drug addiction.}, } @article {pmid30065291, year = {2018}, author = {Meier-Kolthoff, JP and Uchiyama, J and Yahara, H and Paez-Espino, D and Yahara, K}, title = {Investigation of recombination-intense viral groups and their genes in the Earth's virome.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {11496}, pmid = {30065291}, issn = {2045-2322}, support = {16H06429//Ministry of Education, Culture, Sports, Science, and Technology (MEXT)/International ; 16K21723//Ministry of Education, Culture, Science, Sports, and Technology (MEXT) of Japan/International ; 17H05826//Ministry of Education, Culture, Science, Sports, and Technology (MEXT) of Japan/International ; }, mesh = {Bacteria/virology ; Bacteriophages/genetics ; Biodiversity ; DNA, Viral/genetics ; Earth, Planet ; Ecosystem ; Genome, Viral/*genetics ; Host Specificity/genetics ; Humans ; Metagenome/genetics ; Metagenomics/methods ; Mouth/virology ; Recombination, Genetic/*genetics ; Viruses/*genetics ; }, abstract = {Bacteriophages (phages), or bacterial viruses, are the most abundant and diverse biological entities that impact the global ecosystem. Recent advances in metagenomics have revealed their rampant abundance in the biosphere. A fundamental aspect of bacteriophages that remains unexplored in metagenomic data is the process of recombination as a driving force in evolution that occurs among different viruses within the same bacterial host. Here, we systematically examined signatures of recombination in every gene from 211 species-level viral groups in a recently obtained dataset of the Earth's virome that contain corresponding information on the host bacterial species. Our study revealed that signatures of recombination are widespread (84%) among the diverse viral groups. We identified 25 recombination-intense viral groups, widely distributed across the viral taxonomy, and present in bacterial species living in the human oral cavity. We also revealed a significant inverse association between the recombination-intense viral groups and Type II restriction endonucleases, that could be effective in reducing recombination among phages in a cell. Furthermore, we identified recombination-intense genes that are significantly enriched for encoding phage morphogenesis proteins. Changes in the viral genomic sequence by recombination may be important to escape cleavage by the host bacterial immune systems.}, } @article {pmid30065105, year = {2018}, author = {Faria, JP and Rocha, M and Rocha, I and Henry, CS}, title = {Methods for automated genome-scale metabolic model reconstruction.}, journal = {Biochemical Society transactions}, volume = {46}, number = {4}, pages = {931-936}, doi = {10.1042/BST20170246}, pmid = {30065105}, issn = {1470-8752}, mesh = {Automation ; Databases, Genetic ; High-Throughput Nucleotide Sequencing ; Humans ; Metabolic Networks and Pathways ; *Metagenome ; Microbiota ; *Models, Biological ; Software Design ; }, abstract = {In the era of next-generation sequencing and ubiquitous assembly and binning of metagenomes, new putative genome sequences are being produced from isolate and microbiome samples at ever-increasing rates. Genome-scale metabolic models have enormous utility for supporting the analysis and predictive characterization of these genomes based on sequence data. As a result, tools for rapid automated reconstruction of metabolic models are becoming critically important for supporting the analysis of new genome sequences. Many tools and algorithms have now emerged to support rapid model reconstruction and analysis. Here, we are comparing and contrasting the capabilities and output of a variety of these tools, including ModelSEED, Raven Toolbox, PathwayTools, SuBliMinal Toolbox and merlin.}, } @article {pmid30063098, year = {2018}, author = {Kojadinovic-Sirinelli, M and Villain, A and Puppo, C and Fon Sing, S and Prioretti, L and Hubert, P and Grégori, G and Zhang, Y and Sassi, JF and Claverie, JM and Blanc, G and Gontero, B}, title = {Exploring the microbiome of the "star" freshwater diatom Asterionella formosa in a laboratory context.}, journal = {Environmental microbiology}, volume = {20}, number = {10}, pages = {3601-3615}, doi = {10.1111/1462-2920.14337}, pmid = {30063098}, issn = {1462-2920}, support = {ANR-11-IDEX-0001-02//ANR/International ; ANR-10-INBS-0009//ANR/International ; //Aix-Marseille University/International ; 1166-39417//European FEDER Fund/International ; }, mesh = {Bacteria/*isolation & purification ; Bacteroidetes/isolation & purification ; Diatoms/*microbiology ; Fresh Water ; Heterotrophic Processes ; *Microbiota ; Phylogeny ; Proteobacteria/isolation & purification ; Taiwan ; }, abstract = {Most of our knowledge on the mechanisms underlying diatom-bacterial interactions has been acquired through studies involving isolation of culturable partners. Here, we established a laboratory model of intermediate complexity between complex natural communities and laboratory pure culture models. We investigated the whole community formed by the freshwater diatom Asterionella formosa and its associated bacteria in a laboratory context, including both culturable and unculturable bacteria. Combining cellular and molecular approaches, we showed that in laboratory cultures, A. formosa microbiome was dynamic and comprised of numerous bacterial species (mainly Proteobacteria and Bacteroidetes). Using metagenomics, we explored several metabolic potentials present within the bacterial community. Our analyses suggested that bacteria were heterotrophic although a third of them (Alpha- and Beta-proteobacteria) could also be phototrophic. About 60% of the bacteria, phylogenetically diverse, could metabolize glycolate. The capacity to synthesize molecules such as B vitamins appeared unevenly distributed among bacteria. Altogether, our results brought insights into the bacterial diversity found in diatom-bacterial communities and hinted at metabolic interdependencies within the community that could result in diatom-bacterial and bacterial-bacterial interactions. The present work allowed us to explore the functional architecture of the bacterial community associated with A. formosa in culture and is complementary to field studies.}, } @article {pmid30058755, year = {2018}, author = {Díaz-Sánchez, S and Hernández-Jarguín, A and Torina, A and Fernández de Mera, IG and Estrada-Peña, A and Villar, M and La Russa, F and Blanda, V and Vicente, J and Caracappa, S and Gortazar, C and de la Fuente, J}, title = {Biotic and abiotic factors shape the microbiota of wild-caught populations of the arbovirus vector Culicoides imicola.}, journal = {Insect molecular biology}, volume = {27}, number = {6}, pages = {847-861}, doi = {10.1111/imb.12526}, pmid = {30058755}, issn = {1365-2583}, mesh = {Animals ; Ceratopogonidae/*microbiology ; Dogs ; Environment ; Female ; Humans ; Insect Vectors/*microbiology ; Microbiota ; }, abstract = {Biting midges of the genus Culicoides are known vectors of arboviruses affecting human and animal health. However, little is known about Culicoides imicola microbiota and its influence on this insect's biology. In this study, the impact of biotic and abiotic factors on C. imicola microbiota was characterized using shotgun-metagenomic sequencing of whole-body DNA samples. Wild-caught C. imicola adult nulliparous females were sampled in two locations from Sicily, Italy. The climatic variables of temperature and soil moisture from both localities were recorded together with potential host bloodmeal sources. Shared core microbiome among C. imicola populations included Pseudomonas, Escherichia, Halomonas, Candidatus Zinderia, Propionibacterium, and Schizosaccharomyces. Specific and unique taxa were also found in C. imicola from each location, highlighting similarities and differences in microbiome composition between the two populations. DNA and protein identification showed differences in host preferences between the two populations, with Homo sapiens and Canis lupus familiaris L. being the preferred bloodmeal source in both locations. A principal component analysis showed that the combined effect of host preferences (H. sapiens) and local soil moisture factors shape the microbiome composition of wild-caught populations of C. imicola. These results contribute to characterizing the role of the microbiome in insect adaptation and its utility in predicting geographic expansion of Culicoides species with potential implications for the control of vector-borne diseases.}, } @article {pmid30058657, year = {2018}, author = {Yin, J and Li, Y and Han, H and Liu, Z and Zeng, X and Li, T and Yin, Y}, title = {Long-term effects of lysine concentration on growth performance, intestinal microbiome, and metabolic profiles in a pig model.}, journal = {Food & function}, volume = {9}, number = {8}, pages = {4153-4163}, doi = {10.1039/c8fo00973b}, pmid = {30058657}, issn = {2042-650X}, mesh = {Amino Acid Transport Systems/blood ; Amino Acids/blood ; Animals ; Bacteria/genetics/isolation & purification ; Dose-Response Relationship, Drug ; Gastrointestinal Microbiome ; Intestines/*microbiology ; Lysine/administration & dosage/*pharmacology ; Male ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Random Allocation ; Real-Time Polymerase Chain Reaction ; Swine/*growth & development/microbiology ; }, abstract = {Lysine is a common limiting amino acid in human and animal diets and plays an important role in cell proliferation and metabolism. Our previous study suggested that short-term lysine restriction improved feed intake. Herein, we further investigated the long-term effects of lysine restriction on intestinal microbial communities and metabolic profiles in pigs by 16S rDNA sequencing and metabolomic analysis. The results showed that 30% lysine limitation increased the feed intake in piglets but not in growing and finishing pigs. Microbiota sequencing was conducted, and we identified 12 differentiated microbes at the genus level in response to dietary lysine restriction. Metagenomic predictions by PICRUSt suggested that the altered microbiota was mainly involved in the host metabolism, especially in amino acid metabolism. Intestinal metabolomic study identified 20 differentiated metabolites in finishing pigs, which were mapped into 5 metabolic pathways including glutamine and glutamate metabolism, taurine metabolism, alanine, aspartate and glutamate metabolism, vitamin B6 metabolism, and pentose and glucoronate metabolism. Determination of serum amino acids and intestinal amino acid transporters further validated the results obtained from PICRUSt and metabolomic analyses, which showed that long-term lysine restriction influenced amino acid metabolism. Phosphorylation of mTOR in the intestine was not altered in lysine-restricted pigs, whereas lysine limitation markedly inhibited the AMPK signaling. In conclusion, long-term lysine restriction from piglets to finishing pigs affected the amino acid metabolism, which might be associated with gut microbiota and AMPK signaling.}, } @article {pmid30058291, year = {2019}, author = {Bahram, M and Anslan, S and Hildebrand, F and Bork, P and Tedersoo, L}, title = {Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment.}, journal = {Environmental microbiology reports}, volume = {11}, number = {4}, pages = {487-494}, pmid = {30058291}, issn = {1758-2229}, support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; ERC-AdG-669830/ERC_/European Research Council/International ; }, mesh = {Archaea/*classification/genetics ; DNA Primers/*genetics ; DNA, Archaeal/genetics ; *Environmental Microbiology ; Metagenomics ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {High-throughput studies of microbial communities suggest that Archaea are a widespread component of microbial diversity in various ecosystems. However, proper quantification of archaeal diversity and community ecology remains limited, as sequence coverage of Archaea is usually low owing to the inability of available prokaryotic primers to efficiently amplify archaeal compared to bacterial rRNA genes. To improve identification and quantification of Archaea, we designed and validated the utility of several primer pairs to efficiently amplify archaeal 16S rRNA genes based on up-to-date reference genes. We demonstrate that several of these primer pairs amplify phylogenetically diverse Archaea with high sequencing coverage, outperforming commonly used primers. Based on comparing the resulting long 16S rRNA gene fragments with public databases from all habitats, we found several novel family- to phylum-level archaeal taxa from topsoil and surface water. Our results suggest that archaeal diversity has been largely overlooked due to the limitations of available primers, and that improved primer pairs enable to estimate archaeal diversity more accurately.}, } @article {pmid30056386, year = {2018}, author = {Kushugulova, A and Forslund, SK and Costea, PI and Kozhakhmetov, S and Khassenbekova, Z and Urazova, M and Nurgozhin, T and Zhumadilov, Z and Benberin, V and Driessen, M and Hercog, R and Voigt, AY and Benes, V and Kandels-Lewis, S and Sunagawa, S and Letunic, I and Bork, P}, title = {Metagenomic analysis of gut microbial communities from a Central Asian population.}, journal = {BMJ open}, volume = {8}, number = {7}, pages = {e021682}, pmid = {30056386}, issn = {2044-6055}, mesh = {Adult ; Aged ; Case-Control Studies ; Cohort Studies ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Kazakhstan ; Male ; Metabolic Syndrome/microbiology ; Metagenomics ; Middle Aged ; Probiotics/*administration & dosage ; }, abstract = {OBJECTIVE: Changes in the gut microbiota are increasingly recognised to be involved in many diseases. This ecosystem is known to be shaped by many factors, including climate, geography, host nutrition, lifestyle and medication. Thus, knowledge of varying populations with different habits is important for a better understanding of the microbiome.

DESIGN: We therefore conducted a metagenomic analysis of intestinal microbiota from Kazakh donors, recruiting 84 subjects, including male and female healthy subjects and metabolic syndrome (MetS) patients aged 25-75 years, from the Kazakh administrative centre, Astana. We characterise and describe these microbiomes, the first deep-sequencing cohort from Central Asia, in comparison with a global dataset (832 individuals from five countries on three continents), and explore correlations between microbiota, clinical and laboratory parameters as well as with nutritional data from Food Frequency Questionnaires.

RESULTS: We observe that Kazakh microbiomes are relatively different from both European and East Asian counterparts, though similar to other Central Asian microbiomes, with the most striking difference being significantly more samples falling within the Prevotella-rich enterotype, potentially reflecting regional diet and lifestyle. We show that this enterotype designation remains stable within an individual over time in 82% of cases. We further observe gut microbiome features that distinguish MetS patients from controls (eg, significantly reduced Firmicutes to Bacteroidetes ratio, Bifidobacteria and Subdoligranulum, alongside increased Prevotella), though these overlap little with previously published reports and thus may reflect idiosyncrasies of the present cohort.

CONCLUSION: Taken together, this exploratory study describes gut microbiome data from an understudied population, providing a starting point for further comparative work on biogeography and research on widespread diseases.

TRIAL REGISTRATION NUMBER: ISRCTN37346212; Post-results.}, } @article {pmid30056005, year = {2018}, author = {Bankevich, A and Pevzner, PA}, title = {Joint Analysis of Long and Short Reads Enables Accurate Estimates of Microbiome Complexity.}, journal = {Cell systems}, volume = {7}, number = {2}, pages = {192-200.e3}, doi = {10.1016/j.cels.2018.06.009}, pmid = {30056005}, issn = {2405-4712}, mesh = {Algorithms ; Bacteria/genetics ; *Gastrointestinal Microbiome ; Genetic Variation ; *Genome, Bacterial ; Humans ; Metagenome ; Metagenomics/*methods ; Sequence Analysis, DNA ; }, abstract = {Reduced microbiome diversity has been linked to several diseases. However, estimating the diversity of bacterial communities-the number and the total length of distinct genomes within a metagenome-remains an open problem in microbial ecology. Here, we describe an algorithm for estimating the microbial diversity in a metagenomic sample based on a joint analysis of short and long reads. Unlike previous approaches, the algorithm does not make any assumptions on the distribution of the frequencies of genomes within a metagenome (as in parametric methods) and does not require a large database that covers the total diversity (as in non-parametric methods). We estimate that genomes comprising a human gut metagenome have total length varying from 1.3 to 3.5 billion nucleotides, with genomes responsible for 50% of total abundance having total length varying from only 25 to 61 million nucleotides. In contrast, genomes comprising an aquifer sediment metagenome have more than two orders of magnitude larger total length (≈840 billion nucleotides).}, } @article {pmid30055354, year = {2018}, author = {Linard, B and Crampton-Platt, A and Moriniere, J and Timmermans, MJTN and Andújar, C and Arribas, P and Miller, KE and Lipecki, J and Favreau, E and Hunter, A and Gómez-Rodríguez, C and Barton, C and Nie, R and Gillett, CPDT and Breeschoten, T and Bocak, L and Vogler, AP}, title = {The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera.}, journal = {Molecular phylogenetics and evolution}, volume = {128}, number = {}, pages = {1-11}, doi = {10.1016/j.ympev.2018.07.008}, pmid = {30055354}, issn = {1095-9513}, mesh = {Algorithms ; Animals ; Base Sequence ; Coleoptera/classification/*genetics ; Databases, Genetic ; *Metagenomics ; Mitochondria/*genetics ; *Phylogeny ; }, abstract = {A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16,000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.}, } @article {pmid30054809, year = {2019}, author = {Decsi, G and Soki, J and Pap, B and Dobra, G and Harmati, M and Kormondi, S and Pankotai, T and Braunitzer, G and Minarovits, J and Sonkodi, I and Urban, E and Nemeth, IB and Nagy, K and Buzas, K}, title = {Chicken or the Egg: Microbial Alterations in Biopsy Samples of Patients with Oral Potentially Malignant Disorders.}, journal = {Pathology oncology research : POR}, volume = {25}, number = {3}, pages = {1023-1033}, pmid = {30054809}, issn = {1532-2807}, support = {2.3.2-15-2016-00015//GINOP/ ; 2.3.2-15-2016-00011//GINOP/ ; NKFI-6-K funding scheme, 11493 project//National Research, Development and Innovation Fund of Hungary/ ; János Bolyai Research Scholarship//Magyar Tudományos Akadémia/ ; }, mesh = {Aged ; Bacteremia/*complications/microbiology/pathology ; Bacteria/classification/genetics/*pathogenicity ; Biopsy ; Case-Control Studies ; DNA, Bacterial/genetics ; Female ; Follow-Up Studies ; Humans ; Hungary/epidemiology ; Male ; Microbiota ; Middle Aged ; Mouth Mucosa/*microbiology/pathology ; Mouth Neoplasms/epidemiology/*microbiology/pathology ; Prognosis ; Sequence Analysis, DNA ; }, abstract = {Oral carcinogenesis often leads to the alteration of the microbiota at the site of the tumor, but data are scarce regarding the microbial communities of oral potentially malignant disorders (OPMDs). Punch biopsies were taken from healthy and non-healthy mucosa of OPMD patients to analyze the microbiome using metagenome sequencing. In healthy oral mucosa biopsies the bacterial phyla Firmicutes, Fusobacteria, Proteobacteria, Actinobacteria and Bacteroidetes were detected by Ion Torrent sequencing. The same phyla as well as the phyla Fibrobacteres and Spirochaetes were present in the OPMD biopsies. On the species level, there were 10 bacterial species unique to the healthy tissue and 35 species unique to the OPMD lesions whereas eight species were detected in both samples. We observed that the relative abundance of Streptococcus mitis decreased in the OPMD lesions compared to the uninvolved tissue. In contrast, the relative abundance of Fusobacterium nucleatum, implicated in carcinogenesis, was elevated in OPMD. We detected markedly increased bacterial diversity in the OPMD lesions compared to the healthy oral mucosa. The ratio of S. mitis and F. nucleatum are characteristically altered in the OPMD lesions compared to the healthy mucosa.}, } @article {pmid30054365, year = {2018}, author = {Esteban-Torres, M and Santamaría, L and Cabrera-Rubio, R and Plaza-Vinuesa, L and Crispie, F and de Las Rivas, B and Cotter, P and Muñoz, R}, title = {A Diverse Range of Human Gut Bacteria Have the Potential To Metabolize the Dietary Component Gallic Acid.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {19}, pages = {}, pmid = {30054365}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; DNA, Bacterial/genetics ; Feces/microbiology ; Gallic Acid/*metabolism ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The human gut microbiota contains a broad variety of bacteria that possess functional genes, with resultant metabolites that affect human physiology and therefore health. Dietary gallates are phenolic components that are present in many foods and beverages and are regarded as having health-promoting attributes. However, the potential for metabolism of these phenolic compounds by the human microbiota remains largely unknown. The emergence of high-throughput sequencing (HTS) technologies allows this issue to be addressed. In this study, HTS was used to assess the incidence of gallate-decarboxylating bacteria within the gut microbiota of healthy individuals for whom bacterial diversity was previously determined to be high. This process was facilitated by the design and application of degenerate PCR primers to amplify a region encoding the catalytic C subunit of gallate decarboxylase (LpdC) from total metagenomic DNA extracted from human fecal samples. HTS resulted in the generation of a total of 3,261,967 sequence reads and revealed that the primary gallate-decarboxylating microbial phyla in the intestinal microbiota were Firmicutes (74.6%), Proteobacteria (17.6%), and Actinobacteria (7.8%). These reads corresponded to 53 genera, i.e., 47% of the bacterial genera detected previously in these samples. Among these genera, Anaerostipes and Klebsiella accounted for the majority of reads (40%). The usefulness of the HTS-lpdC method was demonstrated by the production of pyrogallol from gallic acid, as expected for functional gallate decarboxylases, among representative strains belonging to species identified in the human gut microbiota by this method.IMPORTANCE Despite the increasing wealth of sequencing data, the health contributions of many bacteria found in the human gut microbiota have yet to be elucidated. This study applies a novel experimental approach to predict the ability of gut microbes to carry out a specific metabolic activity, i.e., gallate metabolism. The study showed that, while gallate-decarboxylating bacteria represented 47% of the bacterial genera detected previously in the same human fecal samples, no gallate decarboxylase homologs were identified from representatives of Bacteroidetes The presence of functional gallate decarboxylases was demonstrated in representative Proteobacteria and Firmicutes strains from the human microbiota, an observation that could be of considerable relevance to the in vivo production of pyrogallol, a physiologically important bioactive compound.}, } @article {pmid30050163, year = {2018}, author = {Ishii, S and Suzuki, S and Tenney, A and Nealson, KH and Bretschger, O}, title = {Comparative metatranscriptomics reveals extracellular electron transfer pathways conferring microbial adaptivity to surface redox potential changes.}, journal = {The ISME journal}, volume = {12}, number = {12}, pages = {2844-2863}, pmid = {30050163}, issn = {1751-7370}, mesh = {Carbon/metabolism ; Cytochrome c Group/genetics/metabolism ; Electric Conductivity ; Electrodes ; Electron Transport ; Geobacter/*genetics/metabolism ; Heme ; *Metabolic Networks and Pathways ; Metagenomics ; *Microbiota ; Oxidation-Reduction ; *Transcriptome ; }, abstract = {Some microbes can capture energy through redox reactions with electron flow to solid-phase electron acceptors, such as metal-oxides or poised electrodes, via extracellular electron transfer (EET). While diverse oxide minerals, exhibiting different surface redox potentials, are widely distributed on Earth, little is known about how microbes sense and use the minerals. Here we show electrochemical, metabolic, and transcriptional responses of EET-active microbial communities established on poised electrodes to changes in the surface redox potentials (as electron acceptors) and surrounding substrates (as electron donors). Combination of genome-centric stimulus-induced metatranscriptomics and metabolic pathway investigation revealed that nine Geobacter/Pelobacter microbes performed EET activity differently according to their preferable surface potentials and substrates. While the Geobacter/Pelobacter microbes coded numerous numbers of multi-heme c-type cytochromes and conductive e-pili, wide variations in gene expression were seen in response to altering surrounding substrates and surface potentials, accelerating EET via poised electrode or limiting EET via an open circuit system. These flexible responses suggest that a wide variety of EET-active microbes utilizing diverse EET mechanisms may work together to provide such EET-active communities with an impressive ability to handle major changes in surface potential and carbon source availability.}, } @article {pmid30048915, year = {2018}, author = {Milanović, V and Osimani, A and Garofalo, C and De Filippis, F and Ercolini, D and Cardinali, F and Taccari, M and Aquilanti, L and Clementi, F}, title = {Profiling white wine seed vinegar bacterial diversity through viable counting, metagenomic sequencing and PCR-DGGE.}, journal = {International journal of food microbiology}, volume = {286}, number = {}, pages = {66-74}, doi = {10.1016/j.ijfoodmicro.2018.07.022}, pmid = {30048915}, issn = {1879-3460}, mesh = {Acetic Acid/*analysis ; Bacteria/*classification/genetics/*isolation & purification ; Biodiversity ; Fermentation ; Metagenomics ; Microbiota/genetics ; Molecular Typing ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Wine/*microbiology ; }, abstract = {The production of traditional vinegar is usually carried out using the so-called "seed vinegar" or "mother of vinegar" that is composed of an undefined and complex pool of microorganisms deriving from a previous vinegar production. To date, there have been relatively few studies on the microbiota of seed vinegars. The present study was carried out to discover the bacterial biota of seed vinegar samples used in the homemade production of local vinegars obtained from the acetic fermentation of white wine. The seed vinegar samples were subjected to viable counting and advanced molecular analyses, namely, Illumina sequencing and PCR-DGGE. The adopted polyphasic approach allowed the bacterial diversity of the analyzed samples to be profiled, thus revealing the presence of acetic acid bacteria ascribed to the genera Acetobacter, Gluconacetobacter, Gluconobacter and Komagataeibacter. Moreover, other microbial genera as Pseudomonas, Bacillus and Clostridium were abundantly found in almost all the samples, together with other minority genera. The results of viable counting confirmed the well-acknowledged limitations inherent with acetic acid bacteria recovery on plate growth media. The overall results confirmed that seed vinegars have a complex and heterogeneous biodiversity, thus encouraging their exploitation for the isolation and future technological characterization of cultures to be selected for the manufacture of mixed starter cultures.}, } @article {pmid30046166, year = {2018}, author = {Ma, B and Zhao, K and Lv, X and Su, W and Dai, Z and Gilbert, JA and Brookes, PC and Faust, K and Xu, J}, title = {Genetic correlation network prediction of forest soil microbial functional organization.}, journal = {The ISME journal}, volume = {12}, number = {10}, pages = {2492-2505}, pmid = {30046166}, issn = {1751-7370}, mesh = {*Forests ; Gene Regulatory Networks ; Metagenome ; Microbiota/*genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Soil ecological functions are largely determined by the activities of soil microorganisms, which, in turn, are regulated by relevant interactions between genes and their corresponding pathways. Therefore, the genetic network can theoretically elucidate the functional organization that supports complex microbial community functions, although this has not been previously attempted. We generated a genetic correlation network based on 5421 genes derived from metagenomes of forest soils, identifying 7191 positive and 123 negative correlation relationships. This network consisted of 27 clusters enriched with sets of genes within specific functions, represented with corresponding cluster hubs. The clusters revealed a hierarchical architecture, reflecting the functional organization in the soil metagenomes. Positive correlations mapped functional associations, whereas negative correlations often mapped regulatory processes. The potential functions of uncharacterized genes were predicted based on the functions of located clusters. The global genetic correlation network highlights the functional organization in soil metagenomes and provides a resource for predicting gene functions. We anticipate that the genetic correlation network may be exploited to comprehensively decipher soil microbial community functions.}, } @article {pmid30046123, year = {2018}, author = {Imchen, M and Kumavath, R and Barh, D and Vaz, A and Góes-Neto, A and Tiwari, S and Ghosh, P and Wattam, AR and Azevedo, V}, title = {Comparative mangrove metagenome reveals global prevalence of heavy metals and antibiotic resistome across different ecosystems.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {11187}, pmid = {30046123}, issn = {2045-2322}, support = {SB-EMEQ-051/2014//DST | Science and Engineering Research Board (SERB)/International ; }, mesh = {Bacteroidetes/genetics ; *Ecosystem ; Firmicutes/genetics ; Geologic Sediments/microbiology ; India ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; Proteobacteria/genetics ; Wetlands ; }, abstract = {The mangrove ecosystem harbors a complex microbial community that plays crucial role in biogeochemical cycles. In this study, we analyzed mangrove sediments from India using de novo whole metagenome next generation sequencing (NGS) and compared their taxonomic and functional community structures to mangrove metagenomics samples from Brazil and Saudi Arabia. The most abundant phyla in the mangroves of all three countries was Proteobacteria, followed by Firmicutes and Bacteroidetes. A total of 1,942 genes were found to be common across all the mangrove sediments from each of the three countries. The mangrove resistome consistently showed high resistance to fluoroquinolone and acriflavine. A comparative study of the mangrove resistome with other ecosystems shows a higher frequency of heavy metal resistance in mangrove and terrestrial samples. Ocean samples had a higher abundance of drug resistance genes with fluoroquinolone and methicillin resistance genes being as high as 28.178% ± 3.619 and 10.776% ± 1.823. Genes involved in cobalt-zinc-cadmium resistance were higher in the mangrove (23.495% ± 4.701) and terrestrial (27.479% ± 4.605) ecosystems. Our comparative analysis of samples collected from a variety of habitats shows that genes involved in resistance to both heavy metals and antibiotics are ubiquitous, irrespective of the ecosystem examined.}, } @article {pmid30044797, year = {2018}, author = {Cornet, L and Meunier, L and Van Vlierberghe, M and Léonard, RR and Durieu, B and Lara, Y and Misztak, A and Sirjacobs, D and Javaux, EJ and Philippe, H and Wilmotte, A and Baurain, D}, title = {Consensus assessment of the contamination level of publicly available cyanobacterial genomes.}, journal = {PloS one}, volume = {13}, number = {7}, pages = {e0200323}, pmid = {30044797}, issn = {1932-6203}, mesh = {Consensus ; Cyanobacteria/*genetics ; *DNA Contamination ; DNA, Bacterial/genetics ; Genes, rRNA/genetics ; Genetic Markers/genetics ; Genome, Bacterial/*genetics ; }, abstract = {Publicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for Cyanobacteria because axenic strains are notoriously difficult to obtain and keep in culture. Yet, despite their great scientific interest, no data are currently available concerning the quality of publicly available cyanobacterial genomes. As reliably detecting contaminants is a complex task, we designed a pipeline combining six methods in a consensus strategy to assess the contamination level of 440 genome assemblies of Cyanobacteria. Two methods are based on published reference databases of ribosomal genes (SSU rRNA 16S and ribosomal proteins), one is indirectly based on a reference database of marker genes (CheckM), and three are based on complete genome analysis. Among those genome-wide methods, Kraken and DIAMOND blastx share the same reference database that we derived from Ensembl Bacteria, whereas CONCOCT does not require any reference database, instead relying on differences in DNA tetramer frequencies. Given that all the six methods appear to have their own strengths and limitations, we used the consensus of their rankings to infer that >5% of cyanobacterial genome assemblies are highly contaminated by foreign DNA (i.e., contaminants were detected by 5 or 6 methods). Our results will help researchers to check the quality of publicly available genomic data before use in their own analyses. Moreover, we argue that journals should make mandatory the submission of raw read data along with genome assemblies in order to facilitate the detection of contaminants in sequence databases.}, } @article {pmid30042392, year = {2018}, author = {Clayton, JB and Al-Ghalith, GA and Long, HT and Tuan, BV and Cabana, F and Huang, H and Vangay, P and Ward, T and Minh, VV and Tam, NA and Dat, NT and Travis, DA and Murtaugh, MP and Covert, H and Glander, KE and Nadler, T and Toddes, B and Sha, JCM and Singer, R and Knights, D and Johnson, TJ}, title = {Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {11159}, pmid = {30042392}, issn = {2045-2322}, support = {T32 DA007097/DA/NIDA NIH HHS/United States ; }, mesh = {Animals ; Bacteroidetes/classification/genetics ; Biodiversity ; Cercopithecidae/*physiology ; Chloroplasts/genetics ; Diet, Vegan ; Dysbiosis ; Endangered Species ; Feces/microbiology ; Firmicutes/classification/genetics ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/microbiology ; *Health Status ; Life Style ; Metagenome ; Models, Animal ; Nutritional Status/*physiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; Statistics, Nonparametric ; }, abstract = {Red-shanked doucs (Pygathrix nemaeus) are endangered, foregut-fermenting colobine primates which are difficult to maintain in captivity. There are critical gaps in our understanding of their natural lifestyle, including dietary habits such as consumption of leaves, unripe fruit, flowers, seeds, and other plant parts. There is also a lack of understanding of enteric adaptations, including their unique microflora. To address these knowledge gaps, we used the douc as a model to study relationships between gastrointestinal microbial community structure and lifestyle. We analyzed published fecal samples as well as detailed dietary history from doucs with four distinct lifestyles (wild, semi-wild, semi-captive, and captive) and determined gastrointestinal bacterial microbiome composition using 16S rRNA sequencing. A clear gradient of microbiome composition was revealed along an axis of natural lifestyle disruption, including significant associations with diet, biodiversity, and microbial function. We also identified potential microbial biomarkers of douc dysbiosis, including Bacteroides and Prevotella, which may be related to health. Our results suggest a gradient-like shift in captivity causes an attendant shift to severe gut dysbiosis, thereby resulting in gastrointestinal issues.}, } @article {pmid30042197, year = {2018}, author = {Murray, AK and Zhang, L and Yin, X and Zhang, T and Buckling, A and Snape, J and Gaze, WH}, title = {Novel Insights into Selection for Antibiotic Resistance in Complex Microbial Communities.}, journal = {mBio}, volume = {9}, number = {4}, pages = {}, pmid = {30042197}, issn = {2150-7511}, support = {BB/L502509/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Cefotaxime/*pharmacology ; *Cephalosporin Resistance ; Cephalosporinase/genetics/metabolism ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Metagenomics ; Microbiota/*drug effects ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Selection, Genetic ; Sequence Analysis, DNA ; Sewage/*microbiology ; }, abstract = {Recent research has demonstrated that selection for antibiotic resistance occurs at very low antibiotic concentrations in single-species experiments, but the relevance of these findings when species are embedded in complex microbial communities is unclear. We show that the strength of selection for naturally occurring resistance alleles in a complex community remains constant from low subinhibitory to above clinically relevant concentrations. Selection increases with antibiotic concentration before reaching a plateau where selection remains constant over a 2-order-magnitude concentration range. This is likely to be due to cross protection of the susceptible bacteria in the community following rapid extracellular antibiotic degradation by the resistant population, shown experimentally through a combination of chemical quantification and bacterial growth experiments. Metagenome and 16S rRNA analyses of sewage-derived bacterial communities evolved under cefotaxime exposure show preferential enrichment for blaCTX-M genes over all other beta-lactamase genes, as well as positive selection and co-selection for antibiotic resistant, opportunistic pathogens. These findings have far-reaching implications for our understanding of the evolution of antibiotic resistance, by challenging the long-standing assumption that selection occurs in a dose-dependent manner.IMPORTANCE Antibiotic resistance is one of the greatest global issues facing society. Still, comparatively little is known about selection for resistance at very low antibiotic concentrations. We show that the strength of selection for clinically important resistance genes within a complex bacterial community can remain constant across a large antibiotic concentration range (wide selective space). Therefore, largely understudied ecological compartments could be just as important as clinical environments for selection of antibiotic resistance.}, } @article {pmid30041921, year = {2018}, author = {Alcorta, J and Espinoza, S and Viver, T and Alcamán-Arias, ME and Trefault, N and Rosselló-Móra, R and Díez, B}, title = {Temperature modulates Fischerella thermalis ecotypes in Porcelana Hot Spring.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {6}, pages = {531-543}, doi = {10.1016/j.syapm.2018.05.006}, pmid = {30041921}, issn = {1618-0984}, mesh = {Chile ; Cyanobacteria/*genetics/isolation & purification ; DNA, Bacterial/genetics ; *Ecotype ; Evolution, Molecular ; Hot Springs/*microbiology ; *Hot Temperature ; Metagenome ; Phylogeny ; Proteome/genetics ; RNA, Ribosomal, 16S/genetics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {In the Porcelana Hot Spring (Northern Patagonia), true-branching cyanobacteria are the dominant primary producers in microbial mats, and they are mainly responsible for carbon and nitrogen fixation. However, little is known about their metabolic and genomic adaptations at high temperatures. Therefore, in this study, a total of 81 Fischerella thermalis strains (also known as Mastigocladus laminosus) were isolated from mat samples in a thermal gradient between 61-46°C. The complementary use of proteomic comparisons from these strains, and comparative genomics of F. thermalis pangenomes, suggested that at least two different ecotypes were present within these populations. MALDI-TOF MS analysis separated the strains into three clusters; two with strains obtained from mats within the upper temperature range (61 and 54°C), and a third obtained from mats within the lower temperature range (51 and 46°C). Both groups possessed different but synonymous nifH alleles. The main proteomic differences were associated with the abundance of photosynthesis-related proteins. Three F. thermalis metagenome assembled genomes (MAGs) were described from 66, 58 and 48°C metagenomes. These pangenomes indicated a divergence of orthologous genes and a high abundance of exclusive genes at 66°C. These results improved the current understanding of thermal adaptation of F. thermalis and the evolution of these thermophilic cyanobacterial species.}, } @article {pmid30041354, year = {2018}, author = {Tiralerdpanich, P and Sonthiphand, P and Luepromchai, E and Pinyakong, O and Pokethitiyook, P}, title = {Potential microbial consortium involved in the biodegradation of diesel, hexadecane and phenanthrene in mangrove sediment explored by metagenomics analysis.}, journal = {Marine pollution bulletin}, volume = {133}, number = {}, pages = {595-605}, doi = {10.1016/j.marpolbul.2018.06.015}, pmid = {30041354}, issn = {1879-3363}, mesh = {Alkanes/*metabolism ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Environmental Pollutants/metabolism ; Gasoline ; Geologic Sediments/*microbiology ; Metagenomics/methods ; Microbial Consortia/genetics/*physiology ; Phenanthrenes/*metabolism ; RNA, Ribosomal, 16S/metabolism ; Thailand ; Wetlands ; }, abstract = {Hydrocarbon contamination is a serious problem that degrades the quality of mangrove ecosystems, and bioremediation using autochthonous bacteria is a promising technology to recover an impacted environment. This research investigates the biodegradation rates of diesel, hexadecane and phenanthrene, by conducting a microcosm study and survey of the autochthonous microbial community in contaminated mangrove sediment, using an Illumina MiSeq platform. The biodegradation rates of diesel, hexadecane and phenanthrene were 82, 86 and 8 mg kg[-1] sediment day[-1], respectively. The removal efficiencies of hexadecane and phenanthrene were >99%, whereas the removal efficiency of diesel was 88%. A 16S rRNA gene amplicon sequence analysis revealed that the major bacterial assemblages detected were Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria. The bacterial compositions were relatively constant, while reductions of the supplemented hydrocarbons were observed. The results imply that the autochthonous microorganisms in the mangrove sediment were responsible for the degradation of the respective hydrocarbons. Diesel-, hexadecane- and phenanthrene-degrading bacteria, namely Bacillus sp., Pseudomonas sp., Acinetobacter sp. and Staphylococcus sp., were also isolated from the mangrove sediment. The mangrove sediment provides a potential resource of effective hydrocarbon-degrading bacteria that can be used as an inoculum or further developed as a ready-to-use microbial consortium for the purpose of bioremediation.}, } @article {pmid30039859, year = {2019}, author = {Lu, J and Shi, P and Li, H}, title = {Generalized linear models with linear constraints for microbiome compositional data.}, journal = {Biometrics}, volume = {75}, number = {1}, pages = {235-244}, doi = {10.1111/biom.12956}, pmid = {30039859}, issn = {1541-0420}, mesh = {Bacteria/*isolation & purification ; Computer Simulation ; Confidence Intervals ; Feces/microbiology ; Humans ; Inflammatory Bowel Diseases/microbiology ; Likelihood Functions ; *Linear Models ; *Microbiota ; Regression Analysis ; }, abstract = {Motivated by regression analysis for microbiome compositional data, this article considers generalized linear regression analysis with compositional covariates, where a group of linear constraints on regression coefficients are imposed to account for the compositional nature of the data and to achieve subcompositional coherence. A penalized likelihood estimation procedure using a generalized accelerated proximal gradient method is developed to efficiently estimate the regression coefficients. A de-biased procedure is developed to obtain asymptotically unbiased and normally distributed estimates, which leads to valid confidence intervals of the regression coefficients. Simulations results show the correctness of the coverage probability of the confidence intervals and smaller variances of the estimates when the appropriate linear constraints are imposed. The methods are illustrated by a microbiome study in order to identify bacterial species that are associated with inflammatory bowel disease (IBD) and to predict IBD using fecal microbiome.}, } @article {pmid30038903, year = {2018}, author = {Estrada-Peña, A and Cabezas-Cruz, A and Pollet, T and Vayssier-Taussat, M and Cosson, JF}, title = {High Throughput Sequencing and Network Analysis Disentangle the Microbial Communities of Ticks and Hosts Within and Between Ecosystems.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {236}, pmid = {30038903}, issn = {2235-2988}, mesh = {Animals ; Arvicolinae/*microbiology/*parasitology ; Bacteria/*classification/genetics ; Cluster Analysis ; Computational Biology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Ecosystem ; High-Throughput Nucleotide Sequencing ; Ixodes/*growth & development/*microbiology ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spleen/microbiology ; }, abstract = {We aimed to develop a framework, based on graph theory, to capture the ecological meaning behind pure pair comparisons of microbiome-derived data. As a proof of concept, we applied the framework to analyze the co-occurrence of bacteria in either Ixodes ricinus ticks or the spleen of one of their main hosts, the vole Myodes glareolus. As a secondary lymphoid organ, the spleen acts as a filter of blood and represents well the exposure to microorganisms circulating in the blood; including those acquired and transmitted by ticks during feeding. The microbiome of 301 and 269 individual tick and vole samples, respectively, were analyzed using next generation sequencing (NGS) of 16S rRNA. To assess the effect of habitat on ecological communities of bacteria associated to ticks and voles, two different biotopes were included in the study, forest, and ecotone. An innovative approach of NGS data analysis combining network analysis and phylogenies of co-occuring of bacteria was used to study associations between bacteria in individual samples. Of the 126 bacterial genera found in ticks and voles, 62% were shared by both species. Communities of co-occurring bacteria were always more phylogenetically diverse in ticks than in voles. Interestingly, ~80% of bacterial phylogenetic diversity was found in ~20% of ticks. This pattern was not observed in vole-associated bacteria. Results revealed that the microbiome of I. ricinus is only slightly related to that of M. glareolus and that the biotope plays the most important role in shaping the bacterial communities of either ticks or voles. The analysis of the phylogenetic signal of the network indexes across the 16S rRNA-derived tree of bacteria suggests that the microbiome of both ticks and voles has high phylogenetic diversity and that closest bacterial genera do not co-occur. This study shows that network analysis is a promising tool to unravel complex microbial communities associated to arthropod vectors and vertebrate hosts.}, } @article {pmid30038310, year = {2018}, author = {Duerkop, BA and Kleiner, M and Paez-Espino, D and Zhu, W and Bushnell, B and Hassell, B and Winter, SE and Kyrpides, NC and Hooper, LV}, title = {Murine colitis reveals a disease-associated bacteriophage community.}, journal = {Nature microbiology}, volume = {3}, number = {9}, pages = {1023-1031}, pmid = {30038310}, issn = {2058-5276}, support = {K01 DK102436/DK/NIDDK NIH HHS/United States ; R01 DK070855/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteriophages/genetics/*isolation & purification ; Cells, Cultured ; Colitis/*pathology/*virology ; Disease Models, Animal ; Dysbiosis/*virology ; Gastrointestinal Microbiome/*physiology ; Genome, Viral/genetics ; Humans ; Intestinal Mucosa/*virology ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; }, abstract = {The dysregulation of intestinal microbial communities is associated with inflammatory bowel diseases (IBD). Studies aimed at understanding the contribution of the microbiota to inflammatory diseases have primarily focused on bacteria, yet the intestine harbours a viral component dominated by prokaryotic viruses known as bacteriophages (phages). Phage numbers are elevated at the intestinal mucosal surface and phages increase in abundance during IBD, suggesting that phages play an unidentified role in IBD. We used a sequence-independent approach for the selection of viral contigs and then applied quantitative metagenomics to study intestinal phages in a mouse model of colitis. We discovered that during colitis the intestinal phage population is altered and transitions from an ordered state to a stochastic dysbiosis. We identified phages specific to pathobiotic hosts associated with intestinal disease, whose abundances are altered during colitis. Additionally, phage populations in healthy and diseased mice overlapped with phages from healthy humans and humans with IBD. Our findings indicate that intestinal phage communities are altered during inflammatory disease, establishing a platform for investigating phage involvement in IBD.}, } @article {pmid30038308, year = {2018}, author = {Munk, P and Knudsen, BE and Lukjancenko, O and Duarte, ASR and Van Gompel, L and Luiken, REC and Smit, LAM and Schmitt, H and Garcia, AD and Hansen, RB and Petersen, TN and Bossers, A and Ruppé, E and , and Lund, O and Hald, T and Pamp, SJ and Vigre, H and Heederik, D and Wagenaar, JA and Mevius, D and Aarestrup, FM}, title = {Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries.}, journal = {Nature microbiology}, volume = {3}, number = {8}, pages = {898-908}, doi = {10.1038/s41564-018-0192-9}, pmid = {30038308}, issn = {2058-5276}, mesh = {Animals ; Bacteria/*classification/drug effects/genetics ; Bacterial Proteins/*genetics ; Biodiversity ; Chickens ; *Drug Resistance, Bacterial ; Europe ; Feces/*microbiology ; Gene Expression Profiling/veterinary ; Metagenomics/methods ; Sequence Analysis, DNA/veterinary ; Species Specificity ; Swine ; }, abstract = {Antimicrobial resistance (AMR) in bacteria and associated human morbidity and mortality is increasing. The use of antimicrobials in livestock selects for AMR that can subsequently be transferred to humans. This flow of AMR between reservoirs demands surveillance in livestock and in humans. We quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, sequencing more than 5,000 Gb of DNA using shotgun metagenomics. We quantified acquired AMR using the ResFinder database and a second database constructed for this study, consisting of AMR genes identified through screening environmental DNA. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than in poultry. We found higher AMR loads in pigs, whereas poultry resistomes were more diverse. We detected several recently described, critical AMR genes, including mcr-1 and optrA, the abundance of which differed both between host species and between countries. We found that the total acquired AMR level was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns had similar resistomes. However, functionally determined AMR genes were not associated with total drug use.}, } @article {pmid30037148, year = {2018}, author = {Cross, ST and Kapuscinski, ML and Perino, J and Maertens, BL and Weger-Lucarelli, J and Ebel, GD and Stenglein, MD}, title = {Co-Infection Patterns in Individual Ixodes scapularis Ticks Reveal Associations between Viral, Eukaryotic and Bacterial Microorganisms.}, journal = {Viruses}, volume = {10}, number = {7}, pages = {}, pmid = {30037148}, issn = {1999-4915}, support = {UL1 TR002535/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/isolation & purification ; Borrelia burgdorferi/genetics/isolation & purification ; Coinfection/epidemiology/*microbiology/*virology ; Eukaryota/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Ixodes/genetics/*microbiology/*virology ; Lyme Disease ; Microbiota/genetics ; Orthobunyavirus/genetics/isolation & purification ; Phlebovirus/genetics/isolation & purification ; Prevalence ; Symbiosis ; Tick Infestations/epidemiology/microbiology/virology ; Tick-Borne Diseases/*epidemiology/microbiology/virology ; Viruses/genetics/isolation & purification ; Wisconsin/epidemiology ; }, abstract = {Ixodes scapularis ticks harbor a variety of microorganisms, including eukaryotes, bacteria and viruses. Some of these can be transmitted to and cause disease in humans and other vertebrates. Others are not pathogenic, but may impact the ability of the tick to harbor and transmit pathogens. A growing number of studies have examined the influence of bacteria on tick vector competence but the influence of the tick virome remains less clear, despite a surge in the discovery of tick-associated viruses. In this study, we performed shotgun RNA sequencing on 112 individual adult I. scapularis collected in Wisconsin, USA. We characterized the abundance, prevalence and co-infection rates of viruses, bacteria and eukaryotic microorganisms. We identified pairs of tick-infecting microorganisms whose observed co-infection rates were higher or lower than would be expected, or whose RNA levels were positively correlated in co-infected ticks. Many of these co-occurrence and correlation relationships involved two bunyaviruses, South Bay virus and blacklegged tick phlebovirus-1. These viruses were also the most prevalent microorganisms in the ticks we sampled, and had the highest average RNA levels. Evidence of associations between microbes included a positive correlation between RNA levels of South Bay virus and Borrelia burgdorferi, the Lyme disease agent. These findings contribute to the rationale for experimental studies on the impact of viruses on tick biology and vector competence.}, } @article {pmid30036363, year = {2018}, author = {Chai, H and Jiang, H and Lin, L and Liu, L}, title = {A marginalized two-part Beta regression model for microbiome compositional data.}, journal = {PLoS computational biology}, volume = {14}, number = {7}, pages = {e1006329}, pmid = {30036363}, issn = {1553-7358}, support = {R01 HS020263/HS/AHRQ HHS/United States ; }, mesh = {Animals ; Colony Count, Microbial ; Likelihood Functions ; *Logistic Models ; Metagenomics ; Mice ; *Microbiota ; Skin/*microbiology ; }, abstract = {In microbiome studies, an important goal is to detect differential abundance of microbes across clinical conditions and treatment options. However, the microbiome compositional data (quantified by relative abundance) are highly skewed, bounded in [0, 1), and often have many zeros. A two-part model is commonly used to separate zeros and positive values explicitly by two submodels: a logistic model for the probability of a specie being present in Part I, and a Beta regression model for the relative abundance conditional on the presence of the specie in Part II. However, the regression coefficients in Part II cannot provide a marginal (unconditional) interpretation of covariate effects on the microbial abundance, which is of great interest in many applications. In this paper, we propose a marginalized two-part Beta regression model which captures the zero-inflation and skewness of microbiome data and also allows investigators to examine covariate effects on the marginal (unconditional) mean. We demonstrate its practical performance using simulation studies and apply the model to a real metagenomic dataset on mouse skin microbiota. We find that under the proposed marginalized model, without loss in power, the likelihood ratio test performs better in controlling the type I error than those under conventional methods.}, } @article {pmid30033973, year = {2018}, author = {Choi, HJ and Jeong, TY and Yoon, H and Oh, BY and Han, YS and Hur, MJ and Kang, S and Kim, JG}, title = {Comparative microbial communities in tidal flats sediment on Incheon, South Korea.}, journal = {The Journal of general and applied microbiology}, volume = {64}, number = {5}, pages = {232-239}, doi = {10.2323/jgam.2017.12.007}, pmid = {30033973}, issn = {1349-8037}, mesh = {Bacteria/*classification/genetics/*isolation & purification ; *Biodiversity ; DNA, Bacterial/genetics ; *Environmental Microbiology ; Geologic Sediments/*microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Republic of Korea ; Seawater/microbiology ; }, abstract = {Coastal ecosystems, play critical ecological roles of which tidal flats are a significant component of coastal wetlands, such as habitat and nutrient cycling in aquatic biology. Microbial communities in tidal flats are known to play vital roles of self-purification. And the microbial ecology of the sediment is easily affected by human activities and pollution. In this paper, we applied pyrosequencing technology to investigate microbial communities in three different tidal flats (Ganghwa Island, Ongnyeon land region and Yeongjong Island) on the Incheon, Korea peninsula. A total of 16,906 sequences were obtained. We used these sequences to identify the dominant phyla in the three tidal flats: Proteobacteria, Chloroflexi, Actinobacteria, and Bacteroidetes. The composition of the bacterial community of Ganghwa Island and the Ongnyeon region were more similar to each other than they were to the bacterial community of Yeongjong Island. Simpson's dominance index of Yeongjong Island was higher than that of the other regions, and the Shannon diversity index of this region was the lowest. Previous research of samples in these regions indicated that the three tidal flats had similar geochemical characteristics. However, their bacterial communities were rather distinct. This might be because the analysis of microbial communities and physiochemical analysis have different perspectives. Therefore, the pyrosequencing of a bacterial community with physiochemical analysis is recommended as an effective monitoring tool for the comprehensive management of tidal flats.}, } @article {pmid30033505, year = {2018}, author = {Edouard, S and Million, M and Bachar, D and Dubourg, G and Michelle, C and Ninove, L and Charrel, R and Raoult, D}, title = {The nasopharyngeal microbiota in patients with viral respiratory tract infections is enriched in bacterial pathogens.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {37}, number = {9}, pages = {1725-1733}, pmid = {30033505}, issn = {1435-4373}, support = {10-IAHU-03//IHU Méditerranée Infection/ ; }, mesh = {Acute Disease/epidemiology ; Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacteria/genetics/isolation & purification/*pathogenicity ; Case-Control Studies ; Child ; Child, Preschool ; Coinfection/microbiology/virology ; Disease Susceptibility/virology ; Female ; Haemophilus influenzae/genetics/isolation & purification/pathogenicity ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenomics ; Microbiota/*genetics ; Middle Aged ; Nasopharynx/*microbiology/virology ; RNA, Ribosomal, 16S/genetics ; Respiratory Tract Infections/epidemiology/*microbiology/*virology ; Staphylococcus aureus/genetics/isolation & purification/pathogenicity ; Streptococcus pneumoniae/genetics/isolation & purification/pathogenicity ; Virus Diseases/*microbiology/virology ; Young Adult ; }, abstract = {The nasopharynx is the primary site of colonization by respiratory pathogen that constitutes the port of entrance in the respiratory tract. The role of mucosal respiratory microbiota in infection has been recently emphasized; therefore, we aimed to assess if a specific respiratory microbiota profile was associated with symptomatic infection and/or with presence of respiratory viruses. We performed a case-control study to characterize the healthy respiratory microbiota and its alteration during acute viral infections. Next-generation sequencing of the 16S rRNA gene was applied to 225 nasopharyngeal samples from 177 patients with viral respiratory infection and 48 matched healthy controls. We evidenced an important decrease of bacterial alpha-diversity in patients with symptomatic respiratory infection and a loss of the healthy core microbiota, specifically anaerobes and Prevotella spp. Moreover, eight respiratory pathogens were enriched in these patients, including Staphylococcus aureus, Haemophilus influenzae, Streptococcus pneumoniae, Moraxella catarrhalis, Dol osigranulum pigrum and Corynebacterium propinquum/pseudodiphtheriticum, whose role in respiratory infection is unclear. The asymptomatic carrier of influenza harbors a microbiota similar to healthy subjects, suggesting a critical role of microbiota in the clinical expression of viruses. These data suggest that the commensal microbiota plays a significant role in susceptibility to viral infection. The frequent co-detection of virus and bacteria raises the question of a strategy to prevent bacterial disease, focusing on the prevention of nasopharyngeal colonization through effective antibiotic treatment. In addition to antibiotics, further studies should test preventive or therapeutic interventions for maintaining or restoring a healthy nasopharyngeal microbiota.}, } @article {pmid30031771, year = {2018}, author = {Wade, RM and Sherwood, AR}, title = {Updating Plakobranchus cf. ianthobapsus (Gastropoda, Sacoglossa) host use: Diverse algal-animal interactions revealed by NGS with implications for invasive species management.}, journal = {Molecular phylogenetics and evolution}, volume = {128}, number = {}, pages = {172-181}, doi = {10.1016/j.ympev.2018.07.010}, pmid = {30031771}, issn = {1095-9513}, mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic ; Gastropoda/*genetics/*parasitology ; Hawaii ; *High-Throughput Nucleotide Sequencing ; *Host-Parasite Interactions ; *Introduced Species ; Likelihood Functions ; Metagenomics ; Phylogeny ; Principal Component Analysis ; }, abstract = {Sacoglossa, the "sap sucking" sea slugs, are highly specialized herbivores and the only metazoans that exhibit kleptoplasty, the sequestration and retention of chloroplasts from algae. Plakobranchus is one of the most generalistic herbivores within this order, with as many as 12 reported "algal host" (i.e. kleptoplast source) species. However, kleptoplast diversity studies conducted on Plakobranchus to date most likely underestimated the full diversity of kleptoplast sources within the studied populations due to limitations of the molecular techniques employed. Here, we apply a high throughput sequencing technique to assess kleptoplast diversity of Plakobranchus cf. ianthobapsus' from 10 sites across the Main Hawaiian Islands during winter and summer seasons. In so doing, we effectively used P. cf. ianthobapsus as a novel sampling tool to explore diminutive algal communities, including the current distribution of the invasive alga "Avrainvillea amadelpha." Our results show that P. cf. ianthobapsus sequesters chloroplasts from 23 algal species from across the siphonous green algal order Bryopsidales. We identified "Avrainvillea amadelpha" and Codium edule as new host species for P. cf. ianthobapusus, but their rarity among the data suggests they were most likely less preferential as hosts and were possibly utilized due to low abundance or unavailability of more preferable species, and therefore a response to starvation risk. Additionally, the identification of the highly invasive siphonous green alga "A. amadelpha" as a kleptoplast source provides new fine-scale range and distribution data for this problematic species. Overall kleptoplast diversity does not differ among sites, except in a coral-dominated, (i.e. not algal dominated) environment, suggesting that siphonous algal assemblages are common in algal-dominated ecosystems in the Hawaiian Islands. Diversity dissimilarity among seasons was recovered from the majority of sites sampled, supporting the need for seasonal data collection in algal diversity assessments. This case study using metabarcoding of sacoglossan kleptoplasts provides deeper insights into these plant-animal interactions with a better understanding of host use than previous studies using traditional molecular methods and illustrates how algal diversity studies on the scale of plastids can have implications for understanding algal community structure and invasive species dynamics.}, } @article {pmid30029052, year = {2018}, author = {Jiang, HY and Zhang, X and Yu, ZH and Zhang, Z and Deng, M and Zhao, JH and Ruan, B}, title = {Altered gut microbiota profile in patients with generalized anxiety disorder.}, journal = {Journal of psychiatric research}, volume = {104}, number = {}, pages = {130-136}, doi = {10.1016/j.jpsychires.2018.07.007}, pmid = {30029052}, issn = {1879-1379}, mesh = {Adult ; Anxiety Disorders/*microbiology/*pathology ; Case-Control Studies ; Cohort Studies ; Cross-Sectional Studies ; Dysbiosis/genetics/metabolism ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; Statistics, Nonparametric ; }, abstract = {Close relationships have recently been established between gut microbiota and some mental disorders. Here, we performed a systematic comparative analysis of the gut microbiome in patients with generalized anxiety disorder (GAD) and healthy controls (HCs). We first conducted a cross-sectional study of 40 patients with GAD in the active state and 36 HCs. Second, subgroup analysis consisting of 12 antidepressant-naive patients and 22 controls was performed to validate the results. Finally, a prospective study was performed in a subgroup of nine patients with GAD who underwent analysis in the active state of anxiety and in remission. Compared with the HCs, we found markedly decreased microbial richness and diversity, distinct metagenomic composition with reduced short-chain fatty acid (SCFA)-producing bacteria (associated with a healthy status) and overgrowth of bacteria, such as Escherichia-Shigella, Fusobacterium and Ruminococcus gnavus. Unexpectedly, these changes in the genera were not reversed in remissive GAD. This study identified microbiota dysbiosis of gut microbiota in GAD patients, suggesting that targeting the microbiome may be a useful therapeutic and preventive target for GAD.}, } @article {pmid30027368, year = {2018}, author = {Miyoshi, J and Sofia, MA and Pierre, JF}, title = {The evidence for fungus in Crohn's disease pathogenesis.}, journal = {Clinical journal of gastroenterology}, volume = {11}, number = {6}, pages = {449-456}, pmid = {30027368}, issn = {1865-7265}, support = {1R01DK113788-01//National Institute of Diabetes and Digestive and Kidney Diseases/ ; }, mesh = {Animals ; Biomarkers/analysis ; Crohn Disease/diagnosis/drug therapy/*microbiology/physiopathology ; Dysbiosis ; Environmental Exposure ; Fungi/*pathogenicity ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Immunity, Innate ; Inflammatory Bowel Diseases/microbiology/physiopathology ; }, abstract = {Current evidence suggests the etiology of inflammatory bowel diseases (IBD) involves the confluence of host genetic, environmental, and microbial factors that lead to chronic, and often refractory, disease in susceptible individuals. The involvement of microbial triggers in IBD, including Crohn's disease (CD), is increasingly evident with supporting data provided with advancements in metagenomic sequencing that have identified perturbations in microbial structure and function-broadly termed dysbiosis-in CD patients compared with healthy subjects. This concept is supported by the finding germ-free animals with CD genetic susceptibility fail to develop disease; demonstrating microorganisms are necessary but not sufficient for CD. The vast majority of CD microbiome research has focused on the complex bacterial communities and microbiome dysbiosis in the gut with 16S metagenomic sequencing. However, emerging data capturing eukaryotes suggest fungal opportunistic pathogens are also associated with IBD pathogenesis and chronicity. This hypothesis is further supported by historical observations that CD patient populations display elevated antibodies against fungal targets, even evident before disease diagnosis. This review discusses the current findings in the field, followed by historical and metagenomic evidence for fungal pathogens in the development and recurrence of CD in adult and pediatric populations.}, } @article {pmid30024917, year = {2018}, author = {De Leon, MP and Montecillo, AD and Pinili, DS and Siringan, MAT and Park, DS}, title = {Bacterial diversity of bat guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines: A first report on the metagenome of Philippine bat guano.}, journal = {PloS one}, volume = {13}, number = {7}, pages = {e0200095}, pmid = {30024917}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Caves/microbiology ; Chiroptera/*microbiology ; Feces/*microbiology ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Philippines ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Bats are highly diverse and ecologically valuable mammals. They serve as host to bacteria, viruses and fungi that are either beneficial or harmful to its colony as well as to other groups of cave organisms. The bacterial diversity of two bat guano samples, C1 and C2, from Cabalyorisa Cave, Mabini, Pangasinan, Philippines were investigated using 16S rRNA gene amplicon sequencing. V3-V4 hypervariable regions were amplified and then sequenced using Illumina MiSeq 250 PE system. Reads were processed using Mothur and QIIME pipelines and assigned 12,345 OTUs for C1 and 5,408 OTUs for C2. The most dominant OTUs in C1 belong to the Proteobacteria (61.7%), Actinobacteria (19.4%), Bacteroidetes (4.2%), Firmicutes (2.7%), Chloroflexi (2.5%), candidate phylum TM7 (2.3%) and Planctomycetes (1.9%) while Proteobacteria (61.7%) and Actinobacteria (34.9%) dominated C2. Large proportion of sequence reads mainly associated with unclassified bacteria indicated possible occurrence of novel bacteria in both samples. XRF spectrophotometric analyses of C1 and C2 guano revealed significant differences in the composition of both major and trace elements. C1 guano recorded high levels of Si, Fe, Mg, Al, Mn, Ti and Cu while C2 samples registered high concentrations of Ca, P, S, Zn and Cr. Community structure of the samples were compared with other published community profiling studies from Finland (SRR868695), Meghalaya, Northeast India (SRR1793374) and Maharashtra State, India (CGS). Core microbiome among samples were determined for comparison. Variations were observed among previously studied guano samples and the Cabalyorisa Cave samples were attributed to either bat sources or age of the guano. This is the first study on bacterial diversity of guano in the Philippines through high-throughput sequencing.}, } @article {pmid30022262, year = {2018}, author = {Miao, Y and Zhang, XX and Jia, S and Liao, R and Li, A}, title = {Comprehensive analyses of functional bacteria and genes in a denitrifying EGSB reactor under Cd(II) stress.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {19}, pages = {8551-8560}, doi = {10.1007/s00253-018-9228-6}, pmid = {30022262}, issn = {1432-0614}, support = {2014BAC08B04//National Key Technology Support Program of China/ ; BK20150019//Jiangsu Science Foundation for Distinguished Young Scholars/ ; 2015-JNHB-001//Six Talent Peaks Project in Jiangsu Province/ ; }, mesh = {Bacteria/*drug effects/*genetics ; Biodiversity ; Bioreactors/*microbiology ; Cadmium/*pharmacology ; Denitrification/drug effects ; Nitrates/metabolism ; Nitrites/metabolism ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Waste Disposal, Fluid/methods ; Wastewater/microbiology ; Water Purification/methods ; }, abstract = {A bench-scale expanded granular sludge bioreactor (EGSB) was continuously operated to treat synthesized high-nitrate industrial wastewater with increasing bivalent cadmium (Cd(II)) stress. The bioreactor showed nearly complete nitrate removal regardless of Cd(II) loadings, while nitrite accumulated in the effluent when influent Cd(II) loading was over 64 mg/L. Mi-seq sequencing of 16S rRNA gene amplicons elucidated that denitrifiers had decreasing abundances while biodiversity showed increasing trend as the Cd(II) loading increased. In the bioreactor, genera Halomonas, Thauera, Pseudomonas, and Zoogloea played major roles in the denitrification under lower Cd(II) loadings (< 32 mg/L), while Halomonas sp. KM-1 and Halomonas sp. BC04 acted as the crucial Cd-resistant denitrifiers under 128 mg/L Cd(II) loading. Metagenomic analyses and real-time quantitative PCR consistently indicated that napA encoding nitrate reductase was the predominant denitrifying gene, that could be mainly functioning on the efficient nitrate removal. Statistical analyses revealed the significantly positive correlation between Halomonas and nirS gene, both of which were functionally responsible for nitrite reduction. The obtained results may be practically useful for regulation and optimization of the biological processes to treat industrial wastewater containing high levels of nitrate and Cd(II).}, } @article {pmid30021874, year = {2018}, author = {Glassman, SI and Martiny, JBH}, title = {Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units.}, journal = {mSphere}, volume = {3}, number = {4}, pages = {}, pmid = {30021874}, issn = {2379-5042}, mesh = {Bacteria/*classification/*genetics ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Environmental Microbiology ; Fungi/*classification/*genetics ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Recent discussion focuses on the best method for delineating microbial taxa, based on either exact sequence variants (ESVs) or traditional operational taxonomic units (OTUs) of marker gene sequences. We sought to test if the binning approach (ESVs versus 97% OTUs) affected the ecological conclusions of a large field study. The data set included sequences targeting all bacteria (16S rRNA) and fungi (internal transcribed spacer [ITS]), across multiple environments diverging markedly in abiotic conditions, over three collection times. Despite quantitative differences in microbial richness, we found that all α and β diversity metrics were highly positively correlated (r > 0.90) between samples analyzed with both approaches. Moreover, the community composition of the dominant taxa did not vary between approaches. Consequently, statistical inferences were nearly indistinguishable. Furthermore, ESVs only moderately increased the genetic resolution of fungal and bacterial diversity (1.3 and 2.1 times OTU richness, respectively). We conclude that for broadscale (e.g., all bacteria or all fungi) α and β diversity analyses, ESV or OTU methods will often reveal similar ecological results. Thus, while there are good reasons to employ ESVs, we need not question the validity of results based on OTUs.IMPORTANCE Microbial ecologists have made exceptional improvements in our understanding of microbiomes in the last decade due to breakthroughs in sequencing technologies. These advances have wide-ranging implications for fields ranging from agriculture to human health. Due to limitations in databases, the majority of microbial ecology studies use a binning approach to approximate taxonomy based on DNA sequence similarity. There remains extensive debate on the best way to bin and approximate this taxonomy. Here we examine two popular approaches using a large field-based data set examining both bacteria and fungi and conclude that there are not major differences in the ecological outcomes. Thus, it appears that standard microbial community analyses are not overly sensitive to the particulars of binning approaches.}, } @article {pmid30019906, year = {2018}, author = {Wang, AY and Thuy-Boun, PS and Stupp, GS and Su, AI and Wolan, DW}, title = {Triflic Acid Treatment Enables LC-MS/MS Analysis of Insoluble Bacterial Biomass.}, journal = {Journal of proteome research}, volume = {17}, number = {9}, pages = {2978-2986}, pmid = {30019906}, issn = {1535-3907}, support = {U54 GM114833/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus subtilis/*chemistry/genetics/metabolism ; Bacterial Proteins/*isolation & purification ; Chromatography, Liquid ; Complex Mixtures/chemistry ; Gastrointestinal Microbiome/genetics ; Humans ; Jurkat Cells ; Membrane Proteins/*isolation & purification ; Mesylates/*chemistry ; Metagenome ; Proteomics/*methods ; Pseudomonas aeruginosa/*chemistry/genetics/metabolism ; Sonication/methods ; Tandem Mass Spectrometry ; }, abstract = {The lysis and extraction of soluble bacterial proteins from cells is a common practice for proteomics analyses, but insoluble bacterial biomasses are often left behind. Here, we show that with triflic acid treatment, the insoluble bacterial biomass of Gram[-] and Gram[+] bacteria can be rendered soluble. We use LC-MS/MS shotgun proteomics to show that bacterial proteins in the soluble and insoluble postlysis fractions differ significantly. Additionally, in the case of Gram[-] Pseudomonas aeruginosa, triflic acid treatment enables the enrichment of cell-envelope-associated proteins. Finally, we apply triflic acid to a human microbiome sample to show that this treatment is robust and enables the identification of a new, complementary subset of proteins from a complex microbial mixture.}, } @article {pmid30018874, year = {2018}, author = {Colabella, C and Corte, L and Roscini, L and Bassetti, M and Tascini, C and Mellor, JC and Meyer, W and Robert, V and Vu, D and Cardinali, G}, title = {NGS barcode sequencing in taxonomy and diagnostics, an application in "Candida" pathogenic yeasts with a metagenomic perspective.}, journal = {IMA fungus}, volume = {9}, number = {1}, pages = {91-105}, pmid = {30018874}, issn = {2210-6340}, abstract = {Species identification of yeasts and other Fungi is currently carried out with Sanger sequences of selected molecular markers, mainly from the ribosomal DNA operon, characterized by hundreds of tandem repeats of the 18S, ITS1, 5.8S, ITS2 and LSU loci. The ITS region has been recently proposed as a primary barcode marker making this region the most used one in taxonomy, phylogeny and diagnostics. The introduction of NGS is providing tools of high efficacy and relatively low cost to amplify two or more markers simultaneously with great sequencing depth. However, the presence of intra-genomic variability between the repeats requires specific analytical procedures and pipelines. In this study, 286 strains belonging to 11 pathogenic yeasts species were analysed with NGS of the region spanning from ITS1 to the D1/D2 domain of the LSU encoding ribosomal DNA. Results showed that relatively high heterogeneity can hamper the use of these sequences for the identification of single strains and even more of complex microbial mixtures. These observations point out that the metagenomics studies could be affected by species inflection at levels higher than currently expected.}, } @article {pmid30017197, year = {2018}, author = {He, F and Liu, D and Zhai, J and Zhang, L and Ma, Y and Xu, Y and Rong, K and Ma, J}, title = {Metagenomic analysis revealed the effects of goat milk feeding and breast feeding on the gut microbiome of Amur tiger cubs.}, journal = {Biochemical and biophysical research communications}, volume = {503}, number = {4}, pages = {2590-2596}, doi = {10.1016/j.bbrc.2018.07.020}, pmid = {30017197}, issn = {1090-2104}, mesh = {Animals ; Animals, Newborn ; Bacteria/isolation & purification ; Feeding Behavior ; *Gastrointestinal Microbiome ; *Goats/microbiology ; Metagenomics/*methods ; *Milk ; *Tigers/microbiology ; }, abstract = {BACKGROUND: Ingredients in breast milk can help establish a healthy community of microorganisms in the infant gut, but no research exists regarding the effects of goat milk feeding and breast feeding on the gut microbiome of the Amur tiger, which is one of the most endangered species in the world.

METHODS: In this study, we used whole-metagenome shotgun sequencing to analyze the effects of two different feeding patterns, goat milk feeding and breast feeding, on the composition and functional structures of gut microbiota in Amur tiger cubs.

RESULTS: Goat milk-fed cubs have fewer beneficial bacteria and more pathogenic bacteria and a higher microbial diversity in their gut than breastfed cubs. A total of 15 genera showed statistically significant differences; the relative abundances of Streptomyces scabiei, Streptomyces avermitilis and Streptomyces davawensis were significantly decreased, whereas those of Niabella soli, Aeromonas media and Brochothrix thermosphacta were significantly increased in the goat milk-fed group compared with those in the breastfed group. At the functional level, carbohydrate metabolism, translation and replication and repair decreased, and amino acid metabolism, membrane transport and metabolism of cofactors and vitamins increased in the gut microbiota of goat milk-fed cubs compared with breastfed cubs.

CONCLUSION: Our results indicate for the first time that the different milk feeding patterns of goat milk feeding and breast feeding can change the composition and functional structures of gut microbiota in Amur tiger cubs and that breastfed tiger cubs and goat milk-fed tiger cubs have distinct microbiotas in their guts.}, } @article {pmid30016149, year = {2018}, author = {Piccolo, BD and Graham, JL and Stanhope, KL and Nookaew, I and Mercer, KE and Chintapalli, SV and Wankhade, UD and Shankar, K and Havel, PJ and Adams, SH}, title = {Diabetes-associated alterations in the cecal microbiome and metabolome are independent of diet or environment in the UC Davis Type 2 Diabetes Mellitus Rat model.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {315}, number = {5}, pages = {E961-E972}, pmid = {30016149}, issn = {1522-1555}, support = {R01 DK050603/DK/NIDDK NIH HHS/United States ; P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 DK078328/DK/NIDDK NIH HHS/United States ; R01 HL121324/HL/NHLBI NIH HHS/United States ; R01 HL121324/HL/NHLBI NIH HHS/United States ; P20 GM121293/GM/NIGMS NIH HHS/United States ; R01 HL107256/HL/NHLBI NIH HHS/United States ; R01 HL091333/HL/NHLBI NIH HHS/United States ; P20 GM125503/GM/NIGMS NIH HHS/United States ; U24 DK092993/DK/NIDDK NIH HHS/United States ; RC1 DK087307/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteroides/isolation & purification ; Cecum/metabolism/*microbiology ; Diabetes Mellitus, Type 2/metabolism/*microbiology ; Diet ; Disease Models, Animal ; Firmicutes/isolation & purification ; Gastrointestinal Microbiome/*physiology ; Male ; *Metabolome ; Metabolomics ; Metagenomics ; Prediabetic State/metabolism/*microbiology ; Rats ; Rats, Sprague-Dawley ; }, abstract = {The composition of the gut microbiome is altered in obesity and type 2 diabetes; however, it is not known whether these alterations are mediated by dietary factors or related to declines in metabolic health. To address this, cecal contents were collected from age-matched, chow-fed male University of California, Davis Type 2 Diabetes Mellitus (UCD-T2DM) rats before the onset of diabetes (prediabetic PD; n = 15), 2 wk recently diabetic (RD; n = 10), 3 mo (D3M; n = 11), and 6 mo (D6M; n = 8) postonset of diabetes. Bacterial species and functional gene counts were assessed by shotgun metagenomic sequencing of bacterial DNA in cecal contents, while metabolites were identified by gas chromatography-quadrupole time-off-flight-mass spectrometry. Metagenomic analysis showed a shift from Firmicutes species in early stages of diabetes (PD + RD) toward an enrichment of Bacteroidetes species in later stages of diabetes (D3M + D6M). In total, 45 bacterial species discriminated early and late stages of diabetes with 25 of these belonging to either Bacteroides or Prevotella genera. Furthermore, 61 bacterial gene clusters discriminated early and later stages of diabetes with elevations of enzymes related to stress response (e.g., glutathione and glutaredoxin) and amino acid, carbohydrate, and bacterial cell wall metabolism. Twenty-five cecal metabolites discriminated early vs. late stages of diabetes, with the largest differences observed in abundances of dehydroabietic acid and phosphate. Alterations in the gut microbiota and cecal metabolome track diabetes progression in UCD-T2DM rats when controlling for diet, age, and housing environment. Results suggest that diabetes-specific host signals impact the ecology and end product metabolites of the gut microbiome when diet is held constant.}, } @article {pmid30015225, year = {2018}, author = {Schnorr, SL}, title = {Meanings, measurements, and musings on the significance of patterns in human microbiome variation.}, journal = {Current opinion in genetics & development}, volume = {53}, number = {}, pages = {43-52}, doi = {10.1016/j.gde.2018.06.014}, pmid = {30015225}, issn = {1879-0380}, mesh = {Bacteria/classification/*genetics ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenomics ; Microbiota/*genetics ; Transcriptome/genetics ; }, abstract = {Variation of the human microbiome is a multidimensional value depending on the question of interest. Unlike traditional human genetics, which most often deals with variation at the level of genes or genetic sequences, microbiome variation may be most relevant at the functional level and can be interrogated a number of ways. Most common methods are marker gene metataxonomic surveys or shotgun metagenomic sequencing, however more direct indicators of microbial activity that are gaining popularity include metabolomic and metatranscriptomic surveys. With all these data and promise in human microbiome research, it requires that we reassess what is meant by variation of the human microbiome and how its significance impacts the ability of microbiome research to be informative on a range of topics from evolutionary theory to clinical outcomes. Learning from mistakes is essential to advancing the field, and new sophisticated analysis tools are helping to crystallize associations between microbiome variation and its drivers so that firm ground supports future explorations of mechanism. However, the body of current data suggests that these may be highly individualized due to the array of interactions between the host, the microbiome, and the environment. As a result, microbiome researchers need to be cognizant of population contexts and the limits these impose on conclusive outcomes.}, } @article {pmid30014616, year = {2018}, author = {Rands, CM and Starikova, EV and Brüssow, H and Kriventseva, EV and Govorun, VM and Zdobnov, EM}, title = {ACI-1 beta-lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages.}, journal = {Environmental microbiology}, volume = {20}, number = {6}, pages = {2288-2300}, doi = {10.1111/1462-2920.14276}, pmid = {30014616}, issn = {1462-2920}, support = {IZLRZ3_163863 16-54-21012//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/International ; //Russian Foundation for Basic Research/International ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/*metabolism ; China ; Drug Resistance, Bacterial/*genetics ; Europe ; Firmicutes/genetics ; *Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; Humans ; Metagenome ; Phylogeny ; Prophages/*genetics ; United States ; beta-Lactamases/genetics/*metabolism ; }, abstract = {Antibiotic resistance is increasing among pathogens, and the human microbiome contains a reservoir of antibiotic resistance genes. Acidaminococcus intestini is the first Negativicute bacterium (Gram-negative Firmicute) shown to be resistant to beta-lactam antibiotics. Resistance is conferred by the aci1 gene, but its evolutionary history and prevalence remain obscure. We discovered that ACI-1 proteins are phylogenetically distinct from beta-lactamases of Gram-positive Firmicutes and that aci1 occurs in bacteria scattered across the Negativicute clade, suggesting lateral gene transfer. In the reference A. intestini RyC-MR95 genome, we found transposons residing within a tailed prophage context are likely vehicles for aci1's mobility. We found aci1 in 56 (4.4%) of 1,267 human gut metagenomes, mostly hosted within A. intestini, and, where could be determined, mostly within a consistent mobile element constellation. These samples are from Europe, China and the USA, showing that aci1 is distributed globally. We found that for most Negativicute assemblies with aci1, the prophage observed in A. instestini is absent, but in all cases aci1 is flanked by varying transposons. The chimeric mobile elements we identify here likely have a complex evolutionary history and potentially provide multiple complementary mechanisms for antibiotic resistance gene transfer both within and between cells.}, } @article {pmid30014577, year = {2018}, author = {Cordier, T and Forster, D and Dufresne, Y and Martins, CIM and Stoeck, T and Pawlowski, J}, title = {Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1381-1391}, doi = {10.1111/1755-0998.12926}, pmid = {30014577}, issn = {1755-0998}, support = {316030_150817//Swiss Network for International Studies/ ; 31003A_179125//Swiss National Science Foundation/ ; STO414/15-1//Deutsche Forschungsgemeinschaft/ ; //Carl Zeiss Foundation/ ; //NVIDIA GPU grant program/ ; }, mesh = {Bacteria/*classification ; *Biodiversity ; Biomarkers/analysis ; Computer Simulation ; DNA Barcoding, Taxonomic/*methods ; Environmental Monitoring/*methods ; Eukaryota/*classification ; Metagenomics/*methods ; RNA, Ribosomal/genetics ; *Supervised Machine Learning ; }, abstract = {Biodiversity monitoring is the standard for environmental impact assessment of anthropogenic activities. Several recent studies showed that high-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) could overcome many limitations of the traditional morphotaxonomy-based bioassessment. Recently, we demonstrated that supervised machine learning (SML) can be used to predict accurate biotic indices values from eDNA metabarcoding data, regardless of the taxonomic affiliation of the sequences. However, it is unknown to which extent the accuracy of such models depends on taxonomic resolution of molecular markers or how SML compares with metabarcoding approaches targeting well-established bioindicator species. In this study, we address these issues by training predictive models upon five different ribosomal bacterial and eukaryotic markers and measuring their performance to assess the environmental impact of marine aquaculture on independent data sets. Our results show that all tested markers are yielding accurate predictive models and that they all outperform the assessment relying solely on taxonomically assigned sequences. Remarkably, we did not find any significant difference in the performance of the models built using universal eukaryotic or prokaryotic markers. Using any molecular marker with a taxonomic range broad enough to comprise different potential bioindicator taxa, SML approach can overcome the limits of taxonomy-based eDNA bioassessment.}, } @article {pmid30013164, year = {2018}, author = {Armstrong, Z and Mewis, K and Liu, F and Morgan-Lang, C and Scofield, M and Durno, E and Chen, HM and Mehr, K and Withers, SG and Hallam, SJ}, title = {Metagenomics reveals functional synergy and novel polysaccharide utilization loci in the Castor canadensis fecal microbiome.}, journal = {The ISME journal}, volume = {12}, number = {11}, pages = {2757-2769}, pmid = {30013164}, issn = {1751-7370}, mesh = {Animals ; Biomass ; Feces/microbiology ; Gastrointestinal Tract/microbiology ; Glycoside Hydrolases/genetics ; Metagenomics ; *Microbiota/genetics ; Polysaccharides/*metabolism ; Rodentia/*microbiology ; }, abstract = {The North American beaver (Castor canadensis) has long been considered an engineering marvel, transforming landscapes and shaping biological diversity through its dam building behavior. While the beaver possesses conspicuous morphological features uniquely adapted for the use of woody plants as construction materials and dietary staples, relatively little is known about the specialized microorganisms inhabiting the beaver gastrointestinal tract and their functional roles in determining host nutrition. Here we use a combination of shotgun metagenomics, functional screening and carbohydrate biochemistry to chart the community structure and metabolic power of the beaver fecal microbiome. We relate this information to the metabolic capacity of other wood feeding and hindgut fermenting organisms and profile the functional repertoire of glycoside hydrolase (GH) families distributed among and between population genome bins. Metagenomic screening revealed novel mechanisms of xylan oligomer degradation involving GH43 enzymes from uncharacterized subfamilies and divergent polysaccharide utilization loci, indicating the potential for synergistic biomass deconstruction. Together, these results open a functional metagenomic window on less conspicuous adaptations enabling the beaver microbiome to efficiently convert woody plants into host nutrition and point toward rational design of enhanced enzyme mixtures for biorefining process streams.}, } @article {pmid30010747, year = {2018}, author = {Nusbaum, DJ and Sun, F and Ren, J and Zhu, Z and Ramsy, N and Pervolarakis, N and Kunde, S and England, W and Gao, B and Fiehn, O and Michail, S and Whiteson, K}, title = {Gut microbial and metabolomic profiles after fecal microbiota transplantation in pediatric ulcerative colitis patients.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {9}, pages = {}, pmid = {30010747}, issn = {1574-6941}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; R56 HL126754/HL/NHLBI NIH HHS/United States ; UL1 TR001414/TR/NCATS NIH HHS/United States ; R01 HD081197/HD/NICHD NIH HHS/United States ; T32 EB009418/EB/NIBIB NIH HHS/United States ; }, mesh = {Child ; Clostridiaceae/classification/genetics/*isolation & purification ; Colitis, Ulcerative/*microbiology/*therapy ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Metabolomics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Ulcerative colitis is a chronic inflammatory disease of the colon that carries a significant disease burden in children. Therefore, new therapeutic approaches are being explored to help children living with this disease. Fecal microbiota transplantation (FMT) has been successful in some children with ulcerative colitis. However, the mechanism of its therapeutic effect in this patient population is not well understood. To characterize changes in gut microbial and metabolomic profiles after FMT, we performed 16S rRNA gene sequencing, shotgun metagenomic sequencing, virome analysis and untargeted metabolomics by gas chromatography-time of flight-mass spectrometry on stool samples collected before and after FMT from four children with ulcerative colitis who responded to this treatment. Alpha diversity of the gut microbiota increased after intervention, with species richness rising from 251 (S.D. 125) to 358 (S.D. 27). In responders, the mean relative abundance of bacteria in the class Clostridia shifted toward donor levels, increasing from 33% (S.D. 11%) to 54% (S.D. 16%). Patient metabolomic and viromic profiles exhibited a similar but less pronounced shift toward donor profiles after FMT. The fecal concentrations of several metabolites were altered after FMT, correlating with clinical improvement. Larger studies using a similar multi-omics approach may suggest novel strategies for the treatment of pediatric ulcerative colitis.}, } @article {pmid30010734, year = {2018}, author = {Geng, S and Cheng, S and Li, Y and Wen, Z and Ma, X and Jiang, X and Wang, Y and Han, X}, title = {Faecal Microbiota Transplantation Reduces Susceptibility to Epithelial Injury and Modulates Tryptophan Metabolism of the Microbial Community in a Piglet Model.}, journal = {Journal of Crohn's & colitis}, volume = {12}, number = {11}, pages = {1359-1374}, doi = {10.1093/ecco-jcc/jjy103}, pmid = {30010734}, issn = {1876-4479}, mesh = {Animals ; Colitis/chemically induced/pathology/*prevention & control ; *Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/*physiology ; Homeostasis ; Indoleacetic Acids/metabolism ; Interleukins/metabolism ; Intestinal Mucosa/metabolism/*pathology ; Lipopolysaccharides ; Mass Spectrometry ; Metabolome ; RNA, Ribosomal, 16S/analysis ; Receptors, Aryl Hydrocarbon/metabolism ; Swine ; Tryptophan/*metabolism ; Interleukin-22 ; }, abstract = {BACKGROUND AND AIMS: Faecal microbiota transplantation [FMT] has shown promise as a treatment for inflammatory bowel disease [IBD]. Using a piglet model, our previous study indicated that exogenous faecal microbiota can increase the expressions of tight junction proteins, mucin and antimicrobial peptide in the intestinal mucosa, suggesting a beneficial effect of FMT on gut barrier and gastrointestinal health. However, specific connections between FMT-induced microbial changes and modulation of the intestinal barrier remain to be fully illustrated. Here, we aimed to determine the potential role of metabolic function of gut microbiota in the beneficial effects of FMT.

METHODS: The influence of FMT on the maintenance of intestinal homeostasis was assessed by early-life gut microbiota intervention on newborn piglets and subsequent lipopolysaccharide [LPS] challenge. Analysis of the gut microbiome and metabolome was carried out by 16S rRNA gene sequencing and multiple mass spectrometry platforms.

RESULTS: FMT modulated the diversity and composition of colonic microbiota and reduced the susceptibility to LPS-induced destruction of epithelial integrity and severe inflammatory response. Metabolomic analysis revealed functional changes of the gut metabolome along with a significant increase of the typical microbiota-derived tryptophan catabolite indole-3-acetic acid in the colonic lumen. In concordance with the metabolome data, metagenomics prediction analysis based on 16S rRNA gene sequencing also demonstrated that FMT modulated the metabolic functions of gut microbiota associated with indole alkaloid biosynthesis, cytochrome P450 and intestinal homeostasis, which coincided with up-regulation of cytokine interleukin-22 and enhanced activation of aryl hydrocarbon receptor in the recipient colon.

CONCLUSIONS: Our data reveal a regulatory effect of FMT on tryptophan metabolism of gut microbiota in the recipient colon, which may play a potential role in maintenance of the intestinal barrier.}, } @article {pmid30009332, year = {2019}, author = {Bag, S and Ghosh, TS and Banerjee, S and Mehta, O and Verma, J and Dayal, M and Desigamani, A and Kumar, P and Saha, B and Kedia, S and Ahuja, V and Ramamurthy, T and Das, B}, title = {Molecular Insights into Antimicrobial Resistance Traits of Commensal Human Gut Microbiota.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {546-557}, pmid = {30009332}, issn = {1432-184X}, support = {BT/MB/THSTI/HMC-SFC/2011//Department of Biotechnology , Ministry of Science and Technology/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics/isolation & purification ; DNA Transposable Elements/genetics ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/*genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*genetics ; Genome, Bacterial ; Genotype ; Humans ; Interspersed Repetitive Sequences/genetics ; Metagenome/genetics ; Microbial Sensitivity Tests ; *Phenotype ; *Symbiosis ; Transformation, Genetic/genetics ; Vibrio cholerae/genetics ; Whole Genome Sequencing ; }, abstract = {Antimicrobial resistance (AMR) among bacterial species that resides in complex ecosystems is a natural phenomenon. Indiscriminate use of antimicrobials in healthcare, livestock, and agriculture provides an evolutionary advantage to the resistant variants to dominate the ecosystem. Ascendency of resistant variants threatens the efficacy of most, if not all, of the antimicrobial drugs commonly used to prevent and/or cure microbial infections. Resistant phenotype is very common in enteric bacteria. The most common mechanisms of AMR are enzymatic modifications to the antimicrobials or their target molecules. In enteric bacteria, most of the resistance traits are acquired by horizontal gene transfer from closely or distantly related bacterial population. AMR traits are generally linked with mobile genetic elements (MGEs) and could rapidly disseminate to the bacterial species through horizontal gene transfer (HGT) from a pool of resistance genes. Although prevalence of AMR genes among pathogenic bacteria is widely studied in the interest of infectious disease management, the resistance profile and the genetic traits that encode resistance to the commensal microbiota residing in the gut of healthy humans are not well-studied. In the present study, we have characterized AMR phenotypes and genotypes of five dominant commensal enteric bacteria isolated from the gut of healthy Indians. Our study revealed that like pathogenic bacteria, enteric commensals are also multidrug-resistant. The genes encoding antibiotic resistance are physically linked with MGEs and could disseminate vertically to the progeny and laterally to the distantly related microbial species. Consequently, the AMR genes present in the chromosome of commensal gut bacteria could be a potential source of resistance functions for other enteric pathogens.}, } @article {pmid30006634, year = {2018}, author = {Kawai, K and Kamochi, R and Oiki, S and Murata, K and Hashimoto, W}, title = {Probiotics in human gut microbiota can degrade host glycosaminoglycans.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10674}, pmid = {30006634}, issn = {2045-2322}, mesh = {Aldose-Ketose Isomerases/genetics/metabolism ; Bacteria/*enzymology/genetics ; Bacterial Proteins/genetics/isolation & purification/*metabolism ; Caco-2 Cells ; Carbohydrate Dehydrogenases/genetics/metabolism ; Coculture Techniques ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Glycosaminoglycans/*metabolism ; Humans ; Metagenomics ; Probiotics/*metabolism ; }, abstract = {Glycosaminoglycans (GAGs) (e.g. heparin, chondroitin sulfate, and hyaluronan) show various significant physiological functions as a major component of extracellular matrix in animals. Some bacteria target GAGs for adhesion and/or infection to host cells, although no probiotics have been known to degrade GAGs. Here, we show GAG degradation by probiotics from human gut microbiota and their adhesion to human intestinal cells through a GAG. GAG-degrading bacteria were isolated from human faeces and identified as Enterococcus faecium, and some typical probiotics such as Lactobacillus casei, Lactobacillus rhamnosus and Enterococcus faecalis were also found to degrade heparin. GAG-degrading lactobacilli and enterococci including the isolated E. faecium possessed a genetic cluster encoding GAG-degrading/metabolising enzymes in the bacterial genome. KduI and KduD enzymes encoded in the GAG cluster of L. rhamnosus functioned as 4-deoxy-l-threo-5-hexosulose-uronate ketol-isomerase and 2-keto-3-deoxy-d-gluconate dehydrogenase, respectively, both of which were crucial for GAG metabolism. GAG-degrading L. rhamnosus and E. faecium attached to human intestinal Caco-2 cells via heparin. Some species of Bacteroides, considered to be the next generation probiotics, degraded chondroitin sulfate C and hyaluronan, and genes coding for the Bacteroides GAG-degrading enzyme were frequently detected from human gut microbiota. This is the first report on GAG-degrading probiotics in human gut microbiota.}, } @article {pmid30006403, year = {2018}, author = {Zhang, H and Wang, K and Shen, L and Chen, H and Hou, F and Zhou, X and Zhang, D and Zhu, X}, title = {Microbial Community Dynamics and Assembly Follow Trajectories of an Early-Spring Diatom Bloom in a Semienclosed Bay.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {18}, pages = {}, pmid = {30006403}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Bays/*microbiology/parasitology ; Diatoms/*growth & development ; Ecosystem ; *Microbiota ; Seasons ; }, abstract = {Harmful algal blooms (HABs) are serious ecological disasters in coastal areas, significantly influencing biogeochemical cycles driven by bacteria. The shifts in microbial communities during HABs have been widely investigated, but the assembly mechanisms of microbial communities during HABs are poorly understood. Here, using 16S rRNA gene amplicon sequencing, we analyzed the microbial communities during an early-spring diatom bloom, in order to investigate the dynamics of microbial assembly processes. Rhodobacteraceae, Flavobacteriaceae, and Microbacteriaceae were the main bacterial families during the bloom. The 30 most abundant operational taxonomic units (OTUs) segregated into 4 clusters according to specific bloom stages, exhibiting clear successional patterns during the bloom process. The succession of microbial communities correlated with changes in the dynamics of algal species. Based on the β-nearest taxon distance, we constructed a simulation model, which demonstrated that the assembly of microbial communities shifted from strong heterogenous selection in the early stage of the bloom to stochasticity in the middle stage and then to strong homogeneous selection in the late and after-bloom stages. These successions were driven mainly by chlorophyll a contents, which were affected mainly by Skeletonema costatum Moreover, functional prediction of microbial communities showed that microbial metabolic functions were significantly related to nitrogen metabolism. In summary, our results clearly suggested a dominant role of determinacy in microbial community assembly in HABs and will facilitate deeper understanding of the ecological processes shaping microbial communities during the algal bloom process.IMPORTANCE Harmful algal blooms (HABs) significantly influence biogeochemical cycles driven by bacteria. The shifts in microbial communities during HABs have been studied intensively, but the assembly mechanisms of microbial communities during HABs are poorly understood, with limited investigation of the balance of deterministic and stochastic processes in shaping microbial communities in HABs. In this study, the dynamics and assembly of microbial communities in an early-spring diatom bloom process were investigated. Our data both confirm previously observed general microbial successional patterns and show new detailed mechanisms for microbial assembly in HABs. These results will facilitate deeper understanding of the ecological processes shaping microbial communities in HABs. In addition, predictions of metabolic potential in this study will facilitate understanding of the influence of HABs on nitrogen metabolism in marine environments.}, } @article {pmid30006398, year = {2018}, author = {Kougias, PG and Campanaro, S and Treu, L and Tsapekos, P and Armani, A and Angelidaki, I}, title = {Spatial Distribution and Diverse Metabolic Functions of Lignocellulose-Degrading Uncultured Bacteria as Revealed by Genome-Centric Metagenomics.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {18}, pages = {}, pmid = {30006398}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Biodiversity ; Bioreactors/microbiology ; *Genome, Bacterial ; Lignin/*metabolism ; Manure/microbiology ; Metagenomics ; Phylogeny ; Swine ; }, abstract = {The mechanisms by which specific anaerobic microorganisms remain firmly attached to lignocellulosic material, allowing them to efficiently decompose organic matter, have yet to be elucidated. To circumvent this issue, microbiomes collected from anaerobic digesters treating pig manure and meadow grass were fractionated to separate the planktonic microbes from those adhered to lignocellulosic substrate. Assembly of shotgun reads, followed by a binning process, recovered 151 population genomes, 80 out of which were completely new and were not previously deposited in any database. Genome coverage allowed the identification of microbial spatial distribution in the engineered ecosystem. Moreover, a composite bioinformatic analysis using multiple databases for functional annotation revealed that uncultured members of the Bacteroidetes and Firmicutes follow diverse metabolic strategies for polysaccharide degradation. The structure of cellulosome in Firmicutes species can differ depending on the number and functional roles of carbohydrate-binding modules. In contrast, members of the Bacteroidetes are able to adhere to and degrade lignocellulose due to the presence of multiple carbohydrate-binding family 6 modules in beta-xylosidase and endoglucanase proteins or S-layer homology modules in unknown proteins. This study combines the concept of variability in spatial distribution with genome-centric metagenomics, allowing a functional and taxonomical exploration of the biogas microbiome.IMPORTANCE This work contributes new knowledge about lignocellulose degradation in engineered ecosystems. Specifically, the combination of the spatial distribution of uncultured microbes with genome-centric metagenomics provides novel insights into the metabolic properties of planktonic and firmly attached to plant biomass bacteria. Moreover, the knowledge obtained in this study enabled us to understand the diverse metabolic strategies for polysaccharide degradation in different species of Bacteroidetes and Clostridiales Even though structural elements of cellulosome were restricted to Clostridiales species, our study identified a putative mechanism in Bacteroidetes species for biomass decomposition, which is based on a gene cluster responsible for cellulose degradation, disaccharide cleavage to glucose, and transport to cytoplasm.}, } @article {pmid30003485, year = {2018}, author = {Li, M and Zhang, X and Yang, H and Li, X and Cui, Z}, title = {Soil sustainable utilization technology: mechanism of flavonols in resistance process of heavy metal.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {26}, pages = {26669-26681}, pmid = {30003485}, issn = {1614-7499}, mesh = {Arabidopsis/genetics/*metabolism/microbiology ; Drug Resistance/genetics ; Flavonols/genetics/*metabolism ; Metabolic Networks and Pathways/drug effects/genetics ; Metagenome/*drug effects ; Metals, Heavy/*toxicity ; Microbiota/*genetics ; Plant Roots/genetics/metabolism/microbiology ; Rhizosphere ; *Soil Microbiology ; Soil Pollutants/*toxicity ; }, abstract = {The soil ecosystem is critical for agricultural production, affecting many aspects of human health. Soil has more unknown biodiversity and edaphic parameters than any other ecosystem especially when polluted. Metagenomics and metatranscriptomics were applied to research on toxicological characteristics of Pb and resistance mechanism of flavonols. Rhizosphere microorganisms-plants system, a unified system closely related to soil environment was taken as research object. Results emphasize gene expression changes in different test groups. Gene ontology enrichment and eggNOG showed that Pb has a toxic effect on gene and protein function which concentrated on ATPase and ATP-dependent activity. Differentially expressed genes in the flavonols group indicated that flavonols regulate amino acid transport and other transportation process related to Pb stress. Kegg analysis represents that Pb interferences energy production process via not only the upstream like glycolysis and tricarboxylic acid (TCA) circle but also oxidative phosphorylation process, which can also produce reactive oxygen species and impact the eliminating process. Flavonols have shown the ability in alleviating toxic effect of Pb and improving the resistance of plants. Flavonols can recover the electronic transmission and other process in TCA and oxidative phosphorylation via ascorbic acid-glutathione metabolism. Flavonols activated antioxidative process and non-specific immunity via vitamins B2-B6 metabolism.}, } @article {pmid30002454, year = {2018}, author = {Phoma, S and Vikram, S and Jansson, JK and Ansorge, IJ and Cowan, DA and Van de Peer, Y and Makhalanyane, TP}, title = {Agulhas Current properties shape microbial community diversity and potential functionality.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10542}, pmid = {30002454}, issn = {2045-2322}, mesh = {Bacteria/*genetics/isolation & purification/metabolism ; *Biodiversity ; DNA, Bacterial/isolation & purification ; Indian Ocean ; Microbiota/*physiology ; Nitrogen Cycle ; Oceanography ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; Sulfur/metabolism ; *Water Movements ; }, abstract = {Understanding the impact of oceanographic features on marine microbial ecosystems remains a major ecological endeavour. Here we assess microbial diversity, community structure and functional capacity along the Agulhas Current system and the Subtropical Front in the South Indian Ocean (SIO). Samples collected from the epipelagic, oxygen minimum and bathypelagic zones were analysed by 16S rRNA gene amplicon and metagenomic sequencing. In contrast to previous studies, we found high taxonomic richness in surface and deep water samples, but generally low richness for OMZ communities. Beta-diversity analysis revealed significant dissimilarity between the three water depths. Most microbial communities were dominated by marine Gammaproteobacteria, with strikingly low levels of picocyanobacteria. Community composition was strongly influenced by specific environmental factors including depth, salinity, and the availability of both oxygen and light. Carbon, nitrogen and sulfur cycling capacity in the SIO was linked to several autotrophic and copiotrophic Alphaproteobacteria and Gammaproteobacteria. Taken together, our data suggest that the environmental conditions in the Agulhas Current system, particularly depth-related parameters, substantially influence microbial community structure. In addition, the capacity for biogeochemical cycling of nitrogen and sulfur is linked primarily to the dominant Gammaproteobacteria taxa, whereas ecologically rare taxa drive carbon cycling.}, } @article {pmid30002438, year = {2018}, author = {Hart, EH and Creevey, CJ and Hitch, T and Kingston-Smith, AH}, title = {Meta-proteomics of rumen microbiota indicates niche compartmentalisation and functional dominance in a limited number of metabolic pathways between abundant bacteria.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10504}, pmid = {30002438}, issn = {2045-2322}, support = {BB/E/W/10964A01//Biotechnology and Biological Sciences Research Council (BBSRC)/International ; }, mesh = {Animal Feed ; Animals ; Bacteria/genetics/isolation & purification/*metabolism ; Bacterial Proteins/*metabolism ; Cattle ; DNA, Bacterial/isolation & purification ; Female ; Fermentation/physiology ; Gastrointestinal Microbiome/*physiology ; Gene Expression Profiling ; Metabolic Networks and Pathways/physiology ; Proteome/*metabolism ; Proteomics/methods ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; }, abstract = {The rumen is a complex ecosystem. It is the primary site for microbial fermentation of ingested feed allowing conversion of a low nutritional feed source into high quality meat and milk products. However, digestive inefficiencies lead to production of high amounts of environmental pollutants; methane and nitrogenous waste. These inefficiencies could be overcome by development of forages which better match the requirements of the rumen microbial population. Although challenging, the application of meta-proteomics has potential for a more complete understanding of the rumen ecosystem than sequencing approaches alone. Here, we have implemented a meta-proteomic approach to determine the association between taxonomies of microbial sources of the most abundant proteins in the rumens of forage-fed dairy cows, with taxonomic abundances typical of those previously described by metagenomics. Reproducible proteome profiles were generated from rumen samples. The most highly abundant taxonomic phyla in the proteome were Bacteriodetes, Firmicutes and Proteobacteria, which corresponded with the most abundant taxonomic phyla determined from 16S rRNA studies. Meta-proteome data indicated differentiation between metabolic pathways of the most abundant phyla, which is in agreement with the concept of diversified niches within the rumen microbiota.}, } @article {pmid30001854, year = {2018}, author = {Berry, D and Loy, A}, title = {Stable-Isotope Probing of Human and Animal Microbiome Function.}, journal = {Trends in microbiology}, volume = {26}, number = {12}, pages = {999-1007}, pmid = {30001854}, issn = {1878-4380}, support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; P 26127/FWF_/Austrian Science Fund FWF/Austria ; P 27831/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Bacterial Physiological Phenomena ; DNA/chemistry ; Gastrointestinal Microbiome/*physiology ; Host Microbial Interactions/*physiology ; Humans ; Isotope Labeling/*methods ; *Isotopes ; Metagenome ; Metagenomics/methods ; Molecular Probes ; RNA/chemistry ; Spectrum Analysis, Raman/methods ; }, abstract = {Humans and animals host diverse communities of microorganisms important to their physiology and health. Despite extensive sequencing-based characterization of host-associated microbiomes, there remains a dramatic lack of understanding of microbial functions. Stable-isotope probing (SIP) is a powerful strategy to elucidate the ecophysiology of microorganisms in complex host-associated microbiotas. Here, we suggest that SIP methodologies should be more frequently exploited as part of a holistic functional microbiomics approach. We provide examples of how SIP has been used to study host-associated microbes in vivo and ex vivo. We highlight recent developments in SIP technologies and discuss future directions that will facilitate deeper insights into the function of human and animal microbiomes.}, } @article {pmid30001519, year = {2018}, author = {Karasov, TL and Almario, J and Friedemann, C and Ding, W and Giolai, M and Heavens, D and Kersten, S and Lundberg, DS and Neumann, M and Regalado, J and Neher, RA and Kemen, E and Weigel, D}, title = {Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales.}, journal = {Cell host & microbe}, volume = {24}, number = {1}, pages = {168-179.e4}, pmid = {30001519}, issn = {1934-6069}, support = {//European Research Council/International ; }, mesh = {Arabidopsis/*microbiology ; *Biological Evolution ; Crops, Agricultural/microbiology ; DNA, Bacterial/*genetics ; Metagenome ; Phylogeny ; Plant Diseases/microbiology ; Plant Leaves/*microbiology ; Pseudomonas/*genetics/pathogenicity ; Pseudomonas Infections/microbiology ; RNA, Ribosomal, 16S/genetics ; Whole Genome Sequencing ; }, abstract = {Crop disease outbreaks are often associated with clonal expansions of single pathogenic lineages. To determine whether similar boom-and-bust scenarios hold for wild pathosystems, we carried out a multi-year, multi-site survey of Pseudomonas in its natural host Arabidopsis thaliana. The most common Pseudomonas lineage corresponded to a ubiquitous pathogenic clade. Sequencing of 1,524 genomes revealed this lineage to have diversified approximately 300,000 years ago, containing dozens of genetically identifiable pathogenic sublineages. There is differentiation at the level of both gene content and disease phenotype, although the differentiation may not provide fitness advantages to specific sublineages. The coexistence of sublineages indicates that in contrast to crop systems, no single strain has been able to overtake the studied A. thaliana populations in the recent past. Our results suggest that selective pressures acting on a plant pathogen in wild hosts are likely to be much more complex than those in agricultural systems.}, } @article {pmid30001517, year = {2018}, author = {Yassour, M and Jason, E and Hogstrom, LJ and Arthur, TD and Tripathi, S and Siljander, H and Selvenius, J and Oikarinen, S and Hyöty, H and Virtanen, SM and Ilonen, J and Ferretti, P and Pasolli, E and Tett, A and Asnicar, F and Segata, N and Vlamakis, H and Lander, ES and Huttenhower, C and Knip, M and Xavier, RJ}, title = {Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life.}, journal = {Cell host & microbe}, volume = {24}, number = {1}, pages = {146-154.e4}, pmid = {30001517}, issn = {1934-6069}, support = {DP3 DK094338/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Bacteroides/*genetics ; Cohort Studies ; DNA, Bacterial/*genetics ; Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Infant ; Infant, Newborn ; Longitudinal Studies ; Male ; Meconium/microbiology ; Metagenomics ; *Mother-Child Relations ; Prospective Studies ; }, abstract = {Bacterial community acquisition in the infant gut impacts immune education and disease susceptibility. We compared bacterial strains across and within families in a prospective birth cohort of 44 infants and their mothers, sampled longitudinally in the first months of each child's life. We identified mother-to-child bacterial transmission events and describe the incidence of family-specific antibiotic resistance genes. We observed two inheritance patterns across multiple species, where often the mother's dominant strain is transmitted to the child, but occasionally her secondary strains colonize the infant gut. In families where the secondary strain of B. uniformis was inherited, a starch utilization gene cluster that was absent in the mother's dominant strain was identified in the child, suggesting the selective advantage of a mother's secondary strain in the infant gut. Our findings reveal mother-to-child bacterial transmission events at high resolution and give insights into early colonization of the infant gut.}, } @article {pmid30460050, year = {2017}, author = {Kim, H and Kim, H and Hwang, HS and Kim, W}, title = {Metagenomic analysis of the marine coastal invertebrates of South Korea as assessed by Ilumina MiSeq.}, journal = {Animal cells and systems}, volume = {21}, number = {1}, pages = {37-44}, pmid = {30460050}, issn = {1976-8354}, abstract = {Metagenomic analysis was carried out for the first time on the marine coastal invertebrates of South Korea. Samples collected from coastal areas of Korea were filtered through a 63 µm mesh, then their 18S rDNA V4 regions were amplified. High-throughput sequencing of PCR amplicons using Illumina MiSeq and BLAST against the SILVA database showed that a total of 319 eukaryotic Operational Taxonomic Units were identified at the species level. Annelida, Arthropoda, Mollusca, Nematoda, and Platyhelminthes and for 92.23% of the total 103 metazoan species belonging to 101 genera, 75 families, and 10 phyla. Of these, several taxa previously unreported to exist in Korea were detected at the family level compared with the integrated database from three main Korean biodiversity DBs (MABIK, KOMBIS, and MRBR). Analysis of beta diversity of the community structure of invertebrates indicated that the composition of marine invertebrates is likely to be affected by habitat type rather than geographical distance. The present study showed that metagenomic high-throughput technology can be used to unravel species diversity and for various studies regarding marine invertebrate community structure.}, } @article {pmid30141594, year = {2016}, author = {Patyka, NV and Kolodyazhnyi, AY and Ibatullin, II}, title = {[The Evaluation of Metagenome and Detection of Functionally Significant Polymorphisms of Prokaryotes of Soil by Method of Pyrosequencingl].}, journal = {Mikrobiolohichnyi zhurnal (Kiev, Ukraine : 1993)}, volume = {78}, number = {2}, pages = {43-51}, pmid = {30141594}, issn = {1028-0987}, mesh = {Archaea/*classification ; Bacteria/*classification ; Biodiversity ; *Metagenome ; *Phylogeny ; Soil ; *Soil Microbiology ; Triticum ; }, abstract = {It was evaluated the metagenome and functionally significant phylogenetic and taxonomic polymorphisms of prokaryotes of typical chernozem in agrocenoses of winter wheat by the method of pyrosequencing. Have been received 1708 operational taxonomic units and identified 335 taxons of prokaryotes. It was established, that the structure of prokaryotes metagenome of typical chernozem includes the representatives of the 2 Archaea and 22 Bacteria phylums, and absolutely dominants among them were Proteobacteria - 79.6 % and Actinobacteria - 12.9 %. The polymorphism of representation of prokaryotic taxons was observed at the level of families, and the dominants were Alcaligenaceae, Pseudomonadaceae, Solirubrobacteraceae, Gaiellaceae, Nitrososphaeraceae. It is shown phylogenetic links between the main representatives of prokaryotes’ metagenome of typical chernozem in agrocenoses of winter wheat. Thus, the use of pyrosequencing, in addition to estimation of structure and diversity, opens new perspectives for the study of functional component of prokaryotes’ metagenome of soil.}, } @article {pmid30001516, year = {2018}, author = {Ferretti, P and Pasolli, E and Tett, A and Asnicar, F and Gorfer, V and Fedi, S and Armanini, F and Truong, DT and Manara, S and Zolfo, M and Beghini, F and Bertorelli, R and De Sanctis, V and Bariletti, I and Canto, R and Clementi, R and Cologna, M and Crifò, T and Cusumano, G and Gottardi, S and Innamorati, C and Masè, C and Postai, D and Savoi, D and Duranti, S and Lugli, GA and Mancabelli, L and Turroni, F and Ferrario, C and Milani, C and Mangifesta, M and Anzalone, R and Viappiani, A and Yassour, M and Vlamakis, H and Xavier, R and Collado, CM and Koren, O and Tateo, S and Soffiati, M and Pedrotti, A and Ventura, M and Huttenhower, C and Bork, P and Segata, N}, title = {Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome.}, journal = {Cell host & microbe}, volume = {24}, number = {1}, pages = {133-145.e5}, pmid = {30001516}, issn = {1934-6069}, support = {716575/ERC_/European Research Council/International ; }, mesh = {Adult ; DNA, Bacterial/*genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; Infant ; Longitudinal Studies ; Metagenomics ; Middle Aged ; *Mother-Child Relations ; Mouth/microbiology ; Skin/microbiology ; Time Factors ; Vagina/microbiology ; }, abstract = {The acquisition and development of the infant microbiome are key to establishing a healthy host-microbiome symbiosis. The maternal microbial reservoir is thought to play a crucial role in this process. However, the source and transmission routes of the infant pioneering microbes are poorly understood. To address this, we longitudinally sampled the microbiome of 25 mother-infant pairs across multiple body sites from birth up to 4 months postpartum. Strain-level metagenomic profiling showed a rapid influx of microbes at birth followed by strong selection during the first few days of life. Maternal skin and vaginal strains colonize only transiently, and the infant continues to acquire microbes from distinct maternal sources after birth. Maternal gut strains proved more persistent in the infant gut and ecologically better adapted than those acquired from other sources. Together, these data describe the mother-to-infant microbiome transmission routes that are integral in the development of the infant microbiome.}, } @article {pmid29996907, year = {2018}, author = {Cariou, M and Ribière, C and Morlière, S and Gauthier, JP and Simon, JC and Peyret, P and Charlat, S}, title = {Comparing 16S rDNA amplicon sequencing and hybridization capture for pea aphid microbiota diversity analysis.}, journal = {BMC research notes}, volume = {11}, number = {1}, pages = {461}, pmid = {29996907}, issn = {1756-0500}, support = {CapSymbArt//Centre National de la Recherche Scientifique/ ; }, mesh = {Animals ; Aphids/*microbiology ; DNA, Ribosomal/*genetics ; High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; Pisum sativum ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVE: Targeted sequencing of 16S rDNA amplicons is routinely used for microbial community profiling but this method suffers several limitations such as bias affinity of universal primers and short read size. Gene capture by hybridization represents a promising alternative. Here we used a metagenomic extract from the pea aphid Acyrthosiphon pisum to compare the performances of two widely used PCR primer pairs with DNA capture, based on solution hybrid selection.

RESULTS: All methods produced an exhaustive description of the 8 bacterial taxa known to be present in this sample. In addition, the methods yielded similar quantitative results, with the number of reads strongly correlating with quantitative PCR controls. Both methods can thus be considered as qualitatively and quantitatively robust on such a sample with low microbial complexity.}, } @article {pmid29995973, year = {2018}, author = {Franke, T and Deppenmeier, U}, title = {Physiology and central carbon metabolism of the gut bacterium Prevotella copri.}, journal = {Molecular microbiology}, volume = {109}, number = {4}, pages = {528-540}, doi = {10.1111/mmi.14058}, pmid = {29995973}, issn = {1365-2958}, mesh = {Acetate-CoA Ligase/metabolism ; Carbon Dioxide/metabolism ; Energy Metabolism/*genetics/physiology ; Formates/metabolism ; Fumarates/metabolism ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/microbiology ; Glycolysis/*genetics ; Humans ; Metabolic Networks and Pathways/genetics/physiology ; Prevotella/genetics/*growth & development/*metabolism ; Pyruvic Acid/metabolism ; Succinic Acid/metabolism ; }, abstract = {The human gut microbiota is a crucial factor for the host's physiology with respect to health and disease. Metagenomic shotgun sequencing of microbial gut communities revealed that Prevotella copri is one of the most important players in the gastrointestinal tract of many individuals. Because of the importance of this bacterium we analyzed the growth behavior and the central metabolic pathways of P. copri. Bioinformatic data, transcriptome profiling and enzyme activity measurements indicated that the major pathways are based on glycolysis and succinate production from fumarate. In addition, pyruvate can be degraded to acetate and formate. Electron transport phosphorylation depends on fumarate respiration with NADH and reduced ferredoxin as electron donors. In contrast to Bacteroides vulgatus, P. copri showed a more pronounced dependency on the addition of CO2 or bicarbonate for biomass formation, which is a remarkable difference between P. copri and Bacteroides spp. with important implication in the context of gut microbial competition. The analysis of substrate consumption and product concentrations from many P. copri cultures with different optical densities allowed a prediction of the carbon and electron flow in the central metabolism and a detailed calculation of growth yields as well as carbon and redox balances.}, } @article {pmid29995839, year = {2019}, author = {Amato, KR and G Sanders, J and Song, SJ and Nute, M and Metcalf, JL and Thompson, LR and Morton, JT and Amir, A and J McKenzie, V and Humphrey, G and Gogul, G and Gaffney, J and L Baden, A and A O Britton, G and P Cuozzo, F and Di Fiore, A and J Dominy, N and L Goldberg, T and Gomez, A and Kowalewski, MM and J Lewis, R and Link, A and L Sauther, M and Tecot, S and A White, B and E Nelson, K and M Stumpf, R and Knight, R and R Leigh, S}, title = {Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes.}, journal = {The ISME journal}, volume = {13}, number = {3}, pages = {576-587}, pmid = {29995839}, issn = {1751-7370}, mesh = {Animals ; *Biological Evolution ; Diet/veterinary ; Gastrointestinal Microbiome/*genetics ; *Metagenomics ; Phylogeny ; Primates/*microbiology/*physiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Over the past decade several studies have reported that the gut microbiomes of mammals with similar dietary niches exhibit similar compositional and functional traits. However, these studies rely heavily on samples from captive individuals and often confound host phylogeny, gut morphology, and diet. To more explicitly test the influence of host dietary niche on the mammalian gut microbiome we use 16S rRNA gene amplicon sequencing and shotgun metagenomics to compare the gut microbiota of 18 species of wild non-human primates classified as either folivores or closely related non-folivores, evenly distributed throughout the primate order and representing a range of gut morphological specializations. While folivory results in some convergent microbial traits, collectively we show that the influence of host phylogeny on both gut microbial composition and function is much stronger than that of host dietary niche. This pattern does not result from differences in host geographic location or actual dietary intake at the time of sampling, but instead appears to result from differences in host physiology. These findings indicate that mammalian gut microbiome plasticity in response to dietary shifts over both the lifespan of an individual host and the evolutionary history of a given host species is constrained by host physiological evolution. Therefore, the gut microbiome cannot be considered separately from host physiology when describing host nutritional strategies and the emergence of host dietary niches.}, } @article {pmid29994027, year = {2019}, author = {Nalbantoglu, OU and Sayood, K}, title = {MIMOSA: Algorithms for Microbial Profiling.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {16}, number = {6}, pages = {2023-2034}, doi = {10.1109/TCBB.2018.2830324}, pmid = {29994027}, issn = {1557-9964}, mesh = {Algorithms ; Biodiversity ; Computer Simulation ; Contig Mapping ; Databases, Genetic ; Female ; Gastrointestinal Microbiome ; *Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Humans ; *Metagenome ; Metagenomics/*methods ; Mimosa ; Models, Biological ; Nucleic Acid Hybridization ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; Vagina/microbiology ; }, abstract = {A significant goal of the study of metagenomes obtained from an environment is to find the microbial diversity and the abundance of each organism in the community. Phylotyping and binning methods which address this problem generally operate using either marker sequences or by classifying each genome fragment individually. However, these approaches might not use all the information contained in the metagenome. We propose an approach based on a Multiple Input Multiple Output (MIMO) communication system model. Results from two different implementations of this approach, one using DNA-DNA hybridization simulations and one using short read mapping are evaluated using simulated and actual metagenomes and compared with other methods of phylotyping. The proposed approaches generally performed better under different scenarios including pathogen detection tasks of community complexity and low and high sequencing coverage while being highly computationally effective. The resulting framework can be integrated to metagenome analysis pipelines for phylogenetic diversity estimation. The approach is modular so that techniques other than hybridization simulations and short read mapping may be integrated. We have observed that even for low coverage samples, the method provides accurate estimates. Therefore, the use of the proposed strategy could enable the task of exploring biodiversity with limited resources.}, } @article {pmid29992707, year = {2018}, author = {Ostrensky, A and Horodesky, A and Faoro, H and Balsanelli, E and Sfeir, MZT and Cozer, N and Pie, MR and Dal Pont, G and Castilho-Westphal, GG}, title = {Metagenomic evaluation of the effects of storage conditions on the bacterial microbiota of oysters Crassostrea gasar (Adanson, 1757).}, journal = {Journal of applied microbiology}, volume = {125}, number = {5}, pages = {1435-1443}, doi = {10.1111/jam.14045}, pmid = {29992707}, issn = {1365-2672}, support = {//Serviço Brasileiro de Apoio às Micro e Pequenas Empresas - Sebrae/ ; }, mesh = {Animals ; Brazil ; Crassostrea/*microbiology ; Food Safety ; Food Storage/*methods ; Humans ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Seafood ; Temperature ; }, abstract = {AIMS: To evaluate the influence of storage conditions on the composition of the bacterial microbiota of living oysters Crassostrea gasar.

METHODS AND RESULTS: The oysters used in this study came from marine farms (Guaratuba Bay, Brazil) and were exposed to two conditions that simulated different storage situations: immersion in water (group I) and exposure to air (group II). The animals were subjected to five different temperatures (5-25°C), for 10 days. The 16S rRNA gene from oysters was amplified and sequenced to determine the taxonomic units and bacterial strains present in the samples. Group I showed higher diversity of bacteria (163 genera) rather than group II (104 genera). In all, 59 bacterial genera potentially pathogenic to humans were identified (n = 56 in group I and n = 45 in group II).

CONCLUSIONS: The storage conditions having a direct influence on the oyster microbiota. Live C. gasar should be stored exposed to air at 5-25°C, because it favours a lower prevalence of bacteria potentially pathogenic to humans.

During the oyster commercialization process, some conditions of storage, time and temperature must be followed in order to reduce the prevalence of bacteria potentially pathogenic to humans.}, } @article {pmid29991350, year = {2018}, author = {Haro-Moreno, JM and López-Pérez, M and de la Torre, JR and Picazo, A and Camacho, A and Rodriguez-Valera, F}, title = {Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {128}, pmid = {29991350}, issn = {2049-2618}, mesh = {Archaea/*classification/isolation & purification ; Bacteria/*classification/isolation & purification ; Mediterranean Sea ; Metagenomics/*methods ; Phylogeny ; Seasons ; Water Microbiology ; }, abstract = {BACKGROUND: The photic zone of aquatic habitats is subjected to strong physicochemical gradients. To analyze the fine-scale variations in the marine microbiome, we collected seven samples from a single offshore location in the Mediterranean at 15 m depth intervals during a period of strong stratification, as well as two more samples during the winter when the photic water column was mixed. We were able to recover 94 new metagenome-assembled genomes (MAGs) from these metagenomes and examine the distribution of key marine microbes within the photic zone using metagenomic recruitment.

RESULTS: Our results showed significant differences in the microbial composition of different layers within the stratified photic water column. The majority of microorganisms were confined to discreet horizontal layers of no more than 30 m (stenobathic). Only a few such as members of the SAR11 clade appeared at all depths (eurybathic). During the winter mixing period, only some groups of bloomers such as Pseudomonas were favored. Although most microbes appeared in both seasons, some groups like the SAR116 clade and some Bacteroidetes and Verrucomicrobia seemed to disappear during the mixing period. Furthermore, we found that some microbes previously considered seasonal (e.g., Archaea or Actinobacteria) were living in deeper layers within the photic zone during the stratification period. A strong depth-related specialization was detected, not only at the taxonomic level but also at the functional level, even within the different clades, for the manipulation and uptake of specific polysaccharides. Rhodopsin sequences (green or blue) also showed narrow depth distributions that correlated with the taxonomy of the microbe in which they were found but not with depth.

CONCLUSIONS: Although limited to a single location in the Mediterranean, this study has profound implications for our understanding of how marine microbial communities vary with depth within the photic zone when stratified. Our results highlight the importance of collecting samples at different depths in the water column when comparing seasonal variations and have important ramifications for global marine studies that most often take samples from only one single depth. Furthermore, our perspective and approaches (metagenomic assembly and recruitment) are broadly applicable to other metagenomic studies.}, } @article {pmid29988145, year = {2018}, author = {Delzenne, NM and Bindels, LB}, title = {Microbiome metabolomics reveals new drivers of human liver steatosis.}, journal = {Nature medicine}, volume = {24}, number = {7}, pages = {906-907}, doi = {10.1038/s41591-018-0126-3}, pmid = {29988145}, issn = {1546-170X}, mesh = {*Fatty Liver ; Female ; Humans ; Metabolomics ; Metagenomics ; *Microbiota ; Obesity ; }, } @article {pmid29988102, year = {2018}, author = {Sfanos, KS and Markowski, MC and Peiffer, LB and Ernst, SE and White, JR and Pienta, KJ and Antonarakis, ES and Ross, AE}, title = {Compositional differences in gastrointestinal microbiota in prostate cancer patients treated with androgen axis-targeted therapies.}, journal = {Prostate cancer and prostatic diseases}, volume = {21}, number = {4}, pages = {539-548}, pmid = {29988102}, issn = {1476-5608}, support = {P30 CA006973/CA/NCI NIH HHS/United States ; T32 OD011089/OD/NIH HHS/United States ; 16CHAL13//Prostate Cancer Foundation (PCF)/International ; W81XWH-13-PCRP-CCA//U.S. Department of Defense (DOD)/International ; }, mesh = {Aged ; Aged, 80 and over ; Androgen Antagonists/*pharmacology/therapeutic use ; Androgens/*metabolism ; Antineoplastic Agents, Hormonal/*pharmacology/therapeutic use ; Biodiversity ; Cross-Sectional Studies ; Gastrointestinal Microbiome/*drug effects ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Molecular Targeted Therapy ; Prostatic Neoplasms/drug therapy/metabolism/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: It is well known that the gastrointestinal (GI) microbiota can influence the metabolism, pharmacokinetics, and toxicity of cancer therapies. Conversely, the effect of cancer treatments on the composition of the GI microbiota is poorly understood. We hypothesized that oral androgen receptor axis-targeted therapies (ATT), including bicalutamide, enzalutamide, and abiraterone acetate, may be associated with compositional differences in the GI microbiota.

METHODS: We profiled the fecal microbiota in a cross-sectional study of 30 patients that included healthy male volunteers and men with different clinical states of prostate cancer (i.e., localized, biochemically recurrent, and metastatic disease) using 16S rDNA amplicon sequencing. Functional inference of identified taxa was performed using PICRUSt.

RESULTS: We report a significant difference in alpha diversity in GI microbiota among men with versus without a prostate cancer diagnosis. Further analysis identified significant compositional differences in the GI microbiota of men taking ATT, including a greater abundance of species previously linked to response to anti-PD-1 immunotherapy such as Akkermansia muciniphila and Ruminococcaceae spp. In functional analyses, we found an enriched representation of bacterial gene pathways involved in steroid biosynthesis and steroid hormone biosynthesis in the fecal microbiota of men taking oral ATT.

CONCLUSIONS: There are measurable differences in the GI microbiota of men receiving oral ATT. We speculate that oral hormonal therapies for prostate cancer may alter the GI microbiota, influence clinical responses to ATT, and/or potentially modulate the antitumor effects of future therapies including immunotherapy. Given our findings, larger, longitudinal studies are warranted.}, } @article {pmid29984842, year = {2018}, author = {Mallott, EK and Amato, KR}, title = {The microbial reproductive ecology of white-faced capuchins (Cebus capucinus).}, journal = {American journal of primatology}, volume = {80}, number = {8}, pages = {e22896}, doi = {10.1002/ajp.22896}, pmid = {29984842}, issn = {1098-2345}, support = {//Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana-Champaign/International ; //Graduate Research Fellowship Program, National Science Foundation/International ; //Department of Anthropology, University of Illinois at Urbana-Champaign/International ; //Northwestern University/International ; //Center for Latin American Studies, University of Illinois at Urbana-Champaign/International ; //Lewis and Clark Fund for Exploration and Research, American Philosophical Society/International ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Cebus/*microbiology/*physiology ; Costa Rica ; Female ; Gastrointestinal Microbiome/*physiology ; Metagenome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Reproduction ; }, abstract = {Changes in reproductive status influence energy and nutrient requirements in female primates. The gut microbiota may buffer changes in energy demands, with shifts in community composition increasing the energy production potential of the gut during pregnancy and lactation. In this study, we examine changes in the gut microbiome of wild, female white-faced capuchins (Cebus capucinus) across different reproductive states. Fecal samples (n = 39) were collected from five adult females over the course of a year. Gut microbial community composition was assessed using 16S rRNA gene sequences, and PICRUSt was used to make metagenomic functional predictions. We found a significant relationship between reproductive state and both the structure and predicted function of the gut microbiome, neither of which were associated with host diet. For example, the relative abundance of Firmicutes was significantly lower in lactating females compared with cycling females; the relative abundance of Actinobacteria was significantly higher in pregnant females compared with lactating females, and there was a trend toward higher relative abundances of Proteobacteria in pregnant females compared with cycling females. The results of this study suggest that, in addition to behavioral and dietary adaptions, the gut microbiota may play a role in allowing female primates to meet their changing energetic needs during reproduction. Further studies of the "microbial reproductive ecology" of primates will help advance our understanding of gut microbial contributions to primate energetics.}, } @article {pmid29984552, year = {2019}, author = {Gulliver, D and Lipus, D and Ross, D and Bibby, K}, title = {Insights into microbial community structure and function from a shallow, simulated CO2 -leakage aquifer demonstrate microbial selection and adaptation.}, journal = {Environmental microbiology reports}, volume = {11}, number = {3}, pages = {338-351}, doi = {10.1111/1758-2229.12675}, pmid = {29984552}, issn = {1758-2229}, mesh = {Archaea/classification/genetics/isolation & purification/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; Biodiversity ; Carbon Cycle/genetics ; Carbon Dioxide/analysis/*metabolism ; Chemoautotrophic Growth/genetics ; Groundwater/chemistry/*microbiology ; Metagenomics ; Microbiota/genetics/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Water Pollutants, Chemical/analysis/*metabolism ; }, abstract = {Geological carbon storage is likely to be a part of a comprehensive strategy to minimize the atmospheric release of carbon dioxide (CO2), raising concerns that injected CO2 will leak into overlying freshwater aquifers. CO2(aq) leakage may impact the dominant microbial community responsible for important ecosystem functions such as nutrient cycling, metal cycling and carbon conversion. Here, we examined the impact of an experimental in situ CO2 -leakage on a freshwater aquifer microbial community. High-throughput 16S rRNA gene sequencing demonstrated lower microbial diversity in freshwater wells with CO2 concentrations above 1.15 g l[-1] . Metagenomic sequencing and population genome binning were used to evaluate the metabolic potential of microbial populations across four CO2 exposed samples and one control sample. Population genome binning resulted in the recovery and annotation of three metagenome assembled genomes (MAGs). Two of the MAGs, most closely related to Curvibacter and Sulfuricurvum, had the functional capacity for CO2 utilization via carbon fixation coupled to sulfur and iron oxidation. The third draft genome was an Archaea, most closely related to Methanoregula, characterized by the metabolic potential for methanogenesis. Together, these findings show that CO2 leakage in a freshwater aquifer poses a strong selection, driving both microbial community structure and metabolic function.}, } @article {pmid29982928, year = {2018}, author = {Zhou, H and Gu, W and Sun, W and Hay, AG}, title = {A microbial community snapshot of windrows from a commercial composting facility.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {18}, pages = {8069-8077}, doi = {10.1007/s00253-018-9201-4}, pmid = {29982928}, issn = {1432-0614}, support = {1011065//National Institute of Food and Agriculture/ ; 31400434//National Natural Science Foundation of China/ ; }, mesh = {Bacteria/classification/genetics/*isolation & purification ; *Biodiversity ; Composting/instrumentation ; DNA, Bacterial/genetics ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {The effect of depth on compost microbial communities is unclear but could be relevant to the management of windrows at commercial facilities. DNA extracted from 64 compost samples from seven windrows at a commercial facility were analyzed via deep 16S rRNA gene sequencing. The relative abundance of eight to nine genera was affected by depth during the transition from cooling to maturation phases between 4 and 6 months, whereas very few genera (0-1) showed a depth dependence in young, actively managed windrows or in mature windrows older than 10 months. Seven novel bacterial operational taxonomic units (OTUs) were detected in compost DNA and also in publicly available compost metagenomes. A compost metagenome was used to construct a metagenome-assembled genome for most of the abundant uncharacterized OTU in our samples and suggests its involvement in carbon cycling.}, } @article {pmid29981578, year = {2018}, author = {Bengtsson-Palme, J}, title = {The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants-but not always.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {125}, pmid = {29981578}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*drug effects/*genetics ; Databases, Genetic ; Drug Resistance, Multiple, Bacterial/*genetics ; Genes, Bacterial/genetics ; Genetic Variation/genetics ; Humans ; Metagenome/*genetics ; Polymerase Chain Reaction ; }, abstract = {BACKGROUND: Antibiotic resistance is considered one of the most urgent threats to modern healthcare, and the role of the environment in resistance development is increasingly recognized. It is often assumed that the abundance and diversity of known resistance genes are representative also for the non-characterized fraction of the resistome in a given environment, but this assumption has not been verified. In this study, this hypothesis is tested, using the resistance gene profiles of 1109 metagenomes from various environments.

RESULTS: This study shows that the diversity and abundance of known antibiotic resistance genes can generally predict the diversity and abundance of undescribed resistance genes. However, the extent of this predictability is dependent on the type of environment investigated. Furthermore, it is shown that carefully selected small sets of resistance genes can describe total resistance gene diversity remarkably well.

CONCLUSIONS: The results of this study suggest that knowledge gained from large-scale quantifications of known resistance genes can be utilized as a proxy for unknown resistance factors. This is important for current and proposed monitoring efforts for environmental antibiotic resistance and has implications for the design of risk ranking strategies and the choices of measures and methods for describing resistance gene abundance and diversity in the environment.}, } @article {pmid29981382, year = {2018}, author = {Imangaliyev, S and Prodan, A and Nieuwdorp, M and Groen, AK and van Riel, NAW and Levin, E}, title = {Domain intelligible models.}, journal = {Methods (San Diego, Calif.)}, volume = {149}, number = {}, pages = {69-73}, doi = {10.1016/j.ymeth.2018.06.011}, pmid = {29981382}, issn = {1095-9130}, mesh = {*Algorithms ; Gastrointestinal Microbiome/*physiology ; Humans ; Metagenome/*physiology ; *Models, Biological ; *Phylogeny ; }, abstract = {Mining biological information from rich "-omics" datasets is facilitated by organizing features into groups that are related to a biological phenomenon or clinical outcome. For example, microorganisms can be grouped based on a phylogenetic tree that depicts their similarities regarding genetic or physical characteristics. Here, we describe algorithms that incorporate auxiliary information in terms of groups of predictors and the relationships between them into the metagenome learning task to build intelligible models. In particular, our cost function guides the feature selection process using auxiliary information by requiring related groups of predictors to provide similar contributions to the final response. We apply the developed algorithms to a recently published dataset analyzing the effects of fecal microbiota transplantation (FMT) in order to identify factors that are associated with improved peripheral insulin sensitivity, leading to accurate predictions of the response to the FMT.}, } @article {pmid29980796, year = {2018}, author = {Wong, HL and White, RA and Visscher, PT and Charlesworth, JC and Vázquez-Campos, X and Burns, BP}, title = {Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes.}, journal = {The ISME journal}, volume = {12}, number = {11}, pages = {2619-2639}, pmid = {29980796}, issn = {1751-7370}, mesh = {Animals ; Archaea/genetics/isolation & purification/metabolism ; Bacteria/genetics/isolation & purification/metabolism ; Bays ; Carbon/metabolism ; Carbon Cycle/genetics ; *Metagenome ; Metagenomics ; Microbial Interactions ; *Microbiota ; Nitrogen/metabolism ; Phosphorus/metabolism ; Sulfur/metabolism ; }, abstract = {The functional metagenomic potential of Shark Bay microbial mats was examined for the first time at a millimeter scale, employing shotgun sequencing of communities via the Illumina NextSeq 500 platform in conjunction with defined chemical analyses. A detailed functional metagenomic profile has elucidated key pathways and facilitated inference of critical microbial interactions. In addition, 87 medium-to-high-quality metagenome-assembled genomes (MAG) were assembled, including potentially novel bins under the deep-branching archaeal Asgard group (Thorarchaetoa and Lokiarchaeota). A range of pathways involved in carbon, nitrogen, sulfur, and phosphorus cycles were identified in mat metagenomes, with the Wood-Ljungdahl pathway over-represented and inferred as a major carbon fixation mode. The top five sets of genes were affiliated to sulfate assimilation (cysNC cysNCD, sat), methanogenesis (hdrABC), Wood-Ljungdahl pathways (cooS, coxSML), phosphate transport (pstB), and copper efflux (copA). Polyhydroxyalkanoate (PHA) synthase genes were over-represented at the surface, with PHA serving as a potential storage of fixed carbon. Sulfur metabolism genes were highly represented, in particular complete sets of genes responsible for both assimilatory and dissimilatory sulfate reduction. Pathways of environmental adaptation (UV, hypersalinity, oxidative stress, and heavy metal resistance) were also delineated, as well as putative viral defensive mechanisms (core genes of the CRISPR, BREX, and DISARM systems). This study provides new metagenome-based models of how biogeochemical cycles and adaptive responses may be partitioned in the microbial mats of Shark Bay.}, } @article {pmid29980437, year = {2018}, author = {Kim, M and Galan, C and Hill, AA and Wu, WJ and Fehlner-Peach, H and Song, HW and Schady, D and Bettini, ML and Simpson, KW and Longman, RS and Littman, DR and Diehl, GE}, title = {Critical Role for the Microbiota in CX3CR1[+] Intestinal Mononuclear Phagocyte Regulation of Intestinal T Cell Responses.}, journal = {Immunity}, volume = {49}, number = {1}, pages = {151-163.e5}, pmid = {29980437}, issn = {1097-4180}, support = {/HHMI/Howard Hughes Medical Institute/United States ; R21 AI123945/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; P30 AI036211/AI/NIAID NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; R01 AI125264/AI/NIAID NIH HHS/United States ; R01 DK114252/DK/NIDDK NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; T32 AI053831/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Antigen Presentation ; Bacterial Adhesion/immunology ; CX3C Chemokine Receptor 1/*metabolism ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/*immunology ; Homeostasis ; Immune Tolerance ; Immunity, Mucosal ; Inflammation/immunology ; Inflammatory Bowel Diseases/immunology ; Interleukin-10/immunology/metabolism ; Intestinal Mucosa/*immunology/microbiology ; Male ; Mice ; Mononuclear Phagocyte System/*immunology ; RAW 264.7 Cells ; T-Lymphocytes, Regulatory/*immunology ; Th1 Cells/*immunology ; }, abstract = {The intestinal barrier is vulnerable to damage by microbiota-induced inflammation that is normally restrained through mechanisms promoting homeostasis. Such disruptions contribute to autoimmune and inflammatory diseases including inflammatory bowel disease. We identified a regulatory loop whereby, in the presence of the normal microbiota, intestinal antigen-presenting cells (APCs) expressing the chemokine receptor CX3CR1 reduced expansion of intestinal microbe-specific T helper 1 (Th1) cells and promoted generation of regulatory T cells responsive to food antigens and the microbiota itself. We identified that disruption of the microbiota resulted in CX3CR1[+] APC-dependent inflammatory Th1 cell responses with increased pathology after pathogen infection. Colonization with microbes that can adhere to the epithelium was able to compensate for intestinal microbiota loss, indicating that although microbial interactions with the epithelium can be pathogenic, they can also activate homeostatic regulatory mechanisms. Our results identify a cellular mechanism by which the microbiota limits intestinal inflammation and promotes tissue homeostasis.}, } @article {pmid29980232, year = {2018}, author = {Hani, J and Abdel Nour, G and Matta, J and Jazzar, B and Pfaffl, MW and Hanna-Wakim, L and Abdel Nour, AM}, title = {Shisha microbiota: the good, the bad and the not so ugly.}, journal = {BMC research notes}, volume = {11}, number = {1}, pages = {446}, pmid = {29980232}, issn = {1756-0500}, mesh = {Adult ; Bacteria/genetics/*isolation & purification ; Equipment Contamination ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S ; Smoking ; Smoking Water Pipes/*microbiology ; Tobacco Products ; }, abstract = {OBJECTIVE: Over the last decade, there has been a rapid expansion of the trendy water pipe smoking around the world especially among younger adults. The initial objective of this study was to identify the microbiota of the shisha, which may either be of no harm for the smoker or enhance the threat on his well-being. The total DNA for the metagenomics study was conducted on three different shishas from three different delivery shops in Jounieh, Lebanon. The microbiota in two solid parts of the shisha, shaft and hose, were analysed including the fresh tobacco and the water in the bowl. All samples were analysed using high-throughput sequencing of 16S rRNA gene amplicons.

RESULTS: Overall, more than 40 bacterial genera were found in the three investigated shishas, some are commensal others are pathogenic. All three shishas showed similar microbial content regarding the bacteria inhabiting in water, shaft, or hose. From the results of this study it appears that a very large quantity of bacteria was found in the water pipes, some are harmful and others beneficial. We assume that the presence of gut dependent microbiota is related to the loose hygienic conditions in which the shisha is prepared.}, } @article {pmid29979780, year = {2018}, author = {Segura-Wang, M and Görzer, I and Jaksch, P and Puchhammer-Stöckl, E}, title = {Temporal dynamics of the lung and plasma viromes in lung transplant recipients.}, journal = {PloS one}, volume = {13}, number = {7}, pages = {e0200428}, pmid = {29979780}, issn = {1932-6203}, mesh = {Adult ; Biodiversity ; Bronchoalveolar Lavage Fluid/virology ; Female ; Follow-Up Studies ; Humans ; Lung/*virology ; *Lung Transplantation ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Phylogeny ; Plasma/*virology ; Retrospective Studies ; Time Factors ; Transplant Recipients ; Young Adult ; }, abstract = {The human virome plays an important role for the clinical outcome of lung transplant recipients (LTRs). While pathogenic viruses may cause severe infections, non-pathogenic viruses may serve as potential markers for the level of immunosuppression. However, neither the complexity of the virome in different compartments nor the dynamics of the virus populations posttransplantation are yet understood. Therefore, in this study the virome was analyzed by metagenomic sequencing in simultaneously withdrawn bronchoalveolar lavage (BAL) and plasma samples of 15 LTRs. In seven patients, also follow-up samples were investigated for abundance and dynamics of virus populations posttransplantation. Five eukaryotic and two prokaryotic virus families were identified in BAL, and nine eukaryotic and two prokaryotic families in plasma. Anelloviruses were the most abundant in both compartments, followed by Herpes- and Coronaviruses. Virus abundance was significantly higher in LTRs than in healthy controls (Kruskal-Wallis test, p<0.001). Up to 48 different anellovirus strains were identified within a single LTR. Analyses in the follow-up patients revealed for the first time a highly complex and unique dynamics of individual anellovirus strains in the posttransplantation period. The abundance of anelloviruses in plasma was inversely correlated with that of other eukaryotic viruses (Pearson correlation coefficient r = -0.605; p<0.05). A broad spectrum of virus strains co-exists in BAL and plasma of LTRs. Especially for the anelloviruses, a high degree of co-infections and a highly individual and complex dynamics after transplantation was observed. The biological impact of these findings and their relation to clinical variables remain to be elucidated by future analyses.}, } @article {pmid29978606, year = {2018}, author = {Xiong, W and Zhan, A}, title = {Testing clustering strategies for metabarcoding-based investigation of community-environment interactions.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1326-1338}, doi = {10.1111/1755-0998.12922}, pmid = {29978606}, issn = {1755-0998}, support = {31572228//National Natural Science Foundation of China/ ; ZDRW-ZS-2016-5-6//The Key Research Program of the Chinese Academy of Sciences/ ; 2015//The Innovation in Cross-functional Team Program of the Chinese Academy of Sciences/ ; 2015ZX07201-008-09//Water Pollution Control and Treatment Special Project/ ; 15K01ESPCR//The State Key Joint Laboratory of Environment Simulation and Pollution Control (RCEES, Chinese Academy of Sciences)/ ; 2017M620927//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; China ; *Cluster Analysis ; Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; *Environmental Exposure ; Environmental Monitoring/*methods ; Metagenomics/*methods ; Rivers ; Water Pollutants/toxicity ; Zooplankton/drug effects ; }, abstract = {The degradation of freshwater ecosystems has become a common ecological and environmental problem globally. Owing to the complexity of biological communities, there remain tremendous technical challenges for investigating influence of environmental stressors (e.g., chemical pollution) on biological communities. High-throughput sequencing-based metabarcoding provides a powerful tool to reveal complex interactions between environments and biological communities. Among many technical issues, the clustering strategies for operational taxonomic units (OTUs) which are crucial for assessing biodiversity of communities, may affect final conclusions. Here, we used zooplankton communities along an environmental pollution gradient in the Chaobai River in Northern China to test different clustering strategies, including nonclustering and clustering with varied thresholds. Our results showed that though the number of OTUs estimated by nonclustering strategies and clustering strategies with divergence thresholds of 99%-97% largely varied, they were able to identify the same set of significant environmental and spatial variables responsible for geographical distributions of zooplankton communities. In addition, the ecological conclusions obtained by clustering thresholds of 99%-97% were consistent with nonclustering strategies, where for all eight clustering scenarios we detected that species sorting predicted by environmental variables overrode dispersal as the dominant factor in structuring zooplankton communities. However, clustering with the divergence thresholds of <95% affected the environmental and spatial variables identified. We conclude that both newly developed nonclustering methods and traditional clustering methods with divergence thresholds ≥97% were reliable to reveal mechanisms of complex community-environment interactions, although different clustering strategies could lead to largely varied biodiversity estimates such as those for α-diversity.}, } @article {pmid29976643, year = {2018}, author = {Chaudhary, A and Kauser, I and Ray, A and Poretsky, R}, title = {Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community.}, journal = {mSphere}, volume = {3}, number = {4}, pages = {}, pmid = {29976643}, issn = {2379-5042}, mesh = {*Biota ; Chicago ; Cluster Analysis ; *Cyclonic Storms ; DNA, Ribosomal/chemistry/genetics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Urban streams are susceptible to stormwater and sewage inputs that can impact their ecological health and water quality. Microbial communities in streams play important functional roles, and their composition and metabolic potential can help assess ecological state and water quality. Although these environments are highly heterogenous, little is known about the influence of isolated perturbations, such as those resulting from rain events on urban stream microbiota. Here, we examined the microbial community composition and diversity in an urban stream during dry and wet weather conditions with both 16S rRNA gene sequencing across multiple years and shotgun metagenomics to more deeply analyze a single storm flow event. Metagenomics was used to assess population-level dynamics as well as shifts in the microbial community taxonomic profile and functional potential before and after a substantial rainfall. The results demonstrated general trends present in the stream under storm flow versus base flow conditions and also highlighted the influence of increased effluent flow following rain in shifting the stream microbial community from abundant freshwater taxa to those more associated with urban/anthropogenic settings. Shifts in the taxonomic composition were also linked to changes in functional gene content, particularly for transmembrane transport and organic substance biosynthesis. We also observed an increase in relative abundance of genes encoding degradation of organic pollutants and antibiotic resistance after rain. Overall, this study highlighted some differences in the microbial community of an urban stream under storm flow conditions and showed the impact of a storm flow event on the microbiome from an environmental and public health perspective.IMPORTANCE Urban streams in various parts of the world are facing increased anthropogenic pressure on their water quality, and storm flow events represent one such source of complex physical, chemical, and biological perturbations. Microorganisms are important components of these streams from both ecological and public health perspectives. Analysis of the effect of perturbations on the stream microbial community can help improve current knowledge on the impact such chronic disturbances can have on these water resources. This study examines microbial community dynamics during rain-induced storm flow conditions in an urban stream of the Chicago Area Waterway System. Additionally, using shotgun metagenomics we identified significant shifts in the microbial community composition and functional gene content following a high-rainfall event, with potential environment and public health implications. Previous work in this area has focused on specific genes/organisms or has not assessed immediate storm flow impact.}, } @article {pmid29976249, year = {2018}, author = {Kayani, MUR and Doyle, SM and Sangwan, N and Wang, G and Gilbert, JA and Christner, BC and Zhu, TF}, title = {Metagenomic analysis of basal ice from an Alaskan glacier.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {123}, pmid = {29976249}, issn = {2049-2618}, mesh = {Alaska ; Bacteria/*classification/genetics/*isolation & purification/metabolism ; Base Sequence ; Biodiversity ; Ecosystem ; Genome, Bacterial/*genetics ; Geologic Sediments/*microbiology ; Ice Cover/*microbiology ; *Metagenomics ; Microbiota/*genetics ; Nitrification/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfur/metabolism ; }, abstract = {BACKGROUND: Glaciers cover ~ 10% of land but are among the least explored environments on Earth. The basal portion of glaciers often harbors unique aquatic microbial ecosystems in the absence of sunlight, and knowledge on the microbial community structures and their metabolic potential is very limited. Here, we provide insights into the microbial lifestyle present at the base of the Matanuska Glacier, Alaska.

RESULTS: DNA and RNA were extracted from samples of the Matanuska Glacier basal ice. Using Illumina MiSeq and HiSeq sequencing, we investigated the microbial diversity with the metagenomic shotgun reads and 16S ribosomal RNA data. We further assembled 9 partial and draft bacterial genomes from the metagenomic assembly, and identified key metabolic pathways such as sulfur oxidation and nitrification. Collectively, our analyses suggest a prevalence of lithotrophic and heterotrophic metabolisms in the subglacial microbiome.

CONCLUSION: Our results present the first metagenomic assembly and bacterial draft genomes for a subglacial environment. These results extend our understanding of the chemical and biological processes in subglacial environments critically influenced by global climate change.}, } @article {pmid29976032, year = {2018}, author = {Vijayakumar, MM and P More, R and Rangasamy, A and R Gandhi, G and Muthugounder, M and Thiruvengadam, V and Samaddar, S and K Jalali, S and Sa, T}, title = {Gut Bacterial Diversity of Insecticide-Susceptible and -Resistant Nymphs of the Brown Planthopper Nilaparvata lugens Stål (Hemiptera: Delphacidae) and Elucidation of Their Putative Functional Roles.}, journal = {Journal of microbiology and biotechnology}, volume = {28}, number = {6}, pages = {976-986}, doi = {10.4014/jmb.1711.11039}, pmid = {29976032}, issn = {1738-8872}, mesh = {Animals ; Bacteria/classification/genetics ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Enzymes/genetics ; Gastrointestinal Tract/microbiology ; Hemiptera/*drug effects/*microbiology ; High-Throughput Nucleotide Sequencing ; *Insecticide Resistance ; Insecticides/*pharmacology ; Metabolic Networks and Pathways/genetics ; Nymph/drug effects/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Knowledge about the gut bacterial communities associated with insects is essential to understand their roles in the physiology of the host. In the present study, the gut bacterial communities of a laboratory-reared insecticide-susceptible (IS), and a field-collected insecticide-resistant (IR) population of a major rice pest, the brown planthopper Nilaparvata lugens, were evaluated. The deep-sequencing analysis of the V3 hypervariable region of the 16S rRNA gene was performed using Illumina and the sequence data were processed using QIIME. The toxicological bioassays showed that compared with the IS population, IR population exhibited 7.9-, 6.7-, 14.8-, and 18.7-fold resistance to acephate, imidacloprid, thiamethoxam, and buprofezin, respectively. The analysis of the alpha diversity indicated a higher bacterial diversity and richness associated with the IR population. The dominant phylum in the IS population was Proteobacteria (99.86%), whereas the IR population consisted of Firmicutes (46.06%), followed by Bacteroidetes (30.8%) and Proteobacteria (15.49%). Morganella, Weissella, and Enterococcus were among the genera shared between the two populations and might form the core bacteria associated with N. lugens. The taxonomic-to-phenotypic mapping revealed the presence of ammonia oxidizers, nitrogen fixers, sulfur oxidizers and reducers, xylan degraders, and aromatic hydrocarbon degraders in the metagenome of N. lugens. Interestingly, the IR population was found to be enriched with bacteria involved in detoxification functions. The results obtained in this study provide a basis for future studies elucidating the roles of the gut bacteria in the insecticide resistance-associated symbiotic relationship and on the design of novel strategies for the management of N. lugens.}, } @article {pmid29975692, year = {2018}, author = {Ge, Y and Guo, G and Ge, B and Yin, H and Yin, H}, title = {The spleen microbiota of small wild mammals reveals distinct patterns with tick-borne bacteria.}, journal = {PLoS neglected tropical diseases}, volume = {12}, number = {7}, pages = {e0006499}, pmid = {29975692}, issn = {1935-2735}, mesh = {Animals ; Animals, Wild/microbiology ; Bacteria/classification/genetics/*isolation & purification ; China ; DNA, Bacterial/genetics ; Disease Reservoirs/microbiology ; Female ; Male ; Mice/*microbiology ; *Microbiota ; Murinae/*microbiology ; Phylogeny ; Rats/*microbiology ; Shrews/*microbiology ; Spleen/*microbiology ; Ticks/microbiology ; }, abstract = {BACKGROUND: Wild mammals serve as reservoirs for a variety of microbes and play an important role in the enzootic cycles of these microbes. Some of them are vector-borne bacteria in the genera Anaplasma, Ehrlichia and Rickettsia of the order Rickettsiales, which can cause febrile illnesses in human beings as well as animals. Anaplasma spp., Ehrlichia spp. and many spotted fever group (SFG) Rickettsia spp. are transmitted to mammalian hosts by tick vectors during blood meals. As a powerful sequencing method, the next generation sequencing can reveal the complexity of bacterial communities in humans and animals. Compared with limited studies on blood microbiota, however, much fewer studies have been carried out on spleen microbiota, which is very scarce in wild mammals. Chongming Island is the third biggest island in China. It was unclear whether there were any vector-borne bacteria in Chongming Island. In the present study, we explored the bacterial microbiota in the spleens of wild mice and shrews from the rural areas of Chongming Island and investigated the prevalence of vector-borne bacteria.

Genomic DNAs were extracted from the spleen samples of 35 mice and shrews. The 16S rDNA V3-V4 regions of the DNA extracts were amplified by PCR and subjected to the 16S rDNA-targeted metagenomic sequencing on an Illumina MiSeq platform. All the 35 spleen samples obtained data with sufficient coverage (99.7-99.9%) for analysis. More than 1,300,000 sequences were obtained after quality control and classified into a total of 1,967 operational taxonomic units (OTUs) clustered at 97% similarity. The two most abundant bacterial phyla were Firmicutes and Proteobacteria according to the analysis of rarefied sequences. Among the bacterial communities detected in this study, Anaplasma, Rickettsia and Coxiella were adjacently clustered by hierarchical analysis. Significant differences in many bacterial features between Anaplasma-positive and Anaplasma-negative samples were identified by LEfSe analysis and Wilcoxon rank-sum test, suggesting that the Anaplasma-infection of small wild mammals was associated with a specific pattern of spleen microbiota.

CONCLUSIONS/SIGNIFICANCE: Our study has comprehensively characterized the complex bacterial profiles in the spleens of wild mice and shrews from Chongming Island, Shanghai city. This work has revealed distinct spleen bacterial communities associated with tick-borne bacteria in wild animals. The detection of tick-borne bacteria highlights the risk of contracting pathogens with public health importance upon tick-exposure in the studied areas.}, } @article {pmid29974156, year = {2018}, author = {Sharma, S and Grewal, S and Vakhlu, J}, title = {Phylogenetic diversity and metabolic potential of microbiome of natural healing clay from Chamliyal (J&K).}, journal = {Archives of microbiology}, volume = {200}, number = {9}, pages = {1333-1343}, doi = {10.1007/s00203-018-1549-4}, pmid = {29974156}, issn = {1432-072X}, support = {38(1269)/10/EMR-II//Council of Scientific and Industrial Research/ ; }, mesh = {Bacteria/classification/genetics/*isolation & purification/*metabolism ; Clay/*analysis/*chemistry ; Fungi/classification/*isolation & purification/*metabolism ; Humans ; India ; Iron/metabolism ; Metagenome ; Microbiota/*physiology ; Molecular Typing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Skin Diseases/therapy ; Sulfur/metabolism ; }, abstract = {Clay therapy for skin disease treatment is an ancient practice popular worldwide as a cheap alternative to pharmaceutical products. Effectiveness of clay against skin problems has been linked to its mineral composition and to microbial activity. The clay-water paste of a holy shrine Chamliyal in the Jammu region of J&K, India is used as an ointment to treat different skin disorders particularly psoriasis. Using the 16 SrDNA amplicon pyrosequencing and whole-metagenome direct shotgun Illumina sequencing, microbial phylogeny and potential metabolic functions were catalogued for Chamliyal's clay. Microbial diversity profile of the Chamliyal's clay is similar to other medicinal clays, particularly Dead Sea; there is some uniqueness as well. Although Proteobacteria, Actinomycetes and Firmicutes are common inhabitants of all the clay types, sulphur- and iron-reducing bacteria like Deferribacterales are particular to clays used for skin healing. In the present study it is proposed that healing properties of clay may be due to the microbes and microbial genes associated with metabolism of minerals like iron and sulphur, that lead to mineral acquisition in the Chamliyal's clay.}, } @article {pmid29973630, year = {2018}, author = {Hart, ML and Ericsson, AC and Lloyd, KCK and Grimsrud, KN and Rogala, AR and Godfrey, VL and Nielsen, JN and Franklin, CL}, title = {Development of outbred CD1 mouse colonies with distinct standardized gut microbiota profiles for use in complex microbiota targeted studies.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10107}, pmid = {29973630}, issn = {2045-2322}, support = {P40 OD010995/OD/NIH HHS/United States ; T32 OD0112639//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/International ; U42 OD010924/OD/NIH HHS/United States ; T32 OD011126/OD/NIH HHS/United States ; K01 OD019924/OD/NIH HHS/United States ; U42 OD012210/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; U2C DK092993/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Breeding/*methods ; Embryo Transfer/methods ; Fecal Microbiota Transplantation/*methods ; Female ; *Gastrointestinal Microbiome ; Housing, Animal ; Male ; Mice ; Mice, Inbred C57BL ; Models, Animal ; }, abstract = {Studies indicate that the gut microbiota (GM) can significantly influence both local and systemic host physiologic processes. With rising concern for optimization of experimental reproducibility and translatability, it is essential to consider the GM in study design. However, GM profiles can vary between rodent producers making consistency between models challenging. To circumvent this, we developed outbred CD1 mouse colonies with stable, complex GM profiles that can be used as donors for a variety of GM transfer techniques including rederivation, co-housing, cross-foster, and fecal microbiota transfer (FMT). CD1 embryos were surgically transferred into CD1 or C57BL/6 surrogate dams that varied by GM composition and complexity to establish four separate mouse colonies harboring GM profiles representative of contemporary mouse producers. Using targeted 16S rRNA amplicon sequencing, subsequent female offspring were found to have similar GM profiles to surrogate dams. Furthermore, breeding colonies of CD1 mice with distinct GM profiles were maintained for nine generations, demonstrating GM stability within these colonies. To confirm GM stability, we shipped cohorts of these four colonies to collaborating institutions and found no significant variation in GM composition. These mice are an invaluable experimental resource that can be used to investigate GM effects on mouse model phenotype.}, } @article {pmid29969843, year = {2019}, author = {Fakhruddin, KS and Ngo, HC and Samaranayake, LP}, title = {Cariogenic microbiome and microbiota of the early primary dentition: A contemporary overview.}, journal = {Oral diseases}, volume = {25}, number = {4}, pages = {982-995}, doi = {10.1111/odi.12932}, pmid = {29969843}, issn = {1601-0825}, mesh = {Bacteria/*isolation & purification ; Child ; Child, Preschool ; Dental Caries/*microbiology/prevention & control ; Dental Plaque/*microbiology ; Humans ; Infant ; *Microbiota ; Saliva/*microbiology ; Sequence Analysis, DNA ; Tooth/*microbiology ; Tooth, Deciduous ; }, abstract = {Recent advances in the field of molecular microbiology provide an unprecedented opportunity to decipher the vast diversity of the oral microbiome in health and disease. Here, we provide a contemporary overview of the oral microbiome and the microbiota of early childhood caries (ECC) with particular reference to newer analytical techniques. A MEDLINE search revealed a total of 20 metagenomic studies describing cariogenic microbiomes of ECC, 10 of which also detailed the healthy microbiomes. In addition, seven studies on site-specific microbiomes, focusing on acidogenic and aciduric microbiota of deep-dentinal lesions, were also reviewed. These studies evaluated plaque and saliva of children aged 1.5-11 years, in cohorts of 12-485 individuals. These studies reveal a very rich and diverse microbial communities, with hundreds of different phylotypes and microbial species, including novel species and phyla such as Scardovia wiggsiae, Slackia exigua, Granulicatella elegans, Firmicutes in the plaque biofilms of children with ECC. On the contrary, bacteria such as Streptococcus cristatus, S. gordonii, S. sanguinis, Corynebacterium matruchotii, and Neisseria flavescens were common in plaque biofilm of noncarious, healthy, tooth surfaces in subjects with caries. The review illustrates the immense complexity and the diversity of the human oral microbiota of the cariogenic plaque microbiome in ECC, and the daunting prospect of its demystification.}, } @article {pmid29968740, year = {2018}, author = {Roldán, C and Murcia-Mascarós, S and López-Montalvo, E and Vilanova, C and Porcar, M}, title = {Proteomic and metagenomic insights into prehistoric Spanish Levantine Rock Art.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10011}, pmid = {29968740}, issn = {2045-2322}, mesh = {Archaeology ; Caves/*microbiology ; *Coloring Agents ; Firmicutes/genetics/*isolation & purification ; Fossils/*microbiology ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics ; *Paintings ; Proteomics/methods ; Spain ; Spectrometry, X-Ray Emission ; Spectrum Analysis, Raman ; }, abstract = {The Iberian Mediterranean Basin is home to one of the largest groups of prehistoric rock art sites in Europe. Despite the cultural relevance of prehistoric Spanish Levantine rock art, pigment composition remains partially unknown, and the nature of the binders used for painting has yet to be disclosed. In this work, we present the first omic analysis applied to one of the flagship Levantine rock art sites: the Valltorta ravine (Castellón, Spain). We used high-throughput sequencing to provide the first description of the bacterial communities colonizing the rock art patina, which proved to be dominated by Firmicutes species and might have a protective effect on the paintings. Proteomic analysis was also performed on rock art microsamples in order to determine the organic binders present in Levantine prehistoric rock art pigments. This information could shed light on the controversial dating of this UNESCO Cultural Heritage, and contribute to defining the chrono-cultural framework of the societies responsible for these paintings.}, } @article {pmid29968731, year = {2018}, author = {Mohammed, WS and Ziganshina, EE and Shagimardanova, EI and Gogoleva, NE and Ziganshin, AM}, title = {Comparison of intestinal bacterial and fungal communities across various xylophagous beetle larvae (Coleoptera: Cerambycidae).}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10073}, pmid = {29968731}, issn = {2045-2322}, mesh = {Animals ; Bacteria/genetics ; Coleoptera/genetics/*microbiology ; Fungi/genetics ; Gastrointestinal Microbiome/*genetics/physiology ; Gastrointestinal Tract/microbiology ; Intestines ; Larva/*microbiology ; Microbiota/genetics ; Mycobiome/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The microbial gut communities associated with various xylophagous beetles offer great potential for different biotechnologies and elaboration of novel pest management strategies. In this research, the intestinal bacterial and fungal communities of various cerambycid larvae, including Acmaeops septentrionis, Acanthocinus aedilis, Callidium coriaceum, Trichoferus campestris and Chlorophorus herbstii, were investigated. The intestinal microbial communities of these Cerambycidae species were mostly represented by members of the bacterial phyla Proteobacteria and Actinobacteria and the fungal phylum Ascomycota. However, the bacterial and fungal communities varied by beetle species and between individual organisms. Furthermore, bacterial communities' metagenomes reconstruction indicated the genes that encode enzymes involved in the lignocellulose degradation (such as peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannosidases, endoglucanases, beta-glucosidases and others) and nitrogen fixation (nitrogenases). Most of the predicted genes potentially related to lignocellulose degradation were enriched in the T. campestris, A. aedilis and A. septentrionis larval gut consortia, whereas predicted genes affiliated with the nitrogenase component proteins were enriched in the T. campestris, A. septentrionis and C. herbstii larval gut consortia. Several bacteria and fungi detected in the current work could be involved in the nutrition of beetle larvae.}, } @article {pmid29968357, year = {2018}, author = {Vuillemin, A and Horn, F and Friese, A and Winkel, M and Alawi, M and Wagner, D and Henny, C and Orsi, WD and Crowe, SA and Kallmeyer, J}, title = {Metabolic potential of microbial communities from ferruginous sediments.}, journal = {Environmental microbiology}, volume = {20}, number = {12}, pages = {4297-4313}, doi = {10.1111/1462-2920.14343}, pmid = {29968357}, issn = {1462-2920}, support = {0487//NSERC/International ; P2GEP2_148621//Swiss National Science Foundation/Switzerland ; //University of Geneva/International ; KA 2293/8-1//Deutsche Forschungsgemeinschaft/International ; VU 94/1-1//Deutsche Forschungsgemeinschaft/International ; OR 417/1-1//Deutsche Forschungsgemeinschaft/International ; }, mesh = {Gene Expression Regulation, Bacterial ; Geologic Sediments/*chemistry/microbiology ; Iron/*chemistry/metabolism ; *Lakes ; Metagenomics ; Methane/metabolism ; *Microbiota ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Sulfates/metabolism ; }, abstract = {Ferruginous (Fe-rich, SO4 -poor) conditions are generally restricted to freshwater sediments on Earth today, but were likely widespread during the Archean and Proterozoic Eons. Lake Towuti, Indonesia, is a large ferruginous lake that likely hosts geochemical processes analogous to those that operated in the ferruginous Archean ocean. The metabolic potential of microbial communities and related biogeochemical cycling under such conditions remain largely unknown. We combined geochemical measurements (pore water chemistry, sulfate reduction rates) with metagenomics to link metabolic potential with geochemical processes in the upper 50 cm of sediment. Microbial diversity and quantities of genes for dissimilatory sulfate reduction (dsrAB) and methanogenesis (mcrA) decrease with increasing depth, as do rates of potential sulfate reduction. The presence of taxa affiliated with known iron- and sulfate-reducers implies potential use of ferric iron and sulfate as electron acceptors. Pore-water concentrations of acetate imply active production through fermentation. Fermentation likely provides substrates for respiration with iron and sulfate as electron donors and for methanogens that were detected throughout the core. The presence of ANME-1 16S and mcrA genes suggests potential for anaerobic methane oxidation. Overall our data suggest that microbial community metabolism in anoxic ferruginous sediments support coupled Fe, S and C biogeochemical cycling.}, } @article {pmid29964641, year = {2017}, author = {Wang, BQ and Li, CY and Lu, W and Fan, H and Zhang, DZ and Wang, Z and Lü, C and Shen, FD}, title = {[Shift of Microbial Communities During the CO2-Brine-Sandstone Interaction Process].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {38}, number = {7}, pages = {2978-2987}, doi = {10.13227/j.hjkx.201612067}, pmid = {29964641}, issn = {0250-3301}, mesh = {Bacteria/*classification ; *Carbon Dioxide ; *Salts ; Solubility ; }, abstract = {In this study, the dynamic variation of the structure, functionality and biodiversity of indigenous microorganism during the CO2-brine-sandstone interaction process was investigated using MiSeq sequencing techniques. The results indicated that some kinds of indigenous microorganisms could grow well under the extreme condition induced by CO2-injection. After injection of CO2, the species of indigenous microorganisms tended to be single and the relative abundance of Proteobacteria reached up to 99.77% after 6 months. The dominant species varied as follows:Pseudomonas sp., Citrobacter sp. and Brevundimonas sp.. Meanwhile, some special genera such as Bacillus sp., Hydrogenophaga sp. and Rhizobium sp. with functionality of iron-reducing and denitrification were found in this study, which may have a potential effect on the capture and storage of CO2. In addition, the Shannon index decreased from 5.3302 to 1.9465 after injection of CO2, suggesting that the biodiversity reduced significantly. Function and main metabolites analysis of bacteria in the CO2-brine-sandstone interaction process showed that bacteria like Bacillus sp., Citrobacter sp. and Pseudomonas sp. could enhance CO2 solubility-trapping process. Bacteria metabolisms could accelerate the dissolution of feldspar and chlorites, and facilitate the formation of transition-state calcite and siderite. Otherwise, the great variation was mainly attributed to the change of condition driven by CO2-brine-sandstone interactions, such as pH and the chemical composition of brine water(anion and cation), etc.}, } @article {pmid29961874, year = {2018}, author = {Behzad, H and Mineta, K and Gojobori, T}, title = {Global Ramifications of Dust and Sandstorm Microbiota.}, journal = {Genome biology and evolution}, volume = {10}, number = {8}, pages = {1970-1987}, pmid = {29961874}, issn = {1759-6653}, mesh = {Agriculture ; *Dust ; Ecosystem ; Geography ; Humans ; *Internationality ; Metagenomics ; *Microbiota ; }, abstract = {Dust and sandstorm events inject substantial quantities of foreign microorganisms into global ecosystems, with the ability to impact distant environments. The majority of these microorganisms originate from deserts and drylands where the soil is laden with highly stress-resistant microbes capable of thriving under extreme environmental conditions, and a substantial portion of them survive long journeys through the atmosphere. This large-scale transmission of highly resilient alien microbial contaminants raises concerns with regards to the invasion of sensitive and/or pristine sink environments, and to human health-concerns exacerbated by increases in the rate of desertification. Further increases in the transport of dust-associated microbiota could extend the spread of foreign microbes to new ecosystems, increase their load in present sink environments, disrupt ecosystem balance, and potentially introduce new pathogens. Our present understanding of these microorganisms, their phylogenic affiliations and functional significance, is insufficient to determine their impact. The purpose of this review is to provide an overview of available data regarding dust and sandstorm microbiota and their potential ramifications on human and ecosystem health. We conclude by discussing current gaps in dust and sandstorm microbiota research, and the need for collaborative studies involving high-resolution meta-omic approaches in conjunction with extensive ecological time-series studies to advance the field towards an improved and sufficient understanding of these invisible atmospheric travelers and their global ramifications.}, } @article {pmid29961061, year = {2018}, author = {Lee, J and Lim, JH and Park, J and Kim, IN}, title = {Temporal and Vertical Variation in Microbial Community Composition in Response to Physicochemical Characteristics in a Water Column of Highly Eutrophied Jinhae Bay, South Korea.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {28}, number = {2}, pages = {65-77}, doi = {10.1159/000489633}, pmid = {29961061}, issn = {1660-2412}, mesh = {Bacteroidetes/genetics/isolation & purification ; Bays/*microbiology ; Cyanobacteria/genetics/isolation & purification ; DNA, Bacterial/genetics/isolation & purification ; *Eutrophication ; *Microbiota ; Proteobacteria/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics/isolation & purification ; Republic of Korea ; Seasons ; Sequence Analysis, DNA ; Water Microbiology ; }, abstract = {Microbial communities play an essential role in marine biogeochemical cycles. Physical and biogeochemical changes in Jinhae Bay, the most anthropogenically eutrophied bay on the coasts of South Korea, are well described, but less is known about the associated changes in microbial communities. Temporal and vertical variation in microbial communities at three depths (surface, middle, and bottom) at seven time points (June to December) at the J1 sampling site were investigated on the MiSeq platform based on the 16S rRNA gene. Overall, the microbial community was dominated by Proteobacteria, Cyanobacteria, and Bacteroidetes from June to November, whereas Firmicutes were dominant in December, especially in the middle and bottom layers. The results indicate that the microbial community composition strongly varied with temporal changes in the physicochemical water properties. Moreover, the community composition differed markedly between the surface and middle layers and the bottom layer in the summer, when the water column was strongly stratified and bottom water hypoxia developed. A redundancy analysis suggested a significant correlation between physicochemical variables (i.e., temperature, salinity, and oxygen concentration) and microbial community composition. This study indicates that temporal changes in water conditions and eutrophication-induced hypoxia effectively shape the structure of the microbial community.}, } @article {pmid29959351, year = {2018}, author = {Mann, AE and Sabin, S and Ziesemer, K and Vågene, ÅJ and Schroeder, H and Ozga, AT and Sankaranarayanan, K and Hofman, CA and Fellows Yates, JA and Salazar-García, DC and Frohlich, B and Aldenderfer, M and Hoogland, M and Read, C and Milner, GR and Stone, AC and Lewis, CM and Krause, J and Hofman, C and Bos, KI and Warinner, C}, title = {Differential preservation of endogenous human and microbial DNA in dental calculus and dentin.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {9822}, pmid = {29959351}, issn = {2045-2322}, mesh = {Bacteria/*genetics ; DNA, Bacterial/*analysis/genetics ; Dental Calculus/*genetics/microbiology ; Dentin/*metabolism/microbiology ; Humans ; *Metagenomics ; Microbiota ; Preservation, Biological/*methods ; }, abstract = {Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is microbial and originates from the oral microbiome; however, a small but consistent proportion of DNA (mean 0.08 ± 0.08%, range 0.007-0.47%) derives from the host genome. Host DNA content within dentin is variable (mean 13.70 ± 18.62%, range 0.003-70.14%), and for a subset of dentin samples (15.21%), oral bacteria contribute > 20% of total DNA. Human DNA in dental calculus is highly fragmented, and is consistently shorter than both microbial DNA in dental calculus and human DNA in paired dentin samples. Finally, we find that microbial DNA fragmentation patterns are associated with guanine-cytosine (GC) content, but not aspects of cellular structure.}, } @article {pmid29956164, year = {2018}, author = {Tang, MS and Bowcutt, R and Loke, P}, title = {Assessing the Mouse Intestinal Microbiota in Settings of Type-2 Immune Responses.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1799}, number = {}, pages = {359-370}, doi = {10.1007/978-1-4939-7896-0_26}, pmid = {29956164}, issn = {1940-6029}, mesh = {Animals ; Gastrointestinal Microbiome/*immunology ; Helminthiasis/diagnosis/immunology/parasitology ; Helminths/immunology ; Host-Pathogen Interactions ; *Immunity ; Metagenome ; Metagenomics/methods ; Mice ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The microbial communities that reside within the mammalian host play important roles in the development of a robust host immune system. With the advent of sequencing technology and barcoding strategy of the bacterial 16S ribosomal RNA (rRNA) gene, microbiota studies are becoming more economical but also more important in many immunology studies. Here, we described a representative study protocol to characterize how the microbiota changes during an intestinal helminth infection, with emphasis on subtle aspects of the experimental design that are critical for data interpretation.}, } @article {pmid29954453, year = {2018}, author = {Parras-Moltó, M and Rodríguez-Galet, A and Suárez-Rodríguez, P and López-Bueno, A}, title = {Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {119}, pmid = {29954453}, issn = {2049-2618}, mesh = {Base Composition/genetics ; DNA Viruses/*genetics ; Genetic Markers/genetics ; Genome, Viral/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/genetics ; Nucleic Acid Amplification Techniques/*methods ; Polymerase Chain Reaction ; Saliva/*virology ; }, abstract = {BACKGROUND: Viruses are key players regulating microbial ecosystems. Exploration of viral assemblages is now possible thanks to the development of metagenomics, the most powerful tool available for studying viral ecology and discovering new viruses. Unfortunately, several sources of bias lead to the misrepresentation of certain viruses within metagenomics workflows, hindering the shift from merely descriptive studies towards quantitative comparisons of communities. Therefore, benchmark studies on virus enrichment and random amplification protocols are required to better understand the sources of bias.

RESULTS: We assessed the bias introduced by viral enrichment on mock assemblages composed of seven DNA viruses, and the bias from random amplification methods on human saliva DNA viromes, using qPCR and deep sequencing, respectively. While iodixanol cushions and 0.45 μm filtration preserved the original composition of nuclease-protected viral genomes, low-force centrifugation and 0.22 μm filtration removed large viruses. Comparison of unamplified and randomly amplified saliva viromes revealed that multiple displacement amplification (MDA) induced stochastic bias from picograms of DNA template. However, the type of bias shifted to systematic using 1 ng, with only a marginal influence by amplification time. Systematic bias consisted of over-amplification of small circular genomes, and under-amplification of those with extreme GC content, a negative bias that was shared with the PCR-based sequence-independent, single-primer amplification (SISPA) method. MDA based on random priming provided by a DNA primase activity slightly outperformed those based on random hexamers and SISPA, which may reflect differences in ability to handle sequences with extreme GC content. SISPA viromes showed uneven coverage profiles, with high coverage peaks in regions with low linguistic sequence complexity. Despite misrepresentation of certain viruses after random amplification, ordination plots based on dissimilarities among contig profiles showed perfect overlapping of related amplified and unamplified saliva viromes and strong separation from unrelated saliva viromes. This result suggests that random amplification bias has a minor impact on beta diversity studies.

CONCLUSIONS: Benchmark analyses of mock and natural communities of viruses improve understanding and mitigate bias in metagenomics surveys. Bias induced by random amplification methods has only a minor impact on beta diversity studies of human saliva viromes.}, } @article {pmid29950381, year = {2018}, author = {Jenior, ML and Leslie, JL and Young, VB and Schloss, PD}, title = {Clostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization.}, journal = {mSphere}, volume = {3}, number = {3}, pages = {}, pmid = {29950381}, issn = {2379-5042}, support = {UL1 TR000433/TR/NCATS NIH HHS/United States ; T32 GM008353/GM/NIGMS NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; T32 GM145304/GM/NIGMS NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*administration & dosage/adverse effects ; Cecum/*chemistry/*microbiology ; Clostridioides difficile/*growth & development ; Clostridium Infections/*microbiology ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Metabolomics ; Metagenomics ; Mice ; }, abstract = {Susceptibility to Clostridium difficile infection (CDI) is primarily associated with previous exposure to antibiotics, which compromise the structure and function of the gut bacterial community. Specific antibiotic classes correlate more strongly with recurrent or persistent C. difficile infection. As such, we utilized a mouse model of infection to explore the effect of distinct antibiotic classes on the impact that infection has on community-level transcription and metabolic signatures shortly following pathogen colonization and how those changes may associate with persistence of C. difficile Untargeted metabolomic analysis revealed that C. difficile infection had significantly larger impacts on the metabolic environment across cefoperazone- and streptomycin-pretreated mice, which became persistently colonized compared to clindamycin-pretreated mice, where infection quickly became undetectable. Through metagenome-enabled metatranscriptomics, we observed that transcripts for genes associated with carbon and energy acquisition were greatly reduced in infected animals, suggesting that those niches were instead occupied by C. difficile Furthermore, the largest changes in transcription were seen in the least abundant species, indicating that C. difficile may "attack the loser" in gut environments where sustained infection occurs more readily. Overall, our results suggest that C. difficile is able to restructure the nutrient-niche landscape in the gut to promote persistent infection.IMPORTANCEClostridium difficile has become the most common single cause of hospital-acquired infection over the last decade in the United States. Colonization resistance to the nosocomial pathogen is primarily provided by the gut microbiota, which is also involved in clearing the infection as the community recovers from perturbation. As distinct antibiotics are associated with different risk levels for CDI, we utilized a mouse model of infection with 3 separate antibiotic pretreatment regimens to generate alternative gut microbiomes that each allowed for C. difficile colonization but varied in clearance rate. To assess community-level dynamics, we implemented an integrative multi-omics approach that revealed that infection significantly changed many aspects of the gut community. The degree to which the community changed was inversely correlated with clearance during the first 6 days of infection, suggesting that C. difficile differentially modifies the gut environment to promote persistence. This is the first time that metagenome-enabled metatranscriptomics have been employed to study the behavior of a host-associated microbiota in response to an infection. Our results allow for a previously unseen understanding of the ecology associated with C. difficile infection and provide the groundwork for identification of context-specific probiotic therapies.}, } @article {pmid29948018, year = {2019}, author = {Kamutando, CN and Vikram, S and Kamgan-Nkuekam, G and Makhalanyane, TP and Greve, M and Le Roux, JJ and Richardson, DM and Cowan, DA and Valverde, A}, title = {The Functional Potential of the Rhizospheric Microbiome of an Invasive Tree Species, Acacia dealbata.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {191-200}, pmid = {29948018}, issn = {1432-184X}, support = {CPRR14071676470//National Research Foundation of South Africa (NRF)/ ; }, mesh = {Acacia/growth & development/*microbiology ; Bacteria/classification/genetics ; Bacterial Proteins/genetics ; Bradyrhizobium/genetics/metabolism ; Carbohydrate Metabolism ; DNA, Bacterial/genetics ; Genes, Bacterial/genetics ; *Introduced Species ; Metagenome ; Microbial Interactions/physiology ; Microbiota/genetics/*physiology ; Nitrogen/metabolism ; Nitrogen Fixation/genetics ; Phylogeny ; Plant Development ; Rhizobium/genetics/physiology ; *Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; South Africa ; Vitamins/metabolism ; }, abstract = {Plant-microbe interactions mediate both the invasiveness of introduced plant species and the impacts that they have in invaded ecosystems. Although the phylogenetic composition of the rhizospheric microbiome of Acacia dealbata (an invasive Australian tree species) has been investigated, little is known about the functional potential of the constituents of these altered microbial communities. We used shotgun DNA sequencing to better understand the link between bacterial community composition and functional capacity in the rhizospheric microbiomes associated with invasive A. dealbata populations in South Africa. Our analysis showed that several genes associated with plant growth-promoting (PGP) traits were significantly overrepresented in the rhizospheric metagenomes compared to neighbouring bulk soils collected away from A. dealbata stands. The majority of these genes are involved in the metabolism of nitrogen, carbohydrates and vitamins, and in various membrane transport systems. Overrepresented genes were linked to a limited number of bacterial taxa, mostly Bradyrhizobium species, the preferred N-fixing rhizobial symbiont of Australian acacias. Overall, these findings suggest that A. dealbata enriches rhizosphere soils with potentially beneficial microbial taxa, and that members of the genus Bradyrhizobium may play an integral role in mediating PGP processes that may influence the success of this invader when colonizing novel environments.}, } @article {pmid29942096, year = {2018}, author = {Hoyles, L and Fernández-Real, JM and Federici, M and Serino, M and Abbott, J and Charpentier, J and Heymes, C and Luque, JL and Anthony, E and Barton, RH and Chilloux, J and Myridakis, A and Martinez-Gili, L and Moreno-Navarrete, JM and Benhamed, F and Azalbert, V and Blasco-Baque, V and Puig, J and Xifra, G and Ricart, W and Tomlinson, C and Woodbridge, M and Cardellini, M and Davato, F and Cardolini, I and Porzio, O and Gentileschi, P and Lopez, F and Foufelle, F and Butcher, SA and Holmes, E and Nicholson, JK and Postic, C and Burcelin, R and Dumas, ME}, title = {Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women.}, journal = {Nature medicine}, volume = {24}, number = {7}, pages = {1070-1080}, pmid = {29942096}, issn = {1546-170X}, support = {MR/L01632X/1/MRC_/Medical Research Council/United Kingdom ; MR/M501797/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Cells, Cultured ; Cohort Studies ; Confounding Factors, Epidemiologic ; Diabetes Mellitus/*genetics ; Fecal Microbiota Transplantation ; Female ; Hepatocytes/metabolism ; Humans ; Metabolome ; Metabolomics ; *Metagenomics ; Mice ; Microbiota ; Non-alcoholic Fatty Liver Disease/*genetics ; Obesity/*genetics ; Phenotype ; Transcriptome/genetics ; }, abstract = {Hepatic steatosis is a multifactorial condition that is often observed in obese patients and is a prelude to non-alcoholic fatty liver disease. Here, we combine shotgun sequencing of fecal metagenomes with molecular phenomics (hepatic transcriptome and plasma and urine metabolomes) in two well-characterized cohorts of morbidly obese women recruited to the FLORINASH study. We reveal molecular networks linking the gut microbiome and the host phenome to hepatic steatosis. Patients with steatosis have low microbial gene richness and increased genetic potential for the processing of dietary lipids and endotoxin biosynthesis (notably from Proteobacteria), hepatic inflammation and dysregulation of aromatic and branched-chain amino acid metabolism. We demonstrated that fecal microbiota transplants and chronic treatment with phenylacetic acid, a microbial product of aromatic amino acid metabolism, successfully trigger steatosis and branched-chain amino acid metabolism. Molecular phenomic signatures were predictive (area under the curve = 87%) and consistent with the gut microbiome having an effect on the steatosis phenome (>75% shared variation) and, therefore, actionable via microbiome-based therapies.}, } @article {pmid29941875, year = {2018}, author = {Buendía, E and Zakzuk, J and San-Juan-Vergara, H and Zurek, E and Ajami, NJ and Caraballo, L}, title = {Gut microbiota components are associated with fixed airway obstruction in asthmatic patients living in the tropics.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {9582}, pmid = {29941875}, issn = {2045-2322}, mesh = {Adult ; Asthma/*microbiology/*physiopathology ; Biodiversity ; Female ; *Gastrointestinal Microbiome ; Humans ; Lung/*physiopathology ; Male ; Phenotype ; *Tropical Climate ; }, abstract = {Microbiome composition has been associated to several inflammatory diseases, including asthma. There are few studies exploring the relationships of gut microbiota with airway obstruction pheonotypes in adult asthma, especially those living in the tropics. We sought to evaluate the relationships of gut microbiota with the airway obstruction and other variables of interest in asthmatic patients living in the tropics according to three phenotypes: No Airway Obstruction (NAO), Reversible Airway Obstruction (RAO) or Fixed Airway Obstruction (FAO). We found that Streptococcaceae:Streptococcus and Enterobacteriaceae:Escherichia-Shigella consistently discriminated asthmatic individuals suffering FAO from NAO or RAO, plus Veillonellaceae:Megasphaera when comparing FAO and RAO (p < 0.05; FDR < 0.05). In the FAO, the network showing the genus relations was less complex and interconnected. Several Rumminococcaceae, Lachnospiraceae and Clostridiales were enriched in patients with low specific IgE levels to mites and Ascaris. All patients shared a common exposure framework; control medication usage and smoking habit were uncommon and equally distributed between them. In conclusion, in this tropical asthmatic population, components of human gut microbiota are associated with the presence of a FAO phenotype and lower specific IgE response to mites and Ascaris.}, } @article {pmid29941576, year = {2018}, author = {Borton, MA and Hoyt, DW and Roux, S and Daly, RA and Welch, SA and Nicora, CD and Purvine, S and Eder, EK and Hanson, AJ and Sheets, JM and Morgan, DM and Wolfe, RA and Sharma, S and Carr, TR and Cole, DR and Mouser, PJ and Lipton, MS and Wilkins, MJ and Wrighton, KC}, title = {Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {28}, pages = {E6585-E6594}, pmid = {29941576}, issn = {1091-6490}, mesh = {Bacteria/classification/*metabolism ; *Hydraulic Fracking ; Microbial Consortia/*physiology ; Natural Gas/*microbiology ; United States ; }, abstract = {Hydraulic fracturing is one of the industrial processes behind the surging natural gas output in the United States. This technology inadvertently creates an engineered microbial ecosystem thousands of meters below Earth's surface. Here, we used laboratory reactors to perform manipulations of persisting shale microbial communities that are currently not feasible in field scenarios. Metaproteomic and metabolite findings from the laboratory were then corroborated using regression-based modeling performed on metagenomic and metabolite data from more than 40 produced fluids from five hydraulically fractured shale wells. Collectively, our findings show that Halanaerobium, Geotoga, and Methanohalophilus strain abundances predict a significant fraction of nitrogen and carbon metabolites in the field. Our laboratory findings also exposed cryptic predatory, cooperative, and competitive interactions that impact microorganisms across fractured shales. Scaling these results from the laboratory to the field identified mechanisms underpinning biogeochemical reactions, yielding knowledge that can be harnessed to potentially increase energy yields and inform management practices in hydraulically fractured shales.}, } @article {pmid29940835, year = {2018}, author = {Devlin, JC and Battaglia, T and Blaser, MJ and Ruggles, KV}, title = {WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {493}, pmid = {29940835}, issn = {1471-2164}, support = {U01 AI22285//Foundation for the National Institutes of Health/ ; }, mesh = {Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {BACKGROUND: Exploration of large data sets, such as shotgun metagenomic sequence or expression data, by biomedical experts and medical professionals remains as a major bottleneck in the scientific discovery process. Although tools for this purpose exist for 16S ribosomal RNA sequencing analysis, there is a growing but still insufficient number of user-friendly interactive visualization workflows for easy data exploration and figure generation. The development of such platforms for this purpose is necessary to accelerate and streamline microbiome laboratory research.

RESULTS: We developed the Workflow Hub for Automated Metagenomic Exploration (WHAM!) as a web-based interactive tool capable of user-directed data visualization and statistical analysis of annotated shotgun metagenomic and metatranscriptomic data sets. WHAM! includes exploratory and hypothesis-based gene and taxa search modules for visualizing differences in microbial taxa and gene family expression across experimental groups, and for creating publication quality figures without the need for command line interface or in-house bioinformatics.

CONCLUSIONS: WHAM! is an interactive and customizable tool for downstream metagenomic and metatranscriptomic analysis providing a user-friendly interface allowing for easy data exploration by microbiome and ecological experts to facilitate discovery in multi-dimensional and large-scale data sets.}, } @article {pmid29937540, year = {2018}, author = {Lagier, JC and Dubourg, G and Million, M and Cadoret, F and Bilen, M and Fenollar, F and Levasseur, A and Rolain, JM and Fournier, PE and Raoult, D}, title = {Culturing the human microbiota and culturomics.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {}, pages = {540-550}, doi = {10.1038/s41579-018-0041-0}, pmid = {29937540}, issn = {1740-1534}, mesh = {Bacteria/*classification/genetics/growth & development/*isolation & purification ; Bacteriological Techniques/*methods/trends ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/methods ; *Microbiota ; }, abstract = {The gut microbiota has an important role in the maintenance of human health and in disease pathogenesis. This importance was realized through the advent of omics technologies and their application to improve our knowledge of the gut microbial ecosystem. In particular, the use of metagenomics has revealed the diversity of the gut microbiota, but it has also highlighted that the majority of bacteria in the gut remain uncultured. Culturomics was developed to culture and identify unknown bacteria that inhabit the human gut as a part of the rebirth of culture techniques in microbiology. Consisting of multiple culture conditions combined with the rapid identification of bacteria, the culturomic approach has enabled the culture of hundreds of new microorganisms that are associated with humans, providing exciting new perspectives on host-bacteria relationships. In this Review, we discuss why and how culturomics was developed. We describe how culturomics has extended our understanding of bacterial diversity and then explore how culturomics can be applied to the study of the human microbiota and the potential implications for human health.}, } @article {pmid29937307, year = {2018}, author = {Coutinho, FH and Gregoracci, GB and Walter, JM and Thompson, CC and Thompson, FL}, title = {Metagenomics Sheds Light on the Ecology of Marine Microbes and Their Viruses.}, journal = {Trends in microbiology}, volume = {26}, number = {11}, pages = {955-965}, doi = {10.1016/j.tim.2018.05.015}, pmid = {29937307}, issn = {1878-4380}, mesh = {Archaea/genetics/physiology ; Bacteria/genetics ; Bacterial Physiological Phenomena/genetics ; Biodiversity ; Biological Evolution ; Classification ; Cyanobacteria/physiology ; *Ecology ; Ecosystem ; Genomics ; Host Microbial Interactions/physiology ; Marine Biology ; *Metagenomics ; Seawater/*microbiology/*virology ; Virus Physiological Phenomena/genetics ; Viruses/genetics ; }, abstract = {Advances brought about by omics-based approaches have revolutionized our understanding of the diversity and ecological processes involving marine archaea, bacteria, and their viruses. This broad review discusses recent examples of how genomics, metagenomics, and ecogenomics have been applied to reveal the ecology of these biological entities. Three major topics are covered in this revision: (i) the novel roles of microorganisms in ecosystem processes; (ii) virus-host associations; and (iii) ecological associations of microeukaryotes and other microbes. We also briefly comment on the discovery of novel taxa from marine ecosystems; development of a robust taxonomic framework for prokaryotes; breakthroughs on the diversity and ecology of cyanobacteria; and advances on ecological modelling. We conclude by discussing limitations of the field and suggesting directions for future research.}, } @article {pmid29934497, year = {2018}, author = {Ji, Y and Zhang, F and Zhang, R and Shen, Y and Liu, L and Wang, J and Yang, J and Tang, Q and Xun, J and Qi, T and Wang, Z and Song, W and Tang, Y and Chen, J and Lu, H}, title = {Changes in intestinal microbiota in HIV-1-infected subjects following cART initiation: influence of CD4+ T cell count.}, journal = {Emerging microbes & infections}, volume = {7}, number = {1}, pages = {113}, pmid = {29934497}, issn = {2222-1751}, support = {81571977//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Adult ; Antiretroviral Therapy, Highly Active ; Biodiversity ; Biomarkers ; *CD4 Lymphocyte Count ; CD4-CD8 Ratio ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome/drug effects ; HIV Infections/drug therapy/*immunology/virology ; HIV-1/*immunology ; Humans ; Male ; Metagenome ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Viral Load ; }, abstract = {The roles of immunodeficiency and combined antiretroviral therapy (cART) in shaping the gut microbiota in HIV-1-infected subjects (HISs) have not been described thoroughly by time-series investigations. In this study, 36 antiretroviral-naïve HISs were enrolled to prospectively assess alterations in the fecal microbiota and plasma markers of microbial translocation and inflammation with cART. At baseline, the species α-diversity of the fecal microbiota was significantly lower in HISs with a CD4[+] T cell count <300/mm[3] than in HISs with a CD4[+] T cell count >300/mm[3] (Shannon index: Median 2.557 vs. 2.981, P = 0.006; Simpson index: Median 0.168 vs. 0.096, P = 0.004). Additionally, the baseline α-diversity indices correlated with CD4[+] T cell counts (Shannon index: r = 0.474, P = 0.004; Simpson index: r = -0.467, P = 0.004) and the specific plasma biomarkers for microbial translocation and inflammation. After cART introduction, the species α-diversity of fecal microbiota in HISs with CD4[+] T cell counts <300/mm[3] was significantly restored (Shannon index: Median 2.557 vs. 2.791, P = 0.007; Simpson index: Median 0.168 vs. 0.112, P = 0.004), while the variances were insignificant among HISs with CD4+ T cell counts >300/mm[3] (Shannon index: Median 2.981 vs. 2.934, P = 0.179; Simpson index: Median 0.096 vs. 0.119, P = 0.082). Meanwhile, with cART introduction, alterations in the gut microbial composition were more significant in the subgroup with CD4[+] T cell counts >300/mm[3], corresponding to increases in the specific plasma inflammatory markers. These findings implicated the interactive roles of immunodeficiency and cART for affecting gut microbiota in HIV-1-infected individuals, providing new insights into intestinal microbiome dysbiosis related to HIV-1 infection.}, } @article {pmid29934437, year = {2018}, author = {Cani, PD}, title = {Human gut microbiome: hopes, threats and promises.}, journal = {Gut}, volume = {67}, number = {9}, pages = {1716-1725}, pmid = {29934437}, issn = {1468-3288}, support = {336452/ERC_/European Research Council/International ; }, mesh = {Diabetes Mellitus/immunology/microbiology ; Dysbiosis/prevention & control ; Evidence-Based Medicine ; Gastrointestinal Microbiome/*immunology ; Humans ; Liver Diseases/immunology/microbiology ; Metabolic Diseases/*immunology/metabolism/*microbiology/prevention & control ; Neoplasms/immunology/microbiology ; Neurodegenerative Diseases/immunology/microbiology ; Obesity/immunology/microbiology ; Prevotella/immunology ; Verrucomicrobia/immunology ; }, abstract = {The microbiome has received increasing attention over the last 15 years. Although gut microbes have been explored for several decades, investigations of the role of microorganisms that reside in the human gut has attracted much attention beyond classical infectious diseases. For example, numerous studies have reported changes in the gut microbiota during not only obesity, diabetes, and liver diseases but also cancer and even neurodegenerative diseases. The human gut microbiota is viewed as a potential source of novel therapeutics. Between 2013 and 2017, the number of publications focusing on the gut microbiota was, remarkably, 12 900, which represents four-fifths of the total number of publications over the last 40 years that investigated this topic. This review discusses recent evidence of the impact of the gut microbiota on metabolic disorders and focus on selected key mechanisms. This review also aims to provide a critical analysis of the current knowledge in this field, identify putative key issues or problems and discuss misinterpretations. The abundance of metagenomic data generated on comparing diseased and healthy subjects can lead to the erroneous claim that a bacterium is causally linked with the protection or the onset of a disease. In fact, environmental factors such as dietary habits, drug treatments, intestinal motility and stool frequency and consistency are all factors that influence the composition of the microbiota and should be considered. The cases of the bacteria Prevotella copri and Akkermansia muciniphila will be discussed as key examples.}, } @article {pmid29934334, year = {2018}, author = {Judd, AM and Matthews, MK and Hughes, R and Veloz, M and Sexton, CE and Chaston, JM}, title = {Bacterial Methionine Metabolism Genes Influence Drosophila melanogaster Starvation Resistance.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {17}, pages = {}, pmid = {29934334}, issn = {1098-5336}, mesh = {Acetobacter/genetics/metabolism ; Animals ; Drosophila melanogaster/*microbiology ; Escherichia coli/genetics/metabolism ; Gastrointestinal Tract/*microbiology ; Lactobacillus/genetics/metabolism ; Methionine/*metabolism ; Microbiota/*genetics ; Starvation/*prevention & control ; Symbiosis ; }, abstract = {Animal-associated microorganisms (microbiota) dramatically influence the nutritional and physiological traits of their hosts. To expand our understanding of such influences, we predicted bacterial genes that influence a quantitative animal trait by a comparative genomic approach, and we extended these predictions via mutant analysis. We focused on Drosophila melanogaster starvation resistance (SR). We first confirmed that D. melanogaster SR responds to the microbiota by demonstrating that bacterium-free flies have greater SR than flies bearing a standard 5-species microbial community, and we extended this analysis by revealing the species-specific influences of 38 genome-sequenced bacterial species on D. melanogaster SR. A subsequent metagenome-wide association analysis predicted bacterial genes with potential influence on D. melanogaster SR, among which were significant enrichments in bacterial genes for the metabolism of sulfur-containing amino acids and B vitamins. Dietary supplementation experiments established that the addition of methionine, but not B vitamins, to the diets significantly lowered D. melanogaster SR in a way that was additive, but not interactive, with the microbiota. A direct role for bacterial methionine metabolism genes in D. melanogaster SR was subsequently confirmed by analysis of flies that were reared individually with distinct methionine cycle Escherichia coli mutants. The correlated responses of D. melanogaster SR to bacterial methionine metabolism mutants and dietary modification are consistent with the established finding that bacteria can influence fly phenotypes through dietary modification, although we do not provide explicit evidence of this conclusion. Taken together, this work reveals that D. melanogaster SR is a microbiota-responsive trait, and specific bacterial genes underlie these influences.IMPORTANCE Extending descriptive studies of animal-associated microorganisms (microbiota) to define causal mechanistic bases for their influence on animal traits is an emerging imperative. In this study, we reveal that D. melanogaster starvation resistance (SR), a model quantitative trait in animal genetics, responds to the presence and identity of the microbiota. Using a predictive analysis, we reveal that the amino acid methionine has a key influence on D. melanogaster SR and show that bacterial methionine metabolism mutants alter normal patterns of SR in flies bearing the bacteria. Our data further suggest that these effects are additive, and we propose the untested hypothesis that, similar to bacterial effects on fruit fly triacylglyceride deposition, the bacterial influence may be through dietary modification. Together, these findings expand our understanding of the bacterial genetic basis for influence on a nutritionally relevant trait of a model animal host.}, } @article {pmid29934134, year = {2018}, author = {Zaheer, M and Wang, C and Bian, F and Yu, Z and Hernandez, H and de Souza, RG and Simmons, KT and Schady, D and Swennes, AG and Pflugfelder, SC and Britton, RA and de Paiva, CS}, title = {Protective role of commensal bacteria in Sjögren Syndrome.}, journal = {Journal of autoimmunity}, volume = {93}, number = {}, pages = {45-56}, pmid = {29934134}, issn = {1095-9157}, support = {P30 CA125123/CA/NCI NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; T32 AI053831/AI/NIAID NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; P30 AI036211/AI/NIAID NIH HHS/United States ; R01 EY026893/EY/NEI NIH HHS/United States ; }, mesh = {Animals ; CD4-Positive T-Lymphocytes/immunology/pathology ; Cornea/*immunology/pathology ; Dacryocystitis/genetics/immunology/*microbiology/pathology ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Female ; Gastrointestinal Microbiome/immunology ; Gene Expression Regulation ; Germ-Free Life ; Goblet Cells/immunology/pathology ; Homeodomain Proteins/genetics/*immunology ; Interferon-gamma/genetics/immunology ; Interleukin-12/genetics/immunology ; Interleukin-2 Receptor alpha Subunit/deficiency/genetics/*immunology ; Lacrimal Apparatus/*immunology/pathology ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Permeability ; Sjogren's Syndrome/genetics/immunology/*microbiology/pathology ; Symbiosis/*immunology ; }, abstract = {CD25 knock-out (CD25KO) mice spontaneously develop Sjögren Syndrome (SS)-like inflammation. We investigated the role of commensal bacteria by comparing CD25KO mice housed in conventional or germ-free conditions. Germ-free CD25KO mice have greater corneal barrier dysfunction, lower goblet cell density, increased total lymphocytic infiltration score, increased expression of IFN-γ, IL-12 and higher a frequency of CD4[+]IFN-γ[+] cells than conventional mice. CD4[+] T cells isolated from female germ-free CD25KO mice adoptively transferred to naive immunodeficient RAG1KO recipients caused more severe Sjögren-like disease than CD4[+] T cells transferred from conventional CD25KO mice. Fecal transplant in germ-free CD25KO mice reversed the spontaneous dry eye phenotype and decreased the generation of pathogenic CD4[+]IFN-γ[+] cells. Our studies indicate that lack of commensal bacteria accelerates the onset and severity of dacryoadenitis and generates autoreactive CD4[+]T cells with greater pathogenicity in the CD25KO model, suggesting that the commensal bacteria or their metabolites products have immunoregulatory properties that protect exocrine glands in the CD25KO SS model.}, } @article {pmid29931479, year = {2018}, author = {Philips, CA and Phadke, N and Ganesan, K and Ranade, S and Augustine, P}, title = {Corticosteroids, nutrition, pentoxifylline, or fecal microbiota transplantation for severe alcoholic hepatitis.}, journal = {Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology}, volume = {37}, number = {3}, pages = {215-225}, pmid = {29931479}, issn = {0975-0711}, mesh = {Administration, Oral ; Adult ; Aged ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Hepatitis, Alcoholic/microbiology/*therapy ; Humans ; Male ; Middle Aged ; *Nutrition Therapy ; Pentoxifylline/*therapeutic use ; Prednisolone/*administration & dosage ; Severity of Illness Index ; Treatment Outcome ; }, abstract = {INTRODUCTION: Alcohol-induced intestinal dysbiosis is central to the development of the severe alcoholic liver disease. We present the first study to compare outcomes in patients of severe alcoholic hepatitis (SAH) on nutritional therapy, corticosteroids, pentoxifylline, and healthy donor fecal transplantation (FMT) and discuss distinct microbial community and microbiome metabolic functional changes after FMT.

METHODS: Out of 1271 liver disease patients, 809 (63.7%) were diagnosed to have the alcoholic liver disease, of which 51 patients (8 treated with corticosteroids, 17 with nutritional support only, 10 with pentoxifylline, 16 receiving FMT) were included. Clinical, biochemical parameters, liver disease, and alcoholic hepatitis severity scores at baseline and mortality at the end of 1 and 3 months were analyzed between groups. Stool microbiota (SM) analysis was performed for healthy controls (HC) and respective recipients after FMT.

RESULTS: All the patients were male. The proportions of patients surviving at the end of 1 and 3 months in the steroids, nutrition, pentoxifylline, and FMT group were 63%, 47%, 40% and 75% [p = 0.179] and 38%, 29%, 30%, and 75% [p = 0.036], respectively. When compared with FMT, relative risk and hazard ratios for death were higher in all the other groups. Following FMT, distinct and beneficial modulation of SM and pathways of dysregulated metabolism, infections, inflammation, and oxidative stress in SAH patients were noted in tandem with improved clinical outcomes.

CONCLUSIONS: Healthy donor FMT for SAH improves survival beyond what is offered by current therapies and can function as a cost-effective bridge to liver transplant (LT) or for improving transplant-free survival. Larger studies and randomized trials are unmet needs.}, } @article {pmid29930350, year = {2018}, author = {Dini-Andreote, F and van Elsas, JD and Olff, H and Salles, JF}, title = {Dispersal-competition tradeoff in microbiomes in the quest for land colonization.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {9451}, pmid = {29930350}, issn = {2045-2322}, mesh = {*Biological Evolution ; *Metagenome ; *Microbiota ; Seawater/microbiology ; *Soil Microbiology ; }, abstract = {Ancestor microbes started colonizing inland habitats approximately 2.7 to 3.5 billion years ago. With some exceptions, the key physiological adaptations of microbiomes associated with marine-to-land transitions have remained elusive. This is essentially caused by the lack of suitable systems that depict changes in microbiomes across sufficiently large time scales. Here, we investigate the adaptive routes taken by microbiomes along a contemporary gradient of land formation. Using functional trait-based metagenomics, we show that a switch from a microbial 'dispersal' to a 'competition' response modus best characterizes the microbial trait changes during this eco-evolutionary trajectory. The 'dispersal' modus prevails in microbiomes at the boundary sites between land and sea. It encompasses traits conferring cell chemosensory and motile behaviors, thus allowing the local microbes to exploit short-lived nutritional patches in high-diffusion microhabitats. A systematic transition towards the 'competition' modus occurs progressively as the soil matures, which is likely due to forces of viscosity or strain that favor traits for competition and chemical defense. Concomitantly, progressive increases in the abundances of genes encoding antibiotic resistance and complex organic substrate degradation were found. Our findings constitute a novel perspective on the ecology and evolution of microbiome traits, tracking back one of the most seminal transitions in the evolutionary history of life.}, } @article {pmid29930201, year = {2018}, author = {Abreu, C and Ortiz Lopez, A and Gore, J}, title = {Pairing off: a bottom-up approach to the human gut microbiome.}, journal = {Molecular systems biology}, volume = {14}, number = {6}, pages = {e8425}, pmid = {29930201}, issn = {1744-4292}, mesh = {*Gastrointestinal Microbiome ; Humans ; Microbial Interactions ; *Microbiota ; }, abstract = {The human gut microbiome has been implicated in a variety of health outcomes, and extensive research has aimed to understand its composition and function, primarily via metagenomic analyses. An examination of how the microbiome develops and interacts through interspecies competition and cooperation has been lacking so far. In their recent work, Venturelli et al (2018) build a synthetic gut community and accurately predict its dynamics with a simple network of pairwise interactions.}, } @article {pmid29929823, year = {2018}, author = {Schott, C and Weigt, SS and Turturice, BA and Metwally, A and Belperio, J and Finn, PW and Perkins, DL}, title = {Bronchiolitis obliterans syndrome susceptibility and the pulmonary microbiome.}, journal = {The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation}, volume = {37}, number = {9}, pages = {1131-1140}, pmid = {29929823}, issn = {1557-3117}, support = {F30 HL137267/HL/NHLBI NIH HHS/United States ; R01 HL138628/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Bronchiolitis Obliterans/*microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Disease Susceptibility ; Female ; Follow-Up Studies ; Humans ; Lung/*microbiology ; *Lung Transplantation ; Male ; *Microbiota ; Middle Aged ; Syndrome ; }, abstract = {BACKGROUND: Lung transplantation outcomes remain complicated by bronchiolitis obliterans syndrome (BOS), a major cause of mortality and retransplantation for patients. A variety of factors linking inflammation and BOS have emerged, meriting further exploration of the microbiome as a source of inflammation. In this analysis, we determined features of the pulmonary microbiome associated with BOS susceptibility.

METHODS: Bronchoalveolar lavage (BAL) samples were collected from 25 patients during standard of care bronchoscopies before BOS onset. Microbial DNA was isolated from BAL fluid and prepared for metagenomics shotgun sequencing. Patient microbiomes were phenotyped using k-means clustering and compared to determine effects on BOS-free survival.

RESULTS: Clustering identified 3 microbiome phenotypes: Actinobacteria dominant (AD), mixed, and Proteobacteria dominant. AD microbiomes, distinguished by enrichment with Gram-positive organisms, conferred reduced odds and risks for patients to develop acute rejection and BOS compared with non-AD microbiomes. These findings were independent of treatment models. Microbiome findings were correlated with BAL cell counts and polymorphonuclear cell percentages.

CONCLUSIONS: In some populations, features of the microbiome may be used to assess BOS susceptibility. Namely, a Gram-positive enriched pulmonary microbiome may predict resilience to BOS.}, } @article {pmid29929226, year = {2018}, author = {Pierart, A and Dumat, C and Maes, AQ and Roux, C and Sejalon-Delmas, N}, title = {Opportunities and risks of biofertilization for leek production in urban areas: Influence on both fungal diversity and human bioaccessibility of inorganic pollutants.}, journal = {The Science of the total environment}, volume = {624}, number = {}, pages = {1140-1151}, doi = {10.1016/j.scitotenv.2017.12.100}, pmid = {29929226}, issn = {1879-1026}, mesh = {Biodiversity ; Environmental Monitoring ; Fertilizers ; Gardening ; Humans ; Mycorrhizae ; Onions/*chemistry/microbiology ; *Soil Microbiology ; Soil Pollutants/analysis/chemistry/*metabolism ; }, abstract = {The influence of biofertilization with arbuscular mycorrhizal fungi (AMF) on trace metal and metalloids (TM) - Pb, Cd and Sb - uptake by leek (Allium porrum L.) grown in contaminated soils was investigated. The effect of biofertilization on human bioaccessibility of the TM in the plants was also examined. Leek were cultivated in one soil with geogenic TM sources and one soil with anthropogenic TM, to assess the influence of pollutant origin on soil-plant transfer. Leek were grown for six months on these contaminated soils, with and without a local AMF based biofertilizer. Fungal communities associated with leek roots were identified by high throughput sequencing (illumina Miseq®) metagenomic analysis. The TM compartmentation was studied using electron microscopy in plants tissues. In all the soils, biofertilization generated a loss of diversity favoring the AM fungal species Rhizophagus irregularis, which could explain the observed modification of metal transfer at the soil-AMF-plant interface. The human bioaccessibility of Sb increased in biofertilized treatments. Consequently, this latter result highlights a potential health risk of the use of this fertilization technique on contaminated soil since further field investigation is performed to better understand the mechanisms governing (1) the effect of AMF on TM bioaccessibility and (2) the evolution of AMF communities in contaminated soils.}, } @article {pmid29926341, year = {2019}, author = {Lladó Fernández, S and Větrovský, T and Baldrian, P}, title = {The concept of operational taxonomic units revisited: genomes of bacteria that are regarded as closely related are often highly dissimilar.}, journal = {Folia microbiologica}, volume = {64}, number = {1}, pages = {19-23}, pmid = {29926341}, issn = {1874-9356}, support = {18-25706S//Czech Science Foundation/ ; LTT17022//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; }, mesh = {Bacteria/*classification/*genetics ; DNA, Bacterial/genetics ; Databases, Nucleic Acid ; Genes, Bacterial/genetics ; Genetic Variation ; Genome, Bacterial/*genetics ; Glycoside Hydrolases/genetics ; *Metagenomics ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The concept of operational taxonomic units (OTUs), which constructs "mathematically" defined taxa, is widely accepted and applied to describe bacterial communities using amplicon sequencing of 16S rRNA gene. OTUs are often used to infer functional traits since they are considered to fairly represent of community members. However, the link between molecular taxa, real taxa, and OTUs seems to be much more complicated. Strains of the same bacterial species (ideally belonging to the same OTU) typically only share some genes (the core genome), while other genes are strain-specific and unique. It is thus unclear to what extent are important functional traits homogeneous within an OTU and how correctly can functional traits be inferred for individual OTU members. Here, we have tested in silico the similarity of all genes and, more specifically, the set of genes encoding for glycoside hydrolases (GH) in bacterial genomes that belong to the same OTU. Genome similarity varied among OTUs, but as many as 5-78% of genes were not shared between the two bacterial genomes in the pair. The complement of GH families (the presence of gene families and the number of genes per family) differed in 95% of OTUs. In average, 43% of GH families either differed in gene counts or were present in one genome and absent in the other. These results show a serious limitation of the OTU-based approaches when used to infer the functional traits of bacterial communities and open the questions how to link environmental sequencing data and microbial functions.}, } @article {pmid29925880, year = {2018}, author = {Galand, PE and Pereira, O and Hochart, C and Auguet, JC and Debroas, D}, title = {A strong link between marine microbial community composition and function challenges the idea of functional redundancy.}, journal = {The ISME journal}, volume = {12}, number = {10}, pages = {2470-2478}, pmid = {29925880}, issn = {1751-7370}, mesh = {Bacteria/*classification/*genetics ; Metagenome ; Metagenomics ; Microbiota/*genetics/*physiology ; Time Factors ; }, abstract = {Marine microbes have tremendous diversity, but a fundamental question remains unanswered: why are there so many microbial species in the sea? The idea of functional redundancy for microbial communities has long been assumed, so that the high level of richness is often explained by the presence of different taxa that are able to conduct the exact same set of metabolic processes and that can readily replace each other. Here, we refute the hypothesis of functional redundancy for marine microbial communities by showing that a shift in the community composition altered the overall functional attributes of communities across different temporal and spatial scales. Our metagenomic monitoring of a coastal northwestern Mediterranean site also revealed that diverse microbial communities harbor a high diversity of potential proteins. Working with all information given by the metagenomes (all reads) rather than relying only on known genes (annotated orthologous genes) was essential for revealing the similarity between taxonomic and functional community compositions. Our finding does not exclude the possibility for a partial redundancy where organisms that share some specific function can coexist when they differ in other ecological requirements. It demonstrates, however, that marine microbial diversity reflects a tremendous diversity of microbial metabolism and highlights the genetic potential yet to be discovered in an ocean of microbes.}, } @article {pmid29925614, year = {2018}, author = {Brothers, CJ and Van Der Pol, WJ and Morrow, CD and Hakim, JA and Koo, H and McClintock, JB}, title = {Ocean warming alters predicted microbiome functionality in a common sea urchin.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1881}, pages = {}, pmid = {29925614}, issn = {1471-2954}, support = {P30 AI027767/AI/NIAID NIH HHS/United States ; P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR001417/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; *Climate Change ; Hot Temperature/*adverse effects ; Lytechinus/*microbiology ; *Microbiota ; Oceans and Seas ; Random Allocation ; Seawater/*analysis ; }, abstract = {The microbiome of sea urchins plays a role in maintaining digestive health and innate immunity. Here, we investigated the effects of long-term (90 day) exposure to elevated seawater temperatures on the microbiome of the common, subtropical sea urchin Lytechinus variegatus The community composition and diversity of microbes varied according to the type of sample collected from the sea urchin (seawater, feed, intestines, coelomic fluid, digested pellet and faeces), with the lowest microbial diversity (predominately the order Campylobacterales) located in the intestinal tissue. Sea urchins exposed to near-future seawater temperatures maintained the community structure and diversity of microbes associated with their tissues. However, marginal, non-significant shifts in microbial community structure with elevated temperature resulted in significant changes in predicted metagenomic functions such as membrane transport and amino acid and carbohydrate metabolism. The predicted changes in key metabolic categories suggest that near-future climate-induced increases in seawater temperature could shift microbial community function and impact sea urchin digestive and immune physiology.}, } @article {pmid29925429, year = {2018}, author = {Tschitschko, B and Erdmann, S and DeMaere, MZ and Roux, S and Panwar, P and Allen, MA and Williams, TJ and Brazendale, S and Hancock, AM and Eloe-Fadrosh, EA and Cavicchioli, R}, title = {Genomic variation and biogeography of Antarctic haloarchaea.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {113}, pmid = {29925429}, issn = {2049-2618}, mesh = {Antarctic Regions ; Archaeal Viruses/*genetics/isolation & purification ; Base Sequence ; Genetic Variation/genetics ; Genome, Archaeal/*genetics ; Genomic Islands/genetics ; Geography ; Halorubrum/classification/*genetics/isolation & purification ; Lakes/microbiology ; Metagenome/genetics ; Microbiota/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The genomes of halophilic archaea (haloarchaea) often comprise multiple replicons. Genomic variation in haloarchaea has been linked to viral infection pressure and, in the case of Antarctic communities, can be caused by intergenera gene exchange. To expand understanding of genome variation and biogeography of Antarctic haloarchaea, here we assessed genomic variation between two strains of Halorubrum lacusprofundi that were isolated from Antarctic hypersaline lakes from different regions (Vestfold Hills and Rauer Islands). To assess variation in haloarchaeal populations, including the presence of genomic islands, metagenomes from six hypersaline Antarctic lakes were characterised.

RESULTS: The sequence of the largest replicon of each Hrr. lacusprofundi strain (primary replicon) was highly conserved, while each of the strains' two smaller replicons (secondary replicons) were highly variable. Intergenera gene exchange was identified, including the sharing of a type I-B CRISPR system. Evaluation of infectivity of an Antarctic halovirus provided experimental evidence for the differential susceptibility of the strains, bolstering inferences that strain variation is important for modulating interactions with viruses. A relationship was found between genomic structuring and the location of variation within replicons and genomic islands, demonstrating that the way in which haloarchaea accommodate genomic variability relates to replicon structuring. Metagenome read and contig mapping and clustering and scaling analyses demonstrated biogeographical patterning of variation consistent with environment and distance effects. The metagenome data also demonstrated that specific haloarchaeal species dominated the hypersaline systems indicating they are endemic to Antarctica.

CONCLUSION: The study describes how genomic variation manifests in Antarctic-lake haloarchaeal communities and provides the basis for future assessments of Antarctic regional and global biogeography of haloarchaea.}, } @article {pmid29925423, year = {2018}, author = {Brooks, B and Olm, MR and Firek, BA and Baker, R and Geller-McGrath, D and Reimer, SR and Soenjoyo, KR and Yip, JS and Dahan, D and Thomas, BC and Morowitz, MJ and Banfield, JF}, title = {The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {112}, pmid = {29925423}, issn = {2049-2618}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; S10 OD018174/OD/NIH HHS/United States ; }, mesh = {Aerosols ; Bacteria/*classification/genetics/*isolation & purification ; Base Sequence ; Dust ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; Infant, Newborn ; Infant, Premature ; Infant, Very Low Birth Weight ; *Intensive Care Units, Neonatal ; Premature Birth ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Skin/*microbiology ; }, abstract = {BACKGROUND: The neonatal intensive care unit (NICU) contains a unique cohort of patients with underdeveloped immune systems and nascent microbiome communities. Patients often spend several months in the same room, and it has been previously shown that the gut microbiomes of these infants often resemble the microbes found in the NICU. Little is known, however, about the identity, persistence, and absolute abundance of NICU room-associated bacteria over long stretches of time. Here, we couple droplet digital PCR (ddPCR), 16S rRNA gene surveys, and recently published metagenomics data from infant gut samples to infer the extent to which the NICU microbiome is shaped by its room occupants.

RESULTS: Over 2832 swabs, wipes, and air samples were collected from 16 private-style NICU rooms housing very low birth weight (< 1500 g), premature (< 31 weeks' gestation) infants. For each infant, room samples were collected daily, Monday through Friday, for 1 month. The first samples from the first infant and the last samples from the last infant were collected 383 days apart. Twenty-two NICU locations spanning room surfaces, hands, electronics, sink basins, and air were collected. Results point to an incredibly simple room community where 5-10 taxa, mostly skin-associated, account for over 50% of the amplicon reads. Biomass estimates reveal four to five orders of magnitude difference between the least to the most dense microbial communities, air, and sink basins, respectively. Biomass trends from bioaerosol samples and petri dish dust collectors suggest occupancy to be a main driver of suspended biological particles within the NICU. Using a machine learning algorithm to classify the origin of room samples, we show that each room has a unique microbial fingerprint. Several important taxa driving this model were dominant gut colonizers of infants housed within each room.

CONCLUSIONS: Despite regular cleaning of hospital surfaces, bacterial biomass was detectable at varying densities. A room-specific microbiome signature was detected, suggesting microbes seeding NICU surfaces are sourced from reservoirs within the room and that these reservoirs contain actively dividing cells. Collectively, the data suggests that hospitalized infants, in combination with their caregivers, shape the microbiome of NICU rooms.}, } @article {pmid29922970, year = {2018}, author = {Li, J and Li, L and Jiang, H and Yuan, L and Zhang, L and Ma, JE and Zhang, X and Cheng, M and Chen, J}, title = {Fecal Bacteriome and Mycobiome in Bats with Diverse Diets in South China.}, journal = {Current microbiology}, volume = {75}, number = {10}, pages = {1352-1361}, pmid = {29922970}, issn = {1432-0991}, support = {2016B070701016//PlanningFunds of Science and Technology of Guangdong Province/ ; 2013B031500006//PlanningFunds of Science and Technology of Guangdong Province/ ; 2016GDASPT-0107//Funds for Environment Construction and Capacity Building of GDAS' Research Platform/ ; 2017GDASCX-0107//GDAS Special Project of Science and Technology Development/ ; }, mesh = {*Animal Feed ; Animals ; Bacteria/classification/genetics ; Biodiversity ; China ; *Chiroptera ; Feces/*microbiology ; Female ; Fungi/classification/genetics ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Bats can be divided into frugivory, nectarivory, insectivory, and sanguivory based on their diets, and are therefore ideal wild animal models to study the relationship between diets and intestinal microflora. Early studies of bat gut bacteria showed that the diversity and structure of intestinal bacterial communities in bats are closely related to dietary changes. Worthy of note, intestinal microbes are composed of bacteria, fungi, protozoa, and archaea. Although the number of gut fungi is much lower than that of gut bacteria, they also play an important role in maintaining the host homeostasis. However, there are still few reports on the relationship between the gut mycobiota and the dietary habits of the host. In addition, bats have also been shown to naturally transmit pathogenic viruses and bacteria through their feces and saliva, but fungal infections from bat are less studied. Here, we used high-throughput sequencing of bacterial 16S and eukaryotic 18S rRNA genes in the V4 and V9 regions to characterize fecal bacterial and fungal microbiota in phytophagous and insectivorous bats in South China. The results show that the gut microbiota in bats were dominated by bacterial phyla Proteobacteria, Firmicutes, Tenericutes and Bacteroidetes, and fungal phyla Ascomycota and Basidiomycota. There was a significant difference in the diversity of bacterial and fungal microbiota between the groups, in addition to specific bacteria and fungi populations on each of them. Of note, the number of fungi in the feces of herbivorous bats is relatively higher. Most of these fungi are foodborne and are also pathogens of humans and other animals. Thus, bats are natural carriers of fungal pathogens. The current study expands the understanding of the bat gut bacterial and fungal mycobiota and provides further insight into the transmission of fungal pathogens.}, } @article {pmid29921329, year = {2018}, author = {Call, L and Stoll, B and Oosterloo, B and Ajami, N and Sheikh, F and Wittke, A and Waworuntu, R and Berg, B and Petrosino, J and Olutoye, O and Burrin, D}, title = {Metabolomic signatures distinguish the impact of formula carbohydrates on disease outcome in a preterm piglet model of NEC.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {111}, pmid = {29921329}, issn = {2049-2618}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; T32 GM088129/GM/NIGMS NIH HHS/United States ; }, mesh = {Animal Feed/analysis ; Animals ; Bacillus/classification/genetics/*isolation & purification ; Clostridium/classification/genetics/*isolation & purification ; *Dietary Carbohydrates ; *Enteral Nutrition ; Enterocolitis, Necrotizing/etiology/microbiology ; Female ; Gammaproteobacteria/classification/genetics/*isolation & purification ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; High Fructose Corn Syrup/*administration & dosage ; Lactose/*administration & dosage ; Pregnancy ; Premature Birth ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; Swine ; }, abstract = {BACKGROUND: Major risk factors for necrotizing enterocolitis (NEC) include premature birth and formula feeding in the context of microbial colonization of the gastrointestinal tract. We previously showed that feeding formula composed of lactose vs. corn syrup solids protects against NEC in preterm pigs; however, the microbial and metabolic effects of these different carbohydrates used in infant formula has not been explored.

OBJECTIVE: Our objective was to characterize the effects of lactose- and corn syrup solid-based formulas on the metabolic and microbial profiles of preterm piglets and to determine whether unique metabolomic or microbiome signatures correlate with severity or incidence of NEC.

DESIGN/METHODS: Preterm piglets (103 days gestation) were given total parenteral nutrition (2 days) followed by gradual (5 days) advancement of enteral feeding of formulas matched in nutrient content but containing either lactose (LAC), corn syrup solids (CSS), or 1:1 mix (MIX). Gut contents and mucosal samples were collected and analyzed for microbial profiles by sequencing the V4 region of the 16S rRNA gene. Metabolomic profiles of cecal contents and plasma were analyzed by LC/GC mass spectrometry.

RESULTS: NEC incidence was 14, 50, and 44% in the LAC, MIX, and CSS groups, respectively. The dominant classes of bacteria were Bacilli, Clostridia, and Gammaproteobacteria. The number of observed OTUs was lowest in colon contents of CSS-fed pigs. CSS-based formula was associated with higher Bacilli and lower Clostridium from clusters XIVa and XI in the colon. NEC was associated with decreased Gammaproteobacteria in the stomach and increased Clostridium sensu stricto in the ileum. Plasma from NEC piglets was enriched with metabolites of purine metabolism, aromatic amino acid metabolism, and bile acids. Markers of glycolysis, e.g., lactate, were increased in the cecal contents of CSS-fed pigs and in plasma of pigs which developed NEC.

CONCLUSIONS: Feeding formula containing lactose is not completely protective against NEC, yet selects for greater microbial richness associated with changes in Bacilli and Clostridium and lower NEC incidence. We conclude that feeding preterm piglets a corn syrup solid vs. lactose-based formula increases the incidence of NEC and produces distinct metabolomic signatures despite modest changes in microbiome profiles.}, } @article {pmid29920927, year = {2019}, author = {Lee, JR and Magruder, M and Zhang, L and Westblade, LF and Satlin, MJ and Robertson, A and Edusei, E and Crawford, C and Ling, L and Taur, Y and Schluter, J and Lubetzky, M and Dadhania, D and Pamer, E and Suthanthiran, M}, title = {Gut microbiota dysbiosis and diarrhea in kidney transplant recipients.}, journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons}, volume = {19}, number = {2}, pages = {488-500}, pmid = {29920927}, issn = {1600-6143}, support = {K23 AI124464/AI/NIAID NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; R37 AI051652/AI/NIAID NIH HHS/United States ; //Chinese American Medical Society/International ; }, mesh = {Adult ; Bacteria/genetics/*growth & development/isolation & purification ; Case-Control Studies ; Cohort Studies ; Diarrhea/*etiology/pathology ; Dysbiosis/*etiology/pathology ; Feces/microbiology ; Female ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Glomerular Filtration Rate ; Graft Rejection/*etiology/pathology ; Graft Survival ; Humans ; Kidney Failure, Chronic/*surgery ; Kidney Function Tests ; Kidney Transplantation/*adverse effects ; Male ; Middle Aged ; Postoperative Complications ; Prognosis ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; }, abstract = {Posttransplant diarrhea is associated with kidney allograft failure and death, but its etiology remains unknown in the majority of cases. Because altered gut microbial ecology is a potential basis for diarrhea, we investigated whether posttransplant diarrhea is associated with gut dysbiosis. We enrolled 71 kidney allograft recipients for serial fecal specimen collections in the first 3 months of transplantation and profiled the gut microbiota using 16S ribosomal RNA (rRNA) gene V4-V5 deep sequencing. The Shannon diversity index was significantly lower in 28 diarrheal fecal specimens from 25 recipients with posttransplant diarrhea than in 112 fecal specimens from 46 recipients without posttransplant diarrhea. We found a lower relative abundance of 13 commensal genera (Benjamini-Hochberg adjusted P ≤ .15) in the diarrheal fecal specimens including the same 4 genera identified in our prior study. The 28 diarrheal fecal specimens were also evaluated by a multiplexed polymerase chain reaction (PCR) assay for 22 bacterial, viral, and protozoan gastrointestinal pathogens, and 26 specimens were negative for infectious etiologies. Using PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) to predict metagenomic functions, we found that diarrheal fecal specimens had a lower abundance of metabolic genes. Our findings suggest that posttransplant diarrhea is not associated with common infectious diarrheal pathogens but with a gut dysbiosis.}, } @article {pmid29920461, year = {2018}, author = {Graham, EB and Crump, AR and Kennedy, DW and Arntzen, E and Fansler, S and Purvine, SO and Nicora, CD and Nelson, W and Tfaily, MM and Stegen, JC}, title = {Multi 'omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone.}, journal = {The Science of the total environment}, volume = {642}, number = {}, pages = {742-753}, doi = {10.1016/j.scitotenv.2018.05.256}, pmid = {29920461}, issn = {1879-1026}, mesh = {Carbon ; Environmental Monitoring/*methods ; Groundwater ; Metabolome/*physiology ; Microbiota ; Rivers ; }, abstract = {Biogeochemical hotspots are pervasive at terrestrial-aquatic interfaces, particularly within groundwater-surface water mixing zones (hyporheic zones), and they are critical to understanding spatiotemporal variation in biogeochemical cycling. Here, we use multi 'omic comparisons of hotspots to low-activity sediments to gain mechanistic insight into hyporheic zone organic matter processing. We hypothesized that microbiome structure and function, as described by metagenomics and metaproteomics, would distinguish hotspots from low-activity sediments by shifting metabolism towards carbohydrate-utilizing pathways and elucidate discrete mechanisms governing organic matter processing in each location. We also expected these differences to be reflected in the metabolome, whereby hotspot carbon (C) pools and metabolite transformations therein would be enriched in sugar-associated compounds. In contrast to expectations, we found pronounced phenotypic plasticity in the hyporheic zone microbiome that was denoted by similar microbiome structure, functional potential, and expression across sediments with dissimilar metabolic rates. Instead, diverse nitrogenous metabolites and biochemical transformations characterized hotspots. Metabolomes also corresponded more strongly to aerobic metabolism than bulk C or N content only (explaining 67% vs. 42% and 37% of variation respectively), and bulk C and N did not improve statistical models based on metabolome composition alone. These results point to organic nitrogen as a significant regulatory factor influencing hyporheic zone organic matter processing. Based on our findings, we propose incorporating knowledge of metabolic pathways associated with different chemical fractions of C pools into ecosystem models will enhance prediction accuracy.}, } @article {pmid29915700, year = {2018}, author = {Carew, ME and Coleman, RA and Hoffmann, AA}, title = {Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding?.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4980}, pmid = {29915700}, issn = {2167-8359}, abstract = {BACKGROUND: High throughput DNA sequencing of bulk invertebrate samples or metabarcoding is becoming increasingly used to provide profiles of biological communities for environmental monitoring. As metabarcoding becomes more widely applied, new reference DNA barcodes linked to individual specimens identified by taxonomists are needed. This can be achieved through using DNA extraction methods that are not only suitable for metabarcoding but also for building reference DNA barcode libraries.

METHODS: In this study, we test the suitability of a rapid non-destructive DNA extraction method for metabarcoding of freshwater invertebrate samples.

RESULTS: This method resulted in detection of taxa from many taxonomic groups, comparable to results obtained with two other tissue-based extraction methods. Most taxa could also be successfully used for subsequent individual-based DNA barcoding and taxonomic identification. The method was successfully applied to field-collected invertebrate samples stored for taxonomic studies in 70% ethanol at room temperature, a commonly used storage method for freshwater samples.

DISCUSSION: With further refinement and testing, non-destructive extraction has the potential to rapidly characterise species biodiversity in invertebrate samples, while preserving specimens for taxonomic investigation.}, } @article {pmid29912385, year = {2018}, author = {Bengtsson-Palme, J and Richardson, RT and Meola, M and Wurzbacher, C and Tremblay, ÉD and Thorell, K and Kanger, K and Eriksson, KM and Bilodeau, GJ and Johnson, RM and Hartmann, M and Nilsson, RH}, title = {Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {23}, pages = {4027-4033}, pmid = {29912385}, issn = {1367-4811}, mesh = {Computational Biology ; *DNA Barcoding, Taxonomic ; *Genetic Markers ; *Metagenomics ; *Phylogeny ; *Software ; }, abstract = {MOTIVATION: Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, no genetic marker gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. This has led to the adoption of a range of genetic markers for DNA metabarcoding. While many taxonomic classification software tools can be re-trained on these genetic markers, they are often designed with assumptions that impair their utility on genes other than the SSU and LSU rRNA. Here, we present an update to Metaxa2 that enables the use of any genetic marker for taxonomic classification of metagenome and amplicon sequence data.

RESULTS: We evaluated the Metaxa2 Database Builder on 11 commonly used barcoding regions and found that while there are wide differences in performance between different genetic markers, our software performs satisfactorily provided that the input taxonomy and sequence data are of high quality.

Freely available on the web as part of the Metaxa2 package at http://microbiology.se/software/metaxa2/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid29911322, year = {2018}, author = {Moon, CD and Young, W and Maclean, PH and Cookson, AL and Bermingham, EN}, title = {Metagenomic insights into the roles of Proteobacteria in the gastrointestinal microbiomes of healthy dogs and cats.}, journal = {MicrobiologyOpen}, volume = {7}, number = {5}, pages = {e00677}, pmid = {29911322}, issn = {2045-8827}, mesh = {Animals ; Bacteria/*classification/*genetics ; Cats ; Dogs ; Feces/*microbiology ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Metagenomics ; }, abstract = {Interests in the impact of the gastrointestinal microbiota on health and wellbeing have extended from humans to that of companion animals. While relatively fewer studies to date have examined canine and feline gut microbiomes, analysis of the metagenomic DNA from fecal communities using next-generation sequencing technologies have provided insights into the microbes that are present, their function, and potential to contribute to overall host nutrition and health. As carnivores, healthy dogs and cats possess fecal microbiomes that reflect the generally higher concentrations of protein and fat in their diets, relative to omnivores and herbivores. The phyla Firmicutes and Bacteroidetes are highly abundant, and Fusobacteria, Actinobacteria, and Proteobacteria also feature prominently. Proteobacteria is the most diverse bacterial phylum and commonly features in the fecal microbiota of healthy dogs and cats, although its reputation is often sullied as its members include a number of well-known opportunistic pathogens, such as Escherichia coli, Salmonella, and Campylobacter, which may impact the health of the host and its owner. Furthermore, in other host species, high abundances of Proteobacteria have been associated with dysbiosis in hosts with metabolic or inflammatory disorders. In this review, we seek to gain further insight into the prevalence and roles of the Proteobacteria within the gastrointestinal microbiomes of healthy dogs and cats. We draw upon the growing number of metagenomic DNA sequence-based studies which now allow us take a culture-independent approach to examine the functions that this more minor, yet important, group contribute to normal microbiome function.}, } @article {pmid29908593, year = {2018}, author = {Rastrojo, A and Alcamí, A}, title = {Viruses in Polar Lake and Soil Ecosystems.}, journal = {Advances in virus research}, volume = {101}, number = {}, pages = {39-54}, doi = {10.1016/bs.aivir.2018.02.002}, pmid = {29908593}, issn = {1557-8399}, mesh = {Antarctic Regions ; Arctic Regions ; Biological Evolution ; *Ecosystem ; Genetic Variation ; Lakes/*virology ; Metagenomics ; *Soil Microbiology ; Virus Physiological Phenomena ; Viruses/classification/*genetics ; }, abstract = {Viruses play an important role in the control of microbial communities, and it has been suggested that the influence of viruses in polar ecosystems, with low nutrients and under extreme environmental conditions, may be greater. Viral metagenomics allows the genetic characterization of complex viral communities without the need to isolate and grow viruses. Recent investigations in Antarctica and the Arctic are uncovering a great diversity of DNA viruses, including bacteriophages, circular single-stranded DNA viruses, algal-infecting phycodnaviruses, and virophages, adapted to these extreme environments. The limited sequence similarity between viruses in Antarctica and the Arctic suggests that viral communities in the two polar regions have evolved independently since the formation of the Antarctic continent, estimated to occur 25 million years ago. The community of RNA viruses in Antarctica is dominated by the order Picornavirales and their quasispecies composition suggests that higher genetic variability may correlate with viral adaptation to new environmental conditions.}, } @article {pmid29907938, year = {2018}, author = {Li, W and Hou, Q and Wang, Y and Ma, H and Liu, Y and Zhao, F and Li, J and Kwok, LY and Yu, J and Sun, Z and Sun, T}, title = {Analysis of the Gut Microbial Diversity of Dairy Cows During Peak Lactation by PacBio Single-Molecule Real-Time (SMRT) Sequencing.}, journal = {Current microbiology}, volume = {75}, number = {10}, pages = {1316-1323}, pmid = {29907938}, issn = {1432-0991}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification/metabolism ; *Biodiversity ; Cattle/*microbiology/physiology ; DNA, Bacterial/genetics ; Fatty Acids, Volatile/metabolism ; Female ; *Gastrointestinal Microbiome ; Intestines/*microbiology ; Lactation ; Metagenome ; Milk/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The gut microbes of dairy cows are strongly associated with their health, but the relationship between milk production and the intestinal microbiota has seldom been studied. Thus, we explored the diversity of the intestinal microbiota during peak lactation of dairy cows.

METHODS: The intestinal microbiota of nine dairy cows at peak lactation was evaluated using the Pacific Biosciences single-molecule real-time (PacBio SMRT) sequencing approach.

RESULTS: A total of 32,670 high-quality 16S rRNA gene sequences were obtained, belonging to 12 phyla, 59 families, 107 genera, and 162 species. Firmicutes (83%) were the dominant phylum, while Bacteroides (6.16%) was the dominant genus. All samples showed a high microbial diversity, with numerous genera of short chain fatty acid (SCFA)-producers. The proportion of SCFA producers was relatively high in relation to the identified core intestinal microbiota. Moreover, the predicted functional metagenome was heavily involved in energy metabolism.

CONCLUSIONS: This study provided novel insights into the link between the dairy cow gut microbiota and milk production.}, } @article {pmid29907097, year = {2018}, author = {Oudah, M and Henschel, A}, title = {Taxonomy-aware feature engineering for microbiome classification.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {227}, pmid = {29907097}, issn = {1471-2105}, mesh = {*Algorithms ; Bacteria/*classification/*genetics/isolation & purification ; Ecology ; Humans ; *Metagenome ; Microbiota/*genetics ; Phylogeny ; *Terminology as Topic ; }, abstract = {BACKGROUND: What is a healthy microbiome? The pursuit of this and many related questions, especially in light of the recently recognized microbial component in a wide range of diseases has sparked a surge in metagenomic studies. They are often not simply attributable to a single pathogen but rather are the result of complex ecological processes. Relatedly, the increasing DNA sequencing depth and number of samples in metagenomic case-control studies enabled the applicability of powerful statistical methods, e.g. Machine Learning approaches. For the latter, the feature space is typically shaped by the relative abundances of operational taxonomic units, as determined by cost-effective phylogenetic marker gene profiles. While a substantial body of microbiome/microbiota research involves unsupervised and supervised Machine Learning, very little attention has been put on feature selection and engineering.

RESULTS: We here propose the first algorithm to exploit phylogenetic hierarchy (i.e. an all-encompassing taxonomy) in feature engineering for microbiota classification. The rationale is to exploit the often mono- or oligophyletic distribution of relevant (but hidden) traits by virtue of taxonomic abstraction. The algorithm is embedded in a comprehensive microbiota classification pipeline, which we applied to a diverse range of datasets, distinguishing healthy from diseased microbiota samples.

CONCLUSION: We demonstrate substantial improvements over the state-of-the-art microbiota classification tools in terms of classification accuracy, regardless of the actual Machine Learning technique while using drastically reduced feature spaces. Moreover, generalized features bear great explanatory value: they provide a concise description of conditions and thus help to provide pathophysiological insights. Indeed, the automatically and reproducibly derived features are consistent with previously published domain expert analyses.}, } @article {pmid29906449, year = {2018}, author = {Tropini, C and Moss, EL and Merrill, BD and Ng, KM and Higginbottom, SK and Casavant, EP and Gonzalez, CG and Fremin, B and Bouley, DM and Elias, JE and Bhatt, AS and Huang, KC and Sonnenburg, JL}, title = {Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota.}, journal = {Cell}, volume = {173}, number = {7}, pages = {1742-1754.e17}, pmid = {29906449}, issn = {1097-4172}, support = {R01 DK101674/DK/NIDDK NIH HHS/United States ; K08 CA184420/CA/NCI NIH HHS/United States ; R01 DK085025/DK/NIDDK NIH HHS/United States ; P50 GM107615/GM/NIGMS NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Bacteroidetes/drug effects/genetics/isolation & purification ; Cecum/chemistry/metabolism/microbiology/pathology ; Colon/chemistry/microbiology/pathology ; Cytokines/metabolism ; Diarrhea/immunology/microbiology/*pathology/veterinary ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Glycoside Hydrolases/metabolism ; Humans ; Immunity, Humoral/drug effects ; Immunoglobulin G/metabolism ; Intestinal Mucosa/microbiology/pathology ; Metagenomics ; Mice ; Osmolar Concentration ; Polyethylene Glycols/metabolism/*pharmacology ; Proteome/analysis ; RNA, Ribosomal, 16S/chemistry/genetics ; Verrucomicrobia/drug effects/genetics/isolation & purification ; }, abstract = {Osmotic diarrhea is a prevalent condition in humans caused by food intolerance, malabsorption, and widespread laxative use. Here, we assess the resilience of the gut ecosystem to osmotic perturbation at multiple length and timescales using mice as model hosts. Osmotic stress caused reproducible extinction of highly abundant taxa and expansion of less prevalent members in human and mouse microbiotas. Quantitative imaging revealed decimation of the mucus barrier during osmotic perturbation, followed by recovery. The immune system exhibited temporary changes in cytokine levels and a lasting IgG response against commensal bacteria. Increased osmolality prevented growth of commensal strains in vitro, revealing one mechanism contributing to extinction. Environmental availability of microbiota members mitigated extinction events, demonstrating how species reintroduction can affect community resilience. Our findings (1) demonstrate that even mild osmotic diarrhea can cause lasting changes to the microbiota and host and (2) lay the foundation for interventions that increase system-wide resilience.}, } @article {pmid29906260, year = {2018}, author = {Albert, K and Rani, A and Sela, DA}, title = {The comparative genomics of Bifidobacterium callitrichos reflects dietary carbohydrate utilization within the common marmoset gut.}, journal = {Microbial genomics}, volume = {4}, number = {6}, pages = {}, pmid = {29906260}, issn = {2057-5858}, mesh = {Animals ; Bifidobacterium/*genetics/isolation & purification ; Callithrix/*microbiology ; Carbohydrate Metabolism ; DNA, Bacterial ; Dietary Carbohydrates/metabolism ; Feces/microbiology ; Firmicutes/genetics/isolation & purification ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Genome, Bacterial ; Genomics ; Metagenomics ; Phylogeny ; Proteobacteria/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics/isolation & purification ; Sequence Analysis, DNA ; }, abstract = {Bifidobacterium is a diverse genus of anaerobic, saccharolytic bacteria that colonize many animals, notably humans and other mammals. The presence of these bacteria in the gastrointestinal tract represents a potential coevolution between the gut microbiome and its mammalian host mediated by diet. To study the relationship between bifidobacterial gut symbionts and host nutrition, we analyzed the genome of two bifidobacteria strains isolated from the feces of a common marmoset (Callithrix jacchus), a primate species studied for its ability to subsist on host-indigestible carbohydrates. Whole genome sequencing identified these isolates as unique strains of Bifidobacterium callitrichos. All three strains, including these isolates and the previously described type strain, contain genes that may enable utilization of marmoset dietary substrates. These include genes predicted to contribute to galactose, arabinose, and trehalose metabolic pathways. In addition, significant genomic differences between strains suggest that bifidobacteria possess distinct roles in carbohydrate metabolism within the same host. Thus, bifidobacteria utilize dietary components specific to their host, both humans and non-human primates alike. Comparative genomics suggests conservation of possible coevolutionary relationships within the primate clade.}, } @article {pmid29903529, year = {2019}, author = {Pérez-Monter, C and Escalona-Nandez, I and Estanes-Hernández, A and Noriega-López, LG and Torre-Delgadillo, A}, title = {Intestinal microbiota assessment in cirrhotic patients from a Mexican mestizo population.}, journal = {Revista de gastroenterologia de Mexico (English)}, volume = {84}, number = {1}, pages = {26-35}, doi = {10.1016/j.rgmx.2018.02.010}, pmid = {29903529}, issn = {2255-534X}, mesh = {Adult ; Bacterial Load ; DNA, Bacterial/genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Indians, Central American ; Liver Cirrhosis/*microbiology ; Liver Function Tests ; Male ; Mexico ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; }, abstract = {INTRODUCTION AND AIMS: The intestinal microbiota is significantly altered in cirrhotic patients, but the composition of the intestinal microbiota in Mexican patients with the pathology has not been reported. The present study is an attempt to determine the type of intestinal microbiota in healthy subjects and in patients of Mexican mestizo origin that present with cirrhosis of the liver.

MATERIALS AND METHODS: Biochemical liver function parameters (ALT, AST, GGT, BIL-T, etc.) were determined in 23 cirrhotic patients and 21 control subjects. The intestinal microbiota was established through 16S ribosomal RNA gene sequencing.

RESULTS: The cirrhotic patients had elevated levels of ALT, AST, GGT (105.2±77.7 vs. 20.99±8.5UI/L, 110±68.6 vs. 23.39±5.2, and 119.1±79.1 vs. 19.3±15.2UI/L, respectively), IL-6 (1.64±0.38pg/ml, P<.001), or TNFα (1.78±0.3, P<.05). The intestinal microbiota of the cirrhotic patients was less diverse, compared with that of the control subjects. At the level of the phylum, there was a significant increase in Proteobacteria and Bacteroidetes in the patients with cirrhosis, compared with the controls (6.2 vs. 4.9% and 44 vs. 46%, respectively, P<.01). In contrast, there was a decrease in Firmicutes, Actinobacteria, and Fusobacteria in the cirrhotic patients. There was an increase in the Campylobacter and Gemella families in the cirrhotic patients, whereas Streptococcus and Veillonella had a positive association with serum ALT or AST levels.

CONCLUSIONS: To the best of our knowledge, the present study is the first to demonstrate the type of intestinal microbiota in Mexican patients with cirrhosis of the liver. The extension of the findings in a larger cohort of subjects and the metagenome analysis will enable the creation of data that can have relevant treatment implications for this group of patients in Mexico.}, } @article {pmid29903041, year = {2018}, author = {Zhao, L and Huang, Y and Lu, L and Yang, W and Huang, T and Lin, Z and Lin, C and Kwan, H and Wong, HLX and Chen, Y and Sun, S and Xie, X and Fang, X and Yang, H and Wang, J and Zhu, L and Bian, Z}, title = {Saturated long-chain fatty acid-producing bacteria contribute to enhanced colonic motility in rats.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {107}, pmid = {29903041}, issn = {2049-2618}, support = {FRG2/15-16/001, FRG2/16-17/003//Faculty Research Grant of Hong Kong Baptist University/International ; C2012-15G//The Research Grants Council of Hong Kong Collaborative Research Fund/International ; 2016A050503039//Guangdong-Hong Kong Technology Cooperation Funding Scheme/International ; }, mesh = {Animals ; Bacteroidetes/*metabolism ; Biodiversity ; Colon/microbiology/physiology ; Disease Models, Animal ; Dysbiosis/microbiology ; Fatty Acids/*analysis ; Fecal Microbiota Transplantation ; Gastrointestinal Microbiome ; Gastrointestinal Motility/*physiology ; Gastrointestinal Tract/microbiology ; Germ-Free Life ; Lactobacillus/*metabolism ; Maternal Deprivation ; Muscle Contraction/physiology ; Prevotella/*metabolism ; Rats ; Rats, Sprague-Dawley ; }, abstract = {BACKGROUND: The gut microbiota is closely associated with gastrointestinal (GI) motility disorder, but the mechanism(s) by which bacteria interact with and affect host GI motility remains unclear. In this study, through using metabolomic and metagenomic analyses, an animal model of neonatal maternal separation (NMS) characterized by accelerated colonic motility and gut dysbiosis was used to investigate the mechanism underlying microbiota-driven motility dysfunction.

RESULTS: An excess of intracolonic saturated long-chain fatty acids (SLCFAs) was associated with enhanced bowel motility in NMS rats. Heptadecanoic acid (C17:0) and stearic acid (C18:0), as the most abundant odd- and even-numbered carbon SLCFAs in the colon lumen, can promote rat colonic muscle contraction and increase stool frequency. Increase of SLCFAs was positively correlated with elevated abundances of Prevotella, Lactobacillus, and Alistipes. Functional annotation found that the level of bacterial LCFA biosynthesis was highly enriched in NMS group. Essential synthetic genes Fabs were largely identified from the genera Prevotella, Lactobacillus, and Alistipes. Pseudo germ-free (GF) rats receiving fecal microbiota from NMS donors exhibited increased defecation frequency and upregulated bacterial production of intracolonic SLCFAs. Modulation of gut dysbiosis by neomycin effectively attenuated GI motility and reduced bacterial SLCFA generation in the colon lumen of NMS rats.

CONCLUSIONS: These findings reveal a previously unknown relationship between gut bacteria, intracolonic SLCFAs, and host GI motility, suggesting the importance of SLCFA-producing bacteria in GI motility disorders. Further exploration of this relationship could lead to a precise medication targeting the gut microbiota for treating GI motility disorders.}, } @article {pmid29902438, year = {2018}, author = {Milshteyn, A and Colosimo, DA and Brady, SF}, title = {Accessing Bioactive Natural Products from the Human Microbiome.}, journal = {Cell host & microbe}, volume = {23}, number = {6}, pages = {725-736}, pmid = {29902438}, issn = {1934-6069}, support = {R01 AT009562/AT/NCCIH NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/metabolism ; Bacteria/genetics/metabolism ; Biological Products/*metabolism/*pharmacology ; Humans ; Indoles/metabolism ; Metabolomics ; Metagenomics ; Microbial Interactions ; Microbiota/genetics/*physiology ; Multigene Family ; Peptides, Cyclic/metabolism ; Pyrrolidonecarboxylic Acid/metabolism ; Thiazolidines/metabolism ; }, abstract = {Natural products have long played a pivotal role in the development of therapeutics for a variety of diseases. Traditionally, soil and marine environments have provided a rich reservoir from which diverse chemical scaffolds could be discovered. Recently, the human microbiome has been recognized as a promising niche from which secondary metabolites with therapeutic potential have begun to be isolated. In this Review, we address how the expansive history of identifying bacterial natural products in other environments is informing the approaches being brought to bear on the study of the human microbiota. We also touch on how these tools can lead to insights about microbe-microbe and host-microbe interactions and help generate biological hypotheses that may lead to developments of new therapeutic modalities.}, } @article {pmid29902201, year = {2018}, author = {Li, X and Naser, SA and Khaled, A and Hu, H and Li, X}, title = {When old metagenomic data meet newly sequenced genomes, a case study.}, journal = {PloS one}, volume = {13}, number = {6}, pages = {e0198773}, pmid = {29902201}, issn = {1932-6203}, support = {R15 GM123407/GM/NIGMS NIH HHS/United States ; }, mesh = {Colitis/genetics/*microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenome ; *Metagenomics ; *Whole Genome Sequencing ; }, abstract = {Dozens of computational methods are developed to identify species present in a metagenomic dataset. Many of these computational methods depend on available sequenced microbial species, which are still far from being representative. To see how newly sequenced genomes affect the analysis results, we re-analyzed a shotgun metagenomic dataset composed of twelve colitis free metagenomic samples and ten colitis-related metagenomic samples. Unexpectedly, we identified at least two new phyla that may relate to colitis development in patients, together with the phylum identified previously. Compared with the previously identified phylum that differed between the two types of samples, the differences associated with the two new phyla are statistically more significant. Moreover, the abundance of the two new phyla correlates more with the severity of colitis. Surprisingly, even by repeating the analyses implemented in the previous study, we found that at least one main conclusion in the previous study is not supported. Our study indicates the importance of re-analysis of the generated metagenomic datasets and the necessity of considering multiple updated tools in metagenomic studies. It also sheds light on the limitations of the popular tools used currently and the importance to infer the presence of taxa without relying upon available sequenced genomes.}, } @article {pmid29901277, year = {2018}, author = {Holland-Moritz, H and Stuart, J and Lewis, LR and Miller, S and Mack, MC and McDaniel, SF and Fierer, N}, title = {Novel bacterial lineages associated with boreal moss species.}, journal = {Environmental microbiology}, volume = {20}, number = {7}, pages = {2625-2638}, doi = {10.1111/1462-2920.14288}, pmid = {29901277}, issn = {1462-2920}, mesh = {Alaska ; Bacteria/classification/genetics/*isolation & purification ; Bryophyta/*microbiology ; Microbiota ; Nitrogen Fixation ; }, abstract = {Mosses are critical components of boreal ecosystems where they typically account for a large proportion of net primary productivity and harbour diverse bacterial communities that can be the major source of biologically-fixed nitrogen in these ecosystems. Despite their ecological importance, we have limited understanding of how microbial communities vary across boreal moss species and the extent to which local site conditions may influence the composition of these bacterial communities. We used marker gene sequencing to analyze bacterial communities associated with seven boreal moss species collected near Fairbanks, AK, USA. We found that host identity was more important than site in determining bacterial community composition and that mosses harbour diverse lineages of potential N2 -fixers as well as an abundance of novel taxa assigned to understudied bacterial phyla (including candidate phylum WPS-2). We performed shotgun metagenomic sequencing to assemble genomes from the WPS-2 candidate phylum and found that these moss-associated bacteria are likely anoxygenic phototrophs capable of carbon fixation via RuBisCo with an ability to utilize byproducts of photorespiration from hosts via a glyoxylate shunt. These results give new insights into the metabolic capabilities of understudied bacterial lineages that associate with mosses and the importance of plant hosts in shaping their microbiomes.}, } @article {pmid29900563, year = {2018}, author = {Coleman, M and Elkins, C and Gutting, B and Mongodin, E and Solano-Aguilar, G and Walls, I}, title = {Microbiota and Dose Response: Evolving Paradigm of Health Triangle.}, journal = {Risk analysis : an official publication of the Society for Risk Analysis}, volume = {38}, number = {10}, pages = {2013-2028}, doi = {10.1111/risa.13121}, pmid = {29900563}, issn = {1539-6924}, mesh = {Animals ; *Bacteria ; *Dysbiosis ; *Gastrointestinal Microbiome ; Genomics ; Humans ; Immunity, Innate ; Immunity, Mucosal ; Intestines/immunology/microbiology ; Mice ; Models, Biological ; Prebiotics ; Probiotics/*analysis ; Risk Assessment/*methods ; }, abstract = {SRA Dose-Response and Microbial Risk Analysis Specialty Groups jointly sponsored symposia that addressed the intersections between the "microbiome revolution" and dose response. Invited speakers presented on innovations and advances in gut and nasal microbiota (normal microbial communities) in the first decade after the Human Microbiome Project began. The microbiota and their metabolites are now known to influence health and disease directly and indirectly, through modulation of innate and adaptive immune systems and barrier function. Disruption of healthy microbiota is often associated with changes in abundance and diversity of core microbial species (dysbiosis), caused by stressors including antibiotics, chemotherapy, and disease. Nucleic-acid-based metagenomic methods demonstrated that the dysbiotic host microbiota no longer provide normal colonization resistance to pathogens, a critical component of innate immunity of the superorganism. Diverse pathogens, probiotics, and prebiotics were considered in human and animal models (in vivo and in vitro). Discussion included approaches for design of future microbial dose-response studies to account for the presence of the indigenous microbiota that provide normal colonization resistance, and the absence of the protective microbiota in dysbiosis. As NextGen risk analysis methodology advances with the "microbiome revolution," a proposed new framework, the Health Triangle, may replace the old paradigm based on the Disease Triangle (focused on host, pathogen, and environment) and germophobia. Collaborative experimental designs are needed for testing hypotheses about causality in dose-response relationships for pathogens present in our environments that clearly compete in complex ecosystems with thousands of bacterial species dominating the healthy superorganism.}, } @article {pmid29899109, year = {2018}, author = {Russo, AG and Eden, JS and Enosi Tuipulotu, D and Shi, M and Selechnik, D and Shine, R and Rollins, LA and Holmes, EC and White, PA}, title = {Viral Discovery in the Invasive Australian Cane Toad (Rhinella marina) Using Metatranscriptomic and Genomic Approaches.}, journal = {Journal of virology}, volume = {92}, number = {17}, pages = {}, pmid = {29899109}, issn = {1098-5514}, mesh = {Animals ; Bufo marinus/*virology ; Gene Expression Profiling ; Metagenomics ; Proviruses/*classification/genetics/*isolation & purification ; Viruses/*classification/genetics/*isolation & purification ; Western Australia ; }, abstract = {Cane toads are a notorious invasive species, inhabiting over 1.2 million km[2] of Australia and threatening native biodiversity. The release of pathogenic cane toad viruses is one possible biocontrol strategy yet is currently hindered by the poorly described cane toad virome. Metatranscriptomic analysis of 16 cane toad livers revealed the presence of a novel and full-length picornavirus, Rhimavirus A (RhiV-A), a member of a reptile- and amphibian-specific cluster of the Picornaviridae basal to the Kobuvirus-like group. In the combined liver transcriptome, we also identified a complete genome sequence of a distinct epsilonretrovirus, Rhinella marina endogenous retrovirus (RMERV). The recently sequenced cane toad genome contains 8 complete RMERV proviruses as well as 21 additional truncated insertions. The oldest full-length RMERV provirus was estimated to have inserted 1.9 million years ago (MYA). To screen for these viral sequences in additional toads, we analyzed publicly available transcriptomes from six diverse Australian locations. RhiV-A transcripts were identified in toads sampled from three locations across 1,000 km of Australia, stretching to the current Western Australia (WA) invasion front, while RMERV transcripts were observed at all six sites. Finally, we scanned the cane toad genome for nonretroviral endogenous viral elements, finding three sequences related to small DNA viruses in the family Circoviridae This shows ancestral circoviral infection with subsequent genomic integration. The identification of these current and past viral infections enriches our knowledge of the cane toad virome, an understanding of which will facilitate future work on infection and disease in this important invasive species.IMPORTANCE Cane toads are poisonous amphibians that were introduced to Australia in 1935 for insect control. Since then, their population has increased dramatically, and they now threaten many native Australian species. One potential method to control the population is to release a cane toad virus with high mortality rates, yet few cane toad viruses have been characterized. This study samples cane toads from different Australian locations and uses an RNA sequencing and computational approach to find new viruses. We report novel complete picornavirus and retrovirus sequences that were genetically similar to viruses infecting frogs, reptiles, and fish. Using data generated in other studies, we show that these viral sequences are present in cane toads from distinct Australian locations. Three sequences related to circoviruses were also found in the toad genome. The identification of new viral sequences will aid future studies that investigate their prevalence and potential as agents for biocontrol.}, } @article {pmid29899081, year = {2019}, author = {Aron-Wisnewsky, J and Prifti, E and Belda, E and Ichou, F and Kayser, BD and Dao, MC and Verger, EO and Hedjazi, L and Bouillot, JL and Chevallier, JM and Pons, N and Le Chatelier, E and Levenez, F and Ehrlich, SD and Dore, J and Zucker, JD and Clément, K}, title = {Major microbiota dysbiosis in severe obesity: fate after bariatric surgery.}, journal = {Gut}, volume = {68}, number = {1}, pages = {70-82}, pmid = {29899081}, issn = {1468-3288}, support = {T32 HL130357/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; *Bariatric Surgery ; Biomarkers/blood ; Chromatography, Liquid ; Comorbidity ; Dysbiosis/*etiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Mass Spectrometry ; Metagenomics ; Obesity, Morbid/*microbiology/*surgery ; Phenotype ; Prospective Studies ; Risk Factors ; }, abstract = {OBJECTIVES: Decreased gut microbial gene richness (MGR) and compositional changes are associated with adverse metabolism in overweight or moderate obesity, but lack characterisation in severe obesity. Bariatric surgery (BS) improves metabolism and inflammation in severe obesity and is associated with gut microbiota modifications. Here, we characterised severe obesity-associated dysbiosis (ie, MGR, microbiota composition and functional characteristics) and assessed whether BS would rescue these changes.

DESIGN: Sixty-one severely obese subjects, candidates for adjustable gastric banding (AGB, n=20) or Roux-en-Y-gastric bypass (RYGB, n=41), were enrolled. Twenty-four subjects were followed at 1, 3 and 12 months post-BS. Gut microbiota and serum metabolome were analysed using shotgun metagenomics and liquid chromatography mass spectrometry (LC-MS). Confirmation groups were included.

RESULTS: Low gene richness (LGC) was present in 75% of patients and correlated with increased trunk-fat mass and comorbidities (type 2 diabetes, hypertension and severity). Seventy-eight metagenomic species were altered with LGC, among which 50% were associated with adverse body composition and metabolic phenotypes. Nine serum metabolites (including glutarate, 3-methoxyphenylacetic acid and L-histidine) and functional modules containing protein families involved in their metabolism were strongly associated with low MGR. BS increased MGR 1 year postsurgery, but most RYGB patients remained with low MGR 1 year post-BS, despite greater metabolic improvement than AGB patients.

CONCLUSIONS: We identified major gut microbiota alterations in severe obesity, which include decreased MGR and related functional pathways linked with metabolic deteriorations. The lack of full rescue post-BS calls for additional strategies to improve the gut microbiota ecosystem and microbiome-host interactions in severe obesity.

TRIAL REGISTRATION NUMBER: NCT01454232.}, } @article {pmid29898983, year = {2018}, author = {Zhu, L and Yang, Z and Yao, R and Xu, L and Chen, H and Gu, X and Wu, T and Yang, X}, title = {Potential Mechanism of Detoxification of Cyanide Compounds by Gut Microbiomes of Bamboo-Eating Pandas.}, journal = {mSphere}, volume = {3}, number = {3}, pages = {}, pmid = {29898983}, issn = {2379-5042}, mesh = {Ailuridae/*microbiology/*physiology ; Animals ; Bacteria/classification/genetics/metabolism ; Biotransformation ; Cyanides/*metabolism ; *Gastrointestinal Microbiome ; Metagenomics ; Ursidae/*microbiology/*physiology ; }, abstract = {Gut microbes can enhance the ability of hosts to consume secondary plant compounds and, therefore, expand the dietary niche breadth of mammalian herbivores. The giant and red pandas are bamboo-eating specialists within the mammalian order Carnivora. Bamboo contains abundant plant secondary metabolites (e.g., cyanide-containing compounds). However, Carnivora species, including the giant panda, have deficient levels of rhodanese (one of the essential cyanide detoxification enzymes) in their tissues compared with the same tissues of herbivores. Here, we make a comparative analysis of 94 gut metagenomes, including 25 from bamboo-eating pandas (19 from giant pandas and 6 from red pandas), 30 from Père David's deer, and 39 from published data for other mammals. The bamboo-eating pandas' gut microbiomes had some common features, such as high proportions of Pseudomonas bacteria. The results revealed that bamboo-eating pandas' gut microbiomes were significantly enriched in putative genes coding for enzymes related to cyanide degradation (e.g., rhodanese) compared with the gut microbiomes of typical herbivorous mammals, which might have coevolved with their special bamboo diets. The enrichment of putative cyanide-digesting gut microbes, in combination with adaptations related to morphology (e.g., pseudothumbs) and genomic signatures, show that the giant panda and red panda have evolved some common traits to adapt to their bamboo diet.IMPORTANCE The giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens), two obligate bamboo feeders, have distinct phylogenetic positions in the order Carnivora. Bamboo is extraordinarily rich in plant secondary metabolites, such as allied phenolic and polyphenolic compounds and even toxic cyanide compounds. Here, the enrichment of putative cyanide-digesting gut microbes, in combination with adaptations related to morphology (e.g., pseudothumbs) and genomic signatures, show that the giant panda and red panda have evolved some common traits to adapt to their bamboo diet. Thus, here is another story of diet-driven gut microbiota in nature.}, } @article {pmid29898804, year = {2018}, author = {Misic, AM and Miedel, EL and Brice, AK and Cole, S and Zhang, GF and Dyer, CD and Secreto, A and Smith, AL and Danet-Desnoyers, G and Beiting, DP}, title = {Culture-independent Profiling of the Fecal Microbiome to Identify Microbial Species Associated with a Diarrheal Outbreak in Immunocompromised Mice.}, journal = {Comparative medicine}, volume = {68}, number = {4}, pages = {261-268}, pmid = {29898804}, issn = {2769-819X}, mesh = {Animals ; Diarrhea/epidemiology/*microbiology ; Disease Outbreaks ; Feces/*microbiology ; Genetic Variation ; Immunocompromised Host ; Metagenomics ; Mice ; Mice, Inbred NOD ; Mice, SCID ; Microbiota/*genetics ; RNA, Ribosomal, 16S/chemistry ; Sequence Analysis, RNA ; Whole Genome Sequencing ; }, abstract = {Immunocompromised mice are used frequently in biomedical research, in part because they accommodate the engraftment and study of primary human cells within a mouse model; however, these animals are susceptible to opportunistic infections and require special husbandry considerations. In 2015, an outbreak marked by high morbidity but low mortality swept through a colony of immunocompromised mice; this outbreak rapidly affected 75% of the colony and ultimately required complete depopulation of the barrier suite. Conventional microbiologic and molecular diagnostics were unsuccessful in determining the cause; therefore, we explored culture-independent methods to broadly profile the microbial community in the feces of affected animals. This approach identified 4 bacterial taxa- Candidatus Arthromitus, Clostridium celatum, Clostridiales bacterium VE202-01, and Bifidobacterium pseudolongum strain PV8-2- that were significantly enriched in the affected mice. Based on these results, specific changes were made to the animal husbandry procedures for immunocompromised mice. This case report highlights the utility of culture-independent methods in laboratory animal diagnostics.}, } @article {pmid29897884, year = {2018}, author = {Platzer, A and Polzin, J and Rembart, K and Han, PP and Rauer, D and Nussbaumer, T}, title = {BioSankey: Visualization of Microbial Communities Over Time.}, journal = {Journal of integrative bioinformatics}, volume = {15}, number = {4}, pages = {}, pmid = {29897884}, issn = {1613-4516}, mesh = {*Computer Graphics ; Databases, Factual ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; *Microbiota ; *Software ; }, abstract = {Metagenomics provides quantitative measurements for microbial species over time. To obtain a global overview of an experiment and to explore the full potential of a given dataset, intuitive and interactive visualization tools are needed. Therefore, we established BioSankey to visualize microbial species in microbiome studies over time as a Sankey diagram. These diagrams are embedded into a project-specific webpage which depends only on JavaScript and Google API to allow searches of interesting species without requiring a web server or connection to a database. BioSankey is a valuable tool to visualize different data elements from single or dual RNA-seq datasets and additionally enables a straightforward exchange of results among collaboration partners.}, } @article {pmid29893876, year = {2018}, author = {Algya, KM and Cross, TL and Leuck, KN and Kastner, ME and Baba, T and Lye, L and de Godoy, MRC and Swanson, KS}, title = {Apparent total-tract macronutrient digestibility, serum chemistry, urinalysis, and fecal characteristics, metabolites and microbiota of adult dogs fed extruded, mildly cooked, and raw diets1.}, journal = {Journal of animal science}, volume = {96}, number = {9}, pages = {3670-3683}, pmid = {29893876}, issn = {1525-3163}, mesh = {Ammonia/metabolism ; *Animal Feed ; Animal Nutritional Physiological Phenomena ; Animals ; *Cooking ; Diet/veterinary ; *Digestion ; *Dogs/physiology ; Feces/chemistry ; *Gastrointestinal Tract/metabolism ; Male ; Microbiota ; Nutrients ; *Raw Foods ; Urinalysis ; }, abstract = {Despite their popularity, little research has been performed on lightly cooked and raw diet formats for pets. Therefore, the objective of this study was to determine the apparent total-tract macronutrient digestibility (ATTD); fecal characteristics, metabolites, and microbiota; serum chemistry metabolites; urinalysis; and voluntary physical activity levels of adult dogs fed commercial diets differing in processing type. The diets included: 1) extruded dry kibble (EXT) diet; 2) high-moisture roasted refrigerated (RR) diet; 3) high-moisture grain-free roasted refrigerated (GFRR) diet; and 4) raw (RAW) diet. Eight dogs (mean age = 3.6; mean BW = 13.0 kg) were used in a replicated 4 × 4 Latin square design. Each period consisted of 28 d, with a 14-d adaptation phase followed by a 7-d phase for measuring voluntary physical activity, 1-d adaptation phase to metabolic cages, 5-d phase for fecal and urine collection, and 1 d for blood collection. Except for microbiota, all data were analyzed statistically by mixed models using SAS. Microbiota data were analyzed using Quantitative Insights Into Microbial Ecology (QIIME) and Statistical Analyses of Metagenomic Profiles (STAMP) software. Many differences in digestibility were observed, including greater (P < 0.05) ATTD of CP and fat in dogs fed GFRR and RR than dogs fed EXT. Dogs fed RAW had the lowest fecal pH and DM %, but fecal scores were not affected. Dogs fed RR had higher (P < 0.05) fecal indole and total phenol and indole concentrations than dogs fed the other diets. Dogs fed RAW had a higher (P < 0.05) fecal ammonia concentration than dogs fed the other diets. Fecal microbial diversity was altered by diet, with dogs fed GFRR and RAW having reduced species richness than dogs fed EXT. Dogs fed RR, GFRR, or RAW had lower (P < 0.05) Actinobacteria and higher (P < 0.05) Fusobacteria than dogs fed EXT. Dogs fed RAW or GFRR had higher (P < 0.05) Proteobacteria than dogs fed EXT or RR. Dogs fed RAW had higher (P < 0.05) Bacteroidetes and lower (P < 0.05) Firmicutes than dogs fed EXT. Serum triglycerides were within reference ranges, but greater (P < 0.05) in dogs fed EXT than dogs fed GFRR and RAW. All diets were well tolerated and dogs remained healthy throughout the study. In conclusion, the lightly cooked and raw diets tested were highly palatable, highly digestible, reduced blood triglycerides, maintained fecal quality and serum chemistry, and modified the fecal microbial community of healthy adult dogs.}, } @article {pmid29891968, year = {2018}, author = {Grey, EK and Bernatchez, L and Cassey, P and Deiner, K and Deveney, M and Howland, KL and Lacoursière-Roussel, A and Leong, SCY and Li, Y and Olds, B and Pfrender, ME and Prowse, TAA and Renshaw, MA and Lodge, DM}, title = {Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8843}, pmid = {29891968}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; DNA/*genetics/*isolation & purification ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; *Environment ; Metagenomics/*methods ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Environmental DNA (eDNA) metabarcoding can greatly enhance our understanding of global biodiversity and our ability to detect rare or cryptic species. However, sampling effort must be considered when interpreting results from these surveys. We explored how sampling effort influenced biodiversity patterns and nonindigenous species (NIS) detection in an eDNA metabarcoding survey of four commercial ports. Overall, we captured sequences from 18 metazoan phyla with minimal differences in taxonomic coverage between 18 S and COI primer sets. While community dissimilarity patterns were consistent across primers and sampling effort, richness patterns were not, suggesting that richness estimates are extremely sensitive to primer choice and sampling effort. The survey detected 64 potential NIS, with COI identifying more known NIS from port checklists but 18 S identifying more operational taxonomic units shared between three or more ports that represent un-recorded potential NIS. Overall, we conclude that eDNA metabarcoding surveys can reveal global similarity patterns among ports across a broad array of taxa and can also detect potential NIS in these key habitats. However, richness estimates and species assignments require caution. Based on results of this study, we make several recommendations for port eDNA sampling design and suggest several areas for future research.}, } @article {pmid29890228, year = {2018}, author = {Poussin, C and Sierro, N and Boué, S and Battey, J and Scotti, E and Belcastro, V and Peitsch, MC and Ivanov, NV and Hoeng, J}, title = {Interrogating the microbiome: experimental and computational considerations in support of study reproducibility.}, journal = {Drug discovery today}, volume = {23}, number = {9}, pages = {1644-1657}, doi = {10.1016/j.drudis.2018.06.005}, pmid = {29890228}, issn = {1878-5832}, mesh = {Animals ; Computational Biology/*methods ; Crowdsourcing ; Data Accuracy ; Humans ; *Metagenome/genetics ; Metagenomics/*methods ; *Microbiota/genetics ; Reproducibility of Results ; *Research Design ; Workflow ; }, abstract = {The microbiome is an important factor in human health and disease and is investigated to develop novel therapeutics. Metagenomics leverages advances in sequencing technologies and computational analysis to identify and quantify the microorganisms present in a sample. This field has, however, not yet reached maturity and the international metagenomics community, aware of the current limitations and of the necessity for standardization, has started investigating sources of variability in experimental and computational workflows. The first studies have already resulted in the identification of crucial steps and factors affecting metagenomics data quality, quantification and interpretation. This review summarizes experimental and computational considerations for interrogating the microbiome and establishing reproducible and robust analysis workflows.}, } @article {pmid29888871, year = {2018}, author = {Wen, ZT and Scott-Anne, K and Liao, S and De, A and Luo, M and Kovacs, C and Narvaez, BS and Faustoferri, RC and Yu, Q and Taylor, CM and Quivey, RG}, title = {Deficiency of BrpA in Streptococcus mutans reduces virulence in rat caries model.}, journal = {Molecular oral microbiology}, volume = {33}, number = {5}, pages = {353-363}, pmid = {29888871}, issn = {2041-1014}, support = {R01 DE013683/DE/NIDCR NIH HHS/United States ; R01 DE019452/DE/NIDCR NIH HHS/United States ; T90 DE021985/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/*genetics ; Biofilms/*growth & development ; Dental Caries/*microbiology ; Dental Plaque/microbiology ; Disease Models, Animal ; Gene Expression Regulation, Bacterial ; Microbiota ; Mutation ; Rats ; Rats, Sprague-Dawley ; Streptococcus mutans/*genetics/*pathogenicity ; Virulence ; }, abstract = {Our recent studies have shown that BrpA in Streptococcus mutans plays a critical role in cell envelope biogenesis, stress responses, and biofilm formation. In this study, a 10-species consortium was used to assess how BrpA deficiency influences the establishment, persistence, and competitiveness of S. mutans during growth in a community under conditions typical of the oral cavity. Results showed that, like the wild-type, the brpA mutant was able to colonize and establish on the surfaces tested. Relative to the wild-type, however, the brpA mutant had a reduced ability to persist and grow in the 10-species consortium (P < .001). A rat caries model was also used to examine the effect of BrpA, as well as Psr, a BrpA paralog, on S. mutans cariogenicity. The results showed no major differences in infectivity between the wild-type and the brpA and psr mutants. Unlike the wild-type, however, infection with the brpA mutant, but not the psr mutant, showed no significant differences in both total numbers of carious lesions and caries severity, compared with the control group that received bacterial growth medium (P > .05). Metagenomic and quantitative polymerase chain reaction analysis showed that S. mutans infection caused major alterations in the composition of the rats' plaque microbiota and that significantly less S. mutans was identified in the rats infected with the brpA mutant compared with those infected with the wild-type and the psr mutant. These results further suggest that BrpA plays a critical role in S. mutans pathophysiology and that BrpA has potential as a therapeutic target in the modulation of S. mutans virulence.}, } @article {pmid29885225, year = {2017}, author = {Chase, MA and Stankowski, S and Streisfeld, MA}, title = {Genomewide variation provides insight into evolutionary relationships in a monkeyflower species complex (Mimulus sect. Diplacus).}, journal = {American journal of botany}, volume = {104}, number = {10}, pages = {1510-1521}, doi = {10.3732/ajb.1700234}, pmid = {29885225}, issn = {1537-2197}, mesh = {Biological Evolution ; *Gene Flow ; *Genetics, Population ; Genome, Plant/*genetics ; Hybridization, Genetic ; *Metagenomics ; Mimulus/*genetics ; Phylogeny ; }, abstract = {PREMISE OF THE STUDY: Evolutionary radiations provide excellent opportunities to study the origins of biodiversity, but rapid divergence and ongoing gene flow make inferring evolutionary relationships among taxa difficult. Consequently, combining morphological and genomic analyses will be necessary to clarify the evolutionary history of radiations. We used an integrative approach to shed light on relationships within a diverse radiation of monkeyflowers (Mimulus section Diplacus) with a controversial taxonomic history.

METHODS: We used genomewide single nucleotide polymorphism data and a combination of phylogenetic and population genomic analyses to infer the evolutionary relationships within the group. Tests for hybridization were performed to reveal sources of shared variation, and multivariate analyses of floral trait data were conducted to examine the correspondence between phenotypic and phylogenetic data.

KEY RESULTS: We identified four primary clades with evidence for some shared variation among them. We also detected evidence for recent gene flow between closely related subclades and populations. Strong discordance between floral trait and molecular data provides evidence for divergent and convergent phenotypic evolution.

CONCLUSIONS: Mimulus section Diplacus has all the hallmarks of a rapid radiation, including diverse taxa that are at different stages of divergence, extensive shared variation among taxa, and complex patterns of phenotypic evolution. Our findings will direct future evolutionary research and have important taxonomic implications that highlight the need for a new revision of section Diplacus.}, } @article {pmid29884754, year = {2018}, author = {Lugli, GA and Mancino, W and Milani, C and Duranti, S and Turroni, F and van Sinderen, D and Ventura, M}, title = {Reconstruction of the Bifidobacterial Pan-Secretome Reveals the Network of Extracellular Interactions between Bifidobacteria and the Infant Gut.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {16}, pages = {}, pmid = {29884754}, issn = {1098-5336}, mesh = {Bifidobacterium/*genetics/*metabolism ; Bifidobacterium longum/genetics/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Glycomics ; Humans ; Infant ; Intestines/*microbiology ; *Metabolome ; Metagenome ; Milk, Human/metabolism ; Oligosaccharides/metabolism ; Proteome ; Symbiosis ; }, abstract = {The repertoire of secreted proteins decoded by a microorganism represents proteins released from or associated with the cell surface. In gut commensals, such as bifidobacteria, these proteins are perceived to be functionally relevant, as they regulate the interaction with the gut environment. In the current study, we screened the predicted proteome of over 300 bifidobacterial strains among the currently recognized bifidobacterial species to generate a comprehensive database encompassing bifidobacterial extracellular proteins. A glycobiome analysis of this predicted bifidobacterial secretome revealed that a correlation exists between particular bifidobacterial species and their capability to hydrolyze human milk oligosaccharides (HMOs) and intestinal glycoconjugates, such as mucin. Furthermore, an exploration of metatranscriptomic data sets of the infant gut microbiota allowed the evaluation of the expression of bifidobacterial genes encoding extracellular proteins, represented by ABC transporter substrate-binding proteins and glycoside hydrolases enzymes involved in the degradation of human milk oligosaccharides and mucin. Overall, this study provides insights into how bifidobacteria interact with their natural yet highly complex environment, the infant gut.IMPORTANCE The ecological success of bifidobacteria relies on the activity of extracellular proteins that are involved in the metabolism of nutrients and the interaction with the environment. To date, information on secreted proteins encoded by bifidobacteria is incomplete and just related to few species. In this study, we reconstructed the bifidobacterial pan-secretome, revealing extracellular proteins that modulate the interaction of bifidobacteria with their natural environment. Furthermore, a survey of the secretion systems between bifidobacterial genomes allowed the identification of a conserved Sec-dependent secretion machinery in all the analyzed genomes and the Tat protein translocation system in the chromosomes of 23 strains belonging to Bifidobacterium longum subsp. longum and Bifidobacterium aesculapii.}, } @article {pmid29882154, year = {2019}, author = {Kerfahi, D and Tripathi, BM and Dong, K and Kim, M and Kim, H and Ferry Slik, JW and Go, R and Adams, JM}, title = {From the High Arctic to the Equator: Do Soil Metagenomes Differ According to Our Expectations?.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {168-185}, pmid = {29882154}, issn = {1432-184X}, support = {0409-20140091//Korea Polar Research Institute/ ; NRF-0409-20150076//National Research Foundation of Korea/ ; }, mesh = {Arctic Regions ; Bacteria/genetics/metabolism ; Biodiversity ; Biota/*genetics/*physiology ; Brunei ; Canada ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; DNA Barcoding, Taxonomic ; Ecosystem ; Eukaryota/genetics/metabolism ; Greenland ; Hydrogen-Ion Concentration ; Malaysia ; Metabolic Networks and Pathways/genetics ; Metagenome/*genetics/*physiology ; Metagenomics/methods ; Microbiota/genetics/physiology ; Rainforest ; Secondary Metabolism/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; Stress, Physiological ; Svalbard ; }, abstract = {Comparing the functional gene composition of soils at opposite extremes of environmental gradients may allow testing of hypotheses about community and ecosystem function. Here, we were interested in comparing how tropical microbial ecosystems differ from those of polar climates. We sampled several sites in the equatorial rainforest of Malaysia and Brunei, and the high Arctic of Svalbard, Canada, and Greenland, comparing the composition and the functional attributes of soil biota between the two extremes of latitude, using shotgun metagenomic Illumina HiSeq2000 sequencing. Based upon "classical" views of how tropical and higher latitude ecosystems differ, we made a series of predictions as to how various gene function categories would differ in relative abundance between tropical and polar environments. Results showed that in some respects our predictions were correct: the polar samples had higher relative abundance of dormancy related genes, and lower relative abundance of genes associated with respiration, and with metabolism of aromatic compounds. The network complexity of the Arctic was also lower than the tropics. However, in various other respects, the pattern was not as predicted; there were no differences in relative abundance of stress response genes or in genes associated with secondary metabolism. Conversely, CRISPR genes, phage-related genes, and virulence disease and defense genes, were unexpectedly more abundant in the Arctic, suggesting more intense biotic interaction. Also, eukaryote diversity and bacterial diversity were higher in the Arctic of Svalbard compared to tropical Brunei, which is consistent with what may expected from amplicon studies in terms of the higher pH of the Svalbard soil. Our results in some respects confirm expectations of how tropical versus polar nature may differ, and in other respects challenge them.}, } @article {pmid29878200, year = {2018}, author = {Lee, FJ and Miller, KI and McKinlay, JB and Newton, ILG}, title = {Differential carbohydrate utilization and organic acid production by honey bee symbionts.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {8}, pages = {}, doi = {10.1093/femsec/fiy113}, pmid = {29878200}, issn = {1574-6941}, mesh = {Acetates/metabolism ; Animals ; Bacteria/genetics/*metabolism ; Bees/*microbiology ; Carbohydrate Metabolism/*physiology ; Carbohydrates ; Fatty Acids, Volatile/biosynthesis/*metabolism ; Gastrointestinal Microbiome/genetics/*physiology ; Lactic Acid/metabolism ; Metagenome ; Symbiosis/physiology ; }, abstract = {The honey bee worker gut hosts a community of bacteria that comprises 8-10 core bacterial species, along with a set of more transient environmental microbes. Collectively, these microbes break down and ferment saccharides present in the host's diet, based on analyses of metagenomes, and metatranscriptomes from this environment. As part of this metabolism, the bacteria produce short-chain fatty acids that may serve as a food source for the host bee, stimulating biological processes that may contribute to host weight gain. To identify metabolic contributions of symbionts within the honey bee gut, we utilized a combination of molecular and biochemical approaches. We show significant variation in the metabolic capabilities of honey bee-associated taxa, highlighting the fact that honey bee gut microbiota members of the same clade are highly variable in their ability to use specific carbohydrates and produce organic acids. Finally, we confirm that the honey bee core microbes are active in vivo, expressing key enzymatic genes critical for utilizing plant-derived molecules and producing organic acids (i.e. acetate and lactate). These results suggest that core taxa may contribute significantly to weight gain in the honey bee, specifically through the production of organic acids.}, } @article {pmid29877042, year = {2018}, author = {Schnell, IB and Bohmann, K and Schultze, SE and Richter, SR and Murray, DC and Sinding, MS and Bass, D and Cadle, JE and Campbell, MJ and Dolch, R and Edwards, DP and Gray, TNE and Hansen, T and Hoa, ANQ and Noer, CL and Heise-Pavlov, S and Sander Pedersen, AF and Ramamonjisoa, JC and Siddall, ME and Tilker, A and Traeholt, C and Wilkinson, N and Woodcock, P and Yu, DW and Bertelsen, MF and Bunce, M and Gilbert, MTP}, title = {Debugging diversity - a pan-continental exploration of the potential of terrestrial blood-feeding leeches as a vertebrate monitoring tool.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1282-1298}, doi = {10.1111/1755-0998.12912}, pmid = {29877042}, issn = {1755-0998}, support = {DNRF94//Danish National Research Foundation/ ; //University of Copenhagen/ ; FT0991741//Australian Research Council Future Fellowship/ ; //KfW Bankengruppe/ ; //WWF Germany/ ; DFF-5051-00140//The Danish Council for Independent Research/ ; 31400470//National Natural Science Foundation of China/ ; 41661144002//National Natural Science Foundation of China/ ; 2012FY110800//Ministry of Science and Technology of China/ ; GREKF13-13//State Key Laboratory of Genetic Resources and Evolution at the Kunming Institute of Zoology/ ; GREKF14-13//State Key Laboratory of Genetic Resources and Evolution at the Kunming Institute of Zoology/ ; GREKF16-09//State Key Laboratory of Genetic Resources and Evolution at the Kunming Institute of Zoology/ ; }, mesh = {Amphibians/parasitology ; Animals ; Birds/parasitology ; Blood Chemical Analysis/*methods ; DNA Barcoding, Taxonomic/*methods ; Environmental Monitoring/*methods ; High-Throughput Nucleotide Sequencing/methods ; Leeches/*growth & development ; Mammals/parasitology ; Metagenomics/*methods ; Reptiles/parasitology ; }, abstract = {The use of environmental DNA (eDNA) has become an applicable noninvasive tool with which to obtain information about biodiversity. A subdiscipline of eDNA is iDNA (invertebrate-derived DNA), where genetic material ingested by invertebrates is used to characterize the biodiversity of the species that served as hosts. While promising, these techniques are still in their infancy, as they have only been explored on limited numbers of samples from only a single or a few different locations. In this study, we investigate the suitability of iDNA extracted from more than 3,000 haematophagous terrestrial leeches as a tool for detecting a wide range of terrestrial vertebrates across five different geographical regions on three different continents. These regions cover almost the full geographical range of haematophagous terrestrial leeches, thus representing all parts of the world where this method might apply. We identify host taxa through metabarcoding coupled with high-throughput sequencing on Illumina and IonTorrent sequencing platforms to decrease economic costs and workload and thereby make the approach attractive for practitioners in conservation management. We identified hosts in four different taxonomic vertebrate classes: mammals, birds, reptiles and amphibians, belonging to at least 42 different taxonomic families. We find that vertebrate blood ingested by haematophagous terrestrial leeches throughout their distribution is a viable source of DNA with which to examine a wide range of vertebrates. Thus, this study provides encouraging support for the potential of haematophagous terrestrial leeches as a tool for detecting and monitoring terrestrial vertebrate biodiversity.}, } @article {pmid29874232, year = {2018}, author = {Higashi, K and Suzuki, S and Kurosawa, S and Mori, H and Kurokawa, K}, title = {Latent environment allocation of microbial community data.}, journal = {PLoS computational biology}, volume = {14}, number = {6}, pages = {e1006143}, pmid = {29874232}, issn = {1553-7358}, mesh = {Computational Biology/*methods ; Databases, Genetic ; Environmental Microbiology ; Humans ; Metagenomics ; *Microbiota/genetics/physiology ; Models, Statistical ; Rivers/microbiology ; }, abstract = {As data for microbial community structures found in various environments has increased, studies have examined the relationship between environmental labels given to retrieved microbial samples and their community structures. However, because environments continuously change over time and space, mixed states of some environments and its effects on community formation should be considered, instead of evaluating effects of discrete environmental categories. Here we applied a hierarchical Bayesian model to paired datasets containing more than 30,000 samples of microbial community structures and sample description documents. From the training results, we extracted latent environmental topics that associate co-occurring microbes with co-occurring word sets among samples. Topics are the core elements of environmental mixtures and the visualization of topic-based samples clarifies the connections of various environments. Based on the model training results, we developed a web application, LEA (Latent Environment Allocation), which provides the way to evaluate typicality and heterogeneity of microbial communities in newly obtained samples without confining environmental categories to be compared. Because topics link words and microbes, LEA also enables to search samples semantically related to the query out of 30,000 microbiome samples.}, } @article {pmid29872163, year = {2018}, author = {Zhu, Y and Zhang, F and Zhang, C and Yang, L and Fan, G and Xu, Y and Sun, B and Li, X}, title = {Dynamic microbial succession of Shanxi aged vinegar and its correlation with flavor metabolites during different stages of acetic acid fermentation.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8612}, pmid = {29872163}, issn = {2045-2322}, mesh = {Acetic Acid/*metabolism ; Bacteria/*classification/*metabolism ; *Biota ; Fermentation ; *Food Microbiology ; High-Throughput Nucleotide Sequencing ; Metabolomics ; Metagenomics ; Volatile Organic Compounds/metabolism ; }, abstract = {Shanxi aged vinegar (SAV), one of the famous Chinese vinegars, is produced by multispecies solid-state fermentation in which the acetic acid fermentation stage (AAF) is especially important. However, how bacterial succession and their metabolites change along with the different stages of AAF is still poorly understood. In this study, we investigated the dynamic bacterial succession and flavor formation in three batches of SAV using high-throughput sequencing and metabolomics approaches. It is interesting to find that AAF can be divided into three stages based on its bacterial community succession (early stage, days 0-4; medium stage, days 5-21; and later stage, days 22-26). Pantoea, Pediococcus, Lactococcus and Rhizobium played an important role in the early stage; Lactobacillus was dominant in the medium stage (67.72%); and Acetobacter, Komagataeibacter and Kroppenstedtia were the key bacteria in the later stage. A total of seven organic acids and 42 volatile constituents (esters, alcohol, ketones and aldehydes) were detected during the AAF. Spearman correlation analysis showed a significant correlation between the bacterial community and these flavor metabolites during the AAF of the SAV. This is the first report to explore the relationships between volatile flavor metabolites and bacterial community succession by a three-staged method and provide theoretical support for a flavor formation mechanism in traditional SAV.}, } @article {pmid29872090, year = {2018}, author = {Paul, F and Otte, J and Schmitt, I and Dal Grande, F}, title = {Comparing Sanger sequencing and high-throughput metabarcoding for inferring photobiont diversity in lichens.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8624}, pmid = {29872090}, issn = {2045-2322}, mesh = {Ascomycota/growth & development ; Chlorophyta/*classification/*genetics/growth & development ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Lichens/*growth & development ; Metagenomics/*methods ; Sequence Analysis, DNA/*methods ; Symbiosis ; }, abstract = {The implementation of HTS (high-throughput sequencing) approaches is rapidly changing our understanding of the lichen symbiosis, by uncovering high bacterial and fungal diversity, which is often host-specific. Recently, HTS methods revealed the presence of multiple photobionts inside a single thallus in several lichen species. This differs from Sanger technology, which typically yields a single, unambiguous algal sequence per individual. Here we compared HTS and Sanger methods for estimating the diversity of green algal symbionts within lichen thalli using 240 lichen individuals belonging to two species of lichen-forming fungi. According to HTS data, Sanger technology consistently yielded the most abundant photobiont sequence in the sample. However, if the second most abundant photobiont exceeded 30% of the total HTS reads in a sample, Sanger sequencing generally failed. Our results suggest that most lichen individuals in the two analyzed species, Lasallia hispanica and L. pustulata, indeed contain a single, predominant green algal photobiont. We conclude that Sanger sequencing is a valid approach to detect the dominant photobionts in lichen individuals and populations. We discuss which research areas in lichen ecology and evolution will continue to benefit from Sanger sequencing, and which areas will profit from HTS approaches to assessing symbiont diversity.}, } @article {pmid29871482, year = {2018}, author = {Reed, S and Knez, M and Uzan, A and Stangoulis, JCR and Glahn, RP and Koren, O and Tako, E}, title = {Alterations in the Gut (Gallus gallus) Microbiota Following the Consumption of Zinc Biofortified Wheat (Triticum aestivum)-Based Diet.}, journal = {Journal of agricultural and food chemistry}, volume = {66}, number = {25}, pages = {6291-6299}, doi = {10.1021/acs.jafc.8b01481}, pmid = {29871482}, issn = {1520-5118}, mesh = {Animal Feed/*analysis ; Animals ; Cecum/metabolism/microbiology ; Chickens/*metabolism/microbiology ; Female ; Food, Fortified/*analysis ; *Gastrointestinal Microbiome ; Male ; Triticum/chemistry/*metabolism ; Zinc/analysis/*metabolism ; }, abstract = {The structure and function of cecal microbiota following the consumption of a zinc (Zn) biofortified wheat diet was evaluated in a well-studied animal model of human nutrition (Gallus gallus) during a six-week efficacy trial. Using 16S rRNA gene sequencing, a significant increase in β- but not α-microbial diversity was observed in the animals receiving the Zn biofortified wheat diet, relative to the control. No significant taxonomic differences were found between the two groups. Linear discriminant analysis revealed a group of metagenomic biomarkers that delineated the Zn replete versus Zn deficient phenotypes, such that enrichment of lactic acid bacteria and concomitant increases in Zn-dependent bacterial metabolic pathways were observed in the Zn biofortified group, and expansion of mucin-degraders and specific bacterial groups able to participate in maintaining host Zn homeostasis were observed in the control group. Additionally, the Ruminococcus genus appeared to be a key player in delineating the Zn replete microbiota from the control group, as it strongly predicts host Zn adequacy. Our data demonstrate that the gut microbiome associated with Zn biofortified wheat ingestion is unique and may influence host Zn status. Microbiota analysis in biofortification trials represents a crucial area for study as Zn biofortified diets are increasingly delivered on a population-wide scale.}, } @article {pmid29870921, year = {2018}, author = {Zou, Y and Lin, M and Xiong, W and Wang, M and Zhang, J and Wang, M and Sun, Y}, title = {Metagenomic insights into the effect of oxytetracycline on microbial structures, functions and functional genes in sediment denitrification.}, journal = {Ecotoxicology and environmental safety}, volume = {161}, number = {}, pages = {85-91}, doi = {10.1016/j.ecoenv.2018.05.045}, pmid = {29870921}, issn = {1090-2414}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics/growth & development/metabolism ; Bacterial Proteins/metabolism ; Bradyrhizobium ; *Denitrification ; Farms ; Genes, Bacterial ; Geologic Sediments ; Metagenomics ; Microbiota ; Nitrate Reductase/metabolism ; Nitrite Reductases/metabolism ; Nitrogen/*metabolism ; Nitrous Oxide/metabolism ; Oxytetracycline/*pharmacology ; Ponds ; Proteobacteria/metabolism ; Pseudomonas ; Sewage ; Water Microbiology ; Water Pollutants, Chemical/metabolism/*pharmacology ; }, abstract = {Denitrification is an indispensable pathway of nitrogen removal in aquatic ecosystems, and plays an important role in decreasing eutrophication induced by excessive reactive nitrogen pollution. Aquatic environments also suffer from antibiotic pollution due to runoff from farms and sewage systems. The aim of this study was to investigate the effect of oxytetracycline stress on denitrifying functional genes, the microbial community and metabolic pathways in sediments using high-throughput sequencing and metagenomic analysis. The oxytetracycline was observed to significantly inhibit the abundance of nirK and nosZ genes (P < 0.001). KEGG pathway annotation indicated that oxytetracycline treatment decreased the abundance of nitrate reductase, nitrite reductase and N2O reductase. Functional annotations revealed that oxytetracycline exposure decreased the abundance of the protein metabolism subsystem in the bacterial community. Metagenomic sequencing demonstrated that the abundance of Proteobacteria and Firmicutes increased with oxytetracycline exposure while the Actinobacteria decreased. In sediments, Pseudomonas and Bradyrhizobium were major contributors to denitrification and oxytetracycline exposure resulted in a decreased abundance of Bradyrhizobium. These results indicated that oxytetracycline residues influences the denitrifier community and may heighten occurrence of reactive nitrogen in aquatic ecosystems.}, } @article {pmid29868024, year = {2018}, author = {Chen, B and Ni, X and Sun, R and Zeng, B and Wei, H and Tian, Z and Wei, H}, title = {Commensal Bacteria-Dependent CD8αβ[+] T Cells in the Intestinal Epithelium Produce Antimicrobial Peptides.}, journal = {Frontiers in immunology}, volume = {9}, number = {}, pages = {1065}, pmid = {29868024}, issn = {1664-3224}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Antimicrobial Cationic Peptides/*biosynthesis ; CD8 Antigens/*immunology ; CD8-Positive T-Lymphocytes/*immunology/metabolism ; Gastrointestinal Microbiome/drug effects/*immunology ; Intestinal Mucosa/*immunology/*metabolism/microbiology ; Lymphocyte Count ; Metagenome ; Metagenomics/methods ; Mice ; Mice, Transgenic ; Toll-Like Receptors/metabolism ; }, abstract = {The epithelium of the intestine functions as the primary "frontline" physical barrier for protection from enteric microbiota. Intraepithelial lymphocytes (IELs) distributed along the intestinal epithelium are predominantly CD8[+] T cells, among which CD8αβ[+] IELs are a large population. In this investigation, the proportion and absolute number of CD8αβ[+] IELs decreased significantly in antibiotic-treated and germ-free mice. Moreover, the number of CD8αβ[+] IELs was correlated closely with the load of commensal microbes, and induced by specific members of commensal bacteria. Microarray analysis revealed that CD8αβ[+] IELs expressed a series of genes encoding potent antimicrobial peptides (AMPs), whereas CD8αβ[+] splenocytes did not. The antimicrobial activity of CD8αβ[+] IELs was confirmed by an antimicrobial-activity assay. In conclusion, microbicidal CD8αβ[+] IELs are regulated by commensal bacteria which, in turn, secrete AMPs that have a vital role in maintaining the homeostasis of the small intestine.}, } @article {pmid29866485, year = {2018}, author = {Garin-Fernandez, A and Pereira-Flores, E and Glöckner, FO and Wichels, A}, title = {The North Sea goes viral: Occurrence and distribution of North Sea bacteriophages.}, journal = {Marine genomics}, volume = {41}, number = {}, pages = {31-41}, doi = {10.1016/j.margen.2018.05.004}, pmid = {29866485}, issn = {1876-7478}, mesh = {Bacteriophages/classification/*physiology ; *Biodiversity ; Metagenomics ; North Sea ; Water Movements ; }, abstract = {Marine viruses are dominated by phages and have an enormous influence on microbial population dynamics, due to lysis and horizontal gene transfer. The aim of this study is to analyze the occurrence and diversity of phages in the North Sea, considering the virus-host interactions and biogeographic factors. The virus community of four sampling stations were described using virus metagenomics (viromes). The results show that the virus community was not evenly distributed throughout the North Sea. The dominant phage members were identified as unclassified phage group, followed by Caudovirales order. Myoviridae was the dominant phage family in the North Sea, which occurrence decreased from the coast to the open sea. In contrast, the occurrence of Podoviridae increased and the occurrence of Siphoviridae was low throughout the North Sea. The occurrence of other groups such as Phycodnaviridae decreased from the coast to the open sea. The coastal virus community was genetically more diverse than the open sea community. The influence of riverine inflow and currents, for instance the English Channel flow affects the genetic virus diversity with the community carrying genes from a variety of metabolic pathways and other functions. The present study offers the first insights in the virus community in the North Sea using viromes and shows the variation in virus diversity and the genetic information moved from coastal to open sea areas.}, } @article {pmid29862448, year = {2018}, author = {Li, H and Qu, J and Li, T and Wirth, S and Zhang, Y and Zhao, X and Li, X}, title = {Diet simplification selects for high gut microbial diversity and strong fermenting ability in high-altitude pikas.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {15}, pages = {6739-6751}, doi = {10.1007/s00253-018-9097-z}, pmid = {29862448}, issn = {1432-0614}, mesh = {Altitude ; Animals ; China ; *Diet ; *Fermentation ; Gastrointestinal Microbiome/*physiology ; Lagomorpha/*microbiology/*physiology ; Tibet ; }, abstract = {The gut microbiota in mammals plays a key role in host metabolism and adaptation. However, relatively little is known regarding to how the animals adapts to extreme environments through regulating gut microbial diversity and function. Here, we investigated the diet, gut microbiota, short-chain fatty acid (SCFA) profiles, and cellulolytic activity from two common pika (Ochotona spp.) species in China, including Plateau pika (Ochotona curzoniae) from the Qinghai-Tibet Plateau and Daurian pika (Ochotona daurica) from the Inner Mongolia Grassland. Despite a partial diet overlap, Plateau pikas harbored lower diet diversity than Daurian pikas. Some bacteria (e.g., Prevotella and Ruminococcus) associated with fiber degradation were enriched in Plateau pikas. They harbored higher gut microbial diversity, total SCFA concentration, and cellulolytic activity than Daurian pikas. Interestingly, cellulolytic activity was positively correlated with the gut microbial diversity and SCFAs. Gut microbial communities and SCFA profiles were segregated structurally between host species. PICRUSt metagenome predictions demonstrated that microbial genes involved in carbohydrate metabolism and energy metabolism were overrepresented in the gut microbiota of Plateau pikas. Our results demonstrate that Plateau pikas harbor a stronger fermenting ability for the plant-based diet than Daurian pikas via gut microbial fermentation. The enhanced ability for utilization of plant-based diets in Plateau pikas may be partly a kind of microbiota adaptation for more energy requirements in cold and hypoxic high-altitude environments.}, } @article {pmid29860637, year = {2019}, author = {Torres, PJ and Thompson, J and McLean, JS and Kelley, ST and Edlund, A}, title = {Discovery of a Novel Periodontal Disease-Associated Bacterium.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {267-276}, pmid = {29860637}, issn = {1432-184X}, support = {R00 DE024543/DE/NIDCR NIH HHS/United States ; U26IHS300292/NH/NIH HHS/United States ; }, mesh = {Alaska Natives ; Bacteroidetes/*classification/genetics/*isolation & purification/*pathogenicity ; California ; Dental Plaque/microbiology ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; Humans ; Indians, North American ; Metagenomics ; Microbiota ; Multigene Family ; Periodontal Diseases/*microbiology ; Periodontitis/microbiology ; *Phylogeny ; Sequence Analysis, DNA ; Virulence Factors/genetics ; }, abstract = {One of the world's most common infectious disease, periodontitis (PD), derives from largely uncharacterized communities of oral bacteria growing as biofilms (a.k.a. plaque) on teeth and gum surfaces in periodontal pockets. Bacteria associated with periodontal disease trigger inflammatory responses in immune cells, which in later stages of the disease cause loss of both soft and hard tissue structures supporting teeth. Thus far, only a handful of bacteria have been characterized as infectious agents of PD. Although deep sequencing technologies, such as whole community shotgun sequencing have the potential to capture a detailed picture of highly complex bacterial communities in any given environment, we still lack major reference genomes for the oral microbiome associated with PD and other diseases. In recent work, by using a combination of supervised machine learning and genome assembly, we identified a genome from a novel member of the Bacteroidetes phylum in periodontal samples. Here, by applying a comparative metagenomics read-classification approach, including 272 metagenomes from various human body sites, and our previously assembled draft genome of the uncultivated Candidatus Bacteroides periocalifornicus (CBP) bacterium, we show CBP's ubiquitous distribution in dental plaque, as well as its strong association with the well-known pathogenic "red complex" that resides in deep periodontal pockets.}, } @article {pmid29858829, year = {2018}, author = {Gupta, SK and Shin, H and Han, D and Hur, HG and Unno, T}, title = {Metagenomic analysis reveals the prevalence and persistence of antibiotic- and heavy metal-resistance genes in wastewater treatment plant.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {56}, number = {6}, pages = {408-415}, pmid = {29858829}, issn = {1976-3794}, mesh = {Anti-Bacterial Agents/*toxicity ; Bacteria/*classification/drug effects/*genetics/isolation & purification ; DNA, Bacterial/genetics ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Metals, Heavy/*toxicity ; Microbial Consortia/genetics ; Phylogeny ; Republic of Korea ; Sequence Analysis ; Sewage/microbiology ; Wastewater/*microbiology ; Water Purification ; }, abstract = {The increased antibiotic resistance among microorganisms has resulted into growing interest for investigating the wastewater treatment plants (WWTPs) as they are reported to be the major source in the dissemination of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in the environment. In this study, we investigated the prevalence and persistence of ARGs and HMRGs as well as bacterial diversity and mobile genetic elements (MGEs) in influent and effluent at the WWTP in Gwangju, South Korea, using high-throughput sequencing based metagenomic approach. A good number of broad-spectrum of resistance genes (both ARG and HMRG) were prevalent and likely persistent, although large portion of them were successfully removed at the wastewater treatment process. The relative abundance of ARGs and MGEs was higher in effluent as compared to that of influent. Our results suggest that the resistance genes with high abundance and bacteria harbouring ARGs and MGEs are likely to persist more through the treatment process. On analyzing the microbial community, the phylum Proteobacteria, especially potentially pathogenic species belonging to the genus Acinetobacter, dominated in WWTP. Overall, our study demonstrates that many ARGs and HMRGs may persist the treatment processes in WWTPs and their association to MGEs may contribute to the dissemination of resistance genes among microorganisms in the environment.}, } @article {pmid29852249, year = {2018}, author = {Jin, J and Guo, L and VonTungeln, L and Vanlandingham, M and Cerniglia, CE and Chen, H}, title = {Smokeless tobacco impacts oral microbiota in a Syrian Golden hamster cheek pouch carcinogenesis model.}, journal = {Anaerobe}, volume = {52}, number = {}, pages = {29-42}, pmid = {29852249}, issn = {1095-8274}, support = {FD999999//Intramural FDA HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Carcinogenesis/*drug effects ; Cricetinae ; DNA, Bacterial/genetics ; Disease Models, Animal ; Humans ; Male ; Mesocricetus ; Microbiota/*drug effects ; Mouth/*microbiology ; Mouth Neoplasms/*etiology/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Tobacco, Smokeless/*adverse effects ; }, abstract = {The use of smokeless tobacco products (STPs) can cause many serious health problems. The oral microbiota plays important roles in oral and systemic health, and the disruption in the oral microbial population is linked to periodontal disease and other health problems. To assess the impact of smokeless tobacco on oral microbiota in vivo, high-throughput sequencing was used to examine the oral microbiota present in Syrian Golden hamster cheek pouches. Sixteen hamsters were divided into four groups and treated with the STP Grizzly snuff (0, 2.5, 25, or 250 mg) twice daily for 4 weeks. After 0, 1, 2, 3, and 4 weeks of treatment, bacterial genomic DNA was extracted from oral swabs sampled from the cheek pouches of the hamsters. The oral bacterial communities present in different hamster groups were characterized by sequencing the hypervariable regions V1-V2 and V4 of 16S rRNA using the Illumina MiSeq platform. Fifteen phyla, 27 classes, 59 orders, 123 families, and 250 genera were identified from 4,962,673 sequence reads from the cheek pouch samples. The bacterial diversity and taxonomic abundances for the different treatment groups were compared to the non-treated hamsters. Bacterial diversity was significantly decreased after 4 weeks of exposure to 2.5 mg, and significantly increased by exposure to 250 mg STP. Treatment with 250 mg STP significantly increased Firmicutes, transiently increased Cyanobacteria and TM7, and decreased Bacteroidetes and Fusobacteria compared to the control group. At the genus level, 4 weeks of administration of 250 mg STP significantly increased Granulicatella, Streptococcus, Oribacterium, Anaerococcus, Acidaminococcus, Actinomyces, Eubacterium, Negativicoccus, and Staphylococcus, and decreased Bacteroides, Buleidia, Dialister, and Leptotrichia, and transiently decreased Arcanobacterium compared to the control group. For the first time, an animal model was used for evaluating the effects of STP on oral microbiota by metagenomic sequencing. Our results provide a view of the shift of the oral microbiota in response to STP exposure in Syrian Golden hamster. Our findings indicate that the use of smokeless tobacco significantly disrupts the oral microbiota.}, } @article {pmid29850933, year = {2019}, author = {Gołębiewski, M and Tarasek, A and Sikora, M and Deja-Sikora, E and Tretyn, A and Niklińska, M}, title = {Rapid Microbial Community Changes During Initial Stages of Pine Litter Decomposition.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {56-75}, pmid = {29850933}, issn = {1432-184X}, support = {UMO-2012/05/NZ8/001362//Narodowe Centrum Nauki/ ; DS758//Uniwersytet Jagielloński w Krakowie/ ; DS759//Uniwersytet Jagielloński w Krakowie/ ; DSC//Uniwersytet Jagielloński w Krakowie/ ; }, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics/metabolism ; *Biodiversity ; DNA/isolation & purification ; DNA, Ribosomal/genetics ; *Decompression ; Ecosystem ; Eukaryota/classification/genetics ; Fungi/classification/genetics ; Metagenomics ; *Microbiota/genetics/physiology ; Pinus/*microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; *Soil Microbiology ; Trees/microbiology ; }, abstract = {Plant litter decomposition is a process enabling biogeochemical cycles closing in ecosystems, and decomposition in forests constitutes the largest part of this process taking place in terrestrial biomes. Microbial communities during litter decomposition were studied mainly with low-throughput techniques not allowing detailed insight, particularly into coniferous litter, as it is more difficult to obtain high quality DNA required for analyses. Motivated by these problems, we analyzed archaeal, bacterial, and eukaryotic communities at three decomposition stages: fresh, 3- and 8-month-old litter by 16/18S rDNA pyrosequencing, aiming at detailed insight into early stages of pine litter decomposition. Archaea were absent from our libraries. Bacterial and eukaryotic diversity was greatest in 8-month-old litter and the same applied to bacterial and fungal rDNA content. Community structure was different at various stages of decomposition, and phyllospheric organisms (bacteria: Acetobacteraceae and Pseudomonadaceae members, fungi: Lophodermium, Phoma) were replaced by communities with metabolic capabilities adapted to the particular stage of decomposition. Sphingomonadaceae and Xanthomonadaceae and fungal genera Sistotrema, Ceuthospora, and Athelia were characteristic for 3-month-old samples, while 8-month-old ones were characterized by Bradyrhizobiaceae and nematodes (Plectus). We suggest that bacterial and eukaryotic decomposer communities change at different stages of pine litter decomposition in a way similar to that in broadleaf litter. Interactions between bacteria and eukaryotes appear to be one of the key drivers of microbial community structure.}, } @article {pmid29850857, year = {2018}, author = {Alfano, M and Ferrarese, R and Locatelli, I and Ventimiglia, E and Ippolito, S and Gallina, P and Cesana, D and Canducci, F and Pagliardini, L and Viganò, P and Clementi, M and Nebuloni, M and Montorsi, F and Salonia, A}, title = {Testicular microbiome in azoospermic men-first evidence of the impact of an altered microenvironment.}, journal = {Human reproduction (Oxford, England)}, volume = {33}, number = {7}, pages = {1212-1217}, pmid = {29850857}, issn = {1460-2350}, mesh = {Azoospermia/*complications/microbiology/pathology ; Cross-Sectional Studies ; Dysbiosis/*complications/microbiology/pathology ; Humans ; Male ; *Microbiota ; Spermatogenesis/physiology ; Testis/*microbiology/pathology ; }, abstract = {STUDY QUESTION: Given the relevant role of the extracellular microenvironment in regulating tissue homeostasis, is testicular bacterial microbiome (BM) associated with germ cell aplasia in idiopathic non-obstructive azoospermia (iNOA)?

SUMMARY ANSWER: A steady increase of dysbiosis was observed among testis with normal spermatogenesis vs. iNOA with positive sperm retrieval and iNOA with complete germ cell aplasia.

WHAT IS KNOWN ALREADY: Tissue-associated BM has been reported to be a biologically important extracellular microenvironment component for numerous body habitats, but not yet for the human testis.

STUDY DESIGN, SIZE, DURATION: Cross-sectional study, investigating tissue-associated BM in the testis of (i) five men with iNOA and negative sperm retrieval at microdissection testicular sperm extraction (microTESE); (ii) five men with iNOA and positive sperm retrieval at microTESE; and (iii) five normozoospermic men upon orchiectomy. Every testicular specimen was histologically classified and analyzed in terms of bacterial community.

Massive ultra-deep pyrosequencing was applied to investigate testis microbiome. Metagenome was analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Tissue-associated bacterial load was quantified by digital droplet PCR.

Normozoospermic men showed small amounts of bacteria in the testis, with Actinobacteria, Bacteroidetes, Firmicutes Proteobacteria as the dominating phyla; iNOA individuals had increased amounts of bacterial DNA (P = 0.02), associated with decreased taxa richness due to the lack of Bacteroidetes and Proteobacteria (P = 2 × 10-5). Specimens with negative sperm retrieval at microTESE depicted complete germ cell aplasia and a further decrease in terms of Firmicutes and Clostridia (P < 0.05), a complete lack of Peptoniphilus asaccharolyticus, but increased amount of Actinobacteria.

The limited number of specimens analyzed in this preliminary study deserves external validation. The paraneoplastic microenvironment could have an impact on the residential bacterial flora.

Human testicular microenvironment is not microbiologically sterile, containing low amounts of Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. A dysbiotic bacterial community was associated with iNOA and complete germ cell aplasia. Novel findings on testicular BM could support future translational therapies of male-factor infertility.

This work was supported by URI-Urological Research Institute free funds. Authors declared no conflict of interest.

TRIAL REGISTRATION NUMBER: N/A.}, } @article {pmid29848762, year = {2018}, author = {Garcia, SL and Buck, M and Hamilton, JJ and Wurzbacher, C and Grossart, HP and McMahon, KD and Eiler, A}, title = {Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.}, journal = {mSphere}, volume = {3}, number = {3}, pages = {}, pmid = {29848762}, issn = {2379-5042}, mesh = {Bacteria/*metabolism ; Fresh Water/*microbiology ; *Metabolism ; *Microbial Consortia ; Microbial Interactions ; }, abstract = {Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.}, } @article {pmid29844409, year = {2018}, author = {Quin, C and Estaki, M and Vollman, DM and Barnett, JA and Gill, SK and Gibson, DL}, title = {Probiotic supplementation and associated infant gut microbiome and health: a cautionary retrospective clinical comparison.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8283}, pmid = {29844409}, issn = {2045-2322}, support = {//CIHR/Canada ; }, mesh = {Adult ; Bifidobacterium ; Breast Feeding ; Dietary Supplements ; Fatty Acids, Volatile ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Immunoglobulin A, Secretory/analysis ; Infant ; Infant, Newborn ; Male ; Microbiota ; Milk, Human ; Mothers ; Probiotics/*adverse effects/*metabolism ; Retrospective Studies ; }, abstract = {While probiotics are a multi-billion dollar industry, there is little evidence to show that supplementing infants provides any health benefits. We conducted an observational study where 35 of 86 participating mothers self-administered probiotics during breastfeeding, as well as directly to their infants. The primary objective was to determine if probiotic exposure influenced the infants' fecal microbiome while the secondary objective assessed associated changes to the mothers' breast milk immunity and infant health. Analysis of infant fecal microbiome throughout the first 6 months of life revealed that probiotics were associated with higher abundances of Bifidobacterium at week 1 only. Short-chain fatty acid production and predicted metagenomic functions of the microbial communities were not altered. While probiotics did not alter breast milk immune markers, fecal sIgA responses were higher among probiotic supplemented infants. Surprisingly, this was not associated with better health outcomes, as the probiotic cohort had higher incidences of mucosal-associated illnesses as toddlers. This retrospective clinical comparison suggests that probiotic exposure during infancy has limited effects on gut microbial composition yet is associated with increased infection later in life. These correlative findings caution against probiotic supplementation during infancy until rigorous controlled follow-up studies determining their safety and efficacy have occurred.}, } @article {pmid29844399, year = {2018}, author = {Ghosh, S and Das, AP}, title = {Metagenomic insights into the microbial diversity in manganese-contaminated mine tailings and their role in biogeochemical cycling of manganese.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8257}, pmid = {29844399}, issn = {2045-2322}, mesh = {Actinobacteria/*physiology ; Biodiversity ; Energy Metabolism/genetics ; Magnesium/metabolism ; Manganese/*metabolism ; Metabolic Networks and Pathways/genetics ; Metagenomics ; Microbial Consortia ; Mining ; Phylogeny ; Proteobacteria/*physiology ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA ; Soil Microbiology ; }, abstract = {To extend the knowledge on the microbial diversity of manganese rich environments, we performed a clone library based study using metagenomic approach. Pyrosequencing based analysis of 16S rRNA genes were carried out on an Illumina platform to gain insights into the bacterial community inhabiting in a manganese mining site and the taxonomic profiles were correlated with the inherent capacities of these strains to solubilise manganese. The application of shot gun sequencing in this study yielded results which revealed the highest prevalence of Proteobacteria (42.47%), followed by Actinobacteria (23.99%) in the area of study. Cluster of orthologous group (COG) functional category has 85,066 predicted functions. Out of which 11% are involved in metabolism of amino acid, 9% are involved in production and conversion of energy while Keto Encyclopedia of Gene and Genomes (KEGG) functional category has 107,388 predicted functions, out of which 55% are involved in cellular metabolism, 15% are environmental and information processing and 12% are genetic information processing in nature. The isolated microbial consortia demonstrated visible growth in presence of high concentrations of Mn. Solubilisation studies resulted in 86% of manganese recovery after 20 days. The result presented in this study has important implications in understanding the microbial diversity in manganese contaminated mine tailings and their role in natural geochemical cycling of Mn.}, } @article {pmid29844325, year = {2018}, author = {Iebba, V and Guerrieri, F and Di Gregorio, V and Levrero, M and Gagliardi, A and Santangelo, F and Sobolev, AP and Circi, S and Giannelli, V and Mannina, L and Schippa, S and Merli, M}, title = {Combining amplicon sequencing and metabolomics in cirrhotic patients highlights distinctive microbiota features involved in bacterial translocation, systemic inflammation and hepatic encephalopathy.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8210}, pmid = {29844325}, issn = {2045-2322}, mesh = {*Bacterial Translocation ; Carbon/metabolism ; Fatty Acids/metabolism ; Feces/microbiology ; *Gene Amplification ; Hepatic Encephalopathy/*metabolism/microbiology ; Humans ; Inflammation/*metabolism ; Liver Cirrhosis/*metabolism/microbiology ; *Metabolomics ; Metagenomics ; Methane/metabolism ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In liver cirrhosis (LC), impaired intestinal functions lead to dysbiosis and possible bacterial translocation (BT). Bacteria or their byproducts within the bloodstream can thus play a role in systemic inflammation and hepatic encephalopathy (HE). We combined 16S sequencing, NMR metabolomics and network analysis to describe the interrelationships of members of the microbiota in LC biopsies, faeces, peripheral/portal blood and faecal metabolites with clinical parameters. LC faeces and biopsies showed marked dysbiosis with a heightened proportion of Enterobacteriaceae. Our approach showed impaired faecal bacterial metabolism of short-chain fatty acids (SCFAs) and carbon/methane sources in LC, along with an enhanced stress-related response. Sixteen species, mainly belonging to the Proteobacteria phylum, were shared between LC peripheral and portal blood and were functionally linked to iron metabolism. Faecal Enterobacteriaceae and trimethylamine were positively correlated with blood proinflammatory cytokines, while Ruminococcaceae and SCFAs played a protective role. Within the peripheral blood and faeces, certain species (Stenotrophomonas pavanii, Methylobacterium extorquens) and metabolites (methanol, threonine) were positively related to HE. Cirrhotic patients thus harbour a 'functional dysbiosis' in the faeces and peripheral/portal blood, with specific keystone species and metabolites related to clinical markers of systemic inflammation and HE.}, } @article {pmid29808965, year = {2019}, author = {Grönroos, M and Parajuli, A and Laitinen, OH and Roslund, MI and Vari, HK and Hyöty, H and Puhakka, R and Sinkkonen, A}, title = {Short-term direct contact with soil and plant materials leads to an immediate increase in diversity of skin microbiota.}, journal = {MicrobiologyOpen}, volume = {8}, number = {3}, pages = {e00645}, pmid = {29808965}, issn = {2045-8827}, mesh = {Bacteria/*classification/*genetics ; *Environmental Exposure ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Microbiota ; Plants ; Skin/*microbiology ; Soil ; }, abstract = {Immune-mediated diseases have increased during the last decades in urban environments. The hygiene hypothesis suggests that increased hygiene level and reduced contacts with natural biodiversity are related to the increase in immune-mediated diseases. We tested whether short-time contact with microbiologically diverse nature-based materials immediately change bacterial diversity on human skin. We tested direct skin contact, as two volunteers rubbed their hands with sixteen soil and plant based materials, and an exposure via fabric packets filled with moss material. Skin swabs were taken before and after both exposures. Next-generation sequencing showed that exposures increased, at least temporarily, the total diversity of skin microbiota and the diversity of Acidobacteria, Actinobacteria, Bacteroidetes, Proteobacteria and Alpha-, Beta- and Gammaproteobacteria suggesting that contact with nature-based materials modify skin microbiome and increase skin microbial diversity. Until now, approaches to cure or prevent immune system disorders using microbe-based treatments have been limited to use of a few microbial species. We propose that nature-based materials with high natural diversity, such as the materials tested here, might be more effective in modifying human skin microbiome, and eventually, in reducing immune system disorders. Future studies should investigate how long-term changes in skin microbiota are achieved and if the exposure induces beneficial changes in the immune system markers.}, } @article {pmid29807988, year = {2018}, author = {Sieber, CMK and Probst, AJ and Sharrar, A and Thomas, BC and Hess, M and Tringe, SG and Banfield, JF}, title = {Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy.}, journal = {Nature microbiology}, volume = {3}, number = {7}, pages = {836-843}, pmid = {29807988}, issn = {2058-5276}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; 5R01AI092531/NH/NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Computational Biology/*methods ; Data Curation ; Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Metagenomics/*methods ; Microbiota ; Soil Microbiology ; User-Computer Interface ; Water Microbiology ; }, abstract = {Microbial communities are critical to ecosystem function. A key objective of metagenomic studies is to analyse organism-specific metabolic pathways and reconstruct community interaction networks. This requires accurate assignment of assembled genome fragments to genomes. Existing binning methods often fail to reconstruct a reasonable number of genomes and report many bins of low quality and completeness. Furthermore, the performance of existing algorithms varies between samples and biotopes. Here, we present a dereplication, aggregation and scoring strategy, DAS Tool, that combines the strengths of a flexible set of established binning algorithms. DAS Tool applied to a constructed community generated more accurate bins than any automated method. Indeed, when applied to environmental and host-associated samples of different complexity, DAS Tool recovered substantially more near-complete genomes, including previously unreported lineages, than any single binning method alone. The ability to reconstruct many near-complete genomes from metagenomics data will greatly advance genome-centric analyses of ecosystems.}, } @article {pmid29806626, year = {2018}, author = {Mihara, T and Koyano, H and Hingamp, P and Grimsley, N and Goto, S and Ogata, H}, title = {Taxon Richness of "Megaviridae" Exceeds those of Bacteria and Archaea in the Ocean.}, journal = {Microbes and environments}, volume = {33}, number = {2}, pages = {162-171}, pmid = {29806626}, issn = {1347-4405}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biodiversity ; Databases, Genetic ; Evolution, Molecular ; Giant Viruses/*classification/genetics ; Metagenomics ; *Oceans and Seas ; *Phylogeny ; RNA Polymerase II/genetics ; }, abstract = {Since the discovery of the giant mimivirus, evolutionarily related viruses have been isolated or identified from various environments. Phylogenetic analyses of this group of viruses, tentatively referred to as the family "Megaviridae", suggest that it has an ancient origin that may predate the emergence of major eukaryotic lineages. Environmental genomics has since revealed that Megaviridae represents one of the most abundant and diverse groups of viruses in the ocean. In the present study, we compared the taxon richness and phylogenetic diversity of Megaviridae, Bacteria, and Archaea using DNA-dependent RNA polymerase as a common marker gene. By leveraging existing microbial metagenomic data, we found higher richness and phylogenetic diversity in this single viral family than in the two prokaryotic domains. We also obtained results showing that the evolutionary rate alone cannot account for the observed high diversity of Megaviridae lineages. These results suggest that the Megaviridae family has a deep co-evolutionary history with diverse marine protists since the early "Big-Bang" radiation of the eukaryotic tree of life.}, } @article {pmid29803476, year = {2018}, author = {González-Escobar, JL and Grajales-Lagunes, A and Smoliński, A and Chagolla-López, A and De Léon-Rodríguez, A and Barba de la Rosa, AP}, title = {Microbiota of edible Liometopum apiculatum ant larvae reveals potential functions related to their nutritional value.}, journal = {Food research international (Ottawa, Ont.)}, volume = {109}, number = {}, pages = {497-505}, doi = {10.1016/j.foodres.2018.04.049}, pmid = {29803476}, issn = {1873-7145}, mesh = {Animals ; Ants/*microbiology ; Bacteria/classification/genetics/*isolation & purification ; Female ; Food Analysis/methods ; Host-Pathogen Interactions ; Larva/microbiology ; Male ; Metagenomics ; *Microbiota ; *Nutritive Value ; Ribotyping ; Symbiosis ; }, abstract = {Edible insects, due to their high nutritive value, are currently considered as a potential renewable source for food and feed production. Liometopum apiculatum ants are widely distributed in arid and semi-arid ecosystems and their larvae (escamoles) are considered as a delicacy, however the microbial importance in L. apiculatum nutritional ecology is unknown. The aim of this research was to characterize the microorganisms associated with both L. apiculatum larvae and the reproductive adult ants using the 16S rRNA gene sequencing and culturomics approaches. The obligate endosymbionts were also investigated through microscopic analysis. The most abundant Phylum identified by sequencing in the larvae was Firmicutes while in adult ants was Proteobacteria. Interestingly, the culturomics results showed 15 genera corresponding to the bacteria identified by sequencing analysis. Particularly, it was observed a large population of nitrogen-fixing bacteria, which could be linked with the high protein content in escamoles. Endosymbionts were detected in bacteoriocytes, these bacteria are related with vitamins and essential amino acids biosynthesis, and both compounds contributing to the high nutritional value of escamoles. This is the first report of the microorganisms present in the escamolera ant ensuring their safety as food and opening new areas of nutritional ecological and food processing.}, } @article {pmid29803134, year = {2018}, author = {Duru, IC and Laine, P and Andreevskaya, M and Paulin, L and Kananen, S and Tynkkynen, S and Auvinen, P and Smolander, OP}, title = {Metagenomic and metatranscriptomic analysis of the microbial community in Swiss-type Maasdam cheese during ripening.}, journal = {International journal of food microbiology}, volume = {281}, number = {}, pages = {10-22}, doi = {10.1016/j.ijfoodmicro.2018.05.017}, pmid = {29803134}, issn = {1879-3460}, mesh = {Cheese/analysis/*microbiology ; Cold Temperature ; Fermentation ; Food Handling ; Gene Expression Regulation, Bacterial ; *Metagenomics ; Microbiota/genetics/*physiology ; Taste ; *Transcriptome ; }, abstract = {In Swiss-type cheeses, characteristic nut-like and sweet flavor develops during the cheese ripening due to the metabolic activities of cheese microbiota. Temperature changes during warm and cold room ripening, and duration of ripening can significantly change the gene expression of the cheese microbiota, which can affect the flavor formation. In this study, a metagenomic and metatranscriptomic analysis of Swiss-type Maasdam cheese was performed on samples obtained during ripening in the warm and cold rooms. We reconstructed four different bacterial genomes (Lactococcus lactis, Lactobacillus rhamnosus, Lactobacillus helveticus, and Propionibacterium freudenreichii subsp. shermanii strain JS) from the Maasdam cheese to near completeness. Based on the DNA and RNA mean coverage, Lc. lactis strongly dominated (~80-90%) within the cheese microbial community. Genome annotation showed the potential for the presence of several flavor forming pathways in these species, such as production of methanethiol, free fatty acids, acetoin, diacetyl, acetate, ethanol, and propionate. Using the metatranscriptomic data, we showed that, with the exception of Lc. lactis, the central metabolism of the microbiota was downregulated during cold room ripening suggesting that fewer flavor compounds such as acetoin and propionate were produced. In contrast, Lc. lactis genes related to the central metabolism, including the vitamin biosynthesis and homolactic fermentation, were upregulated during cold room ripening.}, } @article {pmid29803114, year = {2018}, author = {Wilcox, JJS and Hollocher, H}, title = {Unprecedented Symbiont Eukaryote Diversity Is Governed by Internal Trophic Webs in a Wild Non-Human Primate.}, journal = {Protist}, volume = {169}, number = {3}, pages = {307-320}, doi = {10.1016/j.protis.2018.03.001}, pmid = {29803114}, issn = {1618-0941}, mesh = {Animals ; *Biota ; DNA Barcoding, Taxonomic ; Feces/*parasitology ; Food Chain ; High-Throughput Nucleotide Sequencing ; Macaca fascicularis/*parasitology ; Metagenomics ; Parasites/*classification/*genetics ; Symbiosis ; }, abstract = {Research on host-associated microbiomes has highlighted major divisions between the role of eukaryotes in free-living and symbiont systems. These trends call into question the relevance of macroecological processes to host-associated systems and the relative importance of parasitism, commensalism, and mutualism as evolutionary patterns across the domains of life. However, it is unclear as to whether these apparent differences reflect biological realities or methodologies in community characterization: free-living eukaryotes tend to be characterized using metabarcoding whereas symbiont eukaryotes are typically characterized with microscopy. Here, we utilize an Illumina high-throughput metabarcoding approach to characterize the diversity and dynamics of eukaryotic symbiont communities in the feces of a wild non-human primate, Macaca fascicularis, revealing functionally and taxonomically diverse communities of eukaryotes hitherto unreported from any vertebrate. Importantly, community assembly was consistent with top-down and bottom-up trophic food web dynamics, highlighting the applicability of macroecological principles to these communities. Ultimately, our findings highlight vertebrate-associated symbiont communities of the gut that are much more similar to free-living systems than previously realized. Additionally, our results support a role for symbiosis as a major recurrent life strategy among eukaryotes and highlight the potential for vertebrates to host vast reservoirs of unexplored eukaryotic diversity.}, } @article {pmid29803086, year = {2018}, author = {Gallagher, D and Parker, D and Allen, DJ and Tsesmetzis, N}, title = {Dynamic bacterial and fungal microbiomes during sweet sorghum ensiling impact bioethanol production.}, journal = {Bioresource technology}, volume = {264}, number = {}, pages = {163-173}, doi = {10.1016/j.biortech.2018.05.053}, pmid = {29803086}, issn = {1873-2976}, mesh = {*Biofuels ; Ethanol ; Fermentation ; Lactobacillus ; *Mycobiome ; Silage ; *Sorghum ; }, abstract = {Significant low-cost biofuel production volumes could be achieved from commercial-scale silage by redirecting lactic acid fermentation to ethanol production. A temporal metagenomic analysis on ensiled sweet sorghum inoculated with an ethanologenic yeast has been conducted to understand the underlying microbial processes during bioethanol production. Individual silage buckets approximating silage piles were prepared with freshly harvested material and supplemented with ethanologenic yeast, sulfuric acid or both. The ensiling progress was assessed using high performance liquid chromatography, microbial taxonomic identification and abundance. The combined treatment with Saccharomyces and acid led to a steady reduction of bacterial abundance and microbial diversity with Lactobacillus becoming the dominant genus during the late timepoints. Furthermore, the addition of acid to inhibit bacterial growth hindered Saccharomyces ability to compete with native yeasts like Candida. Knowledge of the response of the in-situ microbial community to the various treatments during ensiling will help improve current methodologies for bioethanol production.}, } @article {pmid29802796, year = {2018}, author = {Bost, A and Martinson, VG and Franzenburg, S and Adair, KL and Albasi, A and Wells, MT and Douglas, AE}, title = {Functional variation in the gut microbiome of wild Drosophila populations.}, journal = {Molecular ecology}, volume = {27}, number = {13}, pages = {2834-2845}, doi = {10.1111/mec.14728}, pmid = {29802796}, issn = {1365-294X}, mesh = {Animals ; Biodiversity ; Drosophila/*genetics/microbiology ; Gammaproteobacteria/genetics ; Gastrointestinal Microbiome/*genetics ; Host Microbial Interactions/*genetics ; Metagenome/genetics ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Transcriptome/*genetics ; }, abstract = {Most of the evidence that the gut microbiome of animals is functionally variable, with consequences for the health and fitness of the animal host, is based on laboratory studies, often using inbred animals under tightly controlled conditions. It is largely unknown whether these microbiome effects would be evident in outbred animal populations under natural conditions. In this study, we quantified the functional traits of the gut microbiota (metagenome) and host (gut transcriptome) and the taxonomic composition of the gut microorganisms (16S rRNA gene sequence) in natural populations of three mycophagous Drosophila species. Variation in microbiome function and composition was driven principally by the period of sample collection, while host function varied mostly with Drosophila species, indicating that variation in microbiome traits is determined largely by environmental factors, and not host taxonomy. Despite this, significant correlations between microbiome and host functional traits were obtained. In particular, microbiome functions dominated by metabolism were positively associated with host functions relating to gut epithelial turnover. Much of the functional variation in the microbiome could be attributed to variation in abundance of Bacteroidetes, rather than the two other abundant groups, the γ-Proteobacteria or Lactobacillales. We conclude that functional variation in the interactions between animals and their gut microbiome can be detectable in natural populations, and, in mycophagous Drosophila, this variation relates primarily to metabolism and homeostasis of the gut epithelium.}, } @article {pmid29802288, year = {2018}, author = {Waite, DW and Dsouza, M and Sekiguchi, Y and Hugenholtz, P and Taylor, MW}, title = {Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8128}, pmid = {29802288}, issn = {2045-2322}, mesh = {Animals ; *Endangered Species ; Feces/*microbiology ; Metagenomics/*methods ; *Microbiota ; Parrots/*genetics/*microbiology ; }, abstract = {The kakapo is a critically endangered, herbivorous parrot endemic to New Zealand. The kakapo hindgut hosts a dense microbial community of low taxonomic diversity, typically dominated by Escherichia fergusonii, and has proven to be a remarkably stable ecosystem, displaying little variation in core membership over years of study. To elucidate mechanisms underlying this robustness, we performed 16S rRNA gene-based co-occurrence network analysis to identify potential interactions between E. fergusonii and the wider bacterial community. Genomic and metagenomic sequencing were employed to facilitate interpretation of potential interactions observed in the network. E. fergusonii maintained very few correlations with other members of the microbiota, and isolates possessed genes for the generation of energy from a wide range of carbohydrate sources, including plant fibres such as cellulose. We surmise that this dominant microorganism is abundant not due to ecological interaction with other members of the microbiota, but its ability to metabolise a wide range of nutrients in the gut. This research represents the first concerted effort to understand the functional roles of the kakapo microbiota, and leverages metagenomic data to contextualise co-occurrence patterns. By combining these two techniques we provide a means for studying the diversity-stability hypothesis in the context of bacterial ecosystems.}, } @article {pmid29801233, year = {2018}, author = {Chen, Y and Jiang, Y and Huang, H and Mou, L and Ru, J and Zhao, J and Xiao, S}, title = {Long-term and high-concentration heavy-metal contamination strongly influences the microbiome and functional genes in Yellow River sediments.}, journal = {The Science of the total environment}, volume = {637-638}, number = {}, pages = {1400-1412}, doi = {10.1016/j.scitotenv.2018.05.109}, pmid = {29801233}, issn = {1879-1026}, mesh = {*Environmental Monitoring ; Geologic Sediments/chemistry ; Metagenome ; Metals, Heavy/*analysis ; Microbiota ; Rivers/chemistry ; Water Pollutants, Chemical/*analysis ; }, abstract = {The world is facing a hard battle against soil pollution such as heavy metals. Metagenome sequencing, 16S rRNA sequencing, and quantitative polymerase chain reaction (qPCR) were used to examine microbial adaptation mechanism to contaminated sediments under natural conditions. Results showed that sediment from a tributary of the Yellow River, which was named Dongdagou River (DDG) supported less bacterial biomass and owned lower richness than sediment from Maqu (MQ), an uncontaminated site in the upper reaches of the Yellow River. Additionally, microbiome structures in these two sites were different. Metagenome sequencing and functional gene annotations revealed that sediment from DDG contains a larger number of genes related to DNA recombination, DNA damage repair, and heavy-metal resistance. KEGG pathway analysis indicated that the sediment of DDG contains a greater number of enzymes associated with heavy-metal resistance and reduction. Additionally, the bacterial phyla Proteobacteria, Bacteroidetes, and Firmicutes, which harbored a larger suite of metal-resistance genes, were found to be the core functional phyla in the contaminated sediments. Furthermore, sediment in DDG owned higher viral abundance, indicating virus-mediated heavy-metal resistance gene transfer might be an adaptation mechanism. In conclusion, microbiome of sediment from DDG has evolved into an integrated system resistant to long-term heavy-metal pollution.}, } @article {pmid29800679, year = {2018}, author = {Feranchuk, S and Belkova, N and Potapova, U and Kuzmin, D and Belikov, S}, title = {Evaluating the use of diversity indices to distinguish between microbial communities with different traits.}, journal = {Research in microbiology}, volume = {169}, number = {4-5}, pages = {254-261}, doi = {10.1016/j.resmic.2018.03.004}, pmid = {29800679}, issn = {1769-7123}, mesh = {*Algorithms ; Bacteria/*classification/*genetics ; *Biodiversity ; Coral Reefs ; DNA, Bacterial/genetics ; Ecosystem ; Metagenomics/*methods ; Microbial Consortia/*genetics ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {Several measures of biodiversity are commonly used to describe microbial communities, analyzed using 16S gene sequencing. A wide range of available experiments on 16S gene sequencing allows us to present a framework for a comparison of various diversity indices. The criterion for the comparison is the statistical significance of the difference in index values for microbial communities with different traits, within the same experiment. The results of the evaluation indicate that Shannon diversity is the most effective measure among the commonly used diversity indices. The results also indicate that, within the present framework, the Gini coefficient as a diversity index is comparable to Shannon diversity, despite the fact that the Gini coefficient, as a diversity estimator, is far less popular in microbiology than several other measures.}, } @article {pmid29800328, year = {2018}, author = {Birkl, P and Bharwani, A and Kjaer, JB and Kunze, W and McBride, P and Forsythe, P and Harlander-Matauschek, A}, title = {Differences in cecal microbiome of selected high and low feather-pecking laying hens.}, journal = {Poultry science}, volume = {97}, number = {9}, pages = {3009-3014}, pmid = {29800328}, issn = {1525-3171}, mesh = {*Aggression ; Animals ; Bacteria/classification ; Cecum/*microbiology ; Chickens/genetics/*microbiology/*physiology ; Feathers ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Selection, Genetic ; Sequence Analysis, RNA/veterinary ; }, abstract = {In mammals, it has become increasingly clear that the gut microbiota influences not only gastrointestinal physiology but also modulates behavior. In domestic birds, ceca have the greatest gastrointestinal microbial population. Feather-pecking (FP) behavior in laying hens is one of the most important unsolved behavioral issues in modern agriculture. The aim of the present study was to assess the cecal microbial community of divergently selected high (HFP; n = 20) and low (LFP; n = 20) feather-pecking birds at 60 wk of age. The cecal samples were subjected to community profiling of 16S rRNA and in silico metagenomics using a modified bar-coded Illumina sequencing method on a MiSeq Illumina sequencer. Our results revealed that compared to HFP birds, LFP birds are characterized by an increased overall microbial diversity (beta diversity) shown by a difference in the Bray-Curtis index (R2 = 0.171, P < 0.05). Furthermore, operational taxonomic unit comparisons showed an increased presence of Clostridiae and decreased presence of Lactobaccillacae in HFP birds when compared to LFP birds (False Discovery Rate < 0.05, Mann-Whitney comparisons). Our data indicate that there may be differences in the cecal profile between these 2 lines of laying hens. More research, building on this first study using sequencing technology for profiling the chicken cecal microbiome, will be needed in order to reveal if and how there exists a functional link between the performance of FP and the cecal microbial community.}, } @article {pmid29796911, year = {2018}, author = {Hojo, M and Asahara, T and Nagahara, A and Takeda, T and Matsumoto, K and Ueyama, H and Matsumoto, K and Asaoka, D and Takahashi, T and Nomoto, K and Yamashiro, Y and Watanabe, S}, title = {Gut Microbiota Composition Before and After Use of Proton Pump Inhibitors.}, journal = {Digestive diseases and sciences}, volume = {63}, number = {11}, pages = {2940-2949}, pmid = {29796911}, issn = {1573-2568}, mesh = {Aged ; Blood/*microbiology ; Carboxylic Acids/analysis ; Dysbiosis/*chemically induced ; Feces/chemistry/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Male ; Middle Aged ; Proton Pump Inhibitors/*adverse effects ; }, abstract = {BACKGROUND: Recently, problems associated with proton pump inhibitor (PPI) use have begun to surface. PPIs influence the gut microbiota; therefore, PPI use may increase the risk of enteric infections and cause bacterial translocation. In this study, we investigated fecal microbiota composition, fecal organic acid concentrations and pH, and gut bacteria in the blood of the same patients before and after PPI use.

METHODS: Twenty patients with reflux esophagitis based on endoscopic examination received 8 weeks of treatment with PPIs. To analyze fecal microbiota composition and gut bacteria in blood and organic acid concentrations, 16S and 23S rRNA-targeted quantitative RT-PCR and high-performance liquid chromatography were conducted.

RESULTS: Lactobacillus species were significantly increased at both 4 and 8 weeks after PPI treatment compared with bacterial counts before treatment (P = 0.011 and P = 0.002, respectively). Among Lactobacillus spp., counts of the L. gasseri subgroup, L. fermentum, the L. reuteri subgroup, and the L. ruminis subgroup were significantly increased at 4 and 8 weeks after treatment compared with counts before treatment. Streptococcus species were also significantly increased at 4 and 8 weeks after PPI treatment compared with counts before treatment (P < 0.01 and P < 0.001, respectively). There was no significant difference in the total organic acid concentrations before and after PPI treatment. Detection rates of bacteria in blood before and after PPI treatment were 22 and 28%, respectively, with no significant differences.

CONCLUSIONS: Our quantitative RT-PCR results showed that gut dysbiosis was caused by PPI use, corroborating previous results obtained by metagenomic analysis.}, } @article {pmid29795644, year = {2018}, author = {Jensen, MS and Fredriksen, L and MacKenzie, AK and Pope, PB and Leiros, I and Chylenski, P and Williamson, AK and Christopeit, T and Østby, H and Vaaje-Kolstad, G and Eijsink, VGH}, title = {Discovery and characterization of a thermostable two-domain GH6 endoglucanase from a compost metagenome.}, journal = {PloS one}, volume = {13}, number = {5}, pages = {e0197862}, pmid = {29795644}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Catalytic Domain ; Cellulase/*chemistry/genetics/*metabolism ; Cellulose/*metabolism ; Cloning, Molecular ; *Composting ; Crystallography, X-Ray ; Enzyme Stability ; Hydrolysis ; Kinetics ; *Metagenome ; Protein Conformation ; Sequence Homology ; Substrate Specificity ; Temperature ; }, abstract = {Enzymatic depolymerization of recalcitrant polysaccharides plays a key role in accessing the renewable energy stored within lignocellulosic biomass, and natural biodiversities may be explored to discover microbial enzymes that have evolved to conquer this task in various environments. Here, a metagenome from a thermophilic microbial community was mined to yield a novel, thermostable cellulase, named mgCel6A, with activity on an industrial cellulosic substrate (sulfite-pulped Norway spruce) and a glucomannanase side activity. The enzyme consists of a glycoside hydrolase family 6 catalytic domain (GH6) and a family 2 carbohydrate binding module (CBM2) that are connected by a linker rich in prolines and threonines. MgCel6A exhibited maximum activity at 85°C and pH 5.0 on carboxymethyl cellulose (CMC), but in prolonged incubations with the industrial substrate, the highest yields were obtained at 60°C, pH 6.0. Differential scanning calorimetry (DSC) indicated a Tm(app) of 76°C. Both functional data and the crystal structure, solved at 1.88 Å resolution, indicate that mgCel6A is an endoglucanase. Comparative studies with a truncated variant of the enzyme showed that the CBM increases substrate binding, while not affecting thermal stability. Importantly, at higher substrate concentrations the full-length enzyme was outperformed by the catalytic domain alone, underpinning previous suggestions that CBMs may be less useful in high-consistency bioprocessing.}, } @article {pmid29795448, year = {2018}, author = {McClure, RS and Overall, CC and Hill, EA and Song, HS and Charania, M and Bernstein, HC and McDermott, JE and Beliaev, AS}, title = {Species-specific transcriptomic network inference of interspecies interactions.}, journal = {The ISME journal}, volume = {12}, number = {8}, pages = {2011-2023}, pmid = {29795448}, issn = {1751-7370}, mesh = {Algorithms ; Bacteria/*genetics/growth & development ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/metabolism ; Cyanobacteria/*genetics/growth & development/physiology ; Gene Regulatory Networks ; Heterotrophic Processes ; Metagenome ; Microbiota ; Species Specificity ; Transcriptome ; }, abstract = {The advent of high-throughput 'omics approaches coupled with computational analyses to reconstruct individual genomes from metagenomes provides a basis for species-resolved functional studies. Here, a mutual information approach was applied to build a gene association network of a commensal consortium, in which a unicellular cyanobacterium Thermosynechococcus elongatus BP1 supported the heterotrophic growth of Meiothermus ruber strain A. Specifically, we used the context likelihood of relatedness (CLR) algorithm to generate a gene association network from 25 transcriptomic datasets representing distinct growth conditions. The resulting interspecies network revealed a number of linkages between genes in each species. While many of the linkages were supported by the existing knowledge of phototroph-heterotroph interactions and the metabolism of these two species several new interactions were inferred as well. These include linkages between amino acid synthesis and uptake genes, as well as carbohydrate and vitamin metabolism, terpenoid metabolism and cell adhesion genes. Further topological examination and functional analysis of specific gene associations suggested that the interactions are likely to center around the exchange of energetically costly metabolites between T. elongatus and M. ruber. Both the approach and conclusions derived from this work are widely applicable to microbial communities for identification of the interactions between species and characterization of community functioning as a whole.}, } @article {pmid29795328, year = {2018}, author = {Knight, R and Vrbanac, A and Taylor, BC and Aksenov, A and Callewaert, C and Debelius, J and Gonzalez, A and Kosciolek, T and McCall, LI and McDonald, D and Melnik, AV and Morton, JT and Navas, J and Quinn, RA and Sanders, JG and Swafford, AD and Thompson, LR and Tripathi, A and Xu, ZZ and Zaneveld, JR and Zhu, Q and Caporaso, JG and Dorrestein, PC}, title = {Best practices for analysing microbiomes.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {7}, pages = {410-422}, doi = {10.1038/s41579-018-0029-9}, pmid = {29795328}, issn = {1740-1534}, mesh = {Animals ; Bacteria/*genetics ; Environmental Microbiology ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Reproducibility of Results ; }, abstract = {Complex microbial communities shape the dynamics of various environments, ranging from the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies and data analysis have provided drastic improvements in microbiome analyses, for example, in taxonomic resolution, false discovery rate control and other properties, over earlier methods. In this Review, we discuss the best practices for performing a microbiome study, including experimental design, choice of molecular analysis technology, methods for data analysis and the integration of multiple omics data sets. We focus on recent findings that suggest that operational taxonomic unit-based analyses should be replaced with new methods that are based on exact sequence variants, methods for integrating metagenomic and metabolomic data, and issues surrounding compositional data analysis, where advances have been particularly rapid. We note that although some of these approaches are new, it is important to keep sight of the classic issues that arise during experimental design and relate to research reproducibility. We describe how keeping these issues in mind allows researchers to obtain more insight from their microbiome data sets.}, } @article {pmid29794413, year = {2018}, author = {Hu, Y and Bai, C and Cai, J and Dai, J and Shao, K and Tang, X and Gao, G}, title = {Co-occurrence Network Reveals the Higher Fragmentation of the Bacterial Community in Kaidu River Than Its Tributaries in Northwestern China.}, journal = {Microbes and environments}, volume = {33}, number = {2}, pages = {127-134}, pmid = {29794413}, issn = {1347-4405}, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; China ; Computational Biology ; DNA, Bacterial ; Ecosystem ; Metagenomics ; *Microbial Interactions ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; *Water Microbiology ; }, abstract = {Rivers and their tributaries sculpt the earth's surface, and play an important role in substance circulation and energy flow. Bacteria are involved in most biogeochemical processes in the fluvial ecosystem; however, their pattern distribution in a river and its tributaries has not yet been investigated in detail. In the present study, high-throughput sequencing was employed to examine bacterial communities and their co-occurrence networks between Kaidu River and its nine tributaries in northwestern China. The results obtained demonstrated that both bacterial communities shared a similar dominant sub-community, mainly consisting of Actinobacteria, Bacteroidetes, and Proteobacteria, with Limnohabitans and Variovorax as the dominant genera. In spite of these commonalities, bacterial community structures still significantly differed between these two habitats, which may be related to the distance-related dispersal limitation. Their co-occurrence networks were generally both positively structured. The structural analysis showed that OTUs from the same phyla were more likely to co-occur. Although the keystone genera were taxonomically different between Kaidu River and its tributaries, they both shared common trophic properties in exploiting niches under oligotrophic conditions. We noted that their relative abundances were less than 1%, indicating the over-proportional roles of rare genera in the bacterial community. In addition, the inferred networks showed less nodes and edges, but higher modularity in Kaidu River than its tributaries, suggesting the higher fragmentation of the bacterial community in the mainstream.}, } @article {pmid29793542, year = {2018}, author = {Li, LG and Yin, X and Zhang, T}, title = {Tracking antibiotic resistance gene pollution from different sources using machine-learning classification.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {93}, pmid = {29793542}, issn = {2049-2618}, support = {172099/14E//Hong Kong General Research Fund/International ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics ; China ; Drug Resistance, Microbial/*genetics ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Machine Learning ; Metagenomics ; Sewage/*microbiology ; Soil Microbiology ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) has been a worldwide public health concern. Current widespread AMR pollution has posed a big challenge in accurately disentangling source-sink relationship, which has been further confounded by point and non-point sources, as well as endogenous and exogenous cross-reactivity under complicated environmental conditions. Because of insufficient capability in identifying source-sink relationship within a quantitative framework, traditional antibiotic resistance gene (ARG) signatures-based source-tracking methods would hardly be a practical solution.

RESULTS: By combining broad-spectrum ARG profiling with machine-learning classification SourceTracker, here we present a novel way to address the question in the era of high-throughput sequencing. Its potential in extensive application was firstly validated by 656 global-scale samples covering diverse environmental types (e.g., human/animal gut, wastewater, soil, ocean) and broad geographical regions (e.g., China, USA, Europe, Peru). Its potential and limitations in source prediction as well as effect of parameter adjustment were then rigorously evaluated by artificial configurations with representative source proportions. When applying SourceTracker in region-specific analysis, excellent performance was achieved by ARG profiles in two sample types with obvious different source compositions, i.e., influent and effluent of wastewater treatment plant. Two environmental metagenomic datasets of anthropogenic interference gradient further supported its potential in practical application. To complement general-profile-based source tracking in distinguishing continuous gradient pollution, a few generalist and specialist indicator ARGs across ecotypes were identified in this study.

CONCLUSION: We demonstrated for the first time that the developed source-tracking platform when coupling with proper experiment design and efficient metagenomic analysis tools will have significant implications for assessing AMR pollution. Following predicted source contribution status, risk ranking of different sources in ARG dissemination will be possible, thereby paving the way for establishing priority in mitigating ARG spread and designing effective control strategies.}, } @article {pmid29793532, year = {2018}, author = {Bilen, M and Dufour, JC and Lagier, JC and Cadoret, F and Daoud, Z and Dubourg, G and Raoult, D}, title = {The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {94}, pmid = {29793532}, issn = {2049-2618}, mesh = {Actinobacteria/isolation & purification ; Archaea/*classification/genetics/*isolation & purification ; Bacteria/*classification/genetics/*isolation & purification ; Bacteroidetes/isolation & purification ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Firmicutes/isolation & purification ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenomics ; Proteobacteria/isolation & purification ; }, abstract = {After a decade of research and metagenomic analyses, our knowledge of the human microbiota appears to have reached a plateau despite promising results. In many studies, culture has proven to be essential in describing new prokaryotic species and filling metagenomic gaps. In 2015, only 2172 different prokaryotic species were reported to have been isolated at least once from the human body as pathogens or commensals. In this review, we update the previous repertoire by reporting the different species isolated from the human body to date, increasing it by 28% to reach a total of 2776 species associated with human beings. They have been classified into 11 different phyla, mostly the Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Finally, culturomics contributed up to 66.2% towards updating this repertoire by reporting 400 species, of which 288 were novel. This demonstrates the need to continue the culturing work, which seems essential in order to decipher the hidden human microbial content.}, } @article {pmid29793117, year = {2018}, author = {Xu, W and Zhang, Y and Cao, H and Sheng, Y and Li, H and Li, Y and Zhao, H and Gui, X}, title = {Metagenomic insights into the microbiota profiles and bioaugmentation mechanism of organics removal in coal gasification wastewater in an anaerobic/anoxic/oxic system by methanol.}, journal = {Bioresource technology}, volume = {264}, number = {}, pages = {106-115}, doi = {10.1016/j.biortech.2018.05.064}, pmid = {29793117}, issn = {1873-2976}, mesh = {Bioreactors ; *Coal ; *Methanol ; *Microbiota ; Waste Disposal, Fluid ; *Wastewater ; Water Pollutants, Chemical ; Water Purification/*methods ; }, abstract = {Coal gasification wastewater is a typical high phenol-containing, toxic and refractory industrial wastewater. Here, lab-scale anaerobic-anoxic-oxic system was employed to treat real coal gasification wastewater, and methanol was added to oxic tank as the co-substrate to enhance the removal of refractory organic pollutants. The results showed that the average COD removal in oxic effluent increased from 24.9% to 36.0% by adding methanol, the total phenols concentration decreased from 54.4 to 44.9 mg/L. GC-MS analysis revealed that contents of phenolic components and polycyclic aromatic hydrocarbons (PAHs) were decreased compared to the control and their degradation intermediates were observed. Microbial community revealed that methanol increased the abundance of phenolics and PAHs degraders such as Comamonas, Burkholderia and Sphingopyxis. Moreover, functional analysis revealed the relative abundance of functional genes associated with toluene, benzoate and PAHs degradation pathways was higher than that of control based on KEGG database.}, } @article {pmid29790949, year = {2018}, author = {Salas-Mani, A and Jeusette, I and Castillo, I and Manuelian, CL and Lionnet, C and Iraculis, N and Sanchez, N and Fernández, S and Vilaseca, L and Torre, C}, title = {Fecal microbiota composition changes after a BW loss diet in Beagle dogs.}, journal = {Journal of animal science}, volume = {96}, number = {8}, pages = {3102-3111}, pmid = {29790949}, issn = {1525-3163}, mesh = {Animals ; Bacteria/*classification/genetics/isolation & purification ; Body Composition ; Body Weight ; Caloric Restriction/*veterinary ; Diet, Fat-Restricted/*veterinary ; Dietary Fiber ; Dogs/*physiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Male ; *Metagenomics ; Obesity/prevention & control/veterinary ; }, abstract = {In developed countries, dogs and cats frequently suffer from obesity. Recently, gut microbiota composition in humans has been related to obesity and metabolic diseases. This study aimed to evaluate changes in body composition, and gut microbiota composition in obese Beagle dogs after a 17-wk BW loss program. A total of six neutered adult Beagle dogs with an average initial BW of 16.34 ± 1.52 kg and BCS of 7.8 ± 0.1 points (9-point scale) were restrictedly fed with a hypocaloric, low-fat and high-fiber dry-type diet. Body composition was assessed with dual-energy X-ray absorptiometry scan, before (T0) and after (T1) BW loss program. Individual stool samples were collected at T0 and T1 for the 16S rRNA analyses of gut microbiota. Taxonomic analysis was done with amplicon-based metagenomic results, and functional analysis of the metabolic potential of the microbial community was done with shotgun metagenomic results. All dogs reached their ideal BW at T1, with an average weekly proportion of BW loss of -1.07 ± 0.03% of starting BW. Body fat (T0, 7.02 ± 0.76 kg) was reduced by half (P < 0.001), while bone (T0, 0.56 ± 0.06 kg) and muscle mass (T0, 8.89 ± 0.80 kg) remained stable (P > 0.05). The most abundant identified phylum was Firmicutes (T0, 74.27 ± 0.08%; T1, 69.38 ± 0.07%), followed by Bacteroidetes (T0, 12.68 ± 0.08%; T1, 16.68 ± 0.05%), Fusobacteria (T0, 7.45 ± 0.02%; T1, 10.18 ± 0.03%), Actinobacteria (T0, 4.53 ± 0.02%; T1, 3.34 ± 0.01%), and Proteobacteria (T0, 1.06 ± 0.01%; T1, 1.40 ± 0.00%). At genus level, the presence of Clostridium, Lactobacillus, and Dorea, at T1 decreased (P = 0.028), while Allobaculum increased (P = 0.046). Although the microbiota communities at T0 and T1 showed a low separation level when compared (Anosim's R value = 0.39), they were significantly biodiverse (P = 0.01). Those differences on microbiota composition could be explained by 13 genus (α = 0.05, linear discriminant analysis (LDA) score > 2.0). Additionally, differences between both communities could also be explained by the expression of 18 enzymes and 27 pathways (α = 0.05, LDA score > 2.0). In conclusion, restricted feeding of a low-fat and high-fiber dry-type diet successfully modifies gut microbiota in obese dogs, increasing biodiversity with a different representation of microbial genus and metabolic pathways.}, } @article {pmid29790941, year = {2018}, author = {Batut, B and Gravouil, K and Defois, C and Hiltemann, S and Brugère, JF and Peyretaillade, E and Peyret, P}, title = {ASaiM: a Galaxy-based framework to analyze microbiota data.}, journal = {GigaScience}, volume = {7}, number = {6}, pages = {}, pmid = {29790941}, issn = {2047-217X}, mesh = {Base Sequence ; Metagenomics ; *Microbiota ; *Software ; *Statistics as Topic ; }, abstract = {BACKGROUND: New generations of sequencing platforms coupled to numerous bioinformatics tools have led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies.

FINDINGS: We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses. ASaiM provides an extensive collection of tools to assemble, extract, explore, and visualize microbiota information from raw metataxonomic, metagenomic, or metatranscriptomic sequences. To guide the analyses, several customizable workflows are included and are supported by tutorials and Galaxy interactive tours, which guide users through the analyses step by step. ASaiM is implemented as a Galaxy Docker flavour. It is scalable to thousands of datasets but also can be used on a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io).

CONCLUSIONS: Based on the Galaxy framework, ASaiM offers a sophisticated environment with a variety of tools, workflows, documentation, and training to scientists working on complex microorganism communities. It makes analysis and exploration analyses of microbiota data easy, quick, transparent, reproducible, and shareable.}, } @article {pmid29789624, year = {2018}, author = {Vázquez-Castellanos, JF and Serrano-Villar, S and Jiménez-Hernández, N and Soto Del Rio, MD and Gayo, S and Rojo, D and Ferrer, M and Barbas, C and Moreno, S and Estrada, V and Rattei, T and Latorre, A and Moya, A and Gosalbes, MJ}, title = {Interplay between gut microbiota metabolism and inflammation in HIV infection.}, journal = {The ISME journal}, volume = {12}, number = {8}, pages = {1964-1976}, pmid = {29789624}, issn = {1751-7370}, mesh = {Bacteria/genetics/isolation & purification/*metabolism ; Bayes Theorem ; Digestive System Diseases/microbiology ; *Gastrointestinal Microbiome ; HIV Infections/*microbiology ; Humans ; Inflammation/microbiology ; Metabolic Networks and Pathways ; Metagenomics ; Transcriptome ; }, abstract = {HIV infection causes a disruption of gut-associated lymphoid tissue, driving a shift in the composition of gut microbiota. A deeper understanding of the metabolic changes and how they affect the interplay with the host is needed. Here, we assessed functional modifications of HIV-associated microbiota by combining metagenomic and metatranscriptomic analyses. The transcriptionally active microbiota was well-adapted to the inflamed environment, overexpressing pathways related to resistance to oxidative stress. Furthermore, gut inflammation was maintained by the Gram-negative nature of the HIV-associated microbiota and underexpression of anti-inflammatory processes, such as short chain fatty acid biosynthesis or indole production. We performed co-occurrence and metabolic network analyses that showed relevance in the microbiota structure of both taxonomic and metabolic HIV-associated biomarkers. The Bayesian network revealed the most determinant pathways for maintaining the structure stability of the bacterial community. In addition, we identified the taxa's contribution to metabolic activities and their interactions with host health.}, } @article {pmid29789574, year = {2018}, author = {Ge, Z and Sheh, A and Feng, Y and Muthupalani, S and Ge, L and Wang, C and Kurnick, S and Mannion, A and Whary, MT and Fox, JG}, title = {Helicobacter pylori-infected C57BL/6 mice with different gastrointestinal microbiota have contrasting gastric pathology, microbial and host immune responses.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8014}, pmid = {29789574}, issn = {2045-2322}, support = {P01 CA028842/CA/NCI NIH HHS/United States ; P30 ES002109/ES/NIEHS NIH HHS/United States ; T32 OD010978/OD/NIH HHS/United States ; }, mesh = {Animals ; Female ; Gastritis/immunology/microbiology/pathology ; *Gastrointestinal Microbiome/immunology ; *Helicobacter Infections/immunology/microbiology/pathology ; Helicobacter pylori/*immunology ; Host-Pathogen Interactions/immunology ; Immunity, Innate/*physiology ; Mice ; Mice, Inbred C57BL ; Species Specificity ; Stomach/immunology/*microbiology/*pathology ; }, abstract = {C57BL/6 (B6) mice from Taconic Sciences (Tac) and the Jackson Laboratory (Jax) were infected with H. pylori PMSS1 (Hp) for 16 week; there was no significant difference in the gastric histologic activity index between Hp infected Tac and Jax B6. However, the degree of gastric mucous metaplasia and Th1-associated IgG2c levels in response to Hp infection were increased in Tac mice over Jax mice, whereas the colonization levels of gastric Hp were higher by 8-fold in Jax B6 compared with Tac B6. Additionally, mRNA expression of gastric Il-1β, Il-17A and RegIIIγ were significantly lower in the infected Tac compared to the infected Jax mice. There were significant differences in the microbial community structures in stomach, colon, and feces between Jax and Tac B6 females. Differences in gastric microbial communities between Jax and Tac B6 females are predicted to affect the metagenome. Moreover, Hp infection perturbed the microbial community structures in the stomach, colon and feces of Jax mice, but only altered the colonic microbial composition of Tac mice. Our data indicate that the GI microbiome of Tac B6 mice is compositionally distinct from Jax B6 mice, which likely resulted in different pathological, immunological, and microbial responses to Hp infection.}, } @article {pmid29789027, year = {2018}, author = {Zhou, J and Xiong, X and Wang, KX and Zou, LJ and Ji, P and Yin, YL}, title = {Ethanolamine enhances intestinal functions by altering gut microbiome and mucosal anti-stress capacity in weaned rats.}, journal = {The British journal of nutrition}, volume = {120}, number = {3}, pages = {241-249}, doi = {10.1017/S0007114518001101}, pmid = {29789027}, issn = {1475-2662}, mesh = {Animals ; Antioxidants/pharmacology ; Bacteria/classification ; Dose-Response Relationship, Drug ; Drinking Water ; Ethanolamine/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Immunity, Mucosal ; Intestinal Mucosa/drug effects ; Intestines/*drug effects/microbiology ; Jejunum/drug effects ; Male ; Oxidative Stress ; Phenotype ; Phosphatidylethanolamines/chemistry ; RNA, Ribosomal, 16S/metabolism ; Rats ; Rats, Sprague-Dawley ; Weaning ; }, abstract = {Ethanolamine (Etn) contained in milk is the base constituent of phosphatidylethanolamine and is required for the proliferation of intestinal epithelial cells and bacteria, which is important for maintenance of the gut microbiome and intestinal development. The present study investigated the effect of Etn on intestinal function and microbiome using 21-d-old Sprague-Dawley rats treated with 0, 250, 500 and 1000 μm Etn in drinking water for 2 weeks immediately after weaning. Growth performance, intestinal morphology, antioxidant capacity and mucosal immunity, as well as gut microbiota community composition, were evaluated. Metagenomic prediction and metabolic phenotype analysis based on 16S RNA sequencing were also carried out to assess changes in metabolic functions. We found that weaned rats administered 500 μm Etn enhanced mucosal antioxidant capacity, as evidenced by higher superoxide dismutase and glutathione peroxidase levels in the jejunum (P<0·05) compared with those in the control group. Predominant microbes including Bacteroidetes, Proteobacteria, Elusimicrobia and Tenericutes were altered by different levels of Etn compared with the control group. An Etn concentration of 500 µm shifted colonic microbial metabolic functions that are in favour of lipid- and sugar-related metabolism and biosynthesis. Etn also altered the metabolic phenotypes such as anaerobic microbial counts, and oxidative stress tolerance at over 250 µm. This is the first report for a role of Etn in modifying gut microbiota and intestinal functions. Our findings highlighted the important role of Etn in shaping gut microbial community and promotes intestinal functions, which may provide a better insight of breast-feeding to infant's gut health.}, } @article {pmid29789015, year = {2018}, author = {Panebianco, C and Andriulli, A and Pazienza, V}, title = {Pharmacomicrobiomics: exploiting the drug-microbiota interactions in anticancer therapies.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {92}, pmid = {29789015}, issn = {2049-2618}, support = {RC1703GA31//Ministero della Salute/International ; RC1503GA40//Ministero della Salute/International ; }, mesh = {Antineoplastic Agents/*metabolism/*therapeutic use ; Bacteria/*metabolism ; Dysbiosis/*chemically induced ; Gastrointestinal Microbiome/*physiology ; Humans ; Intestines/microbiology ; Neoplasms/*drug therapy/microbiology ; Prebiotics ; Probiotics/*therapeutic use ; Synbiotics ; }, abstract = {Cancer is a major health burden worldwide, and despite continuous advances in medical therapies, resistance to standard drugs and adverse effects still represent an important cause of therapeutic failure. There is a growing evidence that gut bacteria can affect the response to chemo- and immunotherapeutic drugs by modulating either efficacy or toxicity. Moreover, intratumor bacteria have been shown to modulate chemotherapy response. At the same time, anticancer treatments themselves significantly affect the microbiota composition, thus disrupting homeostasis and exacerbating discomfort to the patient. Here, we review the existing knowledge concerning the role of the microbiota in mediating chemo- and immunotherapy efficacy and toxicity and the ability of these therapeutic options to trigger dysbiotic condition contributing to the severity of side effects. In addition, we discuss the use of probiotics, prebiotics, synbiotics, postbiotics, and antibiotics as emerging strategies for manipulating the microbiota in order to improve therapeutic outcome or at least ensure patients a better quality of life all along of anticancer treatments.}, } @article {pmid29788417, year = {2018}, author = {Patil, RD and Ellison, MJ and Wolff, SM and Shearer, C and Wright, AM and Cockrum, RR and Austin, KJ and Lamberson, WR and Cammack, KM and Conant, GC}, title = {Poor feed efficiency in sheep is associated with several structural abnormalities in the community metabolic network of their ruminal microbes.}, journal = {Journal of animal science}, volume = {96}, number = {6}, pages = {2113-2124}, pmid = {29788417}, issn = {1525-3163}, mesh = {Animal Feed/*analysis ; Animals ; Female ; *Gastrointestinal Microbiome ; *Metabolic Networks and Pathways ; *Metagenomics ; Rumen/metabolism/microbiology ; Sheep/microbiology/*physiology ; }, abstract = {Ruminant animals have a symbiotic relationship with the microorganisms in their rumens. In this relationship, rumen microbes efficiently degrade complex plant-derived compounds into smaller digestible compounds, a process that is very likely associated with host animal feed efficiency. The resulting simpler metabolites can then be absorbed by the host and converted into other compounds by host enzymes. We used a microbial community metabolic network inferred from shotgun metagenomics data to assess how this metabolic system differs between animals that are able to turn ingested feedstuffs into body mass with high efficiency and those that are not. We conducted shotgun sequencing of microbial DNA from the rumen contents of 16 sheep that differed in their residual feed intake (RFI), a measure of feed efficiency. Metagenomic reads from each sheep were mapped onto a database-derived microbial metabolic network, which was linked to the sheep metabolic network by interface metabolites (metabolites transferred from microbes to host). No single enzyme was identified as being significantly different in abundance between the low and high RFI animals (P > 0.05, Wilcoxon test). However, when we analyzed the metabolic network as a whole, we found several differences between efficient and inefficient animals. Microbes from low RFI (efficient) animals use a suite of enzymes closer in network space to the host's reactions than those of the high RFI (inefficient) animals. Similarly, low RFI animals have microbial metabolic networks that, on average, contain reactions using shorter carbon chains than do those of high RFI animals, potentially allowing the host animals to extract metabolites more efficiently. Finally, the efficient animals possess community networks with greater Shannon diversity among their enzymes than do inefficient ones. Thus, our system approach to the ruminal microbiome identified differences attributable to feed efficiency in the structure of the microbes' community metabolic network that were undetected at the level of individual microbial taxa or reactions.}, } @article {pmid29788084, year = {2018}, author = {Alcamán-Arias, ME and Farías, L and Verdugo, J and Alarcón-Schumacher, T and Díez, B}, title = {Microbial activity during a coastal phytoplankton bloom on the Western Antarctic Peninsula in late summer.}, journal = {FEMS microbiology letters}, volume = {365}, number = {10}, pages = {}, doi = {10.1093/femsle/fny090}, pmid = {29788084}, issn = {1574-6968}, mesh = {Antarctic Regions ; Bacteria/classification/genetics/growth & development/*metabolism ; Bacterial Proteins/genetics/metabolism ; Ecosystem ; Eukaryota/classification/genetics/growth & development/metabolism ; *Microbiota ; Photosynthesis ; Phytoplankton/classification/genetics/growth & development/*metabolism ; Seasons ; Seawater/chemistry/*microbiology ; }, abstract = {Phytoplankton biomass during the austral summer is influenced by freezing and melting cycles as well as oceanographic processes that enable nutrient redistribution in the West Antarctic Peninsula (WAP). Microbial functional capabilities, metagenomic and metatranscriptomic activities as well as inorganic 13C- and 15N-assimilation rates were studied in the surface waters of Chile Bay during two contrasting summer periods in 2014. Concentrations of Chlorophyll a (Chla) varied from 0.3 mg m-3 in February to a maximum of 2.5 mg m-3 in March, together with a decrease in nutrients; however, nutrients were never depleted. The microbial community composition remained similar throughout both sampling periods; however, microbial abundance and activity changed with Chla levels. An increased biomass of Bacillariophyta, Haptophyceae and Cryptophyceae was observed along with night-grazing activity of Dinophyceae and ciliates (Alveolates). During high Chla conditions, HCO3- uptake rates during daytime incubations increased 5-fold (>2516 nmol C L-1 d-1), and increased photosynthetic transcript numbers that were mainly associated with cryptophytes; meanwhile night time NO3- (>706 nmol N L-1 d-1) and NH4+ (41.7 nmol N L-1 d-1) uptake rates were 2- and 3-fold higher, respectively, due to activity from Alpha-/Gammaproteobacteria and Bacteroidetes (Flavobacteriia). Due to a projected acceleration in climate change in the WAP, this information is valuable for predicting the composition and functional changes in Antarctic microbial communities.}, } @article {pmid29786880, year = {2018}, author = {Sánchez-Sanhueza, G and Bello-Toledo, H and González-Rocha, G and Gonçalves, AT and Valenzuela, V and Gallardo-Escárate, C}, title = {Metagenomic study of bacterial microbiota in persistent endodontic infections using Next-generation sequencing.}, journal = {International endodontic journal}, volume = {51}, number = {12}, pages = {1336-1348}, doi = {10.1111/iej.12953}, pmid = {29786880}, issn = {1365-2591}, support = {folio 21130022//CONICYT-PCHA/Doctorado Nacional/2013/ ; N°214.102.016-1 IN//VRID UDEC/ ; }, mesh = {Adult ; Bacteria/*classification/*genetics/*pathogenicity ; Biodiversity ; Chile ; DNA, Bacterial/analysis ; Dental Pulp Cavity/*microbiology ; Female ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Male ; Metagenomics/*methods ; Microbiota/*genetics ; Middle Aged ; Periapical Periodontitis/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Root Canal Therapy ; }, abstract = {AIM: To determine the bacterial microbiota in root canals associated with persistent apical periodontitis and their relationship with the clinical characteristics of patients using next-generation sequencing (NGS).

METHODOLOGY: Bacterial samples from root canals associated with teeth having persistent apical periodontitis were taken from 24 patients undergoing root canal retreatment. Bacterial DNA was extracted, and V3-V4 variable regions of the 16S rRNA gene were amplified. The amplification was deep sequenced by Illumina technology to establish the metagenetic relationships among the bacterial species identified. The composition and diversity of microbial communities in the root canal and their relationships with clinical features were analysed. Parametric and nonparametric tests were used to analyse differences between patient characteristics and microbial data.

RESULTS: A total of 86 different operational taxonomic units (OTUs) were identified and Good's nonparametric coverage estimator method indicated that 99.9 ± 0.00001% diversity was recovered per sample. The largest number of bacteria belonged to the phylum Proteobacteria. According to the medical history from the American Society of Anesthesiologists (ASA) Classification System, ASA II-III had higher richness estimates and distinct phylogenetic relationships compared to ASA I individuals (P < 0.05). Periapical index (PAI) score 5 was associated with increased microbiota diversity in comparison to PAI score 4, and this index was reduced in symptomatic patients.

CONCLUSIONS: Based on the findings of this study, it is possible to suggest a close relationship between several clinical features and greater microbiota diversity with persistent endodontic infections. This work provides a better understanding on how microbial communities interact with their host and vice versa.}, } @article {pmid29784074, year = {2018}, author = {Korte, SW and Franklin, CL and Dorfmeyer, RA and Ericsson, AC}, title = {Effects of Fenbendazole-impregnated Feed and Topical Moxidectin during Quarantine on the Gut Microbiota of C57BL/6 Mice.}, journal = {Journal of the American Association for Laboratory Animal Science : JAALAS}, volume = {57}, number = {3}, pages = {229-235}, pmid = {29784074}, issn = {2769-6677}, support = {U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Administration, Oral ; Animal Feed ; Animals ; Antinematodal Agents/administration & dosage/pharmacology ; Feces/microbiology ; Fenbendazole/administration & dosage/*pharmacology ; Food, Fortified ; Gastrointestinal Microbiome/*drug effects ; Laboratory Animal Science ; Macrolides/administration & dosage/*pharmacology ; Mice ; Mice, Inbred C57BL ; Microbiota ; Quarantine ; Random Allocation ; Reproducibility of Results ; Rodent Diseases/parasitology/prevention & control ; }, abstract = {To protect the biosecurity of research rodent colonies, research institutions frequently require a quarantine period for live animals transferred into their facilities. Quarantine practices often include antibiotic and antiparasitic treatment with drugs such as fenbendazole and macrolide lactones. The influence of these compounds on the resident gut microbiota of mice is unknown, and any effects might subsequently affect model reproducibility. To test the influence of standard quarantine procedures on the composition of the microbiota, C57BL/6 mice, purchased from 2 different commercial suppliers, were randomly assigned to treatment groups (n = 12) by vendor and treated with fenbendazole-supplemented feed, topical moxidectin, both treatments, or no treatment (control), according to our institution's standard treatment regimen and duration. Feces were collected on arrival, immediately after completing the 8-wk treatment, and at 2 and 4 wk after treatment. Fecal DNA was extracted, sequenced, and analyzed to compare the changes in the microbiota of treated and control groups. Although significant main effects of time and treatment and interactions between those variables were detected in comparisons of richness, α-diversity, and β-diversity, the effect sizes associated with any particular treatment were consistently much smaller than that associated with acclimation to a new facility in the absence of any quarantine treatments. This outcome, along with the visual evaluation of principal coordinate analysis based on multiple similarity indices, suggests that time or institution plays a larger role in alterations of the murine gut microbiota than do quarantine treatments on its composition.}, } @article {pmid29783945, year = {2018}, author = {Westreich, ST and Treiber, ML and Mills, DA and Korf, I and Lemay, DG}, title = {SAMSA2: a standalone metatranscriptome analysis pipeline.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {175}, pmid = {29783945}, issn = {1471-2105}, support = {T32-GM008799/NH/NIH HHS/United States ; T32 GM008799/GM/NIGMS NIH HHS/United States ; R01AT008759/NH/NIH HHS/United States ; R01 AT008759/AT/NCCIH NIH HHS/United States ; }, mesh = {Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; Microbiota/genetics ; Sequence Analysis, RNA/*methods ; *Software ; }, abstract = {BACKGROUND: Complex microbial communities are an area of growing interest in biology. Metatranscriptomics allows researchers to quantify microbial gene expression in an environmental sample via high-throughput sequencing. Metatranscriptomic experiments are computationally intensive because the experiments generate a large volume of sequence data and each sequence must be compared with reference sequences from thousands of organisms.

RESULTS: SAMSA2 is an upgrade to the original Simple Annotation of Metatranscriptomes by Sequence Analysis (SAMSA) pipeline that has been redesigned for standalone use on a supercomputing cluster. SAMSA2 is faster due to the use of the DIAMOND aligner, and more flexible and reproducible because it uses local databases. SAMSA2 is available with detailed documentation, and example input and output files along with examples of master scripts for full pipeline execution.

CONCLUSIONS: SAMSA2 is a rapid and efficient metatranscriptome pipeline for analyzing large RNA-seq datasets in a supercomputing cluster environment. SAMSA2 provides simplified output that can be examined directly or used for further analyses, and its reference databases may be upgraded, altered or customized to fit the needs of any experiment.}, } @article {pmid29783653, year = {2018}, author = {Li, H and Liu, X and Chen, F and Zuo, K and Wu, C and Yan, Y and Chen, W and Lin, W and Xie, Q}, title = {Avian Influenza Virus Subtype H9N2 Affects Intestinal Microbiota, Barrier Structure Injury, and Inflammatory Intestinal Disease in the Chicken Ileum.}, journal = {Viruses}, volume = {10}, number = {5}, pages = {}, pmid = {29783653}, issn = {1999-4915}, mesh = {Animals ; Chickens/*virology ; Cytokines/genetics/metabolism ; DNA, Bacterial/genetics ; Enteritis/metabolism ; Escherichia coli/metabolism ; *Gastrointestinal Microbiome ; Influenza A Virus, H9N2 Subtype/*physiology ; Influenza in Birds/immunology/metabolism/*microbiology ; Intestinal Mucosa/*injuries ; Metagenomics ; RNA, Messenger/metabolism ; RNA, Ribosomal, 16S/genetics ; Specific Pathogen-Free Organisms ; }, abstract = {Avian influenza virus subtype H9N2 (H9N2 AIV) has caused significant losses to the poultry industry due to the high mortality associated with secondary infections attributable to E. coli. This study tries to address the underlying secondary mechanisms after H9N2 AIV infection. Initially, nine day-old specific pathogen-free chickens were assigned to control (uninfected) and H9N2-infected groups, respectively. Using Illumina sequencing, histological examination, and quantitative real-time PCR, it was found that H9N2 AIV caused intestinal microbiota disorder, injury, and inflammatory damage to the intestinal mucosa. Notably, the genera Escherichia, especially E. coli, significantly increased (p < 0.01) at five days post-infection (dpi), while Lactobacillus, Enterococcus, and other probiotic organisms were significantly reduced (p < 0.01). Simultaneously, the mRNA expression of tight junction proteins (ZO-1, claudin 3, and occludin), TFF2, and Muc2 were significantly reduced (p < 0.01), indicating the destruction of the intestinal epithelial cell tight junctions and the damage of mucin layer construction. Moreover, the mRNA expression of proinflammatory cytokines IFN-γ, IL-22, IFN-α, and IL-17A in intestinal epithelial cells were significantly upregulated, resulting in the inflammatory response and intestinal injury. Our findings may provide a theoretical basis for observed gastroenteritis-like symptoms such as diarrhea and secondary E. coli infection following H9N2 AIV infection.}, } @article {pmid29782923, year = {2019}, author = {Wong, SH and Kwong, TNY and Wu, CY and Yu, J}, title = {Clinical applications of gut microbiota in cancer biology.}, journal = {Seminars in cancer biology}, volume = {55}, number = {}, pages = {28-36}, doi = {10.1016/j.semcancer.2018.05.003}, pmid = {29782923}, issn = {1096-3650}, mesh = {Computational Biology ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenomics ; Neoplasms/diagnosis/*genetics/microbiology/therapy ; }, abstract = {The involvement of microorganisms in cancer has been increasing recognized. Collectively, microorganisms have been estimated to account for ∼20% of all cancers worldwide. Recent advances in metagenomics and bioinformatics have provided new insights on the microbial ecology in different tumors, pinpointing the roles of microorganisms in cancer formation, development and response to treatments. Furthermore, studies have emphasized the importance of host-microbial and inter-microbial interactions in the cancer microbiota. These studies have not only revolutionized our understanding of cancer biology, but also opened up new opportunities for cancer prevention, diagnosis, prognostication and treatment. This review article aims to summarize the microbiota in various cancers and their treatments, and explore clinical applications for such relevance.}, } @article {pmid29779275, year = {2018}, author = {Sun, TZ and Teng, F and Jia, SB and Tang, YP and Jiang, M and Huang, S and Yuan, X and Li, XL and Yang, F}, title = {[Salivary microbial communities associated with severe early childhood caries].}, journal = {Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology}, volume = {36}, number = {2}, pages = {150-155}, pmid = {29779275}, issn = {2618-0456}, mesh = {Child ; Child, Preschool ; *Dental Caries/microbiology ; Humans ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S ; Saliva ; }, abstract = {OBJECTIVE: To compare the salivary microbial profiles of healthy subjects and those with severe early childhood caries (S-ECC) by using high-throughput sequencing.

METHODS: Salivary samples were obtained from children with S-ECC (group C, n=24) and healthy children (group H, n=24). Total metagenomic DNA was extracted, and DNA amplicons of the V1-V3 hypervariable region of the 16S rRNA gene were generated and subjected to 454 sequencing. The characteristics of oral microbial communities from the two groups were compared based on microbial diversity and taxonomy assignment.

RESULTS: First, the microbial richness was significantly higher in group C than group H (P<0.05). Second, the microbial community structure was significantly different for the groups H and C (P<0.01). In addition, caries microbiota was significantly conserved in group C (P<0.001). High expression of suspected cariogenic microorganisms in group C (P<0.1) and health related microorganisms in group H (P<0.1) were identified. Finally, models of caries risk assessment were proposed to distinguish caries from healthy subjects with over 70% accuracy.

CONCLUSIONS: Salivary microbiota and certain taxa, such as caries-associated taxa (Prevotella), may be useful to screen/assess the children's risk of developing caries.}, } @article {pmid29778701, year = {2018}, author = {Truchado, DA and Williams, RAJ and Benítez, L}, title = {Natural history of avian papillomaviruses.}, journal = {Virus research}, volume = {252}, number = {}, pages = {58-67}, doi = {10.1016/j.virusres.2018.05.014}, pmid = {29778701}, issn = {1872-7492}, mesh = {Animals ; Birds/*virology ; DNA, Viral/genetics ; Genes, Viral ; Genetic Variation ; *Genome, Viral ; Genotype ; Oncogene Proteins, Viral/genetics ; Papillomaviridae/*classification/pathogenicity ; Papillomavirus Infections/diagnosis/*veterinary ; Phylogeny ; }, abstract = {Papillomaviruses (Family: Papillomaviridae) are small non-enveloped viruses that cause skin and mucosa infections in diverse vertebrates. The vast majority have been detected in mammals. However, the number of papillomaviruses described in birds is growing, especially because of metagenomic studies. Seven complete genomes and one partial sequence have been described, corresponding to five papillomavirus genera. These have been detected from various sample types, including skin, internal epithelium, and faecal material, from seven highly diverse wild and captive avian species. This review summarizes the molecular epidemiology of avian papillomaviruses, their genomic organization, evolutionary history and diagnostic techniques used for detection. The most commonly detected avian papillomavirus lesions are cauliflower-shaped papillomas, or warts, found on the tarsus and digits of common chaffinch (Fringilla coelebs) and occasionally brambling (Fringilla montifringilla). Similar warty growths have been detected in African grey parrot (Psittacus erithacus) and northern fulmar (Fulmarus glacialis), on the head and the foot, respectively. Papillomavirus has also been detected in avian tissue with no apparent lesions, similar to findings in humans and other mammals. Papillomavirus involvement was initially suspected to cause other types of lesions, such as internal papillomatosis of parrots (IPP) and proliferative pododermatitis in waterfowl. However, determined efforts failed to demonstrate papillomavirus presence. We briefly describe avian papillomavirus genomic organization and viral gene diversity. Furthermore, we performed a detailed analysis of avian papillomavirus non-coding regions and a preliminary computational analysis of their E9 proteins.}, } @article {pmid29777234, year = {2019}, author = {Hjorth, MF and Blædel, T and Bendtsen, LQ and Lorenzen, JK and Holm, JB and Kiilerich, P and Roager, HM and Kristiansen, K and Larsen, LH and Astrup, A}, title = {Prevotella-to-Bacteroides ratio predicts body weight and fat loss success on 24-week diets varying in macronutrient composition and dietary fiber: results from a post-hoc analysis.}, journal = {International journal of obesity (2005)}, volume = {43}, number = {1}, pages = {149-157}, pmid = {29777234}, issn = {1476-5497}, mesh = {Adult ; Bacteroides/*physiology ; Diet, Reducing ; Dietary Fiber/administration & dosage ; Energy Intake ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Middle Aged ; Nutrients/*administration & dosage ; Overweight/*diet therapy/metabolism/microbiology ; Prevotella/*physiology ; RNA, Ribosomal, 16S ; Retrospective Studies ; Weight Loss/*physiology ; }, abstract = {BACKGROUND/OBJECTIVES: Individuals with high pre-treatment bacterial Prevotella-to-Bacteroides (P/B) ratio have been reported to lose more body weight on diets high in fiber than subjects with a low P/B ratio. Therefore, the aim of the present study was to examine potential differences in dietary weight loss responses between participants with low and high P/B.

SUBJECTS/METHODS: Eighty overweight participants were randomized (52 completed) to a 500 kcal/d energy deficit diet with a macronutrient composition of 30 energy percentage (E%) fat, 52 E% carbohydrate and 18 E% protein either high (≈1500 mg calcium/day) or low ( ≤ 600 mg calcium/day) in dairy products for 24 weeks. Body weight, body fat, and dietary intake (by 7-day dietary records) were determined. Individuals were dichotomized according to their pre-treatment P/B ratio derived from 16S rRNA gene sequencing of collected fecal samples to test the potential modification of dietary effects using linear mixed models.

RESULTS: Independent of the randomized diets, individuals with high P/B lost 3.8 kg (95%CI, 1.8,5.8; P < 0.001) more body weight and 3.8 kg (95% CI, 1.1, 6.5; P = 0.005) more body fat compared to individuals with low P/B. After adjustment for multiple covariates, individuals with high P/B ratio lost 8.3 kg (95% CI, 5.8;10.9, P < 0.001) more body weight when consuming above compared to below 30 g fiber/10MJ whereas this weight loss was 3.2 kg (95% CI, 0.8;5.5, P = 0.008) among individuals with low P/B ratio [Mean difference: 5.1 kg (95% CI, 1.7;8.6, P = 0.003)]. Partial correlation coefficients between fiber intake and weight change was 0.90 (P < 0.001) among individuals with high P/B ratio and 0.25 (P = 0.29) among individuals with low P/B ratio.

CONCLUSIONS: Individuals with high P/B lost more body weight and body fat compared to individuals with low P/B, confirming that individuals with a high P/B are more susceptible to weight loss on a diet rich in fiber.}, } @article {pmid29777052, year = {2018}, author = {Hodgetts, T and Grenyer, R and Greenhough, B and McLeod, C and Dwyer, A and Lorimer, J}, title = {The microbiome and its publics: A participatory approach for engaging publics with the microbiome and its implications for health and hygiene.}, journal = {EMBO reports}, volume = {19}, number = {6}, pages = {}, pmid = {29777052}, issn = {1469-3178}, mesh = {*Community Participation ; Humans ; *Hygiene Hypothesis ; Metagenomics ; Microbiota/*genetics ; *Public Health ; Stakeholder Participation ; }, abstract = {Our project to engage members of the public with metagenomics of microbiota in their households yielded interesting results about their perception of health and hygiene. These findings could direct health‐oriented research and help scientists to navigate the social contexts or microbiome research. [Image: see text]}, } @article {pmid29773876, year = {2018}, author = {Argüello, H and Estellé, J and Zaldívar-López, S and Jiménez-Marín, Á and Carvajal, A and López-Bascón, MA and Crispie, F and O'Sullivan, O and Cotter, PD and Priego-Capote, F and Morera, L and Garrido, JJ}, title = {Early Salmonella Typhimurium infection in pigs disrupts Microbiome composition and functionality principally at the ileum mucosa.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {7788}, pmid = {29773876}, issn = {2045-2322}, mesh = {Animals ; Feces/microbiology ; Ileum/microbiology ; Intestinal Mucosa/microbiology ; *Microbiota ; Salmonella Infections/*microbiology ; Salmonella typhimurium/*pathogenicity ; Swine/*microbiology ; }, abstract = {Salmonella is a major foodborne pathogen which successfully infects animal species for human consumption such as swine. The pathogen has a battery of virulence factors which it uses to colonise and persist within the host. The host microbiota may play a role in resistance to, and may also be indirectly responsible from some of the consequences of, Salmonella infection. To investigate this, we used 16S rRNA metagenomic sequencing to determine the changes in the gut microbiota of pigs in response to infection by Salmonella Typhimurium at three locations: ileum mucosa, ileum content and faeces. Early infection (2 days post-infection) impacted on the microbiome diversity at the mucosa, reflected in a decrease in representatives of the generally regarded as desirable genera (i.e., Bifidobacterium and Lactobacillus). Severe damage in the epithelium of the ileum mucosa correlated with an increase in synergistic (with respect to Salmonella infection; Akkermansia) or opportunistically pathogenic bacteria (Citrobacter) and a depletion in anaerobic bacteria (Clostridium spp., Ruminococcus, or Dialliser). Predictive functional analysis, together with metabolomic analysis revealed changes in glucose and lipid metabolism in infected pigs. The observed changes in commensal healthy microbiota, including the growth of synergistic or potentially pathogenic bacteria and depletion of beneficial or competing bacteria, could contribute to the pathogen's ability to colonize the gut successfully. The findings from this study could be used to form the basis for further research aimed at creating intervention strategies to mitigate the effects of Salmonella infection.}, } @article {pmid29773467, year = {2018}, author = {Daliri, EB and Tango, CN and Lee, BH and Oh, DH}, title = {Human microbiome restoration and safety.}, journal = {International journal of medical microbiology : IJMM}, volume = {308}, number = {5}, pages = {487-497}, doi = {10.1016/j.ijmm.2018.05.002}, pmid = {29773467}, issn = {1618-0607}, mesh = {Anti-Bacterial Agents ; Bacteria/classification/isolation & purification ; Diet ; Dysbiosis/*therapy ; Fecal Microbiota Transplantation/*adverse effects/methods ; Gastrointestinal Microbiome/*physiology ; Humans ; Probiotics/*administration & dosage ; }, abstract = {The human gut microbiome consists of many bacteria which are in symbiotic relationship with human beings. The gut microbial metabolism, as well as the microbial-host co-metabolism, has been found to greatly influence health and disease. Factors such as diet, antibiotic use and lifestyle have been associated with alterations in the gut microbial community and may result in several pathological conditions. For this reason, several strategies including fecal microbiota transplant and probiotic administration have been applied and proven to be feasible and effective in restoring the gut microbiota in humans. Yet, safety concerns such as potential health risks that may arise from such interventions and how these strategies are regulated need to be addressed. Also, it will be important to know if these microbiome restoration strategies can have a profound impact on health. This review provides an overview of our current knowledge of the microbiome restoration strategies and safety issues on how these strategies are regulated.}, } @article {pmid29771345, year = {2018}, author = {Yin, X and Heeney, DD and Srisengfa, YT and Chen, SY and Slupsky, CM and Marco, ML}, title = {Sucrose metabolism alters Lactobacillus plantarum survival and interactions with the microbiota in the digestive tract.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {7}, pages = {}, doi = {10.1093/femsec/fiy084}, pmid = {29771345}, issn = {1574-6941}, mesh = {Animals ; Carbohydrate Metabolism/genetics/*physiology ; Female ; Intestinal Mucosa/*metabolism/microbiology ; Intestines/*microbiology ; Lactate Dehydrogenases/metabolism ; Lactobacillus plantarum/genetics/growth & development/*metabolism ; Mice ; Mice, Inbred BALB C ; Microbial Interactions/*physiology ; Microbiota ; Probiotics/pharmacology ; RNA, Ribosomal, 16S/genetics ; Sucrose/*metabolism ; beta-Fructofuranosidase/genetics ; }, abstract = {We investigated whether sucrose metabolism by probiotic Lactobacillus plantarum influences the intestinal survival and microbial responses to this organism when administered to mice fed a sucrose-rich, Western diet. A L. plantarum mutant unable to metabolize sucrose was constructed by deleting scrB, coding for beta-fructofuranosidase, in a rifampicin-resistant strain of L. plantarum NCIMB8826. The ScrB deficient mutant survived in 8-fold higher numbers compared to the wild-type strain when measured 24 h after administration on two consecutive days. According to 16S rRNA marker gene sequencing, proportions of Faecalibacterium and Streptococcus were elevated in mice fed the L. plantarum ΔscrB mutant. Metagenome predictions also indicated those mice contained a higher abundance of lactate dehydrogenases. This was further supported by a trend in elevated fecal lactate concentrations among mice fed the ΔscrB mutant. L. plantarum also caused other changes to the fecal metabolomes including higher concentrations of glycerol in mice fed the ΔscrB mutant and increased uracil, acetate and propionate levels among mice fed the wild-type strain. Taken together, these results suggest that sucrose metabolism alters the properties of L. plantarum in the digestive tract and that probiotics can differentially influence intestinal metabolomes via their carbohydrate consumption capabilities.}, } @article {pmid29770137, year = {2018}, author = {Stanisavljević, S and Dinić, M and Jevtić, B and Đedović, N and Momčilović, M and Đokić, J and Golić, N and Mostarica Stojković, M and Miljković, Đ}, title = {Gut Microbiota Confers Resistance of Albino Oxford Rats to the Induction of Experimental Autoimmune Encephalomyelitis.}, journal = {Frontiers in immunology}, volume = {9}, number = {}, pages = {942}, pmid = {29770137}, issn = {1664-3224}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cytokines/metabolism ; Disease Models, Animal ; *Disease Resistance/immunology ; Encephalomyelitis, Autoimmune, Experimental/*etiology/metabolism/therapy ; Fecal Microbiota Transplantation/methods ; Female ; *Gastrointestinal Microbiome/drug effects/immunology ; Lymph Nodes/immunology/metabolism ; Metagenome ; Metagenomics/methods ; Peyer's Patches/immunology/metabolism ; Rats ; }, abstract = {Albino Oxford (AO) rats are extremely resistant to induction of experimental autoimmune encephalomyelitis (EAE). EAE is an animal model of multiple sclerosis, a chronic inflammatory disease of the central nervous system (CNS), with established autoimmune pathogenesis. The autoimmune response against the antigens of the CNS is initiated in the peripheral lymphoid tissues after immunization of AO rats with CNS antigens. Subsequently, limited infiltration of the CNS occurs, yet without clinical sequels. It has recently become increasingly appreciated that gut-associated lymphoid tissues (GALT) and gut microbiota play an important role in regulation and propagation of encephalitogenic immune response. Therefore, modulation of AO gut microbiota by antibiotics was performed in this study. The treatment altered composition of gut microbiota in AO rats and led to a reduction in the proportion of regulatory T cells in Peyer's patches, mesenteric lymph nodes, and in lymph nodes draining the site of immunization. Upregulation of interferon-γ and interleukin (IL)-17 production was observed in the draining lymph nodes. The treatment led to clinically manifested EAE in AO rats with more numerous infiltrates and higher production of IL-17 observed in the CNS. Importantly, transfer of AO gut microbiota into EAE-prone Dark Agouti rats ameliorated the disease. These results clearly imply that gut microbiota is an important factor in AO rat resistance to EAE and that gut microbiota transfer is an efficacious way to treat CNS autoimmunity. These findings also support the idea that gut microbiota modulation has a potential as a future treatment of multiple sclerosis.}, } @article {pmid29768738, year = {2019}, author = {Cilleros, K and Valentini, A and Allard, L and Dejean, T and Etienne, R and Grenouillet, G and Iribar, A and Taberlet, P and Vigouroux, R and Brosse, S}, title = {Unlocking biodiversity and conservation studies in high-diversity environments using environmental DNA (eDNA): A test with Guianese freshwater fishes.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {27-46}, doi = {10.1111/1755-0998.12900}, pmid = {29768738}, issn = {1755-0998}, mesh = {Animals ; *Biodiversity ; DNA/chemistry/*genetics/*isolation & purification ; DNA Barcoding, Taxonomic/*methods ; Fishes/*classification/genetics ; Fresh Water/*chemistry ; Guyana ; Metagenomics/*methods ; }, abstract = {Determining the species compositions of local assemblages is a prerequisite to understanding how anthropogenic disturbances affect biodiversity. However, biodiversity measurements often remain incomplete due to the limited efficiency of sampling methods. This is particularly true in freshwater tropical environments that host rich fish assemblages, for which assessments are uncertain and often rely on destructive methods. Developing an efficient and nondestructive method to assess biodiversity in tropical freshwaters is highly important. In this study, we tested the efficiency of environmental DNA (eDNA) metabarcoding to assess the fish diversity of 39 Guianese sites. We compared the diversity and composition of assemblages obtained using traditional and metabarcoding methods. More than 7,000 individual fish belonging to 203 Guianese fish species were collected by traditional sampling methods, and ~17 million reads were produced by metabarcoding, among which ~8 million reads were assigned to 148 fish taxonomic units, including 132 fish species. The two methods detected a similar number of species at each site, but the species identities partially matched. The assemblage compositions from the different drainage basins were better discriminated using metabarcoding, revealing that while traditional methods provide a more complete but spatially limited inventory of fish assemblages, metabarcoding provides a more partial but spatially extensive inventory. eDNA metabarcoding can therefore be used for rapid and large-scale biodiversity assessments, while at a local scale, the two approaches are complementary and enable an understanding of realistic fish biodiversity.}, } @article {pmid29768437, year = {2018}, author = {Willmann, C and Mata, X and Hanghoej, K and Tonasso, L and Tisseyre, L and Jeziorski, C and Cabot, E and Chevet, P and Crubézy, E and Orlando, L and Esclassan, R and Thèves, C}, title = {Oral health status in historic population: Macroscopic and metagenomic evidence.}, journal = {PloS one}, volume = {13}, number = {5}, pages = {e0196482}, pmid = {29768437}, issn = {1932-6203}, mesh = {DNA, Ancient/isolation & purification ; DNA, Bacterial/genetics/history/isolation & purification ; Dental Caries/history/microbiology/pathology ; Female ; France ; Health Status ; History, 18th Century ; Humans ; Male ; Metagenomics ; Microbiota/genetics ; Oral Health/*history ; Paleodontology ; Periodontitis/history/microbiology/pathology ; Rural Population/history ; }, abstract = {Recent developments in High-Throughput DNA sequencing (HTS) technologies and ancient DNA (aDNA) research have opened access to the characterization of the microbial communities within past populations. Most studies have, however, relied on the analysis of dental calculus as one particular material type particularly prone to the molecular preservation of ancient microbial biofilms and potential of entire teeth for microbial characterization, both of healthy communities and pathogens in ancient individuals, remains overlooked. In this study, we used shotgun sequencing to characterize the bacterial composition from historical subjects showing macroscopic evidence of oral pathologies. We first carried out a macroscopic analysis aimed at identifying carious or periodontal diseases in subjects belonging to a French rural population of the 18th century AD. We next examined radiographically six subjects showing specific, characteristic dental pathologies and applied HTS shotgun sequencing to characterize the microbial communities present in and on the dental material. The presence of Streptococcus mutans and also Rothia dentocariosa, Actinomyces viscosus, Porphyromonas gingivalis, Tannerella forsythia, Pseudoramibacter alactolyticus, Olsenella uli and Parvimonas micra was confirmed through the presence of typical signatures of post-mortem DNA damage at an average depth-of-coverage ranging from 0.5 to 7X, with a minimum of 35% (from 35 to 93%) of the positions in the genome covered at least once. Each sampled tooth showed a specific bacterial signature associated with carious or periodontal pathologies. This work demonstrates that from a healthy independent tooth, without visible macroscopic pathology, we can identify a signature of specific pathogens and deduce the oral health status of an individual.}, } @article {pmid29767724, year = {2018}, author = {Magnabosco, C and Timmers, PHA and Lau, MCY and Borgonie, G and Linage-Alvarez, B and Kuloyo, O and Alleva, R and Kieft, TL and Slater, GF and van Heerden, E and Sherwood Lollar, B and Onstott, TC}, title = {Fluctuations in populations of subsurface methane oxidizers in coordination with changes in electron acceptor availability.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {7}, pages = {}, doi = {10.1093/femsec/fiy089}, pmid = {29767724}, issn = {1574-6941}, mesh = {Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; Electrons ; Geologic Sediments/*microbiology ; Metagenomics/methods ; Methane/*metabolism ; Microbiota/*physiology ; Oxidation-Reduction ; Proteomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The concentrations of electron donors and acceptors in the terrestrial subsurface biosphere fluctuate due to migration and mixing of subsurface fluids, but the mechanisms and rates at which microbial communities respond to these changes are largely unknown. Subsurface microbial communities exhibit long cellular turnover times and are often considered relatively static-generating just enough ATP for cellular maintenance. Here, we investigated how subsurface populations of CH4 oxidizers respond to changes in electron acceptor availability by monitoring the biological and geochemical composition in a 1339 m-below-land-surface (mbls) fluid-filled fracture over the course of both longer (2.5 year) and shorter (2-week) time scales. Using a combination of metagenomic, metatranscriptomic, and metaproteomic analyses, we observe that the CH4 oxidizers within the subsurface microbial community change in coordination with electron acceptor availability over time. We then validate these findings through a series of 13C-CH4 laboratory incubation experiments, highlighting a connection between composition of subsurface CH4 oxidizing communities and electron acceptor availability.}, } @article {pmid29762899, year = {2018}, author = {Zhang, X and Chen, Y and Zhu, J and Zhang, M and Ho, CT and Huang, Q and Cao, J}, title = {Metagenomics Analysis of Gut Microbiota in a High Fat Diet-Induced Obesity Mouse Model Fed with (-)-Epigallocatechin 3-O-(3-O-Methyl) Gallate (EGCG3″Me).}, journal = {Molecular nutrition & food research}, volume = {62}, number = {13}, pages = {e1800274}, doi = {10.1002/mnfr.201800274}, pmid = {29762899}, issn = {1613-4133}, mesh = {Animals ; Diet, High-Fat ; Disease Models, Animal ; Gallic Acid/*analogs & derivatives/pharmacology ; *Gastrointestinal Microbiome ; Male ; *Metagenomics ; Mice ; Mice, Inbred C57BL ; Obesity/*microbiology ; }, abstract = {SCOPE: (-)-Epigallocatechin 3-O-(3-O-methyl) gallate (EGCG3″Me) has been shown to have a modulatory effect on human intestinal microbiota, and the relationship between intestinal flora and obesity has attracted more and more attention recently. Here, the potential link between EGCG3″Me and gut microbiota composition, as well as the underlying mechanisms of the anti-obesity activity of EGCG3″Me are investigated.

METHODS AND RESULTS: EGCG3″Me was prepared from oolong tea by column chromatography, and the influence of EGCG3″Me on intestinal microbiota was analyzed using a human-flora-associated high fat diet (HFD)-induced obesity mouse model by metagenomics. EGCG3″Me showed a weight reducing effect, ameliorated the HFD-induced gut dysbiosis, and significantly decreased the ratio of Firmicutes/Bacteroidetes. Moreover, the Kyoto Encyclopedia of Genes and Genomes (KEGG) database provided significant differences in differentially expressed genes in response to EGCG3″Me treatment. The results showed enrichment of genes involved in the biosynthesis of amino acids, the two-component system, ATP-binding cassette (ABC) transporters, purine metabolism, and carbon metabolism.

CONCLUSION: An EGCG3″Me supplemented diet produces promising effects on gut microecology by enhancing beneficial microbial populations and by affecting metabolic pathways including amino acids biosynthesis, the two-component system, and ABC transporters, contributing to the improvement of host health.}, } @article {pmid29762673, year = {2018}, author = {Pan, H and Guo, R and Zhu, J and Wang, Q and Ju, Y and Xie, Y and Zheng, Y and Wang, Z and Li, T and Liu, Z and Lu, L and Li, F and Tong, B and Xiao, L and Xu, X and Li, R and Yuan, Z and Yang, H and Wang, J and Kristiansen, K and Jia, H and Liu, L}, title = {A gene catalogue of the Sprague-Dawley rat gut metagenome.}, journal = {GigaScience}, volume = {7}, number = {5}, pages = {}, pmid = {29762673}, issn = {2047-217X}, mesh = {Animals ; Feces/microbiology ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/*metabolism ; Humans ; Male ; Metagenome/*genetics ; Mice ; Molecular Sequence Annotation ; Rats, Sprague-Dawley ; }, abstract = {BACKGROUND: Laboratory rats such as the Sprague-Dawley (SD) rats are an important model for biomedical studies in relation to human physiological or pathogenic processes. Here we report the first catalog of microbial genes in fecal samples from Sprague-Dawley rats.

FINDINGS: The catalog was established using 98 fecal samples from 49 SD rats, divided in 7 experimental groups, and collected at different time points 30 days apart. The established gene catalog comprises 5,130,167 non-redundant genes with an average length of 750 bp, among which 64.6% and 26.7% were annotated to phylum and genus levels, respectively. Functionally, 53.1%, 21.8%,and 31% of the genes could be annotated to KEGG orthologous groups, modules, and pathways, respectively.

CONCLUSIONS: A comparison of rat gut metagenome catalogue with human or mouse revealed a higher pairwise overlap between rats and humans (2.47%) than between mice and humans (1.19%) at the gene level. Ninety-seven percent of the functional pathways in the human catalog were present in the rat catalogue, underscoring the potential use of rats for biomedical research.}, } @article {pmid29760079, year = {2018}, author = {Wang, GD and Zhang, BL and Zhou, WW and Li, YX and Jin, JQ and Shao, Y and Yang, HC and Liu, YH and Yan, F and Chen, HM and Jin, L and Gao, F and Zhang, Y and Li, H and Mao, B and Murphy, RW and Wake, DB and Zhang, YP and Che, J}, title = {Selection and environmental adaptation along a path to speciation in the Tibetan frog Nanorana parkeri.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {22}, pages = {E5056-E5065}, pmid = {29760079}, issn = {1091-6490}, mesh = {Animals ; Anura/*genetics/*physiology ; Gene Flow/*genetics ; *Genetic Speciation ; Hybridization, Genetic ; Metagenomics ; Phylogeny ; Selection, Genetic ; Tibet ; }, abstract = {Tibetan frogs, Nanorana parkeri, are differentiated genetically but not morphologically along geographical and elevational gradients in a challenging environment, presenting a unique opportunity to investigate processes leading to speciation. Analyses of whole genomes of 63 frogs reveal population structuring and historical demography, characterized by highly restricted gene flow in a narrow geographic zone lying between matrilines West (W) and East (E). A population found only along a single tributary of the Yalu Zangbu River has the mitogenome only of E, whereas nuclear genes of W comprise 89-95% of the nuclear genome. Selection accounts for 579 broadly scattered, highly divergent regions (HDRs) of the genome, which involve 365 genes. These genes fall into 51 gene ontology (GO) functional classes, 14 of which are likely to be important in driving reproductive isolation. GO enrichment analyses of E reveal many overrepresented functional categories associated with adaptation to high elevations, including blood circulation, response to hypoxia, and UV radiation. Four genes, including DNAJC8 in the brain, TNNC1 and ADORA1 in the heart, and LAMB3 in the lung, differ in levels of expression between low- and high-elevation populations. High-altitude adaptation plays an important role in maintaining and driving continuing divergence and reproductive isolation. Use of total genomes enabled recognition of selection and adaptation in and between populations, as well as documentation of evolution along a stepped cline toward speciation.}, } @article {pmid29759899, year = {2018}, author = {Belgini, DRB and Siqueira, VM and Oliveira, DM and Fonseca, SG and Piccin-Santos, V and Dias, RS and Quartaroli, L and Souza, RS and Torres, APR and Sousa, MP and Silva, CM and Silva, CC and De Paula, SO and Oliveira, VM}, title = {Integrated diversity analysis of the microbial community in a reverse osmosis system from a Brazilian oil refinery.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {5}, pages = {473-486}, doi = {10.1016/j.syapm.2018.03.007}, pmid = {29759899}, issn = {1618-0984}, mesh = {Bacteria/*classification/genetics/isolation & purification ; Bacterial Physiological Phenomena ; *Biodiversity ; Biofilms/growth & development ; Brazil ; Fungi/*classification/genetics/isolation & purification/physiology ; Metagenomics ; *Microbial Consortia ; *Oil and Gas Industry ; Osmosis ; Wastewater/*microbiology ; Water Purification/*methods ; }, abstract = {Oil refineries are known for the large volume of water used in their processes, as well as the amount of wastewater generated at the end of the production chain. Due to strict environmental regulations, the recycling of water has now become a viable alternative for refineries. Among the many methods available to treat wastewater for reuse, the use of membranes in reverse osmosis systems stands out due to several economic and environmental benefits. However, these systems are vulnerable to contamination and deposition of microorganisms, mainly because of the feedwater quality. In this study, the microbial diversity of feedwater and reverse osmosis membranes was investigated using a combination of culture-dependent and culture-independent methods in order to characterize the microorganisms colonizing and deteriorating the membranes. In total, 37 bacterial isolates, 17 filamentous fungi and approximately 400 clones were obtained and analyzed. Among the bacterial genera identified, the most represented were Sphingobium, Acidovorax, Microbacterium, Rhizobium and Shinella. The results revealed genera that acted as candidate key players in initial biofilm formation in membrane systems, and provided important information concerning the microbial ecology of oligotrophic aquatic systems.}, } @article {pmid29758429, year = {2018}, author = {Najar, IN and Sherpa, MT and Das, S and Das, S and Thakur, N}, title = {Microbial ecology of two hot springs of Sikkim: Predominate population and geochemistry.}, journal = {The Science of the total environment}, volume = {637-638}, number = {}, pages = {730-745}, doi = {10.1016/j.scitotenv.2018.05.037}, pmid = {29758429}, issn = {1879-1026}, mesh = {Archaea ; Biodiversity ; *Ecology ; Hot Springs/*microbiology ; India ; Phylogeny ; RNA, Ribosomal, 16S ; Sikkim ; }, abstract = {Northeastern regions of India are known for their floral and faunal biodiversity. Especially the state of Sikkim lies in the eastern Himalayan ecological hotspot region. The state harbors many sulfur rich hot springs which have therapeutic and spiritual values. However, these hot springs are yet to be explored for their microbial ecology. The development of neo generation techniques such as metagenomics has provided an opportunity for inclusive study of microbial community of different environment. The present study describes the microbial diversity in two hot springs of Sikkim that is Polok and Borong with the assist of culture dependent and culture independent approaches. The culture independent techniques used in this study were next generation sequencing (NGS) and Phospholipid Fatty Acid Analysis (PLFA). Having relatively distinct geochemistry both the hot springs are thermophilic environments with the temperature range of 50-77 °C and pH range of 5-8. Metagenomic data revealed the dominance of bacteria over archaea. The most abundant phyla were Proteobacteria and Bacteroidetes although other phyla were also present such as Acidobacteria, Nitrospirae, Firmicutes, Proteobacteria, Parcubacteria and Spirochaetes. The PLFA studies have shown the abundance of Gram Positive bacteria followed by Gram negative bacteria. The culture dependent technique was correlative with PLFA studies. Most abundant bacteria as isolated and identified were Gram-positive genus Geobacillus and Anoxybacillus. The genus Geobacillus has been reported for the first time in North-Eastern states of India. The Geobacillus species obtained from the concerned hot springs were Geobacillus toebii, Geobacillus lituanicus, Geobacillus Kaustophillus and the Anoxybacillus species includes Anoxybacillus gonensis and Anoxybacillus Caldiproteolyticus. The distribution of major genera and their statistical correlation analyses with the geochemistry of the springs predicted that the temperature, pH, alkalinity, Ca[2+], Mg[2+], Cl[2+], and sulfur were main environmental variables influencing the microbial community composition and diversity. Also the piper diagram suggested that the water of both the hot springs are Ca-HCO[3-] type and can be predicted as shallow fresh ground waters. This study has provided an insight into the ecological interaction of the diverse microbial communities and associated physicochemical parameters, which will help in determining the future studies on different biogeochemical pathways in these hot springs.}, } @article {pmid29755475, year = {2018}, author = {Zhang, C and Björkman, A and Cai, K and Liu, G and Wang, C and Li, Y and Xia, H and Sun, L and Kristiansen, K and Wang, J and Han, J and Hammarström, L and Pan-Hammarström, Q}, title = {Impact of a 3-Months Vegetarian Diet on the Gut Microbiota and Immune Repertoire.}, journal = {Frontiers in immunology}, volume = {9}, number = {}, pages = {908}, pmid = {29755475}, issn = {1664-3224}, mesh = {Adult ; Bacteria/classification/*metabolism ; Butyrates/metabolism ; *Diet, Vegetarian ; Female ; Gastrointestinal Microbiome/*genetics/*immunology ; High-Throughput Nucleotide Sequencing ; Humans ; Immunity, Mucosal ; Immunoglobulin A ; Inflammation ; Male ; *Metagenome ; Middle Aged ; Probiotics ; Time Factors ; Vegetarians ; }, abstract = {The dietary pattern can influence the immune system directly, but may also modulate it indirectly by regulating the gut microbiota. Here, we investigated the effect of a 3-months lacto-ovo-vegetarian diet on the diversity of gut microbiota and the immune system in healthy omnivorous volunteers, using high-throughput sequencing technologies. The short-term vegetarian diet did not have any major effect on the diversity of the immune system and the overall composition of the metagenome. The prevalence of bacterial genera/species with known beneficial effects on the intestine, including butyrate-producers and probiotic species and the balance of autoimmune-related variable genes/families were, however, altered in the short-term vegetarians. A number of bacterial species that are associated with the expression level of IgA, a key immunoglobulin class that protects the gastrointestinal mucosal system, were also identified. Furthermore, a lower diversity of T-cell repertoire and expression level of IgE, as well as a reduced abundance of inflammation-related genes in the gut microbiota were potentially associated with a control group with long-term vegetarians. Thus, the composition and duration of the diet may have an impact on the balance of pro-/anti-inflammatory factors in the gut microbiota and immune system.}, } @article {pmid29753707, year = {2018}, author = {Fuentes, I and Guttmann-Gruber, C and Tay, ASL and Piñón Hofbauer, J and Denil, SLIJ and Reichelt, J and Palisson, F and Common, JEA and South, AP}, title = {Reduced Microbial Diversity Is a Feature of Recessive Dystrophic Epidermolysis Bullosa-Involved Skin and Wounds.}, journal = {The Journal of investigative dermatology}, volume = {138}, number = {11}, pages = {2492-2495}, doi = {10.1016/j.jid.2018.04.026}, pmid = {29753707}, issn = {1523-1747}, mesh = {Adult ; Aged ; Austria/epidemiology ; Biodiversity ; Chile/epidemiology ; Cohort Studies ; Epidermolysis Bullosa Dystrophica/epidemiology/genetics/*microbiology ; Female ; Genes, Recessive ; Humans ; Male ; Metagenome ; Microbiota/*physiology ; Middle Aged ; Skin/*microbiology/pathology ; Staphylococcaceae/*physiology ; Wounds and Injuries/*microbiology/pathology ; Young Adult ; }, } @article {pmid29753695, year = {2018}, author = {Chu, DM and Seferovic, M and Pace, RM and Aagaard, KM}, title = {The microbiome in preterm birth.}, journal = {Best practice & research. Clinical obstetrics & gynaecology}, volume = {52}, number = {}, pages = {103-113}, doi = {10.1016/j.bpobgyn.2018.03.006}, pmid = {29753695}, issn = {1532-1932}, mesh = {Female ; Humans ; Lactobacillus/metabolism ; Longitudinal Studies ; *Microbiota ; Placenta/microbiology ; Pregnancy ; Premature Birth/*microbiology ; Vagina/microbiology ; }, abstract = {The microbiome is thought to play a role in the maintenance of a healthy pregnancy and thus may either contribute to or protect from preterm birth. Study of the human microbiome has been aided by metagenomic sequencing approaches, providing greater insight into the commensal bacteria that coexist in and on our bodies. The vaginal microbiome has been the most widely studied, though there have been recent efforts to explore the gut, cervical-vaginal, placental and oral microbiomes in the further search of etiologies of preterm birth. To date, a specific microbiome community or microorganism has yet to be reliably associated with preterm birth. This is partly due to the fact that the 'normal' constituents' microbiome can vary widely between healthy individuals. Before our knowledge of the microbiome can be utilized and applied in clinical practice, a greater understanding of the 'healthy' microbiome must be achieved. In particular, we must first appreciate how our microbes influence our biology to promote a healthy pregnancy or alternately render preterm birth.}, } @article {pmid29750384, year = {2019}, author = {Kosnicki, KL and Penprase, JC and Cintora, P and Torres, PJ and Harris, GL and Brasser, SM and Kelley, ST}, title = {Effects of moderate, voluntary ethanol consumption on the rat and human gut microbiome.}, journal = {Addiction biology}, volume = {24}, number = {4}, pages = {617-630}, pmid = {29750384}, issn = {1369-1600}, support = {R21 AA023291/AA/NIAAA NIH HHS/United States ; AA023291/GF/NIH HHS/United States ; }, mesh = {*Alcohol Drinking ; Animals ; Biodiversity ; Central Nervous System Depressants/*administration & dosage ; Dysbiosis/*microbiology ; Ethanol/*administration & dosage ; Gastrointestinal Microbiome/*drug effects ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; RNA, Ribosomal, 16S ; Rats ; Sequence Analysis, RNA ; }, abstract = {Many alcohol-induced health complications are directly attributable to the toxicity of alcohol or its metabolites, but another potential health impact of alcohol may be on the microbial communities of the human gut. Clear distinctions between healthy and diseased-state gut microbiota have been observed in subjects with metabolic diseases, and recent studies suggest that chronic alcoholism is linked to gut microbiome dysbiosis. Here, we investigated the effects of moderate levels of alcohol consumption on the gut microbiome in both rats and humans. The gut microbiota of rats voluntarily consuming a 20 percent ethanol solution, on alternate days, were compared with a non-exposed control group to identify differential taxonomic and functional profiles. Gut microbial diversity profiles were determined using culture-independent amplification, next-generation sequencing and bioinformatic analysis of bacterial 16S ribosomal RNA gene sequence libraries. Our results showed that, compared with controls, ethanol-consuming rats experienced a significant decline in the biodiversity of their gut microbiomes, a state generally associated with dysbiosis. We also observed significant shifts in the overall diversity of the gut microbial communities and a dramatic change in the relative abundance of particular microbes, such as the Lactobacilli. We also compared our results to human fecal microbiome data collected as part of the citizen science American Gut Project. In contrast to the rat data, human drinkers had significantly higher gut microbial biodiversity than non-drinkers. However, we also observed that microbes that differed among the human subjects displayed similar trends in the rat model, including bacteria implicated in metabolic disease.}, } @article {pmid29749926, year = {2018}, author = {Roberts, JMK and Anderson, DL and Durr, PA}, title = {Metagenomic analysis of Varroa-free Australian honey bees (Apis mellifera) shows a diverse Picornavirales virome.}, journal = {The Journal of general virology}, volume = {99}, number = {6}, pages = {818-826}, doi = {10.1099/jgv.0.001073}, pmid = {29749926}, issn = {1465-2099}, mesh = {Animals ; Australia ; Bees/*virology ; *Genome, Viral ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Microbiota ; Phylogeny ; Picornaviridae/*classification/genetics ; RNA, Viral/genetics ; Varroidae ; }, abstract = {The viral landscape of the honey bee (Apismellifera) has changed as a consequence of the global spread of the parasitic mite Varroa destructor and accompanying virulent strains of the iflavirus deformed wing virus (DWV), which the mite vectors. The presence of DWV in honey bee populations is known to influence the occurrence of other viruses, suggesting that the current known virome of A. mellifera may be undercharacterized. Here we tested this hypothesis by examining the honey bee virome in Australia, which is uniquely free of parasitic mites or DWV. Using a high-throughput sequencing (HTS) approach, we examined the RNA virome from nine pools of A. mellifera across Australia. In addition to previously reported honey bee viruses, several other insect viruses were detected, including strains related to aphid lethal paralysis virus (ALPV) and Rhopalosiphum padi virus (RhPV), which have recently been identified as infecting honey bees in the USA, as well as several other viruses recently found in Drosophila spp. A further 42 putative novel insect virus genomes spanning the order Picornavirales were assembled, which significantly increases the known viral diversity in A. mellifera. Among these novel genomes, we identified several that were similar (but different) to key A. mellifera viruses, such as DWV, that warrant further investigation. We propose that A. mellifera may be preferentially infected with viruses of the order Picornavirales and that a diverse population of these viruses may be representative of a Varroa-free landscape.}, } @article {pmid29748902, year = {2018}, author = {Escudero, L and Oetiker, N and Gallardo, K and Tebes-Cayo, C and Guajardo, M and Nuñez, C and Davis-Belmar, C and Pueyo, JJ and Chong Díaz, G and Demergasso, C}, title = {A thiotrophic microbial community in an acidic brine lake in Northern Chile.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {8}, pages = {1403-1419}, doi = {10.1007/s10482-018-1087-8}, pmid = {29748902}, issn = {1572-9699}, support = {1100795//Fondecyt/ ; 32002137//BHP Minerals Americas/ ; }, mesh = {Bacteria/*classification/metabolism ; Biodiversity ; Carbon Cycle ; Chile ; DNA, Bacterial/genetics ; Energy Metabolism ; Geologic Sediments/microbiology ; Lakes/*microbiology ; Metagenomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salts ; Sulfur/*metabolism ; }, abstract = {The endorheic basins of the Northern Chilean Altiplano contain saline lakes and salt flats. Two of the salt flats, Gorbea and Ignorado, have high acidic brines. The causes of the local acidity have been attributed to the occurrence of volcanic native sulfur, the release of sulfuric acid by oxidation, and the low buffering capacity of the rocks in the area. Understanding the microbial community composition and available energy in this pristine ecosystem is relevant in determining the origin of the acidity and in supporting the rationale of conservation policies. Besides, a comparison between similar systems in Australia highlights key microbial components and specific ones associated with geological settings and environmental conditions. Sediment and water samples from the Salar de Gorbea were collected, physicochemical parameters measured and geochemical and molecular biological analyses performed. A low diversity microbial community was observed in brines and sediments dominated by Actinobacteria, Algae, Firmicutes and Proteobacteria. Most of the constituent genera have been reported to be either sulfur oxidizing microorganisms or ones having the potential for sulfur oxidation given available genomic data and information drawn from the literature on cultured relatives. In addition, a link between sulfur oxidation and carbon fixation was observed. In contrast, to acid mine drainage communities, Gorbea microbial diversity is mainly supported by chemolithoheterotrophic, facultative chemolithoautotrophic and oligotrophic sulfur oxidizing populations indicating that microbial activity should also be considered as a causative agent of local acidity.}, } @article {pmid29747892, year = {2018}, author = {Valentine, G and Chu, DM and Stewart, CJ and Aagaard, KM}, title = {Relationships Between Perinatal Interventions, Maternal-Infant Microbiomes, and Neonatal Outcomes.}, journal = {Clinics in perinatology}, volume = {45}, number = {2}, pages = {339-355}, doi = {10.1016/j.clp.2018.01.008}, pmid = {29747892}, issn = {1557-9840}, mesh = {Adult ; Female ; Fetal Diseases/*microbiology ; Humans ; *Infant Health ; Infant, Newborn ; Infant, Newborn, Diseases/*microbiology/therapy ; Male ; *Maternal Health ; Microbiota/immunology/*physiology ; Perinatal Care/methods ; Pregnancy ; Premature Birth/*microbiology ; Prenatal Care/methods ; Probiotics/administration & dosage ; }, abstract = {The human microbiome acquires its vastness and diversity over a relatively short time period during development. Much is unknown, however, about the precise prenatal versus postnatal timing or its sources and determinants. Given early evidence of a role for influences during pregnancy and early neonatal and infant life on the microbiome and subsequent metabolic health, research investigating the development and shaping of the microbiome in the fetus and neonate is an important arena for study. This article reviews the relevant available literature and future questions on what shapes the microbiome during early development and mechanisms for doing so.}, } @article {pmid29746643, year = {2018}, author = {Metzler-Zebeli, BU and Lawlor, PG and Magowan, E and Zebeli, Q}, title = {Interactions between metabolically active bacteria and host gene expression at the cecal mucosa in pigs of diverging feed efficiency.}, journal = {Journal of animal science}, volume = {96}, number = {6}, pages = {2249-2264}, pmid = {29746643}, issn = {1525-3163}, mesh = {Animal Feed ; Animals ; Bacteria/genetics/*metabolism ; Cecum/microbiology ; *Eating ; Female ; Gastrointestinal Microbiome/*physiology ; *Gene Expression Regulation ; High-Throughput Nucleotide Sequencing/veterinary ; Immunity, Innate ; Male ; *Metagenome ; Sequence Analysis, RNA/veterinary ; Swine/genetics/immunology/*microbiology ; }, abstract = {Little is known about the role of the gut mucosal microbiota and microbe-host signaling in the variation of pig's feed efficiency (FE). This study therefore aimed to investigate the FE-related differences in the metabolically active mucosal bacterial microbiota and expression of genes for innate immune response, barrier function, nutrient uptake, and incretins in the cecum of finishing pigs. Pigs (n = 72) were ranked for their residual feed intake (RFI; metric for FE) between days 42 and 91 postweaning and were stratified within litter and sex into high (HRFI; n = 8) and low RFI (LRFI; n = 8). Cecal mucosa and digesta were collected on day 137-141 of life. After isolating total RNA from the mucosa, the RNA was transcribed into cDNA which was used for gene expression analysis, total bacterial quantification, and high-throughput sequencing (Illumina MiSeq) of the hypervariable V3-V4 region of the 16S rRNA gene. The RFI differed by 2.1 kg between low RFI (LRFI; good FE) and high RFI (HRFI; poor FE) pigs (P < 0.001). The cecal mucosa was mainly colonized by Helicobacteraceae, Campylobacteraceae, Veillonellaceae, Lachnospiraceae, and Prevotellaceae. Despite the lack of differences in microbial diversity and absolute abundance, RFI-associated compositional differences were found. The predominant genus Campylobacter tended (P < 0.10) to be 0.4-fold more abundant in LRFI pigs, whereas low abundant Escherichia/Shigella (P < 0.05), Ruminobacter (P < 0.05), and Veillonella (P < 0.10) were 3.4-, 6.6-, and 4.4-fold less abundant at the cecal mucosa of LRFI compared to HRFI pigs. Moreover, mucin 2 and zona occludens-1 were less expressed (P < 0.05) in the cecal mucosa of LRFI compared to HRFI pigs. Cecal mucosal expression of monocarboxylate transporter-1, glucagon-like peptide-1, and peptide YY further tended (P < 0.10) to be downregulated in LRFI compared to HRFI pigs, indicating an enhanced VFA uptake and signaling in HRFI pigs. Sparse partial least square regression and relevance networking support the hypothesis that certain mucosal bacteria and luminal microbial metabolites were more associated than others with differences in RFI and cecal gene expression. However, present results do not allow the determination of whether mucosal bacterial changes contributed to variation in FE or were rather a consequence of FE-related changes in the pig's physiology or feeding behavior.}, } @article {pmid29743119, year = {2018}, author = {Zolfo, M and Asnicar, F and Manghi, P and Pasolli, E and Tett, A and Segata, N}, title = {Profiling microbial strains in urban environments using metagenomic sequencing data.}, journal = {Biology direct}, volume = {13}, number = {1}, pages = {9}, pmid = {29743119}, issn = {1745-6150}, mesh = {Acinetobacter/genetics ; Genome, Bacterial/genetics ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; }, abstract = {BACKGROUND: The microbial communities populating human and natural environments have been extensively characterized with shotgun metagenomics, which provides an in-depth representation of the microbial diversity within a sample. Microbes thriving in urban environments may be crucially important for human health, but have received less attention than those of other environments. Ongoing efforts started to target urban microbiomes at a large scale, but the most recent computational methods to profile these metagenomes have never been applied in this context. It is thus currently unclear whether such methods, that have proven successful at distinguishing even closely related strains in human microbiomes, are also effective in urban settings for tasks such as cultivation-free pathogen detection and microbial surveillance. Here, we aimed at a) testing the currently available metagenomic profiling tools on urban metagenomics; b) characterizing the organisms in urban environment at the resolution of single strain and c) discussing the biological insights that can be inferred from such methods.

RESULTS: We applied three complementary methods on the 1614 metagenomes of the CAMDA 2017 challenge. With MetaMLST we identified 121 known sequence-types from 15 species of clinical relevance. For instance, we identified several Acinetobacter strains that were close to the nosocomial opportunistic pathogen A. nosocomialis. With StrainPhlAn, a generalized version of the MetaMLST approach, we inferred the phylogenetic structure of Pseudomonas stutzeri strains and suggested that the strain-level heterogeneity in environmental samples is higher than in the human microbiome. Finally, we also probed the functional potential of the different strains with PanPhlAn. We further showed that SNV-based and pangenome-based profiling provide complementary information that can be combined to investigate the evolutionary trajectories of microbes and to identify specific genetic determinants of virulence and antibiotic resistances within closely related strains.

CONCLUSION: We show that strain-level methods developed primarily for the analysis of human microbiomes can be effective for city-associated microbiomes. In fact, (opportunistic) pathogens can be tracked and monitored across many hundreds of urban metagenomes. However, while more effort is needed to profile strains of currently uncharacterized species, this work poses the basis for high-resolution analyses of microbiomes sampled in city and mass transportation environments.

REVIEWERS: This article was reviewed by Alexandra Bettina Graf, Daniel Huson and Trevor Cickovski.}, } @article {pmid29740407, year = {2018}, author = {Nooij, S and Schmitz, D and Vennema, H and Kroneman, A and Koopmans, MPG}, title = {Overview of Virus Metagenomic Classification Methods and Their Biological Applications.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {749}, pmid = {29740407}, issn = {1664-302X}, abstract = {Metagenomics poses opportunities for clinical and public health virology applications by offering a way to assess complete taxonomic composition of a clinical sample in an unbiased way. However, the techniques required are complicated and analysis standards have yet to develop. This, together with the wealth of different tools and workflows that have been proposed, poses a barrier for new users. We evaluated 49 published computational classification workflows for virus metagenomics in a literature review. To this end, we described the methods of existing workflows by breaking them up into five general steps and assessed their ease-of-use and validation experiments. Performance scores of previous benchmarks were summarized and correlations between methods and performance were investigated. We indicate the potential suitability of the different workflows for (1) time-constrained diagnostics, (2) surveillance and outbreak source tracing, (3) detection of remote homologies (discovery), and (4) biodiversity studies. We provide two decision trees for virologists to help select a workflow for medical or biodiversity studies, as well as directions for future developments in clinical viral metagenomics.}, } @article {pmid29739908, year = {2018}, author = {Gladieux, P}, title = {Updates in the Language of Histoplasma Biodiversity.}, journal = {mBio}, volume = {9}, number = {3}, pages = {}, pmid = {29739908}, issn = {2150-7511}, mesh = {*Biodiversity ; Biological Evolution ; Genetic Speciation ; *Histoplasma ; Humans ; Metagenomics ; Phylogeny ; }, abstract = {In a recent article, Sepúlveda et al. (mBio 8:e01339-17, 2017, https://doi.org/10.1128/mBio.01339-17) investigated the genetic structure and evolutionary history of the human pathogen Histoplasma Using whole-genome resequencing data, Sepúlveda et al. found that the Histoplasma genus is composed of at least four strongly differentiated lineages. Their tour de force is to use a smart combination of population genomic approaches to show that the advanced stage of intraspecific divergence observed within Histoplasma does not simply reflect population structure, but instead results from previously unidentified speciation events. The four independently evolving Histoplasma lineages are elevated to the species status and assigned names. The newly described species exhibit medically important differences in phenotype, and these findings, therefore, have important epidemiological implications. This work provides a blueprint for phylogenomic species recognition in fungi, opening the way for a new age of enlightenment in which fungal species are diagnosed using highly discriminatory tools within a hypothesis-testing framework.}, } @article {pmid29738477, year = {2018}, author = {Klimenko, NS and Tyakht, AV and Popenko, AS and Vasiliev, AS and Altukhov, IA and Ischenko, DS and Shashkova, TI and Efimova, DA and Nikogosov, DA and Osipenko, DA and Musienko, SV and Selezneva, KS and Baranova, A and Kurilshikov, AM and Toshchakov, SM and Korzhenkov, AA and Samarov, NI and Shevchenko, MA and Tepliuk, AV and Alexeev, DG}, title = {Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project.}, journal = {Nutrients}, volume = {10}, number = {5}, pages = {}, pmid = {29738477}, issn = {2072-6643}, mesh = {Bacteroidetes/genetics/isolation & purification ; Bifidobacterium/genetics/isolation & purification ; Clostridium/genetics/isolation & purification ; Cluster Analysis ; *Diet ; Feces/chemistry/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Methanobrevibacter/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Sample Size ; Sequence Analysis, DNA ; }, abstract = {Personalized nutrition is of increasing interest to individuals actively monitoring their health. The relations between the duration of diet intervention and the effects on gut microbiota have yet to be elucidated. Here we examined the associations of short-term dietary changes, long-term dietary habits and lifestyle with gut microbiota. Stool samples from 248 citizen-science volunteers were collected before and after a self-reported 2-week personalized diet intervention, then analyzed using 16S rRNA sequencing. Considerable correlations between long-term dietary habits and gut community structure were detected. A higher intake of vegetables and fruits was associated with increased levels of butyrate-producing Clostridiales and higher community richness. A paired comparison of the metagenomes before and after the 2-week intervention showed that even a brief, uncontrolled intervention produced profound changes in community structure: resulting in decreased levels of Bacteroidaceae, Porphyromonadaceae and Rikenellaceae families and decreased alpha-diversity coupled with an increase of Methanobrevibacter, Bifidobacterium, Clostridium and butyrate-producing Lachnospiraceae- as well as the prevalence of a permatype (a bootstrapping-based variation of enterotype) associated with a higher diversity of diet. The response of microbiota to the intervention was dependent on the initial microbiota state. These findings pave the way for the development of an individualized diet.}, } @article {pmid29734762, year = {2018}, author = {Semedo-Aguiar, AP and Pereira-Leal, JB and Leite, RB}, title = {Microbial Diversity and Toxin Risk in Tropical Freshwater Reservoirs of Cape Verde.}, journal = {Toxins}, volume = {10}, number = {5}, pages = {}, pmid = {29734762}, issn = {2072-6651}, mesh = {Bacteria/genetics/isolation & purification ; Bacterial Toxins/genetics ; Biodiversity ; Cabo Verde ; DNA, Bacterial/genetics ; Fresh Water/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; }, abstract = {The Cape Verde islands are part of the African Sahelian arid belt that possesses an erratic rain pattern prompting the need for water reservoirs, which are now critical for the country’s sustainability. Worldwide, freshwater cyanobacterial blooms are increasing in frequency due to global climate change and the eutrophication of water bodies, particularly in reservoirs. To date, there have been no risk assessments of cyanobacterial toxin production in these man-made structures. We evaluated this potential risk using 16S rRNA gene amplicon sequencing and full metagenome sequencing in freshwater reservoirs of Cape Verde. Our analysis revealed the presence of several potentially toxic cyanobacterial genera in all sampled reservoirs. Faveta potentially toxic and bloom-forming Microcystis sp., dominated our samples, while a Cryptomonas green algae and Gammaproteobacteria dominated Saquinho and Poil&atilde;o reservoirs. We reconstructed and assembled the Microcystis genome, extracted from the metagenome of bulk DNA from Faveta water. Phylogenetic analysis of Microcystis cf. aeruginosa CV01’s genome revealed its close relationship with other Microcystis genomes, as well as clustering with other continental African strains, suggesting geographical coherency. In addition, it revealed several clusters of known toxin-producing genes. This survey reinforces the need to better understand the country’s microbial ecology as a whole of water reservoirs on the rise.}, } @article {pmid29733457, year = {2018}, author = {Spychala, MS and Venna, VR and Jandzinski, M and Doran, SJ and Durgan, DJ and Ganesh, BP and Ajami, NJ and Putluri, N and Graf, J and Bryan, RM and McCullough, LD}, title = {Age-related changes in the gut microbiota influence systemic inflammation and stroke outcome.}, journal = {Annals of neurology}, volume = {84}, number = {1}, pages = {23-36}, pmid = {29733457}, issn = {1531-8249}, support = {R01 NS094543/NS/NINDS NIH HHS/United States ; R01 NS103592/NS/NINDS NIH HHS/United States ; R21 NS094806/NS/NINDS NIH HHS/United States ; R01 NS080531/NS/NINDS NIH HHS/United States ; RF1 AG058463/AG/NIA NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; }, mesh = {Age Factors ; *Aging ; Animals ; Cytokines/metabolism ; Disease Models, Animal ; Exploratory Behavior ; Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Inflammation/*microbiology/physiopathology ; Mice ; Mice, Inbred C57BL ; Muscle Strength/physiology ; Neurologic Examination ; RNA, Ribosomal, 16S/metabolism ; Stroke/*microbiology/physiopathology ; }, abstract = {OBJECTIVE: Chronic systemic inflammation contributes to the pathogenesis of many age-related diseases. Although not well understood, alterations in the gut microbiota, or dysbiosis, may be responsible for age-related inflammation.

METHODS: Using stroke as a disease model, we tested the hypothesis that a youthful microbiota, when established in aged mice, produces positive outcomes following ischemic stroke. Conversely, an aged microbiota, when established in young mice, produces negative outcomes after stroke. Young and aged male mice had either a young or an aged microbiota established by fecal transplant gavage (FTG). Mice were subjected to ischemic stroke (middle cerebral artery occlusion; MCAO) or sham surgery. During the subsequent weeks, mice underwent behavioral testing and fecal samples were collected for 16S ribosomal RNA analysis of bacterial content.

RESULTS: We found that the microbiota is altered after experimental stroke in young mice and resembles the biome of uninjured aged mice. In aged mice, the ratio of Firmicutes to Bacteroidetes (F:B), two main bacterial phyla in gut microbiota, increased ∼9-fold (p < 0.001) compared to young. This increased F:B ratio in aged mice is indicative of dysbiosis. Altering the microbiota in young by fecal gavage to resemble that of aged mice (∼6-fold increase in F:B ratio, p < 0.001) increased mortality following MCAO, decreased performance in behavioral testing, and increased cytokine levels. Conversely, altering the microbiota in aged to resemble that of young (∼9-fold decrease in F:B ratio, p < 0.001) increased survival and improved recovery following MCAO.

INTERPRETATION: Aged biome increased the levels of systemic proinflammatory cytokines. We conclude that the gut microbiota can be modified to positively impact outcomes from age-related diseases. Ann Neurol 2018;83:23-36.}, } @article {pmid29730317, year = {2018}, author = {Lee, CM and Kim, SY and Song, J and Lee, YS and Sim, JS and Hahn, BS}, title = {Isolation and characterization of a halotolerant and protease-resistant α-galactosidase from the gut metagenome of Hermetia illucens.}, journal = {Journal of biotechnology}, volume = {279}, number = {}, pages = {47-54}, doi = {10.1016/j.jbiotec.2018.05.003}, pmid = {29730317}, issn = {1873-4863}, mesh = {Animals ; Bacterial Proteins/chemistry/*genetics/isolation & purification/metabolism ; Bacteroidetes/enzymology/genetics ; Diptera/*microbiology ; Enzyme Stability ; Escherichia coli/genetics ; Gastrointestinal Microbiome/*genetics ; Metagenome/*genetics ; Metals, Heavy ; Phylogeny ; Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism ; alpha-Galactosidase/chemistry/*genetics/isolation & purification/metabolism ; }, abstract = {Hermetia illucens is a voracious insect scavenger, decomposing food waste efficiently. To survey novel hydrolytic enzymes, we constructed a fosmid metagenome library using unculturable intestinal microorganisms from H. illucens in our previous study (Lee et al., 2014). Functional screening of the library on carboxymethyl cellulose plates identified a fosmid clone the product of which displayed hydrolytic activity. Sequence analysis of the fosmid revealed a novel α-galactosidase gene, Agas2. The Agas2 gene is composed of 2,007 base pairs encoding 668 amino acids with a deduced 25 amino acid N-terminal signal peptide sequence. The conceptual translation and domain analysis of Agas2 showed the highest sequence identity (84%) with the putative α-galactosidase of Dysgonomonas sp. HGC4, exhibiting well-conserved domain homology with glycosyl hydrolase family 97. Phylogenetic analysis indicated that Agas2 may be a currently uncharacterized α-galactosidase. The recombinant protein, rAgas2, was successfully expressed in E. coli. rAgas2 showed the highest activity at 40 °C and pH 7.0. It displayed great pH stability within a pH range of 5-11 for 15 h at 4 °C. rAgas2 was highly stable under stringent conditions, including polar organic solvents, non-ionic detergents, salt, and proteases. rAgas2 hydrolyzed α-d-galactose substrates, showing the maximum enzymatic activity toward p-nitrophenyl α-d-galactopyranoside (specific activity 128.37 U/mg). However, rAgas2 did not hydrolyze substrates linked with β-glucose moieties. Overall, Agas2 may be an attractive candidate for the degradation of α-galactose family oligosaccharides in high-salt, protease-rich and high-organic-solvent processes.}, } @article {pmid29729565, year = {2018}, author = {Chen, L and Hu, C and Lok-Shun Lai, N and Zhang, W and Hua, J and Lam, PKS and Lam, JCW and Zhou, B}, title = {Acute exposure to PBDEs at an environmentally realistic concentration causes abrupt changes in the gut microbiota and host health of zebrafish.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {240}, number = {}, pages = {17-26}, doi = {10.1016/j.envpol.2018.04.062}, pmid = {29729565}, issn = {1873-6424}, mesh = {Animals ; Bacteria ; Female ; Gastrointestinal Microbiome/*drug effects ; Halogenated Diphenyl Ethers/metabolism/*toxicity ; Intestinal Mucosa/metabolism ; Liver/metabolism ; Male ; Metagenomics ; Water Pollutants, Chemical/*toxicity ; Zebrafish/microbiology/*physiology ; }, abstract = {Contamination from lower brominated PBDEs is ubiquitous in the environments. However, their effects on gut microbiota and intestinal health have not yet been investigated. This study exposed adult zebrafish to an environmentally realistic concentration of pentaBDE mixture (DE-71) at 5.0 ng/L for 7 days, after which metagenomic sequencing of the intestinal microbiome was conducted and host physiological activities in the intestine and liver were also examined. The results showed that acute exposure to DE-71 significantly shifted the gut microbial community in a sex-specific manner. Certain genera (e.g., Mycoplasma, Ruminiclostridium, unclassified Firmicutes sensu stricto, and Fusobacterium) disappeared from the DE-71-exposed intestines, resulting in decreased bacterial diversity. Bacterial metabolic functions in guts were also affected by DE-71, namely those covering energy metabolism, virulence, respiration, cell division, cell signaling, and stress response. In addition, measurement of diverse sensitive biomarkers showed that the health of male intestines was remarkably compromised by the DE-71 exposure, as indicated by the disruption to its neural signaling (serotonin), epithelial barrier integrity (tight junction protein 2), inflammatory response (interleukin 1β), oxidative stress and antioxidant capacity, as well as detoxifying potential (ethoxyresorufin-O-deethylase activity). However, female intestines maintained intact physiological activities. Compared to the direct impact on intestines, a latent effect of DE-71 was observed in livers. Co-occurrence network analysis demonstrated that the gut bacteria vigorously interacted to establish the fittest community under DE-71 stress by promoting the reproduction of favorable genera, while diminishing the survival of unfavorable ones. Significant correlations between the zebrafish gut microbiota and physiological activities (e.g., oxidative stress, detoxification, neurotransmission, and epithelial integrity) were also observed. Overall, this study has demonstrated, for the first time, the high susceptibility of gut microbiota and intestinal health of zebrafish to DE-71, thus warranting more work to reveal its mode of toxicity.}, } @article {pmid29729376, year = {2018}, author = {Li, M and Zhou, M and Tian, X and Tan, C and McDaniel, CT and Hassett, DJ and Gu, T}, title = {Microbial fuel cell (MFC) power performance improvement through enhanced microbial electrogenicity.}, journal = {Biotechnology advances}, volume = {36}, number = {4}, pages = {1316-1327}, doi = {10.1016/j.biotechadv.2018.04.010}, pmid = {29729376}, issn = {1873-1899}, mesh = {*Bioelectric Energy Sources ; *Biofilms ; *Microbial Consortia ; Oxidation-Reduction ; Synthetic Biology ; }, abstract = {Within the past 5 years, tremendous advances have been made to maximize the performance of microbial fuel cells (MFCs) for both "clean" bioenergy production and bioremediation. Most research efforts have focused on parameters including (i) optimizing reactor configuration, (ii) electrode construction, (iii) addition of redox-active, electron donating mediators, (iv) biofilm acclimation and feed nutrient adjustment, as well as (v) other parameters that contribute to enhanced MFC performance. To date, tremendous advances have been made, but further improvements are needed for MFCs to be economically practical. In this review, the diversity of electrogenic microorganisms and microbial community changes in mixed cultures are discussed. More importantly, different approaches including chemical/genetic modifications and gene regulation of exoelectrogens, synthetic biology approaches and bacterial community cooperation are reviewed. Advances in recent years in metagenomics and microbiomes have allowed researchers to improve bacterial electrogenicity of robust biofilms in MFCs using novel, unconventional approaches. Taken together, this review provides some important and timely information to researchers who are examining additional means to enhance power production of MFCs.}, } @article {pmid29728382, year = {2018}, author = {Milani, C and Duranti, S and Mangifesta, M and Lugli, GA and Turroni, F and Mancabelli, L and Viappiani, A and Anzalone, R and Alessandri, G and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {Phylotype-Level Profiling of Lactobacilli in Highly Complex Environments by Means of an Internal Transcribed Spacer-Based Metagenomic Approach.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {14}, pages = {}, pmid = {29728382}, issn = {1098-5336}, mesh = {Animals ; Cheese/microbiology ; Chickens ; DNA, Bacterial/genetics ; Female ; Gastrointestinal Microbiome ; Gene Expression Profiling ; Host Microbial Interactions ; Humans ; Lactobacillus/classification/*genetics/*metabolism ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; Vagina/microbiology ; }, abstract = {The genus Lactobacillus is a widespread taxon, members of which are highly relevant to functional and fermented foods, while they are also commonly present in host-associated gut and vaginal microbiota. Substantial efforts have been undertaken to disclose the genetic repertoire of all members of the genus Lactobacillus, and yet their species-level profiling in complex matrices is still undeveloped due to the poor phylotype resolution of profiling approaches based on the 16S rRNA gene. To overcome this limitation, an internal transcribed spacer (ITS)-based profiling method was developed to accurately profile lactobacilli at the species level. This approach encompasses a genus-specific primer pair combined with a database of ITS sequences retrieved from all available Lactobacillus genomes and a script for the QIIME software suite that performs all required steps to reconstruct a species-level profile. This methodology was applied to several environments, i.e., human gut and vagina and the ceca of free-range chickens, as well as whey and fresh cheese. Interestingly, the data collected confirmed a relevant role of lactobacilli present in functional and fermented foods in defining the population harbored by the human gut, while, unsurprisingly perhaps, the ceca of free-range chickens were observed to be dominated by lactobacilli characterized in birds living in natural environments. Moreover, vaginal swabs confirmed the existence of previously hypothesized community state types, while analysis of whey and fresh cheese revealed a dominant presence of single Lactobacillus species used as starters for cheese production. Furthermore, application of this ITS profiling method to a mock Lactobacillus community allowed a minimal resolution level of <0.006 ng/μl.IMPORTANCE The genus Lactobacillus is a large and ubiquitous taxon of high scientific and commercial relevance. Despite the fact that the genetic repertoire of Lactobacillus species has been extensively characterized, the ecology of this genus has been explored by metataxonomic techniques that are accurate down to the genus or phylogenetic group level only. Thus, the distribution of lactobacilli in environmental or processed food samples is relatively unexplored. The profiling protocol described here relies on the use of the internal transcribed spacer to perform an accurate classification in a target population of lactobacilli with a <0.006-ng/μl sensitivity. This approach was used to analyze five sample types collected from both human and animal host-associated microbiota, as well as from the cheese production chain. The availability of a tool for species-level profiling of lactobacilli may be highly useful for both academic research and a wide range of industrial applications.}, } @article {pmid29725134, year = {2018}, author = {ElNaker, NA and Elektorowicz, M and Naddeo, V and Hasan, SW and Yousef, AF}, title = {Assessment of Microbial Community Structure and Function in Serially Passaged Wastewater Electro-Bioreactor Sludge: An Approach to Enhance Sludge Settleability.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {7013}, pmid = {29725134}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics ; Biological Oxygen Demand Analysis ; Bioreactors/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Microbiota ; Phosphorus/analysis ; Phylogeny ; Serial Passage ; Sewage/*microbiology ; Water Purification/*methods ; }, abstract = {Several studies have been carried out to understand bulking phenomena and the importance of environmental factors on sludge settling characteristics. The main objective of this study was to carry out functional characterization of microbial community structure of wastewater electro-bioreactor sludge as it undergoes serial passaging in the presence or absence of a current density over 15 days. Illumina MiSeq sequencing and QIIME were used to assess sludge microbial community shifts over time. (α) and (β) diversity analysis were conducted to assess the microbial diversity in electro-bioreactors. A phylogeny-based weighted UniFrac distance analysis was used to compare between bacterial communities while BIO-ENV trend and Spearman's rank correlation analysis were performed to investigate how reactor operational parameters correlated with bacterial community diversity. Results showed that the removal efficiency of soluble chemical oxygen demand (sCOD) ranged from 91-97%, while phosphorous (PO4[3-]-P) removal was approximately 99%. Phylogenetic analysis revealed stark differences in the development of sludge microbial communities in the control and treatment reactor. There was no mention of any studies aimed at characterizing functional microbial communities under electric field and the results communicated here are the first, to our knowledge, that address this gap in the literature.}, } @article {pmid29725059, year = {2018}, author = {Dittmer, J and Bouchon, D}, title = {Feminizing Wolbachia influence microbiota composition in the terrestrial isopod Armadillidium vulgare.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6998}, pmid = {29725059}, issn = {2045-2322}, mesh = {Animal Structures/*microbiology ; Animals ; Bacteria/classification/genetics ; Isopoda/*microbiology ; Metagenomics ; Microbial Interactions ; *Microbiota ; Wolbachia/*growth & development ; }, abstract = {Wolbachia are widespread heritable endosymbionts of arthropods notorious for their profound effects on host fitness as well as for providing protection against viruses and eukaryotic parasites, indicating that they can interact with other microorganisms sharing the same host environment. Using the terrestrial isopod crustacean Armadillidium vulgare, its highly diverse microbiota (>200 bacterial genera) and its three feminizing Wolbachia strains (wVulC, wVulM, wVulP) as a model system, the present study demonstrates that Wolbachia can even influence the composition of a diverse bacterial community under both laboratory and natural conditions. While host origin is the major determinant of the taxonomic composition of the microbiota in A. vulgare, Wolbachia infection affected both the presence and, more importantly, the abundance of many bacterial taxa within each host population, possibly due to competitive interactions. Moreover, different Wolbachia strains had different impacts on microbiota composition. As such, infection with wVulC affected a higher number of taxa than infection with wVulM, possibly due to intrinsic differences in virulence and titer between these two strains. In conclusion, this study shows that heritable endosymbionts such as Wolbachia can act as biotic factors shaping the microbiota of arthropods, with as yet unknown consequences on host fitness.}, } @article {pmid29725011, year = {2018}, author = {Hicks, AL and Lee, KJ and Couto-Rodriguez, M and Patel, J and Sinha, R and Guo, C and Olson, SH and Seimon, A and Seimon, TA and Ondzie, AU and Karesh, WB and Reed, P and Cameron, KN and Lipkin, WI and Williams, BL}, title = {Gut microbiomes of wild great apes fluctuate seasonally in response to diet.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {1786}, pmid = {29725011}, issn = {2041-1723}, support = {U19 AI109761/AI/NIAID NIH HHS/United States ; U19AI109761/NH/NIH HHS/United States ; }, mesh = {Animal Nutritional Physiological Phenomena ; Animals ; Cercopithecidae/*microbiology ; Diet/*veterinary ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gorilla gorilla/*microbiology ; Herbivory ; Humans ; Male ; Metabolic Networks and Pathways ; Pan troglodytes/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Seasons ; Species Specificity ; }, abstract = {The microbiome is essential for extraction of energy and nutrition from plant-based diets and may have facilitated primate adaptation to new dietary niches in response to rapid environmental shifts. Here we use 16S rRNA sequencing to characterize the microbiota of wild western lowland gorillas and sympatric central chimpanzees and demonstrate compositional divergence between the microbiotas of gorillas, chimpanzees, Old World monkeys, and modern humans. We show that gorilla and chimpanzee microbiomes fluctuate with seasonal rainfall patterns and frugivory. Metagenomic sequencing of gorilla microbiomes demonstrates distinctions in functional metabolic pathways, archaea, and dietary plants among enterotypes, suggesting that dietary seasonality dictates shifts in the microbiome and its capacity for microbial plant fiber digestion versus growth on mucus glycans. These data indicate that great ape microbiomes are malleable in response to dietary shifts, suggesting a role for microbiome plasticity in driving dietary flexibility, which may provide fundamental insights into the mechanisms by which diet has driven the evolution of human gut microbiomes.}, } @article {pmid29721711, year = {2018}, author = {Goodfellow, M and Nouioui, I and Sanderson, R and Xie, F and Bull, AT}, title = {Rare taxa and dark microbial matter: novel bioactive actinobacteria abound in Atacama Desert soils.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {8}, pages = {1315-1332}, doi = {10.1007/s10482-018-1088-7}, pmid = {29721711}, issn = {1572-9699}, mesh = {Actinobacteria/*classification/genetics/isolation & purification/metabolism ; Altitude ; Anti-Bacterial Agents/isolation & purification ; *Biodiversity ; Chile ; *Desert Climate ; Ecosystem ; Metagenomics ; *Phylogeny ; *Soil Microbiology ; Species Specificity ; }, abstract = {An "in house" taxonomic approach to drug discovery led to the isolation of diverse actinobacteria from hyper-arid, extreme hyper-arid and very high altitude Atacama Desert soils. A high proportion of the isolates were assigned to novel taxa, with many showing activity in standard antimicrobial plug assays. The application of more advanced taxonomic and screening strategies showed that strains classified as novel species of Lentzea and Streptomyces synthesised new specialised metabolites thereby underpinning the premise that the extreme abiotic conditions in the Atacama Desert favour the development of a unique actinobacterial diversity which is the basis of novel chemistry. Complementary metagenomic analyses showed that the soils encompassed an astonishing degree of actinobacterial 'dark matter', while rank-abundance analyses showed them to be highly diverse habitats mainly composed of rare taxa that have not been recovered using culture-dependent methods. The implications of these pioneering studies on future bioprospecting campaigns are discussed.}, } @article {pmid29720448, year = {2018}, author = {Fadlallah, J and El Kafsi, H and Sterlin, D and Juste, C and Parizot, C and Dorgham, K and Autaa, G and Gouas, D and Almeida, M and Lepage, P and Pons, N and Le Chatelier, E and Levenez, F and Kennedy, S and Galleron, N and de Barros, JP and Malphettes, M and Galicier, L and Boutboul, D and Mathian, A and Miyara, M and Oksenhendler, E and Amoura, Z and Doré, J and Fieschi, C and Ehrlich, SD and Larsen, M and Gorochov, G}, title = {Microbial ecology perturbation in human IgA deficiency.}, journal = {Science translational medicine}, volume = {10}, number = {439}, pages = {}, doi = {10.1126/scitranslmed.aan1217}, pmid = {29720448}, issn = {1946-6242}, mesh = {Humans ; IgA Deficiency/*immunology/*microbiology ; Immunoglobulin A/metabolism ; Immunoglobulin M/metabolism ; Microbiota/physiology ; }, abstract = {Paradoxically, loss of immunoglobulin A (IgA), one of the most abundant antibodies, does not irrevocably lead to severe infections in humans but rather is associated with relatively mild respiratory infections, atopy, and autoimmunity. IgA might therefore also play covert roles, not uniquely associated with control of pathogens. We show that human IgA deficiency is not associated with massive quantitative perturbations of gut microbial ecology. Metagenomic analysis highlights an expected pathobiont expansion but a less expected depletion in some typically beneficial symbionts. Gut colonization by species usually present in the oropharynx is also reminiscent of spatial microbiota disorganization. IgM only partially rescues IgA deficiency because not all typical IgA targets are efficiently bound by IgM in the intestinal lumen. Together, IgA appears to play a nonredundant role at the forefront of the immune/microbial interface, away from the intestinal barrier, ranging from pathobiont control and regulation of systemic inflammation to preservation of commensal diversity and community networks.}, } @article {pmid29718202, year = {2018}, author = {Wu, L and McCluskey, K and Desmeth, P and Liu, S and Hideaki, S and Yin, Y and Moriya, O and Itoh, T and Kim, CY and Lee, JS and Zhou, Y and Kawasaki, H and Hazbón, MH and Robert, V and Boekhout, T and Lima, N and Evtushenko, L and Boundy-Mills, K and Bunk, B and Moore, ERB and Eurwilaichitr, L and Ingsriswang, S and Shah, H and Yao, S and Jin, T and Huang, J and Shi, W and Sun, Q and Fan, G and Li, W and Li, X and Kurtböke, I and Ma, J}, title = {The global catalogue of microorganisms 10K type strain sequencing project: closing the genomic gaps for the validly published prokaryotic and fungi species.}, journal = {GigaScience}, volume = {7}, number = {5}, pages = {}, pmid = {29718202}, issn = {2047-217X}, mesh = {Bacteria/*genetics ; Fungi/*genetics ; Genomics/*methods ; Prokaryotic Cells/*metabolism ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; }, abstract = {Genomic information is essential for taxonomic, phylogenetic, and functional studies to comprehensively decipher the characteristics of microorganisms, to explore microbiomes through metagenomics, and to answer fundamental questions of nature and human life. However, large gaps remain in the available genomic sequencing information published for bacterial and archaeal species, and the gaps are even larger for fungal type strains. The Global Catalogue of Microorganisms (GCM) leads an internationally coordinated effort to sequence type strains and close gaps in the genomic maps of microorganisms. Hence, the GCM aims to promote research by deep-mining genomic data.}, } @article {pmid29718124, year = {2018}, author = {Inoue, T and Nakayama, J and Moriya, K and Kawaratani, H and Momoda, R and Ito, K and Iio, E and Nojiri, S and Fujiwara, K and Yoneda, M and Yoshiji, H and Tanaka, Y}, title = {Gut Dysbiosis Associated With Hepatitis C Virus Infection.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {67}, number = {6}, pages = {869-877}, doi = {10.1093/cid/ciy205}, pmid = {29718124}, issn = {1537-6591}, mesh = {Aged ; Aged, 80 and over ; Alanine Transaminase/blood ; Bacteria/classification/*isolation & purification ; Case-Control Studies ; DNA, Bacterial/genetics ; Disease Progression ; Dysbiosis/*virology ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Hepacivirus/isolation & purification ; Hepatitis C, Chronic/*complications ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Little is known about the effect of hepatitis C virus (HCV) infection on gut microbiota and the relationship between alteration of gut microbiota and chronic hepatitis C (CHC) progression. We performed a comparative study of gut microbiota composition between CHC patients and healthy individuals.

METHODS: Fecal samples from 166 CHC patients were compared with those from 23 healthy individuals; the gut microbiota community was analyzed using 16S ribosomal RNA gene sequencing. CHC patients were diagnosed with persistently normal serum alanine aminotransferase without evidence of liver cirrhosis (LC) (PNALT, n = 18), chronic hepatitis (CH, n = 84), LC (n = 40), and hepatocellular carcinoma in LC (n = 24).

RESULTS: Compared with healthy individuals, bacterial diversity was lower in persons with HCV infection, with a decrease in the order Clostridiales and an increase in Streptococcus and Lactobacillus. Microbiota dysbiosis already appeared in the PNALT stage with the transient increase in Bacteroides and Enterobacteriaceae. Predicted metagenomics of microbial communities showed an increase in the urease gene mainly encoded by viridans streptococci during CHC progression, consistent with a significantly higher fecal pH in CH and LC patients than in healthy individuals or those in the PNALT stage.

CONCLUSIONS: HCV infection is associated with gut dysbiosis, even in patients with mild liver disease. Additionally, overgrowth of viridans streptococci can account for hyperammonemia in CH and LC. Further studies would help to propose a novel treatment strategy because the gut microbiome can be therapeutically altered, potentially reducing the complications of chronic liver disease.}, } @article {pmid29715508, year = {2018}, author = {Lamichhane, S and Sen, P and Dickens, AM and Orešič, M and Bertram, HC}, title = {Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe.}, journal = {Methods (San Diego, Calif.)}, volume = {149}, number = {}, pages = {3-12}, doi = {10.1016/j.ymeth.2018.04.029}, pmid = {29715508}, issn = {1095-9130}, mesh = {Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/immunology/metabolism ; Host Microbial Interactions/*physiology ; Humans ; Metabolome/*physiology ; Metabolomics/*methods/trends ; }, abstract = {It is well established that gut microbes and their metabolic products regulate host metabolism. The interactions between the host and its gut microbiota are highly dynamic and complex. In this review we present and discuss the metabolomic strategies to study the gut microbial ecosystem. We highlight the metabolic profiling approaches to study faecal samples aimed at deciphering the metabolic product derived from gut microbiota. We also discuss how metabolomics data can be integrated with metagenomics data derived from gut microbiota and how such approaches may lead to better understanding of the microbial functions. Finally, the emerging approaches of genome-scale metabolic modelling to study microbial co-metabolism and host-microbe interactions are highlighted.}, } @article {pmid29713790, year = {2018}, author = {Hassa, J and Maus, I and Off, S and Pühler, A and Scherer, P and Klocke, M and Schlüter, A}, title = {Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {12}, pages = {5045-5063}, pmid = {29713790}, issn = {1432-0614}, support = {22016308, 22017111, 22403816//Bundesministerium für Ernährung und Landwirtschaft/ ; 03SF0381, 03SF0440A//Bundesministerium für Bildung und Forschung/ ; }, mesh = {Archaea/classification/genetics/*physiology ; Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; *Biofuels ; Bioreactors/*microbiology ; *Metagenome ; Proteome ; RNA, Ribosomal, 16S/genetics ; Transcriptome ; }, abstract = {The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.}, } @article {pmid29712968, year = {2018}, author = {Kadnikov, VV and Mardanov, AV and Ivasenko, DA and Antsiferov, DV and Beletsky, AV and Karnachuk, OV and Ravin, NV}, title = {Lignite coal burning seam in the remote Altai Mountains harbors a hydrogen-driven thermophilic microbial community.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6730}, pmid = {29712968}, issn = {2045-2322}, mesh = {Bacteria, Anaerobic/classification/*genetics ; Carbon Dioxide/metabolism ; Coal/*microbiology ; Hot Temperature ; Humans ; Hydrogen/chemistry/metabolism ; *Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Thermal ecosystems associated with underground coal combustion sites are rare and less studied than geothermal features. Here we analysed microbial communities of near-surface ground layer and bituminous substance in an open quarry heated by subsurface coal fire by metagenomic DNA sequencing. Taxonomic classification revealed dominance of only a few groups of Firmicutes. Near-complete genomes of three most abundant species, 'Candidatus Carbobacillus altaicus' AL32, Brockia lithotrophica AL31, and Hydrogenibacillus schlegelii AL33, were assembled. According to the genomic data, Ca. Carbobacillus altaicus AL32 is an aerobic heterotroph, while B. lithotrophica AL31 is a chemolithotrophic anaerobe assimilating CO2 via the Calvin cycle. H. schlegelii AL33 is an aerobe capable of both growth on organic compounds and carrying out CO2 fixation via the Calvin cycle. Phylogenetic analysis of the large subunit of RuBisCO of B. lithotrophica AL31 and H. schlegelii AL33 showed that it belongs to the type 1-E. All three Firmicutes species can gain energy from aerobic or anaerobic oxidation of molecular hydrogen, produced as a result of underground coal combustion along with other coal gases. We propose that thermophilic Firmicutes, whose spores can spread from their original geothermal habitats over long distances, are the first colonizers of this recently formed thermal ecosystem.}, } @article {pmid29709640, year = {2018}, author = {Kobiyama, A and Ikeo, K and Reza, MS and Rashid, J and Yamada, Y and Ikeda, Y and Ikeda, D and Mizusawa, N and Sato, S and Ogata, T and Jimbo, M and Kudo, T and Kaga, S and Watanabe, S and Naiki, K and Kaga, Y and Mineta, K and Bajic, V and Gojobori, T and Watabe, S}, title = {Metagenome-based diversity analyses suggest a strong locality signal for bacterial communities associated with oyster aquaculture farms in Ofunato Bay.}, journal = {Gene}, volume = {665}, number = {}, pages = {149-154}, doi = {10.1016/j.gene.2018.04.073}, pmid = {29709640}, issn = {1879-0038}, mesh = {Animals ; Aquaculture ; *Bacteria/genetics/metabolism ; *Biodiversity ; *Metagenome ; Microbial Consortia/*physiology ; Ostreidae/*microbiology ; *Seasons ; }, abstract = {Ofunato Bay, in Japan, is the home of buoy-and-rope-type oyster aquaculture activities. Since the oysters filter suspended materials and excrete organic matters into the seawater, bacterial communities residing in its vicinity may show dynamic changes depending on the oyster culture activities. We employed a shotgun metagenomic technique to study bacterial communities near oyster aquaculture facilities at the center of the bay (KSt. 2) and compared the results with those of two other localities far from the station, one to the northeast (innermost bay, KSt. 1) and the other to the southwest (bay entrance, KSt. 3). Seawater samples were collected every month from January to December 2015 from the surface (1 m) and deeper (8 or 10 m) layers of the three locations, and the sequentially filtered fraction on 0.2-μm membranes was sequenced on an Illumina MiSeq system. The acquired reads were uploaded to MG-RAST for KEGG functional abundance analysis, while taxonomic analyses at the phylum and genus levels were performed using MEGAN after parsing the BLAST output. Discrimination analyses were then performed using the ROC-AUC value of the cross validation, targeting the depth (shallow or deep), locality [(KSt. 1 + KSt. 2) vs. KSt 3; (KSt. 1 + KSt. 3) vs. KSt. 2 or the (KSt. 2 + KSt. 3) vs. KSt. 1] and seasonality (12 months). The matrix discrimination analysis on the adjacent 2 continuous seasons by ROC-AUC, which was based on the datasets that originated from different depths, localities and months, showed the strongest discrimination signal on the taxonomy matrix at the phylum level for the datasets from July to August compared with those from September to June, while the KEGG matrix showed the strongest signal for the datasets from March to June compared with those from July to February. Then, the locality combination was subjected to the same ROC-AUC discrimination analysis, resulting in significant differences between KSt. 2 and KSt. 1 + KSt. 3 on the KEGG matrix. These results suggest that aquaculture activities markedly affect bacterial functions.}, } @article {pmid29705928, year = {2018}, author = {Bonilla, JO and Kurth, DG and Cid, FD and Ulacco, JH and Gil, RA and Villegas, LB}, title = {Prokaryotic and eukaryotic community structure affected by the presence of an acid mine drainage from an abandoned gold mine.}, journal = {Extremophiles : life under extreme conditions}, volume = {22}, number = {5}, pages = {699-711}, pmid = {29705928}, issn = {1433-4909}, support = {PICT 2013 No. 3170//Agencia Nacional de Promoción Científica y Tecnológica/ ; }, mesh = {Acids/analysis ; Actinobacteria/isolation & purification ; Diatoms/isolation & purification ; *Extreme Environments ; Fungi/isolation & purification ; Gammaproteobacteria/isolation & purification ; Geologic Sediments/chemistry/*microbiology ; Gold/analysis ; Metagenome ; Metals, Heavy/analysis ; *Microbiota ; Mining ; }, abstract = {The acid mine drainage that originates in the abandoned gold mine in San Luis, Argentina, is released into La Carolina stream. The aim of this study was to determine the influence of this mine drainage on the physicochemical parameters of the area studied and on both prokaryotic and eukaryotic community structure. In addition, specific relationships between microbial taxonomic groups and physicochemical parameters were established. The drainage that flows into La Carolina stream acidifies the stream and increases its sulfate, Zn, Cd and Te concentrations. Microbial analysis showed that prokaryotic community structure is mainly affected by pH values. Actinobacteria and Gammaproteobacteria were abundant in samples characterized by low pH values, while Nitrospirae, Chloroflexi, Deltaproteobacteria, Thaumarchaeota and Euryarchaeota were associated with high concentrations of heavy metals. Otherwise, Alphaproteobacteria was present in samples taken in sunlit areas. Regarding eukaryotic community structure, the sunlight had the greatest impact. Inside the mine, in the absence of light, fungi and protists members were the most abundant microorganisms, while those samples taken in the presence of light displayed algae (green algae and diatoms) as the most abundant ones. After receiving the mine drainage, the stream showed a decrease in the diatom abundance and green algae predominated.}, } @article {pmid29705728, year = {2018}, author = {Ticinesi, A and Milani, C and Guerra, A and Allegri, F and Lauretani, F and Nouvenne, A and Mancabelli, L and Lugli, GA and Turroni, F and Duranti, S and Mangifesta, M and Viappiani, A and Ferrario, C and Dodi, R and Dall'Asta, M and Del Rio, D and Ventura, M and Meschi, T}, title = {Understanding the gut-kidney axis in nephrolithiasis: an analysis of the gut microbiota composition and functionality of stone formers.}, journal = {Gut}, volume = {67}, number = {12}, pages = {2097-2106}, doi = {10.1136/gutjnl-2017-315734}, pmid = {29705728}, issn = {1468-3288}, mesh = {Adult ; Aged ; Bacteria/classification/isolation & purification ; Bacterial Typing Techniques ; Biodiversity ; Calcium Oxalate/analysis ; Case-Control Studies ; DNA, Bacterial/analysis ; Energy Intake/physiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Metagenomics/methods ; Middle Aged ; Nephrolithiasis/metabolism/*microbiology ; Oxalates/metabolism ; RNA, Ribosomal, 16S/analysis ; Recurrence ; Young Adult ; }, abstract = {OBJECTIVES: The involvement of the gut microbiota in the pathogenesis of calcium nephrolithiasis has been hypothesised since the discovery of the oxalate-degrading activity of Oxalobacter formigenes, but never comprehensively studied with metagenomics. The aim of this case-control study was to compare the faecal microbiota composition and functionality between recurrent idiopathic calcium stone formers (SFs) and controls.

DESIGN: Faecal samples were collected from 52 SFs and 48 controls (mean age 48±11). The microbiota composition was analysed through 16S rRNA microbial profiling approach. Ten samples (five SFs, five controls) were also analysed with deep shotgun metagenomics sequencing, with focus on oxalate-degrading microbial metabolic pathways. Dietary habits, assessed through a food-frequency questionnaire, and 24-hour urinary excretion of prolithogenic and antilithogenic factors, including calcium and oxalate, were compared between SFs and controls, and considered as covariates in the comparison of microbiota profiles.

RESULTS: SFs exhibited lower faecal microbial diversity than controls (Chao1 index 1460±363vs 1658±297, fully adjusted p=0.02 with stepwise backward regression analysis). At multivariate analyses, three taxa (Faecalibacterium, Enterobacter, Dorea) were significantly less represented in faecal samples of SFs. The Oxalobacter abundance was not different between groups. Faecal samples from SFs exhibited a significantly lower bacterial representation of genes involved in oxalate degradation, with inverse correlation with 24-hour oxalate excretion (r=-0.87, p=0.002). The oxalate-degrading genes were represented in several bacterial species, whose cumulative abundance was inversely correlated with oxaluria (r=-0.85, p=0.02).

CONCLUSIONS: Idiopathic calcium SFs exhibited altered gut microbiota composition and functionality that could contribute to nephrolithiasis physiopathology.}, } @article {pmid29705499, year = {2018}, author = {Bielinska, K and Radkowski, M and Grochowska, M and Perlejewski, K and Huc, T and Jaworska, K and Motooka, D and Nakamura, S and Ufnal, M}, title = {High salt intake increases plasma trimethylamine N-oxide (TMAO) concentration and produces gut dysbiosis in rats.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {54}, number = {}, pages = {33-39}, doi = {10.1016/j.nut.2018.03.004}, pmid = {29705499}, issn = {1873-1244}, mesh = {Animals ; Dysbiosis/*etiology ; Feces/chemistry ; Gastrointestinal Microbiome ; Intestinal Diseases/*etiology ; Male ; Methylamines/*blood ; Rats ; Rats, Sprague-Dawley ; Sodium, Dietary/*adverse effects ; }, abstract = {OBJECTIVE: A high-salt diet is considered a cardiovascular risk factor; however, the mechanisms are not clear. Research suggests that gut bacteria-derived metabolites such as trimethylamine N-oxide (TMAO) are markers of cardiovascular diseases. We evaluated the effect of high salt intake on gut bacteria and their metabolites plasma level.

METHODS: Sprague Dawley rats ages 12-14 wk were maintained on either water (controls) or 0.9% or 2% sodium chloride (NaCl) water solution (isotonic and hypertonic groups, respectively) for 2 wk. Blood plasma, urine, and stool samples were analyzed for concentrations of trimethylamine (TMA; a TMAO precursor), TMAO, and indoxyl sulfate (indole metabolite). The gut-blood barrier permeability to TMA and TMA liver clearance were assessed at baseline and after TMA intracolonic challenge test. Gut bacterial flora was analyzed with a 16S ribosomal ribonucleic acid (rRNA) gene sequence analysis.

RESULTS: The isotonic and hypertonic groups showed a significantly higher plasma TMAO and significantly lower 24-hr TMAO urine excretion than the controls. However, the TMA stool level was similar between the groups. There was no significant difference between the groups in gut-blood barrier permeability and TMA liver clearance. Plasma indoxyl concentration and 24-hr urine indoxyl excretion were similar between the groups. There was a significant difference between the groups in gut bacteria composition.

CONCLUSIONS: High salt intake increases plasma TMAO concentration, which is associated with decreased TMAO urine excretion. Furthermore, high salt intake alters gut bacteria composition. These findings suggest that salt intake affects an interplay between gut bacteria and their host homeostasis.}, } @article {pmid29705422, year = {2018}, author = {Wang, Z and Zhang, W and Wang, B and Zhang, F and Shao, Y}, title = {Influence of Bactrian camel milk on the gut microbiota.}, journal = {Journal of dairy science}, volume = {101}, number = {7}, pages = {5758-5769}, doi = {10.3168/jds.2017-13860}, pmid = {29705422}, issn = {1525-3198}, mesh = {Animals ; Bifidobacterium ; *Camelus ; Gastrointestinal Microbiome/*physiology ; Mice ; Milk/*metabolism ; RNA, Ribosomal, 16S ; }, abstract = {Bactrian camel milk has become popular in the market as an important source of nutrients with diverse functional effects. In this study, the influence of Bactrian camel milk on the gut microbiota of mice was studied using metagenomic-based sequencing of the V3 and V4 hypervariable regions of the 16S rRNA gene. Bioinformatics analysis showed that Firmicutes and Bacteroidetes were the predominant phyla, accounting for more than 80% of the bacteria present. At the genus level, Allobaculum, Akkermansia, Romboutsia, Bifidobacterium, and Lactobacillus were most abundant in the gut microbiota; of these, Allobaculum and Akkermansia were the predominant genera, representing 40.42 and 7.85% of all the bacteria present, respectively. Camel milk was found to reduce relative abundance of Romboutsia, Lactobacillus, Turicibacter, and Desulfovibrio (decreased by 50.88, 34.78, 26.67, and 54.55%, respectively) in the gut microbiota compared with the control. However, some genera such as Allobaculum, Akkermansia, and Bifidobacterium in the gastrointestinal flora increased in abundance in the presence of camel milk; these genera are correlated with beneficial effects for organisms. Our research suggests that the gut microbiota should be taken into account when conducting functional studies on camel milk, and this work provides a useful foundation for further study on functions of camel milk.}, } @article {pmid29705130, year = {2018}, author = {Kudo, T and Kobiyama, A and Rashid, J and Reza, MS and Yamada, Y and Ikeda, Y and Ikeda, D and Mizusawa, N and Ikeo, K and Sato, S and Ogata, T and Jimbo, M and Kaga, S and Watanabe, S and Naiki, K and Kaga, Y and Segawa, S and Mineta, K and Bajic, V and Gojobori, T and Watabe, S}, title = {Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis.}, journal = {Gene}, volume = {665}, number = {}, pages = {174-184}, doi = {10.1016/j.gene.2018.04.072}, pmid = {29705130}, issn = {1879-0038}, mesh = {Animals ; *Bacteria/genetics/metabolism ; Bays/*microbiology ; *Genes, Bacterial ; Metagenomics/methods ; *Seasons ; Seawater/*microbiology ; Sulfonium Compounds/*metabolism ; *Water Microbiology ; }, abstract = {Ofunato Bay is located in the northeastern Pacific Ocean area of Japan, and it has the highest biodiversity of marine organisms in the world, primarily due to tidal influences from the cold Oyashio and warm Kuroshio Currents. Our previous results from performing shotgun metagenomics indicated that Candidatus Pelagibacter ubique and Planktomarina temperata were the dominant bacteria (Reza et al., 2018a, 2018b). These bacteria are reportedly able to catabolize dimethylsulfoniopropionate (DMSP) produced from phytoplankton into dimethyl sulfide (DMS) or methanethiol (MeSH). This study was focused on seasonal changes in the abundances of bacterial genes (dddP, dmdA) related to DMSP catabolism in the seawater of Ofunato Bay by BLAST+ analysis using shotgun metagenomic datasets. We found seasonal changes among the Candidatus Pelagibacter ubique strains, including those of the HTCC1062 type and the Red Sea type. A good correlation was observed between the chlorophyll a concentrations and the abundances of the catabolic genes, suggesting that the bacteria directly interact with phytoplankton in the marine material cycle system and play important roles in producing DMS and MeSH from DMSP as signaling molecules for the possible formation of the scent of the tidewater or as fish attractants.}, } @article {pmid29705129, year = {2018}, author = {Reza, MS and Kobiyama, A and Yamada, Y and Ikeda, Y and Ikeda, D and Mizusawa, N and Ikeo, K and Sato, S and Ogata, T and Jimbo, M and Kudo, T and Kaga, S and Watanabe, S and Naiki, K and Kaga, Y and Mineta, K and Bajic, V and Gojobori, T and Watabe, S}, title = {Basin-scale seasonal changes in marine free-living bacterioplankton community in the Ofunato Bay.}, journal = {Gene}, volume = {665}, number = {}, pages = {185-191}, doi = {10.1016/j.gene.2018.04.074}, pmid = {29705129}, issn = {1879-0038}, mesh = {*Archaea/genetics/growth & development ; *Bacteria/genetics/growth & development ; Bays/*microbiology ; Microbial Consortia/*physiology ; *Plankton/genetics/growth & development ; *Seasons ; *Water Microbiology ; }, abstract = {The Ofunato Bay in the northeastern Pacific Ocean area of Japan possesses the highest biodiversity of marine organisms in the world and has attracted much attention due to its economic and environmental importance. We report here a shotgun metagenomic analysis of the year-round variation in free-living bacterioplankton collected across the entire length of the bay. Phylogenetic differences among spring, summer, autumn and winter bacterioplankton suggested that members of Proteobacteria tended to decrease at high water temperatures and increase at low temperatures. It was revealed that Candidatus Pelagibacter varied seasonally, reaching as much as 60% of all sequences at the genus level in the surface waters during winter. This increase was more evident in the deeper waters, where they reached up to 75%. The relative abundance of Planktomarina also rose during winter and fell during summer. A significant component of the winter bacterioplankton community was Archaea (mainly represented by Nitrosopumilus), as their relative abundance was very low during spring and summer but high during winter. In contrast, Actinobacteria and Cyanobacteria appeared to be higher in abundance during high-temperature periods. It was also revealed that Bacteroidetes constituted a significant component of the summer bacterioplankton community, being the second largest bacterial phylum detected in the Ofunato Bay. Its members, notably Polaribacter and Flavobacterium, were found to be high in abundance during spring and summer, particularly in the surface waters. Principal component analysis and hierarchal clustering analyses showed that the bacterial communities in the Ofunato Bay changed seasonally, likely caused by the levels of organic matter, which would be deeply mixed with surface runoff in the winter.}, } @article {pmid29705124, year = {2018}, author = {Reza, MS and Kobiyama, A and Yamada, Y and Ikeda, Y and Ikeda, D and Mizusawa, N and Ikeo, K and Sato, S and Ogata, T and Jimbo, M and Kudo, T and Kaga, S and Watanabe, S and Naiki, K and Kaga, Y and Mineta, K and Bajic, V and Gojobori, T and Watabe, S}, title = {Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay.}, journal = {Gene}, volume = {665}, number = {}, pages = {192-200}, doi = {10.1016/j.gene.2018.04.075}, pmid = {29705124}, issn = {1879-0038}, mesh = {*Archaea/classification/genetics/growth & development ; *Bacteria/classification/genetics/growth & development ; Bays/*microbiology ; Metagenomics ; Microbial Consortia/*physiology ; *Seasons ; *Water Microbiology ; }, abstract = {The Ofunato Bay in Iwate Prefecture, Japan is a deep coastal bay located at the center of the Sanriku Rias Coast and considered an economically and environmentally important asset. Here, we describe the first whole genome sequencing (WGS) study on the microbial community of the bay, where surface water samples were collected from three stations along its length to cover the entire bay; we preliminarily sequenced a 0.2 μm filter fraction among sequentially size-fractionated samples of 20.0, 5.0, 0.8 and 0.2 μm filters, targeting the free-living fraction only. From the 0.27-0.34 Gb WGS library, 0.9 × 10[6]-1.2 × 10[6] reads from three sampling stations revealed 29 bacterial phyla (~80% of assigned reads), 3 archaeal phyla (~4%) and 59 eukaryotic phyla (~15%). Microbial diversity obtained from the WGS approach was compared with 16S rRNA gene results by mining WGS metagenomes, and we found similar estimates. The most frequently recovered bacterial sequences were Proteobacteria, predominantly comprised of 18.0-19.6% Planktomarina (Family Rhodobacteraceae) and 13.7-17.5% Candidatus Pelagibacter (Family Pelagibacterales). Other dominant bacterial genera, including Polaribacter (3.5-6.1%), Flavobacterium (1.8-2.6%), Sphingobacterium (1.4-1.6%) and Cellulophaga (1.4-2.0%), were members of Bacteroidetes and likely associated with the degradation and turnover of organic matter. The Marine Group I Archaea Nitrosopumilus was also detected. Remarkably, eukaryotic green alga Bathycoccus, Ostreococcus and Micromonas accounted for 8.8-15.2%, 3.6-4.9% and 2.1-3.1% of total read counts, respectively, highlighting their potential roles in the phytoplankton bloom after winter mixing.}, } @article {pmid29704757, year = {2018}, author = {Campanaro, S and Treu, L and Kougias, PG and Luo, G and Angelidaki, I}, title = {Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants.}, journal = {Water research}, volume = {140}, number = {}, pages = {123-134}, doi = {10.1016/j.watres.2018.04.043}, pmid = {29704757}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Biofuels ; Bioreactors/*microbiology ; Manure ; *Metagenome ; Metagenomics/methods ; Microbiota/*physiology ; Sewage/microbiology ; Waste Disposal, Fluid ; Wastewater ; }, abstract = {The aim of this work was to elucidate the microbial ecology in twelve mesophilic and thermophilic full-scale biogas plants using a genome-centric metagenomic approach. In this study both biogas plants treating manure and those treating sludge from waste water treatment plants were considered. The identification of 132 Metagenome-Assembled Genomes (MAGs) and analysis of their abundance profile in different samples allowed the identification of the most abundant core members of the anaerobic digestion microbiome. Canonical correspondence analysis was used to determine the influence of biotic and environmental factors on MAGs abundance and to investigate the methanogenic performance of the biogas plants. Prediction of the functional properties of MAGs was obtained analyzing their KEGG pathways and their carbohydrate active domains. Network analysis allowed investigation of species-species associations and shed light on syntrophic interactions between members belonging to the anaerobic digestion dark matter (phylum Fermentibacteria). By stratifying and comparing different levels of information, it was predicted that some MAGs have a crucial role in the manure-supplemented thermophilic biogas plants and it was highlighted the importance of the glycine cleavage system in complementing the "truncated" Wood-Ljungdahl pathway.}, } @article {pmid29704240, year = {2018}, author = {Liu, Z and Zhou, C and Ontiveros-Valencia, A and Luo, YH and Long, M and Xu, H and Rittmann, BE}, title = {Accurate O2 delivery enabled benzene biodegradation through aerobic activation followed by denitrification-coupled mineralization.}, journal = {Biotechnology and bioengineering}, volume = {115}, number = {8}, pages = {1988-1999}, doi = {10.1002/bit.26712}, pmid = {29704240}, issn = {1097-0290}, mesh = {Aerobiosis ; Benzene/*metabolism ; Biofilms/growth & development ; Bioreactors/microbiology ; Biota ; Biotransformation ; Burkholderiales/classification/isolation & purification ; Denitrification ; Nitrites/*metabolism ; Oxygen/*metabolism ; }, abstract = {Although benzene can be biodegraded when dissolved oxygen is sufficient, delivering oxygen is energy intensive and can lead to air stripping the benzene. Anaerobes can biodegrade benzene by using electron acceptors other than O2 , and this may reduce costs and exposure risks; the drawback is a remarkably slower growth rate. We evaluated a two-step strategy that involved O2 -dependent benzene activation and cleavage followed by intermediate oxidation coupled to NO3[-] respiration. We employed a membrane biofilm reactor (MBfR) featuring nonporous hollow fibers as the means to deliver O2 directly to a biofilm at an accurately controlled rate. Benzene was mineralized aerobically when the O2 -supply rate was more than sufficient for mineralization. As the O2 -supply capacity was systematically lowered, O2 respiration was gradually replaced by NO3[-] respiration. When the maximum O2 -supply capacity was only 20% of the demand for benzene mineralization, O2 was used almost exclusively for benzene activation and cleavage, while respiration was almost only by denitrification. Analyses of microbial community structure and predicted metagenomic function reveal that Burkholderiales was dominant and probably utilized monooxygenase activation, with subsequent mineralization coupled to denitrification; strict anaerobes capable of carboxylative activation were not detected. These results open the door for a promising treatment strategy that simultaneously ameliorates technical and economic challenges of aeration and slow kinetics of anaerobic activation of aromatics.}, } @article {pmid29702634, year = {2018}, author = {Eisenstein, M}, title = {Microbiology: making the best of PCR bias.}, journal = {Nature methods}, volume = {15}, number = {5}, pages = {317-320}, pmid = {29702634}, issn = {1548-7105}, mesh = {DNA, Bacterial/genetics ; *Metagenomics ; Microbiota/*genetics ; Polymerase Chain Reaction/*methods ; Selection Bias ; }, } @article {pmid29701776, year = {2018}, author = {Karimi, E and Slaby, BM and Soares, AR and Blom, J and Hentschel, U and Costa, R}, title = {Metagenomic binning reveals versatile nutrient cycling and distinct adaptive features in alphaproteobacterial symbionts of marine sponges.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {6}, pages = {}, doi = {10.1093/femsec/fiy074}, pmid = {29701776}, issn = {1574-6941}, mesh = {Animals ; Carbon/metabolism ; Genome, Bacterial/genetics ; Metagenome ; Metagenomics ; Microbiota ; Nitrogen/metabolism ; Phylogeny ; Porifera/*microbiology ; Rhodospirillaceae/genetics/*metabolism ; Sulfur/metabolism ; Symbiosis/*physiology ; }, abstract = {Marine sponges are early-branched metazoans known to harbor dense and diverse microbial communities. Yet the role of the so far uncultivable alphaproteobacterial lineages that populate these sessile invertebrates remains unclear. We applied a sequence composition-dependent binning approach to assemble one Rhodospirillaceae genome from the Spongia officinalis microbial metagenome and contrast its functional features with those of closely related sponge-associated and free-living genomes. Both symbiotic and free-living Rhodospirillaceae shared a suite of common features, possessing versatile carbon, nitrogen, sulfur and phosphorus metabolisms. Symbiotic genomes could be distinguished from their free-living counterparts by the lack of chemotaxis and motility traits, enrichment of genes required for the uptake and utilization of organic sulfur compounds-particularly taurine-, higher diversity and abundance of ABC transporters, and a distinct repertoire of genes involved in natural product biosynthesis, plasmid stability, cell detoxification and oxidative stress remediation. These sessile symbionts may more effectively contribute to host fitness via nutrient exchange, and also host detoxification and chemical defense. Considering the worldwide occurrence and high diversity of sponge-associated Rhodospirillaceae verified here using a tailored in silico approach, we suggest that these organisms are not only relevant to holobiont homeostasis but also to nutrient cycling in benthic ecosystems.}, } @article {pmid29700420, year = {2018}, author = {Richardson, JB and Dancy, BCR and Horton, CL and Lee, YS and Madejczyk, MS and Xu, ZZ and Ackermann, G and Humphrey, G and Palacios, G and Knight, R and Lewis, JA}, title = {Exposure to toxic metals triggers unique responses from the rat gut microbiota.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6578}, pmid = {29700420}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; *Heavy Metal Poisoning ; Metagenome ; Metagenomics/methods ; Metals, Heavy/*toxicity ; Rats ; }, abstract = {Our understanding of the interaction between the gut microbiota and host health has recently improved dramatically. However, the effects of toxic metal exposure on the gut microbiota remain poorly characterized. As this microbiota creates a critical interface between the external environment and the host's cells, it may play an important role in host outcomes during exposure. We therefore used 16S ribosomal RNA (rRNA) gene sequencing to track changes in the gut microbiota composition of rats exposed to heavy metals. Rats were exposed daily for five days to arsenic, cadmium, cobalt, chromium, nickel, or a vehicle control. Significant changes to microbiota composition were observed in response to high doses of chromium and cobalt, and significant dose-dependent changes were observed in response to arsenic, cadmium and nickel. Many of these perturbations were not uniform across metals. However, bacteria with higher numbers of iron-importing gene orthologs were overly represented after exposure to arsenic and nickel, suggesting some possibility of a shared response. These findings support the utility of the microbiota as a pre-clinical tool for identifying exposures to specific heavy metals. It is also clear that characterizing changes to the functional capabilities of microbiota is critical to understanding responses to metal exposure.}, } @article {pmid29700349, year = {2018}, author = {Lin, Z and Ye, W and Zu, X and Xie, H and Li, H and Li, Y and Zhang, W}, title = {Integrative metabolic and microbial profiling on patients with Spleen-yang-deficiency syndrome.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6619}, pmid = {29700349}, issn = {2045-2322}, mesh = {Adult ; Aged ; Case-Control Studies ; Computational Biology/methods ; Female ; Gastrointestinal Microbiome ; Humans ; Male ; *Metabolome ; Metabolomics/methods ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Spleen/*immunology/*metabolism ; Syndrome ; Yang Deficiency/diagnosis/*immunology/*metabolism ; Young Adult ; }, abstract = {Gut microbiota is recognized as an indispensable "metabolic organ" that plays crucial roles in maintaining human health or initiating diseases. Spleen-yang-deficiency syndrome (SYDS) is a common syndrome of Traditional Chinese Medicine (TCM) clinic. It is a complex phenotype reflecting the overall changes of metabolism which are mainly caused by digestive disorders. However, little is known about the changes of gut microbiota and metabolism in patients with SYDS, as well as the crosstalk between gut microbiota and host metabolism. In the current study, an integrative metabolic and microbial profiling was performed on plasma, urine and feces from recruited SYDS and healthy individuals by using a LC-QTOFMS-based metabolomic and 16 s rRNA sequencing approaches. Our results showed a potentially significant contribution of gut dysbiosis to the metabolic disorders in SYDS. By integrating the differential gut bacteria with the metabolites, the results revealed some active bacterium of norank_f_CFT112H7, f_lachnospiraceae and bacteroides were closely involved in host mucosal integrity, bile acid metabolism and polysaccharides decomposition. Therefore, our results indicated the probable involvement of gut microbiota in mediating the metabolic changes, which warrants a further investigation on the role of gut microbiota in modulating the pathogenesis of SYDS.}, } @article {pmid29697181, year = {2018}, author = {Srivastava, S and Briggs, BR and Dong, H}, title = {Abundance and taxonomic affiliation of molybdenum transport and utilization genes in Tengchong hot springs, China.}, journal = {Environmental microbiology}, volume = {20}, number = {7}, pages = {2397-2409}, doi = {10.1111/1462-2920.14250}, pmid = {29697181}, issn = {1462-2920}, mesh = {Aldehyde Oxidoreductases/metabolism ; China ; Hot Springs/*microbiology ; *Microbiota/genetics ; Molybdenum/*metabolism ; Multienzyme Complexes/metabolism ; Nitrate Reductase/metabolism ; }, abstract = {The nitrogen, sulfur and carbon cycles all rely on critical microbial transformations that are carried out by enzymes that require molybdenum (Mo) as a cofactor. Despite Mo importance in these biogeochemical cycles, little information exists about microbial Mo utilization in extreme environments where, due to geochemical conditions, bioavailable Mo may be limited. Using metagenomic data from nine hot springs in Tengchong, Yunnan Province, China, which range in temperature from 42°C to 96°C and pH from 2.3 to 9, the effects of pH, temperature and spring geochemistry on the abundance and taxonomic affiliation of genes related to Mo were studied. Dissolved Mo was only detected at sites with circumneutral pH. However, processes and organisms that require Mo were detected at all sites across all temperature and pH gradients. All sites contained xanthine dehydrogenase, formate dehydrogenase, carbon-monoxide dehydrogenase, nitrate reductase, sulfite oxidase and methionine-sulfoxide reductase despite different community compositions. This suggests that different microbial communities, resulting from different physicochemical conditions, may be performing similar metabolic functions. Furthermore, the abundance and taxonomic diversity of Mo-related annotations increased with higher concentrations of Mo. This study shows that despite geochemical conditions that can limit Mo bioavailability, microbes require Mo for a variety of processes.}, } @article {pmid29695035, year = {2018}, author = {Yuan, QS and Yang, P and Wu, AB and Zuo, DY and He, WJ and Guo, MW and Huang, T and Li, HP and Liao, YC}, title = {Variation in the Microbiome, Trichothecenes, and Aflatoxins in Stored Wheat Grains in Wuhan, China.}, journal = {Toxins}, volume = {10}, number = {5}, pages = {}, pmid = {29695035}, issn = {2072-6651}, mesh = {Aflatoxins/*analysis ; Agriculture/methods ; Bacteria/genetics/isolation & purification ; China ; DNA, Bacterial/analysis ; DNA, Fungal/analysis ; Edible Grain/*chemistry/*microbiology ; Environmental Monitoring ; Food Contamination/*analysis ; Fungi/genetics/isolation & purification ; Microbiota ; Trichothecenes/*analysis ; Triticum/*chemistry/*microbiology ; }, abstract = {Contamination by fungal and bacterial species and their metabolites can affect grain quality and health of wheat consumers. In this study, sequence analyses of conserved DNA regions of fungi and bacteria combined with determination of trichothecenes and aflatoxins revealed the microbiome and mycotoxins of wheat from different silo positions (top, middle, and bottom) and storage times (3, 6, 9, and 12 months). The fungal community in wheat on the first day of storage (T0) included 105 classified species (81 genera) and 41 unclassified species. Four species had over 10% of the relative abundance: Alternaria alternata (12%), Filobasidium floriforme (27%), Fusarium graminearum (12%), and Wallemia sebi (12%). Fungal diversity and relative abundance of Fusarium in wheat from top silo positions were significantly lower than at other silo positions during storage. Nivalenol and deoxynivalenol in wheat were 13[-]34% higher in all positions at 3 months compared to T0, and mycotoxins in wheat from middle and bottom positions at 6 to 12 months were 24[-]57% higher than at T0. The relative abundance of toxigenic Aspergillus and aflatoxins were low at T0 and during storage. This study provides information on implementation and design of fungus and mycotoxin management strategies as well as prediction models.}, } @article {pmid29694397, year = {2018}, author = {Søe, MJ and Nejsum, P and Seersholm, FV and Fredensborg, BL and Habraken, R and Haase, K and Hald, MM and Simonsen, R and Højlund, F and Blanke, L and Merkyte, I and Willerslev, E and Kapel, CMO}, title = {Ancient DNA from latrines in Northern Europe and the Middle East (500 BC-1700 AD) reveals past parasites and diet.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195481}, pmid = {29694397}, issn = {1932-6203}, mesh = {Agriculture ; Animals ; Archaeology/methods ; Biodiversity ; *DNA, Ancient ; DNA, Mitochondrial ; DNA, Plant ; *Diet ; Eggs ; Europe ; Feces/*chemistry/*parasitology ; History, Ancient ; Humans ; Metagenome ; Middle East ; Parasites/genetics ; Parasitic Diseases/epidemiology/history ; Phylogeny ; Sequence Analysis, DNA ; *Toilet Facilities ; }, abstract = {High-resolution insight into parasitic infections and diet of past populations in Northern Europe and the Middle East (500 BC- 1700 AD) was obtained by pre-concentration of parasite eggs from ancient latrines and deposits followed by shotgun sequencing of DNA. Complementary profiling of parasite, vertebrate and plant DNA proved highly informative in the study of ancient health, human-animal interactions as well as animal and plant dietary components. Most prominent were finding of soil-borne parasites transmitted directly between humans, but also meat-borne parasites that require consumption of raw or undercooked fish and pork. The detection of parasites for which sheep, horse, dog, pig, and rodents serves as definitive hosts are clear markers of domestic and synanthropic animals living in closer proximity of the respective sites. Finally, the reconstruction of full mitochondrial parasite genomes from whipworm (Ascaris lumbricoides) and roundworm species (Trichuris trichiura and Trichuris muris) and estimates of haplotype frequencies elucidates the genetic diversity and provides insights into epidemiology and parasite biology.}, } @article {pmid29694379, year = {2018}, author = {Garris, HW and Baldwin, SA and Taylor, J and Gurr, DB and Denesiuk, DR and Van Hamme, JD and Fraser, LH}, title = {Short-term microbial effects of a large-scale mine-tailing storage facility collapse on the local natural environment.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0196032}, pmid = {29694379}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics/metabolism ; Biodiversity ; Hydrogen-Ion Concentration ; Metagenomics/*methods ; Mining ; Nitrates/metabolism ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Soil/chemistry ; Water/chemistry ; Wetlands ; }, abstract = {We investigated the impacts of the Mount Polley tailings impoundment failure on chemical, physical, and microbial properties of substrates within the affected watershed, comprised of 70 hectares of riparian wetlands and 40 km of stream and lake shore. We established a biomonitoring network in October of 2014, two months following the disturbance, and evaluated riparian and wetland substrates for microbial community composition and function via 16S and full metagenome sequencing. A total of 234 samples were collected from substrates at 3 depths and 1,650,752 sequences were recorded in a geodatabase framework. These data revealed a wealth of information regarding watershed-scale distribution of microbial community members, as well as community composition, structure, and response to disturbance. Substrates associated with the impact zone were distinct chemically as indicated by elevated pH, nitrate, and sulphate. The microbial community exhibited elevated metabolic capacity for selenate and sulfate reduction and an abundance of chemolithoautotrophs in the Thiobacillus thiophilus/T. denitrificans/T. thioparus clade that may contribute to nitrate attenuation within the affected watershed. The most impacted area (a 6 km stream connecting two lakes) exhibited 30% lower microbial diversity relative to the remaining sites. The tailings impoundment failure at Mount Polley Mine has provided a unique opportunity to evaluate functional and compositional diversity soon after a major catastrophic disturbance to assess metabolic potential for ecosystem recovery.}, } @article {pmid29694348, year = {2018}, author = {Hoffman, KL and Hutchinson, DS and Fowler, J and Smith, DP and Ajami, NJ and Zhao, H and Scheet, P and Chow, WH and Petrosino, JF and Daniel, CR}, title = {Oral microbiota reveals signs of acculturation in Mexican American women.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0194100}, pmid = {29694348}, issn = {1932-6203}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; R25 CA057730/CA/NCI NIH HHS/United States ; CA016672/NH/NIH HHS/United States ; R25CA057730/NH/NIH HHS/United States ; }, mesh = {*Acculturation ; Adult ; Aged ; Emigrants and Immigrants ; Female ; Fusobacterium/*isolation & purification ; Humans ; *Mexican Americans ; Microbiota/*physiology ; Middle Aged ; Mouth/*microbiology ; Prevotella/*isolation & purification ; Streptococcus/*isolation & purification ; Young Adult ; }, abstract = {The oral microbiome has been linked to a number of chronic inflammatory conditions, including obesity, diabetes, periodontitis, and cancers of the stomach and liver. These conditions disproportionately affect Mexican American women, yet few studies have examined the oral microbiota in this at-risk group. We characterized the 16S rDNA oral microbiome in 369 non-smoking women enrolled in the MD Anderson Mano a Mano Mexican American Cohort Study. Lower bacterial diversity, a potential indicator of oral health, was associated with increased age and length of US residency among recent immigrants. Grouping women by overarching bacterial community type (e.g., "Streptococcus," "Fusobacterium," and "Prevotella" clusters), we observed differences across a number of acculturation-related variables, including nativity, age at immigration, time in the US, country of longest residence, and a multi-dimensional acculturation scale. Participants in the cluster typified by higher abundance of Streptococcus spp. exhibited the lowest bacterial diversity and appeared the most acculturated as compared to women in the "Prevotella" group. Computationally-predicted functional analysis suggested the Streptococcus-dominated bacterial community had greater potential for carbohydrate metabolism while biosynthesis of essential amino acids and nitrogen metabolism prevailed among the Prevotella-high group. Findings suggest immigration and adaption to life in the US, a well-established mediator of disease risk, is associated with differences in oral microbial profiles in Mexican American women. These results warrant further investigation into the joint and modifying effects of acculturation and oral bacteria on the health of Mexican American women and other immigrant populations. The oral microbiome presents an easily accessible biomarker of disease risk, spanning biological, behavioral, and environmental factors.}, } @article {pmid29691748, year = {2018}, author = {Yausheva, Е and Miroshnikov, S and Sizova, Е}, title = {Intestinal microbiome of broiler chickens after use of nanoparticles and metal salts.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {18}, pages = {18109-18120}, pmid = {29691748}, issn = {1614-7499}, support = {14-16-00060 P//Russian Science Foundation/ ; }, mesh = {*Animal Feed ; Animals ; Biodiversity ; Cecum/microbiology ; Chickens/*microbiology ; *Diet ; Gastrointestinal Microbiome/*drug effects ; Gram-Negative Bacteria/drug effects/isolation & purification ; Gram-Positive Bacteria/drug effects/isolation & purification ; *Metal Nanoparticles ; Salts ; Trace Elements/chemistry/*pharmacology ; }, abstract = {The research included the study of influence of ultrafine particle preparations (nanoparticles of copper, zinc, iron, CuZn alloy) and metal salts (iron pyrophosphate, copper asparginate, zinc asparginate) on the composition of cecal microbiota of broiler chickens. Before adding the studied nanoparticles and metal salts to the diet, cecal microbiota of broiler chickens was represented by 76% Firmicutes taxon and 16% Bacteroidetes. Numerous among them were the bacteria of the taxa Anaerotruncus spp., Lactobacillus spp., Blautia spp., Alistipes spp., and Bacteroides spp.; they constituted 18, 17, 11, and 6%, respectively. A peculiarity of action of the most analyzed metals in nanoform and in the form of salts was a decrease in the number of phylum Firmicutes bacteria and an increase in the number of microorganisms of the phylum Bacteroidetes. The number of bacteria belonging to the families Ruminococcaceae (III, IV, V, VII, and VIII groups), Bacteroidaceae (in all experimental groups), and Lachnospiraceae (I, IV, V, and VII groups) was registered within the taxa of Firmicutes and Bacteroidetes. At the same time, in some experimental groups, the number of bacteria of the family Lachnospiraceae (II, III, and VIII) decreased in the intestine. The data obtained can be used to assess the possibility of using metal nanoparticles in the poultry diet, as a micronutrient preparation, to correct dysbiosis and to improve the utilization of fodder energy.}, } @article {pmid29691633, year = {2018}, author = {McClelland, J and Koslicki, D}, title = {EMDUniFrac: exact linear time computation of the UniFrac metric and identification of differentially abundant organisms.}, journal = {Journal of mathematical biology}, volume = {77}, number = {4}, pages = {935-949}, pmid = {29691633}, issn = {1432-1416}, mesh = {*Algorithms ; Genome, Microbial ; Humans ; Linear Models ; Mathematical Concepts ; Metagenome ; *Microbiota/genetics ; *Models, Biological ; Phylogeny ; Spatio-Temporal Analysis ; Time Factors ; }, abstract = {Both the weighted and unweighted UniFrac distances have been very successfully employed to assess if two communities differ, but do not give any information about how two communities differ. We take advantage of recent observations that the UniFrac metric is equivalent to the so-called earth mover's distance (also known as the Kantorovich-Rubinstein metric) to develop an algorithm that not only computes the UniFrac distance in linear time and space, but also simultaneously finds which operational taxonomic units are responsible for the observed differences between samples. This allows the algorithm, called EMDUniFrac, to determine why given samples are different, not just if they are different, and with no added computational burden. EMDUniFrac can be utilized on any distribution on a tree, and so is particularly suitable to analyzing both operational taxonomic units derived from amplicon sequencing, as well as community profiles resulting from classifying whole genome shotgun metagenomes. The EMDUniFrac source code (written in python) is freely available at: https://github.com/dkoslicki/EMDUniFrac .}, } @article {pmid29690922, year = {2018}, author = {Jaenicke, S and Albaum, SP and Blumenkamp, P and Linke, B and Stoye, J and Goesmann, A}, title = {Flexible metagenome analysis using the MGX framework.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {76}, pmid = {29690922}, issn = {2049-2618}, mesh = {*Database Management Systems ; *Metagenome ; Metagenomics/*methods ; Microbiota ; Reproducibility of Results ; User-Computer Interface ; Workflow ; }, abstract = {BACKGROUND: The characterization of microbial communities based on sequencing and analysis of their genetic information has become a popular approach also referred to as metagenomics; in particular, the recent advances in sequencing technologies have enabled researchers to study even the most complex communities. Metagenome analysis, the assignment of sequences to taxonomic and functional entities, however, remains a tedious task: large amounts of data need to be processed. There are a number of approaches addressing particular aspects, but scientific questions are often too specific to be answered by a general-purpose method.

RESULTS: We present MGX, a flexible and extensible client/server-framework for the management and analysis of metagenomic datasets; MGX features a comprehensive set of adaptable workflows required for taxonomic and functional metagenome analysis, combined with an intuitive and easy-to-use graphical user interface offering customizable result visualizations. At the same time, MGX allows to include own data sources and devise custom analysis pipelines, thus enabling researchers to perform basic as well as highly specific analyses within a single application.

CONCLUSIONS: With MGX, we provide a novel metagenome analysis platform giving researchers access to the most recent analysis tools. MGX covers taxonomic and functional metagenome analysis, statistical evaluation, and a wide range of visualizations easing data interpretation. Its default taxonomic classification pipeline provides equivalent or superior results in comparison to existing tools.}, } @article {pmid29689301, year = {2018}, author = {Connelly, S and Subramanian, P and Hasan, NA and Colwell, RR and Kaleko, M}, title = {Distinct consequences of amoxicillin and ertapenem exposure in the porcine gut microbiome.}, journal = {Anaerobe}, volume = {53}, number = {}, pages = {82-93}, doi = {10.1016/j.anaerobe.2018.04.012}, pmid = {29689301}, issn = {1095-8274}, mesh = {Administration, Intravenous ; Administration, Oral ; Amoxicillin/*administration & dosage ; Animals ; Anti-Bacterial Agents/*administration & dosage ; Drug Resistance, Bacterial/drug effects ; Ertapenem/*administration & dosage ; Gastrointestinal Microbiome/*drug effects ; Genes, Bacterial ; Membrane Transport Proteins/genetics ; Metagenomics ; Swine ; beta-Lactamases/genetics ; }, abstract = {The gut microbiome influences many, if not all, aspects of human health. Antibiotics, while lifesaving, have the unintended consequence of killing commensal microbiota inhabiting the gastrointestinal (GI) tract, which can lead to overgrowth of opportunistic pathogens such as Clostridium difficile and emergence of antibiotic-resistant organisms. Here, porcine models were developed to evaluate changes to the gut microbiome caused by two distinct types of beta-lactam antibiotics delivered via common administration routes, oral amoxicillin and intravenous ertapenem. Amoxicillin is one of the most often used broad-spectrum antibiotics, frequently prescribed to young children. Ertapenem, a carbapenem considered a last resort antibiotic, is used sparingly in humans and prohibited for use in animals. Cohorts of normal pigs (n = 5) were treated with amoxicillin (20 mg/kg, PO, BID) or ertapenem (30 mg/kg, IV, SID) for seven days. Microbiomes were evaluated using whole genome shotgun metagenomics analyses of fecal DNA collected prior to, during, and after antibiotic treatment. Each antibiotic resulted in significant and distinct changes in the microbiome, causing elimination of key commensal bacterial species and overgrowth of other, potentially pathogenic taxa. In addition, amoxicillin promoted propagation of a broad range of antibiotic resistance genes, many encoding efflux pump components and beta-lactamases, while ertapenem triggered emergence of genes encoding vancomycin resistance, and beta-lactamases, including the carbapenemase, IMP-27. Notably, microbiota alterations and antibiotic resistance gene propagation displayed unique patterns following exposure to amoxicillin or ertapenem. These data underscore the importance of understanding consequences of individual antibiotic use to predict and potentially mitigate adverse outcomes. The porcine models developed here can facilitate evaluation of therapeutic interventions to prevent antibiotic-mediated microbiome disruption.}, } @article {pmid29689266, year = {2018}, author = {Nakatsu, G and Zhou, H and Wu, WKK and Wong, SH and Coker, OO and Dai, Z and Li, X and Szeto, CH and Sugimura, N and Lam, TY and Yu, AC and Wang, X and Chen, Z and Wong, MC and Ng, SC and Chan, MTV and Chan, PKS and Chan, FKL and Sung, JJ and Yu, J}, title = {Alterations in Enteric Virome Are Associated With Colorectal Cancer and Survival Outcomes.}, journal = {Gastroenterology}, volume = {155}, number = {2}, pages = {529-541.e5}, doi = {10.1053/j.gastro.2018.04.018}, pmid = {29689266}, issn = {1528-0012}, mesh = {Austria/epidemiology ; Biomarkers, Tumor/*analysis ; Case-Control Studies ; Cohort Studies ; Colonoscopy ; Colorectal Neoplasms/diagnostic imaging/mortality/pathology/*virology ; Cross-Sectional Studies ; Dysbiosis/diagnostic imaging/*virology ; Feces/virology ; Female ; France/epidemiology ; Gastrointestinal Microbiome/*genetics ; Germany/epidemiology ; Hong Kong/epidemiology ; Humans ; Male ; Metagenomics ; Middle Aged ; Sensitivity and Specificity ; Survival Analysis ; Viruses/*genetics ; }, abstract = {BACKGROUND & AIMS: Patients with colorectal cancer (CRC) have a different gut microbiome signature than individuals without CRC. Little is known about the viral component of CRC-associated microbiome. We aimed to identify and validate viral taxonomic markers of CRC that might be used in detection of the disease or predicting outcome.

METHODS: We performed shotgun metagenomic analyses of viromes of fecal samples from 74 patients with CRC (cases) and 92 individuals without CRC (controls) in Hong Kong (discovery cohort). Viral sequences were classified by taxonomic alignment against an integrated microbial reference genome database. Viral markers associated with CRC were validated using fecal samples from 3 separate cohorts: 111 patients with CRC and 112 controls in Hong Kong, 46 patients with CRC and 63 controls in Austria, and 91 patients with CRC and 66 controls in France and Germany. Using abundance profiles of CRC-associated virome genera, we constructed random survival forest models to identify those associated with patient survival times.

RESULTS: The diversity of the gut bacteriophage community was significantly increased in patients with CRC compared with controls. Twenty-two viral taxa discriminated cases from controls with an area under the receiver operating characteristic curve of 0.802 in the discovery cohort. The viral markers were validated in 3 cohorts, with area under the receiver operating characteristic curves of 0.763, 0.736, and 0.715, respectively. Clinical subgroup analysis showed that dysbiosis of the gut virome was associated with early- and late-stage CRC. A combination of 4 taxonomic markers associated with reduced survival of patients with CRC (log-rank test, P = 8.1 × 10[-6]) independently of tumor stage, lymph node metastases, or clinical parameters. We found altered interactions between bacteriophages and oral bacterial commensals in fecal samples from patients with CRC compared with controls.

CONCLUSIONS: In a metagenomic analysis of fecal samples from patients and controls, we identified virome signatures associated with CRC. These data might be used to develop tools to identify individuals with CRC or predict outcomes.}, } @article {pmid29688343, year = {2018}, author = {Tobin, TC and Shade, A}, title = {A town on fire! Integrating 16S rRNA gene amplicon analyses into an undergraduate microbiology lecture class.}, journal = {FEMS microbiology letters}, volume = {365}, number = {10}, pages = {}, pmid = {29688343}, issn = {1574-6968}, support = {R25 GM115335/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Bacteria/classification/*genetics/isolation & purification ; Computational Biology/*education ; Female ; Humans ; Male ; Metagenomics ; Microbiology/*education ; Microbiota ; Phylogeny ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; Soil Microbiology ; Students ; Teaching ; Young Adult ; }, abstract = {Microbiology increasingly relies upon bioinformatics to understand complex microbial interactions. Nevertheless, biology undergraduates often lack the basic quantitative and computer-based skills required for bioinformatics analyses. To address these issues, the course module 'A Town on Fire! 16S rRNA Gene Amplicon Analysis of Microbial Communities Overlying the Centralia, PA Mine Fire' was developed for an undergraduate microbiology lecture course. In this module, microbiology students used Quantitative Insights into Microbial Ecology to perform taxonomic, phylogenetic and statistical analyses on bacterial communities from three hot mine fire-impacted surface soils using 16S rRNA gene amplicon sequences. Pre- and post-module assessment data for each of 2 years were compiled, and indirect assessment indicated that students' confidence regarding their ability to perform bioinformatics analyses, as well as their ability to interpret bioinformatics data both increased, as did their enthusiasm for bioinformatics. Direct assessment demonstrated that students' understanding of topics that they actually used in the module, such as the statistical analyses that underlie bioinformatics investigations and the ability to infer phylogenetic relationships, improved during the module, but that their underlying understanding of techniques that they did not directly perform, such as sequencing and library construction, did not.}, } @article {pmid29687353, year = {2018}, author = {Allali, I and Boukhatem, N and Bouguenouch, L and Hardi, H and Boudouaya, HA and Cadenas, MB and Ouldim, K and Amzazi, S and Azcarate-Peril, MA and Ghazal, H}, title = {Gut microbiome of Moroccan colorectal cancer patients.}, journal = {Medical microbiology and immunology}, volume = {207}, number = {3-4}, pages = {211-225}, pmid = {29687353}, issn = {1432-1831}, mesh = {Adult ; Aged ; Cluster Analysis ; Colorectal Neoplasms/*complications/*microbiology ; Cytosol/chemistry ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Dysbiosis ; Fatty Acids/analysis ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Morocco ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Surveys and Questionnaires ; Young Adult ; }, abstract = {Although colorectal cancer is the third leading cause of death in Morocco, there are no studies of the microbiome changes associated with the disease in the Moroccan population. The aim of our study was to compare the stool microbiome of Moroccan cancer patients with healthy individuals. We analyzed the microbiome composition of samples from 11 CRC patients and 12 healthy individuals by 16S rRNA amplicon sequencing. Principal coordinate analysis of samples revealed defined cancer versus healthy clusters. Our findings showed that cancer samples had higher proportions of Firmicutes (T = 50.5%; N = 28.4%; p = 0.04), specifically of Clostridia (T = 48.3%; N = 19.0%; p = 0.002), and Fusobacteria (T = 0.1%; N = 0.0%; p = 0.02), especially of Fusobacteriia (T = 0.1%; N = 0.0%; p = 0.02), while Bacteroidetes were enriched in healthy samples (T = 35.1%; N = 62.8%; p = 0.06), particularly the class Bacteroidia (T = 35.1%; N = 62.6%; p = 0.06). Porphyromonas, Clostridium, Ruminococcus, Selenomonas, and Fusobacterium were significantly overrepresented in diseased patients, similarly to other studies. Predicted functional information showed that bacterial motility proteins, flagellar assembly, and fatty acid biosynthesis metabolism were significantly overrepresented in cancer patients, while amino acid metabolism and glycan biosynthesis were overrepresented in controls. This suggests that involvement of these functional metagenomes is similar and relevant in the carcinogenesis process, independent of the origin of the samples. Results from this study allowed identification of bacterial taxa relevant to the Moroccan population and encourages larger studies to facilitate population-directed therapeutic approaches.}, } @article {pmid29686086, year = {2018}, author = {Stringlis, IA and Yu, K and Feussner, K and de Jonge, R and Van Bentum, S and Van Verk, MC and Berendsen, RL and Bakker, PAHM and Feussner, I and Pieterse, CMJ}, title = {MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {22}, pages = {E5213-E5222}, pmid = {29686086}, issn = {1091-6490}, support = {269072/ERC_/European Research Council/International ; }, mesh = {Arabidopsis/metabolism/physiology ; Arabidopsis Proteins/*metabolism ; Fusarium/metabolism ; Iron/metabolism ; Metabolome ; Microbiota/*physiology ; Plant Roots/*metabolism/*microbiology ; Pseudomonas/metabolism ; Rhizosphere ; Scopoletin/*metabolism ; Transcription Factors/*metabolism ; Verticillium/metabolism ; }, abstract = {Plant roots nurture a tremendous diversity of microbes via exudation of photosynthetically fixed carbon sources. In turn, probiotic members of the root microbiome promote plant growth and protect the host plant against pathogens and pests. In the Arabidopsis thaliana-Pseudomonas simiae WCS417 model system the root-specific transcription factor MYB72 and the MYB72-controlled β-glucosidase BGLU42 emerged as important regulators of beneficial rhizobacteria-induced systemic resistance (ISR) and iron-uptake responses. MYB72 regulates the biosynthesis of iron-mobilizing fluorescent phenolic compounds, after which BGLU42 activity is required for their excretion into the rhizosphere. Metabolite fingerprinting revealed the antimicrobial coumarin scopoletin as a dominant metabolite that is produced in the roots and excreted into the rhizosphere in a MYB72- and BGLU42-dependent manner. Shotgun-metagenome sequencing of root-associated microbiota of Col-0, myb72, and the scopoletin biosynthesis mutant f6'h1 showed that scopoletin selectively impacts the assembly of the microbial community in the rhizosphere. We show that scopoletin selectively inhibits the soil-borne fungal pathogens Fusarium oxysporum and Verticillium dahliae, while the growth-promoting and ISR-inducing rhizobacteria P. simiae WCS417 and Pseudomonas capeferrum WCS358 are highly tolerant of the antimicrobial effect of scopoletin. Collectively, our results demonstrate a role for coumarins in microbiome assembly and point to a scenario in which plants and probiotic rhizobacteria join forces to trigger MYB72/BGLU42-dependent scopolin production and scopoletin excretion, resulting in improved niche establishment for the microbial partner and growth and immunity benefits for the host plant.}, } @article {pmid29685968, year = {2018}, author = {Gerhauser, C}, title = {Impact of dietary gut microbial metabolites on the epigenome.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {373}, number = {1748}, pages = {}, pmid = {29685968}, issn = {1471-2970}, mesh = {*Diet ; *Epigenesis, Genetic ; Gastrointestinal Microbiome/*physiology ; Humans ; Metagenome/*physiology ; }, abstract = {Within the past decade, epigenetic mechanisms and their modulation by natural products have gained increasing interest. Dietary bioactive compounds from various sources, including green tea, soya, fruit and berries, cruciferous vegetables, whole grain foods, fish and others, have been shown to target enzymes involved in epigenetic gene regulation, including DNA methyltransferases, histone acetyltransferases, deacetylases and demethylases in vitro and in cell culture. Also, many dietary agents were shown to alter miRNA expression. In vivo studies in animal models and humans are still limited. Recent research has indicated that the gut microbiota and gut microbial metabolites might be important mediators of diet-epigenome interactions. Inter-individual differences in the gut microbiome might affect release, metabolism and bioavailability of dietary agents and explain variability in response to intervention in human studies. Only a few microbial metabolites, including folate, phenolic acids, S-(-)equol, urolithins, isothiocyanates, and short- and long-chain fatty acids have been tested with respect to their potential to influence epigenetic mechanisms. Considering that a complex mixture of intermediary and microbial metabolites is present in human circulation, a more systematic interdisciplinary investigation of nutri-epigenetic activities and their impact on human health is called for.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.}, } @article {pmid29685174, year = {2018}, author = {Fan, X and Peters, BA and Jacobs, EJ and Gapstur, SM and Purdue, MP and Freedman, ND and Alekseyenko, AV and Wu, J and Yang, L and Pei, Z and Hayes, RB and Ahn, J}, title = {Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {59}, pmid = {29685174}, issn = {2049-2618}, support = {R01 CA159036/CA/NCI NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; R01CA159036/CA/NCI NIH HHS/United States ; U01CA182370/CA/NCI NIH HHS/United States ; P30CA016087/CA/NCI NIH HHS/United States ; R21CA183887/CA/NCI NIH HHS/United States ; R21 CA183887/CA/NCI NIH HHS/United States ; R03 CA159414/CA/NCI NIH HHS/United States ; U01 CA182370/CA/NCI NIH HHS/United States ; R01CA164964/CA/NCI NIH HHS/United States ; R01 CA164964/CA/NCI NIH HHS/United States ; R03CA159414/CA/NCI NIH HHS/United States ; Pancreas Cancer Action Network Career Development Award//American Association for Cancer Research/International ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; *Alcohol Drinking ; Female ; Humans ; Male ; Metagenome ; Metagenomics ; *Microbiota ; Middle Aged ; Mouth/*microbiology ; Public Health Surveillance ; RNA, Ribosomal, 16S/genetics ; United States ; }, abstract = {BACKGROUND: Dysbiosis of the oral microbiome can lead to local oral disease and potentially to cancers of the head, neck, and digestive tract. However, little is known regarding exogenous factors contributing to such microbial imbalance.

RESULTS: We examined the impact of alcohol consumption on the oral microbiome in a cross-sectional study of 1044 US adults. Bacterial 16S rRNA genes from oral wash samples were amplified, sequenced, and assigned to bacterial taxa. We tested the association of alcohol drinking level (non-drinker, moderate drinker, or heavy drinker) and type (liquor, beer, or wine) with overall microbial composition and individual taxon abundance. The diversity of oral microbiota and overall bacterial profiles differed between heavy drinkers and non-drinkers (α-diversity richness p = 0.0059 and β-diversity unweighted UniFrac p = 0.0036), and abundance of commensal order Lactobacillales tends to be decreased with higher alcohol consumption (fold changes = 0.89 and 0.94 for heavy and moderate drinkers, p trend = 0.005 [q = 0.064]). Additionally, certain genera were enriched in subjects with higher alcohol consumption, including Actinomyces, Leptotrichia, Cardiobacterium, and Neisseria; some of these genera contain oral pathogens, while Neisseria can synthesize the human carcinogen acetaldehyde from ethanol. Wine drinkers may differ from non-drinkers in microbial diversity and profiles (α-diversity richness p = 0.048 and β-diversity unweighted UniFrac p = 0.059) after controlling for drinking amount, while liquor and beer drinkers did not. All significant differences between drinkers and non-drinkers remained after exclusion of current smokers.

CONCLUSIONS: Our results, from a large human study of alcohol consumption and the oral microbiome, indicate that alcohol consumption, and heavy drinking in particular, may influence the oral microbiome composition. These findings may have implications for better understanding the potential role that oral bacteria play in alcohol-related diseases.}, } @article {pmid29684865, year = {2018}, author = {Kurokawa, S and Kishimoto, T and Mizuno, S and Masaoka, T and Naganuma, M and Liang, KC and Kitazawa, M and Nakashima, M and Shindo, C and Suda, W and Hattori, M and Kanai, T and Mimura, M}, title = {The effect of fecal microbiota transplantation on psychiatric symptoms among patients with irritable bowel syndrome, functional diarrhea and functional constipation: An open-label observational study.}, journal = {Journal of affective disorders}, volume = {235}, number = {}, pages = {506-512}, doi = {10.1016/j.jad.2018.04.038}, pmid = {29684865}, issn = {1573-2517}, mesh = {Adult ; Anxiety Disorders/*psychology ; Constipation/psychology/*therapy ; Depressive Disorder/*psychology ; Diarrhea/psychology/*therapy ; *Fecal Microbiota Transplantation ; Feces/*microbiology ; Female ; Gastrointestinal Diseases ; Gastrointestinal Microbiome ; Humans ; Irritable Bowel Syndrome/psychology/*therapy ; Male ; Middle Aged ; }, abstract = {BACKGROUNDS: The intestinal microbiota is considered as a potential common underpinning pathophysiology of Functional Gastrointestinal Disorders (FGIDs) and psychiatric disorders such as depression and anxiety. Fecal Microbiota Transplantation (FMT) has been reported to have therapeutic effects on diseases related to dysbiosis, but few studies have evaluated its effect on psychiatric symptoms.

METHODS: We followed 17 patients with either Irritable Bowel Syndrome (IBS), Functional Diarrhea (FDr) or Functional Constipation (FC) who underwent FMT for the treatment of gastrointestinal symptoms and observation of psychiatric symptoms. Changes in Hamilton Rating Scale for Depression (HAM-D) and subscale of sleep-related items, Hamilton Rating Scale for Anxiety (HAM-A) and Quick Inventory for Depressive Symptoms (QIDS) between baseline and 4 weeks after FMT, and relationship with the intestinal microbiota were measured.

RESULTS: At baseline, 12 out of 17 patients were rated with HAM-D ≥ 8. Significant improvement in HAM-D total and sleep subscale score, HAM-A and QIDS were observed (p = 0.007, p = 0.007, p = 0.01, p = 0.007, respectively). Baseline Shannon index indicated that microbiota showed lower diversity in patients with HAM-D ≥ 8 compared to those of healthy donors and patients with HAM-D < 8. There was a significant correlation between baseline Shannon index and HAM-D score, and a correlation between Shannon index change and HAM-D improvement after FMT.

LIMITATIONS: The small sample size with no control group.

CONCLUSIONS: Our results suggest that depression and anxiety symptoms may be improved by FMT regardless of gastrointestinal symptom change in patients with IBS, FDr and FC, and the increase of microbiota diversity may help to improve patient's mood.}, } @article {pmid29684641, year = {2018}, author = {Jameson, E and Quareshy, M and Chen, Y}, title = {Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut.}, journal = {Methods (San Diego, Calif.)}, volume = {149}, number = {}, pages = {42-48}, pmid = {29684641}, issn = {1095-9130}, support = {BB/M017982/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Cardiovascular Diseases/etiology/metabolism/microbiology ; Carnitine/adverse effects/*metabolism ; Choline/adverse effects/*metabolism ; Computational Biology/*methods ; Diet/adverse effects/trends ; Gastrointestinal Microbiome/*physiology ; Humans ; Klebsiella pneumoniae/genetics/metabolism ; Methylamines/adverse effects/*metabolism ; Proteus mirabilis/genetics/metabolism ; }, abstract = {The bacterial formation of trimethylamine (TMA) has been linked to cardiovascular disease. This review focuses on the methods employed to investigate the identity of the bacteria responsible for the formation of TMA from dietary choline and carnitine in the human gut. Recent studies have revealed the metabolic pathways responsible for bacterial TMA production, primarily the anaerobic glycyl radical-containing, choline-TMA lyase, CutC and the aerobic carnitine monooxygenase, CntA. Identification of these enzymes has enabled bioinformatics approaches to screen both human-associated bacterial isolate genomes and whole gut metagenomes to determine which bacteria are responsible for TMA formation in the human gut. We centre on several key methodological aspects for identifying the TMA-producing bacteria and report how these pathways can be identified in human gut microbiota through bioinformatics analysis of available bacterial genomes and gut metagenomes.}, } @article {pmid29683411, year = {2019}, author = {Banach, A and Ciesielski, S and Bacza, T and Pieczykolan, M and Ziembińska-Buczyńska, A}, title = {Microbial community composition and methanogens' biodiversity during a temperature shift in a methane fermentation chamber.}, journal = {Environmental technology}, volume = {40}, number = {24}, pages = {3252-3263}, doi = {10.1080/09593330.2018.1468490}, pmid = {29683411}, issn = {1479-487X}, mesh = {Anaerobiosis ; Biodiversity ; Bioreactors ; Fermentation ; *Methane ; *Microbiota ; RNA, Ribosomal, 16S ; Temperature ; }, abstract = {More information on the connection between anaerobic digestion (AD) parameters and composition of the microbial community involved in the AD process is required to gain a better understanding of how a bioreactor functions. The aim of this study was to analyse the composition of microbial communities and the dynamics of methanogens' biodiversity changes during the shift from mesophilic (38°C) to thermophilic (55°C) conditions during biogas production. The total microbial composition was examined via the metagenomic approach based on 16S rRNA gene sequencing, whereas the methanogen communities were analysed using PCR-DGGE (Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis) of mcrA. Even though the temperature is one of the crucial parameters affecting microorganisms involved in the AD process, the results presented here revealed that there were no statistically significant differences in bacterial community composition between the mesophilic and thermophilic phases of the process. The most abundant phyla were found to be Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. However, the methanogens' community genotypic structure as examined by the PCR-DGGE method changed under thermophilic conditions. The temperature had the strongest impact on the archaeal methanogens in the fermentation chamber directly after implementing the temperature shift. A relatively higher biogas yield and average content of CH4 in the produced biogas were observed under thermophilic conditions.}, } @article {pmid29681906, year = {2018}, author = {Iino, C and Shimoyama, T and Chinda, D and Arai, T and Chiba, D and Nakaji, S and Fukuda, S}, title = {Infection of Helicobacter pylori and Atrophic Gastritis Influence Lactobacillus in Gut Microbiota in a Japanese Population.}, journal = {Frontiers in immunology}, volume = {9}, number = {}, pages = {712}, pmid = {29681906}, issn = {1664-3224}, mesh = {Adult ; Aged ; Biomarkers ; Female ; Gastritis, Atrophic/etiology/*immunology ; *Gastrointestinal Microbiome/immunology ; Helicobacter Infections/complications/diagnosis/*immunology/*microbiology ; *Helicobacter pylori/immunology ; Humans ; Japan ; *Lactobacillus/immunology ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Public Health Surveillance ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Suppression of gastric acid by proton pump inhibitors is associated with the increase of Lactobacillus in human gut microbiota. Gastric acid secretion is also suppressed by Helicobacter pylori infection and following atrophic gastritis. However, few studies have examined the association between H. pylori infection and Lactobacillus species in gut microbiota particularly in Japan.

METHODS: A total of 1,123 adult subjects who participated in a health survey in Hirosaki City were studied. Infection of H. pylori was defined by both serum antibody and stool antigen test. The presence and the severity of atrophic gastritis were defined by the serum level of serum pepsinogens. Using 16S ribosomal RNA amplification from fecal samples, the relative abundance of Lactobacillus was calculated, and the composition ratio of each Lactobacillus species was surveyed.

RESULTS: The relative abundance of the Lactobacillus in H. pylori-infected subjects with severe atrophic gastritis was higher comparing with those in subjects with mild atrophic gastritis and without atrophic gastritis (0.591 vs 0.068% and 0.033%, respectively; p < 0.001) and also that of non-infected subjects (0.033%; p < 0.001). In H. pylori non-infected subjects, both gender and age were not associated with the relative abundance of Lactobacillus in fecal samples. The proportion of Lactobacillus salivarius was high in H. pylori-infected subjects while that of Lactobacillus acidophilus was high in non-infected subjects.

CONCLUSION: Lactobacillus in human gut microbiota could be influenced by H. pylori infection and severity of atrophic gastritis in Japanese subjects.}, } @article {pmid29681561, year = {2018}, author = {Tandon, K and Yang, SH and Wan, MT and Yang, CC and Baatar, B and Chiu, CY and Tsai, JW and Liu, WC and Tang, SL}, title = {Bacterial Community in Water and Air of Two Sub-Alpine Lakes in Taiwan.}, journal = {Microbes and environments}, volume = {33}, number = {2}, pages = {120-126}, pmid = {29681561}, issn = {1347-4405}, mesh = {*Air Microbiology ; Bacteria/*classification/genetics ; *Biodiversity ; DNA, Bacterial/genetics ; Ecosystem ; Geologic Sediments/microbiology ; Lakes/*microbiology ; Metagenomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Spatio-Temporal Analysis ; Taiwan ; *Water Microbiology ; }, abstract = {Very few studies have attempted to profile the microbial communities in the air above freshwater bodies, such as lakes, even though freshwater sources are an important part of aquatic ecosystems and airborne bacteria are the most dispersible microorganisms on earth. In the present study, we investigated microbial communities in the waters of two high mountain sub-alpine montane lakes-located 21 km apart and with disparate trophic characteristics-and the air above them. Although bacteria in the lakes had locational differences, their community compositions remained constant over time. However, airborne bacterial communities were diverse and displayed spatial and temporal variance. Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria were dominant in both lakes, with different relative abundances between lakes, and Parcubacteria (OD1) was dominant in air samples for all sampling times, except two. We also identified certain shared taxa between lake water and the air above it. The results obtained on these communities in the present study provide putative candidates to study how airborne communities shape lake water bacterial compositions and vice versa.}, } @article {pmid29680562, year = {2018}, author = {Ribicic, D and Netzer, R and Hazen, TC and Techtmann, SM and Drabløs, F and Brakstad, OG}, title = {Microbial community and metagenome dynamics during biodegradation of dispersed oil reveals potential key-players in cold Norwegian seawater.}, journal = {Marine pollution bulletin}, volume = {129}, number = {1}, pages = {370-378}, doi = {10.1016/j.marpolbul.2018.02.034}, pmid = {29680562}, issn = {1879-3363}, mesh = {Biodegradation, Environmental ; Environmental Monitoring/*methods ; *Metagenome ; Microbial Consortia/*genetics ; Norway ; Petroleum/*analysis ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; Water Pollutants, Chemical/*analysis ; }, abstract = {Oil biodegradation as a weathering process has been extensively investigated over the years, especially after the Deepwater Horizon blowout. In this study, we performed microcosm experiments at 5 °C with chemically dispersed oil in non-amended seawater. We link biodegradation processes with microbial community and metagenome dynamics and explain the succession based on substrate specialization. Reconstructed genomes and 16S rRNA gene analysis revealed that Bermanella and Zhongshania were the main contributors to initial n-alkane breakdown, while subsequent abundances of Colwellia and microorganisms closely related to Porticoccaceae were involved in secondary n‑alkane breakdown and beta‑oxidation. Cycloclasticus, Porticoccaceae and Spongiiabcteraceae were associated with degradation of mono- and poly-cyclic aromatics. Successional pattern of genes coding for hydrocarbon degrading enzymes at metagenome level, and reconstructed genomic content, revealed a high differentiation of bacteria involved in hydrocarbon biodegradation. A cooperation among oil degrading microorganisms is thus needed for the complete substrate transformation.}, } @article {pmid29680553, year = {2018}, author = {Ribicic, D and Netzer, R and Winkler, A and Brakstad, OG}, title = {Microbial communities in seawater from an Arctic and a temperate Norwegian fjord and their potentials for biodegradation of chemically dispersed oil at low seawater temperatures.}, journal = {Marine pollution bulletin}, volume = {129}, number = {1}, pages = {308-317}, doi = {10.1016/j.marpolbul.2018.02.024}, pmid = {29680553}, issn = {1879-3363}, mesh = {Arctic Regions ; Biodegradation, Environmental ; Biotransformation ; Cold Temperature ; *Estuaries ; Hydrocarbons, Aromatic ; Metagenome ; Microbial Consortia/genetics ; Norway ; Petroleum/*analysis ; Seawater/chemistry/*microbiology ; Svalbard ; *Water Microbiology ; Water Pollutants, Chemical/*analysis ; }, abstract = {Biodegradation of chemically dispersed oil at low temperature (0-2 °C) was compared in natural seawater from Arctic (Svalbard) and a temperate (Norway) fjords. The oil was premixed with a dispersant (Corexit 9500) and small-droplet oil dispersions prepared. Faster biotransformation of n-alkanes in the Arctic than in the temperate seawater were associated with the initially higher abundance of the alkane-degrading genus Oleispira in the Arctic than the temperate seawater. Comparable transformation of aromatic hydrocarbons was further associated with the late emergences Cycloclasticus in both seawater sources. The results showed that chemically dispersed oil may be rapidly biodegraded by microbial communities in Arctic seawater. Compared to oil biodegradation studies at higher seawater temperatures, longer lag-periods were experienced here, and may be attributed to both microbial and oil properties at these low seawater temperatures.}, } @article {pmid29679832, year = {2018}, author = {Guo, Y and Chen, X and Wu, Y and Zhang, L and Cheng, J and Wei, G and Lin, Y}, title = {Natural revegetation of a semiarid habitat alters taxonomic and functional diversity of soil microbial communities.}, journal = {The Science of the total environment}, volume = {635}, number = {}, pages = {598-606}, doi = {10.1016/j.scitotenv.2018.04.171}, pmid = {29679832}, issn = {1879-1026}, mesh = {*Biodiversity ; China ; Classification ; Climate ; Ecosystem ; *Environmental Restoration and Remediation ; Microbiota ; Soil ; *Soil Microbiology ; }, abstract = {Revegetation of degraded lands has a profound impact on the maintenance and stability of ecosystem processes. However, the impacts of this land use change on functional diversity of soil microbial communities are poorly understood. Here, using 16S rRNA gene amplicon and shotgun metagenomic sequencing, we compared the taxonomic and functional communities of soil microbiome, and analyzed the effects of plant diversity and soil chemical properties, in a chronosequence of restored ex-farmland that had been naturally revegetated to grassland over periods of 5, 15 and 30years with adjacent farmland, on the Loess Plateau, China. We found that microbial taxonomic diversity was positively correlated with plant diversity and was higher in the revegetated sites. Functional diversity increased significantly in the oldest grassland. Actinobacteria, commonly considered a copiotrophic phylum, was more abundant in the revegetated sites, while Acidobacteria, an oligotrophic phylum, was more abundant in farmland. Furthermore, the structure of taxonomic and functional communities was significantly different between revegetated sites and farmland, and organic matter was the best environmental predictor in determining these microbial communities. Compared with the farmland, revegetation increased the proportion of genes associated with energy metabolism, carbohydrate metabolism and xenobiotics biodegradation and metabolism. Notably, the higher proportion of carbohydrate degradation gene subfamilies in the revegetated sites indicated higher levels of soil nutrient cycling. These results elucidate the significant shifts in belowground microbial taxonomic and functional diversity following vegetation restoration and have implications for ecological restoration programs in arid and semi-arid ecosystems.}, } @article {pmid29679417, year = {2018}, author = {Tankou, SK and Regev, K and Healy, BC and Tjon, E and Laghi, L and Cox, LM and Kivisäkk, P and Pierre, IV and Hrishikesh, L and Gandhi, R and Cook, S and Glanz, B and Stankiewicz, J and Weiner, HL}, title = {A probiotic modulates the microbiome and immunity in multiple sclerosis.}, journal = {Annals of neurology}, volume = {83}, number = {6}, pages = {1147-1161}, pmid = {29679417}, issn = {1531-8249}, support = {R01 NS087226/NS/NINDS NIH HHS/United States ; }, mesh = {Adult ; Bifidobacterium/genetics/*immunology ; Female ; Gastrointestinal Microbiome/physiology ; Humans ; Lactobacillus/genetics/immunology ; Leukocytes, Mononuclear/metabolism ; Male ; Microbiota/genetics/*immunology ; Middle Aged ; Multiple Sclerosis/*genetics/immunology ; Probiotics/*metabolism ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {OBJECTIVE: Effect of a probiotic on the gut microbiome and peripheral immune function in healthy controls and relapsing-remitting multiple sclerosis (MS) patients.

METHODS: MS patients (N = 9) and controls (N = 13) were orally administered a probiotic containing Lactobacillus, Bifidobacterium, and Streptococcus twice-daily for two months. Blood and stool specimens were collected at baseline, after completion of the 2-month treatment, and 3 months after discontinuation of therapy. Frozen peripheral blood mononuclear cells (PBMCs) were used for immune cell profiling. Stool samples were used for 16S rRNA profiling and metabolomics.

RESULTS: Probiotic administration increased the abundance of several taxa known to be depleted in MS such as Lactobacillus. We found that probiotic use decreased the abundance of taxa previously associated with dysbiosis in MS, including Akkermansia and Blautia. Predictive metagenomic analysis revealed a decrease in the abundance of several KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways associated with altered gut microbiota function in MS patients, such as methane metabolism, following probiotic supplementation. At the immune level, probiotic administration induced an anti-inflammatory peripheral immune response characterized by decreased frequency of inflammatory monocytes, decreased mean fluorescence intensity (MFI) of CD80 on classical monocytes, as well as decreased human leukocyte antigen (HLA) D related MFI on dendritic cells. Probiotic administration was also associated with decreased expression of MS risk allele HLA-DQA1 in controls. Probiotic-induced increase in abundance of Lactobacillus and Bifidobacterium was associated with decreased expression of MS risk allele HLA.DPB1 in controls.

INTERPRETATION: Our results suggest that probiotics could have a synergistic effect with current MS therapies. Ann Neurol 2018.}, } @article {pmid29678199, year = {2018}, author = {Huson, DH and Albrecht, B and Bağcı, C and Bessarab, I and Górska, A and Jolic, D and Williams, RBH}, title = {MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs.}, journal = {Biology direct}, volume = {13}, number = {1}, pages = {6}, pmid = {29678199}, issn = {1745-6150}, support = {NSF PHY-1748958//National Science Foundation/International ; }, mesh = {*Algorithms ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Microbiota/genetics ; Sequence Analysis, DNA ; Software ; }, abstract = {BACKGROUND: There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interactively navigate these large datasets. Long read sequencing technologies continue to improve and produce increasing numbers of longer reads (of varying lengths in the range of 10k-1M bps, say), but of low quality. There is an increasing interest in using long reads in microbiome sequencing, and there is a need to adapt short read tools to long read datasets.

METHODS: We describe a new LCA-based algorithm for taxonomic binning, and an interval-tree based algorithm for functional binning, that are explicitly designed for long reads and assembled contigs. We provide a new interactive tool for investigating the alignment of long reads against reference sequences. For taxonomic and functional binning, we propose to use LAST to compare long reads against the NCBI-nr protein reference database so as to obtain frame-shift aware alignments, and then to process the results using our new methods.

RESULTS: All presented methods are implemented in the open source edition of MEGAN, and we refer to this new extension as MEGAN-LR (MEGAN long read). We evaluate the LAST+MEGAN-LR approach in a simulation study, and on a number of mock community datasets consisting of Nanopore reads, PacBio reads and assembled PacBio reads. We also illustrate the practical application on a Nanopore dataset that we sequenced from an anammox bio-rector community.

REVIEWERS: This article was reviewed by Nicola Segata together with Moreno Zolfo, Pete James Lockhart and Serghei Mangul.

CONCLUSION: This work extends the applicability of the widely-used metagenomic analysis software MEGAN to long reads. Our study suggests that the presented LAST+MEGAN-LR pipeline is sufficiently fast and accurate.}, } @article {pmid29676472, year = {2018}, author = {Hao, DC and Zhang, CR and Xiao, PG}, title = {The first Taxus rhizosphere microbiome revealed by shotgun metagenomic sequencing.}, journal = {Journal of basic microbiology}, volume = {58}, number = {6}, pages = {501-512}, doi = {10.1002/jobm.201700663}, pmid = {29676472}, issn = {1521-4028}, mesh = {Archaea/classification/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; Biodegradation, Environmental ; Environmental Pollutants/adverse effects ; Fungi/classification/genetics/isolation & purification ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Genes, Fungal/genetics ; Genes, Viral/genetics ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; Plant Roots/*microbiology ; *Rhizosphere ; *Soil Microbiology ; Taxus/*microbiology ; Viruses/classification/genetics/isolation & purification ; }, abstract = {In the present study, the shotgun high throughput metagenomic sequencing was implemented to globally capture the features of Taxus rhizosphere microbiome. Total reads could be assigned to 6925 species belonging to 113 bacteria phyla and 301 species of nine fungi phyla. For archaea and virus, 263 and 134 species were for the first time identified, respectively. More than 720,000 Unigenes were identified by clean reads assembly. The top five assigned phyla were Actinobacteria (363,941 Unigenes), Proteobacteria (182,053), Acidobacteria (44,527), Ascomycota (fungi; 18,267), and Chloroflexi (15,539). KEGG analysis predicted numerous functional genes; 7101 Unigenes belong to "Xenobiotics biodegradation and metabolism." A total of 12,040 Unigenes involved in defense mechanisms (e.g., xenobiotic metabolism) were annotated by eggNOG. Talaromyces addition could influence not only the diversity and structure of microbial communities of Taxus rhizosphere, but also the relative abundance of functional genes, including metabolic genes, antibiotic resistant genes, and genes involved in pathogen-host interaction, bacterial virulence, and bacterial secretion system. The structure and function of rhizosphere microbiome could be sensitive to non-native microbe addition, which could impact on the pollutant degradation. This study, complementary to the amplicon sequencing, more objectively reflects the native microbiome of Taxus rhizosphere and its response to environmental pressure, and lays a foundation for potential combination of phytoremediation and bioaugmentation.}, } @article {pmid29674608, year = {2018}, author = {Thomas-White, K and Forster, SC and Kumar, N and Van Kuiken, M and Putonti, C and Stares, MD and Hilt, EE and Price, TK and Wolfe, AJ and Lawley, TD}, title = {Culturing of female bladder bacteria reveals an interconnected urogenital microbiota.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {1557}, pmid = {29674608}, issn = {2041-1723}, support = {//Wellcome Trust/United Kingdom ; R01 DK104718/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/genetics/growth & development/*isolation & purification ; Cohort Studies ; Female ; Genome, Bacterial ; Humans ; *Microbiota ; Middle Aged ; Phylogeny ; Urinary Bladder/*microbiology ; Vagina/*microbiology ; Young Adult ; }, abstract = {Metagenomic analyses have indicated that the female bladder harbors an indigenous microbiota. However, there are few cultured reference strains with sequenced genomes available for functional and experimental analyses. Here we isolate and genome-sequence 149 bacterial strains from catheterized urine of 77 women. This culture collection spans 78 species, representing approximately two thirds of the bacterial diversity within the sampled bladders, including Proteobacteria, Actinobacteria, and Firmicutes. Detailed genomic and functional comparison of the bladder microbiota to the gastrointestinal and vaginal microbiotas demonstrates similar vaginal and bladder microbiota, with functional capacities that are distinct from those observed in the gastrointestinal microbiota. Whole-genome phylogenetic analysis of bacterial strains isolated from the vagina and bladder in the same women identifies highly similar Escherichia coli, Streptococcus anginosus, Lactobacillus iners, and Lactobacillus crispatus, suggesting an interlinked female urogenital microbiota that is not only limited to pathogens but is also characteristic of health-associated commensals.}, } @article {pmid29674332, year = {2018}, author = {Du, F and Hinke, SA and Cavanaugh, C and Polidori, D and Wallace, N and Kirchner, T and Jennis, M and Lang, W and Kuo, GH and Gaul, MD and Lenhard, J and Demarest, K and Ajami, NJ and Liang, Y and Hornby, PJ}, title = {Potent Sodium/Glucose Cotransporter SGLT1/2 Dual Inhibition Improves Glycemic Control Without Marked Gastrointestinal Adaptation or Colonic Microbiota Changes in Rodents.}, journal = {The Journal of pharmacology and experimental therapeutics}, volume = {365}, number = {3}, pages = {676-687}, doi = {10.1124/jpet.118.248575}, pmid = {29674332}, issn = {1521-0103}, mesh = {Animals ; Biodiversity ; Blood Glucose/*metabolism ; Colon/*drug effects/metabolism/*microbiology ; Male ; Mice ; Microbiota/*drug effects ; Rats ; Sodium-Glucose Transporter 1/*antagonists & inhibitors ; Sodium-Glucose Transporter 2/*metabolism ; Sodium-Glucose Transporter 2 Inhibitors/metabolism/*pharmacology ; }, abstract = {The sodium/glucose cotransporters (SGLT1 and SGLT2) transport glucose across the intestinal brush border and kidney tubule. Dual SGLT1/2 inhibition could reduce hyperglycemia more than SGLT2-selective inhibition in patients with type 2 diabetes. However, questions remain about altered gastrointestinal (GI) luminal glucose and tolerability, and this was evaluated in slc5a1[-/-] mice or with a potent dual inhibitor (compound 8; SGLT1 Ki = 1.5 ± 0.5 nM 100-fold greater potency than phlorizin; SGLT2 Ki = 0.4 ± 0.2 nM). [13]C6-glucose uptake was quantified in slc5a1[-/-] mice and in isolated rat jejunum. Urinary glucose excretion (UGE), blood glucose (Sprague-Dawley rats), glucagon-like peptide 1 (GLP-1), and hemoglobin A1c (HbA1c) levels (Zucker diabetic fatty rats) were measured. Intestinal adaptation and rRNA gene sequencing was analyzed in C57Bl/6 mice. The blood [13]C6-glucose area under the curve (AUC) was reduced in the absence of SGLT1 by 75% (245 ± 6 vs. 64 ± 6 mg/dl⋅h in wild-type vs. slc5a1[-/-] mice) and compound 8 inhibited its transport up to 50% in isolated rat jejunum. Compound 8 reduced glucose excursion more than SGLT2-selective inhibition (e.g., AUC = 129 ± 3 vs. 249 ± 5 mg/dl⋅h for 1 mg/kg compound 8 vs. dapagliflozin) with similar UGE but a lower renal glucose excretion threshold. In Zucker diabetic fatty rats, compound 8 decreased HbA1c and increased total GLP-1 without changes in jejunum SGLT1 expression, mucosal weight, or villus length. Overall, compound 8 (1 mg/kg for 6 days) did not increase cecal glucose concentrations or bacterial diversity in C57BL/6 mice. In conclusion, potent dual SGLT1/2 inhibition lowers blood glucose by reducing intestinal glucose absorption and the renal glucose threshold but minimally impacts the intestinal mucosa or luminal microbiota in chow-fed rodents.}, } @article {pmid29670218, year = {2018}, author = {Jehrke, L and Stewart, FA and Droste, A and Beller, M}, title = {The impact of genome variation and diet on the metabolic phenotype and microbiome composition of Drosophila melanogaster.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6215}, pmid = {29670218}, issn = {2045-2322}, mesh = {Animals ; Drosophila melanogaster/*genetics/*metabolism/*microbiology ; *Energy Metabolism ; Female ; Genetic Association Studies ; *Genetic Variation ; *Genome ; Genome-Wide Association Study ; Male ; Metabolome ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phenotype ; }, abstract = {The metabolic phenotype of an organism depends on a complex regulatory network, which integrates the plethora of intrinsic and external information and prioritizes the flow of nutrients accordingly. Given the rise of metabolic disorders including obesity, a detailed understanding of this regulatory network is in urgent need. Yet, our level of understanding is far from completeness and complicated by the discovery of additional layers in metabolic regulation, such as the impact of the microbial community present in the gut on the hosts' energy storage levels. Here, we investigate the interplay between genome variation, diet and the gut microbiome in the shaping of a metabolic phenotype. For this purpose, we reared a set of fully sequenced wild type Drosophila melanogaster flies under basal and nutritionally challenged conditions and performed metabolic and microbiome profiling experiments. Our results introduce the fly as a model system to investigate the impact of genome variation on the metabolic response to diet alterations and reveal candidate single nucleotide polymorphisms associated with different metabolic traits, as well as metabolite-metabolite and metabolite-microbe correlations. Intriguingly, the dietary changes affected the microbiome composition less than anticipated. These results challenge the current view of a rapidly changing microbiome in response to environmental fluctuations.}, } @article {pmid29670191, year = {2018}, author = {Le Bastard, Q and Ward, T and Sidiropoulos, D and Hillmann, BM and Chun, CL and Sadowsky, MJ and Knights, D and Montassier, E}, title = {Fecal microbiota transplantation reverses antibiotic and chemotherapy-induced gut dysbiosis in mice.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6219}, pmid = {29670191}, issn = {2045-2322}, mesh = {Animals ; Anti-Bacterial Agents/*adverse effects/pharmacology ; Antineoplastic Agents/*adverse effects/pharmacology ; Biodiversity ; Disease Models, Animal ; Dysbiosis/*etiology/*microbiology/therapy ; *Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Mice ; }, abstract = {Fecal microbiota transplantation (FMT) is now widely used to treat recurrent Clostridium difficile infection, but has been less studied as a means to restore microbiome diversity and composition following antibiotic or chemotherapy treatments. The purpose of our study was to assess the efficacy of FMT to reverse antibiotic- and chemotherapy-induced gut dysbiosis in a mouse model. C57BL/6J mice were treated with ampicillin for 1 week and/or received a single intraperitoneal injection of 5-Fluorouracil. Fresh stool was collected and analyzed using shotgun metagenomics and the Illumina sequencing platform. Ampicillin caused a significant and immediate decrease in bacterial species richness and diversity that persisted for one week. In mice that received FMT, disruption of the intestinal microbiota was reversed immediately. Antibiotic and chemotherapy administration caused significant alteration in species distribution, including a decrease in the relative proportions of Clostridium scindens and Faecalibacterium prausnitzii, and an increase in known pathogenic species. In mice receiving FMT, we observed a significant increase in species known to exhibit anti-inflammatory properties. Moreover, chemotherapy led to a critical decrease in key 'health-promoting' species and to an altered functional profile, especially when chemotherapy was administered in tandem with antibiotics, and that FMT can ameliorate these effects.}, } @article {pmid29669589, year = {2018}, author = {Coelho, LP and Kultima, JR and Costea, PI and Fournier, C and Pan, Y and Czarnecki-Maulden, G and Hayward, MR and Forslund, SK and Schmidt, TSB and Descombes, P and Jackson, JR and Li, Q and Bork, P}, title = {Similarity of the dog and human gut microbiomes in gene content and response to diet.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {72}, pmid = {29669589}, issn = {2049-2618}, support = {686070//Horizon 2020 Framework Programme (BE)/International ; }, mesh = {Animals ; *Diet ; Dogs ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; Mice ; *Microbiota ; Obesity ; Swine ; }, abstract = {BACKGROUND: Gut microbes influence their hosts in many ways, in particular by modulating the impact of diet. These effects have been studied most extensively in humans and mice. In this work, we used whole genome metagenomics to investigate the relationship between the gut metagenomes of dogs, humans, mice, and pigs.

RESULTS: We present a dog gut microbiome gene catalog containing 1,247,405 genes (based on 129 metagenomes and a total of 1.9 terabasepairs of sequencing data). Based on this catalog and taxonomic abundance profiling, we show that the dog microbiome is closer to the human microbiome than the microbiome of either pigs or mice. To investigate this similarity in terms of response to dietary changes, we report on a randomized intervention with two diets (high-protein/low-carbohydrate vs. lower protein/higher carbohydrate). We show that diet has a large and reproducible effect on the dog microbiome, independent of breed or sex. Moreover, the responses were in agreement with those observed in previous human studies.

CONCLUSIONS: We conclude that findings in dogs may be predictive of human microbiome results. In particular, a novel finding is that overweight or obese dogs experience larger compositional shifts than lean dogs in response to a high-protein diet.}, } @article {pmid29668682, year = {2018}, author = {Hannigan, GD and Duhaime, MB and Koutra, D and Schloss, PD}, title = {Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome.}, journal = {PLoS computational biology}, volume = {14}, number = {4}, pages = {e1006099}, pmid = {29668682}, issn = {1553-7358}, support = {T32AI007528/NH/NIH HHS/United States ; T32 AI007528/AI/NIAID NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; P30DK034933/NH/NIH HHS/United States ; U01AI124255/NH/NIH HHS/United States ; U19AI09087/NH/NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Bacteriophages/*genetics/*physiology ; Computational Biology ; Diet ; Humans ; Metagenomics ; Microbial Consortia/genetics/physiology ; Microbiota/*genetics/*physiology ; Models, Biological ; Phylogeography ; Skin/microbiology/virology ; }, abstract = {Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness across the human body. We observed evidence that gut and skin network structures were person-specific and not conserved among cohabitating family members. High-fat diets appeared to be associated with less connected networks. Network structure differed between skin sites, with those exposed to the external environment being less connected and likely more susceptible to network degradation by microbial extinction events. This study quantified and contrasted the diversity of virome-microbiome networks across the human body and illustrated how environmental factors may influence phage-bacteria interactive dynamics. This work provides a baseline for future studies to better understand system perturbations, such as disease states, through ecological networks.}, } @article {pmid29668334, year = {2018}, author = {Amrane, S and Raoult, D and Lagier, JC}, title = {Metagenomics, culturomics, and the human gut microbiota.}, journal = {Expert review of anti-infective therapy}, volume = {16}, number = {5}, pages = {373-375}, doi = {10.1080/14787210.2018.1467268}, pmid = {29668334}, issn = {1744-8336}, mesh = {Culture Techniques/*methods ; Gastrointestinal Microbiome/*physiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; }, } @article {pmid29667371, year = {2019}, author = {Han, Z and Sun, J and Lv, A and Wang, A}, title = {Biases from different DNA extraction methods in intestine microbiome research based on 16S rDNA sequencing: a case in the koi carp, Cyprinus carpio var. Koi.}, journal = {MicrobiologyOpen}, volume = {8}, number = {1}, pages = {e00626}, pmid = {29667371}, issn = {2045-8827}, mesh = {Animals ; Carps/microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics/*isolation & purification ; DNA, Ribosomal/chemistry/genetics/*isolation & purification ; *Gastrointestinal Microbiome ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {This study examined the technical bias associated with different DNA extraction methods used in microbiome research. Three methods were used to extract genomic DNA from the same intestinal microbiota sample that was taken from the koi carp Cyprinus carpio var. koi, after which their microbial diversity and community structure were investigated on the basis of a 16S rDNA high-throughput sequencing analysis. Biased results were observed in relation to the number of reads, alpha diversity indexes and taxonomic composition among the three DNA extraction protocols. A total of 1,381 OTUs from the intestinal bacteria were obtained, with 852, 759, and 698 OTUs acquired, using the Lysozyme and Ultrasonic Lysis method, Zirmil-beating Cell Disruption method, and a QIAamp Fast DNA Stool Mini Kit, respectively. Additionally, 336 OTUs were commonly acquired, using the three methods. The results showed that the alpha diversity indexes (Rarefaction, Shannon, and Chao1) of the community that were determined using the Lysozyme and Ultrasonic Lysis method were higher than those obtained with the Zirmil-beating Cell Disruption method, while the Zirmil method results were higher than those measured, using the QIAamp Fast DNA Stool Mini Kit. Moreover, all the major phyla (ratio>1%) could be identified with all three DNA extraction methods, but the phyla present at a lower abundance (ratio <1%) could not. Similar findings were observed at the genus level. Taken together, these findings indicated that the bias observed in the results about the community structure occurred primarily in OTUs with a lower abundance. The results of this study demonstrate that possible bias exists in community analyses, and researchers should therefore be conservative when drawing conclusions about community structures based on the currently available DNA extraction methods.}, } @article {pmid29667329, year = {2018}, author = {Bista, I and Carvalho, GR and Tang, M and Walsh, K and Zhou, X and Hajibabaei, M and Shokralla, S and Seymour, M and Bradley, D and Liu, S and Christmas, M and Creer, S}, title = {Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.12888}, pmid = {29667329}, issn = {1755-0998}, abstract = {New applications of DNA and RNA sequencing are expanding the field of biodiversity discovery and ecological monitoring, yet questions remain regarding precision and efficiency. Due to primer bias, the ability of metabarcoding to accurately depict biomass of different taxa from bulk communities remains unclear, while PCR-free whole mitochondrial genome (mitogenome) sequencing may provide a more reliable alternative. Here, we used a set of documented mock communities comprising 13 species of freshwater macroinvertebrates of estimated individual biomass, to compare the detection efficiency of COI metabarcoding (three different amplicons) and shotgun mitogenome sequencing. Additionally, we used individual COI barcoding and de novo mitochondrial genome sequencing, to provide reference sequences for OTU assignment and metagenome mapping (mitogenome skimming), respectively. We found that, even though both methods occasionally failed to recover very low abundance species, metabarcoding was less consistent, by failing to recover some species with higher abundances, probably due to primer bias. Shotgun sequencing results provided highly significant correlations between read number and biomass in all but one species. Conversely, the read-biomass relationships obtained from metabarcoding varied across amplicons. Specifically, we found significant relationships for eight of 13 (amplicons B1FR-450 bp, FF130R-130 bp) or four of 13 (amplicon FFFR, 658 bp) species. Combining the results of all three COI amplicons (multiamplicon approach) improved the read-biomass correlations for some of the species. Overall, mitogenomic sequencing yielded more informative predictions of biomass content from bulk macroinvertebrate communities than metabarcoding. However, for large-scale ecological studies, metabarcoding currently remains the most commonly used approach for diversity assessment.}, } @article {pmid29667264, year = {2018}, author = {Xu, Y and Jia, YH and Chen, L and Huang, WM and Yang, DQ}, title = {Metagenomic analysis of oral microbiome in young children aged 6-8 years living in a rural isolated Chinese province.}, journal = {Oral diseases}, volume = {24}, number = {6}, pages = {1115-1125}, doi = {10.1111/odi.12871}, pmid = {29667264}, issn = {1601-0825}, mesh = {Child ; China ; Dentition, Mixed ; Female ; Humans ; Male ; Metagenomics ; *Microbiota ; Mouth/*microbiology ; *Rural Population ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The mixed dentition is an important transition period from primary teeth to permanent teeth. However, the caries prevalence of first permanent molar in mixed dentitions was about 30%, which almost represent the caries rate of permanent teeth in this period of time. Therefore, we assessed the oral bacterial profiles in young children (age 6-8) with mixed dentition with or without first molar caries for providing the research basis of caries etiology.

METHODS: We collected samples of supragingival plaque and saliva from the children living in Guizhou, a rural isolated province in China. Then, we performed DNA extraction and purification followed by 454 pyrosequencing of the V1-V3 hypervariable regions of the 16S rRNA and compared our results with those of previous research.

RESULTS: (i) We analyzed 48,320 unique sequences that represented 18 phyla, 29 classes, 44 orders, 74 families, 129 genera, 15,003 species-level OUT in plaque and saliva samples; (ii) longitudinally, there was the "healthy core microbiome" between healthy deciduous dentition and early mixed dentition, for example, Neisseria, Porphyromonas, Selenomonas etc.; (iii) horizontally, there also existed the "healthy core microbiome" in early mixed dentition, for example, Neisseria, Streptococcus, Prevotella etc.; (iv) the dominant bacteria detected by Lefse in caries group including Actinomycetaceae, Streptobacillus (p < 0.05) and those in caries-free group including Gammaproteobacteria, Pasteurellaceae, Aggregatibacter, Chloroflexi, (p < 0.05).

CONCLUSIONS: The oral cavity is a highly heterogeneous ecosystem with the "healthy core microbiome" in children, although microbial composition shifts along with aging. In addition, the abundance and diversity of microbiota vary between caries and caries-free groups verify the ecological plaque hypothesis.}, } @article {pmid29666288, year = {2018}, author = {Nowicki, EM and Shroff, R and Singleton, JA and Renaud, DE and Wallace, D and Drury, J and Zirnheld, J and Colleti, B and Ellington, AD and Lamont, RJ and Scott, DA and Whiteley, M}, title = {Microbiota and Metatranscriptome Changes Accompanying the Onset of Gingivitis.}, journal = {mBio}, volume = {9}, number = {2}, pages = {}, pmid = {29666288}, issn = {2150-7511}, support = {P20 GM125504/GM/NIGMS NIH HHS/United States ; R01 DE017680/DE/NIDCR NIH HHS/United States ; R01 DE026963/DE/NIDCR NIH HHS/United States ; }, mesh = {Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Dysbiosis ; *Gene Expression Profiling ; Gingivitis/*microbiology/*pathology ; Humans ; *Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; }, abstract = {Over half of adults experience gingivitis, a mild yet treatable form of periodontal disease caused by the overgrowth of oral microbes. Left untreated, gingivitis can progress to a more severe and irreversible disease, most commonly chronic periodontitis. While periodontal diseases are associated with a shift in the oral microbiota composition, it remains unclear how this shift impacts microbiota function early in disease progression. Here, we analyzed the transition from health to gingivitis through both 16S v4-v5 rRNA amplicon and metatranscriptome sequencing of subgingival plaque samples from individuals undergoing an experimental gingivitis treatment. Beta-diversity analysis of 16S rRNA reveals that samples cluster based on disease severity and patient but not by oral hygiene status. Significant shifts in the abundance of several genera occurred during disease transition, suggesting a dysbiosis due to development of gingivitis. Comparing taxonomic abundance with transcriptomic activity revealed concordance of bacterial diversity composition between the two quantification assays in samples originating from both healthy and diseased teeth. Metatranscriptome sequencing analysis indicates that during the early stages of transition to gingivitis, a number of virulence-related transcripts were significantly differentially expressed in individual and across pooled patient samples. Upregulated genes include those involved in proteolytic and nucleolytic processes, while expression levels of those involved in surface structure assembly and other general virulence functions leading to colonization or adaptation within the host are more dynamic. These findings help characterize the transition from health to periodontal disease and identify genes associated with early disease.IMPORTANCE Although more than 50% of adults have some form of periodontal disease, there remains a significant gap in our understanding of its underlying cause. We initiated this study in order to better characterize the progression from oral health to disease. We first analyzed changes in the abundances of specific microorganisms in dental plaque collected from teeth during health and gingivitis, the mildest form of periodontal disease. We found that the clinical score of disease and patient from whom the sample originated but not tooth brushing are significantly correlated with microbial community composition. While a number of virulence-related gene transcripts are differentially expressed in gingivitis samples relative to health, not all are increased, suggesting that the overall activity of the microbiota is dynamic during disease transition. Better understanding of which microbes are present and their function during early periodontal disease can potentially lead to more targeted prophylactic approaches to prevent disease progression.}, } @article {pmid29665523, year = {2018}, author = {Osimani, A and Milanović, V and Garofalo, C and Cardinali, F and Roncolini, A and Sabbatini, R and De Filippis, F and Ercolini, D and Gabucci, C and Petruzzelli, A and Tonucci, F and Clementi, F and Aquilanti, L}, title = {Revealing the microbiota of marketed edible insects through PCR-DGGE, metagenomic sequencing and real-time PCR.}, journal = {International journal of food microbiology}, volume = {276}, number = {}, pages = {54-62}, doi = {10.1016/j.ijfoodmicro.2018.04.013}, pmid = {29665523}, issn = {1879-3460}, mesh = {Animals ; *Biodiversity ; Denaturing Gradient Gel Electrophoresis ; *Food Microbiology ; High-Throughput Nucleotide Sequencing ; Insecta/*microbiology ; *Metagenomics ; Microbiota/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; *Real-Time Polymerase Chain Reaction ; Thailand ; }, abstract = {The present study aimed to identify the microbiota present in six species of processed edible insects produced in Thailand and marketed worldwide via the internet, namely, giant water bugs (Belostoma lutarium), black ants (Polyrhachis), winged termites (alates, Termitoidae), rhino beetles (Hyboschema contractum), mole crickets (Gryllotalpidae), and silkworm pupae (Bombyx mori). For each species, two samples of boiled, dried and salted insects were purchased. The microbial DNA was extracted from the insect samples and subjected to polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), high-throughput sequencing and qualitative real-time PCR assays. The microbiota of the analyzed samples were widely characterized by the presence of spore-forming bacteria mainly represented by the genera Bacillus and Clostridium. Moreover, the genera Anaerobacillus, Paenibacillus, Geobacillus, Pseudomonas, Stenotrophomonas, Massilia, Delftia, Lactobacillus, Staphylococcus, Streptococcus, Vagococcus, and Vibrio were also detected. Real-time PCR allowed for ascertainment of the absence of Coxiella burnetii, Shiga toxin-producing E. coli (STEC), and Pseudomonas aeruginosa in all samples. The results of this study confirm the importance of combining different molecular techniques to characterize the biodiversity of complex ecosystems such as edible insects. The presence of potential human pathogens suggests the need for a careful application of good manufacturing practices during insect processing. This study provides further data that will be useful in risk analyses of edible insects as a novel food source.}, } @article {pmid29664968, year = {2018}, author = {Betiku, OC and Yeoman, CJ and Gaylord, TG and Americus, B and Olivo, S and Duff, GC and Sealey, WM}, title = {Water system is a controlling variable modulating bacterial diversity of gastrointestinal tract and performance in rainbow trout.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195967}, pmid = {29664968}, issn = {1932-6203}, mesh = {Animal Feed ; Animals ; Bacteria/*classification/genetics ; *Biodiversity ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Oncorhynchus mykiss/*microbiology ; Plant Proteins, Dietary ; *Water Microbiology ; }, abstract = {A two-phase feeding study evaluating performance of rainbow trout and comparing luminal and mucosal gastrointestinal tract (GIT) bacterial community compositions when fed two alternative protein diets in two rearing systems was conducted. Alternative protein diets (animal protein and plant protein diets) balanced with crystalline amino acids: lysine, methionine and threonine or unbalanced, were fed to rainbow trout in two separate water systems (recirculating (RR) and flow-through (FF)) for a period of 16 weeks. The four diets, each contained 38% digestible protein and 20% fats, were fed to rainbow trout with an average weight of 12.02 ± 0.61 g, and sorted at 30 fish/tank and 12 tanks per dietary treatment. Phase 1 lasted for 8 weeks after which fish from each tank were randomly divided, with one-half moved to new tanks of the opposing system (i.e. from RR to FF and vice versa). The remaining halves were retained in their initial tank and system, and fed their original diets for another 8 weeks (phase 2). After the 16th week, 3 fish/tank were sampled for each of proximate analysis, body indexes and 16S rRNA analysis of GIT microbiota. Fish weight (P = 0.0008, P = 0.0030, P<0.0010) and body fat (P = 0.0008, P = 0.0041, P = 0.0177) were significantly affected by diet, diet quality (balanced or unbalanced) and system, respectively. Feed intake (P = 0.0008) and body energy (P<0.0010) were altered by system. Body indexes were not affected by dietary treatment and water systems. Compositional dissimilarities existed between samples from the rearing water and GIT locations (ANOSIM: (R = 0.29, P = 0.0010), PERMANOVA: R = 0.39, P = 0.0010), but not in dietary samples (ANOSIM: R = 0.004, P = 0.3140, PERMANOVA: R = 0.008, P = 0.4540). Bacteria were predominantly from the phyla Proteobacteria, Firmicutes and Bacteroidetes. Their abundance differed with more dissimilarity in the luminal samples (ANOSIM: R = 0.40, P = 0.0010, PERMANOVA: R = 0.56, P = 0.0010) than those from the mucosal intestine (ANOSIM: R = 0.37, P = 0.0010, PERMANOVA: R = 0.41, P = 0.0010). Bacteria generally associated with carbohydrate and certain amino acids metabolism were observed in the mucosal intestine while rearing water appeared to serve as the main route of colonization of Aeromonas and Acinetobacter in the rainbow trout.}, } @article {pmid29664912, year = {2018}, author = {Hugenholtz, F and Davids, M and Schwarz, J and Müller, M and Tomé, D and Schaap, P and Hooiveld, GJEJ and Smidt, H and Kleerebezem, M}, title = {Metatranscriptome analysis of the microbial fermentation of dietary milk proteins in the murine gut.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0194066}, pmid = {29664912}, issn = {1932-6203}, mesh = {Animals ; Fatty Acids, Volatile/*metabolism ; Fermentation/*physiology ; Gastrointestinal Microbiome/*physiology ; Intestinal Mucosa/metabolism ; Intestines/microbiology ; *Metagenome ; Mice ; Milk/metabolism ; Milk Proteins/*metabolism ; }, abstract = {Undigestible food ingredients are converted by the microbiota into a large range of metabolites, predominated by short chain fatty acids (SCFA). These microbial metabolites are subsequently available for absorption by the host mucosa and can serve as an energy source. Amino acids fermentation by the microbiota expands the spectrum of fermentation end-products beyond acetate, propionate and butyrate, to include in particular branched-SCFA. Here the long-term effects of high protein-diets on microbial community composition and functionality in mice were analyzed. Determinations of the microbiota composition using phylogenetic microarray (MITChip) technology were complemented with metatranscriptome and SCFA analyses to obtain insight in in situ expression of protein fermentation pathways and the phylogenetic groups involved. High protein diets led to increased luminal concentrations of branched-SCFA, in accordance with protein fermentation in the gut. Bacteria dominantly participating in protein catabolism belonged to the Lachnospiraceae, Erysipelotrichaceae and Clostridiaceae families in both normal- and high- protein diet regimes. This study identifies the microbial groups involved in protein catabolism in the intestine and underpins the value of in situ metatranscriptome analyses as an approach to decipher locally active metabolic networks and pathways as a function of the dietary regime, as well as the phylogeny of the microorganisms executing them.}, } @article {pmid29664320, year = {2018}, author = {Nakano, M}, title = {16S rRNA Gene Primer Validation for Bacterial Diversity Analysis of Vegetable Products.}, journal = {Journal of food protection}, volume = {81}, number = {5}, pages = {848-859}, doi = {10.4315/0362-028X.JFP-17-346}, pmid = {29664320}, issn = {1944-9097}, mesh = {Animals ; Bacteria/genetics ; Bacterial Load ; DNA Primers/genetics ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Microbiota ; RNA, Ribosomal, 16S/*genetics ; Vegetable Products/*microbiology ; }, abstract = {High-throughput sequencing of the 16S rRNA gene enhances understanding of microbial diversity from complex environmental samples. The 16S rRNA gene is currently the most important target in bacterial evolution and ecology studies, particularly for determination of phylogenetic relationships among taxa, exploration of bacterial diversity in a given environment, and quantification of the relative abundance of taxa at various levels. However, some parts of the conserved region of the bacterial 16S rRNA gene are similar to the conserved regions of plant chloroplasts and eukaryotic mitochondria. Therefore, if DNA contains a large amount of nontarget DNA, this nontarget DNA can be coamplified and consequently produce useless sequence reads. We experimentally assessed the primer pair 335f/769r and the widely used bacterial primer pair SD (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21). The primer pair 335f/769r was examined for its ability to amplify bacterial DNA in plant and animal feed samples by using the single-strand confirmation polymorphism method. In our present study, these primer pairs were validated for microbial community structure analysis with complex food matrices by using next-generation sequencing. The sequencing results revealed that the primer pair 335f/769r successfully resulted in fewer chloroplast and mitochondrial sequence reads than generated by the universal primer pair SD and therefore is comparatively suitable for metagenomic analyses of complex food matrices, particularly those that are rich in plant DNA. Additionally, some taxonomic groups were missed entirely when only the SD primer pair was used.}, } @article {pmid29661230, year = {2018}, author = {Gomez-Silvan, C and Leung, MHY and Grue, KA and Kaur, R and Tong, X and Lee, PKH and Andersen, GL}, title = {A comparison of methods used to unveil the genetic and metabolic pool in the built environment.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {71}, pmid = {29661230}, issn = {2049-2618}, support = {G-2015-13977//Alfred P. Sloan Foundation/International ; 11276116//Research Grants Council, University Grants Committee/International ; }, mesh = {*Built Environment ; *Environmental Microbiology ; Humans ; *Metabolomics/methods ; *Metagenomics/methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many exceptions have been noted, the ribosomal RNA fraction of the sample is more likely to represent either viable or metabolically active cells. We examined methodological variations in sample processing using a defined, mock BE microbial community to better understand the scope of technique-based vs. biological-based differences in both ribosomal transcript (rRNA) and gene (DNA) sequence community analysis. Based on in vitro tests, a protocol was adopted for the analysis of the genetic and metabolic pool (DNA vs. rRNA) of air and surface microbiomes within a residential setting.

RESULTS: We observed differences in DNA/RNA co-extraction efficiency for individual microbes, but overall, a greater recovery of rRNA using FastPrep (> 50%). Samples stored with various preservation methods at - 80°C experienced a rapid decline in nucleic acid recovery starting within the first week, although post-extraction rRNA had no significant degradation when treated with RNAStable. We recommend that co-extraction samples be processed as quickly as possible after collection. The in vivo analysis revealed significant differences in the two components (genetic and metabolic pool) in terms of taxonomy, community structure, and microbial association networks. Rare taxa present in the genetic pool showed higher metabolic potential (RNA:DNA ratio), whereas commonly detected taxa of outdoor origins based on DNA sequencing, especially taxa of the Sphingomonadales order, were present in lower relative abundances in the viable community.

CONCLUSIONS: Although methodological variations in sample preparations are high, large differences between the DNA and RNA fractions of the total microbial community demonstrate that direct examination of rRNA isolated from a residential BE microbiome has the potential to identify the more likely viable or active portion of the microbial community. In an environment that has primarily dead and metabolically inactive cells, we suggest that the rRNA fraction of BE samples is capable of providing a more ecologically relevant insight into the factors that drive indoor microbial community dynamics.}, } @article {pmid29660711, year = {2018}, author = {Kotoky, R and Rajkumari, J and Pandey, P}, title = {The rhizosphere microbiome: Significance in rhizoremediation of polyaromatic hydrocarbon contaminated soil.}, journal = {Journal of environmental management}, volume = {217}, number = {}, pages = {858-870}, doi = {10.1016/j.jenvman.2018.04.022}, pmid = {29660711}, issn = {1095-8630}, mesh = {Biodegradation, Environmental ; Hydrocarbons/*metabolism ; Microbiota ; Plant Roots ; *Rhizosphere ; Soil ; *Soil Microbiology ; Soil Pollutants ; }, abstract = {Microbial communities are an essential part of plant rhizosphere and participate in the functioning of plants, including rhizoremediation of petroleum contaminants. Rhizoremediation is a promising technology for removal of polyaromatic hydrocarbons based on interactions between plants and microbiome in the rhizosphere. Root exudation in the rhizosphere provides better nutrient uptake for rhizosphere microbiome, and therefore it is considered to be one of the major factors of microbial community function in the rhizosphere that plays a key role in the enhanced PAH biodegradation. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, the interactions between microbiome and plant roots in the process of rhizosphere mediated remediation of PAH still needs attention. Most of the current researches target PAH degradation by plant or single microorganism, separately, whereas the interactions between plants and whole microbiome are overlooked and its role has been ignored. This review summarizes recent knowledge of PAH degradation in the rhizosphere in the process of plant-microbiome interactions based on emerging omics approaches such as metagenomics, metatranscriptomics, metabolomics and metaproteomics. These omics approaches with combinations to bioinformatics tools provide us a better understanding in integrated activity patterns between plants and rhizosphere microbes, and insight into the biochemical and molecular modification of the meta-organisms (plant-microbiome) to maximize rhizoremediation activity. Moreover, a better understanding of the interactions could lead to the development of techniques to engineer rhizosphere microbiome for better hydrocarbon degradation.}, } @article {pmid29659617, year = {2018}, author = {Mohamed Ramli, N and Giatsis, C and Md Yusoff, F and Verreth, J and Verdegem, M}, title = {Resistance and resilience of small-scale recirculating aquaculture systems (RAS) with or without algae to pH perturbation.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195862}, pmid = {29659617}, issn = {1932-6203}, mesh = {Ammonia/chemistry ; *Aquaculture ; Bacteria/classification/genetics ; Biodiversity ; *Chlorophyta ; *Fresh Water ; *Hydrogen-Ion Concentration ; Metagenome ; Metagenomics/methods ; Nitrogen/chemistry ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; Water Quality ; }, abstract = {The experimental set-up of this study mimicked recirculating aquaculture systems (RAS) where water quality parameters such as dissolved oxygen, pH, temperature, and turbidity were controlled and wastes produced by fish and feeding were converted to inorganic forms. A key process in the RAS was the conversion of ammonia to nitrite and nitrite to nitrate through nitrification. It was hypothesized that algae inclusion in RAS would improve the ammonia removal from the water; thereby improving RAS water quality and stability. To test this hypothesis, the stability of the microbiota community composition in a freshwater RAS with (RAS+A) or without algae (RAS-A) was challenged by introducing an acute pH drop (from pH 7 to 4 during three hours) to the system. Stigeoclonium nanum, a periphytic freshwater microalga was used in this study. No significant effect of the algae presence was found on the resistance to the acute pH drop on ammonia conversion to nitrite and nitrite conversion to nitrate. Also the resilience of the ammonia conversion to the pH drop disruption was not affected by the addition of algae. This could be due to the low biomass of algae achieved in the RAS. However, with regard to the conversion step of nitrite to nitrate, RAS+A was significantly more resilient than RAS-A. In terms of overall bacterial communities, the composition and predictive function of the bacterial communities was significantly different between RAS+A and RAS-A.}, } @article {pmid29658784, year = {2018}, author = {Popic, V and Kuleshov, V and Snyder, M and Batzoglou, S}, title = {Fast Metagenomic Binning via Hashing and Bayesian Clustering.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {25}, number = {7}, pages = {677-688}, doi = {10.1089/cmb.2017.0250}, pmid = {29658784}, issn = {1557-8666}, mesh = {*Bayes Theorem ; Cluster Analysis ; Computational Biology/*statistics & numerical data ; Humans ; Metagenome/genetics ; Metagenomics/*statistics & numerical data ; Microbiota/*genetics ; }, abstract = {We introduce GATTACA, a framework for fast unsupervised binning of metagenomic contigs. Similar to recent approaches, GATTACA clusters contigs based on their coverage profiles across a large cohort of metagenomic samples; however, unlike previous methods that rely on read mapping, GATTACA quickly estimates these profiles from kmer counts stored in a compact index. This approach can result in over an order of magnitude speedup, while matching the accuracy of earlier methods on synthetic and real data benchmarks. It also provides a way to index metagenomic samples (e.g., from public repositories such as the Human Microbiome Project) offline once and reuse them across experiments; furthermore, the small size of the sample indices allows them to be easily transferred and stored. Leveraging the MinHash technique, GATTACA also provides an efficient way to identify publicly available metagenomic data that can be incorporated into the set of reference metagenomes to further improve binning accuracy. Thus, enabling easy indexing and reuse of publicly available metagenomic data sets, GATTACA makes accurate metagenomic analyses accessible to a much wider range of researchers.}, } @article {pmid29657127, year = {2018}, author = {Tilg, H and Adolph, TE and Gerner, RR and Moschen, AR}, title = {The Intestinal Microbiota in Colorectal Cancer.}, journal = {Cancer cell}, volume = {33}, number = {6}, pages = {954-964}, doi = {10.1016/j.ccell.2018.03.004}, pmid = {29657127}, issn = {1878-3686}, support = {P 29379/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; *Carcinogenesis ; *Cell Transformation, Neoplastic ; Colon/microbiology/pathology ; Colorectal Neoplasms/*physiopathology ; Gastrointestinal Microbiome/*physiology ; Humans ; Models, Biological ; Rectum/microbiology/pathology ; Signal Transduction ; }, abstract = {Experimental evidence from the past years highlights a key role for the intestinal microbiota in inflammatory and malignant gastrointestinal diseases. Diet exhibits a strong impact on microbial composition and provides risk for developing colorectal carcinoma (CRC). Large metagenomic studies in human CRC associated microbiome signatures with the colorectal adenoma-carcinoma sequence, suggesting a fundamental role of the intestinal microbiota in the evolution of gastrointestinal malignancy. Basic science established a critical function for the intestinal microbiota in promoting tumorigenesis. Further studies are needed to decipher the mechanisms of tumor promotion and microbial co-evolution in CRC, which may be exploited therapeutically in the future.}, } @article {pmid29656601, year = {2019}, author = {Dashti, N and Ali, N and Salamah, S and Khanafer, M and Al-Shamy, G and Al-Awadhi, H and Radwan, SS}, title = {Culture-independent analysis of hydrocarbonoclastic bacterial communities in environmental samples during oil-bioremediation.}, journal = {MicrobiologyOpen}, volume = {8}, number = {2}, pages = {e00630}, pmid = {29656601}, issn = {2045-8827}, mesh = {Bacteria/*classification/genetics/*metabolism ; Biodegradation, Environmental ; *Biodiversity ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; Environmental Pollutants/*metabolism ; Hydrocarbons/*metabolism ; Metagenomics ; Oils/*metabolism ; Oxidoreductases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {To analyze microbial communities in environmental samples, this study combined Denaturing Gradient Gel Electrophoresis of amplified 16S rRNA-genes in total genomic DNA extracts from those samples with gene sequencing. The environmental samples studied were oily seawater and soil samples, that had been bioaugmented with natural materials rich in hydrocarbonoclastic bacteria. This molecular approach revealed much more diverse bacterial taxa than the culture-dependent method we had used in an earlier study for the analysis of the same samples. The study described the dynamics of bacterial communities during bioremediation. The main limitation associated with this molecular approach, namely of not distinguishing hydrocarbonoclastic taxa from others, was overcome by consulting the literature for the hydrocarbonoclastic potential of taxa related to those identified in this study. By doing so, it was concluded that the hydrocarbonoclastic bacterial taxa were much more diverse than those captured by the culture-dependent approach. The molecular analysis also revealed the frequent occurrence of nifH-genes in the total genomic DNA extracts of all the studied environmental samples, which reflects a nitrogen-fixation potential. Nitrogen fertilization is long known to enhance microbial oil-bioremediation. The study revealed that bioaugmentation using plant rhizospheres or soil with long history of oil-pollution was more effective in oil-removal in the desert soil than in seawater microcosms.}, } @article {pmid29654556, year = {2018}, author = {Jung, DH and Seo, DH and Kim, GY and Nam, YD and Song, EJ and Yoon, S and Park, CS}, title = {The effect of resistant starch (RS) on the bovine rumen microflora and isolation of RS-degrading bacteria.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {11}, pages = {4927-4936}, doi = {10.1007/s00253-018-8971-z}, pmid = {29654556}, issn = {1432-0614}, support = {no. 2017R1A2B4004218//National Research Foundation of Korea/ ; }, mesh = {Animals ; Bacteria/isolation & purification/metabolism ; Cattle ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; Humans ; Rumen/*microbiology ; Starch/*metabolism/*pharmacology ; }, abstract = {Resistant starch (RS) in the diet reaches the large intestine without degradation, where it is decomposed by the commensal microbiota. The fermentation of RS produces secondary metabolites including short-chain fatty acids (SCFAs), which have been linked to a variety of physiological and health effects. Therefore, the availability of RS as a prebiotic is a current issue. The objectives of this study were (1) to use metagenomics to observe microbial flora changes in Bos taurus coreanae rumen fluid in the presence of RS and (2) to isolate RS-degrading microorganisms. The major microbial genus in a general rumen fluid was Succiniclasticum sp., whereas Streptococcus sp. immediately predominated after the addition of RS into the culture medium and was then drastically replaced by Lactobacillus sp. The presence of Bifidobacterium sp. was also observed continuously. Several microorganisms with high RS granule-degrading activity were identified and isolated, including B. choerinum FMB-1 and B. pseudolongum FMB-2. B. choerinum FMB-1 showed the highest RS-hydrolyzing activity and degraded almost 60% of all substrates tested. Coculture experiments demonstrated that Lactobacillus brevis ATCC 14869, which was isolated from human feces, could grow using reducing sugars generated from RS by B. choerinum FMB-1. These results suggest that Bifidobacterium spp., especially B. choerinum FMB-1, are the putative primary degrader of RS in rumen microbial flora and could be further studied as probiotic candidates.}, } @article {pmid29652573, year = {2018}, author = {Laudadio, I and Fulci, V and Palone, F and Stronati, L and Cucchiara, S and Carissimi, C}, title = {Quantitative Assessment of Shotgun Metagenomics and 16S rDNA Amplicon Sequencing in the Study of Human Gut Microbiome.}, journal = {Omics : a journal of integrative biology}, volume = {22}, number = {4}, pages = {248-254}, doi = {10.1089/omi.2018.0013}, pmid = {29652573}, issn = {1557-8100}, mesh = {Adolescent ; Child ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The analysis of microbiota composition in humans, animals, and built environments is important because of emerging roles and applications in a broad range of disease and ecological phenotypes. Next Generation Sequencing is the current method of choice to characterize microbial community composition. The taxonomic profile of a microbial community can be obtained either by shotgun analysis of random DNA fragments or through 16S ribosomal RNA gene (rDNA) amplicon sequencing. It has been previously shown that the 16S rDNA amplicon sequencing approach yields quantitatively and qualitatively different results compared to shotgun metagenomics when the two techniques are used to assess microbial community composition on the same samples. However, most of such comparisons were either based on the recovery of 16S rDNA sequences in the shotgun metagenomics data or limited to a single microbiome or synthetic samples. Direct comparison of shotgun metagenomics and 16S rDNA amplicon sequencing on the same samples was performed only once in the recent literature, suggesting that the two methods yield comparable results. Here, we set out to compare the outcome of these two alternative approaches to the microbiome characterization in human gut microbiomes from stool samples. To this end, we processed six different samples with both techniques. We report here that shotgun next generation sequencing metagenomics allows much deeper characterization of the microbiome complexity, allowing identification of a larger number of species for each sample, compared to 16S rDNA amplicon sequencing. Further comparative studies in independent samples are called for.}, } @article {pmid29651978, year = {2018}, author = {Vigliotti, C and Bicep, C and Bapteste, E and Lopez, P and Corel, E}, title = {Tracking the Rules of Transmission and Introgression with Networks.}, journal = {Microbiology spectrum}, volume = {6}, number = {2}, pages = {}, pmid = {29651978}, issn = {2165-0497}, mesh = {Animals ; Bacteria/genetics ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics/physiology ; Gastrointestinal Tract/*microbiology ; *Gene Regulatory Networks ; Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Interspersed Repetitive Sequences ; Metagenome/genetics ; Microbiota/*genetics/physiology ; Plasmids/genetics ; *Recombination, Genetic ; Sequence Homology ; Viruses/genetics ; }, abstract = {Understanding how an animal organism and its gut microbes form an integrated biological organization, known as a holobiont, is becoming a central issue in biological studies. Such an organization inevitably involves a complex web of transmission processes that occur on different scales in time and space, across microbes and hosts. Network-based models are introduced in this chapter to tackle aspects of this complexity and to better take into account vertical and horizontal dimensions of transmission. Two types of network-based models are presented, sequence similarity networks and bipartite graphs. One interest of these networks is that they can consider a rich diversity of important players in microbial evolution that are usually excluded from evolutionary studies, like plasmids and viruses. These methods bring forward the notion of "gene externalization," which is defined as the presence of redundant copies of prokaryotic genes on mobile genetic elements (MGEs), and therefore emphasizes a related although distinct process from lateral gene transfer between microbial cells. This chapter introduces guidelines to the construction of these networks, reviews their analysis, and illustrates their possible biological interpretations and uses. The application to human gut microbiomes shows that sequences present in a higher diversity of MGEs have both biased functions and a broader microbial and human host range. These results suggest that an "externalized gut metagenome" is partly common to humans and benefits the gut microbial community. We conclude that testing relationships between microbial genes, microbes, and their animal hosts, using network-based methods, could help to unravel additional mechanisms of transmission in holobionts.}, } @article {pmid29651035, year = {2018}, author = {Zaheer, R and Noyes, N and Ortega Polo, R and Cook, SR and Marinier, E and Van Domselaar, G and Belk, KE and Morley, PS and McAllister, TA}, title = {Impact of sequencing depth on the characterization of the microbiome and resistome.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {5890}, pmid = {29651035}, issn = {2045-2322}, support = {T32 OD012201/OD/NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Archaea/classification/drug effects/*genetics/isolation & purification ; Archaeal Proteins/genetics/metabolism ; Bacteria/classification/drug effects/*genetics/isolation & purification ; Bacterial Proteins/genetics/metabolism ; Cattle ; Drug Resistance/*genetics ; Feces/microbiology ; Fungal Proteins/genetics/metabolism ; Fungi/classification/drug effects/*genetics/isolation & purification ; Gastrointestinal Microbiome/drug effects/*genetics ; Gene Expression ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Phylogeny ; Viral Proteins/genetics/metabolism ; Viruses/classification/drug effects/*genetics/isolation & purification ; }, abstract = {Developments in high-throughput next generation sequencing (NGS) technology have rapidly advanced the understanding of overall microbial ecology as well as occurrence and diversity of specific genes within diverse environments. In the present study, we compared the ability of varying sequencing depths to generate meaningful information about the taxonomic structure and prevalence of antimicrobial resistance genes (ARGs) in the bovine fecal microbial community. Metagenomic sequencing was conducted on eight composite fecal samples originating from four beef cattle feedlots. Metagenomic DNA was sequenced to various depths, D1, D0.5 and D0.25, with average sample read counts of 117, 59 and 26 million, respectively. A comparative analysis of the relative abundance of reads aligning to different phyla and antimicrobial classes indicated that the relative proportions of read assignments remained fairly constant regardless of depth. However, the number of reads being assigned to ARGs as well as to microbial taxa increased significantly with increasing depth. We found a depth of D0.5 was suitable to describe the microbiome and resistome of cattle fecal samples. This study helps define a balance between cost and required sequencing depth to acquire meaningful results.}, } @article {pmid29651010, year = {2018}, author = {Ndou, SP and Tun, HM and Kiarie, E and Walsh, MC and Khafipour, E and Nyachoti, CM}, title = {Dietary supplementation with flaxseed meal and oat hulls modulates intestinal histomorphometric characteristics, digesta- and mucosa-associated microbiota in pigs.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {5880}, pmid = {29651010}, issn = {2045-2322}, mesh = {Animals ; *Avena ; Bile Acids and Salts/biosynthesis/genetics ; Dietary Fiber/administration & dosage ; *Dietary Supplements ; Digestion/drug effects/physiology ; *Flax ; Gastrointestinal Microbiome/drug effects ; Gastrointestinal Tract/*drug effects/growth & development ; Intestines/drug effects/microbiology ; Metagenome/drug effects/genetics ; Swine/growth & development ; }, abstract = {The establishment of a healthy gastrointestinal milieu may not only offer an opportunity to reduce swine production costs but could also open the way for a lifetime of human health improvement. This study investigates the effects of feeding soluble fibre from flaxseed meal-containing diet (FM) and insoluble fibre from oat hulls-containing diet (OH) on histomorphological characteristics, digesta- and mucosa-associated microbiota and their associations with metabolites in pig intestines. In comparison with the control (CON) and OH diets, the consumption of FM increased (P < 0.001) the jejunal villi height (VH) and the ratio of VH to crypt depths. The PERMANOVA analyses showed distinct (P < 0.05) microbial communities in ileal digesta and mucosa, and caecal mucosa in CON and FM-diets fed pigs compared to the OH diet-fed pigs. The predicted functional metagenomes indicated that amino acids and butanoate metabolism, lysine degradation, bile acids biosynthesis, and apoptosis were selectively enhanced at more than 2.2 log-folds in intestinal microbiota of pigs fed the FM diet. Taken together, flaxseed meal and oat hulls supplementation in growing pigs' diets altered the gastrointestinal development, as well as the composition and function of microbial communities, depending on the intestinal segment and physicochemical property of the dietary fibre source.}, } @article {pmid29642940, year = {2018}, author = {Dai, Z and Coker, OO and Nakatsu, G and Wu, WKK and Zhao, L and Chen, Z and Chan, FKL and Kristiansen, K and Sung, JJY and Wong, SH and Yu, J}, title = {Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {70}, pmid = {29642940}, issn = {2049-2618}, support = {766613, 14106145, 14111216//RGC-GRF/International ; 2016YFC1303200//135 Program Project China/International ; 2013CB531401//973 Program China/International ; 2014BAI09B05//National Key Technology R&D Program/International ; }, mesh = {Aged ; Bacteria/*classification/*genetics ; Cell Transformation, Neoplastic ; Colorectal Neoplasms/diagnosis/*etiology ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome ; Gene Ontology ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; Middle Aged ; }, abstract = {BACKGROUND: Alterations of gut microbiota are associated with colorectal cancer (CRC) in different populations and several bacterial species were found to contribute to the tumorigenesis. The potential use of gut microbes as markers for early diagnosis has also been reported. However, cohort specific noises may distort the structure of microbial dysbiosis in CRC and lead to inconsistent results among studies. In this regard, our study targeted at exploring changes in gut microbiota that are universal across populations at species level.

RESULTS: Based on the combined analysis of 526 metagenomic samples from Chinese, Austrian, American, and German and French cohorts, seven CRC-enriched bacteria (Bacteroides fragilis, Fusobacterium nucleatum, Porphyromonas asaccharolytica, Parvimonas micra, Prevotella intermedia, Alistipes finegoldii, and Thermanaerovibrio acidaminovorans) have been identified across populations. The seven enriched bacterial markers classified cases from controls with an area under the receiver-operating characteristics curve (AUC) of 0.80 across the different populations. Abundance correlation analysis demonstrated that CRC-enriched and CRC-depleted bacteria respectively formed their own mutualistic networks, in which the latter was disjointed in CRC. The CRC-enriched bacteria have been found to be correlated with lipopolysaccharide and energy biosynthetic pathways.

CONCLUSIONS: Our study identified potential diagnostic bacterial markers that are robust across populations, indicating their potential universal use for non-invasive CRC diagnosis. We also elucidated the ecological networks and functional capacities of CRC-associated microbiota.}, } @article {pmid29636512, year = {2018}, author = {Pechal, JL and Schmidt, CJ and Jordan, HR and Benbow, ME}, title = {A large-scale survey of the postmortem human microbiome, and its potential to provide insight into the living health condition.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {5724}, pmid = {29636512}, issn = {2045-2322}, mesh = {*Autopsy ; Computational Biology/methods ; Cross-Sectional Studies ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Time Factors ; }, abstract = {The microbiome plays many roles in human health, often through the exclusive lens of clinical interest. The inevitable end point for all living hosts, death, has its own altered microbiome configurations. However, little is understood about the ecology and changes of microbial communities after death, or their potential utility for understanding the health condition of the recently living. Here we reveal distinct postmortem microbiomes of human hosts from a large-scale survey of death cases representing a predominantly urban population, and demonstrated these microbiomes reflected antemortem health conditions within 24-48 hours of death. Our results characterized microbial community structure and predicted function from 188 cases representing a cross-section of an industrial-urban population. We found strong niche differentiation of anatomic habitat and microbial community turnover based on topographical distribution. Microbial community stability was documented up to two days after death. Additionally, we observed a positive relationship between cell motility and time since host death. Interestingly, we discovered evidence that microbial biodiversity is a predictor of antemortem host health condition (e.g., heart disease). These findings improve the understanding of postmortem host microbiota dynamics, and provide a robust dataset to test the postmortem microbiome as a tool for assessing health conditions in living populations.}, } @article {pmid29636446, year = {2018}, author = {Zhou, X and Guang, X and Sun, D and Xu, S and Li, M and Seim, I and Jie, W and Yang, L and Zhu, Q and Xu, J and Gao, Q and Kaya, A and Dou, Q and Chen, B and Ren, W and Li, S and Zhou, K and Gladyshev, VN and Nielsen, R and Fang, X and Yang, G}, title = {Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {1276}, pmid = {29636446}, issn = {2041-1723}, mesh = {Adaptation, Biological ; Animals ; Biological Evolution ; China ; Chromosome Mapping ; *Genome ; *Metagenomics ; *Phylogeny ; Porpoises/classification/*genetics ; Reproductive Isolation ; Rivers ; Seawater ; Water-Electrolyte Balance ; }, abstract = {Cetaceans (whales, dolphins, and porpoises) are a group of mammals adapted to various aquatic habitats, from oceans to freshwater rivers. We report the sequencing, de novo assembly and analysis of a finless porpoise genome, and the re-sequencing of an additional 48 finless porpoise individuals. We use these data to reconstruct the demographic history of finless porpoises from their origin to the occupation into the Yangtze River. Analyses of selection between marine and freshwater porpoises identify genes associated with renal water homeostasis and urea cycle, such as urea transporter 2 and angiotensin I-converting enzyme 2, which are likely adaptations associated with the difference in osmotic stress between ocean and rivers. Our results strongly suggest that the critically endangered Yangtze finless porpoises are reproductively isolated from other porpoise populations and harbor unique genetic adaptations, supporting that they should be considered a unique incipient species.}, } @article {pmid29636439, year = {2018}, author = {Brown, CT and Xiong, W and Olm, MR and Thomas, BC and Baker, R and Firek, B and Morowitz, MJ and Hettich, RL and Banfield, JF}, title = {Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles.}, journal = {mBio}, volume = {9}, number = {2}, pages = {}, pmid = {29636439}, issn = {2150-7511}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; R01 GM103600/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*chemistry/classification/genetics ; Biota ; Enterocolitis, Necrotizing/microbiology/pathology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; *Hospitalization ; Humans ; Infant, Newborn ; *Infant, Premature ; Male ; Metagenome ; Metagenomics ; *Microbiota ; Proteome/*analysis ; Proteomics ; }, abstract = {During the first weeks of life, microbial colonization of the gut impacts human immune system maturation and other developmental processes. In premature infants, aberrant colonization has been implicated in the onset of necrotizing enterocolitis (NEC), a life-threatening intestinal disease. To study the premature infant gut colonization process, genome-resolved metagenomics was conducted on 343 fecal samples collected during the first 3 months of life from 35 premature infants housed in a neonatal intensive care unit, 14 of whom developed NEC, and metaproteomic measurements were made on 87 samples. Microbial community composition and proteomic profiles remained relatively stable on the time scale of a week, but the proteome was more variable. Although genetically similar organisms colonized many infants, most infants were colonized by distinct strains with metabolic profiles that could be distinguished using metaproteomics. Microbiome composition correlated with infant, antibiotics administration, and NEC diagnosis. Communities were found to cluster into seven primary types, and community type switched within infants, sometimes multiple times. Interestingly, some communities sampled from the same infant at subsequent time points clustered with those of other infants. In some cases, switches preceded onset of NEC; however, no species or community type could account for NEC across the majority of infants. In addition to a correlation of protein abundances with organism replication rates, we found that organism proteomes correlated with overall community composition. Thus, this genome-resolved proteomics study demonstrated that the contributions of individual organisms to microbiome development depend on microbial community context.IMPORTANCE Humans are colonized by microbes at birth, a process that is important to health and development. However, much remains to be known about the fine-scale microbial dynamics that occur during the colonization period. We conducted a genome-resolved study of microbial community composition, replication rates, and proteomes during the first 3 months of life of both healthy and sick premature infants. Infants were found to be colonized by similar microbes, but each underwent a distinct colonization trajectory. Interestingly, related microbes colonizing different infants were found to have distinct proteomes, indicating that microbiome function is not only driven by which organisms are present, but also largely depends on microbial responses to the unique set of physiological conditions in the infant gut.}, } @article {pmid29635866, year = {2019}, author = {Xie, XT and Kropinski, AM and Tapscott, B and Weese, JS and Turner, PV}, title = {Prevalence of fecal viruses and bacteriophage in Canadian farmed mink (Neovison vison).}, journal = {MicrobiologyOpen}, volume = {8}, number = {1}, pages = {e00622}, pmid = {29635866}, issn = {2045-8827}, mesh = {Animal Husbandry ; Animals ; *Biodiversity ; Feces/*virology ; Mink/*virology ; Ontario ; RNA, Viral/genetics/isolation & purification ; Sequence Analysis, DNA ; Viruses/*classification/genetics/*isolation & purification ; }, abstract = {Recent viral metagenomic studies have demonstrated the diversity of eukaryotic viruses and bacteriophage shed in the feces of domestic species. Although enteric disease is a major concern in the commercial mink farming industry, few etiologic agents have been well characterized. This study aimed to identify viruses shed in the fecal matter of clinically healthy commercial mink from 40 southern Ontario farms. Viral RNA was extracted from 67 pooled fecal samples (30 adult female mink and 37 kit) and amplified for Illumina sequencing on the NextSeq platform, and the resulting contigs were trimmed and assembled using Trimmomatic 0.36.0 and Spades 3.8.0 in iVirus (CyVerse, AZ, USA) and SeqMan NGen 12 (DNAStar, WI, USA). Identification of assembled sequences >100 bp (Geneious 10.1.3) showed an abundance of bacteriophage sequences, mainly from families Siphoviridae (53%), Podoviridae (22%), Myoviridae (20%), Inoviridae (1%), Leviviridae (0.04%), Tectiviridae (0.01%), and Microviridae (0.01%). A diverse range of vertebrate viruses were detected, of which posavirus 3, mink bocavirus, gyroviruses, and avian-associated viruses were most abundant. Additionally, sequences from nonvertebrate viruses with water and soil-associated amebal and algal hosts were also highly prevalent. The results of this study show that viruses shed in the fecal matter of healthy commercial mink are highly diverse and could be closely associated with diet, and that more research is necessary to determine how the detected viruses may impact mink health.}, } @article {pmid29635791, year = {2018}, author = {Liu, X and Fan, P and Che, R and Li, H and Yi, L and Zhao, N and Garber, PA and Li, F and Jiang, Z}, title = {Fecal bacterial diversity of wild Sichuan snub-nosed monkeys (Rhinopithecus roxellana).}, journal = {American journal of primatology}, volume = {80}, number = {4}, pages = {e22753}, doi = {10.1002/ajp.22753}, pmid = {29635791}, issn = {1098-2345}, mesh = {Animals ; Bacteria/*classification/genetics ; China ; Colobinae/*microbiology ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome ; Male ; Phylogeny ; RNA, Ribosomal, 16S ; Sex Factors ; }, abstract = {The gastrointestinal tract of primates harbors a complex microbial community, playing an essential role in the degradation of otherwise indigestible structural carbohydrates. The phylogenetic and functional diversity of the bacterial community in the feces as a surrogate for the gastrointestinal tract of wild Sichuan snub-nosed monkeys (Rhinopithecus roxellana, N = 6) was characterized based on sequence analysis of 16S rRNA genes. A sex comparison was conducted, with a prior hypothesis that the abundances of the bacterial taxa and/or functional categories associated with energy and nutrient metabolism would be higher in adult females (N = 3) due to the higher reproductive costs compared to adult males (N = 3). Ten phyla were identified in all samples, among which Bacteroidetes and Firmicutes were the predominant. Included in the above two phyla, the members of Prevotellaceae (Prevotella in particular) and Ruminococcaceae were highly abundant, which are common bacteria in the gastrointestinal tract of primates and can degrade various structural carbohydrates such as cellulose, hemicellulose, and pectin. This functionality was in line with the high abundances of the metagenomes associated with carbohydrate metabolism. Consistent with our hypothesis, the abundances of the metagenomes associated with energy metabolism, folding/sorting and degradation, glycan biosynthesis and metabolism, and metabolism of amino acids were higher in adult females relative to adult males. Sex differences were also detected in the bacterial community structure, although no sex differences in the proportions of any bacterial taxa were found likely due to the small sample size. These results suggested that gastrointestinal bacterial communities may aid adult females in increasing energy and nutrition utilization efficiencies compared to adult males. Fecal bacterial communities were found to be more similar between individuals in adult females than in adult males. Our study presented the first examination of the fecal bacterial diversity of a little-studied, endangered foregut fermenter.}, } @article {pmid29633335, year = {2018}, author = {Gautam, A and Kumar, R and Chakraborty, N and Muhie, S and Hoke, A and Hammamieh, R and Jett, M}, title = {Altered fecal microbiota composition in all male aggressor-exposed rodent model simulating features of post-traumatic stress disorder.}, journal = {Journal of neuroscience research}, volume = {96}, number = {7}, pages = {1311-1323}, doi = {10.1002/jnr.24229}, pmid = {29633335}, issn = {1097-4547}, mesh = {Animals ; Bacteroidetes/isolation & purification ; Feces/*microbiology ; Firmicutes/isolation & purification ; *Gastrointestinal Microbiome ; Male ; Mice ; Mice, Inbred C57BL ; Models, Animal ; Proteobacteria/isolation & purification ; Stress Disorders, Post-Traumatic/*microbiology ; }, abstract = {The bidirectional role of gut-brain axis that integrates the gut and central nervous system activities has recently been investigated. We studied "cage-within-cage resident-intruder" all-male model, where subject male mice (C57BL/6J) are exposed to aggressor mice (SJL albino), and gut microbiota-derived metabolites were identified in plasma after 10 days of exposure. We assessed 16S ribosomal RNA gene from fecal samples collected daily from these mice during the 10-day study. Alpha diversity using Chao indices indicated no change in diversity in aggressor-exposed samples. The abundance profile showed the top phyla were Firmicutes and Bacteroidetes, Tenericutes, Verrucomicrobia, Actinobacteria and Proteobacteria, respectively. The phyla Firmicutes and Bacteroidetes are vulnerable to PTSD-eliciting stress and the Firmicutes/Bacteroidetes ratio increases with stress. Principal coordinate analysis showed the control and aggressor-exposed samples cluster separately where samples from early time points (day 1-3) clustered together and were distinct from late time points (day 4-9). The genus-based analysis revealed all control time points clustered together and aggressor-exposed samples had multiple clusters. The decrease in proportion of Firmicutes after aggressor exposure persisted throughout the study. The proportion of Verrucomicrobia immediately decreased and was significantly shifted at most of the later time points. The genus Oscillospira, Lactobacillus, Akkermansia and Anaeroplasma are the top four genera that differed between control and stressor-exposed mice. The data showed immediate effect on microbiome composition during a 10 day time period of stress exposure. Studying the longitudinal effects of a stressor is an important step toward an improved mechanistic understanding of the microbiome dynamics.}, } @article {pmid29631628, year = {2018}, author = {Mason, MR and Chambers, S and Dabdoub, SM and Thikkurissy, S and Kumar, PS}, title = {Characterizing oral microbial communities across dentition states and colonization niches.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {67}, pmid = {29631628}, issn = {2049-2618}, support = {T32-DE014320/DE/NIDCR NIH HHS/United States ; R01-DE022579/DE/NIDCR NIH HHS/United States ; F30- DE024940/DE/NIDCR NIH HHS/United States ; R01 DE022579/DE/NIDCR NIH HHS/United States ; P30 CA016058/CA/NCI NIH HHS/United States ; F30 DE024940/DE/NIDCR NIH HHS/United States ; T32 DE014320/DE/NIDCR NIH HHS/United States ; }, mesh = {Biodiversity ; Cross-Sectional Studies ; *Dentition ; Gingiva/microbiology ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; }, abstract = {METHODS: The present study aimed to identify patterns and processes in acquisition of oral bacteria and to characterize the microbiota of different dentition states and habitats. Mucosal, salivary, supragingival, and subgingival biofilm samples were collected from orally and systemically healthy children and mother-child dyads in predentate, primary, mixed, and permanent dentitions. 16S rRNA gene sequences were compared to the Human Oral Microbiome Database (HOMD). Functional potential was inferred using PICRUSt.

RESULTS: Unweighted and weighted UniFrac distances were significantly smaller between each mother-predentate dyad than infant-unrelated female dyads. Predentate children shared a median of 85% of species-level operational taxonomic units (s-OTUs) and 100% of core s-OTUs with their mothers. Maternal smoking, but not gender, mode of delivery, feeding habits, or type of food discriminated between predentate microbial profiles. The primary dentition demonstrated expanded community membership, structure, and function when compared to the predentate stage, as well as significantly lower similarity between mother-child dyads. The primary dentition also included 85% of predentate core s-OTUs. Subsequent dentitions exhibited over 90% similarity to the primary dentition in phylogenetic and functional structure. Species from the predentate mucosa as well as new microbial assemblages were identified in the primary supragingival and subgingival microbiomes. All individuals shared 65% of species between supragingival and subgingival habitats; however, the salivary microbiome exhibited less than 35% similarity to either habitat.

CONCLUSIONS: Within the limitations of a cross-sectional study design, we identified two definitive stages in oral bacterial colonization: an early predentate imprinting and a second wave with the eruption of primary teeth. Bacterial acquisition in the oral microbiome is influenced by the maternal microbiome. Personalization begins with the eruption of primary teeth; however, this is limited to phylogeny; functionally, individuals exhibit few differences, suggesting that microbial assembly may follow a defined schematic that is driven by the functional requirements of the ecosystem. This early microbiome forms the foundation upon which newer communities develop as more colonization niches emerge, and expansion of biodiversity is attributable to both introduction of new species and increase in abundance of predentate organisms.}, } @article {pmid29631623, year = {2018}, author = {Shkoporov, AN and Ryan, FJ and Draper, LA and Forde, A and Stockdale, SR and Daly, KM and McDonnell, SA and Nolan, JA and Sutton, TDS and Dalmasso, M and McCann, A and Ross, RP and Hill, C}, title = {Reproducible protocols for metagenomic analysis of human faecal phageomes.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {68}, pmid = {29631623}, issn = {2049-2618}, support = {SFI/14/SP APC/B3032//Science Foundation Ireland/Ireland ; SFI/12/RC/2273//Science Foundation Ireland/Ireland ; N/A//Janssen Biotech, Inc/International ; }, mesh = {Bacteria/classification/genetics ; Bacteriophages/*genetics ; Feces/*virology ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; }, abstract = {BACKGROUND: Recent studies have demonstrated that the human gut is populated by complex, highly individual and stable communities of viruses, the majority of which are bacteriophages. While disease-specific alterations in the gut phageome have been observed in IBD, AIDS and acute malnutrition, the human gut phageome remains poorly characterised. One important obstacle in metagenomic studies of the human gut phageome is a high level of discrepancy between results obtained by different research groups. This is often due to the use of different protocols for enriching virus-like particles, nucleic acid purification and sequencing. The goal of the present study is to develop a relatively simple, reproducible and cost-efficient protocol for the extraction of viral nucleic acids from human faecal samples, suitable for high-throughput studies. We also analyse the effect of certain potential confounding factors, such as storage conditions, repeated freeze-thaw cycles, and operator bias on the resultant phageome profile. Additionally, spiking of faecal samples with an exogenous phage standard was employed to quantitatively analyse phageomes following metagenomic sequencing. Comparative analysis of phageome profiles to bacteriome profiles was also performed following 16S rRNA amplicon sequencing.

RESULTS: Faecal phageome profiles exhibit an overall greater individual specificity when compared to bacteriome profiles. The phageome and bacteriome both exhibited moderate change when stored at + 4 °C or room temperature. Phageome profiles were less impacted by multiple freeze-thaw cycles than bacteriome profiles, but there was a greater chance for operator effect in phageome processing. The successful spiking of faecal samples with exogenous bacteriophage demonstrated large variations in the total viral load between individual samples.

CONCLUSIONS: The faecal phageome sequencing protocol developed in this study provides a valuable additional view of the human gut microbiota that is complementary to 16S amplicon sequencing and/or metagenomic sequencing of total faecal DNA. The protocol was optimised for several confounding factors that are encountered while processing faecal samples, to reduce discrepancies observed within and between research groups studying the human gut phageome. Rapid storage, limited freeze-thaw cycling and spiking of faecal samples with an exogenous phage standard are recommended for optimum results.}, } @article {pmid29630505, year = {2018}, author = {Panebianco, C and Potenza, A and Andriulli, A and Pazienza, V}, title = {Exploring the microbiota to better understand gastrointestinal cancers physiology.}, journal = {Clinical chemistry and laboratory medicine}, volume = {56}, number = {9}, pages = {1400-1412}, doi = {10.1515/cclm-2017-1163}, pmid = {29630505}, issn = {1437-4331}, mesh = {Antineoplastic Agents/therapeutic use ; Colorectal Neoplasms/microbiology/pathology ; Drug Resistance, Neoplasm ; Esophageal Neoplasms/microbiology/pathology ; Gastrointestinal Neoplasms/drug therapy/microbiology/*pathology ; Humans ; Liver Neoplasms/metabolism/pathology ; *Microbiota ; Pancreatic Neoplasms/microbiology/pathology ; Stomach Neoplasms/microbiology/pathology ; }, abstract = {Gastrointestinal cancers account for around 40% of cancer-related deaths worldwide, representing a global health burden. There is a growing body of evidence highlighting the link between microbiota and gastrointestinal tumorigenesis and/or resistance to therapy. In the present manuscript, we reviewed the published studies on the relationship between the microbiota and the different gastrointestinal tumors, namely, gastric, colorectal and esophageal, including also the cancer of accessory organs such as liver and pancreas. There is an emergent interest in the manipulation of gastrointestinal microflora in order to understand the gastrointestinal tumorigenesis' processes and the establishment of chemoresistance mechanisms.}, } @article {pmid29625975, year = {2018}, author = {Lu, YJ and Sasaki, T and Kuwahara-Arai, K and Uehara, Y and Hiramatsu, K}, title = {Development of a New Application for Comprehensive Viability Analysis Based on Microbiome Analysis by Next-Generation Sequencing: Insights into Staphylococcal Carriage in Human Nasal Cavities.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {11}, pages = {}, pmid = {29625975}, issn = {1098-5336}, mesh = {Adult ; Aged ; Aged, 80 and over ; Carrier State/*microbiology ; Female ; Healthy Volunteers ; *High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Microbial Viability ; *Microbiota ; Middle Aged ; Nasal Cavity/*microbiology ; RNA, Ribosomal, 16S/genetics ; Staphylococcal Infections/microbiology ; Staphylococcus/*genetics/isolation & purification ; Staphylococcus aureus/genetics/isolation & purification ; Staphylococcus epidermidis/genetics/isolation & purification ; Young Adult ; }, abstract = {The nasal carriage rate of Staphylococcus aureus in human is 25 to 30%, and S. aureus sporadically causes severe infections. However, the mechanisms underlying staphylococcal carriage remain largely unknown. In the present study, we constructed an rpoB-based microbiome method for staphylococcal species discrimination. Based on a microbiome scheme targeting viable cell DNA using propidium monoazide (PMA) dye (PMA microbiome method), we also developed a new method to allow the comprehensive viability analysis of any bacterial taxon. To clarify the ecological distribution of staphylococci in the nasal microbiota, we applied these methods in 46 nasal specimens from healthy adults. PMA microbiome results showed that Staphylococcaceae and Corynebacteriaceae were the most predominant viable taxa (average relative abundance: 0.435262 and 0.375195, respectively), and Staphylococcus epidermidis exhibited the highest viability in the nasal microbiota. Staphylococcus aureus detection rates from nasal specimens by rpoB-based conventional and PMA microbiome methods were 84.8% (39 of 46) and 69.5% (32 of 46), respectively, which substantially exceeded the values obtained by a culture method using identical specimens (36.9%). Our results suggest that Staphylococcaceae species, especially S. epidermidis, adapted most successfully to human nasal cavity. High detection of S. aureus DNA by microbiome methods suggests that almost all healthy adults are consistently exposed to S. aureus in everyday life. Furthermore, the large difference in S. aureus detection rates between culture and microbiome methods suggests that S. aureus cells frequently exist in a viable but nonculturable state in nasal cavities. Our method and findings will contribute to a better understanding of the mechanisms underlying carriage of indigenous bacteria.IMPORTANCE Metagenomic analyses, such as 16S rRNA microbiome methods, have provided new insights in various research fields. However, conventional 16S rRNA microbiome methods do not permit taxonomic analysis of only the viable bacteria in a sample and have poor resolving power below the genus level. Our new schemes allowed for viable cell-specific analysis and species discrimination, and nasal microbiome data using these methods provided some interesting findings regarding staphylococcal nasal carriage. According to our comprehensive viability analysis, the high viability of Staphylococcus species, especially Staphylococcus epidermidis, in human nasal carriage suggests that this taxon has adapted most successfully to human nasal tissue. Also, a higher detection rate of S. aureus DNA by microbiome methods (84.8%) than by a culture method (36.9%) suggests that almost all healthy adults are consistently exposed to Staphylococcus aureus in the medium and long term. Our findings will contribute to a better understanding of the mechanisms underlying the carriage of indigenous bacteria.}, } @article {pmid29625974, year = {2018}, author = {Taboada, B and Isa, P and Gutiérrez-Escolano, AL and Del Ángel, RM and Ludert, JE and Vázquez, N and Tapia-Palacios, MA and Chávez, P and Garrido, E and Espinosa, AC and Eguiarte, LE and López, S and Souza, V and Arias, CF}, title = {The Geographic Structure of Viruses in the Cuatro Ciénegas Basin, a Unique Oasis in Northern Mexico, Reveals a Highly Diverse Population on a Small Geographic Scale.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {11}, pages = {}, pmid = {29625974}, issn = {1098-5336}, mesh = {Animals ; Bacteriophages/*classification/isolation & purification ; *Biodiversity ; DNA Viruses/*classification/isolation & purification ; DNA, Bacterial/genetics ; Fishes/*virology ; Genetic Variation ; Geography ; Intestines/virology ; Mexico ; *Microbiota ; Phylogeny ; RNA Viruses/*classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; }, abstract = {The Cuatro Ciénegas Basin (CCB) is located in the Chihuahuan desert in the Mexican state of Coahuila; it has been characterized as a site with high biological diversity despite its extreme oligotrophic conditions. It has the greatest number of endemic species in North America, containing abundant living microbialites (including stromatolites and microbial mats) and diverse microbial communities. With the hypothesis that this high biodiversity and the geographic structure should be reflected in the virome, the viral communities in 11 different locations of three drainage systems, Churince, La Becerra, and Pozas Rojas, and in the intestinal contents of 3 different fish species, were analyzed for both eukaryotic and prokaryotic RNA and DNA viruses using next-generation sequencing methods. Double-stranded DNA (dsDNA) virus families were the most abundant (72.5% of reads), followed by single-stranded DNA (ssDNA) viruses (2.9%) and ssRNA and dsRNA virus families (0.5%). Thirteen families had dsDNA genomes, five had ssDNA, three had dsRNA, and 16 had ssRNA. A highly diverse viral community was found, with an ample range of hosts and a strong geographical structure, with very even distributions and signals of endemicity in the phylogenetic trees from several different virus families. The majority of viruses found were bacteriophages but eukaryotic viruses were also frequent, and the large diversity of viruses related to algae were a surprise, since algae are not evident in the previously analyzed aquatic systems of this ecosystem. Animal viruses were also frequently found, showing the large diversity of aquatic animals in this oasis, where plants, protozoa, and archaea are rare.IMPORTANCE In this study, we tested whether the high biodiversity and geographic structure of CCB is reflected in its virome. CCB is an extraordinarily biodiverse oasis in the Chihuahuan desert, where a previous virome study suggested that viruses had followed the marine ancestry of the marine bacteria and, as a result of their long isolation, became endemic to the site. In this study, which includes a larger sequencing coverage and water samples from other sites within the valley, we confirmed the high virus biodiversity and uniqueness as well as the strong biogeographical diversification of the CCB. In addition, we also analyzed fish intestinal contents, finding that each fish species eats different prey and, as a result, presents different viral compositions even if they coexist in the same pond. These facts highlight the high and novel virus diversity of CCB and its "lost world" status.}, } @article {pmid29624892, year = {2018}, author = {Kaur, K and Saxena, A and Debnath, I and O'Brien, JL and Ajami, NJ and Auchtung, TA and Petrosino, JF and Sougiannis, AJ and Depaep, S and Chumanevich, A and Gummadidala, PM and Omebeyinje, MH and Banerjee, S and Chatzistamou, I and Chakraborty, P and Fayad, R and Berger, FG and Carson, JA and Chanda, A}, title = {Antibiotic-mediated bacteriome depletion in Apc[Min/+] mice is associated with reduction in mucus-producing goblet cells and increased colorectal cancer progression.}, journal = {Cancer medicine}, volume = {7}, number = {5}, pages = {2003-2012}, pmid = {29624892}, issn = {2045-7634}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; P30 GM103336/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenomatous Polyposis Coli/*microbiology/*pathology ; Adenomatous Polyposis Coli Protein/genetics ; Animals ; Anti-Bacterial Agents/*adverse effects/*pharmacology ; Colon/pathology ; Disease Models, Animal ; Disease Progression ; Gastrointestinal Microbiome/*drug effects ; Goblet Cells/*cytology ; Intestinal Mucosa/microbiology/*pathology ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Neomycin/adverse effects/pharmacology ; Streptomycin/adverse effects/pharmacology ; Vancomycin/adverse effects/pharmacology ; }, abstract = {Recent epidemiological evidence suggests that exposure to antibiotics in early-to-middle adulthood is associated with an increased risk of colorectal adenoma. However, mechanistic studies in established preclinical cancer to examine these claims are extremely limited. Therefore, we investigated the effect of long-term exposure of an antibiotic cocktail composed of Vancomycin, Neomycin, and Streptomycin, on tumor development and progression in the Apc[Min/+] mouse, an established genetic model for familial adenomatous polyposis. Clinical pathologies related to tumor development as well as intestinal and colon tissue histopathology were studied at ages 8, 12, and 16 weeks of age, which correspond to the approximate ages of development of neoplasia, gut inflammation with polyposis, and cancer progression, respectively, in this animal model. We show that the antibiotics significantly increase the severity of clinical symptoms, including effects on intestinal histology and goblet cell numbers. In addition, they promote small intestinal polyposis. Finally, metagenomic analysis of fecal samples demonstrated that antibiotic exposure is associated with a significant but nonuniform depletion of the animal's natural gut flora. Overall, these findings support the premise that long-term antibiotic exposure mediates the selected depletion of gut microbial communities and the concomitant thinning of the protective mucus layer, resulting in an increase in tumor development.}, } @article {pmid29624889, year = {2018}, author = {Michał, B and Gagat, P and Jabłoński, S and Chilimoniuk, J and Gaworski, M and Mackiewicz, P and Marcin, Ł}, title = {PhyMet[2] : a database and toolkit for phylogenetic and metabolic analyses of methanogens.}, journal = {Environmental microbiology reports}, volume = {10}, number = {3}, pages = {378-382}, doi = {10.1111/1758-2229.12648}, pmid = {29624889}, issn = {1758-2229}, mesh = {*Databases, Factual ; *Euryarchaeota/classification/physiology ; Metagenomics ; Methane/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The vast biodiversity of the microbial world and how little is known about it, has already been revealed by extensive metagenomics analyses. Our rudimentary knowledge of microbes stems from difficulties concerning their isolation and culture in laboratory conditions, which is necessary for describing their phenotype, among other things, for biotechnological purposes. An important component of the understudied ecosystems is methanogens, archaea producing a potent greenhouse-effect gas methane. Therefore, we created PhyMet[2] , the first database that combines descriptions of methanogens and their culturing conditions with genetic information. The database contains a set of utilities that facilitate interactive data browsing, data comparison, phylogeny exploration and searching for sequence homologues. The most unique feature of the database is the web server MethanoGram, which can be used to significantly reduce the time and cost of searching for the optimal culturing conditions of methanogens by predicting them based on 16S RNA sequences. The database will aid many researchers in exploring the world of methanogens and their applications in biotechnological processes. PhyMet[2] with the MethanoGram predictor is available at http://metanogen.biotech.uni.wroc.pl.}, } @article {pmid29623833, year = {2018}, author = {Di Meo, F and Donato, S and Di Pardo, A and Maglione, V and Filosa, S and Crispi, S}, title = {New Therapeutic Drugs from Bioactive Natural Molecules: The Role of Gut Microbiota Metabolism in Neurodegenerative Diseases.}, journal = {Current drug metabolism}, volume = {19}, number = {6}, pages = {478-489}, doi = {10.2174/1389200219666180404094147}, pmid = {29623833}, issn = {1875-5453}, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Neurodegenerative Diseases/*microbiology ; Polyphenols/therapeutic use ; Prebiotics ; Probiotics/therapeutic use ; }, abstract = {BACKGROUND: The gut-brain axis is considered a neuroendocrine system, which connects the brain and gastrointestinal tract and plays an important role in stress response. The homeostasis of gut-brain axis is important for health conditions and its alterations are associated to neurological disorders and neurodegenerative diseases.

METHOD: We selected recent papers analysing the association among alterations in the homeostasis of the gut-brain axis and neurological disorders. In addition, we described how bioactive natural molecules - such as polyphenols - by influencing gut microbiota composition may help rescue neural signalling pathways impaired in neurodegenerative diseases.

RESULTS: Recent studies show that gut microbiota is a dynamic ecosystem that can be altered by external factors such as diet composition, antibiotics or xenobiotics. Gut bacterial community plays a key role in maintaining normal brain functions. Metagenomic analyses have elucidated that the relationship between gut and brain, either in normal or in pathological conditions, reflects the existence of a "microbiota-gut-brain" axis. Gut microbiota composition can be influenced by dietary ingestion of probiotics or natural bioactive molecules such as prebiotics and polyphenols. Their derivatives coming from microbiota metabolism can affect both the gut bacterial composition and brain biochemistry.

CONCLUSION: This review highlights the role of gut microbiota in regulating regulates brain biochemistry and the role of microbiota metabolites on neuropathologies. Dietary ingestion of probiotics, prebiotics and polyphenols affect gut microbiota composition underlining the key role played by specific metabolites not only in the gut microbiota composition but also in the brain health maintenance.}, } @article {pmid29621980, year = {2018}, author = {Pace, RM and Prince, AL and Ma, J and Belfort, BDW and Harvey, AS and Hu, M and Baquero, K and Blundell, P and Takahashi, D and Dean, T and Kievit, P and Sullivan, EL and Friedman, JE and Grove, K and Aagaard, KM}, title = {Modulations in the offspring gut microbiome are refractory to postnatal synbiotic supplementation among juvenile primates.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {28}, pmid = {29621980}, issn = {1471-2180}, support = {F32 HD082969/HD/NICHD NIH HHS/United States ; R01 HD091731/HD/NICHD NIH HHS/United States ; DP2 OD001500/OD/NIH HHS/United States ; P30 DK020593/DK/NIDDK NIH HHS/United States ; R01 DK089201/DK/NIDDK NIH HHS/United States ; K12GM084897/NH/NIH HHS/United States ; R24 DK090964/DK/NIDDK NIH HHS/United States ; R01 MH107508/MH/NIMH NIH HHS/United States ; K12 GM084897/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification/genetics/*metabolism ; *Diet, High-Fat ; Dysbiosis/microbiology ; Enterococcus/physiology ; Faecalibacterium ; Feces/microbiology ; Female ; Firmicutes ; Gastrointestinal Microbiome/genetics/*physiology ; Lactobacillus/physiology ; Lipids/blood ; Macaca/microbiology ; Male ; Metabolic Networks and Pathways ; Metagenomics ; Primates/*microbiology ; Probiotics ; Psyllium ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; *Synbiotics ; Triglycerides/blood ; }, abstract = {BACKGROUND: We and others have previously shown that alterations in the mammalian gut microbiome are associated with diet, notably early life exposure to a maternal high fat diet (HFD). Here, we aimed to further these studies by examining alterations in the gut microbiome of juvenile Japanese macaques (Macaca fuscata) that were exposed to a maternal HFD, weaned onto a control diet, and later supplemented with a synbiotic comprised of psyllium seed and Enterococcus and Lactobacillus species.

RESULTS: Eighteen month old offspring (n = 7) of 36% HFD fed dams were fed a control (14% fat) diet post weaning, then were synbiotic supplemented for 75 days and longitudinal stool and serum samples were obtained. All stool samples were subjected to 16S rRNA metagenomic sequencing, and microbiome profiles and serum lipids and triglycerides were compared to untreated, healthy age matched and diet matched controls (n = 7). Overall, 16S-based metagenomic analysis revealed that supplementation exerted minimal alterations to the gut microbiome including transient increased abundance of Lactobacillus species and decreased abundance of few bacterial genera, including Faecalibacterium and Anaerovibrio. However, serum lipid analysis revealed significant decreases in triglycerides, cholesterol, and LDL (p < 0.05). Nevertheless, supplemented juveniles challenged 4 months later were not protected from HFD-induced gut dysbiosis.

CONCLUSIONS: Synbiotic supplementation is temporally associated with alterations in the gut microbiome and host lipid profiles of juvenile Japanese macaques that were previously exposed to a maternal HFD. Despite these presumptive temporal benefits, a protective effect against later HFD-challenge gut dysbiosis was not observed.}, } @article {pmid29621268, year = {2018}, author = {Peoples, LM and Donaldson, S and Osuntokun, O and Xia, Q and Nelson, A and Blanton, J and Allen, EE and Church, MJ and Bartlett, DH}, title = {Vertically distinct microbial communities in the Mariana and Kermadec trenches.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195102}, pmid = {29621268}, issn = {1932-6203}, mesh = {Adaptation, Biological ; Biodiversity ; Geologic Sediments/*microbiology ; Hydrostatic Pressure ; Metagenome ; Metagenomics/methods ; *Microbiota ; *Oceans and Seas ; *Water Microbiology ; }, abstract = {Hadal trenches, oceanic locations deeper than 6,000 m, are thought to have distinct microbial communities compared to those at shallower depths due to high hydrostatic pressures, topographical funneling of organic matter, and biogeographical isolation. Here we evaluate the hypothesis that hadal trenches contain unique microbial biodiversity through analyses of the communities present in the bottom waters of the Kermadec and Mariana trenches. Estimates of microbial protein production indicate active populations under in situ hydrostatic pressures and increasing adaptation to pressure with depth. Depth, trench of collection, and size fraction are important drivers of microbial community structure. Many putative hadal bathytypes, such as members related to the Marinimicrobia, Rhodobacteraceae, Rhodospirilliceae, and Aquibacter, are similar to members identified in other trenches. Most of the differences between the two trench microbiomes consists of taxa belonging to the Gammaproteobacteria whose distributions extend throughout the water column. Growth and survival estimates of representative isolates of these taxa under deep-sea conditions suggest that some members may descend from shallower depths and exist as a potentially inactive fraction of the hadal zone. We conclude that the distinct pelagic communities residing in these two trenches, and perhaps by extension other trenches, reflect both cosmopolitan hadal bathytypes and ubiquitous genera found throughout the water column.}, } @article {pmid29615110, year = {2018}, author = {Zhou, X and Li, J and Guo, J and Geng, B and Ji, W and Zhao, Q and Li, J and Liu, X and Liu, J and Guo, Z and Cai, W and Ma, Y and Ren, D and Miao, J and Chen, S and Zhang, Z and Chen, J and Zhong, J and Liu, W and Zou, M and Li, Y and Cai, J}, title = {Gut-dependent microbial translocation induces inflammation and cardiovascular events after ST-elevation myocardial infarction.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {66}, pmid = {29615110}, issn = {2049-2618}, support = {81570335//National Natural Science Foundation of China/International ; 2014CB542302//National Basic Research Program of China/International ; R01 CA209886/CA/NCI NIH HHS/United States ; R01 CA196967/CA/NCI NIH HHS/United States ; CIFMS,2016-12M-1-006//CAMS Innovation Fund for Medical Sciences/International ; 81630014//National Natural Science Foundation of China/International ; 81500383//National Natural Science Foundation of China/International ; 81470541//National Natural Science Foundation of China/International ; }, mesh = {Aged ; Biodiversity ; Biomarkers ; Cardiovascular Diseases/*etiology/metabolism/physiopathology ; Case-Control Studies ; Female ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Humans ; Inflammation/*etiology/metabolism/pathology ; Male ; Middle Aged ; Permeability ; ROC Curve ; ST Elevation Myocardial Infarction/*complications/metabolism/pathology ; Ventricular Function, Left ; }, abstract = {BACKGROUND: Post-infarction cardiovascular remodeling and heart failure are the leading cause of myocardial infarction (MI)-driven death during the past decades. Experimental observations have involved intestinal microbiota in the susceptibility to MI in mice; however, in humans, identifying whether translocation of gut bacteria to systemic circulation contributes to cardiovascular events post-MI remains a major challenge.

RESULTS: Here, we carried out a metagenomic analysis to characterize the systemic bacteria in a cohort of 49 healthy control individuals, 50 stable coronary heart disease (CHD) subjects, and 100 ST-segment elevation myocardial infarction (STEMI) patients. We report for the first time higher microbial richness and diversity in the systemic microbiome of STEMI patients. More than 12% of post-STEMI blood bacteria were dominated by intestinal microbiota (Lactobacillus, Bacteroides, and Streptococcus). The significantly increased product of gut bacterial translocation (LPS and D-lactate) was correlated with systemic inflammation and predicted adverse cardiovascular events. Following experimental MI, compromised left ventricle (LV) function and intestinal hypoperfusion drove gut permeability elevation through tight junction protein suppression and intestinal mucosal injury. Upon abrogation of gut bacterial translocation by antibiotic treatment, both systemic inflammation and cardiomyocyte injury in MI mice were alleviated.

CONCLUSIONS: Our results provide the first evidence that cardiovascular outcomes post-MI are driven by intestinal microbiota translocation into systemic circulation. New therapeutic strategies targeting to protect the gut barrier and eliminate gut bacteria translocation may reduce or even prevent cardiovascular events post-MI.}, } @article {pmid29615108, year = {2018}, author = {Cornuault, JK and Petit, MA and Mariadassou, M and Benevides, L and Moncaut, E and Langella, P and Sokol, H and De Paepe, M}, title = {Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {65}, pmid = {29615108}, issn = {2049-2618}, mesh = {Animals ; Bacteriophages/*physiology/ultrastructure ; Biodiversity ; Colitis/etiology ; DNA Damage ; Dysbiosis ; Faecalibacterium prausnitzii/*virology ; *Gastrointestinal Microbiome ; Genome, Viral ; Humans ; Inflammatory Bowel Diseases/etiology ; Metagenome ; Metagenomics/methods ; Mice ; Retroelements ; Symbiosis ; }, abstract = {BACKGROUND: Viral metagenomic studies have suggested a role for bacteriophages in intestinal dysbiosis associated with several human diseases. However, interpretation of viral metagenomic studies is limited by the lack of knowledge of phages infecting major human gut commensal bacteria, such as Faecalibacterium prausnitzii, a bacterial symbiont repeatedly found depleted in inflammatory bowel disease (IBD) patients. In particular, no complete genomes of phages infecting F. prausnitzii are present in viral databases.

METHODS: We identified 18 prophages in 15 genomes of F. prausnitzii, used comparative genomics to define eight phage clades, and annotated the genome of the type phage of each clade. For two of the phages, we studied prophage induction in vitro and in vivo in mice. Finally, we aligned reads from already published viral metagenomic data onto the newly identified phages.

RESULTS: We show that each phage clade represents a novel viral genus and that a surprisingly large fraction of them (10 of the 18 phages) codes for a diversity-generating retroelement, which could contribute to their adaptation to the digestive tract environment. We obtained either experimental or in silico evidence of activity for at least one member of each genus. In addition, four of these phages are either significantly more prevalent or more abundant in stools of IBD patients than in those of healthy controls.

CONCLUSION: Since IBD patients generally have less F. prausnitzii in their microbiota than healthy controls, the higher prevalence or abundance of some of its phages may indicate that they are activated during disease. This in turn suggests that phages could trigger or aggravate F. prausnitzii depletion in patients. Our results show that prophage detection in sequenced strains of the microbiota can usefully complement viral metagenomic studies.}, } @article {pmid29611114, year = {2018}, author = {Wang, J and Chen, L and Zhao, N and Xu, X and Xu, Y and Zhu, B}, title = {Of genes and microbes: solving the intricacies in host genomes.}, journal = {Protein & cell}, volume = {9}, number = {5}, pages = {446-461}, pmid = {29611114}, issn = {1674-8018}, mesh = {Animals ; Biomedical Research ; *Genes ; *Genetic Variation ; *Genome ; Host-Pathogen Interactions/*genetics ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {Microbiome research is a quickly developing field in biomedical research, and we have witnessed its potential in understanding the physiology, metabolism and immunology, its critical role in understanding the health and disease of the host, and its vast capacity in disease prediction, intervention and treatment. However, many of the fundamental questions still need to be addressed, including the shaping forces of microbial diversity between individuals and across time. Microbiome research falls into the classical nature vs. nurture scenario, such that host genetics shape part of the microbiome, while environmental influences change the original course of microbiome development. In this review, we focus on the nature, i.e., the genetic part of the equation, and summarize the recent efforts in understanding which parts of the genome, especially the human and mouse genome, play important roles in determining the composition and functions of microbial communities, primarily in the gut but also on the skin. We aim to present an overview of different approaches in studying the intricate relationships between host genetic variations and microbes, its underlying philosophy and methodology, and we aim to highlight a few key discoveries along this exploration, as well as current pitfalls. More evidence and results will surely appear in upcoming studies, and the accumulating knowledge will lead to a deeper understanding of what we could finally term a "hologenome", that is, the organized, closely interacting genome of the host and the microbiome.}, } @article {pmid29610942, year = {2018}, author = {Yadav, S and Kumar, A and Gupta, M and Maitra, SS}, title = {Cross-Reactivity of Prokaryotic 16S rDNA-Specific Primers to Eukaryotic DNA: Mistaken Microbial Community Profiling in Environmental Samples.}, journal = {Current microbiology}, volume = {75}, number = {8}, pages = {1038-1045}, pmid = {29610942}, issn = {1432-0991}, support = {PURSE//Department of Science and Technology, GOI/ ; }, mesh = {Animals ; Bacteria/*classification/*genetics/isolation & purification ; Cattle ; DNA Primers/*genetics ; DNA Restriction Enzymes/metabolism ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Denaturing Gradient Gel Electrophoresis ; Eukaryota/*genetics ; Feces/microbiology ; Fungi/*classification/*genetics/isolation & purification ; Gene Expression Profiling ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {16S ribosomal RNA gene sequences are characteristically used as gold-standard genetic marker for the determination of bacterial and/or archaeal biodiversity, and community profiling of environmental samples. The 16S rRNA amplicon analysis till-date is taken as a standard method for investigation and identification of uncultivable bacteria in microbial diversity studies. The accuracy of these analyses strongly depends upon the choice of primers. It is presumed that these primers do not participate in non-specific amplifications. In the present study, by in silico, PCR and denaturing gradient gel electrophoresis (DGGE) analysis, we have shown that primers do cross-react with eukaryotic DNAs as well, eventually leading to overestimation of microbial biodiversity. We further demonstrated that the overestimation is not only due to cross-reaction with eukaryotic mitochondrial or plastid DNA, but also with eukaryotic chromosomal DNA, that is ubiquitous in environmental samples. We tried to establish methanogenic diversity in municipal solid waste (MSW) leachates and cow dung samples before and after enrichment of the prokaryotic DNA from eukaryotic ones. Results revealed that bands disappeared/get lightened in bacterial 16S rRNA-based DGGE community profiles, after prokaryotic DNA enrichment, but not in mcrA-based community profiles.}, } @article {pmid29609653, year = {2018}, author = {De Vrieze, J and Pinto, AJ and Sloan, WT and Ijaz, UZ}, title = {The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {63}, pmid = {29609653}, issn = {2049-2618}, support = {NE/L011956/1//Natural Environment Research Council/International ; EP/M016811/1//Engineering and Physical Sciences Research Council/International ; }, mesh = {*Anaerobiosis ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Biodiversity ; Metagenomics/methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Amplicon sequencing methods targeting the 16S rRNA gene have been used extensively to investigate microbial community composition and dynamics in anaerobic digestion. These methods successfully characterize amplicons but do not distinguish micro-organisms that are actually responsible for the process. In this research, the archaeal and bacterial community of 48 full-scale anaerobic digestion plants were evaluated on DNA (total community) and RNA (active community) level via 16S rRNA (gene) amplicon sequencing.

RESULTS: A significantly higher diversity on DNA compared with the RNA level was observed for archaea, but not for bacteria. Beta diversity analysis showed a significant difference in community composition between the DNA and RNA of both bacteria and archaea. This related with 25.5 and 42.3% of total OTUs for bacteria and archaea, respectively, that showed a significant difference in their DNA and RNA profiles. Similar operational parameters affected the bacterial and archaeal community, yet the differentiating effect between DNA and RNA was much stronger for archaea. Co-occurrence networks and functional prediction profiling confirmed the clear differentiation between DNA and RNA profiles.

CONCLUSIONS: In conclusion, a clear difference in active (RNA) and total (DNA) community profiles was observed, implying the need for a combined approach to estimate community stability in anaerobic digestion.}, } @article {pmid29609258, year = {2018}, author = {Shao, DT and Wei, WW}, title = {[Progress in research of human microbiota for upper gastrointestinal tumors and precancerous lesions].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {39}, number = {3}, pages = {382-386}, doi = {10.3760/cma.j.issn.0254-6450.2018.03.025}, pmid = {29609258}, issn = {0254-6450}, mesh = {Esophageal Neoplasms/*microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Neoplasms/*microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Lactobacillus ; Metagenomics/methods/trends ; *Microbiota ; Precancerous Conditions/*microbiology ; Prognosis ; Research/*trends ; Risk Factors ; Stomach Neoplasms/microbiology ; }, abstract = {With the widely application of the metagenomics, the relationship between microbiota and disease has become a hot research topic. Understanding the potential association between upper gastrointestinal cancer or precancerous lesions and microbiota may play an important role in the early detection, clinical diagnosis and treatment, and prognostic evaluation of upper gastrointestinal cancer. Therefore, a literature retrieval was conducted by using PubMed, Embase and wanfang databases to summarize the latest research progress in the microbiota of upper gastrointestinal cancer, including oral, esophageal, gastric cancer and precancerous lesions. Lower microbial diversity or richness in esophageal cancer and precancerous lesions and specific prognostic biomarkers for esophageal cancer were found. Lactobacillus richness showed an increase trend during the process from gastritis to gastric cancer. This paper summarizes the progress in the research of potential biological etiology of upper gastrointestinal cancer from the perspective of metagenomics in order to provide evidence on the, prevention and control of upper gastrointestinal cancer.}, } @article {pmid29607983, year = {2018}, author = {Katsimichas, T and Ohtani, T and Motooka, D and Tsukamoto, Y and Kioka, H and Nakamoto, K and Konishi, S and Chimura, M and Sengoku, K and Miyawaki, H and Sakaguchi, T and Okumura, R and Theofilis, K and Iida, T and Takeda, K and Nakamura, S and Sakata, Y}, title = {Non-Ischemic Heart Failure With Reduced Ejection Fraction Is Associated With Altered Intestinal Microbiota.}, journal = {Circulation journal : official journal of the Japanese Circulation Society}, volume = {82}, number = {6}, pages = {1640-1650}, doi = {10.1253/circj.CJ-17-1285}, pmid = {29607983}, issn = {1347-4820}, mesh = {Bacteroidetes/isolation & purification ; Case-Control Studies ; Classification ; DNA, Bacterial/isolation & purification ; Gastrointestinal Microbiome/genetics/*physiology ; Heart Failure/*microbiology/physiopathology ; Humans ; RNA, Ribosomal, 16S/analysis ; Streptococcus/isolation & purification ; *Stroke Volume ; Veillonella/isolation & purification ; }, abstract = {BACKGROUND: Research suggests that heart failure with reduced ejection fraction (HFrEF) is a state of systemic inflammation that may be triggered by microbial products passing into the bloodstream through a compromised intestinal barrier. However, whether the intestinal microbiota exhibits dysbiosis in HFrEF patients is largely unknown.

Twenty eight non-ischemic HFrEF patients and 19 healthy controls were assessed by 16S rRNA analysis of bacterial DNA extracted from stool samples. After processing of sequencing data, bacteria were taxonomically classified, diversity indices were used to examine microbial ecology, and relative abundances of common core genera were compared between groups. Furthermore, we predicted gene carriage for bacterial metabolic pathways and inferred microbial interaction networks on multiple taxonomic levels.Bacterial communities of both groups were dominated by the Firmicutes and Bacteroidetes phyla. The most abundant genus in both groups wasBacteroides. Although α diversity did not differ between groups, ordination by β diversity metrics revealed a separation of the groups across components of variation.StreptococcusandVeillonellawere enriched in the common core microbiota of patients, whileSMB53was depleted. Gene families in amino acid, carbohydrate, vitamin, and xenobiotic metabolism showed significant differences between groups. Interaction networks revealed a higher degree of correlations between bacteria in patients.

CONCLUSIONS: Non-ischemic HFrEF patients exhibited multidimensional differences in intestinal microbial communities compared with healthy subjects.}, } @article {pmid29603260, year = {2018}, author = {Mori, K and Konishi, N and Suzuki, Y and Harada, S and Maeda, M and Akase, S and Obata, H and Monma, C and Nagano, M and Kimoto, K and Oda, M and Somura, Y and Hirai, A and Shinkai, T and Noda, M and Sadamasu, K}, title = {Comparison between patients with norovirus-related gastroenteritis and asymptomatic carriers with respect to distribution of antibody-complexed viral particles and intestinal flora.}, journal = {Journal of medical virology}, volume = {90}, number = {12}, pages = {1882-1887}, doi = {10.1002/jmv.25079}, pmid = {29603260}, issn = {1096-9071}, mesh = {Adult ; Antigen-Antibody Complex/*analysis ; Caliciviridae Infections/complications/immunology/*virology ; Carrier State/immunology/*virology ; *Dysbiosis ; Feces/microbiology/virology ; Gastroenteritis/complications/immunology/*virology ; *Gastrointestinal Microbiome ; Humans ; Japan ; Metagenome ; Young Adult ; }, abstract = {Asymptomatic carriers have a major influence on the spreading of norovirus infections. The objective of this study was to examine the characteristics of patients and asymptomatic carriers affected by norovirus-related community gastroenteritis outbreaks. No significant difference between the two groups was observed in terms of the number of norovirus-antibody complexes with respect to total numbers. Principal coordinates analysis of the intestinal flora based on β-diversity analysis, revealed a different bacterial composition between patients and asymptomatic carriers, particularly regarding the genera Pseudomonas, Bacteroides, and Erwinia, as well as the Ruminococcaceae family. Although the proportional changes between these intestinal microorganisms were not sufficient to explain gastroenteritis symptoms, they represent possible markers shared by asymptomatic norovirus carriers.}, } @article {pmid29602784, year = {2018}, author = {Fortney, NW and He, S and Kulkarni, A and Friedrich, MW and Holz, C and Boyd, ES and Roden, EE}, title = {Stable Isotope Probing for Microbial Iron Reduction in Chocolate Pots Hot Spring, Yellowstone National Park.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {11}, pages = {}, pmid = {29602784}, issn = {1098-5336}, mesh = {Bacteria/classification/*metabolism ; Hydrothermal Vents/*microbiology ; Iron/*metabolism ; Isotopes ; *Microbiota ; Oxidation-Reduction ; Parks, Recreational ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Chocolate Pots hot springs (CP) is a circumneutral-pH Fe-rich geothermal feature located in Yellowstone National Park. Previous Fe(III)-reducing enrichment culture studies with CP sediments identified close relatives of known dissimilatory Fe(III)-reducing bacterial (FeRB) taxa, including Geobacter and Melioribacter However, the abundances and activities of such organisms in the native microbial community are unknown. Here, we used stable isotope probing experiments combined with 16S rRNA gene amplicon and shotgun metagenomic sequencing to gain an understanding of the in situ Fe(III)-reducing microbial community at CP. Fe-Si oxide precipitates collected near the hot spring vent were incubated with unlabeled and [13]C-labeled acetate to target active FeRB. We searched reconstructed genomes for homologs of genes involved in known extracellular electron transfer (EET) systems to identify the taxa involved in Fe redox transformations. Known FeRB taxa containing putative EET systems (Geobacter, Ignavibacteria) increased in abundance under acetate-amended conditions, whereas genomes related to Ignavibacterium and Thermodesulfovibrio that contained putative EET systems were recovered from incubations without electron donor. Our results suggest that FeRB play an active role in Fe redox cycling within Fe-Si oxide-rich deposits located at the hot spring vent.IMPORTANCE The identification of past near-surface hydrothermal environments on Mars emphasizes the importance of using modern Earth environments, such as CP, to gain insight into potential Fe-based microbial life on other rocky worlds, as well as ancient Fe-rich Earth ecosystems. By combining stable carbon isotope probing techniques and DNA sequencing technology, we gained insight into the pathways of microbial Fe redox cycling at CP. The results suggest that microbial Fe(III) oxide reduction is prominent in situ, with important implications for the generation of geochemical and stable Fe isotopic signatures of microbial Fe redox metabolism within Fe-rich circumneutral-pH thermal spring environments on Earth and Mars.}, } @article {pmid29601608, year = {2018}, author = {Das, P and Ji, B and Kovatcheva-Datchary, P and Bäckhed, F and Nielsen, J}, title = {In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0195161}, pmid = {29601608}, issn = {1932-6203}, mesh = {Bacteria/genetics/*growth & development ; Coculture Techniques ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Network analysis of large metagenomic datasets generated by current sequencing technologies can reveal significant co-occurrence patterns between microbial species of a biological community. These patterns can be analyzed in terms of pairwise combinations between all species comprising a community. Here, we construct a co-occurrence network for abundant microbial species encompassing the three dominant phyla found in human gut. This was followed by an in vitro evaluation of the predicted microbe-microbe co-occurrences, where we chose species pairs Bifidobacterium adolescentis and Bacteroides thetaiotaomicron, as well as Faecalibacterium prausnitzii and Roseburia inulinivorans as model organisms for our study. We then delineate the outcome of the co-cultures when equal distributions of resources were provided. The growth behavior of the co-culture was found to be dependent on the types of microbial species present, their specific metabolic activities, and resulting changes in the culture environment. Through this reductionist approach and using novel in vitro combinations of microbial species under anaerobic conditions, the results of this work will aid in the understanding and design of synthetic community formulations.}, } @article {pmid29601586, year = {2018}, author = {Ameri, R and Laville, E and Potocki-Véronèse, G and Trabelsi, S and Mezghani, M and Elgharbi, F and Bejar, S}, title = {Two new gene clusters involved in the degradation of plant cell wall from the fecal microbiota of Tunisian dromedary.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194621}, pmid = {29601586}, issn = {1932-6203}, mesh = {Animals ; Camelus/*microbiology ; Cell Wall/*metabolism/*microbiology ; Cellulose/metabolism ; Feces/microbiology ; Microbiota/*genetics ; Molecular Sequence Annotation ; Multigene Family/*genetics ; Plant Cells/*metabolism ; Polysaccharides/metabolism ; Sequence Analysis ; }, abstract = {Dromedaries are capable of digesting plant cell wall with high content of lignocellulose of poor digestibility. Consequently, their intestinal microbiota can be a source of novel carbohydrate-active enzymes (CAZymes). To the best of our knowledge, no data are available describing the biochemical analysis of enzymes in dromedary intestinal microbiota. To investigate new hydrolytic enzymes from the dromedary gut, a fosmid library was constructed using metagenomic DNA from feces of non-domestic adult dromedary camels living in the Tunisian desert. High-throughput functional screening of 13756 clones resulted in 47 hit clones active on a panel of various chromogenic and non-chromogenic glycan substrates. Two of them, harboring multiple activities, were retained for further analysis. Clone 26H3 displayed activity on AZO-CM-cellulose, AZCL Carob galactomannan and Tween 20, while clone 36A23 was active on AZCL carob galactomannan and AZCL barley β-glucan. The functional annotation of their sequences highlighted original metagenomic loci originating from bacteria of the Bacteroidetes/Chlorobi group, involved in the metabolization of mannosides and β-glucans thanks to a complete battery of endo- and exo-acting glycoside hydrolases, esterases, phosphorylases and transporters.}, } @article {pmid29600282, year = {2018}, author = {Auchtung, TA and Fofanova, TY and Stewart, CJ and Nash, AK and Wong, MC and Gesell, JR and Auchtung, JM and Ajami, NJ and Petrosino, JF}, title = {Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi.}, journal = {mSphere}, volume = {3}, number = {2}, pages = {}, pmid = {29600282}, issn = {2379-5042}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; }, mesh = {Adult ; Candida albicans/genetics/isolation & purification ; DNA, Ribosomal Spacer/genetics ; Diet ; Feces/microbiology ; Food Microbiology ; Fungi/*classification/isolation & purification ; Gastrointestinal Tract/*microbiology/physiology ; Healthy Volunteers ; Humans ; Mouth/microbiology ; Mycobiome/*physiology ; RNA, Ribosomal, 18S/genetics ; Saccharomyces cerevisiae/genetics/isolation & purification ; Saliva/microbiology ; Sequence Analysis, DNA ; }, abstract = {A wide diversity of fungi have been detected in the human gastrointestinal (GI) tract with the potential to provide or influence important functions. However, many of the fungi most commonly detected in stool samples are also present in food or the oral cavity. Therefore, to recognize which gut fungi are likely to have a sustained influence on human health, there is a need to separate transient members of the GI tract from true colonizers. To identify colonizing fungi, the eukaryotic rRNA operon's second internal transcribed spacer (ITS2) was sequenced from the stool, saliva, and food of healthy adults following consumption of different controlled diets. Unlike most bacterial 16S rRNA genes, the only fungal ITS2 operational taxonomic units (OTUs) detected in stool DNA across multiple diets were also present in saliva and/or food. Additional analyses, including culture-based approaches and sequencing of the 18S rRNA gene, ITS2 cDNA, and DNA extracted using alternative methods, failed to detect additional fungi. Two abundant fungi, Saccharomyces cerevisiae and Candida albicans, were examined further in healthy volunteers. Saccharomyces became undetectable in stool when a S. cerevisiae-free diet was consumed, and the levels of C. albicans in stool were dramatically reduced by more frequent cleaning of teeth. Extremely low fungal abundance, the inability of fungi to grow under conditions mimicking the distal gut, and evidence from analysis of other public datasets further support the hypothesis that fungi do not routinely colonize the GI tracts of healthy adults. IMPORTANCE We sought to identify the fungi that colonize healthy GI tracts and that have a sustained influence on the diverse functions of the gut microbiome. Instead, we found that all fungi in the stool of healthy volunteers could be explained by their presence in oral and dietary sources and that our results, together with those from other analyses, support the model that there is little or no gastrointestinal colonization by fungi. This may be due to Westernization, primate evolution, fungal ecology, and/or the strong defenses of a healthy immune system. Importantly, fungal colonization of the GI tract may often be indicative of disease. As fungi can cause serious infections in immunocompromised individuals and are found at increased abundance in multiple disorders of the GI tract, understanding normal fungal colonization is essential for proper treatment and prevention of fungal pathogenesis.}, } @article {pmid29599519, year = {2018}, author = {Henson, MW and Lanclos, VC and Faircloth, BC and Thrash, JC}, title = {Cultivation and genomics of the first freshwater SAR11 (LD12) isolate.}, journal = {The ISME journal}, volume = {12}, number = {7}, pages = {1846-1860}, pmid = {29599519}, issn = {1751-7370}, mesh = {Alphaproteobacteria/classification/*genetics/*growth & development/isolation & purification ; Ecosystem ; Ecotype ; Fresh Water/*microbiology ; Genomics ; Phylogeny ; }, abstract = {Evolutionary transitions between fresh and salt water happen infrequently among bacterioplankton. Within the ubiquitous and highly abundant heterotrophic Alphaproteobacteria order Pelagibacterales (SAR11), most members live in marine habitats, but the LD12 subclade has evolved as a unique freshwater lineage. LD12 cells occur as some of the most dominant freshwater bacterioplankton, yet this group has remained elusive to cultivation, hampering a more thorough understanding of its biology. Here, we report the first successful isolation of an LD12 representative, strain LSUCC0530, using high-throughput dilution-to-extinction cultivation methods, and its complete genome sequence. Growth experiments corroborate ecological data suggesting active populations of LD12 in brackish water up to salinities of ~5. LSUCC0530 has the smallest closed genome thus far reported for a SAR11 strain (1.16 Mbp). The genome affirms many previous metabolic predictions from cultivation-independent analyses, like a complete Embden-Meyerhof-Parnas glycolysis pathway, but also provides novel insights, such as the first isocitrate dehydrogenase in LD12, a likely homologous recombination of malate synthase from outside of the SAR11 clade, and analogous substitutions of ion transporters with others that occur throughout the rest of the SAR11 clade. Growth data support metagenomic recruitment results suggesting temperature-based ecotype diversification within LD12. Key gene losses for osmolyte uptake provide a succinct hypothesis for the evolutionary transition of LD12 from salt to freshwater. For strain LSUCC0530, we propose the provisional nomenclature Candidatus fonsibacter ubiquis.}, } @article {pmid29596453, year = {2018}, author = {Konstantinou, D and Gerovasileiou, V and Voultsiadou, E and Gkelis, S}, title = {Sponges-Cyanobacteria associations: Global diversity overview and new data from the Eastern Mediterranean.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0195001}, pmid = {29596453}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Cyanobacteria/classification/genetics/*physiology ; Mediterranean Region ; Phylogeny ; Porifera/classification/genetics/*microbiology ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Sponge-cyanobacteria associations have attracted research interest from an ecological, evolutionary and biotechnological perspective. Current knowledge is, in its majority, "hidden" in metagenomics research studying the entire microbial communities of sponges, while knowledge on these associations is totally missing for certain geographic areas. In this study, we (a) investigated the occurrence of cyanobacteria in 18 sponge species, several of which are studied for the first time for their cyanobionts, from a previously unexplored eastern Mediterranean ecoregion, the Aegean Sea, (b) isolated sponge-associated cyanobacteria, and characterized them based on a polyphasic (morphological-morphometric and molecular phylogenetic analysis) approach, and (c) conducted a meta-analysis on the global diversity of sponge species hosting cyanobacteria, as well as the diversity of cyanobacterial symbionts. Our research provided new records for nine sponge species, previously unknown for this association, while the isolated cyanobacteria were found to form novel clades within Synechococcus, Leptolyngbyaceae, Pseudanabaenaceae, and Schizotrichaceae, whose taxonomic status requires further investigation; this is the first report of a Schizotrichaceae cyanobacterium associated with sponges. The extensive evaluation of the literature along with the new data from the Aegean Sea raised the number of sponge species known for hosting cyanobacteria to 320 and showed that the cyanobacterial diversity reported from sponges is yet underestimated.}, } @article {pmid29593315, year = {2018}, author = {Sun, T and Wang, XQ and Zhao, ZL and Yu, SH and Yang, P and Chen, XM}, title = {A Lethal Fungus Infects the Chinese White Wax Scale Insect and Causes Dramatic Changes in the Host Microbiota.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {5324}, pmid = {29593315}, issn = {2045-2322}, mesh = {Animals ; DNA, Ribosomal Spacer ; Female ; *Fungi/classification/genetics ; Hemiptera/*microbiology ; *Host-Pathogen Interactions ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {The Chinese white wax scale insect (Ericerus pela) is an economically valuable species with an important role in wax production. Recently, in a greenhouse in Kunming, we identified a genus of fungus that infects and kills E. pela females. This study sought to perform the molecular detection of entomopathogens and analyze the changes in the host microbiota after entomopathogen infection. We used library construction, high-throughput sequencing and real-time quantitative polymerase chain reaction (RT-qPCR) to identify the fungi infecting adult E. pela, to understand the changes in the host organism, and to determine the distribution of the entomopathogens. Cladosporium langeronii and C. sphaerospermum were the main pathogenic species that infected the E. pela females, and they were most prevalent in the dorsal cuticle. In vivo, after infection, the proportion of Cladosporium clearly increased. The infection had little influence on the fungal community but had a strong influence on the bacterial community. After infection, Arsenophonus was dominant, and numerous bacterial genera disappeared. However, Rickettsia, instead of Arsenophonus, became dominant in the Cladosporium-infected individuals that had also been infected with Rickettsia. We identified the species that infected E. pela females and determined the influence of infection on the host microorganisms.}, } @article {pmid29593299, year = {2018}, author = {Wang, X and Wang, Z and Jiang, P and He, Y and Mu, Y and Lv, X and Zhuang, L}, title = {Bacterial diversity and community structure in the rhizosphere of four Ferula species.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {5345}, pmid = {29593299}, issn = {2045-2322}, mesh = {*Bacteria/classification ; *Biodiversity ; Ferula/*microbiology ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The medicinal value of the Ferula L. has been recognized for more than a thousand years. Wild stocks of Ferula have declined dramatically because high economic value has led to overharvesting. The objective of this study was to compare the rhizosphere microbial community of four Ferula species [F. syreitschikowii K.-Pol., F. gracilis (Ledeb.) Ledeb., F. ferulaeoides (Steud.) Korov., and F. lehmannii Boiss.] in the northern part of Xinjiang, China. The 16S rRNA sequences of rhizosphere bacteria were obtained with an Illumina paired-end sequence platform. Analysis was conducted to determine the richness and diversity of the rhizosphere bacterial communities. Two-way ANOVA indicated that plant species and soil depth had no significant effect on the alpha diversity of rhizobacteria. Linear discriminant analysis effect size showed that F. lehmannii followed by F. ferulaeoides had the most biomarkers and the highest taxon level, F. syreitschikowii and F. gracilis the least, while F. syreitschikowii and F. gracilis had the least property. This trend is consistent with reports that the medicinal value of F. lehmannii and F. ferulaeoides is greater than that of F. gracilis and F. syreitschikowii. The results of this study provide information that could be used for the commercial cultivation of Ferula spp.}, } @article {pmid29591722, year = {2019}, author = {Wilson, JJ and Brandon-Mong, GJ and Gan, HM and Sing, KW}, title = {High-throughput terrestrial biodiversity assessments: mitochondrial metabarcoding, metagenomics or metatranscriptomics?.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {30}, number = {1}, pages = {60-67}, doi = {10.1080/24701394.2018.1455189}, pmid = {29591722}, issn = {2470-1408}, mesh = {Animals ; Arthropods/genetics ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods/standards ; Electron Transport Complex IV/genetics ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/methods/standards ; Insect Proteins/genetics ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Reference Standards ; *Transcriptome ; }, abstract = {Consensus on the optimal high-throughput sequencing (HTS) approach to examine biodiversity in mixed terrestrial arthropod samples has not been reached. Metatranscriptomics could increase the proportion of taxonomically informative mitochondrial reads in HTS outputs but has not been investigated for terrestrial arthropod samples. We compared the efficiency of 16S rRNA metabarcoding, metagenomics and metatranscriptomics for detecting species in a mixed terrestrial arthropod sample (pooled DNA/RNA from 38 taxa). 16S rRNA metabarcoding and nuclear rRNA-depleted metatranscriptomics had the highest detection rate with 97% of input species detected. Based on cytochrome c oxidase I, metagenomics had the highest detection rate with 82% of input species detected, but metatranscriptomics produced a larger proportion of reads matching (Sanger) reference sequences. Metatranscriptomics with nuclear rRNA depletion may offer advantages over metabarcoding through reducing the number of spurious operational taxonomic units while retaining high detection rates, and offers natural enrichment of mitochondrial sequences which may enable increased species detection rates compared with metagenomics.}, } @article {pmid29590046, year = {2018}, author = {Zhao, L and Zhang, F and Ding, X and Wu, G and Lam, YY and Wang, X and Fu, H and Xue, X and Lu, C and Ma, J and Yu, L and Xu, C and Ren, Z and Xu, Y and Xu, S and Shen, H and Zhu, X and Shi, Y and Shen, Q and Dong, W and Liu, R and Ling, Y and Zeng, Y and Wang, X and Zhang, Q and Wang, J and Wang, L and Wu, Y and Zeng, B and Wei, H and Zhang, M and Peng, Y and Zhang, C}, title = {Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes.}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6380}, pages = {1151-1156}, doi = {10.1126/science.aao5774}, pmid = {29590046}, issn = {1095-9203}, mesh = {Adult ; Aged ; Bacteria/classification/genetics/metabolism ; China ; Diabetes Mellitus, Type 2/*therapy ; Diet ; Dietary Fiber/*metabolism ; Fatty Acids, Volatile/*metabolism ; Feces ; Female ; Fermentation ; *Gastrointestinal Microbiome ; Glucagon-Like Peptide 1/metabolism ; Glycated Hemoglobin/analysis ; Humans ; Hydrogen Sulfide/metabolism ; Indoles/metabolism ; Male ; Metagenomics ; Middle Aged ; }, abstract = {The gut microbiota benefits humans via short-chain fatty acid (SCFA) production from carbohydrate fermentation, and deficiency in SCFA production is associated with type 2 diabetes mellitus (T2DM). We conducted a randomized clinical study of specifically designed isoenergetic diets, together with fecal shotgun metagenomics, to show that a select group of SCFA-producing strains was promoted by dietary fibers and that most other potential producers were either diminished or unchanged in patients with T2DM. When the fiber-promoted SCFA producers were present in greater diversity and abundance, participants had better improvement in hemoglobin A1c levels, partly via increased glucagon-like peptide-1 production. Promotion of these positive responders diminished producers of metabolically detrimental compounds such as indole and hydrogen sulfide. Targeted restoration of these SCFA producers may present a novel ecological approach for managing T2DM.}, } @article {pmid29588360, year = {2018}, author = {Corvelo, A and Clarke, WE and Robine, N and Zody, MC}, title = {taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable time.}, journal = {Genome research}, volume = {28}, number = {5}, pages = {751-758}, pmid = {29588360}, issn = {1549-5469}, mesh = {Bacteria/classification/genetics ; Computational Biology/*methods ; Databases, Nucleic Acid ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Reproducibility of Results ; Rivers/microbiology ; *Software ; Species Specificity ; Water Microbiology ; }, abstract = {High-throughput sequencing is a revolutionary technology for the analysis of metagenomic samples. However, querying large volumes of reads against comprehensive DNA/RNA databases in a sensitive manner can be compute-intensive. Here, we present taxMaps, a highly efficient, sensitive, and fully scalable taxonomic classification tool. Using a combination of simulated and real metagenomics data sets, we demonstrate that taxMaps is more sensitive and more precise than widely used taxonomic classifiers and is capable of delivering classification accuracy comparable to that of BLASTN, but at up to three orders of magnitude less computational cost.}, } @article {pmid29587880, year = {2018}, author = {Gasc, C and Peyret, P}, title = {Hybridization capture reveals microbial diversity missed using current profiling methods.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {61}, pmid = {29587880}, issn = {2049-2618}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biodiversity ; *Metagenome ; *Metagenomics/methods ; *Nucleic Acid Hybridization ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Soil Microbiology ; }, abstract = {BACKGROUND: Microorganisms comprise the majority of living organisms on our planet. For many years, exploration of the composition of microbial communities has been performed through the PCR-based study of the small subunit rRNA gene due to its high conservation across the domains of life. The application of this method has resulted in the discovery of many unexpected evolutionary lineages. However, amplicon sequencing is subject to numerous biases, with some taxa being missed, and is limited by the read length of second-generation sequencing platforms, which drastically reduces the phylogenetic resolution.

RESULTS: Here, we describe a hybridization capture strategy that allows the enrichment of 16S rRNA genes from metagenomic samples and enables an exhaustive identification and a complete reconstruction of the biomarker. Applying this approach to a microbial mock community and a soil sample, we demonstrated that hybridization capture is able to reveal greater microbial diversity than 16S rDNA amplicon sequencing and shotgun sequencing. The reconstruction of full-length 16S rRNA genes facilitated the improvement of phylogenetic resolution and the discovery of novel prokaryotic taxa.

CONCLUSIONS: Our results demonstrate that hybridization capture can lead to major breakthroughs in our understanding of microbial diversity, overcoming the limitations of conventional 16S rRNA gene studies. If applied to a broad range of environmental samples, this innovative approach could reveal the undescribed diversity of the still underexplored microbial communities and could provide a better understanding of ecosystem function.}, } @article {pmid29587819, year = {2018}, author = {Dickson, LB and Ghozlane, A and Volant, S and Bouchier, C and Ma, L and Vega-Rúa, A and Dusfour, I and Jiolle, D and Paupy, C and Mayanja, MN and Kohl, A and Lutwama, JJ and Duong, V and Lambrechts, L}, title = {Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome.}, journal = {Parasites & vectors}, volume = {11}, number = {1}, pages = {207}, pmid = {29587819}, issn = {1756-3305}, support = {ANR-10-LABX-62-IBEID//Investissement d'Avenir program Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases/International ; ANR-16-CE35-0004-01//Agence Nationale de la Recherche/International ; ANR-17-ERC2-0016-01//Agence Nationale de la Recherche/International ; 734584//European Union's Horizon 2020 research and innovation programme under ZikaPLAN/International ; MC_UU_12014/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/MRC_/Medical Research Council/United Kingdom ; ANR10-INBS-09-08//France Génomique consortium/International ; 2015-FED-192//Programme Opérationnel FEDER-Guadeloupe-Conseil Régional/International ; }, mesh = {Aedes/*microbiology ; Animals ; Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Host-associated microbes, collectively known as the microbiota, play an important role in the biology of multicellular organisms. In mosquito vectors of human pathogens, the gut bacterial microbiota influences vectorial capacity and has become the subject of intense study. In laboratory studies of vector biology, genetic effects are often inferred from differences between geographically and genetically diverse colonies of mosquitoes that are reared in the same insectary. It is unclear, however, to what extent genetic effects can be confounded by uncontrolled differences in the microbiota composition among mosquito colonies. To address this question, we used 16S metagenomics to compare the midgut bacterial microbiome of six laboratory colonies of Aedes aegypti recently derived from wild populations representing the geographical range and genetic diversity of the species.

RESULTS: We found that the diversity, abundance, and community structure of the midgut bacterial microbiome was remarkably similar among the six different colonies of Ae. aegypti, regardless of their geographical origin. We also confirmed the relatively low complexity of bacterial communities inhabiting the mosquito midgut.

CONCLUSIONS: Our finding that geographically diverse colonies of Ae. aegypti reared in the same insectary harbor a similar gut bacterial microbiome supports the conclusion that the gut microbiota of adult mosquitoes is environmentally determined regardless of the host genotype. Thus, uncontrolled differences in microbiota composition are unlikely to represent a significant confounding factor in genetic studies of vector biology.}, } @article {pmid29579944, year = {2018}, author = {Qiu, Z and Li, N and Lu, X and Zheng, Z and Zhang, M and Qiao, X}, title = {Characterization of microbial community structure and metabolic potential using Illumina MiSeq platform during the black garlic processing.}, journal = {Food research international (Ottawa, Ont.)}, volume = {106}, number = {}, pages = {428-438}, doi = {10.1016/j.foodres.2017.12.081}, pmid = {29579944}, issn = {1873-7145}, mesh = {Bacteria/classification/genetics/*isolation & purification/metabolism ; Corynebacterium/genetics/isolation & purification/metabolism ; *Fermentation/genetics ; Food Handling/*methods ; Food Microbiology/*methods ; Garlic/*microbiology ; High-Throughput Nucleotide Sequencing ; Hot Temperature ; Humidity ; *Microbiota/genetics ; Phylogeny ; Plant Roots/*microbiology ; Ribotyping ; Streptococcus/genetics/isolation & purification/metabolism ; Thermus/genetics/isolation & purification/metabolism ; }, abstract = {Black garlic is a distinctive garlic deep-processed product made from fresh garlic at high temperature and controlled humidity. To explore microbial community structure, diversity and metabolic potential during the 12days of the black garlic processing, Illumina MiSeq sequencing technology was performed to sequence the 16S rRNA V3-V4 hypervariable region of bacteria. A total of 677,917 high quality reads were yielded with an average read length of 416bp. Operational taxonomic units (OTU) clustering analysis showed that the number of species OTUs ranged from 148 to 1974, with alpha diversity increasing remarkably, indicating the high microbial community abundance and diversity. Taxonomic analysis indicated that bacterial community was classified into 45 phyla and 1125 distinct genera, and the microbiome of black garlic samples based on phylogenetic analysis was dominated by distinct populations of four genera: Thermus, Corynebacterium, Streptococcus and Brevundimonas. The metabolic pathways were predicted for 16S rRNA marker gene sequences based on Kyoto Encyclopedia of Genes and Genomes (KEGG), indicating that amino acid metabolism, carbohydrate metabolism and membrane transport were important for the black garlic fermentation process. Overall, the study was the first to reveal microbial community structure and speculate the composition of functional genes in black garlic samples. The results contributed to further analysis of the interaction between microbial community and black garlic components at different stages, which was of great significance to study the formation mechanism and quality improvement of black garlic in the future.}, } @article {pmid29579049, year = {2018}, author = {Curtis, JT and Assefa, S and Francis, A and Köhler, GA}, title = {Fecal microbiota in the female prairie vole (Microtus ochrogaster).}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0190648}, pmid = {29579049}, issn = {1932-6203}, support = {R15 GM110593/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Arvicolinae/*microbiology ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Pilot Projects ; RNA, Bacterial ; RNA, Ribosomal, 16S ; Siblings ; }, abstract = {We examined the fecal microbiota of female prairie voles. This species is socially and, likely, sexually monogamous, and thus serves as a valuable model in which to examine the interaction between the microbiota-gut-brain axis and social behavior. At present, little is known about the gastrointestinal microbiota of prairie voles; therefore, we performed a first characterization of the fecal microbiota using 16S rRNA gene amplicon sequencing. Semiconductor sequencing technology on an Ion Torrent PGM platform was used to assess the composition of fecal microbiotas from twelve female prairie voles. Following quality filtering, 1,017,756 sequencing reads were classified from phylum to genus level. At the phylum level, Firmicutes, Bacteroidetes, and Saccharibacteria were the predominant taxa, while the Bacteriodales, Erysipelotrichaceae, Ruminococcaceae, and Lachnospiraceae contributed the most dominant microbial groups and genera. Microbial community membership was most similar between vole sibling pairs, but consideration of taxon abundances weakened these associations. The interdependence of host factors such as genetics and behavior with the gastrointestinal microbiota is likely to be particularly pronounced in prairie voles. Our pilot characterization of the prairie vole intestinal microbiota revealed a microbial community composition remarkably consistent with the monogastric alimentary system of these rodents and their diet rich in complex plant carbohydrates. The highly social nature of these animals poses specific challenges to microbiome analyses that nonetheless are valuable for advancing research on the microbiota-gut-brain-behavior axis. Our study provides an important basis for future microbiome research in this emerging model organism for studying social behavior.}, } @article {pmid29577121, year = {2018}, author = {Wang, Z and Jiang, S and Ma, C and Huo, D and Peng, Q and Shao, Y and Zhang, J}, title = {Evaluation of the nutrition and function of cow and goat milk based on intestinal microbiota by metagenomic analysis.}, journal = {Food & function}, volume = {9}, number = {4}, pages = {2320-2327}, doi = {10.1039/c7fo01780d}, pmid = {29577121}, issn = {2042-650X}, mesh = {Animals ; Cattle ; Gastrointestinal Microbiome/genetics/*physiology ; Goats ; Male ; Mice ; Mice, Inbred C57BL ; *Milk ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Milk contains nutrients needed by the body, and the main components of different animal milk vary. Accordingly, we evaluated cow and goat milk's nutrition and their effects on the gut microbiota in mice models using a high-throughput 16S rRNA sequencing technology. The intestinal microbiota of mice changed significantly after the intake of cow and goat milk, and the goat milk had a greater effect on the intestinal microbial community than the cow milk. Bifidobacterium, Allobaculum, Olsenella and Akkermansia grew significantly in both cow and goat milk groups compared with the control group, indicating that milk positively affected their growth. We also found that the citrate cycle (TCA cycle), pyruvate metabolism, and amino sugar and nucleotide sugar metabolism, as well as lipoic acid metabolism, were higher in the goat milk group than in the cow milk group. Association analysis of milk components and their representative intestinal microbiota showed that casein, αs1-casein, and β + κ-casein were positively correlated with Enterococcus and Allobaculum, and negatively correlated with Roseburia. Protein and αs2-casein were positively associated with Akkermansia, Bifidobacterium and Eubacterium.}, } @article {pmid29576590, year = {2018}, author = {Okamoto, H and Koizumi, S and Shimizu, H and Cho, O and Sugita, T}, title = {Characterization of the Axillary Microbiota of Japanese Male Subjects with Spicy and Milky Odor Types by Pyrosequencing.}, journal = {Biocontrol science}, volume = {23}, number = {1}, pages = {1-5}, doi = {10.4265/bio.23.1}, pmid = {29576590}, issn = {1884-0205}, mesh = {Adult ; Axilla/*microbiology ; Bacteria/classification/genetics ; Biodiversity ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; Humans ; Japan ; Male ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; *Odorants ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Malodorants in the human axilla are produced from human biogenic precursors by axillary bacterial enzymes. In the present study, we used pyrosequencing analysis to identify the axillary bacterial microbiota of 13 Japanese male subjects with cumin-like, spicy body odor (C type), and 9 with milky, skin-based body odor (M type). Anaerococcus, Corynebacterium, and Staphylococcus predominated in both C- and M-type subjects, followed by Moraxella and Peptoniphilus. These genera accounted for 96.2-99.9% of the total bacterial population, except in the microbiota of one C-type subject. However, the axillary bacteria in C-type subjects were more abundant than that in M-type subjects. These results suggest that the level of colonization by axillary bacteria is important for the production of malodorants.}, } @article {pmid29575679, year = {2018}, author = {Zhou, Y and Zhu, H and Yao, Q}, title = {Contrasting P acquisition strategies of the bacterial communities associated with legume and grass in subtropical orchard soil.}, journal = {Environmental microbiology reports}, volume = {10}, number = {3}, pages = {310-319}, doi = {10.1111/1758-2229.12641}, pmid = {29575679}, issn = {1758-2229}, mesh = {Bacteria/*classification/isolation & purification/metabolism ; Metagenomics ; Microbiota ; Paspalum/metabolism/*microbiology ; Phosphorus/*metabolism ; Pterocarpus/metabolism/*microbiology ; *Soil Microbiology ; Turkey ; }, abstract = {Phosphorus (P) cycling is a fundamental process driven by microorganisms, and plants can regulate P cycling directly or via their influence on the soil microbial community. However, the differential P cycling patterns associated with legumes and grass are largely unknown. Therefore, we investigated the microbial community involved in P cycling in subtropical soil grown with stylo (Stylosanthes guianensis, legume) or bahiagrass (Paspalum notatum, grass) using metagenomic sequencing. P fractionation indicated that sparingly soluble inorganic P (Pi) accounted for approximately 75% of P pool. Bacteria involved in sparingly soluble Pi solubilization (pqq, gad, JEN) were more abundant in bahiagrass soil, with Candidatus Pelagibacter, Trichodesmium, Neorickettsia, Nitrobacter, Paraburkholderia, Candidatus Solibacter, Burkholderia as major contributors. In contrast, bacteria involved in organic P (Po) mineralization (php, glpQ, phn) were more abundant in stylo soil, consistent with phosphatase activity and Frankia, Kyrpidia, Thermobispora, Streptomyces, Rhodococcus were major contributors. Bacteria taking up low molecular-weight Po were more abundant in stylo soil than in bahiagrass soil, while those taking up Pi were less abundant. These data suggest that bacterial communities associated with legumes and grass develop contrasting P acquisition strategies, highlighting the possibility of intercropping with legumes and grass for better P cycling.}, } @article {pmid29575463, year = {2018}, author = {de Lorenzo, V}, title = {Environmental microbiology to the rescue of planet earth.}, journal = {Environmental microbiology}, volume = {20}, number = {6}, pages = {1910-1916}, doi = {10.1111/1462-2920.14105}, pmid = {29575463}, issn = {1462-2920}, support = {BIO2015-66960-C3-2-R//HELIOS/International ; ERC-2012-ADG-322797//European Union ARISYS/International ; EU-H2020-BIOTEC-2014-2015-6335536//EmPowerPutida/International ; 766975//MADONNA/International ; B2017/BMD-3691//MADONNA/International ; }, mesh = {*Biodegradation, Environmental ; *Conservation of Natural Resources ; *Earth, Planet ; *Environmental Microbiology ; Environmental Monitoring ; Environmental Pollutants/metabolism ; *Environmental Pollution ; Microbiota ; Oceans and Seas ; Plastics ; }, abstract = {Environmental Microbiology has undergone a dramatic transition from being a somewhat marginal branch of Life Sciences to becoming one of the most vibrant and visible areas of contemporary research. The homonymous journal has not only borne witness of the growing interest in environmental microbes that bloomed since the mid-1980s but it has helped also to give visibility to the field and nucleate an active and influential community of authors and readers. During the past 20 years the focus has shifted from individual isolates to communities and microbiomes, from single genomes to metagenomes and from small/medium-scale experimental systems to large/very large scenarios. New challenges that were somewhat marginal when the journal was founded have acquired an unanticipated relevance owing to their impact on the global Earth's homeostasis. They include the unacceptably high atmospheric levels of greenhouse gases, the worrying pollution of the oceans with very recalcitrant plastics and microplastics and the noxious effects of micropollutants on many ecosystems. Global problems ask for global solutions and the environmental microbiome - because of its dimension and its amazing activities - may end up being out best instrument to both counter the impact of industrial development and enable a new, sustainable partnership with Nature.}, } @article {pmid29572891, year = {2018}, author = {Caussy, C and Hsu, C and Lo, MT and Liu, A and Bettencourt, R and Ajmera, VH and Bassirian, S and Hooker, J and Sy, E and Richards, L and Schork, N and Schnabl, B and Brenner, DA and Sirlin, CB and Chen, CH and Loomba, R and , }, title = {Link between gut-microbiome derived metabolite and shared gene-effects with hepatic steatosis and fibrosis in NAFLD.}, journal = {Hepatology (Baltimore, Md.)}, volume = {68}, number = {3}, pages = {918-932}, pmid = {29572891}, issn = {1527-3350}, support = {//American Gastroenterological Association (AGA) Foundation- Sucampo - ASP Designated Research Award in Geriatric Gastroenterology/International ; R01-DK106419//American Gastroenterological Association/International ; //John A. Hartford Foundation/International ; //Société Francophone du Diabète (SFD)/International ; UL1 TR001442/TR/NCATS NIH HHS/United States ; //Atlantic Philanthropies, Inc/International ; //OM/International ; //Philippe Foundation and Monahan Foundation/International ; //Fulbright program/International ; K23 DK090303/DK/NIDDK NIH HHS/United States ; KL2 RR031978/RR/NCRR NIH HHS/United States ; K23-DK090303//American Gastroenterological Association/International ; R01 DK106419/DK/NIDDK NIH HHS/United States ; //T. Franklin Williams Scholarship Award/International ; P42 ES010337/ES/NIEHS NIH HHS/United States ; //Association of Specialty Professors/International ; }, mesh = {Adult ; Aged ; Cross-Sectional Studies ; Female ; *Gastrointestinal Microbiome ; Humans ; Liver Cirrhosis/*blood/microbiology ; Male ; Metformin ; Middle Aged ; Non-alcoholic Fatty Liver Disease/*blood/microbiology ; Phenylpropionates/*blood ; Proof of Concept Study ; }, abstract = {Previous studies have shown that gut-microbiome is associated with nonalcoholic fatty liver disease (NAFLD). We aimed to examine if serum metabolites, especially those derived from the gut-microbiome, have a shared gene-effect with hepatic steatosis and fibrosis. This is a cross-sectional analysis of a prospective discovery cohort including 156 well-characterized twins and families with untargeted metabolome profiling assessment. Hepatic steatosis was assessed using magnetic-resonance-imaging proton-density-fat-fraction (MRI-PDFF) and fibrosis using MR-elastography (MRE). A twin additive genetics and unique environment effects (AE) model was used to estimate the shared gene-effect between metabolites and hepatic steatosis and fibrosis. The findings were validated in an independent prospective validation cohort of 156 participants with biopsy-proven NAFLD including shotgun metagenomics sequencing assessment in a subgroup of the cohort. In the discovery cohort, 56 metabolites including 6 microbial metabolites had a significant shared gene-effect with both hepatic steatosis and fibrosis after adjustment for age, sex and ethnicity. In the validation cohort, 6 metabolites were associated with advanced fibrosis. Among them, only one microbial metabolite, 3-(4-hydroxyphenyl)lactate, remained consistent and statistically significantly associated with liver fibrosis in the discovery and validation cohort (fold-change of higher-MRE versus lower-MRE: 1.78, P < 0.001 and of advanced versus no advanced fibrosis: 1.26, P = 0.037, respectively). The share genetic determination of 3-(4-hydroxyphenyl)lactate with hepatic steatosis was RG :0.57,95%CI:0.27-0.80, P < 0.001 and with fibrosis was RG :0.54,95%CI:0.036-1, P = 0.036. Pathway reconstruction linked 3-(4-hydroxyphenyl)lactate to several human gut-microbiome species. In the validation cohort, 3-(4-hydroxyphenyl)lactate was significantly correlated with the abundance of several gut-microbiome species, belonging only to Firmicutes, Bacteroidetes and Proteobacteria phyla, previously reported as associated with advanced fibrosis. Conclusion: This proof of concept study provides evidence of a link between the gut-microbiome and 3-(4-hydroxyphenyl)lactate that shares gene-effect with hepatic steatosis and fibrosis. (Hepatology 2018).}, } @article {pmid29572583, year = {2018}, author = {Verma, D and Garg, PK and Dubey, AK}, title = {Insights into the human oral microbiome.}, journal = {Archives of microbiology}, volume = {200}, number = {4}, pages = {525-540}, doi = {10.1007/s00203-018-1505-3}, pmid = {29572583}, issn = {1432-072X}, support = {SERB/LS-824/2013//Science and Engineering recruitment Board, New Delhi, India/ ; }, mesh = {Bacteria/genetics ; Health ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Human oral cavity harbors the second most abundant microbiota after the gastrointestinal tract. The expanded Human Oral Microbiome Database (eHOMD) that was last updated on November 22, 2017, contains the information of approximately 772 prokaryotic species, where 70% is cultivable, and 30% belong to the uncultivable class of microorganisms along with whole genome sequences of 482 taxa. Out of 70% culturable species, 57% have already been assigned to their names. The 16S rDNA profiling of the healthy oral cavity categorized the inhabitant bacteria into six broad phyla, viz. Firmicutes, Actinobacteria, Proteobacteria, Fusobacteria, Bacteroidetes and Spirochaetes constituting 96% of total oral bacteria. These hidden oral micro-inhabitants exhibit a direct influence on human health, from host's metabolism to immune responses. Altered oral microflora has been observed in several diseases such as diabetes, bacteremia, endocarditis, cancer, autoimmune disease and preterm births. Therefore, it becomes crucial to understand the oral microbial diversity and how it fluctuates under diseased/perturbed conditions. Advances in metagenomics and next-generation sequencing techniques generate rapid sequences and provide extensive information of inhabitant microorganisms of a niche. Thus, the retrieved information can be utilized for developing microbiome-based biomarkers for their use in early diagnosis of oral and associated diseases. Besides, several apex companies have shown keen interest in oral microbiome for its diagnostic and therapeutic potential indicating a vast market opportunity. This review gives an insight of various associated aspects of the human oral microbiome.}, } @article {pmid29571898, year = {2018}, author = {Rose, DR and Yang, H and Serena, G and Sturgeon, C and Ma, B and Careaga, M and Hughes, HK and Angkustsiri, K and Rose, M and Hertz-Picciotto, I and Van de Water, J and Hansen, RL and Ravel, J and Fasano, A and Ashwood, P}, title = {Differential immune responses and microbiota profiles in children with autism spectrum disorders and co-morbid gastrointestinal symptoms.}, journal = {Brain, behavior, and immunity}, volume = {70}, number = {}, pages = {354-368}, pmid = {29571898}, issn = {1090-2139}, support = {P01 ES011269/ES/NIEHS NIH HHS/United States ; R01 DK048373/DK/NIDDK NIH HHS/United States ; R01 ES015359/ES/NIEHS NIH HHS/United States ; U54 HD079125/HD/NICHD NIH HHS/United States ; R21 HD086669/HD/NICHD NIH HHS/United States ; R21 MH116383/MH/NIMH NIH HHS/United States ; AS7567/AS/Autism Speaks/United States ; UL1 RR024146/RR/NCRR NIH HHS/United States ; ASCN5014/AS/Autism Speaks/United States ; UL1 TR001860/TR/NCATS NIH HHS/United States ; R21 ES025560/ES/NIEHS NIH HHS/United States ; P30 ES023513/ES/NIEHS NIH HHS/United States ; }, mesh = {Autism Spectrum Disorder/immunology/*metabolism/*microbiology ; Child ; Child Development ; Child, Preschool ; Comorbidity ; Cytokines/metabolism ; Female ; Gastrointestinal Diseases ; Gastrointestinal Microbiome/*physiology ; Humans ; Leukocytes, Mononuclear/metabolism ; Male ; Microbiota ; Monocytes/metabolism ; }, abstract = {OBJECTIVES: Many studies have reported the increased presence of gastrointestinal (GI) symptoms in children with autism spectrum disorders (ASD). Altered microbiome profiles, pro-inflammatory responses and impaired intestinal permeability have been observed in children with ASD and co-morbid GI symptoms, yet few studies have compared these findings to ASD children without GI issues or similarly aged typical developing children. The aim of this study was to determine whether there are biological signatures in terms of immune dysfunction and microbiota composition in children with ASD with GI symptoms.

METHODS: Children were enrolled in one of four groups: ASD and GI symptoms of irregular bowel habits (ASD[GI]), children with ASD but without current or previous GI symptoms (ASD[NoGI]), typically developing children with GI symptoms (TD[GI]) and typically developing children without current or previous GI symptoms (TD[NoGI]). Peripheral blood mononuclear cells (PBMC) were isolated from the blood, stimulated and assessed for cytokine production, while stool samples were analyzed for microbial composition.

RESULTS: Following Toll-Like receptor (TLR)-4 stimulation, the ASD[GI] group produced increased levels of mucosa-relevant cytokines including IL-5, IL-15 and IL-17 compared to ASD[NoGI]. The production of the regulatory cytokine TGFβ1 was decreased in the ASD[GI] group compared with both the ASD[NoGI] and TD[NoGI] groups. Analysis of the microbiome at the family level revealed differences in microbiome composition between ASD and TD children with GI symptoms; furthermore, a predictive metagenome functional content analysis revealed that pathways were differentially represented between ASD and TD subjects, independently of the presence of GI symptoms. The ASD[GI] also showed an over-representation of the gene encoding zonulin, a molecule regulating gut permeability, compared to the other groups.

CONCLUSIONS: Overall our findings suggest that children with ASD who experience GI symptoms have an imbalance in their immune response, possibly influenced by or influencing metagenomic changes, and may have a propensity to impaired gut barrier function which may contribute to their symptoms and clinical outcome.}, } @article {pmid29569607, year = {2018}, author = {Jia, G and Zhi, A and Lai, PFH and Wang, G and Xia, Y and Xiong, Z and Zhang, H and Che, N and Ai, L}, title = {The oral microbiota - a mechanistic role for systemic diseases.}, journal = {British dental journal}, volume = {224}, number = {6}, pages = {447-455}, pmid = {29569607}, issn = {1476-5373}, mesh = {Anti-Bacterial Agents/therapeutic use ; Biofilms ; Diet ; Disease Susceptibility/*microbiology ; Humans ; *Microbiota ; Mouth/*microbiology ; Smoking ; Socioeconomic Factors ; }, abstract = {Human oral microbiota is the ecological community of commensal, symbiotic, and pathogenic microorganisms found in the oral cavity. Oral microbiota generally exists in the form of a biofilm and plays a crucial role in maintaining oral homeostasis, protecting the oral cavity and preventing disease development. Human oral microbiota has recently become a new focus research for promoting the progress of disease diagnosis, assisting disease treatment, and developing personalised medicines. In this review, the scientific evidence supporting the association that endogenous and exogenous factors (diet, smoking, drinking, socioeconomic status, antibiotics use and pregnancy) modulate oral microbiota. It provides insights into the mechanistic role in which oral microbiota may influence systemic diseases, and summarises the challenges of clinical diagnosis and treatment based on the microbial community information. It provides information for noninvasive diagnosis and helps develop a new paradigm of personalised medicine. All these benefit human health in the post-metagenomics era.}, } @article {pmid29568746, year = {2018}, author = {Wu, H and Cai, L and Li, D and Wang, X and Zhao, S and Zou, F and Zhou, K}, title = {Metagenomics Biomarkers Selected for Prediction of Three Different Diseases in Chinese Population.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {2936257}, pmid = {29568746}, issn = {2314-6141}, mesh = {Algorithms ; Arthritis, Rheumatoid/*microbiology ; Asian People/*genetics ; Biomarkers/*metabolism ; Diabetes Mellitus, Type 2/*microbiology ; Dysbiosis/genetics ; Female ; Humans ; Liver Cirrhosis/*microbiology ; Male ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Middle Aged ; ROC Curve ; }, abstract = {The dysbiosis of human microbiome has been proven to be associated with the development of many human diseases. Metagenome sequencing emerges as a powerful tool to investigate the effects of microbiome on diseases. Identification of human gut microbiome markers associated with abnormal phenotypes may facilitate feature selection for multiclass classification. Compared with binary classifiers, multiclass classification models deploy more complex discriminative patterns. Here, we developed a pipeline to address the challenging characterization of multilabel samples. In this study, a total of 300 biomarkers were selected from the microbiome of 806 Chinese individuals (383 controls, 170 with type 2 diabetes, 130 with rheumatoid arthritis, and 123 with liver cirrhosis), and then logistic regression prediction algorithm was applied to those markers as the model intrinsic features. The estimated model produced an F1 score of 0.9142, which was better than other popular classification methods, and an average receiver operating characteristic (ROC) of 0.9475 showed a significant correlation between these selected biomarkers from microbiome and corresponding phenotypes. The results from this study indicate that machine learning is a vital tool in data mining from microbiome in order to identify disease-related biomarkers, which may contribute to the application of microbiome-based precision medicine in the future.}, } @article {pmid29567708, year = {2018}, author = {Zitvogel, L and Ma, Y and Raoult, D and Kroemer, G and Gajewski, TF}, title = {The microbiome in cancer immunotherapy: Diagnostic tools and therapeutic strategies.}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6382}, pages = {1366-1370}, doi = {10.1126/science.aar6918}, pmid = {29567708}, issn = {1095-9203}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Immune System ; Immunotherapy/*methods ; Metagenome ; Neoplasms/diagnosis/*microbiology/*therapy ; Treatment Outcome ; }, abstract = {The fine line between human health and disease can be driven by the interplay between host and microbial factors. This "metagenome" regulates cancer initiation, progression, and response to therapies. Besides the capacity of distinct microbial species to modulate the pharmacodynamics of chemotherapeutic drugs, symbiosis between epithelial barriers and their microbial ecosystems has a major impact on the local and distant immune system, markedly influencing clinical outcome in cancer patients. Efficacy of cancer immunotherapy with immune checkpoint antibodies can be diminished with administration of antibiotics, and superior efficacy is observed with the presence of specific gut microbes. Future strategies of precision medicine will likely rely on novel diagnostic and therapeutic tools with which to identify and correct defects in the microbiome that compromise therapeutic efficacy.}, } @article {pmid29567298, year = {2018}, author = {Stensvold, CR and van der Giezen, M}, title = {Associations between Gut Microbiota and Common Luminal Intestinal Parasites.}, journal = {Trends in parasitology}, volume = {34}, number = {5}, pages = {369-377}, doi = {10.1016/j.pt.2018.02.004}, pmid = {29567298}, issn = {1471-5007}, mesh = {Blastocystis/*physiology ; Dientamoeba/*physiology ; *Environmental Biomarkers ; Gastrointestinal Microbiome/*physiology ; Host-Parasite Interactions/*physiology ; Humans ; Intestinal Diseases, Parasitic/*microbiology ; Intestines/microbiology/parasitology ; }, abstract = {The development and integration of DNA-based methods in research and clinical microbiology laboratories have enabled standardised and comprehensive detection and differentiation of the microbes colonising our guts. For instance, the single-celled parasites Blastocystis and Dientamoeba appear to be much more common than previously thought, especially so in healthy individuals. While increasing evidence appears to suggest limited pathogenicity of these parasites, next-generation-sequencing-based studies have helped us to appreciate links between parasite colonisation and certain host phenotypical characteristics and gut microbial profiles. The fundamental question remains as to whether such parasites are merely indicators or active manipulators of gut microbiota structure and function. In this article, we collate existing evidence that these parasites are, at minimum, indicators of intestinal microbiota structure.}, } @article {pmid29567068, year = {2018}, author = {Górska, A and Peter, S and Willmann, M and Autenrieth, I and Schlaberg, R and Huson, DH}, title = {Dynamics of the human gut phageome during antibiotic treatment.}, journal = {Computational biology and chemistry}, volume = {74}, number = {}, pages = {420-427}, doi = {10.1016/j.compbiolchem.2018.03.011}, pmid = {29567068}, issn = {1476-928X}, mesh = {Anti-Bacterial Agents/administration & dosage/*pharmacology ; Ciprofloxacin/administration & dosage/*pharmacology ; Gastrointestinal Microbiome/*drug effects/genetics ; Gastrointestinal Tract/*drug effects/microbiology ; Healthy Volunteers ; Humans ; Metagenomics ; }, abstract = {Bacterial viruses contribute to the dynamics of the microbiome communities, as they are involved in the horizontal gene transfer. Previously we studied changes in the gut microbiome of the two healthy individuals over the course of a 6-days antibiotics treatment and subsequent 28 days recovery time (Willmann et al., 2015). Now, from the same samples, the virus-like particles were isolated and sequenced. As the phage sequences are currently poorly represented in reference databases, the reads had to be assembled, annotated and their abundance had to be evaluated via reads mapping. We analyzed and compared patterns of changes in abundance of the phage scaffolds and scaffolds with antibiotics resistant genes, in both phage and whole-genome metagenomic sets. We observed an increase in abundance of scaffolds carrying antibiotic-resistant genes in response to the treatment.}, } @article {pmid29566905, year = {2017}, author = {Jazayeri, O and Daghighi, SM and Rezaee, F}, title = {Lifestyle alters GUT-bacteria function: Linking immune response and host.}, journal = {Best practice & research. Clinical gastroenterology}, volume = {31}, number = {6}, pages = {625-635}, doi = {10.1016/j.bpg.2017.09.009}, pmid = {29566905}, issn = {1532-1916}, mesh = {Bacteria/*pathogenicity ; Bacterial Physiological Phenomena/*immunology ; Gastrointestinal Microbiome/*immunology ; Humans ; *Life Style ; Microbiota/*immunology ; }, abstract = {Microbiota in human is a "mixture society" of different species (i.e. bacteria, viruses, funguses) populations with a different way of relationship classification to Human. Human GUT serves as the host of the majority of different bacterial populations (GUT flora, more than 500 species), which are with us ("from the beginning") in an innate manner known as the commensal (no harm to each other) and symbiotic (mutual benefit) relationship. A homeostatic balance of host-bacteria relationship is very important and vital for a normal health process. However, this beneficial relationship and delicate homeostatic state can be disrupted by the imbalance of microbiome-composition of gut microbiota, expressing a pathogenic state. A strict homeostatic balance of microbiome-composition strongly depends on several factors; 1- lifestyle, 2- geography, 3- ethnicities, 4- "mom" as prime of the type of bacterial colonization in infant and 5- the disease. With such diversity in individuals combined with huge number of different bacterial species and their interactions, it is wise to perform an in-depth systems biology (e.g. genomics, proteomics, glycomics, and etcetera) analysis of personalized microbiome. Only in this way, we are able to generate a map of complete GUT microbiota and, in turn, to determine its interaction with host and intra-interaction with pathogenic bacteria. A specific microbiome analysis provides us the knowledge to decipher the nature of interactions between the GUT microbiota and the host and its response to the invading bacteria in a pathogenic state. The GUT-bacteria composition is independent of geography and ethnicity but lifestyle well affects GUT-bacteria composition and function. Microbiome knowledge obtained by systems biology also helps us to change the behavior of GUT microbiota in response to the pathogenic microbes as protection. Functional microbiome changes in response to environmental factors will be discussed in this review.}, } @article {pmid29564487, year = {2018}, author = {Pulikkan, J and Maji, A and Dhakan, DB and Saxena, R and Mohan, B and Anto, MM and Agarwal, N and Grace, T and Sharma, VK}, title = {Gut Microbial Dysbiosis in Indian Children with Autism Spectrum Disorders.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {1102-1114}, pmid = {29564487}, issn = {1432-184X}, mesh = {Adolescent ; Autism Spectrum Disorder/*microbiology ; Bacteria/classification/isolation & purification ; Biomarkers/analysis ; Child ; Child, Preschool ; DNA, Bacterial/analysis ; Dysbiosis/*epidemiology/microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; India/epidemiology ; Male ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, RNA ; }, abstract = {Autism spectrum disorder (ASD) is a term associated with a group of neurodevelopmental disorders. The etiology of ASD is not yet completely understood; however, a disorder in the gut-brain axis is emerging as a prominent factor leading to autism. To identify the taxonomic composition and markers associated with ASD, we compared the fecal microbiota of 30 ASD children diagnosed using Childhood Autism Rating Scale (CARS) score, DSM-5 approved AIIMS-modified INCLEN Diagnostic Tool for Autism Spectrum Disorder (INDT-ASD), and Indian Scale for Assessment of Autism (ISAA) tool, with family-matched 24 healthy children from Indian population using next-generation sequencing (NGS) of 16S rRNA gene amplicon. Our study showed prominent dysbiosis in the gut microbiome of ASD children, with higher relative abundances of families Lactobacillaceae, Bifidobacteraceae, and Veillonellaceae, whereas the gut microbiome of healthy children was dominated by the family Prevotellaceae. Comparative meta-analysis with a publicly available dataset from the US population consisting of 20 ASD and 20 healthy control samples from children of similar age, revealed a significantly high abundance of genus Lactobacillus in ASD children from both the populations. The results reveal the microbial dysbiosis and an association of selected Lactobacillus species with the gut microbiome of ASD children.}, } @article {pmid29556105, year = {2018}, author = {Beller, HR and Rodrigues, AV and Zargar, K and Wu, YW and Saini, AK and Saville, RM and Pereira, JH and Adams, PD and Tringe, SG and Petzold, CJ and Keasling, JD}, title = {Discovery of enzymes for toluene synthesis from anoxic microbial communities.}, journal = {Nature chemical biology}, volume = {14}, number = {5}, pages = {451-457}, doi = {10.1038/s41589-018-0017-4}, pmid = {29556105}, issn = {1552-4469}, mesh = {Acidobacteria/enzymology/genetics/isolation & purification ; Anaerobiosis ; Bacteria/*enzymology/genetics ; Biomass ; Carboxy-Lyases/metabolism ; Catalysis ; Genes, Bacterial ; Geologic Sediments/microbiology ; Lakes/microbiology ; Lignin/chemistry ; Likelihood Functions ; Metagenomics ; *Microbiota ; Phenylacetates/chemistry ; Phylogeny ; Proteomics ; Recombinant Proteins/metabolism ; Sewage/microbiology ; Toluene/*metabolism ; }, abstract = {Microbial toluene biosynthesis was reported in anoxic lake sediments more than three decades ago, but the enzyme catalyzing this biochemically challenging reaction has never been identified. Here we report the toluene-producing enzyme PhdB, a glycyl radical enzyme of bacterial origin that catalyzes phenylacetate decarboxylation, and its cognate activating enzyme PhdA, a radical S-adenosylmethionine enzyme, discovered in two distinct anoxic microbial communities that produce toluene. The unconventional process of enzyme discovery from a complex microbial community (>300,000 genes), rather than from a microbial isolate, involved metagenomics- and metaproteomics-enabled biochemistry, as well as in vitro confirmation of activity with recombinant enzymes. This work expands the known catalytic range of glycyl radical enzymes (only seven reaction types had been characterized previously) and aromatic-hydrocarbon-producing enzymes, and will enable first-time biochemical synthesis of an aromatic fuel hydrocarbon from renewable resources, such as lignocellulosic biomass, rather than from petroleum.}, } @article {pmid29555111, year = {2018}, author = {Pandit, RJ and Hinsu, AT and Patel, SH and Jakhesara, SJ and Koringa, PG and Bruno, F and Psifidi, A and Shah, SV and Joshi, CG}, title = {Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {4}, pages = {374-385}, doi = {10.1016/j.syapm.2018.02.002}, pmid = {29555111}, issn = {1618-0984}, mesh = {Animal Feed/*analysis ; Animals ; Bacteria/*classification/genetics ; Cattle ; *Diet ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/genetics ; Rumen/*microbiology ; }, abstract = {Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes. Different proportions of roughage rather than the type of roughage (dry or green) modulated microbiome composition and the expression of its gene pool. Fibre degrading bacteria (i.e. Clostridium, Ruminococcus, Eubacterium, Butyrivibrio, Bacillus and Roseburia) were higher in the solid fraction of rumen (P<0.01) compared to the liquid fraction, whereas bacteria considered to be utilizers of the degraded product (i.e. Prevotella, Bacteroides, Parabacteroides, Paludibacter and Victivallis) were dominant in the liquid fraction (P<0.05). Likewise, expression of fibre degrading enzymes and related carbohydrate binding modules (CBMs) occurred in the solid fraction. When metagenomic and metatranscriptomic data were compared, it was found that some genera and species were transcriptionally more active, although they were in low abundance, making an important contribution to fibre degradation and its further metabolism in the rumen. This study also identified some of the transcriptionally active genera, such as Caldicellulosiruptor and Paludibacter, whose potential has been less-explored in rumen. Overall, the comparison of metagenomic shotgun and metatranscriptomic sequencing appeared to be a much richer source of information compared to conventional metagenomic analysis.}, } @article {pmid29554948, year = {2018}, author = {Walsh, AM and Crispie, F and O'Sullivan, O and Finnegan, L and Claesson, MJ and Cotter, PD}, title = {Species classifier choice is a key consideration when analysing low-complexity food microbiome data.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {50}, pmid = {29554948}, issn = {2049-2618}, support = {SFI/12/RC/2273//Science Foundation Ireland/Ireland ; 11/PI/1137//Science Foundation Ireland/Ireland ; 13/SIRG/2160//Science Foundation Ireland/Ireland ; }, mesh = {Bacteria/classification/*genetics ; Base Sequence/genetics ; Computational Biology/methods ; DNA, Bacterial/*genetics ; Food Microbiology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: The use of shotgun metagenomics to analyse low-complexity microbial communities in foods has the potential to be of considerable fundamental and applied value. However, there is currently no consensus with respect to choice of species classification tool, platform, or sequencing depth. Here, we benchmarked the performances of three high-throughput short-read sequencing platforms, the Illumina MiSeq, NextSeq 500, and Ion Proton, for shotgun metagenomics of food microbiota. Briefly, we sequenced six kefir DNA samples and a mock community DNA sample, the latter constructed by evenly mixing genomic DNA from 13 food-related bacterial species. A variety of bioinformatic tools were used to analyse the data generated, and the effects of sequencing depth on these analyses were tested by randomly subsampling reads.

RESULTS: Compositional analysis results were consistent between the platforms at divergent sequencing depths. However, we observed pronounced differences in the predictions from species classification tools. Indeed, PERMANOVA indicated that there was no significant differences between the compositional results generated by the different sequencers (p = 0.693, R[2] = 0.011), but there was a significant difference between the results predicted by the species classifiers (p = 0.01, R[2] = 0.127). The relative abundances predicted by the classifiers, apart from MetaPhlAn2, were apparently biased by reference genome sizes. Additionally, we observed varying false-positive rates among the classifiers. MetaPhlAn2 had the lowest false-positive rate, whereas SLIMM had the greatest false-positive rate. Strain-level analysis results were also similar across platforms. Each platform correctly identified the strains present in the mock community, but accuracy was improved slightly with greater sequencing depth. Notably, PanPhlAn detected the dominant strains in each kefir sample above 500,000 reads per sample. Again, the outputs from functional profiling analysis using SUPER-FOCUS were generally accordant between the platforms at different sequencing depths. Finally, and expectedly, metagenome assembly completeness was significantly lower on the MiSeq than either on the NextSeq (p = 0.03) or the Proton (p = 0.011), and it improved with increased sequencing depth.

CONCLUSIONS: Our results demonstrate a remarkable similarity in the results generated by the three sequencing platforms at different sequencing depths, and, in fact, the choice of bioinformatics methodology had a more evident impact on results than the choice of sequencer did.}, } @article {pmid29554272, year = {2018}, author = {Rodriguez-Palacios, A and Harding, A and Menghini, P and Himmelman, C and Retuerto, M and Nickerson, KP and Lam, M and Croniger, CM and McLean, MH and Durum, SK and Pizarro, TT and Ghannoum, MA and Ilic, S and McDonald, C and Cominelli, F}, title = {The Artificial Sweetener Splenda Promotes Gut Proteobacteria, Dysbiosis, and Myeloperoxidase Reactivity in Crohn's Disease-Like Ileitis.}, journal = {Inflammatory bowel diseases}, volume = {24}, number = {5}, pages = {1005-1020}, pmid = {29554272}, issn = {1536-4844}, support = {S10 RR026820/RR/NCRR NIH HHS/United States ; P01 DK091222/DK/NIDDK NIH HHS/United States ; P30 DK097948/DK/NIDDK NIH HHS/United States ; R37 DK042191/DK/NIDDK NIH HHS/United States ; R01 DK082437/DK/NIDDK NIH HHS/United States ; R01 DK055812/DK/NIDDK NIH HHS/United States ; R56 DK042191/DK/NIDDK NIH HHS/United States ; R01 DK042191/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteroidetes/drug effects/genetics ; Crohn Disease/metabolism/*pathology ; Disease Models, Animal ; Dysbiosis/*physiopathology ; Female ; Humans ; Ileitis/metabolism/*pathology ; In Situ Hybridization, Fluorescence ; Intestinal Mucosa/metabolism/*pathology ; Male ; Mice ; Mice, Inbred AKR ; Microbiota ; Peroxidase/metabolism ; Proteobacteria/drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; Sucrose/adverse effects/*analogs & derivatives ; Sweetening Agents/*adverse effects ; }, abstract = {BACKGROUND: Epidemiological studies indicate that the use of artificial sweeteners doubles the risk for Crohn's disease (CD). Herein, we experimentally quantified the impact of 6-week supplementation with a commercial sweetener (Splenda; ingredients sucralose maltodextrin, 1:99, w/w) on both the severity of CD-like ileitis and the intestinal microbiome alterations using SAMP1/YitFc (SAMP) mice.

METHODS: Metagenomic shotgun DNA sequencing was first used to characterize the microbiome of ileitis-prone SAMP mice. Then, 16S rRNA microbiome sequencing, quantitative polymerase chain reaction, fluorescent in situ hybridization (FISH), bacterial culture, stereomicroscopy, histology, and myeloperoxidase (MPO) activity analyses were then implemented to compare the microbiome and ileitis phenotype in SAMP with that of control ileitis-free AKR/J mice after Splenda supplementation.

RESULTS: Metagenomics indicated that SAMP mice have a gut microbial phenotype rich in Bacteroidetes, and experiments showed that Helicobacteraceae did not have an exacerbating effect on ileitis. Splenda did not increase the severity of (stereomicroscopic/histological) ileitis; however, biochemically, ileal MPO activity was increased in SAMP treated with Splenda compared with nonsupplemented mice (P < 0.022) and healthy AKR mice. Splenda promoted dysbiosis with expansion of Proteobacteria in all mice, and E. coli overgrowth with increased bacterial infiltration into the ileal lamina propria of SAMP mice. FISH showed increase malX gene-carrying bacterial clusters in the ilea of supplemented SAMP (but not AKR) mice.

CONCLUSIONS: Splenda promoted gut Proteobacteria, dysbiosis, and biochemical MPO reactivity in a spontaneous model of (Bacteroidetes-rich) ileal CD. Our results indicate that although Splenda may promote parallel microbiome alterations in CD-prone and healthy hosts, this did not result in elevated MPO levels in healthy mice, only CD-prone mice. The consumption of sucralose/maltodextrin-containing foods might exacerbate MPO intestinal reactivity only in individuals with a pro-inflammatory predisposition, such as CD.}, } @article {pmid29553575, year = {2018}, author = {Seshadri, R and Leahy, SC and Attwood, GT and Teh, KH and Lambie, SC and Cookson, AL and Eloe-Fadrosh, EA and Pavlopoulos, GA and Hadjithomas, M and Varghese, NJ and Paez-Espino, D and , and Perry, R and Henderson, G and Creevey, CJ and Terrapon, N and Lapebie, P and Drula, E and Lombard, V and Rubin, E and Kyrpides, NC and Henrissat, B and Woyke, T and Ivanova, NN and Kelly, WJ}, title = {Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection.}, journal = {Nature biotechnology}, volume = {36}, number = {4}, pages = {359-367}, pmid = {29553575}, issn = {1546-1696}, support = {322820/ERC_/European Research Council/International ; }, mesh = {Animals ; Archaea/classification/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Biofuels ; Gastrointestinal Microbiome/*genetics ; Humans ; Lignin/chemistry/genetics ; Microbiota/genetics ; Rumen/*microbiology ; }, abstract = {Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ∼75% of the genus-level bacterial and archaeal taxa present in the rumen.}, } @article {pmid29551950, year = {2017}, author = {Oliveira, C and Gunderman, L and Coles, CA and Lochmann, J and Parks, M and Ballard, E and Glazko, G and Rahmatallah, Y and Tackett, AJ and Thomas, DJ}, title = {16S rRNA Gene-Based Metagenomic Analysis of Ozark Cave Bacteria.}, journal = {Diversity}, volume = {9}, number = {3}, pages = {}, pmid = {29551950}, issn = {1424-2818}, support = {P20 GM103429/GM/NIGMS NIH HHS/United States ; P20 RR016460/RR/NCRR NIH HHS/United States ; }, abstract = {The microbial diversity within cave ecosystems is largely unknown. Ozark caves maintain a year-round stable temperature (12-14 °C), but most parts of the caves experience complete darkness. The lack of sunlight and geological isolation from surface-energy inputs generate nutrient-poor conditions that may limit species diversity in such environments. Although microorganisms play a crucial role in sustaining life on Earth and impacting human health, little is known about their diversity, ecology, and evolution in community structures. We used five Ozark region caves as test sites for exploring bacterial diversity and monitoring long-term biodiversity. Illumina MiSeq sequencing of five cave soil samples and a control sample revealed a total of 49 bacterial phyla, with seven major phyla: Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Chloroflexi, Bacteroidetes, and Nitrospirae. Variation in bacterial composition was observed among the five caves studied. Sandtown Cave had the lowest richness and most divergent community composition. 16S rRNA gene-based metagenomic analysis of cave-dwelling microbial communities in the Ozark caves revealed that species abundance and diversity are vast and included ecologically, agriculturally, and economically relevant taxa.}, } @article {pmid29551526, year = {2018}, author = {Santos, JC and Tarvin, RD and O'Connell, LA and Blackburn, DC and Coloma, LA}, title = {Diversity within diversity: Parasite species richness in poison frogs assessed by transcriptomics.}, journal = {Molecular phylogenetics and evolution}, volume = {125}, number = {}, pages = {40-50}, doi = {10.1016/j.ympev.2018.03.015}, pmid = {29551526}, issn = {1095-9513}, mesh = {Animals ; Anura/*genetics/*parasitology ; Biodiversity ; *Gene Expression Profiling ; Genetic Speciation ; Host-Parasite Interactions/genetics ; Parasites/*physiology ; Phylogeny ; Poisons ; Species Specificity ; Transcriptome/genetics ; }, abstract = {Symbionts (e.g., endoparasites and commensals) play an integral role in their host's ecology, yet in many cases their diversity is likely underestimated. Although endoparasites are traditionally characterized using morphology, sequences of conserved genes, and shotgun metagenomics, host transcriptomes constitute an underused resource to identify these organisms' diversity. By isolating non-host transcripts from host transcriptomes, individual host tissues can now simultaneously reveal their endoparasite species richness (i.e., number of different taxa) and provide insights into parasite gene expression. These approaches can be used in host taxa whose endoparasites are mostly unknown, such as those of tropical amphibians. Here, we focus on the poison frogs (Dendrobatidae) as hosts, which are a Neotropical clade known for their bright coloration and defensive alkaloids. These toxins are an effective protection against vertebrate predators (e.g., snakes and birds), bacteria, and skin-biting ectoparasites (e.g., mosquitoes); however, little is known about their deterrence against eukaryotic endoparasites. With de novo transcriptomes of dendrobatids, we developed a bioinformatics pipeline for endoparasite identification that uses host annotated RNA-seq data and set of a priori parasite taxonomic terms, which are used to mine for specific endoparasites. We found a large community of helminths and protozoans that were mostly restricted to the digestive tract and a few systemic parasites (e.g., Trypanosoma). Contrary to our expectations, all dendrobatid frogs regardless of the presence of alkaloid defenses have endoparasites, with their highest species richness located in the frog digestive tract. Some of these organisms (e.g., roundworms) might prove to be generalists, as they were not found to be co-diversifying with their frog hosts. We propose that endoparasites may escape poison frogs' chemical defenses by colonizing tissues with fewer alkaloids than the frog's skin, where most toxins are stored.}, } @article {pmid29549101, year = {2018}, author = {Yan, D and Zhang, T and Su, J and Zhao, LL and Wang, H and Fang, XM and Zhang, YQ and Liu, HY and Yu, LY}, title = {Structural Variation in the Bacterial Community Associated with Airborne Particulate Matter in Beijing, China, during Hazy and Nonhazy Days.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {9}, pages = {}, pmid = {29549101}, issn = {1098-5336}, mesh = {Air Microbiology ; Air Pollutants/*analysis ; Bacteria/classification/*isolation & purification ; Beijing ; *Environmental Monitoring ; *Microbiota ; Particle Size ; Particulate Matter/*analysis ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Weather ; }, abstract = {The structural variation of the bacterial community associated with particulate matter (PM) was assessed in an urban area of Beijing during hazy and nonhazy days. Sampling for different PM fractions (PM2.5 [<2.5 μm], PM10 [<10 μm], and total suspended particulate) was conducted using three portable air samplers from September 2014 to February 2015. The airborne bacterial community in these samples was analyzed using the Illumina MiSeq platform with bacterium-specific primers targeting the 16S rRNA gene. A total of 1,707,072 reads belonging to 6,009 operational taxonomic units were observed. The airborne bacterial community composition was significantly affected by PM fractions (R = 0.157, P < 0.01). In addition, the relative abundances of several genera significantly differed between samples with various haze levels; for example, Methylobacillus, Tumebacillus, and Desulfurispora spp. increased in heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature, SO2 concentration, relative humidity, PM10 concentration, and CO concentration were significant factors that associated with airborne bacterial community composition. Only six genera increased across PM10 samples (Dokdonella, Caenimonas, Geminicoccus, and Sphingopyxis) and PM2.5 samples (Cellulomonas and Rhizobacter), while a large number of taxa significantly increased in total suspended particulate samples, such as Paracoccus, Kocuria, and Sphingomonas Network analysis indicated that Paracoccus, Rubellimicrobium, Kocuria, and Arthrobacter were the key genera in the airborne PM samples. Overall, the findings presented here suggest that diverse airborne bacterial communities are associated with PM and provide further understanding of bacterial community structure in the atmosphere during hazy and nonhazy days.IMPORTANCE The results presented here represent an analysis of the airborne bacterial community associated with particulate matter (PM) and advance our understanding of the structural variation of these communities. We observed a shift in bacterial community composition with PM fractions but no significant difference with haze levels. This may be because the bacterial differences are obscured by high bacterial diversity in the atmosphere. However, we also observed that a few genera (such as Methylobacillus, Tumebacillus, and Desulfurispora) increased significantly on heavy-haze days. In addition, Paracoccus, Rubellimicrobium, Kocuria, and Arthrobacter were the key genera in the airborne PM samples. Accurate and real-time techniques, such as metagenomics and metatranscriptomics, should be developed for a future survey of the relationship of airborne bacteria and haze.}, } @article {pmid29548797, year = {2018}, author = {Hall, JB and Cong, Z and Imamura-Kawasawa, Y and Kidd, BA and Dudley, JT and Thiboutot, DM and Nelson, AM}, title = {Isolation and Identification of the Follicular Microbiome: Implications for Acne Research.}, journal = {The Journal of investigative dermatology}, volume = {138}, number = {9}, pages = {2033-2040}, doi = {10.1016/j.jid.2018.02.038}, pmid = {29548797}, issn = {1523-1747}, mesh = {Acne Vulgaris/genetics/*microbiology/pathology ; Adolescent ; Adult ; Child ; DNA, Bacterial/*analysis ; Female ; Genetic Variation ; Humans ; Male ; Microbiota/*genetics ; Propionibacterium acnes/*genetics/isolation & purification ; Skin/*microbiology/pathology ; Whole Genome Sequencing ; Young Adult ; }, abstract = {Our understanding of the microbiome and the role of Propionibacterium acnes in skin homeostasis and acne pathogenesis is evolving. Multiple methods for sampling and identifying the skin's microbiome exist, and understanding the differences between the abilities of various methods to characterize the microbial landscape is warranted. This study compared the microbial diversity of samples obtained from the cheeks of 20 volunteers, collected by surface swab, pore strips, and cyanoacrylate glue follicular biopsy, all sequenced with 16S rRNA sequencing (V1-V3) and whole-genome metagenomic sequencing. The sequencing method of choice influenced the detection of microbial profiles as whole-genome sequencing captured more species diversity, including viruses, compared with 16S sequencing. The relative abundance of bacterial or fungal species and overall diversity did not differ between sampling methods. However, the viral composition of the skin's surface is unique compared with the follicle, suggesting distinct viral niches within the skin. P. acnes bacteria, ribotypes, and bacteriophages were identified equally by all sampling methods indicating that the sampling method, whether for the skin's surface or follicle, does not impact P. acnes-related characterization and that all may be equally useful for acne-related research studies.}, } @article {pmid29546438, year = {2018}, author = {Rua, CPJ and de Oliveira, LS and Froes, A and Tschoeke, DA and Soares, AC and Leomil, L and Gregoracci, GB and Coutinho, R and Hajdu, E and Thompson, CC and Berlinck, RGS and Thompson, FL}, title = {Microbial and Functional Biodiversity Patterns in Sponges that Accumulate Bromopyrrole Alkaloids Suggest Horizontal Gene Transfer of Halogenase Genes.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {825-838}, pmid = {29546438}, issn = {1432-184X}, support = {CNE E-26/110.735/2013//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; CIMAR 1986/2014//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; BIOTA/BIOprospecTA grant 2013/50228-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2014/17616- 7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, mesh = {Alkaloids/*metabolism ; Animals ; Bacteria/*enzymology/genetics/isolation & purification/metabolism ; Bacterial Proteins/*genetics/metabolism ; *Biodiversity ; Bromine/metabolism ; Gene Transfer, Horizontal ; Hydrolases/*genetics/metabolism ; Phylogeny ; Porifera/chemistry/*microbiology ; Secondary Metabolism ; }, abstract = {Marine sponge holobionts harbor complex microbial communities whose members may be the true producers of secondary metabolites accumulated by sponges. Bromopyrrole alkaloids constitute a typical class of secondary metabolites isolated from sponges that very often display biological activities. Bromine incorporation into secondary metabolites can be catalyzed by either halogenases or haloperoxidases. The diversity of the metagenomes of sponge holobiont species containing bromopyrrole alkaloids (Agelas spp. and Tedania brasiliensis) as well as holobionts devoid of bromopyrrole alkaloids spanning in a vast biogeographic region (approx. Seven thousand km) was studied. The origin and specificity of the detected halogenases was also investigated. The holobionts Agelas spp. and T. brasiliensis did not share microbial halogenases, suggesting a species-specific pattern. Bacteria of diverse phylogenetic origins encoding halogenase genes were found to be more abundant in bromopyrrole-containing sponges. The sponge holobionts (e.g., Agelas spp.) with the greatest number of sequences related to clustered, interspaced, short, palindromic repeats (CRISPRs) exhibited the fewest phage halogenases, suggesting a possible mechanism of protection from phage infection by the sponge host. This study highlights the potential of phages to transport halogenases horizontally across host sponges, particularly in more permissive holobiont hosts, such as Tedania spp.}, } @article {pmid29545525, year = {2018}, author = {Xu, J and Wu, H and Wang, Z and Zheng, F and Lu, X and Li, Z and Ren, Q}, title = {Microbial dynamics and metabolite changes in Chinese Rice Wine fermentation from sorghum with different tannin content.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {4639}, pmid = {29545525}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics/*metabolism ; Fermentation ; Metagenomics ; Microbiota ; Oryza/*microbiology ; Sorghum/classification/*metabolism ; Tannins/*metabolism ; Volatile Organic Compounds/*metabolism ; Wine/*analysis ; }, abstract = {Chinese rice wine (CRW) is the oldest kind of wine in China and is mainly fermented by wheat Qu and yeast with rice, millet, etc. This gives CRW a unique quality, but the flavor components are complex. Its formation is related to microorganisms, but the link between CRW and microorganisms is poorly understood. Here, we used two kinds of sorghum (JZ22 and JB3, of which JZ22 has a higher tannin content) as the raw materials to brew and determined the structural and functional dynamics of the microbiota by metagenomics and flavor analyses. We detected 106 (JZ22) and 109 (JB3) volatile flavor compounds and 8 organic acids. By correlation analysis, we established 687 (JZ22) and 496 (JB3) correlations between the major flavor compounds and microbes. In JZ22, Blautia, Collinsella, Bifidobacterium, Faecalibacterium and Prevotella had the most correlations with flavor production. In JB3, the top 5 genera were Stenotrophomonas, Bdellovibrio, Solibacillus, Sulfuritalea and Achromobacter. In addition, more esters were detected, and more microorganisms correlated with ester generation in JZ22. This study provides a new idea for the micro ecological diversity of CRW fermented with sorghum. This is of significance for improving the quality and broadening the CRW varieties.}, } @article {pmid29544175, year = {2018}, author = {Wang, C and Jiang, K and Zhou, J and Wu, B}, title = {Solidago canadensis invasion affects soil N-fixing bacterial communities in heterogeneous landscapes in urban ecosystems in East China.}, journal = {The Science of the total environment}, volume = {631-632}, number = {}, pages = {702-713}, doi = {10.1016/j.scitotenv.2018.03.061}, pmid = {29544175}, issn = {1879-1026}, mesh = {Biodiversity ; China ; *Ecosystem ; Environmental Monitoring ; *Introduced Species ; Soil/chemistry ; *Soil Microbiology ; Solidago/*growth & development ; }, abstract = {Soil nitrogen-fixing bacterial communities (SNB) can increase the level of available soil N via biological N-fixation to facilitate successful invasion of several invasive plant species (IPS). Meanwhile, landscape heterogeneity can greatly enhance regional invasibility and increase the chances of successful invasion of IPS. Thus, it is important to understand the soil micro-ecological mechanisms driving the successful invasion of IPS in heterogeneous landscapes. This study performed cross-site comparisons, via metagenomics, to comprehensively analyze the effects of Solidago canadensis invasion on SNB in heterogeneous landscapes in urban ecosystems. Rhizospheric soil samples of S. canadensis were obtained from nine urban ecosystems [Three replicate quadrats (including uninvaded sites and invaded sites) for each type of urban ecosystem]. S. canadensis invasion did not significantly affect soil physicochemical properties, the taxonomic diversity of plant communities, or the diversity and richness of SNB. However, some SNB taxa (i.e., f_Micromonosporaceae, f_Oscillatoriaceae, and f_Bacillaceae) changed significantly with S. canadensis invasion. Thus, S. canadensis invasion may alter the community structure, rather than the diversity and richness of SNB, to facilitate its invasion process. Of the nine urban ecosystems, the diversity and richness of SNB was highest in farmland wasteland. Accordingly, the community invasibility of farmland wasteland may be higher than that of the other types of urban ecosystem. In brief, landscape heterogeneity, rather than S. canadensis invasion, was the strongest controlling factor for the diversity and richness of SNB. One possible reason may be the differences in soil electrical conductivity and the taxonomic diversity of plant communities in the nine urban ecosystems, which can cause notable shifts in the diversity and richness of SNB.}, } @article {pmid29543557, year = {2018}, author = {Kiely, CJ and Pavli, P and O'Brien, CL}, title = {The role of inflammation in temporal shifts in the inflammatory bowel disease mucosal microbiome.}, journal = {Gut microbes}, volume = {9}, number = {6}, pages = {477-485}, pmid = {29543557}, issn = {1949-0984}, mesh = {Adult ; Bacteria/classification/genetics/isolation & purification ; *Biodiversity ; Colitis, Ulcerative/microbiology/pathology ; Crohn Disease/microbiology/pathology ; Endoscopy, Gastrointestinal ; *Gastrointestinal Microbiome ; Humans ; Inflammation/pathology ; Inflammatory Bowel Diseases/*microbiology/*pathology ; Intestinal Mucosa/*microbiology/*pathology ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; Time Factors ; }, abstract = {Studies of the human intestinal microbiome in patients with inflammatory bowel disease (IBD) consistently show that there are differences (an abnormal or unbalanced microbiome, "dysbiosis") when compared to healthy subjects. We sought to describe changes in the microbiome in individual patients over time, and determine the clinical factors that are associated with significant alteration. Forty-two mucosal biopsies were collected from 20 patients that were spaced an average of 2.4 years apart. These were analysed using bacterial 16S rRNA gene high-throughput sequencing methods. Presence of active inflammation was determined endoscopically and histologically. Inferred metagenomics analysis was conducted using the PICRUSt package. We found that the differences in the microbiome over time in individual patients were greatest in the presence of ongoing intestinal inflammation, as determined by the Yue and Clayton theta distance between sample pairs (adjusted p = 0.00031). Samples from patients with previous abdominal surgery had lower alpha (within sample) diversity compared with those with no prior operations (mean Shannon index 2.083, 2.510 respectively, p = 0.017). There were no changes in the inferred bacterial metagenomic profile. The microbiome in IBD undergoes considerable fluctuation over time. These changes are greatest when there is histologically confirmed inflammation at both time-points.}, } @article {pmid29543361, year = {2018}, author = {Malone, EW and Perkin, JS and Leckie, BM and Kulp, MA and Hurt, CR and Walker, DM}, title = {Which species, how many, and from where: Integrating habitat suitability, population genomics, and abundance estimates into species reintroduction planning.}, journal = {Global change biology}, volume = {24}, number = {8}, pages = {3729-3748}, doi = {10.1111/gcb.14126}, pmid = {29543361}, issn = {1365-2486}, mesh = {Animals ; *Biodiversity ; Conservation of Natural Resources ; Fishes/*genetics ; Genetic Variation ; Metagenomics ; Population Density ; Rivers ; }, abstract = {Extirpated organisms are reintroduced into their former ranges worldwide to combat species declines and biodiversity losses. The growing field of reintroduction biology provides guiding principles for reestablishing populations, though criticisms remain regarding limited integration of initial planning, modeling frameworks, interdisciplinary collaborations, and multispecies approaches. We used an interdisciplinary, multispecies, quantitative framework to plan reintroductions of three fish species into Abrams Creek, Great Smoky Mountains National Park, USA. We first assessed the appropriateness of habitat at reintroduction sites for banded sculpin (Cottus carolinae), greenside darter (Etheostoma blennioides), and mottled sculpin (Cottus bairdii) using species distribution modeling. Next, we evaluated the relative suitability of nine potential source stock sites using population genomics, abundance estimates, and multiple-criteria decision analysis (MCDA) based on known correlates of reintroduction success. Species distribution modeling identified mottled sculpin as a poor candidate, but banded sculpin and greenside darter as suitable candidates for reintroduction based on species-habitat relationships and habitats available in Abrams Creek. Genotyping by sequencing revealed acceptable levels of genetic diversity at all candidate source stock sites, identified population clusters, and allowed for estimating the number of fish that should be included in translocations. Finally, MCDA highlighted priorities among candidate source stock sites that were most likely to yield successful reintroductions based on differential weightings of habitat assessment, population genomics, and the number of fish available for translocation. Our integrative approach represents a unification of multiple recent advancements in the field of reintroduction biology and highlights the benefit of shifting away from simply choosing nearby populations for translocation to an information-based science with strong a priori planning coupled with several suggested posteriori monitoring objectives. Our framework can be applied to optimize reintroduction successes for a multitude of organisms and advances in the science of reintroduction biology by simultaneously addressing a variety of past criticisms of the field.}, } @article {pmid29540790, year = {2018}, author = {Ushio, M and Murata, K and Sado, T and Nishiumi, I and Takeshita, M and Iwasaki, W and Miya, M}, title = {Demonstration of the potential of environmental DNA as a tool for the detection of avian species.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {4493}, pmid = {29540790}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Birds/*classification/*genetics ; Computational Biology/methods ; *DNA ; DNA Barcoding, Taxonomic ; Metagenomics/methods ; Phylogeny ; }, abstract = {Birds play unique functional roles in the maintenance of ecosystems, such as pollination and seed dispersal, and thus monitoring bird species diversity is a first step towards avoiding undesirable consequences of anthropogenic impacts on bird communities. In the present study, we hypothesized that birds, regardless of their main habitats, must have frequent contact with water and that tissues that contain their DNA that persists in the environment (environmental DNA; eDNA) could be used to detect the presence of avian species. To this end, we applied a set of universal PCR primers (MiBird, a modified version of fish/mammal universal primers) for metabarcoding avian eDNA. We confirmed the versatility of MiBird primers by performing in silico analyses and by amplifying DNAs extracted from bird tissues. Analyses of water samples from zoo cages of birds with known species composition suggested that the use of MiBird primers combined with Illumina MiSeq could successfully detect avian species from water samples. Additionally, analysis of water samples collected from a natural pond detected five avian species common to the sampling areas. The present findings suggest that avian eDNA metabarcoding would be a complementary detection/identification tool in cases where visual census of bird species is difficult.}, } @article {pmid29540768, year = {2018}, author = {Quan, J and Cai, G and Ye, J and Yang, M and Ding, R and Wang, X and Zheng, E and Fu, D and Li, S and Zhou, S and Liu, D and Yang, J and Wu, Z}, title = {A global comparison of the microbiome compositions of three gut locations in commercial pigs with extreme feed conversion ratios.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {4536}, pmid = {29540768}, issn = {2045-2322}, mesh = {Animals ; Bacteria/*classification/genetics ; Cecum/*microbiology ; Chimera/microbiology ; Colon/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Food Industry ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/methods ; Ileum/*microbiology ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA ; Swine ; }, abstract = {In an attempt to increase profits and sustainability in the swine industry, the gut microbiome has become a focus of much research. In this study, we performed a comparative analysis of the gut microbiome in the ileum, cecum, and colon of Duroc × (Landrace × Yorkshire) (DLY) pigs showing two extreme feed conversion ratios (FCRs) using 16S rRNA gene sequencing. The results revealed that the microbial community in the cecum and colon had significantly higher alpha diversity than the ileum. We further identified 11, 55, and 55 operational taxonomic units (OTUs) with significantly different relative abundances between the high and low FCR pigs among the three gut locations, respectively. These OTUs were mainly associated with bacteria that participate in the metabolism of dietary polysaccharides and proteins. We then identified two and nine metabolic pathways that were enriched in the cecum and colon of the high FCR pigs, respectively. The results suggested that the short chain fatty acids and indolic compounds produced by microbial fermentation might influence porcine feed efficiency. These results should improve our understanding of microbiota compositions in the different gut locations of commercial pigs and provide important insights into the effect of gut microbiota on porcine FCRs.}, } @article {pmid29540734, year = {2018}, author = {San-Juan-Vergara, H and Zurek, E and Ajami, NJ and Mogollon, C and Peña, M and Portnoy, I and Vélez, JI and Cadena-Cruz, C and Diaz-Olmos, Y and Hurtado-Gómez, L and Sanchez-Sit, S and Hernández, D and Urruchurtu, I and Di-Ruggiero, P and Guardo-García, E and Torres, N and Vidal-Orjuela, O and Viasus, D and Petrosino, JF and Cervantes-Acosta, G}, title = {A Lachnospiraceae-dominated bacterial signature in the fecal microbiota of HIV-infected individuals from Colombia, South America.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {4479}, pmid = {29540734}, issn = {2045-2322}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Biodiversity ; Case-Control Studies ; *Clostridiaceae/classification/genetics ; Colombia/epidemiology ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; HIV Infections/diagnosis/*epidemiology/immunology/virology ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Young Adult ; }, abstract = {HIV infection has a tremendous impact on the immune system's proper functioning. The mucosa-associated lymphoid tissue (MALT) is significantly disarrayed during HIV infection. Compositional changes in the gut microbiota might contribute to the mucosal barrier disruption, and consequently to microbial translocation. We performed an observational, cross-sectional study aimed at evaluating changes in the fecal microbiota of HIV-infected individuals from Colombia. We analyzed the fecal microbiota of 37 individuals via 16S rRNA gene sequencing; 25 HIV-infected patients and 12 control (non-infected) individuals, which were similar in body mass index, age, gender balance and socioeconomic status. To the best of our knowledge, no such studies have been conducted in Latin American countries. Given its compositional nature, microbiota data were normalized and transformed using Aitchison's Centered Log-Ratio. Overall, a change in the network structure in HIV-infected patients was revealed by using the SPIEC-EASI MB tool. Genera such as Blautia, Dorea, Yersinia, Escherichia-Shigella complex, Staphylococcus, and Bacteroides were highly relevant in HIV-infected individuals. Differential abundance analysis by both sparse Partial Least Square-Discriminant Analysis and Random Forest identified a greater abundance of Lachnospiraceae-OTU69, Blautia, Dorea, Roseburia, and Erysipelotrichaceae in HIV-infected individuals. We show here, for the first time, a predominantly Lachnospiraceae-based signature in HIV-infected individuals.}, } @article {pmid29540507, year = {2018}, author = {Succurro, A and Ebenhöh, O}, title = {Review and perspective on mathematical modeling of microbial ecosystems.}, journal = {Biochemical Society transactions}, volume = {46}, number = {2}, pages = {403-412}, pmid = {29540507}, issn = {1470-8752}, mesh = {*Ecosystem ; Metagenomics ; *Microbiota ; *Models, Biological ; }, abstract = {UNLABELLED: Understanding microbial ecosystems means unlocking the path toward a deeper knowledge of the fundamental mechanisms of life. Engineered microbial communities are also extremely relevant to tackling some of today's grand societal challenges. Advanced meta-omics experimental techniques provide crucial insights into microbial communities, but have been so far mostly used for descriptive, exploratory approaches to answer the initial 'who is there?'

QUESTION: An ecosystem is a complex network of dynamic spatio-temporal interactions among organisms as well as between organisms and the environment. Mathematical models with their abstraction capability are essential to capture the underlying phenomena and connect the different scales at which these systems act. Differential equation models and constraint-based stoichiometric models are deterministic approaches that can successfully provide a macroscopic description of the outcome from microscopic behaviors. In this mini-review, we present classical and recent applications of these modeling methods and illustrate the potential of their integration. Indeed, approaches that can capture multiple scales are needed in order to understand emergent patterns in ecosystems and their dynamics regulated by different spatio-temporal phenomena. We finally discuss promising examples of methods proposing the integration of differential equations with constraint-based stoichiometric models and argue that more work is needed in this direction.}, } @article {pmid29540269, year = {2018}, author = {Villamil, SI and Huerlimann, R and Morianos, C and Sarnyai, Z and Maes, GE}, title = {Adverse effect of early-life high-fat/high-carbohydrate ("Western") diet on bacterial community in the distal bowel of mice.}, journal = {Nutrition research (New York, N.Y.)}, volume = {50}, number = {}, pages = {25-36}, doi = {10.1016/j.nutres.2017.11.008}, pmid = {29540269}, issn = {1879-0739}, mesh = {Animals ; Bacteria/genetics/*growth & development ; Diet, High-Fat/*adverse effects ; Diet, Western/adverse effects ; Dietary Carbohydrates/administration & dosage/*pharmacology ; Dietary Fats/administration & dosage/*pharmacology ; *Feeding Behavior ; *Gastrointestinal Microbiome ; Intestines/*drug effects/microbiology ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S ; }, abstract = {Obesity and other lifestyle diseases in modern society can be related to historical dietary changes from diets balanced in omega-6 and omega-3 to the unbalanced "Western-type" diet. It is recognized that diet influences the murine and human gut microbiome, and most research indicates that microbial diversity and composition are altered by high-fat diets (HFDs). However, good knowledge about the effects of early exposure to HFD on the maturation and structure of the bacterial community is limited. Using mice as model, we hypothesized that an HFD alters the early dynamic of the gut bacterial community toward an unstable/unhealthy state. By sequencing the V3 and V4 regions of the 16S ribosomal ribonucleic acid gene, we investigated the bacterial community in fecal samples of mice fed a control diet and an HFD at weaning (sampling time 1) and after 8 weeks of dietary intervention (11weeks of age; sampling time 2). Natural temporal microbiome maturation was evidenced by a general increase in microbial diversity and shifts in microbial community between sampling times 1 and 2 toward a mature community. However, the HFD led to significant structural segregation of the microbiome compared with controls; the HFD diet repressed health-enhancing bacteria (eg, Bifidobacterium and Akkermansia) and promoted health-detracting bacteria (ie, those associated with gut disorders, eg, Dorea). We suggest that early-life consumption of HFD negatively impacts the natural gut bacterial community maturation leading toward a potentially persistent unhealthy stage.}, } @article {pmid29539590, year = {2018}, author = {Mastrocola, R and Ferrocino, I and Liberto, E and Chiazza, F and Cento, AS and Collotta, D and Querio, G and Nigro, D and Bitonto, V and Cutrin, JC and Rantsiou, K and Durante, M and Masini, E and Aragno, M and Cordero, C and Cocolin, L and Collino, M}, title = {Fructose liquid and solid formulations differently affect gut integrity, microbiota composition and related liver toxicity: a comparative in vivo study.}, journal = {The Journal of nutritional biochemistry}, volume = {55}, number = {}, pages = {185-199}, doi = {10.1016/j.jnutbio.2018.02.003}, pmid = {29539590}, issn = {1873-4847}, mesh = {Animals ; Feces/chemistry ; Fructose/*chemistry/*toxicity/urine ; Gastrointestinal Microbiome/*drug effects/genetics/physiology ; Glucose Transporter Type 2/metabolism ; Glycation End Products, Advanced/metabolism ; Inflammasomes/metabolism ; Lipid Metabolism/drug effects ; Liver Cirrhosis/*chemically induced/metabolism ; Male ; Metagenome/drug effects ; Mice, Inbred C57BL ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; }, abstract = {Despite clinical findings suggesting that the form (liquid versus solid) of the sugars may significantly affect the development of metabolic diseases, no experimental data are available on the impact of their formulations on gut microbiota, integrity and hepatic outcomes. In the present sudy, C57Bl/6j mice were fed a standard diet plus water (SD), a standard diet plus 60% fructose syrup (L-Fr) or a 60% fructose solid diet plus water (S-Fr) for 12 weeks. Gut microbiota was characterized through 16S rRNA phylogenetic profiling and shotgun sequencing of microbial genes in ileum content and related volatilome profiling. Fructose feeding led to alterations of the gut microbiota depending on the fructose formulation, with increased colonization by Clostridium, Oscillospira and Clostridiales phyla in the S-Fr group and Bacteroides, Lactobacillus, Lachnospiraceae and Dorea in the L-Fr. S-Fr evoked the highest accumulation of advanced glycation end products and barrier injury in the ileum intestinal mucosa. These effects were associated to a stronger activation of the lipopolysaccharide-dependent proinflammatory TLR4/NLRP3 inflammasome pathway in the liver of S-Fr mice than of L-Fr mice. In contrast, L-Fr intake induced higher levels of hepatosteatosis and markers of fibrosis than S-Fr. Fructose-induced ex novo lipogenesis with production of SCFA and MCFA was confirmed by metagenomic analysis. These results suggest that consumption of fructose under different forms, liquid or solid, may differently affect gut microbiota, thus leading to impairment in intestinal mucosa integrity and liver homeostasis.}, } @article {pmid29539432, year = {2018}, author = {Fujisaka, S and Avila-Pacheco, J and Soto, M and Kostic, A and Dreyfuss, JM and Pan, H and Ussar, S and Altindis, E and Li, N and Bry, L and Clish, CB and Kahn, CR}, title = {Diet, Genetics, and the Gut Microbiome Drive Dynamic Changes in Plasma Metabolites.}, journal = {Cell reports}, volume = {22}, number = {11}, pages = {3072-3086}, pmid = {29539432}, issn = {2211-1247}, support = {R01 DK033201/DK/NIDDK NIH HHS/United States ; R37 DK031036/DK/NIDDK NIH HHS/United States ; P30 DK036836/DK/NIDDK NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; P30 DK040561/DK/NIDDK NIH HHS/United States ; U01 CA210171/CA/NCI NIH HHS/United States ; R01 DK031036/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Diet, High-Fat/*methods ; Gastrointestinal Microbiome/*genetics ; Humans ; Metabolomics/*methods ; Mice ; Obesity/*genetics/pathology ; }, abstract = {Diet, genetics, and the gut microbiome are determinants of metabolic status, in part through production of metabolites by the gut microbiota. To understand the mechanisms linking these factors, we performed LC-MS-based metabolomic analysis of cecal contents and plasma from C57BL/6J, 129S1/SvImJ, and 129S6/SvEvTac mice on chow or a high-fat diet (HFD) and HFD-treated with vancomycin or metronidazole. Prediction of the functional metagenome of gut bacteria by PICRUSt analysis of 16S sequences revealed dramatic differences in microbial metabolism. Cecal and plasma metabolites showed multifold differences reflecting the combined and integrated effects of diet, antibiotics, host background, and the gut microbiome. Eighteen plasma metabolites correlated positively or negatively with host insulin resistance across strains and diets. Over 1,000 still-unidentified metabolite peaks were also highly regulated by diet, antibiotics, and genetic background. Thus, diet, host genetics, and the gut microbiota interact to create distinct responses in plasma metabolites, which can contribute to regulation of metabolism and insulin resistance.}, } @article {pmid29536131, year = {2018}, author = {Jani, K and Dhotre, D and Bandal, J and Shouche, Y and Suryavanshi, M and Rale, V and Sharma, A}, title = {World's Largest Mass Bathing Event Influences the Bacterial Communities of Godavari, a Holy River of India.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {706-718}, pmid = {29536131}, issn = {1432-184X}, support = {BT/PR/0054/NDB/52/94/2007//Department of Biotechnology , Ministry of Science and Technology/ ; }, mesh = {Bacteria/classification/genetics/*isolation & purification ; Baths ; *Biodiversity ; Humans ; India ; Phylogeny ; Public Health ; Rivers/chemistry/*microbiology ; Water Quality ; }, abstract = {Kumbh Mela is one of the largest religious mass gathering events (MGE) involving bathing in rivers. The exponential rise in the number of devotees, from around 0.4 million in 1903 to 120 million in 2013, bathing in small specified sites can have a dramatic impact on the river ecosystem. Here, we present the spatiotemporal profiling of bacterial communities in Godavari River, Nashik, India, comprising five sites during the Kumbh Mela, held in 2015. Assessment of environmental parameters indicated deterioration of water quality. Targeted amplicon sequencing demonstrates approximately 37.5% loss in microbial diversity because of anthropogenic activity during MGE. A significant decrease in phyla viz. Actinobacteria, Chloroflexi, Proteobacteria, and Bacteroidetes was observed, while we noted substantial increase in prevalence of the phylum Firmicutes (94.6%) during MGE. qPCR estimations suggested nearly 130-fold increase in bacterial load during the event. Bayesian mixing model accounted the source of enormous incorporation of bacterial load of human origin. Further, metagenomic imputations depicted increase in virulence and antibiotic resistance genes during the MGE. These observations suggest the striking impact of the mass bathing on river ecosystem. The subsequent increase in infectious diseases and drug-resistant microbes pose a critical public health concern.}, } @article {pmid29533950, year = {2018}, author = {Tsuji, S and Suruda, C and Hashiyada, M and Kimata, T and Yamanouchi, S and Kitao, T and Kino, J and Akane, A and Kaneko, K}, title = {Gut Microbiota Dysbiosis in Children with Relapsing Idiopathic Nephrotic Syndrome.}, journal = {American journal of nephrology}, volume = {47}, number = {3}, pages = {164-170}, doi = {10.1159/000487557}, pmid = {29533950}, issn = {1421-9670}, mesh = {Butyric Acid/analysis ; Case-Control Studies ; Child ; Child, Preschool ; Dysbiosis/*complications ; Feces/chemistry ; Female ; *Gastrointestinal Microbiome ; Humans ; Lymphocyte Count ; Male ; Nephrotic Syndrome/immunology/*microbiology ; Recurrence ; T-Lymphocytes, Regulatory ; }, abstract = {BACKGROUND: While the etiology of idiopathic nephrotic syndrome (idiopathic nephrotic syndrome [INS]; characterized by repeated relapses and comorbid allergic conditions) remains unknown, recent evidence suggests that dysfunction in regulatory T cells (Tregs) plays an important role in the development of INS as well as allergic diseases. We hypothesized that dysbiosis involving decreased butyric acid-producing gut microbiota leads to defective induction and differentiation of peripherally induced Tregs, resulting in INS relapse.

METHODS: Study subjects were 12 children with INS, 8 classified as relapsing (R group; median age: 3.0 years) and 4 as non-relapsing (NR group; median age: 4.3 years), and 11 healthy children (HC group; median age: 5.1 years) serving as normal controls. Measurement of microbiota was performed using 16S ribosomal RNA metagenomic analysis, and fecal butyric acid was measured using high performance liquid chromatography. Flow-cytometric analysis of Tregs and CD4-positive (CD4+) cells in peripheral blood was also performed.

RESULTS: Metagenomic analysis of gut microbiota using feces showed that the proportion of butyric acid-producing bacteria was significantly lower in R (median 6.36%) than HC (median 18.84%; p = 0.0013), but no different between NR (median 16.71%) and HC (p = 0.29). Fecal organic acid analysis revealed significantly lower butyric acid quantities in R than HC (medians: 0.48 vs. 0.99 mg/g, p = 0.042). Circulating Tregs as a proportion of CD4+ cells were decreased in 75% of R and NR.

CONCLUSION: Pediatric relapsing INS patients show gut microbiota dysbiosis, characterized by a decreased proportion of butyric acid-producing bacteria and lower fecal butyric acid quantities, concomitant with reduced circulatory Tregs.}, } @article {pmid29532103, year = {2018}, author = {Tao, J and Meng, D and Qin, C and Liu, X and Liang, Y and Xiao, Y and Liu, Z and Gu, Y and Li, J and Yin, H}, title = {Integrated network analysis reveals the importance of microbial interactions for maize growth.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {8}, pages = {3805-3818}, doi = {10.1007/s00253-018-8837-4}, pmid = {29532103}, issn = {1432-0614}, support = {31570113//National Nature Science Foundation of China/ ; 41573072//National Nature Science Foundation of China/ ; }, mesh = {Microbial Consortia/*physiology ; Microbial Interactions/*physiology ; Models, Biological ; *Soil Microbiology ; Zea mays/*growth & development/*microbiology ; }, abstract = {Microbes play a critical role in soil global biogeochemical circulation and microbe-microbe interactions have also evoked enormous interests in recent years. Utilization of green manures can stimulate microbial activity and affect microbial composition and diversity. However, few studies focus on the microbial interactions or detect the key functional members in communities. With the advances of metagenomic technologies, network analysis has been used as a powerful tool to detect robust interactions between microbial members. Here, random matrix theory-based network analysis was used to investigate the microbial networks in response to four different green manure fertilization regimes (Vicia villosa, common vetch, milk vetch, and radish) over two growth cycles from October 2012 to September 2014. The results showed that the topological properties of microbial networks were dramatically altered by green manure fertilization. Microbial network under milk vetch amendment showed substantially more intense complexity and interactions than other fertilization systems, indicating that milk vetch provided a favorable condition for microbial interactions and niche sharing. The shift of microbial interactions could be attributed to the changes in some major soil traits and the interactions might be correlated to plant growth and production. With the stimuli of green manures, positive interactions predominated the network eventually and the network complexity was in consistency with maize productivity, which suggested that the complex soil microbial networks might benefit to plants rather than simple ones, because complex networks would hold strong the ability to cope with environment changes or suppress soil-borne pathogen infection on plants. In addition, network analyses discerned some putative keystone taxa and seven of them had directly positive interactions with maize yield, which suggested their important roles in maintaining environmental functions and in improving plant growth.}, } @article {pmid29531366, year = {2018}, author = {Garza, DR and van Verk, MC and Huynen, MA and Dutilh, BE}, title = {Towards predicting the environmental metabolome from metagenomics with a mechanistic model.}, journal = {Nature microbiology}, volume = {3}, number = {4}, pages = {456-460}, doi = {10.1038/s41564-018-0124-8}, pmid = {29531366}, issn = {2058-5276}, mesh = {Bacteria/classification/genetics/*metabolism ; Colon/*microbiology ; Female ; Humans ; Metabolome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Models, Biological ; Molecular Sequence Annotation ; Mouth/*microbiology ; Skin/*microbiology ; Vagina/*microbiology ; }, abstract = {The environmental metabolome and metabolic potential of microorganisms are dominant and essential factors shaping microbial community composition. Recent advances in genome annotation and systems biology now allow us to semiautomatically reconstruct genome-scale metabolic models (GSMMs) of microorganisms based on their genome sequence [1] . Next, growth of these models in a defined metabolic environment can be predicted in silico, mechanistically linking the metabolic fluxes of individual microbial populations to the community dynamics. A major advantage of GSMMs is that no training data is needed, besides information about the metabolic capacity of individual genes (genome annotation) and knowledge of the available environmental metabolites that allow the microorganism to grow. However, the composition of the environment is often not fully determined and remains difficult to measure [2] . We hypothesized that the relative abundance of different bacterial species, as measured by metagenomics, can be combined with GSMMs of individual bacteria to reveal the metabolic status of a given biome. Using a newly developed algorithm involving over 1,500 GSMMs of human-associated bacteria, we inferred distinct metabolomes for four human body sites that are consistent with experimental data. Together, we link the metagenome to the metabolome in a mechanistic framework towards predictive microbiome modelling.}, } @article {pmid29531234, year = {2018}, author = {Penington, JS and Penno, MAS and Ngui, KM and Ajami, NJ and Roth-Schulze, AJ and Wilcox, SA and Bandala-Sanchez, E and Wentworth, JM and Barry, SC and Brown, CY and Couper, JJ and Petrosino, JF and Papenfuss, AT and Harrison, LC and , }, title = {Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {4386}, pmid = {29531234}, issn = {2045-2322}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; }, mesh = {Australia ; Cryopreservation/methods ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Individuality ; RNA, Ribosomal, 16S/*genetics/standards ; Sequence Analysis, DNA ; Specimen Handling/*methods ; United States ; }, abstract = {To optimise fecal sampling for reproducible analysis of the gut microbiome, we compared different methods of sample collection and sequencing of 16S rRNA genes at two centers. Samples collected from six individuals on three consecutive days were placed in commercial collection tubes (OMNIgeneGut OMR-200) or in sterile screw-top tubes in a home fridge or home freezer for 6-24 h, before transfer and storage at -80 °C. Replicate samples were shipped to centers in Australia and the USA for DNA extraction and sequencing by their respective PCR protocols, and analysed with the same bioinformatic pipeline. Variation in gut microbiome was dominated by differences between individuals. Minor differences in the abundance of taxa were found between collection-processing methods and day of collection, and between the two centers. We conclude that collection with storage and transport at 4 °C within 24 h is adequate for 16S rRNA analysis of the gut microbiome. Other factors including differences in PCR and sequencing methods account for relatively minor variation compared to differences between individuals.}, } @article {pmid29528548, year = {2018}, author = {Zhu, L and Wu, Q and Deng, C and Zhang, M and Zhang, C and Chen, H and Lu, G and Wei, F}, title = {Adaptive evolution to a high purine and fat diet of carnivorans revealed by gut microbiomes and host genomes.}, journal = {Environmental microbiology}, volume = {20}, number = {5}, pages = {1711-1722}, doi = {10.1111/1462-2920.14096}, pmid = {29528548}, issn = {1462-2920}, mesh = {Animal Feed/analysis ; Animals ; Bacteria/*classification/metabolism ; *Biological Evolution ; Carnivora/genetics/microbiology/*physiology ; Diet ; Dietary Fats/*administration & dosage/metabolism ; *Gastrointestinal Microbiome ; Genome ; Metagenome ; Purines/*administration & dosage/metabolism ; }, abstract = {Carnivorous members of the Carnivora reside at the apex of food chains and consume meat-only diets, rich in purine, fats and protein. Here, we aimed to identify potential adaptive evolutionary signatures compatible with high purine and fat metabolism based on analysis of host genomes and symbiotic gut microbial metagenomes. We found that the gut microbiomes of carnivorous Carnivora (e.g., Felidae, Canidae) clustered in the same clade, and other clades comprised omnivorous and herbivorous Carnivora (e.g., badgers, bears and pandas). The relative proportions of genes encoding enzymes involved in uric acid degradation were higher in the gut microbiomes of meat-eating carnivorans than plant-eating species. Adaptive amino acid substitutions in two enzymes, carnitine O-palmitoyltransferase 1 (CPT1A) and lipase F (LIPF), which play a role in fat digestion, were identified in Felidae-Candidae species. Carnivorous carnivorans appear to endure diets high in purines and fats via gut microbiomic and genomic adaptations.}, } @article {pmid29526926, year = {2018}, author = {Do, TH and Le, NG and Dao, TK and Nguyen, TMP and Le, TL and Luu, HL and Nguyen, KHV and Nguyen, VL and Le, LA and Phung, TN and van Straalen, NM and Roelofs, D and Truong, NH}, title = {Metagenomic insights into lignocellulose-degrading genes through Illumina-based de novo sequencing of the microbiome in Vietnamese native goats' rumen.}, journal = {The Journal of general and applied microbiology}, volume = {64}, number = {3}, pages = {108-116}, doi = {10.2323/jgam.2017.08.004}, pmid = {29526926}, issn = {1349-8037}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/classification/*enzymology/*genetics ; Base Sequence ; DNA, Bacterial/genetics ; Databases, Genetic ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/genetics ; Glycoside Hydrolases/*genetics/metabolism ; Goats/*microbiology ; Lignin/metabolism ; Metagenome/*genetics ; Metagenomics ; Open Reading Frames ; Rumen/*microbiology ; Vietnam ; }, abstract = {The scarcity of enzymes having an optimal activity in lignocellulose deconstruction is an obstacle for industrial-scale conversion of cellulosic biomass into biofuels. With the aim of mining novel lignocellulolytic enzymes, a ~9 Gb metagenome of bacteria in Vietnamese native goats' rumen was sequenced by Illumina platform. From the data, 821 ORFs encoding carbohydrate esterases (CEs) and polysaccharide lyases (PLs) serving for lignocellulose pre-treatment, 816 ORFs encoding 11 glycoside hydrolase families (GHs) of cellulases, and 2252 ORFs encoding 22 GHs of hemicellulases, were mined. The carbohydrate binding module (CBM) was also abundant with 763 ORFs, of which 480 ORFs are located with lignocellulolytic enzymes. The enzyme modularity analysis showed that CBMs are usually present in endoglucanase, endo 1,3-beta-D-glucosidase, and endoxylanase, whereas fibronectin 3-like module (FN3) mainly represents in GH3 and immunoglobulin-like domain (Ig) was located in GH9 only. Every domain located in each ORF was analyzed in detail to contribute enzymes' modularity which is valuable for modelling, to study the structure, and for recombinant production. With the aim of confirming the annotated results, a mined ORF encoding CBM63 was highly expressed in E. coli in soluble form. The purified recombinant CBM63 exhibited no cellulase activity, but enhanced a commercial cellulase activity in the destruction of a paper filter.}, } @article {pmid29526222, year = {2018}, author = {Andeta, AF and Vandeweyer, D and Woldesenbet, F and Eshetu, F and Hailemicael, A and Woldeyes, F and Crauwels, S and Lievens, B and Ceusters, J and Vancampenhout, K and Van Campenhout, L}, title = {Fermentation of enset (Ensete ventricosum) in the Gamo highlands of Ethiopia: Physicochemical and microbial community dynamics.}, journal = {Food microbiology}, volume = {73}, number = {}, pages = {342-350}, doi = {10.1016/j.fm.2018.02.011}, pmid = {29526222}, issn = {1095-9998}, mesh = {Biodiversity ; Clostridium/classification/genetics/isolation & purification/metabolism ; Ethiopia ; Fermentation ; Hydrogen-Ion Concentration ; Lactobacillales/classification/*isolation & purification/metabolism ; Musaceae/chemistry/metabolism/*microbiology ; Temperature ; }, abstract = {Enset (Ensete ventricosum) provides staple food for 15 million people in Ethiopia after fermentation into kocho. The fermentation process has hardly been investigated and is prone to optimization. The aim of this study was to investigate the physicochemical and microbial dynamics of fermentation practices in the Gamo highlands. These practices show local variation, but two steps were omnipresent: scraping of the pseudostem and fermenting it in a pit or a bamboo basket. Enset plants were fragmented and fermented for two months in order to investigate the physicochemical (temperature, moisture content, pH and titratable acidity) and microbial dynamics (total viable aerobic counts, counts of Enterobacteriaceae, lactic acid bacteria, yeasts and moulds and Clostridium spores counts, and Illumina Miseq sequencing). Samples were taken on days 1, 7, 15, 17, 31 and 60. The pH decreased, whereas the titratable acidity increased during fermentation. Of all counts those of lactic acid bacteria and Clostridium spores increased during fermentation. Leuconostoc mesenteroides initiated the fermentation. Later on, Prevotella paludivivens, Lactobacillus sp. and Bifidobacterium minimum dominated. These three species are potential candidates for the development of a starter culture.}, } @article {pmid29524500, year = {2018}, author = {Ruppé, E and Schrenzel, J}, title = {Messages from the second International Conference on Clinical Metagenomics (ICCMg2).}, journal = {Microbes and infection}, volume = {20}, number = {4}, pages = {222-227}, doi = {10.1016/j.micinf.2018.02.005}, pmid = {29524500}, issn = {1769-714X}, mesh = {Bacteria/genetics/isolation & purification/pathogenicity ; Clinical Laboratory Techniques/standards/trends ; Computational Biology ; Drug Resistance, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/standards/trends ; Humans ; Metagenome/genetics ; *Metagenomics/standards/trends ; Microbiota/genetics ; }, abstract = {Clinical metagenomics (CMg) refers to as the application of metagenomic sequencing of clinical samples in order to recover clinically-relevant information. Due to the increasing access to next-generation sequencing (NGS) facilities, CMg is a gast-growing field. In this context, we held the second International Conference on Clinical Metagenomics (ICCMg2) in Geneva in October 2017. During the two days of the conference, several aspects of CMg were addressed, which we propose to summarize in the present manuscript. Besides, we also discuss the evolution of CMg from the last conference held in 2016. In brief, many technical issues related to CMg are expected to be successfully addressed in the coming years. Conversely, assessing the clinical value of CMg, implementing a quality process, storage of data and the ethics of CMg are emerging challenges.}, } @article {pmid29524068, year = {2018}, author = {Wang, C and Li, Q and Li, J}, title = {Gut microbiota and its implications in small bowel transplantation.}, journal = {Frontiers of medicine}, volume = {12}, number = {3}, pages = {239-248}, pmid = {29524068}, issn = {2095-0225}, mesh = {Biomarkers ; *Gastrointestinal Microbiome ; Graft Rejection/*immunology ; Humans ; Immunity, Mucosal ; Intestine, Small/*microbiology/*transplantation ; Metagenomics ; Transplantation Tolerance/*immunology ; }, abstract = {The gut microbiota is mainly composed of a diverse population of commensal bacterial species and plays a pivotal role in the maintenance of intestinal homeostasis, immune modulation and metabolism. The influence of the gut microbiota on solid organ transplantation has recently been recognized. In fact, several studies indicated that acute and chronic allograft rejection in small bowel transplantation (SBT) is closely associated with the alterations in microbial patterns in the gut. In this review, we focused on the recent findings regarding alterations in the microbiota following SBTand the potential roles of these alterations in the development of acute and chronic allograft rejection. We also reviewed important advances with respect to the interplays between the microbiota and host immune systems in SBT. Furthermore, we explored the potential of the gut microbiota as a microbial marker and/or therapeutic target for the predication and intervention of allograft rejection and chronic dysfunction. Given that current research on the gut microbiota has become increasingly sophisticated and comprehensive, large cohort studies employing metagenomic analysis and multivariate linkage should be designed for the characterization of host-microbe interaction and causality between microbiota alterations and clinical outcomes in SBT. The findings are expected to provide valuable insights into the role of gut microbiota in the development of allograft rejection and other transplant-related complications and introduce novel therapeutic targets and treatment approaches in clinical practice.}, } @article {pmid29523891, year = {2018}, author = {Graham, ED and Heidelberg, JF and Tully, BJ}, title = {Potential for primary productivity in a globally-distributed bacterial phototroph.}, journal = {The ISME journal}, volume = {12}, number = {7}, pages = {1861-1866}, pmid = {29523891}, issn = {1751-7370}, mesh = {Bacteria/classification/isolation & purification/*metabolism/radiation effects ; Biodiversity ; Carbon Cycle ; Light ; Mediterranean Sea ; Metagenomics ; Microbiota ; Photosynthesis ; Phototrophic Processes ; Seawater/*microbiology ; }, abstract = {Aerobic anoxygenic phototrophs (AAnPs) are common in marine environments and are associated with photoheterotrophic activity. To date, AAnPs that possess the potential for carbon fixation have not been identified in the surface ocean. Using the Tara Oceans metagenomic dataset, we have identified draft genomes of nine bacteria that possess the genomic potential for anoxygenic phototrophy, carbon fixation via the Calvin-Benson-Bassham cycle, and the oxidation of sulfite and thiosulfate. Forming a monophyletic clade within the Alphaproteobacteria and lacking cultured representatives, the organisms compose minor constituents of local microbial communities (0.1-1.0%), but are globally distributed, present in multiple samples from the North Pacific, Mediterranean Sea, the East Africa Coastal Province, and the Atlantic. This discovery may require re-examination of the microbial communities in the oceans to understand and constrain the role this group of organisms may play in the global carbon cycle.}, } @article {pmid29523553, year = {2018}, author = {Chen, YL and Fu, HY and Lee, TH and Shih, CJ and Huang, L and Wang, YS and Ismail, W and Chiang, YR}, title = {Estrogen Degraders and Estrogen Degradation Pathway Identified in an Activated Sludge.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {10}, pages = {}, pmid = {29523553}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Estrogens/*metabolism ; Estrone/metabolism ; *Metabolic Networks and Pathways ; Metagenomics ; Phylogeny ; Sewage/*microbiology ; Taiwan ; Wastewater/analysis ; Water Pollutants, Chemical/metabolism ; }, abstract = {The environmental release and fate of estrogens are becoming an increasing public concern. Bacterial degradation has been considered the main process for eliminating estrogens from wastewater treatment plants. Various bacterial isolates are reportedly capable of aerobic estrogen degradation, and several estrogen degradation pathways have been proposed in proteobacteria and actinobacteria. However, the ecophysiological relevance of estrogen-degrading bacteria in the environment is unclear. In this study, we investigated the estrogen degradation pathway and corresponding degraders in activated sludge collected from the Dihua Sewage Treatment Plant, Taipei, Taiwan. Cultivation-dependent and cultivation-independent methods were used to assess estrogen biodegradation in the collected activated sludge. Estrogen metabolite profile analysis revealed the production of pyridinestrone acid and two A/B-ring cleavage products in activated sludge incubated with estrone (1 mM), which are characteristic of the 4,5-seco pathway. PCR-based functional assays detected sequences closely related to alphaproteobacterial oecC, a key gene of the 4,5-seco pathway. Metagenomic analysis suggested that Novosphingobium spp. are major estrogen degraders in estrone-amended activated sludge. Novosphingobium sp. strain SLCC, an estrone-degrading alphaproteobacterium, was isolated from the examined activated sludge. The general physiology and metabolism of this strain were characterized. Pyridinestrone acid and the A/B-ring cleavage products were detected in estrone-grown strain SLCC cultures. The production of pyridinestrone acid was also observed during the aerobic incubation of strain SLCC with 3.7 nM (1 μg/liter) estrone. This concentration is close to that detected in many natural and engineered aquatic ecosystems. The presented data suggest the ecophysiological relevance of Novosphingobium spp. in activated sludge.IMPORTANCE Estrogens, which persistently contaminate surface water worldwide, have been classified as endocrine disruptors and human carcinogens. We contribute new knowledge on the major estrogen biodegradation pathway and estrogen degraders in wastewater treatment plants. This study considerably advances the understanding of environmental estrogen biodegradation, which is instrumental for the efficient elimination of these hazardous pollutants. Moreover, this study substantially improves the understanding of microbial estrogen degradation in the environment.}, } @article {pmid29523545, year = {2018}, author = {Patin, NV and Pratte, ZA and Regensburger, M and Hall, E and Gilde, K and Dove, ADM and Stewart, FJ}, title = {Microbiome Dynamics in a Large Artificial Seawater Aquarium.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {10}, pages = {}, pmid = {29523545}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; *Ecosystem ; Fishes/growth & development ; Georgia ; Metagenome ; *Microbiota ; Phylogeny ; Seawater/*microbiology ; }, abstract = {Artificial habitats for animals have high commercial and societal value. Microbial communities (microbiomes) in such habitats may play ecological roles similar to those in nature. However, this hypothesis remains largely untested. Georgia Aquarium's Ocean Voyager (OV) exhibit is a closed-system aquatic habitat that mimics the oligotrophic open ocean and houses thousands of large marine animals, including fish, sea turtles, and whale sharks. We present a 14-month time series characterizing the OV water column microbiome. The composition and stability of the microbiome differed from those of natural marine environments with similar chemical features. The composition shifted dramatically over the span of 2 weeks and was characterized by bloom events featuring members of two heterotrophic bacterial lineages with cosmopolitan distributions in the oceans. The relative abundances of these lineages were inversely correlated, suggesting an overlap in ecological niches. Transcript mapping to metagenome-assembled genomes (MAGs) of these taxa identified unique characteristics, including the presence and activity of genes for the synthesis and degradation of cyanophycin, an amino acid polymer linked to environmental stress and found frequently in cyanobacteria but rarely in heterotrophic bacteria. The dominant MAGs also contained and transcribed plasmid-associated sequences, suggesting a role for conjugation in adaptation to the OV environment. These findings indicate a highly dynamic microbiome despite the stability of the physical and chemical parameters of the water column. Characterizing how such fluctuations affect microbial function may inform our understanding of animal health in closed aquaculture systems.IMPORTANCE Public aquariums play important societal roles, for example, by promoting science education and helping conserve biodiversity. The health of aquarium animals depends on interactions with the surrounding microbiome. However, the extent to which aquariums recreate a stable and natural microbial ecosystem is uncertain. This study describes the taxonomic composition of the water column microbiome over 14 months in a large indoor aquatic habitat, the Ocean Voyager exhibit at the Georgia Aquarium. Despite stable water column conditions, the exhibit experienced blooms in which the abundance of a single bacterial strain increased to over 65% of the community. Genome analysis indicated that the OV's dominant strains share unique adaptations, notably genes for storage polymers associated with environmental stress. These results, interpreted alongside data from natural ocean systems and another artificial seawater aquarium, suggest a highly dynamic aquarium microbiome and raise questions of how microbiome stability may affect the ecological health of the habitat.}, } @article {pmid29523365, year = {2017}, author = {Lagier, JC and Dubourg, G and Amrane, S and Raoult, D}, title = {Koch Postulate: Why Should we Grow Bacteria?.}, journal = {Archives of medical research}, volume = {48}, number = {8}, pages = {774-779}, doi = {10.1016/j.arcmed.2018.02.003}, pmid = {29523365}, issn = {1873-5487}, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacteria/drug effects/genetics/*isolation & purification ; *Bacterial Infections/diagnosis/drug therapy/microbiology ; *Bacteriological Techniques ; *Cell Culture Techniques ; Humans ; Metagenomics ; Microbial Sensitivity Tests ; Microbiota/*physiology ; }, } @article {pmid29522953, year = {2018}, author = {Cai, L and Chen, TB and Zheng, SW and Liu, HT and Zheng, GD}, title = {Decomposition of lignocellulose and readily degradable carbohydrates during sewage sludge biodrying, insights of the potential role of microorganisms from a metagenomic analysis.}, journal = {Chemosphere}, volume = {201}, number = {}, pages = {127-136}, doi = {10.1016/j.chemosphere.2018.02.177}, pmid = {29522953}, issn = {1879-1298}, mesh = {Carbohydrate Metabolism ; Carbohydrates/*analysis ; Hot Temperature ; Lignin/*analysis ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Sewage/*chemistry/microbiology ; Waste Disposal, Fluid/*methods ; }, abstract = {Sewage sludge biodrying is a waste treatment method that uses bio-heat generated from organic degradation to remove moisture from sewage sludge. Lignocellulose and carbohydrate decomposition is important when assessing biodrying performance. This study investigated lignocellulose and carbohydrate decomposition, and the potential microbial functions during biodrying. We determined the lignocellulose and carbohydrate contents, assayed related enzyme activity, performed a complete metagenomic study on sewage sludge biodrying material during the thermophilic phase, annotated potential genetic function involved in the decomposition, and summarized the key metabolic pathways. The results indicated that lignocellulose, readily degradable carbohydrates, and starch, significantly decomposed after biodrying. During the thermophilic phase, the majority of lignocellulose and carbohydrate-related enzymes showed significantly higher activity, and glycoside hydrolases and glycosyl transferases showed higher gene counts and reads. Moreover, the top five microorganisms enriched with carbohydrate-active enzyme genes, i.e., Bacillus, Intrasporangium, Tetrasphaera, Rhodobacter, and Streptomyces, were also among the top ten ecologically dominant genera. These findings highlight the crucial phases for biodrying process, reveal the ecologically functional diversity of biodrying-originated microbial consortia, and suggest potential candidates for optimizing biodrying decomposition.}, } @article {pmid29522743, year = {2018}, author = {Ferreiro, A and Crook, N and Gasparrini, AJ and Dantas, G}, title = {Multiscale Evolutionary Dynamics of Host-Associated Microbiomes.}, journal = {Cell}, volume = {172}, number = {6}, pages = {1216-1227}, pmid = {29522743}, issn = {1097-4172}, support = {R01 GM099538/GM/NIGMS NIH HHS/United States ; T32 DK077653/DK/NIDDK NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; U01 AI123394/AI/NIAID NIH HHS/United States ; T32 GM007067/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Ecosystem ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Host Specificity ; Humans ; Metagenome/*genetics ; Microbiota/*genetics ; }, abstract = {The composite members of the microbiota face a range of selective pressures and must adapt to persist in the host. We highlight recent work characterizing the evolution and transfer of genetic information across nested scales of host-associated microbiota, which enable resilience to biotic and abiotic perturbations. At the strain level, we consider the preservation and diversification of adaptive information in progeny lineages. At the community level, we consider genetic exchange between distinct microbes in the ecosystem. Finally, we frame microbiomes as open systems subject to acquisition of novel information from foreign ecosystems through invasion by outsider microbes.}, } @article {pmid29522739, year = {2018}, author = {Blaser, MJ}, title = {The Past and Future Biology of the Human Microbiome in an Age of Extinctions.}, journal = {Cell}, volume = {172}, number = {6}, pages = {1173-1177}, doi = {10.1016/j.cell.2018.02.040}, pmid = {29522739}, issn = {1097-4172}, support = {U01 AI122285/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/administration & dosage ; Biology/*methods/trends ; Drug Resistance, Bacterial/genetics ; Gastrointestinal Tract/embryology/growth & development/*microbiology ; Genetic Variation ; *Host Microbial Interactions ; Humans ; Metagenome/*genetics ; Microbiota/*physiology ; }, abstract = {The evolutionary fate of humans is intimately linked with that of our microbiome. Medical and technological advances have caused large-scale changes in the composition and maturation of human-associated microbial communities, increasing our susceptibility to infectious and developmental diseases. Restoration of the human microbiome must become a priority for biomedicine.}, } @article {pmid29521257, year = {2018}, author = {Cano, RJ and Toranzos, GA}, title = {Future Technologies.}, journal = {Microbiology spectrum}, volume = {6}, number = {2}, pages = {}, pmid = {29521257}, issn = {2165-0497}, mesh = {Computational Biology/methods/standards ; Data Analysis ; *Environmental Microbiology ; Environmental Monitoring/*methods/*standards ; Forensic Genetics/*methods/*standards ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods/standards ; Microbiota/*genetics/physiology ; Quality Control ; Reproducibility of Results ; Research ; Research Design ; }, abstract = {Microbiome analysis of environmental samples may represent the next frontier in environmental microbial forensics. Next-generation sequencing technologies significantly increased the available genetic data that could be used as evidentiary material. It is not clear, however, whether the microbiome can scale across institutions using forensic-based evidence due to the data resource requirements and the associated costs of maintaining these databases. A successful microbiome study is impacted by the quality of the information gathered and the steps in sample processing and data analysis. To ascertain the validity of methods and the results obtained, there needs to be a stringent procedure to validate the methods and ensure that the results are comparable and reproducible, not only within the laboratory but also between laboratories conducting similar research. Of primary importance for meaningful microbiome studies is an experimental design that leads to carefully executed, controlled, and reproducible studies. The microbiome literature contains a fair share of anecdotal descriptions of microbial community composition and "diagnostic" relative abundance of the taxa therein. These studies are now being supplemented by experimental designs that feature repeated measurements, error estimates, correlations of microbiota with covariates, and increasingly sophisticated statistical tests that enhance the robustness of data analysis and study conclusions. It is imperative to be careful, especially when carrying out attribution studies, to be fully aware of the possible biases included in a specific sample being analyzed.}, } @article {pmid29520598, year = {2018}, author = {Huang, W and Cheng, Z and Lei, S and Liu, L and Lv, X and Chen, L and Wu, M and Wang, C and Tian, B and Song, Y}, title = {Community composition, diversity, and metabolism of intestinal microbiota in cultivated European eel (Anguilla anguilla).}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {9}, pages = {4143-4157}, doi = {10.1007/s00253-018-8885-9}, pmid = {29520598}, issn = {1432-0614}, support = {2017J01625//the Department of Science and Technology of Fujian Province/ ; 31670125//the National Natural Science Foundation of China/ ; 2016PI-18//the Innovation Program of Fujian Academy of Agricultural Sciences/ ; 2015R1025-8//the Special Scientific Research Funds for Public Scientific Research Institution of Fujian/ ; 2014J01111//the department of science and technology of fujian province/ ; }, mesh = {Anguilla/*microbiology ; Animals ; Bacteria/*classification/genetics/*metabolism ; Biodiversity ; *Gastrointestinal Microbiome ; Intestines/microbiology ; Metagenome/genetics ; Phylogeny ; }, abstract = {The intestinal tract, which harbours tremendous numbers of bacteria, plays a pivotal role in the digestion and absorption of nutrients. Here, high-throughput sequencing technology was used to determine the community composition and complexity of the intestinal microbiota in cultivated European eels during three stages of their lifecycle, after which the metabolic potentials of their intestinal microbial communities were assessed. The results demonstrated that European eel intestinal microbiota were dominated by bacteria in the phyla Proteobacteria and Fusobacteria. Statistical analyses revealed that the three cultured European eel life stages (elver, yellow eel, and silver eel) shared core microbiota dominated by Aeromonas. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predictions of metagenome function revealed that the European eel intestinal microbiota might play significant roles in host nutrient metabolism. Biolog AN MicroPlate™ analysis and extracellular enzyme assays of culturable intestinal bacteria showed that the intestinal microbiota have a marked advantage in the metabolism of starch, which is the main carbohydrate component in European eel formulated feed. Understanding the ecology and functions of the intestinal microbiota during different developmental stages will help us improve the effects of fish-based bacteria on the composition and metabolic capacity of nutrients in European eels.}, } @article {pmid29518419, year = {2018}, author = {Fazlollahi, M and Lee, TD and Andrade, J and Oguntuyo, K and Chun, Y and Grishina, G and Grishin, A and Bunyavanich, S}, title = {The nasal microbiome in asthma.}, journal = {The Journal of allergy and clinical immunology}, volume = {142}, number = {3}, pages = {834-843.e2}, pmid = {29518419}, issn = {1097-6825}, support = {K08 AI093538/AI/NIAID NIH HHS/United States ; R01 AI118833/AI/NIAID NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Asthma/*microbiology ; Bacteria/genetics/isolation & purification ; Child ; Female ; Humans ; Male ; *Microbiota/genetics ; Middle Aged ; Nose/*microbiology ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {BACKGROUND: Nasal microbiota may influence asthma pathobiology.

OBJECTIVE: We sought to characterize the nasal microbiome of subjects with exacerbated asthma, nonexacerbated asthma, and healthy controls to identify nasal microbiota associated with asthma activity.

METHODS: We performed 16S ribosomal RNA sequencing on nasal swabs obtained from 72 primarily adult subjects with exacerbated asthma (n = 20), nonexacerbated asthma (n = 31), and healthy controls (n = 21). Analyses were performed using Quantitative Insights into Microbial (QIIME); linear discriminant analysis effect size (LEfSe); Phylogenetic Investigation of Communities by Reconstruction of Unobserved States; and Statistical Analysis of Metagenomic Profiles (PICRUSt); and Statistical Analysis of Metagenomic Profiles (STAMP). Species found to be associated with asthma activity were validated using quantitative PCR. Metabolic pathways associated with differentially abundant nasal taxa were inferred through metagenomic functional prediction.

RESULTS: Nasal bacterial composition significantly differed among subjects with exacerbated asthma, nonexacerbated asthma, and healthy controls (permutational multivariate ANOVA, P = 2.2 × 10[-2]). Relative to controls, the nasal microbiota of subjects with asthma were enriched with taxa from Bacteroidetes (Wilcoxon-Mann-Whitney, r = 0.33, P = 5.1 × 10[-3]) and Proteobacteria (r = 0.29, P = 1.4 × 10[-2]). Four species were differentially abundant based on asthma status after correction for multiple comparisons: Prevotella buccalis, Padj = 1.0 × 10[-2]; Dialister invisus, Padj = 9.1 × 10[-3]; Gardnerella vaginalis, Padj = 2.8 × 10[-3]; Alkanindiges hongkongensis, Padj = 2.6 × 10[-3]. These phyla and species were also differentially abundant based on asthma activity (exacerbated asthma vs nonexacerbated asthma vs controls). Quantitative PCR confirmed species overrepresentation in asthma relative to controls for Prevotella buccalis (fold change = 130, P = 2.1 × 10[-4]) and Gardnerella vaginalis (fold change = 160, P = 6.8 × 10[-4]). Metagenomic inference revealed differential glycerolipid metabolism (Kruskal-Wallis, P = 1.9 × 10[-4]) based on asthma activity.

CONCLUSIONS: Nasal microbiome composition differs in subjects with exacerbated asthma, nonexacerbated asthma, and healthy controls. The identified nasal taxa could be further investigated for potential mechanistic roles in asthma and as possible biomarkers of asthma activity.}, } @article {pmid29518346, year = {2018}, author = {Solbiati, J and Frias-Lopez, J}, title = {Metatranscriptome of the Oral Microbiome in Health and Disease.}, journal = {Journal of dental research}, volume = {97}, number = {5}, pages = {492-500}, pmid = {29518346}, issn = {1544-0591}, support = {R01 DE021553/DE/NIDCR NIH HHS/United States ; }, mesh = {Chronic Periodontitis/microbiology ; Dental Caries/microbiology ; Dental Plaque/microbiology ; Gene Expression Profiling ; Humans ; Microbiota/*genetics ; Mouth/*microbiology ; Mouth Diseases/*microbiology ; *Transcriptome ; }, abstract = {The last few decades have witnessed an increasing interest in studying the human microbiome and its role in health and disease. The focus of those studies was mainly the characterization of changes in the composition of the microbial communities under different conditions. As a result of those studies, we now know that imbalance in the composition of the microbiome, also referred to as microbial dysbiosis, is directly linked to developing certain conditions. Dysbiosis of the oral microbiome is a prime example of how this imbalance leads to disease in the case of periodontal disease. However, there is considerable overlap in the phylogenetic profiles of microbial communities associated with active and inactive lesions, suggesting that the difference in periodontal status of those sites may not be explained solely by differences in the subgingival microbial composition. These findings suggest that differences in functional activities may be the essential elements that define the dysbiotic process. Researchers have recently begun to study gene expression of the oral microbiome in situ with the goal of identifying changes in functional activities that could explain the transition from health to disease. These initial results suggest that, rather than a specific composition, a better understanding of oral dysbiosis can be obtained from the study of functional activities of the microbial community. In this review, we give a summary of these initial studies, which have opened a new door to our understanding of the dynamics of the oral community during the dysbiotic process in the oral cavity.}, } @article {pmid29516462, year = {2018}, author = {Richarte, V and Rosales, K and Corrales, M and Bellina, M and Fadeuilhe, C and Calvo, E and Ibanez, P and Sanchez-Mora, C and Ribases, M and Ramos-Quiroga, JA}, title = {[The gut-brain axis in attention deficit hyperactivity disorder: the role of the microbiota].}, journal = {Revista de neurologia}, volume = {66}, number = {S01}, pages = {S109-S114}, pmid = {29516462}, issn = {1576-6578}, mesh = {Adult ; Attention Deficit Disorder with Hyperactivity/*microbiology/physiopathology ; Autonomic Nervous System/physiopathology ; Brain/*physiopathology ; Cross-Sectional Studies ; Diet ; Feces/microbiology ; Feeding Behavior ; Female ; Gastrointestinal Microbiome/*physiology ; Genome, Bacterial ; Hippocampus/metabolism ; Humans ; Interview, Psychological ; Male ; Neuropeptides/metabolism ; Solitary Nucleus/physiopathology ; Species Specificity ; Wechsler Scales ; }, abstract = {INTRODUCTION: Attention deficit hyperactivity disorder (ADHD) has a complex aetiology, mainly attributed to a number of susceptibility genes and environmental factors. Genetic association studies, however, have been inconsistent and have identified genetic variants with a moderate effect that explain a small proportion of the estimated inheritability of the disorder (< 10%). Recent studies suggest that the gut microbiota and diet play an important role in the development and symptoms of different mental disorders. Nevertheless, no clear evidence exists on the issue. This project proposes an alternative approach to identify mechanisms by which the intestinal microbial ecosystem and diet could contribute to the presence of ADHD.

AIM: To identify biomarkers for ADHD by examining the gut microbiota.

SUBJECTS AND METHODS: We conducted a cross-sectional study of adult patients with ADHD (n = 100) and control subjects (n = 100). Measures of ADHD evaluation and eating habits were performed in both groups. Samples of faecal material were obtained from which to extract bacterial DNA, then used to characterise the participants' gut microbiota. A meta-genomic association study was later performed to attempt to correlate the bacterial composition of the intestine with the clinical subtypes of the disorder.

RESULTS AND CONCLUSIONS: Comparing the gut microbiota profiles of subjects with ADHD and controls is expected to help account for the clinical heterogeneity of the disorder and identify new mechanisms involved in its development.}, } @article {pmid29515974, year = {2018}, author = {Ewan, VC and Reid, WDK and Shirley, M and Simpson, AJ and Rushton, SP and Wade, WG}, title = {Oropharyngeal Microbiota in Frail Older Patients Unaffected by Time in Hospital.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {42}, pmid = {29515974}, issn = {2235-2988}, support = {G0800440/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Aged ; Aged, 80 and over ; Biodiversity ; Carrier State/*epidemiology ; Cross Infection/epidemiology/microbiology ; Female ; *Geriatric Assessment ; *Hospitalization ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Oropharynx/*microbiology ; Pharyngitis/epidemiology/microbiology ; Time Factors ; }, abstract = {Respiratory tract infections are the commonest nosocomial infections, and occur predominantly in frailer, older patients with multiple comorbidities. The oropharyngeal microbiota is the major reservoir of infection. This study explored the relative contributions of time in hospital and patient demographics to the community structure of the oropharyngeal microbiota in older patients with lower limb fracture. We collected 167 throat swabs from 53 patients (mean age 83) over 14 days after hospitalization, and analyzed these using 16S rRNA gene sequencing. We calculated frailty/comorbidity indices, undertook dental examinations and collected data on respiratory tract infections. We analyzed microbial community composition using correspondence (CA) and canonical correspondence analysis. Ten patients were treated for respiratory tract infection. Microbial community structure was related to frailty, number of teeth and comorbidity on admission, with comorbidity exerting the largest effect. Time in hospital neither significantly changed alpha (t = -0.910, p = 0.365) nor beta diversity (CA1 t = 0.022, p = 0.982; CA2 t = -0.513, p = 0.609) of microbial communities in patient samples. Incidence of respiratory pathogens were not associated with time in hospital (t = -0.207, p = 0.837), nor with alpha diversity of the oral microbiota (t = -1.599, p = 0.113). Patient characteristics at admission, rather than time in hospital, influenced the community structure of the oral microbiota.}, } @article {pmid29515540, year = {2018}, author = {Cuadrat, RRC and Ionescu, D and Dávila, AMR and Grossart, HP}, title = {Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome-Resolved Metagenomics.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {251}, pmid = {29515540}, issn = {1664-302X}, abstract = {Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem.}, } @article {pmid29515151, year = {2018}, author = {Jones, RB and Zhu, X and Moan, E and Murff, HJ and Ness, RM and Seidner, DL and Sun, S and Yu, C and Dai, Q and Fodor, AA and Azcarate-Peril, MA and Shrubsole, MJ}, title = {Inter-niche and inter-individual variation in gut microbial community assessment using stool, rectal swab, and mucosal samples.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {4139}, pmid = {29515151}, issn = {2045-2322}, support = {UL1 TR000445/TR/NCATS NIH HHS/United States ; R01 CA149633/CA/NCI NIH HHS/United States ; R01 DK110166/DK/NIDDK NIH HHS/United States ; R03 CA183019/CA/NCI NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; UL1 RR024975/RR/NCRR NIH HHS/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/*classification/*genetics ; Double-Blind Method ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Intestinal Mucosa/*microbiology ; Male ; *Metagenome ; Middle Aged ; }, abstract = {The purpose of this study is to evaluate similarities and differences in gut bacterial measurements and stability in the microbial communities of three different types of samples that could be used to assess different niches of the gut microbiome: rectal swab, stool, and normal rectal mucosa samples. In swab-stool comparisons, there were substantial taxa differences with some taxa varying largely by sample type (e.g. Thermaceae), inter-individual subject variation (e.g. Desulfovibrionaceae), or by both sample type and participant (e.g. Enterobacteriaceae). Comparing all three sample types with whole-genome metagenome shotgun sequencing, swab samples were much closer to stool samples than mucosa samples although all KEGG functional Level 1 and Level 2 pathways were significantly different across all sample types (e.g. transcription and environmental adaptation). However, the individual signature of participants was also observed and was largely stable between two time points. Thus, we found that while the distribution of some taxa was associated with these different sampling techniques, other taxa largely reflected individual differences in the microbial community that were insensitive to sampling technique. There is substantial variability in the assessment of the gut microbial community according to the type of sample.}, } @article {pmid29513935, year = {2018}, author = {Lopez-Oliva, I and Paropkari, AD and Saraswat, S and Serban, S and Yonel, Z and Sharma, P and de Pablo, P and Raza, K and Filer, A and Chapple, I and Dietrich, T and Grant, MM and Kumar, PS}, title = {Dysbiotic Subgingival Microbial Communities in Periodontally Healthy Patients With Rheumatoid Arthritis.}, journal = {Arthritis & rheumatology (Hoboken, N.J.)}, volume = {70}, number = {7}, pages = {1008-1013}, pmid = {29513935}, issn = {2326-5205}, support = {R01 DE022579/DE/NIDCR NIH HHS/United States ; U01 CA188250/CA/NCI NIH HHS/United States ; PB-PG-0609-19100//Department of Health/United Kingdom ; DRF-2014-07-109//Department of Health/United Kingdom ; PDF-2014-07-055//Department of Health/United Kingdom ; }, mesh = {Adult ; Arthritis, Rheumatoid/*microbiology ; Case-Control Studies ; Citrulline/biosynthesis ; Dysbiosis/*microbiology ; Female ; Gingiva/*microbiology ; Humans ; Male ; Microbiota/physiology ; Middle Aged ; }, abstract = {OBJECTIVE: Studies that demonstrate an association between rheumatoid arthritis (RA) and dysbiotic oral microbiomes are often confounded by the presence of extensive periodontitis in these individuals. This study was undertaken to investigate the role of RA in modulating the periodontal microbiome by comparing periodontally healthy individuals with RA to those without RA.

METHODS: Subgingival plaque was collected from periodontally healthy individuals (22 with RA and 19 without RA), and the 16S gene was sequenced on an Illumina MiSeq platform. Bacterial biodiversity and co-occurrence patterns were examined using the QIIME and PhyloToAST pipelines.

RESULTS: The subgingival microbiomes differed significantly between patients with RA and controls based on both community membership and the abundance of lineages, with 41.9% of the community differing in abundance and 19% in membership. In contrast to the sparse and predominantly congeneric co-occurrence networks seen in controls, RA patients revealed a highly connected grid containing a large intergeneric hub anchored by known periodontal pathogens. Predictive metagenomic analysis (PICRUSt) demonstrated that arachidonic acid and ester lipid metabolism pathways might partly explain the robustness of this clustering. As expected from a periodontally healthy cohort, Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans were not significantly different between groups; however, Cryptobacterium curtum, another organism capable of producing large amounts of citrulline, emerged as a robust discriminant of the microbiome in individuals with RA.

CONCLUSION: Our data demonstrate that the oral microbiome in RA is enriched for inflammophilic and citrulline-producing organisms, which may play a role in the production of autoantigenic citrullinated peptides in RA.}, } @article {pmid29511840, year = {2018}, author = {Gadhave, KR and Devlin, PF and Ebertz, A and Ross, A and Gange, AC}, title = {Soil Inoculation with Bacillus spp. Modifies Root Endophytic Bacterial Diversity, Evenness, and Community Composition in a Context-Specific Manner.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {741-750}, pmid = {29511840}, issn = {1432-184X}, mesh = {Agricultural Inoculants/classification/physiology ; Bacillus/classification/*physiology ; Bacteria/classification/genetics/isolation & purification ; *Biodiversity ; Brassica/growth & development/*microbiology ; Endophytes/classification/genetics/*isolation & purification ; Phylogeny ; Plant Roots/growth & development/*microbiology ; *Soil Microbiology ; Species Specificity ; }, abstract = {The use of microbial inoculants containing plant growth-promoting rhizobacteria as a promoter of plant fitness and health is becoming increasingly popular in agriculture. However, whether and how these bacteria affect indigenous bacterial communities in field conditions is sparsely explored. We studied the effects of seed inoculation and field soil application of ubiquitous soil bacteria, B. cereus, B. subtilis, and B. amyloliquefaciens, on the diversity, evenness, and richness of endophytic bacterial communities in sprouting broccoli roots using high-throughput metagenome sequencing. The multiple operational taxonomic units (OTUs) assigned to different bacterial taxa clearly showed changes in ecological measures and relative abundances of certain taxa between control and treatment groups. The Bacillus inocula, themselves, failed to flourish as endophytes; however, the effects they extended on the endophytic bacterial community were both generic as well as species specific. In each case, Pseudomonadales, Rhizobiales, Xanthomonadales, and Burkholderiales were the most abundant orders in the endosphere. B. amyloliquefaciens drastically reduced the most abundant genus, Pseudomonas, while increasing the relative abundance of a range of minor taxa. The Shannon-Weiner diversity and Buzas and Gibson's evenness indices showed that the diversity and evenness were increased in both B. amyloliquefaciens and mixed treated plants. The UniFrac measurement of beta diversity showed that all treatments affected the specific composition of the endophytic bacterial community, with an apparent interspecies competition in the mixed treatment. Taken together, Bacillus species influenced the diversity, evenness, and composition of the endophytic bacterial community. However, these effects varied between different Bacillus spp. in a context-specific manner.}, } @article {pmid29511208, year = {2018}, author = {Ericsson, AC and Gagliardi, J and Bouhan, D and Spollen, WG and Givan, SA and Franklin, CL}, title = {The influence of caging, bedding, and diet on the composition of the microbiota in different regions of the mouse gut.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {4065}, pmid = {29511208}, issn = {2045-2322}, support = {K01 OD019924/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Animal Husbandry/*methods ; Animals ; Diet/*methods ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Metagenomics ; Mice ; Models, Animal ; Reproducibility of Results ; }, abstract = {Countless studies have identified differences between the gut microbiota of humans affected with myriad conditions and healthy individuals, and animal models are commonly used to determine whether those differences are causative or correlative. Recently, concerns have arisen regarding the reproducibility of animal models between institutions and across time. To determine the influence of three common husbandry-associated factors that vary between institutions, groups of weanling mice were placed in either static or ventilated microisolator caging, with either aspen or paperchip bedding, and with one of three commonly used rodent chows, in a fully crossed study design. After thirteen weeks, samples were collected from multiple regions of the gastrointestinal tract and characterized using culture-independent sequencing methods. Results demonstrated that seemingly benign husbandry factors can interact to induce profound changes in the composition of the microbiota present in certain regions of the gut, most notably the cecum, and that those changes are muted during colonic transit. These findings indicate that differences in factors such as caging and bedding can interact to modulate the gut microbiota that in turn may affect reproducibility of some animal models, and that cecal samples might be optimal when screening environmental effects on the gut microbiota.}, } @article {pmid29511180, year = {2018}, author = {Hu, Y and Sanders, JG and Łukasik, P and D'Amelio, CL and Millar, JS and Vann, DR and Lan, Y and Newton, JA and Schotanus, M and Kronauer, DJC and Pierce, NE and Moreau, CS and Wertz, JT and Engel, P and Russell, JA}, title = {Herbivorous turtle ants obtain essential nutrients from a conserved nitrogen-recycling gut microbiome.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {964}, pmid = {29511180}, issn = {2041-1723}, mesh = {Amino Acids/metabolism ; Ammonia/metabolism ; Animals ; Ants/*microbiology/*physiology ; Diet ; *Gastrointestinal Microbiome/genetics ; Geography ; Herbivory/*physiology ; Metagenome ; Metagenomics ; Nitrogen/*metabolism ; Nitrogen Fixation/genetics ; Nitrogen Isotopes ; Symbiosis ; Urea/metabolism ; Urease/metabolism ; Uric Acid/metabolism ; }, abstract = {Nitrogen acquisition is a major challenge for herbivorous animals, and the repeated origins of herbivory across the ants have raised expectations that nutritional symbionts have shaped their diversification. Direct evidence for N provisioning by internally housed symbionts is rare in animals; among the ants, it has been documented for just one lineage. In this study we dissect functional contributions by bacteria from a conserved, multi-partite gut symbiosis in herbivorous Cephalotes ants through in vivo experiments, metagenomics, and in vitro assays. Gut bacteria recycle urea, and likely uric acid, using recycled N to synthesize essential amino acids that are acquired by hosts in substantial quantities. Specialized core symbionts of 17 studied Cephalotes species encode the pathways directing these activities, and several recycle N in vitro. These findings point to a highly efficient N economy, and a nutritional mutualism preserved for millions of years through the derived behaviors and gut anatomy of Cephalotes ants.}, } @article {pmid29507058, year = {2018}, author = {Kim, S and Goel, R and Kumar, A and Qi, Y and Lobaton, G and Hosaka, K and Mohammed, M and Handberg, EM and Richards, EM and Pepine, CJ and Raizada, MK}, title = {Imbalance of gut microbiome and intestinal epithelial barrier dysfunction in patients with high blood pressure.}, journal = {Clinical science (London, England : 1979)}, volume = {132}, number = {6}, pages = {701-718}, pmid = {29507058}, issn = {1470-8736}, support = {R01 HL033610/HL/NHLBI NIH HHS/United States ; R01 HL056921/HL/NHLBI NIH HHS/United States ; R01 HL132448/HL/NHLBI NIH HHS/United States ; R37 HL033610/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/immunology/*metabolism ; *Blood Pressure ; Butyrates/blood ; Case-Control Studies ; Cholera Toxin/blood ; Disease Models, Animal ; Epithelial Cells/immunology/metabolism/*microbiology ; Fatty Acid-Binding Proteins/blood ; Feces/microbiology ; *Gastrointestinal Microbiome ; Haptoglobins ; Host-Pathogen Interactions ; Humans ; Hypertension/blood/immunology/*microbiology/physiopathology ; Intestinal Mucosa/immunology/metabolism/*microbiology/physiopathology ; Lipopolysaccharides/blood ; Mice, Inbred C57BL ; Permeability ; Protein Precursors ; Rats, Sprague-Dawley ; Th17 Cells/immunology/metabolism ; }, abstract = {Recent evidence indicates a link between gut pathology and microbiome with hypertension (HTN) in animal models. However, whether this association exists in humans is unknown. Thus, our objectives in the present study were to test the hypotheses that high blood pressure (BP) patients have distinct gut microbiomes and that gut-epithelial barrier function markers and microbiome composition could predict systolic BP (SBP). Fecal samples, analyzed by shotgun metagenomics, displayed taxonomic and functional changes, including altered butyrate production between patients with high BP and reference subjects. Significant increases in plasma of intestinal fatty acid binding protein (I-FABP), lipopolysaccharide (LPS), and augmented gut-targetting proinflammatory T helper 17 (Th17) cells in high BP patients demonstrated increased intestinal inflammation and permeability. Zonulin, a gut epithelial tight junction protein regulator, was markedly elevated, further supporting gut barrier dysfunction in high BP. Zonulin strongly correlated with SBP (R[2] = 0.5301, P<0.0001). Two models predicting SBP were built using stepwise linear regression analysis of microbiome data and circulating markers of gut health, and validated in a separate cohort by prediction of SBP from zonulin in plasma (R[2] = 0.4608, P<0.0001). The mouse model of HTN, chronic angiotensin II (Ang II) infusion, was used to confirm the effects of butyrate and gut barrier function on the cardiovascular system and BP. These results support our conclusion that intestinal barrier dysfunction and microbiome function are linked to HTN in humans. They suggest that manipulation of gut microbiome and its barrier functions could be the new therapeutic and diagnostic avenues for HTN.}, } @article {pmid29504486, year = {2018}, author = {Rintala, A and Riikonen, I and Toivonen, A and Pietilä, S and Munukka, E and Pursiheimo, JP and Elo, LL and Arikoski, P and Luopajärvi, K and Schwab, U and Uusitupa, M and Heinonen, S and Savilahti, E and Eerola, E and Ilonen, J}, title = {Early fecal microbiota composition in children who later develop celiac disease and associated autoimmunity.}, journal = {Scandinavian journal of gastroenterology}, volume = {53}, number = {4}, pages = {403-409}, doi = {10.1080/00365521.2018.1444788}, pmid = {29504486}, issn = {1502-7708}, mesh = {Autoantibodies/blood ; Autoimmunity ; Case-Control Studies ; Celiac Disease/genetics/*microbiology ; Child, Preschool ; Duodenum/microbiology ; Feces/*microbiology ; Female ; Finland ; Gastrointestinal Microbiome/*genetics ; Humans ; Infant ; Metagenome ; RNA, Ribosomal, 16S/*analysis ; }, abstract = {OBJECTIVES: Several studies have reported that the intestinal microbiota composition of celiac disease (CD) patients differs from healthy individuals. The possible role of gut microbiota in the pathogenesis of the disease is, however, not known. Here, we aimed to assess the possible differences in early fecal microbiota composition between children that later developed CD and healthy controls matched for age, sex and HLA risk genotype.

MATERIALS AND METHODS: We used 16S rRNA gene sequencing to examine the fecal microbiota of 27 children with high genetic risk of developing CD. Nine of these children developed the disease by the age of 4 years. Stool samples were collected at the age of 9 and 12 months, before any of the children had developed CD. The fecal microbiota composition of children who later developed the disease was compared with the microbiota of the children who did not have CD or associated autoantibodies at the age of 4 years. Delivery mode, early nutrition, and use of antibiotics were taken into account in the analyses.

RESULTS: No statistically significant differences in the fecal microbiota composition were found between children who later developed CD (n = 9) and the control children without disease or associated autoantibodies (n = 18).

CONCLUSIONS: Based on our results, the fecal microbiota composition at the age of 9 and 12 months is not associated with the development of CD. Our results, however, do not exclude the possibility of duodenal microbiota changes or a later microbiota-related trigger for the disease.}, } @article {pmid29501688, year = {2018}, author = {Ravi, A and Avershina, E and Angell, IL and Ludvigsen, J and Manohar, P and Padmanaban, S and Nachimuthu, R and Snipen, L and Rudi, K}, title = {Comparison of reduced metagenome and 16S rRNA gene sequencing for determination of genetic diversity and mother-child overlap of the gut associated microbiota.}, journal = {Journal of microbiological methods}, volume = {149}, number = {}, pages = {44-52}, doi = {10.1016/j.mimet.2018.02.016}, pmid = {29501688}, issn = {1872-8359}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*classification/*genetics ; Cohort Studies ; DNA, Bacterial/genetics/isolation & purification ; Drug Resistance, Bacterial/genetics ; Female ; Gastrointestinal Microbiome/drug effects/*genetics ; Genes, Bacterial/genetics ; *Genetic Variation ; Humans ; Infant, Newborn ; Metagenome/*genetics ; Metagenomics/methods ; *Mother-Child Relations ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {Use of the 16S rRNA gene in microbiota studies is limited by the lack of taxonomic and functional resolution. High resolution analyses are particularly important for understanding transmission and persistence of bacteria. The aim of our work was therefore to compare a novel reduced metagenome sequencing (RMS) approach with 16S rRNA gene sequencing to determine both the metagenome genetic diversity and the mother-to-child sharing of the microbiota in a cohort of 17 mother-child pairs. We found that although both approaches gave comparable results with respect to sample separation and taxonomy, RMS gave higher resolution and the potential for genomic-/functional assignment. Using RMS we estimated that the metagenome size increased from about 60 Mbp for 4-day-old children to about 225 Mbp for mothers. The 4-day-old children shared 7% of the metagenome sequences with the mothers, while the metagenome sequence sharing was >30% among the mothers. We found 15 genomes shared across >50% of the mothers, of which 10 belonged to Clostridia. Only Bacteroides showed a direct mother-child association, with B. vulgatus being abundant in both 4-day-old children and mothers. For the functional assignments, we identified a significant association between antibiotic usage during labor, and quantity of Fosfomycin resistance genes. In conclusion, our results show a higher functional and taxonomic resolution for RMS compared to 16S rRNA gene sequencing, where RMS enabled a detailed description of mother to child gut microbiota transmission - supporting a late recruitment of most gut bacteria and an effect of antibiotic treatment during labor on infant antibiotic resistance gene patterns.}, } @article {pmid29500976, year = {2018}, author = {Tang, X and Guo, Y and Jiang, B and Liu, S}, title = {Metagenomic approaches to understanding bacterial communication during the anammox reactor start-up.}, journal = {Water research}, volume = {136}, number = {}, pages = {95-103}, doi = {10.1016/j.watres.2018.02.054}, pmid = {29500976}, issn = {1879-2448}, mesh = {Ammonium Compounds/*metabolism ; Anaerobiosis ; Bacteria/genetics/*isolation & purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Bioreactors/*microbiology ; Metagenomics ; Nitrogen/chemistry ; Wastewater/chemistry/*microbiology ; }, abstract = {Increasing attention has been paid to the anammox community for its significant function in high-efficiency wastewater treatment. However, bacterial interaction in terms of bacterial communication is still elusive. This study firstly explored the intra- and interspecific communication of bacteria in the anammox community using metagenomic sequence data obtained during bioreactor operation. We verified the existence of multiple bacterial communication gene (BCG) subtypes by alignment with the constructed BCG database containing 11 identified gene subtypes. Bacterial communication was more active at the initial start-up than in the high loading-rate phase, and was correlated with the gradually decreasing bacterial diversity. Hdts, one of the key genes that produced the intraspecific signaling molecule AHL, and RpfF, the key gene that produced the intra- and interspecific signaling molecule DSF, were the primary communication engines in the anammox community because of their high abundance. Anammox bacteria mainly used Hdts genes to communicate with others, while RpfF gene played a core role characterized by their multiple correlations with other BCG subtypes. Interestingly, bacteria with abundant BCGs were more inclined to interact with the bacteria with the same functional traits, indicating the potential communication-related interaction among these bacteria in addition to the frequently reported substrate co-utilization. This highlights the primary importance of AHL and DSF for the anammox community, and thereby hints at a potential strategy for the target regulation of the signals to improve anammox viability and competitive capacity in wastewater treatment.}, } @article {pmid29500689, year = {2018}, author = {Xia, H and Wang, Y and Shi, C and Atoni, E and Zhao, L and Yuan, Z}, title = {Comparative Metagenomic Profiling of Viromes Associated with Four Common Mosquito Species in China.}, journal = {Virologica Sinica}, volume = {33}, number = {1}, pages = {59-66}, pmid = {29500689}, issn = {1995-820X}, mesh = {Animals ; *Biodiversity ; China ; Culicidae/*virology ; Host Specificity ; *Metagenomics ; Mosquito Vectors/*virology ; Viral Tropism ; Viruses/*classification/genetics/*isolation & purification ; }, abstract = {Vast viruses are thought to be associated with mosquitoes. Anopheles sinensis, Armigeres subalbatus, Culex quinquefasciatus, and Culex tritaeniorhynchus are very common mosquito species in China, and whether the virome structure in each species is species-specific has not been evaluated. In this study, a total of 2222 mosquitoes were collected from the same geographic location, and RNAs were sequenced using the Illumina Miseq platform. After querying to the Refseq database, a total of 3,435,781, 2,223,509, 5,727,523, and 6,387,867 paired-end reads were classified under viral sequences from An. sinensis, Ar. subalbatus, Cx. quinquefasciatus, and Cx. tritaeniorhynchus, respectively, with the highest prevalence of virus-associated reads being observed in Cx. quinquefasciatus. The metagenomic comparison analysis showed that the virus-related reads were distributed across 26 virus families, together with an unclassified group of viruses. Anelloviridae, Circoviridae, Genomoviridae, Iridoviridae, Mesoniviridae, Microviridae, Myoviridae, Parvoviridae, Phenuiviridae, and Podoviridae were the top ten significantly different viral families among the four species. Further analysis reveals that the virome is species-specific in four mosquito samples, and several viral sequences which maybe belong to novel viruses are discovered for the first time in those mosquitoes. This investigation provides a basis for a comprehensive knowledge on the mosquito virome status in China.}, } @article {pmid29500262, year = {2018}, author = {Martínez, N and Luque, R and Milani, C and Ventura, M and Bañuelos, O and Margolles, A}, title = {A Gene Homologous to rRNA Methylase Genes Confers Erythromycin and Clindamycin Resistance in Bifidobacterium breve.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {10}, pages = {}, pmid = {29500262}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/*metabolism ; Bifidobacterium breve/*drug effects/*enzymology/genetics ; Clindamycin/*pharmacology ; Drug Resistance, Bacterial ; Erythromycin/*pharmacology ; Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; Humans ; Intestines/microbiology ; Methyltransferases/genetics/*metabolism ; Phylogeny ; }, abstract = {Bifidobacteria are mutualistic intestinal bacteria, and their presence in the human gut has been associated with health-promoting activities. The presence of antibiotic resistance genes in this genus is controversial, since, although bifidobacteria are nonpathogenic microorganisms, they could serve as reservoirs of resistance determinants for intestinal pathogens. However, until now, few antibiotic resistance determinants have been functionally characterized in this genus. In this work, we show that Bifidobacterium breve CECT7263 displays atypical resistance to erythromycin and clindamycin. In order to delimit the genomic region responsible for the observed resistance phenotype, a library of genomic DNA was constructed and a fragment of 5.8 kb containing a gene homologous to rRNA methylase genes was able to confer erythromycin resistance in Escherichia coli This genomic region seems to be very uncommon, and homologs of the gene have been detected in only one strain of Bifidobacterium longum and two other strains of B. breve In this context, analysis of shotgun metagenomics data sets revealed that the gene is also uncommon in the microbiomes of adults and infants. The structural gene and its upstream region were cloned into a B. breve-sensitive strain, which became resistant after acquiring the genetic material. In vitro conjugation experiments did not allow us to detect gene transfer to other recipients. Nevertheless, prediction of genes potentially acquired through horizontal gene transfer events revealed that the gene is located in a putative genomic island.IMPORTANCEBifidobacterium breve is a very common human intestinal bacterium. Often described as a pioneer microorganism in the establishment of early-life intestinal microbiota, its presence has been associated with several beneficial effects for the host, including immune stimulation and protection against infections. Therefore, some strains of this species are considered probiotics. In relation to this, because probiotic bacteria are used for human and animal consumption, one of the safety concerns over these bacteria is the presence of antibiotic resistance genes, since the human gut is a densely populated habitat that could favor the transfer of genetic material to potential pathogens. In this study, we analyzed the genetic basis responsible for the erythromycin and clindamycin resistance phenotype of B. breve CECT7263. We were able to identify and characterize a novel gene homologous to rRNA methylase genes which confers erythromycin and clindamycin resistance. This gene seems to be very uncommon in other bifidobacteria and in the gut microbiomes of both adults and infants. Even though conjugation experiments showed the absence of transferability under in vitro conditions, it has been predicted to be located in a putative genomic island recently acquired by specific bifidobacterial strains.}, } @article {pmid29499759, year = {2018}, author = {Eng, A and Borenstein, E}, title = {Taxa-function robustness in microbial communities.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {45}, pmid = {29499759}, issn = {2049-2618}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; DP2 AT007802-01//National Institutes of Health (US)/International ; }, mesh = {Bacteria/*classification/*genetics ; Biodiversity ; Cellular Microenvironment/*physiology ; Computer Simulation ; Environment ; Female ; Gastrointestinal Tract/microbiology ; Humans ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Vagina/microbiology ; }, abstract = {BACKGROUND: The species composition of a microbial community is rarely fixed and often experiences fluctuations of varying degrees and at varying frequencies. These perturbations to a community's taxonomic profile naturally also alter the community's functional profile-the aggregate set of genes encoded by community members-ultimately altering the community's overall functional capacities. The magnitude of such functional changes and the specific shift that will occur in each function, however, are strongly dependent on how genes are distributed across community members' genomes. This gene distribution, in turn, is determined by the taxonomic composition of the community and would markedly differ, for example, between communities composed of species with similar genomic content vs. communities composed of species whose genomes encode relatively distinct gene sets. Combined, these observations suggest that community functional robustness to taxonomic perturbations could vary widely across communities with different compositions, yet, to date, a systematic study of the inherent link between community composition and robustness is lacking.

RESULTS: In this study, we examined how a community's taxonomic composition influences the robustness of that community's functional profile to taxonomic perturbation (here termed taxa-function robustness) across a wide array of environments. Using a novel simulation-based computational model to quantify this taxa-function robustness in host-associated and non-host-associated communities, we find notable differences in robustness between communities inhabiting different body sites, including significantly higher robustness in gut communities compared to vaginal communities that cannot be attributed solely to differences in species richness. We additionally find between-site differences in the robustness of specific functions, some of which are potentially related to site-specific environmental conditions. These taxa-function robustness differences are most strongly associated with differences in overall functional redundancy, though other aspects of gene distribution also influence taxa-function robustness in certain body environments, and are sufficient to cluster communities by environment. Further analysis revealed a correspondence between our robustness estimates and taxonomic and functional shifts observed across human-associated communities.

CONCLUSIONS: Our analysis approach revealed intriguing taxa-function robustness variation across environments and identified features of community and gene distribution that impact robustness. This approach could be further applied for estimating taxa-function robustness in novel communities and for informing the design of synthetic communities with specific robustness requirements.}, } @article {pmid29498741, year = {2018}, author = {Valeriani, F and Crognale, S and Protano, C and Gianfranceschi, G and Orsini, M and Vitali, M and Spica, VR}, title = {Metagenomic analysis of bacterial community in a travertine depositing hot spring.}, journal = {The new microbiologica}, volume = {41}, number = {2}, pages = {126-135}, pmid = {29498741}, issn = {1121-7138}, mesh = {Bacteria/*genetics/isolation & purification ; Biodiversity ; Computational Biology ; DNA, Bacterial/genetics ; Hot Springs/*microbiology ; Metagenomics/*methods ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; }, abstract = {Several factors influence bacteria biodiversity in hot springs. The impact of biotic and abiotic pathways on travertine deposition plays a key role in microbial ecology and in the final composition of the waterborne microbiota. The metabolism of some bacterial groups such as photoautotrophs or lithoautotrophs influences water chemistry, favoring carbonate precipitation processes. The role of microbial mats in mineral precipitation processes is not fully clarified. For the first time, a comprehensive metagenomic analysis has been undertaken in the historical Bullicame hot spring. Bacterial biodiversity was characterized and biomineralization activities were assigned to different genera. A higher biodiversity in mat samples compared to water samples was observed: Shannon index of 3.34 and 0.86, respectively. Based on the functional assignment of each Operational Taxonomic Unit, the bacteria involved in biologically- induced mineralization are prevalent in mat and released in the water. According to the principle that each geothermal water specimen has distinctive physic-chemical characteristics, our results suggest new interacting bio-actions within these ecosystems. The saturation index and the chemical composition, as the high concentration of sulfur species and HCO3, can be linked to create a selective environment where pioneer communities are able to live and shape the ecosystem.}, } @article {pmid29497869, year = {2018}, author = {Tan, Z and Wang, Y and Yang, T and Ao, H and Chen, S and Xing, K and Zhang, F and Zhao, X and Liu, J and Wang, C}, title = {Differences in gut microbiota composition in finishing Landrace pigs with low and high feed conversion ratios.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {9}, pages = {1673-1685}, pmid = {29497869}, issn = {1572-9699}, support = {BAIC02-2016//Beijing Innovation Consortium of Agriculture Research System/ ; }, mesh = {Amino Acids/metabolism ; Animal Feed/*analysis ; Animals ; Bacteria/*classification/genetics ; *Biodiversity ; Carbohydrate Metabolism ; Cecum/microbiology ; Colon/microbiology ; DNA, Bacterial/genetics ; Discriminant Analysis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Intestine, Small/microbiology ; Metabolic Networks and Pathways ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Swine ; }, abstract = {The goal of this study was to evaluate the microbial communities in the gut and feces from female finishing Landrace pigs with high and low feed conversion ratio (FCR) by 16S rRNA gene amplicon sequencing. Many potential biomarkers can distinguish between high and low FCR groups in the duodenum, ileum, cecum, colon, and rectum, according to linear discriminant analysis effect sizes. The relative abundance of microbes were tested by Mann-Whitney test between the high and low FCR groups in different organs: Campylobacter, Prevotella and Sphaerochaeta were different in the duodenum (P < 0.05); Sanguibacter, Kingella and Anaeroplasma in jejunum; Anaeroplasma, Arthrobacter, Kingella, Megasphaera and SMB53 in the ileum; Butyricicoccus, Campylobacter, Mitsuokella, and Coprobacillus in the cecum; Lactococcus and Peptococcus in the colon; Staphylococcus in the rectum; and Rothia in feces. The prevalence of microbial genera in certain locations could potentially be used as biomarkers to distinguish between high and low FCR. Functional prediction clustering analysis suggested that bacteria in the hindgut mainly participated in carbohydrate metabolism and amino acid metabolism, and different in the relative abundance of metabolic pathways, as predicted from the microbial taxa present, were identified by comparing the high and low groups of each location. The results may provide insights for the alteration of the intestinal microbial communities to improve the growth rate of pigs.}, } @article {pmid29497601, year = {2018}, author = {Lin, W and Jiang, W and Hu, X and Gao, L and Ai, D and Pan, H and Niu, C and Yuan, K and Zhou, X and Xu, C and Huang, Z}, title = {Ecological Shifts of Supragingival Microbiota in Association with Pregnancy.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {24}, pmid = {29497601}, issn = {2235-2988}, mesh = {Adult ; *Biodiversity ; Female ; Gingiva/*microbiology ; Hormones ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; Pregnancy ; RNA, Ribosomal, 16S ; Saliva/microbiology ; }, abstract = {Pregnancy is a physiological process with pronounced hormonal fluctuations in females, and relatively little is known regarding how pregnancy influences the ecological shifts of supragingival microbiota. In this study, supragingival plaques and salivary hormones were collected from 11 pregnant women during pregnancy (P1, ≤14 weeks; P2, 20-25 weeks; P3, 33-37 weeks) and the postpartum period (P4, 6 weeks after childbirth). Seven non-pregnant volunteers were sampled at the same time intervals. The microbial genetic repertoire was obtained by 16S rDNA sequencing. Our results indicated that the Shannon diversity in P3 was significantly higher than in the non-pregnant group. The principal coordinates analysis showed distinct clustering according to gestational status, and the partial least squares discriminant analysis identified 33 genera that may contribute to this difference. There were differentially distributed genera, among which Neisseria, Porphyromonas, and Treponema were over-represented in the pregnant group, while Streptococcus and Veillonella were more abundant in the non-pregnant group. In addition, 53 operational taxonomic units were observed to have positive correlations with sex hormones in a redundancy analysis, with Prevotella spp. and Treponema spp. being most abundant. The ecological events suggest that pregnancy has a role in shaping an at-risk-for-harm microbiota and provide a basis for etiological studies of pregnancy-associated oral dysbiosis.}, } @article {pmid29497412, year = {2018}, author = {Garrido-Sanz, D and Manzano, J and Martín, M and Redondo-Nieto, M and Rivilla, R}, title = {Metagenomic Analysis of a Biphenyl-Degrading Soil Bacterial Consortium Reveals the Metabolic Roles of Specific Populations.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {232}, pmid = {29497412}, issn = {1664-302X}, abstract = {Polychlorinated biphenyls (PCBs) are widespread persistent pollutants that cause several adverse health effects. Aerobic bioremediation of PCBs involves the activity of either one bacterial species or a microbial consortium. Using multiple species will enhance the range of PCB congeners co-metabolized since different PCB-degrading microorganisms exhibit different substrate specificity. We have isolated a bacterial consortium by successive enrichment culture using biphenyl (analog of PCBs) as the sole carbon and energy source. This consortium is able to grow on biphenyl, benzoate, and protocatechuate. Whole-community DNA extracted from the consortium was used to analyze biodiversity by Illumina sequencing of a 16S rRNA gene amplicon library and to determine the metagenome by whole-genome shotgun Illumina sequencing. Biodiversity analysis shows that the consortium consists of 24 operational taxonomic units (≥97% identity). The consortium is dominated by strains belonging to the genus Pseudomonas, but also contains betaproteobacteria and Rhodococcus strains. whole-genome shotgun (WGS) analysis resulted in contigs containing 78.3 Mbp of sequenced DNA, representing around 65% of the expected DNA in the consortium. Bioinformatic analysis of this metagenome has identified the genes encoding the enzymes implicated in three pathways for the conversion of biphenyl to benzoate and five pathways from benzoate to tricarboxylic acid (TCA) cycle intermediates, allowing us to model the whole biodegradation network. By genus assignment of coding sequences, we have also been able to determine that the three biphenyl to benzoate pathways are carried out by Rhodococcus strains. In turn, strains belonging to Pseudomonas and Bordetella are the main responsible of three of the benzoate to TCA pathways while the benzoate conversion into TCA cycle intermediates via benzoyl-CoA and the catechol meta-cleavage pathways are carried out by beta proteobacteria belonging to genera such as Achromobacter and Variovorax. We have isolated a Rhodococcus strain WAY2 from the consortium which contains the genes encoding the three biphenyl to benzoate pathways indicating that this strain is responsible for all the biphenyl to benzoate transformations. The presented results show that metagenomic analysis of consortia allows the identification of bacteria active in biodegradation processes and the assignment of specific reactions and pathways to specific bacterial groups.}, } @article {pmid29497066, year = {2018}, author = {Meale, SJ and Auffret, MD and Watson, M and Morgavi, DP and Cantalapiedra-Hijar, G and Duthie, CA and Roehe, R and Dewhurst, RJ}, title = {Fat accretion measurements strengthen the relationship between feed conversion efficiency and Nitrogen isotopic discrimination while rumen microbial genes contribute little.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {3854}, pmid = {29497066}, issn = {2045-2322}, mesh = {Adipose Tissue/metabolism ; Animal Feed/analysis ; Animal Husbandry/methods ; Animal Nutritional Physiological Phenomena ; Animals ; Body Weight ; Breeding ; Cattle ; Diet ; Gastrointestinal Microbiome/*genetics ; Genes, Microbial/genetics ; Metagenomics/methods ; Nitrogen/*metabolism ; Nitrogen Isotopes/metabolism ; Poaceae/metabolism ; Red Meat ; Rumen/microbiology/*physiology ; Silage/analysis ; Zea mays/metabolism ; }, abstract = {The use of biomarkers for feed conversion efficiency (FCE), such as Nitrogen isotopic discrimination (Δ[15]N), facilitates easier measurement and may be useful in breeding strategies. However, we need to better understand the relationship between FCE and Δ[15]N, particularly the effects of differences in the composition of liveweight gain and rumen N metabolism. Alongside measurements of FCE and Δ[15]N, we estimated changes in body composition and used dietary treatments with and without nitrates, and rumen metagenomics to explore these effects. Nitrate fed steers had reduced FCE and higher Δ[15]N in plasma compared to steers offered non-nitrate containing diets. The negative relationship between FCE and Δ[15]N was strengthened with the inclusion of fat depth change at the 3[rd] lumbar vertebrae, but not with average daily gain. We identified 1,700 microbial genes with a relative abundance >0.01% of which, 26 were associated with Δ[15]N. These genes explained 69% of variation in Δ[15]N and showed clustering in two distinct functional networks. However, there was no clear relationship between their relative abundances and Δ[15]N, suggesting that rumen microbial genes contribute little to Δ[15]N. Conversely, we show that changes in the composition of gain (fat accretion) provide additional strength to the relationship between FCE and Δ[15]N.}, } @article {pmid29496731, year = {2018}, author = {Korpela, K and Costea, P and Coelho, LP and Kandels-Lewis, S and Willemsen, G and Boomsma, DI and Segata, N and Bork, P}, title = {Selective maternal seeding and environment shape the human gut microbiome.}, journal = {Genome research}, volume = {28}, number = {4}, pages = {561-568}, pmid = {29496731}, issn = {1549-5469}, mesh = {Actinobacteria/*genetics ; Bacteroidetes/*genetics ; Clostridiaceae/*genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Infant ; Infant, Newborn ; Microbiota/genetics ; Mother-Child Relations ; Mothers ; Polymorphism, Single Nucleotide/genetics ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Vertical transmission of bacteria from mother to infant at birth is postulated to initiate a life-long host-microbe symbiosis, playing an important role in early infant development. However, only the tracking of strictly defined unique microbial strains can clarify where the intestinal bacteria come from, how long the initial colonizers persist, and whether colonization by other strains from the environment can replace existing ones. Using rare single nucleotide variants in fecal metagenomes of infants and their family members, we show strong evidence of selective and persistent transmission of maternal strain populations to the vaginally born infant and their occasional replacement by strains from the environment, including those from family members, in later childhood. Only strains from the classes Actinobacteria and Bacteroidia, which are essential components of the infant microbiome, are transmitted from the mother and persist for at least 1 yr. In contrast, maternal strains of Clostridia, a dominant class in the mother's gut microbiome, are not observed in the infant. Caesarean-born infants show a striking lack of maternal transmission at birth. After the first year, strain influx from the family environment occurs and continues even in adulthood. Fathers appear to be more frequently donors of novel strains to other family members than receivers. Thus, the infant gut is seeded by selected maternal bacteria, which expand to form a stable community, with a rare but stable continuing strain influx over time.}, } @article {pmid29495531, year = {2018}, author = {Chen, H and Wu, H and Yan, B and Zhao, H and Liu, F and Zhang, H and Sheng, Q and Miao, F and Liang, Z}, title = {Core Microbiome of Medicinal Plant Salvia miltiorrhiza Seed: A Rich Reservoir of Beneficial Microbes for Secondary Metabolism?.}, journal = {International journal of molecular sciences}, volume = {19}, number = {3}, pages = {}, pmid = {29495531}, issn = {1422-0067}, mesh = {Biodiversity ; Genetic Variation ; Metagenome ; Metagenomics/methods ; *Microbiota ; Plants, Medicinal/classification/genetics/metabolism/*microbiology ; RNA, Ribosomal, 16S/genetics ; Salvia miltiorrhiza/classification/genetics/metabolism/*microbiology ; Seeds/metabolism/*microbiology ; }, abstract = {Seed microbiome includes special endophytic or epiphytic microbial taxa associated with seeds, which affects seed germination, plant growth, and health. Here, we analyzed the core microbiome of 21 Salvia miltiorrhiza seeds from seven different geographic origins using 16S rDNA and ITS amplicon sequencing, followed by bioinformatics analysis. The whole bacterial microbiome was classified into 17 microbial phyla and 39 classes. Gammaproteobacteria (67.6%), Alphaproteobacteria (15.6%), Betaproteobacteria (2.6%), Sphingobacteria (5.0%), Bacilli (4.6%), and Actinobacteria (2.9%) belonged to the core bacterial microbiome. Dothideomycetes comprised 94% of core fungal microbiome in S. miltiorrhiza seeds, and another two dominant classes were Leotiomycetes (3.0%) and Tremellomycetes (2.0%). We found that terpenoid backbone biosynthesis, degradation of limonene, pinene, and geraniol, and prenyltransferases, were overrepresented in the core bacterial microbiome using phylogenetic examination of communities by reconstruction of unobserved states (PICRUSt) software. We also found that the bacterial genera Pantoea, Pseudomonas, and Sphingomonas were enriched core taxa and overlapped among S. miltiorrhiza, maize, bean, and rice, while a fungal genus, Alternaria, was shared within S. miltiorrhiza, bean, and Brassicaceae families. These findings highlight that seed-associated microbiomeis an important component of plant microbiomes, which may be a gene reservoir for secondary metabolism in medicinal plants.}, } @article {pmid29494648, year = {2018}, author = {Bhogoju, S and Nahashon, S and Wang, X and Darris, C and Kilonzo-Nthenge, A}, title = {A comparative analysis of microbial profile of Guinea fowl and chicken using metagenomic approach.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0191029}, pmid = {29494648}, issn = {1932-6203}, mesh = {Animal Feed ; Animals ; Galliformes/genetics/*microbiology ; Gastrointestinal Microbiome/*genetics ; *Metagenome ; Metagenomics ; Phylogeny ; Poultry/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {Probiotics are live microbial feed supplements that promote growth and health to the host by minimizing non-essential and pathogenic microorganisms in the host's gastrointestinal tract (GIT). The campaign to minimize excessive use of antibiotics in poultry production has necessitated development of probiotics with broad application in multiple poultry species. Design of such probiotics requires understanding of the diversity or similarity in microbial profiles among avian species of economic importance. Therefore, the objective of this research was to establish and compare the microbial profiles of the GIT of Guinea fowl and chicken and to establish the microbial diversity or similarity between the two avian species. A metagenomic approach consisting of the amplification and sequence analysis of the hypervariable regions V1-V9 of the 16S rRNA gene was used to identify the GIT microbes. Collectively, we detected more than 150 microbial families. The total number of microbial species detected in the chicken GIT was higher than that found in the Guinea Fowl GIT. Our studies also revealed phylogenetic diversity among the microbial species found in chicken and guinea fowl. The phylum Firmicutes was most abundant in both avian species whereas Phylum Actinobacteria was most abundant in chickens than Guinea fowls. The diversity of the microbial profiles found in broiler chickens and Guinea fowls suggest that the design of effective avian probiotics would require species specificity.}, } @article {pmid29494275, year = {2018}, author = {Humphries, A and Daud, A}, title = {The gut microbiota and immune checkpoint inhibitors.}, journal = {Human vaccines & immunotherapeutics}, volume = {14}, number = {9}, pages = {2178-2182}, pmid = {29494275}, issn = {2164-554X}, mesh = {Animals ; CTLA-4 Antigen/*antagonists & inhibitors ; Cancer Vaccines/*immunology ; Gastrointestinal Microbiome/*immunology ; Humans ; Immunotherapy/*methods ; Programmed Cell Death 1 Receptor/*antagonists & inhibitors ; }, abstract = {Although immunotherapy has been remarkably effective across multiple cancer types, there continues to be a significant number of non-responding patients. A possible factor proposed to influence the efficacy of immunotherapies is the gut microbiome. We discuss the results and implications of recent research on the relationship between the gut microbiome, our immune systems, and immune checkpoint inhibitor therapies including anti-CTLA-4 Ab and anti-PD-1 Ab. While the investigations all exhibit interesting results and conclusions, we find little congruence in the specific bacteria that were found favorable for antitumor responses. It is unclear whether the inconsistencies are due to differential approaches in study design (pre-clinical or clinical subjects, anti-CTLA-4 Ab or anti-PD-1 Ab), experimental methods and measurements (metagenomics sequencing and clustering variations) or subject population dynamics (differential cancer types and baseline characteristics). Moreover, we note studies regarding particular bacterial commensals and autoimmune diseases, which challenge findings from these investigations. We conclude that with the current research, clinical investigators can appreciate the critical role of gut microbiota in mediating immunostimulant response. However, prospective research exploring the biochemical mechanisms which commensal bacteria communicate with each other and the immune system is imperative to understand how they can be adjusted properly for higher immunotherapy response.}, } @article {pmid29491015, year = {2018}, author = {Amrane, S and Bachar, D and Lagier, JC and Raoult, D}, title = {Clostridium scindens Is Present in the Gut Microbiota during Clostridium difficile Infection: a Metagenomic and Culturomic Analysis.}, journal = {Journal of clinical microbiology}, volume = {56}, number = {5}, pages = {}, pmid = {29491015}, issn = {1098-660X}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacteriological Techniques ; Child ; Clostridium/*classification/genetics/growth & development/*isolation & purification ; Clostridium Infections/*microbiology ; Diarrhea/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Metagenomics ; Middle Aged ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, } @article {pmid29490879, year = {2019}, author = {Wu, WK and Chen, CC and Panyod, S and Chen, RA and Wu, MS and Sheen, LY and Chang, SC}, title = {Optimization of fecal sample processing for microbiome study - The journey from bathroom to bench.}, journal = {Journal of the Formosan Medical Association = Taiwan yi zhi}, volume = {118}, number = {2}, pages = {545-555}, doi = {10.1016/j.jfma.2018.02.005}, pmid = {29490879}, issn = {0929-6646}, mesh = {DNA/*isolation & purification ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; Reagent Kits, Diagnostic ; Sequence Analysis, DNA ; Specimen Handling/*methods/*standards ; }, abstract = {Although great interest has been displayed by researchers in the contribution of gut microbiota to human health, there is still no standard protocol with consensus to guarantee the sample quality of metagenomic analysis. Here we reviewed existing methodology studies and present suggestions for optimizing research pipeline from fecal sample collection to DNA extraction. First, we discuss strategies of clinical metadata collection as common confounders for microbiome research. Second, we propose general principles for freshly collected fecal sample and its storage and share a DIY stool collection kit protocol based on the manual procedure of Human Microbiome Project (HMP). Third, we provide a useful information of collection kit with DNA stabilization buffers and compare their pros and cons for multi-omic study. Fourth, we offer technical strategies as well as information of novel tools for sample aliquoting before long-term storage. Fifth, we discuss the substantial impact of different DNA extraction protocols on technical variations of metagenomic analysis. And lastly, we point out the limitation of current methods and the unmet needs for better quality control of metagenomic analysis. We hope the information provided here will help investigators in this exciting field to advance their studies while avoiding experimental artifacts.}, } @article {pmid29490093, year = {2018}, author = {Mulukutla, SN and Hsu, JW and Gaba, R and Bohren, KM and Guthikonda, A and Iyer, D and Ajami, NJ and Petrosino, JF and Hampe, CS and Ram, N and Jahoor, F and Balasubramanyam, A}, title = {Arginine Metabolism Is Altered in Adults with A-β + Ketosis-Prone Diabetes.}, journal = {The Journal of nutrition}, volume = {148}, number = {2}, pages = {185-193}, pmid = {29490093}, issn = {1541-6100}, support = {R01 DK026190/DK/NIDDK NIH HHS/United States ; R01 DK101411/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Arginine/administration & dosage/blood/*metabolism ; Blood Glucose/analysis ; Body Mass Index ; Diabetes Mellitus, Type 1/*metabolism/physiopathology ; Diabetes Mellitus, Type 2/physiopathology ; Female ; Gastrointestinal Microbiome/physiology ; Glucose/administration & dosage ; Glucose Clamp Technique ; Humans ; Hyperglycemia ; Insulin/blood/metabolism ; Insulin Secretion ; Insulin-Secreting Cells/*physiology ; Kinetics ; Male ; Metabolomics/methods ; Middle Aged ; Nitric Oxide/metabolism ; Ornithine/blood ; }, abstract = {BACKGROUND: A-β + ketosis-prone diabetes (KPD) is a subset of type 2 diabetes in which patients have severe but reversible β cell dysfunction of unknown etiology. Plasma metabolomic analysis indicates that abnormal arginine metabolism may be involved.

OBJECTIVE: The objective of this study was to determine the relation between gut microbiome and arginine metabolism and the relation between arginine availability and β cell function in KPD patients compared with control participants.

METHODS: Kinetics of arginine and related metabolites were measured with stable isotope tracers, and insulin secretory responses to arginine and glucose were determined under euglycemic and hyperglycemic conditions in 6 KPD patients and 6 age-, gender-, and body mass index-matched control participants. Glucose potentiation of arginine-induced insulin secretion was performed in a different set of 6 KPD and 3 control participants.

RESULTS: Arginine availability was higher in KPD patients during euglycemia [53.5 ± 4.3 (mean ± SEM) compared with 40.3 ± 2.4 μmol · kg lean body mass (LBM)-1 · h-1, P = 0.03] but declined more in response to hyperglycemia (Δ 10.15 ± 2.6 compared with Δ 3.20 ± 1.3 μmol · kg LBM-1 · h-1, P = 0.041). During hyperglycemia, ornithine flux was not different between groups but after an arginine bolus, plasma ornithine AUC trended higher in KPD patients (3360 ± 294 compared with 2584 ± 259 min · μmol · L-1, P = 0.08). In both euglycemia and hyperglycemia, the first-phase insulin responses to glucose stimulation were lower in KPD patients (euglycemic insulin AUC 282 ± 108 compared with 926 ± 257 min · μU · mL-1, P = 0.02; hyperglycemic insulin AUC 358 ± 79 compared with 866 ± 292 min · μU · mL-1, P = 0.05), but exogenous arginine restored first-phase insulin secretion in KPD patients to the level of control participants.

CONCLUSION: Compared with control participants, KPD patients have increased arginine availability in the euglycemic state, indicating a higher requirement. This is compromised during hyperglycemia, with an inadequate supply of arginine to sustain metabolic functions such as insulin secretion. Exogenous arginine administration restores a normal insulin secretory response.}, } @article {pmid29488349, year = {2018}, author = {Lang-Yona, N and Maier, S and Macholdt, DS and Müller-Germann, I and Yordanova, P and Rodriguez-Caballero, E and Jochum, KP and Al-Amri, A and Andreae, MO and Fröhlich-Nowoisky, J and Weber, B}, title = {Insights into microbial involvement in desert varnish formation retrieved from metagenomic analysis.}, journal = {Environmental microbiology reports}, volume = {10}, number = {3}, pages = {264-271}, doi = {10.1111/1758-2229.12634}, pmid = {29488349}, issn = {1758-2229}, mesh = {Actinobacteria/*classification/genetics/isolation & purification/metabolism ; Clay/*microbiology ; Cyanobacteria/*classification/genetics/isolation & purification/metabolism ; Ferric Compounds/*metabolism ; Manganese Compounds/*metabolism ; Metagenomics/methods ; Microbiota/genetics ; Oxides/*metabolism ; Proteobacteria/*classification/genetics/isolation & purification/metabolism ; Sequence Analysis, DNA/methods ; *Soil Microbiology ; }, abstract = {Desert varnishes are dark rock coatings observed in arid environments and might resemble Mn-rich coatings found on Martian rocks. Their formation mechanism is not fully understood and the possible microbial involvement is under debate. In this study, we applied DNA metagenomic Shotgun sequencing of varnish and surrounding soil to evaluate the composition of the microbial community and its potential metabolic function. We found that the α diversity was lower in varnish compared to soil samples (p value < 0.05), suggesting distinct populations with significantly higher abundance of Actinobacteria, Proteobacteria and Cyanobacteria within the varnish. Additionally, we observed increased levels of transition metal metabolic processes in varnish compared to soil samples. Nevertheless, potentially relevant enzymes for varnish formation were detected at low to insignificant levels in both niches, indicating no current direct microbial involvement in Mn oxidation. This finding is supported by quantitative genomic analysis, elemental analysis, fluorescence imaging and scanning transmission X-ray microscopy. We thus conclude that the distinct microbial communities detected in desert varnish originate from settled Aeolian microbes, which colonized this nutrient-enriched niche, and discuss possible indirect contributions of microorganisms to the formation of desert varnish.}, } @article {pmid29486880, year = {2018}, author = {Bodewes, R}, title = {Novel viruses in birds: Flying through the roof or is a cage needed?.}, journal = {Veterinary journal (London, England : 1997)}, volume = {233}, number = {}, pages = {55-62}, doi = {10.1016/j.tvjl.2017.12.023}, pmid = {29486880}, issn = {1532-2971}, mesh = {Animals ; Animals, Domestic/virology ; Animals, Wild/virology ; Bird Diseases/virology ; Birds/*virology ; Chickens/virology ; Columbidae/virology ; Ducks/virology ; Endangered Species ; Virus Diseases/veterinary ; Viruses/isolation & purification/pathogenicity ; }, abstract = {Emerging viral diseases continue to have a major global impact on human beings and animals. To be able to take adequate measures in case of an outbreak of an emerging disease, rapid detection of the causative agent is a crucial first step. In this review, various aspects of virus discovery are discussed, with a special focus on recently discovered viruses in birds. Novel viruses with a potential major impact have been discovered in domestic and wild bird species in recent years using various virus discovery methods. Only a few studies report the detection of novel viruses in endangered bird species, although increased knowledge about viruses circulating in these species is important. Additional studies focusing on the exact role of a novel virus in disease and on the impact of a novel virus on bird populations are often lacking. Intensive collaboration between different disciplines is needed to obtain useful information about the role of these novel viruses.}, } @article {pmid29486796, year = {2018}, author = {Rosa, BA and Supali, T and Gankpala, L and Djuardi, Y and Sartono, E and Zhou, Y and Fischer, K and Martin, J and Tyagi, R and Bolay, FK and Fischer, PU and Yazdanbakhsh, M and Mitreva, M}, title = {Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {33}, pmid = {29486796}, issn = {2049-2618}, support = {R01 AI081803/AI/NIAID NIH HHS/United States ; R56 AI081803/AI/NIAID NIH HHS/United States ; U54 HG003079/HG/NHGRI NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Animals ; Arachidonic Acid/metabolism ; Child ; Clostridiales/*metabolism ; Cross-Sectional Studies ; Double-Blind Method ; Feces/parasitology ; Female ; Gastrointestinal Microbiome/*physiology ; Helminthiasis/*parasitology/*transmission ; Helminths/metabolism ; Humans ; Indonesia ; Intestines/microbiology/parasitology ; Liberia ; Male ; RNA, Ribosomal, 16S/genetics ; Soil/*parasitology ; Young Adult ; }, abstract = {BACKGROUND: The human intestine and its microbiota is the most common infection site for soil-transmitted helminths (STHs), which affect the well-being of ~ 1.5 billion people worldwide. The complex cross-kingdom interactions are not well understood.

RESULTS: A cross-sectional analysis identified conserved microbial signatures positively or negatively associated with STH infections across Liberia and Indonesia, and longitudinal samples analysis from a double-blind randomized trial showed that the gut microbiota responds to deworming but does not transition closer to the uninfected state. The microbiomes of individuals able to self-clear the infection had more alike microbiome assemblages compared to individuals who remained infected. One bacterial taxon (Lachnospiracae) was negatively associated with infection in both countries, and 12 bacterial taxa were significantly associated with STH infection in both countries, including Olsenella (associated with reduced gut inflammation), which also significantly reduced in abundance following clearance of infection. Microbial community gene abundances were also affected by deworming. Functional categories identified as associated with STH infection included arachidonic acid metabolism; arachidonic acid is the precursor for pro-inflammatory leukotrienes that threaten helminth survival, and our findings suggest that some modulation of arachidonic acid activity in the STH-infected gut may occur through the increase of arachidonic acid metabolizing bacteria.

CONCLUSIONS: For the first time, we identify specific members of the gut microbiome that discriminate between moderately/heavily STH-infected and non-infected states across very diverse geographical regions using two different statistical methods. We also identify microbiome-encoded biological functions associated with the STH infections, which are associated potentially with STH survival strategies, and changes in the host environment. These results provide a novel insight of the cross-kingdom interactions in the human gut ecosystem by unlocking the microbiome assemblages at taxonomic, genetic, and functional levels so that advances towards key mechanistic studies can be made.}, } @article {pmid29482661, year = {2018}, author = {Han, M and Hao, L and Lin, Y and Li, F and Wang, J and Yang, H and Xiao, L and Kristiansen, K and Jia, H and Li, J}, title = {A novel affordable reagent for room temperature storage and transport of fecal samples for metagenomic analyses.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {43}, pmid = {29482661}, issn = {2049-2618}, support = {2017YFC0909700//National Key Research and Development Program of China/International ; 31601073//National Natural Science Foundation of China/International ; JSGG20160229172752028//Shenzhen Municipal Government of China/International ; JCYJ20160229172757249//Shenzhen Municipal Government of China/International ; }, mesh = {Bacteria/*genetics/metabolism ; Bromides/*chemistry ; DNA, Bacterial/*genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenomics ; Pyridinium Compounds/*chemistry ; Specimen Handling/*methods ; Temperature ; }, abstract = {BACKGROUND: The number of large-scale studies on the gut microbiota in human cohorts is rapidly increasing. However, the few and expensive options for storage of fecal samples at room temperature have been an obstacle for large-scale metagenomic studies and the development of clinical/commercial personal metagenomic sequencing.

RESULTS: In this study, we systematically tested a novel N-octylpyridinium bromide-based fecal sample preservation method and compared it with other currently used storage methods. We found that the N-octylpyridinium bromide-based method enabled preservation of the bacterial composition in fecal samples transported and stored at room temperature for up to at least 14 days.

CONCLUSIONS: We describe a novel chemical stabilizer that allows cost-effective transportation and storage at room temperature for several days with preservation of bacterial composition. This method will facilitate sample collection even in remote area and also enable transport via normal commercial transportation routes.}, } @article {pmid29482646, year = {2018}, author = {Louca, S and Doebeli, M and Parfrey, LW}, title = {Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {41}, pmid = {29482646}, issn = {2049-2618}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Base Sequence/genetics ; Gene Dosage/*genetics ; Genome, Bacterial/genetics ; Humans ; Metagenomics/methods ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {The 16S ribosomal RNA gene is the most widely used marker gene in microbial ecology. Counts of 16S sequence variants, often in PCR amplicons, are used to estimate proportions of bacterial and archaeal taxa in microbial communities. Because different organisms contain different 16S gene copy numbers (GCNs), sequence variant counts are biased towards clades with greater GCNs. Several tools have recently been developed for predicting GCNs using phylogenetic methods and based on sequenced genomes, in order to correct for these biases. However, the accuracy of those predictions has not been independently assessed. Here, we systematically evaluate the predictability of 16S GCNs across bacterial and archaeal clades, based on ∼ 6,800 public sequenced genomes and using several phylogenetic methods. Further, we assess the accuracy of GCNs predicted by three recently published tools (PICRUSt, CopyRighter, and PAPRICA) over a wide range of taxa and for 635 microbial communities from varied environments. We find that regardless of the phylogenetic method tested, 16S GCNs could only be accurately predicted for a limited fraction of taxa, namely taxa with closely to moderately related representatives (≲15% divergence in the 16S rRNA gene). Consistent with this observation, we find that all considered tools exhibit low predictive accuracy when evaluated against completely sequenced genomes, in some cases explaining less than 10% of the variance. Substantial disagreement was also observed between tools (R[2]<0.5) for the majority of tested microbial communities. The nearest sequenced taxon index (NSTI) of microbial communities, i.e., the average distance to a sequenced genome, was a strong predictor for the agreement between GCN prediction tools on non-animal-associated samples, but only a moderate predictor for animal-associated samples. We recommend against correcting for 16S GCNs in microbiome surveys by default, unless OTUs are sufficiently closely related to sequenced genomes or unless a need for true OTU proportions warrants the additional noise introduced, so that community profiles remain interpretable and comparable between studies.}, } @article {pmid29482639, year = {2018}, author = {Marotz, CA and Sanders, JG and Zuniga, C and Zaramela, LS and Knight, R and Zengler, K}, title = {Improving saliva shotgun metagenomics by chemical host DNA depletion.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {42}, pmid = {29482639}, issn = {2049-2618}, support = {R21 AR071731/AR/NIAMS NIH HHS/United States ; AR071731/AR/NIAMS NIH HHS/United States ; }, mesh = {Azides/*chemistry ; Bacteria/genetics ; DNA/*chemistry ; Fungi/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Propidium/*analogs & derivatives/chemistry ; Saliva/*microbiology ; Sequence Analysis, DNA ; Viruses/genetics ; }, abstract = {BACKGROUND: Shotgun sequencing of microbial communities provides in-depth knowledge of the microbiome by cataloging bacterial, fungal, and viral gene content within a sample, providing an advantage over amplicon sequencing approaches that assess taxonomy but not function and are taxonomically limited. However, mammalian DNA can dominate host-derived samples, obscuring changes in microbial populations because few DNA sequence reads are from the microbial component. We developed and optimized a novel method for enriching microbial DNA from human oral samples and compared its efficiency and potential taxonomic bias with commercially available kits.

RESULTS: Three commercially available host depletion kits were directly compared with size filtration and a novel method involving osmotic lysis and treatment with propidium monoazide (lyPMA) in human saliva samples. We evaluated the percentage of shotgun metagenomic sequencing reads aligning to the human genome, and taxonomic biases of those not aligning, compared to untreated samples. lyPMA was the most efficient method of removing host-derived sequencing reads compared to untreated sample (8.53 ± 0.10% versus 89.29 ± 0.03%). Furthermore, lyPMA-treated samples exhibit the lowest taxonomic bias compared to untreated samples.

CONCLUSION: Osmotic lysis followed by PMA treatment is a cost-effective, rapid, and robust method for enriching microbial sequence data in shotgun metagenomics from fresh and frozen saliva samples and may be extensible to other host-derived sample types.}, } @article {pmid29476620, year = {2018}, author = {Chappell, CR and Fukami, T}, title = {Nectar yeasts: a natural microcosm for ecology.}, journal = {Yeast (Chichester, England)}, volume = {35}, number = {6}, pages = {417-423}, doi = {10.1002/yea.3311}, pmid = {29476620}, issn = {1097-0061}, mesh = {Animals ; Bacteria ; Biota ; Flowers ; Models, Biological ; *Plant Nectar ; Pollination ; *Social Behavior ; *Social Environment ; *Yeasts ; }, abstract = {The species of yeasts that colonize floral nectar can modify the mutualistic relationships between plants and pollinators by changing the chemical properties of nectar. Recent evidence supporting this possibility has led to increased interest among ecologists in studying these fungi as well as the bacteria that interact with them in nectar. Although not fully explored, nectar yeasts also constitute a promising natural microcosm that can be used to facilitate development of general ecological theory. We discuss the methodological and conceptual advantages of using nectar yeasts from this perspective, including simplicity of communities, tractability of dispersal, replicability of community assembly, and the ease with which the mechanisms of species interactions can be studied in complementary experiments conducted in the field and the laboratory. To illustrate the power of nectar yeasts as a study system, we discuss several topics in community ecology, including environmental filtering, priority effects, and metacommunity dynamics. An exciting new direction is to integrate metagenomics and comparative genomics into nectar yeast research to address these fundamental ecological topics.}, } @article {pmid29475869, year = {2018}, author = {Lee, LL and Blumer-Schuette, SE and Izquierdo, JA and Zurawski, JV and Loder, AJ and Conway, JM and Elkins, JG and Podar, M and Clum, A and Jones, PC and Piatek, MJ and Weighill, DA and Jacobson, DA and Adams, MWW and Kelly, RM}, title = {Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic Genus Caldicellulosiruptor by Genomic, Pangenomic, and Metagenomic Analyses.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {9}, pages = {}, pmid = {29475869}, issn = {1098-5336}, support = {T32 GM008776/GM/NIGMS NIH HHS/United States ; }, mesh = {Cellulose/metabolism ; Firmicutes/classification/*genetics/*metabolism ; *Genome, Bacterial ; Genomics ; Lignin/*metabolism ; *Metagenome ; Metagenomics ; }, abstract = {Metagenomic data from Obsidian Pool (Yellowstone National Park, USA) and 13 genome sequences were used to reassess genus-wide biodiversity for the extremely thermophilic Caldicellulosiruptor The updated core genome contains 1,401 ortholog groups (average genome size for 13 species = 2,516 genes). The pangenome, which remains open with a revised total of 3,493 ortholog groups, encodes a variety of multidomain glycoside hydrolases (GHs). These include three cellulases with GH48 domains that are colocated in the glucan degradation locus (GDL) and are specific determinants for microcrystalline cellulose utilization. Three recently sequenced species, Caldicellulosiruptor sp. strain Rt8.B8 (renamed here Caldicellulosiruptor morganii), Thermoanaerobacter cellulolyticus strain NA10 (renamed here Caldicellulosiruptor naganoensis), and Caldicellulosiruptor sp. strain Wai35.B1 (renamed here Caldicellulosiruptor danielii), degraded Avicel and lignocellulose (switchgrass). C. morganii was more efficient than Caldicellulosiruptor bescii in this regard and differed from the other 12 species examined, both based on genome content and organization and in the specific domain features of conserved GHs. Metagenomic analysis of lignocellulose-enriched samples from Obsidian Pool revealed limited new information on genus biodiversity. Enrichments yielded genomic signatures closely related to that of Caldicellulosiruptor obsidiansis, but there was also evidence for other thermophilic fermentative anaerobes (Caldanaerobacter, Fervidobacterium, Caloramator, and Clostridium). One enrichment, containing 89.8% Caldicellulosiruptor and 9.7% Caloramator, had a capacity for switchgrass solubilization comparable to that of C. bescii These results refine the known biodiversity of Caldicellulosiruptor and indicate that microcrystalline cellulose degradation at temperatures above 70°C, based on current information, is limited to certain members of this genus that produce GH48 domain-containing enzymes.IMPORTANCE The genus Caldicellulosiruptor contains the most thermophilic bacteria capable of lignocellulose deconstruction, which are promising candidates for consolidated bioprocessing for the production of biofuels and bio-based chemicals. The focus here is on the extant capability of this genus for plant biomass degradation and the extent to which this can be inferred from the core and pangenomes, based on analysis of 13 species and metagenomic sequence information from environmental samples. Key to microcrystalline hydrolysis is the content of the glucan degradation locus (GDL), a set of genes encoding glycoside hydrolases (GHs), several of which have GH48 and family 3 carbohydrate binding module domains, that function as primary cellulases. Resolving the relationship between the GDL and lignocellulose degradation will inform efforts to identify more prolific members of the genus and to develop metabolic engineering strategies to improve this characteristic.}, } @article {pmid29474068, year = {2018}, author = {Lu, T and Ke, M and Peijnenburg, WJGM and Zhu, Y and Zhang, M and Sun, L and Fu, Z and Qian, H}, title = {Investigation of Rhizospheric Microbial Communities in Wheat, Barley, and Two Rice Varieties at the Seedling Stage.}, journal = {Journal of agricultural and food chemistry}, volume = {66}, number = {11}, pages = {2645-2653}, doi = {10.1021/acs.jafc.7b06155}, pmid = {29474068}, issn = {1520-5118}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; Hordeum/*growth & development/microbiology ; Oryza/*growth & development/microbiology ; Rhizosphere ; Seedlings/growth & development/microbiology ; *Soil Microbiology ; Triticum/*growth & development/microbiology ; }, abstract = {The plant rhizosphere microbiota plays multiple roles in plant growth. We investigated the taxonomic and functional variations in the rhizosphere microbial community, examining both prokaryotes and eukaryotes, of four crops at the seedling stage: wheat, barley, and two rice varieties (indica and japonica) seeded in paddy soil. The diversity of rhizosphere communities in these four species was determined. Results showed that wheat and barley had much stronger selection effects than rice for the rhizosphere microbial community. Functional metagenomic profiling indicated that a series of sequences related to glycan, limonene, and pinene degradation pathways as well as some relatively rare functions related to N or S metabolism were enriched in the rhizosphere soil. We conclude that the four tested crops induced the formation of the microbial community with specific features that may influence the plant growth but stochastic processes also appreciably influenced the functional selection.}, } @article {pmid29472560, year = {2018}, author = {Taş, N and Prestat, E and Wang, S and Wu, Y and Ulrich, C and Kneafsey, T and Tringe, SG and Torn, MS and Hubbard, SS and Jansson, JK}, title = {Landscape topography structures the soil microbiome in arctic polygonal tundra.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {777}, pmid = {29472560}, issn = {2041-1723}, mesh = {Arctic Regions ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Carbon/metabolism ; Climate Change ; Methane/metabolism ; *Microbiota ; Permafrost/*microbiology ; Soil/chemistry ; Soil Microbiology ; Tundra ; }, abstract = {In the Arctic, environmental factors governing microbial degradation of soil carbon (C) in active layer and permafrost are poorly understood. Here we determined the functional potential of soil microbiomes horizontally and vertically across a cryoperturbed polygonal landscape in Alaska. With comparative metagenomics, genome binning of novel microbes, and gas flux measurements we show that microbial greenhouse gas (GHG) production is strongly correlated to landscape topography. Active layer and permafrost harbor contrasting microbiomes, with increasing amounts of Actinobacteria correlating with decreasing soil C in permafrost. While microbial functions such as fermentation and methanogenesis were dominant in wetter polygons, in drier polygons genes for C mineralization and CH4 oxidation were abundant. The active layer microbiome was poised to assimilate N and not to release N2O, reflecting low N2O flux measurements. These results provide mechanistic links of microbial metabolism to GHG fluxes that are needed for the refinement of model predictions.}, } @article {pmid29471863, year = {2018}, author = {Petrosino, JF}, title = {The microbiome in precision medicine: the way forward.}, journal = {Genome medicine}, volume = {10}, number = {1}, pages = {12}, pmid = {29471863}, issn = {1756-994X}, support = {HHSN267200700014C/LM/NLM NIH HHS/United States ; R01 AI108588/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 MH112356/MH/NIMH NIH HHS/United States ; U19 AI116497/AI/NIAID NIH HHS/United States ; }, mesh = {Disease ; Humans ; *Microbiota ; Phenotype ; *Precision Medicine ; }, abstract = {Novel associations between the human microbiome and health and disease are routinely emerging, and important host-microbiome interactions are targets for new diagnostics and therapeutics. Understanding how broadly host-microbe associations are maintained across populations is revealing individualized host-microbiome phenotypes that can be integrated with other 'omics' data sets to enhance precision medicine.}, } @article {pmid29471692, year = {2018}, author = {Knáb, M and Szili-Kovács, T and Márialigeti, K and Móga, J and Borsodi, AK}, title = {Bacterial diversity in soils of different Hungarian karst areas.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {65}, number = {4}, pages = {439-458}, doi = {10.1556/030.65.2018.002}, pmid = {29471692}, issn = {1217-8950}, mesh = {Bacteria/*classification/*isolation & purification ; Bacteriological Techniques ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geography ; Humans ; Hungary ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Karst areas have great environmental importance as sources of subsurface water and often maintain very sensitive ecosystems. In recent years, increasing number of microbiological studies focused on the bacterial communities of karst soils. In this study, diversity examinations on two distinct Hungarian karst areas, Aggtelek and Tapolca, were performed using parallel cultivation and molecular cloning methods. The phylogenetic affiliation of bacterial strains and molecular clones was determined based on their 16S rRNA gene sequences. Bacterial isolates were identified as members of the phyla Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. Besides the taxa identified by cultivation, members of the phyla Chloroflexi, Cyanobacteria, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes were detected by the cloning. The difference in the composition of soil bacterial communities was related to geographic locations and soil types. Both the highest and the lowest bacterial diversities were detected in samples from Aggtelek National Park, characterized by Leptic Luvisol and Rendzic Leptosol soil types. The difference in the composition of bacterial communities between Rendzic Leptosol and Leptic Phaeozem soil types at Tapolca could be the result of human impacts.}, } @article {pmid29471034, year = {2018}, author = {Andermann, TM and Peled, JU and Ho, C and Reddy, P and Riches, M and Storb, R and Teshima, T and van den Brink, MRM and Alousi, A and Balderman, S and Chiusolo, P and Clark, WB and Holler, E and Howard, A and Kean, LS and Koh, AY and McCarthy, PL and McCarty, JM and Mohty, M and Nakamura, R and Rezvani, K and Segal, BH and Shaw, BE and Shpall, EJ and Sung, AD and Weber, D and Whangbo, J and Wingard, JR and Wood, WA and Perales, MA and Jenq, RR and Bhatt, AS and , }, title = {The Microbiome and Hematopoietic Cell Transplantation: Past, Present, and Future.}, journal = {Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation}, volume = {24}, number = {7}, pages = {1322-1340}, pmid = {29471034}, issn = {1523-6536}, support = {U10 HL069294/HL/NHLBI NIH HHS/United States ; UG1 HL069301/HL/NHLBI NIH HHS/United States ; K08 CA184420/CA/NCI NIH HHS/United States ; UG1 HL069315/HL/NHLBI NIH HHS/United States ; U10 HL069330/HL/NHLBI NIH HHS/United States ; R01 HL124112/HL/NHLBI NIH HHS/United States ; UG1 HL069278/HL/NHLBI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; P30 CA014236/CA/NCI NIH HHS/United States ; U24 CA076518/CA/NCI NIH HHS/United States ; U24 HL138660/HL/NHLBI NIH HHS/United States ; UL1 TR001085/TR/NCATS NIH HHS/United States ; UG1 HL069330/HL/NHLBI NIH HHS/United States ; }, mesh = {*Hematopoietic Stem Cell Transplantation ; Humans ; *Microbiota ; }, } @article {pmid29470608, year = {2018}, author = {Cleary, DFR and Polónia, ARM and de Voogd, NJ}, title = {Bacterial Communities Inhabiting the Sponge Biemna fortis, Sediment and Water in Marine Lakes and the Open Sea.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {610-624}, pmid = {29470608}, issn = {1432-184X}, support = {ALW Grant No. 825.12.007//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NL)/ ; PTDC/AAC-AMB/115304/2009//Fundação para a Ciência e a Tecnologia (PT)/ ; UID/AMB/50017//CESAM/ ; SFRH/BPD/117563/2016//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {Animals ; Archaea ; Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; Coral Reefs ; Ecosystem ; Geologic Sediments/*microbiology ; Indonesia ; Lakes/*microbiology ; Phylogeny ; Porifera/*microbiology ; Seawater/*microbiology ; }, abstract = {Marine lakes are small bodies of landlocked seawater that are isolated from the open sea and have been shown to house numerous rare and unique taxa. The environmental conditions of the lakes are also characterised by lower pH and salinity and higher temperatures than generally found in the open sea. In the present study, we used a 16S rRNA gene barcoded pyrosequencing approach and a predictive metagenomic approach (PICRUSt) to examine bacterial composition and function in three distinct biotopes (sediment, water and the sponge species Biemna fortis) in three habitats (two marine lakes and the open sea) of the Berau reef system, Indonesia. Both biotope and habitat were significant predictors of higher taxon abundance and compositional variation. Most of the variation in operational taxonomic unit (OTU) composition was related to the biotope (42% for biotope alone versus 9% for habitat alone and 15% combined). Most OTUs were also restricted to a single biotope (1047 for B. fortis, 6120 for sediment and 471 for water). Only 98 OTUs were shared across all three biotopes. Bacterial communities from B. fortis, sediment and water samples were, however, also distinct in marine lake and open sea habitats. This was evident in the abundance of higher bacterial taxa. For example, the phylum Cyanobacteria was significantly more abundant in samples from marine lakes than from the open sea. This difference was most pronounced in the sponge B. fortis. In line with the compositional differences, there were pronounced differences in predicted relative gene count abundance among biotopes and habitats. Of particular interest was the predicted enrichment in B. fortis from the marine lakes for pathways including DNA replication and repair and the glutathione metabolism. This may facilitate adaptation of host and microbes to life in 'stressful' low pH, low salinity and/or high temperature environments such as those encountered in marine lakes.}, } @article {pmid29469169, year = {2018}, author = {Fountain, MT and Bennett, J and Cobo-Medina, M and Conde Ruiz, R and Deakin, G and Delgado, A and Harrison, R and Harrison, N}, title = {Alimentary microbes of winter-form Drosophila suzukii.}, journal = {Insect molecular biology}, volume = {27}, number = {3}, pages = {383-392}, doi = {10.1111/imb.12377}, pmid = {29469169}, issn = {1365-2583}, mesh = {Animals ; DNA, Ribosomal Spacer/analysis ; Drosophila/*microbiology ; England ; *Gastrointestinal Microbiome ; *Metagenome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Seasons ; }, abstract = {Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is a damaging pest of fruit. Reproductively diapausing adults overwinter in woodlands and remain active on warmer winter days. It is unknown if this adult phase of the lifecycle feeds during the winter period, and what the food source may be. This study characterized the flora in the digestive tract of D. suzukii using a metagenomics approach. Live D. suzukii were trapped in four woodlands in the south of England and their guts dissected for DNA extraction and amplicon-based metagenomics sequencing (internal transcribed spacer and 16S rRNA). Analysis at genus and family taxonomic levels showed high levels of diversity with no differences in digestive tract bacterial or fungal biota between woodland sites of winter-form D. suzukii. Female D. suzukii at one site appeared to have higher bacterial diversity in the alimentary canal than males, but there was a site, sex interaction. Many of the biota were associated with cold, wet climatic conditions and decomposition. This study provides the first evidence that winter-form D. suzukii may be opportunistic feeders during the winter period and are probably exploiting food sources associated with moisture on decomposing vegetation during this time. A core gut microbiome has been identified for winter-form D. suzukii.}, } @article {pmid29468143, year = {2018}, author = {Gigliucci, F and von Meijenfeldt, FAB and Knijn, A and Michelacci, V and Scavia, G and Minelli, F and Dutilh, BE and Ahmad, HM and Raangs, GC and Friedrich, AW and Rossen, JWA and Morabito, S}, title = {Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {25}, pmid = {29468143}, issn = {2235-2988}, mesh = {Biodiversity ; Child, Preschool ; Computational Biology/methods ; Escherichia coli Infections/*microbiology ; Feces/*microbiology ; *Gastrointestinal Microbiome ; *Host-Pathogen Interactions ; Humans ; Infant ; Infant, Newborn ; *Metagenome ; *Metagenomics/methods ; *Shiga-Toxigenic Escherichia coli/genetics/pathogenicity ; Virulence/genetics ; }, abstract = {The human intestinal microbiota is a homeostatic ecosystem with a remarkable impact on human health and the disruption of this equilibrium leads to an increased susceptibility to infection by numerous pathogens. In this study, we used shotgun metagenomic sequencing and two different bioinformatic approaches, based on mapping of the reads onto databases and on the reconstruction of putative draft genomes, to investigate possible changes in the composition of the intestinal microbiota in samples from patients with Shiga Toxin-producing E. coli (STEC) infection compared to healthy and healed controls, collected during an outbreak caused by a STEC O26:H11 infection. Both the bioinformatic procedures used, produced similar result with a good resolution of the taxonomic profiles of the specimens. The stool samples collected from the STEC infected patients showed a lower abundance of the members of Bifidobacteriales and Clostridiales orders in comparison to controls where those microorganisms predominated. These differences seemed to correlate with the STEC infection although a flexion in the relative abundance of the Bifidobacterium genus, part of the Bifidobacteriales order, was observed also in samples from Crohn's disease patients, displaying a STEC-unrelated dysbiosis. The metagenomics also allowed to identify in the STEC positive samples, all the virulence traits present in the genomes of the STEC O26 that caused the outbreak as assessed through isolation of the epidemic strain and whole genome sequencing. The results shown represent a first evidence of the changes occurring in the intestinal microbiota of children in the course of STEC infection and indicate that metagenomics may be a promising tool for the culture-independent clinical diagnosis of the infection.}, } @article {pmid29467398, year = {2018}, author = {Munson-McGee, JH and Peng, S and Dewerff, S and Stepanauskas, R and Whitaker, RJ and Weitz, JS and Young, MJ}, title = {A virus or more in (nearly) every cell: ubiquitous networks of virus-host interactions in extreme environments.}, journal = {The ISME journal}, volume = {12}, number = {7}, pages = {1706-1714}, pmid = {29467398}, issn = {1751-7370}, mesh = {Bacteria/virology ; Clustered Regularly Interspaced Short Palindromic Repeats ; Host Specificity ; *Host-Pathogen Interactions ; Hot Springs/*microbiology/*virology ; Metagenomics ; Microbiota ; *Virus Physiological Phenomena ; Viruses/classification/genetics/isolation & purification ; }, abstract = {The application of viral and cellular metagenomics to natural environments has expanded our understanding of the structure, functioning, and diversity of microbial and viral communities. The high diversity of many communities, e.g., soils, surface ocean waters, and animal-associated microbiomes, make it difficult to establish virus-host associations at the single cell (rather than population) level, assign cellular hosts, or determine the extent of viral host range from metagenomics studies alone. Here, we combine single-cell sequencing with environmental metagenomics to characterize the structure of virus-host associations in a Yellowstone National Park (YNP) hot spring microbial community. Leveraging the relatively low diversity of the YNP environment, we are able to overlay evidence at the single-cell level with contextualized viral and cellular community structure. Combining evidence from hexanucelotide analysis, single cell read mapping, network-based analytics, and CRISPR-based inference, we conservatively estimate that >60% of cells contain at least one virus type and a majority of these cells contain two or more virus types. Of the detected virus types, nearly 50% were found in more than 2 cellular clades, indicative of a broad host range. The new lens provided by the combination of metaviromics and single-cell genomics reveals a network of virus-host interactions in extreme environments, provides evidence that extensive virus-host associations are common, and further expands the unseen impact of viruses on cellular life.}, } @article {pmid29467397, year = {2018}, author = {Anantharaman, K and Hausmann, B and Jungbluth, SP and Kantor, RS and Lavy, A and Warren, LA and Rappé, MS and Pester, M and Loy, A and Thomas, BC and Banfield, JF}, title = {Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle.}, journal = {The ISME journal}, volume = {12}, number = {7}, pages = {1715-1728}, pmid = {29467397}, issn = {1751-7370}, support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; P 25111/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Archaea/classification/genetics/isolation & purification/*metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; *Biodiversity ; Hydrogensulfite Reductase/genetics/metabolism ; Metagenome ; Oxidation-Reduction ; Phylogeny ; Sulfur/*metabolism ; }, abstract = {A critical step in the biogeochemical cycle of sulfur on Earth is microbial sulfate reduction, yet organisms from relatively few lineages have been implicated in this process. Previous studies using functional marker genes have detected abundant, novel dissimilatory sulfite reductases (DsrAB) that could confer the capacity for microbial sulfite/sulfate reduction but were not affiliated with known organisms. Thus, the identity of a significant fraction of sulfate/sulfite-reducing microbes has remained elusive. Here we report the discovery of the capacity for sulfate/sulfite reduction in the genomes of organisms from 13 bacterial and archaeal phyla, thereby more than doubling the number of microbial phyla associated with this process. Eight of the 13 newly identified groups are candidate phyla that lack isolated representatives, a finding only possible given genomes from metagenomes. Organisms from Verrucomicrobia and two candidate phyla, Candidatus Rokubacteria and Candidatus Hydrothermarchaeota, contain some of the earliest evolved dsrAB genes. The capacity for sulfite reduction has been laterally transferred in multiple events within some phyla, and a key gene potentially capable of modulating sulfur metabolism in associated cells has been acquired by putatively symbiotic bacteria. We conclude that current functional predictions based on phylogeny significantly underestimate the extent of sulfate/sulfite reduction across Earth's ecosystems. Understanding the prevalence of this capacity is integral to interpreting the carbon cycle because sulfate reduction is often coupled to turnover of buried organic carbon. Our findings expand the diversity of microbial groups associated with sulfur transformations in the environment and motivate revision of biogeochemical process models based on microbial community composition.}, } @article {pmid29463904, year = {2018}, author = {Lavelle, A and Sokol, H}, title = {Gut microbiota: Beyond metagenomics, metatranscriptomics illuminates microbiome functionality in IBD.}, journal = {Nature reviews. Gastroenterology & hepatology}, volume = {15}, number = {4}, pages = {193-194}, pmid = {29463904}, issn = {1759-5053}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases ; Metagenomics ; *Microbiota ; }, } @article {pmid29463661, year = {2018}, author = {He, Z and Zhang, P and Wu, L and Rocha, AM and Tu, Q and Shi, Z and Wu, B and Qin, Y and Wang, J and Yan, Q and Curtis, D and Ning, D and Van Nostrand, JD and Wu, L and Yang, Y and Elias, DA and Watson, DB and Adams, MWW and Fields, MW and Alm, EJ and Hazen, TC and Adams, PD and Arkin, AP and Zhou, J}, title = {Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.}, journal = {mBio}, volume = {9}, number = {1}, pages = {}, pmid = {29463661}, issn = {2150-7511}, mesh = {Biota/*drug effects ; *Ecosystem ; *Environmental Pollution ; Groundwater/*chemistry/*microbiology ; Hydrogen-Ion Concentration ; Metagenome/drug effects ; Nitrates/analysis ; Tennessee ; Uranium/analysis ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Contamination from anthropogenic activities has significantly impacted Earth's biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly (P < 0.05) as uranium or nitrate increased, and their changes could be used to successfully predict uranium and nitrate contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning.IMPORTANCE Disentangling the relationships between biodiversity and ecosystem functioning is an important but poorly understood topic in ecology. Predicting ecosystem functioning on the basis of biodiversity is even more difficult, particularly with microbial biomarkers. As an exploratory effort, this study used key microbial functional genes as biomarkers to provide predictive understanding of environmental contamination and ecosystem functioning. The results indicated that the overall functional gene richness/diversity decreased as uranium increased in groundwater, while specific key microbial guilds increased significantly as uranium or nitrate increased. These key microbial functional genes could be used to successfully predict environmental contamination and ecosystem functioning. This study represents a significant advance in using functional gene markers to predict the spatial distribution of environmental contaminants and ecosystem functioning toward predictive microbial ecology, which is an ultimate goal of microbial ecology.}, } @article {pmid29463537, year = {2018}, author = {Ajami, NJ and Cope, JL and Wong, MC and Petrosino, JF and Chesnel, L}, title = {Impact of Oral Fidaxomicin Administration on the Intestinal Microbiota and Susceptibility to Clostridium difficile Colonization in Mice.}, journal = {Antimicrobial agents and chemotherapy}, volume = {62}, number = {5}, pages = {}, pmid = {29463537}, issn = {1098-6596}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Clostridioides difficile/*drug effects ; Clostridium Infections/*drug therapy/prevention & control ; Cross Infection/drug therapy/microbiology/prevention & control ; Disease Models, Animal ; Feces/microbiology ; Female ; Fidaxomicin/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Mice ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S/genetics ; Vancomycin/*pharmacology ; }, abstract = {Clostridium difficile infection (CDI), a common cause of hospital-acquired infections, typically occurs after disruption of the normal gut microbiome by broad-spectrum antibiotics. Fidaxomicin is a narrow-spectrum antibiotic that demonstrates a reduced impact on the normal gut microbiota and is approved for the treatment of CDI. To further explore the benefits of this property, we used a murine model to examine the effects of fidaxomicin versus vancomycin on gut microbiota and susceptibility to C. difficile colonization while tracking microbiota recovery over time. Mice were exposed to fidaxomicin or vancomycin by oral gavage for 3 days and subsequently challenged with C. difficile spores at predetermined time points up to 21 days postexposure to antibiotics. Fecal samples were subsequently collected for analysis. Twenty-four hours postchallenge, mice were euthanized and the colon contents harvested. The microbiota was characterized using 16S rRNA gene sequencing. All fidaxomicin-exposed mice (except for one at day 8) were resistant to C. difficile colonization. However, 9 of 15 vancomycin-exposed mice were susceptible to C. difficile colonization until day 12. All vancomycin-exposed mice recovered colonization resistance by day 16. Bacterial diversity was similar prior to antibiotic exposure in both arms and decreased substantially after exposure. A shift in taxonomic structure and composition occurred after both exposures; however, the shift was greater in vancomycin-exposed than in fidaxomicin-exposed mice. In summary, compared with vancomycin, fidaxomicin exposure had less impact on microbiota composition, promoted faster microbial recovery, and had less impact on the loss of C. difficile colonization resistance.}, } @article {pmid29459707, year = {2018}, author = {Zepeda Mendoza, ML and Xiong, Z and Escalera-Zamudio, M and Runge, AK and Thézé, J and Streicker, D and Frank, HK and Loza-Rubio, E and Liu, S and Ryder, OA and Samaniego Castruita, JA and Katzourakis, A and Pacheco, G and Taboada, B and Löber, U and Pybus, OG and Li, Y and Rojas-Anaya, E and Bohmann, K and Carmona Baez, A and Arias, CF and Liu, S and Greenwood, AD and Bertelsen, MF and White, NE and Bunce, M and Zhang, G and Sicheritz-Pontén, T and Gilbert, MPT}, title = {Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat.}, journal = {Nature ecology & evolution}, volume = {2}, number = {4}, pages = {659-668}, pmid = {29459707}, issn = {2397-334X}, support = {/WT_/Wellcome Trust/United Kingdom ; 681396/ERC_/European Research Council/International ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Biological Evolution ; Blood ; Chiroptera/genetics/microbiology/*physiology ; *Diet ; *Gastrointestinal Microbiome ; *Genome ; Phylogeny ; }, abstract = {Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach to the common vampire bat (Desmodus rotundus), one of the only three obligate blood-feeding (sanguivorous) mammals, to study the evolution of its complex dietary adaptation. Specifically, we assembled its high-quality reference genome (scaffold N50 = 26.9 Mb, contig N50 = 36.6 kb) and gut metagenome, and compared them against those of insectivorous, frugivorous and carnivorous bats. Our analyses showed a particular common vampire bat genomic landscape regarding integrated viral elements, a dietary and phylogenetic influence on gut microbiome taxonomic and functional profiles, and that both genetic elements harbour key traits related to the nutritional (for example, vitamin and lipid shortage) and non-nutritional (for example, nitrogen waste and osmotic homeostasis) challenges of sanguivory. These findings highlight the value of a holistic study of both the host and its microbiota when attempting to decipher adaptations underlying radical dietary lifestyles.}, } @article {pmid29459704, year = {2018}, author = {Shi, YC and Guo, H and Chen, J and Sun, G and Ren, RR and Guo, MZ and Peng, LH and Yang, YS}, title = {Initial meconium microbiome in Chinese neonates delivered naturally or by cesarean section.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {3255}, pmid = {29459704}, issn = {2045-2322}, mesh = {Asian People ; Bacteria/*classification/genetics ; Delivery, Obstetric/*methods ; Feces/microbiology ; Female ; Humans ; Infant, Newborn ; Male ; Meconium/*microbiology ; Metagenomics ; *Microbiota ; Sequence Analysis, DNA ; }, abstract = {Previous studies have revealed significant differences in microbiome compositions between infants delivered via cesarean section (C-section) and natural vaginal birth. However, the importance of the delivery mode in the first days of life remains unclear. Importantly, this stage is minimally affected by infant feeding. Here, we used a metagenomic sequencing technique to characterize the meconium microbiome from the feces of a Chinese cohort of vaginally and C-section-delivered infants, including in vitro fertilization (IVF) newborns, during the first 24 h after birth. Meconium microbiome diversity was higher in vaginally delivered infants than that in C-section-delivered infants. Propionibacterium species were most abundant in the vaginally delivered infants, whereas the C-section group had high levels of Bacillus licheniformis. The two IVF newborns delivered by C-section harbored microbial communities similar to the vaginal microbiome in terms of taxonomic composition. Metabolic functions of the C-section group suffered more from the influence of the dominant group (B. licheniformis), whereas the vaginal group was more homogeneous, with a metabolism dominated by multi-microbes. Moreover, different modes of delivery affected the antibiotic resistance gene (ARG) prevalence. These findings provide novel information for the development of strategies to guide a healthy mode of delivery and promote the formation of healthy microbiota.}, } @article {pmid29459499, year = {2018}, author = {Kato, S and Sakai, S and Hirai, M and Tasumi, E and Nishizawa, M and Suzuki, K and Takai, K}, title = {Long-Term Cultivation and Metagenomics Reveal Ecophysiology of Previously Uncultivated Thermophiles Involved in Biogeochemical Nitrogen Cycle.}, journal = {Microbes and environments}, volume = {33}, number = {1}, pages = {107-110}, pmid = {29459499}, issn = {1347-4405}, mesh = {Archaea/*genetics/physiology ; Bacteria/*genetics/metabolism ; *Bacterial Physiological Phenomena ; Biodiversity ; Denitrification ; Ecosystem ; Hot Springs/microbiology ; Metagenome ; *Metagenomics ; Nitrification ; Nitrogen/metabolism ; *Nitrogen Cycle ; Soil Microbiology ; }, abstract = {Many thermophiles thriving in a natural high-temperature environment remain uncultivated, and their ecophysiological functions in the biogeochemical cycle remain unclear. In the present study, we performed long-term continuous cultivation at 65°C and 70°C using a microbial mat sample, collected from a subsurface geothermal stream, as the inoculum, and reconstructed the whole genome of the maintained populations using metagenomics. Some metagenome-assembled genomes (MAGs), affiliated into phylum-level bacterial and archaeal clades without cultivated representatives, contained genes involved in nitrogen metabolism including nitrification and denitrification. Our results show genetic components and their potential interactions for the biogeochemical nitrogen cycle in a subsurface geothermal environment.}, } @article {pmid29458679, year = {2018}, author = {Chiodini, RJ and Dowd, SE and Barron, JN and Galandiuk, S and Davis, B and Glassing, A}, title = {Transitional and temporal changes in the mucosal and submucosal intestinal microbiota in advanced Crohn's disease of the terminal ileum.}, journal = {Journal of medical microbiology}, volume = {67}, number = {4}, pages = {549-559}, doi = {10.1099/jmm.0.000690}, pmid = {29458679}, issn = {1473-5644}, mesh = {Adult ; Aged ; Bacteria/classification/genetics/*isolation & purification ; Bacterial Translocation ; Crohn Disease/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Ileum/*microbiology ; Intestinal Mucosa/microbiology ; Intestines/*microbiology ; Male ; Middle Aged ; Young Adult ; }, abstract = {PURPOSE: Crohn's disease is a chronic debilitating intestinal syndrome of unknown aetiology that is thought to result in part from an imbalance (dysbiosis) of the intestinal microbial populations, known as the microbiota. In this study we sought to compare the microbiota at the mucosal and submucosal levels at the resection margin in Crohn's disease to those in other intestinal dysbiotic disease controls to determine the level of bacterial translocation.

METHODOLOGY: 16S microbiota sequencing was performed on DNA extracted from mucosal and submucosal samples from resected intestinal tissues from Crohn's disease and controls.

RESULTS: Grossly normal appearing tissue at the resection margin showed early signs, suggesting bacterial translocation, with two bacterial families having penetrated the mucosal surfaces. In contrast, 4 and 13 bacterial families were present within submucosal tissues at the disease centre and disease margin, respectively. Although there was no significant difference in biodiversity, there was increased bacterial richness in the Crohn's disease group as compared to non-IBD controls.

CONCLUSION: The presence and/or absence of certain bacteria suggested disease-specific ecological or micro-environmental pressures driving or excluding certain organisms in Crohn's disease. The data suggest that several of the dysbiotic conditions previously reported for Crohn's disease are not unique but common to general dysbiosis. The examination of multiple intestinal sites in advanced disease may provide a spectrum of disease from early onset at the resection margin to active disease at the disease margin and late-stage fibrostenotic disease at the centre of the lesion, and a unique etiopathogenic view of Crohn's disease.}, } @article {pmid29454999, year = {2018}, author = {Wang, J and Tang, L and Zhou, H and Zhou, J and Glenn, TC and Shen, CL and Wang, JS}, title = {Long-term treatment with green tea polyphenols modifies the gut microbiome of female sprague-dawley rats.}, journal = {The Journal of nutritional biochemistry}, volume = {56}, number = {}, pages = {55-64}, pmid = {29454999}, issn = {1873-4847}, support = {R24 TW009489/TW/FIC NIH HHS/United States ; U01 AT006691/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; Antioxidants/pharmacology ; Bacteroidetes ; Body Weight/drug effects ; Female ; Gastrointestinal Microbiome/*drug effects ; Phenotype ; Polyphenols/*chemistry ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; Sequence Analysis, DNA ; Tea/*chemistry ; }, abstract = {Green tea polyphenols (GTP) have been shown to exert a spectrum of health benefits to animals and humans. It is plausible that the beneficial effects of GTP are a result of its interaction with the gut microbiota. This study evaluated the effect of long-term treatment with GTP on the gut microbiota of experimental rats and the potential linkage between changes of the gut microbiota with the beneficial effects of GTP. Six-month-old Sprague-Dawley rats were randomly allocated into three dosing regimens (0, 0.5%, and 1.5% of GTP) and followed for 6 months. At the end of month 3 or month 6, half of the animals from each group were sacrificed and their colon contents were collected for microbiome analysis using 16S ribosomal RNA and shotgun metagenomic community sequencing. GTP treatment significantly decreased the biodiversity and modified the microbial community in a dose-dependent manner; similar patterns were observed at both sampling times. Multiple operational taxonomic units and phylotypes were modified: the phylotypes Bacteroidetes and Oscillospira, previously linked to the lean phenotype in human and animal studies, were enriched; and Peptostreptococcaceae previously linked to colorectal cancer phenotype was depleted in GTP treated groups in a dose-dependent manner. Several microbial gene orthologs were modified, among which genes related to energy production and conversion were consistently enriched in samples from month 6 in a dose-dependent manner. This study showed that long-term treatment with GTP induced a dose-dependent modification of the gut microbiome in experimental rats, which might be linked to beneficial effects of GTP.}, } @article {pmid29454931, year = {2018}, author = {Jansson, JK and Hofmockel, KS}, title = {The soil microbiome-from metagenomics to metaphenomics.}, journal = {Current opinion in microbiology}, volume = {43}, number = {}, pages = {162-168}, doi = {10.1016/j.mib.2018.01.013}, pmid = {29454931}, issn = {1879-0364}, mesh = {Bacteria/*genetics/metabolism ; Bacterial Physiological Phenomena/genetics ; Biodiversity ; Carbon/metabolism ; Metabolic Networks and Pathways ; Metagenomics ; Microbiota/*genetics/physiology ; *Phenotype ; Phylogeny ; *Soil Microbiology ; }, abstract = {Soil microorganisms carry out important processes, including support of plant growth and cycling of carbon and other nutrients. However, the majority of soil microbes have not yet been isolated and their functions are largely unknown. Although metagenomic sequencing reveals microbial identities and functional gene information, it includes DNA from microbes with vastly varying physiological states. Therefore, metagenomics is only predictive of community functional potential. We posit that the next frontier lies in understanding the metaphenome, the product of the combined genetic potential of the microbiome and available resources. Here we describe examples of opportunities towards gaining understanding of the soil metaphenome.}, } @article {pmid29454699, year = {2018}, author = {Schären, M and Frahm, J and Kersten, S and Meyer, U and Hummel, J and Breves, G and Dänicke, S}, title = {Interrelations between the rumen microbiota and production, behavioral, rumen fermentation, metabolic, and immunological attributes of dairy cows.}, journal = {Journal of dairy science}, volume = {101}, number = {5}, pages = {4615-4637}, doi = {10.3168/jds.2017-13736}, pmid = {29454699}, issn = {1525-3198}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Behavior, Animal ; Cattle/*immunology/*microbiology/physiology ; Female ; Fermentation ; *Gastrointestinal Microbiome ; Lactation ; Metagenome ; Milk/metabolism ; Rumen/metabolism/*microbiology ; }, abstract = {Different studies have shown a strong correlation between the rumen microbiome and a range of production traits (e.g., feed efficiency, milk yield and components) in dairy cows. Underlying dynamics concerning cause and effect are, however, still widely unknown and warrant further investigation. The aim of the current study was to describe possible functional interrelations and pathways using a large set of variables describing the production, the metabolic and immunological state, as well as the rumen microbiome and fermentation characteristics of dairy cows in early lactation (n = 36, 56 ± 3 d in milk). It was further hypothesized that the feed intake-associated behavior may influence the ruminal fermentation pattern, and a set of variables describing these individual animal attributes was included. Principal component analysis as well as Spearman's rank correlations were conducted including a total of 265 variables. The attained plots describe several well-known associations between metabolic, immunological, and production traits. Main drivers of variance within the data set included milk production and efficiency as well as rumen fermentation and microbiome diversity attributes, whereas behavioral, metabolic, and immunological variables did not exhibit any strong interrelations with the other variables. The previously well-documented strong correlation of production traits with distinct prokaryote groups was confirmed. This mainly included a negative correlation of operational taxonomic units ascribed to the Prevotella genus with milk and fat yield and feed efficiency. A central role of the animals' feed intake behavior in this context could not be affirmed. Furthermore, different methodological and interpretability aspects concerning the microbiome analysis by 16S rRNA gene sequencing, such as the discrepancy between taxonomic classification and functional communality, as well as the comparability with other studies, are discussed. We concluded that, to further investigate the driving force that causes the difference between efficient and inefficient animals, studies including more sophisticated methods to describe phenotypical traits of the host (e.g., rumen physiology, metabolic and genetic aspects) as well as the rumen microbiome (e.g., metagenome, metatranscriptome, metaproteome, and metabolome analysis) are needed.}, } @article {pmid29453765, year = {2018}, author = {Mahajan, R and Attri, S and Sharma, K and Singh, N and Sharma, D and Goel, G}, title = {Statistical assessment of DNA extraction methodology for culture-independent analysis of microbial community associated with diverse environmental samples.}, journal = {Molecular biology reports}, volume = {45}, number = {3}, pages = {297-308}, pmid = {29453765}, issn = {1573-4978}, support = {INT/RUS/RFBR/P-175//Department of Science and Technology, Ministry of Science and Technology/ ; }, mesh = {Animals ; DNA/genetics/*isolation & purification ; DNA, Bacterial/genetics/isolation & purification ; Feces/chemistry ; Humans ; Metagenomics/methods ; Microbiota/genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; Soil/chemistry ; }, abstract = {Cost-effectiveness, quality, time-effectiveness and ease of the methodology are the most crucial factors in isolating quality DNA from wide variety of samples. Thus, research efforts focusing on the development of an efficient DNA extraction protocol is the need of the hour. The present study therefore, focuses on development of an efficient, rapid and free of inhibitory substances based methodology for extracting metagenomic DNA from diverse environmental samples viz. anaerobic biogas digesta, ruminant stomach, human feces, soil, and microbial starter cultures used for preparation of fermented food. PCR-DGGE based analysis and quality metagenomic library preparation, using DNA extraction methodology, validates the developed protocol. The developed protocol is cost effective, capable of isolating DNA from small sample size (100-1000 µl), time efficient (1.5-2.0 h protocol) and results in significantly higher DNA yield (4-8 times increased yield) when compared to previously available DNA extraction method and a commercial DNA extraction kit. The DNA extracted from the samples using different protocols was evaluated based on its ability to identify diverse microbial species using PCR-DGGE profiles targeting variable region within the 16S rRNA gene. The results of microbial community analysis revealed comparability of the developed protocol to commercial kits, in effectively identifying dominant representatives of the microbial community in different samples. Using the DNA extracted from the presented methodology, metagenomic libraries were prepared, which were found suitable for sequencing on Illumina platform.}, } @article {pmid29453260, year = {2018}, author = {Zhang, X and Sun, Z and Zhang, X and Zhang, M and Li, S}, title = {Hemolymph Microbiomes of Three Aquatic Invertebrates as Revealed by a New Cell Extraction Method.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {8}, pages = {}, pmid = {29453260}, issn = {1098-5336}, mesh = {Analytic Sample Preparation Methods/*methods ; Animals ; Brachyura/*microbiology ; Crassostrea/*microbiology ; Hemolymph/microbiology ; *Microbiota ; Penaeidae/*microbiology ; }, abstract = {Symbiotic microorganisms have been found in the hemolymph (blood) of many aquatic invertebrates, such as crabs, shrimp, and oysters. Hemolymph is a critical site in the host immune response. Currently, studies on hemolymph microorganisms are mostly performed with culture-dependent strategies using selective media (e.g., thiosulfate-citrate-bile salts-sucrose [TCBS], 2216E, and LB) for enumerating and isolating microbial cells. However, doubts remain about the "true" representation of the microbial abundance and diversity of symbiotic microorganisms in hemolymph, particularly for uncultivable microorganisms, which are believed to be more abundant than the cultured microorganisms. To explore this, we developed a culture-independent cell extraction method for separating microbial cells from the hemolymph of three aquatic invertebrates (Scylla paramamosain [mud crab], Litopenaeus vannamei [whiteleg shrimp], and Crassostrea angulata [Portuguese oysters]) involving filtration through a 5-μm-pore-size mesh filter membrane (the filtration method). A combination of the filtration method with fluorescence microscopy and high-throughput sequencing technique provides insight into the abundances and diversity of the total microbiota in the hemolymph of these three invertebrates. More than 2.6 × 10[4] cells/ml of microbial cells dominated by Escherichia-Shigella and Halomonas, Photobacterium and Escherichia-Shigella, and Pseudoalteromonas and Arcobacter were detected in the hemolymph of Scylla paramamosain, Litopenaeus vannamei, and Crassostrea angulata, respectively. A parallel study for investigating the hemolymph microbiomes by comparing the filtration method and a culture-dependent method (the plate count method) showed significantly higher microbial abundances (between 26- and 369-fold difference; P < 0.05) and less biased community structures of the filtration method than those of the plate count method. Furthermore, hemolymph of the three invertebrates harbored many potential pathogens, including Photobacterium, Arcobacter, and Vibrio species. Finally, the filtration method provides a solution that improves the understanding of the metabolic functions of uncultivable hemolymph microorganisms (e.g., metagenomics) devoid of host hemocyte contamination.IMPORTANCE Microorganisms are found in the hemolymph of invertebrates, a critical site in the host immune response. Currently, studies on hemolymph microorganisms are mostly performed with culture-dependent strategies. However, doubts remain about the "true" representation of the hemolymph microbiome. This study developed a culture-independent cell extraction method that could separate microbial cells from the hemolymph of three aquatic invertebrates (S. paramamosain, L. vannamei, and C. angulata) based on filtration through a 5-μm-pore-size mesh filter membrane (the filtration method). A combination of the filtration method with fluorescence microscopy and a high-throughput sequencing technique provides insight into the abundances and diversity of the total microbiota in the hemolymph of these three invertebrates. Our results demonstrate that the hemolymph of aquatic invertebrates harbors a much higher microbial abundance and more distinct microbial community composition than previously estimated. Furthermore, this work provides a less biased solution for studying the metabolic functions of uncultivable hemolymph microbiota devoid of host hemocyte contamination.}, } @article {pmid29446650, year = {2018}, author = {Guilhot, E and Khelaifia, S and La Scola, B and Raoult, D and Dubourg, G}, title = {Methods for culturing anaerobes from human specimen.}, journal = {Future microbiology}, volume = {13}, number = {}, pages = {369-381}, doi = {10.2217/fmb-2017-0170}, pmid = {29446650}, issn = {1746-0921}, mesh = {Antioxidants ; Bacteria, Anaerobic/*growth & development/*isolation & purification ; Bacteriological Techniques ; Coculture Techniques ; Culture Media/chemistry ; Humans ; Metagenomics ; *Microbiota ; Single-Cell Analysis ; Specimen Handling ; }, abstract = {Anaerobes represent the dominating population in the human gut microbiota and play a key role in gut homeostasis. In addition, several anaerobes are now considered as probiotics and they remain essential to several processes in the field of biotechnology. With the implementation of MALDI-TOF MS in routine laboratories, anaerobes are no longer neglected in clinical microbiology, as their identification is made easy. However, the isolation and identification of anaerobic bacteria, remains time consuming, fastidious and costly. Various strategies have been developed, from sampling to culturing human specimens, which will be discussed in this paper. Also, particular attention is paid to isolating species with special medical importance, as for contribution to the field of culturomics.}, } @article {pmid29444186, year = {2018}, author = {Donovan, PD and Gonzalez, G and Higgins, DG and Butler, G and Ito, K}, title = {Identification of fungi in shotgun metagenomics datasets.}, journal = {PloS one}, volume = {13}, number = {2}, pages = {e0192898}, pmid = {29444186}, issn = {1932-6203}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Antarctic Regions ; Ascomycota/classification/genetics/isolation & purification ; Candida tropicalis/genetics/pathogenicity ; Databases, Genetic ; Fungi/classification/*genetics/pathogenicity ; Humans ; Metagenome ; *Metagenomics ; Mice ; Microbiota/genetics ; Phylogeny ; Soil Microbiology ; Swine ; Zoonoses/microbiology ; }, abstract = {Metagenomics uses nucleic acid sequencing to characterize species diversity in different niches such as environmental biomes or the human microbiome. Most studies have used 16S rRNA amplicon sequencing to identify bacteria. However, the decreasing cost of sequencing has resulted in a gradual shift away from amplicon analyses and towards shotgun metagenomic sequencing. Shotgun metagenomic data can be used to identify a wide range of species, but have rarely been applied to fungal identification. Here, we develop a sequence classification pipeline, FindFungi, and use it to identify fungal sequences in public metagenome datasets. We focus primarily on animal metagenomes, especially those from pig and mouse microbiomes. We identified fungi in 39 of 70 datasets comprising 71 fungal species. At least 11 pathogenic species with zoonotic potential were identified, including Candida tropicalis. We identified Pseudogymnoascus species from 13 Antarctic soil samples initially analyzed for the presence of bacteria capable of degrading diesel oil. We also show that Candida tropicalis and Candida loboi are likely the same species. In addition, we identify several examples where contaminating DNA was erroneously included in fungal genome assemblies.}, } @article {pmid29442249, year = {2018}, author = {Wu, Y and Qiu, JW and Qian, PY and Wang, Y}, title = {The vertical distribution of prokaryotes in the surface sediment of Jiaolong cold seep at the northern South China Sea.}, journal = {Extremophiles : life under extreme conditions}, volume = {22}, number = {3}, pages = {499-510}, pmid = {29442249}, issn = {1433-4909}, support = {No. 31460001//National Natural Science Foundation of China/ ; No. 41476104//National Natural Science Foundation of China/ ; }, mesh = {Geologic Sediments/*microbiology ; Methane/metabolism ; *Microbiota ; Nitrates/metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sulfur/metabolism ; }, abstract = {In deep-sea cold seeps, microbial communities are shaped by geochemical components in seepage solutions. In the present study, we report the composition of microbial communities and potential metabolic activities in the surface sediment of Jiaolong cold seep at the northern South China Sea. Pyrosequencing of 16S rRNA gene amplicons revealed that a majority of the microbial inhabitants of the surface layers (0-6 cm) were sulfur oxidizer bacteria Sulfurimonas and archaeal methane consumer ANME-1, while sulfate reducer bacteria SEEP-SRB1, ANME-1 and ANME-2 dominated the bottom layers (8-14 cm). The potential ecological roles of the microorganisms were further supported by the presence of functional genes for methane oxidation, sulfur oxidation, sulfur reduction and nitrate reduction in the metagenomes. Metagenomic analysis revealed a significant correlation between coverage of 16S rRNA gene of sulfur oxidizer bacteria, functional genes involved in sulfur oxidation and nitrate reduction in different layers, indicating that sulfur oxidizing may be coupled to nitrate reducing at the surface layers of Jiaolong seeping site. This is probably related to the sulfur oxidizers of Sulfurimonas and Sulfurovum, which may be the capacity of nitrate reduction or associated with unidentified syntrophic nitrate-reducing microbes in the surface of the cold seep.}, } @article {pmid29441658, year = {2018}, author = {Pent, M and Hiltunen, M and Põldmaa, K and Furneaux, B and Hildebrand, F and Johannesson, H and Ryberg, M and Bahram, M}, title = {Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies.}, journal = {Environmental microbiology}, volume = {20}, number = {5}, pages = {1641-1650}, doi = {10.1111/1462-2920.14069}, pmid = {29441658}, issn = {1462-2920}, mesh = {Ascomycota/*genetics/*physiology ; Fruiting Bodies, Fungal/*physiology ; *Genetic Variation ; *Microbiota ; *Soil Microbiology ; }, abstract = {Despite increasing knowledge on host-associated microbiomes, little is known about mechanisms underlying fungus-microbiome interactions. This study aimed to examine the relative importance of host genetic, geographic and environmental variations in structuring fungus-associated microbiomes. We analyzed the taxonomic composition and function of microbiomes inhabiting fungal fruiting-bodies in relation to host genetic variation, soil pH and geographic distance between samples. For this, we sequenced the metagenomes of 40 fruiting-bodies collected from six fairy rings (i.e., genets) of a saprotrophic fungus Marasmius oreades. Our analyses revealed that fine genetic variations between host fungi could strongly affect their associated microbiome, explaining, respectively, 25% and 37% of the variation in microbiome structure and function, whereas geographic distance and soil pH remained of secondary importance. These results, together with the smaller genome size of fungi compared to other eukaryotes, suggest that fruiting-bodies are suitable for further genome-centric studies on host-microbiome interactions.}, } @article {pmid29440402, year = {2018}, author = {Grébert, T and Doré, H and Partensky, F and Farrant, GK and Boss, ES and Picheral, M and Guidi, L and Pesant, S and Scanlan, DJ and Wincker, P and Acinas, SG and Kehoe, DM and Garczarek, L}, title = {Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {9}, pages = {E2010-E2019}, pmid = {29440402}, issn = {1091-6490}, mesh = {*Acclimatization ; Chlorophyll/chemistry ; Color ; Computer Simulation ; Cyanobacteria/*genetics ; Ecosystem ; Ecotype ; Light ; Likelihood Functions ; Metagenome ; *Oceans and Seas ; Photosynthesis/physiology ; Phycobilisomes/*physiology ; Phylogeny ; Pigmentation ; Seawater/*microbiology ; Synechococcus/*genetics ; }, abstract = {Marine Synechococcus cyanobacteria are major contributors to global oceanic primary production and exhibit a unique diversity of photosynthetic pigments, allowing them to exploit a wide range of light niches. However, the relationship between pigment content and niche partitioning has remained largely undetermined due to the lack of a single-genetic marker resolving all pigment types (PTs). Here, we developed and employed a robust method based on three distinct marker genes (cpcBA, mpeBA, and mpeW) to estimate the relative abundance of all known Synechococcus PTs from metagenomes. Analysis of the Tara Oceans dataset allowed us to reveal the global distribution of Synechococcus PTs and to define their environmental niches. Green-light specialists (PT 3a) dominated in warm, green equatorial waters, whereas blue-light specialists (PT 3c) were particularly abundant in oligotrophic areas. Type IV chromatic acclimaters (CA4-A/B), which are able to dynamically modify their light absorption properties to maximally absorb green or blue light, were unexpectedly the most abundant PT in our dataset and predominated at depth and high latitudes. We also identified populations in which CA4 might be nonfunctional due to the lack of specific CA4 genes, notably in warm high-nutrient low-chlorophyll areas. Major ecotypes within clades I-IV and CRD1 were preferentially associated with a particular PT, while others exhibited a wide range of PTs. Altogether, this study provides important insights into the ecology of Synechococcus and highlights the complex interactions between vertical phylogeny, pigmentation, and environmental parameters that shape Synechococcus community structure and evolution.}, } @article {pmid29439741, year = {2018}, author = {Xiong, W and Wang, Y and Sun, Y and Ma, L and Zeng, Q and Jiang, X and Li, A and Zeng, Z and Zhang, T}, title = {Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {34}, pmid = {29439741}, issn = {2049-2618}, support = {31702290//the National Natural Science Foundation of China/International ; 31672608//the National Natural Science Foundation of China/International ; GRF7201/11E//Hong Kong/International ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*classification/drug effects/genetics/isolation & purification ; Bacterial Proteins/*genetics ; Bifidobacterium/classification/drug effects/genetics/isolation & purification ; Chickens ; Chlortetracycline/pharmacology ; *Drug Resistance, Bacterial ; Escherichia/classification/drug effects/genetics/isolation & purification ; Feces/*microbiology ; Gene Regulatory Networks ; Klebsiella/classification/drug effects/genetics/isolation & purification ; Metagenomics ; Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Antimicrobial agents have been widely used in animal farms to prevent and treat animal diseases and to promote growth. Antimicrobial agents may change the bacterial community and enhance the resistome in animal feces. We used metagenome-wide analysis to investigate the changes in bacterial community, variations in antibiotic resistance genes (ARGs), and their bacterial hosts in the feces of broiler chickens over a full-treatment course of chlortetracycline at low and therapeutic dose levels.

RESULTS: The effects of chlortetracycline on resistome were dependent on the specific ARG subtypes and not simply the overall community-level ARGs. Therapeutic dose of chlortetracycline promoted the abundance of tetracycline resistance genes (tetA and tetW) and inhibited multidrug resistance genes (mdtA, mdtC, mdtK, ompR, and TolC). The therapeutic dose of chlortetracycline led to loss of Proteobacteria mainly due to the decrease of Escherichia/Shigella (from 72 to 58%). Inhibition of Escherichia by chlortetracycline was the primary reason for the decrease of genes resistant to multiple drugs in the therapeutic dose group. The ARG host Bifidobacterium were enriched due to tetW harbored by Bifidobacterium under chlortetracycline treatment. Escherichia was always the major host for multidrug resistance genes, whereas the primary host was changed from Escherichia to Klebsiella for aminoglycoside resistance genes with the treatment of therapeutic dose of chlortetracycline.

CONCLUSIONS: We provided the first metagenomic insights into antibiotic-mediated alteration of ARG-harboring bacterial hosts at community-wide level in chicken feces. These results indicated that the changes in the structure of antibiotic-induced feces microbial communities accompany changes in the abundance of bacterial hosts carrying specific ARGs in the feces microbiota. These findings will help to optimize therapeutic schemes for the effective treatment of antibiotic resistant pathogens in poultry farms. Resistome variations in faecal microbiome of chickens exposed to chlortetracycline.}, } @article {pmid29439665, year = {2018}, author = {Feng, G and Xie, T and Wang, X and Bai, J and Tang, L and Zhao, H and Wei, W and Wang, M and Zhao, Y}, title = {Metagenomic analysis of microbial community and function involved in cd-contaminated soil.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {11}, pmid = {29439665}, issn = {1471-2180}, mesh = {Amino Acids/metabolism ; Bacteria/classification/*drug effects/genetics/metabolism ; Biodiversity ; Cadmium/metabolism/*toxicity ; China ; DNA, Bacterial ; Environmental Pollution ; Fatty Acids/metabolism ; Metabolic Networks and Pathways ; *Metagenomics ; Metals, Heavy/metabolism ; Microbial Consortia/*drug effects ; Nucleotides/metabolism ; Open Reading Frames ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/metabolism/*toxicity ; }, abstract = {BACKGROUND: Soil contaminated with the heavy metal Cadmium (Cd) is a widespread problem in many parts of the world. Based on metagenomic analysis, we investigated the functional potential and structural diversity of the microbial community in Cd-contaminated and non-contaminated soil samples and we explored the associated metabolic pathway network in cluster of orthologous groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG).

RESULTS: The results showed that microorganisms in these soils were quite abundant, and many of them possessed numerous physiological functions. However, Cd-contamination has the potential to reduce the microbial diversity and further alter the community structure in the soil. Notably, function analysis of the crucial microorganisms (e. g. Proteobacteria, Sulfuricella and Thiobacillus) indicated that these bacteria and their corresponding physiological functions were important for the community to cope with Cd pollution. The COG annotation demonstrated that the predominant category was the microbial metabolism cluster in both soil samples, while the relative abundance of metabolic genes was increased in the Cd-contaminated soil. The KEGG annotation results exhibited that the non-contaminated soil had more genes, pathways, modules, orthologies and enzymes involved in metabolic pathways of microbial communities than the Cd-contaminated soil. The relative abundance of some dominant KEGG pathways increased in the Cd contaminated soil, and they were mostly enriched to the metabolism, biosynthesis and degradation of amino acids, fatty acids and nucleotides, which was related to Cd tolerance of the microorganisms.

CONCLUSIONS: Cd-contamination can decrease the taxonomic species of microbes in soil and change the soil microbial composition. The functional pathways involved in the soil change with microbial structure variation, many of which are related to the heavy metal tolerance of soil microbes. The Cd-contaminated soil microbes is a potential resource for exploring cadmium resistant or tolerant bacteria.}, } @article {pmid29438346, year = {2018}, author = {Wang, C and Zaheer, M and Bian, F and Quach, D and Swennes, AG and Britton, RA and Pflugfelder, SC and de Paiva, CS}, title = {Sjögren-Like Lacrimal Keratoconjunctivitis in Germ-Free Mice.}, journal = {International journal of molecular sciences}, volume = {19}, number = {2}, pages = {}, pmid = {29438346}, issn = {1422-0067}, support = {P30 CA125123/CA/NCI NIH HHS/United States ; T32 AI053831/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; P30 AI036211/AI/NIAID NIH HHS/United States ; P30 EY002520/EY/NEI NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; R01 EY026893/EY/NEI NIH HHS/United States ; }, mesh = {Animals ; CD4-Positive T-Lymphocytes/immunology ; Fecal Microbiota Transplantation ; Female ; Germ-Free Life/*immunology ; Homeodomain Proteins/genetics/metabolism ; Immunity, Innate ; Interferon-gamma/metabolism ; Keratoconjunctivitis/immunology/*microbiology/therapy ; Male ; Mice ; Mice, Inbred C57BL ; Microbiota ; }, abstract = {Commensal bacteria play an important role in the formation of the immune system but their role in the maintenance of immune homeostasis at the ocular surface and lacrimal gland remains poorly understood. This study investigated the eye and lacrimal gland phenotype in germ-free and conventional C57BL/6J mice. Our results showed that germ-free mice had significantly greater corneal barrier disruption, greater goblet cell loss, and greater total inflammatory cell and CD4[+] T cell infiltration within the lacrimal gland compared to the conventionally housed group. A greater frequency of CD4[+]IFN-γ[+] cells was observed in germ-free lacrimal glands. Females exhibited a more severe phenotype compared to males. Adoptive transfer of CD4[+] T cells isolated from female germ-free mice into RAG1KO mice transferred Sjögren-like lacrimal keratoconjunctivitis. Fecal microbiota transplant from conventional mice reverted dry eye phenotype in germ-free mice and decreased CD4[+]IFN-γ[+] cells to levels similar to conventional C57BL/6J mice. These findings indicate that germ-free mice have a spontaneous lacrimal keratoconjunctivitis similar to that observed in Sjögren syndrome patients and demonstrate that commensal bacteria function in maintaining immune homeostasis on the ocular surface. Thus, manipulation of intestinal commensal bacteria has the potential to become a novel therapeutic approach to treat Sjögren Syndrome.}, } @article {pmid29436230, year = {2018}, author = {Xiao, J and Tanca, A and Jia, B and Yang, R and Wang, B and Zhang, Y and Li, J}, title = {Metagenomic Taxonomy-Guided Database-Searching Strategy for Improving Metaproteomic Analysis.}, journal = {Journal of proteome research}, volume = {17}, number = {4}, pages = {1596-1605}, doi = {10.1021/acs.jproteome.7b00894}, pmid = {29436230}, issn = {1535-3907}, mesh = {Classification/methods ; Computer Simulation ; Data Mining/*methods ; Databases, Protein ; Metagenomics/*standards ; *Microbiota ; Proteins/*analysis ; Proteomics/*standards ; }, abstract = {Metaproteomics provides a direct measure of the functional information by investigating all proteins expressed by a microbiota. However, due to the complexity and heterogeneity of microbial communities, it is very hard to construct a sequence database suitable for a metaproteomic study. Using a public database, researchers might not be able to identify proteins from poorly characterized microbial species, while a sequencing-based metagenomic database may not provide adequate coverage for all potentially expressed protein sequences. To address this challenge, we propose a metagenomic taxonomy-guided database-search strategy (MT), in which a merged database is employed, consisting of both taxonomy-guided reference protein sequences from public databases and proteins from metagenome assembly. By applying our MT strategy to a mock microbial mixture, about two times as many peptides were detected as with the metagenomic database only. According to the evaluation of the reliability of taxonomic attribution, the rate of misassignments was comparable to that obtained using an a priori matched database. We also evaluated the MT strategy with a human gut microbial sample, and we found 1.7 times as many peptides as using a standard metagenomic database. In conclusion, our MT strategy allows the construction of databases able to provide high sensitivity and precision in peptide identification in metaproteomic studies, enabling the detection of proteins from poorly characterized species within the microbiota.}, } @article {pmid29434314, year = {2018}, author = {Serena, C and Ceperuelo-Mallafré, V and Keiran, N and Queipo-Ortuño, MI and Bernal, R and Gomez-Huelgas, R and Urpi-Sarda, M and Sabater, M and Pérez-Brocal, V and Andrés-Lacueva, C and Moya, A and Tinahones, FJ and Fernández-Real, JM and Vendrell, J and Fernández-Veledo, S}, title = {Elevated circulating levels of succinate in human obesity are linked to specific gut microbiota.}, journal = {The ISME journal}, volume = {12}, number = {7}, pages = {1642-1657}, pmid = {29434314}, issn = {1751-7370}, mesh = {Adult ; Aged ; Bacteria/classification/genetics/isolation & purification/metabolism ; Biomarkers/blood ; Cross-Sectional Studies ; Diabetes Mellitus, Type 2/blood/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; Obesity/blood/*microbiology ; Phylogeny ; Prospective Studies ; Succinic Acid/*blood ; }, abstract = {Gut microbiota-related metabolites are potential clinical biomarkers for cardiovascular disease (CVD). Circulating succinate, a metabolite produced by both microbiota and the host, is increased in hypertension, ischemic heart disease, and type 2 diabetes. We aimed to analyze systemic levels of succinate in obesity, a major risk factor for CVD, and its relationship with gut microbiome. We explored the association of circulating succinate with specific metagenomic signatures in cross-sectional and prospective cohorts of Caucasian Spanish subjects. Obesity was associated with elevated levels of circulating succinate concomitant with impaired glucose metabolism. This increase was associated with specific changes in gut microbiota related to succinate metabolism: a higher relative abundance of succinate-producing Prevotellaceae (P) and Veillonellaceae (V), and a lower relative abundance of succinate-consuming Odoribacteraceae (O) and Clostridaceae (C) in obese individuals, with the (P + V/O + C) ratio being a main determinant of plasma succinate. Weight loss intervention decreased (P + V/O + C) ratio coincident with the reduction in circulating succinate. In the spontaneous evolution after good dietary advice, alterations in circulating succinate levels were linked to specific metagenomic signatures associated with carbohydrate metabolism and energy production with independence of body weight change. Our data support the importance of microbe-microbe interactions for the metabolite signature of gut microbiome and uncover succinate as a potential microbiota-derived metabolite related to CVD risk.}, } @article {pmid29434076, year = {2018}, author = {Hamada, S and Masamune, A and Nabeshima, T and Shimosegawa, T}, title = {Differences in Gut Microbiota Profiles between Autoimmune Pancreatitis and Chronic Pancreatitis.}, journal = {The Tohoku journal of experimental medicine}, volume = {244}, number = {2}, pages = {113-117}, doi = {10.1620/tjem.244.113}, pmid = {29434076}, issn = {1349-3329}, mesh = {Aged ; Autoimmune Diseases/*microbiology ; Bacteria/genetics ; DNA/genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Middle Aged ; Pancreatitis, Chronic/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Host-derived factors alter gut microenvironment, and changes in gut microbiota also affect biological functions of host. Alterations of gut microbiota have been reported in a wide variety of diseases, but the whole picture of alterations in pancreatic diseases remains to be clarified. In particular, the gut microbiota may be affected by malnutrition or impaired exocrine pancreas function that is associated with pancreatic diseases. We here conducted comprehensive analysis of gut microbiota in patients with type 1 autoimmune pancreatitis (AIP), a pancreatic manifestation of the systemic IgG4-related disease, and chronic pancreatitis (CP). The two diseases were selected, because altered immune reactions in AIP and/or long-standing malnutrition in CP may influence the gut microbiota. Fecal samples were obtained from 12 patients with AIP before the steroid therapy and 8 patients with CP. Metagenome DNA was extracted, and microbiota was analyzed by next generation sequencing. Gut microbiota profiles were different between patients with AIP and those with CP; namely, the proportions of Bacteroides, Streptococcus and Clostridium species were higher in patients with CP. The reasons for the increased proportion of these bacterial species remain unknown, but may reflect malabsorption and/or decreased pancreatic enzymes, both of which are associated with CP. Incidentally, the identified Streptococcus species are oral cavity inhabitants and also known as pathogens for endocarditis. Despite the small sample size, this study has shown the differences in gut microbiota profiles between AIP and CP. Comprehensive analysis of the gut microbiota may be useful for the differential diagnosis of pancreatic diseases.}, } @article {pmid29433401, year = {2018}, author = {Alex, CE and Kubiski, SV and Li, L and Sadeghi, M and Wack, RF and McCarthy, MA and Pesavento, JB and Delwart, E and Pesavento, PA}, title = {Amdoparvovirus Infection in Red Pandas (Ailurus fulgens).}, journal = {Veterinary pathology}, volume = {55}, number = {4}, pages = {552-561}, doi = {10.1177/0300985818758470}, pmid = {29433401}, issn = {1544-2217}, mesh = {Ailuridae/*virology ; Animals ; Endangered Species ; Feces/virology ; Female ; *Genetic Variation ; Genome, Viral/*genetics ; In Situ Hybridization/veterinary ; Male ; Metagenomics ; Microscopy, Electron/veterinary ; Parvoviridae Infections/diagnostic imaging/pathology/*veterinary/virology ; Parvovirinae/genetics/*isolation & purification ; Phylogeny ; Polymerase Chain Reaction/veterinary ; Virus Shedding ; }, abstract = {Aleutian mink disease virus is the type species in the genus Amdoparvovirus, and in mink and other Mustelidae can cause either subclinical disease or fatal chronic immune stimulation and immune complex disease. The authors describe a novel amdoparvovirus in the endangered red panda (Ailurus fulgens), discovered using viral metagenomics. The authors analyzed the prevalence, tissue distribution, and disease association by PCR, in situ hybridization, electron microscopy, and histology in a group of 6 red pandas from a single zoological collection. The study incorporates a fecal shedding survey and analysis of tissues from 4 necropsied animals over a 12-year span. The tentatively named red panda amdoparvovirus (RpAPV) was detected in the feces and/or tissues of all animals tested. At necropsy of 1 geriatric animal, infection was associated with pyogranulomatous peritonitis, pancreatitis, and myocarditis. Other animals had detectable low-level viral nucleic acid in lymph nodes and both oral and intestinal epithelium at the time of necropsy. Full-length genome sequences of RpAPV strains from 2 animals had 12% sequence divergence, demonstrating genetic diversity even among in-contact animals. RpAPV is a persistent infection in this cohort of red pandas, and has variable clinical expression.}, } @article {pmid29433218, year = {2018}, author = {Higgins, D and Pal, C and Sulaiman, IM and Jia, C and Zerwekh, T and Dowd, SE and Banerjee, P}, title = {Application of high-throughput pyrosequencing in the analysis of microbiota of food commodities procured from small and large retail outlets in a U.S. metropolitan area - A pilot study.}, journal = {Food research international (Ottawa, Ont.)}, volume = {105}, number = {}, pages = {29-40}, doi = {10.1016/j.foodres.2017.10.057}, pmid = {29433218}, issn = {1873-7145}, support = {U54 FD004330/FD/FDA HHS/United States ; }, mesh = {Aeromonas/isolation & purification ; Bacillus/isolation & purification ; Computational Biology ; DNA, Bacterial/genetics/*isolation & purification ; Enterobacter/isolation & purification ; Firmicutes/isolation & purification ; *Food Microbiology ; *High-Throughput Nucleotide Sequencing ; Meat Products/microbiology ; *Microbiota ; Pantoea/isolation & purification ; Pilot Projects ; Proteobacteria/isolation & purification ; RNA, Ribosomal, 16S/genetics/isolation & purification ; Sequence Analysis, DNA ; Tennessee ; Vegetables/microbiology ; }, abstract = {With the advent of high-throughput sequencing technologies, it is possible to comprehensively analyze the microbial community of foods without culturing them in the laboratory. The estimation of all microbes inhabiting a food commodity (food microbiota) therefore may shed light on the microbial quality and safety of foods. In this study, we utilized high-throughput pyrosequencing of 16S rRNA genes as well as traditional microbiological methods to evaluate the bacterial diversity and the predicted metabolic pathways associated with the bacterial communities of selected foods (romaine lettuce, cabbage, deli meat, and chicken legs, total 200 samples) procured from small and large retail outlets located in Memphis-Shelby County, Tennessee, USA. For high-throughput sequencing, microbial genomic DNA was directly extracted from the food products and subjected to genetic sequencing. Aerobic plate count of all food samples was also performed. Foods from small stores (such as corner stores) were found to contain higher bacterial counts as compared to large stores (such as supermarkets). High-throughput pyrosequencing in tandem with bioinformatics analyses revealed a comprehensive picture of the bacterial ecology of foods at different taxonomic levels. Firmicutes and Proteobacteria were the most abundant phyla across all products. At the genus level, Enterobacter and Pantoea in vegetables, and Bacillus and Aeromonas in animal products were found to be the most abundant. The bacterial predicted metabolic pathways such as inosine-5'-phosphate biosynthesis I, methylglyoxal (MG) degradation pathways, urea cycle, dTDP-l-rhamnose biosynthesis I, and mevalonate pathway I differed in foods procured from small stores as compared to large groceries or supermarkets. The results from this study revealed that the bacterial ecology (both in terms of numbers and types of bacteria) of food commodities might differ based on the vending outlet type (large vs. small) of retail stores. The overall estimation bacterial communities in foods by high-throughput sequencing method may be useful to identify potential taxa responsible for food spoilage. Moreover, the data from pyrosequencing of 16S rRNA genes can also be applied to infer major metabolic pathways in bacteria inhabiting different foods. This may reflect the role of these pathways in food-bacteria interaction and adaptation.}, } @article {pmid29432849, year = {2018}, author = {Joshi, A and Lanjekar, V and Dhakephalkar, PK and Dagar, SS}, title = {Cultivation of multiple genera of hydrogenotrophic methanogens from different environmental niches.}, journal = {Anaerobe}, volume = {50}, number = {}, pages = {64-68}, doi = {10.1016/j.anaerobe.2018.02.001}, pmid = {29432849}, issn = {1095-8274}, mesh = {Animals ; *Environmental Microbiology ; Feces/microbiology ; Geologic Sediments/microbiology ; Hydrogen/*metabolism ; Metagenome ; Metagenomics/methods ; Methane/*metabolism ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Rumen/microbiology ; }, abstract = {Six genera of hydrogenotrophic methanogens, namely Methanobrevibacter, Methanobacterium, Methanocorpusculum, Methanothermobacter, Methanoculleus, and Methanospirillum were cultivated from diverse environmental niches like rumen, feces, gut, and sediments using BY medium. We also report a putative novel genus and two novel species of methanogens isolated from termite, Indian star tortoise, and green iguana.}, } @article {pmid29428461, year = {2018}, author = {Perfumo, A and Banat, IM and Marchant, R}, title = {Going Green and Cold: Biosurfactants from Low-Temperature Environments to Biotechnology Applications.}, journal = {Trends in biotechnology}, volume = {36}, number = {3}, pages = {277-289}, doi = {10.1016/j.tibtech.2017.10.016}, pmid = {29428461}, issn = {1879-3096}, mesh = {Antarctic Regions ; Bacteria/metabolism ; Biodegradation, Environmental ; *Biotechnology ; *Cold Temperature ; Enzymes/biosynthesis ; Glycolipids/*biosynthesis/*chemical synthesis ; Lakes/microbiology ; Metagenomics ; Soil Microbiology ; Surface-Active Agents/*chemical synthesis/metabolism ; Water Microbiology ; }, abstract = {Approximately 80% of the Earth's biosphere is cold, at an average temperature of 5°C, and is populated by a diversity of microorganisms that are a precious source of molecules with high biotechnological potential. Biosurfactants from cold-adapted organisms can interact with multiple physical phases - water, ice, hydrophobic compounds, and gases - at low and freezing temperatures and be used in sustainable (green) and low-energy-impact (cold) products and processes. We review the biodiversity of microbial biosurfactants produced in cold habitats and provide a perspective on the most promising future applications in environmental and industrial technologies. Finally, we encourage exploring the cryosphere for novel types of biosurfactants via both culture screening and functional metagenomics.}, } @article {pmid29427960, year = {2018}, author = {Fontana, A and Campanaro, S and Treu, L and Kougias, PG and Cappa, F and Morelli, L and Angelidaki, I}, title = {Performance and genome-centric metagenomics of thermophilic single and two-stage anaerobic digesters treating cheese wastes.}, journal = {Water research}, volume = {134}, number = {}, pages = {181-191}, doi = {10.1016/j.watres.2018.02.001}, pmid = {29427960}, issn = {1879-2448}, mesh = {Anaerobiosis ; Bacteria/genetics/metabolism ; Bioreactors/*microbiology ; *Cheese ; Metagenomics ; Methane/metabolism ; Wastewater ; }, abstract = {The present research is the first comprehensive study regarding the thermophilic anaerobic degradation of cheese wastewater, which combines the evaluation of different reactor configurations (i.e. single and two-stage continuous stirred tank reactors) on the process efficiency and the in-depth characterization of the microbial community structure using genome-centric metagenomics. Both reactor configurations showed acidification problems under the tested organic loading rates (OLRs) of 3.6 and 2.4 g COD/L-reactor day and the hydraulic retention time (HRT) of 15 days. However, the two-stage design reached a methane yield equal to 95% of the theoretical value, in contrast with the single stage configuration, which reached a maximum of 33% of the theoretical methane yield. The metagenomic analysis identified 22 new population genomes and revealed that the microbial compositions between the two configurations were remarkably different, demonstrating a higher methanogenic biodiversity in the two-stage configuration. In fact, the acidogenic reactor of the serial configuration was almost solely composed by the lactose degrader Bifidobacterium crudilactis UC0001. The predictive functional analyses of the main population genomes highlighted specific metabolic pathways responsible for the AD process and the mechanisms of main intermediates production. Particularly, the acetate accumulation experienced by the single stage configuration was mainly correlated to the low abundant syntrophic acetate oxidizer Tepidanaerobacter acetatoxydans UC0018 and to the absence of aceticlastic methanogens.}, } @article {pmid29427518, year = {2018}, author = {Guirro, M and Costa, A and Gual-Grau, A and Mayneris-Perxachs, J and Torrell, H and Herrero, P and Canela, N and Arola, L}, title = {Multi-omics approach to elucidate the gut microbiota activity: Metaproteomics and metagenomics connection.}, journal = {Electrophoresis}, volume = {39}, number = {13}, pages = {1692-1701}, doi = {10.1002/elps.201700476}, pmid = {29427518}, issn = {1522-2683}, mesh = {Animals ; Cardiovascular Diseases/microbiology ; Dietary Supplements/adverse effects ; *Gastrointestinal Microbiome ; Male ; *Metagenomics ; Obesity/microbiology ; *Proteomics ; Rats ; Rats, Sprague-Dawley ; }, abstract = {Over the last few years, the application of high-throughput meta-omics methods has provided great progress in improving the knowledge of the gut ecosystem and linking its biodiversity to host health conditions, offering complementary support to classical microbiology. Gut microbiota plays a crucial role in relevant diseases such as obesity or cardiovascular disease (CVD), and its regulation is closely influenced by several factors, such as dietary composition. In fact, polyphenol-rich diets are the most palatable treatment to prevent hypertension associated with CVD, although the polyphenol-microbiota interactions have not been completely elucidated. For this reason, the aim of this study was to evaluate microbiota effect in obese rats supplemented by hesperidin, after being fed with cafeteria or standard diet, using a multi meta-omics approaches combining strategy of metagenomics and metaproteomics analysis. We reported that cafeteria diet induces obesity, resulting in changes in the microbiota composition, which are related to functional alterations at proteome level. In addition, hesperidin supplementation alters microbiota diversity and also proteins involved in important metabolic pathways. Overall, going deeper into strategies to integrate omics sciences is necessary to understand the complex relationships between the host, gut microbiota, and diet.}, } @article {pmid29425888, year = {2018}, author = {Rajpoot, M and Sharma, AK and Sharma, A and Gupta, GK}, title = {Understanding the microbiome: Emerging biomarkers for exploiting the microbiota for personalized medicine against cancer.}, journal = {Seminars in cancer biology}, volume = {52}, number = {Pt 1}, pages = {1-8}, doi = {10.1016/j.semcancer.2018.02.003}, pmid = {29425888}, issn = {1096-3650}, mesh = {*Biomarkers, Tumor ; Genetic Variation ; Humans ; Metagenomics/methods/trends ; Microbiota/*genetics ; Neoplasms/*diagnosis/*microbiology ; Precision Medicine/*methods/trends ; Sequence Analysis, DNA/methods ; }, abstract = {The human body is a home to more than 1 trillion microbes with a diverse variety of commensal microbes that play a crucial role towards the health of the individual. These microbes occupy different habitats such as gut, skin, vagina, oral etc. Not only the types and abundance of microbes are different in different organs, but also these may differ in different individuals. The genome of these microbiota and their ecosystem constitute to form a microbiome. Factors such as diet, environment, host genetics etc. may be the reason behind the wide microbial diversity. A number of studies performed on human microbiome have revealed that microbiota present in healthy and diseased individuals are distinct. Altered microbiome is many a times the reason behind the overexpression of genes which may cause complex diseases including cancer. Manipulation of the human microbiome can be done by microbial supplements such as probiotics or synbiotics, diet or prebiotics and microbial suppression strategies using antibiotics. Recent advances in genome sequencing technologies and metagenomic analysis provide us the broader understanding of these commensal microbes and highlighting the distinctive features of microbiome during healthy and disease states. Molecular pathological epidemiology (MPE) studies have been very helpful in providing insights into the pathological process behind disease evolution and progression by determining the specific etiological factors. New emerging field of research targets the microbiome for therapeutic purposes by which personalized medicines can be made for treating various types of tumors. Screening programmes might be helpful in identifying patients who are at the verge of developing cancer and in delivering appropriate approaches according to individual risk modes so that disease could be prevented.}, } @article {pmid29423379, year = {2018}, author = {Li, Q and Wang, C and Tang, C and Zhao, X and He, Q and Li, J}, title = {Identification and Characterization of Blood and Neutrophil-Associated Microbiomes in Patients with Severe Acute Pancreatitis Using Next-Generation Sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {5}, pmid = {29423379}, issn = {2235-2988}, mesh = {Acute Disease ; Adult ; Aged ; Biomarkers ; Comorbidity ; Female ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions/immunology ; Humans ; Male ; Metabolome ; *Metagenome ; *Metagenomics ; *Microbiota ; Middle Aged ; Neutrophils/metabolism/*microbiology ; Pancreatitis/*complications/diagnosis/metabolism ; Phylogeny ; RNA, Ribosomal, 16S ; Sepsis/diagnosis/*etiology/metabolism ; Young Adult ; }, abstract = {Infectious complications are a leading cause of death for patients with severe acute pancreatitis (SAP). Yet, our knowledge about details of the blood microbial landscape in SAP patients remains limited. Recently, some studies have reported that the peripheral circulation harbors a diverse bacterial community in healthy and septic subjects. The objective of this study was to examine the presence of the blood bacterial microbiome in SAP patients and its potential role in the development of infectious complications. Here we conducted a prospective observational study on a cohort of 50 SAP patients and 12 healthy subjects to profile the bacterial composition in the blood. The patients were subgrouped into uninfected (n = 17), infected (n = 16), and septic (n = 17) cases. Applying 16S rDNA-based next-generation sequencing technique, we investigated blood and neutrophil-associated microbiomes in SAP patients, and assessed their connections with immunological alterations. Based on the sequencing data, a diverse bacterial microbiota was found in peripheral blood and neutrophils from the healthy and SAP subjects. As compared to healthy controls, the blood and neutrophil-associated microbiomes in the patients were significantly altered, with an expansion in Bacteroidetes and Firmicutes as well as a decrease in Actinobacteria. Variations in the microbiome composition in patients were associated with immunological disorders, including altered lymphocyte subgroups, elevated levels of serum cytokines and altered proteomic profiles of neutrophils. However, no significant compositional difference was observed between the patient subgroups, implying that the microbiota alterations might not be linked to presence/absence of infectious complications in SAP. Together, we present an initial description of the blood and neutrophil-associated bacterial profiles in SAP patients, offering novel evidence for the existence of the blood microbiome. Identification of the blood microbiome provides novel insights into characteristics and diagnostics of bacteremia in the patients. Further study is required to assess the possible implications of the blood microbiome in health and diseases.}, } @article {pmid29422490, year = {2018}, author = {Xu, W and You, Y and Wang, Z and Chen, W and Zeng, J and Zhao, X and Su, Y}, title = {Dibutyl phthalate alters the metabolic pathways of microbes in black soils.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2605}, pmid = {29422490}, issn = {2045-2322}, mesh = {Dibutyl Phthalate/metabolism/*toxicity ; Environmental Pollutants/metabolism/*toxicity ; Metabolic Networks and Pathways ; Metagenome ; Microbiota/*drug effects ; Soil ; *Soil Microbiology ; Soil Pollutants/metabolism/*toxicity ; }, abstract = {Dibutyl phthalate (DBP) is well known as a high-priority pollutant. This study explored the impacts of DBP on the metabolic pathways of microbes in black soils in the short term (20 days). The results showed that the microbial communities were changed in black soils with DBP. In nitrogen cycling, the abundances of the genes were elevated by DBP. DBP contamination facilitated 3'-phosphoadenosine-5'-phosphosulfate (PAPS) formation, and the gene flux of sulfate metabolism was increased. The total abundances of ABC transporters and the gene abundances of the monosaccharide-transporting ATPases MalK and MsmK were increased by DBP. The total abundance of two-component system (TCS) genes and the gene abundances of malate dehydrogenase, histidine kinase and citryl-CoA lyase were increased after DBP contamination. The total abundance of phosphotransferase system (PTS) genes and the gene abundances of phosphotransferase, Crr and BglF were raised by DBP. The increased gene abundances of ABC transporters, TCS and PTS could be the reasons for the acceleration of nitrogen, carbon and sulfate metabolism. The degrading-genes of DBP were increased markedly in soil exposed to DBP. In summary, DBP contamination altered the microbial community and enhanced the gene abundances of the carbon, nitrogen and sulfur metabolism in black soils in the short term.}, } @article {pmid29416123, year = {2018}, author = {Kim, MS and Bae, JW}, title = {Lysogeny is prevalent and widely distributed in the murine gut microbiota.}, journal = {The ISME journal}, volume = {12}, number = {4}, pages = {1127-1141}, pmid = {29416123}, issn = {1751-7370}, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification ; Bacteriophages/genetics ; CRISPR-Cas Systems ; *Gastrointestinal Microbiome ; *Lysogeny ; Male ; Metagenome ; Mice, Inbred C57BL ; Phylogeny ; Prophages/genetics ; Virus Activation ; }, abstract = {Bacteriophages are central members and potential modulators of the gut microbiome; however, the ecological and evolutionary relationships of gut bacteria and phages are poorly understood. Here we investigated the abundance and diversity of lysogenic bacteria (lysogens) in the bacterial community of C57BL/6J mice by detecting integrated prophages in genomes reconstructed from the metagenome of commensal bacteria. For the activities of lysogens and prophages, we compared the prophage genomes with the metagenome of free phages. The majority of commensal bacteria in different taxa were identified as lysogens. More lysogens were found among Firmicutes and Proteobacteria, than among Bacteroidetes and Actinobacteria. The prophage genomes shared high sequence similarity with the metagenome of free phages, indicating that most lysogens appeared to be active, and that prophages are spontaneously induced as active phages; dietary interventions changed the composition of the induced prophages. By contrast, CRISPR-Cas systems were present in few commensal bacteria, and were rarely active against gut phages. The structure of the bacteria-phage infection networks was "nested-modular", with modularity emerging across taxonomic scales, indicating that temperate phage features have developed over a long phylogenetic timescale. We concluded that phage generalists contribute to the prevalence of lysogeny in the gut ecosystem.}, } @article {pmid29415909, year = {2018}, author = {Utami, YD and Kuwahara, H and Murakami, T and Morikawa, T and Sugaya, K and Kihara, K and Yuki, M and Lo, N and Deevong, P and Hasin, S and Boonriam, W and Inoue, T and Yamada, A and Ohkuma, M and Hongoh, Y}, title = {Phylogenetic Diversity and Single-Cell Genome Analysis of "Melainabacteria", a Non-Photosynthetic Cyanobacterial Group, in the Termite Gut.}, journal = {Microbes and environments}, volume = {33}, number = {1}, pages = {50-57}, pmid = {29415909}, issn = {1347-4405}, mesh = {Animals ; Cyanobacteria/classification/*genetics ; Gastrointestinal Microbiome ; Genetic Variation ; *Genome, Bacterial ; In Situ Hybridization, Fluorescence ; Isoptera/*microbiology ; *Photosynthesis ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Single-Cell Analysis ; Symbiosis ; }, abstract = {Termite guts harbor diverse yet-uncultured bacteria, including a non-photosynthetic cyanobacterial group, the class "Melainabacteria". We herein reported the phylogenetic diversity of "Melainabacteria" in the guts of diverse termites and conducted a single-cell genome analysis of a melainabacterium obtained from the gut of the termite Termes propinquus. We performed amplicon sequencing of 16S rRNA genes from the guts of 60 termite and eight cockroach species, and detected melainabacterial sequences in 48 out of the 68 insect species, albeit with low abundances (0.02-1.90%). Most of the melainabacterial sequences obtained were assigned to the order "Gastranaerophilales" and appeared to form clusters unique to termites and cockroaches. A single-cell genome of a melainabacterium, designated phylotype Tpq-Mel-01, was obtained using a fluorescence-activated cell sorter and whole genome amplification. The genome shared basic features with other melainabacterial genomes previously reconstructed from the metagenomes of human and koala feces. The bacterium had a small genome (~1.6 Mb) and possessed fermentative pathways possibly using sugars and chitobiose as carbon and energy sources, while the pathways for photosynthesis and carbon fixation were not found. The genome contained genes for flagellar components and chemotaxis; therefore, the bacterium is likely motile. A fluorescence in situ hybridization analysis showed that the cells of Tpq-Mel-01 and/or its close relatives are short rods with the dimensions of 1.1±0.2 μm by 0.5±0.1 μm; for these bacteria, we propose the novel species, "Candidatus Gastranaerophilus termiticola". Our results provide fundamental information on "Melainabacteria" in the termite gut and expand our knowledge on this underrepresented, non-photosynthetic cyanobacterial group.}, } @article {pmid29415902, year = {2018}, author = {Kishida, S and Kato-Mori, Y and Hagiwara, K}, title = {Influence of changes in the intestinal microflora on the immune function in mice.}, journal = {The Journal of veterinary medical science}, volume = {80}, number = {3}, pages = {440-446}, pmid = {29415902}, issn = {1347-7439}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Concanavalin A/metabolism ; Cytokines/metabolism ; Flow Cytometry ; Gastrointestinal Microbiome/drug effects/*immunology ; Immunity/immunology/*physiology ; Mice/immunology/microbiology ; Mice, Inbred BALB C/immunology/microbiology ; RNA, Ribosomal, 16S ; Real-Time Polymerase Chain Reaction ; Spleen/cytology ; T-Lymphocyte Subsets/immunology/physiology ; }, abstract = {The composition of the intestinal microbiota is related to the health and immune function of the host. Administration of antibiotics affects the composition of the intestinal microbiota. However, the effects of immune function on the composition of the intestinal microbiota are still unclear. In this study, we investigated the lymphocyte composition and determined the relationships between lymphocyte function and the intestinal microbiota following antibiotic treatment in mice. To change the composition of the intestinal microbiota, mice were treated with or without antibiotics. Analysis of intestinal microbiota was performed by metagenomic analysis targeting 16S rRNA. Lymphocyte subsets of splenocytes were measured by flow cytometry. For functional analysis of T cells, splenocytes were stimulated with concanavalin (Con A), and cytokine gene expression was measured by real-time polymerase chain reaction. Firmicutes were predominant in the control group, whereas Bacteroidetes predominated in the antibiotic-treated group, as determined by metagenomic analysis. The diversity of the microbiota decreased in the antibiotic-treated group. Analysis of lymphocyte subsets showed that CD3[+] cells decreased, whereas CD19[+] cells increased in the antibiotic-treated group. All cytokine genes in splenocytes treated with Con A were downregulated in the antibiotic-treated group; in particular, genes encoding interferon-γ, interleukin (IL)-6, and IL-13 significantly decreased. Taken together, these results revealed that changes in the composition of the intestinal microbiota by antibiotic treatment influenced the population of lymphocytes in splenocytes and affected the immune response.}, } @article {pmid29414445, year = {2018}, author = {Quatrini, R and Johnson, DB}, title = {Microbiomes in extremely acidic environments: functionalities and interactions that allow survival and growth of prokaryotes at low pH.}, journal = {Current opinion in microbiology}, volume = {43}, number = {}, pages = {139-147}, doi = {10.1016/j.mib.2018.01.011}, pmid = {29414445}, issn = {1879-0364}, mesh = {Acids/*pharmacology ; Archaea/genetics/*growth & development/physiology ; Hydrogen-Ion Concentration ; Metagenomics ; Microbial Consortia/drug effects/physiology ; Microbial Viability ; Microbiota/*drug effects/genetics/*physiology ; Phylogeny ; Proteobacteria/genetics/*growth & development/physiology ; }, abstract = {Extremely acidic environments have global distribution and can have natural or, increasingly, anthropogenic origins. Extreme acidophiles grow optimally at pH 3 or less, have multiple strategies for tolerating stresses that accompany high levels of acidity and are scattered in all three domains of the tree of life. Metagenomic studies have expanded knowledge of the diversity of extreme acidophile communities, their ecological networks and their metabolic potentials, both confirmed and inferred. High resolution compositional and functional profiling of these microbiomes have begun to reveal spatial diversity patterns at global, regional, local, zonal and micro-scales. Future integration of genomic and other meta-omic data will offer new opportunities to utilize acidic microbiomes and to engineer beneficial interactions within them in biotechnologies.}, } @article {pmid29414358, year = {2018}, author = {Yang, Y and Wang, W}, title = {Benzyldimethyldodecyl ammonium chloride shifts the proliferation of functional genes and microbial community in natural water from eutrophic lake.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {236}, number = {}, pages = {355-365}, doi = {10.1016/j.envpol.2018.01.059}, pmid = {29414358}, issn = {1873-6424}, mesh = {Benzalkonium Compounds/*toxicity ; Eutrophication ; Genes, Bacterial ; Lakes/*microbiology ; Metagenome/*drug effects ; Microbial Consortia/*drug effects/genetics ; Oxidoreductases/genetics ; Pseudomonas/genetics ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Benzylalkyldimethylethyl ammonium compounds are pervasive in natural environments and toxic at high concentrations. The changes in functional genes and microbial diversity in eutrophic lake samples exposed to benzyldimethyldodecyl ammonium chloride (BAC) were assessed. BAC exerted negative effects on bacteria abundance, particularly at concentrations of 100 μg L[-1] and higher. A significant increase in the number of the quaternary ammonium compound-resistant gene qacA/B was recorded within the 10 μg L[-1] treatment after the first day of exposure. Not all antibiotic resistance genes increased in abundance as the concentrations of BAC increased; rather, gene abundances were dependent on the gene type, concentrations of BAC, and contact time. The nitrogen fixation-related gene nifH and ammonia monooxygenase gene amoA were inhibited by high concentrations of BAC after the first day, whereas an increase of the nitrite reductase gene nirK was stimulated by exposure. Microbial communities within higher treatment levels (1000 and 10 000 μg L[-1]) exhibited significantly different community composition compared to other treatment levels and the control. Selective enrichment of Rheinheimera, Pseudomonas, and Vogesella were found in the higher treatment levels, suggesting that these bacteria have some resistance or degradation capacity to BAC. Genes related with RNA processing and modification, transcription, lipid transport and metabolism, amino acid transport and metabolism, and cell motility of microbial community function were involved in the process exposed to the BAC stress.}, } @article {pmid29408266, year = {2018}, author = {Hemmink, JD and Sitt, T and Pelle, R and de Klerk-Lorist, LM and Shiels, B and Toye, PG and Morrison, WI and Weir, W}, title = {Ancient diversity and geographical sub-structuring in African buffalo Theileria parva populations revealed through metagenetic analysis of antigen-encoding loci.}, journal = {International journal for parasitology}, volume = {48}, number = {3-4}, pages = {287-296}, pmid = {29408266}, issn = {1879-0135}, support = {BB/H009515/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/D/05201234/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004227/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Analysis of Variance ; Animals ; Antigens, Protozoan/*genetics ; Base Sequence ; Buffaloes/*parasitology ; Cattle ; DNA, Ribosomal/chemistry ; Disease Reservoirs/parasitology ; Genes, Protozoan/genetics ; Genetic Variation ; Genetics, Population ; High-Throughput Nucleotide Sequencing/veterinary ; Kenya ; Metagenome/*genetics ; Phylogeny ; Protozoan Vaccines/genetics ; RNA, Ribosomal, 18S/genetics ; South Africa ; Theileria parva/*classification/genetics/immunology ; Theileriasis/*parasitology ; }, abstract = {An infection and treatment protocol involving infection with a mixture of three parasite isolates and simultaneous treatment with oxytetracycline is currently used to vaccinate cattle against Theileria parva. While vaccination results in high levels of protection in some regions, little or no protection is observed in areas where animals are challenged predominantly by parasites of buffalo origin. A previous study involving sequencing of two antigen-encoding genes from a series of parasite isolates indicated that this is associated with greater antigenic diversity in buffalo-derived T. parva. The current study set out to extend these analyses by applying high-throughput sequencing to ex vivo samples from naturally infected buffalo to determine the extent of diversity in a set of antigen-encoding genes. Samples from two populations of buffalo, one in Kenya and the other in South Africa, were examined to investigate the effect of geographical distance on the nature of sequence diversity. The results revealed a number of significant findings. First, there was a variable degree of nucleotide sequence diversity in all gene segments examined, with the percentage of polymorphic nucleotides ranging from 10% to 69%. Second, large numbers of allelic variants of each gene were found in individual animals, indicating multiple infection events. Third, despite the observed diversity in nucleotide sequences, several of the gene products had highly conserved amino acid sequences, and thus represent potential candidates for vaccine development. Fourth, although compelling evidence for population differentiation between the Kenyan and South African T. parva parasites was identified, analysis of molecular variance for each gene revealed that the majority of the underlying nucleotide sequence polymorphism was common to both areas, indicating that much of this aspect of genetic variation in the parasite population arose prior to geographic separation.}, } @article {pmid29408025, year = {2018}, author = {Jeon, SJ and Lima, FS and Vieira-Neto, A and Machado, VS and Lima, SF and Bicalho, RC and Santos, JEP and Galvão, KN}, title = {Shift of uterine microbiota associated with antibiotic treatment and cure of metritis in dairy cows.}, journal = {Veterinary microbiology}, volume = {214}, number = {}, pages = {132-139}, doi = {10.1016/j.vetmic.2017.12.022}, pmid = {29408025}, issn = {1873-2542}, mesh = {Ampicillin/administration & dosage/therapeutic use ; Animals ; Anti-Bacterial Agents/administration & dosage/*therapeutic use ; Bacteria/classification/drug effects/*isolation & purification ; Bacteroidetes/drug effects/isolation & purification ; Cattle ; Cephalosporins/administration & dosage/therapeutic use ; Endometritis/drug therapy/microbiology/*veterinary ; Female ; Microbiota/*drug effects ; Porphyromonas/drug effects/isolation & purification ; Uterus/drug effects/*microbiology ; }, abstract = {Broad-spectrum antibiotics such as ceftiofur and ampicillin are recommended for the treatment of metritis in dairy cows. Nonetheless, little is known about the impacts of antibiotics on the uterine microbiota. Here, we evaluated the shift in uterine microbiota after treating metritic cows with ceftiofur or ampicillin, and also gained insight into the uterine microbiota associated with cure of metritis. Uterine swabs from ceftiofur-treated, ampicillin-treated, and untreated metritic Holstein cows were collected on the day of metritis diagnosis (D1) and on D6 and then used for genomic DNA extraction and sequencing of the V4 hypervariable region of the 16S rRNA gene on the Illumina MiSeq platform. The uterine microbiota consolidated over time by decreasing species richness and increasing evenness; therefore, becoming more homogeneous. The uterine microbial community showed distinct clustering patterns on D6 according to antibiotic treatment, which could be attributed to more dynamic changes in the microbial structure from D1 to D6 in ceftiofur-treated cows. Ceftiofur led to significant changes at the community level, phylum level, and genus level, whereas the changes in ampicillin and untreated cows, although following the same pattern, were mostly non-significant. Bacteroidetes was significantly increased in ceftiofur-treated cows but was not changed after ampicillin and no treatment. Different responses to antibiotics were observed in Porphyromonas, which increased in relative abundance with ceftiofur and decreased with ampicillin. Regardless of treatment group, failure to cure metritis was associated with a decrease in diversity of uterine microbiota and an increase in the relative abundance of Bacteroides, Porphyromonas, and Fusobacterium.}, } @article {pmid29407396, year = {2018}, author = {Wang, Z and Shao, Y}, title = {Effects of microbial diversity on nitrite concentration in pao cai, a naturally fermented cabbage product from China.}, journal = {Food microbiology}, volume = {72}, number = {}, pages = {185-192}, doi = {10.1016/j.fm.2017.12.003}, pmid = {29407396}, issn = {1095-9998}, mesh = {*Biodiversity ; Brassica/chemistry/*microbiology ; China ; Fermentation ; Fermented Foods/*analysis/microbiology ; Food Microbiology ; Lactobacillales/classification/genetics/*isolation & purification/metabolism ; Nitrites/*analysis/metabolism ; Phylogeny ; }, abstract = {Pao cai is a spontaneously fermented cabbage where native bacteria may have an important influence on nitrite content during fermentation. In this research, we used metagenomic-based 16S rRNA gene amplicon sequencing to analyze differences in bacterial composition of pao cai from Hohhot City (northern China) and Guiyang City (southern China). Alongside this, metagenome functional features from the 16S rRNA genes of the microbiome were predicted and correlated with the nitrite content of pao cai. Nitrite-reducing bacterial genera were identified including Lactobacillus (73.37%), Pediococcus (0.93%), Acinetobacter (0.74%), Leuconostoc (0.31%), Weissella (0.14%), Streptococcus (0.09%), Megamonas (0.08%), Enterococcus (0.07%), and Alistipes (0.06%). Lactobacillus was the predominant genus in both the northern and the southern pao cai samples and was significantly negatively correlated with nitrite content; it was more abundant in southern samples than northern samples. Based on determination of alpha and beta diversities of the microbiome in samples, differences in the microbiome of northern and southern pao cai were demonstrated that may influence nitrogen metabolism. This research suggests that 16S rRNA gene amplicon sequencing is an effective way to comprehensively study the microbes with potential nitrite formation or decomposition ability instead of investigating the individual bacterial genera.}, } @article {pmid29405826, year = {2018}, author = {Huang, YY and Martínez-Del Campo, A and Balskus, EP}, title = {Anaerobic 4-hydroxyproline utilization: Discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity.}, journal = {Gut microbes}, volume = {9}, number = {5}, pages = {437-451}, pmid = {29405826}, issn = {1949-0984}, mesh = {Anaerobiosis ; Bacteria/classification/*enzymology/genetics/metabolism ; Bacterial Proteins/genetics/*metabolism ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Humans ; Hydro-Lyases/genetics/*metabolism ; Hydroxyproline/chemistry/*metabolism ; Metabolic Networks and Pathways ; Metagenome ; Microbiota ; Phylogeny ; }, abstract = {The discovery of enzymes responsible for previously unappreciated microbial metabolic pathways furthers our understanding of host-microbe and microbe-microbe interactions. We recently identified and characterized a new gut microbial glycyl radical enzyme (GRE) responsible for anaerobic metabolism of trans-4-hydroxy-l-proline (Hyp). Hyp dehydratase (HypD) catalyzes the removal of water from Hyp to generate Δ[1]-pyrroline-5-carboxylate (P5C). This enzyme is encoded in the genomes of a diverse set of gut anaerobes and is prevalent and abundant in healthy human stool metagenomes. Here, we discuss the roles HypD may play in different microbial metabolic pathways as well as the potential implications of this activity for colonization resistance and pathogenesis within the human gut. Finally, we present evidence of anaerobic Hyp metabolism in sediments through enrichment culturing of Hyp-degrading bacteria, highlighting the wide distribution of this pathway in anoxic environments beyond the human gut.}, } @article {pmid29405134, year = {2017}, author = {Desikan, P}, title = {Our microbial signatures.}, journal = {Indian journal of medical microbiology}, volume = {35}, number = {4}, pages = {443-444}, doi = {10.4103/ijmm.IJMM_17_250}, pmid = {29405134}, issn = {1998-3646}, mesh = {Biological Variation, Individual ; *Dysbiosis ; Healthy Volunteers ; Humans ; Metagenomics ; *Microbiota ; }, } @article {pmid29404836, year = {2018}, author = {Boers, SA and de Zeeuw, M and Jansen, R and van der Schroeff, MP and van Rossum, AMC and Hays, JP and Verhaegh, SJC}, title = {Characterization of the nasopharyngeal and middle ear microbiota in gastroesophageal reflux-prone versus gastroesophageal reflux non-prone children.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {37}, number = {5}, pages = {851-857}, pmid = {29404836}, issn = {1435-4373}, mesh = {Bacterial Typing Techniques ; Biodiversity ; Child ; Child, Preschool ; Ear, Middle/*microbiology ; Female ; Gastroesophageal Reflux/*complications ; Humans ; Infant ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Nasopharyngitis/diagnosis/*etiology ; Nasopharynx/*microbiology ; Otitis Media/diagnosis/*etiology ; RNA, Ribosomal, 16S ; }, abstract = {Otitis media (OM) is one of the most common pediatric infections worldwide, but the complex microbiology associated with OM is poorly understood. Previous studies have shown an association between OM and gastroesophageal reflux (GER) in children. Therefore, in order to bridge the gap in our current understanding of the interaction between GER and OM, we investigated the nasopharyngeal and middle ear microbiota of children suffering from GER-associated OM and OM only, using culture-independent 16S rRNA gene sequencing. Middle ear fluid, nasopharyngeal swabs, and clinical data were collected as part of a prospective pilot study conducted at the Department of Otorhinolaryngology of the Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands. A total of 30 children up to 12 years of age who suffered from recurrent acute otitis media (AOM) (5), chronic otitis media with effusion (OME) (23), or both (2), and who were listed for tympanostomy tube placement, were included in the study. Nine children were included in the GER-associated OM cohort and 21 in the OM-only cohort. We found no obvious effect of GER on the nasopharyngeal and middle ear microbiota between the two groups of children. However, our results highlight the need to assess the true role of Alloiococcus spp. and Turicella spp. in children presenting with a high prevalence of recurrent AOM and chronic OME.}, } @article {pmid29404427, year = {2018}, author = {Hester, ER and Harpenslager, SF and van Diggelen, JMH and Lamers, LL and Jetten, MSM and Lüke, C and Lücker, S and Welte, CU}, title = {Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities.}, journal = {mSystems}, volume = {3}, number = {1}, pages = {}, pmid = {29404427}, issn = {2379-5077}, support = {339880/ERC_/European Research Council/International ; }, abstract = {Wetland ecosystems are important reservoirs of biodiversity and significantly contribute to emissions of the greenhouse gases CO2, N2O, and CH4. High anthropogenic nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity and ecosystem functioning, such as control of greenhouse gas emissions. Therefore, it is important to understand how increased N input into pristine wetlands affects the composition and activity of microorganisms, especially in interaction with dominant wetland plants. In a series of incubations analyzed over 90 days, we disentangled the effects of N fertilization on the microbial community in bulk soil and the rhizosphere of Juncus acutiflorus, a common and abundant graminoid wetland plant. We observed an increase in greenhouse gas emissions when N is increased in incubations with J. acutiflorus, changing the system from a greenhouse gas sink to a source. Using 16S rRNA gene amplicon sequencing, we determined that the bacterial orders Opitutales, subgroup 6 Acidobacteria, and Sphingobacteriales significantly responded to high N availability. Based on metagenomic data, we hypothesize that these groups are contributing to the increased greenhouse gas emissions. These results indicated that increased N input leads to shifts in microbial activity within the rhizosphere, altering N cycling dynamics. Our study provides a framework for connecting environmental conditions of wetland bulk and rhizosphere soil to the structure and metabolic output of microbial communities. IMPORTANCE Microorganisms living within the rhizospheres of wetland plants significantly contribute to greenhouse gas emissions. Understanding how microbes produce these gases under conditions that have been imposed by human activities (i.e., nitrogen pollution) is important to the development of future management strategies. Our results illustrate that within the rhizosphere of the wetland plant Juncus acutiflorus, physiological differences associated with nitrogen availability can influence microbial activity linked to greenhouse gas production. By pairing taxonomic information and environmental conditions like nitrogen availability with functional outputs of a system such as greenhouse gas fluxes, we present a framework to link certain taxa to both nitrogen load and greenhouse gas production. We view this type of combined information as essential in moving forward in our understanding of complex systems such as rhizosphere microbial communities.}, } @article {pmid29404279, year = {2018}, author = {Ziklo, N and Vidgen, ME and Taing, K and Huston, WM and Timms, P}, title = {Dysbiosis of the Vaginal Microbiota and Higher Vaginal Kynurenine/Tryptophan Ratio Reveals an Association with Chlamydia trachomatis Genital Infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {1}, pmid = {29404279}, issn = {2235-2988}, mesh = {Chlamydia Infections/*metabolism/*microbiology ; Chlamydia trachomatis/*physiology ; Cytokines/metabolism ; *Dysbiosis ; Female ; Humans ; Inflammation Mediators/metabolism ; Kynurenine/metabolism ; Metagenome ; Metagenomics/methods ; *Microbiota ; Tryptophan/metabolism ; Vagina/*metabolism/*microbiology ; }, abstract = {The natural course of Chlamydia trachomatis urogenital tract infections varies between individuals. While protective immunity can occur, some women can become reinfected, contributing to the development of severe pathology. While the reasons for these differences are unknown, an individual's response to induced interferon-γ (IFN-γ) is suggested to be critical. IFN-γ induction of the enzyme indoleamine 2,3-dioxygenase, which depletes tryptophan, may be the key. One hypothesis suggests that indole-producing bacteria in the vaginal microbiota can provide a substrate for the Chlamydia to synthesize tryptophan, rescuing the Chlamydia from host IFN-γ attack. We studied a cohort of 25 women who were either, Chlamydia negative, Chlamydia positive with a single infection, or Chlamydia positive with repeated infection, to test our hypothesis. We characterized their vaginal microbiota, cytokine response, as well as their tryptophan, kynurenine and indole concentrations directly in vaginal secretions. We found that C. trachomatis urogenital tract infections either initial or repeat infections, were associated with elevated vaginal kynurenine/tryptophan ratios, primarily as a result of elevated kynurenine levels. In addition, vaginal microbiota of community state type (CST) IV showed significantly lower vaginal tryptophan levels compared to CST I and III, which might be related to a higher abundance of indole producers found within this group. Furthermore, we found a higher abundance of indole producers in women who cleared their Chlamydia infection post antibiotic treatment. This study demonstrates for the first time in vivo, the association between high vaginal kynurenine/tryptophan ratios and C. trachomatis infections. In addition, tryptophan depletion was associated with vaginal microbiota of CST IV.}, } @article {pmid29402898, year = {2018}, author = {Cai, L and Tian, RM and Zhou, G and Tong, H and Wong, YH and Zhang, W and Chui, APY and Xie, JY and Qiu, JW and Ang, PO and Liu, S and Huang, H and Qian, PY}, title = {Exploring coral microbiome assemblages in the South China Sea.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2428}, pmid = {29402898}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Archaea/classification/*genetics/isolation & purification ; Bacteria/classification/*genetics/isolation & purification ; Carbon Cycle/physiology ; China ; Coral Reefs ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Microbiota/*genetics ; Nitrogen Cycle/physiology ; Pacific Ocean ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sulfur/physiology ; Symbiosis/*physiology ; }, abstract = {Coral reefs are significant ecosystems. The ecological success of coral reefs relies on not only coral-algal symbiosis but also coral-microbial partnership. However, microbiome assemblages in the South China Sea corals remain largely unexplored. Here, we compared the microbiome assemblages of reef-building corals Galaxea (G. fascicularis) and Montipora (M. venosa, M. peltiformis, M. monasteriata) collected from five different locations in the South China Sea using massively-parallel sequencing of 16S rRNA gene and multivariate analysis. The results indicated that microbiome assemblages for each coral species were unique regardless of location and were different from the corresponding seawater. Host type appeared to drive the coral microbiome assemblages rather than location and seawater. Network analysis was employed to explore coral microbiome co-occurrence patterns, which revealed 61 and 80 co-occurring microbial species assembling the Galaxea and Montipora microbiomes, respectively. Most of these co-occurring microbial species were commonly found in corals and were inferred to play potential roles in host nutrient metabolism; carbon, nitrogen, sulfur cycles; host detoxification; and climate change. These findings suggest that the co-occurring microbial species explored might be essential to maintain the critical coral-microbial partnership. The present study provides new insights into coral microbiome assemblages in the South China Sea.}, } @article {pmid29397054, year = {2018}, author = {Scanlan, PD and Hill, CJ and Ross, RP and Ryan, CA and Stanton, C and Cotter, PD}, title = {The intestinal protist Blastocystis is not a common member of the healthy infant gut microbiota in a Westernized country (Ireland).}, journal = {Parasitology}, volume = {145}, number = {10}, pages = {1274-1278}, doi = {10.1017/S0031182018000033}, pmid = {29397054}, issn = {1469-8161}, mesh = {Adult ; Blastocystis/genetics/*isolation & purification ; Blastocystis Infections/*epidemiology/transmission ; Disease Transmission, Infectious ; Feces/parasitology ; *Gastrointestinal Microbiome ; Humans ; Infant ; Intestines/*parasitology ; Ireland/epidemiology ; Longitudinal Studies ; Metagenomics ; Polymerase Chain Reaction ; Prevalence ; }, abstract = {Research into the gut microbiota of human infants is necessary in order to better understand how inter-species interactions and ecological succession shape the diversity of the gut microbiota, and in turn, how the specific composition of the gut microbiota impacts on host health both during infancy and in later years. Blastocystis is a ubiquitous intestinal protist that has been linked to a number of intestinal and extra-intestinal diseases. However, emerging data show that asymptomatic carriage is common and that Blastocystis is prevalent in the healthy adult gut microbiota. Nonetheless, little is known about the prevalence and diversity of this microorganism in the healthy infant gut, including when and how individuals become colonized by Blastocystis. Here, we surveyed the prevalence and diversity of Blastocystis in an infant population (n = 59) from an industrialized country (Ireland) using Blastocystis-specific primers at three or more time-points up to 24 months old. Only three infants were positive for Blastocystis (prevalence = 5%) and this was only noted for samples collected at month 24. This rate is comparatively low relative to previously reported prevalence rates in the contemporaneous adult population. These data suggest that infants in Westernized countries that are successfully colonized by Blastocystis most likely acquire this microorganism via horizontal transfer.}, } @article {pmid29396619, year = {2018}, author = {Mehetre, G and Shah, M and Dastager, SG and Dharne, MS}, title = {Untapped bacterial diversity and metabolic potential within Unkeshwar hot springs, India.}, journal = {Archives of microbiology}, volume = {200}, number = {5}, pages = {753-770}, doi = {10.1007/s00203-018-1484-4}, pmid = {29396619}, issn = {1432-072X}, support = {EMR/2014/000483//Science and Engineering Research Board/ ; }, mesh = {Amylases/analysis ; Bacteria/enzymology/genetics/isolation & purification ; Bacterial Proteins/analysis ; Biodiversity ; Hot Springs/*microbiology ; India ; Peptide Hydrolases/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; Xylosidases/analysis ; }, abstract = {Hot springs support diverse and interesting groups of microorganisms adapted to extreme conditions and gaining attention in biotechnological applications. However, due to limitations of cultivation methods, a majority of such extremophiles remain uncultivated and unexplored. The advent of multiple cultivation conditions and specialized culture media could possibly aid to access the unexplored microbial portion of hot springs. In the present study, different media and isolation strategies were applied to isolate hitherto unexplored bacterial taxa in the water samples collected from Unkeshwar hot springs, India. Molecular, phylogenetic and predictive functional characterization of the isolated bacterial population was done using 16S rRNA sequencing coupled with Tax4Fun tools. Furthermore, representative isolates were screened for important enzymes (cellulase, xylanase, amylase, and protease) and heavy metal tolerance (chromium, arsenic) properties. A total of 454 bacterial isolates obtained were mapped into 57 unique bacterial genera and 4 different bacterial phyla. Interestingly, 37 genera not previously isolated from Indian hot springs, were isolated for the first time in the present study. However, most of these genera (23 out of 37) were reported only in metagenomics studies from Indian and global hot springs. Furthermore, around 14 genera not previously cultivated and not detected in metagenomics studies of hot springs are documented here. The metabolic potential was ascertained by determining the abundance of specific genes using in silico based Tax4Fun tool, which identified around 315 metabolic pathways for metabolism of carbohydrates, synthesis of secondary metabolites and degradation of xenobiotic compounds. Bioprospection study revealed that 33 and 25 bacterial genera were positive for enzyme production and resistance to the heavy metals, respectively. The present study revealed the advantages of cultivation methods using a comprehensive multiple isolation approach for exploring untapped and unique bacterial diversity, and also utilities for various biotechnological and environmental applications.}, } @article {pmid29396587, year = {2018}, author = {Mahony, J and Lugli, GA and van Sinderen, D and Ventura, M}, title = {Impact of gut-associated bifidobacteria and their phages on health: two sides of the same coin?.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {5}, pages = {2091-2099}, doi = {10.1007/s00253-018-8795-x}, pmid = {29396587}, issn = {1432-0614}, mesh = {Animals ; Bacteriophages/classification/genetics/isolation & purification/*physiology ; Bifidobacterium/classification/genetics/*physiology/virology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology/*virology ; Humans ; }, abstract = {Bifidobacteria are among the first microbial colonisers of the human infant gut post-partum. Their early appearance and dominance in the human infant gut and the reported health-promoting or probiotic status of several bifidobacterial strains has culminated in intensive research efforts that focus on their activities as part of the gut microbiota and the concomitant implications for human health. In this mini-review, we evaluate current knowledge on the genomics of this diverse bacterial genus, and on the genetic and functional adaptations that have underpinned the success of bifidobacteria in colonising the infant gut. The growing interest in functional genomics of bifidobacteria has also created interest in the interactions of bifidobacteria and their (bacterio)phages. While virulent phages of bifidobacteria have yet to be isolated, the incidence of integrated (pro)phages in bifidobacterial genomes are widely reported and this mini-review considers the role of these so-called bifidoprophages in modulating bifidobacterial populations in the human gastrointestinal tract and the implications for existing and future development of probiotic therapies.}, } @article {pmid29396546, year = {2018}, author = {Gonzalez-Martinez, A and Sihvonen, M and Muñoz-Palazon, B and Rodriguez-Sanchez, A and Mikola, A and Vahala, R}, title = {Microbial ecology of full-scale wastewater treatment systems in the Polar Arctic Circle: Archaea, Bacteria and Fungi.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2208}, pmid = {29396546}, issn = {2045-2322}, mesh = {Archaea/classification/genetics/*isolation & purification ; Arctic Regions ; Bacteria/classification/genetics/*isolation & purification ; Bioreactors/*microbiology ; *Biota ; Finland ; Fungi/classification/genetics/*isolation & purification ; Metagenomics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sewage/microbiology ; Wastewater/*microbiology ; Water Purification ; }, abstract = {Seven full-scale biological wastewater treatment systems located in the Polar Arctic Circle region in Finland were investigated to determine their Archaea, Bacteria and Fungi community structure, and their relationship with the operational conditions of the bioreactors by the means of quantitative PCR, massive parallel sequencing and multivariate redundancy analysis. The results showed dominance of Archaea and Bacteria members in the bioreactors. The activated sludge systems showed strong selection of Bacteria but not for Archaea and Fungi, as suggested by diversity analyses. Core OTUs in influent and bioreactors were classified as Methanobrevibacter, Methanosarcina, Terrestrial Group Thaumarchaeota and unclassified Euryarchaeota member for Archaea; Trichococcus, Leptotrichiaceae and Comamonadaceae family, and Methylorosula for Bacteria and Trichosporonaceae family for Fungi. All influents shared core OTUs in all domains, but in bioreactors this did not occur for Bacteria. Oligotype structure of core OTUs showed several ubiquitous Fungi oligotypes as dominant in sewage and bioreactors. Multivariate redundancy analyses showed that the majority of core OTUs were related to organic matter and nutrients removal. Also, there was evidence of competition among Archaea and Fungi core OTUs, while all Bacteria OTUs were positively correlated among them. The results obtained highlighted interesting features of extremely cold temperature bioreactors.}, } @article {pmid29395346, year = {2018}, author = {Limborg, MT and Alberdi, A and Kodama, M and Roggenbuck, M and Kristiansen, K and Gilbert, MTP}, title = {Applied Hologenomics: Feasibility and Potential in Aquaculture.}, journal = {Trends in biotechnology}, volume = {36}, number = {3}, pages = {252-264}, doi = {10.1016/j.tibtech.2017.12.006}, pmid = {29395346}, issn = {1879-3096}, support = {681396/ERC_/European Research Council/International ; }, mesh = {Animals ; *Aquaculture ; Epigenomics ; *Feasibility Studies ; Fishes/*microbiology ; Food Industry ; Gastrointestinal Microbiome/genetics/immunology ; Genome, Microbial/genetics/immunology ; Humans ; Immune System/immunology/microbiology ; *Metagenomics ; Proteomics ; Transcriptome ; }, abstract = {Aquaculture will play an essential role in feeding a growing human population, but several biological challenges impede sustainable growth of production. Emerging evidence across all areas of life has revealed the importance of the intimate biological interactions between animals and their associated gut microbiota. Based on challenges in aquaculture, we leverage current knowledge in molecular biology and host microbiota interactions to propose an applied holo-omic framework that integrates molecular data including genomes, transcriptomes, epigenomes, proteomes, and metabolomes for analyzing fish and their gut microbiota as interconnected and coregulated systems. With an eye towards aquaculture, we discuss the feasibility and potential of our holo-omic framework to improve growth, health, and sustainability in any area of food production, including livestock and agriculture.}, } @article {pmid29391857, year = {2017}, author = {Chen, WY and Kraková, L and Wu, JH and Pangallo, D and Jeszeová, L and Liu, B and Yasui, H}, title = {Community and Proteomic Analysis of Anaerobic Consortia Converting Tetramethylammonium to Methane.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2017}, number = {}, pages = {2170535}, pmid = {29391857}, issn = {1472-3654}, mesh = {Anaerobiosis ; Archaea/chemistry/*classification/genetics/*metabolism ; Bioreactors/microbiology ; Biotransformation ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; *Metagenome ; Methane/*metabolism ; *Microbial Consortia ; Phylogeny ; Polymerase Chain Reaction ; *Proteome ; Quaternary Ammonium Compounds/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/microbiology ; }, abstract = {Tetramethylammonium-degrading methanogenic consortia from a complete-mixing suspended sludge (CMSS) and an upflow anaerobic sludge blanket (UASB) reactors were studied using multiple PCR-based molecular techniques and shotgun proteomic approach. The prokaryotic 16S rRNA genes of the consortia were analyzed by quantitative PCR, high-throughput sequencing, and DGGE-cloning methods. The results showed that methanogenic archaea were highly predominant in both reactors but differed markedly according to community structure. Community and proteomic analysis revealed that Methanomethylovorans and Methanosarcina were the major players for the demethylation of methylated substrates and methane formation through the reduction pathway of methyl-S-CoM and possibly, acetyl-CoA synthase/decarbonylase-related pathways. Unlike high dominance of one Methanomethylovorans population in the CMSS reactor, diverse methylotrophic Methanosarcina species inhabited in syntrophy-like association with hydrogenotrophic Methanobacterium in the granular sludge of UASB reactor. The overall findings indicated the reactor-dependent community structures of quaternary amines degradation and provided microbial insight for the improved understanding of engineering application.}, } @article {pmid29391526, year = {2018}, author = {Dada, N and Sheth, M and Liebman, K and Pinto, J and Lenhart, A}, title = {Whole metagenome sequencing reveals links between mosquito microbiota and insecticide resistance in malaria vectors.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2084}, pmid = {29391526}, issn = {2045-2322}, mesh = {Animals ; Anopheles/drug effects/genetics/*microbiology ; Disease Vectors ; Female ; Fenitrothion/toxicity ; *Insecticide Resistance ; Insecticides/toxicity ; *Metagenome ; *Microbiota ; }, abstract = {In light of the declining global malaria burden attained largely due to insecticides, a deeper understanding of the factors driving insecticide resistance is needed to mitigate its growing threat to malaria vector control programs. Following evidence of microbiota-mediated insecticide resistance in agricultural pests, we undertook a comparative study of the microbiota in mosquitoes of differing insecticide resistance status. The microbiota of wild-caught Anopheles albimanus, an important Latin American malaria vector, that were resistant (FEN_Res) or susceptible (FEN_Sus) to the organophosphate (OP) insecticide fenitrothion were characterized and compared using whole metagenome sequencing. Results showed differing composition of the microbiota and its functions between FEN_Res and FEN_Sus, with significant enrichment of OP-degrading bacteria and enzymes in FEN_Res compared to FEN_Sus. Lower bacterial diversity was observed in FEN_Res compared to FEN_Sus, suggesting the enrichment of bacterial taxa with a competitive advantage in response to insecticide selection pressure. We report and characterize for the first time whole metagenomes of An. albimanus, revealing associations between the microbiota and phenotypic resistance to the insecticide fenitrothion. This study lays the groundwork for further investigation of the role of the mosquito microbiota in insecticide resistance.}, } @article {pmid29386563, year = {2018}, author = {Treonis, AM and Unangst, SK and Kepler, RM and Buyer, JS and Cavigelli, MA and Mirsky, SB and Maul, JE}, title = {Characterization of soil nematode communities in three cropping systems through morphological and DNA metabarcoding approaches.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2004}, pmid = {29386563}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; *Metagenome ; Soil/*parasitology ; Tylenchida/classification/*genetics ; }, abstract = {We used complementary morphological and DNA metabarcoding approaches to characterize soil nematode communities in three cropping systems, conventional till (CT), no-till (NT) and organic (ORG), from a long-term field experiment. We hypothesized that organic inputs to the ORG system would promote a more abundant nematode community, and that the NT system would show a more structured trophic system (higher Bongers MI) than CT due to decreased soil disturbance. The abundance of Tylenchidae and Cephalobidae both showed positive correlations to soil organic carbon and nitrogen, which were highest in the ORG system. The density of omnivore-predator and bacterial-feeding nematodes was reduced in NT soils compared to CT, while some plant-parasitic taxa increased. NT soils had similar Bongers MI values to CT, suggesting they contained nematode communities associated with soils experiencing comparable levels of disturbance. Metabarcoding revealed within-family differences in nematode diversity. Shannon and Simpson's index values for the Tylenchidae and Rhabditidae were higher in the ORG system than CT. Compared to morphological analysis, metabarcoding over- or underestimated the prevalence of several nematode families and detected some families not observed based on morphology. Discrepancies between the techniques require further investigation to establish the accuracy of metabarcoding for characterization of soil nematode communities.}, } @article {pmid29385453, year = {2018}, author = {Wang, Y and Staubach, F}, title = {Individual variation of natural D.melanogaster-associated bacterial communities.}, journal = {FEMS microbiology letters}, volume = {365}, number = {6}, pages = {}, doi = {10.1093/femsle/fny017}, pmid = {29385453}, issn = {1574-6968}, mesh = {Animals ; Bacteria/classification/genetics ; Biodiversity ; Drosophila melanogaster/*microbiology ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S ; Symbiosis ; }, abstract = {Drosophila melanogaster has become an important model organism to study host-microbe interaction in the laboratory. However, the natural microbial communities that are associated with D. melanogaster have received less attention. Especially, information on inter-individual variation is still lacking, because most studies so far have used pooled material from several flies. Here, we collected bacterial 16S rRNA gene community profiles from a set of 32 individuals from a single population. We simulated pools from the individual data (i) to assess how well the microbiome of a host population is represented by pools, and (ii) to compare variation of Drosophila microbiomes within and between populations. Taxon richness was increased in simulated pools, suggesting that pools paint a more comprehensive picture of the taxa associated with a host population. Furthermore, microbiome composition varied less between pools than between individuals, indicating that differences even out in pools. Variation in microbiome composition was larger between populations than between simulated pools from a single population, adding to the notion that there are population-specific effects on the Drosophila microbiome. Surprisingly, samples from individuals clustered into two groups, suggesting that there are yet unknown factors that affect the composition of natural fly-associated microbial communities and need further research.}, } @article {pmid29382366, year = {2018}, author = {Stoll, ML and Weiss, PF and Weiss, JE and Nigrovic, PA and Edelheit, BS and Bridges, SL and Danila, MI and Spencer, CH and Punaro, MG and Schikler, K and Reiff, A and Kumar, R and Cron, RQ and Morrow, CD and Lefkowitz, EJ}, title = {Age and fecal microbial strain-specific differences in patients with spondyloarthritis.}, journal = {Arthritis research & therapy}, volume = {20}, number = {1}, pages = {14}, pmid = {29382366}, issn = {1478-6362}, support = {P30 AI027767/AI/NIAID NIH HHS/United States ; P30 CA013148/CA/NCI NIH HHS/United States ; K23 AR062100/AR/NIAMS NIH HHS/United States ; R01 AR065538/AR/NIAMS NIH HHS/United States ; UL1 TR001417/TR/NCATS NIH HHS/United States ; P60 AR064172/AR/NIAMS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Age Factors ; Arthritis, Juvenile/*microbiology ; Bacteria/classification/genetics ; Child ; DNA, Bacterial/chemistry/genetics ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Male ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Spondylarthritis/*microbiology ; }, abstract = {BACKGROUND: Prior studies have demonstrated abnormalities in the composition of the gastrointestinal microbiota in pediatric and adult patients with spondyloarthritis (SpA). In particular, diminished fecal abundance of Faecalibacterium prausnitzii and abnormalities in both directions in the abundance of the Bacteroides genus have been identified.

METHODS: We obtained fecal specimens from 30 children with treatment-naïve enthesitis-related arthritis (ERA) and 19 healthy controls, as well as specimens from 11 adult patients with longstanding SpA and 10 adult healthy controls. All of the samples underwent sequencing of the 16S ribosomal DNA. A subset of the pediatric fecal samples was subjected to shotgun metagenomics sequencing.

RESULTS: ERA patients had decreased abundance of the anti-inflammatory F. prausnitzii A2-165 strain (41 ± 28% versus 54 ± 20% of all sequences matching F. prausnitzii, p = 0.084) and an increased abundance of the control F. prausnitzii L2/6 strain (28 ± 28% versus 15 ± 15%, p = 0.038). Similar trends were observed in adults with longstanding SpA (n = 11) and controls (n = 10). In contrast, the fecal abundance of Bacteroides fragilis was increased in ERA subjects (2.0 ± 4.0% versus 0.45 ± 0.7% of all sequences, p = 0.045), yet was diminished in adult subjects (0.2 ± % versus 1.0 ± % of all sequences, p = 0.106). Shotgun metagenomics sequencing of the fecal DNA in the pediatric subjects revealed diminished coverage of the butanoate pathway (abundance normalized to controls of 1 ± 0.48 versus 0.72 ± 0.33 in ERA, p = 0.037).

CONCLUSIONS: The anti-inflammatory F. prausnitzii A2-165 strain appears to be depleted in both pediatric and adult SpA. In contrast, B. fragilis may be depleted in adult disease yet abundant in pediatric SpA, suggesting developmental effects on the immune system.}, } @article {pmid29382070, year = {2018}, author = {D'Argenio, V}, title = {Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies.}, journal = {International journal of molecular sciences}, volume = {19}, number = {2}, pages = {}, pmid = {29382070}, issn = {1422-0067}, mesh = {*Gastrointestinal Microbiome ; Genomics/*methods/standards ; Humans ; *Metagenome ; Transcriptome ; }, abstract = {The study of the human microbiome has become a very popular topic. Our microbial counterpart, in fact, appears to play an important role in human physiology and health maintenance. Accordingly, microbiome alterations have been reported in an increasing number of human diseases. Despite the huge amount of data produced to date, less is known on how a microbial dysbiosis effectively contributes to a specific pathology. To fill in this gap, other approaches for microbiome study, more comprehensive than 16S rRNA gene sequencing, i.e., shotgun metagenomics and metatranscriptomics, are becoming more widely used. Methods standardization and the development of specific pipelines for data analysis are required to contribute to and increase our understanding of the human microbiome relationship with health and disease status.}, } @article {pmid29380873, year = {2018}, author = {Bapatla, KG and Singh, A and Yeddula, S and Patil, RH}, title = {Annotation of gut bacterial taxonomic and functional diversity in Spodoptera litura and Spilosoma obliqua.}, journal = {Journal of basic microbiology}, volume = {58}, number = {3}, pages = {217-226}, doi = {10.1002/jobm.201700462}, pmid = {29380873}, issn = {1521-4028}, mesh = {Animals ; Bacteria/*classification/*genetics ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gastrointestinal Tract/microbiology ; Helianthus/parasitology ; High-Throughput Nucleotide Sequencing ; Lepidoptera/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Glycine max/parasitology ; }, abstract = {The insect gut has been the house of many taxonomically and physiologically diverse groups of microbial colonizers as symbionts and commensals, which are evolving to support the physiological requirement of insects. Lepidoptera is one of the important family of class hexapoda, comprising agriculture insect pest Spodoptera litura and Spilosoma obliqua. Information on gut microbiota and their functional role in these insects was meager to elucidate the wide-ranging survivalist mechanisms. In this context, we analyzed the composition, diversity and functional role of gut bacteria in S. litura and S. obliqua collected from soybean and sunflower crops, respectively, using Next Generation Sequencing of 16S rRNA. A total of 3427 and 206 Operation Taxonomic Units (OTUs) were identified in S. litura and S. obliqua gut metagenome, respectively. Highest number of sequences were annotated to unclassified bacteria (34%), followed by Proteobacteria (27%), and Chlorobi (14%) in S. litura, while S. obliqua has significant representation of Firmicutes (48%), followed by Bacteroidetes (20%), and unclassified bacteria (11%). Functionality of both metagenomes revealed, high abundance of ammonia oxidizers (20.1 58.0%) followed by relative abundance of detoxifying processes - dehalogenation (17.4-41.2%) and aromatic hydrocarbons degradation (1.1-3.1%). This study highlights the significance of the inherent microbiome of two defoliators in shaping the metagenome for nutrition and detoxifying the chemical molecules, and opens an avenue for exploring role of insect gut bacteria in host selection, metabolic endurance of insecticides and synergistic or agonistic mechanisms inside gut of insects feeding on insect-resistant biotech crops.}, } @article {pmid29379216, year = {2018}, author = {Almeida, A and Shao, Y}, title = {Genome watch: Keeping tally in the microbiome.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {3}, pages = {124}, pmid = {29379216}, issn = {1740-1534}, mesh = {Animals ; Bacteria/classification/*genetics/isolation & purification ; Biodiversity ; Gene Expression Profiling/*methods ; *Genome, Bacterial ; Humans ; *Metagenomics ; *Microbiota ; Nucleic Acid Amplification Techniques ; }, abstract = {This month's Genome Watch highlights how the development of new approaches for quantifying the human microbiome may pave the way for a better understanding of microbial shifts in the context of human health and disease.}, } @article {pmid29379124, year = {2018}, author = {Xu, S and Lin, Y and Zeng, D and Zhou, M and Zeng, Y and Wang, H and Zhou, Y and Zhu, H and Pan, K and Jing, B and Ni, X}, title = {Bacillus licheniformis normalize the ileum microbiota of chickens infected with necrotic enteritis.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1744}, pmid = {29379124}, issn = {2045-2322}, mesh = {Animals ; Bacillus licheniformis/*growth & development ; Biological Therapy/methods ; Chickens ; Clostridium Infections/complications/microbiology/therapy/*veterinary ; Clostridium perfringens/growth & development ; Diet/methods ; *Dysbiosis ; Enteritis/complications/microbiology/therapy/*veterinary ; *Gastrointestinal Microbiome ; Ileum/*microbiology ; Metagenomics ; Necrosis/complications/microbiology/therapy/veterinary ; Poultry Diseases/*microbiology ; Sequence Analysis, DNA ; Treatment Outcome ; }, abstract = {Necrotic enteritis (NE) is a severe intestinal disease, which can change gut microbiota and result in a high cost for the poultry industry worldwide. However, little is known regarding how the gut microbiota of NE chicken ileum are changed by Bacillus licheniformis. This study was conducted to investigate how ileum microbiota structure was changed by B. licheniformis in broiler chickens challenged with Clostridium perfringens-induced NE through Illumina MiSeq sequencing. The broilers were randomly separated into four groups: the negative control group (NC), the positive control group (PC), the fishmeal and coccidia group (FC), and the PC group supplied with feed containing B. licheniformis (BL). Compared to the PC and FC, alpha diversity, beta diversity, and the bacterial taxa of the ileum microbiota were more similar in BL and NC. Some genera, which were related to the NE control, became insignificant in BL with NC, such as Lactobacillus, Lactococcus, Bacteroides, Ruminococcus and Helicobacter. The PICRUSt analysis revealed that a tumour suppressor gene, p53, which was negatively correlated with Helicobacter, was enriched in the BL group. Our findings showed that the ileum microbiota disorder caused by NE in chickens was normalized by dietary B. licheniformis supplementation.}, } @article {pmid29378882, year = {2018}, author = {Miller-Ensminger, T and Garretto, A and Brenner, J and Thomas-White, K and Zambom, A and Wolfe, AJ and Putonti, C}, title = {Bacteriophages of the Urinary Microbiome.}, journal = {Journal of bacteriology}, volume = {200}, number = {7}, pages = {}, pmid = {29378882}, issn = {1098-5530}, support = {R01 DK104718/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Bacteriophages/genetics/*isolation & purification ; Coliphages/genetics/isolation & purification ; Computational Biology ; Female ; Genome, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota ; Phylogeny ; Pregnancy ; Prophages/genetics/isolation & purification ; Sequence Analysis, DNA ; Urinary Bladder/microbiology/virology ; Urinary Bladder, Overactive/virology ; Urinary Tract/*microbiology/virology ; }, abstract = {Bacterial viruses (bacteriophages) play a significant role in microbial community dynamics. Within the human gastrointestinal tract, for instance, associations among bacteriophages (phages), microbiota stability, and human health have been discovered. In contrast to the gastrointestinal tract, the phages associated with the urinary microbiota are largely unknown. Preliminary metagenomic surveys of the urinary virome indicate a rich diversity of novel lytic phage sequences at an abundance far outnumbering that of eukaryotic viruses. These surveys, however, exclude the lysogenic phages residing within the bacteria of the bladder. To characterize this phage population, we examined 181 genomes representative of the phylogenetic diversity of bacterial species within the female urinary microbiota and found 457 phage sequences, 226 of which were predicted with high confidence. Phages were prevalent within the bladder bacteria: 86% of the genomes examined contained at least one phage sequence. Most of these phages are novel, exhibiting no discernible sequence homology to sequences in public data repositories. The presence of phages with substantial sequence similarity within the microbiota of different women supports the existence of a core community of phages within the bladder. Furthermore, the observed variation between the phage populations of women with and without overactive bladder symptoms suggests that phages may contribute to urinary health. To complement our bioinformatic analyses, viable phages were cultivated from the bacterial isolates for characterization; a novel coliphage was isolated, which is obligately lytic in the laboratory strain Escherichia coli C. Sequencing of bacterial genomes facilitates a comprehensive cataloguing of the urinary virome and reveals phage-host interactions.IMPORTANCE Bacteriophages are abundant within the human body. However, while some niches have been well surveyed, the phage population within the urinary microbiome is largely unknown. Our study is the first survey of the lysogenic phage population within the urinary microbiota. Most notably, the abundance of prophage exceeds that of the bacteria. Furthermore, many of the prophage sequences identified exhibited no recognizable sequence homology to sequences in data repositories. This suggests a rich diversity of uncharacterized phage species present in the bladder. Additionally, we observed a variation in the abundances of phages between bacteria isolated from asymptomatic "healthy" individuals and those with urinary symptoms, thus suggesting that, like phages within the gut, phages within the bladder may contribute to urinary health.}, } @article {pmid29378630, year = {2018}, author = {Kolde, R and Franzosa, EA and Rahnavard, G and Hall, AB and Vlamakis, H and Stevens, C and Daly, MJ and Xavier, RJ and Huttenhower, C}, title = {Host genetic variation and its microbiome interactions within the Human Microbiome Project.}, journal = {Genome medicine}, volume = {10}, number = {1}, pages = {6}, pmid = {29378630}, issn = {1756-994X}, support = {U54 DK102557/DK/NIDDK NIH HHS/United States ; U54 HG003067/HG/NHGRI NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; 5U54HG003067-13/HG/NHGRI NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; }, mesh = {*Genetic Variation ; Genotype ; Humans ; Metagenome ; Microbiota/*genetics ; Principal Component Analysis ; Sequence Analysis, DNA ; Tissue Donors ; }, abstract = {BACKGROUND: Despite the increasing recognition that microbial communities within the human body are linked to health, we have an incomplete understanding of the environmental and molecular interactions that shape the composition of these communities. Although host genetic factors play a role in these interactions, these factors have remained relatively unexplored given the requirement for large population-based cohorts in which both genotyping and microbiome characterization have been performed.

METHODS: We performed whole-genome sequencing of 298 donors from the Human Microbiome Project (HMP) healthy cohort study to accompany existing deep characterization of their microbiomes at various body sites. This analysis yielded an average sequencing depth of 32x, with which we identified 27 million (M) single nucleotide variants and 2.3 M insertions-deletions.

RESULTS: Taxonomic composition and functional potential of the microbiome covaried significantly with genetic principal components in the gastrointestinal tract and oral communities, but not in the nares or vaginal microbiota. Example associations included validation of known associations between FUT2 secretor status, as well as a variant conferring hypolactasia near the LCT gene, with Bifidobacterium longum abundance in stool. The associations of microbial features with both high-level genetic attributes and single variants were specific to particular body sites, highlighting the opportunity to find unique genetic mechanisms controlling microbiome properties in the microbial communities from multiple body sites.

CONCLUSIONS: This study adds deep sequencing of host genomes to the body-wide microbiome sequences already extant from the HMP healthy cohort, creating a unique, versatile, and well-controlled reference for future studies seeking to identify host genetic modulators of the microbiome.}, } @article {pmid29378627, year = {2018}, author = {Broberg, M and Doonan, J and Mundt, F and Denman, S and McDonald, JE}, title = {Integrated multi-omic analysis of host-microbiota interactions in acute oak decline.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {21}, pmid = {29378627}, issn = {2049-2618}, support = {TH0108//Department for Environment, Food and Rural Affairs/International ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Enterobacteriaceae/genetics/metabolism/*pathogenicity ; Gene Expression Profiling ; Genomics/*methods ; Host-Pathogen Interactions ; Microbiota ; Plant Diseases/*microbiology ; Proteomics ; Quercus/*microbiology ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; Virulence Factors/*genetics/*metabolism ; }, abstract = {BACKGROUND: Britain's native oak species are currently under threat from acute oak decline (AOD), a decline-disease where stem bleeds overlying necrotic lesions in the inner bark and larval galleries of the bark-boring beetle, Agrilus biguttatus, represent the primary symptoms. It is known that complex interactions between the plant host and its microbiome, i.e. the holobiont, significantly influence the health status of the plant. In AOD, necrotic lesions are caused by a microbiome shift to a pathobiome consisting predominantly of Brenneria goodwinii, Gibbsiella quercinecans, Rahnella victoriana and potentially other bacteria. However, the specific mechanistic processes of the microbiota causing tissue necrosis, and the host response, have not been established and represent a barrier to understanding and managing this decline.

RESULTS: We profiled the metagenome, metatranscriptome and metaproteome of inner bark tissue from AOD symptomatic and non-symptomatic trees to characterise microbiota-host interactions. Active bacterial virulence factors such as plant cell wall-degrading enzymes, reactive oxygen species defence and flagella in AOD lesions, along with host defence responses including reactive oxygen species, cell wall modification and defence regulators were identified. B. goodwinii dominated the lesion microbiome, with significant expression of virulence factors such as the phytopathogen effector avrE. A smaller proportion of microbiome activity was attributed to G. quercinecans and R. victoriana. In addition, we describe for the first time the potential role of two previously uncharacterised Gram-positive bacteria predicted from metagenomic binning and identified as active in the AOD lesion metatranscriptome and metaproteome, implicating them in lesion formation.

CONCLUSIONS: This multi-omic study provides novel functional insights into microbiota-host interactions in AOD, a complex arboreal decline disease where polymicrobial-host interactions result in lesion formation on tree stems. We present the first descriptions of holobiont function in oak health and disease, specifically, the relative lesion activity of B. goodwinii, G. quercinecans, Rahnella victoriana and other bacteria. Thus, the research presented here provides evidence of some of the mechanisms used by members of the lesion microbiome and a template for future multi-omic research into holobiont characterisation, plant polymicrobial diseases and pathogen defence in trees.}, } @article {pmid29378252, year = {2019}, author = {Sircana, A and De Michieli, F and Parente, R and Framarin, L and Leone, N and Berrutti, M and Paschetta, E and Bongiovanni, D and Musso, G}, title = {Gut microbiota, hypertension and chronic kidney disease: Recent advances.}, journal = {Pharmacological research}, volume = {144}, number = {}, pages = {390-408}, doi = {10.1016/j.phrs.2018.01.013}, pmid = {29378252}, issn = {1096-1186}, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Hypertension/metabolism/*microbiology/pathology/therapy ; Probiotics/therapeutic use ; Renal Insufficiency, Chronic/metabolism/*microbiology/pathology/therapy ; }, abstract = {A large number of different microbial species populates intestine. Extensive research has studied the entire microbial population and their genes (microbiome) by using metagenomics, metatranscriptomics and metabolomic analysis. Studies suggest that the imbalances of the microbial community causes alterations in the intestinal homeostasis, leading to repercussions on other systems: metabolic, nervous, cardiovascular, immune. These studies have also shown that alterations in the structure and function of the gut microbiota play a key role in the pathogenesis and complications of Hypertension (HTN) and Chronic Kidney Disease (CKD). Increased blood pressure (BP) and CKD are two leading risk factors for cardiovascular disease and their treatment represents a challenge for the clinicians. In this Review, we discuss mechanisms whereby gut microbiota (GM) and its metabolites act on downstream cellular targets to contribute to the pathogenesis of HTN and CKD, and potential therapeutic implications.}, } @article {pmid29371652, year = {2018}, author = {Fernández, L and Rodríguez, A and García, P}, title = {Phage or foe: an insight into the impact of viral predation on microbial communities.}, journal = {The ISME journal}, volume = {12}, number = {5}, pages = {1171-1179}, pmid = {29371652}, issn = {1751-7370}, mesh = {Bacteria/genetics/*metabolism/pathogenicity ; Bacteriophages/*physiology ; Biological Evolution ; Genomics ; Metagenomics ; *Microbial Interactions ; Microbiota ; Proteomics ; }, abstract = {Since their discovery, bacteriophages have been traditionally regarded as the natural enemies of bacteria. However, recent advances in molecular biology techniques, especially data from "omics" analyses, have revealed that the interplay between bacterial viruses and their hosts is far more intricate than initially thought. On the one hand, we have become more aware of the impact of viral predation on the composition and genetic makeup of microbial communities thanks to genomic and metagenomic approaches. Moreover, data obtained from transcriptomic, proteomic, and metabolomic studies have shown that responses to phage predation are complex and diverse, varying greatly depending on the bacterial host, phage, and multiplicity of infection. Interestingly, phage exposure may alter different phenotypes, including virulence and biofilm formation. The complexity of the interactions between microbes and their viral predators is also evidenced by the link between quorum-sensing signaling pathways and bacteriophage resistance. Overall, new data increasingly suggests that both temperate and virulent phages have a positive effect on the evolution and adaptation of microbial populations. From this perspective, further research is still necessary to fully understand the interactions between phage and host under conditions that allow co-existence of both populations, reflecting more accurately the dynamics in natural microbial communities.}, } @article {pmid29371626, year = {2018}, author = {Carradec, Q and Pelletier, E and Da Silva, C and Alberti, A and Seeleuthner, Y and Blanc-Mathieu, R and Lima-Mendez, G and Rocha, F and Tirichine, L and Labadie, K and Kirilovsky, A and Bertrand, A and Engelen, S and Madoui, MA and Méheust, R and Poulain, J and Romac, S and Richter, DJ and Yoshikawa, G and Dimier, C and Kandels-Lewis, S and Picheral, M and Searson, S and , and Jaillon, O and Aury, JM and Karsenti, E and Sullivan, MB and Sunagawa, S and Bork, P and Not, F and Hingamp, P and Raes, J and Guidi, L and Ogata, H and de Vargas, C and Iudicone, D and Bowler, C and Wincker, P}, title = {A global ocean atlas of eukaryotic genes.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {373}, pmid = {29371626}, issn = {2041-1723}, support = {294823/ERC_/European Research Council/International ; }, mesh = {Amino Acid Sequence ; Animals ; *Aquatic Organisms ; Atlases as Topic ; Bacteria/classification/genetics ; Biodiversity ; Ecosystem ; Eukaryota/classification/*genetics ; Eukaryotic Cells/cytology/*metabolism ; *Metagenome ; Metagenomics/methods ; Oceans and Seas ; *Phylogeny ; Phytoplankton/classification/genetics ; Seawater ; Viruses/classification/genetics ; Zooplankton/classification/*genetics ; }, abstract = {While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.}, } @article {pmid29368406, year = {2018}, author = {Chai, ZY and He, ZL and Deng, YY and Yang, YF and Tang, YZ}, title = {Cultivation of seaweed Gracilaria lemaneiformis enhanced biodiversity in a eukaryotic plankton community as revealed via metagenomic analyses.}, journal = {Molecular ecology}, volume = {27}, number = {4}, pages = {1081-1093}, doi = {10.1111/mec.14496}, pmid = {29368406}, issn = {1365-294X}, mesh = {*Biodiversity ; Biomass ; China ; Geography ; Gracilaria/*growth & development ; *Metagenomics ; Phylogeny ; Plankton/*genetics ; Principal Component Analysis ; RNA, Ribosomal, 28S/genetics ; Seaweed/*growth & development ; }, abstract = {Plankton diversity reflects the quality and health of waters and should be monitored as a critical feature of marine ecosystems. This study applied a pair of 28S rRNA gene-specific primers and pyrosequencing to assess the effects of large-scale cultivation of the seaweed Gracilaria lemaneiformis on the biodiversity of eukaryotic plankton community in the coastal water of Guangdong, China. With 1 million sequences (2,221 operational taxonomic units [OTUs]) obtained from 51 samples, we found that the biodiversity of eukaryotic plankton community was significantly higher in the seaweed cultivation area than that in the nearby control area as reflected in OTU richness, evenness (Shannon-Wiener index) and dominance (Simpson index) for total plankton community and its four subcategories when Gracilaria biomass reached the maximum, while no such a significant difference was observed before seaweed inoculation. Our laboratory experiment using an artificial phytoplankton community of nine species observed the same effects of Gracilaria exposure. Principal component analysis and principal coordinates analysis showed the plankton community structure in cultivation area markedly differed from the control area when Gracilaria biomass reached its maximum. Redundancy analysis showed that G. lemaneiformis was the critical factor in controlling the dynamics of eukaryotic plankton communities in the studied coastal ecosystem. Our results explicitly demonstrated G. lemaneiformis cultivation could enhance biodiversity of plankton community via allelopathy, which prevents one or several plankton species from blooming and consequently maintains a relatively higher biodiversity. Our study provided further support for using large-scale G. lemaneiformis cultivation as an effective approach for improving costal ecosystem health.}, } @article {pmid29367606, year = {2018}, author = {Shangpliang, HNJ and Rai, R and Keisam, S and Jeyaram, K and Tamang, JP}, title = {Bacterial community in naturally fermented milk products of Arunachal Pradesh and Sikkim of India analysed by high-throughput amplicon sequencing.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1532}, pmid = {29367606}, issn = {2045-2322}, mesh = {Bacteria/*classification/*genetics ; *Biota ; Cultured Milk Products/*microbiology ; High-Throughput Nucleotide Sequencing ; India ; Metagenomics ; }, abstract = {Naturally fermented milk (NFM) products are popular ethnic fermented foods in Arunachal Pradesh and Sikkim states of India. The present study is the first to have documented the bacterial community in 54 samples of NFM products viz. chhurpi, churkam, dahi and gheu/mar by high-throughput Illumina amplicon sequencing. Metagenomic investigation showed that Firmicutes (Streptococcaceae, Lactobacillaceae) and Proteobacteria (Acetobacteraceae) were the two predominant members of the bacterial communities in these products. Lactococcus lactis and Lactobacillus helveticus were the predominant lactic acid bacteria while Acetobacter spp. and Gluconobacter spp. were the predominant acetic acid bacteria present in these products.}, } @article {pmid29363671, year = {2018}, author = {Lu, P and Sodhi, CP and Yamaguchi, Y and Jia, H and Prindle, T and Fulton, WB and Vikram, A and Bibby, KJ and Morowitz, MJ and Hackam, DJ}, title = {Intestinal epithelial Toll-like receptor 4 prevents metabolic syndrome by regulating interactions between microbes and intestinal epithelial cells in mice.}, journal = {Mucosal immunology}, volume = {11}, number = {3}, pages = {727-740}, pmid = {29363671}, issn = {1935-3456}, support = {R01 DK083752/DK/NIDDK NIH HHS/United States ; R01 DK117186/DK/NIDDK NIH HHS/United States ; R01 GM078238/GM/NIGMS NIH HHS/United States ; T32 DK007713/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Cells, Cultured ; Host-Pathogen Interactions ; Intestinal Mucosa/microbiology/*physiology ; Metabolic Syndrome/*immunology/microbiology ; Mice ; Mice, Knockout ; Microbiota/*immunology ; Muramidase/metabolism ; PPAR gamma/genetics/metabolism ; Signal Transduction ; Toll-Like Receptor 4/*metabolism ; }, abstract = {Little is known about the pathogenesis of metabolic syndrome, although Toll-like receptor 4 (TLR4) has been implicated. We investigated whether TLR4 in the intestinal epithelium regulates metabolic syndrome by coordinating interactions between the luminal microbiota and host genes that regulate metabolism. Mice lacking TLR4 in the intestinal epithelium (TLR4[ΔIEC]), but not mice lacking TLR4 in myeloid cells nor mice lacking TLR4 globally, developed metabolic syndrome; these features were not observed in TLR4[ΔIEC] mice given antibiotics. Metagenomic analysis of the fecal microbiota revealed differences between TLR4[ΔIEC] and wild-type mice, while meta-transcriptome analysis of the microbiota showed that intestinal TLR4 affected the expression of microbial genes involved in the metabolism of lipids, amino acids, and nucleotides. Genes regulated by peroxisome proliferator-activated receptors (PPARs) and the antimicrobial peptide lysozyme were significantly downregulated in TLR4[ΔIEC] mice, suggesting a mechanism by which intestinal TLR4 could exert its effects on the microbiota and metabolic syndrome. Supportingly, antibiotics prevented both downregulation of PPAR genes and the development of metabolic syndrome, while PPAR agonists prevented development of metabolic syndrome in TLR4[ΔIEC] mice. Thus, intestinal epithelial TLR4 regulates metabolic syndrome through altered host-bacterial signaling, suggesting that microbial or PPAR-based strategies might have therapeutic potential for this disease.}, } @article {pmid29362424, year = {2018}, author = {Verma, MK and Ahmed, V and Gupta, S and Kumar, J and Pandey, R and Mandhan, V and Chauhan, NS}, title = {Functional metagenomics identifies novel genes ABCTPP, TMSRP1 and TLSRP1 among human gut enterotypes.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1397}, pmid = {29362424}, issn = {2045-2322}, support = {MC_PC_15029/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacterial Proteins/*genetics ; Bacteroidetes/genetics/*isolation & purification ; Cloning, Molecular ; Gastrointestinal Microbiome ; Gene Expression Regulation, Bacterial ; Humans ; Metagenomics/*methods ; Phylogeny ; *Salt Tolerance ; }, abstract = {Every niche in the biosphere is touched by the seemingly endless capacity of microbes to transform the world around them by adapting swiftly and flexibly to the environmental changes, likewise the gastrointestinal tract is no exception. The ability to cope with rapid changes in external osmolarity is an important aspect of gut microbes for their survival and colonization. Identification of these survival mechanisms is a pivotal step towards understanding genomic suitability of a symbiont for successful human gut colonization. Here we highlight our recent work applying functional metagenomics to study human gut microbiome to identify candidate genes responsible for the salt stress tolerance. A plasmid borne metagenomic library of Bacteroidetes enriched human fecal metagenomic DNA led to identification of unique salt osmotolerance clones SR6 and SR7. Subsequent gene analysis combined with functional studies revealed that TLSRP1 within pSR7 and TMSRP1 and ABCTPP of pSR6 are the active loci responsible for osmotolerance through an energy dependent mechanism. Our study elucidates the novel genetic machinery involved in bestowing osmotolerance in Prevotella and Bacteroidetes, the predominant microbial groups in a North Indian population. This study unravels an alternative method for imparting ionic stress tolerance, which may be prevalent in the human gut microbiome.}, } @article {pmid29361802, year = {2018}, author = {D'Auria, G and Artacho, A and Rojas, RA and Bautista, JS and Méndez, R and Gamboa, MT and Gamboa, JR and Gómez-Cruz, R}, title = {Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs.}, journal = {Genes}, volume = {9}, number = {1}, pages = {}, pmid = {29361802}, issn = {2073-4425}, abstract = {New biotechnology applications require in-depth preliminary studies of biodiversity. The methods of massive sequencing using metagenomics and bioinformatics tools offer us sufficient and reliable knowledge to understand environmental diversity, to know new microorganisms, and to take advantage of their functional genes. Villa Luz caves, in the southern Mexican state of Tabasco, are fed by at least 26 groundwater inlets, containing 300-500 mg L-1 H2S and <0.1 mg L-1 O2. We extracted environmental DNA for metagenomic analysis of collected samples in five selected Villa Luz caves sites, with pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H2S to H2SO4. These include: biovermiculites, a bacterial association that can grow on the rock walls; snottites, that are whitish, viscous biofilms hanging from the rock walls, and sacks or bags of phlegm, which live within the aquatic environment of the springs. Through the emergency food assistance program (TEFAP) pyrosequencing, a total of 20,901 readings of amplification products from hypervariable regions V1 and V3 of 16S rRNA bacterial gene in whole and pure metagenomic DNA samples were generated. Seven bacterial phyla were identified. As a result, Proteobacteria was more frequent than Acidobacteria. Finally, acidophilic Proteobacteria was detected in UJAT5 sample.}, } @article {pmid29356515, year = {2018}, author = {Chen, L and Zhang, W and Hua, J and Hu, C and Lok-Shun Lai, N and Qian, PY and Lam, PKS and Lam, JCW and Zhou, B}, title = {Dysregulation of Intestinal Health by Environmental Pollutants: Involvement of the Estrogen Receptor and Aryl Hydrocarbon Receptor.}, journal = {Environmental science & technology}, volume = {52}, number = {4}, pages = {2323-2330}, doi = {10.1021/acs.est.7b06322}, pmid = {29356515}, issn = {1520-5851}, mesh = {Animals ; *Environmental Pollutants ; Female ; *Gastrointestinal Microbiome ; Intestines ; Male ; *Polychlorinated Biphenyls ; Receptors, Aryl Hydrocarbon ; Receptors, Estrogen ; }, abstract = {To determine how environmental pollutants induce dysbiosis of the gut microbiota, we exposed adult zebrafish to model pollutants with varied modes of action (atrazine, estradiol, polychlorinated biphenyl [PCB]126, and PCB153) for 7 days. Subsequently, metagenomic sequencing of the intestines was performed to compare the gut microbiomes among the groups. We observed clear compound- and sex-specific responses to xenobiotic stress. Principal component analysis revealed involvement of the aryl hydrocarbon receptor (AhR) and, to a lesser extent, the estrogen receptor (ER) in the dysregulation of the intestinal microbiota. The model pollutants differentially impaired intestinal and hepatic physiological activities, as indicated by assessments of gut motility, epithelial permeability, inflammation, and oxidative stress. Correlation analysis showed that abnormal Aeromonas reproduction, especially in the PCB126 groups, was significantly positively associated with oxidative damage. Aeromonas closely interacted with Mannheimia and Blastococcus to regulate intestinal permeability. In summary, we demonstrated that ER and AhR signaling regulated the dynamics of the gut microbiota. Our findings provide new mechanistic insight into the complex interactions between the host metabolism and gut microbiota, which may contribute to the grouped assessment of environmental pollutants in future.}, } @article {pmid29355576, year = {2018}, author = {Johnson, PJ and Hargreaves, LL and Zobrist, CN and Ericsson, AC}, title = {Utility of a portable desiccant system for preservation of fecal samples for downstream 16S rRNA amplicon sequencing.}, journal = {Journal of microbiological methods}, volume = {146}, number = {}, pages = {1-6}, pmid = {29355576}, issn = {1872-8359}, support = {K01 OD019924/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; DNA, Bacterial ; Feces/*microbiology ; Freezing ; Horses ; *Hygroscopic Agents ; Microbiota/genetics ; Preservation, Biological/*methods ; *RNA, Ribosomal, 16S ; Specimen Handling/methods ; }, abstract = {While recent advances in culture-independent sequencing approaches have revitalized the field of microbiology, rapid collection and preservation of microbial DNA in samples like feces is critical to avoid degradation of target DNA via nuclease activity and proliferation of aerotolerant microbes. Common laboratory practices to ameliorate such changes rely on prompt freezing of samples or dispersion in nuclease-inhibiting reagents. As many of the microbial enzymes associated with nuclease activity and bacterial proliferation are hydrolases, prompt desiccation of samples offers an attractive alternative to freezing and liquid reagents for field collection of samples in remote areas. Herein, we evaluated the utility of a portable desiccant chamber with a rechargeable cartridge, for preservation of equine fecal samples for downstream microbial profiling via 16S rRNA amplicon sequencing. Controls included matched samples promptly frozen at -80 °C or left at room temperature for an equivalent period of time. While samples held at room temperature showed a significant reduction in richness and proliferation of several facultative anaerobes, desiccated samples showed minimal change from promptly frozen samples, with the exception of increased abundance of Acinetobacter spp. in desiccated samples relative to frozen samples. The data support the utility of portable desiccant chambers for the preservation of microbial field samples intended for downstream sequencing approaches.}, } @article {pmid29355422, year = {2018}, author = {Mira, A}, title = {Oral Microbiome Studies: Potential Diagnostic and Therapeutic Implications.}, journal = {Advances in dental research}, volume = {29}, number = {1}, pages = {71-77}, doi = {10.1177/0022034517737024}, pmid = {29355422}, issn = {1544-0737}, mesh = {Bacteria/classification ; Biofilms/classification ; Biomarkers/analysis ; Dental Caries/immunology/*microbiology/*prevention & control ; Humans ; In Situ Hybridization, Fluorescence/methods ; Metagenomics ; Microbiota/*physiology ; Microfluidics ; Mouth/*microbiology ; Prebiotics ; Probiotics/pharmacology ; Saliva/microbiology ; }, abstract = {Understanding the microbiology of dental caries is not a mere academic exercise; it provides the basis for preventive, diagnostic, and treatment strategies and gives the dentist a theoretical framework to become a better professional. The last years have seen the development of new research methodologies, ranging from high-throughput sequencing or "omics" techniques to new fluorescence microscopy applications and microfluidics, which have allowed the study of the oral microbiome to an unprecedented level of detail. Those studies have provided new insights about oral biofilm formation, biomarkers of caries risk, microbial etiology, appropriate sampling, identification of health-associated bacteria, and new anticaries strategies, among others. Several pitfalls are associated with the new technologies, including a small number of samples per study group, elevated cost, and genus- or species-based analyses that do not take into consideration intraspecies variability. However, the new data strongly suggest that saliva may not be an appropriate sample for etiological studies or for bacterial caries-risk tests, that microbial composition alone may be insufficient to predict caries risk, and that antimicrobial or immunization strategies targeting single species are unlikely to be effective. Strategies directed toward modulation of the oral biofilm, such as pre- and probiotics, emerge as promising new approaches to prevent tooth decay.}, } @article {pmid29355278, year = {2018}, author = {Cheng, M and Zhang, X and Zhu, J and Cheng, L and Cao, J and Wu, Z and Weng, P and Zheng, X}, title = {A metagenomics approach to the intestinal microbiome structure and function in high fat diet-induced obesity mice fed with oolong tea polyphenols.}, journal = {Food & function}, volume = {9}, number = {2}, pages = {1079-1087}, doi = {10.1039/c7fo01570d}, pmid = {29355278}, issn = {2042-650X}, mesh = {Animals ; Bacteria/classification/drug effects/*genetics/isolation & purification ; Camellia sinensis/*chemistry ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Obesity/*drug therapy/metabolism/microbiology ; Plant Extracts/*administration & dosage ; Polyphenols/*administration & dosage ; Tea/chemistry/metabolism ; }, abstract = {To investigate the modulatory effect of oolong tea polyphenols (OTP) on intestinal microbiota, OTP was prepared by column chromatography and its influence on the gut flora structure was analyzed by high-throughput sequencing with a human flora-associated high fat diet (HFD) induced obesity mouse model. We observed a robust increase in bacterial biodiversity and the abundance of genera known to be butyrate- and acetate-producing bacteria. A large increase in Bacteroidetes with a decrease in Firmicutes was observed after the administration of OTP for 4 weeks, and the corresponding decrease in the Firmicutes/Bacteroidetes ratio reflected the positive modulatory effect of OTP on the intestinal microbiota. In addition, KEGG pathways for the biosynthesis of amino acids, carbon metabolism, and the ribosome were among the most differentially expressed genes after OTP intervention. The current study revealed that OTP rich in tea catechins, especially O-methylated derivatives, may have prebiotic-like activity and can be used as a functional food component with potential therapeutic utility to prevent obesity-related metabolic disorders by manipulating the intestinal microbiota.}, } @article {pmid29354879, year = {2018}, author = {Cerqueira, T and Barroso, C and Froufe, H and Egas, C and Bettencourt, R}, title = {Metagenomic Signatures of Microbial Communities in Deep-Sea Hydrothermal Sediments of Azores Vent Fields.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {387-403}, pmid = {29354879}, issn = {1432-184X}, support = {M3.1.2/F/052/2011//Direção Regional da Ciência e Tecnologia/ ; UID/MAR/04292/2013 granted to MARE//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {Archaea/classification/genetics/metabolism ; Autotrophic Processes ; Azores ; Bacteria/classification/genetics/metabolism ; Biodiversity ; Carbon/metabolism ; Carbon Cycle ; Chemoautotrophic Growth/physiology ; Citric Acid Cycle ; Epsilonproteobacteria/metabolism ; Geologic Sediments/*microbiology ; Hydrothermal Vents/*microbiology ; Metagenome/physiology ; *Metagenomics ; Methane/metabolism ; Microbiota/*physiology ; Nitrogen/metabolism ; Oxidation-Reduction ; Photosynthesis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sulfur/metabolism ; }, abstract = {The organisms inhabiting the deep-seafloor are known to play a crucial role in global biogeochemical cycles. Chemolithoautotrophic prokaryotes, which produce biomass from single carbon molecules, constitute the primary source of nutrition for the higher organisms, being critical for the sustainability of food webs and overall life in the deep-sea hydrothermal ecosystems. The present study investigates the metabolic profiles of chemolithoautotrophs inhabiting the sediments of Menez Gwen and Rainbow deep-sea vent fields, in the Mid-Atlantic Ridge. Differences in the microbial community structure might be reflecting the distinct depth, geology, and distance from vent of the studied sediments. A metagenomic sequencing approach was conducted to characterize the microbiome of the deep-sea hydrothermal sediments and the relevant metabolic pathways used by microbes. Both Menez Gwen and Rainbow metagenomes contained a significant number of genes involved in carbon fixation, revealing the largely autotrophic communities thriving in both sites. Carbon fixation at Menez Gwen site was predicted to occur mainly via the reductive tricarboxylic acid cycle, likely reflecting the dominance of sulfur-oxidizing Epsilonproteobacteria at this site, while different autotrophic pathways were identified at Rainbow site, in particular the Calvin-Benson-Bassham cycle. Chemolithotrophy appeared to be primarily driven by the oxidation of reduced sulfur compounds, whether through the SOX-dependent pathway at Menez Gwen site or through reverse sulfate reduction at Rainbow site. Other energy-yielding processes, such as methane, nitrite, or ammonia oxidation, were also detected but presumably contributing less to chemolithoautotrophy. This work furthers our knowledge of the microbial ecology of deep-sea hydrothermal sediments and represents an important repository of novel genes with potential biotechnological interest.}, } @article {pmid29353803, year = {2018}, author = {Guerra, AB and Oliveira, JS and Silva-Portela, RCB and Araújo, W and Carlos, AC and Vasconcelos, ATR and Freitas, AT and Domingos, YS and de Farias, MF and Fernandes, GJT and Agnez-Lima, LF}, title = {Metagenome enrichment approach used for selection of oil-degrading bacteria consortia for drill cutting residue bioremediation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {235}, number = {}, pages = {869-880}, doi = {10.1016/j.envpol.2018.01.014}, pmid = {29353803}, issn = {1873-6424}, mesh = {Alkanes/metabolism ; Bacteria/*metabolism ; *Biodegradation, Environmental ; Environmental Pollutants/*metabolism ; *Genome, Bacterial ; Hydrocarbons/metabolism ; *Metagenome ; *Microbial Consortia ; Petroleum/*metabolism ; }, abstract = {Drill cuttings leave behind thousands of tons of residues without adequate treatment, generating a large environmental liability. Therefore knowledge about the microbial community of drilling residue may be useful for developing bioremediation strategies. In this work, samples of drilling residue were enriched in different culture media in the presence of petroleum, aiming to select potentially oil-degrading bacteria and biosurfactant producers. Total DNA was extracted directly from the drill cutting samples and from two enriched consortia and sequenced using the Ion Torrent platform. Taxonomic analysis revealed the predominance of Proteobacteria in the metagenome from the drill cuttings, while Firmicutes was enriched in consortia samples. Functional analysis using the Biosurfactants and Biodegradation Database (BioSurfDB) revealed a similar pattern among the three samples regarding hydrocarbon degradation and biosurfactants production pathways. However, some statistical differences were observed between samples. Namely, the pathways related to the degradation of fatty acids, chloroalkanes, and chloroalkanes were enriched in consortia samples. The degradation colorimetric assay using dichlorophenolindophenol as an indicator was positive for several hydrocarbon substrates. The consortia were also able to produce biosurfactants, with biosynthesis of iturin, lichnysin, and surfactin among the more abundant pathways. A microcosms assay followed by gas chromatography analysis showed the efficacy of the consortia in degrading alkanes, as we observed a reduction of around 66% and 30% for each consortium in total alkanes. These data suggest the potential use of these consortia in the bioremediation of drilling residue based on autochthonous bioaugmentation.}, } @article {pmid29351302, year = {2018}, author = {Bzhalava, Z and Hultin, E and Dillner, J}, title = {Extension of the viral ecology in humans using viral profile hidden Markov models.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0190938}, pmid = {29351302}, issn = {1932-6203}, mesh = {Algorithms ; Computational Biology ; Contig Mapping/statistics & numerical data ; Databases, Protein/statistics & numerical data ; Humans ; Markov Chains ; Metagenomics/statistics & numerical data ; *Microbiota ; Phylogeny ; Viral Proteins/genetics ; Viruses/classification/*genetics/*isolation & purification ; }, abstract = {When human samples are sequenced, many assembled contigs are "unknown", as conventional alignments find no similarity to known sequences. Hidden Markov models (HMM) exploit the positions of specific nucleotides in protein-encoding codons in various microbes. The algorithm HMMER3 implements HMM using a reference set of sequences encoding viral proteins, "vFam". We used HMMER3 analysis of "unknown" human sample-derived sequences and identified 510 contigs distantly related to viruses (Anelloviridae (n = 1), Baculoviridae (n = 34), Circoviridae (n = 35), Caulimoviridae (n = 3), Closteroviridae (n = 5), Geminiviridae (n = 21), Herpesviridae (n = 10), Iridoviridae (n = 12), Marseillevirus (n = 26), Mimiviridae (n = 80), Phycodnaviridae (n = 165), Poxviridae (n = 23), Retroviridae (n = 6) and 89 contigs related to described viruses not yet assigned to any taxonomic family). In summary, we find that analysis using the HMMER3 algorithm and the "vFam" database greatly extended the detection of viruses in biospecimens from humans.}, } @article {pmid29350561, year = {2018}, author = {De Filippis, F and Parente, E and Ercolini, D}, title = {Recent Past, Present, and Future of the Food Microbiome.}, journal = {Annual review of food science and technology}, volume = {9}, number = {}, pages = {589-608}, doi = {10.1146/annurev-food-030117-012312}, pmid = {29350561}, issn = {1941-1413}, mesh = {Computational Biology ; Fermentation ; *Food Microbiology ; Food Safety ; Food Technology/*methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics ; Microbiota/*genetics ; }, abstract = {Sequencing technologies have deeply changed our approach to the study of food microbial communities. This review describes recent exploitations of high-throughput sequencing applications to improve our knowledge of food microbial consortia. In the past 10 years, target amplicon sequencing has become routinely used in many food microbiology laboratories, providing a detailed picture of food-associated microbiota. Metagenomics and metatranscriptomics approaches are still underexploited in food microbial ecology, despite their potential to uncover the functionality of complex communities. In a near future, sequencing technologies will surely advance our understanding of how to effectively use the invaluable microbial resources to improve food quality and safety.}, } @article {pmid29350297, year = {2018}, author = {Zaikova, E and Benison, KC and Mormile, MR and Johnson, SS}, title = {Microbial communities and their predicted metabolic functions in a desiccating acid salt lake.}, journal = {Extremophiles : life under extreme conditions}, volume = {22}, number = {3}, pages = {367-379}, pmid = {29350297}, issn = {1433-4909}, mesh = {Bacteria/isolation & purification/metabolism ; Chlorophyta/metabolism ; *Desiccation ; Fungi/isolation & purification/metabolism ; Groundwater/chemistry/microbiology ; Lakes/chemistry/*microbiology ; Metagenome ; *Microbiota ; Salinity ; }, abstract = {The waters of Lake Magic in Western Australia are among the most geochemically extreme on Earth. This ephemeral saline lake is characterized by pH as low as 1.6 salinity as high as 32% total dissolved solids, and unusually complex geochemistry, including extremely high concentrations of aluminum, silica, and iron. We examined the microbial composition and putative function in this extreme acid brine environment by analyzing lake water, groundwater, and sediment samples collected during the austral summer near peak evapoconcentration. Our results reveal that the lake water metagenome, surprisingly, was comprised of mostly eukaryote sequences, particularly fungi and to a lesser extent, green algae. Groundwater and sediment samples were dominated by acidophilic Firmicutes, with eukaryotic community members only detected at low abundances. The lake water bacterial community was less diverse than that in groundwater and sediment, and was overwhelmingly represented by a single OTU affiliated with Salinisphaera. Pathways associated with halotolerance were found in the metagenomes, as were genes associated with biosynthesis of protective carotenoids. During periods of complete desiccation of the lake, we hypothesize that dormancy and entrapment in fluid inclusions in halite crystals may increase long-term survival, leading to the resilience of complex eukaryotes in this extreme environment.}, } @article {pmid29347966, year = {2018}, author = {Zhou, W and Gay, N and Oh, J}, title = {ReprDB and panDB: minimalist databases with maximal microbial representation.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {15}, pmid = {29347966}, issn = {2049-2618}, support = {DP2 GM126893/GM/NIGMS NIH HHS/United States ; K22 AI119231/AI/NIAID NIH HHS/United States ; }, mesh = {Access to Information ; Algorithms ; Computational Biology/methods ; *Databases, Genetic ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/*methods ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Skin/*microbiology ; }, abstract = {BACKGROUND: Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compatible to various metagenomic read mapping tools. Moreover, computational tools to rapidly compile and update such databases to accommodate the rapid increase in new reference genomes do not exist. As a result, database-guided analyses often fail to profile a substantial fraction of metagenomic shotgun sequencing reads from complex microbiomes.

RESULTS: We report pipelines that efficiently traverse all open access microbial genomes and assemble non-redundant genomic information. The pipelines result in two species-resolution microbial reference databases of relatively small sizes: reprDB, which assembles microbial representative or reference genomes, and panDB, for which we developed a novel iterative alignment algorithm to identify and assemble non-redundant genomic regions in multiple sequenced strains. With the databases, we managed to assign taxonomic labels and genome positions to the majority of metagenomic reads from human skin and gut microbiomes, demonstrating a significant improvement over a previous database-guided analysis on the same datasets.

CONCLUSIONS: reprDB and panDB leverage the rapid increases in the number of open access microbial genomes to more fully profile metagenomic samples. Additionally, the databases exclude redundant sequence information to avoid inflated storage or memory space and indexing or analyzing time. Finally, the novel iterative alignment algorithm significantly increases efficiency in pan-genome identification and can be useful in comparative genomic analyses.}, } @article {pmid29346588, year = {2018}, author = {Cridland, JM and Ramirez, SR and Dean, CA and Sciligo, A and Tsutsui, ND}, title = {Genome Sequencing of Museum Specimens Reveals Rapid Changes in the Genetic Composition of Honey Bees in California.}, journal = {Genome biology and evolution}, volume = {10}, number = {2}, pages = {458-472}, pmid = {29346588}, issn = {1759-6653}, support = {S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Bees/*genetics ; California ; Chromosome Mapping ; *Evolution, Molecular ; Genetics, Population ; *Genome, Insect ; Introduced Species ; Metagenomics ; Pollination ; Polymorphism, Single Nucleotide ; Population Dynamics ; }, abstract = {The western honey bee, Apis mellifera, is an enormously influential pollinator in both natural and managed ecosystems. In North America, this species has been introduced numerous times from a variety of different source populations in Europe and Africa. Since then, feral populations have expanded into many different environments across their broad introduced range. Here, we used whole genome sequencing of historical museum specimens and newly collected modern populations from California (USA) to analyze the impact of demography and selection on introduced populations during the past 105 years. We find that populations from both northern and southern California exhibit pronounced genetic changes, but have changed in different ways. In northern populations, honey bees underwent a substantial shift from western European to eastern European ancestry since the 1960s, whereas southern populations are dominated by the introgression of Africanized genomes during the past two decades. Additionally, we identify an isolated island population that has experienced comparatively little change over a large time span. Fine-scale comparison of different populations and time points also revealed SNPs that differ in frequency, highlighting a number of genes that may be important for recent adaptations in these introduced populations.}, } @article {pmid29340947, year = {2018}, author = {Rubiolo, JA and Lozano-Leon, A and Rodriguez-Souto, R and Fol Rodríguez, N and Vieytes, MR and Botana, LM}, title = {The impact of depuration on mussel hepatopancreas bacteriome composition and predicted metagenome.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {7}, pages = {1117-1129}, doi = {10.1007/s10482-018-1015-y}, pmid = {29340947}, issn = {1572-9699}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; Bivalvia/*microbiology ; Genome, Bacterial ; Hepatopancreas/microbiology ; Metagenome ; Shellfish/*microbiology ; }, abstract = {Due to the rapid elimination of bacteria through normal behaviour of filter feeding and excretion, the decontamination of hazardous contaminating bacteria from shellfish is performed by depuration. This process, under conditions that maximize shellfish filtering activity, is a useful method to eliminate microorganisms from bivalves. The microbiota composition in bivalves reflects that of the environment of harvesting waters, so quite different bacteriomes would be expected in shellfish collected in different locations. Bacterial accumulation within molluscan shellfish occurs primarily in the hepatopancreas. In order to assess the effect of the depuration process on these different bacteriomes, in this work we used 16S RNA pyrosequencing and metagenome prediction to assess the impact of 15 h of depuration on the whole hepatopancreas bacteriome of mussels collected in three different locations.}, } @article {pmid29340898, year = {2018}, author = {Mirande, C and Bizine, I and Giannetti, A and Picot, N and van Belkum, A}, title = {Epidemiological aspects of healthcare-associated infections and microbial genomics.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {37}, number = {5}, pages = {823-831}, pmid = {29340898}, issn = {1435-4373}, mesh = {Bacteria/classification/genetics ; Bacterial Typing Techniques/methods ; Cross Infection/*epidemiology/*microbiology/prevention & control ; Disease Outbreaks ; Genome, Bacterial ; Humans ; *Metagenome ; *Metagenomics/methods ; Microbiota/*genetics ; Molecular Epidemiology ; Whole Genome Sequencing ; }, abstract = {Hospital-acquired infections (HAIs) are a cause of continuously increasing morbidity and mortality. Most of these infections are caused by a limited set of bacterial species, which share the capability to efficiently spread from patient to patient and to easily acquire antibiotic resistance determinants. This renders correct and rapid species identification and antibiotic susceptibility testing (AST) important and underscores the relevance of bacterial epidemiological typing. The latter is needed for the sensitive detection and exact tracing of nosocomial spread of these potentially multidrug-resistant microorganisms (MDRO). Many microbial typing technologies have been developed and put to some level of executive practice, but it seems that the continued evolution in methodology has currently reached an apex: there is likely to be scientific and practical consensus on the ultimate typing potential of bacterial whole-genome sequencing (WGS). The possibility to perform pan-genomic nucleotide-to-nucleotide comparisons between strains belonging to a single species and to detect even minute changes in nucleotide order will identify closely related organisms, while upon accumulation of such mutations, independent descend can be assumed. Calibration of difference levels [i.e. number of single nucleotide polymorphisms (SNPs)] into categories of inter-strain relatedness needs to be performed in order to generate robust, portable typing schemes. Here, we will briefly discuss the state of affairs regarding bacterial epidemiology based upon WGS, its relatedness with the nomenclature of former typing approaches and the continuing need for a global typing language.}, } @article {pmid29339611, year = {2018}, author = {Guan, X and Liu, F and Wang, J and Li, C and Zheng, X}, title = {Mechanism of 1,4-dioxane microbial degradation revealed by 16S rRNA and metatranscriptomic analyses.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {77}, number = {1-2}, pages = {123-133}, doi = {10.2166/wst.2017.498}, pmid = {29339611}, issn = {0273-1223}, mesh = {Biodegradation, Environmental/drug effects ; Dioxanes/*analysis/metabolism ; Furans/pharmacology ; Genes, Microbial ; High-Throughput Nucleotide Sequencing ; Metagenome/*genetics ; Microbial Consortia/*genetics ; Oxidoreductases/genetics/metabolism ; RNA, Ribosomal, 16S ; Sewage/*microbiology ; Transcriptome/*genetics ; Water Pollutants, Chemical/*analysis/metabolism ; }, abstract = {1,4-Dioxane (dioxane), a probable human carcinogen, often exists in industrial wastewater and domestic sewage. In this study, we applied 16S rRNA and metatranscriptomic methods to analyze the dioxane biodegradation mechanism by activated sludge. Tetrahydrofuran (THF) was added as an essential co-metabolite to promote the degradation of dioxane. We found the dioxane removal ratio increased with increasing THF concentrations. When the THF concentration increased from 60.0 to 200.0 mg/L, the dioxane degradation rate was stable. Three additions of ∼60.0 mg/L THF resulted in better dioxane degradation than one addition of 200 mg/L THF. Ammonia-oxidizing and denitrifying bacteria with methane monooxygenases (MOs) and ammonia MOs played the most important roles during the degradation of dioxane. Kyoto Encyclopedia of Genes and Genomes metabolic pathway and functional genes analyses showed that the activated sludge system was complex and stable when dioxane was added. In future studies, primers should be designed to identify specific bacteria and functional MO genes, which would help reveal the function of various bacteria and their MOs during dioxane degradation.}, } @article {pmid29339259, year = {2018}, author = {Lee, MJ and Kang, MJ and Lee, SY and Lee, E and Kim, K and Won, S and Suh, DI and Kim, KW and Sheen, YH and Ahn, K and Kim, BS and Hong, SJ}, title = {Perturbations of gut microbiome genes in infants with atopic dermatitis according to feeding type.}, journal = {The Journal of allergy and clinical immunology}, volume = {141}, number = {4}, pages = {1310-1319}, doi = {10.1016/j.jaci.2017.11.045}, pmid = {29339259}, issn = {1097-6825}, mesh = {*Breast Feeding ; Case-Control Studies ; DNA, Bacterial ; Dermatitis, Atopic/immunology/*microbiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics/*immunology ; Humans ; Infant ; Infant Formula/*adverse effects ; Male ; Metagenome ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Perturbations of the infant gut microbiota can shape development of the immune system and link to the risk of allergic diseases.

OBJECTIVE: We sought to understand the role of the gut microbiome in patients with atopic dermatitis (AD). The metagenome of the infant gut microbiome was analyzed according to feeding types.

METHODS: Composition of the gut microbiota was analyzed in fecal samples from 129 infants (6 months old) by using pyrosequencing, including 66 healthy infants and 63 infants with AD. The functional profile of the gut microbiome was analyzed by means of whole-metagenome sequencing (20 control subjects and 20 patients with AD). In addition, the total number of bacteria in the feces was determined by using real-time PCR.

RESULTS: The gut microbiome of 6-month-old infants was different based on feeding types, and 2 microbiota groups (Bifidobacterium species-dominated and Escherichia/Veillonella species-dominated groups) were found in breast-fed and mixed-fed infants. Bacterial cell amounts in the feces were lower in infants with AD than in control infants. Although no specific taxa directly correlated with AD in 16S rRNA gene results, whole-metagenome analysis revealed differences in functional genes related to immune development. The reduction in genes for oxidative phosphorylation, phosphatidylinositol 3-kinase-Akt signaling, estrogen signaling, nucleotide-binding domain-like receptor signaling, and antigen processing and presentation induced by reduced colonization of mucin-degrading bacteria (Akkermansia muciniphila, Ruminococcus gnavus, and Lachnospiraceae bacterium 2_1_58FAA) was significantly associated with stunted immune development in the AD group compared with the control group (P < .05).

CONCLUSIONS: Alterations in the gut microbiome can be associated with AD because of different bacterial genes that can modulate host immune cell function.}, } @article {pmid29336480, year = {2018}, author = {Freilich, MA and Wieters, E and Broitman, BR and Marquet, PA and Navarrete, SA}, title = {Species co-occurrence networks: Can they reveal trophic and non-trophic interactions in ecological communities?.}, journal = {Ecology}, volume = {99}, number = {3}, pages = {690-699}, doi = {10.1002/ecy.2142}, pmid = {29336480}, issn = {0012-9658}, mesh = {Biota ; Chile ; *Ecology ; *Food Chain ; Symbiosis ; }, abstract = {Co-occurrence methods are increasingly utilized in ecology to infer networks of species interactions where detailed knowledge based on empirical studies is difficult to obtain. Their use is particularly common, but not restricted to, microbial networks constructed from metagenomic analyses. In this study, we test the efficacy of this procedure by comparing an inferred network constructed using spatially intensive co-occurrence data from the rocky intertidal zone in central Chile to a well-resolved, empirically based, species interaction network from the same region. We evaluated the overlap in the information provided by each network and the extent to which there is a bias for co-occurrence data to better detect known trophic or non-trophic, positive or negative interactions. We found a poor correspondence between the co-occurrence network and the known species interactions with overall sensitivity (probability of true link detection) equal to 0.469, and specificity (true non-interaction) equal to 0.527. The ability to detect interactions varied with interaction type. Positive non-trophic interactions such as commensalism and facilitation were detected at the highest rates. These results demonstrate that co-occurrence networks do not represent classical ecological networks in which interactions are defined by direct observations or experimental manipulations. Co-occurrence networks provide information about the joint spatial effects of environmental conditions, recruitment, and, to some extent, biotic interactions, and among the latter, they tend to better detect niche-expanding positive non-trophic interactions. Detection of links (sensitivity or specificity) was not higher for well-known intertidal keystone species than for the rest of consumers in the community. Thus, as observed in previous empirical and theoretical studies, patterns of interactions in co-occurrence networks must be interpreted with caution, especially when extending interaction-based ecological theory to interpret network variability and stability. Co-occurrence networks may be particularly valuable for analysis of community dynamics that blends interactions and environment, rather than pairwise interactions alone.}, } @article {pmid29335567, year = {2018}, author = {Metch, JW and Burrows, ND and Murphy, CJ and Pruden, A and Vikesland, PJ}, title = {Metagenomic analysis of microbial communities yields insight into impacts of nanoparticle design.}, journal = {Nature nanotechnology}, volume = {13}, number = {3}, pages = {253-259}, doi = {10.1038/s41565-017-0029-3}, pmid = {29335567}, issn = {1748-3395}, mesh = {Acrylic Resins/chemistry/metabolism ; Bacteria/*genetics/metabolism ; Cetrimonium/chemistry/metabolism ; Gold/chemistry/*metabolism ; Metagenomics ; *Microbiota ; Nanoparticles/chemistry/*metabolism/ultrastructure ; Nanotubes/chemistry/ultrastructure ; Phylogeny ; Sewage/*microbiology ; Surface Properties ; }, abstract = {Next-generation DNA sequencing and metagenomic analysis provide powerful tools for the environmentally friendly design of nanoparticles. Herein we demonstrate this approach using a model community of environmental microbes (that is, wastewater-activated sludge) dosed with gold nanoparticles of varying surface coatings and morphologies. Metagenomic analysis was highly sensitive in detecting the microbial community response to gold nanospheres and nanorods with either cetyltrimethylammonium bromide or polyacrylic acid surface coatings. We observed that the gold-nanoparticle morphology imposes a stronger force in shaping the microbial community structure than does the surface coating. Trends were consistent in terms of the compositions of both taxonomic and functional genes, which include antibiotic resistance genes, metal resistance genes and gene-transfer elements associated with cell stress that are relevant to public health. Given that nanoparticle morphology remained constant, the potential influence of gold dissolution was minimal. Surface coating governed the nanoparticle partitioning between the bioparticulate and aqueous phases.}, } @article {pmid29335555, year = {2018}, author = {Abu-Ali, GS and Mehta, RS and Lloyd-Price, J and Mallick, H and Branck, T and Ivey, KL and Drew, DA and DuLong, C and Rimm, E and Izard, J and Chan, AT and Huttenhower, C}, title = {Metatranscriptome of human faecal microbial communities in a cohort of adult men.}, journal = {Nature microbiology}, volume = {3}, number = {3}, pages = {356-366}, pmid = {29335555}, issn = {2058-5276}, support = {U54 DK102557/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 CA202704/CA/NCI NIH HHS/United States ; U01 CA152904/CA/NCI NIH HHS/United States ; L30 CA209764/CA/NCI NIH HHS/United States ; K24 DK098311/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; UM1 CA167552/CA/NCI NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Feces/*microbiology ; Follow-Up Studies ; Gastrointestinal Microbiome ; *Gene Expression Profiling ; Gene Regulatory Networks ; Humans ; Longitudinal Studies ; Male ; *Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; Prospective Studies ; }, abstract = {The gut microbiome is intimately related to human health, but it is not yet known which functional activities are driven by specific microorganisms' ecological configurations or transcription. We report a large-scale investigation of 372 human faecal metatranscriptomes and 929 metagenomes from a subset of 308 men in the Health Professionals Follow-Up Study. We identified a metatranscriptomic 'core' universally transcribed over time and across participants, often by different microorganisms. In contrast to the housekeeping functions enriched in this core, a 'variable' metatranscriptome included specialized pathways that were differentially expressed both across participants and among microorganisms. Finally, longitudinal metagenomic profiles allowed ecological interaction network reconstruction, which remained stable over the six-month timespan, as did strain tracking within and between participants. These results provide an initial characterization of human faecal microbial ecology into core, subject-specific, microorganism-specific and temporally variable transcription, and they differentiate metagenomically versus metatranscriptomically informative aspects of the human faecal microbiome.}, } @article {pmid29335554, year = {2018}, author = {Mehta, RS and Abu-Ali, GS and Drew, DA and Lloyd-Price, J and Subramanian, A and Lochhead, P and Joshi, AD and Ivey, KL and Khalili, H and Brown, GT and DuLong, C and Song, M and Nguyen, LH and Mallick, H and Rimm, EB and Izard, J and Huttenhower, C and Chan, AT}, title = {Stability of the human faecal microbiome in a cohort of adult men.}, journal = {Nature microbiology}, volume = {3}, number = {3}, pages = {347-355}, pmid = {29335554}, issn = {2058-5276}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; U01 CA152904/CA/NCI NIH HHS/United States ; L30 CA209764/CA/NCI NIH HHS/United States ; K24 DK098311/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; UM1 CA167552/CA/NCI NIH HHS/United States ; R01 HL035464/HL/NHLBI NIH HHS/United States ; K01 DK110267/DK/NIDDK NIH HHS/United States ; R01 CA202704/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Bacteria/classification ; Cohort Studies ; Feces/*microbiology ; Follow-Up Studies ; *Gastrointestinal Microbiome ; *Gene Expression ; Gene Expression Profiling ; Health Personnel/statistics & numerical data ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Prospective Studies ; }, abstract = {Characterizing the stability of the gut microbiome is important to exploit it as a therapeutic target and diagnostic biomarker. We metagenomically and metatranscriptomically sequenced the faecal microbiomes of 308 participants in the Health Professionals Follow-Up Study. Participants provided four stool samples-one pair collected 24-72 h apart and a second pair ~6 months later. Within-person taxonomic and functional variation was consistently lower than between-person variation over time. In contrast, metatranscriptomic profiles were comparably variable within and between subjects due to higher within-subject longitudinal variation. Metagenomic instability accounted for ~74% of corresponding metatranscriptomic instability. The rest was probably attributable to sources such as regulation. Among the pathways that were differentially regulated, most were consistently over- or under-transcribed at each time point. Together, these results suggest that a single measurement of the faecal microbiome can provide long-term information regarding organismal composition and functional potential, but repeated or short-term measures may be necessary for dynamic features identified by metatranscriptomics.}, } @article {pmid29334978, year = {2018}, author = {Wang, H and Li, S and Mahmood, A and Yang, S and Wang, X and Shen, Q and Shan, T and Deng, X and Li, J and Hua, X and Cui, L and Delwart, E and Zhang, W}, title = {Plasma virome of cattle from forest region revealed diverse small circular ssDNA viral genomes.}, journal = {Virology journal}, volume = {15}, number = {1}, pages = {11}, pmid = {29334978}, issn = {1743-422X}, mesh = {Animals ; Biodiversity ; Cattle ; Cattle Diseases/*virology ; DNA Viruses/*genetics ; *DNA, Circular ; *DNA, Viral ; Forests ; *Genetic Variation ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Phylogeny ; Sequence Analysis, DNA ; *Viral Load ; Virus Diseases/*veterinary ; }, abstract = {BACKGROUND: Free-range cattle are common in the Northeast China area, which have close contact with farmers and may carry virus threatening to cattle and farmers.

METHODS: Using viral metagenomics we analyzed the virome in plasma samples collected from 80 cattle from the forested region of Northeast China.

RESULTS: The virome of cattle plasma is composed of the viruses belonging to the families including Parvoviridae, Papillomaviridae, Picobirnaviridae, and divergent viral genomes showing sequence similarity to circular Rep-encoding single stranded (CRESS) DNA viruses. Five such CRESS-DNA genomes were full characterized, with Rep sequences related to circovirus and gemycircularvirus. Three bovine parvoviruses belonging to two different genera were also characterized.

CONCLUSION: The virome in plasma samples of cattle from the forested region of Northeast China was revealed, which further characterized the diversity of viruses in cattle plasma.}, } @article {pmid29334892, year = {2018}, author = {Chen, H and Zhang, W and Li, X and Pan, Y and Yan, S and Wang, Y}, title = {The genome of a prasinoviruses-related freshwater virus reveals unusual diversity of phycodnaviruses.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {49}, pmid = {29334892}, issn = {1471-2164}, support = {41376135//National Natural Science Foundation of China/International ; 31570112//National Natural Science Foundation of China/International ; }, mesh = {Biodiversity ; Fresh Water/virology ; Genes, Viral ; *Genome, Viral ; Histones/genetics ; Phycodnaviridae/classification/*genetics ; Phylogeny ; }, abstract = {BACKGROUND: Phycodnaviruses are widespread algae-infecting large dsDNA viruses and presently contain six genera: Chlorovirus, Prasinovirus, Prymnesiovirus, Phaeovirus, Coccolithovirus and Raphidovirus. The members in Prasinovirus are identified as marine viruses due to their marine algal hosts, while prasinovirus freshwater relatives remain rarely reported.

RESULTS: Here we present the complete genomic sequence of a novel phycodnavirus, Dishui Lake Phycodnavirus 1 (DSLPV1), which was assembled from Dishui Lake metagenomic datasets. DSLPV1 harbors a linear genome of 181,035 bp in length (G + C content: 52.7%), with 227 predicted genes and 2 tRNA encoding regions. Both comparative genomic and phylogenetic analyses indicate that the freshwater algal virus DSLPV1 is closely related to the members in Prasinovirus, a group of marine algae infecting viruses. In addition, a complete eukaryotic histone H3 variant was identified in the genome of DSLPV1, which is firstly detected in phycodnaviruses and contributes to understand the interaction between algal virus and its eukaryotic hosts.

CONCLUSION: It is in a freshwater ecosystem that a novel Prasinovirus-related viral complete genomic sequence is discovered, which sheds new light on the evolution and diversity of the algae infecting Phycodnaviridae.}, } @article {pmid29334812, year = {2018}, author = {Ding, W and Ma, C and Zhang, W and Chiang, H and Tam, C and Xu, Y and Zhang, G and Qian, PY}, title = {Anti-biofilm effect of a butenolide/polymer coating and metatranscriptomic analyses.}, journal = {Biofouling}, volume = {34}, number = {1}, pages = {111-122}, doi = {10.1080/08927014.2017.1409891}, pmid = {29334812}, issn = {1029-2454}, mesh = {4-Butyrolactone/*analogs & derivatives/pharmacology ; Biofilms/*drug effects ; Biofouling/*prevention & control ; Cell Adhesion ; Metagenomics ; Microbial Consortia/*genetics ; Polyesters/*pharmacology ; Polyurethanes/*pharmacology ; Seawater ; Surface Properties ; Transcriptome ; }, abstract = {Butenolide is an environmentally friendly antifouling natural product, but its efficiency and mechanism in preventing biofilm formation have not been examined. Furthermore, controlling the release of butenolide from paints into seawater is technically challenging. A coating was developed by mixing butenolide with a biodegradable polymer, poly (ε-caprolactone)-based polyurethane, and a one-month in situ anti-biofilm test was conducted in a subtidal area. The constant release of butenolide from the surface suggested that its release was well controlled. Direct observation and confocal microscope investigation indicated that the coating was effective against both biofilm formation and attachment of large fouling organisms. Metatranscriptomic analysis of biofilm samples implied that the coating selectively inhibited the adhesion of microbes from a variety of phyla and targeted particular functional pathways including energy metabolism, drug transport and toxin release. These integrated analyses demonstrated the potential application of this butenolide/polymer coating as an anti-biofilm material.}, } @article {pmid29332945, year = {2018}, author = {Byrd, AL and Belkaid, Y and Segre, JA}, title = {The human skin microbiome.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {3}, pages = {143-155}, pmid = {29332945}, issn = {1740-1534}, mesh = {Bacteria/*classification ; Bacterial Physiological Phenomena ; Humans ; *Microbiota ; Skin/*microbiology ; Skin Diseases, Bacterial/microbiology ; }, abstract = {Functioning as the exterior interface of the human body with the environment, skin acts as a physical barrier to prevent the invasion of foreign pathogens while providing a home to the commensal microbiota. The harsh physical landscape of skin, particularly the desiccated, nutrient-poor, acidic environment, also contributes to the adversity that pathogens face when colonizing human skin. Despite this, the skin is colonized by a diverse microbiota. In this Review, we describe amplicon and shotgun metagenomic DNA sequencing studies that have been used to assess the taxonomic diversity of microorganisms that are associated with skin from the kingdom to the strain level. We discuss recent insights into skin microbial communities, including their composition in health and disease, the dynamics between species and interactions with the immune system, with a focus on Propionibacterium acnes, Staphylococcus epidermidis and Staphylococcus aureus.}, } @article {pmid29330574, year = {2018}, author = {Koizumi, T and Hattori, M and Nara, K}, title = {Ectomycorrhizal fungal communities in alpine relict forests of Pinus pumila on Mt. Norikura, Japan.}, journal = {Mycorrhiza}, volume = {28}, number = {2}, pages = {129-145}, pmid = {29330574}, issn = {1432-1890}, support = {25660115//Japan Society for the Promotion of Science/ ; 16J07343//Japan Society for the Promotion of Science/ ; }, mesh = {Altitude ; *Biodiversity ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; *Forests ; Japan ; Mycorrhizae/genetics/*physiology ; Pinus/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Ectomycorrhizal (ECM) symbioses are indispensable for the establishment of host trees, yet available information of ECM symbiosis in alpine forests is scarce. Pinus pumila is a typical ice age relict tree species in Japan and often forms monodominant dwarf vegetation above the tree line in mountains. We studied ECM fungi colonizing P. pumila on Mt. Norikura, Japan, with reference to host developmental stages, i.e., from current-year seedlings to mature trees. ECM fungal species were identified based on rDNA ITS sequences. Ninety-two ECM fungal species were confirmed from a total of 2480 root tips examined. Species in /suillus-rhizopogon and /wilcoxina were dominant in seedling roots. ECM fungal diversity increased with host development, due to the addition of species-rich fungal lineages (/cenococcum, /cortinarius, and /russula-lactarius) in late-successional stages. Such successional pattern of ECM fungi is similar to those in temperate pine systems, suggesting the predominant role of /suillus-rhizopogon in seedling establishment, even in relict alpine habitats fragmented and isolated for a geological time period. Most of the ECM fungi detected were also recorded in Europe or North America, indicating their potential Holarctic distribution and the possibility of their comigration with P. pumila through land bridges during ice ages. In addition, we found significant effects of soil properties on ECM fungal communities, which explained 34.1% of the total variation of the fungal communities. While alpine vegetation is regarded as vulnerable to the ongoing global warming, ECM fungal communities associated with P. pumila could be altered by the edaphic change induced by the warming.}, } @article {pmid29330424, year = {2018}, author = {Cui, X and Ye, L and Li, J and Jin, L and Wang, W and Li, S and Bao, M and Wu, S and Li, L and Geng, B and Zhou, X and Zhang, J and Cai, J}, title = {Metagenomic and metabolomic analyses unveil dysbiosis of gut microbiota in chronic heart failure patients.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {635}, pmid = {29330424}, issn = {2045-2322}, mesh = {Adult ; Aged ; Bacteria/*classification/genetics/isolation & purification ; Butyrates/analysis ; Dysbiosis/*diagnosis ; Female ; Gastrointestinal Microbiome ; Heart Failure/*complications ; Humans ; Male ; Metabolomics/*methods ; Metagenomics/*methods ; Methylamines/analysis ; Middle Aged ; Phylogeny ; }, abstract = {Previous studies suggested a possible gut microbiota dysbiosis in chronic heart failure (CHF). However, direct evidence was lacking. In this study, we investigated the composition and metabolic patterns of gut microbiota in CHF patients to provide direct evidence and comprehensive understanding of gut microbiota dysbiosis in CHF. We enrolled 53 CHF patients and 41 controls. Metagenomic analyses of faecal samples and metabolomic analyses of faecal and plasma samples were then performed. We found that the composition of gut microbiota in CHF was significantly different from controls. Faecalibacterium prausnitzii decrease and Ruminococcus gnavus increase were the essential characteristics in CHF patients' gut microbiota. We also observed an imbalance of gut microbes involved in the metabolism of protective metabolites such as butyrate and harmful metabolites such as trimethylamine N-oxide in CHF patients. Metabolic features of both faecal and plasma samples from CHF patients also significantly changed. Moreover, alterations in faecal and plasma metabolic patterns correlated with gut microbiota dysbiosis in CHF. Taken together, we found that CHF was associated with distinct gut microbiota dysbiosis and pinpointed the specific core bacteria imbalance in CHF, along with correlations between changes in certain metabolites and gut microbes.}, } @article {pmid29330189, year = {2018}, author = {Mythen, SM and Devendran, S and Méndez-García, C and Cann, I and Ridlon, JM}, title = {Targeted Synthesis and Characterization of a Gene Cluster Encoding NAD(P)H-Dependent 3α-, 3β-, and 12α-Hydroxysteroid Dehydrogenases from Eggerthella CAG:298, a Gut Metagenomic Sequence.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {7}, pages = {}, pmid = {29330189}, issn = {1098-5336}, mesh = {3-alpha-Hydroxysteroid Dehydrogenase (B-Specific)/genetics/metabolism ; Actinobacteria/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Gastrointestinal Microbiome/*genetics ; *Genes, Bacterial ; Humans ; Hydroxysteroid Dehydrogenases/genetics/metabolism ; Metagenomics ; Multigene Family/*genetics ; }, abstract = {Gut metagenomic sequences provide a rich source of microbial genes, the majority of which are annotated by homology or unknown. Genes and gene pathways that encode enzymes catalyzing biotransformation of host bile acids are important to identify in gut metagenomic sequences due to the importance of bile acids in gut microbiome structure and host physiology. Hydroxysteroid dehydrogenases (HSDHs) are pyridine nucleotide-dependent enzymes with stereospecificity and regiospecificity for bile acid and steroid hydroxyl groups. HSDHs have been identified in several protein families, including medium-chain and short-chain dehydrogenase/reductase families as well as the aldo-keto reductase family. These protein families are large and contain diverse functionalities, making prediction of HSDH-encoding genes difficult and necessitating biochemical characterization. We located a gene cluster in Eggerthella sp. CAG:298 predicted to encode three HSDHs (CDD59473, CDD59474, and CDD59475) and synthesized the genes for heterologous expression in Escherichia coli We then screened bile acid substrates against the purified recombinant enzymes. CDD59475 is a novel 12α-HSDH, and we determined that CDD59474 (3α-HSDH) and CDD59473 (3β-HSDH) constitute novel enzymes in an iso-bile acid pathway. Phylogenetic analysis of these HSDHs with other gut bacterial HSDHs and closest homologues in the database revealed predictable clustering of HSDHs by function and identified several likely HSDH sequences from bacteria isolated or sequenced from diverse mammalian and avian gut samples.IMPORTANCE Bacterial HSDHs have the potential to significantly alter the physicochemical properties of bile acids, with implications for increased/decreased toxicity for gut bacteria and the host. The generation of oxo-bile acids is known to inhibit host enzymes involved in glucocorticoid metabolism and may alter signaling through nuclear receptors such as farnesoid X receptor and G-protein-coupled receptor TGR5. Biochemical or similar approaches are required to fill in many gaps in our ability to link a particular enzymatic function with a nucleic acid or amino acid sequence. In this regard, we have identified a novel 12α-HSDH and a novel set of genes encoding an iso-bile acid pathway (3α-HSDH and 3β-HSDH) involved in epimerization and detoxification of harmful secondary bile acids.}, } @article {pmid29330119, year = {2018}, author = {Jin, W and Wang, Y and Li, Y and Cheng, Y and Zhu, W}, title = {Temporal changes of the bacterial community colonizing wheat straw in the cow rumen.}, journal = {Anaerobe}, volume = {50}, number = {}, pages = {1-8}, doi = {10.1016/j.anaerobe.2018.01.004}, pmid = {29330119}, issn = {1095-8274}, mesh = {Animal Feed/*microbiology ; Animals ; *Bacteria/classification/ultrastructure ; Biodiversity ; Biomass ; Cattle ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Rumen/*microbiology ; Triticum/*microbiology ; }, abstract = {This study used Miseq pyrosequencing and scanning electron microscopy to investigate the temporal changes in the bacterial community tightly attached to wheat straw in the cow rumen. The wheat straw was incubated in the rumens and samples were recovered at various times. The wheat straw degradation exhibited three phases: the first degradation phase occurred within 0.5 h, and the second degradation phase occurred after 6 h, with a stalling phase occurring between 0.5 and 6 h. Scanning electron microscopy revealed the colonization of the microorganisms on the wheat straw over time. The bacterial communities at 0.5, 6, 24, and 72 h were determined, corresponding to the degradation phases. Firmicutes and Bacteroidetes were the two most dominant phyla in the bacterial communities at the four time points. Principal coordinate analysis (PCoA) showed that the bacterial communities at the four time points were distinct from each other. The wheat straw-associated bacteria stabilized at the phylum level after 0.5 h of rumen incubation, and only modest phylum-level and family-level changes were observed for most taxa between 0.5 h and 72 h. The relative abundance of the dominant genera, Butyrivibrio, Coprococcus, Ruminococcus, Succiniclasticum, Clostridium, Prevotella, YRC22, CF231, and Treponema, changed significantly over time (P < .05). However, at the genus level, unclassified taxa accounted for 70.3% ± 6.1% of the relative abundance, indicating their probable importance in the degradation of wheat straw as well as in the temporal changes of the bacterial community. Thus, understanding the function of these unclassified taxa is of great importance for targeted improvement of forage use efficiency in ruminants. Collectively, our results revealed distinct degradation phases of wheat straw and corresponding changes in the colonized bacterial community.}, } @article {pmid29329230, year = {2018}, author = {Atoni, E and Wang, Y and Karungu, S and Waruhiu, C and Zohaib, A and Obanda, V and Agwanda, B and Mutua, M and Xia, H and Yuan, Z}, title = {Metagenomic Virome Analysis of Culex Mosquitoes from Kenya and China.}, journal = {Viruses}, volume = {10}, number = {1}, pages = {}, pmid = {29329230}, issn = {1999-4915}, mesh = {Animals ; China/epidemiology ; Computational Biology ; Culex/*virology ; *Genome, Viral ; High-Throughput Nucleotide Sequencing ; Insect Viruses/*classification ; Kenya/epidemiology ; *Metagenomics ; *Microbiota ; Phylogeny ; }, abstract = {Many blood-feeding arthropods are known vectors of viruses that are a source of unprecedented global health concern. Mosquitoes are an integral part of these arthropod vectors. Advancements in next-generation sequencing and bioinformatics has expanded our knowledge on the richness of viruses harbored by arthropods. In the present study, we applied a metagenomic approach to determine the intercontinental virome diversity of Culex quinquefasciatus and Culex tritaeniorhynchus in Kwale, Kenya and provinces of Hubei and Yunnan in China. Our results showed that viromes from the three locations were strikingly diverse and comprised 30 virus families specific to vertebrates, invertebrates, plants, and protozoa as well as unclassified group of viruses. Though sampled at different times, both Kwale and Hubei mosquito viromes were dominated by vertebrate viruses, in contrast to the Yunnan mosquito virome, which was dominated by insect-specific viruses. However, each virome was unique in terms of virus proportions partly influenced by type of ingested meals (blood, nectar, plant sap, environment substrates). The dominant vertebrate virus family in the Kwale virome was Papillomaviridae (57%) while in Hubei it was Herpesviridae (30%) and the Yunnan virome was dominated by an unclassified viruses group (27%). Given that insect-specific viruses occur naturally in their hosts, they should be the basis for defining the viromes. Hence, the dominant insect-specific viruses in Kwale, Hubei, and Yunnan were Baculoviridae, Nimaviridae and Iflaviridae, respectively. Our study is preliminary but contributes to growing and much needed knowledge, as mosquito viromes could be manipulated to prevent and control pathogenic arboviruses.}, } @article {pmid29327481, year = {2018}, author = {Bahram, M and Vanderpool, D and Pent, M and Hiltunen, M and Ryberg, M}, title = {The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics.}, journal = {Environmental microbiology reports}, volume = {10}, number = {2}, pages = {155-166}, doi = {10.1111/1758-2229.12612}, pmid = {29327481}, issn = {1758-2229}, mesh = {Agaricales/classification/*genetics/isolation & purification/physiology ; Bacteria/classification/genetics/*isolation & purification ; Bacterial Physiological Phenomena ; Fruiting Bodies, Fungal/classification/genetics/isolation & purification/physiology ; Genome, Fungal ; Metagenomics ; *Microbiota ; Phylogeny ; Symbiosis ; }, abstract = {Recent advances in molecular methods have increased our understanding of various fungal symbioses. However, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Agaricales, Basidiomycota), a largely uncultured ectomycorrhizal clade known to form symbiotic associations with a wide variety of plant species. We used metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr.) Kuyper, to classify fungal and bacterial genomic sequences, and obtained a nearly complete fungal genome containing 93% of core eukaryotic genes. Comparative genomics reveals that I. terrigena is more similar to ectomycorrhizal and brown rot fungi than to white rot fungi. The reduction in lignin degradation capacity has been independent from and significantly faster than in closely related ectomycorrhizal clades supporting that ectomycorrhizal symbiosis evolved independently in Inocybe. The microbiome of I. terrigena fruiting-bodies includes bacteria with known symbiotic functions in other fungal and non-fungal host environments, suggesting potential symbiotic functions of these bacteria in fungal tissues regardless of habitat conditions. Our study demonstrates the usefulness of direct metagenomics analysis of fruiting-body tissues for characterizing fungal genomes and microbiome.}, } @article {pmid29327330, year = {2018}, author = {Miao, L and Liu, Z}, title = {Microbiome analysis and -omics studies of microbial denitrification processes in wastewater treatment: recent advances.}, journal = {Science China. Life sciences}, volume = {61}, number = {7}, pages = {753-761}, doi = {10.1007/s11427-017-9228-2}, pmid = {29327330}, issn = {1869-1889}, mesh = {Bacteria/classification/enzymology/genetics/*metabolism ; Carbon/chemistry/metabolism ; *Denitrification/genetics/physiology ; *Metagenomics ; *Microbiota ; Nitrates/chemistry/metabolism ; Nitrogen/chemistry/metabolism ; Proteomics ; Waste Disposal, Fluid ; Wastewater/chemistry/*microbiology ; }, abstract = {Nitrogen pollution is an increasingly severe worldwide problem because of drainage of nitrogen-containing wastewater and intensive application of nitrogen-containing fertilizers. Denitrification, a key process in nitrogen cycles, is commonly employed for nitrogen removal in engineered wastewater treatment systems. Biological denitrification is performed by denitrifying microbes (bacteria) that use nitrate as terminal electron acceptor. Better understanding the functions of diverse microbial populations in denitrification-based wastewater treatment systems, and the interactions of these populations with operating environments, is essential for improving both treatment performance and system stability. Recent advances in "meta-omics" (e. g., genomics, transcriptomics, proteomics, metabolomics), other molecular biology tools, and microbiome analysis have greatly enhanced such understanding. This minireview summarizes recent findings regarding microbial community structure and composition, key functional microbes and their physiology, functional genes involved in nitrogen cycle, and responses of microbes and their genes to changes of environmental factors or operating parameters, in denitrification processes in wastewater treatment systems. Of particular interest are heterotrophic denitrification systems (which require alternative organic carbon sources) and the autotrophic denitrification systems (which do not require an external carbon source). Integrated microbiome and -omics approaches have great future potential for determination of optimal environmental and biotechnological parameters, novel process development, and improvement of nitrogen removal efficiency and system stability.}, } @article {pmid29322681, year = {2018}, author = {Maji, A and Misra, R and Dhakan, DB and Gupta, V and Mahato, NK and Saxena, R and Mittal, P and Thukral, N and Sharma, E and Singh, A and Virmani, R and Gaur, M and Singh, H and Hasija, Y and Arora, G and Agrawal, A and Chaudhry, A and Khurana, JP and Sharma, VK and Lal, R and Singh, Y}, title = {Gut microbiome contributes to impairment of immunity in pulmonary tuberculosis patients by alteration of butyrate and propionate producers.}, journal = {Environmental microbiology}, volume = {20}, number = {1}, pages = {402-419}, doi = {10.1111/1462-2920.14015}, pmid = {29322681}, issn = {1462-2920}, mesh = {Adult ; Bacteria/classification/*metabolism ; Butyrates/*metabolism ; Dysbiosis ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Middle Aged ; Pilot Projects ; Propionates/*metabolism ; RNA, Ribosomal, 16S ; Tuberculosis, Pulmonary/*immunology/metabolism/*microbiology ; Young Adult ; }, abstract = {Tuberculosis (TB) is primarily associated with decline in immune health status. As gut microbiome (GM) is implicated in the regulation of host immunity and metabolism, here we investigate GM alteration in TB patients by 16S rRNA gene and whole-genome shotgun sequencing. The study group constituted of patients with pulmonary TB and their healthy household contacts as controls (HCs). Significant alteration of microbial taxonomic and functional capacity was observed in patients with active TB as compared to the HCs. We observed that Prevotella and Bifidobacterium abundance were associated with HCs, whereas butyrate and propionate-producing bacteria like Faecalibacterium, Roseburia, Eubacterium and Phascolarctobacterium were significantly enriched in TB patients. Functional analysis showed reduced biosynthesis of vitamins and amino acids in favour of enriched metabolism of butyrate and propionate in TB subjects. The TB subjects were also investigated during the course of treatment, to analyse the variation of GM. Although perturbation in microbial composition was still evident after a month's administration of anti-TB drugs, significant changes were observed in metagenome gene pool that pointed towards recovery in functional capacity. Therefore, the findings from this pilot study suggest that microbial dysbiosis may contribute to pathophysiology of TB by enhancing the anti-inflammatory milieu in the host.}, } @article {pmid29322618, year = {2018}, author = {Kato, S and Shibuya, T and Takaki, Y and Hirai, M and Nunoura, T and Suzuki, K}, title = {Genome-enabled metabolic reconstruction of dominant chemosynthetic colonizers in deep-sea massive sulfide deposits.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {862-877}, doi = {10.1111/1462-2920.14032}, pmid = {29322618}, issn = {1462-2920}, mesh = {Carbon Dioxide/*metabolism ; Deltaproteobacteria/*genetics/*metabolism ; Ecosystem ; Geologic Sediments/*microbiology ; Metagenome/genetics ; Metagenomics ; Microbiota ; Nitrogen Fixation/genetics/*physiology ; Seawater/microbiology ; Sulfides/*metabolism ; Sulfur/*metabolism ; }, abstract = {Deep-sea massive sulfide deposits remaining after ceasing of hydrothermal activity potentially provide energy for a chemosynthetic ecosystem in the dark, cold marine environments. Although yet-uncultivated bacteria in the phylum Nitrospirae and the class Deltaproteobacteria are known to dominate the microbial communities of sulfide deposits at and below the seafloor, their metabolic capabilities remain largely elusive. Here, we reveal the metabolic potential of these yet-uncultivated bacteria in hydrothermally inactive sulfide deposits collected at the Southern Mariana Trough by seafloor drilling. Near-complete genomes of the predominant bacterial members were recovered from shotgun metagenomic sequences. The genomic capabilities for CO2 and N2 fixation suggest that these bacteria are primary producers in the microbial ecosystem. Their genomes also encode versatile chemolithotrophic energy metabolisms, such as the oxidation of H2 , sulfide and intermediate sulfur species including thiosulfate, all of which can be supplied by chemical reactions between seawater and metal sulfides. Notably, the presence of genes involved in thiosulfate oxidation in Nitrospirae and Deltaproteobacteria genomes is unusual. Our study strongly support the presence of a chemosynthetic ecosystem fuelled by the Earth's internal energy in the deep-sea massive sulfide deposits, and illustrates the unexpected metabolic capability of known bacterial taxonomic groups.}, } @article {pmid29321767, year = {2017}, author = {Soliman, T and Reimer, JD and Yang, SY and Villar-Briones, A and Roy, MC and Jenke-Kodama, H}, title = {Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro) in Okinawa Island, Japan.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2451}, pmid = {29321767}, issn = {1664-302X}, abstract = {Microbial community diversity and chemodiversity were investigated in marine sediments adjacent to the Okinawan "Kaichu-Doro" Causeway, which was constructed 46 years ago to connect a group of four islands (Henza-jima, Miyagi-jima, Ikei-jima, Hamahiga-jima) to the Okinawan main island. This causeway was not built on pilings, but by land reclamation; hence, it now acts as a long, thin peninsula. The construction of this causeway was previously shown to have influenced the surrounding marine ecosystem, causing ecosystem fragmentation and loss of water circulation. In this study, we collected sediment cores (n = 10) from five paired sites in 1 m water depths. Each pair of sites consisted of one site each on the immediate north and south sides of the causeway. Originally the members of each pair were much closer to each other (<150 m) than to other pairs, but now the members of each pair are isolated by the causeway. Each core was 60-80 cm long and was divided into 15-cm layers. We examined the vertical diversity of microbial communities and chemical compounds to determine the correlation between chemodiversity and microbial communities among marine sediment cores and layers. Principal coordinate analyses (PCoA) of detected compounds and of bacterial and archaeal operational taxonomic units (OTUs) revealed that the north and south sides of the causeway are relatively isolated, with each side having unique microbial OTUs. Additionally, some bacterial families (e.g., Acidaminobacteraceae, Rhizobiaceae, and Xanthomonadaceae) were found only on the south side of Kaichu-Doro. Interestingly, we found that the relative abundance of OTUs for some microbial families increased from top to bottom, but this was reversed in some other families. We conclude that the causeway has altered microbial community composition and metabolite profiles in marine sediments.}, } @article {pmid29321640, year = {2018}, author = {Ehsani, E and Hernandez-Sanabria, E and Kerckhof, FM and Props, R and Vilchez-Vargas, R and Vital, M and Pieper, DH and Boon, N}, title = {Initial evenness determines diversity and cell density dynamics in synthetic microbial ecosystems.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {340}, pmid = {29321640}, issn = {2045-2322}, mesh = {*Biodiversity ; *Ecosystem ; Metagenome ; Metagenomics/methods ; *Microbiota ; Models, Theoretical ; Phenotype ; }, abstract = {The effect of initial evenness on the temporal trajectory of synthetic communities in comprehensive, low-volume microcosm studies remains unknown. We used flow cytometric fingerprinting and 16S rRNA gene amplicon sequencing to assess the impact of time on community structure in one hundred synthetic ecosystems of fixed richness but varying initial evenness. Both methodologies uncovered a similar reduction in diversity within synthetic communities of medium and high initial evenness classes. However, the results of amplicon sequencing showed that there were no significant differences between and within the communities in all evenness groups at the end of the experiment. Nevertheless, initial evenness significantly impacted the cell density of the community after five medium transfers. Highly even communities retained the highest cell densities at the end of the experiment. The relative abundances of individual species could be associated to particular evenness groups, suggesting that their presence was dependent on the initial evenness of the synthetic community. Our results reveal that using synthetic communities for testing ecological hypotheses requires prior assessment of initial evenness, as it impacts temporal dynamics.}, } @article {pmid29319531, year = {2017}, author = {Czarny, J and Staninska-Pięta, J and Powierska-Czarny, J and Nowak, J and Wolko, Ł and Piotrowska-Cyplik, A}, title = {Metagenomic Analysis of Soil Bacterial Community and Level of Genes Responsible for Biodegradation of Aromatic Hydrocarbons.}, journal = {Polish journal of microbiology}, volume = {66}, number = {3}, pages = {345-352}, doi = {10.5604/01.3001.0010.4865}, pmid = {29319531}, issn = {1733-1331}, mesh = {Alphaproteobacteria/classification/*genetics/*metabolism ; *Biodegradation, Environmental ; DNA, Bacterial/genetics ; Dioxygenases/analysis ; Gammaproteobacteria/classification/*genetics/*metabolism ; Gasoline/analysis ; Metagenomics ; Poland ; Polycyclic Aromatic Hydrocarbons/*metabolism ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {The aim of the studies was to compare the composition of soil bacterial metabiomes originating from urbanized areas and areas con¬taminated with hydrocarbons with those from agricultural soil and forest soil obtained from a protected wild-life park area. It should be noted that hydrocarbons are everywhere therefore bacteria capable of their utilization are present in every soil type. In the hydrocarbon-contaminated soil and in the soil of anthropogenic origin, the bacteria belonging to Gammaproteobacteria were dominant (28.4-36.6%), whereas in the case of agricultural soil and protected wild-life park soil their ratios decreased (22.8-23.0%) and were similar to that of Alphaproteobacteria. No statistically significant changes were observed in terms of the Operational Taxonomic Unit identified in the studies soils, however, based on the determined alpha-diversity it can be established that contaminated soils were characterized by lower biodiversity indices compared to agricultural and forest soils. Furthermore, the dioxygenase level was also evaluated in the studied soils, which are genes encoding crucial enzymes for the decomposition of mono- and polycyclic aromatic hydrocarbons during the biodegradation of diesel oil (PAHRHDαGN, PAHRHDαGP, xylE, Cat 2,3, ndoB). It was concluded that both the population structure of the soil metabiome and the number of genes crucial for biodegradation processes differed significantly between the soils. The level of analysed genes showed a similar trend, as their highest number in relations to genes encoding 16S RNA was determined in urban and hydrocarbon-contaminated soil.}, } @article {pmid29319528, year = {2017}, author = {Wang, H and Wei, Q and Gui, S and Feng, Y and Zhang, Y and Liu, Y and Lu, F}, title = {Metagenomic Profiling of the Bacterial Community Changes from Koji to Mash Stage in the Brewing of Soy Sauce.}, journal = {Polish journal of microbiology}, volume = {66}, number = {4}, pages = {537-541}, doi = {10.5604/01.3001.0010.7097}, pmid = {29319528}, issn = {1733-1331}, mesh = {Bacteria/*classification ; Biodiversity ; *Fermentation ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; *Microbiota ; Polymerase Chain Reaction ; Soy Foods/*microbiology ; Glycine max/microbiology ; Staphylococcus/classification ; Weissella/classification ; }, abstract = {The improvement of soy sauce fermentation is restricted by the insufficient information on bacterial community. In this study, bacterial communities in the koji and mash stage were compared based on next-generation sequencing technology. A total of 29 genera were identified in the koji stage, while 34 in the mash stage. After koji stage, 7 genera disappeared and 12 new genera appeared in the mash stage. The dominant bacteria were Kurthia, Weissella and Staphylococcus in the koji stage and Staphylococcus, Kurthia, Enterococcus and Leuconostoc in the mash stage. The results provided insights into the microbial communities involved in soy sauce fermentation.}, } @article {pmid29319506, year = {2017}, author = {Cłapa, T and Narożna, D and Siuda, R and Borkowski, A and Selwet, M and Mądrzak, CJ and Koźlecka, E}, title = {Bacterial Communities from the Arsenic Mine in Złoty Stok, Sudety Mountains, Poland.}, journal = {Polish journal of microbiology}, volume = {66}, number = {3}, pages = {375-381}, doi = {10.5604/01.3001.0010.4875}, pmid = {29319506}, issn = {1733-1331}, mesh = {*Arsenic ; Bacteria/*classification/*genetics/isolation & purification ; DNA, Bacterial/genetics ; Geologic Sediments/*microbiology ; Microbiota/*genetics ; *Mining ; Poland ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Investigations of bacterial communities and characterization of mineralogy of the environment in the Złoty Stok As-Au deposit were carried out. PXRD analysis revealed the presence of picropharmacolite as the most common secondary arsenic mineral in the mine. Total DNA was extracted from slime streams or slime biofilms samples to investigate the bacterial communities. PCR amplification of 16S rDNA was performed followed by subcloning of its products. Over 170 clones were analyzed by means of RFLP method. Eight group of clones representing different restriction patterns were identified. The nucleotide sequences of their inserts suggest that bacteria present in the mine environment belong to: Flavobacteria, Sphingobacteriia, Bacteroides, Proteobacteria, Mollicutes and Firmicutes. The metagenomic approach allows to demonstrate a higher diversity of microbiota than classical microbiological studies of cultivable isolates.}, } @article {pmid29318631, year = {2018}, author = {Fazlollahi, M and Chun, Y and Grishin, A and Wood, RA and Burks, AW and Dawson, P and Jones, SM and Leung, DYM and Sampson, HA and Sicherer, SH and Bunyavanich, S}, title = {Early-life gut microbiome and egg allergy.}, journal = {Allergy}, volume = {73}, number = {7}, pages = {1515-1524}, pmid = {29318631}, issn = {1398-9995}, support = {U01 AI066560/AI/NIAID NIH HHS/United States ; UL1 TR000039/TR/NCATS NIH HHS/United States ; UL1 RR025005/RR/NCRR NIH HHS/United States ; UM1 AI130781/AI/NIAID NIH HHS/United States ; S10 OD018522/OD/NIH HHS/United States ; U19 AI066738/AI/NIAID NIH HHS/United States ; UL1 TR000067/TR/NCATS NIH HHS/United States ; U01 AI181962/AI/NIAID NIH HHS/United States ; R01 AI118833/AI/NIAID NIH HHS/United States ; UL1 TR000154/TR/NCATS NIH HHS/United States ; K08 AI093538/AI/NIAID NIH HHS/United States ; }, mesh = {Age Factors ; Case-Control Studies ; Egg Hypersensitivity/*etiology ; Female ; *Gastrointestinal Microbiome/immunology ; Humans ; Immunization ; Immunoglobulin E/immunology ; Infant ; Male ; Metagenome ; Metagenomics ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Gut microbiota may play a role in egg allergy. We sought to examine the association between early-life gut microbiota and egg allergy.

METHODS: We studied 141 children with egg allergy and controls from the multicenter Consortium of Food Allergy Research study. At enrollment (age 3 to 16 months), fecal samples were collected, and clinical evaluation, egg-specific IgE measurement, and egg skin prick test were performed. Gut microbiome was profiled by 16S rRNA sequencing. Analyses for the primary outcome of egg allergy at enrollment, and the secondary outcomes of egg sensitization at enrollment and resolution of egg allergy by age 8 years, were performed using Quantitative Insights into Microbial Ecology, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, and Statistical Analysis of Metagenomic Profiles.

RESULTS: Compared to controls, increased alpha diversity and distinct taxa (PERMANOVA P = 5.0 × 10[-4]) characterized the early-life gut microbiome of children with egg allergy. Genera from the Lachnospiraceae, Streptococcaceae, and Leuconostocaceae families were differentially abundant in children with egg allergy. Predicted metagenome functional analyses showed differential purine metabolism by the gut microbiota of egg-allergic subjects (Kruskal-Wallis Padj  = 0.021). Greater gut microbiome diversity and genera from Lachnospiraceae and Ruminococcaceae were associated with egg sensitization (PERMANOVA P = 5.0 × 10[-4]). Among those with egg allergy, there was no association between early-life gut microbiota and egg allergy resolution by age 8 years.

CONCLUSION: The distinct early-life gut microbiota in egg-allergic and egg-sensitized children identified by our study may point to targets for preventive or therapeutic intervention.}, } @article {pmid29317592, year = {2018}, author = {Ong, IM and Gonzalez, JG and McIlwain, SJ and Sawin, EA and Schoen, AJ and Adluru, N and Alexander, AL and Yu, JJ}, title = {Gut microbiome populations are associated with structure-specific changes in white matter architecture.}, journal = {Translational psychiatry}, volume = {8}, number = {1}, pages = {6}, pmid = {29317592}, issn = {2158-3188}, support = {U54 AI117924/AI/NIAID NIH HHS/United States ; P30 HD003352/HD/NICHD NIH HHS/United States ; UL1 TR000427/TR/NCATS NIH HHS/United States ; P30 CA014520/CA/NCI NIH HHS/United States ; T32 CA009206/CA/NCI NIH HHS/United States ; R01 EB022883/EB/NIBIB NIH HHS/United States ; UL1 TR002373/TR/NCATS NIH HHS/United States ; U54 HD090256/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification ; *Diet ; Diffusion Tensor Imaging ; *Gastrointestinal Microbiome ; Male ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; White Matter/diagnostic imaging/*pathology ; }, abstract = {Altered gut microbiome populations are associated with a broad range of neurodevelopmental disorders including autism spectrum disorder and mood disorders. In animal models, modulation of gut microbiome populations via dietary manipulation influences brain function and behavior and has been shown to ameliorate behavioral symptoms. With striking differences in microbiome-driven behavior, we explored whether these behavioral changes are also accompanied by corresponding changes in neural tissue microstructure. Utilizing diffusion tensor imaging, we identified global changes in white matter structural integrity occurring in a diet-dependent manner. Analysis of 16S ribosomal RNA sequencing of gut bacteria also showed changes in bacterial populations as a function of diet. Changes in brain structure were found to be associated with diet-dependent changes in gut microbiome populations using a machine learning classifier for quantitative assessment of the strength of microbiome-brain region associations. These associations allow us to further test our understanding of the gut-brain-microbiota axis by revealing possible links between altered and dysbiotic gut microbiome populations and changes in brain structure, highlighting the potential impact of diet and metagenomic effects in neuroimaging.}, } @article {pmid29312205, year = {2017}, author = {Karimi, E and Ramos, M and Gonçalves, JMS and Xavier, JR and Reis, MP and Costa, R}, title = {Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2499}, pmid = {29312205}, issn = {1664-302X}, abstract = {Current knowledge of sponge microbiome functioning derives mostly from comparative analyses with bacterioplankton communities. We employed a metagenomics-centered approach to unveil the distinct features of the Spongia officinalis endosymbiotic consortium in the context of its two primary environmental vicinities. Microbial metagenomic DNA samples (n = 10) from sponges, seawater, and sediments were subjected to Hiseq Illumina sequencing (c. 15 million 100 bp reads per sample). Totals of 10,272 InterPro (IPR) predicted protein entries and 784 rRNA gene operational taxonomic units (OTUs, 97% cut-off) were uncovered from all metagenomes. Despite the large divergence in microbial community assembly between the surveyed biotopes, the S. officinalis symbiotic community shared slightly greater similarity (p < 0.05), in terms of both taxonomy and function, to sediment than to seawater communities. The vast majority of the dominant S. officinalis symbionts (i.e., OTUs), representing several, so-far uncultivable lineages in diverse bacterial phyla, displayed higher residual abundances in sediments than in seawater. CRISPR-Cas proteins and restriction endonucleases presented much higher frequencies (accompanied by lower viral abundances) in sponges than in the environment. However, several genomic features sharply enriched in the sponge specimens, including eukaryotic-like repeat motifs (ankyrins, tetratricopeptides, WD-40, and leucine-rich repeats), and genes encoding for plasmids, sulfatases, polyketide synthases, type IV secretion proteins, and terpene/terpenoid synthases presented, to varying degrees, higher frequencies in sediments than in seawater. In contrast, much higher abundances of motility and chemotaxis genes were found in sediments and seawater than in sponges. Higher cell and surface densities, sponge cell shedding and particle uptake, and putative chemical signaling processes favoring symbiont persistence in particulate matrices all may act as mechanisms underlying the observed degrees of taxonomic connectivity and functional convergence between sponges and sediments. The reduced frequency of motility and chemotaxis genes in the sponge microbiome reinforces the notion of a prevalent mutualistic mode of living inside the host. This study highlights the S. officinalis "endosymbiome" as a distinct consortium of uncultured prokaryotes displaying a likely "sit-and-wait" strategy to nutrient foraging coupled to sophisticated anti-viral defenses, unique natural product biosynthesis, nutrient utilization and detoxification capacities, and both microbe-microbe and host-microbe gene transfer amenability.}, } @article {pmid29311667, year = {2018}, author = {Trosvik, P and Rueness, EK and de Muinck, EJ and Moges, A and Mekonnen, A}, title = {Ecological plasticity in the gastrointestinal microbiomes of Ethiopian Chlorocebus monkeys.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {20}, pmid = {29311667}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Cercopithecinae ; Chloroplasts/genetics ; *Ecology ; *Gastrointestinal Microbiome ; Geography ; Metagenomics/methods ; Microbiota ; RNA, Ribosomal, 16S ; Seasons ; }, abstract = {Human activities can cause habitat degradation that may alter the types and quality of available food resources and thus influence the microbiomes of wild animal populations. Furthermore, seasonal shifts in food availability may cause adaptive responses in the gut microbiome to meet the need for different metabolic capabilities. Here, we demonstrate local-scale population structure in the gastrointestinal microbiotas of Chlorocebus monkeys, in southern Ethiopia, in response to varying degrees of human encroachment. We further provide evidence of adaptation to ecological conditions associated with the dry and wet seasons, and show seasonal effects to be more pronounced in areas with limited human activity. Finally, we report species-level microbiota differences between the endemic Ethiopian Bale monkey, an ecological specialist, and generalist Chlorocebus species from the same geographical region.}, } @article {pmid29311644, year = {2018}, author = {Schirmer, M and Franzosa, EA and Lloyd-Price, J and McIver, LJ and Schwager, R and Poon, TW and Ananthakrishnan, AN and Andrews, E and Barron, G and Lake, K and Prasad, M and Sauk, J and Stevens, B and Wilson, RG and Braun, J and Denson, LA and Kugathasan, S and McGovern, DPB and Vlamakis, H and Xavier, RJ and Huttenhower, C}, title = {Dynamics of metatranscription in the inflammatory bowel disease gut microbiome.}, journal = {Nature microbiology}, volume = {3}, number = {3}, pages = {337-346}, pmid = {29311644}, issn = {2058-5276}, support = {U54 DK102557/DK/NIDDK NIH HHS/United States ; U01 DK062413/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; P01 DK046763/DK/NIDDK NIH HHS/United States ; UL1 TR001881/TR/NCATS NIH HHS/United States ; P30 DK078392/DK/NIDDK NIH HHS/United States ; R01 DK092405/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Child ; Colitis, Ulcerative/microbiology ; Crohn Disease/microbiology ; Dysbiosis ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Gene Expression Profiling ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Longitudinal Studies ; Male ; *Metagenomics ; Phenotype ; *Transcription, Genetic ; Young Adult ; }, abstract = {Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract that affects millions of people worldwide. Genetic, environmental and microbial factors have been implicated in the onset and exacerbation of IBD. However, the mechanisms associating gut microbial dysbioses and aberrant immune responses remain largely unknown. The integrative Human Microbiome Project seeks to close these gaps by examining the dynamics of microbiome functionality in disease by profiling the gut microbiomes of >100 individuals sampled over a 1-year period. Here, we present the first results based on 78 paired faecal metagenomes and metatranscriptomes, and 222 additional metagenomes from 59 patients with Crohn's disease, 34 with ulcerative colitis and 24 non-IBD control patients. We demonstrate several cases in which measures of microbial gene expression in the inflamed gut can be informative relative to metagenomic profiles of functional potential. First, although many microbial organisms exhibited concordant DNA and RNA abundances, we also detected species-specific biases in transcriptional activity, revealing predominant transcription of pathways by individual microorganisms per host (for example, by Faecalibacterium prausnitzii). Thus, a loss of these organisms in disease may have more far-reaching consequences than suggested by their genomic abundances. Furthermore, we identified organisms that were metagenomically abundant but inactive or dormant in the gut with little or no expression (for example, Dialister invisus). Last, certain disease-specific microbial characteristics were more pronounced or only detectable at the transcript level, such as pathways that were predominantly expressed by different organisms in patients with IBD (for example, Bacteroides vulgatus and Alistipes putredinis). This provides potential insights into gut microbial pathway transcription that can vary over time, inducing phenotypical changes that are complementary to those linked to metagenomic abundances. The study's results highlight the strength of analysing both the activity and the presence of gut microorganisms to provide insight into the role of the microbiome in IBD.}, } @article {pmid29311639, year = {2018}, author = {Segobola, J and Adriaenssens, E and Tsekoa, T and Rashamuse, K and Cowan, D}, title = {Exploring Viral Diversity in a Unique South African Soil Habitat.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {111}, pmid = {29311639}, issn = {2045-2322}, mesh = {Bacteriophages/classification/genetics ; *Biodiversity ; Computational Biology/methods ; Genome, Viral ; Metagenome ; Metagenomics/methods ; Phylogeny ; *Soil Microbiology ; South Africa ; Viruses/*classification/genetics/ultrastructure ; }, abstract = {The Kogelberg Biosphere Reserve in the Cape Floral Kingdom in South Africa is known for its unique plant biodiversity. The potential presence of unique microbial and viral biodiversity associated with this unique plant biodiversity led us to explore the fynbos soil using metaviromic techniques. In this study, metaviromes of a soil community from the Kogelberg Biosphere Reserve has been characterised in detail for the first time. Metaviromic DNA was recovered from soil and sequenced by Next Generation Sequencing. The MetaVir, MG-RAST and VIROME bioinformatics pipelines were used to analyse taxonomic composition, phylogenetic and functional assessments of the sequences. Taxonomic composition revealed members of the order Caudovirales, in particular the family Siphoviridae, as prevalent in the soil samples and other compared viromes. Functional analysis and other metaviromes showed a relatively high frequency of phage-related and structural proteins. Phylogenetic analysis of PolB, PolB2, terL and T7gp17 genes indicated that many viral sequences are closely related to the order Caudovirales, while the remainder were distinct from known isolates. The use of single virome which only includes double stranded DNA viruses limits this study. Novel phage sequences were detected, presenting an opportunity for future studies aimed at targeting novel genetic resources for applied biotechnology.}, } @article {pmid29311585, year = {2018}, author = {Odamaki, T and Bottacini, F and Kato, K and Mitsuyama, E and Yoshida, K and Horigome, A and Xiao, JZ and van Sinderen, D}, title = {Genomic diversity and distribution of Bifidobacterium longum subsp. longum across the human lifespan.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {85}, pmid = {29311585}, issn = {2045-2322}, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Aged, 80 and over ; Bifidobacterium longum/*classification/*genetics ; Child ; Child, Preschool ; Gastrointestinal Microbiome ; Gene Order ; *Genetic Variation ; *Genome, Bacterial ; Humans ; Infant ; Infant, Newborn ; Japan ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; Multigene Family ; Phylogeny ; Young Adult ; }, abstract = {Bifidobacterium longum subsp. longum represents one of the most prevalent bifidobacterial species in the infant, adult and elderly (human) gut. In the current study, we performed a comparative genome analysis involving 145 B. longum representatives, including 113 B. longum subsp. longum strains obtained from healthy Japanese subjects aged between 0 and 98 years. Although MCL clustering did not reveal any correlation between isolated strains and subject age, certain characteristics appear to be more prevalent among strains corresponding to specific host ages, such as genes involved in carbohydrate metabolism and environmental response. Remarkably, a substantial number of strains appeared to have been transmitted across family members, a phenomenon that was shown not to be confined to mother-infant pairs. This suggests that the ubiquitous distribution of B. longum subsp. longum across the human lifespan is at least partly due to extensive transmission between relatives. Our findings form a foundation for future research aimed at unraveling the mechanisms that allow B. longum strains to successfully transfer between human hosts, where they then colonize and persist in the gut environment throughout the host's lifespan.}, } @article {pmid29311457, year = {2018}, author = {Kenzaka, T and Kataoka, K and Fujimitsu, T and Tani, K}, title = {[Intestinal Microbiota in Migrating Barn Swallows around Osaka].}, journal = {Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan}, volume = {138}, number = {1}, pages = {117-122}, doi = {10.1248/yakushi.17-00148}, pmid = {29311457}, issn = {1347-5231}, mesh = {Alcaligenaceae/isolation & purification/pathogenicity ; Animal Migration/*physiology ; Animals ; Asia, Southeastern ; *Disease Vectors ; Enterobacteriaceae/isolation & purification/pathogenicity ; Enterococcaceae/isolation & purification/pathogenicity ; Feces/microbiology ; Intestines/*microbiology ; Japan ; *Microbiota ; Mycoplasmataceae/isolation & purification/pathogenicity ; Pseudomonadaceae/isolation & purification/pathogenicity ; Streptococcaceae/isolation & purification/pathogenicity ; Swallows/*microbiology ; }, abstract = {Migratory birds are considered as vectors of infectious diseases, owing to their potential for transmitting pathogens over large distances. The populations of barn swallow (Hirundo rustica) migrate from Southeast Asia to the Japanese mainland during spring and migrate back to Southeast Asia during autumn. This migratory population is estimated to comprise approximately hundreds to thousands of individuals per year. However, to date, not much is known about the gastrointestinal microbiota of the barn swallow. In this study, we characterized the fecal bacterial community in barn swallow. Using 16S rRNA gene metagenomic sequencing analysis, we examined the presence and composition of potentially pathogenic bacteria in the fecal samples, which were collected during spring season from Osaka. The number (±S.D.) of total bacteria was approximately 2.1(±3.4)×10[8] per gram of feces. In most samples, the bacterial community composition was dominated by families, such as Enterobacteriaceae, Pseudomonadaceae, Mycoplasmataceae, Enterococcaceae, Streptococcaceae, and Alcaligenaceae. However, no relationship was found between the bacterial community composition and geographical area in the fecal samples. Potentially pathogenic bacteria were detected at the rate of >0.1%, which included Pseudomonas spp., Escherichia/Shigella spp., Enterobacter spp., Yersinia spp., Mycoplasma spp., Enterococcus spp., Achromobacter spp., and Serratia spp. Our results suggested that barn swallow is instrumental in the transmission of these genera over large distances.}, } @article {pmid29310749, year = {2018}, author = {Taylor-Brown, A and Madden, D and Polkinghorne, A}, title = {Culture-independent approaches to chlamydial genomics.}, journal = {Microbial genomics}, volume = {4}, number = {2}, pages = {}, pmid = {29310749}, issn = {2057-5858}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Bacteriological Techniques/methods ; Base Sequence ; Biodiversity ; Cell Culture Techniques/*methods ; Chlamydia/classification/*genetics/growth & development ; DNA, Bacterial/isolation & purification ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Metagenomics ; }, abstract = {The expanding field of bacterial genomics has revolutionized our understanding of microbial diversity, biology and phylogeny. For most species, DNA extracted from culture material is used as the template for genome sequencing; however, the majority of microbes are actually uncultivable, and others, such as obligate intracellular bacteria, require laborious tissue culture to yield sufficient genomic material for sequencing. Chlamydiae are one such group of obligate intracellular microbes whose characterization has been hampered by this requirement. To circumvent these challenges, researchers have developed culture-independent sample preparation methods that can be applied to the sample directly or to genomic material extracted from the sample. These methods, which encompass both targeted [immunomagnetic separation-multiple displacement amplification (IMS-MDA) and sequence capture] and non-targeted approaches (host methylated DNA depletion-microbial DNA enrichment and cell-sorting-MDA), have been applied to a range of clinical and environmental samples to generate whole genomes of novel chlamydial species and strains. This review aims to provide an overview of the application, advantages and limitations of these targeted and non-targeted approaches in the chlamydial context. The methods discussed also have broad application to other obligate intracellular bacteria or clinical and environmental samples.}, } @article {pmid29309527, year = {2018}, author = {Drost, HG and Gabel, A and Liu, J and Quint, M and Grosse, I}, title = {myTAI: evolutionary transcriptomics with R.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {9}, pages = {1589-1590}, pmid = {29309527}, issn = {1367-4811}, mesh = {Biological Evolution ; Genomics ; Software ; *Transcriptome ; }, abstract = {MOTIVATION: Next Generation Sequencing (NGS) technologies generate a large amount of high quality transcriptome datasets enabling the investigation of molecular processes on a genomic and metagenomic scale. These transcriptomics studies aim to quantify and compare the molecular phenotypes of the biological processes at hand. Despite the vast increase of available transcriptome datasets, little is known about the evolutionary conservation of those characterized transcriptomes.

RESULTS: The myTAI package implements exploratory analysis functions to infer transcriptome conservation patterns in any transcriptome dataset. Comprehensive documentation of myTAI functions and tutorial vignettes provide step-by-step instructions on how to use the package in an exploratory and computationally reproducible manner.

The open source myTAI package is available at https://github.com/HajkD/myTAI and https://cran.r-project.org/web/packages/myTAI/index.html.

CONTACT: hgd23@cam.ac.uk.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid29306345, year = {2018}, author = {Cremonesi, P and Conte, G and Severgnini, M and Turri, F and Monni, A and Capra, E and Rapetti, L and Colombini, S and Chessa, S and Battelli, G and Alves, SP and Mele, M and Castiglioni, B}, title = {Evaluation of the effects of different diets on microbiome diversity and fatty acid composition of rumen liquor in dairy goat.}, journal = {Animal : an international journal of animal bioscience}, volume = {12}, number = {9}, pages = {1856-1866}, doi = {10.1017/S1751731117003433}, pmid = {29306345}, issn = {1751-732X}, mesh = {Animals ; Diet ; Dietary Supplements ; *Fatty Acids/metabolism ; Female ; *Goats/physiology ; Lactation ; *Microbiota ; Milk ; *Rumen/microbiology ; }, abstract = {Fat supplementation plays an important role in defining milk fatty acids (FA) composition of ruminant products. The use of sources rich in linoleic and α-linolenic acid favors the accumulation of conjugated linoleic acids isomers, increasing the healthy properties of milk. Ruminal microbiota plays a pivotal role in defining milk FA composition, and its profile is affected by diet composition. The aim of this study was to investigate the responses of rumen FA production and microbial structure to hemp or linseed supplementation in diets of dairy goats. Ruminal microbiota composition was determined by 16S amplicon sequencing, whereas FA composition was obtained by gas-chromatography technique. In all, 18 pluriparous Alpine goats fed the same pre-treatment diet for 40±7 days were, then, arranged to three dietary treatments consisting of control, linseed and hemp seeds supplemented diets. Independently from sampling time and diets, bacterial community of ruminal fluid was dominated by Bacteroidetes (about 61.2%) and Firmicutes (24.2%) with a high abundance of Prevotellaceae (41.0%) and Veillonellaceae (9.4%) and a low presence of Ruminococcaceae (5.0%) and Lachnospiraceae (4.3%). Linseed supplementation affected ruminal bacteria population, with a significant reduction of biodiversity; in particular, relative abundance of Prevotella was reduced (-12.0%), whereas that of Succinivibrio and Fibrobacter was increased (+50.0% and +75.0%, respectively). No statistically significant differences were found among the average relative abundance of archaeal genera between each dietary group. Moreover, the addition of linseed and hemp seed induced significant changes in FA concentration in the rumen, as a consequence of shift from C18 : 2n-6 to C18 : 3n-3 biohydrogenation pathway. Furthermore, dimethylacetal composition was affected by fat supplementation, as consequence of ruminal bacteria population modification. Finally, the association study between the rumen FA profile and the bacterial microbiome revealed that Fibrobacteriaceae is the bacterial family showing the highest and significant correlation with FA involved in the biohydrogenation pathway of C18 : 3n-3.}, } @article {pmid29304124, year = {2018}, author = {Krehenwinkel, H and Fong, M and Kennedy, S and Huang, EG and Noriyuki, S and Cayetano, L and Gillespie, R}, title = {The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0189188}, pmid = {29304124}, issn = {1932-6203}, mesh = {Animals ; Arthropods/classification/*genetics/*microbiology ; Biodiversity ; DNA/*analysis/*genetics ; DNA Barcoding, Taxonomic/*methods/statistics & numerical data ; DNA Primers ; Ecosystem ; Hawaii ; Metagenome ; Metagenomics/methods/statistics & numerical data ; Microbiota/*genetics ; Polymerase Chain Reaction/methods ; Selection Bias ; }, abstract = {PCR amplification bias is a well-known problem in metagenomic analysis of arthropod communities. In contrast, variation of DNA degradation rates is a largely neglected source of bias. Differential degradation of DNA molecules could cause underrepresentation of taxa in a community sequencing sample. Arthropods are often collected by passive sampling devices, like malaise traps. Specimens in such a trap are exposed to varying periods of suboptimal storage and possibly different rates of DNA degradation. Degradation bias could thus be a significant issue, skewing diversity estimates. Here, we estimate the effect of differential DNA degradation on the recovery of community diversity of Hawaiian arthropods and their associated microbiota. We use a simple DNA size selection protocol to test for degradation bias in mock communities, as well as passively collected samples from actual Malaise traps. We compare the effect of DNA degradation to that of varying PCR conditions, including primer choice, annealing temperature and cycle number. Our results show that DNA degradation does indeed bias community analyses. However, the effect of this bias is of minor importance compared to that induced by changes in PCR conditions. Analyses of the macro and microbiome from passively collected arthropod samples are thus well worth pursuing.}, } @article {pmid29302014, year = {2018}, author = {Matson, V and Fessler, J and Bao, R and Chongsuwat, T and Zha, Y and Alegre, ML and Luke, JJ and Gajewski, TF}, title = {The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients.}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6371}, pages = {104-108}, pmid = {29302014}, issn = {1095-9203}, support = {F99 CA234946/CA/NCI NIH HHS/United States ; R35 CA210098/CA/NCI NIH HHS/United States ; T32 CA009594/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Antibodies, Monoclonal/therapeutic use ; Bifidobacterium longum/classification/genetics/immunology/isolation & purification ; Enterococcus faecium/classification/genetics/immunology/isolation & purification ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*immunology ; Humans ; Immunotherapy/*methods ; Melanoma/immunology/*therapy ; Mice ; Programmed Cell Death 1 Receptor/*antagonists & inhibitors ; RNA, Ribosomal, 16S/genetics ; Skin Neoplasms/immunology/*therapy ; T-Lymphocytes/immunology ; }, abstract = {Anti-PD-1-based immunotherapy has had a major impact on cancer treatment but has only benefited a subset of patients. Among the variables that could contribute to interpatient heterogeneity is differential composition of the patients' microbiome, which has been shown to affect antitumor immunity and immunotherapy efficacy in preclinical mouse models. We analyzed baseline stool samples from metastatic melanoma patients before immunotherapy treatment, through an integration of 16S ribosomal RNA gene sequencing, metagenomic shotgun sequencing, and quantitative polymerase chain reaction for selected bacteria. A significant association was observed between commensal microbial composition and clinical response. Bacterial species more abundant in responders included Bifidobacterium longum, Collinsella aerofaciens, and Enterococcus faecium. Reconstitution of germ-free mice with fecal material from responding patients could lead to improved tumor control, augmented T cell responses, and greater efficacy of anti-PD-L1 therapy. Our results suggest that the commensal microbiome may have a mechanistic impact on antitumor immunity in human cancer patients.}, } @article {pmid29301588, year = {2018}, author = {Greay, TL and Gofton, AW and Paparini, A and Ryan, UM and Oskam, CL and Irwin, PJ}, title = {Recent insights into the tick microbiome gained through next-generation sequencing.}, journal = {Parasites & vectors}, volume = {11}, number = {1}, pages = {12}, pmid = {29301588}, issn = {1756-3305}, support = {130100050//Australian Research Council/International ; 130100050//Bayer Australia Ltd/International ; 130100050//Bayer AG (Germany)/International ; }, mesh = {Animals ; High-Throughput Nucleotide Sequencing/*statistics & numerical data ; Metagenomics/*methods ; *Microbiota ; Ticks/*microbiology ; }, abstract = {The tick microbiome comprises communities of microorganisms, including viruses, bacteria and eukaryotes, and is being elucidated through modern molecular techniques. The advent of next-generation sequencing (NGS) technologies has enabled the genes and genomes within these microbial communities to be explored in a rapid and cost-effective manner. The advantages of using NGS to investigate microbiomes surpass the traditional non-molecular methods that are limited in their sensitivity, and conventional molecular approaches that are limited in their scalability. In recent years the number of studies using NGS to investigate the microbial diversity and composition of ticks has expanded. Here, we provide a review of NGS strategies for tick microbiome studies and discuss the recent findings from tick NGS investigations, including the bacterial diversity and composition, influential factors, and implications of the tick microbiome.}, } @article {pmid29301569, year = {2018}, author = {Lu, D and Tiezzi, F and Schillebeeckx, C and McNulty, NP and Schwab, C and Shull, C and Maltecca, C}, title = {Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {4}, pmid = {29301569}, issn = {2049-2618}, mesh = {Animals ; Bacteria/*classification/genetics/isolation & purification ; Breeding ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Male ; Phylogeny ; Quantitative Trait Loci ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Swine ; Weaning ; }, abstract = {BACKGROUND: In pigs, gut bacteria have been shown to play important roles in nutritional, physiological, and immunological processes in the host. However, the contribution of their metagenomes or part of them, which are normally reflected by fragments of 16S rRNA-encoding genes, has yet to be fully investigated.

RESULTS: Fecal samples, collected from a population of crossbred pigs at three time points, including weaning, week 15 post weaning (hereafter "week 15"), and end-of-feeding test (hereafter "off-test"), were used to evaluate changes in the composition of the fecal microbiome of each animal over time. This study used 1205, 1295, and 1283 samples collected at weaning, week 15, and off-test, respectively. There were 1039 animals that had samples collected at all three time points and also had phenotypic records on back fat thickness (BF) and average daily body weight gain (ADG). Firmicutes and Bacteroidetes were the most abundant phyla at all three time points. The most abundant genera at all three time points included Clostridium, Escherichia, Bacteroides, Prevotella, Ruminococcus, Fusobacterium, Campylobacter, Eubacterium, and Lactobacillus. Two enterotypes were identified at each time point. However, only enterotypes at week 15 and off-test were significantly associated with BF. We report herein two novel findings: (i) alpha diversity and operational taxonomic unit (OTU) richness were moderately heritable at week 15, h[2] of 0.15 ± 0.06 to 0.16 ± 0.07 and 0.23 ± 0.09 to 0.26 ± 0.08, respectively, as well as at off-test, h[2] of 0.20 ± 0.09 to 0.33 ± 0.10 and 0.17 ± 0.08 to 0.24 ± 0.08, respectively, whereas very low heritability estimates for both measures were detected at weaning; and (ii) alpha diversity at week 15 had strong and negative genetic correlations with BF, - 0.53 ± 0.23 to - 0.45 ± 0.25, as well as with ADG, - 0.53 ± 0.32 to - 0.53 ± 0.29.

CONCLUSIONS: These results are important for efforts to genetically improve the domesticated pig because they suggest fecal microbiota diversity can be used as an indicator trait to improve traits that are expensive to measure.}, } @article {pmid29299394, year = {2017}, author = {Kuzmina, ML and Braukmann, TWA and Fazekas, AJ and Graham, SW and Dewaard, SL and Rodrigues, A and Bennett, BA and Dickinson, TA and Saarela, JM and Catling, PM and Newmaster, SG and Percy, DM and Fenneman, E and Lauron-Moreau, A and Ford, B and Gillespie, L and Subramanyam, R and Whitton, J and Jennings, L and Metsger, D and Warne, CP and Brown, A and Sears, E and Dewaard, JR and Zakharov, EV and Hebert, PDN}, title = {Using herbarium-derived DNAs to assemble a large-scale DNA barcode library for the vascular plants of Canada.}, journal = {Applications in plant sciences}, volume = {5}, number = {12}, pages = {}, pmid = {29299394}, issn = {2168-0450}, abstract = {PREMISE OF THE STUDY: Constructing complete, accurate plant DNA barcode reference libraries can be logistically challenging for large-scale floras. Here we demonstrate the promise and challenges of using herbarium collections for building a DNA barcode reference library for the vascular plant flora of Canada.

METHODS: Our study examined 20,816 specimens representing 5076 of 5190 vascular plant species in Canada (98%). For 98% of the specimens, at least one of the DNA barcode regions was recovered from the plastid loci rbcL and matK and from the nuclear ITS2 region. We used beta regression to quantify the effects of age, type of preservation, and taxonomic affiliation (family) on DNA sequence recovery.

RESULTS: Specimen age and method of preservation had significant effects on sequence recovery for all markers, but influenced some families more (e.g., Boraginaceae) than others (e.g., Asteraceae).

DISCUSSION: Our DNA barcode library represents an unparalleled resource for metagenomic and ecological genetic research working on temperate and arctic biomes. An observed decline in sequence recovery with specimen age may be associated with poor primer matches, intragenomic variation (for ITS2), or inhibitory secondary compounds in some taxa.}, } @article {pmid29298732, year = {2018}, author = {Luna, PN and Hasegawa, K and Ajami, NJ and Espinola, JA and Henke, DM and Petrosino, JF and Piedra, PA and Sullivan, AF and Camargo, CA and Shaw, CA and Mansbach, JM}, title = {The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {2}, pmid = {29298732}, issn = {2049-2618}, support = {UG3 OD-023253/NH/NIH HHS/United States ; R01 AI-114552/NH/NIH HHS/United States ; R01 AI108588/AI/NIAID NIH HHS/United States ; U01 AI-087881/NH/NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; R01 AI-108588/NH/NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; R01 AI114552/AI/NIAID NIH HHS/United States ; UH3 OD023253/OD/NIH HHS/United States ; }, mesh = {Bronchiolitis/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Hospitalization ; Humans ; Infant ; Longitudinal Studies ; Male ; Microbiota ; Nasal Cavity/*microbiology ; Nasopharynx/*microbiology ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Staphylococcus/classification/genetics/*isolation & purification ; }, abstract = {BACKGROUND: The airway microbiome is a subject of great interest for the study of respiratory disease. Anterior nare samples are more accessible than samples from deeper within the nasopharynx. However, the correlation between the microbiota found in the anterior nares and the microbiota found within the nasopharynx is unknown. We assessed the anterior nares and nasopharyngeal microbiota to determine (1) the relation of the microbiota from these two upper airway sites and (2) if associations were maintained between the microbiota from these two sites and two bronchiolitis severity outcomes.

RESULTS: Among 815 infants hospitalized at 17 US centers for bronchiolitis with optimal 16S rRNA gene sequence reads from both nasal swab and nasopharyngeal aspirate samples, there were strong intra-individual correlations in the microbial communities between the two sample types, especially relating to Haemophilus and Moraxella genera. By contrast, we found a high abundance of Staphylococcus genus in the nasal swabs-a pattern not found in the nasopharyngeal samples and not informative when predicting the dominant nasopharyngeal genera. While these disparities may have been due to sample processing differences (i.e., nasal swabs were mailed at ambient temperature to emulate processing of future parent collected swabs while nasopharyngeal aspirates were mailed on dry ice), a previously reported association between Haemophilus-dominant nasopharyngeal microbiota and the increased severity of bronchiolitis was replicated utilizing the nasal swab microbiota and the same outcome measures: intensive care use (adjusted OR 6.43; 95% CI 2.25-20.51; P < 0.001) and hospital length-of-stay (adjusted OR 4.31; 95% CI, 1.73-11.11; P = 0.002). Additionally, Moraxella-dominant nasopharyngeal microbiota was previously identified as protective against intensive care use, a result that was replicated when analyzing the nasal swab microbiota (adjusted OR 0.30; 95% CI, 0.11-0.64; P = 0.01).

CONCLUSIONS: While the microbiota of the anterior nares and the nasopharynx are distinct, there is considerable overlap between the bacterial community compositions from these two anatomic sites. Despite processing differences between the samples, these results indicate that microbiota severity associations from the nasopharynx are recapitulated in the anterior nares, suggesting that nasal swab samples not only are effective sample types, but also can be used to detect microbial risk markers.}, } @article {pmid29297933, year = {2018}, author = {Cinek, O and Mazankova, K and Kramna, L and Odeh, R and Alassaf, A and Ibekwe, MU and Ahmadov, G and Mekki, H and Abdullah, MA and Elmahi, BME and Hyöty, H and Rainetova, P}, title = {Quantitative CrAssphage real-time PCR assay derived from data of multiple geographically distant populations.}, journal = {Journal of medical virology}, volume = {90}, number = {4}, pages = {767-771}, doi = {10.1002/jmv.25012}, pmid = {29297933}, issn = {1096-9071}, mesh = {Africa ; Asia ; Bacteriophages/genetics/*isolation & purification ; DNA Primers/genetics ; Europe ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Oligonucleotide Probes/genetics ; Real-Time Polymerase Chain Reaction/*methods ; Viral Load/*methods ; }, abstract = {After its computational inference from human stool metagenomes, the CrAssphage has proven to be the most prevalent phage in the human gut, with presumably very wide geographic distribution. The currently available molecular assays do not sufficiently reflect the CrAssphage sequence variability. Here, we report a novel real-time PCR assay whose primers and probes are derived from data of multiple CrAssphage strains obtained from gut viral metagenomes of European, Asian, and African subjects. This assay can be useful in analyses of putative bacterial host co-occurence, and in association studies of non-infectious diseases where the phage may modify the content of gut bacteriomes.}, } @article {pmid29297382, year = {2017}, author = {Rozanov, AS and Bryanskaya, AV and Ivanisenko, TV and Malup, TK and Peltek, SE}, title = {Biodiversity of the microbial mat of the Garga hot spring.}, journal = {BMC evolutionary biology}, volume = {17}, number = {Suppl 2}, pages = {254}, pmid = {29297382}, issn = {1471-2148}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biodiversity ; Geography ; Hot Springs/*microbiology ; Likelihood Functions ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Russia ; }, abstract = {BACKGROUND: Microbial mats are a good model system for ecological and evolutionary analysis of microbial communities. There are more than 20 alkaline hot springs on the banks of the Barguzin river inflows. Water temperature reaches 75 °C and pH is usually 8.0-9.0. The formation of microbial mats is observed in all hot springs. Microbial communities of hot springs of the Baikal rift zone are poorly studied. Garga is the biggest hot spring in this area.

RESULTS: In this study, we investigated bacterial and archaeal diversity of the Garga hot spring (Baikal rift zone, Russia) using 16S rRNA metagenomic sequencing. We studied two types of microbial communities: (i) small white biofilms on rocks in the points with the highest temperature (75 °C) and (ii) continuous thick phototrophic microbial mats observed at temperatures below 70 °C. Archaea (mainly Crenarchaeota; 19.8% of the total sequences) were detected only in the small biofilms. The high abundance of Archaea in the sample from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. In the microbial mats, primary products were formed by cyanobacteria of the genus Leptolyngbya. Heterotrophic microorganisms were mostly represented by Actinobacteria and Proteobacteria in all studied samples of the microbial mats. Planctomycetes, Chloroflexi, and Chlorobi were abundant in the middle layer of the microbial mats, while heterotrophic microorganisms represented mostly by Firmicutes (Clostridia, strict anaerobes) dominated in the bottom part. Besides prokaryotes, we detect some species of Algae with help of detection their chloroplasts 16 s rRNA.

CONCLUSIONS: High abundance of Archaea in samples from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. Metagenomic analysis of microbial communities of the microbial mat of Garga hot spring showed that the three studied points sampled at 70 °C, 55 °C, and 45 °C had similar species composition. Cyanobacteria of the genus Leptolyngbya dominated in the upper layer of the microbial mat. Chloroflexi and Chlorobi were less abundant and were mostly observed in the middle part of the microbial mat. We detected domains of heterotrophic organisms in high abundance (Proteobacteria, Firmicutes, Verrucomicrobia, Planctomicetes, Bacteroidetes, Actinobacteria, Thermi), according to metabolic properties of known relatives, which can form complete cycles of carbon, sulphur, and nitrogen in the microbial mat. The studied microbial mats evolved in early stages of biosphere formation. They can live autonomously, providing full cycles of substances and preventing live activity products poisoning.}, } @article {pmid29297295, year = {2017}, author = {Herath, D and Tang, SL and Tandon, K and Ackland, D and Halgamuge, SK}, title = {CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision.}, journal = {BMC bioinformatics}, volume = {18}, number = {Suppl 16}, pages = {571}, pmid = {29297295}, issn = {1471-2105}, mesh = {*Algorithms ; Base Sequence ; Cluster Analysis ; *Contig Mapping ; Databases, Genetic ; Genome ; Humans ; Metagenome ; Metagenomics/*methods ; *Workflow ; }, abstract = {BACKGROUND: In metagenomics, the separation of nucleotide sequences belonging to an individual or closely matched populations is termed binning. Binning helps the evaluation of underlying microbial population structure as well as the recovery of individual genomes from a sample of uncultivable microbial organisms. Both supervised and unsupervised learning methods have been employed in binning; however, characterizing a metagenomic sample containing multiple strains remains a significant challenge. In this study, we designed and implemented a new workflow, Coverage and composition based binning of Metagenomes (CoMet), for binning contigs in a single metagenomic sample. CoMet utilizes coverage values and the compositional features of metagenomic contigs. The binning strategy in CoMet includes the initial grouping of contigs in guanine-cytosine (GC) content-coverage space and refinement of bins in tetranucleotide frequencies space in a purely unsupervised manner. With CoMet, the clustering algorithm DBSCAN is employed for binning contigs. The performances of CoMet were compared against four existing approaches for binning a single metagenomic sample, including MaxBin, Metawatt, MyCC (default) and MyCC (coverage) using multiple datasets including a sample comprised of multiple strains.

RESULTS: Binning methods based on both compositional features and coverages of contigs had higher performances than the method which is based only on compositional features of contigs. CoMet yielded higher or comparable precision in comparison to the existing binning methods on benchmark datasets of varying complexities. MyCC (coverage) had the highest ranking score in F1-score. However, the performances of CoMet were higher than MyCC (coverage) on the dataset containing multiple strains. Furthermore, CoMet recovered contigs of more species and was 18 - 39% higher in precision than the compared existing methods in discriminating species from the sample of multiple strains. CoMet resulted in higher precision than MyCC (default) and MyCC (coverage) on a real metagenome.

CONCLUSIONS: The approach proposed with CoMet for binning contigs, improves the precision of binning while characterizing more species in a single metagenomic sample and in a sample containing multiple strains. The F1-scores obtained from different binning strategies vary with different datasets; however, CoMet yields the highest F1-score with a sample comprised of multiple strains.}, } @article {pmid29297282, year = {2017}, author = {Tran, Q and Pham, DT and Phan, V}, title = {Using 16S rRNA gene as marker to detect unknown bacteria in microbial communities.}, journal = {BMC bioinformatics}, volume = {18}, number = {Suppl 14}, pages = {499}, pmid = {29297282}, issn = {1471-2105}, mesh = {Algorithms ; Bacteria/*genetics/*isolation & purification ; Genetic Markers ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Quantification and identification of microbial genomes based on next-generation sequencing data is a challenging problem in metagenomics. Although current methods have mostly focused on analyzing bacteria whose genomes have been sequenced, such analyses are, however, complicated by the presence of unknown bacteria or bacteria whose genomes have not been sequence.

RESULTS: We propose a method for detecting unknown bacteria in environmental samples. Our approach is unique in its utilization of short reads only from 16S rRNA genes, not from entire genomes. We show that short reads from 16S rRNA genes retain sufficient information for detecting unknown bacteria in oral microbial communities.

CONCLUSION: In our experimentation with bacterial genomes from the Human Oral Microbiome Database, we found that this method made accurate and robust predictions at different read coverages and percentages of unknown bacteria. Advantages of this approach include not only a reduction in experimental and computational costs but also a potentially high accuracy across environmental samples due to the strong conservation of the 16S rRNA gene.}, } @article {pmid29293960, year = {2018}, author = {Fang, C and Zhong, H and Lin, Y and Chen, B and Han, M and Ren, H and Lu, H and Luber, JM and Xia, M and Li, W and Stein, S and Xu, X and Zhang, W and Drmanac, R and Wang, J and Yang, H and Hammarström, L and Kostic, AD and Kristiansen, K and Li, J}, title = {Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing.}, journal = {GigaScience}, volume = {7}, number = {3}, pages = {1-8}, pmid = {29293960}, issn = {2047-217X}, support = {P30 DK036836/DK/NIDDK NIH HHS/United States ; T32 HG002295/HG/NHGRI NIH HHS/United States ; T32 GM074897/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics ; Computational Biology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: More extensive use of metagenomic shotgun sequencing in microbiome research relies on the development of high-throughput, cost-effective sequencing. Here we present a comprehensive evaluation of the performance of the new high-throughput sequencing platform BGISEQ-500 for metagenomic shotgun sequencing and compare its performance with that of 2 Illumina platforms.

FINDINGS: Using fecal samples from 20 healthy individuals, we evaluated the intra-platform reproducibility for metagenomic sequencing on the BGISEQ-500 platform in a setup comprising 8 library replicates and 8 sequencing replicates. Cross-platform consistency was evaluated by comparing 20 pairwise replicates on the BGISEQ-500 platform vs the Illumina HiSeq 2000 platform and the Illumina HiSeq 4000 platform. In addition, we compared the performance of the 2 Illumina platforms against each other. By a newly developed overall accuracy quality control method, an average of 82.45 million high-quality reads (96.06% of raw reads) per sample, with 90.56% of bases scoring Q30 and above, was obtained using the BGISEQ-500 platform. Quantitative analyses revealed extremely high reproducibility between BGISEQ-500 intra-platform replicates. Cross-platform replicates differed slightly more than intra-platform replicates, yet a high consistency was observed. Only a low percentage (2.02%-3.25%) of genes exhibited significant differences in relative abundance comparing the BGISEQ-500 and HiSeq platforms, with a bias toward genes with higher GC content being enriched on the HiSeq platforms.

CONCLUSIONS: Our study provides the first set of performance metrics for human gut metagenomic sequencing data using BGISEQ-500. The high accuracy and technical reproducibility confirm the applicability of the new platform for metagenomic studies, though caution is still warranted when combining metagenomic data from different platforms.}, } @article {pmid29293631, year = {2018}, author = {Villegas, LEM and Campolina, TB and Barnabe, NR and Orfano, AS and Chaves, BA and Norris, DE and Pimenta, PFP and Secundino, NFC}, title = {Zika virus infection modulates the bacterial diversity associated with Aedes aegypti as revealed by metagenomic analysis.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0190352}, pmid = {29293631}, issn = {1932-6203}, mesh = {Aedes/*microbiology/virology ; Animals ; Bacteria/*classification/genetics ; *Biodiversity ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Mosquito Vectors ; RNA, Ribosomal, 16S/genetics ; Zika Virus Infection/*microbiology ; }, abstract = {Zika is a re-emerging infection that has been considered a major threat to global public health. Currently at least 100 countries are at risk of Zika virus (ZIKV) transmission. Aedes aegypti is the main mosquito vector in the Americas. This vector is exposed to, and interacts symbiotically with a variety of microorganisms in its environment, which may result in the formation of a lifetime association. Here, the unknown effect that ZIKV exerts on the dynamic bacterial community harbored by this mosquito vector was investigated using a metagenomic analysis of its microbiota. Groups of Ae. aegypti were experimentally fed on sugar, blood and blood mixed with ZIKV, and held for 3 to 7 days after blood meal and eggs development respectively. The infected groups were processed by qPCR to confirm the presence of ZIKV. All groups were analyzed by metagenomics (Illumina Hiseq Sequencing) and 16S rRNA amplicon sequences were obtained to create bacterial taxonomic profiles. A core microbiota and exclusive bacterial taxa were identified that incorporate 50.5% of the predicted reads from the dataset, with 40 Gram-negative and 9 Gram-positive families. To address how ZIKV invasion may disturb the ecological balance of the Ae. aegypti microbiota, a CCA analysis coupled with an explanatory matrix was performed to support the biological interpretation of shifts in bacterial signatures. Two f-OTUs appeared as potential biomarkers of ZIKV infection: Rhodobacteraceae and Desulfuromonadaceae. Coincidentally, both f-OTUs were exclusively present in the ZIKV- infected blood-fed and ZIKV- infected gravid groups. In conclusion, this study shows that bacterial symbionts act as biomarkers of the insect physiological states and how they respond as a community when ZIKV invades Ae. aegypti. Basic knowledge of local haematophagous vectors and their associated microbiota is relevant when addressing transmission of vector-borne infectious diseases in their regional surroundings.}, } @article {pmid29293174, year = {2018}, author = {Ikeda, M and Shimizu, K and Ogura, H and Kurakawa, T and Umemoto, E and Motooka, D and Nakamura, S and Ichimaru, N and Takeda, K and Takahara, S and Hirano, SI and Shimazu, T}, title = {Hydrogen-Rich Saline Regulates Intestinal Barrier Dysfunction, Dysbiosis, and Bacterial Translocation in a Murine Model of Sepsis.}, journal = {Shock (Augusta, Ga.)}, volume = {50}, number = {6}, pages = {640-647}, doi = {10.1097/SHK.0000000000001098}, pmid = {29293174}, issn = {1540-0514}, mesh = {Animals ; Bacterial Translocation/drug effects ; Disease Models, Animal ; Dysbiosis/*metabolism ; Enterobacteriaceae/genetics ; Hydrogen/pharmacology ; Intestinal Mucosa/*metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Microbiota/drug effects/genetics ; Oxidative Stress/drug effects/genetics ; RNA, Messenger/genetics ; RNA, Ribosomal, 16S/genetics ; Sepsis ; Tight Junction Proteins/genetics/metabolism ; }, abstract = {Bacterial translocation is a major cause of multiple organ dysfunction syndrome in critical illness, and its management is an important therapeutic strategy. In this study, we focused on the key factors responsible for bacterial translocation including the intestinal microbiome and investigated the impact of molecular hydrogen therapy as a countermeasure against bacterial translocation in a murine model of sepsis. The experimental protocols were divided into the sham, saline treatment (control), and hydrogen treatment (H2) groups. In the H2 group, 15 mL/kg of hydrogen-rich saline (7 ppm) was gavaged daily for 7 days following cecal ligation and puncture (CLP). In the control group, normal saline was gavaged in the same way. In the results, the 7-day survival rate was significantly improved in the H2 group versus the control group (69% vs. 31%, P < 0.05). The incidence of bacterial translocation at 24 h after CLP as assessed by cultivation of mesenteric lymph nodes and blood was significantly decreased in the H2 group versus the control group. Administration of hydrogen-rich saline also prevented the expansion of facultative anaerobic Enterobacteriaceae and ameliorated intestinal hyperpermeability at 24 h after CLP. Intestinal tissue levels of inflammatory mediators such as inducible nitric oxide synthases, tumor necrosis factor α, interleukin (IL)-1β, IL-6, and oxidative stress marker malondialdehyde at 6 h after CLP were down-regulated in the H2 group. These results suggest luminal administration of hydrogen-rich saline, which prevents intestinal dysbiosis, hyperpermeability, and bacterial translocation, could potentially be a new therapeutic strategy in critical illness.}, } @article {pmid29292539, year = {2018}, author = {Porter, TM and Hajibabaei, M}, title = {Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis.}, journal = {Molecular ecology}, volume = {27}, number = {2}, pages = {313-338}, doi = {10.1111/mec.14478}, pmid = {29292539}, issn = {1365-294X}, mesh = {*Biodiversity ; Computational Biology/methods ; DNA/*genetics ; DNA Barcoding, Taxonomic/methods ; *Environmental Monitoring ; *Genomics ; High-Throughput Nucleotide Sequencing ; }, abstract = {The purpose of this review is to present the most common and emerging DNA-based methods used to generate data for biodiversity and biomonitoring studies. As environmental assessment and monitoring programmes may require biodiversity information at multiple levels, we pay particular attention to the DNA metabarcoding method and discuss a number of bioinformatic tools and considerations for producing DNA-based indicators using operational taxonomic units (OTUs), taxa at a variety of ranks and community composition. By developing the capacity to harness the advantages provided by the newest technologies, investigators can "scale up" by increasing the number of samples and replicates processed, the frequency of sampling over time and space, and even the depth of sampling such as by sequencing more reads per sample or more markers per sample. The ability to scale up is made possible by the reduced hands-on time and cost per sample provided by the newest kits, platforms and software tools. Results gleaned from broad-scale monitoring will provide opportunities to address key scientific questions linked to biodiversity and its dynamics across time and space as well as being more relevant for policymakers, enabling science-based decision-making, and provide a greater socio-economic impact. As genomic approaches are continually evolving, we provide this guide to methods used in biodiversity genomics.}, } @article {pmid29291350, year = {2018}, author = {Smith, TE and Pond, CD and Pierce, E and Harmer, ZP and Kwan, J and Zachariah, MM and Harper, MK and Wyche, TP and Matainaho, TK and Bugni, TS and Barrows, LR and Ireland, CM and Schmidt, EW}, title = {Accessing chemical diversity from the uncultivated symbionts of small marine animals.}, journal = {Nature chemical biology}, volume = {14}, number = {2}, pages = {179-185}, pmid = {29291350}, issn = {1552-4469}, support = {R01 GM102602/GM/NIGMS NIH HHS/United States ; R01 GM107557/GM/NIGMS NIH HHS/United States ; U01 TW006671/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Anti-HIV Agents/*pharmacology ; Bacteria ; Biological Products/*pharmacology ; DNA/analysis ; *Drug Discovery ; Drug Evaluation, Preclinical ; Genomics ; HIV Infections/*drug therapy ; Humans ; Lysinoalanine/chemistry ; Metagenome ; Metagenomics ; *Microbiota ; Multigene Family ; Peptides/pharmacology ; Structure-Activity Relationship ; *Symbiosis ; Synthetic Biology ; T-Lymphocytes/drug effects ; Urochordata ; }, abstract = {Chemistry drives many biological interactions between the microbiota and host animals, yet it is often challenging to identify the chemicals involved. This poses a problem, as such small molecules are excellent sources of potential pharmaceuticals, pretested by nature for animal compatibility. We discovered anti-HIV compounds from small, marine tunicates from the Eastern Fields of Papua New Guinea. Tunicates are a reservoir for new bioactive chemicals, yet their small size often impedes identification or even detection of the chemicals within. We solved this problem by combining chemistry, metagenomics, and synthetic biology to directly identify and synthesize the natural products. We show that these anti-HIV compounds, the divamides, are a novel family of lanthipeptides produced by symbiotic bacteria living in the tunicate. Neighboring animal colonies contain structurally related divamides that differ starkly in their biological properties, suggesting a role for biosynthetic plasticity in a native context wherein biological interactions take place.}, } @article {pmid29291348, year = {2018}, author = {Karst, SM and Dueholm, MS and McIlroy, SJ and Kirkegaard, RH and Nielsen, PH and Albertsen, M}, title = {Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias.}, journal = {Nature biotechnology}, volume = {36}, number = {2}, pages = {190-195}, pmid = {29291348}, issn = {1546-1696}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Biodiversity ; Eukaryota/classification/genetics ; High-Throughput Nucleotide Sequencing ; Metagenome/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/classification/*genetics ; RNA, Ribosomal, 18S/*genetics ; }, abstract = {Small subunit ribosomal RNA (SSU rRNA) genes, 16S in bacteria and 18S in eukaryotes, have been the standard phylogenetic markers used to characterize microbial diversity and evolution for decades. However, the reference databases of full-length SSU rRNA gene sequences are skewed to well-studied ecosystems and subject to primer bias and chimerism, which results in an incomplete view of the diversity present in a sample. We combine poly(A)-tailing and reverse transcription of SSU rRNA molecules with synthetic long-read sequencing to generate high-quality, full-length SSU rRNA sequences, without primer bias, at high throughput. We apply our approach to samples from seven different ecosystems and obtain more than a million SSU rRNA sequences from all domains of life, with an estimated raw error rate of 0.17%. We observe a large proportion of novel diversity, including several deeply branching phylum-level lineages putatively related to the Asgard Archaea. Our approach will enable expansion of the SSU rRNA reference databases by orders of magnitude, and contribute to a comprehensive census of the tree of life.}, } @article {pmid29288930, year = {2018}, author = {Liu, J and Chen, X and Shu, HY and Lin, XR and Zhou, QX and Bramryd, T and Shu, WS and Huang, LN}, title = {Microbial community structure and function in sediments from e-waste contaminated rivers at Guiyu area of China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {235}, number = {}, pages = {171-179}, doi = {10.1016/j.envpol.2017.12.008}, pmid = {29288930}, issn = {1873-6424}, mesh = {Biodiversity ; China ; Ecosystem ; *Electronic Waste/analysis ; Geologic Sediments/*microbiology ; Metals, Heavy/analysis/pharmacology ; RNA, Ribosomal, 16S/genetics ; Rivers/chemistry/*microbiology ; *Soil Microbiology ; *Water Microbiology ; Water Pollutants/*pharmacology ; }, abstract = {The release of toxic organic pollutants and heavy metals by primitive electronic waste (e-waste) processing to waterways has raised significant concerns, but little is known about their potential ecological effects on aquatic biota especially microorganisms. We characterized the microbial community composition and diversity in sediments sampled along two rivers consistently polluted by e-waste, and explored how community functions may respond to the complex combined pollution. High-throughput 16S rRNA gene sequencing showed that Proteobacteria (particularly Deltaproteobacteria) dominated the sediment microbial assemblages followed by Bacteroidetes, Acidobacteria, Chloroflexi and Firmicutes. PICRUSt metagenome inference provided an initial insight into the metabolic potentials of these e-waste affected communities, speculating that organic pollutants degradation in the sediment might be mainly performed by some of the dominant genera (such as Sulfuricurvum, Thiobacillus and Burkholderia) detected in situ. Statistical analyses revealed that toxic organic compounds contributed more to the observed variations in sediment microbial community structure and predicted functions (24.68% and 8.89%, respectively) than heavy metals (12.18% and 4.68%), and Benzo(a)pyrene, bioavailable lead and electrical conductivity were the key contributors. These results have shed light on the microbial assemblages in e-waste contaminated river sediments, indicating a potential influence of e-waste pollution on the microbial community structure and function in aquatic ecosystems.}, } @article {pmid29287982, year = {2018}, author = {Pienkowska, K and Wiehlmann, L and Tümmler, B}, title = {Airway microbial metagenomics.}, journal = {Microbes and infection}, volume = {20}, number = {9-10}, pages = {536-542}, doi = {10.1016/j.micinf.2017.12.002}, pmid = {29287982}, issn = {1769-714X}, mesh = {Bacteria/classification/genetics/isolation & purification ; Computational Biology ; High-Throughput Nucleotide Sequencing ; Humans ; Lung Diseases/*microbiology ; *Metagenomics ; Microbiota/*genetics ; Respiratory System/*microbiology ; Viruses/classification/genetics/isolation & purification ; }, abstract = {High-throughput untargeted metagenome sequencing provides information about the composition of the microbial communities of viruses, bacteria, archaea and unicellular eukaryotes in the habitat of interest. This review outlines the sampling, processing, sequencing and bioinformatic analysis of secretions of the respiratory tract and summarizes our current knowledge of the upper and lower human airways metagenome in health and disease.}, } @article {pmid29284535, year = {2017}, author = {Pires, ACAM and Villegas, LEM and Campolina, TB and Orfanó, AS and Pimenta, PFP and Secundino, NFC}, title = {Bacterial diversity of wild-caught Lutzomyia longipalpis (a vector of zoonotic visceral leishmaniasis in Brazil) under distinct physiological conditions by metagenomics analysis.}, journal = {Parasites & vectors}, volume = {10}, number = {1}, pages = {627}, pmid = {29284535}, issn = {1756-3305}, support = {305512/2014-5//Brazilian Council for Scientific and Technological Development- CNPq- Research fellowship/International ; 308849/2015-9//Brazilian Council for Scientific and Technological Development- CNPq (Research fellowship)/International ; 00242-12//Fundação de Amparo à Pesquisa do Estado de Minas Gerais (BR) FAPEMIG/International ; }, mesh = {Animals ; Bacteria/*classification/*genetics ; Brazil ; *Gastrointestinal Microbiome ; Insect Vectors/*microbiology ; Metagenomics ; Psychodidae/*microbiology ; }, abstract = {BACKGROUND: The leishmaniases are a group of diseases caused by protozoans of the genus Leishmania, which are transmitted by the bite of phlebotomine sand flies. In the New World, Lutzomyia longipalpis is the most important vector of visceral leishmaniasis and is a proven vector for Leishmania infantum chagasi in Brazil. During development within the vector, Leishmania can interact with a variety of microorganisms such as fungi and bacteria. The presence of bacteria in the midgut of sand flies can influence the development and survival of the parasite.

RESULTS: The bacteria-targeted metagenomic analysis revealed different community compositions between the distinct physiological stages of those tested. The amplicon-oriented metagenomic profiling revealed 64 bacterial genera and 46 families. By crossing the taxa indices from each experimental condition a core composed of 6 genera was identified (Enterobacter, Serratia, Stenotrophomonas, Enhydrobacter, Pseudomonas and Chryseobacterium).

CONCLUSIONS: The observed dynamic nature of the bacterial community expands the knowledge pertaining to the tripartite host-microbiota-pathogen interactions. Further studies addressing how laboratory and field collected communities differ are critical to successfully develop control strategies based on bacterial symbionts and paratransgenesis, as already tested in other arthropod vectors.}, } @article {pmid29282825, year = {2018}, author = {Tsukahara, T and Inoue, R and Nakayama, K and Inatomi, T}, title = {Inclusion of Bacillus amyloliquefaciens strain TOA5001 in the diet of broilers suppresses the symptoms of coccidiosis by modulating intestinal microbiota.}, journal = {Animal science journal = Nihon chikusan Gakkaiho}, volume = {89}, number = {4}, pages = {679-687}, doi = {10.1111/asj.12980}, pmid = {29282825}, issn = {1740-0929}, mesh = {Animals ; *Antibiosis ; *Bacillus amyloliquefaciens/physiology ; Cats ; Cecum/*microbiology ; Chickens/*microbiology ; Clostridium perfringens/*growth & development/*pathogenicity ; Coccidiosis/microbiology/*prevention & control/*veterinary ; Diet/*veterinary ; Enteritis/*microbiology/*veterinary ; Escherichia coli ; Faecalibacterium prausnitzii ; *Gastrointestinal Microbiome ; Intestinal Diseases, Parasitic/*prevention & control/*veterinary ; Parasitic Diseases, Animal/*prevention & control ; Poultry Diseases/*prevention & control ; }, abstract = {Coccidiosis is an intestinal parasitic infection and one of the most prevalent and economically damaging diseases of chickens. Furthermore, coccidia-induced mucogenesis promotes secondary colonization by Clostridium perfringens, a major pathogen of chickens that causes necrotic enteritis. Our previous work found that supernatant of a culture of Bacillus amyloliquefaciens strain TOA5001 (BA) inhibited the growth of C. perfringens on Gifu anaerobic broth medium. Accordingly, we evaluated the effectiveness of dietary BA administration in inhibiting C. perfringens colonization of the intestine in broilers that were experimentally infected with coccidia. Ten healthy broilers from a BA-supplemented (2 × 10[5] colony-forming units/g of feed) broiler group and 10 from a non-treated group were challenged with Eimeria tenella and E. maxima (5000 oocysts of each species/chick) at 28 days old. At 36 days old, five chicks from each group were slaughtered, whereas the remaining five in each group were killed at 49 days old. Dietary BA administration into Eimeria-challenged birds reduced coccidial symptoms such as intestinal lesions. It also modified the cecal microbiota through suppressing C. perfringens and E. coli colonization, and inducing domination of Faecalibacterium prausnitzii, the Lactobacillus group and unknown Lachnospiraceae genera by bacterial DNA-based metagenome analyses. B. amyloliquefaciens TOA5001 supplementation suppressed the symptoms of coccidiosis by modulating cecal microbiota in Eimeria-challenged broilers.}, } @article {pmid29281673, year = {2017}, author = {Finlayson-Trick, ECL and Getz, LJ and Slaine, PD and Thornbury, M and Lamoureux, E and Cook, J and Langille, MGI and Murray, LE and McCormick, C and Rohde, JR and Cheng, Z}, title = {Taxonomic differences of gut microbiomes drive cellulolytic enzymatic potential within hind-gut fermenting mammals.}, journal = {PloS one}, volume = {12}, number = {12}, pages = {e0189404}, pmid = {29281673}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Cellulases/*metabolism ; Cellulose/metabolism ; *Fermentation ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Mammals/classification/*metabolism ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Host diet influences the diversity and metabolic activities of the gut microbiome. Previous studies have shown that the gut microbiome provides a wide array of enzymes that enable processing of diverse dietary components. Because the primary diet of the porcupine, Erethizon dorsatum, is lignified plant material, we reasoned that the porcupine microbiome would be replete with enzymes required to degrade lignocellulose. Here, we report on the bacterial composition in the porcupine microbiome using 16S rRNA sequencing and bioinformatics analysis. We extended this analysis to the microbiomes of 20 additional mammals located in Shubenacadie Wildlife Park (Nova Scotia, Canada), enabling the comparison of bacterial diversity amongst three mammalian taxonomic orders (Rodentia, Carnivora, and Artiodactyla). 16S rRNA sequencing was validated using metagenomic shotgun sequencing on selected herbivores (porcupine, beaver) and carnivores (coyote, Arctic wolf). In the microbiome, functionality is more conserved than bacterial composition, thus we mined microbiome data sets to identify conserved microbial functions across species in each order. We measured the relative gene abundances for cellobiose phosphorylase, endoglucanase, and beta-glucosidase to evaluate the cellulose-degrading potential of select mammals. The porcupine and beaver had higher proportions of genes encoding cellulose-degrading enzymes than the Artic wolf and coyote. These findings provide further evidence that gut microbiome diversity and metabolic capacity are influenced by host diet.}, } @article {pmid29278751, year = {2018}, author = {Kim, HN and Yun, Y and Ryu, S and Chang, Y and Kwon, MJ and Cho, J and Shin, H and Kim, HL}, title = {Correlation between gut microbiota and personality in adults: A cross-sectional study.}, journal = {Brain, behavior, and immunity}, volume = {69}, number = {}, pages = {374-385}, doi = {10.1016/j.bbi.2017.12.012}, pmid = {29278751}, issn = {1090-2139}, mesh = {Adult ; Aged ; Cross-Sectional Studies ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Middle Aged ; Neuroticism ; Personality/*physiology ; Personality Assessment ; Young Adult ; }, abstract = {Personality affects fundamental behavior patterns and has been related with health outcomes and mental disorders. Recent evidence has emerged supporting a relationship between the microbiota and behavior, referred to as brain-gut relationships. Here, we first report correlations between personality traits and gut microbiota. This research was performed using the Revised NEO Personality Inventory and the sequencing data of the 16S rRNA gene in 672 adults. The diversity and the composition of the human gut microbiota exhibited significant difference when stratified by personality traits. We found that personality traits were significantly correlated with diversity of gut microbiota, while their differences were extremely subtle. High neuroticism and low conscientiousness groups were correlated with high abundance of Gammaproteobacteria and Proteobacteria, respectively when covariates, including age, sex, BMI and nutrient intake, were controlled. Additionally, high conscientiousness group also showed increased abundance of some universal butyrate-producing bacteria including Lachnospiraceae. This study was of observational and cross-sectional design and our findings must be further validated through metagenomic or metatranscriptomic methodologies, or metabolomics-based analyses. Our findings will contribute to elucidating potential links between the gut microbiota and personality, and provide useful insights toward developing and testing personality- and microbiota-based interventions for promoting health.}, } @article {pmid29277868, year = {2018}, author = {Maltez Thomas, A and Prata Lima, F and Maria Silva Moura, L and Maria da Silva, A and Dias-Neto, E and Setubal, JC}, title = {Comparative Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1704}, number = {}, pages = {243-260}, doi = {10.1007/978-1-4939-7463-4_8}, pmid = {29277868}, issn = {1940-6029}, mesh = {Computational Biology ; Humans ; Metagenomics/*methods ; *Microbiota ; Mouth Mucosa/*microbiology ; Sequence Analysis, DNA/methods ; Software ; Tongue/*microbiology ; }, abstract = {Thanks in large part to newer, better, and cheaper DNA sequencing technologies, an enormous number of metagenomic sequence datasets have been and continue to be generated, covering a huge variety of environmental niches, including several different human body sites. Comparing these metagenomes and identifying their commonalities and differences is a challenging task, due not only to the large amounts of data, but also because there are several methodological considerations that need to be taken into account to ensure an appropriate and sound comparison between datasets. In this chapter, we describe current techniques aimed at comparing metagenomes generated by 16S ribosomal RNA and shotgun DNA sequencing, emphasizing methodological issues that arise in these comparative studies. We provide a detailed case study to illustrate some of these techniques using data from the Human Microbiome Project comparing the microbial communities from ten buccal mucosa samples with ten tongue dorsum samples in terms of alpha diversity, beta diversity, and their taxonomic and functional profiles.}, } @article {pmid29275129, year = {2018}, author = {Zeineldin, M and Aldridge, B and Lowe, J}, title = {Dysbiosis of the fecal microbiota in feedlot cattle with hemorrhagic diarrhea.}, journal = {Microbial pathogenesis}, volume = {115}, number = {}, pages = {123-130}, doi = {10.1016/j.micpath.2017.12.059}, pmid = {29275129}, issn = {1096-1208}, mesh = {Animals ; Bacteria/*classification/genetics/isolation & purification ; Bacterial Infections/microbiology/*veterinary ; Biodiversity ; Cattle/microbiology ; Cattle Diseases/*microbiology ; DNA, Bacterial/genetics ; Diarrhea/microbiology/*veterinary ; Dysbiosis/*microbiology/*veterinary ; Feces/*microbiology ; *Gastrointestinal Microbiome/genetics ; Housing, Animal ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis ; }, abstract = {The bovine gastrointestinal microbiota is a complex polymicrobial ecosystem that plays an important role in maintaining mucosal health. The role of mucosal microbial populations in the pathogenesis of gastrointestinal diseases has been well established in other species. However, limited information is available about changes in the fecal microbiota that occur under disease conditions, such as hemorrhagic diarrhea in feedlot cattle. The objectives of this study were to characterize the differences in fecal microbiota composition, diversity and functional gene profile between feedlot calves with, and without, hemorrhagic diarrhea. Deep fecal swabs were collected from calves with hemorrhagic diarrhea (n = 5) and from pen matched healthy calves (n = 5). Genomic DNA was extracted, and V1-V3 hypervariable region of 16S rRNA gene was amplified and sequenced using the Illumina MiSeq sequencing. When compared to healthy calves, feedlot cattle with hemorrhagic diarrhea showed significant increases in the relative abundance of Clostridium, Blautia and Escherichia, and significant decreases in the relative abundance of Flavobacterium, Oscillospira, Desulfonauticus, Ruminococcus, Thermodesulfovibrio and Butyricimonas. Linear discriminant analysis effect size (LEfSe) also revealed significant differences in bacterial taxa between healthy calves and hemorrhagic diarrhea calves. This apparent dysbiosis in fecal microbiota was associated with significant differences in the predictive functional metagenome profiles of these microbial communities. In summary, our results revealed a bacterial dysbiosis in fecal samples of calves with hemorrhagic diarrhea, with the diseased calves exhibiting less diversity and fewer observed species compared to healthy controls. Additional studies are warranted in a larger cohort of animals to help elucidate the trajectory of change in fecal microbial communities, and their predictive functional capacity, in calves with other gastrointestinal diseases.}, } @article {pmid29274973, year = {2018}, author = {Gonzalez-Recio, O and Zubiria, I and García-Rodríguez, A and Hurtado, A and Atxaerandio, R}, title = {Short communication: Signs of host genetic regulation in the microbiome composition in 2 dairy breeds: Holstein and Brown Swiss.}, journal = {Journal of dairy science}, volume = {101}, number = {3}, pages = {2285-2292}, doi = {10.3168/jds.2017-13179}, pmid = {29274973}, issn = {1525-3198}, mesh = {Animals ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Bayes Theorem ; Breeding ; Cattle/*genetics/microbiology/parasitology ; Ciliophora/*classification/genetics ; Databases, Genetic ; Female ; Genotype ; *Microbiota ; Rumen/microbiology ; }, abstract = {This study aimed to evaluate whether the host genotype exerts any genetic control on the microbiome composition of the rumen in cattle. Microbial DNA was extracted from 18 samples of ruminal content from 2 breeds (Holstein and Brown Swiss). Reads were processed using mothur (https://www.mothur.org/) in 16S and 18S rRNA gene-based analyses. Then, reads were classified at the genus clade, resulting in 3,579 operational taxonomic units (OTU) aligned against the 16S database and 184 OTU aligned against the 18S database. After filtering on relative abundance (>0.1%) and penetrance (95%), 25 OTU were selected for the analyses (17 bacteria, 1 archaea, and 7 ciliates). Association with the genetic background of the host animal based on the principal components of a genomic relationship matrix based on single nucleotide polymorphism markers was analyzed using Bayesian methods. Fifty percent of the bacteria and archaea genera were associated with the host genetic background, including Butyrivibrio, Prevotella, Paraprevotella, and Methanobrevibacter as main genera. Forty-three percent of the ciliates analyzed were also associated with the genetic background of the host. In total, 48% of microbes were associated with the host genetic background. The results in this study support the hypothesis and provide some evidence that there exists a host genetic component in cattle that can partially regulate the composition of the microbiome.}, } @article {pmid29274958, year = {2018}, author = {Li, F and Neves, ALA and Ghoshal, B and Guan, LL}, title = {Symposium review: Mining metagenomic and metatranscriptomic data for clues about microbial metabolic functions in ruminants.}, journal = {Journal of dairy science}, volume = {101}, number = {6}, pages = {5605-5618}, doi = {10.3168/jds.2017-13356}, pmid = {29274958}, issn = {1525-3198}, mesh = {Animals ; Gene Expression Profiling ; *Metagenomics ; Methane/metabolism ; Microbiota ; Rumen/*microbiology ; *Ruminants ; Transcriptome ; }, abstract = {Metagenomics and metatranscriptomics can capture the whole genome and transcriptome repertoire of microorganisms through sequencing total DNA/RNA from various environmental samples, providing both taxonomic and functional information with high resolution. The unique and complex rumen microbial ecosystem is receiving great research attention because the rumen microbiota coevolves with the host and equips ruminants with the ability to convert cellulosic plant materials to high-protein products for human consumption. To date, hundreds to thousands of microbial phylotypes have been identified in the rumen using culture-independent molecular-based approaches, and genomic information of rumen microorganisms is rapidly accumulating through the single genome sequencing. However, functional characteristics of the rumen microbiome have not been well described because there are numerous uncultivable microorganisms in the rumen. The advent of metagenomics and metatranscriptomics along with advanced bioinformatics methods can help us better understand mechanisms of the rumen fermentation, which is vital for improving nutrient utilization and animal productivity. Therefore, in this review, we summarize a general workflow to conduct rumen metagenomics and metatranscriptomics and discuss how the data can be interpreted to be useful information. Moreover, we review recent literatures studying associations between the rumen microbiome and host phenotypes (e.g., feed efficiency and methane emissions) using these approaches, aiming to provide a useful guide to include studying the rumen microbiome as one of the research objectives using these 2 approaches.}, } @article {pmid29274283, year = {2018}, author = {Kumar, K and Jaiswal, SK and Dhoke, GV and Srivastava, GN and Sharma, AK and Sharma, VK}, title = {Mechanistic and structural insight into promiscuity based metabolism of cardiac drug digoxin by gut microbial enzyme.}, journal = {Journal of cellular biochemistry}, volume = {119}, number = {7}, pages = {5287-5296}, doi = {10.1002/jcb.26638}, pmid = {29274283}, issn = {1097-4644}, mesh = {Actinobacteria/*enzymology/isolation & purification ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/*metabolism ; Cardiotonic Agents/*metabolism ; Digoxin/*metabolism ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/enzymology/*microbiology ; Humans ; Molecular Dynamics Simulation ; Protein Conformation ; Sequence Homology ; }, abstract = {The recent advances in microbiome studies have revealed the role of gut microbiota in altering the pharmacological properties of oral drugs, which contributes to patient-response variation and undesired effect of the drug molecule. These studies are essential to guide us for achieving the desired efficacy and pharmacological activity of the existing drug molecule or for discovering novel and more effective therapeutics. However, one of the main limitations is the lack of atomistic details on the binding and metabolism of these drug molecules by gut-microbial enzymes. Therefore, in this study, for a well-known and important FDA-approved cardiac glycoside drug, digoxin, we report the atomistic details and energy economics for its binding and metabolism by the Cgr2 protein of Eggerthella lenta DSM 2243. It was observed that the binding pocket of digoxin to Cgr2 primarily involved the negatively charged polar amino acids and a few non-polar hydrophobic residues. The drug digoxin was found to bind Cgr2 at the same binding site as that of fumarate, which is the proposed natural substrate. However, digoxin showed a much lower binding energy (17.75 ± 2 Kcal mol[-1]) than the binding energy (42.17 ± 2 Kcal mol[-1]) of fumarate. This study provides mechanistic insights into the structural and promiscuity-based metabolism of widely used cardiac drug digoxin and presents a methodology, which could be useful to confirm the promiscuity-based metabolism of other orally administrated drugs by gut microbial enzymes and also help in designing strategies for improving the efficacy of the drugs.}, } @article {pmid29273717, year = {2017}, author = {Albanese, D and Donati, C}, title = {Strain profiling and epidemiology of bacterial species from metagenomic sequencing.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {2260}, pmid = {29273717}, issn = {2041-1723}, mesh = {Bacteria/*genetics ; Bifidobacterium longum/genetics ; *Computational Biology ; Databases, Genetic ; Enterococcus faecalis/genetics ; Escherichia coli/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; Neisseria meningitidis/genetics ; Polymorphism, Single Nucleotide ; Propionibacterium acnes/genetics ; Staphylococcus aureus/genetics ; Staphylococcus epidermidis/genetics ; Streptococcus pneumoniae/genetics ; }, abstract = {Microbial communities are often composed by complex mixtures of multiple strains of the same species, characterized by a wide genomic and phenotypic variability. Computational methods able to identify, quantify and classify the different strains present in a sample are essential to fully exploit the potential of metagenomic sequencing in microbial ecology, with applications that range from the epidemiology of infectious diseases to the characterization of the dynamics of microbial colonization. Here we present a computational approach that uses the available genomic data to reconstruct complex strain profiles from metagenomic sequencing, quantifying the abundances of the different strains and cataloging them according to the population structure of the species. We validate the method on synthetic data sets and apply it to the characterization of the strain distribution of several important bacterial species in real samples, showing how its application provides novel insights on the structure and complexity of the microbiota.}, } @article {pmid29272899, year = {2017}, author = {Shah, A and Shanahan, E and Macdonald, GA and Fletcher, L and Ghasemi, P and Morrison, M and Jones, M and Holtmann, G}, title = {Systematic Review and Meta-Analysis: Prevalence of Small Intestinal Bacterial Overgrowth in Chronic Liver Disease.}, journal = {Seminars in liver disease}, volume = {37}, number = {4}, pages = {388-400}, doi = {10.1055/s-0037-1608832}, pmid = {29272899}, issn = {1098-8971}, mesh = {Bacteria/*growth & development ; Disease Progression ; *Dysbiosis ; *Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Humans ; Intestine, Small/*microbiology ; Liver Diseases/diagnosis/epidemiology/*microbiology ; Prevalence ; Prognosis ; Risk Factors ; }, abstract = {The authors conducted a meta-analysis of the prevalence of small intestinal bacterial overgrowth (SIBO) in patients with chronic liver disease (CLD) and controls. Using the search terms "small intestinal bacterial overgrowth (SIBO)" and "chronic liver disease (CLD)" or "cirrhosis," 19 case-control studies were identified. Utilizing breath tests, the prevalence of SIBO in CLD was 35.80% (95% CI, 32.60-39.10) compared with 8.0% (95% CI, 5.70-11.00) in controls. Using culture techniques, the prevalence was 68.31% (95% CI, 59.62-76.00) in CLD patients as compared with 7.94% (95% CI, 3.44-12.73) in controls. No difference between cirrhotic and noncirrhotic patients was found. SIBO is significantly more frequent in CLD patients as compared with controls. The association of SIBO and CLD was not confined to patients with advanced CLD, suggesting that SIBO is not a consequence of advanced liver disease but may play a role in the progression of CLD.}, } @article {pmid29272453, year = {2018}, author = {Pérez-Brocal, V and Andremont, A and Moya, A}, title = {Isolation in small populations of Wayampi Amerindians promotes endemicity and homogenisation of their faecal virome, but its distribution is not entirely random.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {2}, pages = {}, doi = {10.1093/femsec/fix184}, pmid = {29272453}, issn = {1574-6941}, mesh = {Adult ; Anti-Bacterial Agents/therapeutic use ; DNA Viruses/classification/*genetics/isolation & purification ; Enterobacteriaceae/genetics/metabolism ; Feces/*virology ; Female ; French Guiana ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; Prophages/classification/*genetics/isolation & purification ; beta-Lactamases/*genetics ; }, abstract = {The isolated community of the Wayampi Amerindians has been extensively studied for the presence of beta lactamase-producing enterobacteria and their gut microbiota. However, no information about their virome was available. This study tries to establish potential associations between the virome and diverse epidemiological data, through the metagenomic study of the faecal prophages and DNA viruses from 31 samples collected in 2010. Taxonomic assignments, composition, abundance and diversity analyses were obtained to characterise the virome and were compared between groups according to several demographic, environmental and medical data. Prophages outnumbered viruses. Composition and abundance of virome indicated relatively low variability. Diversity within samples showed no significant differences, regardless of the group comparison. Significant differences were observed in the beta diversity among samples according to hospitalisation and gender, but not by extended spectrum β-lactamase carriage, antibiotic intake or possession of pets, although some viruses differed in some cases (e.g. immunodeficiency-associated stool virus associated with antibiotic intake). The faecal virome of adult Wayampi is more homogeneous than that from western populations. Not a single factor analysed can explain alone the observed distribution of the virome, but differences by gender (fewer variability in females than males) may reflect differences in life habits and work.}, } @article {pmid29272370, year = {2018}, author = {Laenen, L and Vergote, V and Kafetzopoulou, LE and Wawina, TB and Vassou, D and Cook, JA and Hugot, JP and Deboutte, W and Kang, HJ and Witkowski, PT and Köppen-Rung, P and Krüger, DH and Licková, M and Stang, A and Striešková, L and Szemeš, T and Markowski, J and Hejduk, J and Kafetzopoulos, D and Van Ranst, M and Yanagihara, R and Klempa, B and Maes, P}, title = {A Novel Hantavirus of the European Mole, Bruges Virus, Is Involved in Frequent Nova Virus Coinfections.}, journal = {Genome biology and evolution}, volume = {10}, number = {1}, pages = {45-55}, pmid = {29272370}, issn = {1759-6653}, support = {P20 GM103516/GM/NIGMS NIH HHS/United States ; R01 AI075057/AI/NIAID NIH HHS/United States ; U54 MD007601/MD/NIMHD NIH HHS/United States ; }, mesh = {Animals ; Coinfection ; Europe/epidemiology ; Evolution, Molecular ; Genome, Viral ; Orthohantavirus/*genetics/physiology ; Hantavirus Infections/epidemiology/*virology ; Host-Pathogen Interactions ; Humans ; Moles/*virology ; *Phylogeny ; }, abstract = {Hantaviruses are zoonotic viruses with a complex evolutionary history of virus-host coevolution and cross-species transmission. Although hantaviruses have a broad reservoir host range, virus-host relationships were previously thought to be strict, with a single virus species infecting a single host species. Here, we describe Bruges virus, a novel hantavirus harbored by the European mole (Talpa europaea), which is the well-known host of Nova virus. Phylogenetic analyses of all three genomic segments showed tree topology inconsistencies, suggesting that Bruges virus has emerged from cross-species transmission and ancient reassortment events. A high number of coinfections with Bruges and Nova viruses was detected, but no evidence was found for reassortment between these two hantaviruses. These findings highlight the complexity of hantavirus evolution and the importance of further investigation of hantavirus-reservoir relationships.}, } @article {pmid29271225, year = {2018}, author = {Sebastián Domingo, JJ and Sánchez Sánchez, C}, title = {From the intestinal flora to the microbiome.}, journal = {Revista espanola de enfermedades digestivas}, volume = {110}, number = {1}, pages = {51-56}, doi = {10.17235/reed.2017.4947/2017}, pmid = {29271225}, issn = {1130-0108}, mesh = {Gastroenterology/*history ; Gastrointestinal Diseases/microbiology ; *Gastrointestinal Microbiome ; History, 17th Century ; History, 19th Century ; Humans ; Intestines/*microbiology ; }, abstract = {In this article, the history of the microbiota is reviewed and the related concepts of the microbiota, microbiome, metagenome, pathobiont, dysbiosis, holobiont, phylotype and enterotype are defined. The most precise and current knowledge about the microbiota is presented and the metabolic, nutritional and immunomodulatory functions are reviewed. Some gastrointestinal diseases whose pathogenesis is associated with the intestinal microbiota, including inflammatory bowel disease, irritable bowel syndrome and celiac disease, among others, are briefly discussed. Finally, some prominent and promising data with regard to the fecal microbiota transplantation in certain digestive illness are discussed.}, } @article {pmid29269503, year = {2018}, author = {Chu, BTT and Petrovich, ML and Chaudhary, A and Wright, D and Murphy, B and Wells, G and Poretsky, R}, title = {Metagenomics Reveals the Impact of Wastewater Treatment Plants on the Dispersal of Microorganisms and Genes in Aquatic Sediments.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {5}, pages = {}, pmid = {29269503}, issn = {1098-5336}, mesh = {Bacteria/genetics/*isolation & purification ; Genes, Bacterial ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; *Metagenome ; *Microbiota ; Wastewater/*microbiology ; Wisconsin ; }, abstract = {Wastewater treatment plants (WWTPs) release treated effluent containing mobile genetic elements (MGEs), antibiotic resistance genes (ARGs), and microorganisms into the environment, yet little is known about their influence on nearby microbial communities and the retention of these factors in receiving water bodies. Our research aimed to characterize the genes and organisms from two different WWTPs that discharge into Lake Michigan, as well as from surrounding lake sediments to determine the dispersal and fate of these factors with respect to distance from the effluent outfall. Shotgun metagenomics coupled to distance-decay analyses showed a higher abundance of genes identical to those in WWTP effluent genes in sediments closer to outfall sites than in sediments farther away, indicating their possible WWTP origin. We also found genes attributed to organisms, such as those belonging to Helicobacteraceae, Legionellaceae, Moraxellaceae, and Neisseriaceae, in effluent from both WWTPs and decreasing in abundance in lake sediments with increased distance from WWTPs. Moreover, our results showed that the WWTPs likely influence the ARG composition in lake sediments close to the effluent discharge. Many of these ARGs were located on MGEs in both the effluent and sediment samples, indicating a relatively broad propensity for horizontal gene transfer (HGT). Our approach allowed us to specifically link genes to organisms and their genetic context, providing insight into WWTP impacts on natural microbial communities. Overall, our results suggest a substantial influence of wastewater effluent on gene content and microbial community structure in the sediments of receiving water bodies.IMPORTANCE Wastewater treatment plants (WWTPs) release their effluent into aquatic environments. Although treated, effluent retains many genes and microorganisms that have the potential to influence the receiving water in ways that are poorly understood. Here, we tracked the genetic footprint, including genes specific to antibiotic resistance and mobile genetic elements and their associated organisms, from WWTPs to lake sediments. Our work is novel in that we used metagenomic data sets to comprehensively evaluate total gene content and the genetic and taxonomic context of specific genes in environmental samples putatively impacted by WWTP inputs. Based on two different WWTPs with different treatment processes, our findings point to an influence of WWTPs on the presence, abundance, and composition of these factors in the environment.}, } @article {pmid29268781, year = {2017}, author = {Carda-Diéguez, M and Ghai, R and Rodríguez-Valera, F and Amaro, C}, title = {Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {162}, pmid = {29268781}, issn = {2049-2618}, support = {BES-2012-052361//Secretaría de Estado de Investigación, Desarrollo e Innovación/International ; AGL2014-58933-P (cofunded with FEDER funds)//Secretaría de Estado de Investigación, Desarrollo e Innovación/International ; 17-04828S//Grantová Agentura České Republiky/International ; CGL2016-76273-P [AEI/FEDER, EU]//AEI/FEDER/EU/International ; CGL2015-71523-REDC (Acciones de dinamización "REDES DE EXCELENCIA" CONSOLIDER)//Dirección General de Investigación Científica y Técnica/International ; Prometeo II/2014/012 "AQUAMET"//Generalitat Valenciana/International ; }, mesh = {Anguilla/anatomy & histology/*microbiology ; Animals ; Animals, Wild/microbiology ; Bacteria/genetics/isolation & purification/*pathogenicity ; DNA, Bacterial ; Evolution, Molecular ; Genomic Islands ; Genomics ; Humans ; Metagenomics ; Microbiota/*genetics ; Mucus/*microbiology ; Skin/*microbiology ; Vibrio/genetics/isolation & purification/pathogenicity ; *Water Microbiology ; }, abstract = {BACKGROUND: Fish skin mucosal surfaces (SMS) are quite similar in composition and function to some mammalian MS and, in consequence, could constitute an adequate niche for the evolution of mucosal aquatic pathogens in natural environments. We aimed to test this hypothesis by searching for metagenomic and genomic evidences in the SMS-microbiome of a model fish species (Anguilla Anguilla or eel), from different ecosystems (four natural environments of different water salinity and one eel farm) as well as the water microbiome (W-microbiome) surrounding the host.

RESULTS: Remarkably, potentially pathogenic Vibrio monopolized wild eel SMS-microbiome from natural ecosystems, Vibrio anguillarum/Vibrio vulnificus and Vibrio cholerae/Vibrio metoecus being the most abundant ones in SMS from estuary and lake, respectively. Functions encoded in the SMS-microbiome differed significantly from those in the W-microbiome and allowed us to predict that successful mucus colonizers should have specific genes for (i) attachment (mainly by forming biofilms), (ii) bacterial competence and communication, and (iii) resistance to mucosal innate immunity, predators (amoeba), and heavy metals/drugs. In addition, we found several mobile genetic elements (mainly integrative conjugative elements) as well as a series of evidences suggesting that bacteria exchange DNA in SMS. Further, we isolated and sequenced a V. metoecus strain from SMS. This isolate shares pathogenicity islands with V. cholerae O1 from intestinal infections that are absent in the rest of sequenced V. metoecus strains, all of them from water and extra-intestinal infections.

CONCLUSIONS: We have obtained metagenomic and genomic evidence in favor of the hypothesis on the role of fish mucosal surfaces as a specialized habitat selecting microbes capable of colonizing and persisting on other comparable mucosal surfaces, e.g., the human intestine.}, } @article {pmid29268121, year = {2018}, author = {Damgaard, MTF and Pærregaard, SI and Søgaard, I and Agerholm, M and Paulson, JN and Treebak, JT and Sina, C and Holm, JB and Kristiansen, K and Jensen, BAH}, title = {Age-dependent alterations of glucose clearance and homeostasis are temporally separated and modulated by dietary fat.}, journal = {The Journal of nutritional biochemistry}, volume = {54}, number = {}, pages = {66-76}, doi = {10.1016/j.jnutbio.2017.09.026}, pmid = {29268121}, issn = {1873-4847}, mesh = {Adipose Tissue, White/pathology ; Age Factors ; Animals ; Dietary Fats/*pharmacology ; Fish Oils/*pharmacology ; Gastrointestinal Microbiome ; Gene Expression Regulation ; Gluconeogenesis/genetics ; Glucose/*metabolism ; Homeostasis ; Insulin/metabolism/pharmacology ; Male ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/etiology/pathology ; Obesity/etiology ; Panniculitis/etiology ; Soybean Oil/*pharmacology ; Weight Gain ; }, abstract = {Diet- and age-dependent changes in glucose regulation in mice occur, but the temporal development, mechanisms and influence of dietary fat source remain to be defined. We followed metabolic changes in three groups of mice including a low-fat diet (LFD) reference group and two high-fat, high-sucrose diets based on either fish oil (FOD) or soybean oil (SOD), rich in ω3- and ω6-polyunsaturated fatty acids, respectively, to closely monitor the age-dependent development in glucose regulation in both obese (SOD-fed) and lean (LFD- and FOD-fed) mice. We assessed glucose homeostasis and glucose clearance at week 8, 12, 16, 24, 31, and 39 and performed an insulin tolerance test at week 40. We further analyzed correlations between the gut microbiota and key metabolic parameters. Interestingly, alterations in glucose homeostasis and glucose clearance were temporally separated, while 16S ribosomal gene amplicon sequencing revealed that gut microbial alterations formed correlation clusters with fat mass and either glucose homeostasis or glucose clearance, but rarely both. Importantly, effective glucose clearance was maintained in FOD- and even increased in LFD-fed mice, whereas SOD-fed mice rapidly developed impaired glucose clearance followed by a gradual improvement from week 8 to week 39. All groups had similar responses to insulin 40 weeks post diet initiation despite severe nonalcoholic steatohepatitis in SOD-fed mice. We conclude that age-related alterations in glucose regulation may occur in both lean and obese mice and are modulated by dietary fat as indicated by the sustained metabolic homeostasis observed in mice fed ω3-polyunsaturated fatty acids.}, } @article {pmid29261736, year = {2017}, author = {Camacho-Ortiz, A and Gutiérrez-Delgado, EM and Garcia-Mazcorro, JF and Mendoza-Olazarán, S and Martínez-Meléndez, A and Palau-Davila, L and Baines, SD and Maldonado-Garza, H and Garza-González, E}, title = {Randomized clinical trial to evaluate the effect of fecal microbiota transplant for initial Clostridium difficile infection in intestinal microbiome.}, journal = {PloS one}, volume = {12}, number = {12}, pages = {e0189768}, pmid = {29261736}, issn = {1932-6203}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/genetics ; Biodiversity ; Clostridium Infections/drug therapy/*therapy ; Demography ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Genotype ; Humans ; Male ; Metagenomics ; Microbial Sensitivity Tests ; Middle Aged ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Tissue Donors ; Vancomycin/therapeutic use ; Young Adult ; }, abstract = {OBJECTIVE: The aim of this study was to evaluate the impact of fecal donor-unrelated donor mix (FMT-FURM) transplantation as first-line therapy for C. difficile infection (CDI) in intestinal microbiome.

METHODS: We designed an open, two-arm pilot study with oral vancomycin (250mg every 6 h for 10-14 days) or FMT-FURM as treatments for the first CDI episode in hospitalized adult patients in Hospital Universitario "Dr. Jose Eleuterio Gonzalez". Patients were randomized by a closed envelope method in a 1: 1 ratio to either oral vancomycin or FMT-FURM. CDI resolution was considered when there was a reduction on the Bristol scale of at least 2 points, a reduction of at least 50% in the number of bowel movements, absence of fever, and resolution of abdominal pain (at least two criteria). From each patient, a fecal sample was obtained at days 0, 3, and 7 after treatment. Specimens were cultured to isolate C. difficile, and isolates were characterized by PCR. Susceptibility testing of isolates was performed using the agar dilution method. Fecal samples and FMT-FURM were analyzed by 16S rRNA sequencing.

RESULTS: We included 19 patients; 10 in the vancomycin arm and 9 in the FMT-FURM arm. However, one of the patients in the vancomycin arm and two patients in the FMT-FURM arm were eliminated. Symptoms resolved in 8/9 patients (88.9%) in the vancomycin group, while symptoms resolved in 4/7 patients (57.1%) after the first FMT-FURM dose (P = 0.26) and in 5/7 patients (71.4%) after the second dose (P = 0.55). During the study, no adverse effects attributable to FMT-FURM were observed in patients. Twelve isolates were recovered, most isolates carried tcdB, tcdA, cdtA, and cdtB, with an 18-bp deletion in tcdC. All isolates were resistant to ciprofloxacin and moxifloxacin but susceptible to metronidazole, linezolid, fidaxomicin, and tetracycline. In the FMT-FURM group, the bacterial composition was dominated by Firmicutes, Bacteroidetes, and Proteobacteria at all-time points and the microbiota were remarkably stable over time. The vancomycin group showed a very different pattern of the microbial composition when comparing to the FMT-FURM group over time.

CONCLUSION: The results of this preliminary study showed that FMT-FURM for initial CDI is associated with specific bacterial communities that do not resemble the donors' sample.}, } @article {pmid29259289, year = {2018}, author = {Ogilvie, LA and Nzakizwanayo, J and Guppy, FM and Dedi, C and Diston, D and Taylor, H and Ebdon, J and Jones, BV}, title = {Resolution of habitat-associated ecogenomic signatures in bacteriophage genomes and application to microbial source tracking.}, journal = {The ISME journal}, volume = {12}, number = {4}, pages = {942-958}, pmid = {29259289}, issn = {1751-7370}, support = {G0901553/MRC_/Medical Research Council/United Kingdom ; MR/N006496/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacteriophages/*genetics ; Ecosystem ; Environmental Monitoring ; Feces/virology ; Gastrointestinal Tract/virology ; *Genome, Viral ; Humans ; *Metagenome ; Metagenomics ; Microbiota ; }, abstract = {Just as the expansion in genome sequencing has revealed and permitted the exploitation of phylogenetic signals embedded in bacterial genomes, the application of metagenomics has begun to provide similar insights at the ecosystem level for microbial communities. However, little is known regarding this aspect of bacteriophage associated with microbial ecosystems, and if phage encode discernible habitat-associated signals diagnostic of underlying microbiomes. Here we demonstrate that individual phage can encode clear habitat-related 'ecogenomic signatures', based on relative representation of phage-encoded gene homologues in metagenomic data sets. Furthermore, we show the ecogenomic signature encoded by the gut-associated ɸB124-14 can be used to segregate metagenomes according to environmental origin, and distinguish 'contaminated' environmental metagenomes (subject to simulated in silico human faecal pollution) from uncontaminated data sets. This indicates phage-encoded ecological signals likely possess sufficient discriminatory power for use in biotechnological applications, such as development of microbial source tracking tools for monitoring water quality.}, } @article {pmid29257962, year = {2017}, author = {Narrowe, A and Miller, CS and Lozupone, C}, title = {Microbial Biodiversity: Straight from the Dolphin's Mouth.}, journal = {Current biology : CB}, volume = {27}, number = {24}, pages = {R1307-R1309}, doi = {10.1016/j.cub.2017.10.068}, pmid = {29257962}, issn = {1879-0445}, mesh = {Animals ; Biodiversity ; *Dolphins ; *Microbiota ; Mouth ; Phylogeny ; }, abstract = {Advances in metagenomic sequencing and bioinformatics have vastly expanded our knowledge of microbial phylogenetic and functional diversity. In this issue, Dudek et al. show that shotgun metagenomic sequencing of a less-well-studied environment - dolphin gums - uncovers surprising novelty in the bacterial tree of life, underscoring the promise of future discovery.}, } @article {pmid29255284, year = {2018}, author = {Costea, PI and Hildebrand, F and Arumugam, M and Bäckhed, F and Blaser, MJ and Bushman, FD and de Vos, WM and Ehrlich, SD and Fraser, CM and Hattori, M and Huttenhower, C and Jeffery, IB and Knights, D and Lewis, JD and Ley, RE and Ochman, H and O'Toole, PW and Quince, C and Relman, DA and Shanahan, F and Sunagawa, S and Wang, J and Weinstock, GM and Wu, GD and Zeller, G and Zhao, L and Raes, J and Knight, R and Bork, P}, title = {Enterotypes in the landscape of gut microbial community composition.}, journal = {Nature microbiology}, volume = {3}, number = {1}, pages = {8-16}, pmid = {29255284}, issn = {2058-5276}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; UH2 DK083981/DK/NIDDK NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; R35 GM118038/GM/NIGMS NIH HHS/United States ; MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; P30 DK050306/DK/NIDDK NIH HHS/United States ; BB/L027801/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacteria/*classification/genetics ; Bacterial Typing Techniques ; Biodiversity ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.}, } @article {pmid29255014, year = {2018}, author = {Bergauer, K and Fernandez-Guerra, A and Garcia, JAL and Sprenger, RR and Stepanauskas, R and Pachiadaki, MG and Jensen, ON and Herndl, GJ}, title = {Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {3}, pages = {E400-E408}, pmid = {29255014}, issn = {1091-6490}, support = {268595/ERC_/European Research Council/International ; I 486/FWF_/Austrian Science Fund FWF/Austria ; Z 194/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/*metabolism ; Atlantic Ocean ; Bacteria/genetics/*metabolism ; Bacterial Proteins/*metabolism ; Biodiversity ; Genome, Archaeal ; Genome, Bacterial ; Metagenomics ; Proteomics/*methods ; Seawater ; *Water Microbiology ; }, abstract = {The phylogenetic composition of the heterotrophic microbial community is depth stratified in the oceanic water column down to abyssopelagic layers. In the layers below the euphotic zone, it has been suggested that heterotrophic microbes rely largely on solubilized particulate organic matter as a carbon and energy source rather than on dissolved organic matter. To decipher whether changes in the phylogenetic composition with depth are reflected in changes in the bacterial and archaeal transporter proteins, we generated an extensive metaproteomic and metagenomic dataset of microbial communities collected from 100- to 5,000-m depth in the Atlantic Ocean. By identifying which compounds of the organic matter pool are absorbed, transported, and incorporated into microbial cells, intriguing insights into organic matter transformation in the deep ocean emerged. On average, solute transporters accounted for 23% of identified protein sequences in the lower euphotic and ∼39% in the bathypelagic layer, indicating the central role of heterotrophy in the dark ocean. In the bathypelagic layer, substrate affinities of expressed transporters suggest that, in addition to amino acids, peptides and carbohydrates, carboxylic acids and compatible solutes may be essential substrates for the microbial community. Key players with highest expression of solute transporters were Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria, accounting for 40%, 11%, and 10%, respectively, of relative protein abundances. The in situ expression of solute transporters indicates that the heterotrophic prokaryotic community is geared toward the utilization of similar organic compounds throughout the water column, with yet higher abundances of transporters targeting aromatic compounds in the bathypelagic realm.}, } @article {pmid29253074, year = {2018}, author = {Huang, L and Krüger, J and Sczyrba, A}, title = {Analyzing large scale genomic data on the cloud with Sparkhit.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {9}, pages = {1457-1465}, pmid = {29253074}, issn = {1367-4811}, mesh = {Algorithms ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; *Software ; }, abstract = {MOTIVATION: The increasing amount of next-generation sequencing data poses a fundamental challenge on large scale genomic analytics. Existing tools use different distributed computational platforms to scale-out bioinformatics workloads. However, the scalability of these tools is not efficient. Moreover, they have heavy run time overheads when pre-processing large amounts of data. To address these limitations, we have developed Sparkhit: a distributed bioinformatics framework built on top of the Apache Spark platform.

RESULTS: Sparkhit integrates a variety of analytical methods. It is implemented in the Spark extended MapReduce model. It runs 92-157 times faster than MetaSpark on metagenomic fragment recruitment and 18-32 times faster than Crossbow on data pre-processing. We analyzed 100 terabytes of data across four genomic projects in the cloud in 21 h, which includes the run times of cluster deployment and data downloading. Furthermore, our application on the entire Human Microbiome Project shotgun sequencing data was completed in 2 h, presenting an approach to easily associate large amounts of public datasets with reference data.

Sparkhit is freely available at: https://rhinempi.github.io/sparkhit/.

CONTACT: asczyrba@cebitec.uni-bielefeld.de.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid29251611, year = {2017}, author = {Starikova, EV and Prianichnikov, NA and Zdobnov, E and Govorun, VM}, title = {[Bioinformatics analysis of antimicrobial resistance genes and prophages colocalized in human gut metagenomes].}, journal = {Biomeditsinskaia khimiia}, volume = {63}, number = {6}, pages = {508-512}, doi = {10.18097/PBMC20176306508}, pmid = {29251611}, issn = {2310-6972}, mesh = {Anti-Bacterial Agents ; Anti-Infective Agents ; *Computational Biology ; Drug Resistance, Bacterial/*genetics ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; Prophages/*genetics ; }, abstract = {The constant increase of antibiotic-resistant strains of bacteria is caused by extensive uses of antibiotics in medicine and animal breeding. It was suggested that the gut microbiota serves as a reservoir for antibiotics resistance genes that can be carried from symbiotic bacteria to pathogenic ones, in particular, as a result of transduction. In the current study, we have searched for antibiotics resistance genes that are located inside prophages in human gut microbiota using PHASTER prophage predicting tool and CARD antibiotics resistance database. After analysing metagenomic assemblies of eight samples of antibiotic treated patients, lsaE, mdfA and cpxR/cpxA genes were identified inside prophages. The abovementioned genes confer resistance to antimicrobial peptides, pleuromutilin, lincomycins, streptogramins and multidrug resistance. Three (0.46%) of 659 putative prophages predicted in metagenomic assemblies contained antibiotics resistance genes in their sequences.}, } @article {pmid29247187, year = {2017}, author = {Börnigen, D and Ren, B and Pickard, R and Li, J and Ozer, E and Hartmann, EM and Xiao, W and Tickle, T and Rider, J and Gevers, D and Franzosa, EA and Davey, ME and Gillison, ML and Huttenhower, C}, title = {Alterations in oral bacterial communities are associated with risk factors for oral and oropharyngeal cancer.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {17686}, pmid = {29247187}, issn = {2045-2322}, support = {R01 DE019117/DE/NIDCR NIH HHS/United States ; R01 DE024580/DE/NIDCR NIH HHS/United States ; }, mesh = {Aged ; Alcohol Drinking/adverse effects ; Bacteria/*pathogenicity ; Carcinoma, Squamous Cell/etiology/microbiology ; Case-Control Studies ; Female ; Humans ; Male ; Microbiota/*physiology ; Middle Aged ; Mouth Neoplasms/*etiology/*microbiology ; Oral Hygiene/adverse effects ; Oropharyngeal Neoplasms/*etiology/*microbiology ; Risk Factors ; Smoking/adverse effects ; Tobacco Use/adverse effects ; Tooth Loss/etiology/microbiology ; }, abstract = {Oral squamous cell carcinomas are a major cause of morbidity and mortality, and tobacco usage, alcohol consumption, and poor oral hygiene are established risk factors. To date, no large-scale case-control studies have considered the effects of these risk factors on the composition of the oral microbiome, nor microbial community associations with oral cancer. We compared the composition, diversity, and function of the oral microbiomes of 121 oral cancer patients to 242 age- and gender-matched controls using a metagenomic multivariate analysis pipeline. Significant shifts in composition and function of the oral microbiome were observed with poor oral hygiene, tobacco smoking, and oral cancer. Specifically, we observed dramatically altered community composition and function after tooth loss, with smaller alterations in current tobacco smokers, increased production of antioxidants in individuals with periodontitis, and significantly decreased glutamate metabolism metal transport in oral cancer patients. Although the alterations in the oral microbiome of oral cancer patients were significant, they were of substantially lower effect size relative to microbiome shifts after tooth loss. Alterations following tooth loss, itself a major risk factor for oral cancer, are likely a result of severe ecological disruption due to habitat loss but may also contribute to the development of the disease.}, } @article {pmid29247170, year = {2017}, author = {Wassermann, B and Rybakova, D and Müller, C and Berg, G}, title = {Harnessing the microbiomes of Brassica vegetables for health issues.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {17649}, pmid = {29247170}, issn = {2045-2322}, mesh = {Bacterial Proteins/genetics ; Brassicaceae/*microbiology/physiology ; Disease Resistance/genetics ; Food ; Foodborne Diseases/*prevention & control ; *Genotype ; Glycoside Hydrolases/genetics ; Humans ; Metagenome ; Microbiota/*genetics ; Plants, Edible ; RNA, Ribosomal, 16S/*analysis ; Rhizosphere ; Soil Microbiology ; Vegetables ; }, abstract = {Plant health is strongly connected with plants´ microbiome. In case of raw-eaten plants, the microbiome can also affect human health. To study potential impacts on health issues of both hosts, the microbiome composition of seven different Brassica vegetables, originating from different food processing pathways, was analyzed by a combined approach of amplicon sequencing, metagenomic mining and cultivation. All Brassica vegetables harbored a highly diverse microbiota as identified by 16S rRNA gene amplicon sequencing. The composition of the microbiota was found to be rather driven by the plant genotype than by the processing pathway. We characterized isolates with potential cancer-preventing properties by tracing myrosinase activity as well as isolates with biological control activity towards plant pathogens. We identified a novel strain with myrosinase activity and we found bacterial myrosinase genes to be enriched in rhizosphere and phyllosphere metagenomes of Brassica napus and Eruca sativa in comparison to the surrounding soil. Strains which were able to suppress plant pathogens were isolated from naturally processed vegetables and represent a substantial part (4.1%) of all vegetable microbiomes. Our results shed first light on the microbiome of edible plants and open the door to harnessing the Brassica microbiome for plant disease resistance and human health.}, } @article {pmid29247054, year = {2018}, author = {Peng, K and Jin, L and Niu, YD and Huang, Q and McAllister, TA and Yang, HE and Denise, H and Xu, Z and Acharya, S and Wang, S and Wang, Y}, title = {Condensed Tannins Affect Bacterial and Fungal Microbiomes and Mycotoxin Production during Ensiling and upon Aerobic Exposure.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {5}, pages = {}, pmid = {29247054}, issn = {1098-5336}, mesh = {Aerobiosis ; Bacteria/*metabolism ; *Fermentation ; Fungi/*metabolism ; Mycobiome/*physiology ; Mycotoxins/*metabolism ; Proanthocyanidins/*metabolism ; Silage/analysis ; }, abstract = {Purple prairie clover (PPC; Dalea purpurea Vent.) containing 84.5 g/kg dry matter (DM) of condensed tannin (CT) was ensiled without (control) or with polyethylene glycol (PEG) for 76 days, followed by 14 days of aerobic exposure. Changes in fermentation characteristics were determined, and the composition of bacterial and fungal communities were assessed using metagenomic sequencing. The addition of polyethylene glycol (PEG) that deactivated CT at ensiling increased (P < 0.05 to ∼0.001) soluble N, nonprotein N, lactic acid, total volatile fatty acids, ammonia N, deoxynivalenol (DON), and ochratoxin A (OTA) but decreased (P < 0.001) pH and water-soluble carbohydrates. The concentrations of DON and OTA increased (P < 0.001) for both silages, with the extent of increase being greater for control than for PEG-treated silage during aerobic exposure. The PEG-treated silage exhibited higher (P < 0.01 to ∼0.001) copy numbers of total bacteria, Lactobacillus, yeasts, and fungi than the control. The addition of PEG decreased (P < 0.01) bacterial diversity during both ensiling and aerobic exposure, whereas it increased (P < 0.05) fungal diversity during aerobic exposure. The addition of PEG at ensiling increased (P < 0.05) the abundances of Lactobacillus and Pediococcus species but decreased (P < 0.01) the abundances of Lactococcus and Leuconostoc species. Filamentous fungi were found in the microbiome at ensiling and after aerobic exposure, whereas Bacillus spp. were the dominate bacteria after aerobic exposure. In conclusion, CT decreased protein degradation and improved the aerobic stability of silage. These desirable outcomes likely reflect the ability of PPC CT to inhibit those microorganisms involved in lowering silage quality and in the production of mycotoxins.IMPORTANCE The present study reports the effects of condensed tannins on the complex microbial communities involved in ensiling and aerobic exposure of purple prairie clover. This study documents the ability of condensed tannins to lower mycotoxin production and the associated microbiome. Taxonomic bacterial community profiles were dominated by Lactobacillales after fermentation, with a notable increase in Bacillus spp. as a result of aerobic exposure. It is interesting to observe that condensed tannins decreased bacterial diversity during both ensiling and aerobic exposure but increased fungal diversity during aerobic exposure only. The present study indicates that the effects of condensed tannins on microbial communities lead to reduced lactic acid and total volatile fatty acid production, proteolysis, and mycotoxin concentration in the terminal silage and improved aerobic stability. Condensed tannins could be used as an additive to control unfavorable microbial development and maybe enhanced feed safety.}, } @article {pmid29246178, year = {2017}, author = {Razavi, M and Marathe, NP and Gillings, MR and Flach, CF and Kristiansson, E and Joakim Larsson, DG}, title = {Discovery of the fourth mobile sulfonamide resistance gene.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {160}, pmid = {29246178}, issn = {2049-2618}, support = {942-2015-750//Svenska Forskningsrådet Formas/ ; 521-2013-8633//Vetenskapsrådet/ ; 2015-02492//Vetenskapsrådet (SE)/ ; }, mesh = {Aminoglycosides/pharmacology ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; Bioprospecting ; Cross Infection/microbiology ; Dihydropteroate Synthase/genetics/isolation & purification ; Drug Resistance, Microbial/*genetics ; Escherichia coli/drug effects/genetics ; Genes, Bacterial ; Humans ; India ; *Integrons/genetics ; Metagenomics ; Microbial Consortia/genetics ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/genetics ; Rivers/microbiology ; Sulfonamides/*pharmacology ; beta-Lactams/pharmacology ; }, abstract = {BACKGROUND: Over the past 75 years, human pathogens have acquired antibiotic resistance genes (ARGs), often from environmental bacteria. Integrons play a major role in the acquisition of antibiotic resistance genes. We therefore hypothesized that focused exploration of integron gene cassettes from microbial communities could be an efficient way to find novel mobile resistance genes. DNA from polluted Indian river sediments were amplified using three sets of primers targeting class 1 integrons and sequenced by long- and short-read technologies to maintain both accuracy and context.

RESULTS: Up to 89% of identified open reading frames encode known resistance genes, or variations thereof (> 1000). We identified putative novel ARGs to aminoglycosides, beta-lactams, trimethoprim, rifampicin, and chloramphenicol, including several novel OXA variants, providing reduced susceptibility to carbapenems. One dihydropteroate synthase gene, with less than 34% amino acid identity to the three known mobile sulfonamide resistance genes (sul1-3), provided complete resistance when expressed in Escherichia coli. The mobilized gene, here named sul4, is the first mobile sulfonamide resistance gene discovered since 2003. Analyses of adjacent DNA suggest that sul4 has been decontextualized from a set of chromosomal genes involved in folate synthesis in its original host, likely within the phylum Chloroflexi. The presence of an insertion sequence common region element could provide mobility to the entire integron. Screening of 6489 metagenomic datasets revealed that sul4 is already widespread in seven countries across Asia and Europe.

CONCLUSIONS: Our findings show that exploring integrons from environmental communities with a history of antibiotic exposure can provide an efficient way to find novel, mobile resistance genes. The mobilization of a fourth sulfonamide resistance gene is likely to provide expanded opportunities for sulfonamide resistance to spread, with potential impacts on both human and animal health.}, } @article {pmid29243150, year = {2018}, author = {Naik, OA and Shashidhar, R and Rath, D and Bandekar, JR and Rath, A}, title = {Characterization of multiple antibiotic resistance of culturable microorganisms and metagenomic analysis of total microbial diversity of marine fish sold in retail shops in Mumbai, India.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {7}, pages = {6228-6239}, pmid = {29243150}, issn = {1614-7499}, support = {2012/37B/50/BRNS//Board of Research in Nuclear Sciences/ ; }, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria/*classification/genetics ; Biodiversity ; Drug Resistance, Multiple, Bacterial/*genetics ; Fishes/*microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; India ; Integrons/genetics ; *Metagenomics ; Microbial Sensitivity Tests ; Plasmids/genetics ; }, abstract = {Marine fish species were analyzed for culturable and total metagenomic microbial diversity, antibiotic resistance (AR) pattern, and horizontal gene transfer in culturable microorganisms. We observed a high AR microbial load of 3 to 4 log CFU g[-1]. Many fish pathogens like Providencia, Staphylococcus, Klebsiella pneumoniae, Enterobacter, Vagococcus, and Aeromonas veronii were isolated. Photobacterium and Vibrio were two major fish and human pathogens which were identified in the fish metagenome. Other pathogens that were identified were Shewanella, Acinetobacter, Psychrobacter, and Flavobacterium. Most of these pathogens were resistant to multiple antibiotics such as erythromycin, kanamycin, neomycin, streptomycin, penicillin, cefotaxime, bacitracin, rifampicin, trimethoprim, ciprofloxacin, and doxycycline with a high multiple antibiotic resistance index of 0.54-0.77. The fish microflora showed high prevalence of AR genes like bla TEM, Class I integron, tetA, aph(3')-IIIa, ermB, aadA, and sul1. Nineteen of 26 AR isolates harbored Class I integrons showing high co-resistance to trimethoprim, kanamycin, doxycycline, and cefotaxime. Mobile R-plasmids from 6 of the 12 AR pathogens were transferred to recipient E. coli after conjugation. The transconjugants harbored the same R-plasmid carrying bla CTX-M, dfr1, tetA, bla TEM, and cat genes. This study confirms that fish is a potential carrier of AR pathogens which can enter the human gut via food chain. To the best of our knowledge, this is the first study in the Indian subcontinent reporting a direct evidence of spread of AR pathogens to humans from specific marine fish consumption.}, } @article {pmid29242367, year = {2017}, author = {Costea, PI and Coelho, LP and Sunagawa, S and Munch, R and Huerta-Cepas, J and Forslund, K and Hildebrand, F and Kushugulova, A and Zeller, G and Bork, P}, title = {Subspecies in the global human gut microbiome.}, journal = {Molecular systems biology}, volume = {13}, number = {12}, pages = {960}, pmid = {29242367}, issn = {1744-4292}, mesh = {Escherichia coli/physiology ; *Gastrointestinal Microbiome/genetics ; Genes, Bacterial ; Humans ; *Microbiota/genetics ; Phenotype ; Phylogeography ; Species Specificity ; }, abstract = {Population genomics of prokaryotes has been studied in depth in only a small number of primarily pathogenic bacteria, as genome sequences of isolates of diverse origin are lacking for most species. Here, we conducted a large-scale survey of population structure in prevalent human gut microbial species, sampled from their natural environment, with a culture-independent metagenomic approach. We examined the variation landscape of 71 species in 2,144 human fecal metagenomes and found that in 44 of these, accounting for 72% of the total assigned microbial abundance, single-nucleotide variation clearly indicates the existence of sub-populations (here termed subspecies). A single subspecies (per species) usually dominates within each host, as expected from ecological theory. At the global scale, geographic distributions of subspecies differ between phyla, with Firmicutes subspecies being significantly more geographically restricted. To investigate the functional significance of the delineated subspecies, we identified genes that consistently distinguish them in a manner that is independent of reference genomes. We further associated these subspecies-specific genes with properties of the microbial community and the host. For example, two of the three Eubacterium rectale subspecies consistently harbor an accessory pro-inflammatory flagellum operon that is associated with lower gut community diversity, higher host BMI, and higher blood fasting insulin levels. Using an additional 676 human oral samples, we further demonstrate the existence of niche specialized subspecies in the different parts of the oral cavity. Taken together, we provide evidence for subspecies in the majority of abundant gut prokaryotes, leading to a better functional and ecological understanding of the human gut microbiome in conjunction with its host.}, } @article {pmid29241587, year = {2018}, author = {Arrieta, MC and Arévalo, A and Stiemsma, L and Dimitriu, P and Chico, ME and Loor, S and Vaca, M and Boutin, RCT and Morien, E and Jin, M and Turvey, SE and Walter, J and Parfrey, LW and Cooper, PJ and Finlay, B}, title = {Associations between infant fungal and bacterial dysbiosis and childhood atopic wheeze in a nonindustrialized setting.}, journal = {The Journal of allergy and clinical immunology}, volume = {142}, number = {2}, pages = {424-434.e10}, pmid = {29241587}, issn = {1097-6825}, support = {//Wellcome Trust/United Kingdom ; T32 CA009142/CA/NCI NIH HHS/United States ; 088862/Z/09/Z//Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*genetics ; Carbohydrate Metabolism ; Case-Control Studies ; Child, Preschool ; Cohort Studies ; Dysbiosis/*epidemiology ; Ecuador/epidemiology ; Feces/*microbiology ; Fungi/*physiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Hypersensitivity, Immediate/*epidemiology ; Infant ; RNA, Ribosomal, 16S/genetics ; Respiratory Sounds ; Rural Population ; Taurine/metabolism ; }, abstract = {BACKGROUND: Asthma is the most prevalent chronic disease of childhood. Recently, we identified a critical window early in the life of both mice and Canadian infants during which gut microbial changes (dysbiosis) affect asthma development. Given geographic differences in human gut microbiota worldwide, we studied the effects of gut microbial dysbiosis on atopic wheeze in a population living in a distinct developing world environment.

OBJECTIVE: We sought to determine whether microbial alterations in early infancy are associated with the development of atopic wheeze in a nonindustrialized setting.

METHODS: We conducted a case-control study nested within a birth cohort from rural Ecuador in which we identified 27 children with atopic wheeze and 70 healthy control subjects at 5 years of age. We analyzed bacterial and eukaryotic gut microbiota in stool samples collected at 3 months of age using 16S and 18S sequencing. Bacterial metagenomes were predicted from 16S rRNA data by using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States and categorized by function with Kyoto Encyclopedia of Genes and Genomes ontology. Concentrations of fecal short-chain fatty acids were determined by using gas chromatography.

RESULTS: As previously observed in Canadian infants, microbial dysbiosis at 3 months of age was associated with later development of atopic wheeze. However, the dysbiosis in Ecuadorian babies involved different bacterial taxa, was more pronounced, and also involved several fungal taxa. Predicted metagenomic analysis emphasized significant dysbiosis-associated differences in genes involved in carbohydrate and taurine metabolism. Levels of the fecal short-chain fatty acids acetate and caproate were reduced and increased, respectively, in the 3-month stool samples of children who went on to have atopic wheeze.

CONCLUSIONS: Our findings support the importance of fungal and bacterial microbiota during the first 100 days of life on the development of atopic wheeze and provide additional support for considering modulation of the gut microbiome as a primary asthma prevention strategy.}, } @article {pmid29235707, year = {2018}, author = {Brewer, TE and Fierer, N}, title = {Tales from the tomb: the microbial ecology of exposed rock surfaces.}, journal = {Environmental microbiology}, volume = {20}, number = {3}, pages = {958-970}, doi = {10.1111/1462-2920.14024}, pmid = {29235707}, issn = {1462-2920}, mesh = {Bacteria/*classification/genetics ; Biodiversity ; *Calcium Carbonate ; *Metagenomics ; *Microbiota ; *Silicon Dioxide ; }, abstract = {Although a broad diversity of eukaryotic and bacterial taxa reside on rock surfaces where they can influence the weathering of rocks and minerals, these communities and their contributions to mineral weathering remain poorly resolved. To build a more comprehensive understanding of the diversity, ecology and potential functional attributes of microbial communities living on rock, we sampled 149 tombstones across three continents and analysed their bacterial and eukaryotic communities via marker gene and shotgun metagenomic sequencing. We found that geographic location and climate were important factors structuring the composition of these communities. Moreover, the tombstone-associated microbial communities varied as a function of rock type, with granite and limestone tombstones from the same cemeteries harbouring taxonomically distinct microbial communities. The granite and limestone-associated communities also had distinct functional attributes, with granite-associated bacteria having more genes linked to acid tolerance and chemotaxis, while bacteria on limestone were more likely to be lichen associated and have genes involved in photosynthesis and radiation resistance. Together these results indicate that rock-dwelling microbes exhibit adaptations to survive the stresses of the rock surface, differ based on location, climate and rock type, and seem pre-disposed to different ecological strategies (symbiotic versus free-living lifestyles) depending on the rock type.}, } @article {pmid29235578, year = {2017}, author = {Stary, L and Mezerova, K and Skalicky, P and Zboril, P and Raclavsky, V}, title = {Are we any closer to screening for colorectal cancer using microbial markers?A critical review.}, journal = {Biomedical papers of the Medical Faculty of the University Palacky, Olomouc, Czechoslovakia}, volume = {161}, number = {4}, pages = {333-338}, doi = {10.5507/bp.2017.051}, pmid = {29235578}, issn = {1804-7521}, mesh = {Biomarkers, Tumor/*analysis ; Colorectal Neoplasms/*diagnosis/*microbiology ; DNA, Bacterial/*analysis ; Early Detection of Cancer/*methods ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; }, abstract = {The role of gut microbiota in the development of sporadic colorectal cancer (CRC) is supported by a number of studies, however, the conclusiveness of published metagenomic studies is questioned by technical pitfalls and limited by small cohort sizes. In this review, we evaluate the current knowledge critically and outline practical solutions. We also list candidate CRC risk markers that are - in our opinion - well supported by available data and thus deserve clinical validation. Last but not least, we summarise available knowledge useful for improving care for patients immediately.}, } @article {pmid29235508, year = {2017}, author = {Zeng, Q and Tian, X and Wang, L}, title = {Genetic adaptation of microbial populations present in high-intensity catfish production systems with therapeutic oxytetracycline treatment.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {17491}, pmid = {29235508}, issn = {2045-2322}, mesh = {Adaptation, Biological ; Animals ; Anti-Bacterial Agents/*pharmacology ; Aquaculture ; Bacteria/drug effects/genetics ; Biodiversity ; Catfishes/*microbiology ; Drug Resistance, Bacterial/*genetics ; Metagenome/drug effects ; Microbiota/*drug effects/*genetics ; Oxytetracycline/*pharmacology ; Phylogeny ; Polymorphism, Single Nucleotide ; }, abstract = {Microbial communities that are present in aquaculture production systems play significant roles in degrading organic matter, controlling diseases, and formation of antibiotic resistance. It is important to understand the diversity and abundance of microbial communities and their genetic adaptations associated with environmental physical and chemical changes. Here we collected water and sediment samples from a high-intensity catfish production system and its original water reservoir. The metagenomic analysis showed that Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes were the top five phyla identified from all samples. The aquaculture production system significantly changed the structure of aquatic microbial populations. Substantial changes were also observed in SNP patterns among four sample types. The gene-specific sweep was found to be more common than genome-wide sweep. The selective sweep analysis revealed that 21 antibiotic resistant (AR) genes were under selection, with most belonging to antibiotic efflux pathways. Over 200 AR gene gains and losses were determined by changes in gene frequencies. Most of the AR genes were characterized as ABC efflux pumps, RND efflux pumps, and tetracycline MFS efflux pumps. Results of this study suggested that aquaculture waste, especially waste containing therapeutic antibiotics, has a significant impact on microbial population structures and their genetic structures.}, } @article {pmid29233840, year = {2018}, author = {Byrd, V and Getz, T and Padmanabhan, R and Arora, H and Eng, C}, title = {The microbiome in PTEN hamartoma tumor syndrome.}, journal = {Endocrine-related cancer}, volume = {25}, number = {3}, pages = {233-243}, pmid = {29233840}, issn = {1479-6821}, support = {P01 CA124570/CA/NCI NIH HHS/United States ; U54 NS092090/NS/NINDS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; DNA, Bacterial/genetics ; Dysbiosis ; Feces/microbiology ; Female ; Germ-Line Mutation ; Hamartoma Syndrome, Multiple/*microbiology ; Humans ; Male ; Microbiota/*genetics ; Middle Aged ; Mouth/microbiology ; PTEN Phosphohydrolase/*genetics ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; Urine/microbiology ; Young Adult ; }, abstract = {Germline PTEN mutations defining PTEN hamartoma tumor syndrome (PHTS) confer heritable predisposition to breast, endometrial, thyroid and other cancers with known age-related risks, but it remains impossible to predict if any individual will develop cancer. In the general population, gut microbial dysbiosis has been linked to cancer, yet is unclear whether these are associated in PHTS patients. In this pilot study, we aimed to characterize microbial composition of stool, urine, and oral wash from 32 PTEN mutation-positive individuals using 16S rRNA gene sequencing. PCoA revealed clustering of the fecal microbiome by cancer history (P = 0.03, R[2] = 0.04). Fecal samples from PHTS cancer patients had relatively more abundant operational taxonomic units (OTUs) from family Rikenellaceae and unclassified members of Clostridia compared to those from non-cancer patients, whereas families Peptostreptococcaceae, Enterobacteriaceae, and Bifidobacteriaceae represented relatively more abundant OTUs among fecal samples from PHTS non-cancer patients. Functional metagenomic prediction revealed enrichment of the folate biosynthesis, genetic information processing and cell growth and death pathways among fecal samples from PHTS cancer patients compared to non-cancer patients. We found no major shifts in overall diversity and no clustering by cancer history among oral wash or urine samples. Our observations suggest the utility of an expanded study to interrogate gut dysbiosis as a potential cancer risk modifier in PHTS patients.}, } @article {pmid29232848, year = {2017}, author = {Vernocchi, P and Del Chierico, F and Quagliariello, A and Ercolini, D and Lucidi, V and Putignani, L}, title = {A Metagenomic and in Silico Functional Prediction of Gut Microbiota Profiles May Concur in Discovering New Cystic Fibrosis Patient-Targeted Probiotics.}, journal = {Nutrients}, volume = {9}, number = {12}, pages = {}, pmid = {29232848}, issn = {2072-6643}, mesh = {Bacteria/*genetics ; Case-Control Studies ; Child, Preschool ; Cystic Fibrosis/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics/*methods ; Phylogeny ; *Probiotics ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Cystic fibrosis (CF) is a life-limiting hereditary disorder that results in aberrant mucosa in the lungs and digestive tract, chronic respiratory infections, chronic inflammation, and the need for repeated antibiotic treatments. Probiotics have been demonstrated to improve the quality of life of CF patients. We investigated the distribution of gut microbiota (GM) bacteria to identify new potential probiotics for CF patients on the basis of GM patterns. Fecal samples of 28 CF patients and 31 healthy controls (HC) were collected and analyzed by 16S rRNA-based pyrosequencing analysis of GM, to produce CF-HC paired maps of the distribution of operational taxonomic units (OTUs), and by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) for Kyoto Encyclopedia of Genes and Genomes (KEGG) biomarker prediction. The maps were scanned to highlight the distribution of bacteria commonly claimed as probiotics, such as bifidobacteria and lactobacilli, and of butyrate-producing colon bacteria, such as Eubacterium spp. and Faecalibacterium prausnitzii. The analyses highlighted 24 OTUs eligible as putative probiotics. Eleven and nine species were prevalently associated with the GM of CF and HC subjects, respectively. Their KEGG prediction provided differential CF and HC pathways, indeed associated with health-promoting biochemical activities in the latter case. GM profiling and KEGG biomarkers concurred in the evaluation of nine bacterial species as novel putative probiotics that could be investigated for the nutritional management of CF patients.}, } @article {pmid29229530, year = {2018}, author = {Umadevi, P and Anandaraj, M and Srivastav, V and Benjamin, S}, title = {Trichoderma harzianum MTCC 5179 impacts the population and functional dynamics of microbial community in the rhizosphere of black pepper (Piper nigrum L.).}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {49}, number = {3}, pages = {463-470}, pmid = {29229530}, issn = {1678-4405}, mesh = {Bacteria/classification/genetics/*growth & development/isolation & purification ; *Biodiversity ; Ecosystem ; Fungi/classification/genetics/*growth & development/isolation & purification ; Piper nigrum/growth & development/*microbiology ; Rhizosphere ; *Soil Microbiology ; Trichoderma/genetics/*growth & development/isolation & purification ; Viruses/classification/genetics/*growth & development/isolation & purification ; }, abstract = {Employing Illumina Hiseq whole genome metagenome sequencing approach, we studied the impact of Trichoderma harzianum on altering the microbial community and its functional dynamics in the rhizhosphere soil of black pepper (Piper nigrum L.). The metagenomic datasets from the rhizosphere with (treatment) and without (control) T. harzianum inoculation were annotated using dual approach, i.e., stand alone and MG-RAST. The probiotic application of T. harzianum in the rhizhosphere soil of black pepper impacted the population dynamics of rhizosphere bacteria, archae, eukaryote as reflected through the selective recruitment of bacteria [Acidobacteriaceae bacterium (p=1.24e-12), Candidatus koribacter versatilis (p=2.66e-10)] and fungi [(Fusarium oxysporum (p=0.013), Talaromyces stipitatus (p=0.219) and Pestalotiopsis fici (p=0.443)] in terms of abundance in population and bacterial chemotaxis (p=0.012), iron metabolism (p=2.97e-5) with the reduction in abundance for pathogenicity islands (p=7.30e-3), phages and prophages (p=7.30e-3) with regard to functional abundance. Interestingly, it was found that the enriched functional metagenomic signatures on phytoremediation such as benzoate transport and degradation (p=2.34e-4), and degradation of heterocyclic aromatic compounds (p=3.59e-13) in the treatment influenced the rhizosphere micro ecosystem favoring growth and health of pepper plant. The population dynamics and functional richness of rhizosphere ecosystem in black pepper influenced by the treatment with T. harzianum provides the ecological importance of T. harzianum in the cultivation of black pepper.}, } @article {pmid29228991, year = {2017}, author = {Auffret, MD and Dewhurst, RJ and Duthie, CA and Rooke, JA and John Wallace, R and Freeman, TC and Stewart, R and Watson, M and Roehe, R}, title = {The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {159}, pmid = {29228991}, issn = {2049-2618}, support = {BB/I001107/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/D/20211551/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/D/20211552/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N01720X/1 and BB/N016742/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animal Feed/adverse effects/*analysis ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteriocins/pharmacology ; Bacteroidetes/drug effects/genetics/pathogenicity ; Cattle/*microbiology ; Chloramphenicol/pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Firmicutes/drug effects/genetics/pathogenicity ; *Genes, Bacterial ; Humans ; Metagenomics/methods ; *Microbiota ; Proteobacteria/drug effects/genetics/pathogenicity ; Red Meat/analysis ; Rumen/*microbiology ; Virulence ; }, abstract = {BACKGROUND: The emergence and spread of antimicrobial resistance is the most urgent current threat to human and animal health. An improved understanding of the abundance of antimicrobial resistance genes and genes associated with microbial colonisation and pathogenicity in the animal gut will have a major role in reducing the contribution of animal production to this problem. Here, the influence of diet on the ruminal resistome and abundance of pathogenicity genes was assessed in ruminal digesta samples taken from 50 antibiotic-free beef cattle, comprising four cattle breeds receiving two diets containing different proportions of concentrate.

RESULTS: Two hundred and four genes associated with antimicrobial resistance (AMR), colonisation, communication or pathogenicity functions were identified from 4966 metagenomic genes using KEGG identification. Both the diversity and abundance of these genes were higher in concentrate-fed animals. Chloramphenicol and microcin resistance genes were dominant in samples from forage-fed animals (P < 0.001), while aminoglycoside and streptomycin resistances were enriched in concentrate-fed animals. The concentrate-based diet also increased the relative abundance of Proteobacteria, which includes many animal and zoonotic pathogens. A high ratio of Proteobacteria to (Firmicutes + Bacteroidetes) was confirmed as a good indicator for rumen dysbiosis, with eight cases all from concentrate-fed animals. Finally, network analysis demonstrated that the resistance/pathogenicity genes are potentially useful as biomarkers for health risk assessment of the ruminal microbiome.

CONCLUSIONS: Diet has important effects on the complement of AMR genes in the rumen microbial community, with potential implications for human and animal health.}, } @article {pmid29228901, year = {2017}, author = {Forsell, J and Bengtsson-Palme, J and Angelin, M and Johansson, A and Evengård, B and Granlund, M}, title = {The relation between Blastocystis and the intestinal microbiota in Swedish travellers.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {231}, pmid = {29228901}, issn = {1471-2180}, mesh = {Adult ; Biodiversity ; Blastocystis/*classification/physiology ; Blastocystis Infections/epidemiology/*microbiology/*parasitology/transmission ; Feces/microbiology/parasitology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Prevalence ; Sweden/epidemiology ; *Travel ; Young Adult ; }, abstract = {BACKGROUND: Blastocystis sp. is a unicellular eukaryote that is commonly found in the human intestine. Its ability to cause disease is debated and a subject for ongoing research. In this study, faecal samples from 35 Swedish university students were examined through shotgun metagenomics before and after travel to the Indian peninsula or Central Africa. We aimed at assessing the impact of travel on Blastocystis carriage and seek associations between Blastocystis and the bacterial microbiota.

RESULTS: We found a prevalence of Blastocystis of 16/35 (46%) before travel and 15/35 (43%) after travel. The two most commonly Blastocystis subtypes (STs) found were ST3 and ST4, accounting for 20 of the 31 samples positive for Blastocystis. No mixed subtype carriage was detected. All ten individuals with a typable ST before and after travel maintained their initial ST. The composition of the gut bacterial community was not significantly different between Blastocystis-carriers and non-carriers. Interestingly, the presence of Blastocystis was accompanied with higher abundances of the bacterial genera Sporolactobacillus and Candidatus Carsonella. Blastocystis carriage was positively associated with high bacterial genus richness, and negatively correlated to the Bacteroides-driven enterotype. These associations were both largely dependent on ST4 - a subtype commonly described from Europe - while the globally prevalent ST3 did not show such significant relationships.

CONCLUSIONS: The high rate of Blastocystis subtype persistence found during travel indicates that long-term carriage of Blastocystis is common. The associations between Blastocystis and the bacterial microbiota found in this study could imply a link between Blastocystis and a healthy microbiota as well as with diets high in vegetables. Whether the associations between Blastocystis and the microbiota are resulting from the presence of Blastocystis, or are a prerequisite for colonization with Blastocystis, are interesting questions for further studies.}, } @article {pmid29228244, year = {2018}, author = {Cleary, DFR and Polónia, ARM and de Voogd, NJ}, title = {Prokaryote composition and predicted metagenomic content of two Cinachyrella Morphospecies and water from West Papuan Marine Lakes.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {2}, pages = {}, doi = {10.1093/femsec/fix175}, pmid = {29228244}, issn = {1574-6941}, mesh = {Animals ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Biodiversity ; Indonesia ; Lakes/microbiology ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; Porifera/genetics/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Certain sponge species are difficult to identify using classical taxonomic characters, and other techniques are often necessary. Here we used 454-pyrosequencing of the 16S rRNA gene to investigate bacterial and archaeal communities of two distinct Cinachyrella morphospecies collected from two Indonesian marine lakes with differing degrees of connection to the surrounding sea. Our main goal was to assess whether these morphospecies hosted distinct bacterial and archaeal communities and to what extent these differed from those found in lake water. A recently developed bioinformatic tool (PICRUSt) was used to predict metagenomic gene content of the studied communities. Compositionally, sponge samples clustered according to morphospecies as opposed to marine lake indicating that each morphospecies hosted distinct bacterial and archaeal communities. There were, however, also differences in higher taxon abundance among lakes. In the less connected lake, for example, both Cinachyrella morphospecies had higher levels of the order Synechococcales. With respect to metabolic gene content, although there were pronounced differences in predicted enrichment between both morphospecies, both were putatively enriched for KOs involved in pathways related to stress response, energy metabolism, environmental information processing and the production of secondary metabolites compared to prokaryote communities in water. These morphospecies may thus prove to be interesting sources of novel compounds of potential pharmaceutical and/or biotechnological importance.}, } @article {pmid29227468, year = {2018}, author = {Beaulaurier, J and Zhu, S and Deikus, G and Mogno, I and Zhang, XS and Davis-Richardson, A and Canepa, R and Triplett, EW and Faith, JJ and Sebra, R and Schadt, EE and Fang, G}, title = {Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.}, journal = {Nature biotechnology}, volume = {36}, number = {1}, pages = {61-69}, pmid = {29227468}, issn = {1546-1696}, support = {R01 GM114472/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/genetics ; Cluster Analysis ; DNA Methylation/*genetics ; Environmental Microbiology ; Genome, Bacterial/genetics ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; Plasmids/genetics ; Sequence Analysis, DNA ; }, abstract = {Shotgun metagenomics methods enable characterization of microbial communities in human microbiome and environmental samples. Assembly of metagenome sequences does not output whole genomes, so computational binning methods have been developed to cluster sequences into genome 'bins'. These methods exploit sequence composition, species abundance, or chromosome organization but cannot fully distinguish closely related species and strains. We present a binning method that incorporates bacterial DNA methylation signatures, which are detected using single-molecule real-time sequencing. Our method takes advantage of these endogenous epigenetic barcodes to resolve individual reads and assembled contigs into species- and strain-level bins. We validate our method using synthetic and real microbiome sequences. In addition to genome binning, we show that our method links plasmids and other mobile genetic elements to their host species in a real microbiome sample. Incorporation of DNA methylation information into shotgun metagenomics analyses will complement existing methods to enable more accurate sequence binning.}, } @article {pmid29225146, year = {2018}, author = {Hahn, A and Warnken, S and Pérez-Losada, M and Freishtat, RJ and Crandall, KA}, title = {Microbial diversity within the airway microbiome in chronic pediatric lung diseases.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {63}, number = {}, pages = {316-325}, pmid = {29225146}, issn = {1567-7257}, support = {K12 HL119994/HL/NHLBI NIH HHS/United States ; KL2 TR001877/TR/NCATS NIH HHS/United States ; R01 AI127507/AI/NIAID NIH HHS/United States ; UL1 TR001876/TR/NCATS NIH HHS/United States ; }, mesh = {Asthma/*microbiology/pathology ; Bacteria/classification/*genetics/isolation & purification ; Biodiversity ; Child ; Cystic Fibrosis/*microbiology/pathology ; Humans ; Infant, Newborn ; Lung/microbiology/pathology ; *Metagenome ; Metagenomics/methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Respiratory Distress Syndrome, Newborn/*microbiology/pathology ; Severity of Illness Index ; Sputum/microbiology ; }, abstract = {The study of the airway microbiome in children is an area of emerging research, especially in relation to the role microbial diversity may play in acute and chronic inflammation. Three such pediatric airway diseases include cystic fibrosis, asthma, and chronic lung disease of prematurity. In cystic fibrosis, the presence of Pseudomonas spp. is associated with decreased microbial diversity. Decreasing microbial diversity is also associated with poor lung function. In asthma, early viral infections appear to drive changes in bacterial diversity which may be associated with asthma risk. Premature infants with Ureaplasma spp. are at higher risk for chronic lung disease due to inflammation. Microbiome changes due to prematurity also appear to affect the inflammatory response to viral infections post-natally. Importantly, microbial diversity can be measured using metataxonomic (e.g., 16S rRNA sequencing) and metagenomic (e.g., shotgun sequencing) approaches. A metagenomics approach may be preferable as it can provide further granularity of the sample composition, identifying the bacterial species or strain, information on additional microbial components, including fungal and viral components, information about functional genomics of the microbiome, and information about antimicrobial resistance mutations. Future studies of pediatric airway diseases incorporating these techniques may provide evidence for new treatment approaches for these vulnerable patient populations.}, } @article {pmid29223543, year = {2018}, author = {Cowart, DA and Murphy, KR and Cheng, CC}, title = {Metagenomic sequencing of environmental DNA reveals marine faunal assemblages from the West Antarctic Peninsula.}, journal = {Marine genomics}, volume = {37}, number = {}, pages = {148-160}, doi = {10.1016/j.margen.2017.11.003}, pmid = {29223543}, issn = {1876-7478}, mesh = {Animals ; Antarctic Regions ; Aquatic Organisms ; *Biodiversity ; DNA/*analysis ; High-Throughput Nucleotide Sequencing/methods ; *Invertebrates ; *Metagenome ; Metagenomics/*methods ; *Vertebrates ; }, abstract = {The West Antarctic Peninsula (WAP) is the fastest warming region in Antarctica where climate impact on the cold-adapted marine ecosystem is already visible. To monitor faunal changes in remote vast bodies of Antarctic waters, efficient and informative tools are essential. High-throughput sequencing of environmental DNA (eDNA) has emerged as one such tool for monitoring biodiversity and ecosystems, as it increases detection sensitivity of taxa, and sampling is often simpler and less costly than traditional collection methods. We collected water samples from four WAP shallow (≤300m) shelf regions, recovered the eDNA therein, and performed metagenomic shotgun sequencing and analyses to determine the effectiveness of this method to assess marine benthic faunal diversity; this includes the detection of deep-water predatory king crabs whose potential shoreward expansion to warming shelves has sparked much concern. Using a customized bioinformatics pipeline, we identified abundant signatures of common benthic invertebrate fauna, endemic notothenioid fishes, as well as lithodid king crabs. We also uncovered species richness and diversity comparable to biological inventories compiled by the use of traditional survey methods, supporting the efficacy of the eDNA shotgun sequencing approach. As the rate of eDNA degradation affects faunal detection sensitivity, we also quantified mitochondrial ND2 gene copies in eDNA derived from a WAP icefish and found ND2 copies persisted to at least 20days in the cold WAP water, much longer than values reported for temperate environments. We propose that eDNA metagenomic sequencing complements traditional sampling, and combining both will enable more inclusive biodiversity detection and faunal change monitoring in the vast Southern Ocean.}, } @article {pmid29222756, year = {2018}, author = {Ye, C and Xu, N and Chen, X and Liu, L}, title = {Metabolic Model Reconstruction and Analysis of an Artificial Microbial Ecosystem.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1716}, number = {}, pages = {219-238}, doi = {10.1007/978-1-4939-7528-0_10}, pmid = {29222756}, issn = {1940-6029}, mesh = {Algorithms ; Metabolomics/*methods ; Metagenomics ; Microbial Consortia ; *Models, Biological ; Phylogeny ; }, abstract = {Microbial communities are widespread in the environment, and to isolate and identify species or to determine relations among microorganisms, some 'omics methods like metagenomics, proteomics, and metabolomics have been used. When combined with various 'omics data, models known as artificial microbial ecosystems (AME) are powerful methods that can make functional predictions about microbial communities. Reconstruction of an AME model is the first step for model analysis. Many techniques have been applied to the construction of AME models, e.g., the compartmentalization approach, community objectives method, and dynamic analysis approach. Of these approaches, species compartmentalization is the most relevant to genetics. Besides, some algorithms have been developed for the analysis of AME models. In this chapter, we present a general protocol for the use of the species compartmentalization method to reconstruct a model of microbial communities. Then, the analysis of an AME is discussed.}, } @article {pmid29216488, year = {2018}, author = {Lee, DW and Lee, H and Lee, AH and Kwon, BO and Khim, JS and Yim, UH and Kim, BS and Kim, JJ}, title = {Microbial community composition and PAHs removal potential of indigenous bacteria in oil contaminated sediment of Taean coast, Korea.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {234}, number = {}, pages = {503-512}, doi = {10.1016/j.envpol.2017.11.097}, pmid = {29216488}, issn = {1873-6424}, mesh = {Bacteria/classification/*drug effects/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Biodiversity ; Dioxygenases/genetics/metabolism ; Geologic Sediments/analysis/*microbiology ; Multienzyme Complexes/genetics/metabolism ; Petroleum/analysis ; Petroleum Pollution/analysis ; Polycyclic Aromatic Hydrocarbons/*chemistry ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; }, abstract = {The tidal flats near Sinduri beach in Taean, Korea, have been severely contaminated by heavy crude oils due to the Korea's worst oil spill accident, say the Hebei Spirit Oil Spill, in 2007. Crude oil compounds, including polycyclic aromatic hydrocarbons (PAHs), pose significant environmental damages due to their wide distribution, persistence, high toxicity, mutagenicity, and carcinogenicity. Microbial community of Sinduri beach sediments samples was analyzed by metagenomic data with 16S rRNA gene amplicons. Three phyla (Proteobacteria, Firmicutes, and Bacteroidetes) accounted for approximately ≥93.0% of the total phyla based on metagenomic analysis. Proteobacteria was the dominant phylum in Sinduri beach sediments. Cultivable bacteria were isolated from PAH-enriched cultures, and bacterial diversity was investigated through performing culture characterization followed by molecular biology methods. Sixty-seven isolates were obtained, comprising representatives of Actinobacteria, Firmicutes, α- and γ-Proteobacteria, and Bacteroidetes. PAH catabolism genes, such as naphthalene dioxygenase (NDO) and aromatic ring hydroxylating dioxygenase (ARHDO), were used as genetic markers to assess biodegradation of PAHs in the cultivable bacteria. The ability to degrade PAHs was demonstrated by monitoring the removal of PAHs using a gas chromatography mass spectrometer. Overall, various PAH-degrading bacteria were widely present in Sinduri beach sediments and generally reflected the restored microbial community. Among them, Cobetia marina, Rhodococcus soli, and Pseudoalteromonas agarivorans were found to be significant in degradation of PAHs. This large collection of PAH-degrading strains represents a valuable resource for studies investigating mechanisms of PAH degradation and bioremediation in oil contaminated coastal environment, elsewhere.}, } @article {pmid29214491, year = {2017}, author = {Lee, KC and Kil, DY and Sul, WJ}, title = {Cecal microbiome divergence of broiler chickens by sex and body weight.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {55}, number = {12}, pages = {939-945}, pmid = {29214491}, issn = {1976-3794}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; Body Weight ; Cecum/*microbiology ; Chickens/*growth & development/microbiology ; DNA, Bacterial/genetics ; Female ; *Gastrointestinal Microbiome ; Male ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {The divergence of gut bacterial community on broiler chickens has been reported as potentially possible keys to enhancing nutrient absorption, immune systems, and increasing poultry health and performance. Thus, we compared cecal bacterial communities and functional predictions by sex and body weight regarding the association between cecal microbiota and chicken growth performance. In this study, a total of 12 male and 12 female 1-day-old broiler chickens were raised for 35 days in 2 separate cages. Chickens were divided into 3 subgroups depending on body weight (low, medium, and high) by each sex. We compared chicken cecal microbiota compositions and its predictive functions by sex and body weight difference. We found that bacterial 16S rRNA genes were classified as 3 major phyla (Bacteroidetes, Firmicutes, and Proteobacteria), accounting for > 98% of the total bacterial community. The profiling of different bacterial taxa and predictive metagenome functions derived from 16S rRNA genes were performed over chicken sex and bodyweight. Male chickens were related to the enrichment of Bacteroides while female chickens were to the enrichment of Clostridium and Shigella. Male chickens with high body weight were associated with the enrichment of Faecalibacterium and Shuttleworthia. Carbohydrate and lipid metabolisms were suggested as candidate functions for weight gain in the males. This suggests that the variation of cecal bacterial communities and their functions by sex and body weight may be associated with the differences in the growth potentials of broiler chickens.}, } @article {pmid29211828, year = {2018}, author = {Orakov, AN and Sakenova, NK and Sorokin, A and Goryanin, II}, title = {ASAR: visual analysis of metagenomes in R.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {8}, pages = {1404-1405}, pmid = {29211828}, issn = {1367-4811}, mesh = {Metagenomics/*methods ; Microbiota/*genetics ; *Software ; }, abstract = {MOTIVATION: Functional and taxonomic analyses are critical steps in understanding interspecific interactions within microbial communities. Currently, such analyses are run separately, which complicates interpretation of results. Here we present the ASAR interactive tool for simultaneous analysis of metagenomic data in three dimensions: taxonomy, function, metagenome.

RESULTS: An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is available.

Source code of the ASAR is accessible at GitHub (https://github.com/Askarbek-orakov/ASAR).

CONTACT: askarbek.orakov@nu.edu.kz or goryanin@gmail.com.}, } @article {pmid29211769, year = {2017}, author = {Dong, X and Shulzhenko, N and Lemaitre, J and Greer, RL and Peremyslova, K and Quamruzzaman, Q and Rahman, M and Hasan, OS and Joya, SA and Golam, M and Christiani, DC and Morgun, A and Kile, ML}, title = {Arsenic exposure and intestinal microbiota in children from Sirajdikhan, Bangladesh.}, journal = {PloS one}, volume = {12}, number = {12}, pages = {e0188487}, pmid = {29211769}, issn = {1932-6203}, support = {K01 ES017800/ES/NIEHS NIH HHS/United States ; P30 ES000210/ES/NIEHS NIH HHS/United States ; R01 ES015533/ES/NIEHS NIH HHS/United States ; R01 ES023441/ES/NIEHS NIH HHS/United States ; }, mesh = {Arsenic/*toxicity ; Bangladesh ; Child, Preschool ; Drinking Water/*chemistry ; Drug Resistance, Microbial ; *Environmental Exposure ; Female ; Humans ; Intestines/*microbiology ; Male ; Microbiota/*drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; Water Pollutants, Chemical/*toxicity ; }, abstract = {BACKGROUND: Arsenic has antimicrobial properties at high doses yet few studies have examined its effect on gut microbiota. This warrants investigation since arsenic exposure increases the risk of many diseases in which gut microbiota have been shown to play a role. We examined the association between arsenic exposure from drinking water and the composition of intestinal microbiota in children exposed to low and high arsenic levels during prenatal development and early life.

RESULTS: 16S rRNA gene sequencing revealed that children with high arsenic exposure had a higher abundance of Proteobacteria in their stool compared to matched controls with low arsenic exposure. Furthermore, whole metagenome shotgun sequencing identified 332 bacterial SEED functions that were enriched in the high exposure group. A separate model showed that these genes, which included genes involved in virulence and multidrug resistance, were positively correlated with arsenic concentration within the group of children in the high arsenic group. We performed reference free genome assembly, and identified strains of E.coli as contributors to the arsenic enriched SEED functions. Further genome annotation of the E.coli genome revealed two strains containing two different arsenic resistance operons that are not present in the gut microbiome of a recently described European human cohort (Metagenomics of the Human Intestinal Tract, MetaHIT). We then performed quantification by qPCR of two arsenic resistant genes (ArsB, ArsC). We observed that the expression of these two operons was higher among the children with high arsenic exposure compared to matched controls.

CONCLUSIONS: This preliminary study indicates that arsenic exposure early in life was associated with altered gut microbiota in Bangladeshi children. The enrichment of E.coli arsenic resistance genes in the high exposure group provides an insight into the possible mechanisms of how this toxic compound could affect gut microbiota.}, } @article {pmid29208946, year = {2018}, author = {Mehrshad, M and Rodriguez-Valera, F and Amoozegar, MA and López-García, P and Ghai, R}, title = {The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling.}, journal = {The ISME journal}, volume = {12}, number = {3}, pages = {655-668}, pmid = {29208946}, issn = {1751-7370}, support = {322669/ERC_/European Research Council/International ; }, mesh = {Chloroflexi/classification/genetics/*isolation & purification/*metabolism ; Genomics ; Metagenome ; Metagenomics ; Microbiota ; Oceans and Seas ; Phylogeny ; Seawater/*microbiology ; Sulfur/*metabolism ; }, abstract = {The dark ocean microbiota represents the unknown majority in the global ocean waters. The SAR202 cluster belonging to the phylum Chloroflexi was the first microbial lineage discovered to specifically inhabit the aphotic realm, where they are abundant and globally distributed. The absence of SAR202 cultured representatives is a significant bottleneck towards understanding their metabolic capacities and role in the marine environment. In this work, we use a combination of metagenome-assembled genomes from deep-sea datasets and publicly available single-cell genomes to construct a genomic perspective of SAR202 phylogeny, metabolism and biogeography. Our results suggest that SAR202 cluster members are medium sized, free-living cells with a heterotrophic lifestyle, broadly divided into two distinct clades. We present the first evidence of vertical stratification of these microbes along the meso- and bathypelagic ocean layers. Remarkably, two distinct species of SAR202 cluster are highly abundant in nearly all deep bathypelagic metagenomic datasets available so far. SAR202 members metabolize multiple organosulfur compounds, many appear to be sulfite-oxidizers and are predicted to play a major role in sulfur turnover in the dark water column. This concomitantly suggests an unsuspected availability of these nutrient sources to allow for the high abundance of these microbes in the deep sea.}, } @article {pmid29205917, year = {2018}, author = {Stolze, Y and Bremges, A and Maus, I and Pühler, A and Sczyrba, A and Schlüter, A}, title = {Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants.}, journal = {Microbial biotechnology}, volume = {11}, number = {4}, pages = {667-679}, pmid = {29205917}, issn = {1751-7915}, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; Biofuels/*analysis ; Bioreactors/*microbiology ; Gases/*metabolism ; Methane/*metabolism ; Microbial Consortia ; Phylogeny ; }, abstract = {Biogas production is performed anaerobically by complex microbial communities with key species driving the process. Hence, analyses of their in situ activities are crucial to understand the process. In a previous study, metagenome sequencing and subsequent genome binning for different production-scale biogas plants (BGPs) resulted in four genome bins of special interest, assigned to the phyla Thermotogae, Fusobacteria, Spirochaetes and Cloacimonetes, respectively, that were genetically analysed. In this study, metatranscriptome sequencing of the same BGP samples was conducted, enabling in situ transcriptional activity determination of these genome bins. For this, mapping of metatranscriptome reads on genome bin sequences was performed providing transcripts per million (TPM) values for each gene. This approach revealed an active sugar-based metabolism of the Thermotogae and Spirochaetes bins and an active amino acid-based metabolism of the Fusobacteria and Cloacimonetes bins. The data also hint at syntrophic associations of the four corresponding species with methanogenic Archaea.}, } @article {pmid29205750, year = {2018}, author = {Fortunato, CS and Larson, B and Butterfield, DA and Huber, JA}, title = {Spatially distinct, temporally stable microbial populations mediate biogeochemical cycling at and below the seafloor in hydrothermal vent fluids.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {769-784}, doi = {10.1111/1462-2920.14011}, pmid = {29205750}, issn = {1462-2920}, mesh = {Archaea/*genetics/isolation & purification/*metabolism ; Bacteria/*genetics/isolation & purification/*metabolism ; Carbon/metabolism ; Chemoautotrophic Growth/*genetics ; Geologic Sediments/*microbiology ; Hydrogen/metabolism ; Hydrothermal Vents/*microbiology ; Metagenomics ; Microbiota/genetics ; Nitrogen/metabolism ; Pacific Ocean ; Phylogeny ; Population Dynamics ; Seawater/chemistry/microbiology ; Sulfur/metabolism ; }, abstract = {At deep-sea hydrothermal vents, microbial communities thrive across geochemical gradients above, at, and below the seafloor. In this study, we determined the gene content and transcription patterns of microbial communities and specific populations to understand the taxonomy and metabolism both spatially and temporally across geochemically different diffuse fluid hydrothermal vents. Vent fluids were examined via metagenomic, metatranscriptomic, genomic binning, and geochemical analyses from Axial Seamount, an active submarine volcano on the Juan de Fuca Ridge in the NE Pacific Ocean, from 2013 to 2015 at three different vents: Anemone, Marker 33, and Marker 113. Results showed that individual vent sites maintained microbial communities and specific populations over time, but with spatially distinct taxonomic, metabolic potential, and gene transcription profiles. The geochemistry and physical structure of each vent both played important roles in shaping the dominant organisms and metabolisms present at each site. Genomic binning identified key populations of SUP05, Aquificales and methanogenic archaea carrying out important transformations of carbon, sulfur, hydrogen, and nitrogen, with groups that appear unique to individual sites. This work highlights the connection between microbial metabolic processes, fluid chemistry, and microbial population dynamics at and below the seafloor and increases understanding of the role of hydrothermal vent microbial communities in deep ocean biogeochemical cycles.}, } @article {pmid29204058, year = {2017}, author = {Long, CX and He, L and Guo, YF and Liu, YW and Xiao, NQ and Tan, ZJ}, title = {Diversity of bacterial lactase genes in intestinal contents of mice with antibiotics-induced diarrhea.}, journal = {World journal of gastroenterology}, volume = {23}, number = {42}, pages = {7584-7593}, pmid = {29204058}, issn = {2219-2840}, mesh = {Animals ; Anti-Bacterial Agents/*adverse effects ; Diarrhea/*chemically induced/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; *Genes, Bacterial ; Lactase/genetics/*metabolism ; Male ; Mice ; Random Allocation ; }, abstract = {AIM: To investigate the diversity of bacterial lactase genes in the intestinal contents of mice with antibiotics-induced diarrhea.

METHODS: Following 2 d of adaptive feeding, 12 specific pathogen-free Kunming mice were randomly divided into the control group and model group. The mouse model of antibiotics-induced diarrhea was established by gastric perfusion with mixed antibiotics (23.33 mL·kg[-1]·d[-1]) composed of gentamicin sulfate and cephradine capsules administered for 5 days, and the control group was treated with an equal amount of sterile water. Contents of the jejunum and ileum were then collected and metagenomic DNA was extracted, after which analysis of bacterial lactase genes using operational taxonomic units (OTUs) was carried out after amplification and sequencing.

RESULTS: OTUs were 871 and 963 in the model group and control group, respectively, and 690 of these were identical. There were significant differences in Chao1 and ACE indices between the two groups (P < 0.05). Principal component analysis, principal coordination analysis and nonmetric multidimensional scaling analyses showed that OTUs distribution in the control group was relatively intensive, and differences among individuals were small, while in the model group, they were widely dispersed and more diversified. Bacterial lactase genes from the intestinal contents of the control group were related to Proteobacteria, Actinobacteria, Firmicutes and unclassified bacteria. Of these, Proteobacteria was the most abundant phylum. In contrast, the bacterial population was less diverse and abundant in the model group, as the abundance of Bradyrhizobium sp. BTAi1, Agrobacterium sp. H13-3, Acidovorax sp. KKS102, Azoarcus sp. KH32C and Aeromonas caviae was lower than that in the control group. In addition, of the known species, the control group and model group had their own unique genera, respectively.

CONCLUSION: Antibiotics reduce the diversity of bacterial lactase genes in the intestinal contents, decrease the abundance of lactase gene, change the lactase gene strains, and transform their structures.}, } @article {pmid29198875, year = {2018}, author = {Yu, J and Guo, J and Tao, W and Liu, P and Shang, E and Zhu, Z and Fan, X and Shen, J and Hua, Y and Zhu, KY and Tang, Y and Duan, JA}, title = {Gancao-Gansui combination impacts gut microbiota diversity and related metabolic functions.}, journal = {Journal of ethnopharmacology}, volume = {214}, number = {}, pages = {71-82}, doi = {10.1016/j.jep.2017.11.031}, pmid = {29198875}, issn = {1872-7573}, mesh = {Animals ; Bacteria/classification/*drug effects/genetics/metabolism ; Biomarkers/blood ; Drugs, Chinese Herbal/*toxicity ; Dysbiosis ; Feces/chemistry/microbiology ; Gas Chromatography-Mass Spectrometry ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Regulation, Bacterial ; Genome, Bacterial ; Intestinal Mucosa/metabolism ; Intestines/*drug effects/microbiology ; Lipid Metabolism/drug effects ; Male ; Metabolomics/methods ; Metagenome ; Mice, Inbred ICR ; Ribotyping ; Risk Assessment ; }, abstract = {The theory of "eighteen incompatible medicaments" (EIM) in traditional Chinese medicine (TCM) is the most representative case of herbal-herbal interactions. Gancao and Gansui are one of the incompatible herbal pairs in EIM. Gancao, also known as "licorice", is the most frequently used Chinese herb or food additive. Gansui, the root of Euphorbia kansui T.P. Wang, is another famous Chinese herb usually used to treat edema, ascites and asthma but could induce gastrointestinal (GI) tract irritation. Although Gancao and Gansui are incompatible herbal pairs, they are still used in combination in the famous "Gansui-Banxia" decoction.

AIM OF THE STUDY: This study was conducted to investigate if Gancao-Gansui combination could exacerbate Gansui induced GI tract injury. Moreover, the impact of Gancao-Gansui combination to gut microbiota and related metabolism pathways were evaluated.

MATERIALS AND METHODS: Normal mice were divided into different groups and treated with Gancao extracts, Gansui extracts, and Gancao-Gansui combination extracts for 7 days. Serum biomarkers (diamine oxidase activity, lipopolysaccharide, motilin, IL-1β, IL-6, TNF-α) were determined to reflect GI tract damage. Gut microbiota diversity was studied by 16S rDNA sequencing and metagenomes analysis were also conducted to reflect functional genes expression alteration. Fecal hydrogen sulfide concentrations were measured by spectrophotometry to confirm the alteration of Desulfovibrio genus. Fecal lipid metabolomics study was conducted by GC-MS analysis to confirm the change of metagenomes and Mycoplasma abundance.

RESULTS: Gancao-Gansui combination did not exacerbate GI tract tissue or functional damage but caused gut microbiota dysbiosis and increased some rare genus's abundance including Desulfovibrio and Mycoplasma. Desulfovibrio genus proliferation was confirmed by the disturbance of fecal hydrogen sulfide homeostasis. Gancao-Gansui combination also dys-regulated the metabolic genes in metagenomes. Mycoplasma genus proliferation and the metagenomes changes were both confirmed by metabolic profile analysis of fecal lipids, especially cholesterol.

CONCLUSIONS: Gancao-Gansui combination can impact the gut microbiota diversity and related metabolic functions. Further studies should be carried out when the combination of Gancao-Gansui is used in herbal formulations as this may alter the diversity of the microbiota.}, } @article {pmid29197774, year = {2018}, author = {Ruiz-Sánchez, J and Campanaro, S and Guivernau, M and Fernández, B and Prenafeta-Boldú, FX}, title = {Effect of ammonia on the active microbiome and metagenome from stable full-scale digesters.}, journal = {Bioresource technology}, volume = {250}, number = {}, pages = {513-522}, doi = {10.1016/j.biortech.2017.11.068}, pmid = {29197774}, issn = {1873-2976}, mesh = {*Ammonia ; Anaerobiosis ; *Bioreactors ; Metagenome ; Methane ; *Microbiota ; }, abstract = {Four full-scale anaerobic digesters with a long history of stable operation were characterized in terms of active microbiome and metagenome. Isotopic fractionation of biogas demonstrated that acetotrophy was rather prevalent in reactors operated at <3 gTAN L[-1] while hydrogenotrophy was predominant at >6 gTAN L[-1], suggesting that syntrophic acetate oxidizing bacteria (SAOB) played a significant role in the latter. These results were generally coherent with the observed active bacterial and archaeal communities but no known SAOB were observed. Metagenome descriptions yielded 73 assembled population genomes, of which only 7 could be assigned at the species level. Gene annotation and association to relevant metabolic pathways indicated that the phyla Chloroflexi and Bacteroidales might encompass new, currently undescribed, SAOB/formate producing species that would metabolize acetate via the glycine cleavage system. The predominant hydrogenotrophic counterpart at a high ammonia content belonged to the genus Methanoculleus, which could also grow on acetate to a certain extent.}, } @article {pmid29197424, year = {2017}, author = {Cheng, K and Ning, Z and Zhang, X and Li, L and Liao, B and Mayne, J and Stintzi, A and Figeys, D}, title = {MetaLab: an automated pipeline for metaproteomic data analysis.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {157}, pmid = {29197424}, issn = {2049-2618}, support = {217066//Natural Sciences and Engineering Research Council of Canada/ ; 9408//Genome Canada/Ontario Genomics/ ; }, mesh = {*Computational Biology ; Databases, Protein ; Gastrointestinal Microbiome ; *Metagenomics ; Microbiota ; *Proteomics ; *Software ; Statistics as Topic ; }, abstract = {BACKGROUND: Research involving microbial ecosystems has drawn increasing attention in recent years. Studying microbe-microbe, host-microbe, and environment-microbe interactions are essential for the understanding of microbial ecosystems. Currently, metaproteomics provide qualitative and quantitative information of proteins, providing insights into the functional changes of microbial communities. However, computational analysis of large-scale data generated in metaproteomic studies remains a challenge. Conventional proteomic software have difficulties dealing with the extreme complexity and species diversity present in microbiome samples leading to lower rates of peptide and protein identification. To address this issue, we previously developed the MetaPro-IQ approach for highly efficient microbial protein/peptide identification and quantification.

RESULT: Here, we developed an integrated software platform, named MetaLab, providing a complete and automated, user-friendly pipeline for fast microbial protein identification, quantification, as well as taxonomic profiling, directly from mass spectrometry raw data. Spectral clustering adopted in the pre-processing step dramatically improved the speed of peptide identification from database searches. Quantitative information of identified peptides was used for estimating the relative abundance of taxa at all phylogenetic ranks. Taxonomy result files exported by MetaLab are fully compatible with widely used metagenomics tools. Herein, the potential of MetaLab is evaluated by reanalyzing a metaproteomic dataset from mouse gut microbiome samples.

CONCLUSION: MetaLab is a fully automatic software platform enabling an integrated data-processing pipeline for metaproteomics. The function of sample-specific database generation can be very advantageous for searching peptides against huge protein databases. It provides a seamless connection between peptide determination and taxonomic profiling; therefore, the peptide abundance is readily used for measuring the microbial variations. MetaLab is designed as a versatile, efficient, and easy-to-use tool which can greatly simplify the procedure of metaproteomic data analysis for researchers in microbiome studies.}, } @article {pmid29196767, year = {2017}, author = {Wen, X and Miao, L and Deng, Y and Bible, PW and Hu, X and Zou, Y and Liu, Y and Guo, S and Liang, J and Chen, T and Peng, GH and Chen, W and Liang, L and Wei, L}, title = {The Influence of Age and Sex on Ocular Surface Microbiota in Healthy Adults.}, journal = {Investigative ophthalmology & visual science}, volume = {58}, number = {14}, pages = {6030-6037}, doi = {10.1167/iovs.17-22957}, pmid = {29196767}, issn = {1552-5783}, mesh = {Adult ; Age Factors ; Aged ; Aged, 80 and over ; Bacteria/*genetics/isolation & purification ; Conjunctiva/*microbiology ; DNA, Bacterial/*analysis ; Eye Infections, Bacterial/immunology/*microbiology ; Female ; Healthy Volunteers ; Humans ; *Immunity, Innate ; Male ; *Microbiota ; Middle Aged ; Sequence Analysis, DNA ; Sex Factors ; Young Adult ; }, abstract = {PURPOSE: A growing body of evidence suggests that the microbiome of the ocular surface confers potent immunoregulatory functions and has a key role in the physiologic maintenance of healthy eyes and in the pathogenesis of ocular diseases. Although the microbiome is known to be affected by age and sex, the influence of these factors on ocular surface microbiota in healthy adults remains largely unknown.

METHODS: Ocular surface microbiome samples were obtained from the inferior bulbar conjunctiva of 48 young and 42 old adults at Zhongshan Ophthalmic Center. Using metagenomic shotgun sequencing, we characterized the sex- and age-differences in conjunctival microbiome profiles of healthy adults.

RESULTS: Male and female groups differed only in the β diversity of bacterial communities, while there were significant differences in bacterial composition, metabolic functions, and the abundance of antibiotic resistance genes between young and old adult groups.

CONCLUSIONS: Our findings suggest that age and sex collectively shape the conjunctival microbiome, and may change the immune homeostasis of the ocular surface through alterations of its commensal microbiome.}, } @article {pmid29196717, year = {2017}, author = {Hamad, I and Ranque, S and Azhar, EI and Yasir, M and Jiman-Fatani, AA and Tissot-Dupont, H and Raoult, D and Bittar, F}, title = {Culturomics and Amplicon-based Metagenomic Approaches for the Study of Fungal Population in Human Gut Microbiota.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {16788}, pmid = {29196717}, issn = {2045-2322}, mesh = {Ascomycota/classification/genetics/isolation & purification ; Basidiomycota/classification/genetics/isolation & purification ; Case-Control Studies ; DNA, Fungal/analysis ; DNA, Ribosomal Spacer/*analysis ; Feces/microbiology ; Fungi/*classification/genetics/isolation & purification ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiological Techniques ; Mycobiome ; Mycoses/*microbiology ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Herein, the mycobiota was characterized in fecal samples from sick patients and healthy subjects, collected from different geographical locations and using both culturomics and amplicon-based metagenomics approaches. Using the culturomics approach, a total of 17,800 fungal colonies were isolated from 14 fecal samples, and resulted in the isolation of 41 fungal species, of which 10 species had not been previously reported in the human gut. Deep sequencing of fungal-directed ITS1 and ITS2 amplicons led to the detection of a total of 142 OTUs and 173 OTUs from the ITS1 and ITS2 regions, respectively. Ascomycota composed the largest fraction of the total OTUs analyzed (78.9% and 68.2% of the OTUs from the ITS1 and ITS2 regions, respectively), followed by Basidiomycota (16.9% and 30.1% of the OTUs from the ITS1 and ITS2 regions, respectively). Interestingly, the results demonstrate that the ITS1/ITS2 amplicon sequencing provides different information about gut fungal communities compared to culturomics, though both approaches complete each other in assessing fungal diversity in fecal samples. We also report higher fungal diversity and abundance in patients compared to healthy subjects. In conclusion, combining both culturomic and amplicon-based metagenomic approaches may be a novel strategy towards analyzing fungal compositions in the human gut.}, } @article {pmid29196415, year = {2017}, author = {Peters, BA and Wu, J and Pei, Z and Yang, L and Purdue, MP and Freedman, ND and Jacobs, EJ and Gapstur, SM and Hayes, RB and Ahn, J}, title = {Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers.}, journal = {Cancer research}, volume = {77}, number = {23}, pages = {6777-6787}, pmid = {29196415}, issn = {1538-7445}, support = {R01 CA159036/CA/NCI NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; R21 CA183887/CA/NCI NIH HHS/United States ; R03 CA159414/CA/NCI NIH HHS/United States ; U01 CA182370/CA/NCI NIH HHS/United States ; R01 CA164964/CA/NCI NIH HHS/United States ; }, mesh = {Adenocarcinoma/epidemiology/*microbiology ; Aged ; Carcinoma, Squamous Cell/epidemiology/*microbiology ; Case-Control Studies ; Esophageal Neoplasms/epidemiology/*microbiology ; Esophageal Squamous Cell Carcinoma ; Female ; Humans ; Male ; Microbiota/*genetics ; Middle Aged ; Mouth/*microbiology ; Neisseria/classification/genetics/*isolation & purification ; Porphyromonas gingivalis/classification/genetics/*isolation & purification ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Streptococcus pneumoniae/classification/genetics/*isolation & purification ; Surveys and Questionnaires ; Tannerella forsythia/classification/genetics/*isolation & purification ; }, abstract = {Bacteria may play a role in esophageal adenocarcinoma (EAC) and esophageal squamous cell carcinoma (ESCC), although evidence is limited to cross-sectional studies. In this study, we examined the relationship of oral microbiota with EAC and ESCC risk in a prospective study nested in two cohorts. Oral bacteria were assessed using 16S rRNA gene sequencing in prediagnostic mouthwash samples from n = 81/160 EAC and n = 25/50 ESCC cases/matched controls. Findings were largely consistent across both cohorts. Metagenome content was predicted using PiCRUST. We examined associations between centered log-ratio transformed taxon or functional pathway abundances and risk using conditional logistic regression adjusting for BMI, smoking, and alcohol. We found the periodontal pathogen Tannerella forsythia to be associated with higher risk of EAC. Furthermore, we found that depletion of the commensal genus Neisseria and the species Streptococcus pneumoniae was associated with lower EAC risk. Bacterial biosynthesis of carotenoids was also associated with protection against EAC. Finally, the abundance of the periodontal pathogen Porphyromonas gingivalis trended with higher risk of ESCC. Overall, our findings have potential implications for the early detection and prevention of EAC and ESCC. Cancer Res; 77(23); 6777-87. ©2017 AACR.}, } @article {pmid29196353, year = {2017}, author = {Moffatt, MF and Cookson, WO}, title = {The lung microbiome in health and disease.}, journal = {Clinical medicine (London, England)}, volume = {17}, number = {6}, pages = {525-529}, pmid = {29196353}, issn = {1473-4893}, mesh = {Asthma/microbiology ; Bronchiectasis/microbiology ; Cystic Fibrosis/microbiology ; Humans ; Lung/*microbiology ; Lung Diseases/*microbiology ; Metagenomics ; *Microbiota/genetics ; Pulmonary Disease, Chronic Obstructive/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The Human Microbiome Project began 10 years ago, leading to a significant growth in understanding of the role the human microbiome plays in health and disease. In this article, we explain with an emphasis on the lung, the origins of microbiome research. We discuss how 16S rRNA gene sequencing became the first major molecular tool to examine the bacterial communities present within the human body. We highlight the pitfalls of molecular-based studies, such as false findings resulting from contamination, and the limitations of 16S rRNA gene sequencing. Knowledge about the lung microbiome has evolved from initial scepticism to the realisation that it might have a significant influence on many illnesses. We also discuss the lung microbiome in the context of disease by giving examples of important respiratory conditions. In addition, we draw attention to the challenges for metagenomic studies of respiratory samples and the importance of systematic bacterial isolation to enable host-microbiome interactions to be understood. We conclude by discussing how knowledge of the lung microbiome impacts current clinical diagnostics.}, } @article {pmid29196291, year = {2018}, author = {Ferrocino, I and Bellio, A and Giordano, M and Macori, G and Romano, A and Rantsiou, K and Decastelli, L and Cocolin, L}, title = {Shotgun Metagenomics and Volatilome Profile of the Microbiota of Fermented Sausages.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {3}, pages = {}, pmid = {29196291}, issn = {1098-5336}, mesh = {Acetic Acid/analysis/metabolism ; Acetoin/analysis/metabolism ; Animals ; Colony Count, Microbial ; Enterobacteriaceae/isolation & purification/metabolism ; Fermentation ; Fermented Foods/microbiology ; Food Microbiology ; Lactobacillus/isolation & purification/metabolism ; Meat Products/analysis/*microbiology ; Metabolic Networks and Pathways ; Metagenomics/methods ; Microbiota/*genetics/*physiology ; Odorants/analysis ; Staphylococcus/isolation & purification/metabolism ; Swine ; Volatile Organic Compounds/*analysis ; Volatilization ; }, abstract = {Changes in the microbial gene content and abundance can be analyzed to detect shifts in the microbiota composition due to the use of a starter culture in the food fermentation process, with the consequent shift of key metabolic pathways directly connected with product acceptance. Meat fermentation is a complex process involving microbes that metabolize the main components in meat. The breakdown of carbohydrates, proteins, and lipids can lead to the formation of volatile organic compounds (VOCs) that can drastically affect the organoleptic characteristics of the final products. The present meta-analysis, performed with the shotgun DNA metagenomic approach, focuses on studying the microbiota and its gene content in an Italian fermented sausage produced by using a commercial starter culture (a mix of Lactobacillus sakei and Staphylococcus xylosus), with the aim to discover the connections between the microbiota, microbiome, and the release of volatile metabolites during ripening. The inoculated fermentation with the starter culture limited the development of Enterobacteriaceae and reduced the microbial diversity compared to that from spontaneous fermentation. KEGG database genes associated with the reduction of acetaldehyde to ethanol (EC 1.1.1.1), acetyl phosphate to acetate (EC 2.7.2.1), and 2,3-butanediol to acetoin (EC 1.1.1.4) were most abundant in inoculated samples (I) compared to those in spontaneous fermentation samples (S). The volatilome profiles were highly consistent with the abundance of the genes; elevated acetic acid (1,173.85 μg/kg), ethyl acetate (251.58 μg/kg), and acetoin (1,100.19 μg/kg) were observed in the presence of the starters at the end of fermentation. Significant differences were found in the liking of samples based on flavor and odor, suggesting a higher preference by consumers for the spontaneous fermentation samples. Inoculated samples exhibited the lowest scores for the liking data, which were clearly associated with the highest concentration of acetic acid.IMPORTANCE We present an advance in the understanding of meat fermentation by coupling DNA sequencing metagenomics and metabolomics approaches to describe the microbial function during this process. Very few studies using this global approach have been dedicated to food, and none have examined sausage fermentation, underlying the originality of the study. The starter culture drastically affected the organoleptic properties of the products. This finding underlines the importance of starter culture selection that takes into consideration the functional characteristics of the microorganism to optimize production efficiency and product quality.}, } @article {pmid29195979, year = {2017}, author = {Lee, JJ and Kim, TY and Choi, SH and Kim, BS}, title = {Analysis of the bacterial microbiome in the small octopus, Octopus variabilis, from South Korea to detect the potential risk of foodborne illness and to improve product management.}, journal = {Food research international (Ottawa, Ont.)}, volume = {102}, number = {}, pages = {51-60}, doi = {10.1016/j.foodres.2017.09.084}, pmid = {29195979}, issn = {1873-7145}, mesh = {Animals ; Bacteroidetes/classification/genetics/*isolation & purification ; Food Microbiology/*methods ; Foodborne Diseases/*microbiology/prevention & control ; Humans ; *Microbiota ; Octopodiformes/*microbiology ; Proteobacteria/classification/genetics/*isolation & purification ; Republic of Korea ; Ribotyping ; Risk Assessment ; Risk Factors ; Seafood/adverse effects/*microbiology ; Seasons ; Temperature ; Vibrio vulnificus/genetics/*isolation & purification/pathogenicity ; Water Microbiology ; }, abstract = {The small octopus (Octopus variabilis) is a popular seafood in many countries including South Korea. Because it is often consumed uncooked, the microorganisms in it often cause food poisoning. Therefore, analyzing the microbiome of the small octopus can help to understand the risk of food poisoning and manage octopus products better. A total of 40 small octopuses were collected from four sites in November and August. The microbiota was analyzed using Illumina Miseq sequencing, and the amount of bacteria was quantified by real-time PCR. In addition, we analyzed the influence of Vibrio vulnificus infection on the microbiome of the small octopus through artificial infection experiments. Bacteroidetes was the predominant phylum in August, and Proteobacteria was predominant in November. The composition of the microbiota in octopus depended on sampling region and season. The potential risk of foodborne illness from small octopus consumption might be higher in August than in November due to the abundance of potential pathogens. In the infection experiment, the proportion of V. vulnificus increased only at 27°C. The composition and functional gene profiles of the microbiota varied in a similar manner between non-infected and infected samples over time at the same temperature. These results indicated that the indigenous microbiota in small octopus could inhibit colonization by V. vulnificus during storage. Although further studies are necessary to clarify these results, our results could help us better understand food poisoning through octopus ingestion and manage products.}, } @article {pmid29195140, year = {2018}, author = {Montassier, E and Berthelot, L and Soulillou, JP}, title = {Are the decrease in circulating anti-α1,3-Gal IgG and the lower content of galactosyl transferase A1 in the microbiota of patients with multiple sclerosis a novel environmental risk factor for the disease?.}, journal = {Molecular immunology}, volume = {93}, number = {}, pages = {162-165}, doi = {10.1016/j.molimm.2017.09.016}, pmid = {29195140}, issn = {1872-9142}, mesh = {Autoantibodies/*blood/immunology ; Bacterial Proteins/*analysis ; Environmental Exposure ; Environmental Microbiology ; Epitopes/analysis ; Galactosyltransferases/*analysis ; Gastrointestinal Microbiome/*immunology ; Genes, Bacterial ; Humans ; Immunoglobulin G/*blood/immunology ; Metagenome ; Models, Immunological ; Multiple Sclerosis, Relapsing-Remitting/blood/etiology/immunology/*microbiology ; Ribotyping ; Risk Factors ; }, abstract = {The etiology of multiple sclerosis (MS), particularly the environmental component of the disease, remains speculative. Recent reports have suggested that alterations in the gut microbiota of MS patients could contribute to the etiology or pathophysiology of the disease. In this Viewpoint, using PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) to infer the functional content of the gut microbiota, we show that the gut microbiota of MS patients is characterized by a significant decrease in the relative abundance of the enzyme EC 2.4.1.87, which corresponds to the GGTA1 gene (which codes for the α1,3-Gal epitope and is lacking in humans), against which MS patients also have low levels of IgG antibodies. The decrease in circulating anti-α1,3-Gal IgG and lower content of galactosyl transferase A1 in the microbiota of patients with multiple sclerosis could be a novel environmental risk factor for the disease.}, } @article {pmid29194980, year = {2018}, author = {Tanner, K and Martí, JM and Belliure, J and Fernández-Méndez, M and Molina-Menor, E and Peretó, J and Porcar, M}, title = {Polar solar panels: Arctic and Antarctic microbiomes display similar taxonomic profiles.}, journal = {Environmental microbiology reports}, volume = {10}, number = {1}, pages = {75-79}, doi = {10.1111/1758-2229.12608}, pmid = {29194980}, issn = {1758-2229}, mesh = {Adaptation, Physiological ; Antarctic Regions ; Arctic Regions ; Bacteria/*classification/genetics/radiation effects ; Biodiversity ; Desiccation ; *Ecosystem ; Metagenomics ; *Microbiota ; *Solar Energy ; Ultraviolet Rays ; }, abstract = {Solar panels located on high (Arctic and Antarctic) latitudes combine the harshness of the climate with that of the solar exposure. We report here that these polar solar panels are inhabited by similar microbial communities in taxonomic terms, dominated by Hymenobacter spp., Sphingomonas spp. and Ascomycota. Our results suggest that solar panels, even on high latitudes, can shape a microbial ecosystem adapted to irradiation and desiccation.}, } @article {pmid29194931, year = {2018}, author = {Feng, J and Li, B and Jiang, X and Yang, Y and Wells, GF and Zhang, T and Li, X}, title = {Antibiotic resistome in a large-scale healthy human gut microbiota deciphered by metagenomic and network analyses.}, journal = {Environmental microbiology}, volume = {20}, number = {1}, pages = {355-368}, doi = {10.1111/1462-2920.14009}, pmid = {29194931}, issn = {1462-2920}, mesh = {Adult ; Aged ; Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Microbial ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Genes, Bacterial ; Humans ; Male ; Metagenomics ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S ; Young Adult ; }, abstract = {The human gut microbiota is an important reservoir of antibiotic resistance genes (ARGs). A metagenomic approach and network analysis were used to establish a comprehensive antibiotic resistome catalog and to obtain co-occurrence patterns between ARGs and microbial taxa in fecal samples from 180 healthy individuals from 11 different countries. In total, 507 ARG subtypes belonging to 20 ARG types were detected with abundances ranging from 7.12 × 10[-7] to 2.72 × 10[-1] copy of ARG/copy of 16S-rRNA gene. Tetracycline, multidrug, macrolide-lincosamide-streptogramin, bacitracin, vancomycin, beta-lactam and aminoglycoside resistance genes were the top seven most abundant ARG types. The multidrug ABC transporter, aadE, bacA, acrB, tetM, tetW, vanR and vanS were shared by all 180 individuals, suggesting their common occurrence in the human gut. Compared to populations from the other 10 countries, the Chinese population harboured the most abundant ARGs. Moreover, LEfSe analysis suggested that the MLS resistance type and its subtype 'ermF' were representative ARGs of the Chinese population. Antibiotic inactivation, antibiotic target alteration and antibiotic efflux were the dominant resistance mechanism categories in all populations. Procrustes analysis revealed that microbial phylogeny structured the antibiotic resistome. Co-occurrence patterns obtained via network analysis implied that 12 species might be potential hosts of 58 ARG subtypes.}, } @article {pmid29194919, year = {2018}, author = {Lavy, A and Keren, R and Yu, K and Thomas, BC and Alvarez-Cohen, L and Banfield, JF and Ilan, M}, title = {A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {800-814}, pmid = {29194919}, issn = {1462-2920}, support = {P42 ES004705/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; *Gammaproteobacteria/classification/genetics/metabolism ; Genome, Bacterial/genetics ; Indian Ocean ; Microbiota/genetics ; Nitrogen/metabolism ; Oceans and Seas ; Oxidation-Reduction ; Phylogeny ; Polyketide Synthases/genetics ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sulfides/*metabolism ; Sulfur/*metabolism ; Symbiosis/physiology ; }, abstract = {Sponges are benthic filter feeders that play pivotal roles in coupling benthic-pelagic processes in the oceans that involve transformation of dissolved and particulate organic carbon and nitrogen into biomass. While the contribution of sponge holobionts to the nitrogen cycle has been recognized in past years, their importance in the sulfur cycle, both oceanic and physiological, has only recently gained attention. Sponges in general, and Theonella swinhoei in particular, harbour a multitude of associated microorganisms that could affect sulfur cycling within the holobiont. We reconstructed the genome of a Chromatiales (class Gammaproteobacteria) bacterium from a metagenomic sequence dataset of a T. swinhoei-associated microbial community. This relatively abundant bacterium has the metabolic capability to oxidize sulfide yet displays reduced metabolic potential suggestive of its lifestyle as an obligatory symbiont. This bacterium was detected in multiple sponge orders, according to similarities in key genes such as 16S rRNA and polyketide synthase genes. Due to its sulfide oxidation metabolism and occurrence in many members of the Porifera phylum, we suggest naming the newly described taxon Candidatus Porisulfidus.}, } @article {pmid29194524, year = {2018}, author = {Zhu, C and Miller, M and Marpaka, S and Vaysberg, P and Rühlemann, MC and Wu, G and Heinsen, FA and Tempel, M and Zhao, L and Lieb, W and Franke, A and Bromberg, Y}, title = {Functional sequencing read annotation for high precision microbiome analysis.}, journal = {Nucleic acids research}, volume = {46}, number = {4}, pages = {e23}, pmid = {29194524}, issn = {1362-4962}, mesh = {Algorithms ; Bacterial Proteins/physiology ; Child ; Crohn Disease/microbiology ; Humans ; Metagenomics/*methods ; *Microbiota ; Molecular Sequence Annotation/*methods ; Prader-Willi Syndrome/microbiology ; Sequence Alignment ; }, abstract = {The vast majority of microorganisms on Earth reside in often-inseparable environment-specific communities-microbiomes. Meta-genomic/-transcriptomic sequencing could reveal the otherwise inaccessible functionality of microbiomes. However, existing analytical approaches focus on attributing sequencing reads to known genes/genomes, often failing to make maximal use of available data. We created faser (functional annotation of sequencing reads), an algorithm that is optimized to map reads to molecular functions encoded by the read-correspondent genes. The mi-faser microbiome analysis pipeline, combining faser with our manually curated reference database of protein functions, accurately annotates microbiome molecular functionality. mi-faser's minutes-per-microbiome processing speed is significantly faster than that of other methods, allowing for large scale comparisons. Microbiome function vectors can be compared between different conditions to highlight environment-specific and/or time-dependent changes in functionality. Here, we identified previously unseen oil degradation-specific functions in BP oil-spill data, as well as functional signatures of individual-specific gut microbiome responses to a dietary intervention in children with Prader-Willi syndrome. Our method also revealed variability in Crohn's Disease patient microbiomes and clearly distinguished them from those of related healthy individuals. Our analysis highlighted the microbiome role in CD pathogenicity, demonstrating enrichment of patient microbiomes in functions that promote inflammation and that help bacteria survive it.}, } @article {pmid29194469, year = {2018}, author = {McIver, LJ and Abu-Ali, G and Franzosa, EA and Schwager, R and Morgan, XC and Waldron, L and Segata, N and Huttenhower, C}, title = {bioBakery: a meta'omic analysis environment.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {7}, pages = {1235-1237}, pmid = {29194469}, issn = {1367-4811}, support = {R01 HG005220/HG/NHGRI NIH HHS/United States ; R01 HG005969/HG/NHGRI NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; }, mesh = {Metagenomics/*methods ; Microbiota/*genetics ; Reproducibility of Results ; *Software ; Workflow ; }, abstract = {SUMMARY: bioBakery is a meta'omic analysis environment and collection of individual software tools with the capacity to process raw shotgun sequencing data into actionable microbial community feature profiles, summary reports, and publication-ready figures. It includes a collection of pre-configured analysis modules also joined into workflows for reproducibility.

bioBakery (http://huttenhower.sph.harvard.edu/biobakery) is publicly available for local installation as individual modules and as a virtual machine image. Each individual module has been developed to perform a particular task (e.g. quantitative taxonomic profiling or statistical analysis), and they are provided with source code, tutorials, demonstration data, and validation results; the bioBakery virtual image includes the entire suite of modules and their dependencies pre-installed. Images are available for both Amazon EC2 and Google Compute Engine. All software is open source under the MIT license. bioBakery is actively maintained with a support group at biobakery-users@googlegroups.com and new tools being added upon their release.

CONTACT: chuttenh@hsph.harvard.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid29192628, year = {2017}, author = {Anukam, KC and Agbakoba, NR}, title = {A comparative study of the oral microbiome compositions of healthy postmenopausal, premenopausal, and prepubertal Nigerian females, using 16s rrna metagenomics methods.}, journal = {Nigerian journal of clinical practice}, volume = {20}, number = {10}, pages = {1250-1258}, doi = {10.4103/njcp.njcp_32_17}, pmid = {29192628}, issn = {1119-3077}, mesh = {Adolescent ; Adult ; Aged ; Bacteria/classification/*genetics ; Child ; Female ; Humans ; Metagenomics/*methods ; *Microbiota ; Middle Aged ; Mouth/*microbiology ; Pilot Projects ; *Postmenopause ; *Premenopause ; RNA, Ribosomal, 16S/*genetics ; Young Adult ; }, abstract = {INTRODUCTION: There is a paucity of information on the oral microbiome compositions of Nigerians, mostly due to lack of appropriate molecular techniques. In this pilot study, we sought to determine and characterize the oral bacterial compositions of "healthy" females.

MATERIALS AND METHODS: Oral samples were collected from three randomly selected females aged 56, 28, and 8 years. DNA was extracted and 16S rRNA V4 region was amplified using custom-barcoded primers before sequencing with Illumina MiSeq platform. Quantitative Insights into Microbial Ecology pipeline was used for 16S rRNA recognition. Distribution of taxonomic categories at different levels of resolution was done using the ribosomal RNA similarities to entries in the REFseq protein database. Diversity score was calculated based on the inverse Simpson's index.

RESULTS: The inverse Simpson's diversity index for the postmenopausal, premenopausal, and prepubertal was 7.74, 6.95, and 7.42 respectively. A total of 12 phyla, 70 genera, and 85 species were detected. Firmicutes followed by Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria dominated the oral microbiome of the subjects. Streptococcus thermophilus (33.19%) was the most abundance species in subject 1, while subject 2 was highly predominated by Haemophilus parainfluenzae (80.65%), and subject 3 was predominated by Haemophilus influenzae (23.05%).

CONCLUSION: The study has revealed that bacteria with varying diversities colonized the subjects and it highlighted the importance of metagenomics in deciphering the oral bacterial compositions from females of different age groups. More studies are needed using metagenomics approach, to appreciate these bacterial organisms that are associated with health and disease in our environment.}, } @article {pmid29192335, year = {2018}, author = {Salmaso, N and Albanese, D and Capelli, C and Boscaini, A and Pindo, M and Donati, C}, title = {Diversity and Cyclical Seasonal Transitions in the Bacterial Community in a Large and Deep Perialpine Lake.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {125-143}, pmid = {29192335}, issn = {1432-184X}, support = {Ph.D. fellowship//FIRS>T/ ; }, mesh = {Bacteria/*classification/genetics/growth & development ; *Biodiversity ; Cyanobacteria/classification/growth & development ; DNA, Bacterial/genetics ; Ecosystem ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Lakes/*microbiology ; *Microbiota ; *Phylogeny ; Phytoplankton/classification/growth & development ; RNA, Ribosomal, 16S/genetics ; *Seasons ; Temperature ; *Water Microbiology ; Water Quality ; }, abstract = {High-throughput sequencing (HTS) was used to analyze the seasonal variations in the bacterioplankton community composition (BCC) in the euphotic layer of a large and deep lake south of the Alps (Lake Garda). The BCC was analyzed throughout two annual cycles by monthly samplings using the amplification and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene by the MiSeq Illumina platform. The dominant and most diverse bacterioplankton phyla were among the more frequently reported in freshwater ecosystems, including the Proteobacteria, Cyanobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, and Planctomycetes. As a distinctive feature, the development of the BCC showed a cyclical temporal pattern in the two analyzed years and throughout the euphotic layer. The recurring temporal development was controlled by the strong seasonality in water temperature and thermal stratification, and by cyclical temporal changes in nutrients and, possibly, by the remarkable annual cyclical development of cyanobacteria and eukaryotic phytoplankton hosting bacterioplankton that characterizes Lake Garda. Further downstream analyses of operational taxonomic units associated to cyanobacteria allowed confirming the presence of the most abundant taxa previously identified by microscopy and/or phylogenetic analyses, as well as the presence of other small Synechococcales/Chroococcales and rare Nostocales never identified so far in the deep lakes south of the Alps. The implications of the high diversity and strong seasonality are relevant, opening perspectives for the definition of common and discriminating patterns characterizing the temporal and spatial distribution in the BCC, and for the application of the new sequencing technologies in the monitoring of water quality in large and deep lakes.}, } @article {pmid29192012, year = {2018}, author = {Zalewski, S and Stewart, CJ and Embleton, ND and Berrington, JE}, title = {Brief guide to the analysis, interpretation and presentation of microbiota data.}, journal = {Archives of disease in childhood. Education and practice edition}, volume = {103}, number = {6}, pages = {327-330}, doi = {10.1136/archdischild-2017-313838}, pmid = {29192012}, issn = {1743-0593}, mesh = {Computational Biology/*methods ; Humans ; *Microbiota ; }, } @article {pmid29191900, year = {2017}, author = {Coles, VJ and Stukel, MR and Brooks, MT and Burd, A and Crump, BC and Moran, MA and Paul, JH and Satinsky, BM and Yager, PL and Zielinski, BL and Hood, RR}, title = {Ocean biogeochemistry modeled with emergent trait-based genomics.}, journal = {Science (New York, N.Y.)}, volume = {358}, number = {6367}, pages = {1149-1154}, doi = {10.1126/science.aan5712}, pmid = {29191900}, issn = {1095-9203}, mesh = {Atlantic Ocean ; Biochemical Phenomena/genetics ; Metabolic Networks and Pathways/*genetics ; Metagenome ; *Metagenomics ; Microbial Consortia/*genetics ; Models, Biological ; Seawater/*microbiology ; Transcriptome ; }, abstract = {Marine ecosystem models have advanced to incorporate metabolic pathways discovered with genomic sequencing, but direct comparisons between models and "omics" data are lacking. We developed a model that directly simulates metagenomes and metatranscriptomes for comparison with observations. Model microbes were randomly assigned genes for specialized functions, and communities of 68 species were simulated in the Atlantic Ocean. Unfit organisms were replaced, and the model self-organized to develop community genomes and transcriptomes. Emergent communities from simulations that were initialized with different cohorts of randomly generated microbes all produced realistic vertical and horizontal ocean nutrient, genome, and transcriptome gradients. Thus, the library of gene functions available to the community, rather than the distribution of functions among specific organisms, drove community assembly and biogeochemical gradients in the model ocean.}, } @article {pmid29191163, year = {2017}, author = {Ignasiak, K and Maxwell, A}, title = {Antibiotic-resistant bacteria in the guts of insects feeding on plants: prospects for discovering plant-derived antibiotics.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {223}, pmid = {29191163}, issn = {1471-2180}, support = {BBS/E/J/00000201/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004561/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/chemistry/isolation & purification/*pharmacology ; Bacteria/*drug effects/isolation & purification ; Chromatography, High Pressure Liquid ; Chromatography, Liquid ; Drug Resistance, Bacterial/*drug effects ; Gastrointestinal Tract/microbiology ; Insecta/*microbiology ; Metagenomics ; Microbial Sensitivity Tests ; Microbiota ; Plant Extracts/chemistry/*pharmacology ; Plants/chemistry ; Symbiosis ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: Although plants produce many secondary metabolites, currently none of these are commercial antibiotics. Insects feeding on specific plants can harbour bacterial strains resistant to known antibiotics suggesting that compounds in the plant have stimulated resistance development. We sought to determine whether the occurrence of antibiotic-resistant bacteria in insect guts was a widespread phenomenon, and whether this could be used as a part of a strategy to identify antibacterial compounds from plants.

RESULTS: Six insect/plant pairs were selected and the insect gut bacteria were identified and assessed for antibiotic susceptibilities compared with type strains from culture collections. We found that the gut strains could be more or less susceptible to antibiotics than the type strains, or show no differences. Evidence of antibacterial activity was found in the plant extracts from five of the six plants, and, in one case Catharanthus roseus (Madagascar Periwinkle), compounds with antibacterial activity were identified.

CONCLUSION: Bacterial strains isolated from insect guts show a range of susceptibilities to antibiotics suggesting a complex interplay between species in the insect gut microbiome. Extracts from selected plants can show antibacterial activity but it is not easy to isolate and identify the active components. We found that vindoline, present in Madagascar Periwinkle extracts, possessed moderate antibacterial activity. We suggest that plant-derived antibiotics are a realistic possibility given the advances in genomic and metabolomic methodologies.}, } @article {pmid29189738, year = {2017}, author = {Ticinesi, A and Lauretani, F and Milani, C and Nouvenne, A and Tana, C and Del Rio, D and Maggio, M and Ventura, M and Meschi, T}, title = {Aging Gut Microbiota at the Cross-Road between Nutrition, Physical Frailty, and Sarcopenia: Is There a Gut-Muscle Axis?.}, journal = {Nutrients}, volume = {9}, number = {12}, pages = {}, pmid = {29189738}, issn = {2072-6643}, mesh = {Aging/*physiology ; *Frailty ; *Gastrointestinal Microbiome ; Humans ; Muscle, Skeletal/*physiology ; *Nutritional Status ; *Sarcopenia ; }, abstract = {Inadequate nutrition and physical inactivity are the mainstays of primary sarcopenia-physiopathology in older individuals. Gut microbiota composition is strongly dependent on both of these elements, and conversely, can also influence the host physiology by modulating systemic inflammation, anabolism, insulin sensitivity, and energy production. The bacterial metabolism of nutrients theoretically influences skeletal muscle cell functionality through producing mediators that drive all of these systemic effects. In this study, we review the scientific literature supporting the concept of the involvement of gut microbiota in primary sarcopenia physiopathology. First, we examine studies associating fecal microbiota alterations with physical frailty, i.e., the loss of muscle performance and normal muscle mass. Then, we consider studies exploring the effects of exercise on gut microbiota composition. Finally, we examine studies demonstrating the possible effects of mediators produced by gut microbiota on skeletal muscle, and intervention studies considering the effects of prebiotic or probiotic administration on muscle function. Even if there is no evidence of a distinct gut microbiota composition in older sarcopenic patients, we conclude that the literature supports the possible presence of a "gut-muscle axis", whereby gut microbiota may act as the mediator of the effects of nutrition on muscle cells.}, } @article {pmid29187708, year = {2017}, author = {Hirai, M and Nishi, S and Tsuda, M and Sunamura, M and Takaki, Y and Nunoura, T}, title = {Library Construction from Subnanogram DNA for Pelagic Sea Water and Deep-Sea Sediments.}, journal = {Microbes and environments}, volume = {32}, number = {4}, pages = {336-343}, pmid = {29187708}, issn = {1347-4405}, mesh = {Base Composition/genetics ; Base Sequence ; Biodiversity ; DNA, Archaeal/analysis/*genetics ; DNA, Bacterial/analysis/*genetics ; DNA, Protozoan/analysis/*genetics ; Gene Library ; Geologic Sediments/*microbiology/*parasitology ; Metagenome/*genetics ; Metagenomics/*methods ; Seawater/microbiology/parasitology ; Sequence Analysis, DNA ; }, abstract = {Shotgun metagenomics is a low biased technology for assessing environmental microbial diversity and function. However, the requirement for a sufficient amount of DNA and the contamination of inhibitors in environmental DNA leads to difficulties in constructing a shotgun metagenomic library. We herein examined metagenomic library construction from subnanogram amounts of input environmental DNA from subarctic surface water and deep-sea sediments using two library construction kits: the KAPA Hyper Prep Kit and Nextera XT DNA Library Preparation Kit, with several modifications. The influence of chemical contaminants associated with these environmental DNA samples on library construction was also investigated. Overall, shotgun metagenomic libraries were constructed from 1 pg to 1 ng of input DNA using both kits without harsh library microbial contamination. However, the libraries constructed from 1 pg of input DNA exhibited larger biases in GC contents, k-mers, or small subunit (SSU) rRNA gene compositions than those constructed from 10 pg to 1 ng DNA. The lower limit of input DNA for low biased library construction in this study was 10 pg. Moreover, we revealed that technology-dependent biases (physical fragmentation and linker ligation vs. tagmentation) were larger than those due to the amount of input DNA.}, } @article {pmid29187243, year = {2017}, author = {Boynton, FDD and Ericsson, AC and Uchihashi, M and Dunbar, ML and Wilkinson, JE}, title = {Doxycycline induces dysbiosis in female C57BL/6NCrl mice.}, journal = {BMC research notes}, volume = {10}, number = {1}, pages = {644}, pmid = {29187243}, issn = {1756-0500}, support = {K01 OD019924/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Disease Models, Animal ; Doxycycline/*pharmacology ; Dysbiosis/*chemically induced ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Mice ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVE: This study aims to demonstrate the effect of oral doxycycline on fecal microbiota of mice. Doxycycline is a common effector for control of gene expression using the tet-inducible system in transgenic mice. The effect of oral doxycycline on murine gut microbiota has not been reported. We evaluated the effect of doxycycline treatment by sequencing the V4 hypervariable region of the 16S rRNA gene from fecal samples collected during a 4 week course of treatment at a dose of 2 mg/ml in the drinking water.

RESULTS: The fecal microbiota of treated animals were distinct from control animals; the decreased richness and diversity were characterized primarily by Bacteroides sp. enrichment. These effects persisted when the treatment was temporarily discontinued for 1 week. These data suggest that doxycycline treatment can induce significant dysbiosis, and its effects should be considered when used in animal models that are or maybe sensitive to perturbation of the gut microbiota.}, } @article {pmid29187204, year = {2017}, author = {Mallick, H and Ma, S and Franzosa, EA and Vatanen, T and Morgan, XC and Huttenhower, C}, title = {Experimental design and quantitative analysis of microbial community multiomics.}, journal = {Genome biology}, volume = {18}, number = {1}, pages = {228}, pmid = {29187204}, issn = {1474-760X}, support = {R01 HG005220/HG/NHGRI NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/methods ; DNA Barcoding, Taxonomic ; Gene Expression Profiling/methods ; Humans ; *Metabolomics/methods ; *Metagenomics/methods ; *Microbiota ; *Proteomics/methods ; *Research Design ; }, abstract = {Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the resulting host and microbial data types to human health, several experimental design considerations, data analysis challenges, and statistical epidemiological approaches must be addressed. Here, we survey current best practices for experimental design in microbiome molecular epidemiology, including technologies for generating, analyzing, and integrating microbiome multiomics data. We highlight studies that have identified molecular bioactives that influence human health, and we suggest steps for scaling translational microbiome research to high-throughput target discovery across large populations.}, } @article {pmid29186720, year = {2017}, author = {Pampillón-González, L and Ortiz-Cornejo, NL and Luna-Guido, M and Dendooven, L and Navarro-Noya, YE}, title = {Archaeal and Bacterial Community Structure in an Anaerobic Digestion Reactor (Lagoon Type) Used for Biogas Production at a Pig Farm.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {27}, number = {5}, pages = {306-317}, doi = {10.1159/000479108}, pmid = {29186720}, issn = {1660-2412}, mesh = {Anaerobiosis ; Animals ; Animals, Domestic ; Archaea/*classification/genetics/*metabolism ; Bacteria, Anaerobic/*classification/genetics/*metabolism ; *Biofuels ; *Bioreactors ; Chemical Phenomena ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Farms ; Feces/*microbiology ; *Fermentation ; Metagenome/genetics ; Metagenomics/methods ; Methane/biosynthesis ; Mexico ; Microbial Consortia/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Swine ; Waste Disposal, Fluid ; Wastewater/microbiology ; }, abstract = {Biogas production from animal waste is an economically viable way to reduce environmental pollution and produce valuable products, i.e., methane and a nutrient-rich organic waste product. An anaerobic digestion reactor for biogas production from pig waste was sampled at the entrance, middle (digestion chamber), and exit of a digester, while the bacterial and archaeal community structure was studied by 16S rRNA gene metagenomics. The number of bacterial operational taxonomic units (OTU)-97% was 3-7 times larger than that of archaeal ones. Bacteria and Archaea found in feces of animals (e.g., Clostridiaceae, Lachnospiraceae, Ruminococcaceae, Methanosarcina, Methanolobus, Methanosaeta, and Methanospirillum) dominated the entrance of the digester. The digestion chamber was dominated by anaerobic sugar-fermenting OP9 bacteria and the syntrophic bacteria Candidatus Cloacamonas (Waste Water of Evry 1; WWE1). The methanogens dominant in the digestion chamber were the acetoclastic Methanosaeta and the hydrogenothrophic Methanoculleus and Methanospirillum. Similar bacterial and archaeal groups that dominated in the middle of the digestion chamber were found in the waste that left the digester. Predicted functions associated with degradation of xenobiotic compounds were significantly different between the sampling locations. The microbial community found in an anaerobic digestion reactor loaded with pig manure contained microorganisms with biochemical capacities related to the 4 phases of methane production.}, } @article {pmid29186529, year = {2018}, author = {de Gunzburg, J and Ghozlane, A and Ducher, A and Le Chatelier, E and Duval, X and Ruppé, E and Armand-Lefevre, L and Sablier-Gallis, F and Burdet, C and Alavoine, L and Chachaty, E and Augustin, V and Varastet, M and Levenez, F and Kennedy, S and Pons, N and Mentré, F and Andremont, A}, title = {Protection of the Human Gut Microbiome From Antibiotics.}, journal = {The Journal of infectious diseases}, volume = {217}, number = {4}, pages = {628-636}, pmid = {29186529}, issn = {1537-6613}, mesh = {Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/*administration & dosage/analysis ; Charcoal/*administration & dosage ; Feces/chemistry/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Healthy Volunteers ; Humans ; Male ; Metagenomics ; Microbiota/*drug effects ; Middle Aged ; Moxifloxacin/*administration & dosage/analysis ; Treatment Outcome ; Young Adult ; }, abstract = {BACKGROUND: Antibiotics are life-saving drugs but severely affect the gut microbiome with short-term consequences including diarrhea and selection of antibiotic-resistant bacteria. Long-term links to allergy and obesity are also suggested. We devised a product, DAV132, and previously showed its ability to deliver a powerful adsorbent, activated charcoal, in the late ileum of human volunteers.

METHODS: We performed a randomized controlled trial in 28 human volunteers treated with a 5-day clinical regimen of the fluoroquinolone antibiotic moxifloxacin in 2 parallel groups, with or without DAV132 coadministration. Two control goups of 8 volunteers each receiving DAV132 alone, or a nonactive substitute, were added.

RESULTS: The coadministration of DAV132 decreased free moxifloxacin fecal concentrations by 99%, while plasmatic levels were unaffected. Shotgun quantitative metagenomics showed that the richness and composition of the intestinal microbiota were largely preserved in subjects co-treated with DAV132 in addition to moxifloxacin. No adverse effect was observed. In addition, DAV132 efficiently adsorbed a wide range of clinically relevant antibiotics ex vivo.

CONCLUSIONS: DAV132 was highly effective to protect the gut microbiome of moxifloxacin-treated healthy volunteers and may constitute a clinical breakthrough by preventing adverse health consequences of a wide range of antibiotic treatments.

CLINICAL TRIALS REGISTRATION: NCT02176005.}, } @article {pmid29186317, year = {2019}, author = {Dovrolis, N and Kolios, G and Spyrou, GM and Maroulakou, I}, title = {Computational profiling of the gut-brain axis: microflora dysbiosis insights to neurological disorders.}, journal = {Briefings in bioinformatics}, volume = {20}, number = {3}, pages = {825-841}, doi = {10.1093/bib/bbx154}, pmid = {29186317}, issn = {1477-4054}, mesh = {Brain/*metabolism ; Computational Biology/*methods ; *Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; Nervous System Diseases/*microbiology ; }, abstract = {Almost 2500 years after Hippocrates' observations on health and its direct association to the gastrointestinal tract, a paradigm shift has recently occurred, making the gut and its symbionts (bacteria, fungi, archaea and viruses) a point of convergence for studies. It is nowadays well established that the gut microflora's compositional diversity regulates via its genes (the microbiome) the host's health and provides preliminary insights into disease progression and regulation. The microbiome's involvement is evident in immunological and physiological studies that link changes in its biodiversity to its contributions to the host's phenotype but also in neurological investigations, substantiating the aptly named gut-brain axis. The definitive mechanisms of this last bidirectional interaction will be our main focus because it presents researchers with a new conundrum. In this review, we prospect current literature for computational analysis methodologies that accommodate the need for better understanding of the microbiome-gut-brain interactions and neurological disorder onset and progression, through cross-disciplinary systems biology applications. We will present bioinformatics tools used in exploring these synergies that help build and interpret microbial 16S ribosomal RNA data sets, produced by shotgun and high-throughput sequencing of healthy and neurological disorder samples stored in biological databases. These approaches provide alternative means for researchers to form hypotheses to their inquests faster, cheaper and swith precision. The goal of these studies relies on the integration of combined metagenomics and metabolomics assessments. An accurate characterization of the microbiome and its functionality can support new diagnostic, prognostic and therapeutic strategies for neurological disorders, customized for each individual host.}, } @article {pmid29184540, year = {2017}, author = {Walter, JM and Coutinho, FH and Dutilh, BE and Swings, J and Thompson, FL and Thompson, CC}, title = {Ecogenomics and Taxonomy of Cyanobacteria Phylum.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2132}, pmid = {29184540}, issn = {1664-302X}, abstract = {Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats, although only a few studies have analyzed the association of phylogenomic clades to specific environmental niches. In this study, we adopted an ecogenomics strategy with the aim to delineate ecological niche preferences of Cyanobacteria and integrate them to the genomic taxonomy of these bacteria. First, an appropriate phylogenomic framework was established using a set of genomic taxonomy signatures (including a tree based on conserved gene sequences, genome-to-genome distance, and average amino acid identity) to analyse ninety-nine publicly available cyanobacterial genomes. Next, the relative abundances of these genomes were determined throughout diverse global marine and freshwater ecosystems, using metagenomic data sets. The whole-genome-based taxonomy of the ninety-nine genomes allowed us to identify 57 (of which 28 are new genera) and 87 (of which 32 are new species) different cyanobacterial genera and species, respectively. The ecogenomic analysis allowed the distinction of three major ecological groups of Cyanobacteria (named as i. Low Temperature; ii. Low Temperature Copiotroph; and iii. High Temperature Oligotroph) that were coherently linked to the genomic taxonomy. This work establishes a new taxonomic framework for Cyanobacteria in the light of genomic taxonomy and ecogenomic approaches.}, } @article {pmid29184122, year = {2017}, author = {Lee, WH and Chen, HM and Yang, SF and Liang, C and Peng, CY and Lin, FM and Tsai, LL and Wu, BC and Hsin, CH and Chuang, CY and Yang, T and Yang, TL and Ho, SY and Chen, WL and Ueng, KC and Huang, HD and Huang, CN and Jong, YJ}, title = {Bacterial alterations in salivary microbiota and their association in oral cancer.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {16540}, pmid = {29184122}, issn = {2045-2322}, mesh = {Biodiversity ; Carcinoma, Squamous Cell/diagnosis/epidemiology/etiology ; Computational Biology/methods ; Disease Susceptibility ; Female ; Humans ; Male ; Metagenomics ; *Microbiota ; Mouth Mucosa/microbiology/pathology ; Mouth Neoplasms/diagnosis/*epidemiology/*etiology ; RNA, Ribosomal, 16S ; Saliva/*microbiology ; Taiwan/epidemiology ; }, abstract = {Oral squamous cell carcinoma (OSCC) is the most common malignant neoplasm of the oral cavity and the fourth leading malignancy and cause of cancer-related death in the male population of Taiwan. Most cases are detected at advanced stages, resulting in poor prognosis. Therefore, improved detection of early oral health disorders is indispensable. The involvement of oral bacteria in inflammation and their association with OSCC progression provide a feasible target for diagnosis. Due to the nature of oral neoplasms, the diagnosis of epithelial precursor lesions is relatively easy compared with that of other types of cancer. However, the transition from an epithelial precursor lesion to cancer is slow and requires further and continuous follow-up. In this study, we investigated microbiota differences between normal individuals, epithelial precursor lesion patients, and cancer patients with different lifestyle habits, such as betel chewing and smoking, using next-generation sequencing. Overall, the oral microbiome compositions of five genera, Bacillus, Enterococcus, Parvimonas, Peptostreptococcus, and Slackia, revealed significant differences between epithelial precursor lesion and cancer patients and correlated with their classification into two clusters. These composition changes might have the potential to constitute a biomarker to help in monitoring the oral carcinogenesis transition from epithelial precursor lesion to cancer.}, } @article {pmid29184093, year = {2017}, author = {Stearns, JC and Simioni, J and Gunn, E and McDonald, H and Holloway, AC and Thabane, L and Mousseau, A and Schertzer, JD and Ratcliffe, EM and Rossi, L and Surette, MG and Morrison, KM and Hutton, EK}, title = {Intrapartum antibiotics for GBS prophylaxis alter colonization patterns in the early infant gut microbiome of low risk infants.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {16527}, pmid = {29184093}, issn = {2045-2322}, support = {MSH-136665//CIHR/Canada ; }, mesh = {Adult ; Anti-Bacterial Agents/*administration & dosage ; *Antibiotic Prophylaxis ; Bifidobacterium/drug effects ; Delivery, Obstetric ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant ; Infant, Newborn ; Male ; *Maternal Exposure ; Metagenome ; Metagenomics ; Pregnancy ; Streptococcal Infections/*microbiology/*prevention & control ; Streptococcus agalactiae/*drug effects/physiology ; }, abstract = {Early life microbial colonization and succession is critically important to healthy development with impacts on metabolic and immunologic processes throughout life. A longitudinal prospective cohort was recruited from midwifery practices to include infants born at full term gestation to women with uncomplicated pregnancies. Here we compare bacterial community succession in infants born vaginally, with no exposure to antibiotics (n = 53), with infants who were exposed to intrapartum antibiotic prophylaxis (IAP) for Group B Streptococcus (GBS; n = 14), and infants born by C-section (n = 7). Molecular profiles of the 16 S rRNA genes indicate that there is a delay in the expansion of Bifidobacterium, which was the dominate infant gut colonizer, over the first 12 weeks and a persistence of Escherichia when IAP for GBS exposure is present during vaginal labour. Longer duration of IAP exposure increased the magnitude of the effect on Bifidobacterium populations, suggesting a longer delay in microbial community maturation. As with prior studies, we found altered gut colonisation following C-section that included a notable lack of Bacteroidetes. This study found that exposure of infants to IAP for GBS during vaginal birth affected aspects of gut microbial ecology that, although dramatic at early time points, disappeared by 12 weeks of age in most infants.}, } @article {pmid29184025, year = {2017}, author = {Gnanaprakasam, ET and Lloyd, JR and Boothman, C and Ahmed, KM and Choudhury, I and Bostick, BC and van Geen, A and Mailloux, BJ}, title = {Microbial Community Structure and Arsenic Biogeochemistry in Two Arsenic-Impacted Aquifers in Bangladesh.}, journal = {mBio}, volume = {8}, number = {6}, pages = {}, pmid = {29184025}, issn = {2150-7511}, support = {P42 ES010349/ES/NIEHS NIH HHS/United States ; }, mesh = {Arsenates/analysis ; Arsenic/*metabolism ; Arsenites/analysis ; Bacteria/*classification/*genetics ; Bangladesh ; *Biota ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/chemistry ; Groundwater/*microbiology ; Iron/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Long-term exposure to trace levels of arsenic (As) in shallow groundwater used for drinking and irrigation puts millions of people at risk of chronic disease. Although microbial processes are implicated in mobilizing arsenic from aquifer sediments into groundwater, the precise mechanism remains ambiguous. The goal of this work was to target, for the first time, a comprehensive suite of state-of-the-art molecular techniques in order to better constrain the relationship between indigenous microbial communities and the iron and arsenic mineral phases present in sediments at two well-characterized arsenic-impacted aquifers in Bangladesh. At both sites, arsenate [As(V)] was the major species of As present in sediments at depths with low aqueous As concentrations, while most sediment As was arsenite [As(III)] at depths with elevated aqueous As concentrations. This is consistent with a role for the microbial As(V) reduction in mobilizing arsenic. 16S rRNA gene analysis indicates that the arsenic-rich sediments were colonized by diverse bacterial communities implicated in both dissimilatory Fe(III) and As(V) reduction, while the correlation analyses involved phylogenetic groups not normally associated with As mobilization. Findings suggest that direct As redox transformations are central to arsenic fate and transport and that there is a residual reactive pool of both As(V) and Fe(III) in deeper sediments that could be released by microbial respiration in response to hydrologic perturbation, such as increased groundwater pumping that introduces reactive organic carbon to depth.IMPORTANCE The consumption of arsenic in waters collected from tube wells threatens the lives of millions worldwide and is particularly acute in the floodplains and deltas of southern Asia. The cause of arsenic mobilization from natural sediments within these aquifers to groundwater is complex, with recent studies suggesting that sediment-dwelling microorganisms may be the cause. In the absence of oxygen at depth, specialist bacteria are thought able to use metals within the sediments to support their metabolism. Via these processes, arsenic-contaminated iron minerals are transformed, resulting in the release of arsenic into the aquifer waters. Focusing on a field site in Bangladesh, a comprehensive, multidisciplinary study using state-of-the-art geological and microbiological techniques has helped better understand the microbes that are present naturally in a high-arsenic aquifer and how they may transform the chemistry of the sediment to potentially lethal effect.}, } @article {pmid29184020, year = {2017}, author = {Luo, E and Aylward, FO and Mende, DR and DeLong, EF}, title = {Bacteriophage Distributions and Temporal Variability in the Ocean's Interior.}, journal = {mBio}, volume = {8}, number = {6}, pages = {}, pmid = {29184020}, issn = {2150-7511}, mesh = {Bacteriophages/*classification/genetics/*isolation & purification ; *Biodiversity ; DNA, Viral/analysis/genetics ; Genotype ; Lysogeny ; Metagenomics ; *Oceans and Seas ; Seawater/*virology ; Spatio-Temporal Analysis ; }, abstract = {Bacteriophages are numerically the most abundant DNA-containing entities in the oligotrophic ocean, yet how specific phage populations vary over time and space remains to be fully explored. Here, we conducted a metagenomic time-series survey of double-stranded DNA phages throughout the water column in the North Pacific Subtropical Gyre, encompassing 1.5 years from depths of 25 to 1,000 m. Viral gene sequences were identified in assembled metagenomic samples, yielding an estimated 172,385 different viral gene families. Viral marker gene distributions suggested that lysogeny was more prevalent at mesopelagic depths than in surface waters, consistent with prior prophage induction studies using mitomycin C. A total of 129 ALOHA viral genomes and genome fragments from 20 to 108 kbp were selected for further study, which represented the most abundant phages in the water column. Phage genotypes displayed discrete population structures. Most phages persisted throughout the time-series and displayed a strong depth structure that mirrored the stratified depth distributions of co-occurring bacterial taxa in the water column. Mesopelagic phages were distinct from surface water phages with respect to diversity, gene content, putative life histories, and temporal persistence, reflecting depth-dependent differences in host genomic architectures and phage reproductive strategies. The spatiotemporal distributions of the most abundant open-ocean bacteriophages that we report here provide new insight into viral temporal persistence, life history, and virus-host-environment interactions throughout the open-ocean water column.IMPORTANCE The North Pacific Subtropical Gyre represents one of the largest biomes on the planet, where microbial communities are central mediators of ecosystem dynamics and global biogeochemical cycles. Critical members of these communities are the viruses of marine bacteria, which can alter microbial metabolism and significantly influence their survival and productivity. To better understand these viral assemblages, we conducted genomic analyses of planktonic viruses over a seasonal cycle to ocean depths of 1,000 m. We identified 172,385 different viral gene families and 129 unique virus genotypes in this open-ocean setting. The spatiotemporal distributions of the most abundant open-ocean viruses that we report here provide new insights into viral temporal variability, life history, and virus-host-environment interactions throughout the water column.}, } @article {pmid29184019, year = {2017}, author = {Chatzidaki-Livanis, M and Coyne, MJ and Roelofs, KG and Gentyala, RR and Caldwell, JM and Comstock, LE}, title = {Gut Symbiont Bacteroides fragilis Secretes a Eukaryotic-Like Ubiquitin Protein That Mediates Intraspecies Antagonism.}, journal = {mBio}, volume = {8}, number = {6}, pages = {}, pmid = {29184019}, issn = {2150-7511}, support = {R01 AI093771/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*metabolism ; *Antibiosis ; Bacterial Proteins/genetics/*metabolism ; Bacteroides fragilis/growth & development/metabolism/*physiology ; DNA Transposable Elements ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Gene Deletion ; Humans ; Metagenomics ; Microbiota ; Mutagenesis, Insertional ; Ubiquitin/genetics/*metabolism ; }, abstract = {Human gut Bacteroides species produce different types of toxins that antagonize closely related members of the gut microbiota. Some are toxic effectors delivered by type VI secretion systems, and others are non-contact-dependent secreted antimicrobial proteins. Many strains of Bacteroides fragilis secrete antimicrobial molecules, but only one of these toxins has been described to date (Bacteroidales secreted antimicrobial protein 1 [BSAP-1]). In this study, we describe a novel secreted protein produced by B. fragilis strain 638R that mediated intraspecies antagonism. Using transposon mutagenesis and deletion mutation, we identified a gene encoding a eukaryotic-like ubiquitin protein (BfUbb) necessary for toxin activity against a subset of B. fragilis strains. The addition of ubb into a heterologous background strain conferred toxic activity on that strain. We found this gene to be one of the most highly expressed in the B. fragilis genome. The mature protein is 84% similar to human ubiquitin but has an N-terminal signal peptidase I (SpI) signal sequence and is secreted extracellularly. We found that the mature 76-amino-acid synthetic protein has very potent activity, confirming that BfUbb mediates the activity. Analyses of human gut metagenomic data sets revealed that ubb is present in 12% of the metagenomes that have evidence of B. fragilis As 638R produces both BSAP-1 and BfUbb, we performed a comprehensive analysis of the toxin activity of BSAP-1 and BfUbb against a set of 40 B. fragilis strains, revealing that 75% of B. fragilis strains are targeted by one or the other of these two secreted proteins of strain 638R.IMPORTANCE We are just beginning to understand some of the important interactions that occur between microbes of the human gut microbiota that dictate the composition and abundance of its constituent members. The ability of one member to produce molecules that directly kill a coresident member has been shown among minor gut species and is just starting to be studied in the abundant Bacteroides species. Here, we show that some strains of Bacteroides fragilis have acquired a gene encoding a secreted eukaryotic-like ubiquitin protein with potent inhibitory activity against other B. fragilis stains. This is the first bacterially encoded ubiquitin-like molecule shown to function like a bacterial toxin. This molecule is an example of a gut symbiont acquiring and adapting a eukaryotic molecule likely to increase its competitiveness in the mammalian gut. Understanding antagonistic factors produced by abundant gut symbionts is an important prerequisite to properly engineer strains to colonize the gut for health benefits.}, } @article {pmid29183332, year = {2017}, author = {Hall, AB and Yassour, M and Sauk, J and Garner, A and Jiang, X and Arthur, T and Lagoudas, GK and Vatanen, T and Fornelos, N and Wilson, R and Bertha, M and Cohen, M and Garber, J and Khalili, H and Gevers, D and Ananthakrishnan, AN and Kugathasan, S and Lander, ES and Blainey, P and Vlamakis, H and Xavier, RJ and Huttenhower, C}, title = {A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients.}, journal = {Genome medicine}, volume = {9}, number = {1}, pages = {103}, pmid = {29183332}, issn = {1756-994X}, support = {U54 DK102557/DK/NIDDK NIH HHS/United States ; U54DE023798//National Institutes of Health (US)/ ; P30 DK043351/DK/NIDDK NIH HHS/United States ; P30DK43351//National Institute of Diabetes and Digestive and Kidney Diseases/ ; R01 DK092405/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; K99 DK113224/DK/NIDDK NIH HHS/United States ; R01DK92405//National Institute of Diabetes and Digestive and Kidney Diseases/ ; MCB-1453942//National Science Foundation (US)/ ; }, mesh = {Adult ; Aged ; Feces/microbiology ; Gastrointestinal Microbiome/genetics ; Genome, Bacterial ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Middle Aged ; Oxidative Stress ; Phylogeny ; Ruminococcus/genetics/*isolation & purification ; Species Specificity ; Young Adult ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome. Here, we sought to identify strain-specific functional correlates with IBD outcomes.

METHODS: We performed metagenomic sequencing of monthly stool samples from 20 IBD patients and 12 controls (266 total samples). These were taxonomically profiled with MetaPhlAn2 and functionally profiled using HUMAnN2. Differentially abundant species were identified using MaAsLin and strain-specific pangenome haplotypes were analyzed using PanPhlAn.

RESULTS: We found a significantly higher abundance in patients of facultative anaerobes that can tolerate the increased oxidative stress of the IBD gut. We also detected dramatic, yet transient, blooms of Ruminococcus gnavus in IBD patients, often co-occurring with increased disease activity. We identified two distinct clades of R. gnavus strains, one of which is enriched in IBD patients. To study functional differences between these two clades, we augmented the R. gnavus pangenome by sequencing nine isolates from IBD patients. We identified 199 IBD-specific, strain-specific genes involved in oxidative stress responses, adhesion, iron-acquisition, and mucus utilization, potentially conferring an adaptive advantage for this R. gnavus clade in the IBD gut.

CONCLUSIONS: This study adds further evidence to the hypothesis that increased oxidative stress may be a major factor shaping the dysbiosis of the microbiome observed in IBD and suggests that R. gnavus may be an important member of the altered gut community in IBD.}, } @article {pmid29182421, year = {2018}, author = {McKenney, EA and O'Connell, TM and Rodrigo, A and Yoder, AD}, title = {Feeding strategy shapes gut metagenomic enrichment and functional specialization in captive lemurs.}, journal = {Gut microbes}, volume = {9}, number = {3}, pages = {202-217}, pmid = {29182421}, issn = {1949-0984}, support = {S10 OD018164/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/metabolism ; Biodiversity ; *Diet ; Feces/chemistry/microbiology ; Feeding Methods/veterinary ; Fermentation ; Fruit/chemistry/metabolism ; Gastrointestinal Tract/*microbiology/physiology ; Lemur/metabolism/*microbiology ; Metabolic Networks and Pathways ; *Metagenome ; Microbiota/genetics/*physiology ; Plant Leaves/chemistry/metabolism ; Species Specificity ; Strepsirhini/metabolism/microbiology ; }, abstract = {Many studies have demonstrated the effects of host diet on gut microbial membership, metagenomics, and fermentation individually; but few have attempted to interpret the relationship among these biological phenomena with respect to host features (e.g. gut morphology). We quantitatively compare the fecal microbial communities, metabolic pathways, and fermentation products associated with the nutritional intake of frugivorous (fruit-eating) and folivorous (leaf-eating) lemurs. Our results provide a uniquely multidimensional and comparative perspective on the adaptive dynamics between host and microbiome. Shotgun metagenomic sequencing revealed significant differential taxonomic and metabolic pathway enrichment, tailored to digest and detoxify different diets. Frugivorous metagenomes feature pathways to degrade simple carbohydrates and host-derived glycosaminoglycans, while folivorous metagenomes are equipped to break down phytic acid and other phytochemical compounds in an anaerobic environment. We used nuclear magnetic resonance based metabolic profiling of fecal samples to link metabolic pathways to fermentation products, confirming that the dissimilar substrates provided in each diet select for specific microbial functions. Fecal samples from frugivorous lemurs contained significantly different profiles of short chain fatty acids, alcohol fermentation products, amino acids, glucose, and glycerol compared to folivorous lemurs. We present the relationships between these datasets as an integrated visual framework, which we refer to as microbial geometry. We use microbial geometry to compare empirical gut microbial profiles across different feeding strategies, and suggest additional utility as a tool for hypothesis-generation.}, } @article {pmid29180750, year = {2017}, author = {Brooks, B and Olm, MR and Firek, BA and Baker, R and Thomas, BC and Morowitz, MJ and Banfield, JF}, title = {Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {1814}, pmid = {29180750}, issn = {2041-1723}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; S10 OD018174/OD/NIH HHS/United States ; }, mesh = {Cross Infection/*microbiology ; Environmental Exposure ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/microbiology/*physiology ; Humans ; Infant ; Infant, Newborn ; Infant, Premature/*physiology ; *Intensive Care Units, Neonatal ; Metagenomics/methods ; }, abstract = {Preterm infants exhibit different microbiome colonization patterns relative to full-term infants, and it is speculated that the hospital room environment may contribute to infant microbiome development. Here, we present a genome-resolved metagenomic study of microbial genotypes from the gastrointestinal tracts of infants and from the neonatal intensive care unit (NICU) room environment. Some strains detected in hospitalized infants also occur in sinks and on surfaces, and belong to species such as Staphylococcus epidermidis, Enterococcus faecalis, Pseudomonas aeruginosa, and Klebsiella pneumoniae, which are frequently implicated in nosocomial infection and preterm infant gut colonization. Of the 15 K. pneumoniae strains detected in the study, four were detected in both infant gut and room samples. Time series experiments showed that nearly all strains associated with infant gut colonization can be detected in the room after, and often before, detection in the gut. Thus, we conclude that a component of premature infant gut colonization is the cycle of microbial exchange between the room and the occupant.}, } @article {pmid29180726, year = {2018}, author = {Schulfer, AF and Battaglia, T and Alvarez, Y and Bijnens, L and Ruiz, VE and Ho, M and Robinson, S and Ward, T and Cox, LM and Rogers, AB and Knights, D and Sartor, RB and Blaser, MJ}, title = {Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice.}, journal = {Nature microbiology}, volume = {3}, number = {2}, pages = {234-242}, pmid = {29180726}, issn = {2058-5276}, support = {P01 DK094779/DK/NIDDK NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; P40 OD010995/OD/NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; P30 CA016086/CA/NCI NIH HHS/United States ; R01 DK090989/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*administration & dosage ; Colitis/chemically induced/*microbiology ; Colon/immunology/microbiology/pathology ; Diet, High-Fat ; Disease Models, Animal ; Disease Susceptibility/*microbiology ; Dysbiosis/chemically induced/microbiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Inflammatory Bowel Diseases/chemically induced/*microbiology ; Interleukin-10 ; Metagenome/drug effects ; Mice ; Mice, Inbred C57BL ; Phenotype ; Pregnancy ; }, abstract = {Antibiotic exposure in children has been associated with the risk of inflammatory bowel disease (IBD). Antibiotic use in children or in their pregnant mother can affect how the intestinal microbiome develops, so we asked whether the transfer of an antibiotic-perturbed microbiota from mothers to their children could affect their risk of developing IBD. Here we demonstrate that germ-free adult pregnant mice inoculated with a gut microbial community shaped by antibiotic exposure transmitted their perturbed microbiota to their offspring with high fidelity. Without any direct or continued exposure to antibiotics, this dysbiotic microbiota in the offspring remained distinct from controls for at least 21 weeks. By using both IL-10-deficient and wild-type mothers, we showed that both inoculum and genotype shape microbiota populations in the offspring. Because IL10[-/-] mice are genetically susceptible to colitis, we could assess the risk due to maternal transmission of an antibiotic-perturbed microbiota. We found that the IL10[-/-] offspring that had received the perturbed gut microbiota developed markedly increased colitis. Taken together, our findings indicate that antibiotic exposure shaping the maternal gut microbiota has effects that extend to the offspring, with both ecological and long-term disease consequences.}, } @article {pmid29180374, year = {2018}, author = {Gaby, JC and Rishishwar, L and Valderrama-Aguirre, LC and Green, SJ and Valderrama-Aguirre, A and Jordan, IK and Kostka, JE}, title = {Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {4}, pages = {}, pmid = {29180374}, issn = {1098-5336}, mesh = {Bacteria/classification/*genetics/metabolism ; Bacterial Physiological Phenomena ; Computational Biology ; DNA, Bacterial/genetics ; Ecosystem ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics ; Microbiota/*genetics/physiology ; Nitrogen/metabolism ; *Nitrogen Fixation ; Oxidoreductases/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The dinitrogenase reductase gene (nifH) is the most widely established molecular marker for the study of nitrogen-fixing prokaryotes in nature. A large number of PCR primer sets have been developed for nifH amplification, and the effective deployment of these approaches should be guided by a rapid, easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline. The developed amplicon sequencing workflow is a three-stage PCR-based approach that uses established technologies for incorporating sample-specific barcode sequences and sequencing adapters. Based on our primer evaluation, we recommend the Ando primer set be used with a modified annealing temperature of 58°C, as this approach captured the largest diversity of nifH templates, including paralog cluster IV/V sequences. To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences. In addition, we employed an empirical model to derive optimal operational taxonomic unit (OTU) cutoffs for the nifH gene at the species, genus, and family levels. A comprehensive workflow script named TaxADivA (TAXonomy Assignment and DIVersity Assessment) is provided to ease processing and analysis of nifH amplicons. Our approach is then validated through characterization of diazotroph communities across environmental gradients in beach sands impacted by the Deepwater Horizon oil spill in the Gulf of Mexico, in a peat moss-dominated wetland, and in various plant compartments of a sugarcane field.IMPORTANCE Nitrogen availability often limits ecosystem productivity, and nitrogen fixation, exclusive to prokaryotes, comprises a major source of nitrogen input that sustains food webs. The nifH gene, which codes for the iron protein of the nitrogenase enzyme, is the most widely established molecular marker for the study of nitrogen-fixing microorganisms (diazotrophs) in nature. In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering, and produces output in formats that may be used by programs that facilitate data exploration and analysis. Diazotroph diversity and community composition are linked to ecosystem functioning, and our results advance the phylogenetic characterization of diazotroph communities by providing empirically derived nifH similarity cutoffs for species, genus, and family levels. The utility of our pipeline is validated for diazotroph communities in a variety of ecosystems, including contaminated beach sands, peatland ecosystems, living plant tissues, and rhizosphere soil.}, } @article {pmid29179769, year = {2017}, author = {Ma, L and Li, B and Jiang, XT and Wang, YL and Xia, Y and Li, AD and Zhang, T}, title = {Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {154}, pmid = {29179769}, issn = {2049-2618}, support = {172057/15E//Hong Kong General Research Fund/ ; JCYJ20150831192847649//Shenzhen Knowledge Innovation Program-Basic Research Project/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/*isolation & purification ; China ; Drinking Water/*analysis/*microbiology ; Drug Resistance, Microbial/*genetics ; Drug Resistance, Multiple/genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Hong Kong ; Humans ; Metagenomics/methods ; Microbial Consortia/drug effects/genetics ; Public Health ; Surveys and Questionnaires ; United States ; Water Purification ; }, abstract = {BACKGROUND: Excesses of antibiotic resistance genes (ARGs), which are regarded as emerging environmental pollutants, have been observed in various environments. The incidence of ARGs in drinking water causes potential risks to human health and receives more attention from the public. However, ARGs harbored in drinking water remain largely unexplored. In this study, we aimed at establishing an antibiotic resistome catalogue in drinking water samples from a wide range of regions and to explore the potential hosts of ARGs.

RESULTS: A catalogue of antibiotic resistome in drinking water was established, and the host-tracking of ARGs was conducted through a large-scale survey using metagenomic approach. The drinking water samples were collected at the point of use in 25 cities in mainland China, Hong Kong, Macau, Taiwan, South Africa, Singapore and the USA. In total, 181 ARG subtypes belonging to 16 ARG types were detected with an abundance range of 2.8 × 10[-2] to 4.2 × 10[-1] copies of ARG per cell. The highest abundance was found in northern China (Henan Province). Bacitracin, multidrug, aminoglycoside, sulfonamide, and beta-lactam resistance genes were dominant in drinking water. Of the drinking water samples tested, 84% had a higher ARG abundance than typical environmental ecosystems of sediment and soil. Metagenomic assembly-based host-tracking analysis identified Acidovorax, Acinetobacter, Aeromonas, Methylobacterium, Methyloversatilis, Mycobacterium, Polaromonas, and Pseudomonas as the hosts of ARGs. Moreover, potential horizontal transfer of ARGs in drinking water systems was proposed by network and Procrustes analyses.

CONCLUSIONS: The antibiotic resistome catalogue compiled using a large-scale survey provides a useful reference for future studies on the global surveillance and risk management of ARGs in drinking water. .}, } @article {pmid29179741, year = {2017}, author = {Anderson, CL and Sullivan, MB and Fernando, SC}, title = {Dietary energy drives the dynamic response of bovine rumen viral communities.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {155}, pmid = {29179741}, issn = {2049-2618}, support = {2016-67011-24783//National Institute of Food and Agriculture/ ; 2012-68002-19823//National Institute of Food and Agriculture/ ; 3790.01//Gordon and Betty Moore Foundation/ ; }, mesh = {Animals ; Bacteriophages/genetics ; Cattle ; Cross-Over Studies ; DNA, Viral/genetics ; *Diet ; Food ; Metagenome ; Metagenomics/methods ; Microbiota/drug effects/*genetics ; Rumen/microbiology/*virology ; Sequence Analysis, DNA ; Viruses/classification/drug effects/*genetics/isolation & purification ; Zinc/pharmacology ; }, abstract = {BACKGROUND: Rumen microbes play a greater role in host energy acquisition than that of gut-associated microbes in monogastric animals. Although genome-enabled advancements are providing access to the vast diversity of uncultivated microbes, our understanding of variables shaping rumen microbial communities is in its infancy. Viruses have been shown to impact microbial populations through a myriad of processes, including cell lysis and reprogramming of host metabolism. However, little is known about the processes shaping the distribution of rumen viruses or how viruses may modulate microbial-driven processes in the rumen. To this end, we investigated how rumen bacterial and viral community structure and function responded in five steers fed four randomized dietary treatments in a crossover design.

RESULTS: Total digestible nutrients (TDN), a measure of dietary energy, best explained the variation in bacterial and viral communities. Additional ecological drivers of viral communities included dietary zinc content and microbial functional diversity. Using partial least squares regression, we demonstrate significant associations between the abundances of 267 viral populations and variables driving the variation in rumen viral communities. While rumen viruses were dynamic, 14 near ubiquitous viral populations were identified, suggesting the presence of a core rumen virome largely comprised of novel viruses. Moreover, analysis of virally encoded auxiliary metabolic genes (AMGs) indicates rumen viruses have glycosidic hydrolases to potentially augment the breakdown of complex carbohydrates to increase energy production. Other AMGs identified have a role in redirecting carbon to the pentose phosphate pathway and one carbon pools by folate to boost viral replication.

CONCLUSIONS: We demonstrate that rumen bacteria and viruses have differing responses and ecological drivers to dietary perturbation. Our results show that rumen viruses have implications for understanding the structuring of the previously identified core rumen microbiota and impacting microbial metabolism through a vast array of AMGs. AMGs in the rumen appear to have consequences for microbial metabolism that are largely in congruence with the current paradigm established in marine systems. This study provides a foundation for future hypotheses regarding the dynamics of viral-mediated processes in the rumen.}, } @article {pmid29178920, year = {2017}, author = {Nash, AK and Auchtung, TA and Wong, MC and Smith, DP and Gesell, JR and Ross, MC and Stewart, CJ and Metcalf, GA and Muzny, DM and Gibbs, RA and Ajami, NJ and Petrosino, JF}, title = {The gut mycobiome of the Human Microbiome Project healthy cohort.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {153}, pmid = {29178920}, issn = {2049-2618}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; 2 U54 HG003273//National Human Genome Research Institute/ ; }, mesh = {Candida/classification/genetics/isolation & purification ; Cohort Studies ; DNA, Ribosomal Spacer/genetics ; Feces/microbiology ; Fungi/classification/genetics/*isolation & purification ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; *Healthy Volunteers ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Malassezia/classification/genetics/isolation & purification ; Metagenomics/methods ; *Microbiota ; *Mycobiome ; RNA, Ribosomal, 18S/genetics ; Saccharomyces/classification/genetics/isolation & purification ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, human gut mycobiome studies have primarily been disease centric or in small cohorts of healthy individuals. To contribute to existing knowledge of the human mycobiome, we investigated the gut mycobiome of the Human Microbiome Project (HMP) cohort by sequencing the Internal Transcribed Spacer 2 (ITS2) region as well as the 18S rRNA gene.

RESULTS: Three hundred seventeen HMP stool samples were analyzed by ITS2 sequencing. Fecal fungal diversity was significantly lower in comparison to bacterial diversity. Yeast dominated the samples, comprising eight of the top 15 most abundant genera. Specifically, fungal communities were characterized by a high prevalence of Saccharomyces, Malassezia, and Candida, with S. cerevisiae, M. restricta, and C. albicans operational taxonomic units (OTUs) present in 96.8, 88.3, and 80.8% of samples, respectively. There was a high degree of inter- and intra-volunteer variability in fungal communities. However, S. cerevisiae, M. restricta, and C. albicans OTUs were found in 92.2, 78.3, and 63.6% of volunteers, respectively, in all samples donated over an approximately 1-year period. Metagenomic and 18S rRNA gene sequencing data agreed with ITS2 results; however, ITS2 sequencing provided greater resolution of the relatively low abundance mycobiome constituents.

CONCLUSIONS: Compared to bacterial communities, the human gut mycobiome is low in diversity and dominated by yeast including Saccharomyces, Malassezia, and Candida. Both inter- and intra-volunteer variability in the HMP cohort were high, revealing that unlike bacterial communities, an individual's mycobiome is no more similar to itself over time than to another person's. Nonetheless, several fungal species persisted across a majority of samples, evidence that a core gut mycobiome may exist. ITS2 sequencing data provided greater resolution of the mycobiome membership compared to metagenomic and 18S rRNA gene sequencing data, suggesting that it is a more sensitive method for studying the mycobiome of stool samples.}, } @article {pmid29177936, year = {2018}, author = {Reid, G}, title = {Is bacterial vaginosis a disease?.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {2}, pages = {553-558}, doi = {10.1007/s00253-017-8659-9}, pmid = {29177936}, issn = {1432-0614}, mesh = {*Disease Management ; *Dysbiosis ; Female ; Humans ; Metagenome ; Microbiota ; Probiotics/therapeutic use ; Vagina/*microbiology/physiopathology ; Vaginosis, Bacterial/diagnosis/*physiopathology/prevention & control/therapy ; }, abstract = {Bacterial vaginosis (BV) has been described as a disease, a disorder, a vaginal inflammation, an infection, a microbial dysbiosis, a condition, and in some women, a normal situation. In order to fit the definition of a disease, BV would have to be a disorder of function that produces specific signs or symptoms or affects the vagina in an aberrant way. Yet, there is little consistency in patients reporting signs and symptoms when BV is diagnosed, nor the appearance of aberrations to the vagina. If BV is not a disease, there are implications for its management and coverage of treatment costs, and for the conclusions drawn in a multitude of previous studies. It is time for BV to be redefined and for the various subsets to be given a separate terminology with specific methods of diagnosis and appropriate treatment and preventive strategies.}, } @article {pmid29177508, year = {2018}, author = {Gao, NL and Zhang, C and Zhang, Z and Hu, S and Lercher, MJ and Zhao, XM and Bork, P and Liu, Z and Chen, WH}, title = {MVP: a microbe-phage interaction database.}, journal = {Nucleic acids research}, volume = {46}, number = {D1}, pages = {D700-D707}, pmid = {29177508}, issn = {1362-4962}, mesh = {Archaea/genetics/*virology ; Bacteria/genetics/*virology ; Bacteriophages/classification/genetics/*physiology ; Base Sequence ; DNA, Bacterial/genetics ; DNA, Viral/genetics ; *Databases, Factual ; Databases, Genetic ; Datasets as Topic ; Gastrointestinal Microbiome ; Genome, Viral ; Host Specificity ; Humans ; Metagenomics ; Prophages/genetics ; Sequence Homology, Nucleic Acid ; Species Specificity ; Virus Integration ; }, abstract = {Phages invade microbes, accomplish host lysis and are of vital importance in shaping the community structure of environmental microbiota. More importantly, most phages have very specific hosts; they are thus ideal tools to manipulate environmental microbiota at species-resolution. The main purpose of MVP (Microbe Versus Phage) is to provide a comprehensive catalog of phage-microbe interactions and assist users to select phage(s) that can target (and potentially to manipulate) specific microbes of interest. We first collected 50 782 viral sequences from various sources and clustered them into 33 097 unique viral clusters based on sequence similarity. We then identified 26 572 interactions between 18 608 viral clusters and 9245 prokaryotes (i.e. bacteria and archaea); we established these interactions based on 30 321 evidence entries that we collected from published datasets, public databases and re-analysis of genomic and metagenomic sequences. Based on these interactions, we calculated the host range for each of the phage clusters and accordingly grouped them into subgroups such as 'species-', 'genus-' and 'family-' specific phage clusters. MVP is equipped with a modern, responsive and intuitive interface, and is freely available at: http://mvp.medgenius.info.}, } @article {pmid29176730, year = {2017}, author = {Junqueira, ACM and Ratan, A and Acerbi, E and Drautz-Moses, DI and Premkrishnan, BNV and Costea, PI and Linz, B and Purbojati, RW and Paulo, DF and Gaultier, NE and Subramanian, P and Hasan, NA and Colwell, RR and Bork, P and Azeredo-Espin, AML and Bryant, DA and Schuster, SC}, title = {The microbiomes of blowflies and houseflies as bacterial transmission reservoirs.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {16324}, pmid = {29176730}, issn = {2045-2322}, mesh = {Animals ; Feces/microbiology ; Helicobacter pylori/isolation & purification ; Houseflies/*microbiology ; Metagenomics ; Microbiota/physiology ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Blowflies and houseflies are mechanical vectors inhabiting synanthropic environments around the world. They feed and breed in fecal and decaying organic matter, but the microbiome they harbour and transport is largely uncharacterized. We sampled 116 individual houseflies and blowflies from varying habitats on three continents and subjected them to high-coverage, whole-genome shotgun sequencing. This allowed for genomic and metagenomic analyses of the host-associated microbiome at the species level. Both fly host species segregate based on principal coordinate analysis of their microbial communities, but they also show an overlapping core microbiome. Legs and wings displayed the largest microbial diversity and were shown to be an important route for microbial dispersion. The environmental sequencing approach presented here detected a stochastic distribution of human pathogens, such as Helicobacter pylori, thereby demonstrating the potential of flies as proxies for environmental and public health surveillance.}, } @article {pmid29176696, year = {2017}, author = {}, title = {Overcoming hurdles in sharing microbiome data.}, journal = {Nature microbiology}, volume = {2}, number = {12}, pages = {1573}, doi = {10.1038/s41564-017-0077-3}, pmid = {29176696}, issn = {2058-5276}, mesh = {Computational Biology/*methods ; Information Dissemination/*methods ; Metagenomics/*methods ; *Microbiota ; }, } @article {pmid29176284, year = {2017}, author = {}, title = {[Not Available].}, journal = {Nihon Rinsho Men'eki Gakkai kaishi = Japanese journal of clinical immunology}, volume = {40}, number = {4}, pages = {258a}, doi = {10.2177/jsci.40.258a}, pmid = {29176284}, issn = {1349-7413}, mesh = {Animals ; Autoimmune Diseases/microbiology ; Cardiovascular Diseases/microbiology ; Dysbiosis ; Epigenomics ; Gastrointestinal Microbiome/*genetics/immunology/physiology ; Host-Pathogen Interactions ; Humans ; Inflammatory Bowel Diseases/microbiology ; Metabolic Diseases/microbiology ; Metabolome ; Metagenome ; Transcriptome ; }, } @article {pmid29173869, year = {2018}, author = {Heintz-Buschart, A and Wilmes, P}, title = {Human Gut Microbiome: Function Matters.}, journal = {Trends in microbiology}, volume = {26}, number = {7}, pages = {563-574}, doi = {10.1016/j.tim.2017.11.002}, pmid = {29173869}, issn = {1878-4380}, mesh = {Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/*microbiology ; Host Microbial Interactions/*physiology ; Humans ; Metagenomics ; Microbiota/*physiology ; Transcriptome ; }, abstract = {The human gut microbiome represents a complex ecosystem contributing essential functions to its host. Recent large-scale metagenomic studies have provided insights into its structure and functional potential. However, the functional repertoire which is actually contributed to human physiology remains largely unexplored. Here, by leveraging recent omics datasets, we challenge current assumptions regarding key attributes of the functional gut microbiome, in particular with respect to its variability. We further argue that the closing of existing gaps in functional knowledge should be addressed by a most-wanted gene list, the development and application of molecular and cellular high-throughput measurements, the development and sensible use of experimental models, as well as the direct study of observable molecular effects in the human host.}, } @article {pmid29173057, year = {2018}, author = {Cydzik-Kwiatkowska, A and Zielińska, M}, title = {Microbial composition of biofilm treating wastewater rich in bisphenol A.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering}, volume = {53}, number = {4}, pages = {385-392}, doi = {10.1080/10934529.2017.1404326}, pmid = {29173057}, issn = {1532-4117}, mesh = {Benzhydryl Compounds/*analysis/metabolism ; Biodegradation, Environmental ; Biofilms/*growth & development ; *Microbial Consortia/physiology ; Phenols/*analysis/metabolism ; *Wastewater/chemistry/microbiology ; Water Pollutants, Chemical/*analysis/metabolism ; Water Purification/*methods ; }, abstract = {Although microbial degradation plays a major role in the removal of bisphenol A (BPA) from water environments, there is little information on the effect of BPA on microorganisms in wastewater treatment systems. The aim of this study was to determine the dynamics of the microbial communities in biofilm growing on porous ceramic supports in a column up-flow reactor during exposure to BPA at increasing concentrations from 0 to 10 mg L[-1]. Independent of BPA load, the efficiency of BPA removal was about 90%. Groups of microorganisms that differ in their sensitivity to the presence of BPA in wastewater were identified. The core microbial genera in the biofilm were Acidovorax, Pseudoxanthomonas and Acinetobacter. Arenimonas sp., Thauera sp. and Acidobacterium sp. were the main components of the biofilm in the absence of BPA in wastewater. Increased abundances of Pseudomonas sp., Acidovorax sp. and Luteimonas sp. in BPA-exposed biofilm indicate that these genera may have played important roles in BPA biodegradation. A correlation between Pseudomonas sp. abundance and BPA removal efficiency indicates that BPA was used directly as a source of carbon and energy for growth. This study indicates that the use of the biofilm reactor enables effective BPA removal from wastewater and expands knowledge about the microbial structure of communities responsible for BPA degradation.}, } @article {pmid29171095, year = {2018}, author = {Barko, PC and McMichael, MA and Swanson, KS and Williams, DA}, title = {The Gastrointestinal Microbiome: A Review.}, journal = {Journal of veterinary internal medicine}, volume = {32}, number = {1}, pages = {9-25}, pmid = {29171095}, issn = {1939-1676}, mesh = {Animals ; Dysbiosis/*veterinary ; *Gastrointestinal Microbiome ; Mammals ; Metabolomics ; Metagenomics ; }, abstract = {The gastrointestinal microbiome is a diverse consortium of bacteria, archaea, fungi, protozoa, and viruses that inhabit the gut of all mammals. Studies in humans and other mammals have implicated the microbiome in a range of physiologic processes that are vital to host health including energy homeostasis, metabolism, gut epithelial health, immunologic activity, and neurobehavioral development. The microbial genome confers metabolic capabilities exceeding those of the host organism alone, making the gut microbiome an active participant in host physiology. Recent advances in DNA sequencing technology and computational biology have revolutionized the field of microbiomics, permitting mechanistic evaluation of the relationships between an animal and its microbial symbionts. Changes in the gastrointestinal microbiome are associated with diseases in humans and animals including inflammatory bowel disease, asthma, obesity, metabolic syndrome, cardiovascular disease, immune-mediated conditions, and neurodevelopmental conditions such as autism spectrum disorder. While there remains a paucity of data regarding the intestinal microbiome in small animals, recent studies have helped to characterize its role in host animal health and associated disease states. This review is intended to familiarize small animal veterinarians with recent advances in the field of microbiomics and to prime them for a future in which diagnostic tests and therapies will incorporate these developments into clinical practice.}, } @article {pmid29169786, year = {2018}, author = {Kanokratana, P and Wongwilaiwalin, S and Mhuantong, W and Tangphatsornruang, S and Eurwilaichitr, L and Champreda, V}, title = {Characterization of cellulolytic microbial consortium enriched on Napier grass using metagenomic approaches.}, journal = {Journal of bioscience and bioengineering}, volume = {125}, number = {4}, pages = {439-447}, doi = {10.1016/j.jbiosc.2017.10.014}, pmid = {29169786}, issn = {1347-4421}, mesh = {Anaerobiosis ; Bacteroidetes/genetics/isolation & purification/metabolism ; Biofuels/microbiology ; Cellulose/*metabolism ; Firmicutes/genetics/isolation & purification/metabolism ; Lignin/metabolism ; *Metagenome ; *Metagenomics ; Microbial Consortia/*genetics ; Pennisetum/*metabolism/*microbiology ; Proteobacteria/genetics/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Energy grass is a promising substrate for production of biogas by anaerobic digestion. However, the conversion efficiency is limited by the enzymatically recalcitrant nature of cellulosic wastes. In this study, an active, structurally stable mesophilic lignocellulolytic degrading microbial consortium (Np-LMC) was constructed from forest compost soil microbiota by successive subcultivation on Napier grass under facultative anoxic conditions. According to tagged 16S rRNA gene amplicon sequencing, increasing abundance of facultative Proteobacteria was found in the middle of batch cycle which was then subsequently replaced by the cellulose degraders Firmicutes and Bacteroidetes along with decreasing CMCase, xylanase, and β-glucanase activity profiles in the supernatant after 5 days of incubation. Anaerobic/facultative bacteria Dysgonomonas and Sedimentibacter and aerobic bacteria Comamonas were the major genera found in Np-LMC. The consortium was active on degradation of the native and delignified grass. Direct shotgun sequencing of the consortium metagenome revealed relatively high abundance of genes encoding for various lignocellulose degrading enzymes in 23 glycosyl hydrolase (GH) families compared to previously reported cellulolytic microbial communities in mammalian digestive tracts. Enzymes attacking cellulose and hemicellulose were dominated by GH2, 3, 5, 9, 10, 26, 28 and 43 in addition to a variety of carbohydrate esterases (CE) and auxiliary activities (AA), reflecting adaptation of the enzyme systems to the native herbaceous substrate. The consortium identified here represents the microcosm specifically bred on energy grass, with potential for enhancing degradation of fibrous substrates in bioenergy industry.}, } @article {pmid29169222, year = {2018}, author = {Kim, D and Hong, S and Kim, YT and Ryu, S and Kim, HB and Lee, JH}, title = {Metagenomic Approach to Identifying Foodborne Pathogens on Chinese Cabbage.}, journal = {Journal of microbiology and biotechnology}, volume = {28}, number = {2}, pages = {227-235}, doi = {10.4014/jmb.1710.10021}, pmid = {29169222}, issn = {1738-8872}, mesh = {Bacteria/*classification/genetics/*isolation & purification ; Biodiversity ; Brassica/*microbiology ; DNA, Bacterial/genetics ; Foodborne Diseases/*microbiology ; *Metagenomics ; Microbial Consortia ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; }, abstract = {Foodborne illness represents a major threat to public health and is frequently attributed to pathogenic microorganisms on fresh produce. Recurrent outbreaks often come from vegetables that are grown close to or within the ground. Therefore, the first step to understanding the public health risk of microorganisms on fresh vegetables is to identify and describe microbial communities. We investigated the phyllospheres on Chinese cabbage (Brassica rapa subsp. pekinensis, N = 54). 16S rRNA gene amplicon sequencing targeting the V5-V6 region of 16S rRNA genes was conducted by employing the Illumina MiSeq system. Sequence quality was assessed, and phylogenetic assessments were performed using the RDP classifier implemented in QIIME with a bootstrap cutoff of 80%. Principal coordinate analysis was performed using a weighted Fast UniFrac matrix. The average number of sequence reads generated per sample was 34,584. At the phylum level, bacterial communities were composed primarily of Proteobacteria and Bacteroidetes. The most abundant genera on Chinese cabbages were Chryseobacterium, Aurantimonadaceae_g, Sphingomonas, and Pseudomonas. Diverse potential pathogens, such as Pantoea, Erwinia, Klebsiella, Yersinia, Bacillus, Staphylococcus, Salmonella, and Clostridium were also detected from the samples. Although further epidemiological studies will be required to determine whether the detected potential pathogens are associated with foodborne illness, our results imply that a metagenomic approach can be used to detect pathogenic bacteria on fresh vegetables.}, } @article {pmid29169110, year = {2018}, author = {Liu, Y and Li, J and Yu, J and Wang, Y and Lu, J and Shang, EX and Zhu, Z and Guo, J and Duan, J}, title = {Disorder of gut amino acids metabolism during CKD progression is related with gut microbiota dysbiosis and metagenome change.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {149}, number = {}, pages = {425-435}, doi = {10.1016/j.jpba.2017.11.040}, pmid = {29169110}, issn = {1873-264X}, mesh = {Amino Acids/blood/*metabolism/urine ; Animals ; Bacteria/genetics ; Bacterial Physiological Phenomena ; Cresols/blood/metabolism/urine ; DNA, Bacterial/isolation & purification ; Disease Models, Animal ; Disease Progression ; Dysbiosis/*microbiology ; Feces/chemistry/microbiology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/metabolism/*microbiology ; Humans ; Indoles/blood/metabolism/urine ; Male ; Metabolic Networks and Pathways ; Metagenome/*physiology ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; Renal Insufficiency, Chronic/blood/*metabolism/urine ; Sequence Analysis, DNA ; Specific Pathogen-Free Organisms ; }, abstract = {Chronic kidney disease (CKD) is a worldwide public health problem. Uremic retention solutes such as indoxyl sulfate (IS) and p-cresyl sulfate (PCS) are accumulated in CKD patients and are associated with the incidence of CKD progression. Amino acids are the major precursors of uremic retention solutes in gut. The dynamic change of amino acid metabolism in the gut during CKD progression has not been reported previously. In this paper, we studied the dynamic change of gut IS/PCS precursor and amino acid metabolism profile during CKD progression in 5/6 nephrectomized (5/6Nx) rats model. The related gut microbiota and metagenome profile was also studied. Rat plasma, urine and feces were collected at different time points after nephrectomization. Plasma IS and PCS, fecal indole (the precursor of IS), p-cresol (the precursor of PCS) and 19 kinds of amino acids were analyzed by LC-MS. During CKD progression, 5/6 Nx rats showed increased plasma IS, PCS concentration and increased fecal indole, p-cresol concentration. 5/6 Nx rats also showed disordered gut amino acids metabolism profile which became more significant along with the progession of CKD. The abundance of some specific gut bacteria also changed significantly in 5/6 Nx rats. The 16S rDNA sequencing data of gut microbiota was further analyzed by an online tool PICRUSt, a large-scale computational method for metagenomes prediction with 16S rDNA sequencing data. The content of each gene was compared between the two groups by Mann-Whitney U test, and then the significantly regulated genes in 5/6 Nx group were subjected to KEGG website. The amino acid metabolism related genes were picked out. Most of these genes are more abundant in 5/6 Nx groups. Our study showed that gut amino acids metabolism profile was disordered with CKD progression, which was highly related to the gut microbiota dysbiosis and metagenome change. And that regulation of gut amino acids metabolism pathway may be a possible way to intervene the progression of CKD.}, } @article {pmid29169088, year = {2017}, author = {Maier, L and Typas, A}, title = {Systematically investigating the impact of medication on the gut microbiome.}, journal = {Current opinion in microbiology}, volume = {39}, number = {}, pages = {128-135}, doi = {10.1016/j.mib.2017.11.001}, pmid = {29169088}, issn = {1879-0364}, mesh = {Animals ; Gastrointestinal Microbiome/*drug effects ; Humans ; Models, Biological ; Prescription Drugs/*pharmacology ; }, abstract = {In the recent years, there is accumulating evidence for a strong impact of medication on the gut microbiota composition. This evidence comes from metagenomics-based associations and extends beyond classical antibacterials to a handful of human-targeted drugs. To answer whether such effects are direct and explore their consequences in human health, we need to develop experimental platforms that will allow for systematic profiling of drug-microbiota interactions. Here, we discuss approaches, considerations, experimental setups and strategies that can be used to tackle this need, but can be also readily transmitted to related questions in the microbiome field. A comprehensive understanding of how therapeutics interact with gut microbes will open up the path for further mechanistic dissection of such interactions, and ultimately improve not only our understanding of the gut microbiome, but also drug safety and efficacy.}, } @article {pmid29167556, year = {2018}, author = {Del Bas, JM and Guirro, M and Boqué, N and Cereto, A and Ras, R and Crescenti, A and Caimari, A and Canela, N and Arola, L}, title = {Alterations in gut microbiota associated with a cafeteria diet and the physiological consequences in the host.}, journal = {International journal of obesity (2005)}, volume = {42}, number = {4}, pages = {746-754}, pmid = {29167556}, issn = {1476-5497}, mesh = {Animals ; Diet, High-Fat/*adverse effects ; Gastrointestinal Microbiome/genetics/*physiology ; Insulin Resistance ; Male ; Metabolic Networks and Pathways/physiology ; Metabolic Syndrome/metabolism ; Metagenome/genetics/physiology ; Obesity/*metabolism ; Organ Size/physiology ; Rats ; Rats, Wistar ; }, abstract = {OBJECTIVE: Gut microbiota have been described as key factors in the pathophysiology of obesity and different components of metabolic syndrome (MetS). The cafeteria diet (CAF)-fed rat is a preclinical model that reproduces most of the alterations found in human MetS by simulating a palatable human unbalanced diet. Our objective was to assess the effects of CAF on gut microbiota and their associations with different components of MetS in Wistar rats.

METHODS: Animals were fed a standard diet or CAF for 12 weeks. A partial least square-based methodology was used to reveal associations between gut microbiota, characterized by 16S ribosomal DNA gene sequencing, and biochemical, nutritional and physiological parameters.

RESULTS: CAF feeding resulted in obesity, dyslipidemia, insulin resistance and hepatic steatosis. These changes were accompanied by a significant decrease in gut bacterial diversity, decreased Firmicutes and an increase in Actinobacteria and Proteobacteria abundances, which were concomitant with increased endotoxemia. Associations of different genera with the intake of lipids and carbohydrates were opposed from those associated with the intake of fiber. Changes in gut microbiota were also associated with the different physiological effects of CAF, mainly increased adiposity and altered levels of plasma leptin and glycerol, consistent with altered adipose tissue metabolism. Also hepatic lipid accretion was associated with changes in microbiota, highlighting the relevance of gut microbiota homeostasis in the adipose-liver axis.

CONCLUSIONS: Overall, our results suggest that CAF feeding has a profound impact on the gut microbiome and, in turn, that these changes may be associated with important features of MetS.}, } @article {pmid29165844, year = {2018}, author = {Lassalle, F and Spagnoletti, M and Fumagalli, M and Shaw, L and Dyble, M and Walker, C and Thomas, MG and Bamberg Migliano, A and Balloux, F}, title = {Oral microbiomes from hunter-gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet.}, journal = {Molecular ecology}, volume = {27}, number = {1}, pages = {182-195}, doi = {10.1111/mec.14435}, pmid = {29165844}, issn = {1365-294X}, support = {BB/H008802/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/P007597/1/MRC_/Medical Research Council/United Kingdom ; MR/N010760/1/MRC_/Medical Research Council/United Kingdom ; /DH_/Department of Health/United Kingdom ; }, mesh = {Biodiversity ; *Diet, Paleolithic ; *Farmers ; Genetics, Population ; Geography ; *Host-Pathogen Interactions ; Humans ; *Microbiota/genetics ; Mouth/*microbiology ; Philippines ; Principal Component Analysis ; Species Specificity ; }, abstract = {Maladaptation to modern diets has been implicated in several chronic disorders. Given the higher prevalence of disease such as dental caries and chronic gum diseases in industrialized societies, we sought to investigate the impact of different subsistence strategies on oral health and physiology, as documented by the oral microbiome. To control for confounding variables such as environment and host genetics, we sampled saliva from three pairs of populations of hunter-gatherers and traditional farmers living in close proximity in the Philippines. Deep shotgun sequencing of salivary DNA generated high-coverage microbiomes along with human genomes. Comparing these microbiomes with publicly available data from individuals living on a Western diet revealed that abundance ratios of core species were significantly correlated with subsistence strategy, with hunter-gatherers and Westerners occupying either end of a gradient of Neisseria against Haemophilus, and traditional farmers falling in between. Species found preferentially in hunter-gatherers included microbes often considered as oral pathogens, despite their hosts' apparent good oral health. Discriminant analysis of gene functions revealed vitamin B5 autotrophy and urease-mediated pH regulation as candidate adaptations of the microbiome to the hunter-gatherer and Western diets, respectively. These results suggest that major transitions in diet selected for different communities of commensals and likely played a role in the emergence of modern oral pathogens.}, } @article {pmid29163419, year = {2017}, author = {Cabello-Yeves, PJ and Ghai, R and Mehrshad, M and Picazo, A and Camacho, A and Rodriguez-Valera, F}, title = {Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2131}, pmid = {29163419}, issn = {1664-302X}, abstract = {The phylum Verrucomicrobia contains freshwater representatives which remain poorly studied at the genomic, taxonomic, and ecological levels. In this work we present eighteen new reconstructed verrucomicrobial genomes from two freshwater reservoirs located close to each other (Tous and Amadorio, Spain). These metagenome-assembled genomes (MAGs) display a remarkable taxonomic diversity inside the phylum and comprise wide ranges of estimated genome sizes (from 1.8 to 6 Mb). Among all Verrucomicrobia studied we found some of the smallest genomes of the Spartobacteria and Opitutae classes described so far. Some of the Opitutae family MAGs were small, cosmopolitan, with a general heterotrophic metabolism with preference for carbohydrates, and capable of xylan, chitin, or cellulose degradation. Besides, we assembled large copiotroph genomes, which contain a higher number of transporters, polysaccharide degrading pathways and in general more strategies for the uptake of nutrients and carbohydrate-based metabolic pathways in comparison with the representatives with the smaller genomes. The diverse genomes revealed interesting features like green-light absorbing rhodopsins and a complete set of genes involved in nitrogen fixation. The large diversity in genome sizes and physiological properties emphasize the diversity of this clade in freshwaters enlarging even further the already broad eco-physiological range of these microbes.}, } @article {pmid29161643, year = {2018}, author = {Silbande, A and Adenet, S and Chopin, C and Cornet, J and Smith-Ravin, J and Rochefort, K and Leroi, F}, title = {Effect of vacuum and modified atmosphere packaging on the microbiological, chemical and sensory properties of tropical red drum (Sciaenops ocellatus) fillets stored at 4°C.}, journal = {International journal of food microbiology}, volume = {266}, number = {}, pages = {31-41}, doi = {10.1016/j.ijfoodmicro.2017.10.015}, pmid = {29161643}, issn = {1879-3460}, mesh = {Animals ; Bacteria/isolation & purification ; Biogenic Amines/analysis ; Colony Count, Microbial ; Fishes/*microbiology ; *Food Microbiology ; Food Packaging/*standards ; Metagenomics ; Microbiota ; Nitrogen/analysis ; *Vacuum ; }, abstract = {AIMS: The effect of vacuum (VP - 4°C) and CO2/N2-atmosphere (MAP - 4°C) packaging on the quality of red drum fillets compared with whole gutted iced fish was investigated.

METHODS AND RESULTS: A metagenomic approach, bacterial enumeration and isolation, biochemical and sensory analyses were carried out. The organoleptic rejection of whole fish was observed at day 15 whereas VP and MAP fillets appeared unacceptable only after 29days. At these dates, total mesophilic counts reached 10[7]-10[8]CFU g[-1]. According to Illumina MiSeq sequencing, Arthrobacter, Chryseobacterium, Brevibacterium, Staphylococcus and Kocuria were the main genera of the fresh red drum fillets. At the sensory rejection time, lactic acid bacteria (LAB), particularly Carnobacterium sp., dominated the microbiota of both types of packaging. The pH value of fresh samples was between 5.96 and 6.37 and did not vary greatly in all trials. Total volatile basic nitrogen (TVBN) and trimethylamine (TMA) concentrations were low and not represent reliable indicators of the spoilage, contrary to some biogenic amines (cadaverine, putrescine and tyramine).

CONCLUSION: Chilled packed fillets of red drum have an extended shelf-life compared to whole gutted iced fish. Overall, few differences in sensory and microbial quality were observed between the VP and MAP samples.

Next-Generation Sequencing (NGS) provided data on the microbiota of a tropical fish.}, } @article {pmid29159825, year = {2018}, author = {Hartmann, P and Hochrath, K and Horvath, A and Chen, P and Seebauer, CT and Llorente, C and Wang, L and Alnouti, Y and Fouts, DE and Stärkel, P and Loomba, R and Coulter, S and Liddle, C and Yu, RT and Ling, L and Rossi, SJ and DePaoli, AM and Downes, M and Evans, RM and Brenner, DA and Schnabl, B}, title = {Modulation of the intestinal bile acid/farnesoid X receptor/fibroblast growth factor 15 axis improves alcoholic liver disease in mice.}, journal = {Hepatology (Baltimore, Md.)}, volume = {67}, number = {6}, pages = {2150-2166}, pmid = {29159825}, issn = {1527-3350}, support = {P01 HL088093/HL/NHLBI NIH HHS/United States ; R01 AA020703/AA/NIAAA NIH HHS/United States ; P42 ES010337/ES/NIEHS NIH HHS/United States ; U01 AA021856/AA/NIAAA NIH HHS/United States ; U01 AA024726/AA/NIAAA NIH HHS/United States ; I01 BX002213/BX/BLRD VA/United States ; P30 CA014195/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bile Acids and Salts/*physiology ; Ethanol/*administration & dosage ; Fibroblast Growth Factors/*physiology ; Gastrointestinal Microbiome/*physiology ; Intestinal Mucosa/metabolism ; Intestines/microbiology ; Liver Diseases, Alcoholic/*etiology ; Mice ; Mice, Inbred C57BL ; Receptors, Cytoplasmic and Nuclear/*physiology ; }, abstract = {UNLABELLED: Alcoholic liver disease (ALD) is associated with changes in the intestinal microbiota. Functional consequences of alcohol-associated dysbiosis are largely unknown. The aim of this study was to identify a mechanism of how changes in the intestinal microbiota contribute to ALD. Metagenomic sequencing of intestinal contents demonstrated that chronic ethanol feeding in mice is associated with an over-representation of bacterial genomic DNA encoding choloylglycine hydrolase, which deconjugates bile acids in the intestine. Bile acid analysis confirmed an increased amount of unconjugated bile acids in the small intestine after ethanol administration. Mediated by a lower farnesoid X receptor (FXR) activity in enterocytes, lower fibroblast growth factor (FGF)-15 protein secretion was associated with increased hepatic cytochrome P450 enzyme (Cyp)-7a1 protein expression and circulating bile acid levels. Depletion of the commensal microbiota with nonabsorbable antibiotics attenuated hepatic Cyp7a1 expression and reduced ALD in mice, suggesting that increased bile acid synthesis is dependent on gut bacteria. To restore intestinal FXR activity, we used a pharmacological intervention with the intestine-restricted FXR agonist fexaramine, which protected mice from ethanol-induced liver injury. Whereas bile acid metabolism was only minimally altered, fexaramine treatment stabilized the gut barrier and significantly modulated hepatic genes involved in lipid metabolism. To link the beneficial metabolic effect to FGF15, a nontumorigenic FGF19 variant-a human FGF15 ortholog-was overexpressed in mice using adeno-associated viruses. FGF19 treatment showed similarly beneficial metabolic effects and ameliorated alcoholic steatohepatitis.

CONCLUSION: Taken together, alcohol-associated metagenomic changes result in alterations of bile acid profiles. Targeted interventions improve bile acid-FXR-FGF15 signaling by modulation of hepatic Cyp7a1 and lipid metabolism, and reduce ethanol-induced liver disease in mice. (Hepatology 2018;67:2150-2166).}, } @article {pmid29157743, year = {2018}, author = {Cocolin, L and Mataragas, M and Bourdichon, F and Doulgeraki, A and Pilet, MF and Jagadeesan, B and Rantsiou, K and Phister, T}, title = {Next generation microbiological risk assessment meta-omics: The next need for integration.}, journal = {International journal of food microbiology}, volume = {287}, number = {}, pages = {10-17}, doi = {10.1016/j.ijfoodmicro.2017.11.008}, pmid = {29157743}, issn = {1879-3460}, mesh = {*Computational Biology ; Food Microbiology/*trends ; Metabolomics ; Metagenomics ; Microbiota ; Proteomics ; Risk Assessment/trends ; }, abstract = {The development of a multi-omics approach has provided a new approach to the investigation of microbial communities allowing an integration of data, which can be used to better understand the behaviour of and interactions between community members. Metagenomics, metatranscriptomics, metaproteomics and metabolomics have the potential of producing a large amount of data in a very short time, however an important challenge is how to exploit and interpret these data to assist risk managers in food safety and quality decisions. This can be achieved by integrating multi-omics data in microbiological risk assessment. In this paper we identify limitations and challenges of the multi-omics approach, underlining promising potentials, but also identifying gaps, which should be addressed for its full exploitation. A view on how this new way of investigation will impact the traditional microbiology schemes in the food industry is also presented.}, } @article {pmid29155257, year = {2018}, author = {Fonseca, JP and Hoffmann, L and Cabral, BCA and Dias, VHG and Miranda, MR and de Azevedo Martins, AC and Boschiero, C and Bastos, WR and Silva, R}, title = {Contrasting the microbiomes from forest rhizosphere and deeper bulk soil from an Amazon rainforest reserve.}, journal = {Gene}, volume = {642}, number = {}, pages = {389-397}, doi = {10.1016/j.gene.2017.11.039}, pmid = {29155257}, issn = {1879-0038}, mesh = {Archaea/*classification/genetics/isolation & purification ; Bacteria/*classification/genetics/isolation & purification ; Cluster Analysis ; Fungi/*classification/genetics/isolation & purification ; Metagenomics/methods ; Microbiota ; Rainforest ; Rhizosphere ; Sequence Analysis, DNA/methods ; *Soil Microbiology ; }, abstract = {Pristine forest ecosystems provide a unique perspective for the study of plant-associated microbiota since they host a great microbial diversity. Although the Amazon forest is one of the hotspots of biodiversity around the world, few metagenomic studies described its microbial community diversity thus far. Understanding the environmental factors that can cause shifts in microbial profiles is key to improving soil health and biogeochemical cycles. Here we report a taxonomic and functional characterization of the microbiome from the rhizosphere of Brosimum guianense (Snakewood), a native tree, and bulk soil samples from a pristine Brazilian Amazon forest reserve (Cuniã), for the first time by the shotgun approach. We identified several fungi and bacteria taxon significantly enriched in forest rhizosphere compared to bulk soil samples. For archaea, the trend was the opposite, with many archaeal phylum and families being considerably more enriched in bulk soil compared to forest rhizosphere. Several fungal and bacterial decomposers like Postia placenta and Catenulispora acidiphila which help maintain healthy forest ecosystems were found enriched in our samples. Other bacterial species involved in nitrogen (Nitrobacter hamburgensis and Rhodopseudomonas palustris) and carbon cycling (Oligotropha carboxidovorans) were overrepresented in our samples indicating the importance of these metabolic pathways for the Amazon rainforest reserve soil health. Hierarchical clustering based on taxonomic similar microbial profiles grouped the forest rhizosphere samples in a distinct clade separated from bulk soil samples. Principal coordinate analysis of our samples with publicly available metagenomes from the Amazon region showed grouping into specific rhizosphere and bulk soil clusters, further indicating distinct microbial community profiles. In this work, we reported significant shifts in microbial community structure between forest rhizosphere and bulk soil samples from an Amazon forest reserve that are probably caused by more than one environmental factors such as rhizosphere and soil depth.}, } @article {pmid29153320, year = {2017}, author = {Dudek, NK and Sun, CL and Burstein, D and Kantor, RS and Aliaga Goltsman, DS and Bik, EM and Thomas, BC and Banfield, JF and Relman, DA}, title = {Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome.}, journal = {Current biology : CB}, volume = {27}, number = {24}, pages = {3752-3762.e6}, doi = {10.1016/j.cub.2017.10.040}, pmid = {29153320}, issn = {1879-0445}, mesh = {Animals ; Archaea/*classification ; Bacteria/*classification ; Bottle-Nosed Dolphin/*microbiology ; Female ; *Genome, Archaeal ; *Genome, Bacterial ; Male ; *Metagenome ; Metagenomics ; *Microbiota ; Mouth/microbiology ; }, abstract = {The vast majority of bacterial diversity lies within phylum-level lineages called "candidate phyla," which lack isolated representatives and are poorly understood. These bacteria are surprisingly abundant in the oral cavity of marine mammals. We employed a genome-resolved metagenomic approach to recover and characterize genomes and functional potential from microbes in the oral gingival sulcus of two bottlenose dolphins (Tursiops truncatus). We detected organisms from 24 known bacterial phyla and one archaeal phylum. We also recovered genomes from two deep-branching, previously uncharacterized phylum-level lineages (here named "Candidatus Delphibacteria" and "Candidatus Fertabacteria"). The Delphibacteria lineage is found in both managed and wild dolphins; its metabolic profile suggests a capacity for denitrification and a possible role in dolphin health. We uncovered a rich diversity of predicted Cas9 proteins, including the two longest predicted Cas9 proteins to date. Notably, we identified the first type II CRISPR-Cas systems encoded by members of the Candidate Phyla Radiation. Using their spacer sequences, we subsequently identified and assembled a complete Saccharibacteria phage genome. These findings underscore the immense microbial diversity and functional potential that await discovery in previously unexplored environments.}, } @article {pmid29146901, year = {2017}, author = {Zomorrodi, AR and Segrè, D}, title = {Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {1563}, pmid = {29146901}, issn = {2041-1723}, support = {R01 DE024468/DE/NIDCR NIH HHS/United States ; R01 GM121950/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Ecosystem ; Energy Metabolism/*genetics ; Evolution, Molecular ; *Game Theory ; Metagenome/*genetics ; Microbial Interactions ; Microbiota/*genetics ; Models, Genetic ; }, abstract = {Metabolite exchanges in microbial communities give rise to ecological interactions that govern ecosystem diversity and stability. It is unclear, however, how the rise of these interactions varies across metabolites and organisms. Here we address this question by integrating genome-scale models of metabolism with evolutionary game theory. Specifically, we use microbial fitness values estimated by metabolic models to infer evolutionarily stable interactions in multi-species microbial "games". We first validate our approach using a well-characterized yeast cheater-cooperator system. We next perform over 80,000 in silico experiments to infer how metabolic interdependencies mediated by amino acid leakage in Escherichia coli vary across 189 amino acid pairs. While most pairs display shared patterns of inter-species interactions, multiple deviations are caused by pleiotropy and epistasis in metabolism. Furthermore, simulated invasion experiments reveal possible paths to obligate cross-feeding. Our study provides genomically driven insight into the rise of ecological interactions, with implications for microbiome research and synthetic ecology.}, } @article {pmid29146247, year = {2018}, author = {Vepštaitė-Monstavičė, I and Lukša, J and Stanevičienė, R and Strazdaitė-Žielienė, Ž and Yurchenko, V and Serva, S and Servienė, E}, title = {Distribution of apple and blackcurrant microbiota in Lithuania and the Czech Republic.}, journal = {Microbiological research}, volume = {206}, number = {}, pages = {1-8}, doi = {10.1016/j.micres.2017.09.004}, pmid = {29146247}, issn = {1618-0623}, mesh = {Bacteria/classification/genetics/isolation & purification ; Czech Republic ; DNA, Bacterial/isolation & purification ; DNA, Fungal/isolation & purification ; Ecology ; Fruit/microbiology ; Fungi/classification/genetics/isolation & purification ; Lithuania ; Malus/*microbiology ; Metagenomics/methods ; *Microbial Consortia ; *Microbiota/genetics ; Phylogeny ; Ribes/*microbiology ; }, abstract = {The microbial assemblies on the surface of plants correlate with specific climatic features, suggesting a direct link between environmental conditions and microbial inhabitation patterns. At the same time however, microbial communities demonstrate distinct profiles depending on the plant species and region of origin. In this study, we report Next Generation Sequencing-based metagenomic analysis of microbial communities associated with apple and blackcurrant fruits harvested from Lithuania and the Czech Republic. Differences in the taxonomic composition of eukaryotic and prokaryotic microorganisms were observed between plant types. Our results revealed limited geographic differentiation between the bacterial and fungal communities associated with apples. In contrast, blackcurrant berries harvested from different regions demonstrated high diversity in both bacterial and fungal microbiota structures. Among fungal and bacterial microorganisms, we identified both potentially beneficial (Cryptococcus, Hanseniaspora, Massilia, Rhodotorula, Sphingomonas) and phytopathogenic microorganisms (Cladosporium, Pantoea, Phoma, Pseudomonas, Septoria, Taphrina) indicating their important roles in ecological and evolutionary processes.}, } @article {pmid29142285, year = {2017}, author = {Mehrpouya-Bahrami, P and Chitrala, KN and Ganewatta, MS and Tang, C and Murphy, EA and Enos, RT and Velazquez, KT and McCellan, J and Nagarkatti, M and Nagarkatti, P}, title = {Blockade of CB1 cannabinoid receptor alters gut microbiota and attenuates inflammation and diet-induced obesity.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15645}, pmid = {29142285}, issn = {2045-2322}, support = {K01 AT007824/AT/NCCIH NIH HHS/United States ; R01 MH094755/MH/NIMH NIH HHS/United States ; R01 ES019313/ES/NIEHS NIH HHS/United States ; P20 GM103641/GM/NIGMS NIH HHS/United States ; P01 AT003961/AT/NCCIH NIH HHS/United States ; R01 AT006888/AT/NCCIH NIH HHS/United States ; }, mesh = {Adipose Tissue/metabolism/pathology ; Animals ; Cannabinoid Receptor Antagonists/*pharmacology ; Cell Movement/drug effects ; Cytokines/metabolism ; Gastrointestinal Microbiome/*drug effects ; Inflammation/drug therapy/metabolism/pathology ; Macrophages/metabolism ; Male ; Mice ; Obesity/*drug therapy/etiology/metabolism ; Receptor, Cannabinoid, CB1/*antagonists & inhibitors/metabolism ; Rimonabant/*pharmacology ; }, abstract = {Obesity is characterized by chronic low-grade, systemic inflammation, altered gut microbiota, and gut barrier disruption. Additionally, obesity is associated with increased activity of endocannabinoid system (eCB). However, the clear connection between gut microbiota and the eCB system in the regulation of energy homeostasis and adipose tissue inflammation and metabolism, remains to be established. We investigated the effect of treatment of mice with a cannabinoid receptor 1 (CB1) antagonist on Diet-Induced Obesity (DIO), specifically whether such a treatment that blocks endocannabinoid activity can induce changes in gut microbiota and anti-inflammatory state in adipose tissue. Blockade of CB1 attenuated DIO, inflammatory cytokines and trafficking of M1 macrophages into adipose tissue. Decreased inflammatory tone was associated with a lower intestinal permeability and decreased metabolic endotoxemia as evidenced by reduced plasma LPS level, and improved hyperglycemia and insulin resistance. 16S rRNA metagenomics sequencing revealed that CB1 blockade dramatically increased relative abundance of Akkermansia muciniphila and decreased Lanchnospiraceae and Erysipelotrichaceae in the gut. Together, the current study suggests that blocking of CB1 ameliorates Diet-Induced Obesity and metabolic disorder by modulating macrophage inflammatory mediators, and that this effect is associated with alterations in gut microbiota and their metabolites.}, } @article {pmid29142271, year = {2017}, author = {Stadlbauer, V and Horvath, A and Ribitsch, W and Schmerböck, B and Schilcher, G and Lemesch, S and Stiegler, P and Rosenkranz, AR and Fickert, P and Leber, B}, title = {Structural and functional differences in gut microbiome composition in patients undergoing haemodialysis or peritoneal dialysis.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15601}, pmid = {29142271}, issn = {2045-2322}, support = {P 24362/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Aged ; C-Reactive Protein/genetics ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Inflammation/genetics/*microbiology/pathology ; Kidney Failure, Chronic/*genetics/microbiology/pathology ; Male ; Middle Aged ; Peritoneal Dialysis/adverse effects ; Renal Dialysis/adverse effects ; }, abstract = {Complications of end-stage renal disease (ESRD) are critically related to inflammation. The gut microbiome is a key driver of inflammation. Since dialysis modalities may differently influence the gut microbiome, we aimed to compare the effects of haemodialysis (HD) and peritoneal dialysis (PD) on patients' gut microbiome composition and function. We therefore studied faecal microbiome composition and function as well as inflammation and gut permeability in 30 patients with ESRD (15 HD, 15 PD) and compared to 21 healthy controls. We found an increase in potentially pathogenic species and a decrease in beneficial species in patients on HD and to a lesser extend in patients on PD when compared to controls. These changes in taxonomic composition also resulted in differences in predicted metagenome functions of the faecal microbiome. In HD but not in PD, changes in microbiome composition were associated with an increase in c-reactive protein (CRP) but not with intestinal inflammation or gut permeability. In conclusion microbiome composition in ESRD differs from healthy controls but also between modes of dialysis. These differences are associated with systemic inflammation and cannot completely be explained by dialysis vintage. The mode of renal replacement therapy seems to be an important driver of dysbiosis in ESRD.}, } @article {pmid29141885, year = {2017}, author = {Ni, J and Shen, TD and Chen, EZ and Bittinger, K and Bailey, A and Roggiani, M and Sirota-Madi, A and Friedman, ES and Chau, L and Lin, A and Nissim, I and Scott, J and Lauder, A and Hoffmann, C and Rivas, G and Albenberg, L and Baldassano, RN and Braun, J and Xavier, RJ and Clish, CB and Yudkoff, M and Li, H and Goulian, M and Bushman, FD and Lewis, JD and Wu, GD}, title = {A role for bacterial urease in gut dysbiosis and Crohn's disease.}, journal = {Science translational medicine}, volume = {9}, number = {416}, pages = {}, pmid = {29141885}, issn = {1946-6242}, support = {P30 DK040561/DK/NIDDK NIH HHS/United States ; UH2 DK083981/DK/NIDDK NIH HHS/United States ; UH3 DK083981/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; K24 DK078228/DK/NIDDK NIH HHS/United States ; P30 DK050306/DK/NIDDK NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; T32 DK007066/DK/NIDDK NIH HHS/United States ; R01 GM080279/GM/NIGMS NIH HHS/United States ; U54 HD086984/HD/NICHD NIH HHS/United States ; R01 GM103591/GM/NIGMS NIH HHS/United States ; P01 DK046763/DK/NIDDK NIH HHS/United States ; K23 DK109136/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/*metabolism ; Crohn Disease/*metabolism/*microbiology ; Dysbiosis/*metabolism/*microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Mice ; Urease/*metabolism ; }, abstract = {Gut dysbiosis during inflammatory bowel disease involves alterations in the gut microbiota associated with inflammation of the host gut. We used a combination of shotgun metagenomic sequencing and metabolomics to analyze fecal samples from pediatric patients with Crohn's disease and found an association between disease severity, gut dysbiosis, and bacterial production of free amino acids. Nitrogen flux studies using [15]N in mice showed that activity of bacterial urease, an enzyme that releases ammonia by hydrolysis of host urea, led to the transfer of murine host-derived nitrogen to the gut microbiota where it was used for amino acid synthesis. Inoculation of a conventional murine host (pretreated with antibiotics and polyethylene glycol) with commensal Escherichia coli engineered to express urease led to dysbiosis of the gut microbiota, resulting in a predominance of Proteobacteria species. This was associated with a worsening of immune-mediated colitis in these animals. A potential role for altered urease expression and nitrogen flux in the development of gut dysbiosis suggests that bacterial urease may be a potential therapeutic target for inflammatory bowel diseases.}, } @article {pmid29138475, year = {2017}, author = {Lin, JJ and Wang, FY and Li, WH and Wang, TY}, title = {The rises and falls of opsin genes in 59 ray-finned fish genomes and their implications for environmental adaptation.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15568}, pmid = {29138475}, issn = {2045-2322}, mesh = {Animals ; *Evolution, Molecular ; Fishes/*genetics ; Genome/genetics ; Metagenomics ; Opsins/classification/*genetics ; Phylogeny ; Rod Opsins/classification/*genetics ; Synteny/genetics ; }, abstract = {We studied the evolution of opsin genes in 59 ray-finned fish genomes. We identified the opsin genes and adjacent genes (syntenies) in each genome. Then we inferred the changes in gene copy number (N), syntenies, and tuning sites along each phylogenetic branch during evolution. The Exorh (rod opsin) gene has been retained in 56 genomes. Rh1, the intronless rod opsin gene, first emerged in ancestral Actinopterygii, and N increased to 2 by the teleost-specific whole genome duplication, but then decreased to 1 in the ancestor of Neoteleostei fishes. For cone opsin genes, the rhodopsin-like (Rh2) and long-wave-sensitive (LWS) genes showed great variation in N among species, ranging from 0 to 5 and from 0 to 4, respectively. The two short-wave-sensitive genes, SWS1 and SWS2, were lost in 23 and 6 species, respectively. The syntenies involving LWS, SWS2 and Rh2 underwent complex changes, while the evolution of the other opsin gene syntenies was much simpler. Evolutionary adaptation in tuning sites under different living environments was discussed. Our study provides a detailed view of opsin gene gains and losses, synteny changes and tuning site changes during ray-finned fish evolution.}, } @article {pmid29138298, year = {2017}, author = {Koskinen, K and Pausan, MR and Perras, AK and Beck, M and Bang, C and Mora, M and Schilhabel, A and Schmitz, R and Moissl-Eichinger, C}, title = {First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin.}, journal = {mBio}, volume = {8}, number = {6}, pages = {}, pmid = {29138298}, issn = {2150-7511}, mesh = {Archaea/*classification/genetics/*isolation & purification ; Gastrointestinal Tract/*microbiology ; Humans ; Lung/*microbiology ; Metagenomics/methods ; *Microbiota ; Nose/*microbiology ; Polymerase Chain Reaction/methods ; Skin/*microbiology ; }, abstract = {Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes. Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with parts of the human body other than the gastrointestinal tract and oral cavity. Currently, methodological issues impede the full assessment of the human archaeome, as bacteria-targeting protocols are unsuitable for characterization of the full spectrum of Archaea The goal of this study was to establish conservative protocols based on specifically archaea-targeting, PCR-based methods to retrieve first insights into the archaeomes of the human gastrointestinal tract, lung, nose, and skin. Detection of Archaea was highly dependent on primer selection and the sequence processing pipeline used. Our results enabled us to retrieve a novel picture of the human archaeome, as we found for the first time Methanobacterium and Woesearchaeota (DPANN superphylum) to be associated with the human gastrointestinal tract and the human lung, respectively. Similar to bacteria, human-associated archaeal communities were found to group biogeographically, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal gastrointestinal tract, (iii) a mixed skin-gastrointestinal tract landscape for the nose, and (iv) a woesearchaeal lung landscape. On the basis of the protocols we used, we were able to detect unexpectedly high diversity of archaea associated with different body parts.IMPORTANCE In summary, our study highlights the importance of the primers and data processing pipeline used to study the human archaeome. We were able to establish protocols that revealed the presence of previously undetected Archaea in all of the tissue samples investigated and to detect biogeographic patterns of the human archaeome in the gastrointestinal tract and on the skin and for the first time in the respiratory tract, i.e., the nose and lungs. Our results are a solid basis for further investigation of the human archaeome and, in the long term, discovery of the potential role of archaea in human health and disease.}, } @article {pmid29136413, year = {2017}, author = {Degois, J and Clerc, F and Simon, X and Bontemps, C and Leblond, P and Duquenne, P}, title = {First Metagenomic Survey of the Microbial Diversity in Bioaerosols Emitted in Waste Sorting Plants.}, journal = {Annals of work exposures and health}, volume = {61}, number = {9}, pages = {1076-1086}, doi = {10.1093/annweh/wxx075}, pmid = {29136413}, issn = {2398-7316}, mesh = {Aerosols/*analysis ; *Air Microbiology ; Bacteria/genetics/*isolation & purification ; Biodiversity ; DNA, Ribosomal/analysis ; Environmental Monitoring/*methods ; Feasibility Studies ; Fungi/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Occupational Exposure/analysis ; Proteobacteria/isolation & purification ; Reproducibility of Results ; }, abstract = {Waste sorting activities are source of occupational bioaerosol exposures that are associated with several health disorders. New analytical tools, based on next-generation sequencing (NGS) technologies, provide powerful methods to assess the microbial composition of bioaerosols. The objectives of the study were (i) to assess the feasibility and the repeatability of NGS-based biodiversity measurements and (ii) to study the microbial biodiversity using NGS in bioaerosols emitted in a waste sorting plant (WSP). Three stationary parallel samples were collected in a sorting cabin using closed-face cassettes equipped with polycarbonate membranes. Bacterial and fungal diversity was assessed by sequencing 16S and 18S rDNA genes using either Illumina sequencing or 454 pyrosequencing methods. At sampling point, airborne bacteria were dominated by Proteobacteria, Firmicutes, and Actinobacteria with prevailing genera assigned to unclassified Enterobacteriaceae, Staphylococcus, Acinetobacter, Leuconostoc, Pseudomonas, and Lactobacillus. Airborne fungi were dominated by Ascomycota with prevailing genera assigned to Penicillium, Aspergillus, Rhizopus, Wallemia, and Hemicarpenteles. The NGS biodiversity measurements revealed a higher biodiversity bioaerosols that previously reported for WSP in studies carried out using culture methods followed by identification of microorganisms. These results provide the first survey about taxonomic biodiversity in bioaerosols from WSPs using high-throughput sequencing.}, } @article {pmid29135334, year = {2018}, author = {Mann, PE and Huynh, K and Widmer, G}, title = {Maternal high fat diet and its consequence on the gut microbiome: A rat model.}, journal = {Gut microbes}, volume = {9}, number = {2}, pages = {143-154}, pmid = {29135334}, issn = {1949-0984}, support = {R21 AI125891/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; Biodiversity ; Body Weight ; DNA, Bacterial/genetics ; Diet, High-Fat/*adverse effects ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Lactation ; Maternal Nutritional Physiological Phenomena/*physiology ; Metagenome ; Models, Animal ; Overweight/microbiology ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; }, abstract = {The biological changes that occur during pregnancy in the female mammal include shifts in hormonal regulation in preparation for parturition and lactation, and changes in energy metabolism. In women, studies have also shown that during pregnancy there is a reduction in bacterial species richness in the gut. In the current experiment rats were used to model the interaction of diet, reproductive status, and intestinal bacterial microbiota during pregnancy and lactation. In Experiment 1 rats were exposed to either standard chow or high-fat chow (60%) and were divided into two groups: unmated (NULL) or mated (RE). In Experiment 2, both NULL and RE rats were exposed to high-fat chow for a 30-day period. High-throughput sequencing of the 16S rRNA gene revealed that pregnancy impacted the gut microbiota in a similar manner to humans. The impact of reproductive status on microbiota composition, however, was stronger in rats fed a high-fat (HF) diet. Diet-induced changes replicated some of the changes observed in humans, such as increasing the Firmicutes/Bacteroidetes ratio. However, in contrast to humans, pregnancy in rats did not increase β-diversity between microbiota from different animals. These results indicate that during pregnancy in rats, the gut microbiota is altered in a similar manner to that which occurs in women, and that these changes are further exaggerated by exposure to a HF diet. Thus, the rat may allow modelling the effects of consumption of HF food during pregnancy and enable future studies to determine the risks of HF diets during pregnancy and its consequences on the offspring.}, } @article {pmid29134939, year = {2018}, author = {Haran, JP and Bucci, V and Dutta, P and Ward, D and McCormick, B}, title = {The nursing home elder microbiome stability and associations with age, frailty, nutrition and physical location.}, journal = {Journal of medical microbiology}, volume = {67}, number = {1}, pages = {40-51}, pmid = {29134939}, issn = {1473-5644}, support = {K23 AG057790/AG/NIA NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; R03 AG056356/AG/NIA NIH HHS/United States ; R15 AI112985/AI/NIAID NIH HHS/United States ; }, mesh = {Aged, 80 and over ; Escherichia coli/isolation & purification ; Female ; Frailty/*microbiology/*physiopathology ; Humans ; Longitudinal Studies ; Male ; Microbiota/*physiology ; Nursing Homes ; Nutritional Status/*physiology ; Prospective Studies ; }, abstract = {PURPOSE: The microbiome from nursing home (NH) residents is marked by a loss in diversity that is associated with increased frailty. Our objective was to explore the associations of NH environment, frailty, nutritional status and residents' age to microbiome composition and potential metabolic function.

METHODOLOGY: We conducted a prospective longitudinal cohort study of 23 residents, 65 years or older, from one NH that had four floors: two separate medical intensive floors and two floors with active elders. Residents were assessed using the mini nutritional assessment tool and clinical frailty scale. Bacterial composition and metabolic potential of residents' stool samples was determined by metagenomic sequencing. We performed traditional unsupervised correspondence analysis and linear mixed effect modelling regression to assess the bacteria and functional pathways significantly affected by these covariates.Results/Key findings. NH resident microbiomes demonstrated temporal stability (PERMANOVA P=0.001) and differing dysbiotic associations with increasing age, frailty and malnutrition scores. As residents aged, the abundance of microbiota-encoded genes and pathways related to essential amino acid, nitrogenous base and vitamin B production declined. With increasing frailty, residents had lower abundances of butyrate-producing organisms, which are associated with increased health and higher abundances of known dysbiotic species. As residents became malnourished, butyrate-producing organisms declined and dysbiotic bacterial species increased. Finally, the microbiome of residents living in proximity shared similar species and, as demonstrated for Escherichia coli, similar strains.

CONCLUSION: These findings support the conclusion that a signature 'NH' microbiota may exist that is affected by the residents' age, frailty, nutritional status and physical location.}, } @article {pmid29133882, year = {2018}, author = {Yutin, N and Makarova, KS and Gussow, AB and Krupovic, M and Segall, A and Edwards, RA and Koonin, EV}, title = {Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut.}, journal = {Nature microbiology}, volume = {3}, number = {1}, pages = {38-46}, pmid = {29133882}, issn = {2058-5276}, support = {Z01 LM000073-12//Intramural NIH HHS/United States ; }, mesh = {Bacteriophages/*classification/*genetics ; Bacteroidetes/virology ; Databases, Protein ; Gastrointestinal Microbiome/*genetics ; Genome, Viral/genetics ; *Genomics ; Humans ; *Metagenomics ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, Protein ; Viral Proteins/chemistry/genetics ; }, abstract = {Metagenomic sequence analysis is rapidly becoming the primary source of virus discovery [1-3] . A substantial majority of the currently available virus genomes come from metagenomics, and some of these represent extremely abundant viruses, even if never grown in the laboratory. A particularly striking case of a virus discovered via metagenomics is crAssphage, which is by far the most abundant human-associated virus known, comprising up to 90% of sequences in the gut virome [4] . Over 80% of the predicted proteins encoded in the approximately 100 kilobase crAssphage genome showed no significant similarity to available protein sequences, precluding classification of this virus and hampering further study. Here we combine a comprehensive search of genomic and metagenomic databases with sensitive methods for protein sequence analysis to identify an expansive, diverse group of bacteriophages related to crAssphage and predict the functions of the majority of phage proteins, in particular those that comprise the structural, replication and expression modules. Most, if not all, of the crAss-like phages appear to be associated with diverse bacteria from the phylum Bacteroidetes, which includes some of the most abundant bacteria in the human gut microbiome and that are also common in various other habitats. These findings provide for experimental characterization of the most abundant but poorly understood members of the human-associated virome.}, } @article {pmid29129355, year = {2018}, author = {Li, J and Fu, R and Yang, Y and Horz, HP and Guan, Y and Lu, Y and Lou, H and Tian, L and Zheng, S and Liu, H and Shi, M and Tang, K and Wang, S and Xu, S}, title = {A metagenomic approach to dissect the genetic composition of enterotypes in Han Chinese and two Muslim groups.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {1}, pages = {1-12}, doi = {10.1016/j.syapm.2017.09.006}, pmid = {29129355}, issn = {1618-0984}, mesh = {Asian People ; Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Ethnicity ; *Gastrointestinal Microbiome ; Genetic Association Studies ; Healthy Volunteers ; Humans ; Islam ; Lysophospholipase/genetics ; *Metagenomics ; *Microbiota ; Phylogeny ; Polymorphism, Single Nucleotide ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Distinct enterotypes have been observed in the human gut but little is known about the genetic basis of the microbiome. Moreover, it is not clear how many genetic differences exist between enterotypes within or between populations. In this study, both the 16S rRNA gene and the metagenomes of the gut microbiota were sequenced from 48 Han Chinese, 48 Kazaks, and 96 Uyghurs, and taxonomies were assigned after de novo assembly. Single nucleotide polymorphisms were also identified by referring to data from the Human Microbiome Project. Systematic analysis of the gut communities in terms of their abundance and genetic composition was also performed, together with a genome-wide association study of the host genomes. The gut microbiota of 192 subjects was clearly classified into two enterotypes (Bacteroides and Prevotella). Interestingly, both enterotypes showed a clear genetic differentiation in terms of their functional catalogue of genes, especially for genes involved in amino acid and carbohydrate metabolism. In addition, several differentiated genera and genes were found among the three populations. Notably, one human variant (rs878394) was identified that showed significant association with the abundance of Prevotella, which is linked to LYPLAL1, a gene associated with body fat distribution, the waist-hip ratio and insulin sensitivity. Taken together, considerable differentiation was observed in gut microbes between enterotypes and among populations that was reflected in both the taxonomic composition and the genetic makeup of their functional genes, which could have been influenced by a variety of factors, such as diet and host genetic variation.}, } @article {pmid29128292, year = {2017}, author = {Herzog, B and Dötsch, A and Lemmer, H and Horn, H and Müller, E}, title = {Profiling 5-tolyltriazole biodegrading sludge communities using next-generation sequencing and denaturing gradient gel electrophoresis.}, journal = {Systematic and applied microbiology}, volume = {40}, number = {8}, pages = {508-515}, doi = {10.1016/j.syapm.2017.09.007}, pmid = {29128292}, issn = {1618-0984}, mesh = {Betaproteobacteria/classification/isolation & purification/metabolism ; Biodegradation, Environmental ; Bioreactors/*microbiology ; Comamonadaceae/isolation & purification/metabolism ; Denaturing Gradient Gel Electrophoresis/methods ; Flavobacterium/isolation & purification/metabolism ; High-Throughput Nucleotide Sequencing ; Phyllobacteriaceae/classification/isolation & purification/metabolism ; Pseudomonas/isolation & purification/metabolism ; Sewage/*microbiology ; Triazoles/analysis/*metabolism ; Water Pollutants, Chemical/analysis/*metabolism ; }, abstract = {Efficient biodegradation of 5-tolyltriazole (5-TTri) in wastewater treatment would minimize its potential detrimental effects on aquatic systems. Therefore, in order to profile 5-TTri biodegrading activated sludge communities (ASC) by DGGE and NGS, acclimation experiments with (i) easily degradable substrates, and (ii) various complex substrates mimicking wastewater conditions were performed. DGGE revealed four genera: Aminobacter (family Phyllobacteriaceae), Flavobacterium (family Flavobacteriaceae), Pseudomonas (family Pseudomonaceae), and Hydrogenophaga (family Comamonadaceae). Metagenomics (DNA) revealed the dominant families Alcaligenaceae, Pseudomonadaceae and Comamonadaceae that also represented the most active families at the RNA level (metatranscriptomics), which might indicate their importance for 5-TTri biodegradation. ASC acclimation and the composition of the substrate significantly affected 5-TTri biodegradation and the development of biodegrading communities. Using acetate only, a moderate 5-TTri degrading community was detected with a very low biodiversity and Pseudomonas spp. as dominant organisms. In contrast, setups fed 'sludge supernatant' (a complex substrate) efficiently biodegraded 5-TTri and formed a more diverse microbial community but with Hydrogenophaga spp. as the dominant group. Finally, a hypothetical 5-TTri biodegradation pathway was constructed based exclusively on the detected, biodegradation-related, Hydrogenophaga spp. genes.}, } @article {pmid29126267, year = {2017}, author = {Mancabelli, L and Milani, C and Lugli, GA and Turroni, F and Cocconi, D and van Sinderen, D and Ventura, M}, title = {Identification of universal gut microbial biomarkers of common human intestinal diseases by meta-analysis.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {12}, pages = {}, doi = {10.1093/femsec/fix153}, pmid = {29126267}, issn = {1574-6941}, mesh = {Bacteria/*classification/genetics/*isolation & purification ; Biodiversity ; Biomarkers ; Colitis, Ulcerative/*microbiology ; Crohn Disease/*microbiology ; Enterocolitis, Pseudomembranous/*microbiology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Intestines/microbiology/pathology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Intestinal diseases, such as Crohn's disease (CD), ulcerative colitis (UC) and pseudomembranous colitis (CDI), are among the most common diseases in humans and may lead to more serious pathologies, e.g. colorectal cancer (CRC). Next generation sequencing has in recent years allowed the identification of correlations between intestinal bacteria and diseases, although the formulation of universal gut microbial biomarkers for such diseases is only in its infancy. In the current study, we selected and reanalyzed a total of 3048 public datasets obtained from 16S rRNA profiling of individuals affected by CD, UC, CDI and CRC. This meta-analysis revealed possible biases in the reconstruction of the gut microbiota composition due to the use of different primer pairs employed for PCR of 16S rRNA gene fragments. Notably, this approach also identified common features of individuals affected by gut diseases (DS), including lower biodiversity compared to control subjects. Moreover, potential universal intestinal disease microbial biomarkers were identified through cross-disease comparisons. In detail, CTRL showed high abundance of the genera Barnesiella, Ruminococcaceae UCG-005, Alistipes, Christensenellaceae R-7 group and unclassified member of Lachnospiraceae family, while DS exhibited high abundance of Lactobacillus, unclassified member of Erysipelotrichaceae family and Streptococcus genera.}, } @article {pmid29126050, year = {2018}, author = {Abia, ALK and Alisoltani, A and Keshri, J and Ubomba-Jaswa, E}, title = {Metagenomic analysis of the bacterial communities and their functional profiles in water and sediments of the Apies River, South Africa, as a function of land use.}, journal = {The Science of the total environment}, volume = {616-617}, number = {}, pages = {326-334}, doi = {10.1016/j.scitotenv.2017.10.322}, pmid = {29126050}, issn = {1879-1026}, mesh = {Bacteria/classification ; Biodiversity ; DNA, Bacterial/isolation & purification ; Geologic Sediments/*microbiology ; *Metagenomics ; RNA, Ribosomal, 16S ; Rivers/*microbiology ; South Africa ; *Water Microbiology ; }, abstract = {Water quality is an important public health issue given that the presence of pathogenic organisms in such waters can adversely affect human and animal health. Despite the numerous studies conducted to assess the quality of environmental waters in many countries, limited efforts have been put on investigating the microbial quality of the sediments in developing countries and how this relates to different land uses. The present study evaluated the bacterial diversity in water and sediments in a highly used South African river to find out how the different land uses influenced the bacterial diversity, and to verify the human diseases functional classes of the bacterial populations. Samples were collected on river stretches influenced by an informal, a peri-urban and a rural settlement. Genomic DNA was extracted from water and sediment samples and sequenced on an Illumina® MiSeq platform targeting the 16S rRNA gene variable region V3-V4 from the genomic DNA. Metagenomic data analysis revealed that there was a great diversity in the microbial populations associated with the different land uses, with the informal settlement having the most considerable influence on the bacterial diversity in the water and sediments of the Apies River. The Proteobacteria (69.8%), Cyanobacteria (4.3%), Bacteroidetes (2.7%), and Actinobacteria (2.7%) were the most abundant phyla; the Alphaproteobacteria, Betaproteobacteria and Anaerolineae were the most recorded classes. Also, the sediments had a greater diversity and abundance in bacterial population than the water column. The functional profiles of the bacterial populations revealed an association with many human diseases including cancer pathways. Further studies that would isolate these potentially pathogenic organisms in the aquatic environment are therefore needed as this would help in protecting the lives of communities using such rivers, especially against emerging bacterial pathogens.}, } @article {pmid29124861, year = {2018}, author = {Certner, RH and Vollmer, SV}, title = {Inhibiting bacterial quorum sensing arrests coral disease development and disease-associated microbes.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {645-657}, doi = {10.1111/1462-2920.13991}, pmid = {29124861}, issn = {1462-2920}, mesh = {4-Butyrolactone/analogs & derivatives/antagonists & inhibitors ; Animals ; Anthozoa/*microbiology ; Caribbean Region ; Coral Reefs ; Flavobacteriaceae/drug effects ; Gammaproteobacteria/growth & development ; Microbiota/*drug effects ; Quorum Sensing/*drug effects ; RNA, Ribosomal, 16S ; Symbiosis ; }, abstract = {Among the greatest threats to coral reefs are coral epizootics, which are increasing in frequency and severity across many reef ecosystems. In particular, white band disease (WBD) has devastated Caribbean acroporid populations since its initial outbreak in 1979. However, despite its widespread and damaging effects, the aetiology of WBD remains largely unresolved. Here, we examine the role of quorum sensing within bacterial communities associated with WBD-infected Acropora cervicornis. Microbial communities isolated from WBD-infected corals were exposed to quorum sensing inhibitor (QSI) - a N-acyl homoserine lactone autoinducer antagonist - and then dosed onto healthy test corals. WBD-associated bacteria supplemented with QSI lost the ability to establish disease, while healthy corals exposed to uninhibited WBD bacterial communities became infected within two days. Microbial 16S rRNA metagenomic sequencing analyses were then used to identify shifts in bacterial communities due to QSI exposure on WBD-associated bacterial communities. Our results demonstrated that Vibrionaceae and Flavobacteriaceae abundances were strongly inhibited by the addition of QSI to WBD-infected corals, whereas putative coral symbiont Endozoicomonas and Halomonadaceae abundances decrease dramatically in diseased corals.}, } @article {pmid29124770, year = {2018}, author = {Dulski, T and Zakęś, Z and Ciesielski, S}, title = {Characterization of the gut microbiota in early life stages of pikeperch Sander lucioperca.}, journal = {Journal of fish biology}, volume = {92}, number = {1}, pages = {94-104}, doi = {10.1111/jfb.13496}, pmid = {29124770}, issn = {1095-8649}, mesh = {Animals ; Aquaculture ; DNA, Bacterial/chemistry ; *Gastrointestinal Microbiome ; Metagenomics ; Perches/genetics/growth & development/*microbiology ; Proteobacteria ; RNA, Ribosomal, 16S/genetics ; }, abstract = {This study characterized the gastrointestinal microbiome of nine juvenile farmed pikeperch Sander lucioperca using a metagenomics approach based on bacterial 16S rRNA gene sequencing. Potential changes in the gut microbiota during 2 months of S. lucioperca juvenile life were investigated. Results revealed that gut microbiota was dominated by Proteobacteria (95-92%), while other phyla Firmicutes (1-1·5%) and Actinobacteria (0·9-1·5%) were less abundant. At the family level, fish-gut microbiota were dominated by Enterobacteriaceae, which constituted c. 83% of all DNA sequence reads. Such a situation was present in all of the examined fish except one, which showed a different proportion of particular microbial taxa than the other fish. In this fish, a higher relative abundance (%) of Fusobacteria (21·0%), Bacteroidetes (9·5%) and Firmicutes (7·5%) was observed. There were no significant differences in the gut microbiome structure at different stages of development in the examined fish. This may indicate that Proteobacteria inhabiting the gut microbiota at an early stage of life are a necessary component of the pikeperch microbiome that may support proper nutrition of the fish. The information obtained on the gut microbiome could be useful in determining juvenile S. lucioperca health and improving rearing conditions by welfare monitoring in aquaculture.}, } @article {pmid29124307, year = {2018}, author = {Hugenholtz, F and de Vos, WM}, title = {Mouse models for human intestinal microbiota research: a critical evaluation.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {75}, number = {1}, pages = {149-160}, pmid = {29124307}, issn = {1420-9071}, mesh = {Animals ; Bacteria/classification/genetics/*growth & development ; *Diet ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Mice ; Mice, Inbred Strains ; Mice, Transgenic ; Research/standards/statistics & numerical data ; Species Specificity ; }, abstract = {Since the early days of the intestinal microbiota research, mouse models have been used frequently to study the interaction of microbes with their host. However, to translate the knowledge gained from mouse studies to a human situation, the major spatio-temporal similarities and differences between intestinal microbiota in mice and humans need to be considered. This is done here with specific attention for the comparative physiology of the intestinal tract, the effect of dietary patterns and differences in genetics. Detailed phylogenetic and metagenomic analysis showed that while many common genera are found in the human and murine intestine, these differ strongly in abundance and in total only 4% of the bacterial genes are found to share considerable identity. Moreover, a large variety of murine strains is available yet most of the microbiota research is performed in wild-type, inbred strains and their transgenic derivatives. It has become increasingly clear that the providers, rearing facilities and the genetic background of these mice have a significant impact on the microbial composition and this is illustrated with recent experimental data. This may affect the reproducibility of mouse microbiota studies and their conclusions. Hence, future studies should take these into account to truly show the effect of diet, genotype or environmental factors on the microbial composition.}, } @article {pmid29123168, year = {2017}, author = {Zheng, S and Shao, S and Qiao, Z and Chen, X and Piao, C and Yu, Y and Gao, F and Zhang, J and Du, J}, title = {Clinical Parameters and Gut Microbiome Changes Before and After Surgery in Thoracic Aortic Dissection in Patients with Gastrointestinal Complications.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15228}, pmid = {29123168}, issn = {2045-2322}, mesh = {Aortic Dissection/*surgery ; Bacteria/*classification/genetics ; Blood Chemical Analysis ; Cytokines/blood ; Gastrointestinal Diseases/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Microbiota ; Postoperative Complications/*microbiology ; }, abstract = {Thoracic aortic dissection (TAAD) is one of the most common types of aortic diseases. Although surgery remains the main method of treatment, the high rate of postoperative gastrointestinal complications significantly influences the effects of surgery and the recovery process. Moreover, the mechanisms underlying this disease remain unclear. To address these problems, we examined changes in the gut microbiota in 40 thoracic aortic dissection patients with abdominal complications after surgery. Levels of white blood cells (WBC), neutrophile granulocytes (NE), alanine aminotransferase (ALT), and aspartate aminotransferase (AST) were higher in all patients after surgery. Levels of inflammatory cytokines, including interleukin (IL)-2, IL-6, IL-8, and IL-10, were also higher after surgery. A metagenome analysis revealed that levels of Oscillibacter, Anaerotruncus, Alistipes, and Clostridium difficile were higher after the operation. The abundance of functional genes, such as the spermidine/putrescine transport system permease protein, the flagellar motor switch protein, and branched-chain amino acid transport system proteins, was also higher post-surgery. These changes likely contribute to diarrhea, bloating, gastrointestinal bleeding, and other abdominal complications after surgery, and our research opens up new treatment possibilities for patients suffering from abdominal complications after surgical treatment.}, } @article {pmid29120486, year = {2017}, author = {Miossec, MJ and Valenzuela, SL and Mendez, KN and Castro-Nallar, E}, title = {Computational Methods for Human Microbiome Analysis.}, journal = {Current protocols in microbiology}, volume = {47}, number = {}, pages = {1E.14.1-1E.14.17}, doi = {10.1002/cpmc.41}, pmid = {29120486}, issn = {1934-8533}, mesh = {Computational Biology/*methods ; Humans ; Metagenomics/*methods ; *Microbiota ; }, abstract = {As the field of microbiomics advances, the burden of computational work that scientists need to perform in order to extract biological insight has grown accordingly. Likewise, while human microbiome analyses are increasingly shifting toward a greater integration of various high-throughput data types, a core number of methods form the basis of nearly every study. In this unit, we present step-by-step protocols for five core stages of human microbiome research. The protocols presented in this unit provide a base case for human microbiome analysis, complete with sufficient detail for researchers to tailor certain aspects of the protocols to the specificities of their data. © 2017 by John Wiley & Sons, Inc.}, } @article {pmid29118316, year = {2017}, author = {Iraola, G and Forster, SC and Kumar, N and Lehours, P and Bekal, S and García-Peña, FJ and Paolicchi, F and Morsella, C and Hotzel, H and Hsueh, PR and Vidal, A and Lévesque, S and Yamazaki, W and Balzan, C and Vargas, A and Piccirillo, A and Chaban, B and Hill, JE and Betancor, L and Collado, L and Truyers, I and Midwinter, AC and Dagi, HT and Mégraud, F and Calleros, L and Pérez, R and Naya, H and Lawley, TD}, title = {Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {1367}, pmid = {29118316}, issn = {2041-1723}, support = {//Wellcome Trust/United Kingdom ; 098051//Wellcome Trust/United Kingdom ; PF451//Medical Research Council/United Kingdom ; }, mesh = {Animals ; Campylobacter Infections/*transmission/veterinary ; Campylobacter fetus/*genetics/*pathogenicity ; Cattle ; Cattle Diseases/microbiology/transmission ; Feces/microbiology ; *Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Humans ; Male ; Phylogeny ; }, abstract = {Campylobacter fetus is a venereal pathogen of cattle and sheep, and an opportunistic human pathogen. It is often assumed that C. fetus infection occurs in humans as a zoonosis through food chain transmission. Here we show that mammalian C. fetus consists of distinct evolutionary lineages, primarily associated with either human or bovine hosts. We use whole-genome phylogenetics on 182 strains from 17 countries to provide evidence that C. fetus may have originated in humans around 10,500 years ago and may have "jumped" into cattle during the livestock domestication period. We detect C. fetus genomes in 8% of healthy human fecal metagenomes, where the human-associated lineages are the dominant type (78%). Thus, our work suggests that C. fetus is an unappreciated human intestinal pathobiont likely spread by human to human transmission. This genome-based evolutionary framework will facilitate C. fetus epidemiology research and the development of improved molecular diagnostics and prevention schemes for this neglected pathogen.}, } @article {pmid29118049, year = {2017}, author = {Milani, C and Duranti, S and Bottacini, F and Casey, E and Turroni, F and Mahony, J and Belzer, C and Delgado Palacio, S and Arboleya Montes, S and Mancabelli, L and Lugli, GA and Rodriguez, JM and Bode, L and de Vos, W and Gueimonde, M and Margolles, A and van Sinderen, D and Ventura, M}, title = {The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {81}, number = {4}, pages = {}, pmid = {29118049}, issn = {1098-5557}, mesh = {Biomarkers/analysis ; Breast Feeding ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/*microbiology ; Humans ; Immune System/*microbiology ; Infant ; *Infant Health ; Intestinal Diseases/microbiology ; *Maternal-Fetal Exchange ; Milk, Human/chemistry ; Pregnancy ; Probiotics/therapeutic use ; Symbiosis ; Whole Genome Sequencing ; }, abstract = {The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.}, } @article {pmid29117585, year = {2018}, author = {Zainun, MY and Simarani, K}, title = {Metagenomics profiling for assessing microbial diversity in both active and closed landfills.}, journal = {The Science of the total environment}, volume = {616-617}, number = {}, pages = {269-278}, doi = {10.1016/j.scitotenv.2017.10.266}, pmid = {29117585}, issn = {1879-1026}, mesh = {Archaea/classification ; Bacteria/classification ; Biodiversity ; DNA, Archaeal/isolation & purification ; DNA, Bacterial/isolation & purification ; Malaysia ; *Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/isolation & purification ; *Soil Microbiology ; *Waste Disposal Facilities ; }, abstract = {The municipal landfill is an example of human-made environment that harbours some complex diversity of microorganism communities. To evaluate this complexity, the structures of bacterial communities in active (operational) and closed (non-operational) landfills in Malaysia were analysed with culture independent metagenomics approaches. Several points of soil samples were collected from 0 to 20cm depth and were subjected to physicochemical test, such as temperature, pH, and moisture content. In addition, the heavy metal contamination was determined by using ICPMS. The bacterial enumeration was examined on nutrient agar (NA) plates aerobically at 30°C. The soil DNA was extracted, purified and amplified prior to sequence the 16S rRNA gene for statistical and bioinformatics analyses. As a result, the average of bacteria for the closed landfill was higher compared to that for the active landfill at 9.16×10[7] and 1.50×10[7], respectively. The higher bacterial OTUs sequenced was also recorded in closed landfills compared to active landfill i.e. 6625 and 4552 OTUs respectively. The data from both landfills showed that the predominant phyla belonged to Proteobacteria (55.7%). On average, Bacteroidetes was the second highest phylum followed by Firmicutes for the active landfill. While the phyla for communities in closed landfill were dominated by phyla from Acidobacteria and Actinobacteria. There was also Euryarchaeota (Archaea) which became a minor phylum that was detected in active landfill, but almost completely absent in closed landfill. As such, the composition of bacterial communities suggests some variances between the bacterial communities found in active and closed landfills. Thus, this study offers new clues pertaining to bacterial diversity pattern between the varied types of landfills studied.}, } @article {pmid29115413, year = {2018}, author = {Meng, F and Chen, T and Wang, X and Wang, X and Wei, H and Tian, P and Wang, H and Zhao, X and Shen, L and Xin, H}, title = {Evaluation of the accuracy and sensitivity of high‑throughput sequencing technology using known microbiota.}, journal = {Molecular medicine reports}, volume = {17}, number = {1}, pages = {408-413}, doi = {10.3892/mmr.2017.7849}, pmid = {29115413}, issn = {1791-3004}, mesh = {Biodiversity ; Computational Biology/methods ; Genome, Bacterial ; Genomics/methods ; *High-Throughput Nucleotide Sequencing/methods/standards ; *Metagenome ; *Metagenomics/methods/standards ; *Microbiota ; }, abstract = {Next generation sequencing provides an excellent platform to explore microbiota in any given environment, and little work is required to evaluate the accuracy and sensitivity of high‑throughput sequencing technology. In the present study, a known microbiota containing Escherichia coli, Lactobacillus plantarum, Streptococcus thermophilus, Bifidobacterium bifidum, Bacillus subtilis, Enterococcus faecalis and Salmonella typhimurium was used to evaluate the high‑throughput sequencing technology. The results suggested that there were 122.7 operational taxonomic units (OTUs) in all groups, which is 17.5‑fold (the whole OTU number/the actual bacterial number) greater compared with the actual microbial number in each group, and the Venn method indicated that only 46.38% (64/138), 58.70% (81/138), 86.13% (118/137), 83.57% (117/140) and 89.29% (125/140) of the common OTUs were identified in groups A, B, C, D and E, of which the majority of OTUs did not belong to known bacteria. In addition, the DNA extraction and amplification efficiency failed to identify bacteria at the phylum, class, order, family, genus and species levels, which may further increase false information of microbial analysis. In conclusion, the present study provided basic datato investigate the potential drawbacks of high‑throughput sequencing technology, which will help researchers to avoid exaggerating the bacterial number when this technology is applied to study microbiota in particular environments.}, } @article {pmid29115058, year = {2018}, author = {Randle-Boggis, RJ and Ashton, PD and Helgason, T}, title = {Increasing flooding frequency alters soil microbial communities and functions under laboratory conditions.}, journal = {MicrobiologyOpen}, volume = {7}, number = {1}, pages = {}, pmid = {29115058}, issn = {2045-8827}, mesh = {Archaea/*classification/*growth & development ; Bacteria/*classification/*growth & development ; *Biota ; *Floods ; Metabolic Networks and Pathways/genetics ; Metabolism ; Models, Theoretical ; *Soil Microbiology ; }, abstract = {The impacts of increased flooding frequency on soil microbial communities and potential functions, in line with predicted environmental changes, were investigated in a laboratory-controlled environment. More frequent flooding events altered microbial community composition and significantly increased the resolved species alpha-diversity (Shannon index). The Bacteria:Archaea ratio was greater at the end of the experiment than at the start, more-so after only one flood. Significant changes in taxa and functional gene abundances were identified and quantified. These include genes related to the reduction and oxidation of substances associated with anoxia, for example, those involved in nitrogen and sulfur cycling. No significant changes were observed in the methanogenesis pathway, another function associated with anoxia and which contributes to the emission of greenhouse gases.}, } @article {pmid29113654, year = {2017}, author = {Mima, K and Ogino, S and Nakagawa, S and Sawayama, H and Kinoshita, K and Krashima, R and Ishimoto, T and Imai, K and Iwatsuki, M and Hashimoto, D and Baba, Y and Sakamoto, Y and Yamashita, YI and Yoshida, N and Chikamoto, A and Ishiko, T and Baba, H}, title = {The role of intestinal bacteria in the development and progression of gastrointestinal tract neoplasms.}, journal = {Surgical oncology}, volume = {26}, number = {4}, pages = {368-376}, pmid = {29113654}, issn = {1879-3320}, support = {R35 CA197735/CA/NCI NIH HHS/United States ; }, mesh = {Bacteria/*growth & development/*metabolism ; Disease Progression ; Gastrointestinal Microbiome ; Gastrointestinal Neoplasms/epidemiology/*etiology/*prevention & control ; Gastrointestinal Tract/*microbiology ; Humans ; }, abstract = {More than 100 trillion microorganisms inhabit the human intestinal tract and play important roles in health conditions and diseases, including cancer. Accumulating evidence demonstrates that specific bacteria and bacterial dysbiosis in the gastrointestinal tract can potentiate the development and progression of gastrointestinal tract neoplasms by damaging DNA, activating oncogenic signaling pathways, producing tumor-promoting metabolites such as secondary bile acids, and suppressing antitumor immunity. Other bacterial species have been shown to produce short-chain fatty acids such as butyrate, which can suppress inflammation and carcinogenesis in the gastrointestinal tract. Consistent with these lines of evidence, clinical studies using metagenomic analyses have shown associations of specific bacteria and bacterial dysbiosis with gastrointestinal tract cancers, including esophageal, gastric, and colorectal cancers. Emerging data demonstrate that intestinal bacteria can modulate the efficacy of cancer chemotherapies and novel targeted immunotherapies such as anti-CTLA4 and anti-CD274 therapies, the process of absorption, and the occurrence of complications after gastrointestinal surgery. A better understanding of the mechanisms by which the gut microbiota influence tumor development and progression in the intestine would provide opportunities to develop new prevention and treatment strategies for patients with gastrointestinal tract cancers by targeting the intestinal microflora.}, } @article {pmid29113561, year = {2017}, author = {Rahman, MA and LaPierre, N and Rangwala, H and Barbara, D}, title = {Metagenome sequence clustering with hash-based canopies.}, journal = {Journal of bioinformatics and computational biology}, volume = {15}, number = {6}, pages = {1740006}, doi = {10.1142/S0219720017400066}, pmid = {29113561}, issn = {1757-6334}, mesh = {*Algorithms ; *Biodiversity ; Cluster Analysis ; Databases, Factual ; Gastrointestinal Microbiome/genetics ; Humans ; Liver Cirrhosis/microbiology ; *Metagenome ; Metagenomics/*methods ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; RNA, Ribosomal, 18S ; Sequence Analysis, RNA/methods ; Soil Microbiology ; }, abstract = {Metagenomics is the collective sequencing of co-existing microbial communities which are ubiquitous across various clinical and ecological environments. Due to the large volume and random short sequences (reads) obtained from community sequences, analysis of diversity, abundance and functions of different organisms within these communities are challenging tasks. We present a fast and scalable clustering algorithm for analyzing large-scale metagenome sequence data. Our approach achieves efficiency by partitioning the large number of sequence reads into groups (called canopies) using hashing. These canopies are then refined by using state-of-the-art sequence clustering algorithms. This canopy-clustering (CC) algorithm can be used as a pre-processing phase for computationally expensive clustering algorithms. We use and compare three hashing schemes for canopy construction with five popular and state-of-the-art sequence clustering methods. We evaluate our clustering algorithm on synthetic and real-world 16S and whole metagenome benchmarks. We demonstrate the ability of our proposed approach to determine meaningful Operational Taxonomic Units (OTU) and observe significant speedup with regards to run time when compared to different clustering algorithms. We also make our source code publicly available on Github. [a].}, } @article {pmid29113023, year = {2018}, author = {Andújar, C and Arribas, P and Gray, C and Bruce, C and Woodward, G and Yu, DW and Vogler, AP}, title = {Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill.}, journal = {Molecular ecology}, volume = {27}, number = {1}, pages = {146-166}, doi = {10.1111/mec.14410}, pmid = {29113023}, issn = {1365-294X}, mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; *Environmental Monitoring ; *Fresh Water ; High-Throughput Nucleotide Sequencing ; Invertebrates/*drug effects ; *Metagenomics ; Pesticides/*toxicity ; Species Specificity ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Biomonitoring underpins the environmental assessment of freshwater ecosystems and guides management and conservation. Current methodology for surveys of (macro)invertebrates uses coarse taxonomic identification where species-level resolution is difficult to obtain. Next-generation sequencing of entire assemblages (metabarcoding) provides a new approach for species detection, but requires further validation. We used metabarcoding of invertebrate assemblages with two fragments of the cox1 "barcode" and partial nuclear ribosomal (SSU) genes, to assess the effects of a pesticide spill in the River Kennet (southern England). Operational taxonomic unit (OTU) recovery was tested under 72 parameters (read denoising, filtering, pair merging and clustering). Similar taxonomic profiles were obtained under a broad range of parameters. The SSU marker recovered Platyhelminthes and Nematoda, missed by cox1, while Rotifera were only amplified with cox1. A reference set was created from all available barcode entries for Arthropoda in the BOLD database and clustered into OTUs. The River Kennet metabarcoding produced matches to 207 of these reference OTUs, five times the number of species recognized with morphological monitoring. The increase was due to the following: greater taxonomic resolution (e.g., splitting a single morphotaxon "Chironomidae" into 55 named OTUs); splitting of Linnaean binomials into multiple molecular OTUs; and the use of a filtration-flotation protocol for extraction of minute specimens (meiofauna). Community analyses revealed strong differences between "impacted" vs. "control" samples, detectable with each gene marker, for each major taxonomic group, and for meio- and macrofaunal samples separately. Thus, highly resolved taxonomic data can be extracted at a fraction of the time and cost of traditional nonmolecular methods, opening new avenues for freshwater invertebrate biodiversity monitoring and molecular ecology.}, } @article {pmid29112885, year = {2018}, author = {Neville, BA and Forster, SC and Lawley, TD}, title = {Commensal Koch's postulates: establishing causation in human microbiota research.}, journal = {Current opinion in microbiology}, volume = {42}, number = {}, pages = {47-52}, doi = {10.1016/j.mib.2017.10.001}, pmid = {29112885}, issn = {1879-0364}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Gastrointestinal Microbiome/genetics/physiology ; Humans ; Metagenomics/methods ; *Microbiota ; Research ; *Symbiosis ; }, abstract = {Advances in high-throughput sequencing technologies and the development of sophisticated bioinformatics analysis methods, algorithms, and pipelines to handle the large amounts of data generated have driven the field of human microbiome research forward. This specialist knowledge has been crucial to thoroughly mine the human gut microbiota, particularly in the absence of methods for the routine cultivation of most enteric microorganisms. In recent years, however, significant efforts have been made to address the 'great plate count anomaly' and to overcome the barriers to cultivation of the fastidious and mostly strictly anaerobic bacteria that reside in the human gut. As a result, many new species have been discovered, characterised, genome sequenced, and deposited in culture collections. These continually expanding resources enable experimental investigation of the human gut microbiota, validation of hypotheses made with sequence-based analyses, and phenotypic characterisation of its constituent microbes. Herein we propose a variant of Koch's postulates, aimed at providing a framework to establish causation in microbiome studies, with a particular focus on demonstrating the health-promoting role of the commensal gut microbiota.}, } @article {pmid29112720, year = {2018}, author = {Zhu, C and Mahlich, Y and Miller, M and Bromberg, Y}, title = {fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks.}, journal = {Nucleic acids research}, volume = {46}, number = {D1}, pages = {D535-D541}, pmid = {29112720}, issn = {1362-4962}, mesh = {Bacteria/classification/genetics ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/physiology ; Biodiversity ; *Databases, Factual ; Databases, Genetic ; Environmental Microbiology ; Gene Transfer, Horizontal ; Humans ; Internet ; Metadata ; Metagenomics ; Microbiota/*physiology ; Phylogeny ; Synechococcus/classification/genetics/physiology ; User-Computer Interface ; }, abstract = {Microbial functional diversification is driven by environmental factors, i.e. microorganisms inhabiting the same environmental niche tend to be more functionally similar than those from different environments. In some cases, even closely phylogenetically related microbes differ more across environments than across taxa. While microbial similarities are often reported in terms of taxonomic relationships, no existing databases directly link microbial functions to the environment. We previously developed a method for comparing microbial functional similarities on the basis of proteins translated from their sequenced genomes. Here, we describe fusionDB, a novel database that uses our functional data to represent 1374 taxonomically distinct bacteria annotated with available metadata: habitat/niche, preferred temperature, and oxygen use. Each microbe is encoded as a set of functions represented by its proteome and individual microbes are connected via common functions. Users can search fusionDB via combinations of organism names and metadata. Moreover, the web interface allows mapping new microbial genomes to the functional spectrum of reference bacteria, rendering interactive similarity networks that highlight shared functionality. fusionDB provides a fast means of comparing microbes, identifying potential horizontal gene transfer events, and highlighting key environment-specific functionality.}, } @article {pmid29110156, year = {2018}, author = {Medina-Silva, R and Oliveira, RR and Trindade, FJ and Borges, LGA and Lopes Simão, TL and Augustin, AH and Valdez, FP and Constant, MJ and Simundi, CL and Eizirik, E and Groposo, C and Miller, DJ and da Silva, PR and Viana, AR and Ketzer, JMM and Giongo, A}, title = {Microbiota associated with tubes of Escarpia sp. from cold seeps in the southwestern Atlantic Ocean constitutes a community distinct from that of surrounding marine sediment and water.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {4}, pages = {533-550}, doi = {10.1007/s10482-017-0975-7}, pmid = {29110156}, issn = {1572-9699}, mesh = {Animals ; Atlantic Ocean ; Bacteria/*classification ; *Biodiversity ; Chemoautotrophic Growth ; DNA Barcoding, Taxonomic ; Ecosystem ; Geologic Sediments/*microbiology ; Metagenome/genetics ; Microbiota/*physiology ; Planctomycetales ; Polychaeta/*microbiology/ultrastructure ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {As the depth increases and the light fades in oceanic cold seeps, a variety of chemosynthetic-based benthic communities arise. Previous assessments reported polychaete annelids belonging to the family Siboglinidae as part of the fauna at cold seeps, with the 'Vestimentifera' clade containing specialists that depend on microbial chemosynthetic endosymbionts for nutrition. Little information exists concerning the microbiota of the external portion of the vestimentiferan trunk wall. We employed 16S rDNA-based metabarcoding to describe the external microbiota of the chitin tubes from the vestimentiferan Escarpia collected from a chemosynthetic community in a cold seep area at the southwestern Atlantic Ocean. The most abundant operational taxonomic unit (OTU) belonged to the family Pirellulaceae (phylum Planctomycetes), and the second most abundant OTU belonged to the order Methylococcales (phylum Proteobacteria), composing an average of 21.1 and 15.4% of the total reads on tubes, respectively. These frequencies contrasted with those from the surrounding environment (sediment and water), where they represent no more than 0.1% of the total reads each. Moreover, some taxa with lower abundances were detected only in Escarpia tube walls. These data constitute on the first report of an epibiont microbial community found in close association with external surface of a cold-seep metazoan, Escarpia sp., from a chemosynthetic community in the southwestern Atlantic Ocean.}, } @article {pmid29109478, year = {2018}, author = {Kolinko, S and Wu, YW and Tachea, F and Denzel, E and Hiras, J and Gabriel, R and Bäcker, N and Chan, LJG and Eichorst, SA and Frey, D and Chen, Q and Azadi, P and Adams, PD and Pray, TR and Tanjore, D and Petzold, CJ and Gladden, JM and Simmons, BA and Singer, SW}, title = {A bacterial pioneer produces cellulase complexes that persist through community succession.}, journal = {Nature microbiology}, volume = {3}, number = {1}, pages = {99-107}, pmid = {29109478}, issn = {2058-5276}, support = {S10 OD018530/OD/NIH HHS/United States ; }, mesh = {Bacteria/*classification/*enzymology/metabolism ; Bacterial Proteins/analysis/isolation & purification ; Biological Evolution ; Cellulase/*analysis/isolation & purification ; Cellulose/*metabolism ; Composting ; Genome, Bacterial/genetics ; Glycoside Hydrolases/analysis/isolation & purification ; Glycosylation ; Heterotrophic Processes ; Metagenomics ; Microbial Consortia/*physiology ; Models, Biological ; Multienzyme Complexes/*analysis/isolation & purification ; *Phylogeny ; Soil Microbiology ; }, abstract = {Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, 'Candidatus Reconcilibacillus cellulovorans', possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the 'Ca. Reconcilibacillus cellulovorans' multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures for enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. The provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology.}, } @article {pmid29108974, year = {2018}, author = {Yasir, M}, title = {Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {49}, number = {2}, pages = {248-257}, pmid = {29108974}, issn = {1678-4405}, mesh = {*Antibiosis ; Bacteria/*classification/genetics/growth & development/*isolation & purification ; *Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Euryarchaeota/classification/genetics/growth & development/isolation & purification ; Metagenomics ; Pakistan ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {In this study for the first-time microbial communities in the caves located in the mountain range of Hindu Kush were evaluated. The samples were analyzed using culture-independent (16S rRNA gene amplicon sequencing) and culture-dependent methods. The amplicon sequencing results revealed a broad taxonomic diversity, including 21 phyla and 20 candidate phyla. Proteobacteria were dominant in both caves, followed by Bacteroidetes, Actinobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, and the archaeal phylum Euryarchaeota. Representative operational taxonomic units from Koat Maqbari Ghaar and Smasse-Rawo Ghaar were grouped into 235 and 445 different genera, respectively. Comparative analysis of the cultured bacterial isolates revealed distinct bacterial taxonomic profiles in the studied caves dominated by Proteobacteria in Koat Maqbari Ghaar and Firmicutes in Smasse-Rawo Ghaar. Majority of those isolates were associated with the genera Pseudomonas and Bacillus. Thirty strains among the identified isolates from both caves showed antimicrobial activity. Overall, the present study gave insight into the great bacterial taxonomic diversity and antimicrobial potential of the isolates from the previously uncharacterized caves located in the world's highest mountains range in the Indian sub-continent.}, } @article {pmid29107912, year = {2018}, author = {Oh, S and Hammes, F and Liu, WT}, title = {Metagenomic characterization of biofilter microbial communities in a full-scale drinking water treatment plant.}, journal = {Water research}, volume = {128}, number = {}, pages = {278-285}, doi = {10.1016/j.watres.2017.10.054}, pmid = {29107912}, issn = {1879-2448}, mesh = {Bacteria/genetics ; Biofilms ; Charcoal ; Drinking Water ; Filtration ; *Metagenome ; Metagenomics ; *Microbial Consortia ; Phylogeny ; Silicon Dioxide ; *Water Microbiology ; *Water Purification ; }, abstract = {Microorganisms inhabiting filtration media of a drinking water treatment plant can be beneficial, because they metabolize biodegradable organic matter from source waters and those formed during disinfection processes, leading to the production of biologically stable drinking water. However, which microbial consortia colonize filters and what metabolic capacity they possess remain to be investigated. To gain insights into these issues, we performed metagenome sequencing and analysis of microbial communities in three different filters of a full-scale drinking water treatment plant (DWTP). Filter communities were sampled from a rapid sand filter (RSF), granular activated carbon filter (GAC), and slow sand filter (SSF), and from the Schmutzdecke (SCM, a biologically active scum layer accumulated on top of SSF), respectively. Analysis of community phylogenetic structure revealed that the filter bacterial communities significantly differed from those in the source water and final effluent communities, respectively. Network analysis identified a filter-specific colonization pattern of bacterial groups. Bradyrhizobiaceae were abundant in GAC, whereas Nitrospira were enriched in the sand-associated filters (RSF, SCM, and SSF). The GAC community was enriched with functions associated with aromatics degradation, many of which were encoded by Rhizobiales (∼30% of the total GAC community). Predicting minimum generation time (MGT) of prokaryotic communities suggested that the GAC community potentially select fast-growers (<15 h of MGT) among the four filter communities, consistent with the highest dissolved organic matter removal rate by GAC. Our findings provide new insights into the community phylogenetic structure, colonization pattern, and metabolic capacity that potentially contributes to organic matter removal achieved in the biofiltration stages of the full-scale DWTP.}, } @article {pmid29106455, year = {2018}, author = {Maarala, AI and Bzhalava, Z and Dillner, J and Heljanko, K and Bzhalava, D}, title = {ViraPipe: scalable parallel pipeline for viral metagenome analysis from next generation sequencing reads.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {6}, pages = {928-935}, doi = {10.1093/bioinformatics/btx702}, pmid = {29106455}, issn = {1367-4811}, mesh = {Algorithms ; Computers ; *Genome, Viral ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA/methods ; *Software ; Viruses/*genetics ; }, abstract = {MOTIVATION: Next Generation Sequencing (NGS) technology enables identification of microbial genomes from massive amount of human microbiomes more rapidly and cheaper than ever before. However, the traditional sequential genome analysis algorithms, tools, and platforms are inefficient for performing large-scale metagenomic studies on ever-growing sample data volumes. Currently, there is an urgent need for scalable analysis pipelines that enable harnessing all the power of parallel computation in computing clusters and in cloud computing environments. We propose ViraPipe, a scalable metagenome analysis pipeline that is able to analyze thousands of human microbiomes in parallel in tolerable time. The pipeline is tuned for analyzing viral metagenomes and the software is applicable for other metagenomic analyses as well. ViraPipe integrates parallel BWA-MEM read aligner, MegaHit De novo assembler, and BLAST and HMMER3 sequence search tools. We show the scalability of ViraPipe by running experiments on mining virus related genomes from NGS datasets in a distributed Spark computing cluster.

RESULTS: ViraPipe analyses 768 human samples in 210 minutes on a Spark computing cluster comprising 23 nodes and 1288 cores in total. The speedup of ViraPipe executed on 23 nodes was 11x compared to the sequential analysis pipeline executed on a single node. The whole process includes parallel decompression, read interleaving, BWA-MEM read alignment, filtering and normalizing of non-human reads, De novo contigs assembling, and searching of sequences with BLAST and HMMER3 tools.

CONTACT: ilari.maarala@aalto.fi.

https://github.com/NGSeq/ViraPipe.}, } @article {pmid29105040, year = {2018}, author = {Kiran Kumar Reddy, G and Nancharaiah, YV}, title = {Sustainable bioreduction of toxic levels of chromate in a denitrifying granular sludge reactor.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {2}, pages = {1969-1979}, pmid = {29105040}, issn = {1614-7499}, mesh = {Biomass ; Bioreactors/*microbiology ; Chromates/*analysis ; Denitrification ; Halomonas/genetics/growth & development ; Metagenome ; Microbial Consortia/genetics ; Nitrates/*analysis ; Oxidation-Reduction ; Sewage/*microbiology ; Water Pollutants, Chemical/*analysis ; Water Purification/*methods ; }, abstract = {Biological removal of chromate [Cr(VI)] in the presence or absence of nitrate by granular sludge biofilms was investigated in batch experiments and in a sequencing batch reactor (SBR). Denitrifying granular sludge cultivated from activated sludge was able to directly reduce Cr(VI) in the presence of an electron donor. Bioreduction was dependent on the initial Cr(VI) and the granular sludge concentrations. Bioreduction of Cr(VI) was followed by Cr(III) precipitation or entrapment in the granular sludge which was corroborated with decrease in total soluble Cr and increase in inorganic content of biomass. Batch experiments revealed that Cr(VI) addition has no major influence on high-strength nitrate (3000 mg L[-1]) denitrification, but nitrite denitrification was slowed-down. However, SBR experiment demonstrated successful denitrification as well as Cr(VI) removal due to enrichment of Cr(VI)-tolerant denitrifying bacteria. In fact, stable SBR performance in terms of complete and sustained removal of 0.05, 0.1, 0.2, 0.3, 0.5 and 0.75 mM Cr(VI) and denitrification of 3000 mg L[-1] was observed during 2 months of operation. Active biomass and electron donor-dependent Cr(VI) removal, detection of Cr(III) in the biomass and recovery of ~ 92% of the Cr from the granular sludge biofilms confirms bioreduction followed by precipitation or entrapment of Cr(III) as the principal chromate removal mechanism. Metagenomic bacterial community analysis showed enrichment of Halomonas sp. in denitrifying granular sludge performing either denitrification or simultaneous reduction of nitrate and chromate.}, } @article {pmid29103940, year = {2017}, author = {Nater, A and Mattle-Greminger, MP and Nurcahyo, A and Nowak, MG and de Manuel, M and Desai, T and Groves, C and Pybus, M and Sonay, TB and Roos, C and Lameira, AR and Wich, SA and Askew, J and Davila-Ross, M and Fredriksson, G and de Valles, G and Casals, F and Prado-Martinez, J and Goossens, B and Verschoor, EJ and Warren, KS and Singleton, I and Marques, DA and Pamungkas, J and Perwitasari-Farajallah, D and Rianti, P and Tuuga, A and Gut, IG and Gut, M and Orozco-terWengel, P and van Schaik, CP and Bertranpetit, J and Anisimova, M and Scally, A and Marques-Bonet, T and Meijaard, E and Krützen, M}, title = {Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species.}, journal = {Current biology : CB}, volume = {27}, number = {22}, pages = {3487-3498.e10}, doi = {10.1016/j.cub.2017.09.047}, pmid = {29103940}, issn = {1879-0445}, mesh = {Animals ; Behavior, Animal/physiology ; Biological Evolution ; Endangered Species ; Gene Flow/genetics ; *Genetic Speciation ; Genetic Variation ; Genome ; Genomics ; Hominidae/genetics ; Metagenomics/methods ; Phylogeny ; Pongo/classification/*genetics/physiology ; Pongo abelii/genetics ; Pongo pygmaeus/genetics ; }, abstract = {Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos [1]. However, large gaps remain in our knowledge of fine-scale variation in hominoid morphology, behavior, and genetics, and aspects of great ape taxonomy remain in flux. This is particularly true for orangutans (genus: Pongo), the only Asian great apes and phylogenetically our most distant relatives among extant hominids [1]. Designation of Bornean and Sumatran orangutans, P. pygmaeus (Linnaeus 1760) and P. abelii (Lesson 1827), as distinct species occurred in 2001 [1, 2]. Here, we show that an isolated population from Batang Toru, at the southernmost range limit of extant Sumatran orangutans south of Lake Toba, is distinct from other northern Sumatran and Bornean populations. By comparing cranio-mandibular and dental characters of an orangutan killed in a human-animal conflict to those of 33 adult male orangutans of a similar developmental stage, we found consistent differences between the Batang Toru individual and other extant Ponginae. Our analyses of 37 orangutan genomes provided a second line of evidence. Model-based approaches revealed that the deepest split in the evolutionary history of extant orangutans occurred ∼3.38 mya between the Batang Toru population and those to the north of Lake Toba, whereas both currently recognized species separated much later, about 674 kya. Our combined analyses support a new classification of orangutans into three extant species. The new species, Pongo tapanuliensis, encompasses the Batang Toru population, of which fewer than 800 individuals survive. VIDEO ABSTRACT.}, } @article {pmid29102544, year = {2018}, author = {Kang, Y and Cai, Y}, title = {Gut microbiota and hypertension: From pathogenesis to new therapeutic strategies.}, journal = {Clinics and research in hepatology and gastroenterology}, volume = {42}, number = {2}, pages = {110-117}, doi = {10.1016/j.clinre.2017.09.006}, pmid = {29102544}, issn = {2210-741X}, mesh = {*Gastrointestinal Microbiome ; Humans ; Hypertension/*microbiology/*therapy ; Probiotics/*therapeutic use ; }, abstract = {Hypertension (HTN) has become a global public health concern and a major risk factor for cardiovascular, cerebrovascular, and kidney diseases. The complex interplay of genetic and environmental influences is important for the development of the disease. Accumulating evidence has illustrated the association of dysbiosis of gut microbiota with hypertension. Certain gut microbial strains may play either a pathogenic or a protective role in the development of hypertension. Oral probiotics can therefore represent a therapeutic approach for hypertension treatment. However, the relevant scientific work has only just begun, and the available data in this field remain limited. Fortunately, recent technological developments that permit identification of microbes and their products using culture-independent molecular detection techniques. In this review, we summarize the role of gut microbiota in hypertension progression, and probiotics in the treatment of hypertension.}, } @article {pmid29101651, year = {2017}, author = {Quach, D and Britton, RA}, title = {Gut Microbiota and Bone Health.}, journal = {Advances in experimental medicine and biology}, volume = {1033}, number = {}, pages = {47-58}, doi = {10.1007/978-3-319-66653-2_4}, pmid = {29101651}, issn = {0065-2598}, mesh = {Animals ; Bone Remodeling/*physiology ; Bone and Bones/*physiology ; Brain/physiology ; Gastrointestinal Microbiome/drug effects/*physiology ; Gastrointestinal Tract/microbiology/*physiology ; Humans ; Prebiotics/administration & dosage ; Probiotics/administration & dosage ; Signal Transduction/drug effects ; }, abstract = {The past decade has seen an explosion of research in the area of how the bacteria that inhabit the human body impact health and disease. One of the more surprising concepts to emerge from this work is the ability of the intestinal microbiota to impact virtually all systems in the body. Recently, the role of gut bacteria in bone health and disease has received more significant attention. In this chapter, we review what has been learned about how the gut microbiome impacts bone health and discuss possible mechanisms of how the gut-bone axis may be connected. We also discuss the use of therapeutic microbes in the modulation of bone health. Finally, we propose an emerging field of the gut-brain-bone axis, in which the gut drives bone physiology via regulation of key hormones that are originally synthesized in the brain.}, } @article {pmid29101194, year = {2018}, author = {Orellana, LH and Chee-Sanford, JC and Sanford, RA and Löffler, FE and Konstantinidis, KT}, title = {Year-Round Shotgun Metagenomes Reveal Stable Microbial Communities in Agricultural Soils and Novel Ammonia Oxidizers Responding to Fertilization.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {2}, pages = {}, pmid = {29101194}, issn = {1098-5336}, mesh = {Agriculture ; Ammonia/metabolism ; Archaea/classification/*isolation & purification/metabolism ; Bacteria/classification/*isolation & purification/metabolism ; *Fertilizers ; Illinois ; *Metagenome ; *Microbiota ; Oxidation-Reduction ; *Soil Microbiology ; }, abstract = {The dynamics of individual microbial populations and their gene functions in agricultural soils, especially after major activities such as nitrogen (N) fertilization, remain elusive but are important for a better understanding of nutrient cycling. Here, we analyzed 20 short-read metagenomes collected at four time points during 1 year from two depths (0 to 5 and 20 to 30 cm) in two Midwestern agricultural sites representing contrasting soil textures (sandy versus silty loam) with similar cropping histories. Although the microbial community taxonomic and functional compositions differed between the two locations and depths, they were more stable within a depth/site throughout the year than communities in natural aquatic ecosystems. For example, among the 69 population genomes assembled from the metagenomes, 75% showed a less than 2-fold change in abundance between any two sampling points. Interestingly, six deep-branching Thaumarchaeota and three complete ammonia oxidizer (comammox) Nitrospira populations increased up to 5-fold in abundance upon the addition of N fertilizer. These results indicated that indigenous archaeal ammonia oxidizers may respond faster (are more copiotrophic) to N fertilization than previously thought. None of 29 recovered putative denitrifier genomes encoded the complete denitrification pathway, suggesting that denitrification is carried out by a collection of different populations. Altogether, our study identified novel microbial populations and genes responding to seasonal and human-induced perturbations in agricultural soils that should facilitate future monitoring efforts and N-related studies.IMPORTANCE Even though the impact of agricultural management on the microbial community structure has been recognized, an understanding of the dynamics of individual microbial populations and what functions each population carries are limited. Yet, this information is important for a better understanding of nutrient cycling, with potentially important implications for preserving nitrogen in soils and sustainability. Here, we show that reconstructed metagenome-assembled genomes (MAGs) are relatively stable in their abundance and functional gene content year round, and seasonal nitrogen fertilization has selected for novel Thaumarchaeota and comammox Nitrospira nitrifiers that are potentially less oligotrophic than their marine counterparts previously studied.}, } @article {pmid29101190, year = {2018}, author = {Buryska, T and Babkova, P and Vavra, O and Damborsky, J and Prokop, Z}, title = {A Haloalkane Dehalogenase from a Marine Microbial Consortium Possessing Exceptionally Broad Substrate Specificity.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {2}, pages = {}, pmid = {29101190}, issn = {1098-5336}, mesh = {Bacteria/*enzymology/genetics/metabolism ; Biocatalysis ; Biotechnology ; Catalysis ; Catalytic Domain ; Crystallization ; Hydrogen-Ion Concentration ; Hydrolases/*chemistry/genetics/isolation & purification/*metabolism ; Kinetics ; Metagenome ; Microbial Consortia/genetics/*physiology ; Substrate Specificity ; }, abstract = {The haloalkane dehalogenase enzyme DmmA was identified by marine metagenomic screening. Determination of its crystal structure revealed an unusually large active site compared to those of previously characterized haloalkane dehalogenases. Here we present a biochemical characterization of this interesting enzyme with emphasis on its structure-function relationships. DmmA exhibited an exceptionally broad substrate specificity and degraded several halogenated environmental pollutants that are resistant to other members of this enzyme family. In addition to having this unique substrate specificity, the enzyme was highly tolerant to organic cosolvents such as dimethyl sulfoxide, methanol, and acetone. Its broad substrate specificity, high overexpression yield (200 mg of protein per liter of cultivation medium; 50% of total protein), good tolerance to organic cosolvents, and a broad pH range make DmmA an attractive biocatalyst for various biotechnological applications.IMPORTANCE We present a thorough biochemical characterization of the haloalkane dehalogenase DmmA from a marine metagenome. This enzyme with an unusually large active site shows remarkably broad substrate specificity, high overexpression, significant tolerance to organic cosolvents, and activity under a broad range of pH conditions. DmmA is an attractive catalyst for sustainable biotechnology applications, e.g., biocatalysis, biosensing, and biodegradation of halogenated pollutants. We also report its ability to convert multiple halogenated compounds to corresponding polyalcohols.}, } @article {pmid29101024, year = {2018}, author = {Ong, SY and Kho, HP and Riedel, SL and Kim, SW and Gan, CY and Taylor, TD and Sudesh, K}, title = {An integrative study on biologically recovered polyhydroxyalkanoates (PHAs) and simultaneous assessment of gut microbiome in yellow mealworm.}, journal = {Journal of biotechnology}, volume = {265}, number = {}, pages = {31-39}, doi = {10.1016/j.jbiotec.2017.10.017}, pmid = {29101024}, issn = {1873-4863}, mesh = {Animals ; Cupriavidus necator/*metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Larva/microbiology ; Palm Oil/metabolism ; Polyhydroxyalkanoates/*biosynthesis ; RNA, Ribosomal, 16S/genetics ; Tenebrio/*microbiology ; }, abstract = {Polyhydroxyalkanoates (PHAs) are produced in microbes as a source of carbon and energy storage. They are biodegradable and have properties similar to synthetic plastics, which make them an interesting alternative to petroleum-based plastics. In this study, a refined method of recovering PHA from Cupriavidus necator biomass was proposed by incorporating the use of the yellow mealworm (the larval phase of the mealworm beetle, Tenebrio molitor) as partial purification machinery, followed by washing of the fecal pellets with distilled water and sodium hydroxide. The PHA contents of the cells used in this study were 55wt% (produced from palm olein) and 60 wt% (produced from waste animal fats). The treatment of distilled water and NaOH further increased the purity of PHA to 94%. In parallel, analysis of the 16S rRNA metagenomic sequencing of the mealworm gut microbiome has revealed remarkable changes in the bacterial diversity, especially between the mealworms fed with cells produced from palm olein and waste animal fats. This biological recovery of PHA from cells is an attempt to move towards a green and sustainable process with the aim of reducing the use of harmful solvents and strong chemicals during polymer purification. The results obtained show that - purities of >90%, without a reduction in the molecular weight, can be obtained through this integrative biological recovery approach. In addition, this study has successfully shown that the cells, regardless of their origins, were readily consumed by the mealworms, and there is a correlation between the feed type and the mealworm gut microbiome.}, } @article {pmid29099490, year = {2018}, author = {Tully, BJ and Wheat, CG and Glazer, BT and Huber, JA}, title = {A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer.}, journal = {The ISME journal}, volume = {12}, number = {1}, pages = {1-16}, pmid = {29099490}, issn = {1751-7370}, mesh = {Bacteria/classification/genetics/*isolation & purification/metabolism ; *Biodiversity ; Genome, Bacterial ; Groundwater/chemistry/*microbiology ; Iron/metabolism ; Metagenome ; Oxidation-Reduction ; Phylogeny ; }, abstract = {The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb3- and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer.}, } @article {pmid29099096, year = {2017}, author = {Barrington, WT and Lusis, AJ}, title = {Atherosclerosis: Association between the gut microbiome and atherosclerosis.}, journal = {Nature reviews. Cardiology}, volume = {14}, number = {12}, pages = {699-700}, pmid = {29099096}, issn = {1759-5010}, support = {P01 HL028481/HL/NHLBI NIH HHS/United States ; P01 HL030568/HL/NHLBI NIH HHS/United States ; }, mesh = {*Atherosclerosis/etiology/metabolism/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Metagenomics/*methods ; }, abstract = {The gut microbiota has been associated with many different disorders, including cardiovascular diseases. A new study by Jie and colleagues is the first large case–control study to examine directly the enrichment of certain communities of gut bacteria in patients with atherosclerotic cardiovascular disease compared with control individuals.}, } @article {pmid29097759, year = {2017}, author = {Meiser, A and Otte, J and Schmitt, I and Grande, FD}, title = {Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {14881}, pmid = {29097759}, issn = {2045-2322}, mesh = {DNA, Fungal/*genetics ; *Genome, Fungal ; Lichens/classification/*genetics ; Metagenomics ; Sequence Analysis, DNA ; Transcriptome ; }, abstract = {The metagenome skimming approach, i.e. low coverage shotgun sequencing of multi-species assemblages and subsequent reconstruction of individual genomes, is increasingly used for in-depth genomic characterization of ecological communities. This approach is a promising tool for reconstructing genomes of facultative symbionts, such as lichen-forming fungi, from metagenomic reads. However, no study has so far tested accuracy and completeness of assemblies based on metagenomic sequences compared to assemblies based on pure culture strains of lichenized fungi. Here we assembled the genomes of Evernia prunastri and Pseudevernia furfuracea based on metagenomic sequences derived from whole lichen thalli. We extracted fungal contigs using two different taxonomic binning methods, and performed gene prediction on the fungal contig subsets. We then assessed quality and completeness of the metagenome-based assemblies using genome assemblies as reference which are based on pure culture strains of the two fungal species. Our comparison showed that we were able to reconstruct fungal genomes from uncultured lichen thalli, and also cover most of the gene space (86-90%). Metagenome skimming will facilitate genome mining, comparative (phylo)genomics, and population genetics of lichen-forming fungi by circumventing the time-consuming, sometimes unfeasible, step of aposymbiotic cultivation.}, } @article {pmid29097494, year = {2018}, author = {Routy, B and Le Chatelier, E and Derosa, L and Duong, CPM and Alou, MT and Daillère, R and Fluckiger, A and Messaoudene, M and Rauber, C and Roberti, MP and Fidelle, M and Flament, C and Poirier-Colame, V and Opolon, P and Klein, C and Iribarren, K and Mondragón, L and Jacquelot, N and Qu, B and Ferrere, G and Clémenson, C and Mezquita, L and Masip, JR and Naltet, C and Brosseau, S and Kaderbhai, C and Richard, C and Rizvi, H and Levenez, F and Galleron, N and Quinquis, B and Pons, N and Ryffel, B and Minard-Colin, V and Gonin, P and Soria, JC and Deutsch, E and Loriot, Y and Ghiringhelli, F and Zalcman, G and Goldwasser, F and Escudier, B and Hellmann, MD and Eggermont, A and Raoult, D and Albiges, L and Kroemer, G and Zitvogel, L}, title = {Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors.}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6371}, pages = {91-97}, doi = {10.1126/science.aan3706}, pmid = {29097494}, issn = {1095-9203}, mesh = {Animals ; Anti-Bacterial Agents/therapeutic use ; Antibodies, Monoclonal/therapeutic use ; CD4 Antigens/immunology ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*immunology ; Humans ; Immunotherapy/*methods ; Interleukin-12/immunology ; Metagenome/genetics ; Mice ; Neoplasms/*therapy ; Programmed Cell Death 1 Receptor/*antagonists & inhibitors ; Receptors, CCR/immunology ; Receptors, CXCR3/immunology ; T-Lymphocytes/immunology ; Verrucomicrobia/genetics/immunology ; }, abstract = {Immune checkpoint inhibitors (ICIs) targeting the PD-1/PD-L1 axis induce sustained clinical responses in a sizable minority of cancer patients. We found that primary resistance to ICIs can be attributed to abnormal gut microbiome composition. Antibiotics inhibited the clinical benefit of ICIs in patients with advanced cancer. Fecal microbiota transplantation (FMT) from cancer patients who responded to ICIs into germ-free or antibiotic-treated mice ameliorated the antitumor effects of PD-1 blockade, whereas FMT from nonresponding patients failed to do so. Metagenomics of patient stool samples at diagnosis revealed correlations between clinical responses to ICIs and the relative abundance of Akkermansia muciniphila Oral supplementation with A. muciniphila after FMT with nonresponder feces restored the efficacy of PD-1 blockade in an interleukin-12-dependent manner by increasing the recruitment of CCR9[+]CXCR3[+]CD4[+] T lymphocytes into mouse tumor beds.}, } @article {pmid29097493, year = {2018}, author = {Gopalakrishnan, V and Spencer, CN and Nezi, L and Reuben, A and Andrews, MC and Karpinets, TV and Prieto, PA and Vicente, D and Hoffman, K and Wei, SC and Cogdill, AP and Zhao, L and Hudgens, CW and Hutchinson, DS and Manzo, T and Petaccia de Macedo, M and Cotechini, T and Kumar, T and Chen, WS and Reddy, SM and Szczepaniak Sloane, R and Galloway-Pena, J and Jiang, H and Chen, PL and Shpall, EJ and Rezvani, K and Alousi, AM and Chemaly, RF and Shelburne, S and Vence, LM and Okhuysen, PC and Jensen, VB and Swennes, AG and McAllister, F and Marcelo Riquelme Sanchez, E and Zhang, Y and Le Chatelier, E and Zitvogel, L and Pons, N and Austin-Breneman, JL and Haydu, LE and Burton, EM and Gardner, JM and Sirmans, E and Hu, J and Lazar, AJ and Tsujikawa, T and Diab, A and Tawbi, H and Glitza, IC and Hwu, WJ and Patel, SP and Woodman, SE and Amaria, RN and Davies, MA and Gershenwald, JE and Hwu, P and Lee, JE and Zhang, J and Coussens, LM and Cooper, ZA and Futreal, PA and Daniel, CR and Ajami, NJ and Petrosino, JF and Tetzlaff, MT and Sharma, P and Allison, JP and Jenq, RR and Wargo, JA}, title = {Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients.}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6371}, pages = {97-103}, pmid = {29097493}, issn = {1095-9203}, support = {R25 CA056452/CA/NCI NIH HHS/United States ; UL1 TR000128/TR/NCATS NIH HHS/United States ; K12 CA088084/CA/NCI NIH HHS/United States ; K08 CA160692/CA/NCI NIH HHS/United States ; P30 CA016672/CA/NCI NIH HHS/United States ; R25 CA057730/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/genetics/*immunology ; Humans ; *Immunotherapy ; Melanoma/immunology/*therapy ; Metagenome ; Mice ; Programmed Cell Death 1 Receptor/*antagonists & inhibitors ; Skin Neoplasms/immunology/*therapy ; }, abstract = {Preclinical mouse models suggest that the gut microbiome modulates tumor response to checkpoint blockade immunotherapy; however, this has not been well-characterized in human cancer patients. Here we examined the oral and gut microbiome of melanoma patients undergoing anti-programmed cell death 1 protein (PD-1) immunotherapy (n = 112). Significant differences were observed in the diversity and composition of the patient gut microbiome of responders versus nonresponders. Analysis of patient fecal microbiome samples (n = 43, 30 responders, 13 nonresponders) showed significantly higher alpha diversity (P < 0.01) and relative abundance of bacteria of the Ruminococcaceae family (P < 0.01) in responding patients. Metagenomic studies revealed functional differences in gut bacteria in responders, including enrichment of anabolic pathways. Immune profiling suggested enhanced systemic and antitumor immunity in responding patients with a favorable gut microbiome as well as in germ-free mice receiving fecal transplants from responding patients. Together, these data have important implications for the treatment of melanoma patients with immune checkpoint inhibitors.}, } @article {pmid29097220, year = {2018}, author = {Gao, B and Chi, L and Tu, P and Bian, X and Thomas, J and Ru, H and Lu, K}, title = {The organophosphate malathion disturbs gut microbiome development and the quorum-Sensing system.}, journal = {Toxicology letters}, volume = {283}, number = {}, pages = {52-57}, doi = {10.1016/j.toxlet.2017.10.023}, pmid = {29097220}, issn = {1879-3169}, mesh = {Animals ; Bacteria/genetics/pathogenicity ; Cell Wall/drug effects ; Gastrointestinal Microbiome/*drug effects ; Genome ; Genomics ; Insecticides/*toxicity ; Malathion/*toxicity ; Male ; Mice ; Mice, Inbred C57BL ; Quorum Sensing/*drug effects/*genetics ; RNA, Ribosomal, 16S/biosynthesis/genetics ; }, abstract = {The gut microbiome has tremendous potential to impact health and disease. Various environmental toxicants, including insecticides, have been shown to alter gut microbiome community structures. However, the mechanism that compositionally and functionally regulates gut microbiota remains unclear. Quorum sensing is known to modulate intra- and interspecies gene expression and coordinate population responses. It is unknown whether quorum sensing is disrupted when environmental toxicants cause perturbations in the gut microbiome community structure. To reveal the response of the quorum-sensing system to environmental exposure, we use a combination of Illumina-based 16S rRNA gene amplicon and shotgun metagenome sequencing to examine the impacts of a widely used organophosphate insecticide, malathion, on the gut microbiome trajectory, quorum sensing system and behaviors related to quorum sensing, such as motility and pathogenicity. Our results demonstrated that malathion perturbed the gut microbiome development, quorum sensing and quorum sensing related behaviors. These findings may provide a novel mechanistic understanding of the role of quorum-sensing in the gut microbiome toxicity of malathion.}, } @article {pmid29096601, year = {2017}, author = {Alcon-Giner, C and Caim, S and Mitra, S and Ketskemety, J and Wegmann, U and Wain, J and Belteki, G and Clarke, P and Hall, LJ}, title = {Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {841}, pmid = {29096601}, issn = {1471-2164}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/J004529/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M011216/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/00044409/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bifidobacterium/drug effects/genetics/isolation & purification/physiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/drug effects/*genetics ; Genomics/*methods ; Humans ; Infant ; *Infant, Extremely Low Birth Weight ; Lactobacillus/drug effects/genetics/isolation & purification/physiology ; Male ; Probiotics/pharmacology ; RNA, Ribosomal, 16S/*genetics ; Risk ; Sequence Analysis, RNA/*methods ; }, abstract = {BACKGROUND: Infants born prematurely, particularly extremely low birth weight infants (ELBW) have altered gut microbial communities. Factors such as maternal health, gut immaturity, delivery mode, and antibiotic treatments are associated with microbiota disturbances, and are linked to an increased risk of certain diseases such as necrotising enterocolitis. Therefore, there is a requirement to optimally characterise microbial profiles in this at-risk cohort, via standardisation of methods, particularly for studying the influence of microbiota therapies (e.g. probiotic supplementation) on community profiles and health outcomes. Profiling of faecal samples using the 16S rRNA gene is a cost-efficient method for large-scale clinical studies to gain insights into the gut microbiota and additionally allows characterisation of cohorts were sample quantities are compromised (e.g. ELBW infants). However, DNA extraction method, and the 16S rRNA region targeted can significantly change bacterial community profiles obtained, and so confound comparisons between studies. Thus, we sought to optimise a 16S rRNA profiling protocol to allow standardisation for studying ELBW infant faecal samples, with or without probiotic supplementation.

METHODS: Using ELBW faecal samples, we compared three different DNA extraction methods, and subsequently PCR amplified and sequenced three hypervariable regions of the 16S rRNA gene (V1 + V2 + V3), (V4 + V5) and (V6 + V7 + V8), and compared two bioinformatics approaches to analyse results (OTU and paired end). Paired shotgun metagenomics was used as a 'gold-standard'.

RESULTS: Results indicated a longer bead-beating step was required for optimal bacterial DNA extraction and that sequencing regions (V1 + V2 + V3) and (V6 + V7 + V8) provided the most representative taxonomic profiles, which was confirmed via shotgun analysis. Samples sequenced using the (V4 + V5) region were found to be underrepresented in specific taxa including Bifidobacterium, and had altered diversity profiles. Both bioinformatics 16S rRNA pipelines used in this study (OTU and paired end) presented similar taxonomic profiles at genus level.

CONCLUSIONS: We determined that DNA extraction from ELBW faecal samples, particularly those infants receiving probiotic supplementation, should include a prolonged beat-beating step. Furthermore, use of the 16S rRNA (V1 + V2 + V3) and (V6 + V7 + V8) regions provides reliable representation of ELBW microbiota profiles, while inclusion of the (V4 + V5) region may not be appropriate for studies where Bifidobacterium constitutes a resident microbiota member.}, } @article {pmid29095820, year = {2017}, author = {Marzano, V and Mancinelli, L and Bracaglia, G and Del Chierico, F and Vernocchi, P and Di Girolamo, F and Garrone, S and Tchidjou Kuekou, H and D'Argenio, P and Dallapiccola, B and Urbani, A and Putignani, L}, title = {"Omic" investigations of protozoa and worms for a deeper understanding of the human gut "parasitome".}, journal = {PLoS neglected tropical diseases}, volume = {11}, number = {11}, pages = {e0005916}, pmid = {29095820}, issn = {1935-2735}, mesh = {Animals ; Entamoeba histolytica/genetics/metabolism ; Gastrointestinal Microbiome ; Gastrointestinal Tract/*parasitology ; *Genomics ; Giardia/genetics/metabolism ; Helminths/genetics/physiology ; *Host-Parasite Interactions ; Humans ; *Metabolomics ; Mice ; Parasites/*physiology ; *Proteomics ; Taenia solium/genetics/metabolism ; }, abstract = {The human gut has been continuously exposed to a broad spectrum of intestinal organisms, including viruses, bacteria, fungi, and parasites (protozoa and worms), over millions of years of coevolution, and plays a central role in human health. The modern lifestyles of Western countries, such as the adoption of highly hygienic habits, the extensive use of antimicrobial drugs, and increasing globalisation, have dramatically altered the composition of the gut milieu, especially in terms of its eukaryotic "citizens." In the past few decades, numerous studies have highlighted the composition and role of human intestinal bacteria in physiological and pathological conditions, while few investigations exist on gut parasites and particularly on their coexistence and interaction with the intestinal microbiota. Studies of the gut "parasitome" through "omic" technologies, such as (meta)genomics, transcriptomics, proteomics, and metabolomics, are herein reviewed to better understand their role in the relationships between intestinal parasites, host, and resident prokaryotes, whether pathogens or commensals. Systems biology-based profiles of the gut "parasitome" under physiological and severe disease conditions can indeed contribute to the control of infectious diseases and offer a new perspective of omics-assisted tropical medicine.}, } @article {pmid29095019, year = {2017}, author = {González, S and Gutie Rrez-Díaz, I and Lo Pez, P and Suárez, A and Fernández-Navarro, T and Sánchez, B and Margolles, A}, title = {Microbiota and oxidant-antioxidant balance in systemic lupus erythematosus.}, journal = {Nutricion hospitalaria}, volume = {34}, number = {4}, pages = {934-941}, doi = {10.20960/nh.546}, pmid = {29095019}, issn = {1699-5198}, mesh = {Adult ; Antioxidants/*metabolism ; Diet ; Female ; Humans ; Lupus Erythematosus, Systemic/*metabolism/*microbiology ; Male ; *Microbiota ; Middle Aged ; Oxidative Stress ; }, abstract = {BACKGROUND: Systemic lupus erythematosus (SLE) is a chronic infl ammatory disease of autoimmune nature, in which oxidative stress is implicated.

AIM: Compare the concentrations of dietary and blood antioxidants, as well as gut microbiota, with serum malondialdehyde (MDA) and C reactive protein (CRP) in 21 subjects suffering from non-active systemic lupus erythematosus (SLE) and 21 age and gender-matched controls.

METHODS: General biochemical parameters and CRP were determined by enzymatic methods: copper, zinc and selenium by inductively coupled plasma mass spectrometry (ICP-MS), MDA and total antioxidant capacity (TAC) by spectrophotometric methods, gut microbiota by metagenomic analyses and dietary intake by means of food frequency questionnaire.

RESULTS: No significant differences were found in diet between lupus patients and the control group, with the exception of trans fatty acids intake, which was higher in patients. In addition, higher concentration of serum copper and lower of zinc in SLE were found. Serum copper was positively associated with CRP and also, this protein with the proportion of Lentisphaerae, ProteobacteriaandVerrucomicrobiain feces. Moreover, MDA levels displayed inverse correlations with the Cyanobacteriaand Firmicutesgroups, while Actinobacteria showed a positive association. The lupus subjects with presence of anti-SSA/Ro were related to higher levels of serum zinc.

CONCLUSION: These results could be useful in the future to go deeper into the understanding of this complex disease.}, } @article {pmid29094115, year = {2017}, author = {Shao, Y and Huo, D and Peng, Q and Pan, Y and Jiang, S and Liu, B and Zhang, J}, title = {Lactobacillus plantarum HNU082-derived improvements in the intestinal microbiome prevent the development of hyperlipidaemia.}, journal = {Food & function}, volume = {8}, number = {12}, pages = {4508-4516}, doi = {10.1039/c7fo00902j}, pmid = {29094115}, issn = {2042-650X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Fatty Acids/biosynthesis ; Female ; *Gastrointestinal Microbiome/drug effects ; Humans ; Hyperlipidemias/microbiology/*prevention & control ; Intestinal Mucosa/metabolism ; Intestines/drug effects/*microbiology ; Lactobacillus plantarum/genetics/*physiology ; Male ; Probiotics/*administration & dosage ; Pyruvic Acid/metabolism ; Rats ; Rats, Sprague-Dawley ; }, abstract = {Restricted by research techniques, the probiotic-derived changes in the microbiome and microbial metabolites correlated with the potential prevention of hyperlipidaemia have remained undiscovered. In the present research, a metagenomic approach was applied to describe Lactobacillus plantarum HNU082 consumption-derived changes in the intestinal microbiome and their correlation with the occurrence and development of hyperlipidaemia. Principal coordinate analysis based on UniFrac distances indicated that the intestinal microbiota was profoundly altered in the hyperlipidaemia group, and probiotic consumption regulated the bias in the intestinal microbial structure in hyperlipidaemia. Bifidobacterium, Lactobacillus, Akkermansia and Faecalibacterium were significantly increased in the probiotic group, and the genera Clostridium, Natranaerovirga and Odoribacter were significantly increased in the hyperlipidaemia group. Further analysis based on metabolic pathways revealed that pyruvate metabolism, glycerolipid metabolism, propanoate metabolism, and fatty acid biosynthesis were enriched in the probiotic and control groups. In contrast, the pathways of secondary bile acid and lipopolysaccharide biosynthesis were enriched in the hyperlipidaemia group. Finally, we constructed a network to better explain the potential mechanism of hyperlipidaemia prevention. The present basic research will promote our understanding of the probiotic action mechanism in hyperlipidaemia therapy and provide new insight into the design and application of probiotic-containing functional foods.}, } @article {pmid29093477, year = {2017}, author = {Zhang, L and Fu, Q and Li, W and Wang, B and Yin, X and Liu, S and Xu, Z and Niu, Q}, title = {Identification and characterization of a novel β-glucosidase via metagenomic analysis of Bursaphelenchus xylophilus and its microbial flora.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {14850}, pmid = {29093477}, issn = {2045-2322}, mesh = {Animals ; Cellulose/metabolism ; Glucosides/metabolism ; Metagenomics/*methods ; Microbiota/genetics ; Nematoda/*enzymology/microbiology ; Pinus/parasitology ; beta-Glucosidase/*isolation & purification/metabolism ; }, abstract = {β-glucosidases catalyze the final step of cellulose hydrolysis and are essential in cellulose degradation. A β-glucosidase gene, cen502, was identified and isolated from a metagenomic library from Bursaphelenchus xylophilus via functional screening. Analyses indicated that cen502 encodes a 465 amino acid polypeptide that contains a catalytic domain belonging to the glycoside hydrolase family 1 (GH1). Cen502 was heterologously expressed, purified, and biochemically characterized. Recombinant Cen502 displayed optimum enzymatic activity at pH 8.0 and 38 °C. The enzyme had highest specific activity to p-nitrophenyl-β-D-glucopyranoside (pNPG; 180.3 U/mg) and had K m and V max values of 2.334 mol/ml and 9.017 μmol/min/mg, respectively. The addition of Fe[2+] and Mn[2+] significantly increased Cen502 β-glucosidase activity by 60% and 50%, respectively, while 10% and 25% loss of β-glucosidase activity was induced by addition of Pb[2+] and K[+], respectively. Cen502 exhibited activity against a broad array of substrates, including cellobiose, lactose, salicin, lichenan, laminarin, and sophorose. However, Cen502 displayed a preference for the hydrolysis of β-1,4 glycosidic bonds rather than β-1,3, β-1,6, or β-1,2 bonds. Our results indicate that Cen502 is a novel β-glucosidase derived from bacteria associated with B. xylophilus and may represent a promising target to enhance the efficiency of cellulose bio-degradation in industrial applications.}, } @article {pmid29092015, year = {2018}, author = {Olekhnovich, EI and Vasilyev, AT and Ulyantsev, VI and Kostryukova, ES and Tyakht, AV}, title = {MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {3}, pages = {434-444}, doi = {10.1093/bioinformatics/btx681}, pmid = {29092015}, issn = {1367-4811}, mesh = {Algorithms ; Bacteria/*genetics ; Drug Resistance, Bacterial/*genetics ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenomics/*methods ; *Software ; }, abstract = {MOTIVATION: Antibiotic resistance is an important global public health problem. Human gut microbiota is an accumulator of resistance genes potentially providing them to pathogens. It is important to develop tools for identifying the mechanisms of how resistance is transmitted between gut microbial species and pathogens.

RESULTS: We developed MetaCherchant-an algorithm for extracting the genomic environment of antibiotic resistance genes from metagenomic data in the form of a graph. The algorithm was validated on a number of simulated and published datasets, as well as applied to new 'shotgun' metagenomes of gut microbiota from patients with Helicobacter pylori who underwent antibiotic therapy. Genomic context was reconstructed for several major resistance genes. Taxonomic annotation of the context suggests that within a single metagenome, the resistance genes can be contained in genomes of multiple species. MetaCherchant allows reconstruction of mobile elements with resistance genes within the genomes of bacteria using metagenomic data. Application of MetaCherchant in differential mode produced specific graph structures suggesting the evidence of possible resistance gene transmission within a mobile element that occurred as a result of the antibiotic therapy. MetaCherchant is a promising tool giving researchers an opportunity to get an insight into dynamics of resistance transmission in vivo basing on metagenomic data.

Source code and binaries are freely available for download at https://github.com/ctlab/metacherchant. The code is written in Java and is platform-independent.

COTANCT: ulyantsev@rain.ifmo.ru.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid29091761, year = {2017}, author = {Nakamoto, N and Amiya, T and Aoki, R and Taniki, N and Koda, Y and Miyamoto, K and Teratani, T and Suzuki, T and Chiba, S and Chu, PS and Hayashi, A and Yamaguchi, A and Shiba, S and Miyake, R and Katayama, T and Suda, W and Mikami, Y and Kamada, N and Ebinuma, H and Saito, H and Hattori, M and Kanai, T}, title = {Commensal Lactobacillus Controls Immune Tolerance during Acute Liver Injury in Mice.}, journal = {Cell reports}, volume = {21}, number = {5}, pages = {1215-1226}, doi = {10.1016/j.celrep.2017.10.022}, pmid = {29091761}, issn = {2211-1247}, mesh = {Alanine Transaminase/blood ; Animals ; Chemical and Drug Induced Liver Injury/*immunology/pathology ; Dendritic Cells/cytology/metabolism ; Gastrointestinal Microbiome ; Histocompatibility Antigens Class II/metabolism ; *Immune Tolerance ; Immunity, Innate ; Interferon-gamma/metabolism ; Interleukin-10/metabolism ; Interleukins/metabolism ; Intestinal Mucosa/metabolism ; Intestines/immunology/microbiology ; Lactobacillus/*immunology/physiology ; Liver/immunology/metabolism/pathology ; Male ; Mice ; Mice, Inbred C57BL ; T-Lymphocytes, Regulatory/cytology/immunology/metabolism ; Toll-Like Receptor 9/metabolism ; Transforming Growth Factor beta/metabolism ; Interleukin-22 ; }, abstract = {Gut-derived microbial antigens trigger the innate immune system during acute liver injury. During recovery, regulatory immunity plays a role in suppressing inflammation; however, the precise mechanism underlying this process remains obscure. Here, we find that recruitment of immune-regulatory classical dendritic cells (cDCs) is crucial for liver tolerance in concanavalin A-induced acute liver injury. Acute liver injury resulted in enrichment of commensal Lactobacillus in the gut. Notably, Lactobacillus activated IL-22 production by gut innate lymphoid cells and raised systemic IL-22 levels. Gut-derived IL-22 enhanced mucosal barrier function and promoted the recruitment of regulatory cDCs to the liver. These cDCs produced IL-10 and TGF-β through TLR9 activation, preventing further liver inflammation. Collectively, our results indicate that beneficial gut microbes influence tolerogenic immune responses in the liver. Therefore, modulation of the gut microbiota might be a potential option to regulate liver tolerance.}, } @article {pmid29089173, year = {2018}, author = {Turroni, F and Milani, C and Duranti, S and Mahony, J and van Sinderen, D and Ventura, M}, title = {Glycan Utilization and Cross-Feeding Activities by Bifidobacteria.}, journal = {Trends in microbiology}, volume = {26}, number = {4}, pages = {339-350}, doi = {10.1016/j.tim.2017.10.001}, pmid = {29089173}, issn = {1878-4380}, mesh = {Adaptation, Biological ; Bifidobacterium/genetics/*physiology ; Biological Evolution ; Carbohydrate Metabolism/physiology ; Ecology ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/microbiology ; Genome, Bacterial ; Humans ; Metagenomics ; Polysaccharides/*metabolism ; Probiotics ; }, abstract = {Bifidobacteria represent one of the first colonizers of the mammalian gut, where such colonization is facilitated by their saccharolytic capabilities. Genomic analyses of bifidobacteria have revealed intriguing genetic strategies employed by these bacteria to access a variety of dietary and host-produced glycans. Bifidobacterial genome evolution therefore represents a fascinating example of how their chromosomes were molded to contain a large number of genes involved in carbohydrate metabolism. One of the reasons as to why bifidobacteria are such dominant and prevalent members of the (early) microbiota is that they may access glycans in the gut through mutualistic cross-feeding or resource-sharing activities, which is indicative of 'social behavior' among bifidobacterial strains.}, } @article {pmid29088131, year = {2017}, author = {Woyke, T and Doud, DFR and Schulz, F}, title = {The trajectory of microbial single-cell sequencing.}, journal = {Nature methods}, volume = {14}, number = {11}, pages = {1045-1054}, pmid = {29088131}, issn = {1548-7105}, mesh = {Metagenomics ; Microbiota/genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Single-Cell Analysis ; }, abstract = {Over the past decade, it has become nearly routine to sequence genomes of individual microbial cells directly isolated from environmental samples ranging from deep-sea hydrothermal vents to insect guts, providing a powerful complement to shotgun metagenomics in microbial community studies. In this review, we address the technical aspects and challenges of single-cell genome sequencing and discuss some of the scientific endeavors that it has enabled. Specifically, we highlight newly added leaves and branches in the genomic tree of bacterial and archaeal life and illustrate the unique and exciting advantages that single-cell genomics offers over metagenomics, both now and in the near future.}, } @article {pmid29088129, year = {2017}, author = {Pasolli, E and Schiffer, L and Manghi, P and Renson, A and Obenchain, V and Truong, DT and Beghini, F and Malik, F and Ramos, M and Dowd, JB and Huttenhower, C and Morgan, M and Segata, N and Waldron, L}, title = {Accessible, curated metagenomic data through ExperimentHub.}, journal = {Nature methods}, volume = {14}, number = {11}, pages = {1023-1024}, pmid = {29088129}, issn = {1548-7105}, support = {P41 HG004059/HG/NHGRI NIH HHS/United States ; R21 AI121784/AI/NIAID NIH HHS/United States ; U24 CA180996/CA/NCI NIH HHS/United States ; U41 HG004059/HG/NHGRI NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Gastrointestinal Microbiome/genetics ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Genome, Fungal/genetics ; Genome, Human/genetics ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; *Software ; Species Specificity ; }, } @article {pmid29085573, year = {2017}, author = {Herath, D and Jayasundara, D and Ackland, D and Saeed, I and Tang, SL and Halgamuge, S}, title = {Assessing Species Diversity Using Metavirome Data: Methods and Challenges.}, journal = {Computational and structural biotechnology journal}, volume = {15}, number = {}, pages = {447-455}, pmid = {29085573}, issn = {2001-0370}, abstract = {Assessing biodiversity is an important step in the study of microbial ecology associated with a given environment. Multiple indices have been used to quantify species diversity, which is a key biodiversity measure. Measuring species diversity of viruses in different environments remains a challenge relative to measuring the diversity of other microbial communities. Metagenomics has played an important role in elucidating viral diversity by conducting metavirome studies; however, metavirome data are of high complexity requiring robust data preprocessing and analysis methods. In this review, existing bioinformatics methods for measuring species diversity using metavirome data are categorised broadly as either sequence similarity-dependent methods or sequence similarity-independent methods. The former includes a comparison of DNA fragments or assemblies generated in the experiment against reference databases for quantifying species diversity, whereas estimates from the latter are independent of the knowledge of existing sequence data. Current methods and tools are discussed in detail, including their applications and limitations. Drawbacks of the state-of-the-art method are demonstrated through results from a simulation. In addition, alternative approaches are proposed to overcome the challenges in estimating species diversity measures using metavirome data.}, } @article {pmid29084347, year = {2018}, author = {Dijkhuizen, LW and Brouwer, P and Bolhuis, H and Reichart, GJ and Koppers, N and Huettel, B and Bolger, AM and Li, FW and Cheng, S and Liu, X and Wong, GK and Pryer, K and Weber, A and Bräutigam, A and Schluepmann, H}, title = {Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N2 but may denitrify.}, journal = {The New phytologist}, volume = {217}, number = {1}, pages = {453-466}, pmid = {29084347}, issn = {1469-8137}, mesh = {Alphaproteobacteria/genetics/isolation & purification/*physiology ; Biomass ; Denitrification ; Endophytes ; Ferns/growth & development/*microbiology ; Metagenome ; Microbiota ; Nitrogen/*metabolism ; Nitrogen Fixation ; Nitrogen Isotopes/analysis ; Nostoc/genetics/isolation & purification/*physiology ; Oxygen/*metabolism ; Plant Leaves/growth & development/microbiology ; Water ; Water Microbiology ; }, abstract = {Dinitrogen fixation by Nostoc azollae residing in specialized leaf pockets supports prolific growth of the floating fern Azolla filiculoides. To evaluate contributions by further microorganisms, the A. filiculoides microbiome and nitrogen metabolism in bacteria persistently associated with Azolla ferns were characterized. A metagenomic approach was taken complemented by detection of N2 O released and nitrogen isotope determinations of fern biomass. Ribosomal RNA genes in sequenced DNA of natural ferns, their enriched leaf pockets and water filtrate from the surrounding ditch established that bacteria of A. filiculoides differed entirely from surrounding water and revealed species of the order Rhizobiales. Analyses of seven cultivated Azolla species confirmed persistent association with Rhizobiales. Two distinct nearly full-length Rhizobiales genomes were identified in leaf-pocket-enriched samples from ditch grown A. filiculoides. Their annotation revealed genes for denitrification but not N2 -fixation. [15] N2 incorporation was active in ferns with N. azollae but not in ferns without. N2 O was not detectably released from surface-sterilized ferns with the Rhizobiales. N2 -fixing N. azollae, we conclude, dominated the microbiome of Azolla ferns. The persistent but less abundant heterotrophic Rhizobiales bacteria possibly contributed to lowering O2 levels in leaf pockets but did not release detectable amounts of the strong greenhouse gas N2 O.}, } @article {pmid29083504, year = {2018}, author = {Puri, P and Liangpunsakul, S and Christensen, JE and Shah, VH and Kamath, PS and Gores, GJ and Walker, S and Comerford, M and Katz, B and Borst, A and Yu, Q and Kumar, DP and Mirshahi, F and Radaeva, S and Chalasani, NP and Crabb, DW and Sanyal, AJ and , }, title = {The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis.}, journal = {Hepatology (Baltimore, Md.)}, volume = {67}, number = {4}, pages = {1284-1302}, pmid = {29083504}, issn = {1527-3350}, support = {U01 AA021883/AA/NIAAA NIH HHS/United States ; U01 AA021840/AA/NIAAA NIH HHS/United States ; UH2 AA026218/AA/NIAAA NIH HHS/United States ; U01 AA021891/AA/NIAAA NIH HHS/United States ; U01 AA021788/AA/NIAAA NIH HHS/United States ; U01 AA026974/AA/NIAAA NIH HHS/United States ; T32 DK007150/DK/NIDDK NIH HHS/United States ; K23 AA021179/AA/NIAAA NIH HHS/United States ; UH3 AA026218/AA/NIAAA NIH HHS/United States ; R37 AA021171/AA/NIAAA NIH HHS/United States ; }, mesh = {Adult ; Alcohol Drinking/adverse effects ; DNA, Bacterial/*blood/genetics ; Endotoxins/blood ; Female ; Hepatitis, Alcoholic/*microbiology ; Humans ; Liver/microbiology/pathology ; Liver Diseases, Alcoholic/*microbiology ; Male ; Metagenomics/*methods ; Microbiota/*genetics ; Middle Aged ; Monocytes/pathology ; }, abstract = {UNLABELLED: Intestinal dysbiosis is implicated in alcoholic hepatitis (AH). However, changes in the circulating microbiome, its association with the presence and severity of AH, and its functional relevance in AH is unknown. Qualitative and quantitative assessment of changes in the circulating microbiome were performed by sequencing bacterial DNA in subjects with moderate AH (MAH) (n = 18) or severe AH (SAH) (n = 19). These data were compared with heavy drinking controls (HDCs) without obvious liver disease (n = 19) and non-alcohol-consuming controls (NACs, n = 20). The data were related to endotoxin levels and markers of monocyte activation. Linear discriminant analysis effect size (LEfSe) analysis, inferred metagenomics, and predictive functional analysis using PICRUSt were performed. There was a significant increase in 16S copies/ng DNA both in MAH (P < 0.01) and SAH (P < 0.001) subjects. Compared with NACs, the relative abundance of phylum Bacteroidetes was significantly decreased in HDCs, MAH, and SAH (P < 0.001). In contrast, all alcohol-consuming groups had enrichment with Fusobacteria; this was greatest for HDCs and decreased progressively in MAH and SAH. Subjects with SAH had significantly higher endotoxemia (P = 0.01). Compared with alcohol-consuming groups, predictive functional metagenomics indicated an enrichment of bacteria with genes related to methanogenesis and denitrification. Furthermore, both HDCs and SAH showed activation of a type III secretion system that has been linked to gram-negative bacterial virulence. Metagenomics in SAH versus NACs predicted increased isoprenoid synthesis via mevalonate and anthranilate degradation, known modulators of gram-positive bacterial growth and biofilm production, respectively.

CONCLUSION: Heavy alcohol consumption appears to be the primary driver of changes in the circulating microbiome associated with a shift in its inferred metabolic functions. (Hepatology 2018;67:1284-1302).}, } @article {pmid29083035, year = {2018}, author = {Laskar, F and Das Purkayastha, S and Sen, A and Bhattacharya, MK and Misra, BB}, title = {Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems.}, journal = {Journal of basic microbiology}, volume = {58}, number = {2}, pages = {101-119}, doi = {10.1002/jobm.201700341}, pmid = {29083035}, issn = {1521-4028}, mesh = {Archaea/*classification/genetics/growth & development/*metabolism ; *Biodiversity ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fresh Water/*microbiology ; Geologic Sediments/microbiology ; Lakes/microbiology ; Metagenomics/*methods ; Methane/*metabolism ; Microbiological Techniques/*methods ; Oxidoreductases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {About half of the global methane (CH4) emission is contributed by the methanogenic archaeal communities leading to a significant increase in global warming. This unprecedented situation has increased the ever growing necessity of evaluating the control measures for limiting CH4 emission to the atmosphere. Unfortunately, research endeavors on the diversity and functional interactions of methanogens are not extensive till date. We anticipate that the study of the diversity of methanogenic community is paramount for understanding the metabolic processes in freshwater lake ecosystems. Although there are several disadvantages of conventional culture-based methods for determining the diversity of methanogenic archaeal communities, in order to understand their ecological roles in natural environments it is required to culture the microbes. Recently different molecular techniques have been developed for determining the structure of methanogenic archaeal communities thriving in freshwater lake ecosystem. The two gene based cloning techniques required for this purpose are 16S rRNA and methyl coenzyme M reductase (mcrA) in addition to the recently developed metagenomics approaches and high throughput next generation sequencing efforts. This review discusses the various methods of culture-dependent and -independent measures of determining the diversity of methanogen communities in lake sediments in lieu of the different molecular approaches and inter-relationships of diversity of methanogenic archaea.}, } @article {pmid29079861, year = {2018}, author = {Velásquez-Mejía, EP and de la Cuesta-Zuluaga, J and Escobar, JS}, title = {Impact of DNA extraction, sample dilution, and reagent contamination on 16S rRNA gene sequencing of human feces.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {1}, pages = {403-411}, doi = {10.1007/s00253-017-8583-z}, pmid = {29079861}, issn = {1432-0614}, mesh = {DNA/genetics/*isolation & purification ; *DNA Contamination ; DNA, Bacterial/genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; *High-Throughput Nucleotide Sequencing ; Humans ; Indicators and Reagents ; Metagenomics/methods ; Microbial Consortia/genetics ; Microbiota/genetics ; RNA, Ribosomal, 16S/chemistry/*genetics ; Sequence Analysis, DNA ; }, abstract = {Culture-independent methods have granted the possibility to study microbial diversity in great detail, but technical issues pose a threat to the accuracy of new findings. Biases introduced during DNA extraction can result in erroneous representations of the microbial community, particularly in samples with low microbial biomass. We evaluated the DNA extraction method, initial sample biomass, and reagent contamination on the assessment of the human gut microbiota. Fecal samples of 200 mg were subjected to 1:10 serial dilutions; total DNA was obtained using two commercial kits and the microbiota assessed by 16S ribosomal RNA (rRNA) gene sequencing. In addition, we sequenced multiple technical controls. The two kits were efficient in extracting DNA from samples with as low as 2 mg of feces. However, in instances of lower biomass, only one kit performed well. The number of reads from negative controls was negligible. Both DNA extraction kits allowed inferring microbial consortia with similar membership but different abundances. Furthermore, we found differences in the taxonomic profile of the microbial community. Unexpectedly, the effect of sample dilution was moderate and did not introduce severe bias into the microbial inference. Indeed, the microbiota inferred from fecal samples was distinguishable from that of negative controls. In most cases, samples as low as 2 mg did not result in a dissimilar representation of the microbial community compared with the undiluted sample. Our results indicate that the gut microbiota inference is not much affected by contamination with laboratory reagents but largely impacted by the protocol to extract DNA.}, } @article {pmid29078342, year = {2017}, author = {Lemetre, C and Maniko, J and Charlop-Powers, Z and Sparrow, B and Lowe, AJ and Brady, SF}, title = {Bacterial natural product biosynthetic domain composition in soil correlates with changes in latitude on a continent-wide scale.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {44}, pages = {11615-11620}, pmid = {29078342}, issn = {1091-6490}, support = {R35 GM122559/GM/NIGMS NIH HHS/United States ; U01 GM110714/GM/NIGMS NIH HHS/United States ; U19 AI109713/AI/NIAID NIH HHS/United States ; }, mesh = {Australia ; Bacteria/*classification/*metabolism ; Biodiversity ; Biological Products/chemistry/*metabolism ; Genetic Variation ; Metagenome ; Molecular Structure ; *Soil Microbiology ; }, abstract = {Although bacterial bioactive metabolites have been one of the most prolific sources of lead structures for the development of small-molecule therapeutics, very little is known about the environmental factors associated with changes in secondary metabolism across natural environments. Large-scale sequencing of environmental microbiomes has the potential to shed light on the richness of bacterial biosynthetic diversity hidden in the environment, how it varies from one environment to the next, and what environmental factors correlate with changes in biosynthetic diversity. In this study, the sequencing of PCR amplicons generated using primers targeting either ketosynthase domains from polyketide biosynthesis or adenylation domains from nonribosomal peptide biosynthesis was used to assess biosynthetic domain composition and richness in soils collected across the Australian continent. Using environmental variables collected at each soil site, we looked for environmental factors that correlated with either high overall domain richness or changes in the domain composition. Among the environmental variables we measured, changes in biosynthetic domain composition correlate most closely with changes in latitude and to a lesser extent changes in pH. Although it is unclear at this time the exact mix of factors that may drive the relationship between biosynthetic domain composition and latitude, from a practical perspective the identification of a latitudinal basis for differences in soil metagenome biosynthetic domain compositions should help guide future natural product discovery efforts.}, } @article {pmid29076296, year = {2017}, author = {de la Calle, F}, title = {Marine microbiome as source of natural products.}, journal = {Microbial biotechnology}, volume = {10}, number = {6}, pages = {1293-1296}, pmid = {29076296}, issn = {1751-7915}, mesh = {Biological Products/*metabolism ; Biotechnology/methods ; Data Mining/methods ; Metabolic Networks and Pathways/genetics ; Metagenomics ; *Microbiota ; Seawater/*microbiology ; }, } @article {pmid29069476, year = {2018}, author = {Mitchell, AL and Scheremetjew, M and Denise, H and Potter, S and Tarkowska, A and Qureshi, M and Salazar, GA and Pesseat, S and Boland, MA and Hunter, FMI and Ten Hoopen, P and Alako, B and Amid, C and Wilkinson, DJ and Curtis, TP and Cochrane, G and Finn, RD}, title = {EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies.}, journal = {Nucleic acids research}, volume = {46}, number = {D1}, pages = {D726-D735}, pmid = {29069476}, issn = {1362-4962}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Algorithms ; Base Sequence ; Classification/methods ; *Databases, Genetic ; Datasets as Topic ; *Metagenomics/methods ; *Microbiota ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Viral/genetics ; Ribotyping ; Software ; Transcriptome ; User-Computer Interface ; Web Browser ; Workflow ; }, abstract = {EBI metagenomics (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the analysis and archiving of sequence data derived from the microbial populations found in a particular environment. Over the past two years, EBI metagenomics has increased the number of datasets analysed 10-fold. In addition to increased throughput, the underlying analysis pipeline has been overhauled to include both new or updated tools and reference databases. Of particular note is a new workflow for taxonomic assignments that has been extended to include assignments based on both the large and small subunit RNA marker genes and to encompass all cellular micro-organisms. We also describe the addition of metagenomic assembly as a new analysis service. Our pilot studies have produced over 2400 assemblies from datasets in the public domain. From these assemblies, we have produced a searchable, non-redundant protein database of over 50 million sequences. To provide improved access to the data stored within the resource, we have developed a programmatic interface that provides access to the analysis results and associated sample metadata. Finally, we have integrated the results of a series of statistical analyses that provide estimations of diversity and sample comparisons.}, } @article {pmid29069412, year = {2017}, author = {De Anda, V and Zapata-Peñasco, I and Poot-Hernandez, AC and Eguiarte, LE and Contreras-Moreira, B and Souza, V}, title = {MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle.}, journal = {GigaScience}, volume = {6}, number = {11}, pages = {1-17}, pmid = {29069412}, issn = {2047-217X}, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Sequence Analysis, DNA/*methods ; *Software ; Sulfur/*metabolism ; }, abstract = {The increasing number of metagenomic and genomic sequences has dramatically improved our understanding of microbial diversity, yet our ability to infer metabolic capabilities in such datasets remains challenging. We describe the Multigenomic Entropy Based Score pipeline (MEBS), a software platform designed to evaluate, compare, and infer complex metabolic pathways in large "omic" datasets, including entire biogeochemical cycles. MEBS is open source and available through https://github.com/eead-csic-compbio/metagenome_Pfam_score. To demonstrate its use, we modeled the sulfur cycle by exhaustively curating the molecular and ecological elements involved (compounds, genes, metabolic pathways, and microbial taxa). This information was reduced to a collection of 112 characteristic Pfam protein domains and a list of complete-sequenced sulfur genomes. Using the mathematical framework of relative entropy (H΄), we quantitatively measured the enrichment of these domains among sulfur genomes. The entropy of each domain was used both to build up a final score that indicates whether a (meta)genomic sample contains the metabolic machinery of interest and to propose marker domains in metagenomic sequences such as DsrC (PF04358). MEBS was benchmarked with a dataset of 2107 non-redundant microbial genomes from RefSeq and 935 metagenomes from MG-RAST. Its performance, reproducibility, and robustness were evaluated using several approaches, including random sampling, linear regression models, receiver operator characteristic plots, and the area under the curve metric (AUC). Our results support the broad applicability of this algorithm to accurately classify (AUC = 0.985) hard-to-culture genomes (e.g., Candidatus Desulforudis audaxviator), previously characterized ones, and metagenomic environments such as hydrothermal vents, or deep-sea sediment. Our benchmark indicates that an entropy-based score can capture the metabolic machinery of interest and can be used to efficiently classify large genomic and metagenomic datasets, including uncultivated/unexplored taxa.}, } @article {pmid29069352, year = {2017}, author = {Keller-Costa, T and Eriksson, D and Gonçalves, JMS and Gomes, NCM and Lago-Lestón, A and Costa, R}, title = {The gorgonian coral Eunicella labiata hosts a distinct prokaryotic consortium amenable to cultivation.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {12}, pages = {}, doi = {10.1093/femsec/fix143}, pmid = {29069352}, issn = {1574-6941}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/genetics ; DNA, Bacterial/genetics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; }, abstract = {Microbial communities inhabiting gorgonian corals are believed to benefit their hosts through nutrient provision and chemical defence; yet much remains to be learned about their phylogenetic uniqueness and cultivability. Here, we determined the prokaryotic community structure and distinctiveness in the gorgonian Eunicella labiata by Illumina sequencing of 16S rRNA genes from gorgonian and seawater metagenomic DNA. Furthermore, we used a 'plate-wash' methodology to compare the phylogenetic diversity of the 'total' gorgonian bacteriome and its 'cultivatable' fraction. With 1016 operational taxonomic units (OTUs), prokaryotic richness was higher in seawater than in E. labiata where 603 OTUs were detected, 68 of which were host-specific. Oceanospirillales and Rhodobacterales predominated in the E. labiata communities. One Oceanospirillales OTU, classified as Endozoicomonas, was particularly dominant, and closest relatives comprised exclusively uncultured clones from other gorgonians. We cultivated a remarkable 62% of the bacterial symbionts inhabiting E. labiata: Ruegeria, Sphingorhabdus, Labrenzia, other unclassified Rhodobacteraceae, Vibrio and Shewanella ranked among the 10 most abundant genera in both the cultivation-independent and dependent samples. In conclusion, the E. labiata microbiome is diverse, distinct from seawater and enriched in (gorgonian)-specific bacterial phylotypes. In contrast to current understanding, many dominant E. labiata symbionts can, indeed, be cultivated.}, } @article {pmid29066788, year = {2017}, author = {Komazaki, R and Katagiri, S and Takahashi, H and Maekawa, S and Shiba, T and Takeuchi, Y and Kitajima, Y and Ohtsu, A and Udagawa, S and Sasaki, N and Watanabe, K and Sato, N and Miyasaka, N and Eguchi, Y and Anzai, K and Izumi, Y}, title = {Periodontal pathogenic bacteria, Aggregatibacter actinomycetemcomitans affect non-alcoholic fatty liver disease by altering gut microbiota and glucose metabolism.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {13950}, pmid = {29066788}, issn = {2045-2322}, mesh = {Aggregatibacter actinomycetemcomitans/immunology/*physiology ; Animals ; Body Weight ; Female ; *Gastrointestinal Microbiome ; Glucose/*metabolism ; Humans ; Immunoglobulin G/immunology ; Insulin Resistance ; Liver/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Middle Aged ; Non-alcoholic Fatty Liver Disease/*metabolism/*microbiology ; }, abstract = {Increasing evidence indicates that periodontitis affects non-alcoholic fatty liver disease (NAFLD). We examined the relationship between periodontal bacterial infection and clinical/biochemical parameters in 52 NAFLD patients. Anti-Aggregatibacter actinomycetemcomitans (Aa) antibody titers correlated positively with visceral fat, fasting plasma insulin, and HOMA-IR; and negatively with the liver/spleen ratio. C57BL/6J mice (8-weeks-old) were given Aa or saline (control) for 6 weeks, and were fed either normal chow (NCAa, NCco) or high-fat diet (HFAa and HFco). NCAa and HFAa mice presented impaired glucose tolerance and insulin resistance compared to control mice. HFAa mice showed higher hepatic steatosis than HFco animals. Liver microarray analysis revealed that 266 genes were differentially expressed between NCAa and NCco mice. Upregulated genes in Aa-administrated mice were enriched for glucagon signaling pathway, adipocytokine signaling pathway and insulin resistance. Consistently, plasma glucagon concentration was higher in NCAa mice. In addition, Akt phosphorylation was lower in the liver of NCAa/HFAa than in NCco/HFco mice. Based on 16S rRNA sequencing, Aa administration changed composition of the gut microbiota. Metagenome prediction in gut microbiota showed upregulation of fatty acid biosynthesis and downregulation of fatty acid degradation in Aa-administered mice. Thus, infection with Aa affects NAFLD by altering the gut microbiota and glucose metabolism.}, } @article {pmid29066755, year = {2017}, author = {Anderson, RE and Reveillaud, J and Reddington, E and Delmont, TO and Eren, AM and McDermott, JM and Seewald, JS and Huber, JA}, title = {Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {1114}, pmid = {29066755}, issn = {2041-1723}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biodiversity ; Biological Evolution ; Contig Mapping ; Ecosystem ; Gene Frequency ; *Genetic Variation ; Genome ; Hydrogen-Ion Concentration ; Hydrothermal Vents/*microbiology ; Marine Biology ; *Metagenome ; Oceans and Seas ; Phylogeny ; Polymorphism, Single Nucleotide ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Temperature ; }, abstract = {Little is known about evolutionary drivers of microbial populations in the warm subseafloor of deep-sea hydrothermal vents. Here we reconstruct 73 metagenome-assembled genomes (MAGs) from two geochemically distinct vent fields in the Mid-Cayman Rise to investigate patterns of genomic variation within subseafloor populations. Low-abundance populations with high intra-population diversity coexist alongside high-abundance populations with low genomic diversity, with taxonomic differences in patterns of genomic variation between the mafic Piccard and ultramafic Von Damm vent fields. Populations from Piccard are significantly enriched in nonsynonymous mutations, suggesting stronger purifying selection in Von Damm relative to Piccard. Comparison of nine Sulfurovum MAGs reveals two high-coverage, low-diversity MAGs from Piccard enriched in unique genes related to the cellular membrane, suggesting these populations were subject to distinct evolutionary pressures that may correlate with genes related to nutrient uptake, biofilm formation, or viral invasion. These results are consistent with distinct evolutionary histories between geochemically different vent fields, with implications for understanding evolutionary processes in subseafloor microbial populations.}, } @article {pmid29065967, year = {2017}, author = {Park, SJ and Kim, JH and Song, MY and Sung, YC and Lee, SW and Park, Y}, title = {PD-1 deficiency protects experimental colitis via alteration of gut microbiota.}, journal = {BMB reports}, volume = {50}, number = {11}, pages = {578-583}, pmid = {29065967}, issn = {1976-670X}, mesh = {Animals ; Bacteria/genetics ; Colitis/chemically induced/*metabolism/pathology/*prevention & control ; Colon/pathology ; Cytokines/metabolism ; Disease Models, Animal ; Gastrointestinal Microbiome/physiology ; Inflammatory Bowel Diseases/metabolism ; Metagenomics/methods ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Programmed Cell Death 1 Ligand 2 Protein/genetics/*metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Programmed cell death-1 (PD-1) is a coinhibitory molecule and plays a pivotal role in immune regulation. Here, we demonstrate a role for PD-1 in pathogenesis of inflammatory bowel disease (IBD). Wild-type (WT) mice had severe wasting disease during experimentally induced colitis, while mice deficient for PD-1 (PD-1-/-) did not develop colon inflammation. Interestingly, PD-1-/- mice cohoused with WT mice became susceptible to colitis, suggesting that resistance of PD-1-/- mice to colitis is dependent on their gut microbiota. 16S rRNA gene-pyrosequencing analysis showed that PD-1-/- mice had altered composition of gut microbiota with significant reduction in Rikenellaceae family. These altered colon bacteria of PD-1-/- mice induced less amount of inflammatory mediators from colon epithelial cells, including interleukin (IL)-6, and inflammatory chemokines. Taken together, our study indicates that PD-1 expression is involved in the resistance to experimental colitis through altered bacterial communities of colon. [BMB Reports 2017; 50(11): 578-583].}, } @article {pmid29065388, year = {2018}, author = {Schmedes, SE and Woerner, AE and Novroski, NMM and Wendt, FR and King, JL and Stephens, KM and Budowle, B}, title = {Targeted sequencing of clade-specific markers from skin microbiomes for forensic human identification.}, journal = {Forensic science international. Genetics}, volume = {32}, number = {}, pages = {50-61}, doi = {10.1016/j.fsigen.2017.10.004}, pmid = {29065388}, issn = {1878-0326}, mesh = {DNA, Bacterial/*genetics ; Female ; Forensic Genetics/methods ; *Genetic Markers ; Humans ; Male ; *Microbiota ; Multiplex Polymerase Chain Reaction ; *Sequence Analysis, DNA ; Skin/*microbiology ; }, abstract = {The human skin microbiome is comprised of diverse communities of bacterial, eukaryotic, and viral taxa and contributes millions of additional genes to the repertoire of human genes, affecting human metabolism and immune response. Numerous genetic and environmental factors influence the microbiome composition and as such contribute to individual-specific microbial signatures which may be exploited for forensic applications. Previous studies have demonstrated the potential to associate skin microbial profiles collected from touched items to their individual owner, mainly using unsupervised methods from samples collected over short time intervals. Those studies utilize either targeted 16S rRNA or shotgun metagenomic sequencing to characterize skin microbiomes; however, these approaches have limited species and strain resolution and susceptibility to stochastic effects, respectively. Clade-specific markers from the skin microbiome, using supervised learning, can predict individual identity using skin microbiomes from their respective donors with high accuracy. In this study the hidSkinPlex is presented, a novel targeted sequencing method using skin microbiome markers developed for human identification. The hidSkinPlex (comprised of 286 bacterial (and phage) family-, genus-, species-, and subspecies-level markers), initially was evaluated on three bacterial control samples represented in the panel (i.e., Propionibacterium acnes, Propionibacterium granulosum, and Rothia dentocariosa) to assess the performance of the multiplex. The hidSkinPlex was further evaluated for prediction purposes. The hidSkinPlex markers were used to attribute skin microbiomes collected from eight individuals from three body sites (i.e., foot (Fb), hand (Hp) and manubrium (Mb)) to their host donor. Supervised learning, specifically regularized multinomial logistic regression and 1-nearest-neighbor classification were used to classify skin microbiomes to their hosts with up to 92% (Fb), 96% (Mb), and 100% (Hp) accuracy. All samples (n=72) regardless of body site origin were correctly classified with up to 94% accuracy, and body site origin could be predicted with up to 86% accuracy. Finally, human short tandem repeat and single-nucleotide polymorphism profiles were generated from skin swab extracts from a single subject to highlight the potential to use microbiome profiling in conjunction with low-biomass samples. The hidSkinPlex is a novel targeted enrichment approach to profile skin microbiomes for human forensic identification purposes and provides a method to further characterize the utility of skin microflora for human identification in future studies, such as the stability and diversity of the personal skin microbiome.}, } @article {pmid29065369, year = {2018}, author = {Brenner, D and Hiergeist, A and Adis, C and Mayer, B and Gessner, A and Ludolph, AC and Weishaupt, JH}, title = {The fecal microbiome of ALS patients.}, journal = {Neurobiology of aging}, volume = {61}, number = {}, pages = {132-137}, doi = {10.1016/j.neurobiolaging.2017.09.023}, pmid = {29065369}, issn = {1558-1497}, mesh = {Aged ; Amyotrophic Lateral Sclerosis/*etiology/*microbiology ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; RNA, Ribosomal, 16S ; Ruminococcus ; Sequence Analysis, RNA ; }, abstract = {Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative motor neuron disease accompanied by both systemic and central nervous system-specific inflammation as well as deregulated energy metabolism. These potential pathogenetic factors have recently been found to mutually interact with the gut microbiota, raising the hypothesis of a link between microbiome alterations and ALS pathogenesis. The aim of our study was to assess whether ALS is associated with an altered composition of the fecal microbiota. We compared the fecal microbiota of 25 ALS patients with 32 age- and gender-matched healthy persons using 16S rRNA gene sequencing analysis. Confounding factors and secondary disease effects on the microbiome were minimized by selection of patients without dysphagia, gastrostomy, noninvasive ventilation, or reduced body mass index. Comparing the 2 carefully matched groups, the diversity and the abundance of the bacterial taxa on the different taxonomic levels as well as PICRUSt-predicted metagenomes were almost indistinguishable. Significant differences between ALS patients and healthy controls were only observed with regard to the overall number of microbial species (operational taxonomic units) and in the abundance of uncultured Ruminococcaceae. Conclusively, ALS patients do not exhibit a substantial alteration of the gut microbiota composition.}, } @article {pmid29063148, year = {2018}, author = {Marcos, MS and Barboza, AD and Keijzer, RM and Laanbroek, HJ}, title = {Tide as Steering Factor in Structuring Archaeal and Bacterial Ammonia-Oxidizing Communities in Mangrove Forest Soils Dominated by Avicennia germinans and Rhizophora mangle.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {997-1008}, pmid = {29063148}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*metabolism ; Avicennia/*microbiology ; Bacteria/classification/genetics/*metabolism ; Florida ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Metagenomics ; Microbiota/*physiology ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizophoraceae/*microbiology ; Soil/chemistry ; *Soil Microbiology ; *Wetlands ; }, abstract = {Mangrove species are adapted to grow at specific zones in a tidal gradient. Here we tested the hypothesis that the archaeal and bacterial ammonia-oxidizing microbial communities differ in soils dominated by the mangrove species Avicennia germinans and Rhizophora mangle. Two of the sampling locations were tidal locations, while the other location was impounded. Differences in the community compositions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were analyzed by denaturing gradient gel electrophoresis (DGGE) of amoA genes and by MiSeq 16S rRNA gene-sequencing. The abundances of AOA and AOB were established by quantitative PCR of amoA genes. In addition, we analyzed the total microbial community composition based on 16S rRNA genes and explored the influence of soil physicochemical properties underneath Avicennia germinans and Rhizophora mangle on microbial communities. AOA were always more abundant than AOB, but the effect of mangrove species on total numbers of ammonia oxidizers was location-specific. The microbial communities including the ammonia oxidizers in soils associated with A. germinans and R. mangle differed only at the tidal locations. In conclusion, potential site-specific effects of mangrove species on soil microbial communities including those of the AOA and AOB are apparently overruled by the absence or presence of tide.}, } @article {pmid29061202, year = {2017}, author = {Volokhov, DV and Becker, DJ and Bergner, LM and Camus, MS and Orton, RJ and Chizhikov, VE and Altizer, SM and Streicker, DG}, title = {Novel hemotropic mycoplasmas are widespread and genetically diverse in vampire bats.}, journal = {Epidemiology and infection}, volume = {145}, number = {15}, pages = {3154-3167}, pmid = {29061202}, issn = {1469-4409}, support = {MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; 102507//Wellcome Trust/United Kingdom ; 102507/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; G0801822/MRC_/Medical Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Belize ; Chiroptera/*microbiology ; DNA, Bacterial/genetics ; Disease Reservoirs/microbiology ; Genetic Variation/genetics ; Mycoplasma/*genetics ; Mycoplasma Infections/microbiology/transmission/*veterinary ; Peru ; Phylogeny ; Polymerase Chain Reaction/veterinary ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bats (Order: Chiroptera) have been widely studied as reservoir hosts for viruses of concern for human and animal health. However, whether bats are equally competent hosts of non-viral pathogens such as bacteria remains an important open question. Here, we surveyed blood and saliva samples of vampire bats from Peru and Belize for hemotropic Mycoplasma spp. (hemoplasmas), bacteria that can cause inapparent infection or anemia in hosts. 16S rRNA gene amplification of blood showed 67% (150/223) of common vampire bats (Desmodus rotundus) were infected by hemoplasmas. Sequencing of the 16S rRNA gene amplicons revealed three novel genotypes that were phylogenetically related but not identical to hemoplasmas described from other (non-vampire) bat species, rodents, humans, and non-human primates. Hemoplasma prevalence in vampire bats was highest in non-reproductive and young individuals, did not differ by country, and was relatively stable over time (i.e., endemic). Metagenomics from pooled D. rotundus saliva from Peru detected non-hemotropic Mycoplasma species and hemoplasma genotypes phylogenetically similar to those identified in blood, providing indirect evidence for potential direct transmission of hemoplasmas through biting or social contacts. This study demonstrates vampire bats host several novel hemoplasmas and sheds light on risk factors for infection and basic transmission routes. Given the high frequency of direct contacts that arise when vampire bats feed on humans, domestic animals, and wildlife, the potential of these bacteria to be transmitted between species should be investigated in future work.}, } @article {pmid29058768, year = {2018}, author = {Hernandez-Rodriguez, J and Arandjelovic, M and Lester, J and de Filippo, C and Weihmann, A and Meyer, M and Angedakin, S and Casals, F and Navarro, A and Vigilant, L and Kühl, HS and Langergraber, K and Boesch, C and Hughes, D and Marques-Bonet, T}, title = {The impact of endogenous content, replicates and pooling on genome capture from faecal samples.}, journal = {Molecular ecology resources}, volume = {18}, number = {2}, pages = {319-333}, pmid = {29058768}, issn = {1755-0998}, support = {U01 MH106874/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; DNA/*genetics/*isolation & purification ; Feces/*chemistry ; Gabon ; Genetics, Population/*methods ; Metagenomics/*methods ; Pan troglodytes ; Sampling Studies ; Uganda ; }, abstract = {Target-capture approach has improved over the past years, proving to be very efficient tool for selectively sequencing genetic regions of interest. These methods have also allowed the use of noninvasive samples such as faeces (characterized by their low quantity and quality of endogenous DNA) to be used in conservation genomic, evolution and population genetic studies. Here we aim to test different protocols and strategies for exome capture using the Roche SeqCap EZ Developer kit (57.5 Mb). First, we captured a complex pool of DNA libraries. Second, we assessed the influence of using more than one faecal sample, extract and/or library from the same individual, to evaluate its effect on the molecular complexity of the experiment. We validated our experiments with 18 chimpanzee faecal samples collected from two field sites as a part of the Pan African Programme: The Cultured Chimpanzee. Those two field sites are in Kibale National Park, Uganda (N = 9) and Loango National Park, Gabon (N = 9). We demonstrate that at least 16 libraries can be pooled, target enriched through hybridization, and sequenced allowing for the genotyping of 951,949 exome markers for population genetic analyses. Further, we observe that molecule richness, and thus, data acquisition, increase when using multiple libraries from the same extract or multiple extracts from the same sample. Finally, repeated captures significantly decrease the proportion of off-target reads from 34.15% after one capture round to 7.83% after two capture rounds, supporting our conclusion that two rounds of target enrichment are advisable when using complex faecal samples.}, } @article {pmid29058217, year = {2017}, author = {Jiang, X and Hu, X}, title = {Data Analysis for Gut Microbiota and Health.}, journal = {Advances in experimental medicine and biology}, volume = {1028}, number = {}, pages = {79-87}, doi = {10.1007/978-981-10-6041-0_5}, pmid = {29058217}, issn = {0065-2598}, mesh = {*Data Mining ; *Gastrointestinal Microbiome ; Health ; Humans ; Statistics as Topic ; }, abstract = {In recent years, data mining and analysis of high-throughput sequencing of microbiomes and metagenomic data enable researchers to discover biological knowledge by characterizing the composition and variation of species across environmental samples and to accumulate a huge amount of data, making it feasible to infer the complex principle of species interactions. The interactions of microbes in a microbial community play an important role in microbial ecological system. Data mining provides diverse approachs to identify the correlations between disease and microbes and how microbial species coexist and interact in a host-associated or natural environment. This is not only important to advance basic microbiology science and other related fields but also important to understand the impacts of microbial communities on human health and diseases.}, } @article {pmid29056339, year = {2017}, author = {Rosshart, SP and Vassallo, BG and Angeletti, D and Hutchinson, DS and Morgan, AP and Takeda, K and Hickman, HD and McCulloch, JA and Badger, JH and Ajami, NJ and Trinchieri, G and Pardo-Manuel de Villena, F and Yewdell, JW and Rehermann, B}, title = {Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance.}, journal = {Cell}, volume = {171}, number = {5}, pages = {1015-1028.e13}, pmid = {29056339}, issn = {1097-4172}, support = {F30 MH103925/MH/NIMH NIH HHS/United States ; U19 AI100625/AI/NIAID NIH HHS/United States ; ZIA DK054508-19/ImNIH/Intramural NIH HHS/United States ; ZIA DK054508-20/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Animals ; Animals, Laboratory ; Animals, Wild ; Carcinogenesis/immunology ; Disease Resistance ; Female ; *Gastrointestinal Microbiome ; Male ; Maryland ; Mice/*classification/immunology/*microbiology ; Mice, Inbred C57BL ; Peromyscus ; Virus Diseases/immunology ; }, abstract = {Laboratory mice, while paramount for understanding basic biological phenomena, are limited in modeling complex diseases of humans and other free-living mammals. Because the microbiome is a major factor in mammalian physiology, we aimed to identify a naturally evolved reference microbiome to better recapitulate physiological phenomena relevant in the natural world outside the laboratory. Among 21 distinct mouse populations worldwide, we identified a closely related wild relative to standard laboratory mouse strains. Its bacterial gut microbiome differed significantly from its laboratory mouse counterpart and was transferred to and maintained in laboratory mice over several generations. Laboratory mice reconstituted with natural microbiota exhibited reduced inflammation and increased survival following influenza virus infection and improved resistance against mutagen/inflammation-induced colorectal tumorigenesis. By demonstrating the host fitness-promoting traits of natural microbiota, our findings should enable the discovery of protective mechanisms relevant in the natural world and improve the modeling of complex diseases of free-living mammals. VIDEO ABSTRACT.}, } @article {pmid29055396, year = {2017}, author = {Kaneko, K and Tsuji, S and Kimata, T}, title = {Role of gut microbiota in idiopathic nephrotic syndrome in children.}, journal = {Medical hypotheses}, volume = {108}, number = {}, pages = {35-37}, doi = {10.1016/j.mehy.2017.07.035}, pmid = {29055396}, issn = {1532-2777}, mesh = {Bacteria ; Child ; Child, Preschool ; Dysbiosis ; Fatty Acids/metabolism ; *Gastrointestinal Microbiome ; Humans ; Hypersensitivity/complications/*microbiology/physiopathology ; Microbiota ; Models, Theoretical ; Nephrotic Syndrome/complications/*microbiology/physiopathology ; Probiotics ; T-Lymphocytes, Regulatory/cytology/pathology ; }, abstract = {Nephrotic syndrome characterized by heavy proteinuria and edema is the most common chronic kidney disease in children. It is classified into three categories, of which the idiopathic type accounts for the vast majority of cases. As indicated by the name, the etiology of idiopathic nephrotic syndrome remains unknown though it has been suggested that impaired T cell function is involved. Recently, evidence has mounted to suggest that dysfunction in regulatory T cells plays an important role in the development of allergic disease, a recognized comorbid condition for children with idiopathic nephrotic syndrome. It is known that regulatory T cells are mainly induced by short chain fatty acids produced by gut microbiota and that children with allergy are reported to have aberrant gut microbiota. On this basis, we hypothesize that an aberrant microbiota, i.e., dysbiosis in the gut resulting in defective induction of regulatory T cells, is also involved in the etiology of idiopathic nephrotic syndrome in children. Our hypothesis can be directly tested by metagenome analysis using bacterial DNA extracted from the feces of patients with idiopathic nephrotic syndrome. Indirect evidence could be obtained by epidemiological survey, such as a comparative study of the environmental factors influencing the initial colonization of gut microbiota between patients with idiopathic nephrotic syndrome and age-matched healthy children. Factors that may disrupt this colonization include a cesarean delivery, formula feeding, excessive use of antibiotics, or the introduction of inappropriate solid foods containing a high amount of saturated fat. Based on this hypothesis, we suggest it would be clinically worthwhile to study whether administration of probiotics composed of commensal bacteria known to efficiently induce regulatory T cells in vitro could control the exacerbation or relapse of INS.}, } @article {pmid29053714, year = {2017}, author = {Turturice, BA and McGee, HS and Oliver, B and Baraket, M and Nguyen, BT and Ascoli, C and Ranjan, R and Rani, A and Perkins, DL and Finn, PW}, title = {Atopic asthmatic immune phenotypes associated with airway microbiota and airway obstruction.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0184566}, pmid = {29053714}, issn = {1932-6203}, support = {R01 AI053878/AI/NIAID NIH HHS/United States ; }, mesh = {Adrenal Cortex Hormones/administration & dosage/pharmacology ; Adult ; *Airway Obstruction ; Asthma/drug therapy/*immunology/metabolism ; Chemokines/metabolism ; Cohort Studies ; Cytokines/metabolism ; Female ; Humans ; *Immunophenotyping ; Male ; *Microbiota ; Young Adult ; }, abstract = {BACKGROUND: Differences in asthma severity may be related to inflammation in the airways. The lower airway microbiota has been associated with clinical features such as airway obstruction, symptom control, and response to corticosteroids.

OBJECTIVE: To assess the relationship between local airway inflammation, severity of disease, and the lower airway microbiota in atopic asthmatics.

METHODS: A cohort of young adult, atopic asthmatics with intermittent or mild/moderate persistent symptoms (n = 13) were assessed via bronchoscopy, lavage, and spirometry. These individuals were compared to age matched non-asthmatic controls (n = 6) and to themselves after six weeks of treatment with fluticasone propionate (FP). Inflammation of the airways was assessed via a cytokine and chemokine panel. Lower airway microbiota composition was determined by metagenomic shotgun sequencing.

RESULTS: Unsupervised clustering of cytokines and chemokines prior to treatment with FP identified two asthmatic phenotypes (AP), termed AP1 and AP2, with distinct bronchoalveolar lavage inflammatory profiles. AP2 was associated with more obstruction, compared to AP1. After treatment with FP reduced MIP-1β and TNF-α and increased IL-2 was observed. A module of highly correlated cytokines that include MIP-1β and TNF-α was identified that negatively correlated with pulmonary function. Independently, IL-2 was positively correlated with pulmonary function. The airway microbiome composition correlated with asthmatic phenotypes. AP2, prior to FP treatment, was enriched with Streptococcus pneumoniae. Unique associations between IL-2 or the cytokine module and the microbiota composition of the airways were observed in asthmatics subjects prior to treatment but not after or in controls.

CONCLUSION: The underlying inflammation in atopic asthma is related to the composition of microbiota and is associated with severity of airway obstruction. Treatment with inhaled corticosteroids was associated with changes in the airway inflammatory response to microbiota.}, } @article {pmid29053686, year = {2017}, author = {Steffan, SA and Dharampal, PS and Diaz-Garcia, L and Currie, CR and Zalapa, J and Hittinger, CT}, title = {Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {128}, pages = {}, pmid = {29053686}, issn = {1940-087X}, mesh = {Animals ; Bees/*physiology ; Fungicides, Industrial/*adverse effects ; Metagenomics/*methods ; Microbiota ; Pollen ; Yeasts ; }, abstract = {Growers often use fungicide sprays during bloom to protect crops against disease, which exposes bees to fungicide residues. Although considered "bee-safe," there is mounting evidence that fungicide residues in pollen are associated with bee declines (for both honey and bumble bee species). While the mechanisms remain relatively unknown, researchers have speculated that bee-microbe symbioses are involved. Microbes play a pivotal role in the preservation and/or processing of pollen, which serves as nutrition for larval bees. By altering the microbial community, it is likely that fungicides disrupt these microbe-mediated services, and thereby compromise bee health. This manuscript describes the protocols used to investigate the indirect mechanism(s) by which fungicides may be causing colony decline. Cage experiments exposing bees to fungicide-treated flowers have already provided the first evidence that fungicides cause profound colony losses in a native bumble bee (Bombus impatiens). Using field-relevant doses of fungicides, a series of experiments have been developed to provide a finer description of microbial community dynamics of fungicide-exposed pollen. Shifts in the structural composition of fungal and bacterial assemblages within the pollen microbiome are investigated by next-generation sequencing and metagenomic analysis. Experiments developed herein have been designed to provide a mechanistic understanding of how fungicides affect the microbiome of pollen-provisions. Ultimately, these findings should shed light on the indirect pathway through which fungicides may be causing colony declines.}, } @article {pmid29053145, year = {2018}, author = {Bernardo, P and Charles-Dominique, T and Barakat, M and Ortet, P and Fernandez, E and Filloux, D and Hartnady, P and Rebelo, TA and Cousins, SR and Mesleard, F and Cohez, D and Yavercovski, N and Varsani, A and Harkins, GW and Peterschmitt, M and Malmstrom, CM and Martin, DP and Roumagnac, P}, title = {Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale.}, journal = {The ISME journal}, volume = {12}, number = {1}, pages = {173-184}, pmid = {29053145}, issn = {1751-7370}, mesh = {*Agriculture ; Biodiversity ; Climate ; Ecosystem ; France ; Metagenomics ; Plant Viruses/classification/genetics/*isolation & purification ; Plants/virology ; South Africa ; }, abstract = {Disease emergence events regularly result from human activities such as agriculture, which frequently brings large populations of genetically uniform hosts into contact with potential pathogens. Although viruses cause nearly 50% of emerging plant diseases, there is little systematic information about virus distribution across agro-ecological interfaces and large gaps in understanding of virus diversity in nature. Here we applied a novel landscape-scale geometagenomics approach to examine relationships between agricultural land use and distributions of plant-associated viruses in two Mediterranean-climate biodiversity hotspots (Western Cape region of South Africa and Rhône river delta region of France). In total, we analysed 1725 geo-referenced plant samples collected over two years from 4.5 × 4.5 km[2] grids spanning farmlands and adjacent uncultivated vegetation. We found substantial virus prevalence (25.8-35.7%) in all ecosystems, but prevalence and identified family-level virus diversity were greatest in cultivated areas, with some virus families displaying strong agricultural associations. Our survey revealed 94 previously unknown virus species, primarily from uncultivated plants. This is the first effort to systematically evaluate plant-associated viromes across broad agro-ecological interfaces. Our findings indicate that agriculture substantially influences plant virus distributions and highlight the extent of current ignorance about the diversity and roles of viruses in nature.}, } @article {pmid29052232, year = {2018}, author = {Kim, BS and Lee, E and Lee, MJ and Kang, MJ and Yoon, J and Cho, HJ and Park, J and Won, S and Lee, SY and Hong, SJ}, title = {Different functional genes of upper airway microbiome associated with natural course of childhood asthma.}, journal = {Allergy}, volume = {73}, number = {3}, pages = {644-652}, doi = {10.1111/all.13331}, pmid = {29052232}, issn = {1398-9995}, mesh = {Asthma/*microbiology ; Child ; Female ; Humans ; Male ; Microbiota/*physiology ; Nasal Mucosa/microbiology ; Transcriptome ; }, abstract = {BACKGROUND: Microbial colonization of the airway plays a role in the pathogenesis of asthma; however, the effect of the upper airway microbiome on childhood asthma is not fully understood. We analyzed the metagenome of airway microbiome to understand the associated role of upper airway microbiome with the natural course of childhood asthma.

METHODS: Nasopharyngeal swabs were collected from children with asthma, those in asthma remission, and control groups. High-throughput sequencing was used to examine the structure and functional dynamics of the airway microbiome with respect to asthma phenotypes.

RESULTS: The composition of microbiota differed among healthy control, asthma, and remission groups. The relative abundance of Streptococcus was negatively associated with FEV1% predicted (P = .023) and that of Staphylococcus was negatively associated with methacholine PC20 (P = .013). Genes related to arachidonic acid metabolites, lysine residues, and glycosaminoglycans in the microbiome could be associated with airway inflammation. In particular, genes related to synthesis of anti-inflammatory prostaglandin E2 (PGE2) were not detected from the airway microbiome in the asthma group.

CONCLUSIONS: These data suggest that alterations in the composition and function of the upper airway microbiome could be related with the natural course of asthma in children.}, } @article {pmid29050881, year = {2017}, author = {Kvas, S and Rahn, J and Engel, K and Neufeld, JD and Villeneuve, PJ and Trevors, JT and Lee, H and Scroggins, RP and Beaudette, LA}, title = {Development of a microbial test suite and data integration method for assessing microbial health of contaminated soil.}, journal = {Journal of microbiological methods}, volume = {143}, number = {}, pages = {66-77}, doi = {10.1016/j.mimet.2017.10.004}, pmid = {29050881}, issn = {1872-8359}, mesh = {Biota/*drug effects ; Canada ; *Data Interpretation, Statistical ; *Environmental Pollution ; Forests ; Metagenomics/methods ; Microbiological Techniques/*methods ; Petroleum/analysis ; *Soil Microbiology ; Soil Pollutants/analysis ; }, abstract = {There is no standard methodology or guideline for assessing soil microbial health for the purposes of contaminant risk assessments. Here we propose a laboratory-based test suite and novel data integration method for evaluating soil microbial health using site-specific contaminated and reference soil. The test suite encompasses experiments for evaluating microbial biomass, activity, and diversity. The results from the tests are then integrated so that a Soil Microbial Health Score (SMHS) may be assigned. This test suite and data integration method was tested on soils from 3 different contaminated sites in Canada. The soil microbial health of a petroleum hydrocarbon (PHC) contaminated site was found to be 'Mildly Impacted' and 'Moderately Impacted' for two soil horizons at a boreal forest site. The soil microbial health of the mixed metal/PHC and mixed metal sites were both found to be 'Not Impacted'. Continued use of this test suite and data integration method will help create guidelines for assessing soil microbial health in ecological risk assessments.}, } @article {pmid29050374, year = {2017}, author = {Jin, T and Wang, Y and Huang, Y and Xu, J and Zhang, P and Wang, N and Liu, X and Chu, H and Liu, G and Jiang, H and Li, Y and Xu, J and Kristiansen, K and Xiao, L and Zhang, Y and Zhang, G and Du, G and Zhang, H and Zou, H and Zhang, H and Jie, Z and Liang, S and Jia, H and Wan, J and Lin, D and Li, J and Fan, G and Yang, H and Wang, J and Bai, Y and Xu, X}, title = {Taxonomic structure and functional association of foxtail millet root microbiome.}, journal = {GigaScience}, volume = {6}, number = {10}, pages = {1-12}, pmid = {29050374}, issn = {2047-217X}, mesh = {Bacteria/classification/genetics ; DNA Barcoding, Taxonomic ; Genome, Bacterial ; *Microbiota ; Millets/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizome/*microbiology ; }, abstract = {The root microbes play pivotal roles in plant productivity, nutrient uptakes, and disease resistance. The root microbial community structure has been extensively investigated by 16S/18S/ITS amplicons and metagenomic sequencing in crops and model plants. However, the functional associations between root microbes and host plant growth are poorly understood. This work investigates the root bacterial community of foxtail millet (Setaria italica) and its potential effects on host plant productivity. We determined the bacterial composition of 2882 samples from foxtail millet rhizoplane, rhizosphere and corresponding bulk soils from 2 well-separated geographic locations by 16S rRNA gene amplicon sequencing. We identified 16 109 operational taxonomic units (OTUs), and defined 187 OTUs as shared rhizoplane core OTUs. The β-diversity analysis revealed that microhabitat was the major factor shaping foxtail millet root bacterial community, followed by geographic locations. Large-scale association analysis identified the potential beneficial bacteria correlated with plant high productivity. Besides, the functional prediction revealed specific pathways enriched in foxtail millet rhizoplane bacterial community. We systematically described the root bacterial community structure of foxtail millet and found its core rhizoplane bacterial members. Our results demonstrated that host plants enrich specific bacteria and functions in the rhizoplane. The potentially beneficial bacteria may serve as a valuable knowledge foundation for bio-fertilizer development in agriculture.}, } @article {pmid29049378, year = {2017}, author = {Oh, S and Yap, GC and Hong, PY and Huang, CH and Aw, MM and Shek, LP and Liu, WT and Lee, BW}, title = {Immune-modulatory genomic properties differentiate gut microbiota of infants with and without eczema.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0184955}, pmid = {29049378}, issn = {1932-6203}, mesh = {Case-Control Studies ; Eczema/*genetics/*immunology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Phylogeny ; Placebos ; }, abstract = {Gut microbiota play an important role in human immunological processes, potentially affecting allergic diseases such as eczema. The diversity and structure of gut microbiota in infants with eczema have been previously documented. This study aims to evaluate by comparative metagenomics differences in genetic content in gut microbiota of infants with eczema and their matched controls. Stools were collected at the age of one month old from twelve infants from an at risk birth cohort in a case control manner. Clinical follow up for atopic outcomes were carried out at the age of 12 and 24 months. Microbial genomic DNA were extracted from stool samples and used for shotgun sequencing. Comparative metagenomic analysis showed that immune-regulatory TCAAGCTTGA motifs were significantly enriched in the six healthy controls (C) communities compared to the six eczema subjects (E), with many encoded by Bifidobacterium (38% of the total motifs in the C communities). Draft genomes of five Bifidobacterium species populations (B. longum, B. bifidum, B. breve, B. dentium, and B. pseudocatenulatum) were recovered from metagenomic datasets. The B. longum BFN-121-2 genome encoded more TCAAGCTTGA motifs (4.2 copies per one million genome sequence) than other Bifidobacterium genomes. Additionally, the communities in the stool of controls (C) were also significantly enriched in functions associated with tetrapyrrole biosynthesis compared to those of eczema (E). Our results show distinct immune-modulatory genomic properties of gut microbiota in infants associated with eczema and provide new insights into potential role of gut microbiota in affecting human immune homeostasis.}, } @article {pmid29047329, year = {2017}, author = {Guo, X and Li, S and Zhang, J and Wu, F and Li, X and Wu, D and Zhang, M and Ou, Z and Jie, Z and Yan, Q and Li, P and Yi, J and Peng, Y}, title = {Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {800}, pmid = {29047329}, issn = {1471-2164}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics ; Humans ; Mammals/*microbiology ; Mice ; Molecular Sequence Annotation ; Verrucomicrobia/drug effects/*genetics/*physiology ; *Whole Genome Sequencing ; }, abstract = {BACKGROUND: Akkermansia muciniphila is one of the most dominant bacteria that resides on the mucus layer of intestinal tract and plays key role in human health, however, little is known about its genomic content.

RESULTS: Herein, we for the first time characterized the genomic architecture of A. muciniphila based on whole-genome sequencing, assembling, and annotating of 39 isolates derived from human and mouse feces. We revealed a flexible open pangenome of A. muciniphila currently consisting of 5644 unique proteins. Phylogenetic analysis identified three species-level A. muciniphila phylogroups exhibiting distinct metabolic and functional features. Based on the comprehensive genome catalogue, we reconstructed 106 newly A. muciniphila metagenome assembled genomes (MAGs) from available metagenomic datasets of human, mouse and pig gut microbiomes, revealing a transcontinental distribution of A. muciniphila phylogroups across mammalian gut microbiotas. Accurate quantitative analysis of A. muciniphila phylogroups in human subjects further demonstrated its strong correlation with body mass index and anti-diabetic drug usage. Furthermore, we found that, during their mammalian gut evolution history, A. muciniphila acquired extra genes, especially antibiotic resistance genes, from symbiotic microbes via recent lateral gene transfer.

CONCLUSIONS: The genome repertoire of A. muciniphila provided insights into population structure, evolutionary and functional specificity of this significant bacterium.}, } @article {pmid29045670, year = {2018}, author = {Houghton, D and Stewart, CJ and Stamp, C and Nelson, A and Aj Ami, NJ and Petrosino, JF and Wipat, A and Trenell, MI and Turnbull, DM and Greaves, LC}, title = {Impact of Age-Related Mitochondrial Dysfunction and Exercise on Intestinal Microbiota Composition.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {73}, number = {5}, pages = {571-578}, pmid = {29045670}, issn = {1758-535X}, support = {G0700718/MRC_/Medical Research Council/United Kingdom ; MR/L016354/1/MRC_/Medical Research Council/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; P30 DK056338/DK/NIDDK NIH HHS/United States ; SRF-2011-04-017/DH_/Department of Health/United Kingdom ; }, mesh = {Animals ; Mice ; *Aging/physiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Mitochondrial Diseases/physiopathology ; *Physical Conditioning, Animal ; Random Allocation ; Sedentary Behavior ; }, abstract = {Mitochondrial dysfunction is prevalent in the aging gastrointestinal tract. We investigated whether mitochondrial function in aging colonic crypts and exercise influences microbial gut communities in mice. Twelve PolgAmut/mut mice were randomly divided into a sedentary and exercise group at 4 months. Seven-aged matched PolgA+/+ mice remained sedentary throughout. Stool samples were collected at 4, 7, and 11 months, and bacterial profiling was achieved through 16S rRNA sequencing profiling. Mitochondrial enzyme activity was assessed in colonic epithelial crypts at 11 months for PolgAmut/mut and PolgA+/+ mice. Sedentary and exercised PolgAmut/mut mice had significantly higher levels of mitochondrial dysfunction than PolgA+/+ mice (78%, 77%, and 1% of crypts, respectively). Bacterial profiles of sedentary PolgAmut/mut mice were significantly different from the sedentary PolgA+/+ mice, with increases in Lactobacillus and Mycoplasma, and decreases in Alistipes, Odoribacter, Anaeroplasma, Rikenella, Parabacteroides, and Allobaculum in the PolgAmut/mut mice. Exercise did not have any impact upon gut mitochondrial dysfunction; however, exercise did increase gut microbiota diversity and significantly increased bacterial genera Mucispirillum and Desulfovibrio. Mitochondrial dysfunction is associated with changes in the gut microbiota. Endurance exercise moderated some of these changes, establishing that environmental factors can influence gut microbiota, despite mitochondrial dysfunction.}, } @article {pmid29042583, year = {2017}, author = {Xie, K and Deng, Y and Zhang, S and Zhang, W and Liu, J and Xie, Y and Zhang, X and Huang, H}, title = {Prokaryotic Community Distribution along an Ecological Gradient of Salinity in Surface and Subsurface Saline Soils.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {13332}, pmid = {29042583}, issn = {2045-2322}, mesh = {Biodiversity ; Environment ; Geologic Sediments/*chemistry/*microbiology ; Metagenome ; Metagenomics/methods ; Microbiota ; *Prokaryotic Cells ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Salinity effects on microbial communities in saline soils is still unclear, and little is known about subsurface soil microbial communities especially in saline or hypersaline ecosystems. Here we presented the survey of the prokaryotic community in saline soils along a salinity gradient (17.3-148.3 dS/m) in surface (0-10 cm) and subsurface (15-30 cm) saline soils of Qarhan Salt Lake, China. Moreover, we compared them with three paired nonsaline normal soils. Using the high-throughput sequencing technology and several statistical methods, we observed no significant community difference between surface soils and subsurface soils. For environmental factors, we found that TOC was the primary driver of the prokaryotic community distribution in surface saline soils, so was pH in subsurface saline soils. Salinity had more effects on the prokaryotic community in subsurface saline soils than in surface saline soils and played a less important role in saline soils than in saline waters or saline sediments. Our research provided references for the prokaryotic community distribution along a salinity gradient in both surface and subsurface saline soils of arid playa areas.}, } @article {pmid29041989, year = {2017}, author = {Dubinkina, VB and Tyakht, AV and Odintsova, VY and Yarygin, KS and Kovarsky, BA and Pavlenko, AV and Ischenko, DS and Popenko, AS and Alexeev, DG and Taraskina, AY and Nasyrova, RF and Krupitsky, EM and Shalikiani, NV and Bakulin, IG and Shcherbakov, PL and Skorodumova, LO and Larin, AK and Kostryukova, ES and Abdulkhakov, RA and Abdulkhakov, SR and Malanin, SY and Ismagilova, RK and Grigoryeva, TV and Ilina, EN and Govorun, VM}, title = {Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {141}, pmid = {29041989}, issn = {2049-2618}, mesh = {Adult ; Alcoholism/*microbiology/physiopathology ; Bifidobacterium/isolation & purification/pathogenicity/physiology ; Dysbiosis ; Enterobacteriaceae/isolation & purification/physiology ; Ethanol/adverse effects/metabolism ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/physiology ; Humans ; Inflammation ; Lactobacillus/isolation & purification/pathogenicity/physiology ; Liver/physiopathology ; Liver Cirrhosis/*microbiology/physiopathology ; Liver Diseases, Alcoholic/*microbiology/physiopathology/therapy ; Male ; Metagenomics/methods ; Middle Aged ; Probiotics/therapeutic use ; Symbiosis ; Virulence Factors ; Young Adult ; }, abstract = {BACKGROUND: Alcohol abuse has deleterious effects on human health by disrupting the functions of many organs and systems. Gut microbiota has been implicated in the pathogenesis of alcohol-related liver diseases, with its composition manifesting expressed dysbiosis in patients suffering from alcoholic dependence. Due to its inherent plasticity, gut microbiota is an important target for prevention and treatment of these diseases. Identification of the impact of alcohol abuse with associated psychiatric symptoms on the gut community structure is confounded by the liver dysfunction. In order to differentiate the effects of these two factors, we conducted a comparative "shotgun" metagenomic survey of 99 patients with the alcohol dependence syndrome represented by two cohorts-with and without liver cirrhosis. The taxonomic and functional composition of the gut microbiota was subjected to a multifactor analysis including comparison with the external control group.

RESULTS: Alcoholic dependence and liver cirrhosis were associated with profound shifts in gut community structures and metabolic potential across the patients. The specific effects on species-level community composition were remarkably different between cohorts with and without liver cirrhosis. In both cases, the commensal microbiota was found to be depleted. Alcoholic dependence was inversely associated with the levels of butyrate-producing species from the Clostridiales order, while the cirrhosis-with multiple members of the Bacteroidales order. The opportunist pathogens linked to alcoholic dependence included pro-inflammatory Enterobacteriaceae, while the hallmarks of cirrhosis included an increase of oral microbes in the gut and more frequent occurrence of abnormal community structures. Interestingly, each of the two factors was associated with the expressed enrichment in many Bifidobacterium and Lactobacillus-but the exact set of the species was different between alcoholic dependence and liver cirrhosis. At the level of functional potential, the patients showed different patterns of increase in functions related to alcohol metabolism and virulence factors, as well as pathways related to inflammation.

CONCLUSIONS: Multiple shifts in the community structure and metabolic potential suggest strong negative influence of alcohol dependence and associated liver dysfunction on gut microbiota. The identified differences in patterns of impact between these two factors are important for planning of personalized treatment and prevention of these pathologies via microbiota modulation. Particularly, the expansion of Bifidobacterium and Lactobacillus suggests that probiotic interventions for patients with alcohol-related disorders using representatives of the same taxa should be considered with caution. Taxonomic and functional analysis shows an increased propensity of the gut microbiota to synthesis of the toxic acetaldehyde, suggesting higher risk of colorectal cancer and other pathologies in alcoholics.}, } @article {pmid29041965, year = {2017}, author = {Noyes, NR and Weinroth, ME and Parker, JK and Dean, CJ and Lakin, SM and Raymond, RA and Rovira, P and Doster, E and Abdo, Z and Martin, JN and Jones, KL and Ruiz, J and Boucher, CA and Belk, KE and Morley, PS}, title = {Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {142}, pmid = {29041965}, issn = {2049-2618}, support = {T32 OD012201/OD/NIH HHS/United States ; }, mesh = {Drug Resistance, Microbial/*genetics ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Virulence/genetics ; Whole Genome Sequencing/methods ; }, abstract = {BACKGROUND: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias.

RESULTS: The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins.

CONCLUSIONS: These results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistome-virulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of microbiome-resistome dynamics.}, } @article {pmid29040451, year = {2018}, author = {Chen, J and King, E and Deek, R and Wei, Z and Yu, Y and Grill, D and Ballman, K and Stegle, O}, title = {An omnibus test for differential distribution analysis of microbiome sequencing data.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {4}, pages = {643-651}, doi = {10.1093/bioinformatics/btx650}, pmid = {29040451}, issn = {1367-4811}, mesh = {Arthritis, Rheumatoid/microbiology ; Humans ; Inflammatory Bowel Diseases/microbiology ; Metagenomics/*methods ; Microbiota/*genetics ; *Models, Statistical ; *Software ; }, abstract = {MOTIVATION: One objective of human microbiome studies is to identify differentially abundant microbes across biological conditions. Previous statistical methods focus on detecting the shift in the abundance and/or prevalence of the microbes and treat the dispersion (spread of the data) as a nuisance. These methods also assume that the dispersion is the same across conditions, an assumption which may not hold in presence of sample heterogeneity. Moreover, the widespread outliers in the microbiome sequencing data make existing parametric models not overly robust. Therefore, a robust and powerful method that allows covariate-dependent dispersion and addresses outliers is still needed for differential abundance analysis.

RESULTS: We introduce a novel test for differential distribution analysis of microbiome sequencing data by jointly testing the abundance, prevalence and dispersion. The test is built on a zero-inflated negative binomial regression model and winsorized count data to account for zero-inflation and outliers. Using simulated data and real microbiome sequencing datasets, we show that our test is robust across various biological conditions and overall more powerful than previous methods.

R package is available at https://github.com/jchen1981/MicrobiomeDDA.

CONTACT: chen.jun2@mayo.edu or zhiwei@njit.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid29040406, year = {2018}, author = {Pericard, P and Dufresne, Y and Couderc, L and Blanquart, S and Touzet, H}, title = {MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {4}, pages = {585-591}, doi = {10.1093/bioinformatics/btx644}, pmid = {29040406}, issn = {1367-4811}, mesh = {Algorithms ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Metagenome ; Metagenomics/methods ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; *Software ; }, abstract = {MOTIVATION: Advances in the sequencing of uncultured environmental samples, dubbed metagenomics, raise a growing need for accurate taxonomic assignment. Accurate identification of organisms present within a community is essential to understanding even the most elementary ecosystems. However, current high-throughput sequencing technologies generate short reads which partially cover full-length marker genes and this poses difficult bioinformatic challenges for taxonomy identification at high resolution.

RESULTS: We designed MATAM, a software dedicated to the fast and accurate targeted assembly of short reads sequenced from a genomic marker of interest. The method implements a stepwise process based on construction and analysis of a read overlap graph. It is applied to the assembly of 16S rRNA markers and is validated on simulated, synthetic and genuine metagenomes. We show that MATAM outperforms other available methods in terms of low error rates and recovered fractions and is suitable to provide improved assemblies for precise taxonomic assignments.

https://github.com/bonsai-team/matam.

CONTACT: pierre.pericard@gmail.com or helene.touzet@univ-lille1.fr.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid29038461, year = {2017}, author = {Lynch, A and Crowley, E and Casey, E and Cano, R and Shanahan, R and McGlacken, G and Marchesi, JR and Clarke, DJ}, title = {The Bacteroidales produce an N-acylated derivative of glycine with both cholesterol-solubilising and hemolytic activity.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {13270}, pmid = {29038461}, issn = {2045-2322}, mesh = {Bacteroides/metabolism ; Bacteroides fragilis/metabolism ; Cholesterol/chemistry/*metabolism ; Escherichia coli/metabolism ; Gastrointestinal Microbiome/genetics/*physiology ; Glycine/chemistry/*metabolism ; Hemolysis ; Phylogeny ; }, abstract = {The contribution of the gut microbiota to the metabolism of cholesterol is not well understood. In this study, we identify 21 fosmid clones from a human gut microbiome metagenomic library that, when expressed in Escherichia coli, produce halos on LB agar supplemented with 0.01% (w/v) cholesterol (LBC agar). Analysis of 14 of these clones revealed that they all share a fragment of DNA with homology to the genome of Bacteroides vulgatus. The gene responsible for halo production on LBC agar, named choA, was identified as an N-acyltransferase known to produce an acylated glycine molecule called commendamide. In this study we show that commendamide is capable of producing a halo on LBC agar suggesting that this molecule is solubilizing the cholesterol micelles in LBC agar. We also show that commendamide is responsible for the previously described hemolytic activity associated with the choA orthologue in Bacteroides fragilis. A functional analysis of ChoA identified 2 amino acids that are important for commendamide biosynthesis and we present phylogenetic and functional data showing that orthologues of choA are found only in the order Bacteroidales. Therefore, the production of commendamide may be an adaptation to the environments colonized by the Bacteroidales, including the mammalian gut.}, } @article {pmid29037173, year = {2017}, author = {Beisser, D and Graupner, N and Grossmann, L and Timm, H and Boenigk, J and Rahmann, S}, title = {TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {787}, pmid = {29037173}, issn = {1471-2164}, mesh = {*Databases, Genetic ; Eukaryota/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics/*standards ; Reference Standards ; Software ; }, abstract = {BACKGROUND: High-throughput sequencing (HTS) technologies are increasingly applied to analyse complex microbial ecosystems by mRNA sequencing of whole communities, also known as metatranscriptome sequencing. This approach is at the moment largely limited to prokaryotic communities and communities of few eukaryotic species with sequenced genomes. For eukaryotes the analysis is hindered mainly by a low and fragmented coverage of the reference databases to infer the community composition, but also by lack of automated workflows for the task.

RESULTS: From the databases of the National Center for Biotechnology Information and Marine Microbial Eukaryote Transcriptome Sequencing Project, 142 references were selected in such a way that the taxa represent the main lineages within each of the seven supergroups of eukaryotes and possess predominantly complete transcriptomes or genomes. From these references, we created an annotated microeukaryotic reference database. We developed a tool called TaxMapper for a reliably mapping of sequencing reads against this database and filtering of unreliable assignments. For filtering, a classifier was trained and tested on each of the following: sequences of taxa in the database, sequences of taxa related to those in the database, and random sequences. Additionally, TaxMapper is part of a metatranscriptomic Snakemake workflow developed to perform quality assessment, functional and taxonomic annotation and (multivariate) statistical analysis including environmental data. The workflow is provided and described in detail to empower researchers to apply it for metatranscriptome analysis of any environmental sample.

CONCLUSIONS: TaxMapper shows superior performance compared to standard approaches, resulting in a higher number of true positive taxonomic assignments. Both the TaxMapper tool and the workflow are available as open-source code at Bitbucket under the MIT license: https://bitbucket.org/dbeisser/taxmapper and as a Bioconda package: https://bioconda.github.io/recipes/taxmapper/README.html .}, } @article {pmid29036597, year = {2018}, author = {Rozov, R and Goldshlager, G and Halperin, E and Shamir, R}, title = {Faucet: streaming de novo assembly graph construction.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {1}, pages = {147-154}, pmid = {29036597}, issn = {1367-4811}, mesh = {Algorithms ; Genomics/*methods ; Humans ; *Metagenome ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {MOTIVATION: We present Faucet, a two-pass streaming algorithm for assembly graph construction. Faucet builds an assembly graph incrementally as each read is processed. Thus, reads need not be stored locally, as they can be processed while downloading data and then discarded. We demonstrate this functionality by performing streaming graph assembly of publicly available data, and observe that the ratio of disk use to raw data size decreases as coverage is increased.

RESULTS: Faucet pairs the de Bruijn graph obtained from the reads with additional meta-data derived from them. We show these metadata-coverage counts collected at junction k-mers and connections bridging between junction pairs-contain most salient information needed for assembly, and demonstrate they enable cleaning of metagenome assembly graphs, greatly improving contiguity while maintaining accuracy. We compared Fauceted resource use and assembly quality to state of the art metagenome assemblers, as well as leading resource-efficient genome assemblers. Faucet used orders of magnitude less time and disk space than the specialized metagenome assemblers MetaSPAdes and Megahit, while also improving on their memory use; this broadly matched performance of other assemblers optimizing resource efficiency-namely, Minia and LightAssembler. However, on metagenomes tested, Faucet,o outputs had 14-110% higher mean NGA50 lengths compared with Minia, and 2- to 11-fold higher mean NGA50 lengths compared with LightAssembler, the only other streaming assembler available.

Faucet is available at https://github.com/Shamir-Lab/Faucet.

CONTACT: rshamir@tau.ac.il or eranhalperin@gmail.com.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid29036588, year = {2018}, author = {Liu, X and Yu, Y and Liu, J and Elliott, CF and Qian, C and Liu, J}, title = {A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {1}, pages = {171-178}, pmid = {29036588}, issn = {1367-4811}, support = {P30 CA177558/CA/NCI NIH HHS/United States ; R01 HG006272/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/genetics ; *Genome, Microbial ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {MOTIVATION: Metagenomic read classification is a critical step in the identification and quantification of microbial species sampled by high-throughput sequencing. Although many algorithms have been developed to date, they suffer significant memory and/or computational costs. Due to the growing popularity of metagenomic data in both basic science and clinical applications, as well as the increasing volume of data being generated, efficient and accurate algorithms are in high demand.

RESULTS: We introduce MetaOthello, a probabilistic hashing classifier for metagenomic sequencing reads. The algorithm employs a novel data structure, called l-Othello, to support efficient querying of a taxon using its k-mer signatures. MetaOthello is an order-of-magnitude faster than the current state-of-the-art algorithms Kraken and Clark, and requires only one-third of the RAM. In comparison to Kaiju, a metagenomic classification tool using protein sequences instead of genomic sequences, MetaOthello is three times faster and exhibits 20-30% higher classification sensitivity. We report comparative analyses of both scalability and accuracy using a number of simulated and empirical datasets.

MetaOthello is a stand-alone program implemented in C ++. The current version (1.0) is accessible via https://doi.org/10.5281/zenodo.808941.

CONTACT: liuj@cs.uky.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid29035796, year = {2018}, author = {Park, JH and Kim, BS and Chon, CM}, title = {Characterization of iron and manganese minerals and their associated microbiota in different mine sites to reveal the potential interactions of microbiota with mineral formation.}, journal = {Chemosphere}, volume = {191}, number = {}, pages = {245-252}, doi = {10.1016/j.chemosphere.2017.10.050}, pmid = {29035796}, issn = {1879-1298}, mesh = {Bacteria/*metabolism ; Chemical Precipitation ; Iron/analysis/*metabolism ; Manganese/analysis/*metabolism ; Metals/isolation & purification/toxicity ; *Microbiota ; Minerals/*chemistry ; Mining ; Oxidation-Reduction ; Rivers/chemistry/microbiology ; Sequence Analysis, DNA ; Water Pollutants, Chemical/analysis/*isolation & purification ; Water Purification/*methods ; }, abstract = {Different environmental conditions such as pH and dissolved elements of mine stream induce precipitation of different minerals and their associated microbial community may vary. Therefore, mine precipitates from various environmental conditions were collected and their associated microbiota were analyzed through metagenomic DNA sequencing. Various Fe and Mn minerals including ferrihydrite, schwertmannite, goethite, birnessite, and Mn-substituted δ-FeOOH (δ-(Fe1-x, Mnx)OOH) were found in the different environmental conditions. The Fe and Mn minerals were enriched with toxic metal(loid)s including As, Cd, Ni and Zn, indicating they can act as scavengers of toxic metal(loid)s in mine streams. Under acidic conditions, Acidobacteria was dominant phylum and Gallionella (Fe oxidizing bacteria) was the predominant genus in these Fe rich environments. Manganese oxidizing bacteria, Hyphomicrobium, was found in birnessite forming environments. Leptolyngbya within Cyanobacteria was found in Fe and Mn oxidizing environments, and might contribute to Fe and Mn oxidation through the production of molecular oxygen. The potential interaction of microbial community with minerals in mine sites can be traced by analysis of microbial community in different Fe and Mn mineral forming environments. Iron and Mn minerals contribute to the removal of toxic metal(loid)s from mine water. Therefore, the understanding characteristics of mine precipitates and their associated microbes helps to develop strategies for the management of contaminated mine water.}, } @article {pmid29032502, year = {2018}, author = {Santoro, A and Ostan, R and Candela, M and Biagi, E and Brigidi, P and Capri, M and Franceschi, C}, title = {Gut microbiota changes in the extreme decades of human life: a focus on centenarians.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {75}, number = {1}, pages = {129-148}, pmid = {29032502}, issn = {1420-9071}, mesh = {Aged ; Aged, 80 and over ; Aging/genetics/*physiology ; *Diet ; Female ; Gastrointestinal Microbiome/*physiology ; Genetics, Population ; Humans ; Longevity/genetics/*physiology ; Male ; }, abstract = {The gut microbiota (GM) is a complex, evolutionarily molded ecological system, which contributes to a variety of physiological functions. The GM is highly dynamic, being sensitive to environmental stimuli, and its composition changes over the host's entire lifespan. However, the basic question of how much these changes may be ascribed to variables such as population, diet, genetics and gender, and/or to the aging process per se is still largely unanswered. We argue that comparison among studies on centenarians-the best model of healthy aging and longevity-recruited from different geographical areas/populations (different genetics and dietary habits) can help to disentangle the contribution of aging and non-aging-related variables to GM remodeling with age. The current review focuses on the role of population, gender and host genetics as possible drivers of GM modification along the human aging process. The feedback impact of age-associated GM variation on the GM-brain axis and GM metabolomics is also discussed. We likewise address the role of GM in neurodegenerative diseases such as Parkinson's and Alzheimer's, and its possible therapeutic use, taking advantage of the fact that centenarians are characterized by an extreme (healthy) phenotype versus patients suffering from age-related pathologies. Finally, it is argued that longitudinal studies combining metagenomics sequencing and in-depth phylogenetic analysis with a comprehensive phenotypic characterization of centenarians and patients using up-to-date omics (metabolomics, transcriptomics and meta-transcriptomics) are urgently needed.}, } @article {pmid29029060, year = {2017}, author = {Berini, F and Casciello, C and Marcone, GL and Marinelli, F}, title = {Metagenomics: novel enzymes from non-culturable microbes.}, journal = {FEMS microbiology letters}, volume = {364}, number = {21}, pages = {}, doi = {10.1093/femsle/fnx211}, pmid = {29029060}, issn = {1574-6968}, mesh = {Bacteria/*enzymology ; *Bacterial Proteins/chemistry/classification/genetics ; Biocatalysis ; Environmental Microbiology ; *Enzymes/chemistry/classification/genetics ; Industrial Microbiology ; Metagenomics/*methods ; *Microbiota ; }, abstract = {In the transition to the post-petroleum economy, there is a growing demand for novel enzymes with high process performances to replace traditional chemistry with a more 'green' approach. To date, microorganisms encompass the richest source of industrial biocatalysts, but the Earth-living microbiota remains largely untapped by using traditional isolation and cultivation methods. Metagenomics, which is culture independent, represents a powerful tool for discovering novel enzymes from unculturable microorganisms. Herein, we summarize the variety of approaches adopted for mining environmental DNA and, based on a systematic literature review, we provide a comprehensive list of 332 industrially relevant enzymes discovered from metagenomes within the last three years.}, } @article {pmid29028897, year = {2018}, author = {Guo, X and Li, Z and Yao, Q and Mueller, RS and Eng, JK and Tabb, DL and Hervey, WJ and Pan, C}, title = {Sipros Ensemble improves database searching and filtering for complex metaproteomics.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {5}, pages = {795-802}, pmid = {29028897}, issn = {1367-4811}, mesh = {Algorithms ; Metagenomics/methods ; Microbiota/genetics ; Proteomics/*methods ; Search Engine ; *Software ; }, abstract = {MOTIVATION: Complex microbial communities can be characterized by metagenomics and metaproteomics. However, metagenome assemblies often generate enormous, and yet incomplete, protein databases, which undermines the identification of peptides and proteins in metaproteomics. This challenge calls for increased discrimination of true identifications from false identifications by database searching and filtering algorithms in metaproteomics.

RESULTS: Sipros Ensemble was developed here for metaproteomics using an ensemble approach. Three diverse scoring functions from MyriMatch, Comet and the original Sipros were incorporated within a single database searching engine. Supervised classification with logistic regression was used to filter database searching results. Benchmarking with soil and marine microbial communities demonstrated a higher number of peptide and protein identifications by Sipros Ensemble than MyriMatch/Percolator, Comet/Percolator, MS-GF+/Percolator, Comet & MyriMatch/iProphet and Comet & MyriMatch & MS-GF+/iProphet. Sipros Ensemble was computationally efficient and scalable on supercomputers.

Freely available under the GNU GPL license at http://sipros.omicsbio.org.

CONTACT: cpan@utk.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid29028892, year = {2018}, author = {Weber, N and Liou, D and Dommer, J and MacMenamin, P and Quiñones, M and Misner, I and Oler, AJ and Wan, J and Kim, L and Coakley McCarthy, M and Ezeji, S and Noble, K and Hurt, DE}, title = {Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {8}, pages = {1411-1413}, pmid = {29028892}, issn = {1367-4811}, mesh = {*Cloud Computing ; Computational Biology/*methods ; Humans ; Metagenomics/methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA ; *Software ; }, abstract = {MOTIVATION: Widespread interest in the study of the microbiome has resulted in data proliferation and the development of powerful computational tools. However, many scientific researchers lack the time, training, or infrastructure to work with large datasets or to install and use command line tools.

RESULTS: The National Institute of Allergy and Infectious Diseases (NIAID) has created Nephele, a cloud-based microbiome data analysis platform with standardized pipelines and a simple web interface for transforming raw data into biological insights. Nephele integrates common microbiome analysis tools as well as valuable reference datasets like the healthy human subjects cohort of the Human Microbiome Project (HMP). Nephele is built on the Amazon Web Services cloud, which provides centralized and automated storage and compute capacity, thereby reducing the burden on researchers and their institutions.

https://nephele.niaid.nih.gov and https://github.com/niaid/Nephele.

CONTACT: darrell.hurt@nih.gov.}, } @article {pmid29028872, year = {2019}, author = {Breitwieser, FP and Lu, J and Salzberg, SL}, title = {A review of methods and databases for metagenomic classification and assembly.}, journal = {Briefings in bioinformatics}, volume = {20}, number = {4}, pages = {1125-1136}, pmid = {29028872}, issn = {1477-4054}, support = {R01 GM083873/GM/NIGMS NIH HHS/United States ; R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Computational Biology/methods ; *Databases, Genetic/statistics & numerical data ; Gene Expression Profiling/statistics & numerical data ; Genetic Markers ; High-Throughput Nucleotide Sequencing/statistics & numerical data ; Metagenome ; Metagenomics/*methods/statistics & numerical data ; Microbiota/genetics ; Phylogeny ; Sequence Alignment/statistics & numerical data ; }, abstract = {Microbiome research has grown rapidly over the past decade, with a proliferation of new methods that seek to make sense of large, complex data sets. Here, we survey two of the primary types of methods for analyzing microbiome data: read classification and metagenomic assembly, and we review some of the challenges facing these methods. All of the methods rely on public genome databases, and we also discuss the content of these databases and how their quality has a direct impact on our ability to interpret a microbiome sample.}, } @article {pmid29028181, year = {2018}, author = {Fosso, B and Pesole, G and Rosselló, F and Valiente, G}, title = {Unbiased Taxonomic Annotation of Metagenomic Samples.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {25}, number = {3}, pages = {348-360}, pmid = {29028181}, issn = {1557-8666}, mesh = {DNA Barcoding, Taxonomic/*methods/standards ; Humans ; *Metagenome ; Microbiota ; *Phylogeny ; *Software ; }, abstract = {The classification of reads from a metagenomic sample using a reference taxonomy is usually based on first mapping the reads to the reference sequences and then classifying each read at a node under the lowest common ancestor of the candidate sequences in the reference taxonomy with the least classification error. However, this taxonomic annotation can be biased by an imbalanced taxonomy and also by the presence of multiple nodes in the taxonomy with the least classification error for a given read. In this article, we show that the Rand index is a better indicator of classification error than the often used area under the receiver operating characteristic (ROC) curve and F-measure for both balanced and imbalanced reference taxonomies, and we also address the second source of bias by reducing the taxonomic annotation problem for a whole metagenomic sample to a set cover problem, for which a logarithmic approximation can be obtained in linear time and an exact solution can be obtained by integer linear programming. Experimental results with a proof-of-concept implementation of the set cover approach to taxonomic annotation in a next release of the TANGO software show that the set cover approach further reduces ambiguity in the taxonomic annotation obtained with TANGO without distorting the relative abundance profile of the metagenomic sample.}, } @article {pmid29028005, year = {2018}, author = {Denman, S and Doonan, J and Ransom-Jones, E and Broberg, M and Plummer, S and Kirk, S and Scarlett, K and Griffiths, AR and Kaczmarek, M and Forster, J and Peace, A and Golyshin, PN and Hassard, F and Brown, N and Kenny, JG and McDonald, JE}, title = {Microbiome and infectivity studies reveal complex polyspecies tree disease in Acute Oak Decline.}, journal = {The ISME journal}, volume = {12}, number = {2}, pages = {386-399}, pmid = {29028005}, issn = {1751-7370}, mesh = {Algorithms ; Animals ; Coleoptera/*microbiology ; Enterobacteriaceae/*genetics/pathogenicity ; Genome, Bacterial ; Genome, Plant ; Metagenome ; *Microbiota ; Necrosis ; Phylogeny ; Plant Diseases/*microbiology ; Quercus/*microbiology ; Rahnella/*genetics/pathogenicity ; Systems Biology ; Transcriptome ; }, abstract = {Decline-diseases are complex and becoming increasingly problematic to tree health globally. Acute Oak Decline (AOD) is characterized by necrotic stem lesions and galleries of the bark-boring beetle, Agrilus biguttatus, and represents a serious threat to oak. Although multiple novel bacterial species and Agrilus galleries are associated with AOD lesions, the causative agent(s) are unknown. The AOD pathosystem therefore provides an ideal model for a systems-based research approach to address our hypothesis that AOD lesions are caused by a polymicrobial complex. Here we show that three bacterial species, Brenneria goodwinii, Gibbsiella quercinecans and Rahnella victoriana, are consistently abundant in the lesion microbiome and possess virulence genes used by canonical phytopathogens that are expressed in AOD lesions. Individual and polyspecies inoculations on oak logs and trees demonstrated that B. goodwinii and G. quercinecans cause tissue necrosis and, in combination with A. biguttatus, produce the diagnostic symptoms of AOD. We have proved a polybacterial cause of AOD lesions, providing new insights into polymicrobial interactions and tree disease. This work presents a novel conceptual and methodological template for adapting Koch's postulates to address the role of microbial communities in disease.}, } @article {pmid29028000, year = {2018}, author = {Mendes, LW and Raaijmakers, JM and de Hollander, M and Mendes, R and Tsai, SM}, title = {Influence of resistance breeding in common bean on rhizosphere microbiome composition and function.}, journal = {The ISME journal}, volume = {12}, number = {1}, pages = {212-224}, pmid = {29028000}, issn = {1751-7370}, mesh = {Bacteria/genetics/isolation & purification ; Disease Resistance ; Fusarium/physiology ; Metagenome ; *Microbiota ; Phaseolus/*microbiology ; Plant Breeding ; Plant Diseases/microbiology ; Plant Roots/*microbiology ; *Rhizosphere ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The rhizosphere microbiome has a key role in plant growth and health, providing a first line of defense against root infections by soil-borne pathogens. Here, we investigated the composition and metabolic potential of the rhizobacterial community of different common bean (Phaseolus vulgaris) cultivars with variable levels of resistance to the fungal root pathogen Fusarium oxysporum (Fox). For the different bean cultivars grown in two soils with contrasting physicochemical properties and microbial diversity, rhizobacterial abundance was positively correlated with Fox resistance. Pseudomonadaceae, bacillaceae, solibacteraceae and cytophagaceae were more abundant in the rhizosphere of the Fox-resistant cultivar. Network analyses showed a modular topology of the rhizosphere microbiome of the Fox-resistant cultivar, suggesting a more complex and highly connected bacterial community than in the rhizosphere of the Fox-susceptible cultivar. Metagenome analyses further revealed that specific functional traits such as protein secretion systems and biosynthesis genes of antifungal phenazines and rhamnolipids were more abundant in the rhizobacterial community of the Fox-resistant cultivar. Our findings suggest that breeding for Fox resistance in common bean may have co-selected for other unknown plant traits that support a higher abundance of specific beneficial bacterial families in the rhizosphere with functional traits that reinforce the first line of defense.}, } @article {pmid29027998, year = {2018}, author = {Arkhipova, K and Skvortsov, T and Quinn, JP and McGrath, JW and Allen, CC and Dutilh, BE and McElarney, Y and Kulakov, LA}, title = {Temporal dynamics of uncultured viruses: a new dimension in viral diversity.}, journal = {The ISME journal}, volume = {12}, number = {1}, pages = {199-211}, pmid = {29027998}, issn = {1751-7370}, mesh = {Bacteria/isolation & purification ; Bacteriophages/genetics/isolation & purification ; Biodiversity ; Ecosystem ; *Genome, Viral ; Lakes/microbiology/virology ; Metagenomics ; Viruses/*genetics/isolation & purification ; }, abstract = {Recent work has vastly expanded the known viral genomic sequence space, but the seasonal dynamics of viral populations at the genome level remain unexplored. Here we followed the viral community in a freshwater lake for 1 year using genome-resolved viral metagenomics, combined with detailed analyses of the viral community structure, associated bacterial populations and environmental variables. We reconstructed 8950 complete and partial viral genomes, the majority of which were not persistent in the lake throughout the year, but instead continuously succeeded each other. Temporal analysis of 732 viral genus-level clusters demonstrated that one-fifth were undetectable at specific periods of the year. Based on host predictions for a subset of reconstructed viral genomes, we for the first time reveal three distinct patterns of host-pathogen dynamics, where the viruses may peak before, during or after the peak in their host's abundance, providing new possibilities for modelling of their interactions. Time series metagenomics opens up a new dimension in viral profiling, which is essential to understand the full scale of viral diversity and evolution, and the ecological roles of these important factors in the global ecosystem.}, } @article {pmid29026883, year = {2017}, author = {Martinez, KA and Devlin, JC and Lacher, CR and Yin, Y and Cai, Y and Wang, J and Dominguez-Bello, MG}, title = {Increased weight gain by C-section: Functional significance of the primordial microbiome.}, journal = {Science advances}, volume = {3}, number = {10}, pages = {eaao1874}, pmid = {29026883}, issn = {2375-2548}, support = {P30 CA016087/CA/NCI NIH HHS/United States ; T32 AI007180/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Biodiversity ; Body Weight ; *Cesarean Section ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Mice ; *Microbiota ; Obesity/etiology ; *Weight Gain ; }, abstract = {Epidemiological evidence supports a direct association between early microbiota impact-including C-section-and obesity. We performed antibiotic-free, fostered C-sections and determined the impact on the early microbiota and body weight during development. Mice in the C-section group gained more body mass after weaning, with a stronger phenotype in females. C-section-born mice lacked the dynamic developmental gut microbiota changes observed in control mice. The results demonstrate a causal relationship between C-section and increased body weight, supporting the involvement of maternal vaginal bacteria in normal metabolic development.}, } @article {pmid29020628, year = {2017}, author = {Tamura, K and Hemsworth, GR and Déjean, G and Rogers, TE and Pudlo, NA and Urs, K and Jain, N and Davies, GJ and Martens, EC and Brumer, H}, title = {Molecular Mechanism by which Prominent Human Gut Bacteroidetes Utilize Mixed-Linkage Beta-Glucans, Major Health-Promoting Cereal Polysaccharides.}, journal = {Cell reports}, volume = {21}, number = {2}, pages = {417-430}, pmid = {29020628}, issn = {2211-1247}, support = {BB/I014802/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 GM099513/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteroides/genetics/*metabolism ; Edible Grain/chemistry ; *Gastrointestinal Microbiome ; *Genes, Bacterial ; Humans ; Metabolism ; Metagenome ; beta-Glucans/*metabolism ; }, abstract = {Microbial utilization of complex polysaccharides is a major driving force in shaping the composition of the human gut microbiota. There is a growing appreciation that finely tuned polysaccharide utilization loci enable ubiquitous gut Bacteroidetes to thrive on the plethora of complex polysaccharides that constitute "dietary fiber." Mixed-linkage β(1,3)/β(1,4)-glucans (MLGs) are a key family of plant cell wall polysaccharides with recognized health benefits but whose mechanism of utilization has remained unclear. Here, we provide molecular insight into the function of an archetypal MLG utilization locus (MLGUL) through a combination of biochemistry, enzymology, structural biology, and microbiology. Comparative genomics coupled with growth studies demonstrated further that syntenic MLGULs serve as genetic markers for MLG catabolism across commensal gut bacteria. In turn, we surveyed human gut metagenomes to reveal that MLGULs are ubiquitous in human populations globally, which underscores the importance of gut microbial metabolism of MLG as a common cereal polysaccharide.}, } @article {pmid29020222, year = {2018}, author = {Leung, V and Vincent, C and Edens, TJ and Miller, M and Manges, AR}, title = {Antimicrobial Resistance Gene Acquisition and Depletion Following Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {66}, number = {3}, pages = {456-457}, pmid = {29020222}, issn = {1537-6591}, mesh = {Anti-Bacterial Agents/pharmacology ; Clostridium Infections/*therapy ; Drug Resistance, Multiple, Bacterial/*genetics ; Fecal Microbiota Transplantation/*adverse effects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genes, Bacterial ; *Genes, MDR ; High-Throughput Nucleotide Sequencing ; Humans ; Recurrence ; }, abstract = {Fecal microbiota transplantation (FMT) may be a novel approach to eliminate multidrug-resistant bacteria from the gut and to prevent future infections. Using whole metagenome sequencing data from 8 FMT donor-recipient pairs, we identified 37 and 95 antimicrobial resistance genes that were acquired by or removed from FMT recipients, respectively.}, } @article {pmid29019934, year = {2017}, author = {Kakuta, M and Suzuki, S and Izawa, K and Ishida, T and Akiyama, Y}, title = {A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data.}, journal = {International journal of molecular sciences}, volume = {18}, number = {10}, pages = {}, pmid = {29019934}, issn = {1422-0067}, mesh = {Algorithms ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Mouth/*microbiology ; Sequence Analysis, DNA/*methods ; *Sequence Homology, Nucleic Acid ; *Software ; }, abstract = {Sequence similarity searches have been widely used in the analyses of metagenomic sequencing data. Finding homologous sequences in a reference database enables the estimation of taxonomic and functional characteristics of each query sequence. Because current metagenomic sequencing data consist of a large number of nucleotide sequences, the time required for sequence similarity searches account for a large proportion of the total time. This time-consuming step makes it difficult to perform large-scale analyses. To analyze large-scale metagenomic data, such as those found in the human oral microbiome, we developed GHOST-MP (Genome-wide HOmology Search Tool on Massively Parallel system), a parallel sequence similarity search tool for massively parallel computing systems. This tool uses a fast search algorithm based on suffix arrays of query and database sequences and a hierarchical parallel search to accelerate the large-scale sequence similarity search of metagenomic sequencing data. The parallel computing efficiency and the search speed of this tool were evaluated. GHOST-MP was shown to be scalable over 10,000 CPU (Central Processing Unit) cores, and achieved over 80-fold acceleration compared with mpiBLAST using the same computational resources. We applied this tool to human oral metagenomic data, and the results indicate that the oral cavity, the oral vestibule, and plaque have different characteristics based on the functional gene category.}, } @article {pmid29018275, year = {2017}, author = {Ray, K}, title = {Gut microbiota: Human faecal sample processing in metagenomic studies: striving for standards.}, journal = {Nature reviews. Gastroenterology & hepatology}, volume = {14}, number = {11}, pages = {631}, pmid = {29018275}, issn = {1759-5053}, mesh = {Feces ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; }, } @article {pmid29018189, year = {2017}, author = {Jie, Z and Xia, H and Zhong, SL and Feng, Q and Li, S and Liang, S and Zhong, H and Liu, Z and Gao, Y and Zhao, H and Zhang, D and Su, Z and Fang, Z and Lan, Z and Li, J and Xiao, L and Li, J and Li, R and Li, X and Li, F and Ren, H and Huang, Y and Peng, Y and Li, G and Wen, B and Dong, B and Chen, JY and Geng, QS and Zhang, ZW and Yang, H and Wang, J and Wang, J and Zhang, X and Madsen, L and Brix, S and Ning, G and Xu, X and Liu, X and Hou, Y and Jia, H and He, K and Kristiansen, K}, title = {The gut microbiome in atherosclerotic cardiovascular disease.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {845}, pmid = {29018189}, issn = {2041-1723}, mesh = {Atherosclerosis/*microbiology ; Case-Control Studies ; Fermentation ; *Gastrointestinal Microbiome/drug effects ; Genome-Wide Association Study ; Humans ; Inflammation/microbiology ; Liver Cirrhosis/microbiology ; *Metagenome ; Metagenomics ; }, abstract = {The gut microbiota has been linked to cardiovascular diseases. However, the composition and functional capacity of the gut microbiome in relation to cardiovascular diseases have not been systematically examined. Here, we perform a metagenome-wide association study on stools from 218 individuals with atherosclerotic cardiovascular disease (ACVD) and 187 healthy controls. The ACVD gut microbiome deviates from the healthy status by increased abundance of Enterobacteriaceae and Streptococcus spp. and, functionally, in the potential for metabolism or transport of several molecules important for cardiovascular health. Although drug treatment represents a confounding factor, ACVD status, and not current drug use, is the major distinguishing feature in this cohort. We identify common themes by comparison with gut microbiome data associated with other cardiometabolic diseases (obesity and type 2 diabetes), with liver cirrhosis, and rheumatoid arthritis. Our data represent a comprehensive resource for further investigations on the role of the gut microbiome in promoting or preventing ACVD as well as other related diseases.The gut microbiota may play a role in cardiovascular diseases. Here, the authors perform a metagenome-wide association study on stools from individuals with atherosclerotic cardiovascular disease and healthy controls, identifying microbial strains and functions associated with the disease.}, } @article {pmid29016661, year = {2017}, author = {Yan, YW and Zou, B and Zhu, T and Hozzein, WN and Quan, ZX}, title = {Modified RNA-seq method for microbial community and diversity analysis using rRNA in different types of environmental samples.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0186161}, pmid = {29016661}, issn = {1932-6203}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Datasets as Topic ; Drinking Water/microbiology ; Fungi/classification/*genetics ; Gene Library ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Microbial Consortia/genetics ; *Phylogeny ; Plant Leaves/microbiology ; RNA, Ribosomal, 16S/*genetics ; Reverse Transcription ; Sequence Analysis, DNA/*methods ; Wetlands ; }, abstract = {RNA-seq-based SSU (small subunit) rRNA (ribosomal RNA) analysis has provided a better understanding of potentially active microbial community within environments. However, for RNA-seq library construction, high quantities of purified RNA are typically required. We propose a modified RNA-seq method for SSU rRNA-based microbial community analysis that depends on the direct ligation of a 5' adaptor to RNA before reverse-transcription. The method requires only a low-input quantity of RNA (10-100 ng) and does not require a DNA removal step. The method was initially tested on three mock communities synthesized with enriched SSU rRNA of archaeal, bacterial and fungal isolates at different ratios, and was subsequently used for environmental samples of high or low biomass. For high-biomass salt-marsh sediments, enriched SSU rRNA and total nucleic acid-derived RNA-seq datasets revealed highly consistent community compositions for all of the SSU rRNA sequences, and as much as 46.4%-59.5% of 16S rRNA sequences were suitable for OTU (operational taxonomic unit)-based community and diversity analyses with complete coverage of V1-V2 regions. OTU-based community structures for the two datasets were also highly consistent with those determined by all of the 16S rRNA reads. For low-biomass samples, total nucleic acid-derived RNA-seq datasets were analyzed, and highly active bacterial taxa were also identified by the OTU-based method, notably including members of the previously underestimated genus Nitrospira and phylum Acidobacteria in tap water, members of the phylum Actinobacteria on a shower curtain, and members of the phylum Cyanobacteria on leaf surfaces. More than half of the bacterial 16S rRNA sequences covered the complete region of primer 8F, and non-coverage rates as high as 38.7% were obtained for phylum-unclassified sequences, providing many opportunities to identify novel bacterial taxa. This modified RNA-seq method will provide a better snapshot of diverse microbial communities, most notably by OTU-based analysis, even communities with low-biomass samples.}, } @article {pmid28992056, year = {2017}, author = {Leggett, RM and Clark, MD}, title = {A world of opportunities with nanopore sequencing.}, journal = {Journal of experimental botany}, volume = {68}, number = {20}, pages = {5419-5429}, doi = {10.1093/jxb/erx289}, pmid = {28992056}, issn = {1460-2431}, support = {BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Computational Biology/instrumentation/*methods ; Genome, Human/genetics ; Genome, Plant/*genetics ; Humans ; Microbiota/genetics ; *Nanopores ; Plants/*genetics ; Sequence Analysis, DNA/instrumentation/*methods ; }, abstract = {Oxford Nanopore Technologies' MinION sequencer was launched in pre-release form in 2014 and represents an exciting new sequencing paradigm. The device offers multi-kilobase reads and a streamed mode of operation that allows processing of reads as they are generated. Crucially, it is an extremely compact device that is powered from the USB port of a laptop computer, enabling it to be taken out of the lab and facilitating previously impossible in-field sequencing experiments to be undertaken. Many of the initial publications concerning the platform focused on provision of tools to access and analyse the new sequence formats and then demonstrating the assembly of microbial genomes. More recently, as throughput and accuracy have increased, it has been possible to begin work involving more complex genomes and metagenomes. With the release of the high-throughput GridION X5 and PromethION platforms, the sequencing of large genomes will become more cost efficient, and enable the leveraging of extremely long (>100 kb) reads for resolution of complex genomic structures. This review provides a brief overview of nanopore sequencing technology, describes the growing range of nanopore bioinformatics tools, and highlights some of the most influential publications that have emerged over the last 2 years. Finally, we look to the future and the potential the platform has to disrupt work in human, microbiome, and plant genomics.}, } @article {pmid28983638, year = {2018}, author = {Turroni, F and Milani, C and Duranti, S and Ferrario, C and Lugli, GA and Mancabelli, L and van Sinderen, D and Ventura, M}, title = {Bifidobacteria and the infant gut: an example of co-evolution and natural selection.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {75}, number = {1}, pages = {103-118}, pmid = {28983638}, issn = {1420-9071}, mesh = {Bifidobacterium/genetics/*physiology ; Evolution, Molecular ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/metabolism/*microbiology ; Humans ; Infant ; Microbial Interactions/genetics/*physiology ; Polysaccharides/metabolism ; Selection, Genetic ; Time Factors ; }, abstract = {Throughout the human life, the gut microbiota interacts with us in a number of different ways, thereby influencing our health status. The acquisition of such an interactive gut microbiota commences at birth. Medical and environmental factors including diet, antibiotic exposure and mode of delivery are major factors that shape the composition of the microbial communities in the infant gut. Among the most abundant members of the infant microbiota are species belonging to the Bifidobacterium genus, which are believed to confer beneficial effects upon their host. Bifidobacteria may be acquired directly from the mother by vertical transmission and their persistence in the infant gut is associated with their saccharolytic activity toward glycans that are abundant in the infant gut. Here, we discuss the establishment of the infant gut microbiota and the contribution of bifidobacteria to this early life microbial consortium.}, } @article {pmid28982089, year = {2018}, author = {Tang, B and Chen, Q and Bin, L and Huang, S and Zhang, W and Fu, F and Li, P}, title = {Insight into the microbial community and its succession of a coupling anaerobic-aerobic biofilm on semi-suspended bio-carriers.}, journal = {Bioresource technology}, volume = {247}, number = {}, pages = {591-598}, doi = {10.1016/j.biortech.2017.09.147}, pmid = {28982089}, issn = {1873-2976}, mesh = {Bacteria ; Biodiversity ; *Biofilms ; *Bioreactors ; }, abstract = {This work aims at establishing a coupling anaerobic-aerobic biofilm within a single bioreactor and revealing its microbial community and succession. By using a semi-suspended bio-carrier fabricated with 3D printing technique, an obvious DO gradient was gradually created within the biofilm, which demonstrated that a coupling anaerobic-aerobic biofilm was successfully established on the surface of bio-carriers. The results of metagenomic analysis revealed that the microbial community on the bio-carriers experienced a continuous succession in its structure and dominant species along with the operational time. The formed coupling biofilm created suitable micro multi-habitats for the co-existence of these microorganisms, including nitrifying and denitrifying bacteria, which were beneficial to the removing of organic pollutants and converting nutrients. Along with the succession, the microbial community was gradually dominated by several functional microorganisms. Overall, the results presented an approach to improve the microbial biodiversity by constructing a new structure and floating status of bio-carriers.}, } @article {pmid28978929, year = {2017}, author = {Ren, Z and Gao, H and Elser, JJ and Zhao, Q}, title = {Microbial functional genes elucidate environmental drivers of biofilm metabolism in glacier-fed streams.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {12668}, pmid = {28978929}, issn = {2045-2322}, mesh = {Biodiversity ; Biofilms/growth & development ; Climate Change ; *Ecosystem ; Genes, Bacterial/*genetics ; Hydrogen-Ion Concentration ; Metagenome/*genetics ; Nitrogen/metabolism ; RNA, Ribosomal, 16S/*genetics ; Sulfur/metabolism ; }, abstract = {Benthic biofilms in glacier-fed streams harbor diverse microorganisms driving biogeochemical cycles and, consequently, influencing ecosystem-level processes. Benthic biofilms are vulnerable to glacial retreat induced by climate change. To investigate microbial functions of benthic biofilms in glacier-fed streams, we predicted metagenomes from 16s rRNA gene sequence data using PICRUSt and identified functional genes associated with nitrogen and sulfur metabolisms based on KEGG database and explored the relationships between metabolic pathways and abiotic factors in glacier-fed streams in the Tianshan Mountains in Central Asia. Results showed that the distribution of functional genes was mainly associated with glacier area proportion, glacier source proportion, total nitrogen, dissolved organic carbon, and pH. For nitrogen metabolism, the relative abundance of functional genes associated with dissimilatory pathways was higher than those for assimilatory pathways. The relative abundance of functional genes associated with assimilatory sulfate reduction was higher than those involved with the sulfur oxidation system and dissimilatory sulfate reduction. Hydrological factors had more significant correlations with nitrogen metabolism than physicochemical factors and anammox was the most sensitive nitrogen cycling pathway responding to variation of the abiotic environment in these glacial-fed streams. In contrast, sulfur metabolism pathways were not sensitive to variations of abiotic factors in these systems.}, } @article {pmid28978331, year = {2017}, author = {Shamarina, D and Stoyantcheva, I and Mason, CE and Bibby, K and Elhaik, E}, title = {Communicating the promise, risks, and ethics of large-scale, open space microbiome and metagenome research.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {132}, pmid = {28978331}, issn = {2049-2618}, support = {R01 ES021006/ES/NIEHS NIH HHS/United States ; R25 EB020393/EB/NIBIB NIH HHS/United States ; }, mesh = {Environment Design ; *Ethics, Research ; Humans ; *Metagenome ; Metagenomics ; *Microbiota ; Public Opinion ; *Public Relations ; *Research ; }, abstract = {The public commonly associates microorganisms with pathogens. This suspicion of microorganisms is understandable, as historically microorganisms have killed more humans than any other agent while remaining largely unknown until the late seventeenth century with the works of van Leeuwenhoek and Kircher. Despite our improved understanding regarding microorganisms, the general public are apt to think of diseases rather than of the majority of harmless or beneficial species that inhabit our bodies and the built and natural environment. As long as microbiome research was confined to labs, the public's exposure to microbiology was limited. The recent launch of global microbiome surveys, such as the Earth Microbiome Project and MetaSUB (Metagenomics and Metadesign of Subways and Urban Biomes) project, has raised ethical, financial, feasibility, and sustainability concerns as to the public's level of understanding and potential reaction to the findings, which, done improperly, risk negative implications for ongoing and future investigations, but done correctly, can facilitate a new vision of "smart cities." To facilitate improved future research, we describe here the major concerns that our discussions with ethics committees, community leaders, and government officials have raised, and we expound on how to address them. We further discuss ethical considerations of microbiome surveys and provide practical recommendations for public engagement.}, } @article {pmid28976007, year = {2017}, author = {Rosen, CE and Palm, NW}, title = {Functional Classification of the Gut Microbiota: The Key to Cracking the Microbiota Composition Code: Functional classifications of the gut microbiota reveal previously hidden contributions of indigenous gut bacteria to human health and disease.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {12}, pages = {}, doi = {10.1002/bies.201700032}, pmid = {28976007}, issn = {1521-1878}, mesh = {Dysbiosis/genetics/*immunology/microbiology ; Gastrointestinal Microbiome/*immunology ; Gastrointestinal Tract/immunology/*microbiology ; Humans ; *Immunity, Innate ; Immunoglobulin A/genetics ; Metabolome/immunology ; Metagenome/*immunology ; Microbial Consortia/immunology ; Terminology as Topic ; }, abstract = {The last decade has seen an explosion of research on the gut microbiota-the trillions of microorganisms that colonize the human gut. It is now clear that interindividual diversity in microbiota composition plays an important role in determining susceptibility to a wide variety of diseases. However, identifying the precise changes in microbiota composition that play causal roles has remained a largely unrealized goal. Here, we propose that functional classifications of microbes based on their interactions with and effects on the host-particularly the host immune system-will illuminate the role of the microbiota in shaping human physiology. We outline the benefits of "functional" classification compared to phylogenetic classifications, and review current efforts at functional classification of the microbiota. Finally, we outline a theoretical framework for classifying host-microbiota interactions. Future advances enabling broader functional classifications of the microbiota promise to revolutionize our understanding of the role of gut microbes in health and disease.}, } @article {pmid28974215, year = {2017}, author = {Lalremruata, A and Jeyaraj, S and Engleitner, T and Joanny, F and Lang, A and Bélard, S and Mombo-Ngoma, G and Ramharter, M and Kremsner, PG and Mordmüller, B and Held, J}, title = {Species and genotype diversity of Plasmodium in malaria patients from Gabon analysed by next generation sequencing.}, journal = {Malaria journal}, volume = {16}, number = {1}, pages = {398}, pmid = {28974215}, issn = {1475-2875}, mesh = {*Biodiversity ; Gabon ; Genetic Variation ; *Genotype ; High-Throughput Nucleotide Sequencing ; Humans ; Malaria/diagnosis/parasitology ; Plasmodium/genetics/*physiology ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; }, abstract = {BACKGROUND: Six Plasmodium species are known to naturally infect humans. Mixed species infections occur regularly but morphological discrimination by microscopy is difficult and multiplicity of infection (MOI) can only be evaluated by molecular methods. This study investigated the complexity of Plasmodium infections in patients treated for microscopically detected non-falciparum or mixed species malaria in Gabon.

METHODS: Ultra-deep sequencing of nucleus (18S rRNA), mitochondrion, and apicoplast encoded genes was used to evaluate Plasmodium species diversity and MOI in 46 symptomatic Gabonese patients with microscopically diagnosed non-falciparum or mixed species malaria.

RESULTS: Deep sequencing revealed a large complexity of confections in patients with uncomplicated malaria, both on species and genotype levels. Mixed infections involved up to four parasite species (Plasmodium falciparum, Plasmodium malariae, Plasmodium ovale curtisi, and P. ovale wallikeri). Multiple genotypes from each species were determined from the asexual 18S rRNA gene. 17 of 46 samples (37%) harboured multiple genotypes of at least one Plasmodium species. The number of genotypes per sample (MOI) was highest in P. malariae (n = 4), followed by P. ovale curtisi (n = 3), P. ovale wallikeri (n = 3), and P. falciparum (n = 2). The highest combined genotype complexity in samples that contained mixed-species infections was seven.

CONCLUSIONS: Ultra-deep sequencing showed an unexpected breadth of Plasmodium species and within species diversity in clinical samples. MOI of P. ovale curtisi, P. ovale wallikeri and P. malariae infections were higher than anticipated and contribute significantly to the burden of malaria in Gabon.}, } @article {pmid28973555, year = {2017}, author = {Chi, L and Bian, X and Gao, B and Tu, P and Ru, H and Lu, K}, title = {The Effects of an Environmentally Relevant Level of Arsenic on the Gut Microbiome and Its Functional Metagenome.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {160}, number = {2}, pages = {193-204}, pmid = {28973555}, issn = {1096-0929}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 ES024950/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Arsenites/*toxicity ; Bacteria/classification/*drug effects/genetics ; Dysbiosis ; Environmental Pollutants/*toxicity ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Gene Expression Regulation, Bacterial ; Intestines/*drug effects/microbiology ; Metagenome/*drug effects/genetics ; Mice, Inbred C57BL ; Ribotyping ; Sodium Compounds/*toxicity ; Time Factors ; }, abstract = {Multiple environmental factors induce dysbiosis in the gut microbiome and cause a variety of human diseases. Previously, we have first demonstrated that arsenic alters the composition of the gut microbiome. However, the functional impact of arsenic on the gut microbiome has not been adequately assessed, particularly at environmentally relevant concentrations. In this study, we used 16S rRNA sequencing and metagenomics sequencing to investigate how exposure to 100 ppb arsenic for 13 weeks alters the composition and functional capacity of the gut microbiome in mice. Arsenic exposure altered the alpha and beta diversities as well as the composition profile of the gut microbiota. Metagenomics data revealed that the abundances of genes involved in carbohydrate metabolism, especially pyruvate fermentation, short-chain fatty acid synthesis, and starch utilization, and were significantly changed. Moreover, lipopolysaccharide biosynthesis genes, multiple stress response genes, and DNA repair genes were significantly increased in the gut microbiome of arsenic-exposed mice. The genes involved in the production or processing of multiple vitamins, including folic acid and vitamins B6, B12, and K2, were also enriched in arsenic-treated mice. In, addition, genes involved in multidrug resistance and conjugative transposon proteins were highly increased after treatment with arsenic. In conclusion, we demonstrate that arsenic exposure, at an environmentally relevant dose, not only perturbed the communal composition of the gut microbiome but also profoundly altered a variety of important bacterial functional pathways.}, } @article {pmid28973392, year = {2017}, author = {Chen, YC and Greenbaum, J and Shen, H and Deng, HW}, title = {Association Between Gut Microbiota and Bone Health: Potential Mechanisms and Prospective.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {102}, number = {10}, pages = {3635-3646}, pmid = {28973392}, issn = {1945-7197}, support = {R01 AR059781/AR/NIAMS NIH HHS/United States ; R01 AR069055/AR/NIAMS NIH HHS/United States ; D43 TW009107/TW/FIC NIH HHS/United States ; R01 GM109068/GM/NIGMS NIH HHS/United States ; R01 AR057049/AR/NIAMS NIH HHS/United States ; U19 AG055373/AG/NIA NIH HHS/United States ; P50 AR055081/AR/NIAMS NIH HHS/United States ; P20 GM109036/GM/NIGMS NIH HHS/United States ; R01 MH104680/MH/NIMH NIH HHS/United States ; R01 MH107354/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Animals, Laboratory ; Anti-Bacterial Agents/pharmacology ; Bone Resorption/microbiology ; Bone and Bones/drug effects/*metabolism ; Gastrointestinal Microbiome/*physiology ; Germ-Free Life ; Health ; Humans ; Prebiotics ; Probiotics/pharmacology ; }, abstract = {CONTEXT: It has been well established that the human gut microbiome plays a critical role in the regulation of important biological processes and the mechanisms underlying numerous complex diseases. Although researchers have only recently begun to study the relationship between the gut microbiota and bone metabolism, early efforts have provided increased evidence to suggest an important association.

EVIDENCE ACQUISITION: In this study, we attempt to comprehensively summarize the relationship between the gut microbiota and bone metabolism by detailing the regulatory effects of the microbiome on various biological processes, including nutrient absorption and the intestinal mucosal barrier, immune system functionality, the gut-brain axis, and excretion of functional byproducts. In this review, we incorporate evidence from various types of studies, including observational, in vitro and in vivo animal experiments, as well as small efficacy clinic trails.

EVIDENCE SYNTHESIS: We review the various potential mechanisms of influence for the gut microbiota on the regulation of bone metabolism and discuss the importance of further examining the potential effects of the gut microbiota on the risk of osteoporosis in humans. Furthermore, we outline some useful tools/approaches for metagenomics research and present some prominent examples of metagenomics association studies in humans.

CONCLUSION: Current research efforts, although limited, clearly indicate that the gut microbiota may be implicated in bone metabolism, and therefore, further exploration of this relationship is a promising area of focus in bone health and osteoporosis research. Although most existing studies investigate this relationship using animal models, human studies are both needed and on the horizon.}, } @article {pmid28971238, year = {2018}, author = {Rodrigues, EM and Morais, DK and Pylro, VS and Redmile-Gordon, M and de Oliveira, JA and Roesch, LFW and Cesar, DE and Tótola, MR}, title = {Aliphatic Hydrocarbon Enhances Phenanthrene Degradation by Autochthonous Prokaryotic Communities from a Pristine Seawater.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {688-700}, pmid = {28971238}, issn = {1432-184X}, support = {405544/2012-0//CNPq/ ; }, mesh = {Alkanes ; Alphaproteobacteria/drug effects/metabolism ; Bacteria/classification/*drug effects/genetics/*metabolism ; Biodegradation, Environmental ; Biodiversity ; Brazil ; DNA, Bacterial/genetics ; Ecosystem ; Gammaproteobacteria/drug effects/metabolism ; High-Throughput Nucleotide Sequencing ; Hydrocarbons/*adverse effects ; Islands ; Metagenomics ; Microbial Consortia/*drug effects/genetics/*physiology ; Petroleum Pollution/adverse effects ; Phenanthrenes/*metabolism ; Polycyclic Aromatic Hydrocarbons/pharmacology ; Pyrenes ; RNA, Ribosomal, 16S/metabolism ; Seawater/*microbiology ; Water Pollutants ; }, abstract = {The microbial diversity and functioning around oceanic islands is poorly described, despite its importance for ecosystem homeostasis. Here, we aimed to verify the occurrence of microbe-driven phenanthrene co-oxidation in the seawater surrounding the Trindade Island (Brazil). We also used Next-Generation Sequencing to evaluate the effects of aliphatic and polycyclic aromatic hydrocarbons (PAHs) on these microbial community assemblies. Microcosms containing seawater from the island enriched with either labelled (9-[14]C) or non-labelled phenanthrene together with hexadecane, weathered oil, fluoranthene or pyrene, and combinations of these compounds were incubated. Biodegradation of phenanthrene-9-[14]C was negatively affected in the presence of weathered oil and PAHs but increased in the presence of hexadecane. PAH contamination caused shifts in the seawater microbial community-from a highly diverse one dominated by Alphaproteobacteria to less diverse communities dominated by Gammaproteobacteria. Furthermore, the combination of PAHs exerted a compounded negative influence on the microbial community, reducing its diversity and thus functional capacity of the ecosystem. These results advance our understanding of bacterial community dynamics in response to contrasting qualities of hydrocarbon contamination. This understanding is fundamental in the application and monitoring of bioremediation strategies if accidents involving oil spillages occur near Trindade Island and similar ecosystems.}, } @article {pmid28970223, year = {2017}, author = {Xiao, C and Lu, ZM and Zhang, XJ and Wang, ST and Ao, L and Shen, CH and Shi, JS and Xu, ZH}, title = {Bio-Heat Is a Key Environmental Driver Shaping the Microbial Community of Medium-Temperature Daqu.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {23}, pages = {}, pmid = {28970223}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; Biodiversity ; China ; Edible Grain/microbiology ; *Microbiota ; Temperature ; Wine/analysis/*microbiology ; }, abstract = {"Daqu" is a saccharifying and fermenting agent commonly used in the traditional solid-state fermentation industry (e.g., baijiu and vinegar). The patterns of microbial community succession and flavor formation are highly similar among batches, yet the mechanisms promoting temporal succession in the Daqu microbial ecology remain unclear. Here, we first correlated temporal profiles of microbial community succession with environmental variables (temperature, moisture, and titratable acidity) in medium temperature Daqu (MT-Daqu) throughout fermentation. Temperature dynamics significantly correlated (P < 0.05) with the quick succession of MT-Daqu microbiota in the first 12 d of fermentation, while the community structure was relatively stable after 12 d. Then, we explored the effect of temperature on the MT-Daqu community assembly. In the first 4 d of fermentation, the rapid propagation of most bacterial taxa and several fungal taxa, including Candida, Wickerhamomyces, and unclassified Dipodascaceae and Saccharomycetales species, significantly increased MT-Daqu temperature to 55°C. Subsequently, sustained bio-heat generated by microbial metabolism (53 to 56°C) within MT-Daqu inhibited the growth of most microbes from day 4 to day 12, while thermotolerant taxa, including Bacillus, unclassified Streptophyta, Weissella, Thermoactinomyces, Thermoascus, and Thermomyces survived or kept on growing. Furthermore, temperature as a major driving force on the shaping of MT-Daqu microbiota was validated. Lowering the fermentation temperature by placing the MT-Daqu in a 37°C incubator resulted in decreased relative abundances of thermotolerant taxa, including Bacillus, Thermoactinomyces, and Thermoascus, in the MT-Daqu microbiota. This study revealed that bio-heat functioned as a primary endogenous driver promoting the formation of functional MT-Daqu microbiota.IMPORTANCE Humans have mastered the Daqu preparation technique of cultivating functional microbiota on starchy grains over thousands of years, and it is well known that the metabolic activity of these microbes is key to the flavor production of Chinese baijiu. The pattern of microbial community succession and flavor formation remains highly similar between batches, yet mechanistic insight into these patterns and into microbial population fidelity to specific environmental conditions remains unclear. Our study revealed that bio-heat was generated within Daqu bricks in the first 4 d of fermentation, concomitant with rapid microbial propagation and metabolism. The sustained bio-heat may then function as a major endogenous driving force promoting the formation of the MT-Daqu microbiota from day 4 to day 12. The bio-heat-driven growth of thermotolerant microorganisms might contribute to the formation of flavor metabolites. This study provides useful information for the temperature-based modulation of microbiota function during the fermentation of Daqu.}, } @article {pmid28969605, year = {2017}, author = {Zhai, P and Yang, L and Guo, X and Wang, Z and Guo, J and Wang, X and Zhu, H}, title = {MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics.}, journal = {BMC bioinformatics}, volume = {18}, number = {1}, pages = {434}, pmid = {28969605}, issn = {1471-2105}, mesh = {Data Interpretation, Statistical ; Gene Expression Profiling/methods ; Genes, Microbial ; Humans ; Metabolomics/methods ; Metagenomics/*methods ; Microbiota/genetics ; Proteomics/methods ; *Software ; }, abstract = {BACKGROUND: During the past decade, the development of high throughput nucleic sequencing and mass spectrometry analysis techniques have enabled the characterization of microbial communities through metagenomics, metatranscriptomics, metaproteomics and metabolomics data. To reveal the diversity of microbial communities and interactions between living conditions and microbes, it is necessary to introduce comparative analysis based upon integration of all four types of data mentioned above. Comparative meta-omics, especially comparative metageomics, has been established as a routine process to highlight the significant differences in taxon composition and functional gene abundance among microbiota samples. Meanwhile, biologists are increasingly concerning about the correlations between meta-omics features and environmental factors, which may further decipher the adaptation strategy of a microbial community.

RESULTS: We developed a graphical comprehensive analysis software named MetaComp comprising a series of statistical analysis approaches with visualized results for metagenomics and other meta-omics data comparison. This software is capable to read files generated by a variety of upstream programs. After data loading, analyses such as multivariate statistics, hypothesis testing of two-sample, multi-sample as well as two-group sample and a novel function-regression analysis of environmental factors are offered. Here, regression analysis regards meta-omic features as independent variable and environmental factors as dependent variables. Moreover, MetaComp is capable to automatically choose an appropriate two-group sample test based upon the traits of input abundance profiles. We further evaluate the performance of its choice, and exhibit applications for metagenomics, metaproteomics and metabolomics samples.

CONCLUSION: MetaComp, an integrative software capable for applying to all meta-omics data, originally distills the influence of living environment on microbial community by regression analysis. Moreover, since the automatically chosen two-group sample test is verified to be outperformed, MetaComp is friendly to users without adequate statistical training. These improvements are aiming to overcome the new challenges under big data era for all meta-omics data. MetaComp is available at: http://cqb.pku.edu.cn/ZhuLab/MetaComp/ and https://github.com/pzhaipku/MetaComp/ .}, } @article {pmid28969463, year = {2019}, author = {Wilczyńska, P and Skarżyńska, E and Lisowska-Myjak, B}, title = {Meconium microbiome as a new source of information about long-term health and disease: questions and answers.}, journal = {The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians}, volume = {32}, number = {4}, pages = {681-686}, doi = {10.1080/14767058.2017.1387888}, pmid = {28969463}, issn = {1476-4954}, mesh = {Amniotic Fluid/microbiology ; Animals ; Biomarkers/analysis ; Feces/*microbiology ; Female ; Fetus/microbiology ; *Gastrointestinal Microbiome ; Humans ; Meconium/*microbiology ; Pregnancy ; }, abstract = {OBJECTIVE: The objective of this study is to assess the diagnostic role of meconium microbiota as a source of information about the intrauterine environment of the developing fetus and possibly health and disease in later life.

METHODS: The literature review of over 30 papers published in international journals in the years 2001-2017, on the bacterial composition of meconium and early feces, investigated by metagenomic DNA sequencing in experimental studies on animals and clinical studies in neonates born after normal and pathological pregnancies.

RESULTS: The bacterial composition of meconium reflects the in utero microbial environment. Bacterial colonization of the fetal gut is a source of microbial stimulation and may provide a primary signal for the maturation of a balanced postnatal innate and adaptive immune system. Clarification of a possible relationship between the presence of specific bacteria in meconium and their active role in the abnormal course of pregnancy may improve our knowledge of the pathomechanisms modifying the intrauterine environment with short- and long-term effects on the immune system and metabolic pathways.

CONCLUSION: Diversified intrauterine microbiome may modify the environment of the developing fetus with possible short- and long-term impact on the individual's health and disease. Meconium which provides the individual-specific information about the intrauterine microbiome composition is a biological material with potential uses in routine clinical diagnostic practice.}, } @article {pmid28968799, year = {2018}, author = {Äijö, T and Müller, CL and Bonneau, R}, title = {Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {3}, pages = {372-380}, pmid = {28968799}, issn = {1367-4811}, mesh = {Bacteria/genetics/*isolation & purification ; Gastrointestinal Microbiome/*genetics ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; *Models, Statistical ; RNA, Ribosomal, 16S/*analysis ; Sequence Analysis, DNA/methods ; }, abstract = {MOTIVATION: The number of microbial and metagenomic studies has increased drastically due to advancements in next-generation sequencing-based measurement techniques. Statistical analysis and the validity of conclusions drawn from (time series) 16S rRNA and other metagenomic sequencing data is hampered by the presence of significant amount of noise and missing data (sampling zeros). Accounting uncertainty in microbiome data is often challenging due to the difficulty of obtaining biological replicates. Additionally, the compositional nature of current amplicon and metagenomic data differs from many other biological data types adding another challenge to the data analysis.

RESULTS: To address these challenges in human microbiome research, we introduce a novel probabilistic approach to explicitly model overdispersion and sampling zeros by considering the temporal correlation between nearby time points using Gaussian Processes. The proposed Temporal Gaussian Process Model for Compositional Data Analysis (TGP-CODA) shows superior modeling performance compared to commonly used Dirichlet-multinomial, multinomial and non-parametric regression models on real and synthetic data. We demonstrate that the nonreplicative nature of human gut microbiota studies can be partially overcome by our method with proper experimental design of dense temporal sampling. We also show that different modeling approaches have a strong impact on ecological interpretation of the data, such as stationarity, persistence and environmental noise models.

A Stan implementation of the proposed method is available under MIT license at https://github.com/tare/GPMicrobiome.

CONTACT: taijo@flatironinstitute.org or rb113@nyu.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid28968737, year = {2019}, author = {Olson, ND and Treangen, TJ and Hill, CM and Cepeda-Espinoza, V and Ghurye, J and Koren, S and Pop, M}, title = {Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes.}, journal = {Briefings in bioinformatics}, volume = {20}, number = {4}, pages = {1140-1150}, pmid = {28968737}, issn = {1477-4054}, support = {R01 AI100947/AI/NIAID NIH HHS/United States ; R01 HG004885/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Computational Biology ; Databases, Genetic/statistics & numerical data ; High-Throughput Nucleotide Sequencing/statistics & numerical data ; *Metagenome ; Metagenomics/*methods/statistics & numerical data/trends ; Microbiota/*genetics ; Software ; }, abstract = {Metagenomic samples are snapshots of complex ecosystems at work. They comprise hundreds of known and unknown species, contain multiple strain variants and vary greatly within and across environments. Many microbes found in microbial communities are not easily grown in culture making their DNA sequence our only clue into their evolutionary history and biological function. Metagenomic assembly is a computational process aimed at reconstructing genes and genomes from metagenomic mixtures. Current methods have made significant strides in reconstructing DNA segments comprising operons, tandem gene arrays and syntenic blocks. Shorter, higher-throughput sequencing technologies have become the de facto standard in the field. Sequencers are now able to generate billions of short reads in only a few days. Multiple metagenomic assembly strategies, pipelines and assemblers have appeared in recent years. Owing to the inherent complexity of metagenome assembly, regardless of the assembly algorithm and sequencing method, metagenome assemblies contain errors. Recent developments in assembly validation tools have played a pivotal role in improving metagenomics assemblers. Here, we survey recent progress in the field of metagenomic assembly, provide an overview of key approaches for genomic and metagenomic assembly validation and demonstrate the insights that can be derived from assemblies through the use of assembly validation strategies. We also discuss the potential for impact of long-read technologies in metagenomics. We conclude with a discussion of future challenges and opportunities in the field of metagenomic assembly and validation.}, } @article {pmid28968517, year = {2017}, author = {Bagarolli, RA and Tobar, N and Oliveira, AG and Araújo, TG and Carvalho, BM and Rocha, GZ and Vecina, JF and Calisto, K and Guadagnini, D and Prada, PO and Santos, A and Saad, STO and Saad, MJA}, title = {Probiotics modulate gut microbiota and improve insulin sensitivity in DIO mice.}, journal = {The Journal of nutritional biochemistry}, volume = {50}, number = {}, pages = {16-25}, doi = {10.1016/j.jnutbio.2017.08.006}, pmid = {28968517}, issn = {1873-4847}, mesh = {Adipose Tissue, White/immunology/metabolism/pathology ; Animals ; Appetite Regulation ; Bifidobacterium bifidum/classification/growth & development/immunology/isolation & purification ; Cell Membrane Permeability ; Diabetes Mellitus, Type 2/etiology/immunology/microbiology/*prevention & control ; Diet, High-Fat/adverse effects ; Dysbiosis/etiology/immunology/microbiology/*prevention & control ; Feces/microbiology ; *Gastrointestinal Microbiome/immunology ; Glucose Clamp Technique ; *Insulin Resistance ; Intestinal Mucosa/immunology/metabolism/microbiology/*physiopathology ; Lactobacillus acidophilus/classification/growth & development/immunology/isolation & purification ; Lacticaseibacillus rhamnosus/classification/growth & development/immunology/isolation & purification ; Liver/immunology/metabolism/pathology ; Male ; Mice ; Molecular Typing ; Obesity/*diet therapy/metabolism/pathology/physiopathology ; Probiotics/*therapeutic use ; Random Allocation ; }, abstract = {Obesity and type 2 diabetes are characterized by subclinical inflammatory process. Changes in composition or modulation of the gut microbiota may play an important role in the obesity-associated inflammatory process. In the current study, we evaluated the effects of probiotics (Lactobacillus rhamnosus, L. acidophilus and Bifidobacterium bifidumi) on gut microbiota, changes in permeability, and insulin sensitivity and signaling in high-fat diet and control animals. More importantly, we investigated the effects of these gut modulations on hypothalamic control of food intake, and insulin and leptin signaling. Swiss mice were submitted to a high-fat diet (HFD) with probiotics or pair-feeding for 5 weeks. Metagenome analyses were performed on DNA samples from mouse feces. Blood was drawn to determine levels of glucose, insulin, LPS, cytokines and GLP-1. Liver, muscle, ileum and hypothalamus tissue proteins were analyzed by Western blotting and real-time polymerase chain reaction. In addition, liver and adipose tissues were analyzed using histology and immunohistochemistry. The HFD induced huge alterations in gut microbiota accompanied by increased intestinal permeability, LPS translocation and systemic low-grade inflammation, resulting in decreased glucose tolerance and hyperphagic behavior. All these obesity-related features were reversed by changes in the gut microbiota profile induced by probiotics. Probiotics also induced an improvement in hypothalamic insulin and leptin resistance. Our data demonstrate that the intestinal microbiome is a key modulator of inflammatory and metabolic pathways in both peripheral and central tissues. These findings shed light on probiotics as an important tool to prevent and treat patients with obesity and insulin resistance.}, } @article {pmid28967228, year = {2017}, author = {Rampelli, S and Turroni, S and Schnorr, SL and Soverini, M and Quercia, S and Barone, M and Castagnetti, A and Biagi, E and Gallinella, G and Brigidi, P and Candela, M}, title = {Characterization of the human DNA gut virome across populations with different subsistence strategies and geographical origin.}, journal = {Environmental microbiology}, volume = {19}, number = {11}, pages = {4728-4735}, doi = {10.1111/1462-2920.13938}, pmid = {28967228}, issn = {1462-2920}, mesh = {Adolescent ; Adult ; Aged ; Biological Evolution ; Child ; DNA Viruses/*genetics ; DNA, Viral/*analysis ; Gastrointestinal Microbiome/*genetics ; Geography ; Humans ; Italy ; Metagenome ; Middle Aged ; Young Adult ; }, abstract = {It is a matter of fact that the human gut microbiome also includes a non-bacterial fraction represented by eukaryotic cells and viruses. To further explore the gut microbiome variation in human populations, here we characterized the human DNA viral community from publicly available gut metagenome data sets from human populations with different geographical origin and lifestyle. In particular, such data sets encompass microbiome information from two western urban societies (USA and Italy), as well as two traditional hunter-gatherer communities (the Hadza from Tanzania and Matses from Peru) and one pre-agricultural tribe (Tunapuco from Peru). Our results allowed for the first taxonomic reconstruction of the complex viral metacommunities within the human gut. The core virome structure included herpesviruses, papillomaviruses, polyomaviruses, adenoviruses and anelloviruses. Using Random Forests and a co-occurrence analysis approach, we identified the viruses that distinguished populations according to their geographical origin and/or lifestyle. This paves the way for new research aimed at investigating the biological role of the gut virome in human physiology, and the importance of our viral counterpart in the microbiome-host co-evolutionary process.}, } @article {pmid28967204, year = {2017}, author = {Ferrario, C and Alessandri, G and Mancabelli, L and Gering, E and Mangifesta, M and Milani, C and Lugli, GA and Viappiani, A and Duranti, S and Turroni, F and Ossiprandi, MC and Hiyashi, R and Mackie, R and van Sinderen, D and Ventura, M}, title = {Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses.}, journal = {Environmental microbiology}, volume = {19}, number = {11}, pages = {4771-4783}, doi = {10.1111/1462-2920.13943}, pmid = {28967204}, issn = {1462-2920}, mesh = {Animals ; Bacteria/*classification/genetics/*isolation & purification ; Cecum/*microbiology ; Chickens/*microbiology ; Diet ; Gastrointestinal Microbiome/*genetics ; Geography ; Humans ; Metagenomics ; }, abstract = {Different factors may modulate the gut microbiota of animals. In any particular environment, diet, genetic factors and human influences can shape the bacterial communities residing in the gastrointestinal tract. Metagenomic approaches have significantly expanded our knowledge on microbiota dynamics inside hosts, yet cultivation and isolation of bacterial members of these complex ecosystems may still be necessary to fully understand interactions between bacterial communities and their host. A dual approach, involving culture-independent and -dependent techniques, was used here to decipher the microbiota communities that inhabit the gastro intestinal tract of free-range, broiler and feral chickens. In silico analysis revealed the presence of a core microbiota that is typical of those animals that live in different geographical areas and that have limited contact with humans. Anthropic influences guide the metabolic potential and the presence of antibiotic resistance genes of these different bacterial communities. Culturomics attempts, based on different cultivation conditions, were applied to reconstruct in vitro the microbiota of feral chickens. A unique strain collection representing members of the four major phyla of the poultry microbiota was assembled, including bacterial strains that are not typically retrieved from the chicken gut.}, } @article {pmid28967193, year = {2018}, author = {De Corte, D and Srivastava, A and Koski, M and Garcia, JAL and Takaki, Y and Yokokawa, T and Nunoura, T and Elisabeth, NH and Sintes, E and Herndl, GJ}, title = {Metagenomic insights into zooplankton-associated bacterial communities.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {492-505}, pmid = {28967193}, issn = {1462-2920}, support = {268595/ERC_/European Research Council/International ; I 486/FWF_/Austrian Science Fund FWF/Austria ; Z 194/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Atlantic Ocean ; Bacteria/classification/*genetics/isolation & purification/*metabolism ; *Metagenome ; Metagenomics ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Zooplankton/*microbiology ; }, abstract = {Zooplankton and microbes play a key role in the ocean's biological cycles by releasing and consuming copious amounts of particulate and dissolved organic matter. Additionally, zooplankton provide a complex microhabitat rich in organic and inorganic nutrients in which bacteria thrive. In this study, we assessed the phylogenetic composition and metabolic potential of microbial communities associated with crustacean zooplankton species collected in the North Atlantic. Using Illumina sequencing of the 16S rRNA gene, we found significant differences between the microbial communities associated with zooplankton and those inhabiting the surrounding seawater. Metagenomic analysis of the zooplankton-associated microbial community revealed a highly specialized bacterial community able to exploit zooplankton as microhabitat and thus, mediating biogeochemical processes generally underrepresented in the open ocean. The zooplankton-associated bacterial community is able to colonize the zooplankton's internal and external surfaces using a large set of adhesion mechanisms and to metabolize complex organic compounds released or exuded by the zooplankton such as chitin, taurine and other complex molecules. Moreover, the high number of genes involved in iron and phosphorus metabolisms in the zooplankton-associated microbiome suggests that this zooplankton-associated bacterial community mediates specific biogeochemical processes (through the proliferation of specific taxa) that are generally underrepresented in the ambient waters.}, } @article {pmid28961809, year = {2017}, author = {Goss-Souza, D and Mendes, LW and Borges, CD and Baretta, D and Tsai, SM and Rodrigues, JLM}, title = {Soil microbial community dynamics and assembly under long-term land use change.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {10}, pages = {}, doi = {10.1093/femsec/fix109}, pmid = {28961809}, issn = {1574-6941}, mesh = {Archaea/classification/isolation & purification ; Bacteria/classification/isolation & purification ; Biodiversity ; Conservation of Natural Resources ; *Forests ; Grassland ; Metagenome ; *Soil Microbiology ; }, abstract = {We evaluated the bacterial and archaeal community dynamics and assembly in soils under forest, grassland and no-till cropping, using a high-throughput shotgun metagenomics approach. No significant alterations in alpha diversity were observed among different land uses, but beta diversity in grassland was lower than that observed in forest and no-till soils. Grassland communities showed assembly that predominantly followed the neutral model, i.e. high homogenizing selection with moderate dispersion, leading to biotic homogenization. Both no-till and forest soil communities were found to have assembly that predominantly followed a niche model, i.e. low rates of dispersal and weak homogenizing selection, resulting in maintenance of higher beta diversity relative to grasslands, indicating niche specialization or variable selection. Taken together, our results indicate that the patterns of assembly and their governing processes are dependent on the land use employed after deforestation, with consequences for taxa turnover and microbial functional potential.}, } @article {pmid28961409, year = {2017}, author = {Williamson, KE and Fuhrmann, JJ and Wommack, KE and Radosevich, M}, title = {Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory.}, journal = {Annual review of virology}, volume = {4}, number = {1}, pages = {201-219}, doi = {10.1146/annurev-virology-101416-041639}, pmid = {28961409}, issn = {2327-0578}, mesh = {*Biodiversity ; DNA, Single-Stranded/isolation & purification ; *Ecosystem ; Food Chain ; Gene Transfer, Horizontal ; Genome, Viral ; Humans ; Metagenomics ; *Soil Microbiology ; Virus Physiological Phenomena ; Viruses/*genetics ; }, abstract = {Viral abundance in soils can range from below detection limits in hot deserts to over 1 billion per gram in wetlands. Abundance appears to be strongly influenced by water availability and temperature, but a lack of informational standards creates difficulties for cross-study analysis. Soil viral diversity is severely underestimated and undersampled, although current measures of viral richness are higher for soils than for aquatic ecosystems. Both morphometric and metagenomic analyses have raised questions about the prevalence of nontailed, ssDNA viruses in soils. Soil is complex and critically important to terrestrial biodiversity and human civilization, but impacts of viral activities on soil ecosystem services are poorly understood. While information from aquatic systems and medical microbiology suggests the potential for viral influences on nutrient cycles, food web interactions, gene transfer, and other key processes in soils, very few empirical data are available. To understand the soil virome, much work remains.}, } @article {pmid28955471, year = {2017}, author = {van Nieuwenhuijzen, EJ and Houbraken, JAMP and Punt, PJ and Roeselers, G and Adan, OCG and Samson, RA}, title = {The fungal composition of natural biofinishes on oil-treated wood.}, journal = {Fungal biology and biotechnology}, volume = {4}, number = {}, pages = {2}, pmid = {28955471}, issn = {2054-3085}, abstract = {BACKGROUND: Biofinished wood is considered to be a decorative and protective material for outdoor constructions, showing advantages compared to traditional treated wood in terms of sustainability and self-repair. Natural dark wood staining fungi are essential to biofinish formation on wood. Although all sorts of outdoor situated timber are subjected to fungal staining, the homogenous dark staining called biofinish has only been detected on specific vegetable oil-treated substrates. Revealing the fungal composition of various natural biofinishes on wood is a first step to understand and control biofinish formation for industrial application.

RESULTS: A culture-based survey of fungi in natural biofinishes on oil-treated wood samples showed the common wood stain fungus Aureobasidium and the recently described genus Superstratomyces to be predominant constituents. A culture-independent approach, based on amplification of the internal transcribed spacer regions, cloning and Sanger sequencing, resulted in clone libraries of two types of biofinishes. Aureobasidium was present in both biofinish types, but was only predominant in biofinishes on pine sapwood treated with raw linseed oil. Most cloned sequences of the other biofinish type (pine sapwood treated with olive oil) could not be identified. In addition, a more in-depth overview of the fungal composition of biofinishes was obtained with Illumina amplicon sequencing that targeted the internal transcribed spacer region 1. All investigated samples, that varied in wood species, (oil) treatments and exposure times, contained Aureobasidium and this genus was predominant in the biofinishes on pine sapwood treated with raw linseed oil. Lapidomyces was the predominant genus in most of the other biofinishes and present in all other samples. Surprisingly, Superstratomyces, which was predominantly detected by the cultivation-based approach, could not be found with the Illumina sequencing approach, while Lapidomyces was not detected in the culture-based approach.

CONCLUSIONS: Overall, the culture-based approach and two culture-independent methods that were used in this study revealed that natural biofinishes were composed of multiple fungal genera always containing the common wood staining mould Aureobasidium. Besides Aureobasidium, the use of other fungal genera for the production of biofinished wood has to be considered.}, } @article {pmid28955177, year = {2017}, author = {Ericsson, AC and Montonye, DR and Smith, CR and Franklin, CL}, title = {Modeling a Superorganism - Considerations Regarding the Use of "Dirty" Mice in Biomedical Research .}, journal = {The Yale journal of biology and medicine}, volume = {90}, number = {3}, pages = {361-371}, pmid = {28955177}, issn = {1551-4056}, support = {K01 OD019924/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Animals ; Biomedical Research ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Microbiota/genetics/physiology ; T-Lymphocytes/metabolism/physiology ; }, abstract = {An ever-expanding body of evidence in both humans and animal models demonstrates the influence of the resident gut microbiota on host health and disease susceptibility. However, as unwanted bacterial, viral, protozoal, and parasitic agents have gradually been eliminated from colonies of purpose-bred laboratory mice, the resident microbiota has lost richness and complexity. Recent studies have shown that the ultra-hygienic environment of traditional laboratory mice and lack of antigenic exposure during development results in mice with an immune system more akin to that of a neonate than an adult human. In contrast, wild mice or mice purchased from pet stores are exposed to much greater antigen burdens and their immune system reflects this with significantly greater numbers of memory T cells and more robust vaccine responses. The current review explores the use of alternative sources for research rodents, with an emphasis on the differences in resident gut microbiota and pathogen burden between wild mice, pet store-origin mice, and traditional laboratory mice. Specifically, the literature is compared and contrasted to our own data reflecting the endogenous gut microbiota and pathogen load of wild and pet store mice, as well as the changes in both during and after procedures intended to eliminate certain zoonotic agents present in pet store mice. These data demonstrate that, while alternative sources of research rodents will likely provide models that are more translatable to the human condition, there are also several real-world considerations for scientists including contamination of research facilities and human health risks such as zoonotic diseases.}, } @article {pmid28954247, year = {2018}, author = {Grohmann, A and Fehrmann, S and Vainshtein, Y and Haag, NL and Wiese, F and Stevens, P and Naegele, HJ and Oechsner, H and Hartsch, T and Sohn, K and Grumaz, C}, title = {Microbiome dynamics and adaptation of expression signatures during methane production failure and process recovery.}, journal = {Bioresource technology}, volume = {247}, number = {}, pages = {347-356}, doi = {10.1016/j.biortech.2017.08.214}, pmid = {28954247}, issn = {1873-2976}, mesh = {Acclimatization ; Anaerobiosis ; Archaea ; Biofuels ; *Bioreactors ; *Methane ; Microbiota ; }, abstract = {This study aimed to uncover microbial dynamics and transcriptional adaptations during mesophilic AD of maize silage and slurry. While one digester performed under optimal conditions, the investigations also evaluated the microbiome during a temperature drop mediated process failure accompanied by acidification and how it contributed to a process recovery. Composition and pathway activities were analyzed by whole genome shotgun (WGS) and metatranscriptome sequencing, respectively. A biodiversity of 112 species was observed with noticeable shifts over process time. Although four distinct groups of microbes could be identified with a correlating versatility according to substrate and to process disturbance, also tremendous effects on gene expression were monitored especially of the archaeal methane metabolism. Particularly, the expression of acetogenotrophic methanogenesis related genes was identified to be relevant for process regeneration.}, } @article {pmid28953883, year = {2017}, author = {Lloyd-Price, J and Mahurkar, A and Rahnavard, G and Crabtree, J and Orvis, J and Hall, AB and Brady, A and Creasy, HH and McCracken, C and Giglio, MG and McDonald, D and Franzosa, EA and Knight, R and White, O and Huttenhower, C}, title = {Strains, functions and dynamics in the expanded Human Microbiome Project.}, journal = {Nature}, volume = {550}, number = {7674}, pages = {61-66}, pmid = {28953883}, issn = {1476-4687}, support = {U54 HG004973/HG/NHGRI NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; U01 HG006537/HG/NHGRI NIH HHS/United States ; U54 AI084844/AI/NIAID NIH HHS/United States ; U01 HG004866/HG/NHGRI NIH HHS/United States ; U54 HG004968/HG/NHGRI NIH HHS/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; U54 HG003079/HG/NHGRI NIH HHS/United States ; U54 HG004969/HG/NHGRI NIH HHS/United States ; }, mesh = {Datasets as Topic ; Humans ; Metagenome/genetics/physiology ; Microbiota/genetics/*physiology ; Molecular Sequence Annotation ; National Institutes of Health (U.S.) ; Organ Specificity ; *Phylogeny ; Spatio-Temporal Analysis ; Time Factors ; United States ; }, abstract = {The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, diversity, biogeography, and molecular function. The National Institutes of Health Human Microbiome Project has provided one of the broadest such characterizations so far. Here we introduce a second wave of data from the study, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to provide new characterizations of microbiome personalization. Strain identification revealed subspecies clades specific to body sites; it also quantified species with phylogenetic diversity under-represented in isolate genomes. Body-wide functional profiling classified pathways into universal, human-enriched, and body site-enriched subsets. Finally, temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. This study furthers our knowledge of baseline human microbial diversity and enables an understanding of personalized microbiome function and dynamics.}, } @article {pmid28952686, year = {2017}, author = {Kuzmin, MD and Peshkova, YI and Pashkova, TM and Kartashova, OL and Pashinina, OA and Meshcheryakov, AO}, title = {[Structure of microorganism species cultured from urine of urolithiasis patients].}, journal = {Urologiia (Moscow, Russia : 1999)}, volume = {}, number = {4}, pages = {18-21}, pmid = {28952686}, issn = {1728-2985}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/genetics/*isolation & purification ; Female ; Humans ; Male ; Microbiota ; Middle Aged ; Urolithiasis/*microbiology/urine ; Young Adult ; }, abstract = {AIM: To investigate the incidence of microorganisms of different taxonomic groups and their associations in the pelvic and bladder urine of adult urolithiasis patients.

MATERIALS AND METHODS: A bacteriological method and metagenomic sequencing were used to investigate the bacterial spectrum of microflora cultured from pelvic and bladder urine sampled during surgical interventions in urolithiasis patients.

RESULTS: The both microbiotas had approximately the same spectrum, but in 26.1% of patients it was inconsistent. Metagenomic analysis detected DNA of microorganisms in urine samples which were found free of microflora by the bacteriological method.

CONCLUSION: The study findings showed species diversity of microorganisms cultured from pelvic and bladder urine sampled during surgical interventions in urolithiasis patients.}, } @article {pmid28950879, year = {2017}, author = {Valseth, K and Nesbø, CL and Easterday, WR and Turner, WC and Olsen, JS and Stenseth, NC and Haverkamp, THA}, title = {Temporal dynamics in microbial soil communities at anthrax carcass sites.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {206}, pmid = {28950879}, issn = {1471-2180}, mesh = {Animals ; Anthrax/*microbiology/*veterinary ; Bacillus anthracis/classification/genetics/isolation & purification/*physiology ; Biodiversity ; Cadaver ; DNA, Bacterial/analysis ; Ecology ; Equidae/microbiology ; Genes, rRNA ; Metagenomics ; Namibia ; Soil ; *Soil Microbiology ; Spores, Bacterial/genetics ; }, abstract = {BACKGROUND: Anthrax is a globally distributed disease affecting primarily herbivorous mammals. It is caused by the soil-dwelling and spore-forming bacterium Bacillus anthracis. The dormant B. anthracis spores become vegetative after ingestion by grazing mammals. After killing the host, B. anthracis cells return to the soil where they sporulate, completing the lifecycle of the bacterium. Here we present the first study describing temporal microbial soil community changes in Etosha National Park, Namibia, after decomposition of two plains zebra (Equus quagga) anthrax carcasses. To circumvent state-associated-challenges (i.e. vegetative cells/spores) we monitored B. anthracis throughout the period using cultivation, qPCR and shotgun metagenomic sequencing.

RESULTS: The combined results suggest that abundance estimation of spore-forming bacteria in their natural habitat by DNA-based approaches alone is insufficient due to poor recovery of DNA from spores. However, our combined approached allowed us to follow B. anthracis population dynamics (vegetative cells and spores) in the soil, along with closely related organisms from the B. cereus group, despite their high sequence similarity. Vegetative B. anthracis abundance peaked early in the time-series and then dropped when cells either sporulated or died. The time-series revealed that after carcass deposition, the typical semi-arid soil community (e.g. Frankiales and Rhizobiales species) becomes temporarily dominated by the orders Bacillales and Pseudomonadales, known to contain plant growth-promoting species.

CONCLUSION: Our work indicates that complementing DNA based approaches with cultivation may give a more complete picture of the ecology of spore forming pathogens. Furthermore, the results suggests that the increased vegetation biomass production found at carcass sites is due to both added nutrients and the proliferation of microbial taxa that can be beneficial for plant growth. Thus, future B. anthracis transmission events at carcass sites may be indirectly facilitated by the recruitment of plant-beneficial bacteria.}, } @article {pmid28947833, year = {2017}, author = {Thomas, M and Webb, M and Ghimire, S and Blair, A and Olson, K and Fenske, GJ and Fonder, AT and Christopher-Hennings, J and Brake, D and Scaria, J}, title = {Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {12257}, pmid = {28947833}, issn = {2045-2322}, mesh = {*Animal Feed ; Animals ; Anti-Bacterial Agents/*administration & dosage ; Bacteria/classification/genetics ; Cattle ; *Dietary Supplements ; Drug Resistance, Bacterial/*drug effects ; Gastrointestinal Microbiome/*drug effects ; Genes, Bacterial ; Metagenomics ; North America ; }, abstract = {In North America, antibiotic feed additives such as monensin and tylosin are added to the finishing diets of feedlot cattle to counter the ill-effects of feeding diets with rapidly digestible carbohydrates. While these feed additives have been proven to improve feed efficiency and reduce liver abscess incidence, how these products impact the gastrointestinal microbiota is not completely understood. In this study, we analyzed the impact of providing antibiotic feed additives to feedlot cattle using metagenome sequencing of treated and control animals. Our results indicate that use of antibiotic feed additives does not produce discernable changes at the phylum level. However, treated cattle had reduced abundance of gram-positive bacteria at the genus level. The abundance of Ruminococcus, Erysipelotrichaceae and Lachnospiraceae in the gut of treated steers was reduced. Functional analysis of the data indicates that there was only minimal impact due to the treatment in the rumen. Genes involved in detoxification were significantly increased in the rumen of AB steers. But the relative abundance of these genes was < 0.3%. However, our results did not show any correlation between the presence of antimicrobial resistance genes in the gut microbiota and the administration of antibiotic feed additives.}, } @article {pmid28947818, year = {2017}, author = {Stat, M and Huggett, MJ and Bernasconi, R and DiBattista, JD and Berry, TE and Newman, SJ and Harvey, ES and Bunce, M}, title = {Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {12240}, pmid = {28947818}, issn = {2045-2322}, mesh = {Animals ; Aquatic Organisms/*classification/*genetics ; DNA/analysis/genetics ; Environmental Monitoring/*methods ; Metagenomics/*methods ; Seawater/chemistry ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Tropical Climate ; }, abstract = {Effective marine management requires comprehensive data on the status of marine biodiversity. However, efficient methods that can document biodiversity in our oceans are currently lacking. Environmental DNA (eDNA) sourced from seawater offers a new avenue for investigating the biota in marine ecosystems. Here, we investigated the potential of eDNA to inform on the breadth of biodiversity present in a tropical marine environment. Directly sequencing eDNA from seawater using a shotgun approach resulted in only 0.34% of 22.3 million reads assigning to eukaryotes, highlighting the inefficiency of this method for assessing eukaryotic diversity. In contrast, using 'tree of life' (ToL) metabarcoding and 20-fold fewer sequencing reads, we could detect 287 families across the major divisions of eukaryotes. Our data also show that the best performing 'universal' PCR assay recovered only 44% of the eukaryotes identified across all assays, highlighting the need for multiple metabarcoding assays to catalogue biodiversity. Lastly, focusing on the fish genus Lethrinus, we recovered intra- and inter-specific haplotypes from seawater samples, illustrating that eDNA can be used to explore diversity beyond taxon identifications. Given the sensitivity and low cost of eDNA metabarcoding we advocate this approach be rapidly integrated into biomonitoring programs.}, } @article {pmid28945499, year = {2018}, author = {Baek, K and Ji, S and Choi, Y}, title = {Complex Intratissue Microbiota Forms Biofilms in Periodontal Lesions.}, journal = {Journal of dental research}, volume = {97}, number = {2}, pages = {192-200}, pmid = {28945499}, issn = {1544-0591}, mesh = {Adult ; Biofilms/*classification ; Chronic Periodontitis/*microbiology ; DNA, Bacterial/analysis ; Dental Plaque/*microbiology ; Female ; Humans ; Male ; Microbiota/*physiology ; Microscopy, Atomic Force ; Periodontal Index ; RNA, Ribosomal, 16S/analysis ; Republic of Korea ; }, abstract = {Periodontitis is caused by dysbiotic subgingival bacterial communities that may lead to increased bacterial invasion into gingival tissues. Although shifts in community structures associated with transition from health to periodontitis have been well characterized, the nature of bacteria present within the gingival tissue of periodontal lesions is not known. To characterize microbiota within tissues of periodontal lesions and compare them with plaque microbiota, gingival tissues and subgingival plaques were obtained from 7 patients with chronic periodontitis. A sequencing analysis of the 16S rRNA gene revealed that species richness and diversity were not significantly different between the 2 groups. However, intersubject variability of intratissue communities was smaller than that of plaque communities. In addition, when compared with the plaque communities, intratissue communities were characterized by decreased abundance of Firmicutes and increased abundance of Fusobacteria and Chloroflexi. In particular, Fusobacterium nucleatum and Porphyromonas gingivalis were highly enriched within the tissue, composing 15% to 40% of the total bacteria. Furthermore, biofilms, as visualized by alcian blue staining and atomic force microscopy, were observed within the tissue where the degradation of connective tissue fibers was prominent. In conclusion, very complex bacterial communities exist in the form of biofilms within the gingival tissue of periodontal lesions, which potentially serve as a reservoir for persistent infection. This novel finding may prompt new research on therapeutic strategies to treat periodontitis.}, } @article {pmid28941534, year = {2017}, author = {Mourani, PM and Sontag, MK}, title = {Ventilator-Associated Pneumonia in Critically Ill Children: A New Paradigm.}, journal = {Pediatric clinics of North America}, volume = {64}, number = {5}, pages = {1039-1056}, doi = {10.1016/j.pcl.2017.06.005}, pmid = {28941534}, issn = {1557-8240}, support = {R01 HL124103/HL/NHLBI NIH HHS/United States ; UG1 HD083171/HD/NICHD NIH HHS/United States ; }, mesh = {Child ; Critical Care/methods ; Critical Illness ; Humans ; Lung/microbiology ; Metagenomics ; Microbiota ; *Pneumonia, Ventilator-Associated/diagnosis/etiology/therapy ; Proteomics ; Risk Factors ; }, abstract = {Ventilator-associated pneumonia (VAP) is a serious complication of critical illness. Surveillance definitions have undergone revisions for more objective and consistent reporting. The 1 organism-1 disease paradigm for microbial involvement may not adequately apply to many cases of VAP, in which pathogens are introduced to a pre-existing and often complex microbial community that facilitates or hinders the potential pathogen, consequently determining whether progression to VAP occurs. As omics technology is applied to VAP, a paradigm is emerging incorporating simultaneous assessments of microbial populations and their activity, as well as the host response, to personalize prevention and treatment.}, } @article {pmid28940049, year = {2018}, author = {Tremlett, H and Waubant, E}, title = {The Gut Microbiota and Pediatric Multiple Sclerosis: Recent Findings.}, journal = {Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics}, volume = {15}, number = {1}, pages = {102-108}, pmid = {28940049}, issn = {1878-7479}, mesh = {Biomarkers ; Child ; *Gastrointestinal Microbiome ; Humans ; Multiple Sclerosis/immunology/*microbiology ; Recurrence ; }, abstract = {Pediatric multiple sclerosis (MS) is a chronic, life-long neurological condition associated with inflammation and degeneration in the brain and spinal cord. Fortunately, < 5% of people with MS have their onset in childhood years. However, studying these very-early-onset cases of MS offers key advantages. In particular, with fewer years lived, children have had a limited range of exposures, potentially enhancing our ability to identify what might cause MS. Further, as the actual timing of the biological MS onset is unknown, the possibility to study these children much closer to the real onset of disease is far greater than in the typical adult with MS. Whether MS (in children or adults) can be prevented is unknown and the available drugs are only modestly effective in modifying the disease course and are not without risk. Emerging evidence is providing insight into the gut microbiota's potential role in triggering and shaping neurological conditions such as MS. The limited number of studies in humans with MS and absence of prior work in pediatric MS motivated the following 3 fundamental questions, addressed in 2 cross-sectional and 1 longitudinal investigation in children with and without MS: 1) Does the gut microbiota composition differ between children with and without MS? 2) Is there an association between the gut microbiota and host immune markers in children with and without MS? 3) Is the gut microbiota associated with the future risk of a MS relapse?}, } @article {pmid28938903, year = {2017}, author = {O'Hara, NB and Reed, HJ and Afshinnekoo, E and Harvin, D and Caplan, N and Rosen, G and Frye, B and Woloszynek, S and Ounit, R and Levy, S and Butler, E and Mason, CE}, title = {Metagenomic characterization of ambulances across the USA.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {125}, pmid = {28938903}, issn = {2049-2618}, support = {R01 AI125416/AI/NIAID NIH HHS/United States ; }, mesh = {*Ambulances ; Bacteria/classification/genetics/*isolation & purification/pathogenicity ; Cross Infection/microbiology ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Hospitals ; Humans ; *Metagenome ; *Metagenomics ; *Microbial Consortia/genetics ; *Microbiota/genetics ; United States ; }, abstract = {BACKGROUND: Microbial communities in our built environments have great influence on human health and disease. A variety of built environments have been characterized using a metagenomics-based approach, including some healthcare settings. However, there has been no study to date that has used this approach in pre-hospital settings, such as ambulances, an important first point-of-contact between patients and hospitals.

RESULTS: We sequenced 398 samples from 137 ambulances across the USA using shotgun sequencing. We analyzed these data to explore the microbial ecology of ambulances including characterizing microbial community composition, nosocomial pathogens, patterns of diversity, presence of functional pathways and antimicrobial resistance, and potential spatial and environmental factors that may contribute to community composition. We found that the top 10 most abundant species are either common built environment microbes, microbes associated with the human microbiome (e.g., skin), or are species associated with nosocomial infections. We also found widespread evidence of antimicrobial resistance markers (hits ~ 90% samples). We identified six factors that may influence the microbial ecology of ambulances including ambulance surfaces, geographical-related factors (including region, longitude, and latitude), and weather-related factors (including temperature and precipitation).

CONCLUSIONS: While the vast majority of microbial species classified were beneficial, we also found widespread evidence of species associated with nosocomial infections and antimicrobial resistance markers. This study indicates that metagenomics may be useful to characterize the microbial ecology of pre-hospital ambulance settings and that more rigorous testing and cleaning of ambulances may be warranted.}, } @article {pmid28937980, year = {2017}, author = {Seo, M and Heo, J and Yoon, J and Kim, SY and Kang, YM and Yu, J and Cho, S and Kim, H}, title = {Methanobrevibacter attenuation via probiotic intervention reduces flatulence in adult human: A non-randomised paired-design clinical trial of efficacy.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184547}, pmid = {28937980}, issn = {1932-6203}, mesh = {Adult ; Bifidobacterium/genetics ; Electric Impedance ; Feces/microbiology ; Female ; Flatulence/complications/*diet therapy/*microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Lactobacillus/genetics ; Male ; *Methanobrevibacter/genetics ; Middle Aged ; Obesity/complications/diet therapy/microbiology ; Phenotype ; Probiotics/*therapeutic use ; Surveys and Questionnaires ; Treatment Outcome ; Young Adult ; }, abstract = {TRIAL DESIGN: The aim of this study was to investigate which of the gut microbes respond to probiotic intervention, as well as study whether they are associated with gastrointestinal symptoms in a healthy adult human. For the experimental purpose, twenty-one healthy adults were recruited and received probiotic mixture, which is composed of five Lactobacilli strains and two Bifidobacteria strains, once a day for 60 days. Defecation survey and Bioelectrical Impedance Analysis were conducted pre- and post-administration to measure phenotypic differences. Stool samples of the subjects were collected twice.

METHODS: The statistical analysis was performed for pair designed metagenome data with 11 phenotypic records of the bioelectrical impedance body composition analyzer and 6 responses of the questionnaires about gastrointestinal symptom. Furthemore, correlation-based network analysis was conducted for exploring complex relationships among microbiome communities.

RESULTS: The abundances of Citrobacter, Klebsiella, and Methanobrevibacter were significantly reduced, which are strong candidates to be highly affected by the probiotic administration. In addition, interaction effects were observed between flatulence symptom attenuation and decreasing patterns of the Methanobrevibacter abundance.

CONCLUSIONS: These results reveal that probiotic intervention modulated the composition of gut microbiota and reduced the abundance of potential pathogens (i.e. Citrobacter and Klebsiella). In addition, methanogens (i.e. Methanobrevibacter) associated with the gastrointestinal symptom in an adult human.}, } @article {pmid28936948, year = {2017}, author = {Collins, J and Auchtung, JM}, title = {Control of Clostridium difficile Infection by Defined Microbial Communities.}, journal = {Microbiology spectrum}, volume = {5}, number = {5}, pages = {}, pmid = {28936948}, issn = {2165-0497}, support = {R21 AI121522/AI/NIAID NIH HHS/United States ; R33 AI121522/AI/NIAID NIH HHS/United States ; U01 AI124290/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Clostridioides difficile/genetics/isolation & purification/*physiology ; Clostridium Infections/*microbiology/*therapy ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Gastrointestinal Microbiome ; Humans ; }, abstract = {Each year in the United States, billions of dollars are spent combating almost half a million Clostridium difficile infections (CDIs) and trying to reduce the ∼29,000 patient deaths in which C. difficile has an attributed role. In Europe, disease prevalence varies by country and level of surveillance, though yearly costs are estimated at €3 billion. One factor contributing to the significant health care burden of C. difficile is the relatively high frequency of recurrent CDIs. Recurrent CDI, i.e., a second episode of symptomatic CDI occurring within 8 weeks of successful initial CDI treatment, occurs in ∼25% of patients, with 35 to 65% of these patients experiencing multiple episodes of recurrent disease. Using microbial communities to treat recurrent CDI, either as whole fecal transplants or as defined consortia of bacterial isolates, has shown great success (in the case of fecal transplants) or potential promise (in the case of defined consortia of isolates). This review will briefly summarize the epidemiology and physiology of C. difficile infection, describe our current understanding of how fecal microbiota transplants treat recurrent CDI, and outline potential ways that knowledge can be used to rationally design and test alternative microbe-based therapeutics.}, } @article {pmid28934976, year = {2017}, author = {Quince, C and Delmont, TO and Raguideau, S and Alneberg, J and Darling, AE and Collins, G and Eren, AM}, title = {DESMAN: a new tool for de novo extraction of strains from metagenomes.}, journal = {Genome biology}, volume = {18}, number = {1}, pages = {181}, pmid = {28934976}, issn = {1474-760X}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Genome, Bacterial/genetics ; Haplotypes ; *Metagenome ; Microbiota/genetics ; Polymorphism, Genetic ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain. We validated DESMAN on a complex 50-species 210-genome 96-sample synthetic mock data set and then applied it to the Tara Oceans microbiome.}, } @article {pmid28934964, year = {2017}, author = {McIntyre, ABR and Ounit, R and Afshinnekoo, E and Prill, RJ and Hénaff, E and Alexander, N and Minot, SS and Danko, D and Foox, J and Ahsanuddin, S and Tighe, S and Hasan, NA and Subramanian, P and Moffat, K and Levy, S and Lonardi, S and Greenfield, N and Colwell, RR and Rosen, GL and Mason, CE}, title = {Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.}, journal = {Genome biology}, volume = {18}, number = {1}, pages = {182}, pmid = {28934964}, issn = {1474-760X}, support = {R01 AI125416/AI/NIAID NIH HHS/United States ; R01 ES021006/ES/NIEHS NIH HHS/United States ; R25 EB020393/EB/NIBIB NIH HHS/United States ; }, mesh = {Benchmarking/*methods/standards ; Contig Mapping/*methods/standards ; DNA Barcoding, Taxonomic/*methods/standards ; Humans ; *Metagenome ; Microbiota ; Phylogeny ; Sequence Analysis, DNA/*methods/standards ; *Software ; }, abstract = {BACKGROUND: One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited.

RESULTS: In this study, we use the largest-to-date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of 11 metagenomic classifiers. Tools were characterized on the basis of their ability to identify taxa at the genus, species, and strain levels, quantify relative abundances of taxa, and classify individual reads to the species level. Strikingly, the number of species identified by the 11 tools can differ by over three orders of magnitude on the same datasets. Various strategies can ameliorate taxonomic misclassification, including abundance filtering, ensemble approaches, and tool intersection. Nevertheless, these strategies were often insufficient to completely eliminate false positives from environmental samples, which are especially important where they concern medically relevant species. Overall, pairing tools with different classification strategies (k-mer, alignment, marker) can combine their respective advantages.

CONCLUSIONS: This study provides positive and negative controls, titrated standards, and a guide for selecting tools for metagenomic analyses by comparing ranges of precision, accuracy, and recall. We show that proper experimental design and analysis parameters can reduce false positives, provide greater resolution of species in complex metagenomic samples, and improve the interpretation of results.}, } @article {pmid28934322, year = {2017}, author = {Moussa, TAA and Al-Zahrani, HS and Almaghrabi, OA and Abdelmoneim, TS and Fuller, MP}, title = {Comparative metagenomics approaches to characterize the soil fungal communities of western coastal region, Saudi Arabia.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0185096}, pmid = {28934322}, issn = {1932-6203}, mesh = {Biodiversity ; Classification ; Fungi/*genetics ; *Metagenomics ; Oceans and Seas ; Phylogeny ; Polymerase Chain Reaction ; Saudi Arabia ; Sequence Analysis, DNA ; Soil ; *Soil Microbiology ; }, abstract = {A total of 145007 reads were obtained from pyrosequencing for all the 4 samples. The total count ranged from 11,301,014 (Mecca old road) to 23,503,512 bp (Thuwal). A total of 460 fungal species belonging to 133 genera, 58 families, 33 orders, 13 classes and 4 phyla was identified across the four sites. The most abundant phylum at all four sites was Ascomycota followed by Basidiomycota. Four phyla (Ascomycota-99.31%, Basidiomycota-0.59%, Chytridiomycota-0.04%, Glomeromycota-0.03%) were detected in Khulais. Except for Glomeromycota, all phyla were detected at Mecca old road (Ascomycota-74.26%, Basidiomycota-25.71%, Chytridiomycota-0.01%) and Thuwal (Ascomycota-99.59%, Basidiomycota-0.40%, Chytridiomycota-0.002%); while only Ascomycota-90.98% and Basidiomycota-9.01% were detected in Asfan road. At the class level, Sordariomycetes was predominantly observed at Asfan road-59.88%, Khulais-68.26% and Thuwal-94.84%; while Pezizomycetes was dominant at Mecca old road-56.01%, was absent at Asfan road. Agaricomycetes was present only at Mecca old road-25.73%; while Tremellomycetes-5.77%, Malasseizomycetes-2.13% and Microbotryomycetes-1.10% were found only at Asfan road. The phylogenetic trees revealed that clear genus level differences are visible across all the four sites, with an overall predominance of Thielavia followed by Madurella, Aspergillus, and Gelasinospora. Chaetomium sp., Aspergillus caespitosus and Aspergillus sp. were found in moderate (Mecca old road and Thuwal) to abundant (Asfan road and Khulais) quantities. Thielavia sp., Thielavia hyalocarpa and Madurella sp. are found in moderate quantities at Khulais and Mecca old road, while in abundant levels at Asfan road and Thuwal. Fusarium equisati and F. oxysporum were detected at Thuwal and Khulais. Sordaria araneosa was present at Khulais, while Malasseiza globosa species was detected in moderate quantities across all sites except Khulais.}, } @article {pmid28931073, year = {2017}, author = {Li, O and Xiao, R and Sun, L and Guan, C and Kong, D and Hu, X}, title = {Bacterial and diazotrophic diversities of endophytes in Dendrobium catenatum determined through barcoded pyrosequencing.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184717}, pmid = {28931073}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Dendrobium/*microbiology ; Endophytes/*classification/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Phylogeny ; Plant Roots/*microbiology ; Sequence Analysis, DNA/*methods ; }, abstract = {As an epiphyte orchid, Dendrobium catenatum relies on microorganisms for requisite nutrients. Metagenome pyrosequencing based on 16S rRNA and nifH genes was used to characterize the bacterial and diazotrophic communities associated with D. catenatum collected from 5 districts in China. Based on Meta-16S rRNA sequencing, 22 bacterial phyla and 699 genera were identified, distributed as 125 genera from 8 phyla and 319 genera from 10 phyla shared by all the planting bases and all the tissues, respectively. The predominant Proteobacteria varied from 71.81% (GZ) to 96.08% (YN), and Delftia (10.39-38.42%), Burkholderia (2.71-15.98%), Escherichia/Shigella (4.90-25.12%), Pseudomonas (2.68-30.72%) and Sphingomonas (1.83-2.05%) dominated in four planting bases. Pseudomonas (17.94-22.06%), Escherichia/Shigella (6.59-11.59%), Delftia (9.65-22.14%) and Burkholderia (3.12-11.05%) dominated in all the tissues. According to Meta-nifH sequencing, 4 phyla and 45 genera were identified, while 17 genera and 24 genera from 4 phyla were shared by all the planting bases and all the tissues, respectively. Burkholderia and Bradyrhizobium were the most popular in the planting bases, followed by Methylovirgula and Mesorhizobium. Mesorhizobium was the most popular in different tissues, followed by Beijerinckia, Xanthobacter, and Burkholderia. Among the genera, 39 were completely overlapped with the results based on the 16S rRNA gene. In conclusion, abundant bacteria and diazotrophs were identified in common in different tissues of D. catenatum from five planting bases, which might play a great role in the supply of nutrients such as nitrogen. The exact abundance of phylum and genus on the different tissues from different planting bases need deeper sequencing with more samples.}, } @article {pmid28929212, year = {2018}, author = {Parmar, K and Dafale, N and Pal, R and Tikariha, H and Purohit, H}, title = {An Insight into Phage Diversity at Environmental Habitats using Comparative Metagenomics Approach.}, journal = {Current microbiology}, volume = {75}, number = {2}, pages = {132-141}, pmid = {28929212}, issn = {1432-0991}, mesh = {Bacteriophages/*classification/genetics/*isolation & purification ; *Biodiversity ; *Ecosystem ; Metagenomics ; *Water Microbiology ; }, abstract = {Bacteriophages play significant role in driving microbial diversity; however, little is known about the diversity of phages in different ecosystems. A dynamic predator-prey mechanism called "kill the winner" suggests the elimination of most active bacterial populations through phages. Thus, interaction between phage and host has an effect on the composition of microbial communities in ecosystems. In this study, secondary phage metagenome data from aquatic habitats: wastewater treatment plant (WWTP), fresh, marine, and hot water spring habitat were analyzed using MG-RAST and STAMP tools to explore the diversity of the viruses. Differential relative abundance of phage families-Siphoviridae (34%) and Myoviridae (26%) in WWTP, Myoviridae (30%) and Podoviridae (23%) in fresh water, and Myoviridae (41%) and Podoviridae (8%) in marine-was found to be a discriminating factor among four habitats while Rudiviridae (9%), Globuloviridae (8%), and Lipothrixviridae (1%) were exclusively observed in hot water spring. Subsequently, at genera level, Bpp-1-like virus, Chlorovirus, and T4-like virus were found abundant in WWTP, fresh, and marine habitat, respectively. PCA analysis revealed completely disparate composition of phage in hot water spring from other three ecosystems. Similar analysis of relative abundance of functional features corroborated observations from taxa analysis. Functional features corresponding to phage packaging machinery, replication, integration and excision, and gene transfer discriminated among four habitats. The comparative metagenomics approach exhibited genetically distinct phage communities among four habitats. Results revealed that selective distribution of phage communities would help in understanding the role of phages in food chains, nutrient cycling, and microbial ecology. Study of specific phages would also help in controlling environmental pathogens including MDR bacterial populations using phage therapy approach by selective mining and isolation of phages against specific pathogens persisting in a given environment.}, } @article {pmid28927227, year = {2017}, author = {Cannon, K and Byrne, B and Happe, J and Wu, K and Ward, L and Chesnel, L and Louie, T}, title = {Enteric microbiome profiles during a randomized Phase 2 clinical trial of surotomycin versus vancomycin for the treatment of Clostridium difficile infection.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {12}, pages = {3453-3461}, doi = {10.1093/jac/dkx318}, pmid = {28927227}, issn = {1460-2091}, mesh = {Administration, Oral ; Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/administration & dosage/*adverse effects ; Bacteria/classification/*isolation & purification ; Bacterial Load ; Bacteriological Techniques ; Clostridium Infections/*drug therapy ; Double-Blind Method ; Dysbiosis/*chemically induced ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Lipopeptides/administration & dosage/*adverse effects ; Male ; Metagenomics ; Middle Aged ; Peptides, Cyclic/administration & dosage/*adverse effects ; Real-Time Polymerase Chain Reaction ; Time Factors ; Vancomycin/administration & dosage/*adverse effects ; Young Adult ; }, abstract = {OBJECTIVES: The effects of surotomycin (CB-183,315, MK-4261), a bactericidal cyclic lipopeptide, and vancomycin, the current standard-of-care for Clostridium difficile infection (CDI), on intestinal pathogens and microbiota were evaluated parallel to a Phase 2 randomized, double-blind clinical trial.

METHODS: The single-centre cohort included 26 patients receiving surotomycin [125 or 250 mg twice daily (n = 9 each)] or oral vancomycin [125 mg four times daily (n = 8)] for 10 days. Faecal samples were collected at days 0-42 to quantify both C. difficile by conventional culture and the major components of the microbiome by quantitative PCR.

RESULTS: Surotomycin 250 mg twice daily or vancomycin 125 mg four times daily reduced faecal C. difficile counts from ∼105-107 log10 cfu/g at baseline to ≤ 102 cfu/g by days 4-10 of treatment. Day 10 counts of C. difficile in 3/9 patients receiving surotomycin 125 mg twice daily remained detectable, including one patient who failed to achieve clinical cure. Bacteroidetes and Prevotella mean counts increased 0.7 log10 or remained unchanged with surotomycin 125 and 250 mg twice daily, respectively, whereas vancomycin reduced counts by 2.5-3.2 log10 (P < 0.02). Vancomycin reduced Firmicutes counts by 2.5-2.8 log10; surotomycin moderately suppressed these microbes in a dose-dependent manner.

CONCLUSIONS: In this Phase 2 trial substudy, compared with vancomycin 125 mg four times daily, surotomycin 250 mg twice daily is as active in vivo against C. difficile, but was more sparing of microbiota. Surotomycin is no longer in development due to failed Phase 3 efficacy results.}, } @article {pmid28925579, year = {2018}, author = {In 't Zandt, MH and Beckmann, S and Rijkers, R and Jetten, MSM and Manefield, M and Welte, CU}, title = {Nutrient and acetate amendment leads to acetoclastic methane production and microbial community change in a non-producing Australian coal well.}, journal = {Microbial biotechnology}, volume = {11}, number = {4}, pages = {626-638}, pmid = {28925579}, issn = {1751-7915}, mesh = {Acetates/*metabolism ; Australia ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Coal Mining ; Fungi/classification/genetics/isolation & purification/*metabolism ; Geologic Sediments/analysis/*microbiology ; Metagenome ; Methane/*metabolism ; *Microbiota ; }, abstract = {Coal mining is responsible for 11% of total anthropogenic methane emission thereby contributing considerably to climate change. Attempts to harvest coalbed methane for energy production are challenged by relatively low methane concentrations. In this study, we investigated whether nutrient and acetate amendment of a non-producing sub-bituminous coal well could transform the system to a methane source. We tracked cell counts, methane production, acetate concentration and geochemical parameters for 25 months in one amended and one unamended coal well in Australia. Additionally, the microbial community was analysed with 16S rRNA gene amplicon sequencing at 17 and 25 months after amendment and complemented by metagenome sequencing at 25 months. We found that cell numbers increased rapidly from 3.0 × 10[4] cells ml[-1] to 9.9 × 10[7] in the first 7 months after amendment. However, acetate depletion with concomitant methane production started only after 12-19 months. The microbial community was dominated by complex organic compound degraders (Anaerolineaceae, Rhodocyclaceae and Geobacter spp.), acetoclastic methanogens (Methanothrix spp.) and fungi (Agaricomycetes). Even though the microbial community had the functional potential to convert coal to methane, we observed no indication that coal was actually converted within the time frame of the study. Our results suggest that even though nutrient and acetate amendment stimulated relevant microbial species, it is not a sustainable way to transform non-producing coal wells into bioenergy factories.}, } @article {pmid28924190, year = {2017}, author = {Cornejo-Granados, F and Lopez-Zavala, AA and Gallardo-Becerra, L and Mendoza-Vargas, A and Sánchez, F and Vichido, R and Brieba, LG and Viana, MT and Sotelo-Mundo, RR and Ochoa-Leyva, A}, title = {Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11783}, pmid = {28924190}, issn = {2045-2322}, mesh = {Animals ; *Aquaculture ; *Bacteria/classification/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; Penaeidae/growth & development/*microbiology ; }, abstract = {Crustaceans form the second largest subphylum on Earth, which includes Litopeneaus vannamei (Pacific whiteleg shrimp), one of the most cultured shrimp worldwide. Despite efforts to study the shrimp microbiota, little is known about it from shrimp obtained from the open sea and the role that aquaculture plays in microbiota remodeling. Here, the microbiota from the hepatopancreas and intestine of wild type (wt) and aquacultured whiteleg shrimp and pond sediment from hatcheries were characterized using sequencing of seven hypervariable regions of the 16S rRNA gene. Cultured shrimp with AHPND/EMS disease symptoms were also included. We found that (i) microbiota and their predicted metagenomic functions were different between wt and cultured shrimp; (ii) independent of the shrimp source, the microbiota of the hepatopancreas and intestine was different; (iii) the microbial diversity between the sediment and intestines of cultured shrimp was similar; and (iv) associated to an early development of AHPND/EMS disease, we found changes in the microbiome and the appearance of disease-specific bacteria. Notably, under cultured conditions, we identified bacterial taxa enriched in healthy shrimp, such as Faecalibacterium prausnitzii and Pantoea agglomerans, and communities enriched in diseased shrimp, such as Aeromonas taiwanensis, Simiduia agarivorans and Photobacterium angustum.}, } @article {pmid28923537, year = {2017}, author = {Frankel, AE and Coughlin, LA and Kim, J and Froehlich, TW and Xie, Y and Frenkel, EP and Koh, AY}, title = {Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients.}, journal = {Neoplasia (New York, N.Y.)}, volume = {19}, number = {10}, pages = {848-855}, pmid = {28923537}, issn = {1476-5586}, support = {P30 CA142543/CA/NCI NIH HHS/United States ; R01 CA152301/CA/NCI NIH HHS/United States ; R01 CA172211/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Antineoplastic Agents, Immunological/pharmacology/therapeutic use ; Biomarkers, Tumor ; Chromatography, High Pressure Liquid ; Cluster Analysis ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Melanoma/drug therapy/*etiology/*metabolism/pathology ; *Metabolomics/methods ; *Metagenome ; *Metagenomics/methods ; Middle Aged ; Molecular Targeted Therapy ; Neoplasm Metastasis ; Neoplasm Staging ; Prognosis ; Tandem Mass Spectrometry ; Treatment Outcome ; }, abstract = {This is the first prospective study of the effects of human gut microbiota and metabolites on immune checkpoint inhibitor (ICT) response in metastatic melanoma patients. Whereas many melanoma patients exhibit profound response to ICT, there are fewer options for patients failing ICT-particularly with BRAF-wild-type disease. In preclinical studies, specific gut microbiota promotes regression of melanoma in mice. We therefore conducted a study of the effects of pretreatment gut microbiota and metabolites on ICT Response Evaluation Criteria in Solid Tumors response in 39 metastatic melanoma patients treated with ipilimumab, nivolumab, ipilimumab plus nivolumab (IN), or pembrolizumab (P). IN yielded 67% responses and 8% stable disease; P achieved 23% responses and 23% stable disease. ICT responders for all types of therapies were enriched for Bacteroides caccae. Among IN responders, the gut microbiome was enriched for Faecalibacterium prausnitzii, Bacteroides thetaiotamicron, and Holdemania filiformis. Among P responders, the microbiome was enriched for Dorea formicogenerans. Unbiased shotgun metabolomics revealed high levels of anacardic acid in ICT responders. Based on these pilot studies, both additional confirmatory clinical studies and preclinical testing of these bacterial species and metabolites are warranted to confirm their ICT enhancing activity.}, } @article {pmid28917117, year = {2017}, author = {Jing, Y and Campanaro, S and Kougias, P and Treu, L and Angelidaki, I and Zhang, S and Luo, G}, title = {Anaerobic granular sludge for simultaneous biomethanation of synthetic wastewater and CO with focus on the identification of CO-converting microorganisms.}, journal = {Water research}, volume = {126}, number = {}, pages = {19-28}, doi = {10.1016/j.watres.2017.09.018}, pmid = {28917117}, issn = {1879-2448}, mesh = {Anaerobiosis ; Bioreactors/*microbiology ; Carbon Monoxide/*metabolism ; Metagenome ; Methane/*metabolism ; Microbial Consortia/genetics/*physiology ; Sewage ; Waste Disposal, Fluid/instrumentation/methods ; Wastewater/*chemistry ; }, abstract = {CO is a main component of syngas, which can be produced from the gasification of organic wastes and biomass. CO can be converted to methane by anaerobic digestion (AD), however, it is still challenging due to its toxicity to microorganisms and limited knowledge about CO converting microorganisms. In the present study, anaerobic granular sludge (AGS) was used for the simultaneous biomethanation of wastewater and CO. Batch experiments showed that AGS tolerated CO partial pressure as high as 0.5 atm without affecting its ability for synthetic wastewater degradation, which had higher tolerance of CO compared to suspended sludge (less than 0.25 atm) as previously reported. Continuous experiments in upflow anaerobic sludge blanket (UASB) reactors showed AGS could efficiently convert synthetic wastewater and CO into methane by applying gas-recirculation. The addition of CO to UASB reactor enhanced the hydrogenotrophic CO-oxidizing pathway, resulted in the increase of extracellular polymeric substances, changed the morphology of AGS and significantly altered the microbial community compositions of AGS. The microbial species relating with CO conversion and their functions were revealed by metagenomic analysis. It showed that 23 of the 70 reconstructed genome bins (GBs), most of which were not previously characterized at genomic level, were enriched and contained genes involved in CO conversion upon CO addition. CO-converting microorganisms might be taxonomically more diverse than previously known and have multi-functions in the AD process. The reductive tricarboxylic acid (TCA) cycle in combination with the oxidation of the CO was probably crucial for CO utilization by the majority of the GBs in the present study.}, } @article {pmid28915922, year = {2017}, author = {Winglee, K and Howard, AG and Sha, W and Gharaibeh, RZ and Liu, J and Jin, D and Fodor, AA and Gordon-Larsen, P}, title = {Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {121}, pmid = {28915922}, issn = {2049-2618}, support = {R01 DK104371/DK/NIDDK NIH HHS/United States ; R01 HL108427/HL/NHLBI NIH HHS/United States ; R24 HD050924/HD/NICHD NIH HHS/United States ; UL1 TR001111/TR/NCATS NIH HHS/United States ; P30 ES010126/ES/NIEHS NIH HHS/United States ; }, mesh = {Aged ; Bacteria/*genetics/pathogenicity ; China ; *Diet, Western ; Drug Resistance, Microbial/*genetics ; Escherichia coli/genetics/pathogenicity ; Feeding Behavior ; Female ; *Gastrointestinal Microbiome/genetics ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metabolome ; Metagenomics ; Middle Aged ; Shigella/genetics/pathogenicity ; *Urbanization ; Virulence/genetics ; }, abstract = {BACKGROUND: Urbanization is associated with an increased risk for a number of diseases, including obesity, diabetes, and cancer, which all also show associations with the microbiome. While microbial community composition has been shown to vary across continents and in traditional versus Westernized societies, few studies have examined urban-rural differences in neighboring communities within a single country undergoing rapid urbanization. In this study, we compared the gut microbiome, plasma metabolome, dietary habits, and health biomarkers of rural and urban people from a single Chinese province.

RESULTS: We identified significant differences in the microbiota and microbiota-related plasma metabolites in rural versus recently urban subjects from the Hunan province of China. Microbes with higher relative abundance in Chinese urban samples have been associated with disease in other studies and were substantially more prevalent in the Human Microbiome Project cohort of American subjects. Furthermore, using whole metagenome sequencing, we found that urbanization was associated with a loss of microbial diversity and changes in the relative abundances of Viruses, Archaea, and Bacteria. Gene diversity, however, increased with urbanization, along with the proportion of reads associated with antibiotic resistance and virulence, which were strongly correlated with the presence of Escherichia and Shigella.

CONCLUSIONS: Our data suggest that urbanization has produced convergent evolution of the gut microbial composition in American and urban Chinese populations, resulting in similar compositional patterns of abundant microbes through similar lifestyles on different continents, including a loss of potentially beneficial bacteria and an increase in potentially harmful genes via increased relative abundance of Escherichia and Shigella.}, } @article {pmid28912589, year = {2017}, author = {Naghoni, A and Emtiazi, G and Amoozegar, MA and Cretoiu, MS and Stal, LJ and Etemadifar, Z and Shahzadeh Fazeli, SA and Bolhuis, H}, title = {Microbial diversity in the hypersaline Lake Meyghan, Iran.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11522}, pmid = {28912589}, issn = {2045-2322}, mesh = {Archaea/*classification/genetics/growth & development ; Bacteria/*classification/genetics/growth & development ; *Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Iran ; Lakes/chemistry/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Saline Waters ; Sequence Analysis, DNA ; }, abstract = {Lake Meyghan is one of the largest and commercially most important salt lakes in Iran. Despite its inland location and high altitude, Lake Meyghan has a thalassohaline salt composition suggesting a marine origin. Inputs of fresh water by rivers and rainfall formed various basins characterized by different salinities. We analyzed the microbial community composition of three basins by isolation and culturing of microorganisms and by analysis of the metagenome. The basins that were investigated comprised a green ~50 g kg[-1] salinity brine, a red ~180 g kg[-1] salinity brine and a white ~300 g kg[-1] salinity brine. Using different growth media, 57 strains of Bacteria and 48 strains of Archaea were isolated. Two bacterial isolates represent potential novel species with less than 96% 16S rRNA gene sequence identity to known species. Abundant isolates were also well represented in the metagenome. Bacteria dominated the low salinity brine, with Alteromonadales (Gammaproteobacteria) as a particularly important taxon, whereas the high salinity brines were dominated by haloarchaea. Although the brines of Lake Meyghan differ in geochemical composition, their ecosystem function appears largely conserved amongst each other while being driven by different microbial communities.}, } @article {pmid28912574, year = {2017}, author = {Purcell, RV and Visnovska, M and Biggs, PJ and Schmeier, S and Frizelle, FA}, title = {Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11590}, pmid = {28912574}, issn = {2045-2322}, mesh = {Adult ; Aged ; Aged, 80 and over ; *Biomarkers, Tumor ; Colorectal Neoplasms/*etiology/metabolism/*pathology ; Computational Biology ; Female ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Humans ; Male ; Metagenome ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Transcriptome ; }, abstract = {Colorectal cancer (CRC) is a heterogeneous disease and recent advances in subtype classification have successfully stratified the disease using molecular profiling. The contribution of bacterial species to CRC development is increasingly acknowledged, and here, we sought to analyse CRC microbiomes and relate them to tumour consensus molecular subtypes (CMS), in order to better understand the relationship between bacterial species and the molecular mechanisms associated with CRC subtypes. We classified 34 tumours into CRC subtypes using RNA-sequencing derived gene expression and determined relative abundances of bacterial taxonomic groups using 16S rRNA amplicon metabarcoding. 16S rRNA analysis showed enrichment of Fusobacteria and Bacteroidetes, and decreased levels of Firmicutes and Proteobacteria in CMS1. A more detailed analysis of bacterial taxa using non-human RNA-sequencing reads uncovered distinct bacterial communities associated with each molecular subtype. The most highly enriched species associated with CMS1 included Fusobacterium hwasookii and Porphyromonas gingivalis. CMS2 was enriched for Selenomas and Prevotella species, while CMS3 had few significant associations. Targeted quantitative PCR validated these findings and also showed an enrichment of Fusobacterium nucleatum, Parvimonas micra and Peptostreptococcus stomatis in CMS1. In this study, we have successfully associated individual bacterial species to CRC subtypes for the first time.}, } @article {pmid28910638, year = {2017}, author = {Verster, AJ and Ross, BD and Radey, MC and Bao, Y and Goodman, AL and Mougous, JD and Borenstein, E}, title = {The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals Its Role in Community Composition.}, journal = {Cell host & microbe}, volume = {22}, number = {3}, pages = {411-419.e4}, pmid = {28910638}, issn = {1934-6069}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; R35 GM118159/GM/NIGMS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; R01 AI080609/AI/NIAID NIH HHS/United States ; /HHMI_/Howard Hughes Medical Institute/United States ; }, mesh = {Adolescent ; Adult ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Bacteroides/classification/genetics/isolation & purification/metabolism ; Biodiversity ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; Middle Aged ; Phylogeny ; Type VI Secretion Systems/genetics/*metabolism ; Young Adult ; }, abstract = {Although gut microbiome composition is well defined, the mechanisms underlying community assembly remain poorly understood. Bacteroidales possess three genetic architectures (GA1-3) of the type VI secretion system (T6SS), an effector delivery pathway that mediates interbacterial competition. Here we define the distribution and role of GA1-3 in the human gut using metagenomic analysis. We find that adult microbiomes harbor limited effector and cognate immunity genes, suggesting selection for compatibility at the species (GA1 and GA2) and strain (GA3) levels. Bacteroides fragilis GA3 is known to mediate potent inter-strain competition, and we observe GA3 enrichment among strains colonizing infant microbiomes, suggesting competition early in life. Additionally, GA3 is associated with increased Bacteroides abundance, indicating that this system confers an advantage in Bacteroides-rich ecosystems. Collectively, these analyses uncover the prevalence of T6SS-dependent competition and reveal its potential role in shaping human gut microbial composition.}, } @article {pmid28904330, year = {2017}, author = {Xu, K and Jiang, B}, title = {Analysis of Mucosa-Associated Microbiota in Colorectal Cancer.}, journal = {Medical science monitor : international medical journal of experimental and clinical research}, volume = {23}, number = {}, pages = {4422-4430}, pmid = {28904330}, issn = {1643-3750}, mesh = {Adenocarcinoma/pathology ; Adenoma/pathology ; Adult ; Bacteria ; Biomarkers ; Case-Control Studies ; Colon/pathology ; Colonic Neoplasms/pathology ; Colorectal Neoplasms/*microbiology/*pathology ; Escherichia coli ; Female ; Humans ; Intestinal Mucosa/*microbiology/pathology ; Male ; Microbiota/physiology ; Middle Aged ; RNA, Ribosomal, 16S/analysis ; }, abstract = {BACKGROUND The aim of this study was to compare the microbiota community structure, assess differences in intestinal bacterial types, and identify metagenomic biomarkers for disparate stages of colorectal cancer formation. MATERIAL AND METHODS A total of 160 individuals were recruited: 61 cases with non-tumor colon were regarded as the normal group, 47 cases with histology-substantiated colorectal adenomas were regarded as the adenoma group, and 52 cases with invasive adenocarcinomas were regarded as the cancer group. Biopsy on the mucosa was performed on each subject. USEARCH was used to process the sequences data and generate OTUs. Gut mucosal microbiota from healthy controls, adenoma patients, and carcinoma patients were analyzed. RESULTS Principal coordinate analysis of unweighted and weighted UniFrac distance showed a separation in composition of microbiota in the 3 groups. Bacteria with potential tumorigenesis, like Bacteroides fragilis and Fusobacterium, were more common in the carcinoma group, while some SCFA (short chain fatty acids) - producing microbes were enriched in the normal group. The commensal Escherichia were more abundant in adenoma patients. CONCLUSIONS Our study provides insights into possible function of gut microbiota in diagnosis and treatment of colorectal cancer. Some bacteria, such as Butyricicoccus, E. coli, and Fusobacterium, can be used as potential biomarkers for normal, adenoma, and cancer groups, respectively.}, } @article {pmid28904137, year = {2017}, author = {Wu, Q and Wang, X and Ding, Y and Hu, Y and Nie, Y and Wei, W and Ma, S and Yan, L and Zhu, L and Wei, F}, title = {Seasonal variation in nutrient utilization shapes gut microbiome structure and function in wild giant pandas.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1862}, pages = {}, pmid = {28904137}, issn = {1471-2954}, mesh = {Animals ; Diet/*veterinary ; Food ; *Gastrointestinal Microbiome ; Metagenomics ; Plant Leaves ; Plant Shoots ; *Seasons ; Ursidae/*microbiology ; }, abstract = {Wild giant pandas use different parts of bamboo (shoots, leaves and stems) and different bamboo species at different times of the year. Their usage of bamboo can be classified temporally into a distinct leaf stage, shoot stage and transition stage. An association between this usage pattern and variation in the giant panda gut microbiome remains unknown. Here, we found associations using a gut metagenomic approach and nutritional analyses whereby diversity of the gut microbial community in the leaf and shoot stages was significantly different. Functional metagenomic analysis showed that in the leaf stage, bacteria species over-represented genes involved in raw fibre utilization and cell cycle control. Thus, raw fibre utilization by the gut microbiome was guaranteed during the nutrient-deficient leaf stage by reinforcing gut microbiome robustness. During the protein-abundant shoot stage, the functional capacity of the gut microbiome expanded to include prokaryotic secretion and signal transduction activity, suggesting active interactions between the gut microbiome and host. These results illustrate that seasonal nutrient variation in wild giant pandas substantially influences gut microbiome composition and function. Nutritional interactions between gut microbiomes and hosts appear to be complex and further work is needed.}, } @article {pmid28903464, year = {2017}, author = {Bonatelli, ML and Quecine, MC and Silva, MS and Labate, CA}, title = {Characterization of the contaminant bacterial communities in sugarcane first-generation industrial ethanol production.}, journal = {FEMS microbiology letters}, volume = {364}, number = {17}, pages = {}, doi = {10.1093/femsle/fnx159}, pmid = {28903464}, issn = {1574-6968}, mesh = {Acetobacter/genetics/isolation & purification ; Bacteria/*genetics/isolation & purification/metabolism ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ethanol/*metabolism ; Fermentation ; Industrial Microbiology ; Lactobacillus/genetics/isolation & purification ; Microbial Consortia/*genetics/physiology ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Saccharum/*microbiology ; Weissella/genetics/isolation & purification ; }, abstract = {The industrial ethanolic fermentation process is operated in distilleries, either in fed-batch or continuous mode. A consequence of the large industrial ethanol production is bacterial contamination in the fermentation tanks, which is responsible for significant economic losses. To investigate this community, we accessed the profile of bacterial contaminant from two distilleries in Brazil, each operating a different fermentation mode, throughout sugarcane harvest of 2013-2014. Bacterial communities were accessed through Illumina culture-independent 16S rDNA gene sequencing, and qPCR was used to quantify total bacteria abundance. Both ethanol production modes showed similar bacterial abundance, around 105 gene copies/mL. 16S rDNA sequencing showed that 92%-99% of the sequences affiliated to Lactobacillus genus. Operational taxonomic units differently represented belonged mainly to Lactobacillus, but also to Weissella, Pediococcus, Acetobacter and Anaeosporobacter, although in lower abundance. Alpha-diversity only showed a correlation through the fermentation tanks in continuous mode, where it was always higher in the second and third tanks. Beta-diversity clearly separated the two distilleries and metagenome prediction reinforces clusterization within distilleries. Despite certain variations between bacterial community in the distilleries throughout harvest season, Lactobacillus were the main genera reported in both distilleries and bacterial community seemed to persist along time, suggesting bacterial reinfestation.}, } @article {pmid28900280, year = {2017}, author = {Zhang, J and Mao, L and Zhang, L and Loh, KC and Dai, Y and Tong, YW}, title = {Metagenomic insight into the microbial networks and metabolic mechanism in anaerobic digesters for food waste by incorporating activated carbon.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11293}, pmid = {28900280}, issn = {2045-2322}, mesh = {*Anaerobiosis ; Computational Biology/methods ; *Energy Metabolism ; Fermentation ; Food ; Metabolic Networks and Pathways ; *Metagenome ; *Metagenomics/methods ; Methane/biosynthesis ; *Microbiota ; Waste Disposal, Fluid ; }, abstract = {Powdered activated carbon (AC) is commonly used as an effective additive to enhance anaerobic digestion (AD), but little is known about how the metabolic pathways resulting from adding AC change the microbial association network and enhance food waste treatment. In this work, the use of AC in an anaerobic digestion system for food waste was explored. Using bioinformatics analysis, taxonomic trees and the KEGG pathway analysis, changes in microbial network and biometabolic pathways were tracked. The overall effect of these changes were used to explain and validate improved digestion performance. The results showed that AC accelerated the decomposition of edible oil in food waste, enhancing the conversion of food waste to methane with the optimized dosage of 12 g AC per reactor. Specifically, when AC was added, the proponoate metabolic pathway that converts propanoic acid to acetic acid became more prominent, as measured by 16S rRNA in the microbial community. The other two metabolic pathways, Lipid Metabolism and Methane Metabolism, were also enhanced. Bioinformatics analysis revealed that AC promoted the proliferation of syntrophic microorganisms such as Methanosaeta and Geobacter, forming a highly intensive syntrophic microbial network.}, } @article {pmid28900257, year = {2017}, author = {Potter, C and Freeman, C and Golyshin, PN and Ackermann, G and Fenner, N and McDonald, JE and Ehbair, A and Jones, TG and Murphy, LM and Creer, S}, title = {Subtle shifts in microbial communities occur alongside the release of carbon induced by drought and rewetting in contrasting peatland ecosystems.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11314}, pmid = {28900257}, issn = {2045-2322}, support = {BB/M029085/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biodiversity ; Carbon/*metabolism ; *Droughts ; *Ecosystem ; Environment ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Peat represents a globally significant pool of sequestered carbon. However, peatland carbon stocks are highly threatened by anthropogenic climate change, including drought, which leads to a large release of carbon dioxide. Although the enzymatic mechanisms underlying drought-driven carbon release are well documented, the effect of drought on peatland microbial communities has been little studied. Here, we carried out a replicated and controlled drought manipulation using intact peat 'mesocosm cores' taken from bog and fen habitats, and used a combination of community fingerprinting and sequencing of marker genes to identify community changes associated with drought. Community composition varied with habitat and depth. Moreover, community differences between mesocosm cores were stronger than the effect of the drought treatment, emphasising the importance of replication in microbial marker gene studies. While the effect of drought on the overall composition of prokaryotic and eukaryotic communities was weak, a subset of the microbial community did change in relative abundance, especially in the fen habitat at 5 cm depth. 'Drought-responsive' OTUs were disproportionately drawn from the phyla Bacteroidetes and Proteobacteria. Collectively, the data provide insights into the microbial community changes occurring alongside drought-driven carbon release from peatlands, and suggest a number of novel avenues for future research.}, } @article {pmid28900198, year = {2017}, author = {Wu, X and Zhang, H and Chen, J and Shang, S and Yan, J and Chen, Y and Tang, X and Zhang, H}, title = {Analysis and comparison of the wolf microbiome under different environmental factors using three different data of Next Generation Sequencing.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11332}, pmid = {28900198}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Computational Biology/methods ; Dogs ; *Environment ; Feces/microbiology ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; *Wolves ; }, abstract = {Next Generation Sequencing has been widely used to characterize the prevalence of fecal bacteria in many different species. In this study, we attempted to employ a low-cost and high-throughput sequencing model to discern information pertaining to the wolf microbiota. It is hoped that this model will allow researchers to elucidate potential protective factors in relation to endangered wolf species. We propose three high-throughput sequencing models to reveal information pertaining to the micro-ecology of the wolf. Our analyses advised that, among the three models, more than 100,000 sequences are more appropriate to retrieve the communities' richness and diversity of micro-ecology. In addition, the top five wolf microbiome OTUs (99%) were members of the following five phyla: Bacteroidetes, Fusobacteria, Firmicutes, Proteobacteria, and Actinobacteria. While Alloprevotella, Clostridium_sensu_stricto_1, Anaerobiospirillum, Faecalibactreium and Streptococcus were shared by all samples, their relative abundances were differentially represented between domestic dogs and other wolves. Our findings suggest that altitude, human interference, age, and climate all contribute towards the micro-ecology of the wolf. Specifically, we observed that genera Succinivibrio and Turicibacter are significantly related to altitude and human interference (including hunting practices).}, } @article {pmid28899105, year = {2017}, author = {Williams, B and Ghosh, M and Boucher, CAB and Bushman, F and Carrington-Lawrence, S and Collman, RG and Dandekar, S and Dang, Q and Malaspina, A and Paredes, R and Wilson, CC and Nowak, P and Klatt, NR and Lagenaur, L and Landay, AL}, title = {A Summary of the Second Annual HIV Microbiome Workshop.}, journal = {AIDS research and human retroviruses}, volume = {33}, number = {12}, pages = {1258-1264}, pmid = {28899105}, issn = {1931-8405}, support = {P51 OD010425/OD/NIH HHS/United States ; }, mesh = {Bacteria/classification/*isolation & purification ; Fungi/classification/*isolation & purification ; HIV Infections/*pathology/*transmission/virology ; Humans ; Microbial Interactions/*physiology ; Microbiota/*physiology ; Symbiosis/physiology ; }, abstract = {Commensal organisms appear to play significant roles in normal homeostasis as well as in the pathogenesis of HIV infection in a number of different organ systems. On November 17th and 18th, 2016, leading researchers from around the world met to discuss their insights on advances in our understanding of HIV and the microbiome at the National Institutes of Health (NIH) in Bethesda. Dr. Elhanan Borenstein of the University of Washington gave a keynote address where he discussed new developments in systems biology which hold the promise of illuminating the pathways by which these organisms interact with human physiology. He suggested that we need to get past correlations in microbiome research by using models and informatics which incorporate metagenomics to predict functional changes in the microbiome.}, } @article {pmid28898777, year = {2017}, author = {Liu, P and Jia, S and He, X and Zhang, X and Ye, L}, title = {Different impacts of manure and chemical fertilizers on bacterial community structure and antibiotic resistance genes in arable soils.}, journal = {Chemosphere}, volume = {188}, number = {}, pages = {455-464}, doi = {10.1016/j.chemosphere.2017.08.162}, pmid = {28898777}, issn = {1879-1298}, mesh = {Agriculture/methods ; China ; Drug Resistance, Microbial/*genetics ; *Fertilizers ; Genes, Bacterial ; High-Throughput Screening Assays ; *Manure ; Metagenomics ; Microbiota/*drug effects/genetics ; Soil/*chemistry ; Soil Microbiology/*standards ; }, abstract = {Both manure and chemical fertilizers are widely used in modern agriculture. However, the impacts of different fertilizers on bacterial community structure and antibiotic resistance genes (ARGs) in arable soils still remain unclear. In this study, high-throughput sequencing and quantitative PCR were employed to investigate the bacterial community structure, ARGs and mobile genetic elements (MGEs) influenced by the application of different fertilizers, including chemical fertilizers, piggery manure and straw ash. The results showed that the application of fertilizers could significantly change the soil bacterial community and the abundance of Gaiella under phylum Actinobacteria was significantly reduced from 12.9% in unfertilized soil to 4.1%-7.4% in fertilized soil (P < 0.05). It was also found that the application of manure could cause a transient effect on soil resistome composition and the relative abundance of ARGs increased from 7.37 ppm to 32.10 ppm. The abundance of aminoglycoside, sulfonamide and tetracycline resistance genes greatly increased after manure fertilization and then gradually returned to normal levels with the decay of some intestinal bacteria carrying ARGs. In contrast, the application of chemical fertilizers and straw ash significantly changed the bacterial community structure but exerted little effect on soil resistome. Overall, the results of this study illustrated the different effects of different fertilizers on the soil resistome and revealed that the changes of soil resistome induced by manure application mainly resulted from alteration of bacteria community rather than the horizontal gene transfer.}, } @article {pmid28898292, year = {2017}, author = {Elderman, M and Sovran, B and Hugenholtz, F and Graversen, K and Huijskes, M and Houtsma, E and Belzer, C and Boekschoten, M and de Vos, P and Dekker, J and Wells, J and Faas, M}, title = {The effect of age on the intestinal mucus thickness, microbiota composition and immunity in relation to sex in mice.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184274}, pmid = {28898292}, issn = {1932-6203}, mesh = {Age Factors ; Aging/immunology/metabolism ; Animals ; Biodiversity ; Cell Differentiation/genetics/immunology ; Colon/cytology/immunology/metabolism/microbiology ; Dendritic Cells/cytology/immunology/metabolism ; Female ; Gastrointestinal Microbiome/*immunology ; Gene Expression Profiling ; Gene Expression Regulation ; *Immunity, Mucosal ; Intestinal Mucosa/*cytology/*immunology/metabolism ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Mucus/metabolism ; Peyer's Patches/immunology/metabolism ; Sex Factors ; Signal Transduction ; Spleen/immunology/metabolism ; T-Lymphocytes/cytology/metabolism ; Transcriptome ; }, abstract = {A mucus layer covers and protects the intestinal epithelial cells from direct contact with microbes. This mucus layer not only prevents inflammation but also plays an essential role in microbiota colonization, indicating the complex interplay between mucus composition-microbiota and intestinal health. However, it is unknown whether the mucus layer is influenced by age or sex and whether this contributes to reported differences in intestinal diseases in males and females or with ageing. Therefore, in this study we investigated the effect of age on mucus thickness, intestinal microbiota composition and immune composition in relation to sex. The ageing induced shrinkage of the colonic mucus layer was associated with bacterial penetration and direct contact of bacteria with the epithelium in both sexes. Additionally, several genes involved in the biosynthesis of mucus were downregulated in old mice, especially in males, and this was accompanied by a decrease in abundances of various Lactobacillus species and unclassified Clostridiales type IV and XIV and increase in abundance of the potential pathobiont Bacteroides vulgatus. The changes in mucus and microbiota in old mice were associated with enhanced activation of the immune system as illustrated by a higher percentage of effector T cells in old mice. Our data contribute to a better understanding of the interplay between mucus-microbiota-and immune responses and ultimately may lead to more tailored design of strategies to modulate mucus production in targeted groups.}, } @article {pmid28898207, year = {2017}, author = {Quince, C and Walker, AW and Simpson, JT and Loman, NJ and Segata, N}, title = {Shotgun metagenomics, from sampling to analysis.}, journal = {Nature biotechnology}, volume = {35}, number = {9}, pages = {833-844}, pmid = {28898207}, issn = {1546-1696}, support = {BB/L027801/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; MR/M501621/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Biomedical Research ; *High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; *Microbiota/genetics/physiology ; }, abstract = {Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes have crucial roles in the environment and in human health. However, microbes are frequently difficult to culture in the laboratory, which can confound cataloging of members and understanding of how communities function. High-throughput sequencing technologies and a suite of computational pipelines have been combined into shotgun metagenomics methods that have transformed microbiology. Still, computational approaches to overcome the challenges that affect both assembly-based and mapping-based metagenomic profiling, particularly of high-complexity samples or environments containing organisms with limited similarity to sequenced genomes, are needed. Understanding the functions and characterizing specific strains of these communities offers biotechnological promise in therapeutic discovery and innovative ways to synthesize products using microbial factories and can pinpoint the contributions of microorganisms to planetary, animal and human health.}, } @article {pmid28894921, year = {2017}, author = {Luo, J and Tao, Q and Wu, K and Li, J and Qian, J and Liang, Y and Yang, X and Li, T}, title = {Structural and functional variability in root-associated bacterial microbiomes of Cd/Zn hyperaccumulator Sedum alfredii.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {21}, pages = {7961-7976}, doi = {10.1007/s00253-017-8469-0}, pmid = {28894921}, issn = {1432-0614}, mesh = {Calcium/metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Microbiota ; Phylogeny ; Plant Roots/metabolism/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sedum/metabolism/*microbiology ; Sequence Analysis, DNA ; Soil Microbiology ; Spatial Analysis ; Zinc/metabolism ; }, abstract = {Interactions between roots and microbes affect plant's resistance to abiotic stress. However, the structural and functional variation of root-associated microbiomes and their effects on metal accumulation in hyperaccumulators remain poorly understood. Here, we characterize the root-associated microbiota of a hyperaccumulating (HP) and a non-hyperaccumulating (NHP) genotype of Sedum alfredii by 16S ribosomal RNA gene profiling. We show that distinct microbiomes are observed in four spatially separable compartments: the bulk soil, rhizosphere, rhizoplane, and endosphere. Both the rhizosphere and rhizoplane were preferentially colonized by Proteobacteria, and the endosphere by Actinobacteria. The rhizosphere and endophytic microbiomes were dominated by the family of Sphingomonadaceae and Streptomycetaceae, respectively, which benefited for their survival and adaptation. The bacterial α-diversity decreases along the spatial gradient from the rhizosphere to the endosphere. Soil type and compartment were strongest determinants of root-associated community variation, and host genotype explained a small, but significant amount of variation. The enrichment of Bacteroidetes and depletion of Firmicutes and Planctomycetes in the HP endosphere compared with that of the NHP genotype may affect metal hyperaccumulation. Program PICRUSt predicted moderate functional differences in bacterial consortia across rhizocompartments and soil types. The functional categories involved in membrane transporters (specifically ATP-binding cassette transporters) and energy metabolism were overrepresented in endosphere of HP in comparison with NHP genotypes. Taken together, our study reveals substantial variation in structure and function of microbiomes colonizing different compartments, with the endophytic microbiota potentially playing an important role in heavy metal hyperaccumulation.}, } @article {pmid28894273, year = {2017}, author = {Chen, L and Feng, Q and Li, C and Wei, Y and Zhao, Y and Feng, Y and Zheng, H and Li, F and Li, H}, title = {Impacts of aquaculture wastewater irrigation on soil microbial functional diversity and community structure in arid regions.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11193}, pmid = {28894273}, issn = {2045-2322}, mesh = {Agricultural Irrigation/*methods ; *Aquaculture ; Bacteria/*classification/genetics/*isolation & purification ; Bacterial Typing Techniques ; *Biota ; Desert Climate ; Metagenomics ; Soil/chemistry ; *Soil Microbiology ; *Wastewater ; }, abstract = {Aquaculture wastewater is one of the most important alternative water resources in arid regions where scarcity of fresh water is common. Irrigation with this kind of water may affect soil microbial functional diversity and community structure as changes of soil environment would be significant. Here, we conducted a field sampling to investigate these effects using Biolog and metagenomic methods. The results demonstrated that irrigation with aquaculture wastewater could dramatically reduce soil microbial functional diversity. The values of diversity indices and sole carbon source utilization were all significantly decreased. Increased soil salinity, especially Cl concentration, appeared primarily associated with the decreases. Differently, higher bacterial community diversity was obtained in aquaculture wastewater irrigated soils. More abundant phyla Actinobacteria, Chloroflexi, Acidobacteria, Gemmatimonadetes and fewer members of Proteobacteria, Bacteroidetes and Planctomycetes were found in this kind of soils. Changes in the concentration of soil Cl mainly accounted for the shifts of bacterial community composition. This research can improve our understanding of how aquaculture wastewater irrigation changes soil microbial process and as a result, be useful to manage soil and wastewater resources in arid regions.}, } @article {pmid28894183, year = {2017}, author = {Ticinesi, A and Milani, C and Lauretani, F and Nouvenne, A and Mancabelli, L and Lugli, GA and Turroni, F and Duranti, S and Mangifesta, M and Viappiani, A and Ferrario, C and Maggio, M and Ventura, M and Meschi, T}, title = {Gut microbiota composition is associated with polypharmacy in elderly hospitalized patients.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11102}, pmid = {28894183}, issn = {2045-2322}, mesh = {Aged ; Aged, 80 and over ; Biodiversity ; Biological Variation, Population ; Comorbidity ; Female ; Gastrointestinal Microbiome/*drug effects ; *Hospitalization ; Humans ; Male ; Metagenome ; Metagenomics ; Patient Outcome Assessment ; Phenotype ; *Polypharmacy ; RNA, Ribosomal, 16S ; Survival Analysis ; Symptom Assessment ; }, abstract = {Reduced biodiversity and increased representation of opportunistic pathogens are typical features of gut microbiota composition in aging. Few studies have investigated their correlation with polypharmacy, multimorbidity and frailty. To assess it, we analyzed the fecal microbiota from 76 inpatients, aged 83 ± 8. Microbiome biodiversity (Chao1 index) and relative abundance of individual bacterial taxa were determined by next-generation 16S rRNA microbial profiling. Their correlation with number of drugs, and indexes of multimorbidity and frailty were verified using multivariate linear regression models. The impact of gut microbiota biodiversity on mortality, rehospitalizations and incident sepsis was also assessed after a 2-year follow-up, using Cox regression analysis. We found a significant negative correlation between the number of drugs and Chao1 Index at multivariate analysis. The number of drugs was associated with the average relative abundance of 15 taxa. The drug classes exhibiting the strongest association with single taxa abundance were proton pump inhibitors, antidepressants and antipsychotics. Conversely, frailty and multimorbidity were not significantly associated with gut microbiota biodiversity. Very low Chao1 index was also a significant predictor of mortality, but not of rehospitalizations and sepsis, at follow-up. In aging, polypharmacy may thus represent a determinant of gut microbiota composition, with detrimental clinical consequences.}, } @article {pmid28894161, year = {2017}, author = {Parnell, LA and Briggs, CM and Cao, B and Delannoy-Bruno, O and Schrieffer, AE and Mysorekar, IU}, title = {Microbial communities in placentas from term normal pregnancy exhibit spatially variable profiles.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11200}, pmid = {28894161}, issn = {2045-2322}, support = {T32 GM007067/GM/NIGMS NIH HHS/United States ; T32 HL130357/HL/NHLBI NIH HHS/United States ; UL1 TR000448/TR/NCATS NIH HHS/United States ; UL1 TR002345/TR/NCATS NIH HHS/United States ; }, mesh = {Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Female ; Humans ; *Metagenomics ; *Microbiota ; Phylogeny ; Placenta/*microbiology ; Polymerase Chain Reaction ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spatial Analysis ; }, abstract = {The placenta is the principal organ nurturing the fetus during pregnancy and was traditionally considered to be sterile. Recent work has suggested that the placenta harbours microbial communities, however the location and possible function of these microbes remain to be confirmed and elucidated. Here, we employed genomic DNA sequencing of multiple variable (V) regions of the bacterial 16S ribosomal gene, to interrogate microbial profiles in term pregnancies, from the basal plate, which is in direct contact with maternal uterine, endothelial, and immune cells; placental villi, which are bathed in maternal blood, and fetal membranes, which encapsulate the amniotic cavity. QIIME, R package "Phyloseq" analysis was used to assess alpha and beta diversity and absolute abundance of the 16S rRNA gene per location. We demonstrate that (1) microbiota exhibit spatially distinct profiles depending on the location within the placenta and (2) "semi-composite" 16S profiles using multiple V regions validated by quantitative PCR analysis confirmed that distinct bacterial taxa dominate in different placental niches. Finally, profiles are not altered by mode of delivery. Together these findings suggest that there is niche-specificity to the placental microbiota and placental microbiome studies should consider regional differences, which may affect maternal, fetal, and/or neonatal health and physiology.}, } @article {pmid28893994, year = {2017}, author = {Berer, K and Gerdes, LA and Cekanaviciute, E and Jia, X and Xiao, L and Xia, Z and Liu, C and Klotz, L and Stauffer, U and Baranzini, SE and Kümpfel, T and Hohlfeld, R and Krishnamoorthy, G and Wekerle, H}, title = {Gut microbiota from multiple sclerosis patients enables spontaneous autoimmune encephalomyelitis in mice.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {40}, pages = {10719-10724}, pmid = {28893994}, issn = {1091-6490}, support = {K12 GM081266/GM/NIGMS NIH HHS/United States ; R25 NS070680/NS/NINDS NIH HHS/United States ; }, mesh = {Adult ; Aged ; Animals ; Brain/*immunology/microbiology/pathology ; Cohort Studies ; *Disease Models, Animal ; Encephalomyelitis, Autoimmune, Experimental/*immunology/microbiology/pathology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Mice ; Middle Aged ; Multiple Sclerosis/*immunology/microbiology/pathology ; T-Lymphocytes, Regulatory/*immunology ; Young Adult ; }, abstract = {There is emerging evidence that the commensal microbiota has a role in the pathogenesis of multiple sclerosis (MS), a putative autoimmune disease of the CNS. Here, we compared the gut microbial composition of 34 monozygotic twin pairs discordant for MS. While there were no major differences in the overall microbial profiles, we found a significant increase in some taxa such as Akkermansia in untreated MS twins. Furthermore, most notably, when transplanted to a transgenic mouse model of spontaneous brain autoimmunity, MS twin-derived microbiota induced a significantly higher incidence of autoimmunity than the healthy twin-derived microbiota. The microbial profiles of the colonized mice showed a high intraindividual and remarkable temporal stability with several differences, including Sutterella, an organism shown to induce a protective immunoregulatory profile in vitro. Immune cells from mouse recipients of MS-twin samples produced less IL-10 than immune cells from mice colonized with healthy-twin samples. IL-10 may have a regulatory role in spontaneous CNS autoimmunity, as neutralization of the cytokine in mice colonized with healthy-twin fecal samples increased disease incidence. These findings provide evidence that MS-derived microbiota contain factors that precipitate an MS-like autoimmune disease in a transgenic mouse model. They hence encourage the detailed search for protective and pathogenic microbial components in human MS.}, } @article {pmid28893308, year = {2017}, author = {Michas, A and Vestergaard, G and Trautwein, K and Avramidis, P and Hatzinikolaou, DG and Vorgias, CE and Wilkes, H and Rabus, R and Schloter, M and Schöler, A}, title = {More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {118}, pmid = {28893308}, issn = {2049-2618}, mesh = {Anaerobiosis ; *Biodegradation, Environmental ; Chemoautotrophic Growth ; Geologic Sediments/*microbiology ; High-Throughput Nucleotide Sequencing ; Hydrocarbons/*metabolism ; Lakes/microbiology ; *Metagenome ; Metagenomics/methods ; Methane/*metabolism ; Microbial Interactions ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfates/metabolism ; Time Factors ; }, abstract = {BACKGROUND: Natural oil seeps offer the opportunity to study the adaptation of ecosystems and the associated microbiota to long-term oil exposure. In the current study, we investigated a land-to-sea transition ecosystem called "Keri Lake" in Zakynthos Island, Greece. This ecosystem is unique due to asphalt oil springs found at several sites, a phenomenon already reported 2500 years ago. Sediment microbiomes at Keri Lake were studied, and their structure and functional potential were compared to other ecosystems with oil exposure histories of various time periods.

RESULTS: Replicate sediment cores (up to 3-m depth) were retrieved from one site exposed to oil as well as a non-exposed control site. Samples from three different depths were subjected to chemical analysis and metagenomic shotgun sequencing. At the oil-exposed site, we observed high amounts of asphalt oil compounds and a depletion of sulfate compared to the non-exposed control site. The numbers of reads assigned to genes involved in the anaerobic degradation of hydrocarbons were similar between the two sites. The numbers of denitrifiers and sulfate reducers were clearly lower in the samples from the oil-exposed site, while a higher abundance of methanogens was detected compared to the non-exposed site. Higher abundances of the genes of methanogenesis were also observed in the metagenomes from other ecosystems with a long history of oil exposure, compared to short-term exposed environments.

CONCLUSIONS: The analysis of Keri Lake metagenomes revealed that microbiomes in the oil-exposed sediment have a higher potential for methanogenesis over denitrification/sulfate reduction, compared to those in the non-exposed site. Comparison with metagenomes from various oil-impacted environments suggests that syntrophic interactions of hydrocarbon degraders with methanogens are favored in the ecosystems with a long-term presence of oil.}, } @article {pmid28892512, year = {2017}, author = {Mezzasalma, V and Sandionigi, A and Bruni, I and Bruno, A and Lovicu, G and Casiraghi, M and Labra, M}, title = {Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184615}, pmid = {28892512}, issn = {1932-6203}, mesh = {Agriculture ; Bacteria/classification/genetics ; Biodiversity ; Cluster Analysis ; DNA Barcoding, Taxonomic ; *Environment ; Fungi/classification/genetics ; Geography ; Metagenome ; Metagenomics/methods ; *Microbiota ; Vitis/*microbiology ; *Wine ; }, abstract = {Grape berries harbor a wide range of microbes originating from the vineyard environment, many of which are recognized for their role in the must fermentation process shaping wine quality. To better clarify the contribution of the microbiome of grape fruits during wine fermentation, we used high-throughput sequencing to identify bacterial and fungi communities associated with berries and musts of Cannonau. This is the most important cultivar-wine of Sardinia (Italy) where most vineyards are cultivated without phytochemical treatments. Results suggested that microbiomes of berries collected at four different localities share a core composition characterized by Enterobacteriales, Pseudomonadales, Bacillales, and Rhodospirillales. However, any area seems to enrich berries microbiome with peculiar microbial traits. For example, berries belonging to the biodynamic vineyards of Mamoiada were rich in Bacillales typical of manure (i.e. Lysinibacillus, Bacillus, and Sporosarcina), whereas in the Santadi locality, berries showed soil bacteria such as Pasteurellales and Bacteroidales as well as Rhodospirillales and Lactobacillales which are commonly involved in wine fermentation. In the case of fungi, the most abundant taxa were Dothioraceae, Pleosporaceae, and Saccharomycodaceae, and although the proportion of these families varied among localities, they occurred ubiquitously in all vineyards. During vinification processes performed at the same wine cellar under controlled conditions and without using any yeast starter, more than 50% of bacteria groups of berries reached musts, and each locality had its own private bacteria signature, even if Saccharomyces cerevisiae represented the most abundant fungal species. This work suggests that natural berries microbiome could be influenced by pedoclimatic and anthropologic conditions (e.g., farming management), and the fruits' microorganisms persist during the fermentation process. For these reasons, a reliable wine genotyping should include the entire holobiont (plant and all its symbionts), and bioprospecting activities on grape microbiota could lead to improved viticulture yields and wine quality.}, } @article {pmid28892494, year = {2017}, author = {Jenkins, TP and Rathnayaka, Y and Perera, PK and Peachey, LE and Nolan, MJ and Krause, L and Rajakaruna, RS and Cantacessi, C}, title = {Infections by human gastrointestinal helminths are associated with changes in faecal microbiota diversity and composition.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184719}, pmid = {28892494}, issn = {1932-6203}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Analysis of Variance ; Animals ; *Biodiversity ; Computational Biology/methods ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Helminthiasis/*microbiology/*parasitology ; *Helminths ; Humans ; Intestinal Diseases, Parasitic/*microbiology ; Metagenome ; Metagenomics/methods ; Sri Lanka ; }, abstract = {Investigations of the impact that patent infections by soil-transmitted gastrointestinal nematode parasites exert on the composition of the host gut commensal flora are attracting growing interest by the scientific community. However, information collected to date varies across experiments, and further studies are needed to identify consistent relationships between parasites and commensal microbial species. Here, we explore the qualitative and quantitative differences between the microbial community profiles of cohorts of human volunteers from Sri Lanka with patent infection by one or more parasitic nematode species (H+), as well as that of uninfected subjects (H-) and of volunteers who had been subjected to regular prophylactic anthelmintic treatment (Ht). High-throughput sequencing of the bacterial 16S rRNA gene, followed by bioinformatics and biostatistical analyses of sequence data revealed no significant differences in alpha diversity (Shannon) and richness between groups (P = 0.65, P = 0.13 respectively); however, beta diversity was significantly increased in H+ and Ht when individually compared to H-volunteers (P = 0.04). Among others, bacteria of the families Verrucomicrobiaceae and Enterobacteriaceae showed a trend towards increased abundance in H+, whereas the Leuconostocaceae and Bacteroidaceae showed a relative increase in H- and Ht respectively. Our findings add valuable knowledge to the vast, and yet little explored, research field of parasite-microbiota interactions and will provide a basis for the elucidation of the role such interactions play in pathogenic and immune-modulatory properties of parasitic nematodes in both human and animal hosts.}, } @article {pmid28891744, year = {2018}, author = {Fraumene, C and Manghina, V and Cadoni, E and Marongiu, F and Abbondio, M and Serra, M and Palomba, A and Tanca, A and Laconi, E and Uzzau, S}, title = {Caloric restriction promotes rapid expansion and long-lasting increase of Lactobacillus in the rat fecal microbiota.}, journal = {Gut microbes}, volume = {9}, number = {2}, pages = {104-114}, pmid = {28891744}, issn = {1949-0984}, mesh = {Animals ; Bacteria/classification/genetics/*growth & development ; *Caloric Restriction ; Cluster Analysis ; DNA, Bacterial/genetics ; Diet ; Feces/*microbiology ; Gastrointestinal Microbiome/*physiology ; Lactobacillus/classification/*growth & development ; Models, Animal ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Inbred F344 ; }, abstract = {Previous studies indicated that caloric restricted diet enables to lower significantly the risk of cardiovascular and metabolic diseases. In experimental animal models, life-long lasting caloric restriction (CR) was demonstrated to induce changes of the intestinal microbiota composition, regardless of fat content and/or exercise. To explore the potential impact of short and long-term CR treatment on the gut microbiota, we conducted an analysis of fecal microbiota composition in young and adult Fisher 344 rats treated with a low fat feed under ad libitum (AL) or CR conditions (70%). We report here significant changes of the rat fecal microbiota that arise rapidly in young growing animals after short-term administration of a CR diet. In particular, Lactobacillus increased significantly after 8 weeks of CR treatment and its relative abundance was significantly higher in CR vs AL fed animals after 36 weeks of dietary intervention. Taken together, our data suggest that Lactobacillus intestinal colonization is hampered in AL fed young rats compared to CR fed ones, while health-promoting CR diet intervention enables the expansion of this genus rapidly and persistently up to adulthood.}, } @article {pmid28887679, year = {2018}, author = {Poddar, A and Das, SK}, title = {Microbiological studies of hot springs in India: a review.}, journal = {Archives of microbiology}, volume = {200}, number = {1}, pages = {1-18}, doi = {10.1007/s00203-017-1429-3}, pmid = {28887679}, issn = {1432-072X}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Hot Springs/chemistry/*microbiology ; India ; Microbiota ; Phylogeny ; }, abstract = {The earliest microbiological studies on hot springs in India date from 2003, a much later date compared to global attention in this striking field of study. As of today, 28 out of 400 geothermal springs have been explored following both culturable and non-culturable approaches. The temperatures and pH of the springs are 37-99 °C and 6.8-10, respectively. Several studies have been performed on the description of novel genera and species, characterization of different bio-resources, metagenomics of hot spring microbiome and whole genome analysis of few isolates. 17 strains representing novel species and many thermostable enzymes, including lipase, protease, chitinase, amylase, etc. with potential biotechnological applications have been reported by several authors. Influence of physico-chemical conditions, especially that of temperature, on shaping the hot spring microbiome has been established by metagenomic investigations. Bacteria are the predominant life forms in all the springs with an abundance of phyla Firmicutes, Proteobacteria, Actinobacteria, Thermi, Bacteroidetes, Deinococcus-Thermus and Chloroflexi. In this review, we have discussed the findings on all microbiological studies that have been carried out to date, on the 28 hot springs. Further, the possibilities of extrapolating these studies for practical applications and environmental impact assessment towards protection of natural ecosystem of hot springs have also been discussed.}, } @article {pmid28887570, year = {2017}, author = {Cabral, DJ and Wurster, JI and Flokas, ME and Alevizakos, M and Zabat, M and Korry, BJ and Rowan, AD and Sano, WH and Andreatos, N and Ducharme, RB and Chan, PA and Mylonakis, E and Fuchs, BB and Belenky, P}, title = {The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11040}, pmid = {28887570}, issn = {2045-2322}, support = {P20 GM109035/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/*classification/genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; *Hospitalization ; Humans ; Male ; *Metagenome ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {In recent years, a growing amount of research has begun to focus on the oral microbiome due to its links with health and systemic disease. The oral microbiome has numerous advantages that make it particularly useful for clinical studies, including non-invasive collection, temporal stability, and lower complexity relative to other niches, such as the gut. Despite recent discoveries made in this area, it is unknown how the oral microbiome responds to short-term hospitalization. Previous studies have demonstrated that the gut microbiome is extremely sensitive to short-term hospitalization and that these changes are associated with significant morbidity and mortality. Here, we present a comprehensive pipeline for reliable bedside collection, sequencing, and analysis of the human salivary microbiome. We also develop a novel oral-specific mock community for pipeline validation. Using our methodology, we analyzed the salivary microbiomes of patients before and during hospitalization or azithromycin treatment to profile impacts on this community. Our findings indicate that azithromycin alters the diversity and taxonomic composition of the salivary microbiome; however, we also found that short-term hospitalization does not impact the richness or structure of this community, suggesting that the oral cavity may be less susceptible to dysbiosis during short-term hospitalization.}, } @article {pmid28887527, year = {2017}, author = {Kim, Y and Koh, I and Young Lim, M and Chung, WH and Rho, M}, title = {Pan-genome analysis of Bacillus for microbiome profiling.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10984}, pmid = {28887527}, issn = {2045-2322}, mesh = {Bacillus/classification/*genetics ; Evolution, Molecular ; Genes, Bacterial ; *Genome, Bacterial ; *Genomics/methods ; Metagenome ; Metagenomics/methods ; *Microbiota ; Multilocus Sequence Typing ; Phylogeny ; }, abstract = {Recent advances in high-throughput sequencing technology allow for in-depth studies on microbial genomes and their communities. While multiple strains of the same species could display genomic variations with different gene contents in diverse habitats and hosts, the essential functions for a specific species are conserved as core genes that are shared among strains. We have comprehensively analyzed 238 strains of five different Bacillus species to identify the properties of core and strain-specific genes. Core and strain-specific genes in each Bacillus species show significant differences in their functions and genomic signatures. Using the core genes defined in this study, we have precisely identified the Bacillus species that exist in food microbiomes. Without resorting to culture-based whole genome sequencing, an unexpectedly large portion of the core genes, 98.22% of core genes in B. amyloliquefaciens and 97.77% of B. subtilis, were reconstructed from the microbiome. We have performed a pan-genome analysis on the core gene data of multiple Bacillus species to investigate the Bacillus species in food microbiome. Our findings provide a comprehensive genetic landscape of the Bacillus species, which is also consistent with previous studies on a limited number of strains and species. Analysis based on comprehensive core genes should thus serve as a powerful profiling tool to better understand major constituents in fermented food microbiomes.}, } @article {pmid28887494, year = {2017}, author = {Walker, A and Pfitzner, B and Harir, M and Schaubeck, M and Calasan, J and Heinzmann, SS and Turaev, D and Rattei, T and Endesfelder, D and Castell, WZ and Haller, D and Schmid, M and Hartmann, A and Schmitt-Kopplin, P}, title = {Sulfonolipids as novel metabolite markers of Alistipes and Odoribacter affected by high-fat diets.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11047}, pmid = {28887494}, issn = {2045-2322}, mesh = {Animals ; Bacteroidetes/*chemistry/*metabolism ; Cecum/*microbiology ; Chromatography, Liquid ; *Diet, High-Fat ; Gastrointestinal Microbiome/*drug effects ; Lipids/*analysis ; Mass Spectrometry ; Mice ; }, abstract = {The gut microbiota generates a huge pool of unknown metabolites, and their identification and characterization is a key challenge in metabolomics. However, there are still gaps on the studies of gut microbiota and their chemical structures. In this investigation, an unusual class of bacterial sulfonolipids (SLs) is detected in mouse cecum, which was originally found in environmental microbes. We have performed a detailed molecular level characterization of this class of lipids by combining high-resolution mass spectrometry and liquid chromatography analysis. Eighteen SLs that differ in their capnoid and fatty acid chain compositions were identified. The SL called "sulfobacin B" was isolated, characterized, and was significantly increased in mice fed with high-fat diets. To reveal bacterial producers of SLs, metagenome analysis was acquired and only two bacterial genera, i.e., Alistipes and Odoribacter, were revealed to be responsible for their production. This knowledge enables explaining a part of the molecular complexity introduced by microbes to the mammalian gastrointestinal tract and can be used as chemotaxonomic evidence in gut microbiota.}, } @article {pmid28886166, year = {2017}, author = {Festa, S and Coppotelli, BM and Madueño, L and Loviso, CL and Macchi, M and Neme Tauil, RM and Valacco, MP and Morelli, IS}, title = {Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184505}, pmid = {28886166}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics/*metabolism ; *Biodegradation, Environmental ; DNA, Bacterial/genetics ; Gene Order ; Genes, Bacterial ; Metagenome ; Metagenomics/methods ; *Microbial Consortia ; Phenanthrenes/*metabolism ; Phylogeny ; Proteomics/methods ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {The present study describes the behavior of a natural phenanthrene-degrading consortium (CON), a synthetic consortium (constructed with isolated strains from CON) and an isolated strain form CON (Sphingobium sp. AM) in phenanthrene cultures to understand the interactions among the microorganisms present in the natural consortium during phenanthrene degradation as a sole carbon and energy source in liquid cultures. In the contaminant degradation assay, the defined consortium not only achieved a major phenanthrene degradation percentage (> 95%) but also showed a more efficient elimination of the intermediate metabolite. The opposite behavior occurred in the CON culture where the lowest phenanthrene degradation and the highest HNA accumulation were observed, which suggests the presence of positive and also negative interaction in CON. To consider the uncultured bacteria present in CON, a metagenomic library was constructed with total CON DNA. One of the resulting scaffolds (S1P3) was affiliated with the Betaproteobacteria class and resulted in a significant similarity with a genome fragment from Burkholderia sp. HB1 chromosome 1. A complete gene cluster, which is related to one of the lower pathways (meta-cleavage of catechol) involved in PAH degradation (ORF 31-43), mobile genetic elements and associated proteins, was found. These results suggest the presence of at least one other microorganism in CON besides Sphingobium sp. AM, which is capable of degrading PAH through the meta-cleavage pathway. Burkholderiales order was further found, along with Sphingomonadales order, by a metaproteomic approach, which indicated that both orders were metabolically active in CON. Our results show the presence of negative interactions between bacterial populations found in a natural consortium selected by enrichment techniques; moreover, the synthetic syntrophic processing chain with only one microorganism with the capability of degrading phenanthrene was more efficient in contaminant and intermediate metabolite degradation than a generalist strain (Sphingobium sp. AM).}, } @article {pmid28885183, year = {2018}, author = {Popescu, L and Cao, ZP}, title = {From Microscopy to Genomic Approach in Soil Biodiversity Assessment.}, journal = {Current issues in molecular biology}, volume = {27}, number = {}, pages = {195-198}, doi = {10.21775/cimb.027.195}, pmid = {28885183}, issn = {1467-3045}, mesh = {Animals ; Bacteria/classification/*genetics ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Bacterial/genetics ; Ecosystem ; Fungi/classification/*genetics ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Microbial Consortia/genetics ; Microscopy ; Nematoda/classification/*genetics ; Plant Roots/microbiology ; Plants/microbiology ; *Soil Microbiology ; }, abstract = {Soil biota represents a major component of the earth's biodiversity and for over 200 years, the microscopy approach was the only way to explore it. In the last decade, the DNA-based technique has been adopted in soil ecology. Due to the rapid development of cutting-edge technology, the field is transitioning from barcoding individuals to metabarcoding communities. With the advent of next-generation sequencing and a rapid decline in sequencing cost, it has become feasible to assess soil biodiversity at species level. This review article summarizes current approaches in soil biodiversity research along with their advantages and disadvantages.}, } @article {pmid28884952, year = {2017}, author = {Li, Q and Wu, T and Liu, R and Zhang, M and Wang, R}, title = {Soluble Dietary Fiber Reduces Trimethylamine Metabolism via Gut Microbiota and Co-Regulates Host AMPK Pathways.}, journal = {Molecular nutrition & food research}, volume = {61}, number = {12}, pages = {}, doi = {10.1002/mnfr.201700473}, pmid = {28884952}, issn = {1613-4133}, mesh = {AMP-Activated Protein Kinases/*metabolism ; Animals ; Cholesterol/blood ; Diet ; Dietary Fiber/*pharmacology ; Energy Intake/drug effects ; Fatty Acids, Volatile/metabolism ; Fermented Foods ; Gastrointestinal Microbiome/*drug effects/physiology ; Intestinal Mucosa/metabolism ; Lipids/blood ; Metagenome ; Methylamines/blood/*metabolism ; Mice, Inbred C57BL ; Red Meat ; Solubility ; }, abstract = {SCOPE: Evidence from animal experiments and clinical medicine suggests that high dietary fiber intake, followed by gut microbiota-mediated fermentation, decreases trimethylamine (TMA) metabolism, the mechanism of which, however, remains unclear. The objective of this analysis was to evaluate, using mice fed with red meat, the effects of soluble dietary fiber (SDF) intervention on TMA metabolism.

METHODS AND RESULTS: Low- or high-dose soluble dietary fiber (SDF) from natural wheat bran (LN and HN, low- and high-dose natural SDF), fermented wheat bran (LF and HF, low- and high-dose fermented SDF), and steam-exploded wheat bran (LE and HE, low- and high-dose exploded SDF groups) were used to examine whether SDF interventions in mice fed with red meat can alter TMA and trimethylamine N-oxide (TMAO) metabolism by gut microbial communities in a diet-specific manner. Results demonstrated that SDF-diets could reduce TMA and trimethylamine N-oxide (TMAO) metabolism by 40.6 and 62.6%, respectively. DF feeding, particularly fermented SDF, reshaped gut microbial ecology and promoted the growth of certain beneficial microflora species. SDF-diet decreased energy intake, weight gain, intestinal pH values, and serum lipid and cholesterol levels. SDF-diet also enhanced the production of short chain fatty acids with activation of the intestinal epithelial adenosine monophosphate-activated protein kinase (AMPK).

CONCLUSION: These findings suggest a central mechanism via which SDF-diet may control TMA metabolism by gut microflora and co-regulate the AMPK pathways of the host.}, } @article {pmid28884664, year = {2017}, author = {Langevin, S and Pichon, M and Smith, E and Morrison, J and Bent, Z and Green, R and Barker, K and Solberg, O and Gillet, Y and Javouhey, E and Lina, B and Katze, MG and Josset, L}, title = {Early nasopharyngeal microbial signature associated with severe influenza in children: a retrospective pilot study.}, journal = {The Journal of general virology}, volume = {98}, number = {10}, pages = {2425-2437}, pmid = {28884664}, issn = {1465-2099}, support = {HHSN272201400005C/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/isolation & purification ; Child ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Dysbiosis ; Humans ; Influenza, Human/*complications/*diagnosis ; *Microbiota ; Nasopharynx/*microbiology ; Phylogeny ; Prognosis ; RNA, Ribosomal, 16S/genetics ; Retrospective Studies ; Sequence Analysis, DNA ; }, abstract = {A few studies have highlighted the importance of the respiratory microbiome in modulating the frequency and outcome of viral respiratory infections. However, there are insufficient data on the use of microbial signatures as prognostic biomarkers to predict respiratory disease outcomes. In this study, we aimed to evaluate whether specific bacterial community compositions in the nasopharynx of children at the time of hospitalization are associated with different influenza clinical outcomes. We utilized retrospective nasopharyngeal (NP) samples (n=36) collected at the time of hospital arrival from children who were infected with influenza virus and had been symptomatic for less than 2 days. Based on their clinical course, children were classified into two groups: patients with mild influenza, and patients with severe respiratory or neurological complications. We implemented custom 16S rRNA gene sequencing, metagenomic sequencing and computational analysis workflows to classify the bacteria present in NP specimens at the species level. We found that increased bacterial diversity in the nasopharynx of children was strongly associated with influenza severity. In addition, patients with severe influenza had decreased relative abundance of Staphylococcus aureus and increased abundance of Prevotella (including P. melaninogenica), Streptobacillus, Porphyromonas, Granulicatella (including G. elegans), Veillonella (including V. dispar), Fusobacterium and Haemophilus in their nasopharynx. This pilot study provides proof-of-concept data for the use of microbial signatures as prognostic biomarkers of influenza outcomes. Further large prospective cohort studies are needed to refine and validate the performance of such microbial signatures in clinical settings.}, } @article {pmid28884091, year = {2017}, author = {Yan, Q and Gu, Y and Li, X and Yang, W and Jia, L and Chen, C and Han, X and Huang, Y and Zhao, L and Li, P and Fang, Z and Zhou, J and Guan, X and Ding, Y and Wang, S and Khan, M and Xin, Y and Li, S and Ma, Y}, title = {Alterations of the Gut Microbiome in Hypertension.}, journal = {Frontiers in cellular and infection microbiology}, volume = {7}, number = {}, pages = {381}, pmid = {28884091}, issn = {2235-2988}, mesh = {Bacteria/*classification/genetics/isolation & purification ; Dysbiosis/*microbiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; Hypertension/*microbiology ; Male ; Metagenome/genetics ; Middle Aged ; Whole Genome Sequencing ; }, abstract = {Introduction: Human gut microbiota is believed to be directly or indirectly involved in cardiovascular diseases and hypertension. However, the identification and functional status of the hypertension-related gut microbe(s) have not yet been surveyed in a comprehensive manner. Methods: Here we characterized the gut microbiome in hypertension status by comparing fecal samples of 60 patients with primary hypertension and 60 gender-, age-, and body weight-matched healthy controls based on whole-metagenome shotgun sequencing. Results: Hypertension implicated a remarkable gut dysbiosis with significant reduction in within-sample diversity and shift in microbial composition. Metagenome-wide association study (MGWAS) revealed 53,953 microbial genes that differ in distribution between the patients and healthy controls (false discovery rate, 0.05) and can be grouped into 68 clusters representing bacterial species. Opportunistic pathogenic taxa, such as, Klebsiella spp., Streptococcus spp., and Parabacteroides merdae were frequently distributed in hypertensive gut microbiome, whereas the short-chain fatty acid producer, such as, Roseburia spp. and Faecalibacterium prausnitzii, were higher in controls. The number of hypertension-associated species also showed stronger correlation to the severity of disease. Functionally, the hypertensive gut microbiome exhibited higher membrane transport, lipopolysaccharide biosynthesis and steroid degradation, while in controls the metabolism of amino acid, cofactors and vitamins was found to be higher. We further provided the microbial markers for disease discrimination and achieved an area under the receiver operator characteristic curve (AUC) of 0.78, demonstrating the potential of gut microbiota in prediction of hypertension. Conclusion: These findings represent specific alterations in microbial diversity, genes, species and functions of the hypertensive gut microbiome. Further studies on the causality relationship between hypertension and gut microbiota will offer new prospects for treating and preventing the hypertension and its associated diseases.}, } @article {pmid28883460, year = {2017}, author = {Bridgewater, LC and Zhang, C and Wu, Y and Hu, W and Zhang, Q and Wang, J and Li, S and Zhao, L}, title = {Gender-based differences in host behavior and gut microbiota composition in response to high fat diet and stress in a mouse model.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10776}, pmid = {28883460}, issn = {2045-2322}, mesh = {Animals ; *Behavior, Animal ; Computational Biology/methods ; *Diet, High-Fat ; Female ; *Gastrointestinal Microbiome ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Sex Factors ; *Stress, Physiological ; }, abstract = {Obesity is associated with a high prevalence of mood disorders such as anxiety and depression. Both stress and high fat diet can alter the gut microbiota and contribute to obesity. To examine the interrelationships between obesity, stress, gut microbiota and mood disorders, obesity was induced in mice using a high fat diet, and the mice were subsequently stressed using a chronic unpredictable mild stress protocol. During the experiment, the composition of the gut microbiota was analyzed by 16 S rRNA gene high-throughput sequencing, and anxiety-like behaviors were measured. The results revealed distinct gender differences in the impacts of obesity and stress on anxiety-like behaviors, activity levels, and composition of the gut microbiota. Male mice were more vulnerable to the anxiogenic effects of the high fat diet, and obese male mice showed decreased locomotion activity in response to stress whereas obese female mice did not. In females, stress caused the gut microbiota of lean mice to more closely resemble that of obese mice. Taken together, these results suggest the importance of considering gender as a biological variable in studies on the role of gut microbiota in obesity-related mood disorders.}, } @article {pmid28883399, year = {2017}, author = {Wipperman, MF and Fitzgerald, DW and Juste, MAJ and Taur, Y and Namasivayam, S and Sher, A and Bean, JM and Bucci, V and Glickman, MS}, title = {Antibiotic treatment for Tuberculosis induces a profound dysbiosis of the microbiome that persists long after therapy is completed.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10767}, pmid = {28883399}, issn = {2045-2322}, support = {R15 AI112985/AI/NIAID NIH HHS/United States ; U19 AI111143/AI/NIAID NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; D43 TW010062/TW/FIC NIH HHS/United States ; UL1 TR002384/TR/NCATS NIH HHS/United States ; UL1 TR000457/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Antitubercular Agents/*adverse effects/therapeutic use ; Cross-Sectional Studies ; Drug Therapy, Combination ; Dysbiosis/*etiology ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Haiti ; Humans ; Male ; Middle Aged ; Mycobacterium tuberculosis/drug effects ; Tuberculosis, Pulmonary/*drug therapy ; }, abstract = {Mycobacterium tuberculosis, the cause of Tuberculosis (TB), infects one third of the world's population and causes substantial mortality worldwide. In its shortest format, treatment of TB requires six months of multidrug therapy with a mixture of broad spectrum and mycobacterial specific antibiotics, and treatment of multidrug resistant TB is longer. The widespread use of this regimen makes this one of the largest exposures of humans to antimicrobials, yet the effects of TB treatment on intestinal microbiome composition and long-term stability are unknown. We compared the microbiome composition, assessed by both 16S rDNA and metagenomic DNA sequencing, of TB cases during antimycobacterial treatment and following cure by 6 months of antibiotics. TB treatment does not perturb overall diversity, but nonetheless dramatically depletes multiple immunologically significant commensal bacteria. The microbiomic perturbation of TB therapy can persist for at least 1.2 years, indicating that the effects of TB treatment are long lasting. These results demonstrate that TB treatment has dramatic effects on the intestinal microbiome and highlight unexpected durable consequences of treatment for the world's most common infection on human ecology.}, } @article {pmid28882888, year = {2017}, author = {Versalovic, J and Dore, J and Guarner, F and Luna, RA and Ringel, Y}, title = {Microbiome-Based Diagnostics: Ready for Applications in Laboratory Medicine?.}, journal = {Clinical chemistry}, volume = {63}, number = {11}, pages = {1674-1679}, doi = {10.1373/clinchem.2016.264473}, pmid = {28882888}, issn = {1530-8561}, mesh = {Communicable Diseases/*diagnosis ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/drug effects/genetics/physiology ; Humans ; Noncommunicable Diseases/prevention & control/therapy ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; }, } @article {pmid28882736, year = {2018}, author = {Anupama, R and Mukherjee, A and Babu, S}, title = {Gene-centric metegenome analysis reveals diversity of Pseudomonas aeruginosa biofilm gene orthologs in fresh water ecosystem.}, journal = {Genomics}, volume = {110}, number = {2}, pages = {89-97}, doi = {10.1016/j.ygeno.2017.08.010}, pmid = {28882736}, issn = {1089-8646}, mesh = {*Biofilms ; Fresh Water/microbiology ; *Genes, Bacterial ; *Genetic Variation ; *Metagenome ; Microbiota ; Pseudomonas aeruginosa/*genetics/physiology ; }, abstract = {Metagenomic analysis of biofilm forming bacteria in environmental samples remains challenging due to the non-availability of gene sequences of most of the uncultivable bacteria. Sequences of Pseudomonas aeruginosa PAO1-UW genes involved either directly or indirectly in biofilm formation were analyzed using BLASTn to obtain matching sequences from different strain, species and genus. Conserved regions in the functional domain of the amino acid sequences were used to design common primers for direct PCR analysis of freshwater metagenomes. Seven key genes such as aceA, clpP, typA, cbrA, phoR, rpoS and gacA involved in biofilm formation were validated. The ortholog genes belonged to wide range of Pseudomonas sp. indicating the diversity of biofilm genes and the conservation of protein functional domains. The approach would also help in analyzing the expression of biofilm genes in different bacteria of freshwater systems for monitoring toxic contaminations such as organic or inorganic pollutants.}, } @article {pmid28878025, year = {2017}, author = {Sarashina-Kida, H and Negishi, H and Nishio, J and Suda, W and Nakajima, Y and Yasui-Kato, M and Iwaisako, K and Kang, S and Endo, N and Yanai, H and Asagiri, M and Kida, H and Hattori, M and Kumanogoh, A and Taniguchi, T}, title = {Gallbladder-derived surfactant protein D regulates gut commensal bacteria for maintaining intestinal homeostasis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {38}, pages = {10178-10183}, pmid = {28878025}, issn = {1091-6490}, mesh = {Animals ; Colitis/*metabolism/microbiology ; Forkhead Transcription Factors/metabolism ; Gallbladder/*metabolism ; *Gastrointestinal Microbiome ; Glucocorticoids/biosynthesis ; Homeostasis ; Intestinal Mucosa/immunology ; Liver/metabolism ; Mice, Inbred C57BL ; Pulmonary Surfactant-Associated Protein D/*metabolism ; Symbiosis ; T-Lymphocytes, Regulatory/metabolism ; }, abstract = {The commensal microbiota within the gastrointestinal tract is essential in maintaining homeostasis. Indeed, dysregulation in the repertoire of microbiota can result in the development of intestinal immune-inflammatory diseases. Further, this immune regulation by gut microbiota is important systemically, impacting health and disease of organ systems beyond the local environment of the gut. What has not been explored is how distant organs might in turn shape the microbiota via microbe-targeted molecules. Here, we provide evidence that surfactant protein D (SP-D) synthesized in the gallbladder and delivered into intestinal lumen binds selectively to species of gut commensal bacteria. SP-D-deficient mice manifest intestinal dysbiosis and show a susceptibility to dextran sulfate sodium-induced colitis. Further, fecal transfer from SP-D-deficient mice to wild-type, germ-free mice conveyed colitis susceptibility. Interestingly, colitis caused a notable increase in Sftpd gene expression in the gallbladder, but not in the lung, via the activity of glucocorticoids produced in the liver. These findings describe a unique mechanism of interorgan regulation of intestinal immune homeostasis by SP-D with potential clinical implications such as cholecystectomy.}, } @article {pmid28877164, year = {2017}, author = {Han, K and Bose, S and Wang, JH and Lim, SK and Chin, YW and Kim, YM and Choi, HS and Kim, H}, title = {In vivo therapeutic effect of combination treatment with metformin and Scutellaria baicalensis on maintaining bile acid homeostasis.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0182467}, pmid = {28877164}, issn = {1932-6203}, mesh = {Algorithms ; Animals ; Bile Acids and Salts/*metabolism ; Blood Glucose/metabolism ; Blotting, Western ; Body Weight/drug effects ; Cholesterol/blood ; Cholesterol 7-alpha-Hydroxylase/genetics/metabolism ; Combined Modality Therapy ; Feces/chemistry ; Feeding Behavior/drug effects ; Gastrointestinal Microbiome/drug effects ; Homeostasis/*drug effects ; Insulin Resistance ; Liver/drug effects/metabolism ; Male ; Metagenome ; Metformin/administration & dosage/*pharmacology ; Phylogeny ; Plant Extracts/administration & dosage/*pharmacology ; Principal Component Analysis ; Rats, Inbred OLETF ; Receptors, Cytoplasmic and Nuclear/genetics/metabolism ; Scutellaria baicalensis ; Up-Regulation/drug effects/genetics ; }, abstract = {The radix of Scutellaria baicalensis (SB) is a herb widely used in traditional Chinese medicine to treat metabolic diseases. Several main components, including baicalin and wogonoside, possess anti-dyslipidemia, anti-obesity and anti-diabetic effects. We hypothesized that co-administration of SB extract and metformin exerts a better effect on obesity-induced insulin resistance and lipid metabolism than treatment with metformin alone. We compared the effect of metformin (100 mg/10 mL/kg/day) alone with co-administration of metformin (100 mg/5 mL/kg/day) and SB extract (200 mg/5 mL/kg/day) on Otsuka Long Evans Tokushima Fatty rats, a useful model of type II diabetes with obesity, and used Long-Evans Tokushima Otsuka rats as a control. Weight, fasting glucose, oral glucose tolerance test, intraperitoneal insulin tolerance test, and serum total cholesterol were measured after 12 weeks of drug administration. We observed a synergetic effect of metformin and SB on lowering cholesterol level by excretion of bile acid through feces. We found that this accompanied activation of FXR, CYP7A1 and LDLR genes and repression of HMGCR in the liver. Although there were no significant changes in BSH-active gut microbiota due to high variability, functional prediction with 16S sequences showed increased primary and secondary bile acid biosynthesis in the combination treatment group. Further study is needed to find the specific strains of bacteria which contribute to FXR-related cholesterol and bile acid regulations.}, } @article {pmid28874832, year = {2017}, author = {Minter, MR and Hinterleitner, R and Meisel, M and Zhang, C and Leone, V and Zhang, X and Oyler-Castrillo, P and Zhang, X and Musch, MW and Shen, X and Jabri, B and Chang, EB and Tanzi, RE and Sisodia, SS}, title = {Antibiotic-induced perturbations in microbial diversity during post-natal development alters amyloid pathology in an aged APPSWE/PS1ΔE9 murine model of Alzheimer's disease.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10411}, pmid = {28874832}, issn = {2045-2322}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; }, mesh = {Alzheimer Disease/*etiology/metabolism/pathology ; Amyloid beta-Protein Precursor/*genetics/metabolism ; Amyloidosis/*genetics/metabolism/pathology ; Animals ; Anti-Bacterial Agents/*pharmacology ; Biodiversity ; Biomarkers ; Brain/metabolism/pathology ; Disease Models, Animal ; Gastrointestinal Microbiome ; Inflammation Mediators/metabolism ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Mice, Transgenic ; Microbiota/*drug effects ; Neuroimmunomodulation/drug effects/genetics/immunology ; Plaque, Amyloid/etiology/metabolism/pathology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recent evidence suggests the commensal microbiome regulates host immunity and influences brain function; findings that have ramifications for neurodegenerative diseases. In the context of Alzheimer's disease (AD), we previously reported that perturbations in microbial diversity induced by life-long combinatorial antibiotic (ABX) selection pressure in the APPSWE/PS1ΔE9 mouse model of amyloidosis is commensurate with reductions in amyloid-β (Aβ) plaque pathology and plaque-localised gliosis. Considering microbiota-host interactions, specifically during early post-natal development, are critical for immune- and neuro-development we now examine the impact of microbial community perturbations induced by acute ABX exposure exclusively during this period in APPSWE/PS1ΔE9 mice. We show that early post-natal (P) ABX treatment (P14-P21) results in long-term alterations of gut microbial genera (predominantly Lachnospiraceae and S24-7) and reduction in brain Aβ deposition in aged APPSWE/PS1ΔE9 mice. These mice exhibit elevated levels of blood- and brain-resident Foxp3[+] T-regulatory cells and display an alteration in the inflammatory milieu of the serum and cerebrospinal fluid. Finally, we confirm that plaque-localised microglia and astrocytes are reduced in ABX-exposed mice. These findings suggest that ABX-induced microbial diversity perturbations during post-natal stages of development coincide with altered host immunity mechanisms and amyloidosis in a murine model of AD.}, } @article {pmid28874721, year = {2017}, author = {Shibagaki, N and Suda, W and Clavaud, C and Bastien, P and Takayasu, L and Iioka, E and Kurokawa, R and Yamashita, N and Hattori, Y and Shindo, C and Breton, L and Hattori, M}, title = {Aging-related changes in the diversity of women's skin microbiomes associated with oral bacteria.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10567}, pmid = {28874721}, issn = {2045-2322}, mesh = {Adult ; Age Factors ; Aged ; Female ; Humans ; *Microbiota ; Middle Aged ; Mouth Mucosa/growth & development/*microbiology ; Propionibacterium/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Skin/growth & development/*microbiology ; }, abstract = {Skin aging is associated with changes in cutaneous physiology including interactions with a skin microbial community. A striking alteration and diversification in the skin microbiome with aging was observed between two different age groups of 37 healthy Japanese women, i.e. younger adults of 21-37 years old and older adults of 60-76 years old, using bacterial 16S rRNA gene sequencing. The analyses revealed that the alpha diversity/species richness was significantly higher in the older than the younger group for the cheek and forehead microbiomes, while the beta diversity in the overall structure significantly differed particularly for the forearm and scalp microbiomes between the two age groups. Taxonomic profiling showed a striking reduction in the relative abundance of the majority skin genus Propionibacterium in the cheek, forearm and forehead microbiomes of the older adults, and identified 38 species including many oral bacteria that significantly differentiated the two age groups with a skin site dependency. Furthermore, we found chronological age-related and unrelated skin clinical parameters that correlate with the observed changes in the skin microbiome diversity. Thus, our data suggested that the diversification of skin microbiomes in adult women was largely affected by chronological and physiological skin aging in association with oral bacteria.}, } @article {pmid28873967, year = {2017}, author = {Kuang, YS and Lu, JH and Li, SH and Li, JH and Yuan, MY and He, JR and Chen, NN and Xiao, WQ and Shen, SY and Qiu, L and Wu, YF and Hu, CY and Wu, YY and Li, WD and Chen, QZ and Deng, HW and Papasian, CJ and Xia, HM and Qiu, X}, title = {Connections between the human gut microbiome and gestational diabetes mellitus.}, journal = {GigaScience}, volume = {6}, number = {8}, pages = {1-12}, pmid = {28873967}, issn = {2047-217X}, support = {MR/P002536/1/MRC_/Medical Research Council/United Kingdom ; R01 AR059781/AR/NIAMS NIH HHS/United States ; R01 AR069055/AR/NIAMS NIH HHS/United States ; }, mesh = {Biomarkers ; Blood Glucose ; Cluster Analysis ; Diabetes, Gestational/*etiology ; Female ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; Models, Biological ; Pregnancy ; ROC Curve ; }, abstract = {The human gut microbiome can modulate metabolic health and affect insulin resistance, and it may play an important role in the etiology of gestational diabetes mellitus (GDM). Here, we compared the gut microbial composition of 43 GDM patients and 81 healthy pregnant women via whole-metagenome shotgun sequencing of their fecal samples, collected at 21-29 weeks, to explore associations between GDM and the composition of microbial taxonomic units and functional genes. A metagenome-wide association study identified 154 837 genes, which clustered into 129 metagenome linkage groups (MLGs) for species description, with significant relative abundance differences between the 2 cohorts. Parabacteroides distasonis, Klebsiella variicola, etc., were enriched in GDM patients, whereas Methanobrevibacter smithii, Alistipes spp., Bifidobacterium spp., and Eubacterium spp. were enriched in controls. The ratios of the gross abundances of GDM-enriched MLGs to control-enriched MLGs were positively correlated with blood glucose levels. A random forest model shows that fecal MLGs have excellent discriminatory power to predict GDM status. Our study discovered novel relationships between the gut microbiome and GDM status and suggests that changes in microbial composition may potentially be used to identify individuals at risk for GDM.}, } @article {pmid28870713, year = {2017}, author = {Zhang, S and Yang, J and Henning, SM and Lee, R and Hsu, M and Grojean, E and Pisegna, R and Ly, A and Heber, D and Li, Z}, title = {Dietary pomegranate extract and inulin affect gut microbiome differentially in mice fed an obesogenic diet.}, journal = {Anaerobe}, volume = {48}, number = {}, pages = {184-193}, doi = {10.1016/j.anaerobe.2017.08.017}, pmid = {28870713}, issn = {1095-8274}, mesh = {*Animal Feed ; Animals ; Biodiversity ; Biomarkers ; Chemokine CCL2/metabolism ; *Dietary Supplements ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; *Inulin/administration & dosage ; Lythraceae/*chemistry ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Obesity/etiology/metabolism ; *Plant Extracts/administration & dosage ; }, abstract = {Growing evidence suggests that dysbiosis of gut microbiota is associated with pathogenesis of a variety of human diseases. Using dietary intervention to shape the composition and metabolism of the gut microbiota is increasingly recognized. In the present study, we investigated the effects of polysaccharide inulin and polyphenol-rich pomegranate extract (PomX) alone or in combination on the cecal microbiota composition and function in a diet induced obesity mouse model. Male C57BL/6 mice were randomly divided into four experimental groups and consumed either high-fat/high-sucrose [HF/HS (32% energy from fat, 25% energy from sucrose, 17% energy from protein)] diet, HF/HS diet supplemented with PomX (0.25%), or inulin (9%) or PomX and inulin in combination for 4 weeks. In mice fed the PomX-diet the proportion of Turicibacteraceae and Ruminococcaceae was significantly increased compared to the control HF/HS diet. Supplementation with inulin alone and inulin + PomX combination significantly increased the proportion of Verrucomicrobiaceae (A. muciniphila) and decreased Clostridiaceae. Only mice fed the inulin diet experienced an increase in serum lipopolysaccharide (LPS) and monocyte chemoattractant protein 1 (MCP-1), which was reversed when feeding the inulin + PomX diet. Feeding the inulin + PomX diet was associated with a significant increase in Bifidobacteriaceae and Rikenellaceae, which may have contributed to the reduction of endotoxemia markers. Inulin supplementation showed lower species richness of gut microbiota compared to mice fed with HF/HS or HF/HS/PomX, and the reduction was reversed by the addition of PomX. Inulin alone and in combination with PomX had distinct microbial clusters determined by both weighted and unweighted UniFrac Beta-Diversity principle coordinate analysis. A total of 19 KEGG biological pathways were significantly regulated in the gut microbiota with PomX and inulin alone or combined treatment. Inulin significantly enhanced KEGG infectious disease-related pathway associated with increase of serum LPS and MCP-1. No changes in gene expression of ileal proinflammatory cytokine and tight junction genes were observed in mice treated with PomX and inulin. Our results demonstrated that the gut microbiota and their biological pathways were differentially effected by dietary PomX and inulin fed combined or alone. It is therefore very important to consider the interaction among bioactive components of food when evaluating potential prebiotic effects.}, } @article {pmid28869283, year = {2017}, author = {Carding, SR and Davis, N and Hoyles, L}, title = {Review article: the human intestinal virome in health and disease.}, journal = {Alimentary pharmacology & therapeutics}, volume = {46}, number = {9}, pages = {800-815}, pmid = {28869283}, issn = {1365-2036}, support = {BB/J004529/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L01632X/1/MRC_/Medical Research Council/United Kingdom ; BB/J004529/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/therapeutic use ; Bacteriophages/isolation & purification ; Feces/virology ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/virology ; Intestines/*virology ; Metagenomics ; Viruses/isolation & purification ; }, abstract = {BACKGROUND: The human virome consists of animal-cell viruses causing transient infections, bacteriophage (phage) predators of bacteria and archaea, endogenous retroviruses and viruses causing persistent and latent infections. High-throughput, inexpensive, sensitive sequencing methods and metagenomics now make it possible to study the contribution dsDNA, ssDNA and RNA virus-like particles make to the human virome, and in particular the intestinal virome.

AIM: To review and evaluate the pioneering studies that have attempted to characterise the human virome and generated an increased interest in understanding how the intestinal virome might contribute to maintaining health, and the pathogenesis of chronic diseases.

METHODS: Relevant virome-related articles were selected for review following extensive language- and date-unrestricted, electronic searches of the literature.

RESULTS: The human intestinal virome is personalised and stable, and dominated by phages. It develops soon after birth in parallel with prokaryotic communities of the microbiota, becoming established during the first few years of life. By infecting specific populations of bacteria, phages can alter microbiota structure by killing host cells or altering their phenotype, enabling phages to contribute to maintaining intestinal homeostasis or microbial imbalance (dysbiosis), and the development of chronic infectious and autoimmune diseases including HIV infection and Crohn's disease, respectively.

CONCLUSIONS: Our understanding of the intestinal virome is fragmented and requires standardised methods for virus isolation and sequencing to provide a more complete picture of the virome, which is key to explaining the basis of virome-disease associations, and how enteric viruses can contribute to disease aetiologies and be rationalised as targets for interventions.}, } @article {pmid28867788, year = {2017}, author = {Dong, B and Yi, Y and Liang, L and Shi, Q}, title = {High Throughput Identification of Antimicrobial Peptides from Fish Gastrointestinal Microbiota.}, journal = {Toxins}, volume = {9}, number = {9}, pages = {}, pmid = {28867788}, issn = {2072-6651}, mesh = {Animals ; Antimicrobial Cationic Peptides/*metabolism ; Bacteria/genetics/isolation & purification/metabolism ; Bacterial Proteins/*metabolism ; Carps/*microbiology ; *Gastrointestinal Microbiome ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; }, abstract = {Antimicrobial peptides (AMPs) are a group of small peptides, which are secreted by almost all creatures in nature. They have been explored in therapeutic and agricultural aspects as they are toxic to many bacteria. A considerable amount of work has been conducted in analyzing 16S and metagenomics of the gastrointestinal (GI) microbiome of grass carp (Ctenopharyngodon idellus). However, these datasets are still untapped resources. In this present study, a homologous search was performed to predict AMPs from our newly generated metagenome of grass carp. We identified five AMPs with high similarities to previously reported bacterial toxins, such as lantibiotic and class II bacteriocins. In addition, we observed that the top abundant genus in the GI microbiota of the grass carp was generally consistent with the putative AMP-producing strains, which are mainly from Lactobacillales. Furthermore, we constructed the phylogenetic relationship of these putative AMP-producing bacteria existing in the GI of grass carp and some popular commercial probiotics (commonly used for microecologics), demonstrating that they are closely related. Thus, these strains have the potential to be developed into novel microecologics. In a word, we provide a high-throughput way to discover AMPs from fish GI microbiota, which can be developed as alternative pathogen antagonists (toxins) for microecologics or probiotic supplements.}, } @article {pmid28866243, year = {2018}, author = {Heeney, DD and Gareau, MG and Marco, ML}, title = {Intestinal Lactobacillus in health and disease, a driver or just along for the ride?.}, journal = {Current opinion in biotechnology}, volume = {49}, number = {}, pages = {140-147}, pmid = {28866243}, issn = {1879-0429}, support = {R01 AT009365/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; Behavior ; Biodiversity ; Cognition ; *Disease ; *Health ; Humans ; Intestines/*microbiology ; Lactobacillus/*physiology ; }, abstract = {Metagenomics and related methods have led to significant advances in our understanding of the human microbiome. Members of the genus Lactobacillus, although best understood for essential roles in food fermentations and applications as probiotics, have also come to the fore in a number of untargeted gut microbiome studies in humans and animals. Even though Lactobacillus is only a minor member of the human colonic microbiota, the proportions of those bacteria are frequently either positively or negatively correlated with human disease and chronic conditions. Recent findings on Lactobacillus species in human and animal microbiome research, together with the increased knowledge on probiotic and other ingested lactobacilli, have resulted in new perspectives on the importance of this genus to human health.}, } @article {pmid28860611, year = {2017}, author = {Bhat, M and Pasini, E and Copeland, J and Angeli, M and Husain, S and Kumar, D and Renner, E and Teterina, A and Allard, J and Guttman, DS and Humar, A}, title = {Impact of Immunosuppression on the Metagenomic Composition of the Intestinal Microbiome: a Systems Biology Approach to Post-Transplant Diabetes.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10277}, pmid = {28860611}, issn = {2045-2322}, mesh = {Animals ; Computational Biology/methods ; Diabetes Mellitus/etiology ; Gastrointestinal Microbiome/*immunology ; Gene Ontology ; Humans ; Hyperglycemia/etiology ; Immunosuppression Therapy/*adverse effects ; Immunosuppressive Agents/adverse effects/therapeutic use ; Insulin Resistance ; Male ; *Metagenome ; *Metagenomics/methods ; RNA, Ribosomal, 16S ; Rats ; Sirolimus/adverse effects/therapeutic use ; Systems Biology/methods ; Tacrolimus/adverse effects/therapeutic use ; Transplantation/adverse effects ; }, abstract = {Solid organ transplantation (SOT) outcomes have continued to improve, although long-term use of immunosuppressants can lead to complications such as diabetes, compromising post-transplant outcomes. In this study, we have characterized the intestinal microbiome (IM) composition at the metagenomic level in the context of hyperglycemia induced by immunosuppressants. Sprague-Dawley rats were subjected to doses of tacrolimus and sirolimus that reliably induce hyperglycemia and an insulin-resistant state. Subsequent exposure to probiotics resulted in reversal of hyperglycemia. 16S rRNA and metagenomic sequencing of stool were done to identify the bacterial genes and pathways enriched in immunosuppression. Bacterial diversity was significantly decreased in sirolimus-treated rats, with 9 taxa significantly less present in both immunosuppression groups: Roseburia, Oscillospira, Mollicutes, Rothia, Micrococcaceae, Actinomycetales and Staphylococcus. Following probiotics, these changes were reversed to baseline. At the metagenomic level, the balance of metabolism was shifted towards the catabolic side with an increase of genes involved in sucrose degradation, similar to diabetes. Conversely, the control rats had greater abundance of anabolic processes and genes involved in starch degradation. Immunosuppression leads to a more catabolic microbial profile, which may influence development of diabetes after SOT. Modulation of the microbiome with probiotics may help in minimizing adverse long-term effects of immunosuppression.}, } @article {pmid28859695, year = {2017}, author = {Cai, Y and Gu, H and Kenney, T}, title = {Learning Microbial Community Structures with Supervised and Unsupervised Non-negative Matrix Factorization.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {110}, pmid = {28859695}, issn = {2049-2618}, support = {250043/ERC_/European Research Council/International ; }, mesh = {Algorithms ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenome ; Metagenomics/*methods ; *Microbial Consortia ; Supervised Machine Learning ; Unsupervised Machine Learning ; }, abstract = {BACKGROUND: Learning the structure of microbial communities is critical in understanding the different community structures and functions of microbes in distinct individuals. We view microbial communities as consisting of many subcommunities which are formed by certain groups of microbes functionally dependent on each other. The focus of this paper is on methods for extracting the subcommunities from the data, in particular Non-Negative Matrix Factorization (NMF). Our methods can be applied to both OTU data and functional metagenomic data. We apply the existing unsupervised NMF method and also develop a new supervised NMF method for extracting interpretable information from classification problems.

RESULTS: The relevance of the subcommunities identified by NMF is demonstrated by their excellent performance for classification. Through three data examples, we demonstrate how to interpret the features identified by NMF to draw meaningful biological conclusions and discover hitherto unidentified patterns in the data. Comparing whole metagenomes of various mammals, (Muegge et al., Science 332:970-974, 2011), the biosynthesis of macrolides pathway is found in hindgut-fermenting herbivores, but not carnivores. This is consistent with results in veterinary science that macrolides should not be given to non-ruminant herbivores. For time series microbiome data from various body sites (Caporaso et al., Genome Biol 12:50, 2011), a shift in the microbial communities is identified for one individual. The shift occurs at around the same time in the tongue and gut microbiomes, indicating that the shift is a genuine biological trait, rather than an artefact of the method. For whole metagenome data from IBD patients and healthy controls (Qin et al., Nature 464:59-65, 2010), we identify differences in a number of pathways (some known, others new).

CONCLUSIONS: NMF is a powerful tool for identifying the key features of microbial communities. These identified features can not only be used to perform difficult classification problems with a high degree of accuracy, they are also very interpretable and can lead to important biological insights into the structure of the communities. In addition, NMF is a dimension-reduction method (similar to PCA) in that it reduces the extremely complex microbial data into a low-dimensional representation, allowing a number of analyses to be performed more easily-for example, searching for temporal patterns in the microbiome. When we are interested in the differences between the structures of two groups of communities, supervised NMF provides a better way to do this, while retaining all the advantages of NMF-e.g. interpretability and a simple biological intuition.}, } @article {pmid28855895, year = {2017}, author = {Novello, G and Gamalero, E and Bona, E and Boatti, L and Mignone, F and Massa, N and Cesaro, P and Lingua, G and Berta, G}, title = {The Rhizosphere Bacterial Microbiota of Vitis vinifera cv. Pinot Noir in an Integrated Pest Management Vineyard.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1528}, pmid = {28855895}, issn = {1664-302X}, abstract = {Microorganisms associated with Vitis vinifera (grapevine) can affect its growth, health and grape quality. The aim of this study was to unravel the biodiversity of the bacterial rhizosphere microbiota of grapevine in an integrated pest management vineyard located in Piedmont, Italy. Comparison between the microbial community structure in the bulk and rhizosphere soil (variable: space) were performed. Moreover, the possible shifts of the bulk and rhizosphere soil microbiota according to two phenological stages such as flowering and early fruit development (variable: time) were characterized. The grapevine microbiota was identified using metagenomics and next-generation sequencing. Biodiversity was higher in the rhizosphere than in the bulk soil, independent of the phenological stage. Actinobacteria were the dominant class with frequencies ≥ 50% in all the soil samples, followed by Proteobacteria, Gemmatimonadetes, and Bacteroidetes. While Actinobacteria and Proteobacteria are well-known as being dominant in soil, this is the first time the presence of Gemmatimonadetes has been observed in vineyard soils. Gaiella was the dominant genus of Actinobacteria in all the samples. Finally, the microbiota associated with grapevine differed from the bulk soil microbiota and these variations were independent of the phenological stage of the plant.}, } @article {pmid28855542, year = {2017}, author = {Shin, JM and Luo, T and Kamarajan, P and Fenno, JC and Rickard, AH and Kapila, YL}, title = {Microbial Communities Associated with Primary and Metastatic Head and Neck Squamous Cell Carcinoma - A High Fusobacterial and Low Streptococcal Signature.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9934}, pmid = {28855542}, issn = {2045-2322}, support = {T32 DE007057/DE/NIDCR NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Bacteria/*classification/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Fusobacteria/isolation & purification ; Head and Neck Neoplasms/*microbiology/secondary ; Humans ; Larynx/microbiology ; Lymph Nodes/microbiology ; Male ; Metagenomics/*methods ; Microbiota ; Middle Aged ; Mouth/microbiology ; Pharynx/microbiology ; RNA, Ribosomal, 16S/genetics ; Sample Size ; Sequence Analysis, DNA/*methods ; Squamous Cell Carcinoma of Head and Neck/*microbiology/secondary ; Streptococcus/isolation & purification ; }, abstract = {Given the potential relationship between head and neck squamous cell carcinoma (HNSCC) and microbial dysbiosis, we profiled the microbiome within healthy normal and tumorous (primary and metastatic) human tissues from the oral cavity, larynx-pharynx, and lymph nodes using 16S rRNA sequencing. Alpha and beta diversity analyses revealed that normal tissues had the greatest richness in community diversity, while the metastatic populations were most closely related to one another. Compared to the normal, the microbiota associated with tumors supported altered abundances in the phyla Fusobacteria, Firmicutes, Actinobacteria and Proteobacteria. Most notably, the relative abundance of Fusobacterium increased whereas Streptococcus decreased in both primary and metastatic samples. Principal coordinate analysis indicated a separation and clustering of samples by tissue status. However, random forest analysis revealed that the microbial profiles alone were a poor predictor for primary and metastatic HNSCC samples. Here, we report that the microbial communities residing in the tumorous tissues are compositionally distinct compared to the normal adjacent tissues. However, likely due to the smaller sample size and sample-to-sample heterogeneity, our prediction models were not able to distinguish by sample types. This work provides a foundation for future studies aimed at understanding the role of the dysbiotic tissue microbiome in HNSCC.}, } @article {pmid28854684, year = {2017}, author = {Li, B and Zhou, X and Zhou, X and Wu, P and Li, M and Feng, M and Peng, X and Ren, B and Cheng, L}, title = {Effects of different substrates/growth media on microbial community of saliva-derived biofilm.}, journal = {FEMS microbiology letters}, volume = {364}, number = {13}, pages = {}, doi = {10.1093/femsle/fnx123}, pmid = {28854684}, issn = {1574-6968}, mesh = {Bacteria/*drug effects/genetics/metabolism ; Biofilms/*drug effects/growth & development ; Culture Media/*pharmacology ; Cysteine/pharmacology ; Dental Plaque/microbiology ; Durapatite/pharmacology ; Glass/chemistry ; Humans ; Linear Models ; Microbial Consortia/*drug effects ; RNA, Ribosomal, 16S ; Saliva/*microbiology ; Saliva, Artificial/pharmacology ; }, abstract = {The aims of this study were to investigate the effects of substrates (glass versus hydroxyapatite [HA]) and growth media (SHI medium versus a modified artificial saliva medium with cysteine) on the microbial community of saliva-derived biofilm in vitro. 16S rRNA gene sequencing technology was used to analyze the microbial community of saliva-derived biofilm cultured for 72 h anaerobically. The metagenomes of biofilms were predicted from the clusters of orthologous groups. No significant difference was found between the saliva-derived biofilms grown on HA and glass in ACE, Chao, Shannon and Simpson indices. The abundances of only a few bacteria on HA were significantly different from those on glass with a low relative abundance (<0.5%). Compared with the biofilms developed in a modified artificial saliva medium with cysteine, biofilms in SHI medium were significantly higher (P < 0.05) in diversity. Linear discriminant analysis coupled with effect size measurement showed that some obligate anaerobic genera (Lactobacillus, Veillonella, Porphyromonas and Leptotrichia) were more abundant in SHI medium biofilms. The biofilms grown in different media were also significantly different in predicted gene categories. In conclusion, the growth media, not the substrates, have significant effects on the microbial community of saliva-derived biofilm in vitro.}, } @article {pmid28853774, year = {2016}, author = {Kadnikov, VV and Ivasenko, DA and Beletsky, AV and Mardanov, AV and Danilova, EV and Pimenov, NV and Karnachuk, OV and Ravin, NV}, title = {A Novel Uncultured Bacterium of the Family Gallionellaceae: Description and Genome Reconstruction Based on the Metagenomic Analysis of Microbial Community in Acid Mine Drainage.}, journal = {Mikrobiologiia}, volume = {85}, number = {4}, pages = {421-435}, pmid = {28853774}, issn = {0026-3656}, mesh = {Acidithiobacillus/classification/genetics/isolation & purification/metabolism ; Acidobacteria/classification/genetics/isolation & purification/metabolism ; Adenosine Triphosphatases/genetics/metabolism ; Electron Transport Chain Complex Proteins/genetics/metabolism ; Electron Transport Complex III/genetics/metabolism ; Electron Transport Complex IV/genetics/metabolism ; Gallionellaceae/classification/*genetics/isolation & purification/metabolism ; Gene Expression ; *Genome, Bacterial ; Humans ; Hydrogen-Ion Concentration ; Iron/metabolism ; Isoenzymes/genetics/metabolism ; *Metagenome ; Metals/chemistry/metabolism ; Microbial Consortia/*genetics ; Mining ; NADH Dehydrogenase/genetics/metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Photosynthesis/genetics ; Phylogeny ; Quinone Reductases/genetics/metabolism ; RNA, Ribosomal, 16S/*genetics ; Siberia ; Sulfate Adenylyltransferase/genetics/metabolism ; Thiobacillus/classification/genetics/isolation & purification/metabolism ; Wastewater/*microbiology ; }, abstract = {Drainage waters at the metal mining areas often have low pH and high content of dissolved metals due to oxidation of sulfide minerals. Extreme conditions limit microbial diversity in- such ecosystems. A drainage water microbial community (6.5'C, pH 2.65) in an open pit at the Sherlovaya Gora polymetallic open-cast mine (Transbaikal region, Eastern Siberia, Russia) was studied using metagenomic techniques. Metagenome sequencing provided information for taxonomic and functional characterization of the micro- bial community. The majority of microorganisms belonged to a single uncultured lineage representing a new Betaproteobacteria species of the genus Gallionella. While no.acidophiles are known among the cultured members of the family Gallionellaceae, similar 16S rRNA gene sequences were detected in acid mine drain- ages. Bacteria ofthe genera Thiobacillus, Acidobacterium, Acidisphaera, and Acidithiobacillus,-which are com- mon in acid mine drainage environments, were the minor components of the community. Metagenomic data were -used to determine the almost complete (-3.4 Mb) composite genome of the new bacterial. lineage desig- nated Candidatus Gallionella acididurans ShG14-8. Genome analysis revealed that Fe(II) oxidation probably involved the cytochromes localized on the outer membrane of the cell. The electron transport chain included NADH dehydrogenase, a cytochrome bc1 complex, an alternative complex III, and cytochrome oxidases of the bd, cbb3, and bo3 types. Oxidation of reduced sulfur compounds probably involved the Sox system, sul- fide-quinone oxidoreductase, adenyl sulfate reductase, and sulfate adenyltransferase. The genes required for autotrophic carbon assimilation via the Calvin cycle were present, while no pathway for nitrogen fixation was revealed. High numbers of RND metal transporters and P type ATPases were probably responsible for resis- tance to heavy metals. The new microorganism was an aerobic chemolithoautotroph of the group of psychrotolerant iron- and sulfur-oxidizing acidophiles of the family Gallionellaceae, which are common in acid mine drainages.}, } @article {pmid28852824, year = {2017}, author = {Bai, Y and Huo, Y and Liao, K and Qu, J}, title = {Influence of microbial community diversity and function on pollutant removal in ecological wastewater treatment.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {19}, pages = {7293-7302}, doi = {10.1007/s00253-017-8464-5}, pmid = {28852824}, issn = {1432-0614}, support = {51578537//National Natural Science Foundation of China/ ; 51420105012//National Natural Science Foundation of China/ ; ZDRW-ZS-2016-5-6//Chinese Academy of Sciences/ ; }, mesh = {Biodegradation, Environmental ; Biomass ; Comamonadaceae/genetics/isolation & purification ; Metagenomics ; *Microbial Consortia ; Nerium/microbiology ; Poaceae/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Waste Disposal, Fluid ; Wastewater/*microbiology ; *Water Purification ; }, abstract = {Traditional wastewater treatments based on activated sludge often encounter the problems of bulking and foaming, as well as malodor. To solve these problems, new treatment technologies have emerged in recent decades, including the ecological wastewater treatment process, which introduces selected local plants into the treatment system. With a focus on the underlying mechanisms of the ecological treatment process, we explored the microbial community biomass, composition, and function in the treatment system to understand the microbial growth in this system and its role in pollutant removal. Flow cytometry analysis revealed that ecological treatment significantly decreased influent bacterial quantity, with around 80% removal. 16S rRNA gene sequencing showed that the ecological treatment also altered the bacterial community structure of the wastewater, leading to a significant change in Comamonadaceae in the effluent. In the internal ecological system, because most of microbes aggregate in the plant rhizosphere and the sludge under plant roots, we selected two plant species (Nerium oleander and Arundo donax) to study the characteristics of rhizosphere and sludge microbes. Metagenomic results showed that the microbial community composition and function differed between the two species, and the microbial communities of A. donax were more sensitive to seasonal effects. Combined with their greater biomass and abundance of metabolic genes, microbes associated with N. oleander showed a greater contribution to pollutant removal. Further, the biodegradation pathways of some micropollutants, e.g., atrazine, were estimated.}, } @article {pmid28852214, year = {2017}, author = {Forster, SC}, title = {Illuminating microbial diversity.}, journal = {Nature reviews. Microbiology}, volume = {15}, number = {10}, pages = {578}, pmid = {28852214}, issn = {1740-1534}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Biodiversity ; Genetic Association Studies ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; *Metagenomics ; Phylogeny ; }, } @article {pmid28852195, year = {2017}, author = {Ozkan, J and Nielsen, S and Diez-Vives, C and Coroneo, M and Thomas, T and Willcox, M}, title = {Temporal Stability and Composition of the Ocular Surface Microbiome.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9880}, pmid = {28852195}, issn = {2045-2322}, mesh = {Adult ; Conjunctiva/*microbiology ; Eyelids/*microbiology ; Female ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S ; }, abstract = {To determine if there is a core ocular surface microbiome and whether there are microbial community changes over time, the conjunctiva of 45 healthy subjects were sampled at three time points over three months and processed using culture-dependent and -independent methods. Contaminant taxa were removed using a linear regression model using taxa abundances in negative controls as predictor of taxa abundances in subject samples. Both cultured cell counts and sequencing indicated low microbial biomass on the ocular surface. No cultured species was found in all subjects at all times or in all subjects at any one time. After removal of contaminant taxa identified in negative controls using a statistical model, the most commonly detected taxon was Corynebacterium (11.1%). No taxa were found in all subjects at all times or in all subjects in any one time, but there were 26 taxa present in at least one or more subjects at all times including Corynebacterium and Streptococcus. The ocular surface contains a low diversity of microorganisms. Using culture dependent and independent methods, the ocular surface does not appear to support a substantial core microbiome. However, consistently present taxa could be observed within individuals suggesting the possibility of individual-specific core microbiomes.}, } @article {pmid28852182, year = {2017}, author = {Mancabelli, L and Milani, C and Lugli, GA and Turroni, F and Mangifesta, M and Viappiani, A and Ticinesi, A and Nouvenne, A and Meschi, T and van Sinderen, D and Ventura, M}, title = {Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9879}, pmid = {28852182}, issn = {2045-2322}, mesh = {Case-Control Studies ; Constipation/*etiology/metabolism ; *Gastrointestinal Microbiome ; Gene Amplification ; Humans ; *Metagenome ; *Metagenomics/methods ; RNA, Ribosomal, 16S ; }, abstract = {Functional constipation (FC) is a gastrointestinal disorder with a high prevalence among the general population. The precise causes of FC are still unknown and are most likely multifactorial. Growing evidence indicates that alterations of gut microbiota composition contribute to constipation symptoms. Nevertheless, many discrepancies exist in literature and no clear link between FC and gut microbiota composition has as yet been identified. In this study, we performed 16 S rRNA-based microbial profiling analysis of 147 stool samples from 68 FC individuals and compared their microbial profiles with those of 79 healthy subjects (HS). Notably, the gut microbiota of FC individuals was shown to be depleted of members belonging to Bacteroides, Roseburia and Coprococcus 3. Furthermore, the metabolic capabilities of the gut microbiomes of five FC and five HS individuals were evaluated through shotgun metagenomics using a MiSeq platform, indicating that HS are enriched in pathways involved in carbohydrate, fatty acid and lipid metabolism as compared to FC. In contrast, the microbiomes corresponding to FC were shown to exhibit high abundance of genes involved in hydrogen production, methanogenesis and glycerol degradation. The identified differences in bacterial composition and metabolic capabilities may play an important role in development of FC symptoms.}, } @article {pmid28852143, year = {2017}, author = {Gribben, PE and Nielsen, S and Seymour, JR and Bradley, DJ and West, MN and Thomas, T}, title = {Microbial communities in marine sediments modify success of an invasive macrophyte.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9845}, pmid = {28852143}, issn = {2045-2322}, mesh = {Australia ; Bacteria ; *Biodiversity ; Ecosystem ; Geologic Sediments/*microbiology ; *Introduced Species ; Metagenome ; Metagenomics/methods ; *Microbiota ; *Oceans and Seas ; *Plants ; }, abstract = {Invasive plants have extensive impacts on ecosystem function and biodiversity globally. Our inability to manage invasive species stems in part from a lack of understanding of the processes that control their successful establishment and spread. To date, studies have largely considered how above-ground processes control native/invasive plant interactions. Emerging research from terrestrial and wetland ecosystems demonstrates that below-ground processes under microbial control can determine the outcome of interactions between native and invasive plants. Whether sediment microbes modify the success of invasive macrophytes in marine ecosystems is untested, despite marine sediment microbes controlling many ecological processes (e.g. nutrient cycling) comparable to those in terrestrial ecosystems. We first show that sediment bacterial communities differ between the native seagrass Zostera capricorni and the invasive alga Caulerpa taxifolia and that those differences relate to functional changes in sulfur cycling between the macrophytes. Second, by experimentally manipulating the microbial communities we show that intact microbial communities in Z. capricorni sediments provide biotic resistance by reducing C. taxifolia fragment growth 119% compared to when they are inactive, and intact microbial communities in C. taxifolia sediments have positive feedbacks by increasing fragment growth 200%. Thus, similar to terrestrial ecosystems, microorganisms appear to indirectly control the success of invasive macrophytes in marine ecosystems.}, } @article {pmid28852134, year = {2017}, author = {Zhou, X and Zhang, Z and Tian, L and Li, X and Tian, C}, title = {Microbial communities in peatlands along a chronosequence on the Sanjiang Plain, China.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9567}, pmid = {28852134}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics ; *Biodiversity ; China ; *Environment ; *Environmental Microbiology ; Geography ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; Soil Microbiology ; }, abstract = {Microbial communities play crucial roles in the global carbon cycle, particularly in peatland ecosystems under climate change. The peatlands of the Sanjiang Plain could be highly vulnerable to global warming because they are mainly located at the southern limit of northern peatlands. In this study, the alpha diversity and composition of bacterial communities in three different minerotrophic fens along a chronosequence were investigated. We captured a rich microbial community that included many rare operational taxonomic units (OTUs) but was dominated by a few bacterial classes that have frequently been detected in other peatland ecosystems. Notably, a large diversity of methanotrophs affiliated with Alpha- and Gammaproteobacteria was also detected. Bacterial alpha diversity and composition varied as a function of peat depth and its associated physical-chemical properties, such as total carbon, total nitrogen, pH and bulk density. We also found that bacterial community turnover (beta diversity) to be significantly correlated with soil age, whereas bacterial alpha diversity was not.}, } @article {pmid28852094, year = {2017}, author = {Debebe, T and Biagi, E and Soverini, M and Holtze, S and Hildebrandt, TB and Birkemeyer, C and Wyohannis, D and Lemma, A and Brigidi, P and Savkovic, V and König, B and Candela, M and Birkenmeier, G}, title = {Unraveling the gut microbiome of the long-lived naked mole-rat.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9590}, pmid = {28852094}, issn = {2045-2322}, mesh = {Animals ; Computational Biology/methods ; *Gastrointestinal Microbiome ; *Longevity ; Metagenome ; Metagenomics/methods ; *Mole Rats ; RNA, Ribosomal, 16S ; }, abstract = {The naked mole-rat (Heterocephalus glaber) is a subterranean mouse-sized African mammal that shows astonishingly few age-related degenerative changes and seems to not be affected by cancer. These features make this wild rodent an excellent model to study the biology of healthy aging and longevity. Here we characterize for the first time the intestinal microbial ecosystem of the naked mole-rat in comparison to humans and other mammals, highlighting peculiarities related to the specific living environment, such as the enrichment in bacteria able to utilize soil sulfate as a terminal electron acceptor to sustain an anaerobic oxidative metabolism. Interestingly, some compositional gut microbiota peculiarities were also shared with human gut microbial ecosystems of centenarians and Hadza hunter-gatherers, considered as models of a healthy gut microbiome and of a homeostatic and highly adaptive gut microbiota-host relationship, respectively. In addition, we found an enrichment of short-chain fatty acids and carbohydrate degradation products in naked mole-rat compared to human samples. These data confirm the importance of the gut microbial ecosystem as an adaptive partner for the mammalian biology and health, independently of the host phylogeny.}, } @article {pmid28852076, year = {2017}, author = {Sharma, AK and Jaiswal, SK and Chaudhary, N and Sharma, VK}, title = {A novel approach for the prediction of species-specific biotransformation of xenobiotic/drug molecules by the human gut microbiota.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9751}, pmid = {28852076}, issn = {2045-2322}, mesh = {Bacteria/classification/*enzymology/genetics/*metabolism ; Biotransformation ; Computational Biology/methods ; Enzymes/*genetics/*metabolism ; *Gastrointestinal Microbiome ; Humans ; Metabolic Networks and Pathways/genetics ; *Microbiota ; Xenobiotics/*metabolism ; }, abstract = {The human gut microbiota is constituted of a diverse group of microbial species harbouring an enormous metabolic potential, which can alter the metabolism of orally administered drugs leading to individual/population-specific differences in drug responses. Considering the large heterogeneous pool of human gut bacteria and their metabolic enzymes, investigation of species-specific contribution to xenobiotic/drug metabolism by experimental studies is a challenging task. Therefore, we have developed a novel computational approach to predict the metabolic enzymes and gut bacterial species, which can potentially carry out the biotransformation of a xenobiotic/drug molecule. A substrate database was constructed for metabolic enzymes from 491 available human gut bacteria. The structural properties (fingerprints) from these substrates were extracted and used for the development of random forest models, which displayed average accuracies of up to 98.61% and 93.25% on cross-validation and blind set, respectively. After the prediction of EC subclass, the specific metabolic enzyme (EC) is identified using a molecular similarity search. The performance was further evaluated on an independent set of FDA-approved drugs and other clinically important molecules. To our knowledge, this is the only available approach implemented as 'DrugBug' tool for the prediction of xenobiotic/drug metabolism by metabolic enzymes of human gut microbiota.}, } @article {pmid28852043, year = {2017}, author = {Mitra, A and MacIntyre, DA and Mahajan, V and Lee, YS and Smith, A and Marchesi, JR and Lyons, D and Bennett, PR and Kyrgiou, M}, title = {Comparison of vaginal microbiota sampling techniques: cytobrush versus swab.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9802}, pmid = {28852043}, issn = {2045-2322}, support = {MR/L009226/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adolescent ; Adult ; Bacterial Load ; Computational Biology/methods ; Cytodiagnosis/methods ; Female ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiological Techniques ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S ; Specimen Handling/methods ; Vagina/*microbiology ; Vaginal Smears/methods ; Young Adult ; }, abstract = {Evidence suggests the vaginal microbiota (VM) may influence risk of persistent Human Papillomavirus (HPV) infection and cervical carcinogenesis. Established cytology biobanks, typically collected with a cytobrush, constitute a unique resource to study such associations longitudinally. It is plausible that compared to rayon swabs; the most commonly used sampling devices, cytobrushes may disrupt biofilms leading to variation in VM composition. Cervico-vaginal samples were collected with cytobrush and rayon swabs from 30 women with high-grade cervical precancer. Quantitative PCR was used to compare bacterial load and Illumina MiSeq sequencing of the V1-V3 regions of the 16S rRNA gene used to compare VM composition. Cytobrushes collected a higher total bacterial load. Relative abundance of bacterial species was highly comparable between sampling devices (R[2] = 0.993). However, in women with a Lactobacillus-depleted, high-diversity VM, significantly less correlation in relative species abundance was observed between devices when compared to those with a Lactobacillus species-dominant VM (p = 0.0049). Cytobrush and swab sampling provide a comparable VM composition. In a small proportion of cases the cytobrush was able to detect underlying high-diversity community structure, not realized with swab sampling. This study highlights the need to consider sampling devices as potential confounders when comparing multiple studies and datasets.}, } @article {pmid28851878, year = {2017}, author = {Colin, Y and Nicolitch, O and Van Nostrand, JD and Zhou, JZ and Turpault, MP and Uroz, S}, title = {Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9604}, pmid = {28851878}, issn = {2045-2322}, mesh = {Carbon/metabolism ; Metagenome ; Metagenomics/methods ; Microbial Interactions ; *Microbiota ; RNA, Ribosomal, 16S ; *Rhizosphere ; Secondary Metabolism ; *Soil Microbiology ; }, abstract = {It has been rarely questioned as to whether the enrichment of specific bacterial taxa found in the rhizosphere of a given plant species changes with different soil types under field conditions and under similar climatic conditions. Understanding tree microbiome interactions is essential because, in contrast to annual plants, tree species require decades to grow and strongly depend on the nutritive resources of the soil. In this context, we tested using a natural toposequence the hypothesis that beech trees select specific taxa and functions in their rhizosphere based on the soil conditions and their nutritive requirements. Our 16S rRNA gene pyrosequencing analyses revealed that the soil type determines the taxa colonizing the beech rhizosphere. A rhizosphere effect was observed in each soil type, but a stronger effect was observed in the nutrient-poor soils. Although the communities varied significantly across the toposequence, we identified a core beech rhizosphere microbiome. Functionally, GeoChip analyses showed a functional redundancy across the toposequence, with genes related to nutrient cycling and to the bacterial immune system being significantly enriched in the rhizosphere. Altogether, the data suggest that, regardless of the soil conditions, trees enrich variable bacterial communities to maintain the functions necessary for their nutrition.}, } @article {pmid28849048, year = {2017}, author = {Chen, H and Xia, Y and Zhu, S and Yang, J and Yao, J and Di, J and Liang, Y and Gao, R and Wu, W and Yang, Y and Shi, C and Hu, D and Qin, H and Wang, Z}, title = {Lactobacillus plantarum LP‑Onlly alters the gut flora and attenuates colitis by inducing microbiome alteration in interleukin‑10 knockout mice.}, journal = {Molecular medicine reports}, volume = {16}, number = {5}, pages = {5979-5985}, pmid = {28849048}, issn = {1791-3004}, mesh = {Actinobacteria/classification/genetics/isolation & purification ; Animals ; Bacteroidetes/classification/genetics/isolation & purification ; Colitis/immunology/microbiology/pathology/*therapy ; DNA, Bacterial/*genetics ; Disease Models, Animal ; Female ; Firmicutes/classification/genetics/isolation & purification ; Gastrointestinal Microbiome/*genetics ; Gene Deletion ; High-Throughput Nucleotide Sequencing ; Homozygote ; Interleukin-10/*deficiency/genetics ; Lactobacillus plantarum/*physiology ; Mice ; Mice, Knockout ; Probiotics/*pharmacology ; Proteobacteria/classification/genetics/isolation & purification ; }, abstract = {The association between inflammatory bowel disease (IBD) and gut microbes has been widely investigated. Our previous study demonstrated that Lactobacillus plantarum LP‑Onlly (LP) applied as a probiotic altered the gut flora and attenuated colitis in interleukin (IL)‑10 knockout (IL‑10‑/‑) mice. In the present study, metagenome sequencing was performed to investigate the gut microbiome in IL‑10‑/‑mice and the influence of oral administration of LP on microbial composition. Metagenomics sequencing was performed to investigate the influence of IBD on the gut microbiome with and without LP treatment. The alteration of the abundances of various taxonomic and functional groups were investigated across these gut microbiomes. The present study demonstrates that Akkermansia muciniphila was significantly enriched in IL‑10‑/‑ mice, and bacteroides were significantly increased following LP administration. In addition, the phylum Bacteroidetes and Firmicutes were significantly influenced by LP administration. Further characterization of functional capacity revealed that in the gut metagenomes of IL‑10‑/‑mice, genes encoding cell cycle control, replication, recombination, repair and cell envelope biogenesis were decreased, but intracellular trafficking, secretion, and vesicular transport were increased. The present findings indicate that the gut metagenome is associated with IBD, and oral administration of LP contributes to prevention of gut inflammation, providing insight into the treatment of IBD.}, } @article {pmid28849032, year = {2017}, author = {Ji, W and Zhu, Y and Kan, P and Cai, Y and Wang, Z and Wu, Z and Yang, P}, title = {Analysis of intestinal microbial communities of cerebral infarction and ischemia patients based on high throughput sequencing technology and glucose and lipid metabolism.}, journal = {Molecular medicine reports}, volume = {16}, number = {4}, pages = {5413-5417}, pmid = {28849032}, issn = {1791-3004}, mesh = {Aged ; Aged, 80 and over ; Blood Glucose ; Brain Ischemia/etiology/*metabolism ; Cerebral Infarction/etiology/*metabolism ; Cluster Analysis ; Female ; *Gastrointestinal Microbiome ; Humans ; *Lipid Metabolism ; Lipids/blood ; Male ; *Metagenome ; *Metagenomics/methods ; Middle Aged ; }, abstract = {Currently, cerebral infarction (CI) is the leading cause of disability and the second leading cause of mortality in China, seriously affecting patient quality of life. Ischemia (IS) is considered to be the early stage of CI. The present study aims to investigate the variation of intestinal microbial communities in patients with CI and IS using high throughput sequencing technology, and then analyze the results to identify a novel potential pathogenic mechanism of CI and IS. In total, 8 patients with CI, 2 patients with IS and 10 healthy volunteers as a control were selected. Throughput sequencing technology was used to analyze the character and microbial population of the gut. The abundance of Escherichia, Bacteroides, Megamonas, Parabacteroides, Akkermansia, Prevotella, Faecalibacterium, Dialister, Bifidobacterium and Ruminococcus was the significant difference in the intestinal microbial communities of the CI and IS patients compared with the healthy group. It was also observed that CI and IS were closely associated with internal glucose metabolism. The intestinal gut disturbance of CI patients may be one of the causes inducing CI by glucose metabolism and maybe considered as a potential method to predict the disease.}, } @article {pmid28848528, year = {2017}, author = {Shih, CJ and Chen, YL and Wang, CH and Wei, ST and Lin, IT and Ismail, WA and Chiang, YR}, title = {Biochemical Mechanisms and Microorganisms Involved in Anaerobic Testosterone Metabolism in Estuarine Sediments.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1520}, pmid = {28848528}, issn = {1664-302X}, abstract = {Current knowledge on the biochemical mechanisms underlying microbial steroid metabolism in anaerobic ecosystems is extremely limited. Sulfate, nitrate, and iron [Fe (III)] are common electron acceptors for anaerobes in estuarine sediments. Here, we investigated anaerobic testosterone metabolism in anaerobic sediments collected from the estuary of Tamsui River, Taiwan. The anaerobic sediment samples were spiked with testosterone (1 mM) and individual electron acceptors (10 mM), including nitrate, Fe[3+], and sulfate. The analysis of androgen metabolites indicated that testosterone biodegradation under denitrifying conditions proceeds through the 2,3-seco pathway, whereas testosterone biodegradation under iron-reducing conditions may proceed through an unidentified alternative pathway. Metagenomic analysis and PCR-based functional assays suggested that Thauera spp. were the major testosterone degraders in estuarine sediment samples incubated with testosterone and nitrate. Thauera sp. strain GDN1, a testosterone-degrading betaproteobacterium, was isolated from the denitrifying sediment sample. This strain tolerates a broad range of salinity (0-30 ppt). Although testosterone biodegradation did not occur under sulfate-reducing conditions, we observed the anaerobic biotransformation of testosterone to estrogens in some testosterone-spiked sediment samples. This is unprecedented since biotransformation of androgens to estrogens is known to occur only under oxic conditions. Our metagenomic analysis suggested that Clostridium spp. might play a role in this anaerobic biotransformation. These results expand our understanding of microbial metabolism of steroids under strictly anoxic conditions.}, } @article {pmid28846439, year = {2018}, author = {Clarke, EL and Lauder, AP and Hofstaedter, CE and Hwang, Y and Fitzgerald, AS and Imai, I and Biernat, W and Rękawiecki, B and Majewska, H and Dubaniewicz, A and Litzky, LA and Feldman, MD and Bittinger, K and Rossman, MD and Patterson, KC and Bushman, FD and Collman, RG}, title = {Microbial Lineages in Sarcoidosis. A Metagenomic Analysis Tailored for Low-Microbial Content Samples.}, journal = {American journal of respiratory and critical care medicine}, volume = {197}, number = {2}, pages = {225-234}, pmid = {28846439}, issn = {1535-4970}, support = {R01 HL113252/HL/NHLBI NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; U01 HL098957/HL/NHLBI NIH HHS/United States ; R61 HL137063/HL/NHLBI NIH HHS/United States ; U01 HL112712/HL/NHLBI NIH HHS/United States ; }, mesh = {Biopsy, Needle ; Case-Control Studies ; DNA, Bacterial/*analysis ; Female ; Humans ; Immunohistochemistry ; Kveim Test ; Male ; Metagenome/*genetics ; Microbiota/*genetics ; Reference Values ; Sarcoidosis/*genetics/*microbiology/pathology ; Sensitivity and Specificity ; Tissue Embedding ; }, abstract = {RATIONALE: The etiology of sarcoidosis is unknown, but microbial agents are suspected as triggers.

OBJECTIVES: We sought to identify bacterial, fungal, or viral lineages in specimens from patients with sarcoidosis enriched relative to control subjects using metagenomic DNA sequencing. Because DNA from environmental contamination contributes disproportionately to samples with low authentic microbial content, we developed improved methods for filtering environmental contamination.

METHODS: We analyzed specimens from subjects with sarcoidosis (n = 93), control subjects without sarcoidosis (n = 72), and various environmental controls (n = 150). Sarcoidosis specimens consisted of two independent sets of formalin-fixed, paraffin-embedded lymph node biopsies, BAL, Kveim reagent, and fresh granulomatous spleen from a patient with sarcoidosis. All specimens were analyzed by bacterial 16S and fungal internal transcribed spacer ribosomal RNA gene sequencing. In addition, BAL was analyzed by shotgun sequencing of fractions enriched for viral particles, and Kveim and spleen were subjected to whole-genome shotgun sequencing.

MEASUREMENTS AND MAIN RESULTS: In one tissue set, fungi in the Cladosporiaceae family were enriched in sarcoidosis compared with nonsarcoidosis tissues; in the other tissue set, we detected enrichment of several bacterial lineages in sarcoidosis but not Cladosporiaceae. BAL showed limited enrichment of Aspergillus fungi. Several microbial lineages were detected in Kveim and spleen, including Cladosporium. No microbial lineage was enriched in more than one sample type after correction for multiple comparisons.

CONCLUSIONS: Metagenomic sequencing revealed enrichment of microbes in single types of sarcoidosis samples but limited concordance across sample types. Statistical analysis accounting for environmental contamination was essential to avoiding false positives.}, } @article {pmid28844808, year = {2017}, author = {Torres-Fuentes, C and Schellekens, H and Dinan, TG and Cryan, JF}, title = {The microbiota-gut-brain axis in obesity.}, journal = {The lancet. Gastroenterology & hepatology}, volume = {2}, number = {10}, pages = {747-756}, doi = {10.1016/S2468-1253(17)30147-4}, pmid = {28844808}, issn = {2468-1253}, mesh = {Affect ; Appetite Regulation ; Brain/*metabolism ; Diet, Reducing ; Energy Metabolism ; Fecal Microbiota Transplantation ; Feeding Behavior/psychology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; Obesity/*metabolism/psychology/therapy ; Prebiotics ; Probiotics/therapeutic use ; Reward ; }, abstract = {Changes in microbial diversity and composition are increasingly associated with several disease states including obesity and behavioural disorders. Obesity-associated microbiota alter host energy harvesting, insulin resistance, inflammation, and fat deposition. Additionally, intestinal microbiota can regulate metabolism, adiposity, homoeostasis, and energy balance as well as central appetite and food reward signalling, which together have crucial roles in obesity. Moreover, some strains of bacteria and their metabolites might target the brain directly via vagal stimulation or indirectly through immune-neuroendocrine mechanisms. Therefore, the gut microbiota is becoming a target for new anti-obesity therapies. Further investigations are needed to elucidate the intricate gut-microbiota-host relationship and the potential of gut-microbiota-targeted strategies, such as dietary interventions and faecal microbiota transplantation, as promising metabolic therapies that help patients to maintain a healthy weight throughout life.}, } @article {pmid28843021, year = {2018}, author = {Heintz-Buschart, A and Pandey, U and Wicke, T and Sixel-Döring, F and Janzen, A and Sittig-Wiegand, E and Trenkwalder, C and Oertel, WH and Mollenhauer, B and Wilmes, P}, title = {The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder.}, journal = {Movement disorders : official journal of the Movement Disorder Society}, volume = {33}, number = {1}, pages = {88-98}, pmid = {28843021}, issn = {1531-8257}, mesh = {Aged ; Case-Control Studies ; Cohort Studies ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Middle Aged ; Nose/*microbiology ; Parkinson Disease/*microbiology ; REM Sleep Behavior Disorder/*microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; RNA, Ribosomal, 18S/genetics/metabolism ; }, abstract = {BACKGROUND: Increasing evidence connects the gut microbiota and the onset and/or phenotype of Parkinson's disease (PD). Differences in the abundances of specific bacterial taxa have been reported in PD patients. It is, however, unknown whether these differences can be observed in individuals at high risk, for example, with idiopathic rapid eye movement sleep behavior disorder, a prodromal condition of α-synuclein aggregation disorders including PD.

OBJECTIVES: To compare microbiota in carefully preserved nasal wash and stool samples of subjects with idiopathic rapid eye movement sleep behavior disorder, manifest PD, and healthy individuals.

METHODS: Microbiota of flash-frozen stool and nasal wash samples from 76 PD patients, 21 idiopathic rapid eye movement sleep behavior disorder patients, and 78 healthy controls were assessed by 16S and 18S ribosomal RNA amplicon sequencing. Seventy variables, related to demographics, clinical parameters including nonmotor symptoms, and sample processing, were analyzed in relation to microbiome variability and controlled differential analyses were performed.

RESULTS: Differentially abundant gut microbes, such as Akkermansia, were observed in PD, but no strong differences in nasal microbiota. Eighty percent of the differential gut microbes in PD versus healthy controls showed similar trends in idiopathic rapid eye movement sleep behavior disorder, for example, Anaerotruncus and several Bacteroides spp., and correlated with nonmotor symptoms. Metagenomic sequencing of select samples enabled the reconstruction of genomes of so far uncharacterized differentially abundant organisms.

CONCLUSION: Our study reveals differential abundances of gut microbial taxa in PD and its prodrome idiopathic rapid eye movement sleep behavior disorder in comparison to the healthy controls, and highlights the potential of metagenomics to identify and characterize microbial taxa, which are enriched or depleted in PD and/or idiopathic rapid eye movement sleep behavior disorder. © 2017 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.}, } @article {pmid28842593, year = {2017}, author = {Ojha, A and Sinha, DK and Padmakumari, AP and Bentur, JS and Nair, S}, title = {Bacterial Community Structure in the Asian Rice Gall Midge Reveals a Varied Microbiome Rich in Proteobacteria.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9424}, pmid = {28842593}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; Diptera/*microbiology ; Metagenome ; Metagenomics/methods ; *Microbiota ; Proteobacteria/*classification/*genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The Asian rice gall midge (ARGM) has emerged as a model gall forming pest of rice. The ARGM infestation of rice results in failure of panicle formation and economic loss. Understanding the molecular basis of ARGM-rice interactions is very crucial in order to control this devastating pest of rice. The current investigation was devised to identify bacterial communities present in the ARGM and in addition the bacterial diversity in the maggots during their interaction with susceptible or resistant rice varieties. Sequencing of 16S rRNA bacterial gene (V3-V4 region) revealed differences in the microflora of the ARGM maggots feeding on susceptible or resistant rice hosts. Results revealed that Wolbachia was the predominant bacterium in pupae and adults while Pseudomonas was predominant in maggots. Further, we observed that members of proteobacteria were predominant across all the samples. There was high species diversity in maggots isolated from susceptible rice and a high representation of unclassified bacteria in maggots isolated from resistant rice. This is the first study that reports variation of microbiome of the ARGM, based on host phenotype from which it was isolated, and results suggest that these variations could have an important role in host's susceptibility.}, } @article {pmid28842259, year = {2018}, author = {van Gelder, S and Röhrig, N and Schattenberg, F and Cichocki, N and Schumann, J and Schmalz, G and Haak, R and Ziebolz, D and Müller, S}, title = {A cytometric approach to follow variation and dynamics of the salivary microbiota.}, journal = {Methods (San Diego, Calif.)}, volume = {134-135}, number = {}, pages = {67-79}, doi = {10.1016/j.ymeth.2017.08.009}, pmid = {28842259}, issn = {1095-9130}, mesh = {Flow Cytometry/*methods ; Humans ; Metagenome/genetics ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics/isolation & purification ; Saliva/*microbiology ; }, abstract = {Microbial flow cytometry is an established fast and economic technique for complex ecosystem studies and enables visualization of rapidly changing community structures by measuring characteristics of single microbial cells. Cytometric evaluation routines are available such as flowCyBar which are useful for automatic data processing. Here, a cytometric workflow was established which allows to routinely analyze salivary microbiomes on the example of ten oral healthy subjects. First, saliva was collected within a 3-month period, cytometrically analyzed and the evolution of the microbiomes followed as well as the calculation of their intra- and inter-subject similarity. Second, the respective microbiomes were stressed by exposition to high sugar or acid concentrations and immediate changes were recorded. Third, bactericide solutions were tested on their impact on the microbiomes. In all three set ups huge intra-individual variations in cytometric community structures were found to be largely absent, even under stress, while inter-individual diversity was obvious. The bacterial cell counts of saliva samples were found to vary between 3.0×10[7] and 6.2×10[8] cells per sample and subject in undisturbed environments. The application of the two bactericides did not cause noteworthy diversity changes but the loss in cell numbers by about 50% was high after treatment. Illumina® sequencing of whole microbiomes or sorted sub-microbiomes revealed typical phyla such as Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria. This approach is useful for fast monitoring of individual salivary microbiomes and automatic calculation of intra- and inter-individual dynamic changes and variability and opens insight into ecological principles leading to their sustainment in their individual environment.}, } @article {pmid28841911, year = {2017}, author = {Jeon, SJ and Cunha, F and Vieira-Neto, A and Bicalho, RC and Lima, S and Bicalho, ML and Galvão, KN}, title = {Blood as a route of transmission of uterine pathogens from the gut to the uterus in cows.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {109}, pmid = {28841911}, issn = {2049-2618}, mesh = {Animals ; Bacteria/classification/*genetics/*isolation & purification/pathogenicity ; Bacteroides/physiology ; Blood/*microbiology ; Cattle/*microbiology ; Feces/*microbiology ; Female ; Gene Regulatory Networks ; Metagenomics ; Microbial Interactions ; *Microbiota ; Polymerase Chain Reaction ; Porphyromonas/physiology ; *Postpartum Period ; Uterus/*microbiology ; Vagina/microbiology ; }, abstract = {BACKGROUND: Metritis is an inflammatory disease of the uterus caused by bacterial infection, particularly Bacteroides, Porphyromonas, and Fusobacterium. Bacteria from the environment, feces, or vagina are believed to be the only sources of uterine contamination. Blood seeps into the uterus after calving; therefore, we hypothesized that blood could also be a seeding source of uterine bacteria. Herein, we compared bacterial communities from blood, feces, and uterine samples from the same cows at 0 and 2 days postpartum using deep sequencing and qPCR. The vaginal microbiome 7 days before calving was also compared.

RESULTS: There was a unique structure of bacterial communities by sample type. Principal coordinate analysis revealed two distinct clusters for blood and feces, whereas vaginal and uterine bacterial communities were more scattered, indicating greater variability. Cluster analysis indicated that uterine bacterial communities were more similar to fecal bacterial communities than vaginal and blood bacterial communities. Nonetheless, there were core genera shared by all blood, feces, vaginal, and uterine samples. Major uterine pathogens such as Bacteroides, Porphyromonas, and Fusobacterium were part of the core genera in blood, feces, and vagina. Other uterine pathogens such as Prevotella and Helcococcus were not part of the core genera in vaginal samples. In addition, uterine pathogens showed a strong and significant interaction with each other in the network of blood microbiota, but not in feces or vagina. These microbial interactions in blood may be an important component of disease etiology. The copy number of total bacteria in blood and uterus was correlated; the same did not occur in other sites. Bacteroides heparinolyticus was more abundant in the uterus on day 0, and both B. heparinolyticus and Fusobacterium necrophorum were more abundant in the uterus than in the blood and feces on day 2. This indicates that B. heparinolyticus has a tropism for the uterus, whereas both pathogens thrive in the uterine environment early postpartum.

CONCLUSIONS: Blood harbored a unique microbiome that contained the main uterine pathogens such as Bacteroides, Porphyromonas, and Fusobacterium. The presence of these pathogens in blood shortly after calving shows the feasibility of hematogenous spread of uterine pathogens in cows.}, } @article {pmid28839269, year = {2017}, author = {Chen, WY and Ng, TH and Wu, JH and Chen, JW and Wang, HC}, title = {Microbiome Dynamics in a Shrimp Grow-out Pond with Possible Outbreak of Acute Hepatopancreatic Necrosis Disease.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9395}, pmid = {28839269}, issn = {2045-2322}, mesh = {Acute Disease ; Animal Diseases/*microbiology ; Animals ; Crustacea/*microbiology ; Disease Outbreaks ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; Ponds/*microbiology ; RNA, Ribosomal, 16S ; Vibrio Infections/*veterinary ; *Vibrio parahaemolyticus ; *Water Microbiology ; }, abstract = {Acute hepatopancreatic necrosis disease (AHPND) (formerly, early mortality syndrome) is a high-mortality-rate shrimp disease prevalent in shrimp farming areas. Although AHPND is known to be caused by pathogenic Vibrio parahaemolyticus hosting the plasmid-related PirAB[vp] toxin gene, the effects of disturbances in microbiome have not yet been studied. We took 62 samples from a grow-out pond during an AHPND developing period from Days 23 to 37 after stocking white postlarvae shrimp and sequenced the 16S rRNA genes with Illumina sequencing technology. The microbiomes of pond seawater and shrimp stomachs underwent varied dynamic succession during the period. Despite copies of PirAB[vp], principal co-ordinates analysis revealed two distinctive stages of change in stomach microbiomes associated with AHPND. AHPND markedly changed the bacterial diversity in the stomachs; it decreased the Shannon index by 53.6% within approximately 7 days, shifted the microbiome with Vibrio and Candidatus Bacilloplasma as predominant populations, and altered the species-to-species connectivity and complexity of the interaction network. The AHPND-causing Vibrio species were predicted to develop a co-occurrence pattern with several resident and transit members within Candidatus Bacilloplasma and Cyanobacteria. This study's insights into microbiome dynamics during AHPND infection can be valuable for minimising this disease in shrimp farming ponds.}, } @article {pmid28837853, year = {2018}, author = {Sarma, SM and Singh, DP and Singh, P and Khare, P and Mangal, P and Singh, S and Bijalwan, V and Kaur, J and Mantri, S and Boparai, RK and Mazumder, K and Bishnoi, M and Bhutani, KK and Kondepudi, KK}, title = {Finger millet arabinoxylan protects mice from high-fat diet induced lipid derangements, inflammation, endotoxemia and gut bacterial dysbiosis.}, journal = {International journal of biological macromolecules}, volume = {106}, number = {}, pages = {994-1003}, doi = {10.1016/j.ijbiomac.2017.08.100}, pmid = {28837853}, issn = {1879-0003}, mesh = {Adipose Tissue, White/drug effects/metabolism ; Animals ; Body Weight ; Diet, High-Fat/adverse effects ; Dysbiosis/*diet therapy/microbiology/pathology ; *Eleusine ; Endotoxemia/*diet therapy/metabolism/pathology ; Gastrointestinal Microbiome/drug effects ; Gene Expression Regulation/drug effects ; Glucose Tolerance Test ; Humans ; Inflammation/*diet therapy/metabolism/pathology ; Lipid Metabolism/drug effects/genetics ; Liver/drug effects/metabolism ; Mice ; Xylans/*administration & dosage/chemistry ; }, abstract = {Arabinoxylan (AX), a non-starch polysaccharide extracted from cereals such as wheat, rice and millets, is known to impart various health promoting effects. Our earlier study suggested that finger millet (FM) could ameliorate high fat diet (HFD)-induced metabolic derangements. The present study is aimed to evaluate the effect of FM-AX supplementation, a key bioactive from finger millet, on HFD-induced metabolic and gut bacterial derangements. Male Swiss albino mice were fed with normal chow diet (NPD) or HFD (60%kcal from fat) for 10 weeks. FM-AX was orally supplemented at doses of 0.5 and 1.0g/kg bodyweight on every alternate day for 10 weeks. Glucose tolerance, serum hormones, hepatic lipid accumulation and inflammation, white adipose tissue marker gene expression, adipocyte size and inflammation; metagenomic alterations in cecal bacteria; cecal short chain fatty acids and colonic tight junction gene expressions were studied. FM-AX supplementation prevented HFD-induced weight gain, alerted glucose tolerance and serum lipid profile, hepatic lipid accumulation and inflammation. Hepatic and white adipose tissue gene expressions were beneficially modulated. Further, AX supplementation prevented metagenomic alterations in cecum; improved ileal and colonic health and overall prevented metabolic endotoxemia. Present work suggests that AX from finger millet can be developed as a nutraceutical for the management of HFD- induced obesity.}, } @article {pmid28835919, year = {2017}, author = {Dickson, LB and Jiolle, D and Minard, G and Moltini-Conclois, I and Volant, S and Ghozlane, A and Bouchier, C and Ayala, D and Paupy, C and Moro, CV and Lambrechts, L}, title = {Carryover effects of larval exposure to different environmental bacteria drive adult trait variation in a mosquito vector.}, journal = {Science advances}, volume = {3}, number = {8}, pages = {e1700585}, pmid = {28835919}, issn = {2375-2548}, mesh = {Animals ; Antibiosis ; *Bacteria ; *Biological Variation, Population ; Breeding ; Dengue/transmission ; Ecosystem ; Environment ; *Environmental Microbiology ; Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Humans ; Larva ; Life Cycle Stages ; Metagenome ; Metagenomics ; Microbiota ; Mosquito Vectors/*growth & development/*microbiology/virology ; *Quantitative Trait, Heritable ; }, abstract = {Conditions experienced during larval development of holometabolous insects can affect adult traits, but whether differences in the bacterial communities of larval development sites contribute to variation in the ability of insect vectors to transmit human pathogens is unknown. We addressed this question in the mosquito Aedes aegypti, a major arbovirus vector breeding in both sylvatic and domestic habitats in Sub-Saharan Africa. Targeted metagenomics revealed differing bacterial communities in the water of natural breeding sites in Gabon. Experimental exposure to different native bacterial isolates during larval development resulted in significant differences in pupation rate and adult body size but not life span. Larval exposure to an Enterobacteriaceae isolate resulted in decreased antibacterial activity in adult hemolymph and reduced dengue virus dissemination titer. Together, these data provide the proof of concept that larval exposure to different bacteria can drive variation in adult traits underlying vectorial capacity. Our study establishes a functional link between larval ecology, environmental microbes, and adult phenotypic variation in a holometabolous insect vector.}, } @article {pmid28835692, year = {2017}, author = {Freitas, AC and Chaban, B and Bocking, A and Rocco, M and Yang, S and Hill, JE and Money, DM and , }, title = {The vaginal microbiome of pregnant women is less rich and diverse, with lower prevalence of Mollicutes, compared to non-pregnant women.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9212}, pmid = {28835692}, issn = {2045-2322}, support = {MOP-82799//CIHR/Canada ; }, mesh = {Adolescent ; Adult ; Bacterial Load ; *Biodiversity ; Female ; Humans ; Lactobacillus ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Phylogeny ; Pregnancy ; RNA, Ribosomal, 16S ; Tenericutes/*classification ; Vagina/*microbiology ; Young Adult ; }, abstract = {The vaginal microbiome plays an important role in maternal and neonatal health. Imbalances in this microbiota (dysbiosis) during pregnancy are associated with negative reproductive outcomes, such as pregnancy loss and preterm birth, but the underlying mechanisms remain poorly understood. Consequently a comprehensive understanding of the baseline microbiome in healthy pregnancy is needed. We characterized the vaginal microbiomes of healthy pregnant women at 11-16 weeks of gestational age (n = 182) and compared them to those of non-pregnant women (n = 310). Profiles were created by pyrosequencing of the cpn60 universal target region. Microbiome profiles of pregnant women clustered into six Community State Types: I, II, III, IVC, IVD and V. Overall microbiome profiles could not be distinguished based on pregnancy status. However, the vaginal microbiomes of women with healthy ongoing pregnancies had lower richness and diversity, lower prevalence of Mycoplasma and Ureaplasma and higher bacterial load when compared to non-pregnant women. Lactobacillus abundance was also greater in the microbiomes of pregnant women with Lactobacillus-dominated CSTs in comparison with non-pregnant women. This study provides further information regarding characteristics of the vaginal microbiome of low-risk pregnant women, providing a baseline for forthcoming studies investigating the diagnostic potential of the microbiome for prediction of adverse pregnancy outcomes.}, } @article {pmid28835659, year = {2017}, author = {Parker, EPK and Praharaj, I and John, J and Kaliappan, SP and Kampmann, B and Kang, G and Grassly, NC}, title = {Changes in the intestinal microbiota following the administration of azithromycin in a randomised placebo-controlled trial among infants in south India.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9168}, pmid = {28835659}, issn = {2045-2322}, support = {//Medical Research Council/United Kingdom ; }, mesh = {Age Factors ; Anti-Bacterial Agents/*administration & dosage ; Azithromycin/*administration & dosage ; Bacteria/classification/drug effects/genetics ; Bacterial Infections/drug therapy/microbiology ; Biodiversity ; Female ; Gastroenteritis/drug therapy/microbiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; India/epidemiology ; Infant ; Infant, Newborn ; Male ; Metagenome ; Metagenomics/methods ; Public Health Surveillance ; Time Factors ; }, abstract = {Macrolides are among the most widely prescribed antibiotics worldwide. However, their impact on the gut's bacterial microbiota remains uncertain. We characterised the intestinal microbiota in 6-11 month-old infants in India who received a 3-day course of azithromycin or placebo during a randomised trial of oral poliovirus vaccine immunogenicity (CTRI/2014/05/004588). In 60 infants per study arm, we sequenced the V4 region of the bacterial 16S rRNA gene in stool samples collected before and 12 days after finishing treatment. We also tested for the presence of common bacterial, viral, and eukaryotic enteropathogens in the same samples using real-time PCR in a Taqman array card (TAC) format. Azithromycin induced a modest decline in microbiota richness and a shift in taxonomic composition driven by a reduction in the relative abundance of Proteobacteria and Verrucomicrobia (specifically Akkermansia muciniphila). The former phylum includes pathogenic strains of Escherichia coli and Campylobacter spp. that declined in prevalence based on the TAC assay. These findings differ from previous observations among older children and adults in Europe and North America, suggesting that the effects of azithromycin on the bacterial microbiota may be specific to the age and geographic setting of its recipients.}, } @article {pmid28835624, year = {2017}, author = {Nie, Z and Zheng, Y and Xie, S and Zhang, X and Song, J and Xia, M and Wang, M}, title = {Unraveling the correlation between microbiota succession and metabolite changes in traditional Shanxi aged vinegar.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9240}, pmid = {28835624}, issn = {2045-2322}, mesh = {Acetic Acid/*metabolism ; Bacteria/classification/genetics ; Biodiversity ; *Fermentation ; *Food Microbiology ; Food Preservation ; Fungi/classification/genetics ; *Metabolomics/methods ; Metagenome ; Metagenomics/methods ; *Microbiota ; Models, Theoretical ; Phylogeny ; }, abstract = {Shanxi aged vinegar (SAV) is a well-known vinegar produced by traditional solid-state fermentation and has been used in China for thousands of years. However, how microorganisms and their metabolites change along with fermentation is unclear. Here, 454 high-throughput sequencing and denaturing gradient gel electrophoresis were used to investigate the composition of microbial community. Metabolites were further analyzed by gas chromatography-mass spectrometry and high-performance liquid chromatography. Results showed that the composition of bacterial community changed dramatically at different stages of fermentation. The bacterial genera (relative abundance > 0.1%) decreased from 17 in daqu (starter used in starch saccharification) to 2 at the 12th day of alcohol fernemtation (AF). 15 bacterial genera at the 1st day of acetic acid fermentation (AAF) decreased to 4 genera, involving Acetobacter (50.9%), Lactobacillus (47.9%), Komagataeibacter (formerly Gluconacetobacter, 0.7%) and Propionibacterium (0.1%) at the 7th day of AAF. The structure of fungal community was more homogeneous. Saccharomyces and Saccharomycopsis were predominant in AF and AAF. A total of 87 kinds of nonvolatile metabolites were detected. Canonical correspondence analysis showed a significant correlation between the microbiota succession and the formation of metabolites during the fermentation of SAV. This study provides detailed information for the fermentation mechanism of traditional SAV.}, } @article {pmid28835538, year = {2017}, author = {Ngugi, DK and Miyake, S and Cahill, M and Vinu, M and Hackmann, TJ and Blom, J and Tietbohl, MD and Berumen, ML and Stingl, U}, title = {Genomic diversification of giant enteric symbionts reflects host dietary lifestyles.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {36}, pages = {E7592-E7601}, pmid = {28835538}, issn = {1091-6490}, mesh = {Animals ; Bacteria/metabolism ; Biomass ; Diet ; Ecology ; Fishes/metabolism/microbiology/physiology ; Genomics/methods ; Herbivory/physiology ; Host-Pathogen Interactions/*physiology ; Life Style ; Metagenomics/methods ; Microbiota/physiology ; Phaeophyceae/metabolism/microbiology/physiology ; Phylogeny ; Polysaccharides/metabolism ; Rhodophyta/metabolism/microbiology/physiology ; Symbiosis/*physiology ; }, abstract = {Herbivorous surgeonfishes are an ecologically successful group of reef fish that rely on marine algae as their principal food source. Here, we elucidated the significance of giant enteric symbionts colonizing these fishes regarding their roles in the digestive processes of hosts feeding predominantly on polysiphonous red algae and brown Turbinaria algae, which contain different polysaccharide constituents. Using metagenomics, single-cell genomics, and metatranscriptomic analyses, we provide evidence of metabolic diversification of enteric microbiota involved in the degradation of algal biomass in these fishes. The enteric microbiota is also phylogenetically and functionally simple relative to the complex lignocellulose-degrading microbiota of terrestrial herbivores. Over 90% of the enzymes for deconstructing algal polysaccharides emanate from members of a single bacterial lineage, "Candidatus Epulopiscium" and related giant bacteria. These symbionts lack cellulases but encode a distinctive and lineage-specific array of mostly intracellular carbohydrases concurrent with the unique and tractable dietary resources of their hosts. Importantly, enzymes initiating the breakdown of the abundant and complex algal polysaccharides also originate from these symbionts. These are also highly transcribed and peak according to the diel lifestyle of their host, further supporting their importance and host-symbiont cospeciation. Because of their distinctive genomic blueprint, we propose the classification of these giant bacteria into three candidate genera. Collectively, our findings show that the acquisition of metabolically distinct "Epulopiscium" symbionts in hosts feeding on compositionally varied algal diets is a key niche-partitioning driver in the nutritional ecology of herbivorous surgeonfishes.}, } @article {pmid28835260, year = {2017}, author = {Dombrowski, N and Seitz, KW and Teske, AP and Baker, BJ}, title = {Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {106}, pmid = {28835260}, issn = {2049-2618}, mesh = {Archaea/classification/*genetics/*metabolism/physiology ; Bacteria/*genetics/*metabolism ; Biodiversity ; DNA, Bacterial/genetics ; Deltaproteobacteria/classification/genetics/metabolism ; Genomics ; Hydrocarbons/*metabolism ; Hydrothermal Vents/*microbiology ; Metagenome ; Metagenomics ; Methane/metabolism ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Deep-sea hydrothermal vents are hotspots for productivity and biodiversity. Thermal pyrolysis and circulation produce fluids rich in hydrocarbons and reduced compounds that stimulate microbial activity in surrounding sediments. Several studies have characterized the diversity of Guaymas Basin (Gulf of California) sediment-inhabiting microorganisms; however, many of the identified taxa lack cultures or genomic representations. Here, we resolved the metabolic potential and community-level interactions of these diverse communities by reconstructing and analyzing microbial genomes from metagenomic sequencing data.

RESULTS: We reconstructed 115 microbial metagenome-assembled genomes comprising 27 distinct archaeal and bacterial phyla. The archaea included members of the DPANN and TACK superphyla, Bathyarchaeota, novel Methanosarcinales (GoM-Arc1), and anaerobic methane-oxidizing lineages (ANME-1). Among the bacterial phyla, members of the Bacteroidetes, Chloroflexi, and Deltaproteobacteria were metabolically versatile and harbored potential pathways for hydrocarbon and lipid degradation and a variety of respiratory processes. Genes encoding enzymes that activate anaerobic hydrocarbons for degradation were detected in Bacteroidetes, Chloroflexi, Latescibacteria, and KSB1 phyla, while the reconstructed genomes for most candidate bacteria phyla (Aminicenantes, Atribacteria, Omnitrophica, and Stahlbacteria) indicated a fermentative metabolism. Newly obtained GoM-Arc1 archaeal genomes encoded novel pathways for short-chain hydrocarbon oxidation by alkyl-coenzyme M formation. We propose metabolic linkages among different functional groups, such as fermentative community members sharing substrate-level interdependencies with sulfur- and nitrogen-cycling microbes.

CONCLUSIONS: Overall, inferring the physiologies of archaea and bacteria from metagenome-assembled genomes in hydrothermal deep-sea sediments has revealed potential mechanisms of carbon cycling in deep-sea sediments. Our results further suggest a network of biogeochemical interdependencies in organic matter utilization, hydrocarbon degradation, and respiratory sulfur cycling among deep-sea-inhabiting microbial communities.}, } @article {pmid28835202, year = {2017}, author = {Bond, SL and Timsit, E and Workentine, M and Alexander, T and Léguillette, R}, title = {Upper and lower respiratory tract microbiota in horses: bacterial communities associated with health and mild asthma (inflammatory airway disease) and effects of dexamethasone.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {184}, pmid = {28835202}, issn = {1471-2180}, mesh = {Animals ; Asthma/drug therapy/*microbiology/veterinary ; Bacteria/classification/*drug effects/isolation & purification/pathogenicity ; Biodiversity ; Bronchoalveolar Lavage Fluid/immunology/microbiology ; DNA, Bacterial ; Dexamethasone/*pharmacology ; Horse Diseases/drug therapy/immunology/*microbiology ; Horses/*microbiology ; Inflammation/drug therapy/microbiology ; Metagenomics ; Microbial Consortia/drug effects ; Microbiota/*drug effects ; Respiratory System/immunology/*microbiology ; }, abstract = {BACKGROUND: The microbial composition of the equine respiratory tract, and differences due to mild equine asthma (also called Inflammatory Airway Disease (IAD)) have not been reported. The primary treatment for control of IAD in horses are corticosteroids. The objectives were to characterize the upper and lower respiratory tract microbiota associated with respiratory health and IAD, and to investigate the effects of dexamethasone on these bacterial communities using high throughput sequencing.

RESULTS: The respiratory microbiota of horses was dominated by four major phyla, Proteobacteria (43.85%), Actinobacteria (21.63%), Firmicutes (16.82%), and Bacteroidetes (13.24%). Fifty genera had a relative abundance > 0.1%, with Sphingomonas and Pantoea being the most abundant. The upper and lower respiratory tract microbiota differed in healthy horses, with a decrease in richness in the lower airways, and 2 OTUs that differed in abundance. There was a separation between bacterial communities in the lower respiratory tract of healthy and IAD horses; 6 OTUs in the tracheal community had different abundance with disease status, with Streptococcus being increased in IAD horses. Treatment with dexamethasone had an effect on the lower respiratory tract microbiota of both heathy and IAD horses, with 8 OTUs increasing in abundance (including Streptococcus) and 1 OTU decreasing.

CONCLUSIONS: The lower respiratory tract microbiota differed between healthy and IAD horses. Further research on the role of Streptococcus in IAD is warranted. Dexamethasone treatment affected the lower respiratory tract microbiota, which suggests that control of bacterial overgrowth in IAD horses treated with dexamethasone could be part of the treatment strategy.}, } @article {pmid28834331, year = {2017}, author = {O' Donnell, MM and Harris, HMB and Ross, RP and O'Toole, PW}, title = {Core fecal microbiota of domesticated herbivorous ruminant, hindgut fermenters, and monogastric animals.}, journal = {MicrobiologyOpen}, volume = {6}, number = {5}, pages = {}, pmid = {28834331}, issn = {2045-8827}, mesh = {Animals ; *Animals, Domestic ; Biodiversity ; Cluster Analysis ; Feces/*microbiology ; Gastrointestinal Microbiome ; *Herbivory ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; *Ruminants ; }, abstract = {In this pilot study, we determined the core fecal microbiota composition and overall microbiota diversity of domesticated herbivorous animals of three digestion types: hindgut fermenters, ruminants, and monogastrics. The 42 animals representing 10 animal species were housed on a single farm in Ireland and all the large herbivores consumed similar feed, harmonizing two of the environmental factors that influence the microbiota. Similar to other mammals, the fecal microbiota of all these animals was dominated by the Firmicutes and Bacteroidetes phyla. The fecal microbiota spanning all digestion types comprised 42% of the genera identified. Host phylogeny and, to a lesser extent, digestion type determined the microbiota diversity in these domesticated herbivores. This pilot study forms a platform for future studies into the microbiota of nonbovine and nonequine domesticated herbivorous animals.}, } @article {pmid28833934, year = {2017}, author = {do Vale Pereira, G and da Cunha, DG and Pedreira Mourino, JL and Rodiles, A and Jaramillo-Torres, A and Merrifield, DL}, title = {Characterization of microbiota in Arapaima gigas intestine and isolation of potential probiotic bacteria.}, journal = {Journal of applied microbiology}, volume = {123}, number = {5}, pages = {1298-1311}, doi = {10.1111/jam.13572}, pmid = {28833934}, issn = {1365-2672}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Fishes/*microbiology ; *Gastrointestinal Microbiome ; Intestines/*microbiology ; Lactobacillales/classification/drug effects/genetics/*isolation & purification ; Probiotics/*isolation & purification ; }, abstract = {AIMS: The aim of this study was to determine the intestinal microbiota of pirarucu (Arapaima gigas) in different growth stages (adult and fingerlings) and to isolate and identify potential probiotic bacteria.

METHODS AND RESULTS: High-throughput sequencing analysis of the intestinal contents revealed that the majority of sequences belonged to the Proteobacteria, Fusobacteria and Firmicutes phyla. At the genus level, the greatest number of sequences belonged to Bradyrhizobium in adult fish, while Cetobacterium was the most abundant in juvenile fish. Twenty-three lactic-acid bacteria (LABs) were isolated on MRS agar from healthy juvenile fish. The isolates were tested in vitro for probiotic properties. Two isolates (identified as strains of Lactococcus lactis subsp. lactis and Enterococcus faecium) displayed antagonism against all 10 pathogens tested, were nonhaemolytic and maintained good viability for at least 3 weeks when supplemented to fish diets. The presence of a number of antibiotic resistance genes (ARGs), conferring resistance to erythromycin, tetracycline and chloramphenicol, was investigated by PCR.

CONCLUSIONS: The absence of ARGs investigated the potential to antagonize pathogens, and favourable growth and survival characteristics indicate that these autochthonous isolates have the potential to be considered probiotics, which will be studied in future in vivo experiments.

This study has demonstrated, for the first time, the normal microbiota in the A. gigas intestine during different life stages and the presence of LAB strains. It also demonstrated LAB antibiotic resistance and antagonistic behaviour against pathogens isolated from the same fish.}, } @article {pmid28831604, year = {2018}, author = {Mendes, LW and Tsai, SM}, title = {Distinct taxonomic and functional composition of soil microbiomes along the gradient forest-restinga-mangrove in southeastern Brazil.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {1}, pages = {101-114}, doi = {10.1007/s10482-017-0931-6}, pmid = {28831604}, issn = {1572-9699}, support = {2007/01859-4//FAPESP/ ; }, mesh = {Biodiversity ; Brazil ; *Forests ; Geography ; *Metagenome ; *Metagenomics/methods ; *Soil Microbiology ; *Wetlands ; }, abstract = {Soil microorganisms play crucial roles in ecosystem functioning, and the central goal in microbial ecology studies is to elucidate which factors shape community structure. A better understanding of the relationship between microbial diversity, functions and environmental parameters would increase our ability to set conservation priorities. Here, the bacterial and archaeal community structure in Atlantic Forest, restinga and mangrove soils was described and compared based on shotgun metagenomics. We hypothesized that each distinct site would harbor a distinct taxonomic and functional soil community, which is influenced by environmental parameters. Our data showed that the microbiome is shaped by soil properties, with pH, base saturation, boron and iron content significantly correlated to overall community structure. When data of specific phyla were correlated to specific soil properties, we demonstrated that parameters such as boron, copper, sulfur, potassium and aluminum presented significant correlation with the most number of bacterial groups. Mangrove soil was the most distinct site and presented the highest taxonomic and functional diversity in comparison with forest and restinga soils. From the total 34 microbial phyla identified, 14 were overrepresented in mangrove soils, including several archaeal groups. Mangrove soils hosted a high abundance of sequences related to replication, survival and adaptation; forest soils included high numbers of sequences related to the metabolism of nutrients and other composts; while restinga soils included abundant genes related to the metabolism of carbohydrates. Overall, our finds show that the microbial community structure and functional potential were clearly different across the environmental gradient, followed by functional adaptation and both were related to the soil properties.}, } @article {pmid28830999, year = {2017}, author = {Kowarsky, M and Camunas-Soler, J and Kertesz, M and De Vlaminck, I and Koh, W and Pan, W and Martin, L and Neff, NF and Okamoto, J and Wong, RJ and Kharbanda, S and El-Sayed, Y and Blumenfeld, Y and Stevenson, DK and Shaw, GM and Wolfe, ND and Quake, SR}, title = {Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {36}, pages = {9623-9628}, pmid = {28830999}, issn = {1091-6490}, mesh = {Cell-Free Nucleic Acids/*blood/*genetics ; DNA, Bacterial/*blood/*genetics ; DNA, Viral/*blood/*genetics ; Genetic Variation ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; Microbiota/*genetics ; Phylogeny ; }, abstract = {Blood circulates throughout the human body and contains molecules drawn from virtually every tissue, including the microbes and viruses which colonize the body. Through massive shotgun sequencing of circulating cell-free DNA from the blood, we identified hundreds of new bacteria and viruses which represent previously unidentified members of the human microbiome. Analyzing cumulative sequence data from 1,351 blood samples collected from 188 patients enabled us to assemble 7,190 contiguous regions (contigs) larger than 1 kbp, of which 3,761 are novel with little or no sequence homology in any existing databases. The vast majority of these novel contigs possess coding sequences, and we have validated their existence both by finding their presence in independent experiments and by performing direct PCR amplification. When their nearest neighbors are located in the tree of life, many of the organisms represent entirely novel taxa, showing that microbial diversity within the human body is substantially broader than previously appreciated.}, } @article {pmid28828756, year = {2017}, author = {Suhaimi, NSM and Goh, SY and Ajam, N and Othman, RY and Chan, KG and Thong, KL}, title = {Diversity of microbiota associated with symptomatic and non-symptomatic bacterial wilt-diseased banana plants determined using 16S rRNA metagenome sequencing.}, journal = {World journal of microbiology & biotechnology}, volume = {33}, number = {9}, pages = {168}, pmid = {28828756}, issn = {1573-0972}, mesh = {Bacteria/*classification/genetics/isolation & purification ; Cyanobacteria/classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Fusarium ; High-Throughput Nucleotide Sequencing/methods ; Malaysia ; Metagenomics/*methods ; Musa/*microbiology ; Phylogeny ; Plant Diseases/*microbiology ; Proteobacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Banana is one of the most important fruits cultivated in Malaysia, and it provides many health benefits. However, bacterial wilt disease, which attacks bananas, inflicts major losses on the banana industry in Malaysia. To understand the complex interactions of the microbiota of bacterial wilt-diseased banana plants, we first determined the bacterial communities residing in the pseudostems of infected (symptomatic) and diseased-free (non-symptomatic) banana plants. We characterized the associated microorganisms using the targeted 16S rRNA metagenomics sequencing on the Illumina MiSeq platform. Taxonomic classifications revealed 17 and nine known bacterial phyla in the tissues of non-symptomatic and symptomatic plants, respectively. Cyanobacteria and Proteobacteria (accounted for more than 99% of the 16S rRNA gene fragments) were the two most abundant phyla in both plants. The five major genera found in both plant samples were Ralstonia, Sphingomonas, Methylobacterium, Flavobacterium, and Pseudomonas. Ralstonia was more abundant in symptomatic plant (59% out of the entire genera) as compared to those in the non-symptomatic plant (only 36%). Our data revealed that 102 bacterial genera were only assigned to the non-symptomatic plant. Overall, this study indicated that more diverse and abundant microbiota were associated with the non-symptomatic bacterial wilt-diseased banana plant as compared to the symptomatic plant. The higher diversity of endophytic microbiota in the non-symptomatic banana plant could be an indication of pathogen suppression which delayed or prevented the disease expression. This comparative study of the microbiota in the two plant conditions might provide caveats for potential biological control strategies.}, } @article {pmid28828247, year = {2017}, author = {Tomczyk-Żak, K and Szczesny, P and Gromadka, R and Zielenkiewicz, U}, title = {Taxonomic and chemical assessment of exceptionally abundant rock mine biofilm.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3635}, pmid = {28828247}, issn = {2167-8359}, abstract = {BACKGROUND: An exceptionally thick biofilm covers walls of ancient gold and arsenic Złoty Stok mine (Poland) in the apparent absence of organic sources of energy.

METHODS AND RESULTS: We have characterized this microbial community using culture-dependent and independent methods. We sequenced amplicons of the 16S rRNA gene obtained using generic primers and additional primers targeted at Archaea and Actinobacteria separately. Also, we have cultured numerous isolates from the biofilm on different media under aerobic and anaerobic conditions. We discovered very high biodiversity, and no single taxonomic group was dominant. The majority of almost 4,000 OTUs were classified above genus level indicating presence of novel species. Elemental analysis, performed using SEM-EDS and X-ray, of biofilm samples showed that carbon, sulphur and oxygen were not evenly distributed in the biofilm and that their presence is highly correlated. However, the distribution of arsenic and iron was more flat, and numerous intrusions of elemental silver and platinum were noted, indicating that microorganisms play a key role in releasing these elements from the rock.

CONCLUSIONS: Altogether, the picture obtained throughout this study shows a very rich, complex and interdependent system of rock biofilm. The chemical heterogeneity of biofilm is a likely explanation as to why this oligotrophic environment is capable of supporting such high microbial diversity.}, } @article {pmid28827739, year = {2017}, author = {Idris, H and Goodfellow, M and Sanderson, R and Asenjo, JA and Bull, AT}, title = {Actinobacterial Rare Biospheres and Dark Matter Revealed in Habitats of the Chilean Atacama Desert.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8373}, pmid = {28827739}, issn = {2045-2322}, mesh = {Actinobacteria/classification/genetics/*isolation & purification ; *Biodiversity ; Chile ; Desert Climate ; *Ecosystem ; Metagenomics ; *Soil Microbiology ; }, abstract = {The Atacama Desert is the most extreme non-polar biome on Earth, the core region of which is considered to represent the dry limit for life and to be an analogue for Martian soils. This study focused on actinobacteria because they are keystone species in terrestrial ecosystems and are acknowledged as an unrivalled source of bioactive compounds. Metagenomic analyses of hyper-arid and extreme hyper-arid soils in this desert revealed a remarkable degree of actinobacterial 'dark matter', evidenced by a detected increase of 34% in families against those that are validly published. Rank-abundance analyses indicated that these soils were high-diversity habitats and that the great majority of designated 'rare' genera (up to 60% of all phylotypes) were always rare. These studies have enabled a core actinobacterial microbiome common to both habitats to be defined. The great majority of detected taxa have not been recovered by culture dependent methods, neither, with very few exceptions, has their functional ecology been explored. A microbial seed bank of this magnitude has significance not just for Atacama soil ecosystem resilience but represents an enormous untapped resource for biotechnology discovery programmes in an era where resistance to existing antibiotics is rapidly becoming a major threat to global health.}, } @article {pmid28827715, year = {2017}, author = {Corinaldesi, C and Tangherlini, M and Dell'Anno, A}, title = {From virus isolation to metagenome generation for investigating viral diversity in deep-sea sediments.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8355}, pmid = {28827715}, issn = {2045-2322}, mesh = {*Biodiversity ; *Ecosystem ; Geologic Sediments/*virology ; *Metagenome ; Seawater/*virology ; Viruses/*genetics/isolation & purification ; }, abstract = {Viruses are the most abundant and, likely, one of the most diverse biological components in the oceans. By infecting their hosts, they play key roles in biogeochemical cycles and ecosystem functioning at a global scale. The ocean interior hosts most of the microbial life, and, despite deep-sea sediments represent the main repository of this component and the largest biome on Earth, viral diversity in these ecosystems remains almost completely unknown. We compared a physical-chemical procedure and a previously published sediment washing-based procedure for isolating viruses from benthic deep-sea ecosystems to generate viromes through high-throughput sequencing. The procedure based on a physical-chemical dislodgment of viral particles from the sediments, followed by vacuum filtration was much more efficient allowing us to recover >85% of the extractable viruses. By using this procedure, a high fraction of viral DNA was recovered and new viromes from different benthic deep-sea sites were generated. Such viromes were diversified in terms of both viral families and putative functions. Overall, the results presented here provide new insights for evaluating benthic deep-sea viral diversity through metagenomic analyses, and reveal that deep-sea sediments are a hot spot of novel viral genotypes and functions.}, } @article {pmid28827587, year = {2017}, author = {Kinross, J and Mirnezami, R and Alexander, J and Brown, R and Scott, A and Galea, D and Veselkov, K and Goldin, R and Darzi, A and Nicholson, J and Marchesi, JR}, title = {A prospective analysis of mucosal microbiome-metabonome interactions in colorectal cancer using a combined MAS 1HNMR and metataxonomic strategy.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8979}, pmid = {28827587}, issn = {2045-2322}, mesh = {Cluster Analysis ; Colorectal Neoplasms/*microbiology/*pathology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/*chemistry/*microbiology ; Magnetic Resonance Spectroscopy ; *Metabolome ; Metabolomics ; Metagenomics ; Microbiota ; Phylogeny ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Colon cancer induces a state of mucosal dysbiosis with associated niche specific changes in the gut microbiota. However, the key metabolic functions of these bacteria remain unclear. We performed a prospective observational study in patients undergoing elective surgery for colon cancer without mechanical bowel preparation (n = 18). Using 16 S rRNA gene sequencing we demonstrated that microbiota ecology appears to be cancer stage-specific and strongly associated with histological features of poor prognosis. Fusobacteria (p < 0.007) and ε- Proteobacteria (p < 0.01) were enriched on tumour when compared to adjacent normal mucosal tissue, and fusobacteria and β-Proteobacteria levels increased with advancing cancer stage (p = 0.014 and 0.002 respecitvely). Metabonomic analysis using 1H Magic Angle Spinning Nuclear Magnetic Resonsance (MAS-NMR) spectroscopy, demonstrated increased abundance of taurine, isoglutamine, choline, lactate, phenylalanine and tyrosine and decreased levels of lipids and triglycerides in tumour relative to adjacent healthy tissue. Network analysis revealed that bacteria associated with poor prognostic features were not responsible for the modification of the cancer mucosal metabonome. Thus the colon cancer mucosal microbiome evolves with cancer stage to meet the demands of cancer metabolism. Passenger microbiota may play a role in the maintenance of cancer mucosal metabolic homeostasis but these metabolic functions may not be stage specific.}, } @article {pmid28827532, year = {2017}, author = {Jiang, J and Song, Z and Yang, X and Mao, Z and Nie, X and Guo, H and Peng, X}, title = {Microbial community analysis of apple rhizosphere around Bohai Gulf.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8918}, pmid = {28827532}, issn = {2045-2322}, mesh = {Biodiversity ; Environment ; Malus/*microbiology ; Metagenome ; Metagenomics ; *Microbiota ; Plant Roots/microbiology ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Bohai Gulf is the main area for apple tree cultivation in China. Consecutive replanting significantly affects the yield and quality of apple trees in this area. Microecological imbalance in apple trees' rhizospheres caused by variation in the soil microbial community is considered the primary cause of apple replant disease (ARD). This study analysed the microbial communities of the rhizospheres of perennial apple trees (PAT) and apple tree saplings under replanting (ATS) around Bohai Gulf using high-throughput sequencing. The results revealed increased populations of typical pathogenic fungi Verticillium and bacteria Xanthomonadaceae, and decreased populations of beneficial bacterial populations Pseudomonas and Bacillus with replanting, suggesting that competition between pathogens and beneficial microbes varies according to the ratio of pathogens to beneficial microbes in rhizosphere soil under the replanting system. Meanwhile, replanting was accompanied by an increase in the antagonistic bacteria Arthrobacter and fungus Chaetomium, suggesting that increased numbers of pathogens can lead to more instances of antagonism. Redundancy analysis (RDA) revealed site position and the main soil properties (pH, organic matter, available N, available K, available P, and moisture) affected the microbial community composition. It found clear differences in soil microbial communities and demonstrated a better understanding of the causes for ARD.}, } @article {pmid28826586, year = {2018}, author = {Lucas, SK and Yang, R and Dunitz, JM and Boyer, HC and Hunter, RC}, title = {16S rRNA gene sequencing reveals site-specific signatures of the upper and lower airways of cystic fibrosis patients.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {17}, number = {2}, pages = {204-212}, pmid = {28826586}, issn = {1873-5010}, support = {R00 HL114862/HL/NHLBI NIH HHS/United States ; T90 DE022732/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Bacterial Load ; Chronic Disease ; Cohort Studies ; Cystic Fibrosis/complications/*microbiology ; Endoscopy ; Gram-Negative Bacteria/*isolation & purification ; Gram-Positive Bacteria/*isolation & purification ; Humans ; Lung/*microbiology ; Microbiota ; Middle Aged ; Paranasal Sinuses/*microbiology ; RNA, Bacterial ; RNA, Ribosomal, 16S ; Sinusitis/*microbiology ; Sputum/microbiology ; Young Adult ; }, abstract = {BACKGROUND: Metastasis of upper airway microbiota may have significant implications in the development of chronic lung disease. Here, we compare bacterial communities of matched sinus and lung mucus samples from cystic fibrosis (CF) subjects undergoing endoscopic surgery for treatment of chronic sinusitis.

METHODS: Mucus from one maxillary sinus and expectorated sputum were collected from twelve patients. 16S rRNA gene sequencing was then performed on sample pairs to compare the structure and function of CF airway microbiota.

RESULTS: Bacterial diversity was comparable between airway sites, though sinuses harbored a higher prevalence of dominant microorganisms. Ordination analyses revealed that samples clustered more consistently by airway niche rather than by individual. Finally, predicted metagenomes suggested that anaerobiosis was enriched in the lung.

CONCLUSIONS: Our findings indicate that while the lung may be seeded by individual sinus pathogens, airway microenvironments harbor distinct bacterial communities that should be considered in selecting antimicrobial therapies.}, } @article {pmid28824177, year = {2017}, author = {Fierer, N}, title = {Embracing the unknown: disentangling the complexities of the soil microbiome.}, journal = {Nature reviews. Microbiology}, volume = {15}, number = {10}, pages = {579-590}, pmid = {28824177}, issn = {1740-1534}, mesh = {Bacteria/classification/genetics ; Eukaryota/classification/genetics ; Fungi/classification/genetics ; Microbiota/*genetics ; Soil/*parasitology ; *Soil Microbiology ; }, abstract = {Soil microorganisms are clearly a key component of both natural and managed ecosystems. Despite the challenges of surviving in soil, a gram of soil can contain thousands of individual microbial taxa, including viruses and members of all three domains of life. Recent advances in marker gene, genomic and metagenomic analyses have greatly expanded our ability to characterize the soil microbiome and identify the factors that shape soil microbial communities across space and time. However, although most soil microorganisms remain undescribed, we can begin to categorize soil microorganisms on the basis of their ecological strategies. This is an approach that should prove fruitful for leveraging genomic information to predict the functional attributes of individual taxa. The field is now poised to identify how we can manipulate and manage the soil microbiome to increase soil fertility, improve crop production and improve our understanding of how terrestrial ecosystems will respond to environmental change.}, } @article {pmid28823860, year = {2017}, author = {Wong, SH and Zhao, L and Zhang, X and Nakatsu, G and Han, J and Xu, W and Xiao, X and Kwong, TNY and Tsoi, H and Wu, WKK and Zeng, B and Chan, FKL and Sung, JJY and Wei, H and Yu, J}, title = {Gavage of Fecal Samples From Patients With Colorectal Cancer Promotes Intestinal Carcinogenesis in Germ-Free and Conventional Mice.}, journal = {Gastroenterology}, volume = {153}, number = {6}, pages = {1621-1633.e6}, doi = {10.1053/j.gastro.2017.08.022}, pmid = {28823860}, issn = {1528-0012}, mesh = {Animals ; Azoxymethane ; Case-Control Studies ; Cell Proliferation ; *Cell Transformation, Neoplastic/metabolism/pathology ; Colon/metabolism/*microbiology/pathology ; Colonic Polyps/chemically induced/metabolism/*microbiology/pathology ; Colorectal Neoplasms/chemically induced/metabolism/*microbiology/pathology ; Disease Models, Animal ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Gene Expression Regulation, Neoplastic ; Germ-Free Life ; Host-Pathogen Interactions ; Humans ; Inflammation Mediators/metabolism ; Ki-67 Antigen/metabolism ; Lymphocytes, Tumor-Infiltrating/metabolism/microbiology ; Male ; Mice, Inbred C57BL ; Th1 Cells/metabolism/microbiology ; Th17 Cells/metabolism/microbiology ; }, abstract = {BACKGROUND & AIMS: Altered gut microbiota is implicated in development of colorectal cancer (CRC). Some intestinal bacteria have been reported to potentiate intestinal carcinogenesis by producing genotoxins, altering the immune response and intestinal microenvironment, and activating oncogenic signaling pathways. We investigated whether stool from patients with CRC could directly induce colorectal carcinogenesis in mice.

METHODS: We obtained stored stool samples from participants in a metagenome study performed in Hong Kong. Conventional (male C57BL/6) mice were given azoxymethane to induce colon neoplasia after receiving a course of antibiotics in drinking water. Mice were gavaged twice weekly with stool from 5 patients with CRC or 5 healthy individuals (controls) for 5 weeks. Germ-free C57BL/6 mice were gavaged once with stool from 5 patients with CRC or 5 controls. We collected intestinal tissues from mice and performed histology, immunohistochemistry, expression microarray, quantitative polymerase chain reaction, immunoblot, and flow cytometry analyses. We performed 16S ribosomal RNA gene sequencing analysis of feces from mice.

RESULTS: Significantly higher proportions of conventional mice fed with stool from individuals with CRC than control stool developed high-grade dysplasia (P < .05) and macroscopic polyps (P < .01). We observed a higher proportion of proliferating (Ki-67-positive) cells in colons of germ-free mice fed with stool from patients with CRC vs those fed with stool from controls (P < .05). Feces from germ-free and conventional mice fed with stool from patients with CRC vs controls contained different microbial compositions, with lower richness in mice fed with stool from patients with CRC. Intestines collected from conventional and germ-free mice fed with stool from patients with CRC had increased expression of cytokines that modulate inflammation, including C-X-C motif chemokine receptor 1, C-X-C motif chemokine receptor 2, interleukin 17A (IL17A), IL22, and IL23A. Intestines from conventional and germ-free mice fed with stool from patients with CRC contained higher proportions of T-helper 1 (Th1) cells (2.25% vs 0.44%) and Th17 cells (2.08% vs 0.31%) (P < .05 for each) than mice fed with stool from controls. Real-time polymerase chain reaction arrays revealed up-regulation of genes involved in cell proliferation, stemness, apoptosis, angiogenesis, invasiveness, and metastasis in mice fed with stool from patients with CRC.

CONCLUSIONS: We fed stool samples from patients with CRC and heathy individuals to germ-free mice and conventional mice with azoxymethane. We found stool from patients with CRC to increase the numbers of polyps, levels of intestinal dysplasia and proliferation, markers of inflammation, and proportions of Th1 and Th17 cells in colon, compared with stool from individuals without CRC. This study provides evidence that the fecal microbiota from patients with CRC can promote tumorigenesis in germ-free mice and mice given a carcinogen.}, } @article {pmid28821976, year = {2017}, author = {Gao, R and Kong, C and Li, H and Huang, L and Qu, X and Qin, N and Qin, H}, title = {Dysbiosis signature of mycobiota in colon polyp and colorectal cancer.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {36}, number = {12}, pages = {2457-2468}, pmid = {28821976}, issn = {1435-4373}, support = {No. 81230057//National Natural Science Foundation of China/ ; No. 81472262//National Natural Science Foundation of China/ ; 81372615//National Natural Science Foundation of China/ ; 81200264//National Natural Science Foundation of China/ ; No.SHDC12012106//Shen Kang Hospital Development Center of Shanghai/ ; No.162385//Tongji University Subject Pilot Program/ ; }, mesh = {Aged ; Biodiversity ; Colonic Polyps/*microbiology/pathology ; Colorectal Neoplasms/*etiology/pathology ; Disease Susceptibility ; *Dysbiosis ; Feces/microbiology ; Female ; *Fungi/classification ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Neoplasm Staging ; Tumor Burden ; }, abstract = {Microbiota refers to a colony of microorganisms, and they are found in all multicellular organisms. This colony plays a major role in both the physiology and disease of the organism it inhabits. Much attention has been paid to host-microbiota interactions, but there has been little investigation on its role in carcinogenesis. In this study, we characterized a fecal mycobiota, also known as fungal signature, for the first time with 131 subjects, comprising polyp and colorectal cancer (CRC) patients, as well as a healthy control population. The data obtained were analyzed to assess the biodiversity and composition of the fungi. The impacts of anatomic position and tumor stage on the mycobiota were also evaluated. Correlations between fungi were investigated using the Spearman test. We observed fungal dysbiosis in colon polyps and CRC, including decreased diversity in polyp patients, an increased Ascomycota/Basidiomycota ratio, and an increased proportion of opportunistic fungi Trichosporon and Malassezia, which might favor the progression of CRC. Subsequent analysis with regard to tumor stage demonstrated a lower diversity and significant mycobiota alteration in early-stage tumors. Finally, the fungal correlation showed a close relationship within the community and concomitantly revealed a dramatically structured discrepancy in each clinical phenotype. In conclusion, our study has uncovered a distinct fungal dysbiosis and an alteration in the fungal network, which could play important roles in polyp and CRC pathogenesis.}, } @article {pmid28821872, year = {2017}, author = {Nakagawa, S and Saito, H and Tame, A and Hirai, M and Yamaguchi, H and Sunata, T and Aida, M and Muto, H and Sawayama, S and Takaki, Y}, title = {Microbiota in the coelomic fluid of two common coastal starfish species and characterization of an abundant Helicobacter-related taxon.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8764}, pmid = {28821872}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; Fish Diseases/microbiology ; Helicobacter/*classification/*genetics ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeography ; RNA, Ribosomal, 16S/genetics ; Starfish/*microbiology ; }, abstract = {Marine invertebrates associate with diverse microorganisms. Microorganisms even inhabit coelomic fluid (CF), namely, the fluid filling the main body cavity of echinoderms. The CF microbiota potentially impacts host health and disease. Here, we analysed the CF microbiota in two common coastal starfish species, Patiria pectinifera and Asterias amurensis. Although microbial community structures were highly variable among individual starfish, those of P. pectinifera were compositionally similar to those in the surrounding seawater. By contrast, many A. amurensis individuals harboured unique microbes in the CF, which was dominated by the unclassified Thiotrichales or previously unknown Helicobacter-related taxon. In some individuals, the Helicobacter-related taxon was the most abundant genus-level taxon, accounting for up to 97.3% of reads obtained from the CF microbial community. Fluorescence in situ hybridization using a Helicobacter-related-taxon-specific probe suggested that probe-reactive cells in A. amurensis were spiral-shaped, morphologically similar to known Helicobacter species. Electron microscopy revealed that the spiral cells had a prosthecate-like polar appendage that has never been reported in Helicobacter species. Although culture of Helicobacter-related taxon was unsuccessful, this is the first report of the dominance of a Helicobacter-related taxon in invertebrates and non-digestive organs, reshaping our knowledge of the phylogeography of Helicobacter-related taxa.}, } @article {pmid28821814, year = {2017}, author = {Fang, D and Shi, D and Lv, L and Gu, S and Wu, W and Chen, Y and Guo, J and Li, A and Hu, X and Guo, F and Ye, J and Li, Y and Li, L}, title = {Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10 attenuate D-galactosamine-induced liver injury by modifying the gut microbiota.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8770}, pmid = {28821814}, issn = {2045-2322}, mesh = {Animals ; Bifidobacterium/*physiology ; Bifidobacterium pseudocatenulatum/*physiology ; Cytokines/blood/metabolism ; Galactosamine/*adverse effects ; Gastrointestinal Microbiome/*drug effects ; Inflammation Mediators/blood/metabolism ; Intestinal Mucosa/drug effects/metabolism/pathology ; Liver Diseases/*etiology/metabolism/pathology ; Male ; Metagenome ; Metagenomics ; Models, Biological ; Rats ; }, abstract = {The gut microbiota is altered in liver diseases, and several probiotics have been shown to reduce the degree of liver damage. We hypothesized that oral administration of specific Bifidobacterium strains isolated from healthy guts could attenuate liver injury. Five strains were tested in this study. Acute liver injury was induced by D-galactosamine after pretreating Sprague-Dawley rats with the Bifidobacterium strains, and liver function, liver and ileum histology, plasma cytokines, bacterial translocation and the gut microbiome were assessed. Two strains, Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10, conferred liver protection, as well as alleviated the increase in plasma M-CSF, MIP-1α and MCP-1 and bacterial translocation. They also ameliorated ileal mucosal injury and gut flora dysbiosis, especially the enrichment of the opportunistic pathogen Parasutterella and the depletion of the SCFA-producing bacteria Anaerostipes, Coprococcus and Clostridium XI. Negative correlations were found between MIP-1α / MCP-1 and Odoribacter (LI09 group) and MIP-1α / M-CSF and Flavonifractor (LI10 group). Our results indicate that the liver protection effects might be mediated through gut microbiota modification, which thus affect the host immune profile. The desirable characteristics of these two strains may enable them to serve as potential probiotics for the prevention or adjuvant treatment of liver injury.}, } @article {pmid28821731, year = {2017}, author = {Glymenaki, M and Barnes, A and O'Hagan, S and Warhurst, G and McBain, AJ and Wilson, ID and Kell, DB and Else, KJ and Cruickshank, SM}, title = {Stability in metabolic phenotypes and inferred metagenome profiles before the onset of colitis-induced inflammation.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8836}, pmid = {28821731}, issn = {2045-2322}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Chromatography, High Pressure Liquid ; Colitis/*etiology/*metabolism ; Disease Models, Animal ; Disease Susceptibility ; *Gastrointestinal Microbiome ; Genotype ; Inflammatory Bowel Diseases/etiology/metabolism ; Male ; Mass Spectrometry ; *Metabolome ; *Metabolomics/methods ; Metagenome ; Metagenomics ; Mice ; Mice, Knockout ; *Phenotype ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Inflammatory bowel disease (IBD) is associated with altered microbiota composition and metabolism, but it is unclear whether these changes precede inflammation or are the result of it since current studies have mainly focused on changes after the onset of disease. We previously showed differences in mucus gut microbiota composition preceded colitis-induced inflammation and stool microbial differences only became apparent at colitis onset. In the present study, we aimed to investigate whether microbial dysbiosis was associated with differences in both predicted microbial gene content and endogenous metabolite profiles. We examined the functional potential of mucus and stool microbial communities in the mdr1a [-/-] mouse model of colitis and littermate controls using PICRUSt on 16S rRNA sequencing data. Our findings indicate that despite changes in microbial composition, microbial functional pathways were stable before and during the development of mucosal inflammation. LC-MS-based metabolic phenotyping (metabotyping) in urine samples confirmed that metabolite profiles in mdr1a [-/-] mice were remarkably unaffected by development of intestinal inflammation and there were no differences in previously published metabolic markers of IBD. Metabolic profiles did, however, discriminate the colitis-prone mdr1a [-/-] genotype from controls. Our results indicate resilience of the metabolic network irrespective of inflammation. Importantly as metabolites differentiated genotype, genotype-differentiating metabolites could potentially predict IBD risk.}, } @article {pmid28821301, year = {2017}, author = {Casero, D and Gill, K and Sridharan, V and Koturbash, I and Nelson, G and Hauer-Jensen, M and Boerma, M and Braun, J and Cheema, AK}, title = {Space-type radiation induces multimodal responses in the mouse gut microbiome and metabolome.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {105}, pmid = {28821301}, issn = {2049-2618}, support = {P01 DK046763/DK/NIDDK NIH HHS/United States ; P20 GM109005/GM/NIGMS NIH HHS/United States ; P30 CA051008/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Carbohydrate Metabolism/radiation effects ; Gastrointestinal Microbiome/genetics/physiology/*radiation effects ; Humans ; Linear Energy Transfer ; Lipopolysaccharides/biosynthesis/radiation effects ; Metabolic Networks and Pathways/radiation effects ; Metabolome/genetics/physiology/*radiation effects ; Metagenome/*radiation effects ; Mice ; Obesity ; *Radiation, Ionizing ; }, abstract = {BACKGROUND: Space travel is associated with continuous low dose rate exposure to high linear energy transfer (LET) radiation. Pathophysiological manifestations after low dose radiation exposure are strongly influenced by non-cytocidal radiation effects, including changes in the microbiome and host gene expression. Although the importance of the gut microbiome in the maintenance of human health is well established, little is known about the role of radiation in altering the microbiome during deep-space travel.

RESULTS: Using a mouse model for exposure to high LET radiation, we observed substantial changes in the composition and functional potential of the gut microbiome. These were accompanied by changes in the abundance of multiple metabolites, which were related to the enzymatic activity of the predicted metagenome by means of metabolic network modeling. There was a complex dynamic in microbial and metabolic composition at different radiation doses, suggestive of transient, dose-dependent interactions between microbial ecology and signals from the host's cellular damage repair processes. The observed radiation-induced changes in microbiota diversity and composition were analyzed at the functional level. A constitutive change in activity was found for several pathways dominated by microbiome-specific enzymatic reactions like carbohydrate digestion and absorption and lipopolysaccharide biosynthesis, while the activity in other radiation-responsive pathways like phosphatidylinositol signaling could be linked to dose-dependent changes in the abundance of specific taxa.

CONCLUSIONS: The implication of microbiome-mediated pathophysiology after low dose ionizing radiation may be an unappreciated biologic hazard of space travel and deserves experimental validation. This study provides a conceptual and analytical basis of further investigations to increase our understanding of the chronic effects of space radiation on human health, and points to potential new targets for intervention in adverse radiation effects.}, } @article {pmid28821012, year = {2017}, author = {Fukuyama, J and Rumker, L and Sankaran, K and Jeganathan, P and Dethlefsen, L and Relman, DA and Holmes, SP}, title = {Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment.}, journal = {PLoS computational biology}, volume = {13}, number = {8}, pages = {e1005706}, pmid = {28821012}, issn = {1553-7358}, support = {R01 AI112401/AI/NIAID NIH HHS/United States ; T15 LM007033/LM/NLM NIH HHS/United States ; }, mesh = {Adult ; DNA, Bacterial/analysis/genetics ; Diarrhea ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Longitudinal Studies ; Male ; Metagenome/*genetics ; Metagenomics/*methods ; Middle Aged ; *Models, Biological ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Our work focuses on the stability, resilience, and response to perturbation of the bacterial communities in the human gut. Informative flash flood-like disturbances that eliminate most gastrointestinal biomass can be induced using a clinically-relevant iso-osmotic agent. We designed and executed such a disturbance in human volunteers using a dense longitudinal sampling scheme extending before and after induced diarrhea. This experiment has enabled a careful multidomain analysis of a controlled perturbation of the human gut microbiota with a new level of resolution. These new longitudinal multidomain data were analyzed using recently developed statistical methods that demonstrate improvements over current practices. By imposing sparsity constraints we have enhanced the interpretability of the analyses and by employing a new adaptive generalized principal components analysis, incorporated modulated phylogenetic information and enhanced interpretation through scoring of the portions of the tree most influenced by the perturbation. Our analyses leverage the taxa-sample duality in the data to show how the gut microbiota recovers following this perturbation. Through a holistic approach that integrates phylogenetic, metagenomic and abundance information, we elucidate patterns of taxonomic and functional change that characterize the community recovery process across individuals. We provide complete code and illustrations of new sparse statistical methods for high-dimensional, longitudinal multidomain data that provide greater interpretability than existing methods.}, } @article {pmid28819272, year = {2017}, author = {Concheri, G and Stevanato, P and Zaccone, C and Shotyk, W and D'Orazio, V and Miano, T and Piffanelli, P and Rizzi, V and Ferrandi, C and Squartini, A}, title = {Rapid peat accumulation favours the occurrence of both fen and bog microbial communities within a Mediterranean, free-floating peat island.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8511}, pmid = {28819272}, issn = {2045-2322}, mesh = {Bacteria/*classification/genetics ; DNA, Bacterial/chemistry/genetics/isolation & purification ; DNA, Fungal/chemistry/genetics/isolation & purification ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Fungi/*classification/genetics ; *Islands ; Italy ; Metagenomics ; *Microbiota ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; Wetlands ; }, abstract = {The unique environment of a 4m-thick, free-floating peat island within the Posta Fibreno lake (Central Italy) was analyzed using DNA-based techniques to assess bacterial and fungal community members identity and abundance. Two depths were sampled at 41 and 279 cm from the surface, the former corresponding to an emerged portion of Sphagnum residues accumulated less than 30 yrs ago, and the latter mainly consisting of silty peat belonging to the deeply submerged part of the island, dating back to 1520-1660 AD. The corresponding communities were very diverse, each of them dominated by a different member of the Delta-proteobacteria class for prokaryotes. Among Eukaryotes, Ascomycota prevailed in the shallow layer while Basidiomycota were abundant in the deep sample. The identity of taxa partitioning between acidic surface layer and neutral core is very reminiscent of the differences reported between bogs and fens respectively, supporting the view of Posta Fibreno as a relic transitional floating mire. Moreover, some microbial taxa show an unusual concurrent species convergence between this sub-Mediterranean site and far Nordic or circumpolar environments. This study represents the first report describing the biotic assemblages of such a peculiar environment, and provides some insights into the possible mechanisms of its evolution.}, } @article {pmid28819242, year = {2017}, author = {Lim, Y and Totsika, M and Morrison, M and Punyadeera, C}, title = {The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8523}, pmid = {28819242}, issn = {2045-2322}, mesh = {Adult ; Bacteria/classification/genetics ; Cluster Analysis ; DNA, Bacterial/analysis/genetics/*isolation & purification ; DNA, Ribosomal/chemistry/genetics ; Healthy Volunteers ; Humans ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Saliva/*microbiology ; Sequence Analysis, DNA ; Specimen Handling/*methods ; Young Adult ; beta-Globins/analysis/genetics ; }, abstract = {Saliva has attracted attention as a diagnostic fluid due to the association of oral microbiota with systemic diseases. However, the lack of standardised methods for saliva collection has led to the slow uptake of saliva in microbiome research. The aim of this study was to systematically evaluate the potential effects on salivary microbiome profiles using different methods of saliva collection, storage and gDNA extraction. Three types of saliva fractions were collected from healthy individuals with or without the gDNA stabilising buffer. Subsequently, three types of gDNA extraction methods were evaluated to determine the gDNA extraction efficiencies from saliva samples. The purity of total bacterial gDNA was evaluated using the ratio of human β-globin to bacterial 16S rRNA PCR while 16S rRNA gene amplicon sequencing was carried out to identify the bacterial profiles present in these samples. The quantity and quality of extracted gDNA were similar among all three gDNA extraction methods and there were no statistically significant differences in the bacterial profiles among different saliva fractions at the genus-level of taxonomic classification. In conclusion, saliva sampling, processing and gDNA preparation do not have major influence on microbiome profiles.}, } @article {pmid28815328, year = {2018}, author = {Mardanov, AV and Gumerov, VM and Beletsky, AV and Ravin, NV}, title = {Microbial diversity in acidic thermal pools in the Uzon Caldera, Kamchatka.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {1}, pages = {35-43}, doi = {10.1007/s10482-017-0924-5}, pmid = {28815328}, issn = {1572-9699}, support = {11-04-00671//Russian Foundation for Basic Research/ ; 14-14-01016//Russian Science Foundation/ ; }, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biodiversity ; Hot Springs/*chemistry/*microbiology ; Hydrogen-Ion Concentration ; *Metagenome ; *Metagenomics/methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Microbial communities of four acidic thermal pools in the Uzon Caldera, Kamchatka, Russia, were studied using amplification and pyrosequencing of 16S rRNA gene fragments. The sites differed in temperature and pH: 1805 (60 °C, pH 3.7), 1810 (90 °C, pH 4.1), 1818 (80 °C, pH 3.5), and 1807 (86 °C, pH 5.6). Archaea of the order Sulfolobales were present among the dominant groups in all four pools. Acidilobales dominated in pool 1818 but were a minor fraction at the higher temperature in pool 1810. Uncultivated Archaea of the Hot Thaumarchaeota-related clade were present in significant quantities in pools 1805 and 1807, but they were not abundant in pools 1810 and 1818, where high temperatures were combined with low pH. Nanoarchaeota were present in all pools, but were more abundant in pools 1810 and 1818. A similar abundance pattern was observed for Halobacteriales. Thermophilic Bacteria were less diverse and were mostly represented by aerobic hydrogen- and sulfur-oxidizers of the phylum Aquificae and sulfur-oxidising Proteobacteria of the genus Acidithiobacillus. Thus we showed that extremely acidic hot pools contain diverse microbial communities comprising different metabolic groups of prokaryotes, including putative lithoautotrophs using energy sources of volcanic origin, and various facultative and obligate heterotrophs.}, } @article {pmid28814344, year = {2017}, author = {Wang, C and Dong, D and Strong, PJ and Zhu, W and Ma, Z and Qin, Y and Wu, W}, title = {Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {103}, pmid = {28814344}, issn = {2049-2618}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteriophages/genetics ; *Composting ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial ; Livestock/microbiology ; Manure/*microbiology ; Metagenomics ; *Microbiota/drug effects/genetics ; *Phylogeny ; RNA Viruses/genetics ; *Soil Microbiology ; Tetracycline Resistance/genetics ; *Transcription, Genetic ; }, abstract = {BACKGROUND: Animal manure is a reservoir of antibiotic resistance genes (ARGs) that pose a potential health risk globally, especially for resistance to the antibiotics commonly used in livestock production (such as tetracycline, sulfonamide, and fluoroquinolone). Currently, the effects of biological treatment (composting) on the transcriptional response of manure ARGs and their microbial hosts are not well characterized. Composting is a dynamic process that consists of four distinct phases that are distinguished by the temperature resulting from microbial activity, namely the mesophilic, thermophilic, cooling, and maturing phases. In this study, changes of resistome expression were determined and related to active microbiome profiles during the dynamic composting process. This was achieved by integrating metagenomic and time series metatranscriptomic data for the evolving microbial community during composting.

RESULTS: Composting noticeably reduced the aggregated expression level of the manure resistome, which primarily consisted of genes encoding for tetracycline, vancomycin, fluoroquinolone, beta-lactam, and aminoglycoside resistance, as well as efflux pumps. Furthermore, a varied transcriptional response of resistome to composting at the ARG levels was highlighted. The expression of tetracycline resistance genes (tetM-tetW-tetO-tetS) decreased during composting, where distinctive shifts in the four phases of composting were related to variations in antibiotic concentration. Composting had no effect on the expression of sulfonamide and fluoroquinolone resistance genes, which increased slightly during the thermophilic phase and then decreased to initial levels. As indigenous populations switched greatly throughout the dynamic composting, the core resistome persisted and their reservoir hosts' composition was significantly correlated with dynamic active microbial phylogenetic structure. Hosts for sulfonamide and fuoroquinolone resistance genes changed notably in phylognetic structure and underwent an initial increase and then a decrease in abundance. By contrast, hosts for tetracycline resistance genes (tetM-tetW-tetO-tetS) exhibited a constant decline through time.

CONCLUSIONS: The transcriptional patterns of a core resistome over the course of composting were identified, and microbial phylogeny was the key determinant in defining the varied transcriptional response of resistome to this dynamic biological process. This research demonstrated the benefits of composting for manure treatment. It reduced the risk of emerging environmental contaminants such as tetracyclines, tetracycline resistance genes, and clinically relevant pathogens carrying ARGs, as well as RNA viruses and bacteriophages.}, } @article {pmid28813664, year = {2017}, author = {Hayashi, A and Mikami, Y and Miyamoto, K and Kamada, N and Sato, T and Mizuno, S and Naganuma, M and Teratani, T and Aoki, R and Fukuda, S and Suda, W and Hattori, M and Amagai, M and Ohyama, M and Kanai, T}, title = {Intestinal Dysbiosis and Biotin Deprivation Induce Alopecia through Overgrowth of Lactobacillus murinus in Mice.}, journal = {Cell reports}, volume = {20}, number = {7}, pages = {1513-1524}, doi = {10.1016/j.celrep.2017.07.057}, pmid = {28813664}, issn = {2211-1247}, mesh = {Alopecia/chemically induced/metabolism/*microbiology/pathology ; Animals ; Anti-Bacterial Agents/pharmacology ; Biotin/*deficiency ; Diet/adverse effects ; Dysbiosis/chemically induced/metabolism/*microbiology/pathology ; Gastrointestinal Microbiome/*genetics ; Intestinal Mucosa/microbiology/pathology ; Lactobacillus/genetics/*growth & development ; Male ; Metagenome ; Mice ; RNA, Ribosomal, 16S/*genetics ; Skin/microbiology/pathology ; Vancomycin/pharmacology ; }, abstract = {Metabolism by the gut microbiota affects host physiology beyond the gastrointestinal tract. Here, we find that antibiotic-induced dysbiosis, in particular, overgrowth of Lactobacillus murinus (L. murinus), impaired gut metabolic function and led to the development of alopecia. While deprivation of dietary biotin per se did not affect skin physiology, its simultaneous treatment with vancomycin resulted in hair loss in specific pathogen-free (SPF) mice. Vancomycin treatment induced the accumulation of L. murinus in the gut, which consumes residual biotin and depletes available biotin in the gut. Consistently, L. murinus induced alopecia when monocolonized in germ-free mice fed a biotin-deficient diet. Supplementation of biotin can reverse established alopecia symptoms in the SPF condition, indicating that L. murinus plays a central role in the induction of hair loss via a biotin-dependent manner. Collectively, our results indicate that luminal metabolic alterations associated with gut dysbiosis and dietary modifications can compromise skin physiology.}, } @article {pmid28813529, year = {2017}, author = {Abecia, L and Jiménez, E and Martínez-Fernandez, G and Martín-García, AI and Ramos-Morales, E and Pinloche, E and Denman, SE and Newbold, CJ and Yáñez-Ruiz, DR}, title = {Natural and artificial feeding management before weaning promote different rumen microbial colonization but not differences in gene expression levels at the rumen epithelium of newborn goats.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0182235}, pmid = {28813529}, issn = {1932-6203}, mesh = {*Animal Feed ; Animals ; Biodiversity ; Biomarkers ; DNA Barcoding, Taxonomic ; Female ; Gastric Mucosa/immunology/*metabolism/*microbiology ; *Gastrointestinal Microbiome ; *Gene Expression ; Goats ; Immunoglobulin A/blood/immunology ; Immunoglobulin G/blood/immunology ; Metagenome ; Metagenomics/methods ; *Nutritional Support ; Pregnancy ; Rumen/immunology/*microbiology ; *Weaning ; }, abstract = {The aim of this work was to evaluate the effect of feeding management during the first month of life (natural with the mother, NAT, or artificial with milk replacer, ART) on the rumen microbial colonization and the host innate immune response. Thirty pregnant goats carrying two fetuses were used. At birth one kid was taken immediately away from the doe and fed milk replacer (ART) while the other remained with the mother (NAT). Kids from groups received colostrum during first 2 days of life. Groups of four kids (from ART and NAT experimental groups) were slaughtered at 1, 3, 7, 14, 21 and 28 days of life. On the sampling day, after slaughtering, the rumen content was sampled and epithelial rumen tissue was collected. Pyrosequencing analyses of the bacterial community structure on samples collected at 3, 7, 14 and 28 days showed that both systems promoted significantly different colonization patterns (P = 0.001). Diversity indices increased with age and were higher in NAT feeding system. Lower mRNA abundance was detected in TLR2, TLR8 and TLR10 in days 3 and 5 compared to the other days (7, 14, 21 and 28). Only TLR5 showed a significantly different level of expression according to the feeding system, presenting higher mRNA abundances in ART kids. PGLYRP1 showed significantly higher abundance levels in days 3, 5 and 7, and then experienced a decline independently of the feeding system. These observations confirmed a highly diverse microbial colonisation from the first day of life in the undeveloped rumen, and show that the colonization pattern substantially differs between pre-ruminants reared under natural or artificial milk feeding systems. However, the rumen epithelial immune development does not differentially respond to distinct microbial colonization patterns.}, } @article {pmid28813450, year = {2017}, author = {Chen, H and Peng, S and Dai, L and Zou, Q and Yi, B and Yang, X and Ma, ZS}, title = {Oral microbial community assembly under the influence of periodontitis.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0182259}, pmid = {28813450}, issn = {1932-6203}, mesh = {Algorithms ; *Biodiversity ; Case-Control Studies ; Datasets as Topic ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Models, Theoretical ; Mouth Mucosa/*microbiology ; Periodontitis/*microbiology ; }, abstract = {Several ecological hypotheses (e.g., specific plaque, non-specific plaque and keystone pathogen) regarding the etiology of periodontitis have been proposed since the 1990s, most of which have been centered on the concept of dysbiosis associated with periodontitis. Nevertheless, none of the existing hypotheses have presented mechanistic interpretations on how and why dysbiosis actually occurs. Hubbell's neutral theory of biodiversity offers a powerful null model to test hypothesis regarding the mechanism of community assembly and diversity maintenance from the metagenomic sequencing data, which can help to understand the forces that shape the community dynamics such as dysbiosis. Here we reanalyze the dataset from Abusleme et al.'s comparative study of the oral microbial communities from periodontitis patients and healthy individuals. Our study demonstrates that 14 out of 61 communities (23%) passed the neutrality test, a percentage significantly higher than the previous reported neutrality rate of 1% in human microbiome (Li & Ma 2016, Scientific Reports). This suggests that, while the niche selection may play a predominant role in the assembly and diversity maintenance in oral microbiome, the effect of neutral dynamics may not be ignored. However, no statistically significant differences in the neutrality passing rates were detected between the periodontitis and healthy treatments with Fisher's exact probability test and multiple testing corrections, suggesting that the mechanism of community assembly is robust against disturbances such as periodontitis. In addition, our study confirmed previous finding that periodontitis patients exhibited higher biodiversity. These findings suggest that while periodontitis may significantly change the community composition measured by diversity (i.e., the exhibition or 'phenotype' of community assembly), it does not seem to cause the 'mutation' of the 'genotype" (mechanism) of community assembly. We argue that the 'phenotypic' changes explain the observed link (not necessarily causal) between periodontitis and community dysbiosis, which is certainly worthy of further investigation.}, } @article {pmid28813445, year = {2017}, author = {Masuoka, H and Shimada, K and Kiyosue-Yasuda, T and Kiyosue, M and Oishi, Y and Kimura, S and Ohashi, Y and Fujisawa, T and Hotta, K and Yamada, A and Hirayama, K}, title = {Transition of the intestinal microbiota of cats with age.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0181739}, pmid = {28813445}, issn = {1932-6203}, mesh = {Age Factors ; Animals ; Bifidobacterium/classification/genetics ; *Biodiversity ; Cats ; DNA, Bacterial/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Lactobacillus/classification/genetics ; Metagenome ; Metagenomics/methods ; }, abstract = {The transition of intestinal microbiota with age has been well described in humans. However, the age-related changes in intestinal microbiota of cats have not been well studied. In the present study, we investigated the composition of intestinal microbiota of cats in 5 different age groups (pre-weanling, weanling, young, aged, senile) with a culture-based method. For lactobacilli and bifidobacteria, we also quantified with molecular-based method, real-time PCR. The results suggested that the composition of the feline intestinal microbiota changes with age, while the changes were different from those of humans and dogs. Bifidobacteria which are predominant in human intestine or lactobacilli which are predominant in dog intestine, did not appear to be important in cat intestines. Enterococci, instead, seem to be major lactic acid producing bacteria in cats. We also identified lactobacilli and bifidobacteria at the species level based on 16S rRNA gene sequences and found that the species composition of Lactobacillus also changed with age.}, } @article {pmid28811583, year = {2017}, author = {Chen, CH and Lin, YL and Chen, KH and Chen, WP and Chen, ZF and Kuo, HY and Hung, HF and Tang, CY and Liou, ML}, title = {Bacterial diversity among four healthcare-associated institutes in Taiwan.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8230}, pmid = {28811583}, issn = {2045-2322}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Cross Infection/epidemiology/microbiology ; *Environmental Microbiology ; *Health Facilities ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/methods ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Taiwan/epidemiology ; }, abstract = {Indoor microbial communities have important implications for human health, especially in health-care institutes (HCIs). The factors that determine the diversity and composition of microbiomes in a built environment remain unclear. Herein, we used 16S rRNA amplicon sequencing to investigate the relationships between building attributes and surface bacterial communities among four HCIs located in three buildings. We examined the surface bacterial communities and environmental parameters in the buildings supplied with different ventilation types and compared the results using a Dirichlet multinomial mixture (DMM)-based approach. A total of 203 samples from the four HCIs were analyzed. Four bacterial communities were grouped using the DMM-based approach, which were highly similar to those in the 4 HCIs. The α-diversity and β-diversity in the naturally ventilated building were different from the conditioner-ventilated building. The bacterial source composition varied across each building. Nine genera were found as the core microbiota shared by all the areas, of which Acinetobacter, Enterobacter, Pseudomonas, and Staphylococcus are regarded as healthcare-associated pathogens (HAPs). The observed relationship between environmental parameters such as core microbiota and surface bacterial diversity suggests that we might manage indoor environments by creating new sanitation protocols, adjusting the ventilation design, and further understanding the transmission routes of HAPs.}, } @article {pmid28811339, year = {2017}, author = {Sasson, G and Kruger Ben-Shabat, S and Seroussi, E and Doron-Faigenboim, A and Shterzer, N and Yaacoby, S and Berg Miller, ME and White, BA and Halperin, E and Mizrahi, I}, title = {Heritable Bovine Rumen Bacteria Are Phylogenetically Related and Correlated with the Cow's Capacity To Harvest Energy from Its Feed.}, journal = {mBio}, volume = {8}, number = {4}, pages = {}, pmid = {28811339}, issn = {2150-7511}, mesh = {Animal Feed ; Animals ; Bacteria/*genetics ; Biomass ; Cattle ; *Energy Metabolism ; Female ; Gastrointestinal Microbiome/*genetics ; Metagenome ; Methane/metabolism ; Phylogeny ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Ruminants sustain a long-lasting obligatory relationship with their rumen microbiome dating back 50 million years. In this unique host-microbiome relationship, the host's ability to digest its feed is completely dependent on its coevolved microbiome. This extraordinary alliance raises questions regarding the dependent relationship between ruminants' genetics and physiology and the rumen microbiome structure, composition, and metabolism. To elucidate this relationship, we examined the association of host genetics with the phylogenetic and functional composition of the rumen microbiome. We accomplished this by studying a population of 78 Holstein-Friesian dairy cows, using a combination of rumen microbiota data and other phenotypes from each animal with genotypic data from a subset of 47 animals. We identified 22 operational taxonomic units (OTUs) whose abundances were associated with rumen metabolic traits and host physiological traits and which showed measurable heritability. The abundance patterns of these microbes can explain high proportions of variance in rumen metabolism and many of the host physiological attributes such as its energy-harvesting efficiency. Interestingly, these OTUs shared higher phylogenetic similarity between themselves than expected by chance, suggesting occupation of a specific ecological niche within the rumen ecosystem. The findings presented here suggest that ruminant genetics and physiology are correlated with microbiome structure and that host genetics may shape the microbiome landscape by enriching for phylogenetically related taxa that may occupy a unique niche.IMPORTANCE Dairy cows are an essential nutritional source for the world's population; as such, they are extensively farmed throughout our planet and subsequently impact our environment. The microbial communities that reside in the upper digestive tract of these animals in a compartment named the rumen degrade and ferment the plant biomass that the animal ingests. Our recent efforts, as well as those of others, have shown that this microbial community's composition and functionality are tightly linked to the cow's capacity to harvest energy from its feed, as well as to other physiological traits. In this study, we identified microbial groups that are heritable and also linked to the cow's production parameters. This finding could potentially allow us to apply selection programs on specific rumen microbial components that are linked to the animal's physiology and beneficial to production. Hence, it is a steppingstone toward microbiome manipulation for increasing food availability while lowering environmental impacts such as methane emission.}, } @article {pmid28811148, year = {2018}, author = {Marshall, IPG and Karst, SM and Nielsen, PH and Jørgensen, BB}, title = {Metagenomes from deep Baltic Sea sediments reveal how past and present environmental conditions determine microbial community composition.}, journal = {Marine genomics}, volume = {37}, number = {}, pages = {58-68}, doi = {10.1016/j.margen.2017.08.004}, pmid = {28811148}, issn = {1876-7478}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Environment ; Geologic Sediments/*analysis ; *Metagenome ; *Microbiota ; Oceans and Seas ; Salinity ; }, abstract = {Microbial communities that lived near the sediment surface in the past become slowly buried and are the source of deep subsurface communities thousands of years later. We used metagenomes to analyse how the composition of buried microbial communities may change to conform to altered environmental conditions at depth. Sediment samples were collected from down to 85m below sea floor during the Integrated Ocean Drilling Program Expedition 347, "Baltic Sea Paleoenvironment". The sediments vary in age, organic carbon content, porewater salinity, and other parameters that reflect the changing Baltic environment from the last ice age and throughout the Holocene. We found microorganisms capable of energy conservation by fermentation, acetogenesis, methanogenesis, anaerobic oxidation of methane, and reductive dehalogenation. Glacial sediments showed a greater relative abundance of genes encoding enzymes in the Wood-Ljungdahl pathway and pyruvate:ferredoxin oxidoreductase than Holocene sediments. Relative abundance of genes conferring salinity tolerance was found to correlate with the present salinity, even in deep late-glacial sediment layers where salinity has increased since the sediment was deposited in a freshwater lake >9000years ago. This suggests that deeply buried and isolated sediment communities can slowly change in composition in response to geochemical changes that happen long after deposition.}, } @article {pmid28810907, year = {2017}, author = {Emerson, JB and Adams, RI and Román, CMB and Brooks, B and Coil, DA and Dahlhausen, K and Ganz, HH and Hartmann, EM and Hsu, T and Justice, NB and Paulino-Lima, IG and Luongo, JC and Lymperopoulou, DS and Gomez-Silvan, C and Rothschild-Mancinelli, B and Balk, M and Huttenhower, C and Nocker, A and Vaishampayan, P and Rothschild, LJ}, title = {Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {86}, pmid = {28810907}, issn = {2049-2618}, mesh = {Bacteria/*isolation & purification ; *Bacterial Physiological Phenomena ; Biomass ; *Ecosystem ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/methods ; Microbial Consortia ; *Microbial Viability ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms. In this review, we describe a number of techniques, from microscopy- to molecular-based, that have been used to test for viability (live/dead determination) and/or activity in various contexts, including newer techniques that are compatible with or complementary to downstream nucleic acid sequencing. We describe the compatibility of these viability assessments with high-throughput quantification techniques, including flow cytometry and quantitative PCR (qPCR). Although bacterial viability-linked community characterizations are now feasible in many environments and thus are the focus of this critical review, further methods development is needed for complex environmental samples and to more fully capture the diversity of microbes (e.g., eukaryotic microbes and viruses) and metabolic states (e.g., spores) of microbes in natural environments.}, } @article {pmid28810737, year = {2018}, author = {Cohen, LJ and Han, S and Huang, YH and Brady, SF}, title = {Identification of the Colicin V Bacteriocin Gene Cluster by Functional Screening of a Human Microbiome Metagenomic Library.}, journal = {ACS infectious diseases}, volume = {4}, number = {1}, pages = {27-32}, pmid = {28810737}, issn = {2373-8227}, support = {K08 DK109287/DK/NIDDK NIH HHS/United States ; T32 GM007739/GM/NIGMS NIH HHS/United States ; U01 GM110714/GM/NIGMS NIH HHS/United States ; }, mesh = {Colicins/*genetics ; Gene Library ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; *Multigene Family ; Sequence Analysis, DNA ; }, abstract = {The forces that shape human microbial ecology are complex. It is likely that human microbiota, similarly to other microbiomes, use antibiotics as one way to establish an ecological niche. In this study, we use functional metagenomics to identify human microbial gene clusters that encode for antibiotic functions. Screening of a metagenomic library prepared from a healthy patient stool sample led to the identification of a family of clones with inserts that are 99% identical to a region of a virulence plasmid found in avian pathogenic Escherichia coli. Characterization of the metagenomic DNA sequence identified a colicin V biosynthetic cluster as being responsible for the observed antibiotic effect of the metagenomic clone against E. coli. This study presents a scalable method to recover antibiotic gene clusters from humans using functional metagenomics and highlights a strategy to study bacteriocins in the human microbiome which can provide a resource for therapeutic discovery.}, } @article {pmid28807046, year = {2017}, author = {Whelan, FJ and Surette, MG}, title = {A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {100}, pmid = {28807046}, issn = {2049-2618}, support = {//CIHR/Canada ; }, mesh = {Algorithms ; Bacteria/classification/*genetics/isolation & purification ; Base Sequence ; Cluster Analysis ; Computational Biology/*methods ; Databases, Genetic ; Gene Library ; *Genes, rRNA ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Microbiota/genetics ; RNA, Ribosomal, 16S/*genetics ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {BACKGROUND: Advances in next-generation sequencing technologies have allowed for detailed, molecular-based studies of microbial communities such as the human gut, soil, and ocean waters. Sequencing of the 16S rRNA gene, specific to prokaryotes, using universal PCR primers has become a common approach to studying the composition of these microbiota. However, the bioinformatic processing of the resulting millions of DNA sequences can be challenging, and a standardized protocol would aid in reproducible analyses.

METHODS: The short-read library 16S rRNA gene sequencing pipeline (sl1p, pronounced "slip") was designed with the purpose of mitigating this lack of reproducibility by combining pre-existing tools into a computational pipeline. This pipeline automates the processing of raw 16S rRNA gene sequencing data to create human-readable tables, graphs, and figures to make the collected data more readily accessible.

RESULTS: Data generated from mock communities were compared using eight OTU clustering algorithms, two taxon assignment approaches, and three 16S rRNA gene reference databases. While all of these algorithms and options are available to sl1p users, through testing with human-associated mock communities, AbundantOTU+, the RDP Classifier, and the Greengenes 2011 reference database were chosen as sl1p's defaults based on their ability to best represent the known input communities.

CONCLUSIONS: sl1p promotes reproducible research by providing a comprehensive log file, and reduces the computational knowledge needed by the user to process next-generation sequencing data. sl1p is freely available at https://bitbucket.org/fwhelan/sl1p .}, } @article {pmid28801639, year = {2017}, author = {Yin, Y and Fan, B and Liu, W and Ren, R and Chen, H and Bai, S and Zhu, L and Sun, G and Yang, Y and Wang, X}, title = {Investigation into the stability and culturability of Chinese enterotypes.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {7947}, pmid = {28801639}, issn = {2045-2322}, mesh = {Adult ; Bacteria/*classification/genetics/*growth & development ; Bacteriological Techniques ; Bacteroides/classification/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Feces/*microbiology ; Gastrointestinal Microbiome ; Healthy Volunteers ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/methods ; Phylogeny ; Prevotella/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Although many gut microbial enterotypes have been reported in Europe, Africa and the U.S., their effects on human health are still not yet clear. Culturing gut microbial enterotypes in vitro will be helpful to study their effects and applications. Here, fecal samples from 13 healthy Chinese volunteers were collected and subjected to next-generation sequencing. The results showed that seven of these samples belong to the Bacteroides enterotype and another six to the Prevotella enterotype. Stability of these Chinese gut microbial enterotypes was also evaluated. Results showed that most of the tested volunteer gut microbiota to be very stable. For one volunteer, the bacterial community returned to the state it was in before intestinal lavage and antibiotics treatment after four months. XP medium was found effective for simulating the Bacteroides enterotype independent of the original gut microbial community in an in vitro chemostat culture system. Although, the Prevotella enterotype was not very well simulated in vitro, different culture elements selectively enriched different gut bacteria. Pectin and xylan were found to be related to the enrichment of the genera Bacteroides, Sutterella, and Flavonifractor in this chemostat culture system.}, } @article {pmid28799900, year = {2017}, author = {Vorholt, JA and Vogel, C and Carlström, CI and Müller, DB}, title = {Establishing Causality: Opportunities of Synthetic Communities for Plant Microbiome Research.}, journal = {Cell host & microbe}, volume = {22}, number = {2}, pages = {142-155}, doi = {10.1016/j.chom.2017.07.004}, pmid = {28799900}, issn = {1934-6069}, mesh = {Bacteria/genetics ; Bacterial Physiological Phenomena ; Ecosystem ; Host-Pathogen Interactions ; Metagenome ; Microbial Consortia/physiology ; Microbial Interactions ; *Microbiota/genetics/physiology ; Plant Roots/microbiology ; Plants/*microbiology ; Soil Microbiology ; }, abstract = {Plant microbiome research highlights the importance of indigenous microbial communities for host phenotypes such as growth and health. It aims to discover the molecular basis by which host-microbe and microbe-microbe interactions shape and maintain microbial communities and to understand the role of individual microorganisms, as well as their collective ecosystem function. Here, we discuss reductionist approaches to disentangle the inherent complexity of interactions in situ. Experimentally tractable, synthetic communities enable testing of hypotheses by targeted manipulation in gnotobiotic systems. Modifications of microbial, host, and environmental parameters allow for the quantitative assessment of host and microbe characteristics with dynamic and spatial resolution. We summarize first insights from this emerging field and discuss current challenges and limitations. Using multifaceted approaches to detect interactions and functions will provide new insights into the fundamental biology of plant-microbe interactions and help to harness the power of the microbiome.}, } @article {pmid28799713, year = {2017}, author = {Dunthorn, M and Kauserud, H and Bass, D and Mayor, J and Mahé, F}, title = {Yeasts dominate soil fungal communities in three lowland Neotropical rainforests.}, journal = {Environmental microbiology reports}, volume = {9}, number = {5}, pages = {668-675}, doi = {10.1111/1758-2229.12575}, pmid = {28799713}, issn = {1758-2229}, mesh = {*Biodiversity ; Fungi/*classification/*genetics ; Metagenome ; Metagenomics/methods ; Phylogeography ; *Rainforest ; *Soil Microbiology ; *Tropical Climate ; }, abstract = {Forest soils typically harbour a vast diversity of fungi, but are usually dominated by filamentous (hyphae-forming) taxa. Compared to temperate and boreal forests, though, we have limited knowledge about the fungal diversity in tropical rainforest soils. Here we show, by environmental metabarcoding of soil samples collected in three Neotropical rainforests, that Yeasts dominate the fungal communities in terms of the number of sequencing reads and OTUs. These unicellular forms are commonly found in aquatic environments, and their hyperdiversity may be the result of frequent inundation combined with numerous aquatic microenvironments in these rainforests. Other fungi that are frequent in aquatic environments, such as the abundant Chytridiomycotina, were also detected. While there was low similarity in OTU composition within and between the three rainforests, the fungal communities in Central America were more similar to each other than the communities in South America, reflecting a general biogeographic pattern also seen in animals, plants and protists.}, } @article {pmid28799297, year = {2017}, author = {Hussein, EI and Jacob, JH and Shakhatreh, MAK and Abd Al-Razaq, MA and Juhmani, AF and Cornelison, CT}, title = {Exploring the microbial diversity in Jordanian hot springs by comparative metagenomic analysis.}, journal = {MicrobiologyOpen}, volume = {6}, number = {6}, pages = {}, pmid = {28799297}, issn = {2045-8827}, mesh = {Archaea/classification/genetics/*isolation & purification ; Bacteria/classification/genetics/*isolation & purification ; *Biodiversity ; Hot Springs/chemistry/*microbiology ; Hydrogen-Ion Concentration ; Jordan ; Metagenome ; Metagenomics ; Phylogeny ; }, abstract = {A culture-independent approach was utilized in this study to reveal the microbial diversity in Jordanian hot springs represented by Ma'in and Afra hot springs. Water samples from Ma'in and Afra hot springs were collected in June 2015. The in situ temperature of water samples range was 38-59°C and the pH range was 7.4-8.4. The metagenome was extracted and analyzed using the next generation technology (bTEFAP[®]). A total of 314,310 sequences were parsed and 288,452 were then clustered. The sequences were predominated by bacteria (>84%) and the relative abundance of archaea in each sample was <1%. Eukaryotic microorganisms were detected but with varying abundances (0.6%-15%). Because most of the detected sequences were found to belong to the domain of bacteria (196,936 sequences out 288,452), the bacterial sequences were utilized for further microbial analyses. With respect to alpha and beta diversity, samples were rarefied to 30,000 sequences and bootstrapped at 10,000 sequences. The Shannon-Wiener Index curve plot reaches a plateau at approximately 3,000 sequences indicating that sequencing depth was sufficient to capture the full scope of microbial diversity. By examining the relative abundance of phyla detected in each sample, it appears that the biota of both Jordanian hot springs sampled are compositionally similar, with over 50% of the microbial community of each sample being comprised of the phylum Proteobacteria. The second most abundant phylum was the phylum Bacteroidetes which represents more than 13% in each sample. The phylum Firmicutes was also detected with a significant abundance. However, lower abundance of Deinococcus, Verrucomicrobia, Planctomycetes, and Chloroflexi was detected. A principal coordinate analysis plot was generated based upon the weighted UniFrac distance matrix. By utilizing Monte Carlo simulations, we were able to determine that there were no significant differences in the microbial diversity between each sample.}, } @article {pmid28798873, year = {2017}, author = {Aswad, A and Katzourakis, A}, title = {A novel viral lineage distantly related to herpesviruses discovered within fish genome sequence data.}, journal = {Virus evolution}, volume = {3}, number = {2}, pages = {vex016}, pmid = {28798873}, issn = {2057-1577}, abstract = {Pathogenic viruses represent a small fraction of viral diversity, and emerging diseases are frequently the result of cross-species transmissions. Therefore, we need to develop high-throughput techniques to investigate a broader range of viral biodiversity across a greater number of species. This is especially important in the context of new practices in agriculture that have arisen to tackle the challenges of global food security, including the rising number of marine and freshwater species that are used in aquaculture. In this study, we demonstrate the utility of combining evolutionary approaches with bioinformatics to mine non-viral genome data for viruses, by adapting methods from paleovirology. We report the discovery of a new lineage of dsDNA viruses that are associated with at least fifteen different species of fish. This approach also enabled us to simultaneously identify sequences that likely represent endogenous viral elements, which we experimentally confirmed in commercial salmon samples. Moreover, genomic analysis revealed that the endogenous sequences have co-opted PiggyBac-like transposable elements, possibly as a mechanism of intragenomic proliferation. The identification of novel viruses from genome data shows that our approach has applications in genomics, virology, and the development of best practices for aquaculture and farming.}, } @article {pmid28798374, year = {2017}, author = {Patel, SH and Vaidya, YH and Patel, RJ and Pandit, RJ and Joshi, CG and Kunjadiya, AP}, title = {Culture independent assessment of human milk microbial community in lactational mastitis.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {7804}, pmid = {28798374}, issn = {2045-2322}, mesh = {Bacteria/*classification/genetics ; Case-Control Studies ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Gene Regulatory Networks ; Humans ; Lactation ; Mastitis/*microbiology ; Metagenomics/*methods ; Microbiota ; Milk, Human/*microbiology ; Odds Ratio ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Breastfeeding undoubtedly provides important benefits to the mother-infant dyad and should be encouraged. Mastitis, one of the common but major cause of premature weaning among lactating women, is an inflammation of connective tissue within the mammary gland. This study reports the influence of mastitis on human milk microbiota by utilizing 16 S rRNA gene sequencing approach. We sampled and sequenced microbiome from 50 human milk samples, including 16 subacute mastitis (SAM), 16 acute mastitis (AM) and 18 healthy-controls. Compared to controls, SAM and AM microbiota were quite distinct and drastically reduced. Genera including, Aeromonas, Staphylococcus, Ralstonia, Klebsiella, Serratia, Enterococcus and Pseudomonas were significantly enriched in SAM and AM samples, while Acinetobacter, Ruminococcus, Clostridium, Faecalibacterium and Eubacterium were consistently depleted. Further analysis of our samples revealed positive aerotolerant odds ratio, indicating dramatic depletion of obligate anaerobes and enrichment of aerotolerant bacteria during the course of mastitis. In addition, predicted functional metagenomics identified several gene pathways related to bacterial proliferation and colonization (e.g. two-component system, bacterial secretion system and motility proteins) in SAM and AM samples. In conclusion, our study confirmed previous hypothesis that mastitis women have lower microbial diversity, increased abundance of opportunistic pathogens and depletion of commensal obligate anaerobes.}, } @article {pmid28797931, year = {2017}, author = {Byerley, LO and Samuelson, D and Blanchard, E and Luo, M and Lorenzen, BN and Banks, S and Ponder, MA and Welsh, DA and Taylor, CM}, title = {Changes in the gut microbial communities following addition of walnuts to the diet.}, journal = {The Journal of nutritional biochemistry}, volume = {48}, number = {}, pages = {94-102}, pmid = {28797931}, issn = {1873-4847}, support = {P01 HL076100/HL/NHLBI NIH HHS/United States ; P60 AA009803/AA/NIAAA NIH HHS/United States ; U54 GM104940/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Body Weight ; Diet ; Eating ; *Gastrointestinal Microbiome/genetics ; *Juglans ; Male ; Metagenome ; Rats, Inbred F344 ; }, abstract = {Walnuts are rich in omega-3 fatty acids, phytochemicals and antioxidants making them unique compared to other foods. Consuming walnuts has been associated with health benefits including a reduced risk of heart disease and cancer. Dysbiosis of the gut microbiome has been linked to several chronic diseases. One potential mechanism by which walnuts may exert their health benefit is through modifying the gut microbiome. This study identified the changes in the gut microbial communities that occur following the inclusion of walnuts in the diet. Male Fischer 344 rats (n=20) were randomly assigned to one of two diets for as long as 10 weeks: (1) walnut (W), and (2) replacement (R) in which the fat, fiber, and protein in walnuts were matched with corn oil, protein casein, and a cellulose fiber source. Intestinal samples were collected from the descending colon, the DNA isolated, and the V3-V4 hypervariable region of 16S rRNA gene deep sequenced on an Illumina MiSeq for characterization of the gut microbiota. Body weight and food intake did not differ significantly between the two diet groups. The diet groups had distinct microbial communities with animals consuming walnuts displaying significantly greater species diversity. Walnuts increased the abundance of Firmicutes and reduced the abundance of Bacteriodetes. Walnuts enriched the microbiota for probiotic-type bacteria including Lactobacillus, Ruminococcaceae, and Roseburia while significantly reducing Bacteroides and Anaerotruncus. The class Alphaproteobacteria was also reduced. Walnut consumption altered the gut microbial community suggesting a new mechanism by which walnuts may confer their beneficial health effects.}, } @article {pmid28797298, year = {2017}, author = {Petersen, LM and Bautista, EJ and Nguyen, H and Hanson, BM and Chen, L and Lek, SH and Sodergren, E and Weinstock, GM}, title = {Community characteristics of the gut microbiomes of competitive cyclists.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {98}, pmid = {28797298}, issn = {2049-2618}, support = {P30 CA034196/CA/NCI NIH HHS/United States ; U54 DE023789/DE/NIDCR NIH HHS/United States ; U54 HG004968/HG/NHGRI NIH HHS/United States ; }, mesh = {Adult ; *Athletes ; Bacteria/classification/*genetics/*isolation & purification ; Bacteroides/genetics/isolation & purification ; *Bicycling ; Carbohydrate Metabolism/genetics ; Diet ; Exercise ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Humans ; Life Style ; Male ; Metabolic Networks and Pathways/genetics ; Metagenome ; Metagenomics ; Methane/*metabolism ; Middle Aged ; Pilot Projects ; Prevotella/genetics/isolation & purification ; }, abstract = {BACKGROUND: Changes in diet and exercise can alter the gut microbiome of humans and mice; however, few studies to date have assessed the microbiomes of highly fit athletes. In this pilot study, we used metagenomic whole genome shotgun (mWGS) and metatranscriptomic (RNA-Seq) sequencing to show what organisms are both present and active in the gut microbiomes of both professional and amateur level competitive cyclists and to determine if any significant differences exist between these two groups.

RESULTS: Using mWGS sequencing data, we showed that the gut microbiomes of 33 cyclists split into three taxonomic clusters, characterized by either high Prevotella, high Bacteroides or a mix of many genera including Bacteroides, Prevotella, Eubacterium, Ruminococcus, and Akkermansia. While no significant correlations could be found between taxonomic cluster and being either a professional or amateur level cyclist, high abundance of the genus Prevotella (≥2.5%) was significantly correlated with time reported exercising during an average week. Increased abundance of Prevotella was correlated with a number of amino acid and carbohydrate metabolism pathways, including branched chain amino acid metabolism. Further analysis of the metatranscriptome revealed significant taxonomic differences when compared to the metagenome. There was increased abundance of Methanobrevibacter smithii transcripts in a number of professional cyclists in comparison to amateur cyclists and this archaeon had upregulation of genes involved in the production of methane. Furthermore, when methane metabolism was upregulated, there was similar upregulation of energy and carbohydrate metabolism pathways.

CONCLUSIONS: These results provide a framework for common constituents of the gut community in individuals who follow an exercise-rich lifestyle. These data also suggest how certain organisms such as M. smithii may beneficially influence the metabolic efficiency of the gut community in professional cyclists due to synergistic metabolic cross-feeding events.}, } @article {pmid28797279, year = {2017}, author = {Zhang, Y and Xu, J and Riera, N and Jin, T and Li, J and Wang, N}, title = {Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {97}, pmid = {28797279}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Burkholderia/physiology ; Citrus/*microbiology ; Gene Expression Profiling/methods ; Host-Pathogen Interactions/genetics ; Metagenomics/methods ; Microbiota/*genetics ; Phylogeny ; Plant Diseases/*microbiology ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizobiaceae/genetics ; Rhizosphere ; *Soil Microbiology ; }, abstract = {BACKGROUND: Roots are the primary site for plant-microbe interactions. Among the three root-associated layers (i.e., rhizosphere, rhizoplane, and endorhiza), the rhizoplane is a key component serving a critical gating role that controls microbial entry into plant roots. The microbial communities colonizing the three layers are believed to be gradually enriched from the bulk soil inoculum. However, it is unknown how this enrichment process, particularly the rhizosphere to rhizoplane step, is affected by biotic stresses, such as disease. In this study, we address this question using the citrus root-associated microbiome as a model.

RESULTS: We identified the rhizosphere-to-rhizoplane-enriched taxonomic and functional properties of the citrus root-associated microbiome and determined how they were affected by Huanglongbing (HLB), a severe systemic disease caused by Candidatus Liberibacter asiaticus, using metagenomic and metatranscriptomic approaches. Multiple rhizoplane-enriched genera were identified, with Bradyrhizobium and Burkholderia being the most dominant. Plant-derived carbon sources are an important driving force for the enrichment process. The enrichment of functional attributes, such as motility, chemotaxis, secretion systems, and lipopolysaccharide (LPS) synthesis, demonstrated more active microbe-plant interactions on the rhizoplane than the rhizosphere. We observed that HLB impaired the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome in three ways: (1) by decreasing the relative abundance of most rhizoplane-enriched genera; (2) by reducing the relative abundance and/or expression activity of the functional attributes involved in microbe-plant interactions; and (3) by recruiting more functional features involved in autotrophic life cycle adaptation, such as carbon fixation and nitrogen nitrification in the HLB rhizoplane microbiome. Finally, our data showed that inoculation of Burkholderia strains isolated from the healthy citrus root-associated microbiome could trigger the expression of genes involved in induced systemic resistance in inoculated plants.

CONCLUSIONS: HLB causes decreased relative abundance and/or expression activity of rhizoplane-enriched taxonomic and functional properties, collectively resulting in impaired plant host-microbiome interactions. Manipulation of the citrus root-associated microbiome, for instance, by inoculating citrus roots with beneficial Burkholderia strains, has potential to promote plant health. Our results provide novel insights for understanding the contributions of the community enrichment process of the root-associated microbiome to the plant hosts.}, } @article {pmid28796793, year = {2017}, author = {Reed, S and Neuman, H and Glahn, RP and Koren, O and Tako, E}, title = {Characterizing the gut (Gallus gallus) microbiota following the consumption of an iron biofortified Rwandan cream seeded carioca (Phaseolus Vulgaris L.) bean-based diet.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0182431}, pmid = {28796793}, issn = {1932-6203}, mesh = {Administration, Oral ; *Animal Feed ; Animals ; Cecum/microbiology ; Chickens/*microbiology ; Diet ; Dietary Supplements ; Female ; *Food, Fortified ; Gastrointestinal Microbiome/*genetics ; Iron/*administration & dosage ; Male ; Metagenome ; Molecular Typing ; Phaseolus/genetics/metabolism ; }, abstract = {Biofortification is a plant breeding method that introduces increased concentrations of minerals in staple food crops (e.g., legumes, cereal grains), and has shown success in alleviating insufficient Fe intake in various human populations. Unlike other strategies utilized to alleviate Fe deficiency, studies of the gut microbiota in the context of Fe biofortification have not yet been reported, although the consumption of Fe biofortified staple food crops has increased significantly over time. Hence, in this study, we performed a 6-week feeding trial in Gallus gallus (n = 14), aimed to investigate the alterations in the gut microbiome following administration of an Fe biofortified bean-based diet (biofortified, BFe) versus a bean based diet with poorly-bioavailable Fe (standard, SFe). Cream seeded carioca bean based diets were designed in an identical fashion to those used in a recent human clinical trial of Fe biofortified beans in Rwanda. We hypothesized that the different dietary Fe contents in the beans based diets will alter the composition and function of the intestinal microbiome. The primary outcomes were changes in the gut microbiome composition and function analyzed by 16S rRNA gene sequencing. We observed no significant changes in phylogenetic diversity between groups. There were significant differences in the composition of the microbiota between groups, with the BFe group harboring fewer taxa participating in bacterial Fe uptake, increased abundance of bacteria involved in phenolic catabolism, and increased abundance of beneficial butyrate-producing bacteria. Additionally, depletion of key bacterial pathways responsible for bacterial viability and Fe uptake suggest that improvements in Fe bioavailability, in addition to increases in Fe-polyphenol and Fe-phytate complexes due to biofortification, led to decreased concentrations of cecal Fe available for bacterial utilization. Our findings demonstrate that Fe biofortification may improve Fe status without negatively altering the structure and function of the gut microbiota, as is observed with other nutritional methods of Fe supplementation. These results may be used to further improve the efficacy and safety of future biofortification efforts in eradicating global Fe deficiency.}, } @article {pmid28793929, year = {2017}, author = {Broman, E and Sjöstedt, J and Pinhassi, J and Dopson, M}, title = {Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {96}, pmid = {28793929}, issn = {2049-2618}, mesh = {Bacteria/classification/*genetics/isolation & purification/*metabolism ; Bacterial Physiological Phenomena/genetics ; Baltic States ; Gene Expression Profiling ; Geologic Sediments/*chemistry/*microbiology ; Hydrogen Sulfide/metabolism ; Metagenomics ; Methane/metabolism ; Microbial Consortia/*genetics/physiology ; Oceans and Seas ; Oxidation-Reduction ; Oxygen/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability. Here, coastal Baltic Sea sediments sampled from oxic and anoxic sites, plus an intermediate area subjected to episodic oxygenation, were experimentally exposed to oxygen shifts. Chemical, 16S rRNA gene, metagenomic, and metatranscriptomic analyses were conducted to investigate changes in chemistry fluxes, microbial community structure, and metabolic functions in the sediment surface.

RESULTS: Compared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated as sqr, fccB, and dsrA involved in sulfide oxidation. In addition, the importance of cryptic sulfur cycling was highlighted by the oxidative genes listed above as well as dsvA, ttrB, dmsA, and ddhAB that encode reductive processes being identified in anoxic and intermediate sediments turned oxic. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic matter degradation.

CONCLUSIONS: These novel data emphasize that genetic expression analyses has the power to identify key molecular mechanisms that regulate microbial community responses upon oxygenation of dead zones. Moreover, these results highlight that microbial responses, and therefore ultimately remediation efforts, depend largely on the oxygenation history of sites. Furthermore, it was shown that re-oxygenation efforts to remediate dead zones could ultimately be facilitated by in situ microbial molecular mechanisms involved in removal of toxic H2S and the potent greenhouse gas methane.}, } @article {pmid28792501, year = {2017}, author = {Takayasu, L and Suda, W and Watanabe, E and Fukuda, S and Takanashi, K and Ohno, H and Takayasu, M and Takayasu, H and Hattori, M}, title = {A 3-dimensional mathematical model of microbial proliferation that generates the characteristic cumulative relative abundance distributions in gut microbiomes.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0180863}, pmid = {28792501}, issn = {1932-6203}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Cell Proliferation/physiology ; Colon/drug effects/metabolism/microbiology/pathology ; Computer Simulation ; Diabetes Mellitus, Type 2/metabolism/microbiology ; Diet, Vegetarian ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; Humans ; Infant ; Infant, Newborn ; Inflammatory Bowel Diseases/metabolism/microbiology ; Intestine, Small/drug effects/metabolism/microbiology/pathology ; Mice ; *Models, Biological ; Multiple Sclerosis/metabolism/microbiology ; RNA, Ribosomal, 16S/metabolism ; }, abstract = {The gut microbiome is highly variable among individuals, largely due to differences in host lifestyle and physiology. However, little is known about the underlying processes or rules that shape the complex microbial community. In this paper, we show that the cumulative relative abundance distribution (CRAD) of microbial species can be approximated by a power law function, and found that the power exponent of CRADs generated from 16S rRNA gene and metagenomic data for normal gut microbiomes of humans and mice was similar consistently with ∼0.9. A similarly robust power exponent was observed in CRADs of gut microbiomes during dietary interventions and several diseases. However, the power exponent was found to be ∼0.6 in CRADs from gut microbiomes characterized by lower species richness, such as those of human infants and the small intestine of mice. In addition, the CRAD of gut microbiomes of mice treated with antibiotics differed slightly from those of infants and the small intestines of mice. Based on these observations, in addition to data on the spatial distribution of microbes in the digestive tract, we developed a 3-dimensional mathematical model of microbial proliferation that reproduced the experimentally observed CRAD patterns. Our model indicated that the CRAD may be determined by the ratio of emerging to pre-existing species during non-uniform spatially competitive proliferation, independent of species composition.}, } @article {pmid28790452, year = {2017}, author = {Claesson, MJ and Clooney, AG and O'Toole, PW}, title = {A clinician's guide to microbiome analysis.}, journal = {Nature reviews. Gastroenterology & hepatology}, volume = {14}, number = {10}, pages = {585-595}, pmid = {28790452}, issn = {1759-5053}, mesh = {Computational Biology/*methods ; *Gastrointestinal Microbiome ; Genetic Techniques ; Humans ; Metagenomics/*methods ; Research Design ; }, abstract = {Microbiome analysis involves determining the composition and function of a community of microorganisms in a particular location. For the gastroenterologist, this technology opens up a rapidly evolving set of challenges and opportunities for generating novel insights into the health of patients on the basis of microbiota characterizations from intestinal, hepatic or extraintestinal samples. Alterations in gut microbiota composition correlate with intestinal and extraintestinal disease and, although only a few mechanisms are known, the microbiota are still an attractive target for developing biomarkers for disease detection and management as well as potential therapeutic applications. In this Review, we summarize the major decision points confronting new entrants to the field or for those designing new projects in microbiome research. We provide recommendations based on current technology options and our experience of sequencing platform choices. We also offer perspectives on future applications of microbiome research, which we hope convey the promise of this technology for clinical applications.}, } @article {pmid28790203, year = {2017}, author = {Johnson, TA and Looft, T and Severin, AJ and Bayles, DO and Nasko, DJ and Wommack, KE and Howe, A and Allen, HK}, title = {The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription in the Swine Gut Microbiome.}, journal = {mBio}, volume = {8}, number = {4}, pages = {}, pmid = {28790203}, issn = {2150-7511}, mesh = {Animal Feed ; Animals ; Anti-Infective Agents/*administration & dosage ; Bacteriophages/drug effects/*genetics ; Carbadox/*administration & dosage ; Drug Resistance, Microbial ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; Gene Expression Profiling ; Metagenome/drug effects ; Prophages/genetics ; Sus scrofa/*microbiology/virology ; Swine ; Transcription, Genetic/*drug effects ; }, abstract = {Carbadox is a quinoxaline-di-N-oxide antibiotic fed to over 40% of young pigs in the United States that has been shown to induce phage DNA transduction in vitro; however, the effects of carbadox on swine microbiome functions are poorly understood. We investigated the in vivo longitudinal effects of carbadox on swine gut microbial gene expression (fecal metatranscriptome) and phage population dynamics (fecal dsDNA viromes). Microbial metagenome, transcriptome, and virome sequences were annotated for taxonomic inference and gene function by using FIGfam (isofunctional homolog sequences) and SEED subsystems databases. When the beta diversities of microbial FIGfam annotations were compared, the control and carbadox communities were distinct 2 days after carbadox introduction. This effect was driven by carbadox-associated lower expression of FIGfams (n = 66) related to microbial respiration, carbohydrate utilization, and RNA metabolism (q < 0.1), suggesting bacteriostatic or bactericidal effects within certain populations. Interestingly, carbadox treatment caused greater expression of FIGfams related to all stages of the phage lytic cycle 2 days following the introduction of carbadox (q ≤0.07), suggesting the carbadox-mediated induction of prophages and phage DNA recombination. These effects were diminished by 7 days of continuous carbadox in the feed, suggesting an acute impact. Additionally, the viromes included a few genes that encoded resistance to tetracycline, aminoglycoside, and beta-lactam antibiotics but these did not change in frequency over time or with treatment. The results show decreased bacterial growth and metabolism, prophage induction, and potential transduction of bacterial fitness genes in swine gut bacterial communities as a result of carbadox administration.IMPORTANCE FDA regulations on agricultural antibiotic use have focused on antibiotics that are important for human medicine. Carbadox is an antibiotic not used in humans but frequently used on U.S. pig farms. It is important to study possible side effects of carbadox use because it has been shown to promote bacterial evolution, which could indirectly impact antibiotic resistance in bacteria of clinical importance. Interestingly, the present study shows greater prophage gene expression in feces from carbadox-fed animals than in feces from nonmedicated animals 2 days after the initiation of in-feed carbadox treatment. Importantly, the phage genetic material isolated in this study contained genes that could provide resistance to antibiotics that are important in human medicine, indicating that human-relevant antibiotic resistance genes are mobile between bacteria via phages. This study highlights the collateral effects of antibiotics and demonstrates the need to consider diverse antibiotic effects whenever antibiotics are being used or new regulations are considered.}, } @article {pmid28789673, year = {2017}, author = {Kamke, J and Soni, P and Li, Y and Ganesh, S and Kelly, WJ and Leahy, SC and Shi, W and Froula, J and Rubin, EM and Attwood, GT}, title = {Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep.}, journal = {BMC research notes}, volume = {10}, number = {1}, pages = {367}, pmid = {28789673}, issn = {1756-0500}, mesh = {Animals ; Bacteria/classification/*genetics/isolation & purification/metabolism ; Bacterial Proteins/*genetics/metabolism ; Culture Media/chemistry ; Fermentation ; Gastrointestinal Microbiome/genetics ; *Gene Expression Regulation, Bacterial ; Gene Ontology ; Metabolic Networks and Pathways/genetics ; Metagenome ; Methane/*biosynthesis ; Methanobrevibacter/genetics/isolation & purification/metabolism ; Molecular Sequence Annotation ; Phylogeny ; Rumen/microbiology ; Sheep ; Succinivibrionaceae/genetics/isolation & purification/metabolism ; *Transcriptome ; Type III Secretion Systems/*genetics/metabolism ; }, abstract = {BACKGROUND: Ruminants are important contributors to global methane emissions via microbial fermentation in their reticulo-rumens. This study is part of a larger program, characterising the rumen microbiomes of sheep which vary naturally in methane yield (g CH4/kg DM/day) and aims to define differences in microbial communities, and in gene and transcript abundances that can explain the animal methane phenotype.

METHODS: Rumen microbiome metagenomic and metatranscriptomic data were analysed by Gene Set Enrichment, sparse partial least squares regression and the Wilcoxon Rank Sum test to estimate correlations between specific KEGG bacterial pathways/genes and high methane yield in sheep. KEGG genes enriched in high methane yield sheep were reassembled from raw reads and existing contigs and analysed by MEGAN to predict their phylogenetic origin. Protein coding sequences from Succinivibrio dextrinosolvens strains were analysed using Effective DB to predict bacterial type III secreted proteins. The effect of S. dextrinosolvens strain H5 growth on methane formation by rumen methanogens was explored using co-cultures.

RESULTS: Detailed analysis of the rumen microbiomes of high methane yield sheep shows that gene and transcript abundances of bacterial type III secretion system genes are positively correlated with methane yield in sheep. Most of the bacterial type III secretion system genes could not be assigned to a particular bacterial group, but several genes were affiliated with the genus Succinivibrio, and searches of bacterial genome sequences found that strains of S. dextrinosolvens were part of a small group of rumen bacteria that encode this type of secretion system. In co-culture experiments, S. dextrinosolvens strain H5 showed a growth-enhancing effect on a methanogen belonging to the order Methanomassiliicoccales, and inhibition of a representative of the Methanobrevibacter gottschalkii clade.

CONCLUSIONS: This is the first report of bacterial type III secretion system genes being associated with high methane emissions in ruminants, and identifies these secretions systems as potential new targets for methane mitigation research. The effects of S. dextrinosolvens on the growth of rumen methanogens in co-cultures indicate that bacteria-methanogen interactions are important modulators of methane production in ruminant animals.}, } @article {pmid28787780, year = {2017}, author = {Noronha, MF and Lacerda Júnior, GV and Gilbert, JA and de Oliveira, VM}, title = {Taxonomic and functional patterns across soil microbial communities of global biomes.}, journal = {The Science of the total environment}, volume = {609}, number = {}, pages = {1064-1074}, doi = {10.1016/j.scitotenv.2017.07.159}, pmid = {28787780}, issn = {1879-1026}, mesh = {Biodiversity ; Classification ; *Ecosystem ; Metagenomics ; Soil ; *Soil Microbiology ; }, } @article {pmid28786955, year = {2017}, author = {Arafat, Y and Wei, X and Jiang, Y and Chen, T and Saqib, HSA and Lin, S and Lin, W}, title = {Spatial Distribution Patterns of Root-Associated Bacterial Communities Mediated by Root Exudates in Different Aged Ratooning Tea Monoculture Systems.}, journal = {International journal of molecular sciences}, volume = {18}, number = {8}, pages = {}, pmid = {28786955}, issn = {1422-0067}, mesh = {Bacteria/*classification/genetics ; Biodiversity ; Chromatography, High Pressure Liquid ; Cluster Analysis ; Computational Biology/methods ; *Exudates and Transudates ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Plant Roots/*chemistry/*microbiology ; *Rhizosphere ; Soil/chemistry ; Soil Microbiology ; Spectrometry, Mass, Electrospray Ionization ; *Tea ; }, abstract = {Positive plant-soil feedback depends on beneficial interactions between roots and microbes for nutrient acquisition; growth promotion; and disease suppression. Recent pyrosequencing approaches have provided insight into the rhizosphere bacterial communities in various cropping systems. However; there is a scarcity of information about the influence of root exudates on the composition of root-associated bacterial communities in ratooning tea monocropping systems of different ages. In Southeastern China; tea cropping systems provide the unique natural experimental environment to compare the distribution of bacterial communities in different rhizo-compartments. High performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS) was performed to identify and quantify the allelochemicals in root exudates. A high-throughput sequence was used to determine the structural dynamics of the root-associated bacterial communities. Although soil physiochemical properties showed no significant differences in nutrients; long-term tea cultivation resulted in the accumulation of catechin-containing compounds in the rhizosphere and a lowering of pH. Moreover; distinct distribution patterns of bacterial taxa were observed in all three rhizo-compartments of two-year and 30-year monoculture tea; mediated strongly by soil pH and catechin-containing compounds. These results will help to explore the reasons why soil quality and fertility are disturbed in continuous ratooning tea monocropping systems; and to clarify the associated problems.}, } @article {pmid28785422, year = {2017}, author = {Gundogdu, A and Nalbantoglu, U}, title = {Human genome-microbiome interaction: metagenomics frontiers for the aetiopathology of autoimmune diseases.}, journal = {Microbial genomics}, volume = {3}, number = {4}, pages = {e000112}, pmid = {28785422}, issn = {2057-5858}, mesh = {Autoimmune Diseases/*genetics/*microbiology ; Autoimmunity/*genetics ; Genetic Variation ; Genome, Human ; Host Microbial Interactions/*genetics ; Humans ; Machine Learning ; Metagenomics ; Microbiota/*genetics ; Systems Biology ; }, abstract = {A short while ago, the human genome and microbiome were analysed simultaneously for the first time as a multi-omic approach. The analyses of heterogeneous population cohorts showed that microbiome components were associated with human genome variations. In-depth analysis of these results reveals that the majority of those relationships are between immune pathways and autoimmune disease-associated microbiome components. Thus, it can be hypothesized that autoimmunity may be associated with homeostatic disequilibrium of the human-microbiome interactome. Further analysis of human genome-human microbiome relationships in disease contexts with tailored systems biology approaches may yield insights into disease pathogenesis and prognosis.}, } @article {pmid28785417, year = {2016}, author = {Jameson, E and Doxey, AC and Airs, R and Purdy, KJ and Murrell, JC and Chen, Y}, title = {Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems.}, journal = {Microbial genomics}, volume = {2}, number = {9}, pages = {e000080}, pmid = {28785417}, issn = {2057-5858}, mesh = {Actinobacteria/enzymology/*genetics ; *Data Mining ; *Ecosystem ; Gastrointestinal Microbiome/*genetics ; Geologic Sediments/microbiology ; Humans ; *Metagenomics ; Methylamines/*metabolism ; Oxidoreductases, N-Demethylating/genetics ; Proteobacteria/enzymology/*genetics ; }, abstract = {Existing metagenome datasets from many different environments contain untapped potential for understanding metabolic pathways and their biological impact. Our interest lies in the formation of trimethylamine (TMA), a key metabolite in both human health and climate change. Here, we focus on bacterial degradation pathways for choline, carnitine, glycine betaine and trimethylamine N-oxide (TMAO) to TMA in human gut and marine metagenomes. We found the TMAO reductase pathway was the most prevalent pathway in both environments. Proteobacteria were found to contribute the majority of the TMAO reductase pathway sequences, except in the stressed gut, where Actinobacteria dominated. Interestingly, in the human gut metagenomes, a high proportion of the Proteobacteria hits were accounted for by the genera Klebsiella and Escherichia. Furthermore Klebsiella and Escherichia harboured three of the four potential TMA-production pathways (choline, carnitine and TMAO), suggesting they have a key role in TMA cycling in the human gut. In addition to the intensive TMAO-TMA cycling in the marine environment, our data suggest that carnitine-to-TMA transformation plays an overlooked role in aerobic marine surface waters, whereas choline-to-TMA transformation is important in anaerobic marine sediments. Our study provides new insights into the potential key microbes and metabolic pathways for TMA formation in two contrasting environments.}, } @article {pmid28783248, year = {2017}, author = {Cui, J and Xiao, M and Liu, M and Wang, Z and Liu, F and Guo, L and Meng, H and Zhang, H and Yang, J and Deng, D and Huang, S and Ma, Y and Liu, C}, title = {Coupling metagenomics with cultivation to select host-specific probiotic micro-organisms for subtropical aquaculture.}, journal = {Journal of applied microbiology}, volume = {123}, number = {5}, pages = {1274-1285}, doi = {10.1111/jam.13555}, pmid = {28783248}, issn = {1365-2672}, mesh = {Animals ; Aquaculture/methods ; Fishes/*microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Lactobacillales/classification/*genetics/*isolation & purification ; Metagenomics ; Probiotics/classification/*isolation & purification ; Shellfish/*microbiology ; Species Specificity ; }, abstract = {AIMS: To demonstrate a nonempirical workflow to select host-specific probiotics for aquaculture industry.

METHODS AND RESULTS: Using both culture-dependent and culture-independent methods, we have systematically investigated, for the first time, the gut microbiota of twelve subtropical aquatic animal species. We found that the diversity, abundance and distribution of gut micro-organisms of these animals were host-specific and that lactic acid bacteria (LAB) were predominant among the indigenous probiotic microbes. Using culturing method, we isolated and characterized ninety-eight LAB strains; however, only a few strains was representative of the dominant LAB OTUs recovered by culture-independent analysis.

CONCLUSIONS: Two cultured LAB strains, Enterococcus faecalis LS1-2 and Enterococcus faecium Z1-2, capturing the major LAB OTUs in the sequencing data set of the most animal samples and showing significant antimicrobial activities against shrimp pathogens, were suggested to be the candidates of shrimp probiotics.

Disease outbreak and the consequential abuse of antibiotics have been the constraints to the aquaculture industry. However, the selection of probiotic bacteria is currently still an empirical process due to our limited knowledge on the gastrointestinal microbiota of aquatic organisms. Our study points to a nonempirical selection process by which host-specific probiotics can be developed.}, } @article {pmid28782803, year = {2017}, author = {Trucchi, E and Frajman, B and Haverkamp, THA and Schönswetter, P and Paun, O}, title = {Genomic analyses suggest parallel ecological divergence in Heliosperma pusillum (Caryophyllaceae).}, journal = {The New phytologist}, volume = {216}, number = {1}, pages = {267-278}, pmid = {28782803}, issn = {1469-8137}, support = {Y 661/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Caryophyllaceae/*genetics ; *Ecosystem ; Ecotype ; *Genetic Variation ; *Genomics ; Likelihood Functions ; }, abstract = {The mosaic distribution of interbreeding taxa with contrasting ecology and morphology offers an opportunity to study microevolutionary dynamics during ecological divergence. We investigate here the evolutionary history of an alpine and a montane ecotype of Heliosperma pusillum (Caryophyllaceae) in the south-eastern Alps. From six pairs of geographically close populations of the two ecotypes (120 individuals) we obtained a high-coverage restriction site associated DNA sequencing (RADseq) dataset that was used for demographic inference to test the hypothesis of parallel evolution of the two ecotypes. The data are consistent with repeated ecological divergence in H. pusillum, uncovering up to five polytopic origins of one ecotype from the other. A complex evolutionary history is evidenced, with local isolation-with-migration in two population pairs and intra-ecotype migration in two others. In all cases, the time of divergence or secondary contact was inferred as postglacial. A metagenomic analysis on exogenous contaminant RAD sequences suggests divergent microbial communities between the ecotypes. The lack of shared genomic regions of high divergence across population pairs illustrates the action of drift and/or local selection in shaping genetic divergence across repeated cases of ecological divergence.}, } @article {pmid28780386, year = {2017}, author = {Acharya, A and Chan, Y and Kheur, S and Jin, LJ and Watt, RM and Mattheos, N}, title = {Salivary microbiome in non-oral disease: A summary of evidence and commentary.}, journal = {Archives of oral biology}, volume = {83}, number = {}, pages = {169-173}, doi = {10.1016/j.archoralbio.2017.07.019}, pmid = {28780386}, issn = {1879-1506}, mesh = {Diet ; Dysbiosis/*microbiology ; Gastrointestinal Microbiome ; Geography ; Humans ; Life Style ; *Microbiota ; Saliva/*microbiology ; }, abstract = {OBJECTIVE: The advent of high-throughput sequencing and 'omic' technologies is facilitating an 'open-ended' understanding of the human microbial community and its interplay with health. This commentary aims to present key perspectives and summarize current evidence from metagenomic studies of salivary microbiota in relation to general health and systemic diseases.

DESIGN: A narrative review of studies that described salivary microbiome composition in relation to various general health conditions was conducted and the main results were summarized.

RESULTS: Currently available evidence shows salivary microbial patterns and fingerprints as related to a range of metabolic, autoimmune and immunodeficiency associated conditions, similar to albeit at a far lower scale than similar studies in the gut microbiome.

CONCLUSIONS: Considering the relative ease of collection, emerging evidence of association with non-oral diseases may imply that saliva microbiome research may have potential diagnostic or prognostic value.}, } @article {pmid28779118, year = {2017}, author = {Yin, X and Lee, B and Zaragoza, J and Marco, ML}, title = {Dietary perturbations alter the ecological significance of ingested Lactobacillus plantarum in the digestive tract.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {7267}, pmid = {28779118}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; *Diet ; Diet, High-Fat ; Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Lactobacillus plantarum/classification/*physiology ; Mice ; Microbial Interactions ; *Probiotics ; Sugars ; }, abstract = {Host diet is a major determinant of the composition and function of the intestinal microbiome. Less understood is the importance of diet on ingested strains with probiotic significance. We investigated the population dynamics of exogenous Lactobacillus plantarum and its interactions with intestinal bacteria in mice undergoing switches between high-fat, high-sugar (HFHSD) and low-fat, plant-polysaccharide rich (LFPPD) diets. The survival and persistence of ingested L. plantarum WCFS1 was significantly improved during mouse consumption of HFHSD and was negatively associated with the numbers of indigenous Lactobacillus species. Diet also rapidly changed the composition of the indigenous microbiota, but with some taxa differentially affected between HFHSD periods. L. plantarum was not integrated into indigenous bacterial community networks according to co-occurrence patterns but still conferred distinct effects on bacterial species diversity and microbiota stability largely in a diet-dependent manner. Metagenome predictions supported the premise that L. plantarum dampens the effects of diet on the microbiome. This strain also consistently altered the predicted genetic content in the distal gut by enriching for genes encoding glyosyltransferases and bile salt hydrolases. Our findings demonstrate the interactions between ingested, transient probiotic bacteria and intestinal bacterial communities and how they can differ depending on host diet.}, } @article {pmid28779076, year = {2017}, author = {Yin, D and Du, E and Yuan, J and Gao, J and Wang, Y and Aggrey, SE and Guo, Y}, title = {Supplemental thymol and carvacrol increases ileum Lactobacillus population and reduces effect of necrotic enteritis caused by Clostridium perfringes in chickens.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {7334}, pmid = {28779076}, issn = {2045-2322}, mesh = {Animals ; Chickens ; Clostridium Infections/*veterinary ; Clostridium perfringens/*drug effects ; Cymenes ; Dietary Supplements ; Enterocolitis, Necrotizing/*veterinary ; Gastrointestinal Microbiome ; Ileum/microbiology ; Lactobacillus/*drug effects/genetics ; Male ; Metagenome ; Metagenomics/methods ; Monoterpenes/*pharmacology ; Poultry Diseases/*drug therapy/*microbiology/mortality/pathology ; Thymol/*pharmacology ; }, abstract = {Necrotic enteritis (NE) caused by Clostridium perfringens is one of the most detrimental infectious diseases in poultry. This study examined the effect of blends of essential oils (BEOs) (25% thymol and 25% carvacrol) on NE and bacterial dynamics and functions in chicks challenged with C. perfringens. Chicks were assigned to a Control diet and BEOs diet (Control diet + 120 mg/kg BEOs), were challenged with C. perfringens from days 14 to 20 and were killed on day 21 for assessment. Supplementation with BEOs decreased the mortality, alleviated gut lesions, and decreased the virulence factors of pathogenic bacteria (VF 0073-ClpE, VF0124-LPS, and VF0350-BSH). Lack of supplementation also changed the nutrient and immunological dynamics of host microbiota in responding to C. perfringens infection. Adding BEOs changed the host ileum microbial population by increasing the numbers of Lactobacillus crispatus and Lactobacillus agilis, and decreasing Lactobacillus salivarius and Lactobacillus johnsonii. The functional roles of these changing host bacterial populations coupled with the putative reduced pathogenicity of C. perfringens by BEOs contributed to the reduction in gut lesions and mortality in infected chickens. It suggests that dietary supplementation with BEOs could significantly reduce the impact of NE caused by C. perfringens on broilers.}, } @article {pmid28775301, year = {2017}, author = {Erwin, PM and Rhodes, RG and Kiser, KB and Keenan-Bateman, TF and McLellan, WA and Pabst, DA}, title = {High diversity and unique composition of gut microbiomes in pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {7205}, pmid = {28775301}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Phylogeny ; *Sperm Whale ; Symbiosis ; *Whales ; }, abstract = {Mammals host diverse bacterial and archaeal symbiont communities (i.e. microbiomes) that play important roles in digestive and immune system functioning, yet cetacean microbiomes remain largely unexplored, in part due to sample collection difficulties. Here, fecal samples from stranded pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales were used to characterize the gut microbiomes of two closely-related species with similar diets. 16S rRNA gene sequencing revealed diverse microbial communities in kogiid whales dominated by Firmicutes and Bacteroidetes. Core symbiont taxa were affiliated with phylogenetic lineages capable of fermentative metabolism and sulfate respiration, indicating potential symbiont contributions to energy acquisition during prey digestion. The diversity and phylum-level composition of kogiid microbiomes differed from those previously reported in toothed whales, which exhibited low diversity communities dominated by Proteobacteria and Actinobacteria. Community structure analyses revealed distinct gut microbiomes in K. breviceps and K. sima, driven by differential relative abundances of shared taxa, and unique microbiomes in kogiid hosts compared to other toothed and baleen whales, driven by differences in symbiont membership. These results provide insight into the diversity, composition and structure of kogiid gut microbiomes and indicate that host identity plays an important role in structuring cetacean microbiomes, even at fine-scale taxonomic levels.}, } @article {pmid28774270, year = {2017}, author = {Galia, W and Leriche, F and Cruveiller, S and Garnier, C and Navratil, V and Dubost, A and Blanquet-Diot, S and Thevenot-Sergentet, D}, title = {Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {574}, pmid = {28774270}, issn = {1471-2164}, mesh = {Amino Acids/biosynthesis/metabolism ; Biological Transport/genetics ; Cell Membrane/metabolism ; Cell Wall/metabolism ; Down-Regulation ; Enterohemorrhagic Escherichia coli/cytology/*genetics/metabolism/*physiology ; *Gene Expression Profiling ; Microbiota/*genetics ; Nitrates/metabolism ; Nitrites/metabolism ; Red Meat/*microbiology ; Species Specificity ; }, abstract = {BACKGROUND: Enterohemorrhagic Escherichia coli (EHEC) are zoonotic agents associated with outbreaks worldwide. Growth of EHEC strains in ground beef could be inhibited by background microbiota that is present initially at levels greater than that of the pathogen E. coli. However, how the microbiota outcompetes the pathogenic bacteria is unknown. Our objective was to identify metabolic pathways of EHEC that were altered by natural microbiota in order to improve our understanding of the mechanisms controlling the growth and survival of EHECs in ground beef.

RESULTS: Based on 16S metagenomics analysis, we identified the microbial community structure in our beef samples which was an essential preliminary for subtractively analyzing the gene expression of the EHEC strains. Then, we applied strand-specific RNA-seq to investigate the effects of this microbiota on the global gene expression of EHEC O2621765 and O157EDL933 strains by comparison with their behavior in beef meat without microbiota. In strain O2621765, the expression of genes connected with nitrate metabolism and nitrite detoxification, DNA repair, iron and nickel acquisition and carbohydrate metabolism, and numerous genes involved in amino acid metabolism were down-regulated. Further, the observed repression of ftsL and murF, involved respectively in building the cytokinetic ring apparatus and in synthesizing the cytoplasmic precursor of cell wall peptidoglycan, might help to explain the microbiota's inhibitory effect on EHECs. For strain O157EDL933, the induced expression of the genes implicated in detoxification and the general stress response and the repressed expression of the peR gene, a gene negatively associated with the virulence phenotype, might be linked to the survival and virulence of O157:H7 in ground beef with microbiota.

CONCLUSION: In the present study, we show how RNA-Seq coupled with a 16S metagenomics analysis can be used to identify the effects of a complex microbial community on relevant functions of an individual microbe within it. These findings add to our understanding of the behavior of EHECs in ground beef. By measuring transcriptional responses of EHEC, we could identify putative targets which may be useful to develop new strategies to limit their shedding in ground meat thus reducing the risk of human illnesses.}, } @article {pmid28771471, year = {2017}, author = {Deck, J and Gaither, MR and Ewing, R and Bird, CE and Davies, N and Meyer, C and Riginos, C and Toonen, RJ and Crandall, ED}, title = {The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples.}, journal = {PLoS biology}, volume = {15}, number = {8}, pages = {e2002925}, pmid = {28771471}, issn = {1545-7885}, mesh = {*Biodiversity ; *Databases, Nucleic Acid ; *Metadata ; *Metagenomics ; }, abstract = {The Genomic Observatories Metadatabase (GeOMe, http://www.geome-db.org/) is an open access repository for geographic and ecological metadata associated with biosamples and genetic data. Whereas public databases have served as vital repositories for nucleotide sequences, they do not accession all the metadata required for ecological or evolutionary analyses. GeOMe fills this need, providing a user-friendly, web-based interface for both data contributors and data recipients. The interface allows data contributors to create a customized yet standard-compliant spreadsheet that captures the temporal and geospatial context of each biosample. These metadata are then validated and permanently linked to archived genetic data stored in the National Center for Biotechnology Information's (NCBI's) Sequence Read Archive (SRA) via unique persistent identifiers. By linking ecologically and evolutionarily relevant metadata with publicly archived sequence data in a structured manner, GeOMe sets a gold standard for data management in biodiversity science.}, } @article {pmid28770172, year = {2017}, author = {Filardo, S and Di Pietro, M and Porpora, MG and Recine, N and Farcomeni, A and Latino, MA and Sessa, R}, title = {Diversity of Cervical Microbiota in Asymptomatic Chlamydia trachomatis Genital Infection: A Pilot Study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {7}, number = {}, pages = {321}, pmid = {28770172}, issn = {2235-2988}, mesh = {*Asymptomatic Diseases ; Cervix Uteri/*microbiology ; Chlamydia Infections/*microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Humans ; Metagenomics ; *Microbiota ; Phylogeny ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Reproductive Tract Infections/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Chlamydia trachomatis genital infection continues to be an important public health problem worldwide due to its increasing incidence. C. trachomatis infection can lead to severe sequelae, such as pelvic inflammatory disease, obstructive infertility, and preterm birth. Recently, it has been suggested that the cervico-vaginal microbiota may be an important defense factor toward C. trachomatis infection as well as the development of chronic sequelae. Therefore, the investigation of microbial profiles associated to chlamydial infection is of the utmost importance. Here we present a pilot study aiming to characterize, through the metagenomic analysis of sequenced 16s rRNA gene amplicons, the cervical microbiota from reproductive age women positive to C. trachomatis infection. The main finding of our study showed a marked increase in bacterial diversity in asymptomatic C. trachomatis positive women as compared to healthy controls in terms of Shannon's diversity and Shannon's evenness (P = 0.031 and P = 0.026, respectively). More importantly, the cervical microbiota from C. trachomatis positive women and from healthy controls significantly separated into two clusters in the weighted UniFrac analysis (P = 0.0027), suggesting that differences between the two groups depended entirely on the relative abundance of bacterial taxa rather than on the types of bacterial taxa present. Furthermore, C. trachomatis positive women showed an overall decrease in Lactobacillus spp. and an increase in anaerobes. These findings are part of an ongoing larger epidemiological study that will evaluate the potential role of distinct bacterial communities of the cervical microbiota in C. trachomatis infection.}, } @article {pmid28768551, year = {2017}, author = {Gao, P and Ma, C and Sun, Z and Wang, L and Huang, S and Su, X and Xu, J and Zhang, H}, title = {Feed-additive probiotics accelerate yet antibiotics delay intestinal microbiota maturation in broiler chicken.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {91}, pmid = {28768551}, issn = {2049-2618}, mesh = {Animal Feed/*microbiology ; Animals ; Anti-Bacterial Agents/administration & dosage/*pharmacology ; Chickens/*microbiology ; Drug Resistance, Bacterial ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; High-Throughput Nucleotide Sequencing ; Intestines/microbiology ; Lactobacillus/growth & development/isolation & purification/physiology ; Metagenome ; Probiotics/*administration & dosage ; }, abstract = {BACKGROUND: Reducing antibiotics overuse in animal agriculture is one key in combat against the spread of antibiotic resistance. Probiotics are a potential replacement of antibiotics in animal feed; however, it is not clear whether and how probiotics and antibiotics differ in impact on physiology and microbial ecology of host animals.

RESULTS: Host phenotype and fecal microbiota of broilers with either antibiotics or probiotics as feed additive were simultaneously sampled at four time points from birth to slaughter and then compared. Probiotic feeding resulted in a lower feed conversion ratio (FCR) and induced the highest level of immunity response, suggesting greater economic benefits in broiler farming. Probiotic use but not antibiotic use recapitulated the characteristics of age-dependent development of gut microbiota in the control group. The maturation of intestinal microbiota was greatly accelerated by probiotic feeding, yet significantly retarded and eventually delayed by antibiotic feeding. LP-8 stimulated the growth of many intestinal Lactobacillus spp. and led to an altered bacterial correlation network where Lactobacillus spp. are negatively correlated with 14 genera and positively linked with none, yet from the start antibiotic feeding featured a less-organized network where such inter-genera interactions were fewer and weaker. Consistently, microbiota-encoded functions as revealed by metagenome sequencing were highly distinct between the two groups. Thus, "intestinal microbiota maturation index" was proposed to quantitatively compare impact of feed additives on animal microecology.

CONCLUSIONS: Our results reveal a tremendous potential of probiotics as antibiotics' substitute in poultry farming.}, } @article {pmid28767318, year = {2018}, author = {Malan-Muller, S and Valles-Colomer, M and Raes, J and Lowry, CA and Seedat, S and Hemmings, SMJ}, title = {The Gut Microbiome and Mental Health: Implications for Anxiety- and Trauma-Related Disorders.}, journal = {Omics : a journal of integrative biology}, volume = {22}, number = {2}, pages = {90-107}, doi = {10.1089/omi.2017.0077}, pmid = {28767318}, issn = {1557-8100}, mesh = {Animals ; Anxiety/genetics/*microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Mental Disorders/genetics/*microbiology ; Mental Health ; RNA, Ribosomal, 16S/genetics ; Trauma and Stressor Related Disorders/genetics/*microbiology ; }, abstract = {Biological psychiatry research has long focused on the brain in elucidating the neurobiological mechanisms of anxiety- and trauma-related disorders. This review challenges this assumption and suggests that the gut microbiome and its interactome also deserve attention to understand brain disorders and develop innovative treatments and diagnostics in the 21st century. The recent, in-depth characterization of the human microbiome spurred a paradigm shift in human health and disease. Animal models strongly suggest a role for the gut microbiome in anxiety- and trauma-related disorders. The microbiota-gut-brain (MGB) axis sits at the epicenter of this new approach to mental health. The microbiome plays an important role in the programming of the hypothalamic-pituitary-adrenal (HPA) axis early in life, and stress reactivity over the life span. In this review, we highlight emerging findings of microbiome research in psychiatric disorders, focusing on anxiety- and trauma-related disorders specifically, and discuss the gut microbiome as a potential therapeutic target. 16S rRNA sequencing has enabled researchers to investigate and compare microbial composition between individuals. The functional microbiome can be studied using methods involving metagenomics, metatranscriptomics, metaproteomics, and metabolomics, as discussed in the present review. Other factors that shape the gut microbiome should be considered to obtain a holistic view of the factors at play in the complex interactome linked to the MGB. In all, we underscore the importance of microbiome science, and gut microbiota in particular, as emerging critical players in mental illness and maintenance of mental health. This new frontier of biological psychiatry and postgenomic medicine should be embraced by the mental health community as it plays an ever-increasing transformative role in integrative and holistic health research in the next decade.}, } @article {pmid28766918, year = {2018}, author = {Sherwani, MA and Tufail, S and Muzaffar, AF and Yusuf, N}, title = {The skin microbiome and immune system: Potential target for chemoprevention?.}, journal = {Photodermatology, photoimmunology & photomedicine}, volume = {34}, number = {1}, pages = {25-34}, pmid = {28766918}, issn = {1600-0781}, support = {R01 AR071157/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; Gastrointestinal Microbiome ; Humans ; *Microbiota/radiation effects ; Prebiotics ; Probiotics/pharmacology ; Skin/*immunology/*microbiology ; Skin Neoplasms/immunology/*microbiology/*prevention & control ; Ultraviolet Rays ; Virus Diseases/complications ; Vitamin D/analogs & derivatives/metabolism ; }, abstract = {There has been increasing interest in understanding the role of the human microbiome in skin diseases. Microbiome studies are being utilized in skin cancer research in numerous ways. Commensal bacteria are being studied as a potential tool to judge the biggest environmental risk of skin cancer, ultraviolet (UV) radiation. Owing to the recognized link of skin microbes in the process of inflammation, there have been theories linking commensal bacteria to skin cancer. Viral metagenomics has also provided insight into virus linked forms of skin cancers. Speculations can be drawn for skin microbiome that in a manner similar to gut microbiome, they can be involved in chemoprevention of skin cancer. Nonetheless, there are definitely huge gaps in our knowledge of the relationship of microbiome and skin cancers, especially in relation to chemoprevention. The utilization of microbiome in skin cancer research seems to be a promising field and may help yield novel skin cancer prevention and treatment options. This review focuses on recent utilization of the microbiome in skin cancer research, and it explores the potential of utilizing the microbiome in prevention, earlier diagnosis, and treatment of skin cancers.}, } @article {pmid28761980, year = {2017}, author = {Jin, W and Xue, C and Liu, J and Yin, Y and Zhu, W and Mao, S}, title = {Effects of Disodium Fumarate on In Vitro Rumen Fermentation, The Production of Lipopolysaccharide and Biogenic Amines, and The Rumen Bacterial Community.}, journal = {Current microbiology}, volume = {74}, number = {11}, pages = {1337-1342}, pmid = {28761980}, issn = {1432-0991}, mesh = {Animals ; Bacteria/classification/genetics/*metabolism ; Biogenic Amines/*biosynthesis ; Cattle ; Cluster Analysis ; Fermentation/*drug effects ; Fumarates/*pharmacology ; Lipopolysaccharides/*biosynthesis ; Metagenome ; Metagenomics/methods ; Microbiota/*drug effects ; Rumen/*microbiology ; }, abstract = {The effect of disodium fumarate (DF) on the ruminal fermentation profiles, the accumulation of lipopolysaccharide (LPS) and bioamines, and the composition of the ruminal bacterial community was investigated by in vitro rumen fermentation. The addition of DF increased the total gas production; the concentrations of propionate, valerate, total volatile fatty acids, and ammonia-nitrogen; and the rumen pH after a 24 h fermentation. By contrast, DF addition decreased the ratio of acetate to propionate and the concentrations of lactate, lipopolysaccharide, methylamine, tryptamine, putrescine, histamine, and tyramine (P < 0.05). Principal coordinates analysis and molecular variance analysis showed that DF altered the ruminal bacterial community (P < 0.05). At the phylum level, DF decreased the proportion of Proteobacteria, and increased the proportions of Spirochaetae and Elusimicrobia (P < 0.05). At the genus level, DF decreased the percentage of Ruminobacter, while increasing the percentage of Succinivibrio and Treponema (P < 0.05). Overall, the results indicate that DF modified rumen fermentation and mitigated the production of several toxic compounds. Thus, DF has great potential for preventing subacute rumen acidosis in dairy cows and for improving the health of ruminants.}, } @article {pmid28761145, year = {2017}, author = {Tessler, M and Neumann, JS and Afshinnekoo, E and Pineda, M and Hersch, R and Velho, LFM and Segovia, BT and Lansac-Toha, FA and Lemke, M and DeSalle, R and Mason, CE and Brugler, MR}, title = {Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6589}, pmid = {28761145}, issn = {2045-2322}, mesh = {Bacteria/*classification/genetics/growth & development ; *Biodiversity ; Biota ; Computational Biology ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/*methods ; *Metagenomics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; *Water Microbiology ; }, abstract = {Modern metagenomic environmental DNA studies are almost completely reliant on next-generation sequencing, making evaluations of these methods critical. We compare two next-generation sequencing techniques - amplicon and shotgun - on water samples across four of Brazil's major river floodplain systems (Amazon, Araguaia, Paraná, and Pantanal). Less than 50% of phyla identified via amplicon sequencing were recovered from shotgun sequencing, clearly challenging the dogma that mid-depth shotgun recovers more diversity than amplicon-based approaches. Amplicon sequencing also revealed ~27% more families. Overall the amplicon data were more robust across both biodiversity and community ecology analyses at different taxonomic scales. Our work doubles the sampling size in similar environmental studies, and novelly integrates environmental data (e.g., pH, temperature, nutrients) from each site, revealing divergent correlations depending on which data are used. While myriad variants on NGS techniques and bioinformatic pipelines are available, our results point to core differences that have not been highlighted in any studies to date. Given the low number of taxa identified when coupling shotgun data with clade-based taxonomic algorithms, previous studies that quantified biodiversity using such bioinformatic tools should be viewed cautiously or re-analyzed. Nonetheless, shotgun has complementary advantages that should be weighed when designing projects.}, } @article {pmid28761060, year = {2017}, author = {Shi, D and Lv, L and Fang, D and Wu, W and Hu, C and Xu, L and Chen, Y and Guo, J and Hu, X and Li, A and Guo, F and Ye, J and Li, Y and Andayani, D and Li, L}, title = {Administration of Lactobacillus salivarius LI01 or Pediococcus pentosaceus LI05 prevents CCl4-induced liver cirrhosis by protecting the intestinal barrier in rats.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6927}, pmid = {28761060}, issn = {2045-2322}, mesh = {Animals ; Carbon Tetrachloride/*adverse effects ; Cytokines/metabolism ; Disease Models, Animal ; Endotoxins/blood ; Gastrointestinal Microbiome ; Gene Expression Regulation/drug effects ; Intestinal Mucosa/drug effects/metabolism/ultrastructure ; Ligilactobacillus salivarius/*physiology ; Liver Cirrhosis/chemically induced/metabolism/microbiology/*prevention & control ; Pediococcus pentosaceus/*physiology ; Probiotics/*administration & dosage/pharmacology ; RNA, Ribosomal, 16S/genetics ; Rats ; }, abstract = {Alterations in the gut microbiome have been reported in liver cirrhosis, and probiotic interventions are considered a potential treatment strategy. This study aimed to evaluate the effects and mechanisms of Lactobacillus salivarius LI01, Pediococcus pentosaceus LI05, Lactobacillus rhamnosus GG, Clostridium butyricum MIYAIRI and Bacillus licheniformis Zhengchangsheng on CCl4-induced cirrhotic rats. Only administration of LI01 or LI05 prevented liver fibrosis and down-regulated the hepatic expression of profibrogenic genes. Serum endotoxins, bacterial translocations (BTs), and destruction of intestinal mucosal ultrastructure were reduced in rats treated with LI01 or LI05, indicating maintenance of the gut barrier as a mechanism; this was further confirmed by the reduction of not only hepatic inflammatory cytokines, such as TNF-α, IL-6, and IL-17A, but also hepatic TLR2, TLR4, TLR5 and TLR9. Metagenomic sequencing of 16S rRNA gene showed an increase in potential beneficial bacteria, such as Elusimicrobium and Prevotella, and a decrease in pathogenic bacteria, such as Escherichia. These alterations in gut microbiome were correlated with profibrogenic genes, gut barrier markers and inflammatory cytokines. In conclusion, L. salivarius LI01 and P. pentosaceus LI05 attenuated liver fibrosis by protecting the intestinal barrier and promoting microbiome health. These results suggest novel strategies for the prevention of liver cirrhosis.}, } @article {pmid28760934, year = {2017}, author = {Spinler, JK and Auchtung, J and Brown, A and Boonma, P and Oezguen, N and Ross, CL and Luna, RA and Runge, J and Versalovic, J and Peniche, A and Dann, SM and Britton, RA and Haag, A and Savidge, TC}, title = {Next-Generation Probiotics Targeting Clostridium difficile through Precursor-Directed Antimicrobial Biosynthesis.}, journal = {Infection and immunity}, volume = {85}, number = {10}, pages = {}, pmid = {28760934}, issn = {1098-5522}, support = {U01 AI124290/AI/NIAID NIH HHS/United States ; U19 AI090872/AI/NIAID NIH HHS/United States ; UL1 TR000071/TR/NCATS NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R21 DK096323/DK/NIDDK NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*biosynthesis/pharmacology/therapeutic use ; Bacterial Proteins/genetics ; Clostridioides difficile/drug effects/*growth & development ; Clostridium Infections/immunology/*prevention & control/therapy ; Drug Discovery/methods ; Drug Resistance, Bacterial ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome ; Glyceraldehyde/*analogs & derivatives/metabolism/pharmacology/therapeutic use ; Glycerol/*administration & dosage/immunology/metabolism ; Humans ; Limosilactobacillus reuteri/*metabolism ; Metabolomics ; *Probiotics ; Propane/*metabolism/pharmacology/therapeutic use ; Vancomycin/pharmacology ; }, abstract = {Integration of antibiotic and probiotic therapy has the potential to lessen the public health burden of antimicrobial-associated diseases. Clostridium difficile infection (CDI) represents an important example where the rational design of next-generation probiotics is being actively pursued to prevent disease recurrence. Because intrinsic resistance to clinically relevant antibiotics used to treat CDI (vancomycin, metronidazole, and fidaxomicin) is a desired trait in such probiotic species, we screened several bacteria and identified Lactobacillus reuteri to be a promising candidate for adjunct therapy. Human-derived L. reuteri bacteria convert glycerol to the broad-spectrum antimicrobial compound reuterin. When supplemented with glycerol, strains carrying the pocR gene locus were potent reuterin producers, with L. reuteri 17938 inhibiting C. difficile growth at a level on par with the level of growth inhibition by vancomycin. Targeted pocR mutations and complementation studies identified reuterin to be the precursor-induced antimicrobial agent. Pathophysiological relevance was demonstrated when the codelivery of L. reuteri with glycerol was effective against C. difficile colonization in complex human fecal microbial communities, whereas treatment with either glycerol or L. reuteri alone was ineffective. A global unbiased microbiome and metabolomics analysis independently confirmed that glycerol precursor delivery with L. reuteri elicited changes in the composition and function of the human microbial community that preferentially targets C. difficile outgrowth and toxicity, a finding consistent with glycerol fermentation and reuterin production. Antimicrobial resistance has thus been successfully exploited in the natural design of human microbiome evasion of C. difficile, and this method may provide a prototypic precursor-directed probiotic approach. Antibiotic resistance and substrate bioavailability may therefore represent critical new determinants of probiotic efficacy in clinical trials.}, } @article {pmid28759053, year = {2017}, author = {Legoff, J and Resche-Rigon, M and Bouquet, J and Robin, M and Naccache, SN and Mercier-Delarue, S and Federman, S and Samayoa, E and Rousseau, C and Piron, P and Kapel, N and Simon, F and Socié, G and Chiu, CY}, title = {The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease.}, journal = {Nature medicine}, volume = {23}, number = {9}, pages = {1080-1085}, pmid = {28759053}, issn = {1546-170X}, mesh = {Adolescent ; Adult ; Aged ; Anelloviridae/genetics/immunology ; DNA, Viral/*analysis ; Feces/chemistry ; Female ; Gastrointestinal Microbiome/genetics/*immunology ; Graft vs Host Disease/*immunology ; *Hematopoietic Stem Cell Transplantation ; Herpesviridae/genetics/immunology ; Humans ; Intestinal Diseases/*immunology ; Intestines/*virology ; Leukocyte L1 Antigen Complex/metabolism ; Male ; Metagenomics ; Middle Aged ; Papillomaviridae/genetics/immunology ; Picobirnavirus/genetics/immunology ; Polyomaviridae/genetics/immunology ; Proportional Hazards Models ; Risk Factors ; Severity of Illness Index ; Transplantation, Homologous ; Young Adult ; alpha 1-Antitrypsin/metabolism ; }, abstract = {Much attention has been focused on the role of the bacterial microbiome in human health, but the virome is understudied. Although previously investigated in individuals with inflammatory bowel diseases or solid-organ transplants, virome dynamics in allogeneic hematopoietic stem cell transplantation (HSCT) and enteric graft-versus-host disease (GVHD) remain unexplored. Here we characterize the longitudinal gut virome in 44 recipients of HSCT using metagenomics. A viral 'bloom' was identified, and significant increases were demonstrated in the overall proportion of vertebrate viral sequences following transplantation (P = 0.02). Increases in both the rates of detection (P < 0.0001) and number of sequences (P = 0.047) of persistent DNA viruses (anelloviruses, herpesviruses, papillomaviruses and polyomaviruses) over time were observed in individuals with enteric GVHD relative to those without, a finding accompanied by a reduced phage richness (P = 0.01). Picobirnaviruses were detected in 18 individuals (40.9%), more frequently before or within a week after transplant than at later time points (P = 0.008). In a time-dependent Cox proportional-hazards model, picobirnaviruses were predictive of the occurrence of severe enteric GVHD (hazard ratio, 2.66; 95% confidence interval (CI) = 1.46-4.86; P = 0.001), and correlated with higher fecal levels of two GVHD severity markers, calprotectin and α1-antitrypsin. These results reveal a progressive expansion of vertebrate viral infections over time following HSCT, and they suggest an unexpected association of picobirnaviruses with early post-transplant GVHD.}, } @article {pmid28758937, year = {2017}, author = {Bacci, G and Mengoni, A and Fiscarelli, E and Segata, N and Taccetti, G and Dolce, D and Paganin, P and Morelli, P and Tuccio, V and De Alessandri, A and Lucidi, V and Bevivino, A}, title = {A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease.}, journal = {International journal of molecular sciences}, volume = {18}, number = {8}, pages = {}, pmid = {28758937}, issn = {1422-0067}, mesh = {Adolescent ; Adult ; Bacteria/*genetics ; *Cystic Fibrosis/genetics/microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Female ; *Genes, Bacterial ; Humans ; Lung/microbiology/pathology ; Male ; Microbiota/*genetics ; Middle Aged ; Severity of Illness Index ; Virulence Factors/*genetics ; }, abstract = {In recent years, next-generation sequencing (NGS) was employed to decipher the structure and composition of the microbiota of the airways in cystic fibrosis (CF) patients. However, little is still known about the overall gene functions harbored by the resident microbial populations and which specific genes are associated with various stages of CF lung disease. In the present study, we aimed to identify the microbial gene repertoire of CF microbiota in twelve patients with severe and normal/mild lung disease by performing sputum shotgun metagenome sequencing. The abundance of metabolic pathways encoded by microbes inhabiting CF airways was reconstructed from the metagenome. We identified a set of metabolic pathways differently distributed in patients with different pulmonary function; namely, pathways related to bacterial chemotaxis and flagellar assembly, as well as genes encoding efflux-mediated antibiotic resistance mechanisms and virulence-related genes. The results indicated that the microbiome of CF patients with low pulmonary function is enriched in virulence-related genes and in genes encoding efflux-mediated antibiotic resistance mechanisms. Overall, the microbiome of severely affected adults with CF seems to encode different mechanisms for the facilitation of microbial colonization and persistence in the lung, consistent with the characteristics of multidrug-resistant microbial communities that are commonly observed in patients with severe lung disease.}, } @article {pmid28758342, year = {2017}, author = {Rodgers, TW and Xu, CCY and Giacalone, J and Kapheim, KM and Saltonstall, K and Vargas, M and Yu, DW and Somervuo, P and McMillan, WO and Jansen, PA}, title = {Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: Evidence from a known tropical mammal community.}, journal = {Molecular ecology resources}, volume = {17}, number = {6}, pages = {e133-e145}, doi = {10.1111/1755-0998.12701}, pmid = {28758342}, issn = {1755-0998}, mesh = {Animal Feed/*analysis ; Animals ; Biodiversity ; DNA/*genetics/isolation & purification ; DNA Barcoding, Taxonomic/*methods ; Diptera/*physiology ; *Feeding Behavior ; Mammals/*classification/genetics ; Metagenomics/*methods ; Panama ; }, abstract = {Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well-known mammal community, and compared our results against diurnal transect counts and camera trapping. We collected 1,084 flies in 29 sampling days, conducted metabarcoding with mammal-specific (16S) and vertebrate-specific (12S) primers, and sequenced amplicons on Illumina MiSeq. For taxonomic assignment, we compared blast with the new program protax, and we found that protax improved species identifications. We detected 20 mammal, four bird, and one lizard species from carrion fly metabarcoding, all but one of which are known from BCI. Fly metabarcoding detected more mammal species than concurrent transect counts (29 sampling days, 13 species) and concurrent camera trapping (84 sampling days, 17 species), and detected 67% of the number of mammal species documented by 8 years of transect counts and camera trapping combined, although fly metabarcoding missed several abundant species. This study demonstrates that carrion fly metabarcoding is a powerful tool for mammal biodiversity surveys and has the potential to detect a broader range of species than more commonly used methods.}, } @article {pmid28755263, year = {2017}, author = {Liu, R and Qi, R and Wang, J and Zhang, Y and Liu, X and Rossetti, S and Tandoi, V and Yang, M}, title = {Phage-host associations in a full-scale activated sludge plant during sludge bulking.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {16}, pages = {6495-6504}, doi = {10.1007/s00253-017-8429-8}, pmid = {28755263}, issn = {1432-0614}, mesh = {Actinobacteria/genetics/isolation & purification ; Bacteria/genetics/isolation & purification ; Bacteriophages/*physiology ; Genome, Viral ; Metagenome ; Microbial Consortia/genetics/physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology/*virology ; Wastewater/microbiology/virology ; *Water Purification ; }, abstract = {Sludge bulking, a notorious microbial issue in activated sludge plants, is always accompanied by dramatic changes in the bacterial community. Despite large numbers of phages in sludge systems, their responses to sludge bulking and phage-host associations during bulking are unknown. In this study, high-throughput sequencing of viral metagenomes and bacterial 16S rRNA genes were employed to characterize viral and bacterial communities in a sludge plant under different sludge conditions (sludge volume index (SVI) of 180, 132, and 73 ml/g). Bulking sludges (SVI > 125 ml/g) taken about 10 months apart exhibited similar bacterial and viral composition. This reflects ecological resilience of the sludge microbial community and indicates that changes in viral and bacterial populations correlate closely with each other. Overgrowth of "Candidatus Microthrix parvicella" led to filamentous bulking, but few corresponding viral genotypes were identified. In contrast, sludge viromes were characterized by numerous contigs associated with "Candidatus Accumulibacter phosphatis," suggesting an abundance of corresponding phages in the sludge viral community. Notably, while nitrifiers (mainly Nitrosomonadaceae and Nitrospiraceae) declined significantly along with sludge bulking, their corresponding viral contigs were identified more frequently and with greater abundance in the bulking viromes, implying that phage-mediated lysis might contribute to the loss of autotrophic nitrifiers under bulking conditions.}, } @article {pmid28754704, year = {2017}, author = {Muhammed, MK and Kot, W and Neve, H and Mahony, J and Castro-Mejía, JL and Krych, L and Hansen, LH and Nielsen, DS and Sørensen, SJ and Heller, KJ and van Sinderen, D and Vogensen, FK}, title = {Metagenomic Analysis of Dairy Bacteriophages: Extraction Method and Pilot Study on Whey Samples Derived from Using Undefined and Defined Mesophilic Starter Cultures.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {19}, pages = {}, pmid = {28754704}, issn = {1098-5336}, mesh = {Animals ; Bacteriophages/classification/genetics/*isolation & purification/ultrastructure ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Milk/*virology ; Pilot Projects ; Siphoviridae/classification/genetics/*isolation & purification/ultrastructure ; Whey/*virology ; }, abstract = {Despite being potentially highly useful for characterizing the biodiversity of phages, metagenomic studies are currently not available for dairy bacteriophages, partly due to the lack of a standard procedure for phage extraction. We optimized an extraction method that allows the removal of the bulk protein from whey and milk samples with losses of less than 50% of spiked phages. The protocol was applied to extract phages from whey in order to test the notion that members of Lactococcus lactis 936 (now Sk1virus), P335, c2 (now C2virus) and Leuconostoc phage groups are the most frequently encountered in the dairy environment. The relative abundance and diversity of phages in eight and four whey mixtures from dairies using undefined mesophilic mixed-strain cultures containing Lactococcus lactis subsp. lactis biovar diacetylactis and Leuconostoc species (i.e., DL starter cultures) and defined cultures, respectively, were assessed. Results obtained from transmission electron microscopy and high-throughput sequence analyses revealed the dominance of Lc. lactis 936 phages (order Caudovirales, family Siphoviridae) in dairies using undefined DL starter cultures and Lc. lactis c2 phages (order Caudovirales, family Siphoviridae) in dairies using defined cultures. The 936 and Leuconostoc phages demonstrated limited diversity. Possible coinduction of temperate P335 prophages and satellite phages in one of the whey mixtures was also observed.IMPORTANCE The method optimized in this study could provide an important basis for understanding the dynamics of the phage community (abundance, development, diversity, evolution, etc.) in dairies with different sizes, locations, and production strategies. It may also enable the discovery of previously unknown phages, which is crucial for the development of rapid molecular biology-based methods for phage burden surveillance systems. The dominance of only a few phage groups in the dairy environment signifies the depth of knowledge gained over the past decades, which served as the basis for designing current phage control strategies. The presence of a correlation between phages and the type of starter cultures being used in dairies might help to improve the selection and/or design of suitable, custom, and cost-efficient phage control strategies.}, } @article {pmid28751714, year = {2017}, author = {Fouhy, F and Ronan, NJ and O'Sullivan, O and McCarthy, Y and Walsh, AM and Murphy, DM and Daly, M and Flanagan, ET and Fleming, C and McCarthy, M and Shortt, C and Eustace, JA and Shanahan, F and Rea, MC and Ross, RP and Stanton, C and Plant, BJ}, title = {A pilot study demonstrating the altered gut microbiota functionality in stable adults with Cystic Fibrosis.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6685}, pmid = {28751714}, issn = {2045-2322}, mesh = {Adult ; Aged ; Case-Control Studies ; Cystic Fibrosis/*microbiology ; *Gastrointestinal Microbiome/genetics ; Gene Ontology ; Humans ; Metabolic Networks and Pathways ; Middle Aged ; Phylogeny ; Pilot Projects ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Xenobiotics/metabolism ; Young Adult ; }, abstract = {Cystic Fibrosis (CF) and its treatment result in an altered gut microbiota composition compared to non-CF controls. However, the impact of this on gut microbiota functionality has not been extensively characterised. Our aim was to conduct a proof-of-principle study to investigate if measurable changes in gut microbiota functionality occur in adult CF patients compared to controls. Metagenomic DNA was extracted from faecal samples from six CF patients and six non-CF controls and shotgun metagenomic sequencing was performed on the MiSeq platform. Metabolomic analysis using gas chromatography-mass spectrometry was conducted on faecal water. The gut microbiota of the CF group was significantly different compared to the non-CF controls, with significantly increased Firmicutes and decreased Bacteroidetes. Functionality was altered, with higher pathway abundances and gene families involved in lipid (e.g. PWY 6284 unsaturated fatty acid biosynthesis (p = 0.016)) and xenobiotic metabolism (e.g. PWY-5430 meta-cleavage pathway of aromatic compounds (p = 0.004)) in CF patients compared to the controls. Significant differences in metabolites occurred between the two groups. This proof-of-principle study demonstrates that measurable changes in gut microbiota functionality occur in CF patients compared to controls. Larger studies are thus needed to interrogate this further.}, } @article {pmid28750650, year = {2017}, author = {Wen, C and Zheng, Z and Shao, T and Liu, L and Xie, Z and Le Chatelier, E and He, Z and Zhong, W and Fan, Y and Zhang, L and Li, H and Wu, C and Hu, C and Xu, Q and Zhou, J and Cai, S and Wang, D and Huang, Y and Breban, M and Qin, N and Ehrlich, SD}, title = {Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis.}, journal = {Genome biology}, volume = {18}, number = {1}, pages = {142}, pmid = {28750650}, issn = {1474-760X}, mesh = {Adolescent ; Adult ; Aged ; Autoimmune Diseases/immunology/*microbiology/pathology ; Bacteroides/classification/genetics/isolation & purification ; Bifidobacterium/classification/genetics/isolation & purification ; Biomarkers/metabolism ; Case-Control Studies ; Dysbiosis/immunology/*microbiology/pathology ; Female ; Gastrointestinal Microbiome/*genetics ; *Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics/*methods ; Middle Aged ; Phylogeny ; Prevotella/classification/genetics/isolation & purification ; Spondylitis, Ankylosing/immunology/*microbiology/pathology ; }, abstract = {BACKGROUND: The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence showed that ankylosing spondylitis may be a microbiome-driven disease.

RESULTS: To investigate the relationship between the gut microbiome and ankylosing spondylitis, a quantitative metagenomics study based on deep shotgun sequencing was performed, using gut microbial DNA from 211 Chinese individuals. A total of 23,709 genes and 12 metagenomic species were shown to be differentially abundant between ankylosing spondylitis patients and healthy controls. Patients were characterized by a form of gut microbial dysbiosis that is more prominent than previously reported cases with inflammatory bowel disease. Specifically, the ankylosing spondylitis patients demonstrated increases in the abundance of Prevotella melaninogenica, Prevotella copri, and Prevotella sp. C561 and decreases in Bacteroides spp. It is noteworthy that the Bifidobacterium genus, which is commonly used in probiotics, accumulated in the ankylosing spondylitis patients. Diagnostic algorithms were established using a subset of these gut microbial biomarkers.

CONCLUSIONS: Alterations of the gut microbiome are associated with development of ankylosing spondylitis. Our data suggest biomarkers identified in this study might participate in the pathogenesis or development process of ankylosing spondylitis, providing new leads for the development of new diagnostic tools and potential treatments.}, } @article {pmid28750626, year = {2017}, author = {Oliveira, JS and Araújo, WJ and Figueiredo, RM and Silva-Portela, RCB and de Brito Guerra, A and da Silva Araújo, SC and Minnicelli, C and Carlos, AC and de Vasconcelos, ATR and Freitas, AT and Agnez-Lima, LF}, title = {Biogeographical distribution analysis of hydrocarbon degrading and biosurfactant producing genes suggests that near-equatorial biomes have higher abundance of genes with potential for bioremediation.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {168}, pmid = {28750626}, issn = {1471-2180}, mesh = {Bacteria/classification/*genetics/isolation & purification/*metabolism ; Bacterial Proteins/*genetics/metabolism ; Biodegradation, Environmental ; Ecosystem ; Hydrocarbons/*metabolism ; Metagenomics ; Microbial Consortia ; Petroleum/*microbiology ; Phylogeny ; Surface-Active Agents/*metabolism ; }, abstract = {BACKGROUND: Bacterial and Archaeal communities have a complex, symbiotic role in crude oil bioremediation. Their biosurfactants and degradation enzymes have been in the spotlight, mainly due to the awareness of ecosystem pollution caused by crude oil accidents and their use. Initially, the scientific community studied the role of individual microbial species by characterizing and optimizing their biosurfactant and oil degradation genes, studying their individual distribution. However, with the advances in genomics, in particular with the use of New-Generation-Sequencing and Metagenomics, it is now possible to have a macro view of the complex pathways related to the symbiotic degradation of hydrocarbons and surfactant production. It is now possible, although more challenging, to obtain the DNA information of an entire microbial community before automatically characterizing it. By characterizing and understanding the interconnected role of microorganisms and the role of degradation and biosurfactant genes in an ecosystem, it becomes possible to develop new biotechnological approaches for bioremediation use. This paper analyzes 46 different metagenome samples, spanning 20 biomes from different geographies obtained from different research projects.

RESULTS: A metagenomics bioinformatics pipeline, focused on the biodegradation and biosurfactant-production pathways, genes and organisms, was applied. Our main results show that: (1) surfactation and degradation are correlated events, and therefore should be studied together; (2) terrestrial biomes present more degradation genes, especially cyclic compounds, and less surfactation genes, when compared to water biomes; and (3) latitude has a significant influence on the diversity of genes involved in biodegradation and biosurfactant production. This suggests that microbiomes found near the equator are richer in genes that have a role in these processes and thus have a higher biotechnological potential.

CONCLUSION: In this work we have focused on the biogeographical distribution of hydrocarbon degrading and biosurfactant producing genes. Our principle results can be seen as an important step forward in the application of bioremediation techniques, by considering the biostimulation, optimization or manipulation of a starting microbial consortia from the areas with higher degradation and biosurfactant producing genetic diversity.}, } @article {pmid28750065, year = {2017}, author = {Zapata-Pérez, R and Martínez-Moñino, AB and García-Saura, AG and Cabanes, J and Takami, H and Sánchez-Ferrer, Á}, title = {Biochemical characterization of a new nicotinamidase from an unclassified bacterium thriving in a geothermal water stream microbial mat community.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0181561}, pmid = {28750065}, issn = {1932-6203}, mesh = {Aldehydes/metabolism ; Amino Acid Sequence ; Bacteria/*enzymology ; Enzyme Inhibitors/pharmacology ; Enzyme Stability/drug effects ; Hot Springs/*microbiology ; Hydrogen-Ion Concentration ; Kinetics ; *Microbiota ; Models, Molecular ; Mutant Proteins/metabolism ; Nicotinamidase/antagonists & inhibitors/chemistry/*metabolism ; Phylogeny ; Rivers/*microbiology ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; Temperature ; *Water Microbiology ; }, abstract = {Nicotinamidases are amidohydrolases that convert nicotinamide into nicotinic acid, contributing to NAD+ homeostasis in most organisms. In order to increase the number of nicotinamidases described to date, this manuscript characterizes a nicotinamidase obtained from a metagenomic library fosmid clone (JFF054_F02) obtained from a geothermal water stream microbial mat community in a Japanese epithermal mine. The enzyme showed an optimum temperature of 90°C, making it the first hyperthermophilic bacterial nicotinamidase to be characterized, since the phylogenetic analysis of this fosmid clone placed it in a clade of uncultured geothermal bacteria. The enzyme, named as UbNic, not only showed an alkaline optimum pH, but also a biphasic pH dependence of its kcat, with a maximum at pH 9.5-10.0. The two pKa values obtained were 4.2 and 8.6 for pKes1 and pKes2, respectively. These results suggest a possible flexible catalytic mechanism for nicotinamidases, which reconciles the two previously proposed mechanisms. In addition, the enzyme showed a high catalytic efficiency, not only toward nicotinamide, but also toward other nicotinamide analogs. Its mutational analysis showed that a tryptophan (W83) is needed in one of the faces of the active site to maintain low Km values toward all the substrates tested. Furthermore, UbNic proved to contain a Fe2+ ion in its metal binding site, and was revealed to belong to a new nicotinamidase subgroup. All these characteristics, together with its high pH- and thermal stability, distinguish UbNic from previously described nicotinamidases, and suggest that a wide diversity of enzymes remains to be discovered in extreme environments.}, } @article {pmid28748273, year = {2017}, author = {She, R and Li, TT and Luo, D and Li, JB and Yin, LY and Li, H and Liu, YM and Li, XZ and Yan, QG}, title = {Changes in the Intestinal Microbiota of Gibel Carp (Carassius gibelio) Associated with Cyprinid herpesvirus 2 (CyHV-2) Infection.}, journal = {Current microbiology}, volume = {74}, number = {10}, pages = {1130-1136}, pmid = {28748273}, issn = {1432-0991}, support = {IRT0848//the Program for Changjiang Scholars and Innovative Research Team in University, China/ ; }, mesh = {Animals ; Biodiversity ; Fish Diseases/*microbiology/*virology ; *Gastrointestinal Microbiome ; *Herpesviridae ; Herpesviridae Infections/*veterinary ; *Host-Pathogen Interactions ; Metagenome ; Metagenomics/methods ; RNA, Ribosomal, 16S ; ROC Curve ; }, abstract = {Gut microbiota are integral to the host, and have received increased attention in recent years. However, information regarding the intestinal microbiota of many aquaculture animals is insufficient; elucidating the dynamics of the intestinal microbiota can be beneficial for nutrition, immunity, and disease control. In this study, we used 16S rRNA sequencing to observe changes in the intestinal microbiota of gibel carp (Carassius auratus gibelio) associated with cyprinid herpesvirus 2 (CyHV-2) infection. Our results indicate that the diversity of the intestinal microbiota was strongly reduced, and the composition was dramatically altered following CyHV-2 infection. The most dominant species in healthy fish were Cetobacterium, Rhodobacter, and Crenothrix; meanwhile, Cetobacterium, Plesiomonas, Bacteroides, and Flavobacterium were the most abundant species in sick fish. Plesiomonas was highly abundant in infected samples, and could be used as a microbial biomarker for CyHV-2 infection. Chemical properties of the aquaculture water were significantly correlated with the microbial community structure; however, it is difficult to determine whether these changes are a cause or consequence of infection. However, it may be possible to use probiotics or prebiotics to restore the richness of the host intestinal microbiota in infected animals to maintain host health.}, } @article {pmid28747798, year = {2017}, author = {Pearman, JK and Ellis, J and Irigoien, X and Sarma, YVB and Jones, BH and Carvalho, S}, title = {Microbial planktonic communities in the Red Sea: high levels of spatial and temporal variability shaped by nutrient availability and turbulence.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6611}, pmid = {28747798}, issn = {2045-2322}, mesh = {*Biota ; Eukaryota/*classification/genetics ; Indian Ocean ; Metagenomics ; *Plankton ; Prokaryotic Cells/*classification ; RNA, Ribosomal/genetics ; Seawater/*microbiology ; Spatio-Temporal Analysis ; }, abstract = {The semi-enclosed nature of the Red Sea (20.2°N-38.5°N) makes it a natural laboratory to study the influence of environmental gradients on microbial communities. This study investigates the composition and structure of microbial prokaryotes and eukaryotes using molecular methods, targeting ribosomal RNA genes across different regions and seasons. The interaction between spatial and temporal scales results in different scenarios of turbulence and nutrient conditions allowing for testing of ecological theory that categorizes the response of the plankton community to these variations. The prokaryotic reads are mainly comprised of Cyanobacteria and Proteobacteria (Alpha and Gamma), with eukaryotic reads dominated by Dinophyceae and Syndiniophyceae. Periodic increases in the proportion of Mamiellophyceae and Bacillariophyceae reads were associated with alterations in the physical oceanography leading to nutrient increases either through the influx of Gulf of Aden Intermediate Water (south in the fall) or through water column mixing processes (north in the spring). We observed that in general dissimilarity amongst microbial communities increased when nutrient concentrations were higher, whereas richness (observed OTUs) was higher in scenarios of higher turbulence. Maximum abundance models showed the differential responses of dominant taxa to temperature giving an indication how taxa will respond as waters become warmer and more oligotrophic.}, } @article {pmid28747705, year = {2017}, author = {Kamutando, CN and Vikram, S and Kamgan-Nkuekam, G and Makhalanyane, TP and Greve, M and Roux, JJL and Richardson, DM and Cowan, D and Valverde, A}, title = {Soil nutritional status and biogeography influence rhizosphere microbial communities associated with the invasive tree Acacia dealbata.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6472}, pmid = {28747705}, issn = {2045-2322}, mesh = {Acacia/*growth & development ; Bacteria/*classification/genetics/isolation & purification ; Bacterial Proteins/genetics ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; Fungal Proteins/genetics ; Fungi/*classification/genetics/isolation & purification ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Fungal ; High-Throughput Nucleotide Sequencing/*methods ; Introduced Species ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Sequence Analysis, DNA/*methods ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {Invasiveness and the impacts of introduced plants are known to be mediated by plant-microbe interactions. Yet, the microbial communities associated with invasive plants are generally poorly understood. Here we report on the first comprehensive investigation of the bacterial and fungal communities inhabiting the rhizosphere and the surrounding bulk soil of a widespread invasive tree, Acacia dealbata. Amplicon sequencing data indicated that rhizospheric microbial communities differed significantly in structure and composition from those of the bulk soil. Two bacterial (Alphaproteobacteria and Gammaproteobacteria) and two fungal (Pezizomycetes and Agaricomycetes) classes were enriched in the rhizosphere compared with bulk soils. Changes in nutritional status, possibly induced by A. dealbata, primarily shaped rhizosphere soil communities. Despite a high degree of geographic variability in the diversity and composition of microbial communities, invasive A. dealbata populations shared a core of bacterial and fungal taxa, some of which are known to be involved in N and P cycling, while others are regarded as plant pathogens. Shotgun metagenomic analysis also showed that several functional genes related to plant growth promotion were overrepresented in the rhizospheres of A. dealbata. Overall, results suggest that rhizosphere microbes may contribute to the widespread success of this invader in novel environments.}, } @article {pmid28747215, year = {2017}, author = {Hasegawa, K and Stewart, CJ and Mansbach, JM and Linnemann, RW and Ajami, NJ and Petrosino, JF and Camargo, CA}, title = {Sphingolipid metabolism potential in fecal microbiome and bronchiolitis in infants: a case-control study.}, journal = {BMC research notes}, volume = {10}, number = {1}, pages = {325}, pmid = {28747215}, issn = {1756-0500}, support = {R01 AI127507/AI/NIAID NIH HHS/United States ; R01 AI108588/AI/NIAID NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; R21 HL129909/HL/NHLBI NIH HHS/United States ; R01 AI114552/AI/NIAID NIH HHS/United States ; UH3 OD023253/OD/NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; }, mesh = {Bronchiolitis/*microbiology ; Case-Control Studies ; *Feces ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; *Metabolic Networks and Pathways ; Sphingolipids/*metabolism ; }, abstract = {OBJECTIVE: Emerging evidence demonstrated that the structure of fecal microbiome is associated with the likelihood of bronchiolitis in infants. However, no study has examined functional profiles of fecal microbiome in infants with bronchiolitis. In this context, we conducted a case-control study. As a part of multicenter prospective study, we collected stool samples from 40 infants hospitalized with bronchiolitis (cases). We concurrently enrolled 115 age-matched healthy controls.

RESULTS: First, by applying 16S rRNA gene sequencing to these 155 fecal samples, we identified the taxonomic profiles of fecal microbiome. Next, based on the taxonomy data, we inferred the functional capabilities of fecal microbiome and tested for differences in the functional capabilities between cases and controls. Overall, the median age was 3 months and 45% were female. Among 274 metabolic pathways surveyed, there were significant differences between bronchiolitis cases and healthy controls for 37 pathways, including lipid metabolic pathways (false discovery rate [FDR] <0.05). Particularly, the fecal microbiome of bronchiolitis cases had consistently higher abundances of gene function related to the sphingolipid metabolic pathways compared to that of controls (FDR <0.05). These pathways were more abundant in infants with Bacteroides-dominant microbiome profile compared to the others (FDR <0.001). On the basis of the predicted metagenome in this case-control study, we found significant differences in the functional potential of fecal microbiome between infants with bronchiolitis and healthy controls. Although causal inferences remain premature, our data suggest a potential link between the bacteria-derived metabolites, modulations of host immune response, and development of bronchiolitis.}, } @article {pmid28742928, year = {2017}, author = {Choo, LQ and Crampton-Platt, A and Vogler, AP}, title = {Shotgun mitogenomics across body size classes in a local assemblage of tropical Diptera: Phylogeny, species diversity and mitochondrial abundance spectrum.}, journal = {Molecular ecology}, volume = {26}, number = {19}, pages = {5086-5098}, doi = {10.1111/mec.14258}, pmid = {28742928}, issn = {1365-294X}, mesh = {Animals ; *Body Size ; Borneo ; Contig Mapping ; DNA, Mitochondrial/genetics ; Diptera/anatomy & histology/*classification ; *Genome, Mitochondrial ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Mitochondrial genomes can be assembled readily from shotgun-sequenced DNA mixtures of mass-trapped arthropods ("mitochondrial metagenomics"), speeding up the taxonomic characterization. Bulk sequencing was conducted on some 800 individuals of Diptera obtained by canopy fogging of a single tree in Borneo dominated by small (<1.5 mm) individuals. Specimens were split into five body size classes for DNA extraction, to equalize read numbers across specimens and to study how body size, a key ecological trait, interacts with species and phylogenetic diversity. Genome assembly produced 304 orthologous mitochondrial contigs presumed to each represent a different species. The small-bodied fraction was the by far most species-rich (187 contigs). Identification of contigs was through phylogenetic analysis together with 56 reference mitogenomes, which placed most of the Bornean community into seven clades of small-bodied species, indicating phylogenetic conservation of body size. Mapping of shotgun reads against the mitogenomes showed wide ranges of read abundances within each size class. Ranked read abundance plots were largely log-linear, indicating a uniformly filled abundance spectrum, especially for small-bodied species. Small-bodied species differed greatly from other size classes in neutral metacommunity parameters, exhibiting greater levels of immigration, besides greater total community size. We suggest that the established uses of mitochondrial metagenomics for analysis of species and phylogenetic diversity can be extended to parameterize recent theories of community ecology and biodiversity, and by focusing on the number mitochondria, rather than individuals, a new theoretical framework for analysis of mitochondrial abundance spectra can be developed that incorporates metabolic activity approximated by the count of mitochondria.}, } @article {pmid28740337, year = {2017}, author = {Ponziani, FR and Zocco, MA and D'Aversa, F and Pompili, M and Gasbarrini, A}, title = {Eubiotic properties of rifaximin: Disruption of the traditional concepts in gut microbiota modulation.}, journal = {World journal of gastroenterology}, volume = {23}, number = {25}, pages = {4491-4499}, pmid = {28740337}, issn = {2219-2840}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; Bacteria/*pathogenicity ; Communicable Diseases/*drug therapy ; Drug Resistance, Bacterial/drug effects ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Permeability ; Rifamycins/*pharmacology/therapeutic use ; Rifaximin ; Virulence/drug effects ; }, abstract = {Antibiotics are usually prescribed to cure infections but they also have significant modulatory effects on the gut microbiota. Several alterations of the intestinal bacterial community have been reported during antibiotic treatment, including the reduction of beneficial bacteria as well as of microbial alpha-diversity. Although after the discontinuation of antibiotic therapies it has been observed a trend towards the restoration of the original condition, the new steady state is different from the previous one, as if antibiotics induced some kind of irreversible perturbation of the gut microbial community. The poorly absorbed antibiotic rifaximin seem to be different from the other antibiotics, because it exerts non-traditional effects additional to the bactericidal/bacteriostatic activity on the gut microbiota. Rifaximin is able to reduce bacterial virulence and translocation, has anti-inflammatory properties and has been demonstrated to positively modulate the gut microbial composition. Animal models, culture studies and metagenomic analyses have demonstrated an increase in Bifidobacterium, Faecalibacterium prausnitzii and Lactobacillus abundance after rifaximin treatment, probably consequent to the induction of bacterial resistance, with no major change in the overall gut microbiota composition. Antibiotics are therefore modulators of the symbiotic relationship between the host and the gut microbiota. Specific antibiotics, such as rifaximin, can also induce eubiotic changes in the intestinal ecosystem; this additional property may represent a therapeutic advantage in specific clinical settings.}, } @article {pmid28732571, year = {2017}, author = {Stefanaki, C and Peppa, M and Mastorakos, G and Chrousos, GP}, title = {Examining the gut bacteriome, virome, and mycobiome in glucose metabolism disorders: Are we on the right track?.}, journal = {Metabolism: clinical and experimental}, volume = {73}, number = {}, pages = {52-66}, doi = {10.1016/j.metabol.2017.04.014}, pmid = {28732571}, issn = {1532-8600}, mesh = {Animals ; Gastrointestinal Microbiome/*physiology ; *Glucose Metabolism Disorders ; Humans ; Hyperglycemia ; Microbiota/*physiology ; Mycobiome/*physiology ; }, abstract = {Human gut microbiome is defined as the gene complement of the gut microbial community, measured via laboratory metagenomic techniques. It includes bacteriome, virome and mycobiome, which represent, respectively, the assemblages of bacteria, viruses and fungi, living in the human gut. Gut microbiota function as a living "organ" that interacts with the gastro-intestinal environment, provides nutrients and vitamins to the organism and transduces hormonal messages, essentially influencing the main metabolic pathways, including drug metabolism. A clear association between gut, and glucose metabolism disorders has recently emerged. Medications acting on glucose absorption in the gut, or enhancing gut hormone activity are already extensively employed in the therapy of diabetes. Moreover, the gut is characterized by immune, and autonomous neuronal features, which play a critical role in maintaining glucose metabolism homeostasis. Gut microbes respond to neuroendocrine, and immune biochemical messages, affecting the health, and behavior of the host. There is vast heterogeneity in the studies included in this review, hence a meta-analysis, or a systematic review were not applicable. In this article, we attempt to reveal the interplay between human gut microbiota physiology, and hyperglycemic states, synthesizing, and interpreting findings from human studies.}, } @article {pmid28732171, year = {2017}, author = {Eaton, WD and Shokralla, S and McGee, KM and Hajibabaei, M}, title = {Using metagenomics to show the efficacy of forest restoration in the New Jersey Pine Barrens.}, journal = {Genome}, volume = {60}, number = {10}, pages = {825-836}, doi = {10.1139/gen-2015-0199}, pmid = {28732171}, issn = {1480-3321}, mesh = {Animals ; Biomass ; Carbon/metabolism ; Chamaecyparis ; Ecosystem ; Environmental Restoration and Remediation/*methods ; *Forests ; High-Throughput Nucleotide Sequencing ; Invertebrates/genetics ; Metagenomics/*methods ; Mycorrhizae/genetics ; New Jersey ; *Soil Microbiology ; Vaccinium macrocarpon ; Wetlands ; }, abstract = {The Franklin Parker Preserve within the New Jersey Pine Barrens contains 5000 acres of wetlands habitat, including old-growth Atlantic white cedar (or AWC; Chamaecyparis thyoides) swamps, cranberry bogs, and former cranberry bogs undergoing restoration into AWC forests. This study showed that the C-use efficiency was greater in the old-growth AWC soils than in soils from 8-year-old mid-stage restored AWC stands, which were greater than found in soil from 4-year-old AWC stands-the latter two stands being restored from long-term cranberry bogs. A metagenomic analysis of eDNA extracted from these soils showed that the C-cycle trends were associated with increases in the relative numbers of DNA sequences from several copiotrophic bacterial groups (Bacteroidetes and Proteobacteria), complex C-decomposing fungal groups (Sordiomycetes, Mortierellales, and Thelephorales), and collembolan and formicid invertebrates. All groups are indicators of successionally more advanced soils, and critical for soil C-cycle activities. These data suggest that the restoration activities studied are enhancing critical guilds of soil biota, and increasing C-use efficiency in the soils of restored habitats, and that the use of metagenomic analysis of soil eDNA can be used in the development of assessment models for soil recovery of wetlands following restoration.}, } @article {pmid28731475, year = {2017}, author = {Suzuki, S and Ishii, S and Hoshino, T and Rietze, A and Tenney, A and Morrill, PL and Inagaki, F and Kuenen, JG and Nealson, KH}, title = {Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars.}, journal = {The ISME journal}, volume = {11}, number = {11}, pages = {2584-2598}, pmid = {28731475}, issn = {1751-7370}, mesh = {Alkalies/*metabolism ; Archaea/classification/genetics/*isolation & purification/*metabolism ; Bacteria/classification/genetics/*isolation & purification/*metabolism ; Biodiversity ; Metagenomics ; Natural Springs/analysis/*microbiology ; Phylogeny ; }, abstract = {Water from The Cedars springs that discharge from serpentinized ultramafic rocks feature highly basic (pH=~12), highly reducing (Eh<-550 mV) conditions with low ionic concentrations. These conditions make the springs exceptionally challenging for life. Here, we report the metagenomic data and recovered draft genomes from two different springs, GPS1 and BS5. GPS1, which was fed solely by a deep groundwater source within the serpentinizing system, was dominated by several bacterial taxa from the phyla OD1 ('Parcubacteria') and Chloroflexi. Members of the GPS1 community had, for the most part, the smallest genomes reported for their respective taxa, and encoded only archaeal (A-type) ATP synthases or no ATP synthases at all. Furthermore, none of the members encoded respiration-related genes and some of the members also did not encode key biosynthesis-related genes. In contrast, BS5, fed by shallow water, appears to have a community driven by hydrogen metabolism and was dominated by a diverse group of Proteobacteria similar to those seen in many terrestrial serpentinization sites. Our findings indicated that the harsh ultrabasic geological setting supported unexpectedly diverse microbial metabolic strategies and that the deep-water-fed springs supported a community that was remarkable in its unusual metagenomic and genomic constitution.}, } @article {pmid28731473, year = {2017}, author = {Svartström, O and Alneberg, J and Terrapon, N and Lombard, V and de Bruijn, I and Malmsten, J and Dalin, AM and El Muller, E and Shah, P and Wilmes, P and Henrissat, B and Aspeborg, H and Andersson, AF}, title = {Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.}, journal = {The ISME journal}, volume = {11}, number = {11}, pages = {2538-2551}, pmid = {28731473}, issn = {1751-7370}, support = {322820/ERC_/European Research Council/International ; }, mesh = {Animal Feed/analysis ; Animals ; Bacteria/classification/*genetics/*isolation & purification/metabolism ; Biomass ; Deer/metabolism/*microbiology ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Lignin/metabolism ; Metagenome ; Metagenomics ; Phylogeny ; Poaceae/metabolism ; Rumen/metabolism/*microbiology ; }, abstract = {The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes and were overall overrepresented in the moose microbiome compared with other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a large numbers of dockerins, a module usually associated with cellulosomes. The Bacteroidetes dockerins were often linked to CAZymes and sometimes encoded inside polysaccharide utilization loci, which has never been reported before. The almost 100 CAZyme-annotated genomes reconstructed in this study provide an in-depth view of an efficient lignocellulose-degrading microbiome and prospects for developing enzyme technology for biorefineries.}, } @article {pmid28730710, year = {2017}, author = {Otten, TG and Paerl, HW and Dreher, TW and Kimmerer, WJ and Parker, AE}, title = {The molecular ecology of Microcystis sp. blooms in the San Francisco Estuary.}, journal = {Environmental microbiology}, volume = {19}, number = {9}, pages = {3619-3637}, doi = {10.1111/1462-2920.13860}, pmid = {28730710}, issn = {1462-2920}, mesh = {Animals ; Biodiversity ; DNA, Bacterial/genetics ; Ecology ; Estuaries ; Fishes ; Food Chain ; *Harmful Algal Bloom ; *Microbiota ; Microcystins/biosynthesis ; Microcystis/*classification/genetics/*isolation & purification/virology ; Real-Time Polymerase Chain Reaction ; San Francisco ; Water Microbiology ; }, abstract = {Harmful blooms of the cyanobacterium Microcystis sp. have become increasingly pervasive in the San Francisco Estuary Delta (USA) since the early 2000s and their rise has coincided with substantial decreases in several important fish species. Direct and indirect effects Microcystis blooms may have on the Delta food web were investigated. The Microcystis population was tracked for 2 years at six sites throughout the Delta using quantitative PCR. High-throughput amplicon sequencing and colony PCR sequencing revealed the presence of 10 different strains of Microcystis, including 6 different microcystin-producing strains. Shotgun metagenomic analysis identified a variety of Microcystis secondary metabolite pathways, including those for the biosynthesis of: aeruginosin, cyanopeptolin, microginin, microviridin and piricyclamide. A sizable reduction was observed in microbial community diversity during a large Microcystis bloom (H' = 0.61) relative to periods preceding (H' = 2.32) or following (H' = 3.71) the bloom. Physicochemical conditions of the water column were stable throughout the bloom period. The elevated abundance of a cyanomyophage with high similarity to previously sequenced isolates known to infect Microcystis sp. was implicated in the bloom's collapse. Network analysis was employed to elucidate synergistic and antagonistic relationships between Microcystis and other bacteria and indicated that only very few taxa were positively correlated with Microcystis.}, } @article {pmid28730541, year = {2017}, author = {Vasar, M and Andreson, R and Davison, J and Jairus, T and Moora, M and Remm, M and Young, JPW and Zobel, M and Öpik, M}, title = {Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi.}, journal = {Mycorrhiza}, volume = {27}, number = {8}, pages = {761-773}, pmid = {28730541}, issn = {1432-1890}, mesh = {*Biodiversity ; DNA, Fungal/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Mycorrhizae/*genetics ; }, abstract = {The arrival of 454 sequencing represented a major breakthrough by allowing deeper sequencing of environmental samples than was possible with existing Sanger approaches. Illumina MiSeq provides a further increase in sequencing depth but shorter read length compared with 454 sequencing. We explored whether Illumina sequencing improves estimates of arbuscular mycorrhizal (AM) fungal richness in plant root samples, compared with 454 sequencing. We identified AM fungi in root samples by sequencing amplicons of the SSU rRNA gene with 454 and Illumina MiSeq paired-end sequencing. In addition, we sequenced metagenomic DNA without prior PCR amplification. Amplicon-based Illumina sequencing yielded two orders of magnitude higher sequencing depth per sample than 454 sequencing. Initial analysis with minimal quality control recorded five times higher AM fungal richness per sample with Illumina sequencing. Additional quality control of Illumina samples, including restriction of the marker region to the most variable amplicon fragment, revealed AM fungal richness values close to those produced by 454 sequencing. Furthermore, AM fungal richness estimates were not correlated with sequencing depth between 300 and 30,000 reads per sample, suggesting that the lower end of this range is sufficient for adequate description of AM fungal communities. By contrast, metagenomic Illumina sequencing yielded very few AM fungal reads and taxa and was dominated by plant DNA, suggesting that AM fungal DNA is present at prohibitively low abundance in colonised root samples. In conclusion, Illumina MiSeq sequencing yielded higher sequencing depth, but similar richness of AM fungi in root samples, compared with 454 sequencing.}, } @article {pmid28730353, year = {2018}, author = {Vieira, FR and Pecchia, JA}, title = {An Exploration into the Bacterial Community under Different Pasteurization Conditions during Substrate Preparation (Composting-Phase II) for Agaricus bisporus Cultivation.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {318-330}, pmid = {28730353}, issn = {1432-184X}, support = {005707/2012-05//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, mesh = {Agaricus/*growth & development/metabolism ; Bacteria/classification/genetics/growth & development/*isolation & purification ; Biodiversity ; Composting ; Culture Media/*chemistry/metabolism ; DNA, Bacterial/genetics ; Hot Temperature ; Pasteurization/instrumentation/*methods ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {Substrate preparation (i.e., composting) for Agaricus bisporus cultivation is the most critical point of mushroom production. Among many factors involved in the composting process, the microbial ecology of the system is the underlying drive of composting and can be influenced by composting management techniques. Pasteurization temperature at the beginning of phase II, in theory, may influence the bacterial community and subsequently the "selectivity" and nutrition of the final substrate. Therefore, this hypothesis was tested by simulation in bioreactors under different pasteurization conditions (57 °C/6 h, 60 °C/2 h, and 68 °C/2 h), simulating conditions adopted by many producers. Bacterial diversity, based on 16S ribosomal RNA obtained by high-throughput sequencing and classified in operational taxonomic units (OTUs), was greater than previously reported using culture-dependent methods. Alpha diversity estimators show a lower diversity of OTUs under a high-temperature pasteurization condition. Bacillales order shows a relatively higher OTU abundance under a high-pasteurization temperature, which also was related to high ammonia emission measurements. On the other hand, beta diversity analysis showed no significantly changes in the bacterial community structure under different conditions. Agaricus bisporus mycelium growth during a standard spawn run period was significantly slower in the compost pasteurized at high temperature. Since the bacterial community structure was not greatly affected by different pasteurization conditions but by-products left (e.g., ammonia) at the end of compost conditioning varied, further studies need to be conducted to determine the functional role of the microbial communities found during substrate preparation for Agaricus bisporus cultivation.}, } @article {pmid28729863, year = {2017}, author = {Chan, CS and Chan, KG and Ee, R and Hong, KW and Urbieta, MS and Donati, ER and Shamsir, MS and Goh, KM}, title = {Effects of Physiochemical Factors on Prokaryotic Biodiversity in Malaysian Circumneutral Hot Springs.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1252}, pmid = {28729863}, issn = {1664-302X}, abstract = {Malaysia has a great number of hot springs, especially along the flank of the Banjaran Titiwangsa mountain range. Biological studies of the Malaysian hot springs are rare because of the lack of comprehensive information on their microbial communities. In this study, we report a cultivation-independent census to describe microbial communities in six hot springs. The Ulu Slim (US), Sungai Klah (SK), Dusun Tua (DT), Sungai Serai (SS), Semenyih (SE), and Ayer Hangat (AH) hot springs exhibit circumneutral pH with temperatures ranging from 43°C to 90°C. Genomic DNA was extracted from environmental samples and the V3-V4 hypervariable regions of 16S rRNA genes were amplified, sequenced, and analyzed. High-throughput sequencing analysis showed that microbial richness was high in all samples as indicated by the detection of 6,334-26,244 operational taxonomy units. In total, 59, 61, 72, 73, 65, and 52 bacterial phyla were identified in the US, SK, DT, SS, SE, and AH hot springs, respectively. Generally, Firmicutes and Proteobacteria dominated the bacterial communities in all hot springs. Archaeal communities mainly consisted of Crenarchaeota, Euryarchaeota, and Parvarchaeota. In beta diversity analysis, the hot spring microbial memberships were clustered primarily on the basis of temperature and salinity. Canonical correlation analysis to assess the relationship between the microbial communities and physicochemical variables revealed that diversity patterns were best explained by a combination of physicochemical variables, rather than by individual abiotic variables such as temperature and salinity.}, } @article {pmid28729652, year = {2017}, author = {Johnston, EC and Forsman, ZH and Flot, JF and Schmidt-Roach, S and Pinzón, JH and Knapp, ISS and Toonen, RJ}, title = {A genomic glance through the fog of plasticity and diversification in Pocillopora.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5991}, pmid = {28729652}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*genetics ; Bayes Theorem ; *Biodiversity ; Genome, Mitochondrial ; *Genomics ; Likelihood Functions ; Open Reading Frames/genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Time Factors ; }, abstract = {Scleractinian corals of the genus Pocillopora (Lamarck, 1816) are notoriously difficult to identify morphologically with considerable debate on the degree to which phenotypic plasticity, introgressive hybridization and incomplete lineage sorting obscure well-defined taxonomic lineages. Here, we used RAD-seq to resolve the phylogenetic relationships among seven species of Pocillopora represented by 15 coral holobiont metagenomic libraries. We found strong concordance between the coral holobiont datasets, reads that mapped to the Pocillopora damicornis (Linnaeus, 1758) transcriptome, nearly complete mitochondrial genomes, 430 unlinked high-quality SNPs shared across all Pocillopora taxa, and a conspecificity matrix of the holobiont dataset. These datasets also show strong concordance with previously published clustering of the mitochondrial clades based on the mtDNA open reading frame (ORF). We resolve seven clear monophyletic groups, with no evidence for introgressive hybridization among any but the most recently derived sister species. In contrast, ribosomal and histone datasets, which are most commonly used in coral phylogenies to date, were less informative and contradictory to these other datasets. These data indicate that extant Pocillopora species diversified from a common ancestral lineage within the last ~3 million years. Key to this evolutionary success story may be the high phenotypic plasticity exhibited by Pocillopora species.}, } @article {pmid28729646, year = {2017}, author = {Orsi, WD and Coolen, MJL and Wuchter, C and He, L and More, KD and Irigoien, X and Chust, G and Johnson, C and Hemingway, JD and Lee, M and Galy, V and Giosan, L}, title = {Climate oscillations reflected within the microbiome of Arabian Sea sediments.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6040}, pmid = {28729646}, issn = {2045-2322}, mesh = {*Climate ; Geologic Sediments/*microbiology ; Metagenome ; Metagenomics/methods ; *Microbiota ; Oceans and Seas ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {Selection of microorganisms in marine sediment is shaped by energy-yielding electron acceptors for respiration that are depleted in vertical succession. However, some taxa have been reported to reflect past depositional conditions suggesting they have experienced weak selection after burial. In sediments underlying the Arabian Sea oxygen minimum zone (OMZ), we performed the first metagenomic profiling of sedimentary DNA at centennial-scale resolution in the context of a multi-proxy paleoclimate reconstruction. While vertical distributions of sulfate reducing bacteria and methanogens indicate energy-based selection typical of anoxic marine sediments, 5-15% of taxa per sample exhibit depth-independent stratigraphies indicative of paleoenvironmental selection over relatively short geological timescales. Despite being vertically separated, indicator taxa deposited under OMZ conditions were more similar to one another than those deposited in bioturbated intervals under intervening higher oxygen. The genomic potential for denitrification also correlated with palaeo-OMZ proxies, independent of sediment depth and available nitrate and nitrite. However, metagenomes revealed mixed acid and Entner-Dourdoroff fermentation pathways encoded by many of the same denitrifier groups. Fermentation thus may explain the subsistence of these facultatively anaerobic microbes whose stratigraphy follows changing paleoceanographic conditions. At least for certain taxa, our analysis provides evidence of their paleoenvironmental selection over the last glacial-interglacial cycle.}, } @article {pmid28729641, year = {2017}, author = {Fernández-González, AJ and Martínez-Hidalgo, P and Cobo-Díaz, JF and Villadas, PJ and Martínez-Molina, E and Toro, N and Tringe, SG and Fernández-López, M}, title = {The rhizosphere microbiome of burned holm-oak: potential role of the genus Arthrobacter in the recovery of burned soils.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6008}, pmid = {28729641}, issn = {2045-2322}, mesh = {Arthrobacter/classification/genetics ; Biodiversity ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; Plant Roots/*microbiology ; *Quercus ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; *Wildfires ; }, abstract = {After a forest wildfire, the microbial communities have a transient alteration in their composition. The role of the soil microbial community in the recovery of an ecosystem following such an event remains poorly understood. Thus, it is necessary to understand the plant-microbe interactions that occur in burned soils. By high-throughput sequencing, we identified the main bacterial taxa of burnt holm-oak rhizosphere, then we obtained an isolate collection of the most abundant genus and its growth promoting activities were characterised. 16S rRNA amplicon sequencing showed that the genus Arthrobacter comprised more than 21% of the total community. 55 Arthrobacter strains were isolated and characterized using RAPDs and sequencing of the almost complete 16S rRNA gene. Our results indicate that isolated Arthrobacter strains present a very high genetic diversity, and they could play an important ecological role in interaction with the host plant by enhancing aerial growth. Most of the selected strains exhibited a great ability to degrade organic polymers in vitro as well as possibly presenting a direct mechanism for plant growth promotion. All the above data suggests that Arthrobacter can be considered as an excellent PGP rhizobacterium that may play an important role in the recovery of burned holm-oak forests.}, } @article {pmid28724443, year = {2017}, author = {Su, JQ and An, XL and Li, B and Chen, QL and Gillings, MR and Chen, H and Zhang, T and Zhu, YG}, title = {Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {84}, pmid = {28724443}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/pharmacology ; Antimicrobial Stewardship ; Bacteria/classification/*drug effects/*genetics/isolation & purification ; China ; Drug Resistance, Bacterial/*genetics ; Gastrointestinal Microbiome/genetics ; *Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Urban Renewal ; }, abstract = {BACKGROUND: Antibiotic-resistant pathogens are challenging treatment of infections worldwide. Urban sewage is potentially a major conduit for dissemination of antibiotic resistance genes into various environmental compartments. However, the diversity and abundance of such genes in wastewater are not well known.

METHODS: Here, seasonal and geographical distributions of antibiotic resistance genes and their host bacterial communities from Chinese urban sewage were characterized, using metagenomic analyses and 16S rRNA gene-based Illumina sequencing, respectively.

RESULTS: In total, 381 different resistance genes were detected, and these genes were extensively shared across China, with no geographical clustering. Seasonal variation in abundance of resistance genes was observed, with average concentrations of 3.27 × 10[11] and 1.79 × 10[12] copies/L in summer and winter, respectively. Bacterial communities did not exhibit geographical clusters, but did show a significant distance-decay relationship (P < 0.01). The core, shared resistome accounted for 57.7% of the total resistance genes, and was significantly associated with the core microbial community (P < 0.01). The core human gut microbiota was also strongly associated with the shared resistome, demonstrating the potential contribution of human gut microbiota to the dissemination of resistance elements via sewage disposal.

CONCLUSIONS: This study provides a baseline for investigating environmental dissemination of resistance elements and raises the possibility of using the abundance of resistance genes in sewage as a tool for antibiotic stewardship.}, } @article {pmid28724401, year = {2017}, author = {Cernava, T and Erlacher, A and Aschenbrenner, IA and Krug, L and Lassek, C and Riedel, K and Grube, M and Berg, G}, title = {Deciphering functional diversification within the lichen microbiota by meta-omics.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {82}, pmid = {28724401}, issn = {2049-2618}, support = {I 882/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Alphaproteobacteria/genetics ; Ascomycota/genetics ; Bacteria/classification/genetics ; Chlorophyta/genetics ; Gene Expression Profiling ; Lichens/genetics/metabolism/*microbiology ; *Metagenomics ; Microbial Consortia/genetics/physiology ; *Microbiota ; Phylogeny ; *Proteomics ; *Symbiosis ; }, abstract = {BACKGROUND: Recent evidence of specific bacterial communities extended the traditional concept of fungal-algal lichen symbioses by a further organismal kingdom. Although functional roles were already assigned to dominant members of the highly diversified microbiota, a substantial fraction of the ubiquitous colonizers remained unexplored. We employed a multi-omics approach to further characterize functional guilds in an unconventional model system.

RESULTS: The general community structure of the lichen-associated microbiota was shown to be highly similar irrespective of the employed omics approach. Five highly abundant bacterial orders-Sphingomonadales, Rhodospirillales, Myxococcales, Chthoniobacterales, and Sphingobacteriales-harbor functions that are of substantial importance for the holobiome. Identified functions range from the provision of vitamins and cofactors to the degradation of phenolic compounds like phenylpropanoid, xylenols, and cresols.

CONCLUSIONS: Functions that facilitate the persistence of Lobaria pulmonaria under unfavorable conditions were present in previously overlooked fractions of the microbiota. So far, unrecognized groups like Chthoniobacterales (Verrucomicrobia) emerged as functional protectors in the lichen microbiome. By combining multi-omics and imaging techniques, we highlight previously overlooked participants in the complex microenvironment of the lichens.}, } @article {pmid28723981, year = {2017}, author = {Passos, MDCF and Moraes-Filho, JP}, title = {INTESTINAL MICROBIOTA IN DIGESTIVE DISEASES.}, journal = {Arquivos de gastroenterologia}, volume = {54}, number = {3}, pages = {255-262}, doi = {10.1590/S0004-2803.201700000-31}, pmid = {28723981}, issn = {1678-4219}, mesh = {Gastrointestinal Diseases/*microbiology ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Obesity/*microbiology ; }, abstract = {BACKGROUND: In recent years, especially after the development of sophisticated metagenomic studies, research on the intestinal microbiota has increased, radically transforming our knowledge about the microbiome and its association with health maintenance and disease development in humans. Increasing evidence has shown that a permanent alteration in microbiota composition or function (dysbiosis) can alter immune responses, metabolism, intestinal permeability, and digestive motility, thereby promoting a proinflammatory state. Such alterations can mainly impair the host's immune and metabolic functions, thus favoring the onset of diseases such as diabetes, obesity, digestive, neurological, autoimmune, and neoplastic diseases. This comprehensive review is a compilation of the available literature on the formation of the complex intestinal ecosystem and its impact on the incidence of diseases such as obesity, non-alcoholic steatohepatitis, irritable bowel syndrome, inflammatory bowel disease, celiac disease, and digestive neoplasms.

CONCLUSION:: Alterations in the composition and function of the gastrointestinal microbiota (dysbiosis) have a direct impact on human health and seem to have an important role in the pathogenesis of several gastrointestinal diseases, whether inflammatory, metabolic, or neoplastic ones.}, } @article {pmid28721658, year = {2017}, author = {Vieira, AS and Ramalho, MO and Martins, C and Martins, VG and Bueno, OC}, title = {Microbial Communities in Different Tissues of Atta sexdens rubropilosa Leaf-cutting Ants.}, journal = {Current microbiology}, volume = {74}, number = {10}, pages = {1216-1225}, pmid = {28721658}, issn = {1432-0991}, support = {157837/2015-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 306910/2011-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 007343/2014-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 2012/12541-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, mesh = {Animals ; Ants/*microbiology ; Biodiversity ; Metagenome ; Metagenomics ; *Microbiota ; Organ Specificity ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bacterial endosymbionts are common in all insects, and symbiosis has played an integral role in ant evolution. Atta sexdens rubropilosa leaf-cutting ants cultivate their symbiotic fungus using fresh leaves. They need to defend themselves and their brood against diseases, but they also need to defend their obligate fungus gardens, their primary food source, from infection, parasitism, and usurpation by competitors. This study aimed to characterize the microbial communities in whole workers and different tissues of A. sexdens rubropilosa queens using Ion Torrent NGS. Our results showed that the microbial community in the midgut differs in abundance and diversity from the communities in the postpharyngeal gland of the queen and in whole workers. The main microbial orders in whole workers were Lactobacillales, Clostridiales, Enterobacteriales, Actinomycetales, Burkholderiales, and Bacillales. In the tissues of the queens, the main orders were Burkholderiales, Clostridiales, Syntrophobacterales, Lactobacillales, Bacillales, and Actinomycetales (midgut) and Entomoplasmatales, unclassified γ-proteobacteria, and Actinomycetales (postpharyngeal glands). The high abundance of Entomoplasmatales in the postpharyngeal glands (77%) of the queens was an unprecedented finding. We discuss the role of microbial communities in different tissues and castes. Bacteria are likely to play a role in nutrition and immune defense as well as helping antimicrobial defense in this ant species.}, } @article {pmid28721504, year = {2018}, author = {LeBrun, ES and King, RS and Back, JA and Kang, S}, title = {Microbial Community Structure and Function Decoupling Across a Phosphorus Gradient in Streams.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {64-73}, pmid = {28721504}, issn = {1432-184X}, mesh = {Archaea/classification/genetics/*isolation & purification/metabolism ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Biodiversity ; Ecosystem ; Metagenome ; *Microbiota ; Phosphorus/*analysis/metabolism ; Phylogeny ; Rivers/chemistry/*microbiology ; }, abstract = {Phosphorus (P) is a key biological element with important and unique biogeochemical cycling in natural ecosystems. Anthropogenic phosphorus inputs have been shown to greatly affect natural ecosystems, and this has been shown to be especially true of freshwater systems. While the importance of microbial communities in the P cycle is widely accepted, the role, composition, and relationship to P of these communities in freshwater systems still hold many secrets. Here, we investigated combined bacterial and archaeal communities utilizing 16S ribosomal RNA (rRNA) gene sequencing and computationally predicted functional metagenomes (PFMs) in 25 streams representing a strong P gradient. We discovered that 16S rRNA community structure and PFMs demonstrate a degree of decoupling between structure and function in the system. While we found that total phosphorus (TP) was correlated to the structure and functional capability of bacterial and archaeal communities in the system, turbidity had a stronger, but largely independent, correlation. At TP levels of approximately 55 μg/L, we see sharp differences in the abundance of numerous ecologically important taxa related to vegetation, agriculture, sediment, and other ecosystem inhabitants.}, } @article {pmid28720895, year = {2017}, author = {Liu, J and Techtmann, SM and Woo, HL and Ning, D and Fortney, JL and Hazen, TC}, title = {Rapid Response of Eastern Mediterranean Deep Sea Microbial Communities to Oil.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5762}, pmid = {28720895}, issn = {2045-2322}, mesh = {Archaea/classification/genetics/metabolism ; Bacteria/classification/genetics/metabolism ; Biodegradation, Environmental ; Biodiversity ; Geography ; Mediterranean Sea ; Metagenomics/methods ; Microbiota/*drug effects/genetics ; Petroleum/*toxicity ; Petroleum Pollution/*analysis ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Deep marine oil spills like the Deepwater Horizon (DWH) in the Gulf of Mexico have the potential to drastically impact marine systems. Crude oil contamination in marine systems remains a concern, especially for countries around the Mediterranean Sea with off shore oil production. The goal of this study was to investigate the response of indigenous microbial communities to crude oil in the deep Eastern Mediterranean Sea (E. Med.) water column and to minimize potential bias associated with storage and shifts in microbial community structure from sample storage. 16S rRNA amplicon sequencing was combined with GeoChip metagenomic analysis to monitor the microbial community changes to the crude oil and dispersant in on-ship microcosms set up immediately after water collection. After 3 days of incubation at 14 °C, the microbial communities from two different water depths: 824 m and 1210 m became dominated by well-known oil degrading bacteria. The archaeal population and the overall microbial community diversity drastically decreased. Similarly, GeoChip metagenomic analysis revealed a tremendous enrichment of genes related to oil biodegradation, which was consistent with the results from the DWH oil spill. These results highlight a rapid microbial adaption to oil contamination in the deep E. Med., and indicate strong oil biodegradation potential.}, } @article {pmid28720679, year = {2017}, author = {Koh, AY}, title = {Potential for Monitoring Gut Microbiota for Diagnosing Infections and Graft-versus-Host Disease in Cancer and Stem Cell Transplant Patients.}, journal = {Clinical chemistry}, volume = {63}, number = {11}, pages = {1685-1694}, pmid = {28720679}, issn = {1530-8561}, support = {R01 AI123163/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Infections/complications/*diagnosis ; *Gastrointestinal Microbiome ; Graft vs Host Disease/complications/*diagnosis ; Humans ; *Microbiota ; Neoplasms/*complications ; RNA, Ribosomal, 16S/genetics ; *Stem Cell Transplantation ; }, abstract = {BACKGROUND: Gut microbiota, the collective community of microorganisms inhabiting the intestine, have been shown to provide many beneficial functions for the host. Recent advances in next-generation sequencing and advanced molecular biology approaches have allowed researchers to identify gut microbiota signatures associated with disease processes and, in some cases, establish causality and elucidate underlying mechanisms.

CONTENT: This report reviews 3 commonly used methods for studying the gut microbiota and microbiome (the collective genomes of the gut microorganisms): 16S rRNA gene sequencing, bacterial group or species-specific quantitative polymerase chain reaction (qPCR), and metagenomic shotgun sequencing (MSS). The technical approaches and resources needed for each approach are outlined, and advantages and disadvantages for each approach are summarized. The findings regarding the role of the gut microbiota in the health of patients with cancer and stem cell transplant (SCT) patients (specifically in modulating the development of gut-derived bacterial infections and a posttransplant immune-mediated complication known as graft-vs-host-disease) are reviewed. Finally, there is discussion of the potential viability of these approaches in the actual clinical treatment of cancer and SCT patients.

SUMMARY: Advances in next-generation sequencing have revolutionized our understanding of the importance of the gut microbiome to human health. Both 16S rRNA gene sequencing and MSS are currently too labor-intensive or computationally burdensome to incorporate into real-time clinical monitoring of gut microbiomes. Yet, the lessons learned from these technologies could be adapted to currently used methods (e.g., qPCR) that could then be rigorously tested in the clinical care of these patients.}, } @article {pmid28719637, year = {2017}, author = {Siqueira, FM and Pérez-Wohlfeil, E and Carvalho, FM and Trelles, O and Schrank, IS and Vasconcelos, ATR and Zaha, A}, title = {Microbiome overview in swine lungs.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0181503}, pmid = {28719637}, issn = {1932-6203}, mesh = {Animals ; Lung/*microbiology ; *Microbiota/genetics ; Sequence Analysis ; Swine ; }, abstract = {Mycoplasma hyopneumoniae is the etiologic agent of swine enzootic pneumonia. However other mycoplasma species and secondary bacteria are found as inhabitants of the swine respiratory tract, which can be also related to disease. In the present study we have performed a total DNA metagenomic analysis from the lungs of pigs kept in a field condition, with suggestive signals of enzootic pneumonia and without any infection signals to evaluate the bacteria variability of the lungs microbiota. Libraries from metagenomic DNA were prepared and sequenced using total DNA shotgun metagenomic pyrosequencing. The metagenomic distribution showed a great abundance of bacteria. The most common microbial families identified from pneumonic swine's lungs were Mycoplasmataceae, Flavobacteriaceae and Pasteurellaceae, whereas in the carrier swine's lungs the most common families were Mycoplasmataceae, Bradyrhizobiaceae and Flavobacteriaceae. Analysis of community composition in both samples confirmed the high prevalence of M. hyopneumoniae. Moreover, the carrier lungs had more diverse family population, which should be related to the lungs normal flora. In summary, we provide a wide view of the bacterial population from lungs with signals of enzootic pneumonia and lungs without signals of enzootic pneumonia in a field situation. These bacteria patterns provide information that may be important for the establishment of disease control measures and to give insights for further studies.}, } @article {pmid28718274, year = {2017}, author = {Suárez Moya, A}, title = {[Microbiome and next generation sequencing].}, journal = {Revista espanola de quimioterapia : publicacion oficial de la Sociedad Espanola de Quimioterapia}, volume = {30}, number = {5}, pages = {305-311}, pmid = {28718274}, issn = {1988-9518}, mesh = {Biodiversity ; DNA, Bacterial/*analysis ; *High-Throughput Nucleotide Sequencing ; Humans ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The human microbiome is an internal ecosystem that refers to the community of microorganisms that populate the human body. These microorganisms are essential to support his health, because the interaction between the host immune system and microorganisms, provide the host with protection against pathogens, and contributes to the preservation of health. Bacteriological culture has been the basis for traditional microbiology; however, most of the bacterial forms observed in nature cannot be isolated with laboratory culture methods. At present, metagenomic applies a suite of genomic technologies, where the microorganisms are identified by their genomic fingerprint. The 16S rRNA subunit is considered as the universal target for bacterial identification from DNA with the aid of sequencing. Sanger sequencing technology had a great impact on the first generation sequencing due to its simplicity and precision. Platforms high-throughput known as second generation secuencing technologies are capable to generate hundreds of thousands of sequence reactions in a faster and economic way. However, thanks to the third generation sequencing the greatest advances in nanotechnology have been made. Using the reference gene, the massive sequencing techniques and bioinformatics tools used for the data processing, there has been an important development of the human microbiome, achieving an unprecedented detail level on the taxonomy and microbial function. This has meant an authentic revolution not only in their knowledge but also in their involvement in the health or illness of the human being.}, } @article {pmid28716113, year = {2017}, author = {Be, NA and Avila-Herrera, A and Allen, JE and Singh, N and Checinska Sielaff, A and Jaing, C and Venkateswaran, K}, title = {Whole metagenome profiles of particulates collected from the International Space Station.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {81}, pmid = {28716113}, issn = {2049-2618}, mesh = {Archaea/classification/*genetics/isolation & purification ; Astronauts ; Bacteria/classification/*genetics/isolation & purification ; Dust/*analysis ; Environment Design ; Environment, Controlled ; High-Throughput Nucleotide Sequencing ; Humans ; International Agencies ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Phylogeny ; Space Flight ; *Spacecraft ; Weightlessness ; }, abstract = {BACKGROUND: The built environment of the International Space Station (ISS) is a highly specialized space in terms of both physical characteristics and habitation requirements. It is unique with respect to conditions of microgravity, exposure to space radiation, and increased carbon dioxide concentrations. Additionally, astronauts inhabit a large proportion of this environment. The microbial composition of ISS particulates has been reported; however, its functional genomics, which are pertinent due to potential impact of its constituents on human health and operational mission success, are not yet characterized.

METHODS: This study examined the whole metagenome of ISS microbes at both species- and gene-level resolution. Air filter and dust samples from the ISS were analyzed and compared to samples collected in a terrestrial cleanroom environment. Furthermore, metagenome mining was carried out to characterize dominant, virulent, and novel microorganisms. The whole genome sequences of select cultivable strains isolated from these samples were extracted from the metagenome and compared.

RESULTS: Species-level composition in the ISS was found to be largely dominated by Corynebacterium ihumii GD7, with overall microbial diversity being lower in the ISS relative to the cleanroom samples. When examining detection of microbial genes relevant to human health such as antimicrobial resistance and virulence genes, it was found that a larger number of relevant gene categories were observed in the ISS relative to the cleanroom. Strain-level cross-sample comparisons were made for Corynebacterium, Bacillus, and Aspergillus showing possible distinctions in the dominant strain between samples.

CONCLUSION: Species-level analyses demonstrated distinct differences between the ISS and cleanroom samples, indicating that the cleanroom population is not necessarily reflective of space habitation environments. The overall population of viable microorganisms and the functional diversity inherent to this unique closed environment are of critical interest with respect to future space habitation. Observations and studies such as these will be important to evaluating the conditions required for long-term health of human occupants in such environments.}, } @article {pmid28716079, year = {2017}, author = {Sundin, OH and Mendoza-Ladd, A and Zeng, M and Diaz-Arévalo, D and Morales, E and Fagan, BM and Ordoñez, J and Velez, P and Antony, N and McCallum, RW}, title = {The human jejunum has an endogenous microbiota that differs from those in the oral cavity and colon.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {160}, pmid = {28716079}, issn = {1471-2180}, support = {R01 EY013610/EY/NEI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Bacteria/classification/genetics/growth & development/*isolation & purification ; Colon/*microbiology ; Female ; Humans ; Jejunum/*microbiology ; Male ; *Microbiota ; Middle Aged ; Mouth/*microbiology ; }, abstract = {BACKGROUND: The upper half of the human small intestine, known as the jejunum, is the primary site for absorption of nutrient-derived carbohydrates, amino acids, small peptides, and vitamins. In contrast to the colon, which contains 10[11]-10[12] colony forming units of bacteria per ml (CFU/ml), the normal jejunum generally ranges from 10[3] to 10[5] CFU per ml. Because invasive procedures are required to access the jejunum, much less is known about its bacterial microbiota. Bacteria inhabiting the jejunal lumen have been investigated by classical culture techniques, but not by culture-independent metagenomics.

RESULTS: The lumen of the upper jejunum was sampled during enteroscopy of 20 research subjects. Culture on aerobic and anaerobic media gave live bacterial counts ranging from 5.8 × 10[3] CFU/ml to 8.0 × 10[6] CFU/ml. DNA from the same samples was analyzed by 16S rRNA gene-specific quantitative PCR, yielding values from 1.5 × 10[5] to 3.1 × 10[7] bacterial genomes per ml. When calculated for each sample, estimated bacterial viability ranged from effectively 100% to a low of 0.3%. 16S rRNA metagenomic analysis of uncultured bacteria by Illumina MiSeq sequencing gave detailed microbial composition by phylum, genus and species. The genera Streptococcus, Prevotella, Veillonella and Fusobacterium, were especially abundant, as well as non-oral genera including Escherichia, Klebsiella, and Citrobacter. The jejunum was devoid of the genera Alistipes, Ruminococcus, Faecalibacterium, and other extreme anaerobes abundant in the colon. In patients with higher bacterial loads, there was no significant change in microbial species composition.

CONCLUSIONS: The jejunal lumen contains a distinctive bacterial population consisting primarily of facultative anaerobes and oxygen-tolerant obligate anaerobes similar to those found in the oral cavity. However, the frequent abundance of Enterobacteriaceae represents a major difference from oral microbiota. Although a few genera are shared with the colon, we found no evidence for retrograde movement of the most abundant colonic microbes to the jejunum. Some individuals had much higher bacterial loads, but this was not correlated with decreases in bacterial species diversity or other evidence of dysbiosis.}, } @article {pmid28715458, year = {2017}, author = {Hirai, J and Nagai, S and Hidaka, K}, title = {Evaluation of metagenetic community analysis of planktonic copepods using Illumina MiSeq: Comparisons with morphological classification and metagenetic analysis using Roche 454.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0181452}, pmid = {28715458}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Classification ; Computational Biology ; Copepoda/*genetics ; High-Throughput Nucleotide Sequencing/*instrumentation ; Metagenome/*genetics ; Metagenomics/*instrumentation ; Oceans and Seas ; Plankton/*genetics ; }, abstract = {Metagenetics is a rapid and taxonomically comprehensive method for revealing community structures within environmental samples, based on large amounts of sequence data produced by high-throughput sequencers. Because community structures of planktonic copepods are important in the ocean owing to their high diversity and abundance, a metagenetic analysis of the 28S D2 region using Roche 454 was previously developed. However, the Illumina MiSeq platform with a high sequence output is being used more frequently in metagenetics, and non-calanoid copepods have not previously been fully evaluated. Here, we evaluated an Illumina MiSeq-based metagenetic analysis using a mock community and field-collected samples that were examined in a previous study using Roche 454, and the community structure, including non-calanoid copepods, was compared among morphological and metagenetic analyses. We removed a singleton read and applied an appropriate abundance threshold to remove erroneous Molecular Operational Taxonomic Units (MOTUs) with low-abundance sequences in the MiSeq-based analysis. Results showed that the copepod community was successfully characterized using Illumina MiSeq. Higher-quality sequences were obtained using MiSeq than by Roche 454, which reduced the overestimation of diversity, especially at a strict 99% similarity threshold for MOTU clustering. Taxonomic compositions in terms of both biomass and presence/absence of species, including non-calanoids, were more appropriately represented in the MiSeq- than in Roche 454-based analysis. Our data showed that metagenetic analysis using Illumina MiSeq is more useful for revealing copepod communities than Roche 454, owing to the lower cost and higher quality.}, } @article {pmid28714286, year = {2017}, author = {Bozic, J and Capone, A and Pediconi, D and Mensah, P and Cappelli, A and Valzano, M and Mancini, MV and Scuppa, P and Martin, E and Epis, S and Rossi, P and Favia, G and Ricci, I}, title = {Mosquitoes can harbour yeasts of clinical significance and contribute to their environmental dissemination.}, journal = {Environmental microbiology reports}, volume = {9}, number = {5}, pages = {642-648}, doi = {10.1111/1758-2229.12569}, pmid = {28714286}, issn = {1758-2229}, mesh = {Animals ; Culicidae/*microbiology ; *Environment ; Female ; *Host-Pathogen Interactions ; Male ; Metagenome ; Metagenomics/methods ; Microbiota ; Polymerase Chain Reaction ; *Yeasts/classification/genetics/isolation & purification ; }, abstract = {There is still a lack of studies on fungal microbiota in mosquitoes, compared with the number available on bacterial microbiota. This study reports the identification of yeasts of clinical significance in laboratory mosquito species: Anopheles gambiae, Anopheles stephensi, Culex quinquefasciatus, Aedes albopictus and Aedes aegypti. Among the yeasts isolated, they focused on the opportunistic pathogen Candida parapsilosis, since there is a need to better understand breakthrough candidaemia with resistance to the usual antifungals, which requires careful consideration in the broad-spectrum therapy, as documented in many clinical reports. C. parapsilosis occurs widely and has been isolated from diverse sources, including insects, which may contribute to its dissemination. In this study, it was isolated from the gut of An. gambiae and its presence in developmental stages and organs of different mosquito species was studied. Our results indicated that there was a stable association between C. parapsilosis and reared mosquitoes during the entire life cycle, and in adult male and female gut and gonads. A wide occurrence of C. parapsilosis was also documented in several populations of wild mosquitoes. Based on these findings, it can be said that mosquitoes might participate in the spreading of this opportunistic pathogen, not only as a carrier.}, } @article {pmid28711820, year = {2017}, author = {Chen, Z and Zheng, Y and Ding, C and Ren, X and Yuan, J and Sun, F and Li, Y}, title = {Integrated metagenomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops.}, journal = {Ecotoxicology and environmental safety}, volume = {145}, number = {}, pages = {111-118}, doi = {10.1016/j.ecoenv.2017.07.019}, pmid = {28711820}, issn = {1090-2414}, mesh = {Biodegradation, Environmental ; *Biofuels ; Cadmium/*analysis/metabolism ; *Metagenomics ; Microbial Consortia/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil Microbiology/standards ; Soil Pollutants/*analysis/metabolism ; Glycine max/*growth & development/metabolism ; Zea mays/*growth & development/metabolism ; }, abstract = {Two energy crops (maize and soybean) were used in the remediation of cadmium-contaminated soils. These crops were used because they are fast growing, have a large biomass and are good sources for bioenergy production. The total accumulation of cadmium in maize and soybean plants was 393.01 and 263.24μg pot[-1], respectively. The rhizosphere bacterial community composition was studied by MiSeq sequencing. Phylogenetic analysis was performed using 16S rRNA gene sequences. The rhizosphere bacteria were divided into 33 major phylogenetic groups according to phyla. The dominant phylogenetic groups included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes. Based on principal component analysis (PCA) and unweighted pair group with arithmetic mean (UPGMA) analysis, we found that the bacterial community was influenced by cadmium addition and bioenergy cropping. Three molecular ecological networks were constructed for the unplanted, soybean- and maize-planted bacterial communities grown in 50mgkg[-1] cadmium-contaminated soils. The results indicated that bioenergy cropping increased the complexity of the bacterial community network as evidenced by a higher total number of nodes, the average geodesic distance (GD), the modularity and a shorter geodesic distance. Proteobacteria and Acidobacteria were the keystone bacteria connecting different co-expressed operational taxonomic units (OTUs). The results showed that bioenergy cropping altered the topological roles of individual OTUs and keystone populations. This is the first study to reveal the effects of bioenergy cropping on microbial interactions in the phytoremediation of cadmium-contaminated soils by network reconstruction. This method can greatly enhance our understanding of the mechanisms of plant-microbe-metal interactions in metal-polluted ecosystems.}, } @article {pmid28710513, year = {2017}, author = {Zhao, H and Sun, W and Wang, Z and Zhang, T and Fan, Y and Gu, H and Li, G}, title = {Mink (Mustela vison) Gut Microbial Communities from Northeast China and Its Internal Relationship with Gender and Food Additives.}, journal = {Current microbiology}, volume = {74}, number = {10}, pages = {1169-1177}, pmid = {28710513}, issn = {1432-0991}, support = {No. 20150101112JC//Natural Science Foundation of Science and Technology Department of Jilin Province, China/ ; }, mesh = {Animals ; Biodiversity ; Computational Biology ; Evolution, Molecular ; Female ; Food Additives ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Male ; *Metagenome ; *Metagenomics/methods ; Mink/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sex Factors ; }, abstract = {It is well documented that the microbial interactions and biodiversity play an important role in health and disease in mammalian species. There is a rare study about gut microbiota of Mustelidae family. In this study, 40 male and female minks from Northeast China were divided into three groups and fed until they reached maturity. The V3 region of 16S rRNA genes was amplified and sequenced using NGS. There were 526 OTUs principally concentrated among five bacterial phyla. Two points about mink's body weight gaining were observed: (1) the weight of male individuals increased more rapidly than female individuals; (2) the weight of individuals whose feed was supplemented with Chinese herb additives increased more rapidly than individuals without giving food additives. The differences of microorganism abundance were shown in two points: (1) two genera which had ≥2-fold change difference were found between male and female minks. (2) Ten genera which had a ≥2-fold change difference were found among minks with and without Chinese herb additive. Findings from this study provide new and fundamental knowledge on the gut microbiota composition of minks farmed in Northeast China, which can contribute to the general well-being of minks worldwide.}, } @article {pmid28709472, year = {2017}, author = {Tanca, A and Abbondio, M and Palomba, A and Fraumene, C and Manghina, V and Cucca, F and Fiorillo, E and Uzzau, S}, title = {Potential and active functions in the gut microbiota of a healthy human cohort.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {79}, pmid = {28709472}, issn = {2049-2618}, support = {HHSN271201100005C/DA/NIDA NIH HHS/United States ; N01AG12109/AG/NIA NIH HHS/United States ; }, mesh = {Adult ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Biosynthetic Pathways ; Carbohydrate Metabolism ; Cohort Studies ; Faecalibacterium/genetics/isolation & purification/metabolism ; Fatty Acids, Volatile/metabolism ; Female ; Firmicutes/genetics/isolation & purification/metabolism ; *Gastrointestinal Microbiome/genetics/physiology ; Healthy Volunteers ; Homeostasis ; Humans ; Italy ; Male ; Metagenome ; *Metagenomics ; Middle Aged ; *Proteomics ; Young Adult ; }, abstract = {BACKGROUND: The study of the gut microbiota (GM) is rapidly moving towards its functional characterization by means of shotgun meta-omics. In this context, there is still no consensus on which microbial functions are consistently and constitutively expressed in the human gut in physiological conditions. Here, we selected a cohort of 15 healthy subjects from a native and highly monitored Sardinian population and analyzed their GMs using shotgun metaproteomics, with the aim of investigating GM functions actually expressed in a healthy human population. In addition, shotgun metagenomics was employed to reveal GM functional potential and to compare metagenome and metaproteome profiles in a combined taxonomic and functional fashion.

RESULTS: Metagenomic and metaproteomic data concerning the taxonomic structure of the GM under study were globally comparable. On the contrary, a considerable divergence between genetic potential and functional activity of the human healthy GM was observed, with the metaproteome displaying a higher plasticity, compared to the lower inter-individual variability of metagenome profiles. The taxon-specific contribution to functional activities and metabolic tasks was also examined, giving insights into the peculiar role of several GM members in carbohydrate metabolism (including polysaccharide degradation, glycan transport, glycolysis, and short-chain fatty acid production). Noteworthy, Firmicutes-driven butyrogenesis (mainly due to Faecalibacterium spp.) was shown to be the metabolic activity with the highest expression rate and the lowest inter-individual variability in the study cohort, in line with the previously reported importance of the biosynthesis of this microbial product for the gut homeostasis.

CONCLUSIONS: Our results provide detailed and taxon-specific information regarding functions and pathways actively working in a healthy GM. The reported discrepancy between expressed functions and functional potential suggests that caution should be used before drawing functional conclusions from metagenomic data, further supporting metaproteomics as a fundamental approach to characterize the human GM metabolic functions and activities.}, } @article {pmid28704556, year = {2017}, author = {Wang, HL and Zhang, J and Sun, QL and Lian, C and Sun, L}, title = {A comparative study revealed first insights into the diversity and metabolisms of the microbial communities in the sediments of Pacmanus and Desmos hydrothermal fields.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0181048}, pmid = {28704556}, issn = {1932-6203}, mesh = {Carbon Dioxide/metabolism ; Gammaproteobacteria/genetics/isolation & purification/metabolism ; Geologic Sediments/*microbiology ; Hydrothermal Vents/*microbiology ; *Microbiota ; Nitrogen/metabolism ; Proteobacteria/genetics/isolation & purification/metabolism ; Sulfur/metabolism ; }, abstract = {Currently, little is known about the microbial diversity in the sediments of Pacmanus and Desmos hydrothermal fields in Manus Basin. In this study, Illumina-based sequencing of 16S rRNA gene amplicons and metagenomic analysis were conducted to investigate the microbial populations and metabolic profiles in the sediments from four different regions in Pacmanus and Desmos hydrothermal fields. It was found that Gammaproteobacteria and Thaumarchaeota were the most abundant bacterial and archaeal populations, respectively. The autotrophic prokaryotes in the four communities probably fixed CO2 via four major pathways, i.e. Calvin-Benson-Bassham cycle, reductive acetyl-CoA cycle, rTCA cycle, and 3-hydroxypropionate/4-hydroxybutyrate cycle. Ammonia-oxidizing Thaumarchaeota, nitrifiers, denitrifiers, and sulfur oxidizers belonging to the subgroups of Proteobacteria (e.g., alpha, beta, gamma, and epsilon), Nitrospira, and Nitrospina, and sulfate-reducing Desulfobacterales likely played critical roles in nitrogen and sulfur cycling, in which ammonia, sulfur compounds, and hydrogen could be utilized as potential energy sources. These findings revealed new insights into the operational mechanism of the microbial communities associated with Pacmanus and Desmos hydrothermal fields.}, } @article {pmid28704437, year = {2017}, author = {Lai, PS and Allen, JG and Hutchinson, DS and Ajami, NJ and Petrosino, JF and Winters, T and Hug, C and Wartenberg, GR and Vallarino, J and Christiani, DC}, title = {Impact of environmental microbiota on human microbiota of workers in academic mouse research facilities: An observational study.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0180969}, pmid = {28704437}, issn = {1932-6203}, support = {K23 ES023700/ES/NIEHS NIH HHS/United States ; P30 ES000002/ES/NIEHS NIH HHS/United States ; T32 ES007069/ES/NIEHS NIH HHS/United States ; T42 OH008416/OH/NIOSH CDC HHS/United States ; }, mesh = {Air Pollutants, Occupational/analysis ; Animal Technicians ; Animals ; Bacteria/*classification/genetics ; DNA, Bacterial/genetics ; Endotoxins/*genetics ; Humans ; Medical Laboratory Personnel ; Mice ; *Microbiota ; Mouth/microbiology ; Nose/microbiology ; Occupational Exposure/*classification ; RNA, Ribosomal, 16S/*genetics ; Skin/microbiology ; }, abstract = {OBJECTIVES: To characterize the microbial environment of workers in academic mouse research facilities using endotoxin, 16S qPCR, and 16S amplicon sequencing. To determine whether the work microbiome contributes to the human microbiome of workers.

METHODS: We performed area air sampling from the animal rooms, dirty, middle, and setup cage wash locations in four academic mouse research facilities. 10 workers in the dirty cage wash area underwent personal air sampling as well as repeated collection of nasal, oral, and skin samples before and after the work shift. Environmental samples underwent measurement of endotoxin, mouse allergen, bacteria copy number via 16S qPCR, and microbial identification via 16S rDNA sequencing. 16S rDNA sequencing was also performed on human samples before and after the work shift. SourceTracker was used to identify the contribution of the work microbiome to the human microbiome.

RESULTS: Median endotoxin levels ranged from undetectable to 1.0 EU/m3. Significant differences in mouse allergen levels, bacterial copy number, microbial richness, and microbial community structure were identified between animal, dirty, middle, and setup cage wash locations. Endotoxin levels had only a moderate correlation with microbial composition. Location within a facility was a stronger predictor of microbial community composition (R2 = 0.41, p = 0.002) than facility. The contribution of the work microbiome to the pre-shift human microbiome of workers was estimated to be 0.1 ± 0.1% for the oral microbiome; 3.1 ± 1.9% for the nasal microbiome; and 3.0 ± 1.5% for the skin microbiome.

CONCLUSIONS: The microbial environment of academic animal care facilities varies significantly by location rather than facility. Endotoxin is not a proxy for assessment of environmental microbial exposures using 16S qPCR or 16S rDNA sequencing. The work microbiome contributes to the composition of the nasal and skin microbiome of workers; the clinical implications of this observation should be further studied.}, } @article {pmid28703874, year = {2017}, author = {Tao, Y and Wang, X and Li, X and Wei, N and Jin, H and Xu, Z and Tang, Q and Zhu, X}, title = {The functional potential and active populations of the pit mud microbiome for the production of Chinese strong-flavour liquor.}, journal = {Microbial biotechnology}, volume = {10}, number = {6}, pages = {1603-1615}, pmid = {28703874}, issn = {1751-7915}, mesh = {Alcoholic Beverages/analysis/*microbiology ; Aluminum Silicates/*chemistry ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Caproates/analysis/metabolism ; China ; Clay ; Fermentation ; Flavoring Agents/analysis/*metabolism ; *Microbiota ; }, abstract = {The popular distilled Chinese strong-flavour liquor (CSFL) is produced by solid fermentation in the ground pit. Microbes inhabiting in the pit mud (PM) on the walls of the fermentation pit are responsible for the production of caproic acid (CA) that determines the quality of CSFL to a large degree. However, little is known about the active microbial populations and metabolic potential of the PM microbiome. Here, we investigated the overall metabolic features of the PM microbiome and its active microbial components by combining metagenomics and MiSeq-sequencing analyses of the 16S rRNA genes from DNA and RNA (cDNA). Results showed that prokaryotes were predominant populations in the PM microbiome, accounting for 95.3% of total metagenomic reads, while eukaryotic abundance was only 1.8%. The dominant prokaryotic phyla were Firmicutes, Euryarchaeota, Bacteroidetes, Actinobacteria and Proteobacteria, accounting for 48.0%, 19.0%, 13.5%, 2.5% and 2.1% of total metagenomic reads respectively. Most genes encoding putative metabolic pathways responsible for the putative CA production via chain elongation pathway were detected. This indicated that the PM microbiome owned functional potential for synthesizing CA from ethanol or lactate. Some key genes encoding enzymes involved in hydrogenotrophic and acetoclastic methanogenesis pathways were detected in the PM metagenome, suggesting the possible occurrence of interspecies hydrogen transfer between CA-producing bacteria and methanogens. The 16S rDNA and 16S rRNA profiles showed that the Clostridial cluster IV, Lactobacillus, Caloramator, Clostridium, Sedimentibacter, Bacteroides and Porphyromonas were active populations in situ, in which Clostridial cluster IV and Clostridium were likely involved in the CA production. This study improved our understandings on the active populations and metabolic pathways of the PM microbiome involved in the CA synthesis in the CSFL fermentation.}, } @article {pmid28702706, year = {2018}, author = {Espínola, F and Dionisi, HM and Borglin, S and Brislawn, CJ and Jansson, JK and Mac Cormack, WP and Carroll, J and Sjöling, S and Lozada, M}, title = {Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {123-139}, pmid = {28702706}, issn = {1432-184X}, support = {CSP proposal ID 328//Joint Genome Institute/ ; ANPCyT PICT2008 Nº 0468//National Agency for the Promotion of Science and Technology of Argentina/ ; 112-200801-01736//CONICET/ ; UBA 20020100100378//Secretaria de Ciencia y Tecnica, Universidad de Buenos Aires/ ; grant No. 228107//Research Council of Norway/ ; DE-AC05-76RL01830//Laboratory Directed Research and Development Program at PNNL/ ; }, mesh = {Anaerobiosis ; Bacteria/classification/*genetics/isolation & purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Cold Climate ; DNA, Bacterial/genetics ; Geologic Sediments/*microbiology ; Hydrocarbons/*metabolism ; Metagenomics ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.}, } @article {pmid28701177, year = {2017}, author = {Stewart, CJ and Embleton, ND and Marrs, ECL and Smith, DP and Fofanova, T and Nelson, A and Skeath, T and Perry, JD and Petrosino, JF and Berrington, JE and Cummings, SP}, title = {Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {75}, pmid = {28701177}, issn = {2049-2618}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; }, mesh = {Acetic Acid/metabolism ; Bacterial Translocation ; Bifidobacterium/isolation & purification/physiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/*physiology ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Infant, Premature, Diseases/diagnosis/*microbiology ; *Metabolome ; Metabolomics/methods ; Neonatal Sepsis/diagnosis/*microbiology ; Raffinose/metabolism ; Sucrose/metabolism ; }, abstract = {BACKGROUND: Late onset sepsis (LOS) in preterm infants is associated with considerable morbidity and mortality. While studies have implicated gut bacteria in the aetiology of the disease, functional analysis and mechanistic insights are generally lacking. We performed temporal bacterial (n = 613) and metabolomic (n = 63) profiling on extensively sampled stool from 7 infants with LOS and 28 matched healthy (no LOS or NEC) controls.

RESULTS: The bacteria isolated in diagnostic blood culture usually corresponded to the dominant bacterial genera in the gut microbiome. Longitudinal changes were monitored based on preterm gut community types (PGCTs), where control infants had an increased number of PGCTs compared to LOS infants (P = 0.011). PGCT 6, characterised by Bifidobacteria dominance, was only present in control infants. Metabolite profiles differed between LOS and control infants at diagnosis and 7 days later, but not 7 days prior to diagnosis. Bifidobacteria was positively correlated with control metabolites, including raffinose, sucrose, and acetic acid.

CONCLUSIONS: Using multi-omic analysis, we show that the gut microbiome is involved in the pathogenesis of LOS. While the causative agent of LOS varies, it is usually abundant in the gut. Bifidobacteria dominance was associated with control infants, and the presence of this organism may directly protect, or act as a marker for protection, against gut epithelial translocation. While the metabolomic data is preliminary, the findings support that gut development and protection in preterm infants is associated with increased in prebiotic oligosaccharides (e.g. raffinose) and the growth of beneficial bacteria (e.g. Bifidobacterium).}, } @article {pmid28700218, year = {2017}, author = {Sun, W and Xiao, E and Xiao, T and Krumins, V and Wang, Q and Häggblom, M and Dong, Y and Tang, S and Hu, M and Li, B and Xia, B and Liu, W}, title = {Response of Soil Microbial Communities to Elevated Antimony and Arsenic Contamination Indicates the Relationship between the Innate Microbiota and Contaminant Fractions.}, journal = {Environmental science & technology}, volume = {51}, number = {16}, pages = {9165-9175}, doi = {10.1021/acs.est.7b00294}, pmid = {28700218}, issn = {1520-5851}, mesh = {*Antimony ; *Arsenic ; China ; Environmental Monitoring ; Humans ; Microbiota ; RNA, Ribosomal, 16S ; Soil ; *Soil Microbiology ; *Soil Pollutants ; }, abstract = {Mining of sulfide ore deposits containing metalloids, such as antimony and arsenic, has introduced serious soil contamination around the world, posing severe threats to food safety and human health. Hence, it is important to understand the behavior and composition of the microbial communities that control the mobilization or sequestration of these metal(loid)s. Here, we selected two sites in Southwest China with different levels of Sb and As contamination to study interactions among various Sb and As fractions and the soil microbiota, with a focus on the microbial response to metalloid contamination. Comprehensive geochemical analyses and 16S rRNA gene amplicon sequencing demonstrated distinct soil taxonomic inventories depending on Sb and As contamination levels. Stochastic gradient boosting indicated that citric acid extractable Sb(V) and As(V) contributed 5% and 15%, respectively, to influencing the community diversity. Random forest predicted that low concentrations of Sb(V) and As(V) could enhance the community diversity but generally, the Sb and As contamination impairs microbial diversity. Co-occurrence network analysis indicated a strong correlation between the indigenous microbial communities and various Sb and As fractions. A number of taxa were identified as core genera due to their elevated abundances and positive correlation with contaminant fractions (total Sb and As concentrations, bioavailable Sb and As extractable fractions, and Sb and As redox species). Shotgun metagenomics indicated that Sb and As biogeochemical redox reactions may exist in contaminated soils. All these observations suggest the potential for bioremediation of Sb- and As-contaminated soils.}, } @article {pmid28699116, year = {2017}, author = {Thomas, P and Sekhar, AC and Shaik, SP}, title = {High taxonomic diversity of cultivation-recalcitrant endophytic bacteria in grapevine field shoots, their in vitro introduction, and unsuspected persistence.}, journal = {Planta}, volume = {246}, number = {5}, pages = {879-898}, pmid = {28699116}, issn = {1432-2048}, support = {AMASS project//National Bureau of Agriculturally Important Microorganisms/ ; }, mesh = {Bacteria/classification/*genetics/isolation & purification ; Biodiversity ; Endophytes ; *Metagenomics ; Plant Shoots/microbiology ; Polymerase Chain Reaction ; Tissue Culture Techniques ; Vitis/*microbiology ; }, abstract = {Molecular and microscopic analyses reveal enormous non-cultivable endophytic bacteria in grapevine field shoots with functional significance. Diverse bacteria enter tissue cultures through surface-sterilized tissues and survive surreptitiously with varying taxonomic realignments. The study was envisaged to assess the extent of endophytic bacterial association with field shoot tissues of grapevine and the likelihood of introduction of such internally colonizing bacteria in vitro adopting molecular techniques targeting the non-cultivable bacterial community. PowerFood[®]-kit derived DNA from surface-sterilized field shoot tips of grapevine Flame Seedless was employed in a preliminary bacterial class-specific PCR screening proving positive for major prokaryotic taxa including Archaea. Taxonomic and functional diversity were analyzed through whole metagenome profiling (WMG) which revealed predominantly phylum Actinobacteria, Proteobacteria, and minor shares of Firmicutes, Bacteroidetes, and Deinococcus-Thermus with varying functional roles ascribable to the whole bacterial community. Field shoot tip tissues and callus derived from stem segments were further employed in 16S rRNA V3-V4 amplicon taxonomic profiling. This revealed elevated taxonomic diversity in field shoots over WMG, predominantly Proteobacteria succeeded by Actinobacteria, Firmicutes, Bacteroidetes, and 15 other phyla including several candidate phyla (135 families, 179 genera). Callus stocks also displayed broad bacterial diversity (16 phyla; 96 families; 141 genera) bearing resemblance to field tissues with Proteobacterial dominance but a reduction in its share, enrichment of Actinobacteria and Firmicutes, disappearance of some field-associated phyla and detection of a few additional taxonomic groups over field community. Similar results were documented during 16S V3-V4 amplicon taxonomic profiling on Thompson Seedless field shoot tip and callus tissues. Video microscopy on tissue homogenates corroborated enormous endophytic bacteria. This study elucidates a vast diversity of cultivation-recalcitrant endophytic bacteria prevailing in grapevine field shoots, their in vitro introduction, and unsuspecting sustenance with possible silent participation in tissue culture processes.}, } @article {pmid28698277, year = {2017}, author = {He, T and Li, H and Zhang, X}, title = {Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions.}, journal = {mBio}, volume = {8}, number = {4}, pages = {}, pmid = {28698277}, issn = {2150-7511}, mesh = {Archaea/genetics/*metabolism/virology ; Bacteria/genetics/*metabolism/virology ; Bacteriophages/genetics/*metabolism ; Ecosystem ; Hydrothermal Vents/*microbiology/*virology ; Metagenomics ; *Microbial Interactions ; Microbiota/genetics ; Oceans and Seas ; Phylogeny ; Seawater/*microbiology ; Symbiosis ; }, abstract = {Viruses are believed to be responsible for the mortality of host organisms. However, some recent investigations reveal that viruses may be essential for host survival. To date, it remains unclear whether viruses are beneficial or harmful to their hosts. To reveal the roles of viruses in the virus-host interactions, viromes and microbiomes of sediment samples from three deep-sea hydrothermal vents were explored in this study. To exclude the influence of exogenous DNAs on viromes, the virus particles were purified with nuclease (DNase I and RNase A) treatments and cesium chloride density gradient centrifugation. The metagenomic analysis of viromes without exogenous DNA contamination and microbiomes of vent samples indicated that viruses had compensation effects on the metabolisms of their host microorganisms. Viral genes not only participated in most of the microbial metabolic pathways but also formed branched pathways in microbial metabolisms, including pyrimidine metabolism; alanine, aspartate, and glutamate metabolism; nitrogen metabolism and assimilation pathways of the two-component system; selenocompound metabolism; aminoacyl-tRNA biosynthesis; and amino sugar and nucleotide sugar metabolism. As is well known, deep-sea hydrothermal vent ecosystems exist in relatively isolated environments which are barely influenced by other ecosystems. The metabolic compensation of hosts mediated by viruses might represent a very important aspect of virus-host interactions.IMPORTANCE Viruses are the most abundant biological entities in the oceans and have very important roles in regulating microbial community structure and biogeochemical cycles. The relationship between virus and host microbes is broadly thought to be that of predator and prey. Viruses can lyse host cells to control microbial population sizes and affect community structures of hosts by killing specific microbes. However, viruses also influence their hosts through manipulation of bacterial metabolism. We found that viral genes not only participated in most microbial metabolic pathways but also formed branched pathways in microbial metabolisms. The metabolic compensation of hosts mediated by viruses may help hosts to adapt to extreme environments and may be essential for host survival.}, } @article {pmid28696422, year = {2017}, author = {Slaby, BM and Hackl, T and Horn, H and Bayer, K and Hentschel, U}, title = {Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization.}, journal = {The ISME journal}, volume = {11}, number = {11}, pages = {2465-2478}, pmid = {28696422}, issn = {1751-7370}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Bacterial Physiological Phenomena ; Metagenomics ; Microbiota ; Phylogeny ; Porifera/*microbiology/physiology ; Symbiosis ; }, abstract = {Marine sponges are ancient metazoans that are populated by distinct and highly diverse microbial communities. In order to obtain deeper insights into the functional gene repertoire of the Mediterranean sponge Aplysina aerophoba, we combined Illumina short-read and PacBio long-read sequencing followed by un-targeted metagenomic binning. We identified a total of 37 high-quality bins representing 11 bacterial phyla and two candidate phyla. Statistical comparison of symbiont genomes with selected reference genomes revealed a significant enrichment of genes related to bacterial defense (restriction-modification systems, toxin-antitoxin systems) as well as genes involved in host colonization and extracellular matrix utilization in sponge symbionts. A within-symbionts genome comparison revealed a nutritional specialization of at least two symbiont guilds, where one appears to metabolize carnitine and the other sulfated polysaccharides, both of which are abundant molecules in the sponge extracellular matrix. A third guild of symbionts may be viewed as nutritional generalists that perform largely the same metabolic pathways but lack such extraordinary numbers of the relevant genes. This study characterizes the genomic repertoire of sponge symbionts at an unprecedented resolution and it provides greater insights into the molecular mechanisms underlying microbial-sponge symbiosis.}, } @article {pmid28696003, year = {2018}, author = {Malanoski, AP and Lin, B and Eddie, BJ and Wang, Z and Hervey, WJ and Glaven, SM}, title = {Relative abundance of 'Candidatus Tenderia electrophaga' is linked to cathodic current in an aerobic biocathode community.}, journal = {Microbial biotechnology}, volume = {11}, number = {1}, pages = {98-111}, pmid = {28696003}, issn = {1751-7915}, mesh = {*Bioelectric Energy Sources ; *Biota ; Carbon Dioxide/metabolism ; Chromatiaceae/classification/genetics/*isolation & purification/*metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrodes/*microbiology ; Metagenomics ; Oxidation-Reduction ; Oxygen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Biocathode microbial communities are proposed to catalyse a range of useful reactions. Unlike bioanodes, model biocathode organisms have not yet been successfully cultivated in isolation highlighting the need for culture-independent approaches to characterization. Biocathode MCL (Marinobacter, Chromatiaceae, Labrenzia) is a microbial community proposed to couple CO2 fixation to extracellular electron transfer and O2 reduction. Previous metagenomic analysis of a single MCL bioelectrochemical system (BES) resulted in resolution of 16 bin genomes. To further resolve bin genomes and compare community composition across replicate MCL BES, we performed shotgun metagenomic and 16S rRNA gene (16S) sequencing at steady-state current. Clustering pooled reads from replicate BES increased the number of resolved bin genomes to 20, over half of which were > 90% complete. Direct comparison of unassembled metagenomic reads and 16S operational taxonomic units (OTUs) predicted higher community diversity than the assembled/clustered metagenome and the predicted relative abundances did not match. However, when 16S OTUs were mapped to bin genomes and genome abundance was scaled by 16S gene copy number, estimated relative abundance was more similar to metagenomic analysis. The relative abundance of the bin genome representing 'Ca. Tenderia electrophaga' was correlated with increasing current, further supporting the hypothesis that this organism is the electroautotroph.}, } @article {pmid29878736, year = {2016}, author = {Lin, Z and Zu, XP and Xie, HS and Jin, HZ and Yang, N and Liu, XR and Zhang, WD}, title = {[Research progress in mechanism of intestinal microorganisms in human diseases].}, journal = {Yao xue xue bao = Acta pharmaceutica Sinica}, volume = {51}, number = {6}, pages = {843-852}, pmid = {29878736}, issn = {0513-4870}, mesh = {*Gastrointestinal Microbiome ; Humans ; Intestines/*microbiology ; *Metagenomics ; Symbiosis ; }, abstract = {The international cooperated research projects of the Human Microbiome Project (HMP) and Metagenomics of The Human Intestinal Tract (MetaHIT) were officially launched in 2007, which indicated the era of metagenomics research of microorganisms in human gastrointestinal tract had been coming. Each human body is a superorganism which is composed of 90% commensal microorganisms, especially the intestinal microorganisms. The intestinal microorganisms play an important role on health maintenance since they are involved in the absorption and metabolism of nutrients in the human bodies. Herein, we review the research progress in the mechanism of intestinal microorganisms in human diseases. Our purpose is to provide novel ideas on human health and therapeutic targets of diseases.}, } @article {pmid28879736, year = {2016}, author = {Ning, Y and Li, YL and Zhou, GY and Yang, LC and Xu, WH}, title = {[Community composition and diversity of endophytic fungi from roots of Sinopodophyllum hexandrum in forest of Upper-north mountain of Qinghai province].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {41}, number = {7}, pages = {1227-1234}, doi = {10.4268/cjcmm20160712}, pmid = {28879736}, issn = {1001-5302}, mesh = {Berberidaceae/*microbiology ; Biodiversity ; China ; DNA, Fungal ; Endophytes/classification ; *Forests ; Fungi/*classification ; High-Throughput Nucleotide Sequencing ; Metagenome ; Plant Roots/*microbiology ; *Soil Microbiology ; }, abstract = {High throughput sequencing technology is also called Next Generation Sequencing (NGS), which can sequence hundreds and thousands sequences in different samples at the same time. In the present study, the culture-independent high throughput sequencing technology was applied to sequence the fungi metagenomic DNA of the fungal internal transcribed spacer 1(ITS 1) in the root of Sinopodophyllum hexandrum. Sequencing data suggested that after the quality control, 22 565 reads were remained. Cluster similarity analysis was done based on 97% sequence similarity, which obtained 517 OTUs for the three samples (LD1, LD2 and LD3). All the fungi which identified from all the reads of OTUs based on 0.8 classification thresholds using the software of RDP classifier were classified as 13 classes, 35 orders, 44 family, 55 genera. Among these genera, the genus of Tetracladium was the dominant genera in all samples(35.49%, 68.55% and 12.96%).The Shannon's diversity indices and the Simpson indices of the endophytic fungi in the samples ranged from 1.75-2.92, 0.11-0.32, respectively.This is the first time for applying high through put sequencing technol-ogyto analyze the community composition and diversity of endophytic fungi in the medicinal plant, and the results showed that there were hyper diver sity and high community composition complexity of endophytic fungi in the root of S. hexandrum. It is also proved that the high through put sequencing technology has great advantage for analyzing ecommunity composition and diversity of endophtye in the plant.}, } @article {pmid28695665, year = {2017}, author = {Auer, L and Mariadassou, M and O'Donohue, M and Klopp, C and Hernandez-Raquet, G}, title = {Analysis of large 16S rRNA Illumina data sets: Impact of singleton read filtering on microbial community description.}, journal = {Molecular ecology resources}, volume = {17}, number = {6}, pages = {e122-e132}, doi = {10.1111/1755-0998.12700}, pmid = {28695665}, issn = {1755-0998}, mesh = {Cluster Analysis ; Computational Biology/*methods ; DNA, Ribosomal/chemistry/genetics ; Metagenomics/*methods ; *Microbiota ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Next-generation sequencing technologies give access to large sets of data, which are extremely useful in the study of microbial diversity based on 16S rRNA gene. However, the production of such large data sets is not only marred by technical biases and sequencing noise but also increases computation time and disc space use. To improve the accuracy of OTU predictions and overcome both computations, storage and noise issues, recent studies and tools suggested removing all single reads and low abundant OTUs, considering them as noise. Although the effect of applying an OTU abundance threshold on α- and β-diversity has been well documented, the consequences of removing single reads have been poorly studied. Here, we test the effect of singleton read filtering (SRF) on microbial community composition using in silico simulated data sets as well as sequencing data from synthetic and real communities displaying different levels of diversity and abundance profiles. Scalability to large data sets is also assessed using a complete MiSeq run. We show that SRF drastically reduces the chimera content and computational time, enabling the analysis of a complete MiSeq run in just a few minutes. Moreover, SRF accurately determines the actual community diversity: the differences in α- and β-community diversity obtained with SRF and standard procedures are much smaller than the intrinsic variability of technical and biological replicates.}, } @article {pmid28693612, year = {2017}, author = {Xiong, W and Brown, CT and Morowitz, MJ and Banfield, JF and Hettich, RL}, title = {Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {72}, pmid = {28693612}, issn = {2049-2618}, support = {R01 GM103600/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acids/metabolism ; Bacterial Proteins/classification/genetics/isolation & purification/metabolism ; Carbohydrate Metabolism ; Fatty Acids, Volatile/biosynthesis ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics/physiology ; Humans ; Infant, Newborn ; *Infant, Premature ; Lipid Metabolism ; Metagenomics ; Proteome ; *Proteomics ; Species Specificity ; }, abstract = {BACKGROUND: Establishment of the human gut microbiota begins at birth. This early-life microbiota development can impact host physiology during infancy and even across an entire life span. However, the functional stability and population structure of the gut microbiota during initial colonization remain poorly understood. Metaproteomics is an emerging technology for the large-scale characterization of metabolic functions in complex microbial communities (gut microbiota).

RESULTS: We applied a metagenome-informed metaproteomic approach to study the temporal and inter-individual differences of metabolic functions during microbial colonization of preterm human infants' gut. By analyzing 30 individual fecal samples, we identified up to 12,568 protein groups for each of four infants, including both human and microbial proteins. With genome-resolved matched metagenomics, proteins were confidently identified at the species/strain level. The maximum percentage of the proteome detected for the abundant organisms was ~45%. A time-dependent increase in the relative abundance of microbial versus human proteins suggested increasing microbial colonization during the first few weeks of early life. We observed remarkable variations and temporal shifts in the relative protein abundances of each organism in these preterm gut communities. Given the dissimilarity of the communities, only 81 microbial EggNOG orthologous groups and 57 human proteins were observed across all samples. These conserved microbial proteins were involved in carbohydrate, energy, amino acid and nucleotide metabolism while conserved human proteins were related to immune response and mucosal maturation. We identified seven proteome clusters for the communities and showed infant gut proteome profiles were unstable across time and not individual-specific. Applying a gut-specific metabolic module (GMM) analysis, we found that gut communities varied primarily in the contribution of nutrient (carbohydrates, lipids, and amino acids) utilization and short-chain fatty acid production.

CONCLUSIONS: Overall, this study reports species-specific proteome profiles and metabolic functions of human gut microbiota during early colonization. In particular, our work contributes to reveal microbiota-associated shifts and variations in the metabolism of three major nutrient sources and short-chain fatty acid during colonization of preterm infant gut.}, } @article {pmid28692666, year = {2017}, author = {Sui, S and Yang, Y and Sun, Y and Wang, X and Wang, G and Shan, G and Wang, J and Yu, J}, title = {On the core bacterial flora of Ixodes persulcatus (Taiga tick).}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0180150}, pmid = {28692666}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/genetics ; Female ; Ixodes/*microbiology ; *Microbiota ; Phylogeny ; Sequence Analysis, DNA ; *Taiga ; }, abstract = {Ixodes persulcatus is a predominant hard tick species that transmits a wide range of human and animal pathogens. Since bacterial flora of the tick dwelling in the wild always vary according to their hosts and the environment, it is highly desirable that species-associated microbiomes are fully determined by using next-generation sequencing and based on comparative metagenomics. Here, we examine such metagenomic changes of I. persulcatus starting with samples collected from the wild ticks and followed by the reared animals under pathogen-free laboratory conditions over multiple generations. Based on high-coverage genomic sequences from three experimental groups-wild, reared for a single generation or R1, and reared for eight generations or R8 -we identify the core bacterial flora of I. persulcatus, which contains 70 species that belong to 69 genera of 8 phyla; such a core is from the R8 group, which is reduced from 4625 species belonging to 1153 genera of 29 phyla in the wild group. Our study provides a novel example of tick core bacterial flora acquired based on wild-to-reared comparison, which paves a way for future research on tick metagenomics and tick-borne disease pandemics.}, } @article {pmid28692665, year = {2017}, author = {Ellis, GA and Thomas, CS and Chanana, S and Adnani, N and Szachowicz, E and Braun, DR and Harper, MK and Wyche, TP and Bugni, TS}, title = {Brackish habitat dictates cultivable Actinobacterial diversity from marine sponges.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0176968}, pmid = {28692665}, issn = {1932-6203}, support = {R01 GM104192/GM/NIGMS NIH HHS/United States ; }, mesh = {Actinobacteria/genetics/*isolation & purification ; Animals ; *Biodiversity ; Biological Assay ; Cluster Analysis ; Discriminant Analysis ; *Ecosystem ; Least-Squares Analysis ; Metabolome ; Phylogeny ; Porifera/*microbiology ; Principal Component Analysis ; *Saline Waters ; Seawater/*microbiology ; Tropical Climate ; }, abstract = {Bacterial communities associated with marine invertebrates such as sponges and ascidians have demonstrated potential as sources of bio-medically relevant small molecules. Metagenomic analysis has shown that many of these invertebrates harbor populations of Actinobacteria, many of which are cultivable. While some populations within invertebrates are transmitted vertically, others are obtained from the environment. We hypothesized that cultivable diversity from sponges living in brackish mangrove habitats have associations with Actinobacterial populations that differ from those found in clear tropical waters. In this study, we analyzed the cultivable Actinobacterial populations from sponges found in these two distinct habitats with the aim of understanding the secondary metabolite potential. Importantly, we wanted to broadly evaluate the potential differences among these groups to guide future Actinobacterial collection strategies for the purposes of drug discovery.}, } @article {pmid28689814, year = {2017}, author = {Song, YH and Lee, KT and Baek, JY and Kim, MJ and Kwon, MR and Kim, YJ and Park, MR and Ko, H and Lee, JS and Kim, KS}, title = {Isolation and characterization of a novel endo-β-1,4-glucanase from a metagenomic library of the black-goat rumen.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {48}, number = {4}, pages = {801-808}, pmid = {28689814}, issn = {1678-4405}, mesh = {Animals ; Bacteria/classification/*enzymology/genetics/isolation & purification ; Bacterial Proteins/*chemistry/*genetics/metabolism ; Cellulase/*chemistry/*genetics/metabolism ; Cloning, Molecular ; Enzyme Stability ; Gastrointestinal Microbiome ; Goats ; Hydrogen-Ion Concentration ; Metagenome ; Metagenomics ; Rumen/*microbiology ; }, abstract = {The various types of lignocellulosic biomass found in plants comprise the most abundant renewable bioresources on Earth. In this study, the ruminal microbial ecosystem of black goats was explored because of their strong ability to digest lignocellulosic forage. A metagenomic fosmid library containing 115,200 clones was prepared from the black-goat rumen and screened for a novel cellulolytic enzyme. The KG35 gene, containing a novel glycosyl hydrolase family 5 cellulase domain, was isolated and functionally characterized. The novel glycosyl hydrolase family 5 cellulase gene is composed of a 963-bp open reading frame encoding a protein of 320 amino acid residues (35.1kDa). The deduced amino acid sequence showed the highest sequence identity (58%) for sequences from the glycosyl hydrolase family 5 cellulases. The novel glycosyl hydrolase family 5 cellulase gene was overexpressed in Escherichia coli. Substrate specificity analysis revealed that this recombinant glycosyl hydrolase family 5 cellulase functions as an endo-β-1,4-glucanase. The recombinant KG35 endo-β-1,4-glucanase showed optimal activity within the range of 30-50°C at a pH of 6-7. The thermostability was retained and the pH was stable in the range of 30-50°C at a pH of 5-7.}, } @article {pmid28686852, year = {2017}, author = {Kaysen, A and Heintz-Buschart, A and Muller, EEL and Narayanasamy, S and Wampach, L and Laczny, CC and Graf, N and Simon, A and Franke, K and Bittenbring, J and Wilmes, P and Schneider, JG}, title = {Integrated meta-omic analyses of the gastrointestinal tract microbiome in patients undergoing allogeneic hematopoietic stem cell transplantation.}, journal = {Translational research : the journal of laboratory and clinical medicine}, volume = {186}, number = {}, pages = {79-94.e1}, doi = {10.1016/j.trsl.2017.06.008}, pmid = {28686852}, issn = {1878-1810}, mesh = {Adult ; Aged ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; *Hematopoietic Stem Cell Transplantation ; Humans ; Male ; *Metabolomics ; Microbiota/*physiology ; Middle Aged ; }, abstract = {In patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT), treatment-induced changes to the gastrointestinal tract (GIT) microbiome have been linked to adverse outcomes, most notably graft-versus-host disease (GvHD). However, it is presently unknown whether this relationship is causal or consequential. Here, we performed an integrated meta-omic analysis to probe deeper into the GIT microbiome changes during allo-HSCT and its accompanying treatments. We used 16S and 18S rRNA gene amplicon sequencing to resolve archaea, bacteria, and eukaryotes within the GIT microbiomes of 16 patients undergoing allo-HSCT for the treatment of hematologic malignancies. These results revealed a major shift in the GIT microbiome after allo-HSCT including a marked reduction in bacterial diversity, accompanied by only limited changes in eukaryotes and archaea. An integrated analysis of metagenomic and metatranscriptomic data was performed on samples collected from a patient before and after allo-HSCT for acute myeloid leukemia. This patient developed severe GvHD, leading to death 9 months after allo-HSCT. In addition to drastically decreased bacterial diversity, the post-treatment microbiome showed a higher overall number and higher expression levels of antibiotic resistance genes (ARGs). One specific Escherichia coli strain causing a paravertebral abscess was linked to GIT dysbiosis, suggesting loss of intestinal barrier integrity. The apparent selection for bacteria expressing ARGs suggests that prophylactic antibiotic administration may adversely affect the overall treatment outcome. We therefore assert that such analyses including information about the selection of pathogenic bacteria expressing ARGs may assist clinicians in "personalizing" regimens for individual patients to improve overall outcomes.}, } @article {pmid28686659, year = {2017}, author = {Williams, KE and Huyvaert, KP and Piaggio, AJ}, title = {Clearing muddied waters: Capture of environmental DNA from turbid waters.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0179282}, pmid = {28686659}, issn = {1932-6203}, mesh = {Animals ; DNA/chemistry/genetics/*isolation & purification ; *Ecosystem ; Endangered Species ; Introduced Species ; Metagenomics/*methods ; Swine/*genetics ; Water/chemistry ; }, abstract = {Understanding the differences in efficiencies of various methods to concentrate, extract, and amplify environmental DNA (eDNA) is vital for best performance of eDNA detection. Aquatic systems vary in characteristics such as turbidity, eDNA concentration, and inhibitor load, thus affecting eDNA capture efficiency. Application of eDNA techniques to the detection of terrestrial invasive or endangered species may require sampling at intermittent water sources that are used for drinking and cooling; these water bodies may often be stagnant and turbid. We present our best practices technique for the detection of wild pig eDNA in water samples, a protocol that will have wide applicability to the detection of elusive vertebrate species. We determined the best practice for eDNA capture in a turbid water system was to concentrate DNA from a 15 mL water sample via centrifugation, purify DNA with the DNeasy mericon Food kit, and remove inhibitors with Zymo Inhibitor Removal Technology columns. Further, we compared the sensitivity of conventional PCR to quantitative PCR and found that quantitative PCR was more sensitive in detecting lower concentrations of eDNA. We show significant differences in efficiencies among methods in each step of eDNA capture, emphasizing the importance of optimizing best practices for the system of interest.}, } @article {pmid28686571, year = {2017}, author = {Chistoserdova, L}, title = {Application of Omics Approaches to Studying Methylotrophs and Methylotroph Comunities.}, journal = {Current issues in molecular biology}, volume = {24}, number = {}, pages = {119-142}, doi = {10.21775/cimb.024.119}, pmid = {28686571}, issn = {1467-3045}, mesh = {Aerobiosis ; Anaerobiosis ; Bacteria/*metabolism ; Metabolomics/methods ; Metagenomics/*methods ; Methane/chemistry/*metabolism ; Methanol/chemistry/*metabolism ; *Microbial Consortia ; Proteomics/methods ; }, abstract = {This review covers some recent advances in application of omics technologies to studying methylotrophs, with special reference to their activities in natural environments. Some of the developments highlighted in this review are the new outlook at the role of the XoxF-type, lanthanum-dependent methanol dehydrogenase in natural habitats, new mechanistic details of methane oxidation through the reverse methanogenesis pathway, propensity of 'aerobic' methanotrophs to thrive in hypoxic environments and potential connection of this process to denitrification, and a novel outlook at methane oxidation as a community function.}, } @article {pmid28686570, year = {2017}, author = {Mendes, LW and Braga, LPP and Navarrete, AA and Souza, DG and Silva, GGZ and Tsai, SM}, title = {Using Metagenomics to Connect Microbial Community Biodiversity and Functions.}, journal = {Current issues in molecular biology}, volume = {24}, number = {}, pages = {103-118}, doi = {10.21775/cimb.024.103}, pmid = {28686570}, issn = {1467-3045}, mesh = {Bacteria/classification/*genetics/*metabolism ; *Biodiversity ; *Ecosystem ; Metagenomics/*methods ; Phylogeny ; *Soil Microbiology ; }, abstract = {Microbes constitute about a third of the Earth's biomass and are composed by an enormous genetic diversity. In a majority of environments the microbial communities play crucial roles for the ecosystem functioning, where a drastic biodiversity alteration or loss could lead to negative effects on the environment and sustainability. A central goal in microbiome studies is to elucidate the relation between microbial diversity to functions. A better understanding of the relation diversity-function would increase the ability to manipulate that diversity to improve plant and animal health and also setting conservation priorities. The recent advances in genomic methodologies in microbial ecology have provide means to assess highly complex communities in detail, making possible the link between diversity and the functions performed by the microbes. In this work we first explore some advances in bioinformatics tools to connect the microbial community biodiversity to their potential metabolism and after present some examples of how this information can be useful for a better understanding of the microbial role in the environment.}, } @article {pmid28686567, year = {2017}, author = {Sudarikov, K and Tyakht, A and Alexeev, D}, title = {Methods for The Metagenomic Data Visualization and Analysis.}, journal = {Current issues in molecular biology}, volume = {24}, number = {}, pages = {37-58}, doi = {10.21775/cimb.024.037}, pmid = {28686567}, issn = {1467-3045}, mesh = {Bacteria/*genetics ; *Computer Graphics ; Databases, Genetic ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; }, abstract = {Surveys of environmental microbial communities using metagenomic approach produce vast volumes of multidimensional data regarding the phylogenetic and functional composition of the microbiota. Faced with such complex data, a metagenomic researcher needs to select the means for data analysis properly. Data visualization became an indispensable part of the exploratory data analysis and serves a key to the discoveries. While the molecular-genetic analysis of even a single bacterium presents multiple layers of data to be properly displayed and perceived, the studies of microbiota are significantly more challenging. Here we present a review of the state-of-art methods for the visualization of metagenomic data in a multi-level manner: from the methods applicable to an in-depth analysis of a single metagenome to the techniques appropriate for large-scale studies containing hundreds of environmental samples.}, } @article {pmid28686566, year = {2017}, author = {Odintsova, V and Tyakht, A and Alexeev, D}, title = {Guidelines to Statistical Analysis of Microbial Composition Data Inferred from Metagenomic Sequencing.}, journal = {Current issues in molecular biology}, volume = {24}, number = {}, pages = {17-36}, doi = {10.21775/cimb.024.017}, pmid = {28686566}, issn = {1467-3045}, mesh = {Algorithms ; Computational Biology/*methods ; Data Interpretation, Statistical ; *Guidelines as Topic ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; *Microbiota ; *Software ; }, abstract = {Metagenomics, the application of high-throughput DNA sequencing for surveys of environmental samples, has revolutionized our view on the taxonomic and genetic composition of complex microbial communities. An enormous richness of microbiota keeps unfolding in the context of various fields ranging from biomedicine and food industry to geology. Primary analysis of metagenomic reads allows to infer semi-quantitative data describing the community structure. However, such compositional data possess statistical specific properties that are important to be considered during preprocessing, hypothesis testing and interpreting the results of statistical tests. Failure to account for these specifics may lead to essentially wrong conclusions as a result of the survey. Here we present a researcher introduced to the field of metagenomics with the basic properties of microbial compositional data including statistical power and proposed distribution models, perform a review of the publicly available software tools developed specifically for such data and outline the recommendations for the application of the methods.}, } @article {pmid28686565, year = {2017}, author = {Marco, D}, title = {Integration of Ecology and Environmental Metagenomics Conceptual and Methodological Frameworks.}, journal = {Current issues in molecular biology}, volume = {24}, number = {}, pages = {1-16}, doi = {10.21775/cimb.024.001}, pmid = {28686565}, issn = {1467-3045}, mesh = {*Biodiversity ; Computational Biology/*methods ; Ecology/*methods ; Ecosystem ; Environment ; Humans ; Metagenomics/*methods ; Models, Theoretical ; }, abstract = {Although from its origin metagenomics was concerned with composition of communities of microbial OTUs (Operational Taxonomic Units) living in a given habitat and their diversity and functional heterogeneity (concepts already well rooted in ecology), the new field was more 'environmentally' than 'ecologically' oriented. Probably by circumstantial reasons, metagenomics and ecology followed rather independent trajectories and conceptual and methodological gaps appeared. Recently, calls for the need of integrating the theoretical basis and methodologies coming from metagenomics (and other meta-omics) and ecology have been made. Here I will address some of the principles and methods of field ecology that, although useful in the context of environmental metagenomic studies, have been rather disregarded. In particular, I will emphasize the contribution of some well established concepts and methods of field ecology to a an appropriate field sampling and experimental design of environmental metagenomic studies.}, } @article {pmid28683828, year = {2017}, author = {Ren, J and Ahlgren, NA and Lu, YY and Fuhrman, JA and Sun, F}, title = {VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {69}, pmid = {28683828}, issn = {2049-2618}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology/methods ; DNA, Viral/*genetics ; Gastrointestinal Microbiome ; *Genome, Viral ; Humans ; Liver Cirrhosis/virology ; Machine Learning ; Metagenome ; Metagenomics/*methods ; Phylogeny ; Sequence Analysis, DNA ; *Software ; }, abstract = {BACKGROUND: Identifying viral sequences in mixed metagenomes containing both viral and host contigs is a critical first step in analyzing the viral component of samples. Current tools for distinguishing prokaryotic virus and host contigs primarily use gene-based similarity approaches. Such approaches can significantly limit results especially for short contigs that have few predicted proteins or lack proteins with similarity to previously known viruses.

METHODS: We have developed VirFinder, the first k-mer frequency based, machine learning method for virus contig identification that entirely avoids gene-based similarity searches. VirFinder instead identifies viral sequences based on our empirical observation that viruses and hosts have discernibly different k-mer signatures. VirFinder's performance in correctly identifying viral sequences was tested by training its machine learning model on sequences from host and viral genomes sequenced before 1 January 2014 and evaluating on sequences obtained after 1 January 2014.

RESULTS: VirFinder had significantly better rates of identifying true viral contigs (true positive rates (TPRs)) than VirSorter, the current state-of-the-art gene-based virus classification tool, when evaluated with either contigs subsampled from complete genomes or assembled from a simulated human gut metagenome. For example, for contigs subsampled from complete genomes, VirFinder had 78-, 2.4-, and 1.8-fold higher TPRs than VirSorter for 1, 3, and 5 kb contigs, respectively, at the same false positive rates as VirSorter (0, 0.003, and 0.006, respectively), thus VirFinder works considerably better for small contigs than VirSorter. VirFinder furthermore identified several recently sequenced virus genomes (after 1 January 2014) that VirSorter did not and that have no nucleotide similarity to previously sequenced viruses, demonstrating VirFinder's potential advantage in identifying novel viral sequences. Application of VirFinder to a set of human gut metagenomes from healthy and liver cirrhosis patients reveals higher viral diversity in healthy individuals than cirrhosis patients. We also identified contig bins containing crAssphage-like contigs with higher abundance in healthy patients and a putative Veillonella genus prophage associated with cirrhosis patients.

CONCLUSIONS: This innovative k-mer based tool complements gene-based approaches and will significantly improve prokaryotic viral sequence identification, especially for metagenomic-based studies of viral ecology.}, } @article {pmid28683448, year = {2018}, author = {Lopetuso, LR and Petito, V and Graziani, C and Schiavoni, E and Paroni Sterbini, F and Poscia, A and Gaetani, E and Franceschi, F and Cammarota, G and Sanguinetti, M and Masucci, L and Scaldaferri, F and Gasbarrini, A}, title = {Gut Microbiota in Health, Diverticular Disease, Irritable Bowel Syndrome, and Inflammatory Bowel Diseases: Time for Microbial Marker of Gastrointestinal Disorders.}, journal = {Digestive diseases (Basel, Switzerland)}, volume = {36}, number = {1}, pages = {56-65}, doi = {10.1159/000477205}, pmid = {28683448}, issn = {1421-9875}, mesh = {Adult ; Biomarkers/*metabolism ; Diverticular Diseases/*microbiology ; Female ; *Gastrointestinal Microbiome ; *Health ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Irritable Bowel Syndrome/*microbiology ; Male ; Middle Aged ; Phylogeny ; Principal Component Analysis ; Species Specificity ; }, abstract = {Few data exist on differences in gut microbiota composition among principal gastrointestinal (GI) diseases. We evaluated the differences in gut microbiota composition among uncomplicated diverticular disease (DD), irritable bowel syndrome (IBS) and inflammatory bowel diseases (IBD) patients. DD, IBS, and IBD patients along with healthy controls (CT) were enrolled in our Italian GI outpatient clinic. Stool samples were collected. Microbiota composition was evaluated through a metagenomic gene-targeted approach. GI pathology represented a continuous spectrum of diseases where IBD displayed one extreme, while CT displayed the other. Among Phyla, Biplot PC2/PC3 and dendogram plot showed major differences in samples from IBS and IBD. DD resembled species CT composition, but not for Bacteroides fragilis. In IBS, Dialister spp. and then Faecalibacterium prausnitzii were the most representative species. Ulcerative colitis showed a reduced concentration of Clostridium difficile and an increase of Bacteroides fragilis. In Crohn's disease, Parabacteroides distasonis was the most represented, while Faecalibacterium prausnitzii and Bacteroides fragilis were significantly reduced. Each disorder has its definite overall microbial signature, which produces a clear differentiation from the others. On the other hand, shared alterations constitute the "core dysbiosis" of GI diseases. The assessment of these microbial markers represents a parameter that may complete the diagnostic assessment.}, } @article {pmid28681284, year = {2017}, author = {Wolinska, A and Frąc, M and Oszust, K and Szafranek-Nakonieczna, A and Zielenkiewicz, U and Stępniewska, Z}, title = {Microbial biodiversity of meadows under different modes of land use: catabolic and genetic fingerprinting.}, journal = {World journal of microbiology & biotechnology}, volume = {33}, number = {8}, pages = {154}, pmid = {28681284}, issn = {1573-0972}, mesh = {Bacteria/*classification/*genetics/*metabolism ; *Biodiversity ; Carbon/metabolism ; DNA Fingerprinting ; DNA, Bacterial/analysis/genetics ; Ecosystem ; *Grassland ; High-Throughput Nucleotide Sequencing ; Metagenome ; Phylogeny ; Poland ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The main goal of the study was to find differences in the bacterial community structure resulting from different ways of meadow management in order to get the first insight into microbial biodiversity in meadow samples. The next generation sequencing technique (454-pyrosequencing) was accompanied with the community level physiological profiling (CLPP) method in order to acquire combined knowledge of both genetic and catabolic bacterial fingerprinting of two studied meadows (hayland and pasture). Soil samples (FAO: Mollic Gleysol) were taken in April 2015 from the surface layer (0-20 cm). Significant differences of the bacterial community structure between the two analyzed meadows resulted from different land mode were evidenced by pyrosequencing and CLPP techniques. It was found that Alpha- and Gammaproteobacteria dominated in the hayland, whereas Delta- and Betaproteobacteria prevailed in the pasture. Additionally, the hayland displayed lower Firmicutes diversity than the pasture. Predominant bacterial taxa: Acidobacteria, together with Chloroflexi and Bacteroidetes seemed to be insensitive to the mode of land use, because their abundance remained at a similar level in the both studied meadows. The CLPP analysis confirmed much faster degradation of the carbon sources by microorganisms from the hayland rather than from the pasture. Amino acids were the most favoured carbon source groups utilized by microorganisms in contrast to carbohydrates, which were utilized to the lowest extent. The study clearly proved that the consequences of even moderate anthropogenic management are always changes in bacterial community structure and their metabolic activity. Bacterial taxa that are sensitive and resistant on modes of land use were determined.}, } @article {pmid28680419, year = {2017}, author = {Cabello-Yeves, PJ and Haro-Moreno, JM and Martin-Cuadrado, AB and Ghai, R and Picazo, A and Camacho, A and Rodriguez-Valera, F}, title = {Novel Synechococcus Genomes Reconstructed from Freshwater Reservoirs.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1151}, pmid = {28680419}, issn = {1664-302X}, abstract = {Freshwater picocyanobacteria including Synechococcus remain poorly studied at the genomic level, compared to their marine representatives. Here, using a metagenomic assembly approach we discovered two novel Synechococcus sp. genomes from two freshwater reservoirs Tous and Lake Lanier, both sharing 96% average nucleotide identity and displaying high abundance levels in these two lakes located at similar altitudes and temperate latitudes. These new genomes have the smallest estimated size (2.2 Mb) and average intergenic spacer length (20 bp) of any previously sequenced freshwater Synechococcus, which may contribute to their success in oligotrophic freshwater systems. Fluorescent in situ hybridization confirmed that Synechococcus sp. Tous comprises small cells (0.987 ± 0.139 μm length, 0.723 ± 0.119 μm width) that amount to 90% of the picocyanobacteria in Tous. They appear together in a phylogenomic tree with Synechococcus sp. RCC307 strain, the main representative of sub-cluster 5.3 that has itself one of the smallest marine Synechococcus genomes. We detected a type II phycobilisome (PBS) gene cluster in both genomes, which suggests that they belong to a phycoerythrin-rich pink low-light ecotype. The decrease of acidic proteins and the higher content of basic transporters and membrane proteins in the novel Synechococcus genomes, compared to marine representatives, support their freshwater specialization. A sulfate Cys transporter which is absent in marine but has been identified in many freshwater cyanobacteria was also detected in Synechococcus sp. Tous. The RuBisCo subunits from this microbe are phylogenetically close to the freshwater amoeba Paulinella chromatophora symbiont, hinting to a freshwater origin of the carboxysome operon of this protist. The novel genomes enlarge the known diversity of freshwater Synechococcus and improve the overall knowledge of the relationships among members of this genus at large.}, } @article {pmid28679747, year = {2017}, author = {Malik, AA and Thomson, BC and Whiteley, AS and Bailey, M and Griffiths, RI}, title = {Bacterial Physiological Adaptations to Contrasting Edaphic Conditions Identified Using Landscape Scale Metagenomics.}, journal = {mBio}, volume = {8}, number = {4}, pages = {}, pmid = {28679747}, issn = {2150-7511}, mesh = {*Adaptation, Physiological ; Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Biodiversity ; Ecosystem ; Genome, Bacterial ; Hydrogen-Ion Concentration ; Metagenomics/*methods ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; United Kingdom ; }, abstract = {Environmental factors relating to soil pH are important regulators of bacterial taxonomic biodiversity, yet it remains unclear if such drivers affect community functional potential. To address this, we applied whole-genome metagenomics to eight geographically distributed soils at opposing ends of a landscape soil pH gradient (where "low-pH" is ~pH 4.3 and "high-pH" is ~pH 8.3) and evaluated functional differences with respect to functionally annotated genes. First, differences in taxonomic and functional diversity between the two pH categories were assessed with respect to alpha diversity (mean sample richness) and gamma diversity (total richness pooled for each pH category). Low-pH soils, also exhibiting higher organic matter and moisture, consistently had lower taxonomic alpha and gamma diversity, but this was not apparent in assessments of functional alpha and gamma diversity. However, coherent changes in the relative abundances of annotated genes between low- and high-pH soils were identified; with strong multivariate clustering of samples according to pH independent of geography. Assessment of indicator genes revealed that the acidic organic-rich soils possessed a greater abundance of cation efflux pumps, C and N direct fixation systems, and fermentation pathways, indicating adaptations to both acidity and anaerobiosis. Conversely, high-pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings highlight the distinctive physiological adaptations required for bacteria to survive in soils of various nutrient availability and edaphic conditions and more generally indicate that bacterial functional versatility with respect to functional gene annotations may not be constrained by taxonomy.IMPORTANCE Over a set of soil samples spanning Britain, the widely reported reductions in bacterial taxonomic richness at low pH were found not to be accompanied by significant reductions in the richness of functional genes. However, consistent changes in the abundance of related functional genes were observed, characteristic of differential ecological and nutrient acquisition strategies between high-pH mineral soils and low-pH organic anaerobic soils. Our assessment at opposing ends of a soil gradient encapsulates the limits of functional diversity in temperate climates and identifies key pathways that may serve as indicators for soil element cycling and C storage processes in other soil systems. To this end, we make available a data set identifying functional indicators of the different soils; as well as raw sequences, which given the geographic scale of our sampling should be of value in future studies assessing novel genetic diversity of a wide range of soil functional attributes.}, } @article {pmid28677677, year = {2017}, author = {Coutinho, FH and Silveira, CB and Gregoracci, GB and Thompson, CC and Edwards, RA and Brussaard, CPD and Dutilh, BE and Thompson, FL}, title = {Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {15955}, pmid = {28677677}, issn = {2041-1723}, abstract = {Marine viruses are key drivers of host diversity, population dynamics and biogeochemical cycling and contribute to the daily flux of billions of tons of organic matter. Despite recent advancements in metagenomics, much of their biodiversity remains uncharacterized. Here we report a data set of 27,346 marine virome contigs that includes 44 complete genomes. These outnumber all currently known phage genomes in marine habitats and include members of previously uncharacterized lineages. We designed a new method for host prediction based on co-occurrence associations that reveals these viruses infect dominant members of the marine microbiome such as Prochlorococcus and Pelagibacter. A negative association between host abundance and the virus-to-host ratio supports the recently proposed Piggyback-the-Winner model of reduced phage lysis at higher host densities. An analysis of the abundance patterns of viruses throughout the oceans revealed how marine viral communities adapt to various seasonal, temperature and photic regimes according to targeted hosts and the diversity of auxiliary metabolic genes.}, } @article {pmid28677326, year = {2017}, author = {Jacob, JH and Hussein, EI and Shakhatreh, MAK and Cornelison, CT}, title = {Microbial community analysis of the hypersaline water of the Dead Sea using high-throughput amplicon sequencing.}, journal = {MicrobiologyOpen}, volume = {6}, number = {5}, pages = {}, pmid = {28677326}, issn = {2045-8827}, mesh = {Bacteria/classification/genetics ; Biodiversity ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; *Salinity ; Seawater/*chemistry/*microbiology ; *Water Microbiology ; }, abstract = {Amplicon sequencing using next-generation technology (bTEFAP[®]) has been utilized in describing the diversity of Dead Sea microbiota. The investigated area is a well-known salt lake in the western part of Jordan found in the lowest geographical location in the world (more than 420 m below sea level) and characterized by extreme salinity (approximately, 34%) in addition to other extreme conditions (low pH, unique ionic composition different from sea water). DNA was extracted from Dead Sea water. A total of 314,310 small subunit RNA (SSU rRNA) sequences were parsed, and 288,452 sequences were then clustered. For alpha diversity analysis, sample was rarefied to 3,000 sequences. The Shannon-Wiener index curve plot reached a plateau at approximately 3,000 sequences indicating that sequencing depth was sufficient to capture the full scope of microbial diversity. Archaea was found to be dominating the sequences (52%), whereas Bacteria constitute 45% of the sequences. Altogether, prokaryotic sequences (which constitute 97% of all sequences) were found to predominate. The findings expand on previous studies by using high-throughput amplicon sequencing to describe the microbial community in an environment which in recent years has been shown to hide some interesting diversity.}, } @article {pmid28677262, year = {2017}, author = {Mikaelyan, A and Thompson, CL and Meuser, K and Zheng, H and Rani, P and Plarre, R and Brune, A}, title = {High-resolution phylogenetic analysis of Endomicrobia reveals multiple acquisitions of endosymbiotic lineages by termite gut flagellates.}, journal = {Environmental microbiology reports}, volume = {9}, number = {5}, pages = {477-483}, doi = {10.1111/1758-2229.12565}, pmid = {28677262}, issn = {1758-2229}, mesh = {Animals ; Bacteria/classification/genetics ; DNA, Intergenic ; *Gastrointestinal Microbiome ; Insecta/microbiology ; *Metagenome ; *Metagenomics/methods ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; *Symbiosis ; }, abstract = {Bacteria of the class Endomicrobia form a deep-branching clade in the Elusimicrobia phylum. They are found almost exclusively in the intestinal tract of animals and are particularly abundant in many termites, where they reside as intracellular symbionts in the cellulolytic gut flagellates. Although small populations of putatively free-living lineages have been detected in faunated and flagellate-free hosts, the evolutionary origin of the endosymbionts is obscured by the limited amount of phylogenetic information provided by the 16S rRNA gene fragment amplified with Endomicrobia-specific primers. Here, we present a robust phylogenetic framework based on the near-full-length 16S-23S rRNA gene region of a diverse set of Endomicrobia from termites and cockroaches, which also allowed us to classify the shorter reads from previous studies. Our data revealed that endosymbionts arose independently at least four times from different free-living lineages, which were already present in ancestral cockroaches but became associated with their respective hosts long after the digestive symbiosis between termites and flagellates had been established. Pyrotag sequencing revealed that the proportion of putatively free-living lineages increased, when all flagellates and their symbionts were removed from the gut of lower termites by starvation, starch feeding or hyperbaric oxygen, but results varied between different methods.}, } @article {pmid28677239, year = {2017}, author = {Wagner, R and Zona, D and Oechel, W and Lipson, D}, title = {Microbial community structure and soil pH correspond to methane production in Arctic Alaska soils.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {3398-3410}, doi = {10.1111/1462-2920.13854}, pmid = {28677239}, issn = {1462-2920}, mesh = {Alaska ; Arctic Regions ; Bacteria/classification/genetics/*metabolism ; Biodiversity ; Carbon Dioxide/*metabolism ; Environment ; Genome, Bacterial/genetics ; Metagenome/genetics ; Methane/chemistry/*metabolism ; Microbiota/genetics ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {While there is no doubt that biogenic methane production in the Arctic is an important aspect of global methane emissions, the relative roles of microbial community characteristics and soil environmental conditions in controlling Arctic methane emissions remains uncertain. Here, relevant methane-cycling microbial groups were investigated at two remote Arctic sites with respect to soil potential methane production (PMP). Percent abundances of methanogens and iron-reducing bacteria correlated with increased PMP, while methanotrophs correlated with decreased PMP. Interestingly, α-diversity of the methanogens was positively correlated with PMP, while β-diversity was unrelated to PMP. The β-diversity of the entire microbial community, however, was related to PMP. Shannon diversity was a better correlate of PMP than Simpson diversity across analyses, while rarefied species richness was a weak correlate of PMP. These results demonstrate the following: first, soil pH and microbial community structure both probably control methane production in Arctic soils. Second, there may be high functional redundancy in the methanogens with regard to methane production. Third, iron-reducing bacteria co-occur with methanogens in Arctic soils, and iron-reduction-mediated effects on methanogenesis may be controlled by α- and β-diversity. And finally, species evenness and rare species abundances may be driving relationships between microbial groups, influencing Arctic methane production.}, } @article {pmid28676106, year = {2017}, author = {Yun, Y and Kim, HN and Kim, SE and Heo, SG and Chang, Y and Ryu, S and Shin, H and Kim, HL}, title = {Comparative analysis of gut microbiota associated with body mass index in a large Korean cohort.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {151}, pmid = {28676106}, issn = {1471-2180}, mesh = {Adult ; Bacteria/*classification/genetics ; Body Mass Index ; Cross-Sectional Studies ; DNA, Bacterial/genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Middle Aged ; Obesity/*microbiology ; Overweight/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Gut microbiota plays an important role in the harvesting, storage, and expenditure of energy obtained from one's diet. Our cross-sectional study aimed to identify differences in gut microbiota according to body mass index (BMI) in a Korean population. 16S rRNA gene sequence data from 1463 subjects were categorized by BMI into normal, overweight, and obese groups. Fecal microbiotas were compared to determine differences in diversity and functional inference analysis related with BMI. The correlation between genus-level microbiota and BMI was tested using zero-inflated Gaussian mixture models, with or without covariate adjustment of nutrient intake.

RESULTS: We confirmed differences between 16Sr RNA gene sequencing data of each BMI group, with decreasing diversity in the obese compared with the normal group. According to analysis of inferred metagenomic functional content using PICRUSt algorithm, a highly significant discrepancy in metabolism and immune functions (P < 0.0001) was predicted in the obese group. Differential taxonomic components in each BMI group were greatly affected by nutrient adjustment, whereas signature bacteria were not influenced by nutrients in the obese compared with the overweight group.

CONCLUSIONS: We found highly significant statistical differences between normal, overweight and obese groups using a large sample size with or without diet confounding factors. Our informative dataset sheds light on the epidemiological study on population microbiome.}, } @article {pmid28673401, year = {2017}, author = {Renz, H and Holt, PG and Inouye, M and Logan, AC and Prescott, SL and Sly, PD}, title = {An exposome perspective: Early-life events and immune development in a changing world.}, journal = {The Journal of allergy and clinical immunology}, volume = {140}, number = {1}, pages = {24-40}, doi = {10.1016/j.jaci.2017.05.015}, pmid = {28673401}, issn = {1097-6825}, mesh = {Animals ; Diet ; *Environmental Exposure ; Gastrointestinal Tract/microbiology ; Humans ; Immune System/*growth & development ; Microbiota ; }, abstract = {Advances in metagenomics, proteomics, metabolomics, and systems biology are providing a new emphasis in research; interdisciplinary work suggests that personalized medicine is on the horizon. These advances are illuminating sophisticated interactions between human-associated microbes and the immune system. The result is a transformed view of future prevention and treatment of chronic noncommunicable diseases, including allergy. Paradigm-shifting gains in scientific knowledge are occurring at a time of rapid global environmental change, urbanization, and biodiversity losses. Multifactorial and multigenerational implications of total environmental exposures, the exposome, require coordinated interdisciplinary efforts. It is clear that the genome alone cannot provide answers to urgent questions. Here we review the historical origins of exposome research and define a new concept, the metaexposome, which considers the bidirectional effect of the environment on human subjects and the human influence on all living systems and their genomes. The latter is essential for human health. We place the metaexposome in the context of early-life immune functioning and describe how various aspects of a changing environment, especially through microbiota exposures, can influence health and disease over the life course.}, } @article {pmid28673041, year = {2017}, author = {Bengtsson-Palme, J and Larsson, DGJ and Kristiansson, E}, title = {Using metagenomics to investigate human and environmental resistomes.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {10}, pages = {2690-2703}, doi = {10.1093/jac/dkx199}, pmid = {28673041}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Chromosome Mapping/methods ; Data Interpretation, Statistical ; Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Gastrointestinal Microbiome/genetics ; Genes, Bacterial/drug effects ; Geologic Sediments/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Lakes/microbiology ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {Antibiotic resistance is a global health concern declared by the WHO as one of the largest threats to modern healthcare. In recent years, metagenomic DNA sequencing has started to be applied as a tool to study antibiotic resistance in different environments, including the human microbiota. However, a multitude of methods exist for metagenomic data analysis, and not all methods are suitable for the investigation of resistance genes, particularly if the desired outcome is an assessment of risks to human health. In this review, we outline the current state of methods for sequence handling, mapping to databases of resistance genes, statistical analysis and metagenomic assembly. In addition, we provide an overview of important considerations related to the analysis of resistance genes, and recommend some of the currently used tools and methods that are best equipped to inform research and clinical practice related to antibiotic resistance.}, } @article {pmid28673033, year = {2017}, author = {Corcoll, N and Österlund, T and Sinclair, L and Eiler, A and Kristiansson, E and Backhaus, T and Eriksson, KM}, title = {Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing.}, journal = {FEMS microbiology letters}, volume = {364}, number = {14}, pages = {}, doi = {10.1093/femsle/fnx139}, pmid = {28673033}, issn = {1574-6968}, mesh = {Bacteria/*genetics ; Biodiversity ; *Biofilms ; DNA, Bacterial/analysis/genetics/*isolation & purification ; DNA, Ribosomal/analysis/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Molecular Biology/*methods ; Periphyton/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {High-throughput DNA sequencing technologies are increasingly used for the metagenomic characterisation of microbial biodiversity. However, basic issues, such as the choice of an appropriate DNA extraction method, are still not resolved for non-model microbial communities. This study evaluates four commonly used DNA extraction methods for marine periphyton biofilms in terms of DNA yield, efficiency, purity, integrity and resulting 16S rRNA bacterial diversity. Among the tested methods, the Plant DNAzol® Reagent (PlantDNAzol) and the FastDNA® SPIN Kit for Soil (FastDNA Soil) methods were best suited to extract high quantities of DNA (77-130 μg g wet wt-1). Lower amounts of DNA were obtained (<37 μg g wet wt-1) with the Power Plant® Pro DNA Isolation Kit (PowerPlant) and the Power Biofilm® DNA Isolation Kit (PowerBiofilm) methods, but integrity and purity of the extracted DNA were higher. Results from 16S rRNA amplicon sequencing demonstrate that the choice of a DNA extraction method significantly influences the bacterial community profiles generated. A higher number of bacterial OTUs were detected when DNA was extracted with the PowerBiofilm and the PlantDNAzol methods. Overall, this study demonstrates the potential bias in metagenomic diversity estimates associated with different DNA extraction methods.}, } @article {pmid28671295, year = {2017}, author = {Xu, L and Zhu, Y and Ren, L and Xu, B and Liu, C and Xie, Z and Shen, K}, title = {Characterization of the nasopharyngeal viral microbiome from children with community-acquired pneumonia but negative for Luminex xTAG respiratory viral panel assay detection.}, journal = {Journal of medical virology}, volume = {89}, number = {12}, pages = {2098-2107}, pmid = {28671295}, issn = {1096-9071}, mesh = {Child, Preschool ; Community-Acquired Infections/*virology ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Infant ; Male ; Metagenomics/methods ; Microbiota/*genetics ; Molecular Diagnostic Techniques ; Nasopharynx/*virology ; Parainfluenza Virus 3, Human/genetics/isolation & purification ; Pneumonia/diagnosis/*virology ; Respiratory System/virology ; Respiratory Tract Infections/virology ; Sensitivity and Specificity ; Viruses/classification/genetics/*isolation & purification ; }, abstract = {In the present study, 50 nasopharyngeal swabs from children with community-acquired pneumonia (CAP) but negative for 18 common respiratory viruses, as measured by the Luminex xTAG Respiratory Viral Panel Assay, were subjected to multiplex metagenomic analyses using a next-generation sequencing platform. Taxonomic analysis showed that all sequence reads could be assigned to a specific species. An average of 95.13% were assigned to the Bacteria kingdom, whereas, only 0.72% were potentially virus derived. This snapshot of the respiratory tract virome revealed most viral reads to be respiratory tract related, classified into four known virus families: Paramyxoviridae, Herpesviridae, Anelloviridae, and Polyomaviridae. Importantly, we detected a novel human parainfluenza virus 3 (HPIV 3) strain with a 32-bp insertion in the haemagglutinin-neuraminidase (HN) gene that produced a negative result in the Luminex assay, highlighting the strength of virome metagenomic analysis to identify not only novel viruses but also viruses likely to be missed by ordinary clinical tests. Thus, virome metagenomic analysis could become a viable clinical diagnostic method.}, } @article {pmid28669650, year = {2017}, author = {Malone, M and Johani, K and Jensen, SO and Gosbell, IB and Dickson, HG and Hu, H and Vickery, K}, title = {Next Generation DNA Sequencing of Tissues from Infected Diabetic Foot Ulcers.}, journal = {EBioMedicine}, volume = {21}, number = {}, pages = {142-149}, pmid = {28669650}, issn = {2352-3964}, mesh = {Aged ; Biodiversity ; Diabetic Foot/diagnosis/*microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; }, abstract = {We used next generation DNA sequencing to profile the microbiome of infected Diabetic Foot Ulcers (DFUs). The microbiota was correlated to clinical parameters and treatment outcomes to determine if directed antimicrobial therapy based on conventional microbiological cultures are relevant based on genomic analysis. Patients≥18years presenting with a new Diabetic Foot Infection (DFI) who had not received topical or oral antimicrobials in the two weeks prior to presentation, were eligible for enrolment. Tissue punch biopsies were obtained from infected DFUs for analysis. Demographics, clinical and laboratory data were collected and correlated against microbiota data. Thirty-nine patients with infected DFUs were recruited over twelve-months. Shorter duration DFUs (
OBJECTIVE: To compare the relative amounts of Akkermansia muciniphila, Clostridium leptum, Faecalibacterium prausnitzii, and Enterobacteriaceae as members of gut microbiota among patients with chronic urticaria (CU) and healthy controls.

METHODS: A total of 20 patients with CU and 20 healthy individuals matched by age and sex participated in the study. Fresh fecal samples were collected, and DNA extracted from stool samples was analyzed by real-time polymerase chain reaction for the qualitative and quantitative assays of the so-called bacteria.

RESULTS: The frequencies of A muciniphila, C leptum, and F prausnitzii in healthy controls' stool samples were significantly more than those of patients with CU (P < .001, P < .01, and P < .05, respectively), whereas the Enterobacteriaceae family was detected in all patients and healthy controls' stool samples. The relative amounts of A muciniphila in healthy control positive samples were significantly higher than those of samples from patients with CU (P < .001). Furthermore, there was a corresponding increase of relative amounts of C leptum and F prausnitzii in healthy control positive samples compared with those of patients with CU (P = .09 and P = .08, respectively). The mean of the relative amounts of Enterobacteriaceae family in the stool samples from patients with CU was more than that of healthy controls; however, the difference was nearly significant (P = .12).

CONCLUSION: The results reveal a change of frequency and relative amounts of A muciniphila, C leptum, and F prausnitzii in patients with CU compared with healthy controls. This is the first study, to our knowledge, to show the change of microbiota composition in patients with CU.}, } @article {pmid28665922, year = {2017}, author = {Ravi, A and Estensmo, ELF and Abée-Lund, TML and Foley, SL and Allgaier, B and Martin, CR and Claud, EC and Rudi, K}, title = {Association of the gut microbiota mobilome with hospital location and birth weight in preterm infants.}, journal = {Pediatric research}, volume = {82}, number = {5}, pages = {829-838}, pmid = {28665922}, issn = {1530-0447}, mesh = {*Birth Weight ; Case-Control Studies ; Computational Biology ; DNA, Bacterial/*genetics ; Databases, Genetic ; Enterocolitis, Necrotizing/diagnosis/epidemiology/*microbiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Genome, Bacterial ; Gestational Age ; Humans ; Infant, Newborn ; *Infant, Premature ; *Infant, Very Low Birth Weight ; *Interspersed Repetitive Sequences ; Male ; Metagenome ; Metagenomics/methods ; Premature Birth/diagnosis/epidemiology/*microbiology ; Ribotyping ; United States/epidemiology ; }, abstract = {BackgroundThe preterm infant gut microbiota is vulnerable to different biotic and abiotic factors. Although the development of this microbiota has been extensively studied, the mobilome-i.e. the mobile genetic elements (MGEs) in the gut microbiota-has not been considered. Therefore, the aim of this study was to investigate the association of the mobilome with birth weight and hospital location in the preterm infant gut microbiota.MethodsThe data set consists of fecal samples from 62 preterm infants with and without necrotizing enterocolitis (NEC) from three different hospitals. We analyzed the gut microbiome by using 16S rRNA amplicon sequencing, shot-gun metagenome sequencing, and quantitative PCR. Predictive models and other data analyses were performed using MATLAB and QIIME.ResultSThe microbiota composition was significantly different between NEC-positive and NEC-negative infants and significantly different between hospitals. An operational taxanomic unit (OTU) showed strong positive and negative correlation with NEC and birth weight, respectively, whereas none showed significance for mode of delivery. Metagenome analyses revealed high levels of conjugative plasmids with MGEs and virulence genes. Results from quantitative PCR showed that the plasmid signature genes were significantly different between hospitals and in NEC-positive infants.ConclusionOur results point toward an association of the mobilome with hospital location in preterm infants.}, } @article {pmid28663049, year = {2017}, author = {Heyer, R and Schallert, K and Zoun, R and Becher, B and Saake, G and Benndorf, D}, title = {Challenges and perspectives of metaproteomic data analysis.}, journal = {Journal of biotechnology}, volume = {261}, number = {}, pages = {24-36}, doi = {10.1016/j.jbiotec.2017.06.1201}, pmid = {28663049}, issn = {1873-4863}, mesh = {Environmental Microbiology ; Mass Spectrometry ; *Metagenomics ; *Microbial Consortia ; *Proteomics ; Software ; }, abstract = {In nature microorganisms live in complex microbial communities. Comprehensive taxonomic and functional knowledge about microbial communities supports medical and technical application such as fecal diagnostics as well as operation of biogas plants or waste water treatment plants. Furthermore, microbial communities are crucial for the global carbon and nitrogen cycle in soil and in the ocean. Among the methods available for investigation of microbial communities, metaproteomics can approximate the activity of microorganisms by investigating the protein content of a sample. Although metaproteomics is a very powerful method, issues within the bioinformatic evaluation impede its success. In particular, construction of databases for protein identification, grouping of redundant proteins as well as taxonomic and functional annotation pose big challenges. Furthermore, growing amounts of data within a metaproteomics study require dedicated algorithms and software. This review summarizes recent metaproteomics software and addresses the introduced issues in detail.}, } @article {pmid28662574, year = {2017}, author = {Phillips, CD and Hanson, J and Wilkinson, JE and Koenig, L and Rees, E and Webala, P and Kingston, T}, title = {Microbiome Structural and Functional Interactions across Host Dietary Niche Space.}, journal = {Integrative and comparative biology}, volume = {57}, number = {4}, pages = {743-755}, doi = {10.1093/icb/icx011}, pmid = {28662574}, issn = {1557-7023}, mesh = {Animals ; Chiroptera/*microbiology ; *Diet ; *Gastrointestinal Microbiome ; Kenya ; Metagenome ; Species Specificity ; }, abstract = {Host-associated microbiomes are integral components of host health, but microbiome community structure varies among and within hosts. Reconciling community variability with the apparent dependence of hosts on community function, and characterizing how functional divergence proceeds across niches, remains challenging. Here, through the study of gut microbiomes and diets of three insectivorous bat species we characterize how community structure is shaped by predicted functional properties of community members. We found that while host diet and microbiome community composition do not significantly relate to each other, host diet and metagenome function do, suggesting that diet directly selects metagenomic functions rather than communities. We use a novel inference framework to show how the discordance between community structure and functional variation derives from functional equivalence and is influenced by the continuum of shared and derived gene sets across microbial lineages. Our findings help clarify how metagenome community structure-function relationships contribute to deterministic processes in community assembly, and describe the basis for metagenomic differences across ecologically similar hosts.}, } @article {pmid28662572, year = {2017}, author = {Dearing, MD and Kohl, KD}, title = {Beyond Fermentation: Other Important Services Provided to Endothermic Herbivores by their Gut Microbiota.}, journal = {Integrative and comparative biology}, volume = {57}, number = {4}, pages = {723-731}, doi = {10.1093/icb/icx020}, pmid = {28662572}, issn = {1557-7023}, mesh = {Animal Nutritional Physiological Phenomena ; Animals ; Bacterial Physiological Phenomena ; Birds/*microbiology/physiology ; Digestion ; *Gastrointestinal Microbiome ; *Herbivory ; Mammals/*microbiology/physiology ; }, abstract = {For decades, comparative biologists have recognized the importance of microbial partners in facilitating herbivory as a successful feeding strategy. Most of this success is attributed to the ability of gut microbes to digest recalcitrant dietary fiber and provides usable nutrients to their hosts. Gut microbes can also provide numerous other functions, such as vitamin synthesis, nitrogen recycling, and the detoxification of plant secondary compounds. Here, we review these microbial functions in herbivorous mammals and birds, highlighting studies that utilize recently developed metagenomic techniques. Several of these studies emphasize that microbial services are the product of interactions and exchanges within a complex microbial community, rather than the product of an individual member. Additionally, a number of these microbial functions are interdependent. For example, levels of dietary nitrogen or plant toxins can influence fiber digestibility. Further studies into the variety of microbial services provided to herbivorous hosts, and how these services might interact will broaden our understanding of host-microbe interactions.}, } @article {pmid28660691, year = {2017}, author = {Sambles, C and Moore, K and Lux, TM and Jones, K and Littlejohn, GR and Gouveia, JD and Aves, SJ and Studholme, DJ and Lee, R and Love, J}, title = {Metagenomic analysis of the complex microbial consortium associated with cultures of the oil-rich alga Botryococcus braunii.}, journal = {MicrobiologyOpen}, volume = {6}, number = {4}, pages = {}, pmid = {28660691}, issn = {2045-8827}, support = {WT097835MF/WT_/Wellcome Trust/United Kingdom ; BB/K003240/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/K003240/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; WT101650MA/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/M008924/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacteria/*classification/genetics/growth & development/*isolation & purification ; Chlorophyta/*growth & development ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Metagenomics ; *Microbial Consortia ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Microalgae are widely viewed as a promising and sustainable source of renewable chemicals and biofuels. Botryococcus braunii synthesizes and secretes significant amounts of long-chain (C30 -C40) hydrocarbons that can be subsequently converted into gasoline, diesel, and aviation fuel. B. braunii cultures are not axenic and the effects of co-cultured microorganisms on B. braunii growth and hydrocarbon yield are important, but sometimes contradictory. To understand the composition of the B. braunii microbial consortium, we used high throughput Illumina sequencing of metagenomic DNA to profile the microbiota within a well established, stable B. braunii culture and characterized the demographic changes in the microcosm following modification to the culture conditions. DNA sequences attributed to B. braunii were present in equal quantities in all treatments, whereas sequences assigned to the associated microbial community were dramatically altered. Bacterial species least affected by treatments, and more robustly associated with the algal cells, included members of Rhizobiales, comprising Bradyrhizobium and Methylobacterium, and representatives of Dyadobacter, Achromobacter and Asticcacaulis. The presence of bacterial species identified by metagenomics was confirmed by additional 16S rDNA analysis of bacterial isolates. Our study demonstrates the advantages of high throughput sequencing and robust metagenomic analyses to define microcosms and further our understanding of microbial ecology.}, } @article {pmid28659635, year = {2017}, author = {Hosomi, K and Ohno, H and Murakami, H and Natsume-Kitatani, Y and Tanisawa, K and Hirata, S and Suzuki, H and Nagatake, T and Nishino, T and Mizuguchi, K and Miyachi, M and Kunisawa, J}, title = {Method for preparing DNA from feces in guanidine thiocyanate solution affects 16S rRNA-based profiling of human microbiota diversity.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4339}, pmid = {28659635}, issn = {2045-2322}, mesh = {Adult ; Bacteria/classification/genetics ; *Biodiversity ; Feces/microbiology ; Female ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Metagenomic analysis based on the 16S rRNA gene is generally performed to examine the diversity and abundance of commensal bacteria in feces, which is now recognized to be associated with human health and diseases. Guanidine thiocyanate (GuSCN) solution is used as a less onerous way compared with a frozen method to transport and stock fecal samples at room temperature for DNA analysis; however, optimal methods to measure fecal bacterial composition in GuSCN solution remain to be investigated. Here, we examined the influence of various factors such as pretreatment (e.g., removing GuSCN solution and washing feces with phosphate-buffered saline (PBS) before mechanical lysis), fecal concentration in the GuSCN solution, storage time, and position of fecal subsampling on the 16S rRNA-based analysis of fecal bacteria in GuSCN solution. We found that pretreatment and fecal concentration affected the bacterial composition, and a little change was noted with subsampling position. Based on these results, we propose a basic protocol, including fecal sampling, sample storage, and DNA extraction, for the 16S rRNA-based analysis of bacterial composition in feces suspended in GuSCN solution.}, } @article {pmid28655556, year = {2017}, author = {Koo, H and Hakim, JA and Morrow, CD and Eipers, PG and Davila, A and Andersen, DT and Bej, AK}, title = {Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica.}, journal = {Journal of microbiological methods}, volume = {140}, number = {}, pages = {15-22}, pmid = {28655556}, issn = {1872-8359}, support = {NNX08AO19G/NASA/NASA/United States ; P30 AI027767/AI/NIAID NIH HHS/United States ; P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR001417/TR/NCATS NIH HHS/United States ; }, mesh = {Antarctic Regions ; Computational Biology/*methods ; Cyanobacteria/genetics ; Databases, Factual ; *Genetic Variation ; High-Throughput Nucleotide Sequencing ; Lakes/*microbiology ; Metagenome ; Metagenomics/methods ; Microbial Consortia/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In this study, using NextGen sequencing of the collective 16S rRNA genes obtained from two sets of samples collected from Lake Obersee, Antarctica, we compared and contrasted two bioinformatics tools, PICRUSt and Tax4Fun. We then developed an R script to assess the taxonomic and predictive functional profiles of the microbial communities within the samples. Taxa such as Pseudoxanthomonas, Planctomycetaceae, Cyanobacteria Subsection III, Nitrosomonadaceae, Leptothrix, and Rhodobacter were exclusively identified by Tax4Fun that uses SILVA database; whereas PICRUSt that uses Greengenes database uniquely identified Pirellulaceae, Gemmatimonadetes A1-B1, Pseudanabaena, Salinibacterium and Sinobacteraceae. Predictive functional profiling of the microbial communities using Tax4Fun and PICRUSt separately revealed common metabolic capabilities, while also showing specific functional IDs not shared between the two approaches. Combining these functional predictions using a customized R script revealed a more inclusive metabolic profile, such as hydrolases, oxidoreductases, transferases; enzymes involved in carbohydrate and amino acid metabolisms; and membrane transport proteins known for nutrient uptake from the surrounding environment. Our results present the first molecular-phylogenetic characterization and predictive functional profiles of the microbial mat communities in Lake Obersee, while demonstrating the efficacy of combining both the taxonomic assignment information and functional IDs using the R script created in this study for a more streamlined evaluation of predictive functional profiles of microbial communities.}, } @article {pmid28655159, year = {2017}, author = {He, Q and Gao, Y and Jie, Z and Yu, X and Laursen, JM and Xiao, L and Li, Y and Li, L and Zhang, F and Feng, Q and Li, X and Yu, J and Liu, C and Lan, P and Yan, T and Liu, X and Xu, X and Yang, H and Wang, J and Madsen, L and Brix, S and Wang, J and Kristiansen, K and Jia, H}, title = {Two distinct metacommunities characterize the gut microbiota in Crohn's disease patients.}, journal = {GigaScience}, volume = {6}, number = {7}, pages = {1-11}, pmid = {28655159}, issn = {2047-217X}, mesh = {Adolescent ; Adult ; Case-Control Studies ; Crohn Disease/diet therapy/*microbiology ; Enteral Nutrition/adverse effects/methods ; Fatty Acids/metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; Lipopolysaccharides/metabolism ; Male ; Metagenome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The inflammatory intestinal disorder Crohn's disease (CD) has become a health challenge worldwide. The gut microbiota closely interacts with the host immune system, but its functional impact in CD is unclear. Except for studies on a small number of CD patients, analyses of the gut microbiota in CD have used 16S rDNA amplicon sequencing. Here we employed metagenomic shotgun sequencing to provide a detailed characterization of the compositional and functional features of the CD microbiota, comprising also unannotated bacteria, and investigated its modulation by exclusive enteral nutrition. Based on signature taxa, CD microbiotas clustered into 2 distinct metacommunities, indicating individual variability in CD microbiome structure. Metacommunity-specific functional shifts in CD showed enrichment in producers of the pro-inflammatory hexa-acylated lipopolysaccharide variant and a reduction in the potential to synthesize short-chain fatty acids. Disruption of ecological networks was evident in CD, coupled with reduction in growth rates of many bacterial species. Short-term exclusive enteral nutrition elicited limited impact on the overall composition of the CD microbiota, although functional changes occurred following treatment. The microbiotas in CD patients can be stratified into 2 distinct metacommunities, with the most severely perturbed metacommunity exhibiting functional potentials that deviate markedly from that of the healthy individuals, with possible implication in relation to CD pathogenesis.}, } @article {pmid28654183, year = {2017}, author = {Zhang, Y and Oh, S and Liu, WT}, title = {Impact of drinking water treatment and distribution on the microbiome continuum: an ecological disturbance's perspective.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {3163-3174}, doi = {10.1111/1462-2920.13800}, pmid = {28654183}, issn = {1462-2920}, mesh = {Bacteria/classification/genetics/growth & development/*isolation & purification ; Disinfection ; Drinking Water/*microbiology ; Groundwater/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Water Purification/*methods ; }, abstract = {While microbes are known to be present at different stages of a drinking water system, their potential functions and ability to grow in such systems are poorly understood. In this study, we demonstrated that treatment and distribution processes could be viewed as ecological disturbances exhibited over space on the microbiome continuum in a groundwater-derived system. Results from 16S rRNA gene amplicon analysis and metagenomics suggested that disturbances in the system were intense as the community diversity was substantially reduced during the treatment steps. Specifically, syntrophs and methanogens dominant in raw water (RW) disappeared after water abstraction, accompanied by a substantial decrease in both the abundance and number of functional genes related to methanogenesis. The softening effluent was dominated by an Exiguobacterium-related population, likely due to its ability to use the phosphotransferase system (PTS) as regulatory machinery to control the energy conditions of the cell. After disinfection and entering the distribution system, community-level functionality remained relatively stable, whereas the community structure differed from those taken in the treatment steps. The diversity and high abundance of some eukaryotic groups in the system suggested that predation could be a disturbance to the bacterial microbiome, which could further drive the diversification of the bacterial community.}, } @article {pmid28654083, year = {2017}, author = {Siegwald, L and Audebert, C and Even, G and Viscogliosi, E and Caboche, S and Chabé, M}, title = {Targeted metagenomic sequencing data of human gut microbiota associated with Blastocystis colonization.}, journal = {Scientific data}, volume = {4}, number = {}, pages = {170081}, pmid = {28654083}, issn = {2052-4463}, mesh = {*Blastocystis ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenomics ; Sequence Analysis ; }, abstract = {In the past decade, metagenomics studies have become widespread due to the arrival of second-generation sequencing platforms characterized by low costs, high throughput and short read lengths. Today, although benchtop sequencers are considered to be accurate platforms to deliver data for targeted metagenomics studies, the limiting factor has become the analysis of these data. In a previous paper, we performed an Ion Torrent PGM 16S rDNA gene sequencing of faecal DNAs from 48 Blastocystis-colonized patients and 48 Blastocystis-negative subjects, in order to decipher the impact of this widespread protist on gut microbiota composition and diversity. We report here on the Ion Torrent targeted metagenomic sequencing and analysis of these 96 human faecal samples, and the complete datasets from raw to analysed data. We also provide the key steps of the bioinformatic analyses, from library preparation to data filtering and OTUs tables generation. This data represents a valuable resource for the scientific community, enabling re-processing of these targeted metagenomic datasets through various pipelines and a comparative evaluation of microbiota analysis methods.}, } @article {pmid28651652, year = {2017}, author = {Andersen, VD and DE Knegt, LV and Munk, P and Jensen, MS and Agersø, Y and Aarestrup, FM and Vigre, H}, title = {The association between measurements of antimicrobial use and resistance in the faeces microbiota of finisher batches.}, journal = {Epidemiology and infection}, volume = {145}, number = {13}, pages = {2827-2837}, pmid = {28651652}, issn = {1469-4409}, mesh = {Animals ; Anti-Infective Agents/administration & dosage/*pharmacology ; Denmark ; *Drug Resistance, Microbial ; Feces/*microbiology ; Microbial Sensitivity Tests/veterinary ; Microbiota/*drug effects ; Sus scrofa/*microbiology ; }, abstract = {The objectives were to present three approaches for calculating antimicrobial (AM) use in pigs that take into account the rearing period and rearing site, and to study the association between these measurements and phenotypical resistance and abundance of resistance genes in faeces samples from 10 finisher batches. The AM use was calculated relative to the rearing period of the batches as (i) 'Finisher Unit Exposure' at unit level, (ii) 'Lifetime Exposure' at batch level and (iii) 'Herd Exposure' at herd level. A significant effect on the occurrence of tetracycline resistance measured by cultivation was identified for Lifetime Exposure for the AM class: tetracycline. Furthermore, for Lifetime Exposure for the AM classes: macrolide, broad-spectrum penicillin, sulfonamide and tetracycline use as well as Herd Unit Exposure for the AM classes: aminoglycoside, lincosamide and tetracycline use, a significant effect was observed on the occurrence of genes coding for the AM resistance classes: aminoglycoside, lincosamide, macrolide, β-lactam, sulfonamide and tetracycline. No effect was observed for Finisher Unit Exposure. Overall, the study shows that Lifetime Exposure is an efficient measurement of AM use in finisher batches, and has a significant effect on the occurrence of resistance, measured either by cultivation or metagenomics.}, } @article {pmid28648853, year = {2017}, author = {Anbalagan, R and Srikanth, P and Mani, M and Barani, R and Seshadri, KG and Janarthanan, R}, title = {Next generation sequencing of oral microbiota in Type 2 diabetes mellitus prior to and after neem stick usage and correlation with serum monocyte chemoattractant-1.}, journal = {Diabetes research and clinical practice}, volume = {130}, number = {}, pages = {204-210}, doi = {10.1016/j.diabres.2017.06.009}, pmid = {28648853}, issn = {1872-8227}, mesh = {Adult ; Aged ; Chemokine CCL2/*blood ; Diabetes Mellitus, Type 2/blood/*microbiology ; Female ; Glycerides/*therapeutic use ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Microbiota/*drug effects ; Middle Aged ; Mouth/*microbiology ; RNA, Ribosomal, 16S/metabolism ; Saliva/microbiology ; Terpenes/*therapeutic use ; }, abstract = {INTRODUCTION: Oral microbiome impacts health and disease. T2DM and periodontitis are associated. Neem (Azadiracta indica) has antibacterial activity against oral microbiota.

OBJECTIVES: To characterize oral microbiota (OMB) in saliva samples of T2DM patients by Next generation sequencing. To analyze MCP-1 levels among the T2DM patients before and after a month of neem stick usage as a toothbrush.

MATERIALS AND METHODS: Blood and saliva samples were collected from adult T2DM patients before and after the neem stick usage. Metagenomic sequencing was performed on saliva samples targeting V6 region of 16s rRNA. Serum MCP-1 levels were determined using a quantitative sandwich Human MCP-1 standard ABTS development kit (Peprotech, USA).

RESULTS: The profile of oral microbiota of T2DM patients (n=24) consists of Streptococcus (95.8%) counts ranging from 2644 to 27,214, Veillonella (72.2%, counts 25-19,709, Neisseria (87.5%) 453-33,445), Rothia (63.6%, 233-6734), Actinomycetes (25%, 161-3730), Fusobacterium (21%, 2252-21,334), and Pigmentiphaga (12.5% 3-16,644). Oral microbiota in healthy controls (n=10), consists of Streptococcus (26.1%), Veillonella (21.9%), Neisseria (16.9%), Haemophilus (10.7%), Actinomycetes (2.6%), Rothia (3.1%), Oribacterium (1.7%). Post neem samples showed drastic reduction in the load of bacteria which was statistically significant. The mean serum MCP-1 before the use of neem stick was 265.18±79.44 (range 141.6-980.5pg/ml) and dropped to 33.6±7.35 after a month of neem stick usage (P value>0.001).

CONCLUSION: OMB of T2DM patients and healthy controls were similar, however bacterial loads were significantly higher in T2DM patients. Use of neem stick has a statistically significant reduction on bacterial loads and MCP-1 levels in T2DM patients.}, } @article {pmid28647755, year = {2018}, author = {Scola, V and Ramond, JB and Frossard, A and Zablocki, O and Adriaenssens, EM and Johnson, RM and Seely, M and Cowan, DA}, title = {Namib Desert Soil Microbial Community Diversity, Assembly, and Function Along a Natural Xeric Gradient.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {193-203}, pmid = {28647755}, issn = {1432-184X}, support = {N00113-95565//National Research Foundation of South Africa/ ; }, mesh = {Bacteria/*classification/genetics/*isolation & purification ; Biodiversity ; Desert Climate ; *Microbiota ; Namibia ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The hyperarid Namib desert is a coastal desert in southwestern Africa and one of the oldest and driest deserts on the planet. It is characterized by a west/east increasing precipitation gradient and by regular coastal fog events (extending up to 75 km inland) that can also provide soil moisture. In this study, we evaluated the role of this natural aridity and xeric gradient on edaphic microbial community structure and function in the Namib desert. A total of 80 individual soil samples were collected at 10-km intervals along a 190-km transect from the fog-dominated western coastal region to the eastern desert boundary. Seventeen physicochemical parameters were measured for each soil sample. Soil parameters reflected the three a priori defined climatic/xeric zones along the transect ("fog," "low rain," and "high rain"). Microbial community structures were characterized by terminal restriction fragment length polymorphism fingerprinting and shotgun metaviromics, and their functional capacities were determined by extracellular enzyme activity assays. Both microbial community structures and activities differed significantly between the three xeric zones. The deep sequencing of surface soil metavirome libraries also showed shifts in viral composition along the xeric transect. While bacterial community assembly was influenced by soil chemistry and stochasticity along the transect, variations in community "function" were apparently tuned by xeric stress.}, } @article {pmid28646918, year = {2017}, author = {Staley, C and Ferrieri, AP and Tfaily, MM and Cui, Y and Chu, RK and Wang, P and Shaw, JB and Ansong, CK and Brewer, H and Norbeck, AD and Markillie, M and do Amaral, F and Tuleski, T and Pellizzaro, T and Agtuca, B and Ferrieri, R and Tringe, SG and Paša-Tolić, L and Stacey, G and Sadowsky, MJ}, title = {Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {65}, pmid = {28646918}, issn = {2049-2618}, mesh = {Arabidopsis/genetics ; Arabidopsis Proteins/genetics ; Bacteria/classification/genetics/metabolism ; Bacterial Physiological Phenomena ; Biodiversity ; Brachypodium/genetics ; Carbon/*metabolism ; *Circadian Rhythm ; High-Throughput Nucleotide Sequencing ; Microbiota/*physiology ; Plant Development/physiology ; RNA, Ribosomal, 16S ; *Rhizosphere ; *Soil Microbiology ; Transcription Factors/genetics ; }, abstract = {BACKGROUND: The circadian clock regulates plant metabolic functions and is an important component in plant health and productivity. Rhizosphere bacteria play critical roles in plant growth, health, and development and are shaped primarily by soil communities. Using Illumina next-generation sequencing and high-resolution mass spectrometry, we characterized bacterial communities of wild-type (Col-0) Arabidopsis thaliana and an acyclic line (OX34) ectopically expressing the circadian clock-associated cca1 transcription factor, relative to a soil control, to determine how cycling dynamics affected the microbial community. Microbial communities associated with Brachypodium distachyon (BD21) were also evaluated.

RESULTS: Significantly different bacterial community structures (P = 0.031) were observed in the rhizosphere of wild-type plants between light and dark cycle samples. Furthermore, 13% of the community showed cycling, with abundances of several families, including Burkholderiaceae, Rhodospirillaceae, Planctomycetaceae, and Gaiellaceae, exhibiting fluctuation in abundances relative to the light cycle. However, limited-to-no cycling was observed in the acyclic CCAox34 line or in soil controls. Significant cycling was also observed, to a lesser extent, in Brachypodium. Functional gene inference revealed that genes involved in carbohydrate metabolism were likely more abundant in near-dawn, dark samples. Additionally, the composition of organic matter in the rhizosphere showed a significant variation between dark and light cycles.

CONCLUSIONS: The results of this study suggest that the rhizosphere bacterial community is regulated, to some extent, by the circadian clock and is likely influenced by, and exerts influences, on plant metabolism and productivity. The timing of bacterial cycling in relation to that of Arabidopsis further suggests that diurnal dynamics influence plant-microbe carbon metabolism and exchange. Equally important, our results suggest that previous studies done without relevance to time of day may need to be reevaluated with regard to the impact of diurnal cycles on the rhizosphere microbial community.}, } @article {pmid28646502, year = {2018}, author = {Yip, LY and Aw, CC and Lee, SH and Hong, YS and Ku, HC and Xu, WH and Chan, JMX and Cheong, EJY and Chng, KR and Ng, AHQ and Nagarajan, N and Mahendran, R and Lee, YK and Browne, ER and Chan, ECY}, title = {The liver-gut microbiota axis modulates hepatotoxicity of tacrine in the rat.}, journal = {Hepatology (Baltimore, Md.)}, volume = {67}, number = {1}, pages = {282-295}, doi = {10.1002/hep.29327}, pmid = {28646502}, issn = {1527-3350}, mesh = {Animals ; Biopsy, Needle ; Chemical and Drug Induced Liver Injury/*etiology/pathology ; Disease Models, Animal ; Dose-Response Relationship, Drug ; Gastrointestinal Microbiome/*drug effects ; Immunohistochemistry ; Liver Function Tests ; Male ; Random Allocation ; Rats ; Rats, Inbred Strains ; Reference Values ; Severity of Illness Index ; Tacrine/pharmacokinetics/pharmacology/*toxicity ; }, abstract = {UNLABELLED: The gut microbiota possesses diverse metabolic activities, but its contribution toward heterogeneous toxicological responses is poorly understood. In this study, we investigated the role of the liver-gut microbiota axis in underpinning the hepatotoxicity of tacrine. We employed an integrated strategy combining pharmacokinetics, toxicology, metabonomics, genomics, and metagenomics to elucidate and validate the mechanism of tacrine-induced hepatotoxicity in Lister hooded rats. Pharmacokinetic studies in rats demonstrated 3.3-fold higher systemic exposure to tacrine in strong responders that experienced transaminitis, revealing enhanced enterohepatic recycling of deglucuronidated tacrine in this subgroup, not attributable to variation in hepatic disposition gene expression. Metabonomic studies implicated variations in gut microbial activities that mapped onto tacrine-induced transaminitis. Metagenomics delineated greater deglucuronidation capabilities in strong responders, based on differential gut microbial composition (e.g., Lactobacillus, Bacteroides, and Enterobacteriaceae) and approximately 9% higher β-glucuronidase gene abundance compared with nonresponders. In the validation study, coadministration with oral β-glucuronidase derived from Escherichia coli and pretreatment with vancomycin and imipenem significantly modulated the susceptibility to tacrine-induced transaminitis in vivo.

CONCLUSION: This study establishes pertinent gut microbial influences in modifying the hepatotoxicity of tacrine, providing insights for personalized medicine initiatives. (Hepatology 2018;67:282-295).}, } @article {pmid28643787, year = {2017}, author = {Martinez-Hernandez, F and Fornas, O and Lluesma Gomez, M and Bolduc, B and de la Cruz Peña, MJ and Martínez, JM and Anton, J and Gasol, JM and Rosselli, R and Rodriguez-Valera, F and Sullivan, MB and Acinas, SG and Martinez-Garcia, M}, title = {Single-virus genomics reveals hidden cosmopolitan and abundant viruses.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {15892}, pmid = {28643787}, issn = {2041-1723}, mesh = {Atlantic Ocean ; Biodiversity ; Data Mining/methods ; Flow Cytometry/methods ; Genome, Viral ; Genomics/*methods ; Mediterranean Sea ; Metagenome ; Polymorphism, Single Nucleotide ; Proteomics/methods ; Seawater/*virology ; Viruses/*genetics/isolation & purification ; }, abstract = {Microbes drive ecosystems under constraints imposed by viruses. However, a lack of virus genome information hinders our ability to answer fundamental, biological questions concerning microbial communities. Here we apply single-virus genomics (SVGs) to assess whether portions of marine viral communities are missed by current techniques. The majority of the here-identified 44 viral single-amplified genomes (vSAGs) are more abundant in global ocean virome data sets than published metagenome-assembled viral genomes or isolates. This indicates that vSAGs likely best represent the dsDNA viral populations dominating the oceans. Species-specific recruitment patterns and virome simulation data suggest that vSAGs are highly microdiverse and that microdiversity hinders the metagenomic assembly, which could explain why their genomes have not been identified before. Altogether, SVGs enable the discovery of some of the likely most abundant and ecologically relevant marine viral species, such as vSAG 37-F6, which were overlooked by other methodologies.}, } @article {pmid28642609, year = {2017}, author = {Banerjee, S and Tian, T and Wei, Z and Peck, KN and Shih, N and Chalian, AA and O'Malley, BW and Weinstein, GS and Feldman, MD and Alwine, J and Robertson, ES}, title = {Microbial Signatures Associated with Oropharyngeal and Oral Squamous Cell Carcinomas.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4036}, pmid = {28642609}, issn = {2045-2322}, support = {P30 CA016520/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics ; Carcinoma, Squamous Cell/epidemiology/*etiology ; Computational Biology/methods ; Host-Parasite Interactions ; Host-Pathogen Interactions ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth Neoplasms/epidemiology/*etiology ; Mutagenesis, Insertional ; Oropharyngeal Neoplasms/epidemiology/*etiology ; Parasites/classification/genetics ; Reproducibility of Results ; }, abstract = {The microbiome is fundamentally one of the most unique organs in the human body. Dysbiosis can result in critical inflammatory responses and result in pathogenesis contributing to neoplastic events. We used a pan-pathogen array technology (PathoChip) coupled with next-generation sequencing to establish microbial signatures unique to human oral and oropharyngeal squamous cell carcinomas (OCSCC/OPSCC). Signatures for DNA and RNA viruses including oncogenic viruses, gram positive and negative bacteria, fungi and parasites were detected. Cluster and topological analyses identified 2 distinct groups of microbial signatures related to OCSCCs/OPSCCs. Results were validated by probe capture next generation sequencing; the data from which also provided a comprehensive map of integration sites and chromosomal hotspots for micro-organism genomic insertions. Identification of these microbial signatures and their integration sites may provide biomarkers for OCSCC/OPSCC diagnosis and prognosis as well as novel avenues for study of their potential role in OCSCCs/OPSCCs.}, } @article {pmid28640804, year = {2017}, author = {Claussen, JC and Skiecevičienė, J and Wang, J and Rausch, P and Karlsen, TH and Lieb, W and Baines, JF and Franke, A and Hütt, MT}, title = {Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome.}, journal = {PLoS computational biology}, volume = {13}, number = {6}, pages = {e1005361}, pmid = {28640804}, issn = {1553-7358}, mesh = {Bacterial Load/methods/statistics & numerical data ; Computer Simulation ; Data Interpretation, Statistical ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenome ; Microbial Interactions/*physiology ; Microbiota/*physiology ; *Models, Biological ; *Models, Statistical ; Pattern Recognition, Automated ; }, abstract = {The analysis of microbiome compositions in the human gut has gained increasing interest due to the broader availability of data and functional databases and substantial progress in data analysis methods, but also due to the high relevance of the microbiome in human health and disease. While most analyses infer interactions among highly abundant species, the large number of low-abundance species has received less attention. Here we present a novel analysis method based on Boolean operations applied to microbial co-occurrence patterns. We calibrate our approach with simulated data based on a dynamical Boolean network model from which we interpret the statistics of attractor states as a theoretical proxy for microbiome composition. We show that for given fractions of synergistic and competitive interactions in the model our Boolean abundance analysis can reliably detect these interactions. Analyzing a novel data set of 822 microbiome compositions of the human gut, we find a large number of highly significant synergistic interactions among these low-abundance species, forming a connected network, and a few isolated competitive interactions.}, } @article {pmid28640714, year = {2017}, author = {Wen, SW and Wong, CHY}, title = {An unexplored brain-gut microbiota axis in stroke.}, journal = {Gut microbes}, volume = {8}, number = {6}, pages = {601-606}, pmid = {28640714}, issn = {1949-0984}, mesh = {Animals ; Bacteria/classification ; *Bacterial Physiological Phenomena ; Bacterial Translocation ; *Disease Models, Animal ; Dysbiosis/etiology/*microbiology ; Escherichia coli/physiology ; Gastrointestinal Tract/microbiology ; *Host-Pathogen Interactions ; Humans ; Lung/microbiology ; Mice ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Specific Pathogen-Free Organisms ; Stroke/complications/*microbiology ; }, abstract = {Microbiota research, in particular that of the gut, has recently gained much attention in medical research owing to technological advances in metagenomics and metabolomics. Despite this, much of the research direction has focused on long-term or chronic effects of microbiota manipulation on health and disease. In this addendum, we reflect on our recent publication that reported findings addressing a rather unconventional hypothesis. Bacterial pneumonia is highly prevalent and is one of the leading contributors to stroke morbidity and mortality worldwide. However, microbiological cultures of samples taken from stroke patient with a suspected case of pneumonia often return with a negative result. Therefore, we proposed that post-stroke infection may be due to the presence of anaerobic bacteria, possibly those originated from the host gut microbiota. Supporting this, we showed that stroke promotes intestinal barrier breakdown and robust microbiota changes, and the subsequent translocation of selective bacterial strain from the host gut microbiota to peripheral tissues (i.e. lung) induces post-stroke infections. Our findings were further supported by various elegant studies published in the past 12 months. Here, we discuss and provide an overview of our key findings, supporting studies, and the implications for future advances in stroke research.}, } @article {pmid28637485, year = {2017}, author = {Singh, N and Vats, A and Sharma, A and Arora, A and Kumar, A}, title = {The development of lower respiratory tract microbiome in mice.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {61}, pmid = {28637485}, issn = {2049-2618}, mesh = {Achromobacter/genetics/isolation & purification ; Actinobacteria/genetics/isolation & purification ; *Aging ; Animals ; Animals, Newborn ; Bacteroidetes/genetics/isolation & purification ; Firmicutes/genetics/isolation & purification ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Lactobacillus/genetics/isolation & purification ; Lung/*microbiology/physiology ; *Metagenome ; Mice ; Mice, Inbred C57BL ; Microbiota/genetics/*physiology ; Proteobacteria/genetics/isolation & purification ; RNA, Ribosomal, 16S ; Respiratory System/*microbiology ; }, abstract = {BACKGROUND: Although culture-independent methods have paved the way for characterization of the lung microbiome, the dynamic changes in the lung microbiome from neonatal stage to adult age have not been investigated.

RESULTS: In this study, we tracked changes in composition and diversity of the lung microbiome in C57BL/6N mice, starting from 1-week-old neonates to 8-week-old mice. Towards this, the lungs were sterilely excised from mice of different ages from 1 to 8 weeks. High-throughput DNA sequencing of the 16S rRNA gene followed by composition and diversity analysis was utilized to decipher the microbiome in these samples. Microbiome analysis suggests that the changes in the lung microbiome correlated with age. The lung microbiome was primarily dominated by phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria in all the stages from week 1 to week 8 after birth. Although Defluvibacter was the predominant genus in 1-week-old neonatal mice, Streptococcus became the dominant genus at the age of 2 weeks. Lactobacillus, Defluvibacter, Streptococcus, and Achromobacter were the dominant genera in 3-week-old mice, while Lactobacillus and Achromobacter were the most abundant genera in 4-week-old mice. Interestingly, relatively greater diversity (at the genus level) during the age of 5 to 6 weeks was observed as compared to the earlier weeks. The diversity of the lung microbiome remained stable between 6 and 8 weeks of age.

CONCLUSIONS: In summary, we have tracked the development of the lung microbiome in mice from an early age of 1 week to adulthood. The lung microbiome is dominated by the phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. However, dynamic changes were observed at the genus level. Relatively higher richness in the microbial diversity was achieved by age of 6 weeks and then maintained at later ages. We believe that this study improves our understanding of the development of the mice lung microbiome and will facilitate further analyses of the role of the lung microbiome in chronic lung diseases.}, } @article {pmid28636759, year = {2018}, author = {Nam, JH and Yun, Y and Kim, HS and Kim, HN and Jung, HJ and Chang, Y and Ryu, S and Shin, H and Kim, HL and Kim, WS}, title = {Rosacea and its association with enteral microbiota in Korean females.}, journal = {Experimental dermatology}, volume = {27}, number = {1}, pages = {37-42}, doi = {10.1111/exd.13398}, pmid = {28636759}, issn = {1600-0625}, mesh = {Acidaminococcus ; Adult ; Case-Control Studies ; Citrobacter ; Cross-Sectional Studies ; Desulfovibrio ; Female ; *Gastrointestinal Microbiome ; Humans ; *Inflammation ; Megasphaera ; Metagenome ; Methanobrevibacter ; Middle Aged ; Peptococcaceae ; RNA, Ribosomal, 16S/analysis ; Republic of Korea ; Rosacea/epidemiology/*microbiology ; Skin Diseases/immunology/microbiology ; }, abstract = {Rosacea is a chronic inflammatory dermatosis affecting the face and eyes. An association between systemic comorbidities and rosacea has been reported, but the link to enteral microbiota is uncertain. We aimed to investigate the link between rosacea and enteral microbiota. A cross-sectional study was performed in a sample of Korean women who participated in a health check-up programme at the Kangbuk Samsung Hospital Health Screening Center between 23 June 2014 and 5 September 2014. The gut microbiome was evaluated by 16S rRNA gene and metagenome sequence analyses. A total of 12 rosacea patients and 251 controls were enrolled. We identified links between rosacea and several changes in gut microbiota: reduced abundance of Peptococcaceae family unknown genus, Methanobrevibacter (genus), Slackia (genus), Coprobacillus (genus), Citrobacter (genus), and Desulfovibrio (genus), and increased abundance of Acidaminococcus (genus), Megasphaera (genus), and Lactobacillales order unknown family unknown genus. A link between rosacea and enteral microbiota was observed in this metagenomic study. A large and elaborate study is needed to confirm these findings and to elucidate the mechanisms involved.}, } @article {pmid28636668, year = {2017}, author = {Borgo, F and Riva, A and Benetti, A and Casiraghi, MC and Bertelli, S and Garbossa, S and Anselmetti, S and Scarone, S and Pontiroli, AE and Morace, G and Borghi, E}, title = {Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests.}, journal = {PloS one}, volume = {12}, number = {6}, pages = {e0179739}, pmid = {28636668}, issn = {1932-6203}, mesh = {Alanine Transaminase/blood ; Anorexia Nervosa/*microbiology/*psychology ; Anxiety Disorders/diagnosis ; Aspartate Aminotransferases/blood ; Body Mass Index ; Butyrates/metabolism ; Case-Control Studies ; Clostridium/genetics/isolation & purification ; DNA, Bacterial/chemistry/isolation & purification/metabolism ; Depressive Disorder/diagnosis ; Diet ; Dysbiosis/microbiology ; Fatty Acids, Volatile/blood ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; *Microbiota ; Propionates/metabolism ; Psychological Tests ; Ruminococcus/genetics/isolation & purification ; Sequence Analysis, DNA ; }, abstract = {Anorexia nervosa (AN) is a psychiatric disease with devastating physical consequences, with a pathophysiological mechanism still to be elucidated. Metagenomic studies on anorexia nervosa have revealed profound gut microbiome perturbations as a possible environmental factor involved in the disease. In this study we performed a comprehensive analysis integrating data on gut microbiota with clinical, anthropometric and psychological traits to gain new insight in the pathophysiology of AN. Fifteen AN women were compared with fifteen age-, sex- and ethnicity-matched healthy controls. AN diet was characterized by a significant lower energy intake, but macronutrient analysis highlighted a restriction only in fats and carbohydrates consumption. Next generation sequencing showed that AN intestinal microbiota was significantly affected at every taxonomic level, showing a significant increase of Enterobacteriaceae, and of the archeon Methanobrevibacter smithii compared with healthy controls. On the contrary, the genera Roseburia, Ruminococcus and Clostridium, were depleted, in line with the observed reduction in AN of total short chain fatty acids, butyrate, and propionate. Butyrate concentrations inversely correlated with anxiety levels, whereas propionate directly correlated with insulin levels and with the relative abundance of Roseburia inulinivorans, a known propionate producer. BMI represented the best predictive value for gut dysbiosis and metabolic alterations, showing a negative correlation with Bacteroides uniformis (microbiota), with alanine aminotransferase (liver function), and with psychopathological scores (obsession-compulsion, anxiety, and depression), and a positive correlation with white blood cells count. In conclusion, our findings corroborate the hypothesis that the gut dysbiosis could take part in the AN neurobiology, in particular in sustaining the persistence of alterations that eventually result in relapses after renourishment and psychological therapy, but causality still needs to be proven.}, } @article {pmid28633517, year = {2017}, author = {Shin, J and Kim, YB and Jeon, JH and Choi, S and Park, IK and Kim, YM}, title = {Biomethanation of Sewage Sludge with Food Waste Leachate Via Co-Digestion.}, journal = {Journal of microbiology and biotechnology}, volume = {27}, number = {8}, pages = {1513-1518}, doi = {10.4014/jmb.1705.05048}, pmid = {28633517}, issn = {1738-8872}, mesh = {Anaerobiosis ; Archaea/growth & development/metabolism ; Bacteria/growth & development/metabolism ; Biota ; Metagenome ; Methane/*metabolism ; Sewage/*microbiology ; *Water Purification ; }, abstract = {Anaerobic mono- and co-digestion of sewage sludge and food waste leachate (FWL) were performed by assessing methane production and characterizing microbial communities. Anaerobic digestion (AD) of waste activated sludge (WAS) alone produced the lowest methane (281 ml CH4), but an approximately 80% increase in methane production was achieved via co-digestion of WAS and FWL (506 ml CH4). There were less differences in the diversity of bacterial communities in anaerobic digesters, while archaeal (ARC) and bacterial (BAC) amounts reflected AD performance. Compared with the total ARC and BAC amounts in the mono-digestion of WAS, the ARC and BAC amounts increased two and three times, respectively, during co-digestion of FWL and WAS. In characterized archaeal communities, the dominant ratio of hydrogenotrophic methanogens in the mono-digestion of WAS approached nearly a 1:1 ratio of the two acetoclastic and hydrogenotrophic methanogens in the co-digestion of FWL and WAS. The ARC/BAC ratio in the digesters varied in the range of 5.9% to 9.1%, indicating a positive correlation with the methane production of AD.}, } @article {pmid28632934, year = {2018}, author = {Savage, JH and Lee-Sarwar, KA and Sordillo, J and Bunyavanich, S and Zhou, Y and O'Connor, G and Sandel, M and Bacharier, LB and Zeiger, R and Sodergren, E and Weinstock, GM and Gold, DR and Weiss, ST and Litonjua, AA}, title = {A prospective microbiome-wide association study of food sensitization and food allergy in early childhood.}, journal = {Allergy}, volume = {73}, number = {1}, pages = {145-152}, pmid = {28632934}, issn = {1398-9995}, support = {R01 HL091528/HL/NHLBI NIH HHS/United States ; R01 HL108818/HL/NHLBI NIH HHS/United States ; T32 AI007306/AI/NIAID NIH HHS/United States ; R01 AI118833/AI/NIAID NIH HHS/United States ; K23 AI110522/AI/NIAID NIH HHS/United States ; }, mesh = {Allergens/immunology ; Biodiversity ; Child, Preschool ; Female ; Food Hypersensitivity/*epidemiology/*immunology ; Gastrointestinal Microbiome ; Humans ; *Immunization ; Immunoglobulin E/immunology ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota/immunology ; }, abstract = {BACKGROUND: Alterations in the intestinal microbiome are prospectively associated with the development of asthma; less is known regarding the role of microbiome alterations in food allergy development.

METHODS: Intestinal microbiome samples were collected at age 3-6 months in children participating in the follow-up phase of an interventional trial of high-dose vitamin D given during pregnancy. At age 3, sensitization to foods (milk, egg, peanut, soy, wheat, walnut) was assessed. Food allergy was defined as caretaker report of healthcare provider-diagnosed allergy to the above foods prior to age 3 with evidence of IgE sensitization. Analysis was performed using Phyloseq and DESeq2; P-values were adjusted for multiple comparisons.

RESULTS: Complete data were available for 225 children; there were 87 cases of food sensitization and 14 cases of food allergy. Microbial diversity measures did not differ between food sensitization and food allergy cases and controls. The genera Haemophilus (log2 fold change -2.15, P=.003), Dialister (log2 fold change -2.22, P=.009), Dorea (log2 fold change -1.65, P=.02), and Clostridium (log2 fold change -1.47, P=.002) were underrepresented among subjects with food sensitization. The genera Citrobacter (log2 fold change -3.41, P=.03), Oscillospira (log2 fold change -2.80, P=.03), Lactococcus (log2 fold change -3.19, P=.05), and Dorea (log2 fold change -3.00, P=.05) were underrepresented among subjects with food allergy.

CONCLUSIONS: The temporal association between bacterial colonization and food sensitization and allergy suggests that the microbiome may have a causal role in the development of food allergy. Our findings have therapeutic implications for the prevention and treatment of food allergy.}, } @article {pmid28631400, year = {2017}, author = {Sutcliffe, B and Chariton, AA and Harford, AJ and Hose, GC and Greenfield, P and Elbourne, LDH and Oytam, Y and Stephenson, S and Midgley, DJ and Paulsen, IT}, title = {Effects of uranium concentration on microbial community structure and functional potential.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {3323-3341}, doi = {10.1111/1462-2920.13839}, pmid = {28631400}, issn = {1462-2920}, mesh = {ATP-Binding Cassette Transporters/genetics ; Australia ; Bacteria/classification/*genetics/metabolism ; Base Sequence ; Carbon/metabolism ; Carbon Cycle/*genetics ; Ecosystem ; Geologic Sediments/*chemistry/microbiology ; Metagenomics ; Methane/metabolism ; Microbial Consortia/*drug effects ; Mining ; Nitrogen/metabolism ; Nitrogen Cycle/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Uranium/metabolism/pharmacology ; }, abstract = {Located in the Northern Territory of Australia, Ranger uranium mine is directly adjacent to the UNESCO World Heritage listed Kakadu National Park, with rehabilitation targets needed to ensure the site can be incorporated into the park following the mine's closure in 2026. This study aimed to understand the impact of uranium concentration on microbial communities, in order to identify and describe potential breakpoints in microbial ecosystem services. This is the first study to report in situ deployment of uranium-spiked sediments along a concentration gradient (0-4000 mg U kg[-1]), with the study design maximising the advantages of both field surveys and laboratory manipulative studies. Changes to microbial communities were characterised through the use of amplicon and shotgun metagenomic next-generation sequencing. Significant changes to taxonomic and functional community assembly occurred at a concentration of 1500 mg U kg[-1] sediment and above. At uranium concentrations of ≥ 1500 mg U kg[-1] , genes associated with methanogenic consortia and processes increased in relative abundance, while numerous significant changes were also seen in the relative abundances of genes involved in nitrogen cycling. Such alterations in carbon and nitrogen cycling pathways suggest that taxonomic and functional changes to microbial communities may result in changes in ecosystem processes and resilience.}, } @article {pmid28628622, year = {2017}, author = {Bossa, L and Kline, K and McDougald, D and Lee, BB and Rice, SA}, title = {Urinary catheter-associated microbiota change in accordance with treatment and infection status.}, journal = {PloS one}, volume = {12}, number = {6}, pages = {e0177633}, pmid = {28628622}, issn = {1932-6203}, mesh = {Biofilms/growth & development ; DNA, Bacterial/chemistry/metabolism ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Microbiota ; Middle Aged ; Polymerase Chain Reaction ; Probiotics ; RNA, Ribosomal, 16S/genetics/metabolism ; Sequence Analysis, DNA ; Spinal Cord Injuries/complications ; Urinary Catheters/microbiology ; Urinary Tract/*microbiology ; Urinary Tract Infections/complications/*diagnosis/microbiology/*prevention & control ; }, abstract = {The use of long-term catheterisation to manage insensate bladders, often associated with spinal cord injury (SCI), increases the risk of microbial colonisation and infection of the urinary tract. Urinary tract infection (UTI) is typically diagnosed and treated based on the culturing of organisms from the urine, although this approach overlooks low titer, slow growing and non-traditional pathogens. Here, we present an investigation of the urinary tract microbiome in catheterised SCI individuals, using T-RFLP and metagenomic sequencing of the microbial community. We monitored three neurogenic patients over a period of 12 months, who were part of a larger study investigating the efficacy of probiotics in controlling UTIs, to determine how their urinary tract microbial community composition changed over time and in relation to probiotic treatment regimens. Bacterial biofilms adherent to urinary catheters were examined as a proxy for bladder microbes. The microbial community composition of the urinary tract differed significantly between individuals. Probiotic therapy resulted in a significant change in the microbial community associated with the catheters. The community also changed as a consequence of UTI and this shift in community composition preceded the clinical diagnosis of infection. Changes in the microbiota due to probiotic treatment or infection were transient, resolving to microbial communities similar to their pre-treatment communities, suggesting that the native community was highly resilient. Based on these results, we propose that monitoring a patient's microbial community can be used to track the health of chronically catheterized patients and thus, can be used as part of a health-status monitoring program.}, } @article {pmid28628112, year = {2017}, author = {Liu, R and Hong, J and Xu, X and Feng, Q and Zhang, D and Gu, Y and Shi, J and Zhao, S and Liu, W and Wang, X and Xia, H and Liu, Z and Cui, B and Liang, P and Xi, L and Jin, J and Ying, X and Wang, X and Zhao, X and Li, W and Jia, H and Lan, Z and Li, F and Wang, R and Sun, Y and Yang, M and Shen, Y and Jie, Z and Li, J and Chen, X and Zhong, H and Xie, H and Zhang, Y and Gu, W and Deng, X and Shen, B and Xu, X and Yang, H and Xu, G and Bi, Y and Lai, S and Wang, J and Qi, L and Madsen, L and Wang, J and Ning, G and Kristiansen, K and Wang, W}, title = {Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention.}, journal = {Nature medicine}, volume = {23}, number = {7}, pages = {859-868}, pmid = {28628112}, issn = {1546-170X}, mesh = {Adiposity ; Adult ; Animals ; Bacteroides/genetics ; Bacteroides thetaiotaomicron/genetics ; Bariatric Surgery ; Case-Control Studies ; DNA, Bacterial/*analysis ; Dysbiosis/metabolism/*microbiology ; Female ; Fusobacterium/genetics ; Gastrectomy ; Gastrointestinal Microbiome/*genetics ; Glutamic Acid/blood ; Humans ; Male ; *Metabolome ; Metagenome ; Mice ; Obesity/metabolism/*microbiology/surgery ; Weight Gain ; Young Adult ; }, abstract = {Emerging evidence has linked the gut microbiome to human obesity. We performed a metagenome-wide association study and serum metabolomics profiling in a cohort of lean and obese, young, Chinese individuals. We identified obesity-associated gut microbial species linked to changes in circulating metabolites. The abundance of Bacteroides thetaiotaomicron, a glutamate-fermenting commensal, was markedly decreased in obese individuals and was inversely correlated with serum glutamate concentration. Consistently, gavage with B. thetaiotaomicron reduced plasma glutamate concentration and alleviated diet-induced body-weight gain and adiposity in mice. Furthermore, weight-loss intervention by bariatric surgery partially reversed obesity-associated microbial and metabolic alterations in obese individuals, including the decreased abundance of B. thetaiotaomicron and the elevated serum glutamate concentration. Our findings identify previously unknown links between intestinal microbiota alterations, circulating amino acids and obesity, suggesting that it may be possible to intervene in obesity by targeting the gut microbiota.}, } @article {pmid28625159, year = {2017}, author = {Marotz, C and Amir, A and Humphrey, G and Gaffney, J and Gogul, G and Knight, R}, title = {DNA extraction for streamlined metagenomics of diverse environmental samples.}, journal = {BioTechniques}, volume = {62}, number = {6}, pages = {290-293}, doi = {10.2144/000114559}, pmid = {28625159}, issn = {1940-9818}, mesh = {Bacteria/*genetics/isolation & purification ; DNA, Bacterial/genetics/*isolation & purification ; Feces/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; Sequence Analysis, DNA/methods ; Skin/microbiology ; Soil Microbiology ; Water Microbiology ; }, abstract = {A major bottleneck for metagenomic sequencing is rapid and efficient DNA extraction. Here, we compare the extraction efficiencies of three magnetic bead-based platforms (KingFisher, epMotion, and Tecan) to a standardized column-based extraction platform across a variety of sample types, including feces, oral, skin, soil, and water. Replicate sample plates were extracted and prepared for 16S rRNA gene amplicon sequencing in parallel to assess extraction bias and DNA quality. The data demonstrate that any effect of extraction method on sequencing results was small compared with the variability across samples; however, the KingFisher platform produced the largest number of high-quality reads in the shortest amount of time. Based on these results, we have identified an extraction pipeline that dramatically reduces sample processing time without sacrificing bacterial taxonomic or abundance information.}, } @article {pmid28624689, year = {2017}, author = {Clavel, T and Lagkouvardos, I and Stecher, B}, title = {From complex gut communities to minimal microbiomes via cultivation.}, journal = {Current opinion in microbiology}, volume = {38}, number = {}, pages = {148-155}, doi = {10.1016/j.mib.2017.05.013}, pmid = {28624689}, issn = {1879-0364}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Mammals ; Metagenomics/*methods ; Microbiological Techniques/*methods ; }, abstract = {The mammalian gut microbiota is dominated by populations of bacteria, mostly strict anaerobes. Because these bacteria can influence the health of their host, it is important to investigate their diversity and functions, which can be done via culture-based or molecular approaches. In recent years, microbiologists have very often preferred the use of molecular techniques, as they do not limit the analysis to the fraction of communities that can be grown in the laboratory. In reality, cultivation and molecular methods are complementary, and we are now witnessing a period of unification. Obtaining strains that can be grown in vitro is currently indispensable for the description of novel diversity and eventually the improvement of taxonomic and sequence databases. Moreover, cultivation allows using host-specific minimal consortia of microbes that are helpful for detailed and standardized studies of gut microbial communities and microbe-host interactions. Molecular techniques are helpful because they can provide insights into strain-level diversity and the functional potential of organisms. Furthermore, genomic and metagenomic data allow inferring growth conditions for uncultured bacteria and also enable detailed genetic studies. In the present manuscript, we highlight recent work on culture-based investigation of mammalian gut bacteria and microbe-host interactions and give our opinions on challenges and perspectives in the field.}, } @article {pmid28624548, year = {2017}, author = {Morris, DJ and Ridlon, JM}, title = {Glucocorticoids and gut bacteria: "The GALF Hypothesis" in the metagenomic era.}, journal = {Steroids}, volume = {125}, number = {}, pages = {1-13}, doi = {10.1016/j.steroids.2017.06.002}, pmid = {28624548}, issn = {1878-5867}, mesh = {Animals ; Colorectal Neoplasms/metabolism/microbiology ; *Gastrointestinal Microbiome ; Glucocorticoids/*metabolism ; Humans ; Hypertension/metabolism/microbiology ; }, abstract = {A new concept is emerging in biomedical sciences: the gut microbiota is a virtual 'organ' with endocrine function. Here, we explore the literature pertaining to the role of gut microbial metabolism of endogenous adrenocorticosteroids as a contributing factor in the etiology of essential hypertension. A body of literature demonstrates that bacterial products of glucocorticoid metabolism are absorbed into the portal circulation, and pass through the kidney before excretion into urine. Apparent mineralocorticoid excess (AME) syndrome patients were found to have congenital mutations resulting in non-functional renal 11β-hydroxysteroid dehydrogenase-2 (11β-HSD2) and severe hypertension often lethal in childhood. 11β-HSD2 acts as a "guardian" enzyme protecting the mineralocorticoid receptor from excess cortisol, preventing sodium and water retention in the normotensive state. Licorice root, whose active ingredient, glycerrhetinic acid (GA), inhibits renal 11β-HSD2, and thereby causes hypertension in some individuals. Bacterially derived glucocorticoid metabolites may cause hypertension in some patients by a similar mechanism. Parallel observations in gut microbiology coupled with screening of endogenous steroids as inhibitors of 11β-HSD2 have implicated particular gut bacteria in essential hypertension through the production of glycerrhetinic acid-like factors (GALFs). A protective role of GALFs produced by gut bacteria in the etiology of colorectal cancer is also explored.}, } @article {pmid28623321, year = {2017}, author = {Deng, ZL and Szafrański, SP and Jarek, M and Bhuju, S and Wagner-Döbler, I}, title = {Dysbiosis in chronic periodontitis: Key microbial players and interactions with the human host.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3703}, pmid = {28623321}, issn = {2045-2322}, mesh = {Archaea ; Case-Control Studies ; Chronic Periodontitis/*microbiology/parasitology/virology ; Computational Biology/methods ; *Dysbiosis ; Gene Expression Regulation, Bacterial ; Host-Pathogen Interactions ; Humans ; Metagenome ; Metagenomics/methods ; Microbiota ; Nucleophosmin ; RNA, Ribosomal, 18S/genetics ; RNA, Viral ; Virulence Factors ; }, abstract = {Periodontitis is an extremely prevalent disease worldwide and is driven by complex dysbiotic microbiota. Here we analyzed the transcriptional activity of the periodontal pocket microbiota from all domains of life as well as the human host in health and chronic periodontitis. Bacteria showed strong enrichment of 18 KEGG functional modules in chronic periodontitis, including bacterial chemotaxis, flagellar assembly, type III secretion system, type III CRISPR-Cas system, and two component system proteins. Upregulation of these functions was driven by the red-complex pathogens and candidate pathogens, e.g. Filifactor alocis, Prevotella intermedia, Fretibacterium fastidiosum and Selenomonas sputigena. Nine virulence factors were strongly up-regulated, among them the arginine deiminase arcA from Porphyromonas gingivalis and Mycoplasma arginini. Viruses and archaea accounted for about 0.1% and 0.22% of total putative mRNA reads, respectively, and a protozoan, Entamoeba gingivalis, was highly enriched in periodontitis. Fourteen human transcripts were enriched in periodontitis, including a gene for a ferric iron binding protein, indicating competition with the microbiota for iron, and genes associated with cancer, namely nucleolar phosphoprotein B23, ankyrin-repeat domain 30B-like protein and beta-enolase. The data provide evidence on the level of gene expression in vivo for the potentially severe impact of the dysbiotic microbiota on human health.}, } @article {pmid28623024, year = {2017}, author = {Weisse, T}, title = {Functional diversity of aquatic ciliates.}, journal = {European journal of protistology}, volume = {61}, number = {Pt B}, pages = {331-358}, doi = {10.1016/j.ejop.2017.04.001}, pmid = {28623024}, issn = {1618-0429}, mesh = {*Biodiversity ; Ciliophora/*classification/*physiology ; Fresh Water ; }, abstract = {This paper first reviews the concept of functional diversity in general terms and then applies it to free-living aquatic ciliates. Ciliates are extremely versatile organisms and display an enormous functional diversity as key elements of pelagic food webs, acting as predators of bacteria, algae, other protists and even some metazoans. Planktonic ciliates are important food for zooplankton, and mixotrophic and functionally autotrophic species may significantly contribute to primary production in the ocean and in lakes. The co-occurrence of many ciliate species in seemingly homogenous environments indicates a wide range of their ecological niches. Variation in space and time may foster co-occurrence and prevent violating the competitive exclusion principle among ciliates using the same resources. Considering that many ciliates may be dormant and/or rare in many habitats, ciliate species diversity must be higher than can be deduced from simple sampling techniques; molecular methods of identification clearly point to this hidden diversity. From a functional point of view, the question is how much of this diversity represents redundancy. A key challenge for future research is to link the ecophysiological performance of naturally co-occurring ciliates to their functional genes. To this end, more experimental research is needed with with functionally different species.}, } @article {pmid28620208, year = {2017}, author = {Xu, Y and Xie, Z and Wang, H and Shen, Z and Guo, Y and Gao, Y and Chen, X and Wu, Q and Li, X and Wang, K}, title = {Bacterial Diversity of Intestinal Microbiota in Patients with Substance Use Disorders Revealed by 16S rRNA Gene Deep Sequencing.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3628}, pmid = {28620208}, issn = {2045-2322}, mesh = {Adult ; Bacteria/*classification/*genetics ; Biodiversity ; Case-Control Studies ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Phylogeny ; *RNA, Ribosomal, 16S ; Substance-Related Disorders/*etiology ; Young Adult ; }, abstract = {Substance abuse and addiction are worldwide concerns. In China, populated with over 1.3 billion people, emerging studies show a steady increase in substance abuse and substance-related problems. Some of the major challenges include a lack of an effective evaluation platform to determine the health status of substance-addicted subjects. It is known that the intestinal microbiota is associated to the occurrence and development of human diseases. However, the changes of bacterial diversity of intestinal microbiota in substance-addicted subjects have not been clearly characterized. Herein, we examined the composition and diversity of intestinal microbiota in 45 patients with substance use disorders (SUDs) and in 48 healthy controls (HCs). The results show that the observed species diversity index and the abundance of Thauera, Paracoccus, and Prevotella are significantly higher in SUDs compared to HCs. The functional diversity of the putative metagenomes analysis reveals that pathways including translation, DNA replication and repair, and cell growth and death are over-represented while cellular processes and signaling, and metabolism are under-represented in SUDs. Overall, the analyses show that there seem to be changes in the microbiota that are associated with substance use across an array of SUDs, providing fundamental knowledge for future research in substance-addiction assessment tests.}, } @article {pmid28612429, year = {2017}, author = {Tanner, K and Vilanova, C and Porcar, M}, title = {Bioprospecting challenges in unusual environments.}, journal = {Microbial biotechnology}, volume = {10}, number = {4}, pages = {671-673}, pmid = {28612429}, issn = {1751-7915}, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; Biodiversity ; Bioprospecting/*trends ; Biotechnology ; *Environmental Microbiology ; Metagenomics ; }, } @article {pmid28610994, year = {2017}, author = {Chi, L and Gao, B and Bian, X and Tu, P and Ru, H and Lu, K}, title = {Manganese-induced sex-specific gut microbiome perturbations in C57BL/6 mice.}, journal = {Toxicology and applied pharmacology}, volume = {331}, number = {}, pages = {142-153}, pmid = {28610994}, issn = {1096-0333}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 ES024950/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Female ; Gastrointestinal Microbiome/*drug effects/physiology ; Gastrointestinal Tract/drug effects/physiology ; Male ; Manganese/*administration & dosage/*toxicity ; Mice ; Mice, Inbred C57BL ; *Sex Characteristics ; }, abstract = {Overexposure to manganese (Mn) leads to toxic effects, such as promoting the development of Parkinson's-like neurological disorders. The gut microbiome is deeply involved in immune development, host metabolism, and xenobiotics biotransformation, and significantly influences central nervous system (CNS) via the gut-brain axis, i.e. the biochemical signaling between the gastrointestinal tract and the CNS. However, it remains unclear whether Mn can affect the gut microbiome and its metabolic functions, particularly those linked to neurotoxicity. In addition, sex-specific effects of Mn have been reported, with no mechanism being identified yet. Recently, we have shown that the gut microbiome is largely different between males and females, raising the possibility that differential gut microbiome responses may contribute to sex-selective toxicity of Mn. Here, we applied high-throughput sequencing and gas chromatography-mass spectrometry (GC-MS) metabolomics to explore how Mn[2+] exposure affects the gut microbiome and its metabolism in C57BL/6 mice. Mn[2+] exposure perturbed the gut bacterial compositions, functional genes and fecal metabolomes in a highly sex-specific manner. In particular, bacterial genes and/or key metabolites of neurotransmitter synthesis and pro-inflammatory mediators are significantly altered by Mn[2+] exposure, which can potentially affect chemical signaling of gut-brain interactions. Likewise, functional genes involved in iron homeostasis, flagellar motility, quorum sensing, and Mn transportation/oxidation are also widely changed by Mn[2+] exposure. Taken together, this study has demonstrated that Mn[2+] exposure perturbs the gut microbiome and its metabolic functions, which highlights the potential role of the gut microbiome in Mn[2+] toxicity, particularly its sex-specific toxic effects.}, } @article {pmid28609785, year = {2017}, author = {Philips, A and Stolarek, I and Kuczkowska, B and Juras, A and Handschuh, L and Piontek, J and Kozlowski, P and Figlerowicz, M}, title = {Comprehensive analysis of microorganisms accompanying human archaeological remains.}, journal = {GigaScience}, volume = {6}, number = {7}, pages = {1-13}, pmid = {28609785}, issn = {2047-217X}, mesh = {Archaeology/*methods ; Bone and Bones/microbiology ; *DNA, Ancient ; Fossils/microbiology ; Humans ; Metagenome ; *Microbiota ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenome analysis has become a common source of information about microbial communities that occupy a wide range of niches, including archaeological specimens. It has been shown that the vast majority of DNA extracted from ancient samples come from bacteria (presumably modern contaminants). However, characterization of microbial DNA accompanying human remains has never been done systematically for a wide range of different samples. We used metagenomic approaches to perform comparative analyses of microorganism communities present in 161 archaeological human remains. DNA samples were isolated from the teeth of human skeletons dated from 100 AD to 1200 AD. The skeletons were collected from 7 archaeological sites in Central Europe and stored under different conditions. The majority of identified microbes were ubiquitous environmental bacteria that most likely contaminated the host remains not long ago. We observed that the composition of microbial communities was sample-specific and not correlated with its temporal or geographical origin. Additionally, traces of bacteria and archaea typical for human oral/gut flora, as well as potential pathogens, were identified in two-thirds of the samples. The genetic material of human-related species, in contrast to the environmental species that accounted for the majority of identified bacteria, displayed DNA damage patterns comparable with endogenous human ancient DNA, which suggested that these microbes might have accompanied the individual before death. Our study showed that the microbiome observed in an individual sample is not reliant on the method or duration of sample storage. Moreover, shallow sequencing of DNA extracted from ancient specimens and subsequent bioinformatics analysis allowed both the identification of ancient microbial species, including potential pathogens, and their differentiation from contemporary species that colonized human remains more recently.}, } @article {pmid28609295, year = {2017}, author = {Miller, M and Zhu, C and Bromberg, Y}, title = {clubber: removing the bioinformatics bottleneck in big data analyses.}, journal = {Journal of integrative bioinformatics}, volume = {14}, number = {2}, pages = {}, pmid = {28609295}, issn = {1613-4516}, support = {U01 GM115486/GM/NIGMS NIH HHS/United States ; }, mesh = {Automation ; Bathing Beaches ; Computational Biology/*methods ; *Computing Methodologies ; Datasets as Topic ; Gulf of Mexico ; Metagenome/genetics ; Microbiota/genetics ; Molecular Sequence Annotation ; Petroleum Pollution/adverse effects ; *Software ; }, abstract = {With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. clubber is our automated cluster-load balancing system developed for optimizing these "big data" analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. clubber's goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC) resources. Notably, the latter can be added on demand, including cloud-based resources, and/or featuring heterogeneous environments. The second goal of making HPCs user-friendly is facilitated by an interactive web interface and a RESTful API, allowing for job monitoring and result retrieval. We used clubber to speed up our pipeline for annotating molecular functionality of metagenomes. Here, we analyzed the Deepwater Horizon oil-spill study data to quantitatively show that the beach sands have not yet entirely recovered. Further, our analysis of the CAMI-challenge data revealed that microbiome taxonomic shifts do not necessarily correlate with functional shifts. These examples (21 metagenomes processed in 172 min) clearly illustrate the importance of clubber in the everyday computational biology environment.}, } @article {pmid28607413, year = {2017}, author = {Xiao, Y and Yan, H and Diao, H and Yu, B and He, J and Yu, J and Zheng, P and Mao, X and Luo, Y and Chen, D}, title = {Early Gut Microbiota Intervention Suppresses DSS-Induced Inflammatory Responses by Deactivating TLR/NLR Signalling in Pigs.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3224}, pmid = {28607413}, issn = {2045-2322}, mesh = {Animals ; Colitis/chemically induced/*genetics/metabolism ; Cytokines/metabolism ; Dextran Sulfate ; Fecal Microbiota Transplantation/methods ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Gene Expression ; Genotype ; NLR Proteins/*genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Signal Transduction/*genetics ; Species Specificity ; Swine/classification/*genetics/metabolism ; Toll-Like Receptors/*genetics/metabolism ; }, abstract = {Recent metagenomic studies suggest that innate and adaptive immune phenotypes can be programmed via gut microbiota-host interactions mediated via activation of pattern recognition receptors (PRRs) on host cells. In this study, we used two extremely different pig lines (the Yorkshire and the Tibetan) to test the hypothesis that the transplantation of gut microbiota could transfer certain immunologic characteristics from donor to recipient. The faecal microbiota of these two pig lines was transplanted in healthy commercial hybrid newborn piglets to establish the "Tibetan-intervened" and "Yorkshire-intervened" porcine models. Then, acute colitis was induced using dextran sulphate sodium (DSS), which activated Toll-/NOD-like receptor (TLR/NLR) signalling in the colonic tissues of the "Yorkshire-intervened" piglets, leading to increases in pro-inflammatory cytokines and immune cells and causing intestinal injuries. Conversely, DSS administration had little influence on the "Tibetan-intervened" piglets, which showed no significant inflammation and no changes in cytokines, immune cells, or signalling molecules, including TLRs, NLRs, MYD88 and NF-κB, after DSS treatment. These results indicate that pigs inoculated with the Tibetan microbiota acquired relatively strong resistance to experimental colitis, suggesting that the genotype of the host contributes to the uniqueness of its intestinal microbial community, whereas the microbiota plays a vital role in programming the immune phenotypes of the host.}, } @article {pmid28607352, year = {2017}, author = {Zhou, J and Jiang, X and Wei, D and Zhao, B and Ma, M and Chen, S and Cao, F and Shen, D and Guan, D and Li, J}, title = {Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3267}, pmid = {28607352}, issn = {2045-2322}, mesh = {Bacteria/*classification/genetics ; Biodiversity ; China ; Crops, Agricultural ; Fertilizers/*analysis ; Metagenome ; Metagenomics/methods ; Nitrogen/*analysis ; RNA, Ribosomal, 16S ; *Seasons ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Long-term use of inorganic nitrogen (N) fertilization has greatly influenced the bacterial community in black soil of northeast China. It is unclear how N affects the bacterial community in two successive crop seasons in the same field for this soil type. We sampled soils from a long-term fertilizer experimental field in Harbin city with three N gradients. We applied sequencing and quantitative PCR targeting at the 16S rRNA gene to examine shifts in bacterial communities and test consistent shifts and driving-factors bacterial responses to elevated N additions. N addition decreased soil pH and bacterial 16S rDNA copy numbers, and increased soil N and crop yield. N addition consistently decreased bacterial diversity and altered bacterial community composition, by increasing the relative abundance of Proteobacteria, and decreasing that of Acidobacteria and Nitrospirae in both seasons. Consistent changes in the abundant classes and genera, and the structure of the bacterial communities across both seasons were observed. Our results suggest that increases in N inputs had consistent effects on the richness, diversity and composition of soil bacterial communities across the crop seasons in two continuous years, and the N addition and the subsequent edaphic changes were important factors in shaping bacterial community structures.}, } @article {pmid28606169, year = {2017}, author = {Gao, B and Tu, P and Bian, X and Chi, L and Ru, H and Lu, K}, title = {Profound perturbation induced by triclosan exposure in mouse gut microbiome: a less resilient microbial community with elevated antibiotic and metal resistomes.}, journal = {BMC pharmacology & toxicology}, volume = {18}, number = {1}, pages = {46}, pmid = {28606169}, issn = {2050-6511}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 ES024950/ES/NIEHS NIH HHS/United States ; }, mesh = {Administration, Oral ; Animals ; Anti-Infective Agents, Local/*pharmacology ; Drinking Water ; Drug Resistance, Microbial/genetics ; Gastrointestinal Microbiome/*drug effects/genetics ; Metagenomics ; Metals, Heavy/toxicity ; Mice, Inbred C57BL ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Triclosan/*pharmacology ; }, abstract = {BACKGROUND: Environmental chemical-induced perturbations of gut microbiome are associated with a series of adverse health outcomes. The effects of triclosan on human health have been controversial in recent years. The purpose of this study is to investigate the functional impact of triclosan on the mouse gut microbiome and the link between triclosan exposure and resistomes in gut bacteria.

METHODS: We combined 16S rRNA gene sequencing and shotgun metagenomics sequencing to examine the compositional and functional impact of triclosan exposure on the gut microbiota of C57BL/6 mice.

RESULTS: 16S rRNA sequencing results revealed that 13-week triclosan exposure in drinking water induced significant perturbations in mouse gut bacterial assemblages with distinct trajectories compared to controls. Metagenomics sequencing results indicated a remarkable enrichment of gut bacterial genes related to triclosan resistance, stress response, antibiotic resistance and heavy metal resistance.

CONCLUSIONS: Triclosan exposure has a profound impact on the mouse gut microbiome by inducing perturbations at both compositional and functional levels. To our best knowledge, this is the first evidence regarding the functional alterations of gut microbiome induced by triclosan exposure, which may provide novel mechanistic insights into triclosan exposure and associated diseases.}, } @article {pmid28605130, year = {2017}, author = {Martín-Peláez, S and Camps-Bossacoma, M and Massot-Cladera, M and Rigo-Adrover, M and Franch, À and Pérez-Cano, FJ and Castell, M}, title = {Effect of cocoa's theobromine on intestinal microbiota of rats.}, journal = {Molecular nutrition & food research}, volume = {61}, number = {10}, pages = {}, doi = {10.1002/mnfr.201700238}, pmid = {28605130}, issn = {1613-4133}, mesh = {Animals ; Bifidobacterium/drug effects/isolation & purification ; Butyric Acid/metabolism ; Cacao/*chemistry ; Clostridium histolyticum/drug effects/isolation & purification ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Diet ; Escherichia coli/drug effects/isolation & purification ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; Immunoglobulin A/metabolism ; In Situ Hybridization, Fluorescence ; Lactic Acid/metabolism ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Inbred Lew ; Streptococcus/drug effects/isolation & purification ; Theobromine/*pharmacology ; }, abstract = {SCOPE: To establish the role of cocoa theobromine on gut microbiota composition and fermentation products after cocoa consumption in rats.

METHODS AND RESULTS: Lewis rats were fed either a standard diet (RF diet), a diet containing 10% cocoa (CC diet) or a diet including 0.25% theobromine (TB diet) for 15 days. Gut microbiota (fluorescence in situ hybridization coupled to flow cytometry and metagenomics analysis), SCFA and IgA-coated bacteria were analyzed in fecal samples. CC and TB diets induced lower counts of E. coli whereas TB diet led to lower counts of Bifidobacterium spp., Streptococcus spp. and Clostridium histolyticum-C. perfingens group compared to RF diet. Metagenomics analysis also revealed a different microbiota pattern among the studied groups. The SCFA content was higher after both CC and TB diets, which was mainly due to enhanced butyric acid production. Furthermore, both diets decreased the proportion of IgA-coated bacteria.

CONCLUSION: Cocoa's theobromine plays a relevant role in some effects related to cocoa intake, such as the lower proportion of IgA-coated bacteria. Moreover, theobromine modifies gut microbiota although other cocoa compounds could also act on intestinal bacteria, attenuating or enhancing the theobromine effects.}, } @article {pmid28604259, year = {2018}, author = {Tansirichaiya, S and Reynolds, LJ and Cristarella, G and Wong, LC and Rosendahl, K and Roberts, AP}, title = {Reduced Susceptibility to Antiseptics Is Conferred by Heterologous Housekeeping Genes.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {24}, number = {2}, pages = {105-112}, doi = {10.1089/mdr.2017.0105}, pmid = {28604259}, issn = {1931-8448}, mesh = {Amino Acid Sequence ; Anti-Infective Agents, Local/*pharmacology ; Cetrimonium ; Cetrimonium Compounds/pharmacology ; Cetylpyridinium/pharmacology ; Clone Cells ; Drug Resistance, Bacterial/genetics ; Enoyl-(Acyl-Carrier-Protein) Reductase (NADH)/*genetics/metabolism ; Escherichia coli/*drug effects/enzymology/genetics ; Escherichia coli Proteins/*genetics/metabolism ; Fatty Acid Synthase, Type II/genetics/metabolism ; Gastrointestinal Microbiome/drug effects/genetics ; *Gene Expression Regulation, Bacterial ; *Genes, Essential ; Humans ; Microbial Sensitivity Tests ; Mouth/microbiology ; Sequence Alignment ; Sequence Homology, Amino Acid ; Static Electricity ; Triclosan/pharmacology ; UDPglucose 4-Epimerase/*genetics/metabolism ; Veillonella/drug effects/enzymology/genetics ; }, abstract = {Antimicrobial resistance is common in the microbial inhabitants of the human oral cavity. Antimicrobials are commonly encountered by oral microbes as they are present in our diet, both naturally and anthropogenically, and also used in oral healthcare products and amalgam fillings. We aimed to determine the presence of genes in the oral microbiome conferring reduced susceptibility to common antimicrobials. From an Escherichia coli library, 12,277 clones were screened and ten clones with reduced susceptibility to triclosan were identified. The genes responsible for this phenotype were identified as fabI, originating from a variety of different bacteria. The gene fabI encodes an enoyl-acyl carrier protein reductase (ENR), which is essential for fatty acid synthesis in bacteria. Triclosan binds to ENR, preventing fatty acid synthesis. By introducing the inserts containing fabI, ENR is likely overexpressed in E. coli, reducing the inhibitory effect of triclosan. Another clone was found to have reduced susceptibility to cetyltrimethylammonium bromide and cetylpyridinium chloride. This phenotype was conferred by a UDP-glucose 4-epimerase gene, galE, homologous to one from Veillonella parvula. The product of galE is involved in lipopolysaccharide production. Analysis of the E. coli host cell surface showed that the charge was more positive in the presence of galE, which likely reduces the binding of these positively charged antiseptics to the bacteria. This is the first time galE has been shown to confer resistance against quaternary ammonium compounds and represents a novel, epimerase-based, global cell adaptation, which confers resistance to cationic antimicrobials.}, } @article {pmid28603873, year = {2017}, author = {Ushio, M and Fukuda, H and Inoue, T and Makoto, K and Kishida, O and Sato, K and Murata, K and Nikaido, M and Sado, T and Sato, Y and Takeshita, M and Iwasaki, W and Yamanaka, H and Kondoh, M and Miya, M}, title = {Environmental DNA enables detection of terrestrial mammals from forest pond water.}, journal = {Molecular ecology resources}, volume = {17}, number = {6}, pages = {e63-e75}, doi = {10.1111/1755-0998.12690}, pmid = {28603873}, issn = {1755-0998}, mesh = {Animals ; DNA/genetics/*isolation & purification ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; *Forests ; Japan ; Mammals/*classification/genetics ; Metagenomics/*methods ; *Ponds ; Water/*analysis ; }, abstract = {Terrestrial animals must have frequent contact with water to survive, implying that environmental DNA (eDNA) originating from those animals should be detectable from places containing water in terrestrial ecosystems. Aiming to detect the presence of terrestrial mammals using forest water samples, we applied a set of universal PCR primers (MiMammal, a modified version of fish universal primers) for metabarcoding mammalian eDNA. The versatility of MiMammal primers was tested in silico and by amplifying DNAs extracted from tissues. The results suggested that MiMammal primers are capable of amplifying and distinguishing a diverse group of mammalian species. In addition, analyses of water samples from zoo cages of mammals with known species composition suggested that MiMammal primers could successfully detect mammalian species from water samples in the field. Then, we performed an experiment to detect mammals from natural ecosystems by collecting five 500-ml water samples from ponds in two cool-temperate forests in Hokkaido, northern Japan. MiMammal amplicon libraries were constructed using eDNA extracted from water samples, and sequences generated by Illumina MiSeq were subjected to data processing and taxonomic assignment. We thereby detected multiple species of mammals common to the sampling areas, including deer (Cervus nippon), mouse (Mus musculus), vole (Myodes rufocanus), raccoon (Procyon lotor), rat (Rattus norvegicus) and shrew (Sorex unguiculatus). Many previous applications of the eDNA metabarcoding approach have been limited to aquatic/semiaquatic systems, but the results presented here show that the approach is also promising even for forest mammal biodiversity surveys.}, } @article {pmid28602995, year = {2017}, author = {Wang, H and Zheng, H and Browne, F and Roehe, R and Dewhurst, RJ and Engel, F and Hemmje, M and Lu, X and Walsh, P}, title = {Integrated metagenomic analysis of the rumen microbiome of cattle reveals key biological mechanisms associated with methane traits.}, journal = {Methods (San Diego, Calif.)}, volume = {124}, number = {}, pages = {108-119}, doi = {10.1016/j.ymeth.2017.05.029}, pmid = {28602995}, issn = {1095-9130}, mesh = {Animals ; Archaeal Proteins/classification/*genetics/metabolism ; Bacterial Proteins/classification/*genetics/metabolism ; Cattle ; Fungal Proteins/classification/*genetics/metabolism ; Gastrointestinal Microbiome/*genetics ; Gene Ontology ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Metagenomics/methods ; Methane/*biosynthesis ; Molecular Sequence Annotation ; Oxidoreductases/classification/genetics/metabolism ; Protozoan Proteins/classification/*genetics/metabolism ; Rumen/microbiology ; }, abstract = {Methane is one of the major contributors to global warming. The rumen microbiota is directly involved in methane production in cattle. The link between variation in rumen microbial communities and host genetics has important applications and implications in bioscience. Having the potential to reveal the full extent of microbial gene diversity and complex microbial interactions, integrated metagenomics and network analysis holds great promise in this endeavour. This study investigates the rumen microbial community in cattle through the integration of metagenomic and network-based approaches. Based on the relative abundance of 1570 microbial genes identified in a metagenomics analysis, the co-abundance network was constructed and functional modules of microbial genes were identified. One of the main contributions is to develop a random matrix theory-based approach to automatically determining the correlation threshold used to construct the co-abundance network. The resulting network, consisting of 549 microbial genes and 3349 connections, exhibits a clear modular structure with certain trait-specific genes highly over-represented in modules. More specifically, all the 20 genes previously identified to be associated with methane emissions are found in a module (hypergeometric test, p<10[-11]). One third of genes are involved in methane metabolism pathways. The further examination of abundance profiles across 8 samples of genes highlights that the revealed pattern of metagenomics abundance has a strong association with methane emissions. Furthermore, the module is significantly enriched with microbial genes encoding enzymes that are directly involved in methanogenesis (hypergeometric test, p<10[-9]).}, } @article {pmid28597821, year = {2017}, author = {El-Jurdi, N and Ghannoum, MA}, title = {The Mycobiome: Impact on Health and Disease States.}, journal = {Microbiology spectrum}, volume = {5}, number = {3}, pages = {}, pmid = {28597821}, issn = {2165-0497}, mesh = {Bacterial Physiological Phenomena ; Cell Transplantation ; *Disease ; Dysbiosis/microbiology ; Fungi/pathogenicity/physiology ; *Health Status ; Host-Pathogen Interactions/immunology/physiology ; Humans ; Metabolome/genetics/physiology ; Metagenome ; Microbial Interactions/immunology/physiology ; Microbiota/genetics/immunology/physiology ; Mycobiome/genetics/immunology/*physiology ; Neoplasms/microbiology ; Symbiosis ; }, abstract = {The term "microbiome" refers to microorganisms (microbiota) and their genomes (metagenome) coexisting with their hosts. Some researchers coined the term "second genome" to underscore the importance of the microbiota and its collective metagenome on their host's health and/or disease. It is now undeniable that the commensal fungal microorganisms, alongside the other components of the microbiota, play a central role in association with the human host. In recognition, projects were launched nationally and internationally to unify efforts to characterize the microbiome and elucidate the functional role of the microbiota and the mechanism(s) by which these organisms and their metabolites (metabolome) may affect health and disease states. In this article, we will highlight the role of the fungal community as an indispensable component of the microbiome.}, } @article {pmid28597254, year = {2017}, author = {Gopal, M and Bhute, SS and Gupta, A and Prabhu, SR and Thomas, GV and Whitman, WB and Jangid, K}, title = {Changes in structure and function of bacterial communities during coconut leaf vermicomposting.}, journal = {Antonie van Leeuwenhoek}, volume = {110}, number = {10}, pages = {1339-1355}, doi = {10.1007/s10482-017-0894-7}, pmid = {28597254}, issn = {1572-9699}, support = {BT/PR/0054/NDB/52/94/2007//Department of Biotechnology , Ministry of Science and Technology/ ; }, mesh = {Animals ; Bacteria/classification/genetics ; Bacterial Proteins/metabolism ; *Biodiversity ; *Cocos ; *Composting ; DNA, Bacterial/genetics ; Metagenomics/methods ; *Microbiota ; Oligochaeta/*metabolism/microbiology ; Plant Leaves/*metabolism ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {To understand bacterial community dynamics during the vermicomposting of lignin-rich coconut leaves using an indigenous isolate of an epigeic earthworm, Eudrilus sp., we employed amplicon-based pyrosequencing of the V1 to V3 region of the 16S rRNA genes. Total community DNA was isolated from two separate vermicomposting tanks in triplicate at four different stages of the process: pre-decomposition (15th day), initial vermicomposting (45th day), 50-70% vermicomposting (75th day) and mature vermicompost (105th day). Alpha diversity measurements revealed an increase in bacterial diversity till the 75th day, which then declined in the mature vermicompost. Beta diversity comparisons showed formation of distinct, stage-specific communities. In terms of relative abundance, the Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, Planctomycetes, TM7 and WS3 groups increased until the 50-70% vermicomposting stage (p = 0.05). During the same time, the abundance of Bacteroidetes and Proteobacteria decreased. In contrast, the levels of Firmicutes increased throughout the 105-day vermicomposting process. The distribution of the most abundant OTUs revealed that each stage of the vermicomposting process possessed its own unique microbiome. Predictions based on the OTUs present by PICRUSt suggested a functional shift in the microbiome during vermicomposting. Enzymes and pathways of lipid and lignin metabolism were predicted to be initially abundant, but by the end of the process, biosynthesis of secondary metabolites and plant beneficial properties were enriched. The study revealed that bacterial communities undergo a continuous change throughout the vermicomposting process and that certain OTUs associated with specific stages could be targets for further improvements in the process.}, } @article {pmid28595639, year = {2017}, author = {Wolff, SM and Ellison, MJ and Hao, Y and Cockrum, RR and Austin, KJ and Baraboo, M and Burch, K and Lee, HJ and Maurer, T and Patil, R and Ravelo, A and Taxis, TM and Truong, H and Lamberson, WR and Cammack, KM and Conant, GC}, title = {Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {60}, pmid = {28595639}, issn = {2049-2618}, mesh = {Animal Feed/analysis ; Animals ; *Diet ; Digestion/physiology ; Edible Grain ; Feeding Behavior ; Gastrointestinal Microbiome/*physiology ; *Metabolic Networks and Pathways ; *Metagenomics ; Rumen/*microbiology/physiology ; Sheep/*microbiology/physiology ; }, abstract = {BACKGROUND: Grazing mammals rely on their ruminal microbial symbionts to convert plant structural biomass into metabolites they can assimilate. To explore how this complex metabolic system adapts to the host animal's diet, we inferred a microbiome-level metabolic network from shotgun metagenomic data.

RESULTS: Using comparative genomics, we then linked this microbial network to that of the host animal using a set of interface metabolites likely to be transferred to the host. When the host sheep were fed a grain-based diet, the induced microbial metabolic network showed several critical differences from those seen on the evolved forage-based diet. Grain-based (e.g., concentrate) diets tend to be dominated by a smaller set of reactions that employ metabolites that are nearer in network space to the host's metabolism. In addition, these reactions are more central in the network and employ substrates with shorter carbon backbones. Despite this apparent lower complexity, the concentrate-associated metabolic networks are actually more dissimilar from each other than are those of forage-fed animals. Because both groups of animals were initially fed on a forage diet, we propose that the diet switch drove the appearance of a number of different microbial networks, including a degenerate network characterized by an inefficient use of dietary nutrients. We used network simulations to show that such disparate networks are not an unexpected result of a diet shift.

CONCLUSION: We argue that network approaches, particularly those that link the microbial network with that of the host, illuminate aspects of the structure of the microbiome not seen from a strictly taxonomic perspective. In particular, different diets induce predictable and significant differences in the enzymes used by the microbiome. Nonetheless, there are clearly a number of microbiomes of differing structure that show similar functional properties. Changes such as a diet shift uncover more of this type of diversity.}, } @article {pmid28594392, year = {2017}, author = {Manrique, P and Dills, M and Young, MJ}, title = {The Human Gut Phage Community and Its Implications for Health and Disease.}, journal = {Viruses}, volume = {9}, number = {6}, pages = {}, pmid = {28594392}, issn = {1999-4915}, support = {R01 GM117361/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*virology ; Bacteriophages/genetics/*physiology ; Dysbiosis ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*physiopathology/*virology ; Humans ; Lysogeny ; Metagenome ; Mice ; Prophages/genetics/physiology ; }, abstract = {In this review, we assess our current understanding of the role of bacteriophages infecting the human gut bacterial community in health and disease. In general, bacteriophages contribute to the structure of their microbial communities by driving host and viral diversification, bacterial evolution, and by expanding the functional diversity of ecosystems. Gut bacteriophages are an ensemble of unique and shared phages in individuals, which encompass temperate phages found predominately as prophage in gut bacteria (prophage reservoir) and lytic phages. In healthy individuals, only a small fraction of the prophage reservoir is activated and found as extracellular phages. Phage community dysbiosis is characterized by a shift in the activated prophage community or an increase of lytic phages, and has been correlated with disease, suggesting that a proper balance between lysis and lysogeny is needed to maintain health. Consequently, the concept of microbial dysbiosis might be extended to the phage component of the microbiome as well. Understanding the dynamics and mechanisms to restore balance after dysbiosis is an active area of research. The use of phage transplants to re-establish health suggests that phages can be used as disease treatment. Such advances represent milestones in our understanding of gut phages in human health and should fuel research on their role in health and disease.}, } @article {pmid28593475, year = {2017}, author = {Ottoni, JR and Cabral, L and de Sousa, STP and Júnior, GVL and Domingos, DF and Soares Junior, FL and da Silva, MCP and Marcon, J and Dias, ACF and de Melo, IS and de Souza, AP and Andreote, FD and de Oliveira, VM}, title = {Functional metagenomics of oil-impacted mangrove sediments reveals high abundance of hydrolases of biotechnological interest.}, journal = {World journal of microbiology & biotechnology}, volume = {33}, number = {7}, pages = {141}, pmid = {28593475}, issn = {1573-0972}, mesh = {Bacteria/*classification/enzymology/genetics/isolation & purification ; Bacterial Proteins/genetics ; Biodiversity ; Brazil ; Genomic Library ; Geologic Sediments/*microbiology ; High-Throughput Nucleotide Sequencing ; Hydrolases/*genetics ; Metagenomics/*methods ; Petroleum Pollution/adverse effects ; Phylogeny ; Sequence Analysis, DNA ; Soil Microbiology ; Wetlands ; }, abstract = {Mangroves are located in coastal wetlands and are susceptible to the consequences of oil spills, what may threaten the diversity of microorganisms responsible for the nutrient cycling and the consequent ecosystem functioning. Previous reports show that high concentration of oil favors the incidence of epoxide hydrolases and haloalkane dehalogenases in mangroves. This finding has guided the goals of this study in an attempt to broaden the analysis to other hydrolases and thereby verify whether oil contamination interferes with the prevalence of particular hydrolases and their assigned microorganisms. For this, an in-depth survey of the taxonomic and functional microbial diversity recovered in a fosmid library (Library_Oil Mgv) constructed from oil-impacted Brazilian mangrove sediment was carried out. Fosmid DNA of the whole library was extracted and submitted to Illumina HiSeq sequencing. The resulting Library Oil_Mgv dataset was further compared with those obtained by direct sequencing of environmental DNA from Brazilian mangroves (from distinct regions and affected by distinct sources of contamination), focusing on hydrolases with potential use in biotechnological processes. The most abundant hydrolases found were proteases, esterases and amylases, with similar occurrence profile in all datasets. The main microbial groups harboring such hydrolase-encoding genes were distinct in each mangrove, and in the fosmid library these enzymes were mainly assigned to Chloroflexaceae (for amylases), Planctomycetaceae (for esterases) and Bradyrhizobiaceae (for proteases). Assembly and analysis of Library_Oil Mgv reads revealed three potentially novel enzymes, one epoxide hydrolase, one xylanase and one amylase, to be further investigated via heterologous expression assays.}, } @article {pmid28592823, year = {2017}, author = {Cardoso, DC and Sandionigi, A and Cretoiu, MS and Casiraghi, M and Stal, L and Bolhuis, H}, title = {Comparison of the active and resident community of a coastal microbial mat.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2969}, pmid = {28592823}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Seawater ; *Water Microbiology ; }, abstract = {Coastal microbial mats form a nearly closed micro-scale ecosystem harboring a complex microbial community. Previous DNA based analysis did not necessarily provide information about the active fraction of the microbial community because it includes dormant, inactive cells as well as a potential stable pool of extracellular DNA. Here we focused on the active microbial community by comparing 16S rRNA sequences obtained from the ribosomal RNA pool with gene sequences obtained from the DNA fraction. In addition, we aimed to establish an optimal and feasible sampling protocol that takes potential spatial and temporal heterogeneity into account. The coastal microbial mat investigated here was sampled randomly and at regular time points during one 24-h period. DNA and RNA was extracted and after conversion of the RNA fraction to cDNA, the V1-V3 and the V3-V4 regions of the 16S rRNA gene were targeted for high-throughput amplicon sequencing. We show that the community composition varies little in time and space whereas two amplified 16S regions gave significant different results. The largest differences were found when comparing the "resident community" (DNA) with the "active community" (cDNA/RNA); in the latter, Cyanobacteria dominated for almost 95% while they represented 60% of the resident fraction.}, } @article {pmid28591831, year = {2017}, author = {Blasco, G and Moreno-Navarrete, JM and Rivero, M and Pérez-Brocal, V and Garre-Olmo, J and Puig, J and Daunis-I-Estadella, P and Biarnés, C and Gich, J and Fernández-Aranda, F and Alberich-Bayarri, Á and Moya, A and Pedraza, S and Ricart, W and López, M and Portero-Otin, M and Fernandez-Real, JM}, title = {The Gut Metagenome Changes in Parallel to Waist Circumference, Brain Iron Deposition, and Cognitive Function.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {102}, number = {8}, pages = {2962-2973}, doi = {10.1210/jc.2017-00133}, pmid = {28591831}, issn = {1945-7197}, mesh = {Adult ; Bacteroidetes ; Brain/diagnostic imaging/*metabolism ; Case-Control Studies ; *Cognition ; Cross-Sectional Studies ; Female ; Firmicutes ; Gastrointestinal Microbiome/*genetics ; Humans ; Image Processing, Computer-Assisted ; Iron/*metabolism ; Longitudinal Studies ; Magnetic Resonance Imaging ; Male ; Metagenome/*genetics ; Middle Aged ; Neuropsychological Tests ; Obesity/metabolism/*microbiology/psychology ; Tenericutes ; *Waist Circumference ; }, abstract = {CONTEXT: Microbiota perturbations seem to exert modulatory effects on emotional behavior, stress-, and pain-modulation systems in adult animals; however, limited information is available in humans.

OBJECTIVE: To study potential relationships among the gut metagenome, brain microstructure, and cognitive performance in middle-aged, apparently healthy, obese and nonobese subjects after weight changes.

DESIGN: This is a longitudinal study over a 2-year period.

SETTING: A tertiary public hospital.

Thirty-five (18 obese) apparently healthy subjects.

INTERVENTION(S): Diet counseling was provided to all subjects. Obese subjects were followed every 6 months.

MAIN OUTCOME MEASURE(S): Brain relaxometry (using magnetic resonance R2*), cognitive performance (by means of cognitive tests), and gut microbiome composition (shotgun).

RESULTS: R2* increased in both obese and nonobese subjects, independent of weight variations. Changes in waist circumference, but not in body mass index, were associated with brain iron deposition (R2*) in the striatum, amygdala, and hippocampus in parallel to visual-spatial constructional ability and circulating beta amyloid Aβ42 levels. These changes were linked to shifts in gut microbiome in which the relative abundance of bacteria belonging to Caldiserica and Thermodesulfobacteria phyla were reciprocally associated with raised R2* in different brain nuclei. Of note, the increase in bacteria belonging to Tenericutes phylum was parallel to decreased R2* gain in the striatum, serum Aβ42 levels, and spared visual-spatial constructional ability. Interestingly, metagenome functions associated with circulating and brain iron stores are involved in bacterial generation of siderophores.

CONCLUSIONS: Changes in the gut metagenome are associated longitudinally with cognitive function and brain iron deposition.}, } @article {pmid28588309, year = {2017}, author = {Jiang, S and Xie, S and Lv, D and Wang, P and He, H and Zhang, T and Zhou, Y and Lin, Q and Zhou, H and Jiang, J and Nie, J and Hou, F and Chen, Y}, title = {Alteration of the gut microbiota in Chinese population with chronic kidney disease.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2870}, pmid = {28588309}, issn = {2045-2322}, mesh = {Adult ; Aged ; Bacteria/classification/genetics ; Biomarkers ; Butyrates/metabolism ; Case-Control Studies ; China/epidemiology ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome ; Humans ; Kidney Failure, Chronic/epidemiology ; Kidney Function Tests ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Population Surveillance ; Renal Insufficiency, Chronic/diagnosis/*epidemiology/metabolism ; }, abstract = {We evaluated differences in the compositions of faecal microbiota between 52 end stage renal disease (ESRD) patients and 60 healthy controls in southern China using quantitative real-time polymerase chain reaction (qPCR) and high-throughput sequencing (16S ribosomal RNA V4-6 region) methods. The absolute quantification of total bacteria was significantly reduced in ESRD patients (p < 0.01). In three enterotypes, Prevotella was enriched in the healthy group whereas Bacteroides were prevalent in the ESRD group (LDA score > 4.5). 11 bacterial taxa were significantly overrepresented in samples from ESRD and 22 bacterial taxa were overrepresented in samples from healthy controls. The butyrate producing bacteria, Roseburia, Faecalibacterium, Clostridium, Coprococcus and Prevotella were reduced in the ESRD group (LDA values > 2.0). Canonical correspondence analysis (CCA) indicated that Cystatin C (CysC), creatinine and eGFR appeared to be the most important environmental parameters to influence the overall microbial communities. In qPCR analysis, The butyrate producing species Roseburia spp., Faecalibacterium prausnitzii, Prevotella and Universal bacteria, were negatively related to CRP and CysC. Total bacteria in faeces were reduced in patients with ESRD compared to that in healthy individuals. The enterotypes change from Prevotella to Bacteroides in ESRD patients. The gut microbiota was associated with the inflammatory state and renal function of chronic kidney disease.}, } @article {pmid28588199, year = {2017}, author = {Gomez-Arango, LF and Barrett, HL and McIntyre, HD and Callaway, LK and Morrison, M and Nitert, MD}, title = {Contributions of the maternal oral and gut microbiome to placental microbial colonization in overweight and obese pregnant women.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2860}, pmid = {28588199}, issn = {2045-2322}, mesh = {Adult ; Biomarkers ; Female ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; Mouth/*microbiology ; Obesity/*etiology ; Overweight/*etiology ; Phylogeny ; Placenta/*microbiology ; Pregnancy ; *Pregnancy Complications ; }, abstract = {A distinct bacterial signature of the placenta was reported, providing evidence that the fetus does not develop in a sterile environment. The oral microbiome was suggested as a possible source of the bacterial DNA present in the placenta based on similarities to the oral non-pregnant microbiome. Here, the possible origin of the placental microbiome was assessed, examining the gut, oral and placental microbiomes from the same pregnant women. Microbiome profiles from 37 overweight and obese pregnant women were examined by 16SrRNA sequencing. Fecal and oral contributions to the establishment of the placental microbiome were evaluated. Core phylotypes between body sites and metagenome predictive functionality were determined. The placental microbiome showed a higher resemblance and phylogenetic proximity with the pregnant oral microbiome. However, similarity decreased at lower taxonomic levels and microbiomes clustered based on tissue origin. Core genera: Prevotella, Streptococcus and Veillonella were shared between all body compartments. Pathways encoding tryptophan, fatty-acid metabolism and benzoate degradation were highly enriched specifically in the placenta. Findings demonstrate that the placental microbiome exhibits a higher resemblance with the pregnant oral microbiome. Both oral and gut microbiomes contribute to the microbial seeding of the placenta, suggesting that placental colonization may have multiple niche sources.}, } @article {pmid28588195, year = {2017}, author = {Kang, J and Ma, X and He, S}, title = {Population genetics analysis of the Nujiang catfish Creteuchiloglanis macropterus through a genome-wide single nucleotide polymorphisms resource generated by RAD-seq.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2813}, pmid = {28588195}, issn = {2045-2322}, mesh = {Animals ; Catfishes/*genetics ; Genome/genetics ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; }, abstract = {Advances in genome scanning using high-throughput sequencing technologies has led to a revolution in studies of non-model organisms. The glyptosternoid fish Creteuchiloglanis macropterus, is widely distributed in the main stem and tributaries of the Nujiang River basin. Here, we analyzed IIB restriction-site-associated DNA (2b-RAD) sequences and mitochondrial DNA sequences, to assess the genomic signature of adaptation by detecting and estimating the degree of genetic differentiation among ten Creteuchiloglanis macropterus populations from the Nujiang River. The analyses revealed significant population differentiation among the up-tributaries, main stem, mid-tributary and low-tributary. Annotation of contigs containing outlier SNPs revealed that the candidate genes showed significant enrichment in several important biological process terms between up-tributaries and low-tributary, and exhibited prominent enrichment in the term macromolecular metabolic process between all tributaries and the main stem. Population dynamics analyses indicated that the Late Pleistocene glaciations strongly influenced the demographic history of C. macropterus. Our results provide strong evidence for the utility of RAD-seq in population genetics studies, and our generated SNP resource should provide a valuable tool for population genomics studies of C. macropterus in the future.}, } @article {pmid28586542, year = {2017}, author = {Andújar, C and Arribas, P and Vogler, AP}, title = {Terra incognita of soil biodiversity: unseen invasions under our feet.}, journal = {Molecular ecology}, volume = {26}, number = {12}, pages = {3087-3089}, doi = {10.1111/mec.14112}, pmid = {28586542}, issn = {1365-294X}, mesh = {Animals ; *Arthropods ; Biodiversity ; DNA, Mitochondrial ; Ecosystem ; *Introduced Species ; Islands ; Metagenomics ; Phylogeny ; Soil ; }, abstract = {Whilst cartographers of the 19th century endeavoured to chart the last unknown lands, the great challenge for biologists in the 21st century is to fill the gaps on the biodiversity map of the Earth. And one of the largest gaps concerns the biodiversity of soils, a terra incognita right under our feet. The study of soil biodiversity, and particularly the complex communities of small invertebrates, has suffered from a severe 'taxonomic impediment' (Decaëns) leading to great uncertainties about total species richness, phylogenetic diversity, geographical structure, temporal dynamics of soil organisms, and consequently about their role on ecosystem function (Bardgett & van der Putten). However, the revolution in high-throughput sequencing is now revealing the hidden biodiversity of the soil with unprecedented detail (e.g. Arribas et al.). In a noteworthy from the Cover article in this issue of Molecular Ecology, Cicconardi et al. () apply these new tools to study soil communities of Collembola in three distant oceanic islands of volcanic origin, obtaining a striking result: only 38 of 70 species (54%) are exclusively found in a single island, with the remaining shared among islands or with other distant regions, suggesting a massive recent introduction of soil species, whose impact is entirely unknown.}, } @article {pmid28585938, year = {2017}, author = {Borrel, G and McCann, A and Deane, J and Neto, MC and Lynch, DB and Brugère, JF and O'Toole, PW}, title = {Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome.}, journal = {The ISME journal}, volume = {11}, number = {9}, pages = {2059-2074}, pmid = {28585938}, issn = {1751-7370}, mesh = {Aged ; Aged, 80 and over ; Animals ; Archaea/classification/*genetics/isolation & purification/*metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Genomics ; Humans ; Male ; Metagenome ; Metagenomics ; Methylamines/*metabolism ; Microbiota ; Phylogeny ; }, abstract = {The biological significance of Archaea in the human gut microbiota is largely unclear. We recently reported genomic and biochemical analyses of the Methanomassiliicoccales, a novel order of methanogenic Archaea dwelling in soil and the animal digestive tract. We now show that these Methanomassiliicoccales are present in published microbiome data sets from eight countries. They are represented by five Operational Taxonomic Units present in at least four cohorts and phylogenetically distributed into two clades. Genes for utilizing trimethylamine (TMA), a bacterial precursor to an atherosclerogenic human metabolite, were present in four of the six novel Methanomassiliicoccales genomes assembled from ELDERMET metagenomes. In addition to increased microbiota TMA production capacity in long-term residential care subjects, abundance of TMA-utilizing Methanomassiliicoccales correlated positively with bacterial gene count for TMA production and negatively with fecal TMA concentrations. The two large Methanomassiliicoccales clades have opposite correlations with host health status in the ELDERMET cohort and putative distinct genomic signatures for gut adaptation.}, } @article {pmid28585356, year = {2017}, author = {Zhang, X and Johnston, ER and Barberán, A and Ren, Y and Lü, X and Han, X}, title = {Decreased plant productivity resulting from plant group removal experiment constrains soil microbial functional diversity.}, journal = {Global change biology}, volume = {23}, number = {10}, pages = {4318-4332}, doi = {10.1111/gcb.13783}, pmid = {28585356}, issn = {1365-2486}, mesh = {*Biodiversity ; China ; Ecosystem ; *Plant Development ; Soil ; *Soil Microbiology ; }, abstract = {Anthropogenic environmental changes are accelerating the rate of biodiversity loss on Earth. Plant diversity loss is predicted to reduce soil microbial diversity primarily due to the decreased variety of carbon/energy resources. However, this intuitive hypothesis is supported by sparse empirical evidence, and most underlying mechanisms remain underexplored or obscure altogether. We constructed four diversity gradients (0-3) in a five-year plant functional group removal experiment in a steppe ecosystem in Inner Mongolia, China, and quantified microbial taxonomic and functional diversity with shotgun metagenome sequencing. The treatments had little effect on microbial taxonomic diversity, but were found to decrease functional gene diversity. However, the observed decrease in functional gene diversity was more attributable to a loss in plant productivity, rather than to the loss of any individual plant functional group per se. Reduced productivity limited fresh plant resources supplied to microorganisms, and thus, intensified the pressure of ecological filtering, favoring genes responsible for energy production/conversion, material transport/metabolism and amino acid recycling, and accordingly disfavored many genes with other functions. Furthermore, microbial respiration was correlated with the variation in functional composition but not taxonomic composition. Overall, the amount of carbon/energy resources driving microbial gene diversity was identified to be the critical linkage between above- and belowground communities, contrary to the traditional framework of linking plant clade/taxonomic diversity to microbial taxonomic diversity.}, } @article {pmid28584301, year = {2017}, author = {Pootakham, W and Mhuantong, W and Yoocha, T and Putchim, L and Sonthirod, C and Naktang, C and Thongtham, N and Tangphatsornruang, S}, title = {High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2774}, pmid = {28584301}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/*genetics ; Biodiversity ; *Metagenomics/methods ; *Microbiota ; Phylogeny ; Phylogeography ; *RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Thailand ; }, abstract = {Coral reefs are a complex ecosystem consisting of coral animals and a vast array of associated symbionts including the dinoflagellate Symbiodinium, fungi, viruses and bacteria. Several studies have highlighted the importance of coral-associated bacteria and their fundamental roles in fitness and survival of the host animal. The scleractinian coral Porites lutea is one of the dominant reef-builders in the Indo-West Pacific. Currently, very little is known about the composition and structure of bacterial communities across P. lutea reefs. The purpose of this study is twofold: to demonstrate the advantages of using PacBio circular consensus sequencing technology in microbial community studies and to investigate the diversity and structure of P. lutea-associated microbiome in the Indo-Pacific. This is the first metagenomic study of marine environmental samples that utilises the PacBio sequencing system to capture full-length 16S rRNA sequences. We observed geographically distinct coral-associated microbial profiles between samples from the Gulf of Thailand and Andaman Sea. Despite the geographical and environmental impacts on the coral-host interactions, we identified a conserved community of bacteria that were present consistently across diverse reef habitats. Finally, we demonstrated the superior performance of full-length 16S rRNA sequences in resolving taxonomic uncertainty of coral associates at the species level.}, } @article {pmid28576763, year = {2017}, author = {Gill, AS and Lee, A and McGuire, KL}, title = {Phylogenetic and Functional Diversity of Total (DNA) and Expressed (RNA) Bacterial Communities in Urban Green Infrastructure Bioswale Soils.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {16}, pages = {}, pmid = {28576763}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/*isolation & purification/metabolism ; Biodiversity ; DNA, Bacterial/genetics ; Hydrocarbons/metabolism ; New York City ; *Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Urban Renewal ; }, abstract = {New York City (NYC) is pioneering green infrastructure with the use of bioswales and other engineered soil-based habitats to provide stormwater infiltration and other ecosystem functions. In addition to avoiding the environmental and financial costs of expanding traditional built infrastructure, green infrastructure is thought to generate cobenefits in the form of diverse ecological processes performed by its plant and microbial communities. Yet, although plant communities in these habitats are closely managed, we lack basic knowledge about how engineered ecosystems impact the distribution and functioning of soil bacteria. We sequenced amplicons of the 16S ribosomal subunit, as well as seven genes associated with functional pathways, generated from both total (DNA-based) and expressed (RNA) soil communities in the Bronx, NYC, NY, in order to test whether bioswale soils host characteristic bacterial communities with evidence for enriched microbial functioning, compared to nonengineered soils in park lawns and tree pits. Bioswales had distinct, phylogenetically diverse bacterial communities, including taxa associated with nutrient cycling and metabolism of hydrocarbons and other pollutants. Bioswale soils also had a significantly greater diversity of genes involved in several functional pathways, including carbon fixation (cbbL-R [cbbL gene, red-like subunit] and apsA), nitrogen cycling (noxZ and amoA), and contaminant degradation (bphA); conversely, no functional genes were significantly more abundant in nonengineered soils. These results provide preliminary evidence that urban land management can shape the diversity and activity of soil communities, with positive consequences for genetic resources underlying valuable ecological functions, including biogeochemical cycling and degradation of common urban pollutants.IMPORTANCE Management of urban soil biodiversity by favoring taxa associated with decontamination or other microbial metabolic processes is a powerful prospect, but it first requires an understanding of how engineered soil habitats shape patterns of microbial diversity. This research adds to our understanding of urban microbial biogeography by providing data on soil bacteria in bioswales, which had relatively diverse and compositionally distinct communities compared to park and tree pit soils. Bioswales also contained comparatively diverse pools of genes related to carbon sequestration, nitrogen cycling, and contaminant degradation, suggesting that engineered soils may serve as effective reservoirs of functional microbial biodiversity. We also examined both total (DNA-based) and expressed (RNA) communities, revealing that total bacterial communities (the exclusive targets in the vast majority of soil studies) were poor predictors of expressed community diversity, pointing to the value of quantifying RNA, especially when ecological functioning is considered.}, } @article {pmid28576366, year = {2017}, author = {Lee, M and Song, JH and Jung, MY and Lee, SH and Chang, JY}, title = {Large-scale targeted metagenomics analysis of bacterial ecological changes in 88 kimchi samples during fermentation.}, journal = {Food microbiology}, volume = {66}, number = {}, pages = {173-183}, doi = {10.1016/j.fm.2017.05.002}, pmid = {28576366}, issn = {1095-9998}, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; *Biodiversity ; Brassica/metabolism/*microbiology ; Fermentation ; Metagenomics ; Vegetables/metabolism/*microbiology ; }, abstract = {The microbial communities in kimchi vary widely, but the precise effects of differences in region of origin, ingredients, and preparation method on the microbiota are unclear. We analyzed the bacterial community composition of household (n = 69) and commercial (n = 19) kimchi samples obtained from six Korean provinces between April and August 2015. Samples were analyzed by barcoded pyrosequencing targeting the V1-V3 region of the 16S ribosomal RNA gene. The initial pH of the kimchi samples was 5.00-6.39, and the salt concentration was 1.72-4.42%. Except for sampling locality, all categorical variables, i.e., salt concentration, major ingredient, fermentation period, sampling time, and manufacturing process, influenced the bacterial community composition. Particularly, samples were highly clustered by sampling time and salt concentration in non-metric multidimensional scaling plots and an analysis of similarity. These results indicated that the microbial community differed according to fermentation conditions such as salt concentration, major ingredient, fermentation period, and sampling time. Furthermore, fermentation properties, including pH, acidity, salt concentration, and microbial abundance differed between kimchi samples from household and commercial sources. Analyses of changes in bacterial ecology during fermentation will improve our understanding of the biological properties of kimchi, as well as the relationships between these properties and the microbiota of kimchi.}, } @article {pmid28576115, year = {2017}, author = {Esmaeili Taheri, A and Chatterton, S and Gossen, BD and McLaren, DL}, title = {Metagenomic analysis of oomycete communities from the rhizosphere of field pea on the Canadian prairies.}, journal = {Canadian journal of microbiology}, volume = {63}, number = {9}, pages = {758-768}, doi = {10.1139/cjm-2017-0099}, pmid = {28576115}, issn = {1480-3275}, mesh = {Biodiversity ; Canada ; Grassland ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Oomycetes/classification/*genetics/*isolation & purification ; Pisum sativum/growth & development/*parasitology ; Plant Roots/parasitology ; Rhizosphere ; Soil/*parasitology ; }, abstract = {Oomycetes are a diverse group of microorganisms; however, little is known about their composition and biodiversity in agroecosystems. Illumina MiSeq was used to determine the type and abundance of oomycetes associated with pea root rot in the Canadian prairies. Additional objectives of the study were to identify differences in oomycete communities associated with pea root health and compare oomycete communities among the 3 prairie provinces, where field peas are commonly cultivated. Samples of soil from the rhizosphere of field pea (Pisum sativum L.) were collected from patches of asymptomatic or diseased plants from 26 commercial fields in 2013 and 2014. Oomycete communities were characterized using metagenomic analysis of the ITS1 region on Illumina MiSeq. From 105 identified operational taxonomic units (OTUs), 45 and 16 oomycete OTUs were identified at species and genus levels, respectively. Pythium was the most prevalent genus and Pythium heterothallicum the most prevalent species in all 3 provinces in both 2013 and 2014. Aphanomyces euteiches, a very important pea root rot pathogen in regions of the prairies, was detected in 57% of sites but at very low abundance (<0.2%). Multivariate analysis revealed differences in the relative abundance of species in oomycete communities between asymptomatic and diseased sites, and among years and provinces. This study demonstrated that deep amplicon sequencing can provide information on the composition and diversity of oomycete communities in agricultural soils.}, } @article {pmid28571861, year = {2017}, author = {Bao, YJ and Xu, Z and Li, Y and Yao, Z and Sun, J and Song, H}, title = {High-throughput metagenomic analysis of petroleum-contaminated soil microbiome reveals the versatility in xenobiotic aromatics metabolism.}, journal = {Journal of environmental sciences (China)}, volume = {56}, number = {}, pages = {25-35}, doi = {10.1016/j.jes.2016.08.022}, pmid = {28571861}, issn = {1001-0742}, mesh = {Bacteria/genetics ; Biodegradation, Environmental ; China ; Metagenome/physiology ; Microbiota/*genetics ; Petroleum/*metabolism ; Petroleum Pollution ; Phylogeny ; *Soil Microbiology ; Soil Pollutants/*metabolism ; Xenobiotics/*metabolism ; }, abstract = {The soil with petroleum contamination is one of the most studied soil ecosystems due to its rich microorganisms for hydrocarbon degradation and broad applications in bioremediation. However, our understanding of the genomic properties and functional traits of the soil microbiome is limited. In this study, we used high-throughput metagenomic sequencing to comprehensively study the microbial community from petroleum-contaminated soils near Tianjin Dagang oilfield in eastern China. The analysis reveals that the soil metagenome is characterized by high level of community diversity and metabolic versatility. The metageome community is predominated by γ-Proteobacteria and α-Proteobacteria, which are key players for petroleum hydrocarbon degradation. The functional study demonstrates over-represented enzyme groups and pathways involved in degradation of a broad set of xenobiotic aromatic compounds, including toluene, xylene, chlorobenzoate, aminobenzoate, DDT, methylnaphthalene, and bisphenol. A composite metabolic network is proposed for the identified pathways, thus consolidating our identification of the pathways. The overall data demonstrated the great potential of the studied soil microbiome in the xenobiotic aromatics degradation. The results not only establish a rich reservoir for novel enzyme discovery but also provide putative applications in bioremediation.}, } @article {pmid28571671, year = {2017}, author = {Millar, M and Seale, J and Greenland, M and Hardy, P and Juszczak, E and Wilks, M and Panton, N and Costeloe, K and Wade, WG}, title = {The Microbiome of Infants Recruited to a Randomised Placebo-controlled Probiotic Trial (PiPS Trial).}, journal = {EBioMedicine}, volume = {20}, number = {}, pages = {255-262}, pmid = {28571671}, issn = {2352-3964}, mesh = {Bifidobacterium ; Dysbiosis ; Enterocolitis, Necrotizing/etiology/*prevention & control ; Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Metagenome ; Metagenomics ; *Microbiota ; Odds Ratio ; Outcome Assessment, Health Care ; Probiotics/*administration & dosage ; RNA, Ribosomal, 16S ; Time-to-Treatment ; }, abstract = {The microbial dysbiosis associated with necrotizing enterocolitis (NEC) in preterm infants suggests that early exposure to probiotics may decrease and antibiotics may increase NEC risk. However, administration of Bifidobacterium breve strain BBG-001 to preterm infants did not affect NEC incidence in a multicenter randomised controlled phase 3 trial (PiPS trial). Using a subset of these subjects we compared the fecal microbiome of probiotic and placebo groups and assessed the impact of early antibiotic treatment. Extracted DNA from 103 fecal samples collected at 36weeks post-menstrual age underwent PCR amplification of a fragment of the 16S rRNA gene. Heatmaps were constructed showing the proportions of sequences from bacterial families present at >1% of the community. Stepwise logistic regression assessed the association between early antibiotic exposure and microbiome group. There was no difference in the microbial richness and diversity of the microbiome of preterm infants following treatment with probiotic or a placebo. Conversely, early antimicrobial exposure was associated with different patterns of colonisation, specifically a relative abundance of Proteobacteria. These findings highlight that the potential influence of probiotics on the microbiome of preterm infants remains unclear whereas the modulatory effect of antibiotic exposure on microbial colonisation requires further research.}, } @article {pmid28570897, year = {2017}, author = {Subedi, G and Taylor, J and Hatam, I and Baldwin, SA}, title = {Simultaneous selenate reduction and denitrification by a consortium of enriched mine site bacteria.}, journal = {Chemosphere}, volume = {183}, number = {}, pages = {536-545}, doi = {10.1016/j.chemosphere.2017.05.144}, pmid = {28570897}, issn = {1879-1298}, mesh = {Bacteria, Anaerobic/genetics/growth & development ; Denitrification ; Kinetics ; *Microbial Consortia ; *Mining ; Nitrates/*analysis ; Oxidation-Reduction ; Oxidoreductases/genetics ; Selenic Acid/*analysis ; Water Pollutants, Chemical/*analysis ; Water Purification/*methods ; }, abstract = {Increasing selenium concentrations in aquatic environments downstream of mine sites is of great concern due to selenium's bioaccumulation propensity and teratogenic toxicity. Removal of selenium from mine influenced water is complicated by the presence of nitrate, which is also elevated in mine influenced water due to the use of explosives in mining. In many biological treatment processes, nitrate as a thermodynamically more preferable electron acceptor inhibits selenate reduction. Here we report on an enrichment of a bacterial assemblage from a mine impacted natural marsh sediment that was capable of simultaneous selenate reduction and denitrification. Selenate reduction followed first order kinetics with respect to the concentration of total dissolved selenium. The kinetic rate constant was independent of initial nitrate concentration over the range 3-143 mg L[-1]-NO3[-]-N. The initial concentration of selenate inhibited selenate reduction kinetics over the range 1-24 mg-Se L[-1]. Dominant taxa that grew in selenate only medium were classified in the genera Pseudomonas, Lysinibacillus and Thauera. When nitrate was introduced in addition to selenate, previously rare taxa that became dominant were relatives of Exiguobacterium, Tissierella and Clostridium. Open reading frames (ORFs) associated with dissimilatory denitrification were identified for Pseudomonas, Thauera and Clostridium. In addition, ORFs were found that were homologous with known selenate reductase subunits (SerA and SerB). These findings suggest that native mine site bacteria can be used for removing selenate and nitrate from mine wastewater.}, } @article {pmid28562180, year = {2018}, author = {Gutleben, J and Chaib De Mares, M and van Elsas, JD and Smidt, H and Overmann, J and Sipkema, D}, title = {The multi-omics promise in context: from sequence to microbial isolate.}, journal = {Critical reviews in microbiology}, volume = {44}, number = {2}, pages = {212-229}, doi = {10.1080/1040841X.2017.1332003}, pmid = {28562180}, issn = {1549-7828}, mesh = {Metabolomics/*methods ; Metagenomics/*methods ; Microbiological Techniques/*methods ; *Microbiota ; Proteomics/*methods ; }, abstract = {The numbers and diversity of microbes in ecosystems within and around us is unmatched, yet most of these microorganisms remain recalcitrant to in vitro cultivation. Various high-throughput molecular techniques, collectively termed multi-omics, provide insights into the genomic structure and metabolic potential as well as activity of complex microbial communities. Nonetheless, pure or defined cultures are needed to (1) decipher microbial physiology and thus test multi-omics-based ecological hypotheses, (2) curate and improve database annotations and (3) realize novel applications in biotechnology. Cultivation thus provides context. In turn, we here argue that multi-omics information awaits integration into the development of novel cultivation strategies. This can build the foundation for a new era of omics information-guided microbial cultivation technology and reduce the inherent trial-and-error search space. This review discusses how information that can be extracted from multi-omics data can be applied for the cultivation of hitherto uncultured microorganisms. Furthermore, we summarize groundbreaking studies that successfully translated information derived from multi-omics into specific media formulations, screening techniques and selective enrichments in order to obtain novel targeted microbial isolates. By integrating these examples, we conclude with a proposed workflow to facilitate future omics-aided cultivation strategies that are inspired by the microbial complexity of the environment.}, } @article {pmid28558788, year = {2017}, author = {Schoster, A and Staempfli, HR and Guardabassi, LG and Jalali, M and Weese, JS}, title = {Comparison of the fecal bacterial microbiota of healthy and diarrheic foals at two and four weeks of life.}, journal = {BMC veterinary research}, volume = {13}, number = {1}, pages = {144}, pmid = {28558788}, issn = {1746-6148}, mesh = {Animals ; Animals, Newborn/microbiology ; Diarrhea/microbiology/*veterinary ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Horse Diseases/*microbiology ; Horses ; Male ; }, abstract = {BACKGROUND: Diarrhea in foals affects up to 60% of foals during the first six months of life. The effect of diarrhea on the fecal bacterial microbiota in foals has not been investigated. Little is known on the fecal bacterial microbial richness and diversity of foals at a young age. The objective was to compare the fecal bacterial microbiota of healthy foals to foals with diarrhea at two and four weeks of life.

METHODS: Fecal samples were collected from foals (n = 20) at 1-14 (T1) and 15-28 (T2) days of age and analyzed using high throughput sequencing. Differences in relative abundance of bacterial taxa, alpha diversity and beta diversity indices were assessed between age-matched foals with diarrhea (n = 9) and healthy foals (n = 11), and between time points.

RESULTS: Differences in microbial community composition based on time point and health status were observed on all taxonomic levels. Of 117 enriched species in healthy foals at T2, 50 (48%) were Lachnospiraceae or Ruminococcaceae. The Chao richness index was increased in healthy foals at T2 compared to T1 (p = 0.02). Foals with diarrhea had a significantly lower richness index than non-diarrheic foals at T2 (p = 0.04). Diarrhea had an inconsistent effect, while time point had a consistent effect on microbial community structure.

CONCLUSIONS: Preventative and therapeutic measures for diarrhea should focus on maintaining bacterial microbiota richness. Lachnospiraceae and Ruminococcaceae were underrepresented in foals with diarrhea. These should be evaluated further as potential therapeutic options.}, } @article {pmid28557300, year = {2017}, author = {Lin, W and Pan, Y and Bazylinski, DA}, title = {Diversity and ecology of and biomineralization by magnetotactic bacteria.}, journal = {Environmental microbiology reports}, volume = {9}, number = {4}, pages = {345-356}, doi = {10.1111/1758-2229.12550}, pmid = {28557300}, issn = {1758-2229}, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; *Biodiversity ; Ecosystem ; Ferrosoferric Oxide/*metabolism ; Iron/*metabolism ; Magnetosomes/metabolism ; Phylogeny ; Sulfides/*metabolism ; }, abstract = {Magnetotactic bacteria (MTB) biomineralize intracellular, membrane-bounded crystals of magnetite (Fe3 O4) and/or greigite (Fe3 S4) called magnetosomes. MTB play important roles in the geochemical cycling of iron, sulfur, nitrogen and carbon. Significantly, they also represent an intriguing model system not just for the study of microbial biomineralization but also for magnetoreception, prokaryotic organelle formation and microbial biogeography. Here we review current knowledge on the ecology of and biomineralization by MTB, with an emphasis on more recent reports of unexpected ecological and phylogenetic findings regarding MTB. In this study, we conducted a search of public metagenomic databases and identified six novel magnetosome gene cluster-containing genomic fragments affiliated with the Deltaproteobacteria and Gammaproteobacteria classes of the Proteobacteria phylum, the Nitrospirae phylum and the Planctomycetes phylum from the deep subseafloor, marine oxygen minimum zone, groundwater biofilm and estuary sediment, thereby extending our knowledge on the diversity and distribution of MTB as well deriving important information as to their ecophysiology. We point out that the increasing availability of sequence data will facilitate researchers to systematically explore the ecology and biomineralization of MTB even further.}, } @article {pmid28552653, year = {2018}, author = {Mesuere, B and Van der Jeugt, F and Willems, T and Naessens, T and Devreese, B and Martens, L and Dawyndt, P}, title = {High-throughput metaproteomics data analysis with Unipept: A tutorial.}, journal = {Journal of proteomics}, volume = {171}, number = {}, pages = {11-22}, doi = {10.1016/j.jprot.2017.05.022}, pmid = {28552653}, issn = {1876-7737}, mesh = {Databases, Protein ; Feces/microbiology ; Female ; Humans ; Metadata ; *Metagenome ; Microbiota ; Peptides/analysis ; Proteome/*analysis/classification ; Proteomics/*methods ; *Software ; }, abstract = {In recent years, shotgun metaproteomics has established itself as an important tool to study the composition of complex ecosystems and microbial communities. Two key steps in metaproteomics data analysis are the inference of proteins from the identified peptides, and the determination of the taxonomic origin and function of these proteins. This tutorial therefore introduces the Unipept command line interface (http://unipept.ugent.be/clidocs) as a platform-independent tool for such metaproteomics data analyses. First, a detailed overview is given of the available Unipept commands and their functions. Next, the power of the Unipept command line interface is illustrated using two case studies that analyze a single tryptic peptide, and a set of peptides retrieved from a shotgun metaproteomics experiment, respectively. Finally, the analysis results obtained using these command line tools are compared with the interactive taxonomic analysis that is available on the Unipept website.}, } @article {pmid28545131, year = {2017}, author = {Gontang, EA and Aylward, FO and Carlos, C and Glavina Del Rio, T and Chovatia, M and Fern, A and Lo, CC and Malfatti, SA and Tringe, SG and Currie, CR and Kolter, R}, title = {Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.}, journal = {PloS one}, volume = {12}, number = {5}, pages = {e0177189}, pmid = {28545131}, issn = {1932-6203}, support = {F32 GM087941/GM/NIGMS NIH HHS/United States ; R01 GM082137/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Ants/microbiology ; Biodiversity ; Cockroaches/*microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/*microbiology ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach's food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.}, } @article {pmid28544522, year = {2017}, author = {Rasigraf, O and Schmitt, J and Jetten, MSM and Lüke, C}, title = {Metagenomic potential for and diversity of N-cycle driving microorganisms in the Bothnian Sea sediment.}, journal = {MicrobiologyOpen}, volume = {6}, number = {4}, pages = {}, pmid = {28544522}, issn = {2045-8827}, mesh = {Aerobiosis ; Anaerobiosis ; Archaea/classification/*enzymology/genetics ; Bacteria/classification/*enzymology/genetics ; *Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/*microbiology ; Metagenome ; Nitrogen/*metabolism ; *Nitrogen Cycle ; Oceans and Seas ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The biological nitrogen cycle is driven by a plethora of reactions transforming nitrogen compounds between various redox states. Here, we investigated the metagenomic potential for nitrogen cycle of the in situ microbial community in an oligotrophic, brackish environment of the Bothnian Sea sediment. Total DNA from three sediment depths was isolated and sequenced. The characterization of the total community was performed based on 16S rRNA gene inventory using SILVA database as reference. The diversity of diagnostic functional genes coding for nitrate reductases (napA;narG), nitrite:nitrate oxidoreductase (nxrA), nitrite reductases (nirK;nirS;nrfA), nitric oxide reductase (nor), nitrous oxide reductase (nosZ), hydrazine synthase (hzsA), ammonia monooxygenase (amoA), hydroxylamine oxidoreductase (hao), and nitrogenase (nifH) was analyzed by blastx against curated reference databases. In addition, Polymerase chain reaction (PCR)-based amplification was performed on the hzsA gene of anammox bacteria. Our results reveal high genomic potential for full denitrification to N2 , but minor importance of anaerobic ammonium oxidation and dissimilatory nitrite reduction to ammonium. Genomic potential for aerobic ammonia oxidation was dominated by Thaumarchaeota. A higher diversity of anammox bacteria was detected in metagenomes than with PCR-based technique. The results reveal the importance of various N-cycle driving processes and highlight the advantage of metagenomics in detection of novel microbial key players.}, } @article {pmid28543918, year = {2017}, author = {Berasategui, A and Salem, H and Paetz, C and Santoro, M and Gershenzon, J and Kaltenpoth, M and Schmidt, A}, title = {Gut microbiota of the pine weevil degrades conifer diterpenes and increases insect fitness.}, journal = {Molecular ecology}, volume = {26}, number = {15}, pages = {4099-4110}, doi = {10.1111/mec.14186}, pmid = {28543918}, issn = {1365-294X}, mesh = {Animals ; Diterpenes/*metabolism ; Europe ; *Gastrointestinal Microbiome ; Genetic Fitness ; Picea/chemistry ; Weevils/genetics/*microbiology ; }, abstract = {The pine weevil (Hylobius abietis), a major pest of conifer forests throughout Europe, feeds on the bark and cambium, tissues rich in terpenoid resins that are toxic to many insect herbivores. Here, we report the ability of the pine weevil gut microbiota to degrade the diterpene acids of Norway spruce. The diterpene acid levels present in ingested bark were substantially reduced on passage through the pine weevil gut. This reduction was significantly less upon antibiotic treatment, and supplementing the diet with gut suspensions from untreated insects restored the ability to degrade diterpenes. In addition, cultured bacteria isolated from pine weevil guts were shown to degrade a Norway spruce diterpene acid. In a metagenomic survey of the insect's bacterial community, we were able to annotate several genes of a previously described diterpene degradation (dit) gene cluster. Antibiotic treatment disrupted the core bacterial community of H. abietis guts and eliminated nearly all dit genes concordant with its reduction in diterpene degradation. Pine weevils reared on an artificial diet spiked with diterpenes, but without antibiotics, were found to lay more eggs with a higher hatching rate than weevils raised on diets with antibiotics or without diterpenes. These results suggest that gut symbionts contribute towards host fitness, but not by detoxification of diterpenes, as these compounds do not show toxic effects with or without antibiotics. Rather the ability to thrive in a terpene-rich environment appears to allow gut microbes to benefit the weevil in other ways, such as increasing the nutritional properties of their diet.}, } @article {pmid28543439, year = {2017}, author = {Iliev, I and Yahubyan, G and Marhova, M and Apostolova, E and Gozmanova, M and Gecheva, G and Kostadinova, S and Ivanova, A and Baev, V}, title = {Metagenomic profiling of the microbial freshwater communities in two Bulgarian reservoirs.}, journal = {Journal of basic microbiology}, volume = {57}, number = {8}, pages = {669-679}, doi = {10.1002/jobm.201700137}, pmid = {28543439}, issn = {1521-4028}, mesh = {Actinobacteria/classification/genetics ; Bacteria/classification/*genetics ; Bacteroidetes/classification/genetics ; Biodiversity ; Bulgaria ; Ecosystem ; Fresh Water/*microbiology ; High-Throughput Nucleotide Sequencing ; Lakes/microbiology ; *Metagenomics ; *Microbial Consortia ; Phylogeny ; Plankton/classification/*genetics ; Proteobacteria/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Microorganisms inhabiting freshwater environments are an integral part of the aquatic ecosystems. Very few data are available regarding the profiles of the microbial communities in the reservoirs in Bulgaria, despite their key role in the biogeochemical processes. In the present study, we provide the first comprehensive metagenomic analysis on the planktonic bacterial diversity of two large and economically important Bulgarian reservoirs (Batak and Tsankov Kamak) using next-generation sequencing of 16S ribosomal RNA gene (16S rRNA). Analysis of the metagenomic amplicon datasets, including quality filtering, clustering of Operational Taxonomic Units and taxonomy assignment revealed that 78.45% of the microbial communities between the two reservoirs were overlapping. The diversity (H) and Pielou's evenness (J) indices declined along the longitudinal axis of both reservoirs. The estimated values for the Shannon diversity index are typically observed in oligotrophic lakes. The microbial communities of both reservoirs were dominated by Proteobacteria, followed by Actinobacteria and Bacteroidetes all comprised over 95% of the relative abundance, regardless of the reservoir's large hydrogeological differences. The bacterioplankton was characterized by high phylogenetic heterogeneity in the taxonomic structure, being distributed among 211 genera. The genera Limnohabitans and Rhodoferax held the absolute predominance, implying their significance in the aquatic food webs. The obtained data can contribute to the better systematic understanding of the microbial diversity of freshwater environments.}, } @article {pmid28543188, year = {2017}, author = {Chitrala, KN and Guan, H and Singh, NP and Busbee, B and Gandy, A and Mehrpouya-Bahrami, P and Ganewatta, MS and Tang, C and Chatterjee, S and Nagarkatti, P and Nagarkatti, M}, title = {CD44 deletion leading to attenuation of experimental autoimmune encephalomyelitis results from alterations in gut microbiome in mice.}, journal = {European journal of immunology}, volume = {47}, number = {7}, pages = {1188-1199}, pmid = {28543188}, issn = {1521-4141}, support = {R01 AI129788/AI/NIAID NIH HHS/United States ; R01 MH094755/MH/NIMH NIH HHS/United States ; R01 ES019313/ES/NIEHS NIH HHS/United States ; P20 GM103641/GM/NIGMS NIH HHS/United States ; P01 AT003961/AT/NCCIH NIH HHS/United States ; R01 AT006888/AT/NCCIH NIH HHS/United States ; R01 AI123947/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteroidetes/genetics/immunology/isolation & purification ; Disease Models, Animal ; Dysbiosis ; Encephalomyelitis, Autoimmune, Experimental/*immunology/physiopathology ; Fatty Acids, Volatile/immunology ; Fecal Microbiota Transplantation ; Feces/microbiology ; Firmicutes/genetics/immunology/isolation & purification ; Gastrointestinal Microbiome/genetics/*immunology ; Gene Deletion ; Hyaluronan Receptors/*genetics/*immunology ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Propionates/metabolism ; RNA, Ribosomal, 16S ; }, abstract = {Dysbiosis in gut microbiome has been shown to be associated with inflammatory and autoimmune diseases. Previous studies from our laboratory demonstrated the pivotal role played by CD44 in the regulation of EAE, a murine model of multiple sclerosis. In the current study, we determined whether these effects resulted from an alteration in gut microbiota and the short-chain fatty acid (SCFA) production in CD44 knockout (CD44KO) mice. Fecal transfer from naïve CD44KO but not C57BL/6 wild type (CD44WT) mice, into EAE-induced CD44WT mice, led to significant amelioration of EAE. High-throughput bacterial 16S rRNA gene sequencing, followed by clustering sequences into operational taxonomic units (OTUs) and biochemical analysis, revealed that EAE-induced CD44KO mice showed significant diversity, richness, and evenness when compared to EAE-induced CD44WT mice at the phylum level, with dominant Bacteroidetes (68.5%) and low Firmicutes (26.8%). Further, data showed a significant change in the abundance of SCFAs, propionic acid, and i-butyric acid in EAE-CD44KO compared to EAE-CD44WT mice. In conclusion, our results demonstrate that the attenuation of EAE seen following CD44 gene deletion in mice may result from alterations in the gut microbiota and SCFAs. Furthermore, our studies also demonstrate that the phenotype of gene knock-out animals may be shaped by gut microbiota.}, } @article {pmid28542523, year = {2017}, author = {Zaza, G and Dalla Gassa, A and Felis, G and Granata, S and Torriani, S and Lupo, A}, title = {Impact of maintenance immunosuppressive therapy on the fecal microbiome of renal transplant recipients: Comparison between an everolimus- and a standard tacrolimus-based regimen.}, journal = {PloS one}, volume = {12}, number = {5}, pages = {e0178228}, pmid = {28542523}, issn = {1932-6203}, mesh = {Adult ; Aged ; Everolimus/adverse effects/*therapeutic use ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Humans ; Immunosuppressive Agents/adverse effects/*therapeutic use ; *Kidney Transplantation ; Maintenance Chemotherapy/adverse effects ; Male ; Metagenomics ; Middle Aged ; Mycophenolic Acid/therapeutic use ; Tacrolimus/adverse effects/*therapeutic use ; }, abstract = {BACKGROUND: The gut microbiome is the full set of microbes living in the gastrointestinal tract and is emerging as an important dynamic/fluid system that, if altered by environmental, dietetic or pharmacological factors, could considerably influence drug response. However, the immunosuppressive drug-induced modifications of this system are still poorly defined.

METHODS: We employed an innovative bioinformatics approach to assess differences in the whole-gut microbial metagenomic profile of 20 renal transplant recipients undergoing maintenance treatment with two different immunosuppressive protocols. Nine patients were treated with everolimus plus mycophenolate mofetil (EVE+MMF group), and 11 patients were treated with a standard therapy with tacrolimus plus mycophenolate mofetil (TAC+MMF group).

RESULTS: A statistical analysis of comparative high-throughput data demonstrated that although similar according to the degree of Shannon diversity (alpha diversity) at the taxonomic level, three functional genes clearly discriminated EVE+MMF versus TAC+MMF (cutoff: log2 fold change≥1, FDR≤0.05). Flagellar motor switch protein (fliNY) and type IV pilus assembly protein pilM (pilM) were significantly enriched in TAC+MMF-treated patients, while macrolide transport system mrsA (msrA) was more abundant in patients treated with EVE+MMF. Finally, PERMANOVA revealed that among the variables analyzed and included in our model, only the consumption of sugar significantly influenced beta diversity.

CONCLUSIONS: Our study, although performed on a relatively small number of patients, showed, for the first time, specific immunosuppressive-related effects on fecal microbiome of renal transplant recipients and it suggested that the analysis of the gut microbes community could represent a new tool to better understand the effects of drugs currently employed in organ transplantations. However, multicenter studies including healthy controls should be undertaken to better address this objective.}, } @article {pmid28542458, year = {2017}, author = {Cameron, SJS and Lewis, KE and Huws, SA and Hegarty, MJ and Lewis, PD and Pachebat, JA and Mur, LAJ}, title = {A pilot study using metagenomic sequencing of the sputum microbiome suggests potential bacterial biomarkers for lung cancer.}, journal = {PloS one}, volume = {12}, number = {5}, pages = {e0177062}, pmid = {28542458}, issn = {1932-6203}, mesh = {Aged ; Bacteria/*genetics ; Biomarkers, Tumor/*genetics ; Female ; Humans ; Lung Neoplasms/*microbiology ; Male ; Metagenomics/methods ; Microbiota/*genetics ; Middle Aged ; Pilot Projects ; Sputum/*microbiology ; }, abstract = {Lung cancer (LC) is the most prevalent cancer worldwide, and responsible for over 1.3 million deaths each year. Currently, LC has a low five year survival rates relative to other cancers, and thus, novel methods to screen for and diagnose malignancies are necessary to improve patient outcomes. Here, we report on a pilot-sized study to evaluate the potential of the sputum microbiome as a source of non-invasive bacterial biomarkers for lung cancer status and stage. Spontaneous sputum samples were collected from ten patients referred with possible LC, of which four were eventually diagnosed with LC (LC+), and six had no LC after one year (LC-). Of the seven bacterial species found in all samples, Streptococcus viridans was significantly higher in LC+ samples. Seven further bacterial species were found only in LC-, and 16 were found only in samples from LC+. Additional taxonomic differences were identified in regards to significant fold changes between LC+ and LC-cases, with five species having significantly higher abundances in LC+, with Granulicatella adiacens showing the highest level of abundance change. Functional differences, evident through significant fold changes, included polyamine metabolism and iron siderophore receptors. G. adiacens abundance was correlated with six other bacterial species, namely Enterococcus sp. 130, Streptococcus intermedius, Escherichia coli, S. viridans, Acinetobacter junii, and Streptococcus sp. 6, in LC+ samples only, which could also be related to LC stage. Spontaneous sputum appears to be a viable source of bacterial biomarkers which may have utility as biomarkers for LC status and stage.}, } @article {pmid28539641, year = {2017}, author = {Alessi, AM and Bird, SM and Bennett, JP and Oates, NC and Li, Y and Dowle, AA and Polikarpov, I and Young, JPW and McQueen-Mason, SJ and Bruce, NC}, title = {Revealing the insoluble metasecretome of lignocellulose-degrading microbial communities.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2356}, pmid = {28539641}, issn = {2045-2322}, support = {BB/I018492/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/K020358/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J014443/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/1018492/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biomass ; Lignin/*metabolism ; Mass Spectrometry ; Metagenome/genetics ; Metagenomics/methods ; *Microbiota ; Oryza/growth & development/microbiology ; Proteome/genetics/*metabolism ; Proteomics/*methods ; Transcriptome/genetics ; Triticum/growth & development/microbiology ; }, abstract = {Microbial communities metabolize plant biomass using secreted enzymes; however, identifying extracellular proteins tightly bound to insoluble lignocellulose in these microbiomes presents a challenge, as the rigorous extraction required to elute these proteins also lyses the microbes associated with the plant biomass releasing intracellular proteins that contaminate the metasecretome. Here we describe a technique for targeting the extracellular proteome, which was used to compare the metasecretome and meta-surface-proteome of two lignocellulose-degrading communities grown on wheat straw and rice straw. A combination of mass spectrometry-based proteomics coupled with metatranscriptomics enabled the identification of a unique secretome pool from these lignocellulose-degrading communities. This method enabled us to efficiently discriminate the extracellular proteins from the intracellular proteins by improving detection of actively secreted and transmembrane proteins. In addition to the expected carbohydrate active enzymes, our new method reveals a large number of unknown proteins, supporting the notion that there are major gaps in our understanding of how microbial communities degrade lignocellulosic substrates.}, } @article {pmid28539477, year = {2017}, author = {Lax, S and Sangwan, N and Smith, D and Larsen, P and Handley, KM and Richardson, M and Guyton, K and Krezalek, M and Shogan, BD and Defazio, J and Flemming, I and Shakhsheer, B and Weber, S and Landon, E and Garcia-Houchins, S and Siegel, J and Alverdy, J and Knight, R and Stephens, B and Gilbert, JA}, title = {Bacterial colonization and succession in a newly opened hospital.}, journal = {Science translational medicine}, volume = {9}, number = {391}, pages = {}, pmid = {28539477}, issn = {1946-6242}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/genetics/*isolation & purification ; Bayes Theorem ; *Hospitals ; Humans ; Microbiota ; Propionibacterium/genetics/isolation & purification ; Staphylococcus/genetics/isolation & purification ; }, abstract = {The microorganisms that inhabit hospitals may influence patient recovery and outcome, although the complexity and diversity of these bacterial communities can confound our ability to focus on potential pathogens in isolation. To develop a community-level understanding of how microorganisms colonize and move through the hospital environment, we characterized the bacterial dynamics among hospital surfaces, patients, and staff over the course of 1 year as a new hospital became operational. The bacteria in patient rooms, particularly on bedrails, consistently resembled the skin microbiota of the patient occupying the room. Bacterial communities on patients and room surfaces became increasingly similar over the course of a patient's stay. Temporal correlations in community structure demonstrated that patients initially acquired room-associated taxa that predated their stay but that their own microbial signatures began to influence the room community structure over time. The α- and β-diversity of patient skin samples were only weakly or nonsignificantly associated with clinical factors such as chemotherapy, antibiotic usage, and surgical recovery, and no factor except for ambulatory status affected microbial similarity between the microbiotas of a patient and their room. Metagenomic analyses revealed that genes conferring antimicrobial resistance were consistently more abundant on room surfaces than on the skin of the patients inhabiting those rooms. In addition, persistent unique genotypes of Staphylococcus and Propionibacterium were identified. Dynamic Bayesian network analysis suggested that hospital staff were more likely to be a source of bacteria on the skin of patients than the reverse but that there were no universal patterns of transmission across patient rooms.}, } @article {pmid28536926, year = {2017}, author = {Li, W and Wu, X and Hu, X and Wang, T and Liang, S and Duan, Y and Jin, F and Qin, B}, title = {Structural changes of gut microbiota in Parkinson's disease and its correlation with clinical features.}, journal = {Science China. Life sciences}, volume = {60}, number = {11}, pages = {1223-1233}, doi = {10.1007/s11427-016-9001-4}, pmid = {28536926}, issn = {1869-1889}, mesh = {Aged ; Bacteria/classification ; Brain/pathology ; DNA, Bacterial ; Disease Progression ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/*microbiology ; Host-Pathogen Interactions ; Humans ; Male ; Metagenome/genetics/*physiology ; Parkinson Disease/*microbiology/*physiopathology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The aim of this study was to compare the structure of gut microbiota in Parkinson's disease (PD) patients and healthy controls; and to explore correlations between gut microbiota and PD clinical features. We analyzed fecal bacterial composition of 24 PD patients and 14 healthy volunteers by using 16S rRNA sequencing. There were significant differences between PD and healthy controls, as well as among different PD stages. The putative cellulose degrading bacteria from the genera Blautia (P=0.018), Faecalibacterium (P=0.048) and Ruminococcus (P=0.019) were significantly decreased in PD compared to healthy controls. The putative pathobionts from the genera Escherichia-Shigella (P=0.038), Streptococcus (P=0.01), Proteus (P=0.022), and Enterococcus (P=0.006) were significantly increased in PD subjects. Correlation analysis indicated that disease severity and PD duration negatively correlated with the putative cellulose degraders, and positively correlated with the putative pathobionts. The results suggest that structural changes of gut microbiota in PD are characterized by the decreases of putative cellulose degraders and the increases of putative pathobionts, which may potentially reduce the production of short chain fatty acids, and produce more endotoxins and neurotoxins; and these changes is potentially associated with the development of PD pathology.}, } @article {pmid28536449, year = {2017}, author = {Choi, S and Song, H and Tripathi, BM and Kerfahi, D and Kim, H and Adams, JM}, title = {Effect of experimental soil disturbance and recovery on structure and function of soil community: a metagenomic and metagenetic approach.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2260}, pmid = {28536449}, issn = {2045-2322}, mesh = {Biodiversity ; *Biota ; Ecosystem ; *Metagenome ; *Metagenomics/methods ; Microbiota ; *Soil ; *Soil Microbiology ; }, abstract = {There has been little study of effects of disturbance on soil biota combining closely controlled experimental conditions and DNA-based methods. We sampled pots of soil at varying times following an initial simulated mass mortality event. Soil DNA was extracted at intervals up to 24 weeks after the event, and shotgun metagenomes sequenced using NextSeq. Compared to initial conditions, we found: consistent, sequential changes in functional metagenome and community structure over time, indicating successional niche differentiation amongst soil biota. As predicted, early successional systems had greater abundance of genes associated with motility, but fewer genes relating to DNA/RNA/protein metabolism, cell division and cell cycle. Contrary to predictions, there were no significant differences in cell signaling, virulence and defense-related genes. Also, stress related genes were less abundant in later succession. The early successional system had lower taxonomic diversity but higher functional gene diversity. Over time, community characteristics changed progressively, but by the end of the experiment had not returned to the 'original' state of the system before disturbance. Results indicated a predictable sequence of gene functions and taxa following disturbance, analogous to ecosystem succession for large organisms. It is unclear if and when the system would return to its pre-disturbance state.}, } @article {pmid28535299, year = {2017}, author = {Escobedo-Hinojosa, W and Pardo-López, L}, title = {Analysis of bacterial metagenomes from the Southwestern Gulf of Mexico for pathogens detection.}, journal = {Pathogens and disease}, volume = {75}, number = {5}, pages = {}, doi = {10.1093/femspd/ftx058}, pmid = {28535299}, issn = {2049-632X}, mesh = {Bacteria/*classification/*genetics/isolation & purification ; *Biota ; Gulf of Mexico ; *Metagenome ; Seawater/*microbiology ; }, abstract = {Little is known about the diversity of bacteria in the Southwestern Gulf of Mexico. The aim of the study illustrated in this perspective was to search for the presence of bacterial pathogens in this ecosystem, using metagenomic data recently generated by the Mexican research group known as the Gulf of Mexico Research Consortium. Several genera of bacteria annotated as pathogens were detected in water and sediment marine samples. As expected, native and ubiquitous pathogenic bacteria genera such as Burkolderia, Halomonas, Pseudomonas, Shewanella and Vibrio were highly represented. Surprisingly, non-native genera of public health concern were also detected, including Borrelia, Ehrlichia, Leptospira, Mycobacterium, Mycoplasma, Salmonella, Staphylococcus, Streptococcus and Treponema. While there are no previous metagenomics studies of this environment, the potential influences of natural, anthropogenic and ecological factors on the diversity of putative pathogenic bacteria found in it are reviewed. The taxonomic annotation herein reported provides a starting point for an improved understanding of bacterial biodiversity in the Southwestern Gulf of Mexico. It also represents a useful tool in public health as it may help identify infectious diseases associated with exposure to marine water and ingestion of fish or shellfish, and thus may be useful in predicting and preventing waterborne disease outbreaks.}, } @article {pmid28534987, year = {2017}, author = {Chen, T and Shi, Y and Wang, X and Wang, X and Meng, F and Yang, S and Yang, J and Xin, H}, title = {High‑throughput sequencing analyses of oral microbial diversity in healthy people and patients with dental caries and periodontal disease.}, journal = {Molecular medicine reports}, volume = {16}, number = {1}, pages = {127-132}, pmid = {28534987}, issn = {1791-3004}, mesh = {Adolescent ; Adult ; Biodiversity ; Child ; Computational Biology/methods ; Dental Caries/*microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; Mouth/*microbiology ; Periodontal Diseases/*microbiology ; Young Adult ; }, abstract = {Recurrence of oral diseases caused by antibiotics has brought about an urgent requirement to explore the oral microbial diversity in the human oral cavity. In the present study, the high‑throughput sequencing method was adopted to compare the microbial diversity of healthy people and oral patients and sequence analysis was performed by UPARSE software package. The Venn results indicated that a mean of 315 operational taxonomic units (OTUs) was obtained, and 73, 64, 53, 19 and 18 common OTUs belonging to Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria, respectively, were identified in healthy people. Moreover, the reduction of Firmicutes and the increase of Proteobacteria in the children group, and the increase of Firmicutes and the reduction of Proteobacteria in the youth and adult groups, indicated that the age bracket and oral disease had largely influenced the tooth development and microbial development in the oral cavity. In addition, the traditional 'pathogenic bacteria' of Firmicutes, Proteobacteria and Bacteroidetes (accounted for >95% of the total sequencing number in each group) indicated that the 'harmful' bacteria may exert beneficial effects on oral health. Therefore, the data will provide certain clues for curing some oral diseases by the strategy of adjusting the disturbed microbial compositions in oral disease to healthy level.}, } @article {pmid28533514, year = {2017}, author = {Yohda, M and Ikegami, K and Aita, Y and Kitajima, M and Takechi, A and Iwamoto, M and Fukuda, T and Tamura, N and Shibasaki, J and Koike, S and Komatsu, D and Miyagi, S and Nishimura, M and Uchino, Y and Shiroma, A and Shimoji, M and Tamotsu, H and Ashimine, N and Shinzato, M and Ohki, S and Nakano, K and Teruya, K and Satou, K and Hirano, T and Yagi, O}, title = {Isolation and genomic characterization of a Dehalococcoides strain suggests genomic rearrangement during culture.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2230}, pmid = {28533514}, issn = {2045-2322}, mesh = {Chloroflexi/classification/*genetics/metabolism ; Ethylene Dichlorides/metabolism ; Ethylenes/metabolism ; *Gene Rearrangement ; *Genome, Bacterial ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Microbial Consortia ; Vinyl Chloride/metabolism ; }, abstract = {We have developed and characterized a bacterial consortium that reductively dechlorinates trichloroethene to ethene. Quantitative PCR analysis for the 16S rRNA and reductive dehalogenase genes showed that the consortium is highly enriched with Dehalococcoides spp. that have two vinyl chloride reductive dehalogenase genes, bvcA and vcrA, and a trichloroethene reductive dehalogenase gene, tceA. The metagenome analysis of the consortium by the next generation sequencer SOLiD 3 Plus suggests that a Dehalococcoides sp. that is highly homologous to D. mccartyi 195 and equipped with vcrA and tceA exists in the consortium. We isolated this Dehalococcoides sp. and designated it as D. mccartyi UCH-ATV1. As the growth of D. mccartyi UCH-ATV1 is too slow under isolated conditions, we constructed a consortium by mixing D. mccartyi UCH-ATV1 with several other bacteria and performed metagenomic sequencing using the single molecule DNA sequencer PacBio RS II. We successfully determined the complete genome sequence of D. mccartyi UCH-ATV1. The strain is equipped with vcrA and tceA, but lacks bvcA. Comparison with tag sequences of SOLiD 3 Plus from the original consortium shows a few differences between the sequences. This suggests that a genome rearrangement of Dehalococcoides sp. occurred during culture.}, } @article {pmid28532414, year = {2017}, author = {Koliada, A and Syzenko, G and Moseiko, V and Budovska, L and Puchkov, K and Perederiy, V and Gavalko, Y and Dorofeyev, A and Romanenko, M and Tkach, S and Sineok, L and Lushchak, O and Vaiserman, A}, title = {Association between body mass index and Firmicutes/Bacteroidetes ratio in an adult Ukrainian population.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {120}, pmid = {28532414}, issn = {1471-2180}, mesh = {Actinobacteria/genetics/isolation & purification ; Adult ; Bacteria/classification/genetics ; Bacteroidetes/genetics/*isolation & purification ; *Body Mass Index ; DNA, Bacterial ; Exercise ; Feces/microbiology ; Female ; Firmicutes/genetics/*isolation & purification ; *Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/*microbiology ; Humans ; Life Style ; Male ; Middle Aged ; Obesity/*microbiology ; Tobacco Smoking ; Ukraine ; }, abstract = {BACKGROUND: Metagenomic studies confirm that obesity is associated with a composition of gut microbiota. There are some controversies, however, about the composition of gut microbial communities in obese individuals in different populations. To examine the association between body mass index and microbiota composition in Ukrainian population, fecal concentrations of Bacteroidetes, Firmicutes, Actinobacteria and Firmicutes/Bacteroidetes (F/B) ratio were analyzed in 61 adult individuals.

RESULTS: The relative abundance of Actinobacteria was small (5-7%) and comparable in different BMI categories. The content of Firmicutes was gradually increased while the content of Bacteroidetes was decreased with increasing body mass index (BMI). The F/B ratio also raised with increasing BMI. In an unadjusted logistic regression model, F/B ratio was significantly associated with BMI (OR = 1.23, 95% CI 1,09-1,38). This association continued to be significant after adjusting for confounders such as age, sex, tobacco smoking and physical activity (OR = 1.33, 95% CI 1,11-1,60).

CONCLUSIONS: The obtained data indicate that obese persons in Ukraine adult population have a significantly higher level of Firmicutes and lower level of Bacteroidetes compared to normal-weight and lean adults.}, } @article {pmid28530702, year = {2017}, author = {Wu, H and Esteve, E and Tremaroli, V and Khan, MT and Caesar, R and Mannerås-Holm, L and Ståhlman, M and Olsson, LM and Serino, M and Planas-Fèlix, M and Xifra, G and Mercader, JM and Torrents, D and Burcelin, R and Ricart, W and Perkins, R and Fernàndez-Real, JM and Bäckhed, F}, title = {Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug.}, journal = {Nature medicine}, volume = {23}, number = {7}, pages = {850-858}, pmid = {28530702}, issn = {1546-170X}, mesh = {Animals ; Bile Acids and Salts/metabolism ; DNA, Bacterial/*analysis ; Diabetes Mellitus, Type 2/*drug therapy/microbiology ; Double-Blind Method ; Fatty Acids, Volatile/metabolism ; Fecal Microbiota Transplantation ; Feces/chemistry/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Germ-Free Life ; Glucose Tolerance Test ; Humans ; Hypoglycemic Agents/*therapeutic use ; In Vitro Techniques ; Male ; Metagenomics ; Metformin/*therapeutic use ; Mice ; Middle Aged ; }, abstract = {Metformin is widely used in the treatment of type 2 diabetes (T2D), but its mechanism of action is poorly defined. Recent evidence implicates the gut microbiota as a site of metformin action. In a double-blind study, we randomized individuals with treatment-naive T2D to placebo or metformin for 4 months and showed that metformin had strong effects on the gut microbiome. These results were verified in a subset of the placebo group that switched to metformin 6 months after the start of the trial. Transfer of fecal samples (obtained before and 4 months after treatment) from metformin-treated donors to germ-free mice showed that glucose tolerance was improved in mice that received metformin-altered microbiota. By directly investigating metformin-microbiota interactions in a gut simulator, we showed that metformin affected pathways with common biological functions in species from two different phyla, and many of the metformin-regulated genes in these species encoded metalloproteins or metal transporters. Our findings provide support for the notion that altered gut microbiota mediates some of metformin's antidiabetic effects.}, } @article {pmid28530140, year = {2017}, author = {Stewart, CJ and Mansbach, JM and Wong, MC and Ajami, NJ and Petrosino, JF and Camargo, CA and Hasegawa, K}, title = {Associations of Nasopharyngeal Metabolome and Microbiome with Severity among Infants with Bronchiolitis. A Multiomic Analysis.}, journal = {American journal of respiratory and critical care medicine}, volume = {196}, number = {7}, pages = {882-891}, pmid = {28530140}, issn = {1535-4970}, support = {R01 AI127507/AI/NIAID NIH HHS/United States ; R01 AI108588/AI/NIAID NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; R21 HL129909/HL/NHLBI NIH HHS/United States ; R01 AI114552/AI/NIAID NIH HHS/United States ; UH3 OD023253/OD/NIH HHS/United States ; }, mesh = {Bronchiolitis/*metabolism/*microbiology/therapy ; Cohort Studies ; Continuous Positive Airway Pressure/statistics & numerical data ; Female ; Humans ; Infant ; Male ; Metabolome/*physiology ; Microbiota/*physiology ; Nasopharynx/*metabolism/*microbiology ; Prospective Studies ; Severity of Illness Index ; }, abstract = {RATIONALE: Bronchiolitis is the most common lower respiratory infection in infants; however, it remains unclear which infants with bronchiolitis will develop severe illness. In addition, although emerging evidence indicates associations of the upper-airway microbiome with bronchiolitis severity, little is known about the mechanisms linking airway microbes and host response to disease severity.

OBJECTIVES: To determine the relations among the nasopharyngeal airway metabolome profiles, microbiome profiles, and severity in infants with bronchiolitis.

METHODS: We conducted a multicenter prospective cohort study of infants (age <1 yr) hospitalized with bronchiolitis. By applying metabolomic and metagenomic (16S ribosomal RNA gene and whole-genome shotgun sequencing) approaches to 144 nasopharyngeal airway samples collected within 24 hours of hospitalization, we determined metabolome and microbiome profiles and their association with higher severity, defined by the use of positive pressure ventilation (i.e., continuous positive airway pressure and/or intubation).

MEASUREMENTS AND MAIN RESULTS: Nasopharyngeal airway metabolome profiles significantly differed by bronchiolitis severity (P < 0.001). Among 254 metabolites identified, a panel of 25 metabolites showed high sensitivity (84%) and specificity (86%) in predicting the use of positive pressure ventilation. The intensity of these metabolites was correlated with relative abundance of Streptococcus pneumoniae. In the pathway analysis, sphingolipid metabolism was the most significantly enriched subpathway in infants with positive pressure ventilation use compared with those without (P < 0.001). Enrichment of sphingolipid metabolites was positively correlated with the relative abundance of S. pneumoniae.

CONCLUSIONS: Although further validation is needed, our multiomic analyses demonstrate the potential of metabolomics to predict bronchiolitis severity and better understand microbe-host interaction.}, } @article {pmid28528426, year = {2017}, author = {Nielsen, J and Archer, J and Essack, M and Bajic, VB and Gojobori, T and Mijakovic, I}, title = {Building a bio-based industry in the Middle East through harnessing the potential of the Red Sea biodiversity.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {12}, pages = {4837-4851}, pmid = {28528426}, issn = {1432-0614}, mesh = {Bacillus/physiology ; *Biodiversity ; *Bioelectric Energy Sources ; Cyanobacteria/physiology ; Indian Ocean ; Metabolic Engineering/economics/methods/statistics & numerical data ; Metagenomics/economics/methods ; Middle East ; Synthetic Biology/economics/methods ; }, abstract = {The incentive for developing microbial cell factories for production of fuels and chemicals comes from the ability of microbes to deliver these valuable compounds at a reduced cost and with a smaller environmental impact compared to the analogous chemical synthesis. Another crucial advantage of microbes is their great biological diversity, which offers a much larger "catalog" of molecules than the one obtainable by chemical synthesis. Adaptation to different environments is one of the important drives behind microbial diversity. We argue that the Red Sea, which is a rather unique marine niche, represents a remarkable source of biodiversity that can be geared towards economical and sustainable bioproduction processes in the local area and can be competitive in the international bio-based economy. Recent bioprospecting studies, conducted by the King Abdullah University of Science and Technology, have established important leads on the Red Sea biological potential, with newly isolated strains of Bacilli and Cyanobacteria. We argue that these two groups of local organisms are currently most promising in terms of developing cell factories, due to their ability to operate in saline conditions, thus reducing the cost of desalination and sterilization. The ability of Cyanobacteria to perform photosynthesis can be fully exploited in this particular environment with one of the highest levels of irradiation on the planet. We highlight the importance of new experimental and in silico methodologies needed to overcome the hurdles of developing efficient cell factories from the Red Sea isolates.}, } @article {pmid28527760, year = {2017}, author = {Shi, Y and Zhai, Q and Li, D and Mao, B and Liu, X and Zhao, J and Zhang, H and Chen, W}, title = {Restoration of cefixime-induced gut microbiota changes by Lactobacillus cocktails and fructooligosaccharides in a mouse model.}, journal = {Microbiological research}, volume = {200}, number = {}, pages = {14-24}, doi = {10.1016/j.micres.2017.04.001}, pmid = {28527760}, issn = {1618-0623}, mesh = {Animals ; Blood Chemical Analysis ; Cecum/chemistry/microbiology/pathology ; Cefixime/administration & dosage/*pharmacology ; Cell Adhesion/drug effects ; Colon/microbiology/pathology ; DNA, Bacterial/genetics ; Disease Models, Animal ; Fatty Acids, Volatile/analysis ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/drug effects/microbiology ; HT29 Cells ; Humans ; Ileum/microbiology/pathology ; Intestines ; Lactobacillus/classification/isolation & purification/metabolism/*physiology ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Microbial Consortia/*drug effects ; Oligosaccharides/*pharmacology ; Probiotics/pharmacology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Probiotics have been used to rebuild the antibiotic-induced dysfunction in gut microbiota, but whether the different strains of probiotics result in similar or reverse effects remains unclear. In this study, the different recovery effects of two cocktails (each contains four strains) of Lactobacillus and fructooligosaccharide against cefixime-induced change of gut microbiota were evaluated in C57BL/6J mice. The results show that the use of cefixime caused a reduction in the diversities of the microbial community and led to significantly decreasing to one preponderant Firmicutes phylum, which was difficult to restore naturally in the short term. The gut microbiota compositions of the groups treated with the probiotic cocktails were much more diverse than those of the natural recovery group. The effects of Lactobacillus cocktails against the cefixime-induced gut microbiota change may mainly be due to the beneficial SCFAs production in vivo and also be related to the good cell adhesion properties performed in vitro. Meanwhile, the restoration of the cefixime-induced gut microbiota was significantly different between two Lactobacillus groups since the Lactobacillus strains with high levels of fructooligosaccharide use and better cell adhesion properties performed considerably better than the Lactobacillus strains with high survival rates in the gastrointestinal tract. The contents of short-chain fatty acids in ceca were increased to 26.483±1.925 and 25.609±2.782μmol/g in the two probiotic cocktail groups respectively compared to 15.791±0.833μmol/g (P<0.05) in control group. Moreover, intestinal inflammation was alleviated by administration of the Lactobacillus cocktails. However, fructooligasaccharide administration showed certain effects on gut microbiota restoration (such as an increase of Akkermansia), although its effect on the entire microbiome structure is not so obvious.}, } @article {pmid28525602, year = {2017}, author = {Boudreau, MD and Olson, GR and Tryndyak, VP and Bryant, MS and Felton, RP and Beland, FA}, title = {From the Cover: Aloin, a Component of the Aloe Vera Plant Leaf, Induces Pathological Changes and Modulates the Composition of Microbiota in the Large Intestines of F344/N Male Rats.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {158}, number = {2}, pages = {302-318}, pmid = {28525602}, issn = {1096-0929}, mesh = {Aloe/*chemistry ; Animals ; Colon/*drug effects/microbiology/pathology ; Dose-Response Relationship, Drug ; Emodin/administration & dosage/*analogs & derivatives/toxicity ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Growth ; Male ; Plant Extracts/*toxicity ; Plant Leaves/*chemistry ; Rats ; Rats, Inbred F344 ; }, abstract = {In a previous study, the oral administration of an Aloe vera whole leaf extract induced dose-related mucosal and goblet cell hyperplasia in the rat colon after 13 weeks and colon cancer after 2 years. The primary goal of this study was to determine whether or not the administration of aloin, a component of the Aloe vera plant leaf, would replicate the pathophysiological effects that were observed in rats in the previous study with an Aloe vera whole leaf extract. Groups of 10 male F344/N rats were administered aloin at 0, 6.95, 13.9, 27.8, 55.7, 111, 223, and 446 mg/kg drinking water for 13 weeks. At the end of study, rat feces were collected, and the composition of fecal bacteria was investigated by next generation sequencing of the PCR-amplified V3/V4 region of the 16S rRNA gene. At necropsy, blood was collected by cardiac puncture and organs and sections of the large intestine were collected for histopathology. Aloin induced dose-related increased incidences and severities of mucosal and goblet cell hyperplasia that extended from the cecum to the rectum, with increased incidences and severities detected at aloin doses ≥55.7 mg/kg drinking water. Analysis of the 16S rRNA metagenomics sequencing data revealed marked shifts in the structure of the gut microbiota in aloin-treated rats at each taxonomic rank. This study highlights the similarities in effects observed for aloin and the Aloe vera whole leaf extract, and points to a potential mechanism of action to explain the observed pathological changes via modulation of the gut microbiota composition.}, } @article {pmid28524867, year = {2017}, author = {Kashtan, N and Roggensack, SE and Berta-Thompson, JW and Grinberg, M and Stepanauskas, R and Chisholm, SW}, title = {Fundamental differences in diversity and genomic population structure between Atlantic and Pacific Prochlorococcus.}, journal = {The ISME journal}, volume = {11}, number = {9}, pages = {1997-2011}, pmid = {28524867}, issn = {1751-7370}, mesh = {Atlantic Ocean ; Bermuda ; *Biodiversity ; Ecology ; Genomics ; Hawaii ; Metagenomics ; Pacific Ocean ; Phylogeny ; Prochlorococcus/classification/*genetics/isolation & purification ; Seawater/*microbiology ; }, abstract = {The Atlantic and Pacific Oceans represent different biogeochemical regimes in which the abundant marine cyanobacterium Prochlorococcus thrives. We have shown that Prochlorococcus populations in the Atlantic are composed of hundreds of genomically, and likely ecologically, distinct coexisting subpopulations with distinct genomic backbones. Here we ask if differences in the ecology and selection pressures between the Atlantic and Pacific are reflected in the diversity and genomic composition of their indigenous Prochlorococcus populations. We applied large-scale single-cell genomics and compared the cell-by-cell genomic composition of wild populations of co-occurring cells from samples from Station ALOHA off Hawaii, and from Bermuda Atlantic Time Series Station off Bermuda. We reveal fundamental differences in diversity and genomic structure of populations between the sites. The Pacific populations are more diverse than those in the Atlantic, composed of significantly more coexisting subpopulations and lacking dominant subpopulations. Prochlorococcus from the two sites seem to be composed of mostly non-overlapping distinct sets of subpopulations with different genomic backbones-likely reflecting different sets of ocean-specific micro-niches. Furthermore, phylogenetically closely related strains carry ocean-associated nutrient acquisition genes likely reflecting differences in major selection pressures between the oceans. This differential selection, along with geographic separation, clearly has a significant role in shaping these populations.}, } @article {pmid28524866, year = {2017}, author = {Vigneron, A and Alsop, EB and Lomans, BP and Kyrpides, NC and Head, IM and Tsesmetzis, N}, title = {Succession in the petroleum reservoir microbiome through an oil field production lifecycle.}, journal = {The ISME journal}, volume = {11}, number = {9}, pages = {2141-2154}, pmid = {28524866}, issn = {1751-7370}, mesh = {Bacteria/classification/genetics/*isolation & purification/metabolism ; Ecosystem ; *Microbiota ; Nitrates/metabolism ; North Sea ; Oil and Gas Fields/*microbiology ; Petroleum/metabolism ; Seawater/microbiology ; Sulfides/metabolism ; }, abstract = {Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth's surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system. Analysis of the entire Halfdan oil field in the North Sea (32 producing wells in production for 1-15 years) using quantitative PCR, multigenic sequencing, comparative metagenomic and genomic bins reconstruction revealed systematic shifts in microbial community composition and metabolic potential, as well as changing ecological strategies in response to anthropogenic perturbation of the oil field ecosystem, related to length of time in production. The microbial communities were initially dominated by slow growing anaerobes such as members of the Thermotogales and Clostridiales adapted to living on hydrocarbons and complex refractory organic matter. However, as seawater and nitrate injection (used for secondary oil production) delivered oxidants, the microbial community composition progressively changed to fast growing opportunists such as members of the Deferribacteres, Delta-, Epsilon- and Gammaproteobacteria, with energetically more favorable metabolism (for example, nitrate reduction, H2S, sulfide and sulfur oxidation). This perturbation has profound consequences for understanding the microbial ecology of the system and is of considerable practical importance as it promotes detrimental processes such as reservoir souring and metal corrosion. These findings provide a new conceptual framework for understanding the petroleum reservoir biosphere and have consequences for developing strategies to manage microbiological problems in the oil industry.}, } @article {pmid28523623, year = {2017}, author = {Rudrashetti, AP and Jadeja, NB and Gandhi, D and Juwarkar, AA and Sharma, A and Kapley, A and Pandey, RA}, title = {Microbial population shift caused by sulfamethoxazole in engineered-Soil Aquifer Treatment (e-SAT) system.}, journal = {World journal of microbiology & biotechnology}, volume = {33}, number = {6}, pages = {121}, pmid = {28523623}, issn = {1573-0972}, mesh = {Bacteria/*classification/genetics/*metabolism ; Bacterial Physiological Phenomena ; *Biodegradation, Environmental ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal ; Groundwater/*microbiology ; India ; Metagenome/genetics ; Microbial Consortia/genetics ; Phylogeny ; Sequence Analysis ; Soil/chemistry ; *Soil Microbiology ; Sulfamethoxazole/*metabolism ; Wastewater/microbiology ; }, abstract = {The engineered-Soil Aquifer Treatment (e-SAT) system was exploited for the biological degradation of Sulfamethoxazole (SMX) which is known to bio-accumulate in the environment. The fate of SMX in soil column was studied through laboratory simulation for a period of 90 days. About 20 ppm SMX concentration could be removed in four consecutive cycles in e-SAT. To understand the microbial community change and biological degradation of SMX in e-SAT system, metagenomic analysis was performed for the soil samples before (A-EBD) and after SMX exposure (B-EBD) in the e-SAT. Four bacterial phyla were found to be present in both the samples, with sample B-EBD showing increased abundance for Actinobacteria, Bacteroidetes, Firmicutes and decreased Proteobacterial abundance compared to A-EBD. The unclassified bacteria were found to be abundant in B-EBD compared to A-EBD. At class level, classes such as Bacilli, Negativicutes, Deltaproteobacteria, and Bacteroidia emerged in sample B-EBD owing to SMX treatment, while Burkholderiales and Nitrosomonadales appeared to be dominant at order level after SMX treatment. Furthermore, in response to SMX treatment, the family Nitrosomonadaceae appeared to be dominant. Pseudomonas was the most dominating bacterial genus in A-EBD whereas Cupriavidus dominated in sample B-EBD. Additionally, the sulfur oxidizing bacteria were enriched in the B-EBD sample, signifying efficient electron transfer and hence organic molecule degradation in the e-SAT system. Results of this study offer new insights into understanding of microbial community shift during the biodegradation of SMX.}, } @article {pmid28523395, year = {2017}, author = {Han, GG and Lee, JY and Jin, GD and Park, J and Choi, YH and Chae, BJ and Kim, EB and Choi, YJ}, title = {Evaluating the association between body weight and the intestinal microbiota of weaned piglets via 16S rRNA sequencing.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {14}, pages = {5903-5911}, doi = {10.1007/s00253-017-8304-7}, pmid = {28523395}, issn = {1432-0614}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Bacteroidetes/genetics/isolation & purification ; *Body Weight ; Feces/microbiology ; Firmicutes/genetics/isolation & purification ; *Gastrointestinal Microbiome/genetics ; Genes, rRNA ; High-Throughput Nucleotide Sequencing ; Lactococcus/genetics/isolation & purification ; Metabolic Networks and Pathways ; Metagenomics ; RNA, Ribosomal, 16S/*genetics ; Swine/*microbiology/*physiology ; Weaning ; Xenobiotics ; }, abstract = {Due to the ban on the use of antimicrobial growth promoters in livestock feeds, understanding the relationship between intestinal microbiota and the physiology of the host has become very important for improving livestock performance. In this study, we investigated the relationship between intestinal microbiota and body weights of weaned piglets. Lighter (n = 9) and heavier (n = 9) 9-week-old weaned piglets were selected from approximately one hundred individuals based on their body weights. Their fecal microbial communities were analyzed by sequencing the V4 region of the 16S rRNA gene. The microbial richness estimators of the heavier piglets were significantly higher than those of the lighter piglets. At the phylum level, the microbiota of the heavier group had significantly higher levels of Firmicutes and a higher Firmicutes-to-Bacteroidetes ratio than that of the lighter group. At the genus level, the levels of several genera, such as Anaerococcus and Lactococcus, were significantly different in the two groups. In particular, the lighter group had significantly higher levels of opportunistic pathogenic bacteria, such as Anaerotruncus and Bacteroides, compared with those of the heavier group. Moreover, the levels of bacteria expressing the components of several metabolic pathways were significantly different in the two groups. The microbiota of the heavier group had a significantly higher involvement in three KEGG pathways concerned with xenobiotic degradation than that of the lighter group. These results may provide insights into host-microbe interactions occurring in the piglet intestine and will be useful in establishing a strategy for improving growth performance in the swine industry.}, } @article {pmid28520993, year = {2017}, author = {McDonald, LC}, title = {Effects of short- and long-course antibiotics on the lower intestinal microbiome as they relate to traveller's diarrhea.}, journal = {Journal of travel medicine}, volume = {24}, number = {suppl_1}, pages = {S35-S38}, pmid = {28520993}, issn = {1708-8305}, support = {CC999999//Intramural CDC HHS/United States ; }, mesh = {Anti-Bacterial Agents/administration & dosage/*pharmacology/therapeutic use ; Diarrhea/*drug therapy ; Gastrointestinal Microbiome/*drug effects ; Humans ; *Travel ; }, abstract = {BACKGROUND: Antibiotics have profound and lasting effects on the lower intestinal (gut) microbiome that can both promote resistance and increase susceptibility to colonization and infection; knowledge of these changes is important to the prevention and treatment of traveler's diarrhea.

METHODS: Recent data from epidemiologic and modern metagenomics studies were reviewed in regard to how such findings could inform the prevention and treatment of traveler's diarrhea.

RESULTS: Although it is well recognized that antibiotics increase the risk for Clostridium difficile infection, it is less recognized how they predispose patients to typically foodborne pathogens such as Salmonella or Camplyobacter spp. While these pathogens account for only a fraction of traveler's diarrhea, such predisposition reflects how antibiotic exposure that precedes or occurs during travel may increase the risk for infection with other more common pathogens, even possibly enterotoxigenic Eschericia coli, especially in the setting of acquired resistance. Even short antibiotic exposures disrupt the gut microbiome up to a year or more and repeated exposures appear to attenuate recovery from ever occurring. One bacterial phylum that commonly increases in the gut following antibiotics are the proteobacteria including Enterobacteriacea; these are pro-inflammatory and often carry antibiotic resistance genes, the number and diversity of these genes (i.e. the resistome) commonly expands following antibiotics. The gut resistome among healthy community-dwelling adults reflects geographic variability in antibiotic use practices in both humans and food-producing animals as well as possibly the transmission of antibiotic resistance genes through the food supply.

CONCLUSIONS: Because antibiotic use among travelers will influence the resistome and thereby promote geographic spread of resistance, it is important that antibiotic use recommendations for travelers be guided by resistance surveillance data as well as a careful assessment of the risks and benefits to both the individual and society.}, } @article {pmid28515299, year = {2017}, author = {Remnant, EJ and Shi, M and Buchmann, G and Blacquière, T and Holmes, EC and Beekman, M and Ashe, A}, title = {A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations.}, journal = {Journal of virology}, volume = {91}, number = {16}, pages = {}, pmid = {28515299}, issn = {1098-5514}, mesh = {Animals ; Bees/parasitology/*virology ; *Biodiversity ; *Genetic Variation ; RNA Viruses/*classification/genetics/*isolation & purification ; Varroidae/virology ; }, abstract = {Understanding the diversity and consequences of viruses present in honey bees is critical for maintaining pollinator health and managing the spread of disease. The viral landscape of honey bees (Apis mellifera) has changed dramatically since the emergence of the parasitic mite Varroa destructor, which increased the spread of virulent variants of viruses such as deformed wing virus. Previous genomic studies have focused on colonies suffering from infections by Varroa and virulent viruses, which could mask other viral species present in honey bees, resulting in a distorted view of viral diversity. To capture the viral diversity within colonies that are exposed to mites but do not suffer the ultimate consequences of the infestation, we examined populations of honey bees that have evolved naturally or have been selected for resistance to Varroa This analysis revealed seven novel viruses isolated from honey bees sampled globally, including the first identification of negative-sense RNA viruses in honey bees. Notably, two rhabdoviruses were present in three geographically diverse locations and were also present in Varroa mites parasitizing the bees. To characterize the antiviral response, we performed deep sequencing of small RNA populations in honey bees and mites. This provided evidence of a Dicer-mediated immune response in honey bees, while the viral small RNA profile in Varroa mites was novel and distinct from the response observed in bees. Overall, we show that viral diversity in honey bee colonies is greater than previously thought, which encourages additional studies of the bee virome on a global scale and which may ultimately improve disease management.IMPORTANCE Honey bee populations have become increasingly susceptible to colony losses due to pathogenic viruses spread by parasitic Varroa mites. To date, 24 viruses have been described in honey bees, with most belonging to the order Picornavirales Collapsing Varroa-infected colonies are often overwhelmed with high levels of picornaviruses. To examine the underlying viral diversity in honey bees, we employed viral metatranscriptomics analyses on three geographically diverse Varroa-resistant populations from Europe, Africa, and the Pacific. We describe seven novel viruses from a range of diverse viral families, including two viruses that are present in all three locations. In honey bees, small RNA sequences indicate that these viruses are processed by Dicer and the RNA interference pathway, whereas Varroa mites produce strikingly novel small RNA patterns. This work increases the number and diversity of known honey bee viruses and will ultimately contribute to improved disease management in our most important agricultural pollinator.}, } @article {pmid28513633, year = {2017}, author = {Thomas, H}, title = {NAFLD: A gut microbiome signature for advanced fibrosis diagnosis in NAFLD.}, journal = {Nature reviews. Gastroenterology & hepatology}, volume = {14}, number = {7}, pages = {388}, pmid = {28513633}, issn = {1759-5053}, mesh = {Dysbiosis ; Fibrosis ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Non-alcoholic Fatty Liver Disease ; }, } @article {pmid28512003, year = {2018}, author = {Krüger, A and Schäfers, C and Schröder, C and Antranikian, G}, title = {Towards a sustainable biobased industry - Highlighting the impact of extremophiles.}, journal = {New biotechnology}, volume = {40}, number = {Pt A}, pages = {144-153}, doi = {10.1016/j.nbt.2017.05.002}, pmid = {28512003}, issn = {1876-4347}, mesh = {*Conservation of Natural Resources ; *Extremophiles/genetics/metabolism ; Metagenome ; Oil and Gas Industry/*organization & administration ; }, abstract = {The transition of the oil-based economy towards a sustainable economy completely relying on biomass as renewable feedstock requires the concerted action of academia, industry, politics and civil society. An interdisciplinary approach of various fields such as microbiology, molecular biology, chemistry, genetics, chemical engineering and agriculture in addition to cross-sectional technologies such as economy, logistics and digitalization is necessary to meet the future global challenges. The genomic era has contributed significantly to the exploitation of naturés biodiversity also from extreme habitats. By applying modern technologies it is now feasible to deliver robust enzymes (extremozymes) and robust microbial systems that are active at temperatures up to 120°C, at pH 0 and 12 and at 1000bar. In the post-genomic era, different sophisticated "omics" analyses will allow the identification of countless novel enzymes regardless of the lack of cultivability of most microorganisms. Furthermore, elaborate protein-engineering methods are clearing the way towards tailor-made robust biocatalysts. Applying environmentally friendly and efficient biological processes, terrestrial and marine biomass can be converted to high value products e.g. chemicals, building blocks, biomaterials, pharmaceuticals, food, feed and biofuels. Thus, further application of extremophiles has the potential to improve sustainability of existing biotechnological processes towards a greener biobased industry.}, } @article {pmid28511691, year = {2017}, author = {Larousse, M and Rancurel, C and Syska, C and Palero, F and Etienne, C and Industri, B and Nesme, X and Bardin, M and Galiana, E}, title = {Tomato root microbiota and Phytophthora parasitica-associated disease.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {56}, pmid = {28511691}, issn = {2049-2618}, mesh = {Bacteria/*classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Gene Expression Regulation, Plant ; High-Throughput Nucleotide Sequencing/*methods ; Solanum lycopersicum/*microbiology ; Microbiota ; Phylogeny ; Phytophthora/*pathogenicity ; Plant Diseases ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Symbiosis ; }, abstract = {BACKGROUND: Interactions between pathogenic oomycetes and microbiota residing on the surface of the host plant root are unknown, despite being critical to inoculum constitution. The nature of these interactions was explored for the polyphagous and telluric species Phytophthora parasitica.

RESULTS: Composition of the rhizospheric microbiota of Solanum lycopersicum was characterized using deep re-sequencing of 16S rRNA gene to analyze tomato roots either free of or partly covered with P. parasitica biofilm. Colonization of the host root surface by the oomycete was associated with a shift in microbial community involving a Bacteroidetes/Proteobacteria transition and Flavobacteriaceae as the most abundant family. Identification of members of the P. parasitica-associated microbiota interfering with biology and oomycete infection was carried out by screening for bacteria able to (i) grow on a P. parasitica extract-based medium (ii), exhibit in vitro probiotic or antibiotic activity towards the oomycete (iii), have an impact on the oomycete infection cycle in a tripartite interaction S. lycopersicum-P. parasitica-bacteria. One Pseudomonas phylotype was found to exacerbate disease symptoms in tomato plants. The lack of significant gene expression response of P. parasitica effectors to Pseudomonas suggested that the increase in plant susceptibility was not associated with an increase in virulence. Our results reveal that Pseudomonas spp. establishes commensal interactions with the oomycete. Bacteria preferentially colonize the surface of the biofilm rather than the roots, so that they can infect plant cells without any apparent infection of P. parasitica.

CONCLUSIONS: The presence of the pathogenic oomycete P. parasitica in the tomato rhizosphere leads to a shift in the rhizospheric microbiota composition. It contributes to the habitat extension of Pseudomonas species mediated through a physical association between the oomycete and the bacteria.}, } @article {pmid28509857, year = {2017}, author = {Poli, A and Finore, I and Romano, I and Gioiello, A and Lama, L and Nicolaus, B}, title = {Microbial Diversity in Extreme Marine Habitats and Their Biomolecules.}, journal = {Microorganisms}, volume = {5}, number = {2}, pages = {}, pmid = {28509857}, issn = {2076-2607}, abstract = {Extreme marine environments have been the subject of many studies and scientific publications. For many years, these environmental niches, which are characterized by high or low temperatures, high-pressure, low pH, high salt concentrations and also two or more extreme parameters in combination, have been thought to be incompatible to any life forms. Thanks to new technologies such as metagenomics, it is now possible to detect life in most extreme environments. Starting from the discovery of deep sea hydrothermal vents up to the study of marine biodiversity, new microorganisms have been identified, and their potential uses in several applied fields have been outlined. Thermophile, halophile, alkalophile, psychrophile, piezophile and polyextremophile microorganisms have been isolated from these marine environments; they proliferate thanks to adaptation strategies involving diverse cellular metabolic mechanisms. Therefore, a vast number of new biomolecules such as enzymes, polymers and osmolytes from the inhabitant microbial community of the sea have been studied, and there is a growing interest in the potential returns of several industrial production processes concerning the pharmaceutical, medical, environmental and food fields.}, } @article {pmid28506730, year = {2017}, author = {Lepage, P}, title = {[The human gut microbiota: Interactions with the host and dysfunctions].}, journal = {Revue des maladies respiratoires}, volume = {34}, number = {10}, pages = {1085-1090}, doi = {10.1016/j.rmr.2016.11.003}, pmid = {28506730}, issn = {1776-2588}, mesh = {Dysbiosis/*etiology/microbiology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology ; Host-Pathogen Interactions/*physiology ; Humans ; Inflammation/*etiology ; Inflammatory Bowel Diseases/microbiology ; Metabolic Diseases/microbiology ; }, abstract = {The human intestinal microbiota is composed of approximately 100,000 billion microorganisms with the average total number of different commensal bacterial species estimated at over 500 per individual. The human intestinal microbiota can be considered as an organ within another, which co-evolved with its host to achieve a symbiotic relationship leading to physiological homeostasis. The host provides an environment enriched in nutrients and the microbiota provides essential functions. Dysbiosis of the intestinal microbiota (changes in bacterial composition) has been associated with local dysfunctions of the gastrointestinal tract, such as inflammatory bowel disease or irritable bowel syndrome but also with obesity and metabolic diseases. However, a better understanding of the human intestinal ecosystem is still needed to understand the exact role of the microbiota in health and disease. Most intestinal bacteria are anaerobic and therefore, for the large majority, impossible to culture at present. Consequently, their function cannot be inferred from data on their composition. Today, with the help of a metagenomic approach, the bacterial genomic content of an ecosystem and the associated functions can be directly accessed from the environment without culture.}, } @article {pmid28506638, year = {2017}, author = {Hao, L and Xia, Z and Yang, H and Wang, J and Han, M}, title = {Ionic liquid-based reagents improve the stability of midterm fecal sample storage.}, journal = {Journal of microbiological methods}, volume = {139}, number = {}, pages = {68-73}, doi = {10.1016/j.mimet.2017.05.005}, pmid = {28506638}, issn = {1872-8359}, mesh = {Feces/chemistry/*microbiology ; Humans ; Indicators and Reagents ; Ionic Liquids/*chemistry ; Metagenomics/methods ; *Microbiota/genetics ; Preservation, Biological/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Specimen Handling/*methods ; Temperature ; Time Factors ; }, abstract = {Fecal samples are widely used in metagenomic research, which aims to elucidate the relationship between human health and the intestinal microbiota. However, the best conditions for stable and reliable storage and transport of these samples at room temperature are still unknown, and whether samples stored at room temperature for several days will maintain their microbiota composition is still unknown. Here, we established and tested a preservation method using reagents containing imidazolium- or pyridinium-based ionic liquids. We stored human fecal samples in these reagents for up to 7 days at different temperatures. Subsequently, all samples were sequenced and compared with fresh samples and/or samples treated under other conditions. The 16S rRNA sequencing results suggested that ionic liquid-based reagents could stabilize the composition of the microbiota in fecal samples during a 7-day storage period, particularly when stored at room temperature. Thus, this method may have implications in the storage of fecal samples for metagenomic research.}, } @article {pmid28506279, year = {2017}, author = {Rath, S and Heidrich, B and Pieper, DH and Vital, M}, title = {Uncovering the trimethylamine-producing bacteria of the human gut microbiota.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {54}, pmid = {28506279}, issn = {2049-2618}, mesh = {Bacteria/*classification/enzymology/isolation & purification/metabolism ; Bacterial Proteins/genetics ; Biosynthetic Pathways ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/*methods ; Methylamines/*metabolism ; Multilocus Sequence Typing ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Trimethylamine (TMA), produced by the gut microbiota from dietary quaternary amines (mainly choline and carnitine), is associated with atherosclerosis and severe cardiovascular disease. Currently, little information on the composition of TMA producers in the gut is available due to their low abundance and the requirement of specific functional-based detection methods as many taxa show disparate abilities to produce that compound.

RESULTS: In order to examine the TMA-forming potential of microbial communities, we established databases for the key genes of the main TMA-synthesis pathways, encoding choline TMA-lyase (cutC) and carnitine oxygenase (cntA), using a multi-level screening approach on 67,134 genomes revealing 1107 and 6738 candidates to exhibit cutC and cntA, respectively. Gene-targeted assays enumerating the TMA-producing community by quantitative PCR and characterizing its composition via Illumina sequencing were developed and applied on human fecal samples (n = 50) where all samples contained potential TMA producers (cutC was detected in all individuals, whereas only 26% harbored cntA) constituting, however, only a minor part of the total community (below 1% in most samples). Obtained cutC amplicons were associated with various taxa, in particular with Clostridium XIVa strains and Eubacterium sp. strain AB3007, though a bulk of sequences displayed low nucleotide identities to references (average 86% ± 7%) indicating that key human TMA producers are yet to be isolated. Co-occurrence analysis revealed specific groups governing the community structure of cutC-exhibiting taxa across samples. CntA amplicons displayed high identities (~99%) to Gammaproteobacteria-derived references, primarily from Escherichia coli. Metagenomic analysis of samples provided by the Human Microbiome Project (n = 154) confirmed the abundance patterns as well as overall taxonomic compositions obtained with our assays, though at much lower resolution, whereas 16S ribosomal RNA gene sequence analysis could not adequately uncover the TMA-producing potential.

CONCLUSIONS: In this study, we developed a diagnostic framework that enabled the quantification and comprehensive characterization of the TMA-producing potential in human fecal samples. The key players were identified, and together with predictions on their environmental niches using functional genomics on most closely related reference strains, we provide crucial information for the development of specific treatment strategies to restrain TMA producers and limit their proliferation.}, } @article {pmid28506246, year = {2017}, author = {Lin, J and Kramna, L and Autio, R and Hyöty, H and Nykter, M and Cinek, O}, title = {Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {378}, pmid = {28506246}, issn = {1471-2164}, mesh = {Genetic Variation ; Genomics/*methods ; *High-Throughput Nucleotide Sequencing ; Humans ; *Internet ; Microbiota/genetics ; *Software ; Viruses/*genetics ; }, abstract = {BACKGROUND: Next generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical methods: this is especially important in studies of multifactorial diseases, or in parallel comparison of laboratory protocols.

RESULTS: We have developed a web-based application allowing direct upload of sequences from multiple virome samples using custom parameters. The samples are then processed in parallel using an identical protocol, and can be easily reanalyzed. The pipeline performs de-novo assembly, taxonomic classification of viruses as well as sample analyses based on user-defined grouping categories. Tables of virus abundance are produced from cross-validation by remapping the sequencing reads to a union of all observed reference viruses. In addition, read sets and reports are created after processing unmapped reads against known human and bacterial ribosome references. Secured interactive results are dynamically plotted with population and diversity charts, clustered heatmaps and a sortable and searchable abundance table.

CONCLUSIONS: The Vipie web application is a unique tool for multi-sample metagenomic analysis of viral data, producing searchable hits tables, interactive population maps, alpha diversity measures and clustered heatmaps that are grouped in applicable custom sample categories. Known references such as human genome and bacterial ribosomal genes are optionally removed from unmapped ('dark matter') reads. Secured results are accessible and shareable on modern browsers. Vipie is a freely available web-based tool whose code is open source.}, } @article {pmid28503851, year = {2017}, author = {Zumsteg, A and Urwyler, SK and Glaubitz, J}, title = {Characterizing bacterial communities in paper production-troublemakers revealed.}, journal = {MicrobiologyOpen}, volume = {6}, number = {4}, pages = {}, pmid = {28503851}, issn = {2045-8827}, mesh = {Biofilms/*growth & development ; *Biota ; Burkholderiales/classification/genetics/*isolation & purification/physiology ; Chryseobacterium/classification/genetics/*isolation & purification/physiology ; *Manufacturing and Industrial Facilities ; *Paper ; }, abstract = {Biofilm formation is a major cause of reduced paper quality and increased down time during paper manufacturing. This study uses Illumina next-generation sequencing to identify the microbial populations causing quality issues due to their presence in biofilms and slimes. The paper defects investigated contained traces of the films and/or slime of mainly two genera, Tepidimonas and Chryseobacterium. The Tepidimonas spp. found contributed on average 68% to the total bacterial population. Both genera have been described previously to be associated with biofilms in paper mills. There was indication that Tepidimonas spp. were present as compact biofilm in the head box of one paper machine and was filtered out by the paper web during production. On the other hand Tepidimonas spp. were also present to a large extent in the press and white waters of two nonproblematic paper machines. Therefore, the mere presence of a known biofilm producer alone is not sufficient to cause slimes and therefore paper defects and other critical factors are additionally at play. For instance, we identified Acidovorax sp., which is an early colonizer of paper machines, exhibiting the ability to form extracellular DNA matrices for attachment and biofilm formation.}, } @article {pmid28500338, year = {2017}, author = {Al-Hebshi, NN and Nasher, AT and Maryoud, MY and Homeida, HE and Chen, T and Idris, AM and Johnson, NW}, title = {Inflammatory bacteriome featuring Fusobacterium nucleatum and Pseudomonas aeruginosa identified in association with oral squamous cell carcinoma.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1834}, pmid = {28500338}, issn = {2045-2322}, support = {R37 DE016937/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Aged ; Biodiversity ; Carcinoma, Squamous Cell/*etiology/pathology ; Case-Control Studies ; Female ; Fusobacterium Infections/*complications/*microbiology ; *Fusobacterium nucleatum/classification/genetics ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Mouth Neoplasms/*etiology/pathology ; Pseudomonas Infections/*complications/*microbiology ; *Pseudomonas aeruginosa/classification/genetics ; }, abstract = {Studies on the possible association between bacteria and oral squamous cell carcinoma (OSCC) remain inconclusive, largely due to methodological variations/limitations. The objective of this study was to characterize the species composition as well as functional potential of the bacteriome associated with OSCC. DNA obtained from 20 fresh OSCC biopsies (cases) and 20 deep-epithelium swabs (matched control subjects) was sequenced for the V1-V3 region using Illumina's 2 × 300 bp chemistry. High quality, non-chimeric merged reads were classified to species level using a prioritized BLASTN-algorithm. Downstream analyses were performed using QIIME, PICRUSt, and LEfSe. Fusobacterium nucleatum subsp. polymorphum was the most significantly overrepresented species in the tumors followed by Pseudomonas aeruginosa and Campylobacter sp. Oral taxon 44, while Streptococcus mitis, Rothia mucilaginosa and Haemophilus parainfluenzae were the most significantly abundant in the controls. Functional prediction showed that genes involved in bacterial mobility, flagellar assembly, bacterial chemotaxis and LPS synthesis were enriched in the tumors while those responsible for DNA repair and combination, purine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, ribosome biogenesis and glycolysis/gluconeogenesis were significantly associated with the controls. This is the first epidemiological evidence for association of F. nucleatum and P. aeruginosa with OSCC. Functionally, an "inflammatory bacteriome" is enriched in OSSC.}, } @article {pmid28494786, year = {2017}, author = {Cope, EK and Goldberg, AN and Pletcher, SD and Lynch, SV}, title = {Compositionally and functionally distinct sinus microbiota in chronic rhinosinusitis patients have immunological and clinically divergent consequences.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {53}, pmid = {28494786}, issn = {2049-2618}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/*classification/genetics/*immunology ; Endoscopy ; Female ; Humans ; Male ; Microbiota ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhinitis/immunology/*microbiology/surgery ; Sequence Analysis, DNA/*methods ; Sinusitis/immunology/*microbiology/surgery ; Young Adult ; }, abstract = {BACKGROUND: Chronic rhinosinusitis (CRS) is a heterogeneous disease characterized by persistent sinonasal inflammation and sinus microbiome dysbiosis. The basis of this heterogeneity is poorly understood. We sought to address the hypothesis that a limited number of compositionally distinct pathogenic bacterial microbiota exist in CRS patients and invoke discrete immune responses and clinical phenotypes in CRS patients.

RESULTS: Sinus brushings from patients with CRS (n = 59) and healthy individuals (n = 10) collected during endoscopic sinus surgery were analyzed using 16S rRNA gene sequencing, predicted metagenomics, and RNA profiling of the mucosal immune response. We show that CRS patients cluster into distinct sub-groups (DSI-III), each defined by specific pattern of bacterial co-colonization (permutational multivariate analysis of variance (PERMANOVA); p = 0.001, r [2] = 0.318). Each sub-group was typically dominated by a pathogenic family: Streptococcaceae (DSI), Pseudomonadaceae (DSII), Corynebacteriaceae [DSIII(a)], or Staphylococcaceae [DSIII(b)]. Each pathogenic microbiota was predicted to be functionally distinct (PERMANOVA; p = 0.005, r [2] = 0.217) and encode uniquely enriched gene pathways including ansamycin biosynthesis (DSI), tryptophan metabolism (DSII), two-component response [DSIII(b)], and the PPAR-γ signaling pathway [DSIII(a)]. Each is also associated with significantly distinct host immune responses; DSI, II, and III(b) invoked a variety of pro-inflammatory, TH1 responses, while DSIII(a), which exhibited significantly increased incidence of nasal polyps (Fisher's exact; p = 0.034, relative risk = 2.16), primarily induced IL-5 expression (Kruskal Wallis; q = 0.045).

CONCLUSIONS: A large proportion of CRS patient heterogeneity may be explained by the composition of their sinus bacterial microbiota and related host immune response-features which may inform strategies for tailored therapy in this patient population.}, } @article {pmid28494241, year = {2017}, author = {Ananthakrishnan, AN and Luo, C and Yajnik, V and Khalili, H and Garber, JJ and Stevens, BW and Cleland, T and Xavier, RJ}, title = {Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases.}, journal = {Cell host & microbe}, volume = {21}, number = {5}, pages = {603-610.e3}, pmid = {28494241}, issn = {1934-6069}, support = {K23 DK097142/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 DK092405/DK/NIDDK NIH HHS/United States ; }, mesh = {Antibodies, Monoclonal, Humanized/*therapeutic use ; *Biological Therapy ; Butyrates/metabolism ; Colitis, Ulcerative/drug therapy ; Crohn Disease/drug therapy ; Feces/chemistry/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Inflammatory Bowel Diseases/*therapy ; Integrins/drug effects ; Metagenome ; Prospective Studies ; Treatment Outcome ; }, abstract = {The gut microbiome plays a central role in inflammatory bowel diseases (IBDs) pathogenesis and propagation. To determine whether the gut microbiome may predict responses to IBD therapy, we conducted a prospective study with Crohn's disease (CD) or ulcerative colitis (UC) patients initiating anti-integrin therapy (vedolizumab). Disease activity and stool metagenomes at baseline, and weeks 14, 30, and 54 after therapy initiation were assessed. Community α-diversity was significantly higher, and Roseburia inulinivorans and a Burkholderiales species were more abundant at baseline among CD patients achieving week 14 remission. Several significant associations were identified with microbial function; 13 pathways including branched chain amino acid synthesis were significantly enriched in baseline samples from CD patients achieving remission. A neural network algorithm, vedoNet, incorporating microbiome and clinical data, provided highest classifying power for clinical remission. We hypothesize that the trajectory of early microbiome changes may be a marker of response to IBD treatment.}, } @article {pmid28492362, year = {2017}, author = {Cortés-Acha, B and Figueiredo, R and Seminago, R and Roig, FJ and Llorens, C and Valmaseda-Castellón, E}, title = {Microbiota Analysis of Biofilms on Experimental Abutments Mimicking Dental Implants: An In Vivo Model.}, journal = {Journal of periodontology}, volume = {88}, number = {10}, pages = {1090-1104}, doi = {10.1902/jop.2017.170051}, pmid = {28492362}, issn = {1943-3670}, mesh = {Aged ; Aged, 80 and over ; Bacteria/*classification ; *Biofilms ; DNA, Bacterial/analysis ; Dental Abutments/*microbiology ; Dental Implants/*microbiology ; Female ; Humans ; Implants, Experimental ; Male ; *Microbiota ; Middle Aged ; Periodontitis/microbiology ; RNA, Ribosomal, 16S/analysis ; }, abstract = {BACKGROUND: The microbiota colonizing dental implants has been said to be similar to the microbiome surrounding teeth. In the absence of inflammation, a biofilm with pathologic bacteria can cover implant surfaces exposed to the oral cavity, for example, due to a remodeling process. The aim of the present study is to identify microbiota surrounding exposed dental implants in patients with and without a history of periodontitis through a deep-sequencing approach.

METHODS: An experimental abutment with the same surface and structure as a commercially available dental implant was used. Bacterial DNA was isolated, and the 16S ribosomal RNA gene was amplified and sequenced. Multiplexed tag-encoded sequencing of DNA from the samples was performed, and the reads were processed by metagenomic rapid annotation.

RESULTS: A wide variety of bacteria, 96 species, were identified. The most frequently found bacteria were Fusobacterium nucleatum and Prevotella denticola. Some species generally associated with periodontitis were found to a greater extent in patients without a history of periodontitis. Some bacteria that have never been described as part of the oral microbiome were identified in the present sample.

CONCLUSIONS: Analysis of data suggests that the bacteria surrounding exposed dental implants form a diverse microbiome regardless of the periodontal profile of patients. Further research is needed to clarify the role of these microorganisms in the oral environment.}, } @article {pmid28489411, year = {2017}, author = {Fang, H and Huang, C and Zhao, H and Deng, M}, title = {gCoda: Conditional Dependence Network Inference for Compositional Data.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {24}, number = {7}, pages = {699-708}, pmid = {28489411}, issn = {1557-8666}, mesh = {*Algorithms ; Animals ; Computer Simulation ; High-Throughput Nucleotide Sequencing ; *Likelihood Functions ; Metagenomics ; Mice ; *Microbial Interactions ; *Microbiota ; RNA, Ribosomal, 16S/analysis ; Skin/*microbiology ; }, abstract = {The increasing quality and the reducing cost of high-throughput sequencing technologies for 16S rRNA gene profiling enable researchers to directly analyze microbe communities in natural environments. The direct interactions among microbial species of a given ecological system can help us understand the principles of community assembly and maintenance under various conditions. Compositionality and dimensionality of microbiome data are two main challenges for inferring the direct interaction network of microbes. In this article, we use the logistic normal distribution to model the background mechanism of microbiome data, which can appropriately deal with the compositional nature of the data. The direct interaction relationships are then modeled via the conditional dependence network under this logistic normal assumption. We then propose a novel penalized maximum likelihood method called gCoda to estimate the sparse structure of inverse covariance for latent normal variables to address the high dimensionality of the microbiome data. An effective Majorization-Minimization algorithm is proposed to solve the optimization problem in gCoda. Simulation studies show that gCoda outperforms existing methods (e.g., SPIEC-EASI) in edge recovery of inverse covariance for compositional data under a variety of scenarios. gCoda also performs better than SPIEC-EASI for inferring direct microbial interactions of mouse skin microbiome data.}, } @article {pmid28488798, year = {2017}, author = {Niemeyer, B and Epp, LS and Stoof-Leichsenring, KR and Pestryakova, LA and Herzschuh, U}, title = {A comparison of sedimentary DNA and pollen from lake sediments in recording vegetation composition at the Siberian treeline.}, journal = {Molecular ecology resources}, volume = {17}, number = {6}, pages = {e46-e62}, doi = {10.1111/1755-0998.12689}, pmid = {28488798}, issn = {1755-0998}, mesh = {Biodiversity ; DNA Barcoding, Taxonomic/methods ; DNA, Plant/*genetics/*isolation & purification ; *Geologic Sediments ; *Lakes ; Metagenomics/*methods ; Plants/*classification/genetics ; Pollen/*classification ; Siberia ; }, abstract = {Reliable information on past and present vegetation is important to project future changes, especially for rapidly transitioning areas such as the boreal treeline. To study past vegetation, pollen analysis is common, while current vegetation is usually assessed by field surveys. Application of detailed sedimentary DNA (sedDNA) records has the potential to enhance our understanding of vegetation changes, but studies systematically investigating the power of this proxy are rare to date. This study compares sedDNA metabarcoding and pollen records from surface sediments of 31 lakes along a north-south gradient of increasing forest cover in northern Siberia (Taymyr peninsula) with data from field surveys in the surroundings of the lakes. sedDNA metabarcoding recorded 114 plant taxa, about half of them to species level, while pollen analyses identified 43 taxa, both exceeding the 31 taxa found by vegetation field surveys. Increasing Larix percentages from north to south were consistently recorded by all three methods and principal component analyses based on percentage data of vegetation surveys and DNA sequences separated tundra from forested sites. Comparisons of the ordinations using procrustes and protest analyses show a significant fit among all compared pairs of records. Despite similarities of sedDNA and pollen records, certain idiosyncrasies, such as high percentages of Alnus and Betula in all pollen and high percentages of Salix in all sedDNA spectra, are observable. Our results from the tundra to single-tree tundra transition zone show that sedDNA analyses perform better than pollen in recording site-specific richness (i.e., presence/absence of taxa in the vicinity of the lake) and perform as well as pollen in tracing vegetation composition.}, } @article {pmid28488795, year = {2017}, author = {Marshall, IPG and Starnawski, P and Cupit, C and Fernández Cáceres, E and Ettema, TJG and Schramm, A and Kjeldsen, KU}, title = {The novel bacterial phylum Calditrichaeota is diverse, widespread and abundant in marine sediments and has the capacity to degrade detrital proteins.}, journal = {Environmental microbiology reports}, volume = {9}, number = {4}, pages = {397-403}, doi = {10.1111/1758-2229.12544}, pmid = {28488795}, issn = {1758-2229}, support = {310039/ERC_/European Research Council/International ; }, mesh = {Bacteria/*classification/genetics/*isolation & purification/metabolism ; Biodiversity ; DNA, Bacterial/genetics ; Geologic Sediments/*microbiology ; Metagenome ; Phylogeny ; Proteins/*metabolism ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; }, abstract = {Calditrichaeota is a recently recognized bacterial phylum with three cultured representatives, isolated from hydrothermal vents. Here we expand the phylogeny and ecology of this novel phylum with metagenome-derived and single-cell genomes from six uncultivated bacteria previously not recognized as members of Calditrichaeota. Using 16S rRNA gene sequences from these genomes, we then identified 322 16S rRNA gene sequences from cultivation-independent studies that can now be classified as Calditrichaeota for the first time. This dataset was used to re-analyse a collection of 16S rRNA gene amplicon datasets from marine sediments showing that the Calditrichaeota are globally distributed in the seabed at high abundance, making up to 6.7% of the total bacterial community. This wide distribution and high abundance of Calditrichaeota in cold marine sediment has gone unrecognized until now. All Calditrichaeota genomes show indications of a chemoorganoheterotrophic metabolism with the potential to degrade detrital proteins through the use of extracellular peptidases. Most of the genomes contain genes encoding proteins that confer O2 tolerance, consistent with the relatively high abundance of Calditrichaeota in surficial bioturbated part of the seabed and, together with the genes encoding extracellular peptidases, suggestive of a general ecophysiological niche for this newly recognized phylum in marine sediment.}, } @article {pmid28488752, year = {2017}, author = {Louca, S and Jacques, SMS and Pires, APF and Leal, JS and González, AL and Doebeli, M and Farjalla, VF}, title = {Functional structure of the bromeliad tank microbiome is strongly shaped by local geochemical conditions.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {3132-3151}, doi = {10.1111/1462-2920.13788}, pmid = {28488752}, issn = {1462-2920}, mesh = {Archaea/classification/genetics/*isolation & purification ; Brazil ; Bromeliaceae/*microbiology ; Fresh Water/microbiology ; *Microbiota ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Phytotelmata in tank-forming Bromeliaceae plants are regarded as potential miniature models for aquatic ecology, but detailed investigations of their microbial communities are rare. Hence, the biogeochemistry in bromeliad tanks remains poorly understood. Here we investigate the structure of bacterial and archaeal communities inhabiting the detritus within the tanks of two bromeliad species, Aechmea nudicaulis and Neoregelia cruenta, from a Brazilian sand dune forest. We used metagenomic sequencing for functional community profiling and 16S sequencing for taxonomic profiling. We estimated the correlation between functional groups and various environmental variables, and compared communities between bromeliad species. In all bromeliads, microbial communities spanned a metabolic network adapted to oxygen-limited conditions, including all denitrification steps, ammonification, sulfate respiration, methanogenesis, reductive acetogenesis and anoxygenic phototrophy. Overall, CO2 reducers dominated in abundance over sulfate reducers, and anoxygenic phototrophs largely outnumbered oxygenic photoautotrophs. Functional community structure correlated strongly with environmental variables, between and within a single bromeliad species. Methanogens and reductive acetogens correlated with detrital volume and canopy coverage, and exhibited higher relative abundances in N. cruenta. A comparison of bromeliads to freshwater lake sediments and soil from around the world, revealed stark differences in terms of taxonomic as well as functional microbial community structure.}, } @article {pmid28484095, year = {2017}, author = {Zhou, YJ and Zhao, DD and Liu, H and Chen, HT and Li, JJ and Mu, XQ and Liu, Z and Li, X and Tang, L and Zhao, ZY and Wu, JH and Cai, YX and Huang, YZ and Wang, PG and Jia, YY and Liang, PQ and Peng, X and Chen, SY and Yue, ZL and Yuan, XY and Lu, T and Yao, BQ and Li, YG and Liu, GR and Liu, SL}, title = {Cancer killers in the human gut microbiota: diverse phylogeny and broad spectra.}, journal = {Oncotarget}, volume = {8}, number = {30}, pages = {49574-49591}, pmid = {28484095}, issn = {1949-2553}, mesh = {Adolescent ; Adult ; Animals ; Bacteria/classification/genetics ; Bacterial Physiological Phenomena ; Cell Survival ; Child ; Child, Preschool ; Disease Models, Animal ; Feces/microbiology ; Female ; Gas Chromatography-Mass Spectrometry ; *Gastrointestinal Microbiome ; HeLa Cells ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Neoplasms/*etiology/pathology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Cancer as a large group of complex diseases is believed to result from the interactions of numerous genetic and environmental factors but may develop in people without any known genetic or environmental risks, suggesting the existence of other powerful factors to influence the carcinogenesis process. Much attention has been focused recently on particular members of the intestinal microbiota for their potential roles in promoting carcinogenesis. Here we report the identification and characterization of intestinal bacteria that exhibited potent anti-malignancy activities on a broad range of solid cancers and leukemia. We collected fecal specimens from healthy individuals of different age groups (preschool children and university students), inspected their effects on cancer cells, and obtained bacteria with potent anti-malignancy activities. The bacteria mostly belonged to Actinobacteria but also included lineages of other phyla such as Proteobacteria and Firmicutes. In animal cancer models, sterile culture supernatant from the bacteria highly effectively inhibited tumor growth. Remarkably, intra-tumor administration of the bacterial products prevented metastasis and even cleared cancer cells at remote locations from the tumor site. This work demonstrates the prevalent existence of potent malignancy-killers in the human intestinal microbiota, which may routinely clear malignant cells from the body before they form cancers.}, } @article {pmid28481971, year = {2018}, author = {Niu, SY and Yang, J and McDermaid, A and Zhao, J and Kang, Y and Ma, Q}, title = {Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes.}, journal = {Briefings in bioinformatics}, volume = {19}, number = {6}, pages = {1415-1429}, doi = {10.1093/bib/bbx051}, pmid = {28481971}, issn = {1477-4054}, mesh = {*Computational Biology ; *Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Transcriptome ; }, abstract = {Metagenomic and metatranscriptomic sequencing approaches are more frequently being used to link microbiota to important diseases and ecological changes. Many analyses have been used to compare the taxonomic and functional profiles of microbiota across habitats or individuals. While a large portion of metagenomic analyses focus on species-level profiling, some studies use strain-level metagenomic analyses to investigate the relationship between specific strains and certain circumstances. Metatranscriptomic analysis provides another important insight into activities of genes by examining gene expression levels of microbiota. Hence, combining metagenomic and metatranscriptomic analyses will help understand the activity or enrichment of a given gene set, such as drug-resistant genes among microbiome samples. Here, we summarize existing bioinformatics tools of metagenomic and metatranscriptomic data analysis, the purpose of which is to assist researchers in deciding the appropriate tools for their microbiome studies. Additionally, we propose an Integrated Meta-Function mapping pipeline to incorporate various reference databases and accelerate functional gene mapping procedures for both metagenomic and metatranscriptomic analyses.}, } @article {pmid28481406, year = {2017}, author = {Bhatt, AP and Redinbo, MR and Bultman, SJ}, title = {The role of the microbiome in cancer development and therapy.}, journal = {CA: a cancer journal for clinicians}, volume = {67}, number = {4}, pages = {326-344}, pmid = {28481406}, issn = {1542-4863}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 CA125237/CA/NCI NIH HHS/United States ; R01 DK109559/DK/NIDDK NIH HHS/United States ; R01 CA207416/CA/NCI NIH HHS/United States ; T32 DK007737/DK/NIDDK NIH HHS/United States ; R01 CA098468/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Carcinogenesis ; Disease Models, Animal ; Disease Progression ; Disease Susceptibility ; Dysbiosis ; Humans ; Metagenomics ; *Microbiota ; Neoplasms/*microbiology/*therapy ; Precision Medicine ; }, abstract = {Answer questions and earn CME/CNE The human body harbors enormous numbers of microbiota that influence cancer susceptibility, in part through their prodigious metabolic capacity and their profound influence on immune cell function. Microbial pathogens drive tumorigenesis in 15% to 20% of cancer cases. Even larger numbers of malignancies are associated with an altered composition of commensal microbiota (dysbiosis) based on microbiome studies using metagenomic sequencing. Although association studies cannot distinguish whether changes in microbiota are causes or effects of cancer, a causative role is supported by rigorously controlled preclinical studies using gnotobiotic mouse models colonized with one or more specific bacteria. These studies demonstrate that microbiota can alter cancer susceptibility and progression by diverse mechanisms, such as modulating inflammation, inducing DNA damage, and producing metabolites involved in oncogenesis or tumor suppression. Evidence is emerging that microbiota can be manipulated for improving cancer treatment. By incorporating probiotics as adjuvants for checkpoint immunotherapy or by designing small molecules that target microbial enzymes, microbiota can be harnessed to improve cancer care. CA Cancer J Clin 2017;67:326-344. © 2017 American Cancer Society.}, } @article {pmid28479399, year = {2017}, author = {Udayangani, RMC and Dananjaya, SHS and Nikapitiya, C and Heo, GJ and Lee, J and De Zoysa, M}, title = {Metagenomics analysis of gut microbiota and immune modulation in zebrafish (Danio rerio) fed chitosan silver nanocomposites.}, journal = {Fish & shellfish immunology}, volume = {66}, number = {}, pages = {173-184}, doi = {10.1016/j.fsi.2017.05.018}, pmid = {28479399}, issn = {1095-9947}, mesh = {Adjuvants, Immunologic/*pharmacology ; Animal Feed/analysis ; Animals ; *Chitosan/pharmacology ; Diet/veterinary ; Fish Proteins/genetics/metabolism ; Gastrointestinal Microbiome/*drug effects ; Goblet Cells/immunology ; Immunity, Innate/*drug effects ; Metagenome/*drug effects ; *Nanocomposites ; Silver/*pharmacology ; Zebrafish/*immunology/*microbiology ; }, abstract = {In this study, we evaluated the effects of chitosan silver nanocomposites (CAgNCs) supplemented diet on gut microbial community, goblet cell density, gut morphometry and mRNA expression of immune related and mucin encoding genes in zebrafish. Zebrafish gut microbiota analysis results clearly showed the reduction of phylum Proteobacteria. However, they remained as the major bacterial group in gut with CAgNCs supplemented diet, while the abundance of phylum Fusobacteria and phylum Bacteroidetes were increased notably compared to the control diet fed fish. Total goblet cell density was significantly increased at 30 and 60 days in CAgNCs supplemented group (1.6-fold and 2.0-fold, respectively) compared to the control group indicating enhanced immune function in the gut. CAgNCs supplementation has also increased villi height significantly in the zebrafish mid gut at the end of 30 (95.5 ± 3.7 μm) and 60 days (144.40 ± 4.8 μm) compared to control diet fed fish at 30 (86.90 ± 3.7 μm) and 60 days (96.2 ± 4.8 μm). Furthermore, mRNA expression of immune related genes such as TNF-α (6.2-fold), IL-10 (5.0-fold), IL-12 (9.2-fold), IRF-1 (5.2-fold), Defbl1 (3-fold), Lyz (5.1-fold) and mucin encoding genes were significantly upregulated (above 2-fold) compared to that of control group. The current study revealed that CAgNCs supplemented diet engenders promising effects on fish gut immunity by enhancing beneficial microbial populations, goblet cell density, villi length, and transcriptional regulation of immune related and mucin encoding genes.}, } @article {pmid28479280, year = {2017}, author = {Abele, D and Vazquez, S and Buma, AGJ and Hernandez, E and Quiroga, C and Held, C and Frickenhaus, S and Harms, L and Lopez, JL and Helmke, E and Mac Cormack, WP}, title = {Pelagic and benthic communities of the Antarctic ecosystem of Potter Cove: Genomics and ecological implications.}, journal = {Marine genomics}, volume = {33}, number = {}, pages = {1-11}, doi = {10.1016/j.margen.2017.05.001}, pmid = {28479280}, issn = {1876-7478}, mesh = {Antarctic Regions ; Aquatic Organisms/*genetics ; Biodiversity ; *Ecosystem ; Genetic Techniques ; Genome ; Genomics ; Ice Cover ; Phylogeography ; }, abstract = {Molecular technologies are more frequently applied in Antarctic ecosystem research and the growing amount of sequence-based information available in databases adds a new dimension to understanding the response of Antarctic organisms and communities to environmental change. We apply molecular techniques, including fingerprinting, and amplicon and metagenome sequencing, to understand biodiversity and phylogeography to resolve adaptive processes in an Antarctic coastal ecosystem from microbial to macrobenthic organisms and communities. Interpretation of the molecular data is not only achieved by their combination with classical methods (pigment analyses or microscopy), but furthermore by combining molecular with environmental data (e.g., sediment characteristics, biogeochemistry or oceanography) in space and over time. The studies form part of a long-term ecosystem investigation in Potter Cove on King-George Island, Antarctica, in which we follow the effects of rapid retreat of the local glacier on the cove ecosystem. We formulate and encourage new approaches to integrate molecular tools into Antarctic ecosystem research, environmental conservation actions, and polar ocean observatories.}, } @article {pmid28477337, year = {2017}, author = {Birer, C and Tysklind, N and Zinger, L and Duplais, C}, title = {Comparative analysis of DNA extraction methods to study the body surface microbiota of insects: A case study with ant cuticular bacteria.}, journal = {Molecular ecology resources}, volume = {17}, number = {6}, pages = {e34-e45}, doi = {10.1111/1755-0998.12688}, pmid = {28477337}, issn = {1755-0998}, mesh = {Animals ; Ants/*microbiology ; Bacteria/*classification/*genetics ; DNA, Bacterial/*isolation & purification ; Metagenomics/*methods ; *Microbiota ; }, abstract = {High-throughput sequencing of the 16S rRNA gene has considerably helped revealing the essential role of bacteria living on insect cuticles in the ecophysiology and behaviour of their hosts. However, our understanding of host-cuticular microbiota feedbacks remains hampered by the difficulties of working with low bacterial DNA quantities as with individual insect cuticle samples, which are more prone to molecular biases and contaminations. Herein, we conducted a methodological benchmark on the cuticular bacterial loads retrieved from two Neotropical ant species of different body size and ecology: Atta cephalotes (~15 mm) and Pseudomyrmex penetrator (~5 mm). We evaluated the richness and composition of the cuticular microbiota, as well as the amount of biases and contamination produced by four DNA extraction protocols. We also addressed how bacterial community characteristics would be affected by the number of individuals or individual body size used for DNA extraction. Most extraction methods yielded similar results in terms of bacterial diversity and composition for A. cephalotes (~15 mm). In contrast, greater amounts of artefactual sequences and contaminations, as well as noticeable differences in bacterial community characteristics were observed between extraction methods for P. penetrator (~5 mm). We also found that large (~15 mm) and small (~5 mm) A. cephalotes individuals harbour different bacterial communities. Our benchmark suggests that cuticular microbiota of single individual insects can be reliably retrieved provided that blank controls, appropriate data cleaning, and individual body size and functional role within insect society are considered in the experiment.}, } @article {pmid28476139, year = {2017}, author = {Kim, D and Hofstaedter, CE and Zhao, C and Mattei, L and Tanes, C and Clarke, E and Lauder, A and Sherrill-Mix, S and Chehoud, C and Kelsen, J and Conrad, M and Collman, RG and Baldassano, R and Bushman, FD and Bittinger, K}, title = {Optimizing methods and dodging pitfalls in microbiome research.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {52}, pmid = {28476139}, issn = {2049-2618}, support = {P30 AI045008/AI/NIAID NIH HHS/United States ; R01 HL113252/HL/NHLBI NIH HHS/United States ; T32 AI007632/AI/NIAID NIH HHS/United States ; T32 DK101371/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Humans ; Metagenomics ; Microbiological Techniques/*methods/standards ; Microbiota ; Reproducibility of Results ; Research Design/*standards ; }, abstract = {Research on the human microbiome has yielded numerous insights into health and disease, but also has resulted in a wealth of experimental artifacts. Here, we present suggestions for optimizing experimental design and avoiding known pitfalls, organized in the typical order in which studies are carried out. We first review best practices in experimental design and introduce common confounders such as age, diet, antibiotic use, pet ownership, longitudinal instability, and microbial sharing during cohousing in animal studies. Typically, samples will need to be stored, so we provide data on best practices for several sample types. We then discuss design and analysis of positive and negative controls, which should always be run with experimental samples. We introduce a convenient set of non-biological DNA sequences that can be useful as positive controls for high-volume analysis. Careful analysis of negative and positive controls is particularly important in studies of samples with low microbial biomass, where contamination can comprise most or all of a sample. Lastly, we summarize approaches to enhancing experimental robustness by careful control of multiple comparisons and to comparing discovery and validation cohorts. We hope the experimental tactics summarized here will help researchers in this exciting field advance their studies efficiently while avoiding errors.}, } @article {pmid28475713, year = {2017}, author = {Stedtfeld, RD and Stedtfeld, TM and Fader, KA and Williams, MR and Bhaduri, P and Quensen, J and Zacharewski, TR and Tiedje, JM and Hashsham, SA}, title = {TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {5}, pages = {}, pmid = {28475713}, issn = {1574-6941}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/*genetics ; Dysbiosis/*chemically induced ; Enterobacteriaceae/*drug effects/*genetics ; Female ; Gastrointestinal Microbiome/*drug effects ; Interspersed Repetitive Sequences/genetics ; Mice ; Mice, Inbred C57BL ; Polychlorinated Dibenzodioxins/*pharmacology ; Receptors, Aryl Hydrocarbon/antagonists & inhibitors ; }, abstract = {Dysbiosis of the gut microbiome via antibiotics, changes in diet and infection can select for bacterial groups that more frequently harbor antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). However, the impact of environmental toxicants on the reservoir of ARGs in the gut microbiome has received less attention. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a potent aryl hydrocarbon receptor (AhR) agonist with multiple toxic health effects including immune dysfunction. The selective pressure of TCDD on the abundance of ARG and MGE-harboring gut populations was examined using C57BL/6 mice exposed to 0-30 μg/kg TCDD for 28 and 92 days with the latter having a 30-day recovery period. DNA extracted from temporally collected fecal pellets was characterized using a qPCR array with 384 assays targeting ARGs and MGEs. Fourteen genes, typically observed in Enterobacteriaceae, increased significantly within 8 days of initial dosing, persisted throughout the treatment period, and remained induced 30 days post dosing. A qPCR primer set targeting Enterobacteriaceae also showed 10- to 100-fold higher abundance in TCDD-treated groups, which was further verified using metagenomics. Results show a bloom of ARG-harboring bacterial groups in the gut due to a xenobiotic compound that is not a metal, biocide or antimicrobial.}, } @article {pmid28473032, year = {2017}, author = {Taillefumier, T and Posfai, A and Meir, Y and Wingreen, NS}, title = {Microbial consortia at steady supply.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, pmid = {28473032}, issn = {2050-084X}, support = {R01 GM082938/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biomass ; Humans ; *Metabolism ; *Microbial Consortia ; Models, Biological ; *Population Dynamics ; }, abstract = {Metagenomics has revealed hundreds of species in almost all microbiota. In a few well-studied cases, microbial communities have been observed to coordinate their metabolic fluxes. In principle, microbes can divide tasks to reap the benefits of specialization, as in human economies. However, the benefits and stability of an economy of microbial specialists are far from obvious. Here, we physically model the population dynamics of microbes that compete for steadily supplied resources. Importantly, we explicitly model the metabolic fluxes yielding cellular biomass production under the constraint of a limited enzyme budget. We find that population dynamics generally leads to the coexistence of different metabolic types. We establish that these microbial consortia act as cartels, whereby population dynamics pins down resource concentrations at values for which no other strategy can invade. Finally, we propose that at steady supply, cartels of competing strategies automatically yield maximum biomass, thereby achieving a collective optimum.}, } @article {pmid28472118, year = {2017}, author = {De Cesare, A and Sirri, F and Manfreda, G and Moniaci, P and Giardini, A and Zampiga, M and Meluzzi, A}, title = {Effect of dietary supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) on caecum microbioma and productive performance in broiler chickens.}, journal = {PloS one}, volume = {12}, number = {5}, pages = {e0176309}, pmid = {28472118}, issn = {1932-6203}, mesh = {Animals ; Cecum/*microbiology ; Chickens ; *Dietary Supplements ; Lactobacillus acidophilus/*physiology ; *Microbiota ; }, abstract = {This study examines the effects of the dietary supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) (LA) on productive performances, incidence of foot pad dermatitis and caecum microbioma in broiler chickens. A total of 1,100 one-day old male Ross 308 chicks were divided into 2 groups of 16 replicates with 25 birds each and reared from 1-41 d. One group was fed a basal diet (CON) and the other group the same diet supplemented with LA. Caecum contents were collected from 4 selected birds at day one and 5 selected birds at the end of the rearing period. Then, they were submitted to DNA extraction and whole DNA shotgun metagenomic sequencing. Overall, the LA supplementation produced a significant beneficial effect on body weight gain between 15-28 d and improved feed conversion rate in the overall period. On the contrary, litter moisture, pH and incidence of the foot pad lesions were not affected by LA. Birds treated with LA showed a lower occurrence of pasty vent at both 14 and 28 d. At the end of the rearing period, Lachanospiraceae were significantly higher in LA birds in comparison to CON (17.07 vs 14.39%; P = 0.036). Moreover, Ruminococcus obeum, Clostridium clostridioforme, Roseburia intestinalis, Lachnospiraceae bacterium 14-2T and Coprococcus eutactus were significantly higher in LA birds in comparison to CON. The relative abundance of Lactobacillus acidophilus was comparable between LA and CON groups. However, a positive effect was observed in relation to the metabolic functions in the treated group, with particular reference to the higher abundance of β-glucosidase. In conclusion, the LA supplementation improved broiler productive performances and metabolic functions promoting animal health.}, } @article {pmid28467925, year = {2017}, author = {Loomba, R and Seguritan, V and Li, W and Long, T and Klitgord, N and Bhatt, A and Dulai, PS and Caussy, C and Bettencourt, R and Highlander, SK and Jones, MB and Sirlin, CB and Schnabl, B and Brinkac, L and Schork, N and Chen, CH and Brenner, DA and Biggs, W and Yooseph, S and Venter, JC and Nelson, KE}, title = {Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease.}, journal = {Cell metabolism}, volume = {25}, number = {5}, pages = {1054-1062.e5}, pmid = {28467925}, issn = {1932-7420}, support = {P01 HL088093/HL/NHLBI NIH HHS/United States ; R01 HL105278/HL/NHLBI NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; P42 ES010337/ES/NIEHS NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; U01 AA024726/AA/NIAAA NIH HHS/United States ; R37 DK057978/DK/NIDDK NIH HHS/United States ; U01 DK061734/DK/NIDDK NIH HHS/United States ; I01 BX002213/BX/BLRD VA/United States ; P01 HL147835/HL/NHLBI NIH HHS/United States ; R01 DK121378/DK/NIDDK NIH HHS/United States ; R01 DK106419/DK/NIDDK NIH HHS/United States ; T32 DK007202/DK/NIDDK NIH HHS/United States ; K23 DK090303/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Aged ; Bacteria/genetics/*isolation & purification ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Liver Cirrhosis/diagnosis/*microbiology ; Male ; Metagenomics/methods ; Middle Aged ; Non-alcoholic Fatty Liver Disease/diagnosis/*microbiology ; Prognosis ; Prospective Studies ; }, abstract = {The presence of advanced fibrosis in nonalcoholic fatty liver disease (NAFLD) is the most important predictor of liver mortality. There are limited data on the diagnostic accuracy of gut microbiota-derived signature for predicting the presence of advanced fibrosis. In this prospective study, we characterized the gut microbiome compositions using whole-genome shotgun sequencing of DNA extracted from stool samples. This study included 86 uniquely well-characterized patients with biopsy-proven NAFLD, of which 72 had mild/moderate (stage 0-2 fibrosis) NAFLD, and 14 had advanced fibrosis (stage 3 or 4 fibrosis). We identified a set of 40 features (p < 0.006), which included 37 bacterial species that were used to construct a Random Forest classifier model to distinguish mild/moderate NAFLD from advanced fibrosis. The model had a robust diagnostic accuracy (AUC 0.936) for detecting advanced fibrosis. This study provides preliminary evidence for a fecal-microbiome-derived metagenomic signature to detect advanced fibrosis in NAFLD.}, } @article {pmid28466442, year = {2017}, author = {Guo, L and Hua, X and Zhang, W and Yang, S and Shen, Q and Hu, H and Li, J and Liu, Z and Wang, X and Wang, H and Zhou, C and Cui, L}, title = {Viral metagenomics analysis of feces from coronary heart disease patients reveals the genetic diversity of the Microviridae.}, journal = {Virologica Sinica}, volume = {32}, number = {2}, pages = {130-138}, pmid = {28466442}, issn = {1995-820X}, mesh = {Aged ; Aged, 80 and over ; *Biodiversity ; Coronary Disease/*virology ; Feces/*virology ; Humans ; Metagenomics ; Middle Aged ; Viruses/*classification/*genetics ; }, abstract = {Recent studies have declared that members of the ssDNA virus family Microviridae play an important role in multiple environments, as they have been found taking a dominant position in the human gut. The aim of this study was to analyze the overall composition of the gut virome in coronary heart disease (CHD) patients, and try to discover the potential link between the human gut virome and CHD. Viral metagenomics methods were performed to detect the viral sequences in fecal samples collected from CHD inpatients and healthy persons as controls. We present the analysis of the virome composition in these CHD patients and controls. Our data shows that the virome composition may be linked to daily living habits and the medical therapy of CHD. Virgaviridae and Microviridae were the two dominant types of viruses found in the enteric virome of CHD patients. Fourteen divergent viruses belonging to the family Microviridae were found, twelve of which were grouped into the subfamily Gokushovirinae, while the remaining two strains might represent two new subfamilies within Microviridae, according to the phylogenetic analysis. In addition, the genomic organization of these viruses has been characterized.}, } @article {pmid28466051, year = {2017}, author = {Alexyuk, MS and Turmagambetova, AS and Alexyuk, PG and Bogoyavlenskiy, AP and Berezin, VE}, title = {Comparative study of viromes from freshwater samples of the Ile-Balkhash region of Kazakhstan captured through metagenomic analysis.}, journal = {Virusdisease}, volume = {28}, number = {1}, pages = {18-25}, pmid = {28466051}, issn = {2347-3584}, abstract = {Viruses are the most abundant biological entities on Earth and can be found in a variety of environments. A high prevalence of viruses in marine and freshwater systems was initially reported by Spencer in 1955, but the ecological significance of viruses is insufficiently known even until the present day. Viruses are known to play a key role in the biology of freshwater bacteria: controlling the bacterial abundance, composition of species, and acting as intermediaries in the transfer of genes between bacterial populations. In our study a variety of viromes of the Ile-Balkhash water basin were identified. It was found that the composition of viruses of the Ile-Balkhash region is made up not only of a wide variety of autochthonous viruses typical for phytoplankton hydro ecosystems, but also of representatives of allochthonous viruses-such families as Coronaviridae, Reoviridae and Herpesviridae-indicating anthropogenic pollution of the basin. The research designed to investigate the viral abundance, spread, infectious cycle, seasonal dynamics, composition of the viral community, and the influence of viruses on the bacteria, phytoplankton and recycling of nutrients, as well as the impact of environmental factors on the viral ecology in a variety of marine and freshwater systems is very relevant nowadays.}, } @article {pmid28465056, year = {2017}, author = {Guo, J and Ni, BJ and Han, X and Chen, X and Bond, P and Peng, Y and Yuan, Z}, title = {Unraveling microbial structure and diversity of activated sludge in a full-scale simultaneous nitrogen and phosphorus removal plant using metagenomic sequencing.}, journal = {Enzyme and microbial technology}, volume = {102}, number = {}, pages = {16-25}, doi = {10.1016/j.enzmictec.2017.03.009}, pmid = {28465056}, issn = {1879-0909}, mesh = {Biodegradation, Environmental ; Biodiversity ; Industrial Microbiology ; Metagenomics ; Microbial Consortia/genetics ; Nitrogen/isolation & purification/metabolism ; Phosphorus/isolation & purification/metabolism ; Sewage/*microbiology ; Waste Disposal, Fluid/methods ; Wastewater/chemistry ; Water Pollutants, Chemical/isolation & purification/metabolism ; }, abstract = {Activated sludge contains highly complex microbial communities, which play crucial roles in pollutant removal performance in wastewater treatment plants (WWTPs). Metagenomic sequencing was applied to characterize microbial community and functional profiles within activated sludge from a full-scale municipal WWTP carrying out simultaneous nitrogen and phosphorous removal (SNPR). We applied the assembled contigs (N90 of 591bp) and predicted genes to conduct taxonomic and function annotations, respectively. Results revealed the extraordinary microbial diversity of activated sludge, which included detection of minority populations that are difficult to be explored by traditional molecular methods. Taxonomic analysis indicated that the dominant bacterial phyla were Proteobacteria, Nitrospirae, Bacteroidetes, Actinobacteria and Firmicutes. The abundance of the key organisms involved in nitrogen and phosphorous removal were qualified. Aerobic ammonia-oxidizing bacteria distinctly dominate over ammonia-oxidizing archaea and anaerobic ammonium oxidation bacteria. Various key enzymes involved in the global nitrogen cycle were annotated in the activated sludge. High abundance of the known polyphosphate accumulating organisms was detected (approximately 4.89% of the overall population reads), supporting good phosphorous removal performance. This study provides a comprehensive insight into the community structure and diversity of the SNPR system, and will provide foundation for optimal operation of nutrient removal systems.}, } @article {pmid28464793, year = {2017}, author = {Broeksema, B and Calusinska, M and McGee, F and Winter, K and Bongiovanni, F and Goux, X and Wilmes, P and Delfosse, P and Ghoniem, M}, title = {ICoVeR - an interactive visualization tool for verification and refinement of metagenomic bins.}, journal = {BMC bioinformatics}, volume = {18}, number = {1}, pages = {233}, pmid = {28464793}, issn = {1471-2105}, mesh = {*Algorithms ; *Databases, Genetic ; Gastrointestinal Microbiome/genetics ; Genome, Microbial/genetics ; Humans ; Infant ; Metagenome/*genetics ; Metagenomics/*methods ; *Software ; }, abstract = {BACKGROUND: Recent advances in high-throughput sequencing allow for much deeper exploitation of natural and engineered microbial communities, and to unravel so-called "microbial dark matter" (microbes that until now have evaded cultivation). Metagenomic analyses result in a large number of genomic fragments (contigs) that need to be grouped (binned) in order to reconstruct draft microbial genomes. While several contig binning algorithms have been developed in the past 2 years, they often lack consensus. Furthermore, these software tools typically lack a provision for the visualization of data and bin characteristics.

RESULTS: We present ICoVeR, the Interactive Contig-bin Verification and Refinement tool, which allows the visualization of genome bins. More specifically, ICoVeR allows curation of bin assignments based on multiple binning algorithms. Its visualization window is composed of two connected and interactive main views, including a parallel coordinates view and a dimensionality reduction plot. To demonstrate ICoVeR's utility, we used it to refine disparate genome bins automatically generated using MetaBAT, CONCOCT and MyCC for an anaerobic digestion metagenomic (AD microbiome) dataset. Out of 31 refined genome bins, 23 were characterized with higher completeness and lower contamination in comparison to their respective, automatically generated, genome bins. Additionally, to benchmark ICoVeR against a previously validated dataset, we used Sharon's dataset representing an infant gut metagenome.

CONCLUSIONS: ICoVeR is an open source software package that allows curation of disparate genome bins generated with automatic binning algorithms. It is freely available under the GPLv3 license at https://git.list.lu/eScience/ICoVeR . The data management and analytical functions of ICoVeR are implemented in R, therefore the software can be easily installed on any system for which R is available. Installation and usage guide together with the example files ready to be visualized are also provided via the project wiki. ICoVeR running instance preloaded with AD microbiome and Sharon's datasets can be accessed via the website.}, } @article {pmid28460196, year = {2017}, author = {Warinner, C and Herbig, A and Mann, A and Fellows Yates, JA and Weiß, CL and Burbano, HA and Orlando, L and Krause, J}, title = {A Robust Framework for Microbial Archaeology.}, journal = {Annual review of genomics and human genetics}, volume = {18}, number = {}, pages = {321-356}, pmid = {28460196}, issn = {1545-293X}, support = {R01 GM089886/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaea/genetics/*isolation & purification ; Archaeology/methods ; Bacteria/genetics/*isolation & purification ; DNA, Ancient/*analysis ; Genome, Archaeal ; Genome, Bacterial ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Microbial archaeology is flourishing in the era of high-throughput sequencing, revealing the agents behind devastating historical plagues, identifying the cryptic movements of pathogens in prehistory, and reconstructing the ancestral microbiota of humans. Here, we introduce the fundamental concepts and theoretical framework of the discipline, then discuss applied methodologies for pathogen identification and microbiome characterization from archaeological samples. We give special attention to the process of identifying, validating, and authenticating ancient microbes using high-throughput DNA sequencing data. Finally, we outline standards and precautions to guide future research in the field.}, } @article {pmid28458095, year = {2017}, author = {Moeller, AH}, title = {The shrinking human gut microbiome.}, journal = {Current opinion in microbiology}, volume = {38}, number = {}, pages = {30-35}, doi = {10.1016/j.mib.2017.04.002}, pmid = {28458095}, issn = {1879-0364}, mesh = {Biological Evolution ; *Gastrointestinal Microbiome ; Humans ; Life Style ; *Microbiota ; }, abstract = {Mammals harbor complex assemblages of gut bacteria that are deeply integrated with their hosts' digestive, immune, and neuroendocrine systems. Recent work has revealed that there has been a substantial loss of gut bacterial diversity from humans since the divergence of humans and chimpanzees. This bacterial depauperation began in humanity's ancient evolutionary past and has accelerated in recent years with the advent of modern lifestyles. Today, humans living in industrialized societies harbor the lowest levels of gut bacterial diversity of any primate for which metagenomic data are available, a condition that may increase risk of infections, autoimmune disorders, and metabolic syndrome. Some missing gut bacteria may remain within under-sampled human populations, whereas others may be globally extinct and unrecoverable.}, } @article {pmid28457984, year = {2017}, author = {Tang, L and Xia, Y and Wu, X and Chen, X and Zhang, X and Li, H}, title = {Screening and characterization of a novel thermostable lipase with detergent-additive potential from the metagenomic library of a mangrove soil.}, journal = {Gene}, volume = {625}, number = {}, pages = {64-71}, doi = {10.1016/j.gene.2017.04.046}, pmid = {28457984}, issn = {1879-0038}, mesh = {Bacterial Proteins/chemistry/genetics/*metabolism ; Cations, Divalent/chemistry ; Detergents/chemistry ; Enzyme Stability ; Hot Temperature ; Lipase/chemistry/genetics/*metabolism ; *Microbiota ; Myristic Acid/chemistry ; Phylogeny ; *Soil Microbiology ; Substrate Specificity ; *Wetlands ; }, abstract = {One clone (Lip906) exhibiting lipase activity was screened from a metagenomic library by using a medium containing tricaprylin. A novel lipase gene from the inserted fragment of Lip906 was obtained by sequencing. The phylogenetic analysis of Lip906 lipase exhibited 34% and 32% homologue to lipases from Streptomyces sp. MspMP-M5 and Rhodopirellula europaea. This gene was expressed in Escherichia coli (E. coli) BL21 (DE3), and the recombinant protein was purified and characterized. The best substrate of the recombinant Lip906 lipase was p-nitrophenyl myristate (C14). The lipase expressed maximum activity at 74°C and pH7.8, and it was found to be stable at pH values and temperatures ranging from 6.0-8.0 and 4-78°C, respectively. Furthermore, the lipase was found to be highly resistant to commercial detergent, DMSO, and EDTA, whereas its activity was stimulated in the presence of methanol and ethanol at low concentrations. The lipase showed enhanced activity in the presence of Hg[2+], whereas the presence of the metal ions Fe[2+], Ca[2+], Co[2+], and Mg[2+] inhibited the activity. These beneficial characteristics of Lip906 lipase provide some advantages for its potential application in industry.}, } @article {pmid28457228, year = {2017}, author = {Labus, JS and Hollister, EB and Jacobs, J and Kirbach, K and Oezguen, N and Gupta, A and Acosta, J and Luna, RA and Aagaard, K and Versalovic, J and Savidge, T and Hsiao, E and Tillisch, K and Mayer, EA}, title = {Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {49}, pmid = {28457228}, issn = {2049-2618}, support = {R01 DK048351/DK/NIDDK NIH HHS/United States ; P30 DK041301/DK/NIDDK NIH HHS/United States ; F31 MH090749/MH/NIMH NIH HHS/United States ; R01 AT007137/AT/NCCIH NIH HHS/United States ; R21 HD086737/HD/NICHD NIH HHS/United States ; P50 DK064539/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Bacteria/*classification/genetics/isolation & purification ; Brain/*diagnostic imaging ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Irritable Bowel Syndrome/diagnostic imaging/*microbiology ; Male ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Young Adult ; }, abstract = {BACKGROUND: Preclinical and clinical evidence supports the concept of bidirectional brain-gut microbiome interactions. We aimed to determine if subgroups of irritable bowel syndrome (IBS) subjects can be identified based on differences in gut microbial composition, and if there are correlations between gut microbial measures and structural brain signatures in IBS.

METHODS: Behavioral measures, stool samples, and structural brain images were collected from 29 adult IBS and 23 healthy control subjects (HCs). 16S ribosomal RNA (rRNA) gene sequencing was used to profile stool microbial communities, and various multivariate analysis approaches were used to quantitate microbial composition, abundance, and diversity. The metagenomic content of samples was inferred from 16S rRNA gene sequence data using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). T1-weighted brain images were acquired on a Siemens Allegra 3T scanner, and morphological measures were computed for 165 brain regions.

RESULTS: Using unweighted Unifrac distances with hierarchical clustering on microbial data, samples were clustered into two IBS subgroups within the IBS population (IBS1 (n = 13) and HC-like IBS (n = 16)) and HCs (n = 23) (AUROC = 0.96, sensitivity 0.95, specificity 0.67). A Random Forest classifier provided further support for the differentiation of IBS1 and HC groups. Microbes belonging to the genera Faecalibacterium, Blautia, and Bacteroides contributed to this subclassification. Clinical features distinguishing the groups included a history of early life trauma and duration of symptoms (greater in IBS1), but not self-reported bowel habits, anxiety, depression, or medication use. Gut microbial composition correlated with structural measures of brain regions including sensory- and salience-related regions, and with a history of early life trauma.

CONCLUSIONS: The results confirm previous reports of gut microbiome-based IBS subgroups and identify for the first time brain structural alterations associated with these subgroups. They provide preliminary evidence for the involvement of specific microbes and their predicted metabolites in these correlations.}, } @article {pmid28454900, year = {2017}, author = {Wei, ZG and Zhang, SW}, title = {DBH: A de Bruijn graph-based heuristic method for clustering large-scale 16S rRNA sequences into OTUs.}, journal = {Journal of theoretical biology}, volume = {425}, number = {}, pages = {80-87}, doi = {10.1016/j.jtbi.2017.04.019}, pmid = {28454900}, issn = {1095-8541}, mesh = {Algorithms ; Cluster Analysis ; Computational Biology/methods ; Gastrointestinal Microbiome/genetics ; *Heuristics ; Humans ; Metagenomics/*methods ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Recent sequencing revolution driven by high-throughput technologies has led to rapid accumulation of 16S rRNA sequences for microbial communities. Clustering short sequences into operational taxonomic units (OTUs) is an initial crucial process in analyzing metagenomic data. Although many heuristic methods have been proposed for OTU inferences with low computational complexity, they just select one sequence as the seed for each cluster and the results are sensitive to the selected sequences that represent the clusters. To address this issue, we present a de Bruijn graph-based heuristic clustering method (DBH) for clustering massive 16S rRNA sequences into OTUs by introducing a novel seed selection strategy and greedy clustering approach. Compared with existing widely used methods on several simulated and real-life metagenomic datasets, the results show that DBH has higher clustering performance and low memory usage, facilitating the overestimation of OTUs number. DBH is more effective to handle large-scale metagenomic datasets. The DBH software can be freely downloaded from https://github.com/nwpu134/DBH.git for academic users.}, } @article {pmid28454776, year = {2017}, author = {Jiao, D and Han, W and Ye, Y}, title = {Functional association prediction by community profiling.}, journal = {Methods (San Diego, Calif.)}, volume = {129}, number = {}, pages = {8-17}, pmid = {28454776}, issn = {1095-9130}, support = {R01 AI108888/AI/NIAID NIH HHS/United States ; }, mesh = {Algorithms ; Computational Biology/methods ; Databases, Genetic ; Genome, Bacterial ; *Metagenomics ; Microbial Consortia/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {Recent years have witnessed unprecedented accumulation of DNA sequences and therefore protein sequences (predicted from DNA sequences), due to the advances of sequencing technology. One of the major sources of the hypothetical proteins is the metagenomics research. Current annotation of metagenomes (collections of short metagenomic sequences or assemblies) relies on similarity searches against known gene/protein families, based on which functional profiles of microbial communities can be built. This practice, however, leaves out the hypothetical proteins, which may outnumber the known proteins for many microbial communities. On the other hand, we may ask: what can we gain from the large number of metagenomes made available by the metagenomic studies, for the annotation of metagenomic sequences as well as functional annotation of hypothetical proteins in general? Here we propose a community profiling approach for predicting functional associations between proteins: two proteins are predicted to be associated if they share similar presence and absence profiles (called community profiles) across microbial communities. Community profiling is conceptually similar to the phylogenetic profiling approach to functional prediction, however with fundamental differences. We tested different profile construction methods, the selection of reference metagenomes, and correlation metrics, among others, to optimize the performance of this new approach. We demonstrated that the community profiling approach alone slightly outperforms the phylogenetic profiling approach for associating proteins in species that are well represented by sequenced genomes, and combining phylogenetic and community profiling further improves (though only marginally) the prediction of functional association. Further we showed that community profiling method significantly outperforms phylogenetic profiling, revealing more functional associations, when applied to a more recently sequenced bacterial genome.}, } @article {pmid28454706, year = {2017}, author = {Haferburg, G and Gröning, JAD and Schmidt, N and Kummer, NA and Erquicia, JC and Schlömann, M}, title = {Microbial diversity of the hypersaline and lithium-rich Salar de Uyuni, Bolivia.}, journal = {Microbiological research}, volume = {199}, number = {}, pages = {19-28}, doi = {10.1016/j.micres.2017.02.007}, pmid = {28454706}, issn = {1618-0623}, mesh = {Archaea/classification/drug effects/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; *Biodiversity ; Bolivia ; Boron/chemistry ; DNA, Archaeal/analysis/genetics ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal/genetics ; Geographic Mapping ; Halobacteriaceae/classification/drug effects/genetics ; Hydrogen-Ion Concentration ; Lakes/microbiology ; Lithium/*chemistry ; Metagenomics ; *Microbial Consortia ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Salts/chemistry ; Sequence Analysis, DNA ; Sodium Chloride/metabolism ; Soil Microbiology ; Water Microbiology ; }, abstract = {Salar de Uyuni, situated in the Southwest of the Bolivian Altiplano, is the largest salt flat on Earth. Brines of this athalassohaline hypersaline environment are rich in lithium and boron. Due to the ever- increasing commodity demand, the industrial exploitation of brines for metal recovery from the world's biggest lithium reservoir is likely to increase substantially in the near future. Studies on the composition of halophilic microbial communities in brines of the salar have not been published yet. Here we report for the first time on the prokaryotic diversity of four brine habitats across the salar. The brine is characterized by salinity values between 132 and 177 PSU, slightly acidic to near-neutral pH and lithium and boron concentrations of up to 2.0 and 1.4g/L, respectively. Community analysis was performed after sequencing the V3-V4 region of the 16S rRNA genes employing the Illumina MiSeq technology. The mothur software package was used for sequence processing and data analysis. Metagenomic analysis revealed the occurrence of an exclusively archaeal community comprising 26 halobacterial genera including only recently identified genera like Halapricum, Halorubellus and Salinarchaeum. Despite the high diversity of the halobacteria-dominated community in sample P3 (Shannon-Weaver index H'=3.12 at 3% OTU cutoff) almost 40% of the Halobacteriaceae-assigned sequences could not be classified on the genus level under stringent filtering conditions. Even if the limited taxonomic resolution of the V3-V4 region for halobacteria is considered, it seems likely to discover new, hitherto undescribed genera of the family halobacteriaceae in this particular habitat of Salar de Uyuni in future.}, } @article {pmid28453579, year = {2017}, author = {Granja-Salcedo, YT and Ramirez-Uscategui, RA and Machado, EG and Duarte Messana, J and Takeshi Kishi, L and Lino Dias, AV and Berchielli, TT}, title = {Studies on bacterial community composition are affected by the time and storage method of the rumen content.}, journal = {PloS one}, volume = {12}, number = {4}, pages = {e0176701}, pmid = {28453579}, issn = {1932-6203}, mesh = {Animals ; Bacteria/genetics/*isolation & purification ; Bacterial Physiological Phenomena ; Biodiversity ; Cattle ; Cryopreservation/*methods ; DNA, Bacterial ; Fluorometry ; Freeze Drying ; Freezing ; *Gastrointestinal Microbiome ; Rumen/*microbiology ; Sequence Analysis, DNA ; Spectrophotometry ; Time Factors ; }, abstract = {The objective of this study was to investigate three storage methods and four storage times for rumen sampling in terms of quality and yield of extracted metagenomic DNA as well as the composition of the rumen bacterial community. One Nellore steer fitted with a ruminal silicone-type cannula was used as a donor of ruminal contents. The experiment comprised 11 experimental groups: pellet control (PC), lyophilized control (LC), P-20: pellet stored frozen at -20°C for a period of 3, 6, and 12 months, P-80: pellet stored frozen at -80°C for a period of 3, 6, and 12 months, and L-20: lyophilized sample stored frozen at -20°C for a period of 3, 6, and 12 months. Metagenomic DNA concentrations were measured spectrophotometrically and fluorometrically and ion torrent sequencing was used to assess the bacterial community composition. The L-20 method could not maintain the yield of DNA during storage. In addition, the P-80 group showed a greater yield of metagenomic DNA than the other groups after 6 months of storage. Rumen samples stored as pellets (P-20 and P-80) resulted in lower richness Chao 1, ACE, and Shannon Wiener indices when compared to PC, while LC and PC were only different in richness ACE. The storage method and storage time influenced the proportions of 14 of 17 phyla identified by sequencing. In the P-20 group, the proportion of Cyanobacteria, Elusimicrobia, Fibrobacteres, Lentisphaerae, Proteobacteria, and Spirochaetes phyla identified was lower than 1%. In the P-80 group, there was an increase in the proportion of the Bacteroidetes phylum (p = 0.010); however, the proportion of Actinobacteria, Chloroflexi, SR1, Synergistetes, TM7, and WPS.2 phyla were unchanged compared to the PC group (p > 0.05). The class Clostridium was the most abundant in all stored groups and increased in its proportion, especially in the L-20 group. The rumen sample storage time significantly reduced the yield of metagenomic DNA extracted. Therefore, the storage method can influence the abundance of phyla, classes, and bacterial families studied in rumen samples and affect the richness and diversity index.}, } @article {pmid28449715, year = {2017}, author = {Bedarf, JR and Hildebrand, F and Coelho, LP and Sunagawa, S and Bahram, M and Goeser, F and Bork, P and Wüllner, U}, title = {Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.}, journal = {Genome medicine}, volume = {9}, number = {1}, pages = {39}, pmid = {28449715}, issn = {1756-994X}, mesh = {Aged ; Bacteria/*genetics/isolation & purification ; Gastrointestinal Microbiome/*genetics ; Humans ; Levodopa ; Male ; *Metagenome ; Middle Aged ; Parkinson Disease/*microbiology/virology ; Sequence Analysis, DNA ; Viruses/*genetics/isolation & purification ; }, abstract = {BACKGROUND: Parkinson's disease (PD) presently is conceptualized as a protein aggregation disease in which pathology involves both the enteric and the central nervous system, possibly spreading from one to another via the vagus nerves. As gastrointestinal dysfunction often precedes or parallels motor symptoms, the enteric system with its vast diversity of microorganisms may be involved in PD pathogenesis. Alterations in the enteric microbial taxonomic level of L-DOPA-naïve PD patients might also serve as a biomarker.

METHODS: We performed metagenomic shotgun analyses and compared the fecal microbiomes of 31 early stage, L-DOPA-naïve PD patients to 28 age-matched controls.

RESULTS: We found increased Verrucomicrobiaceae (Akkermansia muciniphila) and unclassified Firmicutes, whereas Prevotellaceae (Prevotella copri) and Erysipelotrichaceae (Eubacterium biforme) were markedly lowered in PD samples. The observed differences could reliably separate PD from control with a ROC-AUC of 0.84. Functional analyses of the metagenomes revealed differences in microbiota metabolism in PD involving the ẞ-glucuronate and tryptophan metabolism. While the abundances of prophages and plasmids did not differ between PD and controls, total virus abundance was decreased in PD participants. Based on our analyses, the intake of either a MAO inhibitor, amantadine, or a dopamine agonist (which in summary relates to 90% of PD patients) had no overall influence on taxa abundance or microbial functions.

CONCLUSIONS: Our data revealed differences of colonic microbiota and of microbiota metabolism between PD patients and controls at an unprecedented detail not achievable through 16S sequencing. The findings point to a yet unappreciated aspect of PD, possibly involving the intestinal barrier function and immune function in PD patients. The influence of the parkinsonian medication should be further investigated in the future in larger cohorts.}, } @article {pmid28449106, year = {2017}, author = {Dhariwal, A and Chong, J and Habib, S and King, IL and Agellon, LB and Xia, J}, title = {MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data.}, journal = {Nucleic acids research}, volume = {45}, number = {W1}, pages = {W180-W188}, pmid = {28449106}, issn = {1362-4962}, mesh = {Computational Biology/*methods ; Computer Graphics ; DNA Barcoding, Taxonomic/methods ; Datasets as Topic ; Female ; Gastrointestinal Tract/microbiology ; Humans ; Internet ; Male ; Meta-Analysis as Topic ; Metabolic Networks and Pathways/*genetics ; Metagenomics/methods/*statistics & numerical data ; Microbiota/*genetics ; Mouth/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Skin/microbiology ; *Software ; Vagina/microbiology ; }, abstract = {The widespread application of next-generation sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling of the genetic contents of microbial communities. How to analyze the resulting large complex datasets remains a key challenge in current microbiome studies. Over the past decade, powerful computational pipelines and robust protocols have been established to enable efficient raw data processing and annotation. The focus has shifted toward downstream statistical analysis and functional interpretation. Here, we introduce MicrobiomeAnalyst, a user-friendly tool that integrates recent progress in statistics and visualization techniques, coupled with novel knowledge bases, to enable comprehensive analysis of common data outputs produced from microbiome studies. MicrobiomeAnalyst contains four modules - the Marker Data Profiling module offers various options for community profiling, comparative analysis and functional prediction based on 16S rRNA marker gene data; the Shotgun Data Profiling module supports exploratory data analysis, functional profiling and metabolic network visualization of shotgun metagenomics or metatranscriptomics data; the Taxon Set Enrichment Analysis module helps interpret taxonomic signatures via enrichment analysis against >300 taxon sets manually curated from literature and public databases; finally, the Projection with Public Data module allows users to visually explore their data with a public reference data for pattern discovery and biological insights. MicrobiomeAnalyst is freely available at http://www.microbiomeanalyst.ca.}, } @article {pmid28448623, year = {2017}, author = {Pammi, M and O'Brien, JL and Ajami, NJ and Wong, MC and Versalovic, J and Petrosino, JF}, title = {Development of the cutaneous microbiome in the preterm infant: A prospective longitudinal study.}, journal = {PloS one}, volume = {12}, number = {4}, pages = {e0176669}, pmid = {28448623}, issn = {1932-6203}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; U01 CA170930/CA/NCI NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/adverse effects ; Female ; Gestational Age ; Humans ; Infant, Newborn ; *Infant, Premature ; Linear Models ; Longitudinal Studies ; Male ; *Microbiota ; Neonatal Sepsis/prevention & control ; Skin/*microbiology ; }, abstract = {BACKGROUND: Neonatal sepsis in preterm infants is often due to organisms that colonize the skin including Staphylococcus spp. and Candida spp. Development and maturation of the skin microbiome in the neonatal period, especially in preterm infants, may be critical in preventing colonization with pathogens and subsequent progression to neonatal sepsis. Development of the skin microbiome in preterm infants or its determinants in the first 4 weeks of life has not been evaluated.

METHODS: We evaluated the skin microbiome from three body sites, antecubital fossa, forehead and gluteal region, in a prospective cohort of 15 preterm (birth weight < 1500 g and < 32 weeks of gestation) and 15 term neonates. The microbiome community membership and relative abundance were evaluated by amplification and sequencing the bacterial V3-V5 region of the16S rRNA gene on the 454 GS FLX platform. We used linear mixed effects models to analyze longitudinal data.

RESULTS: The structure and composition of the skin microbiome did not differ between the three sampling sites for term and preterm infants in the neonatal period. However, skin bacterial richness was positively associated with gestational age in the first four weeks of life. Intravenous antibiotics negatively impacted the bacterial diversity of the skin but we did not see differences with respect to feeding or mode of delivery.

CONCLUSIONS: Gestational age, which influences the maturity of skin structure and function, is associated with the development of the preterm cutaneous microbiome. Understanding the maturation of a healthy skin microbiome, prevention of pathogen colonization and its role in the development of immunity will be pivotal in the development of novel interventions to prevent infections in critically ill preterm infants.}, } @article {pmid28448616, year = {2017}, author = {Yarygin, K and Tyakht, A and Larin, A and Kostryukova, E and Kolchenko, S and Bitner, V and Alexeev, D}, title = {Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses.}, journal = {PloS one}, volume = {12}, number = {4}, pages = {e0176154}, pmid = {28448616}, issn = {1932-6203}, mesh = {Algorithms ; Anti-Bacterial Agents/pharmacology ; Gastrointestinal Microbiome/drug effects/*genetics ; *Gene Expression Profiling ; *Metagenomics ; }, abstract = {The gut microbiota is essentially a multifunctional bioreactor within a human being. The exploration of its enormous metabolic potential provides insights into the mechanisms underlying microbial ecology and interactions with the host. The data obtained using "shotgun" metagenomics capture information about the whole spectrum of microbial functions. However, each new study presenting new sequencing data tends to extract only a little of the information concerning the metabolic potential and often omits specific functions. A meta-analysis of the available data with an emphasis on biomedically relevant gene groups can unveil new global trends in the gut microbiota. As a step toward the reuse of metagenomic data, we developed a method for the quantitative profiling of user-defined groups of genes in human gut metagenomes. This method is based on the quick analysis of a gene coverage matrix obtained by pre-mapping the metagenomic reads to a global gut microbial catalogue. The method was applied to profile the abundance of several gene groups related to antibiotic resistance, phages, biosynthesis clusters and carbohydrate degradation in 784 metagenomes from healthy populations worldwide and patients with inflammatory bowel diseases and obesity. We discovered country-wise functional specifics in gut resistome and virome compositions. The most distinct features of the disease microbiota were found for Crohn's disease, followed by ulcerative colitis and obesity. Profiling of the genes belonging to crAssphage showed that its abundance varied across the world populations and was not associated with clinical status. We demonstrated temporal resilience of crAssphage and the influence of the sample preparation protocol on its detected abundance. Our approach offers a convenient method to add value to accumulated "shotgun" metagenomic data by helping researchers state and assess novel biological hypotheses.}, } @article {pmid28445246, year = {2017}, author = {Jacob, V and Crawford, C and Cohen-Mekelburg, S and Viladomiu, M and Putzel, GG and Schneider, Y and Chabouni, F and OʼNeil, S and Bosworth, B and Woo, V and Ajami, NJ and Petrosino, JF and Gerardin, Y and Kassam, Z and Smith, M and Iliev, ID and Sonnenberg, GF and Artis, D and Scherl, E and Longman, RS}, title = {Single Delivery of High-Diversity Fecal Microbiota Preparation by Colonoscopy Is Safe and Effective in Increasing Microbial Diversity in Active Ulcerative Colitis.}, journal = {Inflammatory bowel diseases}, volume = {23}, number = {6}, pages = {903-911}, pmid = {28445246}, issn = {1536-4844}, support = {K08 DK099381/DK/NIDDK NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Aged ; CD4-Positive T-Lymphocytes/cytology ; Colitis, Ulcerative/*microbiology/*therapy ; Colonoscopy ; Fecal Microbiota Transplantation/*methods ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; New York ; Pilot Projects ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Rectum/pathology ; Remission Induction ; Treatment Outcome ; Young Adult ; }, abstract = {BACKGROUND: Recent trials suggest fecal microbiota transplantation (FMT) with repeated enemas and high-diversity FMT donors is a promising treatment to induce remission in ulcerative colitis.

METHODS: We designed a prospective, open-label pilot study to assess the safety, clinical efficacy, and microbial engraftment of single FMT delivery by colonoscopy for active ulcerative colitis using a 2-donor fecal microbiota preparation (FMP). Safety and clinical endpoints of response, remission, and mucosal healing at week 4 were assessed. Fecal DNA and rectal biopsies were used to characterize the microbiome and mucosal CD4 T cells, respectively, before and after FMT.

RESULTS: Of the 20 patients enrolled in this study, 7 patients (35%) achieved a clinical response by week 4. Three patients (15%) were in remission at week 4 and 2 of these patients (10%) achieved mucosal healing. Three patients (15%) required escalation of care. No serious adverse events were observed. Microbiome analysis revealed that restricted diversity of recipients pre-FMT was significantly increased by high-diversity 2-donor FMP. The microbiome of recipients post-transplant was more similar to the donor FMP than the pretransplant recipient sample in both responders and nonresponders. Notably, donor composition correlated with clinical response. Mucosal CD4 T-cell analysis revealed a reduction in both Th1 and regulatory T-cells post-FMT.

CONCLUSIONS: High-diversity, 2-donor FMP delivery by colonoscopy seems safe and effective in increasing fecal microbial diversity in patients with active ulcerative colitis. Donor composition correlated with clinical response and further characterization of immunological parameters may provide insight into factors influencing clinical outcome.}, } @article {pmid28444190, year = {2017}, author = {Maffei, VJ and Kim, S and Blanchard, E and Luo, M and Jazwinski, SM and Taylor, CM and Welsh, DA}, title = {Biological Aging and the Human Gut Microbiota.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {72}, number = {11}, pages = {1474-1482}, pmid = {28444190}, issn = {1758-535X}, support = {P60 AA009803/AA/NIAAA NIH HHS/United States ; T32 AA007577/AA/NIAAA NIH HHS/United States ; K01 AG027905/AG/NIA NIH HHS/United States ; P01 AG022064/AG/NIA NIH HHS/United States ; R24 AA019661/AA/NIAAA NIH HHS/United States ; P01 HL076100/HL/NHLBI NIH HHS/United States ; P20 GM103629/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aging/*physiology ; Algorithms ; Computational Biology/methods ; Female ; Gastrointestinal Microbiome/*physiology ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics/*methods ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The human gastrointestinal microbiota plays a key homeostatic role in normal functioning of physiologic processes commonly undermined by aging. We used a previously validated 34-item frailty index (FI34) to identify changes in gut microbiota community structure associated with biological age of community-dwelling adults. Stool 16S rRNA cDNA libraries from 85 subjects ranging in age (43-79) and FI34 score (0-0.365) were deep sequenced, denoised, and clustered using DADA2. Subject biological age but not chronological age correlated with a decrease in stool microbial diversity. Specific microbial genera were differentially abundant in the lower, middle, and upper 33rd percentiles of biological age. Using Sparse Inverse Covariance Estimation for Ecological Association and Statistical Inference (SPIEC-EASI) and Weighted Gene Co-Expression Network Analysis (WGCNA), we identified modules of coabundant microbial genera that distinguished biological from chronological aging. A biological age-associated module composed of Eggerthella, Ruminococcus, and Coprobacillus genera was robust to correction for subject age, sex, body mass index, antibiotic usage, and other confounders. Subject FI34 score positively correlated with the abundance of this module, which exhibited a distinct inferred metagenome as predicted by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). We conclude that increasing biological age in community-dwelling adults is associated with gastrointestinal dysbiosis.}, } @article {pmid28442730, year = {2017}, author = {Wang, S and Hou, X and Su, H}, title = {Exploration of the relationship between biogas production and microbial community under high salinity conditions.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1149}, pmid = {28442730}, issn = {2045-2322}, mesh = {Biofuels/*microbiology ; Biota/*drug effects ; Carbon Dioxide/metabolism ; High-Throughput Nucleotide Sequencing ; Hydrogen-Ion Concentration ; Metagenomics ; Methane/*metabolism ; *Salinity ; Sewage/*microbiology ; Sodium Chloride/metabolism ; }, abstract = {High salinity frequently causes inhibition and even failure in anaerobic digestion. To explore the impact of increasing NaCl concentrations on biogas production, and reveal the microbial community variations in response to high salinity stress, the Illumina high-throughput sequencing technology was employed. The results showed that a NaCl concentration of 20 g/L (H group) exhibited a similar level of VFAs and specific CO2 production rate with that in the blank group, thus indicating that the bacterial activity in acidogenesis might not be inhibited. However, the methanogenic activity in the H group was significantly affected compared with that in the blank group, causing a 42.2% decrease in CH4 production, a 37.12% reduction in the specific CH4 generation rate and a lower pH value. Illumina sequencing revealed that microbial communities between the blank and H groups were significantly different. Bacteroides, Clostridium and BA021 uncultured were the dominant species in the blank group while some halotolerant genera, such as Thermovirga, Soehngenia and Actinomyces, dominated and complemented the hydrolytic and acidogenetic abilities in the H group. Additionally, the most abundant archaeal species included Methanosaeta, Methanolinea, Methanospirillum and Methanoculleus in both groups, but hydrogenotrophic methanogens showed a lower resistance to high salinity than aceticlastic methanogens.}, } @article {pmid28441565, year = {2017}, author = {Luber, JM and Kostic, AD}, title = {Gut Microbiota: Small Molecules Modulate Host Cellular Functions.}, journal = {Current biology : CB}, volume = {27}, number = {8}, pages = {R307-R310}, doi = {10.1016/j.cub.2017.03.026}, pmid = {28441565}, issn = {1879-0445}, mesh = {*Gastrointestinal Microbiome ; Humans ; Metagenome ; *Microbiota ; Multigene Family ; Peptide Hydrolases ; }, abstract = {The human gut metagenome was recently discovered to encode vast collections of biosynthetic gene clusters with diverse chemical potential, almost none of which are yet functionally validated. Recent work elucidates common microbiome-derived biosynthetic gene clusters encoding peptide aldehydes that inhibit human proteases.}, } @article {pmid28441394, year = {2017}, author = {Bruce-Keller, AJ and Fernandez-Kim, SO and Townsend, RL and Kruger, C and Carmouche, R and Newman, S and Salbaum, JM and Berthoud, HR}, title = {Maternal obese-type gut microbiota differentially impact cognition, anxiety and compulsive behavior in male and female offspring in mice.}, journal = {PloS one}, volume = {12}, number = {4}, pages = {e0175577}, pmid = {28441394}, issn = {1932-6203}, support = {P30 DK072476/DK/NIDDK NIH HHS/United States ; U54 GM104940/GM/NIGMS NIH HHS/United States ; R01 DK047348/DK/NIDDK NIH HHS/United States ; P50 AT002776/AT/NCCIH NIH HHS/United States ; P30 GM118430/GM/NIGMS NIH HHS/United States ; }, mesh = {Adiposity ; Animal Communication ; Animals ; Animals, Newborn ; Anxiety/*etiology/microbiology ; *Cognition ; Compulsive Behavior/*etiology/microbiology ; Female ; *Gastrointestinal Microbiome ; Male ; Maternal Nutritional Physiological Phenomena ; Mice, Inbred C57BL ; Obesity/*microbiology ; Pregnancy ; Prenatal Exposure Delayed Effects/*etiology/microbiology ; }, abstract = {Maternal obesity is known to predispose offspring to metabolic and neurodevelopmental abnormalities. While the mechanisms underlying these phenomena are unclear, high fat diets dramatically alter intestinal microbiota, and gut microbiota can impact physiological function. To determine if maternal diet-induced gut dysbiosis can disrupt offspring neurobehavioral function, we transplanted high fat diet- (HFD) or control low fat diet-associated (CD) gut microbiota to conventionally-housed female mice. Recipient mice were then bred and the behavioral phenotype of male and female offspring was tracked. While maternal behavior was unaffected, neonatal offspring from HFD dams vocalized less upon maternal separation than pups from CD dams. Furthermore, weaned male offspring from HFD dams had significant and selective disruptions in exploratory, cognitive, and stereotypical/compulsive behavior compared to male offspring from CD dams; while female offspring from HFD dams had increases in body weight and adiposity. 16S metagenomic analyses confirmed establishment of divergent microbiota in CD and HFD dams, with alterations in diversity and taxonomic distribution throughout pregnancy and lactation. Likewise, significant alterations in gut microbial diversity and distribution were noted in offspring from HFD dams compared to CD dams, and in males compared to females. Regression analyses of behavioral performance against differentially represented taxa suggest that decreased representation of specific members of the Firmicutes phylum predict behavioral decline in male offspring. Collectively, these data establish that high fat diet-induced maternal dysbiosis is sufficient to disrupt behavioral function in murine offspring in a sex-specific manner. Thus these data reinforce the essential link between maternal diet and neurologic programming in offspring and suggest that intestinal dysbiosis could link unhealthy modern diets to the increased prevalence of neurodevelopmental and childhood disorders.}, } @article {pmid28440278, year = {2017}, author = {Wexler, AG and Goodman, AL}, title = {An insider's perspective: Bacteroides as a window into the microbiome.}, journal = {Nature microbiology}, volume = {2}, number = {}, pages = {17026}, pmid = {28440278}, issn = {2058-5276}, support = {DP2 GM105456/GM/NIGMS NIH HHS/United States ; R35 GM118159/GM/NIGMS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {*Bacteroides/genetics/physiology ; Firmicutes/genetics/physiology ; Gastrointestinal Microbiome/genetics/physiology ; Gastrointestinal Tract/microbiology/physiology ; Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Microbiota ; Symbiosis ; }, abstract = {Over the last decade, our appreciation for the contribution of resident gut microorganisms-the gut microbiota-to human health has surged. However, progress is limited by the sheer diversity and complexity of these microbial communities. Compounding the challenge, the majority of our commensal microorganisms are not close relatives of Escherichia coli or other model organisms and have eluded culturing and manipulation in the laboratory. In this Review, we discuss how over a century of study of the readily cultured, genetically tractable human gut Bacteroides has revealed important insights into the biochemistry, genomics and ecology that make a gut bacterium a gut bacterium. While genome and metagenome sequences are being produced at breakneck speed, the Bacteroides provide a significant 'jump-start' on uncovering the guiding principles that govern microbiota-host and inter-bacterial associations in the gut that will probably extend to many other members of this ecosystem.}, } @article {pmid28439121, year = {2017}, author = {Mukherjee, A and Chettri, B and Langpoklakpam, JS and Basak, P and Prasad, A and Mukherjee, AK and Bhattacharyya, M and Singh, AK and Chattopadhyay, D}, title = {Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1108}, pmid = {28439121}, issn = {2045-2322}, mesh = {Bacteria/classification/*drug effects ; Biota/*drug effects ; Cluster Analysis ; Computational Biology/*methods ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Environmental Pollutants/*metabolism ; Metagenomics/*methods ; Petroleum/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Microbial remediation of oil polluted habitats remains one of the foremost methods for restoration of petroleum hydrocarbon contaminated environments. The development of effective bioremediation strategies however, require an extensive understanding of the resident microbiome of these habitats. Recent developments such as high-throughput sequencing has greatly facilitated the advancement of microbial ecological studies in oil polluted habitats. However, effective interpretation of biological characteristics from these large datasets remain a considerable challenge. In this study, we have implemented recently developed bioinformatic tools for analyzing 65 16S rRNA datasets from 12 diverse hydrocarbon polluted habitats to decipher metagenomic characteristics of the resident bacterial communities. Using metagenomes predicted from 16S rRNA gene sequences through PICRUSt, we have comprehensively described phylogenetic and functional compositions of these habitats and additionally inferred a multitude of metagenomic features including 255 taxa and 414 functional modules which can be used as biomarkers for effective distinction between the 12 oil polluted sites. Additionally, we show that significantly over-represented taxa often contribute to either or both, hydrocarbon degradation and additional important functions. Our findings reveal significant differences between hydrocarbon contaminated sites and establishes the importance of endemic factors in addition to petroleum hydrocarbons as driving factors for sculpting hydrocarbon contaminated bacteriomes.}, } @article {pmid28438217, year = {2017}, author = {Koh, H and Blaser, MJ and Li, H}, title = {A powerful microbiome-based association test and a microbial taxa discovery framework for comprehensive association mapping.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {45}, pmid = {28438217}, issn = {2049-2618}, support = {P30 CA016087/CA/NCI NIH HHS/United States ; R01 DK090989/DK/NIDDK NIH HHS/United States ; R01 DK110014/DK/NIDDK NIH HHS/United States ; U01 CA182370/CA/NCI NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/*classification/genetics/*growth & development ; Computational Biology/*methods ; Humans ; *Metagenome ; Microbial Consortia ; Microbial Interactions ; Microbial Viability ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Regression Analysis ; }, abstract = {BACKGROUND: The role of the microbiota in human health and disease has been increasingly studied, gathering momentum through the use of high-throughput technologies. Further identification of the roles of specific microbes is necessary to better understand the mechanisms involved in diseases related to microbiome perturbations.

METHODS: Here, we introduce a new microbiome-based group association testing method, optimal microbiome-based association test (OMiAT). OMiAT is a data-driven testing method which takes an optimal test throughout different tests from the sum of powered score tests (SPU) and microbiome regression-based kernel association test (MiRKAT). We illustrate that OMiAT efficiently discovers significant association signals arising from varying microbial abundances and different relative contributions from microbial abundance and phylogenetic information. We also propose a way to apply it to fine-mapping of diverse upper-level taxa at different taxonomic ranks (e.g., phylum, class, order, family, and genus), as well as the entire microbial community, within a newly introduced microbial taxa discovery framework, microbiome comprehensive association mapping (MiCAM).

RESULTS: Our extensive simulations demonstrate that OMiAT is highly robust and powerful compared with other existing methods, while correctly controlling type I error rates. Our real data analyses also confirm that MiCAM is especially efficient for the assessment of upper-level taxa by integrating OMiAT as a group analytic method.

CONCLUSIONS: OMiAT is attractive in practice due to the high complexity of microbiome data and the unknown true nature of the state. MiCAM also provides a hierarchical association map for numerous microbial taxa and can also be used as a guideline for further investigation on the roles of discovered taxa in human health and disease.}, } @article {pmid28436439, year = {2017}, author = {Song, C and Wang, B and Tan, J and Zhu, L and Lou, D}, title = {Discovery of tauroursodeoxycholic acid biotransformation enzymes from the gut microbiome of black bears using metagenomics.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {45495}, pmid = {28436439}, issn = {2045-2322}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/enzymology/isolation & purification ; Bile Acids and Salts/chemistry/metabolism ; Cloning, Molecular ; DNA, Bacterial/isolation & purification/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; Hydroxysteroid Dehydrogenases/chemistry/genetics/*metabolism ; Kinetics ; *Metagenomics ; Protein Stability ; Recombinant Proteins/biosynthesis/isolation & purification ; Sequence Alignment ; Stereoisomerism ; Taurochenodeoxycholic Acid/*metabolism ; Ursidae ; }, abstract = {Tauroursodeoxycholic acid (TUDCA) has been used to treat many diseases effectively. 7α-hydroxysteroid dehydrogenase (7α-HSDH) and 7β-hydroxysteroid dehydrogenase (7β-HSDH) are two key enzymes that drive the efficient biosynthesis of TUDCA from taurochenodeoxycholic acid (TCDCA) in vitro. In this study, a metagenomic approach was used to isolate 7α- and 7β-HSDHs from fecal samples of black bears. Five new 7α-HSDHs and one new 7β-HSDH enzyme were discovered and identified from the gut microbiota of black bears, and four of them presented good enzymatic properties. Our data also suggest cooperation in the biotransformation of TUDCA by the gut microbiota in black bears. In conclusion, this work expands the natural enzyme bank of HSDHs, provides promising candidate enzymes for application in the biosynthesis TUDCA and the epimerization reaction of bile acids at the C-7 position, and provides a data set for the discovery of novel enzymes in the gut micriobiome of black bears.}, } @article {pmid28434745, year = {2017}, author = {Moore, SG and Ericsson, AC and Poock, SE and Melendez, P and Lucy, MC}, title = {Hot topic: 16S rRNA gene sequencing reveals the microbiome of the virgin and pregnant bovine uterus.}, journal = {Journal of dairy science}, volume = {100}, number = {6}, pages = {4953-4960}, pmid = {28434745}, issn = {1525-3198}, support = {K01 OD019924/OD/NIH HHS/United States ; }, mesh = {Amniotic Fluid/microbiology ; Analysis of Variance ; Animals ; Bacteroidetes/genetics ; Cattle ; Cervix Uteri/microbiology ; Female ; Firmicutes/genetics ; Microbiota/*genetics ; Placenta/microbiology ; Postpartum Period ; Pregnancy ; Principal Component Analysis ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/methods/*veterinary ; Uterus/*microbiology ; }, abstract = {We tested the hypothesis that the uterus of virgin heifers and pregnant cows possessed a resident microbiome by 16S rRNA gene sequencing of the virgin and pregnant bovine uterus. The endometrium of 10 virgin heifers in estrus and the amniotic fluid, placentome, intercotyledonary placenta, cervical lumen, and external cervix surface (control) of 5 pregnant cows were sampled using aseptic techniques. The DNA was extracted, the V4 hypervariable region of the 16S rRNA gene was amplified, and amplicons were sequenced using Illumina MiSeq technology (Illumina Inc., San Diego, CA). Operational taxonomic units (OTU) were generated from the sequences using Qiime v1.8 software, and taxonomy was assigned using the Greengenes database. The effect of tissue on the microbial composition within the pregnant uterus was tested using univariate (mixed model) and multivariate (permutational multivariate ANOVA) procedures. Amplicons of 16S rRNA gene were generated in all samples, supporting the contention that the uterus of virgin heifers and pregnant cows contained a microbiome. On average, 53, 199, 380, 382, 525, and 13,589 reads annotated as 16, 35, 43, 63, 48, and 176 OTU in the placentome, virgin endometrium, amniotic fluid, cervical lumen, intercotyledonary placenta, and external surface of the cervix, respectively, were generated. The 3 most abundant phyla in the uterus of the virgin heifers and pregnant cows were Firmicutes, Bacteroidetes, and Proteobacteria, and they accounted for approximately 40, 35, and 10% of the sequences, respectively. Phyla abundance was similar between the tissues of the pregnant uterus. Principal component analysis, one-way PERMANOVA analysis of the Bray-Curtis similarity index, and mixed model analysis of the Shannon diversity index and Chao1 index demonstrated that the microbiome of the control tissue (external surface of the cervix) was significantly different from that of the amniotic fluid, intercotyledonary placenta, and placentome tissues. Interestingly, many bacterial species associated with postpartum uterine disease (i.e., Trueperella spp., Acinetobacter spp., Fusobacteria spp., Proteus spp., Prevotella spp., and Peptostreptococcus spp.) were also present in the uterus of virgin heifers and of pregnant cows. The presence of 16S rRNA gene sequence reads in the samples from the current study suggests that the uterine microbiome is established by the time a female reaches reproductive maturity, and that pregnancies are established and maintained in the presence of a uterine microbiome.}, } @article {pmid28434033, year = {2017}, author = {Brunkwall, L and Orho-Melander, M}, title = {The gut microbiome as a target for prevention and treatment of hyperglycaemia in type 2 diabetes: from current human evidence to future possibilities.}, journal = {Diabetologia}, volume = {60}, number = {6}, pages = {943-951}, pmid = {28434033}, issn = {1432-0428}, mesh = {Diabetes Mellitus, Type 2/drug therapy/genetics/*metabolism/*microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*radiation effects ; Humans ; Metformin/therapeutic use ; }, abstract = {The totality of microbial genomes in the gut exceeds the size of the human genome, having around 500-fold more genes that importantly complement our coding potential. Microbial genes are essential for key metabolic processes, such as the breakdown of indigestible dietary fibres to short-chain fatty acids, biosynthesis of amino acids and vitamins, and production of neurotransmitters and hormones. During the last decade, evidence has accumulated to support a role for gut microbiota (analysed from faecal samples) in glycaemic control and type 2 diabetes. Mechanistic studies in mice support a causal role for gut microbiota in metabolic diseases, although human data favouring causality is insufficient. As it may be challenging to sort the human evidence from the large number of animal studies in the field, there is a need to provide a review of human studies. Thus, the aim of this review is to cover the current and future possibilities and challenges of using the gut microbiota, with its capacity to be modified, in the development of preventive and treatment strategies for hyperglycaemia and type 2 diabetes in humans. We discuss what is known about the composition and functionality of human gut microbiota in type 2 diabetes and summarise recent evidence of current treatment strategies that involve, or are based on, modification of gut microbiota (diet, probiotics, metformin and bariatric surgery). We go on to review some potential future gut-based glucose-lowering approaches involving microbiota, including the development of personalised nutrition and probiotic approaches, identification of therapeutic components of probiotics, targeted delivery of propionate in the proximal colon, targeted delivery of metformin in the lower gut, faecal microbiota transplantation, and the incorporation of genetically modified bacteria that express therapeutic factors into microbiota. Finally, future avenues and challenges for understanding the interplay between human nutrition, genetics and microbial genetics, and the need for integration of human multi-omic data (such as genetics, transcriptomics, epigenetics, proteomics and metabolomics) with microbiome data (such as strain-level variation, transcriptomics, proteomics and metabolomics) to make personalised treatments a successful future reality are discussed.}, } @article {pmid28431529, year = {2017}, author = {Österlund, T and Jonsson, V and Kristiansson, E}, title = {HirBin: high-resolution identification of differentially abundant functions in metagenomes.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {316}, pmid = {28431529}, issn = {1471-2164}, mesh = {Algorithms ; Cluster Analysis ; Diabetes Mellitus, Type 2/genetics/pathology ; High-Throughput Nucleotide Sequencing ; Humans ; Internet ; Intestines/microbiology ; Male ; Metagenomics/*methods ; Microbiota ; User-Computer Interface ; }, abstract = {BACKGROUND: Gene-centric analysis of metagenomics data provides information about the biochemical functions present in a microbiome under a certain condition. The ability to identify significant differences in functions between metagenomes is dependent on accurate classification and quantification of the sequence reads (binning). However, biological effects acting on specific functions may be overlooked if the classes are too general.

METHODS: Here we introduce High-Resolution Binning (HirBin), a new method for gene-centric analysis of metagenomes. HirBin combines supervised annotation with unsupervised clustering to bin sequence reads at a higher resolution. The supervised annotation is performed by matching sequence fragments to genes using well-established protein domains, such as TIGRFAM, PFAM or COGs, followed by unsupervised clustering where each functional domain is further divided into sub-bins based on sequence similarity. Finally, differential abundance of the sub-bins is statistically assessed.

RESULTS: We show that HirBin is able to identify biological effects that are only present at more specific functional levels. Furthermore we show that changes affecting more specific functional levels are often diluted at the more general level and therefore overlooked when analyzed using standard binning approaches.

CONCLUSIONS: HirBin improves the resolution of the gene-centric analysis of metagenomes and facilitates the biological interpretation of the results. HirBin is implemented as a Python package and is freely available for download at http://bioinformatics.math.chalmers.se/hirbin .}, } @article {pmid28429164, year = {2017}, author = {Otto, CC and Chen, LH and He, T and Tang, YW and Babady, NE}, title = {Detection of gastrointestinal pathogens in oncology patients by highly multiplexed molecular panels.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {36}, number = {9}, pages = {1665-1672}, pmid = {28429164}, issn = {1435-4373}, support = {P30 CA008748/CA/NCI NIH HHS/United States ; P30 CA008748//National Cancer Institute/ ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; Feces/microbiology ; Female ; Gastroenteritis/diagnosis/*etiology ; *Gastrointestinal Microbiome ; Hematopoietic Stem Cell Transplantation/adverse effects ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Neoplasms/*complications/therapy ; Young Adult ; }, abstract = {We compared the frequency of gastrointestinal (GI) pathogen detection in an oncology patient population by two multiplexed molecular assays, the Luminex xTAG® Gastrointestinal Pathogen Panel (GPP, which identifies 14 GI pathogens) and the BioFire Gastrointestinal Panel (BFGP, which identifies 22 GI pathogens). We additionally reviewed the clinical characteristics of patients tested with both panels. A total of 200 prospectively collected and 81 archived stool samples were tested by both panels. In the prospective cohort, the GPP and BFGP identified a pathogen in 33.5% [95% confidence interval (CI): 27.3-40.35%] and 39.6% (95% CI: 33.0%-46.6%) of samples, respectively (p = 0.25). The BFGP detected significantly more pathogens than the GPP (p = 0.038), with 21.3% of samples positive for targets only detected by the BFGP. The concordance between the assays was very good at 91.1% (κ = 0.8, 95% CI: 0.7-0.9) when considering only pathogens detected by both assays. The most frequent pathogens detected were Clostridium difficile, norovirus, Campylobacter, and Salmonella species. On the archived samples, the BFGP was positive in 92.6% of samples but detected more pathogens than the GPP (86 vs. 97, p = 0.033), including both targets unique to the BFGP and targets common to both panels. A pathogen was more frequently detected in patients with hematological malignancies than solid tumors and in ambulatory patients compared to hospitalized patients, but these differences were not statistically significant. Overall, the detection rates were similar for both the GPP and the BFGP, and the latter detected more than one pathogen in additional patients. The impact of increased detection of GI pathogens by multiplexed panels on the clinical care of oncology patients will require further investigation.}, } @article {pmid28425942, year = {2017}, author = {Johannessen, TV and Larsen, A and Bratbak, G and Pagarete, A and Edvardsen, B and Egge, ED and Sandaa, RA}, title = {Seasonal Dynamics of Haptophytes and dsDNA Algal Viruses Suggest Complex Virus-Host Relationship.}, journal = {Viruses}, volume = {9}, number = {4}, pages = {}, pmid = {28425942}, issn = {1999-4915}, mesh = {Biodiversity ; Haptophyta/*growth & development/*virology ; *Host-Parasite Interactions ; Phycodnaviridae/*growth & development ; Population Density ; Seasons ; }, abstract = {Viruses influence the ecology and diversity of phytoplankton in the ocean. Most studies of phytoplankton host-virus interactions have focused on bloom-forming species like Emiliania huxleyi or Phaeocystis spp. The role of viruses infecting phytoplankton that do not form conspicuous blooms have received less attention. Here we explore the dynamics of phytoplankton and algal viruses over several sequential seasons, with a focus on the ubiquitous and diverse phytoplankton division Haptophyta, and their double-stranded DNA viruses, potentially with the capacity to infect the haptophytes. Viral and phytoplankton abundance and diversity showed recurrent seasonal changes, mainly explained by hydrographic conditions. By 454 tag-sequencing we revealed 93 unique haptophyte operational taxonomic units (OTUs), with seasonal changes in abundance. Sixty-one unique viral OTUs, representing Megaviridae and Phycodnaviridae, showed only distant relationship with currently isolated algal viruses. Haptophyte and virus community composition and diversity varied substantially throughout the year, but in an uncoordinated manner. A minority of the viral OTUs were highly abundant at specific time-points, indicating a boom-bust relationship with their host. Most of the viral OTUs were very persistent, which may represent viruses that coexist with their hosts, or able to exploit several host species.}, } @article {pmid28425179, year = {2017}, author = {Gajigan, AP and Diaz, LA and Conaco, C}, title = {Resilience of the prokaryotic microbial community of Acropora digitifera to elevated temperature.}, journal = {MicrobiologyOpen}, volume = {6}, number = {4}, pages = {}, pmid = {28425179}, issn = {2045-8827}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/genetics/*radiation effects ; Biota/*radiation effects ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Temperature ; }, abstract = {The coral is a holobiont formed by the close interaction between the coral animal and a diverse community of microorganisms, including dinoflagellates, bacteria, archaea, fungi, and viruses. The prokaryotic symbionts of corals are important for host fitness but are also highly sensitive to changes in the environment. In this study, we used 16S ribosomal RNA (rRNA) sequencing to examine the response of the microbial community associated with the coral, Acropora digitifera, to elevated temperature. The A. digitifera microbial community is dominated by operational taxonomic unit (OTUs) affiliated with classes Alphaproteobacteria and Gammaproteobacteria. The prokaryotic community in the coral tissue is distinct from that of the mucus and the surrounding seawater. Remarkably, the overall microbial community structure of A. digitifera remained stable for 10 days of continuous exptosure at 32°C compared to corals maintained at 27°C. However, the elevated temperature regime resulted in a decrease in the abundance of OTUs affiliated with certain groups of bacteria, such as order Rhodobacterales. On the other hand, some OTUs affiliated with the orders Alteromonadales, Vibrionales, and Flavobacteriales, which are often associated with diseased and stressed corals, increased in abundance. Thus, while the A. digitifera bacterial community structure appears resilient to higher temperature, prolonged exposure and intensified stress results in changes in the abundance of specific microbial community members that may affect the overall metabolic state and health of the coral holobiont.}, } @article {pmid28424669, year = {2017}, author = {Weng, FC and Shaw, GT and Weng, CY and Yang, YJ and Wang, D}, title = {Inferring Microbial Interactions in the Gut of the Hong Kong Whipping Frog (Polypedates megacephalus) and a Validation Using Probiotics.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {525}, pmid = {28424669}, issn = {1664-302X}, abstract = {The concerted activity of intestinal microbes is crucial to the health and development of their host organisms. Investigation of microbial interactions in the gut should deepen our understanding of how these micro-ecosystems function. Due to advances in Next Generation Sequencing (NGS) technologies, various bioinformatic strategies have been proposed to investigate these microbial interactions. However, due to the complexity of the intestinal microbial community and difficulties in monitoring their interactions, at present there is a gap between the theory and biological application. In order to construct and validate microbial relationships, we first induce a community shift from simple to complex by manipulating artificial hibernation (AH) in the treefrog Polypedates megacephalus. To monitor community growth and microbial interactions, we further performed a time-course screen using a 16S rRNA amplicon approach and a Lotka-Volterra model. Lotka-Volterra models, also known as predator-prey equations, predict the dynamics of microbial communities and how communities are structured and sustained. An interaction network of gut microbiota at the genus level in the treefrog was constructed using Metagenomic Microbial Interaction Simulator (MetaMIS) package. The interaction network obtained had 1,568 commensal, 1,737 amensal, 3,777 mutual, and 3,232 competitive relationships, e.g., Lactococcus garvieae has a commensal relationship with Corynebacterium variabile. To validate the interacting relationships, the gut microbe composition was analyzed after probiotic trials using single strain (L. garvieae, C. variabile, and Bacillus coagulans, respectively) and a combination of L. garvieae, C. variabile, and B. coagulans, because of the cooperative relationship among their respective genera identified in the interaction network. After a 2 week trial, we found via 16S rRNA amplicon analysis that the combination of cooperative microbes yielded significantly higher probiotic concentrations than single strains, and the immune response (interleukin-10 expression) also significantly changed in a manner consistent with improved probiotic effects. By taking advantage of microbial community shift from simple to complex, we thus constructed a reliable microbial interaction network, and validated it using probiotic strains as a test system.}, } @article {pmid28419931, year = {2017}, author = {Pham, HL and Ho, CL and Wong, A and Lee, YS and Chang, MW}, title = {Applying the design-build-test paradigm in microbiome engineering.}, journal = {Current opinion in biotechnology}, volume = {48}, number = {}, pages = {85-93}, doi = {10.1016/j.copbio.2017.03.021}, pmid = {28419931}, issn = {1879-0429}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Bioengineering/*methods ; Humans ; Inflammation/genetics/microbiology/*therapy ; *Metagenome ; *Microbiota ; *Probiotics ; }, abstract = {The recently discovered roles of human microbiome in health and diseases have inspired research efforts across many disciplines to engineer microbiome for health benefits. In this review, we highlight recent progress in human microbiome research and how modifications to the microbiome could result in implications to human health. Furthermore, we discuss the application of a 'design-build-test' framework to expedite microbiome engineering efforts by reviewing current literature on three key aspects: design principles to engineer the human microbiome, methods to engineer microbiome with desired functions, and analytical techniques to examine complex microbiome samples.}, } @article {pmid28419766, year = {2017}, author = {Zozaya-Valdés, E and Roth-Schulze, AJ and Egan, S and Thomas, T}, title = {Microbial community function in the bleaching disease of the marine macroalgae Delisea pulchra.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {3012-3024}, doi = {10.1111/1462-2920.13758}, pmid = {28419766}, issn = {1462-2920}, mesh = {Anti-Infective Agents ; Biofilms/growth & development ; Flavobacteriaceae/*classification/genetics/isolation & purification ; Genome, Bacterial/genetics ; Metagenome/genetics ; Microbiota/genetics ; Plant Diseases/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rhodobacteraceae/*classification/genetics/isolation & purification ; Rhodophyta/*microbiology ; Seaweed/*microbiology ; Virulence Factors/genetics ; Water Microbiology ; }, abstract = {Disease is increasingly viewed as a major factor impacting the health of both natural and cultured populations of marine organisms, including macroalgae. The red macroalga Delisea pulchra suffers from a bleaching disease resulting from host stress and infection by opportunistic bacterial pathogens. However, how pathogens cause the disease and how the entire macro algal-associated community is involved in the process is unclear. Here, we perform a metagenomic analysis of microbial communities associated with diseased and healthy D. pulchra across multiple bleaching events. Analysis of reconstructed 16S rRNA gene sequences showed that bacteria belonging to the families Rhodobacteraceae, Saprospiraceae and Flavobacteriaceae, including bacteria previously implicated in algal bleaching, to be enriched in diseased D. pulchra. Genes with predicted functions related to chemotaxis, motility, oxidative stress response, vitamin biosynthesis and nutrient acquisition were also prevalent in microbiomes of bleached algae, which may have a role in pathogenicity. Reconstruction of genomes that were abundant on bleached samples revealed that no single organism contains all bleaching-enriched functional genes. This observation indicates that potential virulence traits are distributed across multiple bacteria and that the disease in D. pulchra may result from a consortium of opportunistic pathogens, analogous to dysbiotic or polymicrobial diseases.}, } @article {pmid28419748, year = {2017}, author = {Lidbury, IDEA and Fraser, T and Murphy, ARJ and Scanlan, DJ and Bending, GD and Jones, AME and Moore, JD and Goodall, A and Tibbett, M and Hammond, JP and Wellington, EMH}, title = {The 'known' genetic potential for microbial communities to degrade organic phosphorus is reduced in low-pH soils.}, journal = {MicrobiologyOpen}, volume = {6}, number = {4}, pages = {}, pmid = {28419748}, issn = {2045-8827}, support = {BB/L026074/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Genetic Variation ; Hydrogen-Ion Concentration ; Metagenome ; *Microbiota ; Organic Chemicals/*metabolism ; Phosphoric Monoester Hydrolases/genetics/*metabolism ; Phosphorus/*metabolism ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {In soil, bioavailable inorganic orthophosphate is found at low concentrations and thus limits biological growth. To overcome this phosphorus scarcity, plants and bacteria secrete numerous enzymes, namely acid and alkaline phosphatases, which cleave orthophosphate from various organic phosphorus substrates. Using profile hidden Markov modeling approaches, we investigated the abundance of various non specific phosphatases, both acid and alkaline, in metagenomes retrieved from soils with contrasting pH regimes. This analysis uncovered a marked reduction in the abundance and diversity of various alkaline phosphatases in low-pH soils that was not counterbalanced by an increase in acid phosphatases. Furthermore, it was also discovered that only half of the bacterial strains from different phyla deposited in the Integrated Microbial Genomes database harbor alkaline phosphatases. Taken together, our data suggests that these 'phosphatase lacking' isolates likely increase in low-pH soils and future research should ascertain how these bacteria overcome phosphorus scarcity.}, } @article {pmid28419691, year = {2017}, author = {Viver, T and Orellana, LH and Hatt, JK and Urdiain, M and Díaz, S and Richter, M and Antón, J and Avian, M and Amann, R and Konstantinidis, KT and Rosselló-Móra, R}, title = {The low diverse gastric microbiome of the jellyfish Cotylorhiza tuberculata is dominated by four novel taxa.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {3039-3058}, doi = {10.1111/1462-2920.13763}, pmid = {28419691}, issn = {1462-2920}, mesh = {Animals ; Biodiversity ; Chlamydia/*classification/genetics/isolation & purification ; Female ; Gastrointestinal Microbiome ; In Situ Hybridization, Fluorescence ; Male ; Mediterranean Sea ; Mycoplasma/*classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Scyphozoa/*microbiology ; Spiroplasma/*classification/genetics/isolation & purification ; Tenacibaculum/*classification/genetics/isolation & purification ; }, abstract = {Cotylorhiza tuberculata is an important scyphozoan jellyfish producing population blooms in the Mediterranean probably due to pelagic ecosystem's decay. Its gastric cavity can serve as a simple model of microbial-animal digestive associations, yet poorly characterized. Using state-of-the-art metagenomic population binning and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), we show that only four novel clonal phylotypes were consistently associated with multiple jellyfish adults. Two affiliated close to Spiroplasma and Mycoplasma genera, one to chlamydial 'Candidatus Syngnamydia', and one to bacteroidetal Tenacibaculum, and were at least one order of magnitude more abundant than any other bacteria detected. Metabolic modelling predicted an aerobic heterotrophic lifestyle for the chlamydia, which were found intracellularly in Onychodromopsis-like ciliates. The Spiroplasma-like organism was predicted to be an anaerobic fermenter associated to some jellyfish cells, whereas the Tenacibaculum-like as free-living aerobic heterotroph, densely colonizing the mesogleal axis inside the gastric filaments. The association between the jellyfish and its reduced microbiome was close and temporally stable, and possibly related to food digestion and protection from pathogens. Based on the genomic and microscopic data, we propose three candidate taxa: 'Candidatus Syngnamydia medusae', 'Candidatus Medusoplasma mediterranei' and 'Candidatus Tenacibaculum medusae'.}, } @article {pmid28418094, year = {2017}, author = {Doane, MP and Haggerty, JM and Kacev, D and Papudeshi, B and Dinsdale, EA}, title = {The skin microbiome of the common thresher shark (Alopias vulpinus) has low taxonomic and gene function β-diversity.}, journal = {Environmental microbiology reports}, volume = {9}, number = {4}, pages = {357-373}, doi = {10.1111/1758-2229.12537}, pmid = {28418094}, issn = {1758-2229}, mesh = {Animals ; Bacteria/*classification/genetics/*isolation & purification/metabolism ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Metagenomics ; *Microbiota ; Open Reading Frames ; Phylogeny ; Sharks/*microbiology ; Skin/*microbiology ; }, abstract = {The health of sharks, like all organisms, is linked to their microbiome. At the skin interface, sharks have dermal denticles that protrude above the mucus, which may affect the types of microbes that occur here. We characterized the microbiome from the skin of the common thresher shark (Alopias vulpinus) to investigate the structure and composition of the skin microbiome. On average 618 812 (80.9% ± S.D. 0.44%) reads per metagenomic library contained open reading frames; of those, between 7.6% and 12.8% matched known protein sequences. Genera distinguishing the A. vulpinus microbiome from the water column included, Pseudoalteromonas (12.8% ± 4.7 of sequences), Erythrobacter (5. 3% ± 0.5) and Idiomarina (4.2% ± 1.2) and distinguishing gene pathways included, cobalt, zinc and cadmium resistance (2.2% ± 0.1); iron acquisition (1.2% ± 0.1) and ton/tol transport (1.3% ± 0.08). Taxonomic community overlap (100 - dissimilarity index) was greater in the skin microbiome (77.6), relative to the water column microbiome (70.6) and a reference host-associated microbiome (algae: 71.5). We conclude the A. vulpinus skin microbiome is influenced by filtering processes, including biochemical and biophysical components of the shark skin and result in a structured microbiome.}, } @article {pmid28417460, year = {2017}, author = {Jiao, S and Cao, H and Dai, Y and Wu, J and Lv, J and Du, R and Han, B}, title = {Effect of high-fat diet and growth stage on the diversity and composition of intestinal microbiota in healthy bovine livestock.}, journal = {Journal of the science of food and agriculture}, volume = {97}, number = {14}, pages = {5004-5013}, doi = {10.1002/jsfa.8380}, pmid = {28417460}, issn = {1097-0010}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; Cattle/*growth & development/*metabolism/microbiology ; Diet, High-Fat ; Fats/*metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Male ; }, abstract = {BACKGROUND: This study aimed to investigate the composition of bacteria in the bovine rectum and their functions during growth, in relation to different diets. Fecal samples were collected from 6-, 12-, 18- and 24-month cattle fed high-fat diet, and healthy female parents fed regular diet. Total DNA was amplified (V3-V4 of 16S rRNA) and submitted to barcode-DNA pyrosequencing. Intestinal microbiota profiles and functions were then analyzed.

RESULTS: A total of 114 512 operational taxonomic units were detected from the 1 802 243 sequences obtained. In 6-month-old and female parent groups, the top three abundant phyla were Bacteroidetes (37.6%, 32.2%), Firmicutes (34.4%, 48.2%) and Proteobacteria (9.1%, 6.3%); in the 12-, 18- and 24-month groups, they were Proteobacteria (45.5%, 47.1%, 38.8%), Firmicutes (27.4%, 22.2%, 20.1%) and Bacteroidetes (14.9%, 19.4%, 17.7%), respectively. Paludibacter and Desulfopila in abundance showed negative (P < 0.001) and positive (P < 0.05) correlation, respectively, to cattle weight gain through metagenomic functional prediction of methane, cysteine and methionine metabolism. Meanwhile, cofactor/vitamin and amino acid metabolic processes were significantly higher in bacteria from the regular diet group than high-fat diet groups, with markedly lower cellular processes and signaling, and reduced glycan biosynthesis and metabolism (P < 0.01).

CONCLUSIONS: The 6-month cattle and female parents shared similar intestinal bacteria; the community structure of fecal microbiota was significantly affected by high-fat diet in older cattle. © 2017 Society of Chemical Industry.}, } @article {pmid28415628, year = {2017}, author = {Yang, Y and Chen, G and Yang, Q and Ye, J and Cai, X and Tsering, P and Cheng, X and Hu, C and Zhang, S and Cao, P}, title = {Gut microbiota drives the attenuation of dextran sulphate sodium-induced colitis by Huangqin decoction.}, journal = {Oncotarget}, volume = {8}, number = {30}, pages = {48863-48874}, pmid = {28415628}, issn = {1949-2553}, mesh = {Animals ; Anti-Inflammatory Agents/pharmacology ; Colitis/drug therapy/*etiology/*pathology ; Colitis, Ulcerative/drug therapy/etiology/metabolism/pathology ; Cytokines/genetics/metabolism ; Dextran Sulfate/*adverse effects ; Disease Models, Animal ; Drugs, Chinese Herbal/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Regulation/drug effects ; High-Throughput Nucleotide Sequencing ; Intestinal Mucosa/drug effects/metabolism/microbiology/pathology ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Scutellaria baicalensis/*chemistry ; }, abstract = {The gut microbiota, including probiotics and pathogenic microorganisms, is involved in ulcerative colitis (UC) by regulating pathogenic microorganisms and the production of intestinal mucosal antibodies. Huangqin decoction (HQD), a traditional Chinese formula chronicled in the Shanghan lun, has been recognized as an effective drug for UC, owing to its anti-inflammatory and anti-oxidative properties. In the present study, we investigated whether HQD ameliorates dextran sulphate sodium (DSS)-induced colitis through alteration of the gut microbiota. We found that HQD significantly inhibited colitis, alleviating the loss of body weight, disease activity index, colon shortening, tissue injury, and inflammatory cytokine changes induced by DSS treatment. Principal component analysis and principal co-ordinate analysis showed an obvious difference among the groups, with increased diversity in the DSS and DSS+HQD groups. Linear discriminant analysis effect size was used to determine differences between the groups. The relative abundance of Lactococcus was higher in the DSS+HQD group than in the DSS group, whereas Desulfovibrio and Helicobacter were decreased. Furthermore, the protective effect of HQD was attenuated only in antibiotic-treated mice. In conclusion, our results suggest that HQD could ameliorate DSS-induced inflammation through alteration of the gut microbiota.}, } @article {pmid28410379, year = {2017}, author = {Oberbach, A and Schlichting, N and Feder, S and Lehmann, S and Kullnick, Y and Buschmann, T and Blumert, C and Horn, F and Neuhaus, J and Neujahr, R and Bagaev, E and Hagl, C and Pichlmaier, M and Rodloff, AC and Gräber, S and Kirsch, K and Sandri, M and Kumbhari, V and Behzadi, A and Behzadi, A and Correia, JC and Mohr, FW and Friedrich, M}, title = {New insights into valve-related intramural and intracellular bacterial diversity in infective endocarditis.}, journal = {PloS one}, volume = {12}, number = {4}, pages = {e0175569}, pmid = {28410379}, issn = {1932-6203}, mesh = {Aged ; Aged, 80 and over ; Bacteria/*genetics/isolation & purification ; Endocarditis/diagnosis/*microbiology ; Female ; Heart Valves/*microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenome ; Microscopy, Electron, Scanning ; Middle Aged ; Phenotype ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {AIMS: In infective endocarditis (IE), a severe inflammatory disease of the endocardium with an unchanged incidence and mortality rate over the past decades, only 1% of the cases have been described as polymicrobial infections based on microbiological approaches. The aim of this study was to identify potential biodiversity of bacterial species from infected native and prosthetic valves. Furthermore, we compared the ultrastructural micro-environments to detect the localization and distribution patterns of pathogens in IE.

MATERIAL AND METHODS: Using next-generation sequencing (NGS) of 16S rDNA, which allows analysis of the entire bacterial community within a single sample, we investigated the biodiversity of infectious bacterial species from resected native and prosthetic valves in a clinical cohort of 8 IE patients. Furthermore, we investigated the ultrastructural infected valve micro-environment by focused ion beam scanning electron microscopy (FIB-SEM).

RESULTS: Biodiversity was detected in 7 of 8 resected heart valves. This comprised 13 bacterial genera and 16 species. In addition to 11 pathogens already described as being IE related, 5 bacterial species were identified as having a novel association. In contrast, valve and blood culture-based diagnosis revealed only 4 species from 3 bacterial genera and did not show any relevant antibiotic resistance. The antibiotics chosen on this basis for treatment, however, did not cover the bacterial spectra identified by our amplicon sequencing analysis in 4 of 8 cases. In addition to intramural distribution patterns of infective bacteria, intracellular localization with evidence of bacterial immune escape mechanisms was identified.

CONCLUSION: The high frequency of polymicrobial infections, pathogen diversity, and intracellular persistence of common IE-causing bacteria may provide clues to help explain the persistent and devastating mortality rate observed for IE. Improved bacterial diagnosis by 16S rDNA NGS that increases the ability to tailor antibiotic therapy may result in improved outcomes.}, } @article {pmid28407078, year = {2017}, author = {Zhu, L and Qin, S and Zhai, S and Gao, Y and Li, L}, title = {Inulin with different degrees of polymerization modulates composition of intestinal microbiota in mice.}, journal = {FEMS microbiology letters}, volume = {364}, number = {10}, pages = {}, doi = {10.1093/femsle/fnx075}, pmid = {28407078}, issn = {1574-6968}, mesh = {Animals ; DNA, Bacterial/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Intestines/*drug effects/microbiology ; Inulin/chemistry/*pharmacology ; Male ; Mice ; Mice, Inbred C57BL ; Mucins/metabolism ; Oligosaccharides/pharmacology ; Polymerization ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Verrucomicrobia/isolation & purification/metabolism ; }, abstract = {The study aimed to analyze the global influences of dietary inulin with different degrees of polymerization (DP) on intestinal microbial communities. Six-week-old male C57BL/6J mice were treated with fructo-oligosaccharides and inulin for 6 weeks. Fecal samples were obtained at time point 0 and 6th week. 16S rRNA sequence analysis was used to measure intestinal microbiota performed on the Illumina MiSeq platform. Influences of dietary inulin on intestinal microbiota were more complex effects than bifidogenic effects, relative abundance of butyrate-producing bacteria increased after interventions. Akkermansia muciniphila, belonging to mucin-degrading species, became a dominant species in Verrucomicrobia phylum after treatment with fructo-oligosaccharides and inulin. Modulation effects of intestinal microbiota were positively correlated with DP. Lower DP interventions exhibited better effects than higher DP treatment on stimulation of probiotics. We hypothesized that Akkermansia muciniphila played an important role on maintaining balance between mucin and short chain fatty acids.}, } @article {pmid28406159, year = {2017}, author = {Hatzenbuhler, C and Kelly, JR and Martinson, J and Okum, S and Pilgrim, E}, title = {Sensitivity and accuracy of high-throughput metabarcoding methods for early detection of invasive fish species.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {46393}, pmid = {28406159}, issn = {2045-2322}, mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Fish Proteins/genetics ; Fishes/*classification/embryology/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Introduced Species ; Limit of Detection ; Metagenomics ; Sequence Analysis, DNA/methods ; }, abstract = {High-throughput DNA metabarcoding has gained recognition as a potentially powerful tool for biomonitoring, including early detection of aquatic invasive species (AIS). DNA based techniques are advancing, but our understanding of the limits to detection for metabarcoding complex samples is inadequate. For detecting AIS at an early stage of invasion when the species is rare, accuracy at low detection limits is key. To evaluate the utility of metabarcoding in future fish community monitoring programs, we conducted several experiments to determine the sensitivity and accuracy of routine metabarcoding methods. Experimental mixes used larval fish tissue from multiple "common" species spiked with varying proportions of tissue from an additional "rare" species. Pyrosequencing of genetic marker, COI (cytochrome c oxidase subunit I) and subsequent sequence data analysis provided experimental evidence of low-level detection of the target "rare" species at biomass percentages as low as 0.02% of total sample biomass. Limits to detection varied interspecifically and were susceptible to amplification bias. Moreover, results showed some data processing methods can skew sequence-based biodiversity measurements from corresponding relative biomass abundances and increase false absences. We suggest caution in interpreting presence/absence and relative abundance in larval fish assemblages until metabarcoding methods are optimized for accuracy and precision.}, } @article {pmid28404738, year = {2017}, author = {Galla, S and Chakraborty, S and Mell, B and Vijay-Kumar, M and Joe, B}, title = {Microbiotal-Host Interactions and Hypertension.}, journal = {Physiology (Bethesda, Md.)}, volume = {32}, number = {3}, pages = {224-233}, pmid = {28404738}, issn = {1548-9221}, support = {R01 HL020176/HL/NHLBI NIH HHS/United States ; R37 HL020176/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Humans ; Hypertension/*genetics/*microbiology ; *Metagenome ; Mice ; *Microbiota ; }, abstract = {Hypertension, or elevated blood pressure (BP), has been extensively researched over decades and clearly demonstrated to be caused due to a combination of host genetic and environmental factors. Although much research remains to be conducted to pin-point the precise genetic elements on the host genome that control BP, new lines of evidence are emerging to indicate that, besides the host genome, the genomes of all indigenous commensal micro-organisms, collectively referred to as the microbial metagenome or microbiome, are important, but largely understudied, determinants of BP. Unlike the rigid host genome, the microbiome or the "second genome" can be altered by diet or microbiotal transplantation in the host. This possibility is attractive from the perspective of exploiting the microbiotal composition for clinical management of inherited hypertension. Thus, focusing on the limited current literature supporting a role for the microbiome in BP regulation, this review highlights the need to further explore the role of the co-existence of host and the microbiota as an organized biological unit called the "holobiont" in the context of BP regulation.}, } @article {pmid28404649, year = {2017}, author = {Faner, R and Sibila, O and Agustí, A and Bernasconi, E and Chalmers, JD and Huffnagle, GB and Manichanh, C and Molyneaux, PL and Paredes, R and Pérez Brocal, V and Ponomarenko, J and Sethi, S and Dorca, J and Monsó, E}, title = {The microbiome in respiratory medicine: current challenges and future perspectives.}, journal = {The European respiratory journal}, volume = {49}, number = {4}, pages = {}, doi = {10.1183/13993003.02086-2016}, pmid = {28404649}, issn = {1399-3003}, mesh = {Animals ; Bacteroidetes/*classification ; Bronchiectasis/microbiology ; Cystic Fibrosis/microbiology ; Dysbiosis ; Host-Pathogen Interactions ; Humans ; Idiopathic Interstitial Pneumonias/microbiology ; Lung/*microbiology ; Mice ; *Microbiota ; Proteobacteria/*classification ; Pulmonary Disease, Chronic Obstructive/microbiology ; *Pulmonary Medicine ; Risk Factors ; Terminology as Topic ; }, abstract = {The healthy lung has previously been considered to be a sterile organ because standard microbiological culture techniques consistently yield negative results. However, culture-independent techniques report that large numbers of microorganisms coexist in the lung. There are many unknown aspects in the field, but available reports show that the lower respiratory tract microbiota: 1) is similar in healthy subjects to the oropharyngeal microbiota and dominated by members of the Firmicutes, Bacteroidetes and Proteobacteria phyla; 2) shows changes in smokers and well-defined differences in chronic respiratory diseases, although the temporal and spatial kinetics of these changes are only partially known; and 3) shows relatively abundant non-cultivable bacteria in chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, cystic fibrosis and bronchiectasis, with specific patterns for each disease. In all of these diseases, a loss of diversity, paralleled by an over-representation of Proteobacteria (dysbiosis), has been related to disease severity and exacerbations. However, it is unknown whether dysbiosis is a cause or a consequence of the damage to bronchoalveolar surfaces.Finally, little is known about bacterial functionality and the interactions between viruses, fungi and bacteria. It is expected that future research in bacterial gene expressions, metagenomics longitudinal analysis and host-microbiome animal models will help to move towards targeted microbiome interventions in respiratory diseases.}, } @article {pmid28402790, year = {2017}, author = {LeBlanc, N and Kinkel, L and Kistler, HC}, title = {Plant diversity and plant identity influence Fusarium communities in soil.}, journal = {Mycologia}, volume = {109}, number = {1}, pages = {128-139}, doi = {10.1080/00275514.2017.1281697}, pmid = {28402790}, issn = {0027-5514}, mesh = {*Biodiversity ; Chemical Phenomena ; Cluster Analysis ; Fusarium/*classification/*isolation & purification ; *Genetic Variation ; Genotype ; Metagenomics ; Plants/*classification/*microbiology ; RNA Polymerase II/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Fusarium communities play important functional roles in soil and in plants as pathogens, endophytes, and saprotrophs. This study tests how rhizosphere Fusarium communities may vary with plant species, changes in the diversity of the surrounding plant community, and soil physiochemical characteristics. Fusarium communities in soil associated with the roots of two perennial prairie plant species maintained as monocultures or growing within polyculture plant communities were characterized using targeted metagenomics. Amplicon libraries targeting the RPB2 locus were generated from rhizosphere soil DNAs and sequenced using pyrosequencing. Sequences were clustered into operational taxonomic units (OTUs) and assigned a taxonomy using the Evolutionary Placement Algorithm. Fusarium community composition was differentiated between monoculture and polyculture plant communities, and by plant species in monoculture, but not in polyculture. Taxonomic classification of the Fusarium OTUs showed a predominance of F. tricinctum and F. oxysporum as well of the presence of a clade previously only found in the Southern Hemisphere. Total Fusarium richness was not affected by changes in plant community richness or correlated with soil physiochemical characteristics. However, OTU richness within two predominant phylogenetic lineages within the genus was positively or negatively correlated with soil physiochemical characteristics among samples within each lineage. This work shows that plant species, plant community richness, and soil physiochemical characteristics may all influence the composition and richness of Fusarium communities in soil.}, } @article {pmid28402209, year = {2018}, author = {Kambouris, ME and Pavlidis, C and Skoufas, E and Arabatzis, M and Kantzanou, M and Velegraki, A and Patrinos, GP}, title = {Culturomics: A New Kid on the Block of OMICS to Enable Personalized Medicine.}, journal = {Omics : a journal of integrative biology}, volume = {22}, number = {2}, pages = {108-118}, doi = {10.1089/omi.2017.0017}, pmid = {28402209}, issn = {1557-8100}, mesh = {Animals ; Genomics/methods ; Humans ; Metabolomics/methods ; Metagenomics/methods ; Microbiota/*drug effects/*physiology ; Precision Medicine/*methods ; Proteomics/methods ; }, abstract = {This innovation analysis highlights the underestimated and versatile potential of the new field of culturomics and examines its relation to other OMICS system sciences such as infectiomics, metabolomics, phenomics, and pharmacomicrobiomics. The advent of molecular biology, followed by the emergence of various disciplines of the genomics, and most importantly metagenomics, brought about the sharp decline of conventional microbiology methods. Emergence of culturomics has a natural synergy with therapeutic and clinical genomic approaches so as to realize personalized medicine. Notably, the concept of culturomics expands on that of phenomics and allows a reintroduction of the culture-based phenotypic characterization into the 21st century research repertoire, bolstered by robust technology for automated and massive execution, but its potential is largely unappreciated at present; the few available references show unenthusiastic pursuit and in narrow applications. This has not to be so: depending on the specific brand of culturomics, the scope of applications may extend to medicine, agriculture, environmental sciences, pharmacomicrobiomics, and biotechnology innovation. Moreover, culturomics may produce Big Data. This calls for a new generation of data scientists and innovative ways of harnessing and valorizing Big Data beyond classical genomics. Much more detailed and objective classification and identification of microbiota may soon be at hand through culturomics, thus enabling precision diagnosis toward truly personalized medicine. Culturomics may both widen the scope of microbiology and improve its contributions to diagnostics and personalized medicine, characterizing microbes and determining their associations with health and disease dynamics.}, } @article {pmid28401612, year = {2017}, author = {Kropáčková, L and Těšický, M and Albrecht, T and Kubovčiak, J and Čížková, D and Tomášek, O and Martin, JF and Bobek, L and Králová, T and Procházka, P and Kreisinger, J}, title = {Codiversification of gastrointestinal microbiota and phylogeny in passerines is not explained by ecological divergence.}, journal = {Molecular ecology}, volume = {26}, number = {19}, pages = {5292-5304}, doi = {10.1111/mec.14144}, pmid = {28401612}, issn = {1365-294X}, mesh = {Animals ; Bacteria/*classification ; Czech Republic ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Passeriformes/classification/*microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Vertebrate gut microbiota (GM) is comprised of a taxonomically diverse consortium of symbiotic and commensal microorganisms that have a pronounced effect on host physiology, immune system function and health status. Despite much research on interactions between hosts and their GM, the factors affecting inter- and intraspecific GM variation in wild populations are still poorly known. We analysed data on faecal microbiota composition in 51 passerine species (319 individuals) using Illumina MiSeq sequencing of bacterial 16S rRNA (V3-V4 variable region). Despite pronounced interindividual variation, GM composition exhibited significant differences at the interspecific level, accounting for approximately 20%-30% of total GM variation. We also observed a significant correlation between GM composition divergence and host's phylogenetic divergence, with strength of correlation higher than that of GM vs. ecological or life history traits and geographic variation. The effect of host's phylogeny on GM composition was significant, even after statistical control for these confounding factors. Hence, our data do not support codiversification of GM and passerine phylogeny solely as a by-product of their ecological divergence. Furthermore, our findings do not support that GM vs. host's phylogeny codiversification is driven primarily through trans-generational GM transfer as the GM vs. phylogeny correlation does not increase with higher sequence similarity used when delimiting operational taxonomic units. Instead, we hypothesize that the GM vs. phylogeny correlation may arise as a consequence of interspecific divergence of genes that directly or indirectly modulate composition of GM.}, } @article {pmid28399822, year = {2017}, author = {De Mandal, S and Chatterjee, R and Kumar, NS}, title = {Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {90}, pmid = {28399822}, issn = {1471-2180}, mesh = {Amino Acids/metabolism ; Ammonia/metabolism ; Bacteria/*classification/genetics/*isolation & purification/*metabolism ; Base Sequence ; Biodiversity ; Carbohydrate Metabolism ; Carbon/metabolism ; Carbon Cycle/*physiology ; Caves/*microbiology ; Classification ; DNA, Bacterial ; Ecology ; Ferric Compounds/metabolism ; Geologic Sediments/chemistry/microbiology ; India ; Metabolic Networks and Pathways/physiology ; Metagenome ; Metagenomics ; Nitrates/metabolism ; Nitrification ; Nitrogen/metabolism ; Nitrogen Cycle/*physiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis ; Soil Microbiology ; Survival ; }, abstract = {BACKGROUND: Bacteria present in cave often survive by modifying their metabolic pathway or other mechanism. Understanding these adopted bacteria and their survival strategy inside the cave is an important aspect of microbial ecology. Present study focuses on the bacterial community and geochemistry in five caves of Mizoram, Northeast India. The objective of this study was to explore the taxonomic composition and presumed functional diversity of cave sediment metagenomes using paired end Illumina sequencing using V3 region of 16S rRNA gene and bioinformatics pipeline.

RESULTS: Actinobacteria, Proteobacteria, Verrucomicrobia and Acidobacteria were the major phyla in all the five cave sediment samples. Among the five caves the highest diversity is found in Lamsialpuk with a Shannon index 12.5 and the lowest in Bukpuk (Shannon index 8.22). In addition, imputed metagenomic approach was used to predict the functional role of microbial community in biogeochemical cycling in the cave environments. Functional module showed high representation of genes involved in Amino Acid Metabolism in (20.9%) and Carbohydrate Metabolism (20.4%) in the KEGG pathways. Genes responsible for carbon degradation, carbon fixation, methane metabolism, nitrification, nitrate reduction and ammonia assimilation were also predicted in the present study.

CONCLUSION: The cave sediments of the biodiversity hotspot region possessing a oligotrophic environment harbours high phylogenetic diversity dominated by Actinobacteria and Proteobacteria. Among the geochemical factors, ferric oxide was correlated with increased microbial diversity. In-silico analysis detected genes involved in carbon, nitrogen, methane metabolism and complex metabolic pathways responsible for the survival of the bacterial community in nutrient limited cave environments. Present study with Paired end Illumina sequencing along with bioinformatics analysis revealed the essential ecological role of the cave bacterial communities. These results will be useful in documenting the biospeleology of this region and systematic understanding of bacterial communities in natural sediment environments as well.}, } @article {pmid28398290, year = {2017}, author = {Hahn, AS and Altman, T and Konwar, KM and Hanson, NW and Kim, D and Relman, DA and Dill, DL and Hallam, SJ}, title = {A geographically-diverse collection of 418 human gut microbiome pathway genome databases.}, journal = {Scientific data}, volume = {4}, number = {}, pages = {170035}, pmid = {28398290}, issn = {2052-4463}, support = {R01 GM099534/GM/NIGMS NIH HHS/United States ; T32 GM008412/GM/NIGMS NIH HHS/United States ; }, mesh = {Crohn Disease/microbiology ; *Databases, Genetic ; Diabetes Mellitus, Type 2/microbiology ; *Gastrointestinal Microbiome ; Geography, Medical ; Humans ; Inflammatory Bowel Diseases/microbiology ; *Metabolic Networks and Pathways ; Metagenome ; Metagenomics ; }, abstract = {Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of human microbiome samples sourced from multiple studies are now publicly available. However, idiosyncratic data processing methods between studies introduce systematic differences that confound comparative analyses. To overcome these challenges, we developed GutCyc, a compendium of environmental pathway genome databases (ePGDBs) constructed from 418 assembled human microbiome datasets using MetaPathways, enabling reproducible functional metagenomic annotation. We also generated metabolic network reconstructions for each metagenome using the Pathway Tools software, empowering researchers and clinicians interested in visualizing and interpreting metabolic pathways encoded by the human gut microbiome. For the first time, GutCyc provides consistent annotations and metabolic pathway predictions, making possible comparative community analyses between health and disease states in inflammatory bowel disease, Crohn's disease, and type 2 diabetes. GutCyc data products are searchable online, or may be downloaded and explored locally using MetaPathways and Pathway Tools.}, } @article {pmid28397879, year = {2017}, author = {Chen, SY and Tsai, CN and Lee, YS and Lin, CY and Huang, KY and Chao, HC and Lai, MW and Chiu, CH}, title = {Intestinal microbiome in children with severe and complicated acute viral gastroenteritis.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {46130}, pmid = {28397879}, issn = {2045-2322}, mesh = {Acute Disease ; Biodiversity ; Caliciviridae Infections/microbiology ; Case-Control Studies ; Child ; Gastroenteritis/*microbiology/*virology ; *Gastrointestinal Microbiome/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; Rotavirus Infections/microbiology ; Sequence Analysis, RNA ; *Severity of Illness Index ; }, abstract = {The aim of the present study was to evaluate the microbiota of children with severe or complicated acute viral gastroenteritis (AGE). To that end, next-generation sequencing (NGS) technology was used to sequence the 16S ribosomal RNA (16S rRNA) gene in 20 hospitalized pediatric patients with severe or complicated AGE and a further 20 otherwise healthy children; the fecal microbiome was then assessed. Comparative metagenomics data were analyzed by a Wilcoxon rank-sum test and hierarchical clustering analysis of bacterial reads. The statistical analyses showed a significantly decreased Shannon diversity index (entropy score) of the intestinal microbiota in patients with severe AGE compared with normal controls (P = 0.017) and patients with mild-to-moderate AGE (P = 0.011). The intestinal microbiota score of the 5 patients with rotavirus AGE was significantly lower than that of those with norovirus infection (P = 0.048). Greater richness in Campylobacteraceae (P = 0.0003), Neisseriaceae (P = 0.0115), Methylobacteriaceae (P = 0.0004), Sphingomonadaceae (P = 0.0221), and Enterobacteriaceae (P = 0.0451) was found in patients with complicated AGE compared with normal controls. The data suggest a significant reduction in intestinal microbial diversity in patients with severe AGE, particularly those with rotavirus infection.}, } @article {pmid28397271, year = {2017}, author = {Minami, SB and Mutai, H and Suzuki, T and Horii, A and Oishi, N and Wasano, K and Katsura, M and Tanaka, F and Takiguchi, T and Fujii, M and Kaga, K}, title = {Microbiomes of the normal middle ear and ears with chronic otitis media.}, journal = {The Laryngoscope}, volume = {127}, number = {10}, pages = {E371-E377}, doi = {10.1002/lary.26579}, pmid = {28397271}, issn = {1531-4995}, mesh = {Actinobacteria/isolation & purification ; Adolescent ; Adult ; Aged ; Bacteroidetes/isolation & purification ; Child ; Child, Preschool ; Chronic Disease ; Ear, Middle/*microbiology ; Female ; Firmicutes/isolation & purification ; Humans ; Infant ; Male ; *Microbiota ; Middle Aged ; Otitis Media/*microbiology/surgery ; Prospective Studies ; Proteobacteria/isolation & purification ; RNA, Ribosomal, 16S/analysis ; Tympanoplasty ; Young Adult ; }, abstract = {OBJECTIVE: The aim of this study was to profile and compare the middle ear microbiomes of human subjects with and without chronic otitis media.

STUDY DESIGN: Prospective multicenter cohort study.

METHODS: All consecutive patients undergoing tympanoplasty surgery for chronic otitis media or ear surgery for conditions other than otitis media were recruited. Sterile swab samples were collected from the middle ear mucosa during surgery. The variable region 4 of the 16S rRNA gene in each sample were amplified using region-specific primers adapted for the Illumina MiSeq sequencer (Illumina, CA, USA)). The sequences were subjected to local blast and classified using Metagenome@KIN (World Fusion, Tokyo, Japan).

RESULTS: In total, 155 participants were recruited from seven medical centers. Of these, 88 and 67 had chronic otitis media and normal middle ears, respectively. The most abundant bacterial phyla on the mucosal surfaces of the normal middle ears were Proteobacteria, followed by Actinobacteria, Firmicutes, and Bacteroidetes. The children and adults with normal middle ears differed significantly in terms of middle ear microbiomes. Subjects with chronic otitis media without active inflammation (dry ear) had similar middle ear microbiomes as the normal middle ears group. Subjects with chronic otitis media with active inflammation (wet ear) had a lower prevalence of Proteobacteria and a higher prevalence of Firmicutes than the normal middle ears.

CONCLUSION: The human middle ear is inhabited by more diverse microbial communities than was previously thought. Alteration of the middle ear microbiome may contribute to the pathogenesis of chronic otitis media with active inflammation.

LEVEL OF EVIDENCE: 2b. Laryngoscope, 127:E371-E377, 2017.}, } @article {pmid28396267, year = {2017}, author = {Puehler, A and Kalinowski, J}, title = {Microbial genomics and metagenomics in human health and disease.}, journal = {Journal of biotechnology}, volume = {250}, number = {}, pages = {1}, doi = {10.1016/j.jbiotec.2017.04.007}, pmid = {28396267}, issn = {1873-4863}, mesh = {Bacteria/genetics ; Bacterial Infections/*genetics ; Bacteriophages/genetics ; *Genome, Bacterial ; Genomics ; Humans ; Microbiota ; Sequence Analysis, DNA ; }, } @article {pmid28393285, year = {2018}, author = {Rowland, I and Gibson, G and Heinken, A and Scott, K and Swann, J and Thiele, I and Tuohy, K}, title = {Gut microbiota functions: metabolism of nutrients and other food components.}, journal = {European journal of nutrition}, volume = {57}, number = {1}, pages = {1-24}, pmid = {28393285}, issn = {1436-6215}, mesh = {Bacteria/enzymology/*metabolism ; Bile Acids and Salts/metabolism ; Diet ; Dietary Carbohydrates/metabolism ; Dietary Proteins/metabolism ; Fatty Acids/metabolism ; *Food ; Gastrointestinal Microbiome/*physiology ; *Health Promotion ; Humans ; Metagenomics ; Models, Theoretical ; Phytochemicals/metabolism ; Plants, Edible/chemistry/metabolism ; Polyphenols/metabolism ; Proteomics ; Vitamins/biosynthesis ; }, abstract = {The diverse microbial community that inhabits the human gut has an extensive metabolic repertoire that is distinct from, but complements the activity of mammalian enzymes in the liver and gut mucosa and includes functions essential for host digestion. As such, the gut microbiota is a key factor in shaping the biochemical profile of the diet and, therefore, its impact on host health and disease. The important role that the gut microbiota appears to play in human metabolism and health has stimulated research into the identification of specific microorganisms involved in different processes, and the elucidation of metabolic pathways, particularly those associated with metabolism of dietary components and some host-generated substances. In the first part of the review, we discuss the main gut microorganisms, particularly bacteria, and microbial pathways associated with the metabolism of dietary carbohydrates (to short chain fatty acids and gases), proteins, plant polyphenols, bile acids, and vitamins. The second part of the review focuses on the methodologies, existing and novel, that can be employed to explore gut microbial pathways of metabolism. These include mathematical models, omics techniques, isolated microbes, and enzyme assays.}, } @article {pmid28390576, year = {2017}, author = {Buttó, LF and Haller, D}, title = {Functional relevance of microbiome signatures: The correlation era requires tools for consolidation.}, journal = {The Journal of allergy and clinical immunology}, volume = {139}, number = {4}, pages = {1092-1098}, doi = {10.1016/j.jaci.2017.02.010}, pmid = {28390576}, issn = {1097-6825}, mesh = {Animals ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenome/*genetics ; Metagenomics/*methods/*standards/trends ; Models, Biological ; }, abstract = {Compelling research over the past decade identified a fundamental role of the intestinal microbiome on human health. Compositional and functional changes of this microbial ecosystem are correlated with a variety of human pathologies. Metagenomic resolution and bioinformatic tools considerably improved, allowing even strain-level analysis. However, the search for microbial risk patterns in human cohorts is often confounded by environmental factors (eg, medication) and host status (eg, disease relapse), questioning the prognostic and therapeutic value of the currently available information. In addition to a better stratification of human phenotypes, the implementation of standardized protocols for sampling and analysis is needed to improve the reproducibility and comparability of microbiome signatures at a meaningful taxonomic resolution. At the level of mechanistic understanding, the molecular integration of pleiotropic signals coming from this complex and dynamically changing ecosystem is one of the biggest challenges in this field. The first successful attempts to apply reverse genetics based on the available metagenomic information yielded identification of small molecules and metabolites with functional relevance for microbe-host interactions. Further expansion on the isolation of bacteria from the "unculturable biomass" will help characterize microbiome signatures in model systems, finally aiming at the development of clinically relevant synthetic consortia with safe and functionally well-defined strains. In conclusion and beyond reasonable enthusiasm, the mechanistic implementation and clinical relevance of microbiome alterations on disease susceptibility is still in its infancy, but the integration of all the above-mentioned strategies will help overcome the correlation era in microbiome research and lead to a rational evaluation of clinical strategies relevant for targeted microbial intervention.}, } @article {pmid28390108, year = {2017}, author = {Jacquiod, S and Brejnrod, A and Morberg, SM and Abu Al-Soud, W and Sørensen, SJ and Riber, L}, title = {Deciphering conjugative plasmid permissiveness in wastewater microbiomes.}, journal = {Molecular ecology}, volume = {26}, number = {13}, pages = {3556-3571}, doi = {10.1111/mec.14138}, pmid = {28390108}, issn = {1365-294X}, mesh = {Bacteria/*genetics ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Microbiota ; Plasmids/*genetics ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; Wastewater/*microbiology ; }, abstract = {Wastewater treatment plants (WWTPs) are designed to robustly treat polluted water. They are characterized by ceaseless flows of organic, chemical and microbial matter, followed by treatment steps before environmental release. WWTPs are hotspots of horizontal gene transfer between bacteria via conjugative plasmids, leading to dissemination of potentially hazardous genetic material such as antimicrobial resistance genes (AMRGs). While current focus is on the threat of AMRGs spreading and their environmental maintenance, conjugative plasmid transfer dynamics within and between bacterial communities still remains largely uncharted. Furthermore, current in vitro methods used to assess conjugation in complex microbiomes do not include in situ behaviours of recipient cells, resulting in partial understanding of transfers. We investigated the in vitro conjugation capacities of WWTP microbiomes from inlet sewage and outlet treated water using the broad-host range IncP-1 conjugative plasmid, pKJK5. A thorough molecular approach coupling metagenomes to 16S rRNA DNA/cDNA amplicon sequencing was established to characterize microbiomes using the ecological concept of functional response groups. A broad diversity of recipient bacterial phyla for the plasmid was observed, especially in WWTP outlets. We also identified permissive bacteria potentially able to cross WWTPs and engage in conjugation before and after water treatment. Bacterial activity and lifestyle seem to influence conjugation extent, as treated water copiotrophs were the most represented strategist amongst transconjugants. Correlation analysis highlighted possible plasmid transmission routes into communities between the sewage to the environment, with identification of keystone members (e.g., Arcobacter) potentially involved in cross-border exchanges between distant Gram-positive and Gram-negative phyla.}, } @article {pmid28390093, year = {2018}, author = {Aw, W and Fukuda, S}, title = {Understanding the role of the gut ecosystem in diabetes mellitus.}, journal = {Journal of diabetes investigation}, volume = {9}, number = {1}, pages = {5-12}, pmid = {28390093}, issn = {2040-1124}, mesh = {Animals ; Diabetes Mellitus, Type 1/metabolism/*microbiology ; Diabetes Mellitus, Type 2/metabolism/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Metabolome ; Metabolomics ; Metagenome ; }, abstract = {Diabetes mellitus is a type of metabolic disorder whereby patients are unable to regulate glycemia. It is currently a worldwide public health issue, and is a burden to society because of its disabling and common complications. Diabetes is multifactorial, and also induces the onset of other diseases. In the present report, we review the labyrinth encompassing the gut microbiota and gut microbiota-derived metabolites in type 1 diabetes and type 2 diabetes pathogenesis. There have been exceptional improvements in deoxyribonucleic acid sequencing and mass spectrometry technologies throughout these past years, and these have allowed the comprehensive collection of information on our unique gut ecosystem. We would like to advocate incorporating metagenome and metabolome information for a comprehensive perspective of the complex interrelationships between the gut environment, host metabolism and diabetes pathogenesis. We hope that with this improved understanding we would be able to provide exciting novel therapeutic approaches to engineer an ideal gut ecosystem for optimal health.}, } @article {pmid28390070, year = {2017}, author = {Gomez, DE and Arroyo, LG and Costa, MC and Viel, L and Weese, JS}, title = {Characterization of the Fecal Bacterial Microbiota of Healthy and Diarrheic Dairy Calves.}, journal = {Journal of veterinary internal medicine}, volume = {31}, number = {3}, pages = {928-939}, pmid = {28390070}, issn = {1939-1676}, mesh = {Animals ; Case-Control Studies ; Cattle ; Cattle Diseases/*microbiology ; Diarrhea/microbiology/*veterinary ; Feces/*microbiology ; Female ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Neonatal diarrhea accounts for more than 50% of total deaths in dairy calves. Few population-based studies of cattle have investigated how the microbiota is impacted during diarrhea.

OBJECTIVES: To characterize the fecal microbiota and predict the functional potential of the microbial communities in healthy and diarrheic calves.

METHODS: Fifteen diarrheic calves between the ages of 1 and 30 days and 15 age-matched healthy control calves were enrolled from 2 dairy farms. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene (Illumina, San Diego, CA).

RESULTS: Significant differences in community membership and structure were identified among healthy calves from different farms. Differences in community membership and structure also were identified between healthy and diarrheic calves within each farm. Based on linear discriminant analysis effect size (LEfSe), the genera Bifidobacterium, Megamonas, and a genus of the family Bifidobacteriaceae were associated with health at farm 1, whereas Lachnospiraceae incertae sedis, Dietzia and an unclassified genus of the family Veillonellaceae were significantly associated with health at farm 2. The Phylogenetic Investigation of Communities Reconstruction of Unobserved States (PICRUSt) analysis indicated that diarrheic calves had decreased abundances of genes responsible for metabolism of various vitamins, amino acids, and carbohydrate.

CLINICAL RELEVANCE: The fecal microbiota of healthy dairy calves appeared to be farm specific as were the changes observed during diarrhea. The differences in microbiota structure and membership between healthy and diarrheic calves suggest that dysbiosis can occur in diarrheic calves and it is associated with changes in predictive metagenomic function.}, } @article {pmid28389755, year = {2017}, author = {Szabó, A and Korponai, K and Kerepesi, C and Somogyi, B and Vörös, L and Bartha, D and Márialigeti, K and Felföldi, T}, title = {Soda pans of the Pannonian steppe harbor unique bacterial communities adapted to multiple extreme conditions.}, journal = {Extremophiles : life under extreme conditions}, volume = {21}, number = {3}, pages = {639-649}, pmid = {28389755}, issn = {1433-4909}, mesh = {*Adaptation, Physiological ; Alphaproteobacteria/genetics/isolation & purification ; Extreme Environments ; Lakes/chemistry/*microbiology ; *Metagenome ; *Microbiota ; Osmotic Pressure ; }, abstract = {Soda pans of the Pannonian steppe are unique environments regarding their physical and chemical characteristics: shallowness, high turbidity, intermittent character, alkaline pH, polyhumic organic carbon concentration, hypertrophic condition, moderately high salinity, sodium and carbonate ion dominance. The pans are highly productive environments with picophytoplankton predominance. Little is known about the planktonic bacterial communities inhabiting these aquatic habitats; therefore, amplicon sequencing and shotgun metagenomics were applied to reveal their composition and functional properties. Results showed a taxonomically complex bacterial community which was distinct from other soda lakes regarding its composition, e.g. the dominance of class Alphaproteobacteria was observed within phylum Proteobacteria. The shotgun metagenomic analysis revealed several functional gene components related to the harsh and at the same time hypertrophic environmental conditions, e.g. proteins involved in stress response, transport and hydrolase systems targeting phytoplankton-derived organic matter. This is the first detailed report on the indigenous planktonic bacterial communities coping with the multiple extreme conditions present in the unique soda pans of the Pannonian steppe.}, } @article {pmid28389704, year = {2017}, author = {Abdallah, RA and Beye, M and Diop, A and Bakour, S and Raoult, D and Fournier, PE}, title = {The impact of culturomics on taxonomy in clinical microbiology.}, journal = {Antonie van Leeuwenhoek}, volume = {110}, number = {10}, pages = {1327-1337}, doi = {10.1007/s10482-017-0871-1}, pmid = {28389704}, issn = {1572-9699}, mesh = {Bacteria/*classification/genetics/*growth & development/isolation & purification ; Bacterial Infections/*microbiology ; *Bacterial Typing Techniques ; *Culture Techniques ; Gastrointestinal Tract/microbiology ; Humans ; Metagenome ; Microbiota ; Phylogeny ; Proteome ; }, abstract = {Over the past decade, new culture methods coupled to genome and metagenome sequencing have enabled the number of isolated bacterial species with standing in nomenclature to rise to more than 15,000 whereas it was only 1791 in 1980. 'Culturomics', a new approach based on the diversification of culture conditions, has enabled the isolation of more than 1000 distinct human-associated bacterial species since 2012, including 247 new species. This strategy was demonstrated to be complementary to metagenome sequencing for the exhaustive study of the human microbiota and its roles in health and diseases. However, by identifying a large number of new bacterial species in a short time, culturomics has highlighted a need for taxonomic approaches adapted to clinical microbiology that would include the use of modern and reproducible tools, including high throughput genomic and proteomic analyses. Herein, we review the development of culturomics and genomics in the clinical microbiology field and their impact on bacterial taxonomy.}, } @article {pmid28389566, year = {2017}, author = {Martinez, KB and Leone, V and Chang, EB}, title = {Microbial metabolites in health and disease: Navigating the unknown in search of function.}, journal = {The Journal of biological chemistry}, volume = {292}, number = {21}, pages = {8553-8559}, pmid = {28389566}, issn = {1083-351X}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; R01 DK097268/DK/NIDDK NIH HHS/United States ; R56 DK102872/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Diabetes Mellitus/genetics/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Host-Pathogen Interactions ; Humans ; *Inflammatory Bowel Diseases/genetics/metabolism/microbiology ; *Irritable Bowel Syndrome/genetics/metabolism/microbiology ; *Non-alcoholic Fatty Liver Disease/genetics/metabolism/microbiology ; *Obesity/genetics/metabolism/microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The gut microbiota has been implicated in the development of a number of chronic gastrointestinal and systemic diseases. These include inflammatory bowel diseases, irritable bowel syndrome, and metabolic (i.e. obesity, non-alcoholic fatty liver disease, and diabetes) and neurological diseases. The advanced understanding of host-microbe interactions has largely been due to new technologies such as 16S rRNA sequencing to identify previously unknown microbial communities and, more importantly, their functional characteristics through metagenomic sequencing and other multi-omic technologies, such as metatranscriptomics, metaproteomics, and metabolomics. Given the vast array of newly acquired knowledge in the field and technological advances, it is expected that mechanisms underlying several disease states involving the interactions between microbes, their metabolites, and the host will be discovered. The identification of these mechanisms will allow for the development of more precise therapies to prevent or manage chronic disease. This review discusses the functional characterization of the microbiome, highlighting the advances in identifying bioactive microbial metabolites that have been directly linked to gastrointestinal and peripheral diseases.}, } @article {pmid28384412, year = {2017}, author = {Nascimento, MM and Zaura, E and Mira, A and Takahashi, N and Ten Cate, JM}, title = {Second Era of OMICS in Caries Research: Moving Past the Phase of Disillusionment.}, journal = {Journal of dental research}, volume = {96}, number = {7}, pages = {733-740}, pmid = {28384412}, issn = {1544-0591}, support = {K23 DE023579/DE/NIDCR NIH HHS/United States ; }, mesh = {Biofilms ; Computational Biology/*methods ; Dental Caries/*microbiology/*prevention & control ; *Dental Research ; Diffusion of Innovation ; Genomics/methods ; Humans ; *Metabolome ; Metabolomics/methods ; Metagenome ; *Microbiota ; Proteomics/methods ; }, abstract = {Novel approaches using OMICS techniques enable a collective assessment of multiple related biological units, including genes, gene expression, proteins, and metabolites. In the past decade, next-generation sequencing (NGS) technologies were improved by longer sequence reads and the development of genome databases and user-friendly pipelines for data analysis, all accessible at lower cost. This has generated an outburst of high-throughput data. The application of OMICS has provided more depth to existing hypotheses as well as new insights in the etiology of dental caries. For example, the determination of complete bacterial microbiomes of oral samples rather than selected species, together with oral metatranscriptome and metabolome analyses, supports the viewpoint of dysbiosis of the supragingival biofilms. In addition, metabolome studies have been instrumental in disclosing the contributions of major pathways for central carbon and amino acid metabolisms to biofilm pH homeostasis. New, often noncultured, oral streptococci have been identified, and their phenotypic characterization has revealed candidates for probiotic therapy. Although findings from OMICS research have been greatly informative, problems related to study design, data quality, integration, and reproducibility still need to be addressed. Also, the emergence and continuous updates of these computationally demanding technologies require expertise in advanced bioinformatics for reliable interpretation of data. Despite the obstacles cited above, OMICS research is expected to encourage the discovery of novel caries biomarkers and the development of next-generation diagnostics and therapies for caries control. These observations apply equally to the study of other oral diseases.}, } @article {pmid28383679, year = {2017}, author = {Czeczko, P and Greenway, SC and de Koning, APJ}, title = {EzMap: a simple pipeline for reproducible analysis of the human virome.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {16}, pages = {2573-2574}, doi = {10.1093/bioinformatics/btx202}, pmid = {28383679}, issn = {1367-4811}, mesh = {Computational Biology/methods ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; *Software ; Viruses/*genetics ; }, abstract = {SUMMARY: In solid-organ transplant recipients, a delicate balance between immunosuppression and immunocompetence must be achieved, which can be difficult to monitor in real-time. Shotgun sequencing of cell-free DNA (cfDNA) has been recently proposed as a new way to indirectly assess immune function in transplant recipients through analysis of the status of the human virome. To facilitate exploration of the utility of the human virome as an indicator of immune status, and to enable rapid, straightforward analyses by clinicians, we developed a fully automated computational pipeline, EzMap, for performing metagenomic analysis of the human virome. EzMap combines a number of tools to clean, filter, and subtract WGS reads by mapping to a reference human assembly. The relative abundance of each virus present is estimated using a maximum likelihood approach that accounts for genome size, and results are presented with interactive visualizations and taxonomy-based summaries that enable rapid insights. The pipeline is automated to run on both workstations and computing clusters for all steps. EzMap automates an otherwise tedious and time-consuming protocol and aims to facilitate rapid and reproducible insights from cfDNA.

EzMap is freely available at https://github.com/dekoning-lab/ezmap.

CONTACT: jason.dekoning@ucalgary.ca.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid28383519, year = {2017}, author = {Li, M and Zhou, H and Pan, X and Xu, T and Zhang, Z and Zi, X and Jiang, Y}, title = {Cassava foliage affects the microbial diversity of Chinese indigenous geese caecum using 16S rRNA sequencing.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {45697}, pmid = {28383519}, issn = {2045-2322}, mesh = {*Animal Feed ; Animals ; Biota/*drug effects ; Cecum/*microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Diet/*methods ; Geese/*microbiology ; *Manihot ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Geese are extremely adept in utilizing plant-derived roughage within their diet. However, the intestinal microbiome of geese remains limited, especially the dietary effect on microbial diversity. Cassava foliage was widely used in animal feed, but little information is available for geese. In this study, the geese were fed with control diet (CK), experimental diet supplemented with 5% cassava foliage (CF5) or 10% (CF10) for 42 days, respectively. The cecal samples were collected after animals were killed. High-throughput sequencing technology was used to investigate the microbial diversity in the caecum of geese with different dietary supplements. Taxonomic analysis indicated that the predominant phyla were distinct with different dietary treatments. The phyla Firmicutes (51.4%), Bacteroidetes (29.55%) and Proteobacteria (7.90%) were dominant in the CK group, but Bacteroidetes (65.19% and 67.29%,) Firmicutes (18.01% and 17.39%), Proteobacteria (8.72% and 10.18%), Synergistete (2.51% and 1.76%) and Spirochaetes (2.60% and 1.46%) were dominant in CF5 and CF10 groups. The abundance of Firmicutes was negatively correlated with the supplementation of cassava foliage. However, the abundance of Bacteroidetes and Proteobacteria were positively correlated with the supplementation of cassava foliage. Our study also revealed that the microbial communities were significantly different at genus levels. Genes related to nutrient and energy metabolism, immunity and signal transduction pathways were primarily enriched by the microbiome.}, } @article {pmid28382231, year = {2017}, author = {Castañeda, LE and Barbosa, O}, title = {Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3098}, pmid = {28382231}, issn = {2167-8359}, abstract = {Mediterranean biomes are biodiversity hotspots, and vineyards are important components of the Mediterranean landscape. Over the last few decades, the amount of land occupied by vineyards has augmented rapidly, thereby increasing threats to Mediterranean ecosystems. Land use change and agricultural management have important effects on soil biodiversity, because they change the physical and chemical properties of soil. These changes may also have consequences on wine production considering that soil is a key component of terroir. Here, we describe the taxonomic diversity and metabolic functions of bacterial and fungal communities present in forest and vineyard soils in Chile. To accomplish this goal, we collected soil samples from organic vineyards in central Chile and employed a shotgun metagenomic approach to sequence the microbial DNA. Additionally, we studied the surrounding native forest to obtain a baseline of the soil conditions in the area prior to the establishment of the vineyard. Our metagenomic analyses revealed that both habitats shared most of the soil microbial species. The most abundant genera in the two habitats were the bacteria Candidatus Solibacter and Bradyrhizobium and the fungus Gibberella. Our results suggest that the soil microbial communities are similar in these forests and vineyards. Therefore, we hypothesize that native forests surrounding the vineyards may be acting as a microbial reservoir buffering the effects of the land conversion. Regarding the metabolic diversity, we found that genes pertaining to the metabolism of amino acids, fatty acids, and nucleotides as well as genes involved in secondary metabolism were enriched in forest soils. On the other hand, genes related to miscellaneous functions were more abundant in vineyard soils. These results suggest that the metabolic function of microbes found in these habitats differs, though differences are not related to taxonomy. Finally, we propose that the implementation of environmentally friendly practices by the wine industry may help to maintain the microbial diversity and ecosystem functions associated with natural habitats.}, } @article {pmid28379433, year = {2017}, author = {Nazzal, L and Roberts, J and Singh, P and Jhawar, S and Matalon, A and Gao, Z and Holzman, R and Liebes, L and Blaser, MJ and Lowenstein, J}, title = {Microbiome perturbation by oral vancomycin reduces plasma concentration of two gut-derived uremic solutes, indoxyl sulfate and p-cresyl sulfate, in end-stage renal disease.}, journal = {Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association}, volume = {32}, number = {11}, pages = {1809-1817}, doi = {10.1093/ndt/gfx029}, pmid = {28379433}, issn = {1460-2385}, mesh = {Administration, Oral ; Adult ; Aged ; Anti-Bacterial Agents/*administration & dosage/adverse effects ; Biomarkers/blood ; Cresols/*blood ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Indican/*blood ; Kidney Failure, Chronic/*blood ; Male ; Metagenome ; Middle Aged ; Molecular Typing ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Sulfuric Acid Esters/*blood ; Vancomycin/*administration & dosage/adverse effects ; }, abstract = {BACKGROUND: Observational studies have suggested a relationship between the plasma concentration of indoxyl sulfate (IS) and p-cresyl sulfate (PCS), small gut-derived 'uremic solutes', and the high incidence of uremic cardiomyopathy in patients with end-stage renal disease (ESRD). IS and PCS are derived from the metabolism of dietary components (tryptophan and tyrosine) by gut bacteria. This pilot study was designed to examine the effects of a poorly absorbable antibiotic (vancomycin) on the plasma concentration of two gut-derived 'uremic solutes', IS and PCS, and on the composition of the gut microbiome.

METHODS: Plasma concentrations of IS and PCS were measured by MS-HPLC. The gut microbiome was assessed in stool specimens sequenced for the 16S rRNA gene targeting the V4 region.

RESULTS: The pre-dialysis mean plasma concentrations of both IS and PCS were markedly elevated. Following the administration of vancomycin (Day 0), the IS and PCS concentrations decreased at Day 2 or Day 5 and returned to baseline by Day 28. Following vancomycin administration, several changes in the gut microbiome were observed. Most striking was the decrease in diversity, a finding that was evident on Day 7 and was still evident at Day 28. There was little change at the phylum level but at the genus level, broad population changes were noted. Changes in the abundance of several genera appeared to parallel the concentration of IS and PCS.

CONCLUSIONS: These findings suggest that alteration of the gut microbiome, by an antibiotic, might provide an important strategy in reducing the levels of IS and PCS in ESRD.}, } @article {pmid28379372, year = {2017}, author = {Guet-Revillet, H and Jais, JP and Ungeheuer, MN and Coignard-Biehler, H and Duchatelet, S and Delage, M and Lam, T and Hovnanian, A and Lortholary, O and Nassif, X and Nassif, A and Join-Lambert, O}, title = {The Microbiological Landscape of Anaerobic Infections in Hidradenitis Suppurativa: A Prospective Metagenomic Study.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {65}, number = {2}, pages = {282-291}, doi = {10.1093/cid/cix285}, pmid = {28379372}, issn = {1537-6591}, mesh = {Adult ; Bacteria, Anaerobic/*genetics/isolation & purification/physiology ; Female ; Gram-Negative Bacteria/*genetics/isolation & purification ; Hidradenitis Suppurativa/*microbiology/physiopathology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; *Metagenomics ; Microbiota ; Prevotella/isolation & purification ; Prospective Studies ; Quality of Life ; Skin/microbiology/pathology ; Soft Tissue Infections/microbiology ; }, abstract = {BACKGROUND: Hidradenitis suppurativa (HS) is a frequent and severe disease of the skin, characterized by recurrent or chronic skinfold suppurative lesions with a high impact on quality of life. Although considered inflammatory, antimicrobial treatments can improve or lead to clinical remission of HS, suggesting triggering microbial factors. Indeed, mixed anaerobic microbiota are associated with a majority of HS lesions. Our aim in this study was to characterize the landscape of anaerobic infections in HS using high-throughput sequencing.

METHODS: We sampled and cultured 149 lesions and 175 unaffected control skinfold areas from 65 adult HS patients. The microbiome of 80 anaerobic lesions was compared to that of 88 control samples by 454 high-throughput sequencing after construction of 16S ribosomal RNA gene libraries.

RESULTS: Bacterial cultures detected anaerobes in 83% of lesions vs 53% of control samples, combined with milleri group streptococci and actinomycetes in 33% and 26% of cases, respectively. High-throughput sequencing identified 43 taxa associated with HS lesions. Two gram-negative anaerobic rod taxa, Prevotella and Porphyromonas, predominated, contrasting with a reduced abundance of aerobic commensals. These rare taxa of normal skinfold microbiota were associated with lesions independently of gender, duration and familial history of HS, body mass index, and location. Two main additional taxa, Fusobacterium and Parvimonas, correlated with the clinical severity of HS.

CONCLUSIONS: In this study we reveal the high prevalence and particular landscape of mixed anaerobic infection in HS, paving the way for rationale targeted antimicrobial treatments.}, } @article {pmid28378789, year = {2017}, author = {Boers, SA and Hays, JP and Jansen, R}, title = {Novel micelle PCR-based method for accurate, sensitive and quantitative microbiota profiling.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {45536}, pmid = {28378789}, issn = {2045-2322}, mesh = {Bacteria/*classification/*genetics ; DNA, Ribosomal/genetics ; Metagenomics/*methods/standards ; *Microbiota ; Polymerase Chain Reaction/*methods/standards ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In the last decade, many researchers have embraced 16S rRNA gene sequencing techniques, which has led to a wealth of publications and documented differences in the composition of microbial communities derived from many different ecosystems. However, comparison between different microbiota studies is currently very difficult due to the lack of a standardized 16S rRNA gene sequencing protocol. Here we report on a novel approach employing micelle PCR (micPCR) in combination with an internal calibrator that allows for standardization of microbiota profiles via their absolute abundances. The addition of an internal calibrator allows the researcher to express the resulting operational taxonomic units (OTUs) as a measure of 16S rRNA gene copies by correcting the number of sequences of each individual OTU in a sample for efficiency differences in the NGS process. Additionally, accurate quantification of OTUs obtained from negative extraction control samples allows for the subtraction of contaminating bacterial DNA derived from the laboratory environment or chemicals/reagents used. Using equimolar synthetic microbial community samples and low biomass clinical samples, we demonstrate that the calibrated micPCR/NGS methodology possess a much higher precision and a lower limit of detection compared with traditional PCR/NGS, resulting in more accurate microbiota profiles suitable for multi-study comparison.}, } @article {pmid28378160, year = {2017}, author = {Hu, Q and Zhang, J and Xu, C and Li, C and Liu, S}, title = {The Dynamic Microbiota Profile During Pepper (Piper nigrum L.) Peeling by Solid-State Fermentation.}, journal = {Current microbiology}, volume = {74}, number = {6}, pages = {739-746}, pmid = {28378160}, issn = {1432-0991}, mesh = {Acetylesterase/metabolism ; Acinetobacter/classification/*genetics/isolation & purification ; Aspergillus niger/classification/*genetics/isolation & purification ; Carboxylic Ester Hydrolases/metabolism ; China ; Fermentation/*physiology ; Food Handling/methods ; High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; Piper nigrum/*microbiology ; Pseudomonas/classification/*genetics/isolation & purification ; Vegetables/*microbiology ; }, abstract = {White pepper (Piper nigrum L.), a well-known spice, is the main pepper processing product in Hainan province, China. The solid-state method of fermentation can peel pepper in a highly efficient manner and yield high-quality white pepper. In the present study, we used next-generation sequencing to reveal the dynamic changes in the microbiota during pepper peeling by solid-state fermentation. The results suggested that the inoculated Aspergillus niger was dominant throughout the fermentation stage, with its strains constituting more than 95% of the fungi present; thus, the fungal community structure was relatively stable. The bacterial community structure fluctuated across different fermentation periods; among the bacteria present, Pseudomonas, Tatumella, Pantoea, Acinetobacter, Lactococcus, and Enterobacter accounted for more than 95% of all bacteria. Based on the correlations among the microbial community, we found that Pseudomonas and Acinetobacter were significantly positively related with A. niger, which showed strong synergy with them. In view of the microbial functional gene analysis, we found that these three bacteria and fungi were closely related to the production of pectin esterase (COG4677) and acetyl xylan esterase (COG3458), the key enzymes for pepper peeling. The present research clarifies the solid-state fermentation method of pepper peeling and lays a theoretical foundation to promote the development of the pepper peeling process and the production of high-quality white pepper.}, } @article {pmid28375652, year = {2017}, author = {Knight, R and Callewaert, C and Marotz, C and Hyde, ER and Debelius, JW and McDonald, D and Sogin, ML}, title = {The Microbiome and Human Biology.}, journal = {Annual review of genomics and human genetics}, volume = {18}, number = {}, pages = {65-86}, doi = {10.1146/annurev-genom-083115-022438}, pmid = {28375652}, issn = {1545-293X}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Humans ; *Immune System ; *Metabolome ; *Metagenome ; Microbiota/*genetics ; *Sequence Analysis, DNA ; }, abstract = {Over the past few years, microbiome research has dramatically reshaped our understanding of human biology. New insights range from an enhanced understanding of how microbes mediate digestion and disease processes (e.g., in inflammatory bowel disease) to surprising associations with Parkinson's disease, autism, and depression. In this review, we describe how new generations of sequencing technology, analytical advances coupled to new software capabilities, and the integration of animal model data have led to these new discoveries. We also discuss the prospects for integrating studies of the microbiome, metabolome, and immune system, with the goal of elucidating mechanisms that govern their interactions. This systems-level understanding will change how we think about ourselves as organisms.}, } @article {pmid28369659, year = {2017}, author = {Gao, B and Bian, X and Chi, L and Tu, P and Ru, H and Lu, K}, title = {Editor's Highlight: OrganophosphateDiazinon Altered Quorum Sensing, Cell Motility, Stress Response, and Carbohydrate Metabolism of Gut Microbiome.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {157}, number = {2}, pages = {354-364}, pmid = {28369659}, issn = {1096-0929}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 ES024950/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Bacterial Translocation/*drug effects/genetics ; Carbohydrate Metabolism/*drug effects/genetics ; Diazinon/*toxicity ; Down-Regulation ; Gastrointestinal Microbiome/*drug effects/genetics ; Gastrointestinal Tract/drug effects/microbiology ; Genes, Bacterial ; Insecticides/*toxicity ; Male ; Metagenome ; Mice, Inbred C57BL ; Quorum Sensing/*drug effects/genetics ; Stress, Physiological/*drug effects/genetics ; Up-Regulation ; }, abstract = {The gut microbiome plays a key role in energy production, immune system development, and host resistance against invading pathogens, etc. Disruption of gut bacterial homeostasis is associated with a number of human diseases. Several environmental chemicals have been reported to induce alterations of the gut microbiome. Diazinon, one of important organophosphate insecticides, has been widely used in agriculture. Diazinon and its metabolites are readily detected in different environmental settings and human urine. The toxicity of organophosphates has been a long-standing public health concern. We recently demonstrated that organophosphate insecticide diazinon perturbed the gut microbiome composition of mice. However, the functional impact of exposure on the gut microbiome has not been adequately assessed yet. In particular, the molecular mechanism responsible for exposure-induced microbial profile and community structure changes has not been identified. Therefore, in this study, we used metatranscriptomics to examine the effects of diazinon exposure on the gut metatranscriptome in C57BL/6 mice. Herein, we demonstrated for the first time that organophosphate diazinon modulated quorum sensing, which may serve as a key mechanism to regulate bacterial population, composition, and more importantly, their functional genes. In addition, we also found that diazinon exposure activated diverse stress response pathways and profoundly impaired energy metabolism of gut bacteria. These findings provide new understandings of the functional interplay between the gut microbiome and environmental chemicals, such as organophosphates.}, } @article {pmid28369246, year = {2017}, author = {Torres, PJ and Edwards, RA and McNair, KA}, title = {PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {15}, pages = {2389-2391}, pmid = {28369246}, issn = {1367-4811}, mesh = {Bacteria/*genetics ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Molecular Sequence Annotation/methods ; Sequence Analysis, DNA/methods ; *Software ; Viruses/*genetics ; }, abstract = {MOTIVATION: The Sequence Read Archive (SRA) contains raw data from many different types of sequence projects. As of 2017, the SRA contained approximately ten petabases of DNA sequence (10 16 bp). Annotations of the data are provided by the submitter, and mining the data in the SRA is complicated by both the amount of data and the detail within those annotations. Here, we introduce PARTIE, a partition engine optimized to differentiate sequence read data into metagenomic (random) and amplicon (targeted) sequence data sets.

RESULTS: PARTIE subsamples reads from the sequencing file and calculates four different statistics: k -mer frequency, 16S abundance, prokaryotic- and viral-read abundance. These metrics are used to create a RandomForest decision tree to classify the sequencing data, and PARTIE provides mechanisms for both supervised and unsupervised classification. We demonstrate the accuracy of PARTIE for classifying SRA data, discuss the probable error rates in the SRA annotations and introduce a resource assessing SRA data.

PARTIE and reclassified metagenome SRA entries are available from https://github.com/linsalrob/partie.

CONTACT: redwards@mail.sdsu.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid28367917, year = {2017}, author = {Narihiro, T and Kamagata, Y}, title = {Genomics and Metagenomics in Microbial Ecology: Recent Advances and Challenges.}, journal = {Microbes and environments}, volume = {32}, number = {1}, pages = {1-4}, pmid = {28367917}, issn = {1347-4405}, mesh = {Biota ; *Environmental Microbiology ; Genome, Microbial ; *Genomics/trends ; Host Microbial Interactions ; *Metagenomics/trends ; Microbial Interactions ; }, } @article {pmid28366817, year = {2017}, author = {Forsman, ZH and Knapp, ISS and Tisthammer, K and Eaton, DAR and Belcaid, M and Toonen, RJ}, title = {Coral hybridization or phenotypic variation? Genomic data reveal gene flow between Porites lobata and P. Compressa.}, journal = {Molecular phylogenetics and evolution}, volume = {111}, number = {}, pages = {132-148}, doi = {10.1016/j.ympev.2017.03.023}, pmid = {28366817}, issn = {1095-9513}, mesh = {Animals ; Anthozoa/*genetics ; Gene Flow/*genetics ; Genome, Mitochondrial ; Genomics/*methods ; Geography ; Hawaii ; *Hybridization, Genetic ; Likelihood Functions ; Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Principal Component Analysis ; Sequence Alignment ; Species Specificity ; }, abstract = {Major gaps remain in our understanding of the ecology, evolution, biodiversity, biogeography, extinction risk, and adaptive potential of reef building corals. One of the central challenges remains that there are few informative genetic markers for studying boundaries between species, and variation within species. Reduced representation sequencing approaches, such as RADseq (Restriction site Associated DNA sequencing) have great potential for resolving such relationships. However, it is necessary to identify loci in order to make inferences for endosymbiotic organisms such as corals. Here, we examined twenty-one coral holobiont ezRAD libraries from Hawai'i, focusing on P. lobata and P. compressa, two species with contrasting morphology and habitat preference that previous studies have not resolved. We used a combination of de novo assembly and reference mapping approaches to identify and compare loci: we used reference mapping to extract and compare nearly complete mitochondrial genomes, ribosomal arrays, and histone genes. We used de novo clustering and phylogenomic methods to compare the complete holobiont data set with coral and symbiont subsets that map to transcriptomic data. In addition, we used reference assemblies to examine genetic structure from SNPs (Single Nucleotide Polymorphisms). All approaches resolved outgroup taxa but failed to resolve P. lobata and P. compressa as distinct, with mito-nuclear discordance and shared mitochondrial haplotypes within the species complex. The holobiont and 'coral transcriptomic' datasets were highly concordant, revealing stronger genetic structure between sites than between coral morphospecies. These results suggest that either branching morphology is a polymorphic trait, or that these species frequently hybridize. This study provides examples of several approaches to acquire, identify, and compare loci across metagenomic samples such as the coral holobiont while providing insights into the nature of coral variability.}, } @article {pmid28361695, year = {2017}, author = {Balvočiūtė, M and Huson, DH}, title = {SILVA, RDP, Greengenes, NCBI and OTT - how do these taxonomies compare?.}, journal = {BMC genomics}, volume = {18}, number = {Suppl 2}, pages = {114}, pmid = {28361695}, issn = {1471-2164}, mesh = {*Algorithms ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Databases, Genetic ; Gene Ontology/*statistics & numerical data ; Metagenomics/methods/statistics & numerical data ; Microbiota/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: A key step in microbiome sequencing analysis is read assignment to taxonomic units. This is often performed using one of four taxonomic classifications, namely SILVA, RDP, Greengenes or NCBI. It is unclear how similar these are and how to compare analysis results that are based on different taxonomies.

RESULTS: We provide a method and software for mapping taxonomic entities from one taxonomy onto another. We use it to compare the four taxonomies and the Open Tree of life Taxonomy (OTT).

CONCLUSIONS: While we find that SILVA, RDP and Greengenes map well into NCBI, and all four map well into the OTT, mapping the two larger taxonomies on to the smaller ones is problematic.}, } @article {pmid28360096, year = {2018}, author = {Barton, W and Penney, NC and Cronin, O and Garcia-Perez, I and Molloy, MG and Holmes, E and Shanahan, F and Cotter, PD and O'Sullivan, O}, title = {The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level.}, journal = {Gut}, volume = {67}, number = {4}, pages = {625-633}, doi = {10.1136/gutjnl-2016-313627}, pmid = {28360096}, issn = {1468-3288}, support = {CDF-2017-10-032/DH_/Department of Health/United Kingdom ; PDF-2012-05-456/DH_/Department of Health/United Kingdom ; }, mesh = {*Athletes ; Body Mass Index ; Case-Control Studies ; *Exercise ; Feces/*microbiology ; *Feeding Behavior ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Young Adult ; }, abstract = {OBJECTIVE: It is evident that the gut microbiota and factors that influence its composition and activity effect human metabolic, immunological and developmental processes. We previously reported that extreme physical activity with associated dietary adaptations, such as that pursued by professional athletes, is associated with changes in faecal microbial diversity and composition relative to that of individuals with a more sedentary lifestyle. Here we address the impact of these factors on the functionality/metabolic activity of the microbiota which reveals even greater separation between exercise and a more sedentary state.

DESIGN: Metabolic phenotyping and functional metagenomic analysis of the gut microbiome of professional international rugby union players (n=40) and controls (n=46) was carried out and results were correlated with lifestyle parameters and clinical measurements (eg, dietary habit and serum creatine kinase, respectively).

RESULTS: Athletes had relative increases in pathways (eg, amino acid and antibiotic biosynthesis and carbohydrate metabolism) and faecal metabolites (eg, microbial produced short-chain fatty acids (SCFAs) acetate, propionate and butyrate) associated with enhanced muscle turnover (fitness) and overall health when compared with control groups.

CONCLUSIONS: Differences in faecal microbiota between athletes and sedentary controls show even greater separation at the metagenomic and metabolomic than at compositional levels and provide added insight into the diet-exercise-gut microbiota paradigm.}, } @article {pmid28355207, year = {2017}, author = {Fraihi, W and Fares, W and Perrin, P and Dorkeld, F and Sereno, D and Barhoumi, W and Sbissi, I and Cherni, S and Chelbi, I and Durvasula, R and Ramalho-Ortigao, M and Gtari, M and Zhioua, E}, title = {An integrated overview of the midgut bacterial flora composition of Phlebotomus perniciosus, a vector of zoonotic visceral leishmaniasis in the Western Mediterranean Basin.}, journal = {PLoS neglected tropical diseases}, volume = {11}, number = {3}, pages = {e0005484}, pmid = {28355207}, issn = {1935-2735}, mesh = {Animals ; Bacteria/*classification/*genetics/isolation & purification ; Bacteriological Techniques ; *Gastrointestinal Microbiome ; *Insect Vectors ; Mediterranean Region ; Metagenomics ; Phlebotomus/*microbiology ; Seasons ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The Leishmania developmental life cycle within its sand fly vector occurs exclusively in the lumen of the insect's digestive tract in the presence of symbiotic bacteria. The composition of the gut microbiota and the factors that influence its composition are currently poorly understood. A set of factors, including the host and its environment, may influence this composition. It has been demonstrated that the insect gut microbiota influences the development of several human pathogens, such as Plasmodium falciparum. For sand flies and Leishmania, understanding the interactions between the parasite and the microbial environment of the vector midgut can provide new tools to control Leishmania transmission.

The midguts of female Phlebotomus perniciosus from laboratory colonies or from the field were collected during the months of July, September and October 2011 and dissected. The midguts were analyzed by culture-dependent and culture-independent methods. A total of 441 and 115 cultivable isolates were assigned to 30 and 11 phylotypes from field-collected and colonized P. perniciosus, respectively. Analysis of monthly variations in microbiota composition shows a species diversity decline in October, which is to the end of the Leishmania infantum transmission period. In parallel, a compilation and a meta-analysis of all available data concerning the microbiota of two Psychodidae genera, namely Phlebotomus and Lutzomyia, was performed and compared to P. perniciosus, data obtained herein. This integrated analysis did not reveal any substantial divergences between Old and New world sand flies with regards to the midgut bacterial phyla and genera diversity. But clearly, most bacterial species (>76%) are sparsely distributed between Phlebotominae species.

CONCLUSION/SIGNIFICANCE: Our results pinpoint the need for a more exhaustive understanding of the bacterial richness and abundance at the species level in Phlebotominae sand flies in order to capture the role of midgut bacteria during Leishmania development and transmission. The occurrence of Bacillus subtilis in P. perniciosus and at least two other sand fly species studied so far suggests that this bacterial species is a potential candidate for paratransgenic or biolological approaches for the control of sand fly populations in order to prevent Leishmania transmission.}, } @article {pmid28351915, year = {2017}, author = {Zapka, C and Leff, J and Henley, J and Tittl, J and De Nardo, E and Butler, M and Griggs, R and Fierer, N and Edmonds-Wilson, S}, title = {Comparison of Standard Culture-Based Method to Culture-Independent Method for Evaluation of Hygiene Effects on the Hand Microbiome.}, journal = {mBio}, volume = {8}, number = {2}, pages = {}, pmid = {28351915}, issn = {2150-7511}, mesh = {Adolescent ; Adult ; Bacteriological Techniques/*methods ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Hand Disinfection/*methods ; Humans ; Metagenomics/*methods ; Microbiota/*drug effects ; Montana ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Treatment Outcome ; Young Adult ; }, abstract = {Hands play a critical role in the transmission of microbiota on one's own body, between individuals, and on environmental surfaces. Effectively measuring the composition of the hand microbiome is important to hand hygiene science, which has implications for human health. Hand hygiene products are evaluated using standard culture-based methods, but standard test methods for culture-independent microbiome characterization are lacking. We sampled the hands of 50 participants using swab-based and glove-based methods prior to and following four hand hygiene treatments (using a nonantimicrobial hand wash, alcohol-based hand sanitizer [ABHS], a 70% ethanol solution, or tap water). We compared results among culture plate counts, 16S rRNA gene sequencing of DNA extracted directly from hands, and sequencing of DNA extracted from culture plates. Glove-based sampling yielded higher numbers of unique operational taxonomic units (OTUs) but had less diversity in bacterial community composition than swab-based sampling. We detected treatment-induced changes in diversity only by using swab-based samples (P < 0.001); we were unable to detect changes with glove-based samples. Bacterial cell counts significantly decreased with use of the ABHS (P < 0.05) and ethanol control (P < 0.05). Skin hydration at baseline correlated with bacterial abundances, bacterial community composition, pH, and redness across subjects. The importance of the method choice was substantial. These findings are important to ensure improvement of hand hygiene industry methods and for future hand microbiome studies. On the basis of our results and previously published studies, we propose recommendations for best practices in hand microbiome research.IMPORTANCE The hand microbiome is a critical area of research for diverse fields, such as public health and forensics. The suitability of culture-independent methods for assessing effects of hygiene products on microbiota has not been demonstrated. This is the first controlled laboratory clinical hand study to have compared traditional hand hygiene test methods with newer culture-independent characterization methods typically used by skin microbiologists. This study resulted in recommendations for hand hygiene product testing, development of methods, and future hand skin microbiome research. It also demonstrated the importance of inclusion of skin physiological metadata in skin microbiome research, which is atypical for skin microbiome studies.}, } @article {pmid28350876, year = {2017}, author = {Zou, B and Li, J and Zhou, Q and Quan, ZX}, title = {MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0174609}, pmid = {28350876}, issn = {1932-6203}, mesh = {Algorithms ; Computational Biology/*methods ; DNA Primers ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Polymerase Chain Reaction/methods ; RNA, Ribosomal/*genetics ; Reproducibility of Results ; Software ; }, abstract = {An understanding of microbial community structure is an important issue in the field of molecular ecology. The traditional molecular method involves amplification of small subunit ribosomal RNA (SSU rRNA) genes by polymerase chain reaction (PCR). However, PCR-based amplicon approaches are affected by primer bias and chimeras. With the development of high-throughput sequencing technology, unbiased SSU rRNA gene sequences can be mined from shotgun sequencing-based metagenomic or metatranscriptomic datasets to obtain a reflection of the microbial community structure in specific types of environment and to evaluate SSU primers. However, the use of short reads obtained through next-generation sequencing for primer evaluation has not been well resolved. The software MIPE (MIcrobiota metagenome Primer Explorer) was developed to adapt numerous short reads from metagenomes and metatranscriptomes. Using metagenomic or metatranscriptomic datasets as input, MIPE extracts and aligns rRNA to reveal detailed information on microbial composition and evaluate SSU rRNA primers. A mock dataset, a real Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) test dataset, two PrimerProspector test datasets and a real metatranscriptomic dataset were used to validate MIPE. The software calls Mothur (v1.33.3) and the SILVA database (v119) for the alignment and classification of rRNA genes from a metagenome or metatranscriptome. MIPE can effectively extract shotgun rRNA reads from a metagenome or metatranscriptome and is capable of classifying these sequences and exhibiting sensitivity to different SSU rRNA PCR primers. Therefore, MIPE can be used to guide primer design for specific environmental samples.}, } @article {pmid28350798, year = {2017}, author = {Busby, PE and Soman, C and Wagner, MR and Friesen, ML and Kremer, J and Bennett, A and Morsy, M and Eisen, JA and Leach, JE and Dangl, JL}, title = {Research priorities for harnessing plant microbiomes in sustainable agriculture.}, journal = {PLoS biology}, volume = {15}, number = {3}, pages = {e2001793}, pmid = {28350798}, issn = {1545-7885}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Agriculture/*methods ; Conservation of Natural Resources/*trends ; Food Supply ; *Microbiota ; Plants/*microbiology ; *Research ; Research Design ; }, abstract = {Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One way to assist in achieving these goals is to integrate beneficial plant microbiomes-i.e., those enhancing plant growth, nutrient use efficiency, abiotic stress tolerance, and disease resistance-into agricultural production. This integration will require a large-scale effort among academic researchers, industry researchers, and farmers to understand and manage plant-microbiome interactions in the context of modern agricultural systems. Here, we identify priorities for research in this area: (1) develop model host-microbiome systems for crop plants and non-crop plants with associated microbial culture collections and reference genomes, (2) define core microbiomes and metagenomes in these model systems, (3) elucidate the rules of synthetic, functionally programmable microbiome assembly, (4) determine functional mechanisms of plant-microbiome interactions, and (5) characterize and refine plant genotype-by-environment-by-microbiome-by-management interactions. Meeting these goals should accelerate our ability to design and implement effective agricultural microbiome manipulations and management strategies, which, in turn, will pay dividends for both the consumers and producers of the world food supply.}, } @article {pmid28349946, year = {2017}, author = {Yan, W and Sun, C and Yuan, J and Yang, N}, title = {Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {45308}, pmid = {28349946}, issn = {2045-2322}, mesh = {Amino Acids/metabolism ; Animal Feed ; Animals ; Bacteria/genetics/isolation & purification ; Biodiversity ; Cecum/microbiology ; Chickens ; Duodenum/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Lactobacillus/genetics/*isolation & purification ; *Metagenomics ; Phenotype ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {Interactions between the host and gut microbiota can affect gut metabolism. In this study, the individual performances of 252 hens were recorded to evaluate feed efficiency. Hens with contrasting feed efficiencies (14 birds per group) were selected to investigate their duodenal, cecal and fecal microbial composition by sequencing the 16S rRNA gene V4 region. The results showed that the microbial community in the cecum was quite different from those in the duodenum and feces. The highest biodiversity and all differentially abundant taxa between the different efficiency groups were observed in the cecal microbial community with false discovery rate (FDR) <0.05. Of these differentially abundant cecal microbes, Lactobacillus accounted for a greater proportion than the others. The abundances of Lactobacillus and Akkermansia were significantly higher while that of Faecalibacterium was lower (FDR < 0.05) in the better feed efficiency (BFE) group. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis revealed that the functions relating to glycometabolism and amino acid metabolism were enriched in the cecal microbiota of the BFE group. These results indicated the prominent role of cecal microbiota in the feed efficiency of chickens and suggested plausible uses of Lactobacillus to improve the feed efficiency of host.}, } @article {pmid28349932, year = {2017}, author = {Nunes-Alves, C}, title = {Microbial communities rock.}, journal = {Nature microbiology}, volume = {2}, number = {}, pages = {17041}, doi = {10.1038/nmicrobiol.2017.41}, pmid = {28349932}, issn = {2058-5276}, mesh = {Biotransformation ; *Environmental Microbiology ; Metabolic Networks and Pathways ; Metagenomics/methods/trends ; Microbiological Techniques/methods/trends ; Microbiology/trends ; *Microbiota ; Minerals/metabolism ; }, } @article {pmid28346340, year = {2017}, author = {Waterworth, SC and Jiwaji, M and Kalinski, JJ and Parker-Nance, S and Dorrington, RA}, title = {A Place to Call Home: An Analysis of the Bacterial Communities in Two Tethya rubra Samaai and Gibbons 2005 Populations in Algoa Bay, South Africa.}, journal = {Marine drugs}, volume = {15}, number = {4}, pages = {}, pmid = {28346340}, issn = {1660-3397}, mesh = {Animals ; Bacteria/*genetics ; Bays/*microbiology ; Biodiversity ; DNA, Bacterial/genetics ; Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA/methods ; South Africa ; }, abstract = {Sponges are important sources of bioactive secondary metabolites. These compounds are frequently synthesized by bacterial symbionts, which may be recruited from the surrounding seawater or transferred to the sponge progeny by the parent. In this study, we investigated the bacterial communities associated with the sponge Tethya rubra Samaai and Gibbons 2005. Sponge specimens were collected from Evans Peak and RIY Banks reefs in Algoa Bay, South Africa and taxonomically identified by spicule analysis and molecular barcoding. Crude chemical extracts generated from individual sponges were profiled by ultraviolet high performance liquid chromatography (UV-HPLC) and subjected to bioactivity assays in mammalian cells. Next-generation sequencing analysis of 16S rRNA gene sequences was used to characterize sponge-associated bacterial communities. T. rubra sponges collected from the two locations were morphologically and genetically indistinguishable. Chemical extracts from sponges collected at RIY banks showed mild inhibition of the metabolic activity of mammalian cells and their UV-HPLC profiles were distinct from those of sponges collected at Evans Peak. Similarly, the bacterial communities associated with sponges from the two locations were distinct with evidence of vertical transmission of symbionts from the sponge parent to its embryos. We conclude that these distinct bacterial communities may be responsible for the differences observed in the chemical profiles of the two Algoa Bay T. rubra Samaai and Gibbons 2005 populations.}, } @article {pmid28345793, year = {2017}, author = {Ehrmann, M and Kaiser, M}, title = {Small Molecules from Deep within the Gut.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {18}, number = {11}, pages = {967-968}, doi = {10.1002/cbic.201700165}, pmid = {28345793}, issn = {1439-7633}, mesh = {Humans ; Metagenomics/methods ; Microbiota/*physiology ; Multigene Family ; Peptide Synthases/analysis/genetics ; Physiological Phenomena/*physiology ; Protease Inhibitors ; }, abstract = {Although the influence of the human microbiome on host functions is widely recognized, the underlying molecular mechanisms are still largely unknown. A recent study by the Fischbach group now provides an experimental workflow for characterizing and evaluating the impact of microbiome-derived small molecules on host physiology.}, } @article {pmid28345673, year = {2017}, author = {Xie, G and Wang, X and Zhao, A and Yan, J and Chen, W and Jiang, R and Ji, J and Huang, F and Zhang, Y and Lei, S and Ge, K and Zheng, X and Rajani, C and Alegado, RA and Liu, J and Liu, P and Nicholson, J and Jia, W}, title = {Sex-dependent effects on gut microbiota regulate hepatic carcinogenic outcomes.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {45232}, pmid = {28345673}, issn = {2045-2322}, support = {P30 CA071789/CA/NCI NIH HHS/United States ; U01 CA188387/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification ; Bile Acids and Salts/metabolism ; Carcinoma, Hepatocellular/chemically induced/drug therapy/genetics/*microbiology ; Cholestyramine Resin/pharmacology/therapeutic use ; Diet, High-Fat/*adverse effects ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/drug effects ; Gene Expression Regulation, Neoplastic/drug effects ; Humans ; Incidence ; Liver Neoplasms/chemically induced/genetics/*microbiology ; Male ; Metagenomics/*methods ; Mice ; MicroRNAs/genetics ; Non-alcoholic Fatty Liver Disease/drug therapy/etiology/metabolism/*microbiology ; Sex Factors ; Streptozocin/*adverse effects ; }, abstract = {Emerging evidence points to a strong association between sex and gut microbiota, bile acids (BAs), and gastrointestinal cancers. Here, we investigated the mechanistic link between microbiota and hepatocellular carcinogenesis using a streptozotocin-high fat diet (STZ-HFD) induced nonalcoholic steatohepatitis-hepatocellular carcinoma (NASH-HCC) murine model and compared results for both sexes. STZ-HFD feeding induced a much higher incidence of HCC in male mice with substantially increased intrahepatic retention of hydrophobic BAs and decreased hepatic expression of tumor-suppressive microRNAs. Metagenomic analysis showed differences in gut microbiota involved in BA metabolism between normal male and female mice, and such differences were amplified when mice of both sexes were exposed to STZ-HFD. Treating STZ-HFD male mice with 2% cholestyramine led to significant improvement of hepatic BA retention, tumor-suppressive microRNA expressions, microbial gut communities, and prevention of HCC. Additionally the sex-dependent differences in BA profiles in the murine model can be correlated to the differential BA profiles between men and women during the development of HCC. These results uncover distinct male and female profiles for gut microbiota, BAs, and microRNAs that may contribute to sex-based disparity in liver carcinogenesis, and suggest new possibilities for preventing and controlling human obesity-related gastrointestinal cancers that often exhibit sex differences.}, } @article {pmid28345370, year = {2017}, author = {Pham, DT and Gao, S and Phan, V}, title = {An accurate and fast alignment-free method for profiling microbial communities.}, journal = {Journal of bioinformatics and computational biology}, volume = {15}, number = {3}, pages = {1740001}, doi = {10.1142/S0219720017400017}, pmid = {28345370}, issn = {1757-6334}, mesh = {Databases, Genetic ; Genetic Markers ; Genome ; Metagenomics/*methods ; Microbial Consortia/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Determining abundances of microbial genomes in metagenomic samples is an important problem in analyzing metagenomic data. Although homology-based methods are popular, they have shown to be computationally expensive due to the alignment of tens of millions of reads from metagenomic samples to reference genomes of hundreds to thousands of environmental microbial species. We introduce an efficient alignment-free approach to estimate abundances of microbial genomes in metagenomic samples. The approach is based on solving linear and quadratic programs, which are represented by genome-specific markers (GSM). We compared our method against popular alignment-free and homology-based methods. Without contamination, our method was more accurate than other alignment-free methods while being much faster than a homology-based method. In more realistic settings where samples were contaminated with human DNA, our method was the most accurate method in predicting abundance at varying levels of contamination. We achieve higher accuracy than both alignment-free and homology-based methods.}, } @article {pmid28345059, year = {2017}, author = {Martí, JM and Martínez-Martínez, D and Rubio, T and Gracia, C and Peña, M and Latorre, A and Moya, A and P Garay, C}, title = {Health and Disease Imprinted in the Time Variability of the Human Microbiome.}, journal = {mSystems}, volume = {2}, number = {2}, pages = {}, pmid = {28345059}, issn = {2379-5077}, abstract = {The animal microbiota (including the human microbiota) plays an important role in keeping the physiological status of the host healthy. Research seeks greater insight into whether changes in the composition and function of the microbiota are associated with disease. We analyzed published 16S rRNA and shotgun metagenomic sequencing (SMS) data pertaining to the gut microbiotas of 99 subjects monitored over time. Temporal fluctuations in the microbial composition revealed significant differences due to factors such as dietary changes, antibiotic intake, age, and disease. This article shows that a fluctuation scaling law can describe the temporal changes in the gut microbiota. This law estimates the temporal variability of the microbial population and quantitatively characterizes the path toward disease via a noise-induced phase transition. Estimation of the systemic parameters may be of clinical utility in follow-up studies and have more general applications in fields where it is important to know whether a given community is stable or not. IMPORTANCE The human microbiota correlates closely with the health status of its host. This article analyzes the microbial composition of several subjects under different conditions over time spans that ranged from days to months. Using the Langevin equation as the basis of our mathematical framework to evaluate microbial temporal stability, we proved that stable microbiotas can be distinguished from unstable microbiotas. This initial step will help us to determine how temporal microbiota stability is related to a subject's health status and to develop a more comprehensive framework that will provide greater insight into this complex system.}, } @article {pmid28344519, year = {2017}, author = {Ahsanuddin, S and Afshinnekoo, E and Gandara, J and Hakyemezoğlu, M and Bezdan, D and Minot, S and Greenfield, N and Mason, CE}, title = {Assessment of REPLI-g Multiple Displacement Whole Genome Amplification (WGA) Techniques for Metagenomic Applications.}, journal = {Journal of biomolecular techniques : JBT}, volume = {28}, number = {1}, pages = {46-55}, pmid = {28344519}, issn = {1943-4731}, support = {R01 AI125416/AI/NIAID NIH HHS/United States ; R01 ES021006/ES/NIEHS NIH HHS/United States ; R01 NS076465/NS/NINDS NIH HHS/United States ; R25 EB020393/EB/NIBIB NIH HHS/United States ; }, mesh = {Base Composition ; DNA, Bacterial/genetics/isolation & purification ; *Environmental Microbiology ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics ; Microbiota/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Amplification of minute quantities of DNA is a fundamental challenge in low-biomass metagenomic and microbiome studies because of potential biases in coverage, guanine-cytosine (GC) content, and altered species abundances. Whole genome amplification (WGA), although widely used, is notorious for introducing artifact sequences, either by amplifying laboratory contaminants or by nonrandom amplification of a sample's DNA. In this study, we investigate the effect of REPLI-g multiple displacement amplification (MDA; Qiagen, Valencia, CA, USA) on sequencing data quality and species abundance detection in 8 paired metagenomic samples and 1 titrated, mixed control sample. We extracted and sequenced genomic DNA (gDNA) from 8 environmental samples and compared the quality of the sequencing data for the MDA and their corresponding non-MDA samples. The degree of REPLI-g MDA bias was evaluated by sequence metrics, species composition, and cross-validating observed species abundance and species diversity estimates using the One Codex and MetaPhlAn taxonomic classification tools. Here, we provide evidence of the overall efficacy of REPLI-g MDA on retaining sequencing data quality and species abundance measurements while providing increased yields of high-fidelity DNA. We find that species abundance estimates are largely consistent across samples, even with REPLI-g amplification, as demonstrated by the Spearman's rank order coefficient (R[2] > 0.8). However, REPLI-g MDA often produced fewer classified reads at the species, genera, and family level, resulting in decreased species diversity. We also observed some areas with the PCR "jackpot effect," with varying input DNA values for the Metagenomics Research Group (MGRG) controls at specific genomic loci. We visualize this effect in whole genome coverage plots and with sequence composition analyses and note these caveats of the MDA method. Despite overall concordance of species abundance between the amplified and unamplified samples, these results demonstrate that amplification of DNA using the REPLI-g method has some limitations. These concerns could be addressed by future improvements in the enzymes or methods for REPLI-g to be considered a >99% robust method for increasing the amount of high-fidelity DNA from low-biomass samples or at the very least, accounted for during computational analysis of MDA samples.}, } @article {pmid28342734, year = {2017}, author = {Chen, B and Sun, L and Zhang, X}, title = {Integration of microbiome and epigenome to decipher the pathogenesis of autoimmune diseases.}, journal = {Journal of autoimmunity}, volume = {83}, number = {}, pages = {31-42}, doi = {10.1016/j.jaut.2017.03.009}, pmid = {28342734}, issn = {1095-9157}, mesh = {Animals ; Autoimmune Diseases/*immunology/microbiology ; Dysbiosis/*immunology ; Epigenesis, Genetic ; Epigenomics ; Gastrointestinal Microbiome/*immunology ; Gene-Environment Interaction ; Humans ; Microbiota/*immunology ; T-Lymphocytes, Regulatory/*immunology ; Th17 Cells/*immunology ; Toll-Like Receptors/metabolism ; }, abstract = {The interaction between genetic predisposition and environmental factors are of great significance in the pathogenesis and development of autoimmune diseases (AIDs). The human mucosa is the most frequent site that interacts with the exterior environment, and commensal microbiota at the gut and other human mucosal cavities play a crucial role in the regulation of immune system. Growing evidence has shown that the compositional and functional changes of mucosal microbiota are closely related to AIDs. Gut dysbiosis not only influence the expression level of Toll-like receptors (TLRs) of antigen presenting cells, but also contribute to Th17/Treg imbalance. Epigenetic modifications triggered by environmental factors is an important mechanism that leads to altered gene expression. Researches addressing the role of DNA methylation, histone modification and non-coding RNA in AIDs have been increasing in recent years. Furthermore, studies showed that human microbiota and their metabolites can regulate immune cells and cytokines via epigenomic modifications. For example, short-chain fatty acids (SCFAs) produced by gut microbiota promote the differentiation of naïve T cell into Treg by suppressing histone deacetylases (HDACs). Therefore, we propose that dysbiosis and resulting metabolites may cause aberrant immune responses via epigenetic modifications, and lead to AIDs. With the development of high-throughput sequencing, metagenome analysis has been applied to investigate the dysbiosis in AIDs patients. We have tested the fecal, dental and salivary samples from treatment-naïve rheumatoid arthritis (RA) individuals by metagenomic shotgun sequencing and a metagenome-wide association study. Dysbiosis was detected in the gut and oral microbiomes of RA patients, but it was partially restored after treatment. We also found functional changes of microbiota and molecular mimicry of human antigens in RA individuals. By integrating the analysis of multi-omics of microbiome and epigenome, we could explore the interaction between human immune system and microbiota, and thereby unmasking specific and more sensitive biomarkers as well as potential therapeutic targets. Future studies aiming at the crosstalk between human dysbiosis and epigenetic modifications and their influences on AIDs will facilitate our understanding and better managing of these debilitating AIDs.}, } @article {pmid28338745, year = {2017}, author = {Takayasu, L and Suda, W and Takanashi, K and Iioka, E and Kurokawa, R and Shindo, C and Hattori, Y and Yamashita, N and Nishijima, S and Oshima, K and Hattori, M}, title = {Circadian oscillations of microbial and functional composition in the human salivary microbiome.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {24}, number = {3}, pages = {261-270}, pmid = {28338745}, issn = {1756-1663}, mesh = {Adult ; Bacteria/genetics/*isolation & purification/metabolism ; Bacterial Physiological Phenomena ; *Circadian Rhythm ; Fatty Acids/biosynthesis ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Male ; Metagenome ; RNA, Bacterial ; RNA, Ribosomal, 16S ; Saliva/*microbiology ; Vitamins/biosynthesis ; }, abstract = {The human microbiomes across the body evidently interact with various signals in response to biogeographical physiological conditions. To understand such interactions in detail, we investigated how the salivary microbiome in the oral cavity would be regulated by host-related signals. Here, we show that the microbial abundance and gene participating in keeping the human salivary microbiome exhibit global circadian rhythm. Analysis of the 16S rRNA sequences of salivary microbial samples of six healthy adults collected at 4-h intervals for three days revealed that the microbial genera accounting for 68.4-89.6% of the total abundance were observed to significantly oscillate with the periodicity of ∼24 h. These oscillation patterns showed high variations amongst individuals, and the extent of circadian variations in individuals was generally lower than that of interindividual variations. Of the microbial categories oscillated, those classified by aerobic/anaerobic growth and Gram staining, Firmicutes including Streptococcus and Gemella, and Bacteroidetes including Prevotella showed high association with the circadian oscillation. The circadian oscillation was completely abolished by incubating the saliva in vitro, suggesting that host's physiological changes mostly contributed to the microbial oscillation. Further metagenomic analysis showed that circadian oscillation enriched the functions of environmental responses such as various transporters and two-component regulatory systems in the evening, and those of metabolisms such as the biosynthesis of vitamins and fatty acids in the morning.}, } @article {pmid28338677, year = {2017}, author = {Moitinho-Silva, L and Díez-Vives, C and Batani, G and Esteves, AI and Jahn, MT and Thomas, T}, title = {Integrated metabolism in sponge-microbe symbiosis revealed by genome-centered metatranscriptomics.}, journal = {The ISME journal}, volume = {11}, number = {7}, pages = {1651-1666}, pmid = {28338677}, issn = {1751-7370}, mesh = {Animals ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Gene Expression Regulation/physiology ; In Situ Hybridization, Fluorescence ; *Metagenomics ; Microbiota ; Phylogeny ; Porifera/genetics/*microbiology ; Symbiosis/*physiology ; }, abstract = {Despite an increased understanding of functions in sponge microbiomes, the interactions among the symbionts and between symbionts and host are not well characterized. Here we reconstructed the metabolic interactions within the sponge Cymbastela concentrica microbiome in the context of functional features of symbiotic diatoms and the host. Three genome bins (CcPhy, CcNi and CcThau) were recovered from metagenomic data of C. concentrica, belonging to the proteobacterial family Phyllobacteriaceae, the Nitrospira genus and the thaumarchaeal order Nitrosopumilales. Gene expression was estimated by mapping C. concentrica metatranscriptomic reads. Our analyses indicated that CcPhy is heterotrophic, while CcNi and CcThau are chemolithoautotrophs. CcPhy expressed many transporters for the acquisition of dissolved organic compounds, likely available through the sponge's filtration activity and symbiotic carbon fixation. Coupled nitrification by CcThau and CcNi was reconstructed, supported by the observed close proximity of the cells in fluorescence in situ hybridization. CcPhy facultative anaerobic respiration and assimilation by diatoms may consume the resulting nitrate. Transcriptional analysis of diatom and sponge functions indicated that these organisms are likely sources of organic compounds, for example, creatine/creatinine and dissolved organic carbon, for other members of the symbiosis. Our results suggest that organic nitrogen compounds, for example, creatine, creatinine, urea and cyanate, fuel the nitrogen cycle within the sponge. This study provides an unprecedented view of the metabolic interactions within sponge-microbe symbiosis, bridging the gap between cell- and community-level knowledge.}, } @article {pmid28337070, year = {2017}, author = {Tighe, S and Afshinnekoo, E and Rock, TM and McGrath, K and Alexander, N and McIntyre, A and Ahsanuddin, S and Bezdan, D and Green, SJ and Joye, S and Stewart Johnson, S and Baldwin, DA and Bivens, N and Ajami, N and Carmical, JR and Herriott, IC and Colwell, R and Donia, M and Foox, J and Greenfield, N and Hunter, T and Hoffman, J and Hyman, J and Jorgensen, E and Krawczyk, D and Lee, J and Levy, S and Garcia-Reyero, N and Settles, M and Thomas, K and Gómez, F and Schriml, L and Kyrpides, N and Zaikova, E and Penterman, J and Mason, CE}, title = {Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP).}, journal = {Journal of biomolecular techniques : JBT}, volume = {28}, number = {1}, pages = {31-39}, pmid = {28337070}, issn = {1943-4731}, support = {R01 AI125416/AI/NIAID NIH HHS/United States ; R01 ES021006/ES/NIEHS NIH HHS/United States ; R01 NS076465/NS/NINDS NIH HHS/United States ; R25 EB020393/EB/NIBIB NIH HHS/United States ; }, mesh = {DNA, Bacterial/genetics/isolation & purification ; *Environmental Microbiology ; Extreme Environments ; Metagenome ; Microbiota/*genetics ; Molecular Typing/standards ; RNA, Bacterial/genetics/isolation & purification ; Reference Standards ; Sequence Analysis, DNA/standards ; }, abstract = {The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines. Here, we highlight the different ongoing projects that we have been working on, as well as details on the various methods we use to characterize the microbiome and metagenome of these complex samples. In particular, we present data of a novel multienzyme extraction protocol that we developed, called Polyzyme or MetaPolyZyme. Presently, the XMP is characterizing sample sites around the world with the intent of discovering new species, genes, and gene clusters. Once a project site is complete, the resulting data will be publically available. Sites include Lake Hillier in Western Australia, the "Door to Hell" crater in Turkmenistan, deep ocean brine lakes of the Gulf of Mexico, deep ocean sediments from Greenland, permafrost tunnels in Alaska, ancient microbial biofilms from Antarctica, Blue Lagoon Iceland, Ethiopian toxic hot springs, and the acidic hypersaline ponds in Western Australia.}, } @article {pmid28336973, year = {2017}, author = {Wang, R and Zhang, H and Sun, L and Qi, G and Chen, S and Zhao, X}, title = {Microbial community composition is related to soil biological and chemical properties and bacterial wilt outbreak.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {343}, pmid = {28336973}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics/*isolation & purification ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fungi/classification/genetics/*isolation & purification ; Hydrogen-Ion Concentration ; Metagenomics ; Phosphorus/analysis ; Phylogeny ; Plant Diseases/*microbiology ; Potassium/analysis ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Soil microbes play important roles in plant growth and health. Little is known about the differences of soil microbes between healthy and bacterial wilt infected soils with Ralstonia solanacearum. By Illumina-MiSeq sequencing of 16S rRNA and 18S rRNA gene amplicons, we found the soil microbial composition and diversity were distinct between healthy and bacterial wilt infected soils. Soil microbial community varied at different plant growth stages due to changes of root exudates composition and soil pH. Healthy soils exhibited higher microbial diversity than the bacterial wilt infected soils. More abundant beneficial microbes including Bacillus, Agromyces, Micromonospora, Pseudonocardia, Acremonium, Lysobacter, Mesorhizobium, Microvirga, Bradyrhizobium, Acremonium and Chaetomium were found in the healthy soils rather than the bacterial wilt infected soils. Compared to bacterial wilt infected soils, the activities of catalase, invertase and urease, as well as soil pH, available phosphorous and potassium content, were all significantly increased in the healthy soils. In a conclusion, the higher abundance of beneficial microbes are positively related the higher soil quality, including better plant growth, lower disease incidence, and higher nutrient contents, soil enzyme activities and soil pH.}, } @article {pmid28335651, year = {2017}, author = {Gonzalez, CG and Zhang, L and Elias, JE}, title = {From mystery to mechanism: can proteomics build systems-level understanding of our gut microbes?.}, journal = {Expert review of proteomics}, volume = {14}, number = {6}, pages = {473-476}, doi = {10.1080/14789450.2017.1311211}, pmid = {28335651}, issn = {1744-8387}, mesh = {*Gastrointestinal Microbiome ; Humans ; Metagenome ; Proteome/genetics/metabolism ; Proteomics/*methods ; Systems Biology/*methods ; }, } @article {pmid28334267, year = {2017}, author = {Yarygin, KS and Kovarsky, BA and Bibikova, TS and Melnikov, DS and Tyakht, AV and Alexeev, DG}, title = {ResistoMap-online visualization of human gut microbiota antibiotic resistome.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {14}, pages = {2205-2206}, pmid = {28334267}, issn = {1367-4811}, mesh = {Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial ; Gastrointestinal Microbiome/*drug effects ; Humans ; Metagenome ; Microbiota/*drug effects ; *Software ; }, abstract = {ABSTRACT: We created ResistoMap—a Web-based interactive visualization of the presence of genetic determinants conferring resistance to antibiotics, biocides and heavy metals in human gut microbiota. ResistoMap displays the data on more than 1500 published gut metagenomes of world populations including both healthy subjects and patients. Multiparameter display filters allow visual assessment of the associations between the meta-data and proportions of resistome. The geographic map navigation layer allows to state hypotheses regarding the global trends of antibiotic resistance and correlates the gut resistome variations with the national clinical guidelines on antibiotics application.

ResistoMap was implemented using AngularJS, CoffeeScript, D3.js and TopoJSON. The tool is publicly available at http://resistomap.rcpcm.org.

CONTACT: yarygin@phystech.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid28334218, year = {2017}, author = {Mysara, M and Vandamme, P and Props, R and Kerckhof, FM and Leys, N and Boon, N and Raes, J and Monsieurs, P}, title = {Reconciliation between operational taxonomic units and species boundaries.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {4}, pages = {}, pmid = {28334218}, issn = {1574-6941}, mesh = {Biological Evolution ; Classification ; Cluster Analysis ; DNA Primers ; *Genetic Variation ; *High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The development of high-throughput sequencing technologies has revolutionised the field of microbial ecology via 16S rRNA gene amplicon sequencing approaches. Clustering those amplicon sequencing reads into operational taxonomic units (OTUs) using a fixed cut-off is a commonly used approach to estimate microbial diversity. A 97% threshold was chosen with the intended purpose that resulting OTUs could be interpreted as a proxy for bacterial species. Our results show that the robustness of such a generalised cut-off is questionable when applied to short amplicons only covering one or two variable regions of the 16S rRNA gene. It will lead to biases in diversity metrics and makes it hard to compare results obtained with amplicons derived with different primer sets. The method introduced within this work takes into account the differential evolutional rates of taxonomic lineages in order to define a dynamic and taxonomic-dependent OTU clustering cut-off score. For a taxonomic family consisting of species showing high evolutionary conservation in the amplified variable regions, the cut-off will be more stringent than 97%. By taking into consideration the amplified variable regions and the taxonomic family when defining this cut-off, such a threshold will lead to more robust results and closer correspondence between OTUs and species. This approach has been implemented in a publicly available software package called DynamiC.}, } @article {pmid28331945, year = {2017}, author = {Pereira, MR and Maester, TC and Mercaldi, GF and de Macedo Lemos, EG and Hyvönen, M and Balan, A}, title = {From a metagenomic source to a high-resolution structure of a novel alkaline esterase.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {12}, pages = {4935-4949}, doi = {10.1007/s00253-017-8226-4}, pmid = {28331945}, issn = {1432-0614}, mesh = {Butyrates/metabolism ; Cloning, Molecular ; Crystallization ; Crystallography, X-Ray ; Enzyme Stability ; Esterases/*chemistry/genetics/isolation & purification/*metabolism ; Gene Library ; Hydrogen-Ion Concentration ; Hydrolysis ; Lipase/genetics/isolation & purification/metabolism ; Lipolysis ; *Metagenomics ; Microbial Consortia/*genetics ; Nitrophenols/metabolism ; Recombinant Proteins/chemistry/isolation & purification/metabolism ; Substrate Specificity ; }, abstract = {Esterases catalyze the cleavage and formation of ester bonds and are members of the diverse family of α/β hydrolase fold. They are useful in industries from different sectors, such as food, detergent, fine chemicals, and biofuel production. In a previous work, 30 positive clones for lipolytic activity were identified from a metagenomic library of a microbial consortium specialized in diesel oil degradation. In this study, a putative gene encoding an esterase/lipase, denominated est8, has been cloned and the corresponding protein expressed recombinantly, purified to homogeneity and characterized functional and structurally. We show that the protein codified by est8 gene, denominated Est8, is an alkaline esterase with high catalytic efficiency against p-nitrophenyl acetate and stable in the presence of up to 10% dimethyl sulfoxide. The three-dimensional structure of Est8 was determined at 1.85-Ǻ resolution, allowing the characterization of the substrate-binding pocket and features that rationalize the preference of Est8 for short-chain substrates. In an attempt to increase the size of ligand-binding pocket and enzyme activity against distinct substrates of long chain, we mutated two residues (Met[213] and Phe[217]) that block the substrate channel. A small increase in the reaction velocity for p-nitrophenyl butyrate and p-nitrophenyl valerate hydrolysis was observed. Activity against p-nitrophenyl acetate was reduced. The functional and structural characterization of Est8 is explored in comparison with orthologues.}, } @article {pmid28330508, year = {2017}, author = {Bradley, PH and Pollard, KS}, title = {Proteobacteria explain significant functional variability in the human gut microbiome.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {36}, pmid = {28330508}, issn = {2049-2618}, mesh = {Bacteroidetes/*genetics ; Biodiversity ; Feces/microbiology ; Firmicutes/*genetics ; Gastrointestinal Microbiome/*genetics ; Genetic Variation/*genetics ; Humans ; Metagenome/genetics ; Models, Theoretical ; Proteobacteria/*genetics ; }, abstract = {BACKGROUND: While human gut microbiomes vary significantly in taxonomic composition, biological pathway abundance is surprisingly invariable across hosts. We hypothesized that healthy microbiomes appear functionally redundant due to factors that obscure differences in gene abundance between individuals.

RESULTS: To account for these biases, we developed a powerful test of gene variability called CCoDA, which is applicable to shotgun metagenomes from any environment and can integrate data from multiple studies. Our analysis of healthy human fecal metagenomes from three separate cohorts revealed thousands of genes whose abundance differs significantly and consistently between people, including glycolytic enzymes, lipopolysaccharide biosynthetic genes, and secretion systems. Even housekeeping pathways contain a mix of variable and invariable genes, though most highly conserved genes are significantly invariable. Variable genes tend to be associated with Proteobacteria, as opposed to taxa used to define enterotypes or the dominant phyla Bacteroidetes and Firmicutes.

CONCLUSIONS: These results establish limits on functional redundancy and predict specific genes and taxa that may explain physiological differences between gut microbiomes.}, } @article {pmid28327377, year = {2017}, author = {Kloepfer, KM and Sarsani, VK and Poroyko, V and Lee, WM and Pappas, TE and Kang, T and Grindle, KA and Bochkov, YA and Janga, SC and Lemanske, RF and Gern, JE}, title = {Community-acquired rhinovirus infection is associated with changes in the airway microbiome.}, journal = {The Journal of allergy and clinical immunology}, volume = {140}, number = {1}, pages = {312-315.e8}, pmid = {28327377}, issn = {1097-6825}, support = {U19 AI070503/AI/NIAID NIH HHS/United States ; T32 AI007635/AI/NIAID NIH HHS/United States ; UL1 RR025011/RR/NCRR NIH HHS/United States ; U19 AI104317/AI/NIAID NIH HHS/United States ; P01 HL070831/HL/NHLBI NIH HHS/United States ; K12 HD068371/HD/NICHD NIH HHS/United States ; L40 AI096442/AI/NIAID NIH HHS/United States ; }, mesh = {Community-Acquired Infections/*virology ; Humans ; Metagenome ; Metagenomics ; *Microbial Interactions ; *Microbiota ; Picornaviridae Infections/*virology ; Respiratory Mucosa/*microbiology/*virology ; *Rhinovirus ; }, } @article {pmid28323391, year = {2018}, author = {Martinez-Sañudo, I and Simonato, M and Squartini, A and Mori, N and Marri, L and Mazzon, L}, title = {Metagenomic analysis reveals changes of the Drosophila suzukii microbiota in the newly colonized regions.}, journal = {Insect science}, volume = {25}, number = {5}, pages = {833-846}, doi = {10.1111/1744-7917.12458}, pmid = {28323391}, issn = {1744-7917}, support = {613678//European Union's Seventh Framework Programme/ ; }, mesh = {*Animal Distribution ; Animals ; Bacteria/*classification ; China ; Drosophila/*microbiology ; Europe ; *Gastrointestinal Microbiome ; *Introduced Species ; Japan ; *Metagenome ; Metagenomics ; United States ; }, abstract = {The spotted wing drosophila, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is a highly polyphagous pest of a wide variety of wild or cultivated berry and stone fruit. Originating from Southeast Asia, it has recently invaded a wide range of regions in Europe and North America. It is well known that insect microbiotas may significantly influence several aspects of the host biology and play an important role in invasive species introduction into new areas. However, in spite of the great economic importance of D. suzukii, a limited attention has been given so far to its microbiota. In this study, we present the first in-depth characterization of gut bacterial diversity from field (native and invasive range) and lab-reared populations of this insect. The gut bacterial communities of field insects were dominated, regardless of their origin, by 2 families of the phylum Proteobacteria: Acetobacteraceae and Enterobacteriaceae, while Firmicutes, mainly represented by the family Staphylococcaceae, prevailed in lab-reared population. Locality was the most significant factor in shaping the microbiota of wild flies. Moreover, a negative correlation between diversity and abundance of Enterobacteriaceae and the time elapsed since the establishment of D. suzukii in a new region was observed. Altogether our results indicate that habitat, food resources as well as the colonization phase of a new region contribute to shape the bacterial communities of the invasive species which, in turn, by evolving more quickly, could influence host adaptation in a new environment.}, } @article {pmid28323135, year = {2017}, author = {Ozbayram, EG and Kleinsteuber, S and Nikolausz, M and Ince, B and Ince, O}, title = {Effect of bioaugmentation by cellulolytic bacteria enriched from sheep rumen on methane production from wheat straw.}, journal = {Anaerobe}, volume = {46}, number = {}, pages = {122-130}, doi = {10.1016/j.anaerobe.2017.03.013}, pmid = {28323135}, issn = {1095-8274}, mesh = {Anaerobiosis ; Animals ; Bacteria/*metabolism ; *Biodegradation, Environmental ; *Biotransformation ; Cellulose/*metabolism ; Hydrolysis ; Metagenome ; Metagenomics/methods ; Methane/biosynthesis ; Microbiota ; Rumen/*microbiology ; Sheep ; Triticum/*metabolism/*microbiology ; }, abstract = {The aim of this study was to determine the potential of bioaugmentation with cellulolytic rumen microbiota to enhance the anaerobic digestion of lignocellulosic feedstock. An anaerobic cellulolytic culture was enriched from sheep rumen fluid using wheat straw as substrate under mesophilic conditions. To investigate the effects of bioaugmentation on methane production from straw, the enrichment culture was added to batch reactors in proportions of 2% (Set-1) and 4% (Set-2) of the microbial cell number of the standard inoculum slurry. The methane production in the bioaugmented reactors was higher than in the control reactors. After 30 days of batch incubation, the average methane yield was 154 mLN CH4 gVS[-1] in the control reactors. Addition of 2% enrichment culture did not enhance methane production, whereas in Set-2 the methane yield was increased by 27%. The bacterial communities were examined by 454 amplicon sequencing of 16S rRNA genes, while terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of mcrA genes was applied to analyze the methanogenic communities. The results highlighted that relative abundances of Ruminococcaceae and Lachnospiraceae increased during the enrichment. However, Cloacamonaceae, which were abundant in the standard inoculum, dominated the bacterial communities of all batch reactors. T-RFLP profiles revealed that Methanobacteriales were predominant in the rumen fluid, whereas the enrichment culture was dominated by Methanosarcinales. In the batch rectors, the most abundant methanogens were affiliated to Methanobacteriales and Methanomicrobiales. Our results suggest that bioaugmentation with sheep rumen enrichment cultures can enhance the performance of digesters treating lignocellulosic feedstock.}, } @article {pmid28322295, year = {2017}, author = {Li, TH and Qin, Y and Sham, PC and Lau, KS and Chu, KM and Leung, WK}, title = {Alterations in Gastric Microbiota After H. Pylori Eradication and in Different Histological Stages of Gastric Carcinogenesis.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {44935}, pmid = {28322295}, issn = {2045-2322}, mesh = {Biodiversity ; *Cell Transformation, Neoplastic ; Female ; Gastric Mucosa/*microbiology/*physiology ; Helicobacter Infections/*complications/*microbiology ; *Helicobacter pylori ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Microbiota ; Stomach Neoplasms/*etiology/*pathology ; }, abstract = {The role of bacteria other than Helicobacter pylori (HP) in the stomach remains elusive. We characterized the gastric microbiota in individuals with different histological stages of gastric carcinogenesis and after receiving HP eradication therapy. Endoscopic gastric biopsies were obtained from subjects with HP gastritis, gastric intestinal metaplasia (IM), gastric cancer (GC) and HP negative controls. Gastric microbiota was characterized by Illumina MiSeq platform targeting the 16 S rDNA. Apart from dominant H. pylori, we observed other Proteobacteria including Haemophilus, Serratia, Neisseria and Stenotrophomonas as the major components of the human gastric microbiota. Although samples were largely converged according to the relative abundance of HP, a clear separation of GC and other samples was recovered. Whilst there was a strong inverse association between HP relative abundance and bacterial diversity, this association was weak in GC samples which tended to have lower bacterial diversity compared with other samples with similar HP levels. Eradication of HP resulted in an increase in bacterial diversity and restoration of the relative abundance of other bacteria to levels similar to individuals without HP. In conclusion, HP colonization results in alterations of gastric microbiota and reduction in bacterial diversity, which could be restored by antibiotic treatment.}, } @article {pmid28320307, year = {2017}, author = {Schokker, D and Jansman, AJ and Veninga, G and de Bruin, N and Vastenhouw, SA and de Bree, FM and Bossers, A and Rebel, JM and Smits, MA}, title = {Perturbation of microbiota in one-day old broiler chickens with antibiotic for 24 hours negatively affects intestinal immune development.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {241}, pmid = {28320307}, issn = {1471-2164}, mesh = {Animals ; Animals, Newborn ; Anti-Bacterial Agents/*pharmacology ; Biodiversity ; Chickens/genetics/*immunology/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/*immunology ; Gene Expression Profiling ; Immunohistochemistry ; Immunomodulation/*drug effects ; Male ; Metagenome ; Metagenomics/methods ; Transcriptome ; }, abstract = {BACKGROUND: Gut microbial colonization and development of immune competence are intertwined and are influenced by early-life nutritional, environmental, and management factors. Perturbation of the gut microbiome at young age affects the crosstalk between intestinal bacteria and host cells of the intestinal mucosa.

RESULTS: We investigated the effect of a perturbation of the normal early life microbial colonization of the jejunum in 1-day old chickens. Perturbation was induced by administering 0.8 mg amoxicillin per bird per day) via the drinking water for a period of 24 h. Effects of the perturbation were measured by 16S rRNA profiling of the microbiome and whole genome gene expression analysis. In parallel to what has been observed for other animal species, we hypothesized that such an intervention may have negative impact on immune development. Trends were observed in changes of the composition and diversity of the microbiome when comparing antibiotic treated birds with their controls. in the jejunum, the expression of numerous genes changed, which potentially leads to changes in biological activities of the small intestinal mucosa. Validation of the predicted functional changes was performed by staining immune cells in the small intestinal mucosa and a reduction in the number of macrophage-like (KUL01[+]) cells was observed due to a direct or indirect effect of the antibiotic treatment. We provide evidence that a short, early life antibiotic treatment affects both the intestinal microbiota (temporarily) and mucosal gene expression over a period of 2 weeks.

CONCLUSION: These results underscore the importance of early life microbial colonization of the gut in relation to immune development and the necessity to explore the capabilities of a variety of early life dietary and/or environmental factors to modulate the programming for immune competence in broilers.}, } @article {pmid28318535, year = {2017}, author = {Halderman, AA and Lane, AP}, title = {Organism and Microbiome Analysis: Techniques and Implications for Chronic Rhinosinusitis.}, journal = {Otolaryngologic clinics of North America}, volume = {50}, number = {3}, pages = {521-532}, doi = {10.1016/j.otc.2017.01.004}, pmid = {28318535}, issn = {1557-8259}, mesh = {Bacteria/classification/genetics ; Chronic Disease ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/genetics ; *Microbiota ; Paranasal Sinuses/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rhinitis/*microbiology ; Sinusitis/*microbiology ; }, abstract = {Modern advances in DNA sequencing have allowed for the development of culture-independent techniques with application to infectious and inflammatory conditions, such as rhinosinusitis. Although paradigm-changing discoveries have resulted from molecular microbiologic methods for a number of diseases, insights provided into the role of bacteria in chronic rhinosinusitis have yet to be fully understood to the point of impacting clinical diagnosis and management. As culture-independent techniques continue to evolve and become more refined, it is likely that a better understanding will emerge of how the microbiome influences chronic rhinosinusitis pathogenesis and response to therapy.}, } @article {pmid28318115, year = {2017}, author = {Smith, MW and Herfort, L and Fortunato, CS and Crump, BC and Simon, HM}, title = {Microbial players and processes involved in phytoplankton bloom utilization in the water column of a fast-flowing, river-dominated estuary.}, journal = {MicrobiologyOpen}, volume = {6}, number = {4}, pages = {}, pmid = {28318115}, issn = {2045-8827}, mesh = {Bacteria/*growth & development ; Bacteriophages/*growth & development ; *Biota ; *Estuaries ; Eukaryota/*growth & development ; Metagenomics ; *Water Microbiology ; }, abstract = {Fueled by seasonal phytoplankton blooms, the Columbia River estuary is a natural bioreactor for organic matter transformations. Prior metagenome analyses indicated high abundances of diverse Bacteroidetes taxa in estuarine samples containing phytoplankton. To examine the hypothesis that Bacteroidetes taxa have important roles in phytoplankton turnover, we further analyzed metagenomes from water collected along a salinity gradient at 0, 5, 15, 25, and 33 PSU during bloom events. Size fractions were obtained by using a 3-μm prefilter and 0.2-μm collection filter. Although this approach targeted bacteria by removing comparatively large eukaryotic cells, the metagenome from the ES-5 sample (5 PSU) nevertheless contained an abundance of diatom DNA. Biogeochemical measurements and prior studies indicated that this finding resulted from the leakage of cellular material due to freshwater diatom lysis at low salinity. Relative to the other metagenomes, the bacterial fraction of ES-5 was dramatically depleted of genes annotated as Bacteroidetes and lysogenic bacteriophages, but was overrepresented in DNA of protists and Myxococcales bacterivores. We suggest the following equally plausible scenarios for the microbial response to phytoplankton lysis: (1) Bacteroidetes depletion in the free-living fraction may at least in part be caused by their attachment to fluvial diatoms as the latter are lysed upon contact with low-salinity estuarine waters; (2) diatom particle colonization is likely followed by rapid bacterial growth and lytic phage infection, resulting in depletion of lysogenic bacteriophages and host bacteria; and (3) the subsequent availability of labile organic matter attracted both grazers and predators to feed in this estuarine biogeochemical "hotspot," which may have additionally depleted Bacteroidetes populations. These results represent the first detailed molecular analysis of the microbial response to phytoplankton lysis at the freshwater-brackish water interface in the fast-flowing Columbia River estuary.}, } @article {pmid28306146, year = {2017}, author = {Hasegawa, K and Mansbach, JM and Ajami, NJ and Petrosino, JF and Freishtat, RJ and Teach, SJ and Piedra, PA and Camargo, CA}, title = {The relationship between nasopharyngeal CCL5 and microbiota on disease severity among infants with bronchiolitis.}, journal = {Allergy}, volume = {72}, number = {11}, pages = {1796-1800}, pmid = {28306146}, issn = {1398-9995}, support = {R01 AI127507/AI/NIAID NIH HHS/United States ; R01 AI108588/AI/NIAID NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; R21 HL129909/HL/NHLBI NIH HHS/United States ; R01 AI114552/AI/NIAID NIH HHS/United States ; UH3 OD023253/OD/NIH HHS/United States ; }, mesh = {Bronchiolitis/etiology/*pathology ; Chemokine CCL5 ; Haemophilus ; Humans ; Infant ; Infant, Newborn ; Intensive Care Units ; Length of Stay ; *Microbiota ; Moraxella ; Nasopharynx/*chemistry/microbiology ; }, abstract = {Emerging evidence suggests that the airway microbiota plays an important role in viral bronchiolitis pathobiology. However, little is known about the combined role of airway microbiota and CCL5 in infants with bronchiolitis. In this multicenter prospective cohort study of 1005 infants (age <1 year) hospitalized for bronchiolitis during 2011-2014, we observed statistically significant interactions between nasopharyngeal airway CCL5 levels and microbiota profiles with regard to the risk of both intensive care use (Pinteraction =.02) and hospital length-of-stay ≥3 days (Pinteraction =.03). Among infants with lower CCL5 levels, the Haemophilus-dominant microbiota profile was associated with a higher risk of intensive care use (OR, 3.20; 95%CI, 1.18-8.68; P=.02) and hospital length-of-stay ≥3 days (OR, 4.14; 95%CI, 2.08-8.24; P<.001) compared to the Moraxella-dominant profile. Conversely, among those with higher CCL5 levels, there were no significant associations between the microbiota profiles and these severity outcomes (all P≥.10).}, } @article {pmid28304358, year = {2017}, author = {Flaviani, F and Schroeder, DC and Balestreri, C and Schroeder, JL and Moore, K and Paszkiewicz, K and Pfaff, MC and Rybicki, EP}, title = {A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater.}, journal = {Viruses}, volume = {9}, number = {3}, pages = {}, pmid = {28304358}, issn = {1999-4915}, mesh = {Bacteria/*classification/genetics ; Eukaryota/*classification/genetics ; *Microbiota ; Seawater/*microbiology ; Viruses/*classification/genetics ; }, abstract = {The aquatic microbiome is composed of a multi-phylotype community of microbes, ranging from the numerically dominant viruses to the phylogenetically diverse unicellular phytoplankton. They influence key biogeochemical processes and form the base of marine food webs, becoming food for secondary consumers. Due to recent advances in next-generation sequencing, this previously overlooked component of our hydrosphere is starting to reveal its true diversity and biological complexity. We report here that 250 mL of seawater is sufficient to provide a comprehensive description of the microbial diversity in an oceanic environment. We found that there was a dominance of the order Caudovirales (59%), with the family Myoviridae being the most prevalent. The families Phycodnaviridae and Mimiviridae made up the remainder of pelagic double-stranded DNA (dsDNA) virome. Consistent with this analysis, the Cyanobacteria dominate (52%) the prokaryotic diversity. While the dinoflagellates and their endosymbionts, the superphylum Alveolata dominates (92%) the microbial eukaryotic diversity. A total of 834 prokaryotic, 346 eukaryotic and 254 unique virus phylotypes were recorded in this relatively small sample of water. We also provide evidence, through a metagenomic-barcoding comparative analysis, that viruses are the likely source of microbial environmental DNA (meDNA). This study opens the door to a more integrated approach to oceanographic sampling and data analysis.}, } @article {pmid28296353, year = {2017}, author = {Walker, DM and Leys, JE and Dunham, KE and Oliver, JC and Schiller, EE and Stephenson, KS and Kimrey, JT and Wooten, J and Rogers, MW}, title = {Methodological considerations for detection of terrestrial small-body salamander eDNA and implications for biodiversity conservation.}, journal = {Molecular ecology resources}, volume = {17}, number = {6}, pages = {1223-1230}, doi = {10.1111/1755-0998.12667}, pmid = {28296353}, issn = {1755-0998}, mesh = {Animals ; *Biodiversity ; DNA/genetics/isolation & purification ; Feces/chemistry ; Metagenomics/*methods ; Real-Time Polymerase Chain Reaction ; Skin/chemistry ; Soil/chemistry ; Urodela/*classification/*genetics ; }, abstract = {Environmental DNA (eDNA) can be used as an assessment tool to detect populations of threatened species and provide fine-scale data required to make management decisions. The objectives of this project were to use quantitative PCR (qPCR) to: (i) detect spiked salamander DNA in soil, (ii) quantify eDNA degradation over time, (iii) determine detectability of salamander eDNA in a terrestrial environment using soil, faeces, and skin swabs, (iv) detect salamander eDNA in a mesocosm experiment. Salamander eDNA was positively detected in 100% of skin swabs and 66% of faecal samples and concentrations did not differ between the two sources. However, eDNA was not detected in soil samples collected from directly underneath wild-caught living salamanders. Salamander genomic DNA (gDNA) was detected in all qPCR reactions when spiked into soil at 10.0, 5.0, and 1.0 ng/g soil and spike concentration had a significant effect on detected concentrations. Only 33% of samples showed recoverable eDNA when spiked with 0.25 ng/g soil, which was the low end of eDNA detection. To determine the rate of eDNA degradation, gDNA (1 ng/g soil) was spiked into soil and quantified over seven days. Salamander eDNA concentrations decreased across days, but eDNA was still amplifiable at day 7. Salamander eDNA was detected in two of 182 mesocosm soil samples over 12 weeks (n = 52 control samples; n = 65 presence samples; n = 65 eviction samples). The discrepancy in detection success between experiments indicates the potential challenges for this method to be used as a monitoring technique for small-bodied wild terrestrial salamander populations.}, } @article {pmid28296259, year = {2017}, author = {Apothéloz-Perret-Gentil, L and Cordonier, A and Straub, F and Iseli, J and Esling, P and Pawlowski, J}, title = {Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring.}, journal = {Molecular ecology resources}, volume = {17}, number = {6}, pages = {1231-1242}, doi = {10.1111/1755-0998.12668}, pmid = {28296259}, issn = {1755-0998}, mesh = {*Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Diatoms/classification/*genetics ; Metagenomics/*methods ; Rivers/microbiology ; Switzerland ; }, abstract = {Current biodiversity assessment and biomonitoring are largely based on the morphological identification of selected bioindicator taxa. Recently, several attempts have been made to use eDNA metabarcoding as an alternative tool. However, until now, most applied metabarcoding studies have been based on the taxonomic assignment of sequences that provides reference to morphospecies ecology. Usually, only a small portion of metabarcoding data can be used due to a limited reference database and a lack of phylogenetic resolution. Here, we investigate the possibility to overcome these limitations using a taxonomy-free approach that allows the computing of a molecular index directly from eDNA data without any reference to morphotaxonomy. As a case study, we use the benthic diatoms index, commonly used for monitoring the biological quality of rivers and streams. We analysed 87 epilithic samples from Swiss rivers, the ecological status of which was established based on the microscopic identification of diatom species. We compared the diatom index derived from eDNA data obtained with or without taxonomic assignment. Our taxonomy-free approach yields promising results by providing a correct assessment for 77% of examined sites. The main advantage of this method is that almost 95% of OTUs could be used for index calculation, compared to 35% in the case of the taxonomic assignment approach. Its main limitations are under-sampling and the need to calibrate the index based on the microscopic assessment of diatoms communities. However, once calibrated, the taxonomy-free molecular index can be easily standardized and applied in routine biomonitoring, as a complementary tool allowing fast and cost-effective assessment of the biological quality of watercourses.}, } @article {pmid28295427, year = {2017}, author = {Alcántara-Hernández, RJ and Taş, N and Carlos-Pinedo, S and Durán-Moreno, A and Falcón, LI}, title = {Microbial dynamics in anaerobic digestion reactors for treating organic urban residues during the start-up process.}, journal = {Letters in applied microbiology}, volume = {64}, number = {6}, pages = {438-445}, doi = {10.1111/lam.12734}, pmid = {28295427}, issn = {1472-765X}, mesh = {Anaerobiosis ; Archaea/genetics/*physiology ; Bacteria, Anaerobic/genetics/*physiology ; Biofuels/microbiology ; Bioreactors/*microbiology ; Fermentation ; Methane/metabolism ; Mexico ; Microbial Consortia/genetics/*physiology ; Sewage/*microbiology ; Waste Disposal, Fluid ; Wastewater/microbiology ; }, abstract = {UNLABELLED: Anaerobic digestion of organic residues offers economic benefits via biogas production, still methane (CH4) yield relies on the development of a robust microbial consortia for adequate substrate degradation, among other factors. In this study, we monitor biogas production and changes in the microbial community composition in two semi-continuous stirred tank reactors during the setting process under mesophilic conditions (35°C) using a 16S rDNA high-throughput sequencing method. Reactors were initially inoculated with anaerobic granular sludge from a brewery wastewater treatment plant, and gradually fed organic urban residues (4·0 kg VS m[-3] day[-1]) . The inocula and biomass samples showed changes related to adaptations of the community to urban organic wastes including a higher relative proportion of Clostridiales, with Ruminococcus spp. and Syntrophomonas spp. as recurrent species. Candidatus Cloacamonas spp. (Spirochaetes) also increased from ~2·2% in the inoculum to >10% in the reactor biomass. The new community consolidated the cellulose degradation and the propionate and amino acids fermentation processes. Acetoclastic methanogens were more abundant in the reactor, where Methanosaeta spp. was found as a key player. This study demonstrates a successful use of brewery treatment plant granular sludge to obtain a robust consortium for methane production from urban organic solid waste in Mexico.

This study describes the selection of relevant bacteria and archaea in anaerobic digesters inoculated with anaerobic granular sludge from a brewery wastewater treatment plant. Generally, these sludge granules are used to inoculate reactors digesting organic urban wastes. Though, it is still not clearly understood how micro-organisms respond to substrate variations during the reactor start-up process. After feeding two reactors with organic urban residues, it was found that a broader potential for cellulose degradation was developed including Bacteroidetes, Firmicutes and Spirochaetes. These results clarify the bacterial processes behind new reactors establishment for treating organic wastes in urban areas.}, } @article {pmid28293710, year = {2017}, author = {Xiao, M and Yang, J and Feng, Y and Zhu, Y and Chai, X and Wang, Y}, title = {Metaproteomic strategies and applications for gut microbial research.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {8}, pages = {3077-3088}, doi = {10.1007/s00253-017-8215-7}, pmid = {28293710}, issn = {1432-0614}, mesh = {Bacterial Proteins/genetics/*isolation & purification ; Biomedical Research ; *Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/metabolism/microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Mass Spectrometry ; *Metagenome ; Proteome/genetics/metabolism ; *Proteomics ; }, abstract = {The human intestine hosts various complex microbial communities that are closely associated with multiple health and disease processes. Determining the composition and function of these microbial communities is critical to unveil disease mechanisms and promote human health. Recently, meta-omic strategies have been developed that use high-throughput techniques to provide a wealth of information, thus accelerating the study of gut microbes. Metaproteomics is a newly emerged analytical approach that aims to identify proteins on a large scale in complex environmental microbial communities (e.g., the gut microbiota). This review introduces the recent analytical strategies and applications of metaproteomics, with a focus on advances in gut microbiota research, including a discussion of the limitations and challenges of these approaches.}, } @article {pmid28288568, year = {2017}, author = {Shen-Gunther, J and Wang, Y and Lai, Z and Poage, GM and Perez, L and Huang, TH}, title = {Deep sequencing of HPV E6/E7 genes reveals loss of genotypic diversity and gain of clonal dominance in high-grade intraepithelial lesions of the cervix.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {231}, pmid = {28288568}, issn = {1471-2164}, support = {SC1 GM100806/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; DNA, Viral/chemistry/isolation & purification/metabolism ; Evolution, Molecular ; Female ; Genetic Loci ; Genotype ; High-Throughput Nucleotide Sequencing ; Humans ; Neoplasm Grading ; Oncogene Proteins, Viral/classification/*genetics ; Papillomaviridae/*genetics/metabolism ; Papillomavirus E7 Proteins/classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Uterine Cervical Neoplasms/pathology/virology ; }, abstract = {BACKGROUND: Human papillomavirus (HPV) is the carcinogen of almost all invasive cervical cancer and a major cause of oral and other anogenital malignancies. HPV genotyping by dideoxy (Sanger) sequencing is currently the reference method of choice for clinical diagnostics. However, for samples with multiple HPV infections, genotype identification is singular and occasionally imprecise or indeterminable due to overlapping chromatograms. Our aim was to explore and compare HPV metagenomes in abnormal cervical cytology by deep sequencing for correlation with disease states.

RESULTS: Low- and high-grade intraepithelial lesion (LSIL and HSIL) cytology samples were DNA extracted for PCR-amplification of the HPV E6/E7 genes. HPV+ samples were sequenced by dideoxy and deep methods. Deep sequencing revealed ~60% of all samples (n = 72) were multi-HPV infected. Among LSIL samples (n = 43), 27 different genotypes were found. The 3 dominant (most abundant) genotypes were: HPV-39, 11/43 (26%); -16, 9/43 (21%); and -35, 4/43 (9%). Among HSIL (n = 29), 17 HPV genotypes were identified; the 3 dominant genotypes were: HPV-16, 21/29 (72%); -35, 4/29 (14%); and -39, 3/29 (10%). Phylogenetically, type-specific E6/E7 genetic distances correlated with carcinogenic potential. Species diversity analysis between LSIL and HSIL revealed loss of HPV diversity and domination by HPV-16 in HSIL samples.

CONCLUSIONS: Deep sequencing resolves HPV genotype composition within multi-infected cervical cytology. Biodiversity analysis reveals loss of diversity and gain of dominance by carcinogenic genotypes in high-grade cytology. Metagenomic profiles may therefore serve as a biomarker of disease severity and a population surveillance tool for emerging genotypes.}, } @article {pmid28285978, year = {2017}, author = {Raoult, D}, title = {The study of microbiota needs both microbiologists and medical doctors.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {23}, number = {8}, pages = {500-501}, doi = {10.1016/j.cmi.2017.03.002}, pmid = {28285978}, issn = {1469-0691}, mesh = {Bacteria, Aerobic/classification/growth & development ; Bacteria, Anaerobic/classification/growth & development ; Colon/microbiology ; Feces/microbiology ; Humans ; Metagenomics/methods ; *Microbiology/education/trends ; *Microbiota ; *Physicians ; }, } @article {pmid28285599, year = {2017}, author = {Ryan, PM and London, LE and Bjorndahl, TC and Mandal, R and Murphy, K and Fitzgerald, GF and Shanahan, F and Ross, RP and Wishart, DS and Caplice, NM and Stanton, C}, title = {Microbiome and metabolome modifying effects of several cardiovascular disease interventions in apo-E[-/-] mice.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {30}, pmid = {28285599}, issn = {2049-2618}, support = {K01 DK002970/DK/NIDDK NIH HHS/United States ; }, mesh = {Acetates/metabolism ; Animals ; Apolipoproteins E/*deficiency ; Atherosclerosis ; Atorvastatin/administration & dosage ; Butyrates/metabolism ; Cardiovascular Diseases/drug therapy ; Carnitine/analogs & derivatives/blood ; Cholesterol/metabolism ; Cholesterol, Dietary/administration & dosage ; Diet, High-Fat ; Dietary Supplements ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Hemiterpenes ; Limosilactobacillus reuteri ; Male ; *Metabolome ; Mice ; Obesity ; Pentanoic Acids/metabolism ; Probiotics ; beta-Glucans/administration & dosage ; }, abstract = {BACKGROUND: There is strong evidence indicating that gut microbiota have the potential to modify, or be modified by the drugs and nutritional interventions that we rely upon. This study aims to characterize the compositional and functional effects of several nutritional, neutraceutical, and pharmaceutical cardiovascular disease interventions on the gut microbiome, through metagenomic and metabolomic approaches. Apolipoprotein-E-deficient mice were fed for 24 weeks either high-fat/cholesterol diet alone (control, HFC) or high-fat/cholesterol in conjunction with one of three dietary interventions, as follows: plant sterol ester (PSE), oat β-glucan (OBG) and bile salt hydrolase-active Lactobacillus reuteri APC 2587 (BSH), or the drug atorvastatin (STAT). The gut microbiome composition was then investigated, in addition to the host fecal and serum metabolome.

RESULTS: We observed major shifts in the composition of the gut microbiome of PSE mice, while OBG and BSH mice displayed more modest fluctuations, and STAT showed relatively few alterations. Interestingly, these compositional effects imparted by PSE were coupled with an increase in acetate and reduction in isovalerate (p < 0.05), while OBG promoted n-butyrate synthesis (p < 0.01). In addition, PSE significantly dampened the microbial production of the proatherogenic precursor compound, trimethylamine (p < 0.05), attenuated cholesterol accumulation, and nearly abolished atherogenesis in the model (p < 0.05). However, PSE supplementation produced the heaviest mice with the greatest degree of adiposity (p < 0.05). Finally, PSE, OBG, and STAT all appeared to have considerable impact on the host serum metabolome, including alterations in several acylcarnitines previously associated with a state of metabolic dysfunction (p < 0.05).

CONCLUSIONS: We observed functional alterations in microbial and host-derived metabolites, which may have important implications for systemic metabolic health, suggesting that cardiovascular disease interventions may have a significant impact on the microbiome composition and functionality. This study indicates that the gut microbiome-modifying effects of novel therapeutics should be considered, in addition to the direct host effects.}, } @article {pmid28284522, year = {2017}, author = {Jose, VL and More, RP and Appoothy, T and Arun, AS}, title = {In depth analysis of rumen microbial and carbohydrate-active enzymes profile in Indian crossbred cattle.}, journal = {Systematic and applied microbiology}, volume = {40}, number = {3}, pages = {160-170}, doi = {10.1016/j.syapm.2017.02.003}, pmid = {28284522}, issn = {1618-0984}, mesh = {Animals ; Biodiversity ; Cattle ; Cluster Analysis ; Data Mining ; *Hydrolases/classification/genetics ; Metagenome ; Metagenomics ; *Microbiota ; Rumen/*microbiology ; }, abstract = {Rumen houses a plethora of symbiotic microorganisms empowering the host to hydrolyze plant lignocellulose. In this study, NGS based metagenomic approach coupled with bioinformatic analysis was employed to gain an insight into the deconstruction of lignocellulose by carbohydrate-active enzymes (CAZymes) in Indian crossbred Holstein-Friesian cattle. Cattle rumen metagenomic DNA was sequenced using Illumina-MiSeq and 1.9 gigabases of data generated with an average read length of 871 bp. Analysis of the assembled sequences by Pfam-based Carbohydrate-active enzyme Analysis Toolkit identified 17,164 putative protein-encoding CAZymes belonging to different families of glycoside hydrolases (7574), glycosyltransferases (5185), carbohydrate-binding modules (2418), carbohydrate esterases (1516), auxiliary activities (434) and polysaccharide lyases (37). Phylogenetic analysis of putative CAZymes revealed that a significant proportion of CAZymes were contributed by bacteria belonging to the phylum Bacteroidetes (40%), Firmicutes (30%) and Proteobacteria (10%). The comparative analysis of HF cross rumen metagenome with other herbivore metagenomes indicated that Indian crossbred cattle rumen is endowed with a battery of CAZymes that may play a central role in lignocellulose deconstruction. The extensive catalog of enzymes reported in our study that hydrolyzes plant lignocellulose biomass, can be further explored for the better feed utilization in ruminants and also for different industrial applications.}, } @article {pmid28283029, year = {2017}, author = {Weil, T and De Filippo, C and Albanese, D and Donati, C and Pindo, M and Pavarini, L and Carotenuto, F and Pasqui, M and Poto, L and Gabrieli, J and Barbante, C and Sattler, B and Cavalieri, D and Miglietta, F}, title = {Legal immigrants: invasion of alien microbial communities during winter occurring desert dust storms.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {32}, pmid = {28283029}, issn = {2049-2618}, mesh = {Africa, Northern ; *Air Microbiology ; Bacteria/classification/genetics/*isolation & purification/pathogenicity ; Biodiversity ; Climate Change ; *Desert Climate ; Dust/*analysis ; Ecosystem ; Global Warming ; Italy ; Metagenomics ; Microbial Consortia ; *Microbiota ; Public Health ; Seasons ; Silicon Dioxide ; *Wind ; }, abstract = {BACKGROUND: A critical aspect regarding the global dispersion of pathogenic microorganisms is associated with atmospheric movement of soil particles. Especially, desert dust storms can transport alien microorganisms over continental scales and can deposit them in sensitive sink habitats. In winter 2014, the largest ever recorded Saharan dust event in Italy was efficiently deposited on the Dolomite Alps and was sealed between dust-free snow. This provided us the unique opportunity to overcome difficulties in separating dust associated from "domestic" microbes and thus, to determine with high precision microorganisms transported exclusively by desert dust.

RESULTS: Our metagenomic analysis revealed that sandstorms can move not only fractions but rather large parts of entire microbial communities far away from their area of origin and that this microbiota contains several of the most stress-resistant organisms on Earth, including highly destructive fungal and bacterial pathogens. In particular, we provide first evidence that winter-occurring dust depositions can favor a rapid microbial contamination of sensitive sink habitats after snowmelt.

CONCLUSIONS: Airborne microbial depositions accompanying extreme meteorological events represent a realistic threat for ecosystem and public health. Therefore, monitoring the spread and persistence of storm-travelling alien microbes is a priority while considering future trajectories of climatic anomalies as well as anthropogenically driven changes in land use in the source regions.}, } @article {pmid28282386, year = {2017}, author = {Pages-Monteiro, L and Marti, R and Commun, C and Alliot, N and Bardel, C and Meugnier, H and Perouse-de-Montclos, M and Reix, P and Durieu, I and Durupt, S and Vandenesch, F and Freney, J and Cournoyer, B and Doleans-Jordheim, A}, title = {Strong incidence of Pseudomonas aeruginosa on bacterial rrs and ITS genetic structures of cystic fibrosis sputa.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0173022}, pmid = {28282386}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics/isolation & purification ; Cluster Analysis ; Cystic Fibrosis/*complications/diagnosis ; DNA, Bacterial/genetics/*metabolism ; Electrophoresis, Gel, Pulsed-Field ; Genetic Variation ; Humans ; Incidence ; Metagenomics ; Microbial Sensitivity Tests ; Microbiota ; Polymerase Chain Reaction ; Pseudomonas Infections/*complications/epidemiology/microbiology ; Pseudomonas aeruginosa/drug effects/genetics/isolation & purification ; RNA, Ribosomal/genetics/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; Sputum/*microbiology ; }, abstract = {Cystic fibrosis (CF) lungs harbor a complex community of interacting microbes, including pathogens like Pseudomonas aeruginosa. Meta-taxogenomic analysis based on V5-V6 rrs PCR products of 52 P. aeruginosa-positive (Pp) and 52 P. aeruginosa-negative (Pn) pooled DNA extracts from CF sputa suggested positive associations between P. aeruginosa and Stenotrophomonas and Prevotella, but negative ones with Haemophilus, Neisseria and Burkholderia. Internal Transcribed Spacer analyses (RISA) from individual DNA extracts identified three significant genetic structures within the CF cohorts, and indicated an impact of P. aeruginosa. RISA clusters Ip and IIIp contained CF sputa with a P. aeruginosa prevalence above 93%, and of 24.2% in cluster IIp. Clusters Ip and IIIp showed lower RISA genetic diversity and richness than IIp. Highly similar cluster IIp RISA profiles were obtained from two patients harboring isolates of a same P. aeruginosa clone, suggesting convergent evolution in the structure of their microbiota. CF patients of cluster IIp had received significantly less antibiotics than patients of clusters Ip and IIIp but harbored the most resistant P. aeruginosa strains. Patients of cluster IIIp were older than those of Ip. The effects of P. aeruginosa on the RISA structures could not be fully dissociated from the above two confounding factors but several trends in these datasets support the conclusion of a strong incidence of P. aeruginosa on the genetic structure of CF lung microbiota.}, } @article {pmid28280715, year = {2017}, author = {de Moraes, AC and Fernandes, GR and da Silva, IT and Almeida-Pititto, B and Gomes, EP and Pereira, AD and Ferreira, SR}, title = {Enterotype May Drive the Dietary-Associated Cardiometabolic Risk Factors.}, journal = {Frontiers in cellular and infection microbiology}, volume = {7}, number = {}, pages = {47}, pmid = {28280715}, issn = {2235-2988}, mesh = {Adult ; Bacteria/classification/genetics ; Brazil/epidemiology ; Cardiovascular Diseases/*epidemiology ; Cholesterol, LDL/*blood ; Cross-Sectional Studies ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Feeding Behavior ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; Sequence Analysis, DNA ; }, abstract = {Analyses of typical bacterial clusters in humans named enterotypes may facilitate understanding the host differences in the cardiometabolic profile. It stills unknown whether the three previously described enterotypes were present in populations living below the equator. We examined how the identification of enterotypes could be useful to explain the dietary associations with cardiometabolic risk factors in Brazilian subjects. In this cross-sectional study, a convenience sample of 268 adults (54.2% women) reported their dietary habits and had clinical and biological samples collected. In this study, we analyzed biochemical data and metagenomics of fecal microbiota (16SrRNA sequencing, V4 region). Continuous variables were compared using ANOVA, and categorical variables using chi-square test. Vsearch clustered the operational taxonomic units, and Silva Database provided the taxonomic signatures. Spearman coefficient was used to verify the correlation between bacteria abundances within each enterotype. One hundred subjects were classified as omnivore, 102 lacto-ovo-vegetarians, and 66 strict vegetarians. We found the same structure as the three previously described enterotypes: 111 participants were assigned to Bacteroides, 55 to Prevotella, and 102 to Ruminococcaceae enterotype. The Prevotella cluster contained higher amount of strict vegetarians individuals than the other enterotypes (40.0 vs. 20.7 and 20.6, p = 0.04). Subjects in this enterotype had a similar anthropometric profile but a lower mean LDL-c concentration than the Bacteroides enterotype (96 ± 23 vs. 109 ± 32 mg/dL, p = 0.04). We observed significant correlations between bacterial abundances and cardiometabolic risk factors, but coefficients differed depending on the enterotype. In Prevotella enterotype, Eubacterium ventriosum (r BMI = -0.33, p = 0.03, and r HDL-c = 0.33, p = 0.04), Akkermansia (r 2h glucose = -0.35, p = 0.02), Roseburia (r BMI = -0.36, p = 0.02 and r waist = -0.36, p = 0.02), and Faecalibacterium (r insulin = -0.35, p = 0.02) abundances were associated to better cardiometabolic profile. The three enterotypes previously described are present in Brazilians, supporting that those bacterial clusters are not population-specific. Diet-independent lower LDL-c levels in subjects from Prevotella than in other enterotypes suggest that a protective bacterial cluster in the former should be driving this association. Enterotypes seem to be useful to understand the impact of daily diet exposure on cardiometabolic risk factors. Prospective studies are needed to confirm their utility for predicting phenotypes in humans.}, } @article {pmid28279330, year = {2017}, author = {Turnbaugh, PJ}, title = {Microbes and Diet-Induced Obesity: Fast, Cheap, and Out of Control.}, journal = {Cell host & microbe}, volume = {21}, number = {3}, pages = {278-281}, pmid = {28279330}, issn = {1934-6069}, support = {P30 DK063720/DK/NIDDK NIH HHS/United States ; P30 DK098722/DK/NIDDK NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Cytosol/chemistry ; Diet/*adverse effects/*methods ; Gastrointestinal Microbiome/*drug effects ; Humans ; *Obesity ; }, abstract = {Here I revisit our early experiments published in Cell Host & Microbe (Turnbaugh et al., 2008) showing that a diet rich in fat and simple sugars alters the gut microbiome in a manner that contributes to host adiposity, and reflect upon the remarkable advances and remaining challenges in this field.}, } @article {pmid28279152, year = {2017}, author = {Burke, DG and Fouhy, F and Harrison, MJ and Rea, MC and Cotter, PD and O'Sullivan, O and Stanton, C and Hill, C and Shanahan, F and Plant, BJ and Ross, RP}, title = {The altered gut microbiota in adults with cystic fibrosis.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {58}, pmid = {28279152}, issn = {1471-2180}, mesh = {Administration, Intravenous ; Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/*classification ; Bacteroidetes ; Biodiversity ; Classification ; Cystic Fibrosis/*complications/*microbiology ; DNA, Bacterial ; Feces/microbiology ; Female ; Firmicutes ; *Gastrointestinal Microbiome/drug effects ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; Metagenome ; Middle Aged ; Phenotype ; Probiotics ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {BACKGROUND: Cystic Fibrosis (CF) is an autosomal recessive disease that affects the function of a number of organs, principally the lungs, but also the gastrointestinal tract. The manifestations of cystic fibrosis transmembrane conductance regulator (CFTR) dysfunction in the gastrointestinal tract, as well as frequent antibiotic exposure, undoubtedly disrupts the gut microbiota. To analyse the effects of CF and its management on the microbiome, we compared the gut microbiota of 43 individuals with CF during a period of stability, to that of 69 non-CF controls using 454-pyrosequencing of the 16S rRNA gene. The impact of clinical parameters, including antibiotic therapy, on the results was also assessed.

RESULTS: The CF-associated microbiome had reduced microbial diversity, an increase in Firmicutes and a reduction in Bacteroidetes compared to the non-CF controls. While the greatest number of differences in taxonomic abundances of the intestinal microbiota was observed between individuals with CF and the healthy controls, gut microbiota differences were also reported between people with CF when grouped by clinical parameters including % predicted FEV1 (measure of lung dysfunction) and the number of intravenous (IV) antibiotic courses in the previous 12 months. Notably, CF individuals presenting with severe lung dysfunction (% predicted FEV1 ≤ 40%) had significantly (p < 0.05) reduced gut microbiota diversity relative to those presenting with mild or moderate dysfunction. A significant negative correlation (-0.383, Simpson's Diversity Index) was also observed between the number of IV antibiotic courses and gut microbiota diversity.

CONCLUSIONS: This is one of the largest single-centre studies on gut microbiota in stable adults with CF and demonstrates the significantly altered gut microbiota, including reduced microbial diversity seen in CF patients compared to healthy controls. The data show the impact that CF and it's management have on gut microbiota, presenting the opportunity to develop CF specific probiotics to minimise microbiota alterations.}, } @article {pmid28279074, year = {2019}, author = {Tricò, D and Di Sessa, A and Caprio, S and Chalasani, N and Liu, W and Liang, T and Graf, J and Herzog, RI and Johnson, CD and Umano, GR and Feldstein, AE and Santoro, N}, title = {Oxidized Derivatives of Linoleic Acid in Pediatric Metabolic Syndrome: Is Their Pathogenic Role Modulated by the Genetic Background and the Gut Microbiota?.}, journal = {Antioxidants & redox signaling}, volume = {30}, number = {2}, pages = {241-250}, pmid = {28279074}, issn = {1557-7716}, support = {R01 DK049230/DK/NIDDK NIH HHS/United States ; R01 DK111038/DK/NIDDK NIH HHS/United States ; P30 DK045735/DK/NIDDK NIH HHS/United States ; R01 DK101984/DK/NIDDK NIH HHS/United States ; R01 HD028016/HD/NICHD NIH HHS/United States ; R01 HD040787/HD/NICHD NIH HHS/United States ; UL1 RR024139/RR/NCRR NIH HHS/United States ; }, mesh = {Adolescent ; Age Factors ; Biomarkers ; Child ; Delta-5 Fatty Acid Desaturase ; *Disease Susceptibility ; Fatty Acid Desaturases/genetics/metabolism ; Female ; Gastrointestinal Microbiome ; Genetic Background ; Genetic Predisposition to Disease ; Haplotypes ; Humans ; Linoleic Acid/*metabolism ; Lipid Metabolism ; Lipoproteins/metabolism ; Male ; Metabolic Syndrome/blood/*etiology/*metabolism ; Metabolome ; Obesity/complications/metabolism ; *Oxidation-Reduction ; }, abstract = {We tested whether oxidized linoleic acid metabolites (OXLAM) are associated with pediatric metabolic syndrome (MetS) and a proatherogenic lipoprotein profile in 122 obese adolescents. Furthermore, we examined whether genetic and metagenomic factors can modulate plasma OXLAM concentrations by genotyping the fatty acid desaturase 1/2 (FADS) gene and by characterizing the gut microbiota. Subjects with MetS (n = 50) showed higher concentrations of 9- and 13-oxo-octadecadienoic acid (9- and 13-oxo-ODE) than subjects without MetS (n = 72). Both metabolites were associated with an adverse lipoprotein profile that was characterized by elevated very small-dense low-density lipoprotein (p < 0.005) and large very low-density lipoprotein particles (p = 0.01). Plasma 9- and 13-oxo-ODE were higher in subjects carrying the haplotype AA of the FADS gene cluster (p = 0.030 and p = 0.048, respectively). Furthermore, the reduced gut bacterial load was associated with higher 9-oxo-ODE concentrations (p = 0.035). This is the first study showing that high plasma OXLAM concentrations are associated with MetS and suggesting that the leading factors for high plasma concentrations of OXLAM might be the genetic background and the composition of the gut microbiota. In conclusion, high concentrations of 9- and 13-oxo-ODE, which may be the result of a genetic predisposition and a reduced gut bacterial load, are associated with MetS and with a proatherogenic lipoprotein profile in obese adolescents.}, } @article {pmid28278278, year = {2017}, author = {Vientós-Plotts, AI and Ericsson, AC and Rindt, H and Grobman, ME and Graham, A and Bishop, K and Cohn, LA and Reinero, CR}, title = {Dynamic changes of the respiratory microbiota and its relationship to fecal and blood microbiota in healthy young cats.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0173818}, pmid = {28278278}, issn = {1932-6203}, support = {K01 OD019924/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria ; Biomarkers/*analysis ; Blood/*microbiology ; Cats ; DNA, Bacterial/genetics ; Feces/*microbiology ; Female ; Male ; *Microbiota ; Respiratory Mucosa/*metabolism/*microbiology ; }, abstract = {Advances in the field of metagenomics using culture-independent methods of microbial identification have allowed characterization of rich and diverse communities of bacteria in the lungs of healthy humans, mice, dogs, sheep and pigs. These data challenge the long held belief that the lungs are sterile and microbial colonization is synonymous with pathology. Studies in humans and animals demonstrate differences in the composition of airway microbiota in health versus disease suggesting respiratory dysbiosis occurs. Using 16S rRNA amplicon sequencing of DNA extracted from rectal and oropharyngeal (OP) swabs, bronchoalveolar lavage fluid (BALF), and blood, our objective was to characterize the fecal, OP, blood, and lower airway microbiota over time in healthy cats. This work in healthy cats, a species in which a respiratory microbiota has not yet been characterized, sets the stage for future studies in feline asthma in which cats serve as a comparative and translational model for humans. Fecal, OP and BALF samples were collected from six healthy research cats at day 0, week 2, and week 10; blood was collected at week 10. DNA was extracted, amplified via PCR, and sequenced using the Illumina MiSeq platform. Representative operational taxonomic units (OTUs) were identified and microbial richness and diversity were assessed. Principal component analysis (PCA) was used to visualize relatedness of samples and PERMANOVA was used to test for significant differences in microbial community composition. Fecal and OP swabs provided abundant DNA yielding a mean±SEM of 65,653±6,145 and 20,6323±4,360 sequences per sample, respectively while BALF and blood samples had lower coverage (1,489±430 and 269±18 sequences per sample, respectively). Oropharyngeal and fecal swabs were significantly richer than BALF (mean number OTUs 93, 88 and 36, respectively; p < 0.001) with no significant difference (p = 0.180) in richness between time points. PCA revealed site-specific microbial communities in the feces, and upper and lower airways. In comparison, blood had an apparent compositional similarity with BALF with regard to a few dominant taxa, but shared more OTUs with feces. Samples clustered more by time than by individual, with OP swabs having subjectively greater variation than other samples. In summary, healthy cats have a rich and distinct lower airway microbiome with dynamic bacterial populations. The microbiome is likely to be altered by factors such as age, environmental influences, and disease states. Further data are necessary to determine how the distinct feline microbiomes from the upper and lower airways, feces and blood are established and evolve. These data are relevant for comparisons between healthy cats and cats with respiratory disease.}, } @article {pmid28274256, year = {2017}, author = {Pammi, M and Cope, J and Tarr, PI and Warner, BB and Morrow, AL and Mai, V and Gregory, KE and Kroll, JS and McMurtry, V and Ferris, MJ and Engstrand, L and Lilja, HE and Hollister, EB and Versalovic, J and Neu, J}, title = {Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {31}, pmid = {28274256}, issn = {2049-2618}, support = {UL1 RR024992/RR/NCRR NIH HHS/United States ; UH3 AI083265/AI/NIAID NIH HHS/United States ; R01 HD059140/HD/NICHD NIH HHS/United States ; UL1 RR025758/RR/NCRR NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; K23 NR011320/NR/NINR NIH HHS/United States ; }, mesh = {Bacteria/isolation & purification ; Bacteroides/genetics/isolation & purification ; *Dysbiosis ; Enterocolitis, Necrotizing/*microbiology ; Feces/*microbiology ; Firmicutes/genetics/isolation & purification ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Infant, Premature ; Infant, Premature, Diseases ; Intestines/microbiology/*physiopathology ; Proteobacteria/genetics/isolation & purification ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Necrotizing enterocolitis (NEC) is a catastrophic disease of preterm infants, and microbial dysbiosis has been implicated in its pathogenesis. Studies evaluating the microbiome in NEC and preterm infants lack power and have reported inconsistent results.

METHODS AND RESULTS: Our objectives were to perform a systematic review and meta-analyses of stool microbiome profiles in preterm infants to discern and describe microbial dysbiosis prior to the onset of NEC and to explore heterogeneity among studies. We searched MEDLINE, PubMed, CINAHL, and conference abstracts from the proceedings of Pediatric Academic Societies and reference lists of relevant identified articles in April 2016. Studies comparing the intestinal microbiome in preterm infants who developed NEC to those of controls, using culture-independent molecular techniques and reported α and β-diversity metrics, and microbial profiles were included. In addition, 16S ribosomal ribonucleic acid (rRNA) sequence data with clinical meta-data were requested from the authors of included studies or searched in public data repositories. We reprocessed the 16S rRNA sequence data through a uniform analysis pipeline, which were then synthesized by meta-analysis. We included 14 studies in this review, and data from eight studies were available for quantitative synthesis (106 NEC cases, 278 controls, 2944 samples). The age of NEC onset was at a mean ± SD of 30.1 ± 2.4 weeks post-conception (n = 61). Fecal microbiome from preterm infants with NEC had increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes prior to NEC onset. Alpha- or beta-diversity indices in preterm infants with NEC were not consistently different from controls, but we found differences in taxonomic profiles related to antibiotic exposure, formula feeding, and mode of delivery. Exploring heterogeneity revealed differences in microbial profiles by study and the target region of the 16S rRNA gene (V1-V3 or V3-V5).

CONCLUSIONS: Microbial dysbiosis preceding NEC in preterm infants is characterized by increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes. Microbiome optimization may provide a novel strategy for preventing NEC.}, } @article {pmid28272447, year = {2017}, author = {Jia, H and Hanate, M and Aw, W and Itoh, H and Saito, K and Kobayashi, S and Hachimura, S and Fukuda, S and Tomita, M and Hasebe, Y and Kato, H}, title = {Eggshell membrane powder ameliorates intestinal inflammation by facilitating the restitution of epithelial injury and alleviating microbial dysbiosis.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43993}, pmid = {28272447}, issn = {2045-2322}, mesh = {Animals ; Antimicrobial Cationic Peptides/metabolism/*pharmacology/therapeutic use ; Caco-2 Cells ; Cell Proliferation/drug effects ; Colitis/chemically induced/pathology/prevention & control/veterinary ; Dextran Sulfate/toxicity ; *Dysbiosis ; Egg Shell/*metabolism ; Energy Metabolism/drug effects ; Enterobacteriaceae/drug effects/genetics ; Gastrointestinal Microbiome/*drug effects ; Humans ; Interleukin-6/metabolism ; Intestinal Mucosa/drug effects/*metabolism ; Lipopolysaccharides/toxicity ; Male ; Mice ; Mice, Inbred C57BL ; Th17 Cells/cytology/drug effects/metabolism ; Transcriptome/drug effects ; }, abstract = {Gut microbiota is an essential factor in the shaping of intestinal immune system development and driving inflammation in inflammatory bowel disease (IBD). We report the effects and microbe-host interactions underlying an intervention using fine powder of eggshell membrane (ESM) against IBD. ESM attenuated lipopolysaccharide-induced inflammatory cytokine production and promoted the Caco-2 cell proliferation by up-regulating growth factors in vitro. In a murine model of dextran sodium sulphate-induced colitis, ESM significantly suppressed the disease activity index and colon shortening. These effects were associated with significant ameliorations of gene expressions of inflammatory mediators, intestinal epithelial cell proliferation, restitution-related factors and antimicrobial peptides. Multifaceted integrated omics analyses revealed improved levels of energy metabolism-related genes, proteins and metabolites. Concomitantly, cecal metagenomic information established an essential role of ESM in improving dysbiosis characterized by increasing the diversity of bacteria and decreasing absolute numbers of pathogenic bacteria such as Enterobacteriaceae and E. coli, as well as in the regulation of the expansion of Th17 cells by suppressing the overgrowth of segmented filamentous bacteria. Such modulations have functional effects on the host; i.e., repairing the epithelium, regulating energy requirements and eventually alleviating mucosal inflammation. These findings are first insights into ESM's modulation of microbiota and IBD suppression, providing new perspectives on the prevention/treatment of IBD.}, } @article {pmid28272161, year = {2017}, author = {Robinson, A and Fiechtner, L and Roche, B and Ajami, NJ and Petrosino, JF and Camargo, CA and Taveras, EM and Hasegawa, K}, title = {Association of Maternal Gestational Weight Gain With the Infant Fecal Microbiota.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {65}, number = {5}, pages = {509-515}, pmid = {28272161}, issn = {1536-4801}, support = {P30 DK040561/DK/NIDDK NIH HHS/United States ; R25 DK103579/DK/NIDDK NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; R21 HL129909/HL/NHLBI NIH HHS/United States ; R01 AI114552/AI/NIAID NIH HHS/United States ; UH3 OD023253/OD/NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; K12 HS022986/HS/AHRQ HHS/United States ; }, mesh = {Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Pregnancy ; Prenatal Exposure Delayed Effects/*microbiology ; Prospective Studies ; *Weight Gain ; }, abstract = {OBJECTIVES: Pregnancy characteristics may influence the infant fecal microbiota during early life. We aimed to examine associations of maternal gestational weight gain with infant fecal microbiota composition, bacterial community richness, and Shannon diversity index.

METHODS: We analyzed data from a prospective cohort study of healthy infants. We collected prenatal data, including report of mother's gestational weight gain, and infant fecal samples from 84 infant-mother dyads. By applying 16S rRNA gene sequencing and an unbiased clustering by partitioning around medoids using Bray-Curtis distances, we identified 4 fecal microbiota profiles, and examined the associations of maternal gestational weight gain with the 4 fecal microbiota profiles, bacterial community richness, and Shannon diversity index.

RESULTS: Overall, the median age of infants was 4.0 months and 43% were girls. The mothers of the 84 infants gained a mean of 14.2 kg (standard deviation, 5.4 kg) during pregnancy. We identified 4 distinct microbiota profiles: Bifidobacterium-dominant (42%), Enterobacter/Veillonella-dominant (23%), Bacteroides-dominant (19%), and Escherichia-dominant (17%). Infants whose mothers had higher gestational weight gain were less likely to have a Bacteroides-dominant profile, corresponding to a relative risk ratio of 0.83 (95% confidence interval, 0.71-0.96; P = 0.01) per 1 kg increase in weight. In addition, higher gestational weight gain was also associated with lower bacterial community richness and Shannon diversity index (P < 0.05).

CONCLUSIONS: In this prospective cohort study of healthy infants, maternal gestational weight gain was associated with the infant fecal microbiota profiles, bacterial community richness, and Shannon diversity index.}, } @article {pmid28266933, year = {2017}, author = {Franasiak, JM and Scott, RT}, title = {Endometrial microbiome.}, journal = {Current opinion in obstetrics & gynecology}, volume = {29}, number = {3}, pages = {146-152}, doi = {10.1097/GCO.0000000000000357}, pmid = {28266933}, issn = {1473-656X}, mesh = {Endometrium/*microbiology ; Female ; Humans ; *Microbiota ; Pregnancy ; Pregnancy Outcome ; Reproductive Techniques, Assisted ; Vagina/microbiology ; }, abstract = {PURPOSE OF REVIEW: There have been great improvements in assisted reproduction in the recent decade; however, there are still a significant number of chromosomally normal blastocysts that fail to produce live births. The human microbiome is the totality of the microbes and their genomes that exist in and on the host. The understanding of its impact on health and human disease, particularly in human reproduction, is evolving.

RECENT FINDINGS: New technologies have empowered metagenomic sample analysis that allows for more fully characterizing the reproductive tract microbiome. With these technologies, we have determined not only that sites previously thought to be sterile in fact have robust microbiomes, but also have better characterized the normal and abnormal vaginal and endometrial microbiome.

SUMMARY: The understanding of the microbiome in health and human disease, in particular in relation to human reproduction, is in its infancy. As the reproductive tract dysbiosis are better characterized and understood, we may be better equipped to manipulate it more expertly.}, } @article {pmid28265513, year = {2017}, author = {O'Donnell, JL and Kelly, RP and Shelton, AO and Samhouri, JF and Lowell, NC and Williams, GD}, title = {Spatial distribution of environmental DNA in a nearshore marine habitat.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3044}, pmid = {28265513}, issn = {2167-8359}, abstract = {In the face of increasing threats to biodiversity, the advancement of methods for surveying biological communities is a major priority for ecologists. Recent advances in molecular biological technologies have made it possible to detect and sequence DNA from environmental samples (environmental DNA or eDNA); however, eDNA techniques have not yet seen widespread adoption as a routine method for biological surveillance primarily due to gaps in our understanding of the dynamics of eDNA in space and time. In order to identify the effective spatial scale of this approach in a dynamic marine environment, we collected marine surface water samples from transects ranging from the intertidal zone to four kilometers from shore. Using PCR primers that target a diverse assemblage of metazoans, we amplified a region of mitochondrial 16S rDNA from the samples and sequenced the products on an Illumina platform in order to detect communities and quantify their spatial patterns using a variety of statistical tools. We find evidence for multiple, discrete eDNA communities in this habitat, and show that these communities decrease in similarity as they become further apart. Offshore communities tend to be richer but less even than those inshore, though diversity was not spatially autocorrelated. Taxon-specific relative abundance coincided with our expectations of spatial distribution in taxa lacking a microscopic, pelagic life-history stage, though most of the taxa detected do not meet these criteria. Finally, we use carefully replicated laboratory procedures to show that laboratory treatments were remarkably similar in most cases, while allowing us to detect a faulty replicate, emphasizing the importance of replication to metabarcoding studies. While there is much work to be done before eDNA techniques can be confidently deployed as a standard method for ecological monitoring, this study serves as a first analysis of diversity at the fine spatial scales relevant to marine ecologists and confirms the promise of eDNA in dynamic environments.}, } @article {pmid28259411, year = {2017}, author = {Bicalho, MLS and Lima, S and Higgins, CH and Machado, VS and Lima, FS and Bicalho, RC}, title = {Genetic and functional analysis of the bovine uterine microbiota. Part II: Purulent vaginal discharge versus healthy cows.}, journal = {Journal of dairy science}, volume = {100}, number = {5}, pages = {3863-3874}, doi = {10.3168/jds.2016-12061}, pmid = {28259411}, issn = {1525-3198}, mesh = {Animals ; Cattle ; Cattle Diseases/*microbiology ; Endometritis/*veterinary ; Female ; Microbiota ; Postpartum Period ; Vaginal Discharge/veterinary ; }, abstract = {The aim of this study was to characterize, using metagenomic shotgun DNA sequencing, the intrauterine microbial population and its predicted functional diversity within healthy cows and cows presenting purulent vaginal discharge (PVD). Twenty Holstein dairy cows from a single farm were enrolled in the study at 25 to 35 d postpartum. Purulent vaginal discharge was diagnosed by retrieving and scoring vaginal discharge using the Metricheck device (Simcro, Hamilton, New Zealand). Intrauterine samples for metagenomic analysis were collected by the cytobrush technique from 8 cows diagnosed with PVD and 12 healthy cows. Pair-end sequencing was performed using the Illumina MiSeq platform (Illumina Inc., San Diego, CA). Metagenomic sequences were analyzed using the MG-RAST server (metagenomic rapid annotations using subsystems technology; http://metagenomics.anl.gov/), and the STAMP software (http://kiwi.cs.dal.ca/Software/STAMP) was used to study statistically significant differential abundance of taxonomic and functional features between the 2 metagenomes. Additionally, the total number of bacterial 16S rDNA copies was estimated by real-time PCR. Taxonomic analysis revealed that Bacteroidetes was the most abundant phylum in the uterine microbiota from cows with PVD, and Fusobacteria was almost completely absent in the healthy uterine microbiota. Moreover, species belonging to the genus Trueperella were present only in the uterine microbiota of PVD cows. The increased abundance of Fusobacteria and the unique presence of Trueperella in the PVD cows highlight the important role of these bacteria in the pathogenesis of PVD. Genes encoding cytolethal distending toxin were exclusive to the microbiota of PVD cows. Similarly, genes associated with lipid A modification were present only in samples from PVD cows; such modification is associated with greater resistance to cationic antimicrobial peptides. Conversely, genes encoding bacteriocins and ribosomally antibacterial peptide were exclusively found in the healthy uterine microbiota and dominated by tolerance to colicin E2. No difference was observed in total bacterial load between the 2 microbiotas. This study provides deep insight into the uterine microbial community in health and disease. The observations that the healthy microbiota is tolerant to colicin E2, whereas the uterine microbiota of PVD cows produces cytolethal distending toxins and modifies its lipopolysaccharides suggest that species-intrinsic factors may be more relevant than bacterial abundance to the development of disease or maintenance of health in the dairy cow postpartum uterus.}, } @article {pmid28259404, year = {2017}, author = {Bicalho, MLS and Machado, VS and Higgins, CH and Lima, FS and Bicalho, RC}, title = {Genetic and functional analysis of the bovine uterine microbiota. Part I: Metritis versus healthy cows.}, journal = {Journal of dairy science}, volume = {100}, number = {5}, pages = {3850-3862}, doi = {10.3168/jds.2016-12058}, pmid = {28259404}, issn = {1525-3198}, mesh = {Animals ; Cattle ; Cattle Diseases/microbiology ; Endometritis/*veterinary ; Female ; *Lactation ; Microbiota ; Postpartum Period ; Uterine Diseases/veterinary ; }, abstract = {Metritis is a uterine disease that affects 10 to 30% of all lactating dairy cows and has detrimental effects on reproductive performance, milk production, and survival. Data regarding the identity and abundance of bacterial genes governing traits such as virulence, antibiotic resistance, and stress responses could enable identification of previously unknown agents that play a role in metritis pathogenesis. Moreover, such knowledge could lead to the development of improved treatments or preventive methods. Therefore, the objectives of this study were to characterize the uterine microbial population and to differentiate, for the first time, the microbial functional diversity in cows with metritis versus healthy cows. In addition, we aimed to identify relationships between microbial genes and postpartum uterine health. Uterine swabs were collected from 24 cows within 3 to 12 d in milk; 12 cows were diagnosed with metritis and the other 12 were healthy. Metritis was defined as a watery, reddish or brownish uterine discharge having a fetid smell, and rectal temperature greater than 39.5°C. Cows with a clear and viscous uterine discharge, not fetid or mucopurulent, were classified as healthy. Microbial metagenomic DNA from uterine swab samples was subjected to whole-genome shotgun sequencing on the Illumina MiSeq platform (Illumina Inc., San Diego, CA). The MG-RAST server (metagenomic rapid annotations using subsystems technology; http://metagenomics.anl.gov/) and STAMP software (http://kiwi.cs.dal.ca/Software/STAMP) were used to detect statistically significant differences in the abundance of taxonomic and functional features between the uterine microbial metagenomes of metritic and healthy cows. Our results showed an increased abundance of Fusobacteria and Bacteroidetes in metritic cows, confirming the potential role of those 2 taxa in the pathogenesis of metritis. The MG-RAST analysis revealed a significantly higher abundance of genes for protein transport across the cytoplasmic membrane and type VI bacterial secretion systems in the metritic microbiota. Additionally, genes coding for resistance to acid stress were exclusive to the metritis microbiota, suggesting that microbial resistance to acid stress is important for microbial survival in the infected uterus. On the other hand, genes coding for adhesion molecules, bacteriocins, and antibacterial peptides were significantly associated with the uterine microbiota of healthy cows, as was tolerance to colicin E2.}, } @article {pmid28258138, year = {2017}, author = {Wang, Y and Hatt, JK and Tsementzi, D and Rodriguez-R, LM and Ruiz-Pérez, CA and Weigand, MR and Kizer, H and Maresca, G and Krishnan, R and Poretsky, R and Spain, JC and Konstantinidis, KT}, title = {Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {8}, pages = {}, pmid = {28258138}, issn = {1098-5336}, mesh = {2,4-Dichlorophenoxyacetic Acid/metabolism/pharmacology ; Archaea/classification/genetics/metabolism ; Bacteria/classification/genetics/metabolism ; Biodegradation, Environmental ; *Biodiversity ; Caffeine/metabolism/pharmacology ; *Ecosystem ; Fresh Water/*microbiology ; Georgia ; Lakes/microbiology ; Metagenomics ; Microbial Consortia/drug effects/genetics/*physiology ; Nitrophenols/metabolism/pharmacology ; Phylogeny ; RNA, Ribosomal, 16S ; Real-Time Polymerase Chain Reaction ; Water Pollutants, Chemical/chemistry/*metabolism/*pharmacology ; }, abstract = {A single liter of water contains hundreds, if not thousands, of bacterial and archaeal species, each of which typically makes up a very small fraction of the total microbial community (<0.1%), the so-called "rare biosphere." How often, and via what mechanisms, e.g., clonal amplification versus horizontal gene transfer, the rare taxa and genes contribute to microbial community response to environmental perturbations represent important unanswered questions toward better understanding the value and modeling of microbial diversity. We tested whether rare species frequently responded to changing environmental conditions by establishing 20-liter planktonic mesocosms with water from Lake Lanier (Georgia, USA) and perturbing them with organic compounds that are rarely detected in the lake, including 2,4-dichlorophenoxyacetic acid (2,4-D), 4-nitrophenol (4-NP), and caffeine. The populations of the degraders of these compounds were initially below the detection limit of quantitative PCR (qPCR) or metagenomic sequencing methods, but they increased substantially in abundance after perturbation. Sequencing of several degraders (isolates) and time-series metagenomic data sets revealed distinct cooccurring alleles of degradation genes, frequently carried on transmissible plasmids, especially for the 2,4-D mesocosms, and distinct species dominating the post-enrichment microbial communities from each replicated mesocosm. This diversity of species and genes also underlies distinct degradation profiles among replicated mesocosms. Collectively, these results supported the hypothesis that the rare biosphere can serve as a genetic reservoir, which can be frequently missed by metagenomics but enables community response to changing environmental conditions caused by organic pollutants, and they provided insights into the size of the pool of rare genes and species.IMPORTANCE A single liter of water or gram of soil contains hundreds of low-abundance bacterial and archaeal species, the so called rare biosphere. The value of this astonishing biodiversity for ecosystem functioning remains poorly understood, primarily due to the fact that microbial community analysis frequently focuses on abundant organisms. Using a combination of culture-dependent and culture-independent (metagenomics) techniques, we showed that rare taxa and genes commonly contribute to the microbial community response to organic pollutants. Our findings should have implications for future studies that aim to study the role of rare species in environmental processes, including environmental bioremediation efforts of oil spills or other contaminants.}, } @article {pmid28256031, year = {2017}, author = {Gonçalves, AT and Gallardo-Escárate, C}, title = {Microbiome dynamic modulation through functional diets based on pre- and probiotics (mannan-oligosaccharides and Saccharomyces cerevisiae) in juvenile rainbow trout (Oncorhynchus mykiss).}, journal = {Journal of applied microbiology}, volume = {122}, number = {5}, pages = {1333-1347}, doi = {10.1111/jam.13437}, pmid = {28256031}, issn = {1365-2672}, mesh = {Animal Feed/analysis/*microbiology ; Animals ; Aquaculture ; Bacteria/classification/genetics/*isolation & purification ; Dietary Supplements/analysis ; *Gastrointestinal Microbiome ; Intestinal Mucosa/microbiology ; Mannans/metabolism ; Oligosaccharides/*administration & dosage ; Oncorhynchus mykiss/growth & development/*microbiology ; Prebiotics/*administration & dosage ; Probiotics/*administration & dosage/metabolism ; RNA, Ribosomal, 16S/genetics ; Saccharomyces cerevisiae/genetics/isolation & purification/*physiology ; }, abstract = {AIMS: This study used high-throughput sequencing to evaluate the intestinal microbiome dynamics in rainbow trout (Oncorhynchus mykiss) fed commercial diets supplemented with either pre- or probiotics (0·6% mannan-oligosaccharides and 0·5% Saccharomyces cerevisiae respectively) or the mixture of both.

METHODS AND RESULTS: A total of 57 fish whole intestinal mucosa and contents bacterial communities were characterized by high-throughput sequencing and analysis of the V3-V4 region of the 16S rRNA gene, as well as the relationship between plasma biochemical health indicators and microbiome diversity. This was performed at 7, 14 and 30 days after start feeding functional diets, and microbiome diversity increased when fish fed functional diets after 7 days and it was positively correlated with plasma cholesterol levels. Dominant phyla were, in descending order, Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria, Bacteroidetes and Fusobacteria. However, functional diets reduced the abundance of Gammaproteobacteria to favour abundances of organisms from Firmicutes and Fusobacteria, two phyla with members that confer beneficial effects. A dynamic shift of the microbiome composition was observed with changes after 7 days of feeding and the modulation by functional diets tend to cluster the corresponding groups apart from CTRL group. The core microbiome showed an overall stability with functional diets, except genus such as Escherichia-Shigella that suffered severe reductions on their abundances when feeding any of the functional diets.

CONCLUSIONS: Functional diets based on pre- or probiotics dynamically modulate intestinal microbiota of juvenile trout engaging taxonomical abundance shifts that might impact fish physiological performance.

This study shows for the first time the microbiome modulation dynamics by functional diets based on mannan-oligosaccharides and S. cerevisiae and their synergy using culture independent high-throughput sequencing technology, revealing the complexity behind the dietary modulation with functional feeds in aquatic organisms.}, } @article {pmid28255158, year = {2017}, author = {Jandhyala, SM and Madhulika, A and Deepika, G and Rao, GV and Reddy, DN and Subramanyam, C and Sasikala, M and Talukdar, R}, title = {Altered intestinal microbiota in patients with chronic pancreatitis: implications in diabetes and metabolic abnormalities.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43640}, pmid = {28255158}, issn = {2045-2322}, mesh = {Adult ; Biodiversity ; Case-Control Studies ; Diabetes Mellitus, Type 2/diagnosis/*etiology ; Disease Progression ; *Dysbiosis ; Energy Metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolic Diseases/diagnosis/*etiology ; Metagenome ; Metagenomics/methods ; Middle Aged ; Pancreatitis, Chronic/*complications/diagnosis ; }, abstract = {Intestinal dysbiosis and its functional implications in chronic pancreatitis (CP) have not been elaborately studied. We evaluated the taxonomic and functional alterations in intestinal microbiota in 30 well-characterised patients with CP (16 without, 14 with diabetes) and 10 healthy controls. The patients with CP and diabetes had significantly longer disease duration and greater degree of malnutrition. There was increase in plasma endotoxin concentrations from controls to CP non-diabetics to CP diabetics. We observed significant differences in richness and alpha diversity between the groups. We also observed increase in the Firmicutes:Bacteroidetes ratio in CP patients without and with diabetes. There was reduction in abundance of Faecalibacterium prausnitzii and Ruminococcus bromii from controls to CP non-diabetics to CP diabetics. On the other hand, there was increase in LPS (endotoxin) synthetic pathways (KEGG orthology) in the groups. Faecalibacterium prausnitzii abundance correlated negatively with plasma endotoxin and glycemic status; while plasma endotoxin correlated positively with blood glucose and negatively with plasma insulin. Our results have important implications for future studies exploring mechanistic insights on secondary diabetes in CP.}, } @article {pmid28252037, year = {2017}, author = {Aoki, R and Kamikado, K and Suda, W and Takii, H and Mikami, Y and Suganuma, N and Hattori, M and Koga, Y}, title = {A proliferative probiotic Bifidobacterium strain in the gut ameliorates progression of metabolic disorders via microbiota modulation and acetate elevation.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43522}, pmid = {28252037}, issn = {2045-2322}, mesh = {Acetates/*metabolism ; Animals ; Bifidobacterium/*metabolism ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Glucose/metabolism ; Glucose Intolerance/metabolism/therapy ; Male ; Metabolic Diseases/etiology/*metabolism/therapy ; Metagenome ; Metagenomics/methods ; Mice ; *Probiotics ; }, abstract = {The gut microbiota is an important contributor to the worldwide prevalence of metabolic syndrome (MS), which includes obesity and diabetes. The anti-MS effects exerted by Bifidobacterium animalis ssp. lactis GCL2505 (BlaG), a highly proliferative Bifidobacterium strain in the gut, and B. longum ssp. longum JCM1217[T] (BloJ) were comparatively examined. BlaG treatment reduced visceral fat accumulation and improved glucose tolerance, whereas BloJ had no effect on these parameters. Gut microbial analysis revealed that BlaG exerted stronger effects on the overall bacterial structure of the gut microbiota than BloJ, including enrichment of the genus Bifidobacterium. The levels of acetate and glucagon-like peptide-1 were increased by BlaG treatment in both the gut and plasma, but not by BloJ treatment. Correlation analysis suggested that the elevation of gut acetate levels by BlaG treatment plays a pivotal role in the BlaG-induced anti-MS effects. These findings indicated that BlaG, a highly viable and proliferative probiotic, improves metabolic disorders by modulating gut microbiota, which results in the elevation of SCFAs, especially acetate.}, } @article {pmid28246922, year = {2017}, author = {VanMensel, D and Chaganti, SR and Boudens, R and Reid, T and Ciborowski, J and Weisener, C}, title = {Investigating the Microbial Degradation Potential in Oil Sands Fluid Fine Tailings Using Gamma Irradiation: A Metagenomic Perspective.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {362-372}, pmid = {28246922}, issn = {1432-184X}, mesh = {Biodegradation, Environmental ; *Gamma Rays ; *Metagenome ; *Microbial Consortia ; Mining ; Oil and Gas Fields/*microbiology ; Ponds ; }, abstract = {Open-pit mining of the Athabasca oil sands has generated large volumes of waste termed fluid fine tailings (FFT), stored in tailings ponds. Accumulation of toxic organic substances in the tailings ponds is one of the biggest concerns. Gamma irradiation (GI) treatment could accelerate the biodegradation of toxic organic substances. Hence, this research investigates the response of the microbial consortia in GI-treated FFT materials with an emphasis on changes in diversity and organism-related stimuli. FFT materials from aged and fresh ponds were used in the study under aerobic and anaerobic conditions. Variations in the microbial diversity in GI-treated FFT materials were monitored for 52 weeks and significant stimuli (p < 0.05) were observed. Chemoorganotrophic organisms dominated in fresh and aged ponds and showed increased relative abundance resulting from GI treatment. GI-treated anaerobic FFTaged reported stimulus of organisms with biodegradation potential (e.g., Pseudomonas, Enterobacter) and methylotrophic capabilities (e.g., Syntrophus, Smithella). In comparison, GI-treated anaerobic FFTfresh stimulated Desulfuromonas as the principle genus at 52 weeks. Under aerobic conditions, GI-treated FFTaged showed stimulation of organisms capable of sulfur and iron cycling (e.g., Geobacter). However, GI-treated aerobic FFTfresh showed no stimulus at 52 weeks. This research provides an enhanced understanding of oil sands tailings biogeochemistry and the impacts of GI treatment on microorganisms as an effect for targeting toxic organics. The outcomes of this study highlight the potential for this approach to accelerate stabilization and reclamation end points. Graphical Abstract.}, } @article {pmid28246123, year = {2017}, author = {Amon, P and Sanderson, I}, title = {What is the microbiome?.}, journal = {Archives of disease in childhood. Education and practice edition}, volume = {102}, number = {5}, pages = {257-260}, doi = {10.1136/archdischild-2016-311643}, pmid = {28246123}, issn = {1743-0593}, mesh = {Adolescent ; Child ; Child, Preschool ; Female ; Host-Pathogen Interactions/*physiology ; *Human Body ; Humans ; Infant ; Infant, Newborn ; Male ; Microbiota/*physiology ; *Pediatrics ; }, } @article {pmid28246035, year = {2017}, author = {Hinsu, AT and Parmar, NR and Nathani, NM and Pandit, RJ and Patel, AB and Patel, AK and Joshi, CG}, title = {Functional gene profiling through metaRNAseq approach reveals diet-dependent variation in rumen microbiota of buffalo (Bubalus bubalis).}, journal = {Anaerobe}, volume = {44}, number = {}, pages = {106-116}, doi = {10.1016/j.anaerobe.2017.02.021}, pmid = {28246035}, issn = {1095-8274}, mesh = {Animal Feed ; Animals ; Buffaloes/*microbiology ; Computational Biology ; Diet/*methods ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; *Metagenomics ; Rumen/*microbiology ; }, abstract = {Recent advances in next generation sequencing technology have enabled analysis of complex microbial community from genome to transcriptome level. In the present study, metatranscriptomic approach was applied to elucidate functionally active bacteria and their biological processes in rumen of buffalo (Bubalus bubalis) adapted to different dietary treatments. Buffaloes were adapted to a diet containing 50:50, 75:25 and 100:0 forage to concentrate ratio, each for 6 weeks, before ruminal content sample collection. Metatranscriptomes from rumen fiber adherent and fiber-free active bacteria were sequenced using Ion Torrent PGM platform followed by annotation using MG-RAST server and CAZYmes (Carbohydrate active enzymes) analysis toolkit. In all the samples Bacteroidetes was the most abundant phylum followed by Firmicutes. Functional analysis using KEGG Orthology database revealed Metabolism as the most abundant category at level 1 within which Carbohydrate metabolism was dominating. Diet treatments also exerted significant differences in proportion of enzymes involved in metabolic pathways for VFA production. Carbohydrate Active Enzyme(CAZy) analysis revealed the abundance of genes encoding glycoside hydrolases with the highest representation of GH13 CAZy family in all the samples. The findings provide an overview of the activities occurring in the rumen as well as active bacterial population and the changes occurring through different dietary treatments.}, } @article {pmid28246016, year = {2017}, author = {Hong, CP and Park, A and Yang, BG and Yun, CH and Kwak, MJ and Lee, GW and Kim, JH and Jang, MS and Lee, EJ and Jeun, EJ and You, G and Kim, KS and Choi, Y and Park, JH and Hwang, D and Im, SH and Kim, JF and Kim, YK and Seoh, JY and Surh, CD and Kim, YM and Jang, MH}, title = {Gut-Specific Delivery of T-Helper 17 Cells Reduces Obesity and Insulin Resistance in Mice.}, journal = {Gastroenterology}, volume = {152}, number = {8}, pages = {1998-2010}, doi = {10.1053/j.gastro.2017.02.016}, pmid = {28246016}, issn = {1528-0012}, mesh = {*Adoptive Transfer ; Animals ; Cells, Cultured ; Diet, High-Fat ; Disease Models, Animal ; Feces/microbiology ; Gastrointestinal Microbiome/immunology ; Genotype ; Homeodomain Proteins/genetics/metabolism ; Host-Pathogen Interactions ; *Immunity, Mucosal ; *Insulin Resistance ; Integrin beta Chains/genetics/metabolism ; Interleukin-17/deficiency/genetics ; Intestine, Small/*immunology/metabolism/microbiology ; Male ; Metabolic Syndrome/genetics/immunology/microbiology/*prevention & control ; Mice, Inbred C57BL ; Mice, Knockout ; Obesity/genetics/immunology/microbiology/*prevention & control ; Phenotype ; Th17 Cells/immunology/microbiology/*transplantation ; Time Factors ; Vitamin A Deficiency/complications ; }, abstract = {BACKGROUND & AIMS: Obesity and metabolic syndrome have been associated with alterations to the intestinal microbiota. However, few studies examined the effects of obesity on the intestinal immune system. We investigated changes in subsets of intestinal CD4[+] T-helper (TH) cells with obesity and the effects of gut-tropic TH17 cells in mice on a high-fat diet (HFD).

METHODS: We isolated immune cells from small intestine and adipose tissue of C57BL/6 mice fed a normal chow diet or a HFD for 10 weeks and analyzed the cells by flow cytometry. Mice fed a vitamin A-deficient HFD were compared with mice fed a vitamin A-sufficient HFD. Obese RAG1-deficient mice were given injections of only regulatory T cells or a combination of regulatory T cells and TH17 cells (wild type or deficient in integrin β7 subunit or interleukin 17 [IL17]). Mice were examined for weight gain, fat mass, fatty liver, glucose tolerance, and insulin resistance. Fecal samples were collected before and after T cell transfer and analyzed for microbiota composition by metagenomic DNA sequencing and quantitative polymerase chain reaction.

RESULTS: Mice placed on a HFD became obese, which affected the distribution of small intestinal CD4[+] TH cells. Intestinal tissues from obese mice had significant reductions in the proportion of TH17 cells but increased proportion of TH1 cells, compared with intestinal tissues from nonobese mice. Depletion of vitamin A in obese mice further reduced the proportion of TH17 cells in small intestine; this reduction correlated with more weight gain and worsening of glucose intolerance and insulin resistance. Adoptive transfer of in vitro-differentiated gut-tropic TH17 cells to obese mice reduced these metabolic defects, which required the integrin β7 subunit and IL17. Delivery of TH17 cells to intestines of mice led to expansion of commensal microbes associated with leanness.

CONCLUSIONS: In mice, intestinal TH17 cells contribute to development of a microbiota that maintains metabolic homeostasis, via IL17. Gut-homing TH17 cells might be used to reduce metabolic disorders in obese individuals.}, } @article {pmid28245856, year = {2017}, author = {Galloway-Peña, JR and Smith, DP and Sahasrabhojane, P and Wadsworth, WD and Fellman, BM and Ajami, NJ and Shpall, EJ and Daver, N and Guindani, M and Petrosino, JF and Kontoyiannis, DP and Shelburne, SA}, title = {Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients.}, journal = {Genome medicine}, volume = {9}, number = {1}, pages = {21}, pmid = {28245856}, issn = {1756-994X}, support = {L30 CA209245/CA/NCI NIH HHS/United States ; P30 CA016672/CA/NCI NIH HHS/United States ; T32 CA096520/CA/NCI NIH HHS/United States ; }, mesh = {Aged ; Anti-Bacterial Agents/*pharmacology ; Antineoplastic Agents/*pharmacology/therapeutic use ; Bacteria/genetics/isolation & purification/metabolism ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Leukemia, Myeloid, Acute/drug therapy/*microbiology ; Male ; Middle Aged ; RNA, Ribosomal, 16S ; Saliva/microbiology ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Understanding longitudinal variability of the microbiome in ill patients is critical to moving microbiome-based measurements and therapeutics into clinical practice. However, the vast majority of data regarding microbiome stability are derived from healthy subjects. Herein, we sought to determine intra-patient temporal microbiota variability, the factors driving such variability, and its clinical impact in an extensive longitudinal cohort of hospitalized cancer patients during chemotherapy.

METHODS: The stool (n = 365) and oral (n = 483) samples of 59 patients with acute myeloid leukemia (AML) undergoing induction chemotherapy (IC) were sampled from initiation of chemotherapy until neutrophil recovery. Microbiome characterization was performed via analysis of 16S rRNA gene sequencing. Temporal variability was determined using coefficients of variation (CV) of the Shannon diversity index (SDI) and unweighted and weighted UniFrac distances per patient, per site. Measurements of intra-patient temporal variability and patient stability categories were analyzed for their correlations with genera abundances. Groups of patients were analyzed to determine if patients with adverse outcomes had significantly different levels of microbiome temporal variability. Potential clinical drivers of microbiome temporal instability were determined using multivariable regression analyses.

RESULTS: Our cohort evidenced a high degree of intra-patient temporal instability of stool and oral microbial diversity based on SDI CV. We identified statistically significant differences in the relative abundance of multiple taxa amongst individuals with different levels of microbiota temporal stability. Increased intra-patient temporal variability of the oral SDI was correlated with increased risk of infection during IC (P = 0.02), and higher stool SDI CVs were correlated with increased risk of infection 90 days post-IC (P = 0.04). Total days on antibiotics was significantly associated with increased temporal variability of both oral microbial diversity (P = 0.03) and community structure (P = 0.002).

CONCLUSIONS: These data quantify the longitudinal variability of the oral and gut microbiota in AML patients, show that increased variability was correlated with adverse clinical outcomes, and offer the possibility of using stabilizing taxa as a method of focused microbiome repletion. Furthermore, these results support the importance of longitudinal microbiome sampling and analyses, rather than one time measurements, in research and future clinical practice.}, } @article {pmid28245817, year = {2017}, author = {Sandri, M and Dal Monego, S and Conte, G and Sgorlon, S and Stefanon, B}, title = {Raw meat based diet influences faecal microbiome and end products of fermentation in healthy dogs.}, journal = {BMC veterinary research}, volume = {13}, number = {1}, pages = {65}, pmid = {28245817}, issn = {1746-6148}, mesh = {*Animal Feed ; Animals ; Diet/*veterinary ; Dogs/*microbiology ; Feces/*microbiology ; Female ; Fermentation ; Male ; *Meat ; *Microbiota ; *Raw Foods ; Vegetables ; }, abstract = {BACKGROUND: Dietary intervention studies are required to deeper understand the variability of gut microbial ecosystem in healthy dogs under different feeding conditions and to improve diet formulations. The aim of the study was to investigate in dogs the influence of a raw based diet supplemented with vegetable foods on faecal microbiome in comparison with extruded food.

METHODS: Eight healthy adult Boxer dogs were recruited and randomly divided in two experimental blocks of 4 individuals. Dogs were regularly fed a commercial extruded diet (RD) and starting from the beginning of the trial, one group received the raw based diet (MD) and the other group continued to be fed with the RD diet (CD) for a fortnight. After 14 days, the two groups were inverted, the CD group shifted to the MD and the MD shifted to the CD, for the next 14 days. Faeces were collected at the beginning of the study (T0), after 14 days (T14) before the change of diet and at the end of experimental period (T28) for DNA extraction and analysis of metagenome by sequencing 16SrRNA V3 and V4 regions, short chain fatty acids (SCFA), lactate and faecal score.

RESULTS: A decreased proportion of Lactobacillus, Paralactobacillus (P < 0.01) and Prevotella (P < 0.05) genera was observed in the MD group while Shannon biodiversity Index significantly increased (3.31 ± 0.15) in comparison to the RD group (2.92 ± 0.31; P < 0.05). The MD diet significantly (P < 0.05) decreased the Faecal Score and increased the lactic acid concentration in the feces in comparison to the RD treatment (P < 0.01). Faecal acetate was negatively correlated with Escherichia/Shigella and Megamonas (P < 0.01), whilst butyrate was positively correlated with Blautia and Peptococcus (P < 0.05). Positive correlations were found between lactate and Megamonas (P < 0.05), Escherichia/Shigella (P < 0.01) and Lactococcus (P < 0.01).

CONCLUSION: These results suggest that the diet composition modifies faecal microbial composition and end products of fermentation. The administration of MD diet promoted a more balanced growth of bacterial communities and a positive change in the readouts of healthy gut functions in comparison to RD diet.}, } @article {pmid28242677, year = {2017}, author = {Starnawski, P and Bataillon, T and Ettema, TJ and Jochum, LM and Schreiber, L and Chen, X and Lever, MA and Polz, MF and Jørgensen, BB and Schramm, A and Kjeldsen, KU}, title = {Microbial community assembly and evolution in subseafloor sediment.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {11}, pages = {2940-2945}, pmid = {28242677}, issn = {1091-6490}, support = {294200/ERC_/European Research Council/International ; }, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Biodiversity ; *Biological Evolution ; Biomass ; Genetic Variation ; Geologic Sediments/*microbiology ; *Metagenomics/methods ; *Microbiota ; Mutation ; }, abstract = {Bacterial and archaeal communities inhabiting the subsurface seabed live under strong energy limitation and have growth rates that are orders of magnitude slower than laboratory-grown cultures. It is not understood how subsurface microbial communities are assembled and whether populations undergo adaptive evolution or accumulate mutations as a result of impaired DNA repair under such energy-limited conditions. Here we use amplicon sequencing to explore changes of microbial communities during burial and isolation from the surface to the >5,000-y-old subsurface of marine sediment and identify a small core set of mostly uncultured bacteria and archaea that is present throughout the sediment column. These persisting populations constitute a small fraction of the entire community at the surface but become predominant in the subsurface. We followed patterns of genome diversity with depth in four dominant lineages of the persisting populations by mapping metagenomic sequence reads onto single-cell genomes. Nucleotide sequence diversity was uniformly low and did not change with age and depth of the sediment. Likewise, there was no detectable change in mutation rates and efficacy of selection. Our results indicate that subsurface microbial communities predominantly assemble by selective survival of taxa able to persist under extreme energy limitation.}, } @article {pmid28240318, year = {2017}, author = {Lee, ST and Davy, SK and Tang, SL and Kench, PS}, title = {Water flow buffers shifts in bacterial community structure in heat-stressed Acropora muricata.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43600}, pmid = {28240318}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*microbiology/*physiology ; Bacteria/*classification/genetics ; *Biodiversity ; Environment ; *Hot Temperature ; Metagenome ; Metagenomics/methods ; Seasons ; Seawater ; *Stress, Physiological ; *Symbiosis ; Temperature ; Vibrio/classification/genetics ; }, abstract = {Deterioration of coral health and associated change in the coral holobiont's bacterial community are often a result of different environmental stressors acting synergistically. There is evidence that water flow is important for a coral's resistance to elevated seawater temperature, but there is no information on how water flow affects the coral-associated bacterial community under these conditions. In a laboratory cross-design experiment, Acropora muricata nubbins were subjected to interactive effects of seawater temperature (27 °C to 31 °C) and water flow (0.20 m s[-1] and 0.03 m s[-1]). In an in situ experiment, water flow manipulation was conducted with three colonies of A. muricata during the winter and summer, by partially enclosing each colony in a clear plastic mesh box. 16S rRNA amplicon pyrosequencing showed an increase in the relative abundance of Flavobacteriales and Rhodobacterales in the laboratory experiment, and Vibrio spp. in the in situ experiment when corals were exposed to elevated temperature and slow water flow. In contrast, corals that were exposed to faster water flow under laboratory and in situ conditions had a stable bacterial community. These findings indicate that water flow plays an important role in the maintenance of specific coral-bacteria associations during times of elevated thermal stress.}, } @article {pmid28239436, year = {2017}, author = {Camps-Bossacoma, M and Pérez-Cano, FJ and Franch, À and Castell, M}, title = {Gut Microbiota in a Rat Oral Sensitization Model: Effect of a Cocoa-Enriched Diet.}, journal = {Oxidative medicine and cellular longevity}, volume = {2017}, number = {}, pages = {7417505}, pmid = {28239436}, issn = {1942-0994}, mesh = {Animals ; *Cacao ; Chocolate ; *Diet ; Disease Models, Animal ; Feces/chemistry/microbiology ; Female ; Food Hypersensitivity/*microbiology/pathology ; *Gastrointestinal Microbiome/drug effects ; Immunoglobulin A/metabolism ; Intestines/drug effects/immunology/microbiology ; Polyphenols/pharmacology ; Rats ; Rats, Inbred Lew ; }, abstract = {Increasing evidence is emerging suggesting a relation between dietary compounds, microbiota, and the susceptibility to allergic diseases, particularly food allergy. Cocoa, a source of antioxidant polyphenols, has shown effects on gut microbiota and the ability to promote tolerance in an oral sensitization model. Taking these facts into consideration, the aim of the present study was to establish the influence of an oral sensitization model, both alone and together with a cocoa-enriched diet, on gut microbiota. Lewis rats were orally sensitized and fed with either a standard or 10% cocoa diet. Faecal microbiota was analysed through metagenomics study. Intestinal IgA concentration was also determined. Oral sensitization produced few changes in intestinal microbiota, but in those rats fed a cocoa diet significant modifications appeared. Decreased bacteria from the Firmicutes and Proteobacteria phyla and a higher percentage of bacteria belonging to the Tenericutes and Cyanobacteria phyla were observed. In conclusion, a cocoa diet is able to modify the microbiota bacterial pattern in orally sensitized animals. As cocoa inhibits the synthesis of specific antibodies and also intestinal IgA, those changes in microbiota pattern, particularly those of the Proteobacteria phylum, might be partially responsible for the tolerogenic effect of cocoa.}, } @article {pmid28235871, year = {2017}, author = {Li, F and Guan, LL}, title = {Metatranscriptomic Profiling Reveals Linkages between the Active Rumen Microbiome and Feed Efficiency in Beef Cattle.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {9}, pages = {}, pmid = {28235871}, issn = {1098-5336}, mesh = {*Animal Feed ; Animals ; Archaea/classification/enzymology/genetics ; Bacteria/classification/enzymology/genetics ; Cattle ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Diet ; Enzymes/genetics ; *Gastrointestinal Microbiome ; *Gene Expression Profiling ; Metabolic Networks and Pathways/genetics ; *Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Exploring compositional and functional characteristics of the rumen microbiome can improve the understanding of its role in rumen function and cattle feed efficiency. In this study, we applied metatranscriptomics to characterize the active rumen microbiomes of beef cattle with different feed efficiencies (efficient, n = 10; inefficient, n = 10) using total RNA sequencing. Active bacterial and archaeal compositions were estimated based on 16S rRNAs, and active microbial metabolic functions including carbohydrate-active enzymes (CAZymes) were assessed based on mRNAs from the same metatranscriptomic data sets. In total, six bacterial phyla (Proteobacteria, Firmicutes, Bacteroidetes, Spirochaetes, Cyanobacteria, and Synergistetes), eight bacterial families (Succinivibrionaceae, Prevotellaceae, Ruminococcaceae, Lachnospiraceae, Veillonellaceae, Spirochaetaceae, Dethiosulfovibrionaceae, and Mogibacteriaceae), four archaeal clades (Methanomassiliicoccales, Methanobrevibacter ruminantium, Methanobrevibacter gottschalkii, and Methanosphaera), 112 metabolic pathways, and 126 CAZymes were identified as core components of the active rumen microbiome. As determined by comparative analysis, three bacterial families (Lachnospiraceae, Lactobacillaceae, and Veillonellaceae) tended to be more abundant in low-feed-efficiency (inefficient) animals (P < 0.10), and one archaeal taxon (Methanomassiliicoccales) tended to be more abundant in high-feed-efficiency (efficient) cattle (P < 0.10). Meanwhile, 32 microbial metabolic pathways and 12 CAZymes were differentially abundant (linear discriminant analysis score of >2 with a P value of <0.05) between two groups. Among them, 30 metabolic pathways and 11 CAZymes were more abundant in the rumen of inefficient cattle, while 2 metabolic pathways and 1 CAZyme were more abundant in efficient animals. These findings suggest that the rumen microbiomes of inefficient cattle have more diverse activities than those of efficient cattle, which may be related to the host feed efficiency variation.IMPORTANCE This study applied total RNA-based metatranscriptomics and showed the linkage between the active rumen microbiome and feed efficiency (residual feed intake) in beef cattle. The data generated from the current study provide fundamental information on active rumen microbiome at both compositional and functional levels, which serve as a foundation to study rumen function and its role in cattle feed efficiency. The findings that the active rumen microbiome may contribute to variations in feed efficiency of beef cattle highlight the possibility of enhancing nutrient utilization and improve cattle feed efficiency through modification of rumen microbial functions.}, } @article {pmid28234468, year = {2017}, author = {Gao, B and Chi, L and Mahbub, R and Bian, X and Tu, P and Ru, H and Lu, K}, title = {Multi-Omics Reveals that Lead Exposure Disturbs Gut Microbiome Development, Key Metabolites, and Metabolic Pathways.}, journal = {Chemical research in toxicology}, volume = {30}, number = {4}, pages = {996-1005}, pmid = {28234468}, issn = {1520-5010}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 ES024950/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/isolation & purification/metabolism ; Bacterial Proteins/metabolism ; Bile Acids and Salts/metabolism ; Carrier Proteins/metabolism ; Energy Metabolism/drug effects ; Female ; Gas Chromatography-Mass Spectrometry ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/*microbiology ; Lead/*toxicity ; Metabolic Networks and Pathways/*drug effects ; Metabolome/*drug effects ; Metabolomics ; Mice ; Mice, Inbred C57BL ; Nitrite Reductases/metabolism ; Oxidative Stress/drug effects ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Sequence Analysis, DNA ; Vitamin E/metabolism ; }, abstract = {Lead exposure remains a global public health issue, and the recent Flint water crisis has renewed public concern about lead toxicity. The toxicity of lead has been well established in a variety of systems and organs. The gut microbiome has been shown to be highly involved in many critical physiological processes, including food digestion, immune system development, and metabolic homeostasis. However, despite the key role of the gut microbiome in human health, the functional impact of lead exposure on the gut microbiome has not been studied. The aim of this study is to define gut microbiome toxicity induced by lead exposure in C57BL/6 mice using multiomics approaches, including 16S rRNA sequencing, whole genome metagenomics sequencing, and gas chromatography-mass spectrometry (GC-MS) metabolomics. 16S rRNA sequencing revealed that lead exposure altered the gut microbiome trajectory and phylogenetic diversity. Metagenomics sequencing and metabolomics profiling showed that numerous metabolic pathways, including vitamin E, bile acids, nitrogen metabolism, energy metabolism, oxidative stress, and the defense/detoxification mechanism, were significantly disturbed by lead exposure. These perturbed molecules and pathways may have important implications for lead toxicity in the host. Taken together, these results demonstrated that lead exposure not only altered the gut microbiome community structures/diversity but also greatly affected metabolic functions, leading to gut microbiome toxicity.}, } @article {pmid28233813, year = {2017}, author = {Weigel, BL and Erwin, PM}, title = {Effects of reciprocal transplantation on the microbiome and putative nitrogen cycling functions of the intertidal sponge, Hymeniacidon heliophila.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43247}, pmid = {28233813}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; *Microbiota ; *Nitrogen Cycle ; Porifera/*metabolism/*microbiology ; Symbiosis ; }, abstract = {Microbial symbionts in sponges are ubiquitous, forming complex and highly diverse host-specific communities. Conspecific sponges display remarkable stability in their symbiont communities, both spatially and temporally, yet extreme fluctuations in environmental factors can cause shifts in host-symbiont associations. We previously demonstrated that the marine sponge Hymeniacidon heliophila displayed significant community-level differences in microbial symbiont diversity, structure and composition when sampled from intertidal and subtidal environments. Here, we conducted a 70-day reciprocal transplant experiment to directly test the effect of tidal exposure on the microbiome of H. heliophila, using next-generation Illumina sequencing of 16S rRNA gene sequences to characterize symbiont communities. While sponges transplanted between habitats displayed shifts in microbial communities after 70 days, temporal variation was the dominant factor affecting microbial community composition. Further, we identified core symbionts that persisted across these spatio-temporal scales and used a metagenomic approach to show that these dominant members of the microbiome of H. heliophila represent nitrogen cycling taxa that have the potential to contribute to a diverse array of nitrogen transformations in the sponge holobiont. Together, these results indicate that despite moderate spatio-temporal shifts in symbiont composition, core symbiont functions (e.g. nitrogen cycling) can be maintained in sponge microbiomes through functional redundancy.}, } @article {pmid28232956, year = {2017}, author = {Marbouty, M and Baudry, L and Cournac, A and Koszul, R}, title = {Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay.}, journal = {Science advances}, volume = {3}, number = {2}, pages = {e1602105}, pmid = {28232956}, issn = {2375-2548}, support = {260822/ERC_/European Research Council/International ; }, mesh = {Animals ; *Bacteria/genetics/metabolism/virology ; *Bacteriophages/genetics/metabolism ; *Gastrointestinal Microbiome ; *Genome, Bacterial ; *Genome, Viral ; Male ; Mice ; }, abstract = {The biochemical activities of microbial communities, or microbiomes, are essential parts of environmental and animal ecosystems. The dynamics, balance, and effects of these communities are strongly influenced by phages present in the population. Being able to characterize bacterium-phage relationships is therefore essential to investigate these ecosystems to the full extent of their complexity. However, this task is currently limited by (i) the ability to characterize complete bacterial and viral genomes from a complex mix of species and (ii) the difficulty to assign phage sequences to their bacterial hosts. We show that both limitations can be circumvented using meta3C, an experimental and computational approach that exploits the physical contacts between DNA molecules to infer their proximity. In a single experiment, dozens of bacterial and phage genomes present in a complex mouse gut microbiota were assembled and scaffolded de novo. The phage genomes were then assigned to their putative bacterial hosts according to the physical contacts between the different DNA molecules, opening new perspectives for a comprehensive picture of the genomic structure of the gut flora. Therefore, this work holds far-reaching implications for human health studies aiming to bridge the virome to the microbiome.}, } @article {pmid28230723, year = {2017}, author = {Wang, L and Hu, L and Xu, Q and Yin, B and Fang, D and Wang, G and Zhao, J and Zhang, H and Chen, W}, title = {Bifidobacterium adolescentis Exerts Strain-Specific Effects on Constipation Induced by Loperamide in BALB/c Mice.}, journal = {International journal of molecular sciences}, volume = {18}, number = {2}, pages = {}, pmid = {28230723}, issn = {1422-0067}, mesh = {Animals ; Antidiarrheals/*adverse effects ; Bacterial Adhesion ; Bifidobacterium adolescentis/drug effects/*physiology ; Biomarkers ; Constipation/diagnosis/*etiology/therapy ; Defecation ; Disease Models, Animal ; Fatty Acids, Volatile/chemistry/metabolism ; Feces/chemistry/microbiology ; Gastric Juice ; HT29 Cells ; Humans ; Loperamide/*adverse effects ; Melena ; Mice ; Microbiota ; *Probiotics/administration & dosage ; }, abstract = {Constipation is one of the most common gastrointestinal complaints worldwide. This study was performed to determine whether Bifidobacterium adolescentis exerts inter-strain differences in alleviating constipation induced by loperamide in BALB/c mice and to analyze the main reasons for these differences. BALB/c mice underwent gavage with B. adolescentis (CCFM 626, 667, and 669) once per day for 17 days. The primary outcome measures included related constipation indicators, and the secondary outcome measures were the basic biological characteristics of the strains, the concentration changes of short-chain fatty acids in feces, and the changes in the fecal flora. B. adolescentis CCFM 669 and 667 relieved constipation symptoms by adhering to intestinal epithelial cells, growing quickly in vitro and increasing the concentrations of propionic and butyric acids. The effect of B. adolescentis on the gut microbiota in mice with constipation was investigated via 16S rRNA metagenomic analysis. The results revealed that the relative abundance of Lactobacillus increased and the amount of Clostridium decreased in the B. adolescentis CCFM 669 and 667 treatment groups. In conclusion, B. adolescentis exhibits strain-specific effects in the alleviation of constipation, mostly due to the strains' growth rates, adhesive capacity and effects on the gut microbiome and microenvironment.}, } @article {pmid28229558, year = {2017}, author = {Delforno, TP and Lacerda Júnior, GV and Noronha, MF and Sakamoto, IK and Varesche, MBA and Oliveira, VM}, title = {Microbial diversity of a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment: integration of 16S rRNA gene amplicon and shotgun metagenomic sequencing.}, journal = {MicrobiologyOpen}, volume = {6}, number = {3}, pages = {}, pmid = {28229558}, issn = {2045-8827}, mesh = {*Abattoirs ; Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Bacteriophages/classification/genetics ; Bioreactors/*microbiology ; *Biota ; Chickens ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Wastewater ; *Water Purification ; }, abstract = {The 16S rRNA gene amplicon and whole-genome shotgun metagenomic (WGSM) sequencing approaches were used to investigate wide-spectrum profiles of microbial composition and metabolic diversity from a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment. The data were generated by using MiSeq 2 × 250 bp and HiSeq 2 × 150 bp Illumina sequencing platforms for 16S amplicon and WGSM sequencing, respectively. Each approach revealed a distinct microbial community profile, with Pseudomonas and Psychrobacter as predominant genus for the WGSM dataset and Clostridium and Methanosaeta for the 16S rRNA gene amplicon dataset. The virome characterization revealed the presence of two viral families with Bacteria and Archaea as host, Myoviridae, and Siphoviridae. A wide functional diversity was found with predominance of genes involved in the metabolism of acetone, butanol, and ethanol synthesis; and one-carbon metabolism (e.g., methanogenesis). Genes related to the acetotrophic methanogenesis pathways were more abundant than methylotrophic and hydrogenotrophic, corroborating the taxonomic results that showed the prevalence of the acetotrophic genus Methanosaeta. Moreover, the dataset indicated a variety of metabolic genes involved in sulfur, nitrogen, iron, and phosphorus cycles, with many genera able to act in all cycles. BLAST analysis against Antibiotic Resistance Genes Database (ARDB) revealed that microbial community contained 43 different types of antibiotic resistance genes, some of them were associated with growth chicken promotion (e.g., bacitracin, tetracycline, and polymyxin).}, } @article {pmid28229543, year = {2017}, author = {Davis, LR and Bigler, L and Woodhams, DC}, title = {Developmental trajectories of amphibian microbiota: response to bacterial therapy depends on initial community structure.}, journal = {Environmental microbiology}, volume = {19}, number = {4}, pages = {1502-1517}, doi = {10.1111/1462-2920.13707}, pmid = {28229543}, issn = {1462-2920}, mesh = {Animals ; Anura/*microbiology ; Biodiversity ; Fungi ; Larva/microbiology ; Metagenomics ; *Microbiota/drug effects ; Probiotics ; Skin/microbiology ; Switzerland ; Symbiosis ; }, abstract = {Improving host health through microbial manipulation requires untangling factors that shape the microbiome. There is currently little understanding of how initial community structure may drive the microbiota trajectory across host development or influence bacterial therapy outcomes. Probiotic baths of surface symbionts, Pseudomonas fluorescens and Flavobacterium johnsoniae were administered to 240 tadpoles of the midwife toad, Alytes obstetricans in semi-natural outdoor mesocosms originating from geographically and genetically distinct populations in Switzerland. Host bacterial and fungal assemblages were compared in tadpoles from the pond of origin, across metamorphosis, and in toadlets via microbial fingerprinting. Bacterial and fungal community structures differed significantly among populations and a microbial population signature persisted from the tadpole stage, through metamorphosis, and following probiotic treatment. A minimal core surface microbiota is described by persistence through development and by shared membership across populations. The impact of F. johnsoniae on the tadpole surface microbiome was assessed with shotgun metagenomics. Bacterial therapy reduced abundance, diversity, and functional repertoire compared to untreated controls. A correlation between host skin peptides and microbiota suggests a mechanism of host-directed symbiosis throughout development. Early developmental stages are ideal targets for amphibian bacterial therapy that can govern a microbiome trajectory at critical timepoints and may impact susceptibility to disease.}, } @article {pmid28222236, year = {2017}, author = {Aschenbrenner, IA and Cernava, T and Erlacher, A and Berg, G and Grube, M}, title = {Differential sharing and distinct co-occurrence networks among spatially close bacterial microbiota of bark, mosses and lichens‬‬.}, journal = {Molecular ecology}, volume = {26}, number = {10}, pages = {2826-2838}, doi = {10.1111/mec.14070}, pmid = {28222236}, issn = {1365-294X}, mesh = {Bacteria/*classification ; Bryophyta/*microbiology ; Ecology ; Ecosystem ; Lichens/*microbiology ; *Microbiota ; Plant Bark/*microbiology ; Trees ; }, abstract = {Knowledge of bacterial community host-specificity has increased greatly in recent years. However, the intermicrobiome relationships of unrelated but spatially close organisms remain little understood. Trunks of trees covered by epiphytes represent complex habitats with a mosaic of ecological niches. In this context, we investigated the structure, diversity and interactions of microbiota associated with lichens, mosses and the bare tree bark. Comparative analysis revealed significant differences in the habitat-associated community structures. Corresponding co-occurrence analysis indicated that the lichen microbial network is less complex and less densely interconnected than the moss- and bark-associated networks. Several potential generalists and specialists were identified for the selected habitats. Generalists belonged mainly to Proteobacteria, with Sphingomonas as the most abundant genus. The generalists comprise microorganisms with generally beneficial features, such as nitrogen fixation or other supporting functions, according to a metagenomic analysis. We argue that beneficial strains shared among hosts contribute to ecological stability of the host biocoenoses.}, } @article {pmid28222161, year = {2017}, author = {Ijaz, UZ and Quince, C and Hanske, L and Loman, N and Calus, ST and Bertz, M and Edwards, CA and Gaya, DR and Hansen, R and McGrogan, P and Russell, RK and Gerasimidis, K}, title = {The distinct features of microbial 'dysbiosis' of Crohn's disease do not occur to the same extent in their unaffected, genetically-linked kindred.}, journal = {PloS one}, volume = {12}, number = {2}, pages = {e0172605}, pmid = {28222161}, issn = {1932-6203}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; MR/M501621/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adolescent ; Adult ; Bacteria/genetics/isolation & purification/metabolism ; Child ; Crohn Disease/genetics/*microbiology ; Dysbiosis/etiology/genetics/*microbiology ; *Family Health ; Fatty Acids, Volatile/analysis ; Feces/chemistry/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Leukocyte L1 Antigen Complex/analysis ; Male ; Metabolic Networks and Pathways ; Metagenomics ; Parents ; Ribotyping ; Siblings ; }, abstract = {BACKGROUND/AIMS: Studying the gut microbiota in unaffected relatives of people with Crohn's disease (CD) may advance our understanding of the role of bacteria in disease aetiology.

METHODS: Faecal microbiota composition (16S rRNA gene sequencing), genetic functional capacity (shotgun metagenomics) and faecal short chain fatty acids (SCFA) were compared in unaffected adult relatives of CD children (CDR, n = 17) and adult healthy controls, unrelated to CD patients (HUC, n = 14). The microbiota characteristics of 19 CD children were used as a benchmark of CD 'dysbiosis'.

RESULTS: The CDR microbiota was less diverse (p = 0.044) than that of the HUC group. Local contribution of β-diversity analysis showed no difference in community structure between the CDR and HUC groups. Twenty one of 1,243 (1.8%) operational taxonomic units discriminated CDR from HUC. The metagenomic functional capacity (p = 0.207) and SCFA concentration or pattern were similar between CDR and HUC (p>0.05 for all SCFA). None of the KEGG metabolic pathways were different between these two groups. Both of these groups (HUC and CDR) had a higher microbiota α-diversity (CDR, p = 0.026 and HUC, p<0.001) with a community structure (β-diversity) distinct from that of children with CD.

CONCLUSIONS: While some alterations were observed, a distinct microbial 'dysbiosis', characteristic of CD patients, was not observed in their unaffected, genetically linked kindred.}, } @article {pmid28219786, year = {2017}, author = {Poszytek, K and Pyzik, A and Sobczak, A and Lipinski, L and Sklodowska, A and Drewniak, L}, title = {The effect of the source of microorganisms on adaptation of hydrolytic consortia dedicated to anaerobic digestion of maize silage.}, journal = {Anaerobe}, volume = {46}, number = {}, pages = {46-55}, doi = {10.1016/j.anaerobe.2017.02.011}, pmid = {28219786}, issn = {1095-8274}, mesh = {*Anaerobiosis ; Animals ; *Biodegradation, Environmental ; Biodiversity ; Cattle ; Hydrolysis ; Metagenomics/methods ; Methane/biosynthesis ; *Microbial Consortia ; Silage/*microbiology ; Zea mays/*chemistry/*microbiology ; }, abstract = {The main aim of this study was to evaluate the effect of the source of microorganisms on the selection of hydrolytic consortia dedicated to anaerobic digestion of maize silage. The selection process was investigated based on the analysis of changes in the hydrolytic activity and the diversity of microbial communities derived from (i) a hydrolyzer of a commercial agricultural biogas plant, (ii) cattle slurry and (iii) raw sewage sludge, during a series of 10 passages. Following the selection process, the adapted consortia were thoroughly analyzed for their ability to utilize maize silage and augmentation of anaerobic digestion communities. The results of selection of the consortia showed that every subsequent passage of each consortium leads to their adaptation to degradation of maize silage, which was manifested by the increased hydrolytic activity of the adapted consortia. Biodiversity analysis (based on the 16S rDNA amplicon sequencing) confirmed the changes microbial community of each consortium, and showed that after the last (10th) passage all microbial communities were dominated by the representatives of Lactobacillaceae, Prevotellaceae, Veillonellaceae. The results of the functional analyses showed that the adapted consortia improved the efficiency of maize silage degradation, as indicated by the increase in the concentration of glucose and volatile fatty acids (VFAs), as well as the soluble chemical oxygen demand (sCOD). Moreover, bioaugmentation of anaerobic digestion communities by the adapted hydrolytic consortia increased biogas yield by 10-29%, depending on the origin of the community. The obtained results also indicate that substrate input (not community origin) was the driving force responsible for the changes in the community structure of hydrolytic consortia dedicated to anaerobic digestion.}, } @article {pmid28218694, year = {2017}, author = {Matobole, RM and van Zyl, LJ and Parker-Nance, S and Davies-Coleman, MT and Trindade, M}, title = {Antibacterial Activities of Bacteria Isolated from the Marine Sponges Isodictya compressa and Higginsia bidentifera Collected from Algoa Bay, South Africa.}, journal = {Marine drugs}, volume = {15}, number = {2}, pages = {}, pmid = {28218694}, issn = {1660-3397}, mesh = {Animals ; Anti-Bacterial Agents/isolation & purification/*pharmacology ; Bacteria/*chemistry/genetics/isolation & purification ; Base Sequence ; Bays ; Biodiversity ; Biological Products/isolation & purification/*pharmacology ; Drug Resistance, Multiple, Bacterial/drug effects ; Escherichia coli/*drug effects ; Porifera/*microbiology ; South Africa ; Symbiosis ; }, abstract = {Due to the rise in multi-drug resistant pathogens and other diseases, there is renewed interest in marine sponge endosymbionts as a rich source of natural products (NPs). The South African marine environment is rich in marine biota that remains largely unexplored and may represent an important source for the discovery of novel NPs. We first investigated the bacterial diversity associated with five South African marine sponges, whose microbial populations had not previously been investigated, and select the two sponges (Isodictya compressa and Higginsia bidentifera) with highest species richness to culture bacteria. By employing 33 different growth conditions 415 sponge-associated bacterial isolates were cultured and screened for antibacterial activity. Thirty-five isolates showed antibacterial activity, twelve of which exhibited activity against the multi-drug resistant Escherichia coli 1699, implying that some of the bioactive compounds could be novel. Genome sequencing of two of these isolates confirmed that they harbour uncharacterized biosynthetic pathways that may encode novel chemical structures.}, } @article {pmid28217901, year = {2017}, author = {Zielińska, S and Radkowski, P and Blendowska, A and Ludwig-Gałęzowska, A and Łoś, JM and Łoś, M}, title = {The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis.}, journal = {MicrobiologyOpen}, volume = {6}, number = {4}, pages = {}, pmid = {28217901}, issn = {2045-8827}, mesh = {*Biota ; DNA/chemistry/genetics/*isolation & purification ; Metagenomics/*methods/standards ; *Soil Microbiology ; }, abstract = {Metagenomics approaches and recent improvements in the next-generation sequencing methods, have become a method of choice in establishing a microbial population structure. Many commercial soil DNA extraction kits are available and due to their efficiency they are replacing traditional extraction protocols. However, differences in the physicochemical properties of soil samples require optimization of DNA extraction techniques for each sample separately. The aim of this study was to compare the efficiency, quality, and diversity of genetic material extracted with the use of commonly used kits. The comparative analysis of microbial community composition, displayed differences in microbial community structure depending on which kit was used. Statistical analysis indicated significant differences in recovery of the genetic material for 24 out of 32 analyzed phyla, and the most pronounced differences were seen for Actinobacteria. Also, diversity indexes and reproducibility of DNA extraction with the use of a given kit, varied among the tested methods. As the extraction protocol may influence the apparent structure of a microbial population, at the beginning of each project many extraction kits should be tested in order to choose one that would yield the most representative results and present the closest view to the actual structure of microbial population.}, } @article {pmid28215046, year = {2017}, author = {Rahman, SF and Kantor, RS and Huddy, R and Thomas, BC and van Zyl, AW and Harrison, STL and Banfield, JF}, title = {Genome-resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings.}, journal = {MicrobiologyOpen}, volume = {6}, number = {3}, pages = {}, pmid = {28215046}, issn = {2045-8827}, mesh = {*Biodegradation, Environmental ; Biotransformation ; Metagenomics ; *Microbial Consortia ; Thiocyanates/*metabolism ; *Water Microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Thiocyanate (SCN[-]) is a toxic compound that forms when cyanide (CN[-]), used to recover gold, reacts with sulfur species. SCN[-] -degrading microbial communities have been studied, using bioreactors fed synthetic wastewater. The inclusion of suspended solids in the form of mineral tailings, during the development of the acclimatized microbial consortium, led to the selection of an active planktonic microbial community. Preliminary analysis of the community composition revealed reduced microbial diversity relative to the laboratory-based reactors operated without suspended solids. Despite minor upsets during the acclimation period, the SCN[-] degradation performance was largely unchanged under stable operating conditions. Here, we characterized the microbial community in the SCN[-] degrading bioreactor that included solid particulate tailings and determined how it differed from the biofilm-based communities in solids-free reactor systems inoculated from the same source. Genome-based analysis revealed that the presence of solids decreased microbial diversity, selected for different strains, suppressed growth of thiobacilli inferred to be primarily responsible for SCN[-] degradation, and promoted growth of Trupera, an organism not detected in the reactors without solids. In the solids reactor community, heterotrophy and aerobic respiration represent the dominant metabolisms. Many organisms have genes for denitrification and sulfur oxidation, but only one Thiobacillus sp. in the solids reactor has SCN[-] degradation genes. The presence of the solids prevented floc and biofilm formation, leading to the observed reduced microbial diversity. Collectively the presence of the solids and lack of biofilm community may result in a process with reduced resilience to process perturbations, including fluctuations in the influent composition and pH. The results from this investigation have provided novel insights into the community composition of this industrially relevant community, giving potential for improved process control and operation through ongoing process monitoring.}, } @article {pmid28211884, year = {2017}, author = {Li, Z and Lu, L and Guo, J and Yang, J and Zhang, J and He, B and Xu, L}, title = {Responses of spatial-temporal dynamics of bacterioplankton community to large-scale reservoir operation: a case study in the Three Gorges Reservoir, China.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42469}, pmid = {28211884}, issn = {2045-2322}, mesh = {*Bacteroidetes ; *Biodiversity ; China ; Chlorophyll/analysis ; Environment ; Geography ; Metagenome ; Metagenomics/methods ; *Plankton ; Rivers/*microbiology ; Spatio-Temporal Analysis ; *Water Microbiology ; }, abstract = {Large rivers are commonly regulated by damming, yet the effects of such disruption on bacterioplankton community structures have not been adequately studied. The aim of this study was to explore the biogeographical patterns present under dam regulation and to uncover the major drivers structuring bacterioplankton communities. Bacterioplankton assemblages in the Three Gorges Reservoir (TGR) were analyzed using Illumina Miseq sequencing by comparing seven sites located within the TGR before and after impoundment. This approach revealed ecological and spatial-temporal variations in bacterioplankton community composition along the longitudinal axis. The community was dynamic and dominated by Proteobacteria and Actinobacteria phyla, encompassing 39.26% and 37.14% of all sequences, respectively, followed by Bacteroidetes (8.67%) and Cyanobacteria (3.90%). The Shannon-Wiener index of the bacterioplankton community in the flood season (August) was generally higher than that in the impoundment season (November). Principal Component Analysis of the bacterioplankton community compositions showed separation between different seasons and sampling sites. Results of the relationship between bacterioplankton community compositions and environmental variables highlighted that ecological processes of element cycling and large dam disturbances are of prime importance in driving the assemblages of riverine bacterioplankton communities.}, } @article {pmid28207851, year = {2017}, author = {Kala, A and Kamra, DN and Kumar, A and Agarwal, N and Chaudhary, LC and Joshi, CG}, title = {Impact of levels of total digestible nutrients on microbiome, enzyme profile and degradation of feeds in buffalo rumen.}, journal = {PloS one}, volume = {12}, number = {2}, pages = {e0172051}, pmid = {28207851}, issn = {1932-6203}, mesh = {*Animal Feed ; *Animal Nutritional Physiological Phenomena ; Animals ; Bacteria/classification/genetics ; Buffaloes/*genetics/*microbiology ; *Digestion ; Fermentation ; Male ; Metagenome ; *Microbiota ; Rumen/*enzymology/*microbiology ; }, abstract = {The present study was aimed at understanding a shift in rumen microbiome of buffaloes fed various levels of total digestible nutrients. To understand the process, the metagenomics of rumen microbes, in vivo and in vitro rumen fermentation studies were carried out. Three rumen fistulated adult male Murrah buffaloes were fed three isonitrogenous diets varying in total digestible nutrients (70, 85 and 100% of TDN requirement) in 3X3 switch over design. On dry matter basis, wheat straw/ roughage content were 81, 63 and 51% and that of maize grain was 8, 16 and 21% in three diets respectively. After 20 d of feeding, rumen liquor and rumen contents were sampled just before (0h) and 4h post feeding. Ruminococcus flavefaciens and R. albus (estimated with real time PCR) were higher in high roughage diets. The predominant phyla in all the three groups were Bacteroidetes, Firmicutes followed by Proteobacteria, Actinobacteria and Fibrobacteres. A core group of more than fifty rumen bacteria was present in all the animals with very little variations due to level of TDN. The most predominant bacterial genera reported in order of decreasing abundance were: Prevotella, Bacteroides, Clostridium, Ruminococcus, Eubacterium, Parabacteroides, Fibrobacter, Butyrivibrio etc. The higher diversity of the enyzmes families GH 23, GH 28, GH 39, GH 97, GH 106, and GH 127 (the enzymes active in fibre and starch degradation) were significantly higher on 100%TDN diet while CE 14 (required for the hydrolysis of bond between carbohydrate and lignin) was higher on low TDN (70%) diet, indicating ester bond cleavage was better in animals fed high roughage (wheat straw) diet.}, } @article {pmid28198697, year = {2017}, author = {Silverman, JD and Washburne, AD and Mukherjee, S and David, LA}, title = {A phylogenetic transform enhances analysis of compositional microbiota data.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, pmid = {28198697}, issn = {2050-084X}, support = {T32 GM007171/GM/NIGMS NIH HHS/United States ; T32 GM071340/GM/NIGMS NIH HHS/United States ; T32 GM145449/GM/NIGMS NIH HHS/United States ; }, mesh = {Biostatistics/*methods ; Computational Biology/*methods ; Humans ; *Microbiota ; }, abstract = {Surveys of microbial communities (microbiota), typically measured as relative abundance of species, have illustrated the importance of these communities in human health and disease. Yet, statistical artifacts commonly plague the analysis of relative abundance data. Here, we introduce the PhILR transform, which incorporates microbial evolutionary models with the isometric log-ratio transform to allow off-the-shelf statistical tools to be safely applied to microbiota surveys. We demonstrate that analyses of community-level structure can be applied to PhILR transformed data with performance on benchmarks rivaling or surpassing standard tools. Additionally, by decomposing distance in the PhILR transformed space, we identified neighboring clades that may have adapted to distinct human body sites. Decomposing variance revealed that covariation of bacterial clades within human body sites increases with phylogenetic relatedness. Together, these findings illustrate how the PhILR transform combines statistical and phylogenetic models to overcome compositional data challenges and enable evolutionary insights relevant to microbial communities.}, } @article {pmid28198673, year = {2017}, author = {Liang, C and Tseng, HC and Chen, HM and Wang, WC and Chiu, CM and Chang, JY and Lu, KY and Weng, SL and Chang, TH and Chang, CH and Weng, CT and Wang, HM and Huang, HD}, title = {Diversity and enterotype in gut bacterial community of adults in Taiwan.}, journal = {BMC genomics}, volume = {18}, number = {Suppl 1}, pages = {932}, pmid = {28198673}, issn = {1471-2164}, mesh = {Adult ; *Biodiversity ; Cluster Analysis ; Decision Trees ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; Phenotype ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Gastrointestinal microbiota, particularly gut microbiota, is associated with human health. The biodiversity of gut microbiota is affected by ethnicities and environmental factors such as dietary habits or medicine intake, and three enterotypes of the human gut microbiome were announced in 2011. These enterotypes are not significantly correlated with gender, age, or body weight but are influenced by long-term dietary habits. However, to date, only two enterotypes (predominantly consisting of Bacteroides and Prevotella) have shown these characteristics in previous research; the third enterotype remains ambiguous. Understanding the enterotypes can improve the knowledge of the relationship between microbiota and human health.

RESULTS: We obtained 181 human fecal samples from adults in Taiwan. Microbiota compositions were analyzed using next-generation sequencing (NGS) technology, which is a culture-independent method of constructing microbial community profiles by sequencing 16S ribosomal DNA (rDNA). In these samples, 17,675,898 sequencing reads were sequenced, and on average, 215 operational taxonomic units (OTUs) were identified for each sample. In this study, the major bacteria in the enterotypes identified from the fecal samples were Bacteroides, Prevotella, and Enterobacteriaceae, and their correlation with dietary habits was confirmed. A microbial interaction network in the gut was observed on the basis of the amount of short-chain fatty acids, pH value of the intestine, and composition of the bacterial community (enterotypes). Finally, a decision tree was derived to provide a predictive model for the three enterotypes. The accuracies of this model in training and independent testing sets were 97.2 and 84.0%, respectively.

CONCLUSIONS: We used NGS technology to characterize the microbiota and constructed a predictive model. The most significant finding was that Enterobacteriaceae, the predominant subtype, could be a new subtype of enterotypes in the Asian population.}, } @article {pmid28198672, year = {2017}, author = {Ai, D and Huang, R and Wen, J and Li, C and Zhu, J and Xia, LC}, title = {Integrated metagenomic data analysis demonstrates that a loss of diversity in oral microbiota is associated with periodontitis.}, journal = {BMC genomics}, volume = {18}, number = {Suppl 1}, pages = {1041}, pmid = {28198672}, issn = {1471-2164}, support = {R01 HG006137/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; *Biodiversity ; Case-Control Studies ; Cluster Analysis ; Computational Biology/*methods ; Dental Plaque ; Gingiva/microbiology ; Humans ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; Mouth/microbiology ; Periodontitis/*microbiology ; Phylogeny ; Workflow ; }, abstract = {BACKGROUND: Periodontitis is an inflammatory disease affecting the tissues supporting teeth (periodontium). Integrative analysis of metagenomic samples from multiple periodontitis studies is a powerful way to examine microbiota diversity and interactions within host oral cavity.

METHODS: A total of 43 subjects were recruited to participate in two previous studies profiling the microbial community of human subgingival plaque samples using shotgun metagenomic sequencing. We integrated metagenomic sequence data from those two studies, including six healthy controls, 14 sites representative of stable periodontitis, 16 sites representative of progressing periodontitis, and seven periodontal sites of unknown status. We applied phylogenetic diversity, differential abundance, and network analyses, as well as clustering, to the integrated dataset to compare microbiological community profiles among the different disease states.

RESULTS: We found alpha-diversity, i.e., mean species diversity in sites or habitats at a local scale, to be the single strongest predictor of subjects' periodontitis status (P < 0.011). More specifically, healthy subjects had the highest alpha-diversity, while subjects with stable sites had the lowest alpha-diversity. From these results, we developed an alpha-diversity logistic model-based naive classifier able to perfectly predict the disease status of the seven subjects with unknown periodontal status (not used in training). Phylogenetic profiling resulted in the discovery of nine marker microbes, and these species are able to differentiate between stable and progressing periodontitis, achieving an accuracy of 94.4%. Finally, we found that the reduction of negatively correlated species is a notable signature of disease progression.

CONCLUSIONS: Our results consistently show a strong association between the loss of oral microbiota diversity and the progression of periodontitis, suggesting that metagenomics sequencing and phylogenetic profiling are predictive of early periodontitis, leading to potential therapeutic intervention. Our results also support a keystone pathogen-mediated polymicrobial synergy and dysbiosis (PSD) model to explain the etiology of periodontitis. Apart from P. gingivalis, we identified three additional keystone species potentially mediating the progression of periodontitis progression based on pathogenic characteristics similar to those of known keystone pathogens.}, } @article {pmid28198670, year = {2017}, author = {Yan, J and Chuai, G and Qi, T and Shao, F and Zhou, C and Zhu, C and Yang, J and Yu, Y and Shi, C and Kang, N and He, Y and Liu, Q}, title = {MetaTopics: an integration tool to analyze microbial community profile by topic model.}, journal = {BMC genomics}, volume = {18}, number = {Suppl 1}, pages = {962}, pmid = {28198670}, issn = {1471-2164}, mesh = {Computational Biology/*methods ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; *Software ; Web Browser ; }, abstract = {BACKGROUND: Deciphering taxonomical structures based on high dimensional sequencing data is still challenging in metagenomics study. Moreover, the common workflow processed in this field fails to identify microbial communities and their effect on a specific disease status. Even the relationships and interactions between different bacteria in a microbial community keep unknown.

RESULTS: MetaTopics can efficiently extract the latent microbial communities which reflect the intrinsic relations or interactions among several major microbes. Furthermore, a quantitative measurement, Quetelet Index, is defined to estimate the influence of a latent sub-community on a certain disease status for given samples. An analysis of our in-house oral metagenomics data and public gut microbe data was presented to demonstrate the application and usefulness of MetaTopics. To preset a user-friendly R package, we have built a dedicated website, https://github.com/bm2-lab/MetaTopics , which includes free downloads, detailed tutorials and illustration examples.

CONCLUSIONS: MetaTopics is the first interactive R package to integrate the state-of-arts topic model derived from statistical learning community to analyze and visualize the metagenomics taxonomy data.}, } @article {pmid28198425, year = {2017}, author = {Leite, MF and Pan, Y and Bloem, J and Berge, HT and Kuramae, EE}, title = {Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42634}, pmid = {28198425}, issn = {2045-2322}, mesh = {Bacteria ; Carbon/chemistry/metabolism ; Fungi ; Metagenome ; Metagenomics/methods ; Microbiota ; Nitrogen/*chemistry/*metabolism ; *Soil Microbiology ; }, abstract = {Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.}, } @article {pmid28198423, year = {2017}, author = {Montella, S and Ventorino, V and Lombard, V and Henrissat, B and Pepe, O and Faraco, V}, title = {Discovery of genes coding for carbohydrate-active enzyme by metagenomic analysis of lignocellulosic biomasses.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42623}, pmid = {28198423}, issn = {2045-2322}, mesh = {Biodegradation, Environmental ; *Biomass ; Biotransformation ; Carbohydrate Metabolism/*genetics ; Cellulases/*genetics/*metabolism ; Computational Biology/methods ; Crops, Agricultural ; Gene Expression Profiling ; Glycoside Hydrolases/genetics/metabolism ; High-Throughput Nucleotide Sequencing ; Hydrolysis ; Lignin/*metabolism ; *Metagenome ; *Metagenomics/methods ; Microbiota ; Open Reading Frames ; Polysaccharides/metabolism ; }, abstract = {In this study, a high-throughput sequencing approach was applied to discover novel biocatalysts for lignocellulose hydrolysis from three dedicated energy crops, Arundo donax, Eucalyptus camaldulensis and Populus nigra, after natural biodegradation. The microbiomes of the three lignocellulosic biomasses were dominated by bacterial species (approximately 90%) with the highest representation by the Streptomyces genus both in the total microbial community composition and in the microbial diversity related to GH families of predicted ORFs. Moreover, the functional clustering of the predicted ORFs showed a prevalence of poorly characterized genes, suggesting these lignocellulosic biomasses are potential sources of as yet unknown genes. 1.2%, 0.6% and 3.4% of the total ORFs detected in A. donax, E. camaldulensis and P. nigra, respectively, were putative Carbohydrate-Active Enzymes (CAZymes). Interestingly, the glycoside hydrolases abundance in P. nigra (1.8%) was higher than that detected in the other biomasses investigated in this study. Moreover, a high percentage of (hemi)cellulases with different activities and accessory enzymes (mannanases, polygalacturonases and feruloyl esterases) was detected, confirming that the three analyzed samples were a reservoir of diversified biocatalysts required for an effective lignocellulose saccharification.}, } @article {pmid28198087, year = {2017}, author = {Mancabelli, L and Milani, C and Lugli, GA and Turroni, F and Ferrario, C and van Sinderen, D and Ventura, M}, title = {Meta-analysis of the human gut microbiome from urbanized and pre-agricultural populations.}, journal = {Environmental microbiology}, volume = {19}, number = {4}, pages = {1379-1390}, doi = {10.1111/1462-2920.13692}, pmid = {28198087}, issn = {1462-2920}, mesh = {Agriculture ; Asia ; Europe ; Feces ; *Gastrointestinal Microbiome ; Genetic Variation ; Humans ; Metagenomics ; North America ; Rural Population ; Urban Population ; }, abstract = {Metagenomic studies of the human gut microbiome have only recently begun to explore the differences in taxonomic composition between subjects from diverse geographical origins. Here, we compared taxonomy, resistome and functional metabolic properties of publicly available shotgun datasets of human fecal samples collected from different geographical regions (Europe, North America, Asia and Oceania). Such datasets encompassed gut microbiota information corresponding to 13 developed/industrialized societies, as well as two traditional hunter-gatherer, pre-agricultural communities (Tanzanian and Peruvian individuals). Assessment of the retrieved taxonomic profiles allowed the most updated reconstruction of the global core-microbiome as based on currently available data, as well as the identification and targeted genome reconstruction of bacterial taxa that appear to have been lost and/or acquired during urbanization/industrialization. Functional characterization of these metagenomic datasets indicates that the urbanization/industrialization process which occurred in recent human history has shaped the gut microbiota through the acquisition and/or loss of specific gut microbes, thereby potentially impacting on the overall functionality of the gut microbiome.}, } @article {pmid28196961, year = {2017}, author = {Dickson, RP and Erb-Downward, JR and Freeman, CM and McCloskey, L and Falkowski, NR and Huffnagle, GB and Curtis, JL}, title = {Bacterial Topography of the Healthy Human Lower Respiratory Tract.}, journal = {mBio}, volume = {8}, number = {1}, pages = {}, pmid = {28196961}, issn = {2150-7511}, support = {UL1 TR000433/TR/NCATS NIH HHS/United States ; T32 HL007749/HL/NHLBI NIH HHS/United States ; I01 BX001389/BX/BLRD VA/United States ; R01 HL114447/HL/NHLBI NIH HHS/United States ; I01 CX000911/CX/CSRD VA/United States ; U01 HL098961/HL/NHLBI NIH HHS/United States ; K23 HL130641/HL/NHLBI NIH HHS/United States ; I01 CX001553/CX/CSRD VA/United States ; }, mesh = {Adult ; Aged ; Bacteria/classification/*genetics/*isolation & purification ; Bronchoalveolar Lavage/instrumentation/standards ; Bronchoalveolar Lavage Fluid/*microbiology ; Bronchoscopy/adverse effects/standards ; DNA, Bacterial/genetics ; Female ; Healthy Volunteers ; Humans ; Lung/*microbiology ; Male ; *Metagenome ; *Microbiota/genetics ; Middle Aged ; Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Although culture-independent techniques have refuted lung sterility in health, controversy about contamination during bronchoscope passage through the upper respiratory tract (URT) has impeded research progress. We sought to establish whether bronchoscopic sampling accurately reflects the lung microbiome in health and to distinguish between two proposed routes of authentic microbial immigration, (i) dispersion along contiguous respiratory mucosa and (ii) subclinical microaspiration. During bronchoscopy of eight adult volunteers without lung disease, we performed seven protected specimen brushings (PSB) and bilateral bronchoalveolar lavages (BALs) per subject. We amplified, sequenced, and analyzed the bacterial 16S rRNA gene V4 regions by using the Illumina MiSeq platform. Rigorous attention was paid to eliminate potential sources of error or contamination, including a randomized processing order and the inclusion and analysis of exhaustive procedural and sequencing control specimens. Indices of mouth-lung immigration (mouth-lung community similarity, bacterial burden, and community richness) were all significantly greater in airway and alveolar specimens than in bronchoscope contamination control specimens, indicating minimal evidence of pharyngeal contamination. Ecological indices of mouth-lung immigration peaked at or near the carina, as predicted for a primary immigration route of microaspiration. Bacterial burden, diversity, and mouth-lung similarity were greater in BAL than PSB samples, reflecting differences in the sampled surface areas. (This study has been registered at ClinicalTrials.gov under registration no. NCT02392182.)IMPORTANCE This study defines the bacterial topography of the healthy human respiratory tract and provides ecological evidence that bacteria enter the lungs in health primarily by microaspiration, with potential contribution in some subjects by direct dispersal along contiguous mucosa. By demonstrating that contamination contributes negligibly to microbial communities in bronchoscopically acquired specimens, we validate the use of bronchoscopy to investigate the lung microbiome.}, } @article {pmid28192251, year = {2017}, author = {Simms-Waldrip, TR and Sunkersett, G and Coughlin, LA and Savani, MR and Arana, C and Kim, J and Kim, M and Zhan, X and Greenberg, DE and Xie, Y and Davies, SM and Koh, AY}, title = {Antibiotic-Induced Depletion of Anti-inflammatory Clostridia Is Associated with the Development of Graft-versus-Host Disease in Pediatric Stem Cell Transplantation Patients.}, journal = {Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation}, volume = {23}, number = {5}, pages = {820-829}, doi = {10.1016/j.bbmt.2017.02.004}, pmid = {28192251}, issn = {1523-6536}, mesh = {Adolescent ; Animals ; Anti-Bacterial Agents/*adverse effects ; Anti-Inflammatory Agents/adverse effects ; Child ; Child, Preschool ; Clindamycin/adverse effects/pharmacology ; Clostridium/pathogenicity ; Gastrointestinal Microbiome/drug effects ; Graft vs Host Disease/*chemically induced/etiology/microbiology ; Hematopoietic Stem Cell Transplantation/*adverse effects ; Humans ; Infant ; Mice ; Pilot Projects ; }, abstract = {Adult stem cell transplantation (SCT) patients with graft-versus-host-disease (GVHD) exhibit significant disruptions in gut microbial communities. These changes are associated with higher overall mortality and appear to be driven by specific antibiotic therapies. It is unclear whether pediatric SCT patients who develop GVHD exhibit similar antibiotic-induced gut microbiota community changes. Here, we show that pediatric SCT patients (from Children's Medical Center Dallas, n = 8, and Cincinnati Children's Hospital, n = 7) who developed GVHD showed a significant decline, up to 10-log fold, in gut anti-inflammatory Clostridia (AIC) compared with those without GVHD. In fact, the development of GVHD is significantly associated with this AIC decline and with cumulative antibiotic exposure, particularly antibiotics effective against anaerobic bacteria (P = .003, Firth logistic regression analysis). Using metagenomic shotgun sequencing analysis, we were able to identify specific commensal bacterial species, including AIC, that were significantly depleted in GVHD patients. We then used a preclinical GVHD model to verify our clinical observations. Clindamycin depleted AIC and exacerbated GVHD in mice, whereas oral AIC supplementation increased gut AIC levels and mitigated GVHD in mice. Together, these data suggest that an antibiotic-induced AIC depletion in the gut microbiota is associated with the development of GVHD in pediatric SCT patients.}, } @article {pmid28189830, year = {2017}, author = {Kohrs, F and Heyer, R and Bissinger, T and Kottler, R and Schallert, K and Püttker, S and Behne, A and Rapp, E and Benndorf, D and Reichl, U}, title = {Proteotyping of laboratory-scale biogas plants reveals multiple steady-states in community composition.}, journal = {Anaerobe}, volume = {46}, number = {}, pages = {56-68}, doi = {10.1016/j.anaerobe.2017.02.005}, pmid = {28189830}, issn = {1095-8274}, mesh = {Ammonia/analysis ; Anaerobiosis ; *Biofuels/analysis ; Bioreactors ; Cluster Analysis ; Fatty Acids, Volatile/analysis ; Metagenomics/methods ; Methane/biosynthesis ; *Microbiota ; Plants/*metabolism/*microbiology ; *Proteomics/methods ; Tandem Mass Spectrometry ; Temperature ; }, abstract = {Complex microbial communities are the functional core of anaerobic digestion processes taking place in biogas plants (BGP). So far, however, a comprehensive characterization of the microbiomes involved in methane formation is technically challenging. As an alternative, enriched communities from laboratory-scale experiments can be investigated that have a reduced number of organisms and are easier to characterize by state of the art mass spectrometric-based (MS) metaproteomic workflows. Six parallel laboratory digesters were inoculated with sludge from a full-scale BGP to study the development of enriched microbial communities under defined conditions. During the first three month of cultivation, all reactors (R1-R6) were functionally comparable regarding biogas productions (375-625 NL Lreactor volume[-1] d[-1]), methane yields (50-60%), pH values (7.1-7.3), and volatile fatty acids (VFA, <5 mM). Nevertheless, a clear impact of the temperature (R3, R4) and ammonia (R5, R6) shifts was observed for the respective reactors. In both reactors operated under thermophilic regime, acetic and propionic acid (10-20 mM) began to accumulate. While R4 recovered quickly from acidification, the levels of VFA remained to be high in R3 resulting in low pH values of 6.5-6.9. The digesters R5 and R6 operated under the high ammonia regime (>1 gNH3 L[-1]) showed an increase to pH 7.5-8.0, accumulation of acetate (>10 mM), and decreasing biogas production (<125 NL Lreactor volume[-1] d[-1]). Tandem MS (MS/MS)-based proteotyping allowed the identification of taxonomic abundances and biological processes. Although all reactors showed similar performances, proteotyping and terminal restriction fragment length polymorphisms (T-RFLP) fingerprinting revealed significant differences in the composition of individual microbial communities, indicating multiple steady-states. Furthermore, cellulolytic enzymes and cellulosomal proteins of Clostridium thermocellum were identified to be specific markers for the thermophilic reactors (R3, R4). Metaproteins found in R3 indicated hydrogenothrophic methanogenesis, whereas metaproteins of acetoclastic methanogenesis were identified in R4. This suggests not only an individual evolution of microbial communities even for the case that BGPs are started at the same initial conditions under well controlled environmental conditions, but also a high compositional variance of microbiomes under extreme conditions.}, } @article {pmid28189315, year = {2017}, author = {Bicalho, MLS and Santin, T and Rodrigues, MX and Marques, CE and Lima, SF and Bicalho, RC}, title = {Dynamics of the microbiota found in the vaginas of dairy cows during the transition period: Associations with uterine diseases and reproductive outcome.}, journal = {Journal of dairy science}, volume = {100}, number = {4}, pages = {3043-3058}, doi = {10.3168/jds.2016-11623}, pmid = {28189315}, issn = {1525-3198}, mesh = {Animals ; Cattle ; Cattle Diseases/*microbiology ; Endometritis/veterinary ; Female ; Microbiota ; Postpartum Period ; RNA, Ribosomal, 16S/*genetics ; Uterine Diseases/veterinary ; Vagina ; }, abstract = {We investigated the microbiota found in the vaginas of Holstein dairy cows during the transition period and described the differences in bacterial composition and total bacterial load (TBL) associated with disease and fertility. Vaginal swabs were collected at -7, 0, 3, and 7 d relative to parturition from 111 dairy cows housed on a commercial dairy farm near Ithaca, New York. Microbiota were characterized by next-generation DNA sequencing of the bacterial 16S rRNA gene, and TBL was determined by real-time quantitative PCR. We applied repeated-measures ANOVA to evaluate the associations of uterine disease and related risk factors with the microbiota and TBL. We estimated phylum-specific bacterial load by multiplying the TBL by the relative abundance of each phylum observed in the metagenomics results. We confirmed the validity of this approach for estimating bacterial load by enumerating the number of bacteria in an artificial sample mixed in vitro and in clinical and healthy vaginal samples. Phyla associated with uterine disease and related risk factors were Proteobacteria, Fusobacteria, and Bacteroidetes. Cows with retained placenta and healthy cows had similar TBL at the day of parturition, but at d 7 postpartum, cows with retained placenta showed a significantly higher TBL, mainly driven by higher estimated loads of Fusobacteria and Bacteroidetes. Cows diagnosed with metritis had a significantly higher estimated load of Proteobacteria at d -7 and at calving and higher estimated loads of Fusobacteria in the postpartum samples. Additionally, the estimated load of Bacteroidetes at d 7 postpartum was higher for cows diagnosed with endometritis at 35 days in milk. Higher estimated loads of Fusobacteria and Bacteroidetes were also evident in cows with postpartum fever, in primiparous cows, in cows with assisted parturition, and in cows that gave birth to twins. Our findings demonstrated that microbiota composition and TBL were associated with known periparturient risk factors of uterine diseases and reproductive failure, including parity, assisted parturition, and retained fetal membranes.}, } @article {pmid28188205, year = {2017}, author = {Men, Y and Yu, K and Bælum, J and Gao, Y and Tremblay, J and Prestat, E and Stenuit, B and Tringe, SG and Jansson, J and Zhang, T and Alvarez-Cohen, L}, title = {Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {8}, pages = {}, pmid = {28188205}, issn = {1098-5336}, support = {P42 ES004705/ES/NIEHS NIH HHS/United States ; R01 ES024255/ES/NIEHS NIH HHS/United States ; S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; }, mesh = {Bacteria/metabolism ; Biodegradation, Environmental ; Biosynthetic Pathways/genetics ; Chloroflexi/drug effects/*genetics/*metabolism ; Corrinoids/metabolism ; *Gene Expression Profiling ; Genome, Bacterial ; Halogenation ; *Metagenomics ; *Microbial Consortia/drug effects/genetics ; Trichloroethylene/metabolism ; Veillonellaceae/genetics/metabolism ; Vitamin B 12/*metabolism/pharmacology ; }, abstract = {The aim of this study is to obtain a systems-level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoid de novo biosynthesis pathway was also assigned to the Veillonellaceae bin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway of Dehalococcoides was upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions.IMPORTANCE The key chloroethene-dechlorinating bacterium Dehalococcoides mccartyi is a cobalamin auxotroph, thus acquiring corrinoids from other community members. Therefore, it is important to investigate the microbe-microbe interactions between Dehalococcoides and the corrinoid-providing microorganisms in a community. This study provides systems-level information, i.e., taxonomic and functional compositions and dynamics of the supportive microorganisms in dechlorinating communities under different cobalamin conditions. The findings shed light on the important roles of Veillonellaceae species in the communities compared to other coexisting community members in producing and providing corrinoids for Dehalococcoides species under cobalamin-limited conditions.}, } @article {pmid28187782, year = {2017}, author = {Feigelman, R and Kahlert, CR and Baty, F and Rassouli, F and Kleiner, RL and Kohler, P and Brutsche, MH and von Mering, C}, title = {Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {20}, pmid = {28187782}, issn = {2049-2618}, mesh = {Bacteria/*genetics/isolation & purification/pathogenicity ; Cystic Fibrosis/*microbiology ; Drug Resistance, Bacterial/genetics ; Genetic Variation ; Genomic Islands ; *High-Throughput Nucleotide Sequencing ; Humans ; Lung/*microbiology ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; Multilocus Sequence Typing ; Respiratory Tract Infections/microbiology ; Sputum/*microbiology ; }, abstract = {BACKGROUND: Cystic fibrosis (CF) is a life-threatening genetic disorder, characterized by chronic microbial lung infections due to abnormally viscous mucus secretions within airways. The clinical management of CF typically involves regular respiratory-tract cultures in order to identify pathogens and to guide treatment. However, culture-based methods can miss atypical or slow-growing microbes. Furthermore, the isolated microbes are often not classified at the strain level due to limited taxonomic resolution.

RESULTS: Here, we show that untargeted metagenomic sequencing of sputum DNA can provide valuable information beyond the possibilities of culture-based diagnosis. We sequenced the sputum of six CF patients and eleven control samples (including healthy subjects and chronic obstructive pulmonary disease patients) without prior depletion of human DNA or cell size selection, thus obtaining the most unbiased and comprehensive characterization of CF respiratory tract microbes to date. We present detailed descriptions of the CF and healthy lung microbiome, reconstruct near complete pathogen genomes, and confirm that the CF lungs consistently exhibit reduced microbial diversity. Crucially, the obtained genomic sequences enabled a detailed identification of the exact pathogen strain types, when analyzed in conjunction with existing multi-locus sequence typing databases. We also detected putative pathogenicity islands and indicators of antibiotic resistance, in good agreement with independent clinical tests.

CONCLUSIONS: Unbiased sputum metagenomics provides an in-depth profile of the lung pathogen microbiome, which is complementary to and more detailed than standard culture-based reporting. Furthermore, functional and taxonomic features of the dominant pathogens, including antibiotics resistances, can be deduced-supporting accurate and non-invasive clinical diagnosis.}, } @article {pmid28183913, year = {2017}, author = {Levin, BJ and Huang, YY and Peck, SC and Wei, Y and Martínez-Del Campo, A and Marks, JA and Franzosa, EA and Huttenhower, C and Balskus, EP}, title = {A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline.}, journal = {Science (New York, N.Y.)}, volume = {355}, number = {6325}, pages = {}, pmid = {28183913}, issn = {1095-9203}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; }, mesh = {Amino Acid Motifs ; Anaerobiosis ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; Hydroxyproline/*metabolism ; Metagenome ; Proline Oxidase/*chemistry/*genetics/metabolism ; Propanediol Dehydratase/chemistry/genetics ; Protein Processing, Post-Translational ; Sequence Alignment ; }, abstract = {The human microbiome encodes vast numbers of uncharacterized enzymes, limiting our functional understanding of this community and its effects on host health and disease. By incorporating information about enzymatic chemistry into quantitative metagenomics, we determined the abundance and distribution of individual members of the glycyl radical enzyme superfamily among the microbiomes of healthy humans. We identified many uncharacterized family members, including a universally distributed enzyme that enables commensal gut microbes and human pathogens to dehydrate trans-4-hydroxy-l-proline, the product of the most abundant human posttranslational modification. This "chemically guided functional profiling" workflow can therefore use ecological context to facilitate the discovery of enzymes in microbial communities.}, } @article {pmid28182951, year = {2017}, author = {Hughes, ER and Winter, MG and Duerkop, BA and Spiga, L and Furtado de Carvalho, T and Zhu, W and Gillis, CC and Büttner, L and Smoot, MP and Behrendt, CL and Cherry, S and Santos, RL and Hooper, LV and Winter, SE}, title = {Microbial Respiration and Formate Oxidation as Metabolic Signatures of Inflammation-Associated Dysbiosis.}, journal = {Cell host & microbe}, volume = {21}, number = {2}, pages = {208-219}, pmid = {28182951}, issn = {1934-6069}, support = {R01 AI118807/AI/NIAID NIH HHS/United States ; K01 DK102436/DK/NIDDK NIH HHS/United States ; R01 DK070855/DK/NIDDK NIH HHS/United States ; T32 AI007520/AI/NIAID NIH HHS/United States ; R01 AI095500/AI/NIAID NIH HHS/United States ; R01 AI122749/AI/NIAID NIH HHS/United States ; T32 GM109776/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Colitis/microbiology ; Disease Models, Animal ; Dysbiosis/*microbiology ; Escherichia coli/*metabolism ; Female ; Formates/*metabolism ; Gastrointestinal Microbiome ; Inflammation/*microbiology ; Intestines/microbiology ; Male ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Proteobacteria/metabolism ; }, abstract = {Intestinal inflammation is frequently associated with an alteration of the gut microbiota, termed dysbiosis, which is characterized by a reduced abundance of obligate anaerobic bacteria and an expansion of facultative Proteobacteria such as commensal E. coli. The mechanisms enabling the outgrowth of Proteobacteria during inflammation are incompletely understood. Metagenomic sequencing revealed bacterial formate oxidation and aerobic respiration to be overrepresented metabolic pathways in a chemically induced murine model of colitis. Dysbiosis was accompanied by increased formate levels in the gut lumen. Formate was of microbial origin since no formate was detected in germ-free mice. Complementary studies using commensal E. coli strains as model organisms indicated that formate dehydrogenase and terminal oxidase genes provided a fitness advantage in murine models of colitis. In vivo, formate served as electron donor in conjunction with oxygen as the terminal electron acceptor. This work identifies bacterial formate oxidation and oxygen respiration as metabolic signatures for inflammation-associated dysbiosis.}, } @article {pmid28180325, year = {2017}, author = {Orellana, LH and Rodriguez-R, LM and Konstantinidis, KT}, title = {ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores.}, journal = {Nucleic acids research}, volume = {45}, number = {3}, pages = {e14}, pmid = {28180325}, issn = {1362-4962}, mesh = {Aquatic Organisms/genetics ; Computational Biology/methods ; Databases, Genetic/statistics & numerical data ; Ecosystem ; Metagenomics/*statistics & numerical data ; Microbial Consortia/genetics ; Phylogeny ; ROC Curve ; Soil Microbiology ; }, abstract = {Functional annotation of metagenomic and metatranscriptomic data sets relies on similarity searches based on e-value thresholds resulting in an unknown number of false positive and negative matches. To overcome these limitations, we introduce ROCker, aimed at identifying position-specific, most-discriminant thresholds in sliding windows along the sequence of a target protein, accounting for non-discriminative domains shared by unrelated proteins. ROCker employs the receiver operating characteristic (ROC) curve to minimize false discovery rate (FDR) and calculate the best thresholds based on how simulated shotgun metagenomic reads of known composition map onto well-curated reference protein sequences and thus, differs from HMM profiles and related methods. We showcase ROCker using ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ) genes, mediating oxidation of ammonia and the reduction of the potent greenhouse gas, N2O, to inert N2, respectively. ROCker typically showed 60-fold lower FDR when compared to the common practice of using fixed e-values. Previously uncounted ‘atypical’ nosZ genes were found to be two times more abundant, on average, than their typical counterparts in most soil metagenomes and the abundance of bacterial amoA was quantified against the highly-related particulate methane monooxygenase (pmoA). Therefore, ROCker can reliably detect and quantify target genes in short-read metagenomes.}, } @article {pmid28179006, year = {2017}, author = {Manor, O and Borenstein, E}, title = {Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {19}, pmid = {28179006}, issn = {2049-2618}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; P30 DK089507/DK/NIDDK NIH HHS/United States ; R01 DK095869/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Computational Biology/*methods ; DNA, Bacterial/genetics ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Genetic Variation/genetics ; Humans ; Metagenomics/*methods ; }, abstract = {BACKGROUND: Recent metagenomic analyses of the human gut microbiome identified striking variability in its taxonomic composition across individuals. Notably, however, these studies often reported marked functional uniformity, with relatively little variation in the microbiome's gene composition or in its overall metabolic capacity.

RESULTS: Here, we address this surprising discrepancy between taxonomic and functional variations and set out to track its origins. Specifically, we demonstrate that the functional uniformity observed in microbiome studies can be attributed, at least partly, to common computational metagenomic processing procedures that mask true functional variation across microbiome samples. We identify several such procedures, including commonly used practices for gene abundance normalization, mapping of gene families to functional pathways, and gene family aggregation. We show that accounting for these factors and using revised metagenomic processing procedures uncovers such hidden functional variation, significantly increasing observed variation in the abundance of functional elements across samples. Importantly, we find that this uncovered variation is biologically meaningful and that it is associated with both host identity and health.

CONCLUSIONS: Accurate characterization of functional variation in the microbiome is essential for comparative metagenomic analyses in health and disease. Our finding that metagenomic processing procedures mask underlying and biologically meaningful functional variation therefore highlights an important challenge such studies may face. Alternative schemes for metagenomic processing that uncover this hidden functional variation can facilitate improved metagenomic analysis and help pinpoint disease- and host-associated shifts in the microbiome's functional capacity.}, } @article {pmid28178315, year = {2017}, author = {Tayabali, AF and Coleman, G and Crosthwait, J and Nguyen, KC and Zhang, Y and Shwed, P}, title = {Composition and pathogenic potential of a microbial bioremediation product used for crude oil degradation.}, journal = {PloS one}, volume = {12}, number = {2}, pages = {e0171911}, pmid = {28178315}, issn = {1932-6203}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Biodegradation, Environmental ; Biodiversity ; Cell Line ; Cytokines/metabolism ; Environmental Exposure/adverse effects ; Humans ; Inflammation Mediators/metabolism ; Leukocytes/drug effects/metabolism ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Microbial Sensitivity Tests ; Microbial Viability ; Petroleum/*microbiology/toxicity ; }, abstract = {A microbial bioremediation product (MBP) used for large-scale oil degradation was investigated for microbial constituents and possible pathogenicity. Aerobic growth on various media yielded >108 colonies mL-1. Full-length 16S rDNA sequencing and fatty acid profiling from morphologically distinct colonies revealed ≥13 distinct genera. Full-length 16S rDNA library sequencing, by either Sanger or long-read PacBio technology, suggested that up to 21% of the MBP was composed of Arcobacter. Other high abundance microbial constituents (>6%) included the genera Proteus, Enterococcus, Dysgonomonas and several genera in the order Bacteroidales. The MBP was most susceptible to ciprofloxacin, doxycycline, gentamicin, and meropenam. MBP exposure of human HT29 and A549 cells caused significant cytotoxicity, and bacterial growth and adherence. An acellular MBP filtrate was also cytotoxic to HT29, but not A549. Both MBP and filtrate exposures elevated the neutrophil chemoattractant IL-8. In endotracheal murine exposures, bacterial pulmonary clearance was complete after one-week. Elevation of pro-inflammatory cytokines IL-1β, IL-6, and TNF-α, and chemokines KC and MCP-1 occurred between 2h and 48h post-exposure, followed by restoration to baseline levels at 96h. Cytokine/chemokine signalling was accompanied by elevated blood neutrophils and monocytes at 4h and 48h, respectively. Peripheral acute phase response markers were maximal at 24h. All indicators examined returned to baseline values by 168h. In contrast to HT29, but similar to A549 observations, MBP filtrate did not induce significant murine effects with the indicators examined. The results demonstrated the potentially complex nature of MBPs and transient immunological effects during exposure. Products containing microbes should be scrutinized for pathogenic components and subjected to characterisation and quality validation prior to commercial release.}, } @article {pmid28176868, year = {2017}, author = {Yergeau, E and Michel, C and Tremblay, J and Niemi, A and King, TL and Wyglinski, J and Lee, K and Greer, CW}, title = {Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42242}, pmid = {28176868}, issn = {2045-2322}, mesh = {Arctic Regions ; Canada ; Databases, Genetic ; Geography ; Ice Cover/*microbiology ; Metagenomics/*methods ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {Climate change has resulted in an accelerated decline of Arctic sea ice since 2001 resulting in primary production increases and prolongation of the ice-free season within the Northwest Passage. The taxonomic and functional microbial community composition of the seawater and sea ice of the Canadian Arctic is not very well known. Bacterial communities from the bottom layer of sea ice cores and surface water from 23 locations around Cornwallis Island, NU, Canada, were extensively screened. The bacterial 16S rRNA gene was sequenced for all samples while shotgun metagenomics was performed on selected samples. Bacterial community composition showed large variation throughout the sampling area both for sea ice and seawater. Seawater and sea ice samples harbored significantly distinct microbial communities, both at different taxonomic levels and at the functional level. A key difference between the two sample types was the dominance of algae in sea ice samples, as visualized by the higher relative abundance of algae and photosynthesis-related genes in the metagenomic datasets and the higher chl a concentrations. The relative abundance of various OTUs and functional genes were significantly correlated with multiple environmental parameters, highlighting many potential environmental drivers and ecological strategies.}, } @article {pmid28176851, year = {2017}, author = {Zhang, J and Xu, C and Huo, D and Hu, Q and Peng, Q}, title = {Comparative study of the gut microbiome potentially related to milk protein in Murrah buffaloes (Bubalus bubalis) and Chinese Holstein cattle.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42189}, pmid = {28176851}, issn = {2045-2322}, mesh = {Amino Acids/metabolism ; Animals ; Bacteroidetes/classification/isolation & purification/*metabolism ; Buffaloes/*microbiology/physiology ; Burkholderiales/classification/isolation & purification/*metabolism ; Cattle ; China ; Clostridiales/classification/isolation & purification/*metabolism ; Coenzymes/metabolism ; Female ; Gastrointestinal Microbiome/*physiology ; Lactation/physiology ; Lipopolysaccharides/metabolism ; Milk Proteins/biosynthesis/*chemistry ; Phylogeny ; Pyruvic Acid/metabolism ; Vitamins/metabolism ; }, abstract = {Previous studies suggested a close relationship between ruminant gut microbes and the mammary gland. In this study, shotgun metagenomic sequencing was used to reveal the differences in the intestinal microbiome potentially related to milk components in Murrah buffaloes and Chinese Holstein cattle. A PCoA based on the weighted Unifrac distances showed an apparent clustering pattern in the structure of intestinal microbiota between buffalo and cattle. We could attribute the structural difference to the genera of Sutterella, Coprococcus and Dorea. A further analysis of microbial functional features revealed that the biosynthesis of amino acids (including lysine, valine, leucine and isoleucine), lipopolysaccharide biosynthesis and cofactor/vitamin biosynthesis were enriched in the buffalo. In contrast, dairy cattle had higher levels of pyruvate metabolism and carbon fixation in photosynthetic organisms. A further correlation analysis based on different milk components and the typical microbiome uncovered a significant positive correlation between milk protein and the microbial biosynthesis of amino acids, which was also positively correlated in the genera of Parabacteroides, Dorea and Sutterella. This study will expand our understanding of the intestinal microbiome of buffalo and cattle as representative ruminants, as well as provide new views about how to improve the production and nutritional qualities of animal milk.}, } @article {pmid28170428, year = {2017}, author = {Bai, S and Chen, H and Zhu, L and Liu, W and Yu, HD and Wang, X and Yin, Y}, title = {Comparative study on the in vitro effects of Pseudomonas aeruginosa and seaweed alginates on human gut microbiota.}, journal = {PloS one}, volume = {12}, number = {2}, pages = {e0171576}, pmid = {28170428}, issn = {1932-6203}, support = {P20 GM103434/GM/NIGMS NIH HHS/United States ; R43 GM113545/GM/NIGMS NIH HHS/United States ; UL1 TR000117/TR/NCATS NIH HHS/United States ; }, mesh = {Alginates/chemistry/*pharmacology ; Batch Cell Culture Techniques ; DNA Transposable Elements ; Fatty Acids/biosynthesis ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; Humans ; In Vitro Techniques ; Metagenome ; Metagenomics ; Mutation ; Pseudomonas aeruginosa/genetics/*metabolism ; RNA, Ribosomal, 16S/genetics ; Seaweed/*chemistry ; }, abstract = {Alginates pertain to organic polysaccharides that have been extensively used in food- and medicine-related industries. The present study obtained alginates from an alginate overproducing Pseudomonas aeruginosa PAO1 mutant by screening transposon mutagenesis libraries. The interaction between bacterial and seaweed alginates and gut microbiota were further studied by using an in vitro batch fermentation system. Thin-layer chromatography (TLC) analysis indicated that both bacterial and seaweed alginates can be completely degraded by fecal bacteria isolated from study volunteers, indicating that a minor structural difference between bacterial and seaweed alginates (O-acetylation and lack of G-G blocks) didn't affect the digestion of alginates by human microbiota. Although, the digestion of bacterial and seaweed alginates was attributed to different Bacteroides xylanisolvens strains, they harbored similar alginate lyase genes. Genus Bacteroides with alginate-degrading capability were enriched in growth medium containing bacterial or seaweed alginates after in vitro fermentation. Short-chain fatty acid (SCFA) production in both bacterial and seaweed alginates was also comparable, but was significantly higher than the same medium using starch. In summary, the present study has isolated an alginate-overproducing P. aeruginosa mutant strain. Both seaweed and bacterial alginates were degraded by human gut microbiota, and their regulatory function on gut microbiota was similar.}, } @article {pmid28170403, year = {2017}, author = {Cox, MJ and Turek, EM and Hennessy, C and Mirza, GK and James, PL and Coleman, M and Jones, A and Wilson, R and Bilton, D and Cookson, WO and Moffatt, MF and Loebinger, MR}, title = {Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-cystic fibrosis bronchiectasis patients.}, journal = {PloS one}, volume = {12}, number = {2}, pages = {e0170622}, pmid = {28170403}, issn = {1932-6203}, support = {/WT_/Wellcome Trust/United Kingdom ; G1000758/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Aged ; Bronchiectasis/*complications/diagnosis/etiology ; Bronchitis/*diagnosis/*etiology/physiopathology ; Cross-Sectional Studies ; Humans ; Metagenomics/methods ; *Microbiota ; Middle Aged ; *RNA, Ribosomal, 16S ; Respiratory Function Tests ; Risk Factors ; Sputum/*microbiology ; Tomography, X-Ray Computed ; }, abstract = {BACKGROUND: Bronchiectasis is accompanied by chronic bronchial infection that may drive disease progression. However, the evidence base for antibiotic therapy is limited. DNA based methods offer better identification and quantification of microbial constituents of sputum than standard clinical culture and may help inform patient management strategies. Our study objective was to determine the longitudinal variability of the non-cystic fibrosis (CF) bronchiectasis microbiome in sputum with respect to clinical variables. Eighty-five patients with non-CF bronchiectasis and daily sputum production were recruited from outpatient clinics and followed for six months. Monthly sputum samples and clinical measurements were taken, together with additional samples during exacerbations. 16S rRNA gene sequencing of the sputum microbiota was successful for 381 samples from 76 patients and analysed in conjunction with clinical data.

RESULTS: Microbial communities were highly individual in composition and stability, usually with limited diversity and often containing multiple pathogens. When compared to DNA sequencing, microbial culture had restricted sensitivity in identifying common pathogens such as Pseudomonas aeruginosa, Haemophilus influenzae, Moraxella catarrhalis. With some exceptions, community characteristics showed poor correlations with clinical features including underlying disease, antibiotic use and exacerbations, with the subject showing the strongest association with community structure. When present, the pathogens mucoid Pseudomonas aeruginosa and Haemophilus influenzae may also shape the structure of the rest of the microbial community.

CONCLUSIONS: The use of microbial community analysis of sputum added to information from microbial culture. A simple model of exacerbations driven by bacterial overgrowth was not supported, suggesting a need for revision of principles for antibiotic therapy. In individual patients, the management of chronic bronchial infection may be improved by therapy specific to their microbiome, taking into account pathogen load, community stability, and acute and chronic community responses to antibiotics.}, } @article {pmid28169321, year = {2017}, author = {Xu, J and Wei, Y and Jia, H and Xiao, L and Gong, D}, title = {A new perspective on studying burial environment before archaeological excavation: analyzing bacterial community distribution by high-throughput sequencing.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41691}, pmid = {28169321}, issn = {2045-2322}, mesh = {*Archaeology ; Bacteria/classification/genetics ; Biodiversity ; *Burial ; High-Throughput Nucleotide Sequencing ; Hydrogen-Ion Concentration ; Metagenome ; Metagenomics/methods ; Microbiota ; Phylogeny ; Salinity ; Soil/chemistry ; *Soil Microbiology ; Water/chemistry ; }, abstract = {Burial conditions play a crucial role in archaeological heritage preservation. Especially, the microorganisms were considered as the leading causes which incurred degradation and vanishment of historic materials. In this article, we analyzed bacterial diversity and community structure from M1 of Wangshanqiao using 16 S rRNA gene amplicon sequencing. The results indicated that microbial communities in burial conditions were diverse among four different samples. The samples from the robber hole varied most obviously in community structure both in Alpha and Beta diversity. In addition, the dominant phylum in different samples were Proteobacteria, Actinobacteria and Bacteroidetes, respectively. Moreover, the study implied that historical materials preservation conditions had connections with bacterial community distribution. At the genus level, Acinetobacter might possess high ability in degrading organic culture heritage in burial conditions, while Bacteroides were associated closely with favorable preservation conditions. This method contributes to fetch information which would never recover after excavation, and it will help to explore microbial degradation on precious organic culture heritage and further our understanding of archaeological burial environment. The study also indicates that robbery has a serious negative impact on burial remains.}, } @article {pmid28167665, year = {2017}, author = {Truong, DT and Tett, A and Pasolli, E and Huttenhower, C and Segata, N}, title = {Microbial strain-level population structure and genetic diversity from metagenomes.}, journal = {Genome research}, volume = {27}, number = {4}, pages = {626-638}, pmid = {28167665}, issn = {1549-5469}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 HG005969/HG/NHGRI NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; }, mesh = {Algorithms ; Bacteroides/genetics/isolation & purification ; Eubacterium/genetics/isolation & purification ; *Genome, Human ; Humans ; *Metagenome ; *Microbiota ; Molecular Typing/methods ; Polymorphism, Genetic ; Prevotella/genetics/isolation & purification ; Sequence Analysis, DNA/methods ; }, abstract = {Among the human health conditions linked to microbial communities, phenotypes are often associated with only a subset of strains within causal microbial groups. Although it has been critical for decades in microbial physiology to characterize individual strains, this has been challenging when using culture-independent high-throughput metagenomics. We introduce StrainPhlAn, a novel metagenomic strain identification approach, and apply it to characterize the genetic structure of thousands of strains from more than 125 species in more than 1500 gut metagenomes drawn from populations spanning North and South American, European, Asian, and African countries. The method relies on per-sample dominant sequence variant reconstruction within species-specific marker genes. It identified primarily subject-specific strain variants (<5% inter-subject strain sharing), and we determined that a single strain typically dominated each species and was retained over time (for >70% of species). Microbial population structure was correlated in several distinct ways with the geographic structure of the host population. In some cases, discrete subspecies (e.g., for Eubacterium rectale and Prevotella copri) or continuous microbial genetic variations (e.g., for Faecalibacterium prausnitzii) were associated with geographically distinct human populations, whereas few strains occurred in multiple unrelated cohorts. We further estimated the genetic variability of gut microbes, with Bacteroides species appearing remarkably consistent (0.45% median number of nucleotide variants between strains), whereas P. copri was among the most plastic gut colonizers. We thus characterize here the population genetics of previously inaccessible intestinal microbes, providing a comprehensive strain-level genetic overview of the gut microbial diversity.}, } @article {pmid28167213, year = {2017}, author = {Koo, H and Hakim, JA and Powell, ML and Kumar, R and Eipers, PG and Morrow, CD and Crowley, M and Lefkowitz, EJ and Watts, SA and Bej, AK}, title = {Metagenomics approach to the study of the gut microbiome structure and function in zebrafish Danio rerio fed with gluten formulated diet.}, journal = {Journal of microbiological methods}, volume = {135}, number = {}, pages = {69-76}, pmid = {28167213}, issn = {1872-8359}, support = {P30 AI027767/AI/NIAID NIH HHS/United States ; P30 CA013148/CA/NCI NIH HHS/United States ; UL1 TR001417/TR/NCATS NIH HHS/United States ; P30 DK056336/DK/NIDDK NIH HHS/United States ; P30 AR050948/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification/*metabolism/pathogenicity ; Bile Acids and Salts/metabolism ; Biodiversity ; Computational Biology/instrumentation ; DNA, Bacterial/isolation & purification ; *Diet ; Ecosystem ; Gastrointestinal Diseases/microbiology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/metabolism/*microbiology ; Genes, Bacterial ; Glutens/*metabolism ; Glycine/metabolism ; Metagenomics/*methods ; Microbial Consortia ; Models, Animal ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Serine/metabolism ; Threonine/metabolism ; Vitamin B 12/biosynthesis ; Zebrafish/*microbiology ; }, abstract = {In this study, we report the gut microbial composition and predictive functional profiles of zebrafish, Danio rerio, fed with a control formulated diet (CFD), and a gluten formulated diet (GFD) using a metagenomics approach and bioinformatics tools. The microbial communities of the GFD-fed D. rerio displayed heightened abundances of Legionellales, Rhizobiaceae, and Rhodobacter, as compared to the CFD-fed counterparts. Predicted metagenomics of microbial communities (PICRUSt) in GFD-fed D. rerio showed KEGG functional categories corresponding to bile secretion, secondary bile acid biosynthesis, and the metabolism of glycine, serine, and threonine. The CFD-fed D. rerio exhibited KEGG functional categories of bacteria-mediated cobalamin biosynthesis, which was supported by the presence of cobalamin synthesizers such as Bacteroides and Lactobacillus. Though these bacteria were absent in GFD-fed D. rerio, a comparable level of the cobalamin biosynthesis KEGG functional category was observed, which could be contributed by the compensatory enrichment of Cetobacterium. Based on these results, we conclude D. rerio to be a suitable alternative animal model for the use of a targeted metagenomics approach along with bioinformatics tools to further investigate the relationship between the gluten diet and microbiome profile in the gut ecosystem leading to gastrointestinal diseases and other undesired adverse health effects.}, } @article {pmid28165194, year = {2017}, author = {Tanca, A and Fraumene, C and Manghina, V and Palomba, A and Abbondio, M and Deligios, M and Pagnozzi, D and Addis, MF and Uzzau, S}, title = {Diversity and functions of the sheep faecal microbiota: a multi-omic characterization.}, journal = {Microbial biotechnology}, volume = {10}, number = {3}, pages = {541-554}, pmid = {28165194}, issn = {1751-7915}, mesh = {Animals ; Archaea/*classification/genetics/metabolism ; Bacteria/*classification/genetics/metabolism ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Intestine, Large/*microbiology ; Metabolic Networks and Pathways ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sheep/*microbiology ; }, abstract = {Little is currently known on the microbial populations colonizing the sheep large intestine, despite their expected key role in host metabolism, physiology and immunity. This study reports the first characterization of the sheep faecal microbiota composition and functions, obtained through the application of a multi-omic strategy. An optimized protocol was first devised for DNA extraction and amplification from sheep stool samples. Then, 16S rDNA sequencing, shotgun metagenomics and shotgun metaproteomics were applied to unravel taxonomy, genetic potential and actively expressed functions and pathways respectively. Under a taxonomic perspective, the sheep faecal microbiota appeared globally comparable to that of other ruminants, with Firmicutes being the main phylum. In functional terms, we detected 2097 gene and 441 protein families, finding that the sheep faecal microbiota was primarily involved in catabolism. We investigated carbohydrate transport and degradation activities and identified phylum-specific pathways, such as methanogenesis for Euryarchaeota and acetogenesis for Firmicutes. Furthermore, our approach enabled the identification of proteins expressed by the eukaryotic component of the microbiota. Taken together, these findings unveil structure and role of the distal gut microbiota in sheep, and open the way to further studies aimed at elucidating its connections with management and dietary variables in sheep farming.}, } @article {pmid28164855, year = {2017}, author = {O'Toole, PW and Flemer, B}, title = {From Culture to High-Throughput Sequencing and Beyond: A Layperson's Guide to the "Omics" and Diagnostic Potential of the Microbiome.}, journal = {Gastroenterology clinics of North America}, volume = {46}, number = {1}, pages = {9-17}, doi = {10.1016/j.gtc.2016.09.003}, pmid = {28164855}, issn = {1558-1942}, mesh = {Bacteriological Techniques ; Colorectal Neoplasms/*diagnosis ; Computational Biology/methods ; DNA, Bacterial/*analysis/isolation & purification ; Gastrointestinal Microbiome/*genetics/physiology ; High-Throughput Nucleotide Sequencing ; Humans ; Inflammatory Bowel Diseases/diagnosis ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Detailed knowledge of the community of organisms in the gut has become possible in recent years because of the development of culture-independent methods. Largely based on latest DNA sequencing platforms, it is now possible to establish the composition of the microbiota and the repertoire of biochemical functions it encodes. Variations in either or both of these parameters have been linked to intestinal and extraintestinal disease. This article summarizes how these methods are applied, with special reference to gastroenterology, and describes the achievements and future potential of microbiota analysis as a diagnostic tool.}, } @article {pmid28161736, year = {2017}, author = {Mu, C and Zhang, L and He, X and Smidt, H and Zhu, W}, title = {Dietary fibres modulate the composition and activity of butyrate-producing bacteria in the large intestine of suckling piglets.}, journal = {Antonie van Leeuwenhoek}, volume = {110}, number = {5}, pages = {687-696}, doi = {10.1007/s10482-017-0836-4}, pmid = {28161736}, issn = {1572-9699}, mesh = {Animal Feed ; Animals ; Animals, Newborn ; Bacteria/*classification/genetics ; Biota/*drug effects ; Butyrates/*metabolism ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Dietary Fiber/*administration & dosage ; Intestine, Large/*microbiology ; Metabolic Networks and Pathways/genetics ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Swine ; }, abstract = {Dietary fibres have been shown to affect early-life microbiota colonization in the large intestine of suckling piglets, however, much less is known as to whether they also modulate the composition and activity of butyrate-producing bacteria. Here, we investigated the effect of dietary fibres on the abundance, composition, and activity of butyrate-producing bacteria in suckling piglets. Piglets were fed a control diet or creep feeds containing alfalfa, wheat bran, or pure cellulose, respectively, from postnatal day 7 to 22. Large intestinal digesta and mucosa samples were collected for quantitative analysis of bacterial group-specific 16S ribosomal RNA- and butyrate production-related genes, and digesta samples for quantification of short-chain fatty acids. The alfalfa diet increased (P < 0.05) Clostridium cluster XIVa abundance, copies of genes encoding proteins involved in butyrate production (butyryl-CoA:acetate CoA-transferase, butyrate kinase), and butyrate concentration compared to the wheat bran diet in the digesta of the proximal colon. In the distal colonic digesta, animals fed the alfalfa diet had the highest number of butyryl-CoA:acetate CoA-transferase gene copies (P < 0.05) and numerically the highest butyrate concentration, albeit not significant (P > 0.05), compared to other groups. In the distal colonic mucosa, the cellulose diet increased (P < 0.05) the abundance of Clostridium cluster XIVa and copies of the butyryl-CoA:acetate CoA-transferase gene compared to the alfalfa diet. These results indicated that dietary fibres modulate the abundance and activity of butyrate-producing bacteria in the large intestine of suckling piglets, and that a moderate supplementation of alfalfa and cellulose may benefit early-life gut health through the delivery of butyrate to the mucosa.}, } @article {pmid28159795, year = {2017}, author = {Lipus, D and Vikram, A and Ross, D and Bain, D and Gulliver, D and Hammack, R and Bibby, K}, title = {Predominance and Metabolic Potential of Halanaerobium spp. in Produced Water from Hydraulically Fractured Marcellus Shale Wells.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {8}, pages = {}, pmid = {28159795}, issn = {1098-5336}, mesh = {Biofouling ; Firmicutes/genetics/isolation & purification/*metabolism ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways ; Metagenome ; *Microbial Consortia ; Oil and Gas Fields/*microbiology ; Pennsylvania ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Wastewater/*microbiology ; }, abstract = {Microbial activity in the produced water from hydraulically fractured oil and gas wells may potentially interfere with hydrocarbon production and cause damage to the well and surface infrastructure via corrosion, sulfide release, and fouling. In this study, we surveyed the microbial abundance and community structure of produced water sampled from 42 Marcellus Shale wells in southwestern Pennsylvania (well age ranged from 150 to 1,846 days) to better understand the microbial diversity of produced water. We sequenced the V4 region of the 16S rRNA gene to assess taxonomy and utilized quantitative PCR (qPCR) to evaluate the microbial abundance across all 42 produced water samples. Bacteria of the order Halanaerobiales were found to be the most abundant organisms in the majority of the produced water samples, emphasizing their previously suggested role in hydraulic fracturing-related microbial activity. Statistical analyses identified correlations between well age and biocide formulation and the microbial community, in particular, the relative abundance of Halanaerobiales We further investigated the role of members of the order Halanaerobiales in produced water by reconstructing and annotating a Halanaerobium draft genome (named MDAL1), using shotgun metagenomic sequencing and metagenomic binning. The recovered draft genome was found to be closely related to the species H. congolense, an oil field isolate, and Halanaerobium sp. strain T82-1, also recovered from hydraulic fracturing produced water. Reconstruction of metabolic pathways revealed Halanaerobium sp. strain MDAL1 to have the potential for acid production, thiosulfate reduction, and biofilm formation, suggesting it to have the ability to contribute to corrosion, souring, and biofouling events in the hydraulic fracturing infrastructure.IMPORTANCE There are an estimated 15,000 unconventional gas wells in the Marcellus Shale region, each generating up to 8,000 liters of hypersaline produced water per day throughout its lifetime (K. Gregory, R. Vidic, and D. Dzombak, Elements 7:181-186, 2011, https://doi.org/10.2113/gselements.7.3.181; J. Arthur, B. Bohm, and M. Layne, Gulf Coast Assoc Geol Soc Trans 59:49-59, 2009; https://www.marcellusgas.org/index.php). Microbial activity in produced waters could lead to issues with corrosion, fouling, and souring, potentially interfering with hydraulic fracturing operations. Previous studies have found microorganisms contributing to corrosion, fouling, and souring to be abundant across produced water samples from hydraulically fractured wells; however, these findings were based on a limited number of samples and well sites. In this study, we investigated the microbial community structure in produced water samples from 42 unconventional Marcellus Shale wells, confirming the dominance of the genus Halanaerobium in produced water and its metabolic potential for acid and sulfide production and biofilm formation.}, } @article {pmid28158639, year = {2017}, author = {Westbrook, A and Ramsdell, J and Schuelke, T and Normington, L and Bergeron, RD and Thomas, WK and MacManes, MD}, title = {PALADIN: protein alignment for functional profiling whole metagenome shotgun data.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {10}, pages = {1473-1478}, pmid = {28158639}, issn = {1367-4811}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Algorithms ; Bacteria/genetics/metabolism ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Sequence Alignment/*methods ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {MOTIVATION: Whole metagenome shotgun sequencing is a powerful approach for assaying the functional potential of microbial communities. We currently lack tools that efficiently and accurately align DNA reads against protein references, the technique necessary for constructing a functional profile. Here, we present PALADIN-a novel modification of the Burrows-Wheeler Aligner that provides accurate alignment, robust reporting capabilities and orders-of-magnitude improved efficiency by directly mapping in protein space.

RESULTS: We compared the accuracy and efficiency of PALADIN against existing tools that employ nucleotide or protein alignment algorithms. Using simulated reads, PALADIN consistently outperformed the popular DNA read mappers BWA and NovoAlign in detected proteins, percentage of reads mapped and ontological similarity. We also compared PALADIN against four existing protein alignment tools: BLASTX, RAPSearch2, DIAMOND and Lambda, using empirically obtained reads. PALADIN yielded results seven times faster than the best performing alternative, DIAMOND and nearly 8000 times faster than BLASTX. PALADIN's accuracy was comparable to all tested solutions.

PALADIN was implemented in C, and its source code and documentation are available at https://github.com/twestbrookunh/paladin.

CONTACT: anthonyw@wildcats.unh.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid28155661, year = {2016}, author = {Weng, FC and Yang, YJ and Wang, D}, title = {Functional analysis for gut microbes of the brown tree frog (Polypedates megacephalus) in artificial hibernation.}, journal = {BMC genomics}, volume = {17}, number = {Suppl 13}, pages = {1024}, pmid = {28155661}, issn = {1471-2164}, mesh = {Animals ; Anura/*physiology ; Bacteria/classification/genetics ; Biodiversity ; Cluster Analysis ; *Gastrointestinal Microbiome ; *Hibernation ; Metagenome ; Metagenomics ; }, abstract = {BACKGROUND: Annual hibernation is an adaptation that helps many animals conserve energy during food shortage in winter. This natural cycle is also accompanied by a remodeling of the intestinal immune system, which is an aspect of host biology that is both influenced by, and can itself influence, the microbiota. In amphibians, the bacteria in the intestinal tract show a drop in bacterial counts. The proportion of pathogenic bacteria is greater in hibernating frogs than that found in nonhibernating frogs. This suggests that some intestinal gut microbes in amphibians can be maintained and may contribute to the functions in this closed ecosystem during hibernation. However, these results were derived from culture-based approaches that only covered a small portion of bacteria in the intestinal tract.

METHODS: In this study, we use a more comprehensive analysis, including bacterial appearance and functional prediction, to reveal the global changes in gut microbiota during artificial hibernation via high-throughput sequencing technology.

RESULTS: Our results suggest that artificial hibernation in the brown tree frog (Polypedates megacephalus) could reduce microbial diversity, and artificially hibernating frogs tend to harbor core operational taxonomic units that are rarely distributed among nonhibernating frogs. In addition, artificial hibernation increased significantly the relative abundance of the red-leg syndrome-related pathogenic genus Citrobacter. Furthermore, functional predictions via PICRUSt and Tax4Fun suggested that artificial hibernation has effects on metabolism, disease, signal transduction, bacterial infection, and primary immunodeficiency.

CONCLUSIONS: We infer that artificial hibernation may impose potential effects on primary immunodeficiency and increase the risk of bacterial infections in the brown tree frog.}, } @article {pmid28150710, year = {2017}, author = {Nguyen, D and Boberg, J and Cleary, M and Bruelheide, H and Hönig, L and Koricheva, J and Stenlid, J}, title = {Foliar fungi of Betula pendula: impact of tree species mixtures and assessment methods.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41801}, pmid = {28150710}, issn = {2045-2322}, mesh = {Betula/classification/*microbiology ; Biodiversity ; Ecosystem ; Fungi/*classification/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Plant Leaves/microbiology ; }, abstract = {Foliar fungi of silver birch (Betula pendula) in an experimental Finnish forest were investigated across a gradient of tree species richness using molecular high-throughput sequencing and visual macroscopic assessment. We hypothesized that the molecular approach detects more fungal taxa than visual assessment, and that there is a relationship among the most common fungal taxa detected by both techniques. Furthermore, we hypothesized that the fungal community composition, diversity, and distribution patterns are affected by changes in tree diversity. Sequencing revealed greater diversity of fungi on birch leaves than the visual assessment method. One species showed a linear relationship between the methods. Species-specific variation in fungal community composition could be partially explained by tree diversity, though overall fungal diversity was not affected by tree diversity. Analysis of specific fungal taxa indicated tree diversity effects at the local neighbourhood scale, where the proportion of birch among neighbouring trees varied, but not at the plot scale. In conclusion, both methods may be used to determine tree diversity effects on the foliar fungal community. However, high-throughput sequencing provided higher resolution of the fungal community, while the visual macroscopic assessment detected functionally active fungal species.}, } @article {pmid28146577, year = {2017}, author = {Traykova, D and Schneider, B and Chojkier, M and Buck, M}, title = {Blood Microbiome Quantity and the Hyperdynamic Circulation in Decompensated Cirrhotic Patients.}, journal = {PloS one}, volume = {12}, number = {2}, pages = {e0169310}, pmid = {28146577}, issn = {1932-6203}, support = {R01 DK084139/DK/NIDDK NIH HHS/United States ; R41 HL122022/HL/NHLBI NIH HHS/United States ; R41 HL127919/HL/NHLBI NIH HHS/United States ; RC1 DK087031/DK/NIDDK NIH HHS/United States ; }, mesh = {Aged ; Bacteria/classification/genetics ; Biomarkers ; Case-Control Studies ; Cytokines/genetics/metabolism ; Gastrointestinal Microbiome ; Gene Expression Regulation ; *Hemodynamics ; Humans ; Liver Cirrhosis/*complications/diagnosis/etiology/*physiopathology ; Liver Function Tests ; Macrophages/immunology/metabolism ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; Nitric Oxide/metabolism ; Sepsis/*etiology ; }, abstract = {BACKGROUND: Recently, a complex microbiome was comprehensibly characterized in the serum and ascitic fluid of cirrhotic patients. In the current study, we investigated for the first time the induction of inflammatory pathways and Nitric Oxide, as well as the systemic hemodynamics in conjunction with the blood microbiome in a Child-Pugh class B cirrhotic cohort.

METHODS AND FINDINGS: We used the Intestinal Infections Microbial DNA qPCR Array to screen for 53 bacterial DNA from the gut in the blood. Assays were designed using the 16S rRNA gene as a target, and PCR amplification primers (based on the Human Microbiome Project) and hydrolysis-probe detection. Eighteen systemic hemodynamic parameters were measured non-invasively by impedance cardiography using the BioZ ICG monitor. The inflammatory response was assessed by measuring blood cytokines, Nitric Oxide RNA arrays, and Nitric Oxide. In the blood of this cirrhotic cohort, we detected 19 of 53 bacterial species tested. The number of bacterial species was markedly increased in the blood of cirrhotic patients compared to control individuals (0.2+/-0.4 vs 3.1+/-2.3; 95% CI: 1.3 to 4.9; P = 0.0030). The total bacterial DNA was also increased in the blood of cirrhotic subjects compared to control subjects (0.2+/- 1.1 vs 41.8+/-132.1; 95% CI: 6.0 to 77.2; P = 0.0022). In the cirrhotic cohort, the Cardiac Output increased by 37% and the Systemic Vascular Resistance decreased by 40% (P< 0.00001 for both compared to control subjects). Systemic Vascular Resistance was inversely correlated to blood bacterial DNA quantity (- 0.621; 95% CI -0.843 to -0.218; P = 0.0060), blood bacterial species number (- 0.593; 95% CI -0.83 to -0.175; P = 0.0095; logistic regression: Chi Square = 5.8877; P = 0.0152), and serum Nitric Oxide (- 0.705; 95% CI -0.881 to -0.355; P = 0.0011). Many members of the Nitric Oxide signaling pathway gene family were increased in cirrhotic subjects.

CONCLUSIONS: Our study identified blood bacterial DNA in ~ 90% of the cirrhotic patients without clinical evidences of infection, and suggests that the quantity of bacterial DNA in blood may stimulate signaling pathways, including Nitric Oxide, that could decrease systemic vascular resistance and increase cardiac output.}, } @article {pmid28143587, year = {2017}, author = {Li, J and Zhao, F and Wang, Y and Chen, J and Tao, J and Tian, G and Wu, S and Liu, W and Cui, Q and Geng, B and Zhang, W and Weldon, R and Auguste, K and Yang, L and Liu, X and Chen, L and Yang, X and Zhu, B and Cai, J}, title = {Gut microbiota dysbiosis contributes to the development of hypertension.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {14}, pmid = {28143587}, issn = {2049-2618}, mesh = {Animals ; Blood Pressure/*physiology ; Cohort Studies ; Dysbiosis ; Essential Hypertension ; *Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Germ-Free Life ; Humans ; Hypertension/*microbiology ; Klebsiella/genetics/isolation & purification ; Male ; Mice ; Mice, Inbred C57BL ; Prehypertension/*microbiology ; Prevotella/genetics/isolation & purification ; Prospective Studies ; }, abstract = {BACKGROUND: Recently, the potential role of gut microbiome in metabolic diseases has been revealed, especially in cardiovascular diseases. Hypertension is one of the most prevalent cardiovascular diseases worldwide, yet whether gut microbiota dysbiosis participates in the development of hypertension remains largely unknown. To investigate this issue, we carried out comprehensive metagenomic and metabolomic analyses in a cohort of 41 healthy controls, 56 subjects with pre-hypertension, 99 individuals with primary hypertension, and performed fecal microbiota transplantation from patients to germ-free mice.

RESULTS: Compared to the healthy controls, we found dramatically decreased microbial richness and diversity, Prevotella-dominated gut enterotype, distinct metagenomic composition with reduced bacteria associated with healthy status and overgrowth of bacteria such as Prevotella and Klebsiella, and disease-linked microbial function in both pre-hypertensive and hypertensive populations. Unexpectedly, the microbiome characteristic in pre-hypertension group was quite similar to that in hypertension. The metabolism changes of host with pre-hypertension or hypertension were identified to be closely linked to gut microbiome dysbiosis. And a disease classifier based on microbiota and metabolites was constructed to discriminate pre-hypertensive and hypertensive individuals from controls accurately. Furthermore, by fecal transplantation from hypertensive human donors to germ-free mice, elevated blood pressure was observed to be transferrable through microbiota, and the direct influence of gut microbiota on blood pressure of the host was demonstrated.

CONCLUSIONS: Overall, our results describe a novel causal role of aberrant gut microbiota in contributing to the pathogenesis of hypertension. And the significance of early intervention for pre-hypertension was emphasized.}, } @article {pmid28143583, year = {2017}, author = {Chen, Y and Li, Z and Hu, S and Zhang, J and Wu, J and Shao, N and Bo, X and Ni, M and Ying, X}, title = {Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in Bacteroides coprocola.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {15}, pmid = {28143583}, issn = {2049-2618}, mesh = {Bacteroides/*genetics ; *Diabetes Mellitus, Type 2 ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; Hydrolases/genetics ; Metagenomics/methods ; Polymorphism, Single Nucleotide/*genetics ; alpha-Glucosidases/genetics ; }, abstract = {BACKGROUND: Gut microbes play a critical role in human health and disease, and researchers have begun to characterize their genomes, the so-called gut metagenome. Thus far, metagenomics studies have focused on genus- or species-level composition and microbial gene sets, while strain-level composition and single-nucleotide polymorphism (SNP) have been overlooked. The gut metagenomes of type 2 diabetes (T2D) patients have been found to be enriched with butyrate-producing bacteria and sulfate reduction functions. However, it is not known whether the gut metagenomes of T2D patients have characteristic strain patterns or SNP distributions.

FINDINGS: We downloaded public gut metagenome datasets from 170 T2D patients and 174 healthy controls and performed a systematic comparative analysis of their metagenome SNPs. We found that Bacteroides coprocola, whose relative abundance did not differ between the groups, had a characteristic distribution of SNPs in the T2D patient group. We identified 65 genes, all in B. coprocola, that had remarkably different enrichment of SNPs. The first and sixth ranked genes encode glycosyl hydrolases (GenBank accession EDU99824.1 and EDV02301.1). Interestingly, alpha-glucosidase, which is also a glycosyl hydrolase located in the intestine, is an important drug target of T2D. These results suggest that different strains of B. coprocola may have different roles in human gut and a specific set of B. coprocola strains are correlated with T2D.}, } @article {pmid28143486, year = {2017}, author = {Alshawaqfeh, M and Bashaireh, A and Serpedin, E and Suchodolski, J}, title = {Consistent metagenomic biomarker detection via robust PCA.}, journal = {Biology direct}, volume = {12}, number = {1}, pages = {4}, pmid = {28143486}, issn = {1745-6150}, mesh = {Algorithms ; Animals ; Bacteria/classification/genetics ; Colitis, Ulcerative/diagnosis/microbiology ; Dog Diseases/diagnosis/microbiology ; Dogs ; *Genetic Markers ; Inflammatory Bowel Diseases/diagnosis/microbiology/veterinary ; Metagenomics/*methods ; Mice ; Microbiota/*genetics ; Models, Genetic ; Principal Component Analysis/methods ; Reproducibility of Results ; }, abstract = {BACKGROUND: Recent developments of high throughput sequencing technologies allow the characterization of the microbial communities inhabiting our world. Various metagenomic studies have suggested using microbial taxa as potential biomarkers for certain diseases. In practice, the number of available samples varies from experiment to experiment. Therefore, a robust biomarker detection algorithm is needed to provide a set of potential markers irrespective of the number of available samples. Consistent performance is essential to derive solid biological conclusions and to transfer these findings into clinical applications. Surprisingly, the consistency of a metagenomic biomarker detection algorithm with respect to the variation in the experiment size has not been addressed by the current state-of-art algorithms.

RESULTS: We propose a consistency-classification framework that enables the assessment of consistency and classification performance of a biomarker discovery algorithm. This evaluation protocol is based on random resampling to mimic the variation in the experiment size. Moreover, we model the metagenomic data matrix as a superposition of two matrices. The first matrix is a low-rank matrix that models the abundance levels of the irrelevant bacteria. The second matrix is a sparse matrix that captures the abundance levels of the bacteria that are differentially abundant between different phenotypes. Then, we propose a novel Robust Principal Component Analysis (RPCA) based biomarker discovery algorithm to recover the sparse matrix. RPCA belongs to the class of multivariate feature selection methods which treat the features collectively rather than individually. This provides the proposed algorithm with an inherent ability to handle the complex microbial interactions. Comprehensive comparisons of RPCA with the state-of-the-art algorithms on two realistic datasets are conducted. Results show that RPCA consistently outperforms the other algorithms in terms of classification accuracy and reproducibility performance.

CONCLUSIONS: The RPCA-based biomarker detection algorithm provides a high reproducibility performance irrespective of the complexity of the dataset or the number of selected biomarkers. Also, RPCA selects biomarkers with quite high discriminative accuracy. Thus, RPCA is a consistent and accurate tool for selecting taxanomical biomarkers for different microbial populations.

REVIEWERS: This article was reviewed by Masanori Arita and Zoltan Gaspari.}, } @article {pmid28139751, year = {2017}, author = {Jia, HR and Dai, PL and Geng, LL and Jack, CJ and Li, YH and Wu, YY and Diao, QY and Ellis, JD}, title = {No effect of Bt Cry1Ie toxin on bacterial diversity in the midgut of the Chinese honey bees, Apis cerana cerana (Hymenoptera, Apidae).}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41688}, pmid = {28139751}, issn = {2045-2322}, mesh = {Animals ; Bacillus thuringiensis ; Bacterial Toxins/*pharmacology ; Bees/*drug effects/*microbiology ; *Biodiversity ; Cluster Analysis ; Gastrointestinal Microbiome/*drug effects ; Metagenome ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cry1Ie protein derived from Bacillus thuringiensis (Bt) has been proposed as a promising candidate for the development of a new Bt-maize variety to control maize pests in China. We studied the response of the midgut bacterial community of Apis cerana cerana to Cry1Ie toxin under laboratory conditions. Newly emerged bees were fed one of the following treatments for 15 and 30 days: three concentrations of Cry1Ie toxin (20 ng/mL, 200 ng/mL, and 20 μg/mL) in sugar syrup, pure sugar syrup as a negative control and 48 ng/mL imidacloprid as a positive control. The relative abundance of 16S rRNA genes was measured by Quantitative Polymerase Chain Reaction and no apparent differences were found among treatments for any of these counts at any time point. Furthermore, the midgut bacterial structure and compositions were determined using high-throughput sequencing targeting the V3-V4 regions of the 16S rDNA. All core honey bee intestinal bacterial genera such as Lactobacillus, Bifidobacterium, Snodgrassella, and Gilliamella were detected, and no significant changes were found in the species diversity and richness for any bacterial taxa among treatments at different time points. These results suggest that Cry1Ie toxin may not affect gut bacterial communities of Chinese honey bees.}, } @article {pmid28139037, year = {2017}, author = {Cicconardi, F and Borges, PAV and Strasberg, D and Oromí, P and López, H and Pérez-Delgado, AJ and Casquet, J and Caujapé-Castells, J and Fernández-Palacios, JM and Thébaud, C and Emerson, BC}, title = {MtDNA metagenomics reveals large-scale invasion of belowground arthropod communities by introduced species.}, journal = {Molecular ecology}, volume = {26}, number = {12}, pages = {3104-3115}, doi = {10.1111/mec.14037}, pmid = {28139037}, issn = {1365-294X}, mesh = {Animals ; Arthropods/*classification ; *Biodiversity ; DNA, Mitochondrial/*genetics ; Forests ; *Introduced Species ; Islands ; *Metagenomics ; }, abstract = {Using a series of standardized sampling plots within forest ecosystems in remote oceanic islands, we reveal fundamental differences between the structuring of aboveground and belowground arthropod biodiversity that are likely due to large-scale species introductions by humans. Species of beetle and spider were sampled almost exclusively from single islands, while soil-dwelling Collembola exhibited more than tenfold higher species sharing among islands. Comparison of Collembola mitochondrial metagenomic data to a database of more than 80 000 Collembola barcode sequences revealed almost 30% of sampled island species are genetically identical, or near identical, to individuals sampled from often very distant geographic regions of the world. Patterns of mtDNA relatedness among Collembola implicate human-mediated species introductions, with minimum estimates for the proportion of introduced species on the sampled islands ranging from 45% to 88%. Our results call for more attention to soil mesofauna to understand the global extent and ecological consequences of species introductions.}, } @article {pmid28134326, year = {2017}, author = {Liu, H and Carvalhais, LC and Schenk, PM and Dennis, PG}, title = {Effects of jasmonic acid signalling on the wheat microbiome differ between body sites.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41766}, pmid = {28134326}, issn = {2045-2322}, mesh = {Biodiversity ; Biomass ; Cyclopentanes/*metabolism ; Metagenome ; Metagenomics/methods ; Microbiota/*genetics ; Oxylipins/*metabolism ; Plant Roots/metabolism/microbiology ; Plant Shoots/metabolism/microbiology ; Rhizosphere ; *Signal Transduction ; Soil Microbiology ; Triticum/genetics/*metabolism/*microbiology ; }, abstract = {Jasmonic acid (JA) signalling helps plants to defend themselves against necrotrophic pathogens and herbivorous insects and has been shown to influence the root microbiome of Arabidopsis thaliana. In this study, we determined whether JA signalling influences the diversity and functioning of the wheat (Triticum aestivum) microbiome and whether these effects are specific to particular parts of the plant. Activation of the JA pathway was achieved via exogenous application of methyl jasmonate and was confirmed by significant increases in the abundance of 10 JA-signalling-related gene transcripts. Phylogenetic marker gene sequencing revealed that JA signalling reduced the diversity and changed the composition of root endophytic but not shoot endophytic or rhizosphere bacterial communities. The total enzymatic activity and substrate utilisation profiles of rhizosphere bacterial communities were not affected by JA signalling. Our findings indicate that the effects of JA signalling on the wheat microbiome are specific to individual plant compartments.}, } @article {pmid28134269, year = {2017}, author = {Zhou, X and Zhang, J and Gao, D and Gao, H and Guo, M and Li, L and Zhao, M and Wu, F}, title = {Conversion from long-term cultivated wheat field to Jerusalem artichoke plantation changed soil fungal communities.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41502}, pmid = {28134269}, issn = {2045-2322}, mesh = {Agriculture ; Biodiversity ; *Fungi/classification/genetics ; Helianthus/growth & development/*microbiology ; Metagenome ; Metagenomics/methods ; *Soil Microbiology ; *Triticum/growth & development/microbiology ; }, abstract = {Understanding soil microbial communities in agroecosystems has the potential to contribute to the improvement of agricultural productivity and sustainability. Effects of conversion from long-term wheat plantation to Jerusalem artichoke (JA) plantation on soil fungal communities were determined by amplicon sequencing of total fungal ITS regions. Quantitative PCR and PCR-denaturing gradient gel electrophoresis were also used to analyze total fungal and Trichoderma spp. ITS regions and Fusarium spp. Ef1α genes. Results showed that soil organic carbon was higher in the first cropping of JA and Olsen P was lower in the third cropping of JA. Plantation conversion changed soil total fungal and Fusarium but not Trichoderma spp. community structures and compositions. The third cropping of JA had the lowest total fungal community diversity and Fusarium spp. community abundance, but had the highest total fungal and Trichoderma spp. community abundances. The relative abundances of potential fungal pathogens of wheat were higher in the wheat field. Fungal taxa with plant growth promoting, plant pathogen or insect antagonistic potentials were enriched in the first and second cropping of JA. Overall, short-term conversion from wheat to JA plantation changed soil fungal communities, which is related to changes in soil organic carbon and Olsen P contents.}, } @article {pmid28131442, year = {2017}, author = {Doré, J and Multon, MC and Béhier, JM and , }, title = {The human gut microbiome as source of innovation for health: Which physiological and therapeutic outcomes could we expect?.}, journal = {Therapie}, volume = {72}, number = {1}, pages = {21-38}, doi = {10.1016/j.therap.2016.12.007}, pmid = {28131442}, issn = {0040-5957}, mesh = {Clostridioides difficile ; Clostridium Infections/therapy ; Diet ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Humans ; Oxidative Stress/physiology ; Probiotics/therapeutic use ; }, abstract = {From the moment of birth, each human being builds a microbe-host symbiosis which is key for the preservation of its health and well-being. This personal symbiotic coexistence is the result of progressive enrichments in microorganism diversity through external supplies. This diversity is nowadays massively overthrown by drastic changes related to clinical practice in birth management, environmental exposure, nutrition and healthcare behaviors. The last two generations have been the frame of massive modifications in life and food habits, with people being more and more sedentary, overfed and permeated with drugs and pollutants. We are now able to measure the impact of these changes on the gut microbiota diversity. Concomitantly, these modifications of lifestyle were associated with a dramatic increase in incidence of immune-mediated diseases including metabolic, allergic and inflammatory diseases and most likely neurodegenerative and psychiatric disorders. Microbiota is becoming a hot topic in the scientific community and in the mainstream media. The number of scientific publications increased by up to a factor three over the last five years, with gastrointestinal and metabolic diseases being the most productive areas. In the intellectual property landscape, the patent families on microbiota have more than doubled in the meantime. In parallel, funding either from National Institutes (e.g. from NIH which funds research mainly in the field of allergies, infections, cancer and cardiovascular diseases, from the White House which launched the national microbiome initiative) or by pharmaceutical companies follow the same trend, showing a boost and a strong support in the research field on microbiota. All major health players are investing in microbiome research as shown by the number of deals signed and by funding during 2015. The Giens round table addressed how the medicine of tomorrow, considering human beings as a human-microbe symbiotic supraorganism, could leverage microbiome knowledge and tools. The rationale for our working group has been structured around four domains of innovation that could derive from ongoing efforts in deciphering the interactions between human cells and intestinal microbiome as a central component of human health, namely: (1) development of stratification and monitoring tools; (2) identification of new target and drug discovery, as a part of our supra-genome; (4) exploitation of microbiota as a therapeutic target that can be modulated; (4) and finally as a source of live biotherapeutics and adjuvants. These four streams will exemplify how microbiota has changed the way we consider a wide range of chronic and incurable diseases and the consequences of long-lasting dysbiosis. In-depth microbiota analysis is opening one of the broadest fields of investigation for improving human and animal health and will be a source of major therapeutic innovations for tackling today's medical unmet needs. We thus propose a range of recommendations for basic researchers, care givers as well as for health authorities to gain reliability in microbiome analysis and accelerate discovery processes and their translation into applications for the benefits of the people. Finally, les Ateliers de Giens round table on microbiota benefited from the richness of the French ecosystem. France represents a center of excellence in the microbiota research field, with French institutions as Institut national de la recherche agronomique (INRA [Metagenopolis, Micalis]), Centre national de la recherché scientifique (CNRS), Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), Institut of Cardiometabolism and Nutrition (ICAN), Institut des maladies métaboliques et cardiovasculaires (I2MC), Institut national de la santé et de la recherche médicale (Inserm), Pasteur Institute and Gustave-Roussy being top-players for the number of publications.}, } @article {pmid28130230, year = {2017}, author = {Fosso, B and Santamaria, M and D'Antonio, M and Lovero, D and Corrado, G and Vizza, E and Passaro, N and Garbuglia, AR and Capobianchi, MR and Crescenzi, M and Valiente, G and Pesole, G}, title = {MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {11}, pages = {1730-1732}, pmid = {28130230}, issn = {1367-4811}, mesh = {Algorithms ; Bacteria/classification/genetics ; Fungi/classification/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; *Software ; Viruses/classification/genetics ; Workflow ; }, abstract = {SUMMARY: Shotgun metagenomics by high-throughput sequencing may allow deep and accurate characterization of host-associated total microbiomes, including bacteria, viruses, protists and fungi. However, the analysis of such sequencing data is still extremely challenging in terms of both overall accuracy and computational efficiency, and current methodologies show substantial variability in misclassification rate and resolution at lower taxonomic ranks or are limited to specific life domains (e.g. only bacteria). We present here MetaShot, a workflow for assessing the total microbiome composition from host-associated shotgun sequence data, and show its overall optimal accuracy performance by analyzing both simulated and real datasets.

https://github.com/bfosso/MetaShot.

CONTACT: graziano.pesole@uniba.it.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid28129383, year = {2017}, author = {Vörös, J and Márton, O and Schmidt, BR and Gál, JT and Jelić, D}, title = {Surveying Europe's Only Cave-Dwelling Chordate Species (Proteus anguinus) Using Environmental DNA.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0170945}, pmid = {28129383}, issn = {1932-6203}, mesh = {Amphibians/genetics ; Animals ; Caves ; Croatia ; DNA/chemistry/*genetics/isolation & purification ; Europe ; Metagenomics ; Proteus/chemistry/*genetics ; Species Specificity ; Water/chemistry ; }, abstract = {In surveillance of subterranean fauna, especially in the case of rare or elusive aquatic species, traditional techniques used for epigean species are often not feasible. We developed a non-invasive survey method based on environmental DNA (eDNA) to detect the presence of the red-listed cave-dwelling amphibian, Proteus anguinus, in the caves of the Dinaric Karst. We tested the method in fifteen caves in Croatia, from which the species was previously recorded or expected to occur. We successfully confirmed the presence of P. anguinus from ten caves and detected the species for the first time in five others. Using a hierarchical occupancy model we compared the availability and detection probability of eDNA of two water sampling methods, filtration and precipitation. The statistical analysis showed that both availability and detection probability depended on the method and estimates for both probabilities were higher using filter samples than for precipitation samples. Combining reliable field and laboratory methods with robust statistical modeling will give the best estimates of species occurrence.}, } @article {pmid28127053, year = {2017}, author = {Pekas, A and Palevsky, E and Sumner, JC and Perotti, MA and Nesvorna, M and Hubert, J}, title = {Comparison of bacterial microbiota of the predatory mite Neoseiulus cucumeris (Acari: Phytoseiidae) and its factitious prey Tyrophagus putrescentiae (Acari: Acaridae).}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2}, pmid = {28127053}, issn = {2045-2322}, mesh = {Acari/*microbiology ; Animals ; Bacteria/*classification/*genetics ; Metagenomics ; *Microbiota ; Symbiosis ; }, abstract = {Neoseiulus cucumeris is a predatory mite used for biological control of arthropod pests. Mass-reared predators are fed with factitious prey mites such as Tyrophagus putrescentiae. Although some information on certain endosymbionts of N. cucumeris and T. putrescentiae exists, it is unclear whether both species share bacterial communities. The bacterial communities in populations of predator and prey mites, as well as the occurence of potential acaropathogenic bacteria were analyzed. The comparisons were based on the following groups: (i) N. cucumeris mass-production; (ii) N. cucumeris laboratory population with disease symptoms; (iii) T. putrescentiae pure populations and; (iv) T. putrescentiae from rearing units of N. cucumeris. Only 15% of OTUs were present in all samples from predatory and prey mite populations (core OTUs): the intracellular symbionts Wolbachia, Cardinium, plus other Blattabacterium-like, Solitalea-like, and Bartonella-like symbionts. Environmental bacteria were more abundant in predatory mites, while symbiotic bacteria prevailed in prey mites. Relative numbers of certain bacterial taxa were significantly different between the microbiota of prey mites reared with and without N. cucumeris. No significant differences were found in the bacterial communities of healthy N. cucumeris compared to N. cucumeris showing disease symptoms. We did not identify any confirmed acaropathogenic bacteria among microbiota.}, } @article {pmid28125788, year = {2017}, author = {Yang, Y and Chen, N and Chen, T}, title = {Inference of Environmental Factor-Microbe and Microbe-Microbe Associations from Metagenomic Data Using a Hierarchical Bayesian Statistical Model.}, journal = {Cell systems}, volume = {4}, number = {1}, pages = {129-137.e5}, doi = {10.1016/j.cels.2016.12.012}, pmid = {28125788}, issn = {2405-4712}, mesh = {Algorithms ; Animals ; Bacteria/classification/genetics ; Bayes Theorem ; Computational Biology/methods ; Computer Simulation ; Gene-Environment Interaction ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Models, Statistical ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {The inference of associations between environmental factors and microbes and among microbes is critical to interpreting metagenomic data, but compositional bias, indirect associations resulting from common factors, and variance within metagenomic sequencing data limit the discovery of associations. To account for these problems, we propose metagenomic Lognormal-Dirichlet-Multinomial (mLDM), a hierarchical Bayesian model with sparsity constraints, to estimate absolute microbial abundance and simultaneously infer both conditionally dependent associations among microbes and direct associations between microbes and environmental factors. We empirically show the effectiveness of the mLDM model using synthetic data, data from the TARA Oceans project, and a colorectal cancer dataset. Finally, we apply mLDM to 16S sequencing data from the western English Channel and report several associations. Our model can be used on both natural environmental and human metagenomic datasets, promoting the understanding of associations in the microbial community.}, } @article {pmid28125344, year = {2017}, author = {Walsh, AM and Crispie, F and Claesson, MJ and Cotter, PD}, title = {Translating Omics to Food Microbiology.}, journal = {Annual review of food science and technology}, volume = {8}, number = {}, pages = {113-134}, doi = {10.1146/annurev-food-030216-025729}, pmid = {28125344}, issn = {1941-1413}, mesh = {*Food Microbiology ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; Probiotics ; *Transcriptome ; }, abstract = {This review examines the applications of omics technologies in food microbiology, with a primary focus on high-throughput sequencing (HTS) technologies. We discuss the different sequencing approaches applicable to the study of food-related microbial isolates and mixed microbial communities in foods, and we provide an overview of the sequencing platforms suitable for each approach. We highlight the potential for genomics, metagenomics, and metatranscriptomics to guide efforts to optimize food fermentations. Additionally, we explore the use of comparative and functional genomics to further our understanding of the mechanisms of probiotic action and we describe the applicability of HTS as a food safety measure. Finally, we consider the use of HTS to investigate the effects that ingested microbes have on the human gut microbiota.}, } @article {pmid28122610, year = {2017}, author = {Huson, DH and Tappu, R and Bazinet, AL and Xie, C and Cummings, MP and Nieselt, K and Williams, R}, title = {Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {11}, pmid = {28122610}, issn = {2049-2618}, mesh = {Algorithms ; Amino Acid Sequence ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics/*methods ; *Microbiota ; *Sequence Alignment ; Sequence Analysis, DNA/methods ; *Software ; }, abstract = {BACKGROUND: Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. The assembly of whole genomes from metagenomic sequencing reads is a very difficult problem. However, for some questions, only specific genes of interest need to be assembled. This is then a gene-centric assembly where the goal is to assemble reads into contigs for a family of orthologous genes.

METHODS: We present a new method for performing gene-centric assembly, called protein-alignment-guided assembly, and provide an implementation in our metagenome analysis tool MEGAN. Genes are assembled on the fly, based on the alignment of all reads against a protein reference database such as NCBI-nr. Specifically, the user selects a gene family based on a classification such as KEGG and all reads binned to that gene family are assembled.

RESULTS: Using published synthetic community metagenome sequencing reads and a set of 41 gene families, we show that the performance of this approach compares favorably with that of full-featured assemblers and that of a recently published HMM-based gene-centric assembler, both in terms of the number of reference genes detected and of the percentage of reference sequence covered.

CONCLUSIONS: Protein-alignment-guided assembly of orthologous gene families complements whole-metagenome assembly in a new and very useful way.}, } @article {pmid28122030, year = {2017}, author = {Hwang, J and Park, SY and Park, M and Lee, S and Lee, TK}, title = {Seasonal Dynamics and Metagenomic Characterization of Marine Viruses in Goseong Bay, Korea.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0169841}, pmid = {28122030}, issn = {1932-6203}, mesh = {Bays/*virology ; *Biodiversity ; Genetic Variation ; Metagenomics ; Republic of Korea ; Seasons ; Seawater/*virology ; Viruses/*genetics ; }, abstract = {Viruses are the most abundant biological entities in the oceans, and account for a significant amount of the genetic diversity of marine ecosystems. However, there is little detailed information about the biodiversity of viruses in marine environments. Rapid advances in metagenomics have enabled the identification of previously unknown marine viruses. We performed metagenomic profiling of seawater samples collected at 6 sites in Goseong Bay (South Sea, Korea) during the spring, summer, autumn, and winter of 2014. The results indicated the presence of highly diverse virus communities. The DNA libraries from samples collected during four seasons were sequenced using Illumina HiSeq 2000. The number of viral reads was 136,850 during March, 70,651 during June, 66,165 during September, and 111,778 during December. Species identification indicated that Pelagibacter phage HTVC010P, Ostreococcus lucimarinus OIV5 and OIV1, and Roseobacter phage SIO1 were the most common species in all samples. For viruses with at least 10 reads, there were 204 species during March, 189 during June, 170 during September, and 173 during December. Analysis of virus families indicated that the Myoviridae was the most common during all four seasons, and viruses in the Polyomaviridae were only present during March. Viruses in the Iridoviridae were only present during three seasons. Additionally, viruses in the Iridoviridae, Herpesviridae, and Poxviridae, which may affect fish and marine animals, appeared during different seasons. These results suggest that seasonal changes in temperature contribute to the dynamic structure of the viral community in the study area. The information presented here will be useful for comparative analyses with other marine viral communities.}, } @article {pmid28120929, year = {2017}, author = {Soppa, J}, title = {Polyploidy and community structure.}, journal = {Nature microbiology}, volume = {2}, number = {}, pages = {16261}, doi = {10.1038/nmicrobiol.2016.261}, pmid = {28120929}, issn = {2058-5276}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; *Biota ; Eukaryota/classification/*genetics ; Metagenomics/methods ; *Polyploidy ; }, } @article {pmid28119120, year = {2017}, author = {Wiehlmann, L and Pienkowska, K and Hedtfeld, S and Dorda, M and Tümmler, B}, title = {Impact of sample processing on human airways microbial metagenomes.}, journal = {Journal of biotechnology}, volume = {250}, number = {}, pages = {51-55}, doi = {10.1016/j.jbiotec.2017.01.001}, pmid = {28119120}, issn = {1873-4863}, mesh = {Artifacts ; Bacterial Typing Techniques/*methods ; DNA/chemistry/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Lung/*microbiology ; Metagenome/*genetics ; Microbial Consortia/*genetics ; Reproducibility of Results ; Sample Size ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods ; Specimen Handling/*methods ; }, abstract = {Whole metagenome shotgun sequencing provides information about the gene content and the composition of microbial communities provided that the processing of the samples does not introduce a methodology-driven bias. We tested the impact of DNA isolation and storage period on the metagenome profile. Deep throat swabs were collected from healthy adults and an infected infant. DNA was isolated by sonification or enzymatic lysis either immediately or after 24h storage in agar gel Amies transport medium at room temperature. Disruption of cells and subsequent fragmentation of DNA by sonification was as suitable as the common enzymatic lysis to generate high-quality metagenomes particularly for low total DNA input of less than ten nanograms. Conversely, storage of samples for 24h produced severely distorted metagenomes. The majority of species became less abundant or even extinct, whereas a few Streptococcus, Neisseria and Haemophilus spp. proliferated so that the total number of bacterial reads increased at the expense of human reads. We recommend that samples for metagenome analysis should be immediately processed or frozen at -80°C.}, } @article {pmid28114568, year = {2017}, author = {Zhang, H and Zhao, F and Hutchinson, DS and Sun, W and Ajami, NJ and Lai, S and Wong, MC and Petrosino, JF and Fang, J and Jiang, J and Chen, W and Reinach, PS and Qu, J and Zeng, C and Zhang, D and Zhou, X}, title = {Conjunctival Microbiome Changes Associated With Soft Contact Lens and Orthokeratology Lens Wearing.}, journal = {Investigative ophthalmology & visual science}, volume = {58}, number = {1}, pages = {128-136}, doi = {10.1167/iovs.16-20231}, pmid = {28114568}, issn = {1552-5783}, mesh = {Adult ; Bacteria/*genetics ; Conjunctiva/*microbiology ; Contact Lenses, Hydrophilic/*adverse effects/microbiology ; DNA, Bacterial/*analysis ; Eye Infections, Bacterial/genetics/*microbiology ; Female ; Follow-Up Studies ; Humans ; Male ; Microbiota/*physiology ; Myopia/therapy ; Orthokeratologic Procedures/*adverse effects ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/genetics/metabolism ; Time Factors ; }, abstract = {PURPOSE: Usage of different types of contact lenses is associated with increased risk of sight-threatening complications. Changes in the ocular microbiome caused by contact lens wear are suggested to affect infection development in those individuals. To address this question, this study compares conjunctival microbial communities in contact lens wearers with those in noncontact lens wearers.

METHODS: Paired-end sequencing of the V3 region of the 16S rRNA gene was used to characterize the bacterial communities on the conjunctival surfaces of contact lens wearers and nonwearers.

RESULTS: No differences in microbial diversity were detected between contact lens wearers and nonwearers. Nevertheless, some slight microbe variability was evident between these two different groups. Bacillus, Tatumella and Lactobacillus abundance was less in orthokeratology lens (OKL) wearers than in nonwearers. In soft contact lenses (SCL) wearers, Delftia abundance decreased whereas Elizabethkingia levels increased. The difference in the SCL and nonwearer group was smaller than that in the OKL group. Variations in the conjunctival taxonomic composition between SCL wearers were larger than those in other groups. Sex differences in the conjunctival microbiota makeup were only evident among nonwearers.

CONCLUSIONS: Even though there were slight percentage changes between contact lens wearers and nonwearers in some microbes, there were no differences in their diversity. On the other hand, contact lens usage might cause relative abundance of some taxa to change. Our results will help assess whether or not conjunctival microbiome changes caused by contact lens wear affect infection risk.}, } @article {pmid28113163, year = {2016}, author = {Fischer, S}, title = {What Lies Within: The Human Body Might Well Be One of the Best Sources for New Antibiotics.}, journal = {IEEE pulse}, volume = {7}, number = {5}, pages = {16-19}, doi = {10.1109/MPUL.2016.2592621}, pmid = {28113163}, issn = {2154-2317}, mesh = {*Anti-Bacterial Agents ; Bacteria/drug effects/genetics/metabolism ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; Microbial Interactions ; }, abstract = {In 1991, a group of Italian researchers announced that they had isolated a new antibiotic from a chemical soup brewed with a soil-dwelling bacteria called Planobispora rosea. The drug was a type of thiopeptide, effective against grampositive bacteria like Staphylococcus aureus, P. acnes, and C. difficile but uncooperative in terms of being harnessed for human medicines. Little came of that work until around 2012, when pharma giant Novartis reported that it had begun to experiment with the original drug's structure, ultimately creating a semisynthetic version with enough solubility that it could be effectively administered to human patients. In 2015, that antibiotic successfully made it through a multicenter phase II clinical trial, where it proved to be both safe and reasonably effective in the 30 C. difficile patients who completed the study.}, } @article {pmid28112736, year = {2017}, author = {Chu, DM and Ma, J and Prince, AL and Antony, KM and Seferovic, MD and Aagaard, KM}, title = {Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery.}, journal = {Nature medicine}, volume = {23}, number = {3}, pages = {314-326}, pmid = {28112736}, issn = {1546-170X}, support = {U54 HG004973/HG/NHGRI NIH HHS/United States ; F32 HD082969/HD/NICHD NIH HHS/United States ; R01 HD091731/HD/NICHD NIH HHS/United States ; DP2 OD001500/OD/NIH HHS/United States ; T32 GM007330/GM/NIGMS NIH HHS/United States ; R01 NR014792/NR/NINR NIH HHS/United States ; T32 GM088129/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; *Cesarean Section ; Cross-Sectional Studies ; *Delivery, Obstetric ; Female ; Gastrointestinal Microbiome/*genetics ; Gingiva/microbiology ; Humans ; Infant ; Infant, Newborn ; Longitudinal Studies ; Male ; Meconium/microbiology ; Metagenomics ; Nasal Mucosa/microbiology ; Pregnancy ; Pregnancy Trimester, Third ; Prospective Studies ; RNA, Ribosomal, 16S/*genetics ; Skin/microbiology ; Young Adult ; }, abstract = {Human microbial communities are characterized by their taxonomic, metagenomic and metabolic diversity, which varies by distinct body sites and influences human physiology. However, when and how microbial communities within each body niche acquire unique taxonomical and functional signatures in early life remains underexplored. We thus sought to determine the taxonomic composition and potential metabolic function of the neonatal and early infant microbiota across multiple body sites and assess the effect of the mode of delivery and its potential confounders or modifiers. A cohort of pregnant women in their early third trimester (n = 81) were prospectively enrolled for longitudinal sampling through 6 weeks after delivery, and a second matched cross-sectional cohort (n = 81) was additionally recruited for sampling once at the time of delivery. Samples across multiple body sites, including stool, oral gingiva, nares, skin and vagina were collected for each maternal-infant dyad. Whole-genome shotgun sequencing and sequencing analysis of the gene encoding the 16S rRNA were performed to interrogate the composition and function of the neonatal and maternal microbiota. We found that the neonatal microbiota and its associated functional pathways were relatively homogeneous across all body sites at delivery, with the notable exception of the neonatal meconium. However, by 6 weeks after delivery, the infant microbiota structure and function had substantially expanded and diversified, with the body site serving as the primary determinant of the composition of the bacterial community and its functional capacity. Although minor variations in the neonatal (immediately at birth) microbiota community structure were associated with the cesarean mode of delivery in some body sites (oral gingiva, nares and skin; R[2] = 0.038), this was not true for neonatal stool (meconium; Mann-Whitney P > 0.05), and there was no observable difference in community function regardless of delivery mode. For infants at 6 weeks of age, the microbiota structure and function had expanded and diversified with demonstrable body site specificity (P < 0.001, R[2] = 0.189) but without discernable differences in community structure or function between infants delivered vaginally or by cesarean surgery (P = 0.057, R[2] = 0.007). We conclude that within the first 6 weeks of life, the infant microbiota undergoes substantial reorganization, which is primarily driven by body site and not by mode of delivery.}, } @article {pmid28112173, year = {2017}, author = {Ji, P and Zhang, Y and Wang, J and Zhao, F}, title = {MetaSort untangles metagenome assembly by reducing microbial community complexity.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {14306}, pmid = {28112173}, issn = {2041-1723}, mesh = {Bacteria/*genetics ; Computational Biology ; Genome, Bacterial ; Genome, Microbial ; Kelp/*microbiology ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; *Software ; }, abstract = {Most current approaches to analyse metagenomic data rely on reference genomes. Novel microbial communities extend far beyond the coverage of reference databases and de novo metagenome assembly from complex microbial communities remains a great challenge. Here we present a novel experimental and bioinformatic framework, metaSort, for effective construction of bacterial genomes from metagenomic samples. MetaSort provides a sorted mini-metagenome approach based on flow cytometry and single-cell sequencing methodologies, and employs new computational algorithms to efficiently recover high-quality genomes from the sorted mini-metagenome by the complementary of the original metagenome. Through extensive evaluations, we demonstrated that metaSort has an excellent and unbiased performance on genome recovery and assembly. Furthermore, we applied metaSort to an unexplored microflora colonized on the surface of marine kelp and successfully recovered 75 high-quality genomes at one time. This approach will greatly improve access to microbial genomes from complex or novel communities.}, } @article {pmid28111203, year = {2017}, author = {Manor, O and Borenstein, E}, title = {Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome.}, journal = {Cell host & microbe}, volume = {21}, number = {2}, pages = {254-267}, pmid = {28111203}, issn = {1934-6069}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; }, mesh = {Actinobacteria/classification ; Bacteroides/classification ; Communicable Diseases/microbiology ; *Computational Biology ; Databases, Genetic ; Diabetes Mellitus, Type 2/microbiology ; Firmicutes/classification ; Genome, Microbial ; Humans ; Metagenomics ; *Microbiota ; Phylogeny ; Proteobacteria/classification ; *Software ; }, abstract = {Comparative analyses of the human microbiome have identified both taxonomic and functional shifts that are associated with numerous diseases. To date, however, microbiome taxonomy and function have mostly been studied independently and the taxonomic drivers of functional imbalances have not been systematically identified. Here, we present FishTaco, an analytical and computational framework that integrates taxonomic and functional comparative analyses to accurately quantify taxon-level contributions to disease-associated functional shifts. Applying FishTaco to several large-scale metagenomic cohorts, we show that shifts in the microbiome's functional capacity can be traced back to specific taxa. Furthermore, the set of taxa driving functional shifts and their contribution levels vary markedly between functions. We additionally find that similar functional imbalances in different diseases are driven by both disease-specific and shared taxa. Such integrated analysis of microbiome ecological and functional dynamics can inform future microbiome-based therapy, pinpointing putative intervention targets for manipulating the microbiome's functional capacity.}, } @article {pmid28111075, year = {2017}, author = {Guo, CJ and Chang, FY and Wyche, TP and Backus, KM and Acker, TM and Funabashi, M and Taketani, M and Donia, MS and Nayfach, S and Pollard, KS and Craik, CS and Cravatt, BF and Clardy, J and Voigt, CA and Fischbach, MA}, title = {Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases.}, journal = {Cell}, volume = {168}, number = {3}, pages = {517-526.e18}, pmid = {28111075}, issn = {1097-4172}, support = {R01 GM104659/GM/NIGMS NIH HHS/United States ; R37 CA087660/CA/NCI NIH HHS/United States ; R01 DK101674/DK/NIDDK NIH HHS/United States ; R01 AT009874/AT/NCCIH NIH HHS/United States ; T32 GM067547/GM/NIGMS NIH HHS/United States ; F32 GM111012/GM/NIGMS NIH HHS/United States ; R01 DK110174/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacillus subtilis/genetics ; Bacteria/classification/genetics/*metabolism ; Escherichia coli/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Peptide Synthases/genetics/*metabolism ; Phylogeny ; Pyrazines/*metabolism ; }, abstract = {The gut microbiota modulate host biology in numerous ways, but little is known about the molecular mediators of these interactions. Previously, we found a widely distributed family of nonribosomal peptide synthetase gene clusters in gut bacteria. Here, by expressing a subset of these clusters in Escherichia coli or Bacillus subtilis, we show that they encode pyrazinones and dihydropyrazinones. At least one of the 47 clusters is present in 88% of the National Institutes of Health Human Microbiome Project (NIH HMP) stool samples, and they are transcribed under conditions of host colonization. We present evidence that the active form of these molecules is the initially released peptide aldehyde, which bears potent protease inhibitory activity and selectively targets a subset of cathepsins in human cell proteomes. Our findings show that an approach combining bioinformatics, synthetic biology, and heterologous gene cluster expression can rapidly expand our knowledge of the metabolic potential of the microbiota while avoiding the challenges of cultivating fastidious commensals.}, } @article {pmid28103917, year = {2017}, author = {Cox, JW and Ballweg, RA and Taft, DH and Velayutham, P and Haslam, DB and Porollo, A}, title = {A fast and robust protocol for metataxonomic analysis using RNAseq data.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {7}, pmid = {28103917}, issn = {2049-2618}, support = {R01 HL119190/HL/NHLBI NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Bacteria/*classification/genetics ; Base Sequence ; Databases, Genetic ; Fungi/*classification/genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Mice ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; Viruses/*classification/genetics ; }, abstract = {BACKGROUND: Metagenomics is a rapidly emerging field aimed to analyze microbial diversity and dynamics by studying the genomic content of the microbiota. Metataxonomics tools analyze high-throughput sequencing data, primarily from 16S rRNA gene sequencing and DNAseq, to identify microorganisms and viruses within a complex mixture. With the growing demand for analysis of the functional microbiome, metatranscriptome studies attract more interest. To make metatranscriptomic data sufficient for metataxonomics, new analytical workflows are needed to deal with sparse and taxonomically less informative sequencing data.

RESULTS: We present a new protocol, IMSA+A, for accurate taxonomy classification based on metatranscriptome data of any read length that can efficiently and robustly identify bacteria, fungi, and viruses in the same sample. The new protocol improves accuracy by using a conservative reference database, employing a new counting scheme, and by assembling shotgun reads. Assembly also reduces analysis runtime. Simulated data were utilized to evaluate the protocol by permuting common experimental variables. When applied to the real metatranscriptome data for mouse intestines colonized by ASF, the protocol showed superior performance in detection of the microorganisms compared to the existing metataxonomics tools. IMSA+A is available at https://github.com/JeremyCoxBMI/IMSA-A .

CONCLUSIONS: The developed protocol addresses the need for taxonomy classification from RNAseq data. Previously not utilized, i.e., unmapped to a reference genome, RNAseq reads can now be used to gather taxonomic information about the microbiota present in a biological sample without conducting additional sequencing. Any metatranscriptome pipeline that includes assembly of reads can add this analysis with minimal additional cost of compute time. The new protocol also creates an opportunity to revisit old metatranscriptome data, where taxonomic content may be important but was not analyzed.}, } @article {pmid28103814, year = {2017}, author = {Millares, L and Bermudo, G and Pérez-Brocal, V and Domingo, C and Garcia-Nuñez, M and Pomares, X and Moya, A and Monsó, E}, title = {The respiratory microbiome in bronchial mucosa and secretions from severe IgE-mediated asthma patients.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {20}, pmid = {28103814}, issn = {1471-2180}, mesh = {Asthma/*immunology/microbiology ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Biopsy ; Bronchi/*microbiology ; Bronchoscopy ; Cross-Sectional Studies ; DNA, Bacterial/genetics ; Female ; Humans ; *Immunoglobulin E ; Male ; Metagenome ; Microbial Consortia/genetics/*immunology ; Middle Aged ; Mucous Membrane/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sputum/microbiology ; }, abstract = {BACKGROUND: The bronchial microbiome in chronic lung diseases presents an abnormal pattern, but its microbial composition and regional differences in severe asthma have not been sufficiently addressed. The aim of the study was to describe the bacterial community in bronchial mucosa and secretions of patients with severe chronic asthma chronically treated with corticosteroids in addition to usual care according to Global Initiative for Asthma. Bacterial community composition was obtained by 16S rRNA gene amplification and sequencing, and functional capabilities through PICRUSt.

RESULTS: Thirteen patients with severe asthma were included and provided 11 bronchial biopsies (BB) and 12 bronchial aspirates (BA) suitable for sequence analyses. Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria showed relative abundances (RAs) over 5% in BB, a cutoff that was reached by Streptococcus and Prevotella at genus level. Legionella genus attained a median RA of 2.7 (interquartile range 1.1-4.7) in BB samples. In BA a higher RA of Fusobacteria was found, when compared with BB [8.7 (5.9-11.4) vs 4.2 (0.8-7.5), p = 0.037], while the RA of Proteobacteria was lower in BA [4.3 (3.7-6.5) vs 17.1 (11.2-33.4), p = 0.005]. RA of the Legionella genus was also significantly lower in BA [0.004 (0.001-0.02) vs. 2.7 (1.1-4.7), p = 0.005]. Beta-diversity analysis confirmed the differences between the microbial communities in BA and BB (R[2] = 0.20, p = 0.001, Adonis test), and functional analysis revealed also statistically significant differences between both types of sample on Metabolism, Cellular processes, Human diseases, Organismal systems and Genetic information processing pathways.

CONCLUSIONS: The microbiota in the bronchial mucosa of severe asthma has a specific pattern that is not accurately represented in bronchial secretions, which must be considered a different niche of bacteria growth.}, } @article {pmid28100819, year = {2017}, author = {Longdon, B and Day, JP and Schulz, N and Leftwich, PT and de Jong, MA and Breuker, CJ and Gibbs, M and Obbard, DJ and Wilfert, L and Smith, SC and McGonigle, JE and Houslay, TM and Wright, LI and Livraghi, L and Evans, LC and Friend, LA and Chapman, T and Vontas, J and Kambouraki, N and Jiggins, FM}, title = {Vertically transmitted rhabdoviruses are found across three insect families and have dynamic interactions with their hosts.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1847}, pages = {}, pmid = {28100819}, issn = {1471-2954}, support = {/WT_/Wellcome Trust/United Kingdom ; 281668/ERC_/European Research Council/International ; BB/K000489/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 109356/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Butterflies/virology ; Ceratitis capitata/virology ; Drosophila/virology ; *Infectious Disease Transmission, Vertical ; Insecta/*virology ; *Rhabdoviridae ; }, abstract = {A small number of free-living viruses have been found to be obligately vertically transmitted, but it remains uncertain how widespread vertically transmitted viruses are and how quickly they can spread through host populations. Recent metagenomic studies have found several insects to be infected with sigma viruses (Rhabdoviridae). Here, we report that sigma viruses that infect Mediterranean fruit flies (Ceratitis capitata), Drosophila immigrans, and speckled wood butterflies (Pararge aegeria) are all vertically transmitted. We find patterns of vertical transmission that are consistent with those seen in Drosophila sigma viruses, with high rates of maternal transmission, and lower rates of paternal transmission. This mode of transmission allows them to spread rapidly in populations, and using viral sequence data we found the viruses in D. immigrans and C. capitata had both recently swept through host populations. The viruses were common in nature, with mean prevalences of 12% in C. capitata, 38% in D. immigrans and 74% in P. aegeria We conclude that vertically transmitted rhabdoviruses may be widespread in a broad range of insect taxa, and that these viruses can have dynamic interactions with their hosts.}, } @article {pmid28099457, year = {2017}, author = {Vollmers, J and Wiegand, S and Kaster, AK}, title = {Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist's Perspective - Not Only Size Matters!.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0169662}, pmid = {28099457}, issn = {1932-6203}, mesh = {Biodiversity ; Forests ; High-Throughput Nucleotide Sequencing/methods ; Macrocystis/genetics ; *Metagenome ; Metagenomics/*methods ; Phylogeny ; *Software ; Soil Microbiology ; }, abstract = {With the constant improvement in cost-efficiency and quality of Next Generation Sequencing technologies, shotgun-sequencing approaches -such as metagenomics- have nowadays become the methods of choice for studying and classifying microorganisms from various habitats. The production of data has dramatically increased over the past years and processing and analysis steps are becoming more and more of a bottleneck. Limiting factors are partly the availability of computational resources, but mainly the bioinformatics expertise in establishing and applying appropriate processing and analysis pipelines. Fortunately, a large diversity of specialized software tools is nowadays available. Nevertheless, choosing the most appropriate methods for answering specific biological questions can be rather challenging, especially for non-bioinformaticians. In order to provide a comprehensive overview and guide for the microbiological scientific community, we assessed the most common and freely available metagenome assembly tools with respect to their output statistics, their sensitivity for low abundant community members and variability in resulting community profiles as well as their ease-of-use. In contrast to the highly anticipated "Critical Assessment of Metagenomic Interpretation" (CAMI) challenge, which uses general mock community-based assembler comparison we here tested assemblers on real Illumina metagenome sequencing data from natural communities of varying complexity sampled from forest soil and algal biofilms. Our observations clearly demonstrate that different assembly tools can prove optimal, depending on the sample type, available computational resources and, most importantly, the specific research goal. In addition, we present detailed descriptions of the underlying principles and pitfalls of publically available assembly tools from a microbiologist's perspective, and provide guidance regarding the user-friendliness, sensitivity and reliability of the resulting phylogenetic profiles.}, } @article {pmid28099455, year = {2017}, author = {Vesty, A and Biswas, K and Taylor, MW and Gear, K and Douglas, RG}, title = {Evaluating the Impact of DNA Extraction Method on the Representation of Human Oral Bacterial and Fungal Communities.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0169877}, pmid = {28099455}, issn = {1932-6203}, mesh = {Biodiversity ; Chemical Fractionation/methods ; DNA, Bacterial/*isolation & purification ; DNA, Fungal/*isolation & purification ; Humans ; Metagenomics/*methods ; *Microbiota ; Mouth/*microbiology ; RNA, Ribosomal, 16S ; Saliva/microbiology ; }, abstract = {The application of high-throughput, next-generation sequencing technologies has greatly improved our understanding of the human oral microbiome. While deciphering this diverse microbial community using such approaches is more accurate than traditional culture-based methods, experimental bias introduced during critical steps such as DNA extraction may compromise the results obtained. Here, we systematically evaluate four commonly used microbial DNA extraction methods (MoBio PowerSoil® DNA Isolation Kit, QIAamp® DNA Mini Kit, Zymo Bacterial/Fungal DNA Mini PrepTM, phenol:chloroform-based DNA isolation) based on the following criteria: DNA quality and yield, and microbial community structure based on Illumina amplicon sequencing of the V3-V4 region of the 16S rRNA gene of bacteria and the internal transcribed spacer (ITS) 1 region of fungi. Our results indicate that DNA quality and yield varied significantly with DNA extraction method. Representation of bacterial genera in plaque and saliva samples did not significantly differ across DNA extraction methods and DNA extraction method showed no effect on the recovery of fungal genera from plaque. By contrast, fungal diversity from saliva was affected by DNA extraction method, suggesting that not all protocols are suitable to study the salivary mycobiome.}, } @article {pmid28096483, year = {2017}, author = {Kelly, PH and Bahr, SM and Serafim, TD and Ajami, NJ and Petrosino, JF and Meneses, C and Kirby, JR and Valenzuela, JG and Kamhawi, S and Wilson, ME}, title = {The Gut Microbiome of the Vector Lutzomyia longipalpis Is Essential for Survival of Leishmania infantum.}, journal = {mBio}, volume = {8}, number = {1}, pages = {}, pmid = {28096483}, issn = {2150-7511}, support = {P50 AI074321/AI/NIAID NIH HHS/United States ; P50 AI030639/AI/NIAID NIH HHS/United States ; I01 BX001983/BX/BLRD VA/United States ; T32 AI007511/AI/NIAID NIH HHS/United States ; R01 AI076233/AI/NIAID NIH HHS/United States ; I01 BX000536/BX/BLRD VA/United States ; }, mesh = {Animals ; Bacteria/classification/genetics ; Cell Survival ; DNA, Ribosomal/chemistry/genetics ; *Disease Vectors ; *Gastrointestinal Microbiome ; Leishmania infantum/*physiology ; Psychodidae/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {UNLABELLED: The vector-borne disease leishmaniasis, caused by Leishmania species protozoa, is transmitted to humans by phlebotomine sand flies. Development of Leishmania to infective metacyclic promastigotes in the insect gut, a process termed metacyclogenesis, is an essential prerequisite for transmission. Based on the hypothesis that vector gut microbiota influence the development of virulent parasites, we sequenced midgut microbiomes in the sand fly Lutzomyia longipalpis with or without Leishmania infantum infection. Sucrose-fed sand flies contained a highly diverse, stable midgut microbiome. Blood feeding caused a decrease in microbial richness that eventually recovered. However, bacterial richness progressively decreased in L. infantum-infected sand flies. Acetobacteraceae spp. became dominant and numbers of Pseudomonadaceae spp. diminished coordinately as the parasite underwent metacyclogenesis and parasite numbers increased. Importantly, antibiotic-mediated perturbation of the midgut microbiome rendered sand flies unable to support parasite growth and metacyclogenesis. Together, these data suggest that the sand fly midgut microbiome is a critical factor for Leishmania growth and differentiation to its infective state prior to disease transmission.

IMPORTANCE: Leishmania infantum, a parasitic protozoan causing fatal visceral leishmaniasis, is transmitted to humans through the bite of the sand fly Lutzomyia longipalpis Development of the parasite to its virulent metacyclic state occurs in the sand fly gut. In this study, the microbiota within the Lu. longipalpis midgut was delineated by 16S ribosomal DNA (rDNA) sequencing, revealing a highly diverse community composition that lost diversity as parasites developed to their metacyclic state and increased in abundance in infected flies. Perturbing sand fly gut microbiota with an antibiotic cocktail, which alone had no effect on either the parasite or the fly, arrested both the development of virulent parasites and parasite expansion. These findings indicate the importance of bacterial commensals within the insect vector for the development of virulent pathogens, and raise the possibility that impairing the microbial composition within the vector might represent a novel approach to control of vector-borne diseases.}, } @article {pmid28096258, year = {2017}, author = {Ussar, S and Haering, MF and Fujisaka, S and Lutter, D and Lee, KY and Li, N and Gerber, GK and Bry, L and Kahn, CR}, title = {Regulation of Glucose Uptake and Enteroendocrine Function by the Intestinal Epithelial Insulin Receptor.}, journal = {Diabetes}, volume = {66}, number = {4}, pages = {886-896}, pmid = {28096258}, issn = {1939-327X}, support = {R01 DK033201/DK/NIDDK NIH HHS/United States ; R37 DK031036/DK/NIDDK NIH HHS/United States ; P30 DK036836/DK/NIDDK NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; T32 DK007260/DK/NIDDK NIH HHS/United States ; R01 DK031036/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Blotting, Western ; DNA, Ribosomal/genetics ; Fluorescent Antibody Technique ; Gastric Inhibitory Polypeptide/genetics/metabolism ; Gastrointestinal Microbiome/genetics/*physiology ; Glucose/*metabolism ; Glucose Transporter Type 2/genetics/metabolism ; Intestinal Mucosa/*metabolism ; Intestines/growth & development ; Male ; Mice ; RNA, Messenger/*metabolism ; Real-Time Polymerase Chain Reaction ; Receptor, IGF Type 1/*genetics ; Receptor, Insulin/*genetics ; Sodium-Glucose Transporter 1/genetics/metabolism ; }, abstract = {Insulin receptors (IRs) and IGF-I receptors (IGF-IR) are major regulators of metabolism and cell growth throughout the body; however, their roles in the intestine remain controversial. Here we show that genetic ablation of the IR or IGF-IR in intestinal epithelial cells of mice does not impair intestinal growth or development or the composition of the gut microbiome. However, the loss of IRs alters intestinal epithelial gene expression, especially in pathways related to glucose uptake and metabolism. More importantly, the loss of IRs reduces intestinal glucose uptake. As a result, mice lacking the IR in intestinal epithelium retain normal glucose tolerance during aging compared with controls, which show an age-dependent decline in glucose tolerance. Loss of the IR also results in a reduction of glucose-dependent insulinotropic polypeptide (GIP) expression from enteroendocrine K-cells and decreased GIP release in vivo after glucose ingestion but has no effect on glucagon-like peptide 1 expression or secretion. Thus, the IR in the intestinal epithelium plays important roles in intestinal gene expression, glucose uptake, and GIP production, which may contribute to pathophysiological changes in individuals with diabetes, metabolic syndrome, and other insulin-resistant states.}, } @article {pmid28096237, year = {2017}, author = {Rajagopala, SV and Vashee, S and Oldfield, LM and Suzuki, Y and Venter, JC and Telenti, A and Nelson, KE}, title = {The Human Microbiome and Cancer.}, journal = {Cancer prevention research (Philadelphia, Pa.)}, volume = {10}, number = {4}, pages = {226-234}, doi = {10.1158/1940-6207.CAPR-16-0249}, pmid = {28096237}, issn = {1940-6215}, mesh = {*Gastrointestinal Microbiome ; Humans ; Neoplasms/*microbiology ; }, abstract = {Recent scientific advances have significantly contributed to our understanding of the complex connection between the microbiome and cancer. Our bodies are continuously exposed to microbial cells, both resident and transient, as well as their byproducts, including toxic metabolites. Circulation of toxic metabolites may contribute to cancer onset or progression at locations distant from where a particular microbe resides. Moreover, microbes may migrate to other locations in the human body and become associated with tumor development. Several case-control metagenomics studies suggest that dysbiosis in the commensal microbiota is also associated with inflammatory disorders and various cancer types throughout the body. Although the microbiome influences carcinogenesis through mechanisms independent of inflammation and immune system, the most recognizable link is between the microbiome and cancer via the immune system, as the resident microbiota plays an essential role in activating, training, and modulating the host immune response. Immunologic dysregulation is likely to provide mechanistic explanations as to how our microbiome influences cancer development and cancer therapies. In this review, we discuss recent developments in understanding the human gut microbiome's relationship with cancer and the feasibility of developing novel cancer diagnostics based on microbiome profiles. Cancer Prev Res; 10(4); 226-34. ©2017 AACR.}, } @article {pmid28094305, year = {2017}, author = {Zinkernagel, MS and Zysset-Burri, DC and Keller, I and Berger, LE and Leichtle, AB and Largiadèr, CR and Fiedler, GM and Wolf, S}, title = {Association of the Intestinal Microbiome with the Development of Neovascular Age-Related Macular Degeneration.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40826}, pmid = {28094305}, issn = {2045-2322}, mesh = {Aged ; Bacteroides/isolation & purification ; Case-Control Studies ; Female ; *Gastrointestinal Microbiome ; Humans ; Macular Degeneration/epidemiology/*microbiology ; Male ; Middle Aged ; Ruminococcus/isolation & purification ; }, abstract = {Age-related macular degeneration (AMD) is the most frequent cause of blindness in the elderly. There is evidence that nutrition, inflammation and genetic risk factors play an important role in the development of AMD. Recent studies suggest that the composition of the intestinal microbiome is associated with metabolic diseases through modulation of inflammation and host metabolism. To investigate whether compositional and functional alterations of the intestinal microbiome are associated with AMD, we sequenced the gut metagenomes of patients with AMD and controls. The genera Anaerotruncus and Oscillibacter as well as Ruminococcus torques and Eubacterium ventriosum were relatively enriched in patients with AMD, whereas Bacteroides eggerthii was enriched in controls. Patient's intestinal microbiomes were enriched in genes of the L-alanine fermentation, glutamate degradation and arginine biosynthesis pathways and decreased in genes of the fatty acid elongation pathway. These findings suggest that modifications in the intestinal microbiome are associated with AMD, inferring that this common sight threatening disease may be targeted by microbiome-altering interventions.}, } @article {pmid28094284, year = {2017}, author = {Murphy, K and Curley, D and O'Callaghan, TF and O'Shea, CA and Dempsey, EM and O'Toole, PW and Ross, RP and Ryan, CA and Stanton, C}, title = {The Composition of Human Milk and Infant Faecal Microbiota Over the First Three Months of Life: A Pilot Study.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40597}, pmid = {28094284}, issn = {2045-2322}, mesh = {Biodiversity ; Feces/*microbiology ; Humans ; Infant ; Infant, Newborn ; Metagenome ; Metagenomics/methods ; *Microbiota ; Milk, Human/*microbiology ; Pilot Projects ; }, abstract = {Human milk contains a diverse array of bioactives and is also a source of bacteria for the developing infant gut. The aim of this study was to characterize the bacterial communities in human milk and infant faeces over the first 3 months of life, in 10 mother-infant pairs. The presence of viable Bifidobacterium and Lactobacillus in human milk was also evaluated. MiSeq sequencing revealed a large diversity of the human milk microbiota, identifying over 207 bacterial genera in milk samples. The phyla Proteobacteria and Firmicutes and the genera Pseudomonas, Staphylococcus and Streptococcus were the predominant bacterial groups. A core of 12 genera represented 81% of the microbiota relative abundance in milk samples at week 1, 3 and 6, decreasing to 73% at week 12. Genera shared between infant faeces and human milk samples accounted for 70-88% of the total relative abundance in infant faecal samples, supporting the hypothesis of vertical transfer of bacteria from milk to the infant gut. In addition, identical strains of Bifidobacterium breve and Lactobacillus plantarum were isolated from the milk and faeces of one mother-infant pair. Vertical transfer of bacteria via breastfeeding may contribute to the initial establishment of the microbiota in the developing infant intestine.}, } @article {pmid28093622, year = {2017}, author = {Nittami, T and Speirs, LBM and Yamada, T and Suzuki, I and Fukuda, J and Kurisu, F and Seviour, RJ}, title = {Quantification of Chloroflexi Eikelboom morphotype 1851 for prediction and control of bulking events in municipal activated sludge plants in Japan.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {9}, pages = {3861-3869}, doi = {10.1007/s00253-016-8077-4}, pmid = {28093622}, issn = {1432-0614}, mesh = {*Bacterial Load ; *Biota ; Chloroflexi/genetics/*isolation & purification ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; In Situ Hybridization, Fluorescence ; Japan ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sewage/*microbiology ; Wastewater/microbiology ; }, abstract = {The dominant filamentous bacteria associated with bulking incidents in Japanese activated sludge plants with nutrient removal were identified and their quantitative correlations with sludge settleability were assessed, with the aim of controlling bulking incidents by specifically suppressing bacterial growth. Fluorescence in situ hybridization (FISH) analyses using existing oligonucleotide FISH probes indicated that the presence of Eikelboom type 1851 filamentous bacteria belonging to the phylum Chloroflexi is correlated with biomass settleability in the municipal wastewater treatment plants examined. Real-time quantitative PCR (qPCR) assays developed in this study also showed a linear correlation between type 1851 filament members and sludge settleability, with the exception of some winter samples. The real-time qPCR assays and 16S ribosomal RNA gene amplicon sequencing to reveal the microbial community of activated sludge showed that the abundance of type 1851 at 200 mL g[-1] of sludge volume index was estimated to be about 1.9% of the total microbial cells. The abundance of type 1851 served as a bulking indicator in plants where type 1851 was dominant.}, } @article {pmid28092820, year = {2017}, author = {Saubade, F and Humblot, C and Hemery, YM and Guyot, JP}, title = {PCR screening of an African fermented pearl-millet porridge metagenome to investigate the nutritional potential of its microbiota.}, journal = {International journal of food microbiology}, volume = {244}, number = {}, pages = {103-110}, doi = {10.1016/j.ijfoodmicro.2016.12.020}, pmid = {28092820}, issn = {1879-3460}, mesh = {Bioreactors ; Burkina Faso ; Carotenoids/biosynthesis ; Edible Grain/*microbiology ; Fermentation ; Folic Acid/biosynthesis ; Food Microbiology ; Hydrolysis ; Limosilactobacillus fermentum/*genetics/metabolism ; Metagenome/*genetics ; Microbiota/*genetics ; Nutritive Value ; Pennisetum/*microbiology ; Polyphenols/metabolism ; Real-Time Polymerase Chain Reaction ; Riboflavin/biosynthesis ; Starch/metabolism ; Yeasts/*genetics/metabolism ; }, abstract = {Cereals are staple foods in most African countries, and many African cereal-based foods are spontaneously fermented. The nutritional quality of cereal products can be enhanced through fermentation, and traditional cereal-based fermented foods (CBFFs) are possible sources of lactic acid bacteria (LAB) with useful nutritional properties. The nutritional properties of LAB vary depending on the species and even on the strain, and the microbial composition of traditional CBFFs varies from one traditional production unit (TPU) to another. The nutritional quality of traditional CBFFs may thus vary depending on their microbial composition. As the isolation of potentially useful LAB from traditional CBFFs can be very time consuming, the aim of this study was to use PCR to assess the nutritional potential of LAB directly on the metagenomes of pearl-millet based fermented porridges (ben-saalga) from Burkina Faso. Genes encoding enzymes involved in different nutritional activities were screened in 50 metagenomes extracted from samples collected in 10 TPUs in Ouagadougou. The variability of the genetic potential was recorded. Certain genes were never detected in the metagenomes (genes involved in carotenoid synthesis) while others were frequently detected (genes involved in folate and riboflavin production, starch hydrolysis, polyphenol degradation). Highly variable microbial composition - assessed by real-time PCR - was observed among samples collected in different TPUs, but also among samples from the same TPU. The high frequency of the presence of genes did not necessarily correlate with in situ measurements of the expected products. Indeed, no significant correlation was found between the microbial variability and the variability of the genetic potential. In spite of the high rate of detection (80%) of both genes folP and folK, encoding enzymes involved in folate synthesis, the folate content in ben-saalga was rather low (median: 0.5μg/100g fresh weight basis). This work highlighted the limit of evaluating the nutritional potential of the microbiota of traditional fermented foods by the only screening of genes in metagenomes, and suggests that such a screening should be completed by a functional analysis.}, } @article {pmid28091525, year = {2017}, author = {Patrascu, O and Béguet-Crespel, F and Marinelli, L and Le Chatelier, E and Abraham, AL and Leclerc, M and Klopp, C and Terrapon, N and Henrissat, B and Blottière, HM and Doré, J and Béra-Maillet, C}, title = {A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40248}, pmid = {28091525}, issn = {2045-2322}, support = {322820/ERC_/European Research Council/International ; }, mesh = {Bacteroides/metabolism ; Carbohydrate Metabolism ; Carboxymethylcellulose Sodium/metabolism ; Chromosome Mapping ; Clostridiales/metabolism ; Dietary Fiber/*metabolism/*microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Ileum/*microbiology ; Metagenome ; Metagenomics ; Xylans/metabolism ; }, abstract = {The digestion of dietary fibers is a major function of the human intestinal microbiota. So far this function has been attributed to the microorganisms inhabiting the colon, and many studies have focused on this distal part of the gastrointestinal tract using easily accessible fecal material. However, microbial fermentations, supported by the presence of short-chain fatty acids, are suspected to occur in the upper small intestine, particularly in the ileum. Using a fosmid library from the human ileal mucosa, we screened 20,000 clones for their activities against carboxymethylcellulose and xylans chosen as models of the major plant cell wall (PCW) polysaccharides from dietary fibres. Eleven positive clones revealed a broad range of CAZyme encoding genes from Bacteroides and Clostridiales species, as well as Polysaccharide Utilization Loci (PULs). The functional glycoside hydrolase genes were identified, and oligosaccharide break-down products examined from different polysaccharides including mixed-linkage β-glucans. CAZymes and PULs were also examined for their prevalence in human gut microbiome. Several clusters of genes of low prevalence in fecal microbiome suggested they belong to unidentified strains rather specifically established upstream the colon, in the ileum. Thus, the ileal mucosa-associated microbiota encompasses the enzymatic potential for PCW polysaccharide degradation in the small intestine.}, } @article {pmid28089325, year = {2017}, author = {Baker, JL and Bor, B and Agnello, M and Shi, W and He, X}, title = {Ecology of the Oral Microbiome: Beyond Bacteria.}, journal = {Trends in microbiology}, volume = {25}, number = {5}, pages = {362-374}, pmid = {28089325}, issn = {1878-4380}, support = {F32 DE025548/DE/NIDCR NIH HHS/United States ; F32 DE026947/DE/NIDCR NIH HHS/United States ; R01 DE020102/DE/NIDCR NIH HHS/United States ; T90 DE022734/DE/NIDCR NIH HHS/United States ; R00 DE027719/DE/NIDCR NIH HHS/United States ; R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 DE026186/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/genetics/metabolism ; Bacteriophages/genetics/metabolism ; Biodiversity ; Fungi/genetics/metabolism ; Humans ; Metagenome ; *Microbiota ; Mouth/*microbiology ; Viruses/genetics/metabolism ; }, abstract = {Although great strides have been made in understanding the complex bacterial community inhabiting the human oral cavity, for a variety of (mainly technical) reasons the ecological contributions of oral fungi, viruses, phages, and the candidate phyla radiation (CPR) group of ultrasmall bacteria have remained understudied. Several recent reports have illustrated the diversity and importance of these organisms in the oral cavity, while TM7x and Candida albicans have served as crucial paradigms for CPR species and oral fungi, respectively. A comprehensive understanding of the oral microbiota and its influence on host health and disease will require a holistic view that emphasizes interactions among different residents within the oral community, as well as their interaction with the host.}, } @article {pmid28088719, year = {2017}, author = {Young, B and Delatolla, R and Kennedy, K and Laflamme, E and Stintzi, A}, title = {Low temperature MBBR nitrification: Microbiome analysis.}, journal = {Water research}, volume = {111}, number = {}, pages = {224-233}, doi = {10.1016/j.watres.2016.12.050}, pmid = {28088719}, issn = {1879-2448}, mesh = {Ammonia/metabolism ; Biofilms ; Bioreactors/microbiology ; Microbiota ; *Nitrification ; Nitrites/metabolism ; *Temperature ; }, abstract = {This study aims to investigate post carbon removal moving bed biofilm reactor (MBBR) nitrification through the transition from 20 °C to 1 °C and during through long term operation at 1 °C. Four pilot nitrifying MBBR reactors were operated at various ammonia loading rates to elucidate the temperature effects on ammonia removal rates, cell viability and bacterial communities. The transition from 20 °C to 1 °C and during long term operation at 1 °C were modeled using Arrhenius temperature correction coefficients. Specifically, the steady state removal rates at 1 °C on average were 22.8% of the maximum ammonia removal rate at 20 °C, which corresponds to an Arrhenius temperature correction of 1.086 during steady operation at 1 °C. The microbial communities of the nitrifying MBBR biofilm were shown to be significantly more diverse at 20 °C as compared to 1 °C operation. Although less diverse at 1 °C, 2000 species of bacteria were identified in the nitrifying biofilm during operation at this low temperature. Nitrosomonads were shown to be the dominant ammonia oxidizing bacteria (AOB) and Nitrospira was shown to be the dominant nitrite oxidizing bacteria (NOB) in all the pilot MBBR reactors at all temperatures. The performance of the post carbon removal nitrifying MBBR systems were shown to be enhanced at 1 °C by an increase in the viable embedded biomass as well as thicker biofilm. This effectively increases the number of viable cell present during low temperature operation, which partially compensates for the significant decrease in rate of ammonia removal per nitrifying cell. Operation at the highest loading conditions tested in this study at 1 °C were shown to reduce the ammonia removal rate compared to lower loading conditions at 1 °C. The lower performance at higher loading conditions at 1 °C demonstrated an enrichment in the stress response metagenomics pathways of the system.}, } @article {pmid28085878, year = {2017}, author = {Satten, GA and Tyx, RE and Rivera, AJ and Stanfill, S}, title = {Restoring the Duality between Principal Components of a Distance Matrix and Linear Combinations of Predictors, with Application to Studies of the Microbiome.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0168131}, pmid = {28085878}, issn = {1932-6203}, mesh = {*Algorithms ; Bacteria/classification/*genetics ; Computational Biology/*methods ; *Metagenome ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Tobacco, Smokeless/*microbiology ; }, abstract = {Appreciation of the importance of the microbiome is increasing, as sequencing technology has made it possible to ascertain the microbial content of a variety of samples. Studies that sequence the 16S rRNA gene, ubiquitous in and nearly exclusive to bacteria, have proliferated in the medical literature. After sequences are binned into operational taxonomic units (OTUs) or species, data from these studies are summarized in a data matrix with the observed counts from each OTU for each sample. Analysis often reduces these data further to a matrix of pairwise distances or dissimilarities; plotting the first two or three principal components (PCs) of this distance matrix often reveals meaningful groupings in the data. However, once the distance matrix is calculated, it is no longer clear which OTUs or species are important to the observed clustering; further, the PCs are hard to interpret and cannot be calculated for subsequent observations. We show how to construct approximate decompositions of the data matrix that pair PCs with linear combinations of OTU or species frequencies, and show how these decompositions can be used to construct biplots, select important OTUs and partition the variability in the data matrix into contributions corresponding to PCs of an arbitrary distance or dissimilarity matrix. To illustrate our approach, we conduct an analysis of the bacteria found in 45 smokeless tobacco samples.}, } @article {pmid28085156, year = {2017}, author = {Rubino, F and Carberry, C and M Waters, S and Kenny, D and McCabe, MS and Creevey, CJ}, title = {Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome.}, journal = {The ISME journal}, volume = {11}, number = {4}, pages = {932-944}, pmid = {28085156}, issn = {1751-7370}, support = {BB/E/W/10964A01//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacteria/*classification/*genetics ; Bacterial Physiological Phenomena ; Cattle ; Digestion/physiology ; Female ; Metagenomics/methods ; Microbiota/*genetics ; Rumen/*microbiology ; }, abstract = {Many microbes in complex competitive environments share genes for acquiring and utilising nutrients, questioning whether niche specialisation exists and if so, how it is maintained. We investigated the genomic signatures of niche specialisation in the rumen microbiome, a highly competitive, anaerobic environment, with limited nutrient availability determined by the biomass consumed by the host. We generated individual metagenomic libraries from 14 cows fed an ad libitum diet of grass silage and calculated functional isoform diversity for each microbial gene identified. The animal replicates were used to calculate confidence intervals to test for differences in diversity of functional isoforms between microbes that may drive niche specialisation. We identified 153 genes with significant differences in functional isoform diversity between the two most abundant bacterial genera in the rumen (Prevotella and Clostridium). We found Prevotella possesses a more diverse range of isoforms capable of degrading hemicellulose, whereas Clostridium for cellulose. Furthermore, significant differences were observed in key metabolic processes indicating that isoform diversity plays an important role in maintaining their niche specialisation. The methods presented represent a novel approach for untangling complex interactions between microorganisms in natural environments and have resulted in an expanded catalogue of gene targets central to rumen cellulosic biomass degradation.}, } @article {pmid28083922, year = {2017}, author = {Zhang, N and Mao, X and Li, RW and Hou, E and Wang, Y and Xue, C and Tang, Q}, title = {Neoagarotetraose protects mice against intense exercise-induced fatigue damage by modulating gut microbial composition and function.}, journal = {Molecular nutrition & food research}, volume = {61}, number = {8}, pages = {}, doi = {10.1002/mnfr.201600585}, pmid = {28083922}, issn = {1613-4133}, mesh = {Animals ; Dietary Supplements ; Fatigue/etiology/*prevention & control ; Fatty Acids, Volatile/metabolism ; Galactosides/*pharmacology ; Gastrointestinal Microbiome/*drug effects/genetics ; Jejunum/drug effects/pathology ; Male ; Mice, Inbred BALB C ; Oligosaccharides/*pharmacology ; Physical Conditioning, Animal/adverse effects ; RNA, Ribosomal, 16S ; }, abstract = {SCOPE: Exhaustive exercise stress has emerged as an important health issue, and gastrointestinal problems are a common concern during intense exercise. In this study, we investigated the potential antifatigue effects of neoagarotetraose (NAT) in mice under intense exercise stress.

MATERIALS AND METHODS: Exhaustive exercise stress significantly weakened several physiological and physical parameters of the mice, including decreased food intake, reduced body weight, and impaired integrity of the intestinal epithelial barrier. Our data showed that a 16-day NAT treatment resulted in a profound change in microbiome composition, which subsequently led to widespread shifts in the functional potential of the gut microbiome. Furthermore, NAT administration significantly increased the fecal concentration of total short-chain fatty acids (p < 0.01).

CONCLUSION: Together, our findings suggest that NAT may protect mice against intense exercise-induced fatigue and provide insights into the mechanisms of NAT as a potential prebiotic.}, } @article {pmid28083919, year = {2018}, author = {Ishihara, K}, title = {New approach for studying mobile genes using metagenomic analysis.}, journal = {Oral diseases}, volume = {24}, number = {4}, pages = {494-496}, doi = {10.1111/odi.12640}, pmid = {28083919}, issn = {1601-0825}, mesh = {Bacteria/*genetics ; Drug Resistance, Bacterial/genetics ; Fiji ; Gastrointestinal Microbiome/genetics ; Gene Transfer, Horizontal ; Humans ; *Metagenome ; Metagenomics ; Mouth/*microbiology ; Mouth Diseases/*microbiology ; North America ; }, } @article {pmid28081445, year = {2017}, author = {Vázquez-Baeza, Y and Gonzalez, A and Smarr, L and McDonald, D and Morton, JT and Navas-Molina, JA and Knight, R}, title = {Bringing the Dynamic Microbiome to Life with Animations.}, journal = {Cell host & microbe}, volume = {21}, number = {1}, pages = {7-10}, doi = {10.1016/j.chom.2016.12.009}, pmid = {28081445}, issn = {1934-6069}, mesh = {Clostridioides difficile/genetics ; Enterocolitis, Pseudomembranous/microbiology/transmission ; Humans ; *Internet ; Metagenome/*genetics ; Microbiota/*genetics ; }, abstract = {Our bodies and natural environment contain complex microbial communities, colloquially termed microbiomes. We previously created a web-based application, EMPeror, for visualizing ordinations derived from comparisons of these microbiome communities. We have now improved EMPeror to create interactive animations that connect successive samples to highlight patterns over time.}, } @article {pmid28079128, year = {2017}, author = {Jing, G and Sun, Z and Wang, H and Gong, Y and Huang, S and Ning, K and Xu, J and Su, X}, title = {Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40371}, pmid = {28079128}, issn = {2045-2322}, support = {R34 AA021502/AA/NIAAA NIH HHS/United States ; }, mesh = {Adult ; Base Sequence ; Biodiversity ; Biomarkers/metabolism ; Child ; Computer Simulation ; Databases, Genetic ; Humans ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Time Factors ; }, abstract = {The number of metagenomes is increasing rapidly. However, current methods for metagenomic analysis are limited by their capability for in-depth data mining among a large number of microbiome each of which carries a complex community structure. Moreover, the complexity of configuring and operating computational pipeline also hinders efficient data processing for the end users. In this work we introduce Parallel-META 3, a comprehensive and fully automatic computational toolkit for rapid data mining among metagenomic datasets, with advanced features including 16S rRNA extraction for shotgun sequences, 16S rRNA copy number calibration, 16S rRNA based functional prediction, diversity statistics, bio-marker selection, interaction network construction, vector-graph-based visualization and parallel computing. Application of Parallel-META 3 on 5,337 samples with 1,117,555,208 sequences from diverse studies and platforms showed it could produce similar results as QIIME and PICRUSt with much faster speed and lower memory usage, which demonstrates its ability to unravel the taxonomical and functional dynamics patterns across large datasets and elucidate ecological links between microbiome and the environment. Parallel-META 3 is implemented in C/C++ and R, and integrated into an executive package for rapid installation and easy access under Linux and Mac OS X. Both binary and source code packages are available at http://bioinfo.single-cell.cn/parallel-meta.html.}, } @article {pmid28074247, year = {2017}, author = {Tripathi, BM and Moroenyane, I and Sherman, C and Lee, YK and Adams, JM and Steinberger, Y}, title = {Trends in Taxonomic and Functional Composition of Soil Microbiome Along a Precipitation Gradient in Israel.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {168-176}, pmid = {28074247}, issn = {1432-184X}, mesh = {Climate Change ; *Ecosystem ; Israel ; *Microbiota ; Soil ; *Soil Microbiology ; Water ; }, abstract = {The soil microbiome is important for the functioning of terrestrial ecosystems. However, the impacts of climate on taxonomic and functional diversity of soil microbiome are not well understood. A precipitation gradient along regional scale transects may offer a model setting for understanding the effect of climate on the composition and function of the soil microbiome. Here, we compared taxonomic and functional attributes of soil microorganisms in arid, semiarid, Mediterranean, and humid Mediterranean climatic conditions of Israel using shotgun metagenomic sequencing. We hypothesized that there would be a distinct taxonomic and functional soil community for each precipitation zone, with arid environments having lower taxonomic and functional diversity, greater relative abundance of stress response and sporulation-related genes, and lower relative abundance of genes related to nutrient cycling and degradation of complex organic compounds. As hypothesized, our results showed a distinct taxonomic and functional community in each precipitation zone, revealing differences in soil taxonomic and functional selection in the different climates. Although the taxonomic diversity remained similar across all sites, the functional diversity was-as hypothesized-lower in the arid environments, suggesting that functionality is more constrained in "extreme" environments. Also, with increasing aridity, we found a significant increase in genes related to dormancy/sporulation and a decrease in those related to nutrient cycling (genes related to nitrogen, potassium, and sulfur metabolism), respectively. However, relative abundance of genes related to stress response were lower in arid soils. Overall, these results indicate that climatic conditions play an important role in shaping taxonomic and functional attributes of soil microbiome. These findings have important implications for understanding the impacts of climate change (e.g., precipitation change) on structure and function of the soil microbiome.}, } @article {pmid28074233, year = {2017}, author = {Schmautz, Z and Graber, A and Jaenicke, S and Goesmann, A and Junge, R and Smits, TH}, title = {Microbial diversity in different compartments of an aquaponics system.}, journal = {Archives of microbiology}, volume = {199}, number = {4}, pages = {613-620}, doi = {10.1007/s00203-016-1334-1}, pmid = {28074233}, issn = {1432-072X}, mesh = {Animals ; *Aquaculture ; Bacteria/classification/*isolation & purification ; Biodiversity ; Biofilms ; Fishes/*microbiology ; *Hydroponics ; Nitrification ; Plant Roots/*microbiology ; }, abstract = {Aquaponics is a solution for sustainable production of fish and plants in a single semi-closed system, where nutrient-rich water from the aquaculture provides nutrients for plant growth. We examined the microbial communities within an experimental aquaponics system. Whereas the fish feces contained a separate community dominated by bacteria of the genus Cetobacterium, the samples from plant roots, biofilter, and periphyton were more similar to each other, while the communities were more diverse. Detailed examination of the data gave the first indications to functional groups of organisms in the different compartments of the aquaponic system. As other nitrifiers other than members of the genus Nitrospira were only present at low numbers, it was anticipated that Nitrospirae may perform the nitrification process in the biofilm.}, } @article {pmid28073918, year = {2017}, author = {Olm, MR and Brown, CT and Brooks, B and Firek, B and Baker, R and Burstein, D and Soenjoyo, K and Thomas, BC and Morowitz, M and Banfield, JF}, title = {Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates.}, journal = {Genome research}, volume = {27}, number = {4}, pages = {601-612}, pmid = {28073918}, issn = {1549-5469}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; }, mesh = {Citrobacter koseri/*genetics/growth & development/isolation & purification/pathogenicity ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Infant, Extremely Low Birth Weight ; Infant, Newborn ; Infant, Premature ; Mouth/*microbiology ; Polymorphism, Genetic ; Skin/*microbiology ; }, abstract = {The initial microbiome impacts the health and future development of premature infants. Methodological limitations have led to gaps in our understanding of the habitat range and subpopulation complexity of founding strains, as well as how different body sites support microbial growth. Here, we used metagenomics to reconstruct genomes of strains that colonized the skin, mouth, and gut of two hospitalized premature infants during the first month of life. Seven bacterial populations, considered to be identical given whole-genome average nucleotide identity of >99.9%, colonized multiple body sites, yet none were shared between infants. Gut-associated Citrobacter koseri genomes harbored 47 polymorphic sites that we used to define 10 subpopulations, one of which appeared in the gut after 1 wk but did not spread to other body sites. Differential genome coverage was used to measure bacterial population replication rates in situ. In all cases where the same bacterial population was detected in multiple body sites, replication rates were faster in mouth and skin compared to the gut. The ability of identical strains to colonize multiple body sites underscores the habit flexibility of initial colonists, whereas differences in microbial replication rates between body sites suggest differences in host control and/or resource availability. Population genomic analyses revealed microdiversity within bacterial populations, implying initial inoculation by multiple individual cells with distinct genotypes. Overall, however, the overlap of strains across body sites implies that the premature infant microbiome can exhibit very low microbial diversity.}, } @article {pmid28072853, year = {2017}, author = {Priyamvada, H and Akila, M and Singh, RK and Ravikrishna, R and Verma, RS and Philip, L and Marathe, RR and Sahu, LK and Sudheer, KP and Gunthe, SS}, title = {Terrestrial Macrofungal Diversity from the Tropical Dry Evergreen Biome of Southern India and Its Potential Role in Aerobiology.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0169333}, pmid = {28072853}, issn = {1932-6203}, mesh = {*Biodiversity ; *Ecosystem ; Environmental Microbiology ; *Fungi/classification/genetics/ultrastructure ; Incidence ; India ; Metagenome ; Metagenomics/methods ; Plants/*microbiology ; Seasons ; Spores, Fungal/ultrastructure ; *Tropical Climate ; }, abstract = {Macrofungi have long been investigated for various scientific purposes including their food and medicinal characteristics. Their role in aerobiology as a fraction of the primary biological aerosol particles (PBAPs), however, has been poorly studied. In this study, we present a source of macrofungi with two different but interdependent objectives: (i) to characterize the macrofungi from a tropical dry evergreen biome in southern India using advanced molecular techniques to enrich the database from this region, and (ii) to assess whether identified species of macrofungi are a potential source of atmospheric PBAPs. From the DNA analysis, we report the diversity of the terrestrial macrofungi from a tropical dry evergreen biome robustly supported by the statistical analyses for diversity conclusions. A total of 113 macrofungal species belonging to 54 genera and 23 families were recorded, with Basidiomycota and Ascomycota constituting 96% and 4% of the species, respectively. The highest species richness was found in the family Agaricaceae (25.3%) followed by Polyporaceae (15.3%) and Marasmiaceae (10.8%). The difference in the distribution of commonly observed macrofungal families over this location was compared with other locations in India (Karnataka, Kerala, Maharashtra, and West Bengal) using two statistical tests. The distributions of the terrestrial macrofungi were distinctly different in each ecosystem. We further attempted to demonstrate the potential role of terrestrial macrofungi as a source of PBAPs in ambient air. In our opinion, the findings from this ecosystem of India will enhance our understanding of the distribution, diversity, ecology, and biological prospects of terrestrial macrofungi as well as their potential to contribute to airborne fungal aerosols.}, } @article {pmid28072776, year = {2017}, author = {Shankar, V}, title = {Gut microbiome profiling tests propelled by customer demand.}, journal = {Nature biotechnology}, volume = {35}, number = {1}, pages = {9}, doi = {10.1038/nbt0117-9}, pmid = {28072776}, issn = {1546-1696}, mesh = {Diagnostic Techniques and Procedures/trends ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Humans ; Mass Screening/*trends ; Metagenome/*genetics ; RNA, Ribosomal, 16S/genetics ; }, } @article {pmid28070087, year = {2017}, author = {Takino, T and Kato-Mori, Y and Motooka, D and Nakamura, S and Iida, T and Hagiwara, K}, title = {Postnatal changes in the relative abundance of intestinal Lactobacillus spp. in newborn calves.}, journal = {The Journal of veterinary medical science}, volume = {79}, number = {3}, pages = {452-455}, pmid = {28070087}, issn = {1347-7439}, mesh = {Animals ; Animals, Newborn ; Bacteria/isolation & purification ; Cattle/*microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Intestines/microbiology ; Lactobacillus/*growth & development/isolation & purification ; Molecular Typing ; }, abstract = {The intestinal microbiota of newborn calves changes during the early postnatal period and influences their health and immune function. We studied the compositional changes in the intestinal microbiome of newborn calves during the first week after birth by metagenomic analysis. In feces from newborn calves, we identified 4 bacterial phyla, namely, Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The relative abundance of Lactobacillaceae significantly increased from day 1 to day 7. We evaluated Lactobacillus spp. colony numbers using selective agar plates and confirmed that the abundance of Lactobacillus spp. significantly increased during the first 7 days after birth. In conclusion, Lactobacillus spp. colonized the intestinal tract of calves during the first 7 days after birth.}, } @article {pmid28067829, year = {2017}, author = {D'Argenio, V and Torino, M and Precone, V and Casaburi, G and Esposito, MV and Iaffaldano, L and Malapelle, U and Troncone, G and Coto, I and Cavalcanti, P and De Rosa, G and Salvatore, F and Sacchetti, L}, title = {The Cause of Death of a Child in the 18th Century Solved by Bone Microbiome Typing Using Laser Microdissection and Next Generation Sequencing.}, journal = {International journal of molecular sciences}, volume = {18}, number = {1}, pages = {}, pmid = {28067829}, issn = {1422-0067}, mesh = {Actinobacteria/genetics/isolation & purification ; Bacteroidetes/genetics/isolation & purification ; Bone and Bones/*microbiology ; Cause of Death ; Child ; Firmicutes/genetics/isolation & purification ; Genotype ; *High-Throughput Nucleotide Sequencing ; History, 18th Century ; Humans ; *Laser Capture Microdissection ; Male ; *Microbiota ; Osteomyelitis/history/microbiology ; Proteobacteria/genetics/isolation & purification ; Pseudomonas/genetics/isolation & purification ; Pseudomonas Infections/history/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The history of medicine abounds in cases of mysterious deaths, especially by infectious diseases, which were probably unresolved because of the lack of knowledge and of appropriate technology. The aim of this study was to exploit contemporary technologies to try to identify the cause of death of a young boy who died from a putative "infection" at the end of the 18th century, and for whom an extraordinarily well-preserved minute bone fragment was available. After confirming the nature of the sample, we used laser microdissection to select the most "informative" area to be examined. Tissue genotyping indicated male gender, thereby confirming the notary's report. 16S ribosomal RNA sequencing showed that Proteobacteria and Actinobacteria were more abundant than Firmicutes and Bacteroidetes, and that Pseudomonas was the most abundant bacterial genus in the Pseudomonadaceae family. These data suggest that the patient most likely died from Pseudomonas osteomyelitis. This case is an example of how new technological approaches, like laser microdissection and next-generation sequencing, can resolve ancient cases of uncertain etiopathology. Lastly, medical samples may contain a wealth of information that may not be accessible until more sophisticated technology becomes available. Therefore, one may envisage the possibility of systematically storing medical samples for evaluation by future generations.}, } @article {pmid28063827, year = {2017}, author = {Thiele, S and Richter, M and Balestra, C and Glöckner, FO and Casotti, R}, title = {Taxonomic and functional diversity of a coastal planktonic bacterial community in a river-influenced marine area.}, journal = {Marine genomics}, volume = {32}, number = {}, pages = {61-69}, doi = {10.1016/j.margen.2016.12.003}, pmid = {28063827}, issn = {1876-7478}, mesh = {Archaea/*classification ; Bacteria/*classification ; Italy ; Mediterranean Sea ; *Microbiota ; Plankton/*classification ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Salinity ; }, abstract = {The Gulf of Naples is a dynamical area with intense exchanges between offshore oligotrophic and coastal eutrophic waters with frequent freshwater inputs. The Sarno River, one of the most polluted rivers in Europe, strongly contributes to the pollution of the area, discharging high amounts of heavy metals and organic wastes from heavily cultivated and industrial areas. This paper reports on the diversity and community structure of the marine residential Bacteria and Archaea of the Gulf of Naples in an area close to the river Sarno plume and investigates their small-scale taxonomic diversity and expression patterns as a proxy of potential metabolic activity using metagenomics and metatranscriptomics. Bacteria and Archaea were mainly represented by marine clades, with only minor contributors from freshwater ones. The community was dominated by Alpha- and Gammaproteobacteria, of which Rhodospirillales, Pelagibacteriales, and Oceanospirilalles were most represented. However, Alteromonadales and Rhodobacterales were the most active, despite their relative lower abundance, suggesting that they are important for overall ecosystem functioning and nutrient cycling. Nitrification and a reversed form of dissimilatory sulfate reduction were the major metabolic processes found in the metatrascriptomes and were mainly associated to Nitrosopumilales and Pelagibacter, respectively. No clear indication of transcripts related to stress induced by heavy metals or organic pollutants was found. In general, despite the high loads of pollutants discharged continuously by the Sarno River, the microbial community did not show marks of stress-induced changes neither structural nor functional, thus suggesting that this river has little or no effect on the planktonic bacterial community of the Gulf of Naples.}, } @article {pmid28062969, year = {2017}, author = {de Araujo, AS and Bezerra, WM and Dos Santos, VM and Rocha, SM and Carvalho, ND and de Lyra, MD and Figueiredo, MD and de Almeida Lopes, ÂC and Melo, VM}, title = {Distinct bacterial communities across a gradient of vegetation from a preserved Brazilian Cerrado.}, journal = {Antonie van Leeuwenhoek}, volume = {110}, number = {4}, pages = {457-469}, doi = {10.1007/s10482-016-0815-1}, pmid = {28062969}, issn = {1572-9699}, mesh = {Acidobacteria/classification/genetics/*isolation & purification ; Actinobacteria/classification/genetics/*isolation & purification ; Biodiversity ; Brazil ; Ecosystem ; Firmicutes/classification/genetics/*isolation & purification ; Planctomycetales/classification/genetics/*isolation & purification ; Plants/microbiology ; Proteobacteria/classification/genetics/*isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Verrucomicrobia/classification/genetics/*isolation & purification ; }, abstract = {The Cerrado biome in the Sete Cidades National Park, an Ecological Reserve in Northeastern Brazil, has conserved its native biodiversity and presents a variety of plants found in other savannas in Brazil. Despite this finding the soil microbial diversity and community structure are poorly understood. Therefore, we described soil bacterial diversity and distribution along a savanna vegetation gradient taking into account the prevailing environmental factors. The bacterial composition was retrieved by sequencing a fragment of the 16S ribosomal RNA gene. The bacterial operational taxonomic units (OTUs) were assigned to 37 different phyla, 96 classes, and 83 genera. At the phylum level, a core comprised by Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Verrucomicrobia and Planctomycetes, was detected in all areas of Cerrado. 'Cerrado stricto sensu' and 'Cerradao' share more similarities between edaphic properties and vegetation and also present more similar bacterial communities, while 'Floresta decidual' and 'Campo graminoide' show the largest environmental differences and also more distinct bacterial communities. Proteobacteria (26%), Acidobacteria (21%) and Actinobacteria (21%) were the most abundant phyla within the four areas. All the samples present similar bacteria richness (alpha diversity) and the observed differences among them (beta diversity) were more related to the abundance of specific taxon OTUs compared to their presence or absence. Total organic C, N and P are the main abiotic factors structuring the bacterial communities. In summary, our findings show the bacterial community structure was clearly different across the Cerrado gradient, but that these environments share a bacterial phylum-core comprising Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia and Planctomycetes with other Brazilian savannas.}, } @article {pmid28062856, year = {2017}, author = {van der Helm, E and Imamovic, L and Hashim Ellabaan, MM and van Schaik, W and Koza, A and Sommer, MOA}, title = {Rapid resistome mapping using nanopore sequencing.}, journal = {Nucleic acids research}, volume = {45}, number = {8}, pages = {e61}, pmid = {28062856}, issn = {1362-4962}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Infections/drug therapy/microbiology ; Drug Resistance, Microbial/*genetics ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/genetics ; Gastrointestinal Tract/*microbiology ; Gene Library ; Humans ; Intensive Care Units ; Metagenome/drug effects/*genetics ; Microbial Sensitivity Tests ; Nanopores ; Sequence Analysis, DNA/*methods ; }, abstract = {The emergence of antibiotic resistance in human pathogens has become a major threat to modern medicine. The outcome of antibiotic treatment can be affected by the composition of the gut. Accordingly, knowledge of the gut resistome composition could enable more effective and individualized treatment of bacterial infections. Yet, rapid workflows for resistome characterization are lacking. To address this challenge we developed the poreFUME workflow that deploys functional metagenomic selections and nanopore sequencing to resistome mapping. We demonstrate the approach by functionally characterizing the gut resistome of an ICU (intensive care unit) patient. The accuracy of the poreFUME pipeline is with >97% sufficient for the annotation of antibiotic resistance genes. The poreFUME pipeline provides a promising approach for efficient resistome profiling that could inform antibiotic treatment decisions in the future.}, } @article {pmid28061817, year = {2017}, author = {Snelling, TJ and Wallace, RJ}, title = {The rumen microbial metaproteome as revealed by SDS-PAGE.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {9}, pmid = {28061817}, issn = {1471-2180}, mesh = {Animal Feed/analysis ; Animals ; Archaea/enzymology/metabolism ; Bacteria/enzymology/metabolism ; Cattle/*microbiology ; Diet/veterinary ; Digestion ; Electrophoresis, Polyacrylamide Gel/*methods ; Fermentation ; Finland ; Metagenomics/*methods ; Microbiota/*genetics ; Poaceae ; Reproducibility of Results ; Rumen/*metabolism/*microbiology ; Scotland ; Sheep/*microbiology ; Silage ; Sweden ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: Ruminal digestion is carried out by large numbers of bacteria, archaea, protozoa and fungi. Understanding the microbiota is important because ruminal fermentation dictates the efficiency of feed utilisation by the animal and is also responsible for major emissions of the greenhouse gas, methane. Recent metagenomic and metatranscriptomic studies have helped to elucidate many features of the composition and activity of the microbiota. The metaproteome provides complementary information to these other -omics technologies. The aim of this study was to explore the metaproteome of bovine and ovine ruminal digesta using 2D SDS-PAGE.

RESULTS: Digesta samples were taken via ruminal fistulae and by gastric intubation, or at slaughter, and stored in glycerol at -80 °C. A protein extraction protocol was developed to maximise yield and representativeness of the protein content. The proteome of ruminal digesta taken from dairy cows fed a high concentrate diet was dominated by a few very highly expressed proteins, which were identified by LC-MS/MS to be structural proteins, such as actin and α- and β-tubulins, derived from ciliate protozoa. Removal of protozoa from digesta before extraction of proteins revealed the prokaryotic metaproteome, which was dominated by enzymes involved in glycolysis, such as glyceraldehyde-3-phosphate dehydrogenase, phosphoenolpyruvate carboxykinase, phosphoglycerate kinase and triosephosphate isomerase. The enzymes were predominantly from the Firmicutes and Bacteroidetes phyla. Enzymes from methanogenic archaea were also abundant, consistent with the importance of methane formation in the rumen. Gels from samples from dairy cows fed a high proportion of grass silage were consistently obscured by co-staining of humic compounds. Samples from beef cattle and fattening lambs receiving a predominantly concentrate diet produced clearer gels, but the pattern of spots was inconsistent between samples, making comparisons difficult.

CONCLUSION: This work demonstrated for the first time that 2D-PAGE reveals key structural proteins and enzymes in the rumen microbial community, despite its high complexity, and that taxonomic information can be deduced from the analysis. However, technical issues associated with feed material contamination, which affects the reproducibility of electrophoresis of different samples, limits its value.}, } @article {pmid28059627, year = {2017}, author = {Fourie, NH and Wang, D and Abey, SK and Creekmore, AL and Hong, S and Martin, CG and Wiley, JW and Henderson, WA}, title = {Structural and functional alterations in the colonic microbiome of the rat in a model of stress induced irritable bowel syndrome.}, journal = {Gut microbes}, volume = {8}, number = {1}, pages = {33-45}, pmid = {28059627}, issn = {1949-0984}, support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; R01 DK098205/DK/NIDDK NIH HHS/United States ; ZIA NR000023/NR/NINR NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Colon/*microbiology ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/microbiology ; Irritable Bowel Syndrome/*microbiology ; Male ; Metagenomics ; Rats ; Rats, Sprague-Dawley ; }, abstract = {Stress is known to perturb the microbiome and exacerbate irritable bowel syndrome (IBS) associated symptoms. Characterizing structural and functional changes in the microbiome is necessary to understand how alterations affect the biomolecular environment of the gut in IBS. Repeated water avoidance (WA) stress was used to induce IBS-like symptoms in rats. The colon-mucosa associated microbiome was characterized in 13 stressed and control animals by 16S sequencing. In silico analysis of the functional domains of microbial communities was done by inferring metagenomic profiles from 16S data. Microbial communities and functional profiles were compared between conditions. WA animals exhibited higher α-diversity and moderate divergence in community structure (β-diversity) compared with controls. Specific clades and taxa were consistently and significantly modified in the WA animals. The WA microbiome was particularly enriched in Proteobacteria and depleted in several beneficial taxa. A decreased capacity in metabolic domains, including energy- and lipid-metabolism, and an increased capacity for fatty acid and sulfur metabolism was inferred for the WA microbiome. The stressed condition favored the proliferation of a greater diversity of microbes that appear to be functionally similar, resulting in a functionally poorer microbiome with implications for epithelial health. Taxa, with known beneficial effects, were found to be depleted, which supports their relevance as therapeutic agents to restore microbial health. Microbial sulfur metabolism may form a key component of visceral nerve sensitization pathways and is therefore of interest as a target metabolic domain in microbial ecological restoration.}, } @article {pmid28057680, year = {2017}, author = {Luo, D and Ziebell, S and An, L}, title = {An informative approach on differential abundance analysis for time-course metagenomic sequencing data.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {9}, pages = {1286-1292}, doi = {10.1093/bioinformatics/btw828}, pmid = {28057680}, issn = {1367-4811}, mesh = {Animals ; Bacteria/*genetics ; *Diet ; Diet, Fat-Restricted ; Diet, Western ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Male ; Metagenomics/*methods ; Mice ; Sequence Analysis, DNA/*methods ; Statistics as Topic/*methods ; }, abstract = {MOTIVATION: The advent of high-throughput next generation sequencing technology has greatly promoted the field of metagenomics where previously unattainable information about microbial communities can be discovered. Detecting differentially abundant features (e.g. species or genes) plays a critical role in revealing the contributors (i.e. pathogens) to the biological or medical status of microbial samples. However, currently available statistical methods lack power in detecting differentially abundant features contrasting different biological or medical conditions, in particular, for time series metagenomic sequencing data. We have proposed a novel procedure, metaDprof, which is built upon a spline-based method assuming heterogeneous error, to meet the challenges of detecting differentially abundant features from metagenomic samples by comparing different biological/medical conditions across time. It contains two stages: (i) global detection on features and (ii) time interval detection for significant features. The detection procedures in both stages are based on sound statistical support.

RESULTS: Compared with existing methods the new method metaDprof shows the best performance in comprehensive simulation studies. Not only can it accurately detect features relating to the biological condition or disease status of samples but it also can accurately detect the starting and ending time points when the differences arise. The proposed method is also applied to a real metagenomic dataset and the results provide an interesting angle to understand the relationship between the microbiota in mouse gut and diet type.

R code and an example dataset are available at https://cals.arizona.edu/∼anling/sbg/software.htm.

CONTACT: anling@email.arizona.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid28057558, year = {2017}, author = {Zhu, X and Treu, L and Kougias, PG and Campanaro, S and Angelidaki, I}, title = {Characterization of the planktonic microbiome in upflow anaerobic sludge blanket reactors during adaptation of mesophilic methanogenic granules to thermophilic operational conditions.}, journal = {Anaerobe}, volume = {46}, number = {}, pages = {69-77}, doi = {10.1016/j.anaerobe.2016.12.015}, pmid = {28057558}, issn = {1095-8274}, mesh = {*Anaerobiosis ; Bioreactors/*microbiology ; Cluster Analysis ; *Fermentation ; High-Throughput Nucleotide Sequencing ; Hydrolysis ; Metagenomics/methods ; Methane/biosynthesis ; Microbial Interactions ; *Microbiota ; Plankton/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; }, abstract = {Upflow anaerobic sludge blanket (UASB) technology refers to reactor technology where granules, i.e. self-immobilised microbial associations, are the biological catalysts involved in the anaerobic digestion process. During the start-up period, UASB reactors operate at relatively long HRT and therefore the liquid phase of the reactor becomes a favourable environment for microbial growth. The current study aimed to elucidate the dynamicity of the suspended microbial community in UASB reactors, during the transition from mesophilic to thermophilic conditions. High throughput 16S rRNA amplicon sequencing was used to characterize the taxonomic composition of the microbiome. The results showed that the microbial community was mainly composed by hydrolytic and fermentative bacteria. Results revealed relevant shifts in the microbial community composition, which is mainly determined by the operational conditions and the reactor performance. Finally, shared OTUs between the microbial consortia of the suspended and the granular sludge showed that planktonic microbiota is significantly influencing the granule microbial community composition.}, } @article {pmid28053166, year = {2017}, author = {Wu, L and Sun, Q and Desmeth, P and Sugawara, H and Xu, Z and McCluskey, K and Smith, D and Alexander, V and Lima, N and Ohkuma, M and Robert, V and Zhou, Y and Li, J and Fan, G and Ingsriswang, S and Ozerskaya, S and Ma, J}, title = {World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide.}, journal = {Nucleic acids research}, volume = {45}, number = {D1}, pages = {D611-D618}, pmid = {28053166}, issn = {1362-4962}, mesh = {Biodiversity ; Computational Biology/*methods ; Data Mining ; *Databases, Factual ; Metagenomics/methods ; *Microbiology ; *Microbiota ; Phylogeny ; *Software ; Web Browser ; Workflow ; }, abstract = {The World Data Centre for Microorganisms (WDCM) was established 50 years ago as the data center of the World Federation for Culture Collections (WFCC)-Microbial Resource Center (MIRCEN). WDCM aims to provide integrated information services using big data technology for microbial resource centers and microbiologists all over the world. Here, we provide an overview of WDCM including all of its integrated services. Culture Collections Information Worldwide (CCINFO) provides metadata information on 708 culture collections from 72 countries and regions. Global Catalogue of Microorganism (GCM) gathers strain catalogue information and provides a data retrieval, analysis, and visualization system of microbial resources. Currently, GCM includes >368 000 strains from 103 culture collections in 43 countries and regions. Analyzer of Bioresource Citation (ABC) is a data mining tool extracting strain related publications, patents, nucleotide sequences and genome information from public data sources to form a knowledge base. Reference Strain Catalogue (RSC) maintains a database of strains listed in International Standards Organization (ISO) and other international or regional standards. RSC allocates a unique identifier to strains recommended for use in diagnosis and quality control, and hence serves as a valuable cross-platform reference. WDCM provides free access to all these services at www.wdcm.org.}, } @article {pmid28052195, year = {2017}, author = {Mayers, MD and Moon, C and Stupp, GS and Su, AI and Wolan, DW}, title = {Quantitative Metaproteomics and Activity-Based Probe Enrichment Reveals Significant Alterations in Protein Expression from a Mouse Model of Inflammatory Bowel Disease.}, journal = {Journal of proteome research}, volume = {16}, number = {2}, pages = {1014-1026}, pmid = {28052195}, issn = {1535-3907}, support = {R21 CA181027/CA/NCI NIH HHS/United States ; T32 AI007244/AI/NIAID NIH HHS/United States ; U54 GM114833/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/genetics/*isolation & purification/metabolism ; Chromatography, Liquid ; Disease Models, Animal ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Gene Deletion ; Gene Expression ; Homeodomain Proteins/genetics/metabolism ; Humans ; Inflammatory Bowel Diseases/genetics/*microbiology/pathology ; Intestines/microbiology/pathology ; Isotope Labeling ; *Metagenome ; Mice ; Proteome/genetics/*isolation & purification/metabolism ; Tandem Mass Spectrometry ; }, abstract = {Tandem mass spectrometry based shotgun proteomics of distal gut microbiomes is exceedingly difficult due to the inherent complexity and taxonomic diversity of the samples. We introduce two new methodologies to improve metaproteomic studies of microbiome samples. These methods include the stable isotope labeling in mammals to permit protein quantitation across two mouse cohorts as well as the application of activity-based probes to enrich and analyze both host and microbial proteins with specific functionalities. We used these technologies to study the microbiota from the adoptive T cell transfer mouse model of inflammatory bowel disease (IBD) and compare these samples to an isogenic control, thereby limiting genetic and environmental variables that influence microbiome composition. The data generated highlight quantitative alterations in both host and microbial proteins due to intestinal inflammation and corroborates the observed phylogenetic changes in bacteria that accompany IBD in humans and mouse models. The combination of isotope labeling with shotgun proteomics resulted in the total identification of 4434 protein clusters expressed in the microbial proteomic environment, 276 of which demonstrated differential abundance between control and IBD mice. Notably, application of a novel cysteine-reactive probe uncovered several microbial proteases and hydrolases overrepresented in the IBD mice. Implementation of these methods demonstrated that substantial insights into the identity and dysregulation of host and microbial proteins altered in IBD can be accomplished and can be used in the interrogation of other microbiome-related diseases.}, } @article {pmid28051919, year = {2017}, author = {Sadowsky, MJ and Staley, C and Heiner, C and Hall, R and Kelly, CR and Brandt, L and Khoruts, A}, title = {Analysis of gut microbiota - An ever changing landscape.}, journal = {Gut microbes}, volume = {8}, number = {3}, pages = {268-275}, pmid = {28051919}, issn = {1949-0984}, mesh = {Animals ; Clostridium Infections/therapy ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {In the last two decades, the field of metagenomics has greatly expanded due to improvement in sequencing technologies allowing for a more comprehensive characterization of microbial communities. The use of these technologies has led to an unprecedented understanding of human, animal, and environmental microbiomes and have shown that the gut microbiota are comparable to an organ that is intrinsically linked with a variety of diseases. Characterization of microbial communities using next-generation sequencing-by-synthesis approaches have revealed important shifts in microbiota associated with debilitating diseases such as Clostridium difficile infection. But due to limitations in sequence read length, primer biases, and the quality of databases, genus- and species-level classification have been difficult. Third-generation technologies, such as Pacific Biosciences' single molecule, real-time (SMRT) approach, allow for unbiased, more specific identification of species that are likely clinically relevant. Comparison of Illumina next-generation characterization and SMRT sequencing of samples from patients treated for C. difficile infection revealed similarities in community composition at the phylum and family levels, but SMRT sequencing further allowed for species-level characterization - permitting a better understanding of the microbial ecology of this disease. Thus, as sequencing technologies continue to advance, new species-level insights can be gained in the study of complex and clinically-relevant microbial communities.}, } @article {pmid28049409, year = {2017}, author = {Zhang, X and Mallick, H and Tang, Z and Zhang, L and Cui, X and Benson, AK and Yi, N}, title = {Negative binomial mixed models for analyzing microbiome count data.}, journal = {BMC bioinformatics}, volume = {18}, number = {1}, pages = {4}, pmid = {28049409}, issn = {1471-2105}, support = {R01 GM069430/GM/NIGMS NIH HHS/United States ; R03 DE024198/DE/NIDCR NIH HHS/United States ; RC1 DK087346/DK/NIDDK NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Internet ; Intestines/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; *Microbiota ; *Models, Statistical ; RNA, Ribosomal, 16S/chemistry/metabolism ; User-Computer Interface ; }, abstract = {BACKGROUND: Recent advances in next-generation sequencing (NGS) technology enable researchers to collect a large volume of metagenomic sequencing data. These data provide valuable resources for investigating interactions between the microbiome and host environmental/clinical factors. In addition to the well-known properties of microbiome count measurements, for example, varied total sequence reads across samples, over-dispersion and zero-inflation, microbiome studies usually collect samples with hierarchical structures, which introduce correlation among the samples and thus further complicate the analysis and interpretation of microbiome count data.

RESULTS: In this article, we propose negative binomial mixed models (NBMMs) for detecting the association between the microbiome and host environmental/clinical factors for correlated microbiome count data. Although having not dealt with zero-inflation, the proposed mixed-effects models account for correlation among the samples by incorporating random effects into the commonly used fixed-effects negative binomial model, and can efficiently handle over-dispersion and varying total reads. We have developed a flexible and efficient IWLS (Iterative Weighted Least Squares) algorithm to fit the proposed NBMMs by taking advantage of the standard procedure for fitting the linear mixed models.

CONCLUSIONS: We evaluate and demonstrate the proposed method via extensive simulation studies and the application to mouse gut microbiome data. The results show that the proposed method has desirable properties and outperform the previously used methods in terms of both empirical power and Type I error. The method has been incorporated into the freely available R package BhGLM (http://www.ssg.uab.edu/bhglm/ and http://github.com/abbyyan3/BhGLM), providing a useful tool for analyzing microbiome data.}, } @article {pmid28045579, year = {2017}, author = {Zárate-Bladés, CR and Horai, R and Mattapallil, MJ and Ajami, NJ and Wong, M and Petrosino, JF and Itoh, K and Chan, CC and Caspi, RR}, title = {Gut microbiota as a source of a surrogate antigen that triggers autoimmunity in an immune privileged site.}, journal = {Gut microbes}, volume = {8}, number = {1}, pages = {59-66}, pmid = {28045579}, issn = {1949-0984}, mesh = {Animals ; Antigens/*immunology ; Autoimmune Diseases/immunology/*microbiology ; Autoimmunity ; *Gastrointestinal Microbiome ; Humans ; Retina/immunology ; T-Lymphocytes/immunology ; Uveitis/*immunology/*microbiology ; }, abstract = {Recent discoveries on the role of commensal microbiota have significantly changed our understanding of human physiology. The host-microbiota interplay is now an important aspect to take into account to understand immune responses and immunological diseases. Autoimmune uveitis is a sight-threatening disease that arises without a known infectious etiology. It is unknown where and how autoreactive T cells become primed to trigger disease in the eye, which is an immune privileged site. We recently reported data supporting the notion that retina-specific T cells receive a signal in the gut from commensal microbiota-derived cross-reactive antigen(s) and trigger autoimmune uveitis in the R161H mouse model. Here we discuss our published findings, as well as our recent attempts to identify the responsible microbe(s) by using different antibiotic treatments, 16S rDNA sequencing and homology searches for candidate antigenic mimic(s) of the retinal antigen.}, } @article {pmid28039159, year = {2017}, author = {Knoll, RL and Forslund, K and Kultima, JR and Meyer, CU and Kullmer, U and Sunagawa, S and Bork, P and Gehring, S}, title = {Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {312}, number = {4}, pages = {G327-G339}, doi = {10.1152/ajpgi.00293.2016}, pmid = {28039159}, issn = {1522-1547}, mesh = {Adolescent ; Child ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Intestinal Mucosa/*microbiology ; Male ; *Metagenome ; Siblings ; Young Adult ; }, abstract = {Current treatment for pediatric inflammatory bowel disease (IBD) patients is often ineffective, with serious side effects. Manipulating the gut microbiota via fecal microbiota transplantation (FMT) is an emerging treatment approach but remains controversial. We aimed to assess the composition of the fecal microbiome through a comparison of pediatric IBD patients to their healthy siblings, evaluating risks and prospects for FMT in this setting. A case-control (sibling) study was conducted analyzing fecal samples of six children with Crohn's disease (CD), six children with ulcerative colitis (UC) and 12 healthy siblings by metagenomic sequencing. In addition, lifetime antibiotic intake was retrospectively determined. Species richness and diversity were significantly reduced in UC patients compared with control [Mann-Whitney U-test false discovery rate (MWU FDR) = 0.011]. In UC, bacteria positively influencing gut homeostasis, e.g., Eubacterium rectale and Faecalibacterium prausnitzii, were significantly reduced in abundance (MWU FDR = 0.05). Known pathobionts like Escherichia coli were enriched in UC patients (MWU FDR = 0.084). Moreover, E. coli abundance correlated positively with that of several virulence genes (SCC > 0.65, FDR < 0.1). A shift toward antibiotic-resistant taxa in both IBD groups distinguished them from controls [MWU Benjamini-Hochberg-Yekutieli procedure (BY) FDR = 0.062 in UC, MWU BY FDR = 0.019 in CD). The collected results confirm a microbial dysbiosis in pediatric UC, and to a lesser extent in CD patients, replicating associations found previously using different methods. Taken together, these observations suggest microbiotal remodeling therapy from family donors, at least for children with UC, as a viable option.NEW & NOTEWORTHY In this sibling study, prior reports of microbial dysbiosis in IBD patients from 16S rRNA sequencing was verified using deep shotgun sequencing and augmented with insights into the abundance of bacterial virulence genes and bacterial antibiotic resistance determinants, seen against the background of data on the specific antibiotic intake of each of the study participants. The observed dysbiosis, which distinguishes patients from siblings, highlights such siblings as potential donors for microbiotal remodeling therapy in IBD.}, } @article {pmid28034306, year = {2016}, author = {Gregory, KE and Samuel, BS and Houghteling, P and Shan, G and Ausubel, FM and Sadreyev, RI and Walker, WA}, title = {Influence of maternal breast milk ingestion on acquisition of the intestinal microbiome in preterm infants.}, journal = {Microbiome}, volume = {4}, number = {1}, pages = {68}, pmid = {28034306}, issn = {2049-2618}, support = {R01 HD012437/HD/NICHD NIH HHS/United States ; P30 DK040561/DK/NIDDK NIH HHS/United States ; P01 DK033506/DK/NIDDK NIH HHS/United States ; F32 DK083885/DK/NIDDK NIH HHS/United States ; K23 NR011320/NR/NINR NIH HHS/United States ; R01 HD059126/HD/NICHD NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics ; Base Sequence ; Birth Weight ; *Breast Feeding ; DNA, Bacterial/genetics ; Gastrointestinal Microbiome/*genetics ; Gestational Age ; Humans ; *Infant Formula ; *Infant Nutritional Physiological Phenomena ; Infant, Newborn ; *Infant, Premature ; Intestines/*microbiology ; *Milk, Human ; Nutritional Status ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The initial acquisition and early development of the intestinal microbiome during infancy are important to human health across the lifespan. Mode of birth, antibiotic administration, environment of care, and nutrition have all been shown to play a role in the assembly of the intestinal microbiome during early life. For preterm infants, who are disproportionately at risk of inflammatory intestinal disease (i.e., necrotizing enterocolitis), a unique set of clinical factors influence the establishment of the microbiome. The purpose of this study was to establish the influence of nutritional exposures on the intestinal microbiome in a cohort of preterm infants early in life.

RESULTS: Principal component analysis of 199 samples from 30 preterm infants (<32 weeks) over the first 60 days following birth showed that the intestinal microbiome was influenced by postnatal time (p < 0.001, R [2] = 0.13), birth weight (p < 0.001, R [2] = 0.08), and nutrition (p < 0.001, R [2] = 0.21). Infants who were fed breast milk had a greater initial bacterial diversity and a more gradual acquisition of diversity compared to infants who were fed infant formula. The microbiome of infants fed breast milk were more similar regardless of birth weight (p = 0.049), in contrast to the microbiome of infants fed infant formula, which clustered differently based on birth weight (p < 0.001). By adjusting for differences in gut maturity, an ordered succession of microbial phylotypes was observed in breast milk-fed infants, which appeared to be disrupted in those fed infant formula. Supplementation with pasteurized donor human milk was partially successful in promoting a microbiome more similar to breast milk-fed infants and moderating rapid increases in bacterial diversity.

CONCLUSIONS: The preterm infant intestinal microbiome is influenced by postnatal time, birth weight, gestational age, and nutrition. Feeding with breast milk appears to mask the influence of birth weight, suggesting a protective effect against gut immaturity in the preterm infant. These findings suggest not only a microbial mechanism underpinning the body of evidence showing that breast milk promotes intestinal health in the preterm infant but also a dynamic interplay of host and dietary factors that facilitate the colonization of and enrichment for specific microbes during establishment of the preterm infant microbiota.}, } @article {pmid28034304, year = {2016}, author = {Stewart, CJ and Embleton, ND and Marrs, EC and Smith, DP and Nelson, A and Abdulkadir, B and Skeath, T and Petrosino, JF and Perry, JD and Berrington, JE and Cummings, SP}, title = {Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease.}, journal = {Microbiome}, volume = {4}, number = {1}, pages = {67}, pmid = {28034304}, issn = {2049-2618}, mesh = {Bacteria/*classification/genetics/isolation & purification/metabolism ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Enterocolitis, Necrotizing/metabolism/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Infant, Premature ; Infant, Premature, Diseases/metabolism/*microbiology ; Linoleic Acid/metabolism ; Longitudinal Studies ; Male ; Metabolic Networks and Pathways ; Phylogeny ; Proteomics/*methods ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: The preterm microbiome is crucial to gut health and may contribute to necrotising enterocolitis (NEC), which represents the most significant pathology affecting preterm infants. From a cohort of 318 infants, <32 weeks gestation, we selected 7 infants who developed NEC (defined rigorously) and 28 matched controls. We performed detailed temporal bacterial (n = 641) and metabolomic (n = 75) profiling of the gut microbiome throughout the disease.

RESULTS: A core community of Klebsiella, Escherichia, Staphyloccocus, and Enterococcus was present in all samples. Gut microbiota profiles grouped into six distinct clusters, termed preterm gut community types (PGCTs). Each PGCT reflected dominance by the core operational taxonomic units (OTUs), except of PGCT 6, which had high diversity and was dominant in bifidobacteria. While PGCTs 1-5 were present in infants prior to NEC diagnosis, PGCT 6 was comprised exclusively of healthy samples. NEC infants had significantly more PGCT transitions prior to diagnosis. Metabolomic profiling identified significant pathways associated with NEC onset, with metabolites involved in linoleate metabolism significantly associated with NEC diagnosis. Notably, metabolites associated with NEC were the lowest in PGCT 6.

CONCLUSIONS: This is the first study to integrate sequence and metabolomic stool analysis in preterm neonates, demonstrating that NEC does not have a uniform microbial signature. However, a diverse gut microbiome with a high abundance of bifidobacteria may protect preterm infants from disease. These results may inform biomarker development and improve understanding of gut-mediated mechanisms of NEC.}, } @article {pmid28032623, year = {2016}, author = {Marx, V}, title = {Microbiology: the return of culture.}, journal = {Nature methods}, volume = {14}, number = {1}, pages = {37-40}, pmid = {28032623}, issn = {1548-7105}, mesh = {Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; In Situ Hybridization, Fluorescence ; Metagenomics/*methods ; Microbiological Techniques/*methods ; RNA, Ribosomal, 16S ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Workflow ; }, } @article {pmid28030619, year = {2016}, author = {Nguyen, LD and Deschaght, P and Merlin, S and Loywick, A and Audebert, C and Van Daele, S and Viscogliosi, E and Vaneechoutte, M and Delhaes, L}, title = {Effects of Propidium Monoazide (PMA) Treatment on Mycobiome and Bacteriome Analysis of Cystic Fibrosis Airways during Exacerbation.}, journal = {PloS one}, volume = {11}, number = {12}, pages = {e0168860}, pmid = {28030619}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Anti-Bacterial Agents/pharmacology ; Azides/*pharmacology ; Biodiversity ; Cystic Fibrosis/drug therapy/genetics/*microbiology ; DNA, Bacterial/genetics ; Disease Progression ; Female ; Forced Expiratory Volume ; High-Throughput Nucleotide Sequencing ; Humans ; Lung/drug effects/*microbiology/physiopathology ; Male ; Metagenome ; Microbiota/drug effects/*genetics ; Middle Aged ; Mycobiome/drug effects/*genetics ; Propidium/*analogs & derivatives/pharmacology ; Prospective Studies ; Respiratory System/drug effects/metabolism/*microbiology ; Sputum/microbiology ; Young Adult ; }, abstract = {INTRODUCTION AND PURPOSE: Propidium monoazide (PMA)-pretreatment has increasingly been applied to remove the bias from dead or damaged cell artefacts, which could impact the microbiota analysis by high-throughput sequencing. Our study aimed to determine whether a PMA-pretreatment coupled with high-throughput sequencing analysis provides a different picture of the airway mycobiome and bacteriome.

RESULTS AND DISCUSSION: We compared deep-sequencing data of mycobiota and microbiota of 15 sputum samples from 5 cystic fibrosis (CF) patients with and without prior PMA-treatment of the DNA-extracts. PMA-pretreatment had no significant effect on the entire and abundant bacterial community (genera expressed as operational taxonomic units (OTUs) with a relative abundance greater than or equal to 1%), but caused a significant difference in the intermediate community (less than 1%) when analyzing the alpha biodiversity Simpson index (p = 0.03). Regarding PMA impact on the airway mycobiota evaluated for the first time here; no significant differences in alpha diversity indexes between PMA-treated and untreated samples were observed. Regarding beta diversity analysis, the intermediate communities also differed more dramatically than the total and abundant ones when studying both mycobiome and bacteriome. Our results showed that only the intermediate (or low abundance) population diversity is impacted by PMA-treatment, and therefore that abundant taxa are mostly viable during acute exacerbation in CF. Given such a cumbersome protocol (PMA-pretreatment coupled with high-throughput sequencing), we discuss its potential interest within the follow-up of CF patients. Further studies using PMA-pretreatment are warranted to improve our "omic" knowledge of the CF airways.}, } @article {pmid28028921, year = {2017}, author = {Gophna, U and Konikoff, T and Nielsen, HB}, title = {Oscillospira and related bacteria - From metagenomic species to metabolic features.}, journal = {Environmental microbiology}, volume = {19}, number = {3}, pages = {835-841}, doi = {10.1111/1462-2920.13658}, pmid = {28028921}, issn = {1462-2920}, mesh = {Animals ; Butyrates/metabolism ; Clostridiales/*classification/genetics ; Clostridium/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Metabolic Networks and Pathways ; Metagenomics ; RNA, Ribosomal, 16S ; }, abstract = {Oscillospira is an under-studied anaerobic bacterial genus from Clostridial cluster IV that has resisted cultivation for over a century since the first time it was observed. In recent years its 16S rRNA gene was identified in several human gut microbiota studies where it was often associated with interesting traits, especially leanness. However, very little is known about its metabolism or physiology. Here we used nearly complete genomes derived from shot-gun metagenomic data from the human gut to analyze Oscillospira and related bacteria. We used sequence similarity, gene neighbourhood information and manual metabolic pathway curation to decipher key metabolic features of this intriguing bacterial genus. We infer that Oscillospira species are butyrate producers, and at least some of them have the ability to utilize glucuronate, a common animal-derived sugar that is both produced by the human host and consumed by that host in diets rich in animal products. These findings could help explain diet-related inter-individual variation in faecal Oscillospira levels as well as the observation that the presence of this genus is reduced in diseases that involve inflammation.}, } @article {pmid28025221, year = {2017}, author = {Husseneder, C and Park, JS and Howells, A and Tikhe, CV and Davis, JA}, title = {Bacteria Associated With Piezodorus guildinii (Hemiptera: Pentatomidae), With Special Reference to Those Transmitted by Feeding.}, journal = {Environmental entomology}, volume = {46}, number = {1}, pages = {159-166}, doi = {10.1093/ee/nvw112}, pmid = {28025221}, issn = {1938-2936}, mesh = {Animals ; Bacteria/*classification/genetics ; Feeding Behavior ; Hemiptera/*microbiology ; Louisiana ; *Metagenome ; *Microbiota ; Plant Diseases/microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; }, abstract = {The redbanded stink bug, Piezodorus guildinii (Westwood) (Hemiptera: Heteroptera: Pentatomidae), is a rapidly growing pest damaging southern US agriculture. Pentatomid stink bugs are known to vector bacterial, fungal, and viral plant diseases. However, bacteria associated with redbanded stink bugs and their vector potential have not yet been assessed. In this study, we 1) cultured and identified bacteria transmitted by feeding of redbanded stink bug and 2) described bacteria from guts of redbanded stink bug individuals using next-generation sequencing of 16S rRNA genes. Nineteen bacteria transmitted by feeding of redbanded stink bug on soybean agar were isolated and identified via Sanger sequencing of near full length 16S RNA genes. The transmitted bacteria belonged to at least a dozen species in eight genera and included potential plant pathogens (Phaseolibacter flectens), plant beneficials (Bacillus atropheus), and possible insect beneficials (Acinetobacter sp. and Citrobacter farmeri). A total of 284,448 reads were captured from Illumina MiSeq sequencing of the uncultured gut bacteria community. Fifty-one putative bacteria species (74% of the estimated total species richness) were identified via matches to NCBI databases. The bacteria metagenome contained potential plant and insect pathogens (Erwinia persicina, E. rhaponici, Brenneria nigrifluens, Ralstonia picketti, and Serratia marcescens) and beneficials (Pantoea dispersa, Klebsiella oxytoca, Clostridium butyricum, and Citrobacter farmeri).}, } @article {pmid28025202, year = {2017}, author = {Zakrzewski, M and Proietti, C and Ellis, JJ and Hasan, S and Brion, MJ and Berger, B and Krause, L}, title = {Calypso: a user-friendly web-server for mining and visualizing microbiome-environment interactions.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {5}, pages = {782-783}, pmid = {28025202}, issn = {1367-4811}, mesh = {Data Mining/*methods ; *Environment ; Humans ; Internet ; *Metagenome ; Microbiota/genetics/*physiology ; Plants ; RNA, Ribosomal, 16S ; *Software ; Statistics as Topic ; Supervised Machine Learning ; Symbiosis ; }, abstract = {UNLABELLED: Calypso is an easy-to-use online software suite that allows non-expert users to mine, interpret and compare taxonomic information from metagenomic or 16S rDNA datasets. Calypso has a focus on multivariate statistical approaches that can identify complex environment-microbiome associations. The software enables quantitative visualizations, statistical testing, multivariate analysis, supervised learning, factor analysis, multivariable regression, network analysis and diversity estimates. Comprehensive help pages, tutorials and videos are provided via a wiki page.

The web-interface is accessible via http://cgenome.net/calypso/ . The software is programmed in Java, PERL and R and the source code is available from Zenodo (https://zenodo.org/record/50931). The software is freely available for non-commercial users.

CONTACT: l.krause@uq.edu.au.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid28025198, year = {2017}, author = {Jiang, L and Dong, Y and Chen, N and Chen, T}, title = {DACE: a scalable DP-means algorithm for clustering extremely large sequence data.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {6}, pages = {834-842}, doi = {10.1093/bioinformatics/btw722}, pmid = {28025198}, issn = {1367-4811}, mesh = {Algorithms ; Cluster Analysis ; Eukaryota/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/methods ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {MOTIVATION: Advancements in next-generation sequencing technology have produced large amounts of reads at low cost in a short time. In metagenomics, 16S and 18S rRNA gene have been widely used as marker genes to profile diversity of microorganisms in environmental samples. Through clustering of sequencing reads we can determine both number of OTUs and their relative abundance. In many applications, clustering of very large sequencing data with high efficiency and accuracy is essential for downstream analysis.

RESULTS: Here, we report a scalable D irichlet Process Means (DP-means) a lgorithm for c lustering e xtremely large sequencing data, termed . With an efficient random projection partition strategy for parallel clustering, DACE can cluster billions of sequences within a couple of hours. Experimental results show that DACE runs between 6 and 80 times faster than state-of-the-art programs, while maintaining overall better clustering accuracy. Using 80 cores, DACE clustered the Lake Taihu 16S rRNA gene sequencing data (∼316M reads, 30 GB) in 25 min, and the Ocean TARA Eukaryotic 18S rRNA gene sequencing data (∼500M reads, 88 GB) into ∼100 000 clusters within an hour. When applied to the IGC gene catalogs in human gut microbiome (∼10M genes), DACE produced 9.8M clusters with 52K redundant genes in 1.5 hours of running time.

DACE is available at https://github.com/tinglab/DACE .

CONTACTS: tingchen@mail.tsinghua.edu.cn or ningchen@mail.tsinghua.edu.cn.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid28025179, year = {2018}, author = {Finotello, F and Mastrorilli, E and Di Camillo, B}, title = {Measuring the diversity of the human microbiota with targeted next-generation sequencing.}, journal = {Briefings in bioinformatics}, volume = {19}, number = {4}, pages = {679-692}, doi = {10.1093/bib/bbw119}, pmid = {28025179}, issn = {1477-4054}, support = {T 974/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/*classification/*genetics/isolation & purification ; Computational Biology/*methods ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The human microbiota is a complex ecological community of commensal, symbiotic and pathogenic microorganisms harboured by the human body. Next-generation sequencing (NGS) technologies, in particular targeted amplicon sequencing of the 16S ribosomal RNA gene (16S-seq), are enabling the identification and quantification of human-resident microorganisms at unprecedented resolution, providing novel insights into the role of the microbiota in health and disease. Once microbial abundances are quantified through NGS data analysis, diversity indices provide valuable mathematical tools to describe the ecological complexity of a single sample or to detect species differences between samples. However, diversity is not a determined physical quantity for which a consensus definition and unit of measure have been established, and several diversity indices are currently available. Furthermore, they were originally developed for macroecology and their robustness to the possible bias introduced by sequencing has not been characterized so far. To assist the reader with the selection and interpretation of diversity measures, we review a panel of broadly used indices, describing their mathematical formulations, purposes and properties, and characterize their behaviour and criticalities in dependence of the data features using simulated data as ground truth. In addition, we make available an R package, DiversitySeq, which implements in a unified framework the full panel of diversity indices and a simulator of 16S-seq data, and thus represents a valuable resource for the analysis of diversity from NGS count data and for the benchmarking of computational methods for 16S-seq.}, } @article {pmid28009005, year = {2016}, author = {Choma, M and Bárta, J and Šantrůčková, H and Urich, T}, title = {Low abundance of Archaeorhizomycetes among fungi in soil metatranscriptomes.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {38455}, pmid = {28009005}, issn = {2045-2322}, mesh = {Biodiversity ; Gene Regulatory Networks ; Glomeromycota/classification/*genetics ; Metagenome/*genetics ; Phylogeny ; *Soil Microbiology ; Transcriptome/*genetics ; }, abstract = {The Archaeorhizomycetes are recently discovered fungi with poorly resolved ecology. Even their abundance in soil fungal communities is currently disputed. Here we applied a PCR-independent, RNA-based metatranscriptomic approach to determine their abundance among fungi in eleven different soils across Europe. Using small subunit (SSU) ribosomal RNA transcripts as marker, we detected Archaeorhizomycetes in 17 out of 28 soil metatranscriptomes. They had average relative SSU rRNA abundance of 2.0% with a maximum of 9.4% among fungal SSU rRNAs. Network analysis revealed that they co-occur with arbuscular mycorrhizal Glomerales, which is in line with their previously suggested association with plant roots. Moreover, Archaeorhizomycetes ranked among the potential keystone taxa. This metatranscriptomic survey exemplifies the usage of non-targeted molecular approaches for the study of soil fungi. It provides PCR- and DNA-independent evidence for the low abundance of Archaeorhizomycetes in soil fungal communities, although they might be non-negligible players despite their low abundance.}, } @article {pmid28008835, year = {2016}, author = {Burcelin, R and Nicolas, S and Blasco-Baque, V}, title = {[Microbiotes and metabolic diseases: the bases for therapeutic strategies].}, journal = {Medecine sciences : M/S}, volume = {32}, number = {11}, pages = {952-960}, doi = {10.1051/medsci/20163211010}, pmid = {28008835}, issn = {1958-5381}, mesh = {Animals ; Gastrointestinal Tract/metabolism/microbiology ; Humans ; Metabolic Diseases/diagnosis/*etiology/*therapy ; Metagenome/physiology ; Metagenomics/methods/trends ; Microbiota/*physiology ; }, abstract = {After more than one and a half century, i.e. since Louis Pasteur work on microbes, fermentation, and diseases, biological science has made a giant step in bacteria knowledge. Thanks to an ultra-powerful "microscope", i.e. ultra-fast DNA sequencing, scientists have been able to read and group within a catalog over the last decade, the gene code of bacteria, i.e. the metagenome at the surface of our epithelia. More recently, live bacteria within adipose tissue, defining a tissue microbiota, as well as bacterial fragments such as DNA within the liver, the brain and the blood have been identified. Metagenomic analyses from large cohorts of patients have uncovered tight correlations between bacterial genes within our intestine and mouth and diseases such as metabolic diseases, diabetes, obesity, some liver diseases, kidney and heart failure as well as vascular diseases. Some causal mechanisms have been proposed in rodents and can set the soil for novel therapeutic strategies that could interfere with both the microbes and the corresponding host targets.}, } @article {pmid28008834, year = {2016}, author = {Blottière, HM and Doré, J}, title = {[Impact of newly developed metagenomic tools on our knowledge of the gut microbiota and its role in human health: diagnostic and therapeutic issues].}, journal = {Medecine sciences : M/S}, volume = {32}, number = {11}, pages = {944-951}, doi = {10.1051/medsci/20163211009}, pmid = {28008834}, issn = {1958-5381}, mesh = {Animals ; Dysbiosis/*diagnosis/*therapy ; Gastrointestinal Microbiome/*physiology ; *Health ; Humans ; Metagenomics/*methods/trends ; }, abstract = {Over the last years, our vision of the intestinal microbiota and its contribution to human physiology has been fully revisited, thanks to metagenomics. Next generation sequencing allowed a full characterization of the microbiome. Quantitative metagenomic permitted a deep understanding of the intestinal ecosystem, its structure, and potential dysbiosis in several human pathologies. The microbiome may be used as biomarker of disease or of risk to progress toward a disease. A good understanding of the mechanisms of interaction between gut microbiota and its host is needed; functional metagenomic is a useful tool to identify genes and metabolites able to interact with host's cells. Overall, the microbiome science that is developing opens new avenue for diagnosis, discovery of new drugs and potential therapeutic approaches. It is also a target for modulation by food, with potential impact on health.}, } @article {pmid28008833, year = {2016}, author = {Weissenbach, J and Sghir, A}, title = {[Microbiotes and metagenomics].}, journal = {Medecine sciences : M/S}, volume = {32}, number = {11}, pages = {937-943}, doi = {10.1051/medsci/20163211008}, pmid = {28008833}, issn = {1958-5381}, mesh = {Animals ; Gastrointestinal Microbiome/genetics/physiology ; Humans ; Metagenome/physiology ; Metagenomics/*methods ; Microbiota/*genetics/physiology ; RNA, Ribosomal/analysis/genetics ; }, abstract = {Major technical advances were introduced in the study of microflora and microbial communities in the nineties. These are essentially analytical approaches conducted as frequently by brute force. What conclusions can be drawn from these analyses twenty years later? In terms of microbial compositions, monitoring and diagnosis, the results are impressive. But what do all these microorganisms do? What are the factors behind their associations and their maintenance? Gene inventories are approaching completion; they allow us to deepen some physiological processes but do not say much more. We have even begun to manipulate microbiota. But as often in the dialectic between theory and practice, it works but we are far from understanding how!}, } @article {pmid28008829, year = {2016}, author = {Lagier, JC and Raoult, D}, title = {[Culturomics: a method to study human gut microbiota].}, journal = {Medecine sciences : M/S}, volume = {32}, number = {11}, pages = {923-925}, doi = {10.1051/medsci/20163211004}, pmid = {28008829}, issn = {1958-5381}, mesh = {Ecosystem ; *Gastrointestinal Microbiome/genetics ; Humans ; *Metagenome ; Metagenomics/methods ; Microbiological Techniques/*methods ; }, } @article {pmid28008828, year = {2016}, author = {}, title = {[Not Available].}, journal = {Medecine sciences : M/S}, volume = {32}, number = {11}, pages = {922}, doi = {10.1051/medsci/20163211003}, pmid = {28008828}, issn = {1958-5381}, mesh = {*Host-Pathogen Interactions/genetics/immunology ; Humans ; *Metagenomics/classification/methods ; Microbiota/*physiology ; *Terminology as Topic ; }, } @article {pmid28008827, year = {2016}, author = {Gilgenkrantz, H and Teillaud, JL}, title = {[The coordinators' word].}, journal = {Medecine sciences : M/S}, volume = {32}, number = {11}, pages = {921}, doi = {10.1051/medsci/20163211002}, pmid = {28008827}, issn = {1958-5381}, mesh = {Fecal Microbiota Transplantation/trends ; Host-Pathogen Interactions/immunology ; Humans ; Metagenomics ; Microbiota/*physiology ; Prebiotics/microbiology ; Probiotics/therapeutic use ; *Symbiosis/genetics ; }, } @article {pmid28008826, year = {2016}, author = {Debré, P}, title = {[The microbiota's challenges].}, journal = {Medecine sciences : M/S}, volume = {32}, number = {11}, pages = {919-920}, doi = {10.1051/medsci/20163211001}, pmid = {28008826}, issn = {1958-5381}, mesh = {Animals ; Biological Evolution ; Cattle ; Female ; Gastrointestinal Tract/immunology/metabolism/microbiology ; Helicobacter pylori/pathogenicity/physiology ; Host-Pathogen Interactions/genetics/immunology ; Humans ; Infant, Newborn ; Infectious Disease Transmission, Vertical ; Metagenomics/methods/trends ; Microbiota/*physiology ; Pregnancy ; Symbiosis/genetics/immunology ; }, } @article {pmid28005526, year = {2017}, author = {Yoon, SH and Ha, SM and Kwon, S and Lim, J and Kim, Y and Seo, H and Chun, J}, title = {Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {67}, number = {5}, pages = {1613-1617}, pmid = {28005526}, issn = {1466-5034}, mesh = {Archaea/*classification ; Bacteria/*classification ; Base Composition ; Computational Biology ; *Databases, Nucleic Acid ; Genomics ; Humans ; Microbiota ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The recent advent of DNA sequencing technologies facilitates the use of genome sequencing data that provide means for more informative and precise classification and identification of members of the Bacteria and Archaea. Because the current species definition is based on the comparison of genome sequences between type and other strains in a given species, building a genome database with correct taxonomic information is of paramount need to enhance our efforts in exploring prokaryotic diversity and discovering novel species as well as for routine identifications. Here we introduce an integrated database, called EzBioCloud, that holds the taxonomic hierarchy of the Bacteria and Archaea, which is represented by quality-controlled 16S rRNA gene and genome sequences. Whole-genome assemblies in the NCBI Assembly Database were screened for low quality and subjected to a composite identification bioinformatics pipeline that employs gene-based searches followed by the calculation of average nucleotide identity. As a result, the database is made of 61 700 species/phylotypes, including 13 132 with validly published names, and 62 362 whole-genome assemblies that were identified taxonomically at the genus, species and subspecies levels. Genomic properties, such as genome size and DNA G+C content, and the occurrence in human microbiome data were calculated for each genus or higher taxa. This united database of taxonomy, 16S rRNA gene and genome sequences, with accompanying bioinformatics tools, should accelerate genome-based classification and identification of members of the Bacteria and Archaea. The database and related search tools are available at www.ezbiocloud.net/.}, } @article {pmid28004480, year = {2017}, author = {Ni, Y and Wong, VH and Tai, WC and Li, J and Wong, WY and Lee, MM and Fong, FL and El-Nezami, H and Panagiotou, G}, title = {A metagenomic study of the preventive effect of Lactobacillus rhamnosus GG on intestinal polyp formation in Apc[Min/+] mice.}, journal = {Journal of applied microbiology}, volume = {122}, number = {3}, pages = {770-784}, doi = {10.1111/jam.13386}, pmid = {28004480}, issn = {1365-2672}, mesh = {Adenomatous Polyposis Coli Protein/genetics ; Animals ; Humans ; Intestinal Polyps/*prevention & control ; Lacticaseibacillus rhamnosus/*growth & development ; Metagenomics/methods ; Mice ; Microbiota/*drug effects ; Phylogeny ; Probiotics/pharmacology/*therapeutic use ; Specific Pathogen-Free Organisms ; Sulindac/pharmacology/*therapeutic use ; }, abstract = {AIMS: To investigate the in vivo effects of Lactobacillus rhamnosus GG (LGG) on intestinal polyp development and the interaction between this single-organism probiotic and the gut microbiota therein.

METHODS AND RESULTS: The Apc[Min/+] mouse model was used to study the potential preventive effect of LGG on intestinal polyposis, while shotgun metagenomic sequencing was employed to characterize both taxonomic and functional changes within the gut microbial community. We found that the progression of intestinal polyps in the control group altered the community functional profile remarkably despite small variation in the taxonomic diversity. In comparison, the consumption of LGG helped maintain the overall functional potential and taxonomic profile in the resident microbes, thereby leading to a 25% decrease of total polyp counts. Furthermore, we found that LGG enriched those microbes or microbial activities related to short-chain fatty acid production (e.g. Roseburia and Coprococcus), as well as suppressed the ones that can lead to inflammation (e.g. Bilophila wadsworthia).

CONCLUSIONS: Our study using shotgun metagenomics highlights how single probiotic LGG may exert its beneficial effects and decrease polyp formation in mice by maintaining gut microbial functionality.

This probiotic intervention targeting microbiota may be used in conjugation with other dietary supplements or drugs as part of prevention strategies for early-stage colon cancer, after further clinical validations in human.}, } @article {pmid28000755, year = {2016}, author = {Barnard, E and Shi, B and Kang, D and Craft, N and Li, H}, title = {The balance of metagenomic elements shapes the skin microbiome in acne and health.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {39491}, pmid = {28000755}, issn = {2045-2322}, support = {R01 GM099530/GM/NIGMS NIH HHS/United States ; UH2 AR057503/AR/NIAMS NIH HHS/United States ; }, mesh = {Acne Vulgaris/*microbiology ; Adolescent ; Adult ; Aged ; Bacteriophages/*isolation & purification ; Case-Control Studies ; Cohort Studies ; Healthy Volunteers ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Middle Aged ; Propionibacterium acnes/*isolation & purification/virology ; Sequence Analysis, DNA ; Skin/*microbiology ; Virulence ; Young Adult ; }, abstract = {Studies have emphasized the importance of disease-associated microorganisms in perturbed communities, however, the protective roles of commensals are largely under recognized and poorly understood. Using acne as a model disease, we investigated the determinants of the overall virulence property of the skin microbiota when disease- and health-associated organisms coexist in the community. By ultra-deep metagenomic shotgun sequencing, we revealed higher relative abundances of propionibacteria and Propionibacterium acnes phage in healthy skin. In acne patients, the microbiome composition at the species level and at P. acnes strain level was more diverse than in healthy individuals, with enriched virulence-associated factors and reduced abundance of metabolic synthesis genes. Based on the abundance profiles of the metagenomic elements, we constructed a quantitative prediction model, which classified the clinical states of the host skin with high accuracy in both our study cohort (85%) and an independent sample set (86%). Our results suggest that the balance between metagenomic elements, not the mere presence of disease-associated strains, shapes the overall virulence property of the skin microbiota. This study provides new insights into the microbial mechanism of acne pathogenesis and suggests probiotic and phage therapies as potential acne treatments to modulate the skin microbiota and to maintain skin health.}, } @article {pmid28000336, year = {2017}, author = {Cao, HT and Gibson, TE and Bashan, A and Liu, YY}, title = {Inferring human microbial dynamics from temporal metagenomics data: Pitfalls and lessons.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {2}, pages = {}, doi = {10.1002/bies.201600188}, pmid = {28000336}, issn = {1521-1878}, mesh = {Bacteria/*genetics ; *Biota ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenomics/*methods ; Microbial Interactions ; *Models, Biological ; }, abstract = {The human gut microbiota is a very complex and dynamic ecosystem that plays a crucial role in health and well-being. Inferring microbial community structure and dynamics directly from time-resolved metagenomics data is key to understanding the community ecology and predicting its temporal behavior. Many methods have been proposed to perform the inference. Yet, as we point out in this review, there are several pitfalls along the way. Indeed, the uninformative temporal measurements and the compositional nature of the relative abundance data raise serious challenges in inference. Moreover, the inference results can be largely distorted when only focusing on highly abundant species by ignoring or grouping low-abundance species. Finally, the implicit assumptions in various regularization methods may not reflect reality. Those issues have to be seriously considered in ecological modeling of human gut microbiota.}, } @article {pmid27998035, year = {2017}, author = {Wang, W and Zheng, S and Sharshov, K and Sun, H and Yang, F and Wang, X and Li, L and Xiao, Z}, title = {Metagenomic profiling of gut microbial communities in both wild and artificially reared Bar-headed goose (Anser indicus).}, journal = {MicrobiologyOpen}, volume = {6}, number = {2}, pages = {}, pmid = {27998035}, issn = {2045-8827}, mesh = {Actinobacteria/*classification/genetics ; Amino Acids/metabolism ; Animals ; Bacteroidetes/*classification/genetics ; Base Sequence ; Biological Transport/genetics ; Carbohydrate Metabolism/genetics ; Feces/microbiology ; Firmicutes/*classification/genetics ; Gastrointestinal Microbiome/*genetics ; Geese/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenome/*genetics ; Metagenomics/methods ; Proteobacteria/*classification/genetics ; Sequence Analysis, DNA ; }, abstract = {Bar-headed goose (Anser indicus), a species endemic to Asia, has become one of the most popular species in recent years for rare bird breeding industries in several provinces of China. There has been no information on the gut metagenome configuration in both wild and artificially reared Bar-headed geese, even though the importance of gut microbiome in vertebrate nutrient and energy metabolism, immune homeostasis and reproduction is widely acknowledged. In this study, metagenomic methods have been used to describe the microbial community structure and composition of functional genes associated with both wild and artificially reared Bar-headed goose. Taxonomic analyses revealed that Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes were the four most abundant phyla in the gut of Bar-headed geese. Bacteroidetes were significantly abundant in the artificially reared group compared to wild group. Through functional profiling, we found that artificially reared Bar-headed geese had higher bacterial gene content related to carbohydrate transport and metabolism, energy metabolism and coenzyme transport, and metabolism. A comprehensive gene catalog of Bar-headed geese metagenome was built, and the metabolism of carbohydrate, amino acid, nucleotide, and energy were found to be the four most abundant categories. These results create a baseline for future Bar-headed goose microbiology research, and make an original contribution to the artificial rearing of this bird.}, } @article {pmid27997751, year = {2017}, author = {Jackrel, SL and Owens, SM and Gilbert, JA and Pfister, CA}, title = {Identifying the plant-associated microbiome across aquatic and terrestrial environments: the effects of amplification method on taxa discovery.}, journal = {Molecular ecology resources}, volume = {17}, number = {5}, pages = {931-942}, doi = {10.1111/1755-0998.12645}, pmid = {27997751}, issn = {1755-0998}, mesh = {Bacteria/*classification/*genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Metagenomics/*methods ; *Microbiota ; Plants/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Plants in terrestrial and aquatic environments contain a diverse microbiome. Yet, the chloroplast and mitochondria organelles of the plant eukaryotic cell originate from free-living cyanobacteria and Rickettsiales. This represents a challenge for sequencing the plant microbiome with universal primers, as ~99% of 16S rRNA sequences may consist of chloroplast and mitochondrial sequences. Peptide nucleic acid clamps offer a potential solution by blocking amplification of host-associated sequences. We assessed the efficacy of chloroplast and mitochondria-blocking clamps against a range of microbial taxa from soil, freshwater and marine environments. While we found that the mitochondrial blocking clamps appear to be a robust method for assessing animal-associated microbiota, Proteobacterial 16S rRNA binds to the chloroplast-blocking clamp, resulting in a strong sequencing bias against this group. We attribute this bias to a conserved 14-bp sequence in the Proteobacteria that matches the 17-bp chloroplast-blocking clamp sequence. By scanning the Greengenes database, we provide a reference list of nearly 1500 taxa that contain this 14-bp sequence, including 48 families such as the Rhodobacteraceae, Phyllobacteriaceae, Rhizobiaceae, Kiloniellaceae and Caulobacteraceae. To determine where these taxa are found in nature, we mapped this taxa reference list against the Earth Microbiome Project database. These taxa are abundant in a variety of environments, particularly aquatic and semiaquatic freshwater and marine habitats. To facilitate informed decisions on effective use of organelle-blocking clamps, we provide a searchable database of microbial taxa in the Greengenes and Silva databases matching various n-mer oligonucleotides of each PNA sequence.}, } @article {pmid27994068, year = {2017}, author = {He, B and Hoang, TK and Wang, T and Ferris, M and Taylor, CM and Tian, X and Luo, M and Tran, DQ and Zhou, J and Tatevian, N and Luo, F and Molina, JG and Blackburn, MR and Gomez, TH and Roos, S and Rhoads, JM and Liu, Y}, title = {Resetting microbiota by Lactobacillus reuteri inhibits T reg deficiency-induced autoimmunity via adenosine A2A receptors.}, journal = {The Journal of experimental medicine}, volume = {214}, number = {1}, pages = {107-123}, pmid = {27994068}, issn = {1540-9538}, support = {P01 HL114457/HL/NHLBI NIH HHS/United States ; R01 AT007083/AT/NCCIH NIH HHS/United States ; R01 HL113304/HL/NHLBI NIH HHS/United States ; R03 AI117442/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Autoimmunity ; Cell Differentiation ; Female ; *Gastrointestinal Microbiome ; Inosine/pharmacology ; *Limosilactobacillus reuteri ; Male ; Metabolomics ; Mice ; Mice, Inbred C57BL ; Receptor, Adenosine A2A/*physiology ; T-Lymphocytes, Regulatory/*immunology ; Th1 Cells/cytology ; Th2 Cells/cytology ; }, abstract = {Regulatory T (T reg) cell deficiency causes lethal, CD4[+] T cell-driven autoimmune diseases. Stem cell transplantation is used to treat these diseases, but this procedure is limited by the availability of a suitable donor. The intestinal microbiota drives host immune homeostasis by regulating the differentiation and expansion of T reg, Th1, and Th2 cells. It is currently unclear if T reg cell deficiency-mediated autoimmune disorders can be treated by targeting the enteric microbiota. Here, we demonstrate that Foxp3[+] T reg cell deficiency results in gut microbial dysbiosis and autoimmunity over the lifespan of scurfy (SF) mouse. Remodeling microbiota with Lactobacillus reuteri prolonged survival and reduced multiorgan inflammation in SF mice. L. reuteri changed the metabolomic profile disrupted by T reg cell deficiency, and a major effect was to restore levels of the purine metabolite inosine. Feeding inosine itself prolonged life and inhibited multiorgan inflammation by reducing Th1/Th2 cells and their associated cytokines. Mechanistically, the inhibition of inosine on the differentiation of Th1 and Th2 cells in vitro depended on adenosine A2A receptors, which were also required for the efficacy of inosine and of L. reuteri in vivo. These results reveal that the microbiota-inosine-A2A receptor axis might represent a potential avenue for combatting autoimmune diseases mediated by T reg cell dysfunction.}, } @article {pmid27993618, year = {2017}, author = {Sweet, M and Bythell, J}, title = {The role of viruses in coral health and disease.}, journal = {Journal of invertebrate pathology}, volume = {147}, number = {}, pages = {136-144}, doi = {10.1016/j.jip.2016.12.005}, pmid = {27993618}, issn = {1096-0805}, mesh = {Animals ; Anthozoa/*virology ; Biodiversity ; Genetic Variation ; Microbiota/genetics ; Symbiosis ; Virus Diseases/classification/epidemiology ; }, abstract = {Metagenomic and electron microscopy studies confirm that the coral microbiome contains a rich diversity and abundance of viruses. While there have been no definitive tests of disease causation by viruses in corals, viruses have been implicated as coral pathogens in a number of studies. Growing evidence also indicates that latent viral infections can compromise the algal symbionts under environmental stress and may be involved in the coral bleaching response. Conversely, bacteriophages and archaeal phage viruses are abundant in the microbiome of healthy corals and are likely to be involved in complex ecological networks, genetic material transfer and selective co-evolution within the surface mucus layers and tissues. The relative importance of viral control of bacterial and archaeal populations is unknown, but they are almost certain to be exerting some level of control on the composition and maintenance of the coral microbiome. While rapid leaps in the capability to detect viruses have been made due to advances in metagenomics and bioinformatics, these approaches need now to be integrated with in vitro culture and challenge experiments to assess the functional roles of viruses in health and disease, and it is imperative that interactions with other members of the coral microbiome are taken into account when assessing disease causation.}, } @article {pmid27992426, year = {2016}, author = {Berlemont, R and Martiny, AC}, title = {Glycoside Hydrolases across Environmental Microbial Communities.}, journal = {PLoS computational biology}, volume = {12}, number = {12}, pages = {e1005300}, pmid = {27992426}, issn = {1553-7358}, support = {UL1 GM118979/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/enzymology/genetics ; Bacterial Proteins/*genetics/metabolism ; Carbohydrate Metabolism ; *Environmental Microbiology ; Glycoside Hydrolases/*genetics/metabolism ; *Metagenomics ; *Microbial Consortia ; Substrate Specificity ; }, abstract = {Across many environments microbial glycoside hydrolases support the enzymatic processing of carbohydrates, a critical function in many ecosystems. Little is known about how the microbial composition of a community and the potential for carbohydrate processing relate to each other. Here, using 1,934 metagenomic datasets, we linked changes in community composition to variation of potential for carbohydrate processing across environments. We were able to show that each ecosystem-type displays a specific potential for carbohydrate utilization. Most of this potential was associated with just 77 bacterial genera. The GH content in bacterial genera is best described by their taxonomic affiliation. Across metagenomes, fluctuations of the microbial community structure and GH potential for carbohydrate utilization were correlated. Our analysis reveals that both deterministic and stochastic processes contribute to the assembly of complex microbial communities.}, } @article {pmid27988122, year = {2017}, author = {Gaeta, NC and Lima, SF and Teixeira, AG and Ganda, EK and Oikonomou, G and Gregory, L and Bicalho, RC}, title = {Deciphering upper respiratory tract microbiota complexity in healthy calves and calves that develop respiratory disease using shotgun metagenomics.}, journal = {Journal of dairy science}, volume = {100}, number = {2}, pages = {1445-1458}, doi = {10.3168/jds.2016-11522}, pmid = {27988122}, issn = {1525-3198}, mesh = {Animals ; Cattle ; Cattle Diseases/microbiology ; Female ; *Mannheimia haemolytica ; *Metagenomics ; Microbiota ; Pasteurella multocida ; Respiratory System/*microbiology ; }, abstract = {Bovine respiratory disease (BRD) is a multifactorial disorder responsible for severe economic losses in dairy and feedlot herds. Advances in next-generation sequencing mean that microbial communities in clinical samples, including non-culturable bacteria, can be characterized. Our aim was to evaluate the microbiota of the upper respiratory tract of healthy calves and calves with BRD using whole-genome sequencing (shotgun metagenomics). We performed deep nasopharyngeal swabs on 16 Holstein heifer calves (10 healthy and 6 diagnosed with BRD during the study) at 14 and 28 d of life in 1 dairy herd near Ithaca, New York. Total DNA was extracted, and whole-genome sequencing was performed using the MiSeq Illumina platform (Illumina Inc., San Diego, CA). Samples included 5 predominant phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Tenericutes. At the genus level, we observed differences between groups for Pseudomonas spp. At the species level, Mannheimia haemolytica was the most abundant bacterium detected. We detected significant differences between groups of calves in the relative abundance of Pseudomonas fluorescens. Pasteurella multocida was among the 20 most abundant species, and Moraxella catarrhalis, commonly associated with pneumonia in humans, was detected in all groups. Analysis of resistance to antibiotics and compounds profiling revealed differences in cobalt-zinc-cadmium resistance. Further research to elucidate the role of Moraxella catarrhalis in BRD is warranted. Genes that were resistant to cobalt-zinc-cadmium, observed mostly in calves with BRD, might be associated with difficulties in antibiotic treatment.}, } @article {pmid27987268, year = {2017}, author = {Carew, ME and Metzeling, L and St Clair, R and Hoffmann, AA}, title = {Detecting invertebrate species in archived collections using next-generation sequencing.}, journal = {Molecular ecology resources}, volume = {17}, number = {5}, pages = {915-930}, doi = {10.1111/1755-0998.12644}, pmid = {27987268}, issn = {1755-0998}, mesh = {Animals ; Aquatic Organisms ; *Body Remains ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing ; Invertebrates/*classification/*genetics ; Metagenomics/*methods ; *Preservation, Biological ; }, abstract = {Invertebrate biodiversity measured at mostly family level is widely used in biological monitoring programmes to assess anthropogenic impacts on ecosystems. However, next-generation sequencing (NGS) could allow development of new more sensitive biomonitoring tools by allowing rapid species identification. This could be accelerated if archived invertebrate collections and environmental information from past programmes are used to understand species distributions and their environmental responses. In this study, we take archived macroinvertebrate samples from two sites collected on multiple occasions and test whether NGS can successfully detect species. Samples had been stored in 70% ethanol at room temperature for up to 12 years. Three amplicons ranging from 197 to 274 bps within the DNA barcode region were amplified from samples and compared to DNA barcoding libraries to identify species. We were able to amplify partial DNA barcodes from most samples, and species were often detected with multiple amplicons. However, some singletons and taxa poorly covered by DNA barcoding were missed. This suggests additional DNA barcodes will be required to fill 'gaps' in current DNA barcode libraries for aquatic macroinvertebrates and/or that it may not be possible to detect all taxa in a sample. Furthermore, older samples often detected fewer taxa and were less reliable for amplification, suggesting NGS is best used on samples within 8 years of collection. Nevertheless, many common taxa with existing DNA barcodes were reliably identified with NGS and were often present at sites across multiple years, showing the potential of NGS for detecting common and abundant species in archived material.}, } @article {pmid27987263, year = {2017}, author = {Lopes, CM and Sasso, T and Valentini, A and Dejean, T and Martins, M and Zamudio, KR and Haddad, CFB}, title = {eDNA metabarcoding: a promising method for anuran surveys in highly diverse tropical forests.}, journal = {Molecular ecology resources}, volume = {17}, number = {5}, pages = {904-914}, doi = {10.1111/1755-0998.12643}, pmid = {27987263}, issn = {1755-0998}, mesh = {Animals ; Anura/*classification/*genetics ; Brazil ; DNA/chemistry/genetics/isolation & purification ; DNA Barcoding, Taxonomic/*methods ; Forests ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Polymerase Chain Reaction ; Tropical Climate ; Water/chemistry ; }, abstract = {Understanding the geographical distribution and community composition of species is crucial to monitor species persistence and define effective conservation strategies. Environmental DNA (eDNA) has emerged as a powerful noninvasive tool for species detection. However, most eDNA survey methods have been developed and applied in temperate zones. We tested the feasibility of using eDNA to survey anurans in tropical streams in the Brazilian Atlantic forest and compared the results with short-term visual and audio surveys. We detected all nine species known to inhabit our focal streams with one single visit for eDNA sampling. We found a higher proportion of sequence reads and larger number of positive PCR replicates for more common species and for those with life cycles closely associated with the streams, factors that may contribute to increased release of DNA in the water. However, less common species were also detected in eDNA samples, demonstrating the detection power of this method. Filtering larger volumes of water resulted in a higher probability of detection. Our data also show it is important to sample multiple sites along streams, particularly for detection of target species with lower population densities. For the three focal species in our study, the eDNA metabarcoding method had a greater capacity of detection per sampling event than our rapid field surveys, and thus, has the potential to circumvent some of the challenges associated with traditional approaches. Our results underscore the utility of eDNA metabarcoding as an efficient method to survey anuran species in tropical streams of the highly biodiverse Brazilian Atlantic forest.}, } @article {pmid27986827, year = {2017}, author = {Lacerda Júnior, GV and Noronha, MF and de Sousa, ST and Cabral, L and Domingos, DF and Sáber, ML and de Melo, IS and Oliveira, VM}, title = {Potential of semiarid soil from Caatinga biome as a novel source for mining lignocellulose-degrading enzymes.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {2}, pages = {}, doi = {10.1093/femsec/fiw248}, pmid = {27986827}, issn = {1574-6941}, mesh = {Actinobacteria/metabolism ; Animals ; Biofuels ; Biomass ; Brazil ; Cellulose/metabolism ; Glycoside Hydrolases ; Hydrolysis ; Lignin/*metabolism ; *Microbiota ; Phylogeny ; Proteobacteria/metabolism ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The litterfall is the major organic material deposited in soil of Brazilian Caatinga biome, thus providing the ideal conditions for plant biomass-degrading microorganisms to thrive. Herein, the phylogenetic composition and lignocellulose-degrading capacity have been explored for the first time from a fosmid library dataset of Caatinga soil by sequence-based screening. A complex bacterial community dominated by Proteobacteria and Actinobacteria was unraveled. SEED subsystems-based annotations revealed a broad range of genes assigned to carbohydrate and aromatic compounds metabolism, indicating microbial ability to utilize plant-derived material. CAZy-based annotation identified 7275 genes encoding 37 glycoside hydrolases (GHs) families related to hydrolysis of cellulose, hemicellulose, oligosaccharides and other lignin-modifying enzymes. Taxonomic affiliation of genes showed high genetic potential of the phylum Acidobacteria for hemicellulose degradation, whereas Actinobacteria members appear to play an important role in celullose hydrolysis. Additionally, comparative analyses revealed greater GHs profile similarity among soils as compared to the digestive tract of animals capable of digesting plant biomass, particularly in the hemicellulases content. Combined results suggest a complex synergistic interaction of community members required for biomass degradation into fermentable sugars. This large repertoire of lignocellulolytic enzymes opens perspectives for mining potential candidates of biochemical catalysts for biofuels production from renewable resources and other environmental applications.}, } @article {pmid27986083, year = {2016}, author = {Narayanasamy, S and Jarosz, Y and Muller, EE and Heintz-Buschart, A and Herold, M and Kaysen, A and Laczny, CC and Pinel, N and May, P and Wilmes, P}, title = {IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses.}, journal = {Genome biology}, volume = {17}, number = {1}, pages = {260}, pmid = {27986083}, issn = {1474-760X}, mesh = {Algorithms ; Computational Biology ; Genomics ; Metagenome/*genetics ; Microbiota/*genetics ; *Software ; Transcriptome/*genetics ; Workflow ; }, abstract = {Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data. IMP incorporates robust read preprocessing, iterative co-assembly, analyses of microbial community structure and function, automated binning, as well as genomic signature-based visualizations. The IMP-based data integration strategy enhances data usage, output volume, and output quality as demonstrated using relevant use-cases. Finally, IMP is encapsulated within a user-friendly implementation using Python and Docker. IMP is available at http://r3lab.uni.lu/web/imp/ (MIT license).}, } @article {pmid27984592, year = {2016}, author = {Raguideau, S and Plancade, S and Pons, N and Leclerc, M and Laroche, B}, title = {Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota.}, journal = {PLoS computational biology}, volume = {12}, number = {12}, pages = {e1005252}, pmid = {27984592}, issn = {1553-7358}, mesh = {Algorithms ; Bacteria/genetics/metabolism ; Carbohydrate Metabolism/genetics/physiology ; Dietary Fiber/metabolism ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenomics/*methods ; }, abstract = {Whole Genome Shotgun (WGS) metagenomics is increasingly used to study the structure and functions of complex microbial ecosystems, both from the taxonomic and functional point of view. Gene inventories of otherwise uncultured microbial communities make the direct functional profiling of microbial communities possible. The concept of community aggregated trait has been adapted from environmental and plant functional ecology to the framework of microbial ecology. Community aggregated traits are quantified from WGS data by computing the abundance of relevant marker genes. They can be used to study key processes at the ecosystem level and correlate environmental factors and ecosystem functions. In this paper we propose a novel model based approach to infer combinations of aggregated traits characterizing specific ecosystemic metabolic processes. We formulate a model of these Combined Aggregated Functional Traits (CAFTs) accounting for a hierarchical structure of genes, which are associated on microbial genomes, further linked at the ecosystem level by complex co-occurrences or interactions. The model is completed with constraints specifically designed to exploit available genomic information, in order to favor biologically relevant CAFTs. The CAFTs structure, as well as their intensity in the ecosystem, is obtained by solving a constrained Non-negative Matrix Factorization (NMF) problem. We developed a multicriteria selection procedure for the number of CAFTs. We illustrated our method on the modelling of ecosystemic functional traits of fiber degradation by the human gut microbiota. We used 1408 samples of gene abundances from several high-throughput sequencing projects and found that four CAFTs only were needed to represent the fiber degradation potential. This data reduction highlighted biologically consistent functional patterns while providing a high quality preservation of the original data. Our method is generic and can be applied to other metabolic processes in the gut or in other ecosystems.}, } @article {pmid27984120, year = {2017}, author = {Huson, DH and Steel, M and El-Hadidi, M and Mitra, S and Peter, S and Willmann, M}, title = {A simple statistical test of taxonomic or functional homogeneity using replicated microbiome sequencing samples.}, journal = {Journal of biotechnology}, volume = {250}, number = {}, pages = {45-50}, doi = {10.1016/j.jbiotec.2016.10.020}, pmid = {27984120}, issn = {1873-4863}, mesh = {*Algorithms ; Bacteria/classification/*genetics/*isolation & purification ; Bacterial Typing Techniques/*methods ; Computer Simulation ; *Data Interpretation, Statistical ; Feces/microbiology ; High-Throughput Screening Assays/methods ; Humans ; Microbiota/*genetics ; Models, Statistical ; Reproducibility of Results ; Sample Size ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods ; }, abstract = {One important question in microbiome analysis is how to assess the homogeneity of the microbial composition in a given environment, with respect to a given analysis method. Do different microbial samples taken from the same environment follow the same taxonomic distribution of organisms, or the same distribution of functions? Here we provide a non-parametric statistical "triangulation test" to address this type of question. The test requires that multiple replicates are available for each of the biological samples, and it is based on three-way computational comparisons of samples. To illustrate the application of the test, we collected three biological samples taken from different locations in one piece of human stool, each represented by three replicates, and analyzed them using MEGAN. (Despite its name, the triangulation test does not require that the number of biological samples or replicates be three.) The triangulation test rejects the null hypothesis that the three biological samples exhibit the same distribution of taxa or function (error probability ≤0.05), indicating that the microbial composition of the investigated human stool is not homogenous on a macroscopic scale, suggesting that pooling material from multiple locations is a reasonable practice. We provide an implementation of the test in our open source program MEGAN Community Edition.}, } @article {pmid27983720, year = {2017}, author = {Drago, L and Toscano, M and De Grandi, R and Grossi, E and Padovani, EM and Peroni, DG}, title = {Microbiota network and mathematic microbe mutualism in colostrum and mature milk collected in two different geographic areas: Italy versus Burundi.}, journal = {The ISME journal}, volume = {11}, number = {4}, pages = {875-884}, pmid = {27983720}, issn = {1751-7370}, mesh = {Bacteria/classification/*isolation & purification ; Burundi ; Colostrum ; Female ; Humans ; Infant, Newborn ; Italy ; Microbiota ; Milk, Human/*microbiology ; Pregnancy ; Symbiosis ; }, abstract = {Human milk is essential for the initial development of newborns, as it provides all nutrients and vitamins, such as vitamin D, and represents a great source of commensal bacteria. Here we explore the microbiota network of colostrum and mature milk of Italian and Burundian mothers using the auto contractive map (AutoCM), a new methodology based on artificial neural network (ANN) architecture. We were able to demonstrate the microbiota of human milk to be a dynamic, and complex, ecosystem with different bacterial networks among different populations containing diverse microbial hubs and central nodes, which change during the transition from colostrum to mature milk. Furthermore, a greater abundance of anaerobic intestinal bacteria in mature milk compared with colostrum samples has been observed. The association of complex mathematic systems such as ANN and AutoCM adopted to metagenomics analysis represents an innovative approach to investigate in detail specific bacterial interactions in biological samples.}, } @article {pmid27981347, year = {2017}, author = {Gómez-Acata, S and Esquivel-Ríos, I and Pérez-Sandoval, MV and Navarro-Noya, Y and Rojas-Valdez, A and Thalasso, F and Luna-Guido, M and Dendooven, L}, title = {Bacterial community structure within an activated sludge reactor added with phenolic compounds.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {8}, pages = {3405-3414}, doi = {10.1007/s00253-016-8000-z}, pmid = {27981347}, issn = {1432-0614}, mesh = {Actinobacteria/classification/drug effects/genetics/physiology ; Bacteria/classification/*drug effects/genetics/*metabolism ; Bacteroidetes/classification/drug effects/genetics/physiology ; *Biodegradation, Environmental ; *Bioreactors ; Chlorophenols/metabolism/pharmacology ; Cresols/metabolism/pharmacology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Microbial Consortia/*drug effects/genetics/physiology ; Phenol/metabolism/pharmacology ; Phenols/*metabolism/*pharmacology ; Proteobacteria/classification/drug effects/genetics/physiology ; RNA, Ribosomal, 16S ; Sewage/analysis/*microbiology ; }, abstract = {Biodegradation of phenolic compounds in bioreactors is well documented, but the changes in the bacterial populations dynamics during degradation were not that often. A glass bubble column used as reactor was inoculated with activated sludge, spiked with 2-chlorophenol, phenol and m-cresol after 28 days and maintained for an additional 56 days, while the 16S rRNA gene from metagenomic DNA was monitored. Proteobacteria (68.1%) dominated the inoculum, but the bacterial composition changed rapidly. The relative abundance of Bacteroidetes and Firmicutes decreased from 4.8 and 9.4 to <0.1 and 0.2% respectively, while that of Actinobacteria and TM7 increased from 4.8 and 2.0 to 19.2 and 16.1% respectively. Phenol application increased the relative abundance of Proteobacteria to 94.2% (mostly Brevundimonas 17.6%), while that of Bacteroidetes remained low (1.2%) until day 42. It then increased to 47.3% (mostly Leadbetterella 46.9%) at day 84. It was found that addition of phenolic compounds did not affect the relative abundance of the Alphaproteobacteria initially, but it decreased slowly while that of the Bacteroidetes increased towards the end.}, } @article {pmid27980100, year = {2017}, author = {Tourlousse, DM and Yoshiike, S and Ohashi, A and Matsukura, S and Noda, N and Sekiguchi, Y}, title = {Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing.}, journal = {Nucleic acids research}, volume = {45}, number = {4}, pages = {e23}, pmid = {27980100}, issn = {1362-4962}, mesh = {Bacteria/classification/genetics ; Computational Biology ; Environmental Microbiology ; *High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods/standards ; Microbiota ; RNA, Ribosomal, 16S/*genetics ; Reference Standards ; }, abstract = {High-throughput sequencing of 16S rRNA gene amplicons (16S-seq) has become a widely deployed method for profiling complex microbial communities but technical pitfalls related to data reliability and quantification remain to be fully addressed. In this work, we have developed and implemented a set of synthetic 16S rRNA genes to serve as universal spike-in standards for 16S-seq experiments. The spike-ins represent full-length 16S rRNA genes containing artificial variable regions with negligible identity to known nucleotide sequences, permitting unambiguous identification of spike-in sequences in 16S-seq read data from any microbiome sample. Using defined mock communities and environmental microbiota, we characterized the performance of the spike-in standards and demonstrated their utility for evaluating data quality on a per-sample basis. Further, we showed that staggered spike-in mixtures added at the point of DNA extraction enable concurrent estimation of absolute microbial abundances suitable for comparative analysis. Results also underscored that template-specific Illumina sequencing artifacts may lead to biases in the perceived abundance of certain taxa. Taken together, the spike-in standards represent a novel bioanalytical tool that can substantially improve 16S-seq-based microbiome studies by enabling comprehensive quality control along with absolute quantification.}, } @article {pmid27976718, year = {2016}, author = {Bletz, MC and Goedbloed, DJ and Sanchez, E and Reinhardt, T and Tebbe, CC and Bhuju, S and Geffers, R and Jarek, M and Vences, M and Steinfartz, S}, title = {Amphibian gut microbiota shifts differentially in community structure but converges on habitat-specific predicted functions.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {13699}, pmid = {27976718}, issn = {2041-1723}, mesh = {Animals ; *Ecosystem ; Environment ; Gastrointestinal Microbiome/*genetics ; Larva/*microbiology ; Metagenome/genetics ; Microbiota/genetics ; *Ponds ; RNA, Ribosomal, 16S/*genetics ; *Rivers ; Salamandra/*microbiology ; Skin/*microbiology ; }, abstract = {Complex microbial communities inhabit vertebrate digestive systems but thorough understanding of the ecological dynamics and functions of host-associated microbiota within natural habitats is limited. We investigate the role of environmental conditions in shaping gut and skin microbiota under natural conditions by performing a field survey and reciprocal transfer experiments with salamander larvae inhabiting two distinct habitats (ponds and streams). We show that gut and skin microbiota are habitat-specific, demonstrating environmental factors mediate community structure. Reciprocal transfer reveals that gut microbiota, but not skin microbiota, responds differentially to environmental change. Stream-to-pond larvae shift their gut microbiota to that of pond-to-pond larvae, whereas pond-to-stream larvae change to a community structure distinct from both habitat controls. Predicted functions, however, match that of larvae from the destination habitats in both cases. Thus, microbial function can be matched without taxonomic coherence and gut microbiota appears to exhibit metagenomic plasticity.}, } @article {pmid27974658, year = {2016}, author = {Brown, JM}, title = {Eating to boost gut microbial diversity.}, journal = {Science translational medicine}, volume = {8}, number = {369}, pages = {369ec198}, doi = {10.1126/scitranslmed.aal3696}, pmid = {27974658}, issn = {1946-6242}, mesh = {Eating ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; RNA, Ribosomal, 16S ; }, } @article {pmid27965413, year = {2017}, author = {Ainsworth, D and Sternberg, MJE and Raczy, C and Butcher, SA}, title = {k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets.}, journal = {Nucleic acids research}, volume = {45}, number = {4}, pages = {1649-1656}, pmid = {27965413}, issn = {1362-4962}, support = {MR/L01632X/1/MRC_/Medical Research Council/United Kingdom ; BB/I01585X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Algorithms ; Case-Control Studies ; Computational Biology/*methods/standards ; DNA Barcoding, Taxonomic/*methods/standards ; Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Liver Cirrhosis/microbiology ; *Metagenome ; Metagenomics/*methods/standards ; Reproducibility of Results ; Shiga-Toxigenic Escherichia coli/classification/genetics ; }, abstract = {k-SLAM is a highly efficient algorithm for the characterization of metagenomic data. Unlike other ultra-fast metagenomic classifiers, full sequence alignment is performed allowing for gene identification and variant calling in addition to accurate taxonomic classification. A k-mer based method provides greater taxonomic accuracy than other classifiers and a three orders of magnitude speed increase over alignment based approaches. The use of alignments to find variants and genes along with their taxonomic origins enables novel strains to be characterized. k-SLAM's speed allows a full taxonomic classification and gene identification to be tractable on modern large data sets. A pseudo-assembly method is used to increase classification accuracy by up to 40% for species which have high sequence homology within their genus.}, } @article {pmid27965238, year = {2016}, author = {Harrison, JG and Forister, ML and Parchman, TL and Koch, GW}, title = {Vertical stratification of the foliar fungal community in the world's tallest trees.}, journal = {American journal of botany}, volume = {103}, number = {12}, pages = {2087-2095}, doi = {10.3732/ajb.1600277}, pmid = {27965238}, issn = {1537-2197}, mesh = {Biodiversity ; California ; DNA, Fungal/chemistry/genetics ; Endophytes ; Fungi/genetics/*isolation & purification/physiology ; Geography ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Plant Leaves/microbiology ; Sequence Analysis, DNA ; Sequoia/*microbiology ; Trees/microbiology ; }, abstract = {PREMISE OF THE STUDY: The aboveground tissues of plants host numerous, ecologically important fungi, yet patterns in the spatial distribution of these fungi remain little known. Forest canopies in particular are vast reservoirs of fungal diversity, but intracrown variation in fungal communities has rarely been explored. Knowledge of how fungi are distributed throughout tree crowns will contribute to our understanding of interactions between fungi and their host trees and is a first step toward investigating drivers of community assembly for plant-associated fungi. Here we describe spatial patterns in fungal diversity within crowns of the world's tallest trees, coast redwoods (Sequoia sempervirens).

METHODS: We took a culture-independent approach, using the Illumina MiSeq platform, to characterize the fungal assemblage at multiple heights within the crown across the geographical range of the coast redwood.

KEY RESULTS: Within each tree surveyed, we uncovered evidence for vertical stratification in the fungal community; different portions of the tree crown harbored different assemblages of fungi. We also report between-tree variation in the fungal community within redwoods.

CONCLUSIONS: Our results suggest the potential for vertical stratification of fungal communities in the crowns of other tall tree species and should prompt future study of the factors giving rise to this stratification.}, } @article {pmid27959345, year = {2017}, author = {Solden, LM and Hoyt, DW and Collins, WB and Plank, JE and Daly, RA and Hildebrand, E and Beavers, TJ and Wolfe, R and Nicora, CD and Purvine, SO and Carstensen, M and Lipton, MS and Spalinger, DE and Firkins, JL and Wolfe, BA and Wrighton, KC}, title = {New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11.}, journal = {The ISME journal}, volume = {11}, number = {3}, pages = {691-703}, pmid = {27959345}, issn = {1751-7370}, mesh = {Animals ; Arctic Regions ; Bacteria/classification ; Bacteroidetes/classification/*metabolism ; Climate Change ; Deer/classification/*microbiology ; Digestion ; Fatty Acids, Volatile/metabolism ; Fermentation ; *Gastrointestinal Microbiome ; Lignin/metabolism ; Metagenomics/methods ; Phylogeny ; Polysaccharides/*metabolism ; Rumen/*microbiology ; Seasons ; }, abstract = {Ruminants have co-evolved with their gastrointestinal microbial communities that digest plant materials to provide energy for the host. Some arctic and boreal ruminants have already shown to be vulnerable to dietary shifts caused by changing climate, yet we know little about the metabolic capacity of the ruminant microbiome in these animals. Here, we use meta-omics approaches to sample rumen fluid microbial communities from Alaskan moose foraging along a seasonal lignocellulose gradient. Winter diets with increased hemicellulose and lignin strongly enriched for BS11, a Bacteroidetes family lacking cultivated or genomically sampled representatives. We show that BS11 are cosmopolitan host-associated bacteria prevalent in gastrointestinal tracts of ruminants and other mammals. Metagenomic reconstruction yielded the first four BS11 genomes; phylogenetically resolving two genera within this previously taxonomically undefined family. Genome-enabled metabolic analyses uncovered multiple pathways for fermenting hemicellulose monomeric sugars to short-chain fatty acids (SCFA), metabolites vital for ruminant energy. Active hemicellulosic sugar fermentation and SCFA production was validated by shotgun proteomics and rumen metabolites, illuminating the role BS11 have in carbon transformations within the rumen. Our results also highlight the currently unknown metabolic potential residing in the rumen that may be vital for sustaining host energy in response to a changing vegetative environment.}, } @article {pmid27943013, year = {2017}, author = {Wang, X and Xu, X and Xia, Y}, title = {Further analysis reveals new gut microbiome markers of type 2 diabetes mellitus.}, journal = {Antonie van Leeuwenhoek}, volume = {110}, number = {3}, pages = {445-453}, doi = {10.1007/s10482-016-0805-3}, pmid = {27943013}, issn = {1572-9699}, mesh = {China/epidemiology ; Cohort Studies ; Diabetes Mellitus, Type 2/epidemiology/*microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Genetic Markers/genetics ; Genome, Microbial ; Humans ; Metagenome ; Metagenomics/methods ; }, abstract = {In recent years, metagenome-wide association studies have revealed potential relationships between intestinal microbiomes and the pathogenesis of type 2 diabetes mellitus (T2DM). However, considering the increase in volume of gene catalogues and algorithms, an updated analysis would be expected to confirm previous discoveries and provide new knowledge. We therefore constructed new profiles after mapping the recent catalogue of reference genes in the human gut microbiome to reanalyze samples from T2DM cases and controls in the Chinese population. We identified different compositions between Chinese controls and T2DM patients at the species and genus levels, especially in the case of butyrate-producing bacteria, Haemophilus, and Lactobacillus. An effective metagenomic linkage group random forest model was built to differentiate controls from T2DM cases in different cohorts. Functional markers from the Kyoto Encyclopedia of Genes and Genomes database were identified using new annotations. We also report 16 virulence factor markers and 22 antibiotic resistance markers associated with T2DM.}, } @article {pmid27941985, year = {2016}, author = {Yadav, KK and Datta, S and Naglot, A and Bora, A and Hmuaka, V and Bhagyawant, S and Gogoi, HK and Veer, V and Raju, PS}, title = {Diversity of Cultivable Midgut Microbiota at Different Stages of the Asian Tiger Mosquito, Aedes albopictus from Tezpur, India.}, journal = {PloS one}, volume = {11}, number = {12}, pages = {e0167409}, pmid = {27941985}, issn = {1932-6203}, mesh = {*Aedes ; Animals ; Bacteria/classification/genetics ; Biodiversity ; Female ; *Gastrointestinal Microbiome ; India ; *Life Cycle Stages ; Male ; Metagenome ; Metagenomics/methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Aedes aegypti and Ae. albopictus are among the most important vectors of arboviral diseases, worldwide. Recent studies indicate that diverse midgut microbiota of mosquitoes significantly affect development, digestion, metabolism, and immunity of their hosts. Midgut microbiota has also been suggested to modulate the competency of mosquitoes to transmit arboviruses, malaria parasites etc. Interestingly, the midgut microbial flora is dynamic and the diversity changes with the development of vectors, in addition to other factors such as species, sex, life-stage, feeding behavior and geographical origin. The aim of the present study was to investigate the midgut bacterial diversity among larva, adult male, sugar fed female and blood fed female Ae. albopictus collected from Tezpur, Northeastern India. Based on colony morphological characteristics, we selected 113 cultivable bacterial isolates for 16S rRNA gene sequence based molecular identification. Of the 113 isolates, we could identify 35 bacterial species belonging to 18 distinct genera under four major phyla, namely Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Phyla Proteobacteria and Firmicutes accounted for majority (80%) of the species, while phylum Actinobacteria constituted 17% of the species. Bacteroidetes was the least represented phylum, characterized by a single species- Chryseobacterium rhizoplanae, isolated from blood fed individuals. Dissection of midgut microbiota diversity at different developmental stages of Ae. albopictus will be helpful in better understanding mosquito-borne diseases, and for designing effective strategies to manage mosquito-borne diseases.}, } @article {pmid27941956, year = {2016}, author = {Antunes, LP and Martins, LF and Pereira, RV and Thomas, AM and Barbosa, D and Lemos, LN and Silva, GM and Moura, LM and Epamino, GW and Digiampietri, LA and Lombardi, KC and Ramos, PL and Quaggio, RB and de Oliveira, JC and Pascon, RC and Cruz, JB and da Silva, AM and Setubal, JC}, title = {Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {38915}, pmid = {27941956}, issn = {2045-2322}, mesh = {Bacteria/genetics ; Biodegradation, Environmental ; Biomass ; *Composting ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Lignin/metabolism ; Metagenomics ; *Microbial Consortia ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Composting is a promising source of new organisms and thermostable enzymes that may be helpful in environmental management and industrial processes. Here we present results of metagenomic- and metatranscriptomic-based analyses of a large composting operation in the São Paulo Zoo Park. This composting exhibits a sustained thermophilic profile (50 °C to 75 °C), which seems to preclude fungal activity. The main novelty of our study is the combination of time-series sampling with shotgun DNA, 16S rRNA gene amplicon, and metatranscriptome high-throughput sequencing, enabling an unprecedented detailed view of microbial community structure, dynamics, and function in this ecosystem. The time-series data showed that the turning procedure has a strong impact on the compost microbiota, restoring to a certain extent the population profile seen at the beginning of the process; and that lignocellulosic biomass deconstruction occurs synergistically and sequentially, with hemicellulose being degraded preferentially to cellulose and lignin. Moreover, our sequencing data allowed near-complete genome reconstruction of five bacterial species previously found in biomass-degrading environments and of a novel biodegrading bacterial species, likely a new genus in the order Bacillales. The data and analyses provided are a rich source for additional investigations of thermophilic composting microbiology.}, } @article {pmid27941918, year = {2016}, author = {Robinson, G and Caldwell, GS and Wade, MJ and Free, A and Jones, CLW and Stead, SM}, title = {Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {38850}, pmid = {27941918}, issn = {2045-2322}, support = {BB/J01141X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Aquaculture/*methods ; Bacteria/classification/genetics/*isolation & purification/metabolism ; *Biodegradation, Environmental ; Biodiversity ; Biomass ; Genes, Bacterial ; Geologic Sediments/*microbiology ; Holothuria/*growth & development ; Metagenomics ; Oxidation-Reduction ; Oxygen/analysis ; Ribotyping ; Temperature ; }, abstract = {Deposit-feeding invertebrates are proposed bioremediators in microbial-driven sediment-based aquaculture effluent treatment systems. We elucidate the role of the sediment reduction-oxidation (redox) regime in structuring benthic bacterial communities, having direct implications for bioremediation potential and deposit-feeder nutrition. The sea cucumber Holothuria scabra was cultured on sediments under contrasting redox regimes; fully oxygenated (oxic) and redox stratified (oxic-anoxic). Taxonomically, metabolically and functionally distinct bacterial communities developed between the redox treatments with the oxic treatment supporting the greater diversity; redox regime and dissolved oxygen levels were the main environmental drivers. Oxic sediments were colonised by nitrifying bacteria with the potential to remediate nitrogenous wastes. Percolation of oxygenated water prevented the proliferation of anaerobic sulphate-reducing bacteria, which were prevalent in the oxic-anoxic sediments. At the predictive functional level, bacteria within the oxic treatment were enriched with genes associated with xenobiotics metabolism. Oxic sediments showed the greater bioremediation potential; however, the oxic-anoxic sediments supported a greater sea cucumber biomass. Overall, the results indicate that bacterial communities present in fully oxic sediments may enhance the metabolic capacity and bioremediation potential of deposit-feeder microbial systems. This study highlights the benefits of incorporating deposit-feeding invertebrates into effluent treatment systems, particularly when the sediment is oxygenated.}, } @article {pmid27941835, year = {2016}, author = {Mello, BL and Alessi, AM and McQueen-Mason, S and Bruce, NC and Polikarpov, I}, title = {Nutrient availability shapes the microbial community structure in sugarcane bagasse compost-derived consortia.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {38781}, pmid = {27941835}, issn = {2045-2322}, support = {BB/I018492/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biodiversity ; Cellulose/*metabolism ; *Composting ; Microbial Consortia/*physiology ; Saccharum/*metabolism ; }, abstract = {Microbial communities (MCs) create complex metabolic networks in natural habitats and respond to environmental changes by shifts in the community structure. Although members of MCs are often not amenable for cultivation in pure culture, it is possible to obtain a greater diversity of species in the laboratory setting when microorganisms are grown as mixed cultures. In order to mimic the environmental conditions, an appropriate growth medium must be applied. Here, we examined the hypothesis that a greater diversity of microorganisms can be sustained under nutrient-limited conditions. Using a 16 S rRNA amplicon metagenomic approach, we explored the structure of a compost-derived MC. During a five-week time course the MC grown in minimal medium with sugarcane bagasse (SCB) as a sole carbon source showed greater diversity and enrichment in lignocellulose-degrading microorganisms. In contrast, a MC grown in nutrient rich medium with addition of SCB had a lower microbial diversity and limited number of lignocellulolytic species. Our approach provides evidence that factors such as nutrient availability has a significant selective pressure on the biodiversity of microorganisms in MCs. Consequently, nutrient-limited medium may displace bacterial generalist species, leading to an enriched source for mining novel enzymes for biotechnology applications.}, } @article {pmid27940546, year = {2017}, author = {Müller, CA and Perz, V and Provasnek, C and Quartinello, F and Guebitz, GM and Berg, G}, title = {Discovery of Polyesterases from Moss-Associated Microorganisms.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {4}, pages = {}, pmid = {27940546}, issn = {1098-5336}, mesh = {Bacteria/*enzymology ; Butyrates/metabolism ; Esterases/*genetics/*metabolism ; Hydrolysis ; Microbiota/genetics/physiology ; Polyesters/*metabolism ; Sphagnopsida/*microbiology ; }, abstract = {UNLABELLED: The growing pollution of the environment with plastic debris is a global threat which urgently requires biotechnological solutions. Enzymatic recycling not only prevents pollution but also would allow recovery of valuable building blocks. Therefore, we explored the existence of microbial polyesterases in microbial communities associated with the Sphagnum magellanicum moss, a key species within unexploited bog ecosystems. This resulted in the identification of six novel esterases, which were isolated, cloned, and heterologously expressed in Escherichia coli The esterases were found to hydrolyze the copolyester poly(butylene adipate-co-butylene terephthalate) (PBAT) and the oligomeric model substrate bis[4-(benzoyloxy)butyl] terephthalate (BaBTaBBa). Two promising polyesterase candidates, EstB3 and EstC7, which clustered in family VIII of bacterial lipolytic enzymes, were purified and characterized using the soluble esterase substrate p-nitrophenyl butyrate (Km values of 46.5 and 3.4 μM, temperature optima of 48°C and 50°C, and pH optima of 7.0 and 8.5, respectively). In particular, EstC7 showed outstanding activity and a strong preference for hydrolysis of the aromatic ester bond in PBAT. Our study highlights the potential of plant-associated microbiomes from extreme natural ecosystems as a source for novel hydrolytic enzymes hydrolyzing polymeric compounds.

IMPORTANCE: In this study, we describe the discovery and analysis of new enzymes from microbial communities associated with plants (moss). The recovered enzymes show the ability to hydrolyze not only common esterase substrates but also the synthetic polyester poly(butylene adipate-co-butylene terephthalate), which is a common material employed in biodegradable plastics. The widespread use of such synthetic polyesters in industry and society requires the development of new sustainable technological solutions for their recycling. The discovered enzymes have the potential to be used as catalysts for selective recovery of valuable building blocks from this material.}, } @article {pmid27940464, year = {2016}, author = {Zhao, L and Li, Y and Jiang, L and Deng, F}, title = {Determination of fungal community diversity in fresh and traditional Chinese fermented pepper by pyrosequencing.}, journal = {FEMS microbiology letters}, volume = {363}, number = {24}, pages = {}, doi = {10.1093/femsle/fnw273}, pmid = {27940464}, issn = {1574-6968}, mesh = {*Biota ; Capsicum/*microbiology ; China ; *Food Microbiology ; Fungi/*classification/*genetics ; Metagenomics ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Fermented pepper is one of the traditional Chinese fermented vegetables. The production mainly relies on the fermentation by natural microorganisms. This fermentation system is a unique and dynamic microecological environment, and involved microbial communities are very complex. In this study, 454 pyrosequencing was first used to investigate the fungal communities in fresh pepper and different fermentation phases. The results showed that fungal communities in fresh pepper (sample M_0) were more abundant than later fermented phases. Taxa in proportions >0.01% could be assigned to 21 different genera. Taxa in proportions >1% were Trichosporon 24.11%, Rhodotorula 7.4%, Cladosporium 4.26%, Debarvomvces 3.94%, Mucor 2.51% and Cryptococcus 1.86%. There were a large number of unknown fungi (47.99%) in the sample waiting to be identified. Along with the fermentation, microbial communities became less diverse. Hanseniaspora and Pichia became the dominant fungal genera, while Trichosporon decreased from a maximum 24.11% to a minimum 0.1%. On the seventh fermentation day, the percentage of Hanseniaspora reached 89.3%. On the 20th fermentation day, taxa in proportions >1% were Hanseniaspora 69.25%, Unclassified 12.23%, Pichia 8.95%, Debaryomyces 6.22% and Rhodotorula 1.31%.}, } @article {pmid27936055, year = {2016}, author = {Mukherjee, N and Bartelli, D and Patra, C and Chauhan, BV and Dowd, SE and Banerjee, P}, title = {Microbial Diversity of Source and Point-of-Use Water in Rural Haiti - A Pyrosequencing-Based Metagenomic Survey.}, journal = {PloS one}, volume = {11}, number = {12}, pages = {e0167353}, pmid = {27936055}, issn = {1932-6203}, support = {U54 FD004330/FD/FDA HHS/United States ; }, mesh = {Bacteria/classification/genetics/*isolation & purification ; Bacteroidetes/classification/genetics/isolation & purification ; Biodiversity ; Firmicutes/classification/genetics/isolation & purification ; Haiti ; Humans ; *Metagenomics ; Proteobacteria/classification/genetics/isolation & purification ; RNA, Bacterial/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics/*isolation & purification ; *Water Microbiology ; }, abstract = {Haiti endures the poorest water and sanitation infrastructure in the Western Hemisphere, where waterborne diseases cause significant morbidity and mortality. Most of these diseases are reported to be caused by waterborne pathogens. In this study, we examined the overall bacterial diversity of selected source and point-of-use water from rural areas in Central Plateau, Haiti using pyrosequencing of 16s rRNA genes. Taxonomic composition of water samples revealed an abundance of Firmicutes phyla, followed by Proteobacteria and Bacteroidetes. A total of 38 bacterial families and 60 genera were identified. The presence of several Klebsiella spp. (tentatively, K. pneumoniae, K. variicola and other Klebsiella spp.) was detected in most water samples. Several other human pathogens such as Aeromonas, Bacillus, Clostridium, and Yersinia constituted significantly higher proportion of bacterial communities in the point-of-use water samples compared to source water. Bacterial genera traditionally associated with biofilm formation, such as Chryseobacterium, Fusobacterium, Prevotella, Pseudomonas were found in the point-of-use waters obtained from water filters or domestic water storage containers. Although the pyrosequencing method utilized in this study did not reveal the viability status of these pathogens, the abundance of genetic footprints of the pathogens in water samples indicate the probable risk of bacterial transmission to humans. Therefore, the importance of appropriate handling, purification, and treatment of the source water needed to be clearly communicated to the communities in rural Haiti to ensure the water is safe for their daily use and intake.}, } @article {pmid27935837, year = {2016}, author = {Vineis, JH and Ringus, DL and Morrison, HG and Delmont, TO and Dalal, S and Raffals, LH and Antonopoulos, DA and Rubin, DT and Eren, AM and Chang, EB and Sogin, ML}, title = {Patient-Specific Bacteroides Genome Variants in Pouchitis.}, journal = {mBio}, volume = {7}, number = {6}, pages = {}, pmid = {27935837}, issn = {2150-7511}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; R01 DK047722/DK/NIDDK NIH HHS/United States ; R37 DK047722/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteroides/classification/*genetics/isolation & purification ; Bacteroides fragilis/genetics/isolation & purification ; Colitis, Ulcerative/complications/microbiology ; Colonic Pouches/microbiology ; Cross-Sectional Studies ; *Genetic Variation ; *Genome, Bacterial ; *Host-Pathogen Interactions ; Humans ; Ileum/anatomy & histology/microbiology ; Inflammation ; Longitudinal Studies ; Metagenomics/methods ; *Microbiota ; Mucous Membrane/microbiology ; Pouchitis/drug therapy/*microbiology ; Prospective Studies ; }, abstract = {UNLABELLED: A 2-year longitudinal microbiome study of 22 patients who underwent colectomy with an ileal pouch anal anastomosis detected significant increases in distinct populations of Bacteroides during 9 of 11 patient visits that coincided with inflammation (pouchitis). Oligotyping and metagenomic short-read annotation identified Bacteroides populations that occurred in early samples, bloomed during inflammation, and reappeared after antibiotic treatment. Targeted cultivation of Bacteroides isolates from the same individual at multiple time points and from several patients detected subtle genomic changes, including the identification of rapidly evolving genomic elements that differentiate isogenic strains of Bacteroides fragilis from the mucosa versus lumen. Each patient harbored Bacteroides spp. that are closely related to commonly occurring clinical isolates, including Bacteroides ovatus, B. thetaiotaomicron, B. vulgatus, and B. fragilis, which contained unique loci in different patients for synthesis of capsular polysaccharides. The presence of unique Bacteroides capsular polysaccharide loci within different hosts and between the lumen and mucosa may represent adaptations to stimulate, suppress, and evade host-specific immune responses at different microsites of the ileal pouch.

IMPORTANCE: This longitudinal study provides an opportunity to describe shifts in the microbiomes of individual patients who suffer from ulcerative colitis (UC) prior to and following inflammation. Pouchitis serves as a model for UC with a predictable incidence of disease onset and enables prospective longitudinal investigations of UC etiology prior to inflammation. Because of insufficient criteria for predicting which patients will develop UC or pouchitis, the interpretation of cross-sectional study designs suffers from lack of information about the microbiome structure and host gene expression patterns that directly correlate with the onset of disease. Our unique longitudinal study design allows each patient to serve as their own control, providing information about the state of the microbiome and host prior to and during the course of disease. Of significance to the broader community, this study identifies microbial strains that may have genetic elements that trigger the onset of disease in susceptible hosts.}, } @article {pmid27935222, year = {2017}, author = {Marcus, DN and Pinto, A and Anantharaman, K and Ruberg, SA and Kramer, EL and Raskin, L and Dick, GJ}, title = {Diverse manganese(II)-oxidizing bacteria are prevalent in drinking water systems.}, journal = {Environmental microbiology reports}, volume = {9}, number = {2}, pages = {120-128}, doi = {10.1111/1758-2229.12508}, pmid = {27935222}, issn = {1758-2229}, mesh = {Bacteria/*classification/genetics/*isolation & purification/metabolism ; Bacteriological Techniques ; *Biodiversity ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Drinking Water/*microbiology ; Manganese/*metabolism ; Metagenomics ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Manganese (Mn) oxides are highly reactive minerals that influence the speciation, mobility, bioavailability and toxicity of a wide variety of organic and inorganic compounds. Although Mn(II)-oxidizing bacteria are known to catalyze the formation of Mn oxides, little is known about the organisms responsible for Mn oxidation in situ, especially in engineered environments. Mn(II)-oxidizing bacteria are important in drinking water systems, including in biofiltration and water distribution systems. Here, we used cultivation dependent and independent approaches to investigate Mn(II)-oxidizing bacteria in drinking water sources, a treatment plant and associated distribution system. We isolated 29 strains of Mn(II)-oxidizing bacteria and found that highly similar 16S rRNA gene sequences were present in all culture-independent datasets and dominant in the studied drinking water treatment plant. These results highlight a potentially important role for Mn(II)-oxidizing bacteria in drinking water systems, where biogenic Mn oxides may affect water quality in terms of aesthetic appearance, speciation of metals and oxidation of organic and inorganic compounds. Deciphering the ecology of these organisms and the factors that regulate their Mn(II)-oxidizing activity could yield important insights into how microbial communities influence the quality of drinking water.}, } @article {pmid27925857, year = {2016}, author = {Samuelson, DR and Charles, TP and de la Rua, NM and Taylor, CM and Blanchard, EE and Luo, M and Shellito, JE and Welsh, DA}, title = {Analysis of the intestinal microbial community and inferred functional capacities during the host response to Pneumocystis pneumonia.}, journal = {Experimental lung research}, volume = {42}, number = {8-10}, pages = {425-439}, pmid = {27925857}, issn = {1521-0499}, support = {P01 HL076100/HL/NHLBI NIH HHS/United States ; P60 AA009803/AA/NIAAA NIH HHS/United States ; R24 AA019661/AA/NIAAA NIH HHS/United States ; U54 GM104940/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Carbohydrate Metabolism ; Energy Metabolism ; *Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Mice ; Mice, Inbred C57BL ; Pneumonia, Pneumocystis/metabolism/*microbiology ; Signal Transduction ; Xenobiotics ; }, abstract = {BACKGROUND: Pneumocystis pneumonia is a major cause of morbidity and mortality in patients infected with HIV/AIDS. In this study, we evaluated the intestinal microbial communities associated with the development of experimental Pneumocystis pneumonia, as there is growing evidence that the intestinal microbiota is critical for host defense against fungal pathogens.

METHODS: C57BL/6 mice were infected with live Pneumocystis murina (P. murina) via intratracheal inoculation and sacrificed 7 and 14 days postinfection for microbiota analysis. In addition, we evaluated the intestinal microbiota from CD4+ T cell depleted mice infected with P. murina.

RESULTS: We found that the diversity of the intestinal microbial community was significantly altered by respiratory infection with P. murina. Specifically, mice infected with P. murina had altered microbial populations, as judged by changes in diversity metrics and relative taxa abundances. We also found that CD4+ T cell depleted mice infected with P. murina exhibited significantly altered intestinal microbiota that was distinct from immunocompetent mice infected with P. murina, suggesting that loss of CD4+ T cells may also affects the intestinal microbiota in the setting of Pneumocystis pneumonia. Finally, we employed a predictive metagenomics approach to evaluate various microbial features. We found that Pneumocystis pneumonia significantly alters the intestinal microbiota's inferred functional potential for carbohydrate, energy, and xenobiotic metabolism, as well as signal transduction pathways.

CONCLUSIONS: Our study provides insight into specific-microbial clades and inferred microbial functional pathways associated with Pneumocystis pneumonia. Our data also suggest a role for the gut-lung axis in host defense in the lung.}, } @article {pmid27924593, year = {2017}, author = {Lawley, B and Tannock, GW}, title = {Analysis of 16S rRNA Gene Amplicon Sequences Using the QIIME Software Package.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1537}, number = {}, pages = {153-163}, doi = {10.1007/978-1-4939-6685-1_9}, pmid = {27924593}, issn = {1940-6029}, mesh = {Algorithms ; Biodiversity ; *Computational Biology/methods ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; RNA, Ribosomal, 16S/*genetics ; *Software ; Web Browser ; }, abstract = {The study of microbial ecology has undergone a paradigm shift in recent years, with rapid advances in molecular and bioinformatic tools allowing researchers with wide-ranging interests and backgrounds access to community profiling methods. While these advances have undoubtedly led to exciting new understanding of many systems, the array of protocols available and the idiosyncrasies of particular approaches can lead to confusion or, at worst, erroneous interpretation of results. Here, we describe a workflow from raw 16S rRNA gene amplicon sequence data, generated on an Illumina MiSeq instrument, to microbial community taxonomy profiles and basic diversity measures. The workflow can be adapted to input from major sequence platforms and uses freely available open source software that can be implemented on a range of operating systems.}, } @article {pmid27924592, year = {2017}, author = {Siqueira, JF and Sakamoto, M and Rosado, AS}, title = {Microbial Community Profiling Using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and Denaturing Gradient Gel Electrophoresis (DGGE).}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1537}, number = {}, pages = {139-152}, doi = {10.1007/978-1-4939-6685-1_8}, pmid = {27924592}, issn = {1940-6029}, mesh = {*Denaturing Gradient Gel Electrophoresis/methods ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Mouth/microbiology ; Polymerase Chain Reaction ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In their natural environments, microorganisms usually live in organized communities. Profiling analysis of microbial communities has recently assumed special relevance as it allows a thorough understanding of the diversity of the microbiota, its behavior over time, and the establishment of patterns associated with health and disease. The application of molecular biology approaches holds the advantage of including culture-difficult and as-yet-uncultivated phylotypes in the profiles, providing a more comprehensive picture of the microbial community. This chapter focuses on two particular techniques, namely, terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE), both of which have been widely used in environmental studies and have been successfully used by the authors in the study of the oral microbial communities associated with conditions of health and disease.}, } @article {pmid27924591, year = {2017}, author = {Siqueira, JF and Rôças, IN}, title = {The Oral Microbiota in Health and Disease: An Overview of Molecular Findings.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1537}, number = {}, pages = {127-138}, doi = {10.1007/978-1-4939-6685-1_7}, pmid = {27924591}, issn = {1940-6029}, mesh = {Animals ; Bacteria/classification/genetics ; Biodiversity ; *Disease Susceptibility ; Host-Pathogen Interactions ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Mouth/*microbiology ; Mouth Diseases/microbiology ; Tooth Diseases/microbiology ; }, abstract = {Culture-independent nucleic acid technologies have been extensively applied to the analysis of oral bacterial communities associated with healthy and diseased conditions. These methods have confirmed and substantially expanded the findings from culture studies to reveal the oral microbial inhabitants and candidate pathogens associated with the major oral diseases. Over 1000 bacterial distinct species-level taxa have been identified in the oral cavity and studies using next-generation DNA sequencing approaches indicate that the breadth of bacterial diversity may be even much larger. Nucleic acid technologies have also been helpful in profiling bacterial communities and identifying disease-related patterns. This chapter provides an overview of the diversity and taxonomy of oral bacteria associated with health and disease.}, } @article {pmid27923606, year = {2017}, author = {Durand, GA and Pham, T and Ndongo, S and Traore, SI and Dubourg, G and Lagier, JC and Michelle, C and Armstrong, N and Fournier, PE and Raoult, D and Million, M}, title = {Blautia massiliensis sp. nov., isolated from a fresh human fecal sample and emended description of the genus Blautia.}, journal = {Anaerobe}, volume = {43}, number = {}, pages = {47-55}, doi = {10.1016/j.anaerobe.2016.12.001}, pmid = {27923606}, issn = {1095-8274}, mesh = {Adult ; Clostridiales/*classification/genetics/isolation & purification ; DNA, Bacterial/chemistry/genetics ; Fatty Acids/analysis ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genome, Bacterial/*genetics ; Humans ; Male ; Metagenome ; Molecular Sequence Annotation ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/genetics ; Sequence Analysis, DNA ; }, abstract = {The strain GD9[T] is the type strain of the newly proposed species Blautia massiliensis sp. nov., belonging to the family Lachnospiraceae. It was isolated from a fresh stool sample collected from a healthy human using the culturomics strategy. Cells are Gram-negative rods, oxygen intolerant, non-motile and non-spore forming. The 16S rRNA gene sequencing showed that strain GD9[T] was closely related to Blautia luti, with a 97.8% sequence similarity. Major fatty acids were C14:0 (19.8%) and C16:0 (53.2%). Strain GD9[T] exhibits a genome of 3,717,339 bp that contains 3,346 protein-coding genes and 81 RNAs genes including 63 tRNAs. The features of this organism are described here, with its complete genome sequence and annotation. Compared with other Blautia species which are Gram positive, the strain was Gram negative justifying an emended description of the genus Blautia.}, } @article {pmid27918579, year = {2016}, author = {Tang, H and Li, S and Ye, Y}, title = {A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics.}, journal = {PLoS computational biology}, volume = {12}, number = {12}, pages = {e1005224}, pmid = {27918579}, issn = {1553-7358}, support = {R01 AI108888/AI/NIAID NIH HHS/United States ; R01 GM103725/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Peptides/classification/genetics ; Proteins/*classification/*genetics ; Proteomics/*methods ; Tandem Mass Spectrometry ; }, abstract = {Metaproteomic studies adopt the common bottom-up proteomics approach to investigate the protein composition and the dynamics of protein expression in microbial communities. When matched metagenomic and/or metatranscriptomic data of the microbial communities are available, metaproteomic data analyses often employ a metagenome-guided approach, in which complete or fragmental protein-coding genes are first directly predicted from metagenomic (and/or metatranscriptomic) sequences or from their assemblies, and the resulting protein sequences are then used as the reference database for peptide/protein identification from MS/MS spectra. This approach is often limited because protein coding genes predicted from metagenomes are incomplete and fragmental. In this paper, we present a graph-centric approach to improving metagenome-guided peptide and protein identification in metaproteomics. Our method exploits the de Bruijn graph structure reported by metagenome assembly algorithms to generate a comprehensive database of protein sequences encoded in the community. We tested our method using several public metaproteomic datasets with matched metagenomic and metatranscriptomic sequencing data acquired from complex microbial communities in a biological wastewater treatment plant. The results showed that many more peptides and proteins can be identified when assembly graphs were utilized, improving the characterization of the proteins expressed in the microbial communities. The additional proteins we identified contribute to the characterization of important pathways such as those involved in degradation of chemical hazards. Our tools are released as open-source software on github at https://github.com/COL-IU/Graph2Pro.}, } @article {pmid27918230, year = {2017}, author = {Velly, H and Britton, RA and Preidis, GA}, title = {Mechanisms of cross-talk between the diet, the intestinal microbiome, and the undernourished host.}, journal = {Gut microbes}, volume = {8}, number = {2}, pages = {98-112}, pmid = {27918230}, issn = {1949-0984}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; T32 DK007664/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Malnutrition/metabolism/*microbiology ; }, abstract = {Undernutrition remains one of the most pressing global health challenges today, contributing to nearly half of all deaths in children under five years of age. Although insufficient dietary intake and environmental enteric dysfunction are often inciting factors, evidence now suggests that unhealthy gut microbial populations perpetuate the vicious cycle of pathophysiology that results in persistent growth impairment in children. The metagenomics era has facilitated new research identifying an altered microbiome in undernourished hosts and has provided insight into a number of mechanisms by which these alterations may affect growth. This article summarizes a range of observational studies that highlight differences in the composition and function of gut microbiota between undernourished and healthy children; discusses dietary, environmental and host factors that shape this altered microbiome; examines the consequences of these changes on host physiology; and considers opportunities for microbiome-targeting therapies to combat the global challenge of child undernutrition.}, } @article {pmid27916477, year = {2016}, author = {Devlin, AS and Marcobal, A and Dodd, D and Nayfach, S and Plummer, N and Meyer, T and Pollard, KS and Sonnenburg, JL and Fischbach, MA}, title = {Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota.}, journal = {Cell host & microbe}, volume = {20}, number = {6}, pages = {709-715}, pmid = {27916477}, issn = {1934-6069}, support = {R01 DK085025/DK/NIDDK NIH HHS/United States ; R01 DK101674/DK/NIDDK NIH HHS/United States ; T32 GM067547/GM/NIGMS NIH HHS/United States ; }, mesh = {Animal Feed ; Animals ; Bacteria/drug effects/enzymology/genetics/metabolism ; Bacteroides/enzymology/genetics ; Diet ; Disease Models, Animal ; Disease Progression ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/*microbiology ; Genetic Engineering ; Germ-Free Life/drug effects ; Humans ; Indican/*metabolism/*toxicity ; Indoles/metabolism ; Metagenome ; Mice ; Microbiota/genetics ; Renal Insufficiency, Chronic ; Toxins, Biological/biosynthesis/urine ; Tryptophan/metabolism ; Tryptophanase/metabolism ; }, abstract = {Renal disease is growing in prevalence and has striking co-morbidities with metabolic and cardiovascular disease. Indoxyl sulfate (IS) is a toxin that accumulates in plasma when kidney function declines and contributes to the progression of chronic kidney disease. IS derives exclusively from the gut microbiota. Bacterial tryptophanases convert tryptophan to indole, which is absorbed and modified by the host to produce IS. Here, we identify a widely distributed family of tryptophanases in the gut commensal Bacteroides and find that deleting this gene eliminates the production of indole in vitro. By altering the status or abundance of the Bacteroides tryptophanase, we can modulate IS levels in gnotobiotic mice and in the background of a conventional murine gut community. Our results demonstrate that it is possible to control host IS levels by targeting the microbiota and suggest a possible strategy for treating renal disease.}, } @article {pmid27915377, year = {2017}, author = {Kim, J and Seok, SH and Hong, E and Yoo, TH and Seo, MD and Ryu, Y}, title = {Crystal structure and characterization of esterase Est25 mutants reveal improved enantioselectivity toward (S)-ketoprofen ethyl ester.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {6}, pages = {2333-2342}, doi = {10.1007/s00253-016-7989-3}, pmid = {27915377}, issn = {1432-0614}, mesh = {Anti-Inflammatory Agents, Non-Steroidal ; Bacterial Proteins/*chemistry/genetics/metabolism ; Cloning, Molecular ; Crystallography, X-Ray ; Escherichia coli/genetics/metabolism ; Esterases/*chemistry/genetics/metabolism ; Esters ; Gene Expression ; Genomic Library ; Ketoprofen/*chemistry/metabolism ; Kinetics ; *Metagenome ; Microbial Consortia/genetics ; Models, Molecular ; Mutation ; Protein Domains ; Protein Structure, Secondary ; Recombinant Proteins/chemistry/genetics/metabolism ; *Soil Microbiology ; Stereoisomerism ; Substrate Specificity ; }, abstract = {Esterases comprise a group of enzymes that catalyze the cleavage and synthesis of ester bonds. They are important in biotechnological applications owing to their enantioselectivity, regioselectivity, broad substrate specificity, and the fact that they do not require cofactors. In a previous study, we isolated the esterase Est25 from a metagenomic library. Est25 showed catalytic activity toward the (R,S)-ketoprofen ethyl ester but had low enantioselectivity toward the (S)-ketoprofen ethyl ester. Because (S)-ketoprofen has stronger anti-inflammatory effects and fewer side effects than (R)-ketoprofen, enantioselectivity of this esterase is important. In this study, we generated Est25 mutants with improved enantioselectivity toward the (S)-ketoprofen ethyl ester; improved enantioselectivity of mutants was established by analysis of their crystal structures. The enantioselectivity of mutants was influenced by substitution of Phe72 and Leu255. Substituting these residues changed the size of the binding pocket and the entrance hole that leads to the active site. The enantioselectivity of Est25 (E = 1.1 ± 0.0) was improved in the mutants F72G (E = 1.9 ± 0.2), L255W (E = 16.1 ± 1.1), and F72G/L255W (E = 60.1 ± 0.5). Finally, characterization of Est25 mutants was performed by determining the optimum reaction conditions, thermostability, effect of additives, and substrate specificity after substituting Phe72 and Leu255.}, } @article {pmid27915284, year = {2017}, author = {Kashinskaya, EN and Andree, KB and Simonov, EP and Solovyev, MM}, title = {DNA extraction protocols may influence biodiversity detected in the intestinal microbiome: a case study from wild Prussian carp, Carassius gibelio.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {2}, pages = {}, doi = {10.1093/femsec/fiw240}, pmid = {27915284}, issn = {1574-6941}, mesh = {Animals ; Bacteria/genetics ; Biodiversity ; Carps/*microbiology/physiology ; DNA ; Fresh Water ; Gastrointestinal Microbiome/*genetics ; Intestines/*microbiology ; }, abstract = {In this investigation, we examined the influence of different DNA extraction protocols on results obtained for intestinal microbiota of Prussian carp. We showed that significant differences were observed in numbers of reads, OTUs, Shannon index and taxonomic composition between two different DNA extraction protocols for intestine of Prussian carp (Carassius gibelio), and differences were also evident between microbial communities in the intestinal mucosa and intestinal content. Statistical analyses of 25 published articles also revealed a significant relationship between methods of DNA extraction and bacterial diversity in fish intestine of freshwater species. Microbial diversity, community structure, proportions of read numbers derived from each OTU and the total number of OTU's obtained by different DNA extraction protocols could lead to a bias in results obtained in some cases, and therefore researchers should be conservative in conclusions about community structures.}, } @article {pmid27912785, year = {2016}, author = {Ly, M and Jones, MB and Abeles, SR and Santiago-Rodriguez, TM and Gao, J and Chan, IC and Ghose, C and Pride, DT}, title = {Transmission of viruses via our microbiomes.}, journal = {Microbiome}, volume = {4}, number = {1}, pages = {64}, pmid = {27912785}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/administration & dosage/pharmacology ; Bacteriophages/classification/*isolation & purification ; Family Characteristics ; Feces/microbiology/*virology ; Humans ; Metagenome/drug effects ; Microbiota ; Saliva/microbiology/*virology ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Bacteria inhabiting the human body have important roles in a number of physiological processes and are known to be shared amongst genetically-related individuals. Far less is known about viruses inhabiting the human body, but their ecology suggests they may be shared between close contacts.

RESULTS: Here, we report the ecology of viruses in the guts and mouths of a cohort and demonstrate that substantial numbers of gut and oral viruses were shared amongst genetically unrelated, cohabitating individuals. Most of these viruses were bacteriophages, and each individual had distinct oral and gut viral ecology from their housemates despite the fact that some of their bacteriophages were shared. The distribution of bacteriophages over time within households indicated that they were frequently transmitted between the microbiomes of household contacts.

CONCLUSIONS: Because bacteriophages may shape human oral and gut bacterial ecology, their transmission to household contacts suggests they could have substantial roles in shaping the microbiota within a household.}, } @article {pmid27912059, year = {2016}, author = {Thaiss, CA and Levy, M and Korem, T and Dohnalová, L and Shapiro, H and Jaitin, DA and David, E and Winter, DR and Gury-BenAri, M and Tatirovsky, E and Tuganbaev, T and Federici, S and Zmora, N and Zeevi, D and Dori-Bachash, M and Pevsner-Fischer, M and Kartvelishvily, E and Brandis, A and Harmelin, A and Shibolet, O and Halpern, Z and Honda, K and Amit, I and Segal, E and Elinav, E}, title = {Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations.}, journal = {Cell}, volume = {167}, number = {6}, pages = {1495-1510.e12}, doi = {10.1016/j.cell.2016.11.003}, pmid = {27912059}, issn = {1097-4172}, mesh = {Animals ; Chromatin/metabolism ; *Circadian Rhythm ; Colon/metabolism/*microbiology ; *Gastrointestinal Microbiome ; Germ-Free Life ; Liver/metabolism ; Mice ; Microscopy, Electron, Scanning ; *Transcriptome ; }, abstract = {The intestinal microbiota undergoes diurnal compositional and functional oscillations that affect metabolic homeostasis, but the mechanisms by which the rhythmic microbiota influences host circadian activity remain elusive. Using integrated multi-omics and imaging approaches, we demonstrate that the gut microbiota features oscillating biogeographical localization and metabolome patterns that determine the rhythmic exposure of the intestinal epithelium to different bacterial species and their metabolites over the course of a day. This diurnal microbial behavior drives, in turn, the global programming of the host circadian transcriptional, epigenetic, and metabolite oscillations. Surprisingly, disruption of homeostatic microbiome rhythmicity not only abrogates normal chromatin and transcriptional oscillations of the host, but also incites genome-wide de novo oscillations in both intestine and liver, thereby impacting diurnal fluctuations of host physiology and disease susceptibility. As such, the rhythmic biogeography and metabolome of the intestinal microbiota regulates the temporal organization and functional outcome of host transcriptional and epigenetic programs.}, } @article {pmid27911822, year = {2016}, author = {Charlop-Powers, Z and Pregitzer, CC and Lemetre, C and Ternei, MA and Maniko, J and Hover, BM and Calle, PY and McGuire, KL and Garbarino, J and Forgione, HM and Charlop-Powers, S and Brady, SF}, title = {Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {51}, pages = {14811-14816}, pmid = {27911822}, issn = {1091-6490}, support = {F32 AI110029/AI/NIAID NIH HHS/United States ; U01 GM110714/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Biodiversity ; Biological Products ; Drug Design ; Metagenome ; Microbiota ; New York City ; *Parks, Recreational ; Phylogeny ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Numerous therapeutically relevant small molecules have been identified from the screening of natural products (NPs) produced by environmental bacteria. These discovery efforts have principally focused on culturing bacteria from natural environments rich in biodiversity. We sought to assess the biosynthetic capacity of urban soil environments using a phylogenetic analysis of conserved NP biosynthetic genes amplified directly from DNA isolated from New York City park soils. By sequencing genes involved in the biosynthesis of nonribosomal peptides and polyketides, we found that urban park soil microbiomes are both rich in biosynthetic diversity and distinct from nonurban samples in their biosynthetic gene composition. A comparison of sequences derived from New York City parks to genes involved in the biosynthesis of biomedically important NPs produced by bacteria originally collected from natural environments around the world suggests that bacteria producing these same families of clinically important antibiotics, antifungals, and anticancer agents are actually present in the soils of New York City. The identification of new bacterial NPs often centers on the systematic exploration of bacteria present in natural environments. Here, we find that the soil microbiomes found in large cities likely hold similar promise as rich unexplored sources of clinically relevant NPs.}, } @article {pmid27907121, year = {2016}, author = {Gourmelon, V and Maggia, L and Powell, JR and Gigante, S and Hortal, S and Gueunier, C and Letellier, K and Carriconde, F}, title = {Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach.}, journal = {PloS one}, volume = {11}, number = {12}, pages = {e0167405}, pmid = {27907121}, issn = {1932-6203}, mesh = {Bacteria/genetics ; *Ecosystem ; Fungi/genetics ; Genetic Variation ; *Metagenomics ; New Caledonia ; RNA, Ribosomal, 16S/*genetics ; *Soil Microbiology ; }, abstract = {Soil microorganisms play key roles in ecosystem functioning and are known to be influenced by biotic and abiotic factors, such as plant cover or edaphic parameters. New Caledonia, a biodiversity hotspot located in the southwest Pacific, is one-third covered by ultramafic substrates. These types of soils are notably characterised by low nutrient content and high heavy metal concentrations. Ultramafic outcrops harbour diverse vegetation types and remarkable plant diversity. In this study, we aimed to assess soil bacterial and fungal diversity in New Caledonian ultramafic substrates and to determine whether floristic composition, edaphic parameters and geographical factors affect this microbial diversity. Therefore, four plant formation types at two distinct sites were studied. These formations represent different stages in a potential chronosequence. Soil cores, according to a given sampling procedure, were collected to assess microbial diversity using a metagenomic approach, and to characterise the physico-chemical parameters. A botanical inventory was also performed. Our results indicated that microbial richness, composition and abundance were linked to the plant cover type and the dominant plant species. Furthermore, a large proportion of Ascomycota phylum (fungi), mostly in non-rainforest formations, and Planctomycetes phylum (bacteria) in all formations were observed. Interestingly, such patterns could be indicators of past disturbances that occurred on different time scales. Furthermore, the bacteria and fungi were influenced by diverse edaphic parameters as well as by the interplay between these two soil communities. Another striking finding was the existence of a site effect. Differences in microbial communities between geographical locations may be explained by dispersal limitation in the context of the biogeographical island theory. In conclusion, each plant formation at each site possesses is own microbial community resulting from multiple interactions between abiotic and biotic factors.}, } @article {pmid27901108, year = {2016}, author = {Vannier, T and Leconte, J and Seeleuthner, Y and Mondy, S and Pelletier, E and Aury, JM and de Vargas, C and Sieracki, M and Iudicone, D and Vaulot, D and Wincker, P and Jaillon, O}, title = {Survey of the green picoalga Bathycoccus genomes in the global ocean.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {37900}, pmid = {27901108}, issn = {2045-2322}, mesh = {Chlorophyta/*genetics ; Ecotype ; Genomics/methods ; Metagenome/*genetics ; Metagenomics/methods ; Microalgae/*genetics ; Oceans and Seas ; Phylogeny ; Phytoplankton/*genetics ; RNA, Ribosomal, 18S/genetics ; Seawater ; Surveys and Questionnaires ; }, abstract = {Bathycoccus is a cosmopolitan green micro-alga belonging to the Mamiellophyceae, a class of picophytoplankton that contains important contributors to oceanic primary production. A single species of Bathycoccus has been described while the existence of two ecotypes has been proposed based on metagenomic data. A genome is available for one strain corresponding to the described phenotype. We report a second genome assembly obtained by a single cell genomics approach corresponding to the second ecotype. The two Bathycoccus genomes are divergent enough to be unambiguously distinguishable in whole DNA metagenomic data although they possess identical sequence of the 18S rRNA gene including in the V9 region. Analysis of 122 global ocean whole DNA metagenome samples from the Tara-Oceans expedition reveals that populations of Bathycoccus that were previously identified by 18S rRNA V9 metabarcodes are only composed of these two genomes. Bathycoccus is relatively abundant and widely distributed in nutrient rich waters. The two genomes rarely co-occur and occupy distinct oceanic niches in particular with respect to depth. Metatranscriptomic data provide evidence for gain or loss of highly expressed genes in some samples, suggesting that the gene repertoire is modulated by environmental conditions.}, } @article {pmid27900698, year = {2017}, author = {Reen, FJ and Gutiérrez-Barranquero, JA and O'Gara, F}, title = {Mining Microbial Signals for Enhanced Biodiscovery of Secondary Metabolites.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1539}, number = {}, pages = {287-300}, doi = {10.1007/978-1-4939-6691-2_19}, pmid = {27900698}, issn = {1940-6029}, mesh = {*Biodiversity ; Biosensing Techniques ; Chromatography, High Pressure Liquid ; Data Mining/*methods ; Gene Library ; High-Throughput Screening Assays ; Mass Spectrometry ; Metabolomics/methods ; Metagenomics/methods ; *Microbial Interactions ; *Microbiota ; Quorum Sensing/genetics ; *Secondary Metabolism ; *Signal Transduction ; }, abstract = {The advent of metagenomics based biodiscovery has provided researchers with previously unforeseen access to the rich tapestry of natural bioactivity that exists in the biosphere. Unhindered by the "culturable bottleneck" that has severely limited the translation of the genetic potential that undoubtedly exists in nature, metagenomics nonetheless requires ongoing technological developments to maximize its efficacy and applicability to the discovery of new chemical entities.Here we describe methodologies for the detection and isolation of quorum sensing (QS) signal molecules from metagenomics libraries. QS signals have already shown considerable potential for the activation and "awakening" of biosynthetic gene clusters, bridging the existing divide between the natural product repertoire and the natural biosynthetic biodiversity hinted at by nature's blueprint. The QS pipeline from high-throughput robotics to functional screening and hit isolation is detailed, highlighting the multidisciplinary nature of progressive biodiscovery programs.}, } @article {pmid27900685, year = {2017}, author = {Wemheuer, B and Wemheuer, F}, title = {Assessing Bacterial and Fungal Diversity in the Plant Endosphere.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1539}, number = {}, pages = {75-84}, doi = {10.1007/978-1-4939-6691-2_6}, pmid = {27900685}, issn = {1940-6029}, mesh = {Bacteria/*classification/*genetics ; Biodiversity ; Computational Biology/methods ; DNA Barcoding, Taxonomic ; *Endophytes ; Fungi/*classification/*genetics ; Metagenome ; Metagenomics/methods ; Phylogeny ; Plants/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Plants are colonized various microorganisms including endophytes. These microbes can play an important role in agricultural production as they promote plant growth and/or enhance the resistance of their host plant against diseases and environmental stress conditions. Although culture-independent molecular approaches such as DNA barcoding have greatly enhanced our understanding of bacterial and fungal endophyte communities, there are some methodical problems when investigating endophyte diversity. One main issue are sequence contaminations such as plastid-derived rRNA gene sequences which are co-amplified due to their high homology to bacterial 16S rRNA genes. The same is true for plant and fungal ITS sequences. The application of highly specific-primers suppressing co-amplification of these sequence contaminations is a good solution for this issue. Here, we describe a detailed protocol for assessing bacterial and fungal endophyte diversity in plants using these primers in combination with next-generation sequencing.}, } @article {pmid27900684, year = {2017}, author = {Jameson, E and Taubert, M and Coyotzi, S and Chen, Y and Eyice, Ö and Schäfer, H and Murrell, JC and Neufeld, JD and Dumont, MG}, title = {DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1539}, number = {}, pages = {57-74}, doi = {10.1007/978-1-4939-6691-2_5}, pmid = {27900684}, issn = {1940-6029}, mesh = {*Biomarkers ; DNA/chemistry/genetics ; Gene Expression Profiling/methods ; *High-Throughput Screening Assays ; *Isotope Labeling/methods ; Metagenome ; Metagenomics/methods ; *Microbiota ; *Molecular Probes ; Proteins/chemistry ; Proteomics/methods ; RNA/chemistry/genetics ; }, abstract = {Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of [13]C, [18]O, or [15]N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labeled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labeled populations by targeted gene analysis. Such approaches usually involved fingerprint-based analyses or sequencing of clone libraries containing 16S rRNA genes or functional marker gene amplicons. Although molecular fingerprinting remains a valuable approach for rapid confirmation of isotope labeling, recent advances in sequencing technology mean that it is possible to obtain affordable and comprehensive amplicon profiles, metagenomes, or metatranscriptomes from SIP experiments. Not only can the abundance of microbial groups be inferred from metagenomes, but researchers can bin, assemble, and explore individual genomes to build hypotheses about the metabolic capabilities of labeled microorganisms. Analysis of labeled mRNA is a more recent advance that can provide independent metatranscriptome-based analysis of active microorganisms. The power of metatranscriptomics is that mRNA abundance often correlates closely with the corresponding activity of encoded enzymes, thus providing insight into microbial metabolism at the time of sampling. Together, these advances have improved the sensitivity of SIP methods and allow the use of labeled substrates at ecologically relevant concentrations. Particularly as methods improve and costs continue to drop, we expect that the integration of SIP with multiple omics-based methods will become prevalent components of microbial ecology studies, leading to further breakthroughs in our understanding of novel microbial populations and elucidation of the metabolic function of complex microbial communities. In this chapter we provide protocols for obtaining labeled DNA, RNA, and proteins that can be used for downstream omics-based analyses.}, } @article {pmid27900682, year = {2017}, author = {Weiland-Bräuer, N and Langfeldt, D and Schmitz, RA}, title = {Construction and Screening of Marine Metagenomic Large Insert Libraries.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1539}, number = {}, pages = {23-42}, doi = {10.1007/978-1-4939-6691-2_3}, pmid = {27900682}, issn = {1940-6029}, mesh = {Aquatic Organisms/classification/*genetics ; *Gene Library ; Genetic Vectors ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; *Mutagenesis, Insertional ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Water Microbiology ; }, abstract = {The marine environment covers more than 70 % of the world's surface. Marine microbial communities are highly diverse and have evolved during extended evolutionary processes of physiological adaptations under the influence of a variety of ecological conditions and selection pressures. They harbor an enormous diversity of microbes with still unknown and probably new physiological characteristics. In the past, marine microbes, mostly bacteria of microbial consortia attached to marine tissues of multicellular organisms, have proven to be a rich source of highly potent bioactive compounds, which represent a considerable number of drug candidates. However, to date, the biodiversity of marine microbes and the versatility of their bioactive compounds and metabolites have not been fully explored. This chapter describes sampling in the marine environment, construction of metagenomic large insert libraries from marine habitats, and exemplarily one function based screen of metagenomic clones for identification of quorum quenching activities.}, } @article {pmid27900681, year = {2017}, author = {Schneider, D and Wemheuer, F and Pfeiffer, B and Wemheuer, B}, title = {Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a cDNA as Universal Template for Marker Gene Studies.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1539}, number = {}, pages = {13-22}, doi = {10.1007/978-1-4939-6691-2_2}, pmid = {27900681}, issn = {1940-6029}, mesh = {Aquatic Organisms/*genetics ; Biodiversity ; *DNA ; *DNA, Complementary ; Genetic Markers ; Marine Biology/methods ; *Metagenome ; *Metagenomics/methods ; *RNA ; }, abstract = {Microbial communities play an important role in marine ecosystem processes. Although the number of studies targeting marker genes such as the 16S rRNA gene has been increased in the last few years, the vast majority of marine diversity is rather unexplored. Moreover, most studies focused on the entire bacterial community and thus disregarded active microbial community players. Here, we describe a detailed protocol for the simultaneous extraction of DNA and RNA from marine water samples and for the generation of cDNA from the isolated RNA which can be used as a universal template in various marker gene studies.}, } @article {pmid27899624, year = {2017}, author = {Vallenet, D and Calteau, A and Cruveiller, S and Gachet, M and Lajus, A and Josso, A and Mercier, J and Renaux, A and Rollin, J and Rouy, Z and Roche, D and Scarpelli, C and Médigue, C}, title = {MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.}, journal = {Nucleic acids research}, volume = {45}, number = {D1}, pages = {D517-D528}, pmid = {27899624}, issn = {1362-4962}, mesh = {Computational Biology/methods ; *Databases, Genetic ; Evolution, Molecular ; Metabolome ; Metabolomics/methods ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Multigene Family ; Polymorphism, Single Nucleotide ; Software ; }, abstract = {The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can be extracted from genomes and metabolic models. Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Effective comparative analysis requires a consistent and complete view of biological data, and therefore, support for reviewing the quality of functional annotation is critical. MicroScope allows users to analyze microbial (meta)genomes together with post-genomic experiment results if any (i.e. transcriptomics, re-sequencing of evolved strains, mutant collections, phenotype data). It combines tools and graphical interfaces to analyze genomes and to perform the expert curation of gene functions in a comparative context. Starting with a short overview of the MicroScope system, this paper focuses on some major improvements of the Web interface, mainly for the submission of genomic data and on original tools and pipelines that have been developed and integrated in the platform: computation of pan-genomes and prediction of biosynthetic gene clusters. Today the resource contains data for more than 6000 microbial genomes, and among the 2700 personal accounts (65% of which are now from foreign countries), 14% of the users are performing expert annotations, on at least a weekly basis, contributing to improve the quality of microbial genome annotations.}, } @article {pmid27898265, year = {2017}, author = {Mazzola, M and Freilich, S}, title = {Prospects for Biological Soilborne Disease Control: Application of Indigenous Versus Synthetic Microbiomes.}, journal = {Phytopathology}, volume = {107}, number = {3}, pages = {256-263}, doi = {10.1094/PHYTO-09-16-0330-RVW}, pmid = {27898265}, issn = {0031-949X}, mesh = {Agriculture ; Biological Control Agents ; *Microbiota ; Pest Control, Biological/*methods ; Plant Diseases/microbiology/*prevention & control ; Rhizosphere ; Soil ; *Soil Microbiology ; }, abstract = {Biological disease control of soilborne plant diseases has traditionally employed the biopesticide approach whereby single strains or strain mixtures are introduced into production systems through inundative/inoculative release. The approach has significant barriers that have long been recognized, including a generally limited spectrum of target pathogens for any given biocontrol agent and inadequate colonization of the host rhizosphere, which can plague progress in the utilization of this resource in commercial field-based crop production systems. Thus, although potential exists, this model has continued to lag in its application. New omics' tools have enabled more rapid screening of microbial populations allowing for the identification of strains with multiple functional attributes that may contribute to pathogen suppression. Similarly, these technologies also enable the characterization of consortia in natural systems which provide the framework for construction of synthetic microbiomes for disease control. Harnessing the potential of the microbiome indigenous to agricultural soils for disease suppression through application of specific management strategies has long been a goal of plant pathologists. Although this tactic also possesses limitation, our enhanced understanding of functional attributes of suppressive soil systems through application of community and metagenomic analysis methods provide opportunity to devise effective resource management schemes. As these microbial communities in large part are fostered by the resources endemic to soil and the rhizosphere, substrate mediated recruitment of disease-suppressive microbiomes constitutes a practical means to foster their establishment in crop production systems.}, } @article {pmid27897429, year = {2017}, author = {Franzetti, A and Navarra, F and Tagliaferri, I and Gandolfi, I and Bestetti, G and Minora, U and Azzoni, RS and Diolaiuti, G and Smiraglia, C and Ambrosini, R}, title = {Temporal variability of bacterial communities in cryoconite on an alpine glacier.}, journal = {Environmental microbiology reports}, volume = {9}, number = {2}, pages = {71-78}, doi = {10.1111/1758-2229.12499}, pmid = {27897429}, issn = {1758-2229}, mesh = {Bacteria/*classification/*genetics ; *Biota ; High-Throughput Nucleotide Sequencing ; Ice Cover/*microbiology ; Italy ; Metagenomics ; Seasons ; }, abstract = {Cryoconite holes, that is, small ponds that form on glacier surface, are considered the most biologically active environments on glaciers. Bacterial communities in these environments have been extensively studied, but often through snapshot studies based on the assumption of a general stability of community structure. In this study, the temporal variation of bacterial communities in cryoconite holes on the Forni Glacier (Italian Alps) was investigated by high throughput DNA sequencing. A temporal change of bacterial communities was observed with autotrophic Cyanobacteria populations dominating communities after snowmelt, and heterotrophic Sphingobacteriales populations increasing in abundance later in the season. Bacterial communities also varied according to hole depth and area, amount of organic matter in the cryoconite and oxygen concentration. However, variation in environmental features explained a lower fraction of the variation in bacterial communities than temporal variation. Temporal change along ablation season seems therefore more important than local environmental conditions in shaping bacterial communities of cryoconite of the Forni Glacier. These findings challenge the assumption that bacterial communities of cryoconite holes are stable.}, } @article {pmid27894254, year = {2016}, author = {Ding, J and Zhao, L and Wang, L and Zhao, W and Zhai, Z and Leng, L and Wang, Y and He, C and Zhang, Y and Zhang, H and Li, H and Meng, H}, title = {Divergent selection-induced obesity alters the composition and functional pathways of chicken gut microbiota.}, journal = {Genetics, selection, evolution : GSE}, volume = {48}, number = {1}, pages = {93}, pmid = {27894254}, issn = {1297-9686}, mesh = {Animals ; Biodiversity ; *Body Composition ; Chickens ; Cluster Analysis ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Genetic Variation ; Male ; Metagenome ; Metagenomics/methods ; Molecular Sequence Annotation ; Obesity/*etiology ; RNA, Bacterial ; RNA, Ribosomal, 16S/genetics ; *Selection, Genetic ; }, abstract = {BACKGROUND: The gastrointestinal tract is populated by a complex and vast microbial network, with a composition that reflects the relationships of the symbiosis, co-metabolism, and co-evolution of these microorganisms with their host. The mechanism that underlies such interactions between the genetics of the host and gut microbiota remains elusive.

RESULTS: To understand how genetic variation of the host shapes the gut microbiota and interacts with it to affect the metabolic phenotype of the host, we compared the abundance of microbial taxa and their functional performance between two lines of chickens (fat and lean) that had undergone long-term divergent selection for abdominal fat pad weight, which resulted in a 4.5-fold increase in the fat line compared to the lean line. Our analysis revealed that the proportions of Fusobacteria and Proteobacteria differed significantly between the two lines (8 vs. 18% and 33 vs. 24%, respectively) at the phylum level. Eight bacterial genera and 11 species were also substantially influenced by the host genotype. Differences between the two lines in the frequency of host alleles at loci that influence accumulation of abdominal fat were associated with differences in the abundance and composition of the gut microbiota. Moreover, microbial genome functional analysis showed that the gut microbiota was involved in pathways that are associated with fat metabolism such as lipid and glycan biosynthesis, as well as amino acid and energy metabolism. Interestingly, citrate cycle and peroxisome proliferator activated receptor (PPAR) signaling pathways that play important roles in lipid storage and metabolism were more prevalent in the fat line than in the lean line.

CONCLUSIONS: Our study demonstrates that long-term divergent selection not only alters the composition of the gut microbiota, but also influences its functional performance by enriching its relative abundance in microbial taxa. These results support the hypothesis that the host and gut microbiota interact at the genetic level and that these interactions result in their co-evolution.}, } @article {pmid27894251, year = {2016}, author = {Oki, K and Toyama, M and Banno, T and Chonan, O and Benno, Y and Watanabe, K}, title = {Comprehensive analysis of the fecal microbiota of healthy Japanese adults reveals a new bacterial lineage associated with a phenotype characterized by a high frequency of bowel movements and a lean body type.}, journal = {BMC microbiology}, volume = {16}, number = {1}, pages = {284}, pmid = {27894251}, issn = {1471-2180}, mesh = {Activities of Daily Living ; Adult ; Aged ; Aged, 80 and over ; Bacteria/*classification/genetics/*isolation & purification ; DNA, Bacterial/genetics ; Defecation ; Feces/*microbiology ; Feeding Behavior ; Female ; Gastrointestinal Microbiome ; Humans ; Japan ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Phenotype ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Somatotypes ; }, abstract = {BACKGROUND: In Japan, a variety of traditional dietary habits and daily routines have developed in many regions. The effects of these behaviors, and the regional differences in the composition of the gut microbiota, are yet to be sufficiently studied. To characterize the Japanese gut microbiota and identify the factors shaping its composition, we conducted 16S metagenomics analysis of fecal samples collected from healthy Japanese adults residing in various regions of Japan. Each participant also completed a 94-question lifestyle questionnaire.

RESULTS: We collected fecal samples from 516 healthy Japanese adults (325 females, 191 males; age, 21-88). Heatmap and biplot analyses based on the bacterial family composition of the fecal microbiota showed that subjects' region of residence or gender were not strongly correlated with the general composition of the fecal microbiota. Although clustering analysis for the whole cohort did not reveal any distinct clusters, two enterotype-like clusters were observed in the male, but not the female, subjects. In the whole subject population, the scores for bowel movement frequency were significantly correlated with the abundances of Christensenellaceae, Mogibacteriaceae, and Rikenellaceae in the fecal microbiota (P < 0.001). These three bacterial families were also significantly more abundant (P < 0.05 or 0.01) in lean subjects (body mass index (BMI) < 25) than in obese subjects (BMI > 30), which is consistent with previously published results. However, a previously reported correlation between BMI and bowel movement frequency was not observed. In addition, the abundances of these three families were positively correlated with each other and comprised a correlative network with 14 other bacterial families.

CONCLUSIONS: The present study showed that the composition of the fecal microbiota of healthy Japanese adults at the national level was not strongly correlated with subjects' area of residence or gender. In addition, enterotype partitioning was ambiguous in this cohort of healthy Japanese adults. Finally, the results implied that the abundances of Christensenellaceae, Mogibacteriaceae, and Rikenellaceae, along with several other bacterial components that together comprised a correlative network, contributed to a phenotype characterized by a high frequency of bowel movements and a lean body type.}, } @article {pmid27893703, year = {2017}, author = {Magnúsdóttir, S and Heinken, A and Kutt, L and Ravcheev, DA and Bauer, E and Noronha, A and Greenhalgh, K and Jäger, C and Baginska, J and Wilmes, P and Fleming, RM and Thiele, I}, title = {Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota.}, journal = {Nature biotechnology}, volume = {35}, number = {1}, pages = {81-89}, doi = {10.1038/nbt.3703}, pmid = {27893703}, issn = {1546-1696}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Bacterial Proteins/*genetics ; Chromosome Mapping/*methods ; Gastrointestinal Microbiome/*genetics ; Genetic Variation/genetics ; Genome, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Metabolome/*genetics ; Proteome/genetics ; }, abstract = {Genome-scale metabolic models derived from human gut metagenomic data can be used as a framework to elucidate how microbial communities modulate human metabolism and health. We present AGORA (assembly of gut organisms through reconstruction and analysis), a resource of genome-scale metabolic reconstructions semi-automatically generated for 773 human gut bacteria. Using this resource, we identified a defined growth medium for Bacteroides caccae ATCC 34185. We also showed that interactions among modeled species depend on both the metabolic potential of each species and the nutrients available. AGORA reconstructions can integrate either metagenomic or 16S rRNA sequencing data sets to infer the metabolic diversity of microbial communities. AGORA reconstructions could provide a starting point for the generation of high-quality, manually curated metabolic reconstructions. AGORA is fully compatible with Recon 2, a comprehensive metabolic reconstruction of human metabolism, which will facilitate studies of host-microbiome interactions.}, } @article {pmid27890642, year = {2017}, author = {Porras, D and Nistal, E and Martínez-Flórez, S and Pisonero-Vaquero, S and Olcoz, JL and Jover, R and González-Gallego, J and García-Mediavilla, MV and Sánchez-Campos, S}, title = {Protective effect of quercetin on high-fat diet-induced non-alcoholic fatty liver disease in mice is mediated by modulating intestinal microbiota imbalance and related gut-liver axis activation.}, journal = {Free radical biology & medicine}, volume = {102}, number = {}, pages = {188-202}, doi = {10.1016/j.freeradbiomed.2016.11.037}, pmid = {27890642}, issn = {1873-4596}, mesh = {Animals ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Gastrointestinal Microbiome/drug effects/genetics ; Humans ; Insulin Resistance/genetics ; Intestines/microbiology ; Lipid Metabolism/genetics ; Liver/metabolism/pathology ; Metabolic Syndrome/*drug therapy/metabolism/microbiology/pathology ; Mice ; Non-alcoholic Fatty Liver Disease/*drug therapy/metabolism/microbiology/pathology ; Obesity/*drug therapy/metabolism/microbiology/pathology ; Quercetin/*administration & dosage ; Signal Transduction/drug effects ; Toll-Like Receptor 4/genetics/*metabolism ; }, abstract = {Gut microbiota is involved in obesity, metabolic syndrome and the progression of nonalcoholic fatty liver disease (NAFLD). It has been recently suggested that the flavonoid quercetin may have the ability to modulate the intestinal microbiota composition, suggesting a prebiotic capacity which highlights a great therapeutic potential in NAFLD. The present study aims to investigate benefits of experimental treatment with quercetin on gut microbial balance and related gut-liver axis activation in a nutritional animal model of NAFLD associated to obesity. C57BL/6J mice were challenged with high fat diet (HFD) supplemented or not with quercetin for 16 weeks. HFD induced obesity, metabolic syndrome and the development of hepatic steatosis as main hepatic histological finding. Increased accumulation of intrahepatic lipids was associated with altered gene expression related to lipid metabolism, as a result of deregulation of their major modulators. Quercetin supplementation decreased insulin resistance and NAFLD activity score, by reducing the intrahepatic lipid accumulation through its ability to modulate lipid metabolism gene expression, cytochrome P450 2E1 (CYP2E1)-dependent lipoperoxidation and related lipotoxicity. Microbiota composition was determined via 16S ribosomal RNA Illumina next-generation sequencing. Metagenomic studies revealed HFD-dependent differences at phylum, class and genus levels leading to dysbiosis, characterized by an increase in Firmicutes/Bacteroidetes ratio and in Gram-negative bacteria, and a dramatically increased detection of Helicobacter genus. Dysbiosis was accompanied by endotoxemia, intestinal barrier dysfunction and gut-liver axis alteration and subsequent inflammatory gene overexpression. Dysbiosis-mediated toll-like receptor 4 (TLR-4)-NF-κB signaling pathway activation was associated with inflammasome initiation response and reticulum stress pathway induction. Quercetin reverted gut microbiota imbalance and related endotoxemia-mediated TLR-4 pathway induction, with subsequent inhibition of inflammasome response and reticulum stress pathway activation, leading to the blockage of lipid metabolism gene expression deregulation. Our results support the suitability of quercetin as a therapeutic approach for obesity-associated NAFLD via its anti-inflammatory, antioxidant and prebiotic integrative response.}, } @article {pmid27889153, year = {2017}, author = {Wu, LH and Lu, ZM and Zhang, XJ and Wang, ZM and Yu, YJ and Shi, JS and Xu, ZH}, title = {Metagenomics reveals flavour metabolic network of cereal vinegar microbiota.}, journal = {Food microbiology}, volume = {62}, number = {}, pages = {23-31}, doi = {10.1016/j.fm.2016.09.010}, pmid = {27889153}, issn = {1095-9998}, mesh = {Acetic Acid/*metabolism ; Flavoring Agents/*chemistry ; Food Microbiology ; Indicators and Reagents ; *Metabolic Networks and Pathways/genetics ; Metagenomics/methods ; *Microbiota/genetics/physiology ; *Taste ; }, abstract = {Multispecies microbial community formed through centuries of repeated batch acetic acid fermentation (AAF) is crucial for the flavour quality of traditional vinegar produced from cereals. However, the metabolism to generate and/or formulate the essential flavours by the multispecies microbial community is hardly understood. Here we used metagenomic approach to clarify in situ metabolic network of key microbes responsible for flavour synthesis of a typical cereal vinegar, Zhenjiang aromatic vinegar, produced by solid-state fermentation. First, we identified 3 organic acids, 7 amino acids, and 20 volatiles as dominant vinegar metabolites. Second, we revealed taxonomic and functional composition of the microbiota by metagenomic shotgun sequencing. A total of 86 201 predicted protein-coding genes from 35 phyla (951 genera) were involved in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of Metabolism (42.3%), Genetic Information Processing (28.3%), and Environmental Information Processing (10.1%). Furthermore, a metabolic network for substrate breakdown and dominant flavour formation in vinegar microbiota was constructed, and microbial distribution discrepancy in different metabolic pathways was charted. This study helps elucidating different metabolic roles of microbes during flavour formation in vinegar microbiota.}, } @article {pmid27888579, year = {2017}, author = {Schaeffer, RN and Vannette, RL and Brittain, C and Williams, NM and Fukami, T}, title = {Non-target effects of fungicides on nectar-inhabiting fungi of almond flowers.}, journal = {Environmental microbiology reports}, volume = {9}, number = {2}, pages = {79-84}, doi = {10.1111/1758-2229.12501}, pmid = {27888579}, issn = {1758-2229}, mesh = {Bacteria/classification/drug effects/genetics ; Biota/*drug effects ; Flowers/*microbiology ; Fungi/*classification/*drug effects/genetics ; Fungicides, Industrial/*metabolism ; Metagenomics ; Metschnikowia ; *Plant Nectar ; Prunus dulcis/*microbiology ; }, abstract = {Nectar mediates interactions between plants and pollinators in natural and agricultural systems. Specialized microorganisms are common nectar inhabitants, and potentially important mediators of plant-pollinator interactions. However, their diversity and role in mediating pollination services in agricultural systems are poorly characterized. Moreover, agrochemicals are commonly applied to minimize crop damage, but may present ecological consequences for non-target organisms. Assessment of ecological risk has tended to focus on beneficial macroorganisms such as pollinators, with less attention paid to microorganisms. Here, using culture-independent methods, we assess the impact of two widely-used fungicides on nectar microbial community structure in the mass-flowering crop almond (Prunus dulcis). We predicted that fungicide application would reduce fungal richness and diversity, whereas competing bacterial richness would increase, benefitting from negative effects on fungi. We found that fungicides reduced fungal richness and diversity in exposed flowers, but did not significantly affect bacterial richness, diversity, or community composition. The relative abundance of Metschnikowia OTUs, nectar specialists that can impact pollination, was reduced by both fungicides. Given growing recognition of the importance of nectar microorganisms as mediators of plant-pollinator mutualisms, future research should consider the impact of management practices on plant-associated microorganisms and consequences for pollination services in agricultural landscapes.}, } @article {pmid27888152, year = {2016}, author = {Kumar, J and Kumar, M and Gupta, S and Ahmed, V and Bhambi, M and Pandey, R and Chauhan, NS}, title = {An Improved Methodology to Overcome Key Issues in Human Fecal Metagenomic DNA Extraction.}, journal = {Genomics, proteomics & bioinformatics}, volume = {14}, number = {6}, pages = {371-378}, pmid = {27888152}, issn = {2210-3244}, mesh = {Bacteria/genetics/isolation & purification ; DNA/chemistry/isolation & purification/*metabolism ; Feces/*microbiology ; Humans ; Metagenomics/*methods ; *Microbiota ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Microbes are ubiquitously distributed in nature, and recent culture-independent studies have highlighted the significance of gut microbiota in human health and disease. Fecal DNA is the primary source for the majority of human gut microbiome studies. However, further improvement is needed to obtain fecal metagenomic DNA with sufficient amount and good quality but low host genomic DNA contamination. In the current study, we demonstrate a quick, robust, unbiased, and cost-effective method for the isolation of high molecular weight (>23kb) metagenomic DNA (260/280 ratio >1.8) with a good yield (55.8±3.8ng/mg of feces). We also confirm that there is very low human genomic DNA contamination (eubacterial: human genomic DNA marker genes=2[27.9]:1) in the human feces. The newly-developed method robustly performs for fresh as well as stored fecal samples as demonstrated by 16S rRNA gene sequencing using 454 FLX+. Moreover, 16S rRNA gene analysis indicated that compared to other DNA extraction methods tested, the fecal metagenomic DNA isolated with current methodology retains species richness and does not show microbial diversity biases, which is further confirmed by qPCR with a known quantity of spike-in genomes. Overall, our data highlight a protocol with a balance between quality, amount, user-friendliness, and cost effectiveness for its suitability toward usage for culture-independent analysis of the human gut microbiome, which provides a robust solution to overcome key issues associated with fecal metagenomic DNA isolation in human gut microbiome studies.}, } @article {pmid27887570, year = {2016}, author = {Shaw, GT and Pao, YY and Wang, D}, title = {MetaMIS: a metagenomic microbial interaction simulator based on microbial community profiles.}, journal = {BMC bioinformatics}, volume = {17}, number = {1}, pages = {488}, pmid = {27887570}, issn = {1471-2105}, mesh = {*Algorithms ; Bacteria/*classification/*genetics ; Computational Biology/*methods ; Ecology ; Feces/*microbiology ; Female ; Humans ; Male ; Metagenome/*genetics ; Microbial Interactions ; Microbiota/*genetics ; Software ; }, abstract = {BACKGROUND: The complexity and dynamics of microbial communities are major factors in the ecology of a system. With the NGS technique, metagenomics data provides a new way to explore microbial interactions. Lotka-Volterra models, which have been widely used to infer animal interactions in dynamic systems, have recently been applied to the analysis of metagenomic data.

RESULTS: In this paper, we present the Lotka-Volterra model based tool, the Metagenomic Microbial Interacticon Simulator (MetaMIS), which is designed to analyze the time series data of microbial community profiles. MetaMIS first infers underlying microbial interactions from abundance tables for operational taxonomic units (OTUs) and then interprets interaction networks using the Lotka-Volterra model. We also embed a Bray-Curtis dissimilarity method in MetaMIS in order to evaluate the similarity to biological reality. MetaMIS is designed to tolerate a high level of missing data, and can estimate interaction information without the influence of rare microbes. For each interaction network, MetaMIS systematically examines interaction patterns (such as mutualism or competition) and refines the biotic role within microbes. As a case study, we collect a human male fecal microbiome and show that Micrococcaceae, a relatively low abundance OTU, is highly connected with 13 dominant OTUs and seems to play a critical role. MetaMIS is able to organize multiple interaction networks into a consensus network for comparative studies; thus we as a case study have also identified a consensus interaction network between female and male fecal microbiomes.

CONCLUSIONS: MetaMIS provides an efficient and user-friendly platform that may reveal new insights into metagenomics data. MetaMIS is freely available at: https://sourceforge.net/projects/metamis/ .}, } @article {pmid27886907, year = {2017}, author = {Dreyfus, DH}, title = {Differential Diagnosis of Chronic Urticaria and Angioedema Based on Molecular Biology, Pharmacology, and Proteomics.}, journal = {Immunology and allergy clinics of North America}, volume = {37}, number = {1}, pages = {201-215}, doi = {10.1016/j.iac.2016.08.010}, pmid = {27886907}, issn = {1557-8607}, mesh = {Adaptive Immunity ; Angioedema/*diagnosis ; Autoantibodies/blood ; Chronic Disease ; Complement System Proteins/metabolism ; Diagnosis, Differential ; Humans ; Microbiota ; Pathology, Molecular ; Proteomics ; Receptors, Pattern Recognition/metabolism ; Urticaria/*diagnosis ; }, abstract = {Differential diagnosis of urticaria and angioedema has been based on the phenotype as either acute or chronic depending on the duration of more than 6 to 8 weeks, respectively. Additional subdivisions include poorly defined terms such as idiopathic, spontaneous, or autoimmune. In this article, the author suggests that an increased understanding of the acquired and innate immune system and data from novel proteomic technology have blurred the lines between these categories of diagnosis. Specific molecular pathways and response to specific medications should be incorporated in classification and diagnosis schemes.}, } @article {pmid27884820, year = {2016}, author = {Aagaard, K and Stewart, CJ and Chu, D}, title = {Una destinatio, viae diversae: Does exposure to the vaginal microbiota confer health benefits to the infant, and does lack of exposure confer disease risk?.}, journal = {EMBO reports}, volume = {17}, number = {12}, pages = {1679-1684}, pmid = {27884820}, issn = {1469-3178}, mesh = {*Cesarean Section/adverse effects ; Disease Susceptibility/*etiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Pregnancy ; Risk Factors ; Vagina/*microbiology ; }, abstract = {There are lingering concerns that Cesarean surgery could impede on the child's health due to a lack of exposure to the mother's vaginal microbiota. However, the evidence so far is not sufficient to affirm whether the mode of birth influences disease risk or whether it is other causes.[Image: see text]}, } @article {pmid27881416, year = {2017}, author = {Huang, AD and Luo, C and Pena-Gonzalez, A and Weigand, MR and Tarr, CL and Konstantinidis, KT}, title = {Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {3}, pages = {}, pmid = {27881416}, issn = {1098-5336}, mesh = {Alabama/epidemiology ; Coinfection/*epidemiology/microbiology ; Colorado/epidemiology ; *Disease Outbreaks ; Escherichia coli/isolation & purification ; Feces/microbiology ; Foodborne Diseases/*epidemiology/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; Salmonella Infections/*epidemiology/microbiology ; Salmonella enterica/*isolation & purification ; Staphylococcus aureus/isolation & purification ; }, abstract = {UNLABELLED: Diagnostic testing for foodborne pathogens relies on culture-based techniques that are not rapid enough for real-time disease surveillance and do not give a quantitative picture of pathogen abundance or the response of the natural microbiome. Powerful sequence-based culture-independent approaches, such as shotgun metagenomics, could sidestep these limitations and potentially reveal a pathogen-specific signature on the microbiome that would have implications not only for diagnostics but also for better understanding disease progression and pathogen ecology. However, metagenomics have not yet been validated for foodborne pathogen detection. Toward closing these gaps, we applied shotgun metagenomics to stool samples collected from two geographically isolated (Alabama and Colorado) foodborne outbreaks, where the etiologic agents were identified by culture-dependent methods as distinct strains of Salmonella enterica subsp. enterica serovar Heidelberg. Metagenomic investigations were consistent with the culture-based findings and revealed, in addition, the in situ abundance and level of intrapopulation diversity of the pathogen, the possibility of coinfections with Staphylococcus aureus, overgrowth of commensal Escherichia coli, and significant shifts in the gut microbiome during infection relative to reference healthy samples. Additionally, we designed our bioinformatics pipeline to deal with several challenges associated with the analysis of clinical samples, such as the high frequency of coeluting human DNA sequences and assessment of the virulence potential of pathogens. Comparisons of these results to those of other studies revealed that in several, but not all, cases of diarrheal outbreaks, the disease and healthy states of the gut microbial community might be distinguishable, opening new possibilities for diagnostics.

IMPORTANCE: Diagnostic testing for enteric pathogens has relied for decades on culture-based techniques, but a total of 38.4 million cases of foodborne illness per year cannot be attributed to specific causes. This study describes new culture-independent metagenomic approaches and the associated bioinformatics pipeline to detect and type the causative agents of microbial disease with unprecedented accuracy, opening new possibilities for the future development of health technologies and diagnostics. Our tools and approaches should be applicable to other microbial diseases in addition to foodborne diarrhea.}, } @article {pmid27880869, year = {2017}, author = {Champion, CJ and Xu, J}, title = {The impact of metagenomic interplay on the mosquito redox homeostasis.}, journal = {Free radical biology & medicine}, volume = {105}, number = {}, pages = {79-85}, pmid = {27880869}, issn = {1873-4596}, support = {SC1 AI112786/AI/NIAID NIH HHS/United States ; SC2 GM092789/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Culicidae/*genetics/metabolism/microbiology ; Gastrointestinal Microbiome ; Heme/physiology ; Homeostasis ; Humans ; Metagenome ; *Oxidative Stress ; Reactive Oxygen Species/metabolism ; Signal Transduction ; Transcription, Genetic ; }, abstract = {Mosquitoes are exposed to oxidative challenges throughout their life cycle. The primary challenge comes from a blood meal. The blood digestion turns the midgut into an oxidative environment, which imposes pressure not only on mosquito fecundity and other physiological traits but also on the microbiota in the midgut. During evolution, mosquitoes have developed numerous oxidative defense mechanisms to maintain redox homeostasis in the midgut. In addition to antioxidants, SOD, catalase, and glutathione system, sufficient supply of the reducing agent, NADPH, is vital for a successful defense against oxidative stress. Increasing evidence indicates that in response to oxidative stress, cells reconfigure metabolic pathways to increase the generation of NADPH through NADP-reducing networks including the pentose phosphate pathway and others. The microbial homeostasis is critical for the functional contributions to various host phenotypes. The symbiotic microbiota is regulated largely by the Duox-ROS pathway in Drosophila. In mosquitoes, Duox-ROS pathway, heme-mediated signaling, antimicrobial peptide production and C-type lectins work in concert to maintain the dynamic microbial community in the midgut. Microbial mechanisms against oxidative stress in this context are not well understood. Emerging evidence that microbial metabolites trigger host oxidative response warrants further study on the metagenomic interplay in an oxidative environment like mosquito gut ecosystem. Besides the classical Drosophila model, hematophagous insects like mosquitoes provide an alternative model system to study redox homeostasis in a symbiotic metagenomic context.}, } @article {pmid27876778, year = {2016}, author = {Hou, Q and Kwok, LY and Zheng, Y and Wang, L and Guo, Z and Zhang, J and Huang, W and Wang, Y and Leng, L and Li, H and Zhang, H}, title = {Differential fecal microbiota are retained in broiler chicken lines divergently selected for fatness traits.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {37376}, pmid = {27876778}, issn = {2045-2322}, mesh = {Animals ; Bacteria/classification/*genetics/metabolism ; Chickens/genetics/microbiology ; Feces/*microbiology ; Gastrointestinal Tract/microbiology ; Lipogenesis/*genetics ; Metabolic Networks and Pathways/genetics ; Metagenome/*genetics ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Whole Genome Sequencing ; }, abstract = {Our study combined 16S rRNA-pyrosequencing and whole genome sequencing to analyze the fecal metagenomes of the divergently selected lean (LL) and fat (FL) line chickens. Significant structural differences existed in both the phylogenic and functional metagenomes between the two chicken lines. At phylum level, the FL group had significantly less Bacteroidetes. At genus level, fourteen genera of different relative abundance were identified, with some known short-chain fatty acid producers (including Subdoligranulum, Butyricicoccus, Eubacterium, Bacteroides, Blautia) and a potentially pathogenic genus (Enterococcus). Redundancy analysis identified 190 key responsive operational taxonomic units (OTUs) that accounted for the structural differences between the phylogenic metagenome of the two groups. Four Cluster of Orthologous Group (COG) categories (Amino acid transport and metabolism, E; Nucleotide transport and metabolism, F; Coenzyme transport and metabolism, H; and Lipid transport and metabolism, I) were overrepresented in LL samples. Fifteen differential metabolic pathways (Biosynthesis of amino acids, Pyruvate metabolism, Nitrotoluene degradation, Lipopolysaccharide biosynthesis, Peptidoglycan biosynthesis, Pantothenate and CoA biosynthesis, Glycosaminoglycan degradation, Thiamine metabolism, Phosphotransferase system, Two-component system, Bacterial secretion system, Flagellar assembly, Bacterial chemotaxis, Ribosome, Sulfur relay system) were identified. Our data highlighted interesting variations between the gut metagenomes of these two chicken lines.}, } @article {pmid27876768, year = {2017}, author = {Dickson, I}, title = {Gut microbiota: Culturomics: illuminating microbial dark matter.}, journal = {Nature reviews. Gastroenterology & hepatology}, volume = {14}, number = {1}, pages = {3}, pmid = {27876768}, issn = {1759-5053}, mesh = {*Gastrointestinal Microbiome ; *Gastrointestinal Tract ; Humans ; Metagenomics ; }, } @article {pmid27876765, year = {2016}, author = {Young, W and Moon, CD and Thomas, DG and Cave, NJ and Bermingham, EN}, title = {Pre- and post-weaning diet alters the faecal metagenome in the cat with differences in vitamin and carbohydrate metabolism gene abundances.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {34668}, pmid = {27876765}, issn = {2045-2322}, mesh = {Actinobacteria/classification/genetics/isolation & purification ; Animal Nutritional Physiological Phenomena ; Animals ; Bifidobacterium/classification/genetics/isolation & purification ; Cats ; Diet/*methods ; Energy Intake/physiology ; Feces/microbiology ; Food, Preserved/*analysis ; Gastrointestinal Microbiome/*genetics ; Lactobacillus/classification/genetics/isolation & purification ; Male ; *Metagenome ; Time Factors ; Vitamins/administration & dosage/*metabolism ; Weaning ; }, abstract = {Dietary format, and its role in pet nutrition, is of interest to pet food manufacturers and pet owners alike. The aim of the present study was to investigate the effects of pre- and post-weaning diets (kibbled or canned) on the composition and function of faecal microbiota in the domestic cat by shotgun metagenomic sequencing and gene taxonomic and functional assignment using MG-RAST. Post-weaning diet had a dramatic effect on community composition; 147 of the 195 bacterial species identified had significantly different mean relative abundances between kittens fed kibbled and canned diets. The kittens fed kibbled diets had relatively higher abundances of Lactobacillus (>100-fold), Bifidobacterium (>100-fold), and Collinsella (>9-fold) than kittens fed canned diets. There were relatively few differences in the predicted microbiome functions associated with the pre-weaning diet. Post-weaning diet affected the abundance of functional gene groups. Genes involved in vitamin biosynthesis, metabolism, and transport, were significantly enriched in the metagenomes of kittens fed the canned diet. The impact of post-weaning diet on the metagenome in terms of vitamin biosynthesis functions suggests that modulation of the microbiome function through diet may be an important avenue for improving the nutrition of companion animals.}, } @article {pmid27875688, year = {2016}, author = {Gawryluk, RMR and Del Campo, J and Okamoto, N and Strassert, JFH and Lukeš, J and Richards, TA and Worden, AZ and Santoro, AE and Keeling, PJ}, title = {Morphological Identification and Single-Cell Genomics of Marine Diplonemids.}, journal = {Current biology : CB}, volume = {26}, number = {22}, pages = {3053-3059}, doi = {10.1016/j.cub.2016.09.013}, pmid = {27875688}, issn = {1879-0445}, support = {MOP-42517//CIHR/Canada ; }, mesh = {Amino Acid Sequence ; Biodiversity ; California ; Euglenozoa/*classification/cytology/*genetics ; *Genome, Protozoan ; Metagenomics ; Pacific Ocean ; Phylogeny ; Plankton/*classification/cytology/*genetics ; RNA, Protozoan/genetics ; Sequence Alignment ; }, abstract = {Recent global surveys of marine biodiversity have revealed that a group of organisms known as "marine diplonemids" constitutes one of the most abundant and diverse planktonic lineages [1]. Though discovered over a decade ago [2, 3], their potential importance was unrecognized, and our knowledge remains restricted to a single gene amplified from environmental DNA, the 18S rRNA gene (small subunit [SSU]). Here, we use single-cell genomics (SCG) and microscopy to characterize ten marine diplonemids, isolated from a range of depths in the eastern North Pacific Ocean. Phylogenetic analysis confirms that the isolates reflect the entire range of marine diplonemid diversity, and comparisons to environmental SSU surveys show that sequences from the isolates range from rare to superabundant, including the single most common marine diplonemid known. SCG generated a total of ∼915 Mbp of assembled sequence across all ten cells and ∼4,000 protein-coding genes with homologs in the Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology database, distributed across categories expected for heterotrophic protists. Models of highly conserved genes indicate a high density of non-canonical introns, lacking conventional GT-AG splice sites. Mapping metagenomic datasets [4] to SCG assemblies reveals virtually no overlap, suggesting that nuclear genomic diversity is too great for representative SCG data to provide meaningful phylogenetic context to metagenomic datasets. This work provides an entry point to the future identification, isolation, and cultivation of these elusive yet ecologically important cells. The high density of nonconventional introns, however, also portends difficulty in generating accurate gene models and highlights the need for the establishment of stable cultures and transcriptomic analyses.}, } @article {pmid27874095, year = {2016}, author = {Ganda, EK and Bisinotto, RS and Lima, SF and Kronauer, K and Decter, DH and Oikonomou, G and Schukken, YH and Bicalho, RC}, title = {Longitudinal metagenomic profiling of bovine milk to assess the impact of intramammary treatment using a third-generation cephalosporin.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {37565}, pmid = {27874095}, issn = {2045-2322}, mesh = {Animals ; Bacteria/classification/*genetics/isolation & purification/pathogenicity ; Cattle ; Cephalosporins/pharmacology ; Female ; Mastitis, Bovine/*drug therapy/microbiology/pathology ; *Metagenomics ; Microbiota/*genetics ; Milk/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Antimicrobial usage in food animals has a direct impact on human health, and approximately 80% of the antibiotics prescribed in the dairy industry are used to treat bovine mastitis. Here we provide a longitudinal description of the changes in the microbiome of milk that are associated with mastitis and antimicrobial therapy. Next-generation sequencing, 16 S rRNA gene quantitative real-time PCR, and aerobic culturing were applied to assess the effect of disease and antibiotic therapy on the milk microbiome. Cows diagnosed with clinical mastitis associated with Gram-negative pathogens or negative aerobic culture were randomly allocated into 5 days of Ceftiofur intramammary treatment or remained as untreated controls. Serial milk samples were collected from the affected quarter and the ipsilateral healthy quarter of the same animal. Milk from the mastitic quarter had a higher bacterial load and reduced microbial diversity compared to healthy milk. Resolution of the disease was accompanied by increases in diversity indexes and a decrease in pathogen relative abundance. Escherichia coli-associated mastitic milk samples had a remarkably distinct bacterial profile, dominated by Enterobacteriaceae, when compared to healthy milk. However, no differences were observed in culture-negative mastitis samples when compared to healthy milk. Antimicrobial treatment had no significant effect on clinical cure, bacteriological cure, pathogen clearance rate or bacterial load.}, } @article {pmid27872949, year = {2017}, author = {Guidolin, AS and Cônsoli, FL}, title = {Symbiont Diversity of Aphis (Toxoptera) citricidus (Hemiptera: Aphididae) as Influenced by Host Plants.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {201-210}, pmid = {27872949}, issn = {1432-184X}, mesh = {Animals ; Aphids/*microbiology ; Biodiversity ; Buchnera/genetics/*isolation & purification ; Enterobacteriaceae/genetics/*isolation & purification ; Proteobacteria/genetics/*isolation & purification ; Symbiosis ; }, abstract = {Aphids are well known for their association with endosymbiont bacteria. Almost all aphids harbor Buchnera aphidicola as an obligate symbiont and several other bacteria as facultative symbionts. Associations of facultative symbionts and aphids are quite variable in terms of diversity and prevalence across aphid species. Facultative symbionts can have a major impact on aphid bioecological traits. A number of factors shape the outcome of the facultative symbiont-aphid association, including aphid clone, bacterial genotype, geography, and host plant association. The effects of host plant on aphid-facultative symbiont associations are the least understood. We performed deep sequencing of the bacterial community associated with field populations of the oligophagous aphid Aphis (Toxoptera) citricidus collected from different host plants. We demonstrate that (i) A. citricidus has low symbiont diversity, (ii) symbiont diversity is affected by host plant, and (iii) host plants affect the relative abundance of the obligate symbiont Buchnera and an unknown genus of Enterobacteriaceae.}, } @article {pmid27869789, year = {2016}, author = {Brugiroux, S and Beutler, M and Pfann, C and Garzetti, D and Ruscheweyh, HJ and Ring, D and Diehl, M and Herp, S and Lötscher, Y and Hussain, S and Bunk, B and Pukall, R and Huson, DH and Münch, PC and McHardy, AC and McCoy, KD and Macpherson, AJ and Loy, A and Clavel, T and Berry, D and Stecher, B}, title = {Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium.}, journal = {Nature microbiology}, volume = {2}, number = {}, pages = {16215}, doi = {10.1038/nmicrobiol.2016.215}, pmid = {27869789}, issn = {2058-5276}, support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; P 26127/FWF_/Austrian Science Fund FWF/Austria ; P 27831/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; *Antibiosis ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Mice ; Salmonella Infections, Animal/*prevention & control ; Salmonella typhimurium/*physiology ; }, abstract = {Protection against enteric infections, also termed colonization resistance, results from mutualistic interactions of the host and its indigenous microbes. The gut microbiota of humans and mice is highly diverse and it is therefore challenging to assign specific properties to its individual members. Here, we have used a collection of murine bacterial strains and a modular design approach to create a minimal bacterial community that, once established in germ-free mice, provided colonization resistance against the human enteric pathogen Salmonella enterica serovar Typhimurium (S. Tm). Initially, a community of 12 strains, termed Oligo-Mouse-Microbiota (Oligo-MM[12]), representing members of the major bacterial phyla in the murine gut, was selected. This community was stable over consecutive mouse generations and provided colonization resistance against S. Tm infection, albeit not to the degree of a conventional complex microbiota. Comparative (meta)genome analyses identified functions represented in a conventional microbiome but absent from the Oligo-MM[12]. By genome-informed design, we created an improved version of the Oligo-MM community harbouring three facultative anaerobic bacteria from the mouse intestinal bacterial collection (miBC) that provided conventional-like colonization resistance. In conclusion, we have established a highly versatile experimental system that showed efficacy in an enteric infection model. Thus, in combination with exhaustive bacterial strain collections and systems-based approaches, genome-guided design can be used to generate insights into microbe-microbe and microbe-host interactions for the investigation of ecological and disease-relevant mechanisms in the intestine.}, } @article {pmid27867014, year = {2017}, author = {Ghosh, S and Kuisiene, N and Cheeptham, N}, title = {The cave microbiome as a source for drug discovery: Reality or pipe dream?.}, journal = {Biochemical pharmacology}, volume = {134}, number = {}, pages = {18-34}, doi = {10.1016/j.bcp.2016.11.018}, pmid = {27867014}, issn = {1873-2968}, mesh = {Animals ; Bacterial Physiological Phenomena/*drug effects/genetics ; Biological Products/*isolation & purification/pharmacology ; Caves/*microbiology ; Drug Discovery/*methods/trends ; Humans ; *Microbiota/genetics ; }, abstract = {This review highlights cave habitats, cave microbiomes and their potential for drug discovery. Such studies face many challenges, including access to remote and pristine caves, and sample collection and transport. Inappropriate physical and chemical growth conditions in the laboratory for the isolation and cultivation of cave microorganisms pose many complications including length of cultivation; some cave microorganisms can take weeks and even months to grow. Additionally, DNA extraction from cave environmental samples may be difficult due to the high concentration of various minerals that are natural DNA blocking agents. Once cave microorganisms are grown in the lab, other problems often arise, such as maintenance of pure culture, consistency of antimicrobial activity and fermentation conditions for antimicrobial production. In this review, we suggest that, although based on what has been done in the field, there is potential in using cave microorganisms to produce antimicrobial agents, one needs to be highly committed and prepared.}, } @article {pmid27863092, year = {2017}, author = {Tachibana, K and Sakurai, K and Watanabe, M and Miyaso, H and Mori, C}, title = {Associations between changes in the maternal gut microbiome and differentially methylated regions of diabetes-associated genes in fetuses: A pilot study from a birth cohort study.}, journal = {Journal of diabetes investigation}, volume = {8}, number = {4}, pages = {550-553}, pmid = {27863092}, issn = {2040-1124}, mesh = {Adult ; Cohort Studies ; *DNA Methylation ; Diabetes Mellitus/genetics ; Female ; Fetus/*metabolism ; Firmicutes/isolation & purification ; *Gastrointestinal Microbiome ; Humans ; KCNQ1 Potassium Channel/*genetics ; Pilot Projects ; Pregnancy ; Prenatal Exposure Delayed Effects ; Ubiquitin-Conjugating Enzymes/*genetics ; }, abstract = {Several intrauterine environmental factors can increase the future risk of type 2 diabetes. The microbiome can influence the balance between health and disease. However, the influence of the maternal gut microbiome on the future risk of diabetes in the fetus is unknown. The present study investigated the associations between maternal gut microbiome and differentially methylated regions of diabetes-associated genes in umbilical cord samples. The present study included 10 pregnant participants from a birth cohort study. 16S ribosomal ribonucleic acid metagenome analysis of maternal stool samples and deoxyribonucleic acid methylation assays of umbilical cord samples were carried out. The present study found that changes in the UBE2E2 and KCNQ1 methylation rates in umbilical cord samples were associated with the proportion of Firmicutes in the maternal gut, albeit with marginal correlations after adjustment for age and body mass index. These findings suggest a link between the methylation of diabetes-associated genes in fetuses and maternal microbiota components during pregnancy.}, } @article {pmid27861554, year = {2016}, author = {Paramel Jayaprakash, T and Wagner, EC and van Schalkwyk, J and Albert, AY and Hill, JE and Money, DM and , }, title = {High Diversity and Variability in the Vaginal Microbiome in Women following Preterm Premature Rupture of Membranes (PPROM): A Prospective Cohort Study.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0166794}, pmid = {27861554}, issn = {1932-6203}, mesh = {Adult ; *Biodiversity ; Canada ; Cluster Analysis ; Female ; *Fetal Membranes, Premature Rupture ; Gestational Age ; Humans ; Infant, Newborn ; Metagenome ; Metagenomics/methods ; *Microbial Viability ; *Microbiota ; Pregnancy ; Pregnancy Outcome ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; Vagina/*microbiology ; Young Adult ; }, abstract = {OBJECTIVE: To characterize the vaginal microbiota of women following preterm premature rupture of membranes (PPROM), and determine if microbiome composition predicts latency duration and perinatal outcomes.

DESIGN: A prospective cohort study.

SETTING: Canada.

POPULATION: Women with PPROM between 24+0 and 33+6 weeks gestational age (GA).

METHODS: Microbiome profiles, based on pyrosequencing of the cpn60 universal target, were generated from vaginal samples at time of presentation with PPROM, weekly thereafter, and at delivery.

MAIN OUTCOME MEASURES: Vaginal microbiome composition, latency duration, gestational age at delivery, perinatal outcomes.

RESULTS: Microbiome profiles were generated from 70 samples from 36 women. Mean GA at PPROM was 28.8 wk (mean latency 2.7 wk). Microbiome profiles were highly diverse but sequences representing Megasphaera type 1 and Prevotella spp. were detected in all vaginal samples. Only 13/70 samples were dominated by Lactobacillus spp. Microbiome profiles at the time of membrane rupture did not cluster by gestational age at PPROM, latency duration, presence of chorioamnionitis or by infant outcomes. Mycoplasma and/or Ureaplasma were detected by PCR in 81% (29/36) of women, and these women had significantly lower GA at delivery and correspondingly lower birth weight infants than Mycoplasma and/or Ureaplasma negative women.

CONCLUSION: Women with PPROM had mixed, abnormal vaginal microbiota but the microbiome profile at PPROM did not correlate with latency duration. Prevotella spp. and Megasphaera type I were ubiquitous. The presence of Mollicutes in the vaginal microbiome was associated with lower GA at delivery. The microbiome was remarkably unstable during the latency period.}, } @article {pmid27861539, year = {2016}, author = {Izuno, A and Kanzaki, M and Artchawakom, T and Wachrinrat, C and Isagi, Y}, title = {Vertical Structure of Phyllosphere Fungal Communities in a Tropical Forest in Thailand Uncovered by High-Throughput Sequencing.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0166669}, pmid = {27861539}, issn = {1932-6203}, mesh = {*Biodiversity ; DNA Barcoding, Taxonomic ; *Ecosystem ; *Environmental Microbiology ; *Forests ; Fungi/*classification/*genetics ; Geography ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Plants/microbiology ; Thailand ; *Tropical Climate ; }, abstract = {Phyllosphere fungi harbor a tremendous species diversity and play important ecological roles. However, little is known about their distribution patterns within forest ecosystems. We examined how species diversity and community composition of phyllosphere fungi change along a vertical structure in a tropical forest in Thailand. Fungal communities in 144 leaf samples from 19 vertical layers (1.28-34.4 m above ground) of 73 plant individuals (27 species) were investigated by metabarcoding analysis using Ion Torrent sequencing. In total, 1,524 fungal operational taxonomic units (OTUs) were detected among 890,710 reads obtained from the 144 leaf samples. Taxonomically diverse fungi belonging to as many as 24 orders of Ascomycota and 21 orders of Basidiomycota were detected, most of which inhabited limited parts of the lowest layers closest to the forest floor. Species diversity of phyllosphere fungi was the highest in the lowest layers closest to the forest floor, decreased with increasing height, and lowest in the canopy; 742 and 55 fungal OTUs were detected at the lowest and highest layer, respectively. On the layers close to the forest floor, phyllosphere fungal communities were mainly composed of low frequency OTUs and largely differentiated among plant individuals. Conversely, in the canopy, fungal communities consisted of similar OTUs across plant individuals, and as many as 86.1%-92.7% of the OTUs found in the canopy (≥22 m above ground) were also distributed in the lower layers. Overall, our study showed the variability of phyllosphere fungal communities along the vertical gradient of plant vegetation and environmental conditions, suggesting the significance of biotic and abiotic variation for the species diversity of phyllosphere fungi.}, } @article {pmid27861486, year = {2016}, author = {Toju, H and Kishida, O and Katayama, N and Takagi, K}, title = {Networks Depicting the Fine-Scale Co-Occurrences of Fungi in Soil Horizons.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0165987}, pmid = {27861486}, issn = {1932-6203}, mesh = {Biodiversity ; Computational Biology/methods ; DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer ; Ecosystem ; *Fungi/classification/genetics ; Japan ; Metagenome ; Metagenomics/methods ; *Soil Microbiology ; }, abstract = {Fungi in soil play pivotal roles in nutrient cycling, pest controls, and plant community succession in terrestrial ecosystems. Despite the ecosystem functions provided by soil fungi, our knowledge of the assembly processes of belowground fungi has been limited. In particular, we still have limited knowledge of how diverse functional groups of fungi interact with each other in facilitative and competitive ways in soil. Based on the high-throughput sequencing data of fungi in a cool-temperate forest in northern Japan, we analyzed how taxonomically and functionally diverse fungi showed correlated fine-scale distributions in soil. By uncovering pairs of fungi that frequently co-occurred in the same soil samples, networks depicting fine-scale co-occurrences of fungi were inferred at the O (organic matter) and A (surface soil) horizons. The results then led to the working hypothesis that mycorrhizal, endophytic, saprotrophic, and pathogenic fungi could form compartmentalized (modular) networks of facilitative, antagonistic, and/or competitive interactions in belowground ecosystems. Overall, this study provides a research basis for further understanding how interspecific interactions, along with sharing of niches among fungi, drive the dynamics of poorly explored biospheres in soil.}, } @article {pmid27860093, year = {2017}, author = {Lyons, PP and Turnbull, JF and Dawson, KA and Crumlish, M}, title = {Phylogenetic and functional characterization of the distal intestinal microbiome of rainbow trout Oncorhynchus mykiss from both farm and aquarium settings.}, journal = {Journal of applied microbiology}, volume = {122}, number = {2}, pages = {347-363}, doi = {10.1111/jam.13347}, pmid = {27860093}, issn = {1365-2672}, mesh = {Animals ; Aquaculture ; Bacteria/*classification/genetics ; Fresh Water ; *Gastrointestinal Microbiome ; Intestines/*microbiology ; Oncorhynchus mykiss/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {AIMS: This study focused on comparing the phylogenetic composition and functional potential of the intestinal microbiome of rainbow trout sourced from both farm and aquarium settings.

METHODS AND RESULTS: Samples of distal intestinal contents were collected from fish and subjected to high throughput 16S rRNA sequencing, to accurately determine the composition of the intestinal microbiome. The predominant phyla identified from both groups were Tenericutes, Firmicutes, Proteobacteria, Spirochaetae and Bacteroidetes. A novel metagenomic tool, PICRUSt, was used to determine the functional potential of the bacterial communities present in the rainbow trout intestine. Pathways concerning membrane transport activity were dominant in the intestinal microbiome of all fish samples. Furthermore, this analysis revealed that gene pathways relating to metabolism, and in particular amino acid and carbohydrate metabolism, were upregulated in the rainbow trout intestinal microbiome.

CONCLUSIONS: The results suggest that the structure of the intestinal microbiome in farmed rainbow trout may be similar regardless of where the fish are located and hence could be shaped by host factors. Differences were, however, noted in the microbial community membership within the intestine of both fish populations, suggesting that more sporadic taxa could be unique to each environment and may have the ability to colonize the rainbow trout gastrointestinal tract. Finally, the functional analysis provides evidence that the microbiome of rainbow trout contains genes that could contribute to the metabolism of dietary ingredients and therefore may actively influence the digestive process in these fish.

To better understand and exploit the intestinal microbiome and its impact on fish health, it is vital to determine its structure, diversity and potential functional capacity. This study improves our knowledge of these areas and suggests that the intestinal microbiome of rainbow trout may play an important role in the digestive physiology of these fish.}, } @article {pmid27858139, year = {2017}, author = {Park, S and Ji, Y and Jung, HY and Park, H and Kang, J and Choi, SH and Shin, H and Hyun, CK and Kim, KT and Holzapfel, WH}, title = {Lactobacillus plantarum HAC01 regulates gut microbiota and adipose tissue accumulation in a diet-induced obesity murine model.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {4}, pages = {1605-1614}, doi = {10.1007/s00253-016-7953-2}, pmid = {27858139}, issn = {1432-0614}, mesh = {Adipose Tissue/*metabolism ; Animals ; Diet, High-Fat/adverse effects ; Gastrointestinal Microbiome/*physiology ; Lactobacillus plantarum/*physiology ; Mice ; Obesity/etiology/*metabolism/*microbiology ; }, abstract = {The functional features of Lactobacillus plantarum HAC01 (HAC01), isolated from fermented Korean kimchi, were studied with regard to the fat mass, immunometabolic biomarkers and dysbiosis in a diet-induced obesity (DIO) murine model. L. rhamnosus GG (LGG) served as reference strain and a PBS-treated group as control. The administration of L. plantarum HAC01 resulted in reduction of the mesenteric adipose depot, the conjunctive tissue closely associated with the gastrointestinal tract, where lipid oxidative gene expression was upregulated compared to the control group. Metagenome analysis of intestinal microbiota showed that both strains HAC01 and LGG influenced specific bacterial families such as the Lachnospiraceae and Ruminococcaceae rather than the phyla Firmicutes and Bacteroidetes as a whole. The relative abundance of the Lachnospiraceae (phylum Firmicutes) was significantly higher in both LAB-treated groups than in the control. Comparing the impact of the two Lactobacillus strains on microbial composition in the gut also suggests strain-specific effects. The study emphasises the need for deeper studies into functional specificity of a probiotic organism at the strain level. Alleviation of obesity-associated dysbiosis by modulation of the gut microbiota appears to be associated with "indicator" bacterial taxa such as the family Lachnospiraceae. This may provide further insight into mechanisms basic to the mode of probiotic action against obesity and associated dysbiosis.}, } @article {pmid27856001, year = {2017}, author = {Younge, N and Yang, Q and Seed, PC}, title = {Enteral High Fat-Polyunsaturated Fatty Acid Blend Alters the Pathogen Composition of the Intestinal Microbiome in Premature Infants with an Enterostomy.}, journal = {The Journal of pediatrics}, volume = {181}, number = {}, pages = {93-101.e6}, pmid = {27856001}, issn = {1097-6833}, support = {K12 HD043494/HD/NICHD NIH HHS/United States ; R01 GM108494/GM/NIGMS NIH HHS/United States ; T32 HD060558/HD/NICHD NIH HHS/United States ; }, mesh = {*Dietary Supplements ; Enteral Nutrition/*methods ; *Enterostomy ; Fatty Acids, Unsaturated/*administration & dosage ; Female ; Fish Oils/administration & dosage ; *Gastrointestinal Microbiome ; Gestational Age ; Humans ; Infant, Newborn ; Infant, Premature ; Male ; Reference Values ; Risk Assessment ; Safflower Oil/administration & dosage ; Treatment Outcome ; }, abstract = {OBJECTIVE: To determine the effect of enteral fish oil and safflower oil supplementation on the intestinal microbiome in infants with an enterostomy born premature.

STUDY DESIGN: Infants with an enterostomy born premature were randomized to receive early enteral supplementation with a high-fat polyunsaturated fatty acid (HF-PUFA) blend of fish oil and safflower oil vs standard nutritional therapy. We used 16S rRNA gene sequencing for longitudinal profiling of the microbiome from the time of study entry until bowel reanastomosis. We used weighted gene coexpression network analysis to identify microbial community modules that differed between study groups over time. We performed imputed metagenomic analysis to determine metabolic pathways associated with the microbial genes.

RESULTS: Sixteen infants were randomized to receive enteral HF-PUFA supplementation, and 16 infants received standard care. The intestinal microbiota of infants in the treatment group differed from those in the control group, with greater bacterial diversity and lower abundance of Streptococcus, Clostridium, and many pathogenic genera within the Enterobacteriaceae family. We identified 4 microbial community modules with significant differences between groups over time. Imputed metagenomic analysis of the microbial genes revealed metabolic pathways that differed between groups, including metabolism of amino acids, carbohydrates, fatty acids, and secondary bile acid synthesis.

CONCLUSION: Enteral HF-PUFA supplementation was associated with decreased abundance of pathogenic bacteria, greater bacterial diversity, and shifts in the potential metabolic functions of intestinal microbiota.

TRIAL REGISTRATION: ClinicalTrials.gov:NCT01306838.}, } @article {pmid27852235, year = {2016}, author = {Ottesen, A and Ramachandran, P and Reed, E and White, JR and Hasan, N and Subramanian, P and Ryan, G and Jarvis, K and Grim, C and Daquiqan, N and Hanes, D and Allard, M and Colwell, R and Brown, E and Chen, Y}, title = {Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak.}, journal = {BMC microbiology}, volume = {16}, number = {1}, pages = {275}, pmid = {27852235}, issn = {1471-2180}, mesh = {Bacteriological Techniques/methods ; DNA, Bacterial/genetics/isolation & purification ; Disease Outbreaks ; Food Microbiology/*methods/standards ; Foodborne Diseases/microbiology ; Humans ; Ice Cream/*microbiology ; Listeria monocytogenes/genetics/*isolation & purification ; Listeriosis/*microbiology ; *Microbiota ; United States ; United States Department of Agriculture ; United States Food and Drug Administration ; }, abstract = {BACKGROUND: Microbiota that co-enrich during efforts to recover pathogens from foodborne outbreaks interfere with efficient detection and recovery. Here, dynamics of co-enriching microbiota during recovery of Listeria monocytogenes from naturally contaminated ice cream samples linked to an outbreak are described for three different initial enrichment formulations used by the Food and Drug Administration (FDA), the International Organization of Standardization (ISO), and the United States Department of Agriculture (USDA). Enrichment cultures were analyzed using DNA extraction and sequencing from samples taken every 4 h throughout 48 h of enrichment. Resphera Insight and CosmosID analysis tools were employed for high-resolution profiling of 16S rRNA amplicons and whole genome shotgun data, respectively.

RESULTS: During enrichment, other bacterial taxa were identified, including Anoxybacillus, Geobacillus, Serratia, Pseudomonas, Erwinia, and Streptococcus spp. Surprisingly, incidence of L. monocytogenes was proportionally greater at hour 0 than when tested 4, 8, and 12 h later with all three enrichment schemes. The corresponding increase in Anoxybacillus and Geobacillus spp.indicated these taxa co-enriched in competition with L. monocytogenes during early enrichment hours. L. monocytogenes became dominant after 24 h in all three enrichments. DNA sequences obtained from shotgun metagenomic data of Listeria monocytogenes at 48 h were assembled to produce a consensus draft genome which appeared to have a similar tracking utility to pure culture isolates of L. monocytogenes.

CONCLUSIONS: All three methods performed equally well for enrichment of Listeria monocytogenes. The observation of potential competitive exclusion of L. mono by Anoxybacillus and Geobacillus in early enrichment hours provided novel information that may be used to further optimize enrichment formulations. Application of Resphera Insight for high-resolution analysis of 16S amplicon sequences accurately identified L. monocytogenes. Both shotgun and 16S rRNA data supported the presence of three slightly variable genomes of L. monocytogenes. Moreover, the draft assembly of a consensus genome of L. monocytogenes from shotgun metagenomic data demonstrated the potential utility of this approach to expedite trace-back of outbreak-associated strains, although further validation will be needed to confirm this utility.}, } @article {pmid27852226, year = {2016}, author = {Gregory, AC and Solonenko, SA and Ignacio-Espinoza, JC and LaButti, K and Copeland, A and Sudek, S and Maitland, A and Chittick, L and Dos Santos, F and Weitz, JS and Worden, AZ and Woyke, T and Sullivan, MB}, title = {Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {930}, pmid = {27852226}, issn = {1471-2164}, mesh = {Bacteriophages/classification/*genetics ; Biological Evolution ; Comparative Genomic Hybridization ; DNA/metabolism ; DNA, Viral/chemistry/isolation & purification/metabolism ; Gene Transfer, Horizontal/*genetics ; Genetic Linkage ; *Genome, Viral ; Host Specificity ; Metagenomics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Genetic recombination is a driving force in genome evolution. Among viruses it has a dual role. For genomes with higher fitness, it maintains genome integrity in the face of high mutation rates. Conversely, for genomes with lower fitness, it provides immediate access to sequence space that cannot be reached by mutation alone. Understanding how recombination impacts the cohesion and dissolution of individual whole genomes within viral sequence space is poorly understood across double-stranded DNA bacteriophages (a.k.a phages) due to the challenges of obtaining appropriately scaled genomic datasets.

RESULTS: Here we explore the role of recombination in both maintaining and differentiating whole genomes of 142 wild double-stranded DNA marine cyanophages. Phylogenomic analysis across the 51 core genes revealed ten lineages, six of which were well represented. These phylogenomic lineages represent discrete genotypic populations based on comparisons of intra- and inter- lineage shared gene content, genome-wide average nucleotide identity, as well as detected gaps in the distribution of pairwise differences between genomes. McDonald-Kreitman selection tests identified putative niche-differentiating genes under positive selection that differed across the six well-represented genotypic populations and that may have driven initial divergence. Concurrent with patterns of recombination of discrete populations, recombination analyses of both genic and intergenic regions largely revealed decreased genetic exchange across individual genomes between relative to within populations.

CONCLUSIONS: These findings suggest that discrete double-stranded DNA marine cyanophage populations occur in nature and are maintained by patterns of recombination akin to those observed in bacteria, archaea and in sexual eukaryotes.}, } @article {pmid27846901, year = {2016}, author = {Zhou, X and Nardini, C}, title = {A method for automated pathogenic content estimation with application to rheumatoid arthritis.}, journal = {BMC systems biology}, volume = {10}, number = {1}, pages = {107}, pmid = {27846901}, issn = {1752-0509}, mesh = {Arthritis, Rheumatoid/*microbiology ; Automation ; Biodiversity ; Computational Biology/*methods ; Gastrointestinal Microbiome ; Humans ; }, abstract = {BACKGROUND: Sequencing technologies applied to mammals' microbiomes have revolutionized our understanding of health and disease. Hence, to assess diseases' progression as well as therapies longterm effects, the impact of maladies and drugs on the gut-intestinal (GI) microbiome has to be evaluated. Typical metagenomic analyses are run to associate to a condition (disease, therapy, diet) a pool of bacteria, whose eubiotic/dysbiotic potential is assessed either by α-diversity, a measure of the varieties populating the microbiome, or by Firmicutes to Bacteroides ratio, associated to systemic inflammation, and finally by manual and direct inspection of bacteria's biological functions, when known. These approaches lead to results sometimes difficult to interpret in terms of the evolution towards a specific microbial composition, harmed by large areas of unknown.

RESULTS: We propose to additionally evaluate a microbiome based on its global composition, by automatic annotation of pathogenic genera and statistical assessment of the net varied frequency of harmless versus harmful organisms. This application is intuitive, quantitative and computationally efficient and designed to cope with the currently incomplete species' functional knowledge. Our results, applied to human GI-microbiome data exemplify how this layer of information provides additional insights into treatments' impact on the GI microbiome, allowing to characterize a more physiologic effects of Prednisone versus Methotrexate, two treatments for rheumatoid arthritis (RA) a complex autoimmune systemic disease.

CONCLUSIONS: Our quantitative analysis integrates with previous approaches offering an additional systemic level of interpretation here applied, for its potential to translate into clinically relevant information, to the therapies for RA.}, } @article {pmid27846295, year = {2016}, author = {Ericsson, AC and Johnson, PJ and Lopes, MA and Perry, SC and Lanter, HR}, title = {A Microbiological Map of the Healthy Equine Gastrointestinal Tract.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0166523}, pmid = {27846295}, issn = {1932-6203}, support = {K01 OD019924/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/*genetics ; Bacterial Typing Techniques ; Cecum/microbiology ; Colon/microbiology ; Duodenum/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Horses/*microbiology ; Ileum/microbiology ; Jejunum/microbiology ; Male ; Organ Specificity ; Principal Component Analysis ; RNA, Ribosomal, 16S/*genetics ; Stomach/microbiology ; Symbiosis/physiology ; }, abstract = {Horses are exquisitely sensitive to non-specific gastrointestinal disturbances as well as systemic and extraintestinal conditions related to gut health, yet minimal data are available regarding the composition of the microbiota present in the equine stomach, small intestine, and cecum and their relation to fecal microbiota. Moreover, there is minimal information regarding the concordance of the luminal and mucosal microbial communities throughout the equine gut. Illumina-based 16S rRNA gene amplicon sequencing of the luminal and mucosal microbiota present in seven regions of the gastrointestinal tract of nine healthy adult horses revealed a distinct compositional divide between the small and large intestines. This disparity in composition was more pronounced within the luminal contents, but was also detected within mucosal populations. Moreover, the uniformity of the gut microbiota was much higher in the cecum and colon relative to that in the stomach, jejunum and ileum, despite a significantly higher number of unique sequences detected in the colon. Collectively, the current data suggest that while colonic samples (a proxy for feces) may provide a reasonable profile of the luminal contents of the healthy equine large intestine, they are not informative with regard to the contents of the stomach or small intestine. In contrast to the distinct difference between the highly variable upper gastrointestinal tract microbiota and relatively uniform large bowel microbiota present within the lumen, these data also demonstrate a regional continuity present in mucosal microbial communities throughout the length of the equine gut.}, } @article {pmid27842515, year = {2016}, author = {Wagner, J and Coupland, P and Browne, HP and Lawley, TD and Francis, SC and Parkhill, J}, title = {Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification.}, journal = {BMC microbiology}, volume = {16}, number = {1}, pages = {274}, pmid = {27842515}, issn = {1471-2180}, support = {/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; G0701039/MRC_/Medical Research Council/United Kingdom ; G1002369/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Base Sequence ; Biodiversity ; Computational Biology/methods ; DNA, Bacterial/*genetics ; DNA, Ribosomal/genetics ; Female ; Genetic Variation ; High-Throughput Nucleotide Sequencing/instrumentation/*methods ; Humans/microbiology ; Metagenome ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/*classification/*genetics ; Sequence Analysis, DNA ; Staphylococcus aureus/genetics ; Vagina/microbiology ; }, abstract = {BACKGROUND: Currently, bacterial 16S rRNA gene analyses are based on sequencing of individual variable regions of the 16S rRNA gene (Kozich, et al Appl Environ Microbiol 79:5112-5120, 2013).This short read approach can introduce biases. Thus, full-length bacterial 16S rRNA gene sequencing is needed to reduced biases. A new alternative for full-length bacterial 16S rRNA gene sequencing is offered by PacBio single molecule, real-time (SMRT) technology. The aim of our study was to validate PacBio P6 sequencing chemistry using three approaches: 1) sequencing the full-length bacterial 16S rRNA gene from a single bacterial species Staphylococcus aureus to analyze error modes and to optimize the bioinformatics pipeline; 2) sequencing the full-length bacterial 16S rRNA gene from a pool of 50 different bacterial colonies from human stool samples to compare with full-length bacterial 16S rRNA capillary sequence; and 3) sequencing the full-length bacterial 16S rRNA genes from 11 vaginal microbiome samples and compare with in silico selected bacterial 16S rRNA V1V2 gene region and with bacterial 16S rRNA V1V2 gene regions sequenced using the Illumina MiSeq.

RESULTS: Our optimized bioinformatics pipeline for PacBio sequence analysis was able to achieve an error rate of 0.007% on the Staphylococcus aureus full-length 16S rRNA gene. Capillary sequencing of the full-length bacterial 16S rRNA gene from the pool of 50 colonies from stool identified 40 bacterial species of which up to 80% could be identified by PacBio full-length bacterial 16S rRNA gene sequencing. Analysis of the human vaginal microbiome using the bacterial 16S rRNA V1V2 gene region on MiSeq generated 129 operational taxonomic units (OTUs) from which 70 species could be identified. For the PacBio, 36,000 sequences from over 58,000 raw reads could be assigned to a barcode, and the in silico selected bacterial 16S rRNA V1V2 gene region generated 154 OTUs grouped into 63 species, of which 62% were shared with the MiSeq dataset. The PacBio full-length bacterial 16S rRNA gene datasets generated 261 OTUs, which were grouped into 52 species, of which 54% were shared with the MiSeq dataset. Alpha diversity index reported a higher diversity in the MiSeq dataset.

CONCLUSION: The PacBio sequencing error rate is now in the same range of the previously widely used Roche 454 sequencing platform and current MiSeq platform. Species-level microbiome analysis revealed some inconsistencies between the full-length bacterial 16S rRNA gene capillary sequencing and PacBio sequencing.}, } @article {pmid27842027, year = {2016}, author = {Puranik, S and Pal, RR and More, RP and Purohit, HJ}, title = {Metagenomic approach to characterize soil microbial diversity of Phumdi at Loktak Lake.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {74}, number = {9}, pages = {2075-2086}, doi = {10.2166/wst.2016.370}, pmid = {27842027}, issn = {0273-1223}, mesh = {Bacteria/*genetics ; Biodegradation, Environmental ; Biodiversity ; Biomass ; Ecosystem ; Genome, Bacterial ; India ; Islands ; Lakes/*microbiology ; *Metagenomics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Loktak, one of the largest freshwater lakes of India, is known for floating islands (Phumdi), being made up of a heterogeneous biomass of vegetation and soil. This ecological site represents an exclusive environmental habitat wherein the rhizospheric microbial community of Phumdi plays a key role in biogeochemical cycling of nutrients. A culture-independent whole genome shotgun sequencing based metagenomic approach was employed to unravel the composition of the microbial community and its corresponding functional potential at this environmental habitat. Proteobacteria (51%) was found to be the most dominant bacterial phylum followed by Acidobacteria (10%), Actinobacteria (9%) and Bacteroidetes (7%). Furthermore, Loktak metagenome data were compared with available metagenomes from four other aquatic habitats, varying from pristine to highly polluted eutrophic habitats. The comparative metagenomics approach aided by statistical analysis revealed that Candidatus Solibacter, Bradyrhizobium, Candidatus Koribacter, Pedosphaera, Methylobacterium, Anaeromyxobacter, Sorangium, Opitutus and Acidobacterium genera are selectively dominant at this habitat. Correspondingly, 12 different functional categories were found to be exclusively prevalent at Phumdi compared to other freshwater habitats. These differential features have been attributed to the unique habitat at Phumdi and correlated to the phenomenon of bioremediation at Loktak Lake.}, } @article {pmid27833995, year = {2017}, author = {Thomas, P and Sekhar, AC}, title = {Cultivation Versus Molecular Analysis of Banana (Musa sp.) Shoot-Tip Tissue Reveals Enormous Diversity of Normally Uncultivable Endophytic Bacteria.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {885-899}, pmid = {27833995}, issn = {1432-184X}, mesh = {Bacteria/*classification/*genetics/isolation & purification ; Biodiversity ; Chloroplasts/genetics ; DNA, Bacterial/genetics/isolation & purification ; DNA, Ribosomal/genetics ; Ecosystem ; Endophytes/*classification/*genetics/isolation & purification ; India ; Metagenome ; Metagenomics/methods ; Microbiota ; Mitochondria/genetics ; Musa/*microbiology ; *Phylogeny ; Plant Shoots/*growth & development/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {The interior of plants constitutes a unique environment for microorganisms with various organisms inhabiting as endophytes. Unlike subterranean plant parts, aboveground parts are relatively less explored for endophytic microbial diversity. We employed a combination of cultivation and molecular approaches to study the endophytic bacterial diversity in banana shoot-tips. Cultivable bacteria from 20 sucker shoot-tips of cv. Grand Naine included 37 strains under 16 genera and three phyla (Proteobacteria, Actinobacteria, Firmicutes). 16S rRNA gene-ribotyping approach on 799f and 1492r PCR-amplicons to avoid plant organelle sequences was ineffective showing limited bacterial diversity. 16S rRNA metagene profiling targeting the V3-V4 hypervariable region after filtering out the chloroplast (74.2 %), mitochondrial (22.9 %), and unknown sequences (1.1 %) revealed enormous bacterial diversity. Proteobacteria formed the predominant phylum (64 %) succeeded by Firmicutes (12.1 %), Actinobacteria (9.5 %), Bacteroidetes (6.4 %), Planctomycetes, Cyanobacteria, and minor shares (<1 %) of 14 phyla including several candidate phyla besides the domain Euryarchaeota (0.2 %). Microbiome analysis of single shoot-tips through 16S rRNA V3 region profiling showed similar taxonomic richness and diversity and was less affected by plant sequence interferences. DNA extraction kit ominously influenced the phylogenetic diversity. The study has revealed vast diversity of normally uncultivable endophytic bacteria prevailing in banana shoot-tips (20 phyla, 46 classes) with about 2.6 % of the deciphered 269 genera and 1.5 % of the 656 observed species from the same source of shoot-tips attained through cultivation. The predominant genera included several agriculturally important bacteria. The study reveals an immense ecosystem of endophytic bacteria in banana shoot tissues endorsing the earlier documentation of intracellular "Cytobacts" and "Peribacts" with possible roles in plant holobiome and hologenome.}, } @article {pmid27830675, year = {2016}, author = {Rusin, LY}, title = {[Metagenomics and biodiversity of sphagnum bogs].}, journal = {Molekuliarnaia biologiia}, volume = {50}, number = {5}, pages = {730-734}, doi = {10.7868/S0026898416050153}, pmid = {27830675}, issn = {0026-8984}, mesh = {*Biodiversity ; Metagenomics/*methods/trends ; *Wetlands ; }, abstract = {Biodiversity of sphagnum bogs is one of the richest and less studied, while these ecosystems are among the top ones in ecological, conservation, and economic value. Recent studies focused on the prokaryotic consortia associated with sphagnum mosses, and revealed the factors that maintain sustainability and productivity of bog ecosystems. High-throughput sequencing technologies provided insight into functional diversity of moss microbial communities (microbiomes), and helped to identify the biochemical pathways and gene families that facilitate the spectrum of adaptive strategies and largely foster the very successful colonization of the Northern hemisphere by sphagnum mosses. Rich and valuable information obtained on microbiomes of peat bogs sets off the paucity of evidence on their eukaryotic diversity. Prospects and expectations of reliable assessment of taxonomic profiles, relative abundance of taxa, and hidden biodiversity of microscopic eukaryotes in sphagnum bog ecosystems are briefly outlined in the context of today's metagenomics.}, } @article {pmid27829306, year = {2016}, author = {Xu, J}, title = {Fungal DNA barcoding.}, journal = {Genome}, volume = {59}, number = {11}, pages = {913-932}, doi = {10.1139/gen-2016-0046}, pmid = {27829306}, issn = {1480-3321}, mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic/methods/standards ; DNA, Fungal ; DNA, Intergenic ; Databases, Nucleic Acid/standards ; Environmental Microbiology ; Food Microbiology ; Fungi/*classification/*genetics/metabolism ; Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; Microbiota ; Mouth/microbiology ; Research ; Sequence Analysis, DNA/methods ; Soil Microbiology ; }, abstract = {Fungi are ubiquitous in both natural and human-made environments. They play important roles in the health of plants, animals, and humans, and in broad ecosystem functions. Thus, having an efficient species-level identification system could significantly enhance our ability to treat fungal diseases and to monitor the spatial and temporal patterns of fungal distributions and migrations. DNA barcoding is a potent approach for rapid identification of fungal specimens, generating novel species hypothesis, and guiding biodiversity and ecological studies. In this mini-review, I briefly summarize (i) the history of DNA sequence-based fungal identification; (ii) the emergence of the ITS region as the consensus primary fungal barcode; (iii) the use of the ITS barcodes to address a variety of issues on fungal diversity from local to global scales, including generating a large number of species hypothesis; and (iv) the problems with the ITS barcode region and the approaches to overcome these problems. Similar to DNA barcoding research on plants and animals, significant progress has been achieved over the last few years in terms of both the questions being addressed and the foundations being laid for future research endeavors. However, significant challenges remain. I suggest three broad areas of research to enhance the usefulness of fungal DNA barcoding to meet the current and future challenges: (i) develop a common set of primers and technologies that allow the amplification and sequencing of all fungi at both the primary and secondary barcode loci; (ii) compile a centralized reference database that includes all recognized fungal species as well as species hypothesis, and allows regular updates from the research community; and (iii) establish a consensus set of new species recognition criteria based on barcode DNA sequences that can be applied across the fungal kingdom.}, } @article {pmid27825829, year = {2016}, author = {Bouhajja, E and Agathos, SN and George, IF}, title = {Metagenomics: Probing pollutant fate in natural and engineered ecosystems.}, journal = {Biotechnology advances}, volume = {34}, number = {8}, pages = {1413-1426}, doi = {10.1016/j.biotechadv.2016.10.006}, pmid = {27825829}, issn = {1873-1899}, mesh = {*Biodegradation, Environmental ; *Ecosystem ; *Environmental Pollutants/analysis/chemistry/isolation & purification/metabolism ; Metabolic Networks and Pathways/genetics ; Metagenome/*genetics ; *Metagenomics ; Microbial Consortia/*genetics ; }, abstract = {Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field. In this review, we survey the main steps of metagenomics applied to environments contaminated with organic compounds or heavy metals. We emphasize technical solutions proposed to overcome encountered obstacles. We then compare two metagenomic approaches, i.e. library-based targeted metagenomics and direct sequencing of metagenomes. In the former, environmental DNA is cloned inside a host, and then clones of interest are selected based on (i) their expression of biodegradative functions or (ii) sequence homology with probes and primers designed from relevant, already known sequences. The highest score for the discovery of novel genes and degradation pathways has been achieved so far by functional screening of large clone libraries. On the other hand, direct sequencing of metagenomes without a cloning step has been more often applied to polluted environments for characterization of the taxonomic and functional composition of microbial communities and their dynamics. In this case, the analysis has focused on 16S rRNA genes and marker genes of biodegradation. Advances in next generation sequencing and in bioinformatic analysis of sequencing data have opened up new opportunities for assessing the potential of biodegradation by microbes, but annotation of collected genes is still hampered by a limited number of available reference sequences in databases. Although metagenomics is still facing technical and computational challenges, our review of the recent literature highlights its value as an aid to efficiently monitor the clean-up of contaminated environments and develop successful strategies to mitigate the impact of pollutants on ecosystems.}, } @article {pmid27824342, year = {2017}, author = {Biggs, MB and Medlock, GL and Moutinho, TJ and Lees, HJ and Swann, JR and Kolling, GL and Papin, JA}, title = {Systems-level metabolism of the altered Schaedler flora, a complete gut microbiota.}, journal = {The ISME journal}, volume = {11}, number = {2}, pages = {426-438}, pmid = {27824342}, issn = {1751-7370}, support = {T35 AI060528/AI/NIAID NIH HHS/United States ; T32 LM012416/LM/NLM NIH HHS/United States ; T32 GM008715/GM/NIGMS NIH HHS/United States ; R01 GM108501/GM/NIGMS NIH HHS/United States ; T32 GM145443/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/growth & development/*metabolism ; Culture Media ; Gastrointestinal Microbiome/genetics/*physiology ; Host-Pathogen Interactions ; Humans ; Metagenome ; Mice ; Models, Biological ; }, abstract = {The altered Schaedler flora (ASF) is a model microbial community with both in vivo and in vitro relevance. Here we provide the first characterization of the ASF community in vitro, independent of a murine host. We compared the functional genetic content of the ASF to wild murine metagenomes and found that the ASF functionally represents wild microbiomes better than random consortia of similar taxonomic composition. We developed a chemically defined medium that supported growth of seven of the eight ASF members. To elucidate the metabolic capabilities of these ASF species-including potential for interactions such as cross-feeding-we performed a spent media screen and analyzed the results through dynamic growth measurements and non-targeted metabolic profiling. We found that cross-feeding is relatively rare (32 of 3570 possible cases), but is enriched between Clostridium ASF356 and Parabacteroides ASF519. We identified many cases of emergent metabolism (856 of 3570 possible cases). These data will inform efforts to understand ASF dynamics and spatial distribution in vivo, to design pre- and probiotics that modulate relative abundances of ASF members, and will be essential for validating computational models of ASF metabolism. Well-characterized, experimentally tractable microbial communities enable research that can translate into more effective microbiome-targeted therapies to improve human health.}, } @article {pmid27821485, year = {2017}, author = {Viennois, E and Merlin, D and Gewirtz, AT and Chassaing, B}, title = {Dietary Emulsifier-Induced Low-Grade Inflammation Promotes Colon Carcinogenesis.}, journal = {Cancer research}, volume = {77}, number = {1}, pages = {27-40}, pmid = {27821485}, issn = {1538-7445}, support = {IK6 BX004476/BX/BLRD VA/United States ; R01 DK071594/DK/NIDDK NIH HHS/United States ; R01 DK083890/DK/NIDDK NIH HHS/United States ; R01 DK099071/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Carboxymethylcellulose Sodium/toxicity ; Cell Transformation, Neoplastic/*chemically induced ; Colitis/*chemically induced/microbiology ; Colonic Neoplasms/*chemically induced/microbiology ; Disease Models, Animal ; Emulsifying Agents/*toxicity ; Food Additives/*toxicity ; Gastrointestinal Microbiome/drug effects ; Male ; Mice ; Mice, Inbred C57BL ; Polysorbates/toxicity ; }, abstract = {The increased risks conferred by inflammatory bowel disease (IBD) to the development of colorectal cancer gave rise to the term "colitis-associated cancer" and the concept that inflammation promotes colon tumorigenesis. A condition more common than IBD is low-grade inflammation, which correlates with altered gut microbiota composition and metabolic syndrome, both present in many cases of colorectal cancer. Recent findings suggest that low-grade inflammation in the intestine is promoted by consumption of dietary emulsifiers, a ubiquitous component of processed foods, which alter the composition of gut microbiota. Here, we demonstrate in a preclinical model of colitis-induced colorectal cancer that regular consumption of dietary emulsifiers, carboxymethylcellulose or polysorbate-80, exacerbated tumor development. Enhanced tumor development was associated with an altered microbiota metagenome characterized by elevated levels of lipopolysaccharide and flagellin. We found that emulsifier-induced alterations in the microbiome were necessary and sufficient to drive alterations in major proliferation and apoptosis signaling pathways thought to govern tumor development. Overall, our findings support the concept that perturbations in host-microbiota interactions that cause low-grade gut inflammation can promote colon carcinogenesis. Cancer Res; 77(1); 27-40. ©2016 AACR.}, } @article {pmid27821063, year = {2016}, author = {Chan, YK and Brar, MS and Kirjavainen, PV and Chen, Y and Peng, J and Li, D and Leung, FC and El-Nezami, H}, title = {High fat diet induced atherosclerosis is accompanied with low colonic bacterial diversity and altered abundances that correlates with plaque size, plasma A-FABP and cholesterol: a pilot study of high fat diet and its intervention with Lactobacillus rhamnosus GG (LGG) or telmisartan in ApoE[-/-] mice.}, journal = {BMC microbiology}, volume = {16}, number = {1}, pages = {264}, pmid = {27821063}, issn = {1471-2180}, mesh = {Animals ; Apolipoproteins E/deficiency/genetics ; Atherosclerosis/*drug therapy/metabolism/microbiology/pathology ; Benzimidazoles/*administration & dosage ; Benzoates/*administration & dosage ; Cholesterol/*blood ; Colon/*microbiology ; Diet, High-Fat/adverse effects ; Fatty Acid-Binding Proteins/*blood ; Female ; *Gastrointestinal Microbiome ; Humans ; Lacticaseibacillus rhamnosus/*physiology ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Pilot Projects ; Probiotics/*administration & dosage ; Telmisartan ; }, abstract = {BACKGROUND: Atherosclerosis appears to have multifactorial causes - microbial component like lipopolysaccharides (LPS) and other pathogen associated molecular patterns may be plausible factors. The gut microbiota is an ample source of such stimulants, and its dependent metabolites and altered gut metagenome has been an established link to atherosclerosis. In this exploratory pilot study, we aimed to elucidate whether microbial intervention with probiotics L. rhamnosus GG (LGG) or pharmaceuticals telmisartan (TLM) could improve atherosclerosis in a gut microbiota associated manner.

METHODS: Atherosclerotic phenotype was established by 12 weeks feeding of high fat (HF) diet as opposed to normal chow diet (ND) in apolipoprotein E knockout (ApoE[-/-]) mice. LGG or TLM supplementation to HF diet was studied.

RESULTS: Both LGG and TLM significantly reduced atherosclerotic plaque size and improved various biomarkers including endotoxin to different extents. Colonial microbiota analysis revealed that TLM restored HF diet induced increase in Firmicutes/Bacteroidetes ratio and decrease in alpha diversity; and led to a more distinct microbial clustering closer to ND in PCoA plot. Eubacteria, Anaeroplasma, Roseburia, Oscillospira and Dehalobacteria appeared to be protective against atherosclerosis and showed significant negative correlation with atherosclerotic plaque size and plasma adipocyte - fatty acid binding protein (A-FABP) and cholesterol.

CONCLUSION: LGG and TLM improved atherosclerosis with TLM having a more distinct alteration in the colonic gut microbiota. Altered bacteria genera and reduced alpha diversity had significant correlations to atherosclerotic plaque size, plasma A-FABP and cholesterol. Future studies on such bacterial functional influence in lipid metabolism will be warranted.}, } @article {pmid27820856, year = {2016}, author = {Iwai, S and Weinmaier, T and Schmidt, BL and Albertson, DG and Poloso, NJ and Dabbagh, K and DeSantis, TZ}, title = {Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0166104}, pmid = {27820856}, issn = {1932-6203}, support = {R01 CA131286/CA/NCI NIH HHS/United States ; R01 DE019796/DE/NIDCR NIH HHS/United States ; R21 CA163019/CA/NCI NIH HHS/United States ; TL1 RR024129/RR/NCRR NIH HHS/United States ; }, mesh = {Algorithms ; Databases, Factual ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S ; Software ; }, abstract = {Functional analysis of a clinical microbiome facilitates the elucidation of mechanisms by which microbiome perturbation can cause a phenotypic change in the patient. The direct approach for the analysis of the functional capacity of the microbiome is via shotgun metagenomics. An inexpensive method to estimate the functional capacity of a microbial community is through collecting 16S rRNA gene profiles then indirectly inferring the abundance of functional genes. This inference approach has been implemented in the PICRUSt and Tax4Fun software tools. However, those tools have important limitations since they rely on outdated functional databases and uncertain phylogenetic trees and require very specific data pre-processing protocols. Here we introduce Piphillin, a straightforward algorithm independent of any proposed phylogenetic tree, leveraging contemporary functional databases and not obliged to any singular data pre-processing protocol. When all three inference tools were evaluated against actual shotgun metagenomics, Piphillin was superior in predicting gene composition in human clinical samples compared to both PICRUSt and Tax4Fun (p<0.01 and p<0.001, respectively) and Piphillin's ability to predict disease associations with specific gene orthologs exhibited a 15% increase in balanced accuracy compared to PICRUSt. From laboratory animal samples, no performance advantage was observed for any one of the tools over the others and for environmental samples all produced unsatisfactory predictions. Our results demonstrate that functional inference using the direct method implemented in Piphillin is preferable for clinical biospecimens. Piphillin is publicly available for academic use at http://secondgenome.com/Piphillin.}, } @article {pmid27819664, year = {2016}, author = {Brown, CT and Olm, MR and Thomas, BC and Banfield, JF}, title = {Measurement of bacterial replication rates in microbial communities.}, journal = {Nature biotechnology}, volume = {34}, number = {12}, pages = {1256-1263}, pmid = {27819664}, issn = {1546-1696}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; }, mesh = {*Algorithms ; Bacteria/*genetics/isolation & purification ; Bacterial Load/*genetics/*methods ; Cell Proliferation/genetics ; Chromosome Mapping/*methods ; Genome, Bacterial/genetics ; Microbial Consortia/*physiology ; Reproducibility of Results ; Sensitivity and Specificity ; }, abstract = {Culture-independent microbiome studies have increased our understanding of the complexity and metabolic potential of microbial communities. However, to understand the contribution of individual microbiome members to community functions, it is important to determine which bacteria are actively replicating. We developed an algorithm, iRep, that uses draft-quality genome sequences and single time-point metagenome sequencing to infer microbial population replication rates. The algorithm calculates an index of replication (iRep) based on the sequencing coverage trend that results from bi-directional genome replication from a single origin of replication. We apply this method to show that microbial replication rates increase after antibiotic administration in human infants. We also show that uncultivated, groundwater-associated, Candidate Phyla Radiation bacteria only rarely replicate quickly in subsurface communities undergoing substantial changes in geochemistry. Our method can be applied to any genome-resolved microbiome study to track organism responses to varying conditions, identify actively growing populations and measure replication rates for use in modeling studies.}, } @article {pmid27819657, year = {2016}, author = {Lagier, JC and Khelaifia, S and Alou, MT and Ndongo, S and Dione, N and Hugon, P and Caputo, A and Cadoret, F and Traore, SI and Seck, EH and Dubourg, G and Durand, G and Mourembou, G and Guilhot, E and Togo, A and Bellali, S and Bachar, D and Cassir, N and Bittar, F and Delerce, J and Mailhe, M and Ricaboni, D and Bilen, M and Dangui Nieko, NP and Dia Badiane, NM and Valles, C and Mouelhi, D and Diop, K and Million, M and Musso, D and Abrahão, J and Azhar, EI and Bibi, F and Yasir, M and Diallo, A and Sokhna, C and Djossou, F and Vitton, V and Robert, C and Rolain, JM and La Scola, B and Fournier, PE and Levasseur, A and Raoult, D}, title = {Culture of previously uncultured members of the human gut microbiota by culturomics.}, journal = {Nature microbiology}, volume = {1}, number = {}, pages = {16203}, doi = {10.1038/nmicrobiol.2016.203}, pmid = {27819657}, issn = {2058-5276}, mesh = {Archaea/classification/genetics/*growth & development/*isolation & purification ; Bacteria/classification/genetics/*growth & development/*isolation & purification ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Microbiological Techniques/*methods ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; }, abstract = {Metagenomics revolutionized the understanding of the relations among the human microbiome, health and diseases, but generated a countless number of sequences that have not been assigned to a known microorganism[1]. The pure culture of prokaryotes, neglected in recent decades, remains essential to elucidating the role of these organisms[2]. We recently introduced microbial culturomics, a culturing approach that uses multiple culture conditions and matrix-assisted laser desorption/ionization-time of flight and 16S rRNA for identification[2]. Here, we have selected the best culture conditions to increase the number of studied samples and have applied new protocols (fresh-sample inoculation; detection of microcolonies and specific cultures of Proteobacteria and microaerophilic and halophilic prokaryotes) to address the weaknesses of the previous studies[3-5]. We identified 1,057 prokaryotic species, thereby adding 531 species to the human gut repertoire: 146 bacteria known in humans but not in the gut, 187 bacteria and 1 archaea not previously isolated in humans, and 197 potentially new species. Genome sequencing was performed on the new species. By comparing the results of the metagenomic and culturomic analyses, we show that the use of culturomics allows the culture of organisms corresponding to sequences previously not assigned. Altogether, culturomics doubles the number of species isolated at least once from the human gut.}, } @article {pmid27819120, year = {2016}, author = {Li, Z and Wang, Y and Li, J and Liu, F and He, L and He, Y and Wang, S}, title = {Metagenomic Analysis of Genes Encoding Nutrient Cycling Pathways in the Microbiota of Deep-Sea and Shallow-Water Sponges.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {18}, number = {6}, pages = {659-671}, pmid = {27819120}, issn = {1436-2236}, mesh = {Animals ; Archaea/classification/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Biological Evolution ; Carbon/metabolism ; Fungi/classification/*genetics/metabolism ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Microbiota/genetics ; Nitrogen/metabolism ; Phosphorus/metabolism ; Phylogeny ; Porifera/classification/genetics/*microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Stramenopiles/classification/*genetics/metabolism ; Sulfur/metabolism ; Symbiosis/physiology ; }, abstract = {Sponges host complex symbiotic communities, but to date, the whole picture of the metabolic potential of sponge microbiota remains unclear, particularly the difference between the shallow-water and deep-sea sponge holobionts. In this study, two completely different sponges, shallow-water sponge Theonella swinhoei from the South China Sea and deep-sea sponge Neamphius huxleyi from the Indian Ocean, were selected to compare their whole symbiotic communities and metabolic potential, particularly in element transformation. Phylogenetically diverse bacteria, archaea, fungi, and algae were detected in both shallow-water sponge T. swinhoei and deep-sea sponge N. huxleyi, and different microbial community structures were indicated between these two sponges. Metagenome-based gene abundance analysis indicated that, though the two sponge microbiota have similar core functions, they showed different potential strategies in detailed metabolic processes, e.g., in the transformation and utilization of carbon, nitrogen, phosphorus, and sulfur by corresponding microbial symbionts. This study provides insight into the putative metabolic potentials of the microbiota associated with the shallow-water and deep-sea sponges at the whole community level, extending our knowledge of the sponge microbiota's functions, the association of sponge- microbes, as well as the adaption of sponge microbiota to the marine environment.}, } @article {pmid27817942, year = {2017}, author = {Ceugniez, A and Taminiau, B and Coucheney, F and Jacques, P and Delcenserie, V and Daube, G and Drider, D}, title = {Use of a metagenetic approach to monitor the bacterial microbiota of "Tomme d'Orchies" cheese during the ripening process.}, journal = {International journal of food microbiology}, volume = {247}, number = {}, pages = {65-69}, doi = {10.1016/j.ijfoodmicro.2016.10.034}, pmid = {27817942}, issn = {1879-3460}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Cattle ; Cheese/*microbiology ; Food Handling ; Lactococcus/metabolism ; Metagenomics ; *Microbiota ; Milk/*microbiology ; Streptococcus/metabolism ; }, abstract = {The study of microbial ecosystems in artisanal foodstuffs is important to complete in order to unveil its diversity. The number of studies performed on dairy products has increased during the last decade, particularly those performed on milk and cheese derivative products. In this work, we investigated the bacterial content of "Tomme d'Orchies" cheese, an artisanal pressed and uncooked French cheese. To this end, a metagenetic analysis, using Illumina technology, was utilized on samples taken from the surface and core of the cheese at 0, 1, 3, 14 and 21days of ripening process. In addition to the classical microbiota found in cheese, various strains likely from environmental origin were identified. A large difference between the surface and the core content was observed within samples withdrawn during the ripening process. The main species encountered in the core of the cheese were Lactococcus spp. and Streptococcus spp., with an inversion of this ratio during the ripening process. Less than 2.5% of the whole population was composed of strains issued from environmental origin, as Lactobacillales, Corynebacterium and Brevibacterium. In the core, about 85% of the microbiota was attributed to the starters used for the cheese making. In turn, the microbiota of the surface contained less than 30% of these starters and interestingly displayed more diversity. The predominant genus was Corynebacterium sp., likely originating from the environment. The less abundant microbiota of the surface was composed of Bifidobacteria, Brevibacterium and Micrococcales. To summarize, the "Tomme d'Orchies" cheese displayed a high diversity of bacterial species, especially on the surface, and this diversity is assumed to arise from the production environment and subsequent ripening process.}, } @article {pmid27817188, year = {2017}, author = {Li, X and Liu, YH and Zhang, X and Ge, CM and Piao, RZ and Wang, WD and Cui, ZJ and Zhao, HY}, title = {Evaluation of Biogas Production Performance and Dynamics of the Microbial Community in Different Straws.}, journal = {Journal of microbiology and biotechnology}, volume = {27}, number = {3}, pages = {524-534}, doi = {10.4014/jmb.1608.08062}, pmid = {27817188}, issn = {1738-8872}, mesh = {*Biodegradation, Environmental ; Biodiversity ; *Biofuels ; Bioreactors ; Crops, Agricultural ; *Environmental Microbiology ; *Fermentation ; Metagenome ; Metagenomics ; Methane/biosynthesis ; Microbiota ; Volatile Organic Compounds ; }, abstract = {The development and utilization of crop straw biogas resources can effectively alleviate the shortage of energy, environmental pollution, and other issues. This study performed a continuous batch test at 35°C to assess the methane production potential and volatile organic acid contents using the modified Gompertz equation. Illumina MiSeq platform sequencing, which is a sequencing method based on sequencing-by-synthesis, was used to compare the archaeal community diversity, and denaturing gradient gel electrophoresis (DGGE) was used to analyze the bacterial community diversity in rice straw, dry maize straw, silage maize straw, and tobacco straw. The results showed that cumulative gas production values for silage maize straw, rice straw, dry maize straw, and tobacco straw were 4,870, 4,032.5, 3,907.5, and 3,628.3 ml/g ·VS , respectively, after 24 days. Maximum daily gas production values of silage maize straw and rice straw were 1,025 and 904.17 ml/g ·VS, respectively, followed by tobacco straw and dry maize straw. The methane content of all four kinds of straws was > 60%, particularly that of silage maize straw, which peaked at 67.3%. Biogas production from the four kinds of straw was in the order silage maize straw > rice straw > dry maize straw > tobacco straw, and the values were 1,166.7, 1,048.4, 890, and 637.4 ml/g ·VS, respectively. The microbial community analysis showed that metabolism was mainly carried out by acetate-utilizing methanogens, and that Methanosarcina was the dominant archaeal genus in the four kinds of straw, and the DGGE bands belonged to the phyla Firmicutes, Bacteroidetes, and Chloroflexi. Silage maize is useful for biogas production because it contains four kinds of straw.}, } @article {pmid27815277, year = {2017}, author = {Doyle, CJ and Gleeson, D and O'Toole, PW and Cotter, PD}, title = {Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {2}, pages = {}, pmid = {27815277}, issn = {1098-5336}, mesh = {Animals ; *Cattle ; Dairying/*methods ; Feces/microbiology ; Female ; Food Microbiology ; High-Throughput Nucleotide Sequencing ; *Housing, Animal ; Mammary Glands, Animal/*microbiology ; Microbiota/*physiology ; Milk/*microbiology ; *Seasons ; }, abstract = {UNLABELLED: In pasture-based systems, changes in dairy herd habitat due to seasonality results in the exposure of animals to different environmental niches. These niches contain distinct microbial communities that may be transferred to raw milk, with potentially important food quality and safety implications for milk producers. It is postulated that the extent to which these microorganisms are transferred could be limited by the inclusion of a teat preparation step prior to milking. High-throughput sequencing on a variety of microbial niches on farms was used to study the patterns of microbial movement through the dairy production chain and, in the process, to investigate the impact of seasonal housing and the inclusion/exclusion of a teat preparation regime on the raw milk microbiota from the same herd over two sampling periods, i.e., indoor and outdoor. Beta diversity and network analyses showed that environmental and milk microbiotas separated depending on whether they were sourced from an indoor or outdoor environment. Within these respective habitats, similarities between the milk microbiota and that of teat swab samples and, to a lesser extent, fecal samples were apparent. Indeed, SourceTracker identified the teat surface as the most significant source of contamination, with herd feces being the next most prevalent source of contamination. In milk from cows grazing outdoors, teat prep significantly increased the numbers of total bacteria present. In summary, sequence-based microbiota analysis identified possible sources of raw milk contamination and highlighted the influence of environment and farm management practices on the raw milk microbiota.

IMPORTANCE: The composition of the raw milk microbiota is an important consideration from both a spoilage perspective and a food safety perspective and has implications for milk targeted for direct consumption and for downstream processing. Factors that influence contamination have been examined previously, primarily through the use of culture-based techniques. We describe here the extensive application of high-throughput DNA sequencing technologies to study the relationship between the milk production environment and the raw milk microbiota. The results show that the environment in which the herd was kept was the primary driver of the composition of the milk microbiota composition.}, } @article {pmid27815274, year = {2017}, author = {Hagen, LH and Frank, JA and Zamanzadeh, M and Eijsink, VGH and Pope, PB and Horn, SJ and Arntzen, MØ}, title = {Quantitative Metaproteomics Highlight the Metabolic Contributions of Uncultured Phylotypes in a Thermophilic Anaerobic Digester.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {2}, pages = {}, pmid = {27815274}, issn = {1098-5336}, mesh = {Anaerobiosis ; Bacteria/classification/genetics/*metabolism ; Biofuels ; Bioreactors/*microbiology ; Firmicutes/classification/genetics/metabolism ; Garbage ; Metabolic Networks and Pathways ; *Microbial Consortia ; Proteomics ; Sequence Analysis, DNA ; }, abstract = {UNLABELLED: In this study, we used multiple meta-omic approaches to characterize the microbial community and the active metabolic pathways of a stable industrial biogas reactor with food waste as the dominant feedstock, operating at thermophilic temperatures (60°C) and elevated levels of free ammonia (367 mg/liter NH3-N). The microbial community was strongly dominated (76% of all 16S rRNA amplicon sequences) by populations closely related to the proteolytic bacterium Coprothermobacter proteolyticus. Multiple Coprothermobacter-affiliated strains were detected, introducing an additional level of complexity seldom explored in biogas studies. Genome reconstructions provided metabolic insight into the microbes that performed biomass deconstruction and fermentation, including the deeply branching phyla Dictyoglomi and Planctomycetes and the candidate phylum "Atribacteria" These biomass degraders were complemented by a synergistic network of microorganisms that convert key fermentation intermediates (fatty acids) via syntrophic interactions with hydrogenotrophic methanogens to ultimately produce methane. Interpretation of the proteomics data also suggested activity of a Methanosaeta phylotype acclimatized to high ammonia levels. In particular, we report multiple novel phylotypes proposed as syntrophic acetate oxidizers, which also exert expression of enzymes needed for both the Wood-Ljungdahl pathway and β-oxidation of fatty acids to acetyl coenzyme A. Such an arrangement differs from known syntrophic oxidizing bacteria and presents an interesting hypothesis for future studies. Collectively, these findings provide increased insight into active metabolic roles of uncultured phylotypes and presents new synergistic relationships, both of which may contribute to the stability of the biogas reactor.

IMPORTANCE: Biogas production through anaerobic digestion of organic waste provides an attractive source of renewable energy and a sustainable waste management strategy. A comprehensive understanding of the microbial community that drives anaerobic digesters is essential to ensure stable and efficient energy production. Here, we characterize the intricate microbial networks and metabolic pathways in a thermophilic biogas reactor. We discuss the impact of frequently encountered microbial populations as well as the metabolism of newly discovered novel phylotypes that seem to play distinct roles within key microbial stages of anaerobic digestion in this stable high-temperature system. In particular, we draft a metabolic scenario whereby multiple uncultured syntrophic acetate-oxidizing bacteria are capable of syntrophically oxidizing acetate as well as longer-chain fatty acids (via the β-oxidation and Wood-Ljundahl pathways) to hydrogen and carbon dioxide, which methanogens subsequently convert to methane.}, } @article {pmid27814723, year = {2016}, author = {Akinyemi, IA and Wang, F and Zhou, B and Qi, S and Wu, Q}, title = {Ecogenomic survey of plant viruses infecting Tobacco by Next generation sequencing.}, journal = {Virology journal}, volume = {13}, number = {1}, pages = {181}, pmid = {27814723}, issn = {1743-422X}, mesh = {China ; Computational Biology ; *Ecotype ; *Genetic Variation ; Metagenomics ; Plant Viruses/*classification/genetics/*isolation & purification ; Sequence Analysis, DNA ; Nicotiana/*virology ; }, abstract = {BACKGROUND: The invasion of plant by viruses cause major damage to plants and reduces crop yield and integrity. Devastating plant virus infection has been experienced at different times all over the world, which are attributed to different events of mutation, re-assortment and recombination occurring in the viruses. Strategies for proper virus management has been mostly limited to eradicating the vectors that spreads the plant viruses. However, development of prompt and effective diagnostic methods are required to monitor emerging and re-emerging diseases that may be symptomatic or asymptomatic in the plant as well as the genetic variation and evolution in the plant viruses. A survey of plant viruses infecting field-grown Tobacco crop was conducted in Anhui Province of China by the deep sequencing of sRNAs.

METHODS: Survey of plant viruses infecting Tobacco was carried based on 104 samples collected across the province. Nine different sRNA libraries was prepared and custom-made bioinformatics pipeline coupled with molecular techniques was developed to sequence, assemble and analyze the siRNAs for plant virus discovery. We also carried out phylogenetic and recombination analysis of the identified viruses.

RESULTS: Twenty two isolates from eight different virus species including Cucumber mosaic virus, Potato virus Y, Tobacco mosaic virus, Tobacco vein banding Mosaic virus, Pepper mottle virus, Brassica yellow virus, Chilli venial mottle virus, Broad bean wilt virus 2 were identified in tobacco across the survey area. The near-complete genome sequence of the 22 new isolates were determined and analyzed. The isolates were grouped together with known strains in the phylogenetic tree. Molecular variation in the isolates indicated the conserved coding regions have majorly a nucleotide sequence identity of 80-94 % with previously identified isolates. Various events of recombination were discovered among some of the isolates indicating that two or more viruses or different isolates of one virus infect the same host cell.

CONCLUSION: This study describes the discovery of a consortium of plant viruses infecting Tobacco that are broadly distributed in Anhui province of China. It also demonstrates the effectiveness of NGS in identifying plant viruses without a prior knowledge of the virus and the genetic diversity that enhanced mixed infection.}, } @article {pmid27814509, year = {2016}, author = {Schirmer, M and Smeekens, SP and Vlamakis, H and Jaeger, M and Oosting, M and Franzosa, EA and Ter Horst, R and Jansen, T and Jacobs, L and Bonder, MJ and Kurilshikov, A and Fu, J and Joosten, LAB and Zhernakova, A and Huttenhower, C and Wijmenga, C and Netea, MG and Xavier, RJ}, title = {Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.}, journal = {Cell}, volume = {167}, number = {4}, pages = {1125-1136.e8}, pmid = {27814509}, issn = {1097-4172}, support = {322698/ERC_/European Research Council/International ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 DK092405/DK/NIDDK NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Bacteria/classification/immunology ; Blood/immunology ; Cytokines/*immunology ; Dysbiosis/immunology/microbiology ; Feces/microbiology ; Female ; Fungi/classification/immunology ; *Gastrointestinal Microbiome ; Gene-Environment Interaction ; Human Genome Project ; Humans ; Infections/immunology/microbiology ; Inflammation/*immunology ; Leukocytes, Mononuclear/immunology ; Male ; *Microbiota ; Middle Aged ; }, abstract = {Gut microbial dysbioses are linked to aberrant immune responses, which are often accompanied by abnormal production of inflammatory cytokines. As part of the Human Functional Genomics Project (HFGP), we investigate how differences in composition and function of gut microbial communities may contribute to inter-individual variation in cytokine responses to microbial stimulations in healthy humans. We observe microbiome-cytokine interaction patterns that are stimulus specific, cytokine specific, and cytokine and stimulus specific. Validation of two predicted host-microbial interactions reveal that TNFα and IFNγ production are associated with specific microbial metabolic pathways: palmitoleic acid metabolism and tryptophan degradation to tryptophol. Besides providing a resource of predicted microbially derived mediators that influence immune phenotypes in response to common microorganisms, these data can help to define principles for understanding disease susceptibility. The three HFGP studies presented in this issue lay the groundwork for further studies aimed at understanding the interplay between microbial, genetic, and environmental factors in the regulation of the immune response in humans. PAPERCLIP.}, } @article {pmid27812801, year = {2017}, author = {Suriya, J and Chandra Shekar, M and Nathani, NM and Suganya, T and Bharathiraja, S and Krishnan, M}, title = {Assessment of bacterial community composition in response to uranium levels in sediment samples of sacred Cauvery River.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {2}, pages = {831-841}, doi = {10.1007/s00253-016-7945-2}, pmid = {27812801}, issn = {1432-0614}, mesh = {Bacteria/*classification/genetics ; *Biota ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/*chemistry/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers ; Sequence Analysis, DNA ; Uranium/*analysis ; }, abstract = {Global industrialization is a major cause of effluent discharge from industries up to alarming concentrations. Especially, uranium concentrations in water bodies are of great concern, as its radioactivity significantly affects the persistent diversity of microbiota. Recently, continuous application of pesticides in the agricultural lands and accumulation of quartz that enter the Cauvery River has significantly increased the concentration of uranium (U) and other heavy metals. To perceive the impact of uranium on bacterial diversity in Cauvery River, sediment samples collected from polluted (UP) site with 32.4 Bq/K of U concentration and control (UNP) site were scrutinized for bacterial diversity through metagenomic analysis of the V3 region of 16S rDNA by Illumina sequencing. Taxonomic assignment revealed that the unpolluted sample was dominated by Bacteroidetes (27.7 %), and Firmicutes (25.9 %), while sediment sample from the highly polluted site revealed abundance of Proteobacteria (47.5 %) followed by Bacteroidetes (22.4 %) and Firmicutes (14.6 %). Among Proteobacteria, Gammaproteobacteria was the most prevalent group followed by alpha, delta, epsilon, and beta in the uranium-polluted sample. Rare and abundant species analysis revealed that species like Idiomarina loihiensis was abundant in the pollutant sample; however, it was rare (<0.1 %) in the sample from pristine environment. Similarly, the species distribution in both the samples varied, with the bacteria potentially active in redox activity and biosorption potential dominating in the polluted sample. Outcomes of the present study demonstrated the impact of uranium and metal accumulation on the bacterial communities and further confirmed the promising candidature of specific bacterial species as bioindicators of contamination.}, } @article {pmid27807746, year = {2016}, author = {Han, M and Yang, P and Zhou, H and Li, H and Ning, K}, title = {Metagenomics and Single-Cell Omics Data Analysis for Human Microbiome Research.}, journal = {Advances in experimental medicine and biology}, volume = {939}, number = {}, pages = {117-137}, doi = {10.1007/978-981-10-1503-8_6}, pmid = {27807746}, issn = {0065-2598}, mesh = {DNA Barcoding, Taxonomic/*methods ; Genotype ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Phenotype ; Polymorphism, Single Nucleotide ; Single-Cell Analysis/*methods ; }, abstract = {Microbes are ubiquitous on our planet, and it is well known that the total number of microbial cells on earth is huge. These organisms usually live in communities, and each of these communities has a different taxonomical structure. As such, microbial communities would serve as the largest reservoir of genes and genetic functions for a vast number of applications in "bio"-related disciplines, especially in biomedicine. Human microbiome is the area in which the relationships between ourselves as hosts and our microbiomes have been examined.In this chapter, we have first reviewed the researches in microbes on community, population and single-cell levels in general. Then we have focused on the effects of recent metagenomics and single-cell advances on human microbiome research, as well as their effects on translational biomedical research. We have also foreseen that with the advancement of big-data analysis techniques, deeper understanding of human microbiome, as well as its broader applications, could be realized.}, } @article {pmid27807645, year = {2017}, author = {Argiroff, WA and Zak, DR and Lanser, CM and Wiley, MJ}, title = {Microbial Community Functional Potential and Composition Are Shaped by Hydrologic Connectivity in Riverine Floodplain Soils.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {630-644}, pmid = {27807645}, issn = {1432-184X}, mesh = {Base Sequence ; *Floods ; Gene Library ; High-Throughput Nucleotide Sequencing ; *Hydrology ; Metagenome/genetics ; Microbiota/*genetics ; Nitrogen/metabolism ; Rivers/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; *Wetlands ; }, abstract = {Riverine floodplains are ecologically and economically valuable ecosystems that are heavily threatened by anthropogenic stressors. Microbial communities in floodplain soils mediate critical biogeochemical processes, yet we understand little about the relationship between these communities and variation in hydrologic connectivity related to land management or topography. Here, we present metagenomic evidence that differences among microbial communities in three floodplain soils correspond to a long-term gradient of hydrologic connectivity. Specifically, all strictly anaerobic taxa and metabolic pathways were positively associated with increased hydrologic connectivity and flooding frequency. In contrast, most aerobic taxa and all strictly aerobic pathways were negatively related to hydrologic connectivity and flooding frequency. Furthermore, the genetic potential to metabolize organic compounds tended to decrease as hydrologic connectivity increased, which may reflect either the observed concomitant decline of soil organic matter or the parallel increase in both anaerobic taxa and pathways. A decline in soil N, accompanied by an increased genetic potential for oligotrophic N acquisition subsystems, suggests that soil nutrients also shape microbial communities in these soils. We conclude that differences among floodplain soil microbial communities can be conceptualized along a gradient of hydrologic connectivity. Additionally, we show that these differences are likely due to connectivity-related variation in flooding frequency, soil organic matter, and soil N. Our findings are particularly relevant to the restoration and management of microbially mediated biogeochemical processes in riverine floodplain wetlands.}, } @article {pmid27807621, year = {2017}, author = {Jiang, X and Takacs-Vesbach, CD}, title = {Microbial community analysis of pH 4 thermal springs in Yellowstone National Park.}, journal = {Extremophiles : life under extreme conditions}, volume = {21}, number = {1}, pages = {135-152}, pmid = {27807621}, issn = {1433-4909}, mesh = {Bacteria/classification/genetics/isolation & purification ; Genome, Bacterial ; Hot Springs/*microbiology ; Metagenome ; *Microbiota ; }, abstract = {The pH of the majority of thermal springs in Yellowstone National Park (YNP) is from 1 to 3 and 6 to 10; relatively few springs (~5%) have a pH range of 4-5. We used 16S rRNA gene pyrosequencing to investigate microbial communities sampled from four pH 4 thermal springs collected from four regions of YNP that differed in their fluid temperature and geochemistry. Our results revealed that the composition of bacterial communities varied among the sites, despite sharing similar pH values. The taxonomic composition and metabolic functional potential of the site with the lowest temperature (55 °C), a thermal spring from the Seven Mile Hole (SMH) area, were further investigated using shotgun metagenome sequencing. The taxonomic classification, based on 372 Mbp of unassembled metagenomic reads, indicated that this community included a high proportion of Chloroflexi, Bacteroidetes, Proteobacteria, and Firmicutes. Functional comparison with other YNP thermal spring metagenomes indicated that the SMH metagenome was enriched in genes related to energy production and conversion, transcription, and carbohydrate transport. Analysis of genes involved in nitrogen metabolism revealed assimilatory and dissimilatory nitrate reduction pathways, whereas the majority of genes involved in sulfur metabolism were related to the reduction of sulfate to adenylylsulfate, sulfite, and H2S. Given that pH 4 thermal springs are relatively less common in YNP and thermal areas worldwide, they may harbor novel microbiota and the communities that inhabit them deserve further investigation.}, } @article {pmid27807600, year = {2017}, author = {Li, W and Han, Y and Yuan, X and Wang, G and Wang, Z and Pan, Q and Gao, Y and Qu, Y}, title = {Metagenomic analysis reveals the influences of milk containing antibiotics on the rumen microbes of calves.}, journal = {Archives of microbiology}, volume = {199}, number = {3}, pages = {433-443}, doi = {10.1007/s00203-016-1311-8}, pmid = {27807600}, issn = {1432-072X}, mesh = {Animal Feed/analysis ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; Biodiversity ; Cattle ; Gastrointestinal Microbiome/*drug effects ; Genome, Bacterial/*genetics ; Metagenomics ; Milk/*chemistry ; Population Density ; Rumen/*microbiology ; }, abstract = {Milk containing antibiotics is used as cost-effective feed for calves, which may lead to antibiotic residues-associated food safety problems. This study aims to investigate the influence of antibiotics on rumen microbes. Through metagenomic sequencing, the rumen microbial communities of calves fed with pasteurized milk containing antibiotics (B1), milk containing antibiotics (B2) and fresh milk (B3) were explored. Each milk group included calves in 2 (T1), 3 (T2) and 6 (T3) months of age. Using FastQC software and SOAPdenovo 2, the filtered data, respectively, were performed with quality control and sequence splicing. Following KEGG annotation was conducted for the uploaded sequences using KAAS software. Using R software, both species abundance analysis and differential abundance analysis were performed. In the B1 samples, the species abundance of Bacteroidetes gradually decreased along with the extension of feeding time, while that of Fibrobacteres gradually increased. The species abundances of Proteobacteria (p value = 0.01) and Spirochaetes (p value = 0.03) had significant differences among T1, T2 and T3 samples. Meanwhile, only the species abundance of Spirochaetes (p value = 0.04) had significant difference among B1, B2 and B3 samples. Cell cycle involving GSK3β, CDK2 and CDK7 was significantly enriched for the differentially expressed genes in the T1 versus T2 and T1 versus T3 comparison groups. Milk containing antibiotics might have a great influence on these rumen microbes and lead to antibiotic residues-associated food safety problems. Furthermore, GSK3β, CDK2 and CDK7 in rumen bacteria might affect milk fat metabolism in early growth stages of calves.}, } @article {pmid27723427, year = {2016}, author = {Johnson, KV and Burnet, PW}, title = {Microbiome: Should we diversify from diversity?.}, journal = {Gut microbes}, volume = {7}, number = {6}, pages = {455-458}, pmid = {27723427}, issn = {1949-0984}, mesh = {Bacteria/*classification/genetics/isolation & purification ; *Biodiversity ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Health ; Humans ; }, abstract = {Studies on microbiome diversity are flooding the current literature, yet lessons from ecology clearly demonstrate that diversity is just one factor to consider when analyzing an ecosystem, along with its stability, structure and function. Measures of diversity may be a useful tool for interpreting metagenomic data but the question remains as to how informative they are and what insight they may provide into the state of the microbiome. A study utilizing mathematical modeling to investigate the ecological dynamics of microbial communities has shown that diversity and stability may not always be concomitant. This finding is pertinent to the gut microbiome field, especially since diversity comparisons between healthy and pathological states frequently yield contradictory results. There is a need to broaden our approach to the analysis of microbiome data if we are to better understand this complex ecological community and its role in human health and disease.}, } @article {pmid27484237, year = {2016}, author = {Santos-Cortez, RL and Reyes-Quintos, MR and Tantoco, ML and Abbe, I and Llanes, EG and Ajami, NJ and Hutchinson, DS and Petrosino, JF and Padilla, CD and Villarta, RL and Gloria-Cruz, TL and Chan, AL and Cutiongco-de la Paz, EM and Chiong, CM and Leal, SM and Abes, GT}, title = {Genetic and Environmental Determinants of Otitis Media in an Indigenous Filipino Population.}, journal = {Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery}, volume = {155}, number = {5}, pages = {856-862}, pmid = {27484237}, issn = {1097-6817}, support = {R01 DC003594/DC/NIDCD NIH HHS/United States ; R01 DC011651/DC/NIDCD NIH HHS/United States ; R01 DC015004/DC/NIDCD NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; Cross-Sectional Studies ; Environmental Exposure/*adverse effects ; Female ; Genetic Predisposition to Disease ; Genotype ; Humans ; Male ; Microbiota ; Otitis Media/*epidemiology/*genetics/microbiology ; Otoscopy ; Philippines/epidemiology ; Prevalence ; Risk Factors ; alpha-Macroglobulins/*genetics ; }, abstract = {OBJECTIVE: To identify genetic and environmental risk factors for otitis media in an indigenous Filipino population.

STUDY DESIGN: Cross-sectional study.

SETTING: Indigenous Filipino community.

SUBJECTS AND METHODS: Clinical history and information on breastfeeding, tobacco smoke exposure, and swimming were obtained from community members. Heads of households were interviewed for family history and personal beliefs on ear health. Height and weight were measured. Otoscopic findings were described for the presence and character of perforation or discharge. An A2ML1 duplication variant that confers otitis media susceptibility was Sanger sequenced in all DNA samples. Co-occurrence of middle ear bacteria detected by 16S rRNA gene sequencing was determined according to A2ML1 genotype and social cluster.

RESULTS: The indigenous Filipino population has a ~50% prevalence of otitis media. Young age was associated with otitis media (4 age strata; P = .004); however, age was nonsignificant as a bistratal or continuous variable. There was no association between otitis media and sex, body mass index, breastfeeding, tobacco exposure, or deep swimming. In multivariate analyses, A2ML1 genotype is the strongest predictor of otitis media, with an odds ratio of 3.7 (95% confidence interval: 1.3-10.8; P = .005). When otitis media diagnoses were plotted across ages, otitis media was observed within the first year of life, and chronic otitis media persisted up to adulthood, particularly in A2ML1-variant carriers.

CONCLUSION: Among indigenous Filipinos, A2ML1 genotype is the primary risk factor for otitis media and main determinant of disease progression, although age, the middle ear microbiome, and social clusters might modulate the effect of the A2ML1 genotype.}, } @article {pmid27802303, year = {2016}, author = {Jeon, SJ and Cunha, F and Ma, X and Martinez, N and Vieira-Neto, A and Daetz, R and Bicalho, RC and Lima, S and Santos, JE and Jeong, KC and Galvão, KN}, title = {Uterine Microbiota and Immune Parameters Associated with Fever in Dairy Cows with Metritis.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0165740}, pmid = {27802303}, issn = {1932-6203}, mesh = {Animals ; Cattle ; *Cattle Diseases ; *Dairying ; Female ; Fever/complications/*immunology/*microbiology ; *Microbiota ; Respiratory Burst ; Uterus/*immunology/*microbiology ; }, abstract = {OBJECTIVE: This study aimed to evaluate bacterial and host factors causing a fever in cows with metritis. For that, we investigated uterine microbiota using a metagenomic sequencing of the 16S rRNA gene (Study 1), and immune response parameters (Study 2) in metritic cows with and without a fever.

PRINCIPAL FINDINGS (STUDY1): Bacterial communities were similar between the MNoFever and MFever groups based on distance metrics of relative abundance of bacteria. Metritic cows showed a greater prevalence of Bacteroidetes, and Bacteroides and Porphyromonas were the largest contributors to that difference. A comparison of relative abundance at the species level pointed to Bacteroides pyogenes as a fever-related species which was significantly abundant in the MFever than the MNoFever and Healthy groups; however, absolute abundance of Bacteroides pyogenes determined by droplet digital PCR (ddPCR) was similar between MFever and MNoFever groups, but higher than the Healthy group. The same trend was observed in the total number of bacteria.

PRINCIPAL FINDINGS (STUDY2): The activity of polymorphonuclear leukocyte (PMN) and the production of TNFα, PGE2 metabolite, and PGE2 were evaluated in serum, before disease onset, at 0 and 3 DPP. Cows in the MNoFever had decreased proportion of PMN undergoing phagocytosis and oxidative burst compared with the MFever. The low PMN activity in the MNoFever was coupled with the low production of TNFα, but similar PGE2 metabolite and circulating PGE2.

CONCLUSION/SIGNIFICANCE: Our study is the first to show a similar microbiome between metritic cows with and without a fever, which indicates that the host response may be more important for fever development than the microbiome. Bacteroides pyogenes was identified as an important pathogen for the development of metritis but not fever. The decreased inflammatory response may explain the lack of a febrile response in the MNoFever group.}, } @article {pmid27802157, year = {2016}, author = {Tilg, H and Cani, PD and Mayer, EA}, title = {Gut microbiome and liver diseases.}, journal = {Gut}, volume = {65}, number = {12}, pages = {2035-2044}, doi = {10.1136/gutjnl-2016-312729}, pmid = {27802157}, issn = {1468-3288}, mesh = {Cholangitis, Sclerosing/metabolism/prevention & control ; Dysbiosis/metabolism ; Evidence-Based Medicine ; *Gastrointestinal Microbiome ; Hepatic Encephalopathy/prevention & control ; Humans ; Inflammation/metabolism ; Liver Cirrhosis/metabolism/prevention & control ; Liver Diseases/diagnosis/*metabolism/microbiology/*prevention & control ; Liver Diseases, Alcoholic/metabolism/prevention & control ; Prebiotics/administration & dosage ; Probiotics/*therapeutic use ; Severity of Illness Index ; }, abstract = {The gut microbiota has recently evolved as a new important player in the pathophysiology of many intestinal and extraintestinal diseases. The liver is the organ which is in closest contact with the intestinal tract, and is exposed to a substantial amount of bacterial components and metabolites. Various liver disorders such as alcoholic liver disease, non-alcoholic liver disease and primary sclerosing cholangitis have been associated with an altered microbiome. This dysbiosis may influence the degree of hepatic steatosis, inflammation and fibrosis through multiple interactions with the host's immune system and other cell types. Whereas few results from clinical metagenomic studies in liver disease are available, evidence is accumulating that in liver cirrhosis an oral microbiome is overrepresented in the lower intestinal tract, potentially contributing to disease process and severity. A major role for the gut microbiota in liver disorders is also supported by the accumulating evidence that several complications of severe liver disease such as hepatic encephalopathy are efficiently treated by various prebiotics, probiotics and antibiotics. A better understanding of the gut microbiota and its components in liver diseases might provide a more complete picture of these complex disorders and also form the basis for novel therapies.}, } @article {pmid27801992, year = {2016}, author = {Shukla, SP and Sanders, JG and Byrne, MJ and Pierce, NE}, title = {Gut microbiota of dung beetles correspond to dietary specializations of adults and larvae.}, journal = {Molecular ecology}, volume = {25}, number = {24}, pages = {6092-6106}, doi = {10.1111/mec.13901}, pmid = {27801992}, issn = {1365-294X}, mesh = {Animals ; Coleoptera/*microbiology ; *Diet ; Feces ; Female ; *Gastrointestinal Microbiome ; Larva/*microbiology ; Male ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Vertebrate dung is central to the dung beetle life cycle, constituting food for adults and a protective and nutritive refuge for their offspring. Adult dung beetles have soft mandibles and feed primarily on nutritionally rich dung particles, while larvae have sclerotized mandibles and consume coarser dung particles with a higher C/N ratio. Here, using the dung beetles Euoniticellus intermedius and E. triangulatus, we show that these morphological adaptations in mandibular structure are also correlated with differences in basic gut structure and gut bacterial communities between dung beetle life stages. Metagenome functional predictions based on 16S rDNA characterization further indicated that larval gut communities are enriched in genes involved in cellulose degradation and nitrogen fixation compared to adult guts. Larval gut communities are more similar to female gut communities than they are to those of males, and bacteria present in maternally provisioned brood balls and maternal 'gifts' (secretions deposited in the brood ball along with the egg) are also more similar to larval gut communities than to those of males. Maternal secretions and maternally provisioned brood balls, as well as dung, were important factors shaping the larval gut community. Differences between gut microbiota in the adults and larvae are likely to contribute to differences in nutrient assimilation from ingested dung at different life history stages.}, } @article {pmid27801835, year = {2016}, author = {Mohan, M and Chow, CT and Ryan, CN and Chan, LS and Dufour, J and Aye, PP and Blanchard, J and Moehs, CP and Sestak, K}, title = {Dietary Gluten-Induced Gut Dysbiosis Is Accompanied by Selective Upregulation of microRNAs with Intestinal Tight Junction and Bacteria-Binding Motifs in Rhesus Macaque Model of Celiac Disease.}, journal = {Nutrients}, volume = {8}, number = {11}, pages = {}, pmid = {27801835}, issn = {2072-6643}, support = {P51 OD011104/OD/NIH HHS/United States ; T32 OD011124/OD/NIH HHS/United States ; R01 DA042524/DA/NIDA NIH HHS/United States ; R01 DK083929/DK/NIDDK NIH HHS/United States ; R42 DK097976/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Biomarkers/metabolism ; Celiac Disease/immunology/*metabolism/microbiology/pathology ; Claudin-1/antagonists & inhibitors/genetics/metabolism ; *Disease Models, Animal ; Dysbiosis/immunology/*metabolism/microbiology/pathology ; Feces/chemistry/microbiology ; Female ; Gastrointestinal Microbiome/immunology ; Gene Expression Regulation ; Glutens/*adverse effects ; Intestinal Mucosa/immunology/*metabolism/microbiology/pathology ; Jejunum/immunology/metabolism/microbiology/pathology ; Macaca mulatta ; Male ; MicroRNAs/chemistry/*metabolism ; Nucleotide Motifs ; Plant Proteins, Dietary/*adverse effects ; RNA, Bacterial/metabolism ; RNA, Ribosomal, 16S/metabolism ; Specific Pathogen-Free Organisms ; Tight Junctions/immunology/metabolism/pathology ; }, abstract = {The composition of the gut microbiome reflects the overall health status of the host. In this study, stool samples representing the gut microbiomes from 6 gluten-sensitive (GS) captive juvenile rhesus macaques were compared with those from 6 healthy, age- and diet-matched peers. A total of 48 samples representing both groups were studied using V4 16S rRNA gene DNA analysis. Samples from GS macaques were further characterized based on type of diet administered: conventional monkey chow, i.e., wheat gluten-containing diet (GD), gluten-free diet (GFD), barley gluten-derived diet (BOMI) and reduced gluten barley-derived diet (RGB). It was hypothesized that the GD diet would lower the gut microbial diversity in GS macaques. This is the first report illustrating the reduction of gut microbial alpha-diversity (p < 0.05) following the consumption of dietary gluten in GS macaques. Selected bacterial families (e.g., Streptococcaceae and Lactobacillaceae) were enriched in GS macaques while Coriobacteriaceae was enriched in healthy animals. Within several weeks after the replacement of the GD by the GFD diet, the composition (beta-diversity) of gut microbiome in GS macaques started to change (p = 0.011) towards that of a normal macaque. Significance for alpha-diversity however, was not reached by the day 70 when the feeding experiment ended. Several inflammation-associated microRNAs (miR-203, -204, -23a, -23b and -29b) were upregulated (p < 0.05) in jejunum of 4 biopsied GS macaques fed GD with predicted binding sites on 16S ribosomal RNA of Lactobacillus reuteri (accession number: NR_025911), Prevotella stercorea (NR_041364) and Streptococcus luteciae (AJ297218) that were overrepresented in feces. Additionally, claudin-1, a validated tight junction protein target of miR-29b was significantly downregulated in jejunal epithelium of GS macaques. Taken together, we predict that with the introduction of effective treatments in future studies the diversity of gut microbiomes in GS macaques will approach those of healthy individuals. Further studies are needed to elucidate the regulatory pathways of inflammatory miRNAs in intestinal mucosa of GS macaques and to correlate their expression with gut dysbiosis.}, } @article {pmid27799386, year = {2016}, author = {Hasegawa, K and Mansbach, JM and Ajami, NJ and Espinola, JA and Henke, DM and Petrosino, JF and Piedra, PA and Shaw, CA and Sullivan, AF and Camargo, CA and , }, title = {Association of nasopharyngeal microbiota profiles with bronchiolitis severity in infants hospitalised for bronchiolitis.}, journal = {The European respiratory journal}, volume = {48}, number = {5}, pages = {1329-1339}, pmid = {27799386}, issn = {1399-3003}, support = {R01 AI127507/AI/NIAID NIH HHS/United States ; R01 AI108588/AI/NIAID NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; R21 HL129909/HL/NHLBI NIH HHS/United States ; R01 AI114552/AI/NIAID NIH HHS/United States ; UH3 OD023253/OD/NIH HHS/United States ; }, mesh = {Bronchiolitis/*microbiology ; Critical Care ; Female ; Haemophilus ; Hospitalization ; Humans ; Infant ; Infant, Newborn ; Length of Stay ; Male ; *Microbiota ; Moraxella ; Nasopharynx/*microbiology ; Odds Ratio ; Prevotella ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Staphylococcus ; Streptococcus ; Treatment Outcome ; United States ; }, abstract = {Little is known about the relationship between the specific airway microbiota composition and severity of bronchiolitis. We aimed to identify nasopharyngeal microbiota profiles and link these profiles to acute severity in infants hospitalised for bronchiolitis.We conducted a multicentre prospective cohort study of 1005 infants (age <1 year) hospitalised for bronchiolitis over three winters, 2011-2014. By applying a 16S rRNA gene sequence and clustering approach to the nasopharyngeal aspirates collected within 24 h of hospitalisation, we determined nasopharyngeal microbiota profiles and their association with bronchiolitis severity. The primary outcome was intensive care use, i.e. admission to an intensive care unit or use of mechanical ventilation.We identified four nasopharyngeal microbiota profiles: three profiles were dominated by one of Haemophilus, Moraxella or Streptococcus, while the fourth profile had the highest bacterial richness. The rate of intensive care use was highest in infants with a Haemophilus-dominant profile and lowest in those with a Moraxella-dominant profile (20.2% versus 12.3%; unadjusted OR 1.81, 95% CI 1.07-3.11, p=0.03). After adjusting for 11 patient-level confounders, the rate remained significantly higher in infants with Haemophilus-dominant profiles (OR 1.98, 95% CI 1.08-3.62, p=0.03). These findings were externally validated in a separate cohort of 307 children hospitalised for bronchiolitis.}, } @article {pmid27799062, year = {2016}, author = {Santos-Cortez, RL and Hutchinson, DS and Ajami, NJ and Reyes-Quintos, MR and Tantoco, ML and Labra, PJ and Lagrana, SM and Pedro, M and Llanes, EG and Gloria-Cruz, TL and Chan, AL and Cutiongco-de la Paz, EM and Belmont, JW and Chonmaitree, T and Abes, GT and Petrosino, JF and Leal, SM and Chiong, CM}, title = {Middle ear microbiome differences in indigenous Filipinos with chronic otitis media due to a duplication in the A2ML1 gene.}, journal = {Infectious diseases of poverty}, volume = {5}, number = {1}, pages = {97}, pmid = {27799062}, issn = {2049-9957}, support = {K18 DC013564/DC/NIDCD NIH HHS/United States ; R01 DC003594/DC/NIDCD NIH HHS/United States ; R01 DC011651/DC/NIDCD NIH HHS/United States ; R01 DC015004/DC/NIDCD NIH HHS/United States ; }, mesh = {Adolescent ; Child ; Child, Preschool ; DNA, Bacterial/*genetics ; Ear, Middle/*microbiology ; Female ; Genes, Duplicate/*genetics ; Humans ; Male ; *Microbiota ; Otitis Media/*genetics/microbiology ; Philippines ; Population Groups ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Young Adult ; alpha-Macroglobulins/*genetics/metabolism ; }, abstract = {BACKGROUND: Previously rare A2ML1 variants were identified to confer otitis media susceptibility in an indigenous Filipino community and in otitis-prone US children. The goal of this study is to describe differences in the middle ear microbiome between carriers and non-carriers of an A2ML1 duplication variant that increases risk for chronic otitis media among indigenous Filipinos with poor health care access.

METHODS: Ear swabs were obtained from 16 indigenous Filipino individuals with chronic otitis media, of whom 11 carry the A2ML1 duplication variant. Ear swabs were submitted for 16S rRNA gene sequencing.

RESULTS: Genotype-based differences in microbial richness, structure, and composition were identified, but were not statistically significant. Taxonomic analysis revealed that the relative abundance of the phyla Fusobacteria and Bacteroidetes, and genus Fusobacterium were nominally increased in carriers compared to non-carriers, but were non-significant after correction for multiple testing. We also detected rare bacteria including Oligella that was reported only once in the middle ear.

CONCLUSIONS: These findings suggest that A2ML1-related otitis media susceptibility may be mediated by changes in the middle ear microbiome. Knowledge of middle ear microbial profiles according to genetic background can be potentially useful for therapeutic and prophylactic interventions for otitis media and can guide public health interventions towards decreasing otitis media prevalence within the indigenous Filipino community.}, } @article {pmid27798455, year = {2017}, author = {Pevsner-Fischer, M and Blacher, E and Tatirovsky, E and Ben-Dov, IZ and Elinav, E}, title = {The gut microbiome and hypertension.}, journal = {Current opinion in nephrology and hypertension}, volume = {26}, number = {1}, pages = {1-8}, doi = {10.1097/MNH.0000000000000293}, pmid = {27798455}, issn = {1473-6543}, mesh = {Animals ; *Blood Pressure ; Dysbiosis/*physiopathology ; Gastrointestinal Microbiome/*physiology ; Humans ; Hypertension/drug therapy/*physiopathology ; }, abstract = {PURPOSE OF REVIEW: The mammalian mucosal surfaces are densely inhabited by a diverse microbial ecosystem termed the microbiota. Among these highly heterogeneous populations, the largest and richest is the gut microbiota, recently suggested to affect various physiological traits and susceptibility to disease. Novel metagenomic and metabolomic approaches, which have been developed in the past decade, have enabled the elucidation of the contribution of the microbiota to metabolic, immunologic, neurologic and endocrine homeostasis.

RECENT FINDINGS: Dysbiosis, the alteration in the gut microbiota composition and function, has been lately associated with the pathogenesis of multifactorial diseases such as obesity, diabetes and cardiovascular disorders. Recent studies have also suggested associations between dysbiosis and essential hypertension, a common chronic medical condition affecting 20% or more of the adult population worldwide, which is considered a major causative factor for heart disease, stroke, chronic renal failure, blindness and dementia.

SUMMARY: In this review, we discuss the accumulating research pointing to possible interplays between the gut microbiome and hypertension and highlight future prospects by which utilization of microbiome-related techniques may be incorporated into the diagnosis and therapeutic arsenal of hypertension management.}, } @article {pmid27797774, year = {2017}, author = {Kuntal, BK and Mande, SS}, title = {Web-igloo: a web based platform for multivariate data visualization.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {4}, pages = {615-617}, doi = {10.1093/bioinformatics/btw669}, pmid = {27797774}, issn = {1367-4811}, mesh = {Data Mining ; Humans ; Internet ; Metagenomics/*methods ; Microbiota/*genetics ; *Software ; }, abstract = {MOTIVATION: The majority of data generated routinely from various experiments are essentially multivariate, often categorized with multiple experimental metadata. Analyzing such results with interactive visualizations often yields interesting and intuitive results which otherwise remains undisclosed.

RESULTS: In this paper, we present Web-Igloo-a GUI based interactive 'feature decomposition independent' multivariate data visualization platform. Web-Igloo is likely to be a valuable contribution in the field of visual data mining, especially for researchers working with but not limited to multi-omics data. To demonstrate its utility, we have used a metagenomic dataset pertaining to the effect of multiple doses of antibiotic treatment on the human gut microbiome.

http://metagenomics.atc.tcs.com/webigloo and http://121.241.184.233/webigloo [Freely available for academic use].

CONTACT: sharmila@atc.tcs.com.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid27796931, year = {2016}, author = {Marfil-Santana, MD and O'Connor-Sánchez, A and Ramírez-Prado, JH and De Los Santos-Briones, C and López-Aguiar, LK and Rojas-Herrera, R and Lago-Lestón, A and Prieto-Davó, A}, title = {A computationally simplistic poly-phasic approach to explore microbial communities from the Yucatan aquifer as a potential sources of novel natural products.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {54}, number = {11}, pages = {774-781}, pmid = {27796931}, issn = {1976-3794}, mesh = {Biological Products/chemistry/*isolation & purification ; Computational Biology/methods ; Drug Discovery/methods ; Fresh Water/microbiology ; Genetic Variation ; *Groundwater/microbiology ; Metagenome ; *Metagenomics ; Microbial Consortia/*genetics ; Phylogeny ; Polyketide Synthases/*genetics ; Secondary Metabolism/genetics ; }, abstract = {The need for new antibiotics has sparked a search for the microbes that might potentially produce them. Current sequencing technologies allow us to explore the biotechnological potential of microbial communities in diverse environments without the need for cultivation, benefitting natural product discovery in diverse ways. A relatively recent method to search for the possible production of novel compounds includes studying the diverse genes belonging to polyketide synthase pathways (PKS), as these complex enzymes are an important source of novel therapeutics. In order to explore the biotechnological potential of the microbial community from the largest underground aquifer in the world located in the Yucatan, we used a polyphasic approach in which a simple, non-computationally intensive method was coupled with direct amplification of environmental DNA to assess the diversity and novelty of PKS type I ketosynthase (KS) domains. Our results suggest that the bioinformatic method proposed can indeed be used to assess the novelty of KS enzymes; nevertheless, this in silico study did not identify some of the KS diversity due to primer bias and stringency criteria outlined by the metagenomics pipeline. Therefore, additionally implementing a method involving the direct cloning of KS domains enhanced our results. Compared to other freshwater environments, the aquifer was characterized by considerably less diversity in relation to known ketosynthase domains; however, the metagenome included a family of KS type I domains phylogenetically related, but not identical, to those found in the curamycin pathway, as well as an outstanding number of thiolases. Over all, this first look into the microbial community found in this large Yucatan aquifer and other fresh water free living microbial communities highlights the potential of these previously overlooked environments as a source of novel natural products.}, } @article {pmid27795388, year = {2016}, author = {Kastman, EK and Kamelamela, N and Norville, JW and Cosetta, CM and Dutton, RJ and Wolfe, BE}, title = {Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species.}, journal = {mBio}, volume = {7}, number = {5}, pages = {}, pmid = {27795388}, issn = {2150-7511}, support = {P50 GM068763/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biota ; *Food Microbiology ; Gene Expression Profiling ; Genomics ; Iron/metabolism ; *Microbial Interactions ; Scopulariopsis/*growth & development/metabolism ; Staphylococcus/*growth & development/metabolism ; }, abstract = {UNLABELLED: Many metagenomic sequencing studies have observed the presence of closely related bacterial species or genotypes in the same microbiome. Previous attempts to explain these patterns of microdiversity have focused on the abiotic environment, but few have considered how biotic interactions could drive patterns of microbiome diversity. We dissected the patterns, processes, and mechanisms shaping the ecological distributions of three closely related Staphylococcus species in cheese rind biofilms. Paradoxically, the most abundant species (S. equorum) is the slowest colonizer and weakest competitor based on growth and competition assays in the laboratory. Through in vitro community reconstructions, we determined that biotic interactions with neighboring fungi help resolve this paradox. Species-specific stimulation of the poor competitor by fungi of the genus Scopulariopsis allows S. equorum to dominate communities in vitro as it does in situ Results of comparative genomic and transcriptomic experiments indicate that iron utilization pathways, including a homolog of the S. aureus staphyloferrin B siderophore operon pathway, are potential molecular mechanisms underlying Staphylococcus-Scopulariopsis interactions. Our integrated approach demonstrates that fungi can structure the ecological distributions of closely related bacterial species, and the data highlight the importance of bacterium-fungus interactions in attempts to design and manipulate microbiomes.

IMPORTANCE: Decades of culture-based studies and more recent metagenomic studies have demonstrated that bacterial species in agriculture, medicine, industry, and nature are unevenly distributed across time and space. The ecological processes and molecular mechanisms that shape these distributions are not well understood because it is challenging to connect in situ patterns of diversity with mechanistic in vitro studies in the laboratory. Using tractable cheese rind biofilms and a focus on coagulase-negative staphylococcus (CNS) species, we demonstrate that fungi can mediate the ecological distributions of closely related bacterial species. One of the Staphylococcus species studied, S. saprophyticus, is a common cause of urinary tract infections. By identifying processes that control the abundance of undesirable CNS species, cheese producers will have more precise control on the safety and quality of their products. More generally, Staphylococcus species frequently co-occur with fungi in mammalian microbiomes, and similar bacterium-fungus interactions may structure bacterial diversity in these systems.}, } @article {pmid27795313, year = {2017}, author = {Battenberg, K and Wren, JA and Hillman, J and Edwards, J and Huang, L and Berry, AM}, title = {The Influence of the Host Plant Is the Major Ecological Determinant of the Presence of Nitrogen-Fixing Root Nodule Symbiont Cluster II Frankia Species in Soil.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {1}, pages = {}, pmid = {27795313}, issn = {1098-5336}, mesh = {Biological Evolution ; California ; Climate ; Ecosystem ; Frankia/classification/*genetics/*metabolism ; Glutamate-Ammonia Ligase/genetics ; Hydrogen-Ion Concentration ; Metagenomics ; Microbiota/genetics ; *Nitrogen Fixation ; Phylogeny ; RNA, Ribosomal, 16S ; Rhizosphere ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; Symbiosis ; }, abstract = {UNLABELLED: The actinobacterial genus Frankia establishes nitrogen-fixing root nodule symbioses with specific hosts within the nitrogen-fixing plant clade. Of four genetically distinct subgroups of Frankia, cluster I, II, and III strains are capable of forming effective nitrogen-fixing symbiotic associations, while cluster IV strains generally do not. Cluster II Frankia strains have rarely been detected in soil devoid of host plants, unlike cluster I or III strains, suggesting a stronger association with their host. To investigate the degree of host influence, we characterized the cluster II Frankia strain distribution in rhizosphere soil in three locations in northern California. The presence/absence of cluster II Frankia strains at a given site correlated significantly with the presence/absence of host plants on the site, as determined by glutamine synthetase (glnA) gene sequence analysis, and by microbiome analysis (16S rRNA gene) of a subset of host/nonhost rhizosphere soils. However, the distribution of cluster II Frankia strains was not significantly affected by other potential determinants such as host-plant species, geographical location, climate, soil pH, or soil type. Rhizosphere soil microbiome analysis showed that cluster II Frankia strains occupied only a minute fraction of the microbiome even in the host-plant-present site and further revealed no statistically significant difference in the α-diversity or in the microbiome composition between the host-plant-present or -absent sites. Taken together, these data suggest that host plants provide a factor that is specific for cluster II Frankia strains, not a general growth-promoting factor. Further, the factor accumulates or is transported at the site level, i.e., beyond the host rhizosphere.

IMPORTANCE: Biological nitrogen fixation is a bacterial process that accounts for a major fraction of net new nitrogen input in terrestrial ecosystems. Transfer of fixed nitrogen to plant biomass is especially efficient via root nodule symbioses, which represent evolutionarily and ecologically specialized mutualistic associations. Frankia spp. (Actinobacteria), especially cluster II Frankia spp., have an extremely broad host range, yet comparatively little is known about the soil ecology of these organisms in relation to the host plants and their rhizosphere microbiomes. This study reveals a strong influence of the host plant on soil distribution of cluster II Frankia spp.}, } @article {pmid27795310, year = {2017}, author = {Morrow, KM and Bromhall, K and Motti, CA and Munn, CB and Bourne, DG}, title = {Allelochemicals Produced by Brown Macroalgae of the Lobophora Genus Are Active against Coral Larvae and Associated Bacteria, Supporting Pathogenic Shifts to Vibrio Dominance.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {1}, pages = {}, pmid = {27795310}, issn = {1098-5336}, mesh = {Animals ; Anthozoa/drug effects/*microbiology ; Archaea/drug effects/genetics/growth & development/isolation & purification ; Bacteria/drug effects/genetics/growth & development/pathogenicity ; Coral Reefs ; Ecosystem ; Larva/drug effects ; Metagenomics ; Microbial Consortia/drug effects/genetics ; Microbiota/*drug effects/genetics ; Phaeophyceae/*chemistry/physiology ; Pheromones/biosynthesis/chemistry/*pharmacology ; Population Dynamics ; RNA, Ribosomal, 16S ; Seaweed/chemistry/growth & development/*physiology ; Vibrio/*isolation & purification/pathogenicity/physiology ; }, abstract = {UNLABELLED: Pervasive environmental stressors on coral reefs are attributed with shifting the competitive balance in favor of alternative dominants, such as macroalgae. Previous studies have demonstrated that macroalgae compete with corals via a number of mechanisms, including the production of potent primary and secondary metabolites that can influence coral-associated microbial communities. The present study investigates the effects of the Pacific brown macroalga Lobophora sp. (due to the shifting nature of the Lobophora species complex, it will be referred to here as Lobophora sp.) on coral bacterial isolates, coral larvae, and the microbiome associated with the coral Porites cylindrica. Crude aqueous and organic macroalgal extracts were found to inhibit the growth of coral-associated bacteria. Extracts and fractions were also shown to inhibit coral larval settlement and cause mortality at concentrations lower (<0.3 mg · ml[-1]) than calculated natural concentrations (4.4 mg · ml[-1]). Microbial communities associated with coral tissues exposed to aqueous (e.g., hydrophilic) crude extracts demonstrated a significant shift to Vibrio dominance and a loss of sequences related to the putative coral bacterial symbiont, Endozoicomonas sp., based on 16S rRNA amplicon sequencing. This study contributes to growing evidence that macroalgal allelochemicals, dissolved organic material, and native macroalgal microbial assemblages all play a role in shifting the microbial equilibrium of the coral holobiont away from a beneficial state, contributing to a decline in coral fitness and a shift in ecosystem structure.

IMPORTANCE: Diverse microbial communities associate with coral tissues and mucus, providing important protective and nutritional services, but once disturbed, the microbial equilibrium may shift from a beneficial state to one that is detrimental or pathogenic. Macroalgae (e.g., seaweeds) can physically and chemically interact with corals, causing abrasion, bleaching, and overall stress. This study contributes to a growing body of evidence suggesting that macroalgae play a critical role in shifting the coral holobiont equilibrium, which may promote the invasion of opportunistic pathogens and cause coral mortality, facilitating additional macroalgal growth and invasion in the reef. Thus, macroalgae not only contribute to a decline in coral fitness but also influence coral reef ecosystem structure.}, } @article {pmid27793826, year = {2017}, author = {De Bruyn, F and Zhang, SJ and Pothakos, V and Torres, J and Lambot, C and Moroni, AV and Callanan, M and Sybesma, W and Weckx, S and De Vuyst, L}, title = {Exploring the Impacts of Postharvest Processing on the Microbiota and Metabolite Profiles during Green Coffee Bean Production.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {1}, pages = {}, pmid = {27793826}, issn = {1098-5336}, mesh = {Acetic Acid/metabolism ; Acetobacter/isolation & purification ; Bacteria/classification/isolation & purification/*metabolism ; Candida/isolation & purification ; Coffea/*microbiology ; Desiccation ; Endosperm/chemistry/microbiology ; Enterobacteriaceae/isolation & purification ; Fermentation ; *Food Handling ; Fungi/isolation & purification/*metabolism ; Lactic Acid/metabolism ; Lactobacillus/isolation & purification/metabolism ; Mannitol/metabolism ; *Microbiota ; Pichia/isolation & purification ; Seeds/anatomy & histology/chemistry/*microbiology ; Yeasts/isolation & purification ; }, abstract = {UNLABELLED: The postharvest treatment and processing of fresh coffee cherries can impact the quality of the unroasted green coffee beans. In the present case study, freshly harvested Arabica coffee cherries were processed through two different wet and dry methods to monitor differences in the microbial community structure and in substrate and metabolite profiles. The changes were followed throughout the postharvest processing chain, from harvest to drying, by implementing up-to-date techniques, encompassing multiple-step metagenomic DNA extraction, high-throughput sequencing, and multiphasic metabolite target analysis. During wet processing, a cohort of lactic acid bacteria (i.e., Leuconostoc, Lactococcus, and Lactobacillus) was the most commonly identified microbial group, along with enterobacteria and yeasts (Pichia and Starmerella). Several of the metabolites associated with lactic acid bacterial metabolism (e.g., lactic acid, acetic acid, and mannitol) produced in the mucilage were also found in the endosperm. During dry processing, acetic acid bacteria (i.e., Acetobacter and Gluconobacter) were most abundant, along with Pichia and non-Pichia (Candida, Starmerella, and Saccharomycopsis) yeasts. Accumulation of associated metabolites (e.g., gluconic acid and sugar alcohols) took place in the drying outer layers of the coffee cherries. Consequently, both wet and dry processing methods significantly influenced the microbial community structures and hence the composition of the final green coffee beans. This systematic approach to dissecting the coffee ecosystem contributes to a deeper understanding of coffee processing and might constitute a state-of-the-art framework for the further analysis and subsequent control of this complex biotechnological process.

IMPORTANCE: Coffee production is a long process, starting with the harvest of coffee cherries and the on-farm drying of their beans. In a later stage, the dried green coffee beans are roasted and ground in order to brew a cup of coffee. The on-farm, postharvest processing method applied can impact the quality of the green coffee beans. In the present case study, freshly harvested Arabica coffee cherries were processed through wet and dry processing in four distinct variations. The microorganisms present and the chemical profiles of the coffee beans were analyzed throughout the postharvest processing chain. The up-to-date techniques implemented facilitated the investigation of differences related to the method applied. For instance, different microbial groups were associated with wet and dry processing methods. Additionally, metabolites associated with the respective microorganisms accumulated on the final green coffee beans.}, } @article {pmid27789535, year = {2017}, author = {Mašínová, T and Bahnmann, BD and Větrovský, T and Tomšovský, M and Merunková, K and Baldrian, P}, title = {Drivers of yeast community composition in the litter and soil of a temperate forest.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {2}, pages = {}, doi = {10.1093/femsec/fiw223}, pmid = {27789535}, issn = {1574-6941}, mesh = {*Biodiversity ; Fagus/microbiology ; *Forests ; Fungi/genetics ; Picea/microbiology ; Saccharomyces cerevisiae ; Soil/chemistry ; *Soil Microbiology ; Trees/microbiology ; Yeasts/*classification/genetics/growth & development ; }, abstract = {Fungi represent a group of soil microorganisms fulfilling important ecological functions. Although several studies have shown that yeasts represent a significant proportion of fungal communities, our current knowledge is based mainly on cultivation experiments. In this study, we used amplicon sequencing of environmental DNA to describe the composition of yeast communities in European temperate forest and to identify the potential biotic and abiotic drivers of community assembly. Based on the analysis of ITS2 PCR amplicons, yeasts represented a substantial proportion of fungal communities ranging from 0.4 to 14.3% of fungal sequences in soil and 0.2 to 9.9% in litter. The species richness at individual sites was 28 ± 9 in soil and 31 ± 11 in litter. The basidiomycetous yeasts dominated over ascomycetous ones. In litter, yeast communities differed significantly among beech-, oak- and spruce-dominated stands. Drivers of community assembly are probably more complex in soils and comprise the effects of environmental conditions and vegetation.}, } @article {pmid27794467, year = {2016}, author = {Yunes, RA and Poluektova, EU and Dyachkova, MS and Klimina, KM and Kovtun, AS and Averina, OV and Orlova, VS and Danilenko, VN}, title = {GABA production and structure of gadB/gadC genes in Lactobacillus and Bifidobacterium strains from human microbiota.}, journal = {Anaerobe}, volume = {42}, number = {}, pages = {197-204}, doi = {10.1016/j.anaerobe.2016.10.011}, pmid = {27794467}, issn = {1095-8274}, mesh = {Bacterial Proteins/*genetics/metabolism ; Bacteroidetes/drug effects/genetics/isolation & purification/metabolism ; Bifidobacterium/drug effects/*genetics/isolation & purification/metabolism ; DNA, Bacterial/genetics ; Firmicutes/drug effects/genetics/isolation & purification/metabolism ; Gastrointestinal Microbiome/drug effects/*genetics ; Gastrointestinal Tract/microbiology ; Gene Expression ; Glutamate Decarboxylase/*genetics/metabolism ; Humans ; Lactobacillus/drug effects/*genetics/isolation & purification/metabolism ; Membrane Proteins/*genetics/metabolism ; Metagenome ; Proteobacteria/drug effects/genetics/isolation & purification/metabolism ; Pyridoxal Phosphate/metabolism/pharmacology ; Sodium Glutamate/metabolism/pharmacology ; gamma-Aminobutyric Acid/*biosynthesis ; }, abstract = {Gamma-amino butyric acid (GABA) is an active biogenic substance synthesized in plants, fungi, vertebrate animals and bacteria. Lactic acid bacteria are considered the main producers of GABA among bacteria. GABA-producing lactobacilli are isolated from food products such as cheese, yogurt, sourdough, etc. and are the source of bioactive properties assigned to those foods. The ability of human-derived lactobacilli and bifidobacteria to synthesize GABA remains poorly characterized. In this paper, we screened our collection of 135 human-derived Lactobacillus and Bifidobacterium strains for their ability to produce GABA from its precursor monosodium glutamate. Fifty eight strains were able to produce GABA. The most efficient GABA-producers were Bifidobacterium strains (up to 6 g/L). Time profiles of cell growth and GABA production as well as the influence of pyridoxal phosphate on GABA production were studied for L. plantarum 90sk, L. brevis 15f, B. adolescentis 150 and B. angulatum GT102. DNA of these strains was sequenced; the gadB and gadC genes were identified. The presence of these genes was analyzed in 14 metagenomes of healthy individuals. The genes were found in the following genera of bacteria: Bacteroidetes (Bacteroides, Parabacteroides, Alistipes, Odoribacter, Prevotella), Proteobacterium (Esherichia), Firmicutes (Enterococcus), Actinobacteria (Bifidobacterium). These data indicate that gad genes as well as the ability to produce GABA are widely distributed among lactobacilli and bifidobacteria (mainly in L. plantarum, L. brevis, B. adolescentis, B. angulatum, B. dentium) and other gut-derived bacterial species. Perhaps, GABA is involved in the interaction of gut microbiota with the macroorganism and the ability to synthesize GABA may be an important feature in the selection of bacterial strains - psychobiotics.}, } @article {pmid27746285, year = {2016}, author = {Li, L and Wang, Z and He, P and Ma, S and Du, J and Jiang, R}, title = {Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients.}, journal = {Genomics, proteomics & bioinformatics}, volume = {14}, number = {5}, pages = {314-324}, pmid = {27746285}, issn = {2210-3244}, support = {R01 AA020401/AA/NIAAA NIH HHS/United States ; }, mesh = {Diabetes Mellitus, Type 2/*genetics/microbiology/pathology ; Gastrointestinal Microbiome/*genetics/immunology ; Gene Expression Regulation, Bacterial ; *Gene Regulatory Networks ; Host-Pathogen Interactions ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Although networks of microbial species have been widely used in the analysis of 16S rRNA sequencing data of a microbiome, the construction and analysis of a complete microbial gene network are in general problematic because of the large number of microbial genes in metagenomics studies. To overcome this limitation, we propose to map microbial genes to functional units, including KEGG orthologous groups and the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) orthologous groups, to enable the construction and analysis of a microbial functional network. We devised two statistical methods to infer pairwise relationships between microbial functional units based on a deep sequencing dataset of gut microbiome from type 2 diabetes (T2D) patients as well as healthy controls. Networks containing such functional units and their significant interactions were constructed subsequently. We conducted a variety of analyses of global properties, local properties, and functional modules in the resulting functional networks. Our data indicate that besides the observations consistent with the current knowledge, this study provides novel biological insights into the gut microbiome associated with T2D.}, } @article {pmid27794201, year = {2017}, author = {Barroso, E and Muñoz-González, I and Jiménez, E and Bartolomé, B and Moreno-Arribas, MV and Peláez, C and Del Carmen Martínez-Cuesta, M and Requena, T}, title = {Phylogenetic profile of gut microbiota in healthy adults after moderate intake of red wine.}, journal = {Molecular nutrition & food research}, volume = {61}, number = {3}, pages = {}, doi = {10.1002/mnfr.201600620}, pmid = {27794201}, issn = {1613-4133}, mesh = {Adult ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Healthy Volunteers ; Humans ; *Phylogeny ; RNA, Ribosomal, 16S/analysis ; *Wine ; }, abstract = {SCOPE: There is growing interest in understanding how human colonic microbiota can be modified by dietary habits. We examined the influence of moderate red wine intake on the colonic microbiota of 15 healthy volunteers, related to the high concentration of polyphenols present in this beverage. The volunteers were classified into high, moderate, and low polyphenol metabolizers (metabotypes) due to their ability to metabolize polyphenols and the results were compared with that of five control (no wine intake) subjects.

METHODS AND RESULTS: We analyzed the composition, diversity, and dynamics of their fecal microbiota before and after 1 month of wine consumption. The 16S rDNA sequencing allowed detection of 2324 phylotypes, of which only 30 were found over the 0.5% of mean relative frequency, representing 84.6% of the total taxonomical assignments. The samples clustered more strongly by individuals than by wine intake or metabotypes, however an increase in diversity, after the wine intake, was observed.

CONCLUSION: The results of this study suggest an increase in the global fecal microbial diversity associated to the consumption of red wine, confirm the high variability of the microbiota from different individuals, and show the stability of their singular microbiota composition to small and short-term dietary changes.}, } @article {pmid27793585, year = {2016}, author = {Garoutte, A and Cardenas, E and Tiedje, J and Howe, A}, title = {Methodologies for probing the metatranscriptome of grassland soil.}, journal = {Journal of microbiological methods}, volume = {131}, number = {}, pages = {122-129}, doi = {10.1016/j.mimet.2016.10.018}, pmid = {27793585}, issn = {1872-8359}, mesh = {Computational Biology ; Crops, Agricultural ; Databases, Genetic ; Gene Expression Profiling/methods ; Gene Library ; *Grassland ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; Michigan ; Microbiota/*genetics ; Molecular Sequence Annotation/methods ; RNA, Ribosomal/genetics ; Sequence Alignment ; *Soil ; *Soil Microbiology ; Transcriptome/*genetics ; }, abstract = {Metatranscriptomics provides an opportunity to identify active microbes and expressed genes in complex soil communities in response to particular conditions. Currently, there are a limited number of soil metatranscriptome studies to provide guidance for using this approach in this challenging matrix. Hence, we evaluated the technical challenges of applying soil metatranscriptomics to a highly diverse, low activity natural system. We used a non-targeted rRNA removal approach, duplex nuclease specific (DSN) normalization, to generate a metatranscriptomic library from field collected soil supporting a perennial grass, Miscanthus x giganteus (a biofuel crop), and evaluated its ability to provide insight into its active community members and their expressed protein-coding genes. We also evaluated various bioinformatics approaches for analyzing our soil metatranscriptome, including annotation of unassembled transcripts, de novo assembly, and aligning reads to known genomes. Further, we evaluated various databases for their ability to provide annotations for our metatranscriptome. Overall, our results emphasize that low activity, highly genetically diverse and relatively stable microbiomes, like soil, requires very deep sequencing to sample the transcriptome beyond the common core functions. We identified several key areas that metatranscriptomic analyses will benefit from including increased rRNA removal, assembly of short read transcripts, and more relevant reference bases while providing a priority set of expressed genes for functional assessment.}, } @article {pmid27791473, year = {2017}, author = {Diaz, PI and Hong, BY and Dupuy, AK and Strausbaugh, LD}, title = {Mining the oral mycobiome: Methods, components, and meaning.}, journal = {Virulence}, volume = {8}, number = {3}, pages = {313-323}, pmid = {27791473}, issn = {2150-5608}, support = {R01 DE021578/DE/NIDCR NIH HHS/United States ; }, mesh = {Fungi/*classification/*isolation & purification ; Metagenomics/*methods ; Microbiological Techniques/*methods ; *Microbiota ; Mouth/*microbiology ; *Mycobiome ; }, abstract = {Research on oral fungi has centered on Candida. However, recent internal transcribed spacer (ITS)-based studies revealed a vast number of fungal taxa as potential oral residents. We review DNA-based studies of the oral mycobiome and contrast them with cultivation-based surveys, showing that most genera encountered by cultivation have also been detected molecularly. Some taxa such as Malassezia, however, appear in high prevalence and abundance in molecular studies but have not been cultivated. Important technical and bioinformatic challenges to ITS-based oral mycobiome studies are discussed. These include optimization of sample lysis, variability in length of ITS amplicons, high intra-species ITS sequence variability, high inter-species variability in ITS copy number and challenges in nomenclature and maintenance of curated reference databases. Molecular surveys are powerful first steps to characterize the oral mycobiome but further research is needed to unravel which fungi detected by DNA are true oral residents and what role they play in oral homeostasis.}, } @article {pmid27712009, year = {2017}, author = {Bensoussan, L and Moraïs, S and Dassa, B and Friedman, N and Henrissat, B and Lombard, V and Bayer, EA and Mizrahi, I}, title = {Broad phylogeny and functionality of cellulosomal components in the bovine rumen microbiome.}, journal = {Environmental microbiology}, volume = {19}, number = {1}, pages = {185-197}, pmid = {27712009}, issn = {1462-2920}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Bacterial Proteins/genetics/metabolism ; Cattle ; Cellulosomes/*enzymology/genetics ; *Gastrointestinal Microbiome ; Metagenome ; Multienzyme Complexes/genetics/metabolism ; *Phylogeny ; Rumen/*microbiology ; }, abstract = {The cellulosome is an extracellular multi-enzyme complex that is considered one of the most efficient plant cell wall-degrading strategies devised by nature. Its unique modular architecture, achieved by high affinity and specific interaction between protein modules (cohesins and dockerins) enables formation of various enzyme combinations. Extensive research has been dedicated to the mechanistic nature of the cellulosome complex. Nevertheless, little is known regarding its distribution and abundance among microbes in natural plant fibre-rich environments. Here, we explored these questions in bovine rumen microbial communities, specialized in efficient degradation of lignocellulosic plant material. We bioinformatically screened for cellulosomal modules in this complex environment using a previously published ultra-deep fibre-adherent rumen metagenome. Intriguingly, a large portion of the functions of the dockerin-containing proteins were related to alternative biological processes, and not necessarily to the classic fibre degradation function. Our analysis was experimentally validated by characterizing specific interactions between selected cohesins and dockerins and revealed that cellulosome is a more generalized strategy used by diverse bacteria, some of which were not previously associated with cellulosome production. Remarkably, our results provide additional proof of similarity among rumen microbial communities worldwide. This study suggests a broader and widespread role for the cellulosomal machinery in nature.}, } @article {pmid27613679, year = {2016}, author = {Hu, Y and Yang, X and Li, J and Lv, N and Liu, F and Wu, J and Lin, IY and Wu, N and Weimer, BC and Gao, GF and Liu, Y and Zhu, B}, title = {The Bacterial Mobile Resistome Transfer Network Connecting the Animal and Human Microbiomes.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {22}, pages = {6672-6681}, pmid = {27613679}, issn = {1098-5336}, mesh = {Animals ; Animals, Domestic/microbiology ; Bacteria/genetics/pathogenicity ; Drug Resistance, Bacterial/*genetics ; Ecosystem ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; *Metagenome ; Microbiota/*genetics ; Phylogeny ; Proteobacteria/genetics ; RNA, Ribosomal, 16S ; *Soil Microbiology ; }, abstract = {UNLABELLED: Horizontally acquired antibiotic resistance genes (ARGs) in bacteria are highly mobile and have been ranked as principal risk resistance determinants. However, the transfer network of the mobile resistome and the forces driving mobile ARG transfer are largely unknown. Here, we present the whole profile of the mobile resistome in 23,425 bacterial genomes and explore the effects of phylogeny and ecology on the recent transfer (≥99% nucleotide identity) of mobile ARGs. We found that mobile ARGs are mainly present in four bacterial phyla and are significantly enriched in Proteobacteria The recent mobile ARG transfer network, which comprises 703 bacterial species and 16,859 species pairs, is shaped by the bacterial phylogeny, while an ecological barrier also exists, especially when interrogating bacteria colonizing different human body sites. Phylogeny is still a driving force for the transfer of mobile ARGs between farm animals and the human gut, and, interestingly, the mobile ARGs that are shared between the human and animal gut microbiomes are also harbored by diverse human pathogens. Taking these results together, we suggest that phylogeny and ecology are complementary in shaping the bacterial mobile resistome and exert synergistic effects on the development of antibiotic resistance in human pathogens.

IMPORTANCE: The development of antibiotic resistance threatens our modern medical achievements. The dissemination of antibiotic resistance can be largely attributed to the transfer of bacterial mobile antibiotic resistance genes (ARGs). Revealing the transfer network of these genes in bacteria and the forces driving the gene flow is of great importance for controlling and predicting the emergence of antibiotic resistance in the clinic. Here, by analyzing tens of thousands of bacterial genomes and millions of human and animal gut bacterial genes, we reveal that the transfer of mobile ARGs is mainly controlled by bacterial phylogeny but under ecological constraints. We also found that dozens of ARGs are transferred between the human and animal gut and human pathogens. This work demonstrates the whole profile of mobile ARGs and their transfer network in bacteria and provides further insight into the evolution and spread of antibiotic resistance in nature.}, } @article {pmid27590813, year = {2016}, author = {Pold, G and Billings, AF and Blanchard, JL and Burkhardt, DB and Frey, SD and Melillo, JM and Schnabel, J and van Diepen, LT and DeAngelis, KM}, title = {Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {22}, pages = {6518-6530}, pmid = {27590813}, issn = {1098-5336}, mesh = {Actinobacteria/genetics/metabolism ; Bacteria/classification/isolation & purification/*metabolism ; *Carbohydrate Metabolism ; Carbon/metabolism ; Carbon Cycle ; Carbon Dioxide/metabolism ; Cellulose/metabolism ; *Climate Change ; Ecosystem ; Eukaryota/genetics/metabolism ; *Forests ; *Global Warming ; Metagenomics/methods ; Microbial Consortia/genetics/physiology ; *Soil Microbiology ; Time Factors ; Xylans/metabolism ; }, abstract = {UNLABELLED: As Earth's climate warms, soil carbon pools and the microbial communities that process them may change, altering the way in which carbon is recycled in soil. In this study, we used a combination of metagenomics and bacterial cultivation to evaluate the hypothesis that experimentally raising soil temperatures by 5°C for 5, 8, or 20 years increased the potential for temperate forest soil microbial communities to degrade carbohydrates. Warming decreased the proportion of carbohydrate-degrading genes in the organic horizon derived from eukaryotes and increased the fraction of genes in the mineral soil associated with Actinobacteria in all studies. Genes associated with carbohydrate degradation increased in the organic horizon after 5 years of warming but had decreased in the organic horizon after warming the soil continuously for 20 years. However, a greater proportion of the 295 bacteria from 6 phyla (10 classes, 14 orders, and 34 families) isolated from heated plots in the 20-year experiment were able to depolymerize cellulose and xylan than bacterial isolates from control soils. Together, these findings indicate that the enrichment of bacteria capable of degrading carbohydrates could be important for accelerated carbon cycling in a warmer world.

IMPORTANCE: The massive carbon stocks currently held in soils have been built up over millennia, and while numerous lines of evidence indicate that climate change will accelerate the processing of this carbon, it is unclear whether the genetic repertoire of the microbes responsible for this elevated activity will also change. In this study, we showed that bacteria isolated from plots subject to 20 years of 5°C of warming were more likely to depolymerize the plant polymers xylan and cellulose, but that carbohydrate degradation capacity is not uniformly enriched by warming treatment in the metagenomes of soil microbial communities. This study illustrates the utility of combining culture-dependent and culture-independent surveys of microbial communities to improve our understanding of the role changing microbial communities may play in soil carbon cycling under climate change.}, } @article {pmid27787576, year = {2016}, author = {Manook, A and Hiergeist, A and Rupprecht, R and Baghai, TC}, title = {[Gut microbiome and major depressive disorder : The other side of ourselves].}, journal = {Der Nervenarzt}, volume = {87}, number = {11}, pages = {1227-1240}, pmid = {27787576}, issn = {1433-0407}, mesh = {Depressive Disorder, Major/*microbiology/*physiopathology ; Gastrointestinal Microbiome/*physiology ; Humans ; Hypothalamo-Hypophyseal System/microbiology/*physiopathology ; Models, Biological ; Pituitary-Adrenal System/*microbiology/*physiopathology ; }, abstract = {Microbiological ecology and its ambition to describe the complete genome of complex living communities as a whole, have given us powerful tools to characterize the human gut microbiome on a genetic and, hence, taxonomic and abundance level; for a decade now, they have become sufficiently inexpensive, fast and feasible. Thus, opportunities arose to have a fresh and closer look at the microbiota-gut-brain-axis and its impact on human health; this axis comprises a complex multisystemic network of multidirectional interactions between brain and gut including influences beyond one generation. Gnotobiotic animal models have become essential for specific research targets. Combining gut microbiome analysis with observations on the hypothalamus-pituitary-adrenal axis and various aspects of inflammation helped to gain first insights into the role of the microbiota-gut-brain-axis in depressive disorders. Therapeutic endeavors with psychobiotics have not yet shown their value in clinical studies.}, } @article {pmid27786295, year = {2016}, author = {Mukherjee, S and Mitra, R and Maitra, A and Gupta, S and Kumaran, S and Chakrabortty, A and Majumder, PP}, title = {Sebum and Hydration Levels in Specific Regions of Human Face Significantly Predict the Nature and Diversity of Facial Skin Microbiome.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {36062}, pmid = {27786295}, issn = {2045-2322}, mesh = {Bacteria/*classification/genetics ; Cheek/*microbiology ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Forehead/*microbiology ; Healthy Volunteers ; Humans ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sebum/*metabolism ; Sequence Analysis, DNA ; Skin/chemistry/*microbiology ; Water/*analysis ; }, abstract = {The skin microbiome varies across individuals. The causes of these variations are inadequately understood. We tested the hypothesis that inter-individual variation in facial skin microbiome can be significantly explained by variation in sebum and hydration levels in specific facial regions of humans. We measured sebum and hydration from forehead and cheek regions of healthy female volunteers (n = 30). Metagenomic DNA from skin swabs were sequenced for V3-V5 regions of 16S rRNA gene. Altogether, 34 phyla were identified; predominantly Actinobacteria (66.3%), Firmicutes (17.7%), Proteobacteria (13.1%) and Bacteroidetes (1.4%). About 1000 genera were identified; predominantly Propionibacterium (58.6%), Staphylococcus (8.6%), Streptococcus (4.0%), Corynebacterium (3.6%) and Paracoccus (3.3%). A subset (n = 24) of individuals were sampled two months later. Stepwise multiple regression analysis showed that cheek sebum level was the most significant predictor of microbiome composition and diversity followed by forehead hydration level; forehead sebum and cheek hydration levels were not. With increase in cheek sebum, the prevalence of Actinobacteria (p = 0.001)/Propionibacterium (p = 0.002) increased, whereas microbiome diversity decreased (Shannon Index, p = 0.032); this was opposite for other phyla/genera. These trends were reversed for forehead hydration levels. Therefore, the nature and diversity of facial skin microbiome is jointly determined by site-specific lipid and water levels in the stratum corneum.}, } @article {pmid27785541, year = {2017}, author = {Bouhajja, E and McGuire, M and Liles, MR and Bataille, G and Agathos, SN and George, IF}, title = {Identification of novel toluene monooxygenase genes in a hydrocarbon-polluted sediment using sequence- and function-based screening of metagenomic libraries.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {2}, pages = {797-808}, doi = {10.1007/s00253-016-7934-5}, pmid = {27785541}, issn = {1432-0614}, mesh = {Cloning, Molecular ; *Environmental Microbiology ; Environmental Pollutants/*metabolism ; Genetic Testing ; Germany ; Metagenomics ; Mixed Function Oxygenases/*analysis/*genetics ; Nucleic Acid Hybridization ; Sequence Analysis, DNA ; Toluene/*metabolism ; }, abstract = {The microbial potential for toluene degradation within sediments from a tar oil-contaminated site in Flingern, Germany, was assessed using a metagenomic approach. High molecular weight environmental DNA from contaminated sediments was extracted, purified, and cloned into fosmid and BAC vectors and transformed into Escherichia coli. The fosmid library was screened by hybridization with a PCR amplicon of the α-subunit of the toluene 4-monooxygenase gene to identify genes and pathways encoding toluene degradation. Fourteen clones were recovered from the fosmid library, among which 13 were highly divergent from known tmoA genes and several had the closest relatives among Acinetobacter species. The BAC library was transferred to the heterologous hosts Cupriavidus metallidurans (phylum Proteobacteria) and Edaphobacter aggregans (phylum Acidobacteria). The resulting libraries were screened for expression of toluene degradation in the non-degradative hosts. From expression in C. metallidurans, three novel toluene monooxygenase-encoding operons were identified that were located on IncP1 plasmids. The E. aggregans-hosted BAC library led to the isolation of a cloned genetic locus putatively derived from an Acidobacteria taxon that contained genes involved in aerobic and anaerobic toluene degradation. These data suggest the important role of plasmids in the spread of toluene degradative capacity and indicate putative novel tmoA genes present in this hydrocarbon-polluted environment.}, } @article {pmid27694959, year = {2016}, author = {Bonder, MJ and Kurilshikov, A and Tigchelaar, EF and Mujagic, Z and Imhann, F and Vila, AV and Deelen, P and Vatanen, T and Schirmer, M and Smeekens, SP and Zhernakova, DV and Jankipersadsing, SA and Jaeger, M and Oosting, M and Cenit, MC and Masclee, AA and Swertz, MA and Li, Y and Kumar, V and Joosten, L and Harmsen, H and Weersma, RK and Franke, L and Hofker, MH and Xavier, RJ and Jonkers, D and Netea, MG and Wijmenga, C and Fu, J and Zhernakova, A}, title = {The effect of host genetics on the gut microbiome.}, journal = {Nature genetics}, volume = {48}, number = {11}, pages = {1407-1412}, doi = {10.1038/ng.3663}, pmid = {27694959}, issn = {1546-1718}, mesh = {Adolescent ; Adult ; Aged ; Animals ; Cohort Studies ; Female ; *Gastrointestinal Microbiome ; *Genome, Human ; Genome-Wide Association Study ; Humans ; Immunity/genetics ; Male ; Mice ; Middle Aged ; Polymorphism, Single Nucleotide ; Young Adult ; }, abstract = {The gut microbiome is affected by multiple factors, including genetics. In this study, we assessed the influence of host genetics on microbial species, pathways and gene ontology categories, on the basis of metagenomic sequencing in 1,514 subjects. In a genome-wide analysis, we identified associations of 9 loci with microbial taxonomies and 33 loci with microbial pathways and gene ontology terms at P < 5 × 10[-8]. Additionally, in a targeted analysis of regions involved in complex diseases, innate and adaptive immunity, or food preferences, 32 loci were identified at the suggestive level of P < 5 × 10[-6]. Most of our reported associations are new, including genome-wide significance for the C-type lectin molecules CLEC4F-CD207 at 2p13.3 and CLEC4A-FAM90A1 at 12p13. We also identified association of a functional LCT SNP with the Bifidobacterium genus (P = 3.45 × 10[-8]) and provide evidence of a gene-diet interaction in the regulation of Bifidobacterium abundance. Our results demonstrate the importance of understanding host-microbe interactions to gain better insight into human health.}, } @article {pmid27564131, year = {2016}, author = {Plichta, DR and Juncker, AS and Bertalan, M and Rettedal, E and Gautier, L and Varela, E and Manichanh, C and Fouqueray, C and Levenez, F and Nielsen, T and Doré, J and Machado, AM and de Evgrafov, MC and Hansen, T and Jørgensen, T and Bork, P and Guarner, F and Pedersen, O and , and Sommer, MO and Ehrlich, SD and Sicheritz-Pontén, T and Brunak, S and Nielsen, HB}, title = {Transcriptional interactions suggest niche segregation among microorganisms in the human gut.}, journal = {Nature microbiology}, volume = {1}, number = {11}, pages = {16152}, pmid = {27564131}, issn = {2058-5276}, mesh = {ATP-Binding Cassette Transporters/genetics ; Bifidobacterium bifidum/genetics/metabolism ; Butyrates/metabolism ; Carbon Dioxide/metabolism ; Denmark ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics/physiology ; *Gene Expression Profiling ; Humans ; Metabolic Networks and Pathways/genetics ; *Metagenome ; *Microbial Interactions/genetics/physiology ; Spain ; Systems Analysis ; }, abstract = {The human gastrointestinal (GI) tract is the habitat for hundreds of microbial species, of which many cannot be cultivated readily, presumably because of the dependencies between species[1]. Studies of microbial co-occurrence in the gut have indicated community substructures that may reflect functional and metabolic interactions between cohabiting species[2,3]. To move beyond species co-occurrence networks, we systematically identified transcriptional interactions between pairs of coexisting gut microbes using metagenomics and microarray-based metatranscriptomics data from 233 stool samples from Europeans. In 102 significantly interacting species pairs, the transcriptional changes led to a reduced expression of orthologous functions between the coexisting species. Specific species-species transcriptional interactions were enriched for functions important for H2 and CO2 homeostasis, butyrate biosynthesis, ATP-binding cassette (ABC) transporters, flagella assembly and bacterial chemotaxis, as well as for the metabolism of carbohydrates, amino acids and cofactors. The analysis gives the first insight into the microbial community-wide transcriptional interactions, and suggests that the regulation of gene expression plays an important role in species adaptation to coexistence and that niche segregation takes place at the transcriptional level.}, } @article {pmid27062087, year = {2016}, author = {Aguilar, M and Richardson, E and Tan, B and Walker, G and Dunfield, PF and Bass, D and Nesbø, C and Foght, J and Dacks, JB}, title = {Next-Generation Sequencing Assessment of Eukaryotic Diversity in Oil Sands Tailings Ponds Sediments and Surface Water.}, journal = {The Journal of eukaryotic microbiology}, volume = {63}, number = {6}, pages = {732-743}, doi = {10.1111/jeu.12320}, pmid = {27062087}, issn = {1550-7408}, mesh = {Biodiversity ; Eukaryota/classification/*genetics/*isolation & purification ; Geologic Sediments/*parasitology ; High-Throughput Nucleotide Sequencing ; Oil and Gas Fields ; Phylogeny ; Ponds/*parasitology ; }, abstract = {Tailings ponds in the Athabasca oil sands (Canada) contain fluid wastes, generated by the extraction of bitumen from oil sands ores. Although the autochthonous prokaryotic communities have been relatively well characterized, almost nothing is known about microbial eukaryotes living in the anoxic soft sediments of tailings ponds or in the thin oxic layer of water that covers them. We carried out the first next-generation sequencing study of microbial eukaryotic diversity in oil sands tailings ponds. In metagenomes prepared from tailings sediment and surface water, we detected very low numbers of sequences encoding eukaryotic small subunit ribosomal RNA representing seven major taxonomic groups of protists. We also produced and analysed three amplicon-based 18S rRNA libraries prepared from sediment samples. These revealed a more diverse set of taxa, 169 different OTUs encompassing up to eleven higher order groups of eukaryotes, according to detailed classification using homology searching and phylogenetic methods. The 10 most abundant OTUs accounted for > 90% of the total of reads, vs. large numbers of rare OTUs (< 1% abundance). Despite the anoxic and hydrocarbon-enriched nature of the environment, the tailings ponds harbour complex communities of microbial eukaryotes indicating that these organisms should be taken into account when studying the microbiology of the oil sands.}, } @article {pmid27783988, year = {2016}, author = {Xiao, L and Yang, B and Liu, X and Luo, Y and Ji, Q and Wen, Z and Liu, Z and Yang, PC}, title = {Kinetic changes of intestinal microbiota in the course of intestinal sensitization.}, journal = {Oncotarget}, volume = {7}, number = {49}, pages = {81197-81207}, pmid = {27783988}, issn = {1949-2553}, mesh = {Animals ; Bacteria/classification/genetics/*growth & development/immunology ; CD4-Positive T-Lymphocytes/immunology/microbiology ; Cells, Cultured ; DNA, Bacterial/genetics ; Dendritic Cells/immunology/microbiology ; Disease Models, Animal ; Dysbiosis ; Food Hypersensitivity/immunology/*microbiology ; *Gastrointestinal Microbiome/immunology ; Intestinal Mucosa/immunology/*microbiology ; Jejunum/immunology/*microbiology ; Kinetics ; Metagenome ; Mice, Inbred BALB C ; Phenotype ; Ribotyping ; }, abstract = {Food allergy (FA) is an adverse immune response to certain innocent food. It is estimated about 2% to 6% of the general population suffer from FA. Symptoms of a food allergic reaction may involve the gastrointestinal tract or/and other organs. The gut microbiota plays a critical role in diet-induced health problems. Whether the changes in the composition of the intestinal microbiota regulate allergic responses to food remains poorly understood. Thus, we created an FA animal model, sequenced the V4-V5 regions of 16S rRNA genes to characterize the genera abundance of gut microbiota. The results showed that mice under FA condition showed different gut bacterial structures. Diverse distribution of the bacterial species was identified between FA and control groups. FA altered the components of intestinal Microbiota in mice. The dysbiosis of the gut metagenome correlated with the development of the FA.}, } @article {pmid27782174, year = {2016}, author = {Samad, MS and Biswas, A and Bakken, LR and Clough, TJ and de Klein, CA and Richards, KG and Lanigan, GJ and Morales, SE}, title = {Phylogenetic and functional potential links pH and N2O emissions in pasture soils.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {35990}, pmid = {27782174}, issn = {2045-2322}, mesh = {Agriculture ; Biodiversity ; Denitrification/genetics ; Genes, Microbial ; Greenhouse Gases/analysis ; Hydrogen-Ion Concentration ; Metagenome ; Microbial Consortia/genetics ; Nitrogen/analysis ; Nitrous Oxide/analysis ; Phylogeny ; RNA, Ribosomal, 16S/analysis/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Denitrification is mediated by microbial, and physicochemical, processes leading to nitrogen loss via N2O and N2 emissions. Soil pH regulates the reduction of N2O to N2, however, it can also affect microbial community composition and functional potential. Here we simultaneously test the link between pH, community composition, and the N2O emission ratio (N2O/(NO + N2O + N2)) in 13 temperate pasture soils. Physicochemical analysis, gas kinetics, 16S rRNA amplicon sequencing, metagenomic and quantitative PCR (of denitrifier genes: nirS, nirK, nosZI and nosZII) analysis were carried out to characterize each soil. We found strong evidence linking pH to both N2O emission ratio and community changes. Soil pH was negatively associated with N2O emission ratio, while being positively associated with both community diversity and total denitrification gene (nir &nos) abundance. Abundance of nosZII was positively linked to pH, and negatively linked to N2O emissions. Our results confirm that pH imposes a general selective pressure on the entire community and that this results in changes in emission potential. Our data also support the general model that with increased microbial diversity efficiency increases, demonstrated in this study with lowered N2O emission ratio through more efficient conversion of N2O to N2.}, } @article {pmid27780257, year = {2016}, author = {Valverde, JR and Gullón, S and Pérez Mellado, R}, title = {Looking for Rhizobacterial Ecological Indicators in Agricultural Soils Using 16S rRNA metagenomic Amplicon Data.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0165204}, pmid = {27780257}, issn = {1932-6203}, mesh = {Crops, Agricultural/growth & development ; DNA, Ribosomal/genetics ; Ecosystem ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Rhizobiaceae/*classification/genetics/isolation & purification ; Sequence Analysis, DNA/methods ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {INTRODUCTION: Biological communities present in soil are essential to sustainable and productive agricultural practices; however, an accurate determination of the ecological status of agricultural soils remains to date an elusive task. An ideal indicator should be pervasive, play a relevant role in the ecosystem, show a rapid and proportional answer to external perturbations and be easily and economically measurable. Rhizobacteria play a major role in determining soil properties, becoming an attractive candidate for the detection of ecological indicators. The application of massive sequencing technologies to metagenomic analysis is providing an increasingly more precise view of the structure and composition of soil communities. In this work, we analyse soil rhizobacterial composition under various stress levels to search for potential ecological indicators.

Our results suggest that the Shannon index requires observation of a relatively large number of individuals to be representative of the true population diversity, and that the Simpson index may underestimate rare taxa in rhizobacterial environments.

Detection of indicator taxa requires comparison of taxonomical classification of sequences. We have compared RDP classifier, RTAX and similarity-based taxonomical classification and selected the latter for taxonomical assignment because it provides larger detail.

The study of significant variations in common, clearly identified, taxa, using paired datasets allows minimization of non-treatment effects and avoidance of false positives. We have identified taxa associated to specific perturbations as well as taxa generally affected in treated soils. Changes in these taxa, or combinations of them, may be used as ecological indicators of soil health. The overall number and magnitude of changes detected in taxonomic groups does also increase with stress. These changes constitute an alternative indicator to measuring specific taxa, although their determination requires large sample sizes, better obtained by massive sequencing.

SUMMARY: The main ecological indicators available are the Shannon index, OTU counts and estimators, overall detection of the number and proportion of changes, and changes of specific indicator taxa. Massive sequencing remains the most accurate tool to measure rhizobacterial ecological indicators. When massive sequencing is not an option, various cultivable taxonomic groups, such as specific groups in the Actinobacteria tree, are attractive as potential indicators of large disruptions to the rhizobiome.}, } @article {pmid27777091, year = {2016}, author = {Yu, HJ and Deng, H and Ma, J and Huang, SJ and Yang, JM and Huang, YF and Mu, XP and Zhang, L and Wang, Q}, title = {Clinical metagenomic analysis of bacterial communities in breast abscesses of granulomatous mastitis.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {53}, number = {}, pages = {30-33}, doi = {10.1016/j.ijid.2016.10.015}, pmid = {27777091}, issn = {1878-3511}, mesh = {Abscess/*microbiology ; Adult ; Breast/*microbiology ; Corynebacterium/genetics/*isolation & purification ; Corynebacterium Infections/*microbiology ; DNA, Ribosomal/chemistry/genetics ; Female ; Granulomatous Mastitis/*microbiology ; Humans ; *Metagenomics ; *Microbiota ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Granulomatous mastitis (GM) is a chronic inflammatory breast lesion. Its etiology remains incompletely defined. Although mounting evidence suggests the involvement of Corynebacterium in GM, there has been no systematic study of GM bacteriology using -omics technology.

METHODS: The bacterial diversity and relative abundances in breast abscesses from 19 women with GM were investigated using 16S rDNA metagenomic sequencing and Sanger sequencing. A quantitative PCR (qPCR) assay was also developed to identify Corynebacterium kroppenstedtii.

RESULTS: A bioinformatic analysis revealed that Corynebacterium was present in the 19 GM patients, with abundances ranging from 1.1% to 58.9%. Of note, Corynebacterium was the most abundant taxon in seven patients (more than a third of the subjects). The predominance of Corynebacterium kroppenstedtii infection (11 of 19 patients, 57.9%) was confirmed with Sanger sequencing and the qPCR assay.

CONCLUSIONS: This study profiled the microbiota of patients with GM and indicated an important role for Corynebacterium, and in particular C. kroppenstedtii, in the pathogenesis of this disease.}, } @article {pmid27743904, year = {2016}, author = {He, C and Yang, Z and Cheng, D and Xie, C and Zhu, Y and Ge, Z and Luo, Z and Lu, N}, title = {Helicobacter pylori Infection Aggravates Diet-induced Insulin Resistance in Association With Gut Microbiota of Mice.}, journal = {EBioMedicine}, volume = {12}, number = {}, pages = {247-254}, pmid = {27743904}, issn = {2352-3964}, mesh = {Animals ; Biomarkers ; Cytokines/blood ; *Diet, High-Fat/adverse effects ; Disease Models, Animal ; Disease Progression ; *Gastrointestinal Microbiome ; Glucose/metabolism ; Helicobacter Infections/*metabolism/*microbiology ; *Helicobacter pylori ; Homeostasis ; Inflammation Mediators/blood ; Insulin/blood/metabolism ; *Insulin Resistance ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Obesity, Abdominal/etiology/metabolism ; }, abstract = {Emerging evidence suggests that Helicobacter pylori infection is associated with insulin resistance (IR) yet the underlying mechanisms are still obscure. The vital role of gut microbiota in triggering IR has been increasingly reported, however, no study has explored the correlation of gut microbiota and H. pylori-associated IR. Using H. pylori-infected mice model fed different diet structures, we demonstrated that H. pylori infection significantly aggravated high-fat diet (HFD)-induced metabolic disorders at the early stage, the extent of which was close to the effect of long-term HFD. Interestingly, we observed dynamic alterations in gut microbiota that were consistent with the changes in the metabolic phenotype induced by H. pylori and HFD. There may be an interaction among H. pylori, diet and gut microbiota, which dysregulates the host metabolic homeostasis, and treatment of H. pylori may be beneficial to the patients with impaired glucose tolerance in addition to diet control.}, } @article {pmid27773914, year = {2016}, author = {Kristoffersen, C and Jensen, RB and Avershina, E and Austbø, D and Tauson, AH and Rudi, K}, title = {Diet-Dependent Modular Dynamic Interactions of the Equine Cecal Microbiota.}, journal = {Microbes and environments}, volume = {31}, number = {4}, pages = {378-386}, pmid = {27773914}, issn = {1347-4405}, mesh = {*Animal Feed ; Animals ; Bacteria/*classification/*isolation & purification ; Carbohydrates/analysis ; Cecum/*microbiology ; Diet/*methods ; Fatty Acids/analysis ; *Gastrointestinal Microbiome ; Horses ; }, abstract = {Knowledge on dynamic interactions in microbiota is pivotal for understanding the role of bacteria in the gut. We herein present comprehensive dynamic models of the horse cecal microbiota, which include short-chained fatty acids, carbohydrate metabolic networks, and taxonomy. Dynamic models were derived from time-series data in a crossover experiment in which four cecum-cannulated horses were fed a starch-rich diet of hay supplemented with barley (starch intake 2 g kg[-1] body weight per day) and a fiber-rich diet of only hay. Cecal contents were sampled via the cannula each h for 24 h for both diets. We observed marked differences in the microbial dynamic interaction patterns for Fibrobacter succinogenes, Lachnospiraceae, Streptococcus, Treponema, Anaerostipes, and Anaerovibrio between the two diet groups. Fluctuations and microbiota interactions were the most pronounced for the starch rich diet, with Streptococcus spp. and Anaerovibrio spp. showing the largest fluctuations. Shotgun metagenome sequencing revealed that diet differences may be explained by modular switches in metabolic cross-feeding between microbial consortia in which fermentation is linked to sugar alcohols and amino sugars for the starch-rich diet and monosaccharides for the fiber-rich diet. In conclusion, diet may not only affect the composition of the cecal microbiota, but also dynamic interactions and metabolic cross-feeding.}, } @article {pmid27694800, year = {2016}, author = {Genee, HJ and Bali, AP and Petersen, SD and Siedler, S and Bonde, MT and Gronenberg, LS and Kristensen, M and Harrison, SJ and Sommer, MO}, title = {Functional mining of transporters using synthetic selections.}, journal = {Nature chemical biology}, volume = {12}, number = {12}, pages = {1015-1022}, pmid = {27694800}, issn = {1552-4469}, mesh = {Bacteria/enzymology/metabolism ; Biosensing Techniques/*methods ; Gastrointestinal Microbiome ; High-Throughput Screening Assays ; Ligands ; Membrane Transport Proteins/*isolation & purification/*metabolism ; *Metagenome ; Soil Microbiology ; Synthetic Biology/methods ; Thiamine Pyrophosphate/*metabolism ; Xanthines/*metabolism ; }, abstract = {Only 25% of bacterial membrane transporters have functional annotation owing to the difficulty of experimental study and of accurate prediction of their function. Here we report a sequence-independent method for high-throughput mining of novel transporters. The method is based on ligand-responsive biosensor systems that enable selective growth of cells only if they encode a ligand-specific importer. We developed such a synthetic selection system for thiamine pyrophosphate and mined soil and gut metagenomes for thiamine-uptake functions. We identified several members of a novel class of thiamine transporters, PnuT, which is widely distributed across multiple bacterial phyla. We demonstrate that with modular replacement of the biosensor, we could expand our method to xanthine and identify xanthine permeases from gut and soil metagenomes. Our results demonstrate how synthetic-biology approaches can effectively be deployed to functionally mine metagenomes and elucidate sequence-function relationships of small-molecule transport systems in bacteria.}, } @article {pmid27770110, year = {2017}, author = {Silbergeld, EK}, title = {The Microbiome.}, journal = {Toxicologic pathology}, volume = {45}, number = {1}, pages = {190-194}, doi = {10.1177/0192623316672073}, pmid = {27770110}, issn = {1533-1601}, mesh = {Animals ; Gene-Environment Interaction ; Humans ; Metabolomics ; Metagenomics ; Microbiota/drug effects/genetics/*physiology ; Pharmacology/*methods ; Research Design ; Toxicology/*methods ; Xenobiotics/pharmacokinetics/pharmacology/toxicity ; }, abstract = {The microbiome is increasingly recognized as a critical component in human development, health, and disease. Its relevance to toxicology and pharmacology involves challenges to current concepts related to absorption, metabolism, gene:environment, and pathways of response. Framing testable hypotheses for experimental and epidemiological studies will require attention to study designs, biosampling, data analysis, and attention to confounders.}, } @article {pmid27769810, year = {2017}, author = {Sartor, RB and Wu, GD}, title = {Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches.}, journal = {Gastroenterology}, volume = {152}, number = {2}, pages = {327-339.e4}, pmid = {27769810}, issn = {1528-0012}, support = {P01 DK094779/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/metabolism ; Colitis, Ulcerative/metabolism/microbiology ; Crohn Disease/metabolism/microbiology ; Dysbiosis/metabolism/*microbiology ; Fungi/genetics/metabolism ; Gastrointestinal Microbiome/*genetics ; Humans ; Inflammatory Bowel Diseases/metabolism/*microbiology ; Metabolome ; Metagenome ; Pouchitis/metabolism/microbiology ; Viruses/genetics/metabolism ; }, abstract = {Intestinal microbiota are involved in the pathogenesis of Crohn's disease, ulcerative colitis, and pouchitis. We review the mechanisms by which these gut bacteria, fungi, and viruses mediate mucosal homeostasis via their composite genes (metagenome) and metabolic products (metabolome). We explain how alterations to their profiles and functions under conditions of dysbiosis contribute to inflammation and effector immune responses that mediate inflammatory bowel diseases (IBD) in humans and enterocolitis in mice. It could be possible to engineer the intestinal environment by modifying the microbiota community structure or function to treat patients with IBD-either with individual agents, via dietary management, or as adjuncts to immunosuppressive drugs. We summarize the latest information on therapeutic use of fecal microbial transplantation and propose improved strategies to selectively normalize the dysbiotic microbiome in personalized approaches to treatment.}, } @article {pmid27768825, year = {2017}, author = {Adu-Oppong, B and Gasparrini, AJ and Dantas, G}, title = {Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes.}, journal = {Annals of the New York Academy of Sciences}, volume = {1388}, number = {1}, pages = {42-58}, pmid = {27768825}, issn = {1749-6632}, support = {DP2 DK098089/DK/NIDDK NIH HHS/United States ; R01 GM099538/GM/NIGMS NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; U01 AI123394/AI/NIAID NIH HHS/United States ; T32 GM007067/GM/NIGMS NIH HHS/United States ; }, mesh = {*Anti-Infective Agents ; Drug Resistance/*genetics ; Genomics/*methods ; Microbiota/*genetics ; }, abstract = {Microbial communities contain diverse bacteria that play important roles in every environment. Advances in sequencing and computational methodologies over the past decades have illuminated the phylogenetic and functional diversity of microbial communities from diverse habitats. Among the activities encoded in microbiomes are the abilities to synthesize and resist small molecules, yielding antimicrobial activity. These functions are of particular interest when viewed in light of the public health emergency posed by the increase in clinical antimicrobial resistance and the dwindling antimicrobial discovery and approval pipeline, and given the intimate ecological and evolutionary relationship between antimicrobial biosynthesis and resistance. Here, we review genomic and functional methods that have been developed for accessing the antimicrobial biosynthesis and resistance capacity of microbiomes and highlight outstanding examples of their applications.}, } @article {pmid27768750, year = {2016}, author = {Zhang, J and Hu, Q and Xu, C and Liu, S and Li, C}, title = {Key Microbiota Identification Using Functional Gene Analysis during Pepper (Piper nigrum L.) Peeling.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0165206}, pmid = {27768750}, issn = {1932-6203}, mesh = {Bacteria/classification ; Biodiversity ; *Genes, Plant ; *Microbiota ; Piper nigrum/*genetics ; }, abstract = {Pepper pericarp microbiota plays an important role in the pepper peeling process for the production of white pepper. We collected pepper samples at different peeling time points from Hainan Province, China, and used a metagenomic approach to identify changes in the pericarp microbiota based on functional gene analysis. UniFrac distance-based principal coordinates analysis revealed significant changes in the pericarp microbiota structure during peeling, which were attributed to increases in bacteria from the genera Selenomonas and Prevotella. We identified 28 core operational taxonomic units at each time point, mainly belonging to Selenomonas, Prevotella, Megasphaera, Anaerovibrio, and Clostridium genera. The results were confirmed by quantitative polymerase chain reaction. At the functional level, we observed significant increases in microbial features related to acetyl xylan esterase and pectinesterase for pericarp degradation during peeling. These findings offer a new insight into biodegradation for pepper peeling and will promote the development of the white pepper industry.}, } @article {pmid27766749, year = {2017}, author = {Ranchou-Peyruse, M and Gasc, C and Guignard, M and Aüllo, T and Dequidt, D and Peyret, P and Ranchou-Peyruse, A}, title = {The sequence capture by hybridization: a new approach for revealing the potential of mono-aromatic hydrocarbons bioattenuation in a deep oligotrophic aquifer.}, journal = {Microbial biotechnology}, volume = {10}, number = {2}, pages = {469-479}, pmid = {27766749}, issn = {1751-7915}, mesh = {Biota ; Biotransformation ; Groundwater/*microbiology ; High-Throughput Nucleotide Sequencing ; Hydrocarbons, Aromatic/*metabolism ; Metagenomics/*methods ; Nucleic Acid Hybridization ; Peptococcaceae/genetics/*isolation & purification/*metabolism ; Sequence Analysis, DNA ; }, abstract = {The formation water of a deep aquifer (853 m of depth) used for geological storage of natural gas was sampled to assess the mono-aromatic hydrocarbons attenuation potential of the indigenous microbiota. The study of bacterial diversity suggests that Firmicutes and, in particular, sulphate-reducing bacteria (Peptococcaceae) predominate in this microbial community. The capacity of the microbial community to biodegrade toluene and m- and p-xylenes was demonstrated using a culture-based approach after several hundred days of incubation. In order to reveal the potential for biodegradation of these compounds within a shorter time frame, an innovative approach named the solution hybrid selection method, which combines sequence capture by hybridization and next-generation sequencing, was applied to the same original water sample. The bssA and bssA-like genes were investigated as they are considered good biomarkers for the potential of toluene and xylene biodegradation. Unlike a PCR approach which failed to detect these genes directly from formation water, this innovative strategy demonstrated the presence of the bssA and bssA-like genes in this oligotrophic ecosystem, probably harboured by Peptococcaceae. The sequence capture by hybridization shows significant potential to reveal the presence of genes of functional interest which have low-level representation in the biosphere.}, } @article {pmid27766372, year = {2017}, author = {Willmann, M and Peter, S}, title = {Translational metagenomics and the human resistome: confronting the menace of the new millennium.}, journal = {Journal of molecular medicine (Berlin, Germany)}, volume = {95}, number = {1}, pages = {41-51}, pmid = {27766372}, issn = {1432-1440}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacterial Infections/diagnosis/drug therapy/microbiology ; *Drug Resistance, Microbial ; Humans ; Infection Control ; *Metagenome ; *Metagenomics/methods ; Microbiota/*drug effects/*genetics ; Translational Research, Biomedical ; }, abstract = {The increasing threat of antimicrobial resistance poses one of the greatest challenges to modern medicine. The collection of all antimicrobial resistance genes carried by various microorganisms in the human body is called the human resistome and represents the source of resistance in pathogens that can eventually cause life-threatening and untreatable infections. A deep understanding of the human resistome and its multilateral interaction with various environments is necessary for developing proper measures that can efficiently reduce the spread of resistance. However, the human resistome and its evolution still remain, for the most part, a mystery to researchers. Metagenomics, particularly in combination with next-generation-sequencing technology, provides a powerful methodological approach for studying the human microbiome as well as the pathogenome, the virolume and especially the resistome. We summarize below current knowledge on how the human resistome is shaped and discuss how metagenomics can be employed to improve our understanding of these complex processes, particularly as regards a rapid translation of new findings into clinical diagnostics, infection control and public health.}, } @article {pmid27723493, year = {2016}, author = {Fujii, T and Kyoui, D and Takahashi, H and Kuda, T and Kimura, B and Washizu, Y and Emoto, E and Hiramoto, T}, title = {Pyrosequencing analysis of the microbiota of kusaya gravy obtained from Izu Islands.}, journal = {International journal of food microbiology}, volume = {238}, number = {}, pages = {320-325}, doi = {10.1016/j.ijfoodmicro.2016.09.030}, pmid = {27723493}, issn = {1879-3460}, mesh = {Animals ; Firmicutes/*classification/genetics/*isolation & purification ; Fish Products/*microbiology ; Fishes ; Food Microbiology ; *Geography ; Islands ; Japan ; Metagenome ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Kusaya is a salted, dried fish product traditionally produced on the Izu Islands in Japan. Fish are added to kusaya gravy repeatedly and intermittently, and used over several hundred years, which makes unique microbiota and unique flavors. In this study, we performed a metagenomic analysis to compare the composition of the microbiota of kusaya gravy between different islands. Twenty samples obtained from a total of 13 manufacturers on three islands (Hachijojima, Niijima, and Oshima Islands) were analyzed. The statistical analysis revealed that the microbiota in kusaya gravy maintain a stable composition regardless of the production steps, and that the microbiota are characteristic to the particular islands. The bacterial taxa common to all of the samples were not necessarily the dominant ones. On the other hand, the genera Halanaerobium and Tissierella were found to be characteristic to the microbiota of one or two islands. Because these genera are known to be present in the natural environment, it is likely that the bacterial strains peculiar to an island had colonized kusaya gravy for many years. The results of this study revealed an influence of geographical conditions on the microbiota in fermented food.}, } @article {pmid27614122, year = {2016}, author = {Oguntoyinbo, FA and Cho, GS and Trierweiler, B and Kabisch, J and Rösch, N and Neve, H and Bockelmann, W and Frommherz, L and Nielsen, DS and Krych, L and Franz, CM}, title = {Fermentation of African kale (Brassica carinata) using L. plantarum BFE 5092 and L. fermentum BFE 6620 starter strains.}, journal = {International journal of food microbiology}, volume = {238}, number = {}, pages = {103-112}, doi = {10.1016/j.ijfoodmicro.2016.08.030}, pmid = {27614122}, issn = {1879-3460}, mesh = {Africa ; Ascorbic Acid/chemistry ; Brassica/*microbiology ; Enterobacteriaceae/growth & development ; *Fermentation ; Food Microbiology ; Genotype ; Hydrogen-Ion Concentration ; Lactic Acid/chemistry ; Limosilactobacillus fermentum/*growth & development ; Lactobacillus plantarum/*growth & development ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Random Amplified Polymorphic DNA Technique ; Solubility ; Vegetables/microbiology ; Vitamins/chemistry ; }, abstract = {Vegetables produced in Africa are sources of much needed micronutrients and fermentation is one way to enhance the shelf life of these perishable products. To prevent post-harvest losses and preserve African leafy vegetables, Lactobacillus plantarum BFE 5092 and Lactobacillus fermentum BFE 6620 starter strains were investigated for their application in fermentation of African kale (Brassica carinata) leaves. They were inoculated at 1×10[7]cfu/ml and grew to a maximum level of 10[8]cfu/ml during 24h submerged fermentation. The strains utilized simple sugars (i.e., glucose, fructose, and sucrose) in the kale to quickly reduce the pH from pH6.0 to pH3.6 within 24h. The strains continued to produce both d and l lactic acid up to 144h, reaching a maximum concentration of 4.0g/l. Fermentations with pathogens inoculated at 10[4]cfu/ml showed that the quick growth of the starters inhibited the growth of Listeria monocytogenes and Salmonella Enteritidis, as well as other enterobacteria. Denaturing gradient gel electrophoresis and 16S rRNA gene (V3-V4-region) amplicon sequencing showed that in the spontaneous fermentations a microbial succession took place, though with marked differences in biodiversity from fermentation to fermentation. The fermentations inoculated with starters however were clearly dominated by both the inoculated strains throughout the fermentations. RAPD-PCR fingerprinting showed that the strains established themselves at approx. equal proportions. Although vitamins C, B1 and B2 decreased during the fermentation, the final level of vitamin C in the product was an appreciable concentration of 35mg/100g. In conclusion, controlled fermentation of kale offers a promising avenue to prevent spoilage and improve the shelf life and safety.}, } @article {pmid27762295, year = {2016}, author = {Sommeria-Klein, G and Zinger, L and Taberlet, P and Coissac, E and Chave, J}, title = {Inferring neutral biodiversity parameters using environmental DNA data sets.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {35644}, pmid = {27762295}, issn = {2045-2322}, mesh = {*Biodiversity ; Biostatistics ; Computer Simulation ; DNA/*analysis/*genetics ; DNA Barcoding, Taxonomic/methods ; *Ecosystem ; Metagenomics/methods ; Polymerase Chain Reaction ; }, abstract = {The DNA present in the environment is a unique and increasingly exploited source of information for conducting fast and standardized biodiversity assessments for any type of organisms. The datasets resulting from these surveys are however rarely compared to the quantitative predictions of biodiversity models. In this study, we simulate neutral taxa-abundance datasets, and artificially noise them by simulating noise terms typical of DNA-based biodiversity surveys. The resulting noised taxa abundances are used to assess whether the two parameters of Hubbell's neutral theory of biodiversity can still be estimated. We find that parameters can be inferred provided that PCR noise on taxa abundances does not exceed a certain threshold. However, inference is seriously biased by the presence of artifactual taxa. The uneven contribution of organisms to environmental DNA owing to size differences and barcode copy number variability does not impede neutral parameter inference, provided that the number of sequence reads used for inference is smaller than the number of effectively sampled individuals. Hence, estimating neutral parameters from DNA-based taxa abundance patterns is possible but requires some caution. In studies that include empirical noise assessments, our comprehensive simulation benchmark provides objective criteria to evaluate the robustness of neutral parameter inference.}, } @article {pmid27760854, year = {2016}, author = {Hibbett, D and Abarenkov, K and Kõljalg, U and Öpik, M and Chai, B and Cole, J and Wang, Q and Crous, P and Robert, V and Helgason, T and Herr, JR and Kirk, P and Lueschow, S and O'Donnell, K and Nilsson, RH and Oono, R and Schoch, C and Smyth, C and Walker, DM and Porras-Alfaro, A and Taylor, JW and Geiser, DM}, title = {Sequence-based classification and identification of Fungi.}, journal = {Mycologia}, volume = {108}, number = {6}, pages = {1049-1068}, doi = {10.3852/16-130}, pmid = {27760854}, issn = {0027-5514}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Fungi/*classification/*genetics ; Metagenomics/*methods ; *Phylogeny ; }, abstract = {Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes. To realize the full potential of fungal SBCI it will be necessary to make advances in multiple areas. Improvements in sequencing methods, including long-read and single-cell technologies, will empower fungal molecular ecologists to look beyond ITS and current shotgun metagenomics approaches. Data quality and accessibility will be enhanced by attention to data and metadata standards and rigorous enforcement of policies for deposition of data and workflows. Taxonomic communities will need to develop best practices for molecular characterization in their focal clades, while also contributing to globally useful datasets including ITS. Changes to nomenclatural rules are needed to enable validPUBLICation of sequence-based taxon descriptions. Finally, cultural shifts are necessary to promote adoption of SBCI and to accord professional credit to individuals who contribute to community resources.}, } @article {pmid27760570, year = {2016}, author = {Kamke, J and Kittelmann, S and Soni, P and Li, Y and Tavendale, M and Ganesh, S and Janssen, PH and Shi, W and Froula, J and Rubin, EM and Attwood, GT}, title = {Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation.}, journal = {Microbiome}, volume = {4}, number = {1}, pages = {56}, pmid = {27760570}, issn = {2049-2618}, mesh = {Animals ; Bacteria/*classification/genetics/*metabolism ; Base Sequence ; Butyrates/metabolism ; Fatty Acids/metabolism ; Fermentation ; Global Warming ; Hexoses/*metabolism ; High-Throughput Nucleotide Sequencing ; Lactic Acid/*metabolism ; Lactobacillaceae/genetics/*metabolism ; Metagenome/genetics ; Methane/*metabolism ; Microbiota/genetics ; Propionates/metabolism ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology/physiology ; Sequence Analysis, DNA ; Sheep ; }, abstract = {BACKGROUND: Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed to ensure sustainable animal production in the future. Methane yield varies naturally in sheep and is a heritable trait that can be used to select animals that yield less methane per unit of feed eaten. We previously demonstrated elevated expression of hydrogenotrophic methanogenesis pathway genes of methanogenic archaea in the rumens of high methane yield (HMY) sheep compared to their low methane yield (LMY) counterparts. Methane production in the rumen is strongly connected to microbial hydrogen production through fermentation processes. In this study, we investigate the contribution that rumen bacteria make to methane yield phenotypes in sheep.

RESULTS: Using deep sequence metagenome and metatranscriptome datasets in combination with 16S rRNA gene amplicon sequencing from HMY and LMY sheep, we show enrichment of lactate-producing Sharpea spp. in LMY sheep bacterial communities. Increased gene and transcript abundances for sugar import and utilisation and production of lactate, propionate and butyrate were also observed in LMY animals. Sharpea azabuensis and Megasphaera spp. act as important drivers of lactate production and utilisation according to phylogenetic analysis and read mappings.

CONCLUSIONS: Our findings show that the rumen microbiome in LMY animals supports a rapid heterofermentative growth, leading to lactate production. We postulate that lactate is subsequently metabolised mainly to butyrate in LMY animals, producing 2 mol of hydrogen and 0.5 mol of methane per mol hexose, which represents 24 % less than the 0.66 mol of methane formed from the 2.66 mol of hydrogen produced if hexose fermentation was directly to acetate and butyrate. These findings are consistent with the theory that a smaller rumen size with a higher turnover rate, where rapid heterofermentative growth would be an advantage, results in lower hydrogen production and lower methane formation. Together with previous methanogen gene expression data, this builds a strong concept of how animal traits and microbial communities shape the methane phenotype in sheep.}, } @article {pmid27760077, year = {2016}, author = {Dunn, KA and Moore-Connors, J and MacIntyre, B and Stadnyk, A and Thomas, NA and Noble, A and Mahdi, G and Rashid, M and Otley, AR and Bielawski, JP and Van Limbergen, J}, title = {The Gut Microbiome of Pediatric Crohn's Disease Patients Differs from Healthy Controls in Genes That Can Influence the Balance Between a Healthy and Dysregulated Immune Response.}, journal = {Inflammatory bowel diseases}, volume = {22}, number = {11}, pages = {2607-2618}, doi = {10.1097/MIB.0000000000000949}, pmid = {27760077}, issn = {1536-4844}, support = {CMF-108026//CIHR/Canada ; }, mesh = {Adolescent ; Case-Control Studies ; Child ; Crohn Disease/immunology/*microbiology/therapy ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics/*immunology ; Humans ; Immunity, Innate ; Male ; Metagenomics ; Remission Induction ; }, abstract = {BACKGROUND: Exclusive enteral nutrition (EEN) is a first-line therapy in pediatric Crohn's disease (CD) thought to induce remission through changes in the gut microbiome. With microbiome assessment largely focused on microbial taxonomy and diversity, it remains unclear to what extent EEN induces functional changes that thereby contribute to its therapeutic effect.

METHODS: Fecal samples were collected from 15 pediatric CD patients prior to and after EEN treatment, as well as from 5 healthy controls. Metagenomic data were obtained via next-generation sequencing, and nonhuman reads were mapped to KEGG pathways, where possible. Pathway abundance was compared between CD patients and controls, and between CD patients that sustained remission (SR) and those that did not sustain remission (NSR).

RESULTS: Of 132 KEGG pathways identified, 8 pathways differed significantly between baseline CD patients and controls. Examination of these eight pathways showed SR patients had greater similarity to controls than NSR patients in all cases. Pathways fell into one of three groups: 1) no prior connection to IBD, 2) previously reported connection to IBD, and 3) known roles in innate immunity and immunoregulation.

CONCLUSIONS: The microbiota of CD patients and controls represent alternative ecological states that have broad differences in functional capabilities, including xenobiotic and environmental pollutant degradation, succinate metavolism, and bacterial HtpG, all of which can affect barrier integrity and immune regulation. Moreover, our finding that SR patients were more similar to healthy controls suggests that community microbial function, as inferred from fecal microbiomes, could serve as a valuable diagnostic tool.}, } @article {pmid27759035, year = {2016}, author = {Hou, S and Pfreundt, U and Miller, D and Berman-Frank, I and Hess, WR}, title = {mdRNA-Seq analysis of marine microbial communities from the northern Red Sea.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {35470}, pmid = {27759035}, issn = {2045-2322}, mesh = {*Aquatic Organisms ; Biodiversity ; Environment ; Gene Expression Regulation ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Nucleic Acid Conformation ; RNA, Ribosomal, 16S/genetics ; Riboswitch/genetics ; Seawater/*microbiology ; Transcriptome ; *Water Microbiology ; }, abstract = {Metatranscriptomic differential RNA-Seq (mdRNA-Seq) identifies the suite of active transcriptional start sites at single-nucleotide resolution through enrichment of primary transcript 5' ends. Here we analyzed the microbial community at 45 m depth at Station A in the northern Gulf of Aqaba, Red Sea, during 500 m deep mixing in February 2012 using mdRNA-Seq and a parallel classical RNA-Seq approach. We identified promoters active in situ for five different pico-planktonic genera (the SAR11 clade of Alphaproteobacteria, Synechococcus of Cyanobacteria, Euryarchaeota, Thaumarchaeota, and Micromonas as an example for picoeukaryotic algae), showing the applicability of this approach to highly diverse microbial communities. 16S rDNA quantification revealed that 24% of the analyzed community were group II marine Euryarchaeota in which we identified a highly abundant non-coding RNA, Tan1, and detected very high expression of genes encoding intrinsically disordered proteins, as well as enzymes for the synthesis of specific B vitamins, extracellular peptidases, carbohydrate-active enzymes, and transport systems. These results highlight previously unknown functions of Euryarchaeota with community-wide relevance. The complementation of metatranscriptomic studies with mdRNA-Seq provides substantial additional information regarding transcriptional start sites, promoter activities, and the identification of non-coding RNAs.}, } @article {pmid27596621, year = {2016}, author = {Carlström, CI and Lucas, LN and Rohde, RA and Haratian, A and Engelbrektson, AL and Coates, JD}, title = {Characterization of an anaerobic marine microbial community exposed to combined fluxes of perchlorate and salinity.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {22}, pages = {9719-9732}, doi = {10.1007/s00253-016-7780-5}, pmid = {27596621}, issn = {1432-0614}, mesh = {Anaerobiosis ; Aquatic Organisms/*drug effects ; Archaea/classification/*drug effects/genetics ; Bacteria/classification/*drug effects/genetics ; Biota/*drug effects ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/*microbiology ; Perchlorates/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Sequence Analysis, DNA ; Sodium Chloride/metabolism ; }, abstract = {The recent recognition of the environmental prevalence of perchlorate and its discovery on Mars, Earth's moon, and in meteorites, in addition to its novel application to controlling oil reservoir sulfidogenesis, has resulted in a renewed interest in this exotic ion and its associated microbiology. However, while plentiful data exists on freshwater perchlorate respiring organisms, information on their halophilic counterparts and microbial communities is scarce. Here, we investigated the temporal evolving structure of perchlorate respiring communities under a range of NaCl concentrations (1, 3, 5, 7, and 10 % wt/vol) using marine sediment amended with acetate and perchlorate. In general, perchlorate consumption rates were inversely proportional to NaCl concentration with the most rapid rate observed at 1 % NaCl. At 10 % NaCl, no perchlorate removal was observed. Transcriptional analysis of the 16S rRNA gene indicated that salinity impacted microbial community structure and the most active members were in families Rhodocyclaceae (1 and 3 % NaCl), Pseudomonadaceae (1 NaCl), Campylobacteraceae (1, 5, and 7 % NaCl), Sedimenticolaceae (3 % NaCl), Desulfuromonadaceae (5 and 7 % NaCl), Pelobacteraceae (5 % NaCl), Helicobacteraceae (5 and 7 % NaCl), and V1B07b93 (7 %). Novel isolates of genera Sedimenticola, Marinobacter, Denitromonas, Azoarcus, and Pseudomonas were obtained and their perchlorate respiring capacity confirmed. Although the obligate anaerobic, sulfur-reducing Desulfuromonadaceae species were dominant at 5 and 7 % NaCl, their enrichment may result from biological sulfur cycling, ensuing from the innate ability of DPRB to oxidize sulfide. Additionally, our results demonstrated enrichment of an archaeon of phylum Parvarchaeota at 5 % NaCl. To date, this phylum has only been described in metagenomic experiments of acid mine drainage and is unexpected in a marine community. These studies identify the intrinsic capacity of marine systems to respire perchlorate and significantly expand the known diversity of organisms capable of this novel metabolism.}, } @article {pmid27753534, year = {2017}, author = {Petrovskaya, LE and Novototskaya-Vlasova, KA and Gapizov, SS and Spirina, EV and Durdenko, EV and Rivkina, EM}, title = {New member of the hormone-sensitive lipase family from the permafrost microbial community.}, journal = {Bioengineered}, volume = {8}, number = {4}, pages = {420-423}, pmid = {27753534}, issn = {2165-5987}, mesh = {Enzyme Activation ; Enzyme Stability ; Metagenome/*genetics ; Microbial Consortia/*physiology ; Permafrost/*microbiology ; Siberia ; Sterol Esterase/*chemistry/*genetics ; }, abstract = {Siberian permafrost is a unique environment inhabited with diverse groups of microorganisms. Among them, there are numerous producers of biotechnologically relevant enzymes including lipases and esterases. Recently, we have constructed a metagenomic library from a permafrost sample and identified in it several genes coding for potential lipolytic enzymes. In the current work, properties of the recombinant esterases obtained from this library are compared with the previously characterized lipase from Psychrobacter cryohalolentis and other representatives of the hormone-sensitive lipase family.}, } @article {pmid27751665, year = {2017}, author = {Yao, XF and Zhang, JM and Tian, L and Guo, JH}, title = {The effect of heavy metal contamination on the bacterial community structure at Jiaozhou Bay, China.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {48}, number = {1}, pages = {71-78}, pmid = {27751665}, issn = {1678-4405}, mesh = {*Bacteria/classification ; Bays ; *Biodiversity ; China ; Cluster Analysis ; Environment ; *Environmental Microbiology ; *Environmental Pollutants ; *Environmental Pollution ; Geologic Sediments/*chemistry/*microbiology ; *Metals, Heavy ; }, abstract = {In this study, determination of heavy metal parameters and microbiological characterization of marine sediments obtained from two heavily polluted sites and one low-grade contaminated reference station at Jiaozhou Bay in China were carried out. The microbial communities found in the sampled marine sediments were studied using PCR-DGGE (denaturing gradient gel electrophoresis) fingerprinting profiles in combination with multivariate analysis. Clustering analysis of DGGE and matrix of heavy metals displayed similar occurrence patterns. On this basis, 17 samples were classified into two clusters depending on the presence or absence of the high level contamination. Moreover, the cluster of highly contaminated samples was further classified into two sub-groups based on the stations of their origin. These results showed that the composition of the bacterial community is strongly influenced by heavy metal variables present in the sediments found in the Jiaozhou Bay. This study also suggested that metagenomic techniques such as PCR-DGGE fingerprinting in combination with multivariate analysis is an efficient method to examine the effect of metal contamination on the bacterial community structure.}, } @article {pmid27266978, year = {2016}, author = {Liu, Y and Zhang, L and Wang, X and Wang, Z and Zhang, J and Jiang, R and Wang, X and Wang, K and Liu, Z and Xia, Z and Xu, Z and Nie, Y and Lv, X and Wu, X and Zhu, H and Duan, L}, title = {Similar Fecal Microbiota Signatures in Patients With Diarrhea-Predominant Irritable Bowel Syndrome and Patients With Depression.}, journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association}, volume = {14}, number = {11}, pages = {1602-1611.e5}, doi = {10.1016/j.cgh.2016.05.033}, pmid = {27266978}, issn = {1542-7714}, mesh = {Adult ; Biopsy ; *Biota ; China ; Colon ; Colon, Sigmoid/pathology ; Depression/microbiology ; Diarrhea/*microbiology ; Feces/*microbiology ; Female ; Histocytochemistry ; Humans ; Irritable Bowel Syndrome/*microbiology ; Male ; Metagenomics ; Middle Aged ; Young Adult ; }, abstract = {BACKGROUND & AIMS: Patients with irritable bowel syndrome (IBS) often have psychiatric comorbidities. Alterations in the intestinal microbiota have been associated with IBS and depression, but it is not clear if there is a microbial relationship between these disorders. We studied the profiles of fecal microbiota samples from patients with IBS, depression, or comorbidities of IBS and depression; we determined the relationships among these profiles and clinical and pathophysiological features of these disorders.

METHODS: We used 454 pyrosequencing to analyze fecal microbiota samples from 100 subjects (40 with diarrhea-predominant IBS [IBS-D], 15 with depression, 25 with comorbidities of IBS and depression, and 20 healthy individuals [controls]), recruited at Peking University. Abdominal and psychological symptoms were evaluated with validated questionnaires. Visceral sensitivity was evaluated using a barostat. Colonic mucosal inflammation was assayed by immunohistochemical analyses of sigmoid tissue biopsy specimens.

RESULTS: Fecal microbiota signatures were similar between patients with IBS-D and depression in that they were less diverse than samples from controls and had similar abundances of alterations. They were characterized by high proportions of Bacteroides (type I), Prevotella (type II), or nondominant microbiota (type III). Most patients with IBS-D or depression had type I or type II profiles (IBS-D had 85% type I and type II profiles, depression had 80% type I and type II profiles). Colon tissues from patients with type I or type II profiles had higher levels of inflammatory markers than colon tissues from patients with type III profiles. The level of colon inflammation correlated with the severity of IBS symptoms.

CONCLUSIONS: Patients with IBS-D and depression have similar alterations in fecal microbiota; these might be related to the pathogenesis of these disorders. We identified 3 microbial profiles in patients that could indicate different subtypes of IBS and depression or be used as diagnostic biomarkers.}, } @article {pmid27744476, year = {2017}, author = {Lu, XM and Chen, C and Zheng, TL}, title = {Metagenomic Insights into Effects of Chemical Pollutants on Microbial Community Composition and Function in Estuarine Sediments Receiving Polluted River Water.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {791-800}, pmid = {27744476}, issn = {1432-184X}, mesh = {Acetolactate Synthase/metabolism ; Aconitate Hydratase/metabolism ; Amino Acids/metabolism ; Bacteria/*classification/enzymology/*genetics/metabolism ; Base Sequence ; Carbon Cycle ; China ; *Estuaries ; Fresh Water ; Geologic Sediments/chemistry/*microbiology ; Ketone Oxidoreductases/metabolism ; Metabolic Networks and Pathways ; Metagenomics/*methods ; Microbial Consortia/drug effects/*genetics ; Nitrobenzenes/adverse effects ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/adverse effects ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Salinity ; Sequence Analysis ; Water Pollutants, Chemical/*analysis/chemistry ; }, abstract = {Pyrosequencing and metagenomic profiling were used to assess the phylogenetic and functional characteristics of microbial communities residing in sediments collected from the estuaries of Rivers Oujiang (OS) and Jiaojiang (JS) in the western region of the East China Sea. Another sediment sample was obtained from near the shore far from estuaries, used for contrast (CS). Characterization of estuary sediment bacterial communities showed that toxic chemicals potentially reduced the natural variability in microbial communities, while they increased the microbial metabolic enzymes and pathways. Polycyclic aromatic hydrocarbons (PAHs) and nitrobenzene were negatively correlated with the bacterial community variation. The dominant class in the sediments was Gammaproteobacteria. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) enzyme profiles, dominant enzymes were found in estuarine sediments, which increased greatly, such as 2-oxoglutarate synthase, acetolactate synthase, inorganic diphosphatase, and aconitate hydratase. In KEGG pathway profiles, most of the pathways were also dominated by specific metabolism in these sediments and showed a marked increase, for instance alanine, aspartate, and glutamate metabolism, carbon fixation pathways in prokaryotes, and aminoacyl-tRNA biosynthesis. The estuarine sediment bacterial diversity varied with the polluted river water inputs. In the estuary receiving river water from the more seriously polluted River Oujiang, the sediment bacterial community function was more severely affected.}, } @article {pmid27741163, year = {2016}, author = {Valsecchi, C and Carlotta Tagliacarne, S and Castellazzi, A}, title = {Gut Microbiota and Obesity.}, journal = {Journal of clinical gastroenterology}, volume = {50 Suppl 2, Proceedings from the 8th Probiotics, Prebiotics & New Foods for Microbiota and Human Health meeting held in Rome, Italy on September 13-15, 2015}, number = {}, pages = {S157-S158}, doi = {10.1097/MCG.0000000000000715}, pmid = {27741163}, issn = {1539-2031}, mesh = {Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenome ; Obesity/*microbiology ; }, abstract = {Intestinal microbiota is composed by symbiotic innocuous bacteria and potential pathogens also called pathobionts. The human gut normally hosts roughly 1014 bacterial organisms of up to 1000 different species. The genome size of this microbial organ, collectively named microbiome, exceeds the size of the human nuclear genome by 2 orders of magnitude.}, } @article {pmid27740610, year = {2017}, author = {Martiny, JB and Martiny, AC and Weihe, C and Lu, Y and Berlemont, R and Brodie, EL and Goulden, ML and Treseder, KK and Allison, SD}, title = {Microbial legacies alter decomposition in response to simulated global change.}, journal = {The ISME journal}, volume = {11}, number = {2}, pages = {490-499}, pmid = {27740610}, issn = {1751-7370}, mesh = {Bacteria/*classification/genetics/growth & development ; Carbohydrate Metabolism ; *Climate Change ; Ecosystem ; Fungi/*classification/genetics/growth & development ; Metagenomics ; *Microbial Consortia ; Nitrogen/metabolism ; Plant Leaves/microbiology ; Rain ; Seasons ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Terrestrial ecosystem models assume that microbial communities respond instantaneously, or are immediately resilient, to environmental change. Here we tested this assumption by quantifying the resilience of a leaf litter community to changes in precipitation or nitrogen availability. By manipulating composition within a global change experiment, we decoupled the legacies of abiotic parameters versus that of the microbial community itself. After one rainy season, more variation in fungal composition could be explained by the original microbial inoculum than the litterbag environment (18% versus 5.5% of total variation). This compositional legacy persisted for 3 years, when 6% of the variability in fungal composition was still explained by the microbial origin. In contrast, bacterial composition was generally more resilient than fungal composition. Microbial functioning (measured as decomposition rate) was not immediately resilient to the global change manipulations; decomposition depended on both the contemporary environment and rainfall the year prior. Finally, using metagenomic sequencing, we showed that changes in precipitation, but not nitrogen availability, altered the potential for bacterial carbohydrate degradation, suggesting why the functional consequences of the two experiments may have differed. Predictions of how terrestrial ecosystem processes respond to environmental change may thus be improved by considering the legacies of microbial communities.}, } @article {pmid27739431, year = {2016}, author = {Bagnoud, A and Chourey, K and Hettich, RL and de Bruijn, I and Andersson, AF and Leupin, OX and Schwyn, B and Bernier-Latmani, R}, title = {Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {12770}, pmid = {27739431}, issn = {2041-1723}, mesh = {*Aluminum Silicates ; Autotrophic Processes ; Bacteria/classification/genetics/metabolism ; Carbon Cycle ; Clay ; Ecosystem ; Geography ; Heterotrophic Processes ; Hydrogen/*metabolism ; *Metabolic Networks and Pathways ; Metagenomics/*methods ; *Microbial Consortia ; RNA, Ribosomal, 16S/genetics ; Radioactive Waste ; *Soil Microbiology ; Switzerland ; }, abstract = {The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present.}, } @article {pmid27738970, year = {2017}, author = {Murphy, R and Tsai, P and Jüllig, M and Liu, A and Plank, L and Booth, M}, title = {Differential Changes in Gut Microbiota After Gastric Bypass and Sleeve Gastrectomy Bariatric Surgery Vary According to Diabetes Remission.}, journal = {Obesity surgery}, volume = {27}, number = {4}, pages = {917-925}, pmid = {27738970}, issn = {1708-0428}, mesh = {Adult ; Diabetes Mellitus, Type 2/complications/*microbiology/*surgery ; Female ; Follow-Up Studies ; *Gastrectomy/methods ; *Gastric Bypass/methods ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Laparoscopy ; Male ; Middle Aged ; Obesity/complications/*microbiology/*surgery ; Postoperative Period ; Remission Induction ; Treatment Outcome ; }, abstract = {BACKGROUND: It is unclear whether specific gut microbiota is associated with remission of type 2 diabetes (T2D) after distinct types of bariatric surgery.

AIMS: The aim of this study is to examine gut microbiota changes after laparoscopic Roux-en-Y gastric bypass (RYGB) or sleeve gastrectomy (SG) surgery in obese patients with T2D.

METHODS: Whole-metagenome shotgun sequencing of DNA fragments using Illumina HiSeq2000 was obtained from stool samples collected from 14 obese T2D patients pre-operatively (while on very low calorie diet) and 1 year after randomisation to laparoscopic SG (n = 7) or RYGB (n = 7). Resulting shotgun reads were annotated with Kyoto Encyclopedia of Genes and Genomes (KEGG).

RESULTS: Body weight reduction and dietary change was similar 1 year after both surgery types. Identical proportions (n = 5/7) achieved diabetes remission (HbA1c < 48 mmol/mol without medications) 1 year after RYGB and SG. RYGB resulted in increased Firmicutes and Actinobacteria phyla but decreased Bacteroidetes phyla. SG resulted in increased Bacteroidetes phyla. Only an increase in Roseburia species was observed among those achieving diabetes remission, common to both surgery types. KEGG Orthology and pathway analysis predicted contrasting and greater gut microbiota metabolism changes after diabetes remission following RYGB than after SG. Those with persistent diabetes post-operatively had higher Desulfovibrio species pre-operatively.

CONCLUSIONS: Overall, RYGB produces greater and more predicted favourable changes in gut microbiota functional capacity than SG. An increase in Roseburia species was the only compositional change common to both types of surgery among those achieving diabetes remission.}, } @article {pmid27738135, year = {2017}, author = {Chen, IA and Markowitz, VM and Chu, K and Palaniappan, K and Szeto, E and Pillay, M and Ratner, A and Huang, J and Andersen, E and Huntemann, M and Varghese, N and Hadjithomas, M and Tennessen, K and Nielsen, T and Ivanova, NN and Kyrpides, NC}, title = {IMG/M: integrated genome and metagenome comparative data analysis system.}, journal = {Nucleic acids research}, volume = {45}, number = {D1}, pages = {D507-D516}, pmid = {27738135}, issn = {1362-4962}, support = {U01 HG004866/HG/NHGRI NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; *Software ; Web Browser ; }, abstract = {The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support for examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review (ER) companion system (IMG/M ER: https://img.jgi.doe.gov/mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system.}, } @article {pmid27734937, year = {2016}, author = {Chen, YL and Wang, CH and Yang, FC and Ismail, W and Wang, PH and Shih, CJ and Wu, YC and Chiang, YR}, title = {Identification of Comamonas testosteroni as an androgen degrader in sewage.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {35386}, pmid = {27734937}, issn = {2045-2322}, mesh = {Aerobiosis ; Androgens/*metabolism ; Bacterial Proteins/genetics ; Biodegradation, Environmental ; Chromatography, High Pressure Liquid ; Cloning, Molecular ; Comamonas testosteroni/genetics/isolation & purification/*metabolism ; DNA Primers ; Metagenomics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Taiwan ; Tandem Mass Spectrometry ; Testosterone/metabolism ; }, abstract = {Numerous studies have reported the masculinization of freshwater wildlife exposed to androgens in polluted rivers. Microbial degradation is a crucial mechanism for eliminating steroid hormones from contaminated ecosystems. The aerobic degradation of testosterone was observed in various bacterial isolates. However, the ecophysiological relevance of androgen-degrading microorganisms in the environment is unclear. Here, we investigated the biochemical mechanisms and corresponding microorganisms of androgen degradation in aerobic sewage. Sewage samples collected from the Dihua Sewage Treatment Plant (Taipei, Taiwan) were aerobically incubated with testosterone (1 mM). Androgen metabolite analysis revealed that bacteria adopt the 9, 10-seco pathway to degrade testosterone. A metagenomic analysis indicated the apparent enrichment of Comamonas spp. (mainly C. testosteroni) and Pseudomonas spp. in sewage incubated with testosterone. We used the degenerate primers derived from the meta-cleavage dioxygenase gene (tesB) of various proteobacteria to track this essential catabolic gene in the sewage. The amplified sequences showed the highest similarity (87-96%) to tesB of C. testosteroni. Using quantitative PCR, we detected a remarkable increase of the 16S rRNA and catabolic genes of C. testosteroni in the testosterone-treated sewage. Together, our data suggest that C. testosteroni, the model microorganism for aerobic testosterone degradation, plays a role in androgen biodegradation in aerobic sewage.}, } @article {pmid27734124, year = {2017}, author = {Tu, Q and Li, J and Shi, Z and Chen, Y and Lin, L and Li, J and Wang, H and Yan, J and Zhou, Q and Li, X and Li, L and Zhou, J and He, Z}, title = {HuMiChip2 for strain level identification and functional profiling of human microbiomes.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {1}, pages = {423-435}, doi = {10.1007/s00253-016-7910-0}, pmid = {27734124}, issn = {1432-0614}, mesh = {Humans ; Liver Cirrhosis ; Metagenomics/*methods ; Microarray Analysis/*methods ; Microbiological Techniques/*methods ; *Microbiota ; Nucleic Acid Hybridization/*methods ; Sensitivity and Specificity ; }, abstract = {With the massive data generated by the Human Microbiome Project, how to transform such data into useful information and knowledge remains challenging. Here, with currently available sequencing information (reference genomes and metagenomes), we have developed a comprehensive microarray, HuMiChip2, for strain-level identification and functional characterization of human microbiomes. HuMiChip2 was composed of 29,467 strain-specific probes targeting 2063 microbial strains/species and 133,924 sequence- and group-specific probes targeting 157 key functional gene families involved in various metabolic pathways and host-microbiome interaction processes. Computational evaluation of strain-specific probes suggested that they were not only specific to mock communities of sequenced microorganisms and metagenomes from different human body sites but also to non-sequenced microbial strains. Experimental evaluation of strain-specific probes using single strains/species and mock communities suggested a high specificity of these probes with their corresponding targets. Application of HuMiChip2 to human gut microbiome samples showed the patient microbiomes of alcoholic liver cirrhosis significantly (p < 0.05) shifted their functional structure from the healthy individuals, and the relative abundance of 21 gene families significantly (p < 0.1) differed between the liver cirrhosis patients and healthy individuals. At the strain level, five Bacteroides strains were significantly (p < 0.1) and more frequently detected in liver cirrhosis patients. These results suggest that the developed HuMiChip2 is a useful microbial ecological microarray for both strain-level identification and functional profiling of human microbiomes.}, } @article {pmid27723761, year = {2016}, author = {Heintz-Buschart, A and May, P and Laczny, CC and Lebrun, LA and Bellora, C and Krishna, A and Wampach, L and Schneider, JG and Hogan, A and de Beaufort, C and Wilmes, P}, title = {Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes.}, journal = {Nature microbiology}, volume = {2}, number = {}, pages = {16180}, doi = {10.1038/nmicrobiol.2016.180}, pmid = {27723761}, issn = {2058-5276}, mesh = {Diabetes Mellitus, Type 1/*microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Gene Expression Profiling ; Humans ; Metagenomics ; *Microbiota ; Proteome/analysis ; }, abstract = {The gastrointestinal microbiome is a complex ecosystem with functions that shape human health. Studying the relationship between taxonomic alterations and functional repercussions linked to disease remains challenging. Here, we present an integrative approach to resolve the taxonomic and functional attributes of gastrointestinal microbiota at the metagenomic, metatranscriptomic and metaproteomic levels. We apply our methods to samples from four families with multiple cases of type 1 diabetes mellitus (T1DM). Analysis of intra- and inter-individual variation demonstrates that family membership has a pronounced effect on the structural and functional composition of the gastrointestinal microbiome. In the context of T1DM, consistent taxonomic differences were absent across families, but certain human exocrine pancreatic proteins were found at lower levels. The associated microbial functional signatures were linked to metabolic traits in distinct taxa. The methodologies and results provide a foundation for future large-scale integrated multi-omic analyses of the gastrointestinal microbiome in the context of host-microbe interactions in human health and disease.}, } @article {pmid27717408, year = {2016}, author = {Pal, C and Bengtsson-Palme, J and Kristiansson, E and Larsson, DG}, title = {The structure and diversity of human, animal and environmental resistomes.}, journal = {Microbiome}, volume = {4}, number = {1}, pages = {54}, pmid = {27717408}, issn = {2049-2618}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Gastrointestinal Microbiome/drug effects/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Interspersed Repetitive Sequences/*genetics ; Metals/pharmacology ; Selection, Genetic/drug effects/*genetics ; Sewage/microbiology ; Smog ; Soil Microbiology ; Tetracycline Resistance/genetics ; }, abstract = {BACKGROUND: Antibiotic resistance genes (ARGs) are widespread but cause problems only when present in pathogens. Environments where selection and transmission of antibiotic resistance frequently take place are likely to be characterized by high abundance and diversity of horizontally transferable ARGs. Large-scale quantitative data on ARGs is, however, lacking for most types of environments, including humans and animals, as is data on resistance genes to potential co-selective agents, such as biocides and metals. This paucity prevents efficient identification of risk environments.

RESULTS: We provide a comprehensive characterization of resistance genes, mobile genetic elements (MGEs) and bacterial taxonomic compositions for 864 metagenomes from humans (n = 350), animals (n = 145) and external environments (n = 369), all deeply sequenced using Illumina technology. Environment types showed clear differences in both resistance profiles and bacterial community compositions. Human and animal microbial communities were characterized by limited taxonomic diversity and low abundance and diversity of biocide/metal resistance genes and MGEs but a relatively high abundance of ARGs. In contrast, external environments showed consistently high taxonomic diversity which in turn was linked to high diversity of both biocide/metal resistance genes and MGEs. Water, sediment and soil generally carried low relative abundance and few varieties of known ARGs, whereas wastewater/sludge was on par with the human gut. The environments with the largest relative abundance and/or diversity of ARGs, including genes encoding resistance to last resort antibiotics, were those subjected to industrial antibiotic pollution and a limited set of deeply sequenced air samples from a Beijing smog event.

CONCLUSIONS: Our study identifies air and antibiotic-polluted environments as under-investigated transmission routes and reservoirs for antibiotic resistance. The high taxonomic and genetic diversity of external environments supports the hypothesis that these also form vast sources of unknown resistance genes, with potential to be transferred to pathogens in the future.}, } @article {pmid27716148, year = {2016}, author = {Wei, X and Jiang, S and Chen, Y and Zhao, X and Li, H and Lin, W and Li, B and Wang, X and Yuan, J and Sun, Y}, title = {Cirrhosis related functionality characteristic of the fecal microbiota as revealed by a metaproteomic approach.}, journal = {BMC gastroenterology}, volume = {16}, number = {1}, pages = {121}, pmid = {27716148}, issn = {1471-230X}, mesh = {Amino Acids, Branched-Chain/metabolism ; Carbohydrate Metabolism ; Coenzyme A/metabolism ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Liver Cirrhosis/*microbiology/physiopathology ; Male ; Metagenome/physiology ; Middle Aged ; Pantothenic Acid/metabolism ; Proteomics/methods ; Severity of Illness Index ; Spouses ; }, abstract = {BACKGROUND: Intestinal microbiota operated as a whole and was closely related with human health. Previous studies had suggested close relationship between liver cirrhosis (LC) and gut microbiota.

METHODS: To determine the functional characteristic of the intestinal microbiota specific for liver cirrhosis, the fecal metaproteome of three LC patients with Child-Turcotte-Pugh (CTP) score of A, B, and C, and their spouse were first compared using high-throughput approach based on denaturing polyacrylamide gel electrophoresis and liquid chromatography-tandem mass spectrometry in our study.

RESULTS: A total of 5,020 proteins (88 % from bacteria, 12 % form human) were identified and annotated based on the GO and KEGG classification. Our results indicated that the LC patients possessed a core metaproteome including 119 proteins, among which 14 proteins were enhanced expressed and 7 proteins were unique for LC patients compared with the normal, which were dominant at the function of carbohydrate metabolism. In addition, LC patients have unique biosynthesis of branched chain amino acid (BCAA), pantothenate, and CoA, enhanced as CTP scores increased. Those three substances were all important in a wide array of key and essential biological roles of life.

CONCLUSIONS: We observed a highly comparable cirrhosis-specific metaproteome clustering of fecal microbiota and provided the first supportive evidence for the presence of a LC-related substantial functional core mainly involved in carbohydrate, BCAA, pantothenate, and CoA metabolism, suggesting the compensation of intestinal microbiota for the fragile and innutritious body of cirrhotic patients.}, } @article {pmid27713958, year = {2016}, author = {Nguyen, SG and Kim, J and Guevarra, RB and Lee, JH and Kim, E and Kim, SI and Unno, T}, title = {Laminarin favorably modulates gut microbiota in mice fed a high-fat diet.}, journal = {Food & function}, volume = {7}, number = {10}, pages = {4193-4201}, doi = {10.1039/c6fo00929h}, pmid = {27713958}, issn = {2042-650X}, mesh = {Animals ; Dietary Fats/*administration & dosage ; Female ; Gastrointestinal Microbiome/*drug effects ; Glucans/administration & dosage/*pharmacology ; Mice ; Mice, Inbred BALB C ; Random Allocation ; Weight Gain/drug effects ; }, abstract = {We investigated the anti-obesity effects of the potential prebiotic, laminarin, on mice fed a high-fat diet. A metagenomics approach was applied to characterize the ecological and functional differences of gut microbiota among mice fed a normal diet (CTL), a high-fat diet (HFD), and a laminarin-supplemented high-fat diet (HFL). The HFL mice showed a slower weight gain than the HFD mice during the laminarin-feeding period, but the rate of weight gain increased after the termination of laminarin supplementation. Gut microbial community analysis showed clear differences between the CTL and HFD mice, whereas the HFL mice were between the two. A higher abundance of carbohydrate active enzymes was observed in the HFL mice compared to the HFD mice, with especially notable increases in glycoside hydrolase and polysaccharide lyases. A significant decrease in Firmicutes and an increase in the Bacteroidetes phylum, especially the genus Bacteroides, were observed during laminarin ingestion. Laminarin ingestion altered the gut microbiota at the species level, which was re-shifted after termination of laminarin ingestion. Therefore, supplementing laminarin could reduce the adverse effects of a high-fat diet by shifting the gut microbiota towards a higher energy metabolism. Thus, laminarin could be used to develop anti-obesity functional foods. Our results also suggest that laminarin would need to be consumed regularly in order to prevent or manage obesity.}, } @article {pmid27712920, year = {2017}, author = {Hicks, N and Vik, U and Taylor, P and Ladoukakis, E and Park, J and Kolisis, F and Jakobsen, KS}, title = {Using Prokaryotes for Carbon Capture Storage.}, journal = {Trends in biotechnology}, volume = {35}, number = {1}, pages = {22-32}, doi = {10.1016/j.tibtech.2016.06.011}, pmid = {27712920}, issn = {1879-3096}, mesh = {Air Pollutants/isolation & purification/*metabolism ; Biodegradation, Environmental ; Biological Assay/*methods ; Carbon Dioxide/*isolation & purification/*metabolism ; Carbon Sequestration/*physiology ; Environmental Monitoring/*methods ; Greenhouse Effect ; Microbiota/*physiology ; }, abstract = {Geological storage of CO2 is a fast-developing technology that can mitigate rising carbon emissions. However, there are environmental concerns with the long-term storage and implications of a leak from a carbon capture storage (CCS) site. Traditional monitoring lacks clear protocols and relies heavily on physical methods. Here, we discuss the potential of biotechnology, focusing on microbes with a natural ability to utilize and assimilate CO2 through different metabolic pathways. We propose the use of natural microbial communities for CCS monitoring and CO2 utilization, and, with examples, demonstrate how synthetic biology may maximize CO2 uptake within and above storage sites. An integrated physical and biological approach, combined with metagenomics data and biotechnological advances, will enhance CO2 sequestration and prevent large-scale leakages.}, } @article {pmid27710940, year = {2016}, author = {Summers, EL and Moon, CD and Atua, R and Arcus, VL}, title = {The structure of a glycoside hydrolase 29 family member from a rumen bacterium reveals unique, dual carbohydrate-binding domains.}, journal = {Acta crystallographica. Section F, Structural biology communications}, volume = {72}, number = {Pt 10}, pages = {750-761}, pmid = {27710940}, issn = {2053-230X}, mesh = {Amino Acid Sequence ; Animals ; Carbohydrates/*chemistry ; Catalytic Domain ; Cattle ; Cloning, Molecular ; Crystallography, X-Ray ; Escherichia coli/genetics/metabolism ; Female ; Gastrointestinal Microbiome/*genetics ; Gene Expression ; Glycoside Hydrolases/*chemistry/genetics/metabolism ; Hydrolysis ; *Metagenome ; Models, Molecular ; Plasmids/chemistry/metabolism ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Recombinant Proteins/chemistry/genetics/metabolism ; Rumen/*microbiology ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; }, abstract = {Glycoside hydrolase (GH) family 29 consists solely of α-L-fucosidases. These enzymes catalyse the hydrolysis of glycosidic bonds. Here, the structure of GH29_0940, a protein cloned from metagenomic DNA from the rumen of a cow, has been solved, which reveals a multi-domain arrangement that has only recently been identified in bacterial GH29 enzymes. The microbial species that provided the source of this enzyme is unknown. This enzyme contains a second carbohydrate-binding domain at its C-terminal end in addition to the typical N-terminal catalytic domain and carbohydrate-binding domain arrangement of GH29-family proteins. GH29_0940 is a monomer and its overall structure consists of an N-terminal TIM-barrel-like domain, a central β-sandwich domain and a C-terminal β-sandwich domain. The TIM-barrel-like catalytic domain exhibits a (β/α)8/7 arrangement in the core instead of the typical (β/α)8 topology, with the `missing' α-helix replaced by a long meandering loop that `closes' the barrel structure and suggests a high degree of structural flexibility in the catalytic core. This feature was also noted in all six other structures of GH29 enzymes that have been deposited in the PDB. Based on sequence and structural similarity, the residues Asp162 and Glu220 are proposed to serve as the catalytic nucleophile and the proton donor, respectively. Like other GH29 enzymes, the GH29_0940 structure shows five strictly conserved residues in the catalytic pocket. The structure shows two glycerol molecules in the active site, which have also been observed in other GH29 structures, suggesting that the enzyme catalyses the hydrolysis of small carbohydrates. The two binding domains are classed as family 32 carbohydrate-binding modules (CBM32). These domains have residues involved in ligand binding in the loop regions at the edge of the β-sandwich. The predicted substrate-binding residues differ between the modules, suggesting that different modules bind to different groups on the substrate(s). Enzymes that possess multiple copies of CBMs are thought to have a complex mechanism of ligand recognition. Defined electron density identifying a long 20-amino-acid hydrophilic loop separating the two CBMs was observed. This suggests that the additional C-terminal domain may have a dynamic range of movement enabled by the loop, allowing a unique mode of action for a GH29 enzyme that has not been identified previously.}, } @article {pmid27709807, year = {2017}, author = {De Filippis, F and Parente, E and Ercolini, D}, title = {Metagenomics insights into food fermentations.}, journal = {Microbial biotechnology}, volume = {10}, number = {1}, pages = {91-102}, pmid = {27709807}, issn = {1751-7915}, mesh = {Computational Biology ; *Fermentation ; *Food Microbiology ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; *Microbial Consortia ; }, abstract = {This review describes the recent advances in the study of food microbial ecology, with a focus on food fermentations. High-throughput sequencing (HTS) technologies have been widely applied to the study of food microbial consortia and the different applications of HTS technologies were exploited in order to monitor microbial dynamics in food fermentative processes. Phylobiomics was the most explored application in the past decade. Metagenomics and metatranscriptomics, although still underexploited, promise to uncover the functionality of complex microbial consortia. The new knowledge acquired will help to understand how to make a profitable use of microbial genetic resources and modulate key activities of beneficial microbes in order to ensure process efficiency, product quality and safety.}, } @article {pmid27709286, year = {2017}, author = {Lin, CH and Chen, YH and Tsai, TY and Pan, TM}, title = {Effects of deep sea water and Lactobacillus paracasei subsp. paracasei NTU 101 on hypercholesterolemia hamsters gut microbiota.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {1}, pages = {321-329}, doi = {10.1007/s00253-016-7868-y}, pmid = {27709286}, issn = {1432-0614}, mesh = {Animals ; Cecum/microbiology ; Cricetinae ; Denaturing Gradient Gel Electrophoresis ; Disease Models, Animal ; Dysbiosis/*therapy ; *Gastrointestinal Microbiome ; Hypercholesterolemia/*complications ; Lacticaseibacillus paracasei/*growth & development ; Metagenomics ; Seawater/*microbiology ; }, abstract = {Hypercholesterolemia is a common metabolic syndrome in modern human society. Despite that the alteration of host gut microbiota has been linked to hypercholesterolemia in previous studies, the key host-microbiota interaction of hypercholesterolemia remains elusive. Lactobacillus paracasei subsp. paracasei NTU 101 (NTU 101) and deep sea water (DSW) were known for cholesterol-lowering potential. The impact of NTU 101 and DSW on hamster gut microbiota was investigated side-by-side using denaturing gradient gel electrophoresis (DGGE) and metagenomic analysis in this study. These two cholesterol-lowering substances altered hamster cecal microbiota in a very different way with similar cholesterol-lowering effects. Bacteroidetes was the only bacterial population that significantly correlated to host lipid profile (serum total cholesterol and serum low-density lipoprotein). Allobaculum and Clostridium XIVa were associated with beneficial effect of NTU 101. Parasutterella was only associated with consumption of DSW. The major bacterial taxa Akkermansia is associated with high-cholesterol diet but not host cholesterol level. This phenomenon suggested that cholesterol-lowering effect is not necessarily linked to specific bacteria-host interaction, and the conclusion of causal relationships among bacterial abundance, diet, and host physiology should be more rigorously investigated.}, } @article {pmid27708409, year = {2016}, author = {Suryavanshi, MV and Bhute, SS and Jadhav, SD and Bhatia, MS and Gune, RP and Shouche, YS}, title = {Hyperoxaluria leads to dysbiosis and drives selective enrichment of oxalate metabolizing bacterial species in recurrent kidney stone endures.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {34712}, pmid = {27708409}, issn = {2045-2322}, mesh = {Bacteria/*classification/genetics/metabolism ; Case-Control Studies ; Dysbiosis/*etiology/microbiology ; Gastrointestinal Microbiome ; Humans ; Hyperoxaluria/*complications/urine ; Kidney Calculi/*microbiology/urine ; Male ; Metagenomics ; Oxalates/urine ; Oxalobacter formigenes/genetics/isolation & purification/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Hyperoxaluria due to endogenously synthesized and exogenously ingested oxalates is a leading cause of recurrent oxalate stone formations. Even though, humans largely rely on gut microbiota for oxalate homeostasis, hyperoxaluria associated gut microbiota features remain largely unknown. Based on 16S rRNA gene amplicons, targeted metagenomic sequencing of formyl-CoA transferase (frc) gene and qPCR assay, we demonstrate a selective enrichment of Oxalate Metabolizing Bacterial Species (OMBS) in hyperoxaluria condition. Interestingly, higher than usual concentration of oxalate was found inhibitory to many gut microbes, including Oxalobacter formigenes, a well-characterized OMBS. In addition a concomitant enrichment of acid tolerant pathobionts in recurrent stone sufferers is observed. Further, specific enzymes participating in oxalate metabolism are found augmented in stone endures. Additionally, hyperoxaluria driven dysbiosis was found to be associated with oxalate content, stone episodes and colonization pattern of Oxalobacter formigenes. Thus, we rationalize the first in-depth surveillance of OMBS in the human gut and their association with hyperoxaluria. Our findings can be utilized in the treatment of hyperoxaluria associated recurrent stone episodes.}, } @article {pmid27708392, year = {2016}, author = {Liu, W and Zhang, J and Wu, C and Cai, S and Huang, W and Chen, J and Xi, X and Liang, Z and Hou, Q and Zhou, B and Qin, N and Zhang, H}, title = {Unique Features of Ethnic Mongolian Gut Microbiome revealed by metagenomic analysis.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {34826}, pmid = {27708392}, issn = {2045-2322}, mesh = {Actinobacteria/genetics/physiology ; Adult ; Asian People ; Bifidobacterium/genetics/physiology ; Butyrates/metabolism ; Cardiovascular Diseases/microbiology ; Feeding Behavior ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Metagenome ; Mongolia ; }, abstract = {The human gut microbiota varies considerably among world populations due to a variety of factors including genetic background, diet, cultural habits and socioeconomic status. Here we characterized 110 healthy Mongolian adults gut microbiota by shotgun metagenomic sequencing and compared the intestinal microbiome among Mongolians, the Hans and European cohorts. The results showed that the taxonomic profile of intestinal microbiome among cohorts revealed the Actinobaceria and Bifidobacterium were the key microbes contributing to the differences among Mongolians, the Hans and Europeans at the phylum level and genus level, respectively. Metagenomic species analysis indicated that Faecalibacterium prausnitzii and Coprococcus comeswere enrich in Mongolian people which might contribute to gut health through anti-inflammatory properties and butyrate production, respectively. On the other hand, the enriched genus Collinsella, biomarker in symptomatic atherosclerosis patients, might be associated with the high morbidity of cardiovascular and cerebrovascular diseases in Mongolian adults. At the functional level, a unique microbial metabolic pathway profile was present in Mongolian's gut which mainly distributed in amino acid metabolism, carbohydrate metabolism, energy metabolism, lipid metabolism, glycan biosynthesis and metabolism. We can attribute the specific signatures of Mongolian gut microbiome to their unique genotype, dietary habits and living environment.}, } @article {pmid27707993, year = {2017}, author = {Isaac, S and Scher, JU and Djukovic, A and Jiménez, N and Littman, DR and Abramson, SB and Pamer, EG and Ubeda, C}, title = {Short- and long-term effects of oral vancomycin on the human intestinal microbiota.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {1}, pages = {128-136}, pmid = {27707993}, issn = {1460-2091}, support = {K23 AR064318/AR/NIAMS NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; R01 AI042135/AI/NIAID NIH HHS/United States ; RC2 AR058986/AR/NIAMS NIH HHS/United States ; }, mesh = {Administration, Oral ; Animals ; Anti-Bacterial Agents/*administration & dosage ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/methods ; Mice ; Microbiota/*drug effects ; Models, Animal ; Time ; Vancomycin/*administration & dosage ; }, abstract = {BACKGROUND: Oral vancomycin remains the mainstay of therapy for severe infections produced by Clostridium difficile, the most prevalent cause of healthcare-associated infectious diarrhoea in developed countries. However, its short- and long-term effects on the human intestinal microbiota remain largely unknown.

METHODS: We utilized high-throughput sequencing to analyse the effects of vancomycin on the faecal human microbiota up to 22 weeks post-antibiotic cessation. The clinical relevance of the observed microbiota perturbations was studied in mice.

RESULTS: During vancomycin therapy, most intestinal microbiota genera and operational taxonomic units (OTUs) were depleted in all analysed subjects, including all baseline OTUs from the phylum Bacteroidetes. This was accompanied by a vast expansion of genera associated with infections, including Klebsiella and Escherichia/Shigella. Following antibiotic cessation, marked differences in microbiota resilience were observed among subjects. While some individuals recovered a microbiota close to baseline composition, in others, up to 89% of abundant OTUs could no longer be detected. The clinical relevance of the observed microbiota changes was further demonstrated in mice, which developed analogous microbiota alterations. During vancomycin treatment, mice were highly susceptible to intestinal colonization by an antibiotic-resistant pathogen and, upon antibiotic cessation, a less-resilient microbiota allowed higher levels of pathogen colonization.

CONCLUSIONS: Oral vancomycin induces drastic and consistent changes in the human intestinal microbiota. Upon vancomycin cessation, the microbiota recovery rate varied considerably among subjects, which could influence, as validated in mice, the level of susceptibility to pathogen intestinal colonization. Our results demonstrate the negative long-term effects of vancomycin, which should be considered as a fundamental aspect of the cost-benefit equation for antibiotic prescription.}, } @article {pmid27703805, year = {2016}, author = {Khan, MJ and Gerasimidis, K and Edwards, CA and Shaikh, MG}, title = {Role of Gut Microbiota in the Aetiology of Obesity: Proposed Mechanisms and Review of the Literature.}, journal = {Journal of obesity}, volume = {2016}, number = {}, pages = {7353642}, pmid = {27703805}, issn = {2090-0716}, mesh = {Gastrointestinal Tract/*microbiology ; Humans ; *Microbiota ; Obesity, Morbid/etiology/*microbiology ; }, abstract = {The aetiology of obesity has been attributed to several factors (environmental, dietary, lifestyle, host, and genetic factors); however none of these fully explain the increase in the prevalence of obesity worldwide. Gut microbiota located at the interface of host and environment in the gut are a new area of research being explored to explain the excess accumulation of energy in obese individuals and may be a potential target for therapeutic manipulation to reduce host energy storage. Several mechanisms have been suggested to explain the role of gut microbiota in the aetiology of obesity such as short chain fatty acid production, stimulation of hormones, chronic low-grade inflammation, lipoprotein and bile acid metabolism, and increased endocannabinoid receptor system tone. However, evidence from animal and human studies clearly indicates controversies in determining the cause or effect relationship between the gut microbiota and obesity. Metagenomics based studies indicate that functionality rather than the composition of gut microbiota may be important. Further mechanistic studies controlling for environmental and epigenetic factors are therefore required to help unravel obesity pathogenesis.}, } @article {pmid27703179, year = {2016}, author = {Zantow, J and Just, S and Lagkouvardos, I and Kisling, S and Dübel, S and Lepage, P and Clavel, T and Hust, M}, title = {Mining gut microbiome oligopeptides by functional metaproteome display.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {34337}, pmid = {27703179}, issn = {2045-2322}, mesh = {Animals ; Chronic Disease ; *Gastrointestinal Microbiome ; *Ileitis/genetics/metabolism/microbiology ; *Metagenome ; Mice ; Mice, Transgenic ; Oligopeptides/*genetics/metabolism ; *Peptide Library ; Proteome/*genetics/metabolism ; }, abstract = {Pathogen infections, autoimmune diseases, and chronic inflammatory disorders are associated with systemic antibody responses from the host immune system. Disease-specific antibodies can be important serum biomarkers, but the identification of antigens associated with specific immune reactions is challenging, in particular if complex communities of microorganisms are involved in the disease progression. Despite promising new diagnostic opportunities, the discovery of these serological markers becomes more difficult with increasing complexity of microbial communities. In the present work, we used a metagenomic M13 phage display approach to select immunogenic oligopeptides from the gut microbiome of transgenic mice suffering from chronic ileitis. We constructed three individual metaproteome phage display libraries with a library size of approximately 10[7] clones each. Using serum antibodies, we selected and validated three oligopeptides that induced specific antibody responses in the mouse model. This proof-of-concept study provides the first successful application of functional metaproteome display for the study of protein-protein interactions and the discovery of potential disease biomarkers.}, } @article {pmid27701454, year = {2016}, author = {Morikawa, M and Tsujibe, S and Kiyoshima-Shibata, J and Watanabe, Y and Kato-Nagaoka, N and Shida, K and Matsumoto, S}, title = {Microbiota of the Small Intestine Is Selectively Engulfed by Phagocytes of the Lamina Propria and Peyer's Patches.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0163607}, pmid = {27701454}, issn = {1932-6203}, mesh = {Animals ; Biomarkers ; Computational Biology/methods ; Cytokines/genetics/metabolism ; Gastrointestinal Microbiome/*immunology ; Gene Expression ; Immunophenotyping ; Intestinal Mucosa/*immunology/metabolism/*microbiology ; Metagenome ; Metagenomics ; Mice ; Peyer's Patches/cytology/*immunology/metabolism ; Phagocytes/*immunology/metabolism/*microbiology ; Phagocytosis/immunology ; Phenotype ; RNA, Ribosomal, 16S ; T-Lymphocyte Subsets/immunology/metabolism ; }, abstract = {Phagocytes such as dendritic cells and macrophages, which are distributed in the small intestinal mucosa, play a crucial role in maintaining mucosal homeostasis by sampling the luminal gut microbiota. However, there is limited information regarding microbial uptake in a steady state. We investigated the composition of murine gut microbiota that is engulfed by phagocytes of specific subsets in the small intestinal lamina propria (SILP) and Peyer's patches (PP). Analysis of bacterial 16S rRNA gene amplicon sequences revealed that: 1) all the phagocyte subsets in the SILP primarily engulfed Lactobacillus (the most abundant microbe in the small intestine), whereas CD11bhi and CD11bhiCD11chi cell subsets in PP mostly engulfed segmented filamentous bacteria (indigenous bacteria in rodents that are reported to adhere to intestinal epithelial cells); and 2) among the Lactobacillus species engulfed by the SILP cell subsets, L. murinus was engulfed more frequently than L. taiwanensis, although both these Lactobacillus species were abundant in the small intestine under physiological conditions. These results suggest that small intestinal microbiota is selectively engulfed by phagocytes that localize in the adjacent intestinal mucosa in a steady state. These observations may provide insight into the crucial role of phagocytes in immune surveillance of the small intestinal mucosa.}, } @article {pmid27701448, year = {2016}, author = {Kia, E and Wagner Mackenzie, B and Middleton, D and Lau, A and Waite, DW and Lewis, G and Chan, YK and Silvestre, M and Cooper, GJ and Poppitt, SD and Taylor, MW}, title = {Integrity of the Human Faecal Microbiota following Long-Term Sample Storage.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0163666}, pmid = {27701448}, issn = {1932-6203}, mesh = {Biodiversity ; DNA, Bacterial ; Feces/*microbiology ; Humans ; Metagenome ; Metagenomics ; *Microbial Viability ; *Microbiota ; *Preservation, Biological ; RNA, Ribosomal, 16S ; Time Factors ; }, abstract = {In studies of the human microbiome, faecal samples are frequently used as a non-invasive proxy for the study of the intestinal microbiota. To obtain reliable insights, the need for bacterial DNA of high quality and integrity following appropriate faecal sample collection and preservation steps is paramount. In a study of dietary mineral balance in the context of type 2 diabetes (T2D), faecal samples were collected from healthy and T2D individuals throughout a 13-day residential trial. These samples were freeze-dried, then stored mostly at -20°C from the trial date in 2000/2001 until the current research in 2014. Given the relative antiquity of these samples (~14 years), we sought to evaluate DNA quality and comparability to freshly collected human faecal samples. Following the extraction of bacterial DNA, gel electrophoresis indicated that our DNA extracts were more sheared than extracts made from freshly collected faecal samples, but still of sufficiently high molecular weight to support amplicon-based studies. Likewise, spectrophotometric assessment of extracts revealed that they were of high quality and quantity. A subset of bacterial 16S rRNA gene amplicons were sequenced using Illumina MiSeq and compared against publicly available sequence data representing a similar cohort analysed by the American Gut Project (AGP). Notably, our bacterial community profiles were highly consistent with those from the AGP data. Our results suggest that when faecal specimens are stored appropriately, the microbial profiles are preserved and robust to extended storage periods.}, } @article {pmid27699405, year = {2016}, author = {Doan, T and Akileswaran, L and Andersen, D and Johnson, B and Ko, N and Shrestha, A and Shestopalov, V and Lee, CS and Lee, AY and Van Gelder, RN}, title = {Paucibacterial Microbiome and Resident DNA Virome of the Healthy Conjunctiva.}, journal = {Investigative ophthalmology & visual science}, volume = {57}, number = {13}, pages = {5116-5126}, pmid = {27699405}, issn = {1552-5783}, support = {K23 EY024921/EY/NEI NIH HHS/United States ; P30 EY001730/EY/NEI NIH HHS/United States ; R01 EY022038/EY/NEI NIH HHS/United States ; }, mesh = {Adult ; Bacteria/*genetics/isolation & purification ; Conjunctiva/*microbiology ; DNA, Bacterial/*analysis ; Eye Infections, Bacterial/*microbiology ; Female ; Healthy Volunteers ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Microbiota ; Middle Aged ; Prospective Studies ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {PURPOSE: To characterize the ocular surface microbiome of healthy volunteers using a combination of microbial culture and high-throughput DNA sequencing techniques.

METHODS: Conjunctival swab samples from 107 healthy volunteers were analyzed by bacterial culture, 16S rDNA gene deep sequencing (n = 89), and biome representational in silico karyotyping (BRiSK; n = 80). Swab samples of the facial skin (n = 42), buccal mucosa (n = 50), and environmental controls (n = 27) were processed in parallel. 16S rDNA gene quantitative PCR was used to calculate the bacterial load in each site. Bacteria were characterized by site using principal coordinate analysis of metagenomics data. BRiSK data were analyzed for presence of fungi and viruses.

RESULTS: Corynebacteria, Propionibacteria, and coagulase-negative Staphylococci were the predominant organisms identified by all three techniques. Quantitative 16S PCR demonstrated approximately 0.1 bacterial 16S rDNA/human actin copy on the ocular surface compared with greater than 10 16S rDNA/human actin copy for facial skin or the buccal mucosa. The conjunctival bacterial community structure is distinct compared with the facial skin (R = 0.474, analysis of similarities P = 0.0001), the buccal mucosa (R = 0.893, P = 0.0001), and environmental control samples (R = 0.536, P = 0.0001). 16S metagenomics revealed substantially more bacterial diversity on the ocular surface than other techniques, which appears to be artifactual. BRiSK revealed presence of torque teno virus (TTV) on the healthy ocular surface, which was confirmed by direct PCR to be present in 65% of all conjunctiva samples tested.

CONCLUSIONS: Relative to adjacent skin or other mucosa, healthy ocular surface microbiome is paucibacterial. Its flora are distinct from adjacent skin. Torque teno virus is a frequent constituent of the ocular surface microbiome. (ClinicalTrials.gov number, NCT02298881.).}, } @article {pmid27697996, year = {2017}, author = {Liang, Q and Chiu, J and Chen, Y and Huang, Y and Higashimori, A and Fang, J and Brim, H and Ashktorab, H and Ng, SC and Ng, SSM and Zheng, S and Chan, FKL and Sung, JJY and Yu, J}, title = {Fecal Bacteria Act as Novel Biomarkers for Noninvasive Diagnosis of Colorectal Cancer.}, journal = {Clinical cancer research : an official journal of the American Association for Cancer Research}, volume = {23}, number = {8}, pages = {2061-2070}, doi = {10.1158/1078-0432.CCR-16-1599}, pmid = {27697996}, issn = {1557-3265}, mesh = {Adult ; Aged ; Area Under Curve ; Biomarkers, Tumor/*analysis ; Colorectal Neoplasms/*diagnosis/*microbiology ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; ROC Curve ; Real-Time Polymerase Chain Reaction ; Sensitivity and Specificity ; }, abstract = {Purpose: Gut microbiota have been implicated in the development of colorectal cancer. We evaluated the utility of fecal bacterial marker candidates identified by our metagenome sequencing analysis for colorectal cancer diagnosis.Experimental Design: Subjects (total 439; 203 colorectal cancer and 236 healthy subjects) from two independent Asian cohorts were included. Probe-based duplex quantitative PCR (qPCR) assays were established for the quantification of bacterial marker candidates.Results: Candidates identified by metagenome sequencing, including Fusobacterium nucleatum (Fn), Bacteroides clarus (Bc), Roseburia intestinalis (Ri), Clostridium hathewayi (Ch), and one undefined species (labeled as m7), were examined in fecal samples of 203 colorectal cancer patients and 236 healthy controls by duplex-qPCR. Strong positive correlations were demonstrated between the quantification of each candidate by our qPCR assays and metagenomics approach (r = 0.801-0.934, all P < 0.0001). Fn was significantly more abundant in colorectal cancer than controls (P < 0.0001), with AUROC of 0.868 (P < 0.0001). At the best cut-off value maximizing sum of sensitivity and specificity, Fn discriminated colorectal cancer from controls with a sensitivity of 77.7%, and specificity of 79.5% in cohort I. A simple linear combination of four bacteria (Fn + Ch + m7-Bc) showed an improved diagnostic ability compared with Fn alone (AUROC = 0.886, P < 0.0001) in cohort I. These findings were further confirmed in an independent cohort II. In particular, improved diagnostic performances of Fn alone (sensitivity 92.8%, specificity 79.8%) and four bacteria (sensitivity 92.8%, specificity 81.5%) were achieved in combination with fecal immunochemical testing for the detection of colorectal cancer.Conclusions: Stool-based colorectal cancer-associated bacteria can serve as novel noninvasive diagnostic biomarkers for colorectal cancer. Clin Cancer Res; 23(8); 2061-70. ©2016 AACR.}, } @article {pmid27697693, year = {2017}, author = {Koopman, JE and Hoogenkamp, MA and Buijs, MJ and Brandt, BW and Keijser, BJ and Crielaard, W and Ten Cate, JM and Zaura, E}, title = {Changes in the oral ecosystem induced by the use of 8% arginine toothpaste.}, journal = {Archives of oral biology}, volume = {73}, number = {}, pages = {79-87}, doi = {10.1016/j.archoralbio.2016.09.008}, pmid = {27697693}, issn = {1879-1506}, mesh = {Adult ; Arginine/*pharmacology ; Female ; Healthy Volunteers ; Humans ; Hydrogen-Ion Concentration ; Male ; Microbiota/*drug effects ; Mouth/*drug effects/*microbiology ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; Sequence Analysis ; Toothpastes/*pharmacology ; }, abstract = {OBJECTIVE: Bacterial metabolism of arginine in the oral cavity has a pH-raising and thus, potential anti-caries effect. However, the influence of arginine on the oral microbial ecosystem remains largely unresolved.

DESIGN: In this pilot study, nine healthy individuals used toothpaste containing 8% arginine for eight weeks. Saliva was collected to determine arginolytic potential and sucrose metabolic activity at the Baseline, Week 4, Week 8 and after a two weeks Wash-out period. To follow the effects on microbial ecology, 16S rDNA sequencing on saliva and plaque samples at Baseline and Week 8 and metagenome sequencing on selected saliva samples of the same time-points was performed.

RESULTS: During the study period, the arginolytic potential of saliva increased, while the sucrose metabolism in saliva decreased. These effects were reversed during the Wash-out period. Although a few operational taxonomic units (OTUs) in plaque changed in abundance during the study period, there was no real shift in the plaque microbiome. In the saliva microbiome there was a significant compositional shift, specifically the genus Veillonella had increased significantly in abundance at Week 8.

CONCLUSION: Indeed, the presence of arginine in toothpaste affects the arginolytic capacity of saliva and reduces its sucrose metabolic activity. Additionally, it leads to a shift in the salivary microbiome composition towards a healthy ecology from a caries point of view. Therefore, arginine can be regarded as a genuine oral prebiotic.}, } @article {pmid27697111, year = {2016}, author = {Moon, JH and Lee, JH}, title = {Probing the diversity of healthy oral microbiome with bioinformatics approaches.}, journal = {BMB reports}, volume = {49}, number = {12}, pages = {662-670}, pmid = {27697111}, issn = {1976-670X}, mesh = {Aging ; Bacteria/genetics ; Climate ; *Computational Biology ; Databases, Genetic ; Humans ; *Microbiota ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The human oral cavity contains a highly personalized microbiome essential to maintaining health, but capable of causing oral and systemic diseases. Thus, an in-depth definition of "healthy oral microbiome" is critical to understanding variations in disease states from preclinical conditions, and disease onset through progressive states of disease. With rapid advances in DNA sequencing and analytical technologies, population-based studies have documented the range and diversity of both taxonomic compositions and functional potentials observed in the oral microbiome in healthy individuals. Besides factors specific to the host, such as age and race/ethnicity, environmental factors also appear to contribute to the variability of the healthy oral microbiome. Here, we review bioinformatic techniques for metagenomic datasets, including their strengths and limitations. In addition, we summarize the interpersonal and intrapersonal diversity of the oral microbiome, taking into consideration the recent large-scale and longitudinal studies, including the Human Microbiome Project. [BMB Reports 2016; 49(12): 662-670].}, } @article {pmid27695121, year = {2016}, author = {Umu, ÖC and Bäuerl, C and Oostindjer, M and Pope, PB and Hernández, PE and Pérez-Martínez, G and Diep, DB}, title = {The Potential of Class II Bacteriocins to Modify Gut Microbiota to Improve Host Health.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0164036}, pmid = {27695121}, issn = {1932-6203}, mesh = {Animals ; *Antibiosis ; *Bacterial Physiological Phenomena ; Bacteriocins/*metabolism/pharmacology ; Biodiversity ; Biomarkers ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Homeostasis ; Metagenome ; Metagenomics ; Mice ; RNA, Ribosomal, 16S ; }, abstract = {Production of bacteriocins is a potential probiotic feature of many lactic acid bacteria (LAB) as it can help prevent the growth of pathogens in gut environments. However, knowledge on bacteriocin producers in situ and their function in the gut of healthy animals is still limited. In this study, we investigated five bacteriocin-producing strains of LAB and their isogenic non-producing mutants for probiotic values. The LAB bacteriocins, sakacin A (SakA), pediocin PA-1 (PedPA-1), enterocins P, Q and L50 (enterocins), plantaricins EF and JK (plantaricins) and garvicin ML (GarML), are all class II bacteriocins, but they differ greatly from each other in terms of inhibition spectrum and physicochemical properties. The strains were supplemented to mice through drinking water and changes on the gut microbiota composition were interpreted using 16S rRNA gene analysis. In general, we observed that overall structure of the gut microbiota remained largely unaffected by the treatments. However, at lower taxonomic levels, some transient but advantageous changes were observed. Some potentially problematic bacteria were inhibited (e.g., Staphylococcus by enterocins, Enterococcaceae by GarML, and Clostridium by plantaricins) and the proportion of LAB was increased in the presence of SakA-, plantaricins- and GarML-producing bacteria. Moreover, the treatment with GarML-producing bacteria co-occurred with decreased triglyceride levels in the host mice. Taken together, our results indicate that several of these bacteriocin producers have potential probiotic properties at diverse levels as they promote favorable changes in the host without major disturbance in gut microbiota, which is important for normal gut functioning.}, } @article {pmid27695034, year = {2016}, author = {Das, A and Srinivasan, M and Ghosh, TS and Mande, SS}, title = {Xenobiotic Metabolism and Gut Microbiomes.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0163099}, pmid = {27695034}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Bacteria/classification/enzymology/*genetics ; Child ; Child, Preschool ; Enzymes/genetics/*metabolism ; Ethnicity/genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Enzymologic ; Humans ; Inactivation, Metabolic/*genetics ; Infant ; Infant, Newborn ; Male ; Metabolic Networks and Pathways/genetics ; Metagenome/genetics ; Middle Aged ; Xenobiotics/*metabolism ; }, abstract = {Humans are exposed to numerous xenobiotics, a majority of which are in the form of pharmaceuticals. Apart from human enzymes, recent studies have indicated the role of the gut bacterial community (microbiome) in metabolizing xenobiotics. However, little is known about the contribution of the plethora of gut microbiome in xenobiotic metabolism. The present study reports the results of analyses on xenobiotic metabolizing enzymes in various human gut microbiomes. A total of 397 available gut metagenomes from individuals of varying age groups from 8 nationalities were analyzed. Based on the diversities and abundances of the xenobiotic metabolizing enzymes, various bacterial taxa were classified into three groups, namely, least versatile, intermediately versatile and highly versatile xenobiotic metabolizers. Most interestingly, specific relationships were observed between the overall drug consumption profile and the abundance and diversity of the xenobiotic metabolizing repertoire in various geographies. The obtained differential abundance patterns of xenobiotic metabolizing enzymes and bacterial genera harboring them, suggest their links to pharmacokinetic variations among individuals. Additional analyses of a few well studied classes of drug modifying enzymes (DMEs) also indicate geographic as well as age specific trends.}, } @article {pmid27693307, year = {2016}, author = {Maldonado-Gómez, MX and Martínez, I and Bottacini, F and O'Callaghan, A and Ventura, M and van Sinderen, D and Hillmann, B and Vangay, P and Knights, D and Hutkins, RW and Walter, J}, title = {Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome.}, journal = {Cell host & microbe}, volume = {20}, number = {4}, pages = {515-526}, doi = {10.1016/j.chom.2016.09.001}, pmid = {27693307}, issn = {1934-6069}, mesh = {Administration, Oral ; Bifidobacterium longum/*growth & development ; *Carrier State ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Probiotics/*administration & dosage ; Time Factors ; }, abstract = {Live bacteria (such as probiotics) have long been used to modulate gut microbiota and human physiology, but their colonization is mostly transient. Conceptual understanding of the ecological principles as they apply to exogenously introduced microbes in gut ecosystems is lacking. We find that, when orally administered to humans, Bifidobacterium longum AH1206 stably persists in the gut of 30% of individuals for at least 6 months without causing gastrointestinal symptoms or impacting the composition of the resident gut microbiota. AH1206 engraftment was associated with low abundance of resident B. longum and underrepresentation of specific carbohydrate utilization genes in the pre-treatment microbiome. Thus, phylogenetic limiting and resource availability are two factors that control the niche opportunity for AH1206 colonization. These findings suggest that bacterial species and functional genes absent in the gut microbiome of individual humans can be reestablished, providing opportunities for precise and personalized microbiome reconstitution.}, } @article {pmid27692708, year = {2016}, author = {Liu, J and Zhang, M and Xue, C and Zhu, W and Mao, S}, title = {Characterization and comparison of the temporal dynamics of ruminal bacterial microbiota colonizing rice straw and alfalfa hay within ruminants.}, journal = {Journal of dairy science}, volume = {99}, number = {12}, pages = {9668-9681}, doi = {10.3168/jds.2016-11398}, pmid = {27692708}, issn = {1525-3198}, mesh = {Animal Feed ; Animals ; Cattle ; Female ; Medicago sativa ; Microbiota ; *Oryza ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rumen/*metabolism/*microbiology ; Ruminants ; }, abstract = {Three ruminally cannulated Holstein cows were used to characterize the dynamics of bacterial colonization of rice straw and alfalfa hay and to assess the differences in the composition and inferred gene function of the colonized microbiota between these 2 forages. Nonincubated (0h) rice straw and alfalfa hay samples and residues in nylon bags incubated for 0.5, 2, 6, 16, and 48h were analyzed for dry matter and were used for DNA extraction and MiSeq (Illumina Inc., San Diego, CA) sequencing of the 16S rRNA gene. The microbial communities that colonized the air-dried and nonincubated (0h) rice straw and alfalfa hay were both dominated by members of the Proteobacteria (contributing toward 70.47% of the 16S RNA reads generated). In situ incubation of the 2 forages revealed major shifts in the community composition: Proteobacteria were replaced within 30min by members belonging to the Bacteroidetes and Firmicutes, contributing toward 51.9 and 36.6% of the 16S rRNA reads generated, respectively. A second significant shift was observed after 6h of rumen incubation, when members of the Spirochaetes and Fibrobacteria phyla became abundant in the forage-adherent community. During the first 30min of rumen incubation, ~20.7 and 36.1% of the rice straw and alfalfa hay, respectively, were degraded, whereas little biomass degradation occurred between 30min and 2h after the rice straw or alfalfa hay was placed in the rumen. Significant differences were noted in attached bacterial community structure between the 2 forage groups, and the abundances of dominant genera Anaeroplasma, Butyrivibrio, Fibrobacter, and Prevotella were affected by the forage types. Real-time PCR results showed that the 16S rRNA copies of total bacteria attached to these 2 forages were affected by the forage types and incubation time, and higher numbers of attached bacterial 16S rRNA were observed in the alfalfa hay samples than in the rice straw from 0.5 to 16h of incubation. The metagenomes predicted by phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) revealed that the forage types significantly affected 21 metabolic pathways identified in the Kyoto Encyclopedia of Genes and Genomes, and 33 were significantly changed over time. Collectively, our results reveal a difference in the dynamics of bacterial colonization and the inferred gene function of microbiota associated with rice straw and alfalfa hay within the rumen. These findings are of great importance for the targeted improvement of forage nutrient use efficiency in ruminants.}, } @article {pmid27681902, year = {2016}, author = {Dickinson, I and Goodall-Copestake, W and Thorne, MA and Schlitt, T and Ávila-Jiménez, ML and Pearce, DA}, title = {Extremophiles in an Antarctic Marine Ecosystem.}, journal = {Microorganisms}, volume = {4}, number = {1}, pages = {}, pmid = {27681902}, issn = {2076-2607}, abstract = {Recent attempts to explore marine microbial diversity and the global marine microbiome have indicated a large proportion of previously unknown diversity. However, sequencing alone does not tell the whole story, as it relies heavily upon information that is already contained within sequence databases. In addition, microorganisms have been shown to present small-to-large scale biogeographical patterns worldwide, potentially making regional combinations of selection pressures unique. Here, we focus on the extremophile community in the boundary region located between the Polar Front and the Southern Antarctic Circumpolar Current in the Southern Ocean, to explore the potential of metagenomic approaches as a tool for bioprospecting in the search for novel functional activity based on targeted sampling efforts. We assessed the microbial composition and diversity from a region north of the current limit for winter sea ice, north of the Southern Antarctic Circumpolar Front (SACCF) but south of the Polar Front. Although, most of the more frequently encountered sequences were derived from common marine microorganisms, within these dominant groups, we found a proportion of genes related to secondary metabolism of potential interest in bioprospecting. Extremophiles were rare by comparison but belonged to a range of genera. Hence, they represented interesting targets from which to identify rare or novel functions. Ultimately, future shifts in environmental conditions favoring more cosmopolitan groups could have an unpredictable effect on microbial diversity and function in the Southern Ocean, perhaps excluding the rarer extremophiles.}, } @article {pmid27681823, year = {2016}, author = {Miller, IJ and Weyna, TR and Fong, SS and Lim-Fong, GE and Kwan, JC}, title = {Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {34362}, pmid = {27681823}, issn = {2045-2322}, support = {R21 AI121704/AI/NIAID NIH HHS/United States ; }, abstract = {Direct, untargeted sequencing of environmental samples (metagenomics) and de novo genome assembly enable the study of uncultured and phylogenetically divergent organisms. However, separating individual genomes from a mixed community has often relied on the differential-coverage analysis of multiple, deeply sequenced samples. In the metagenomic investigation of the marine bryozoan Bugula neritina, we uncovered seven bacterial genomes associated with a single B. neritina individual that appeared to be transient associates, two of which were unique to one individual and undetectable using certain "universal" 16S rRNA primers and probes. We recovered high quality genome assemblies for several rare instances of "microbial dark matter," or phylogenetically divergent bacteria lacking genomes in reference databases, from a single tissue sample that was not subjected to any physical or chemical pre-treatment. One of these rare, divergent organisms has a small (593 kbp), poorly annotated genome with low GC content (20.9%) and a 16S rRNA gene with just 65% sequence similarity to the closest reference sequence. Our findings illustrate the importance of sampling strategy and de novo assembly of metagenomic reads to understand the extent and function of bacterial biodiversity.}, } @article {pmid27679525, year = {2017}, author = {Fitzstevens, JL and Smith, KC and Hagadorn, JI and Caimano, MJ and Matson, AP and Brownell, EA}, title = {Systematic Review of the Human Milk Microbiota.}, journal = {Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition}, volume = {32}, number = {3}, pages = {354-364}, doi = {10.1177/0884533616670150}, pmid = {27679525}, issn = {1941-2452}, mesh = {*Food Microbiology ; Humans ; Infant ; *Microbiota ; Milk, Human/*microbiology ; Staphylococcus/classification/isolation & purification ; Streptococcus/classification/isolation & purification ; }, abstract = {Human milk-associated microbes are among the first to colonize the infant gut and may help to shape both short- and long-term infant health outcomes. We performed a systematic review to characterize the microbiota of human milk. Relevant primary studies were identified through a comprehensive search of PubMed (January 1, 1964, to June 31, 2015). Included studies were conducted among healthy mothers, were written in English, identified bacteria in human milk, used culture-independent methods, and reported primary results at the genus level. Twelve studies satisfied inclusion criteria. All varied in geographic location and human milk collection/storage/analytic methods. Streptococcus was identified in human milk samples in 11 studies (91.6%) and Staphylococcus in 10 (83.3%); both were predominant genera in 6 (50%). Eight of the 12 studies used conventional ribosomal RNA (rRNA) polymerase chain reaction (PCR), of which 7 (87.5%) identified Streptococcus and 6 (80%) identified Staphylococcus as present. Of these 8 studies, 2 (25%) identified Streptococcus and Staphylococcus as predominant genera. Four of the 12 studies used next-generation sequencing (NGS), all of which identified Streptococcus and Staphylococcus as present and predominant genera. Relative to conventional rRNA PCR, NGS is a more sensitive method to identify/quantify bacterial genera in human milk, suggesting the predominance of Streptococcus and Staphylococcus may be underestimated in studies using older methods. These genera, Streptococcus and Staphylococcus, may be universally predominant in human milk, regardless of differences in geographic location or analytic methods. Primary studies designed to evaluate the effect of these 2 genera on short- and long-term infant outcomes are warranted.}, } @article {pmid27677892, year = {2017}, author = {Ishaq, SL and Johnson, SP and Miller, ZJ and Lehnhoff, EA and Olivo, S and Yeoman, CJ and Menalled, FD}, title = {Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {417-434}, pmid = {27677892}, issn = {1432-184X}, mesh = {Agriculture ; Avena ; Bacteria/*classification/genetics ; Base Sequence ; Biodiversity ; Biota ; Classification ; Crops, Agricultural/*microbiology ; DNA, Bacterial/analysis/genetics ; Genes, Bacterial ; Metagenomics ; *Microbial Consortia ; Montana ; Nitrogen Fixation ; *Phylogeny ; Plant Development ; Plant Weeds ; Plants/classification/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Farming practices affect the soil microbial community, which in turn impacts crop growth and crop-weed interactions. This study assessed the modification of soil bacterial community structure by organic or conventional cropping systems, weed species identity [Amaranthus retroflexus L. (redroot pigweed) or Avena fatua L. (wild oat)], and living or sterilized inoculum. Soil from eight paired USDA-certified organic and conventional farms in north-central Montana was used as living or autoclave-sterilized inoculant into steam-pasteurized potting soil, planted with Am. retroflexus or Av. fatua and grown for two consecutive 8-week periods to condition soil nutrients and biota. Subsequently, the V3-V4 regions of the microbial 16S rRNA gene were sequenced by Illumina MiSeq. Treatments clustered significantly, with living or sterilized inoculum being the strongest delineating factor, followed by organic or conventional cropping system, then individual farm. Living inoculum-treated soil had greater species richness and was more diverse than sterile inoculum-treated soil (observed OTUs, Chao, inverse Simpson, Shannon, P < 0.001) and had more discriminant taxa delineating groups (linear discriminant analysis). Living inoculum soil contained more Chloroflexi and Acidobacteria, while the sterile inoculum soil had more Bacteroidetes, Firmicutes, Gemmatimonadetes, and Verrucomicrobia. Organically farmed inoculum-treated soil had greater species richness, more diversity (observed OTUs, Chao, Shannon, P < 0.05), and more discriminant taxa than conventionally farmed inoculum-treated soil. Cyanobacteria were higher in pots growing Am. retroflexus, regardless of inoculum type, for three of the four organic farms. Results highlight the potential of cropping systems and species identity to modify soil bacterial communities, subsequently modifying plant growth and crop-weed competition.}, } @article {pmid27672151, year = {2016}, author = {Pédron, T and Nigro, G and Sansonetti, PJ}, title = {From homeostasis to pathology: decrypting microbe-host symbiotic signals in the intestinal crypt.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {371}, number = {1707}, pages = {}, pmid = {27672151}, issn = {1471-2970}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Gastrointestinal Microbiome/*physiology ; Homeostasis ; Humans ; Intestines/*microbiology/pathology/*physiology ; *Symbiosis ; }, abstract = {Metagenomic analysis of the human intestinal microbiome has provided a wealth of information that allowed an exceptionally detailed description of its microbial content and physiological potential. It also set the basis for studies allowing correlation of alterations in the balance of this microbiota and the occurrence of a certain number of emerging diseases, such as inflammatory bowel diseases, obesity and diabetes, and possibly colorectal cancer. The time has come to give the intestinal microbiota in symbiosis with its host an experimental dimension. This brief review summarizes our attempt at developing a cellular microbiology of the mutualistic symbiosis established between the gut microbiota and the host intestinal surface. Particular attention is paid to the intestinal crypt, due to its role in epithelial regeneration.This article is part of the themed issue 'The new bacteriology'.}, } @article {pmid27671809, year = {2017}, author = {Kinsman-Costello, LE and Sheik, CS and Sheldon, ND and Allen Burton, G and Costello, DM and Marcus, D and Uyl, PA and Dick, GJ}, title = {Groundwater shapes sediment biogeochemistry and microbial diversity in a submerged Great Lake sinkhole.}, journal = {Geobiology}, volume = {15}, number = {2}, pages = {225-239}, doi = {10.1111/gbi.12215}, pmid = {27671809}, issn = {1472-4669}, mesh = {*Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/*chemistry/*microbiology ; *Groundwater ; North America ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {For a large part of earth's history, cyanobacterial mats thrived in low-oxygen conditions, yet our understanding of their ecological functioning is limited. Extant cyanobacterial mats provide windows into the putative functioning of ancient ecosystems, and they continue to mediate biogeochemical transformations and nutrient transport across the sediment-water interface in modern ecosystems. The structure and function of benthic mats are shaped by biogeochemical processes in underlying sediments. A modern cyanobacterial mat system in a submerged sinkhole of Lake Huron (LH) provides a unique opportunity to explore such sediment-mat interactions. In the Middle Island Sinkhole (MIS), seeping groundwater establishes a low-oxygen, sulfidic environment in which a microbial mat dominated by Phormidium and Planktothrix that is capable of both anoxygenic and oxygenic photosynthesis, as well as chemosynthesis, thrives. We explored the coupled microbial community composition and biogeochemical functioning of organic-rich, sulfidic sediments underlying the surface mat. Microbial communities were diverse and vertically stratified to 12 cm sediment depth. In contrast to previous studies, which used low-throughput or shotgun metagenomic approaches, our high-throughput 16S rRNA gene sequencing approach revealed extensive diversity. This diversity was present within microbial groups, including putative sulfate-reducing taxa of Deltaproteobacteria, some of which exhibited differential abundance patterns in the mats and with depth in the underlying sediments. The biological and geochemical conditions in the MIS were distinctly different from those in typical LH sediments of comparable depth. We found evidence for active cycling of sulfur, methane, and nutrients leading to high concentrations of sulfide, ammonium, and phosphorus in sediments underlying cyanobacterial mats. Indicators of nutrient availability were significantly related to MIS microbial community composition, while LH communities were also shaped by indicators of subsurface groundwater influence. These results show that interactions between the mats and sediments are crucial for sustaining this hot spot of biological diversity and biogeochemical cycling.}, } @article {pmid27670113, year = {2016}, author = {Lagkouvardos, I and Pukall, R and Abt, B and Foesel, BU and Meier-Kolthoff, JP and Kumar, N and Bresciani, A and Martínez, I and Just, S and Ziegler, C and Brugiroux, S and Garzetti, D and Wenning, M and Bui, TP and Wang, J and Hugenholtz, F and Plugge, CM and Peterson, DA and Hornef, MW and Baines, JF and Smidt, H and Walter, J and Kristiansen, K and Nielsen, HB and Haller, D and Overmann, J and Stecher, B and Clavel, T}, title = {The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota.}, journal = {Nature microbiology}, volume = {1}, number = {10}, pages = {16131}, pmid = {27670113}, issn = {2058-5276}, support = {R01 GM099525/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; *Biodiversity ; *Biological Specimen Banks ; Gastrointestinal Microbiome/genetics/*physiology ; Genome, Bacterial ; *Host Specificity ; Intestines/*microbiology ; Mice ; }, abstract = {Intestinal bacteria influence mammalian physiology, but many types of bacteria are still uncharacterized. Moreover, reference strains of mouse gut bacteria are not easily available, although mouse models are extensively used in medical research. These are major limitations for the investigation of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (miBC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50-75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization and molecular studies. The resource is available at www.dsmz.de/miBC.}, } @article {pmid27670112, year = {2016}, author = {Gionfriddo, CM and Tate, MT and Wick, RR and Schultz, MB and Zemla, A and Thelen, MP and Schofield, R and Krabbenhoft, DP and Holt, KE and Moreau, JW}, title = {Microbial mercury methylation in Antarctic sea ice.}, journal = {Nature microbiology}, volume = {1}, number = {10}, pages = {16127}, pmid = {27670112}, issn = {2058-5276}, mesh = {Antarctic Regions ; Bacteria/genetics/isolation & purification/*metabolism ; Bacterial Physiological Phenomena ; Ice Cover/chemistry/*microbiology ; Mercury/*metabolism ; Metagenomics ; Methylation ; Methylmercury Compounds/*analysis ; Microbial Consortia/genetics/*physiology ; Seawater/*microbiology ; Snow/microbiology ; }, abstract = {Atmospheric deposition of mercury onto sea ice and circumpolar sea water provides mercury for microbial methylation, and contributes to the bioaccumulation of the potent neurotoxin methylmercury in the marine food web. Little is known about the abiotic and biotic controls on microbial mercury methylation in polar marine systems. However, mercury methylation is known to occur alongside photochemical and microbial mercury reduction and subsequent volatilization. Here, we combine mercury speciation measurements of total and methylated mercury with metagenomic analysis of whole-community microbial DNA from Antarctic snow, brine, sea ice and sea water to elucidate potential microbially mediated mercury methylation and volatilization pathways in polar marine environments. Our results identify the marine microaerophilic bacterium Nitrospina as a potential mercury methylator within sea ice. Anaerobic bacteria known to methylate mercury were notably absent from sea-ice metagenomes. We propose that Antarctic sea ice can harbour a microbial source of methylmercury in the Southern Ocean.}, } @article {pmid27669488, year = {2017}, author = {Rani, A and Ranjan, R and McGee, HS and Andropolis, KE and Panchal, DV and Hajjiri, Z and Brennan, DC and Finn, PW and Perkins, DL}, title = {Urinary microbiome of kidney transplant patients reveals dysbiosis with potential for antibiotic resistance.}, journal = {Translational research : the journal of laboratory and clinical medicine}, volume = {181}, number = {}, pages = {59-70}, pmid = {27669488}, issn = {1878-1810}, support = {T32 HL082547/HL/NHLBI NIH HHS/United States ; R01 AI075317/AI/NIAID NIH HHS/United States ; K24 DK002886/DK/NIDDK NIH HHS/United States ; R01 HL081663/HL/NHLBI NIH HHS/United States ; R01 AI053878/AI/NIAID NIH HHS/United States ; P30 DK079333/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Aged ; Biodiversity ; Case-Control Studies ; *Drug Resistance, Microbial ; Dysbiosis/*microbiology/*urine ; Female ; Folic Acid/metabolism ; Humans ; Kidney Failure, Chronic/diagnosis/microbiology ; *Kidney Transplantation ; Male ; Metabolic Networks and Pathways ; *Microbiota ; Middle Aged ; Phylogeny ; Principal Component Analysis ; Urinary Tract Infections/microbiology ; }, abstract = {Recent studies have established that a complex community of microbes colonize the human urinary tract; however, their role in kidney transplant patients treated with prophylactic antibiotics remains poorly investigated. Our aim was to investigate the urinary microbiome of kidney transplant recipients. Urine samples from 21 patients after kidney transplantation and 8 healthy controls were collected. All patients received prophylactic treatment with the antibiotic combination trimethoprim-sulfamethoxazole. Metagenomic DNA was isolated from urine samples, sequenced using shotgun sequencing approach on Illumina HiSeq 2000 platform, and analyzed for microbial taxonomic and functional annotations. Our results demonstrate that the urine microbiome of kidney transplants was markedly different at all taxonomic levels from phyla to species, had decreased microbial diversity, and increased abundance of potentially pathogenic species compared with healthy controls. Specifically, at the phylum level, we detected a significant decrease in Actinobacteria and increase in Firmicutes due to increases in Enterococcus faecalis. In addition, there was an increase in the Proteobacteria due to increases in Escherichia coli. Analysis of predicted functions of the urinary metagenome revealed increased abundance of enzymes in the folate pathway including dihydrofolate synthase that are not inhibited by trimethoprim-sulfamethoxazole, but can augment folate metabolism. This report characterizes the urinary microbiome of kidney transplants using shotgun metagenomics approach. Our results indicate that the urinary microbiota may be modified in the context of prophylactic antibiotics, indicating that a therapeutic intervention may shift the urinary microbiota to select bacterial species with increased resistance to antibiotics. The evaluation and development of optimal prophylactic regimens that do not promote antibiotic resistance is an important future goal.}, } @article {pmid27665238, year = {2016}, author = {Bruder, LM and Dörkes, M and Fuchs, BM and Ludwig, W and Liebl, W}, title = {Flow cytometric sorting of fecal bacteria after in situ hybridization with polynucleotide probes.}, journal = {Systematic and applied microbiology}, volume = {39}, number = {7}, pages = {464-475}, doi = {10.1016/j.syapm.2016.08.005}, pmid = {27665238}, issn = {1618-0984}, mesh = {Animals ; Enterococcus faecalis/*genetics ; Feces/*microbiology ; Flow Cytometry/*methods ; Gastrointestinal Microbiome/*genetics ; Germ-Free Life ; In Situ Hybridization, Fluorescence ; Mice ; Nucleic Acid Hybridization/*methods ; Oligonucleotide Probes/*genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; }, abstract = {The gut microbiome represents a key contributor to human physiology, metabolism, immune function, and nutrition. Elucidating the composition and genetics of the gut microbiota under various conditions is essential to understand how microbes function individually and as a community. Metagenomic analyses are increasingly used to study intestinal microbiota. However, for certain scientific questions it is sufficient to examine taxon-specific submetagenomes, covering selected bacterial genera in a targeted manner. Here we established a new variant of fluorescence in situ hybridization (FISH) combined with fluorescence-activated cell sorting (FACS), providing access to the genomes of specific taxa belonging to the complex community of the intestinal microbiota. In contrast to standard oligonucleotide probes, the RNA polynucleotide probe used here, which targets domain III of the 23S rRNA gene, extends the resolution power in environmental samples by increasing signal intensity. Furthermore, cells hybridized with the polynucleotide probe are not subjected to harsh pretreatments, and their genetic information remains intact. The protocol described here was tested on genus-specifically labeled cells in various samples, including complex fecal samples from different laboratory mouse types that harbor diverse intestinal microbiota. Specifically, as an example for the protocol described here, RNA polynucleotide probes could be used to label Enterococcus cells for subsequent sorting by flow cytometry. To detect and quantify enterococci in fecal samples prior to enrichment, taxon-specific PCR and qPCR detection systems have been developed. The accessibility of the genomes from taxon-specifically sorted cells for subsequent molecular analyses was demonstrated by amplification of functional genes.}, } @article {pmid27664737, year = {2016}, author = {Antony, R and Sanyal, A and Kapse, N and Dhakephalkar, PK and Thamban, M and Nair, S}, title = {Microbial communities associated with Antarctic snow pack and their biogeochemical implications.}, journal = {Microbiological research}, volume = {192}, number = {}, pages = {192-202}, doi = {10.1016/j.micres.2016.07.004}, pmid = {27664737}, issn = {1618-0623}, mesh = {Antarctic Regions ; Archaea/classification ; Bacteria/classification ; Biodiversity ; *Ecosystem ; *Environmental Microbiology ; Fungi/classification ; Metagenome ; Metagenomics/methods ; *Microbiota ; Snow/*microbiology ; }, abstract = {Snow ecosystems represent a large part of the Earth's biosphere and harbour diverse microbial communities. Despite our increased knowledge of snow microbial communities, the question remains as to their functional potential, particularly with respect to their role in adapting to and modifying the specific snow environment. In this work, we investigated the diversity and functional capabilities of microorganisms from 3 regions of East Antarctica, with respect to compounds present in snow and tested whether their functional signature reflected the snow environment. A diverse assemblage of bacteria (Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Deinococcus-Thermus, Planctomycetes, Verrucomicrobia), archaea (Euryarchaeota), and eukarya (Basidiomycota, Ascomycota, Cryptomycota and Rhizaria) were detected through culture-dependent and -independent methods. Although microbial communities observed in the three snow samples were distinctly different, all isolates tested produced one or more of the following enzymes: lipase, protease, amylase, β-galactosidase, cellulase, and/or lignin modifying enzyme. This indicates that the snow pack microbes have the capacity to degrade organic compounds found in Antarctic snow (proteins, lipids, carbohydrates, lignin), thus highlighting their potential to be involved in snow chemistry.}, } @article {pmid27662586, year = {2016}, author = {Zeber-Lubecka, N and Kulecka, M and Ambrozkiewicz, F and Paziewska, A and Goryca, K and Karczmarski, J and Rubel, T and Wojtowicz, W and Mlynarz, P and Marczak, L and Tomecki, R and Mikula, M and Ostrowski, J}, title = {Limited prolonged effects of rifaximin treatment on irritable bowel syndrome-related differences in the fecal microbiome and metabolome.}, journal = {Gut microbes}, volume = {7}, number = {5}, pages = {397-413}, pmid = {27662586}, issn = {1949-0984}, mesh = {Adult ; Bacteria/classification/*drug effects/genetics/*isolation & purification ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestinal Mucosa/metabolism ; Intestines/microbiology ; Irritable Bowel Syndrome/*drug therapy/metabolism/microbiology ; Male ; Metabolome/*drug effects ; Middle Aged ; Rifamycins/*administration & dosage ; Rifaximin ; Time Factors ; Young Adult ; }, abstract = {Irritable bowel syndrome (IBS) is a chronic functional disorder and its development may be linked, directly and indirectly, to intestinal dysbiosis. Here we investigated the interactions between IBS symptoms and the gut microbiome, including the relation to rifaximin (1200 mg daily; 11.2 g per a treatment). We recruited 72 patients, including 31 with IBS-D (diarrhea), 11 with IBS-C (constipation), and 30 with IBS-M (mixed constipation and diarrhea) and 30 healthy controls (HCs). Of them, 68%, 64%, and 53% patients with IBS-D, IBS-C, and IBS-M, respectively, achieved 10-12 week-term improvement after the rifaximin treatment. Stool samples were collected before and after the treatment, and fecal microbiotic profiles were analyzed by deep sequencing of 16S rRNA, while stool metabolic profiles were studied by hydrogen 1-nuclear magnetic resonance ((1)H-NMR) and gas chromatography-mass spectrometry (GC-MS). Of 26 identified phyla, only Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria were consistently found in all samples. Bacteroidetes was predominant in fecal samples from HCs and IBS-D and IBS-M subjects, whereas Firmicutes was predominant in samples from IBS-C subjects. Species richness, but not community diversity, differentiated all IBS patients from HCs. Metabolic fingerprinting, using NMR spectra, distinguished HCs from all IBS patients. Thirteen metabolites identified by GC-MS differed HCs and IBS patients. However, neither metagenomics nor metabolomics analyses identified significant differences between patients with and without improvement after treatment.}, } @article {pmid27657714, year = {2016}, author = {Burton, EN and O'Connor, E and Ericsson, AC and Franklin, CL}, title = {Evaluation of Fecal Microbiota Transfer as Treatment for Postweaning Diarrhea in Research-Colony Puppies.}, journal = {Journal of the American Association for Laboratory Animal Science : JAALAS}, volume = {55}, number = {5}, pages = {582-587}, pmid = {27657714}, issn = {2769-6677}, support = {K01 OD019924/OD/NIH HHS/United States ; }, mesh = {Animals ; Diarrhea/therapy/*veterinary ; Dog Diseases/microbiology/*therapy ; Dogs ; Feces/*microbiology ; Female ; Gastrointestinal Diseases/microbiology/therapy/*veterinary ; Microbiota ; RNA, Ribosomal, 16S ; Research ; *Weaning ; }, abstract = {Frequently just prior to or at weaning (approximate age, 6 to 8 wk), puppies in research settings often develop diarrheal disease, which may be due, in part, to an immature and unstable intestinal microbiota that is permissive to opportunistic pathogens. The overall objective of this study was to assess whether fecal microbiota transfer (FMT) increased the transmission of a stable maternal microbiota to pups and decreased the incidence of postweaning diarrhea. Puppies were designated by litter as treated (FMT) or sham-treated. The FMT group received fecal inoculum orally for 5 consecutive days during weaning (at 6 to 8 wk of age). Diarrhea was evaluated according to a published scoring system for 11 d during the weaning period. Fresh feces were collected from dams and puppies at 3 d before weaning and 3, 10, and 24 d after weaning for analysis of the fecal microbiota by using 16S rRNA amplicon sequencing. The composition of fecal inoculum refrigerated at 3 to 5 °C was stable for at least 5 d. No diarrhea was reported in either group during the study period, making comparison of treated and control groups problematic. However, 16S rRNA gene analysis revealed microbial variability across time in both groups. Therefore, although the fecal microbiota of neither group of puppies mirrored the dam at any of the designated time points, the data provided fundamental and novel information regarding the dynamic maturation process of the fecal microbiota of puppies after weaning.}, } @article {pmid27655888, year = {2016}, author = {Louca, S and Hawley, AK and Katsev, S and Torres-Beltran, M and Bhatia, MP and Kheirandish, S and Michiels, CC and Capelle, D and Lavik, G and Doebeli, M and Crowe, SA and Hallam, SJ}, title = {Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {40}, pages = {E5925-E5933}, pmid = {27655888}, issn = {1091-6490}, mesh = {Base Sequence ; Calibration ; DNA ; Genomics/*methods ; Metabolic Networks and Pathways/*drug effects/*genetics ; Oxygen/*metabolism/*pharmacology ; RNA, Messenger/genetics/metabolism ; Time Factors ; }, abstract = {Microorganisms are the most abundant lifeform on Earth, mediating global fluxes of matter and energy. Over the past decade, high-throughput molecular techniques generating multiomic sequence information (DNA, mRNA, and protein) have transformed our perception of this microcosmos, conceptually linking microorganisms at the individual, population, and community levels to a wide range of ecosystem functions and services. Here, we develop a biogeochemical model that describes metabolic coupling along the redox gradient in Saanich Inlet-a seasonally anoxic fjord with biogeochemistry analogous to oxygen minimum zones (OMZs). The model reproduces measured biogeochemical process rates as well as DNA, mRNA, and protein concentration profiles across the redox gradient. Simulations make predictions about the role of ubiquitous OMZ microorganisms in mediating carbon, nitrogen, and sulfur cycling. For example, nitrite "leakage" during incomplete sulfide-driven denitrification by SUP05 Gammaproteobacteria is predicted to support inorganic carbon fixation and intense nitrogen loss via anaerobic ammonium oxidation. This coupling creates a metabolic niche for nitrous oxide reduction that completes denitrification by currently unidentified community members. These results quantitatively improve previous conceptual models describing microbial metabolic networks in OMZs. Beyond OMZ-specific predictions, model results indicate that geochemical fluxes are robust indicators of microbial community structure and reciprocally, that gene abundances and geochemical conditions largely determine gene expression patterns. The integration of real observational data, including geochemical profiles and process rate measurements as well as metagenomic, metatranscriptomic and metaproteomic sequence data, into a biogeochemical model, as shown here, enables holistic insight into the microbial metabolic network driving nutrient and energy flow at ecosystem scales.}, } @article {pmid27653942, year = {2016}, author = {Mitchell, AB and Oliver, BG and Glanville, AR}, title = {Translational Aspects of the Human Respiratory Virome.}, journal = {American journal of respiratory and critical care medicine}, volume = {194}, number = {12}, pages = {1458-1464}, doi = {10.1164/rccm.201606-1278CI}, pmid = {27653942}, issn = {1535-4970}, mesh = {Humans ; Microbiota/*physiology ; Respiratory System/*virology ; Respiratory Tract Infections/*virology ; Translational Research, Biomedical/*methods ; }, abstract = {Despite the dominant role of community-acquired respiratory viruses as etiological agents of disease, there has been little focus to date on the translation of rapidly developing diagnostic modalities, such as next-generation sequencing techniques in the examination of lower respiratory tract samples. When applied, these techniques should inform strategies to both understand the nexus between health and disease states of the respiratory virome, and drive a paradigm shift in how the practicing pulmonologist views the conceptual framework of respiratory infections. The lower respiratory tract was once thought to be a sanctuary site from microbiological colonization owing to the efficacy of upper airway-protective mechanisms and the host mucosal barrier function of the lower airways, combined with both innate and adaptive immune responses. As a small number of recent studies confirm, this is a naive vision of the lung, the viral component of which parallels recent revelations from respiratory microbiome studies. Hence, it is now timely to revise our thinking regarding the constituents, diversity, and changing nature of the respiratory virome in health and disease. One area worthy of focus is the interface between community-acquired respiratory viruses and the respiratory virome to better understand the dynamics in acute infection, as well as the factors that may lead to viral persistence and chronic disease. Given recent advances in metagenomics, the tools are now at hand to accomplish these goals.}, } @article {pmid27651451, year = {2017}, author = {Zolfo, M and Tett, A and Jousson, O and Donati, C and Segata, N}, title = {MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples.}, journal = {Nucleic acids research}, volume = {45}, number = {2}, pages = {e7}, pmid = {27651451}, issn = {1362-4962}, mesh = {Algorithms ; Alleles ; Bacteria/classification/genetics ; Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Metagenome ; Metagenomics/*methods ; Multilocus Sequence Typing/*methods ; Reproducibility of Results ; *Software ; Web Browser ; }, abstract = {Metagenomic characterization of microbial communities has the potential to become a tool to identify pathogens in human samples. However, software tools able to extract strain-level typing information from metagenomic data are needed. Low-throughput molecular typing schema such as Multilocus Sequence Typing (MLST) are still widely used and provide a wealth of strain-level information that is currently not exploited by metagenomic methods. We introduce MetaMLST, a software tool that reconstructs the MLST loci of microorganisms present in microbial communities from metagenomic data. Tested on synthetic and spiked-in real metagenomes, the pipeline was able to reconstruct the MLST sequences with >98.5% accuracy at coverages as low as 1×. On real samples, the pipeline showed higher sensitivity than assembly-based approaches and it proved successful in identifying strains in epidemic outbreaks as well as in intestinal, skin and gastrointestinal microbiome samples.}, } @article {pmid27650378, year = {2016}, author = {Lebret, K and Schroeder, J and Balestreri, C and Highfield, A and Cummings, D and Smyth, T and Schroeder, D}, title = {Choice of molecular barcode will affect species prevalence but not bacterial community composition.}, journal = {Marine genomics}, volume = {29}, number = {}, pages = {39-43}, pmid = {27650378}, issn = {1876-7478}, mesh = {Bacteria/classification/*genetics ; *Biodiversity ; Genomics/*methods ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Seasons ; *Sequence Analysis, RNA ; }, abstract = {The rapid advancement of next generation sequencing protocols in recent years has led to the diversification in the methods used to study microbial communities; however, how comparable the data generated from these different methods are, remains unclear. In this study we compared the taxonomic composition and seasonal dynamics of the bacterial community determined by two distinct 16s amplicon sequencing protocols: sequencing of the V6 region of the 16s rRNA gene using 454 pyrosequencing vs the V4 region of the 16s rRNA gene using the Illumina Hiseq 2500 platform. Significant differences between relative abundances at all taxonomic levels were observed; however, their seasonal dynamics between phyla were largely consistent between methods. This study highlights that care must be taken when comparing datasets generated from different methods.}, } @article {pmid27650273, year = {2016}, author = {Kaiser, K and Wemheuer, B and Korolkow, V and Wemheuer, F and Nacke, H and Schöning, I and Schrumpf, M and Daniel, R}, title = {Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {33696}, pmid = {27650273}, issn = {2045-2322}, mesh = {Bacteria/*classification ; *Biodiversity ; Ecosystem ; *Forests ; Germany ; *Grassland ; Hydrogen-Ion Concentration ; Metagenome ; Metagenomics/methods ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management.}, } @article {pmid27647198, year = {2016}, author = {Wang, HX and Wang, YP}, title = {Gut Microbiota-brain Axis.}, journal = {Chinese medical journal}, volume = {129}, number = {19}, pages = {2373-2380}, pmid = {27647198}, issn = {2542-5641}, mesh = {Animals ; Brain/*metabolism/physiology ; Central Nervous System/metabolism/physiology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/microbiology ; Humans ; Hypothalamo-Hypophyseal System/metabolism/physiology ; Pituitary-Adrenal System/metabolism/physiology ; }, abstract = {OBJECTIVE: To systematically review the updated information about the gut microbiota-brain axis.

DATA SOURCES: All articles about gut microbiota-brain axis published up to July 18, 2016, were identified through a literature search on PubMed, ScienceDirect, and Web of Science, with the keywords of "gut microbiota", "gut-brain axis", and "neuroscience".

STUDY SELECTION: All relevant articles on gut microbiota and gut-brain axis were included and carefully reviewed, with no limitation of study design.

RESULTS: It is well-recognized that gut microbiota affects the brain's physiological, behavioral, and cognitive functions although its precise mechanism has not yet been fully understood. Gut microbiota-brain axis may include gut microbiota and their metabolic products, enteric nervous system, sympathetic and parasympathetic branches within the autonomic nervous system, neural-immune system, neuroendocrine system, and central nervous system. Moreover, there may be five communication routes between gut microbiota and brain, including the gut-brain's neural network, neuroendocrine-hypothalamic-pituitary-adrenal axis, gut immune system, some neurotransmitters and neural regulators synthesized by gut bacteria, and barrier paths including intestinal mucosal barrier and blood-brain barrier. The microbiome is used to define the composition and functional characteristics of gut microbiota, and metagenomics is an appropriate technique to characterize gut microbiota.

CONCLUSIONS: Gut microbiota-brain axis refers to a bidirectional information network between the gut microbiota and the brain, which may provide a new way to protect the brain in the near future.}, } @article {pmid27646687, year = {2016}, author = {Wang, P and Zhang, H and Zuo, J and Zhao, D and Zou, X and Zhu, Z and Jeelani, N and Leng, X and An, S}, title = {A Hardy Plant Facilitates Nitrogen Removal via Microbial Communities in Subsurface Flow Constructed Wetlands in Winter.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {33600}, pmid = {27646687}, issn = {2045-2322}, mesh = {Bacteria ; Biodiversity ; Biomass ; Ecosystem ; Metagenome ; Metagenomics ; *Microbiota ; Nitrogen/*metabolism ; *Plants ; RNA, Ribosomal, 16S/genetics ; *Seasons ; *Wetlands ; }, abstract = {The plants effect in subsurface flow constructed wetlands (SSF-CWs) is controversial, especially at low temperatures. Consequently, several SSF-CWs planted with Iris pseudacorus (CWI) or Typha orientalis Presl. (CWT) and several unplanted ones (CWC) were set up and fed with secondary effluent of sewage treatment plant during the winter in Eastern China. The 16S rDNA Illumina Miseq sequencing analysis indicated the positive effects of I. pseudacorus on the bacterial community richness and diversity in the substrate. Moreover, the community compositions of the bacteria involved with denitrification presented a significant difference in the three systems. Additionally, higher relative abundances of nitrifying bacteria (0.4140%, 0.2402% and 0.4318% for Nitrosomonas, Nitrosospira and Nitrospira, respectively) were recorded in CWI compared with CWT (0.2074%, 0.0648% and 0.0181%, respectively) and CWC (0.3013%, 0.1107% and 0.1185%, respectively). Meanwhile, the average removal rates of NH4(+)-N and TN in CWI showed a prominent advantage compared to CWC, but no distinct advantage was found in CWT. The hardy plant I. pseudacorus, which still had active root oxygen release in cold temperatures, positively affected the abundance of nitrifying bacteria in the substrate, and accordingly was supposed to contribute to a comparatively high nitrogen removal efficiency of the system during the winter.}, } @article {pmid27644050, year = {2016}, author = {Smith-Brown, P and Morrison, M and Krause, L and Davies, PS}, title = {Mothers Secretor Status Affects Development of Childrens Microbiota Composition and Function: A Pilot Study.}, journal = {PloS one}, volume = {11}, number = {9}, pages = {e0161211}, pmid = {27644050}, issn = {1932-6203}, mesh = {Adult ; Bacteroides/genetics/isolation & purification ; Bifidobacterium/genetics/isolation & purification ; *Breast Feeding ; Child, Preschool ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Microbiota ; Milk, Human/*chemistry ; Oligosaccharides/*analysis ; Pilot Projects ; RNA, Ribosomal, 16S/genetics/isolation & purification ; Saliva/chemistry ; Young Adult ; }, abstract = {BACKGROUND: One mechanism by which early life environment may influence long term health is through modulation of the gut microbiota. It is widely accepted that the optimal source of nutrition in early life is breast milk, with Human Milk Oligosaccharides (HMOs) thought to play an important role in nourishing the developing microbiota. However, mothers with inactive secretor genes have altered HMO composition and quantities in their breast milk. In this pilot study we examine the influence of secretor status and breast-feeding on microbiota composition at 2 to 3 years of age.

METHODS: 37 children and 17 eligible mothers were recruited. Secretor status was determined from blood and saliva samples using hemagglutination inhibition technique and faecal microbiota composition was examined by 16S rRNA gene sequencing.

RESULTS: Secretor status was determined for 28 eligible children with 20 being secretors (S, 71.4%). Eleven of the 17 mothers were secretors (S, 64.7%). Unweighted UniFrac distances were significantly associated with child secretor status (R2 = 0.069, p = 0.030) and with mother secretor status in children exclusively breastfed for at least 4 months (R2 = 0.167, p = 0.028), suggesting an influence on the presence/absence of microbes, with Prevotella not detected in samples from secretor children and children of secretor mothers. In children who were exclusively breast-fed for at least 4 months of life the abundance of the known HMO consumers Bifidobacterium were increased in the children of secretor mothers compared to non-secretor mothers. The relative abundance of an OTU related to Bacteroides plebeius, a bacterium noted for its capacity to utilise sulphated polysaccharides for growth, was decreased in these children.

CONCLUSIONS: Child and mothers' secretor status have an impact on childrens' microbiota composition at 2 to 3 years of age.}, } @article {pmid27642121, year = {2016}, author = {Al-Amoudi, S and Razali, R and Essack, M and Amini, MS and Bougouffa, S and Archer, JA and Lafi, FF and Bajic, VB}, title = {Metagenomics as a preliminary screen for antimicrobial bioprospecting.}, journal = {Gene}, volume = {594}, number = {2}, pages = {248-258}, doi = {10.1016/j.gene.2016.09.021}, pmid = {27642121}, issn = {1879-0038}, mesh = {Bacteria/*genetics/metabolism ; Indian Ocean ; *Metagenome ; Microbiota/*genetics ; *Water Microbiology ; }, abstract = {Since the composition of soil directs the diversity of the contained microbiome and its potential to produce bioactive compounds, many studies has been focused on sediment types with unique features characteristic of extreme environments. However, not much is known about the potential of microbiomes that inhabit the highly saline and hot Red Sea lagoons. This case study explores mangrove mud and the microbial mat of sediments collected from the Rabigh harbor lagoon and Al Kharrar lagoon for antimicrobial bioprospecting. Rabigh harbor lagoon appears the better location, and the best sediment type for this purpose is mangrove mud. On the other hand, Al Kharrar lagoon displayed increased anaerobic hydrocarbon degradation and an abundance of bacterial DNA associated with antibiotic resistance. Moreover, our findings show an identical shift in phyla associated with historic hydrocarbon contamination exposure reported in previous studies (that is, enrichment of Gamma- and Delta-proteobacteria), but we also report that bacterial DNA sequences associated with antibiotic synthesis enzymes are derived from Gamma-, Delta- and Alpha-proteobacteria. This suggests that selection pressure associated with hydrocarbon contamination tend to enrich the bacterial classes DNA associated with antibiotic synthesis enzymes. Although Actinobacteria tends to be the common target for research when it comes to antimicrobial bioprospecting, our study suggests that Firmicutes (Bacilli and Clostridia), Bacteroidetes, Cyanobacteria, and Proteobacteria should be antimicrobial bioprospecting targets as well. To the best of our knowledge, this is the first metagenomic study that analyzed the microbiomes in Red Sea lagoons for antimicrobial bioprospecting.}, } @article {pmid27639192, year = {2016}, author = {Lelouvier, B and Servant, F and Païssé, S and Brunet, AC and Benyahya, S and Serino, M and Valle, C and Ortiz, MR and Puig, J and Courtney, M and Federici, M and Fernández-Real, JM and Burcelin, R and Amar, J}, title = {Changes in blood microbiota profiles associated with liver fibrosis in obese patients: A pilot analysis.}, journal = {Hepatology (Baltimore, Md.)}, volume = {64}, number = {6}, pages = {2015-2027}, doi = {10.1002/hep.28829}, pmid = {27639192}, issn = {1527-3350}, mesh = {Cross-Sectional Studies ; Feces/*microbiology ; Female ; Humans ; Liver Cirrhosis/*blood/*complications/microbiology ; Male ; *Microbiota ; Middle Aged ; Obesity/*blood/*complications/microbiology ; Pilot Projects ; }, abstract = {UNLABELLED: The early detection of liver fibrosis among patients with nonalcoholic fatty liver disease (NAFLD) is an important clinical need. In view of the suggested role played by bacterial translocation in liver disease and obesity, we sought to investigate the relationship between blood microbiota and liver fibrosis (LF) in European cohorts of patients with severe obesity. We carried out a cross-sectional study of obese patients, well characterized with respect to the severity of the NAFLD, in the cohort FLORINASH. This cohort has been divided into a discovery cohort comprising 50 Spanish patients and then in a validation cohort of 71 Italian patients. Blood bacterial DNA was analyzed both quantitatively by 16S ribosomal DNA (rDNA) quantitative polymerase chain reaction and qualitatively by 16S rDNA targeted metagenomic sequencing and functional metagenome prediction. Spanish plasma bile acid contents were analyzed by liquid chromatography/mass spectrometry. The 16S rDNA concentration was significantly higher in patients of the discovery cohort with LF. By 16S sequencing, we found specific differences in the proportion of several bacterial taxa in both blood and feces that correlate with the presence of LF, thus defining a specific signature of the liver disease. Several secondary/primary bile acid ratios were also decreased with LF in the discovery cohort. We confirmed, in the validation cohort, the correlation between blood 16S rDNA concentration and LF, whereas we did not confirm the specific bacterial taxa signature, despite a similar trend in patients with more-severe fibrosis.

CONCLUSION: Changes in blood microbiota are associated with LF in obese patients. Blood microbiota analysis provides potential biomarkers for the detection of LF in this population. (Hepatology 2016;64:2015-2027).}, } @article {pmid27639161, year = {2016}, author = {Fauver, JR and Grubaugh, ND and Krajacich, BJ and Weger-Lucarelli, J and Lakin, SM and Fakoli, LS and Bolay, FK and Diclaro, JW and Dabiré, KR and Foy, BD and Brackney, DE and Ebel, GD and Stenglein, MD}, title = {West African Anopheles gambiae mosquitoes harbor a taxonomically diverse virome including new insect-specific flaviviruses, mononegaviruses, and totiviruses.}, journal = {Virology}, volume = {498}, number = {}, pages = {288-299}, doi = {10.1016/j.virol.2016.07.031}, pmid = {27639161}, issn = {1096-0341}, support = {R01 AI094349/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Anopheles/*virology ; Biodiversity ; Burkina Faso ; Flavivirus/classification/genetics ; Genes, Viral ; Genome, Viral ; Insect Vectors/virology ; Insect Viruses/*classification/genetics ; Liberia ; Metagenome ; Metagenomics ; *Microbiota ; Open Reading Frames ; Phylogeny ; RNA Viruses/classification/genetics ; Senegal ; Totivirus/classification/genetics ; }, abstract = {Anopheles gambiae are a major vector of malaria in sub-Saharan Africa. Viruses that naturally infect these mosquitoes may impact their physiology and ability to transmit pathogens. We therefore used metagenomics sequencing to search for viruses in adult Anopheles mosquitoes collected from Liberia, Senegal, and Burkina Faso. We identified a number of virus and virus-like sequences from mosquito midgut contents, including 14 coding-complete genome segments and 26 partial sequences. The coding-complete sequences define new viruses in the order Mononegavirales, and the families Flaviviridae, and Totiviridae. The identification of a flavivirus infecting Anopheles mosquitoes broadens our understanding of the evolution and host range of this virus family. This study increases our understanding of virus diversity in general, begins to define the virome of a medically important vector in its natural setting, and lays groundwork for future studies examining the potential impact of these viruses on anopheles biology and disease transmission.}, } @article {pmid27638139, year = {2017}, author = {Hasegawa, K and Linnemann, RW and Mansbach, JM and Ajami, NJ and Espinola, JA and Fiechtner, LG and Petrosino, JF and Camargo, CA}, title = {Household siblings and nasal and fecal microbiota in infants.}, journal = {Pediatrics international : official journal of the Japan Pediatric Society}, volume = {59}, number = {4}, pages = {473-481}, pmid = {27638139}, issn = {1442-200X}, support = {R01 AI108588/AI/NIAID NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; R21 HL129909/HL/NHLBI NIH HHS/United States ; R01 AI114552/AI/NIAID NIH HHS/United States ; UH3 OD023253/OD/NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; }, mesh = {Cross-Sectional Studies ; Feces/*microbiology ; Female ; Humans ; Infant ; Male ; *Microbiota ; Nasal Mucosa/*microbiology ; *Siblings ; }, abstract = {BACKGROUND: Early-life exposure to older siblings is associated with a lower risk of asthma. To date, no study has addressed the impact of having siblings on both the airway and fecal microbiota during infancy. The aim of this study was therefore to profile the nasal airway and fecal microbiota in infants, and to examine the association between having siblings and microbiota profile.

METHODS: We conducted a cross-sectional study of 105 healthy infants (aged <1 year). Using 16S rRNA gene sequencing and an unbiased clustering approach to the nasal airway and fecal samples, we identified microbiota profiles and then determined the association between having siblings and microbiome profile.

RESULTS: Overall, the median age was 3.4 months (IQR, 2.0-4.7 months); 43% had siblings in the household. Unbiased clustering of nasal airway microbiota identified three profiles: Moraxella dominant (43%), Corynebacterium/Dolosigranulum dominant (36%), and mixed (21%). Infants with siblings were more likely to have a Moraxella-dominant profile than Corynebacterium/Dolosigranulum-dominant profile (76% vs 18%), while those without siblings had the opposite pattern (18% vs 50%; P < 0.001, multivariable-adjusted). Fecal microbiota consisted of three profiles: Bifidobacterium dominant (39%), Escherichia dominant (31%), and Enterobacter dominant (30%). Infants with siblings were more likely to have a Bifidobacterium-dominant profile than Escherichia-dominant profile (49% vs 24%) while those without siblings had the opposite pattern (32% vs 37%; P = 0.04, multivariable-adjusted).

CONCLUSIONS: In this cross-sectional study, infants with siblings were more likely to have a Moraxella-dominant nasal microbiota profile and Bifidobacterium-dominant fecal microbiota profile. These findings should facilitate further investigation of the interplay between early-life environmental exposure, the microbiome, and childhood asthma.}, } @article {pmid27633144, year = {2016}, author = {DiLoreto, ZA and Weber, PA and Olds, W and Pope, J and Trumm, D and Chaganti, SR and Heath, DD and Weisener, CG}, title = {Novel cost effective full scale mussel shell bioreactors for metal removal and acid neutralization.}, journal = {Journal of environmental management}, volume = {183}, number = {Pt 3}, pages = {601-612}, doi = {10.1016/j.jenvman.2016.09.023}, pmid = {27633144}, issn = {1095-8630}, mesh = {Acids/metabolism ; Animal Shells/*microbiology ; Animals ; Bacteria/genetics/*metabolism ; Bioreactors/*microbiology ; Bivalvia ; Hydrogen-Ion Concentration ; Metals/analysis/*metabolism ; Microbial Consortia ; Mining ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Sulfur/analysis/*metabolism ; Water Pollutants, Chemical/analysis/*metabolism ; }, abstract = {Acid mine drainage (AMD) impacted waters are a worldwide concern for the mining industry and countries dealing with this issue; both active and passive technologies are employed for the treatment of such waters. Mussel shell bioreactors (MSB) represent a passive technology that utilizes waste from the shellfish industry as a novel substrate. The aim of this study is to provide insight into the biogeochemical dynamics of a novel full scale MSB for AMD treatment. A combination of water quality data, targeted geochemical extractions, and metagenomic analyses were used to evaluate MSB performance. The MSB raised the effluent pH from 3.4 to 8.3 while removing up to ∼99% of the dissolved Al, and Fe and >90% Ni, Tl, and Zn. A geochemical gradient was observed progressing from oxidized to reduced conditions with depth. The redox conditions helped define the microbial consortium that consists of a specialized niche of organisms that influence elemental cycling (i.e. complex Fe and S cycling). MSB technology represents an economic and effective means of full scale, passive AMD treatment that is an attractive alternative for developing economies due to its low cost and ease of implementation.}, } @article {pmid27632908, year = {2016}, author = {Pirbaglou, M and Katz, J and de Souza, RJ and Stearns, JC and Motamed, M and Ritvo, P}, title = {Probiotic supplementation can positively affect anxiety and depressive symptoms: a systematic review of randomized controlled trials.}, journal = {Nutrition research (New York, N.Y.)}, volume = {36}, number = {9}, pages = {889-898}, doi = {10.1016/j.nutres.2016.06.009}, pmid = {27632908}, issn = {1879-0739}, mesh = {*Affect ; Animals ; Anxiety/*drug therapy ; Depression/*drug therapy ; Dietary Supplements ; *Gastrointestinal Microbiome ; Humans ; *Mental Health ; Probiotics/*therapeutic use ; }, abstract = {Gastrointestinal microbiota, consisting of microbial communities in the gastrointestinal tract, play an important role in digestive, metabolic, and immune functioning. Preclinical studies on rodents have linked behavioral and neurochemical changes in the central nervous system with deficits or alterations in these bacterial communities. Moreover, probiotic supplementation in rodents has been shown to markedly change behavior, with correlated changes in central neurochemistry. While such studies have documented behavioral and mood-related supplementation effects, the significance of these effects in humans, especially in relation to anxiety and depression symptoms, are relatively unknown. Thus, the purpose of this paper was to systematically evaluate current literature on the impact of probiotic supplementation on anxiety and depression symptoms in humans. To this end, multiple databases, including Medline, PsycINFO, PubMed, Scopus, and Web of Science were searched for randomized controlled trials published between January 1990 and January 2016. Search results led to a total of 10 randomized controlled trials (4 in clinically diagnosed and 6 in non-clinical samples) that provided limited support for the use of some probiotics in reducing human anxiety and depression. Despite methodological limitations of the included trials and the complex nature of gut-brain interactions, results suggest the detection of apparent psychological benefits from probiotic supplementation. Nevertheless a better understanding of developmental, modulatory, and metagenomic influences on the GI microbiota, specifically as they relate to mood and mental health, represent strong priorities for future research in this area.}, } @article {pmid27628595, year = {2017}, author = {Gomez, A and Nelson, KE}, title = {The Oral Microbiome of Children: Development, Disease, and Implications Beyond Oral Health.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {492-503}, pmid = {27628595}, issn = {1432-184X}, support = {R01 DE019665/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/metabolism/pathogenicity ; Biodiversity ; Biomarkers ; Child ; Dental Caries/microbiology/therapy ; Ecology ; Humans ; Metagenome ; Microbiota/*physiology ; Mouth/*microbiology ; Mouth Diseases/immunology/*microbiology/therapy ; *Oral Health ; Risk Assessment ; Risk Factors ; }, abstract = {In the era of applied meta-omics and personalized medicine, the oral microbiome is a valuable asset. From biomarker discovery to being a powerful source of therapeutic targets and to presenting an opportunity for developing non-invasive approaches to health care, it has become clear that oral microbes may hold the answer for understanding disease, even beyond the oral cavity. Although our understanding of oral microbiome diversity has come a long way in the past 50 years, there are still many areas that need to be fine-tuned for better risk assessment and diagnosis, especially in early developmental stages of human life. Here, we discuss the factors that impact development of the oral microbiome and explore oral markers of disease, with a focus on the early oral cavity. Our ultimate goal is to put different experimental and methodological views into perspective for better assessment of early oral and systemic disease at an early age and discuss how oral microbiomes-at the community level-could provide improved assessment in individuals and populations at risk.}, } @article {pmid27628212, year = {2016}, author = {Xie, Y and Xia, P and Wang, H and Yu, H and Giesy, JP and Zhang, Y and Mora, MA and Zhang, X}, title = {Effects of captivity and artificial breeding on microbiota in feces of the red-crowned crane (Grus japonensis).}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {33350}, pmid = {27628212}, issn = {2045-2322}, mesh = {Analysis of Variance ; Animals ; Bacteria/genetics ; Biodiversity ; Birds/growth & development/*microbiology ; *Breeding ; Feces/*microbiology ; High-Throughput Nucleotide Sequencing ; Life Cycle Stages ; *Microbiota ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Zoonoses/microbiology ; }, abstract = {Reintroduction of the threatened red-crowned crane has been unsuccessful. Although gut microbiota correlates with host health, there is little information on gut microbiota of cranes under different conservation strategies. The study examined effects of captivity, artificial breeding and life stage on gut microbiota of red-crown cranes. The gut microbiotas of wild, captive adolescent, captive adult, artificially bred adolescent and artificially bred adult cranes were characterized by next-generation sequencing of 16S rRNA gene amplicons. The gut microbiotas were dominated by three phyla: Firmicutes (62.9%), Proteobacteria (29.9%) and Fusobacteria (9.6%). Bacilli dominated the 'core' community consisting of 198 operational taxonomic units (OTUs). Both captivity and artificial breeding influenced the structures and diversities microbiota of the gut. Especially, wild cranes had distinct compositions of gut microbiota from captive and artificially bred cranes. The greatest alpha diversity was found in captive cranes, while wild cranes had the least. According to the results of ordination analysis, influences of captivity and artificial breeding were greater than that of life stage. Overall, captivity and artificial breeding influenced the gut microbiota, potentially due to changes in diet, vaccination, antibiotics and living conditions. Metagenomics can serve as a supplementary non-invasive screening tool for disease control.}, } @article {pmid27624970, year = {2016}, author = {Turroni, S and Fiori, J and Rampelli, S and Schnorr, SL and Consolandi, C and Barone, M and Biagi, E and Fanelli, F and Mezzullo, M and Crittenden, AN and Henry, AG and Brigidi, P and Candela, M}, title = {Fecal metabolome of the Hadza hunter-gatherers: a host-microbiome integrative view.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {32826}, pmid = {27624970}, issn = {2045-2322}, mesh = {Adolescent ; Adult ; Aged ; Biological Evolution ; Cluster Analysis ; Cohort Studies ; Diet ; Ecosystem ; Feces/chemistry/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Italy ; Life Style ; *Metabolome ; Metabolomics ; Metagenomics ; *Microbiota ; Middle Aged ; Principal Component Analysis ; Tanzania ; Young Adult ; }, abstract = {The recent characterization of the gut microbiome of traditional rural and foraging societies allowed us to appreciate the essential co-adaptive role of the microbiome in complementing our physiology, opening up significant questions on how the microbiota changes that have occurred in industrialized urban populations may have altered the microbiota-host co-metabolic network, contributing to the growing list of Western diseases. Here, we applied a targeted metabolomics approach to profile the fecal metabolome of the Hadza of Tanzania, one of the world's few remaining foraging populations, and compared them to the profiles of urban living Italians, as representative of people in the post-industrialized West. Data analysis shows that during the rainy season, when the diet is primarily plant-based, Hadza are characterized by a distinctive enrichment in hexoses, glycerophospholipids, sphingolipids, and acylcarnitines, while deplete in the most common natural amino acids and derivatives. Complementary to the documented unique metagenomic features of their gut microbiome, our findings on the Hadza metabolome lend support to the notion of an alternate microbiome configuration befitting of a nomadic forager lifestyle, which helps maintain metabolic homeostasis through an overall scarcity of inflammatory factors, which are instead highly represented in the Italian metabolome.}, } @article {pmid27623553, year = {2017}, author = {Ferretti, P and Farina, S and Cristofolini, M and Girolomoni, G and Tett, A and Segata, N}, title = {Experimental metagenomics and ribosomal profiling of the human skin microbiome.}, journal = {Experimental dermatology}, volume = {26}, number = {3}, pages = {211-219}, doi = {10.1111/exd.13210}, pmid = {27623553}, issn = {1600-0625}, mesh = {Computational Biology/*methods ; DNA, Bacterial/*analysis ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*analysis ; Sequence Analysis, DNA/methods ; Skin/*microbiology ; }, abstract = {The skin is the largest organ in the human body, and it is populated by a large diversity of microbes, most of which are co-evolved with the host and live in symbiotic harmony. There is increasing evidence that the skin microbiome plays a crucial role in the defense against pathogens, immune system training and homoeostasis, and microbiome perturbations have been associated with pathological skin conditions. Studying the skin resident microbial community is thus essential to better understand the microbiome-host crosstalk and to associate its specific configurations with cutaneous diseases. Several community profiling approaches have proved successful in unravelling the composition of the skin microbiome and overcome the limitations of cultivation-based assays, but these tools remain largely inaccessible to the clinical and medical dermatology communities. The study of the skin microbiome is also characterized by specific technical challenges, such as the low amount of microbial biomass and the extensive human DNA contamination. Here, we review the available community profiling approaches to study the skin microbiome, specifically focusing on the practical experimental and analytical tools necessary to generate and analyse skin microbiome data. We describe all the steps from the initial samples collection to the final data interpretation, with the goal of enabling clinicians and researchers who are not familiar with the microbiome field to perform skin profiling experiments.}, } @article {pmid27621225, year = {2017}, author = {Davis, DJ and Hecht, PM and Jasarevic, E and Beversdorf, DQ and Will, MJ and Fritsche, K and Gillespie, CH}, title = {Sex-specific effects of docosahexaenoic acid (DHA) on the microbiome and behavior of socially-isolated mice.}, journal = {Brain, behavior, and immunity}, volume = {59}, number = {}, pages = {38-48}, doi = {10.1016/j.bbi.2016.09.003}, pmid = {27621225}, issn = {1090-2139}, mesh = {Animals ; Anxiety/psychology ; Behavior, Animal/*drug effects ; Depression/psychology ; Diet ; Docosahexaenoic Acids/*pharmacology ; Feces/chemistry ; Female ; Food Preferences/drug effects ; Gastrointestinal Microbiome ; Male ; Mice ; Mice, Inbred C57BL ; Microbiota/*drug effects ; Motor Activity/drug effects ; Sex Characteristics ; *Social Isolation ; }, abstract = {Dietary supplementation with the long-chain omega-3 polyunsaturated fatty acid docosahexaenoic acid (DHA) has been shown to have a beneficial effect on reducing the symptoms associated with several neuropsychiatric conditions including anxiety and depression. However, the mechanisms underlying this effect remain largely unknown. Increasing evidence suggests that the vast repertoire of commensal bacteria within the gut plays a critical role in regulating various biological processes in the brain and may contribute to neuropsychiatric disease risk. The present study determined the contribution of DHA on anxiety and depressive-like behaviors through modulation of the gut microbiota in a paradigm of social isolation. Adult male and female mice were subjected to social isolation for 28days and then placed either on a control diet or a diet supplemented with 0.1% or 1.0% DHA. Fecal pellets were collected both 24h and 7days following the introduction of the new diets. Behavioral testing revealed that male mice fed a DHA diet, regardless of dose, exhibited reduced anxiety and depressive-like behaviors compared to control fed mice while no differences were observed in female mice. As the microbiota-brain-axis has been recently implicated in behavior, composition of microbial communities were analyzed to examine if these sex-specific effects of DHA may be associated with changes in the gut microbiota (GM). Clear sex differences were observed with males and females showing distinct microbial compositions prior to DHA supplementation. The introduction of DHA into the diet also induced sex-specific interactions on the GM with the fatty acid producing a significant effect on the microbial profiles in males but not in females. Interestingly, levels of Allobaculum and Ruminococcus were found to significantly correlate with the behavioral changes observed in the male mice. Predictive metagenome analysis using PICRUSt was performed on the fecal samples collected from males and identified enrichment in functional KEGG pathway terms relevant to processes such as the biosynthesis of unsaturated fatty acids and antioxidant metabolism. These results indicate that DHA alters commensal community composition and produces beneficial effects on anxiety and depressive-like behaviors in a sex-specific manner. The present study provides insight into the mechanistic role that gut microbes may play in the regulation of anxiety and depressive-like behaviors and how dietary intervention can modulate these effects.}, } @article {pmid27617059, year = {2016}, author = {Robbins, RJ and Krishtalka, L and Wooley, JC}, title = {Advances in biodiversity: metagenomics and the unveiling of biological dark matter.}, journal = {Standards in genomic sciences}, volume = {11}, number = {1}, pages = {69}, pmid = {27617059}, issn = {1944-3277}, abstract = {BACKGROUND: Efforts to harmonize genomic data standards used by the biodiversity and metagenomic research communities have shown that prokaryotic data cannot be understood or represented in a traditional, classical biological context for conceptual reasons, not technical ones.

RESULTS: Biology, like physics, has a fundamental duality-the classical macroscale eukaryotic realm vs. the quantum microscale microbial realm-with the two realms differing profoundly, and counter-intuitively, from one another. Just as classical physics is emergent from and cannot explain the microscale realm of quantum physics, so classical biology is emergent from and cannot explain the microscale realm of prokaryotic life. Classical biology describes the familiar, macroscale realm of multi-cellular eukaryotic organisms, which constitute a highly derived and constrained evolutionary subset of the biosphere, unrepresentative of the vast, mostly unseen, microbial world of prokaryotic life that comprises at least half of the planet's biomass and most of its genetic diversity. The two realms occupy fundamentally different mega-niches: eukaryotes interact primarily mechanically with the environment, prokaryotes primarily physiologically. Further, many foundational tenets of classical biology simply do not apply to prokaryotic biology.

CONCLUSIONS: Classical genetics one held that genes, arranged on chromosomes like beads on a string, were the fundamental units of mutation, recombination, and heredity. Then, molecular analysis showed that there were no fundamental units, no beads, no string. Similarly, classical biology asserts that individual organisms and species are fundamental units of ecology, evolution, and biodiversity, composing an evolutionary history of objectively real, lineage-defined groups in a single-rooted tree of life. Now, metagenomic tools are forcing a recognition that there are no completely objective individuals, no unique lineages, and no one true tree. The newly revealed biosphere of microbial dark matter cannot be understood merely by extending the concepts and methods of eukaryotic macrobiology. The unveiling of biological dark matter is allowing us to see, for the first time, the diversity of the entire biosphere and, to paraphrase Darwin, is providing a new view of life. Advancing and understanding that view will require major revisions to some of the most fundamental concepts and theories in biology.}, } @article {pmid27616558, year = {2016}, author = {Hand, TW}, title = {The Role of the Microbiota in Shaping Infectious Immunity.}, journal = {Trends in immunology}, volume = {37}, number = {10}, pages = {647-658}, pmid = {27616558}, issn = {1471-4981}, support = {K22 AI108719/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Host-Pathogen Interactions ; Humans ; Immunomodulation ; Infections/*immunology/microbiology ; Inflammation/*immunology ; Intestinal Mucosa/*immunology/microbiology ; Metagenome/immunology ; Microbiota/*immunology ; Opportunistic Infections/*immunology/microbiology ; }, abstract = {Humans are meta-organisms that maintain a diverse population of microorganisms on their barrier surfaces, collectively named the microbiota. Since most pathogens either cross or inhabit barrier surfaces, the microbiota plays a critical and often protective role during infections, both by modulating immune system responses and by mediating colonization resistance. However, the microbiota can also act as a reservoir for opportunistic microorganisms that can 'bloom', significantly complicating diseases of barrier surfaces by contributing to inflammatory immune responses. This review discusses our current understanding of the complex interactions between the host, its microbiota, and pathogenic organisms, focusing in particular on the intestinal mucosa.}, } @article {pmid27615066, year = {2017}, author = {Godoy-Vitorino, F and Rodriguez-Hilario, A and Alves, AL and Gonçalves, F and Cabrera-Colon, B and Mesquita, CS and Soares-Castro, P and Ferreira, M and Marçalo, A and Vingada, J and Eira, C and Santos, PM}, title = {The microbiome of a striped dolphin (Stenella coeruleoalba) stranded in Portugal.}, journal = {Research in microbiology}, volume = {168}, number = {1}, pages = {85-93}, doi = {10.1016/j.resmic.2016.08.004}, pmid = {27615066}, issn = {1769-7123}, mesh = {Aerobiosis ; Anaerobiosis ; Animal Structures/microbiology ; Animals ; Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Microbiota ; Phylogeny ; Portugal ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Stenella/*microbiology ; }, abstract = {Infectious diseases with epizootic consequences have not been fully studied in marine mammals. Presently, the unprecedented depth of sequencing, made available by high-throughput approaches, allows detailed comparisons of the microbiome in health and disease. This is the first report of the striped dolphin microbiome in different body sites. Samples from one striped female edematous dolphin were acquired from a variety of body niches, including the blowhole, oral cavity, oral mucosa, tongue, stomach, intestines and genital mucosa. Detailed 16S rRNA analysis of over half a million sequences identified 235 OTUs. Beta diversity analyses indicated that microbial communities vary in structure and cluster by sample origin. Pathogenic, Gram-negative, facultative and obligate anaerobic taxa were significantly detected, including Cetobacterium, Fusobacterium and Ureaplasma. Phocoenobacter and Arcobacter dominated the oral-type samples, while Cardiobacteriaceae and Vibrio were associated with the blowhole and Photobacterium were abundant in the gut. We report for the first time the association of Epulopiscium with a marine mammal gut. The striped dolphin microbiota shows variation in structure and diversity according to the organ type. The high dominance of Gram-negative anaerobic pathogens evidences a cetacean microbiome affected by human-related bacteria.}, } @article {pmid27613488, year = {2017}, author = {Häfner, S}, title = {The last of the organs.}, journal = {Microbes and infection}, volume = {19}, number = {1}, pages = {1-4}, doi = {10.1016/j.micinf.2016.08.006}, pmid = {27613488}, issn = {1769-714X}, mesh = {Clostridioides difficile/isolation & purification ; Clostridium Infections/immunology/microbiology ; *Gastrointestinal Tract/immunology/microbiology ; Humans ; Hypersensitivity, Immediate/immunology/microbiology ; *Metagenome ; Metagenomics ; *Microbiota ; }, } @article {pmid27613296, year = {2017}, author = {Tessler, M and Brugler, MR and DeSalle, R and Hersch, R and Velho, LFM and Segovia, BT and Lansac-Toha, FA and Lemke, MJ}, title = {A Global eDNA Comparison of Freshwater Bacterioplankton Assemblages Focusing on Large-River Floodplain Lakes of Brazil.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {61-74}, pmid = {27613296}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/growth & development ; Biodiversity ; Brazil ; DNA, Bacterial/genetics ; Ecosystem ; Floods ; Lakes/*microbiology ; Plankton/*classification/genetics/growth & development ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; }, abstract = {With its network of lotic and lentic habitats that shift during changes in seasonal connection, the tropical and subtropical large-river systems represent possibly the most dynamic of all aquatic environments. Pelagic water samples were collected from Brazilian floodplain lakes (total n = 58) in four flood-pulsed systems (Amazon [n = 21], Araguaia [n = 14], Paraná [n = 15], and Pantanal [n = 8]) in 2011-2012 and sequenced via 454 for bacterial environmental DNA using 16S amplicons; additional abiotic field and laboratory measurements were collected for the assayed lakes. We report here a global comparison of the bacterioplankton makeup of freshwater systems, focusing on a comparison of Brazilian lakes with similar freshwater systems across the globe. The results indicate a surprising similarity at higher taxonomic levels of the bacterioplankton in Brazilian freshwater with global sites. However, substantial novel diversity at the family level was also observed for the Brazilian freshwater systems. Brazilian freshwater bacterioplankton richness was relatively average globally. Ordination results indicate that Brazilian bacterioplankton composition is unique from other areas of the globe. Using Brazil-only ordinations, floodplain system differentiation most strongly correlated with dissolved oxygen, pH, and phosphate. Our data on Brazilian freshwater systems in combination with analysis of a collection of freshwater environmental samples from across the globe offers the first regional picture of bacterioplankton diversity in these important freshwater systems.}, } @article {pmid27611571, year = {2016}, author = {Davison, M and Treangen, TJ and Koren, S and Pop, M and Bhaya, D}, title = {Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.}, journal = {PloS one}, volume = {11}, number = {9}, pages = {e0160574}, pmid = {27611571}, issn = {1932-6203}, support = {R01 HG004885/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteriophages/classification/genetics ; Biofilms ; Catalytic Domain/genetics ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Computational Biology/methods ; Endopeptidases/*genetics ; Environmental Microbiology ; Gene Targeting ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Molecular Sequence Annotation ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The polymicrobial biofilm communities in Mushroom and Octopus Spring in Yellowstone National Park (YNP) are well characterized, yet little is known about the phage populations. Dominant species, Synechococcus sp. JA-2-3B'a(2-13), Synechococcus sp. JA-3-3Ab, Chloroflexus sp. Y-400-fl, and Roseiflexus sp. RS-1, contain multiple CRISPR-Cas arrays, suggesting complex interactions with phage predators. To analyze phage populations from Octopus Spring biofilms, we sequenced a viral enriched fraction. To assemble and analyze phage metagenomic data, we developed a custom module, VIRITAS, implemented within the MetAMOS framework. This module bins contigs into groups based on tetranucleotide frequencies and CRISPR spacer-protospacer matching and ORF calling. Using this pipeline we were able to assemble phage sequences into contigs and bin them into three clusters that corroborated with their potential host range. The virome contained 52,348 predicted ORFs; some were clearly phage-like; 9319 ORFs had a recognizable Pfam domain while the rest were hypothetical. Of the recognized domains with CRISPR spacer matches, was the phage endolysin used by lytic phage to disrupt cells. Analysis of the endolysins present in the thermophilic cyanophage contigs revealed a subset of characterized endolysins as well as a Glyco_hydro_108 (PF05838) domain not previously associated with sequenced cyanophages. A search for CRISPR spacer matches to all identified phage endolysins demonstrated that a majority of endolysin domains were targets. This strategy provides a general way to link host and phage as endolysins are known to be widely distributed in bacteriophage. Endolysins can also provide information about host cell wall composition and have the additional potential to be used as targets for novel therapeutics.}, } @article {pmid27609714, year = {2016}, author = {Hahn, A and Sanyal, A and Perez, GF and Colberg-Poley, AM and Campos, J and Rose, MC and Pérez-Losada, M}, title = {Different next generation sequencing platforms produce different microbial profiles and diversity in cystic fibrosis sputum.}, journal = {Journal of microbiological methods}, volume = {130}, number = {}, pages = {95-99}, pmid = {27609714}, issn = {1872-8359}, support = {K12 HL119994/HL/NHLBI NIH HHS/United States ; UL1 TR000075/TR/NCATS NIH HHS/United States ; }, mesh = {Bacteria/*classification/*genetics/pathogenicity ; Base Sequence ; Biodiversity ; Classification ; Computational Biology/methods ; Cystic Fibrosis/*microbiology ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Lung/*microbiology ; Metagenome ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sputum/*microbiology ; }, abstract = {BACKGROUND: Cystic fibrosis (CF) is an autosomal recessive disease characterized by recurrent lung infections. Studies of the lung microbiome have shown an association between decreasing diversity and progressive disease. 454 pyrosequencing has frequently been used to study the lung microbiome in CF, but will no longer be supported. We sought to identify the benefits and drawbacks of using two state-of-the-art next generation sequencing (NGS) platforms, MiSeq and PacBio RSII, to characterize the CF lung microbiome. Each has its advantages and limitations.

METHODS: Twelve samples of extracted bacterial DNA were sequenced on both MiSeq and PacBio NGS platforms. DNA was amplified for the V4 region of the 16S rRNA gene and libraries were sequenced on the MiSeq sequencing platform, while the full 16S rRNA gene was sequenced on the PacBio RSII sequencing platform. Raw FASTQ files generated by the MiSeq and PacBio platforms were processed in mothur v1.35.1.

RESULTS: There was extreme discordance in alpha-diversity of the CF lung microbiome when using the two platforms. Because of its depth of coverage, sequencing of the 16S rRNA V4 gene region using MiSeq allowed for the observation of many more operational taxonomic units (OTUs) and higher Chao1 and Shannon indices than the PacBio RSII. Interestingly, several patients in our cohort had Escherichia, an unusual pathogen in CF. Also, likely because of its coverage of the complete 16S rRNA gene, only PacBio RSII was able to identify Burkholderia, an important CF pathogen.

CONCLUSION: When comparing microbiome diversity in clinical samples from CF patients using 16S sequences, MiSeq and PacBio NGS platforms may generate different results in microbial community composition and structure. It may be necessary to use different platforms when trying to correctly identify dominant pathogens versus measuring alpha-diversity estimates, and it would be important to use the same platform for comparisons to minimize errors in interpretation.}, } @article {pmid27608918, year = {2016}, author = {Gao, G and Zhao, X and Li, Q and He, C and Zhao, W and Liu, S and Ding, J and Ye, W and Wang, J and Chen, Y and Wang, H and Li, J and Luo, Y and Su, J and Huang, Y and Liu, Z and Dai, R and Shi, Y and Meng, H and Wang, Q}, title = {Genome and metagenome analyses reveal adaptive evolution of the host and interaction with the gut microbiota in the goose.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {32961}, pmid = {27608918}, issn = {2045-2322}, mesh = {*Adaptation, Biological ; Animals ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Geese/*genetics/microbiology ; Genomics ; Metabolic Networks and Pathways/genetics ; Metagenomics ; Symbiosis ; }, abstract = {The goose is an economically important waterfowl that exhibits unique characteristics and abilities, such as liver fat deposition and fibre digestion. Here, we report de novo whole-genome assemblies for the goose and swan goose and describe the evolutionary relationships among 7 bird species, including domestic and wild geese, which diverged approximately 3.4~6.3 million years ago (Mya). In contrast to chickens as a proximal species, the expanded and rapidly evolving genes found in the goose genome are mainly involved in metabolism, including energy, amino acid and carbohydrate metabolism. Further integrated analysis of the host genome and gut metagenome indicated that the most widely shared functional enrichment of genes occurs for functions such as glycolysis/gluconeogenesis, starch and sucrose metabolism, propanoate metabolism and the citrate cycle. We speculate that the unique physiological abilities of geese benefit from the adaptive evolution of the host genome and symbiotic interactions with gut microbes.}, } @article {pmid27607552, year = {2016}, author = {Bull, AT and Asenjo, JA and Goodfellow, M and Gómez-Silva, B}, title = {The Atacama Desert: Technical Resources and the Growing Importance of Novel Microbial Diversity.}, journal = {Annual review of microbiology}, volume = {70}, number = {}, pages = {215-234}, doi = {10.1146/annurev-micro-102215-095236}, pmid = {27607552}, issn = {1545-3251}, mesh = {Bacteria/classification/genetics/*isolation & purification/metabolism ; *Biodiversity ; Chile ; Desert Climate ; Ecosystem ; Environment ; }, abstract = {The Atacama Desert of northern Chile is the oldest and most arid nonpolar environment on Earth. It is a coastal desert covering approximately 180,000 km(2), and together with the greater Atacama region it comprises a dramatically wide range of ecological niches. Long known and exploited for its mineral resources, the Atacama Desert harbors a rich microbial diversity that has only recently been discovered; the great majority of it has not yet been recovered in culture or even taxonomically identified. This review traces the progress of microbiology research in the Atacama and dispels the popular view that this region is virtually devoid of life. We examine reasons for such research activity and demonstrate that microbial life is the latest recognized and least explored resource in this inspiring biome.}, } @article {pmid27607550, year = {2016}, author = {Rascovan, N and Duraisamy, R and Desnues, C}, title = {Metagenomics and the Human Virome in Asymptomatic Individuals.}, journal = {Annual review of microbiology}, volume = {70}, number = {}, pages = {125-141}, doi = {10.1146/annurev-micro-102215-095431}, pmid = {27607550}, issn = {1545-3251}, mesh = {Asymptomatic Diseases ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; *Microbiota ; Virus Diseases/classification/*genetics/*virology ; Viruses/genetics/*isolation & purification/metabolism ; }, abstract = {High-throughput sequencing technologies have revolutionized how we think about viruses. Investigators can now go beyond pathogenic viruses and have access to the thousands of viruses that inhabit our bodies without causing clinical symptoms. By studying their interactions with each other, with other microbes, and with host genetics and immune systems, we can learn how they affect health and disease. This article reviews current knowledge of the composition and diversity of the human virome in physiologically healthy individuals. It focuses on recent results from metagenomics studies and discusses the contribution of bacteriophages and eukaryotic viruses to human health.}, } @article {pmid27604252, year = {2016}, author = {Duranti, S and Gaiani, F and Mancabelli, L and Milani, C and Grandi, A and Bolchi, A and Santoni, A and Lugli, GA and Ferrario, C and Mangifesta, M and Viappiani, A and Bertoni, S and Vivo, V and Serafini, F and Barbaro, MR and Fugazza, A and Barbara, G and Gioiosa, L and Palanza, P and Cantoni, AM and de'Angelis, GL and Barocelli, E and de'Angelis, N and van Sinderen, D and Ventura, M and Turroni, F}, title = {Elucidating the gut microbiome of ulcerative colitis: bifidobacteria as novel microbial biomarkers.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {12}, pages = {}, doi = {10.1093/femsec/fiw191}, pmid = {27604252}, issn = {1574-6941}, mesh = {Animals ; Bifidobacterium/genetics/immunology/*isolation & purification ; Biomarkers ; Colitis, Ulcerative/chemically induced/*microbiology ; Dysbiosis/*microbiology ; Female ; Fimbriae, Bacterial/*immunology ; Gastrointestinal Microbiome/genetics/*immunology ; Humans ; Intestinal Mucosa/*microbiology/pathology ; Mice ; Mice, Inbred BALB C ; Probiotics ; RNA, Ribosomal, 16S/genetics ; T-Lymphocytes/immunology ; }, abstract = {Ulcerative colitis (UC) is associated with a substantial alteration of specific gut commensals, some of which may be involved in microbiota-mediated protection. In this study, microbiota cataloging of UC patients by 16S rRNA microbial profiling revealed a marked reduction of bifidobacteria, in particular the Bifidobacterium bifidum species, thus suggesting that this taxon plays a biological role in the aetiology of UC. We investigated this further through an in vivo trial by testing the effects of oral treatment with B. bifidum PRL2010 in a wild-type murine colitis model. TNBS-treated mice receiving 10(9) cells of B. bifidum PRL2010 showed a marked reduction of all colitis-associated histological indices as well as maintenance of mucosal integrity as it was shown by the increase in the expression of many tight junction-encoding genes. The protective role of B. bifidum PRL2010, as well as its sortase-dependent pili, appears to be established through the induction of an innate immune response of the host. These results highlight the importance of B. bifidum as a microbial biomarker for UC, revealing its role in protection against experimentally induced colitis.}, } @article {pmid27599587, year = {2016}, author = {Hartmann, EM and Hickey, R and Hsu, T and Betancourt Román, CM and Chen, J and Schwager, R and Kline, J and Brown, GZ and Halden, RU and Huttenhower, C and Green, JL}, title = {Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome.}, journal = {Environmental science & technology}, volume = {50}, number = {18}, pages = {9807-9815}, pmid = {27599587}, issn = {1520-5851}, support = {R01 ES020889/ES/NIEHS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; *Anti-Infective Agents ; Drug Resistance, Microbial/genetics ; Dust ; Humans ; Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Antibiotic resistance is increasingly widespread, largely due to human influence. Here, we explore the relationship between antibiotic resistance genes and the antimicrobial chemicals triclosan, triclocarban, and methyl-, ethyl-, propyl-, and butylparaben in the dust microbiome. Dust samples from a mixed-use athletic and educational facility were subjected to microbial and chemical analyses using a combination of 16S rRNA amplicon sequencing, shotgun metagenome sequencing, and liquid chromatography tandem mass spectrometry. The dust resistome was characterized by identifying antibiotic resistance genes annotated in the Comprehensive Antibiotic Resistance Database (CARD) from the metagenomes of each sample using the Short, Better Representative Extract Data set (ShortBRED). The three most highly abundant antibiotic resistance genes were tet(W), blaSRT-1, and erm(B). The complete dust resistome was then compared against the measured concentrations of antimicrobial chemicals, which for triclosan ranged from 0.5 to 1970 ng/g dust. We observed six significant positive associations between the concentration of an antimicrobial chemical and the relative abundance of an antibiotic resistance gene, including one between the ubiquitous antimicrobial triclosan and erm(X), a 23S rRNA methyltransferase implicated in resistance to several antibiotics. This study is the first to look for an association between antibiotic resistance genes and antimicrobial chemicals in dust.}, } @article {pmid27585583, year = {2016}, author = {Szczepaniak, Z and Czarny, J and Staninska-Pięta, J and Lisiecki, P and Zgoła-Grześkowiak, A and Cyplik, P and Chrzanowski, Ł and Wolko, Ł and Marecik, R and Juzwa, W and Glazar, K and Piotrowska-Cyplik, A}, title = {Influence of soil contamination with PAH on microbial community dynamics and expression level of genes responsible for biodegradation of PAH and production of rhamnolipids.}, journal = {Environmental science and pollution research international}, volume = {23}, number = {22}, pages = {23043-23056}, pmid = {27585583}, issn = {1614-7499}, mesh = {Bacteria/metabolism ; Biodegradation, Environmental ; Gene Expression ; Glycolipids/*metabolism ; Microbial Consortia/*drug effects ; Polycyclic Aromatic Hydrocarbons/metabolism/*toxicity ; Soil ; *Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {The aim of this study was to evaluate the effect of bioaugmentation and addition of rhamnolipids on the biodegradation of PAHs in artificially contaminated soil, expression of genes crucial for the biodegradation process (PAHRHDαGN, PAHRHDαGP), and the synthesis of rhamnolipids as well as population changes in the soil bacterial metabiome. The positive effect of bioaugmentation and addition of rhamnolipids on the bioremediation of the majority of PAHs was confirmed during the early stages of treatment, especially in case of the most structurally complicated compounds. The results of metagenomic analysis indicated that the initial changes in the soil metabiome caused by bioaugmentation diminished after 3 months and that the community structure in treated soil was similar to control. The survival period of bacteria introduced into the soil via bioaugmentation reached a maximum of 3 months. The increased expression of genes observed after addition of PAH into the soil also returned to the initial conditions after 3 months.}, } @article {pmid27583441, year = {2016}, author = {Zhou, S and Xu, R and He, F and Zhou, J and Wang, Y and Zhou, J and Wang, M and Zhou, W}, title = {Diversity of Gut Microbiota Metabolic Pathways in 10 Pairs of Chinese Infant Twins.}, journal = {PloS one}, volume = {11}, number = {9}, pages = {e0161627}, pmid = {27583441}, issn = {1932-6203}, mesh = {Aging/metabolism ; *Asian People ; *Biodiversity ; Carcinoma, Renal Cell/metabolism/microbiology ; Child ; Child, Preschool ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Kidney Neoplasms/metabolism/microbiology ; Male ; *Metabolic Networks and Pathways ; Metagenome ; Prion Diseases/metabolism/microbiology ; *Twins, Dizygotic ; *Twins, Monozygotic ; }, abstract = {Early colonization of gut microbiota in human gut is a complex process. It remains unclear when gut microbiota colonization occurs and how it proceeds. In order to study gut microbiota composition in human early life, the present study recruited 10 healthy pairs of twins, including five monozygotic (MZ) and five dizygotic (DZ) twin pairs, whose age ranged from 0 to 6 years old. 20 fecal samples from these twins were processed by shotgun metagenomic sequencing, and their averaged data outputs were generated as 2G per sample. We used MEGAN5 to perform taxonomic and functional annotation of the metagenomic data, and systematically analyzed those 20 samples, including Jaccard index similarity, principle component, clustering, and correlation analyses. Our findings indicated that within our study group: 1) MZ-twins share more microbes than DZ twins or non-twin pairs, 2) gut microbiota distribution is relatively stable at metabolic pathways level, 3) age represents the strongest factor that can account for variation in gut microbiota, and 4) a clear metabolic pathway shift can be observed, which speculatively occurs around the age of 1 year old. This research will serve as a base for future studies of gut microbiota-related disease research.}, } @article {pmid27581036, year = {2017}, author = {Wolińska, A and Kuźniar, A and Zielenkiewicz, U and Banach, A and Izak, D and Stępniewska, Z and Błaszczyk, M}, title = {Metagenomic Analysis of Some Potential Nitrogen-Fixing Bacteria in Arable Soils at Different Formation Processes.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {162-176}, pmid = {27581036}, issn = {1432-184X}, mesh = {Agriculture ; Biodiversity ; Cyanobacteria/*classification/genetics/*isolation & purification ; Metagenome/genetics ; Nitrogen-Fixing Bacteria/*classification/genetics/*metabolism ; Poland ; Proteobacteria/*classification/genetics/*isolation & purification ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The main goal of the study was to determine the diversity of the potential nitrogen-fixing (PNF) bacteria inhabiting agricultural (A) soils versus wastelands serving as controls (C). The soils were classified into three groups based on the formation process: autogenic soils (Albic Luvisols, Brunic Arenosols, Haplic Phaeozem) formed on loess material, hydrogenic soils (Mollic Gleysols, Eutric Fluvisol, Eutric Histosol) formed under the effect of stagnant water and lithogenic soils (Rendzina Leptosols) formed on limestone. In order to determine the preferable conditions for PNF bacteria, the relationships between the soil chemical features and bacterial operational taxonomic units (OTUs) were tested. Additionally, the nitrogen content and fertilisation requirement of the lithogenic (LG), autogenic (AG) and hydrogenic (HG) soils were discussed. The composition of the bacterial communities was analysed with the next-generation sequencing (NGS) by the Ion Torrent™ technology. The sequences were clustered into OTU based on a 99 % similarity threshold. The arable soils tested were distinctly dominated by β-Proteobacteria representatives of PNF bacteria belonging to the genus Burkholderia. Bacteria from the α-Proteobacteria class and Devosia genus were subdominants. A free-living Cyanobacteria population dominated in A rather than in C soils. We have found that both soil agricultural management and soil formation processes are the most conducive factors for PNF bacteria, as a majority of these microorganisms inhabit the AG group of soils, whilst the LG soils with the lowest abundance of PNF bacteria revealed the need for additional mineral fertilisation. Our studies have also indicated that there are close relationships between soil classification with respect to soil formation processes and PNF bacteria preference for occupation of soil niches.}, } @article {pmid27578483, year = {2016}, author = {Zhang, J and Wang, X and Huo, D and Li, W and Hu, Q and Xu, C and Liu, S and Li, C}, title = {Metagenomic approach reveals microbial diversity and predictive microbial metabolic pathways in Yucha, a traditional Li fermented food.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {32524}, pmid = {27578483}, issn = {2045-2322}, mesh = {Animals ; China ; Clostridium/classification/genetics/isolation & purification/metabolism ; Enterococcus/classification/genetics/isolation & purification/metabolism ; Fermented Foods/*microbiology ; Fishes ; Food Microbiology ; Humans ; Lactobacillus/classification/genetics/isolation & purification/*metabolism ; Metabolic Networks and Pathways/*genetics ; *Metagenomics ; Microbiota/genetics ; Oryza ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Weissella/classification/genetics/isolation & purification/metabolism ; }, abstract = {Yucha is a typical traditional fermented food of the Li population in the Hainan province of China, and it is made up of cooked rice and fresh fish. In the present study, metagenomic approach and culture-dependent technology were applied to describe the diversity of microbiota and identify beneficial microbes in the Yucha. At the genus level, Lactobacillus was the most abundant genus (43.82% of the total reads), followed by Lactococcus, Enterococcus, Vibrio, Weissella, Pediococcus, Enterobacter, Salinivibrio, Acinetobacter, Macrococcus, Kluyvera and Clostridium; this result was confirmed by q-PCR. PCoA based on Weighted UniFrac distances showed an apparent clustering pattern for Yucha samples from different locations, and Lactobacillus sakei, Lactobacillus saniviri and Staphylococcus sciuri represented OTUs according to the major identified markers. At the microbial functional level, it was observed that there was an enrichment of metabolic functional features, including amino acid and carbohydrate metabolism, which implied that the microbial metabolism in the Yucha samples tended to be vigorous. Accordingly, we further investigated the correlation between the predominant microbes and metabolic functional features. Thirteen species of Lactobacillus (147 strains) were isolated, and Lactobacillus plantarum (60 isolates) and Lactobacillus pentosus (34 isolates) were isolated from every sample.}, } @article {pmid27577966, year = {2016}, author = {Cummings, ME and Barbé, D and Leao, TF and Korobeynikov, A and Engene, N and Glukhov, E and Gerwick, WH and Gerwick, L}, title = {A novel uncultured heterotrophic bacterial associate of the cyanobacterium Moorea producens JHB.}, journal = {BMC microbiology}, volume = {16}, number = {1}, pages = {198}, pmid = {27577966}, issn = {1471-2180}, support = {R01 CA108874/CA/NCI NIH HHS/United States ; R01 GM107550/GM/NIGMS NIH HHS/United States ; }, mesh = {Acidobacteria/classification/genetics ; Base Sequence ; Coculture Techniques ; Cyanobacteria/*classification/*genetics/metabolism ; DNA, Bacterial/genetics ; Genome, Bacterial ; Heterotrophic Processes ; Marine Biology ; Metagenomics ; Microbial Consortia ; Microscopy, Electron, Transmission ; Nitrates/metabolism ; Nitrogen/metabolism ; Phylogeny ; Polysaccharides, Bacterial/metabolism ; Proteogenomics ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {BACKGROUND: Filamentous tropical marine cyanobacteria such as Moorea producens strain JHB possess a rich community of heterotrophic bacteria on their polysaccharide sheaths; however, these bacterial communities have not yet been adequately studied or characterized.

RESULTS AND DISCUSSION: Through efforts to sequence the genome of this cyanobacterial strain, the 5.99 MB genome of an unknown bacterium emerged from the metagenomic information, named here as Mor1. Analysis of its genome revealed that the bacterium is heterotrophic and belongs to the phylum Acidobacteria, subgroup 22; however, it is only 85 % identical to the nearest cultured representative. Comparative genomics further revealed that Mor1 has a large number of genes involved in transcriptional regulation, is completely devoid of transposases, is not able to synthesize the full complement of proteogenic amino acids and appears to lack genes for nitrate uptake. Mor1 was found to be present in lab cultures of M. producens collected from various locations, but not other cyanobacterial species. Diverse efforts failed to culture the bacterium separately from filaments of M. producens JHB. Additionally, a co-culturing experiment between M. producens JHB possessing Mor1 and cultures of other genera of cyanobacteria indicated that the bacterium was not transferable.

CONCLUSION: The data presented support a specific relationship between this novel uncultured bacterium and M. producens, however, verification of this proposed relationship cannot be done until the "uncultured" bacterium can be cultured.}, } @article {pmid27573828, year = {2016}, author = {Manrique, P and Bolduc, B and Walk, ST and van der Oost, J and de Vos, WM and Young, MJ}, title = {Healthy human gut phageome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {37}, pages = {10400-10405}, pmid = {27573828}, issn = {1091-6490}, support = {R01 GM117361/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophages/classification/genetics/*isolation & purification ; Computational Biology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/microbiology ; Humans ; Inflammatory Bowel Diseases/genetics/*microbiology ; *Metagenomics ; Microbiota/genetics ; }, abstract = {The role of bacteriophages in influencing the structure and function of the healthy human gut microbiome is unknown. With few exceptions, previous studies have found a high level of heterogeneity in bacteriophages from healthy individuals. To better estimate and identify the shared phageome of humans, we analyzed a deep DNA sequence dataset of active bacteriophages and available metagenomic datasets of the gut bacteriophage community from healthy individuals. We found 23 shared bacteriophages in more than one-half of 64 healthy individuals from around the world. These shared bacteriophages were found in a significantly smaller percentage of individuals with gastrointestinal/irritable bowel disease. A network analysis identified 44 bacteriophage groups of which 9 (20%) were shared in more than one-half of all 64 individuals. These results provide strong evidence of a healthy gut phageome (HGP) in humans. The bacteriophage community in the human gut is a mixture of three classes: a set of core bacteriophages shared among more than one-half of all people, a common set of bacteriophages found in 20-50% of individuals, and a set of bacteriophages that are either rarely shared or unique to a person. We propose that the core and common bacteriophage communities are globally distributed and comprise the HGP, which plays an important role in maintaining gut microbiome structure/function and thereby contributes significantly to human health.}, } @article {pmid27573446, year = {2016}, author = {Tauzin, AS and Laville, E and Xiao, Y and Nouaille, S and Le Bourgeois, P and Heux, S and Portais, JC and Monsan, P and Martens, EC and Potocki-Veronese, G and Bordes, F}, title = {Functional characterization of a gene locus from an uncultured gut Bacteroides conferring xylo-oligosaccharides utilization to Escherichia coli.}, journal = {Molecular microbiology}, volume = {102}, number = {4}, pages = {579-592}, doi = {10.1111/mmi.13480}, pmid = {27573446}, issn = {1365-2958}, support = {R01 GM090080/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Outer Membrane Proteins/metabolism ; Bacteroides/*genetics/*metabolism ; Escherichia coli/*genetics/*metabolism ; Feces/microbiology ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Glycoside Hydrolases/metabolism ; Humans ; Membrane Transport Proteins/metabolism ; Oligosaccharides/metabolism ; Polysaccharides/metabolism ; Symbiosis ; Xylosidases/metabolism ; }, abstract = {In prominent gut Bacteroides strains, sophisticated strategies have been evolved to achieve the complete degradation of dietary polysaccharides such as xylan, which is one of the major components of the plant cell wall. Polysaccharide Utilization Loci (PULs) consist of gene clusters encoding different proteins with a vast arsenal of functions, including carbohydrate binding, transport and hydrolysis. Transport is often attributed to TonB-dependent transporters, although major facilitator superfamily (MFS) transporters have also been identified in some PULs. However, until now, few of these transporters have been biochemically characterized. Here, we targeted a PUL-like system from an uncultivated Bacteroides species that is highly prevalent in the human gut metagenome. It encodes three glycoside-hydrolases specific for xylo-oligosaccharides, a SusC/SusD tandem homolog and a MFS transporter. We combined PUL rational engineering, metabolic and transcriptional analysis in Escherichia coli to functionally characterize this genomic locus. We demonstrated that the SusC and the MFS transporters are specific for internalization of linear xylo-oligosaccharides of polymerization degree up to 3 and 4 respectively. These results were strengthened by the study of growth dynamics and transcriptional analyses in response to XOS induction of the PUL in the native strain, Bacteroides vulgatus.}, } @article {pmid27573112, year = {2016}, author = {Vilanova, C and Porcar, M}, title = {Are multi-omics enough?.}, journal = {Nature microbiology}, volume = {1}, number = {8}, pages = {16101}, pmid = {27573112}, issn = {2058-5276}, mesh = {Bacteria/*classification/*genetics/metabolism ; Biodiversity ; Computational Biology ; Gene Expression Profiling ; Humans ; *Metagenomics ; *Proteomics ; Transcriptome/*genetics ; }, } @article {pmid27573110, year = {2016}, author = {Vieira-Silva, S and Falony, G and Darzi, Y and Lima-Mendez, G and Garcia Yunta, R and Okuda, S and Vandeputte, D and Valles-Colomer, M and Hildebrand, F and Chaffron, S and Raes, J}, title = {Species-function relationships shape ecological properties of the human gut microbiome.}, journal = {Nature microbiology}, volume = {1}, number = {8}, pages = {16088}, pmid = {27573110}, issn = {2058-5276}, mesh = {*Ecosystem ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Metabolic Networks and Pathways/*genetics ; Metagenomics ; *Microbiota ; }, abstract = {Despite recent progress, the organization and ecological properties of the intestinal microbial ecosystem remain under-investigated. Here, using a manually curated metabolic module framework for (meta-)genomic data analysis, we studied species-function relationships in gut microbial genomes and microbiomes. Half of gut-associated species were found to be generalists regarding overall substrate preference, but we observed significant genus-level metabolic diversification linked to bacterial life strategies. Within each genus, metabolic consistency varied significantly, being low in Firmicutes genera and higher in Bacteroides. Differentiation of fermentable substrate degradation potential contributed to metagenomic functional repertoire variation between individuals, with different enterotypes showing distinct saccharolytic/proteolytic/lipolytic profiles. Finally, we found that module-derived functional redundancy was reduced in the low-richness Bacteroides enterotype, potentially indicating a decreased resilience to perturbation, in line with its frequent association to dysbiosis. These results provide insights into the complex structure of gut microbiome-encoded metabolic properties and emphasize the importance of functional and ecological assessment of gut microbiome variation in clinical studies.}, } @article {pmid27572971, year = {2016}, author = {Donati, C and Zolfo, M and Albanese, D and Tin Truong, D and Asnicar, F and Iebba, V and Cavalieri, D and Jousson, O and De Filippo, C and Huttenhower, C and Segata, N}, title = {Uncovering oral Neisseria tropism and persistence using metagenomic sequencing.}, journal = {Nature microbiology}, volume = {1}, number = {7}, pages = {16070}, pmid = {27572971}, issn = {2058-5276}, support = {R01 HG005969/HG/NHGRI NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; }, mesh = {Computers, Molecular ; Genome, Bacterial ; Gingiva/microbiology ; Humans ; *Metagenome ; Metagenomics/methods ; Microbiota ; Mouth/*microbiology ; Multilocus Sequence Typing ; Neisseria/classification/genetics/isolation & purification/*physiology ; Pharynx/microbiology ; Phylogeny ; Polymorphism, Single Nucleotide ; *Sequence Analysis, DNA ; Tongue/microbiology ; *Viral Tropism ; }, abstract = {Microbial epidemiology and population genomics have previously been carried out near-exclusively for organisms grown in vitro. Metagenomics helps to overcome this limitation, but it is still challenging to achieve strain-level characterization of microorganisms from culture-independent data with sufficient resolution for epidemiological modelling. Here, we have developed multiple complementary approaches that can be combined to profile and track individual microbial strains. To specifically profile highly recombinant neisseriae from oral metagenomes, we integrated four metagenomic analysis techniques: single nucleotide polymorphisms in the clade's core genome, DNA uptake sequence signatures, metagenomic multilocus sequence typing and strain-specific marker genes. We applied these tools to 520 oral metagenomes from the Human Microbiome Project, finding evidence of site tropism and temporal intra-subject strain retention. Although the opportunistic pathogen Neisseria meningitidis is enriched for colonization in the throat, N. flavescens and N. subflava populate the tongue dorsum, and N. sicca, N. mucosa and N. elongata the gingival plaque. The buccal mucosa appeared as an intermediate ecological niche between the plaque and the tongue. The resulting approaches to metagenomic strain profiling are generalizable and can be extended to other organisms and microbiomes across environments.}, } @article {pmid27572648, year = {2016}, author = {Jansson, JK and Baker, ES}, title = {A multi-omic future for microbiome studies.}, journal = {Nature microbiology}, volume = {1}, number = {}, pages = {16049}, pmid = {27572648}, issn = {2058-5276}, mesh = {*Gene Expression Profiling ; Humans ; *Metabolomics ; *Metagenomics ; *Microbiota ; *Proteomics ; }, } @article {pmid27572443, year = {2016}, author = {Gibson, MK and Wang, B and Ahmadi, S and Burnham, CA and Tarr, PI and Warner, BB and Dantas, G}, title = {Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome.}, journal = {Nature microbiology}, volume = {1}, number = {}, pages = {16024}, pmid = {27572443}, issn = {2058-5276}, support = {P30 DK052574/DK/NIDDK NIH HHS/United States ; R01 GM099538/GM/NIGMS NIH HHS/United States ; UH3 AI083265/AI/NIAID NIH HHS/United States ; UL1 TR000448/TR/NCATS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*therapeutic use ; *Drug Resistance, Bacterial ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/*microbiology ; Genes, Bacterial ; Humans ; Infant, Premature ; Longitudinal Studies ; Sequence Analysis, DNA ; }, abstract = {Development of the preterm infant gut microbiota is emerging as a critical research priority(1). Since preterm infants almost universally receive early and often extended antibiotic therapy(2), it is important to understand how these interventions alter gut microbiota development(3-6). Analysis of 401 stools from 84 longitudinally sampled preterm infants demonstrates that meropenem, cefotaxime and ticarcillin-clavulanate are associated with significantly reduced species richness. In contrast, vancomycin and gentamicin, the antibiotics most commonly administered to preterm infants, have non-uniform effects on species richness, but these can be predicted with 85% accuracy based on the relative abundance of only two bacterial species and two antibiotic resistance (AR) genes at treatment initiation. To investigate resistome development, we functionally selected resistance to 16 antibiotics from 21 faecal metagenomic expression libraries. Of the 794 AR genes identified, 79% had not previously been classified as AR genes. Combined with deep shotgun sequencing of all stools, we find that multidrug-resistant members of the genera Escherichia, Klebsiella and Enterobacter, genera commonly associated with nosocomial infections, dominate the preterm infant gut microbiota. AR genes that are enriched following specific antibiotic treatments are generally unique to the specific treatment and are highly correlated with the abundance of a single species. The most notable exceptions include ticarcillin-clavulanate and ampicillin, both of which enrich for a large number of overlapping AR genes, and are correlated with Klebsiella pneumoniae. We find that all antibiotic treatments are associated with widespread collateral microbiome impact by enrichment of AR genes that have no known activity against the specific antibiotic driver.}, } @article {pmid27572438, year = {2016}, author = {Eloe-Fadrosh, EA and Ivanova, NN and Woyke, T and Kyrpides, NC}, title = {Metagenomics uncovers gaps in amplicon-based detection of microbial diversity.}, journal = {Nature microbiology}, volume = {1}, number = {}, pages = {15032}, pmid = {27572438}, issn = {2058-5276}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; *Biodiversity ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Metagenome ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Our view of microbial diversity has expanded greatly over the past 40 years, primarily through the wide application of PCR-based surveys of the small-subunit ribosomal RNA (SSU rRNA) gene. Yet significant gaps in knowledge remain due to well-recognized limitations of this method. Here, we systematically survey primer fidelity in SSU rRNA gene sequences recovered from over 6,000 assembled metagenomes sampled globally. Our findings show that approximately 10% of environmental microbial sequences might be missed from classical PCR-based SSU rRNA gene surveys, mostly members of the Candidate Phyla Radiation (CPR) and as yet uncharacterized Archaea. These results underscore the extent of uncharacterized microbial diversity and provide fruitful avenues for describing additional phylogenetic lineages.}, } @article {pmid27571981, year = {2016}, author = {Schimel, J}, title = {Microbial ecology: Linking omics to biogeochemistry.}, journal = {Nature microbiology}, volume = {1}, number = {}, pages = {15028}, pmid = {27571981}, issn = {2058-5276}, mesh = {*Ecology ; *Ecosystem ; Metagenomics ; Microbial Consortia ; Proteomics ; }, } @article {pmid27571759, year = {2016}, author = {Stulberg, E and Fravel, D and Proctor, LM and Murray, DM and LoTempio, J and Chrisey, L and Garland, J and Goodwin, K and Graber, J and Harris, MC and Jackson, S and Mishkind, M and Porterfield, DM and Records, A}, title = {An assessment of US microbiome research.}, journal = {Nature microbiology}, volume = {1}, number = {}, pages = {15015}, pmid = {27571759}, issn = {2058-5276}, mesh = {Biomedical Research/methods/*trends ; *Biota ; Capital Financing ; Computational Biology/methods ; Humans ; Metagenomics/methods ; Microbiological Techniques/standards ; Microbiology/*trends ; United States ; }, abstract = {Genome-enabled technologies have supported a dramatic increase in our ability to study microbial communities in environments and hosts. Taking stock of previously funded microbiome research can help to identify common themes, under-represented areas and research priorities to consider moving forward. To assess the status of US microbiome research, a team of government scientists conducted an analysis of federally funded microbiome research. Microbiomes were defined as host-, ecosystem- or habitat-associated communities of microorganisms, and microbiome research was defined as those studies that emphasize community-level analyses using 'omics technologies. Single pathogen, single strain and culture-based studies were not included, except symbiosis studies that served as models for more complex communities. Fourteen governmental organizations participated in the data call. The analysis examined three broad research themes, eight environments and eight microbial categories. Human microbiome research was larger than any other environment studied, and the basic biology research theme accounted for half of the total research activities. Computational biology and bioinformatics, reference databases and biorepositories, standardized protocols and high-throughput tools were commonly identified needs. Longitudinal and functional studies and interdisciplinary research were also identified as needs. This study has implications for the funding of future microbiome research, not only in the United States but beyond.}, } @article {pmid27570125, year = {2017}, author = {Verma, P and Raghavan, RV and Jeon, CO and Lee, HJ and Priya, PV and Dharani, G and Kirubagaran, R}, title = {Complex bacterial communities in the deep-sea sediments of the Bay of Bengal and volcanic Barren Island in the Andaman Sea.}, journal = {Marine genomics}, volume = {31}, number = {}, pages = {33-41}, doi = {10.1016/j.margen.2016.08.003}, pmid = {27570125}, issn = {1876-7478}, mesh = {Bacteria/*genetics ; *Biodiversity ; DNA, Bacterial/genetics ; Geologic Sediments/*microbiology ; India ; Islands ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Deep-sea environments are gaining global attention as potential sources of useful microorganisms, thereby warranting a better understanding of the diversity and genomic potential of the microbes present. To this end, here we provide the first insights into the composition of the bacterial communities in deep-sea sediment samples from the southwestern Bay of Bengal and the geographically distinct volcanic Barren Island in the Andaman Sea. High-throughput 16S rRNA gene sequencing of the sediments revealed the presence of >44,000 operational taxonomic units (OTUs) in each of the samples, suggesting high bacterial diversity. Actinobacteria was the most dominant phylum, representing >20% of the taxonomically assignable OTUs, followed by Firmicutes, Proteobacteria, and Chloroflexi. Numerous bacteria that are potentially involved in the sulfur cycle were observed in the Barren Island sediment sample, while bacteria with clinical and industrial potential were observed in the samples from the southwestern Bay of Bengal. Correlation analysis of the biotic and abiotic parameters showed that the differences in bacterial richness and community composition between the sampling sites were mainly dependent on sediment texture. Using a predictive functional metagenomic approach, this study also discusses the genetic variations that may provide an adaptive advantage to sediment bacterial communities for survival in these extreme deep-sea environments. The results from this study should aid future studies focused on bioprospecting and geochemical cycling in the deep sea.}, } @article {pmid27566512, year = {2016}, author = {Weerasekara, AW and Jenkins, S and Abbott, LK and Waite, I and McGrath, JW and Larma, I and Eroglu, E and O'Donnell, A and Whiteley, AS}, title = {Microbial phylogenetic and functional responses within acidified wastewater communities exhibiting enhanced phosphate uptake.}, journal = {Bioresource technology}, volume = {220}, number = {}, pages = {55-61}, doi = {10.1016/j.biortech.2016.08.037}, pmid = {27566512}, issn = {1873-2976}, mesh = {Betaproteobacteria/genetics ; Gammaproteobacteria/genetics/metabolism ; High-Throughput Nucleotide Sequencing ; Hydrogen-Ion Concentration ; Kinetics ; Microbial Consortia/genetics/*physiology ; Phosphorus/metabolism ; *Phylogeny ; Polyphosphates/*metabolism ; Ponds ; Wastewater/*chemistry/*microbiology ; Western Australia ; }, abstract = {Acid stimulated accumulation of insoluble phosphorus within microbial cells is highly beneficial to wastewater treatment but remains largely unexplored. Using single cell analyses and next generation sequencing, the response of active polyphosphate accumulating microbial communities under conditions of enhanced phosphorus uptake under both acidic and aerobic conditions was characterised. Phosphorus accumulation activities were highest under acidic conditions (pH 5.5>8.5), where a significant positive effect on bioaccumulation was observed at pH 5.5 when compared to pH 8.5. In contrast to the Betaproteobacteria and Actinobacteria dominated enhanced biological phosphorus removal process, the functionally active polyP accumulators at pH 5.5 belonged to the Gammaproteobacteria, with key accumulators identified as members of the families Aeromonadaceae and Enterobacteriaceae. This study demonstrated a significant enrichment of key polyphosphate kinase and exopolyphosphatase genes within the community metagenome after acidification, concomitant with an increase in P accumulation kinetics.}, } @article {pmid27565581, year = {2016}, author = {Sampaio-Maia, B and Simões-Silva, L and Pestana, M and Araujo, R and Soares-Silva, IJ}, title = {The Role of the Gut Microbiome on Chronic Kidney Disease.}, journal = {Advances in applied microbiology}, volume = {96}, number = {}, pages = {65-94}, doi = {10.1016/bs.aambs.2016.06.002}, pmid = {27565581}, issn = {0065-2164}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Renal Insufficiency, Chronic/*microbiology ; }, abstract = {Chronic kidney disease (CKD) is estimated to affect nearly 500 million people worldwide and cardiovascular (CV) disease is a major cause of death in this population. However, therapeutic interventions targeting traditional CV risks are not effective at lowering the incidence of CV events or at delaying the progression of the disease in CKD patients. In recent years, disturbances of normal gut microbiome were recognized in the pathogenesis of diverse chronic diseases. Gut dysbiosis is being unraveled in CKD and pointed as a nontraditional risk factor for CV risk and CKD progression. The most often reported changes in gut microbiome in CKD are related to the lower levels of Bifidobacteriaceae and Lactobacillaceae and to higher levels of Enterobacteriaceae. Although metagenomics brought us an amplified vision on the microbial world that inhabits the human host, it still lacks the sensitivity to characterize the microbiome up to species level, not revealing alterations that occur within specific genus. Here, we review the current state-of-the-art concerning gut dysbiosis in CKD and its role in pathophysiological mechanisms in CKD, particularly in relation with CV risk. Also, the strategies towards prevention and treatment of gut dysbiosis in CKD progression will be discussed.}, } @article {pmid27565341, year = {2016}, author = {Nayfach, S and Pollard, KS}, title = {Toward Accurate and Quantitative Comparative Metagenomics.}, journal = {Cell}, volume = {166}, number = {5}, pages = {1103-1116}, pmid = {27565341}, issn = {1097-4172}, support = {R21 AI108953/AI/NIAID NIH HHS/United States ; T32 GM067547/GM/NIGMS NIH HHS/United States ; }, mesh = {Classification ; Computational Biology ; Humans ; *Metagenome ; Metagenomics/*standards ; Microbiota/*genetics ; Models, Statistical ; }, abstract = {Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized.}, } @article {pmid27562258, year = {2016}, author = {Chng, KR and Tay, AS and Li, C and Ng, AH and Wang, J and Suri, BK and Matta, SA and McGovern, N and Janela, B and Wong, XF and Sio, YY and Au, BV and Wilm, A and De Sessions, PF and Lim, TC and Tang, MB and Ginhoux, F and Connolly, JE and Lane, EB and Chew, FT and Common, JE and Nagarajan, N}, title = {Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare.}, journal = {Nature microbiology}, volume = {1}, number = {9}, pages = {16106}, pmid = {27562258}, issn = {2058-5276}, mesh = {Adaptive Immunity ; Adult ; Animals ; Dendritic Cells/pathology ; Dermatitis, Atopic/immunology/*microbiology ; Disease Susceptibility ; Female ; Humans ; Interleukin-1/immunology ; Male ; *Metagenome ; Metagenomics ; Mice, Inbred C57BL ; Microbiota/*genetics ; Skin/immunology ; Staphylococcal Infections/immunology/*microbiology ; Staphylococcus aureus/*immunology ; Staphylococcus epidermidis/*immunology ; Young Adult ; }, abstract = {Whole metagenome analysis has the potential to reveal functional triggers of skin diseases, but issues of cost, robustness and sampling efficacy have limited its application. Here, we have established an alternative, clinically practical and robust metagenomic analysis protocol and applied it to 80 skin microbiome samples epidemiologically stratified for atopic dermatitis (AD). We have identified distinct non-flare, baseline skin microbiome signatures enriched for Streptococcus and Gemella but depleted for Dermacoccus in AD-prone versus normal healthy skin. Bacterial challenge assays using keratinocytes and monocyte-derived dendritic cells established distinct IL-1-mediated, innate and Th1-mediated adaptive immune responses with Staphylococcus aureus and Staphylococcus epidermidis. Bacterial differences were complemented by perturbations in the eukaryotic community and functional shifts in the microbiome-wide gene repertoire, which could exacerbate a dry and alkaline phenotype primed for pathogen growth and inflammation in AD-susceptible skin. These findings provide insights into how the skin microbial community, skin surface microenvironment and immune system cross-modulate each other, escalating the destructive feedback cycle between them that leads to AD flare.}, } @article {pmid27559117, year = {2016}, author = {von Wintersdorff, CJ and Wolffs, PF and van Niekerk, JM and Beuken, E and van Alphen, LB and Stobberingh, EE and Oude Lashof, AM and Hoebe, CJ and Savelkoul, PH and Penders, J}, title = {Detection of the plasmid-mediated colistin-resistance gene mcr-1 in faecal metagenomes of Dutch travellers.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {12}, pages = {3416-3419}, doi = {10.1093/jac/dkw328}, pmid = {27559117}, issn = {1460-2091}, mesh = {Adult ; Africa, Southern ; Aged ; Anti-Bacterial Agents/*pharmacology ; Asia, Southeastern ; Colistin/*pharmacology ; *Drug Resistance, Bacterial ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome ; *Genes, Bacterial ; Humans ; Male ; *Metagenomics ; Middle Aged ; Netherlands ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Travel ; Young Adult ; }, abstract = {BACKGROUND: Recently, the first plasmid-mediated colistin-resistance gene, mcr-1, was reported. Colistin is increasingly used as an antibiotic of last resort for the treatment of infections caused by carbapenem-resistant bacteria, which have been rapidly disseminating worldwide in recent years.

OBJECTIVES: The reported carriage rate of mcr-1 in humans remains sporadic thus far, except for those reported in Chinese populations. We aimed to determine its presence in the faecal metagenomes of healthy Dutch travellers between 2010 and 2012.

METHODS: Faecal metagenomic DNA of pre- and post-travel samples from 122 healthy Dutch long-distance travellers was screened for the presence of mcr-1 using a TaqMan quantitative PCR assay, which was designed in this study. All positive samples were confirmed by sequencing of the amplicons.

RESULTS: The mcr-1 gene was detected in 6 (4.9%, 95% CI = 2.1%-10.5%) of 122 healthy Dutch long-distance travellers after they had visited destinations in South(-east) Asia or southern Africa between 2011 and 2012. One of these participants was already found to be positive before travel.

CONCLUSIONS: Our study highlights the potential of PCR-based targeted metagenomics as an unbiased and sensitive method to screen for the carriage of the mcr-1 gene and suggests that mcr-1 is widespread in various parts of the world. The observation that one participant was found to be positive before travel suggests that mcr-1 may already have disseminated to the microbiomes of Dutch residents at a low prevalence, warranting a more extensive investigation of its prevalence in the general population and possible sources.}, } @article {pmid27559027, year = {2016}, author = {Santiago-Rodriguez, TM and Fornaciari, G and Luciani, S and Dowd, SE and Toranzos, GA and Marota, I and Cano, RJ}, title = {Taxonomic and predicted metabolic profiles of the human gut microbiome in pre-Columbian mummies.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {11}, pages = {}, doi = {10.1093/femsec/fiw182}, pmid = {27559027}, issn = {1574-6941}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Adult ; Bacillales/*isolation & purification ; Chagas Disease/diagnosis ; Clostridiales/classification/genetics/*isolation & purification ; DNA, Bacterial/genetics ; DNA, Protozoan/genetics ; Female ; Firmicutes/*isolation & purification ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Leishmania donovani/genetics/*isolation & purification ; Male ; Metabolome/genetics ; Metagenome/genetics ; Metagenomics/methods ; Mummies/*microbiology ; RNA, Ribosomal, 16S/genetics ; Trypanosoma cruzi/genetics/*isolation & purification ; Young Adult ; }, abstract = {Characterization of naturally mummified human gut remains could potentially provide insights into the preservation and evolution of commensal and pathogenic microorganisms, and metabolic profiles. We characterized the gut microbiome of two pre-Columbian Andean mummies dating to the 10-15th centuries using 16S rRNA gene high-throughput sequencing and metagenomics, and compared them to a previously characterized gut microbiome of an 11th century AD pre-Columbian Andean mummy. Our previous study showed that the Clostridiales represented the majority of the bacterial communities in the mummified gut remains, but that other microbial communities were also preserved during the process of natural mummification, as shown with the metagenomics analyses. The gut microbiome of the other two mummies were mainly comprised by Clostridiales or Bacillales, as demonstrated with 16S rRNA gene amplicon sequencing, many of which are facultative anaerobes, possibly consistent with the process of natural mummification requiring low oxygen levels. Metagenome analyses showed the presence of other microbial groups that were positively or negatively correlated with specific metabolic profiles. The presence of sequences similar to both Trypanosoma cruzi and Leishmania donovani could suggest that these pathogens were prevalent in pre-Columbian individuals. Taxonomic and functional profiling of mummified human gut remains will aid in the understanding of the microbial ecology of the process of natural mummification.}, } @article {pmid27558582, year = {2016}, author = {Magalhães, MJ and Pontes, G and Serra, PT and Balieiro, A and Castro, D and Pieri, FA and Crainey, JL and Nogueira, PA and Orlandi, PP}, title = {Multidrug resistant Pseudomonas aeruginosa survey in a stream receiving effluents from ineffective wastewater hospital plants.}, journal = {BMC microbiology}, volume = {16}, number = {1}, pages = {193}, pmid = {27558582}, issn = {1471-2180}, mesh = {Amikacin/pharmacology ; Ampicillin/pharmacology ; Anti-Bacterial Agents/pharmacology ; Biodiversity ; Biofilms ; Brazil ; DNA Fingerprinting ; Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Hospitals ; Microbial Sensitivity Tests ; Pseudomonas aeruginosa/*drug effects/*isolation & purification/physiology ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Wastewater/*microbiology ; }, abstract = {BACKGROUND: Multi-drug resistant forms of Pseudomonas aeruginosa (MDRPA) are a major source of nosocomial infections and when discharged into streams and rivers from hospital wastewater treatment plants (HWWTP) they are known to be able to persist for extended periods. In the city of Manaus (Western Brazilian Amazon), the effluent of three HWWTPs feed into the urban Mindu stream which crosses the city from its rainforest source before draining into the Rio Negro. The stream is routinely used by Manaus residents for bathing and cleaning (of clothes as well as domestic utensils) and, during periods of flooding, can contaminate wells used for drinking water.

RESULTS: 16S rRNA metagenomic sequence analysis of 293 cloned PCR fragments, detected an abundance of Pseudomonas aeruginosa (P. aeruginosa) at the stream's Rio Negro drainage site, but failed to detect it at the stream's source. An array of antimicrobial resistance profiles and resistance to all 14 tested antimicrobials was detected among P. aeruginosa cultures prepared from wastewater samples taken from water entering and being discharged from a Manaus HWWTP. Just one P. aeruginosa antimicrobial resistance profile, however, was detected from cultures made from Mindu stream isolates. Comparisons made between P. aeruginosa isolates' genomic DNA restriction enzyme digest fingerprints, failed to determine if any of the P. aeruginosa found in the Mindu stream were of HWWTP origin, but suggested that Mindu stream P. aeruginosa are from diverse origins. Culturing experiments also showed that P. aeruginosa biofilm formation and the extent of biofilm formation produced were both significantly higher in multi drug resistant forms of P. aeruginosa.

CONCLUSIONS: Our results show that a diverse range of MDRPA are being discharged in an urban stream from a HWWTP in Manaus and that P. aeruginosa strains with ampicillin and amikacin can persist well within it.}, } @article {pmid27558434, year = {2016}, author = {Wu, Y and Zhao, C and Xiao, Z and Lin, H and Ruan, L and Liu, B}, title = {Metagenomic and Proteomic Analyses of a Mangrove Microbial Community Following Green Macroalgae Enteromorpha prolifera Degradation.}, journal = {Journal of microbiology and biotechnology}, volume = {26}, number = {12}, pages = {2127-2137}, doi = {10.4014/jmb.1607.07025}, pmid = {27558434}, issn = {1738-8872}, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; Biodegradation, Environmental ; Biodiversity ; Metagenomics ; Proteomics ; Seaweed/metabolism/*microbiology ; Ulva/metabolism/*microbiology ; Wetlands ; }, abstract = {A mangrove microbial community was analyzed at the gene and protein levels using metagenomic and proteomic methods with the green macroalgae Enteromorpha prolifera as the substrate. Total DNA was sequenced on the Illumina HiSeq 2000 PE-100 platform. Two-dimensional gel electrophoresis in combination with liquid chromatography tandem mass spectrometry was used for proteomic analysis. The metagenomic data revealed that the orders Pseudomonadales, Rhizobiales, and Sphingomonadales were the most prevalent in the mangrove microbial community. By monitoring changes at the functional level, proteomic analyses detected ATP synthase and transporter proteins, which were expressed mainly by members of the phyla Proteobacteria and Bacteroidetes. Members of the phylum Proteobacteria expressed a high number of sugar transporters and demonstrated specialized and efficient digestion of various glycans. A few glycoside hydrolases were detected in members of the phylum Firmicutes, which appeared to be the main cellulose-degrading bacteria. This is the first report of multiple "omics" analysis of E. prolifera degradation. These results support the fact that key enzymes of glycoside hydrolase family were expressed in large quantities, indicating the high metabolic activity of the community.}, } @article {pmid27555581, year = {2016}, author = {Zhou, X and Meng, X and Liu, Z and Chang, J and Wang, B and Li, M and Wengel, PO and Tian, S and Wen, C and Wang, Z and Garber, PA and Pan, H and Ye, X and Xiang, Z and Bruford, MW and Edwards, SV and Cao, Y and Yu, S and Gao, L and Cao, Z and Liu, G and Ren, B and Shi, F and Peterfi, Z and Li, D and Li, B and Jiang, Z and Li, J and Gladyshev, VN and Li, R and Li, M}, title = {Population Genomics Reveals Low Genetic Diversity and Adaptation to Hypoxia in Snub-Nosed Monkeys.}, journal = {Molecular biology and evolution}, volume = {33}, number = {10}, pages = {2670-2681}, doi = {10.1093/molbev/msw150}, pmid = {27555581}, issn = {1537-1719}, mesh = {Acclimatization/genetics ; Adaptation, Biological/genetics ; Adaptation, Physiological/*genetics ; Animals ; Base Sequence ; Colobinae/*genetics ; Ecosystem ; Genetic Variation ; Hypoxia/genetics/metabolism/*veterinary ; Metagenomics/methods ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA/veterinary ; }, abstract = {Snub-nosed monkeys (genus Rhinopithecus) are a group of endangered colobines endemic to South Asia. Here, we re-sequenced the whole genomes of 38 snub-nosed monkeys representing four species within this genus. By conducting population genomic analyses, we observed a similar load of deleterious variation in snub-nosed monkeys living in both smaller and larger populations and found that genomic diversity was lower than that reported in other primates. Reconstruction of Rhinopithecus evolutionary history suggested that episodes of climatic variation over the past 2 million years, associated with glacial advances and retreats and population isolation, have shaped snub-nosed monkey demography and evolution. We further identified several hypoxia-related genes under selection in R. bieti (black snub-nosed monkey), a species that exploits habitats higher than any other nonhuman primate. These results provide the first detailed and comprehensive genomic insights into genetic diversity, demography, genetic burden, and adaptation in this radiation of endangered primates.}, } @article {pmid27554980, year = {2016}, author = {Lai, KP and Chung, YT and Li, R and Wan, HT and Wong, CK}, title = {Bisphenol A alters gut microbiome: Comparative metagenomics analysis.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {218}, number = {}, pages = {923-930}, doi = {10.1016/j.envpol.2016.08.039}, pmid = {27554980}, issn = {1873-6424}, mesh = {Animals ; Benzhydryl Compounds/pharmacokinetics/*toxicity ; Clostridium/genetics/growth & development ; Diet, High-Fat/*adverse effects ; Environmental Pollutants/pharmacokinetics/*toxicity ; Gastrointestinal Microbiome/*genetics ; Heliconiaceae/genetics/growth & development ; Intestinal Mucosa/metabolism ; Intestines/drug effects/*microbiology ; Liver/metabolism ; Male ; Metagenomics/*methods ; Mice ; Microbiota/genetics ; Phenols/pharmacokinetics/*toxicity ; Proteobacteria/genetics/growth & development ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Mounting evidence has shown that an alteration of the gut microbiota is associated with diet, and plays an important role in animal health and metabolic diseases. However, little is known about the influence of environmental contaminants on the gut microbial community. Bisphenol A (BPA), which is widely used for manufacturing plastic products, has recently been classified as an environmental obesogen. Although many studies have demonstrated the metabolic-disrupting effects of BPA on liver and pancreatic functions, the possible effects of this synthetic compound on the metabolic diversity of the intestinal microbiota is unknown. Using 16S rRNA gene sequencing analysis on caecum samples of CD-1 mice, the present study aimed to test the hypothesis that dietary BPA intake may influence the gut microbiota composition and functions, an important attributing factor to development of the metabolic syndrome. A high-fat diet (HFD) and high-sucrose diet (HSD) were included as the positive controls for comparing the changes in the intestinal microbial profiles. Our results demonstrated a significant reduction of species diversity in the gut microbiota of BPA-fed mice. Alpha and beta diversity analyses showed that dietary BPA intake led to a similar gut microbial community structure as that induced by HFD and HSD in mice. In addition, comparative analysis of the microbial communities revealed that both BPA and a HFD favored the growth of Proteobacteria, a microbial marker of dysbiosis. Consistently, growth induction of the family Helicobacteraceae and reduction of the Firmicutes and Clostridia populations were observed in the mice fed BPA or a HFD. Collectively, our study highlighted that the effects of dietary BPA intake on the shift of microbial community structure were similar to those of a HFD and HSD, and revealed microbial markers for the development of diseases associated with an unstable microbiota.}, } @article {pmid27554344, year = {2016}, author = {Igai, K and Itakura, M and Nishijima, S and Tsurumaru, H and Suda, W and Tsutaya, T and Tomitsuka, E and Tadokoro, K and Baba, J and Odani, S and Natsuhara, K and Morita, A and Yoneda, M and Greenhill, AR and Horwood, PF and Inoue, J and Ohkuma, M and Hongoh, Y and Yamamoto, T and Siba, PM and Hattori, M and Minamisawa, K and Umezaki, M}, title = {Nitrogen fixation and nifH diversity in human gut microbiota.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {31942}, pmid = {27554344}, issn = {2045-2322}, mesh = {Acetylene/chemistry/metabolism ; Adult ; Bacterial Proteins/classification/genetics/*metabolism ; Clostridiales/enzymology/genetics/isolation & purification ; Databases, Factual ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Klebsiella/enzymology/genetics/isolation & purification ; Male ; Metagenomics ; Nitrogen/chemistry/*metabolism ; Nitrogen Fixation ; Nitrogen Isotopes/metabolism ; Oxidoreductases/classification/genetics/*metabolism ; Phylogeny ; RNA, Bacterial/chemistry/isolation & purification/metabolism ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {It has been hypothesized that nitrogen fixation occurs in the human gut. However, whether the gut microbiota truly has this potential remains unclear. We investigated the nitrogen-fixing activity and diversity of the nitrogenase reductase (NifH) genes in the faecal microbiota of humans, focusing on Papua New Guinean and Japanese individuals with low to high habitual nitrogen intake. A (15)N2 incorporation assay showed significant enrichment of (15)N in all faecal samples, irrespective of the host nitrogen intake, which was also supported by an acetylene reduction assay. The fixed nitrogen corresponded to 0.01% of the standard nitrogen requirement for humans, although our data implied that the contribution in the gut in vivo might be higher than this value. The nifH genes recovered in cloning and metagenomic analyses were classified in two clusters: one comprising sequences almost identical to Klebsiella sequences and the other related to sequences of Clostridiales members. These results are consistent with an analysis of databases of faecal metagenomes from other human populations. Collectively, the human gut microbiota has a potential for nitrogen fixation, which may be attributable to Klebsiella and Clostridiales strains, although no evidence was found that the nitrogen-fixing activity substantially contributes to the host nitrogen balance.}, } @article {pmid27554148, year = {2016}, author = {Bal, J and Yun, SH and Yeo, SH and Kim, JM and Kim, DH}, title = {Metagenomic analysis of fungal diversity in Korean traditional wheat-based fermentation starter nuruk.}, journal = {Food microbiology}, volume = {60}, number = {}, pages = {73-83}, doi = {10.1016/j.fm.2016.07.002}, pmid = {27554148}, issn = {1095-9998}, mesh = {Alcoholic Beverages/*microbiology ; *Fermentation ; Food Microbiology ; Fungi/*genetics/physiology ; *Genetic Variation ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Microbial Consortia ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Temperature ; Triticum/microbiology ; }, abstract = {Nuruk, a traditional natural starter, is extensively used in the brewing of Makgeolli, one of Korea's most popular alcoholic beverages that has been recently gaining global popularity. Thus, the quality of traditional nuruk needs to be enhanced. The nuruk mycobiome greatly influences both fermentation process as well as palatability enhancement. Limitations of culture-dependent identification restrict an accurate analysis of fungal diversity and distribution in nuruks. 454 pyrosequencing of two traditional wheat-based nuruks, prepared at two representative temperature conditions revealed a total of 153 and 53 OTUs for nuruks A and B, respectively, from a total of 33,157 ITS sequences. Phylogenetic assignments indicated that nuruk A mycobiota was dominated by the genera Aspergillus and Mucorales, whereas nuruk B by Rhizomucor. Species-level identification indicated that Mucorales sp., Aspergillus candidus, and Aspergillus cibarius predominated in nuruk A mycoflora whereas Rhizomucor pusillus, Mucorales sp., and Thermoascus crustaceus in nuruk B. The alpha diversity indices suggest nuruk A mycobiota to be more diverse than that of nuruk B at almost all time points of fermentation. Resemblances of patterns of predominant species composition and succession between culture-dependent and -independent phylogenetic analysis creates the potential to reconstruct the nuruk mycobiome in vitro, which allows the establishment of a standard inoculum for scientific comparison.}, } @article {pmid27554147, year = {2016}, author = {Silbande, A and Adenet, S and Smith-Ravin, J and Joffraud, JJ and Rochefort, K and Leroi, F}, title = {Quality assessment of ice-stored tropical yellowfin tuna (Thunnus albacares) and influence of vacuum and modified atmosphere packaging.}, journal = {Food microbiology}, volume = {60}, number = {}, pages = {62-72}, doi = {10.1016/j.fm.2016.06.016}, pmid = {27554147}, issn = {1095-9998}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Brochothrix/genetics/isolation & purification ; Colony Count, Microbial ; Consumer Product Safety ; Food Microbiology ; Food Packaging/*standards ; Food Storage/methods/*standards ; Genes, rRNA ; Histamine/analysis ; Ice ; Metagenomics ; Microbiota/genetics/physiology ; Nitrogen/analysis ; Quality Control ; RNA, Ribosomal, 16S/genetics ; Seafood/analysis/*microbiology ; Taste ; Tuna/*microbiology ; Vacuum ; }, abstract = {Metagenomic, microbial, chemical and sensory analyses of Thunnus albacares from Martinique stored in ice (AIR - 0 °C), vacuum (VP - 4/8 °C) and modified atmosphere packaging (MAP - 4/8 °C) (70% CO2 - 30% O2) were carried out. The organoleptic rejection of AIR tuna was observed at day 13 when total bacterial counts equaled 10(6)-10(7) CFU g(-1). No extension of shelf-life was provided by VP and MAP. According to 16S rRNA gene sequence analyzed by Illumina MiSeq and PCR-TTGE, Rhodanobacter terrae was the main species of the freshly caught tuna. At the sensory rejection time, Brochothrix thermosphacta and Pseudomonas dominated the AIR products while B. thermosphacta alone or a mix of B. thermosphacta, Enterobacteriaceae and lactic acid bacteria (LAB) dominated the microbiota of MAP and VP products, respectively. The pH value remained stable in all trials, ranging from 5.77 to 5.97. Total volatile basic nitrogen (TVBN) and trimethylamine (TMA-N) concentrations were weak and not significantly different between batches. Lipid oxidation increased in the samples containing O2 (MAP > AIR). The initial concentration of histamine was high (75-78 mg kg(-1)) and stable up to 8 days but then significantly decreased in all trials to reach 25-30 mg kg(-1), probably due to the presence of histamine-decomposing bacteria.}, } @article {pmid27553882, year = {2016}, author = {Yang, C and Schaefer, DA and Liu, W and Popescu, VD and Yang, C and Wang, X and Wu, C and Yu, DW}, title = {Higher fungal diversity is correlated with lower CO2 emissions from dead wood in a natural forest.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {31066}, pmid = {27553882}, issn = {2045-2322}, mesh = {*Biota ; Carbon Dioxide/*metabolism ; China ; DNA Barcoding, Taxonomic ; Forests ; Fungi/*classification/genetics/*metabolism ; Metagenomics ; Wood/*microbiology ; }, abstract = {Wood decomposition releases almost as much CO2 to the atmosphere as does fossil-fuel combustion, so the factors regulating wood decomposition can affect global carbon cycling. We used metabarcoding to estimate the fungal species diversities of naturally colonized decomposing wood in subtropical China and, for the first time, compared them to concurrent measures of CO2 emissions. Wood hosting more diverse fungal communities emitted less CO2, with Shannon diversity explaining 26 to 44% of emissions variation. Community analysis supports a 'pure diversity' effect of fungi on decomposition rates and thus suggests that interference competition is an underlying mechanism. Our findings extend the results of published experiments using low-diversity, laboratory-inoculated wood to a high-diversity, natural system. We hypothesize that high levels of saprotrophic fungal biodiversity could be providing globally important ecosystem services by maintaining dead-wood habitats and by slowing the atmospheric contribution of CO2 from the world's stock of decomposing wood. However, large-scale surveys and controlled experimental tests in natural settings will be needed to test this hypothesis.}, } @article {pmid27551796, year = {2016}, author = {Iyer, N}, title = {Methods in microbiome research.}, journal = {Lab animal}, volume = {45}, number = {9}, pages = {323-326}, pmid = {27551796}, issn = {1548-4475}, mesh = {Germ-Free Life ; Humans ; Metagenomics/methods ; Microbiota/*genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA/methods ; }, } @article {pmid27551280, year = {2016}, author = {Stubbendieck, RM and Vargas-Bautista, C and Straight, PD}, title = {Bacterial Communities: Interactions to Scale.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1234}, pmid = {27551280}, issn = {1664-302X}, abstract = {In the environment, bacteria live in complex multispecies communities. These communities span in scale from small, multicellular aggregates to billions or trillions of cells within the gastrointestinal tract of animals. The dynamics of bacterial communities are determined by pairwise interactions that occur between different species in the community. Though interactions occur between a few cells at a time, the outcomes of these interchanges have ramifications that ripple through many orders of magnitude, and ultimately affect the macroscopic world including the health of host organisms. In this review we cover how bacterial competition influences the structures of bacterial communities. We also emphasize methods and insights garnered from culture-dependent pairwise interaction studies, metagenomic analyses, and modeling experiments. Finally, we argue that the integration of multiple approaches will be instrumental to future understanding of the underlying dynamics of bacterial communities.}, } @article {pmid27550859, year = {2016}, author = {Liu, L and Zhao, X and Wang, Q and Sun, X and Xia, L and Wang, Q and Yang, B and Zhang, Y and Montgomery, S and Meng, H and Geng, T and Gong, D}, title = {Prosteatotic and Protective Components in a Unique Model of Fatty Liver: Gut Microbiota and Suppressed Complement System.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {31763}, pmid = {27550859}, issn = {2045-2322}, mesh = {Animals ; Complement System Proteins/*metabolism ; Fatty Liver/*metabolism ; *Gastrointestinal Microbiome ; Geese ; Gene Expression Regulation ; Hepatocyte Nuclear Factor 1-alpha/metabolism ; Inflammation ; Lactic Acid/blood ; Lactobacillus/genetics/*metabolism ; Liver/metabolism ; Metagenome ; MicroRNAs/metabolism ; Transcriptome ; Tumor Necrosis Factor-alpha/metabolism ; }, abstract = {Goose can develop severe hepatic steatosis without overt injury, thus it may serve as a unique model for uncovering how steatosis-related injury is prevented. To identify the markedly prosteatotic and protective mechanisms, we performed an integrated analysis of liver transcriptomes and gut microbial metagenomes using samples collected from overfed and normally-fed geese at different time points. The results indicated that the fatty liver transcriptome, initially featuring a 'metabolism' pathway, was later joined by 'cell growth and death' and 'immune diseases' pathways. Gut microbiota played a synergistic role in the liver response as microbial and hepatic genes affected by overfeeding shared multiple pathways. Remarkably, the complement system, an inflammatory component, was comprehensively suppressed in fatty liver, which was partially due to increased blood lactic acid from enriched Lactobacillus. Data from in vitro studies suggested that lactic acid suppressed TNFα via the HNF1α/C5 pathway. In conclusion, gut microbes and their hosts respond to excess energy influx as an organic whole, severe steatosis and related tolerance of goose liver may be partially attributable to gut microbiotic products and suppressed complement system, and lactic acid from gut microbiota participates in the suppression of hepatic TNFα/inflammation through the HNF1α/C5 pathway.}, } @article {pmid27548380, year = {2016}, author = {Walter, JM and Tschoeke, DA and Meirelles, PM and de Oliveira, L and Leomil, L and Tenório, M and Valle, R and Salomon, PS and Thompson, CC and Thompson, FL}, title = {Taxonomic and Functional Metagenomic Signature of Turfs in the Abrolhos Reef System (Brazil).}, journal = {PloS one}, volume = {11}, number = {8}, pages = {e0161168}, pmid = {27548380}, issn = {1932-6203}, mesh = {Ammonia/metabolism ; Animals ; Anthozoa/physiology ; Bacteroidetes ; Biodiversity ; Brazil ; Coral Reefs ; Cyanobacteria/classification/*genetics/metabolism ; DNA Barcoding, Taxonomic ; DNA, Bacterial/*genetics ; *Metagenomics ; Microbial Consortia/genetics ; Microbiota/*genetics ; Nitrogen/metabolism ; Photosynthesis ; *Phylogeny ; Pigments, Biological/biosynthesis ; Principal Component Analysis ; Proteobacteria/classification/*genetics/metabolism ; Seawater/microbiology ; Sulfonium Compounds/metabolism ; Sulfur/metabolism ; }, abstract = {Turfs are widespread assemblages (consisting of microbes and algae) that inhabit reef systems. They are the most abundant benthic component in the Abrolhos reef system (Brazil), representing greater than half the coverage of the entire benthic community. Their presence is associated with a reduction in three-dimensional coral reef complexity and decreases the habitats available for reef biodiversity. Despite their importance, the taxonomic and functional diversity of turfs remain unclear. We performed a metagenomics and pigments profile characterization of turfs from the Abrolhos reefs. Turf microbiome primarily encompassed Proteobacteria (mean 40.57% ± s.d. 10.36, N = 1.548,192), Cyanobacteria (mean 35.04% ± s.d. 15.5, N = 1.337,196), and Bacteroidetes (mean 11.12% ± s.d. 4.25, N = 424,185). Oxygenic and anoxygenic phototrophs, chemolithotrophs, and aerobic anoxygenic phototrophic (AANP) bacteria showed a conserved functional trait of the turf microbiomes. Genes associated with oxygenic photosynthesis, AANP, sulfur cycle (S oxidation, and DMSP consumption), and nitrogen metabolism (N2 fixation, ammonia assimilation, dissimilatory nitrate and nitrite ammonification) were found in the turf microbiomes. Principal component analyses of the most abundant taxa and functions showed that turf microbiomes differ from the other major Abrolhos benthic microbiomes (i.e., corals and rhodoliths) and seawater. Taken together, these features suggest that turfs have a homogeneous functional core across the Abrolhos Bank, which holds diverse microbial guilds when comparing with other benthic organisms.}, } @article {pmid27542753, year = {2016}, author = {Gkanogiannis, A and Gazut, S and Salanoubat, M and Kanj, S and Brüls, T}, title = {A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes.}, journal = {BMC bioinformatics}, volume = {17}, number = {1}, pages = {311}, pmid = {27542753}, issn = {1471-2105}, mesh = {*Algorithms ; Biomarkers/*chemistry ; Datasets as Topic ; Humans ; *Metagenome ; *Metagenomics ; Microbiota/*genetics ; }, abstract = {BACKGROUND: Metagenomics holds great promises for deepening our knowledge of key bacterial driven processes, but metagenome assembly remains problematic, typically resulting in representation biases and discarding significant amounts of non-redundant sequence information. In order to alleviate constraints assembly can impose on downstream analyses, and/or to increase the fraction of raw reads assembled via targeted assemblies relying on pre-assembly binning steps, we developed a set of binning modules and evaluated their combination in a new "assembly-free" binning protocol.

RESULTS: We describe a scalable multi-tiered binning algorithm that combines frequency and compositional features to cluster unassembled reads, and demonstrate i) significant runtime performance gains of the developed modules against state of the art software, obtained through parallelization and the efficient use of large lock-free concurrent hash maps, ii) its relevance for clustering unassembled reads from high complexity (e.g., harboring 700 distinct genomes) samples, iii) its relevance to experimental setups involving multiple samples, through a use case consisting in the "de novo" identification of sequences from a target genome (e.g., a pathogenic strain) segregating at low levels in a cohort of 50 complex microbiomes (harboring 100 distinct genomes each), in the background of closely related strains and the absence of reference genomes, iv) its ability to correctly identify clusters of sequences from the E. coli O104:H4 genome as the most strongly correlated to the infection status in 53 microbiomes sampled from the 2011 STEC outbreak in Germany, and to accurately cluster contigs of this pathogenic strain from a cross-assembly of these 53 microbiomes.

CONCLUSIONS: We present a set of sequence clustering ("binning") modules and their application to biomarker (e.g., genomes of pathogenic organisms) discovery from large synthetic and real metagenomics datasets. Initially designed for the "assembly-free" analysis of individual metagenomic samples, we demonstrate their extension to setups involving multiple samples via the usage of the "alignment-free" d2S statistic to relate clusters across samples, and illustrate how the clustering modules can otherwise be leveraged for de novo "pre-assembly" tasks by segregating sequences into biologically meaningful partitions.}, } @article {pmid27542127, year = {2016}, author = {Opstelten, JL and Plassais, J and van Mil, SW and Achouri, E and Pichaud, M and Siersema, PD and Oldenburg, B and Cervino, AC}, title = {Gut Microbial Diversity Is Reduced in Smokers with Crohn's Disease.}, journal = {Inflammatory bowel diseases}, volume = {22}, number = {9}, pages = {2070-2077}, pmid = {27542127}, issn = {1536-4844}, mesh = {Adult ; Bacteria/*classification/isolation & purification ; Case-Control Studies ; Crohn Disease/*microbiology ; DNA, Bacterial/genetics ; Feces/chemistry/microbiology ; Female ; France ; *Gastrointestinal Microbiome ; Humans ; Leukocyte L1 Antigen Complex/analysis ; Male ; Netherlands ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Smoking/*adverse effects ; }, abstract = {BACKGROUND: Smoking has a negative impact on Crohn's disease (CD), but the mechanisms underlying this association are unclear. We compared the gut microbiota composition of smoking with nonsmoking patients with CD using a metagenomic approach.

METHODS: Stool samples and clinical data were collected from current smokers and nonsmokers with CD from France and the Netherlands, matched for country, gender, age, disease activity, and body mass index. Fecal DNA was sequenced on an Illumina HiSeq 2500. On average, 40 million paired-end reads were generated per sample. Gene richness and the Shannon index were computed to assess microbial diversity. Wilcoxon's signed-rank tests for paired samples were performed to detect differences between the 2 groups.

RESULTS: In total, 21 smoking and 21 nonsmoking patients with CD were included. Compared with nonsmoking patients, gut microbial gene richness (P = 0.01), genus diversity (P < 0.01), and species diversity (P = 0.01) were decreased in smoking patients. This was accompanied by a reduced relative abundance of the genera Collinsella (P = 0.02), Enterorhabdus (P = 0.02), and Gordonibacter (P = 0.02) in smokers. No statistically significant differences at the species level were observed, although smokers had lower proportions of Faecalibacterium prausnitzii (P = 0.10).

CONCLUSIONS: Gut microbial diversity is reduced in smokers with CD compared with nonsmokers with CD. The microbial profile differs between these groups at the genus level. Future studies should evaluate whether intestinal microbes mediate the adverse effects of smoking in CD.}, } @article {pmid27533034, year = {2016}, author = {Paez-Espino, D and Eloe-Fadrosh, EA and Pavlopoulos, GA and Thomas, AD and Huntemann, M and Mikhailova, N and Rubin, E and Ivanova, NN and Kyrpides, NC}, title = {Uncovering Earth's virome.}, journal = {Nature}, volume = {536}, number = {7617}, pages = {425-430}, pmid = {27533034}, issn = {1476-4687}, mesh = {Animals ; Aquatic Organisms/virology ; Bacteriophages/genetics ; Biodiversity ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; DNA, Viral/analysis/genetics ; Datasets as Topic ; *Earth, Planet ; *Ecosystem ; Genes, Viral ; Genome, Viral/*genetics ; Host Specificity ; Host-Pathogen Interactions ; Humans ; Metagenome/genetics ; *Metagenomics ; Phylogeny ; Phylogeography ; RNA, Transfer/genetics ; Sequence Analysis ; Viruses/classification/*genetics/isolation & purification ; }, abstract = {Viruses are the most abundant biological entities on Earth, but challenges in detecting, isolating, and classifying unknown viruses have prevented exhaustive surveys of the global virome. Here we analysed over 5 Tb of metagenomic sequence data from 3,042 geographically diverse samples to assess the global distribution, phylogenetic diversity, and host specificity of viruses. We discovered over 125,000 partial DNA viral genomes, including the largest phage yet identified, and increased the number of known viral genes by 16-fold. Half of the predicted partial viral genomes were clustered into genetically distinct groups, most of which included genes unrelated to those in known viruses. Using CRISPR spacers and transfer RNA matches to link viral groups to microbial host(s), we doubled the number of microbial phyla known to be infected by viruses, and identified viruses that can infect organisms from different phyla. Analysis of viral distribution across diverse ecosystems revealed strong habitat-type specificity for the vast majority of viruses, but also identified some cosmopolitan groups. Our results highlight an extensive global viral diversity and provide detailed insight into viral habitat distribution and host–virus interactions.}, } @article {pmid27530840, year = {2016}, author = {Jitwasinkul, T and Suriyaphol, P and Tangphatsornruang, S and Hansen, MA and Hansen, LH and Sørensen, SJ and Permpikul, C and Rongrungruang, Y and Tribuddharat, C}, title = {Plasmid metagenomics reveals multiple antibiotic resistance gene classes among the gut microbiomes of hospitalised patients.}, journal = {Journal of global antimicrobial resistance}, volume = {6}, number = {}, pages = {57-66}, doi = {10.1016/j.jgar.2016.03.001}, pmid = {27530840}, issn = {2213-7173}, mesh = {Animals ; Anti-Bacterial Agents ; Cattle ; Drug Resistance, Multiple, Bacterial/*genetics ; *Gastrointestinal Microbiome ; *Genes, Bacterial ; Humans ; Inpatients ; Metagenomics ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Sequence Analysis, DNA ; Thailand ; }, abstract = {Antibiotic resistance genes are rapidly spread between pathogens and the normal flora, with plasmids playing an important role in their circulation. This study aimed to investigate antibiotic resistance plasmids in the gut microbiome of hospitalised patients. Stool samples were collected from seven inpatients at Siriraj Hospital (Bangkok, Thailand) and were compared with a sample from a healthy volunteer. Plasmids from the gut microbiomes extracted from the stool samples were subjected to high-throughput DNA sequencing (GS Junior). Newbler-assembled DNA reads were categorised into known and unknown sequences (using >80% alignment length as the cut-off), and ResFinder was used to classify the antibiotic resistance gene pools. Plasmid replicon modules were used for plasmid typing. Forty-six genes conferring resistance to several classes of antibiotics were identified in the stool samples. Several antibiotic resistance genes were shared by the patients; interestingly, most were reported previously in food animals and healthy humans. Four antibiotic resistance genes were found in the healthy subject. One gene (aph3-III) was identified in the patients and the healthy subject and was related to that in cattle. Uncommon genes of hospital origin such as blaTEM-124-like and fosA, which confer resistance to extended-spectrum β-lactams and fosfomycin, respectively, were identified. The resistance genes did not match the patients' drug treatments. In conclusion, several plasmid types were identified in the gut microbiome; however, it was difficult to link these to the antibiotic resistance genes identified. That the antibiotic resistance genes came from hospital and community environments is worrying.}, } @article {pmid27530749, year = {2016}, author = {Hansen, TA and Mollerup, S and Nguyen, NP and White, NE and Coghlan, M and Alquezar-Planas, DE and Joshi, T and Jensen, RH and Fridholm, H and Kjartansdóttir, KR and Mourier, T and Warnow, T and Belsham, GJ and Bunce, M and Willerslev, E and Nielsen, LP and Vinner, L and Hansen, AJ}, title = {High diversity of picornaviruses in rats from different continents revealed by deep sequencing.}, journal = {Emerging microbes & infections}, volume = {5}, number = {8}, pages = {e90}, pmid = {27530749}, issn = {2222-1751}, support = {K24 DK002800/DK/NIDDK NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Denmark/epidemiology ; *Disease Reservoirs ; Feces/*virology ; *Gastrointestinal Microbiome ; *Genetic Variation ; *Genome, Viral ; High-Throughput Nucleotide Sequencing ; Hong Kong/epidemiology ; Humans ; Malaysia/epidemiology ; Metagenomics ; Phylogeny ; Picornaviridae/classification/*genetics/isolation & purification ; Picornaviridae Infections/*epidemiology/transmission ; RNA, Viral ; Rats/*virology ; Viral Proteins/chemistry/genetics ; Zoonoses ; }, abstract = {Outbreaks of zoonotic diseases in humans and livestock are not uncommon, and an important component in containment of such emerging viral diseases is rapid and reliable diagnostics. Such methods are often PCR-based and hence require the availability of sequence data from the pathogen. Rattus norvegicus (R. norvegicus) is a known reservoir for important zoonotic pathogens. Transmission may be direct via contact with the animal, for example, through exposure to its faecal matter, or indirectly mediated by arthropod vectors. Here we investigated the viral content in rat faecal matter (n=29) collected from two continents by analyzing 2.2 billion next-generation sequencing reads derived from both DNA and RNA. Among other virus families, we found sequences from members of the Picornaviridae to be abundant in the microbiome of all the samples. Here we describe the diversity of the picornavirus-like contigs including near-full-length genomes closely related to the Boone cardiovirus and Theiler's encephalomyelitis virus. From this study, we conclude that picornaviruses within R. norvegicus are more diverse than previously recognized. The virome of R. norvegicus should be investigated further to assess the full potential for zoonotic virus transmission.}, } @article {pmid27522532, year = {2016}, author = {Medeiros, JD and Cantão, ME and Cesar, DE and Nicolás, MF and Diniz, CG and Silva, VL and Vasconcelos, AT and Coelho, CM}, title = {Comparative metagenome of a stream impacted by the urbanization phenomenon.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {47}, number = {4}, pages = {835-845}, pmid = {27522532}, issn = {1678-4405}, mesh = {DNA Barcoding, Taxonomic ; Ecosystem ; Energy Metabolism ; Humans ; Metabolic Networks and Pathways ; *Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; *Urbanization ; *Water Microbiology ; }, abstract = {Rivers and streams are important reservoirs of freshwater for human consumption. These ecosystems are threatened by increasing urbanization, because raw sewage discharged into them alters their nutrient content and may affect the composition of their microbial community. In the present study, we investigate the taxonomic and functional profile of the microbial community in an urban lotic environment. Samples of running water were collected at two points in the São Pedro stream: an upstream preserved and non-urbanized area, and a polluted urbanized area with discharged sewage. The metagenomic DNA was sequenced by pyrosequencing. Differences were observed in the community composition at the two sites. The non-urbanized area was overrepresented by genera of ubiquitous microbes that act in the maintenance of environments. In contrast, the urbanized metagenome was rich in genera pathogenic to humans. The functional profile indicated that the microbes act on the metabolism of methane, nitrogen and sulfur, especially in the urbanized area. It was also found that virulence/defense (antibiotic resistance and metal resistance) and stress response-related genes were disseminated in the urbanized environment. The structure of the microbial community was altered by uncontrolled anthropic interference, highlighting the selective pressure imposed by high loads of urban sewage discharged into freshwater environments.}, } @article {pmid27518033, year = {2016}, author = {Ye, J and Song, Z and Wang, L and Zhu, J}, title = {Metagenomic analysis of microbiota structure evolution in phytoremediation of a swine lagoon wastewater.}, journal = {Bioresource technology}, volume = {219}, number = {}, pages = {439-444}, doi = {10.1016/j.biortech.2016.08.013}, pmid = {27518033}, issn = {1873-2976}, mesh = {Animals ; *Bacteria/genetics/metabolism ; *Biodegradation, Environmental ; Chlorella ; Manure/*microbiology ; Metagenome ; Microalgae ; Microbiota/*genetics ; *Sewage/chemistry/microbiology ; Swine ; Water Purification/*methods ; }, abstract = {Pytoremediation was studied in this project to treat swine manure lagoon wastewater characteristic of high concentrations of organic carbon, ammonium (N) and phosphorus (P). The impacts of introducing exogenous microalgae Chlorella into the lagoon wastewater on the removal of major nutrients and the transformation of the native wastewater microbiota structure were explored under two phytoremediation modes (shake flask and CO2-air bubbling). The results showed that the inoculation of microalgae could significantly enhance N and P removal. Metagenomic analysis of the native microbiota composition in the wastewater affected by algae inoculation revealed that a substantial population of algicidal bacteria was developed in the shake flask system, while in the CO2-air bubbling system, a niche for more mutualistic bacteria was created, which benefited the maximal algal growth with the simultaneous optimal N and P removal. To our knowledge, this study presents, the first reported case of applying metagenomic approach to a phytoremediation system treating real swine lagoon wastewater.}, } @article {pmid27515514, year = {2016}, author = {Ni, Y and Li, J and Panagiotou, G}, title = {COMAN: a web server for comprehensive metatranscriptomics analysis.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {622}, pmid = {27515514}, issn = {1471-2164}, mesh = {Computational Biology/*methods/statistics & numerical data ; High-Throughput Nucleotide Sequencing ; Humans ; Internet ; Metagenomics/*methods/statistics & numerical data ; Microbiota/*genetics ; Sequence Analysis, RNA ; *Software ; *Transcriptome ; }, abstract = {BACKGROUND: Microbiota-oriented studies based on metagenomic or metatranscriptomic sequencing have revolutionised our understanding on microbial ecology and the roles of both clinical and environmental microbes. The analysis of massive metatranscriptomic data requires extensive computational resources, a collection of bioinformatics tools and expertise in programming.

RESULTS: We developed COMAN (Comprehensive Metatranscriptomics Analysis), a web-based tool dedicated to automatically and comprehensively analysing metatranscriptomic data. COMAN pipeline includes quality control of raw reads, removal of reads derived from non-coding RNA, followed by functional annotation, comparative statistical analysis, pathway enrichment analysis, co-expression network analysis and high-quality visualisation. The essential data generated by COMAN are also provided in tabular format for additional analysis and integration with other software. The web server has an easy-to-use interface and detailed instructions, and is freely available at http://sbb.hku.hk/COMAN/ CONCLUSIONS: COMAN is an integrated web server dedicated to comprehensive functional analysis of metatranscriptomic data, translating massive amount of reads to data tables and high-standard figures. It is expected to facilitate the researchers with less expertise in bioinformatics in answering microbiota-related biological questions and to increase the accessibility and interpretation of microbiota RNA-Seq data.}, } @article {pmid27513472, year = {2016}, author = {Lê Cao, KA and Costello, ME and Lakis, VA and Bartolo, F and Chua, XY and Brazeilles, R and Rondeau, P}, title = {MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities.}, journal = {PloS one}, volume = {11}, number = {8}, pages = {e0160169}, pmid = {27513472}, issn = {1932-6203}, mesh = {*Algorithms ; Atherosclerosis/genetics/*microbiology ; Bacteria/*genetics ; Computational Biology/*methods ; Healthy Volunteers ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; *Models, Statistical ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Culture independent techniques, such as shotgun metagenomics and 16S rRNA amplicon sequencing have dramatically changed the way we can examine microbial communities. Recently, changes in microbial community structure and dynamics have been associated with a growing list of human diseases. The identification and comparison of bacteria driving those changes requires the development of sound statistical tools, especially if microbial biomarkers are to be used in a clinical setting. We present mixMC, a novel multivariate data analysis framework for metagenomic biomarker discovery. mixMC accounts for the compositional nature of 16S data and enables detection of subtle differences when high inter-subject variability is present due to microbial sampling performed repeatedly on the same subjects, but in multiple habitats. Through data dimension reduction the multivariate methods provide insightful graphical visualisations to characterise each type of environment in a detailed manner. We applied mixMC to 16S microbiome studies focusing on multiple body sites in healthy individuals, compared our results with existing statistical tools and illustrated added value of using multivariate methodologies to fully characterise and compare microbial communities.}, } @article {pmid27513210, year = {2017}, author = {Noecker, C and McNally, CP and Eng, A and Borenstein, E}, title = {High-resolution characterization of the human microbiome.}, journal = {Translational research : the journal of laboratory and clinical medicine}, volume = {179}, number = {}, pages = {7-23}, pmid = {27513210}, issn = {1878-1810}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; T32 HG000035/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; Metagenome/genetics ; Metagenomics ; Microbiota/*genetics ; Molecular Sequence Annotation ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The human microbiome plays an important and increasingly recognized role in human health. Studies of the microbiome typically use targeted sequencing of the 16S rRNA gene, whole metagenome shotgun sequencing, or other meta-omic technologies to characterize the microbiome's composition, activity, and dynamics. Processing, analyzing, and interpreting these data involve numerous computational tools that aim to filter, cluster, annotate, and quantify the obtained data and ultimately provide an accurate and interpretable profile of the microbiome's taxonomy, functional capacity, and behavior. These tools, however, are often limited in resolution and accuracy and may fail to capture many biologically and clinically relevant microbiome features, such as strain-level variation or nuanced functional response to perturbation. Over the past few years, extensive efforts have been invested toward addressing these challenges and developing novel computational methods for accurate and high-resolution characterization of microbiome data. These methods aim to quantify strain-level composition and variation, detect and characterize rare microbiome species, link specific genes to individual taxa, and more accurately characterize the functional capacity and dynamics of the microbiome. These methods and the ability to produce detailed and precise microbiome information are clearly essential for informing microbiome-based personalized therapies. In this review, we survey these methods, highlighting the challenges each method sets out to address and briefly describing methodological approaches.}, } @article {pmid27511137, year = {2016}, author = {Shanahan, ER and Zhong, L and Talley, NJ and Morrison, M and Holtmann, G}, title = {Letter: investigating the intestinal mucosa-associated microbiota - relevance and potential pitfalls. Authors' reply.}, journal = {Alimentary pharmacology & therapeutics}, volume = {44}, number = {6}, pages = {648-649}, doi = {10.1111/apt.13741}, pmid = {27511137}, issn = {1365-2036}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Intestinal Mucosa ; Microbiota ; }, } @article {pmid27507346, year = {2016}, author = {Auchtung, JM and Robinson, CD and Farrell, K and Britton, RA}, title = {MiniBioReactor Arrays (MBRAs) as a Tool for Studying C. difficile Physiology in the Presence of a Complex Community.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1476}, number = {}, pages = {235-258}, doi = {10.1007/978-1-4939-6361-4_18}, pmid = {27507346}, issn = {1940-6029}, support = {U19 AI090872/AI/NIAID NIH HHS/United States ; }, mesh = {Anaerobiosis ; Anti-Bacterial Agents/pharmacology ; Bioreactors ; Clindamycin/analogs & derivatives/pharmacology ; Clostridioides difficile/*drug effects/growth & development/pathogenicity ; Culture Media/chemistry/*pharmacology ; Equipment Design ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Microbial Consortia/*drug effects/physiology ; *Models, Biological ; }, abstract = {The commensal microbiome plays an important role in the dynamics of Clostridium difficile infection. In this chapter, we describe minibioreactor arrays (MBRAs), an in vitro cultivation system that we developed that allows for C. difficile physiology to be assayed in the presence of complex fecal microbial communities. The small size of the bioreactors within the MBRAs allows for dozens of reactors to be run simultaneously and therefore several different variables can be tested with limited time and cost. When coupled with experiments in animal models of C. difficile infection, MBRAs can provide important insights into C. difficile physiology and pathogenesis.}, } @article {pmid27507222, year = {2016}, author = {Kelly, TN and Bazzano, LA and Ajami, NJ and He, H and Zhao, J and Petrosino, JF and Correa, A and He, J}, title = {Gut Microbiome Associates With Lifetime Cardiovascular Disease Risk Profile Among Bogalusa Heart Study Participants.}, journal = {Circulation research}, volume = {119}, number = {8}, pages = {956-964}, pmid = {27507222}, issn = {1524-4571}, support = {P20 GM109036/GM/NIGMS NIH HHS/United States ; R01 AG041200/AG/NIA NIH HHS/United States ; R21 AG051914/AG/NIA NIH HHS/United States ; RF1 AG041200/AG/NIA NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Cardiovascular Diseases/*epidemiology/*genetics ; Child ; Child, Preschool ; Cohort Studies ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Longitudinal Studies ; Louisiana/epidemiology ; Male ; Middle Aged ; RNA, Ribosomal, 16S/*genetics ; Risk Factors ; Young Adult ; }, abstract = {RATIONALE: Few studies have systematically assessed the influence of gut microbiota on cardiovascular disease (CVD) risk.

OBJECTIVE: To examine the association between gut microbiota and lifetime CVD risk profile among 55 Bogalusa Heart Study participants with the highest and 57 with the lowest lifetime burdens of CVD risk factors.

METHODS AND RESULTS: 16S ribosomal RNA sequencing was conducted on microbial DNA extracted from stool samples of the Bogalusa Heart Study participants. α Diversity, including measures of richness and evenness, and individual genera were tested for associations with lifetime CVD risk profile. Multivariable regression techniques were used to adjust for age, sex, and race (model 1), along with body mass index (model 2) and both body mass index and diet (model 3). In model 1, odds ratios (95% confidence intervals) for each SD increase in richness, measured by the number of observed operational taxonomic units, Chao 1 index, and abundance-based coverage estimator, were 0.62 (0.39-0.99), 0.61 (0.38-0.98), and 0.63 (0.39-0.99), respectively. Associations were consistent in models 2 and 3. Four genera were enriched among those with high versus low CVD risk profile in all models. Model 1 P values were 2.12×10(-3), 7.95×10(-5), 4.39×10(-4), and 1.51×10(-4) for Prevotella 2, Prevotella 7, Tyzzerella, and Tyzzerella 4, respectively. Two genera were depleted among those with high versus low CVD risk profile in all models. Model 1 P values were 2.96×10(-6) and 1.82×10(-4) for Alloprevotella and Catenibacterium, respectively.

CONCLUSIONS: The current study identified associations of overall microbial richness and 6 microbial genera with lifetime CVD risk.}, } @article {pmid27506856, year = {2016}, author = {Dann, LM and Rosales, S and McKerral, J and Paterson, JS and Smith, RJ and Jeffries, TC and Oliver, RL and Mitchell, JG}, title = {Marine and giant viruses as indicators of a marine microbial community in a riverine system.}, journal = {MicrobiologyOpen}, volume = {5}, number = {6}, pages = {1071-1084}, pmid = {27506856}, issn = {2045-8827}, mesh = {Aquatic Organisms/isolation & purification/virology ; Fresh Water/*virology ; Giant Viruses/*classification/genetics/*isolation & purification ; Metagenome/genetics ; Metagenomics ; Microbiota ; Water Microbiology ; }, abstract = {Viral communities are important for ecosystem function as they are involved in critical biogeochemical cycles and controlling host abundance. This study investigates riverine viral communities around a small rural town that influences local water inputs. Myoviridae, Siphoviridae, Phycodnaviridae, Mimiviridae, Herpesviridae, and Podoviridae were the most abundant families. Viral species upstream and downstream of the town were similar, with Synechoccocus phage, salinus, Prochlorococcus phage, Mimivirus A, and Human herpes 6A virus most abundant, contributing to 4.9-38.2% of average abundance within the metagenomic profiles, with Synechococcus and Prochlorococcus present in metagenomes as the expected hosts for the phage. Overall, the majority of abundant viral species were or were most similar to those of marine origin. At over 60 km to the river mouth, the presence of marine communities provides some support for the Baas-Becking hypothesis "everything is everywhere, but, the environment selects." We conclude marine microbial species may occur more frequently in freshwater systems than previously assumed, and hence may play important roles in some freshwater ecosystems within tens to a hundred kilometers from the sea.}, } @article {pmid27503299, year = {2016}, author = {Le, PT and Makhalanyane, TP and Guerrero, LD and Vikram, S and Van de Peer, Y and Cowan, DA}, title = {Comparative Metagenomic Analysis Reveals Mechanisms for Stress Response in Hypoliths from Extreme Hyperarid Deserts.}, journal = {Genome biology and evolution}, volume = {8}, number = {9}, pages = {2737-2747}, pmid = {27503299}, issn = {1759-6653}, mesh = {Actinobacteria/genetics/isolation & purification ; Antarctic Regions ; Bacteroidetes/genetics/isolation & purification ; Cyanobacteria/genetics/isolation & purification ; Desert Climate ; *Extreme Environments ; *Metagenome ; *Microbiota ; Proteobacteria/genetics/isolation & purification ; *Stress, Physiological ; }, abstract = {Understanding microbial adaptation to environmental stressors is crucial for interpreting broader ecological patterns. In the most extreme hot and cold deserts, cryptic niche communities are thought to play key roles in ecosystem processes and represent excellent model systems for investigating microbial responses to environmental stressors. However, relatively little is known about the genetic diversity underlying such functional processes in climatically extreme desert systems. This study presents the first comparative metagenome analysis of cyanobacteria-dominated hypolithic communities in hot (Namib Desert, Namibia) and cold (Miers Valley, Antarctica) hyperarid deserts. The most abundant phyla in both hypolith metagenomes were Actinobacteria, Proteobacteria, Cyanobacteria and Bacteroidetes with Cyanobacteria dominating in Antarctic hypoliths. However, no significant differences between the two metagenomes were identified. The Antarctic hypolithic metagenome displayed a high number of sequences assigned to sigma factors, replication, recombination and repair, translation, ribosomal structure, and biogenesis. In contrast, the Namib Desert metagenome showed a high abundance of sequences assigned to carbohydrate transport and metabolism. Metagenome data analysis also revealed significant divergence in the genetic determinants of amino acid and nucleotide metabolism between these two metagenomes and those of soil from other polar deserts, hot deserts, and non-desert soils. Our results suggest extensive niche differentiation in hypolithic microbial communities from these two extreme environments and a high genetic capacity for survival under environmental extremes.}, } @article {pmid27502158, year = {2016}, author = {Estaki, M and Pither, J and Baumeister, P and Little, JP and Gill, SK and Ghosh, S and Ahmadi-Vand, Z and Marsden, KR and Gibson, DL}, title = {Cardiorespiratory fitness as a predictor of intestinal microbial diversity and distinct metagenomic functions.}, journal = {Microbiome}, volume = {4}, number = {1}, pages = {42}, pmid = {27502158}, issn = {2049-2618}, support = {//CIHR/Canada ; }, mesh = {Adult ; Bacteria/*classification/genetics/isolation & purification ; Base Sequence ; Butyrates/*isolation & purification ; Cardiorespiratory Fitness/*physiology ; Chromatography, Gas ; Exercise/physiology ; Fatty Acids, Volatile/*analysis ; Feces/chemistry/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Intestines/*microbiology ; Male ; Metagenome/genetics ; Pulmonary Gas Exchange ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {BACKGROUND: Reduced microbial diversity in human intestines has been implicated in various conditions such as diabetes, colorectal cancer, and inflammatory bowel disease. The role of physical fitness in the context of human intestinal microbiota is currently not known. We used high-throughput sequencing to analyze fecal microbiota of 39 healthy participants with similar age, BMI, and diets but with varying cardiorespiratory fitness levels. Fecal short-chain fatty acids were analyzed using gas chromatography.

RESULTS: We showed that peak oxygen uptake (VO2peak), the gold standard measure of cardiorespiratory fitness, can account for more than 20 % of the variation in taxonomic richness, after accounting for all other factors, including diet. While VO2peak did not explain variation in beta diversity, it did play a significant role in explaining variation in the microbiomes' predicted metagenomic functions, aligning positively with genes related to bacterial chemotaxis, motility, and fatty acid biosynthesis. These predicted functions were supported by measured increases in production of fecal butyrate, a short-chain fatty acid associated with improved gut health, amongst physically fit participants. We also identified increased abundances of key butyrate-producing taxa (Clostridiales, Roseburia, Lachnospiraceae, and Erysipelotrichaceae) amongst these individuals, which likely contributed to the observed increases in butyrate levels.

CONCLUSIONS: Results from this study show that cardiorespiratory fitness is correlated with increased microbial diversity in healthy humans and that the associated changes are anchored around a set of functional cores rather than specific taxa. The microbial profiles of fit individuals favor the production of butyrate. As increased microbiota diversity and butyrate production is associated with overall host health, our findings warrant the use of exercise prescription as an adjuvant therapy in combating dysbiosis-associated diseases.}, } @article {pmid27499042, year = {2016}, author = {Shiba, T and Watanabe, T and Kachi, H and Koyanagi, T and Maruyama, N and Murase, K and Takeuchi, Y and Maruyama, F and Izumi, Y and Nakagawa, I}, title = {Distinct interacting core taxa in co-occurrence networks enable discrimination of polymicrobial oral diseases with similar symptoms.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {30997}, pmid = {27499042}, issn = {2045-2322}, mesh = {Aged ; Bacteria/*classification/*genetics ; Cluster Analysis ; Coinfection/*microbiology ; DNA, Ribosomal/chemistry/genetics ; Female ; Humans ; In Situ Hybridization ; Male ; Metagenomics ; *Microbial Consortia ; Middle Aged ; Periodontal Diseases/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Polymicrobial diseases, which can be life threatening, are caused by the presence and interactions of multiple microbes. Peri-implantitis and periodontitis are representative polymicrobial diseases that show similar clinical symptoms. To establish a means of differentiating between them, we compared microbial species and functional genes in situ by performing metatranscriptomic analyses of peri-implantitis and periodontitis samples obtained from the same subjects (n = 12 each). Although the two diseases differed in terms of 16S rRNA-based taxonomic profiles, they showed similarities with respect to functional genes and taxonomic and virulence factor mRNA profiles. The latter-defined as microbial virulence types-differed from those of healthy periodontal sites. We also showed that networks based on co-occurrence relationships of taxonomic mRNA abundance (co-occurrence networks) were dissimilar between the two diseases. Remarkably, these networks consisted mainly of taxa with a high relative mRNA-to-rRNA ratio, with some showing significant co-occurrence defined as interacting core taxa, highlighting differences between the two groups. Thus, peri-implantitis and periodontitis have shared as well as distinct microbiological characteristics. Our findings provide insight into microbial interactions in polymicrobial diseases with unknown etiologies.}, } @article {pmid27495902, year = {2016}, author = {Li, Y and Zou, CG and Fu, Y and Li, Y and Zhou, Q and Liu, B and Zhang, Z and Liu, J}, title = {Oral microbial community typing of caries and pigment in primary dentition.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {558}, pmid = {27495902}, issn = {1471-2164}, mesh = {Cluster Analysis ; Dental Caries/*microbiology ; Dental Plaque/microbiology ; Humans ; *Metagenome ; *Metagenomics ; *Microbiota ; *Pigmentation ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; Selection, Genetic ; Tooth, Deciduous/*microbiology/*pathology ; }, abstract = {BACKGROUND: Black extrinsic discoloration in primary dentition is a common clinical and aesthetic problem that can co-occur with dental caries, the most common oral diseases in childhood. Although the role of bacteria in the formation of pigment and caries in primary dentition is important, their basic features still remain a further mystery.

METHODS: Using targeted sequencing of the V1-V3 hypervariable regions of bacterial 16S ribosomal RNA (rRNA) genes, we obtained a dataset consisting of 831,381 sequences from 111 saliva samples and 110 supragingival plaque samples from 40 patients with pigment (black extrinsic stain), 20 with caries (obvious decay), and 25 with both pigment and caries and from 26 healthy individuals. We applied a Dirichlet multinomial mixture (DMM)-based community typing approach to investigate oral microbial community types.

RESULTS: Our results revealed significant structural segregation of microbial communities, as indicated by the identification of two plaque community types (A and B) and three saliva community types (C-E). We found that the independent occurrence of the two plaque community types, A and B, was potentially associated with our oral diseases of interest. For type A, three co-occurring bacterial genus pairs could separately play a potential role in the formation of pigment (Leptotrichia and Fusobacterium), caries (unclassified Gemellales and Granulicatella), and mixed caries and pigment (Streptococcus and Mogibacterium). For type B, three co-occurring bacterial genera (unclassified Clostridiaceae, Peptostreptococcus, and Clostridium) were related to mixed pigment and caries. Three dominant bacterial genera (Selenomonas, Gemella, and Streptobacillus) were linked to the presence of caries.

CONCLUSIONS: Our study demonstrates that plaque-associated oral microbial communities could majorly contribute to the formation of pigment and caries in primary dentition and suggests potential clinical applications of monitoring oral microbiota as an indicator for disease diagnosis and prognosis.}, } @article {pmid27494088, year = {2016}, author = {Raymond, F and Déraspe, M and Boissinot, M and Bergeron, MG and Corbeil, J}, title = {Partial recovery of microbiomes after antibiotic treatment.}, journal = {Gut microbes}, volume = {7}, number = {5}, pages = {428-434}, pmid = {27494088}, issn = {1949-0984}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Bacteria/*drug effects/genetics/isolation & purification/metabolism ; Bacterial Infections/*drug therapy/microbiology ; Bacterial Proteins/genetics/metabolism ; Cephalosporins/*therapeutic use ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/drug effects/microbiology ; Humans ; Cefprozil ; }, abstract = {Antibiotics profoundly affect the gut microbiome and modulate microbial communities. We recently observed that antimicrobial drugs also impact the abundance and distribution of antibiotic resistance genes. In this addendum, we reanalyze our ∼1 trillion nucleotide shotgun metagenomic dataset to quantify comprehensive genomic differences at the sequence level before and after antibiotic treatment. We show that 7 day exposure to cefprozil leads to a statistically significant loss of metagenome sequences. Recovery of gut microbiomes 3 months after antibiotherapy was characterized by the emergence of new genome sequences not observed prior to antibiotic exposure. Participants with low initial gut microbiome diversity had an increased amount of sequences related to antibiotic resistance. Therefore, we suggest that while the taxonomical composition of microbiomes is partially affected by the antibiotic, the genomic content and population structure of bacterial communities is noticeably impacted.}, } @article {pmid27493014, year = {2016}, author = {Coit, P and Sawalha, AH}, title = {The human microbiome in rheumatic autoimmune diseases: A comprehensive review.}, journal = {Clinical immunology (Orlando, Fla.)}, volume = {170}, number = {}, pages = {70-79}, doi = {10.1016/j.clim.2016.07.026}, pmid = {27493014}, issn = {1521-7035}, mesh = {Autoimmune Diseases/*immunology/microbiology ; Bacteria/classification/genetics/immunology ; Dysbiosis/*immunology/microbiology ; Host-Pathogen Interactions/immunology ; Humans ; Microbiota/genetics/*immunology/physiology ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; Rheumatic Diseases/*immunology/microbiology ; Sequence Analysis, DNA ; }, abstract = {The human microbiome consists of the total diversity of microbiota and their genes. High-throughput sequencing has allowed for inexpensive and rapid evaluation of taxonomic representation and functional capability of the microbiomes of human body sites. Autoimmune and inflammatory rheumatic diseases are characterized by dysbiosis of the microbiome. Microbiome dysbiosis can be influenced by host genetics and environmental factors. Dysbiosis is also associated with shifts in certain functional pathways. The goal of this article is to provide a current and comprehensive review of the unique characteristics of the microbiome of patients with autoimmune and inflammatory rheumatic diseases, measured using high-throughput sequencing. We also highlight the need for broader studies utilizing a longitudinal approach to better understand how the human microbiome contributes to disease susceptibility, and to characterize the role of the interaction between host genetics and microbial diversity in the pathogenesis of autoimmune diseases, disease manifestations, and progression.}, } @article {pmid27490955, year = {2016}, author = {Blaya, J and Marhuenda, FC and Pascual, JA and Ros, M}, title = {Microbiota Characterization of Compost Using Omics Approaches Opens New Perspectives for Phytophthora Root Rot Control.}, journal = {PloS one}, volume = {11}, number = {8}, pages = {e0158048}, pmid = {27490955}, issn = {1932-6203}, mesh = {Bacteria/genetics/isolation & purification/metabolism ; Crops, Agricultural ; DNA, Bacterial/chemistry/isolation & purification/metabolism ; DNA, Fungal/chemistry/isolation & purification/metabolism ; Fusarium/genetics/isolation & purification/metabolism ; Magnetic Resonance Spectroscopy ; Metabolome ; *Metagenomics ; *Microbiota ; Phytophthora/*growth & development/isolation & purification/metabolism ; Plant Diseases/parasitology ; Principal Component Analysis ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; Sordariales/genetics/isolation & purification/metabolism ; }, abstract = {Phytophthora root rot caused by Phytophthora nicotianae is an economically important disease in pepper crops. The use of suppressive composts is a low environmental impact method for its control. Although attempts have been made to reveal the relationship between microbiota and compost suppressiveness, little is known about the microorganisms associated with disease suppression. Here, an Ion Torrent platform was used to assess the microbial composition of composts made of different agro-industrial waste and with different levels of suppressiveness against P. nicotianae. Both bacterial and fungal populations responded differently depending on the chemical heterogeneity of materials used during the composting process. High proportions (67-75%) of vineyard pruning waste were used in the most suppressive composts, COM-A and COM-B. This material may have promoted the presence of higher relative abundance of Ascomycota as well as higher microbial activity, which have proved to be essential for controlling the disease. Although no unique fungi or bacteria have been detected in neither suppressive nor conducive composts, relatively high abundance of Fusarium and Zopfiella were found in compost COM-B and COM-A, respectively. To the best of our knowledge, this is the first work that studies compost metabolome. Surprisingly, composts and peat clustered together in principal component analysis of the metabolic data according to their levels of suppressiveness achieved. This study demonstrated the need for combining the information provided by different techniques, including metagenomics and metametabolomics, to better understand the ability of compost to control plant diseases.}, } @article {pmid27490110, year = {2016}, author = {Abdelfattah, A and Wisniewski, M and Li Destri Nicosia, MG and Cacciola, SO and Schena, L}, title = {Metagenomic Analysis of Fungal Diversity on Strawberry Plants and the Effect of Management Practices on the Fungal Community Structure of Aerial Organs.}, journal = {PloS one}, volume = {11}, number = {8}, pages = {e0160470}, pmid = {27490110}, issn = {1932-6203}, mesh = {*Biodiversity ; *Botrytis/classification/genetics ; *Cladosporium/classification/genetics ; Flowers/*microbiology ; Fragaria/*microbiology ; Fruit/*microbiology ; Metagenomics ; }, abstract = {An amplicon metagenomic approach based on the ITS2 region of fungal rDNA was used to identify the composition of fungal communities associated with different strawberry organs (leaves, flowers, immature and mature fruits), grown on a farm using management practices that entailed the routine use of various chemical pesticides. ITS2 sequences clustered into 316 OTUs and Ascomycota was the dominant phyla (95.6%) followed by Basidiomycota (3.9%). Strawberry plants supported a high diversity of microbial organisms, but two genera, Botrytis and Cladosporium, were the most abundant, representing 70-99% of the relative abundance (RA) of all detected sequences. According to alpha and beta diversity analyses, strawberry organs displayed significantly different fungal communities with leaves having the most diverse fungal community, followed by flowers, and fruit. The interruption of chemical treatments for one month resulted in a significant modification in the structure of the fungal community of leaves and flowers while immature and mature fruit were not significantly affected. Several plant pathogens of other plant species, that would not be intuitively expected to be present on strawberry plants such as Erysiphe, were detected, while some common strawberry pathogens, such as Rhizoctonia, were less evident or absent.}, } @article {pmid27489239, year = {2017}, author = {Zhong, L and Shanahan, ER and Raj, A and Koloski, NA and Fletcher, L and Morrison, M and Walker, MM and Talley, NJ and Holtmann, G}, title = {Dyspepsia and the microbiome: time to focus on the small intestine.}, journal = {Gut}, volume = {66}, number = {6}, pages = {1168-1169}, doi = {10.1136/gutjnl-2016-312574}, pmid = {27489239}, issn = {1468-3288}, mesh = {*Dyspepsia ; Helicobacter Infections ; Humans ; *Intestine, Small ; Microbiota ; Proton Pump Inhibitors ; }, } @article {pmid27485508, year = {2016}, author = {Allen, HK and Bayles, DO and Looft, T and Trachsel, J and Bass, BE and Alt, DP and Bearson, SM and Nicholson, T and Casey, TA}, title = {Pipeline for amplifying and analyzing amplicons of the V1-V3 region of the 16S rRNA gene.}, journal = {BMC research notes}, volume = {9}, number = {}, pages = {380}, pmid = {27485508}, issn = {1756-0500}, mesh = {Computational Biology/methods ; DNA, Archaeal/*genetics ; DNA, Bacterial/*genetics ; Data Mining ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Microbial Consortia/*genetics ; Molecular Sequence Annotation ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Profiling of 16S rRNA gene sequences is an important tool for testing hypotheses in complex microbial communities, and analysis methods must be updated and validated as sequencing technologies advance. In host-associated bacterial communities, the V1-V3 region of the 16S rRNA gene is a valuable region to profile because it provides a useful level of taxonomic resolution; however, use of Illumina MiSeq data for experiments targeting this region needs validation.

RESULTS: Using a MiSeq machine and the version 3 (300 × 2) chemistry, we sequenced the V1-V3 region of the 16S rRNA gene within a mock community. Nineteen bacteria and one archaeon comprised the mock community, and 12 replicate amplifications of the community were performed and sequenced. Sequencing the large fragment (490 bp) that encompasses V1-V3 yielded a higher error rate (3.6 %) than has been reported when using smaller fragment sizes. This higher error rate was due to a large number of sequences that occurred only one or two times among all mock community samples. Removing sequences that occurred one time among all samples (singletons) reduced the error rate to 1.4 %. Diversity estimates of the mock community containing all sequences were inflated, whereas estimates following singleton removal more closely reflected the actual mock community membership. A higher percentage of the sequences could be taxonomically assigned after singleton and doubleton sequences were removed, and the assignments reflected the membership of the input DNA.

CONCLUSIONS: Sequencing the V1-V3 region of the 16S rRNA gene on the MiSeq platform may require additional sequence curation in silico, and improved error rates and diversity estimates show that removing low-frequency sequences is reasonable. When datasets have a high number of singletons, these singletons can be removed from the analysis without losing statistical power while reducing error and improving microbiota assessment.}, } @article {pmid27484946, year = {2016}, author = {Zafra, G and Taylor, TD and Absalón, AE and Cortés-Espinosa, DV}, title = {Comparative metagenomic analysis of PAH degradation in soil by a mixed microbial consortium.}, journal = {Journal of hazardous materials}, volume = {318}, number = {}, pages = {702-710}, doi = {10.1016/j.jhazmat.2016.07.060}, pmid = {27484946}, issn = {1873-3336}, mesh = {Bacteria/enzymology/genetics/metabolism ; *Biodegradation, Environmental ; Computational Biology ; Cytochrome P-450 Enzyme System/metabolism ; Environmental Restoration and Remediation ; Fungi/enzymology/genetics/metabolism ; *Metagenomics ; Microbiota/*genetics ; Polycyclic Aromatic Hydrocarbons/*metabolism ; *Soil Microbiology ; Soil Pollutants ; }, abstract = {In this study, we used a taxonomic and functional metagenomic approach to analyze some of the effects (e.g. displacement, permanence, disappearance) produced between native microbiota and a previously constructed Polycyclic Aromatic Hydrocarbon (PAH)-degrading microbial consortium during the bioremediation process of a soil polluted with PAHs. Bioaugmentation with a fungal-bacterial consortium and biostimulation of native microbiota using corn stover as texturizer produced appreciable changes in the microbial diversity of polluted soils, shifting native microbial communities in favor of degrading specific populations. Functional metagenomics showed changes in gene abundance suggesting a bias towards aromatic hydrocarbon and intermediary degradation pathways, which greatly favored PAH mineralization. In contrast, pathways favoring the formation of toxic intermediates such as cytochrome P450-mediated reactions were found to be significantly reduced in bioaugmented soils. PAH biodegradation in soil using the microbial consortium was faster and reached higher degradation values (84% after 30 d) as a result of an increased co-metabolic degradation when compared with other mixed microbial consortia. The main differences between inoculated and non-inoculated soils were observed in aromatic ring-hydroxylating dioxygenases, laccase, protocatechuate, salicylate and benzoate-degrading enzyme genes. Based on our results, we propose that several concurrent metabolic pathways are taking place in soils during PAH degradation.}, } @article {pmid27482928, year = {2017}, author = {Yan, Y and Kuramae, EE and de Hollander, M and Klinkhamer, PG and van Veen, JA}, title = {Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere.}, journal = {The ISME journal}, volume = {11}, number = {1}, pages = {56-66}, pmid = {27482928}, issn = {1751-7370}, mesh = {Bacteria/classification/genetics/*isolation & purification/metabolism ; Biodiversity ; Plant Roots/microbiology ; Plants/microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {We studied the impact of community diversity on the selection of bacterial communities in the rhizosphere by comparing the composition and the functional traits of these communities in soil and rhizosphere. Differences in diversity were established by inoculating into sterilized soils diluted suspensions of the same soil. We used 16S ribosomal RNA amplicon sequencing to determine the taxonomical structure of the bacterial communities and a shotgun metagenomics approach to investigate the potential functional diversity of the communities. By comparing the bacterial communities in soil and rhizosphere, the selective power of the plant was observed both at the taxonomic and functional level, although the diversity indices of soil and rhizosphere samples showed a highly variable, irregular pattern. Lesser variation, that is, more homogenization, was found for both the taxonomic structure and the functional profile of the rhizosphere communities as compared to the communities of the bulk soil. Network analysis revealed stronger interactions among bacterial operational taxonomic units in the rhizosphere than in the soil. The enrichment processes in the rhizosphere selected microbes with particular functional genes related to transporters, the Embden-Meyerhof-Parnas pathway and hydrogen metabolism. This selection was not random across bacteria with these functional traits, but it was species specific. Overall, this suggests that functional traits are a key to the assembly of bacterial rhizosphere communities.}, } @article {pmid27482891, year = {2016}, author = {King, P and Pham, LK and Waltz, S and Sphar, D and Yamamoto, RT and Conrad, D and Taplitz, R and Torriani, F and Forsyth, RA}, title = {Longitudinal Metagenomic Analysis of Hospital Air Identifies Clinically Relevant Microbes.}, journal = {PloS one}, volume = {11}, number = {8}, pages = {e0160124}, pmid = {27482891}, issn = {1932-6203}, mesh = {Air/analysis ; *Air Microbiology ; Aspergillus/classification/*genetics/isolation & purification ; Cluster Analysis ; Cross Infection/prevention & control ; Genotype ; High-Throughput Nucleotide Sequencing ; Hospitals ; Humans ; Longitudinal Studies ; *Metagenome ; Microbial Consortia/*genetics ; Penicillium/classification/*genetics/isolation & purification ; Sequence Analysis, DNA ; Stenotrophomonas maltophilia/classification/*genetics/isolation & purification ; }, abstract = {We describe the sampling of sixty-three uncultured hospital air samples collected over a six-month period and analysis using shotgun metagenomic sequencing. Our primary goals were to determine the longitudinal metagenomic variability of this environment, identify and characterize genomes of potential pathogens and determine whether they are atypical to the hospital airborne metagenome. Air samples were collected from eight locations which included patient wards, the main lobby and outside. The resulting DNA libraries produced 972 million sequences representing 51 gigabases. Hierarchical clustering of samples by the most abundant 50 microbial orders generated three major nodes which primarily clustered by type of location. Because the indoor locations were longitudinally consistent, episodic relative increases in microbial genomic signatures related to the opportunistic pathogens Aspergillus, Penicillium and Stenotrophomonas were identified as outliers at specific locations. Further analysis of microbial reads specific for Stenotrophomonas maltophilia indicated homology to a sequenced multi-drug resistant clinical strain and we observed broad sequence coverage of resistance genes. We demonstrate that a shotgun metagenomic sequencing approach can be used to characterize the resistance determinants of pathogen genomes that are uncharacteristic for an otherwise consistent hospital air microbial metagenomic profile.}, } @article {pmid27481780, year = {2016}, author = {Baker, CC and Bittleston, LS and Sanders, JG and Pierce, NE}, title = {Dissecting host-associated communities with DNA barcodes.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {371}, number = {1702}, pages = {}, pmid = {27481780}, issn = {1471-2970}, mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; *Symbiosis ; }, abstract = {DNA barcoding and metabarcoding methods have been invaluable in the study of interactions between host organisms and their symbiotic communities. Barcodes can help identify individual symbionts that are difficult to distinguish using morphological characters, and provide a way to classify undescribed species. Entire symbiont communities can be characterized rapidly using barcoding and especially metabarcoding methods, which is often crucial for isolating ecological signal from the substantial variation among individual hosts. Furthermore, barcodes allow the evolutionary histories of symbionts and their hosts to be assessed simultaneously and in reference to one another. Here, we describe three projects illustrating the utility of barcodes for studying symbiotic interactions: first, we consider communities of arthropods found in the ant-occupied domatia of the East African ant-plant Vachellia (Acacia) drepanolobium; second, we examine communities of arthropod and protozoan inquilines in three species of Nepenthes pitcher plant in South East Asia; third, we investigate communities of gut bacteria of South American ants in the genus Cephalotes Advances in sequencing and computation, and greater database connectivity, will continue to expand the utility of barcoding methods for the study of species interactions, especially if barcoding can be approached flexibly by making use of alternative genetic loci, metagenomes and whole-genome data.This article is part of the themed issue 'From DNA barcodes to biomes'.}, } @article {pmid27476207, year = {2016}, author = {Mamaeva, EV and Galach'yants, YP and Khabudaev, KV and Petrova, DP and Pogodaeva, TV and Khodzher, TB and Zemskaya, TI}, title = {[Metagenomic Analysis of Microbial Communities of the Sediments of the Kara Sea Shelf and the Yenisei Bay].}, journal = {Mikrobiologiia}, volume = {85}, number = {2}, pages = {187-198}, pmid = {27476207}, issn = {0026-3656}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Bays/*microbiology ; *Biodiversity ; Metagenome/*physiology ; *Water Microbiology ; }, abstract = {Microbial diversity in the sediments of the Kara Sea shelf and the southern Yenisei Bay, differing in pore water mineralization, was studied using massive parallel pyrosequencing according to the 454 (Roche) technology. Members of the same phyla (Cyanobacteria, Verrucomicrobia, Actinobacteria, Proteobacteria, and Bacteroidetes) predominated in bacterial communities of the sediments, while their ratio and taxonomic composition varied within the phyla and depended on pore water mineralization. Increasing salinity gradient was found to coincide with increased share of the γ-Proteobacteria and decreased abundance of α- and β-Proteo- bacteria, as well as of the phyla Verrucomicrobia, Chloroflexi, Chlorobi, and Acidobacteria. Archaeal diversity was lower, with Thaumarchaeota predominant in the sediments with high and low mineralization, while Crenarchaeota predominated in moderately mineralized sediments. Microbial communities of the Kara Sea shelf and Yenisei Gulf sediments were found to contain the organisms capable of utilization of a broad spectrum of carbon sources, including gaseous and petroleum hydrocarbons.}, } @article {pmid27474719, year = {2016}, author = {Burch, AY and Do, PT and Sbodio, A and Suslow, TV and Lindow, SE}, title = {High-Level Culturability of Epiphytic Bacteria and Frequency of Biosurfactant Producers on Leaves.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {19}, pages = {5997-6009}, pmid = {27474719}, issn = {1098-5336}, mesh = {Bacteria/*genetics/metabolism ; High-Throughput Screening Assays ; *Metagenome ; *Microbiota ; Plant Leaves/*microbiology ; Surface-Active Agents/*metabolism ; }, abstract = {UNLABELLED: To better characterize the bacterial community members capable of biosurfactant production on leaves, we distinguished culturable biosurfactant-producing bacteria from nonproducers and used community sequencing to compare the composition of these distinct cultured populations with that from DNA directly recovered from leaves. Communities on spinach, romaine, and head lettuce leaves were compared with communities from adjacent samples of soil and irrigation source water. Soil communities were poorly described by culturing, with recovery of cultured representatives from only 21% of the prevalent operational taxonomic units (OTUs) (>0.2% reads) identified. The dominant biosurfactant producers cultured from soil included bacilli and pseudomonads. In contrast, the cultured communities from leaves are highly representative of the culture-independent communities, with over 85% of the prevalent OTUs recovered. The dominant taxa of surfactant producers from leaves were pseudomonads as well as members of the infrequently studied genus Chryseobacterium The proportions of bacteria cultured from head lettuce and romaine leaves that produce biosurfactants were directly correlated with the culture-independent proportion of pseudomonads in a given sample, whereas spinach harbored a wider diversity of biosurfactant producers. A subset of the culturable bacteria in irrigation water also became enriched on romaine leaves that were irrigated overhead. Although our study was designed to identify surfactant producers on plants, we also provide evidence that most bacteria in some habitats, such as agronomic plant surfaces, are culturable, and these communities can be readily investigated and described by more classical culturing methods.

IMPORTANCE: The importance of biosurfactant production to the bacteria that live on waxy leaf surfaces as well as their ability to be accurately assessed using culture-based methodologies was determined by interrogating epiphytic populations by both culture-dependent and culture-independent methods. Biosurfactant production was much more frequently observed in cultured communities on leaves than in other nearby habitats, such as soil and water, suggesting that this trait is important to life on a leaf by altering either the leaf itself or the interaction of bacteria with water. While pseudomonads were the most common biosurfactant producers isolated, this habitat also selects for taxa, such as Chryseobacterium, for which this trait was previously unrecognized. The finding that most epiphytic bacterial taxa were culturable validates strategies using more classical culturing methodologies for their study in this habitat.}, } @article {pmid27473689, year = {2016}, author = {Degli Esposti, M and Cortez, D and Lozano, L and Rasmussen, S and Nielsen, HB and Martinez Romero, E}, title = {Alpha proteobacterial ancestry of the [Fe-Fe]-hydrogenases in anaerobic eukaryotes.}, journal = {Biology direct}, volume = {11}, number = {}, pages = {34}, pmid = {27473689}, issn = {1745-6150}, mesh = {Alphaproteobacteria/*genetics ; Amino Acid Sequence ; Bacterial Proteins/*genetics ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics ; Humans ; Hydrogenase/*genetics ; Phylogeny ; Rhodospirillaceae/genetics ; }, abstract = {UNLABELLED: Eukaryogenesis, a major transition in evolution of life, originated from the symbiogenic fusion of an archaea with a metabolically versatile bacterium. By general consensus, the latter organism belonged to α proteobacteria, subsequently evolving into the mitochondrial organelle of our cells. The consensus is based upon genetic and metabolic similarities between mitochondria and aerobic α proteobacteria but fails to explain the origin of several enzymes found in the mitochondria-derived organelles of anaerobic eukaryotes such as Trichomonas and Entamoeba. These enzymes are thought to derive from bacterial lineages other than α proteobacteria, e.g., Clostridium - an obligate anaerobe. [FeFe]-hydrogenase constitues the characteristic enzyme of this anaerobic metabolism and is present in different types also in Entamoeba and other anaerobic eukaryotes. Here we show that α proteobacteria derived from metagenomic studies possess both the cytosolic and organellar type of [FeFe]-hydrogenase, as well as all the proteins required for hydrogenase maturation. These organisms are related to cultivated members of the Rhodospirillales order previously suggested to be close relatives of mitochondrial ancestors. For the first time, our evidence supports an α proteobacterial ancestry for both the anaerobic and the aerobic metabolism of eukaryotes.

REVIEWERS: This article was reviewed by William Martin and Nick Lane, both suggested by the Authors.}, } @article {pmid27473172, year = {2016}, author = {Cao, Y and Wang, Y and Zheng, X and Li, F and Bo, X}, title = {RevEcoR: an R package for the reverse ecology analysis of microbiomes.}, journal = {BMC bioinformatics}, volume = {17}, number = {1}, pages = {294}, pmid = {27473172}, issn = {1471-2105}, mesh = {Algorithms ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; Ecology/methods ; Metabolic Networks and Pathways ; Metagenomics ; Microbial Interactions ; *Microbiota ; *Software ; }, abstract = {BACKGROUND: All species live in complex ecosystems. The structure and complexity of a microbial community reflects not only diversity and function, but also the environment in which it occurs. However, traditional ecological methods can only be applied on a small scale and for relatively well-understood biological systems. Recently, a graph-theory-based algorithm called the reverse ecology approach has been developed that can analyze the metabolic networks of all the species in a microbial community, and predict the metabolic interface between species and their environment.

RESULTS: Here, we present RevEcoR, an R package and a Shiny Web application that implements the reverse ecology algorithm for determining microbe-microbe interactions in microbial communities. This software allows users to obtain large-scale ecological insights into species' ecology directly from high-throughput metagenomic data. The software has great potential for facilitating the study of microbiomes.

CONCLUSIONS: RevEcoR is open source software for the study of microbial community ecology. The RevEcoR R package is freely available under the GNU General Public License v. 2.0 at http://cran.r-project.org/web/packages/RevEcoR/ with the vignette and typical usage examples, and the interactive Shiny web application is available at http://yiluheihei.shinyapps.io/shiny-RevEcoR , or can be installed locally with the source code accessed from https://github.com/yiluheihei/shiny-RevEcoR .}, } @article {pmid27473171, year = {2016}, author = {Strati, F and Cavalieri, D and Albanese, D and De Felice, C and Donati, C and Hayek, J and Jousson, O and Leoncini, S and Pindo, M and Renzi, D and Rizzetto, L and Stefanini, I and Calabrò, A and De Filippo, C}, title = {Altered gut microbiota in Rett syndrome.}, journal = {Microbiome}, volume = {4}, number = {1}, pages = {41}, pmid = {27473171}, issn = {2049-2618}, mesh = {Bacteria/*classification/genetics ; Biodiversity ; Constipation/pathology ; Dysbiosis/*microbiology ; Fatty Acids/metabolism ; Fungi/*classification/genetics ; Gastrointestinal Microbiome/*physiology ; Humans ; Inflammation/pathology ; Intestines/*microbiology ; Metabolomics/methods ; Metagenomics/methods ; Methyl-CpG-Binding Protein 2/genetics ; Rett Syndrome/genetics/*microbiology/*physiopathology ; }, abstract = {BACKGROUND: The human gut microbiota directly affects human health, and its alteration can lead to gastrointestinal abnormalities and inflammation. Rett syndrome (RTT), a progressive neurological disorder mainly caused by mutations in MeCP2 gene, is commonly associated with gastrointestinal dysfunctions and constipation, suggesting a link between RTT's gastrointestinal abnormalities and the gut microbiota. The aim of this study was to evaluate the bacterial and fungal gut microbiota in a cohort of RTT subjects integrating clinical, metabolomics and metagenomics data to understand if changes in the gut microbiota of RTT subjects could be associated with gastrointestinal abnormalities and inflammatory status.

RESULTS: Our findings revealed the occurrence of an intestinal sub-inflammatory status in RTT subjects as measured by the elevated values of faecal calprotectin and erythrocyte sedimentation rate. We showed that, overall, RTT subjects harbour bacterial and fungal microbiota altered in terms of relative abundances from those of healthy controls, with a reduced microbial richness and dominated by microbial taxa belonging to Bifidobacterium, several Clostridia (among which Anaerostipes, Clostridium XIVa, Clostridium XIVb) as well as Erysipelotrichaceae, Actinomyces, Lactobacillus, Enterococcus, Eggerthella, Escherichia/Shigella and the fungal genus Candida. We further observed that alterations of the gut microbiota do not depend on the constipation status of RTT subjects and that this dysbiotic microbiota produced altered short chain fatty acids profiles.

CONCLUSIONS: We demonstrated for the first time that RTT is associated with a dysbiosis of both the bacterial and fungal component of the gut microbiota, suggesting that impairments of MeCP2 functioning favour the establishment of a microbial community adapted to the costive gastrointestinal niche of RTT subjects. The altered production of short chain fatty acids associated with this microbiota might reinforce the constipation status of RTT subjects and contribute to RTT gastrointestinal physiopathology.}, } @article {pmid27471001, year = {2016}, author = {Sul, WJ and Kim, IS and Ekpeghere, KI and Song, B and Kim, BS and Kim, HG and Kim, JT and Koh, SC}, title = {Metagenomic insight of nitrogen metabolism in a tannery wastewater treatment plant bioaugmented with the microbial consortium BM-S-1.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering}, volume = {51}, number = {13}, pages = {1164-1172}, doi = {10.1080/10934529.2016.1206387}, pmid = {27471001}, issn = {1532-4117}, mesh = {Ammonium Compounds/metabolism ; Bacteroidetes/metabolism ; DNA, Bacterial/isolation & purification ; Denitrification ; Firmicutes/metabolism ; *Genes, Bacterial ; *Microbial Consortia ; Molecular Sequence Annotation ; Nitrogen/isolation & purification/*metabolism ; Proteobacteria/metabolism ; Sewage/chemistry/*microbiology ; Waste Disposal, Fluid/methods ; }, abstract = {Nitrogen (N) removal in a tannery wastewater treatment plant was significantly enhanced by the bioaugmentation of the novel consortium BM-S-1. In order to identify dominant taxa responsible for N metabolisms in the different stages of the treatment process, Illumina MiSeq Sequencer was used to conduct metagenome sequencing of the microbial communities in the different stages of treatment system, including influent (I), buffering (B), primary aeration (PA), secondary aeration (SA) and sludge digestion (SD). Based on MG-RAST analysis, the dominant phyla were Proteobacteria, Bacteroidetes and Firmicutes in B, PA, SA and SD, whereas Firmicutes was the most dominant in I before augmentation. The augmentation increased the abundance of the denitrification genes found in the genera such as Ralstonia (nirS, norB and nosZ), Pseudomonas (narG, nirS and norB) and Escherichia (narG) in B and PA. In addition, Bacteroides, Geobacter, Porphyromonasand Wolinella carrying nrfA gene encoding dissimilatory nitrate reduction to ammonium were abundantly present in B and PA. This was corroborated with the higher total N removal in these two stages. Thus, metagenomic analysis was able to identify the dominant taxa responsible for dissimilatory N metabolisms in the tannery wastewater treatment system undergoing bioaugmentation. This metagenomic insight into the nitrogen metabolism will contribute to a successful monitoring and operation of the eco-friendly tannery wastewater treatment system.}, } @article {pmid27469346, year = {2016}, author = {Geach, T}, title = {Gut microbiota: Antibiotics do not affect metabolism in obesity.}, journal = {Nature reviews. Endocrinology}, volume = {12}, number = {10}, pages = {558}, pmid = {27469346}, issn = {1759-5037}, mesh = {*Anti-Bacterial Agents ; *Gastrointestinal Microbiome ; Gastrointestinal Tract ; Humans ; Metagenome ; Microbiota ; Obesity/genetics ; }, } @article {pmid27468850, year = {2016}, author = {Yu, G and Gail, MH and Consonni, D and Carugno, M and Humphrys, M and Pesatori, AC and Caporaso, NE and Goedert, JJ and Ravel, J and Landi, MT}, title = {Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features.}, journal = {Genome biology}, volume = {17}, number = {1}, pages = {163}, pmid = {27468850}, issn = {1474-760X}, mesh = {Aged ; Aged, 80 and over ; Biodiversity ; DNA Barcoding, Taxonomic ; Female ; Humans ; Lung/*microbiology ; Lung Neoplasms/complications/epidemiology/pathology ; Male ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; Neoplasm Staging ; Organ Specificity ; RNA, Ribosomal, 16S/genetics ; Reproductive Tract Infections/complications/epidemiology/microbiology ; Risk Factors ; }, abstract = {BACKGROUND: The human lung tissue microbiota remains largely uncharacterized, although a number of studies based on airway samples suggest the existence of a viable human lung microbiota. Here we characterized the taxonomic and derived functional profiles of lung microbiota in 165 non-malignant lung tissue samples from cancer patients.

RESULTS: We show that the lung microbiota is distinct from the microbial communities in oral, nasal, stool, skin, and vagina, with Proteobacteria as the dominant phylum (60 %). Microbiota taxonomic alpha diversity increases with environmental exposures, such as air particulates, residence in low to high population density areas, and pack-years of tobacco smoking and decreases in subjects with history of chronic bronchitis. Genus Thermus is more abundant in tissue from advanced stage (IIIB, IV) patients, while Legionella is higher in patients who develop metastases. Moreover, the non-malignant lung tissues have higher microbiota alpha diversity than the paired tumors.

CONCLUSIONS: Our results provide insights into the human lung microbiota composition and function and their link to human lifestyle and clinical outcomes. Studies among subjects without lung cancer are needed to confirm our findings.}, } @article {pmid27464827, year = {2016}, author = {Ju, F and Wang, Y and Lau, FT and Fung, WC and Huang, D and Xia, Y and Zhang, T}, title = {Anaerobic digestion of chemically enhanced primary treatment (CEPT) sludge and the microbial community structure.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {20}, pages = {8975-8982}, doi = {10.1007/s00253-016-7730-2}, pmid = {27464827}, issn = {1432-0614}, mesh = {Aluminum Chloride ; Aluminum Compounds/metabolism ; Anaerobiosis ; Bacteria/*classification/*metabolism ; *Biofuels ; *Biota ; Chemical Precipitation ; Chlorides/metabolism ; Ferric Compounds/metabolism ; Metagenomics ; Sewage/*microbiology ; }, abstract = {The effectiveness and treatment conditions of FeCl3- and AlCl3-coagulated municipal sewage sludge from chemically enhanced primary treatment (CEPT) using anaerobic digestion (AD) and the structure of microbial community were investigated. The results based on 297 measurements under different operational conditions demonstrate good average AD performance of CEPT sludge, that is, percent volatile solid reduction of 58 %, specific biogas production (or biogas yield) of 0.92 m(3)/kg volatile solids (VS) destroyed, and methane content of 65.4 %. FeCl3 dosing, organic loading rate, temperature, and hydraulic retention time all significantly affected AD performance. FeCl3 dosing greatly improved specific methane production (methane yield) by 38-54 % and significantly reduced hydrogen sulfide (H2S) content in biogas (from up to 13,250 to <200 ppm), contributing to higher methane recovery and simplified biogas cleaning for power generation. Metagenomic analysis suggested that anaerobic digesters of both CEPT sludge and combined primary and secondary sludge were dominated by Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria, Thermotogae, and Chloroflexi. However, Methanomicrobia methanogens were better enriched in the anaerobic digesters of CEPT sludge than in the combined sludge. Further, different sources of CEPT sludge with various chemical properties nurtured shared and unique microbial community composition. Combined, this study supports AD as an efficient technology for CEPT sludge treatment and poses first insights into the microbial community structure.}, } @article {pmid27462326, year = {2016}, author = {Trivedi, P and Delgado-Baquerizo, M and Anderson, IC and Singh, BK}, title = {Response of Soil Properties and Microbial Communities to Agriculture: Implications for Primary Productivity and Soil Health Indicators.}, journal = {Frontiers in plant science}, volume = {7}, number = {}, pages = {990}, pmid = {27462326}, issn = {1664-462X}, abstract = {Agricultural intensification is placing tremendous pressure on the soil's capacity to maintain its functions leading to large-scale ecosystem degradation and loss of productivity in the long term. Therefore, there is an urgent need to find early indicators of soil health degradation in response to agricultural management. In recent years, major advances in soil meta-genomic and spatial studies on microbial communities and community-level molecular characteristics can now be exploited as 'biomarker' indicators of ecosystem processes for monitoring and managing sustainable soil health under global change. However, a continental scale, cross biome approach assessing soil microbial communities and their functional potential to identify the unifying principles governing the susceptibility of soil biodiversity to land conversion is lacking. We conducted a meta-analysis from a dataset generated from 102 peer-reviewed publications as well as unpublished data to explore how properties directly linked to soil nutritional health (total C and N; C:N ratio), primary productivity (NPP) and microbial diversity and composition (relative abundance of major bacterial phyla determined by next generation sequencing techniques) are affected in response to agricultural management across the main biomes of Earth (arid, continental, temperate and tropical). In our analysis, we found strong statistical trends in the relative abundance of several bacterial phyla in agricultural (e.g., Actinobacteria and Chloroflexi) and natural (Acidobacteria, Proteobacteria, and Cyanobacteria) systems across all regions and these trends correlated well with many soil properties. However, main effects of agriculture on soil properties and productivity were biome-dependent. Our meta-analysis provides evidence on the predictable nature of the microbial community responses to vegetation type. This knowledge can be exploited in future for developing a new set of indicators for primary productivity and soil health.}, } @article {pmid27460447, year = {2016}, author = {Zhang, G and Liu, P and Zhang, L and Wei, W and Wang, X and Wei, D and Wang, W}, title = {Bioprospecting metagenomics of a microbial community on cotton degradation: Mining for new glycoside hydrolases.}, journal = {Journal of biotechnology}, volume = {234}, number = {}, pages = {35-42}, doi = {10.1016/j.jbiotec.2016.07.017}, pmid = {27460447}, issn = {1873-4863}, mesh = {Biomass ; *Bioprospecting ; Cellulose/metabolism ; Enzyme Activation ; Escherichia coli/genetics ; Glycoside Hydrolases/*genetics/metabolism ; Gossypium/*metabolism ; *Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {Glycoside hydrolases (GHases) of higher performance are immediately needed for efficient degradation of plant biomass into fermentable sugars in industrial processes. The current study represents functional characterization of the enzymatic repertoire involved in crude cotton biomass degradation. Physical contact between cells and substrate is necessary for efficient hydrolysis of cellulose. Cytophagales, which plays a major role in cotton biomass decomposition, was identified as a prevalent community member by 16S rRNA analysis. From the metagenome data, 2058 GHase homologs were identified, of which sixteen were successfully expressed in E. coli. Four enzymes showed activities on p-nitrophenyl-β-d-xylopyranoside, four showed activities on p-nitrophenyl-β-d-glucopyranoside, two had activities against p-nitrophenyl-β-d-glucuronide, one showed activity on laminarin, three had activities against p-nitrophenyl-N-acetyl-β-d-glucosaminide, one had activity towards carboxymethyl cellulose, and one towards p-nitrophenyl-β-d-mannopyranoside. Metagenomics provides a good resource for mining novel biomass degrading enzymes. The sixteen GHases that were cloned may have potential application for biomass conversion and bioproduct production. Functional characterization of the enzymatic repertoire in cotton biomass degradation and analysis of the GHases provide insight into the composition and interaction of enzymes and pathways of plant biomass degradation.}, } @article {pmid27458785, year = {2017}, author = {Wang, H and Sangwan, N and Li, HY and Su, JQ and Oyang, WY and Zhang, ZJ and Gilbert, JA and Zhu, YG and Ping, F and Zhang, HL}, title = {The antibiotic resistome of swine manure is significantly altered by association with the Musca domestica larvae gut microbiome.}, journal = {The ISME journal}, volume = {11}, number = {1}, pages = {100-111}, pmid = {27458785}, issn = {1751-7370}, mesh = {Agriculture ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics/isolation & purification ; *Drug Resistance, Bacterial ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/microbiology ; Houseflies/*microbiology ; Larva/microbiology ; Manure/*microbiology ; Swine ; }, abstract = {The overuse of antibiotics as veterinary feed additives is potentially contributing to a significant reservoir of antibiotic resistance in agricultural farmlands via the application of antibiotic-contaminated manure. Vermicomposting of swine manure using housefly larvae is a promising biotechnology for waste reduction and control of antibiotic pollution. To determine how vermicomposting influences antibiotic resistance traits in swine manure, we explored the resistome and associated bacterial community dynamics during larvae gut transit over 6 days of treatment. In total, 94 out of 158 antibiotic resistance genes (ARGs) were significantly attenuated (by 85%), while 23 were significantly enriched (3.9-fold) following vermicomposting. The manure-borne bacterial community showed a decrease in the relative abundance of Bacteroidetes, and an increase in Proteobacteria, specifically Ignatzschineria, following gut transit. ARG attenuation was significantly correlated with changes in microbial community succession, especially reduction in Clostridiales and Bacteroidales. Six genomes were assembled from the manure, vermicompost (final product) and gut samples, including Pseudomonas, Providencia, Enterococcus, Bacteroides and Alcanivorax. Transposon-linked ARGs were more abundant in gut-associated bacteria compared with those from manure and vermicompost. Further, ARG-transposon gene cassettes had a high degree of synteny between metagenomic assemblies from gut and vermicompost samples, highlighting the significant contribution of gut microbiota through horizontal gene transfer to the resistome of vermicompost. In conclusion, the larvae gut microbiome significantly influences manure-borne community succession and the antibiotic resistome during animal manure processing.}, } @article {pmid27456340, year = {2016}, author = {Gerasimidis, K and Bertz, M and Quince, C and Brunner, K and Bruce, A and Combet, E and Calus, S and Loman, N and Ijaz, UZ}, title = {The effect of DNA extraction methodology on gut microbiota research applications.}, journal = {BMC research notes}, volume = {9}, number = {}, pages = {365}, pmid = {27456340}, issn = {1756-0500}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; MR/M501621/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Benchmarking ; Chloroform/chemistry ; DNA/genetics/*isolation & purification ; DNA Barcoding, Taxonomic/*standards ; DNA, Bacterial/genetics/*isolation & purification ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Liquid Phase Microextraction/methods ; Phenol/chemistry ; RNA, Ribosomal, 16S/*genetics ; Real-Time Polymerase Chain Reaction/standards ; }, abstract = {BACKGROUND: The effect that traditional and modern DNA extraction methods have on applications to study the role of gut microbiota in health and disease is a topic of current interest. Genomic DNA was extracted from three faecal samples and one probiotic capsule using three popular methods; chaotropic (CHAO) method, phenol/chloroform (PHEC) extraction, proprietary kit (QIAG). The performance of each of these methods on DNA yield and quality, microbiota composition using quantitative PCR, deep sequencing of the 16S rRNA gene, and sequencing analysis pipeline was evaluated.

RESULTS: The CHAO yielded the highest and the QIAG kit the lowest amount of double-stranded DNA, but the purity of isolated nucleic acids was better for the latter method. The CHAO method yielded a higher concentration of bacterial taxa per mass (g) of faeces. Sequencing coverage was higher in CHAO method but a higher proportion of the initial sequencing reads were retained for assignments to operational taxonomic unit (OTU) in the QIAG kit compared to the other methods. The QIAG kit appeared to have longer trimmed reads and shorter regions of worse quality than the other two methods. A distinct separation of α-diversity indices between different DNA extraction methods was not observed. When compositional dissimilarities between samples were explored, a strong separation was observed according to sample type. The effect of the extraction method was either marginal (Bray-Curtis distance) or none (unweighted Unifrac distance). Taxon membership and abundance in each sample was independent of the DNA extraction method used.

CONCLUSIONS: We have benchmarked several DNA extraction methods commonly used in gut microbiota research and their differences depended on the downstream applications intended for use. Caution should be paid when the intention is to pool and analyse samples or data from studies which have used different DNA extraction methods.}, } @article {pmid27450246, year = {2016}, author = {Rothenberg, SE and Anders, M and Ajami, NJ and Petrosino, JF and Balogh, E}, title = {Water management impacts rice methylmercury and the soil microbiome.}, journal = {The Science of the total environment}, volume = {572}, number = {}, pages = {608-617}, pmid = {27450246}, issn = {1879-1026}, support = {L30 ES023165/ES/NIEHS NIH HHS/United States ; R15 ES022409/ES/NIEHS NIH HHS/United States ; }, mesh = {Agricultural Irrigation/*methods ; Agriculture/methods ; Food Contamination/analysis ; Mercury/analysis/metabolism ; Methylmercury Compounds/*analysis ; Microbiota/genetics/physiology ; Oryza/*chemistry/growth & development ; RNA, Ribosomal, 16S ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/*analysis ; }, abstract = {Rice farmers are pressured to grow rice using less water. The impacts of water-saving rice cultivation methods on rice methylmercury concentrations are uncertain. Rice (Oryza sativa L. cv. Nipponbare) was cultivated in fields using four water management treatments, including flooded (no dry-downs), alternating wetting and drying (AWD) (with one or three dry-downs), and furrow-irrigated fields (nine dry-downs) (n=16 fields). Anoxic bulk soil was collected from rice roots during the rice maturation phase, and rice grain was harvested after fields were dried. Total mercury and methylmercury concentrations were determined in soil and polished rice samples, and the soil microbiome was analyzed using 16S (v4) rRNA gene profiling. Soil total mercury did not differ between fields. However, compared to continuously flooded fields, soil and rice methylmercury concentrations averaged 51% and 38% lower in the AWD fields, respectively, and 95% and 96% lower in the furrow-irrigated fields, respectively. Compared to flooded fields, grain yield was reduced on average by <1% in the AWD fields and 34% in the furrow-irrigated fields. Additionally, using 16S (v4) rRNA gene profiling, the relative abundance of genera (i.e., highest resolution via this method) known to contain mercury methylators averaged 2.9-fold higher in flooded and AWD fields compared to furrow-irrigated fields. These results reinforce the benefits of AWD in reducing rice methylmercury concentrations with minimal changes in rice production yields. In the furrow-irrigated fields, a lower relative abundance of genera known to contain mercury methylators suggests an association between lower concentrations of soil and rice methylmercury and specific soil microbiomes.}, } @article {pmid27450128, year = {2016}, author = {Fontana, A and Patrone, V and Puglisi, E and Morelli, L and Bassi, D and Garuti, M and Rossi, L and Cappa, F}, title = {Effects of geographic area, feedstock, temperature, and operating time on microbial communities of six full-scale biogas plants.}, journal = {Bioresource technology}, volume = {218}, number = {}, pages = {980-990}, doi = {10.1016/j.biortech.2016.07.058}, pmid = {27450128}, issn = {1873-2976}, mesh = {Animal Feed ; Animals ; Biofuels/*microbiology ; Bioreactors/*microbiology ; Cattle ; Cheese ; Manure ; Temperature ; }, abstract = {The objective of this study was to investigate the effect of different animal feedings operated in two distinct PDO (protected designation of origin) cheese production areas (Parmigiano Reggiano and Grana Padano) on the microbiome of six full-scale biogas plants, by means of Illumina sequencing and qPCR techniques. The effects of feedstock (cattle slurry manure, energy crops, agro-industrial by-products), temperature (mesophilic/thermophilic), and operating time were also examined, as were the relationships between the predominant bacterial and archaeal taxa and process parameters. The different feedstocks and temperatures strongly affected the microbiomes. A more biodiverse archaeal population was highlighted in Parmigiano Reggiano area plants, suggesting an influence of the different animal feedings. Methanosarcina and Methanosaeta showed an opposite distribution among anaerobic plants, with the former found to be related to ammonium concentration. The Methanoculleus genus was more abundant in the thermophilic digester whereas representation of the Thermotogales order correlated with hydraulic retention time.}, } @article {pmid27447987, year = {2017}, author = {Shenoy, MK and Iwai, S and Lin, DL and Worodria, W and Ayakaka, I and Byanyima, P and Kaswabuli, S and Fong, S and Stone, S and Chang, E and Davis, JL and Faruqi, AA and Segal, MR and Huang, L and Lynch, SV}, title = {Immune Response and Mortality Risk Relate to Distinct Lung Microbiomes in Patients with HIV and Pneumonia.}, journal = {American journal of respiratory and critical care medicine}, volume = {195}, number = {1}, pages = {104-114}, pmid = {27447987}, issn = {1535-4970}, support = {T32 AI060537/AI/NIAID NIH HHS/United States ; R01 HL128156/HL/NHLBI NIH HHS/United States ; U01 HL098964/HL/NHLBI NIH HHS/United States ; K24 HL087713/HL/NHLBI NIH HHS/United States ; R01 HL090335/HL/NHLBI NIH HHS/United States ; }, mesh = {Bronchoalveolar Lavage Fluid/microbiology ; Coinfection/immunology/microbiology/*mortality ; Female ; HIV Infections/complications/immunology/microbiology/*mortality ; Humans ; Lung/*microbiology ; Male ; Microbiota/genetics/*immunology ; Pneumonia, Bacterial/complications/immunology/*mortality ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; }, abstract = {RATIONALE: The potential role of the airway microbiota in dictating immune responses and infection outcomes in HIV-associated pneumonia is largely unknown.

OBJECTIVES: To investigate whether microbiologically and immunologically distinct subsets of patients with HIV and pneumonia exist and are related to mortality.

METHODS: Bronchoalveolar lavage samples from Ugandan patients with HIV and pneumonia (n = 182) were obtained at study enrollment (following antibiotic treatment); patient demographics including 8- and 70-day mortality were collected. Lower airway bacterial community composition was assessed via amplification and sequencing of the V4 region of the 16S ribosomal RNA gene. Host immune response gene expression profiles were generated by quantitative polymerase chain reaction using RNA extracted from bronchoalveolar lavage fluid. Liquid and gas chromatography mass spectrometry was used to profile serum metabolites.

MEASUREMENTS AND MAIN RESULTS: Based on airway microbiome composition, most patients segregated into three distinct groups, each of which were predicted to encode metagenomes capable of producing metabolites characteristically enriched in paired serum samples from these patients. These three groups also exhibited differences in mortality; those with the highest rate had increased ceftriaxone administration and culturable Aspergillus, and demonstrated significantly increased induction of airway T-helper cell type 2 responses. The group with the lowest mortality was characterized by increased expression of T-cell immunoglobulin and mucin domain 3, which down-regulates T-helper cell type 1 proinflammatory responses and is associated with chronic viral infection.

CONCLUSIONS: These data provide evidence that compositionally and structurally distinct lower airway microbiomes are associated with discrete local host immune responses, peripheral metabolic reprogramming, and different rates of mortality.}, } @article {pmid27446044, year = {2016}, author = {Vilanova, C and Baixeras, J and Latorre, A and Porcar, M}, title = {The Generalist Inside the Specialist: Gut Bacterial Communities of Two Insect Species Feeding on Toxic Plants Are Dominated by Enterococcus sp.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1005}, pmid = {27446044}, issn = {1664-302X}, abstract = {Some specialist insects feed on plants rich in secondary compounds, which pose a major selective pressure on both the phytophagous and the gut microbiota. However, microbial communities of toxic plant feeders are still poorly characterized. Here, we show the bacterial communities of the gut of two specialized Lepidoptera, Hyles euphorbiae and Brithys crini, which exclusively feed on latex-rich Euphorbia sp. and alkaloid-rich Pancratium maritimum, respectively. A metagenomic analysis based on high-throughput sequencing of the 16S rRNA gene revealed that the gut microbiota of both insects is dominated by the phylum Firmicutes, and especially by the common gut inhabitant Enterococcus sp. Staphylococcus sp. are also found in H. euphorbiae though to a lesser extent. By scanning electron microscopy, we found a dense ring-shaped bacterial biofilm in the hindgut of H. euphorbiae, and identified the most prominent bacterium in the biofilm as Enterococcus casseliflavus through molecular techniques. Interestingly, this species has previously been reported to contribute to the immobilization of latex-like molecules in the larvae of Spodoptera litura, a highly polyphagous lepidopteran. The E. casseliflavus strain was isolated from the gut and its ability to tolerate natural latex was tested under laboratory conditions. This fact, along with the identification of less frequent bacterial species able to degrade alkaloids and/or latex, suggest a putative role of bacterial communities in the tolerance of specialized insects to their toxic diet.}, } @article {pmid27442850, year = {2016}, author = {Medina, E and Ruiz-Bellido, MA and Romero-Gil, V and Rodríguez-Gómez, F and Montes-Borrego, M and Landa, BB and Arroyo-López, FN}, title = {Assessment of the bacterial community in directly brined Aloreña de Málaga table olive fermentations by metagenetic analysis.}, journal = {International journal of food microbiology}, volume = {236}, number = {}, pages = {47-55}, doi = {10.1016/j.ijfoodmicro.2016.07.014}, pmid = {27442850}, issn = {1879-3460}, mesh = {Bacteria/*genetics ; Biodiversity ; Fermentation ; *Food Microbiology ; Humans ; Metagenome ; Olea/*microbiology ; RNA, Ribosomal, 16S ; Salts ; Spain ; Yeasts/*genetics ; }, abstract = {This study uses an "omics" approach to evaluate the bacterial biodiversity changes during fermentation process of natural green cracked Aloreña de Málaga table olives, from raw material to fermented fruit. For this purpose, two industries separated by almost 20km in Guadalhorce Valley (Málaga, Spain) were analysed for obtaining both brines and fruit samples at different moments of fermentation (0, 7, 30 and 120days). Physicochemical and microbial counts during fermentation showed the typical evolution of this type of processes, apparently dominated by yeasts. However, high-throughput barcoded pyrosequencing analysis of V2-V3 hypervariable region of the bacterial 16S rRNA gene showed at 97% identity the presence of 131 bacterial genera included in 357 operational taxonomic units, not detected by the conventional approach. The bacterial biodiversity was clearly higher in the olives at the moment of reception in the industry and during the first days of fermentation, while decreased considerably as elapse the fermentation process. The presence of Enterobacteriaceae and Lactobacillaceae species was scarce during the four months of study. On the contrary, the most important genus at the end of fermentation was Celerinatantimonas in both brine (95.3% of frequency) and fruit (89.4%) samples, while the presence of well-known spoilage microorganisms (Pseudomonas and Propionibacterium) and halophilic bacteria (Modestobacter, Rhodovibrio, Salinibacter) was also common during the course of fermentation. Among the most important bacterial pathogens related to food, only Staphylococcus genus was found at low frequencies (<0.02% of total sequences). Results show the need of this type of studies to enhance our knowledge of the microbiology of table olive fermentations. It is also necessary to determine the role played by these species not previously detected in table olives on the quality and safety of this fermented vegetable.}, } @article {pmid27437861, year = {2017}, author = {Zhang, HG and Lv, MH and Yi, WB and Zhu, WB and Bu, WJ}, title = {Species diversity can be overestimated by a fixed empirical threshold: insights from DNA barcoding of the genus Cletus (Hemiptera: Coreidae) and the meta-analysis of COI data from previous phylogeographical studies.}, journal = {Molecular ecology resources}, volume = {17}, number = {2}, pages = {314-323}, doi = {10.1111/1755-0998.12571}, pmid = {27437861}, issn = {1755-0998}, mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Heteroptera/*classification/enzymology/*genetics ; Metagenomics/*methods ; }, abstract = {The use of genetic distances to identify species within the framework of DNA barcoding has to some extent improved the development of biodiversity studies. However, using a fixed empirical threshold to delimit species may lead to overestimating species diversity. In this study, we use a new data set of COI sequences for 366 specimens within the genus of Cletus as well as conduct an analysis on the same genetic data for collected morphologically defined species from previous phylogeographical studies, to test whether high intraspecific genetic divergences are common with the premises of comprehensive sampling. The results indicate C. graminis Hsiao & Cheng , is the same species with C. punctiger (Dallas, 1852) and should be synonymized and that the distributional record of C. pugnator (Fabricius, 1787) in China is correct. High intraspecific genetic differentiations (0%-4.35%) were found in C. punctiger. Furthermore, as to the mined data, the maximum intraspecific K2P distances of 186 species (48.44% of 384) exceed 3%, and 101 species (26.30%) can be divided into two or more clusters with a threshold of 3% in cluster analysis. If genetic distance is used to delimit species boundaries, the minimum interspecific K2P distance of the congeneric species should be considered rather than only using the fixed empirical value; otherwise, the species richness may be overestimated in some cases.}, } @article {pmid27428540, year = {2016}, author = {Lee, SW and Kuan, CS and Wu, LS and Weng, JT}, title = {Metagenome and Metatranscriptome Profiling of Moderate and Severe COPD Sputum in Taiwanese Han Males.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0159066}, pmid = {27428540}, issn = {1932-6203}, mesh = {Aged ; Aged, 80 and over ; Bacteria/classification/*genetics/isolation & purification ; Bacterial Infections/*complications/*microbiology ; DNA, Bacterial/genetics/isolation & purification ; Genome, Bacterial ; Humans ; Lung/*microbiology ; Male ; Metagenome ; *Microbiota ; Middle Aged ; Pulmonary Disease, Chronic Obstructive/epidemiology/*microbiology ; RNA, Bacterial/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics/isolation & purification ; Sputum/*microbiology ; Taiwan/epidemiology ; Transcriptome ; }, abstract = {Chronic obstructive pulmonary disease (COPD) is an inflammatory lung disorder characterized by the progressive obstruction of airflow and is currently the fourth leading cause of death in the world. The pathogenesis of COPD is thought to involve bacterial infections and inflammations. Owing to advancement in sequencing technology, evidence is emerging that supports an association between the lung microbiome and COPD. However, few studies have looked into the expression profile of the bacterial communities in the COPD lungs. In this study, we analyzed the sputum microbiome of four moderate and four severe COPD male patients both at the DNA and RNA level, using next generation sequencing technology. We found that bacterial composition determined by 16S rRNA gene sequencing may not directly translate to the set of actively expressing bacteria as defined by transcriptome sequencing. The two sequencing data agreed on Prevotella, Rothia, Neisseria, Porphyromonas, Veillonella, Fusobacterium and Streptococcus being among the most differentially abundant genera between the moderate and severe COPD samples, supporting their association with COPD severity. However, the two sequencing analyses disagreed on the relative abundance of these bacteria in the two COPD groups, implicating the importance of studying the actively expressing bacteria for enriching our understanding of COPD. Though we have described the metatranscriptome profiles of the lung microbiome in moderate and severe COPD, further investigations are required to determine the functional basis underlying the relationship between the microbial species in the lungs and pathogenesis of COPD.}, } @article {pmid27428430, year = {2016}, author = {Chng, KR and Chan, SH and Ng, AHQ and Li, C and Jusakul, A and Bertrand, D and Wilm, A and Choo, SP and Tan, DMY and Lim, KH and Soetinko, R and Ong, CK and Duda, DG and Dima, S and Popescu, I and Wongkham, C and Feng, Z and Yeoh, KG and Teh, BT and Yongvanit, P and Wongkham, S and Bhudhisawasdi, V and Khuntikeo, N and Tan, P and Pairojkul, C and Ngeow, J and Nagarajan, N}, title = {Tissue Microbiome Profiling Identifies an Enrichment of Specific Enteric Bacteria in Opisthorchis viverrini Associated Cholangiocarcinoma.}, journal = {EBioMedicine}, volume = {8}, number = {}, pages = {195-202}, pmid = {27428430}, issn = {2352-3964}, support = {P01 CA080124/CA/NCI NIH HHS/United States ; R01 CA159258/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Animals ; Bile Duct Neoplasms/*etiology ; Biodiversity ; Cell Transformation, Neoplastic ; Cholangiocarcinoma/*etiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Opisthorchiasis/*complications/*parasitology ; *Opisthorchis ; Organ Specificity ; RNA, Ribosomal, 16S ; }, abstract = {Cholangiocarcinoma (CCA) is the primary cancer of the bile duct system. The role of bile duct tissue microbiomes in CCA tumorigenesis is unestablished. To address this, sixty primary CCA tumors and matched normals, from both liver fluke (Opisthorchis viverrini) associated (OVa, n=28) and non-O. viverrini associated (non-OVa, n=32) cancers, were profiled using high-throughput 16S rRNA sequencing. A distinct, tissue-specific microbiome dominated by the bacterial families Dietziaceae, Pseudomonadaceae and Oxalobacteraceae was observed in bile duct tissues. Systemic perturbation of the microbiome was noted in tumor and paired normal samples (vs non-cancer normals) for several bacterial families with a significant increase in Stenotrophomonas species distinguishing tumors vs paired normals. Comparison of parasite associated (OVa) vs non-associated (non-OVa) groups identified enrichment for specific enteric bacteria (Bifidobacteriaceae, Enterobacteriaceae and Enterococcaceae). One of the enriched families, Bifidobacteriaceae, was found to be dominant in the O. viverrini microbiome, providing a mechanistic link to the parasite. Functional analysis and comparison of CCA microbiomes revealed higher potential for producing bile acids and ammonia in OVa tissues, linking the altered microbiota to carcinogenesis. These results define how the unique microbial communities resident in the bile duct, parasitic infections and the tissue microenvironment can influence each other, and contribute to cancer.}, } @article {pmid27420030, year = {2017}, author = {Thompson, LR and Williams, GJ and Haroon, MF and Shibl, A and Larsen, P and Shorenstein, J and Knight, R and Stingl, U}, title = {Metagenomic covariation along densely sampled environmental gradients in the Red Sea.}, journal = {The ISME journal}, volume = {11}, number = {1}, pages = {138-151}, pmid = {27420030}, issn = {1751-7370}, mesh = {Bacteria/classification/*genetics/*isolation & purification ; Environment ; Indian Ocean ; Marine Biology ; Metagenome ; Metagenomics ; Phylogeny ; Salinity ; Seawater/analysis/*microbiology ; Temperature ; }, abstract = {Oceanic microbial diversity covaries with physicochemical parameters. Temperature, for example, explains approximately half of global variation in surface taxonomic abundance. It is unknown, however, whether covariation patterns hold over narrower parameter gradients and spatial scales, and extending to mesopelagic depths. We collected and sequenced 45 epipelagic and mesopelagic microbial metagenomes on a meridional transect through the eastern Red Sea. We asked which environmental parameters explain the most variation in relative abundances of taxonomic groups, gene ortholog groups, and pathways-at a spatial scale of <2000 km, along narrow but well-defined latitudinal and depth-dependent gradients. We also asked how microbes are adapted to gradients and extremes in irradiance, temperature, salinity, and nutrients, examining the responses of individual gene ortholog groups to these parameters. Functional and taxonomic metrics were equally well explained (75-79%) by environmental parameters. However, only functional and not taxonomic covariation patterns were conserved when comparing with an intruding water mass with different physicochemical properties. Temperature explained the most variation in each metric, followed by nitrate, chlorophyll, phosphate, and salinity. That nitrate explained more variation than phosphate suggested nitrogen limitation, consistent with low surface N:P ratios. Covariation of gene ortholog groups with environmental parameters revealed patterns of functional adaptation to the challenging Red Sea environment: high irradiance, temperature, salinity, and low nutrients. Nutrient-acquisition gene ortholog groups were anti-correlated with concentrations of their respective nutrient species, recapturing trends previously observed across much larger distances and environmental gradients. This dataset of metagenomic covariation along densely sampled environmental gradients includes online data exploration supplements, serving as a community resource for marine microbial ecology.}, } @article {pmid27418359, year = {2016}, author = {Jiménez, DJ and de Lima Brossi, MJ and Schückel, J and Kračun, SK and Willats, WG and van Elsas, JD}, title = {Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {24}, pages = {10463-10477}, pmid = {27418359}, issn = {1432-0614}, mesh = {Aerobiosis ; Bacteria/*classification/enzymology/genetics ; Biotransformation ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Enzymes/metabolism ; Lignin/*metabolism ; *Metagenomics ; *Microbial Consortia ; Panicum/chemistry ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Triticum/chemistry ; Zea mays/chemistry ; }, abstract = {The selection of microbes by enrichment on plant biomass has been proposed as an efficient way to develop new strategies for lignocellulose saccharification. Here, we report an in-depth analysis of soil-derived microbial consortia that were trained to degrade once-used wheat straw (WS1-M), switchgrass (SG-M) and corn stover (CS-M) under aerobic and mesophilic conditions. Molecular fingerprintings, bacterial 16S ribosomal RNA (rRNA) gene amplicon sequencing and metagenomic analyses showed that the three microbial consortia were taxonomically distinct. Based on the taxonomic affiliation of protein-encoding sequences, members of the Bacteroidetes (e.g. Chryseobacterium, Weeksella, Flavobacterium and Sphingobacterium) were preferentially selected on WS1-M, whereas SG-M and CS-M favoured members of the Proteobacteria (e.g. Caulobacter, Brevundimonas, Stenotrophomonas and Xanthomonas). The highest degradation rates of lignin (~59 %) were observed with SG-M, whereas CS-M showed a high consumption of cellulose and hemicellulose. Analyses of the carbohydrate-active enzymes in the three microbial consortia showed the dominance of glycosyl hydrolases (e.g. of families GH3, GH43, GH13, GH10, GH29, GH28, GH16, GH4 and GH92). In addition, proteins of families AA6, AA10 and AA2 were detected. Analysis of secreted protein fractions (metasecretome) for each selected microbial consortium mainly showed the presence of enzymes able to degrade arabinan, arabinoxylan, xylan, β-glucan, galactomannan and rhamnogalacturonan. Notably, these metasecretomes contain enzymes that enable us to produce oligosaccharides directly from wheat straw, sugarcane bagasse and willow. Thus, the underlying microbial consortia constitute valuable resources for the production of enzyme cocktails for the efficient saccharification of plant biomass.}, } @article {pmid27417702, year = {2016}, author = {Hause, BM and Padmanabhan, A and Pedersen, K and Gidlewski, T}, title = {Feral swine virome is dominated by single-stranded DNA viruses and contains a novel Orthopneumovirus which circulates both in feral and domestic swine.}, journal = {The Journal of general virology}, volume = {97}, number = {9}, pages = {2090-2095}, doi = {10.1099/jgv.0.000554}, pmid = {27417702}, issn = {1465-2099}, mesh = {Animals ; Antibodies, Viral/blood ; *Biodiversity ; Metagenomics ; Nasal Mucosa/virology ; Sus scrofa/*virology ; United States ; Viruses/*classification/genetics/*isolation & purification ; }, abstract = {Feral swine are known reservoirs for various pathogens that can adversely affect domestic animals. To assess the viral ecology of feral swine in the USA, metagenomic sequencing was performed on 100 pooled nasal swabs. The virome was dominated by small, ssDNA viruses belonging to the families Circoviridae, Anelloviridae and Parvovirinae. Only four RNA viruses were identified: porcine kobuvirus, porcine sapelovirus, atypical porcine pestivirus and a novel Orthopneumovirus, provisionally named swine orthopneumovirus (SOV). SOV shared ~90 % nucleotide identity to murine pneumonia virus (MPV) and canine pneumovirus. A modified, commercially available ELISA for MPV found that approximately 30 % of both feral and domestic swine sera were positive for antibodies cross-reactive with MPV. Quantitative reverse transcription-PCR identified two (2 %) and four (5.0 %) positive nasal swab pools from feral and domestic swine, respectively, confirming that SOV circulates in both herds.}, } @article {pmid27417261, year = {2016}, author = {Abreu, NA and Taga, ME}, title = {Decoding molecular interactions in microbial communities.}, journal = {FEMS microbiology reviews}, volume = {40}, number = {5}, pages = {648-663}, pmid = {27417261}, issn = {1574-6976}, support = {DP2 AI117984/AI/NIAID NIH HHS/United States ; }, mesh = {Aquatic Organisms/*genetics ; Bacteria/*genetics/*metabolism ; Base Sequence ; DNA, Bacterial/genetics ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenomics/methods ; Microbial Interactions/*genetics ; Oceans and Seas ; Sequence Analysis, DNA ; }, abstract = {Microbial communities govern numerous fundamental processes on earth. Discovering and tracking molecular interactions among microbes is critical for understanding how single species and complex communities impact their associated host or natural environment. While recent technological developments in DNA sequencing and functional imaging have led to new and deeper levels of understanding, we are limited now by our inability to predict and interpret the intricate relationships and interspecies dependencies within these communities. In this review, we highlight the multifaceted approaches investigators have taken within their areas of research to decode interspecies molecular interactions that occur between microbes. Understanding these principles can give us greater insight into ecological interactions in natural environments and within synthetic consortia.}, } @article {pmid27416516, year = {2016}, author = {Latorre, M and Cortés, MP and Travisany, D and Di Genova, A and Budinich, M and Reyes-Jara, A and Hödar, C and González, M and Parada, P and Bobadilla-Fazzini, RA and Cambiazo, V and Maass, A}, title = {The bioleaching potential of a bacterial consortium.}, journal = {Bioresource technology}, volume = {218}, number = {}, pages = {659-666}, doi = {10.1016/j.biortech.2016.07.012}, pmid = {27416516}, issn = {1873-2976}, mesh = {Acidithiobacillus/*metabolism ; Acidithiobacillus thiooxidans/*metabolism ; Bacteria/metabolism ; Copper/*isolation & purification ; Iron/metabolism ; *Metagenome ; Metals/metabolism ; *Microbial Consortia ; Oxidation-Reduction ; Sulfides/metabolism ; Sulfur Compounds/metabolism ; }, abstract = {This work presents the molecular foundation of a consortium of five efficient bacteria strains isolated from copper mines currently used in state of the art industrial-scale biotechnology. The strains Acidithiobacillus thiooxidans Licanantay, Acidiphilium multivorum Yenapatur, Leptospirillum ferriphilum Pañiwe, Acidithiobacillus ferrooxidans Wenelen and Sulfobacillus thermosulfidooxidans Cutipay were selected for genome sequencing based on metal tolerance, oxidation activity and bioleaching of copper efficiency. An integrated model of metabolic pathways representing the bioleaching capability of this consortium was generated. Results revealed that greater efficiency in copper recovery may be explained by the higher functional potential of L. ferriphilum Pañiwe and At. thiooxidans Licanantay to oxidize iron and reduced inorganic sulfur compounds. The consortium had a greater capacity to resist copper, arsenic and chloride ion compared to previously described biomining strains. Specialization and particular components in these bacteria provided the consortium a greater ability to bioleach copper sulfide ores.}, } @article {pmid27411898, year = {2016}, author = {Shin, J and Lee, S and Go, MJ and Lee, SY and Kim, SC and Lee, CH and Cho, BK}, title = {Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {29681}, pmid = {27411898}, issn = {2045-2322}, mesh = {Animals ; Bacteria/*genetics ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Male ; Metagenome/genetics ; Mice ; Mice, Inbred C57BL ; Nanopores ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Demands for faster and more accurate methods to analyze microbial communities from natural and clinical samples have been increasing in the medical and healthcare industry. Recent advances in next-generation sequencing technologies have facilitated the elucidation of the microbial community composition with higher accuracy and greater throughput than was previously achievable; however, the short sequencing reads often limit the microbial composition analysis at the species level due to the high similarity of 16S rRNA amplicon sequences. To overcome this limitation, we used the nanopore sequencing platform to sequence full-length 16S rRNA amplicon libraries prepared from the mouse gut microbiota. A comparison of the nanopore and short-read sequencing data showed that there were no significant differences in major taxonomic units (89%) except one phylotype and three taxonomic units. Moreover, both sequencing data were highly similar at all taxonomic resolutions except the species level. At the species level, nanopore sequencing allowed identification of more species than short-read sequencing, facilitating the accurate classification of the bacterial community composition. Therefore, this method of full-length 16S rRNA amplicon sequencing will be useful for rapid, accurate and efficient detection of microbial diversity in various biological and clinical samples.}, } @article {pmid27409811, year = {2016}, author = {Pedersen, HK and Gudmundsdottir, V and Nielsen, HB and Hyotylainen, T and Nielsen, T and Jensen, BA and Forslund, K and Hildebrand, F and Prifti, E and Falony, G and Le Chatelier, E and Levenez, F and Doré, J and Mattila, I and Plichta, DR and Pöhö, P and Hellgren, LI and Arumugam, M and Sunagawa, S and Vieira-Silva, S and Jørgensen, T and Holm, JB and Trošt, K and , and Kristiansen, K and Brix, S and Raes, J and Wang, J and Hansen, T and Bork, P and Brunak, S and Oresic, M and Ehrlich, SD and Pedersen, O}, title = {Human gut microbes impact host serum metabolome and insulin sensitivity.}, journal = {Nature}, volume = {535}, number = {7612}, pages = {376-381}, pmid = {27409811}, issn = {1476-4687}, mesh = {Amino Acids, Branched-Chain/biosynthesis/metabolism ; Animals ; Bacteroides/physiology ; Cardiovascular Diseases/metabolism/microbiology ; Fasting/blood/metabolism ; Gastrointestinal Microbiome/*physiology ; Glucose Intolerance/blood/microbiology ; Humans ; *Insulin Resistance ; Male ; *Metabolome ; Metagenome ; Mice ; Mice, Inbred C57BL ; Netherlands ; Prevotella/physiology ; Serum/*metabolism ; }, abstract = {Insulin resistance is a forerunner state of ischaemic cardiovascular disease and type 2 diabetes. Here we show how the human gut microbiome impacts the serum metabolome and associates with insulin resistance in 277 non-diabetic Danish individuals. The serum metabolome of insulin-resistant individuals is characterized by increased levels of branched-chain amino acids (BCAAs), which correlate with a gut microbiome that has an enriched biosynthetic potential for BCAAs and is deprived of genes encoding bacterial inward transporters for these amino acids. Prevotella copri and Bacteroides vulgatus are identified as the main species driving the association between biosynthesis of BCAAs and insulin resistance, and in mice we demonstrate that P. copri can induce insulin resistance, aggravate glucose intolerance and augment circulating levels of BCAAs. Our findings suggest that microbial targets may have the potential to diminish insulin resistance and reduce the incidence of common metabolic and cardiovascular disorders.}, } @article {pmid27409808, year = {2016}, author = {Brito, IL and Yilmaz, S and Huang, K and Xu, L and Jupiter, SD and Jenkins, AP and Naisilisili, W and Tamminen, M and Smillie, CS and Wortman, JR and Birren, BW and Xavier, RJ and Blainey, PC and Singh, AK and Gevers, D and Alm, EJ}, title = {Mobile genes in the human microbiome are structured from global to individual scales.}, journal = {Nature}, volume = {535}, number = {7612}, pages = {435-439}, pmid = {27409808}, issn = {1476-4687}, support = {U54 HG003067/HG/NHGRI NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; U54HG003067/HG/NHGRI NIH HHS/United States ; T32 GM087237/GM/NIGMS NIH HHS/United States ; R01 DE020891/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteriophages/genetics ; Cohort Studies ; DNA Transposable Elements/genetics ; Diet ; Fiji ; Gene Pool ; Gene Transfer, Horizontal/*genetics ; *Gene-Environment Interaction ; Genetic Variation/*genetics ; Humans ; *Metagenomics ; Microbiota/*genetics ; North America ; Plasmids/genetics ; Recombination, Genetic/genetics ; Selection, Genetic/*genetics ; Single-Cell Analysis ; }, abstract = {Recent work has underscored the importance of the microbiome in human health, and has largely attributed differences in phenotype to differences in the species present among individuals. However, mobile genes can confer profoundly different phenotypes on different strains of the same species. Little is known about the function and distribution of mobile genes in the human microbiome, and in particular whether the gene pool is globally homogenous or constrained by human population structure. Here, we investigate this question by comparing the mobile genes found in the microbiomes of 81 metropolitan North Americans with those of 172 agrarian Fiji islanders using a combination of single-cell genomics and metagenomics. We find large differences in mobile gene content between the Fijian and North American microbiomes, with functional variation that mirrors known dietary differences such as the excess of plant-based starch degradation genes found in Fijian individuals. Notably, we also observed differences between the mobile gene pools of neighbouring Fijian villages, even though microbiome composition across villages is similar. Finally, we observe high rates of recombination leading to individual-specific mobile elements, suggesting that the abundance of some genes may reflect environmental selection rather than dispersal limitation. Together, these data support the hypothesis that human activities and behaviours provide selective pressures that shape mobile gene pools, and that acquisition of mobile genes is important for colonizing specific human populations.}, } @article {pmid27406942, year = {2017}, author = {Piper, HG and Fan, D and Coughlin, LA and Ho, EX and McDaniel, MM and Channabasappa, N and Kim, J and Kim, M and Zhan, X and Xie, Y and Koh, AY}, title = {Severe Gut Microbiota Dysbiosis Is Associated With Poor Growth in Patients With Short Bowel Syndrome.}, journal = {JPEN. Journal of parenteral and enteral nutrition}, volume = {41}, number = {7}, pages = {1202-1212}, doi = {10.1177/0148607116658762}, pmid = {27406942}, issn = {1941-2444}, support = {P30 CA142543/CA/NCI NIH HHS/United States ; R01 CA152301/CA/NCI NIH HHS/United States ; R01 CA172211/CA/NCI NIH HHS/United States ; R01 CA152301/CA/NCI NIH HHS/United States ; R01 CA172211/CA/NCI NIH HHS/United States ; P30 CA142543/CA/NCI NIH HHS/United States ; }, mesh = {*Bacteria/genetics ; Child ; Child, Preschool ; Clostridiales/genetics ; Dysbiosis/*complications/metabolism/microbiology ; Enterobacteriaceae/genetics ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Growth Disorders/*etiology/metabolism/microbiology ; Humans ; Infant ; Inflammation/microbiology ; Intestine, Small/metabolism/*microbiology/pathology ; Male ; Short Bowel Syndrome/*complications/metabolism/microbiology ; *Weight Gain ; }, abstract = {BACKGROUND: Children with short bowel syndrome (SBS) can vary significantly in their growth trajectory. Recent data have shown that children with SBS possess a unique gut microbiota signature compared with healthy controls. We hypothesized that children with SBS and poor growth would exhibit more severe gut microbiota dysbiosis compared with those with SBS who are growing adequately, despite similar intestinal anatomy.

MATERIALS AND METHODS: Stool samples were collected from children with SBS (n = 8) and healthy controls (n = 3) over 3 months. Gut microbiota populations (16S ribosomal RNA sequencing and metagenomic shotgun sequencing) were compared, including a more in-depth analysis of SBS children exhibiting poor and good growth. Statistical analysis was performed using Mann-Whitney, Kruskal-Wallis, and χ[2] tests as appropriate.

RESULTS: Children with SBS had a significant deficiency of the commensal Firmicutes order Clostridiales (P = .025, Kruskal-Wallis) compared with healthy children. Furthermore, children with SBS and poor growth were deficient in beneficial bacteria known to produce short-chain fatty acids and had expansion of proinflammatory Enterobacteriaceae (P = .038, Kruskal-Wallis) compared with children with SBS who were growing adequately. Using metabolic function analyses, SBS/poor growth microbiomes were deficient in genes needed for gluconeogenesis but enriched in branched and aromatic amino acid synthesis and citrate cycle pathway genes.

CONCLUSIONS: Patients with SBS, particularly those with suboptimal growth, have a marked gut dysbiosis characterized by a paucity of beneficial commensal anaerobes, resulting in a deficiency of key metabolic enzymes found in the gut microbiomes of healthy children.}, } @article {pmid27404280, year = {2016}, author = {Armanhi, JS and de Souza, RS and de Araújo, LM and Okura, VK and Mieczkowski, P and Imperial, J and Arruda, P}, title = {Multiplex amplicon sequencing for microbe identification in community-based culture collections.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {29543}, pmid = {27404280}, issn = {2045-2322}, mesh = {Culture Techniques ; DNA, Bacterial ; *Genetics, Microbial ; Metagenomics/*methods ; *Microbiological Techniques ; *Microbiota ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; Saccharum/microbiology ; Sequence Analysis, DNA/*methods ; }, abstract = {Microbiome analysis using metagenomic sequencing has revealed a vast microbial diversity associated with plants. Identifying the molecular functions associated with microbiome-plant interaction is a significant challenge concerning the development of microbiome-derived technologies applied to agriculture. An alternative to accelerate the discovery of the microbiome benefits to plants is to construct microbial culture collections concomitant with accessing microbial community structure and abundance. However, traditional methods of isolation, cultivation, and identification of microbes are time-consuming and expensive. Here we describe a method for identification of microbes in culture collections constructed by picking colonies from primary platings that may contain single or multiple microorganisms, which we named community-based culture collections (CBC). A multiplexing 16S rRNA gene amplicon sequencing based on two-step PCR amplifications with tagged primers for plates, rows, and columns allowed the identification of the microbial composition regardless if the well contains single or multiple microorganisms. The multiplexing system enables pooling amplicons into a single tube. The sequencing performed on the PacBio platform led to recovery near-full-length 16S rRNA gene sequences allowing accurate identification of microorganism composition in each plate well. Cross-referencing with plant microbiome structure and abundance allowed the estimation of diversity and abundance representation of microorganism in the CBC.}, } @article {pmid27400279, year = {2016}, author = {Pasolli, E and Truong, DT and Malik, F and Waldron, L and Segata, N}, title = {Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights.}, journal = {PLoS computational biology}, volume = {12}, number = {7}, pages = {e1004977}, pmid = {27400279}, issn = {1553-7358}, support = {R21 AI121784/AI/NIAID NIH HHS/United States ; U24 CA180996/CA/NCI NIH HHS/United States ; }, mesh = {Colorectal Neoplasms/genetics ; Computational Biology/methods ; Gastrointestinal Microbiome/*genetics ; Humans ; Inflammatory Bowel Diseases/genetics ; *Machine Learning ; Metagenome/*genetics ; Metagenomics/*methods ; Obesity/genetics ; Software ; }, abstract = {Shotgun metagenomic analysis of the human associated microbiome provides a rich set of microbial features for prediction and biomarker discovery in the context of human diseases and health conditions. However, the use of such high-resolution microbial features presents new challenges, and validated computational tools for learning tasks are lacking. Moreover, classification rules have scarcely been validated in independent studies, posing questions about the generality and generalization of disease-predictive models across cohorts. In this paper, we comprehensively assess approaches to metagenomics-based prediction tasks and for quantitative assessment of the strength of potential microbiome-phenotype associations. We develop a computational framework for prediction tasks using quantitative microbiome profiles, including species-level relative abundances and presence of strain-specific markers. A comprehensive meta-analysis, with particular emphasis on generalization across cohorts, was performed in a collection of 2424 publicly available metagenomic samples from eight large-scale studies. Cross-validation revealed good disease-prediction capabilities, which were in general improved by feature selection and use of strain-specific markers instead of species-level taxonomic abundance. In cross-study analysis, models transferred between studies were in some cases less accurate than models tested by within-study cross-validation. Interestingly, the addition of healthy (control) samples from other studies to training sets improved disease prediction capabilities. Some microbial species (most notably Streptococcus anginosus) seem to characterize general dysbiotic states of the microbiome rather than connections with a specific disease. Our results in modelling features of the "healthy" microbiome can be considered a first step toward defining general microbial dysbiosis. The software framework, microbiome profiles, and metadata for thousands of samples are publicly available at http://segatalab.cibio.unitn.it/tools/metaml.}, } @article {pmid27398939, year = {2016}, author = {Montagna, M and Mereghetti, V and Gargari, G and Guglielmetti, S and Faoro, F and Lozzia, G and Locatelli, D and Limonta, L}, title = {Evidence of a bacterial core in the stored products pest Plodia interpunctella: the influence of different diets.}, journal = {Environmental microbiology}, volume = {18}, number = {12}, pages = {4961-4973}, doi = {10.1111/1462-2920.13450}, pmid = {27398939}, issn = {1462-2920}, mesh = {Animals ; Bacteria/*classification/*genetics/isolation & purification ; *Diet ; *Feeding Behavior ; Microbiota/*genetics ; Moths/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The potential influence of insects' feeding behaviour on their associated bacterial communities is currently a matter of debate. Using the major pest of commodities, Plodia interpunctella, as a model and adopting a culture-independent approach, the impact of different diets on the host-associated microbiota was evaluated. An analysis of similarity showed differences among the microbiotas of moths fed with five substrates and provided evidence that diet represents the only tested factor that explains this dissimilarity. Bacteria shared between food and insects provide evidence for a limited conveyance to the host of the bacteria derived from the diet; more likely, the content of carbohydrates and proteins in the diets promotes changes in the insect's microbiota. Moth microbiotas were characterized by two robust entomotypes, respectively, associated with a carbohydrate-rich diet and a protein-rich diet. These results were also confirmed by the predicted metagenome functional potential. A core microbiota, composed of six taxa, was shared between eggs and adults, regardless of the origin of the population. Finally, the identification of possible human and animal pathogens on chili and associated with the moths that feed on it highlights the possibility that these bacteria may be conveyed by moth frass.}, } @article {pmid27396978, year = {2016}, author = {May, DH and Timmins-Schiffman, E and Mikan, MP and Harvey, HR and Borenstein, E and Nunn, BL and Noble, WS}, title = {An Alignment-Free "Metapeptide" Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing.}, journal = {Journal of proteome research}, volume = {15}, number = {8}, pages = {2697-2705}, pmid = {27396978}, issn = {1535-3907}, support = {P41 GM103533/GM/NIGMS NIH HHS/United States ; }, mesh = {Aquatic Organisms/*chemistry/genetics ; Biodiversity ; Databases, Protein ; Metagenomics/*methods ; *Microbiota/genetics ; Peptides/*analysis ; Proteomics/*methods ; Sequence Analysis, DNA ; Specimen Handling ; Tandem Mass Spectrometry ; }, abstract = {In principle, tandem mass spectrometry can be used to detect and quantify the peptides present in a microbiome sample, enabling functional and taxonomic insight into microbiome metabolic activity. However, the phylogenetic diversity constituting a particular microbiome is often unknown, and many of the organisms present may not have assembled genomes. In ocean microbiome samples, with particularly diverse and uncultured bacterial communities, it is difficult to construct protein databases that contain the bulk of the peptides in the sample without losing detection sensitivity due to the overwhelming number of candidate peptides for each tandem mass spectrum. We describe a method for deriving "metapeptides" (short amino acid sequences that may be represented in multiple organisms) from shotgun metagenomic sequencing of microbiome samples. In two ocean microbiome samples, we constructed site-specific metapeptide databases to detect more than one and a half times as many peptides as by searching against predicted genes from an assembled metagenome and roughly three times as many peptides as by searching against the NCBI environmental proteome database. The increased peptide yield has the potential to enrich the taxonomic and functional characterization of sample metaproteomes.}, } @article {pmid27396567, year = {2016}, author = {Wang, J and Jia, H}, title = {Metagenome-wide association studies: fine-mining the microbiome.}, journal = {Nature reviews. Microbiology}, volume = {14}, number = {8}, pages = {508-522}, pmid = {27396567}, issn = {1740-1534}, mesh = {Arthritis, Rheumatoid/diagnosis/microbiology/prevention & control ; Bacteria/*genetics ; Colorectal Neoplasms/diagnosis/microbiology/prevention & control ; Diabetes Mellitus, Type 2/diagnosis/microbiology/prevention & control ; Gastrointestinal Tract/microbiology ; *Genome-Wide Association Study ; High-Throughput Nucleotide Sequencing ; Humans ; Liver Cirrhosis/diagnosis/microbiology/prevention & control ; *Metagenome ; *Microbiota ; Obesity/diagnosis/microbiology/prevention & control ; RNA, Ribosomal, 16S/genetics ; ROC Curve ; }, abstract = {Metagenome-wide association studies (MWAS) have enabled the high-resolution investigation of associations between the human microbiome and several complex diseases, including type 2 diabetes, obesity, liver cirrhosis, colorectal cancer and rheumatoid arthritis. The associations that can be identified by MWAS are not limited to the identification of taxa that are more or less abundant, as is the case with taxonomic approaches, but additionally include the identification of microbial functions that are enriched or depleted. In this Review, we summarize recent findings from MWAS and discuss how these findings might inform the prevention, diagnosis and treatment of human disease in the future. Furthermore, we highlight the need to better characterize the biology of many of the bacteria that are found in the human microbiota as an essential step in understanding how bacterial strains that have been identified by MWAS are associated with disease.}, } @article {pmid27392501, year = {2016}, author = {Shamriz, O and Mizrahi, H and Werbner, M and Shoenfeld, Y and Avni, O and Koren, O}, title = {Microbiota at the crossroads of autoimmunity.}, journal = {Autoimmunity reviews}, volume = {15}, number = {9}, pages = {859-869}, doi = {10.1016/j.autrev.2016.07.012}, pmid = {27392501}, issn = {1873-0183}, mesh = {Animals ; Autoimmune Diseases/*immunology/microbiology ; *Autoimmunity ; Diet ; Gastrointestinal Microbiome/*immunology ; Humans ; }, abstract = {Autoimmune diseases have a multifactorial etiology including genetic and environmental factors. Recently, there has been increased appreciation of the critical involvement of the microbiota in the pathogenesis of autoimmunity, although in many cases, the cause and the consequence are not easy to distinguish. Here, we suggest that many of the known cues affecting the function of the immune system, such as genetics, gender, pregnancy and diet, which are consequently involved in autoimmunity, exert their effects by influencing, at least in part, the microbiota composition and activity. This, in turn, modulates the immune response in a way that increases the risk for autoimmunity in predisposed individuals. We further discuss current microbiota-based therapies.}, } @article {pmid27391119, year = {2016}, author = {Uyaguari-Diaz, MI and Chan, M and Chaban, BL and Croxen, MA and Finke, JF and Hill, JE and Peabody, MA and Van Rossum, T and Suttle, CA and Brinkman, FS and Isaac-Renton, J and Prystajecky, NA and Tang, P}, title = {A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples.}, journal = {Microbiome}, volume = {4}, number = {1}, pages = {20}, pmid = {27391119}, issn = {2049-2618}, support = {//CIHR/Canada ; }, mesh = {Bacteria/*classification/genetics ; Base Sequence/genetics ; British Columbia ; DNA, Intergenic/genetics ; Eukaryota/*classification/genetics ; Fresh Water/*microbiology ; High-Throughput Nucleotide Sequencing/methods ; Metagenome/genetics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA/methods ; Viruses/*classification/genetics ; Water Microbiology ; Water Pollution/*analysis ; }, abstract = {BACKGROUND: Studies of environmental microbiota typically target only specific groups of microorganisms, with most focusing on bacteria through taxonomic classification of 16S rRNA gene sequences. For a more holistic understanding of a microbiome, a strategy to characterize the viral, bacterial, and eukaryotic components is necessary.

RESULTS: We developed a method for metagenomic and amplicon-based analysis of freshwater samples involving the concentration and size-based separation of eukaryotic, bacterial, and viral fractions. Next-generation sequencing and culture-independent approaches were used to describe and quantify microbial communities in watersheds with different land use in British Columbia. Deep amplicon sequencing was used to investigate the distribution of certain viruses (g23 and RdRp), bacteria (16S rRNA and cpn60), and eukaryotes (18S rRNA and ITS). Metagenomic sequencing was used to further characterize the gene content of the bacterial and viral fractions at both taxonomic and functional levels.

CONCLUSION: This study provides a systematic approach to separate and characterize eukaryotic-, bacterial-, and viral-sized particles. Methodologies described in this research have been applied in temporal and spatial studies to study the impact of land use on watershed microbiomes in British Columbia.}, } @article {pmid27391011, year = {2016}, author = {Brittnacher, MJ and Heltshe, SL and Hayden, HS and Radey, MC and Weiss, EJ and Damman, CJ and Zisman, TL and Suskind, DL and Miller, SI}, title = {GUTSS: An Alignment-Free Sequence Comparison Method for Use in Human Intestinal Microbiome and Fecal Microbiota Transplantation Analysis.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0158897}, pmid = {27391011}, issn = {1932-6203}, support = {P30 DK089507/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Child ; *Crohn Disease/genetics/microbiology/therapy ; *Fecal Microbiota Transplantation ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; *Living Donors ; Male ; *Metagenome ; *Metagenomics ; *Sequence Alignment ; }, abstract = {BACKGROUND: Comparative analysis of gut microbiomes in clinical studies of human diseases typically rely on identification and quantification of species or genes. In addition to exploring specific functional characteristics of the microbiome and potential significance of species diversity or expansion, microbiome similarity is also calculated to study change in response to therapies directed at altering the microbiome. Established ecological measures of similarity can be constructed from species abundances, however methods for calculating these commonly used ecological measures of similarity directly from whole genome shotgun (WGS) metagenomic sequence are lacking.

RESULTS: We present an alignment-free method for calculating similarity of WGS metagenomic sequences that is analogous to the Bray-Curtis index for species, implemented by the General Utility for Testing Sequence Similarity (GUTSS) software application. This method was applied to intestinal microbiomes of healthy young children to measure developmental changes toward an adult microbiome during the first 3 years of life. We also calculate similarity of donor and recipient microbiomes to measure establishment, or engraftment, of donor microbiota in fecal microbiota transplantation (FMT) studies focused on mild to moderate Crohn's disease. We show how a relative index of similarity to donor can be calculated as a measure of change in a patient's microbiome toward that of the donor in response to FMT.

CONCLUSION: Because clinical efficacy of the transplant procedure cannot be fully evaluated without analysis methods to quantify actual FMT engraftment, we developed a method for detecting change in the gut microbiome that is independent of species identification and database bias, sensitive to changes in relative abundance of the microbial constituents, and can be formulated as an index for correlating engraftment success with clinical measures of disease. More generally, this method may be applied to clinical evaluation of human microbiomes and provide potential diagnostic determination of individuals who may be candidates for specific therapies directed at alteration of the microbiome.}, } @article {pmid27388460, year = {2016}, author = {Ormerod, KL and Wood, DL and Lachner, N and Gellatly, SL and Daly, JN and Parsons, JD and Dal'Molin, CG and Palfreyman, RW and Nielsen, LK and Cooper, MA and Morrison, M and Hansbro, PM and Hugenholtz, P}, title = {Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals.}, journal = {Microbiome}, volume = {4}, number = {1}, pages = {36}, pmid = {27388460}, issn = {2049-2618}, mesh = {Animals ; Bacteroidetes/genetics/isolation & purification/*physiology ; Feces/*microbiology ; Gastrointestinal Tract/microbiology ; Genome, Bacterial ; Guinea Pigs ; Host-Pathogen Interactions ; Humans ; Metagenomics/*methods ; Mice ; Microbiota ; Phascolarctidae/microbiology ; Phylogeny ; Polysaccharides/metabolism ; }, abstract = {BACKGROUND: Our view of host-associated microbiota remains incomplete due to the presence of as yet uncultured constituents. The Bacteroidales family S24-7 is a prominent example of one of these groups. Marker gene surveys indicate that members of this family are highly localized to the gastrointestinal tracts of homeothermic animals and are increasingly being recognized as a numerically predominant member of the gut microbiota; however, little is known about the nature of their interactions with the host.

RESULTS: Here, we provide the first whole genome exploration of this family, for which we propose the name "Candidatus Homeothermaceae," using 30 population genomes extracted from fecal samples of four different animal hosts: human, mouse, koala, and guinea pig. We infer the core metabolism of "Ca. Homeothermaceae" to be that of fermentative or nanaerobic bacteria, resembling that of related Bacteroidales families. In addition, we describe three trophic guilds within the family, plant glycan (hemicellulose and pectin), host glycan, and α-glucan, each broadly defined by increased abundance of enzymes involved in the degradation of particular carbohydrates.

CONCLUSIONS: "Ca. Homeothermaceae" representatives constitute a substantial component of the murine gut microbiota, as well as being present within the human gut, and this study provides important first insights into the nature of their residency. The presence of trophic guilds within the family indicates the potential for niche partitioning and specific roles for each guild in gut health and dysbiosis.}, } @article {pmid27387069, year = {2016}, author = {Hunt, KA and Jennings, RD and Inskeep, WP and Carlson, RP}, title = {Stoichiometric modelling of assimilatory and dissimilatory biomass utilisation in a microbial community.}, journal = {Environmental microbiology}, volume = {18}, number = {12}, pages = {4946-4960}, pmid = {27387069}, issn = {1462-2920}, support = {U01 EB019416/EB/NIBIB NIH HHS/United States ; }, mesh = {Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; *Biomass ; Carbon/metabolism ; *Ecosystem ; Eukaryota/classification/genetics/*metabolism ; Food Chain ; Microbial Consortia/genetics/*physiology ; }, abstract = {Assimilatory and dissimilatory utilisation of autotroph biomass by heterotrophs is a fundamental mechanism for the transfer of nutrients and energy across trophic levels. Metagenome data from a tractable, thermoacidophilic microbial community in Yellowstone National Park was used to build an in silico model to study heterotrophic utilisation of autotroph biomass using elementary flux mode analysis and flux balance analysis. Assimilatory and dissimilatory biomass utilisation was investigated using 29 forms of biomass-derived dissolved organic carbon (DOC) including individual monomer pools, individual macromolecular pools and aggregate biomass. The simulations identified ecologically competitive strategies for utilizing DOC under conditions of varying electron donor, electron acceptor or enzyme limitation. The simulated growth environment affected which form of DOC was the most competitive use of nutrients; for instance, oxygen limitation favoured utilisation of less reduced and fermentable DOC while carbon-limited environments favoured more reduced DOC. Additionally, metabolism was studied considering two encompassing metabolic strategies: simultaneous versus sequential use of DOC. Results of this study bound the transfer of nutrients and energy through microbial food webs, providing a quantitative foundation relevant to most microbial ecosystems.}, } @article {pmid27386965, year = {2016}, author = {Yan, Q and Cui, S and Chen, C and Li, S and Sha, S and Wan, X and Yang, R and Xin, Y and Ma, Y}, title = {Metagenomic Analysis of Sputum Microbiome as a Tool toward Culture-Independent Pathogen Detection of Patients with Ventilator-associated Pneumonia.}, journal = {American journal of respiratory and critical care medicine}, volume = {194}, number = {5}, pages = {636-639}, doi = {10.1164/rccm.201601-0034LE}, pmid = {27386965}, issn = {1535-4970}, mesh = {Aged ; Female ; Humans ; Male ; Metagenomics/*methods ; *Microbiota ; Middle Aged ; Pneumonia, Ventilator-Associated/*diagnosis ; Reproducibility of Results ; Sputum/*microbiology ; }, } @article {pmid27386789, year = {2016}, author = {Santiago-Rodriguez, TM and Cano, R and Jiménez-Flores, R}, title = {Potential applications of metagenomics to assess the biological effects of food structure and function.}, journal = {Food & function}, volume = {7}, number = {10}, pages = {4160-4169}, doi = {10.1039/c6fo00317f}, pmid = {27386789}, issn = {2042-650X}, mesh = {Animals ; Digestion ; Humans ; Intestines/*microbiology ; *Metagenomics ; Microbiota/*genetics ; Milk/*chemistry ; }, abstract = {Metagenomics, or the collective study of genomes is an important emerging area in microbiology and related fields, and is increasingly being recognized as a tool to characterize the microbial community structure and function of diverse sample types. Metagenomics compares sequences to existing databases to enable the identification of potential microbial reservoirs and predict specific functions; yet, metagenomics has not been widely applied to understand how changes in the food structure and composition affect microbial communities and their function in the human gut. Studies are needed to understand the digestion of food products, and to measure their effectiveness in preserving a healthy microbiome, as well as intestinal function. We suggest the use of metagenomics with validation techniques such as Polymerase Chain Reaction (PCR), cloning and functional assays to assess the biological effects of food structure and function.}, } @article {pmid27383682, year = {2016}, author = {Hiraoka, S and Yang, CC and Iwasaki, W}, title = {Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond.}, journal = {Microbes and environments}, volume = {31}, number = {3}, pages = {204-212}, pmid = {27383682}, issn = {1347-4405}, mesh = {*Biota ; Computational Biology/*methods ; *Environmental Microbiology ; Metagenomics/*methods ; }, abstract = {Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives.}, } @article {pmid27377622, year = {2016}, author = {Haroon, MF and Thompson, LR and Parks, DH and Hugenholtz, P and Stingl, U}, title = {A catalogue of 136 microbial draft genomes from Red Sea metagenomes.}, journal = {Scientific data}, volume = {3}, number = {}, pages = {160050}, pmid = {27377622}, issn = {2052-4463}, mesh = {Bacteria/genetics ; Ecosystem ; *Genome, Microbial ; Indian Ocean ; *Metagenome ; Metagenomics ; Microbiota ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; Seawater ; Sequence Analysis, DNA ; Temperature ; }, abstract = {Earth is expected to continue warming and the Red Sea is a model environment for understanding the effects of global warming on ocean microbiomes due to its unusually high temperature, salinity and solar irradiance. However, most microbial diversity analyses of the Red Sea have been limited to cultured representatives and single marker gene analyses, hence neglecting the substantial uncultured majority. Here, we report 136 microbial genomes (completion minus contamination is ≥50%) assembled from 45 metagenomes from eight stations spanning the Red Sea and taken from multiple depths between 10 to 500 m. Phylogenomic analysis showed that most of the retrieved genomes belong to seven different phyla of known marine microbes, but more than half representing currently uncultured species. The open-access data presented here is the largest number of Red Sea representative microbial genomes reported in a single study and will help facilitate future studies in understanding the physiology of these microorganisms and how they have adapted to the relatively harsh conditions of the Red Sea.}, } @article {pmid27368709, year = {2016}, author = {Hakim, JA and Koo, H and Kumar, R and Lefkowitz, EJ and Morrow, CD and Powell, ML and Watts, SA and Bej, AK}, title = {The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {9}, pages = {}, pmid = {27368709}, issn = {1574-6941}, support = {P30 AI027767/AI/NIAID NIH HHS/United States ; UL1 TR000165/TR/NCATS NIH HHS/United States ; P30 CA013148/CA/NCI NIH HHS/United States ; P30 DK056336/DK/NIDDK NIH HHS/United States ; UL1 TR001417/TR/NCATS NIH HHS/United States ; P30 AR050948/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; Ecosystem ; Epsilonproteobacteria/isolation & purification/metabolism ; Gammaproteobacteria/isolation & purification/metabolism ; *Gastrointestinal Microbiome ; Lytechinus/*microbiology ; Metabolome ; Metagenomics ; Phylogeny ; Seawater/microbiology ; }, abstract = {In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities. The gut digesta and egested fecal pellets exhibited a microbial profile comprised of Gammaproteobacteria, mainly Vibrio, and Bacteroidetes. Both the seagrass and surrounding sea water revealed Alpha- and Betaproteobacteria. Bray-Curtis distances of microbial communities indicated a clustering profile with low intrasample variation. Predictive metagenomics performed on the microbial communities revealed that the gut tissue had high relative abundances of metabolisms assigned to the KEGG-Level-2 designation of energy metabolisms compared to the gut digesta, which had higher carbohydrate, amino acid and lipid metabolisms. Overall, the results of this study elaborate the spatial distribution of microbial communities in the gut ecosystem of L. variegatus, and specifically a selective attribute for Campylobacteraceae in the gut tissue. Also, the predictive functional significance of bacterial communities in uniquely compartmentalized gut ecosystems of L. variegatus has been described.}, } @article {pmid27366894, year = {2016}, author = {Yigit, E and Feehery, GR and Langhorst, BW and Stewart, FJ and Dimalanta, ET and Pradhan, S and Slatko, B and Gardner, AF and McFarland, J and Sumner, C and Davis, TB}, title = {A Microbiome DNA Enrichment Method for Next-Generation Sequencing Sample Preparation.}, journal = {Current protocols in molecular biology}, volume = {115}, number = {}, pages = {7.26.1-7.26.14}, doi = {10.1002/cpmb.12}, pmid = {27366894}, issn = {1934-3647}, mesh = {Chemical Precipitation ; DNA/genetics/*isolation & purification ; DNA Methylation ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Microbiota ; Sequence Analysis, DNA/*methods ; }, abstract = {"Microbiome" is used to describe the communities of microorganisms and their genes in a particular environment, including communities in association with a eukaryotic host or part of a host. One challenge in microbiome analysis concerns the presence of host DNA in samples. Removal of host DNA before sequencing results in greater sequence depth of the intended microbiome target population. This unit describes a novel method of microbial DNA enrichment in which methylated host DNA such as human genomic DNA is selectively bound and separated from microbial DNA before next-generation sequencing (NGS) library construction. This microbiome enrichment technique yields a higher fraction of microbial sequencing reads and improved read quality resulting in a reduced cost of downstream data generation and analysis. © 2016 by John Wiley & Sons, Inc.}, } @article {pmid27357176, year = {2016}, author = {Purahong, W and Wubet, T and Lentendu, G and Schloter, M and Pecyna, MJ and Kapturska, D and Hofrichter, M and Krüger, D and Buscot, F}, title = {Life in leaf litter: novel insights into community dynamics of bacteria and fungi during litter decomposition.}, journal = {Molecular ecology}, volume = {25}, number = {16}, pages = {4059-4074}, doi = {10.1111/mec.13739}, pmid = {27357176}, issn = {1365-294X}, mesh = {Bacteria/*classification ; DNA, Ribosomal Spacer/genetics ; *Forests ; Fungi/*classification ; Plant Leaves/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Microorganisms play a crucial role in the biological decomposition of plant litter in terrestrial ecosystems. Due to the permanently changing litter quality during decomposition, studies of both fungi and bacteria at a fine taxonomic resolution are required during the whole process. Here we investigated microbial community succession in decomposing leaf litter of temperate beech forest using pyrotag sequencing of the bacterial 16S and the fungal internal transcribed spacer (ITS) rRNA genes. Our results reveal that both communities underwent rapid changes. Proteobacteria, Actinobacteria and Bacteroidetes dominated over the entire study period, but their taxonomic composition and abundances changed markedly among sampling dates. The fungal community also changed dynamically as decomposition progressed, with ascomycete fungi being increasingly replaced by basidiomycetes. We found a consistent and highly significant correlation between bacterial richness and fungal richness (R = 0.76, P < 0.001) and community structure (RM antel = 0.85, P < 0.001), providing evidence of coupled dynamics in the fungal and bacterial communities. A network analysis highlighted nonrandom co-occurrences among bacterial and fungal taxa as well as a shift in the cross-kingdom co-occurrence pattern of their communities from the early to the later stages of decomposition. During this process, macronutrients, micronutrients, C:N ratio and pH were significantly correlated with the fungal and bacterial communities, while bacterial richness positively correlated with three hydrolytic enzymes important for C, N and P acquisition. Overall, we provide evidence that the complex litter decay is the result of a dynamic cross-kingdom functional succession.}, } @article {pmid27354456, year = {2016}, author = {Hasegawa, K and Linnemann, RW and Mansbach, JM and Ajami, NJ and Espinola, JA and Petrosino, JF and Piedra, PA and Stevenson, MD and Sullivan, AF and Thompson, AD and Camargo, CA}, title = {The Fecal Microbiota Profile and Bronchiolitis in Infants.}, journal = {Pediatrics}, volume = {138}, number = {1}, pages = {}, pmid = {27354456}, issn = {1098-4275}, support = {R01 AI108588/AI/NIAID NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; UL1 TR001425/TR/NCATS NIH HHS/United States ; R21 HL129909/HL/NHLBI NIH HHS/United States ; R01 AI114552/AI/NIAID NIH HHS/United States ; }, mesh = {Bronchiolitis/*microbiology ; Case-Control Studies ; Feces/*microbiology ; Female ; Humans ; Infant ; Male ; *Microbiota ; Prospective Studies ; }, abstract = {BACKGROUND: Little is known about the association of gut microbiota, a potentially modifiable factor, with bronchiolitis in infants. We aimed to determine the association of fecal microbiota with bronchiolitis in infants.

METHODS: We conducted a case-control study. As a part of multicenter prospective study, we collected stool samples from 40 infants hospitalized with bronchiolitis. We concurrently enrolled 115 age-matched healthy controls. By applying 16S rRNA gene sequencing and an unbiased clustering approach to these 155 fecal samples, we identified microbiota profiles and determined the association of microbiota profiles with likelihood of bronchiolitis.

RESULTS: Overall, the median age was 3 months, 55% were male, and 54% were non-Hispanic white. Unbiased clustering of fecal microbiota identified 4 distinct profiles: Escherichia-dominant profile (30%), Bifidobacterium-dominant profile (21%), Enterobacter/Veillonella-dominant profile (22%), and Bacteroides-dominant profile (28%). The proportion of bronchiolitis was lowest in infants with the Enterobacter/Veillonella-dominant profile (15%) and highest in the Bacteroides-dominant profile (44%), corresponding to an odds ratio of 4.59 (95% confidence interval, 1.58-15.5; P = .008). In the multivariable model, the significant association between the Bacteroides-dominant profile and a greater likelihood of bronchiolitis persisted (odds ratio for comparison with the Enterobacter/Veillonella-dominant profile, 4.24; 95% confidence interval, 1.56-12.0; P = .005). In contrast, the likelihood of bronchiolitis in infants with the Escherichia-dominant or Bifidobacterium-dominant profile was not significantly different compared with those with the Enterobacter/Veillonella-dominant profile.

CONCLUSIONS: In this case-control study, we identified 4 distinct fecal microbiota profiles in infants. The Bacteroides-dominant profile was associated with a higher likelihood of bronchiolitis.}, } @article {pmid27353502, year = {2016}, author = {Kougias, PG and Treu, L and Campanaro, S and Zhu, X and Angelidaki, I}, title = {Dynamic functional characterization and phylogenetic changes due to Long Chain Fatty Acids pulses in biogas reactors.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {28810}, pmid = {27353502}, issn = {2045-2322}, mesh = {Animals ; Biofuels ; *Bioreactors ; Cattle ; Fatty Acids/*physiology ; Genome, Bacterial ; Manure/microbiology ; Metagenome ; Microbial Consortia/*genetics ; Phylogeny ; }, abstract = {The process stability of biogas plants is often deteriorated by the accumulation of Long Chain Fatty Acids (LCFA). The microbial community shifts due to LCFA disturbances have been poorly understood as the molecular techniques used were not able to identify the genome characteristics of uncultured microorganisms, and additionally, the presence of limited number of reference genomes in public databases prevented the comprehension of specific functional roles characterizing these microorganisms. The present study is the first research which deciphers by means of high throughput shotgun sequencing the dynamics of the microbial community during an inhibitory shock load induced by single pulses of unsaturated LCFA at two different concentrations (i.e. 2 g/L-reactor and 3 g/L-reactor). The metagenomic analysis showed that only the microbes associated with LCFA degradation could encode proteins related to "chemotaxis" and "flagellar assembly", which promoted the ability to move towards the LCFA sources so as to degrade them. Moreover, the syntrophic interactions found between Syntrophomonas sp. together with Methanosarcina sp. were possibly assigned to the menaquinone-electron transfer. Finally, it was proven that a previously exposed to LCFA inoculum is more efficient in the degradation process of LCFA due to the specialization of the microbial consortium.}, } @article {pmid27352007, year = {2016}, author = {Jangi, S and Gandhi, R and Cox, LM and Li, N and von Glehn, F and Yan, R and Patel, B and Mazzola, MA and Liu, S and Glanz, BL and Cook, S and Tankou, S and Stuart, F and Melo, K and Nejad, P and Smith, K and Topçuolu, BD and Holden, J and Kivisäkk, P and Chitnis, T and De Jager, PL and Quintana, FJ and Gerber, GK and Bry, L and Weiner, HL}, title = {Alterations of the human gut microbiome in multiple sclerosis.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {12015}, pmid = {27352007}, issn = {2041-1723}, support = {P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 AI126880/AI/NIAID NIH HHS/United States ; R01 NS087226/NS/NINDS NIH HHS/United States ; R21 NS087867/NS/NINDS NIH HHS/United States ; }, mesh = {Adult ; Breath Tests ; Case-Control Studies ; Female ; *Gastrointestinal Microbiome ; Genes, Bacterial ; Humans ; Immunomodulation ; Male ; Methane/analysis ; Middle Aged ; Monocytes/metabolism ; Multiple Sclerosis, Relapsing-Remitting/immunology/*microbiology/therapy ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; T-Lymphocytes/metabolism ; }, abstract = {The gut microbiome plays an important role in immune function and has been implicated in several autoimmune disorders. Here we use 16S rRNA sequencing to investigate the gut microbiome in subjects with multiple sclerosis (MS, n=60) and healthy controls (n=43). Microbiome alterations in MS include increases in Methanobrevibacter and Akkermansia and decreases in Butyricimonas, and correlate with variations in the expression of genes involved in dendritic cell maturation, interferon signalling and NF-kB signalling pathways in circulating T cells and monocytes. Patients on disease-modifying treatment show increased abundances of Prevotella and Sutterella, and decreased Sarcina, compared with untreated patients. MS patients of a second cohort show elevated breath methane compared with controls, consistent with our observation of increased gut Methanobrevibacter in MS in the first cohort. Further study is required to assess whether the observed alterations in the gut microbiome play a role in, or are a consequence of, MS pathogenesis.}, } @article {pmid27350392, year = {2016}, author = {Colombo, LT and de Oliveira, MN and Carneiro, DG and de Souza, RA and Alvim, MC and Dos Santos, JC and da Silva, CC and Vidigal, PM and da Silveira, WB and Passos, FM}, title = {Applying functional metagenomics to search for novel lignocellulosic enzymes in a microbial consortium derived from a thermophilic composting phase of sugarcane bagasse and cow manure.}, journal = {Antonie van Leeuwenhoek}, volume = {109}, number = {9}, pages = {1217-1233}, doi = {10.1007/s10482-016-0723-4}, pmid = {27350392}, issn = {1572-9699}, mesh = {Animals ; Bacteria/enzymology/genetics ; Bacterial Proteins/genetics/metabolism ; Biomass ; Cattle ; Cellulases/genetics/*metabolism ; Cellulose/*metabolism ; Enzyme Activation ; Ethanol/metabolism ; Lignin/*metabolism ; Manure/*microbiology ; Metagenomics ; Microbial Consortia/*genetics ; Phylogeny ; Saccharum/metabolism/*microbiology ; Sequence Analysis, DNA ; beta-Glucosidase/genetics/metabolism ; }, abstract = {Environments where lignocellulosic biomass is naturally decomposed are sources for discovery of new hydrolytic enzymes that can reduce the high cost of enzymatic cocktails for second-generation ethanol production. Metagenomic analysis was applied to discover genes coding carbohydrate-depleting enzymes from a microbial laboratory subculture using a mix of sugarcane bagasse and cow manure in the thermophilic composting phase. From a fosmid library, 182 clones had the ability to hydrolyse carbohydrate. Sequencing of 30 fosmids resulted in 12 contigs encoding 34 putative carbohydrate-active enzymes belonging to 17 glycosyl hydrolase (GH) families. One third of the putative proteins belong to the GH3 family, which includes β-glucosidase enzymes known to be important in the cellulose-deconstruction process but present with low activity in commercial enzyme preparations. Phylogenetic analysis of the amino acid sequences of seven selected proteins, including three β-glucosidases, showed low relatedness with protein sequences deposited in databases. These findings highlight microbial consortia obtained from a mixture of decomposing biomass residues, such as sugar cane bagasse and cow manure, as a rich resource of novel enzymes potentially useful in biotechnology for saccharification of lignocellulosic substrate.}, } @article {pmid27350143, year = {2016}, author = {Proctor, LM}, title = {The National Institutes of Health Human Microbiome Project.}, journal = {Seminars in fetal & neonatal medicine}, volume = {21}, number = {6}, pages = {368-372}, doi = {10.1016/j.siny.2016.05.002}, pmid = {27350143}, issn = {1878-0946}, mesh = {Humans ; *Microbiota ; National Institutes of Health (U.S.) ; United States ; }, abstract = {This overview describes the impetus for and the goals of the National Institutes of Health (NIH)'s Human Microbiome Project (HMP) and the research resources available through the HMP. As the HMP also serves as a catalyst for human microbiome research at the NIH, NIH Institutes and Centers support for this field is also briefly addressed.}, } @article {pmid27344121, year = {2016}, author = {Geesey, GG and Barkay, T and King, S}, title = {Microbes in mercury-enriched geothermal springs in western North America.}, journal = {The Science of the total environment}, volume = {569-570}, number = {}, pages = {321-331}, doi = {10.1016/j.scitotenv.2016.06.080}, pmid = {27344121}, issn = {1879-1026}, mesh = {Archaea/*classification ; Bacteria/*classification ; Hot Springs/*microbiology ; Mercury/*analysis ; Metagenome ; *Microbiota ; North America ; }, abstract = {Because geothermal environments contain mercury (Hg) from natural sources, microorganisms that evolved in these systems have likely adapted to this element. Knowledge of the interactions between microorganisms and Hg in geothermal systems may assist in understanding the long-term evolution of microbial adaptation to Hg with relevance to other environments where Hg is introduced from anthropogenic sources. A number of microbiological studies with supporting geochemistry have been conducted in geothermal systems across western North America. Approximately 1 in 5 study sites include measurements of Hg. Of all prokaryotic taxa reported across sites with microbiological and accompanying physicochemical data, 42% have been detected at sites in which Hg was measured. Genes specifying Hg reduction and detoxification by microorganisms were detected in a number of hot springs across the region. Archaeal-like sequences, representing two crenarchaeal orders and one order each of the Euryarchaeota and Thaumarchaeota, dominated in metagenomes' MerA (the mercuric reductase protein) inventories, while bacterial homologs were mostly found in one deeply sequenced metagenome. MerA homologs were more frequently found in metagenomes of microbial communities in acidic springs than in circumneutral or high pH geothermal systems, possibly reflecting higher bioavailability of Hg under acidic conditions. MerA homologs were found in hot springs prokaryotic isolates affiliated with Bacteria and Archaea taxa. Acidic sites with high Hg concentrations contain more of Archaea than Bacteria taxa, while the reverse appears to be the case in circumneutral and high pH sites with high Hg concentrations. However, MerA was detected in only a small fraction of the Archaea and Bacteria taxa inhabiting sites containing Hg. Nevertheless, the presence of MerA homologs and their distribution patterns in systems, in which Hg has yet to be measured, demonstrates the potential for detoxification by Hg reduction in these geothermal systems, particularly the low pH springs that are dominated by Archaea.}, } @article {pmid27343061, year = {2016}, author = {Zhang, X and Ning, Z and Mayne, J and Moore, JI and Li, J and Butcher, J and Deeke, SA and Chen, R and Chiang, CK and Wen, M and Mack, D and Stintzi, A and Figeys, D}, title = {MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota.}, journal = {Microbiome}, volume = {4}, number = {1}, pages = {31}, pmid = {27343061}, issn = {2049-2618}, support = {GPH-129340//CIHR/Canada ; }, mesh = {Animals ; Bacteria/*classification/metabolism ; Bacterial Proteins/metabolism ; Computational Biology/methods ; Databases, Genetic ; Diet, High-Fat ; *Gastrointestinal Microbiome/drug effects ; Gene Expression Regulation, Bacterial/drug effects ; Humans ; Metagenomics/*methods ; Mice ; Proteomics/*methods ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: The gut microbiota has been shown to be closely associated with human health and disease. While next-generation sequencing can be readily used to profile the microbiota taxonomy and metabolic potential, metaproteomics is better suited for deciphering microbial biological activities. However, the application of gut metaproteomics has largely been limited due to the low efficiency of protein identification. Thus, a high-performance and easy-to-implement gut metaproteomic approach is required.

RESULTS: In this study, we developed a high-performance and universal workflow for gut metaproteome identification and quantification (named MetaPro-IQ) by using the close-to-complete human or mouse gut microbial gene catalog as database and an iterative database search strategy. An average of 38 and 33 % of the acquired tandem mass spectrometry (MS) spectra was confidently identified for the studied mouse stool and human mucosal-luminal interface samples, respectively. In total, we accurately quantified 30,749 protein groups for the mouse metaproteome and 19,011 protein groups for the human metaproteome. Moreover, the MetaPro-IQ approach enabled comparable identifications with the matched metagenome database search strategy that is widely used but needs prior metagenomic sequencing. The response of gut microbiota to high-fat diet in mice was then assessed, which showed distinct metaproteome patterns for high-fat-fed mice and identified 849 proteins as significant responders to high-fat feeding in comparison to low-fat feeding.

CONCLUSIONS: We present MetaPro-IQ, a metaproteomic approach for highly efficient intestinal microbial protein identification and quantification, which functions as a universal workflow for metaproteomic studies, and will thus facilitate the application of metaproteomics for better understanding the functions of gut microbiota in health and disease.}, } @article {pmid27337135, year = {2016}, author = {Zhang, Y and Skaar, I and Sulyok, M and Liu, X and Rao, M and Taylor, JW}, title = {The Microbiome and Metabolites in Fermented Pu-erh Tea as Revealed by High-Throughput Sequencing and Quantitative Multiplex Metabolite Analysis.}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0157847}, pmid = {27337135}, issn = {1932-6203}, mesh = {Bacteria/classification/genetics ; Biodiversity ; Computational Biology/methods ; *Fermentation ; Fungi/classification/genetics ; High-Throughput Nucleotide Sequencing ; *Metabolome ; *Metabolomics/methods ; Metagenome ; *Metagenomics/methods ; *Microbiota ; Tea/*chemistry/genetics/*microbiology ; }, abstract = {Pu-erh is a tea produced in Yunnan, China by microbial fermentation of fresh Camellia sinensis leaves by two processes, the traditional raw fermentation and the faster, ripened fermentation. We characterized fungal and bacterial communities in leaves and both Pu-erhs by high-throughput, rDNA-amplicon sequencing and we characterized the profile of bioactive extrolite mycotoxins in Pu-erh teas by quantitative liquid chromatography-tandem mass spectrometry. We identified 390 fungal and 629 bacterial OTUs from leaves and both Pu-erhs. Major findings are: 1) fungal diversity drops and bacterial diversity rises due to raw or ripened fermentation, 2) fungal and bacterial community composition changes significantly between fresh leaves and both raw and ripened Pu-erh, 3) aging causes significant changes in the microbial community of raw, but not ripened, Pu-erh, and, 4) ripened and well-aged raw Pu-erh have similar microbial communities that are distinct from those of young, raw Ph-erh tea. Twenty-five toxic metabolites, mainly of fungal origin, were detected, with patulin and asperglaucide dominating and at levels supporting the Chinese custom of discarding the first preparation of Pu-erh and using the wet tea to then brew a pot for consumption.}, } @article {pmid27336782, year = {2016}, author = {Pinheiro de Oliveira, F and Mendes, RH and Dobbler, PT and Mai, V and Pylro, VS and Waugh, SG and Vairo, F and Refosco, LF and Roesch, LF and Schwartz, IV}, title = {Phenylketonuria and Gut Microbiota: A Controlled Study Based on Next-Generation Sequencing.}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0157513}, pmid = {27336782}, issn = {1932-6203}, mesh = {Child ; Child, Preschool ; Cross-Sectional Studies ; Diet ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Phenylketonurias/*diet therapy/*metabolism ; RNA, Ribosomal, 16S ; }, abstract = {Phenylketonuria (PKU) is an inborn error of metabolism associated with high blood levels of phenylalanine (Phe). A Phe-restricted diet supplemented with L-amino acids is the main treatment strategy for this disease; if started early, most neurological abnormalities can be prevented. The healthy human gut contains trillions of commensal bacteria, often referred to as the gut microbiota. The composition of the gut microbiota is known to be modulated by environmental factors, including diet. In this study, we compared the gut microbiota of 8 PKU patients on Phe-restricted dietary treatment with that of 10 healthy individuals. The microbiota were characterized by 16S rRNA sequencing using the Ion Torrent™ platform. The most dominant phyla detected in both groups were Bacteroidetes and Firmicutes. PKU patients showed reduced abundance of the Clostridiaceae, Erysipelotrichaceae, and Lachnospiraceae families, Clostridiales class, Coprococcus, Dorea, Lachnospira, Odoribacter, Ruminococcus and Veillonella genera, and enrichment of Prevotella, Akkermansia, and Peptostreptococcaceae. Microbial function prediction suggested significant differences in starch/glucose and amino acid metabolism between PKU patients and controls. Together, our results suggest the presence of distinct taxonomic groups within the gut microbiome of PKU patients, which may be modulated by their plasma Phe concentration. Whether our findings represent an effect of the disease itself, or a consequence of the modified diet is unclear.}, } @article {pmid27334103, year = {2016}, author = {Herzog, F and Franklin, J}, title = {State-of-the-art practices in farmland biodiversity monitoring for North America and Europe.}, journal = {Ambio}, volume = {45}, number = {8}, pages = {857-871}, pmid = {27334103}, issn = {1654-7209}, mesh = {Agriculture/economics/legislation & jurisprudence/*methods/organization & administration ; Animals ; *Biodiversity ; Conservation of Natural Resources/economics/legislation & jurisprudence/*methods ; Environmental Monitoring/economics/legislation & jurisprudence/*methods ; Farms/economics/legislation & jurisprudence/*organization & administration ; Government Regulation ; North America ; Policy Making ; }, abstract = {Policy makers and farmers need to know the status of farmland biodiversity in order to meet conservation goals and evaluate management options. Based on a review of 11 monitoring programs in Europe and North America and on related literature, we identify the design choices or attributes of a program that balance monitoring costs and usefulness for stakeholders. A useful program monitors habitats, vascular plants, and possibly faunal groups (ecosystem service providers, charismatic species) using a stratified random sample of the agricultural landscape, including marginal and intensive regions. The size of landscape samples varies with the grain of the agricultural landscape; for example, samples are smaller in Europe and larger in North America. Raw data are collected in a rolling survey, which distributes sampling over several years. Sufficient practical experience is now available to implement broad monitoring schemes on both continents. Technological developments in remote sensing, metagenomics, and social media may offer new opportunities for affordable farmland biodiversity monitoring and help to lower the overall costs of monitoring programs.}, } @article {pmid27327495, year = {2016}, author = {Huson, DH and Beier, S and Flade, I and Górska, A and El-Hadidi, M and Mitra, S and Ruscheweyh, HJ and Tappu, R}, title = {MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.}, journal = {PLoS computational biology}, volume = {12}, number = {6}, pages = {e1004957}, pmid = {27327495}, issn = {1553-7358}, mesh = {Genome, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenome/*genetics ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; *Software ; User-Computer Interface ; }, abstract = {There is increasing interest in employing shotgun sequencing, rather than amplicon sequencing, to analyze microbiome samples. Typical projects may involve hundreds of samples and billions of sequencing reads. The comparison of such samples against a protein reference database generates billions of alignments and the analysis of such data is computationally challenging. To address this, we have substantially rewritten and extended our widely-used microbiome analysis tool MEGAN so as to facilitate the interactive analysis of the taxonomic and functional content of very large microbiome datasets. Other new features include a functional classifier called InterPro2GO, gene-centric read assembly, principal coordinate analysis of taxonomy and function, and support for metadata. The new program is called MEGAN Community Edition (CE) and is open source. By integrating MEGAN CE with our high-throughput DNA-to-protein alignment tool DIAMOND and by providing a new program MeganServer that allows access to metagenome analysis files hosted on a server, we provide a straightforward, yet powerful and complete pipeline for the analysis of metagenome shotgun sequences. We illustrate how to perform a full-scale computational analysis of a metagenomic sequencing project, involving 12 samples and 800 million reads, in less than three days on a single server. All source code is available here: https://github.com/danielhuson/megan-ce.}, } @article {pmid27324427, year = {2016}, author = {Cerqueda-García, D and Falcón, LI}, title = {Metabolic potential of microbial mats and microbialites: Autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources.}, journal = {Journal of bioinformatics and computational biology}, volume = {14}, number = {4}, pages = {1650020}, doi = {10.1142/S0219720016500207}, pmid = {27324427}, issn = {1757-6334}, mesh = {Autotrophic Processes ; Biomass ; Carbon/*metabolism ; Carbon Dioxide/*metabolism ; Citric Acid Cycle ; Computer Simulation ; Genomics ; Metabolic Networks and Pathways ; Metagenome ; *Microbiota ; *Models, Biological ; Nitrogen/*metabolism ; Phylogeny ; Reproducibility of Results ; }, abstract = {Microbialites and microbial mats are complex communities with high phylogenetic diversity. These communities are mostly composed of bacteria and archaea, which are the earliest living forms on Earth and relevant to biogeochemical evolution. In this study, we identified the shared metabolic pathways for uptake of inorganic C and N in microbial mats and microbialites based on metagenomic data sets. An in silico analysis for autotrophic pathways was used to trace the paths of C and N to the system, following an elementary flux modes (EFM) approach, resulting in a stoichiometric model. The fragility was analyzed by the minimal cut sets method. We found four relevant pathways for the incorporation of CO2 (Calvin cycle, reverse tricarboxylic acid cycle, reductive acetyl-CoA pathway, and dicarboxylate/4-hydroxybutyrate cycle), some of them present only in archaea, while nitrogen fixation was the most important source of N to the system. The metabolic potential to incorporate nitrate to biomass was also relevant. The fragility of the network was low, suggesting a high redundancy of the autotrophic pathways due to their broad metabolic diversity, and highlighting the relevance of reducing power source. This analysis suggests that microbial mats and microbialites are "metabolic pumps" for the incorporation of inorganic gases and formation of organic matter.}, } @article {pmid27323244, year = {2016}, author = {Pandit, PD and Gulhane, MK and Khardenavis, AA and Purohit, HJ}, title = {Mining of hemicellulose and lignin degrading genes from differentially enriched methane producing microbial community.}, journal = {Bioresource technology}, volume = {216}, number = {}, pages = {923-930}, doi = {10.1016/j.biortech.2016.06.021}, pmid = {27323244}, issn = {1873-2976}, mesh = {Bacteria/genetics/*metabolism ; Biodiversity ; Biofuels ; Bioreactors/*microbiology ; Biotechnology/instrumentation/methods ; Food ; Hydrolysis ; Lignin/genetics/*metabolism ; Metagenome ; Methane/metabolism ; Microbial Consortia/*genetics ; Oryza/metabolism ; Polysaccharides/genetics/*metabolism ; Reproducibility of Results ; }, abstract = {Study creates a scenario for enrichment and selection of ligno-hemicellulose degrading genotypes with anaerobic bioreactor as a model using rice straw, vegetable waste and food waste as substrates. Relative discrimination analysis showed that the hydrolytic pathways and associated microbial communities for ligno-hemicellulose degradation were dominatingly colonized with rice straw as substrate. The dominating bacteria were Caldicellulosiruptor, Fervidobacterium, Cytophaga, Ruminococcus, Thermotoga associated with hemicellulose degradation and Burkholderia, Pandorea, Sphingomonas, Spirochaeta, Pseudomonas for lignocellulose hydrolysis. This was further supported by the abundance of anaerobic aromatic compound degrading genes along with genes for xylanase and xylosidase in rice straw enriched community. The metagenome analysis data was validated by evaluation of the biochemical methane potential for these substrates. Food waste being most amenable substrate yielded 1410mL of biogas/gVS added whereas, biogas yield of 1160mL/gVS and 1080mL/gVS was observed in presence of vegetable waste and rice straw respectively.}, } @article {pmid27322652, year = {2016}, author = {Bell, KL and de Vere, N and Keller, A and Richardson, RT and Gous, A and Burgess, KS and Brosi, BJ}, title = {Pollen DNA barcoding: current applications and future prospects.}, journal = {Genome}, volume = {59}, number = {9}, pages = {629-640}, doi = {10.1139/gen-2015-0200}, pmid = {27322652}, issn = {1480-3321}, mesh = {Allergens/genetics/immunology ; Biodiversity ; Computational Biology/methods ; *DNA Barcoding, Taxonomic ; *DNA, Plant ; Databases, Genetic ; Food Quality ; Genetic Markers ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Plants/*classification/*genetics ; Pollen/*genetics ; }, abstract = {Identification of the species origin of pollen has many applications, including assessment of plant-pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.}, } @article {pmid27321997, year = {2016}, author = {Zhang, Z and Xu, D and Wang, L and Hao, J and Wang, J and Zhou, X and Wang, W and Qiu, Q and Huang, X and Zhou, J and Long, R and Zhao, F and Shi, P}, title = {Convergent Evolution of Rumen Microbiomes in High-Altitude Mammals.}, journal = {Current biology : CB}, volume = {26}, number = {14}, pages = {1873-1879}, doi = {10.1016/j.cub.2016.05.012}, pmid = {27321997}, issn = {1879-0445}, mesh = {Adaptation, Physiological ; Altitude ; Animals ; *Biological Evolution ; Cattle/*microbiology ; China ; *Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Metagenome ; Sheep, Domestic/*microbiology ; }, abstract = {Studies of genetic adaptation, a central focus of evolutionary biology, most often focus on the host's genome and only rarely on its co-evolved microbiome. The Qinghai-Tibetan Plateau (QTP) offers one of the most extreme environments for the survival of human and other mammalian species. Yaks (Bos grunniens) and Tibetan sheep (T-sheep) (Ovis aries) have adaptations for living in this harsh high-altitude environment, where nomadic Tibetan people keep them primarily for food and livelihood [1]. Adaptive evolution affects energy-metabolism-related genes in a way that helps these ruminants live at high altitude [2, 3]. Herein, we report convergent evolution of rumen microbiomes for energy harvesting persistence in two typical high-altitude ruminants, yaks and T-sheep. Both ruminants yield significantly lower levels of methane and higher yields of volatile fatty acids (VFAs) than their low-altitude relatives, cattle (Bos taurus) and ordinary sheep (Ovis aries). Ultra-deep metagenomic sequencing reveals significant enrichment in VFA-yielding pathways of rumen microbial genes in high-altitude ruminants, whereas methanogenesis pathways show enrichment in the cattle metagenome. Analyses of RNA transcriptomes reveal significant upregulation in 36 genes associated with VFA transport and absorption in the ruminal epithelium of high-altitude ruminants. Our study provides novel insights into the contributions of microbiomes to adaptive evolution in mammals and sheds light on the biological control of greenhouse gas emissions from livestock enteric fermentation.}, } @article {pmid27321429, year = {2016}, author = {Lanzén, A and Epelde, L and Blanco, F and Martín, I and Artetxe, U and Garbisu, C}, title = {Multi-targeted metagenetic analysis of the influence of climate and environmental parameters on soil microbial communities along an elevational gradient.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {28257}, pmid = {27321429}, issn = {2045-2322}, mesh = {*Biodiversity ; *Climate Change ; *Metagenomics ; *Soil Microbiology ; Spain ; }, abstract = {Mountain elevation gradients are invaluable sites for understanding the effects of climate change on ecosystem function, community structure and distribution. However, relatively little is known about the impact on soil microbial communities, in spite of their importance for the functioning of the soil ecosystem. Previous studies of microbial diversity along elevational gradients were often limited by confounding variables such as vegetation, pH, and nutrients. Here, we utilised a transect in the Pyrenees established to minimise variation in such parameters, to examine prokaryotic, fungal, protist and metazoan communities throughout three consecutive years. We aimed to determine the influences of climate and environmental parameters on soil microbial community structure; as well as on the relationships between those microbial communities. Further, functional diversity of heterotrophic bacteria was determined using Biolog. Prokaryotic and fungal community structure, but not alpha-diversity, correlated significantly with elevation. However, carbon-to-nitrogen ratio and pH appeared to affect prokaryotic and protist communities more strongly. Both community structure and physicochemical parameters varied considerably between years, illustrating the value of long-term monitoring of the dynamic processes controlling the soil ecosystem. Our study also illustrates both the challenges and strengths of using microbial communities as indicators of potential impacts of climate change.}, } @article {pmid27317862, year = {2016}, author = {Vanwonterghem, I and Jensen, PD and Rabaey, K and Tyson, GW}, title = {Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion.}, journal = {Environmental microbiology}, volume = {18}, number = {9}, pages = {3144-3158}, doi = {10.1111/1462-2920.13382}, pmid = {27317862}, issn = {1462-2920}, mesh = {Anaerobiosis ; Bacteria/classification/*genetics/*metabolism ; Biodiversity ; *Genome, Bacterial ; Metabolic Networks and Pathways ; Metagenomics ; Methane/metabolism ; Phylogeny ; }, abstract = {Our understanding of the complex interconnected processes performed by microbial communities is hindered by our inability to culture the vast majority of microorganisms. Metagenomics provides a way to bypass this cultivation bottleneck and recent advances in this field now allow us to recover a growing number of genomes representing previously uncultured populations from increasingly complex environments. In this study, a temporal genome-centric metagenomic analysis was performed of lab-scale anaerobic digesters that host complex microbial communities fulfilling a series of interlinked metabolic processes to enable the conversion of cellulose to methane. In total, 101 population genomes that were moderate to near-complete were recovered based primarily on differential coverage binning. These populations span 19 phyla, represent mostly novel species and expand the genomic coverage of several rare phyla. Classification into functional guilds based on their metabolic potential revealed metabolic networks with a high level of functional redundancy as well as niche specialization, and allowed us to identify potential roles such as hydrolytic specialists for several rare, uncultured populations. Genome-centric analyses of complex microbial communities across diverse environments provide the key to understanding the phylogenetic and metabolic diversity of these interactive communities.}, } @article {pmid27317857, year = {2017}, author = {Hugon, P and Lagier, JC and Colson, P and Bittar, F and Raoult, D}, title = {Repertoire of human gut microbes.}, journal = {Microbial pathogenesis}, volume = {106}, number = {}, pages = {103-112}, doi = {10.1016/j.micpath.2016.06.020}, pmid = {27317857}, issn = {1096-1208}, mesh = {Animals ; Archaea/classification ; Bacteria/classification/genetics ; Biodiversity ; Coculture Techniques ; Fungi/classification ; *Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/*microbiology ; Giant Viruses ; High-Throughput Screening Assays/methods ; Humans ; Metagenomics ; Mycological Typing Techniques/methods ; Parasites/classification ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis/methods ; Viruses/classification ; }, abstract = {In 1675, Antoni Van Leeuwenhoeck was the first to observe several forms using an optical microscope that he named "animalcules", realizing later that these were microorganisms. The first classification of living organisms proposed by Ehrenberg in 1833 was based on what we could visualize. The failure of this kind of classification arises from viral culture, which preceded direct observations that were finally achieved during the 20th century by electron microscopy. The number of prokaryotic species is estimated at approximately 10 million, although only 1800 were known in 1980, and 14,000 to date, thanks to the advent of 16S rRNA amplification and sequencing. This highlights our inability to access the entire diversity. Indeed, a large number of bacteria are only, known as Operational Taxonomic Units (OTUs) and detected as a result of metagenomics studies, revealing an unexplored world known as the "dark matter". Recently, the rebirth of bacterial culture through the example of culturomics has dramatically increased the human gut repertoire as well as the 18SrRNA sequencing allowed to largely extend the repertoire of Eukaryotes. Finally, filtration and co-culture on free-living protists associated with high-throughput culture elucidated a part of the megavirome. While the majority of studies currently performed on the human gut microbiota focus on bacterial diversity, it appears that several other prokaryotes (including archaea) and eukaryotic populations also inhabit this ecosystem; their detection depending exclusively on the tools used. Rational and comprehensive establishment of this ecosystem will allow the understanding of human health associated with gut microbiota and the potential to change this.}, } @article {pmid27316954, year = {2016}, author = {Perez, M and Juniper, SK}, title = {Insights into Symbiont Population Structure among Three Vestimentiferan Tubeworm Host Species at Eastern Pacific Spreading Centers.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {17}, pages = {5197-5205}, pmid = {27316954}, issn = {1098-5336}, mesh = {Animals ; Biodiversity ; Biological Evolution ; Gammaproteobacteria/classification/genetics/*isolation & purification/*physiology ; Host Specificity ; Hydrothermal Vents/microbiology ; Polychaeta/classification/*microbiology/physiology ; Seawater/microbiology ; Symbiosis ; }, abstract = {UNLABELLED: The symbiotic relationship between vestimentiferan tubeworms and their intracellular chemosynthetic bacteria is one of the more noteworthy examples of adaptation to deep-sea hydrothermal vent environments. The tubeworm symbionts have never been cultured in the laboratory. Nucleotide sequences from the small subunit rRNA gene suggest that the intracellular symbionts of the eastern Pacific vent tubeworms Oasisia alvinae, Riftia pachyptila, Tevnia jerichonana, and Ridgeia piscesae belong to the same phylotype of gammaproteobacteria, "Candidatus Endoriftia persephone." Comparisons of symbiont genomes between the East Pacific Rise tubeworms R. pachyptila and T. jerichonana confirmed that these two hosts share the same symbionts. Two Ridgeia symbiont genomes were assembled from trophosome metagenomes from worms collected from the Juan de Fuca Ridge (one and five individuals, respectively). We compared these assemblies to those of the sequenced Riftia and Tevnia symbionts. Pangenome composition, genome-wide comparisons of the nucleotide sequences, and pairwise comparisons of 2,313 orthologous genes indicated that "Ca Endoriftia persephone" symbionts are structured on large geographical scales but also on smaller scales and possibly through host specificity.

IMPORTANCE: Remarkably, the intracellular symbionts of four to six species of eastern Pacific vent tubeworms all belong to the same phylotype of gammaproteobacteria, "Candidatus Endoriftia persephone." Understanding the structure, dynamism, and interconnectivity of "Ca Endoriftia persephone" populations is important to advancing our knowledge of the ecology and evolution of their host worms, which are often keystone species in vent communities. In this paper, we present the first genomes for symbionts associated with the species R. piscesae, from the Juan de Fuca Ridge. We then combine these genomes with published symbiont genomes from the East Pacific Rise tubeworms R. pachyptila and T. jerichonana to develop a portrait of the "Ca Endoriftia persephone" pangenome and an initial outline of symbiont population structure in the different host species. Our study is the first to apply genome-wide comparisons of "Ca Endoriftia persephone" assemblies in the context of population genetics and molecular evolution.}, } @article {pmid27315483, year = {2016}, author = {Buffington, SA and Di Prisco, GV and Auchtung, TA and Ajami, NJ and Petrosino, JF and Costa-Mattioli, M}, title = {Microbial Reconstitution Reverses Maternal Diet-Induced Social and Synaptic Deficits in Offspring.}, journal = {Cell}, volume = {165}, number = {7}, pages = {1762-1775}, pmid = {27315483}, issn = {1097-4172}, support = {R01 MH096816/MH/NIMH NIH HHS/United States ; R01 MH112356/MH/NIMH NIH HHS/United States ; R01 NS076708/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Autism Spectrum Disorder/*microbiology ; *Diet, High-Fat ; Dysbiosis/physiopathology ; Female ; *Gastrointestinal Microbiome ; Germ-Free Life ; Housing, Animal ; Limosilactobacillus reuteri ; Male ; Mice ; Mice, Inbred C57BL ; Obesity/*complications ; Oxytocin/analysis/metabolism ; Pregnancy ; *Social Behavior ; Ventral Tegmental Area ; }, abstract = {Maternal obesity during pregnancy has been associated with increased risk of neurodevelopmental disorders, including autism spectrum disorder (ASD), in offspring. Here, we report that maternal high-fat diet (MHFD) induces a shift in microbial ecology that negatively impacts offspring social behavior. Social deficits and gut microbiota dysbiosis in MHFD offspring are prevented by co-housing with offspring of mothers on a regular diet (MRD) and transferable to germ-free mice. In addition, social interaction induces synaptic potentiation (LTP) in the ventral tegmental area (VTA) of MRD, but not MHFD offspring. Moreover, MHFD offspring had fewer oxytocin immunoreactive neurons in the hypothalamus. Using metagenomics and precision microbiota reconstitution, we identified a single commensal strain that corrects oxytocin levels, LTP, and social deficits in MHFD offspring. Our findings causally link maternal diet, gut microbial imbalance, VTA plasticity, and behavior and suggest that probiotic treatment may relieve specific behavioral abnormalities associated with neurodevelopmental disorders. VIDEO ABSTRACT.}, } @article {pmid27312700, year = {2016}, author = {Ortseifen, V and Stolze, Y and Maus, I and Sczyrba, A and Bremges, A and Albaum, SP and Jaenicke, S and Fracowiak, J and Pühler, A and Schlüter, A}, title = {An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant.}, journal = {Journal of biotechnology}, volume = {231}, number = {}, pages = {268-279}, doi = {10.1016/j.jbiotec.2016.06.014}, pmid = {27312700}, issn = {1873-4863}, mesh = {Biofuels/*microbiology ; Bioreactors/*microbiology ; Databases, Protein ; Electrophoresis, Gel, Two-Dimensional ; Metagenome/*genetics ; Microbial Consortia/*genetics ; Proteome/*analysis/genetics ; }, abstract = {To study the metaproteome of a biogas-producing microbial community, fermentation samples were taken from an agricultural biogas plant for microbial cell and protein extraction and corresponding metagenome analyses. Based on metagenome sequence data, taxonomic community profiling was performed to elucidate the composition of bacterial and archaeal sub-communities. The community's cytosolic metaproteome was represented in a 2D-PAGE approach. Metaproteome databases for protein identification were compiled based on the assembled metagenome sequence dataset for the biogas plant analyzed and non-corresponding biogas metagenomes. Protein identification results revealed that the corresponding biogas protein database facilitated the highest identification rate followed by other biogas-specific databases, whereas common public databases yielded insufficient identification rates. Proteins of the biogas microbiome identified as highly abundant were assigned to the pathways involved in methanogenesis, transport and carbon metabolism. Moreover, the integrated metagenome/-proteome approach enabled the examination of genetic-context information for genes encoding identified proteins by studying neighboring genes on the corresponding contig. Exemplarily, this approach led to the identification of a Methanoculleus sp. contig encoding 16 methanogenesis-related gene products, three of which were also detected as abundant proteins within the community's metaproteome. Thus, metagenome contigs provide additional information on the genetic environment of identified abundant proteins.}, } @article {pmid27311565, year = {2016}, author = {Gao, J and Hou, L and Zheng, Y and Liu, M and Yin, G and Li, X and Lin, X and Yu, C and Wang, R and Jiang, X and Sun, X}, title = {nirS-Encoding denitrifier community composition, distribution, and abundance along the coastal wetlands of China.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {19}, pages = {8573-8582}, doi = {10.1007/s00253-016-7659-5}, pmid = {27311565}, issn = {1432-0614}, mesh = {Ammonium Compounds/analysis ; *Biota ; China ; *Denitrification ; *Environmental Microbiology ; Metagenomics ; Nitrite Reductases/*analysis/genetics ; *Phylogeography ; Sequence Analysis, DNA ; Sequence Homology ; Temperature ; Water/chemistry ; *Wetlands ; }, abstract = {For the past few decades, human activities have intensively increased the reactive nitrogen enrichment in China's coastal wetlands. Although denitrification is a critical pathway of nitrogen removal, the understanding of denitrifier community dynamics driving denitrification remains limited in the coastal wetlands. In this study, the diversity, abundance, and community composition of nirS-encoding denitrifiers were analyzed to reveal their variations in China's coastal wetlands. Diverse nirS sequences were obtained and more than 98 % of them shared considerable phylogenetic similarity with sequences obtained from aquatic systems (marine/estuarine/coastal sediments and hypoxia sea water). Clone library analysis revealed that the distribution and composition of nirS-harboring denitrifiers had a significant latitudinal differentiation, but without a seasonal shift. Canonical correspondence analysis showed that the community structure of nirS-encoding denitrifiers was significantly related to temperature and ammonium concentration. The nirS gene abundance ranged from 4.3 × 10(5) to 3.7 × 10(7) copies g(-1) dry sediment, with a significant spatial heterogeneity. Among all detected environmental factors, temperature was a key factor affecting not only the nirS gene abundance but also the community structure of nirS-type denitrifiers. Overall, this study significantly enhances our understanding of the structure and dynamics of denitrifying communities in the coastal wetlands of China.}, } @article {pmid27310720, year = {2016}, author = {Fahner, NA and Shokralla, S and Baird, DJ and Hajibabaei, M}, title = {Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers.}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0157505}, pmid = {27310720}, issn = {1932-6203}, mesh = {Alberta ; DNA Barcoding, Taxonomic ; DNA, Intergenic/*genetics ; DNA, Plant/*genetics ; Databases, Genetic ; Ecosystem ; Genetic Markers ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Molecular Sequence Annotation ; *Phylogeny ; Plants/classification/*genetics ; Pollen/genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; Seeds/genetics ; Soil/chemistry ; }, abstract = {In a rapidly changing world we need methods to efficiently assess biodiversity in order to monitor ecosystem trends. Ecological monitoring often uses plant community composition to infer quality of sites but conventional aboveground surveys only capture a snapshot of the actively growing plant diversity. Environmental DNA (eDNA) extracted from soil samples, however, can include taxa represented by both active and dormant tissues, seeds, pollen, and detritus. Analysis of this eDNA through DNA metabarcoding provides a more comprehensive view of plant diversity at a site from a single assessment but it is not clear which DNA markers are best used to capture this diversity. Sequence recovery, annotation, and sequence resolution among taxa were evaluated for four established DNA markers (matK, rbcL, ITS2, and the trnL P6 loop) in silico using database sequences and in situ using high throughput sequencing of 35 soil samples from a remote boreal wetland. Overall, ITS2 and rbcL are recommended for DNA metabarcoding of vascular plants from eDNA when not using customized or geographically restricted reference databases. We describe a new framework for evaluating DNA metabarcodes and, contrary to existing assumptions, we found that full length DNA barcode regions could outperform shorter markers for surveying plant diversity from soil samples. By using current DNA barcoding markers rbcL and ITS2 for plant metabarcoding, we can take advantage of existing resources such as the growing DNA barcode database. Our work establishes the value of standard DNA barcodes for soil plant eDNA analysis in ecological investigations and biomonitoring programs and supports the collaborative development of DNA barcoding and metabarcoding.}, } @article {pmid27306058, year = {2016}, author = {Palleja, A and Kashani, A and Allin, KH and Nielsen, T and Zhang, C and Li, Y and Brach, T and Liang, S and Feng, Q and Jørgensen, NB and Bojsen-Møller, KN and Dirksen, C and Burgdorf, KS and Holst, JJ and Madsbad, S and Wang, J and Pedersen, O and Hansen, T and Arumugam, M}, title = {Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota.}, journal = {Genome medicine}, volume = {8}, number = {1}, pages = {67}, pmid = {27306058}, issn = {1756-994X}, mesh = {*Anastomosis, Roux-en-Y ; Bacteria/*classification/genetics/isolation & purification ; Biodiversity ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; Male ; Metagenomics ; Obesity, Morbid/*microbiology/*surgery ; Sequence Analysis, DNA ; Treatment Outcome ; Weight Loss ; }, abstract = {BACKGROUND: Roux-en-Y gastric bypass (RYGB) is an effective means to achieve sustained weight loss for morbidly obese individuals. Besides rapid weight reduction, patients achieve major improvements of insulin sensitivity and glucose homeostasis. Dysbiosis of gut microbiota has been associated with obesity and some of its co-morbidities, like type 2 diabetes, and major changes of gut microbial communities have been hypothesized to mediate part of the beneficial metabolic effects observed after RYGB. Here we describe changes in gut microbial taxonomic composition and functional potential following RYGB.

METHODS: We recruited 13 morbidly obese patients who underwent RYGB, carefully phenotyped them, and had their gut microbiomes quantified before (n = 13) and 3 months (n = 12) and 12 months (n = 8) after RYGB. Following shotgun metagenomic sequencing of the fecal microbial DNA purified from stools, we characterized the gut microbial composition at species and gene levels followed by functional annotation.

RESULTS: In parallel with the weight loss and metabolic improvements, gut microbial diversity increased within the first 3 months after RYGB and remained high 1 year later. RYGB led to altered relative abundances of 31 species (P < 0.05, q < 0.15) within the first 3 months, including those of Escherichia coli, Klebsiella pneumoniae, Veillonella spp., Streptococcus spp., Alistipes spp., and Akkermansia muciniphila. Sixteen of these species maintained their altered relative abundances during the following 9 months. Interestingly, Faecalibacterium prausnitzii was the only species that decreased in relative abundance. Fifty-three microbial functional modules increased their relative abundance between baseline and 3 months (P < 0.05, q < 0.17). These functional changes included increased potential (i) to assimilate multiple energy sources using transporters and phosphotransferase systems, (ii) to use aerobic respiration, (iii) to shift from protein degradation to putrefaction, and (iv) to use amino acids and fatty acids as energy sources.

CONCLUSIONS: Within 3 months after morbidly obese individuals had undergone RYGB, their gut microbiota featured an increased diversity, an altered composition, an increased potential for oxygen tolerance, and an increased potential for microbial utilization of macro- and micro-nutrients. These changes were maintained for the first year post-RYGB.

TRIAL REGISTRATION: Current controlled trials (ID NCT00810823 , NCT01579981 , and NCT01993511).}, } @article {pmid27304457, year = {2016}, author = {Tansirichaiya, S and Rahman, MA and Antepowicz, A and Mullany, P and Roberts, AP}, title = {Detection of Novel Integrons in the Metagenome of Human Saliva.}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0157605}, pmid = {27304457}, issn = {1932-6203}, mesh = {Adult ; Aged ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Bangladesh ; DNA, Bacterial/chemistry/genetics ; Drug Resistance, Microbial/drug effects/genetics ; Female ; Genes, Bacterial/genetics ; Humans ; Integrons/*genetics ; Male ; Metagenome/*genetics ; Microbiota/*genetics ; Middle Aged ; Open Reading Frames/genetics ; Polymerase Chain Reaction ; Saliva/*microbiology ; Sequence Analysis, DNA ; United Kingdom ; Young Adult ; }, abstract = {Integrons are genetic elements capable of capturing and expressing open reading frames (ORFs) embedded within gene cassettes. They are involved in the dissemination of antibiotic resistance genes (ARGs) in clinically important pathogens. Although the ARGs are common in the oral cavity the association of integrons and antibiotic resistance has not been reported there. In this work, a PCR-based approach was used to investigate the presence of integrons and associated gene cassettes in human oral metagenomic DNA obtained from both the UK and Bangladesh. We identified a diverse array of gene cassettes containing ORFs predicted to confer antimicrobial resistance and other adaptive traits. The predicted proteins include a putative streptogramin A O-acetyltransferase, a bleomycin binding protein, cof-like hydrolase, competence and motility related proteins. This is the first study detecting integron gene cassettes directly from oral metagenomic DNA samples. The predicted proteins are likely to carry out a multitude of functions; however, the function of the majority is yet unknown.}, } @article {pmid27303369, year = {2016}, author = {Kielak, AM and Barreto, CC and Kowalchuk, GA and van Veen, JA and Kuramae, EE}, title = {The Ecology of Acidobacteria: Moving beyond Genes and Genomes.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {744}, pmid = {27303369}, issn = {1664-302X}, abstract = {The phylum Acidobacteria is one of the most widespread and abundant on the planet, yet remarkably our knowledge of the role of these diverse organisms in the functioning of terrestrial ecosystems remains surprisingly rudimentary. This blatant knowledge gap stems to a large degree from the difficulties associated with the cultivation of these bacteria by classical means. Given the phylogenetic breadth of the Acidobacteria, which is similar to the metabolically diverse Proteobacteria, it is clear that detailed and functional descriptions of acidobacterial assemblages are necessary. Fortunately, recent advances are providing a glimpse into the ecology of members of the phylum Acidobacteria. These include novel cultivation and enrichment strategies, genomic characterization and analyses of metagenomic DNA from environmental samples. Here, we couple the data from these complementary approaches for a better understanding of their role in the environment, thereby providing some initial insights into the ecology of this important phylum. All cultured acidobacterial type species are heterotrophic, and members of subdivisions 1, 3, and 4 appear to be more versatile in carbohydrate utilization. Genomic and metagenomic data predict a number of ecologically relevant capabilities for some acidobacteria, including the ability to: use of nitrite as N source, respond to soil macro-, micro nutrients and soil acidity, express multiple active transporters, degrade gellan gum and produce exopolysaccharide (EPS). Although these predicted properties allude to a competitive life style in soil, only very few of these prediction shave been confirmed via physiological studies. The increased availability of genomic and physiological information, coupled to distribution data in field surveys and experiments, should direct future progress in unraveling the ecology of this important but still enigmatic phylum.}, } @article {pmid27301664, year = {2016}, author = {Tanaka, A and Cho, O and Saito, C and Saito, M and Tsuboi, R and Sugita, T}, title = {Comprehensive pyrosequencing analysis of the bacterial microbiota of the skin of patients with seborrheic dermatitis.}, journal = {Microbiology and immunology}, volume = {60}, number = {8}, pages = {521-526}, doi = {10.1111/1348-0421.12398}, pmid = {27301664}, issn = {1348-0421}, mesh = {Adult ; Aged ; Biodiversity ; Dermatitis, Seborrheic/*microbiology ; Female ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; Sequence Analysis, DNA ; Skin/*microbiology ; Young Adult ; }, abstract = {Seborrheic dermatitis (SD) is a chronic inflammatory dermatologic condition in which erythema and itching develop on areas of the body with sebaceous glands, such as the scalp, face and chest. The inflammation is evoked directly by oleic acid, which is hydrolyzed from sebum by lipases secreted by skin microorganisms. Although the skin fungal genus, Malassezia, is thought to be the causative agent of SD, analysis of the bacterial microbiota of skin samples of patients with SD is necessary to clarify any association with Malassezia because the skin microbiota comprises diverse bacterial and fungal genera. In the present study, bacterial microbiotas were analyzed at non-lesional and lesional sites of 24 patients with SD by pyrosequencing and qPCR. Principal coordinate analysis revealed clear separation between the microbiota of non-lesional and lesional sites. Acinetobacter, Corynebacterium, Staphylococcus, Streptococcus and Propionibacterium were abundant at both sites. Propionibacterium was abundant at non-lesional sites, whereas Acinetobacter, Staphylococcus and Streptococcus predominated at lesional sites; however, the extent of Propionibacterium colonization did not differ significantly between lesional and non-lesional sites according to qPCR. Given that these abundant bacteria hydrolyze sebum, they may also contribute to SD development. To the best of our knowledge, this is the first comprehensive analysis of the bacterial microbiotas of the skin of SD patients.}, } @article {pmid27301250, year = {2016}, author = {Hu, J and Raikhel, V and Gopalakrishnan, K and Fernandez-Hernandez, H and Lambertini, L and Manservisi, F and Falcioni, L and Bua, L and Belpoggi, F and L Teitelbaum, S and Chen, J}, title = {Effect of postnatal low-dose exposure to environmental chemicals on the gut microbiome in a rodent model.}, journal = {Microbiome}, volume = {4}, number = {1}, pages = {26}, pmid = {27301250}, issn = {2049-2618}, support = {K01 DK094986/DK/NIDDK NIH HHS/United States ; U01 ES019459/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Bacteroidetes/isolation & purification ; Betaproteobacteria/isolation & purification ; Body Weight/drug effects ; Deltaproteobacteria/isolation & purification ; Environmental Exposure/*adverse effects ; Environmental Pollutants/*pharmacology ; Environmental Pollution/adverse effects ; Feces/microbiology ; Female ; Firmicutes/isolation & purification ; Gastrointestinal Microbiome/*drug effects ; Parabens/*pharmacology ; Phthalic Acids/*pharmacology ; Postpartum Period ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; Triclosan/*pharmacology ; }, abstract = {BACKGROUND: This proof-of-principle study examines whether postnatal, low-dose exposure to environmental chemicals modifies the composition of gut microbiome. Three chemicals that are widely used in personal care products-diethyl phthalate (DEP), methylparaben (MPB), triclosan (TCS)-and their mixture (MIX) were administered at doses comparable to human exposure to Sprague-Dawley rats from birth through adulthood. Fecal samples were collected at two time points: postnatal day (PND) 62 (adolescence) and PND 181 (adulthood). The gut microbiome was profiled by 16S ribosomal RNA gene sequencing, taxonomically assigned and assessed for diversity.

RESULTS: Metagenomic profiling revealed that the low-dose chemical exposure resulted in significant changes in the overall bacterial composition, but in adolescent rats only. Specifically, the individual taxon relative abundance for Bacteroidetes (Prevotella) was increased while the relative abundance of Firmicutes (Bacilli) was reduced in all treated rats compared to controls. Increased abundance was observed for Elusimicrobia in DEP and MPB groups, Betaproteobacteria in MPB and MIX groups, and Deltaproteobacteria in TCS group. Surprisingly, these differences diminished by adulthood (PND 181) despite continuous exposure, suggesting that exposure to the environmental chemicals produced a more profound effect on the gut microbiome in adolescents. We also observed a small but consistent reduction in the bodyweight of exposed rats in adolescence, especially with DEP and MPB treatment (p < 0.05), which is consistent with our findings of a reduced Firmicutes/Bacteroidetes ratio at PND 62 in exposed rats.

CONCLUSIONS: This study provides initial evidence that postnatal exposure to commonly used environmental chemicals at doses comparable to human exposure is capable of modifying the gut microbiota in adolescent rats; whether these changes lead to downstream health effects requires further investigation.}, } @article {pmid27299312, year = {2016}, author = {Marzano, M and Fosso, B and Manzari, C and Grieco, F and Intranuovo, M and Cozzi, G and Mulè, G and Scioscia, G and Valiente, G and Tullo, A and Sbisà, E and Pesole, G and Santamaria, M}, title = {Complexity and Dynamics of the Winemaking Bacterial Communities in Berries, Musts, and Wines from Apulian Grape Cultivars through Time and Space.}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0157383}, pmid = {27299312}, issn = {1932-6203}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Fermentation ; Fruit/microbiology ; Fungi/classification/*genetics/isolation & purification ; High-Throughput Screening Assays ; Metagenomics ; Microbiota ; Vitis/*microbiology ; Wine/*microbiology ; }, abstract = {Currently, there is very little information available regarding the microbiome associated with the wine production chain. Here, we used an amplicon sequencing approach based on high-throughput sequencing (HTS) to obtain a comprehensive assessment of the bacterial community associated with the production of three Apulian red wines, from grape to final product. The relationships among grape variety, the microbial community, and fermentation was investigated. Moreover, the winery microbiota was evaluated compared to the autochthonous species in vineyards that persist until the end of the winemaking process. The analysis highlighted the remarkable dynamics within the microbial communities during fermentation. A common microbial core shared among the examined wine varieties was observed, and the unique taxonomic signature of each wine appellation was revealed. New species belonging to the genus Halomonas were also reported. This study demonstrates the potential of this metagenomic approach, supported by optimized protocols, for identifying the biodiversity of the wine supply chain. The developed experimental pipeline offers new prospects for other research fields in which a comprehensive view of microbial community complexity and dynamics is desirable.}, } @article {pmid27297798, year = {2016}, author = {Zulian, A and Cancello, R and Cesana, E and Rizzi, E and Consolandi, C and Severgnini, M and Panizzo, V and Di Blasio, AM and Micheletto, G and Invitti, C}, title = {Adipose tissue microbiota in humans: an open issue.}, journal = {International journal of obesity (2005)}, volume = {40}, number = {11}, pages = {1643-1648}, pmid = {27297798}, issn = {1476-5497}, mesh = {Adult ; Body Mass Index ; Female ; Gastrointestinal Microbiome/physiology ; Gene Expression Regulation ; Humans ; Inflammation/*microbiology/pathology ; Intestinal Mucosa/*microbiology/pathology ; Intra-Abdominal Fat/*microbiology/pathology ; Male ; Middle Aged ; Obesity/*microbiology/pathology ; RNA, Messenger/metabolism ; RNA, Ribosomal, 16S ; Real-Time Polymerase Chain Reaction ; }, abstract = {BACKGROUND: A specific 'adipose tissue' microbiota has been recently identified in mice and hypothesized in humans. The purpose of this study was to verify the presence of microbiota of human whole adipose tissue and isolated adipocytes by combining culture-dependent and independent methods.

METHODS: Standard microbiological cultural techniques and 16S ribosomal RNA (16S rRNA) gene sequencing (Illumina technology) on DNA and RNA were employed to study (a) whole abdominal subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT) from 14 obese and five normal-weight subjects and (b) mature adipocytes isolated from SAT and VAT after collagenase digestion or mechanical separation. To optimize the 16S rRNA gene detection, we used different DNA extraction methods (lysis with proteinase K, proteinase K+lysozyme and microbeads) and amplification procedures (semi-quantitative standard PCR and real-time quantitative PCR).

RESULTS: Microbiological cultures were negative in all analyzed samples. In enzymatically isolated adipocytes, 90% of the sequenced bacterial DNA belonged to Clostridium histolyticum, the bacterium from which the collagenase enzyme was isolated. Bacterial 16S rRNA gene was not detected from DNA and RNA of whole SAT and VAT, as well as of mechanically isolated mature adipocytes, even after blocking with a specific primer the nonspecific amplification of human mitochondrial 12S rRNA.

CONCLUSIONS: Our results do not support the presence of a human adipose tissue microbiota. In addition, they emphasized the technical problems encountered when applying metagenomic studies to human tissues with very low or absent bacterial load.}, } @article {pmid27297628, year = {2016}, author = {Colston, TJ and Jackson, CR}, title = {Microbiome evolution along divergent branches of the vertebrate tree of life: what is known and unknown.}, journal = {Molecular ecology}, volume = {25}, number = {16}, pages = {3776-3800}, doi = {10.1111/mec.13730}, pmid = {27297628}, issn = {1365-294X}, mesh = {Amphibians/microbiology ; Animals ; *Biological Evolution ; Birds/microbiology ; Diet ; Fishes/microbiology ; High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; Reptiles/microbiology ; Vertebrates/*microbiology ; }, abstract = {Vertebrates harbour microbes both internally and externally, and collectively, these microorganisms (the 'microbiome') contain genes that outnumber the host's genetic information 10-fold. The majority of the microorganisms associated with vertebrates are found within the gut, where they influence host physiology, immunity and development. The development of next-generation sequencing has led to a surge in effort to characterize the microbiomes of various vertebrate hosts, a necessary first step to determine the functional role these communities play in host evolution or ecology. This shift away from a culture-based microbiological approach, limited in taxonomic breadth, has resulted in the emergence of patterns suggesting a core vertebrate microbiome dominated by members of the bacterial phyla Bacteroidetes, Proteobacteria and Firmicutes. Still, there is a substantial variation in the methodology used to characterize the microbiome, from differences in sample type to issues of sampling captive or wild hosts, and the majority (>90%) of studies have characterized the microbiome of mammals, which represent just 8% of described vertebrate species. Here, we review the state of microbiome studies of nonmammalian vertebrates and provide a synthesis of emerging patterns in the microbiome of those organisms. We highlight the importance of collection methods, and the need for greater taxonomic sampling of natural rather than captive hosts, a shift in approach that is needed to draw ecologically and evolutionarily relevant inferences. Finally, we recommend future directions for vertebrate microbiome research, so that attempts can be made to determine the role that microbial communities play in vertebrate biology and evolution.}, } @article {pmid27294780, year = {2016}, author = {Tao, W and Zhang, XX and Zhao, F and Huang, K and Ma, H and Wang, Z and Ye, L and Ren, H}, title = {High Levels of Antibiotic Resistance Genes and Their Correlations with Bacterial Community and Mobile Genetic Elements in Pharmaceutical Wastewater Treatment Bioreactors.}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0156854}, pmid = {27294780}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/*genetics/growth & development ; Biodiversity ; Bioreactors/*microbiology ; Biota/*genetics ; *Drug Industry ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial ; *Interspersed Repetitive Sequences ; Metagenomics ; Microbial Sensitivity Tests ; Waste Disposal, Fluid/instrumentation/methods ; Wastewater/*microbiology ; Water Purification/*instrumentation ; }, abstract = {To understand the diversity and abundance of antibiotic resistance genes (ARGs) in pharmaceutical wastewater treatment bioreactors, the ARGs in sludge from two full-scale pharmaceutical wastewater treatment plants (PWWTPs) were investigated and compared with sludge samples from three sewage treatment plants (STPs) using metagenomic approach. The results showed that the ARG abundances in PWWTP sludge ranged from 54.7 to 585.0 ppm, which were higher than those in STP sludge (27.2 to 86.4 ppm). Moreover, the diversity of ARGs in PWWTP aerobic sludge (153 subtypes) was higher than that in STP aerobic sludge (118 subtypes). In addition, it was found that the profiles of ARGs in PWWTP aerobic sludge were similar to those in STP aerobic sludge but different from those in PWWTP anaerobic sludge, suggesting that dissolve oxygen (DO) could be one of the important factors affecting the profiles of ARGs. In PWWTP aerobic sludge, aminoglycoside, sulfonamide and multidrug resistance genes were frequently detected. While, tetracycline, macrolide-lincosamide-streptogramin and polypeptide resistance genes were abundantly present in PWWTP anaerobic sludge. Furthermore, we investigated the microbial community and the correlation between microbial community and ARGs in PWWTP sludge. And, significant correlations between ARG types and seven bacterial genera were found. In addition, the mobile genetic elements (MGEs) were also examined and correlations between the ARGs and MGEs in PWWTP sludge were observed. Collectively, our results suggested that the microbial community and MGEs, which could be affected by DO, might be the main factors shaping the profiles of ARGs in PWWTP sludge.}, } @article {pmid27295684, year = {2017}, author = {Liu, Y and Hou, T and Kang, B and Liu, F}, title = {Unsupervised Binning of Metagenomic Assembled Contigs Using Improved Fuzzy C-Means Method.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {14}, number = {6}, pages = {1459-1467}, doi = {10.1109/TCBB.2016.2576452}, pmid = {27295684}, issn = {1557-9964}, mesh = {Algorithms ; Cluster Analysis ; Fuzzy Logic ; Gastrointestinal Microbiome/genetics ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Sequence Analysis, DNA/*methods ; Unsupervised Machine Learning ; }, abstract = {Metagenomic contigs binning is a necessary step of metagenome analysis. After assembly, the number of contigs belonging to different genomes is usually unequal. So a metagenomic contigs dataset is a kind of imbalanced dataset and traditional fuzzy c-means method (FCM) fails to handle it very well. In this paper, we will introduce an improved version of fuzzy c-means method (IFCM) into metagenomic contigs binning. First, tetranucleotide frequencies are calculated for every contig. Second, the number of bins is roughly estimated by the distribution of genome lengths of a complete set of non-draft sequenced microbial genomes from NCBI. Then, IFCM is used to cluster DNA contigs with the estimated result. Finally, a clustering validity function is utilized to determine the binning result. We tested this method on a synthetic and two real datasets and experimental results have showed the effectiveness of this method compared with other tools.}, } @article {pmid27294381, year = {2016}, author = {Noble, PA and Park, HD and Olson, BH and Asvapathanagul, P and Hunter, MC and Garrido-Baserba, M and Lee, SH and Rosso, D}, title = {A survey of biofilms on wastewater aeration diffusers suggests bacterial community composition and function vary by substrate type and time.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {14}, pages = {6361-6373}, doi = {10.1007/s00253-016-7604-7}, pmid = {27294381}, issn = {1432-0614}, mesh = {Bacteria/classification/genetics/metabolism ; Biodegradation, Environmental ; *Biofilms ; Biofouling ; DNA, Bacterial/isolation & purification ; Diffusion ; Elastomers/chemistry ; Ethylenes/chemistry ; *Microbial Consortia ; Oxygen/metabolism ; Pilot Projects ; Polyurethanes/chemistry ; Principal Component Analysis ; RNA, Ribosomal, 16S/isolation & purification ; Sequence Analysis, DNA ; Silicones/chemistry ; Surveys and Questionnaires ; Time Factors ; Wastewater/*microbiology ; }, abstract = {Aeration diffusers in wastewater treatment plants generate air bubbles that promote mixing, distribution of dissolved oxygen, and microbial processing of dissolved and suspended matter in bulk solution. Biofouling of diffusers represents a significant problem to wastewater treatment plants because biofilms decrease oxygen transfer efficiency and increase backpressure on the blower. To better understand biofouling, we conducted a pilot study to survey the bacterial community composition and function of biofilms on different diffuser substrates and compare them to those in the bulk solution. DNA was extracted from the surface of ethylene-propylene-diene monomer (EPDM), polyurethane, and silicone diffusers operated for 15 months in a municipal treatment plant and sampled at 3 and 9 months. The bacterial community composition and function of the biofilms and bulk solution were determined by amplifying the 16S rRNA genes and pyrosequencing the amplicons and raw metagenomic DNA. The ordination plots and dendrograms of the 16S rRNA and functional genes showed that while the bacterial community composition and function of the bulk solution was independent of sampling time, the composition and function of the biofilms differed by diffuser type and testing time. For the EPDM and silicone diffusers, the biofilm communities were more similar in composition to the bulk solution at 3 months than 9 months. In contrast, the bacteria on the polyurethane diffusers were more dissimilar to the bulk solution at 3 months than 9 months. Taken together, the survey showed that the community composition and function of bacterial biofilms depend on the diffuser substrate and testing time, which warrants further elucidation.}, } @article {pmid27292825, year = {2016}, author = {Bunyavanich, S and Shen, N and Grishin, A and Wood, R and Burks, W and Dawson, P and Jones, SM and Leung, DYM and Sampson, H and Sicherer, S and Clemente, JC}, title = {Early-life gut microbiome composition and milk allergy resolution.}, journal = {The Journal of allergy and clinical immunology}, volume = {138}, number = {4}, pages = {1122-1130}, pmid = {27292825}, issn = {1097-6825}, support = {U01 AI066560/AI/NIAID NIH HHS/United States ; UL1 TR000039/TR/NCATS NIH HHS/United States ; UL1 RR025005/RR/NCRR NIH HHS/United States ; R01 AI118833/AI/NIAID NIH HHS/United States ; UL1 TR000154/TR/NCATS NIH HHS/United States ; K08 AI093538/AI/NIAID NIH HHS/United States ; UL1 TR001433/TR/NCATS NIH HHS/United States ; UL1 RR024128/RR/NCRR NIH HHS/United States ; U19 AI066738/AI/NIAID NIH HHS/United States ; P30 DK020541/DK/NIDDK NIH HHS/United States ; UL1 TR000067/TR/NCATS NIH HHS/United States ; UL1 TR001082/TR/NCATS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics ; Child ; Child, Preschool ; Dermatitis, Atopic/physiopathology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Immunoglobulin E/blood ; Infant ; Male ; Milk Hypersensitivity/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Gut microbiota may play a role in the natural history of cow's milk allergy.

OBJECTIVE: We sought to examine the association between early-life gut microbiota and the resolution of cow's milk allergy.

METHODS: We studied 226 children with milk allergy who were enrolled at infancy in the Consortium of Food Allergy observational study of food allergy. Fecal samples were collected at age 3 to 16 months, and the children were followed longitudinally with clinical evaluation, milk-specific IgE levels, and milk skin prick test performed at enrollment, 6 months, 12 months, and yearly thereafter up until age 8 years. Gut microbiome was profiled by 16s rRNA sequencing and microbiome analyses performed using Quantitative Insights into Microbial Ecology (QIIME), Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt), and Statistical Analysis of Metagenomic Profiles (STAMP).

RESULTS: Milk allergy resolved by age 8 years in 128 (56.6%) of the 226 children. Gut microbiome composition at age 3 to 6 months was associated with milk allergy resolution by age 8 years (PERMANOVA P = .047), with enrichment of Clostridia and Firmicutes in the infant gut microbiome of subjects whose milk allergy resolved. Metagenome functional prediction supported decreased fatty acid metabolism in the gut microbiome of subjects whose milk allergy resolved (η[2] = 0.43; ANOVA P = .034).

CONCLUSIONS: Early infancy is a window during which gut microbiota may shape food allergy outcomes in childhood. Bacterial taxa within Clostridia and Firmicutes could be studied as probiotic candidates for milk allergy therapy.}, } @article {pmid27291330, year = {2017}, author = {Malone, M and Gosbell, IB and Dickson, HG and Vickery, K and Espedido, BA and Jensen, SO}, title = {Can molecular DNA-based techniques unravel the truth about diabetic foot infections?.}, journal = {Diabetes/metabolism research and reviews}, volume = {33}, number = {1}, pages = {}, doi = {10.1002/dmrr.2834}, pmid = {27291330}, issn = {1520-7560}, mesh = {Bacteria/classification/*genetics ; Bacterial Infections/*diagnosis/genetics/microbiology ; DNA, Bacterial/*genetics ; Diabetic Foot/*microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Metagenomics ; Microbiota/*genetics ; }, abstract = {Diabetes foot infections are a common condition and a major causal pathway to lower extremity amputation. Identification of causative pathogens is vital in directing antimicrobial therapy. Historically, clinicians have relied upon culture-dependent techniques that are now acknowledged as both being selective for microorganisms that thrive under the physiological and nutritional constraints of the microbiology laboratory and that grossly underestimate the microbial diversity of a sample. The amplification and sequence analysis of the 16S rRNA gene has revealed a diversity of microorganisms in diabetes foot infections, extending the view of the diabetic foot microbiome. The interpretation of these findings and their relevance to clinical care remains largely unexplored. The advent of molecular methods that are culture-independent and employ massively parallel DNA sequencing technology represents a potential 'game changer'. Metagenomics and its shotgun approach to surveying all DNA within a sample (whole genome sequencing) affords the possibility to characterize not only the microbial diversity within a diabetes foot infection (i.e. 'which microorganisms are present') but the biological functions of the community such as virulence and pathogenicity (i.e. 'what are the microorganisms capable of doing'), moving the focus from single species as pathogens to groups of species. This review will examine the new molecular techniques for exploration of the microbiome of infected and uninfected diabetic foot ulcers, exploring the potential of these new technologies and postulating how they could translate to improved clinical care. Copyright © 2016 John Wiley & Sons, Ltd.}, } @article {pmid27288420, year = {2016}, author = {Panasevich, MR and Morris, EM and Chintapalli, SV and Wankhade, UD and Shankar, K and Britton, SL and Koch, LG and Thyfault, JP and Rector, RS}, title = {Gut microbiota are linked to increased susceptibility to hepatic steatosis in low-aerobic-capacity rats fed an acute high-fat diet.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {311}, number = {1}, pages = {G166-79}, pmid = {27288420}, issn = {1522-1547}, support = {I01 BX002567/BX/BLRD VA/United States ; IK2 BX001299/BX/BLRD VA/United States ; P40 OD021331/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/*metabolism ; Cecum/*microbiology ; *Diet, High-Fat ; Dietary Carbohydrates/metabolism ; Disease Models, Animal ; Energy Intake ; Energy Metabolism ; *Exercise Tolerance/genetics ; Fatty Acids/metabolism ; *Gastrointestinal Microbiome ; Genetic Predisposition to Disease ; Inflammation Mediators/metabolism ; Liver/*metabolism/pathology ; Non-alcoholic Fatty Liver Disease/genetics/*microbiology/pathology ; Phenotype ; Rats, Inbred Strains ; Running ; Time Factors ; Triglycerides/metabolism ; Weight Gain ; }, abstract = {Poor aerobic fitness is linked to nonalcoholic fatty liver disease and increased all-cause mortality. We previously found that rats with a low capacity for running (LCR) that were fed an acute high-fat diet (HFD; 45% kcal from fat) for 3 days resulted in positive energy balance and increased hepatic steatosis compared with rats that were highly aerobically fit with a high capacity for running (HCR). Here, we tested the hypothesis that poor physiological outcomes in LCR rats following acute HFD feeding are associated with alterations in cecal microbiota. LCR rats exhibited greater body weight, feeding efficiency, 3 days of body weight change, and liver triglycerides after acute HFD feeding compared with HCR rats. Furthermore, compared with HCR rats, LCR rats exhibited reduced expression of intestinal tight junction proteins. Cecal bacterial 16S rDNA revealed that LCR rats had reduced cecal Proteobacteria compared with HCR rats. Microbiota of HCR rats consisted of greater relative abundance of Desulfovibrionaceae and unassigned genera within this family, suggesting increased reduction of endogenous mucins and proteins. Although feeding rats an acute HFD led to reduced Firmicutes in both strains, short-chain fatty acid-producing Phascolarctobacterium was reduced in LCR rats. In addition, Ruminococcae and Ruminococcus were negatively correlated with energy intake in the LCR/HFD rats. Predicted metagenomic function suggested that LCR rats had a greater capacity to metabolize carbohydrate and energy compared with HCR rats. Overall, these data suggest that the populations and metabolic capacity of the microbiota in low-aerobically fit LCR rats may contribute to their susceptibility to acute HFD-induced hepatic steatosis and poor physiologic outcomes.}, } @article {pmid27287850, year = {2016}, author = {Chao, Y and Mao, Y and Yu, K and Zhang, T}, title = {Novel nitrifiers and comammox in a full-scale hybrid biofilm and activated sludge reactor revealed by metagenomic approach.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {18}, pages = {8225-8237}, doi = {10.1007/s00253-016-7655-9}, pmid = {27287850}, issn = {1432-0614}, mesh = {Ammonia/*metabolism ; Bacteria/classification/genetics/metabolism ; Biofilms/*growth & development ; Bioreactors/*microbiology ; *Biota ; *Denitrification ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Nitrification ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; Polymerase Chain Reaction ; Sewage/*microbiology ; Wastewater ; Water Purification ; }, abstract = {Biofilms are widely used in wastewater treatment for their particular enhancement of nitrogen removal and other significant advantages. In this study, the diversity and potential functions of nitrogen removal bacteria in suspended activated sludge (AS) and biofilm of a full-scale hybrid reactor were uncovered by metagenomes (∼34 Gb), coupled with PCR-based 454 reads (>33 K reads). The results indicated that the diversity and abundance of nitrifiers and denitrifiers in biofilm did not surpass that in AS, while more nitrification and denitrification genes were indeed found in biofilm than AS, suggesting that the increased nitrogen removal ability by applying biofilm might be attributed to the enhancement of removal efficiency, rather than the biomass accumulation of nitrogen removal bacteria. The gene annotation and phylogenetic analysis results revealed that AS and biofilm samples consisted of 6.0 % and 9.4 % of novel functional genes for nitrogen removal and 18 % and 30 % of new Nitrospira species for nitrite-oxidizing bacteria, respectively. Moreover, the identification of Nitrospira-like amoA genes provided metagenomic evidence for the presence of complete ammonia oxidizer (comammox) with the functional potential to perform the complete oxidation of ammonia to nitrate. These findings have significant implications in expanding our knowledge of the biological nitrogen transformations in wastewater treatment.}, } @article {pmid27283019, year = {2016}, author = {Chimienti, G and Piredda, R and Pepe, G and van der Werf, ID and Sabbatini, L and Crecchio, C and Ricciuti, P and D'Erchia, AM and Manzari, C and Pesole, G}, title = {Profile of microbial communities on carbonate stones of the medieval church of San Leonardo di Siponto (Italy) by Illumina-based deep sequencing.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {19}, pages = {8537-8548}, doi = {10.1007/s00253-016-7656-8}, pmid = {27283019}, issn = {1432-0614}, mesh = {Bacteria/classification/genetics ; *Biota ; *Carbonates ; Chlorophyta/classification/genetics ; *Environmental Microbiology ; *High-Throughput Nucleotide Sequencing ; Italy ; Metagenomics ; Sequence Analysis, DNA ; }, abstract = {Comprehensive studies of the biodiversity of the microbial epilithic community on monuments may provide critical insights for clarifying factors involved in the colonization processes. We carried out a high-throughput investigation of the communities colonizing the medieval church of San Leonardo di Siponto (Italy) by Illumina-based deep sequencing. The metagenomic analysis of sequences revealed the presence of Archaea, Bacteria, and Eukarya. Bacteria were Actinobacteria, Proteobacteria, Bacteroidetes, Cyanobacteria, Chloroflexi, Firmicutes and Candidatus Saccharibacteria. The predominant phylum was Actinobacteria, with the orders Actynomycetales and Rubrobacteriales, represented by the genera Pseudokineococcus, Sporichthya, Blastococcus, Arthrobacter, Geodermatophilus, Friedmanniella, Modestobacter, and Rubrobacter, respectively. Cyanobacteria sequences showing strong similarity with an uncultured bacterium sequence were identified. The presence of the green algae Oocystaceae and Trebuxiaceae was revealed. The microbial diversity was explored at qualitative and quantitative levels, evaluating the richness (the number of operational taxonomic units (OTUs)) and the abundance of reads associated with each OTU. The rarefaction curves approached saturation, suggesting that the majority of OTUs were recovered. The results highlighted a structured community, showing low diversity, made up of extremophile organisms adapted to desiccation and UV radiation. Notably, the microbiome appeared to be composed not only of microorganisms possibly involved in biodeterioration but also of carbonatogenic bacteria, such as those belonging to the genus Arthrobacter, which could be useful in bioconservation. Our investigation demonstrated that molecular tools, and in particular the easy-to-run next-generation sequencing, are powerful to perform a microbiological diagnosis in order to plan restoration and protection strategies.}, } @article {pmid27282316, year = {2016}, author = {Kazamia, E and Helliwell, KE and Purton, S and Smith, AG}, title = {How mutualisms arise in phytoplankton communities: building eco-evolutionary principles for aquatic microbes.}, journal = {Ecology letters}, volume = {19}, number = {7}, pages = {810-822}, pmid = {27282316}, issn = {1461-0248}, support = {BB/I013164/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biological Evolution ; Ecology/methods ; Food Chain ; Microalgae/metabolism/physiology ; *Microbiota ; *Models, Biological ; Phytoplankton/metabolism/*physiology ; *Symbiosis ; }, abstract = {Extensive sampling and metagenomics analyses of plankton communities across all aquatic environments are beginning to provide insights into the ecology of microbial communities. In particular, the importance of metabolic exchanges that provide a foundation for ecological interactions between microorganisms has emerged as a key factor in forging such communities. Here we show how both studies of environmental samples and physiological experimentation in the laboratory with defined microbial co-cultures are being used to decipher the metabolic and molecular underpinnings of such exchanges. In addition, we explain how metabolic modelling may be used to conduct investigations in reverse, deducing novel molecular exchanges from analysis of large-scale data sets, which can identify persistently co-occurring species. Finally, we consider how knowledge of microbial community ecology can be built into evolutionary theories tailored to these species' unique lifestyles. We propose a novel model for the evolution of metabolic auxotrophy in microorganisms that arises as a result of symbiosis, termed the Foraging-to-Farming hypothesis. The model has testable predictions, fits several known examples of mutualism in the aquatic world, and sheds light on how interactions, which cement dependencies within communities of microorganisms, might be initiated.}, } @article {pmid27279224, year = {2016}, author = {Bashan, A and Gibson, TE and Friedman, J and Carey, VJ and Weiss, ST and Hohmann, EL and Liu, YY}, title = {Universality of human microbial dynamics.}, journal = {Nature}, volume = {534}, number = {7606}, pages = {259-262}, pmid = {27279224}, issn = {1476-4687}, support = {R01 HL091528/HL/NHLBI NIH HHS/United States ; }, mesh = {Clostridioides difficile/physiology ; Clostridium Infections/microbiology ; Computer Simulation ; Cross-Sectional Studies ; Datasets as Topic ; *Ecosystem ; Environment ; Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/physiology ; Healthy Volunteers ; Humans ; Intestines/microbiology ; Metagenomics ; Microbiota/*physiology ; Mouth/microbiology ; Organ Specificity ; Skin/microbiology ; Species Specificity ; }, abstract = {Human-associated microbial communities have a crucial role in determining our health and well-being, and this has led to the continuing development of microbiome-based therapies such as faecal microbiota transplantation. These microbial communities are very complex, dynamic and highly personalized ecosystems, exhibiting a high degree of inter-individual variability in both species assemblages and abundance profiles. It is not known whether the underlying ecological dynamics of these communities, which can be parameterized by growth rates, and intra- and inter-species interactions in population dynamics models, are largely host-independent (that is, universal) or host-specific. If the inter-individual variability reflects host-specific dynamics due to differences in host lifestyle, physiology or genetics, then generic microbiome manipulations may have unintended consequences, rendering them ineffective or even detrimental. Alternatively, microbial ecosystems of different subjects may exhibit universal dynamics, with the inter-individual variability mainly originating from differences in the sets of colonizing species. Here we develop a new computational method to characterize human microbial dynamics. By applying this method to cross-sectional data from two large-scale metagenomic studies--the Human Microbiome Project and the Student Microbiome Project--we show that gut and mouth microbiomes display pronounced universal dynamics, whereas communities associated with certain skin sites are probably shaped by differences in the host environment. Notably, the universality of gut microbial dynamics is not observed in subjects with recurrent Clostridium difficile infection but is observed in the same set of subjects after faecal microbiota transplantation. These results fundamentally improve our understanding of the processes that shape human microbial ecosystems, and pave the way to designing general microbiome-based therapies.}, } @article {pmid27279212, year = {2016}, author = {Stappenbeck, TS and Virgin, HW}, title = {Accounting for reciprocal host-microbiome interactions in experimental science.}, journal = {Nature}, volume = {534}, number = {7606}, pages = {191-199}, pmid = {27279212}, issn = {1476-4687}, mesh = {Animals ; Biomedical Research/*methods/*standards ; Fecal Microbiota Transplantation ; Female ; Humans ; Male ; Metagenome/*genetics ; Mice ; Microbiota/*genetics ; Models, Animal ; Phenotype ; Reference Standards ; Reproducibility of Results ; *Research Design ; Sequence Analysis, DNA ; }, abstract = {Mammals are defined by their metagenome, a combination of host and microbiome genes. This knowledge presents opportunities to further basic biology with translation to human diseases. However, the now-documented influence of the metagenome on experimental results and the reproducibility of in vivo mammalian models present new challenges. Here we provide the scientific basis for calling on all investigators, editors and funding agencies to embrace changes that will enhance reproducible and interpretable experiments by accounting for metagenomic effects. Implementation of new reporting and experimental design principles will improve experimental work, speed discovery and translation, and properly use substantial investments in biomedical research.}, } @article {pmid27277524, year = {2016}, author = {Pop, M and Paulson, JN and Chakraborty, S and Astrovskaya, I and Lindsay, BR and Li, S and Bravo, HC and Harro, C and Parkhill, J and Walker, AW and Walker, RI and Sack, DA and Stine, OC}, title = {Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {440}, pmid = {27277524}, issn = {1471-2164}, support = {R01 AI100947/AI/NIAID NIH HHS/United States ; 098051/WT_/Wellcome Trust/United Kingdom ; R21 GM107683/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R01 GM114267/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Ciprofloxacin/pharmacology/*therapeutic use ; Diarrhea/drug therapy/microbiology ; Enterotoxigenic Escherichia coli/*drug effects/*physiology ; Escherichia coli Infections/*drug therapy/*microbiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; RNA, Ribosomal, 16S ; ROC Curve ; Treatment Outcome ; Young Adult ; }, abstract = {BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhea in inhabitants from low-income countries and in visitors to these countries. The impact of the human intestinal microbiota on the initiation and progression of ETEC diarrhea is not yet well understood.

RESULTS: We used 16S rRNA (ribosomal RNA) gene sequencing to study changes in the fecal microbiota of 12 volunteers during a human challenge study with ETEC (H10407) and subsequent treatment with ciprofloxacin. Five subjects developed severe diarrhea and seven experienced few or no symptoms. Diarrheal symptoms were associated with high concentrations of fecal E. coli as measured by quantitative culture, quantitative PCR, and normalized number of 16S rRNA gene sequences. Large changes in other members of the microbiota varied greatly from individual to individual, whether or not diarrhea occurred. Nonetheless the variation within an individual was small compared to variation between individuals. Ciprofloxacin treatment reorganized microbiota populations; however, the original structure was largely restored at one and three month follow-up visits.

CONCLUSION: Symptomatic ETEC infections, but not asymptomatic infections, were associated with high fecal concentrations of E. coli. Both infection and ciprofloxacin treatment caused variable changes in other bacteria that generally reverted to baseline levels after three months.}, } @article {pmid27271534, year = {2016}, author = {Thies, S and Rausch, SC and Kovacic, F and Schmidt-Thaler, A and Wilhelm, S and Rosenau, F and Daniel, R and Streit, W and Pietruszka, J and Jaeger, KE}, title = {Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {27035}, pmid = {27271534}, issn = {2045-2322}, mesh = {Abattoirs ; Amino Acid Sequence ; Anti-Bacterial Agents/biosynthesis/chemistry/pharmacology ; Bacterial Proteins/genetics ; *Biofilms ; Biosynthetic Pathways ; *Environmental Microbiology ; Escherichia coli/genetics ; Flavobacterium/genetics ; Genes, Bacterial ; Metagenome ; Microbial Consortia/*genetics ; Microbial Sensitivity Tests ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA ; Surface-Active Agents/*chemistry/metabolism/pharmacology ; }, abstract = {DNA derived from environmental samples is a rich source of novel bioactive molecules. The choice of the habitat to be sampled predefines the properties of the biomolecules to be discovered due to the physiological adaptation of the microbial community to the prevailing environmental conditions. We have constructed a metagenomic library in Escherichia coli DH10b with environmental DNA (eDNA) isolated from the microbial community of a slaughterhouse drain biofilm consisting mainly of species from the family Flavobacteriaceae. By functional screening of this library we have identified several lipases, proteases and two clones (SA343 and SA354) with biosurfactant and hemolytic activities. Sequence analysis of the respective eDNA fragments and subsequent structure homology modelling identified genes encoding putative N-acyl amino acid synthases with a unique two-domain organisation. The produced biosurfactants were identified by NMR spectroscopy as N-acyltyrosines with N-myristoyltyrosine as the predominant species. Critical micelle concentration and reduction of surface tension were similar to those of chemically synthesised N-myristoyltyrosine. Furthermore, we showed that the newly isolated N-acyltyrosines exhibit antibiotic activity against various bacteria. This is the first report describing the successful application of functional high-throughput screening assays for the identification of biosurfactant producing clones within a metagenomic library.}, } @article {pmid27269884, year = {2016}, author = {Romano-Bertrand, S and Bourdier, A and Aujoulat, F and Michon, AL and Masnou, A and Parer, S and Marchandin, H and Jumas-Bilak, E}, title = {Skin microbiota is the main reservoir of Roseomonas mucosa, an emerging opportunistic pathogen so far assumed to be environmental.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {22}, number = {8}, pages = {737.e1-7}, doi = {10.1016/j.cmi.2016.05.024}, pmid = {27269884}, issn = {1469-0691}, mesh = {Anti-Bacterial Agents/pharmacology ; Cross Infection/microbiology ; Drug Resistance, Bacterial ; Environmental Microbiology ; Genome, Bacterial ; Gram-Negative Bacterial Infections/*microbiology ; Humans ; Metagenome ; Metagenomics/methods ; *Methylobacteriaceae/classification/drug effects/genetics ; Microbial Sensitivity Tests ; *Microbiota ; Opportunistic Infections/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Skin/*microbiology ; }, abstract = {Roseomonas spp. are increasingly involved in human infectious diseases. The environmental source for infection is generally admitted in published cases owing to the origin of most Roseomonas species and to their affiliation to the family Acetobacteraceae in Rhodospirillales, which mainly groups environmental bacteria. For a better delineation of Roseomonas habitat and infectious reservoir, we related phenotype, phylotype (16S rRNA gene), genomotype (pulsed-field gel electrophoresis) and origin of 33 strains isolated from humans, hospital environment and natural environment. Genetic and metagenomic databases were also surveyed. The population structure of the genus showed clades associated with humans, whereas others grouped environmental strains only. Roseomonas mucosa is the main human-associated species and the study supported the idea that opportunistic infections due to this species are related to the patient skin microbiota rather than to the environment. In contrast, some strains belonging to other species isolated from patients with cystic fibrosis were related to environmental clades, suggesting an exogenous source for patient colonization. Accurate knowledge about the reservoirs of opportunistic pathogens that have long been considered of environmental origin is still needed and would be helpful to improve infection control and epidemiological survey of emerging human pathogens.}, } @article {pmid27268458, year = {2016}, author = {Chi, L and Bian, X and Gao, B and Ru, H and Tu, P and Lu, K}, title = {Sex-Specific Effects of Arsenic Exposure on the Trajectory and Function of the Gut Microbiome.}, journal = {Chemical research in toxicology}, volume = {29}, number = {6}, pages = {949-951}, pmid = {27268458}, issn = {1520-5010}, support = {R01 ES024950/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Arsenic/*toxicity ; Environmental Exposure ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Gastrointestinal Tract/*drug effects/*microbiology ; Male ; Mice ; RNA, Ribosomal, 16S/genetics ; *Sex Characteristics ; Sex Factors ; }, abstract = {The gut microbiome is deeply involved in numerous aspects of human health; however, it can be readily perturbed by environmental toxicants, such as arsenic. Meanwhile, the interaction among host, gut microbiome, and xenobiotics is a very complex dynamic process. Previously, we have demonstrated that gut microbiome phenotypes driven by host genetics and bacterial infection affect the responses to arsenic exposure. The role of host sex in shaping the gut microbiome raises the question whether sex plays a role in exposure-induced microbiome responses. To examine this, we used 16S rRNA sequencing and metagenomics sequencing to analyze the changes of the gut microbiome and its associated functional metagenome in both female and male C57/BL6 mice. Our results clearly demonstrated that arsenic exposure perturbed the trajectory and function of the gut microbiome in a sex-specific manner.}, } @article {pmid27264318, year = {2016}, author = {Eronen-Rasimus, E and Piiparinen, J and Karkman, A and Lyra, C and Gerland, S and Kaartokallio, H}, title = {Bacterial communities in Arctic first-year drift ice during the winter/spring transition.}, journal = {Environmental microbiology reports}, volume = {8}, number = {4}, pages = {527-535}, doi = {10.1111/1758-2229.12428}, pmid = {27264318}, issn = {1758-2229}, mesh = {Arctic Regions ; Bacteria/*classification/*genetics ; *Biota ; *Environmental Microbiology ; *Ice ; Metagenomics ; Seasons ; }, abstract = {Horizontal and vertical variability of first-year drift-ice bacterial communities was investigated along a North-South transect in the Fram Strait during the winter/spring transition. Two different developmental stages were captured along the transect based on the prevailing environmental conditions and the differences in bacterial community composition. The differences in the bacterial communities were likely driven by the changes in sea-ice algal biomass (2.6-5.6 fold differences in chl-a concentrations). Copiotrophic genera common in late spring/summer sea ice, such as Polaribacter, Octadecabacter and Glaciecola, dominated the bacterial communities, supporting the conclusion that the increase in the sea-ice algal biomass was possibly reflected in the sea-ice bacterial communities. Of the dominating bacterial genera, Polaribacter seemed to benefit the most from the increase in algal biomass, since they covered approximately 39% of the total community at the southernmost stations with higher (>6 μg l(-1)) chl-a concentrations and only 9% at the northernmost station with lower chl-a concentrations (<6 μg l(-1)). The sea-ice bacterial communities also varied between the ice horizons at all three stations and thus we recommend that for future studies multiple ice horizons be sampled to cover the variability in sea-ice bacterial communities in spring.}, } @article {pmid27262209, year = {2018}, author = {Tsai, CY and Tang, CY and Tan, TS and Chen, KH and Liao, KH and Liou, ML}, title = {Subgingival microbiota in individuals with severe chronic periodontitis.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {51}, number = {2}, pages = {226-234}, doi = {10.1016/j.jmii.2016.04.007}, pmid = {27262209}, issn = {1995-9133}, mesh = {Bacteria/*classification/genetics/*isolation & purification ; Base Sequence ; Biodiversity ; Chronic Periodontitis/*microbiology ; Gingiva/*microbiology ; Humans ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Taiwan ; }, abstract = {BACKGROUND/PURPOSE: Subgingival microorganisms are potentially associated with periodontal diseases. However, the correlation between the variance in the periodontal microbiome and the prevalence and severity of periodontitis remains unclear. The aim of this study was to determine the subgingival microbiota in Taiwanese individuals with severe chronic periodontitis (SP).

METHODS: The composition of the subgingival microbiota in healthy and diseased individuals was compared using a 16S rRNA metagenomic approach and quantitative polymerase chain reaction (qPCR). A total of 20 samples, including 10 from healthy individuals and 10 from SP patients, were analyzed.

RESULTS: We found high microbial diversity, with an average of 774 classified phylotypes per sample and a total of six bacterial phyla across all samples. Cluster analysis by principal component analysis and heat map showed that the bacterial communities were different in the two groups. Streptococcus dominated across all the healthy samples, whereas Prevotella, Porphyromonas, and Treponema were highly abundant across all diseased samples. At least 13 bacterial genera were conserved among all the samples. Only eight genera, including Lautropia, Parvimonas, Actinomyces, Capnocytophaga, Paludibacter, Streptococcus, Haemophilus, and Corynebacterium, were significantly enriched in the healthy group, and six genera, including Porphyromonas, Treponema, Tannerella, Aggregatibacter, Peptostreptococcus, and Filifactor, were significantly enriched in the diseased group. Furthermore, a trend of abundance of bacteria at the species level measured by qPCR in all samples was consistent with the 16S rRNA metagenomics results.

CONCLUSION: This study is the first in Taiwan to provide a picture of the microbiome in SP via 16S rRNA metagenomics.}, } @article {pmid27259541, year = {2016}, author = {Ulyantsev, VI and Kazakov, SV and Dubinkina, VB and Tyakht, AV and Alexeev, DG}, title = {MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data.}, journal = {Bioinformatics (Oxford, England)}, volume = {32}, number = {18}, pages = {2760-2767}, doi = {10.1093/bioinformatics/btw312}, pmid = {27259541}, issn = {1367-4811}, mesh = {*Algorithms ; Computational Biology/methods ; Databases, Genetic ; Metagenome ; *Metagenomics ; Microbiota ; }, abstract = {MOTIVATION: High-throughput metagenomic sequencing has revolutionized our view on the structure and metabolic potential of microbial communities. However, analysis of metagenomic composition is often complicated by the high complexity of the community and the lack of related reference genomic sequences. As a start point for comparative metagenomic analysis, the researchers require efficient means for assessing pairwise similarity of the metagenomes (beta-diversity). A number of approaches were used to address this task, however, most of them have inherent disadvantages that limit their scope of applicability. For instance, the reference-based methods poorly perform on metagenomes from previously unstudied niches, while composition-based methods appear to be too abstract for straightforward interpretation and do not allow to identify the differentially abundant features.

RESULTS: We developed MetaFast, an approach that allows to represent a shotgun metagenome from an arbitrary environment as a modified de Bruijn graph consisting of simplified components. For multiple metagenomes, the resulting representation is used to obtain a pairwise similarity matrix. The dimensional structure of the metagenomic components preserved in our algorithm reflects the inherent subspecies-level diversity of microbiota. The method is computationally efficient and especially promising for an analysis of metagenomes from novel environmental niches.

Source code and binaries are freely available for download at https://github.com/ctlab/metafast The code is written in Java and is platform independent (tested on Linux and Windows x86_64).

CONTACT: ulyantsev@rain.ifmo.ru

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid27256312, year = {2017}, author = {Lu, YY and Chen, T and Fuhrman, JA and Sun, F}, title = {COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {6}, pages = {791-798}, doi = {10.1093/bioinformatics/btw290}, pmid = {27256312}, issn = {1367-4811}, mesh = {Algorithms ; Bacteria/genetics ; Cluster Analysis ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {MOTIVATION: The advent of next-generation sequencing technologies enables researchers to sequence complex microbial communities directly from the environment. Because assembly typically produces only genome fragments, also known as contigs, instead of an entire genome, it is crucial to group them into operational taxonomic units (OTUs) for further taxonomic profiling and down-streaming functional analysis. OTU clustering is also referred to as binning. We present COCACOLA, a general framework automatically bin contigs into OTUs based on sequence composition and coverage across multiple samples.

RESULTS: The effectiveness of COCACOLA is demonstrated in both simulated and real datasets in comparison with state-of-art binning approaches such as CONCOCT, GroopM, MaxBin and MetaBAT. The superior performance of COCACOLA relies on two aspects. One is using L 1 distance instead of Euclidean distance for better taxonomic identification during initialization. More importantly, COCACOLA takes advantage of both hard clustering and soft clustering by sparsity regularization. In addition, the COCACOLA framework seamlessly embraces customized knowledge to facilitate binning accuracy. In our study, we have investigated two types of additional knowledge, the co-alignment to reference genomes and linkage of contigs provided by paired-end reads, as well as the ensemble of both. We find that both co-alignment and linkage information further improve binning in the majority of cases. COCACOLA is scalable and faster than CONCOCT, GroopM, MaxBin and MetaBAT.

The software is available at https://github.com/younglululu/COCACOLA .

CONTACT: fsun@usc.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid27256005, year = {2016}, author = {Marziah, Z and Mahdzir, A and Musa, MN and Jaafar, AB and Azhim, A and Hara, H}, title = {Abundance of sulfur-degrading bacteria in a benthic bacterial community of shallow sea sediment in the off-Terengganu coast of the South China Sea.}, journal = {MicrobiologyOpen}, volume = {5}, number = {6}, pages = {967-978}, pmid = {27256005}, issn = {2045-8827}, mesh = {Base Sequence ; China ; DNA, Bacterial/genetics ; Epsilonproteobacteria/classification/genetics/*isolation & purification/*metabolism ; Geologic Sediments/*microbiology ; Hydrothermal Vents/microbiology ; *Petroleum Pollution ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sulfur/*metabolism ; Water Microbiology ; Water Pollutants, Chemical/metabolism ; }, abstract = {This study for the first time provides insight into the bacterial community in the benthic region of the Off-Terengganu Coastline, which is considered to be anthropogenically polluted due to heavy fishing vessel commotion. Subsurface bacteria were randomly collected from two locations at different depths and were examined using the 16S rDNA V3-V4 marker gene on the Illumina[™] Miseq platform. In addition, the physiochemical parameters of the sediment were also measured. Surprisingly, the results show a high diversity of sulfur-oxidizing bacteria in the surveyed area, where Sulfurovum sp. was identified to predominate the overall bacterial community. The physiochemical parameters reveal insufficient evidence of hydrothermal vents in the surveyed area. However, there are traces of hydrocarbon pollutants such as gasoline, diesel, and mineral oil in this area. It is assumed that sediment accumulation in the lee of breakwater plays an important role in trapping the runoff from the nearby harbor, which includes oil spills. Based on the common knowledge, Sulvurofum sp. is a native bacterium that exists in deep hydrothermal vents and volcanic territories. Although the reason for the abundance of Sulfurovum sp. in the surveyed area is still unclear, there is a possibility that metabolic adaptation plays an important role in regulating hydrocarbon pollutants for survival. The work presented in this paper therefore has profound implications for future studies on Sulfurovum sp. versatility. However, future research is needed to strengthen the findings of this study and to provide a better evidence regarding the metabolic response of this bacterium toward hydrocarbon pollutants.}, } @article {pmid27255738, year = {2016}, author = {Tsilimigras, MC and Fodor, AA}, title = {Compositional data analysis of the microbiome: fundamentals, tools, and challenges.}, journal = {Annals of epidemiology}, volume = {26}, number = {5}, pages = {330-335}, doi = {10.1016/j.annepidem.2016.03.002}, pmid = {27255738}, issn = {1873-2585}, mesh = {High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; *Models, Statistical ; Needs Assessment ; RNA, Ribosomal, 16S/*genetics ; Selection Bias ; }, abstract = {PURPOSE: Human microbiome studies are within the realm of compositional data with the absolute abundances of microbes not recoverable from sequence data alone. In compositional data analysis, each sample consists of proportions of various organisms with a sum constrained to a constant. This simple feature can lead traditional statistical treatments when naively applied to produce errant results and spurious correlations.

METHODS: We review the origins of compositionality in microbiome data, the theory and usage of compositional data analysis in this setting and some recent attempts at solutions to these problems.

RESULTS: Microbiome sequence data sets are typically high dimensional, with the number of taxa much greater than the number of samples, and sparse as most taxa are only observed in a small number of samples. These features of microbiome sequence data interact with compositionality to produce additional challenges in analysis.

CONCLUSIONS: Despite sophisticated approaches to statistical transformation, the analysis of compositional data may remain a partially intractable problem, limiting inference. We suggest that current research needs include better generation of simulated data and further study of how the severity of compositional effects changes when sampling microbial communities of widely differing diversity.}, } @article {pmid27255518, year = {2016}, author = {Yang, H and Huang, X and Fang, S and Xin, W and Huang, L and Chen, C}, title = {Uncovering the composition of microbial community structure and metagenomics among three gut locations in pigs with distinct fatness.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {27427}, pmid = {27255518}, issn = {2045-2322}, mesh = {Animals ; Bacteria/*genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Male ; Metagenomics/methods ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Swine ; }, abstract = {Uncovering the phylogenetic composition of microbial community and the potential functional capacity of microbiome in different gut locations is of great importance to pig production. Here we performed a comparative analysis of gut microbiota and metagenomics among jejunum, ileum and cecum in pigs with distinct fatness. 16S rRNA gene sequencing revealed dramatic differences of microbial composition, diversity and species abundance between small intestine and cecum. Clostridium and SMB53 were enriched in the small intestine, while Prevotella, Treponema, Ruminococcus and Faecalibacterium showed a higher abundance in the cecum. Functional capacity analysis of gut microbiome revealed that the microbiome of small intestine plays important roles in the metabolism of small molecule nutrients, while the microbiome of cecum has the stronger ability to degrade xylan, pectin and cellulose. We identified tens of fatness associated-bacterial species including Escherichia spp. that showed a notable increase of relative abundance in all three gut locations of high fatness pigs. We further suggested that the potential pathogens, inflammation process, and microbial metabolism and nutrient sensing are involved in the high fatness of pigs. These results improve our knowledge about microbiota compositions in different gut locations, and give an insight into the effect of gut microbiota on porcine fatness.}, } @article {pmid27250856, year = {2016}, author = {Mofiz, E and Holt, DC and Seemann, T and Currie, BJ and Fischer, K and Papenfuss, AT}, title = {Genomic resources and draft assemblies of the human and porcine varieties of scabies mites, Sarcoptes scabiei var. hominis and var. suis.}, journal = {GigaScience}, volume = {5}, number = {1}, pages = {23}, pmid = {27250856}, issn = {2047-217X}, mesh = {Animals ; Australia ; Genome ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/methods ; Microbiota ; Sarcoptes scabiei/*classification/genetics ; Scabies/*veterinary ; Sequence Analysis, DNA/*methods ; Swine/microbiology/parasitology ; Swine Diseases/parasitology ; }, abstract = {BACKGROUND: The scabies mite, Sarcoptes scabiei, is a parasitic arachnid and cause of the infectious skin disease scabies in humans and mange in other animal species. Scabies infections are a major health problem, particularly in remote Indigenous communities in Australia, where secondary group A streptococcal and Staphylococcus aureus infections of scabies sores are thought to drive the high rate of rheumatic heart disease and chronic kidney disease.

RESULTS: We sequenced the genome of two samples of Sarcoptes scabiei var. hominis obtained from unrelated patients with crusted scabies located in different parts of northern Australia using the Illumina HiSeq. We also sequenced samples of Sarcoptes scabiei var. suis from a pig model. Because of the small size of the scabies mite, these data are derived from pools of thousands of mites and are metagenomic, including host and microbiome DNA. We performed cleaning and de novo assembly and present Sarcoptes scabiei var. hominis and var. suis draft reference genomes. We have constructed a preliminary annotation of this reference comprising 13,226 putative coding sequences based on sequence similarity to known proteins.

CONCLUSIONS: We have developed extensive genomic resources for the scabies mite, including reference genomes and a preliminary annotation.}, } @article {pmid27250499, year = {2016}, author = {Sanders, ME}, title = {Probiotics and microbiota composition.}, journal = {BMC medicine}, volume = {14}, number = {1}, pages = {82}, pmid = {27250499}, issn = {1741-7015}, mesh = {Feces/*microbiology ; Gastrointestinal Microbiome/*drug effects ; Homeostasis/drug effects ; Humans ; Microbiota/*drug effects ; Probiotics/*chemistry/*pharmacology ; }, abstract = {Accumulated evidence, corroborated by a new systematic review by Kristensen et al. (Genome Med 8:52, 2016), suggests that probiotics do not significantly impact the fecal microbiota composition of healthy subjects. Nevertheless, physiological benefits have been associated with probiotic consumption by healthy people. Some studies have suggested that probiotics may impact the function of colonizing microbes, although this needs to be further studied. An alternative hypothesis is that probiotics may promote homeostasis of the gut microbiota, rather than change its composition. This hypothesis warrants investigation as a possible mechanism for how probiotics may benefit healthy people.Please see related article: http://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0300-5 .}, } @article {pmid27243603, year = {2016}, author = {Treu, L and Kougias, PG and Campanaro, S and Bassani, I and Angelidaki, I}, title = {Deeper insight into the structure of the anaerobic digestion microbial community; the biogas microbiome database is expanded with 157 new genomes.}, journal = {Bioresource technology}, volume = {216}, number = {}, pages = {260-266}, doi = {10.1016/j.biortech.2016.05.081}, pmid = {27243603}, issn = {1873-2976}, mesh = {*Biofuels ; *Databases, Factual ; Metagenome ; Metagenomics/methods ; *Microbial Consortia ; *Microbiota/genetics ; Phylogeny ; }, abstract = {This research aimed to better characterize the biogas microbiome by means of high throughput metagenomic sequencing and to elucidate the core microbial consortium existing in biogas reactors independently from the operational conditions. Assembly of shotgun reads followed by an established binning strategy resulted in the highest, up to now, extraction of microbial genomes involved in biogas producing systems. From the 236 extracted genome bins, it was remarkably found that the vast majority of them could only be characterized at high taxonomic levels. This result confirms that the biogas microbiome is comprised by a consortium of unknown species. A comparative analysis between the genome bins of the current study and those extracted from a previous metagenomic assembly demonstrated a similar phylogenetic distribution of the main taxa. Finally, this analysis led to the identification of a subset of common microbes that could be considered as the core essential group in biogas production.}, } @article {pmid27243236, year = {2016}, author = {Lv, LX and Fang, DQ and Shi, D and Chen, DY and Yan, R and Zhu, YX and Chen, YF and Shao, L and Guo, FF and Wu, WR and Li, A and Shi, HY and Jiang, XW and Jiang, HY and Xiao, YH and Zheng, SS and Li, LJ}, title = {Alterations and correlations of the gut microbiome, metabolism and immunity in patients with primary biliary cirrhosis.}, journal = {Environmental microbiology}, volume = {18}, number = {7}, pages = {2272-2286}, doi = {10.1111/1462-2920.13401}, pmid = {27243236}, issn = {1462-2920}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/immunology/metabolism/*microbiology ; Humans ; Liver Cirrhosis, Biliary/*immunology/metabolism/microbiology ; Male ; Metagenomics ; Middle Aged ; }, abstract = {We selected 42 early-stage primary biliary cirrhosis (PBC) patients and 30 healthy controls (HC). Metagenomic sequencing of the 16S rRNA gene was used to characterize the fecal microbiome. UPLC-MS/MS assaying of small molecules was used to characterize the metabolomes of the serum, urine and feces. Liquid chip assaying of serum cytokines was used to characterize the immune profiles. The gut of PBC patients were depleted of some potentially beneficial bacteria, such as Acidobacteria, Lachnobacterium sp., Bacteroides eggerthii and Ruminococcus bromii, but were enriched in some bacterial taxa containing opportunistic pathogens, such as γ-Proteobacteria, Enterobacteriaceae, Neisseriaceae, Spirochaetaceae, Veillonella, Streptococcus, Klebsiella, Actinobacillus pleuropneumoniae, Anaeroglobus geminatus, Enterobacter asburiae, Haemophilus parainfluenzae, Megasphaera micronuciformis and Paraprevotella clara. Several altered gut bacterial taxa exhibited potential interactions with PBC through their associations with altered metabolism, immunity and liver function indicators, such as those of Klebsiella with IL-2A and Neisseriaceae with urinary indoleacrylate. Many gut bacteria, such as some members of Bacteroides, were altered in their associations with the immunity and metabolism of PBC patients, although their relative abundances were unchanged. Consequently, the gut microbiome is altered and may be critical for the onset or development of PBC by interacting with metabolism and immunity.}, } @article {pmid27242374, year = {2016}, author = {Kohl, KD and Connelly, JW and Dearing, MD and Forbey, JS}, title = {Microbial detoxification in the gut of a specialist avian herbivore, the Greater Sage-Grouse.}, journal = {FEMS microbiology letters}, volume = {363}, number = {14}, pages = {}, doi = {10.1093/femsle/fnw144}, pmid = {27242374}, issn = {1574-6968}, mesh = {Animals ; Female ; Galliformes/*physiology ; *Gastrointestinal Microbiome ; *Herbivory ; *Inactivation, Metabolic ; Male ; Metabolic Networks and Pathways ; Metagenome ; Metagenomics/methods ; Phenols/metabolism ; }, abstract = {One function of the gut microbiota gaining recent attention, especially in herbivorous mammals and insects, is the metabolism of plant secondary metabolites (PSMs). We investigated whether this function exists within the gut communities of a specialist avian herbivore. We sequenced the cecal metagenome of the Greater Sage-Grouse (Centrocercus urophasianus), which specializes on chemically defended sagebrush (Artemisia spp.). We predicted that the cecal metagenome of the sage-grouse would be enriched in genes associated with the metabolism of PSMs when compared to the metagenome of the domestic chicken. We found that representation of microbial genes associated with 'xenobiotic degradation and metabolism' was 3-fold higher in the sage-grouse cecal metagenomes when compared to that of the domestic chicken. Further, we identified a complete metabolic pathway for the degradation of phenol to pyruvate, which was not detected in the metagenomes of the domestic chicken, bovine rumen or 14 species of mammalian herbivores. Evidence of monoterpene degradation (a major class of PSMs in sagebrush) was less definitive, although we did detect genes for several enzymes associated with this process. Overall, our results suggest that the gut microbiota of specialist avian herbivores plays a similar role to the microbiota of mammalian and insect herbivores in degrading PSMs.}, } @article {pmid27241862, year = {2016}, author = {Hong, X and Chen, J and Liu, L and Wu, H and Tan, H and Xie, G and Xu, Q and Zou, H and Yu, W and Wang, L and Qin, N}, title = {Metagenomic sequencing reveals the relationship between microbiota composition and quality of Chinese Rice Wine.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {26621}, pmid = {27241862}, issn = {2045-2322}, support = {27306C2006/ES/NIEHS NIH HHS/United States ; }, mesh = {*Food Microbiology ; Lactobacillus/*genetics ; *Metagenome ; Microbiota/*genetics ; *Sequence Analysis, DNA ; Wine/*microbiology ; }, abstract = {Chinese Rice Wine (CRW) is a common alcoholic beverage in China. To investigate the influence of microbial composition on the quality of CRW, high throughput sequencing was performed for 110 wine samples on bacterial 16S rRNA gene and fungal Internal Transcribed Spacer II (ITS2). Bioinformatic analyses demonstrated that the quality of yeast starter and final wine correlated with microbial taxonomic composition, which was exemplified by our finding that wine spoilage resulted from a high proportion of genus Lactobacillus. Subsequently, based on Lactobacillus abundance of an early stage, a model was constructed to predict final wine quality. In addition, three batches of 20 representative wine samples selected from a pool of 110 samples were further analyzed in metagenomics. The results revealed that wine spoilage was due to rapid growth of Lactobacillus brevis at the early stage of fermentation. Gene functional analysis indicated the importance of some pathways such as synthesis of biotin, malolactic fermentation and production of short-chain fatty acid. These results led to a conclusion that metabolisms of microbes influence the wine quality. Thus, nurturing of beneficial microbes and inhibition of undesired ones are both important for the mechanized brewery.}, } @article {pmid27241188, year = {2016}, author = {Wang, ZM and Lu, ZM and Shi, JS and Xu, ZH}, title = {Exploring flavour-producing core microbiota in multispecies solid-state fermentation of traditional Chinese vinegar.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {26818}, pmid = {27241188}, issn = {2045-2322}, support = {R01 AA021301/AA/NIAAA NIH HHS/United States ; }, mesh = {Acetic Acid/*chemistry ; Acetobacter/genetics/metabolism ; Aspergillus/genetics/metabolism ; Bacillus/genetics/metabolism ; *Fermentation ; *Food Microbiology ; Gluconacetobacter/genetics/metabolism ; Lactobacillus/genetics/metabolism ; Lactococcus/genetics/metabolism ; Metagenomics ; *Microbiota/genetics ; Staphylococcus/genetics/metabolism ; }, abstract = {Multispecies solid-state fermentation (MSSF), a natural fermentation process driven by reproducible microbiota, is an important technique to produce traditional fermented foods. Flavours, skeleton of fermented foods, was mostly produced by microbiota in food ecosystem. However, the association between microbiota and flavours and flavour-producing core microbiota are still poorly understood. Here, acetic acid fermentation (AAF) of Zhenjiang aromatic vinegar was taken as a typical case of MSSF. The structural and functional dynamics of microbiota during AAF process was determined by metagenomics and favour analyses. The dominant bacteria and fungi were identified as Acetobacter, Lactobacillus, Aspergillus, and Alternaria, respectively. Total 88 flavours including 2 sugars, 9 organic acids, 18 amino acids, and 59 volatile flavours were detected during AAF process. O2PLS-based correlation analysis between microbiota succession and flavours dynamics showed bacteria made more contribution to flavour formation than fungi. Seven genera including Acetobacter, Lactobacillus, Enhydrobacter, Lactococcus, Gluconacetobacer, Bacillus and Staphylococcus were determined as functional core microbiota for production of flavours in Zhenjiang aromatic vinegar, based on their dominance and functionality in microbial community. This study provides a perspective for bridging the gap between the phenotype and genotype of ecological system, and advances our understanding of MSSF mechanisms in Zhenjiang aromatic vinegar.}, } @article {pmid27238636, year = {2016}, author = {Louvel, G and Der Sarkissian, C and Hanghøj, K and Orlando, L}, title = {metaBIT, an integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data.}, journal = {Molecular ecology resources}, volume = {16}, number = {6}, pages = {1415-1427}, doi = {10.1111/1755-0998.12546}, pmid = {27238636}, issn = {1755-0998}, mesh = {Automation ; Computational Biology/*methods ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; *Microbiota ; Sequence Analysis, DNA/*methods ; }, abstract = {Micro-organisms account for most of the Earth's biodiversity and yet remain largely unknown. The complexity and diversity of microbial communities present in clinical and environmental samples can now be robustly investigated in record times and prices thanks to recent advances in high-throughput DNA sequencing (HTS). Here, we develop metaBIT, an open-source computational pipeline automatizing routine microbial profiling of shotgun HTS data. Customizable by the user at different stringency levels, it performs robust taxonomy-based assignment and relative abundance calculation of microbial taxa, as well as cross-sample statistical analyses of microbial diversity distributions. We demonstrate the versatility of metaBIT within a range of published HTS data sets sampled from the environment (soil and seawater) and the human body (skin and gut), but also from archaeological specimens. We present the diversity of outputs provided by the pipeline for the visualization of microbial profiles (barplots, heatmaps) and for their characterization and comparison (diversity indices, hierarchical clustering and principal coordinates analyses). We show that metaBIT allows an automatic, fast and user-friendly profiling of the microbial DNA present in HTS shotgun data sets. The applications of metaBIT are vast, from monitoring of laboratory errors and contaminations, to the reconstruction of past and present microbiota, and the detection of candidate species, including pathogens.}, } @article {pmid27237775, year = {2016}, author = {Thoendel, M and Jeraldo, PR and Greenwood-Quaintance, KE and Yao, JZ and Chia, N and Hanssen, AD and Abdel, MP and Patel, R}, title = {Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing.}, journal = {Journal of microbiological methods}, volume = {127}, number = {}, pages = {141-145}, pmid = {27237775}, issn = {1872-8359}, support = {R01 AI091594/AI/NIAID NIH HHS/United States ; R01 AR056647/AR/NIAMS NIH HHS/United States ; R01 CA179243/CA/NCI NIH HHS/United States ; }, mesh = {DNA, Bacterial/genetics/*isolation & purification ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; Indicators and Reagents ; *Metagenome ; Metagenomics/methods ; Microbiota ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/*genetics ; }, abstract = {Metagenomic whole genome sequencing for detection of pathogens in clinical samples is an exciting new area for discovery and clinical testing. A major barrier to this approach is the overwhelming ratio of human to pathogen DNA in samples with low pathogen abundance, which is typical of most clinical specimens. Microbial DNA enrichment methods offer the potential to relieve this limitation by improving this ratio. Two commercially available enrichment kits, the NEBNext Microbiome DNA Enrichment Kit and the Molzym MolYsis Basic kit, were tested for their ability to enrich for microbial DNA from resected arthroplasty component sonicate fluids from prosthetic joint infections or uninfected sonicate fluids spiked with Staphylococcus aureus. Using spiked uninfected sonicate fluid there was a 6-fold enrichment of bacterial DNA with the NEBNext kit and 76-fold enrichment with the MolYsis kit. Metagenomic whole genome sequencing of sonicate fluid revealed 13- to 85-fold enrichment of bacterial DNA using the NEBNext enrichment kit. The MolYsis approach achieved 481- to 9580-fold enrichment, resulting in 7 to 59% of sequencing reads being from the pathogens known to be present in the samples. These results demonstrate the usefulness of these tools when testing clinical samples with low microbial burden using next generation sequencing.}, } @article {pmid27236827, year = {2016}, author = {Ehrlich, SD}, title = {The human gut microbiome impacts health and disease.}, journal = {Comptes rendus biologies}, volume = {339}, number = {7-8}, pages = {319-323}, doi = {10.1016/j.crvi.2016.04.008}, pmid = {27236827}, issn = {1768-3238}, mesh = {Animals ; Chronic Disease/prevention & control ; DNA/chemistry/genetics ; Dysbiosis/prevention & control ; Gastrointestinal Microbiome/*physiology ; Humans ; Metagenome ; Metagenomics ; Microbiota/genetics/*physiology ; }, abstract = {The human gut microbiome can now be characterized in unprecedented detail by an approach based on high-throughput sequencing of total stool DNA, that we name quantitative metagenomics. Central to the approach is a catalog that lists all the genes of intestinal microbes that are known - 9.9 millions, identified by the analysis of 1267 stool samples. Beyond the gene list, genetic units that carry them begun to be known; many of these correspond to bacterial species that were never isolated and cultured yet. Quantitative metagenomics allows developing powerful algorithms to diagnose a disease, monitor patients and identify individuals at risk to progress towards a disease. This lays ground for developing new approaches to better restore and even preserve the health by modulation of the altered microbiome, which contributes to promote or aggravate a disease.}, } @article {pmid27236321, year = {2016}, author = {Kijpornyongpan, T and Catherine Aime, M}, title = {Rare or rarely detected? Ceraceosorus guamensis sp. nov.: a second described species of Ceraceosorales and the potential for underdetection of rare lineages with common sampling techniques.}, journal = {Antonie van Leeuwenhoek}, volume = {109}, number = {8}, pages = {1127-1139}, doi = {10.1007/s10482-016-0715-4}, pmid = {27236321}, issn = {1572-9699}, mesh = {Basidiomycota/*classification/cytology/genetics/*isolation & purification ; Biodiversity ; Guam ; Hyphae ; Mycological Typing Techniques ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Spores, Fungal/growth & development ; }, abstract = {Ceraceosorales is a monotypic order in Ustilaginomycotina. Its namesake, Ceraceosorus bombacis, was described as a phytopathogen of Bombax ceiba in India. In this study, we describe Ceraceosorus guamensis sp. nov., collected on the South Pacific island of Guam, which appears to represent the second isolation of any member of this order in over 40 years. Ceraceosorus species are monokaryotic and filamentous in culture, producing conidia on potato dextrose agar. However, both species behave yeast-like when cultured on corn meal agar. The internal transcribed spacer (ITS) region (spanning the ITS1-5.8S-ITS2) in both species of Ceraceosorus is highly heterogeneous containing multiple disparate copies that can vary intragenomically by up to 3.5 %. Moreover, this region could not be amplified using the fungal ITS primers most frequently used for culture-independent methods of assessing fungal biodiversity. This fact, combined with the extremely slow growth rates on commonly employed media, may indicate that members of this lineage are potentially underdetected by current sampling methods.}, } @article {pmid27231242, year = {2016}, author = {Zhang, L and Mu, C and He, X and Su, Y and Mao, S and Zhang, J and Smidt, H and Zhu, W}, title = {Effects of dietary fibre source on microbiota composition in the large intestine of suckling piglets.}, journal = {FEMS microbiology letters}, volume = {363}, number = {14}, pages = {}, doi = {10.1093/femsle/fnw138}, pmid = {27231242}, issn = {1574-6968}, mesh = {Animal Feed ; Animals ; Animals, Newborn ; Biodiversity ; Cluster Analysis ; *Dietary Fiber ; *Gastrointestinal Microbiome ; Intestine, Large/*microbiology ; Metagenome ; Metagenomics/methods ; Swine ; }, abstract = {This study aimed to investigate the effects of dietary fibre sources on the gut microbiota in suckling piglets, and to test the hypothesis that a moderate increase of dietary fibre may affect the gut microbiota during the suckling period. Suckling piglets were fed different fibre-containing diets or a control diet from postnatal day 7 to 22. Digesta samples from cecum, proximal colon and distal colon were used for Pig Intestinal Tract Chip analysis. The data showed that the effects of fibre-containing diet on the gut microbiota differed in the fibre source and gut location. The alfalfa diet increased Clostridium cluster XIVb and Sporobacter termitidis in the cecum compared to the pure cellulose diet. Compared to the control diet, the alfalfa diet also increased Coprococcus eutactus in the distal colon, while the pure cellulose diet decreased Eubacterium pyruvativorans in the cecum. The pure cellulose diet increased Prevotella ruminicola compared to the wheat bran diet. Interestingly, the alfalfa group had the lowest abundance of the potential pathogen Streptococcus suis in the cecum and distal colon. These results indicated that a moderate increase in dietary fibres affected the microbial composition in suckling piglets, and that the alfalfa inclusion produced some beneficial effects on the microbial communities.}, } @article {pmid27231050, year = {2016}, author = {Rooks, MG and Garrett, WS}, title = {Gut microbiota, metabolites and host immunity.}, journal = {Nature reviews. Immunology}, volume = {16}, number = {6}, pages = {341-352}, pmid = {27231050}, issn = {1474-1741}, support = {R01 CA154426/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Disease Susceptibility ; Fatty Acids/metabolism ; *Gastrointestinal Microbiome ; Homeostasis ; Host-Pathogen Interactions/immunology ; Humans ; Immune System/cytology/immunology/metabolism ; *Immunity ; Immunomodulation ; Metagenome ; Metagenomics ; Microbiota ; Receptors, Pattern Recognition/metabolism ; Symbiosis/immunology ; }, abstract = {The microbiota - the collection of microorganisms that live within and on all mammals - provides crucial signals for the development and function of the immune system. Increased availability of technologies that profile microbial communities is facilitating the entry of many immunologists into the evolving field of host-microbiota studies. The microbial communities, their metabolites and components are not only necessary for immune homeostasis, they also influence the susceptibility of the host to many immune-mediated diseases and disorders. In this Review, we discuss technological and computational approaches for investigating the microbiome, as well as recent advances in our understanding of host immunity and microbial mutualism with a focus on specific microbial metabolites, bacterial components and the immune system.}, } @article {pmid27230662, year = {2016}, author = {Correa-Fiz, F and Fraile, L and Aragon, V}, title = {Piglet nasal microbiota at weaning may influence the development of Glässer's disease during the rearing period.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {404}, pmid = {27230662}, issn = {1471-2164}, mesh = {Agriculture ; Animals ; Bacteria/classification ; Biodiversity ; Health Status ; *Microbiota ; Nasal Mucosa/*microbiology ; Spain ; Swine ; Swine Diseases/*etiology ; United Kingdom ; *Weaning ; }, abstract = {BACKGROUND: The microbiota, the ensemble of microorganisms on a particular body site, has been extensively studied during the last few years, and demonstrated to influence the development of many diseases. However, these studies focused mainly on the human digestive system, while the populations in the respiratory tract have been poorly assessed, especially in pigs. The nasal mucosa of piglets is colonized by an array of bacteria, many of which are unknown. Among the early colonizers, Haemophilus parasuis also has clinical importance, since it is also the etiological agent of Glässer's disease. This disease produces economical losses in all the countries with pig production, and the factors influencing its development are not totally understood. Hence, the purpose of this work was to characterize the nasal microbiota composition of piglets, and its possible role in Glässer's disease development.

RESULTS: Seven farms from Spain (4 with Glässer's disease and 3 control farms without any respiratory disease) and three farms from UK (all control farms) were studied. Ten piglets from each farm were sampled at 3-4 weeks of age before weaning. The total DNA extracted from nasal swabs was used to amplify the 16S RNA gene for sequencing in Illumina MiSeq. Sequencing data was quality filtered and analyzed using QIIME software. The diversity of the nasal microbiota was low in comparison with other body sites, showing a maximum number of operational taxonomic units (OTUs) per pig of 1,603, clustered in five phyla. Significant differences were found at various taxonomical levels, when the microbiota was compared regarding the farm health status. Healthy status was associated to higher species richness and diversity, and UK farms demonstrated the highest diversity.

CONCLUSIONS: The composition of the nasal microbiota of healthy piglets was uncovered and different phylotypes were shown to be significantly altered in animals depending on the clinical status of the farm of origin. Several OTUs at genus level were identified over-represented in piglets from control farms, indicating their potential as probiotics. Although we provide relevant data, fully metagenomic approaches could give light on the genes and metabolic pathways involved in the roles of the nasal microbiota to prevent respiratory diseases.}, } @article {pmid27226242, year = {2016}, author = {Guo, Y and Li, SH and Kuang, YS and He, JR and Lu, JH and Luo, BJ and Jiang, FJ and Liu, YZ and Papasian, CJ and Xia, HM and Deng, HW and Qiu, X}, title = {Effect of short-term room temperature storage on the microbial community in infant fecal samples.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {26648}, pmid = {27226242}, issn = {2045-2322}, mesh = {Feces/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Male ; Specimen Handling/*methods ; *Temperature ; }, abstract = {Sample storage conditions are important for unbiased analysis of microbial communities in metagenomic studies. Specifically, for infant gut microbiota studies, stool specimens are often exposed to room temperature (RT) conditions prior to analysis. This could lead to variations in structural and quantitative assessment of bacterial communities. To estimate such effects of RT storage, we collected feces from 29 healthy infants (0-3 months) and partitioned each sample into 5 portions to be stored for different lengths of time at RT before freezing at -80 °C. Alpha diversity did not differ between samples with storage time from 0 to 2 hours. The UniFrac distances and microbial composition analysis showed significant differences by testing among individuals, but not by testing between different time points at RT. Changes in the relative abundance of some specific (less common, minor) taxa were still found during storage at room temperature. Our results support previous studies in children and adults, and provided useful information for accurate characterization of infant gut microbiomes. In particular, our study furnished a solid foundation and justification for using fecal samples exposed to RT for less than 2 hours for comparative analyses between various medical conditions.}, } @article {pmid27221669, year = {2016}, author = {Fujinawa, K and Asai, Y and Miyahara, M and Kouzuma, A and Abe, T and Watanabe, K}, title = {Genomic features of uncultured methylotrophs in activated-sludge microbiomes grown under different enrichment procedures.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {26650}, pmid = {27221669}, issn = {2045-2322}, mesh = {Hyphomicrobium/*growth & development ; Methylophilus/*growth & development ; Microbiota/*physiology ; Sewage/*microbiology ; }, abstract = {Methylotrophs are organisms that are able to grow on C1 compounds as carbon and energy sources. They play important roles in the global carbon cycle and contribute largely to industrial wastewater treatment. To identify and characterize methylotrophs that are involved in methanol degradation in wastewater-treatment plants, methanol-fed activated-sludge (MAS) microbiomes were subjected to phylogenetic and metagenomic analyses, and genomic features of dominant methylotrophs in MAS were compared with those preferentially grown in laboratory enrichment cultures (LECs). These analyses consistently indicate that Hyphomicrobium plays important roles in MAS, while Methylophilus occurred predominantly in LECs. Comparative analyses of bin genomes reconstructed for the Hyphomicrobium and Methylophilus methylotrophs suggest that they have different C1-assimilation pathways. In addition, function-module analyses suggest that their cell-surface structures are different. Comparison of the MAS bin genome with genomes of closely related Hyphomicrobium isolates suggests that genes unnecessary in MAS (for instance, genes for anaerobic respiration) have been lost from the genome of the dominant methylotroph. We suggest that genomic features and coded functions in the MAS bin genome provide us with insights into how this methylotroph adapts to activated-sludge ecosystems.}, } @article {pmid27220974, year = {2016}, author = {Pylro, VS and Morais, DK and de Oliveira, FS and Dos Santos, FG and Lemos, LN and Oliveira, G and Roesch, LF}, title = {BMPOS: a Flexible and User-Friendly Tool Sets for Microbiome Studies.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {443-447}, pmid = {27220974}, issn = {1432-184X}, mesh = {Bacteriological Techniques ; Brazil ; Databases, Genetic ; Genetic Markers ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; Sequence Analysis, DNA ; *Software ; }, abstract = {Recent advances in science and technology are leading to a revision and re-orientation of methodologies, addressing old and current issues under a new perspective. Advances in next generation sequencing (NGS) are allowing comparative analysis of the abundance and diversity of whole microbial communities, generating a large amount of data and findings at a systems level. The current limitation for biologists has been the increasing demand for computational power and training required for processing of NGS data. Here, we describe the deployment of the Brazilian Microbiome Project Operating System (BMPOS), a flexible and user-friendly Linux distribution dedicated to microbiome studies. The Brazilian Microbiome Project (BMP) has developed data analyses pipelines for metagenomic studies (phylogenetic marker genes), conducted using the two main high-throughput sequencing platforms (Ion Torrent and Illumina MiSeq). The BMPOS is freely available and possesses the entire requirement of bioinformatics packages and databases to perform all the pipelines suggested by the BMP team. The BMPOS may be used as a bootable live USB stick or installed in any computer with at least 1 GHz CPU and 512 MB RAM, independent of the operating system previously installed. The BMPOS has proved to be effective for sequences processing, sequences clustering, alignment, taxonomic annotation, statistical analysis, and plotting of metagenomic data. The BMPOS has been used during several metagenomic analyses courses, being valuable as a tool for training, and an excellent starting point to anyone interested in performing metagenomic studies. The BMPOS and its documentation are available at http://www.brmicrobiome.org .}, } @article {pmid27217102, year = {2016}, author = {Davis, DJ and Bryda, EC and Gillespie, CH and Ericsson, AC}, title = {Microbial modulation of behavior and stress responses in zebrafish larvae.}, journal = {Behavioural brain research}, volume = {311}, number = {}, pages = {219-227}, pmid = {27217102}, issn = {1872-7549}, support = {K01 OD019924/OD/NIH HHS/United States ; }, mesh = {Animals ; Anxiety/*microbiology/physiopathology ; Behavior, Animal/physiology ; Enzyme-Linked Immunosorbent Assay ; Hydrocortisone/metabolism ; Larva ; Metagenome ; Microbiota/genetics/*physiology ; Models, Animal ; Motor Activity/physiology ; Osmotic Pressure/physiology ; RNA, Messenger/metabolism ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Stress, Psychological/*microbiology/physiopathology ; Zebrafish/growth & development/*microbiology/physiology ; }, abstract = {The influence of the microbiota on behavior and stress responses is poorly understood. Zebrafish larvae have unique characteristics that are advantageous for neuroimmune research, however, they are currently underutilized for such studies. Here, we used germ-free zebrafish to determine the effects of the microbiota on behavior and stress testing. The absence of a microbiota dramatically altered locomotor and anxiety-related behavior. Additionally, characteristic responses to an acute stressor were also obliterated in larvae lacking exposure to microbes. Lastly, treatment with the probiotic Lactobacillus plantarum was sufficient to attenuate anxiety-related behavior in conventionally-raised zebrafish larvae. These results underscore the importance of the microbiota in communicating to the CNS via the microbiome-gut-brain axis and set a foundation for using zebrafish larvae for neuroimmune research.}, } @article {pmid27217061, year = {2016}, author = {Shah, R and Cope, JL and Nagy-Szakal, D and Dowd, S and Versalovic, J and Hollister, EB and Kellermayer, R}, title = {Composition and function of the pediatric colonic mucosal microbiome in untreated patients with ulcerative colitis.}, journal = {Gut microbes}, volume = {7}, number = {5}, pages = {384-396}, pmid = {27217061}, issn = {1949-0984}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Bacteria/classification/genetics/*isolation & purification ; Child ; Child, Preschool ; Colitis, Ulcerative/*microbiology/physiopathology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/*microbiology/physiopathology ; Intestines/microbiology/physiopathology ; Male ; Pediatrics ; Phylogeny ; }, abstract = {Inflammatory bowel diseases (IBD) are chronic intestinal inflammatory disorders characterized by a complex disruption of the physiologic interaction between the host immune system and intestinal microbes precipitated by environmental factors. Numerous observations indicate the altered composition and function of the intestinal microbiome of patients with ulcerative colitis (UC), a subtype of IBD. The accuracy of these results may be limited by confounding factors, such as concurrent medication use. To address these limitations, we examined the colonic mucosal microbiome of pediatric patients with UC prior to initiating treatment. Based on bacterial 16S rRNA gene sequencing, we identified a significant decrease in the phylum Verrucomicrobia in patients with UC. At the genus level, we observed a significant decrease in the short chain fatty acid producer Roseburia. Despite these compositional changes, we did not identify inferred gene content differences between the UC and control groups. To determine if microbial taxa may be associated with clinical outcomes, we retrospectively assessed the clinical course of the UC patients. Despite similar metrics of OTU richness and diversity, multiple OTU differences were observed between patients who responded to therapy and those who did not. Our observations regarding the mucosal microbiome and the associations with differential clinical outcomes support the contributions of gut microbes to disease onset and modulation.}, } @article {pmid27216801, year = {2016}, author = {Addis, MF and Tanca, A and Uzzau, S and Oikonomou, G and Bicalho, RC and Moroni, P}, title = {The bovine milk microbiota: insights and perspectives from -omics studies.}, journal = {Molecular bioSystems}, volume = {12}, number = {8}, pages = {2359-2372}, doi = {10.1039/c6mb00217j}, pmid = {27216801}, issn = {1742-2051}, mesh = {Animals ; Cattle ; Female ; *Food Microbiology ; Mastitis, Bovine/microbiology ; Metabolomics/methods ; Metagenome ; Metagenomics/methods ; *Microbiota ; Milk/*microbiology ; Proteomics/methods ; RNA, Ribosomal, 16S/genetics ; Transcriptome ; }, abstract = {Recent significant progress in culture-independent techniques, together with the parallel development of -omics technologies and data analysis capabilities, have led to a new perception of the milk microbiota as a complex microbial community with great diversity and multifaceted biological roles, living in an environment that was until recently believed to be sterile. In this review, we summarize and discuss the latest findings on the milk microbiota in dairy cows, with a focus on the role it plays in bovine physiology and health. Following an introduction on microbial communities and the importance of their study, we present an overview of the -omics methods currently available for their characterization, and outline the potential offered by a systems biology approach encompassing metatranscriptomics, metaproteomics, and metametabolomics. Then, we review the recent discoveries on the dairy cow milk microbiome enabled by the application of -omics approaches. Learning from studies in humans and in the mouse model, and after a description of the endogenous route hypothesis, we discuss the role of the milk microbiota in the physiology and health of both the mother and the offspring, and report how it can be changed by farming practices and during infection. In conclusion, we shortly outline the impact of the milk microbiota on the quality of milk and of dairy products.}, } @article {pmid27212657, year = {2016}, author = {Noyce, GL and Winsborough, C and Fulthorpe, R and Basiliko, N}, title = {The microbiomes and metagenomes of forest biochars.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {26425}, pmid = {27212657}, issn = {2045-2322}, mesh = {Acidobacteria/genetics/isolation & purification ; Bacteria/*classification/genetics/isolation & purification ; Betaproteobacteria/genetics/isolation & purification ; Charcoal/*analysis ; Forests ; Metagenome ; Microbiota ; Planctomycetales/genetics/isolation & purification ; Sequence Analysis, DNA/*methods ; *Soil Microbiology ; }, abstract = {Biochar particles have been hypothesized to provide unique microhabitats for a portion of the soil microbial community, but few studies have systematically compared biochar communities to bulk soil communities. Here, we used a combination of sequencing techniques to assess the taxonomic and functional characteristics of microbial communities in four-year-old biochar particles and in adjacent soils across three forest environments. Though effects varied between sites, the microbial community living in and around the biochar particles had significantly lower prokaryotic diversity and higher eukaryotic diversity than the surrounding soil. In particular, the biochar bacterial community had proportionally lower abundance of Acidobacteria, Planctomycetes, and β-Proteobacteria taxa, compared to the soil, while the eukaryotic biochar community had an 11% higher contribution of protists belonging to the Aveolata superphylum. Additionally, we were unable to detect a consistent biochar effect on the genetic functional potential of these microbial communities for the subset of the genetic data for which we were able to assign functions through MG-RAST. Overall, these results show that while biochar particles did select for a unique subset of the biota found in adjacent soils, effects on the microbial genetic functional potential appeared to be specific to contrasting forest soil environments.}, } @article {pmid27211518, year = {2016}, author = {Martinez, X and Pozuelo, M and Pascal, V and Campos, D and Gut, I and Gut, M and Azpiroz, F and Guarner, F and Manichanh, C}, title = {MetaTrans: an open-source pipeline for metatranscriptomics.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {26447}, pmid = {27211518}, issn = {2045-2322}, mesh = {Bacteria/classification/*genetics ; Computational Biology/*methods ; Feces/microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Internet ; Metagenomics ; *Microbiota ; Sequence Analysis, RNA ; Transcriptome ; }, abstract = {To date, meta-omic approaches use high-throughput sequencing technologies, which produce a huge amount of data, thus challenging modern computers. Here we present MetaTrans, an efficient open-source pipeline to analyze the structure and functions of active microbial communities using the power of multi-threading computers. The pipeline is designed to perform two types of RNA-Seq analyses: taxonomic and gene expression. It performs quality-control assessment, rRNA removal, maps reads against functional databases and also handles differential gene expression analysis. Its efficacy was validated by analyzing data from synthetic mock communities, data from a previous study and data generated from twelve human fecal samples. Compared to an existing web application server, MetaTrans shows more efficiency in terms of runtime (around 2 hours per million of transcripts) and presents adapted tools to compare gene expression levels. It has been tested with a human gut microbiome database but also proposes an option to use a general database in order to analyze other ecosystems. For the installation and use of the pipeline, we provide a detailed guide at the following website (www.metatrans.org).}, } @article {pmid27210559, year = {2016}, author = {Hennersdorf, P and Mrotzek, G and Abdul-Aziz, MA and Saluz, HP}, title = {Metagenomic analysis between free-living and cultured Epinephelus fuscoguttatus under different environmental conditions in Indonesian waters.}, journal = {Marine pollution bulletin}, volume = {110}, number = {2}, pages = {726-734}, doi = {10.1016/j.marpolbul.2016.05.009}, pmid = {27210559}, issn = {1879-3363}, mesh = {Alphaproteobacteria/genetics/*isolation & purification ; Animals ; Bass/growth & development/*microbiology ; Environmental Monitoring/*methods ; Feces/microbiology ; Fisheries ; Gammaproteobacteria/genetics/*isolation & purification ; Indonesia ; *Metagenomics ; Microbiota/*genetics ; Sequence Analysis, DNA ; }, abstract = {In this study, we analyzed and compared feces of free-living and cultivated fish species, Epinephelus fuscoguttatus under different environmental conditions in Indonesian waters. Metagenome analysis was performed using Illumina MiSeq sequencing of the whole metagenomic DNA isolated from fish feces samples. The analysis covered both prokaryotic and eukaryotic DNA. Feces samples from mariculture fish revealed a highly stable distribution of several orders of bacteria when compared to samples from free-living fish, which were highly diverse and dominated by Vibrionales, Pseudomonales, Rhizobiales and non-classifiable Alphaproteobacteria. The eukaryotic content of the samples was dominated by residues of the host and nine additional fish species that formed a portion of the diet. Investigations on functional annotations for predominant bacterial taxa, using Gene Ontology enrichment, revealed a number of functions related to DNA metabolic processes, especially DNA repair, as well as antibiotic response in the free-living fish species.}, } @article {pmid27208774, year = {2016}, author = {Zhang, Z and Zhang, XX and Wu, B and Yin, J and Yu, Y and Yang, L}, title = {Comprehensive insights into microcystin-LR effects on hepatic lipid metabolism using cross-omics technologies.}, journal = {Journal of hazardous materials}, volume = {315}, number = {}, pages = {126-134}, doi = {10.1016/j.jhazmat.2016.05.011}, pmid = {27208774}, issn = {1873-3336}, mesh = {Animals ; Bacteroidetes/drug effects ; Feces/microbiology ; Firmicutes/drug effects ; Gastrointestinal Microbiome/drug effects ; Genomics ; Lipid Metabolism/*drug effects/genetics ; Liver/*drug effects/metabolism ; Male ; Marine Toxins ; Metabolomics ; Mice, Inbred C57BL ; Microcystins/*toxicity ; RNA, Ribosomal, 16S/genetics ; Transcriptome ; }, abstract = {Microcystin-LR (MC-LR) can induce hepatic tissue damages and molecular toxicities, but its effects on lipid metabolism remain unknown. This study investigated the effects of MC-LR exposure on mice lipid metabolism and uncovered the underlying mechanism through metabonomic, transcriptomic and metagenomic analyses after administration of mice with MC-LR by gavage for 28 d. Increased liver weight and abdominal fat weight, and evident hepatic lipid vacuoles accumulation were observed in the mice fed with 0.2mg/kg/d MC-LR. Serum nuclear magnetic resonance analysis showed that MC-LR treatment altered the levels of serum metabolites including triglyceride, unsaturated fatty acid (UFA) and very low density lipoprotein. Digital Gene Expression technology was used to reveal differential expression of hepatic transcriptomes, demonstrating that MC-LR treatment disturbed hepatic UFA biosynthesis and activated peroxisome proliferator-activated receptor (PPAR) signaling pathways via Pparγ, Fabp1 and Fabp2 over-expression. Metagenomic analyses of gut microbiota revealed that MC-LR exposure also increased abundant ratio of Firmicutes vs. Bacteroidetes in gut and altered biosynthetic pathways of various microbial metabolic and pro-inflammatory molecules. In conclusion, oral MC-LR exposure can induce hepatic lipid metabolism disorder mediated by UFA biosynthesis and PPAR activation, and gut microbial community shift may play an important role in the metabolic disturbance.}, } @article {pmid27206473, year = {2016}, author = {González-Tortuero, E and Rusek, J and Maayan, I and Petrusek, A and Piálek, L and Laurent, S and Wolinska, J}, title = {Genetic diversity of two Daphnia-infecting microsporidian parasites, based on sequence variation in the internal transcribed spacer region.}, journal = {Parasites & vectors}, volume = {9}, number = {1}, pages = {293}, pmid = {27206473}, issn = {1756-3305}, mesh = {Animals ; Czech Republic ; *DNA, Intergenic ; Daphnia/*microbiology ; *Genetic Variation ; Haplotypes ; Metagenomics ; Microsporidia/*genetics ; Phylogeography ; Recombination, Genetic ; }, abstract = {BACKGROUND: Microsporidia are spore-forming obligate intracellular parasites that include both emerging pathogens and economically important disease agents. However, little is known about the genetic diversity of microsporidia. Here, we investigated patterns of geographic population structure, intraspecific genetic variation, and recombination in two microsporidian taxa that commonly infect cladocerans of the Daphnia longispina complex in central Europe. Taken together, this information helps elucidate the reproductive mode and life-cycles of these parasite species.

METHODS: Microsporidia-infected Daphnia were sampled from seven drinking water reservoirs in the Czech Republic. Two microsporidia species (Berwaldia schaefernai and microsporidium lineage MIC1) were sequenced at the internal transcribed spacer (ITS) region, using the 454 pyrosequencing platform. Geographical structure analyses were performed applying Fisher's exact tests, analyses of molecular variance, and permutational MANOVA. To evaluate the genetic diversity of the ITS region, the number of polymorphic sites and Tajima's and Watterson's estimators of theta were calculated. Tajima's D was also used to determine if the ITS in these taxa evolved neutrally. Finally, neighbour similarity score and pairwise homology index tests were performed to detect recombination events.

RESULTS: While there was little variation among Berwaldia parasite strains infecting different host populations, the among-population genetic variation of MIC1 was significant. Likewise, ITS genetic diversity was lower in Berwaldia than in MIC1. Recombination signals were detected only in Berwaldia.

CONCLUSION: Genetic tests showed that parasite populations could have expanded recently after a bottleneck or that the ITS could be under negative selection in both microsporidia species. Recombination analyses might indicate cryptic sex in Berwaldia and pure asexuality in MIC1. The differences observed between the two microsporidian species present an exciting opportunity to study the genetic basis of microsporidia-Daphnia coevolution in natural populations, and to better understand reproduction in these parasites.}, } @article {pmid27203275, year = {2017}, author = {Gao, B and Bian, X and Mahbub, R and Lu, K}, title = {Sex-Specific Effects of Organophosphate Diazinon on the Gut Microbiome and Its Metabolic Functions.}, journal = {Environmental health perspectives}, volume = {125}, number = {2}, pages = {198-206}, pmid = {27203275}, issn = {1552-9924}, support = {R01 ES024950/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Diazinon/*toxicity ; Female ; Gastrointestinal Microbiome/*drug effects/physiology ; Gastrointestinal Tract ; Humans ; Insecticides/*toxicity ; Male ; Metabolome/*drug effects/physiology ; Metagenome/physiology ; Mice ; Mice, Inbred C57BL ; Microbiota/*drug effects/physiology ; Sex Factors ; Toxicity Tests ; }, abstract = {BACKGROUND: There is growing recognition of the significance of the gut microbiome to human health, and the association between a perturbed gut microbiome with human diseases has been established. Previous studies also show the role of environmental toxicants in perturbing the gut microbiome and its metabolic functions. The wide agricultural use of diazinon, an organophosphate insecticide, has raised serious environmental health concerns since it is a potent neurotoxicant. With studies demonstrating the presence of a microbiome-gut-brain axis, it is possible that gut microbiome perturbation may also contribute to diazinon toxicity.

OBJECTIVES: We investigated the impact of diazinon exposure on the gut microbiome composition and its metabolic functions in C57BL/6 mice.

METHODS: We used a combination of 16S rRNA gene sequencing, metagenomics sequencing, and mass spectrometry-based metabolomics profiling in a mouse model to examine the functional impact of diazinon on the gut microbiome.

RESULTS: 16S rRNA gene sequencing revealed that diazinon exposure significantly perturbed the gut microbiome, and metagenomic sequencing found that diazinon exposure altered the functional metagenome. Moreover, metabolomics profiling revealed an altered metabolic profile arising from exposure. Of particular significance, these changes were more pronounced for male mice than for female mice.

CONCLUSIONS: Diazinon exposure perturbed the gut microbiome community structure, functional metagenome, and associated metabolic profiles in a sex-specific manner. These findings may provide novel insights regarding perturbations of the gut microbiome and its functions as a potential new mechanism contributing to diazinon neurotoxicity and, in particular, its sex-selective effects. Citation: Gao B, Bian X, Mahbub R, Lu K. 2017. Sex-specific effects of organophosphate diazinon on the gut microbiome and its metabolic functions. Environ Health Perspect 125:198-206; http://dx.doi.org/10.1289/EHP202.}, } @article {pmid27197692, year = {2016}, author = {Kyrpides, NC and Eloe-Fadrosh, EA and Ivanova, NN}, title = {Microbiome Data Science: Understanding Our Microbial Planet.}, journal = {Trends in microbiology}, volume = {24}, number = {6}, pages = {425-427}, doi = {10.1016/j.tim.2016.02.011}, pmid = {27197692}, issn = {1878-4380}, mesh = {*Information Systems ; Metagenomics ; Microbiology ; *Microbiota ; *Planets ; Research ; *Science ; }, abstract = {Microbiology is experiencing a revolution brought on by recent developments in sequencing technology. The unprecedented volume of microbiome data being generated poses significant challenges that are currently hindering progress in the field. Here, we outline the major bottlenecks and propose a vision to advance microbiome research as a data-driven science.}, } @article {pmid27195106, year = {2016}, author = {Bissett, A and Fitzgerald, A and Court, L and Meintjes, T and Mele, PM and Reith, F and Dennis, PG and Breed, MF and Brown, B and Brown, MV and Brugger, J and Byrne, M and Caddy-Retalic, S and Carmody, B and Coates, DJ and Correa, C and Ferrari, BC and Gupta, VV and Hamonts, K and Haslem, A and Hugenholtz, P and Karan, M and Koval, J and Lowe, AJ and Macdonald, S and McGrath, L and Martin, D and Morgan, M and North, KI and Paungfoo-Lonhienne, C and Pendall, E and Phillips, L and Pirzl, R and Powell, JR and Ragan, MA and Schmidt, S and Seymour, N and Snape, I and Stephen, JR and Stevens, M and Tinning, M and Williams, K and Yeoh, YK and Zammit, CM and Young, A}, title = {Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database.}, journal = {GigaScience}, volume = {5}, number = {}, pages = {21}, pmid = {27195106}, issn = {2047-217X}, mesh = {Archaea/classification/genetics ; Australia ; Bacteria/classification/genetics ; Biodiversity ; *Databases, Factual ; Fungi/classification/genetics ; Metagenomics ; Phylogeny ; Sequence Analysis, DNA/*methods ; *Soil Microbiology ; }, abstract = {BACKGROUND: Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The 'Biomes of Australian Soil Environments' (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function.

FINDINGS: BASE currently provides amplicon sequences and associated contextual data for over 900 sites encompassing all Australian states and territories, a wide variety of bioregions, vegetation and land-use types. Amplicons target bacteria, archaea and general and fungal-specific eukaryotes. The growing database will soon include metagenomics data. Data are provided in both raw sequence (FASTQ) and analysed OTU table formats and are accessed via the project's data portal, which provides a user-friendly search tool to quickly identify samples of interest. Processed data can be visually interrogated and intersected with other Australian diversity and environmental data using tools developed by the 'Atlas of Living Australia'.

CONCLUSIONS: Developed within an open data framework, the BASE project is the first Australian soil microbial diversity database. The database will grow and link to other global efforts to explore microbial, plant, animal, and marine biodiversity. Its design and open access nature ensures that BASE will evolve as a valuable tool for documenting an often overlooked component of biodiversity and the many microbe-driven processes that are essential to sustain soil function and ecosystem services.}, } @article {pmid27193869, year = {2016}, author = {Law, Y and Kirkegaard, RH and Cokro, AA and Liu, X and Arumugam, K and Xie, C and Stokholm-Bjerregaard, M and Drautz-Moses, DI and Nielsen, PH and Wuertz, S and Williams, RB}, title = {Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {25719}, pmid = {27193869}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics/metabolism ; Biodegradation, Environmental ; Bioreactors/microbiology ; Glycogen/metabolism ; In Situ Hybridization, Fluorescence ; Metagenome/genetics ; Microbial Consortia/genetics/*physiology ; Phosphorus/*isolation & purification/metabolism ; Sequence Analysis, DNA ; Sewage/microbiology ; Temperature ; *Tropical Climate ; Waste Disposal, Fluid/methods ; Wastewater/microbiology ; *Water Microbiology ; Water Purification/methods ; }, abstract = {Management of phosphorus discharge from human waste is essential for the control of eutrophication in surface waters. Enhanced biological phosphorus removal (EBPR) is a sustainable, efficient way of removing phosphorus from waste water without employing chemical precipitation, but is assumed unachievable in tropical temperatures due to conditions that favour glycogen accumulating organisms (GAOs) over polyphosphate accumulating organisms (PAOs). Here, we show these assumptions are unfounded by studying comparative community dynamics in a full-scale plant following systematic perturbation of operational conditions, which modified community abundance, function and physicochemical state. A statistically significant increase in the relative abundance of the PAO Accumulibacter was associated with improved EBPR activity. GAO relative abundance also increased, challenging the assumption of competition. An Accumulibacter bin-genome was identified from a whole community metagenomic survey, and comparative analysis against extant Accumulibacter genomes suggests a close relationship to Type II. Analysis of the associated metatranscriptome data revealed that genes encoding proteins involved in the tricarboxylic acid cycle and glycolysis pathways were highly expressed, consistent with metabolic modelling results. Our findings show that tropical EBPR is indeed possible, highlight the translational potential of studying competition dynamics in full-scale waste water communities and carry implications for plant design in tropical regions.}, } @article {pmid27192496, year = {2016}, author = {Koo, OK and Baker, CA and Kim, HJ and Park, SH and Ricke, SC}, title = {Metagenomic assessment of the microbial diversity in ground pork products from markets in the North Central Region of South Korea.}, journal = {Journal of environmental science and health. Part. B, Pesticides, food contaminants, and agricultural wastes}, volume = {51}, number = {9}, pages = {622-627}, doi = {10.1080/03601234.2016.1181910}, pmid = {27192496}, issn = {1532-4109}, mesh = {Animals ; *Food Microbiology ; Food Services ; Metagenomics ; *Microbiota ; Red Meat/*microbiology ; Republic of Korea ; Swine ; }, abstract = {The purpose of this study was to characterize the microbial community in ground pork using molecular approaches. Forty six ground pork products were purchased from local stores in the north central area of South Korea. Aerobic plate counts varied 4.23 ± 5.14 × 10(5) CFU/g with the range between 5.00 × 10(3) and 1.85 × 10(6) CFU/g for ground pork samples. Four ground meat samples were further processed for metagenomic analysis. Pseudomonas species was the most relative abundant with a wide range occurring (1.72 to 77.7%) as part of the microbial genera in ground pork. Bacteria such as Carnobacterium, Yersinia, Photobacterium were also identified in ground pork. Despite the prominence of certain genera across all samples there was still extensive microbial diversity among ground pork products that originated from different slaughter houses and were processed in different markets. Such diversity indicates that designing interventions to extend shelf life may be hampered by the extensive variability in the microbial consortia associated with pork products. However, this diversity may be useful for developing microbial traceability signatures unique to a slaughter house or a particular market.}, } @article {pmid27191725, year = {2016}, author = {Gaulke, CA and Barton, CL and Proffitt, S and Tanguay, RL and Sharpton, TJ}, title = {Triclosan Exposure Is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish.}, journal = {PloS one}, volume = {11}, number = {5}, pages = {e0154632}, pmid = {27191725}, issn = {1932-6203}, support = {P30 ES000210/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Anti-Infective Agents, Local/*pharmacology ; Drug Resistance ; Gastrointestinal Microbiome ; Metagenome ; Metagenomics ; Microbiota/*drug effects ; RNA, Ribosomal, 16S/genetics ; Triclosan/*pharmacology ; Zebrafish/*microbiology ; }, abstract = {Growing evidence indicates that disrupting the microbial community that comprises the intestinal tract, known as the gut microbiome, can contribute to the development or severity of disease. As a result, it is important to discern the agents responsible for microbiome disruption. While animals are frequently exposed to a diverse array of environmental chemicals, little is known about their effects on gut microbiome stability and structure. Here, we demonstrate how zebrafish can be used to glean insight into the effects of environmental chemical exposure on the structure and ecological dynamics of the gut microbiome. Specifically, we exposed forty-five adult zebrafish to triclosan-laden food for four or seven days or a control diet, and analyzed their microbial communities using 16S rRNA amplicon sequencing. Triclosan exposure was associated with rapid shifts in microbiome structure and diversity. We find evidence that several operational taxonomic units (OTUs) associated with the family Enterobacteriaceae appear to be susceptible to triclosan exposure, while OTUs associated with the genus Pseudomonas appeared to be more resilient and resistant to exposure. We also found that triclosan exposure is associated with topological alterations to microbial interaction networks and results in an overall increase in the number of negative interactions per microbe in these networks. Together these data indicate that triclosan exposure results in altered composition and ecological dynamics of microbial communities in the gut. Our work demonstrates that because zebrafish afford rapid and inexpensive interrogation of a large number of individuals, it is a useful experimental system for the discovery of the gut microbiome's interaction with environmental chemicals.}, } @article {pmid27191390, year = {2016}, author = {Liu, L and Zhang, Q and Lin, J and Ma, L and Zhou, Z and He, X and Jia, Y and Chen, F}, title = {Investigating Oral Microbiome Profiles in Children with Cleft Lip and Palate for Prognosis of Alveolar Bone Grafting.}, journal = {PloS one}, volume = {11}, number = {5}, pages = {e0155683}, pmid = {27191390}, issn = {1932-6203}, mesh = {Adolescent ; Alveolar Bone Grafting ; Biodiversity ; Child ; Cleft Lip/*microbiology/surgery ; Cleft Palate/*microbiology/surgery ; Female ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth/*microbiology ; Preoperative Period ; Prognosis ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; }, abstract = {In this study, we sought to investigate the oral microbiota structure of children with cleft lip and palate (CLP) and explore the pre-operative oral bacterial composition related to the prognosis of alveolar bone grafting. In total, 28 patients (19 boys, 9 girls) with CLP who were scheduled to undergo alveolar bone grafting for the first time were recruited. According to the clinical examination of operative sites at the third month after the operation, the individuals were divided into a non-inflammation group (n = 15) and an inflammation group (n = 13). In all, 56 unstimulated saliva samples were collected before and after the operation. The v3-v4 hypervariable regions of the 16S rRNA gene were sequenced using an Illumina MiSeq sequencing platform. Based on the beta diversity of the operational taxonomic units (OTUs) in the inflammation and non-inflammation samples, the microbial variation in the oral cavity differed significantly between the two groups before and after the operation (P < 0.05). Analysis of the relative abundances of pre-operative OTUs revealed 26 OTUs with a relative abundance higher than 0.01%, reflecting a significant difference of the relative abundance between groups (P < 0.05). According to a principal component analysis of the pre-operative samples, the inflammation-related OTUs included Tannerella sp., Porphyromonas sp., Gemella sp., Moraxella sp., Prevotella nigrescens, and Prevotella intermedia, most of which were enriched in the inflammation group and showed a significant positive correlation. A cross-validated random forest model based on the 26 different OTUs before the operation was able to fit the post-operative status of grafted sites and yielded a good classification result. The sensitivity and specificity of this classified model were 76.9% and 86.7%, respectively. These findings show that the oral microbiota profile before alveolar bone grafting may be related to the risk of post-operative inflammation at grafted sites.}, } @article {pmid27188959, year = {2016}, author = {Angelakis, E and Bachar, D and Henrissat, B and Armougom, F and Audoly, G and Lagier, JC and Robert, C and Raoult, D}, title = {Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {26276}, pmid = {27188959}, issn = {2045-2322}, mesh = {Bacteria/genetics ; DNA, Bacterial/genetics/*isolation & purification ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Kwashiorkor/microbiology ; *Metagenomics ; Obesity/microbiology ; Polysaccharides/*chemistry ; Polysaccharides, Bacterial/chemistry ; Protein-Energy Malnutrition/microbiology ; }, abstract = {Exopolysaccharides produced by bacterial species and present in feces are extremely inhibitory to DNA restriction and can cause discrepancies in metagenomic studies. We determined the effects of different DNA extraction methods on the apparent composition of the gut microbiota using Illumina MiSeq deep sequencing technology. DNA was extracted from the stool from an obese female using 10 different methods and the choice of DNA extraction method affected the proportional abundance at the phylum level, species richness (Chao index, 227 to 2,714) and diversity (non parametric Shannon, 1.37 to 4.4). Moreover DNA was extracted from stools obtained from 83 different individuals by the fastest extraction assay and by an extraction assay that degradated exopolysaccharides. The fastest extraction method was able to detect 68% to 100% genera and 42% to 95% species whereas the glycan degradation extraction method was able to detect 56% to 93% genera and 25% to 87% species. To allow a good liberation of DNA from exopolysaccharides commonly presented in stools, we recommend the mechanical lysis of stools plus glycan degradation, used here for the first time. Caution must be taken in the interpretation of current metagenomic studies, as the efficiency of DNA extraction varies widely among stool samples.}, } @article {pmid27184874, year = {2016}, author = {Boers, SA and Jansen, R and Hays, JP}, title = {Suddenly everyone is a microbiota specialist.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {22}, number = {7}, pages = {581-582}, doi = {10.1016/j.cmi.2016.05.002}, pmid = {27184874}, issn = {1469-0691}, mesh = {Humans ; Metagenomics/*methods/*standards ; *Microbiota ; Publications/*standards ; }, } @article {pmid27183895, year = {2016}, author = {Sukumar, S and Roberts, AP and Martin, FE and Adler, CJ}, title = {Metagenomic Insights into Transferable Antibiotic Resistance in Oral Bacteria.}, journal = {Journal of dental research}, volume = {95}, number = {9}, pages = {969-976}, doi = {10.1177/0022034516648944}, pmid = {27183895}, issn = {1544-0591}, mesh = {Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Humans ; *Metagenomics ; Microbiota/*drug effects/genetics ; Mouth/*microbiology ; }, abstract = {Antibiotic resistance is considered one of the greatest threats to global public health. Resistance is often conferred by the presence of antibiotic resistance genes (ARGs), which are readily found in the oral microbiome. In-depth genetic analyses of the oral microbiome through metagenomic techniques reveal a broad distribution of ARGs (including novel ARGs) in individuals not recently exposed to antibiotics, including humans in isolated indigenous populations. This has resulted in a paradigm shift from focusing on the carriage of antibiotic resistance in pathogenic bacteria to a broader concept of an oral resistome, which includes all resistance genes in the microbiome. Metagenomics is beginning to demonstrate the role of the oral resistome and horizontal gene transfer within and between commensals in the absence of selective pressure, such as an antibiotic. At the chairside, metagenomic data reinforce our need to adhere to current antibiotic guidelines to minimize the spread of resistance, as such data reveal the extent of ARGs without exposure to antimicrobials and the ecologic changes created in the oral microbiome by even a single dose of antibiotics. The aim of this review is to discuss the role of metagenomics in the investigation of the oral resistome, including the transmission of antibiotic resistance in the oral microbiome. Future perspectives, including clinical implications of the findings from metagenomic investigations of oral ARGs, are also considered.}, } @article {pmid27183876, year = {2016}, author = {Million, M and Tidjani Alou, M and Khelaifia, S and Bachar, D and Lagier, JC and Dione, N and Brah, S and Hugon, P and Lombard, V and Armougom, F and Fromonot, J and Robert, C and Michelle, C and Diallo, A and Fabre, A and Guieu, R and Sokhna, C and Henrissat, B and Parola, P and Raoult, D}, title = {Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {26051}, pmid = {27183876}, issn = {2045-2322}, mesh = {Asia ; Bacteria/*classification/genetics ; Bacterial Load ; Child ; Child, Preschool ; Dysbiosis/*etiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology/*pathology ; Humans ; Metagenomics ; Niger ; Oxidation-Reduction ; Senegal ; Sequence Analysis, DNA ; Severe Acute Malnutrition/*complications ; }, abstract = {Severe acute malnutrition (SAM) is associated with inadequate diet, low levels of plasma antioxidants and gut microbiota alterations. The link between gut redox and microbial alterations, however, remains unexplored. By sequencing the gut microbiomes of 79 children of varying nutritional status from three centers in Senegal and Niger, we found a dramatic depletion of obligate anaerobes in malnutrition. This was confirmed in an individual patient data meta-analysis including 107 cases and 77 controls from 5 different African and Asian countries. Specifically, several species of the Bacteroidaceae, Eubacteriaceae, Lachnospiraceae and Ruminococceae families were consistently depleted while Enterococcus faecalis, Escherichia coli and Staphylococcus aureus were consistently enriched. Further analyses on our samples revealed increased fecal redox potential, decreased total bacterial number and dramatic Methanobrevibacter smithii depletion. Indeed, M. smithii was detected in more than half of the controls but in none of the cases. No causality was demonstrated but, based on our results, we propose a unifying theory linking microbiota specificity, lacking anaerobes and archaea, to low antioxidant nutrients, and lower food conversion.}, } @article {pmid27183792, year = {2016}, author = {Kaluzhnaya, OV and Itskovich, VB}, title = {[Distinctive Features of the Microbial Diversity and the Polyketide Synthase GenesSpectrum in the Community of the Endemic Baikal Sponge Swartschewskia papyracea].}, journal = {Genetika}, volume = {52}, number = {1}, pages = {47-58}, pmid = {27183792}, issn = {0016-6758}, mesh = {Animals ; Genetic Variation ; Lakes ; Metagenome ; Microbiota/*genetics ; *Phylogeny ; Polyketide Synthases/*genetics ; Porifera/genetics/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The diversity of the symbiotic community of the endemic Baikal sponge Swartschewskia papyracea was studied, and an analysis of the polyketide synthases genes spectrum in sponge-associated microorganisms was carried out. Six bacterial phyla were detected in the S. papyracea microbiome, namely, Verrucomicrobia, Cyanobacteria, Actinobacteria, Bacteroidetes, Proteobacteria, and Planctomycetes. Unlike the microbial associations of other freshwater sponges, the community under study was dominated by the Verrucomicrobia (42.1%) and Cyanobacteria (17.5%) phyla, while the proportion of the Proteobacteria was unusually low (9.7%). In the S. papyracea community metagenome, there were identified 18 polyketide synthases genes fragments, the closest homologs of which included the polyketide synthases of the microorganisms belonging to the bacterial phyla Cyanobacteria, Proteobacteria (Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria classes), and Acidobacteria and to the eukaryotic algae of the Heterokonta phylum (Eustigmatophyceae class). Polyketide synthase sequences from S. papyracea formed three groups on the phylogenetic tree: a group of hybrid NRPS/PKS complexes, a group of cyanobacterial polyketide synthases, and a group of homologs of the eukaryotic alga Nannochloropsis galiana. Notably, the identified polyketide synthase genes fragments showed only a 57-88% similarity to the sequences in the databases, which implies the presence of genes controlling the synthesis of the novel, still unstudied, polyketide compounds in the S. papyracea community. It was proposed that the habitation conditions of S. papyracea affect the taxonomic composition of the microorganisms associated with the sponge, including the diversity of the producers of secondary metabolites.}, } @article {pmid27182596, year = {2016}, author = {Zha, Y and Berga, M and Comte, J and Langenheder, S}, title = {Effects of Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities.}, journal = {PloS one}, volume = {11}, number = {5}, pages = {e0155239}, pmid = {27182596}, issn = {1932-6203}, mesh = {Analysis of Variance ; Bacteria/*classification/genetics ; Bacterial Physiological Phenomena ; *Biodiversity ; Ecosystem ; Environment ; Lakes/microbiology ; Metagenome ; Metagenomics/methods ; Oxygen Consumption ; *Water Microbiology ; }, abstract = {Natural communities are open systems and consequently dispersal can play an important role for the diversity, composition and functioning of communities at the local scale. It is, however, still unclear how effects of dispersal differ depending on the initial diversity of local communities. Here we implemented an experiment where we manipulated the initial diversity of natural freshwater bacterioplankton communities using a dilution-to-extinction approach as well as dispersal from a regional species pool. The aim was further to test whether dispersal effects on bacterial abundance and functional parameters (average community growth rates, respiration rates, substrate utilisation ability) differ in dependence of the initial diversity of the communities. First of all, we found that both initial diversity and dispersal rates had an effect on the recruitment of taxa from a regional source, which was higher in communities with low initial diversity and at higher rates of dispersal. Higher initial diversity and dispersal also promoted higher levels of richness and evenness in local communities and affected, both, separately or interactively, the functional performance of communities. Our study therefore suggests that dispersal can influence the diversity, composition and functioning of bacterial communities and that this effect may be enhanced if the initial diversity of communities is depleted.}, } @article {pmid27180802, year = {2016}, author = {Cernada, M and Bäuerl, C and Serna, E and Collado, MC and Martínez, GP and Vento, M}, title = {Sepsis in preterm infants causes alterations in mucosal gene expression and microbiota profiles compared to non-septic twins.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {25497}, pmid = {27180802}, issn = {2045-2322}, mesh = {Biomarkers ; Computational Biology/methods ; Female ; Gastrointestinal Microbiome ; *Gene Expression ; Gene Expression Profiling ; Gene Expression Regulation ; Humans ; Infant ; Infant, Newborn ; *Infant, Premature ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Models, Biological ; Molecular Sequence Annotation ; Mucous Membrane/*metabolism/*microbiology/pathology ; Sepsis/diagnosis/*genetics/metabolism/*microbiology ; Signal Transduction ; Transcriptome ; }, abstract = {Sepsis is a life-threatening condition in preterm infants. Neonatal microbiota plays a pivotal role in the immune system maturation. Changes in gut microbiota have been associated to inflammatory disorders; however, a link with sepsis in the neonatal period has not yet been established. We aimed to analyze gut microbiota and mucosal gene expression using non-invasively obtained samples to provide with an integrative perspective of host-microbe interactions in neonatal sepsis. For this purpose, a prospective observational case-control study was conducted in septic preterm dizygotic twins and their non-septic twin controls. Fecal samples were used for both microbiota analysis and host genome-wide expression using exfoliated intestinal cells. Gene expression of exfoliated intestinal cells in septic preterm showed an induction of inflammatory and oxidative stress pathways in the gut and pro-oxidant profile that caused dysbiosis in the gut microbiota with predominance of Enterobacteria and reduction of Bacteroides and Bifidobacterium spp.in fecal samples, leading to a global reduction of beneficial anaerobic bacteria. Sepsis in preterm infants induced low-grade inflammation and oxidative stress in the gut mucosa, and also changes in the gut microbiota. This study highlights the role of inflammation and oxidative stress in neonatal sepsis on gut microbial profiles.}, } @article {pmid27180722, year = {2016}, author = {Sun, B and Wang, X and Bernstein, S and Huffman, MA and Xia, DP and Gu, Z and Chen, R and Sheeran, LK and Wagner, RS and Li, J}, title = {Marked variation between winter and spring gut microbiota in free-ranging Tibetan Macaques (Macaca thibetana).}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {26035}, pmid = {27180722}, issn = {2045-2322}, mesh = {Animals ; Carbohydrate Metabolism ; Cellulose/metabolism ; Digestion ; Energy Intake ; Energy Metabolism ; Gastrointestinal Microbiome/*genetics ; *Macaca ; Metagenome ; Nutrigenomics ; Prevotella/*physiology ; Seasons ; Succinivibrionaceae/*genetics/*physiology ; Tibet ; }, abstract = {Variation in the availability and distribution of food resources is a strong selective pressure on wild primates. We explored variation in Tibetan macaque gut microbiota composition during winter and spring seasons. Our results showed that gut microbial composition and diversity varied by season. In winter, the genus Succinivibrio, which promotes the digestion of cellulose and hemicellulose, was significantly increased. In spring, the abundance of the genus Prevotella, which is associated with digestion of carbohydrates and simple sugars, was significantly increased. PICRUSt analysis revealed that the predicted metagenomes related to the glycan biosynthesis and metabolic pathway was significantly increased in winter samples, which would aid in the digestion of glycan extracted from cellulose and hemicellulose. The predicted metagenomes related to carbohydrate and energy metabolic pathways were significantly increased in spring samples, which could facilitate a monkey's recovery from acute energy loss experienced during winter. We propose that shifts in the composition and function of the gut microbiota provide a buffer against seasonal fluctuations in energy and nutrient intake, thus enabling these primates to adapt to variations in food supply and quality.}, } @article {pmid27180112, year = {2016}, author = {Robinson, CK and Brotman, RM and Ravel, J}, title = {Intricacies of assessing the human microbiome in epidemiologic studies.}, journal = {Annals of epidemiology}, volume = {26}, number = {5}, pages = {311-321}, pmid = {27180112}, issn = {1873-2585}, support = {K01 AI080974/AI/NIAID NIH HHS/United States ; R01 AI116799/AI/NIAID NIH HHS/United States ; U19 AI084044/AI/NIAID NIH HHS/United States ; }, mesh = {Biomedical Research/*methods ; *Epidemiologic Studies ; Genes, rRNA/*genetics/physiology ; Humans ; Microbiota/*genetics/physiology ; Molecular Biology ; Reproducibility of Results ; }, abstract = {PURPOSE: In the past decade, remarkable relationships have been documented between dysbiosis of the human microbiota and adverse health outcomes. This review seeks to highlight some of the challenges and pitfalls that may be encountered during all stages of microbiota research, from study design and sample collection, to nucleic acid extraction and sequencing, and bioinformatic and statistical analysis.

METHODS: Literature focused on human microbiota research was reviewed and summarized.

RESULTS: Although most studies have focused on surveying the composition of the microbiota, fewer have explored the causal roles of these bacteria, archaea, viruses, and fungi in affecting disease states. Microbiome research is in its relatively early years and many aspects remain challenging, including the complexity and personalized aspects of microbial communities, the influence of exogenous and often confounding factors, the need to apply fundamental principles of ecology and epidemiology, the necessity for new software tools, and the rapidly evolving genomic, technological, and analytical landscapes.

CONCLUSIONS: Incorporating human microbiome research in large epidemiologic studies will soon help us unravel the intricate relationships that we have with our microbial partners and provide interventional opportunities to improve human health.}, } @article {pmid27180095, year = {2016}, author = {Li, Y and Xie, W and Li, Q}, title = {Characterisation of the bacterial community structures in the intestine of Lampetra morii.}, journal = {Antonie van Leeuwenhoek}, volume = {109}, number = {7}, pages = {979-986}, doi = {10.1007/s10482-016-0699-0}, pmid = {27180095}, issn = {1572-9699}, mesh = {Animals ; Bacteria/*classification/genetics/isolation & purification ; Biodiversity ; Cluster Analysis ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Gastrointestinal Microbiome ; Intestines/*microbiology ; Lampreys/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The metagenomic analysis and 16S rDNA sequencing method were used to investigate the bacterial community in the intestines of Lampetra morii. The bacterial community structure in L. morii intestine was relatively simple. Eight different operational taxonomic units were observed. Chitinophagaceae_unclassified (26.5 %) and Aeromonas spp. (69.6 %) were detected as dominant members at the genus level. The non-dominant genera were as follows: Acinetobacter spp. (1.4 %), Candidatus Bacilloplasma (2.5 %), Enterobacteria spp. (1.5 %), Shewanella spp. (0.04 %), Vibrio spp. (0.09 %), and Yersinia spp. (1.8 %). The Shannon-Wiener (H) and Simpson (1-D) indexes were 0.782339 and 0.5546, respectively. The rarefaction curve representing the bacterial community richness and Shannon-Wiener curve representing the bacterial community diversity reached asymptote, which indicated that the sequence depth were sufficient to represent the majority of species richness and bacterial community diversity. The number of Aeromonas in lamprey intestine was two times higher after stimulation by lipopolysaccharide than PBS. This study provides data for understanding the bacterial community harboured in lamprey intestines and exploring potential key intestinal symbiotic bacteria essential for the L. morii immune response.}, } @article {pmid27179234, year = {2016}, author = {Mustafa, GA and Abd-Elgawad, A and Ouf, A and Siam, R}, title = {The Egyptian Red Sea coastal microbiome: A study revealing differential microbial responses to diverse anthropogenic pollutants.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {214}, number = {}, pages = {892-902}, doi = {10.1016/j.envpol.2016.04.009}, pmid = {27179234}, issn = {1873-6424}, mesh = {Bacteria/drug effects/genetics/growth & development ; Egypt ; Environment ; Indian Ocean ; Microbial Consortia/drug effects/genetics ; Microbiota/*drug effects/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; Water Pollutants, Chemical/*toxicity ; }, abstract = {The Red Sea is considered one of the youngest oceanic systems, with unique physical, geochemical and biological characteristics. Tourism, industrialization, extensive fishing, oil processing and shipping are extensive sources of pollution in the Red Sea. We analyzed the geochemical characteristics and microbial community of sediments along the Egyptian coast of the Red Sea. Our sites mainly included 1) four ports used for shipping aluminum, ilmenite and phosphate; 2) a site previously reported to have suffered extensive oil spills; and 3) a site impacted by tourism. Two major datasets for the sediment of ten Red Sea coastal sites were generated; i) a chemical dataset included measurements of carbon, hydrogen, nitrogen and sulfur, metals and selected semi-volatile oil; and ii) a 16S rRNA Pyrotags bacterial metagenomic dataset. Based on the taxonomic assignments of the 16S rRNA Pyrotags to major bacterial groups, we report 30 taxa constituting an Egyptian Red Sea Coastal Microbiome. Bacteria that degrade hydrocarbons were predominant in the majority of the sites, particularly in two ports where they reached up to 76% of the total identified genera. In contrast, sulfate-reducing and sulfate-oxidizing bacteria dominated two lakes at the expense of other hydrocarbon metabolizers. Despite the reported "Egyptian Red Sea Coastal Microbiome," sites with similar anthropogenic pollutants showed unique microbial community abundances. This suggests that the abundance of a specific bacterial community is an evolutionary mechanism induced in response to selected anthropogenic pollutants.}, } @article {pmid27172044, year = {2016}, author = {Pehrsson, EC and Tsukayama, P and Patel, S and Mejía-Bautista, M and Sosa-Soto, G and Navarrete, KM and Calderon, M and Cabrera, L and Hoyos-Arango, W and Bertoli, MT and Berg, DE and Gilman, RH and Dantas, G}, title = {Interconnected microbiomes and resistomes in low-income human habitats.}, journal = {Nature}, volume = {533}, number = {7602}, pages = {212-216}, pmid = {27172044}, issn = {1476-4687}, support = {MR/K007467/1/MRC_/Medical Research Council/United Kingdom ; R01 GM099538/GM/NIGMS NIH HHS/United States ; R01-GM099538/GM/NIGMS NIH HHS/United States ; }, mesh = {Agriculture ; Bacteria/classification/*genetics ; Developing Countries/*economics ; Drug Resistance, Microbial/*genetics ; *Ecosystem ; El Salvador ; Environmental Monitoring ; Feces/microbiology ; *Gene Transfer, Horizontal ; Humans ; Metagenomics ; Microbiota/*genetics ; Molecular Epidemiology ; Peru ; Phylogeny ; Residence Characteristics ; Risk Assessment ; Sewage/microbiology ; Socioeconomic Factors ; }, abstract = {Antibiotic-resistant infections annually claim hundreds of thousands of lives worldwide. This problem is exacerbated by exchange of resistance genes between pathogens and benign microbes from diverse habitats. Mapping resistance gene dissemination between humans and their environment is a public health priority. Here we characterized the bacterial community structure and resistance exchange networks of hundreds of interconnected human faecal and environmental samples from two low-income Latin American communities. We found that resistomes across habitats are generally structured by bacterial phylogeny along ecological gradients, but identified key resistance genes that cross habitat boundaries and determined their association with mobile genetic elements. We also assessed the effectiveness of widely used excreta management strategies in reducing faecal bacteria and resistance genes in these settings representative of low- and middle-income countries. Our results lay the foundation for quantitative risk assessment and surveillance of resistance gene dissemination across interconnected habitats in settings representing over two-thirds of the world's population.}, } @article {pmid27171468, year = {2016}, author = {Yang, C and Powell, CA and Duan, Y and Shatters, R and Fang, J and Zhang, M}, title = {Deciphering the Bacterial Microbiome in Huanglongbing-Affected Citrus Treated with Thermotherapy and Sulfonamide Antibiotics.}, journal = {PloS one}, volume = {11}, number = {5}, pages = {e0155472}, pmid = {27171468}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects ; Biodiversity ; Citrus/*drug effects/*microbiology ; *Hyperthermia, Induced ; Microbiota/*drug effects ; Phylogeny ; Plant Diseases/*microbiology ; Sulfonamides/*pharmacology ; Temperature ; }, abstract = {Huanglongbing (HLB) is a serious citrus disease that threatens the citrus industry. In previous studies, sulfonamide antibiotics and heat treatment suppressed 'Candidatus Liberibacter asiaticus' (Las), but did not completely eliminate the Las. Furthermore, there are few reports studying the bacterial microbiome of HLB-affected citrus treated by heat and sulfonamide antibiotics. In this study, combinations of heat (45°C or 40°C) and sulfonamide treatment (sulfathiazole sodium-STZ, or sulfadimethoxine sodium-SDX) were applied to HLB-affected citrus. The bacterial microbiome of HLB-affected citrus following thermotherapy and/or chemotherapy was characterized by PhyloChipTMG3-based metagenomics. Our results showed that the combination of thermotherapy at 45°C and chemotherapy with STZ and SDX was more effective against HLB than thermotherapy alone, chemotherapy alone, or a combination of thermotherapy at 40°C and chemotherapy. The PhyloChipTMG3-based results indicated that 311 empirical Operational Taxonomic Units (eOTUs) were detected in 26 phyla. Cyanobacteria (18.01%) were dominant after thermo-chemotherapy. Thermotherapy at 45°C decreased eOTUs (64.43%) in leaf samples, compared with thermotherapy at 40°C (73.96%) or without thermotherapy (90.68%) and it also reduced bacterial family biodiversity. The eOTU in phylum Proteobacteria was reduced significantly and eOTU_28, representing "Candidatus Liberibacter," was not detected following thermotherapy at 45°C. Following antibiotic treatment with SDX and STZ, there was enhanced abundance of specific eOTUs belonging to the families Streptomycetaceae, Desulfobacteraceae, Chitinophagaceae, and Xanthomonadaceae, which may be implicated in increased resistance to plant pathogens. Our study further develops an integrated strategy for combating HLB, and also provides new insight into the bacterial microbiome of HLB-affected citrus treated by heat and sulfonamide antibiotics.}, } @article {pmid27171425, year = {2016}, author = {Vogtmann, E and Hua, X and Zeller, G and Sunagawa, S and Voigt, AY and Hercog, R and Goedert, JJ and Shi, J and Bork, P and Sinha, R}, title = {Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing.}, journal = {PloS one}, volume = {11}, number = {5}, pages = {e0155362}, pmid = {27171425}, issn = {1932-6203}, support = {268985/ERC_/European Research Council/International ; }, mesh = {Case-Control Studies ; Colorectal Neoplasms/*genetics/*microbiology ; District of Columbia ; Female ; Gastrointestinal Microbiome/*genetics ; Genome, Human ; Humans ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; *Sequence Analysis, DNA ; }, abstract = {Accumulating evidence indicates that the gut microbiota affects colorectal cancer development, but previous studies have varied in population, technical methods, and associations with cancer. Understanding these variations is needed for comparisons and for potential pooling across studies. Therefore, we performed whole-genome shotgun sequencing on fecal samples from 52 pre-treatment colorectal cancer cases and 52 matched controls from Washington, DC. We compared findings from a previously published 16S rRNA study to the metagenomics-derived taxonomy within the same population. In addition, metagenome-predicted genes, modules, and pathways in the Washington, DC cases and controls were compared to cases and controls recruited in France whose specimens were processed using the same platform. Associations between the presence of fecal Fusobacteria, Fusobacterium, and Porphyromonas with colorectal cancer detected by 16S rRNA were reproduced by metagenomics, whereas higher relative abundance of Clostridia in cancer cases based on 16S rRNA was merely borderline based on metagenomics. This demonstrated that within the same sample set, most, but not all taxonomic associations were seen with both methods. Considering significant cancer associations with the relative abundance of genes, modules, and pathways in a recently published French metagenomics dataset, statistically significant associations in the Washington, DC population were detected for four out of 10 genes, three out of nine modules, and seven out of 17 pathways. In total, colorectal cancer status in the Washington, DC study was associated with 39% of the metagenome-predicted genes, modules, and pathways identified in the French study. More within and between population comparisons are needed to identify sources of variation and disease associations that can be reproduced despite these variations. Future studies should have larger sample sizes or pool data across studies to have sufficient power to detect associations that are reproducible and significant after correction for multiple testing.}, } @article {pmid27169388, year = {2016}, author = {Wagner-Döbler, I}, title = {Biofilm transplantation in the deep sea.}, journal = {Molecular ecology}, volume = {25}, number = {9}, pages = {1905-1907}, doi = {10.1111/mec.13612}, pmid = {27169388}, issn = {1365-294X}, mesh = {Bacteria/genetics ; *Biofilms ; Indian Ocean ; *Metagenome ; Microbiota ; }, abstract = {A gold rush is currently going on in microbial ecology, which is powered by the possibility to determine the full complexity of microbial communities through next-generation sequencing. Accordingly, enormous efforts are underway to describe microbiomes worldwide, in humans, animals, plants, soil, air and the ocean. While much can be learned from these studies, only experiments will finally unravel mechanisms. One of the key questions is how a microbial community is assembled from a pool of bacteria in the environment, and how it responds to change - be it the increase in CO2 concentration in the ocean, or antibiotic treatment of the gut microbiome. The study by Zhang et al. () in this issue is one of the very few that approaches this problem experimentally in the natural environment. The authors selected a habitat which is both extremely interesting and difficult to access. They studied the Thuwal Seep in the Red Sea at 850 m depth and used a remotely operated vehicle (ROV) to place a steel frame carrying substrata for biofilm growth into the brine pool and into the adjacent normal bottom water (NBW). Biofilms were allowed to develop for 3 days, and then those that had been growing in the brine pool were transported to normal bottom water and stayed there for another 3 days, and vice versa. The 'switched' biofilms were then compared with their source communities by metagenome sequencing. Strikingly, both 'switched' biofilms were now dominated by the same two species. These species were able to cope with conditions in both source ecosystems, as shown by assembly of their genomes and detection of expression of key genes. The biofilms had adapted to environmental change, rather than to brine pools or NBW. The study shows both the resilience and adaptability of biofilm communities and has implications for microbial ecology in general and even for therapeutic approaches such as transplantation of faecal microbiomes.}, } @article {pmid27167411, year = {2016}, author = {Mikelsaar, M and Sepp, E and Štšepetova, J and Songisepp, E and Mändar, R}, title = {Biodiversity of Intestinal Lactic Acid Bacteria in the Healthy Population.}, journal = {Advances in experimental medicine and biology}, volume = {932}, number = {}, pages = {1-64}, pmid = {27167411}, issn = {0065-2598}, mesh = {Biodiversity ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Lactic Acid/metabolism ; Lactobacillus/classification/genetics/*isolation & purification/metabolism ; Probiotics/analysis ; }, abstract = {The complex ecosystem of the gastrointestinal tract involves tight interrelations among host cells, diet, and billions of microbes, both beneficial and opportunistic pathogens. In spite of advanced genomic, metagenomic, and metabonomic approaches, knowledge is still quite limited regarding the biodiversity of beneficial microbiota, including Lactobacillus spp., and its impact on the main biomarkers of general health. In this paper, Lactobacillus biodiversity is demonstrated through its taxonomy, function, and host-microbial interactions. Its prevalence, composition, abundance, intertwined metabolic properties, and relation to host age, genotype, and socioeconomic factors are reviewed based on the literature and original research experience. The species richness, e.g., the biodiversity of gut microbiota, provides the host with a variety of metabolically active species and strains that predict their response for different health conditions and extrinsic interventions. Metabolically active and safe Lactobacillus species and specific strains with particular functional properties increase the biodiversity of the whole intestinal microbiota. The elaborated principles for effective application of probiotics are discussed, aimed at regulating the composition of microbiota simultaneously with blood and urine biomarkers at the borderline of normality. This approach targets the impact of probiotic strains to maintenance of health with anti-infectious, cardiovascular, and metabolic support.}, } @article {pmid27166072, year = {2016}, author = {Milani, C and Ticinesi, A and Gerritsen, J and Nouvenne, A and Lugli, GA and Mancabelli, L and Turroni, F and Duranti, S and Mangifesta, M and Viappiani, A and Ferrario, C and Maggio, M and Lauretani, F and De Vos, W and van Sinderen, D and Meschi, T and Ventura, M}, title = {Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {25945}, pmid = {27166072}, issn = {2045-2322}, mesh = {Aged ; Aged, 80 and over ; Anti-Bacterial Agents/therapeutic use ; Bacteria/*classification/genetics/isolation & purification ; Biodiversity ; Clostridium Infections/*drug therapy/*microbiology ; Cross Infection/*drug therapy/*microbiology ; Cross-Sectional Studies ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Gastrointestinal Microbiome ; Hospitalization ; Humans ; Male ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The gut microbiota composition of elderly hospitalized patients with Clostridium difficile infection (CDI) exposed to previous antibiotic treatment is still poorly investigated. The aim of this study was to compare the microbiota composition by means of 16S rRNA microbial profiling among three groups of hospitalized elderly patients (age ≥ 65) under standard diet including 25 CDI-positive (CDI group), 29 CDI-negative exposed to antibiotic treatment (AB+ group) and 30 CDI-negative subjects not on antibiotic treatment (AB- group). The functional properties of the gut microbiomes of CDI-positive vs CDI-negative subjects were also assessed by shotgun metagenomics. A significantly lower microbial diversity was detected in CDI samples, whose microbiomes clustered separately from CDI-negative specimens. CDI was associated with a significant under-representation of gut commensals with putative protective functionalities, including Bacteroides, Alistipes, Lachnospira and Barnesiella, and over-representation of opportunistic pathogens. These findings were confirmed by functional shotgun metagenomics analyses, including an in-depth profiling of the Peptostreptococcaceae family. In CDI-negative patients, antibiotic treatment was associated with significant depletion of few commensals like Alistipes, but not with a reduction in species richness. A better understanding of the correlations between CDI and the microbiota in high-risk elderly subjects may contribute to identify therapeutic targets for CDI.}, } @article {pmid27159972, year = {2016}, author = {Kristensen, NB and Bryrup, T and Allin, KH and Nielsen, T and Hansen, TH and Pedersen, O}, title = {Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials.}, journal = {Genome medicine}, volume = {8}, number = {1}, pages = {52}, pmid = {27159972}, issn = {1756-994X}, mesh = {Adult ; Bacteria/*classification/genetics ; Feces/*microbiology ; Healthy Volunteers ; Humans ; Microbiota ; Phylogeny ; Probiotics/*administration & dosage/adverse effects ; Randomized Controlled Trials as Topic/standards ; }, abstract = {BACKGROUND: The effects of probiotic supplementation on fecal microbiota composition in healthy adults have not been well established. We aimed to provide a systematic review of the potential evidence for an effect of probiotic supplementation on the composition of human fecal microbiota as assessed by high-throughput molecular approaches in randomized controlled trials (RCTs) of healthy adults.

METHODS: The survey of peer-reviewed papers was performed on 17 August 2015 by a literature search through PubMed, SCOPUS, and ISI Web of Science. Additional papers were identified by checking references of relevant papers. Search terms included healthy adult, probiotic, bifidobacterium, lactobacillus, gut microbiota, fecal microbiota, intestinal microbiota, intervention, and (clinical) trial. RCTs of solely probiotic supplementation and placebo in healthy adults that examined alteration in composition of overall fecal microbiota structure assessed by shotgun metagenomic sequencing, 16S ribosomal RNA sequencing, or phylogenetic microarray methods were included. Independent collection and quality assessment of studies were performed by two authors using predefined criteria including methodological quality assessment of reports of the clinical trials based on revised tools from PRISMA/Cochrane and by the Jadad score.

RESULTS: Seven RCTs investigating the effect of probiotic supplementation on fecal microbiota in healthy adults were identified and included in the present systematic review. The quality of the studies was assessed as medium to high. Still, no effects were observed on the fecal microbiota composition in terms of α-diversity, richness, or evenness in any of the included studies when compared to placebo. Only one study found that probiotic supplementation significantly modified the overall structure of the fecal bacterial community in terms of β-diversity when compared to placebo.

CONCLUSIONS: This systematic review of the pertinent literature demonstrates a lack of evidence for an impact of probiotics on fecal microbiota composition in healthy adults. Future studies would benefit from pre-specifying the primary outcome and transparently reporting the results including effect sizes, confidence intervals, and P values as well as providing a clear distinction of between-group and within-group comparisons.}, } @article {pmid27158046, year = {2016}, author = {Dellagnezze, BM and Vasconcellos, SP and Angelim, AL and Melo, VMM and Santisi, S and Cappello, S and Oliveira, VM}, title = {Bioaugmentation strategy employing a microbial consortium immobilized in chitosan beads for oil degradation in mesocosm scale.}, journal = {Marine pollution bulletin}, volume = {107}, number = {1}, pages = {107-117}, doi = {10.1016/j.marpolbul.2016.04.011}, pmid = {27158046}, issn = {1879-3363}, mesh = {Bacteria/*metabolism ; Biodegradation, Environmental ; Cells, Immobilized/metabolism ; Chitosan ; Hydrocarbons/metabolism ; *Microbial Consortia ; Petroleum/*metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A bacterial consortium composed by four metagenomic clones and Bacillus subtilis strain CBMAI 707, all derived from petroleum reservoirs, was entrapped in chitosan beads and evaluated regarding hydrocarbon degradation capability. Experiments were carried out in mesocosm scale (3000L) with seawater artificially polluted with crude oil. At different time intervals, mesocosms were sampled and subjected to GC-FID and microbiological analyses, as total and heterotrophic culturable bacterial abundance (DAPI and CFU count), biological oxygen demand (BOD) and taxonomic diversity (massive sequencing of 16S rRNA genes). The results obtained showed that degradation of n-alkane hydrocarbons was similar between both treatments. However, aromatic compound degradation was more efficient in bioaugmentation treatment, with biodegradation percentages reaching up to 99% in 30days. Community dynamics was different between treatments and the consortium used in the bioaugmentation treatment contributed to a significant increase in aromatic hydrocarbon degradation.}, } @article {pmid27156744, year = {2016}, author = {Long, PE and Williams, KH and Hubbard, SS and Banfield, JF}, title = {Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes.}, journal = {Trends in microbiology}, volume = {24}, number = {8}, pages = {600-610}, doi = {10.1016/j.tim.2016.04.006}, pmid = {27156744}, issn = {1878-4380}, mesh = {Atmosphere ; Biodiversity ; Carbon/metabolism ; *Climate ; *Ecosystem ; Gases ; Genome, Microbial ; Geologic Sediments ; Greenhouse Effect ; Groundwater ; Metabolic Networks and Pathways/physiology ; *Metagenomics ; Microbial Consortia/genetics/*physiology ; Microbial Interactions/physiology ; Nitrogen/metabolism ; Nitrogen Cycle ; Soil/chemistry ; *Soil Microbiology ; Sulfur/metabolism ; Symbiosis/physiology ; }, abstract = {Microorganisms play key roles in terrestrial system processes, including the turnover of natural organic carbon, such as leaf litter and woody debris that accumulate in soils and subsurface sediments. What has emerged from a series of recent DNA sequencing-based studies is recognition of the enormous variety of little known and previously unknown microorganisms that mediate recycling of these vast stores of buried carbon in subsoil compartments of the terrestrial system. More importantly, the genome resolution achieved in these studies has enabled association of specific members of these microbial communities with carbon compound transformations and other linked biogeochemical processes-such as the nitrogen cycle-that can impact the quality of groundwater, surface water, and atmospheric trace gas concentrations. The emerging view also emphasizes the importance of organism interactions through exchange of metabolic byproducts (e.g., within the carbon, nitrogen, and sulfur cycles) and via symbioses since many novel organisms exhibit restricted metabolic capabilities and an associated extremely small cell size. New, genome-resolved information reshapes our view of subsurface microbial communities and provides critical new inputs for advanced reactive transport models. These inputs are needed for accurate prediction of feedbacks in watershed biogeochemical functioning and their influence on the climate via the fluxes of greenhouse gases, CO2, CH4, and N2O.}, } @article {pmid27154756, year = {2016}, author = {Mitra, N and Cernicchiaro, N and Torres, S and Li, F and Hause, BM}, title = {Metagenomic characterization of the virome associated with bovine respiratory disease in feedlot cattle identified novel viruses and suggests an etiologic role for influenza D virus.}, journal = {The Journal of general virology}, volume = {97}, number = {8}, pages = {1771-1784}, pmid = {27154756}, issn = {1465-2099}, support = {R21 AI107379/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Biodiversity ; Cattle ; Cattle Diseases/*virology ; Metagenomics ; Mexico ; Nasal Mucosa/virology ; RNA, Viral/analysis/genetics ; Real-Time Polymerase Chain Reaction ; Respiratory Tract Infections/*veterinary/virology ; United States ; Viral Load ; Virus Diseases/*veterinary/virology ; Viruses/*classification/genetics/*isolation & purification ; }, abstract = {Bovine respiratory disease (BRD) is the most costly disease affecting the cattle industry. The pathogenesis of BRD is complex and includes contributions from microbial pathogens as well as host, environmental and animal management factors. In this study, we utilized viral metagenomic sequencing to explore the virome of nasal swab samples obtained from feedlot cattle with acute BRD and asymptomatic pen-mates at six and four feedlots in Mexico and the USA, respectively, in April-October 2015. Twenty-one viruses were detected, with bovine rhinitis A (52.7 %) and B (23.7 %) virus, and bovine coronavirus (24.7 %) being the most commonly identified. The emerging influenza D virus (IDV) tended to be significantly associated (P=0.134; odds ratio=2.94) with disease, whereas viruses commonly associated with BRD such as bovine viral diarrhea virus, bovine herpesvirus 1, bovine respiratory syncytial virus and bovine parainfluenza 3 virus were detected less frequently. The detection of IDV was further confirmed using a real-time PCR assay. Nasal swabs from symptomatic animals had significantly more IDV RNA than those collected from healthy animals (P=0.04). In addition to known viruses, new genotypes of bovine rhinitis B virus and enterovirus E were identified and a newly proposed species of bocaparvovirus, Ungulate bocaparvovirus 6, was characterized. Ungulate tetraparvovirus 1 was also detected for the first time in North America to our knowledge. These results illustrate the complexity of the virome associated with BRD and highlight the need for further research into the contribution of other viruses to BRD pathogenesis.}, } @article {pmid27154001, year = {2016}, author = {Warnke-Sommer, J and Ali, H}, title = {Graph mining for next generation sequencing: leveraging the assembly graph for biological insights.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {340}, pmid = {27154001}, issn = {1471-2164}, mesh = {Algorithms ; Computational Biology/methods ; DNA Transposable Elements ; Data Mining/*methods ; Drug Resistance, Bacterial/genetics ; Gastrointestinal Microbiome ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/methods ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; *Sequence Analysis, DNA/methods ; *Software ; User-Computer Interface ; }, abstract = {BACKGROUND: The assembly of Next Generation Sequencing (NGS) reads remains a challenging task. This is especially true for the assembly of metagenomics data that originate from environmental samples potentially containing hundreds to thousands of unique species. The principle objective of current assembly tools is to assemble NGS reads into contiguous stretches of sequence called contigs while maximizing for both accuracy and contig length. The end goal of this process is to produce longer contigs with the major focus being on assembly only. Sequence read assembly is an aggregative process, during which read overlap relationship information is lost as reads are merged into longer sequences or contigs. The assembly graph is information rich and capable of capturing the genomic architecture of an input read data set. We have developed a novel hybrid graph in which nodes represent sequence regions at different levels of granularity. This model, utilized in the assembly and analysis pipeline Focus, presents a concise yet feature rich view of a given input data set, allowing for the extraction of biologically relevant graph structures for graph mining purposes.

RESULTS: Focus was used to create hybrid graphs to model metagenomics data sets obtained from the gut microbiomes of five individuals with Crohn's disease and eight healthy individuals. Repetitive and mobile genetic elements are found to be associated with hybrid graph structure. Using graph mining techniques, a comparative study of the Crohn's disease and healthy data sets was conducted with focus on antibiotics resistance genes associated with transposase genes. Results demonstrated significant differences in the phylogenetic distribution of categories of antibiotics resistance genes in the healthy and diseased patients. Focus was also evaluated as a pure assembly tool and produced excellent results when compared against the Meta-velvet, Omega, and UD-IDBA assemblers.

CONCLUSIONS: Mining the hybrid graph can reveal biological phenomena captured by its structure. We demonstrate the advantages of considering assembly graphs as data-mining support in addition to their role as frameworks for assembly.}, } @article {pmid27153496, year = {2016}, author = {Oh, J and Byrd, AL and Park, M and , and Kong, HH and Segre, JA}, title = {Temporal Stability of the Human Skin Microbiome.}, journal = {Cell}, volume = {165}, number = {4}, pages = {854-866}, pmid = {27153496}, issn = {1097-4172}, support = {Z01 HG000180-08//Intramural NIH HHS/United States ; ZIA BC010938-08//Intramural NIH HHS/United States ; }, mesh = {Bacteria/*classification/isolation & purification ; Bacterial Physiological Phenomena ; DNA Viruses/isolation & purification ; Fungi/*classification/isolation & purification/physiology ; Homeostasis ; Humans ; *Microbiota ; Propionibacterium acnes/isolation & purification ; Skin/*microbiology ; Skin Physiological Phenomena ; Symbiosis ; Virus Physiological Phenomena ; Viruses/*classification/isolation & purification ; }, abstract = {Biogeography and individuality shape the structural and functional composition of the human skin microbiome. To explore these factors' contribution to skin microbial community stability, we generated metagenomic sequence data from longitudinal samples collected over months and years. Analyzing these samples using a multi-kingdom, reference-based approach, we found that despite the skin's exposure to the external environment, its bacterial, fungal, and viral communities were largely stable over time. Site, individuality, and phylogeny were all determinants of stability. Foot sites exhibited the most variability; individuals differed in stability; and transience was a particular characteristic of eukaryotic viruses, which showed little site-specificity in colonization. Strain and single-nucleotide variant-level analysis showed that individuals maintain, rather than reacquire, prevalent microbes from the environment. Longitudinal stability of skin microbial communities generates hypotheses about colonization resistance and empowers clinical studies exploring alterations observed in disease states.}, } @article {pmid27151248, year = {2016}, author = {Candela, M and Biagi, E and Soverini, M and Consolandi, C and Quercia, S and Severgnini, M and Peano, C and Turroni, S and Rampelli, S and Pozzilli, P and Pianesi, M and Fallucca, F and Brigidi, P}, title = {Modulation of gut microbiota dysbioses in type 2 diabetic patients by macrobiotic Ma-Pi 2 diet.}, journal = {The British journal of nutrition}, volume = {116}, number = {1}, pages = {80-93}, pmid = {27151248}, issn = {1475-2662}, mesh = {Adult ; Aged ; Bacteria/*classification ; Diabetes Mellitus, Type 2/*microbiology ; *Diet, Macrobiotic ; Female ; Humans ; Intestines/*microbiology ; Male ; *Microbiota ; Middle Aged ; Overweight ; Young Adult ; }, abstract = {The gut microbiota exerts a role in type 2 diabetes (T2D), and deviations from a mutualistic ecosystem layout are considered a key environmental factor contributing to the disease. Thus, the possibility of improving metabolic control in T2D by correcting gut microbiome dysbioses through diet has been evaluated. Here, we explore the potential of two different energy-restricted dietary approaches - the fibre-rich macrobiotic Ma-Pi 2 diet or a control diet recommended by Italian professional societies for T2D treatment - to correct gut microbiota dysbioses in T2D patients. In a previous 21-d open-label MADIAB trial, fifty-six overweight T2D patients were randomised to the Ma-Pi 2 or the control diet. For the present study, stools were collected before and after intervention from a subset of forty MADIAB participants, allowing us to characterise the gut microbiota by 16S rRNA sequencing and imputed metagenomics. To highlight microbiota dysbioses in T2D, the gut microbiota of thirteen normal-weight healthy controls were characterised. According to our findings, both diets were effective in modulating gut microbiome dysbioses in T2D, resulting in an increase of the ecosystem diversity and supporting the recovery of a balanced community of health-promoting SCFA producers, such as Faecalibacterium, Roseburia, Lachnospira, Bacteroides and Akkermansia. The Ma-Pi 2 diet, but not the control diet, was also effective in counteracting the increase of possible pro-inflammatory groups, such as Collinsella and Streptococcus, in the gut ecosystem, showing the potential to reverse pro-inflammatory dysbioses in T2D, and possibly explaining the greater efficacy in improving the metabolic control.}, } @article {pmid27147260, year = {2016}, author = {Audebert, C and Even, G and Cian, A and , and Loywick, A and Merlin, S and Viscogliosi, E and Chabé, M}, title = {Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {25255}, pmid = {27147260}, issn = {2045-2322}, mesh = {Blastocystis/*growth & development ; Blastocystis Infections/*complications ; Cluster Analysis ; Cross-Sectional Studies ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Dysbiosis/*epidemiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology/*parasitology ; Humans ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Alterations in the composition of commensal bacterial populations, a phenomenon known as dysbiosis, are linked to multiple gastrointestinal disorders, such as inflammatory bowel disease and irritable bowel syndrome, or to infections by diverse enteric pathogens. Blastocystis is one of the most common single-celled eukaryotes detected in human faecal samples. However, the clinical significance of this widespread colonization remains unclear, and its pathogenic potential is controversial. To address the issue of Blastocystis pathogenicity, we investigated the impact of colonization by this protist on the composition of the human gut microbiota. For that purpose, we conducted a cross-sectional study including 48 Blastocystis-colonized patients and 48 Blastocystis-free subjects and performed an Ion Torrent 16S rDNA gene sequencing to decipher the Blastocystis-associated gut microbiota. Here, we report a higher bacterial diversity in faecal microbiota of Blastocystis colonized patients, a higher abundance of Clostridia as well as a lower abundance of Enterobacteriaceae. Our results contribute to suggesting that Blastocystis colonization is usually associated with a healthy gut microbiota, rather than with gut dysbiosis generally observed in metabolic or infectious inflammatory diseases of the lower gastrointestinal tract.}, } @article {pmid27146150, year = {2016}, author = {Nayak, RR and Turnbaugh, PJ}, title = {Mirror, mirror on the wall: which microbiomes will help heal them all?.}, journal = {BMC medicine}, volume = {14}, number = {}, pages = {72}, pmid = {27146150}, issn = {1741-7015}, support = {R01HL122593/HL/NHLBI NIH HHS/United States ; T32 AR007304/AR/NIAMS NIH HHS/United States ; 5T32AR007304-37/AR/NIAMS NIH HHS/United States ; P30 DK098722/DK/NIDDK NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Genome, Human ; Humans ; Metagenomics/methods ; *Microbial Consortia/drug effects/genetics ; Precision Medicine ; }, abstract = {BACKGROUND: Clinicians have known for centuries that there is substantial variability between patients in their response to medications-some individuals exhibit a miraculous recovery while others fail to respond at all. Still others experience dangerous side effects. The hunt for the factors responsible for this variation has been aided by the ability to sequence the human genome, but this just provides part of the picture. Here, we discuss the emerging field of study focused on the human microbiome and how it may help to better predict drug response and improve the treatment of human disease.

DISCUSSION: Various clinical disciplines characterize drug response using either continuous or categorical descriptors that are then correlated to environmental and genetic risk factors. However, these approaches typically ignore the microbiome, which can directly metabolize drugs into downstream metabolites with altered activity, clearance, and/or toxicity. Variations in the ability of each individual's microbiome to metabolize drugs may be an underappreciated source of differences in clinical response. Complementary studies in humans and animal models are necessary to elucidate the mechanisms responsible and to test the feasibility of identifying microbiome-based biomarkers of treatment outcomes. We propose that the predictive power of genetic testing could be improved by taking a more comprehensive view of human genetics that encompasses our human and microbial genomes. Furthermore, unlike the human genome, the microbiome is rapidly altered by diet, pharmaceuticals, and other interventions, providing the potential to improve patient care by re-shaping our associated microbial communities.}, } @article {pmid27144353, year = {2016}, author = {Browne, HP and Forster, SC and Anonye, BO and Kumar, N and Neville, BA and Stares, MD and Goulding, D and Lawley, TD}, title = {Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation.}, journal = {Nature}, volume = {533}, number = {7604}, pages = {543-546}, pmid = {27144353}, issn = {1476-4687}, support = {PF451/MRC_/Medical Research Council/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; G1000214/MRC_/Medical Research Council/United Kingdom ; MR/K000551/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Anaerobiosis ; Bacteria/*classification/drug effects/genetics/*growth & development/isolation & purification ; *Bacterial Typing Techniques ; Cell Culture Techniques ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/genetics/*physiology ; Genome, Bacterial/genetics ; Health ; Humans ; Metagenome/genetics ; Metagenomics ; Oxygen/metabolism/pharmacology ; Phenotype ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Spores, Bacterial/classification/drug effects/growth & development ; }, abstract = {Our intestinal microbiota harbours a diverse bacterial community required for our health, sustenance and wellbeing. Intestinal colonization begins at birth and climaxes with the acquisition of two dominant groups of strict anaerobic bacteria belonging to the Firmicutes and Bacteroidetes phyla. Culture-independent, genomic approaches have transformed our understanding of the role of the human microbiome in health and many diseases. However, owing to the prevailing perception that our indigenous bacteria are largely recalcitrant to culture, many of their functions and phenotypes remain unknown. Here we describe a novel workflow based on targeted phenotypic culturing linked to large-scale whole-genome sequencing, phylogenetic analysis and computational modelling that demonstrates that a substantial proportion of the intestinal bacteria are culturable. Applying this approach to healthy individuals, we isolated 137 bacterial species from characterized and candidate novel families, genera and species that were archived as pure cultures. Whole-genome and metagenomic sequencing, combined with computational and phenotypic analysis, suggests that at least 50-60% of the bacterial genera from the intestinal microbiota of a healthy individual produce resilient spores, specialized for host-to-host transmission. Our approach unlocks the human intestinal microbiota for phenotypic analysis and reveals how a marked proportion of oxygen-sensitive intestinal bacteria can be transmitted between individuals, affecting microbiota heritability.}, } @article {pmid27142672, year = {2016}, author = {Pataky, Z and Genton, L and Spahr, L and Lazarevic, V and Terraz, S and Gaïa, N and Rubbia-Brandt, L and Golay, A and Schrenzel, J and Pichard, C}, title = {Impact of Hypocaloric Hyperproteic Diet on Gut Microbiota in Overweight or Obese Patients with Nonalcoholic Fatty Liver Disease: A Pilot Study.}, journal = {Digestive diseases and sciences}, volume = {61}, number = {9}, pages = {2721-2731}, pmid = {27142672}, issn = {1573-2568}, mesh = {Adipose Tissue/diagnostic imaging ; Alanine Transaminase/metabolism ; Aspartate Aminotransferases/metabolism ; Bacteroides/genetics ; Blood Glucose/metabolism ; Body Composition ; C-Reactive Protein/metabolism ; *Caloric Restriction ; Cholesterol/metabolism ; Cholesterol, HDL/metabolism ; Cholesterol, LDL/metabolism ; Classification ; Clostridiales/genetics ; Cohort Studies ; DNA, Bacterial/analysis ; Dietary Proteins/*therapeutic use ; Electric Impedance ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Intra-Abdominal Fat/diagnostic imaging ; Liver/diagnostic imaging ; Magnetic Resonance Imaging ; Male ; Metagenomics ; Middle Aged ; Non-alcoholic Fatty Liver Disease/*diet therapy/metabolism/microbiology ; Obesity/*diet therapy/metabolism/microbiology ; Overweight/diet therapy/metabolism/microbiology ; Pilot Projects ; Prospective Studies ; Sequence Analysis, DNA ; Triglycerides/metabolism ; gamma-Glutamyltransferase/metabolism ; }, abstract = {BACKGROUND: NAFLD is likely to become the most common cause of chronic liver disease. The first-line treatment includes weight loss.

AIMS: To analyze the impact of a hypocaloric hyperproteic diet (HHD) on gut microbiota in NAFLD patients.

METHODS: Fifteen overweight/obese patients with NAFLD were included. At baseline and after a 3-week HHD (Eurodiets(®), ~1000 kcal/day, ~125 g protein/day), we measured gut microbiota composition and function by shotgun metagenomics; body weight; body composition by bioelectrical impedance analysis; liver and visceral fat by magnetic resonance imaging; plasma C-reactive protein (CRP); and liver tests. Results between both time points, expressed as median (first and third quartile), were compared by Wilcoxon signed-rank tests.

RESULTS: At baseline, age was 50 (47-55) years and body mass index 34.6 (32.4, 36.7) kg/m(2). HDD decreased body weight by 3.6 % (p < 0.001), percent liver fat by 65 % (p < 0.001), and CRP by 19 % (p = 0.014). HDD was associated with a decrease in Lachnospira (p = 0.019), an increase in Blautia (p = 0.026), Butyricicoccus (p = 0.024), and changes in several operational taxonomic units (OTUs) of Bacteroidales and Clostridiales. The reduced liver fat was negatively correlated with bacteria belonging to the Firmicutes and Bacteroidetes phyla (a Ruminococcaceae OTU, r = -0.83; Bacteroides, r = -0.73). The associated metabolic changes concerned mostly enzymes involved in amino acid and carbohydrate metabolism.

CONCLUSIONS: In this pilot study, HHD changes gut microbiota composition and function in overweight/obese NAFLD patients, in parallel with decreased body weight, liver fat, and systemic inflammation. Future studies should aim to confirm these bacterial changes and understand their mode of action.

TRAIL REGISTRATION: Under clinicaltrials.gov: NCT01477307.}, } @article {pmid27142586, year = {2016}, author = {Krishna, P and Jain, A and Bisen, PS}, title = {Microbiome diversity in the sputum of patients with pulmonary tuberculosis.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {35}, number = {7}, pages = {1205-1210}, pmid = {27142586}, issn = {1435-4373}, mesh = {Adult ; Aged ; Biodiversity ; Case-Control Studies ; Cluster Analysis ; Female ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Mycobacterium tuberculosis ; RNA, Ribosomal, 16S/genetics ; Sputum/*microbiology ; Tuberculosis, Pulmonary/diagnosis/*microbiology ; Young Adult ; }, abstract = {TB is a worldwide pandemic. India has the highest burden of TB, with WHO statistics for 2013 giving an estimated incidence figure of 2.1 million cases for India out of a global incidence of 9 million. Microbiota have been shown to be associated with many disease conditions; however, only few studies have been reported for microbiota associated with TB infection. For the first time, we characterized the composition of microbiota of TB patients of India, using high-throughput 16S rRNA gene sequencing and compared it with healthy controls. Phylum-level analysis showed that the relative abundance of Firmicutes and Actinobacteria was significantly higher in TB samples and Neisseria and Veillonella were two dominant genera after Streptococcus. In our study, significantly different core genera in TB and normal population were found as compared with the reported studies. Also, the presence of diverse opportunistic pathogenic microbiota in TB patients increases the complexity and diversity of sputum microbiota. Characterization of the sputum microbiome is likely to provide important pathogenic insights into pulmonary tuberculosis.}, } @article {pmid27142181, year = {2016}, author = {Galloway-Peña, JR and Smith, DP and Sahasrabhojane, P and Ajami, NJ and Wadsworth, WD and Daver, NG and Chemaly, RF and Marsh, L and Ghantoji, SS and Pemmaraju, N and Garcia-Manero, G and Rezvani, K and Alousi, AM and Wargo, JA and Shpall, EJ and Futreal, PA and Guindani, M and Petrosino, JF and Kontoyiannis, DP and Shelburne, SA}, title = {The role of the gastrointestinal microbiome in infectious complications during induction chemotherapy for acute myeloid leukemia.}, journal = {Cancer}, volume = {122}, number = {14}, pages = {2186-2196}, pmid = {27142181}, issn = {1097-0142}, support = {L30 CA209245/CA/NCI NIH HHS/United States ; P30 CA016672/CA/NCI NIH HHS/United States ; T32 CA096520/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Biodiversity ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Induction Chemotherapy/*adverse effects ; Infections/diagnosis/*etiology ; Leukemia, Myeloid, Acute/*complications/drug therapy ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Prognosis ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {BACKGROUND: Despite increasing data on the impact of the microbiome on cancer, the dynamics and role of the microbiome in infection during therapy for acute myelogenous leukemia (AML) are unknown. Therefore, the authors sought to determine correlations between microbiome composition and infectious outcomes in patients with AML who were receiving induction chemotherapy (IC).

METHODS: Buccal and fecal specimens (478 samples) were collected twice weekly from 34 patients with AML who were undergoing IC. Oral and stool microbiomes were characterized by 16S ribosomal RNA V4 sequencing using an Illumina MiSeq system. Microbial diversity and genera composition were associated with clinical outcomes.

RESULTS: Baseline stool α-diversity was significantly lower in patients who developed infections during IC compared with those who did not (P = .047). Significant decreases in both oral and stool microbial α-diversity were observed over the course of IC, with a linear correlation between α-diversity change at the 2 sites (P = .02). Loss of both oral and stool α-diversity was associated significantly with the receipt of a carbapenem P < 0.001. Domination events by the majority of genera were transient (median duration, 1 sample), whereas the number of domination events by pathogenic genera increased significantly over the course of IC (P = .002). Moreover, patients who lost microbial diversity over the course of IC were significantly more likely to contract a microbiologically documented infection within the 90 days after IC neutrophil recovery (P = .04).

CONCLUSIONS: The current data present the largest longitudinal analyses to date of oral and stool microbiomes in patients with AML and suggest that microbiome measurements could assist with the mitigation of infectious complications of AML therapy. Cancer 2016;122:2186-96. © 2016 American Cancer Society.}, } @article {pmid27140533, year = {2016}, author = {Lemas, DJ and Young, BE and Baker, PR and Tomczik, AC and Soderborg, TK and Hernandez, TL and de la Houssaye, BA and Robertson, CE and Rudolph, MC and Ir, D and Patinkin, ZW and Krebs, NF and Santorico, SA and Weir, T and Barbour, LA and Frank, DN and Friedman, JE}, title = {Alterations in human milk leptin and insulin are associated with early changes in the infant intestinal microbiome.}, journal = {The American journal of clinical nutrition}, volume = {103}, number = {5}, pages = {1291-1300}, pmid = {27140533}, issn = {1938-3207}, support = {K12 HD057022/HD/NICHD NIH HHS/United States ; T32 GM008497/GM/NIGMS NIH HHS/United States ; T32 HD007186/HD/NICHD NIH HHS/United States ; UL1 TR001082/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Biomarkers/blood ; Body Composition ; Body Mass Index ; Breast Feeding ; Cohort Studies ; Cross-Sectional Studies ; Fatty Acids, Volatile/analysis ; Feces/chemistry ; Female ; Gammaproteobacteria/isolation & purification ; *Gastrointestinal Microbiome ; Humans ; Infant ; Insulin/*analysis ; Lactobacillales/isolation & purification ; Leptin/*analysis ; Linear Models ; Male ; Milk, Human/*chemistry ; Multivariate Analysis ; Obesity/blood/prevention & control ; Plethysmography ; Pyruvate Kinase/blood ; Risk Factors ; }, abstract = {BACKGROUND: Increased maternal body mass index (BMI) is a robust risk factor for later pediatric obesity. Accumulating evidence suggests that human milk (HM) may attenuate the transfer of obesity from mother to offspring, potentially through its effects on early development of the infant microbiome.

OBJECTIVES: Our objective was to identify early differences in intestinal microbiota in a cohort of breastfeeding infants born to obese compared with normal-weight (NW) mothers. We also investigated relations between HM hormones (leptin and insulin) and both the taxonomic and functional potentials of the infant microbiome.

DESIGN: Clinical data and infant stool and fasting HM samples were collected from 18 NW [prepregnancy BMI (in kg/m(2)) <24.0] and 12 obese (prepregnancy BMI >30.0) mothers and their exclusively breastfed infants at 2 wk postpartum. Infant body composition at 2 wk was determined by air-displacement plethysmography. Infant gastrointestinal microbes were estimated by using 16S amplicon and whole-genome sequencing. HM insulin and leptin were determined by ELISA; short-chain fatty acids (SCFAs) were measured in stool samples by using gas chromatography. Power was set at 80%.

RESULTS: Infants born to obese mothers were exposed to 2-fold higher HM insulin and leptin concentrations (P < 0.01) and showed a significant reduction in the early pioneering bacteria Gammaproteobacteria (P = 0.03) and exhibited a trend for elevated total SCFA content (P < 0.06). Independent of maternal prepregnancy BMI, HM insulin was positively associated with both microbial taxonomic diversity (P = 0.03) and Gammaproteobacteria (e.g., Enterobacteriaceae; P = 0.04) and was negatively associated with Lactobacillales (e.g., Streptococcaceae; P = 0.05). Metagenomic analysis showed that HM leptin and insulin were associated with decreased bacterial proteases, which are implicated in intestinal permeability, and reduced concentrations of pyruvate kinase, a biomarker of pediatric gastrointestinal inflammation.

CONCLUSION: Our results indicate that, although maternal obesity may adversely affect the early infant intestinal microbiome, HM insulin and leptin are independently associated with beneficial microbial metabolic pathways predicted to increase intestinal barrier function and reduce intestinal inflammation. This trial was registered at clinicaltrials.gov as NCT01693406.}, } @article {pmid27138203, year = {2016}, author = {Aydin, S}, title = {Microbial sequencing methods for monitoring of anaerobic treatment of antibiotics to optimize performance and prevent system failure.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {12}, pages = {5313-5321}, doi = {10.1007/s00253-016-7533-5}, pmid = {27138203}, issn = {1432-0614}, mesh = {Anaerobiosis ; Anti-Bacterial Agents/*metabolism/*pharmacology ; Bioreactors ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/methods ; Microbial Consortia/*genetics/*physiology ; Phylogeny ; Sewage ; Waste Disposal, Fluid ; }, abstract = {As a result of developments in molecular technologies and the use of sequencing technologies, the analyses of the anaerobic microbial community in biological treatment process has become increasingly prevalent. This review examines the ways in which microbial sequencing methods can be applied to achieve an extensive understanding of the phylogenetic and functional characteristics of microbial assemblages in anaerobic reactor if the substrate is contaminated by antibiotics which is one of the most important toxic compounds. It will discuss some of the advantages and disadvantages associated with microbial sequencing techniques that are more commonly employed and will assess how a combination of the existing methods may be applied to develop a more comprehensive understanding of microbial communities and improve the validity and depth of the results for the enhancement of the stability of anaerobic reactors.}, } @article {pmid27136381, year = {2016}, author = {Ericsson, AC and Personett, AR and Grobman, ME and Rindt, H and Reinero, CR}, title = {Composition and Predicted Metabolic Capacity of Upper and Lower Airway Microbiota of Healthy Dogs in Relation to the Fecal Microbiota.}, journal = {PloS one}, volume = {11}, number = {5}, pages = {e0154646}, pmid = {27136381}, issn = {1932-6203}, support = {K01 OD019924/OD/NIH HHS/United States ; }, mesh = {Animals ; Bronchoalveolar Lavage Fluid/microbiology ; Clostridium/classification/genetics ; Dogs ; Feces/*microbiology ; Female ; Flavobacterium/classification/genetics ; Gemella/classification/genetics ; Lactobacillus/classification/genetics ; Lung/microbiology ; Microbiota/genetics ; Phylogeny ; Porphyromonas/classification/genetics ; Propionibacterium acnes/classification/genetics ; Prospective Studies ; Proteobacteria/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Respiratory System/*microbiology ; Riemerella/classification/genetics ; }, abstract = {The upper and lower airways of healthy humans are reported to harbor stable and consistent bacterial populations, and the composition of these communities is altered in individuals affected with several respiratory diseases. Data regarding the presence of airway microbiota in other animals are scant and a better understanding of the composition and metabolic function of such bacterial populations is essential for the development of novel therapeutic and diagnostic modalities for use in both veterinary and human medicine. Based on targeted next-generation sequencing of feces and samples collected at multiple levels of the airways from 16 healthy female dogs, we demonstrate that canine airways harbor a topographically continuous microbiota with increasing relative abundance of proteobacterial species from the upper to lower airways. The lung-associated microbiota, as assessed via bronchoalveolar lavage fluid (BALF), was the most consistent between dogs and was dominated by three distinct taxa, two of which were resolved to the species level and one to the level of family. The gene content of the nasal, oropharyngeal, and lung-associated microbiota, predicted using the Phylogenetic Investigations into Communities by Reconstruction of Unobserved States (PICRUSt) software, provided information regarding the glyoxylate and citrate cycle metabolic pathways utilized by these bacterial populations to colonize such nutrient-poor, low-throughput environments. These data generated in healthy subjects provide context for future analysis of diseased canine airways. Moreover, as dogs have similar respiratory anatomy, physiology, and immune systems as humans, are exposed to many of the same environmental stimuli, and spontaneously develop similar respiratory diseases, these data support the use of dogs as a model species for prospective studies of the airway microbiota, with findings translatable to the human condition.}, } @article {pmid27130534, year = {2016}, author = {Putignani, L and Dallapiccola, B}, title = {Foodomics as part of the host-microbiota-exposome interplay.}, journal = {Journal of proteomics}, volume = {147}, number = {}, pages = {3-20}, doi = {10.1016/j.jprot.2016.04.033}, pmid = {27130534}, issn = {1876-7737}, mesh = {Diet/*trends ; Gastrointestinal Microbiome ; Gene Expression Profiling/methods ; Humans ; Metabolomics/methods ; *Microbiota ; Nutritional Status ; Proteomics/methods ; Systems Biology/*methods ; }, abstract = {UNLABELLED: The functional complexity of human gut microbiota and its relationship with host physiology and environmental modulating factors, offers the opportunity to investigate (i) the host and microbiota role in organism-environment relationship; (ii) the individual functional diversity and response to environmental stimuli (exposome); (iii) the host genome and microbiota metagenomes' modifications by diet-mediated epigenomic controls (nutriepigenomics); and (iv) the genotype-phenotype "trajectories" under physiological and disease constraints. Systems biology-based approaches aim at integrating biological data at cellular, tissue and organ organization levels, using computational modeling to interpret diseases' physiopathological mechanisms (i.e., onset and progression). Proteomics improves the existing gene models by profiling molecular phenotypes at protein abundance level, by analyzing post-translational modifications and protein-protein interactions and providing specific pathway information, hence contributing to functional molecular networks. Transcriptomics and metabolomics may determine host ad microbiota changes induced by food ingredients at molecular level, complementing functional genomics and proteomics data. Since foodomics is an -omic wide methodology may feed back all integrative data to foster the omics-based systems medicine field. Hence, coupled to ecological genomics of gut microbial communities, foodomics may highlight health benefits from nutrients, dissecting diet-induced gut microbiota eubiosis mechanisms and significantly contributing to understand and prevent complex disease phenotypes.

BIOLOGICAL SIGNIFICANCE: Besides transcriptomics and proteomics there is a growing interest in applying metabolic profiling to food science for the development of functional foods. Indeed, one of the biggest challenges of modern nutrition is to propose a healthy diet to populations worldwide, intrinsically respecting the high inter-individual variability, driven by complex host/nutrients/microbiota/environment interactions. Therefore, metabolic profiling can assist at various levels for the development of functional foods, starting from screening for food composition to identification of new biomarkers to trace food intake. This current approach can support diet intervention strategies, epidemiological studies, and controlling of metabolic disorders worldwide spreading, hence ensuring healthy aging. With high-throughput molecular technologies driving foodomics, studying bidirectional interactions of host-microbial co-metabolism, innate immune development, dysfunctional nutrient absorption and processing, complex signaling pathways involved in nutritional metabolism, is now likely. In all cases, as microbiome pipeline efforts continue, it is possible that enhanced standardized protocols can be developed, which may lead to new testable biological and clinical hypotheses. This Review provides a comprehensive update on the current state-of-the-art of the integrated -omics route in food, microbiota and host co-metabolism studies, which may revolutionize the design of new dietary intervention strategies.}, } @article {pmid27129965, year = {2016}, author = {Stellato, G and La Storia, A and De Filippis, F and Borriello, G and Villani, F and Ercolini, D}, title = {Overlap of Spoilage-Associated Microbiota between Meat and the Meat Processing Environment in Small-Scale and Large-Scale Retail Distributions.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {13}, pages = {4045-4054}, pmid = {27129965}, issn = {1098-5336}, mesh = {Bacteria/*classification/genetics/*isolation & purification ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Food Contamination ; *Food-Processing Industry ; Meat/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {UNLABELLED: Microbial contamination in food processing plants can play a fundamental role in food quality and safety. The aims of this study were to learn more about the possible influence of the meat processing environment on initial fresh meat contamination and to investigate the differences between small-scale retail distribution (SD) and large-scale retail distribution (LD) facilities. Samples were collected from butcheries (n = 20), including LD (n = 10) and SD (n = 10) facilities, over two sampling campaigns. Samples included fresh beef and pork cuts and swab samples from the knife, the chopping board, and the butcher's hand. The microbiota of both meat samples and environmental swabs were very complex, including more than 800 operational taxonomic units (OTUs) collapsed at the species level. The 16S rRNA sequencing analysis showed that core microbiota were shared by 80% of the samples and included Pseudomonas spp., Streptococcus spp., Brochothrix spp., Psychrobacter spp., and Acinetobacter spp. Hierarchical clustering of the samples based on the microbiota showed a certain separation between meat and environmental samples, with higher levels of Proteobacteria in meat. In particular, levels of Pseudomonas and several Enterobacteriaceae members were significantly higher in meat samples, while Brochothrix, Staphylococcus, lactic acid bacteria, and Psychrobacter prevailed in environmental swab samples. Consistent clustering was also observed when metabolic activities were considered by predictive metagenomic analysis of the samples. An increase in carbohydrate metabolism was predicted for the environmental swabs and was consistently linked to Firmicutes, while increases in pathways related to amino acid and lipid metabolism were predicted for the meat samples and were positively correlated with Proteobacteria Our results highlighted the importance of the processing environment in contributing to the initial microbial levels of meat and clearly showed that the type of retail facility (LD or SD) did not apparently affect the contamination.

IMPORTANCE: The study provides an in-depth description of the microbiota of meat and meat processing environments. It highlights the importance of the environment as a contamination source of spoilage bacteria, and it shows that the size of the retail facility does not affect the level and type of contamination.}, } @article {pmid27129691, year = {2017}, author = {Al Khodor, S and Shatat, IF}, title = {Gut microbiome and kidney disease: a bidirectional relationship.}, journal = {Pediatric nephrology (Berlin, Germany)}, volume = {32}, number = {6}, pages = {921-931}, pmid = {27129691}, issn = {1432-198X}, mesh = {Carbon/therapeutic use ; Child ; Dietary Supplements ; Disease Progression ; Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/*physiology ; Humans ; Hypertension/*physiopathology ; Indican/toxicity ; Indoles/metabolism ; Oxides/therapeutic use ; Renal Dialysis ; Renal Insufficiency, Chronic/*physiopathology/*therapy ; }, abstract = {Recent technological advances and efforts, including powerful metagenomic and metatranscriptomic analyses, have led to a tremendous growth in our understanding of microbial communities. Changes in microbial abundance or composition of human microbial communities impact human health or disease state. However, explorations into the mechanisms underlying host-microbe interactions in health and disease are still in their infancy. Although changes in the gut microbiota have been described in patients with kidney disease, the relationships between pathogenesis, mechanisms of disease progression, and the gut microbiome are still evolving. Here, we review changes in the host-microbiome symbiotic relationship in an attempt to explore the bidirectional relationship in which alterations in the microbiome affect kidney disease progression and how kidney disease may disrupt a balanced microbiome. We also discuss potential targeted interventions that may help re-establish this symbiosis and propose more effective ways to deploy traditional treatments in patients with kidney disease.}, } @article {pmid27126590, year = {2016}, author = {Patel, T and Bhattacharya, P and Das, S}, title = {Gut microbiota: an Indicator to Gastrointestinal Tract Diseases.}, journal = {Journal of gastrointestinal cancer}, volume = {47}, number = {3}, pages = {232-238}, pmid = {27126590}, issn = {1941-6636}, mesh = {Animals ; Gastrointestinal Diseases/*microbiology ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {PURPOSE: Gut microbiota is predicted to play a key role in manifestation of gastrointestinal tract cancers. The human gastrointestinal tract is a complex and abundant network of microbial community. Gut microbiota depicts the microbe population living in our intestine. Humans harbour more than 10(14) microbes in the gut, and the diversity and densities of the microbiota increase from stomach to colon.

METHODS: The beneficial relationship between endogenous microbiota and the eukaryotic hosts helps in maintaining various metabolic activities of the body as well as temperature and pH balance. Studies using culturing methods have suggested that the oesophagus is either sterile or contains only a few transient microbes that originates from the oropharynx by swallowing or from the stomach by gastroesophageal reflux. However, metagenomics suggest that large numbers of uncultured organisms are harboured in the human gut.

RESULTS: Observations suggest that research directed towards manipulation of the gut microbiota can be employed in prevention as well as treatment of these conditions. Well-designed, randomized, placebo-controlled human studies using probiotics and/or prebiotics are necessary to formulate the directions for prevention and therapy.

CONCLUSIONS: Change in gut microbes in gastrointestinal (GI) tract may have major implication in gastric cancer, the fifth most occurring malignancy in the world. Affected population manifests multiple conditions and diseases, which majorly includes inflammatory bowel disease and colorectal malignancy.}, } @article {pmid27126064, year = {2016}, author = {Li, Y and Jia, Z and Sun, Q and Zhan, J and Yang, Y and Wang, D}, title = {Ecological restoration alters microbial communities in mine tailings profiles.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {25193}, pmid = {27126064}, issn = {2045-2322}, mesh = {Bacteria/*classification/*isolation & purification ; *Biota ; *Environmental Restoration and Remediation ; Metagenomics ; Poaceae/*growth & development ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0-30 cm soils and altered the bacterial communities at 0-20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30-60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0-20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings.}, } @article {pmid27126044, year = {2016}, author = {Li, SS and Zhu, A and Benes, V and Costea, PI and Hercog, R and Hildebrand, F and Huerta-Cepas, J and Nieuwdorp, M and Salojärvi, J and Voigt, AY and Zeller, G and Sunagawa, S and de Vos, WM and Bork, P}, title = {Durable coexistence of donor and recipient strains after fecal microbiota transplantation.}, journal = {Science (New York, N.Y.)}, volume = {352}, number = {6285}, pages = {586-589}, doi = {10.1126/science.aad8852}, pmid = {27126044}, issn = {1095-9203}, mesh = {Bacteria/classification/isolation & purification ; Clostridium Infections/microbiology/*therapy ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Symbiosis ; Tissue Donors ; Transplantation, Homologous ; }, abstract = {Fecal microbiota transplantation (FMT) has shown efficacy in treating recurrent Clostridium difficile infection and is increasingly being applied to other gastrointestinal disorders, yet the fate of native and introduced microbial strains remains largely unknown. To quantify the extent of donor microbiota colonization, we monitored strain populations in fecal samples from a recent FMT study on metabolic syndrome patients using single-nucleotide variants in metagenomes. We found extensive coexistence of donor and recipient strains, persisting 3 months after treatment. Colonization success was greater for conspecific strains than for new species, the latter falling within fluctuation levels observed in healthy individuals over a similar time frame. Furthermore, same-donor recipients displayed varying degrees of microbiota transfer, indicating individual patterns of microbiome resistance and donor-recipient compatibilities.}, } @article {pmid27126040, year = {2016}, author = {Zhernakova, A and Kurilshikov, A and Bonder, MJ and Tigchelaar, EF and Schirmer, M and Vatanen, T and Mujagic, Z and Vila, AV and Falony, G and Vieira-Silva, S and Wang, J and Imhann, F and Brandsma, E and Jankipersadsing, SA and Joossens, M and Cenit, MC and Deelen, P and Swertz, MA and , and Weersma, RK and Feskens, EJ and Netea, MG and Gevers, D and Jonkers, D and Franke, L and Aulchenko, YS and Huttenhower, C and Raes, J and Hofker, MH and Xavier, RJ and Wijmenga, C and Fu, J}, title = {Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.}, journal = {Science (New York, N.Y.)}, volume = {352}, number = {6285}, pages = {565-569}, pmid = {27126040}, issn = {1095-9203}, support = {310372/ERC_/European Research Council/International ; 322698/ERC_/European Research Council/International ; P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics/isolation & purification ; Chromogranin A/analysis/metabolism ; Diet ; Enteroendocrine Cells/metabolism ; Feces/chemistry/microbiology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Genetic Markers ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; Netherlands ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Deep sequencing of the gut microbiomes of 1135 participants from a Dutch population-based cohort shows relations between the microbiome and 126 exogenous and intrinsic host factors, including 31 intrinsic factors, 12 diseases, 19 drug groups, 4 smoking categories, and 60 dietary factors. These factors collectively explain 18.7% of the variation seen in the interindividual distance of microbial composition. We could associate 110 factors to 125 species and observed that fecal chromogranin A (CgA), a protein secreted by enteroendocrine cells, was exclusively associated with 61 microbial species whose abundance collectively accounted for 53% of microbial composition. Low CgA concentrations were seen in individuals with a more diverse microbiome. These results are an important step toward a better understanding of environment-diet-microbe-host interactions.}, } @article {pmid27125906, year = {2016}, author = {Clavel, T and Lagkouvardos, I and Hiergeist, A}, title = {Microbiome sequencing: challenges and opportunities for molecular medicine.}, journal = {Expert review of molecular diagnostics}, volume = {16}, number = {7}, pages = {795-805}, doi = {10.1080/14737159.2016.1184574}, pmid = {27125906}, issn = {1744-8352}, mesh = {DNA, Bacterial/chemistry/*genetics ; *Gastrointestinal Microbiome ; Humans ; Molecular Diagnostic Techniques/*methods/standards ; Molecular Typing/*methods/standards ; Sequence Analysis, DNA/*methods/standards ; }, abstract = {INTRODUCTION: Since the discovery of Polymerase Chain Reaction and pioneering work on 16S ribosomal RNA genes in the 1980's, the use of molecular techniques to study microbial ecosystems and pathogenic microorganisms has been increasing exponentially. Because microbial communities inhabiting various body sites such as the skin or the intestine can influence our physiology, there has been a massive interest in studying their diversity, functions, and role in the development of acute and chronic diseases.

AREA COVERED: In the present review, we gather knowledge on sequencing approaches to study microbial communities, especially human body microbiota, and give opinions on their potential and limitations, particularly with respect to clinical applications. Expert commentary: High-throughput sequencing delivered unprecedented views on complex microbial communities, but their popularization is accompanied by substantial technical hurdles that will need to be overcome for efficient implementation in routine clinical procedures.}, } @article {pmid27125587, year = {2016}, author = {Park, CH and Han, DS and Oh, YH and Lee, AR and Lee, YR and Eun, CS}, title = {Role of Fusobacteria in the serrated pathway of colorectal carcinogenesis.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {25271}, pmid = {27125587}, issn = {2045-2322}, mesh = {Adenoma/*microbiology/*physiopathology ; Aged ; *Carcinogenesis ; Cluster Analysis ; Colorectal Neoplasms/*microbiology/*physiopathology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Fusobacteria/*pathogenicity ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Fusobacteria are associated with colorectal cancer (CRC) and are amplified during colorectal carcinogenesis. Compared to the adenoma-carcinoma sequence of carcinogenesis, serrated neoplasm has distinct clinical features and a different molecular background. We aimed to compare the gut microbiome between tubular adenoma (TA) and sessile serrated adenoma/polyp (SSA/P). Patients with TA, SSA/P, or CRC were recruited. Three pieces of colorectal mucosal tissue were obtained from each patient by endoscopic biopsy. 16S rRNA gene pyrosequencing and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) were performed. Among 26 enrolled patients, 8, 10, and 8 had TA, SSA/P, and CRC, respectively. The relative abundance of Fusobacteria did not differ significantly between the TA and SSA/P groups (4.3% and 1.9%, P = 0.739) but was higher in the CRC group (33.8%) than in the TA or SSA/P group, respectively (TA vs. CRC, P = 0.002, false discovery rate [FDR] = 0.023; SSA/P vs. CRC, P < 0.001, FDR = 0.001). PICRUSt revealed that most functions in the TA metagenome were similar to those in the SSA/P metagenome. The gut microbiome, including relative abundance of Fusobacteria, did not differ between TA and SSA/P, suggesting that Fusobacteria may contribute to both the serrated pathway and the adenoma-carcinoma sequence.}, } @article {pmid27124954, year = {2016}, author = {Mahana, D and Trent, CM and Kurtz, ZD and Bokulich, NA and Battaglia, T and Chung, J and Müller, CL and Li, H and Bonneau, RA and Blaser, MJ}, title = {Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet.}, journal = {Genome medicine}, volume = {8}, number = {1}, pages = {48}, pmid = {27124954}, issn = {1756-994X}, support = {P30 CA016087/CA/NCI NIH HHS/United States ; 5T32AI007180-30/AI/NIAID NIH HHS/United States ; T32 AI007180/AI/NIAID NIH HHS/United States ; P30CA016087/CA/NCI NIH HHS/United States ; R01 DK090989/DK/NIDDK NIH HHS/United States ; }, mesh = {*Adiposity/drug effects ; Animals ; Anti-Bacterial Agents/*pharmacology ; Biodiversity ; Body Composition ; Body Weight ; Cytokines/blood ; Diet, High-Fat/*adverse effects ; Disease Models, Animal ; Energy Metabolism/drug effects ; Gastrointestinal Microbiome/*drug effects ; Glucose/metabolism ; Homeostasis/drug effects ; Hormones/blood ; Inflammation Mediators/blood ; Insulin/metabolism ; *Insulin Resistance ; Lipid Metabolism ; Liver Diseases/*etiology/*metabolism/microbiology ; Metagenome ; Metagenomics ; Mice ; Non-alcoholic Fatty Liver Disease/etiology/metabolism/microbiology ; Phenotype ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Time Factors ; }, abstract = {BACKGROUND: Obesity, type 2 diabetes, and non-alcoholic fatty liver disease (NAFLD) are serious health concerns, especially in Western populations. Antibiotic exposure and high-fat diet (HFD) are important and modifiable factors that may contribute to these diseases.

METHODS: To investigate the relationship of antibiotic exposure with microbiome perturbations in a murine model of growth promotion, C57BL/6 mice received lifelong sub-therapeutic antibiotic treatment (STAT), or not (control), and were fed HFD starting at 13 weeks. To characterize microbiota changes caused by STAT, the V4 region of the 16S rRNA gene was examined from collected fecal samples and analyzed.

RESULTS: In this model, which included HFD, STAT mice developed increased weight and fat mass compared to controls. Although results in males and females were not identical, insulin resistance and NAFLD were more severe in the STAT mice. Fecal microbiota from STAT mice were distinct from controls. Compared with controls, STAT exposure led to early conserved diet-independent microbiota changes indicative of an immature microbial community. Key taxa were identified as STAT-specific and several were found to be predictive of disease. Inferred network models showed topological shifts concurrent with growth promotion and suggest the presence of keystone species.

CONCLUSIONS: These studies form the basis for new models of type 2 diabetes and NAFLD that involve microbiome perturbation.}, } @article {pmid27124615, year = {2016}, author = {Kasparovska, J and Pecinkova, M and Dadakova, K and Krizova, L and Hadrova, S and Lexa, M and Lochman, J and Kasparovsky, T}, title = {Effects of Isoflavone-Enriched Feed on the Rumen Microbiota in Dairy Cows.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0154642}, pmid = {27124615}, issn = {1932-6203}, mesh = {Animal Feed/*analysis ; Animal Nutritional Physiological Phenomena/drug effects ; Animals ; Bacteria/*classification/genetics/*isolation & purification ; Bacteroidetes/genetics/isolation & purification ; Betaproteobacteria/genetics/isolation & purification ; Burkholderiaceae/genetics/isolation & purification ; Cattle ; Diet/*veterinary ; *Dietary Supplements ; Female ; Firmicutes/genetics/isolation & purification ; Isoflavones/*pharmacology ; Lactation ; Microbiota ; Milk/*chemistry ; Planctomycetales/genetics/isolation & purification ; Plant Extracts ; Poaceae ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Silage ; Glycine max/metabolism ; Zea mays ; }, abstract = {In this study, we compared the effects of two diets containing different isoflavone concentrations on the isoflavone transfer from feed into milk and on the rumen microbiota in lactating dairy cows. The on-farm experiment was conducted on twelve lactating Czech Fleckvieh x Holstein cows divided into two groups, each with similar mean milk yield. Twice daily, cows were individually fed a diet based on maize silage, meadow hay and supplemental mixture. Control group (CTRL) received the basal diet while the experimental group (EXP) received the basal diet supplemented with 40% soybean isoflavone extract. The average daily isoflavone intake in the EXP group (16 g/day) was twice as high as that in the CTRL group (8.4 g/day, P<0.001). Total isoflavone concentrations in milk from the CTRL and EXP groups were 96.89 and 276.07 μg/L, respectively (P<0.001). Equol concentrations in milk increased from 77.78 μg/L in the CTRL group to 186.30 μg/L in the EXP group (P<0.001). The V3-4 region of bacterial 16S rRNA genes was used for metagenomic analysis of the rumen microbiome. The experimental cows exhibited fewer OTUs at a distance level of 0.03 compared to control cows (P<0.05) and reduced microbial richness compared to control cows based on the calculated Inverse Simpson and Shannon indices. Non-metric multidimensional scaling analysis showed that the major contributor to separation between the experimental and control groups were changes in the representation of bacteria belonging to the phyla Bacteroidetes, Proteobacteria, Firmicutes, and Planctomycetes. Surprisingly, a statistically significant positive correlation was found only between isoflavones and the phyla Burkholderiales (r = 0.65, P<0.05) and unclassified Betaproteobacteria (r = 0.58, P<0.05). Previous mouse and human studies of isoflavone effects on the composition of gastrointestinal microbial populations generally report similar findings.}, } @article {pmid27124399, year = {2016}, author = {Tandon, D and Haque, MM and Mande, SS}, title = {Inferring Intra-Community Microbial Interaction Patterns from Metagenomic Datasets Using Associative Rule Mining Techniques.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0154493}, pmid = {27124399}, issn = {1932-6203}, mesh = {Algorithms ; Data Mining/*methods ; Databases, Genetic ; Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Microbial Interactions ; Web Browser ; }, abstract = {The nature of inter-microbial metabolic interactions defines the stability of microbial communities residing in any ecological niche. Deciphering these interaction patterns is crucial for understanding the mode/mechanism(s) through which an individual microbial community transitions from one state to another (e.g. from a healthy to a diseased state). Statistical correlation techniques have been traditionally employed for mining microbial interaction patterns from taxonomic abundance data corresponding to a given microbial community. In spite of their efficiency, these correlation techniques can capture only 'pair-wise interactions'. Moreover, their emphasis on statistical significance can potentially result in missing out on several interactions that are relevant from a biological standpoint. This study explores the applicability of one of the earliest association rule mining algorithm i.e. the 'Apriori algorithm' for deriving 'microbial association rules' from the taxonomic profile of given microbial community. The classical Apriori approach derives association rules by analysing patterns of co-occurrence/co-exclusion between various '(subsets of) features/items' across various samples. Using real-world microbiome data, the efficiency/utility of this rule mining approach in deciphering multiple (biologically meaningful) association patterns between 'subsets/subgroups' of microbes (constituting microbiome samples) is demonstrated. As an example, association rules derived from publicly available gut microbiome datasets indicate an association between a group of microbes (Faecalibacterium, Dorea, and Blautia) that are known to have mutualistic metabolic associations among themselves. Application of the rule mining approach on gut microbiomes (sourced from the Human Microbiome Project) further indicated similar microbial association patterns in gut microbiomes irrespective of the gender of the subjects. A Linux implementation of the Association Rule Mining (ARM) software (customised for deriving 'microbial association rules' from microbiome data) is freely available for download from the following link: http://metagenomics.atc.tcs.com/arm.}, } @article {pmid27122046, year = {2016}, author = {Lloyd-Price, J and Abu-Ali, G and Huttenhower, C}, title = {The healthy human microbiome.}, journal = {Genome medicine}, volume = {8}, number = {1}, pages = {51}, pmid = {27122046}, issn = {1756-994X}, mesh = {Bacteria/*classification/*genetics ; Genetic Variation ; Healthy Volunteers ; Humans ; Metagenome ; *Microbiota ; Phylogeny ; Phylogeography ; }, abstract = {Humans are virtually identical in their genetic makeup, yet the small differences in our DNA give rise to tremendous phenotypic diversity across the human population. By contrast, the metagenome of the human microbiome-the total DNA content of microbes inhabiting our bodies-is quite a bit more variable, with only a third of its constituent genes found in a majority of healthy individuals. Understanding this variability in the "healthy microbiome" has thus been a major challenge in microbiome research, dating back at least to the 1960s, continuing through the Human Microbiome Project and beyond. Cataloguing the necessary and sufficient sets of microbiome features that support health, and the normal ranges of these features in healthy populations, is an essential first step to identifying and correcting microbial configurations that are implicated in disease. Toward this goal, several population-scale studies have documented the ranges and diversity of both taxonomic compositions and functional potentials normally observed in the microbiomes of healthy populations, along with possible driving factors such as geography, diet, and lifestyle. Here, we review several definitions of a 'healthy microbiome' that have emerged, the current understanding of the ranges of healthy microbial diversity, and gaps such as the characterization of molecular function and the development of ecological therapies to be addressed in the future.}, } @article {pmid27121918, year = {2016}, author = {Li, JG and Shen, MC and Hou, JF and Li, L and Wu, JX and Dong, YH}, title = {Effect of different levels of nitrogen on rhizosphere bacterial community structure in intensive monoculture of greenhouse lettuce.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {25305}, pmid = {27121918}, issn = {2045-2322}, mesh = {Bacteria/*classification/*isolation & purification ; *Biodiversity ; Fertilizers/statistics & numerical data ; Lactuca/*microbiology ; Metagenomics ; Nitrogen/*analysis ; *Rhizosphere ; Seasons ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Pyrosequencing-based analyses revealed significant effects among low (N50), medium (N80), and high (N100) fertilization on community composition involving a long-term monoculture of lettuce in a greenhouse in both summer and winter. The non-fertilized control (CK) treatment was characterized by a higher relative abundance of Actinobacteria, Acidobacteria, and Chloroflexi; however, the average abundance of Firmicutes typically increased in summer, and the relative abundance of Bacteroidetes increased in winter in the N-fertilized treatments. Principle component analysis showed that the distribution of the microbial community was separated by a N gradient with N80 and N100 in the same group in the summer samples, while CK and N50 were in the same group in the winter samples, with the other N-level treatments existing independently. Redundancy analysis revealed that available N, NO3(-)-N, and NH4(+)-N, were the main environmental factors affecting the distribution of the bacterial community. Correlation analysis showed that nitrogen affected the shifts of microbial communities by strongly driving the shifts of Firmicutes, Bacteroidetes, and Proteobacteria in summer samples, and Bacteroidetes, Actinobacteria, and Acidobacteria in winter samples. The study demonstrates a novel example of rhizosphere bacterial diversity and the main factors influencing rizosphere microbial community in continuous vegetable cropping within an intensive greenhouse ecosystem.}, } @article {pmid27121074, year = {2017}, author = {Verma, M}, title = {Mechanistic and Technical Challenges in Studying the Human Microbiome and Cancer Epidemiology.}, journal = {Technology in cancer research & treatment}, volume = {16}, number = {2}, pages = {150-158}, pmid = {27121074}, issn = {1533-0338}, mesh = {Data Mining ; Digestive System Neoplasms/epidemiology/etiology ; Humans ; Metagenomics/methods ; Microbiological Techniques ; *Microbiota ; Neoplasms/*epidemiology/*etiology ; Research Design ; }, abstract = {This article reviews the significance of the microbiome in cancer epidemiology, mechanistic and technical challenges in the field, and characterization of the microbiome in different tumor types to identify biomarkers of risk, progression, and prognosis. Publications on the microbiome and cancer epidemiology were reviewed to analyze sample collection and processing, microbiome taxa characterization by 16S ribosomal RNA sequencing, and microbiome metabolite characterization (metabotyping) by nuclear magnetic resonance and mass spectrometry. The analysis identified methodology types, research design, sample types, and issues in integrating data from different platforms. Aerodigestive cancer epidemiology studies conducted by different groups demonstrated the significance of microbiome information in developing approaches to improve health. Challenges exist in sample preparation and processing (eg, standardization of methods for collection and analysis). These challenges relate to technology, data integration from "omics" studies, inherent bias in primer selection during 16S ribosomal RNA sequencing, the need for large consortia with well-characterized biospecimens, cause and effect issues, resilience of microbiota to exposure events (requires longitudinal studies), and expanding studies for fungal and viral diversity (most studies used bacterial 16S ribosomal RNA sequencing for microbiota characterization). Despite these challenges, microbiome and cancer epidemiology studies are significant and may facilitate cancer risk assessment, diagnosis, and prognosis. In the future, clinical trials likely will use microbiota modifications to improve the efficacy of existing treatments.}, } @article {pmid27118420, year = {2016}, author = {Singh, P and Manning, SD}, title = {Impact of age and sex on the composition and abundance of the intestinal microbiota in individuals with and without enteric infections.}, journal = {Annals of epidemiology}, volume = {26}, number = {5}, pages = {380-385}, pmid = {27118420}, issn = {1873-2585}, support = {U19 AI090872/AI/NIAID NIH HHS/United States ; }, mesh = {Acute Disease ; Adult ; Age Factors ; Biodiversity ; Case-Control Studies ; Child ; Child, Preschool ; Enteritis/*microbiology/physiopathology ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics/physiology ; Gram-Negative Bacteria/pathogenicity ; Gram-Positive Bacteria/pathogenicity ; Humans ; Infant ; Male ; Middle Aged ; RNA, Ribosomal, 16S/*genetics ; Real-Time Polymerase Chain Reaction/methods ; Reference Values ; Sex Factors ; Young Adult ; }, abstract = {PURPOSE: The intestinal microbiome is critical for human health and preventing colonization by enteric pathogens. There are notable differences in the microbiota composition among individuals with and without enteric infections, though the impact that age and gender has on the composition and abundance of intestinal microbes is not known.

METHODS: A comparative 16S rRNA gene sequencing study was performed on stool DNA from 200 patients with enteric infections and 75 healthy family members representing both sexes and multiple age groups.

RESULTS: Microbial community profiles were affected by age and sex in patients with enteric infections and their healthy family members. Overall, we observed an increase in Bacteroides abundance and decrease in Escherichia abundance with age, though these differences were most apparent for patients with enteric infections. Genus Bacteroides was also higher in female communities while Escherichia predominated in males.

CONCLUSIONS: Because Escherichia abundance was previously linked to symptom severity, children with enteric infections may be most susceptible to severe disease outcomes due to high and low abundance of Escherichia and Bacteroides, respectively. Future studies should focus on classifying specific differences in the microbiome using metagenomics and identifying novel methods aimed at shifting the intestinal microbiome to a healthy state.}, } @article {pmid27117007, year = {2016}, author = {Denou, E and Marcinko, K and Surette, MG and Steinberg, GR and Schertzer, JD}, title = {High-intensity exercise training increases the diversity and metabolic capacity of the mouse distal gut microbiota during diet-induced obesity.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {310}, number = {11}, pages = {E982-93}, pmid = {27117007}, issn = {1522-1555}, support = {MSH-136665//CIHR/Canada ; }, mesh = {Animals ; Bacteria/isolation & purification/*metabolism ; Biodiversity ; Diet, High-Fat/adverse effects ; Exercise Therapy/*methods ; Gastrointestinal Microbiome/*physiology ; High-Intensity Interval Training/*methods ; Male ; Metagenome/physiology ; Mice ; Mice, Inbred C57BL ; Obesity/etiology/*microbiology/*therapy ; Physical Conditioning, Animal/methods ; Treatment Outcome ; }, abstract = {Diet and exercise underpin the risk of obesity-related metabolic disease. Diet alters the gut microbiota, which contributes to aspects of metabolic disease during obesity. Repeated exercise provides metabolic benefits during obesity. We assessed whether exercise could oppose changes in the taxonomic and predicted metagenomic characteristics of the gut microbiota during diet-induced obesity. We hypothesized that high-intensity interval training (HIIT) would counteract high-fat diet (HFD)-induced changes in the microbiota without altering obesity in mice. Compared with chow-fed mice, an obesity-causing HFD decreased the Bacteroidetes-to-Firmicutes ratio and decreased the genetic capacity in the fecal microbiota for metabolic pathways such as the tricarboxylic acid (TCA) cycle. After HFD-induced obesity was established, a subset of mice were HIIT for 6 wk, which increased host aerobic capacity but did not alter body or adipose tissue mass. The effects of exercise training on the microbiota were gut segment dependent and more extensive in the distal gut. HIIT increased the alpha diversity and Bacteroidetes/Firmicutes ratio of the distal gut and fecal microbiota during diet-induced obesity. Exercise training increased the predicted genetic capacity related to the TCA cycle among other aspects of metabolism. Strikingly, the same microbial metabolism indexes that were increased by exercise were all decreased in HFD-fed vs. chow diet-fed mice. Therefore, exercise training directly opposed some of the obesity-related changes in gut microbiota, including lower metagenomic indexes of metabolism. Some host and microbial pathways appeared similarly affected by exercise. These exercise- and diet-induced microbiota interactions can be captured in feces.}, } @article {pmid27115757, year = {2016}, author = {Speda, J and Johansson, MA and Jonsson, BH and Karlsson, M}, title = {Applying theories of microbial metabolism for induction of targeted enzyme activity in a methanogenic microbial community at a metabolic steady state.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {18}, pages = {7989-8002}, doi = {10.1007/s00253-016-7547-z}, pmid = {27115757}, issn = {1432-0614}, mesh = {Culture Media/chemistry ; Hydrolases/*metabolism ; Methane/*metabolism ; *Microbial Consortia ; Transcriptional Activation ; }, abstract = {Novel enzymes that are stable in diverse conditions are intensively sought because they offer major potential advantages in industrial biotechnology, and microorganisms in extreme environments are key sources of such enzymes. However, most potentially valuable enzymes are currently inaccessible due to the pure culturing problem of microorganisms. Novel metagenomic and metaproteomic techniques that circumvent the need for pure cultures have theoretically provided possibilities to identify all genes and all proteins in microbial communities, but these techniques have not been widely used to directly identify specific enzymes because they generate vast amounts of extraneous data.In a first step towards developing a metaproteomic approach to pinpoint targeted extracellular hydrolytic enzymes of choice in microbial communities, we have generated and analyzed the necessary conditions for such an approach by the use of a methanogenic microbial community maintained on a chemically defined medium. The results show that a metabolic steady state of the microbial community could be reached, at which the expression of the targeted hydrolytic enzymes were suppressed, and that upon enzyme induction a distinct increase in the targeted enzyme expression was obtained. Furthermore, no cross talk in expression was detected between the two focal types of enzyme activities under their respective inductive conditions. Thus, the described approach should be useful to generate ideal samples, collected before and after selective induction, in controlled microbial communities to clearly discriminate between constituently expressed proteins and extracellular hydrolytic enzymes that are specifically induced, thereby reducing the analysis to only those proteins that are distinctively up-regulated.}, } @article {pmid27115650, year = {2016}, author = {Fabijanić, M and Vlahoviček, K}, title = {Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage Profiles.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1415}, number = {}, pages = {509-531}, doi = {10.1007/978-1-4939-3572-7_26}, pmid = {27115650}, issn = {1940-6029}, mesh = {Codon ; Data Mining ; Evolution, Molecular ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Liver Cirrhosis/*microbiology ; Machine Learning ; Metagenomics/*methods ; Phylogeny ; }, abstract = {Metagenomics projects use next-generation sequencing to unravel genetic potential in microbial communities from a wealth of environmental niches, including those associated with human body and relevant to human health. In order to understand large datasets collected in metagenomics surveys and interpret them in context of how a community metabolism as a whole adapts and interacts with the environment, it is necessary to extend beyond the conventional approaches of decomposing metagenomes into microbial species' constituents and performing analysis on separate components. By applying concepts of translational optimization through codon usage adaptation on entire metagenomic datasets, we demonstrate that a bias in codon usage present throughout the entire microbial community can be used as a powerful analytical tool to predict for community lifestyle-specific metabolism. Here we demonstrate this approach combined with machine learning, to classify human gut microbiome samples according to the pathological condition diagnosed in the human host.}, } @article {pmid27115497, year = {2016}, author = {Turaev, D and Rattei, T}, title = {High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved.}, journal = {Current opinion in biotechnology}, volume = {39}, number = {}, pages = {174-181}, doi = {10.1016/j.copbio.2016.04.011}, pmid = {27115497}, issn = {1879-0429}, mesh = {Bacteria/*classification/*genetics ; Ecology/methods ; Evolution, Molecular ; Genetic Variation ; Genome, Bacterial ; Metagenomics/*methods ; Microbial Consortia/*genetics ; *Systems Biology ; }, abstract = {The systems biology of microbial communities, organismal communities inhabiting all ecological niches on earth, has in recent years been strongly facilitated by the rapid development of experimental, sequencing and data analysis methods. Novel experimental approaches and binning methods in metagenomics render the semi-automatic reconstructions of near-complete genomes of uncultivable bacteria possible, while advances in high-resolution amplicon analysis allow for efficient and less biased taxonomic community characterization. This will also facilitate predictive modeling approaches, hitherto limited by the low resolution of metagenomic data. In this review, we pinpoint the most promising current developments in metagenomics. They facilitate microbial systems biology towards a systemic understanding of mechanisms in microbial communities with scopes of application in many areas of our daily life.}, } @article {pmid27107375, year = {2016}, author = {Kong, HH}, title = {Details Matter: Designing Skin Microbiome Studies.}, journal = {The Journal of investigative dermatology}, volume = {136}, number = {5}, pages = {900-902}, pmid = {27107375}, issn = {1523-1747}, support = {ZIA BC010938-08//Intramural NIH HHS/United States ; ZIA BC010938-09//Intramural NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/*genetics ; Chromosome Mapping ; Humans ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA/methods ; Skin/*microbiology ; }, abstract = {The use of genomic sequencing to investigate microbes has expanded, yet it has also raised questions regarding optimal approaches to studying the skin microbiome. Meisel et al. show that while whole genome shotgun metagenomic sequences were most similar to expected microbial profiles, sequencing of the hypervariable regions V1-V3 of the 16S ribosomal RNA gene had greater accuracy than sequencing of the hypervariable region V4 in determining genus and species level classifications of prominent skin bacteria.}, } @article {pmid27107120, year = {2016}, author = {Fougy, L and Desmonts, MH and Coeuret, G and Fassel, C and Hamon, E and Hézard, B and Champomier-Vergès, MC and Chaillou, S}, title = {Reducing Salt in Raw Pork Sausages Increases Spoilage and Correlates with Reduced Bacterial Diversity.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {13}, pages = {3928-3939}, pmid = {27107120}, issn = {1098-5336}, mesh = {Bacteria/*classification/*drug effects/genetics/growth & development ; Biota/*drug effects ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Food Preservation ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Red Meat/*microbiology ; Sequence Analysis, DNA ; *Sodium Chloride ; Temperature ; Time Factors ; }, abstract = {UNLABELLED: Raw sausages are perishable foodstuffs; reducing their salt content raises questions about a possible increased spoilage of these products. In this study, we evaluated the influence of salt reduction (from 2.0% to 1.5% [wt/wt]), in combination with two types of packaging (modified atmosphere [50% mix of CO2-N2] and vacuum packaging), on the onset of spoilage and on the diversity of spoilage-associated bacteria. After 21 days of storage at 8°C, spoilage was easily observed, characterized by noticeable graying of the products and the production of gas and off-odors defined as rancid, sulfurous, or sour. At least one of these types of spoilage occurred in each sample, and the global spoilage intensity was more pronounced in samples stored under modified atmosphere than under vacuum packaging and in samples with the lower salt content. Metagenetic 16S rRNA pyrosequencing revealed that vacuum-packaged samples contained a higher total bacterial richness (n = 69 operational taxonomic units [OTUs]) than samples under the other packaging condition (n = 46 OTUs). The core community was composed of 6 OTUs (Lactobacillus sakei, Lactococcus piscium, Carnobacterium divergens, Carnobacterium maltaromaticum, Serratia proteamaculans, and Brochothrix thermosphacta), whereas 13 OTUs taxonomically assigned to the Enterobacteriaceae, Enterococcaceae, and Leuconostocaceae families comprised a less-abundant subpopulation. This subdominant community was significantly more abundant when 2.0% salt and vacuum packaging were used, and this correlated with a lower degree of spoilage. Our results demonstrate that salt reduction, particularly when it is combined with CO2-enriched packaging, promotes faster spoilage of raw sausages by lowering the overall bacterial diversity (both richness and evenness).

IMPORTANCE: Our study takes place in the context of raw meat product manufacturing and is linked to a requirement for salt reduction. Health guidelines are calling for a reduction in dietary salt intake. However, salt has been used for a very long time as a hurdle technology, and salt reduction in meat products raises the question of spoilage and waste of food. The study was conceived to assess the role of sodium chloride reduction in meat products, both at the level of spoilage development and at the level of bacterial diversity, using 16S rRNA amplicon sequencing and raw pork sausage as a meat model.}, } @article {pmid27107051, year = {2016}, author = {Kwa, M and Plottel, CS and Blaser, MJ and Adams, S}, title = {The Intestinal Microbiome and Estrogen Receptor-Positive Female Breast Cancer.}, journal = {Journal of the National Cancer Institute}, volume = {108}, number = {8}, pages = {}, pmid = {27107051}, issn = {1460-2105}, support = {R01 DK090989/DK/NIDDK NIH HHS/United States ; R01 CA161891/CA/NCI NIH HHS/United States ; }, mesh = {Adiposity ; Alcohol Drinking ; Anti-Bacterial Agents/therapeutic use ; Breast/microbiology ; Breast Neoplasms/*chemistry/*epidemiology ; Dysbiosis/metabolism ; Estrogens/*metabolism ; Female ; Gastrointestinal Microbiome/drug effects/*physiology ; Humans ; Metabolome/*physiology ; Receptors, Estrogen/*analysis ; Risk Factors ; }, abstract = {The huge communities of residential microbes, including bacteria, viruses, Archaea, and Eukaryotes, that colonize humans are increasingly recognized as playing important roles in health and disease. A complex populous ecosystem, the human gastrointestinal (GI) tract harbors up to 10(11) bacterial cells per gram of luminal content, whose collective genome, the gut metagenome, contains a vastly greater number of individual genes than the human genome. In health, the function of the microbiome might be considered to be in dynamic equilibrium with the host, exerting both local and distant effects. However, 'disequilibrium' may contribute to the emergence of disease, including malignancy. In this review, we discuss how the intestinal bacterial microbiome and in particular how an 'estrobolome,' the aggregate of enteric bacterial genes capable of metabolizing estrogens, might affect women's risk of developing postmenopausal estrogen receptor-positive breast cancer. Estrobolome composition is impacted by factors that modulate its functional activity. Exploring variations in the composition and activities of the estrobolome in healthy individuals and in women with estrogen-driven breast cancer may lead to development of microbiome-based biomarkers and future targeted interventions to attenuate cancer risk.}, } @article {pmid27106050, year = {2016}, author = {Kasiraj, AC and Harmoinen, J and Isaiah, A and Westermarck, E and Steiner, JM and Spillmann, T and Suchodolski, JS}, title = {The effects of feeding and withholding food on the canine small intestinal microbiota.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {6}, pages = {fiw085}, doi = {10.1093/femsec/fiw085}, pmid = {27106050}, issn = {1574-6941}, mesh = {Animals ; Bacteroides/*growth & development ; Betaproteobacteria/*growth & development ; Denaturing Gradient Gel Electrophoresis ; Diet ; Dogs ; *Fasting ; Food ; *Gastrointestinal Microbiome ; Intestine, Small/*microbiology ; Jejunum/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Prolonged lack of enteral feeding has a negative impact on gut physiology, potentially via microbiota modulation. The aims were to investigate the impact of fasting and post-prandial changes in canine jejunal microbiota. To study post-prandial effects, jejunal brushings were analyzed in 8 healthy fistulated dogs 15 min before feeding (baseline) and hourly for 8 h after feeding. To study effects of withholding food (WF), daily samples were collected for 15 days from 5 dogs. The first 5 days (PRE) dogs were fed regular diet. Food was withheld the next 5 days (days 6-10). For days 11-15 (POST), the original diet was reintroduced. Microbiota was characterized via denaturing gradient gel electrophoresis and 454-pyrosequencing of 16S rRNA genes. In the post-prandial study, no changes in microbiome structure were seen after feeding (ANOSIM, P = 0.28), but Betaproteobacteria (P = 0.04) and Bacteroidales decreased compared to baseline. Species richness decreased by 300 min (P = 0.04). During WF, microbiota structure differed from PRE and POST period (P = 0.001). During WF, species richness did not vary over time (P = 0.69). In conclusion, a prolonged period of food withholding results in altered jejunal microbiota. How these changes affect the microbiota metabolism warrants further studies.}, } @article {pmid27105322, year = {2016}, author = {Shimizu, J and Kubota, T and Takada, E and Takai, K and Fujiwara, N and Arimitsu, N and Ueda, Y and Wakisaka, S and Suzuki, T and Suzuki, N}, title = {Bifidobacteria Abundance-Featured Gut Microbiota Compositional Change in Patients with Behcet's Disease.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0153746}, pmid = {27105322}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Aged ; Behcet Syndrome/*microbiology ; Bifidobacterium/*isolation & purification ; Female ; Humans ; Intestines/*microbiology ; Male ; *Microbiota ; Middle Aged ; Young Adult ; }, abstract = {Gut microbiota compositional alteration may have an association with immune dysfunction in patients with Behcet's disease (BD). We conducted a fecal metagenomic analysis of BD patients. We analyzed fecal microbiota obtained from 12 patients with BD and 12 normal individuals by sequencing of 16S ribosomal RNA gene. We compared the relative abundance of bacterial taxa. Direct comparison of the relative abundance of bacterial taxa demonstrated that the genera Bifidobacterium and Eggerthella increased significantly and the genera Megamonas and Prevotella decreased significantly in BD patients compared with normal individuals. A linear discriminant analysis of bacterial taxa showed that the phylum Actinobacteria, including Bifidobacterium, and the family Lactobacillaceae exhibited larger positive effect sizes than other bacteria in patients with BD. The phylum Firmicutes and the class Clostridia had large effect sizes in normal individuals. There was no significant difference in annotated species numbers (as numbers of operational taxonomic unit; OTU) and bacterial diversity of each sample (alpha diversity) between BD patients and normal individuals. We next assigned each sample to a position using three axes by principal coordinates analysis of the OTU table. The two groups had a significant distance as beta diversity in the 3-axis space. Fecal sIgA concentrations increased significantly in BD patients but did not correlate with any bacterial taxonomic abundance. These data suggest that the compositional changes of gut microbes may be one type of dysbiosis (unfavorable microbiota alteration) in patients with BD. The dysbiosis may have an association with the pathophysiology of BD.}, } @article {pmid27104353, year = {2016}, author = {Yamagishi, J and Sato, Y and Shinozaki, N and Ye, B and Tsuboi, A and Nagasaki, M and Yamashita, R}, title = {Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0154389}, pmid = {27104353}, issn = {1932-6203}, mesh = {Adsorption ; DNA, Bacterial/genetics/*isolation & purification ; Dental Plaque/*microbiology ; High-Throughput Nucleotide Sequencing ; Hot Temperature ; Humans ; Liquid Phase Microextraction/instrumentation/*methods ; Male ; Metagenomics/instrumentation/*methods ; Microbiota/genetics ; Pilot Projects ; Principal Component Analysis ; RNA, Ribosomal, 16S/*genetics ; Robotics/*methods ; Sequence Analysis, DNA ; }, abstract = {The rapid improvement of next-generation sequencing performance now enables us to analyze huge sample sets with more than ten thousand specimens. However, DNA extraction can still be a limiting step in such metagenomic approaches. In this study, we analyzed human oral microbes to compare the performance of three DNA extraction methods: PowerSoil (a method widely used in this field), QIAsymphony (a robotics method), and a simple boiling method. Dental plaque was initially collected from three volunteers in the pilot study and then expanded to 12 volunteers in the follow-up study. Bacterial flora was estimated by sequencing the V4 region of 16S rRNA following species-level profiling. Our results indicate that the efficiency of PowerSoil and QIAsymphony was comparable to the boiling method. Therefore, the boiling method may be a promising alternative because of its simplicity, cost effectiveness, and short handling time. Moreover, this method was reliable for estimating bacterial species and could be used in the future to examine the correlation between oral flora and health status. Despite this, differences in the efficiency of DNA extraction for various bacterial species were observed among the three methods. Based on these findings, there is no "gold standard" for DNA extraction. In future, we suggest that the DNA extraction method should be selected on a case-by-case basis considering the aims and specimens of the study.}, } @article {pmid27102666, year = {2016}, author = {Chen, J and Wright, K and Davis, JM and Jeraldo, P and Marietta, EV and Murray, J and Nelson, H and Matteson, EL and Taneja, V}, title = {An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis.}, journal = {Genome medicine}, volume = {8}, number = {1}, pages = {43}, pmid = {27102666}, issn = {1756-994X}, support = {R01 AR030752/AR/NIAMS NIH HHS/United States ; R56 AR030752/AR/NIAMS NIH HHS/United States ; U24 DK100469/DK/NIDDK NIH HHS/United States ; AR30752/AR/NIAMS NIH HHS/United States ; }, mesh = {Adult ; Aged ; Animals ; Arthritis, Rheumatoid/diagnosis/drug therapy/*etiology/metabolism ; Biodiversity ; Case-Control Studies ; Cell Line ; Chemokines ; Computational Biology/methods ; Cytokines/metabolism ; Disease Models, Animal ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/metabolism ; Male ; Metabolome ; Metagenome ; Metagenomics ; Mice ; Middle Aged ; Models, Biological ; Permeability ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; }, abstract = {BACKGROUND: The adaptive immune response in rheumatoid arthritis (RA) is influenced by an interaction between host genetics and environment, particularly the host microbiome. Association of the gut microbiota with various diseases has been reported, though the specific components of the microbiota that affect the host response leading to disease remain unknown. However, there is limited information on the role of gut microbiota in RA. In this study we aimed to define a microbial and metabolite profile that could predict disease status. In addition, we aimed to generate a humanized model of arthritis to confirm the RA-associated microbe.

METHODS: To identify an RA biomarker profile, the 16S ribosomal DNA of fecal samples from RA patients, first-degree relatives (to rule out environment/background as confounding factors), and random healthy non-RA controls were sequenced. Analysis of metabolites and their association with specific taxa was performed to investigate a potential mechanistic link. The role of an RA-associated microbe was confirmed using a human epithelial cell line and a humanized mouse model of arthritis.

RESULTS: Patients with RA exhibited decreased gut microbial diversity compared with controls, which correlated with disease duration and autoantibody levels. A taxon-level analysis suggested an expansion of rare taxa, Actinobacteria, with a decrease in abundant taxa in patients with RA compared with controls. Prediction models based on the random forests algorithm suggested that three genera, Collinsella, Eggerthella, and Faecalibacterium, segregated with RA. The abundance of Collinsella correlated strongly with high levels of alpha-aminoadipic acid and asparagine as well as production of the proinflammatory cytokine IL-17A. A role for Collinsella in altering gut permeability and disease severity was confirmed in experimental arthritis.

CONCLUSIONS: These observations suggest dysbiosis in RA patients resulting from the abundance of certain rare bacterial lineages. A correlation between the intestinal microbiota and metabolic signatures could determine a predictive profile for disease causation and progression.}, } @article {pmid27102665, year = {2016}, author = {Bergkemper, F and Kublik, S and Lang, F and Krüger, J and Vestergaard, G and Schloter, M and Schulz, S}, title = {Novel oligonucleotide primers reveal a high diversity of microbes which drive phosphorous turnover in soil.}, journal = {Journal of microbiological methods}, volume = {125}, number = {}, pages = {91-97}, doi = {10.1016/j.mimet.2016.04.011}, pmid = {27102665}, issn = {1872-8359}, mesh = {6-Phytase/genetics ; Alkaline Phosphatase/genetics ; Bacteria/classification/enzymology/*genetics/metabolism ; Biota/genetics ; *DNA Primers/metabolism ; Forests ; Fungi/classification/enzymology/*genetics/metabolism ; *Genetic Variation ; Glucose 1-Dehydrogenase/genetics ; Phosphorus/*metabolism ; Real-Time Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; *Soil Microbiology ; }, abstract = {Phosphorus (P) is of central importance for cellular life but likewise a limiting macronutrient in numerous environments. Certainly microorganisms have proven their ability to increase the phosphorus bioavailability by mineralization of organic-P and solubilization of inorganic-P. On the other hand they efficiently take up P and compete with other biota for phosphorus. However the actual microbial community that is associated to the turnover of this crucial macronutrient in different ecosystems remains largely anonymous especially taking effects of seasonality and spatial heterogeneity into account. In this study seven oligonucleotide primers are presented which target genes coding for microbial acid and alkaline phosphatases (phoN, phoD), phytases (appA), phosphonatases (phnX) as well as the quinoprotein glucose dehydrogenase (gcd) and different P transporters (pitA, pstS). Illumina amplicon sequencing of soil genomic DNA underlined the high rate of primer specificity towards the respective target gene which usually ranged between 98% and 100% (phoN: 87%). As expected the primers amplified genes from a broad diversity of distinct microorganisms. Using DNA from a beech dominated forest soil, the highest microbial diversity was detected for the alkaline phosphatase (phoD) gene which was amplified from 15 distinct phyla respectively 81 families. Noteworthy the primers also allowed amplification of phoD from 6 fungal orders. The genes coding for acid phosphatase (phoN) and the quinoprotein glucose dehydrogenase (gcd) were amplified from 20 respectively 17 different microbial orders. In comparison the phytase and phosphonatase (appA, phnX) primers covered 13 bacterial orders from 2 different phyla respectively. Although the amplified microbial diversity was apparently limited both primers reliably detected all orders that contributed to the P turnover in the investigated soil as revealed by a previous metagenomic approach. Genes that code for microbial P transporter (pitA, pstS) were amplified from 13 respectively 9 distinct microbial orders. Accordingly the introduced primers represent a valuable tool for further analysis of the microbial community involved in the turnover of phosphorus in soils but most likely also in other environments.}, } @article {pmid27102357, year = {2016}, author = {Liu, W and Zhang, Y and Jiang, S and Deng, Y and Christie, P and Murray, PJ and Li, X and Zhang, J}, title = {Arbuscular mycorrhizal fungi in soil and roots respond differently to phosphorus inputs in an intensively managed calcareous agricultural soil.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {24902}, pmid = {27102357}, issn = {2045-2322}, mesh = {Agriculture/methods ; *Biodiversity ; *Fertilizers ; Fungi ; Metagenomics ; Mycorrhizae/*classification/growth & development/isolation & purification ; *Phosphorus ; Plant Roots/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; Zea mays/*microbiology ; }, abstract = {Understanding the diversity and community structure of arbuscular mycorrhizal fungi (AMF) is important for potentially optimizing their role in mining phosphorus (P) in agricultural ecosystems. Here, we conduct a comprehensive study to investigate the vertical distribution of AMF in a calcareous field and their temporal structure in maize-roots with fertilizer P application over a three-year period. The results showed that soil available-P response to P fertilization but maize yields did not. Phosphorus fertilization had no-significant effect on richness of AMF except at greater soil-depths. High P-supply reduced root colonization while optimum-P tended to increase colonization and fungal richness on all sampling occasions. Crop phenology might override P-supply in determining the community composition of active root inhabiting fungi. Significant differences in the community structure of soil AMF were observed between the controls and P treatments in surface soil and the community shift was attributable mainly to available-P, N/P and pH. Vertical distribution was related mainly to soil electrical conductivity and Na content. Our results indicate that the structure of AMF community assemblages is correlated with P fertilization, soil depth and crop phenology. Importantly, phosphorus management must be integrated with other agricultural-practices to ensure the sustainability of agricultural production in salinized soils.}, } @article {pmid27102203, year = {2016}, author = {Grassl, N and Kulak, NA and Pichler, G and Geyer, PE and Jung, J and Schubert, S and Sinitcyn, P and Cox, J and Mann, M}, title = {Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome.}, journal = {Genome medicine}, volume = {8}, number = {1}, pages = {44}, pmid = {27102203}, issn = {1756-994X}, mesh = {Adult ; Bacteria/classification/genetics/metabolism ; Bacterial Proteins ; Biodiversity ; Chromatography, Liquid ; Female ; Humans ; Male ; Mass Spectrometry ; Metagenome ; Metagenomics ; *Microbiota ; Mouth/*microbiology ; Peptides/metabolism ; Phylogeny ; *Proteome ; *Proteomics/methods ; Saliva/*metabolism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Young Adult ; }, abstract = {BACKGROUND: The oral cavity is home to one of the most diverse microbial communities of the human body and a major entry portal for pathogens. Its homeostasis is maintained by saliva, which fulfills key functions including lubrication of food, pre-digestion, and bacterial defense. Consequently, disruptions in saliva secretion and changes in the oral microbiome contribute to conditions such as tooth decay and respiratory tract infections. Here we set out to quantitatively map the saliva proteome in great depth with a rapid and in-depth mass spectrometry-based proteomics workflow.

METHODS: We used recent improvements in mass spectrometry (MS)-based proteomics to develop a rapid workflow for mapping the saliva proteome quantitatively and at great depth. Standard clinical cotton swabs were used to collect saliva form eight healthy individuals at two different time points, allowing us to study inter-individual differences and interday changes of the saliva proteome. To accurately identify microbial proteins, we developed a method called "split by taxonomy id" that prevents peptides shared by humans and bacteria or between different bacterial phyla to contribute to protein identification.

RESULTS: Microgram protein amounts retrieved from cotton swabs resulted in more than 3700 quantified human proteins in 100-min gradients or 5500 proteins after simple fractionation. Remarkably, our measurements also quantified more than 2000 microbial proteins from 50 bacterial genera. Co-analysis of the proteomics results with next-generation sequencing data from the Human Microbiome Project as well as a comparison to MALDI-TOF mass spectrometry on microbial cultures revealed strong agreement. The oral microbiome differs between individuals and changes drastically upon eating and tooth brushing.

CONCLUSION: Rapid shotgun and robust technology can now simultaneously characterize the human and microbiome contributions to the proteome of a body fluid and is therefore a valuable complement to genomic studies. This opens new frontiers for the study of host-pathogen interactions and clinical saliva diagnostics.}, } @article {pmid27102141, year = {2016}, author = {Huang, Y and Yang, B and Li, W}, title = {Defining the normal core microbiome of conjunctival microbial communities.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {22}, number = {7}, pages = {643.e7-643.e12}, doi = {10.1016/j.cmi.2016.04.008}, pmid = {27102141}, issn = {1469-0691}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/*classification/*genetics ; Conjunctiva/*microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Healthy Volunteers ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metagenome ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Bacterial ocular infections are common. Traditional culture and molecular biological methods have obvious limitations to identify the conjunctival microbiota, while metagenomic studies can avoid the defects of these methods. We used the Illumina high-throughput sequencing technology (MiSeq Illumina Sequencing Platform) to sequence the 16S rDNA V3-V4 hypervariable region of all bacteria in conjunctival swab samples. The operational taxonomic units were obtained from the sequences. The bioinformatic analyses of taxonomy, abundance and alpha diversity were performed. A total of 840 373 high-quality sequencing reads were generated from 31 conjunctival samples. The number of the species operational taxonomic units ranged from 159 to 2042, indicating high microbial diversity. The combined bacterial community was classified into 25 phyla and 526 distinct genera. At the genus level, Corynebacterium (28.22%), Pseudomonas (26.75%), Staphylococcus (5.28%), Acinetobacter (4.74%), Streptococcus (2.85%), Millisia (2.16%), Anaerococcus (1.86%), Finegoldia (1.68%), Simonsiella (1.48%) and Veillonella (1.00%) accounted for over 76% of the microbial community, possibly representing the core genera in normal conjunctival microbiota. The composition and diversity of microbiota in the normal adult human conjunctiva were characterized using high-throughput sequencing. A framework for investigating potential roles played by the diverse microbiota in disease related with the ocular surface was provided.}, } @article {pmid27102132, year = {2016}, author = {Josephs-Spaulding, J and Beeler, E and Singh, OV}, title = {Human microbiome versus food-borne pathogens: friend or foe.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {11}, pages = {4845-4863}, doi = {10.1007/s00253-016-7523-7}, pmid = {27102132}, issn = {1432-0614}, mesh = {Diet ; Fermentation ; Foodborne Diseases/*microbiology/*therapy ; Humans ; Metagenomics ; *Microbiota ; Multilocus Sequence Typing ; Probiotics ; Symbiosis ; }, abstract = {As food safety advances, there is a great need to maintain, distribute, and provide high-quality food to a much broader consumer base. There is also an ever-growing "arms race" between pathogens and humans as food manufacturers. The human microbiome is a collective organ of microbes that have found community niches while associating with their host and other microorganisms. Humans play an important role in modifying the environment of these organisms through their life choices, especially through individual diet. The composition of an individual's diet influences the digestive system-an ecosystem with the greatest number and largest diversity of organisms currently known. Organisms living on and within food have the potential to be either friends or foes to the consumer. Maintenance of this system can have multiple benefits, but lack of maintenance can lead to a host of chronic and preventable diseases. Overall, this dynamic system is influenced by intense competition from food-borne pathogens, lifestyle, overall diet, and presiding host-associated microbiota.}, } @article {pmid27100478, year = {2016}, author = {Wang, F and Zhang, C and Zeng, Q}, title = {Gut microbiota and immunopathogenesis of diabetes mellitus type 1 and 2.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {21}, number = {5}, pages = {900-906}, doi = {10.2741/4427}, pmid = {27100478}, issn = {2768-6698}, mesh = {Animals ; Diabetes Mellitus, Type 1/*etiology/immunology/microbiology ; Diabetes Mellitus, Type 2/*etiology/immunology/microbiology ; Epigenesis, Genetic ; Gastrointestinal Microbiome/genetics/*immunology ; Humans ; Models, Immunological ; Probiotics/therapeutic use ; }, abstract = {Diabetes mellitus (DM) is a major increasing global health burden in the aging population. Understanding the etiology of DM is beneficial for its prevention as well as treatment. In light of the metagenome hypothesis, defined as the overall bacterial genome, gut microbes have attracted increasing attention in the pathogenesis of DM. Many studies have found that gut microbes are involved in the immunopathogenesis of DM. Probiotics strengthen the host's intestinal barrier and modulate the immune system, and have therefore been investigated in DM management. Recent epigenetic findings in context of genes associated with inflammation suggest a possible way in which gut microbiota participate in the immunopathogenesis of DM. In this review, we discuss the role of gut microbiota in the immunopathogenesis of DM.}, } @article {pmid27100052, year = {2017}, author = {Stewart, CJ and Nelson, A and Campbell, MD and Walker, M and Stevenson, EJ and Shaw, JA and Cummings, SP and West, DJ}, title = {Gut microbiota of Type 1 diabetes patients with good glycaemic control and high physical fitness is similar to people without diabetes: an observational study.}, journal = {Diabetic medicine : a journal of the British Diabetic Association}, volume = {34}, number = {1}, pages = {127-134}, doi = {10.1111/dme.13140}, pmid = {27100052}, issn = {1464-5491}, mesh = {Adult ; Bacteroides/growth & development/*isolation & purification ; Case-Control Studies ; Clostridiales/growth & development/*isolation & purification ; Cohort Studies ; Combined Modality Therapy ; Diabetes Mellitus, Type 1/blood/complications/*microbiology/therapy ; Dysbiosis/complications/epidemiology/microbiology/*prevention & control ; England/epidemiology ; Exercise ; Faecalibacterium/growth & development/*isolation & purification ; Feces/microbiology ; *Gastrointestinal Microbiome ; Glycated Hemoglobin/analysis ; Humans ; Hyperglycemia/prevention & control ; Hypoglycemia/prevention & control ; Male ; Oxygen Consumption ; Phylogeny ; Physical Fitness ; Risk ; }, abstract = {AIM: Type 1 diabetes is the product of a complex interplay between genetic susceptibility and exposure to environmental factors. Existing bacterial profiling studies focus on people who are most at risk at the time of diagnosis; there are limited data on the gut microbiota of people with long-standing Type 1 diabetes. This study compared the gut microbiota of patients with Type 1 diabetes and good glycaemic control and high levels of physical-fitness with that of matched controls without diabetes.

METHODS: Ten males with Type 1 diabetes and ten matched controls without diabetes were recruited; groups were matched for gender, age, BMI, peak oxygen uptake (VO2max), and exercise habits. Stool samples were analysed using next-generation sequencing of the 16S rRNA gene to obtain bacterial profiles from each individual. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) was implemented to predict the functional content of the bacterial operational taxonomic units.

RESULTS: Faecalibacterium sp., Roseburia sp. and Bacteroides sp. were typically the most abundant members of the community in both patients with Type 1 diabetes and controls, and were present in every sample in the cohort. Each bacterial profile was relatively individual and no significant difference was reported between the bacterial profiles or the Shannon diversity indices of Type 1 diabetes compared with controls. The functional profiles were more conserved and the Type 1 diabetes group were comparable with the control group.

CONCLUSIONS: We show that both gut microbiota and resulting functional bacterial profiles from patients with long-standing Type 1 diabetes in good glycaemic control and high physical fitness levels are comparable with those of matched people without diabetes.}, } @article {pmid27098841, year = {2016}, author = {Zhang, C and Zhao, L}, title = {Strain-level dissection of the contribution of the gut microbiome to human metabolic disease.}, journal = {Genome medicine}, volume = {8}, number = {1}, pages = {41}, pmid = {27098841}, issn = {1756-994X}, mesh = {Animals ; Bacteria/classification/genetics/metabolism ; Bacterial Physiological Phenomena ; *Gastrointestinal Microbiome ; Humans ; Metabolic Diseases/*etiology/*metabolism ; Metabolome ; Metabolomics ; }, abstract = {The gut microbiota has been linked with metabolic diseases in humans, but demonstration of causality remains a challenge. The gut microbiota, as a complex microbial ecosystem, consists of hundreds of individual bacterial species, each of which contains many strains with high genetic diversity. Recent advances in genomic and metabolomic technologies are facilitating strain-level dissection of the contribution of the gut microbiome to metabolic diseases. Interventional studies and correlation analysis between variations in the microbiome and metabolome, captured by longitudinal sampling, can lead to the identification of specific bacterial strains that may contribute to human metabolic diseases via the production of bioactive metabolites. For example, high-quality draft genomes of prevalent gut bacterial strains can be assembled directly from metagenomic datasets using a canopy-based algorithm. Specific metabolites associated with a disease phenotype can be identified by nuclear magnetic resonance-based metabolomics of urine and other samples. Such multi-omics approaches can be employed to identify specific gut bacterial genomes that are not only correlated with detected metabolites but also encode the genes required for producing the precursors of those metabolites in the gut. Here, we argue that if a causative role can be demonstrated in follow-up mechanistic studies--for example, using gnotobiotic models--such functional strains have the potential to become biomarkers for diagnostics and targets for therapeutics.}, } @article {pmid27095829, year = {2016}, author = {Ferguson, JF and Allayee, H and Gerszten, RE and Ideraabdullah, F and Kris-Etherton, PM and Ordovás, JM and Rimm, EB and Wang, TJ and Bennett, BJ and , }, title = {Nutrigenomics, the Microbiome, and Gene-Environment Interactions: New Directions in Cardiovascular Disease Research, Prevention, and Treatment: A Scientific Statement From the American Heart Association.}, journal = {Circulation. Cardiovascular genetics}, volume = {9}, number = {3}, pages = {291-313}, pmid = {27095829}, issn = {1942-3268}, support = {K22 ES023849/ES/NIEHS NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; R01 HL128572/HL/NHLBI NIH HHS/United States ; }, mesh = {American Heart Association ; Animals ; Biomedical Research/*trends ; Cardiovascular Diseases/blood/genetics/microbiology/*prevention & control ; Diet/adverse effects ; Diffusion of Innovation ; Epigenesis, Genetic ; Forecasting ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; *Gene-Environment Interaction ; Genetic Predisposition to Disease ; *Genetic Variation ; Host-Pathogen Interactions ; Humans ; Metagenomics/trends ; Nutrigenomics/trends ; Nutrition Assessment ; Nutritional Status/*genetics ; Phenotype ; Preventive Health Services/*trends ; Risk Assessment ; Risk Factors ; United States ; }, abstract = {Cardiometabolic diseases are the leading cause of death worldwide and are strongly linked to both genetic and nutritional factors. The field of nutrigenomics encompasses multiple approaches aimed at understanding the effects of diet on health or disease development, including nutrigenetic studies investigating the relationship between genetic variants and diet in modulating cardiometabolic risk, as well as the effects of dietary components on multiple "omic" measures, including transcriptomics, metabolomics, proteomics, lipidomics, epigenetic modifications, and the microbiome. Here, we describe the current state of the field of nutrigenomics with respect to cardiometabolic disease research and outline a direction for the integration of multiple omics techniques in future nutrigenomic studies aimed at understanding mechanisms and developing new therapeutic options for cardiometabolic disease treatment and prevention.}, } @article {pmid27095377, year = {2016}, author = {Noyes, NR and Yang, X and Linke, LM and Magnuson, RJ and Cook, SR and Zaheer, R and Yang, H and Woerner, DR and Geornaras, I and McArt, JA and Gow, SP and Ruiz, J and Jones, KL and Boucher, CA and McAllister, TA and Belk, KE and Morley, PS}, title = {Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {24645}, pmid = {27095377}, issn = {2045-2322}, support = {T32 OD012201/OD/NIH HHS/United States ; UL1 TR001082/TR/NCATS NIH HHS/United States ; T32OD012201/OD/NIH HHS/United States ; }, mesh = {Animals ; Biodiversity ; Canada ; Cattle ; Cluster Analysis ; *Drug Resistance, Microbial ; Livestock ; Manure/*microbiology ; Metagenome ; Metagenomics/methods ; *Soil Microbiology ; United States ; *Waste Products ; Wastewater/*microbiology ; }, abstract = {It has been proposed that livestock production effluents such as wastewater, airborne dust and manure increase the density of antimicrobial resistant bacteria and genes in the environment. The public health risk posed by this proposed outcome has been difficult to quantify using traditional microbiological approaches. We utilized shotgun metagenomics to provide a first description of the resistome of North American dairy and beef production effluents, and identify factors that significantly impact this resistome. We identified 34 mechanisms of antimicrobial drug resistance within 34 soil, manure and wastewater samples from feedlot, ranch and dairy operations. The majority of resistance-associated sequences found in all samples belonged to tetracycline resistance mechanisms. We found that the ranch samples contained significantly fewer resistance mechanisms than dairy and feedlot samples, and that the resistome of dairy operations differed significantly from that of feedlots. The resistome in soil, manure and wastewater differed, suggesting that management of these effluents should be tailored appropriately. By providing a baseline of the cattle production waste resistome, this study represents a solid foundation for future efforts to characterize and quantify the public health risk posed by livestock effluents.}, } @article {pmid27092515, year = {2016}, author = {Amoutzias, GD and Chaliotis, A and Mossialos, D}, title = {Discovery Strategies of Bioactive Compounds Synthesized by Nonribosomal Peptide Synthetases and Type-I Polyketide Synthases Derived from Marine Microbiomes.}, journal = {Marine drugs}, volume = {14}, number = {4}, pages = {}, pmid = {27092515}, issn = {1660-3397}, mesh = {Biodiversity ; Biological Factors/*biosynthesis/metabolism ; Humans ; Metagenomics/methods ; Microbiota/*physiology ; Peptide Synthases/*metabolism ; Polyketide Synthases/*metabolism ; Polyketides/metabolism ; }, abstract = {Considering that 70% of our planet's surface is covered by oceans, it is likely that undiscovered biodiversity is still enormous. A large portion of marine biodiversity consists of microbiomes. They are very attractive targets of bioprospecting because they are able to produce a vast repertoire of secondary metabolites in order to adapt in diverse environments. In many cases secondary metabolites of pharmaceutical and biotechnological interest such as nonribosomal peptides (NRPs) and polyketides (PKs) are synthesized by multimodular enzymes named nonribosomal peptide synthetases (NRPSes) and type-I polyketide synthases (PKSes-I), respectively. Novel findings regarding the mechanisms underlying NRPS and PKS evolution demonstrate how microorganisms could leverage their metabolic potential. Moreover, these findings could facilitate synthetic biology approaches leading to novel bioactive compounds. Ongoing advances in bioinformatics and next-generation sequencing (NGS) technologies are driving the discovery of NRPs and PKs derived from marine microbiomes mainly through two strategies: genome-mining and metagenomics. Microbial genomes are now sequenced at an unprecedented rate and this vast quantity of biological information can be analyzed through genome mining in order to identify gene clusters encoding NRPSes and PKSes of interest. On the other hand, metagenomics is a fast-growing research field which directly studies microbial genomes and their products present in marine environments using culture-independent approaches. The aim of this review is to examine recent developments regarding discovery strategies of bioactive compounds synthesized by NRPS and type-I PKS derived from marine microbiomes and to highlight the vast diversity of NRPSes and PKSes present in marine environments by giving examples of recently discovered bioactive compounds.}, } @article {pmid27090518, year = {2016}, author = {Zozaya, M and Ferris, MJ and Siren, JD and Lillis, R and Myers, L and Nsuami, MJ and Eren, AM and Brown, J and Taylor, CM and Martin, DH}, title = {Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis.}, journal = {Microbiome}, volume = {4}, number = {}, pages = {16}, pmid = {27090518}, issn = {2049-2618}, support = {R01 AI079071/AI/NIAID NIH HHS/United States ; R01AI079071-01A1/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; DNA, Bacterial/genetics ; Female ; Foreskin/microbiology ; Heterosexuality ; Humans ; Male ; Metagenome/*genetics ; Microbiota/*genetics ; Penis/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sexual Behavior ; Sexual Partners ; Urethra/*microbiology ; Vagina/*microbiology ; Vaginosis, Bacterial/*microbiology/pathology ; }, abstract = {BACKGROUND: The epidemiology of bacterial vaginosis (BV) suggests it is sexually transmissible, yet no transmissible agent has been identified. It is probable that BV-associated bacterial communities are transferred from male to female partners during intercourse; however, the microbiota of sexual partners has not been well-studied.

RESULTS: Pyrosequencing analysis of PCR-amplified 16S rDNA was used to examine BV-associated bacteria in monogamous couples with and without BV using vaginal, male urethral, and penile skin specimens. The penile skin and urethral microbiota of male partners of women with BV was significantly more similar to the vaginal microbiota of their female partner compared to the vaginal microbiota of non-partner women with BV. This was not the case for male partners of women with normal vaginal microbiota. Specific BV-associated species were concordant in women with BV and their male partners.

CONCLUSIONS: In monogamous heterosexual couples in which the woman has BV, the significantly higher similarity between the vaginal microbiota and the penile skin and urethral microbiota of the male partner, supports the hypothesis that sexual exchange of BV-associated bacterial taxa is common.}, } @article {pmid27090184, year = {2016}, author = {Sohn, SI and Oh, YJ and Kim, BY and Cho, HS}, title = {Effects of CaMSRB2-Expressing Transgenic Rice Cultivation on Soil Microbial Communities.}, journal = {Journal of microbiology and biotechnology}, volume = {26}, number = {7}, pages = {1303-1310}, doi = {10.4014/jmb.1601.01058}, pmid = {27090184}, issn = {1738-8872}, mesh = {Bacteria/classification/genetics ; Biodiversity ; Cluster Analysis ; *Gene Expression ; *Genes, Plant ; Metagenome ; Metagenomics ; Oryza/*genetics/microbiology ; Phylogeny ; *Plants, Genetically Modified ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Although many studies on the effects of genetically modified (GM) crops on soil microorganisms have been carried out over the past decades, they have provided contradictory information, even for the same GM crop, owing to the diversity of the soil environments in which they were conducted. This inconsistency in results suggests that the effects of GM crops on soil microorganisms should be considered from many aspects. In this study, we investigated the effects of the GM drought-tolerant rice MSRB2-Bar-8, which expresses the CaMSRB2 gene, on soil microorganisms based on the culture-dependent and culture-independent methods. To this end, rhizosphere soils of GM and non-GM (IM) rice were analyzed for soil chemistry, population densities of soil microorganisms, and microbial community structure (using pyrosequencing technology) at three growth stages (seedling, tillering, and maturity). There was no significant difference in the soil chemistry between GM and non-GM rice. The microbial densities of the GM soils were found to be within the range of those of the non-GM rice. In the pyrosequencing analyses, Proteobacteria and Chloroflexi were dominant at the seedling stage, while Chloroflexi showed dominance over Proteobacteria at the maturity stage in both the GM and non-GM soils. An UPGMA dendrogram showed that the soil microbial communities were clustered by growth stage. Taken together, the results from this study suggest that the effects of MSRB2-Bar-8 cultivation on soil microorganisms are not significant.}, } @article {pmid27088626, year = {2016}, author = {Tavares, TC and Normando, LR and de Vasconcelos, AT and Gerber, AL and Agnez-Lima, LF and Melo, VM}, title = {Metagenomic analysis of sediments under seaports influence in the Equatorial Atlantic Ocean.}, journal = {The Science of the total environment}, volume = {557-558}, number = {}, pages = {888-900}, doi = {10.1016/j.scitotenv.2016.03.141}, pmid = {27088626}, issn = {1879-1026}, mesh = {Archaea/genetics ; Atlantic Ocean ; Bacteria/genetics ; *Biodiversity ; Deltaproteobacteria ; *Environmental Monitoring ; Geologic Sediments/chemistry/*microbiology ; *Metagenome ; Metagenomics ; Microbiota ; Proteobacteria ; RNA, Ribosomal, 16S ; Seawater/microbiology ; *Water Microbiology ; }, abstract = {Maritime ports are anthropogenic interventions capable of causing serious alterations in coastal ecosystems. In this study, we examined the benthic microbial diversity and community structure under the influence of two maritime ports, Mucuripe (MUC) and Pecém (PEC), at Equatorial Atlantic Ocean in Northeast Brazil. Those seaports differ in architecture, time of functioning, cargo handling and contamination. The microbiomes from MUC and PEC were also compared in silico to 11 other globally distributed marine microbiomes. The comparative analysis of operational taxonomic units (OTUs) retrieved by PCR-DGGE showed that MUC presents greater richness and β diversity of Bacteria and Archaea than PEC. In line with these results, metagenomic analysis showed that MUC and PEC benthic microbial communities share the main common bacterial phyla found in coastal environments, although can be distinguish by greater abundance of Cyanobacteria in MUC and Deltaproteobacteria in PEC. Both ports differed in Archaea composition, being PEC port sediments dominated by Thaumarchaeota. The microbiomes showed little divergence in their potential metabolic pathways, although shifts on the microbial taxonomic signatures involved in nitrogen and sulphur metabolic pathways were observed. The comparative analysis of different benthic marine metagenomes from Brazil, Australia and Mexico grouped them by the geographic location rather than by the type of ecosystem, although at phylum level seaport sediments share a core microbiome constituted by Proteobacteria, Cyanobacteria, Actinobacteria, Tenericuteres, Firmicutes, Bacteriodetes and Euryarchaeota. Our results suggest that multiple physical and chemical factors acting on sediments as a result of at least 60years of port operation play a role in shaping the benthic microbial communities at taxonomic level, but not at functional level.}, } @article {pmid27087247, year = {2016}, author = {de Paiva, CS and Jones, DB and Stern, ME and Bian, F and Moore, QL and Corbiere, S and Streckfus, CF and Hutchinson, DS and Ajami, NJ and Petrosino, JF and Pflugfelder, SC}, title = {Altered Mucosal Microbiome Diversity and Disease Severity in Sjögren Syndrome.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {23561}, pmid = {27087247}, issn = {2045-2322}, support = {T32 EY007001/EY/NEI NIH HHS/United States ; T32 AI053831/AI/NIAID NIH HHS/United States ; P30 EY002520/EY/NEI NIH HHS/United States ; T32-AI053831/AI/NIAID NIH HHS/United States ; T32-EY07001-37/EY/NEI NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Conjunctiva/*microbiology ; Dry Eye Syndromes/chemically induced/microbiology ; Dysbiosis/microbiology/pathology ; Feces/microbiology ; Female ; Humans ; Intestinal Mucosa/*microbiology ; Mice, Inbred C57BL ; *Microbiota ; Mouth Mucosa/*microbiology ; Scopolamine ; Sjogren's Syndrome/*microbiology/pathology ; Tongue/microbiology ; }, abstract = {There is mounting evidence that the microbiome has potent immunoregulatory functions. We assessed the effects of intestinal dysbiosis in a model of Sjögren syndrome (SS) by subjecting mice to desiccating stress (DS) and antibiotics (ABX). We characterized the conjunctival, tongue and fecal microbiome profiles of patients with SS. Severity of ocular surface and systemic disease was graded. 16S ribosomal RNA gene sequencing characterized the microbiota. ABX + DS mice had a significantly worse dry eye phenotype compared to controls, a decrease in Clostridium and an increase in Enterobacter, Escherichia/Shigella, and Pseudomonas in stool after ABX + DS for 10 days. Goblet cell density was significantly lower in ABX treated groups compared to controls. Stool from SS subjects had greater relative abundances of Pseudobutyrivibrio, Escherichia/Shigella, Blautia, and Streptococcus, while relative abundance of Bacteroides, Parabacteroides, Faecalibacterium, and Prevotella was reduced compared to controls. The severity of SS ocular and systemic disease was inversely correlated with microbial diversity. These findings suggest that SS is marked by a dysbiotic intestinal microbiome driven by low relative abundance of commensal bacteria and high relative abundance of potentially pathogenic genera that is associated with worse ocular mucosal disease in a mouse model of SS and in SS patients.}, } @article {pmid27086880, year = {2016}, author = {Shanahan, ER and Zhong, L and Talley, NJ and Morrison, M and Holtmann, G}, title = {Characterisation of the gastrointestinal mucosa-associated microbiota: a novel technique to prevent cross-contamination during endoscopic procedures.}, journal = {Alimentary pharmacology & therapeutics}, volume = {43}, number = {11}, pages = {1186-1196}, doi = {10.1111/apt.13622}, pmid = {27086880}, issn = {1365-2036}, mesh = {Biopsy ; Duodenum/microbiology ; Endoscopy ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Intestinal Mucosa/*microbiology ; RNA, Ribosomal, 16S/genetics ; Specimen Handling ; }, abstract = {BACKGROUND: The mucosa-associated microbiota appears to be highly relevant to host-microbe interactions in the gastrointestinal (GI) tract. Thus, precise characterisation of the mucosa-associated microbiota may provide important insights for diagnostic and therapeutic development. However, for technical reasons, mucosal biopsies taken during standard endoscopic procedures are potentially contaminated by GI luminal contents.

AIM: To develop and validate a biopsy device that minimises contamination during sampling of the mucosa-associated microbiota.

METHODS: A new, encased biopsy forceps was developed, the Brisbane Aseptic Biopsy Device (BABD). This comprises sterile forceps encased by a sheath with a plug at the tip, allowing targeted, aseptic sampling of the mucosa. Matched duodenal biopsies were obtained using the BABD, standard biopsy forceps, and a sterile brush, from patients undergoing upper GI endoscopy for iron deficiency (n = 6). Total genomic deoxyribonucleic acid (gDNA) was extracted from samples and bacterial 16S rRNA gene libraries sequenced to investigate the mucosa-associated microbiota.

RESULTS: Microbial DNA was recovered from biopsies obtained by the BABD, confirming the presence of a duodenal mucosa-associated microbiota. This microbiota was dominated by the genus Streptococcus, with lower levels of Prevotella, Veillonella and Neisseria. At the individual patient level, substantial differences were observed between matched samples obtained using the different devices. A greater degree of bacterial diversity was observed in samples collected using the standard forceps, indicating the BABD affords collection of samples more representative of the mucosa-associated microbiota, by precluding luminal cross-contamination.

CONCLUSIONS: Cross-contamination can occur when mucosal biopsies are taken during standard endoscopic procedures. Utilising the novel Brisbane Aseptic Biopsy Device can reduce cross-contamination, and it offers improved opportunities to more precisely examine host-mucosa-associated microbiota interactions.}, } @article {pmid27084119, year = {2016}, author = {Yang, JY and Kim, MS and Kim, E and Cheon, JH and Lee, YS and Kim, Y and Lee, SH and Seo, SU and Shin, SH and Choi, SS and Kim, B and Chang, SY and Ko, HJ and Bae, JW and Kweon, MN}, title = {Enteric Viruses Ameliorate Gut Inflammation via Toll-like Receptor 3 and Toll-like Receptor 7-Mediated Interferon-β Production.}, journal = {Immunity}, volume = {44}, number = {4}, pages = {889-900}, doi = {10.1016/j.immuni.2016.03.009}, pmid = {27084119}, issn = {1097-4180}, mesh = {Animals ; Antiviral Agents/pharmacology ; Colitis/chemically induced/*immunology ; Dendritic Cells/immunology ; Dextran Sulfate ; Gastrointestinal Microbiome ; Gastrointestinal Tract/immunology/*virology ; Humans ; Inflammation/immunology ; Interferon-beta/biosynthesis/*immunology ; Membrane Glycoproteins/genetics/*immunology ; Mice ; Mice, Inbred BALB C ; Mice, Knockout ; RNA, Ribosomal, 16S/genetics ; Rotavirus/*immunology ; Toll-Like Receptor 3/genetics/*immunology ; Toll-Like Receptor 7/genetics/*immunology ; }, abstract = {Metagenomic studies show that diverse resident viruses inhabit the healthy gut; however, little is known about the role of these viruses in the maintenance of gut homeostasis. We found that mice treated with antiviral cocktail displayed more severe dextran sulfate sodium (DSS)-induced colitis compared with untreated mice. DSS-induced colitis was associated with altered enteric viral abundance and composition. When wild-type mice were reconstituted with Toll-like receptor 3 (TLR3) or TLR7 agonists or inactivated rotavirus, colitis symptoms were significantly ameliorated. Mice deficient in both TLR3 and TLR7 were more susceptible to DSS-induced experimental colitis. In humans, combined TLR3 and TLR7 genetic variations significantly influenced the severity of ulcerative colitis. Plasmacytoid dendritic cells isolated from inflamed mouse colon produced interferon-β in a TLR3 and TLR7-dependent manner. These results imply that recognition of resident viruses by TLR3 and TLR7 is required for protective immunity during gut inflammation.}, } @article {pmid27080869, year = {2016}, author = {Hao, DC and Song, SM and Mu, J and Hu, WL and Xiao, PG}, title = {Unearthing microbial diversity of Taxus rhizosphere via MiSeq high-throughput amplicon sequencing and isolate characterization.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {22006}, pmid = {27080869}, issn = {2045-2322}, mesh = {*Biodiversity ; Cluster Analysis ; DNA Barcoding, Taxonomic ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; Microbiota ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; *Soil Microbiology ; Taxus/*microbiology ; }, abstract = {The species variability and potential environmental functions of Taxus rhizosphere microbial community were studied by comparative analyses of 15 16S rRNA and 15 ITS MiSeq sequencing libraries from Taxus rhizospheres in subtropical and temperate regions of China, as well as by isolating laccase-producing strains and polycyclic aromatic hydrocarbon (PAH)-degrading strains. Total reads could be assigned to 2,141 Operational Taxonomic Units (OTUs) belonging to 31 bacteria phyla and 2,904 OTUs of at least seven fungi phyla. The abundance of Planctomycetes, Actinobacteria, and Chloroflexi was higher in T. cuspidata var. nana and T. × media rhizospheres than in T. mairei rhizosphere (NF), while Acidobacteria, Proteobacteria, Nitrospirae, and unclassified bacteria were more abundant in the latter. Ascomycota and Zygomycota were predominant in NF, while two temperate Taxus rhizospheres had more unclassified fungi, Basidiomycota, and Chytridiomycota. The bacterial/fungal community richness and diversity were lower in NF than in other two. Three dye decolorizing fungal isolates were shown to be highly efficient in removing three classes of reactive dye, while two PAH-degrading fungi were able to degrade recalcitrant benzo[a]pyrene. The present studies extend the knowledge pedigree of the microbial diversity populating rhizospheres, and exemplify the method shift in research and development of resource plant rhizosphere.}, } @article {pmid27080513, year = {2016}, author = {Ren, W and Xun, Z and Wang, Z and Zhang, Q and Liu, X and Zheng, H and Zhang, Q and Zhang, Y and Zhang, L and Wu, C and Zheng, S and Qin, N and Ehrlich, SD and Li, Y and He, X and Xu, T and Chen, T and Chen, F}, title = {Tongue Coating and the Salivary Microbial Communities Vary in Children with Halitosis.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {24481}, pmid = {27080513}, issn = {2045-2322}, mesh = {Biodiversity ; Case-Control Studies ; Child ; Child, Preschool ; Female ; Halitosis/*epidemiology/*microbiology ; Humans ; Hydrogen Sulfide/metabolism ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Prevalence ; Saliva/*microbiology ; Tongue/*microbiology ; }, abstract = {Halitosis is a common symptom mainly caused by microbial activities in the oral cavity. Here, we used 16S rRNA gene pyrosequencing and metagenomic sequencing to examine oral microbial compositions and their functional variations in children with halitosis. We found that the tongue coating of subjects with halitosis had greater bacterial richness than those of healthy subjects. The relative abundance and prevalence of Leptotrichia wadei and Peptostreptococcus stomatis were higher in tongue coating samples from children with halitosis than those from children without halitosis; Prevotella shahii had higher relative abundance and prevalence in saliva samples from children with halitosis. We present the first comprehensive evaluation of the co-occurrence networks of saliva and tongue coating communities under healthy and halitosis conditions, and investigated patterns of significant differences between these communities. Moreover, we observed that bacterial genes associated with responses to infectious diseases and terpenoid and polyketide metabolism were enriched in subjects with halitosis, but not in healthy subjects. Hydrogen sulphide (H2S)-related metabolic pathways suggested that there was higher microbial production and less usage of H2S in subjects with halitosis. Thus, the mechanism of halitosis was implied for the first time via metagenomic sequencing.}, } @article {pmid27079454, year = {2016}, author = {Chen, L and Luo, Y and Xu, J and Yu, Z and Zhang, K and Brookes, PC}, title = {Assessment of Bacterial Communities and Predictive Functional Profiling in Soils Subjected to Short-Term Fumigation-Incubation.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {240-251}, pmid = {27079454}, issn = {1432-184X}, mesh = {Agriculture/methods ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; DNA, Bacterial/genetics ; Firmicutes/*classification/genetics/isolation & purification ; *Fumigation ; Genes, Bacterial ; Grassland ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Previous investigations observed that when soil was fumigated with ethanol-free CHCl3 for 24 h and then incubated under appropriate conditions, after the initial flush of CO2 was over, soil organic carbon (SOC) mineralization continued at the same rate as in the non-fumigated soil. This indicates that, following fumigation, the much diminished microbial population still retained the same ability to mineralize SOC as the much larger non-fumigated population. We hypothesize that although fumigation drastically alters the soil bacterial community abundance, composition, and diversity, it has little influence on the bacterial C-metabolic functions. Here, we conducted a 30-day incubation experiment involving a grassland soil and an arable soil with and without CHCl3 fumigation. At days 0, 7, and 30 of the incubation, the bacterial abundances were determined by quantitative PCR, and the bacterial community composition and diversity were assessed via the 16S rRNA gene amplicon sequencing. PICRUSt was used to predict the metagenome functional content from the sequence data. Fumigation considerably changed the composition and decreased the abundance and diversity of bacterial community at the end of incubation. At day 30, Firmicutes (mainly Bacilli) accounted for 70.9 and 94.6 % of the total sequences in the fumigated grassland and arable soil communities, respectively. The two fumigated soil communities exhibited large compositional and structural differences during incubation. The families Paenibacillaceae, Bacillaceae, and Symbiobacteriaceae dominated the bacterial community in the grassland soil, and Alicyclobacillaceae in the arable soil. Fumigation had little influence on the predicted abundances of KEGG orthologs (KOs) assigned to the metabolism of the main acid esters, saccharides, amino acids, and lipids in the grassland soil community. The saccharide-metabolizing KO abundances were decreased, but the acid ester- and fatty acid-metabolizing KO abundances were elevated by fumigation in the arable soil community. Our study suggests functional redundancy regarding the bacterial genetic potential associated with SOC mineralization.}, } @article {pmid27077101, year = {2016}, author = {Goedert, JJ}, title = {Effects of HIV, Immune Deficiency, and Confounding on the Distal Gut Microbiota.}, journal = {EBioMedicine}, volume = {5}, number = {}, pages = {14-15}, pmid = {27077101}, issn = {2352-3964}, support = {Z01 CP 010214/CP/NCI NIH HHS/United States ; //Intramural NIH HHS/United States ; }, mesh = {Bacteria ; Biodiversity ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/immunology ; HIV ; HIV Infections/immunology ; Humans ; Immune System ; Immunity, Mucosal ; Immunologic Deficiency Syndromes ; Intestines/immunology ; Metagenome ; Microbiota/*immunology ; Obesity ; Probiotics/therapeutic use ; }, } @article {pmid27074706, year = {2016}, author = {Langdon, A and Crook, N and Dantas, G}, title = {The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation.}, journal = {Genome medicine}, volume = {8}, number = {1}, pages = {39}, pmid = {27074706}, issn = {1756-994X}, support = {DP2 DK098089/DK/NIDDK NIH HHS/United States ; R01 GM099538/GM/NIGMS NIH HHS/United States ; T32 DK077653/DK/NIDDK NIH HHS/United States ; DP2-DK-098089/DK/NIDDK NIH HHS/United States ; R01-GM099538/GM/NIGMS NIH HHS/United States ; UL1 TR000448/TR/NCATS NIH HHS/United States ; TL1 TR000449/TR/NCATS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/adverse effects/*pharmacology/*therapeutic use ; Bacterial Infections/*drug therapy/*microbiology ; Disease Susceptibility ; Host-Pathogen Interactions/drug effects ; Humans ; Metagenome ; Metagenomics ; Microbiota/*drug effects ; Risk Factors ; }, abstract = {The widespread use of antibiotics in the past 80 years has saved millions of human lives, facilitated technological progress and killed incalculable numbers of microbes, both pathogenic and commensal. Human-associated microbes perform an array of important functions, and we are now just beginning to understand the ways in which antibiotics have reshaped their ecology and the functional consequences of these changes. Mounting evidence shows that antibiotics influence the function of the immune system, our ability to resist infection, and our capacity for processing food. Therefore, it is now more important than ever to revisit how we use antibiotics. This review summarizes current research on the short-term and long-term consequences of antibiotic use on the human microbiome, from early life to adulthood, and its effect on diseases such as malnutrition, obesity, diabetes, and Clostridium difficile infection. Motivated by the consequences of inappropriate antibiotic use, we explore recent progress in the development of antivirulence approaches for resisting infection while minimizing resistance to therapy. We close the article by discussing probiotics and fecal microbiota transplants, which promise to restore the microbiota after damage of the microbiome. Together, the results of studies in this field emphasize the importance of developing a mechanistic understanding of gut ecology to enable the development of new therapeutic strategies and to rationally limit the use of antibiotic compounds.}, } @article {pmid27072196, year = {2016}, author = {Liu, H and Guo, X and Gooneratne, R and Lai, R and Zeng, C and Zhan, F and Wang, W}, title = {The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {24340}, pmid = {27072196}, issn = {2045-2322}, mesh = {Animals ; Bacteria/classification/isolation & purification ; Fishes/*microbiology ; Fresh Water ; Intestines/enzymology/*microbiology ; *Microbiota ; Species Specificity ; }, abstract = {Vertebrate gut microbiome often underpins the metabolic capability and provides many beneficial effects on their hosts. However, little was known about how host trophic level influences fish gut microbiota and metabolic activity. In this study, more than 985,000 quality-filtered sequences from 24 16S rRNA libraries were obtained and the results revealed distinct compositions and diversities of gut microbiota in four trophic categories. PCoA test showed that gut bacterial communities of carnivorous and herbivorous fishes formed distinctly different clusters in PCoA space. Although fish in different trophic levels shared a large size of OTUs comprising a core microbiota community, at the genus level a strong distinction existed. Cellulose-degrading bacteria Clostridium, Citrobacter and Leptotrichia were dominant in the herbivorous, while Cetobacterium and protease-producing bacteria Halomonas were dominant in the carnivorous. PICRUSt predictions of metagenome function revealed that fishes in different trophic levels affected the metabolic capacity of their gut microbiota. Moreover, cellulase and amylase activities in herbivorous fishes were significantly higher than in the carnivorous, while trypsin activity in the carnivorous was much higher than in the herbivorous. These results indicated that host trophic level influenced the structure and composition of gut microbiota, metabolic capacity and gut content enzyme activity.}, } @article {pmid27070903, year = {2016}, author = {Kolmeder, CA and Salojärvi, J and Ritari, J and de Been, M and Raes, J and Falony, G and Vieira-Silva, S and Kekkonen, RA and Corthals, GL and Palva, A and Salonen, A and de Vos, WM}, title = {Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0153294}, pmid = {27070903}, issn = {1932-6203}, support = {250172/ERC_/European Research Council/International ; }, mesh = {Adult ; Bacterial Proteins/genetics/isolation & purification ; Cohort Studies ; Double-Blind Method ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Genome, Bacterial ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; Peptide Mapping ; Phylogeny ; Precision Medicine ; Probiotics/*therapeutic use ; Proteomics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Recent metagenomic studies have demonstrated that the overall functional potential of the intestinal microbiome is rather conserved between healthy individuals. Here we assessed the biological processes undertaken in-vivo by microbes and the host in the intestinal tract by conducting a metaproteome analysis from a total of 48 faecal samples of 16 healthy adults participating in a placebo-controlled probiotic intervention trial. Half of the subjects received placebo and the other half consumed Lactobacillus rhamnosus GG for three weeks (1010 cfu per day). Faecal samples were collected just before and at the end of the consumption phase as well as after a three-week follow-up period, and were processed for microbial composition and metaproteome analysis. A common core of shared microbial protein functions could be identified in all subjects. Furthermore, we observed marked differences in expressed proteins between subjects that resulted in the definition of a stable and personalized microbiome both at the mass-spectrometry-based proteome level and the functional level based on the KEGG pathway analysis. No significant changes in the metaproteome were attributable to the probiotic intervention. A detailed taxonomic assignment of peptides and comparison to phylogenetic microarray data made it possible to evaluate the activity of the main phyla as well as key species, including Faecalibacterium prausnitzii. Several correlations were identified between human and bacterial proteins. Proteins of the human host accounted for approximately 14% of the identified metaproteome and displayed variations both between and within individuals. The individually different human intestinal proteomes point to personalized host-microbiota interactions. Our findings indicate that analysis of the intestinal metaproteome can complement gene-based analysis and contributes to a thorough understanding of the activities of the microbiome and the relevant pathways in health and disease.}, } @article {pmid27067514, year = {2016}, author = {Lin, HH and Liao, YC}, title = {Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {24175}, pmid = {27067514}, issn = {2045-2322}, mesh = {Algorithms ; Automation/*methods ; Cluster Analysis ; Computational Biology/*methods ; *Contig Mapping ; Gastrointestinal Microbiome ; Genes ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota ; }, abstract = {Metagenomics, the application of shotgun sequencing, facilitates the reconstruction of the genomes of individual species from natural environments. A major challenge in the genome recovery domain is to agglomerate or 'bin' sequences assembled from metagenomic reads into individual groups. Metagenomic binning without consideration of reference sequences enables the comprehensive discovery of new microbial organisms and aids in the microbial genome reconstruction process. Here we present MyCC, an automated binning tool that combines genomic signatures, marker genes and optional contig coverages within one or multiple samples, in order to visualize the metagenomes and to identify the reconstructed genomic fragments. We demonstrate the superior performance of MyCC compared to other binning tools including CONCOCT, GroopM, MaxBin and MetaBAT on both synthetic and real human gut communities with a small sample size (one to 11 samples), as well as on a large metagenome dataset (over 250 samples). Moreover, we demonstrate the visualization of metagenomes in MyCC to aid in the reconstruction of genomes from distinct bins. MyCC is freely available at http://sourceforge.net/projects/sb2nhri/files/MyCC/.}, } @article {pmid27066712, year = {2016}, author = {Timsit, E and Workentine, M and Schryvers, AB and Holman, DB and van der Meer, F and Alexander, TW}, title = {Evolution of the nasopharyngeal microbiota of beef cattle from weaning to 40 days after arrival at a feedlot.}, journal = {Veterinary microbiology}, volume = {187}, number = {}, pages = {75-81}, doi = {10.1016/j.vetmic.2016.03.020}, pmid = {27066712}, issn = {1873-2542}, mesh = {Animals ; Bacteria/genetics/isolation & purification ; *Biodiversity ; Bovine Respiratory Disease Complex/microbiology ; Cattle ; Disease Susceptibility/microbiology ; Male ; Microbiota/*physiology ; Mycoplasma/genetics/isolation & purification ; Nasopharynx/*microbiology ; RNA, Ribosomal, 16S/genetics ; Weaning ; }, abstract = {Bovine respiratory disease complex (BRDc) is a major cause of morbidity and mortality in beef cattle. There is recent evidence suggesting that the nasopharyngeal microbiota has a key role in respiratory health and disease susceptibility in cattle. However, there is a paucity of knowledge regarding evolution of the nasopharyngeal microbiota when cattle are most likely to develop BRDc (i.e., from weaning to 40days after arrival at a feedlot). The objective was to describe the evolution of the nasopharyngeal microbiota of beef cattle from weaning to 40days after arrival at a feedlot. Deep nasal swabs (DNS) from 30 Angus-cross steers were collected at weaning, on arrival at a feedlot, and at day 40 after arrival. The DNA was extracted from DNS and the hypervariable region V3 of the 16S rRNA gene was amplified and sequenced (Illumina MiSeq platform). Nasopharyngeal microbiota underwent a profound evolution from weaning to arrival at the feedlot and from arrival to day 40, with the abundance of 92 Operational Taxonomic Units (OTUs) significantly changing over time. Mycoplasma (M. dispar and M. bovirhinis) was the most abundant genus in the nasopharynx, accounting for 53% of the total bacterial population. Because an evolving bacterial community may be less capable of resisting colonization by pathogenic bacteria, the instability of the nasopharyngeal microbiota documented in this study might explain why cattle are most likely to be affected with BRDc during the first weeks after weaning and arrival at a feedlot.}, } @article {pmid27063111, year = {2016}, author = {Leake, SL and Pagni, M and Falquet, L and Taroni, F and Greub, G}, title = {The salivary microbiome for differentiating individuals: proof of principle.}, journal = {Microbes and infection}, volume = {18}, number = {6}, pages = {399-405}, doi = {10.1016/j.micinf.2016.03.011}, pmid = {27063111}, issn = {1769-714X}, mesh = {Adult ; Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA-Directed RNA Polymerases ; Forensic Anthropology/*methods ; Forensic Medicine/*methods ; Healthy Volunteers ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Human identification has played a prominent role in forensic science for the past two decades. Identification based on unique genetic traits is driving the field. However, this may have limitations, for instance, for twins. Moreover, high-throughput sequencing techniques are now available and may provide a high amount of data likely useful in forensic science. This study investigates the potential for bacteria found in the salivary microbiome to be used to differentiate individuals. Two different targets (16S rRNA and rpoB) were chosen to maximise coverage of the salivary microbiome and when combined, they increase the power of differentiation (identification). Paired-end Illumina high-throughput sequencing was used to analyse the bacterial composition of saliva from two different people at four different time points (t = 0 and t = 28 days and then one year later at t = 0 and t = 28 days). Five major phyla dominate the samples: Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria. Streptococcus, a Firmicutes, is one of the most abundant aerobic genera found in saliva and targeting Streptococcus rpoB has enabled a deeper characterisation of the different streptococci species, which cannot be differentiated using 16S rRNA alone. We have observed that samples from the same person group together regardless of time of sampling. The results indicate that it is possible to distinguish two people using the bacterial microbiota present in their saliva.}, } @article {pmid27061465, year = {2016}, author = {Cleary, DF and Polónia, AR and Sousa, AI and Lillebø, AI and Queiroga, H and Gomes, NC}, title = {Temporal dynamics of sediment bacterial communities in monospecific stands of Juncus maritimus and Spartina maritima.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {18}, number = {5}, pages = {824-834}, doi = {10.1111/plb.12459}, pmid = {27061465}, issn = {1438-8677}, mesh = {Bacteria/*classification/genetics/isolation & purification/metabolism ; Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Ecosystem ; Geography ; Geologic Sediments/*microbiology ; Magnoliopsida/*microbiology ; *Metagenomics ; *Microbial Consortia ; Poaceae/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Wetlands ; }, abstract = {In the present study, we used 16S rRNA barcoded pyrosequencing to investigate to what extent monospecific stands of different salt marsh plant species (Juncus maritimus and Spartina maritima), sampling site and temporal variation affect sediment bacterial communities. We also used a bioinformatics tool, PICRUSt, to predict metagenome gene functional content. Our results showed that bacterial community composition from monospecific stands of both plant species varied temporally, but both host plant species maintained compositionally distinct communities of bacteria. Juncus sediment was characterised by higher abundances of Alphaproteobacteria, Myxococcales, Rhodospirillales, NB1-j and Ignavibacteriales, while Spartina sediment was characterised by higher abundances of Anaerolineae, Synechococcophycidae, Desulfobacterales, SHA-20 and Rhodobacterales. The differences in composition and higher taxon abundance between the sediment bacterial communities of stands of both plant species may be expected to affect overall metabolic diversity. In line with this expectation, there were also differences in the predicted enrichment of selected metabolic pathways. In particular, bacterial communities of Juncus sediment were predicted to be enriched for pathways related to the degradation of various (xenobiotic) compounds. Bacterial communities of Spartina sediment in turn were predicted to be enriched for pathways related to the biosynthesis of various bioactive compounds. Our study highlights the differences in composition and predicted functions of sediment-associated bacterial communities from two different salt marsh plant species. Loss of salt marsh habitat may thus be expected to both adversely affect microbial diversity and ecosystem functioning and have consequences for environmental processes such as nutrient cycling and pollutant remediation.}, } @article {pmid27061249, year = {2016}, author = {Mansbach, JM and Hasegawa, K and Henke, DM and Ajami, NJ and Petrosino, JF and Shaw, CA and Piedra, PA and Sullivan, AF and Espinola, JA and Camargo, CA}, title = {Respiratory syncytial virus and rhinovirus severe bronchiolitis are associated with distinct nasopharyngeal microbiota.}, journal = {The Journal of allergy and clinical immunology}, volume = {137}, number = {6}, pages = {1909-1913.e4}, pmid = {27061249}, issn = {1097-6825}, support = {R01 AI108588/AI/NIAID NIH HHS/United States ; R21 HL129909/HL/NHLBI NIH HHS/United States ; U01 AI067693/AI/NIAID NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; }, mesh = {Bronchiolitis, Viral/*microbiology ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; *Microbiota ; Nasal Cavity/*microbiology ; Pharynx/*microbiology ; Picornaviridae Infections/*microbiology ; Respiratory Syncytial Virus Infections/*microbiology ; *Respiratory Syncytial Virus, Human ; *Rhinovirus ; }, } @article {pmid27059297, year = {2016}, author = {Greenhalgh, K and Meyer, KM and Aagaard, KM and Wilmes, P}, title = {The human gut microbiome in health: establishment and resilience of microbiota over a lifetime.}, journal = {Environmental microbiology}, volume = {18}, number = {7}, pages = {2103-2116}, pmid = {27059297}, issn = {1462-2920}, support = {R01 NR014792/NR/NINR NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Health ; Humans ; Metagenomics ; }, abstract = {With technological advances in culture-independent molecular methods, we are uncovering a new facet of our natural history by accounting for the vast diversity of microbial life which colonizes the human body. The human microbiome contributes functional genes and metabolites which affect human physiology and are, therefore, considered an important factor for maintaining health. Much has been described in the past decade based primarily on 16S rRNA gene amplicon sequencing regarding the diversity, structure, stability and dynamics of human microbiota in their various body habitats, most notably within the gastrointestinal tract (GIT). Relatively high levels of variation have been described across different stages of life and geographical locations for the GIT microbiome. These observations may prove helpful for the future contextualization of patterns in other body habitats especially in relation to identifying generalizable trends over human lifetime. Given the large degree of complexity and variability, a key challenge will be how to define baseline healthy microbiomes and how to identify features which reflect deviations therefrom in the future. In this context, metagenomics and functional omics will likely play a central role as they will allow resolution of microbiome-conferred functionalities associated with health. Such information will be vital for formulating therapeutic interventions aimed at managing microbiota-mediated health particularly in the GIT over the course of a human lifetime.}, } @article {pmid27056560, year = {2016}, author = {Fyhrquist, N and Salava, A and Auvinen, P and Lauerma, A}, title = {Skin Biomes.}, journal = {Current allergy and asthma reports}, volume = {16}, number = {5}, pages = {40}, pmid = {27056560}, issn = {1534-6315}, mesh = {Animals ; Ecosystem ; Humans ; Metagenome ; *Microbiota ; Skin/*microbiology ; Skin Diseases/*microbiology/pathology ; }, abstract = {The cutaneous microbiome has been investigated broadly in recent years and some traditional perspectives are beginning to change. A diverse microbiome exists on human skin and has a potential to influence pathogenic microbes and modulate the course of skin disorders, e.g. atopic dermatitis. In addition to the known dysfunctions in barrier function of the skin and immunologic disturbances, evidence is rising that frequent skin disorders, e.g. atopic dermatitis, might be connected to a dysbiosis of the microbial community and changes in the skin microbiome. As a future perspective, examining the skin microbiome could be seen as a potential new diagnostic and therapeutic target in inflammatory skin disorders.}, } @article {pmid27056556, year = {2016}, author = {Jervis Bardy, J and Psaltis, AJ}, title = {Next Generation Sequencing and the Microbiome of Chronic Rhinosinusitis: A Primer for Clinicians and Review of Current Research, Its Limitations, and Future Directions.}, journal = {The Annals of otology, rhinology, and laryngology}, volume = {125}, number = {8}, pages = {613-621}, doi = {10.1177/0003489416641429}, pmid = {27056556}, issn = {1943-572X}, mesh = {Anti-Bacterial Agents/therapeutic use ; Chronic Disease ; Corynebacterium/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Microbiota/*genetics ; Nasal Cavity/*microbiology ; Paranasal Sinuses/*microbiology ; Propionibacterium/genetics ; RNA, Ribosomal, 16S/*genetics ; Rhinitis/drug therapy/*microbiology ; Sinusitis/drug therapy/*microbiology ; Staphylococcus/genetics ; }, abstract = {OBJECTIVE: Microbiomics in chronic diseases, including chronic rhinosinusitis (CRS), have undergone rapid advances in recent times. The introduction of Next Generation Sequencing (NGS) technology has produced significant clinical insights regarding the bacteriology of these conditions. We review studies that have used 16S rRNA sequencing to specifically investigate the microbiota profiles of patients with CRS in a variety of contexts.

METHODS: Literature review using the CINAHL, MEDLINE, PUBMED, and the Cochrane databases. Papers utilizing 16S-sequencing technology on CRS specimens published between January 1, 1995, and October 31, 2015, were included. Studies limited to only healthy controls were excluded.

RESULTS: Consistent with published studies using non-NGS techniques, the main genera commonly identified from the sinuses of CRS patients included Staphylococcus, Propionibacterium, and Corynebacterium. The microbiome of CRS patients had lower bacterial diversity compared to controls in a number of studies. Also consistent with non-NGS-based studies, Staphylococcus was implicated as an important genus, with highly colonized patients having worse surgical outcomes. Conflicting reports of antibiotic effects on the CRS microbiome were observed. Sampling methods were well investigated, many of the studies reviewed failed to include important methodological detail.

CONCLUSION: While 16S sequencing is a novel microbiological laboratory method, current studies have confirmed our existing understanding of bacteriology of CRS without providing significant additional clinical insight. Complementing 16S studies with more complex NGS methods while developing robust clinical studies aimed at shifting the disrupted CRS microbiome will provide researches with the opportunity to derive further clinical insight and develop new therapeutic targets.}, } @article {pmid27055030, year = {2016}, author = {Barbosa, A and Balagué, V and Valera, F and Martínez, A and Benzal, J and Motas, M and Diaz, JI and Mira, A and Pedrós-Alió, C}, title = {Age-Related Differences in the Gastrointestinal Microbiota of Chinstrap Penguins (Pygoscelis antarctica).}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0153215}, pmid = {27055030}, issn = {1932-6203}, mesh = {Age Factors ; Animals ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Genetic Variation/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenome ; Spheniscidae/*classification/*genetics/microbiology ; }, abstract = {The gastrointestinal tract microbiota is known to play very important roles in the well being of animals. It is a complex community composed by hundreds of microbial species interacting closely among them and with their host, that is, a microbial ecosystem. The development of high throughput sequencing techniques allows studying the diversity of such communities in a realistic way and considerable work has been carried out in mammals and some birds such as chickens. Wild birds have received less attention and in particular, in the case of penguins, only a few individuals of five species have been examined with molecular techniques. We collected cloacal samples from Chinstrap penguins in the Vapour Col rookery in Deception Island, Antarctica, and carried out pyrosequencing of the V1-V3 region of the 16S rDNA in samples from 53 individuals, 27 adults and 26 chicks. This provided the first description of the Chinstrap penguin gastrointestinal tract microbiota and the most extensive in any penguin species. Firmicutes, Bacteoridetes, Proteobacteria, Fusobacteria, Actinobacteria, and Tenericutes were the main components. There were large differences between chicks and adults. The former had more Firmicutes and the latter more Bacteroidetes and Proteobacteria. In addition, adults had richer and more diverse bacterial communities than chicks. These differences were also observed between parents and their offspring. On the other hand, nests explained differences in bacterial communities only among chicks. We suggest that environmental factors have a higher importance than genetic factors in the microbiota composition of chicks. The results also showed surprisingly large differences in community composition with other Antarctic penguins including the congeneric Adélie and Gentoo penguins.}, } @article {pmid27054497, year = {2016}, author = {Teeling, H and Fuchs, BM and Bennke, CM and Krüger, K and Chafee, M and Kappelmann, L and Reintjes, G and Waldmann, J and Quast, C and Glöckner, FO and Lucas, J and Wichels, A and Gerdts, G and Wiltshire, KH and Amann, RI}, title = {Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms.}, journal = {eLife}, volume = {5}, number = {}, pages = {e11888}, pmid = {27054497}, issn = {2050-084X}, mesh = {Bacteria/*classification/genetics/*isolation & purification ; *Biota ; *Eutrophication ; Germany ; Metagenomics ; North Sea ; Plankton/*microbiology ; Seawater/*microbiology ; }, abstract = {A process of global importance in carbon cycling is the remineralization of algae biomass by heterotrophic bacteria, most notably during massive marine algae blooms. Such blooms can trigger secondary blooms of planktonic bacteria that consist of swift successions of distinct bacterial clades, most prominently members of the Flavobacteriia, Gammaproteobacteria and the alphaproteobacterial Roseobacter clade. We investigated such successions during spring phytoplankton blooms in the southern North Sea (German Bight) for four consecutive years. Dense sampling and high-resolution taxonomic analyses allowed the detection of recurring patterns down to the genus level. Metagenome analyses also revealed recurrent patterns at the functional level, in particular with respect to algal polysaccharide degradation genes. We, therefore, hypothesize that even though there is substantial inter-annual variation between spring phytoplankton blooms, the accompanying succession of bacterial clades is largely governed by deterministic principles such as substrate-induced forcing.}, } @article {pmid27052710, year = {2016}, author = {Escobar-Zepeda, A and Sanchez-Flores, A and Quirasco Baruch, M}, title = {Metagenomic analysis of a Mexican ripened cheese reveals a unique complex microbiota.}, journal = {Food microbiology}, volume = {57}, number = {}, pages = {116-127}, doi = {10.1016/j.fm.2016.02.004}, pmid = {27052710}, issn = {1095-9998}, mesh = {Animals ; Archaea/classification/genetics/*isolation & purification/metabolism ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Biodiversity ; Cattle ; Cheese/*microbiology ; Metagenomics ; *Microbiota ; Milk/*microbiology ; }, abstract = {Cotija cheese is a Mexican handcrafted product made from raw cow milk whose ripening process occurs spontaneously and, presumably, it is influenced by environmental conditions. Its sensory characteristics and safety are probably the result of the balance between microbial populations and their metabolic capacity. In this work, we studied the dominance and richness of the bacteria in the Cotija cheese microbiome, as well as their metabolic potential by high-throughput sequencing. By the analysis of 16S ribosomal sequences, it was found that this metagenome is composed mainly of three dominant genera: Lactobacillus, Leuconostoc and Weissella, and more than 500 of non-dominant genera grouped in 31 phyla of both bacteria and archaea. The analysis of single-copy marker genes reported a similar result for dominant genera, although with greater resolution that reached the species level. Pathogenic bacteria such as Salmonella, Listeria monocytogenes, Brucella or Mycobacterium were not found. The Cotija cheese microbiome has the metabolic capacity for the synthesis of a wide range of flavor compounds, mainly involved with the metabolism of branched chain amino acids and free fatty acids. Genes associated with bacteriocin production and immunity were also found. Arguably, this is one of the most diverse metagenomes among the microbial communities related to fermented products.}, } @article {pmid27052538, year = {2016}, author = {Preidis, GA and Ajami, NJ and Wong, MC and Bessard, BC and Conner, ME and Petrosino, JF}, title = {Microbial-Derived Metabolites Reflect an Altered Intestinal Microbiota during Catch-Up Growth in Undernourished Neonatal Mice.}, journal = {The Journal of nutrition}, volume = {146}, number = {5}, pages = {940-948}, pmid = {27052538}, issn = {1541-6100}, support = {T32 DK007664/DK/NIDDK NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Animals, Newborn ; Bacteria/genetics/growth & development/*metabolism ; Bacteroidetes/growth & development/metabolism ; Biomarkers/metabolism ; Cresols/urine ; Feces ; Female ; Firmicutes/growth & development/metabolism ; *Gastrointestinal Microbiome ; *Growth ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Lactates/blood ; Male ; Metagenomics ; Mice ; Obesity/etiology/microbiology ; Polysaccharides/metabolism ; Protein-Energy Malnutrition/diet therapy/metabolism/*microbiology ; Serotonin/blood ; Sulfuric Acid Esters/urine ; Weaning ; *Weight Gain ; }, abstract = {BACKGROUND: Protein-energy undernutrition during early development confers a lifelong increased risk of obesity-related metabolic disease. Mechanisms by which metabolic abnormalities persist despite catch-up growth are poorly understood.

OBJECTIVE: We sought to determine whether abnormal metabolomic and intestinal microbiota profiles from undernourished neonatal mice remain altered during catch-up growth.

METHODS: Male and female CD1 mouse pups were undernourished by timed separation from lactating dams for 4 h at 5 d of age, 8 h at 6 d of age, and 12 h/d from 7 to 15 d of age, then resumed ad libitum nursing, whereas controls fed uninterrupted. Both groups were weaned simultaneously to a standard unpurified diet. At 3 time points (0, 1, and 3 wk after ending feed deprivation), metabolites in urine, plasma, and stool were identified with the use of mass spectrometry, and fecal microbes were identified with the use of 16S metagenomic sequencing.

RESULTS: Undernourished mice completely recovered deficits of 36% weight and 9% length by 3 wk of refeeding, at which time they had 1.4-fold higher plasma phenyllactate and 2.0-fold higher urinary p-cresol sulfate concentrations than did controls. Plasma serotonin concentrations in undernourished mice were 25% lower at 0 wk but 1.5-fold higher than in controls at 3 wk. Whereas most urine and plasma metabolites normalized with refeeding, 117 fecal metabolites remained altered at 3 wk, including multiple N-linked glycans. Microbiota profiles from undernourished mice also remained distinct, with lower mean proportions of Bacteroidetes (67% compared with 83%) and higher proportions of Firmicutes (26% compared with 16%). Abundances of the mucolytic organisms Akkermansia muciniphila and Mucispirillum schaedleri were altered at 0 and 1 wk. Whereas microbiota from undernourished mice at 0 wk contained 11% less community diversity (P = 0.015), refed mice at 3 wk harbored 1.2-fold greater diversity (P = 0.0006) than did controls.

CONCLUSION: Microbial-derived metabolites and intestinal microbiota remain altered during catch-up growth in undernourished neonatal mice.}, } @article {pmid27051943, year = {2015}, author = {Xin, X and Junzhi, H and Xuedong, Z}, title = {[Oral microbiota: a promising predictor of human oral and systemic diseases].}, journal = {Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology}, volume = {33}, number = {6}, pages = {555-560}, pmid = {27051943}, issn = {1000-1182}, mesh = {*Biomarkers ; Cardiovascular Diseases/microbiology ; Dental Caries/microbiology ; Diabetes Mellitus/microbiology ; Humans ; Metagenomics ; *Microbiota ; Mouth/*microbiology ; Mouth Diseases/microbiology ; Neoplasms/microbiology ; Oral Health ; Periodontal Diseases/microbiology ; }, abstract = {A human oral microbiota is the ecological community of commensal, symbiotic, and pathogenic microorganisms found in human oral cavity. Oral microbiota exists mostly in the form of a biofilm and maintains a dynamic ecological equilibrium with the host body. However, the disturbance of this ecological balance inevitably causes oral infectious diseases, such as dental caries, apical periodontitis, periodontal diseases, pericoronitis, and craniofacial bone osteomyelitis. Oral microbiota is also correlated with many systemic diseases, including cancer, diabetes mellitus, rheumatoid arthritis, cardiovascular diseases, and preterm birth. Hence, oral microbiota has been considered as a potential biomarker of human diseases. The "Human Microbiome Project" and other metagenomic projects worldwide have advanced our knowledge of the human oral microbiota. The integration of these metadata has been the frontier of oral microbiology to improve clinical translation. By reviewing recent progress on studies involving oral microbiota-related oral and systemic diseases, we aimed to propose the essential role of oral microbiota in the prediction of the onset, progression, and prognosis of oral and systemic diseases. An oral microbiota-based prediction model helps develop a new paradigm of personalized medicine and benefits the human health in the post-metagenomics era.}, } @article {pmid27048892, year = {2016}, author = {Chang, C and Lin, H}, title = {Dysbiosis in gastrointestinal disorders.}, journal = {Best practice & research. Clinical gastroenterology}, volume = {30}, number = {1}, pages = {3-15}, doi = {10.1016/j.bpg.2016.02.001}, pmid = {27048892}, issn = {1532-1916}, mesh = {Animals ; Diet ; Dysbiosis/*microbiology/physiopathology ; Gastrointestinal Diseases/*microbiology/physiopathology ; Gastrointestinal Microbiome/physiology ; Humans ; }, abstract = {The recent development of advanced sequencing techniques has revealed the complexity and diverse functions of the gut microbiota. Furthermore, alterations in the composition or balance of the intestinal microbiota, or dysbiosis, are associated with many gastrointestinal diseases. The looming question is whether dysbiosis is a cause or effect of these diseases. In this review, we will evaluate the contribution of intestinal microbiota in obesity, fatty liver, inflammatory bowel disease, and irritable bowel syndrome. Promising results from microbiota or metabolite transfer experiments in animals suggest the microbiota may be sufficient to reproduce disease features in the appropriate host in certain disorders. Less compelling causal associations may reflect complex, multi-factorial disease pathogenesis, in which dysbiosis is a necessary condition. Understanding the contributions of the microbiota in GI diseases should offer novel insight into disease pathophysiology and deliver new treatment strategies such as therapeutic manipulation of the microbiota.}, } @article {pmid27048805, year = {2016}, author = {Hemme, CL and Green, SJ and Rishishwar, L and Prakash, O and Pettenato, A and Chakraborty, R and Deutschbauer, AM and Van Nostrand, JD and Wu, L and He, Z and Jordan, IK and Hazen, TC and Arkin, AP and Kostka, JE and Zhou, J}, title = {Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e02234-15}, pmid = {27048805}, issn = {2150-7511}, mesh = {Gammaproteobacteria/*genetics/metabolism ; *Gene Transfer, Horizontal ; Groundwater/analysis/*microbiology ; Metals, Heavy/*analysis/metabolism ; Microbiota ; Water Pollutants, Chemical/*analysis/metabolism ; }, abstract = {UNLABELLED: Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe(2+)/Pb(2+) permeases, most denitrification enzymes, and cytochrome c553, were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co(2+)/Zn(2+)/Cd(2+) efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome.

IMPORTANCE: Lateral gene transfer (LGT), along with positive selection and gene duplication, are the three main mechanisms that drive adaptive evolution of microbial genomes and communities, but their relative importance is unclear. Some recent studies suggested that LGT is a major adaptive mechanism for microbial populations in response to changing environments, and hence, it could also be critical in shaping microbial community structure. However, direct evidence of LGT and its rates in extant natural microbial communities in response to changing environments is still lacking. Our results presented in this study provide explicit evidence that LGT played a crucial role in driving the evolution of a groundwater microbial community in response to extreme heavy metal contamination. It appears that acquisition of genes critical for survival, growth, and reproduction via LGT is the most rapid and effective way to enable microorganisms and associated microbial communities to quickly adapt to abrupt harsh environmental stresses.}, } @article {pmid27045926, year = {2016}, author = {D'Argenio, V and Casaburi, G and Precone, V and Pagliuca, C and Colicchio, R and Sarnataro, D and Discepolo, V and Kim, SM and Russo, I and Del Vecchio Blanco, G and Horner, DS and Chiara, M and Pesole, G and Salvatore, P and Monteleone, G and Ciacci, C and Caporaso, GJ and Jabrì, B and Salvatore, F and Sacchetti, L}, title = {Metagenomics Reveals Dysbiosis and a Potentially Pathogenic N. flavescens Strain in Duodenum of Adult Celiac Patients.}, journal = {The American journal of gastroenterology}, volume = {111}, number = {6}, pages = {879-890}, pmid = {27045926}, issn = {1572-0241}, mesh = {Actinobacteria/classification/isolation & purification ; Adult ; Biopsy ; Caco-2 Cells ; Celiac Disease/*microbiology ; Diet, Gluten-Free ; Duodenum/*microbiology ; Dysbiosis/*microbiology ; Enzyme-Linked Immunosorbent Assay ; Female ; Fluorescent Antibody Technique ; Humans ; Italy ; Male ; *Metagenomics ; Microbiota ; Neisseria/classification/*isolation & purification ; Proteobacteria/classification/isolation & purification ; }, abstract = {OBJECTIVES: Celiac disease (CD)-associated duodenal dysbiosis has not yet been clearly defined, and the mechanisms by which CD-associated dysbiosis could concur to CD development or exacerbation are unknown. In this study, we analyzed the duodenal microbiome of CD patients.

METHODS: The microbiome was evaluated in duodenal biopsy samples of 20 adult patients with active CD, 6 CD patients on a gluten-free diet, and 15 controls by DNA sequencing of 16S ribosomal RNA libraries. Bacterial species were cultured, isolated and identified by mass spectrometry. Isolated bacterial species were used to infect CaCo-2 cells, and to stimulate normal duodenal explants and cultured human and murine dendritic cells (DCs). Inflammatory markers and cytokines were evaluated by immunofluorescence and ELISA, respectively.

RESULTS: Proteobacteria was the most abundant and Firmicutes and Actinobacteria the least abundant phyla in the microbiome profiles of active CD patients. Members of the Neisseria genus (Betaproteobacteria class) were significantly more abundant in active CD patients than in the other two groups (P=0.03). Neisseria flavescens (CD-Nf) was the most abundant Neisseria species in active CD duodenum. Whole-genome sequencing of CD-Nf and control-Nf showed genetic diversity of the iron acquisition systems and of some hemoglobin-related genes. CD-Nf was able to escape the lysosomal compartment in CaCo-2 cells and to induce an inflammatory response in DCs and in ex-vivo mucosal explants.

CONCLUSIONS: Marked dysbiosis and an abundance of a peculiar CD-Nf strain characterize the duodenal microbiome in active CD patients thus suggesting that the CD-associated microbiota could contribute to the many inflammatory signals in this disorder.}, } @article {pmid27045832, year = {2016}, author = {Land, TA and Fizzano, P and Kodner, RB}, title = {Measuring Cluster Stability in a Large Scale Phylogenetic Analysis of Functional Genes in Metagenomes Using pplacer.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {13}, number = {2}, pages = {341-349}, doi = {10.1109/TCBB.2015.2446470}, pmid = {27045832}, issn = {1557-9964}, mesh = {*Cluster Analysis ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; *Phylogeny ; }, abstract = {Analysis of metagenomic sequence data requires a multi-stage workflow. The results of each intermediate step possess an inherent uncertainty and potentially impact the as-yet-unmeasured statistical significance of downstream analyses. Here, we describe our phylogenetic analysis pipeline which uses the pplacer program to place many shotgun sequences corresponding to a single functional gene onto a fixed phylogenetic tree. We then use the squash clustering method to compare multiple samples with respect to that gene. We approximate the statistical significance of each gene's clustering result by measuring its cluster stability, the consistency of that clustering result when the probabilistic placements made by pplacer are systematically reassigned and then clustered again, as measured by the adjusted Rand Index. We find that among the genes investigated, the majority of analyses are stable, based on the average adjusted Rand Index. We investigated properties of each gene that may explain less stable results. These genes tended to have less convex reference trees, less total reads recruited to the gene, and a greater Expected Distance between Placement Locations as given by pplacer when examined in aggregate. However, for an individual functional gene, these measures alone do not predict cluster stability.}, } @article {pmid27044409, year = {2016}, author = {Wu, G and Zhang, C and Wang, J and Zhang, F and Wang, R and Shen, J and Wang, L and Pang, X and Zhang, X and Zhao, L and Zhang, M}, title = {Diminution of the gut resistome after a gut microbiota-targeted dietary intervention in obese children.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {24030}, pmid = {27044409}, issn = {2045-2322}, mesh = {Anti-Bacterial Agents/chemistry ; Child ; China ; Databases, Genetic ; *Diet ; Drug Resistance, Bacterial/*genetics ; Enterobacter/genetics ; Escherichia/genetics ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Genes, Bacterial ; Humans ; Klebsiella/genetics ; Medicine, Chinese Traditional ; Pediatric Obesity/*diet therapy/*microbiology ; }, abstract = {The gut microbiome represents an important reservoir of antibiotic resistance genes (ARGs). Effective methods are urgently needed for managing the gut resistome to fight against the antibiotic resistance threat. In this study, we show that a gut microbiota-targeted dietary intervention, which shifts the dominant fermentation of gut bacteria from protein to carbohydrate, significantly diminished the gut resistome and alleviated metabolic syndrome in obese children. Of the non-redundant metagenomic gene catalog of ~2 × 10(6) microbial genes, 399 ARGs were identified in 131 gene types and conferred resistance to 47 antibiotics. Both the richness and diversity of the gut resistome were significantly reduced after the intervention. A total of 201 of the 399 ARGs were carried in 120 co-abundance gene groups (CAGs) directly binned from the gene catalog across both pre-and post-intervention samples. The intervention significantly reduced several CAGs in Klebsiella, Enterobacter and Escherichia, which were the major hubs for multiple resistance gene types. Thus, dietary intervention may become a potentially effective method for diminishing the gut resistome.}, } @article {pmid27043715, year = {2016}, author = {Rossi, M and Martínez-Martínez, D and Amaretti, A and Ulrici, A and Raimondi, S and Moya, A}, title = {Mining metagenomic whole genome sequences revealed subdominant but constant Lactobacillus population in the human gut microbiota.}, journal = {Environmental microbiology reports}, volume = {8}, number = {3}, pages = {399-406}, doi = {10.1111/1758-2229.12405}, pmid = {27043715}, issn = {1758-2229}, mesh = {Bacterial Load ; Gastrointestinal Tract/*microbiology ; Humans ; Lactobacillus/*classification/*genetics ; Longitudinal Studies ; *Metagenomics ; *Microbiota ; }, abstract = {The genus Lactobacillus includes over 215 species that colonize plants, foods, sewage and the gastrointestinal tract (GIT) of humans and animals. In the GIT, Lactobacillus population can be made by true inhabitants or by bacteria occasionally ingested with fermented or spoiled foods, or with probiotics. This study longitudinally surveyed Lactobacillus species and strains in the feces of a healthy subject through whole genome sequencing (WGS) data-mining, in order to identify members of the permanent or transient populations. In three time-points (0, 670 and 700 d), 58 different species were identified, 16 of them being retrieved for the first time in human feces. L. rhamnosus, L. ruminis, L. delbrueckii, L. plantarum, L. casei and L. acidophilus were the most represented, with estimated amounts ranging between 6 and 8 Log (cells g(-1)), while the other were detected at 4 or 5 Log (cells g(-1)). 86 Lactobacillus strains belonging to 52 species were identified. 43 seemingly occupied the GIT as true residents, since were detected in a time span of almost 2 years in all the three samples or in 2 samples separated by 670 or 700 d. As a whole, a stable community of lactobacilli was disclosed, with wide and understudied biodiversity.}, } @article {pmid27038948, year = {2016}, author = {Zhang, L and Kang, M and Huang, Y and Yang, L}, title = {Fungal communities from the calcareous deep-sea sediments in the Southwest India Ridge revealed by Illumina sequencing technology.}, journal = {World journal of microbiology & biotechnology}, volume = {32}, number = {5}, pages = {78}, pmid = {27038948}, issn = {1573-0972}, mesh = {*Biodiversity ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fungi/classification/genetics/*isolation & purification ; Geologic Sediments/*microbiology ; India ; Phylogeny ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The diversity and ecological significance of bacteria and archaea in deep-sea environments have been thoroughly investigated, but eukaryotic microorganisms in these areas, such as fungi, are poorly understood. To elucidate fungal diversity in calcareous deep-sea sediments in the Southwest India Ridge (SWIR), the internal transcribed spacer (ITS) regions of rRNA genes from two sediment metagenomic DNA samples were amplified and sequenced using the Illumina sequencing platform. The results revealed that 58-63 % and 36-42 % of the ITS sequences (97 % similarity) belonged to Basidiomycota and Ascomycota, respectively. These findings suggest that Basidiomycota and Ascomycota are the predominant fungal phyla in the two samples. We also found that Agaricomycetes, Leotiomycetes, and Pezizomycetes were the major fungal classes in the two samples. At the species level, Thelephoraceae sp. and Phialocephala fortinii were major fungal species in the two samples. Despite the low relative abundance, unidentified fungal sequences were also observed in the two samples. Furthermore, we found that there were slight differences in fungal diversity between the two sediment samples, although both were collected from the SWIR. Thus, our results demonstrate that calcareous deep-sea sediments in the SWIR harbor diverse fungi, which augment the fungal groups in deep-sea sediments. This is the first report of fungal communities in calcareous deep-sea sediments in the SWIR revealed by Illumina sequencing.}, } @article {pmid27037675, year = {2016}, author = {Willoughby, JR and Wijayawardena, BK and Sundaram, M and Swihart, RK and DeWoody, JA}, title = {The importance of including imperfect detection models in eDNA experimental design.}, journal = {Molecular ecology resources}, volume = {16}, number = {4}, pages = {837-844}, doi = {10.1111/1755-0998.12531}, pmid = {27037675}, issn = {1755-0998}, mesh = {Biostatistics/*methods ; *Biota ; *Environment ; *Metagenome ; Metagenomics/*methods ; *Research Design ; }, abstract = {Environmental DNA (eDNA) is DNA that has been isolated from field samples, and it is increasingly used to infer the presence or absence of particular species in an ecosystem. However, the combination of sampling procedures and subsequent molecular amplification of eDNA can lead to spurious results. As such, it is imperative that eDNA studies include a statistical framework for interpreting eDNA presence/absence data. We reviewed published literature for studies that utilized eDNA where the species density was known and compared the probability of detecting the focal species to the sampling and analysis protocols. Although biomass of the target species and the volume per sample did not impact detectability, the number of field replicates and number of samples from each replicate were positively related to detection. Additionally, increased number of PCR replicates and increased primer specificity significantly increased detectability. Accordingly, we advocate for increased use of occupancy modelling as a method to incorporate effects of sampling effort and PCR sensitivity in eDNA study design. Based on simulation results and the hierarchical nature of occupancy models, we suggest that field replicates, as opposed to molecular replicates, result in better detection probabilities of target species.}, } @article {pmid27037032, year = {2016}, author = {Handley, SA}, title = {The virome: a missing component of biological interaction networks in health and disease.}, journal = {Genome medicine}, volume = {8}, number = {1}, pages = {32}, pmid = {27037032}, issn = {1756-994X}, mesh = {Animals ; Disease Susceptibility ; *Host-Pathogen Interactions/genetics/immunology ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Systems Biology ; Virus Diseases/genetics/immunology/virology ; *Viruses ; }, abstract = {Host-associated viral populations, viromes, have been understudied relative to their contribution to human physiology. Viruses interact with host gene networks, influencing both health and disease. Analysis of host gene networks in the absence of virome analysis risks missing important network information.}, } @article {pmid27035381, year = {2016}, author = {Brumbaugh, DE and Arruda, J and Robbins, K and Ir, D and Santorico, SA and Robertson, CE and Frank, DN}, title = {Mode of Delivery Determines Neonatal Pharyngeal Bacterial Composition and Early Intestinal Colonization.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {63}, number = {3}, pages = {320-328}, doi = {10.1097/MPG.0000000000001124}, pmid = {27035381}, issn = {1536-4801}, mesh = {Adult ; Delivery, Obstetric/adverse effects/*methods ; Feces/*microbiology ; Female ; Humans ; Infant ; Infant, Newborn ; Intestines/*microbiology ; Male ; *Microbiota ; Pharynx/*microbiology ; Pregnancy ; Prospective Studies ; Rectum/microbiology ; Sequence Analysis, DNA ; Skin/microbiology ; Vagina/microbiology ; }, abstract = {OBJECTIVES: Bacterial colonization and succession of the human intestine shape development of immune function and risk for allergic disease, yet these processes remain poorly understood. We investigated the relations between delivery mode, initial bacterial inoculation of the infant oropharynx (OP), and intestinal colonization.

METHODS: We prospectively collected maternal rectal and vaginal swabs, infant OP aspirates, and infant stool from 23 healthy mother/infant pairs delivering by cesarean (CS) or vaginal delivery (VD) in an academic hospital. Bacterial abundance (16S rRNA sequencing) and community similarity between samples were compared by delivery mode. Shotgun DNA metagenomic sequencing of infant stool was performed.

RESULTS: VD infants had higher abundance of Firmicutes (mainly lactobacilli) in OP aspirates whereas CS OP aspirates were enriched in skin bacteria. OP aspirates were more similar to maternal vaginal and rectal microbiomes in VD compared with CS. Bacteroidetes were more abundant through 6 weeks in stool of VD infants. Infant fecal microbiomes in both delivery groups did not resemble maternal rectal or vaginal microbiomes. Differences in fecal bacterial gene potential between CS and VD at 6 weeks clustered in metabolic pathways and were mediated by abundance of Proteobacteria and Bacteroidetes.

CONCLUSIONS: CS infants exhibited different microbiota in the oral inoculum, a chaotic pattern of bacterial succession, and a persistent deficit of intestinal Bacteroidetes. Pioneer OP bacteria transferred from maternal vaginal and intestinal communities were not prominent constituents of the early infant fecal microbiome. Oral inoculation at birth may impact the intestinal microenvironment, thereby modulating early succession of intestinal bacteria.}, } @article {pmid27033535, year = {2016}, author = {Eberly, JO and Indest, KJ and Hancock, DE and Jung, CM and Crocker, FH}, title = {Metagenomic analysis of denitrifying wastewater enrichment cultures able to transform the explosive, 3-nitro-1,2,4-triazol-5-one (NTO).}, journal = {Journal of industrial microbiology & biotechnology}, volume = {43}, number = {6}, pages = {795-805}, pmid = {27033535}, issn = {1476-5535}, mesh = {Clostridiaceae/isolation & purification/metabolism ; *Denitrification ; Firmicutes/isolation & purification/metabolism ; Metagenomics/*methods ; Microbial Consortia ; Nitrates/analysis ; Nitro Compounds/*chemistry ; Proteobacteria/isolation & purification/metabolism ; Pseudomonadaceae/isolation & purification/metabolism ; Triazoles/*chemistry ; Wastewater/*chemistry/microbiology ; }, abstract = {Removal of 3-nitro-1,2,4-triazol-5-one (NTO) was investigated in conjunction with heterotrophic and autotrophic denitrifying growth conditions by a microbial consortium from a wastewater treatment plant. Microcosms were supplemented with molasses, methanol, or thiosulfate. Cultures were passaged twice by transferring 10 % of the culture volume to fresh media on days 11 and 21. Rates of NTO removal were 18.71 ± 0.65, 9.04 ± 2.61, and 4.34 ± 2.72 mg/L/day while rates of nitrate removal were 20.08 ± 1.13, 21.58 ± 1.20, and 24.84 ± 1.26 mg/L/day, respectively, for molasses, methanol, or thiosulfate. Metagenomic analysis showed that Proteobacteria and Firmicutes were the major phyla in the microbial communities. In molasses supplemented cultures, the community profile at the family level changed over time with Pseudomonadaceae the most abundant (67.4 %) at day 11, Clostridiaceae (65.7 %) at day 21, and Sporolactobacillaceae (35.4 %) and Clostridiaceae (41.0 %) at day 29. Pseudomonadaceae was the dominant family in methanol and thiosulfate supplemented cultures from day 21 to 29 with 76.6 and 81.6 % relative abundance, respectively.}, } @article {pmid27033168, year = {2016}, author = {Zhao, P and Irwin, DM and Dong, D}, title = {Host genetics is associated with the gut microbial community membership rather than the structure.}, journal = {Molecular bioSystems}, volume = {12}, number = {5}, pages = {1676-1686}, doi = {10.1039/c5mb00850f}, pmid = {27033168}, issn = {1742-2051}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Animals ; Child ; Child, Preschool ; Evolution, Molecular ; Female ; Gastrointestinal Microbiome/*genetics ; *Genetic Association Studies ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenome ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Support Vector Machine ; Young Adult ; }, abstract = {The issue of what factors shape the gut microbiota has been studied for years. However, questions on the contribution of host genetics to the colonizing process of the gut microbiota and to the extent that host genetics affect the gut microbiota have not yet been clearly answered. Most recently published reports have concluded that host genetics make a smaller contribution than other factors, such as diet, in determining the gut microbiota. Here we have exploited the increasing amount of fecal 16S rRNA gene sequencing data that are becoming available to conduct an analysis to assess the influence of host genetics on the diversity of the gut microbiota. By re-analyzing data obtained from over 5000 stool samples, representing individuals living on five continents and ranging in age from 3 days to 87 years, we found that the strength of the various factors affecting the membership or structure of the gut microbiota are quite different, which leads us to a hypothesis that the presence or absence of taxa is largely controlled by host genetics, whereas non-genetic factors regulate the abundance of each taxon. This hypothesis is supported by the finding that the genome similarity positively correlates with the similarity of community membership. Finally, we showed that only severe perturbations are able to alter the gut microbial community membership. In summary, our work provides new insights into understanding the complexities of the gut microbial community and how it responds to changes imposed on it.}, } @article {pmid27028797, year = {2017}, author = {Del Chierico, F and Nobili, V and Vernocchi, P and Russo, A and De Stefanis, C and Gnani, D and Furlanello, C and Zandonà, A and Paci, P and Capuani, G and Dallapiccola, B and Miccheli, A and Alisi, A and Putignani, L}, title = {Gut microbiota profiling of pediatric nonalcoholic fatty liver disease and obese patients unveiled by an integrated meta-omics-based approach.}, journal = {Hepatology (Baltimore, Md.)}, volume = {65}, number = {2}, pages = {451-464}, doi = {10.1002/hep.28572}, pmid = {27028797}, issn = {1527-3350}, mesh = {Adolescent ; Analysis of Variance ; Case-Control Studies ; Child ; Fatty Liver/microbiology/physiopathology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Multivariate Analysis ; Non-alcoholic Fatty Liver Disease/*microbiology/physiopathology ; Obesity/*microbiology/physiopathology ; Pediatrics ; Proteogenomics/methods ; Reference Values ; Sensitivity and Specificity ; }, abstract = {UNLABELLED: There is evidence that nonalcoholic fatty liver disease (NAFLD) is affected by gut microbiota. Therefore, we investigated its modifications in pediatric NAFLD patients using targeted metagenomics and metabolomics. Stools were collected from 61 consecutive patients diagnosed with nonalcoholic fatty liver (NAFL), nonalcoholic steatohepatitis (NASH), or obesity and 54 healthy controls (CTRLs), matched in a case-control fashion. Operational taxonomic units were pyrosequenced targeting 16S ribosomal RNA and volatile organic compounds determined by solid-phase microextraction gas chromatography-mass spectrometry. The α-diversity was highest in CTRLs, followed by obese, NASH, and NAFL patients; and β-diversity distinguished between patients and CTRLs but not NAFL and NASH. Compared to CTRLs, in NAFLD patients Actinobacteria were significantly increased and Bacteroidetes reduced. There were no significant differences among the NAFL, NASH, and obese groups. Overall NAFLD patients had increased levels of Bradyrhizobium, Anaerococcus, Peptoniphilus, Propionibacterium acnes, Dorea, and Ruminococcus and reduced proportions of Oscillospira and Rikenellaceae compared to CTRLs. After reducing metagenomics and metabolomics data dimensionality, multivariate analyses indicated a decrease of Oscillospira in NAFL and NASH groups and increases of Ruminococcus, Blautia, and Dorea in NASH patients compared to CTRLs. Of the 292 volatile organic compounds, 26 were up-regulated and 2 down-regulated in NAFLD patients. Multivariate analyses found that combination of Oscillospira, Rickenellaceae, Parabacteroides, Bacteroides fragilis, Sutterella, Lachnospiraceae, 4-methyl-2-pentanone, 1-butanol, and 2-butanone could discriminate NAFLD patients from CTRLs. Univariate analyses found significantly lower levels of Oscillospira and higher levels of 1-pentanol and 2-butanone in NAFL patients compared to CTRLs. In NASH, lower levels of Oscillospira were associated with higher abundance of Dorea and Ruminococcus and higher levels of 2-butanone and 4-methyl-2-pentanone compared to CTRLs.

CONCLUSION: An Oscillospira decrease coupled to a 2-butanone up-regulation and increases in Ruminococcus and Dorea were identified as gut microbiota signatures of NAFL onset and NAFL-NASH progression, respectively. (Hepatology 2017;65:451-464).}, } @article {pmid27027646, year = {2016}, author = {Šuranská, H and Raspor, P and Uroić, K and Golić, N and Kos, B and Mihajlović, S and Begović, J and Šušković, J and Topisirović, L and Čadež, N}, title = {Characterisation of the yeast and mould biota in traditional white pickled cheeses by culture-dependent and independent molecular techniques.}, journal = {Folia microbiologica}, volume = {61}, number = {6}, pages = {455-463}, pmid = {27027646}, issn = {1874-9356}, mesh = {*Biodiversity ; Cheese/*microbiology ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fungi/*classification/genetics/*isolation & purification ; Polymorphism, Restriction Fragment Length ; Serbia ; }, abstract = {Artisanal white pickled cheese of Western Serbia is a product of complex microbial community which detection by culture-dependent method only is hampered by its limitations. Thus, in the present study, we used a culture-independent, semi-quantitative technique based on construction of an internal transcribed spacer (ITS)-clone library from metagenomic DNA. This approach, based on direct DNA extraction followed by amplification of fungal internal transcribed regions (ITS) cloned into plasmid and restricted by endonucleases, revealed greater species richness in analysed cheeses and their by-products (17 species in total) compared to the more commonly used techniques of the culture-dependent method (8 species) and LSU-DGGE (10 species). The most frequently occurring yeast species which are commonly associated with cheeses production were Debaryomyces hansenii, Kluyveromyces lactis and Candida zeylanoides. On the other hand, Yarrowia lipolytica and Galactomyces geotrichum were detected only in one cheese sample. Moreover, some species, mainly moulds (Filobasidium globisporum, Cladosporium sp., Aspergillus sp. or Alternaria sp.) were identified only by culture-independent methods. The discrepancies between the techniques were confirmed by low correlation factor and by different indices of general biodiversity and dominance of species. The ITS-clone library approach provides the opportunity to analyse complex fungal communities associated with food products.}, } @article {pmid27027301, year = {2016}, author = {Ponziani, FR and Scaldaferri, F and Petito, V and Paroni Sterbini, F and Pecere, S and Lopetuso, LR and Palladini, A and Gerardi, V and Masucci, L and Pompili, M and Cammarota, G and Sanguinetti, M and Gasbarrini, A}, title = {The Role of Antibiotics in Gut Microbiota Modulation: The Eubiotic Effects of Rifaximin.}, journal = {Digestive diseases (Basel, Switzerland)}, volume = {34}, number = {3}, pages = {269-278}, doi = {10.1159/000443361}, pmid = {27027301}, issn = {1421-9875}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; DNA, Bacterial/isolation & purification ; Gastrointestinal Microbiome/*drug effects ; Humans ; Lactobacillus/drug effects ; Rifamycins/administration & dosage/*pharmacology ; Rifaximin ; }, abstract = {Antibiotics are mainly used in clinical practice for their activity against pathogens, but they also alter the composition of commensal gut microbial community. Rifaximin is a non-absorbable antibiotic with additional effects on the gut microbiota about which very little is known. It is still not clear to what extent rifaximin can be able to modulate gut microbiota composition and diversity in different clinical settings. Studies based on culture-dependent techniques revealed that rifaximin treatment promotes the growth of beneficial bacteria, such as Bifidobacteria and Lactobacilli. Accordingly, our metagenomic analysis carried out on patients with different gastrointestinal and liver diseases highlighted a significant increase in Lactobacilli after rifaximin treatment, persisting in the short time period. This result was independent of the disease background and was not accompanied by a significant alteration of the overall gut microbial ecology. This suggests that rifaximin can exert important eubiotic effects independently of the original disease, producing a favorable gut microbiota perturbation without changing its overall composition and diversity.}, } @article {pmid27026373, year = {2016}, author = {Yu, H and Guo, Z and Shen, S and Shan, W}, title = {Effects of taurine on gut microbiota and metabolism in mice.}, journal = {Amino acids}, volume = {48}, number = {7}, pages = {1601-1617}, doi = {10.1007/s00726-016-2219-y}, pmid = {27026373}, issn = {1438-2199}, mesh = {Animals ; Gastrointestinal Microbiome/*drug effects ; Helicobacter/genetics/*growth & development ; *Metagenome ; Mice ; Mice, Inbred BALB C ; Taurine/*pharmacology ; }, abstract = {As being a necessary amino acid, taurine plays an important role in the regulation of neuroendocrine functions and nutrition. In this study, effects of taurine on mice gut microbes and metabolism were investigated. BALB/C mice were randomly divided into three experimental groups: The first group was administered saline (CK), the second was administered 165 mg/kg natural taurine (NE) and the third one administered 165 mg/kg synthetic taurine (CS). Gut microbiota composition in mice feces was analyzed by metagenomics technology, and the content of short-chain fatty acids (SCFA) in mice feces was detected by gas chromatography (GC), while the concentrations of lipopolysaccharide (LPS) and superoxide dismutase (SOD) were detected by a LPS ELISA kit and a SOD assay kit, respectively. The results showed that the effect of taurine on gut microbiota could reduce the abundance of Proteobacteria, especially Helicobacter. Moreover, we found that the SCFA content was increased in feces of the NE group while LPS content was decreased in serum of the NE group; the SOD activity in serum and livers of the NE and CS groups were not changed significantly compare to that of the CK group. In conclusion, taurine could regulate the gut micro-ecology, which might be of benefit to health by inhibiting the growth of harmful bacteria, accelerating the production of SCFA and reducing LPS concentration.}, } @article {pmid27025836, year = {2016}, author = {Millan, B and Park, H and Hotte, N and Mathieu, O and Burguiere, P and Tompkins, TA and Kao, D and Madsen, KL}, title = {Fecal Microbial Transplants Reduce Antibiotic-resistant Genes in Patients With Recurrent Clostridium difficile Infection.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {62}, number = {12}, pages = {1479-1486}, pmid = {27025836}, issn = {1537-6591}, support = {93675//CIHR/Canada ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/pharmacology ; Clostridioides difficile/*drug effects/genetics ; Drug Resistance, Bacterial/*genetics ; Enterocolitis, Pseudomembranous/microbiology/*therapy ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Middle Aged ; }, abstract = {BACKGROUND: Recurrent Clostridium difficile infection (RCDI) is associated with repeated antibiotic treatment and the enhanced growth of antibiotic-resistant microbes. This study tested the hypothesis that patients with RCDI would harbor large numbers of antibiotic-resistant microbes and that fecal microbiota transplantation (FMT) would reduce the number of antibiotic-resistant genes.

METHODS: In a single center study, patients with RCDI (n = 20) received FMT from universal donors via colonoscopy. Stool samples were collected from donors (n = 3) and patients prior to and following FMT. DNA was extracted and shotgun metagenomics performed. Results as well as assembled libraries from a healthy cohort (n = 87) obtained from the Human Microbiome Project were aligned against the NCBI bacterial taxonomy database and the Comprehensive Antibiotic Resistance Database. Results were corroborated through a DNA microarray containing 354 antibiotic resistance (ABR) genes.

RESULTS: RCDI patients had a greater number and diversity of ABR genes compared with donors and healthy controls. Beta-lactam, multidrug efflux pumps, fluoroquinolone, and antibiotic inactivation ABR genes were increased in RCDI patients, although donors primarily had tetracycline resistance. RCDI patients were dominated by Proteobacteria with Escherichia coli and Klebsiella most prevalent. FMT resulted in a resolution of symptoms that correlated directly with a decreased number and diversity of ABR genes and increased Bacteroidetes and Firmicutes with reduced Proteobacteria. ABR gene profiles were maintained in recipients for up to a year following FMT.

CONCLUSIONS: RCDI patients have increased numbers of antibiotic-resistant organisms. FMT is effective in the eradication of pathogenic antibiotic-resistant organisms and elimination of ABR genes.}, } @article {pmid27025724, year = {2016}, author = {Tejesvi, MV and Uhari, M and Tapiainen, T and Pirttilä, AM and Suokas, M and Lantto, U and Koivunen, P and Renko, M}, title = {Tonsillar microbiota in children with PFAPA (periodic fever, aphthous stomatitis, pharyngitis, and adenitis) syndrome.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {35}, number = {6}, pages = {963-970}, pmid = {27025724}, issn = {1435-4373}, mesh = {Biodiversity ; Case-Control Studies ; Child ; Child, Preschool ; Computational Biology/methods ; Female ; Fever/*etiology ; Humans ; Infant ; Infant, Newborn ; Lymphadenitis/*etiology ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Palatine Tonsil/*microbiology/surgery ; Pharyngitis/*etiology ; Stomatitis, Aphthous/*etiology ; Syndrome ; Tonsillectomy ; }, abstract = {Periodic fever, aphthous stomatitis, pharyngitis, and adenitis (PFAPA) is a childhood febrile syndrome of unknown origin that is often cured with tonsillectomy. We aimed to compare the bacterial microbiota of the tonsils removed from PFAPA patients with those of controls. We used next-generation sequencing technology to investigate the bacterial microbiota of the tonsils of 30 PFAPA patients and 24 controls. We found significant differences in the presence and relative abundance of many bacteria between PFAPA cases and controls. For example, cyanobacteria, potential producers of microcystins and other toxins, were more common in the case samples (14/30, 47 %) than in the controls (4/24, 17 %, p = 0.02), and the mean relative abundance of cyanobacteria was higher in the case samples (0.2 %) than in the controls (0.01 %, p = 0.01). Streptococci were present in all samples in both groups, but their mean relative abundance was lower in the case samples (3.7 %) than in the controls (9.6 %, p = 0.01). Typical nasopharyngeal microbes such as fusobacteria, Prevotella, Tannerella, Porphyromonas, and Parvimonas dominated the microbiota of the tonsils in both groups. The microbiota of the tonsils removed from PFAPA patients differed significantly from those of the controls. Tonsillar microbiota may play a role in triggering the inflammatory processes that lead to symptoms of PFAPA.}, } @article {pmid27025487, year = {2016}, author = {Ilina, LA and Yildirim, EA and Nikonov, IN and Filippova, VA and Laptev, GY and Novikova, NI and Grozina, AA and Lenkova, TN and Manukyan, VA and Egorov, IA and Fisinin, VI}, title = {Metagenomic bacterial community profiles of chicken embryo gastrointestinal tract by using T-RFLP analysis.}, journal = {Doklady. Biochemistry and biophysics}, volume = {466}, number = {}, pages = {47-51}, pmid = {27025487}, issn = {1608-3091}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Animals ; Chick Embryo ; *Genome, Bacterial ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; *Metagenome ; *Microbiota ; Rickettsieae/genetics/isolation & purification ; }, abstract = {Thirty microbial phylotypes of microorganisms were found in the gastrointestinal tract of chicken belonging to the Hajseks White breed, and 38 phylotypes were found in the gastrointestinal tract of chicken belonging to the Hajseks Brown breed. The microbiome of the gastrointestinal tract of the chicken embryos of the Hajseks White breed was dominated by the typical representatives of avian intestinal microflora--bacteria of the family Enterobacteriaceae (47.3%), orders Actinomycetales (13.6%) and Bifidobacteriales (20.6%), and the family Lachnospiraceae (1.1%). The microbiome of the gastrointestinal tract of the chicken embryos of the Hajseks Brown breed was dominated by the pathogenic bacteria of the order Rickettsiales (94.8%). The metagenome of gastrointestinal tract of both breeds also contained a small number of genes of unidentified bacteria.}, } @article {pmid27025191, year = {2016}, author = {Pore, SD and Shetty, D and Arora, P and Maheshwari, S and Dhakephalkar, PK}, title = {Metagenome changes in the biogas producing community during anaerobic digestion of rice straw.}, journal = {Bioresource technology}, volume = {213}, number = {}, pages = {50-53}, doi = {10.1016/j.biortech.2016.03.045}, pmid = {27025191}, issn = {1873-2976}, mesh = {Anaerobiosis ; Bacteria/genetics ; Biofuels/*microbiology ; Euryarchaeota/genetics ; Fatty Acids, Volatile/metabolism ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Metagenomics ; Methane/*metabolism ; *Microbial Consortia ; Oryza/*microbiology ; Oxidoreductases/genetics ; }, abstract = {The present investigation was undertaken to study the microbial community succession in a sour and healthy digester. Ion torrent next-generation sequencing (NGS)-based metagenomic approach indicated abundance of hydrolytic bacteria and exclusion of methanogens and syntrophic bacteria in sour digester. Functional gene analysis revealed higher abundance of enzymes involved in acidogenesis and lower abundance of enzymes associated with methanogenesis like Methyl coenzyme M-reductase, F420 dependent reductase and Formylmethanofuran dehydrogenase in sour digester. Increased abundance of methanogens (Methanomicrobia) and genes involved in methanogenesis was observed in the restored/healthy digester highlighting revival of pH sensitive methanogenic community.}, } @article {pmid27023533, year = {2016}, author = {Houghton, D and Stewart, CJ and Day, CP and Trenell, M}, title = {Gut Microbiota and Lifestyle Interventions in NAFLD.}, journal = {International journal of molecular sciences}, volume = {17}, number = {4}, pages = {447}, pmid = {27023533}, issn = {1422-0067}, support = {189/ALZS_/Alzheimer's Society/United Kingdom ; G0700718/MRC_/Medical Research Council/United Kingdom ; MR/L016354/1/MRC_/Medical Research Council/United Kingdom ; SRF-2011-04-017/DH_/Department of Health/United Kingdom ; }, mesh = {Animals ; Carbohydrate Metabolism ; Diet ; Humans ; Intestines/*microbiology ; *Life Style ; *Microbiota ; Non-alcoholic Fatty Liver Disease/metabolism/*pathology ; Prebiotics/microbiology ; Probiotics/administration & dosage ; }, abstract = {The human digestive system harbors a diverse and complex community of microorganisms that work in a symbiotic fashion with the host, contributing to metabolism, immune response and intestinal architecture. However, disruption of a stable and diverse community, termed "dysbiosis", has been shown to have a profound impact upon health and disease. Emerging data demonstrate dysbiosis of the gut microbiota to be linked with non-alcoholic fatty liver disease (NAFLD). Although the exact mechanism(s) remain unknown, inflammation, damage to the intestinal membrane, and translocation of bacteria have all been suggested. Lifestyle intervention is undoubtedly effective at improving NAFLD, however, not all patients respond to these in the same manner. Furthermore, studies investigating the effects of lifestyle interventions on the gut microbiota in NAFLD patients are lacking. A deeper understanding of how different aspects of lifestyle (diet/nutrition/exercise) affect the host-microbiome interaction may allow for a more tailored approach to lifestyle intervention. With gut microbiota representing a key element of personalized medicine and nutrition, we review the effects of lifestyle interventions (diet and physical activity/exercise) on gut microbiota and how this impacts upon NAFLD prognosis.}, } @article {pmid27023811, year = {2016}, author = {Yausheva, Е and Sizova, Е and Lebedev, S and Skalny, A and Miroshnikov, S and Plotnikov, A and Khlopko, Y and Gogoleva, N and Cherkasov, S}, title = {Influence of zinc nanoparticles on survival of worms Eisenia fetida and taxonomic diversity of the gut microflora.}, journal = {Environmental science and pollution research international}, volume = {23}, number = {13}, pages = {13245-13254}, pmid = {27023811}, issn = {1614-7499}, mesh = {Actinobacteria/genetics ; Animals ; Bacteria/genetics ; Gastrointestinal Microbiome/*drug effects ; Metagenomics ; Nanoparticles/*toxicity ; Oligochaeta/*drug effects/*microbiology ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Zinc/*toxicity ; }, abstract = {The study was conducted to examine the effect of zinc nanoparticles on survival of worms Eisenia fetida and composition of the gut microflora. Analysis of the survival data has shown that the introduction of high doses of the nanoparticles causes death of worms in the second group with 35 % mortality rate and activates protective mechanisms realized as mucous film. DNA from the worm guts was extracted and 16S metagenomic sequencing was fulfilled using MiSeq (Illumina). Regarding the gut microflora of worms in the control group, high diversity of microorganisms (303 OTUs) was noted. Most of those belong to the taxa Firmicutes (51.9 % of the total high-quality united reads), Proteobacteria (24.1 % of the total), and Actinobacteria (13.3 % of the total), which were represented by numerous species of gen. Clostridium (C. saccharobutylicum, C. saccharoperbutylacetonicum, C. beijerinckii), gen. Pseudomonas (P. hydrogenovora, P. aeruginosa, and P. putida), gen. Bacillus (B. megaterium, B. silvestris), gen. Cellulomonas (B. megaterium, B. silvestris), and other numerically smaller genera. Adding of zinc nanoparticles to the substrate decreased the diversity of bacteria (78 OTUs) as well as percentage of bacteria belonging to the taxon Firmicutes (-41.6 %) and increased the proportion of Proteobacteria due to growth in abundance of gen. Verminephrobacter (+46 %) and gen. Ochrobactrum (+19.5 %).}, } @article {pmid27022994, year = {2016}, author = {Hubalek, V and Wu, X and Eiler, A and Buck, M and Heim, C and Dopson, M and Bertilsson, S and Ionescu, D}, title = {Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield.}, journal = {The ISME journal}, volume = {10}, number = {10}, pages = {2447-2458}, pmid = {27022994}, issn = {1751-7370}, mesh = {*Biodiversity ; Carbon Cycle ; Epsilonproteobacteria/classification/genetics/*isolation & purification/*metabolism ; Groundwater/*microbiology ; Metagenomics ; Nitrogen/metabolism ; Phylogeny ; Sulfur/metabolism ; }, abstract = {Little research has been conducted on microbial diversity deep under the Earth's surface. In this study, the microbial communities of three deep terrestrial subsurface aquifers were investigated. Temporal community data over 6 years revealed that the phylogenetic structure and community dynamics were highly dependent on the degree of isolation from the earth surface biomes. The microbial community at the shallow site was the most dynamic and was dominated by the sulfur-oxidizing genera Sulfurovum or Sulfurimonas at all-time points. The microbial community in the meteoric water filled intermediate aquifer (water turnover approximately every 5 years) was less variable and was dominated by candidate phylum OD1. Metagenomic analysis of this water demonstrated the occurrence of key genes for nitrogen and carbon fixation, sulfate reduction, sulfide oxidation and fermentation. The deepest water mass (5000 year old waters) had the lowest taxon richness and surprisingly contained Cyanobacteria. The high relative abundance of phylogenetic groups associated with nitrogen and sulfur cycling, as well as fermentation implied that these processes were important in these systems. We conclude that the microbial community patterns appear to be shaped by the availability of energy and nutrient sources via connectivity to the surface or from deep geological processes.}, } @article {pmid27020245, year = {2016}, author = {Jacquiod, S and Stenbæk, J and Santos, SS and Winding, A and Sørensen, SJ and Priemé, A}, title = {Metagenomes provide valuable comparative information on soil microeukaryotes.}, journal = {Research in microbiology}, volume = {167}, number = {5}, pages = {436-450}, doi = {10.1016/j.resmic.2016.03.003}, pmid = {27020245}, issn = {1769-7123}, mesh = {*Biodiversity ; Computational Biology/*methods ; Eukaryota/*classification/*genetics ; *Metagenome ; *Phylogeny ; *Soil Microbiology ; }, abstract = {Despite the critical ecological roles of microeukaryotes in terrestrial ecosystems, most descriptive studies of soil microbes published so far focused only on specific groups. Meanwhile, the fast development of metagenome sequencing leads to considerable data accumulation in public repositories, providing microbiologists with substantial amounts of accessible information. We took advantage of public metagenomes in order to investigate microeukaryote communities in a well characterized grassland soil. The data gathered allowed the evaluation of several factors impacting the community structure, including the DNA extraction method, the database choice and also the annotation procedure. While most studies on soil microeukaryotes are based on sequencing of PCR-amplified taxonomic markers (18S rRNA genes, ITS regions), this work represents, to our knowledge, the first report based solely on metagenomic microeukaryote DNA. Choosing the correct annotation procedure and reference database has proven to be crucial, as it considerably limits the risk of wrong assignments. In addition, a significant and pronounced effect of the DNA extraction method on the taxonomical structure of soil microeukaryotes has been identified. Our analyses suggest that publicly available metagenome data can provide valuable information on soil microeukaryotes for comparative purposes when handled appropriately, complementing the current view provided by ribosomal amplicon sequencing methods.}, } @article {pmid27015976, year = {2016}, author = {Müller, CA and Obermeier, MM and Berg, G}, title = {Bioprospecting plant-associated microbiomes.}, journal = {Journal of biotechnology}, volume = {235}, number = {}, pages = {171-180}, doi = {10.1016/j.jbiotec.2016.03.033}, pmid = {27015976}, issn = {1873-4863}, mesh = {*Bioprospecting ; *Metagenomics ; *Microbiota ; Plants/*microbiology ; Rhizosphere ; }, abstract = {There is growing demand for new bioactive compounds and biologicals for the pharmaceutical, agro- and food industries. Plant-associated microbes present an attractive and promising source to this end, but are nearly unexploited. Therefore, bioprospecting of plant microbiomes is gaining more and more attention. Due to their highly specialized and co-evolved genetic pool, plant microbiomes host a rich secondary metabolism. This article highlights the potential detection and use of secondary metabolites and enzymes derived from plant-associated microorganisms in biotechnology. As an example we summarize the findings from the moss microbiome with special focus on the genus Sphagnum and its biotechnological potential for the discovery of novel microorganisms and bioactive molecules. The selected examples illustrate unique and yet untapped properties of plant-associated microbiomes, which are an immense treasure box for future research.}, } @article {pmid27015003, year = {2016}, author = {Wu, J and Peters, BA and Dominianni, C and Zhang, Y and Pei, Z and Yang, L and Ma, Y and Purdue, MP and Jacobs, EJ and Gapstur, SM and Li, H and Alekseyenko, AV and Hayes, RB and Ahn, J}, title = {Cigarette smoking and the oral microbiome in a large study of American adults.}, journal = {The ISME journal}, volume = {10}, number = {10}, pages = {2435-2446}, pmid = {27015003}, issn = {1751-7370}, support = {R01 CA159036/CA/NCI NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; U01 CA170948/CA/NCI NIH HHS/United States ; R21 CA183887/CA/NCI NIH HHS/United States ; R03 CA159414/CA/NCI NIH HHS/United States ; U01 CA182370/CA/NCI NIH HHS/United States ; R01 CA164964/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Bacteria/classification/genetics/*isolation & purification ; Dysbiosis/microbiology ; Female ; Humans ; Male ; Metagenome ; Metagenomics ; *Microbiota ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; Smoking/adverse effects ; United States ; Young Adult ; }, abstract = {Oral microbiome dysbiosis is associated with oral disease and potentially with systemic diseases; however, the determinants of these microbial imbalances are largely unknown. In a study of 1204 US adults, we assessed the relationship of cigarette smoking with the oral microbiome. 16S rRNA gene sequencing was performed on DNA from oral wash samples, sequences were clustered into operational taxonomic units (OTUs) using QIIME and metagenomic content was inferred using PICRUSt. Overall oral microbiome composition differed between current and non-current (former and never) smokers (P<0.001). Current smokers had lower relative abundance of the phylum Proteobacteria (4.6%) compared with never smokers (11.7%) (false discovery rate q=5.2 × 10(-7)), with no difference between former and never smokers; the depletion of Proteobacteria in current smokers was also observed at class, genus and OTU levels. Taxa not belonging to Proteobacteria were also associated with smoking: the genera Capnocytophaga, Peptostreptococcus and Leptotrichia were depleted, while Atopobium and Streptococcus were enriched, in current compared with never smokers. Functional analysis from inferred metagenomes showed that bacterial genera depleted by smoking were related to carbohydrate and energy metabolism, and to xenobiotic metabolism. Our findings demonstrate that smoking alters the oral microbiome, potentially leading to shifts in functional pathways with implications for smoking-related diseases.}, } @article {pmid27014224, year = {2016}, author = {Crits-Christoph, A and Robinson, CK and Ma, B and Ravel, J and Wierzchos, J and Ascaso, C and Artieda, O and Souza-Egipsy, V and Casero, MC and DiRuggiero, J}, title = {Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities in Hyper-Arid Environments.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {301}, pmid = {27014224}, issn = {1664-302X}, abstract = {Under extreme water deficit, endolithic (inside rock) microbial ecosystems are considered environmental refuges for life in cold and hot deserts, yet their diversity and functional adaptations remain vastly unexplored. The metagenomic analyses of the communities from two rock substrates, calcite and ignimbrite, revealed that they were dominated by Cyanobacteria, Actinobacteria, and Chloroflexi. The relative distribution of major phyla was significantly different between the two substrates and biodiversity estimates, from 16S rRNA gene sequences and from the metagenomic data, all pointed to a higher taxonomic diversity in the calcite community. While both endolithic communities showed adaptations to extreme aridity and to the rock habitat, their functional capabilities revealed significant differences. ABC transporters and pathways for osmoregulation were more diverse in the calcite chasmoendolithic community. In contrast, the ignimbrite cryptoendolithic community was enriched in pathways for secondary metabolites, such as non-ribosomal peptides (NRP) and polyketides (PK). Assemblies of the metagenome data produced population genomes for the major phyla found in both communities and revealed a greater diversity of Cyanobacteria population genomes for the calcite substrate. Draft genomes of the dominant Cyanobacteria in each community were constructed with more than 93% estimated completeness. The two annotated proteomes shared 64% amino acid identity and a significantly higher number of genes involved in iron update, and NRPS gene clusters, were found in the draft genomes from the ignimbrite. Both the community-wide and genome-specific differences may be related to higher water availability and the colonization of large fissures and cracks in the calcite in contrast to a harsh competition for colonization space and nutrient resources in the narrow pores of the ignimbrite. Together, these results indicated that the habitable architecture of both lithic substrates- chasmoendolithic versus cryptoendolithic - might be an essential element in determining the colonization and the diversity of the microbial communities in endolithic substrates at the dry limit for life.}, } @article {pmid27014222, year = {2016}, author = {Belanche, A and Jones, E and Parveen, I and Newbold, CJ}, title = {A Metagenomics Approach to Evaluate the Impact of Dietary Supplementation with Ascophyllum nodosum or Laminaria digitata on Rumen Function in Rusitec Fermenters.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {299}, pmid = {27014222}, issn = {1664-302X}, abstract = {There is an increasing need to identify alternative feeds for livestock that do not compete with foods for humans. Seaweed might provide such a resource, but there is limited information available on its value as an animal feed. Here we use a multi-omics approach to investigate the value of two brown seaweeds, Ascophyllum nodosum (ASC) and Laminaria digitata (LAM), as alternative feeds for ruminants. These seaweeds were supplemented at 5% inclusion rate into a control diet (CON) in a rumen simulation fermenter. The seaweeds had no substantial effect on rumen fermentation, feed degradability or methane emissions. Concentrations of total bacteria, anaerobic fungi, biodiversity indices and abundances of the main bacterial and methanogen genera were also unaffected. However, species-specific effects of brown seaweed on the rumen function were noted: ASC promoted a substantial decrease in N degradability (-24%) due to its high phlorotannins content. Canonical correspondence analysis of the bacterial community revealed that low N availability led to a change in the structure of the bacterial community. ASC also decreased the concentration of Escherichia coli O157:H7 post-inoculation. In contrast, LAM which has a much lower phlorotannin content did not cause detrimental effects on N degradability nor modified the structure of the bacterial community in comparison to CON. This adaptation of the microbial community to LAM diets led to a greater microbial ability to digest xylan (+70%) and carboxy-methyl-cellulose (+41%). These differences among brown seaweeds resulted in greater microbial protein synthesis (+15%) and non-ammonia N flow (+11%) in LAM than in ASC diets and thus should led to a greater amino acid supply to the intestine of the animal. In conclusion, it was demonstrated that incorporation of brown seaweed into the diet can be considered as a suitable nutritional strategy for ruminants; however, special care must be taken with those seaweeds with high phlorotannin concentrations to prevent detrimental effects on N metabolism. This study highlights the value of combining fermentation and enzyme activity data with molecular characterization of the rumen microbiome in evaluating novel feeds for ruminants. Further experiments are required to determine the maximum seaweed inclusion rate tolerated by rumen microbes.}, } @article {pmid27012914, year = {2016}, author = {Lojkić, I and Biđin, M and Prpić, J and Šimić, I and Krešić, N and Bedeković, T}, title = {Faecal virome of red foxes from peri-urban areas.}, journal = {Comparative immunology, microbiology and infectious diseases}, volume = {45}, number = {}, pages = {10-15}, pmid = {27012914}, issn = {1878-1667}, mesh = {Animals ; Animals, Domestic ; Circovirus/classification/genetics/*isolation & purification ; Croatia ; Disease Reservoirs/veterinary/virology ; Dogs ; Feces/*virology ; Foxes/*virology ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Microbiota ; Parvovirus/classification/genetics/*isolation & purification ; Phylogeny ; Picobirnavirus/classification/genetics/*isolation & purification ; Sequence Analysis, DNA ; Swine ; *Urban Population ; }, abstract = {Red foxes (Vulpes vulpes) are the most abundant carnivore species in the Northern Hemisphere. Since their populations are well established in peri-urban and urban areas, they represent a potential reservoir of viruses that transmit from wildlife to humans or domestic animals. In this study, we evaluated the faecal virome of juvenile and adult foxes from peri-urban areas in central Croatia. The dominating mammalian viruses were fox picobirnavirus and parvovirus. The highest number of viral reads (N=1412) was attributed to a new fox circovirus and complete viral genome was de novo assembled from the high-throughput sequencing data. Fox circovirus is highly similar to dog circoviruses identified in diseased dogs in USA and Italy, and to a recently discovered circovirus of foxes with neurologic disease from the United Kingdom. Our fox picobirnavirus was more closely related to the porcine and human picobirnaviruses than to known fox picobirnaviruses.}, } @article {pmid27012595, year = {2016}, author = {Smirnov, KS and Maier, TV and Walker, A and Heinzmann, SS and Forcisi, S and Martinez, I and Walter, J and Schmitt-Kopplin, P}, title = {Challenges of metabolomics in human gut microbiota research.}, journal = {International journal of medical microbiology : IJMM}, volume = {306}, number = {5}, pages = {266-279}, doi = {10.1016/j.ijmm.2016.03.006}, pmid = {27012595}, issn = {1618-0607}, mesh = {Animals ; Disease Models, Animal ; Feces/*chemistry/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Magnetic Resonance Spectroscopy ; Mass Spectrometry ; Metabolomics/*methods ; *Microbiota ; Reproducibility of Results ; }, abstract = {The review highlights the role of metabolomics in studying human gut microbial metabolism. Microbial communities in our gut exert a multitude of functions with huge impact on human health and disease. Within the meta-omics discipline, gut microbiome is studied by (meta)genomics, (meta)transcriptomics, (meta)proteomics and metabolomics. The goal of metabolomics research applied to fecal samples is to perform their metabolic profiling, to quantify compounds and classes of interest, to characterize small molecules produced by gut microbes. Nuclear magnetic resonance spectroscopy and mass spectrometry are main technologies that are applied in fecal metabolomics. Metabolomics studies have been increasingly used in gut microbiota related research regarding health and disease with main focus on understanding inflammatory bowel diseases. The elucidated metabolites in this field are summarized in this review. We also addressed the main challenges of metabolomics in current and future gut microbiota research. The first challenge reflects the need of adequate analytical tools and pipelines, including sample handling, selection of appropriate equipment, and statistical evaluation to enable meaningful biological interpretation. The second challenge is related to the choice of the right animal model for studies on gut microbiota. We exemplified this using NMR spectroscopy for the investigation of cross-species comparison of fecal metabolite profiles. Finally, we present the problem of variability of human gut microbiota and metabolome that has important consequences on the concepts of personalized nutrition and medicine.}, } @article {pmid27012191, year = {2016}, author = {Kirpich, IA and Petrosino, J and Ajami, N and Feng, W and Wang, Y and Liu, Y and Beier, JI and Barve, SS and Yin, X and Wei, X and Zhang, X and McClain, CJ}, title = {Saturated and Unsaturated Dietary Fats Differentially Modulate Ethanol-Induced Changes in Gut Microbiome and Metabolome in a Mouse Model of Alcoholic Liver Disease.}, journal = {The American journal of pathology}, volume = {186}, number = {4}, pages = {765-776}, pmid = {27012191}, issn = {1525-2191}, support = {R03 DK107912/DK/NIDDK NIH HHS/United States ; U01 AA021893/AA/NIAAA NIH HHS/United States ; U01 AA021901/AA/NIAAA NIH HHS/United States ; P20 GM113226/GM/NIGMS NIH HHS/United States ; R01AA023681/AA/NIAAA NIH HHS/United States ; P50 AA024337/AA/NIAAA NIH HHS/United States ; R21 AA020849-01A1/AA/NIAAA NIH HHS/United States ; R01 AA018869/AA/NIAAA NIH HHS/United States ; U01AA022489/AA/NIAAA NIH HHS/United States ; 1U01AA021901-01/AA/NIAAA NIH HHS/United States ; 1U01AA021893-01/AA/NIAAA NIH HHS/United States ; R21 AA020849/AA/NIAAA NIH HHS/United States ; R01 AA023681/AA/NIAAA NIH HHS/United States ; U01 AA022489/AA/NIAAA NIH HHS/United States ; R01AA018869/AA/NIAAA NIH HHS/United States ; R21 AA022416/AA/NIAAA NIH HHS/United States ; I01 BX000350/BX/BLRD VA/United States ; R01 AA024405/AA/NIAAA NIH HHS/United States ; }, mesh = {Animals ; Dietary Fats/*metabolism ; Dietary Fats, Unsaturated/*metabolism ; Disease Models, Animal ; Ethanol/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Liver/metabolism ; Liver Diseases, Alcoholic/*metabolism ; Male ; Mice, Inbred C57BL ; Triglycerides/metabolism ; }, abstract = {Alcoholic liver disease (ALD) ranks among major causes of morbidity and mortality. Diet and crosstalk between the gut and liver are important determinants of ALD. We evaluated the effects of different types of dietary fat and ethanol on the gut microbiota composition and metabolic activity and the effect of these changes on liver injury in ALD. Compared with ethanol and a saturated fat diet (medium chain triglycerides enriched), an unsaturated fat diet (corn oil enriched) exacerbated ethanol-induced endotoxemia, liver steatosis, and injury. Major alterations in gut microbiota, including a reduction in Bacteroidetes and an increase in Proteobacteria and Actinobacteria, were seen in animals fed an unsaturated fat diet and ethanol but not a saturated fat diet and ethanol. Compared with a saturated fat diet and ethanol, an unsaturated fat diet and ethanol caused major fecal metabolomic changes. Moreover, a decrease in certain fecal amino acids was noted in both alcohol-fed groups. These data support an important role of dietary lipids in ALD pathogenesis and provide insight into mechanisms of ALD development. A diet enriched in unsaturated fats enhanced alcohol-induced liver injury and caused major fecal metagenomic and metabolomic changes that may play an etiologic role in observed liver injury. Dietary lipids can potentially serve as inexpensive interventions for the prevention and treatment of ALD.}, } @article {pmid27010970, year = {2016}, author = {Krishnamurthy, SR and Janowski, AB and Zhao, G and Barouch, D and Wang, D}, title = {Hyperexpansion of RNA Bacteriophage Diversity.}, journal = {PLoS biology}, volume = {14}, number = {3}, pages = {e1002409}, pmid = {27010970}, issn = {1545-7885}, support = {U19 AI078526/AI/NIAID NIH HHS/United States ; AI096040/AI/NIAID NIH HHS/United States ; T32 AI106688/AI/NIAID NIH HHS/United States ; T32 AI 007172 34/AI/NIAID NIH HHS/United States ; AI078526/AI/NIAID NIH HHS/United States ; T32 AI 106688 02/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; OD011170/OD/NIH HHS/United States ; R01 OD011170/OD/NIH HHS/United States ; U19 AI096040/AI/NIAID NIH HHS/United States ; T32 AI007172/AI/NIAID NIH HHS/United States ; }, mesh = {*Genetic Variation ; *Genome, Viral ; Metagenome ; Microbiota ; Phylogeny ; RNA Phages/*genetics ; }, abstract = {Bacteriophage modulation of microbial populations impacts critical processes in ocean, soil, and animal ecosystems. However, the role of bacteriophages with RNA genomes (RNA bacteriophages) in these processes is poorly understood, in part because of the limited number of known RNA bacteriophage species. Here, we identify partial genome sequences of 122 RNA bacteriophage phylotypes that are highly divergent from each other and from previously described RNA bacteriophages. These novel RNA bacteriophage sequences were present in samples collected from a range of ecological niches worldwide, including invertebrates and extreme microbial sediment, demonstrating that they are more widely distributed than previously recognized. Genomic analyses of these novel bacteriophages yielded multiple novel genome organizations. Furthermore, one RNA bacteriophage was detected in the transcriptome of a pure culture of Streptomyces avermitilis, suggesting for the first time that the known tropism of RNA bacteriophages may include gram-positive bacteria. Finally, reverse transcription PCR (RT-PCR)-based screening for two specific RNA bacteriophages in stool samples from a longitudinal cohort of macaques suggested that they are generally acutely present rather than persistent.}, } @article {pmid27008327, year = {2016}, author = {Su, MM and Guo, L and Tao, YL and Zhang, YJ and Wan, FH and Chu, D}, title = {Effects of Host Plant Factors on the Bacterial Communities Associated with Two Whitefly Sibling Species.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0152183}, pmid = {27008327}, issn = {1932-6203}, mesh = {Animals ; Gossypium/microbiology ; Hemiptera/*microbiology/physiology ; Solanum lycopersicum/microbiology ; Metagenomics ; *Microbiota/genetics/physiology ; Plant Viruses/physiology ; }, abstract = {BACKGROUND: Although discrepancy in the specific traits and ecological characteristics of Bemisia tabaci between species are partially attributed to the B. tabaci-associated bacteria, the factors that affect the diversity of B. tabaci-associated bacteria are not well-understood. We used the metagenomic approach to characterize the B. tabaci-associated bacterial community because the approach is an effective tool to identify the bacteria.

METHODOLOGY AND RESULTS: To investigate the effects of the host plant and a virus, tomato yellow leaf curl virus (TYLCV), on the bacterial communities of B. tabaci sibling species B and Q, we analyzed the bacterial communities associated with whitefly B and Q collected from healthy cotton, healthy tomato, and TYLCV-infected tomato. The analysis used miseq-based sequencing of a variable region of the bacterial 16S rDNA gene. For the bacteria associated with B. tabaci, we found that the influence of the host plant species was greater than that of the whitefly cryptic species. With further analysis of host plants infected with the TYLCV, the virus had no significant effects on the B. tabaci-associated bacterial community.

CONCLUSIONS: The effects of different plant hosts and TYLCV-infection on the diversity of B. tabaci-associated bacterial communities were successfully analyzed in this study. To explain why B. tabaci sibling species with different host ranges differ in performance, the analysis of the bacterial community may be essential to the explanation.}, } @article {pmid27007819, year = {2016}, author = {Whitfield-Cargile, CM and Cohen, ND and Chapkin, RS and Weeks, BR and Davidson, LA and Goldsby, JS and Hunt, CL and Steinmeyer, SH and Menon, R and Suchodolski, JS and Jayaraman, A and Alaniz, RC}, title = {The microbiota-derived metabolite indole decreases mucosal inflammation and injury in a murine model of NSAID enteropathy.}, journal = {Gut microbes}, volume = {7}, number = {3}, pages = {246-261}, pmid = {27007819}, issn = {1949-0984}, support = {P30 ES023512/ES/NIEHS NIH HHS/United States ; R01 AI110642/AI/NIAID NIH HHS/United States ; R35 CA197707/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Anti-Inflammatory Agents/*metabolism ; Anti-Inflammatory Agents, Non-Steroidal/administration & dosage/*adverse effects ; Bacteria/classification/isolation & purification ; Biota ; Disease Models, Animal ; Enteritis/chemically induced/*drug therapy ; Feces/chemistry/microbiology ; Gastrointestinal Agents/administration & dosage/*pharmacology ; Histocytochemistry ; Indoles/administration & dosage/*metabolism/*pharmacology ; Inflammation/*pathology ; Leukocyte L1 Antigen Complex/analysis ; Lymph Nodes/pathology ; Mice ; Neutrophils/immunology ; Spleen/pathology ; Treatment Outcome ; }, abstract = {Non-steroidal anti-inflammatory drugs (NSAIDs) are one of the most frequently used classes of medications in the world. Unfortunately, NSAIDs induce an enteropathy associated with high morbidity and mortality. Although the pathophysiology of this condition involves the interaction of the gut epithelium, microbiota, and NSAIDs, the precise mechanisms by which microbiota influence NSAID enteropathy are unclear. One possible mechanism is that the microbiota may attenuate the severity of disease by specific metabolite-mediated regulation of host inflammation and injury. The microbiota-derived tryptophan-metabolite indole is abundant in the healthy mammalian gut and positively influences intestinal health. We thus examined the effects of indole administration on NSAID enteropathy. Mice (n = 5 per group) were treated once daily for 7 days with an NSAID (indomethacin; 5 mg/kg), indole (20 mg/kg), indomethacin plus indole, or vehicle only (control). Outcomes compared among groups included: microscopic pathology; fecal calprotectin concentration; proportion of neutrophils in the spleen and mesenteric lymph nodes; fecal microbiota composition and diversity; small intestinal mucosal transcriptome; and, fecal tryptophan metabolites. Co-administration of indole with indomethacin: significantly reduced mucosal pathology scores, fecal calprotectin concentrations, and neutrophilic infiltration of the spleen and mesenteric lymph nodes induced by indomethacin; modulated NSAID-induced perturbation of the microbiota, fecal metabolites, and inferred metagenome; and, abrogated a pro-inflammatory gene expression profile in the small intestinal mucosa induced by indomethacin. The microbiota-derived metabolite indole attenuated multiple deleterious effects of NSAID enteropathy, including modulating inflammation mediated by innate immune responses and altering indomethacin-induced shift of the microbiota.}, } @article {pmid27007381, year = {2016}, author = {Parages, ML and Gutiérrez-Barranquero, JA and Reen, FJ and Dobson, AD and O'Gara, F}, title = {Integrated (Meta) Genomic and Synthetic Biology Approaches to Develop New Biocatalysts.}, journal = {Marine drugs}, volume = {14}, number = {3}, pages = {}, pmid = {27007381}, issn = {1660-3397}, mesh = {Animals ; Aquatic Organisms/chemistry ; Biocatalysis ; Biodiversity ; Biological Products/isolation & purification/pharmacology ; Biotechnology/methods ; *Drug Design ; Drug Discovery/methods ; Humans ; Metagenomics/*methods ; Molecular Biology/methods ; Synthetic Biology/*methods ; }, abstract = {In recent years, the marine environment has been the subject of increasing attention from biotechnological and pharmaceutical industries as a valuable and promising source of novel bioactive compounds. Marine biodiscovery programmes have begun to reveal the extent of novel compounds encoded within the enormous bacterial richness and diversity of the marine ecosystem. A combination of unique physicochemical properties and spatial niche-specific substrates, in wide-ranging and extreme habitats, underscores the potential of the marine environment to deliver on functionally novel biocatalytic activities. With the growing need for green alternatives to industrial processes, and the unique transformations which nature is capable of performing, marine biocatalysts have the potential to markedly improve current industrial pipelines. Furthermore, biocatalysts are known to possess chiral selectivity and specificity, a key focus of pharmaceutical drug design. In this review, we discuss how the explosion in genomics based sequence analysis, allied with parallel developments in synthetic and molecular biology, have the potential to fast-track the discovery and subsequent improvement of a new generation of marine biocatalysts.}, } @article {pmid27006764, year = {2016}, author = {Crampton-Platt, A and Yu, DW and Zhou, X and Vogler, AP}, title = {Mitochondrial metagenomics: letting the genes out of the bottle.}, journal = {GigaScience}, volume = {5}, number = {}, pages = {15}, pmid = {27006764}, issn = {2047-217X}, mesh = {Animals ; Biodiversity ; DNA, Mitochondrial/chemistry/classification/*genetics ; Genetic Variation ; Genome, Mitochondrial/*genetics ; Humans ; Metagenomics/*methods ; Phylogeny ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; }, abstract = {'Mitochondrial metagenomics' (MMG) is a methodology for shotgun sequencing of total DNA from specimen mixtures and subsequent bioinformatic extraction of mitochondrial sequences. The approach can be applied to phylogenetic analysis of taxonomically selected taxa, as an economical alternative to mitogenome sequencing from individual species, or to environmental samples of mixed specimens, such as from mass trapping of invertebrates. The routine generation of mitochondrial genome sequences has great potential both for systematics and community phylogenetics. Mapping of reads from low-coverage shotgun sequencing of environmental samples also makes it possible to obtain data on spatial and temporal turnover in whole-community phylogenetic and species composition, even in complex ecosystems where species-level taxonomy and biodiversity patterns are poorly known. In addition, read mapping can produce information on species biomass, and potentially allows quantification of within-species genetic variation. The success of MMG relies on the formation of numerous mitochondrial genome contigs, achievable with standard genome assemblers, but various challenges for the efficiency of assembly remain, particularly in the face of variable relative species abundance and intra-specific genetic variation. Nevertheless, several studies have demonstrated the power of mitogenomes from MMG for accurate phylogenetic placement, evolutionary analysis of species traits, biodiversity discovery and the establishment of species distribution patterns; it offers a promising avenue for unifying the ecological and evolutionary understanding of species diversity.}, } @article {pmid27006462, year = {2016}, author = {Shin, H and Price, K and Albert, L and Dodick, J and Park, L and Dominguez-Bello, MG}, title = {Changes in the Eye Microbiota Associated with Contact Lens Wearing.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e00198}, pmid = {27006462}, issn = {2150-7511}, mesh = {Bacteria/*classification/*genetics ; Cluster Analysis ; Conjunctiva/microbiology ; *Contact Lenses ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Eye/*microbiology ; Female ; Hospitals, University ; Humans ; Male ; Metagenomics ; *Microbiota ; New York City ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Skin/microbiology ; }, abstract = {UNLABELLED: Wearing contact lenses has been identified as a risk factor for the development of eye conditions such as giant papillary conjunctivitis and keratitis. We hypothesized that wearing contact lenses is associated with changes in the ocular microbiota. We compared the bacterial communities of the conjunctiva and skin under the eye from 58 subjects and analyzed samples from 20 subjects (9 lens wearers and 11 non-lens wearers) taken at 3 time points using a 16S rRNA gene-based sequencing technique (V4 region; Illumina MiSeq). We found that using anesthetic eye drops before sampling decreases the detected ocular microbiota diversity. Compared to those from non-lens wearers, dry conjunctival swabs from lens wearers had more variable and skin-like bacterial community structures (UniFrac;P value = <0.001), with higher abundances of Methylobacterium,Lactobacillus,Acinetobacter, andPseudomonasand lower abundances of Haemophilus,Streptococcus,Staphylococcus, and Corynebacterium(linear discriminant analysis [LDA] score = >3.0). The results indicate that wearing contact lenses alters the microbial structure of the ocular conjunctiva, making it more similar to that of the skin microbiota. Further research is needed to determine whether the microbiome structure provides less protection from ocular infections.

IMPORTANCE: As in other body sites (i.e., the gut, skin, and mouth), the eye has a normal community of bacteria which are expected to confer resistance that provides protection from invaders. However, the eye microbiome has been largely neglected and is relevant to eye health and understanding eye diseases and to discovery of its functions. This report of a baseline study shows differences in the eye microbiome of contact lens wearers in relation to those of non-lens wearers and has the potential to help future studies explore novel insights into a possible role of the microbiome in the increased risk for eye infections in contact lens wearers.}, } @article {pmid27003245, year = {2016}, author = {Ilott, NE and Bollrath, J and Danne, C and Schiering, C and Shale, M and Adelmann, K and Krausgruber, T and Heger, A and Sims, D and Powrie, F}, title = {Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling.}, journal = {The ISME journal}, volume = {10}, number = {10}, pages = {2389-2404}, pmid = {27003245}, issn = {1751-7370}, support = {095688/Z/11/Z/WT_/Wellcome Trust/United Kingdom ; MR/L022699/1/MRC_/Medical Research Council/United Kingdom ; MC_EX_UU_G1000902/MRC_/Medical Research Council/United Kingdom ; 090532/Z/09/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bacteria/classification/*genetics/isolation & purification/metabolism ; Bacterial Proteins/genetics/metabolism ; Colitis/*genetics/immunology/*microbiology ; Female ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Humans ; Metagenomics ; Mice ; Mice, Inbred C57BL ; }, abstract = {The gut microbiome is significantly altered in inflammatory bowel diseases, but the basis of these changes is not well understood. We have combined metagenomic and metatranscriptomic profiling of the gut microbiome to assess modifications to both bacterial community structure and transcriptional activity in a mouse model of colitis. By using transcriptomic analysis of colonic tissue and luminal RNA derived from the host, we have also characterised how host transcription relates to the microbial transcriptional response in inflammation. In colitis, increased abundance and transcription of diverse microbial gene families involved in responses to nutrient deprivation, antimicrobial peptide production and oxidative stress support an adaptation of multiple commensal genera to withstand a diverse set of environmental stressors in the inflammatory environment. These data are supported by a transcriptional signature of activated macrophages and granulocytes in the gut lumen during colitis, a signature that includes the transcription of the key antimicrobial genes S100a8 and S100a9 (calprotectin). Genes involved in microbial resistance to oxidative stress, including Dps/ferritin, Fe-dependent peroxidase and glutathione S-transferase were identified as changing to a greater extent at the level of transcription than would be predicted by DNA abundance changes, implicating a role for increased oxygen tension and/or host-derived reactive oxygen species in driving transcriptional changes in commensal microbes.}, } @article {pmid27001690, year = {2016}, author = {Meziti, A and Tsementzi, D and Ar Kormas, K and Karayanni, H and Konstantinidis, KT}, title = {Anthropogenic effects on bacterial diversity and function along a river-to-estuary gradient in Northwest Greece revealed by metagenomics.}, journal = {Environmental microbiology}, volume = {18}, number = {12}, pages = {4640-4652}, doi = {10.1111/1462-2920.13303}, pmid = {27001690}, issn = {1462-2920}, mesh = {Bacteria/*genetics ; *Biodiversity ; Ecosystem ; *Estuaries ; Fresh Water ; Greece ; Humans ; Metagenomics ; Plankton/genetics ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Seasons ; *Water Microbiology ; }, abstract = {Studies assessing the effects of anthropogenic inputs on the taxonomic and functional diversity of bacterioplankton communities in lotic ecosystems are limited. Here, we applied 16S rRNA gene amplicon and whole-genome shotgun sequencing to examine the microbial diversity in samples from the Kalamas River (Northwest Greece), a mid-size river that runs through agricultural and NATURA-protected areas, but also receives urban sewage from a large city through a manmade ditch. Samples from three different locations between the exit of the ditch and the estuary, during three different months showed that temporal differences of taxonomic and functional diversity were more pronounced than spatial ones, and <1% of total taxa were shared among all samples, revealing a highly dynamic ecosystem. Comparisons of gene diversity with other aquatic habitats showed that only the high flow winter samples resembled more to freshwater environments while samples during the decreased water flow months were dominated by sewage inputs and soil-related organisms. Notably, microbial human gut signals were detectable over background freshwater and soil/runoff related signals, even at tens of kilometers downstream the city. These findings revealed the significance of allochthonous inputs on the composition and dynamics of river bacterial communities, and highlighted the potential of metagenomics for source tracking purposes.}, } @article {pmid27001503, year = {2016}, author = {Patel, V and Sharma, A and Lal, R and Al-Dhabi, NA and Madamwar, D}, title = {Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates.}, journal = {BMC microbiology}, volume = {16}, number = {}, pages = {50}, pmid = {27001503}, issn = {1471-2180}, mesh = {Bacteria/classification/drug effects/genetics/*isolation & purification ; Biodiversity ; India ; Phylogeny ; Plant Oils/*pharmacology ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/*pharmacology ; }, abstract = {BACKGROUND: Gauging the microbial community structures and functions become imperative to understand the ecological processes. To understand the impact of long-term oil contamination on microbial community structure soil samples were taken from oil fields located in different industrial regions across Kadi, near Ahmedabad, India. Soil collected was hence used for metagenomic DNA extraction to study the capabilities of intrinsic microbial community in tolerating the oil perturbation.

RESULTS: Taxonomic profiling was carried out by two different complementary approaches i.e. 16S rDNA and lowest common ancestor. The community profiling revealed the enrichment of phylum "Proteobacteria" and genus "Chromobacterium," respectively for polluted soil sample. Our results indicated that soil microbial diversity (Shannon diversity index) decreased significantly with contamination. Further, assignment of obtained metagenome reads to Clusters of Orthologous Groups (COG) of protein and Kyoto Encyclopedia of Genes and Genomes (KEGG) hits revealed metabolic potential of indigenous microbial community. Enzymes were mapped on fatty acid biosynthesis pathway to elucidate their roles in possible catalytic reactions.

CONCLUSION: To the best of our knowledge this is first study for influence of edible oil on soil microbial communities via shotgun sequencing. The results indicated that long-term oil contamination significantly affects soil microbial community structure by acting as an environmental filter to decrease the regional differences distinguishing soil microbial communities.}, } @article {pmid26999001, year = {2016}, author = {Scholz, M and Ward, DV and Pasolli, E and Tolio, T and Zolfo, M and Asnicar, F and Truong, DT and Tett, A and Morrow, AL and Segata, N}, title = {Strain-level microbial epidemiology and population genomics from shotgun metagenomics.}, journal = {Nature methods}, volume = {13}, number = {5}, pages = {435-438}, pmid = {26999001}, issn = {1548-7105}, support = {HHSN272200900018C/AI/NIAID NIH HHS/United States ; }, mesh = {Escherichia coli/classification/genetics/isolation & purification/pathogenicity ; Gene Expression Profiling ; Genome, Bacterial ; Germany ; Humans ; Intestinal Mucosa/*microbiology ; Metagenome/*genetics ; Metagenomics/*methods ; Microbial Consortia/*genetics ; *Phylogeny ; Skin/*microbiology ; Software ; Species Specificity ; }, abstract = {Identifying microbial strains and characterizing their functional potential is essential for pathogen discovery, epidemiology and population genomics. We present pangenome-based phylogenomic analysis (PanPhlAn; http://segatalab.cibio.unitn.it/tools/panphlan), a tool that uses metagenomic data to achieve strain-level microbial profiling resolution. PanPhlAn recognized outbreak strains, produced the largest strain-level population genomic study of human-associated bacteria and, in combination with metatranscriptomics, profiled the transcriptional activity of strains in complex communities.}, } @article {pmid26997279, year = {2016}, author = {Ward, DV and Scholz, M and Zolfo, M and Taft, DH and Schibler, KR and Tett, A and Segata, N and Morrow, AL}, title = {Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants.}, journal = {Cell reports}, volume = {14}, number = {12}, pages = {2912-2924}, pmid = {26997279}, issn = {2211-1247}, support = {U54HG004969/HG/NHGRI NIH HHS/United States ; HHSN272200900018C/AI/NIAID NIH HHS/United States ; P01 HD013021/HD/NICHD NIH HHS/United States ; UG1 HD027853/HD/NICHD NIH HHS/United States ; 5UL1RR026314-03/RR/NCRR NIH HHS/United States ; U10 HD027853/HD/NICHD NIH HHS/United States ; P01HD13021/HD/NICHD NIH HHS/United States ; R01 HD059140/HD/NICHD NIH HHS/United States ; UL1 RR026314/RR/NCRR NIH HHS/United States ; R01HD059140/HD/NICHD NIH HHS/United States ; HD27853/HD/NICHD NIH HHS/United States ; U54 HG004969/HG/NHGRI NIH HHS/United States ; UL1 TR001425/TR/NCATS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; DNA, Bacterial/chemistry/genetics/metabolism ; Drug Resistance, Bacterial/drug effects ; Enterocolitis, Necrotizing/microbiology/mortality/*pathology ; Feces/microbiology ; Female ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Intestines/microbiology ; Klebsiella/genetics/isolation & purification/pathogenicity ; Male ; Metagenomics ; Microbiota ; Multilocus Sequence Typing ; Postpartum Period ; Sequence Analysis, DNA ; Survival Rate ; Uropathogenic Escherichia coli/*genetics/isolation & purification/pathogenicity ; }, abstract = {Necrotizing enterocolitis (NEC) afflicts approximately 10% of extremely preterm infants with high fatality. Inappropriate bacterial colonization with Enterobacteriaceae is implicated, but no specific pathogen has been identified. We identify uropathogenic E. coli (UPEC) colonization as a significant risk factor for the development of NEC and subsequent mortality. We describe a large-scale deep shotgun metagenomic sequence analysis of the early intestinal microbiome of 144 preterm and 22 term infants. Using a pan-genomic approach to functionally subtype the E. coli, we identify genes associated with NEC and mortality that indicate colonization by UPEC. Metagenomic multilocus sequence typing analysis further defined NEC-associated strains as sequence types often associated with urinary tract infections, including ST69, ST73, ST95, ST127, ST131, and ST144. Although other factors associated with prematurity may also contribute, this report suggests a link between UPEC and NEC and indicates that further attention to these sequence types as potential causal agents is needed.}, } @article {pmid26996654, year = {2016}, author = {Del Campo, J and Guillou, L and Hehenberger, E and Logares, R and López-García, P and Massana, R}, title = {Ecological and evolutionary significance of novel protist lineages.}, journal = {European journal of protistology}, volume = {55}, number = {Pt A}, pages = {4-11}, pmid = {26996654}, issn = {1618-0429}, support = {322669/ERC_/European Research Council/International ; }, mesh = {Biodiversity ; *Biological Evolution ; *Ecology ; Ecosystem ; Eukaryota/*classification/genetics/*physiology ; Genetic Techniques ; }, abstract = {Environmental molecular surveys targeting protist diversity have unveiled novel and uncultured lineages in a variety of ecosystems, ranging from completely new high-rank lineages, to new taxa moderately related to previously described organisms. The ecological roles of some of these novel taxa have been studied, showing that in certain habitats they may be responsible for critical environmental processes. Moreover, from an evolutionary perspective they still need to be included in a more accurate and wider understanding of the eukaryotic tree of life. These seminal discoveries promoted the development and use of a wide range of more in-depth culture-independent approaches to access this diversity, from metabarcoding and metagenomics to single cell genomics and FISH. Nonetheless, culturing using classical or innovative approaches is also essential to better characterize this new diversity. Ecologists and evolutionary biologists now face the challenge of apprehending the significance of this new diversity within the eukaryotic tree of life.}, } @article {pmid28326980, year = {2016}, author = {Davis, EM}, title = {Gene Sequence Analyses of the Healthy Oral Microbiome in Humans and Companion Animals.}, journal = {Journal of veterinary dentistry}, volume = {33}, number = {2}, pages = {97-107}, doi = {10.1177/0898756416657239}, pmid = {28326980}, issn = {0898-7564}, mesh = {Animals ; Bacteria/*genetics ; DNA, Bacterial/genetics ; Humans ; Microbiota/*genetics ; Mouth/*microbiology ; Oral Health ; *Pets ; RNA, Ribosomal, 16S ; Sequence Analysis ; }, abstract = {It has long been accepted that certain oral bacterial species are responsible for the development of periodontal disease. However, the focus of microbial and immunological research is shifting from studying the organisms associated with disease to examining the indigenous microbial inhabitants that are present in health. Microbiome refers to the aggregate genetic material of all microorganisms living in, or on, a defined habitat. Recent developments in gene sequence analysis have enabled detection and identification of bacteria from polymicrobial samples, including subgingival plaque. Diversity surveys utilizing this technology have demonstrated that bacterial culture techniques have vastly underestimated the richness and diversity of microorganisms in vivo, since only certain bacteria grow in vitro. Surveys using gene sequence analysis have demonstrated that the healthy oral microbiome is composed of an unexpectedly high number of diverse species, including putative pathogens. These findings support the view that coevolution microorganisms and macroscopic hosts has occurred in which certain microorganisms have adapted to survive in the oral cavity and host immune tolerance has allowed the establishment of a symbiotic relationship in which both parties receive benefits (mutualism). This review describes gene sequence analysis as an increasingly common, culture-independent tool for detecting bacteria in vivo and describes the results of recent oral microbiome diversity surveys of clinically healthy humans, dogs, and cats. Six bacterial phyla consistently dominated the healthy oral microbiome of all 3 host species. Previous hypotheses on etiology of periodontitis are reviewed in light of new scientific findings. Finally, the consideration that clinically relevant periodontal disease occurs when immune tolerance of the symbiotic oral microbiome is altered to a proinflammatory response will be discussed.}, } @article {pmid27867467, year = {2015}, author = {Tang, M and Hardman, CJ and Ji, Y and Meng, G and Liu, S and Tan, M and Yang, S and Moss, ED and Wang, J and Yang, C and Bruce, C and Nevard, T and Potts, SG and Zhou, X and Yu, DW}, title = {High-throughput monitoring of wild bee diversity and abundance via mitogenomics.}, journal = {Methods in ecology and evolution}, volume = {6}, number = {9}, pages = {1034-1043}, pmid = {27867467}, issn = {2041-210X}, abstract = {Bee populations and other pollinators face multiple, synergistically acting threats, which have led to population declines, loss of local species richness and pollination services, and extinctions. However, our understanding of the degree, distribution and causes of declines is patchy, in part due to inadequate monitoring systems, with the challenge of taxonomic identification posing a major logistical barrier. Pollinator conservation would benefit from a high-throughput identification pipeline.We show that the metagenomic mining and resequencing of mitochondrial genomes (mitogenomics) can be applied successfully to bulk samples of wild bees. We assembled the mitogenomes of 48 UK bee species and then shotgun-sequenced total DNA extracted from 204 whole bees that had been collected in 10 pan-trap samples from farms in England and been identified morphologically to 33 species. Each sample data set was mapped against the 48 reference mitogenomes.The morphological and mitogenomic data sets were highly congruent. Out of 63 total species detections in the morphological data set, the mitogenomic data set made 59 correct detections (93·7% detection rate) and detected six more species (putative false positives). Direct inspection and an analysis with species-specific primers suggested that these putative false positives were most likely due to incorrect morphological IDs. Read frequency significantly predicted species biomass frequency (R[2] = 24·9%). Species lists, biomass frequencies, extrapolated species richness and community structure were recovered with less error than in a metabarcoding pipeline.Mitogenomics automates the onerous task of taxonomic identification, even for cryptic species, allowing the tracking of changes in species richness and distributions. A mitogenomic pipeline should thus be able to contain costs, maintain consistently high-quality data over long time series, incorporate retrospective taxonomic revisions and provide an auditable evidence trail. Mitogenomic data sets also provide estimates of species counts within samples and thus have potential for tracking population trajectories.}, } @article {pmid27367037, year = {2014}, author = {Hildebrand, F and Tadeo, R and Voigt, AY and Bork, P and Raes, J}, title = {LotuS: an efficient and user-friendly OTU processing pipeline.}, journal = {Microbiome}, volume = {2}, number = {1}, pages = {30}, pmid = {27367037}, issn = {2049-2618}, support = {268985/ERC_/European Research Council/International ; }, mesh = {Algorithms ; Computational Biology/instrumentation/*methods ; DNA, Ribosomal ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis/instrumentation/*methods ; Sequence Analysis, DNA ; *Software ; }, abstract = {BACKGROUND: 16S ribosomal DNA (rDNA) amplicon sequencing is frequently used to analyse the structure of bacterial communities from oceans to the human microbiota. However, computational power is still a major bottleneck in the analysis of continuously enlarging metagenomic data sets. Analysis is further complicated by the technical complexity of current bioinformatics tools.

RESULTS: Here we present the less operational taxonomic units scripts (LotuS), a fast and user-friendly open-source tool to calculate denoised, chimera-checked, operational taxonomic units (OTUs). These are the basis to generate taxonomic abundance tables and phylogenetic trees from multiplexed, next-generation sequencing data (454, illumina MiSeq and HiSeq). LotuS is outstanding in its execution speed, as it can process 16S rDNA data up to two orders of magnitude faster than other existing pipelines. This is partly due to an included stand-alone fast simultaneous demultiplexer and quality filter C++ program, simple demultiplexer (sdm), which comes packaged with LotuS. Additionally, we sequenced two MiSeq runs with the intent to validate future pipelines by sequencing 40 technical replicates; these are made available in this work.

CONCLUSION: We show that LotuS analyses microbial 16S data with comparable or even better results than existing pipelines, requiring a fraction of the execution time and providing state-of-the-art denoising and phylogenetic reconstruction. LotuS is available through the following URL: http://psbweb05.psb.ugent.be/lotus .}, } @article {pmid27008402, year = {2013}, author = {Bhattacharya, D and Price, DC and Bicep, C and Bapteste, E and Sarwade, M and Rajah, VD and Yoon, HS}, title = {Identification of a Marine Cyanophage in a Protist Single-cell Metagenome Assembly.}, journal = {Journal of phycology}, volume = {49}, number = {1}, pages = {207-212}, doi = {10.1111/jpy.12028}, pmid = {27008402}, issn = {0022-3646}, abstract = {Analysis of microbial biodiversity is hampered by a lack of reference genomes from most bacteria, viruses, and algae. This necessitates either the cultivation of a restricted number of species for standard sequencing projects or the analysis of highly complex environmental DNA metagenome data. Single-cell genomics (SCG) offers a solution to this problem by constraining the studied DNA sample to an individual cell and its associated symbionts, prey, and pathogens. We used SCG to study marine heterotrophic amoebae related to Paulinella ovalis (A. Wulff) P.W. Johnson, P.E. Hargraves & J.M. Sieburth (Rhizaria). The genus Paulinella is best known for its photosynthetic members such as P. chromatophora Lauterborn that is the only case of plastid primary endosymbiosis known outside of algae and plants. Here, we studied the phagotrophic sister taxa of P. chromatophora that are related to P. ovalis and found one SCG assembly to contain α-cyanobacterial DNA. These cyanobacterial contigs are presumably derived from prey. We also uncovered an associated cyanophage lineage (provisionally named phage PoL_MC2). Phylogenomic analysis of the fragmented genome assembly suggested a minimum genome size of 200 Kbp for phage PoL_MC2 that encodes 179 proteins and is most closely related to Synechococcus phage S-SM2. For this phage, gene network analysis demonstrates a highly modular genome structure typical of other cyanophages. Our work demonstrates that SCG is a powerful approach for discovering algal and protist biodiversity and for elucidating biotic interactions in natural samples.}, } @article {pmid26875748, year = {2016}, author = {Shinkai, T and Mitsumori, M and Sofyan, A and Kanamori, H and Sasaki, H and Katayose, Y and Takenaka, A}, title = {Comprehensive detection of bacterial carbohydrate-active enzyme coding genes expressed in cow rumen.}, journal = {Animal science journal = Nihon chikusan Gakkaiho}, volume = {87}, number = {11}, pages = {1363-1370}, doi = {10.1111/asj.12585}, pmid = {26875748}, issn = {1740-0929}, mesh = {Animal Feed ; Animals ; Cattle ; Cellulases/*genetics ; Female ; Fibrobacter/*enzymology ; Glycoside Hydrolases/*genetics ; Hydrolysis ; *Microbiota ; Phleum/chemistry ; Polysaccharides/*metabolism ; Rumen/*microbiology ; }, abstract = {To find the abundant and characteristic fibrolytic enzyme-coding gene expressed in fiber-associating microbiota, a metatranscriptomic data set was obtained from fiber-associating microbiota, and it was compared with that of rumen fluid-floating microbiota and two metagenomic data sets. Fibrolytic rumen bacteria associate with plant polysaccharide and hydrolyze it in the rumen. We obtained a metatranscriptomic assembly from fiber-associating microbiota in three ruminally fistulated Holstein cows fed timothy (Phleum pratense) hay. Each metatranscriptomic data set involved over a thousand of the glycoside hydrolase (GH) gene transcripts that accounted for about 1% of total protein coding gene transcripts. Three-quarters of the total GH gene transcripts were dominated by non-structural oligosaccharide-acting hydrolase gene transcripts. In the fiber-associating microbiota, endo-cellulase coding gene families, especially GHs 9 and 5, were abundantly detected, and GHs 9, 11, 30 and 43, carbohydrate esterase 8 and carbohydrate-binding module 6 were characteristically detected. Most fibrolytic gene transcripts assigned to Fibrobacter succinogenes were detected in fiber-associating sections, and GHs 45, 44, 74, 11, 30 and 16 were Fibrobacter-characteristically detected. The metatranscriptomic assembly highlighted the characteristic fibrolytic enzymes expressed in the fiber-associated rumen microbiota and offered access to the fibrolytic activities in each fibrolytic bacteria.}, } @article {pmid26994316, year = {2016}, author = {Tripathi, BM and Edwards, DP and Mendes, LW and Kim, M and Dong, K and Kim, H and Adams, JM}, title = {The impact of tropical forest logging and oil palm agriculture on the soil microbiome.}, journal = {Molecular ecology}, volume = {25}, number = {10}, pages = {2244-2257}, doi = {10.1111/mec.13620}, pmid = {26994316}, issn = {1365-294X}, mesh = {*Agriculture ; Arecaceae/growth & development ; Bacteria/classification ; Biodiversity ; Borneo ; Conservation of Natural Resources ; *Forestry ; Forests ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land-use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once-logged and twice-logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell-cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land-use changes on the interaction of soil microbes.}, } @article {pmid26994078, year = {2016}, author = {Tschitschko, B and Williams, TJ and Allen, MA and Zhong, L and Raftery, MJ and Cavicchioli, R}, title = {Ecophysiological Distinctions of Haloarchaea from a Hypersaline Antarctic Lake as Determined by Metaproteomics.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {11}, pages = {3165-3173}, pmid = {26994078}, issn = {1098-5336}, mesh = {Antarctic Regions ; Archaea/*chemistry/*classification/genetics ; Archaeal Proteins/*analysis ; *Biota ; Lakes/chemistry/*microbiology ; Metagenome ; Proteome/*analysis ; Salinity ; }, abstract = {UNLABELLED: Deep Lake in the Vestfold Hills is hypersaline and the coldest system in Antarctica known to support microbial growth (temperatures as low as -20°C). It represents a strong experimental model because the lake supports a low-complexity community of haloarchaea, with the three most abundant species totaling ∼72%. Moreover, the dominant haloarchaea are cultivatable, and their genomes are sequenced. Here we use metaproteomics linked to metagenome data and the genome sequences of the isolates to characterize the main pathways, trophic strategies, and interactions associated with resource utilization. The dominance of the most abundant member, Halohasta litchfieldiae, appears to be predicated on competitive utilization of substrates (e.g., starch, glycerol, and dihydroxyacetone) produced by Dunaliella, the lake's primary producer, while also possessing diverse mechanisms for acquiring nitrogen and phosphorus. The second most abundant member, strain DL31, is proficient in degrading complex proteinaceous matter. Hht. litchfieldiae and DL31 are inferred to release labile substrates that are utilized by Halorubrum lacusprofundi, the third most abundant haloarchaeon in Deep Lake. The study also linked genome variation to specific protein variants or distinct genetic capacities, thereby identifying strain-level variation indicative of specialization. Overall, metaproteomics revealed that rather than functional differences occurring at different lake depths or through size partitioning, the main lake genera possess major trophic distinctions, and phylotypes (e.g., strains of Hht. litchfieldiae) exhibit a more subtle level of specialization. This study highlights the extent to which the lake supports a relatively uniform distribution of taxa that collectively possess the genetic capacity to effectively exploit available nutrients throughout the lake.

IMPORTANCE: Life on Earth has evolved to colonize a broad range of temperatures, but most of the biosphere (∼85%) exists at low temperatures (≤5°C). By performing unique roles in biogeochemical cycles, environmental microorganisms perform functions that are critical for the rest of life on Earth to survive. Cold environments therefore make a particularly important contribution to maintaining healthy, stable ecosystems. Here we describe the main physiological traits of the dominant microorganisms that inhabit Deep Lake in Antarctica, the coldest aquatic environment known to support life. The hypersaline system enables the growth of halophilic members of the Archaea: haloarchaea. By analyzing proteins of samples collected from the water column, we determined the functions that the haloarchaea were likely to perform. This study showed that the dominant haloarchaea possessed distinct lifestyles yet formed a uniform community throughout the lake that was collectively adept at using available light energy and diverse organic substrates for growth.}, } @article {pmid26992451, year = {2016}, author = {Ertekin, E and Hatt, JK and Konstantinidis, KT and Tezel, U}, title = {Similar Microbial Consortia and Genes Are Involved in the Biodegradation of Benzalkonium Chlorides in Different Environments.}, journal = {Environmental science & technology}, volume = {50}, number = {8}, pages = {4304-4313}, doi = {10.1021/acs.est.5b05959}, pmid = {26992451}, issn = {1520-5851}, mesh = {Benzalkonium Compounds/chemistry/*metabolism ; *Biodegradation, Environmental ; Biotransformation ; Metagenome ; Microbial Consortia/genetics/*physiology ; Pseudomonas/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Sewage/chemistry/microbiology ; Soil/chemistry ; Soil Pollutants/chemistry/*metabolism ; }, abstract = {Benzalkonium chlorides (BACs) are emerging pollutants. Identification of microorganisms and the genes involved in the biodegradation of BACs is crucial for better understanding the fate of BACs in the environment and developing treatment strategies. Four microbial communities degrading BACs were developed from sewage (SEW), activated sludge (AS), soil (SOIL) and sea sediment (SEA) samples. According to 16S rRNA pyrosequencing and shotgun metagenome sequencing analyses, the most abundant species represented uncharacterized members of the Pseudomonas and Achromobacter genera. BAC biotransformation rates of the enriched microbial communities were 2.8, 3.2, 17.8, and 24.3 μM hr(-1) for SEA, AS, SOIL, and SEW, respectively, and were positively correlated with the relative abundance of a particular Pseudomonas sp. strain, BIOMIG1. The strain BIOMIG1 mineralizes BACs at a rate up to 2.40 μmol hr(-1) 10(-11) cells. Genomes of four BAC degrading and nondegrading BIOMIG1 phenotypes were sequenced and differentially compared with each other. As a result, a gene cluster encoding for transporters, an integrase and a dioxygenase were involved in BAC biotransformation. Our results suggest that BIOMIG1 plays a key role on the fate of BACs in the environment and genes, other than those reported to date, are involved in BAC biotransformation in various habitats.}, } @article {pmid26991862, year = {2016}, author = {Oh, B and Kim, JW and Kim, BS}, title = {Changes in the Functional Potential of the Gut Microbiome Following Probiotic Supplementation during Helicobacter Pylori Treatment.}, journal = {Helicobacter}, volume = {21}, number = {6}, pages = {493-503}, doi = {10.1111/hel.12306}, pmid = {26991862}, issn = {1523-5378}, mesh = {Adult ; Anti-Bacterial Agents/*administration & dosage ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Helicobacter Infections/*therapy ; Humans ; Male ; Metagenomics ; Middle Aged ; Probiotics/*administration & dosage ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; }, abstract = {BACKGROUND: Probiotic supplementation is utilized to alleviate the side effects associated with antibiotic therapy for Helicobacter pylori infection. Several studies have described the effects of administration of probiotics on the gut microbiota during antibiotic therapy. However, most of these studies have focused on specific bacteria, thereby providing limited information on the functional roles of the altered microbiota. Therefore, we examined the impact of probiotic supplementation on the structure and functional dynamics of the gut microbiota during H. pylori eradication, using whole-metagenomic sequence analysis.

METHODS: Subjects were divided into two groups: the antibiotics group, which received only antibiotics, and the probiotics group, which received antibiotics with probiotic supplementation. The structural and functional profiles of gut microbiota was analyzed using metagenomic DNA extracted from the feces during treatment by Illumina MiSeq system.

RESULTS: The overall alterations in microbiota, as revealed by whole metagenome sequencing, were similar with results from our previous 16S rRNA gene-based analysis. The proportional shift in functional gene families was greater in the antibiotics group than in the probiotics group. In particular, the proportion of genes related to selenocompound metabolism was reduced in the probiotics group, whereas genes associated with the metabolism of nucleotide sugars were increased.

CONCLUSION: The functional alterations of gut microbiota may link to the reduction in intestinal irritation and maintenance of bacterial diversity observed following probiotic supplementation with antibiotic therapy. The potential beneficial roles of altered gut microbiota following probiotic supplementation are expected a reduction in side effects such as intestinal irritation and antibiotics resistance.}, } @article {pmid26991500, year = {2016}, author = {Yap, TW and Gan, HM and Lee, YP and Leow, AH and Azmi, AN and Francois, F and Perez-Perez, GI and Loke, MF and Goh, KL and Vadivelu, J}, title = {Helicobacter pylori Eradication Causes Perturbation of the Human Gut Microbiome in Young Adults.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0151893}, pmid = {26991500}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Anti-Bacterial Agents/*adverse effects/therapeutic use ; Cohort Studies ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Helicobacter Infections/drug therapy/microbiology ; Humans ; Male ; Metagenomics ; Young Adult ; }, abstract = {BACKGROUND: Accumulating evidence shows that Helicobacter pylori protects against some metabolic and immunological diseases in which the development of these diseases coincide with temporal or permanent dysbiosis. The aim of this study was to assess the effect of H. pylori eradication on the human gut microbiome.

METHODS: As part of the currently on-going ESSAY (Eradication Study in Stable Adults/Youths) study, we collected stool samples from 17 H. pylori-positive young adult (18-30 years-old) volunteers. The same cohort was followed up 6, 12 and 18 months-post H. pylori eradication. The impact of H. pylori on the human gut microbiome pre- and post-eradication was investigated using high throughput 16S rRNA gene (V3-V4 region) sequencing using the Illumina Miseq followed by data analysis using Qiime pipeline.

RESULTS: We compared the composition and diversity of bacterial communities in the fecal microbiome of the H. pylori-positive volunteers, before and after H. pylori eradication therapy. The 16S rRNA gene was sequenced at an average of 150,000-170,000 reads/sample. The microbial diversity were similar pre- and post-H. pylori eradication with no significant differences in richness and evenness of bacterial species. Despite that the general profile of the gut microbiome was similar pre- and post-eradication, some changes in the bacterial communities at the phylum and genus levels were notable, particularly the decrease in relative abundance of Bacterioidetes and corresponding increase in Firmicutes after H. pylori eradication. The significant increase of short-chain fatty acids (SCFA)-producing bacteria genera could also be associated with increased risk of metabolic disorders.

CONCLUSIONS: Our preliminary stool metagenomics study shows that eradication of H. pylori caused perturbation of the gut microbiome and may indirectly affect the health of human. Clinicians should be aware of the effect of broad spectrum antibiotics used in H. pylori eradication regimen and be cautious in the clinical management of H. pylori infection, particularly in immunocompromised patients.}, } @article {pmid26989200, year = {2016}, author = {Hergott, CB and Roche, AM and Tamashiro, E and Clarke, TB and Bailey, AG and Laughlin, A and Bushman, FD and Weiser, JN}, title = {Peptidoglycan from the gut microbiota governs the lifespan of circulating phagocytes at homeostasis.}, journal = {Blood}, volume = {127}, number = {20}, pages = {2460-2471}, pmid = {26989200}, issn = {1528-0020}, support = {107660//Wellcome Trust/United Kingdom ; R01 HL113252/HL/NHLBI NIH HHS/United States ; MR/J006874/1/MRC_/Medical Research Council/United Kingdom ; P30 AI045008/AI/NIAID NIH HHS/United States ; T32 AI060516/AI/NIAID NIH HHS/United States ; R37 AI038446/AI/NIAID NIH HHS/United States ; //Wellcome Trust/United Kingdom ; R01 AI105168/AI/NIAID NIH HHS/United States ; R01 AI038446/AI/NIAID NIH HHS/United States ; }, mesh = {Adoptive Transfer ; Animals ; Animals, Congenic ; Anti-Bacterial Agents/pharmacology ; Apoptosis/drug effects ; Cell Survival/physiology ; Diaminopimelic Acid/analogs & derivatives/pharmacology ; Female ; Gastrointestinal Microbiome/drug effects/*physiology ; Germ-Free Life ; *Homeostasis ; Interleukin-17/physiology ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Monocytes/cytology ; Neutrophils/cytology ; Nod1 Signaling Adaptor Protein/deficiency/physiology ; Nod2 Signaling Adaptor Protein/deficiency/physiology ; Peptidoglycan/*pharmacology ; Phagocytes/*cytology/drug effects ; Toll-Like Receptor 2/deficiency/physiology ; Toll-Like Receptor 4/deficiency/physiology ; }, abstract = {Maintenance of myeloid cell homeostasis requires continuous turnover of phagocytes from the bloodstream, yet whether environmental signals influence phagocyte longevity in the absence of inflammation remains unknown. Here, we show that the gut microbiota regulates the steady-state cellular lifespan of neutrophils and inflammatory monocytes, the 2 most abundant circulating myeloid cells and key contributors to inflammatory responses. Treatment of mice with broad-spectrum antibiotics, or with the gut-restricted aminoglycoside neomycin alone, accelerated phagocyte turnover and increased the rates of their spontaneous apoptosis. Metagenomic analyses revealed that neomycin altered the abundance of intestinal bacteria bearing γ-d-glutamyl-meso-diaminopimelic acid, a ligand for the intracellular peptidoglycan sensor Nod1. Accordingly, signaling through Nod1 was both necessary and sufficient to mediate the stimulatory influence of the flora on myeloid cell longevity. Stimulation of Nod1 signaling increased the frequency of lymphocytes in the murine intestine producing the proinflammatory cytokine interleukin 17A (IL-17A), and liberation of IL-17A was required for transmission of Nod1-dependent signals to circulating phagocytes. Together, these results define a mechanism through which intestinal microbes govern a central component of myeloid homeostasis and suggest perturbations of commensal communities can influence steady-state regulation of cell fate.}, } @article {pmid26985997, year = {2016}, author = {Zepeda Mendoza, ML and Lundberg, J and Ivarsson, M and Campos, P and Nylander, JA and Sallstedt, T and Dalen, L}, title = {Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante's Cave, Northern Sweden.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0151577}, pmid = {26985997}, issn = {1932-6203}, mesh = {Actinobacteria/*genetics ; *Biodiversity ; Caves/*microbiology ; *Metagenome ; Metagenomics ; Sweden ; }, abstract = {Speleothems are secondary mineral deposits normally formed by water supersaturated with calcium carbonate percolating into underground caves, and are often associated with low-nutrient and mostly non-phototrophic conditions. Tjuv-Ante's cave is a shallow-depth cave formed by the action of waves, with granite and dolerite as major components, and opal-A and calcite as part of the speleothems, making it a rare kind of cave. We generated two DNA shotgun sequencing metagenomic datasets from the interior of a speleothem from Tjuv-Ante's cave representing areas of old and relatively recent speleothem formation. We used these datasets to perform i) an evaluation of the use of these speleothems as past biodiversity archives, ii) functional and taxonomic profiling of the speleothem's different formation periods, and iii) taxonomic comparison of the metagenomic results to previous microscopic analyses from a nearby speleothem of the same cave. Our analyses confirm the abundance of Actinobacteria and fungi as previously reported by microscopic analyses on this cave, however we also discovered a larger biodiversity. Interestingly, we identified photosynthetic genes, as well as genes related to iron and sulphur metabolism, suggesting the presence of chemoautotrophs. Furthermore, we identified taxa and functions related to biomineralization. However, we could not confidently establish the use of this type of speleothems as biological paleoarchives due to the potential leaching from the outside of the cave and the DNA damage that we propose has been caused by the fungal chemical etching.}, } @article {pmid26984526, year = {2016}, author = {Zhang, Y and Ji, P and Wang, J and Zhao, F}, title = {RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes.}, journal = {Nucleic acids research}, volume = {44}, number = {10}, pages = {e99}, pmid = {26984526}, issn = {1362-4962}, mesh = {Contig Mapping ; Escherichia coli/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Phaeophyceae/microbiology ; Phylogeny ; *RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; }, abstract = {16S rRNA amplicon analysis and shotgun metagenome sequencing are two main culture-independent strategies to explore the genetic landscape of various microbial communities. Recently, numerous studies have employed these two approaches together, but downstream data analyses were performed separately, which always generated incongruent or conflict signals on both taxonomic and functional classifications. Here we propose a novel approach, RiboFR-Seq (Ribosomal RNA gene flanking region sequencing), for capturing both ribosomal RNA variable regions and their flanking protein-coding genes simultaneously. Through extensive testing on clonal bacterial strain, salivary microbiome and bacterial epibionts of marine kelp, we demonstrated that RiboFR-Seq could detect the vast majority of bacteria not only in well-studied microbiomes but also in novel communities with limited reference genomes. Combined with classical amplicon sequencing and shotgun metagenome sequencing, RiboFR-Seq can link the annotations of 16S rRNA and metagenomic contigs to make a consensus classification. By recognizing almost all 16S rRNA copies, the RiboFR-seq approach can effectively reduce the taxonomic abundance bias resulted from 16S rRNA copy number variation. We believe that RiboFR-Seq, which provides an integrated view of 16S rRNA profiles and metagenomes, will help us better understand diverse microbial communities.}, } @article {pmid26983403, year = {2016}, author = {Souza, RC and Mendes, IC and Reis-Junior, FB and Carvalho, FM and Nogueira, MA and Vasconcelos, AT and Vicente, VA and Hungria, M}, title = {Shifts in taxonomic and functional microbial diversity with agriculture: How fragile is the Brazilian Cerrado?.}, journal = {BMC microbiology}, volume = {16}, number = {}, pages = {42}, pmid = {26983403}, issn = {1471-2180}, mesh = {Agriculture ; Bacteria/*classification/genetics/*isolation & purification/metabolism ; *Biodiversity ; Brazil ; Carbon/analysis/metabolism ; Metagenomics ; Nitrogen/analysis/metabolism ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {BACKGROUND: The Cerrado--an edaphic type of savannah--comprises the second largest biome of the Brazilian territory and is the main area for grain production in the country, but information about the impact of land conversion to agriculture on microbial diversity is still scarce. We used a shotgun metagenomic approach to compare undisturbed (native) soil and soils cropped for 23 years with soybean/maize under conservation tillage--"no-till" (NT)--and conventional tillage (CT) systems in the Cerrado biome.

RESULTS: Soil management and fertilizer inputs with the introduction of agriculture improved chemical properties, but decreased soil macroporosity and microbial biomass of carbon and nitrogen. Principal coordinates analyses confirmed different taxonomic and functional profiles for each treatment. There was predominance of the Bacteria domain, especially the phylum Proteobacteria, with higher numbers of sequences in the NT and CT treatments; Archaea and Viruses also had lower numbers of sequences in the undisturbed soil. Within the Alphaproteobacteria, there was dominance of Rhizobiales and of the genus Bradyrhizobium in the NT and CT systems, attributed to massive inoculation of soybean, and also of Burkholderiales. In contrast, Rhizobium, Azospirillum, Xanthomonas, Pseudomonas and Acidobacterium predominated in the native Cerrado. More Eukaryota, especially of the phylum Ascomycota were detected in the NT. The functional analysis revealed lower numbers of sequences in the five dominant categories for the CT system, whereas the undisturbed Cerrado presented higher abundance.

CONCLUSION: High impact of agriculture in taxonomic and functional microbial diversity in the biome Cerrado was confirmed. Functional diversity was not necessarily associated with taxonomic diversity, as the less conservationist treatment (CT) presented increased taxonomic sequences and reduced functional profiles, indicating a strategy to try to maintain soil functioning by favoring taxa that are probably not the most efficient for some functions. Our results highlight that underneath the rustic appearance of the Cerrado vegetation there is a fragile soil microbial community.}, } @article {pmid26983005, year = {2016}, author = {Ross, DE and Marshall, CW and May, HD and Norman, RS}, title = {Comparative Genomic Analysis of Sulfurospirillum cavolei MES Reconstructed from the Metagenome of an Electrosynthetic Microbiome.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0151214}, pmid = {26983005}, issn = {1932-6203}, mesh = {Epsilonproteobacteria/classification/*genetics ; *Genome, Bacterial ; *Microbiota ; Phylogeny ; }, abstract = {Sulfurospirillum spp. play an important role in sulfur and nitrogen cycling, and contain metabolic versatility that enables reduction of a wide range of electron acceptors, including thiosulfate, tetrathionate, polysulfide, nitrate, and nitrite. Here we describe the assembly of a Sulfurospirillum genome obtained from the metagenome of an electrosynthetic microbiome. The ubiquity and persistence of this organism in microbial electrosynthesis systems suggest it plays an important role in reactor stability and performance. Understanding why this organism is present and elucidating its genetic repertoire provide a genomic and ecological foundation for future studies where Sulfurospirillum are found, especially in electrode-associated communities. Metabolic comparisons and in-depth analysis of unique genes revealed potential ecological niche-specific capabilities within the Sulfurospirillum genus. The functional similarities common to all genomes, i.e., core genome, and unique gene clusters found only in a single genome were identified. Based upon 16S rRNA gene phylogenetic analysis and average nucleotide identity, the Sulfurospirillum draft genome was found to be most closely related to Sulfurospirillum cavolei. Characterization of the draft genome described herein provides pathway-specific details of the metabolic significance of the newly described Sulfurospirillum cavolei MES and, importantly, yields insight to the ecology of the genus as a whole. Comparison of eleven sequenced Sulfurospirillum genomes revealed a total of 6246 gene clusters in the pan-genome. Of the total gene clusters, 18.5% were shared among all eleven genomes and 50% were unique to a single genome. While most Sulfurospirillum spp. reduce nitrate to ammonium, five of the eleven Sulfurospirillum strains encode for a nitrous oxide reductase (nos) cluster with an atypical nitrous-oxide reductase, suggesting a utility for this genus in reduction of the nitrous oxide, and as a potential sink for this potent greenhouse gas.}, } @article {pmid26982568, year = {2016}, author = {Burman, S and Hoedt, EC and Pottenger, S and Mohd-Najman, NS and Ó Cuív, P and Morrison, M}, title = {An (Anti)-Inflammatory Microbiota: Defining the Role in Inflammatory Bowel Disease?.}, journal = {Digestive diseases (Basel, Switzerland)}, volume = {34}, number = {1-2}, pages = {64-71}, doi = {10.1159/000443759}, pmid = {26982568}, issn = {1421-9875}, mesh = {Animals ; Case-Control Studies ; Crohn Disease/immunology/microbiology/prevention & control ; Disease Progression ; Dysbiosis/immunology/microbiology/prevention & control ; Humans ; Inflammatory Bowel Diseases/*immunology/*microbiology/prevention & control ; Metagenomics/methods ; Microbiota/*immunology ; }, abstract = {While it is now accepted that the gut microbiota contribute to the genotype-environment-lifestyle interactions triggering inflammatory bowel disease (IBD) episodes, efforts to identify the pathogen(s) that cause these diseases have met with limited success. The advent of culture-independent techniques for characterizing the structure and/or function of microbial communities (hereafter referred to as metagenomics) has provided new insights into the events associated with the onset, remission and recurrence of IBD. A large number of observational and/or case-control studies of IBD patients have confirmed substantive changes in gut bacterial profiles (dysbiosis) associated with disease. These types of studies have been augmented by new profiling approaches that support the identification of more 'colitogenic' bacteria from numerically predominant taxa. Evidence of alterations in lesser abundant taxa such as the methanogenic archaea, to favor types that are more immunogenic, has also been forthcoming. Several recent longitudinal studies of patients with Crohn's disease have produced additional insights, including evidence for the role of 'anti-inflammatory' microbiota in providing a protective effect and/or promoting remission. In summation, the implications of dysbiosis and restoration of a 'healthy microbiota' in IBD patients requires definition beyond a taxonomic assessment of the changes in the gut microbiota during disease course. The available evidence does suggest that specific members of the gut microbiota can contribute either pro- or anti-inflammatory effects, and their ecological fitness in the large bowel affects the onset and recurrence of IBD. While metagenomics and related approaches offer the potential to provide novel and important insights into these microbiota and thereby the pathophysiology of IBD, we also need to better understand factors affecting the ecological fitness of these microbes, if new treatment of IBD patients are to be delivered.}, } @article {pmid26981376, year = {2016}, author = {Singh, A and Subudhi, E}, title = {Structural insights of microbial community of Deulajhari (India) hot spring using 16s-rRNA based metagenomic sequencing.}, journal = {Genomics data}, volume = {7}, number = {}, pages = {101-102}, pmid = {26981376}, issn = {2213-5960}, abstract = {Insights about the distribution of the microbial community prove to be the major goal of understanding microbial ecology which remains to be fully deciphered. Hot springs being hub for the thermophilic microbiota attract the attention of the microbiologists. Deulajhari hot spring cluster is located in the Angul district of Odisha. Covered within a wooded area, Deulajhari hot spring is also fed by the plant litter resulting in a relatively high amount of total organic content (TOC). For the first time, Illumina sequencing based biodiversity analysis of microbial composition is studied through amplicon metagenome sequencing of 16s rRNA targeting V3-V4 region using metagenomic DNA from the hot spring sediment. Over 28 phyla were detected through the amplicon metagenome sequencing of which the most dominating phyla at the existing physiochemical parameters like; temperature 69 °C, pH 8.09, electroconductivity 0.025 dSm(- 1) and total organic carbon 0.356%, were Proteobacteria (88.12%), Bacteriodetes (10.76%), Firmicutes (0.35%), Spirochetes (0.18%) and chloroflexi (0.11%). Approximately 713 species were observed at the above physiochemical parameters. The analysis of the metagenome provides the quantitative insights into microbial populations based on the sequence data in Deulajhari hot spring. Metagenome sequence is deposited to SRA database which is available at NCBI with accession no. SRX1459736.}, } @article {pmid26979110, year = {2016}, author = {Greer, R and Dong, X and Morgun, A and Shulzhenko, N}, title = {Investigating a holobiont: Microbiota perturbations and transkingdom networks.}, journal = {Gut microbes}, volume = {7}, number = {2}, pages = {126-135}, pmid = {26979110}, issn = {1949-0984}, support = {R01 DK103761/DK/NIDDK NIH HHS/United States ; U01 AI109695/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics/metabolism ; Bacterial Infections/*microbiology ; Computational Biology ; Host-Pathogen Interactions/*drug effects ; Humans ; Microbiota/*drug effects ; }, abstract = {The scientific community has recently come to appreciate that, rather than existing as independent organisms, multicellular hosts and their microbiota comprise a complex evolving superorganism or metaorganism, termed a holobiont. This point of view leads to a re-evaluation of our understanding of different physiological processes and diseases. In this paper we focus on experimental and computational approaches which, when combined in one study, allowed us to dissect mechanisms (traditionally named host-microbiota interactions) regulating holobiont physiology. Specifically, we discuss several approaches for microbiota perturbation, such as use of antibiotics and germ-free animals, including advantages and potential caveats of their usage. We briefly review computational approaches to characterize the microbiota and, more importantly, methods to infer specific components of microbiota (such as microbes or their genes) affecting host functions. One such approach called transkingdom network analysis has been recently developed and applied in our study. (1) Finally, we also discuss common methods used to validate the computational predictions of host-microbiota interactions using in vitro and in vivo experimental systems.}, } @article {pmid26978389, year = {2016}, author = {Temmam, S and Monteil-Bouchard, S and Robert, C and Baudoin, JP and Sambou, M and Aubadie-Ladrix, M and Labas, N and Raoult, D and Mediannikov, O and Desnues, C}, title = {Characterization of Viral Communities of Biting Midges and Identification of Novel Thogotovirus Species and Rhabdovirus Genus.}, journal = {Viruses}, volume = {8}, number = {3}, pages = {77}, pmid = {26978389}, issn = {1999-4915}, mesh = {Animals ; *Biota ; Ceratopogonidae/*virology ; *Disease Vectors ; High-Throughput Nucleotide Sequencing ; RNA Viruses/*classification/*isolation & purification ; Senegal ; }, abstract = {More than two thirds of emerging viruses are of zoonotic origin, and among them RNA viruses represent the majority. Ceratopogonidae (genus Culicoides) are well-known vectors of several viruses responsible for epizooties (bluetongue, epizootic haemorrhagic disease, etc.). They are also vectors of the only known virus infecting humans: the Oropouche virus. Female midges usually feed on a variety of hosts, leading to possible transmission of emerging viruses from animals to humans. In this context, we report here the analysis of RNA viral communities of Senegalese biting midges using next-generation sequencing techniques as a preliminary step toward the identification of potential viral biohazards. Sequencing of the RNA virome of three pools of Culicoides revealed the presence of a significant diversity of viruses infecting plants, insects and mammals. Several novel viruses were detected, including a novel Thogotovirus species, related but genetically distant from previously described tick-borne thogotoviruses. Novel rhabdoviruses were also detected, possibly constituting a novel Rhabdoviridae genus, and putatively restricted to insects. Sequences related to the major viruses transmitted by Culicoides, i.e., African horse sickness, bluetongue and epizootic haemorrhagic disease viruses were also detected. This study highlights the interest in monitoring the emergence and circulation of zoonoses and epizooties using their arthropod vectors.}, } @article {pmid26975620, year = {2016}, author = {Chen, L and Zhang, YH and Huang, T and Cai, YD}, title = {Gene expression profiling gut microbiota in different races of humans.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {23075}, pmid = {26975620}, issn = {2045-2322}, mesh = {Algorithms ; Asian People ; China ; Cluster Analysis ; Europe ; Feeding Behavior/ethnology ; Gastrointestinal Microbiome/*genetics ; Gene Expression Profiling/*methods ; Humans ; Machine Learning ; Metagenome/*genetics ; Metagenomics/*methods ; Oligonucleotide Array Sequence Analysis/methods ; United States ; White People ; }, abstract = {The gut microbiome is shaped and modified by the polymorphisms of microorganisms in the intestinal tract. Its composition shows strong individual specificity and may play a crucial role in the human digestive system and metabolism. Several factors can affect the composition of the gut microbiome, such as eating habits, living environment, and antibiotic usage. Thus, various races are characterized by different gut microbiome characteristics. In this present study, we studied the gut microbiomes of three different races, including individuals of Asian, European and American races. The gut microbiome and the expression levels of gut microbiome genes were analyzed in these individuals. Advanced feature selection methods (minimum redundancy maximum relevance and incremental feature selection) and four machine-learning algorithms (random forest, nearest neighbor algorithm, sequential minimal optimization, Dagging) were employed to capture key differentially expressed genes. As a result, sequential minimal optimization was found to yield the best performance using the 454 genes, which could effectively distinguish the gut microbiomes of different races. Our analyses of extracted genes support the widely accepted hypotheses that eating habits, living environments and metabolic levels in different races can influence the characteristics of the gut microbiome.}, } @article {pmid26975510, year = {2016}, author = {Vincent, C and Miller, MA and Edens, TJ and Mehrotra, S and Dewar, K and Manges, AR}, title = {Bloom and bust: intestinal microbiota dynamics in response to hospital exposures and Clostridium difficile colonization or infection.}, journal = {Microbiome}, volume = {4}, number = {}, pages = {12}, pmid = {26975510}, issn = {2049-2618}, support = {GSD-113375//Canadian Institutes of Health Research/Canada ; }, mesh = {Aged ; Anti-Bacterial Agents/*adverse effects ; Bile Acids and Salts/biosynthesis ; Cephalosporins/adverse effects ; Clostridioides difficile/drug effects/growth & development/*pathogenicity ; Cross Infection/*microbiology/pathology ; Diarrhea/etiology/*microbiology/pathology ; Enterocolitis, Pseudomembranous/etiology/*microbiology/pathology ; Eubacterium/drug effects/growth & development/pathogenicity ; Female ; Fluoroquinolones/adverse effects ; Gastrointestinal Microbiome/*genetics ; Humans ; Laxatives/adverse effects ; Male ; *Metagenome ; Middle Aged ; Prospective Studies ; }, abstract = {BACKGROUND: Clostridium difficile infection (CDI) is the leading infectious cause of nosocomial diarrhea. Hospitalized patients are at increased risk of developing CDI because they are exposed to C. difficile spores through contact with the hospital environment and often receive antibiotics and other medications that can disrupt the integrity of the indigenous intestinal microbiota and impair colonization resistance. Using whole metagenome shotgun sequencing, we examined the diversity and composition of the fecal microbiota in a prospective cohort study of 98 hospitalized patients.

RESULTS: Four patients had asymptomatic C. difficile colonization, and four patients developed CDI. We observed dramatic shifts in the structure of the gut microbiota during hospitalization. In contrast to CDI cases, asymptomatic patients exhibited elevated relative abundance of potentially protective bacterial taxa in their gut at the onset of C. difficile colonization. Use of laxatives was associated with significant reductions in the relative abundance of Clostridium and Eubacterium; species within these genera have previously been shown to enhance resistance to CDI via the production of secondary bile acids. Cephalosporin and fluoroquinolone exposure decreased the frequency of Clostridiales Family XI Incertae Sedis, a bacterial family that has been previously associated with decreased CDI risk.

CONCLUSIONS: This study underscores the detrimental impact of antibiotics as well as other medications, particularly laxatives, on the intestinal microbiota and suggests that co-colonization with key bacterial taxa may prevent C. difficile overgrowth or the transition from asymptomatic C. difficile colonization to CDI.}, } @article {pmid26972977, year = {2016}, author = {Jung, J and Philippot, L and Park, W}, title = {Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {23012}, pmid = {26972977}, issn = {2045-2322}, mesh = {Alkanes/metabolism ; Bacteria/classification/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Biodiversity ; Denitrification ; *Ecosystem ; Environmental Restoration and Remediation/methods ; *Gasoline ; Genetic Variation ; Metagenomics/*methods ; Nitrogen Cycle ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; Soil Microbiology ; Soil Pollutants/metabolism ; }, abstract = {The relationship between microbial biodiversity and soil function is an important issue in ecology, yet most studies have been performed in pristine ecosystems. Here, we assess the role of microbial diversity in ecological function and remediation strategies in diesel-contaminated soils. Soil microbial diversity was manipulated using a removal by dilution approach and microbial functions were determined using both metagenomic analyses and enzymatic assays. A shift from Proteobacteria- to Actinobacteria-dominant communities was observed when species diversity was reduced. Metagenomic analysis showed that a large proportion of functional gene categories were significantly altered by the reduction in biodiversity. The abundance of genes related to the nitrogen cycle was significantly reduced in the low-diversity community, impairing denitrification. In contrast, the efficiency of diesel biodegradation was increased in the low-diversity community and was further enhanced by addition of red clay as a stimulating agent. Our results suggest that the relationship between microbial diversity and ecological function involves trade-offs among ecological processes, and should not be generalized as a positive, neutral, or negative relationship.}, } @article {pmid26972923, year = {2016}, author = {Velázquez, D and López-Bueno, A and Aguirre de Cárcer, D and de los Ríos, A and Alcamí, A and Quesada, A}, title = {Ecosystem function decays by fungal outbreaks in Antarctic microbial mats.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {22954}, pmid = {26972923}, issn = {2045-2322}, mesh = {Antarctic Regions ; Archaea/classification/genetics/growth & development ; Bacteria/classification/genetics/growth & development ; Basidiomycota/classification/genetics/growth & development ; Biodiversity ; Biomass ; *Ecosystem ; *Environmental Microbiology ; Fungi/classification/genetics/*growth & development ; Genetic Variation ; Geography ; Islands ; Metagenomics/methods ; Population Density ; Seasons ; *Temperature ; Viruses/classification/genetics/growth & development ; }, abstract = {Antarctica harbours a remarkably diverse range of freshwater bodies and terrestrial ecosystems, where microbial mats are considered the most important systems in terms of biomass and metabolic capabilities. We describe the presence of lysis plaque-like macroscopic blighted patches within the predominant microbial mats on Livingston Island (Antarctic Peninsula). Those blighting circles are associated with decay in physiological traits as well as nitrogen depletion and changes in the spatial microstructure; these alterations were likely related to disruption of the biogeochemical gradients within the microbial ecosystem caused by an unusually high fungal abundance and consequent physical alterations. This phenomenon has been evidenced at a time of unprecedented rates of local warming in the Antarctic Peninsula area, and decay of these ecosystems is potentially stimulated by warmer temperatures.}, } @article {pmid26972811, year = {2016}, author = {Spanogiannopoulos, P and Bess, EN and Carmody, RN and Turnbaugh, PJ}, title = {The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism.}, journal = {Nature reviews. Microbiology}, volume = {14}, number = {5}, pages = {273-287}, pmid = {26972811}, issn = {1740-1534}, support = {R01 AT008618/AT/NCCIH NIH HHS/United States ; R01HL122593/HL/NHLBI NIH HHS/United States ; F32DK101154/DK/NIDDK NIH HHS/United States ; R01AT008618/AT/NCCIH NIH HHS/United States ; P30 DK098722/DK/NIDDK NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; F32 DK101154/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Diet ; Drug Therapy ; *Gastrointestinal Microbiome/physiology ; Humans ; Immune System/physiology ; Metabolome ; Metagenome ; Pharmaceutical Preparations/*metabolism ; Pharmacogenetics ; Xenobiotics/*metabolism ; }, abstract = {Although the importance of human genetic polymorphisms in therapeutic outcomes is well established, the role of our 'second genome' (the microbiome) has been largely overlooked. In this Review, we highlight recent studies that have shed light on the mechanisms that link the human gut microbiome to the efficacy and toxicity of xenobiotics, including drugs, dietary compounds and environmental toxins. Continued progress in this area could enable more precise tools for predicting patient responses and for the development of a new generation of therapeutics based on, or targeted at, the gut microbiome. Indeed, the admirable goal of precision medicine may require us to first understand the microbial pharmacists within.}, } @article {pmid26969701, year = {2016}, author = {Soto-Giron, MJ and Rodriguez-R, LM and Luo, C and Elk, M and Ryu, H and Hoelle, J and Santo Domingo, JW and Konstantinidis, KT}, title = {Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {9}, pages = {2872-2883}, pmid = {26969701}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/isolation & purification/pathogenicity ; *Bacterial Physiological Phenomena ; Biofilms/*growth & development ; Chlorine ; Cross Infection/*genetics/*microbiology ; Culture Techniques ; DNA, Bacterial/analysis ; Disinfectants/pharmacology ; Disinfection ; Drug Resistance, Bacterial ; Genome, Bacterial ; *Hospitals ; Metagenome ; Microbiota/genetics ; Mycobacterium/physiology ; Ohio ; Phylogeny ; Proteobacteria/physiology ; RNA, Ribosomal, 16S/genetics ; Sphingomonadaceae/physiology ; *Water Microbiology ; Water Supply ; }, abstract = {Although the source of drinking water (DW) used in hospitals is commonly disinfected, biofilms forming on water pipelines are a refuge for bacteria, including possible pathogens that survive different disinfection strategies. These biofilm communities are only beginning to be explored by culture-independent techniques that circumvent the limitations of conventional monitoring efforts. Hence, theories regarding the frequency of opportunistic pathogens in DW biofilms and how biofilm members withstand high doses of disinfectants and/or chlorine residuals in the water supply remain speculative. The aim of this study was to characterize the composition of microbial communities growing on five hospital shower hoses using both 16S rRNA gene sequencing of bacterial isolates and whole-genome shotgun metagenome sequencing. The resulting data revealed a Mycobacterium-like population, closely related to Mycobacterium rhodesiae and Mycobacterium tusciae, to be the predominant taxon in all five samples, and its nearly complete draft genome sequence was recovered. In contrast, the fraction recovered by culture was mostly affiliated with Proteobacteria, including members of the genera Sphingomonas, Blastomonas, and Porphyrobacter.The biofilm community harbored genes related to disinfectant tolerance (2.34% of the total annotated proteins) and a lower abundance of virulence determinants related to colonization and evasion of the host immune system. Additionally, genes potentially conferring resistance to β-lactam, aminoglycoside, amphenicol, and quinolone antibiotics were detected. Collectively, our results underscore the need to understand the microbiome of DW biofilms using metagenomic approaches. This information might lead to more robust management practices that minimize the risks associated with exposure to opportunistic pathogens in hospitals.}, } @article {pmid26965911, year = {2016}, author = {Cannon, MV and Hester, J and Shalkhauser, A and Chan, ER and Logue, K and Small, ST and Serre, D}, title = {In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {22908}, pmid = {26965911}, issn = {2045-2322}, support = {T32 CA094186/CA/NCI NIH HHS/United States ; }, mesh = {Amphibians/classification/genetics ; Animals ; *Biodiversity ; Birds/classification/genetics ; Carps/classification/genetics ; *Classification ; Computer Simulation ; DNA/*genetics/isolation & purification ; Ecosystem ; Environmental Monitoring ; High-Throughput Nucleotide Sequencing ; Mammals/classification/genetics ; *Metagenomics ; Plants/classification ; Rivers ; Species Specificity ; }, abstract = {Analysis of environmental DNA (eDNA) enables the detection of species of interest from water and soil samples, typically using species-specific PCR. Here, we describe a method to characterize the biodiversity of a given environment by amplifying eDNA using primer pairs targeting a wide range of taxa and high-throughput sequencing for species identification. We tested this approach on 91 water samples of 40 mL collected along the Cuyahoga River (Ohio, USA). We amplified eDNA using 12 primer pairs targeting mammals, fish, amphibians, birds, bryophytes, arthropods, copepods, plants and several microorganism taxa and sequenced all PCR products simultaneously by high-throughput sequencing. Overall, we identified DNA sequences from 15 species of fish, 17 species of mammals, 8 species of birds, 15 species of arthropods, one turtle and one salamander. Interestingly, in addition to aquatic and semi-aquatic animals, we identified DNA from terrestrial species that live near the Cuyahoga River. We also identified DNA from one Asian carp species invasive to the Great Lakes but that had not been previously reported in the Cuyahoga River. Our study shows that analysis of eDNA extracted from small water samples using wide-range PCR amplification combined with high-throughput sequencing can provide a broad perspective on biological diversity.}, } @article {pmid26965447, year = {2016}, author = {Prince, AL and Ma, J and Kannan, PS and Alvarez, M and Gisslen, T and Harris, RA and Sweeney, EL and Knox, CL and Lambers, DS and Jobe, AH and Chougnet, CA and Kallapur, SG and Aagaard, KM}, title = {The placental membrane microbiome is altered among subjects with spontaneous preterm birth with and without chorioamnionitis.}, journal = {American journal of obstetrics and gynecology}, volume = {214}, number = {5}, pages = {627.e1-627.e16}, pmid = {26965447}, issn = {1097-6868}, support = {F32 HD082969/HD/NICHD NIH HHS/United States ; R01 HL097064/HL/NHLBI NIH HHS/United States ; DP2 OD001500/OD/NIH HHS/United States ; R01 DK089201/DK/NIDDK NIH HHS/United States ; R01 NR014792/NR/NINR NIH HHS/United States ; }, mesh = {Butyrates/metabolism ; Chorioamnionitis/*microbiology ; Cross-Sectional Studies ; DNA, Bacterial/genetics ; Female ; Glycerophospholipids/metabolism ; Humans ; Metagenomics ; *Microbiota ; Pentose Phosphate Pathway ; Placenta/*microbiology ; Pregnancy ; *Premature Birth ; Riboflavin/metabolism ; Sequence Analysis, DNA ; Severity of Illness Index ; Term Birth ; }, abstract = {BACKGROUND: Preterm birth (PTB) is a leading cause of neonatal morbidity and mortality and is not uncommonly associated with chorioamnionitis. We recently have demonstrated that the placenta harbors a unique microbiome with similar flora to the oral community. We also have shown an association of these placental microbiota with PTB, history of antenatal infection, and excess maternal weight gain. On the basis of these previous observations, we hypothesized that the placental membranes would retain a microbiome community that would vary in association with preterm birth and chorioamnionitis.

OBJECTIVE: In the current study, we aimed to examine the differences in the placental membrane microbiome in association with PTB in both the presence and absence of chorioamnionitis and/or funisitis using state-of-the-science whole-genome shotgun metagenomics.

STUDY DESIGN: This was a cross-sectional analysis with 6 nested spontaneous birth cohorts (n = 9-15 subjects/cohort): Term gestations without chorioamnionitis, term with chorioamnionitis, preterm without chorioamnionitis, preterm with mild chorioamnionitis, preterm with severe chorioamnionitis, and preterm with chorioamnionitis and funisitis. Histologic analysis was performed with Redline's criteria, and inflammatory cytokines were analyzed in the cord blood. DNA from placental membranes was extracted from sterile swabs collected at delivery, and whole-genome shotgun sequencing was performed on the Illumina HiSeq platform. Filtered microbial DNA sequences were annotated and analyzed with MG-RAST (ie, Metagenomic Rapid Annotations using Subsystems Technology) and R.

RESULTS: Subjects were assigned to cohorts on the basis of gestational age at delivery and independent scoring of histologic chorioamnionitis. We found that preterm subjects with severe chorioamnionitis and funisitis had increases in cord blood inflammatory cytokines. Of interest, although the placental membrane microbiome was altered in association with severity of histologic chorioamnionitis (permutational multivariate analysis of variance P = .005), there was no observable impact with either betamethasone or antibiotic treatment. In preterm subjects with chorioamnionitis, we found a high abundance of both urogenital and oral commensal bacteria. These alterations in the microbiome were accompanied by significant variation (P < .05) in microbial metabolic pathways important in the glucose-fed pentose phosphate pathway (term subjects), or glycerophopholipid metabolism, and the biosynthesis of the siderophore group nonribosomal peptides (preterm subjects).

CONCLUSION: Consistent with ours and others previous findings, women who experienced spontaneous PTB harbor placental microbiota that further differed by severity of chorioamnionitis. Integrative metagenomic analysis revealed significant variation in distinct bacterial metabolic pathways, which we speculate may contribute to risk of preterm birth with and without severe chorioamnionitis.}, } @article {pmid26962943, year = {2016}, author = {Handley, SA and Desai, C and Zhao, G and Droit, L and Monaco, CL and Schroeder, AC and Nkolola, JP and Norman, ME and Miller, AD and Wang, D and Barouch, DH and Virgin, HW}, title = {SIV Infection-Mediated Changes in Gastrointestinal Bacterial Microbiome and Virome Are Associated with Immunodeficiency and Prevented by Vaccination.}, journal = {Cell host & microbe}, volume = {19}, number = {3}, pages = {323-335}, pmid = {26962943}, issn = {1934-6069}, support = {U19 AI078526/AI/NIAID NIH HHS/United States ; R01 DK101354/DK/NIDDK NIH HHS/United States ; AI096040/AI/NIAID NIH HHS/United States ; AI078526/AI/NIAID NIH HHS/United States ; R01 AI111918/AI/NIAID NIH HHS/United States ; AI111918/AI/NIAID NIH HHS/United States ; U19 AI096040/AI/NIAID NIH HHS/United States ; AI101354/AI/NIAID NIH HHS/United States ; OD011170/OD/NIH HHS/United States ; R01 OD011170/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification/genetics/*isolation & purification ; CD4-Positive T-Lymphocytes/immunology ; Gastrointestinal Diseases/etiology/microbiology/prevention & control/virology ; *Gastrointestinal Microbiome ; Genetic Variation ; Longitudinal Studies ; Macaca mulatta ; SAIDS Vaccines/administration & dosage/immunology ; Simian Acquired Immunodeficiency Syndrome/complications/immunology/*pathology ; Simian Immunodeficiency Virus/immunology/*pathogenicity ; Viruses/*classification/genetics/*isolation & purification ; }, abstract = {AIDS caused by simian immunodeficiency virus (SIV) infection is associated with gastrointestinal disease, systemic immune activation, and, in cross-sectional studies, changes in the enteric virome. Here we performed a longitudinal study of a vaccine cohort to define the natural history of changes in the fecal metagenome in SIV-infected monkeys. Matched rhesus macaques were either uninfected or intrarectally challenged with SIV, with a subset receiving the Ad26 vaccine, an adenovirus vector expressing the viral Env/Gag/Pol antigens. Progression of SIV infection to AIDS was associated with increased detection of potentially pathogenic viruses and bacterial enteropathogens. Specifically, adenoviruses were associated with an increased incidence of gastrointestinal disease and AIDS-related mortality. Viral and bacterial enteropathogens were largely absent from animals protected by the vaccine. These data suggest that the SIV-associated gastrointestinal disease is associated with the presence of both viral and bacterial enteropathogens and that protection against SIV infection by vaccination prevents enteropathogen emergence.}, } @article {pmid26962896, year = {2016}, author = {Saxena, S and Saxena, VK and Tomar, S and Sapcota, D and Gonmei, G}, title = {Characterisation of caecum and crop microbiota of Indian indigenous chicken targeting multiple hypervariable regions within 16S rRNA gene.}, journal = {British poultry science}, volume = {57}, number = {3}, pages = {381-389}, doi = {10.1080/00071668.2016.1161728}, pmid = {26962896}, issn = {1466-1799}, mesh = {Animals ; Cecum/*microbiology ; Chickens/growth & development/*microbiology ; Crop, Avian/*microbiology ; Gastrointestinal Microbiome/*genetics ; India ; *Metagenome ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA/veterinary ; }, abstract = {A comparative analysis of caecum and crop microbiota of chick, grower and adult stages of Indian indigenous chickens was conducted to investigate the role of the microbiota of the gastrointestinal tract, which play an important role in host performance, health and immunity. High-throughput Illumina sequencing was performed for V3, V4 and V4-V6 hypervariable regions of the 16S rRNA gene. M5RNA and M5NR databases under MG-RAST were used for metagenomic datasets annotation. In the crop, Firmicutes (~78%) and Proteobacteria (~16%) were the predominant phyla whereas in the caecum, Firmicutes (~50%), Bacteroidetes (~29%) and Actinobacteria (~10%) were predominant. The Shannon-Wiener diversity index suggested that sample richness and diversity increased as the chicken aged. For the first time, the presence of Lactobacillus species such as L. frumenti, L. antri, L. mucosae in the chicken crop along with Kineococcus radiotolerans, Desulfohalobium retbaense and L. jensenii in the caecum are reported. Many of these bacterial species have been found to be involved in immune response modulation and disease prevention in pigs and humans. The gut microbiome of the indigenous chicken was enriched with microbes having probiotic potential which might be essential for their adaptability.}, } @article {pmid26961712, year = {2016}, author = {Siles, JA and Margesin, R}, title = {Abundance and Diversity of Bacterial, Archaeal, and Fungal Communities Along an Altitudinal Gradient in Alpine Forest Soils: What Are the Driving Factors?.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {207-220}, pmid = {26961712}, issn = {1432-184X}, mesh = {*Altitude ; Archaea/classification/isolation & purification ; Bacteria/classification/isolation & purification ; *Biodiversity ; Chemical Phenomena ; DNA, Archaeal/genetics/isolation & purification ; DNA, Bacterial/genetics/isolation & purification ; DNA, Fungal/genetics/isolation & purification ; Fungi/classification/isolation & purification ; Italy ; RNA, Ribosomal, 16S/genetics/isolation & purification ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; Temperature ; }, abstract = {Shifts in soil microbial communities over altitudinal gradients and the driving factors are poorly studied. Their elucidation is indispensable to gain a comprehensive understanding of the response of ecosystems to global climate change. Here, we investigated soil archaeal, bacterial, and fungal communities at four Alpine forest sites representing a climosequence, over an altitudinal gradient from 545 to 2000 m above sea level (asl), regarding abundance and diversity by using qPCR and Illumina sequencing, respectively. Archaeal community was dominated by Thaumarchaeota, and no significant shifts were detected in abundance or community composition with altitude. The relative bacterial abundance increased at higher altitudes, which was related to increasing levels of soil organic matter and nutrients with altitude. Shifts in bacterial richness and diversity as well as community structure (comprised basically of Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes) significantly correlated with several environmental and soil chemical factors, especially soil pH. The site at the lowest altitude harbored the highest bacterial richness and diversity, although richness/diversity community properties did not show a monotonic decrease along the gradient. The relative size of fungal community also increased with altitude and its composition comprised Ascomycota, Basidiomycota, and Zygomycota. Changes in fungal richness/diversity and community structure were mainly governed by pH and C/N, respectively. The variation of the predominant bacterial and fungal classes over the altitudinal gradient was the result of the environmental and soil chemical factors prevailing at each site.}, } @article {pmid26958906, year = {2015}, author = {Chow, CE and Suttle, CA}, title = {Biogeography of Viruses in the Sea.}, journal = {Annual review of virology}, volume = {2}, number = {1}, pages = {41-66}, doi = {10.1146/annurev-virology-031413-085540}, pmid = {26958906}, issn = {2327-0578}, mesh = {Ecology ; Seawater/*virology ; Viruses/classification/genetics/*isolation & purification ; }, abstract = {Viral ecology is a rapidly progressing area of research, as molecular methods have improved significantly for targeted research on specific populations and whole communities. To interpret and synthesize global viral diversity and distribution, it is feasible to assess whether macroecology concepts can apply to marine viruses. We review how viral and host life history and physical properties can influence viral distribution in light of biogeography and metacommunity ecology paradigms. We highlight analytical approaches that can be applied to emerging global data sets and meta-analyses to identify individual taxa with global influence and drivers of emergent properties that influence microbial community structure by drawing on examples across the spectrum of viral taxa, from RNA to ssDNA and dsDNA viruses.}, } @article {pmid26954359, year = {2016}, author = {Campbell, SC and Wisniewski, PJ and Noji, M and McGuinness, LR and Häggblom, MM and Lightfoot, SA and Joseph, LB and Kerkhof, LJ}, title = {The Effect of Diet and Exercise on Intestinal Integrity and Microbial Diversity in Mice.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0150502}, pmid = {26954359}, issn = {1932-6203}, support = {U54 AR055073/AR/NIAMS NIH HHS/United States ; U54AR055073/AR/NIAMS NIH HHS/United States ; }, mesh = {*Animal Feed ; Animals ; Bacteria/classification/genetics ; *Biodiversity ; Biomarkers ; Body Weight ; Cadherins/metabolism ; Feces/microbiology ; Intestines/cytology/*microbiology/pathology/*physiology ; Male ; Metagenome ; Mice ; *Microbiota ; Occludin/metabolism ; Phylogeny ; *Physical Conditioning, Animal ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The gut microbiota is now known to play an important role contributing to inflammatory-based chronic diseases. This study examined intestinal integrity/inflammation and the gut microbial communities in sedentary and exercising mice presented with a normal or high-fat diet.

METHODS: Thirty-six, 6-week old C57BL/6NTac male mice were fed a normal or high-fat diet for 12-weeks and randomly assigned to exercise or sedentary groups. After 12 weeks animals were sacrificed and duodenum/ileum tissues were fixed for immunohistochemistry for occludin, E-cadherin, and cyclooxygenase-2 (COX-2). The bacterial communities were assayed in fecal samples using terminal restriction fragment length polymorphism (TRFLP) analysis and pyrosequencing of 16S rRNA gene amplicons.

RESULTS: Lean sedentary (LS) mice presented normal histologic villi while obese sedentary (OS) mice had similar villi height with more than twice the width of the LS animals. Both lean (LX) and obese exercise (OX) mice duodenum and ileum were histologically normal. COX-2 expression was the greatest in the OS group, followed by LS, LX and OX. The TRFLP and pyrosequencing indicated that members of the Clostridiales order were predominant in all diet groups. Specific phylotypes were observed with exercise, including Faecalibacterium prausnitzi, Clostridium spp., and Allobaculum spp.

CONCLUSION: These data suggest that exercise has a strong influence on gut integrity and host microbiome which points to the necessity for more mechanistic studies of the interactions between specific bacteria in the gut and its host.}, } @article {pmid26951067, year = {2016}, author = {Nishijima, S and Suda, W and Oshima, K and Kim, SW and Hirose, Y and Morita, H and Hattori, M}, title = {The gut microbiome of healthy Japanese and its microbial and functional uniqueness.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {23}, number = {2}, pages = {125-133}, pmid = {26951067}, issn = {1756-1663}, mesh = {Adult ; Asian People ; Female ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Geography, Medical ; Humans ; Male ; *Metagenome ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {The human gut microbiome has profound influences on the host's health largely through its interference with various intestinal functions. As recent studies have suggested diversity in the human gut microbiome among human populations, it will be interesting to analyse how gut microbiome is correlated with geographical, cultural, and traditional differences. The Japanese people are known to have several characteristic features such as eating a variety of traditional foods and exhibiting a low BMI and long life span. In this study, we analysed gut microbiomes of the Japanese by comparing the metagenomic data obtained from 106 Japanese individuals with those from 11 other nations. We found that the composition of the Japanese gut microbiome showed more abundant in the phylum Actinobacteria, in particular in the genus Bifidobacterium, than other nations. Regarding the microbial functions, those of carbohydrate metabolism were overrepresented with a concurrent decrease in those for replication and repair, and cell motility. The remarkable low prevalence of genes for methanogenesis with a significant depletion of the archaeon Methanobrevibacter smithii and enrichment of acetogenesis genes in the Japanese gut microbiome compared with others suggested a difference in the hydrogen metabolism pathway in the gut between them. It thus seems that the gut microbiome of the Japanese is considerably different from those of other populations, which cannot be simply explained by diet alone. We postulate possible existence of hitherto unknown factors contributing to the population-level diversity in human gut microbiomes.}, } @article {pmid26948887, year = {2016}, author = {Betrapally, NS and Gillevet, PM and Bajaj, JS}, title = {Changes in the Intestinal Microbiome and Alcoholic and Nonalcoholic Liver Diseases: Causes or Effects?.}, journal = {Gastroenterology}, volume = {150}, number = {8}, pages = {1745-1755.e3}, pmid = {26948887}, issn = {1528-0012}, support = {I01 CX001076/CX/CSRD VA/United States ; R01 DK087913/DK/NIDDK NIH HHS/United States ; }, mesh = {Fatty Liver, Alcoholic/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Intestines/microbiology ; Liver/microbiology ; Liver Cirrhosis/microbiology ; Non-alcoholic Fatty Liver Disease/*microbiology ; }, abstract = {The prevalence of fatty liver diseases is increasing rapidly worldwide; after treatment of hepatitis C virus infection becomes more widespread, fatty liver diseases are likely to become the most prevalent liver disorders. Although fatty liver diseases are associated with alcohol, obesity, and the metabolic syndrome, their mechanisms of pathogenesis are not clear. The development and progression of fatty liver, alcoholic, and nonalcoholic liver disease (NAFLD) all appear to be influenced by the composition of the microbiota. The intestinal microbiota have been shown to affect precirrhotic and cirrhotic stages of liver diseases, which could lead to new strategies for their diagnosis, treatment, and study. We review differences and similarities in the cirrhotic and precirrhotic stages of NAFLD and alcoholic liver disease. Differences have been observed in these stages of alcohol-associated disease in patients who continue to drink compared with those who stop, with respect to the composition and function of the intestinal microbiota and intestinal integrity. NAFLD and the intestinal microbiota also differ between patients with and without diabetes. We also discuss the potential of microbial therapy for patients with NAFLD and ALD.}, } @article {pmid26945826, year = {2016}, author = {Mondot, S and Lepage, P}, title = {The human gut microbiome and its dysfunctions through the meta-omics prism.}, journal = {Annals of the New York Academy of Sciences}, volume = {1372}, number = {1}, pages = {9-19}, doi = {10.1111/nyas.13033}, pmid = {26945826}, issn = {1749-6632}, mesh = {Disease ; Ecosystem ; *Gastrointestinal Microbiome ; Humans ; *Metabolomics ; *Metagenomics ; *Proteomics ; }, abstract = {The microorganisms inhabiting the human gut are abundant (10(14) cells) and diverse (approximately 500 species per individual). It is now acknowledged that the microbiota has coevolved with its host to achieve a symbiotic relationship, leading to physiological homeostasis. The gut microbiota ensures vital functions, such as food digestibility, maturation of the host immune system, and protection against pathogens. Over the last few decades, the gut microbiota has also been associated with numerous diseases, such as inflammatory bowel disease, irritable bowel syndrome, obesity, and metabolic diseases. In most of these pathologies, a microbial dysbiosis has been found, indicating shifts in the taxonomic composition of the gut microbiota and changes in its functionality. Our understanding of the influence of the gut microbiota on human health is still growing. Working with microorganisms residing in the gut is challenging since most of them are anaerobic and a vast majority (approximately 75%) are uncultivable to date. Recently, a wide range of new approaches (meta-omics) has been developed to bypass the uncultivability and reveal the intricate mechanisms that sustain gut microbial homeostasis. After a brief description of these approaches (metagenomics, metatranscriptomics, metaproteomics, and metabolomics), this review will discuss the importance of considering the gut microbiome as a structured ecosystem and the use of meta-omics to decipher dysfunctions of the gut microbiome in diseases.}, } @article {pmid26945643, year = {2016}, author = {Szalkai, B and Grolmusz, V}, title = {Nucleotide 9-mers characterize the type II diabetic gut metagenome.}, journal = {Genomics}, volume = {107}, number = {4}, pages = {120-123}, doi = {10.1016/j.ygeno.2016.02.007}, pmid = {26945643}, issn = {1089-8646}, mesh = {Biomarkers/chemistry ; Case-Control Studies ; Diabetes Mellitus, Type 2/*microbiology ; Female ; Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; *Metagenome ; Nucleotides/*chemistry/isolation & purification ; Obesity/microbiology ; Thinness/microbiology ; }, abstract = {Discoveries of new biomarkers for frequently occurring diseases are of special importance in today's medicine. While fully developed type II diabetes (T2D) can be detected easily, the early identification of high risk individuals is an area of interest in T2D, too. Metagenomic analysis of the human bacterial flora has shown subtle changes in diabetic patients, but no specific microbes are known to cause or promote the disease. Moderate changes were also detected in the microbial gene composition of the metagenomes of diabetic patients, but again, no specific gene was found that is present in disease-related and missing in healthy metagenome. However, these fine differences in microbial taxon- and gene composition are difficult to apply as quantitative biomarkers for diagnosing or predicting type II diabetes. In the present work we report some nucleotide 9-mers with significantly differing frequencies in diabetic and healthy intestinal flora. To our knowledge, it is the first time such short DNA fragments have been associated with T2D. The automated, quantitative analysis of the frequencies of short nucleotide sequences seems to be more feasible than accurate phylogenetic and functional analysis, and thus it might be a promising direction of diagnostic research.}, } @article {pmid26944845, year = {2016}, author = {Finkel, OM and Delmont, TO and Post, AF and Belkin, S}, title = {Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {9}, pages = {2854-2861}, pmid = {26944845}, issn = {1098-5336}, mesh = {Adaptation, Biological/*genetics ; Bacteria/*genetics/isolation & purification ; Biodiversity ; DNA, Bacterial/genetics ; *Desert Climate ; Ecosystem ; Hydrogen-Ion Concentration ; Israel ; Mediterranean Region ; Metagenomics ; Microbial Consortia/genetics ; Phylogeny ; Plant Leaves/metabolism/microbiology ; Salt Tolerance ; Sodium Chloride/*metabolism ; Stress, Physiological/physiology ; Tamaricaceae/microbiology ; Trees/*metabolism/*microbiology ; Ultraviolet Rays ; }, abstract = {UNLABELLED: The leaves of Tamarix aphylla, a globally distributed, salt-secreting desert tree, are dotted with alkaline droplets of high salinity. To successfully inhabit these organic carbon-rich droplets, bacteria need to be adapted to multiple stress factors, including high salinity, high alkalinity, high UV radiation, and periodic desiccation. To identify genes that are important for survival in this harsh habitat, microbial community DNA was extracted from the leaf surfaces of 10 Tamarix aphylla trees along a 350-km longitudinal gradient. Shotgun metagenomic sequencing, contig assembly, and binning yielded 17 genome bins, six of which were >80% complete. These genomic bins, representing three phyla (Proteobacteria,Bacteroidetes, and Firmicutes), were closely related to halophilic and alkaliphilic taxa isolated from aquatic and soil environments. Comparison of these genomic bins to the genomes of their closest relatives revealed functional traits characteristic of bacterial populations inhabiting the Tamarix phyllosphere, independent of their taxonomic affiliation. These functions, most notably light-sensing genes, are postulated to represent important adaptations toward colonization of this habitat.

IMPORTANCE: Plant leaves are an extensive and diverse microbial habitat, forming the main interface between solar energy and the terrestrial biosphere. There are hundreds of thousands of plant species in the world, exhibiting a wide range of morphologies, leaf surface chemistries, and ecological ranges. In order to understand the core adaptations of microorganisms to this habitat, it is important to diversify the type of leaves that are studied. This study provides an analysis of the genomic content of the most abundant bacterial inhabitants of the globally distributed, salt-secreting desert tree Tamarix aphylla Draft genomes of these bacteria were assembled, using the culture-independent technique of assembly and binning of metagenomic data. Analysis of the genomes reveals traits that are important for survival in this habitat, most notably, light-sensing and light utilization genes.}, } @article {pmid26944843, year = {2016}, author = {Graves, CJ and Makrides, EJ and Schmidt, VT and Giblin, AE and Cardon, ZG and Rand, DM}, title = {Functional Responses of Salt Marsh Microbial Communities to Long-Term Nutrient Enrichment.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {9}, pages = {2862-2871}, pmid = {26944843}, issn = {1098-5336}, mesh = {Base Sequence ; Denitrification/genetics ; Ecosystem ; Geologic Sediments/chemistry/*microbiology ; Massachusetts ; Metabolic Networks and Pathways/*genetics ; *Metagenomics ; Microbiota/*genetics ; Nitrates/metabolism ; Phylogeny ; Salinity ; Sequence Homology, Nucleic Acid ; Sewage/microbiology ; *Soil Microbiology ; Water/chemistry ; *Water Microbiology ; *Wetlands ; }, abstract = {UNLABELLED: Environmental nutrient enrichment from human agricultural and waste runoff could cause changes to microbial communities that allow them to capitalize on newly available resources. Currently, the response of microbial communities to nutrient enrichment remains poorly understood, and, while some studies have shown no clear changes in community composition in response to heavy nutrient loading, others targeting specific genes have demonstrated clear impacts. In this study, we compared functional metagenomic profiles from sediment samples taken along two salt marsh creeks, one of which was exposed for more than 40 years to treated sewage effluent at its head. We identified strong and consistent increases in the relative abundance of microbial genes related to each of the biochemical steps in the denitrification pathway at enriched sites. Despite fine-scale local increases in the abundance of denitrification-related genes, the overall community structures based on broadly defined functional groups and taxonomic annotations were similar and varied with other environmental factors, such as salinity, which were common to both creeks. Homology-based taxonomic assignments of nitrous oxide reductase sequences in our data show that increases are spread over a broad taxonomic range, thus limiting detection from taxonomic data alone. Together, these results illustrate a functionally targeted yet taxonomically broad response of microbial communities to anthropogenic nutrient loading, indicating some resolution to the apparently conflicting results of existing studies on the impacts of nutrient loading in sediment communities.

IMPORTANCE: In this study, we used environmental metagenomics to assess the response of microbial communities in estuarine sediments to long-term, nutrient-rich sewage effluent exposure. Unlike previous studies, which have mainly characterized communities based on taxonomic data or primer-based amplification of specific target genes, our whole-genome metagenomics approach allowed an unbiased assessment of the abundance of denitrification-related genes across the entire community. We identified strong and consistent increases in the relative abundance of gene sequences related to denitrification pathways across a broad phylogenetic range at sites exposed to long-term nutrient addition. While further work is needed to determine the consequences of these community responses in regulating environmental nutrient cycles, the increased abundance of bacteria harboring denitrification genes suggests that such processes may be locally upregulated. In addition, our results illustrate how whole-genome metagenomics combined with targeted hypothesis testing can reveal fine-scale responses of microbial communities to environmental disturbance.}, } @article {pmid26943627, year = {2016}, author = {Almeida, M and Pop, M and Le Chatelier, E and Prifti, E and Pons, N and Ghozlane, A and Ehrlich, SD}, title = {Capturing the most wanted taxa through cross-sample correlations.}, journal = {The ISME journal}, volume = {10}, number = {10}, pages = {2459-2467}, pmid = {26943627}, issn = {1751-7370}, support = {R01 AI100947/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics/*isolation & purification ; Humans ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The Human Microbiome Project (HMP) identified the 16S rRNA gene sequences of 'most wanted' taxa-prevalent in the healthy human microbiota but distant from previously known sequences. Since 2012, few of the corresponding genomes have been isolated and sequenced, and only through advanced isolation techniques. We demonstrate that the genomes of the most wanted taxa can be identified computationally through their correlation in abundance across multiple public metagenomic data sets. We link over 200 most wanted sequences with nearly complete genome sequences, including half of the taxa identified as high-priority targets by the HMP. The genomes we identify have strong similarity to genomes reconstructed through expensive isolation techniques, and provide a more complete functional characterization of these organisms than can be extrapolated from their 16S rRNA gene. We also provide insights into the function of organisms for which 16S rRNA gene signatures were recently reported to be associated with health and host genetic factors.}, } @article {pmid26941731, year = {2016}, author = {Vavourakis, CD and Ghai, R and Rodriguez-Valera, F and Sorokin, DY and Tringe, SG and Hugenholtz, P and Muyzer, G}, title = {Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {211}, pmid = {26941731}, issn = {1664-302X}, support = {322551/ERC_/European Research Council/International ; }, abstract = {Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration of sodium carbonates in the absence of major divalent cations. Hypersaline soda brines harbor microbial communities with a high species- and strain-level archaeal diversity and a large proportion of still uncultured poly-extremophiles compared to neutral brines of similar salinities. We present the first "metagenomic snapshots" of microbial communities thriving in the brines of four shallow soda lakes from the Kulunda Steppe (Altai, Russia) covering a salinity range from 170 to 400 g/L. Both amplicon sequencing of 16S rRNA fragments and direct metagenomic sequencing showed that the top-level taxa abundance was linked to the ambient salinity: Bacteroidetes, Alpha-, and Gamma-proteobacteria were dominant below a salinity of 250 g/L, Euryarchaeota at higher salinities. Within these taxa, amplicon sequences related to Halorubrum, Natrinema, Gracilimonas, purple non-sulfur bacteria (Rhizobiales, Rhodobacter, and Rhodobaca) and chemolithotrophic sulfur oxidizers (Thioalkalivibrio) were highly abundant. Twenty-four draft population genomes from novel members and ecotypes within the Nanohaloarchaea, Halobacteria, and Bacteroidetes were reconstructed to explore their metabolic features, environmental abundance and strategies for osmotic adaptation. The Halobacteria- and Bacteroidetes-related draft genomes belong to putative aerobic heterotrophs, likely with the capacity to ferment sugars in the absence of oxygen. Members from both taxonomic groups are likely involved in primary organic carbon degradation, since some of the reconstructed genomes encode the ability to hydrolyze recalcitrant substrates, such as cellulose and chitin. Putative sodium-pumping rhodopsins were found in both a Flavobacteriaceae- and a Chitinophagaceae-related draft genome. The predicted proteomes of both the latter and a Rhodothermaceae-related draft genome were indicative of a "salt-in" strategy of osmotic adaptation. The primary catabolic and respiratory pathways shared among all available reference genomes of Nanohaloarchaea and our novel genome reconstructions remain incomplete, but point to a primarily fermentative lifestyle. Encoded xenorhodopsins found in most drafts suggest that light plays an important role in the ecology of Nanohaloarchaea. Putative encoded halolysins and laccase-like oxidases might indicate the potential for extracellular degradation of proteins and peptides, and phenolic or aromatic compounds.}, } @article {pmid26940651, year = {2016}, author = {Manor, O and Levy, R and Pope, CE and Hayden, HS and Brittnacher, MJ and Carr, R and Radey, MC and Hager, KR and Heltshe, SL and Ramsey, BW and Miller, SI and Hoffman, LR and Borenstein, E}, title = {Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {22493}, pmid = {26940651}, issn = {2045-2322}, support = {P30 DK089507/DK/NIDDK NIH HHS/United States ; R01 DK095869/DK/NIDDK NIH HHS/United States ; }, mesh = {Actinobacteria/*genetics ; Biodiversity ; Child, Preschool ; Cystic Fibrosis/genetics/*microbiology ; DNA Barcoding, Taxonomic ; Dysbiosis/genetics/*microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; Infant ; Infant, Newborn ; Leukocyte L1 Antigen Complex/metabolism ; *Metagenome ; Proteobacteria/*genetics ; }, abstract = {Cystic fibrosis (CF) results in inflammation, malabsorption of fats and other nutrients, and obstruction in the gastrointestinal (GI) tract, yet the mechanisms linking these disease manifestations to microbiome composition remain largely unexplored. Here we used metagenomic analysis to systematically characterize fecal microbiomes of children with and without CF, demonstrating marked CF-associated taxonomic dysbiosis and functional imbalance. We further showed that these taxonomic and functional shifts were especially pronounced in young children with CF and diminished with age. Importantly, the resulting dysbiotic microbiomes had significantly altered capacities for lipid metabolism, including decreased capacity for overall fatty acid biosynthesis and increased capacity for degrading anti-inflammatory short-chain fatty acids. Notably, these functional differences correlated with fecal measures of fat malabsorption and inflammation. Combined, these results suggest that enteric fat abundance selects for pro-inflammatory GI microbiota in young children with CF, offering novel strategies for improving the health of children with CF-associated fat malabsorption.}, } @article {pmid26936188, year = {2016}, author = {Vinturache, AE and Gyamfi-Bannerman, C and Hwang, J and Mysorekar, IU and Jacobsson, B and , }, title = {Maternal microbiome - A pathway to preterm birth.}, journal = {Seminars in fetal & neonatal medicine}, volume = {21}, number = {2}, pages = {94-99}, doi = {10.1016/j.siny.2016.02.004}, pmid = {26936188}, issn = {1878-0946}, mesh = {Cervix Uteri/microbiology ; Dysbiosis/microbiology/*physiopathology ; Female ; Humans ; Intestinal Mucosa/microbiology ; *Microbiota ; Mouth Mucosa/microbiology ; Placenta/microbiology ; Pregnancy ; Premature Birth/*etiology/microbiology ; Vagina/microbiology ; }, abstract = {Despite great medical advances in preventing maternal and infant mortality in the past century, one issue remains unresolved: why do so many women give birth prematurely? A major new field of human microbiome studies has begun to shed light on the impact of microbes (of both the commensal and pathogen varieties) on pregnancy outcomes. Recent advances in next-generation sequencing and metagenomic analysis have revealed that maternal microbiomes at a variety of niches including the oral, vaginal, gut, cervical, and even the placenta itself govern pregnancy outcomes. In this review, we describe how alterations in the microbial biomasses impact preterm birth and we discuss the major research questions concerning the cause and/or interdependent relationships between microbiome, infection, and preterm delivery.}, } @article {pmid26932765, year = {2016}, author = {Rampelli, S and Soverini, M and Turroni, S and Quercia, S and Biagi, E and Brigidi, P and Candela, M}, title = {ViromeScan: a new tool for metagenomic viral community profiling.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {165}, pmid = {26932765}, issn = {1471-2164}, mesh = {Computational Biology ; DNA, Viral ; *Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; *Microbiota ; RNA, Viral/isolation & purification ; Sequence Analysis, DNA ; *Software ; Viruses/*classification/isolation & purification ; }, abstract = {BACKGROUND: Bioinformatics tools available for metagenomic sequencing analysis are principally devoted to the identification of microorganisms populating an ecological niche, but they usually do not consider viruses. Only some software have been designed to profile the viral sequences, however they are not efficient in the characterization of viruses in the context of complex communities, like the intestinal microbiota, containing bacteria, archeabacteria, eukaryotic microorganisms and viruses. In any case, a comprehensive description of the host-microbiota interactions can not ignore the profile of eukaryotic viruses within the virome, as viruses are definitely critical for the regulation of the host immunophenotype.

RESULTS: ViromeScan is an innovative metagenomic analysis tool that characterizes the taxonomy of the virome directly from raw data of next-generation sequencing. The tool uses hierarchical databases for eukaryotic viruses to unambiguously assign reads to viral species more accurately and >1000 fold faster than other existing approaches. We validated ViromeScan on synthetic microbial communities and applied it on metagenomic samples of the Human Microbiome Project, providing a sensitive eukaryotic virome profiling of different human body sites.

CONCLUSIONS: ViromeScan allows the user to explore and taxonomically characterize the virome from metagenomic reads, efficiently denoising samples from reads of other microorganisms. This implies that users can fully characterize the microbiome, including bacteria and viruses, by shotgun metagenomic sequencing followed by different bioinformatic pipelines.}, } @article {pmid26929931, year = {2016}, author = {Bobrova, O and Kristoffersen, JB and Oulas, A and Ivanytsia, V}, title = {Metagenomic 16s rRNA investigation of microbial communities in the Black Sea estuaries in South-West of Ukraine.}, journal = {Acta biochimica Polonica}, volume = {63}, number = {2}, pages = {315-319}, doi = {10.18388/abp.2015_1145}, pmid = {26929931}, issn = {1734-154X}, mesh = {Biodiversity ; Black Sea ; Metagenome ; Molecular Typing ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Seawater/microbiology ; Ukraine ; Water Microbiology ; }, abstract = {The Black Sea estuaries represent interfaces of the sea and river environments. Microorganisms that inhabit estuarine water play an integral role in all biochemical processes that occur there and form unique ecosystems. There are many estuaries located in the Southern-Western part of Ukraine and some of them are already separated from the sea. The aim of this research was to determine the composition of microbial communities in the Khadzhibey, Dniester and Sukhyi estuaries by metagenomic 16S rDNA analysis. This study is the first complex analysis of estuarine microbiota based on isolation of total DNA from a biome that was further subjected to sequencing. DNA was extracted from water samples and sequenced on the Illumina Miseq platform using primers to the V4 variable region of the 16S rRNA gene. Computer analysis of the obtained raw sequences was done with QIIME (Quantitative Insights Into Microbial Ecology) software. As the outcome, 57970 nucleotide sequences were retrieved. Bioinformatic analysis of bacterial community in the studied samples demonstrated a high taxonomic diversity of Prokaryotes at above genus level. It was shown that majority of 16S rDNA bacterial sequences detected in the estuarine samples belonged to phyla Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, Planctomycetes. The Khadhzibey estuary was dominated by the Proteobacteria phylum, while Dniester and Sukhyi estuaries were characterized by dominance of Cyanobacteria. The differences in bacterial populations between the Khadzhibey, Dniester and Sukhyi estuaries were demonstrated through the Beta-diversity analysis. It showed that the Khadzhibey estuary's microbial community significantly varies from the Sukhyi and Dniester estuaries. The majority of identified bacterial species is known as typical inhabitants of marine environments, however, for 2.5% of microbial population members in the studied estuaries no relatives were determined.}, } @article {pmid26929161, year = {2016}, author = {Langenheder, S and Comte, J and Zha, Y and Samad, MS and Sinclair, L and Eiler, A and Lindström, ES}, title = {Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin.}, journal = {Environmental microbiology reports}, volume = {8}, number = {4}, pages = {479-485}, doi = {10.1111/1758-2229.12392}, pmid = {26929161}, issn = {1758-2229}, mesh = {Bacteria/*classification/*genetics ; *Biota ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Some bacteria can be preserved over time in deep sediments where they persist either in dormant or slow-growing vegetative stages. Here, we hypothesized that such cells can be revived when exposed to environmental conditions similar to those before they were buried in the sediments. To test this hypothesis, we collected bacteria from sediment samples of different ages (140-8500 calibrated years before present, cal BP) from three lakes that differed in the timing of their physical isolation from the Baltic Sea following postglacial uplift. After these bacterial communities were grown in sterile water from the Baltic Sea, we determined the proportion of 16S rRNA sequence reads associated with marine habitats by extracting the environment descriptive terms of homologous sequences retrieved from public databases. We found that the proportion of reads associated with marine descriptive term was significantly higher in cultures inoculated with sediment layers formed under Baltic conditions and where salinities were expected to be similar to current levels. Moreover, a similar pattern was found in the original sediment layers. Our study, therefore, suggests that remnants of marine bacterial communities can be preserved in sediments over thousands of years and can be revived from deep sediments in lakes of marine origin.}, } @article {pmid26929102, year = {2016}, author = {Atanasova, NS and Bamford, DH and Oksanen, HM}, title = {Virus-host interplay in high salt environments.}, journal = {Environmental microbiology reports}, volume = {8}, number = {4}, pages = {431-444}, doi = {10.1111/1758-2229.12385}, pmid = {26929102}, issn = {1758-2229}, mesh = {Archaea/*virology ; Bacteria/*virology ; Biota ; Eukaryota/*virology ; *Host-Parasite Interactions ; Seawater/*microbiology/*virology ; Viruses/*isolation & purification ; }, abstract = {Interaction of viruses and cells has tremendous impact on cellular and viral evolution, nutrient cycling and decay of organic matter. Thus, viruses can indirectly affect complex processes such as climate change and microbial pathogenicity. During recent decades, studies on extreme environments have introduced us to archaeal viruses and viruses infecting extremophilic bacteria or eukaryotes. Hypersaline environments are known to contain strikingly high numbers of viruses (∼10(9) particles per ml). Halophilic archaea, bacteria and eukaryotes inhabiting hypersaline environments have only a few cellular predators, indicating that the role of viruses is highly important in these ecosystems. Viruses thriving in high salt are called haloviruses and to date more than 100 such viruses have been described. Virulent, temperate, and persistent halovirus life cycles have been observed among the known isolates including the recently described SNJ1-SNJ2 temperate virus pair which is the first example of an interplay between two haloviruses in one host cell. In addition to direct virus and cell isolations, metagenomics have provided a wealth of information about virus-host dynamics in hypersaline environments suggesting that halovirus populations and halophilic microorganisms are dynamic over time and spatially distributed around the highly saline environments on the Earth.}, } @article {pmid26928707, year = {2016}, author = {Ogino, S and Nishihara, R and VanderWeele, TJ and Wang, M and Nishi, A and Lochhead, P and Qian, ZR and Zhang, X and Wu, K and Nan, H and Yoshida, K and Milner, DA and Chan, AT and Field, AE and Camargo, CA and Williams, MA and Giovannucci, EL}, title = {Review Article: The Role of Molecular Pathological Epidemiology in the Study of Neoplastic and Non-neoplastic Diseases in the Era of Precision Medicine.}, journal = {Epidemiology (Cambridge, Mass.)}, volume = {27}, number = {4}, pages = {602-611}, pmid = {26928707}, issn = {1531-5487}, support = {R35 CA197735/CA/NCI NIH HHS/United States ; R01 CA151993/CA/NCI NIH HHS/United States ; UL1 TR001108/TR/NCATS NIH HHS/United States ; R01 CA137178/CA/NCI NIH HHS/United States ; K24 DK098311/DK/NIDDK NIH HHS/United States ; K07 CA190673/CA/NCI NIH HHS/United States ; }, mesh = {Cardiovascular Diseases/epidemiology/*genetics/metabolism ; Communicable Diseases/epidemiology/genetics/metabolism ; Diabetes Mellitus/epidemiology/*genetics/metabolism ; Drug-Related Side Effects and Adverse Reactions/epidemiology/genetics/metabolism ; Epigenomics ; Gene Expression Profiling ; Genomics ; Humans ; Metabolomics ; Microbiota ; *Molecular Epidemiology ; Neoplasms/epidemiology/*genetics/metabolism ; Obesity/epidemiology/*genetics/metabolism ; *Pathology, Molecular ; *Precision Medicine ; Proteomics ; }, abstract = {Molecular pathology diagnostics to subclassify diseases based on pathogenesis are increasingly common in clinical translational medicine. Molecular pathological epidemiology (MPE) is an integrative transdisciplinary science based on the unique disease principle and the disease continuum theory. While it has been most commonly applied to research on breast, lung, and colorectal cancers, MPE can investigate etiologic heterogeneity in non-neoplastic diseases, such as cardiovascular diseases, obesity, diabetes mellitus, drug toxicity, and immunity-related and infectious diseases. This science can enhance causal inference by linking putative etiologic factors to specific molecular biomarkers as outcomes. Technological advances increasingly enable analyses of various -omics, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, microbiome, immunomics, interactomics, etc. Challenges in MPE include sample size limitations (depending on availability of biospecimens or biomedical/radiological imaging), need for rigorous validation of molecular assays and study findings, and paucities of interdisciplinary experts, education programs, international forums, and standardized guidelines. To address these challenges, there are ongoing efforts such as multidisciplinary consortium pooling projects, the International Molecular Pathological Epidemiology Meeting Series, and the Strengthening the Reporting of Observational Studies in Epidemiology-MPE guideline project. Efforts should be made to build biorepository and biobank networks, and worldwide population-based MPE databases. These activities match with the purposes of the Big Data to Knowledge (BD2K), Genetic Associations and Mechanisms in Oncology (GAME-ON), and Precision Medicine Initiatives of the United States National Institute of Health. Given advances in biotechnology, bioinformatics, and computational/systems biology, there are wide open opportunities in MPE to contribute to public health.}, } @article {pmid26927795, year = {2016}, author = {Skvortsov, T and de Leeuwe, C and Quinn, JP and McGrath, JW and Allen, CC and McElarney, Y and Watson, C and Arkhipova, K and Lavigne, R and Kulakov, LA}, title = {Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0150361}, pmid = {26927795}, issn = {1932-6203}, mesh = {Bacteria/classification/genetics ; Biodiversity ; Eutrophication ; High-Throughput Nucleotide Sequencing ; Ireland ; Lakes/*microbiology/*virology ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; Viruses/classification/*genetics ; }, abstract = {Lough Neagh is the largest and the most economically important lake in Ireland. It is also one of the most nutrient rich amongst the world's major lakes. In this study, 16S rRNA analysis of total metagenomic DNA from the water column of Lough Neagh has revealed a high proportion of Cyanobacteria and low levels of Actinobacteria, Acidobacteria, Chloroflexi, and Firmicutes. The planktonic virome of Lough Neagh has been sequenced and 2,298,791 2×300 bp Illumina reads analysed. Comparison with previously characterised lakes demonstrates that the Lough Neagh viral community has the highest level of sequence diversity. Only about 15% of reads had homologs in the RefSeq database and tailed bacteriophages (Caudovirales) were identified as a major grouping. Within the Caudovirales, the Podoviridae and Siphoviridae were the two most dominant families (34.3% and 32.8% of the reads with sequence homology to the RefSeq database), while ssDNA bacteriophages constituted less than 1% of the virome. Putative cyanophages were found to be abundant. 66,450 viral contigs were assembled with the largest one being 58,805 bp; its existence, and that of another 34,467 bp contig, in the water column was confirmed. Analysis of the contigs confirmed the high abundance of cyanophages in the water column.}, } @article {pmid26922889, year = {2016}, author = {Eun, CS and Kwak, MJ and Han, DS and Lee, AR and Park, DI and Yang, SK and Kim, YS and Kim, JF}, title = {Does the intestinal microbial community of Korean Crohn's disease patients differ from that of western patients?.}, journal = {BMC gastroenterology}, volume = {16}, number = {}, pages = {28}, pmid = {26922889}, issn = {1471-230X}, mesh = {Acidobacteria/genetics ; Actinobacteria/genetics ; Adult ; Anti-Inflammatory Agents, Non-Steroidal/therapeutic use ; Asian People ; Azathioprine/therapeutic use ; Bacteroidetes/genetics ; Case-Control Studies ; Crohn Disease/drug therapy/ethnology/*microbiology ; DNA, Ribosomal/*genetics ; Dysbiosis/ethnology/*microbiology ; Feces/microbiology ; Female ; Firmicutes/genetics ; Fusobacteria/genetics ; Gammaproteobacteria/genetics ; Gastrointestinal Agents/therapeutic use ; Gastrointestinal Microbiome/*genetics ; Humans ; Immunosuppressive Agents/therapeutic use ; Infliximab/therapeutic use ; Intestinal Mucosa/microbiology ; Male ; Mesalamine/therapeutic use ; Prednisolone/therapeutic use ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/*genetics ; Republic of Korea ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; Tumor Necrosis Factor-alpha/antagonists & inhibitors ; }, abstract = {BACKGROUND: Intestinal microbiota play an important role in maintaining the homeostasis of the host immune system. To analyze the alteration of the intestinal microbial community structure in Korean Crohn's disease (CD) patients, we performed a comparative metagenomic analysis between healthy people and CD patients using fecal samples and mucosal tissues of ileocecal valve.

METHODS: 16S rRNA genes from fecal samples or mucosal tissues of 35 CD patients and 15 healthy controls (HC) were amplified using a universal primer set and sequenced with GS FLX Titanium. The microbial composition and diversity of each sample were analyzed with the mothur pipeline, and the association between microbial community and clinical characteristics of the patients were investigated.

RESULTS: The contribution of bacterial groups to the intestinal microbial composition differed between CD and HC, especially in fecal samples. Global structure and individual bacterial abundance of intestinal microbial community were different between feces and ileocecal tissues in HC. In CD patients with active stage, relative abundances of Gammaproteobacteria and Fusobacteria were higher in both fecal and mucosal tissue samples. Moreover, the intestinal microbial community structure was altered by anti-tumor necrosis factor (anti-TNF) treatment.

CONCLUSIONS: Our 16S rRNA sequence data demonstrate intestinal dysbiosis at the community level in Korean CD patients, which is similar to alterations of the intestinal microbial community seen in the western counterparts. Clinical disease activity and anti-TNF treatment might affect the intestinal microbial community structure in CD patients.}, } @article {pmid26919743, year = {2016}, author = {Louis, S and Tappu, RM and Damms-Machado, A and Huson, DH and Bischoff, SC}, title = {Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0149564}, pmid = {26919743}, issn = {1932-6203}, mesh = {Adult ; Bacteroidetes/isolation & purification ; Female ; Firmicutes/isolation & purification ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; Insulin Resistance ; Male ; Metagenome/*genetics ; Middle Aged ; Obesity/*microbiology/therapy ; Weight Loss/*physiology ; }, abstract = {BACKGROUND/OBJECTIVES: Cross-sectional studies suggested that obesity is promoted by the gut microbiota. However, longitudinal data on taxonomic and functional changes in the gut microbiota of obese patients are scarce. The aim of this work is to study microbiota changes in the course of weight loss therapy and the following year in obese individuals with or without co-morbidities, and to asses a possible predictive value of the gut microbiota with regard to weight loss maintenance.

SUBJECTS/METHODS: Sixteen adult patients, who followed a 52-week weight-loss program comprising low calorie diet, exercise and behavioral therapy, were selected according to their weight-loss course. Over two years, anthropometric and metabolic parameters were assessed and microbiota from stool samples was functionally and taxonomically analyzed using DNA shotgun sequencing.

RESULTS: Overall the microbiota responded to the dietetic and lifestyle intervention but tended to return to the initial situation both at the taxonomical and functional level at the end of the intervention after one year, except for an increase in Akkermansia abundance which remained stable over two years (12.7x103 counts, 95%CI: 322-25100 at month 0; 141x103 counts, 95%CI: 49-233x103 at month 24; p = 0.005). The Firmicutes/Bacteroidetes ratio was higher in obese subjects with metabolic syndrome (0.64, 95%CI: 0.34-0.95) than in the "healthy obese" (0.27, 95%CI: 0.08-0.45, p = 0.04). Participants, who succeeded in losing their weight consistently over the two years, had at baseline a microbiota enriched in Alistipes, Pseudoflavonifractor and enzymes of the oxidative phosphorylation pathway compared to patients who were less successful in weight reduction.

CONCLUSIONS: Successful weight reduction in the obese is accompanied with increased Akkermansia numbers in feces. Metabolic co-morbidities are associated with a higher Firmicutes/Bacteroidetes ratio. Most interestingly, microbiota differences might allow discrimination between successful and unsuccessful weight loss prior to intervention.}, } @article {pmid26918330, year = {2016}, author = {Zeber-Lubecka, N and Kulecka, M and Ambrozkiewicz, F and Paziewska, A and Lechowicz, M and Konopka, E and Majewska, U and Borszewska-Kornacka, M and Mikula, M and Cukrowska, B and Ostrowski, J}, title = {Effect of Saccharomyces boulardii and Mode of Delivery on the Early Development of the Gut Microbial Community in Preterm Infants.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0150306}, pmid = {26918330}, issn = {1932-6203}, mesh = {Administration, Oral ; Bacteria/isolation & purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; *Delivery, Obstetric ; Double-Blind Method ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Infant, Premature ; Male ; Metagenome ; *Probiotics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Reagent Kits, Diagnostic ; Ribotyping ; *Saccharomyces ; Symbiosis ; }, abstract = {BACKGROUND: Recent advances in culture-independent approaches have enabled insights into the diversity, complexity, and individual variability of gut microbial communities.

OBJECTIVES: To examine the effect of oral administration of Saccharomyces (S.) boulardii and mode of delivery on the intestinal microbial community in preterm infants.

STUDY DESIGN: Stool samples were collected from preterm newborns randomly divided into two groups: a probiotic-receiving group (n = 18) or a placebo group (n = 21). Samples were collected before probiotic intake (day 0), and after 2 and 6 weeks of supplementation. The composition of colonizing bacteria was assessed by 16S ribosomal RNA (rRNA) gene sequencing of fecal samples using the Ion 16S Metagenomics Kit and the Ion Torrent Personal Genome Machine platform.

RESULTS: A total of 11932257 reads were generated, and were clustered into 459, 187, and 176 operational taxonomic units at 0 days, 2 weeks, and 6 weeks, respectively. Of the 17 identified phyla, Firmicutes Actinobacteria, Proteobacteria, and Bacteroidetes were universal. The microbial community differed at day 0 compared with at 2 weeks and 6 weeks. There was a tendency for increased bacterial diversity at 2 weeks and 6 weeks compared with day 0, and infants with a gestational age of 31 weeks or higher presented increased bacterial diversity prior to S. boulardii administration. Firmicutes and Proteobacteria remained stable during the observation period, whereas Actinobacteria and Bacteroidetes increased in abundance, the latter particularly more sharply in vaginally delivered infants.

CONCLUSION: While the mode of delivery may influence the development of a microbial community, this study had not enough power to detect statistical differences between cohorts supplemented with probiotics, and in a consequence, to speculate on S. boulardii effect on gut microbiome composition in preterm newborns.}, } @article {pmid26917241, year = {2016}, author = {Itävaara, M and Salavirta, H and Marjamaa, K and Ruskeeniemi, T}, title = {Geomicrobiology and Metagenomics of Terrestrial Deep Subsurface Microbiomes.}, journal = {Advances in applied microbiology}, volume = {94}, number = {}, pages = {1-77}, doi = {10.1016/bs.aambs.2015.12.001}, pmid = {26917241}, issn = {0065-2164}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Biodiversity ; Eukaryota/*classification ; Finland ; Geology ; *Metagenomics ; Microbiota/*genetics ; Soil Microbiology ; Viruses/*classification/genetics ; Water Microbiology ; }, abstract = {Fractures in the deep subsurface of Earth's crust are inhabited by diverse microbial communities that participate in biogeochemical cycles of the Earth. Life on Earth, which arose c. 3.5-4.0 billion years ago, reaches down at least 5 km in the crust. Deep mines, caves, and boreholes have provided scientists with opportunities to sample deep subsurface microbiomes and to obtain information on the species diversity and functions. A wide variety of bacteria, archaea, eukaryotes, and viruses are now known to reside in the crust, but their functions are still largely unknown. The crust at different depths has varying geological composition and hosts endemic microbiomes accordingly. The diversity is driven by geological formations and gases evolving from deeper depths. Cooperation among different species is still mostly unexplored, but viruses are known to restrict density of bacterial and archaeal populations. Due to the complex growth requirements of the deep subsurface microbiomes, the new knowledge about their diversity and functions is mostly obtained by molecular methods, eg, meta'omics'. Geomicrobiology is a multidisciplinary research area combining disciplines from geology, mineralogy, geochemistry, and microbiology. Geomicrobiology is concerned with the interaction of microorganisms and geological processes. At the surface of mineralogical or rock surfaces, geomicrobial processes occur mainly under aerobic conditions. In the deep subsurface, however, the environmental conditions are reducing and anaerobic. The present chapter describes the world of microbiomes in deep terrestrial geological environments as well as metagenomic and metatranscriptomic methods suitable for studies of these enigmatic communities.}, } @article {pmid26916597, year = {2016}, author = {Wang, AH and Li, M and Li, CQ and Kou, GJ and Zuo, XL and Li, YQ}, title = {Human colorectal mucosal microbiota correlates with its host niche physiology revealed by endomicroscopy.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {21952}, pmid = {26916597}, issn = {2045-2322}, mesh = {Adult ; Aged ; Bacteria/genetics/*isolation & purification ; Biopsy ; Colon/microbiology/physiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/*microbiology/physiology ; Male ; Microscopy, Confocal ; Middle Aged ; RNA, Ribosomal, 16S ; Rectum/microbiology/physiology ; Sequence Analysis, RNA ; }, abstract = {The human gut microbiota plays a pivotal role in the maintenance of health, but how the microbiota interacts with the host at the colorectal mucosa is poorly understood. We proposed that confocal laser endomicroscopy (CLE) might help to untangle this relationship by providing in vivo physiological information of the mucosa. We used CLE to evaluate the in vivo physiology of human colorectal mucosa, and the mucosal microbiota was quantified using 16 s rDNA pyrosequencing. The human mucosal microbiota agglomerated to three major clusters dominated by Prevotella, Bacteroides and Lactococcus. The mucosal microbiota clusters did not significantly correlate with the disease status or biopsy sites but closely correlated with the mucosal niche physiology, which was non-invasively revealed by CLE. Inflammation tilted two subnetworks within the mucosal microbiota. Infiltration of inflammatory cells significantly correlated with multiple components in the predicted metagenome, such as the VirD2 component of the type IV secretory pathway. Our data suggest that a close correlation exists between the mucosal microbiota and the colorectal mucosal physiology, and CLE is a clinically available tool that can be used to facilitate the study of the in vivo correlation between colorectal mucosal physiology and the mucosal microbiota.}, } @article {pmid26915214, year = {2015}, author = {Zhang, JY and Zhu, BC and Xu, C and Ding, X and Li, JF and Zhang, XG and Lu, ZH}, title = {[Strategy of selecting 16S rRNA hypervariable regions for metagenome-phylogenetic marker genes based analysis].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {26}, number = {11}, pages = {3545-3553}, pmid = {26915214}, issn = {1001-9332}, mesh = {Biodiversity ; *Genetic Markers ; *Genome, Microbial ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The advent of next generation sequencing technology enables parallel analysis of the whole microbial community from multiple samples. Particularly, sequencing 16S rRNA hypervariable tags has become the most efficient and cost-effective method for assessing microbial diversity. Due to its short read length of the 2nd-generation sequencing methods that cannot cover the full 16S rRNA genomic region, specific hypervariable regions or V-regions must be selected to act as the proxy. Over the past decade, selection of V-regions has not been consistent in assessing microbial diversity. Here we evaluated the current strategies of selecting 16S rRNA hypervariable regions for surveying microbial diversity. The environmental condition was considered as one of the important factors for selection of 16S rRNA hypervariable regions. We suggested that a pilot study to test different V-regions is required in bacterial diversity studies based on 16S rRNA genes.}, } @article {pmid26914534, year = {2016}, author = {Crits-Christoph, A and Gelsinger, DR and Ma, B and Wierzchos, J and Ravel, J and Davila, A and Casero, MC and DiRuggiero, J}, title = {Functional interactions of archaea, bacteria and viruses in a hypersaline endolithic community.}, journal = {Environmental microbiology}, volume = {18}, number = {6}, pages = {2064-2077}, doi = {10.1111/1462-2920.13259}, pmid = {26914534}, issn = {1462-2920}, mesh = {Archaea/genetics ; Archaeal Proteins/chemistry ; Bacteria/genetics/*isolation & purification ; Cyanobacteria/genetics/isolation & purification/virology ; *Desert Climate ; Ecosystem ; Euryarchaeota/genetics/*isolation & purification/virology ; Genome, Viral ; Isoelectric Point ; Metagenome ; Microbial Consortia ; Microbial Interactions ; Phylogeny ; *Salinity ; Viruses/genetics/*isolation & purification ; }, abstract = {Halite endoliths in the Atacama Desert represent one of the most extreme ecosystems on Earth. Cultivation-independent methods were used to examine the functional adaptations of the microbial consortia inhabiting halite nodules. The community was dominated by haloarchaea and functional analysis attributed most of the autotrophic CO2 fixation to one unique cyanobacterium. The assembled 1.1 Mbp genome of a novel nanohaloarchaeon, Candidatus Nanopetramus SG9, revealed a photoheterotrophic life style and a low median isoelectric point (pI) for all predicted proteins, suggesting a 'salt-in' strategy for osmotic balance. Predicted proteins of the algae identified in the community also had pI distributions similar to 'salt-in' strategists. The Nanopetramus genome contained a unique CRISPR/Cas system with a spacer that matched a partial viral genome from the metagenome. A combination of reference-independent methods identified over 30 complete or near complete viral or proviral genomes with diverse genome structure, genome size, gene content and hosts. Putative hosts included Halobacteriaceae, Nanohaloarchaea and Cyanobacteria. Despite the dependence of the halite community on deliquescence for liquid water availability, this study exposed an ecosystem spanning three phylogenetic domains, containing a large diversity of viruses and predominance of a 'salt-in' strategy to balance the high osmotic pressure of the environment.}, } @article {pmid26905381, year = {2016}, author = {Yamazaki, Y and Meirelles, PM and Mino, S and Suda, W and Oshima, K and Hattori, M and Thompson, FL and Sakai, Y and Sawabe, T and Sawabe, T}, title = {Individual Apostichopus japonicus fecal microbiome reveals a link with polyhydroxybutyrate producers in host growth gaps.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {21631}, pmid = {26905381}, issn = {2045-2322}, mesh = {Animals ; Body Size ; Feces/*microbiology ; Gastrointestinal Tract/microbiology ; Genes, Bacterial ; Hydroxybutyrates/*metabolism ; Metagenome ; Microbiota/*genetics ; Stichopus/*growth & development/*microbiology ; }, abstract = {Gut microbiome shapes various aspects of a host's physiology, but these functions in aquatic animal hosts have yet to be fully investigated. The sea cucumber Apostichopus japonicus Selenka is one such example. The large growth gap in their body size has delayed the development of intensive aquaculture, nevertheless the species is in urgent need of conservation. To understand possible contributions of the gut microbiome to its host's growth, individual fecal microbiome comparisons were performed. High-throughput 16S rRNA sequencing revealed significantly different microbiota in larger and smaller individuals; Rhodobacterales in particular was the most significantly abundant bacterial group in the larger specimens. Further shotgun metagenome of representative samples revealed a significant abundance of microbiome retaining polyhydroxybutyrate (PHB) metabolism genes in the largest individual. The PHB metabolism reads were potentially derived from Rhodobacterales. These results imply a possible link between microbial PHB producers and potential growth promotion in Deuterostomia marine invertebrates.}, } @article {pmid26903960, year = {2016}, author = {Nesme, J and Achouak, W and Agathos, SN and Bailey, M and Baldrian, P and Brunel, D and Frostegård, Å and Heulin, T and Jansson, JK and Jurkevitch, E and Kruus, KL and Kowalchuk, GA and Lagares, A and Lappin-Scott, HM and Lemanceau, P and Le Paslier, D and Mandic-Mulec, I and Murrell, JC and Myrold, DD and Nalin, R and Nannipieri, P and Neufeld, JD and O'Gara, F and Parnell, JJ and Pühler, A and Pylro, V and Ramos, JL and Roesch, LF and Schloter, M and Schleper, C and Sczyrba, A and Sessitsch, A and Sjöling, S and Sørensen, J and Sørensen, SJ and Tebbe, CC and Topp, E and Tsiamis, G and van Elsas, JD and van Keulen, G and Widmer, F and Wagner, M and Zhang, T and Zhang, X and Zhao, L and Zhu, YG and Vogel, TM and Simonet, P}, title = {Back to the Future of Soil Metagenomics.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {73}, pmid = {26903960}, issn = {1664-302X}, } @article {pmid26896166, year = {2016}, author = {De Nardi, R and Marchesini, G and Li, S and Khafipour, E and Plaizier, KJ and Gianesella, M and Ricci, R and Andrighetto, I and Segato, S}, title = {Metagenomic analysis of rumen microbial population in dairy heifers fed a high grain diet supplemented with dicarboxylic acids or polyphenols.}, journal = {BMC veterinary research}, volume = {12}, number = {}, pages = {29}, pmid = {26896166}, issn = {1746-6148}, mesh = {*Animal Feed ; Animals ; Biodiversity ; Cattle ; Dicarboxylic Acids/*pharmacology ; *Dietary Supplements ; Edible Grain ; *Metagenomics ; Microbiota/*drug effects ; Polyphenols/*pharmacology ; Rumen/drug effects/*microbiology ; }, abstract = {BACKGROUND: The aim of this study was to investigate the effects of two feed supplements on rumen bacterial communities of heifers fed a high grain diet. Six Holstein-Friesian heifers received one of the following dietary treatments according to a Latin square design: no supplement (control, C), 60 g/day of fumarate-malate (organic acid, O) and 100 g/day of polyphenol-essential oil (P). Rumen fluid was analyzed to assess the microbial population using Illumina sequencing and quantitative real time PCR.

RESULTS: The P treatment had the highest number of observed species (P < 0.10), Chao1 index (P < 0.05), abundance based coverage estimated (ACE) (P < 0.05), and Fisher's alpha diversity (P < 0.10). The O treatment had intermediate values between C and P treatments with the exception of the Chao1 index. The PCoA with unweighted Unifrac distance showed a separation among dietary treatments (P = 0.09), above all between the C and P (P = 0.05). The O and P treatments showed a significant increase of the family Christenenellaceae and a decline of Prevotella brevis compared to C. Additionally, the P treatment enhanced the abundance of many taxa belonging to Bacteroidetes, Firmicutes and Tenericutes phyla due to a potential antimicrobial activity of flavonoids that increased competition among bacteria.

CONCLUSIONS: Organic acid and polyphenols significantly modified rumen bacterial populations during high-grain feeding in dairy heifers. In particular the polyphenol treatment increased the richness and diversity of rumen microbiota, which are usually high in conditions of physiological rumen pH and rumen function.}, } @article {pmid26896130, year = {2016}, author = {Terrón-González, L and Martín-Cabello, G and Ferrer, M and Santero, E}, title = {Functional Metagenomics of a Biostimulated Petroleum-Contaminated Soil Reveals an Extraordinary Diversity of Extradiol Dioxygenases.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {8}, pages = {2467-2478}, pmid = {26896130}, issn = {1098-5336}, mesh = {Biphenyl Compounds/metabolism ; Catechols/metabolism ; Cloning, Molecular ; Gene Expression ; Genetic Testing ; *Genetic Variation ; Metagenomics ; Oxygenases/*genetics/*metabolism ; Petroleum/*analysis ; Phylogeny ; Sequence Analysis, DNA ; *Soil Microbiology ; Soil Pollutants/*analysis ; }, abstract = {A metagenomic library of a petroleum-contaminated soil was constructed in a fosmid vector that allowed heterologous expression of metagenomic DNA. The library, consisting of 6.5 Gb of metagenomic DNA, was screened for extradiol dioxygenase (Edo) activity using catechol and 2,3-dihydroxybiphenyl as the substrates. Fifty-eight independent clones encoding extradiol dioxygenase activity were identified. Forty-one different Edo-encoding genes were identified. The population of Edo genes was not dominated by a particular gene or by highly similar genes; rather, the genes had an even distribution and high diversity. Phylogenetic analyses revealed that most of the genes could not be ascribed to previously defined subfamilies of Edos. Rather, the Edo genes led to the definition of 10 new subfamilies of type I Edos. Phylogenetic analysis of type II enzymes defined 7 families, 2 of which harbored the type II Edos that were found in this work. Particularly striking was the diversity found in family I.3 Edos; 15 out of the 17 sequences assigned to this family belonged to 7 newly defined subfamilies. A strong bias was found that depended on the substrate used for the screening: catechol mainly led to the detection of Edos belonging to the I.2 family, while 2,3-dihydroxybiphenyl led to the detection of most other Edos. Members of the I.2 family showed a clear substrate preference for monocyclic substrates, while those from the I.3 family showed a broader substrate range and high activity toward 2,3-dihydroxybiphenyl. This metagenomic analysis has substantially increased our knowledge of the existing biodiversity of Edos.}, } @article {pmid26891056, year = {2016}, author = {Roehe, R and Dewhurst, RJ and Duthie, CA and Rooke, JA and McKain, N and Ross, DW and Hyslop, JJ and Waterhouse, A and Freeman, TC and Watson, M and Wallace, RJ}, title = {Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance.}, journal = {PLoS genetics}, volume = {12}, number = {2}, pages = {e1005846}, pmid = {26891056}, issn = {1553-7404}, support = {BBS/E/D/20211550/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/D/20211553/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004243/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/D/20211551/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; G0900740/MRC_/Medical Research Council/United Kingdom ; BBS/E/D/05191132/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/I001107/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/K001744/1/MRC_/Medical Research Council/United Kingdom ; BBS/E/D/20211552/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animal Feed ; Animal Nutritional Physiological Phenomena ; Animals ; Archaea/genetics/metabolism ; Cattle ; Female ; *Genetic Variation ; Male ; Metagenomics/methods ; Methane/*metabolism ; Microbiota/genetics/*physiology ; Rumen/*microbiology ; }, abstract = {Methane produced by methanogenic archaea in ruminants contributes significantly to anthropogenic greenhouse gas emissions. The host genetic link controlling microbial methane production is unknown and appropriate genetic selection strategies are not developed. We used sire progeny group differences to estimate the host genetic influence on rumen microbial methane production in a factorial experiment consisting of crossbred breed types and diets. Rumen metagenomic profiling was undertaken to investigate links between microbial genes and methane emissions or feed conversion efficiency. Sire progeny groups differed significantly in their methane emissions measured in respiration chambers. Ranking of the sire progeny groups based on methane emissions or relative archaeal abundance was consistent overall and within diet, suggesting that archaeal abundance in ruminal digesta is under host genetic control and can be used to genetically select animals without measuring methane directly. In the metagenomic analysis of rumen contents, we identified 3970 microbial genes of which 20 and 49 genes were significantly associated with methane emissions and feed conversion efficiency respectively. These explained 81% and 86% of the respective variation and were clustered in distinct functional gene networks. Methanogenesis genes (e.g. mcrA and fmdB) were associated with methane emissions, whilst host-microbiome cross talk genes (e.g. TSTA3 and FucI) were associated with feed conversion efficiency. These results strengthen the idea that the host animal controls its own microbiota to a significant extent and open up the implementation of effective breeding strategies using rumen microbial gene abundance as a predictor for difficult-to-measure traits on a large number of hosts. Generally, the results provide a proof of principle to use the relative abundance of microbial genes in the gastrointestinal tract of different species to predict their influence on traits e.g. human metabolism, health and behaviour, as well as to understand the genetic link between host and microbiome.}, } @article {pmid26891226, year = {2016}, author = {Maffeis, C and Martina, A and Corradi, M and Quarella, S and Nori, N and Torriani, S and Plebani, M and Contreas, G and Felis, GE}, title = {Association between intestinal permeability and faecal microbiota composition in Italian children with beta cell autoimmunity at risk for type 1 diabetes.}, journal = {Diabetes/metabolism research and reviews}, volume = {32}, number = {7}, pages = {700-709}, doi = {10.1002/dmrr.2790}, pmid = {26891226}, issn = {1520-7560}, mesh = {Adolescent ; Autoimmunity/*immunology ; Bacteria/genetics/*growth & development ; Biomarkers/analysis ; Case-Control Studies ; Cell Membrane Permeability ; Child ; Diabetes Mellitus, Type 1/*immunology ; Feces/*microbiology ; Female ; Follow-Up Studies ; Humans ; Intestines/*microbiology ; Male ; Metagenome ; Microbiota/*immunology ; Prognosis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Pancreatic organ-specific autoimmunity in subjects at risk for type 1 diabetes (T1D) is associated with increased intestinal permeability and an aberrant gut microbiota, but these factors have not yet been simultaneously investigated in the same subjects. Thus, the aim of this study was to assess both intestinal permeability and gut microbiota composition in an Italian sample of children at risk for T1D.

METHODS: Ten Italian children with beta cell autoimmunity at risk for T1D and 10 healthy children were involved in a case-control study. The lactulose/mannitol test was used to assess intestinal permeability. Analysis of microbiota composition was performed using polymerase chain reaction followed by denaturing gradient gel electrophoresis, based on the 16S rRNA gene.

RESULTS: Intestinal permeability was significantly higher in children at risk for T1D than in healthy controls. Moreover, the gut microbiota of the former differed from that of the latter group: Three microorganisms were detected - Dialister invisus, Gemella sanguinis and Bifidobacterium longum - in association with the pre-pathologic state.

CONCLUSIONS: The results of this study validated the hypothesis that increased intestinal permeability together with differences in microbiota composition are contemporaneously associated with the pre-pathological condition of T1D in a sample of Italian children. Further studies are necessary to confirm the microbial markers identified in this sample of children as well as to clarify the involvement of microbiota modifications in the mechanisms leading to increased permeability and the autoimmune mechanisms that promote diabetes onset. Copyright © 2016 John Wiley & Sons, Ltd.}, } @article {pmid26884067, year = {2016}, author = {Yassour, M and Lim, MY and Yun, HS and Tickle, TL and Sung, J and Song, YM and Lee, K and Franzosa, EA and Morgan, XC and Gevers, D and Lander, ES and Xavier, RJ and Birren, BW and Ko, G and Huttenhower, C}, title = {Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes.}, journal = {Genome medicine}, volume = {8}, number = {1}, pages = {17}, pmid = {26884067}, issn = {1756-994X}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 HG005969/HG/NHGRI NIH HHS/United States ; }, mesh = {Adult ; Diabetes Mellitus, Type 2/*microbiology ; Dysbiosis/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Male ; Middle Aged ; Obesity/*microbiology ; Phylogeny ; Risk Factors ; Twins, Monozygotic ; Verrucomicrobia/*classification/genetics/*isolation & purification ; }, abstract = {BACKGROUND: Obesity and type 2 diabetes (T2D) are linked both with host genetics and with environmental factors, including dysbioses of the gut microbiota. However, it is unclear whether these microbial changes precede disease onset. Twin cohorts present a unique genetically-controlled opportunity to study the relationships between lifestyle factors and the microbiome. In particular, we hypothesized that family-independent changes in microbial composition and metabolic function during the sub-clinical state of T2D could be either causal or early biomarkers of progression.

METHODS: We collected fecal samples and clinical metadata from 20 monozygotic Korean twins at up to two time points, resulting in 36 stool shotgun metagenomes. While the participants were neither obese nor diabetic, they spanned the entire range of healthy to near-clinical values and thus enabled the study of microbial associations during sub-clinical disease while accounting for genetic background.

RESULTS: We found changes both in composition and in function of the sub-clinical gut microbiome, including a decrease in Akkermansia muciniphila suggesting a role prior to the onset of disease, and functional changes reflecting a response to oxidative stress comparable to that previously observed in chronic T2D and inflammatory bowel diseases. Finally, our unique study design allowed us to examine the strain similarity between twins, and we found that twins demonstrate strain-level differences in composition despite species-level similarities.

CONCLUSIONS: These changes in the microbiome might be used for the early diagnosis of an inflamed gut and T2D prior to clinical onset of the disease and will help to advance toward microbial interventions.}, } @article {pmid26881432, year = {2016}, author = {Lopes, FA and Catão, EC and Santana, RH and Cabral, Ade S and Paranhos, R and Rangel, TP and de Rezende, CE and Edwards, RA and Thompson, CC and Thompson, FL and Kruger, RH}, title = {Microbial Community Profile and Water Quality in a Protected Area of the Caatinga Biome.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0148296}, pmid = {26881432}, issn = {1932-6203}, mesh = {Agriculture ; Ammonia/analysis ; Arthrobacter/*classification/genetics ; Brazil ; Burkholderiaceae/*classification/genetics ; Carbon/analysis ; Comamonadaceae/*classification/genetics ; Ecosystem ; Flavobacterium/*classification/genetics ; High-Throughput Nucleotide Sequencing ; Metagenome ; Microbial Consortia/physiology ; Nitrites/analysis ; Particulate Matter/analysis ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Rivers/chemistry/*microbiology ; Seasons ; Silicates/analysis ; *Water Quality ; }, abstract = {The Caatinga is a semi-arid biome in northeast Brazil. The Paraguaçú River is located in the Caatinga biome, and part of its course is protected by the National Park of Chapada Diamantina (PNCD). In this study we evaluated the effect of PNCD protection on the water quality and microbial community diversity of this river by analyzing water samples obtained from points located inside and outside the PNCD in both wet and dry seasons. Results of water quality analysis showed higher levels of silicate, ammonia, particulate organic carbon, and nitrite in samples from the unprotected area compared with those from protected areas. Pyrosequencing of the 16S rRNA genes revealed that Burkholderiales was abundant in samples from all three sites during both seasons and was represented primarily by the genus Polynucleobacter and members of the Comamonadaceae family (e.g., genus Limnohabitans). During the dry season, the unprotected area showed a higher abundance of Flavobacterium sp. and Arthrobacter sp., which are frequently associated with the presence and/or degradation of arsenic and pesticide compounds. In addition, genes that appear to be related to agricultural impacts on the environment, as well as those involved in arsenic and cadmium resistance, copper homeostasis, and propanediol utilization, were detected in the unprotected areas by metagenomic sequencing. Although PNCD protection improves water quality, agricultural activities around the park may affect water quality within the park and may account for the presence of bacteria capable of pesticide degradation and assimilation, evidencing possible anthropogenic impacts on the Caatinga.}, } @article {pmid26876732, year = {2017}, author = {Temmam, S and Davoust, B and Chaber, AL and Lignereux, Y and Michelle, C and Monteil-Bouchard, S and Raoult, D and Desnues, C}, title = {Screening for Viral Pathogens in African Simian Bushmeat Seized at A French Airport.}, journal = {Transboundary and emerging diseases}, volume = {64}, number = {4}, pages = {1159-1167}, pmid = {26876732}, issn = {1865-1682}, mesh = {Africa ; Airports ; Animals ; Bacteriophages/genetics/*isolation & purification ; Commerce ; DNA, Viral/analysis ; *Food Microbiology ; France ; Genome, Viral ; Haplorhini/*virology ; Mass Screening ; Meat/*virology ; Metagenome ; Microscopy, Fluorescence ; RNA, Viral/analysis ; }, abstract = {Illegal bushmeat traffic is an important threat to biodiversity conservation of several endangered species and may contribute to the emergence and spread of infectious diseases in humans. The hunting, manipulation and consumption of wildlife-based products, especially those of primate origin, may be a threat to human health; however, few studies have investigated the role of bushmeat trade and consumption as a potential source of human infections to date. In this study, we report the screening of viral pathogens in African simian game seized by French customs at Toulouse Blagnac Airport. Epifluorescence microscopy revealed the presence of virus-like particles in the samples, and further metagenomic sequencing of the DNA and RNA viromes confirmed the presence of sequences related to the Siphoviridae, Myoviridae and Podoviridae bacteriophage families; some of them infecting bacterial hosts that could be potentially pathogenic for humans. To increase the sensitivity of detection, twelve pan-generic PCRs targeting several viral zoonoses were performed, but no positive signal was detected. A large-scale inventory of bacteria, viruses and parasites is urgently needed to globally assess the risk for human health of the trade, manipulation and consumption of wildlife-related bushmeat.}, } @article {pmid26875998, year = {2017}, author = {Derrien, M and Belzer, C and de Vos, WM}, title = {Akkermansia muciniphila and its role in regulating host functions.}, journal = {Microbial pathogenesis}, volume = {106}, number = {}, pages = {171-181}, doi = {10.1016/j.micpath.2016.02.005}, pmid = {26875998}, issn = {1096-1208}, support = {250172/ERC_/European Research Council/International ; }, mesh = {Animals ; Anti-Bacterial Agents/therapeutic use ; Clinical Studies as Topic ; Feces/microbiology ; *Gastrointestinal Microbiome/immunology ; Humans ; Inflammatory Bowel Diseases/microbiology ; Intestinal Mucosa/microbiology ; Intestines/immunology/*microbiology/physiology ; Metabolic Diseases/microbiology ; Metagenome ; Mice ; Models, Animal ; Obesity/microbiology ; Phylogeny ; Verrucomicrobia/classification/drug effects/growth & development/*physiology ; }, abstract = {Akkermansia muciniphila is an intestinal bacterium that was isolated a decade ago from a human fecal sample. Its specialization in mucin degradation makes it a key organism at the mucosal interface between the lumen and host cells. Although it was isolated quite recently, it has rapidly raised significant interest as A. muciniphila is the only cultivated intestinal representative of the Verrucomicrobia, one of the few phyla in the human gut that can be easily detected in phylogenetic and metagenome analyses. There has also been a growing interest in A. muciniphila, due to its association with health in animals and humans. Notably, reduced levels of A. muciniphila have been observed in patients with inflammatory bowel diseases (mainly ulcerative colitis) and metabolic disorders, which suggests it may have potential anti-inflammatory properties. The aims of this review are to summarize the existing data on the intestinal distribution of A. muciniphila in health and disease, to provide insight into its ecology and its role in founding microbial networks at the mucosal interface, as well as to discuss recent research on its role in regulating host functions that are disturbed in various diseases, with a specific focus on metabolic disorders in both animals and humans.}, } @article {pmid26873931, year = {2016}, author = {Wagner, J and Paulson, JN and Wang, X and Bhattacharjee, B and Corrada Bravo, H}, title = {Privacy-preserving microbiome analysis using secure computation.}, journal = {Bioinformatics (Oxford, England)}, volume = {32}, number = {12}, pages = {1873-1879}, pmid = {26873931}, issn = {1367-4811}, support = {R01 GM114267/GM/NIGMS NIH HHS/United States ; R01 HG005220/HG/NHGRI NIH HHS/United States ; }, mesh = {DNA ; Humans ; Metagenomics ; *Microbiota ; Privacy ; Software ; }, abstract = {MOTIVATION: Developing targeted therapeutics and identifying biomarkers relies on large amounts of research participant data. Beyond human DNA, scientists now investigate the DNA of micro-organisms inhabiting the human body. Recent work shows that an individual's collection of microbial DNA consistently identifies that person and could be used to link a real-world identity to a sensitive attribute in a research dataset. Unfortunately, the current suite of DNA-specific privacy-preserving analysis tools does not meet the requirements for microbiome sequencing studies.

RESULTS: To address privacy concerns around microbiome sequencing, we implement metagenomic analyses using secure computation. Our implementation allows comparative analysis over combined data without revealing the feature counts for any individual sample. We focus on three analyses and perform an evaluation on datasets currently used by the microbiome research community. We use our implementation to simulate sharing data between four policy-domains. Additionally, we describe an application of our implementation for patients to combine data that allows drug developers to query against and compensate patients for the analysis.

The software is freely available for download at: http://cbcb.umd.edu/∼hcorrada/projects/secureseq.html

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

CONTACT: hcorrada@umiacs.umd.edu.}, } @article {pmid26873322, year = {2016}, author = {Esson, KC and Lin, X and Kumaresan, D and Chanton, JP and Murrell, JC and Kostka, JE}, title = {Alpha- and Gammaproteobacterial Methanotrophs Codominate the Active Methane-Oxidizing Communities in an Acidic Boreal Peat Bog.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {8}, pages = {2363-2371}, pmid = {26873322}, issn = {1098-5336}, mesh = {Aerobiosis ; Alphaproteobacteria/classification/genetics/*isolation & purification/metabolism ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Gammaproteobacteria/classification/genetics/*isolation & purification/metabolism ; Metagenome ; Methane/*metabolism ; Minnesota ; Oxidation-Reduction ; Oxygenases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Wetlands ; }, abstract = {The objective of this study was to characterize metabolically active, aerobic methanotrophs in an ombrotrophic peatland in the Marcell Experimental Forest, in Minnesota. Methanotrophs were investigated in the field and in laboratory incubations using DNA-stable isotope probing (SIP), expression studies on particulate methane monooxygenase (pmoA) genes, and amplicon sequencing of 16S rRNA genes. Potential rates of oxidation ranged from 14 to 17 μmol of CH4g dry weight soil(-1)day(-1) Within DNA-SIP incubations, the relative abundance of methanotrophs increased from 4% in situ to 25 to 36% after 8 to 14 days. Phylogenetic analysis of the(13)C-enriched DNA fractions revealed that the active methanotrophs were dominated by the genera Methylocystis(type II;Alphaproteobacteria),Methylomonas, and Methylovulum(both, type I;Gammaproteobacteria). In field samples, a transcript-to-gene ratio of 1 to 2 was observed for pmoA in surface peat layers, which attenuated rapidly with depth, indicating that the highest methane consumption was associated with a depth of 0 to 10 cm. Metagenomes and sequencing of cDNA pmoA amplicons from field samples confirmed that the dominant active methanotrophs were Methylocystis and Methylomonas Although type II methanotrophs have long been shown to mediate methane consumption in peatlands, our results indicate that members of the genera Methylomonas and Methylovulum(type I) can significantly contribute to aerobic methane oxidation in these ecosystems.}, } @article {pmid26873315, year = {2016}, author = {Yang, X and Noyes, NR and Doster, E and Martin, JN and Linke, LM and Magnuson, RJ and Yang, H and Geornaras, I and Woerner, DR and Jones, KL and Ruiz, J and Boucher, C and Morley, PS and Belk, KE}, title = {Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {8}, pages = {2433-2443}, pmid = {26873315}, issn = {1098-5336}, support = {T32 OD012201/OD/NIH HHS/United States ; UL1 TR001082/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification/*genetics ; Cattle ; *Environmental Microbiology ; *Food Handling ; Metagenomics ; *Microbiota ; Red Meat/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Foodborne illnesses associated with pathogenic bacteria are a global public health and economic challenge. The diversity of microorganisms (pathogenic and nonpathogenic) that exists within the food and meat industries complicates efforts to understand pathogen ecology. Further, little is known about the interaction of pathogens within the microbiome throughout the meat production chain. Here, a metagenomic approach and shotgun sequencing technology were used as tools to detect pathogenic bacteria in environmental samples collected from the same groups of cattle at different longitudinal processing steps of the beef production chain: cattle entry to feedlot, exit from feedlot, cattle transport trucks, abattoir holding pens, and the end of the fabrication system. The log read counts classified as pathogens per million reads for Salmonella enterica,Listeria monocytogenes,Escherichia coli,Staphylococcus aureus, Clostridium spp. (C. botulinum and C. perfringens), and Campylobacter spp. (C. jejuni,C. coli, and C. fetus) decreased over subsequential processing steps. Furthermore, the normalized read counts for S. enterica,E. coli, and C. botulinumwere greater in the final product than at the feedlots, indicating that the proportion of these bacteria increased (the effect on absolute numbers was unknown) within the remaining microbiome. From an ecological perspective, data indicated that shotgun metagenomics can be used to evaluate not only the microbiome but also shifts in pathogen populations during beef production. Nonetheless, there were several challenges in this analysis approach, one of the main ones being the identification of the specific pathogen from which the sequence reads originated, which makes this approach impractical for use in pathogen identification for regulatory and confirmation purposes.}, } @article {pmid26873023, year = {2016}, author = {Babujia, LC and Silva, AP and Nakatani, AS and Cantão, ME and Vasconcelos, AT and Visentainer, JV and Hungria, M}, title = {Impact of long-term cropping of glyphosate-resistant transgenic soybean [Glycine max (L.) Merr.] on soil microbiome.}, journal = {Transgenic research}, volume = {25}, number = {4}, pages = {425-440}, pmid = {26873023}, issn = {1573-9368}, mesh = {Biodiversity ; Biomass ; Brazil ; Crop Production/*methods ; Crops, Agricultural ; DNA, Ribosomal ; Genetic Variation ; Glycine/*analogs & derivatives/pharmacology ; Herbicide Resistance ; Metagenome/genetics ; Microbiota/genetics ; *Plants, Genetically Modified ; Soil/chemistry ; *Soil Microbiology ; Glycine max/*genetics/physiology ; Glyphosate ; }, abstract = {The transgenic soybean [Glycine max (L.) Merrill] occupies about 80 % of the global area cropped with this legume, the majority comprising the glyphosate-resistant trait (Roundup Ready(®), GR or RR). However, concerns about possible impacts of transgenic crops on soil microbial communities are often raised. We investigated soil chemical, physical and microbiological properties, and grain yields in long-term field trials involving conventional and nearly isogenic RR transgenic genotypes. The trials were performed at two locations in Brazil, with different edaphoclimatic conditions. Large differences in physical, chemical and classic microbiological parameters (microbial biomass of C and N, basal respiration), as well as in grain production were observed between the sites. Some phyla (Proteobacteria, Actinobacteria, Acidobacteria), classes (Alphaproteobacteria, Actinomycetales, Solibacteres) and orders (Rhizobiales, Burkholderiales, Myxococcales, Pseudomonadales), as well as some functional subsystems (clustering-based subsystems, carbohydrates, amino acids and protein metabolism) were, in general, abundant in all treatments. However, bioindicators related to superior soil fertility and physical properties at Londrina were identified, among them a higher ratio of Proteobacteria:Acidobacteria. Regarding the transgene, the metagenomics showed differences in microbial taxonomic and functional abundances, but lower in magnitude than differences observed between the sites. Besides the site-specific differences, Proteobacteria, Firmicutes and Chlorophyta were higher in the transgenic treatment, as well as sequences related to protein metabolism, cell division and cycle. Although confirming effects of the transgenic trait on soil microbiome, no differences were recorded in grain yields, probably due to the buffering capacity associated with the high taxonomic and functional microbial diversity observed in all treatments.}, } @article {pmid26872143, year = {2016}, author = {Cameron, SJ and Lewis, KE and Huws, SA and Lin, W and Hegarty, MJ and Lewis, PD and Mur, LA and Pachebat, JA}, title = {Metagenomic Sequencing of the Chronic Obstructive Pulmonary Disease Upper Bronchial Tract Microbiome Reveals Functional Changes Associated with Disease Severity.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0149095}, pmid = {26872143}, issn = {1932-6203}, mesh = {Aged ; Bronchi/*microbiology ; Female ; Humans ; Male ; *Metagenome ; Microbiota ; Pulmonary Disease, Chronic Obstructive/*microbiology/pathology ; Sequence Analysis, DNA ; Severity of Illness Index ; }, abstract = {Chronic Obstructive Pulmonary Disease (COPD) is a major source of mortality and morbidity worldwide. The microbiome associated with this disease may be an important component of the disease, though studies to date have been based on sequencing of the 16S rRNA gene, and have revealed unequivocal results. Here, we employed metagenomic sequencing of the upper bronchial tract (UBT) microbiome to allow for greater elucidation of its taxonomic composition, and revealing functional changes associated with the disease. The bacterial metagenomes within sputum samples from eight COPD patients and ten 'healthy' smokers (Controls) were sequenced, and suggested significant changes in the abundance of bacterial species, particularly within the Streptococcus genus. The functional capacity of the COPD UBT microbiome indicated an increased capacity for bacterial growth, which could be an important feature in bacterial-associated acute exacerbations. Regression analyses correlated COPD severity (FEV1% of predicted) with differences in the abundance of Streptococcus pneumoniae and functional classifications related to a reduced capacity for bacterial sialic acid metabolism. This study suggests that the COPD UBT microbiome could be used in patient risk stratification and in identifying novel monitoring and treatment methods, but study of a longitudinal cohort will be required to unequivocally relate these features of the microbiome with COPD severity.}, } @article {pmid26872041, year = {2016}, author = {Yang, FC and Chen, YL and Tang, SL and Yu, CP and Wang, PH and Ismail, W and Wang, CH and Ding, JY and Yang, CY and Yang, CY and Chiang, YR}, title = {Integrated multi-omics analyses reveal the biochemical mechanisms and phylogenetic relevance of anaerobic androgen biodegradation in the environment.}, journal = {The ISME journal}, volume = {10}, number = {8}, pages = {1967-1983}, pmid = {26872041}, issn = {1751-7370}, mesh = {Anaerobiosis ; Androgens/*metabolism ; Biodegradation, Environmental ; Gammaproteobacteria/genetics/*metabolism ; Gene Expression Profiling ; Genome, Bacterial/*genetics ; *Genomics ; Phylogeny ; Sequence Analysis, DNA ; Sewage/microbiology ; Taiwan ; Testosterone/*analogs & derivatives/metabolism ; }, abstract = {Steroid hormones, such as androgens, are common surface-water contaminants. However, literature on the ecophysiological relevance of steroid-degrading organisms in the environment, particularly in anoxic ecosystems, is extremely limited. We previously reported that Steroidobacter denitrificans anaerobically degrades androgens through the 2,3-seco pathway. In this study, the genome of Sdo. denitrificans was completely sequenced. Transcriptomic data revealed gene clusters that were distinctly expressed during anaerobic growth on testosterone. We isolated and characterized the bifunctional 1-testosterone hydratase/dehydrogenase, which is essential for anaerobic degradation of steroid A-ring. Because of apparent substrate preference of this molybdoenzyme, corresponding genes, along with the signature metabolites of the 2,3-seco pathway, were used as biomarkers to investigate androgen biodegradation in the largest sewage treatment plant in Taipei, Taiwan. Androgen metabolite analysis indicated that denitrifying bacteria in anoxic sewage use the 2,3-seco pathway to degrade androgens. Metagenomic analysis and PCR-based functional assays showed androgen degradation in anoxic sewage by Thauera spp. through the action of 1-testosterone hydratase/dehydrogenase. Our integrative 'omics' approach can be used for culture-independent investigations of the microbial degradation of structurally complex compounds where isotope-labeled substrates are not easily available.}, } @article {pmid26871866, year = {2016}, author = {Cuadrat, RR and Ferrera, I and Grossart, HP and Dávila, AM}, title = {Picoplankton Bloom in Global South? A High Fraction of Aerobic Anoxygenic Phototrophic Bacteria in Metagenomes from a Coastal Bay (Arraial do Cabo--Brazil).}, journal = {Omics : a journal of integrative biology}, volume = {20}, number = {2}, pages = {76-87}, pmid = {26871866}, issn = {1557-8100}, mesh = {Aerobiosis ; Bays ; Brazil ; Gene Frequency ; Genes, Bacterial ; Metagenome ; Molecular Sequence Annotation ; Phylogeny ; Phytoplankton/genetics ; Roseobacter/*genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Marine habitats harbor a great diversity of microorganism from the three domains of life, only a small fraction of which can be cultivated. Metagenomic approaches are increasingly popular for addressing microbial diversity without culture, serving as sensitive and relatively unbiased methods for identifying and cataloging the diversity of nucleic acid sequences derived from organisms in environmental samples. Aerobic anoxygenic phototrophic bacteria (AAP) play important roles in carbon and energy cycling in aquatic systems. In oceans, those bacteria are widely distributed; however, their abundance and importance are still poorly understood. The aim of this study was to estimate abundance and diversity of AAPs in metagenomes from an upwelling affected coastal bay in Arraial do Cabo, Brazil, using in silico screening for the anoxygenic photosynthesis core genes. Metagenomes from the Global Ocean Sample Expedition (GOS) were screened for comparative purposes. AAPs were highly abundant in the free-living bacterial fraction from Arraial do Cabo: 23.88% of total bacterial cells, compared with 15% in the GOS dataset. Of the ten most AAP abundant samples from GOS, eight were collected close to the Equator where solar irradiation is high year-round. We were able to assign most retrieved sequences to phylo-groups, with a particularly high abundance of Roseobacter in Arraial do Cabo samples. The high abundance of AAP in this tropical bay may be related to the upwelling phenomenon and subsequent picoplankton bloom. These results suggest a link between upwelling and light abundance and demonstrate AAP even in oligotrophic tropical and subtropical environments. Longitudinal studies in the Arraial do Cabo region are warranted to understand the dynamics of AAP at different locations and seasons, and the ecological role of these unique bacteria for biogeochemical and energy cycling in the ocean.}, } @article {pmid26870888, year = {2016}, author = {Videhult, FK and West, CE}, title = {Nutrition, gut microbiota and child health outcomes.}, journal = {Current opinion in clinical nutrition and metabolic care}, volume = {19}, number = {3}, pages = {208-213}, doi = {10.1097/MCO.0000000000000266}, pmid = {26870888}, issn = {1473-6519}, mesh = {Autoimmune Diseases/etiology/prevention & control ; Breast Feeding ; Celiac Disease/etiology/prevention & control ; Child ; *Child Development ; *Child Nutritional Physiological Phenomena ; Child, Preschool ; Crohn Disease/etiology/prevention & control ; Dysbiosis/immunology/microbiology/physiopathology/prevention & control ; *Evidence-Based Medicine ; *Gastrointestinal Microbiome ; *Health Status ; Humans ; Hypersensitivity/etiology/prevention & control ; Infant ; *Infant Nutritional Physiological Phenomena ; Irritable Bowel Syndrome/etiology/prevention & control ; *Nutritional Status ; }, abstract = {PURPOSE OF REVIEW: Diet is one of the main drivers of the composition and function of the gut microbiota. The scope of this review is to summarize recent studies assessing the role of gut microbiota in clinical pediatric conditions and to review studies using nutritional approaches to favorably modify the gut microbiota to improve health outcomes in children.

RECENT FINDINGS: New studies underscore that breastfeeding and infant diet impact the gut microbiome and metagenome. A comprehensive study using metagenomic shotgun sequencing, suggests that the cessation of breastfeeding rather than the introduction of solid foods, drives the functional maturation of the infant gut microbiome toward an adult-like state. There is further support for the view that a disturbed early gut microbiota is implicated in allergic and autoimmune diseases. New studies using prebiotics, probiotics, and synbiotics in various pediatric disorders have yielded promising results, yet the evidence for specific guidelines on their use is still low.

SUMMARY: Intestinal dysbiosis is associated with several pediatric disorders but a cause-effect relationship remains to be clearly demonstrated in most conditions. Future studies using new systems biology approaches are anticipated to provide further insight into the functional capacities of the gut microbiome and its establishment in childhood. This may then lay the ground for improved treatment and prevention strategies targeting the gut microbiota.}, } @article {pmid26870828, year = {2016}, author = {Hua, X and Goedert, JJ and Pu, A and Yu, G and Shi, J}, title = {Allergy associations with the adult fecal microbiota: Analysis of the American Gut Project.}, journal = {EBioMedicine}, volume = {3}, number = {}, pages = {172-179}, pmid = {26870828}, issn = {2352-3964}, support = {ZIA CP010214//Intramural NIH HHS/United States ; ZIA-CP-010214/CP/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Biodiversity ; Databases, Nucleic Acid ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Hypersensitivity/*epidemiology/*etiology ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Odds Ratio ; RNA, Ribosomal, 16S/genetics ; Risk ; Surveys and Questionnaires ; }, abstract = {BACKGROUND: Alteration of the gut microbial population (dysbiosis) may increase the risk for allergies and other conditions. This study sought to clarify the relationship of dysbiosis with allergies in adults.

METHODS: Publicly available American Gut Project questionnaire and fecal 16S rRNA sequence data were analyzed. Fecal microbiota richness (number of observed species) and composition (UniFrac) were used to compare adults with versus without allergy to foods (peanuts, tree nuts, shellfish, other) and non-foods (drug, bee sting, dander, asthma, seasonal, eczema). Logistic and Poisson regression models adjusted for potential confounders. Odds ratios and 95% confidence intervals (CI) were calculated for lowest vs highest richness tertile. Taxonomy associations considered 122 non-redundant taxa (of 2379 total taxa) with ≥ 0.1% mean abundance.

RESULTS: Self-reported allergy prevalence among the 1879 participants (mean age, 45.5 years; 46.9% male) was 81.5%, ranging from 2.5% for peanuts to 40.5% for seasonal. Fecal microbiota richness was markedly lower with total allergies (P = 10(-9)) and five particular allergies (P ≤ 10(-4)). Richness odds ratios were 1.7 (CI 1.3-2.2) with seasonal, 1.8 (CI 1.3-2.5) with drug, and 7.8 (CI 2.3-26.5) with peanut allergy. These allergic participants also had markedly altered microbial community composition (unweighted UniFrac, P = 10(-4) to 10(-7)). Total food and non-food allergies were significantly associated with 7 and 9 altered taxa, respectively. The dysbiosis was most marked with nut and seasonal allergies, driven by higher Bacteroidales and reduced Clostridiales taxa.

INTERPRETATION: American adults with allergies, especially to nuts and seasonal pollen, have low diversity, reduced Clostridiales, and increased Bacteroidales in their gut microbiota. This dysbiosis might be targeted to improve treatment or prevention of allergy.}, } @article {pmid26870798, year = {2015}, author = {Bahr, SM and Weidemann, BJ and Castro, AN and Walsh, JW and deLeon, O and Burnett, CM and Pearson, NA and Murry, DJ and Grobe, JL and Kirby, JR}, title = {Risperidone-induced weight gain is mediated through shifts in the gut microbiome and suppression of energy expenditure.}, journal = {EBioMedicine}, volume = {2}, number = {11}, pages = {1725-1734}, pmid = {26870798}, issn = {2352-3964}, support = {HL098276/HL/NHLBI NIH HHS/United States ; U24 DK100469/DK/NIDDK NIH HHS/United States ; HL084207/HL/NHLBI NIH HHS/United States ; R00 HL098276/HL/NHLBI NIH HHS/United States ; R01AI108255/AI/NIAID NIH HHS/United States ; R01 AI108255/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Antipsychotic Agents/administration & dosage/*pharmacology ; Energy Metabolism/*drug effects ; Fecal Microbiota Transplantation ; Female ; Gastrointestinal Microbiome/*drug effects ; Metagenome ; Metagenomics/methods ; Mice ; Risperidone/administration & dosage/*pharmacology ; Weight Gain/*drug effects ; Xenobiotics/pharmacology ; }, abstract = {Risperidone is a second-generation antipsychotic that causes weight gain. We hypothesized that risperidone-induced shifts in the gut microbiome are mechanistically involved in its metabolic consequences. Wild-type female C57BL/6J mice treated with risperidone (80 μg/day) exhibited significant excess weight gain, due to reduced energy expenditure, which correlated with an altered gut microbiome. Fecal transplant from risperidone-treated mice caused a 16% reduction in total resting metabolic rate in naïve recipients, attributable to suppression of non-aerobic metabolism. Risperidone inhibited growth of cultured fecal bacteria grown anaerobically more than those grown aerobically. Finally, transplant of the fecal phage fraction from risperidone-treated mice was sufficient to cause excess weight gain in naïve recipients, again through reduced energy expenditure. Collectively, these data highlight a major role for the gut microbiome in weight gain following chronic use of risperidone, and specifically implicates the modulation of non-aerobic resting metabolism in this mechanism.}, } @article {pmid26870025, year = {2016}, author = {Rebollar, EA and Antwis, RE and Becker, MH and Belden, LK and Bletz, MC and Brucker, RM and Harrison, XA and Hughey, MC and Kueneman, JG and Loudon, AH and McKenzie, V and Medina, D and Minbiole, KP and Rollins-Smith, LA and Walke, JB and Weiss, S and Woodhams, DC and Harris, RN}, title = {Using "Omics" and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {68}, pmid = {26870025}, issn = {1664-302X}, abstract = {Emerging infectious diseases in wildlife are responsible for massive population declines. In amphibians, chytridiomycosis caused by Batrachochytrium dendrobatidis, Bd, has severely affected many amphibian populations and species around the world. One promising management strategy is probiotic bioaugmentation of antifungal bacteria on amphibian skin. In vivo experimental trials using bioaugmentation strategies have had mixed results, and therefore a more informed strategy is needed to select successful probiotic candidates. Metagenomic, transcriptomic, and metabolomic methods, colloquially called "omics," are approaches that can better inform probiotic selection and optimize selection protocols. The integration of multiple omic data using bioinformatic and statistical tools and in silico models that link bacterial community structure with bacterial defensive function can allow the identification of species involved in pathogen inhibition. We recommend using 16S rRNA gene amplicon sequencing and methods such as indicator species analysis, the Kolmogorov-Smirnov Measure, and co-occurrence networks to identify bacteria that are associated with pathogen resistance in field surveys and experimental trials. In addition to 16S amplicon sequencing, we recommend approaches that give insight into symbiont function such as shotgun metagenomics, metatranscriptomics, or metabolomics to maximize the probability of finding effective probiotic candidates, which can then be isolated in culture and tested in persistence and clinical trials. An effective mitigation strategy to ameliorate chytridiomycosis and other emerging infectious diseases is necessary; the advancement of omic methods and the integration of multiple omic data provide a promising avenue toward conservation of imperiled species.}, } @article {pmid26869611, year = {2016}, author = {Nova, E and Pérez de Heredia, F and Gómez-Martínez, S and Marcos, A}, title = {The Role of Probiotics on the Microbiota: Effect on Obesity.}, journal = {Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition}, volume = {31}, number = {3}, pages = {387-400}, doi = {10.1177/0884533615620350}, pmid = {26869611}, issn = {1941-2452}, mesh = {Animals ; Bifidobacterium/metabolism ; Gastrointestinal Tract/metabolism/microbiology ; Humans ; Lactobacillus/metabolism ; Mice ; Microbiota/*drug effects ; Obesity/*metabolism/microbiology ; Probiotics/*therapeutic use ; Rats ; }, abstract = {The microbiota and the human host maintain a symbiotic association. Nowadays, metagenomic analyses are providing valuable knowledge on the diversity and functionality of the gut microbiota. However, with regard to the definition of a "healthy microbiota" and the characterization of the dysbiosis linked to obesity, there is still not a clear answer. Despite this fact, attempts have been made to counteract obesity through probiotic supplementation. A literature search of experimental studies relevant to the topic was performed in PubMed database with the keywords "probiotic" and "obesity" and restricted to those with "Lactobacillus" or "Bifidobacterium" in the title. So far, evidence of an antiobesity effect of different lactobacilli and bifidobacteria has been mainly obtained from animal models of dietary-induced obesity. Using these experimental models, a substantial number of studies have reported reductions in weight gain and, in particular, fat tissue mass at different locations following administration of bacteria, as compared with controls. Antiatherogenic and anti-inflammatory effects-including regulation of expression of lipogenic and lipolytic genes in the liver, reduction in liver steatosis, improvement of blood lipid profile and glucose tolerance, decreased endotoxemia, and regulation of inflammatory pathways-are also reported in many of them. The number of human studies focused on probiotic administration for obesity management is still very scarce, and it is too soon to judge their potential efficacy, especially when considering the fact that the actions of probiotics are always strain specific and the individual response varies according to intrinsic factors, the overall composition of diet, and their interactions.}, } @article {pmid26869601, year = {2016}, author = {Kim, J and Guevarra, RB and Nguyen, SG and Lee, JH and Jeong, DK and Unno, T}, title = {Effects of the Antibiotics Growth Promoter Tylosin on Swine Gut Microbiota.}, journal = {Journal of microbiology and biotechnology}, volume = {26}, number = {5}, pages = {876-882}, doi = {10.4014/jmb.1512.12004}, pmid = {26869601}, issn = {1738-8872}, mesh = {Animal Feed ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*classification/*drug effects ; DNA, Bacterial/genetics ; Gastrointestinal Microbiome/*drug effects ; Gram-Positive Bacteria/classification/drug effects ; Growth Substances/pharmacology ; Metagenome ; Models, Animal ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Swine/growth & development/*microbiology ; Tylosin/*pharmacology ; Weight Gain/drug effects ; }, abstract = {Tylosin has been used as a livestock feed additive and antibiotic growth promoter for many years. However, the mode of action by which tylosin enhances animal growth is unclear. We used high-throughput sequencing of 16S rRNA genes to investigate the effects of tylosin as a feed additive on swine gut microbiota. No significant difference in the rate of weight increase was observed between control and tylosin-treated pigs during a 10-week feeding trial. However, tylosin-treated pigs showed rapid increases in the relative abundance of the phylum Firmicutes. Increases in Firmicutes species are associated with (so-called) obese-type gut microbiota. The abundance of species of four families of the phylum Firmicutes (Streptococcaceae, Peptococcaceae, Peptostreptococcaceae, and Clostridiaceae) correlated positively with host weight gain. The abundance of Streptococcaceae family bacteria was least affected by tylosin treatment. Distribution analysis of operational taxonomic units (OTUs) showed that both control and tylosin-treated pigs exhibited similar OTU alterations during growth. However, the tylosin-treated group showed distinctive alterations in gut microbiota when the host weighed approximately 60 kg, whereas similar alterations occurred at around 80 kg in the control group. Our results suggest that use of tylosin accelerates maturation of swine gut microbiota rather than altering its composition.}, } @article {pmid26865079, year = {2016}, author = {Païssé, S and Valle, C and Servant, F and Courtney, M and Burcelin, R and Amar, J and Lelouvier, B}, title = {Comprehensive description of blood microbiome from healthy donors assessed by 16S targeted metagenomic sequencing.}, journal = {Transfusion}, volume = {56}, number = {5}, pages = {1138-1147}, doi = {10.1111/trf.13477}, pmid = {26865079}, issn = {1537-2995}, mesh = {Adolescent ; Adult ; Aged ; Blood/*microbiology ; Blood Donors ; Blood Safety ; DNA, Bacterial/blood/*isolation & purification ; DNA, Ribosomal ; France ; Healthy Volunteers ; Humans ; Metagenomics/*methods ; *Microbiota ; Middle Aged ; Phylogeny ; Public Health Surveillance/methods ; Young Adult ; }, abstract = {BACKGROUND: Recent studies have revealed that the blood of healthy humans is not as sterile as previously supposed. The objective of this study was to provide a comprehensive description of the microbiome present in different fractions of the blood of healthy individuals.

STUDY DESIGN AND METHODS: The study was conducted in 30 healthy blood donors to the French national blood collection center (Établissement Français du Sang). We have set up a 16S rDNA quantitative polymerase chain reaction assay as well as a 16S targeted metagenomics sequencing pipeline specifically designed to analyze the blood microbiome, which we have used on whole blood as well as on different blood fractions (buffy coat [BC], red blood cells [RBCs], and plasma).

RESULTS: Most of the blood bacterial DNA is located in the BC (93.74%), and RBCs contain more bacterial DNA (6.23%) than the plasma (0.03%). The distribution of 16S DNA is different for each fraction and spreads over a relatively broad range among donors. At the phylum level, blood fractions contain bacterial DNA mostly from the Proteobacteria phylum (more than 80%) but also from Actinobacteria, Firmicutes, and Bacteroidetes. At deeper taxonomic levels, there are striking differences between the bacterial profiles of the different blood fractions.

CONCLUSION: We demonstrate that a diversified microbiome exists in healthy blood. This microbiome has most likely an important physiologic role and could be implicated in certain transfusion-transmitted bacterial infections. In this regard, the amount of 16S bacterial DNA or the microbiome profile could be monitored to improve the safety of the blood supply.}, } @article {pmid26862195, year = {2016}, author = {Benjdia, A and Berteau, O}, title = {Sulfatases and radical SAM enzymes: emerging themes in glycosaminoglycan metabolism and the human microbiota.}, journal = {Biochemical Society transactions}, volume = {44}, number = {1}, pages = {109-115}, doi = {10.1042/BST20150191}, pmid = {26862195}, issn = {1470-8752}, mesh = {Glycosaminoglycans/*metabolism ; Host-Pathogen Interactions ; Humans ; *Microbiota ; S-Adenosylmethionine/*metabolism ; Substrate Specificity ; Sulfatases/*metabolism ; }, abstract = {Humans live in a permanent association with bacterial populations collectively called the microbiota. In the last 10 years, major advances in our knowledge of the microbiota have shed light on its critical roles in human physiology. The microbiota has also been shown to be a major factor in numerous pathologies including obesity or inflammatory disorders. Despite tremendous progresses, our understanding of the key functions of the human microbiota and the molecular basis of its interactions with the host remain still poorly understood. Among the factors involved in host colonization, two enzymes families, sulfatases and radical S-adenosyl-L-methionine enzymes, have recently emerged as key enzymes.}, } @article {pmid26861660, year = {2016}, author = {ten Hoopen, P and Amid, C and Buttigieg, PL and Pafilis, E and Bravakos, P and Cerdeño-Tárraga, AM and Gibson, R and Kahlke, T and Legaki, A and Narayana Murthy, K and Papastefanou, G and Pereira, E and Rossello, M and Luisa Toribio, A and Cochrane, G}, title = {Value, but high costs in post-deposition data curation.}, journal = {Database : the journal of biological databases and curation}, volume = {2016}, number = {}, pages = {}, pmid = {26861660}, issn = {1758-0463}, support = {BB/I02612X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Computational Biology/*economics ; Data Collection ; Databases, Nucleic Acid/*economics ; Ecosystem ; Europe ; Geography ; Humans ; *Metagenomics ; Microbiota ; Molecular Sequence Annotation ; Semantics ; Sequence Analysis ; }, abstract = {Discoverability of sequence data in primary data archives is proportional to the richness of contextual information associated with the data. Here, we describe an exercise in the improvement of contextual information surrounding sample records associated with metagenomics sequence reads available in the European Nucleotide Archive. We outline the annotation process and summarize findings of this effort aimed at increasing usability of publicly available environmental data. Furthermore, we emphasize the benefits of such an exercise and detail its costs. We conclude that such a third party annotation approach is expensive and has value as an element of curation, but should form only part of a more sustainable submitter-driven approach. Database URL: http://www.ebi.ac.uk/ena.}, } @article {pmid26861018, year = {2016}, author = {Tsai, YC and Conlan, S and Deming, C and , and Segre, JA and Kong, HH and Korlach, J and Oh, J}, title = {Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing.}, journal = {mBio}, volume = {7}, number = {1}, pages = {e01948-15}, pmid = {26861018}, issn = {2150-7511}, support = {K22 AI119231/AI/NIAID NIH HHS/United States ; //Intramural NIH HHS/United States ; }, mesh = {Bacteriophages/*genetics/isolation & purification ; Corynebacterium/*genetics/isolation & purification/*virology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; *Microbiota ; Molecular Sequence Data ; Sequence Analysis, DNA/methods ; Skin/*microbiology ; }, abstract = {UNLABELLED: Deep metagenomic shotgun sequencing has emerged as a powerful tool to interrogate composition and function of complex microbial communities. Computational approaches to assemble genome fragments have been demonstrated to be an effective tool for de novo reconstruction of genomes from these communities. However, the resultant "genomes" are typically fragmented and incomplete due to the limited ability of short-read sequence data to assemble complex or low-coverage regions. Here, we use single-molecule, real-time (SMRT) sequencing to reconstruct a high-quality, closed genome of a previously uncharacterized Corynebacterium simulans and its companion bacteriophage from a skin metagenomic sample. Considerable improvement in assembly quality occurs in hybrid approaches incorporating short-read data, with even relatively small amounts of long-read data being sufficient to improve metagenome reconstruction. Using short-read data to evaluate strain variation of this C. simulans in its skin community at single-nucleotide resolution, we observed a dominant C. simulans strain with moderate allelic heterozygosity throughout the population. We demonstrate the utility of SMRT sequencing and hybrid approaches in metagenome quantitation, reconstruction, and annotation.

IMPORTANCE: The species comprising a microbial community are often difficult to deconvolute due to technical limitations inherent to most short-read sequencing technologies. Here, we leverage new advances in sequencing technology, single-molecule sequencing, to significantly improve reconstruction of a complex human skin microbial community. With this long-read technology, we were able to reconstruct and annotate a closed, high-quality genome of a previously uncharacterized skin species. We demonstrate that hybrid approaches with short-read technology are sufficiently powerful to reconstruct even single-nucleotide polymorphism level variation of species in this a community.}, } @article {pmid26859770, year = {2016}, author = {Turroni, F and Milani, C and Duranti, S and Mancabelli, L and Mangifesta, M and Viappiani, A and Lugli, GA and Ferrario, C and Gioiosa, L and Ferrarini, A and Li, J and Palanza, P and Delledonne, M and van Sinderen, D and Ventura, M}, title = {Deciphering bifidobacterial-mediated metabolic interactions and their impact on gut microbiota by a multi-omics approach.}, journal = {The ISME journal}, volume = {10}, number = {7}, pages = {1656-1668}, pmid = {26859770}, issn = {1751-7370}, mesh = {Bifidobacterium/*metabolism/physiology ; Carbohydrate Metabolism ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Humans ; Intestines/microbiology ; Polysaccharides/metabolism ; Starch/metabolism ; }, abstract = {The intricacies of cooperation and competition between microorganisms are poorly investigated for particular components of the gut microbiota. In order to obtain insights into the manner by which different bifidobacterial species coexist in the mammalian gut, we investigated possible interactions between four human gut commensals, Bifidobacterium bifidum PRL2010, Bifidobacterium adolescentis 22L, Bifidobacterium breve 12L and Bifidobacterium longum subsp. infantis ATCC15697, in the intestine of conventional mice. The generated information revealed various ecological/metabolic strategies, including glycan-harvesting, glycan-breakdown and cross-feeding behavior, adopted by bifidobacteria in the highly competitive environment of the mammalian intestine. Introduction of two or multiple bifidobacterial strains caused a clear shift in the microbiota composition of the murine cecum. Whole-genome transcription profiling coupled with metagenomic analyses of single, dual or multiple associations of bifidobacterial strains revealed an expansion of the murine gut glycobiome toward enzymatic degradation of plant-derived carbohydrates, such as xylan, arabinoxylan, starch and host-derived glycan substrates. Furthermore, these bifidobacterial communities evoked major changes in the metabolomic profile of the microbiota as observed by shifts in short chain fatty acid production and carbohydrate availability in the murine cecum. Overall, these data support an ecological role of bifidobacteria acting directly or through cross-feeding activities in shaping the gut murine microbiome to instigate an enrichment of saccharolytic microbiota.}, } @article {pmid26859489, year = {2016}, author = {Alcaraz, LD and Martínez-Sánchez, S and Torres, I and Ibarra-Laclette, E and Herrera-Estrella, L}, title = {The Metagenome of Utricularia gibba's Traps: Into the Microbial Input to a Carnivorous Plant.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0148979}, pmid = {26859489}, issn = {1932-6203}, support = {55007646//Howard Hughes Medical Institute/United States ; }, mesh = {Carnivory ; DNA, Plant/genetics ; Gene Library ; Genome, Plant/*genetics ; Lamiales/*genetics/microbiology ; *Metagenome ; Microbiota ; Plant Structures/*genetics/microbiology ; }, abstract = {The genome and transcriptome sequences of the aquatic, rootless, and carnivorous plant Utricularia gibba L. (Lentibulariaceae), were recently determined. Traps are necessary for U. gibba because they help the plant to survive in nutrient-deprived environments. The U. gibba's traps (Ugt) are specialized structures that have been proposed to selectively filter microbial inhabitants. To determine whether the traps indeed have a microbiome that differs, in composition or abundance, from the microbiome in the surrounding environment, we used whole-genome shotgun (WGS) metagenomics to describe both the taxonomic and functional diversity of the Ugt microbiome. We collected U. gibba plants from their natural habitat and directly sequenced the metagenome of the Ugt microbiome and its surrounding water. The total predicted number of species in the Ugt was more than 1,100. Using pan-genome fragment recruitment analysis, we were able to identify to the species level of some key Ugt players, such as Pseudomonas monteilii. Functional analysis of the Ugt metagenome suggests that the trap microbiome plays an important role in nutrient scavenging and assimilation while complementing the hydrolytic functions of the plant.}, } @article {pmid26851966, year = {2016}, author = {Dannemiller, KC and Gent, JF and Leaderer, BP and Peccia, J}, title = {Indoor microbial communities: Influence on asthma severity in atopic and nonatopic children.}, journal = {The Journal of allergy and clinical immunology}, volume = {138}, number = {1}, pages = {76-83.e1}, pmid = {26851966}, issn = {1097-6825}, support = {R01 ES005410/ES/NIEHS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; *Air Microbiology ; Air Pollution, Indoor/*adverse effects ; Allergens/immunology ; Asthma/diagnosis/drug therapy/etiology ; Child ; Female ; Humans ; Hypersensitivity/diagnosis/drug therapy/etiology ; Immunoglobulin E/immunology ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Odds Ratio ; Risk Factors ; Severity of Illness Index ; Young Adult ; }, abstract = {BACKGROUND: Allergic and nonallergic asthma severity in children can be affected by microbial exposures.

OBJECTIVE: We sought to examine associations between exposures to household microbes and childhood asthma severity stratified by atopic status.

METHODS: Participants (n = 196) were selected from a cohort of asthmatic children in Connecticut and Massachusetts. Children were grouped according to asthma severity (mild with no or minimal symptoms and medication or moderate to severe persistent) and atopic status (determined by serum IgE levels). Microbial community structure and concentrations in house dust were determined by using next-generation DNA sequencing and quantitative PCR. Logistic regression was used to explore associations between asthma severity and exposure metrics, including richness, taxa identification and quantification, community composition, and concentration of total fungi and bacteria.

RESULTS: Among all children, increased asthma severity was significantly associated with an increased concentration of summed allergenic fungal species, high total fungal concentrations, and high bacterial richness by using logistic regression in addition to microbial community composition by using the distance comparison t test. Asthma severity in atopic children was associated with fungal community composition (P = .001). By using logistic regression, asthma severity in nonatopic children was associated with total fungal concentration (odds ratio, 2.40; 95% CI, 1.06-5.44). The fungal genus Volutella was associated with increased asthma severity in atopic children (P = .0001, q = 0.04). The yeast genera Kondoa might be protective; Cryptococcus species might also affect asthma severity.

CONCLUSION: Asthma severity among this cohort of children was associated with microbial exposure, and associations differed based on atopic status.}, } @article {pmid26849217, year = {2016}, author = {Clooney, AG and Fouhy, F and Sleator, RD and O' Driscoll, A and Stanton, C and Cotter, PD and Claesson, MJ}, title = {Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0148028}, pmid = {26849217}, issn = {1932-6203}, mesh = {Aged ; DNA Primers/genetics ; Feces/microbiology ; *High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; }, abstract = {Rapid advancements in sequencing technologies along with falling costs present widespread opportunities for microbiome studies across a vast and diverse array of environments. These impressive technological developments have been accompanied by a considerable growth in the number of methodological variables, including sampling, storage, DNA extraction, primer pairs, sequencing technology, chemistry version, read length, insert size, and analysis pipelines, amongst others. This increase in variability threatens to compromise both the reproducibility and the comparability of studies conducted. Here we perform the first reported study comparing both amplicon and shotgun sequencing for the three leading next-generation sequencing technologies. These were applied to six human stool samples using Illumina HiSeq, MiSeq and Ion PGM shotgun sequencing, as well as amplicon sequencing across two variable 16S rRNA gene regions. Notably, we found that the factor responsible for the greatest variance in microbiota composition was the chosen methodology rather than the natural inter-individual variance, which is commonly one of the most significant drivers in microbiome studies. Amplicon sequencing suffered from this to a large extent, and this issue was particularly apparent when the 16S rRNA V1-V2 region amplicons were sequenced with MiSeq. Somewhat surprisingly, the choice of taxonomic binning software for shotgun sequences proved to be of crucial importance with even greater discriminatory power than sequencing technology and choice of amplicon. Optimal N50 assembly values for the HiSeq was obtained for 10 million reads per sample, whereas the applied MiSeq and PGM sequencing depths proved less sufficient for shotgun sequencing of stool samples. The latter technologies, on the other hand, provide a better basis for functional gene categorisation, possibly due to their longer read lengths. Hence, in addition to highlighting methodological biases, this study demonstrates the risks associated with comparing data generated using different strategies. We also recommend that laboratories with particular interests in certain microbes should optimise their protocols to accurately detect these taxa using different techniques.}, } @article {pmid26849041, year = {2016}, author = {Mir, RA and Weppelmann, TA and Elzo, M and Ahn, S and Driver, JD and Jeong, KC}, title = {Colonization of Beef Cattle by Shiga Toxin-Producing Escherichia coli during the First Year of Life: A Cohort Study.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0148518}, pmid = {26849041}, issn = {1932-6203}, mesh = {Age Factors ; Animals ; Bacterial Shedding ; Body Weight ; Cattle/*microbiology ; Cattle Diseases/epidemiology/*microbiology ; DNA, Bacterial/classification/isolation & purification ; Escherichia coli Infections/epidemiology/*veterinary ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics ; Logistic Models ; Male ; Sex Factors ; Shiga-Toxigenic Escherichia coli/*isolation & purification ; }, abstract = {Each year Shiga toxin-producing Escherichia coli (STEC) are responsible for 2.8 million acute illnesses around the world and > 250,000 cases in the US. Lowering the prevalence of this pathogen in animal reservoirs has the potential to reduce STEC outbreaks in humans by controlling its entrance into the food chain. However, factors that modulate the colonization and persistence of STEC in beef cattle remain largely unidentified. This study evaluated if animal physiological factors such as age, breed, sex, and weight gain influenced the shedding of STEC in beef cattle. A cohort of beef calves (n = 260) from a multi-breed beef calf population was sampled every three months after birth to measure prevalence and concentration of STEC during the first year of life. Metagenomic analysis was also used to understand the association between the STEC colonization and the composition of gut microflora. This study identified that beef calves were more likely to shed STEC during the first 6 months and that STEC shedding decreased as the animal matured. Animal breed group, sex of the calf, and average weight gain were not significantly associated with STEC colonization. The metagenomic analysis revealed for the first time that STEC colonization was correlated with a lower diversity of gut microflora, which increases as the cattle matured. Given these findings, intervention strategies that segregate younger animals, more likely to be colonized by STEC from older animals that are ready to be harvested, could be investigated as a method to reduce zoonotic transmission of STEC from cattle to humans.}, } @article {pmid26848678, year = {2016}, author = {Cai, L and Zhang, R and He, Y and Feng, X and Jiao, N}, title = {Metagenomic Analysis of Virioplankton of the Subtropical Jiulong River Estuary, China.}, journal = {Viruses}, volume = {8}, number = {2}, pages = {}, pmid = {26848678}, issn = {1999-4915}, mesh = {Biodiversity ; China ; Estuaries ; Genome, Viral ; Metagenomics ; Molecular Sequence Data ; Phylogeny ; Rivers/*virology ; Viruses/classification/*genetics/*isolation & purification ; }, abstract = {Viruses are the most abundant biological entities in the oceans, and encompass a significant reservoir of genetic diversity. However, little is known about their biodiversity in estuary environments, which represent a highly dynamic and potentially more diverse habitat. Here, we report a metagenomic analysis of the dsDNA viral community from the Jiulong River Estuary (JRE), China, and provide a comparative analysis with other closely related environments. The results showed that the majority of JRE virome did not show any significant similarity to the database. For the major viral group (Caudovirales) detected in the sample, Podoviridae (44.88%) were the most abundant family, followed by Siphoviridae (32.98%) and Myoviridae (17.32%). The two most abundant viruses identified in the virome were phages HTVC010P and HMO-2011, which infect bacteria belonging to marine SAR11 and SAR116 clades, respectively. Two contigs larger than 20 kb, which show similar overall genome architectures to Celeribacter phage P12053L and Thalosomonas phage BA3, respectively, were generated during assembly. Comparative analysis showed that the JRE virome was more similar to marine viromes than to freshwater viromes, and shared a relative coarse-grain genetic overlap (averaging 14.14% ± 1.68%) with other coastal viromes. Our study indicated that the diversity and community structure of the virioplankton found in JRE were mainly affected by marine waters, with less influence from freshwater discharge.}, } @article {pmid26848568, year = {2016}, author = {Nagpal, S and Haque, MM and Mande, SS}, title = {Vikodak--A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0148347}, pmid = {26848568}, issn = {1932-6203}, mesh = {Algorithms ; Automation, Laboratory ; Metabolic Networks and Pathways/*genetics/physiology ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics/physiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The overall metabolic/functional potential of any given environmental niche is a function of the sum total of genes/proteins/enzymes that are encoded and expressed by various interacting microbes residing in that niche. Consequently, prior (collated) information pertaining to genes, enzymes encoded by the resident microbes can aid in indirectly (re)constructing/ inferring the metabolic/ functional potential of a given microbial community (given its taxonomic abundance profile). In this study, we present Vikodak--a multi-modular package that is based on the above assumption and automates inferring and/ or comparing the functional characteristics of an environment using taxonomic abundance generated from one or more environmental sample datasets. With the underlying assumptions of co-metabolism and independent contributions of different microbes in a community, a concerted effort has been made to accommodate microbial co-existence patterns in various modules incorporated in Vikodak.

RESULTS: Validation experiments on over 1400 metagenomic samples have confirmed the utility of Vikodak in (a) deciphering enzyme abundance profiles of any KEGG metabolic pathway, (b) functional resolution of distinct metagenomic environments, (c) inferring patterns of functional interaction between resident microbes, and (d) automating statistical comparison of functional features of studied microbiomes. Novel features incorporated in Vikodak also facilitate automatic removal of false positives and spurious functional predictions.

CONCLUSIONS: With novel provisions for comprehensive functional analysis, inclusion of microbial co-existence pattern based algorithms, automated inter-environment comparisons; in-depth analysis of individual metabolic pathways and greater flexibilities at the user end, Vikodak is expected to be an important value addition to the family of existing tools for 16S based function prediction.

A web implementation of Vikodak can be publicly accessed at: http://metagenomics.atc.tcs.com/vikodak. This web service is freely available for all categories of users (academic as well as commercial).}, } @article {pmid26842811, year = {2016}, author = {Wang, W and Cao, J and Yang, F and Wang, X and Zheng, S and Sharshov, K and Li, L}, title = {High-throughput sequencing reveals the core gut microbiome of Bar-headed goose (Anser indicus) in different wintering areas in Tibet.}, journal = {MicrobiologyOpen}, volume = {5}, number = {2}, pages = {287-295}, pmid = {26842811}, issn = {2045-8827}, mesh = {Animals ; Biodiversity ; Computational Biology ; *Gastrointestinal Microbiome ; *Geese ; *High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; *Seasons ; Tibet ; }, abstract = {Elucidating the spatial dynamic and core gut microbiome related to wild bar-headed goose is of crucial importance for probiotics development that may meet the demands of bar-headed goose artificial breeding industries and accelerate the domestication of this species. However, the core microbial communities in the wild bar-headed geese remain totally unknown. Here, for the first time, we present a comprehensive survey of bar-headed geese gut microbial communities by Illumina high-throughput sequencing technology using nine individuals from three distinct wintering locations in Tibet. A total of 236,676 sequences were analyzed, and 607 OTUs were identified. We show that the gut microbial communities of bar-headed geese have representatives of 14 phyla and are dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The additive abundance of these four most dominant phyla was above 96% across all the samples. At the genus level, the sequences represented 150 genera. A set of 19 genera were present in all samples and considered as core gut microbiome. The top seven most abundant core genera were distributed in that four dominant phyla. Among them, four genera (Lactococcus, Bacillus, Solibacillus, and Streptococcus) belonged to Firmicutes, while for other three phyla, each containing one genus, such as Proteobacteria (genus Pseudomonas), Actinobacteria (genus Arthrobacter), and Bacteroidetes (genus Bacteroides). This broad survey represents the most in-depth assessment, to date, of the gut microbes that associated with bar-headed geese. These data create a baseline for future bar-headed goose microbiology research, and make an original contribution to probiotics development for bar-headed goose artificial breeding industries.}, } @article {pmid26841726, year = {2016}, author = {Moore, JD and Stegemeier, JP and Bibby, K and Marinakos, SM and Lowry, GV and Gregory, KB}, title = {Impacts of Pristine and Transformed Ag and Cu Engineered Nanomaterials on Surficial Sediment Microbial Communities Appear Short-Lived.}, journal = {Environmental science & technology}, volume = {50}, number = {5}, pages = {2641-2651}, doi = {10.1021/acs.est.5b05054}, pmid = {26841726}, issn = {1520-5851}, mesh = {Bacteria/genetics/*metabolism ; Biodiversity ; Biotransformation ; Copper/*chemistry ; Dynamic Light Scattering ; Geologic Sediments/*microbiology ; Metagenome ; Nanostructures/*chemistry ; Nanotechnology/*methods ; Photosynthesis/genetics ; Porosity ; RNA, Ribosomal, 16S/genetics ; Silver/*chemistry ; Static Electricity ; Water ; }, abstract = {Laboratory-based studies have shown that many soluble metal and metal oxide engineered nanomaterials (ENM) exert strong toxic effects on microorganisms. However, laboratory-based studies lack the complexity of natural systems and often use "as manufactured" ENMs rather than more environmentally relevant transformed ENMs, leaving open the question of whether natural ligands and seasonal variation will mitigate ENM impacts. Because ENMs will accumulate in subaquatic sediments, we examined the effects of pristine and transformed Ag and Cu ENMs on surficial sediment microbial communities in simulated freshwater wetlands. Five identical mesocosms were dosed through the water column with either Ag(0), Ag2S, CuO or CuS ENMs (nominal sizes of 4.67 ± 1.4, 18.1 ± 3.2, 31.1 ± 12, and 12.4 ± 4.1, respectively) or Cu(2+). Microbial communities were examined at 0, 7, 30, 90, 180, and 300 d using qPCR and high-throughput 16S rRNA gene sequencing. Results suggest differential short-term impacts of Ag(0) and Ag2S, similarities between CuO and CuS, and differences between Cu ENMs and Cu(2+). PICRUSt-predicted metagenomes displayed differential effects of Ag treatments on photosynthesis and of Cu treatments on methane metabolism. By 300 d, all metrics pointed to reconvergence of ENM-dosed mesocosm microbial community structure and composition, suggesting that the long-term microbial community impacts from a pulse of Ag or Cu ENMs are limited.}, } @article {pmid26833346, year = {2016}, author = {Jaillard, M and Tournoud, M and Meynier, F and Veyrieras, JB}, title = {Optimization of alignment-based methods for taxonomic binning of metagenomics reads.}, journal = {Bioinformatics (Oxford, England)}, volume = {32}, number = {12}, pages = {1779-1787}, doi = {10.1093/bioinformatics/btw040}, pmid = {26833346}, issn = {1367-4811}, mesh = {Algorithms ; Humans ; Metagenome ; *Metagenomics ; Microbiota ; Models, Theoretical ; }, abstract = {MOTIVATION: Alignment-based taxonomic binning for metagenome characterization proceeds in two steps: reads mapping against a reference database (RDB) and taxonomic assignment according to the best hits. Beyond the sequencing technology and the completeness of the RDB, selecting the optimal configuration of the workflow, in particular the mapper parameters and the best hit selection threshold, to get the highest binning performance remains quite empirical.

RESULTS: We developed a statistical framework to perform such optimization at a minimal computational cost. Using an optimization experimental design and simulated datasets for three sequencing technologies, we built accurate prediction models for five performance indicators and then derived the parameter configuration providing the optimal performance. Whatever the mapper and the dataset, we observed that the optimal configuration yielded better performance than the default configuration and that the best hit selection threshold had a large impact on performance. Finally, on a reference dataset from the Human Microbiome Project, we confirmed that the optimized configuration increased the performance compared with the default configuration.

Not applicable.

CONTACT: magali.dancette@biomerieux.com

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid26832204, year = {2016}, author = {Frey, B and Rime, T and Phillips, M and Stierli, B and Hajdas, I and Widmer, F and Hartmann, M}, title = {Microbial diversity in European alpine permafrost and active layers.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {3}, pages = {}, doi = {10.1093/femsec/fiw018}, pmid = {26832204}, issn = {1574-6941}, mesh = {Bacteria/classification/genetics/*isolation & purification/metabolism ; *Biodiversity ; Carbon/analysis/metabolism ; Metagenomics ; Permafrost/chemistry/*microbiology ; Soil Microbiology ; Switzerland ; }, abstract = {Permafrost represents a largely understudied genetic resource. Thawing of permafrost with global warming will not only promote microbial carbon turnover with direct feedback on greenhouse gases, but also unlock an unknown microbial diversity. Pioneering metagenomic efforts have shed light on the permafrost microbiome in polar regions, but temperate mountain permafrost is largely understudied. We applied a unique experimental design coupled to high-throughput sequencing of ribosomal markers to characterize the microbiota at the long-term alpine permafrost study site 'Muot-da-Barba-Peider' in eastern Switzerland with an approximate radiocarbon age of 12 000 years. Compared to the active layers, the permafrost community was more diverse and enriched with members of the superphylum Patescibacteria (OD1, TM7, GN02 and OP11). These understudied phyla with no cultured representatives proposedly feature small streamlined genomes with reduced metabolic capabilities, adaptations to anaerobic fermentative metabolisms and potential ectosymbiotic lifestyles. The permafrost microbiota was also enriched with yeasts and lichenized fungi known to harbour various structural and functional adaptation mechanisms to survive under extreme sub-zero conditions. These data yield an unprecedented view on microbial life in temperate mountain permafrost, which is increasingly important for understanding the biological dynamics of permafrost in order to anticipate potential ecological trajectories in a warming world.}, } @article {pmid26830979, year = {2016}, author = {Bizzarro, S and Laine, ML and Buijs, MJ and Brandt, BW and Crielaard, W and Loos, BG and Zaura, E}, title = {Microbial profiles at baseline and not the use of antibiotics determine the clinical outcome of the treatment of chronic periodontitis.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {20205}, pmid = {26830979}, issn = {2045-2322}, mesh = {Anti-Bacterial Agents/pharmacology/*therapeutic use ; Chronic Periodontitis/diagnosis/*drug therapy/*microbiology ; Colony Count, Microbial ; Female ; Humans ; Male ; Metagenome ; Metagenomics ; *Microbiota/drug effects ; Prognosis ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; }, abstract = {Antibiotics are often used in the treatment of chronic periodontitis, which is a major cause of tooth loss. However, evidence in favour of a microbial indication for the prescription of antibiotics is lacking, which may increase the risk of the possible indiscriminate use of antibiotics, and consequent, microbial resistance. Here, using an open-ended technique, we report the changes in the subgingival microbiome up to one year post-treatment of patients treated with basic periodontal therapy with or without antibiotics. Antibiotics resulted in a greater influence on the microbiome 3 months after therapy, but this difference disappeared at 6 months. Greater microbial diversity, specific taxa and certain microbial co-occurrences at baseline and not the use of antibiotics predicted better clinical treatment outcomes. Our results demonstrate the predictive value of specific subgingival bacterial profiles for the decision to prescribe antibiotics in the treatment of periodontitis, but they also indicate the need for alternative therapies based on ecological approaches.}, } @article {pmid26829039, year = {2016}, author = {Meisel, JS and Hannigan, GD and Tyldsley, AS and SanMiguel, AJ and Hodkinson, BP and Zheng, Q and Grice, EA}, title = {Skin Microbiome Surveys Are Strongly Influenced by Experimental Design.}, journal = {The Journal of investigative dermatology}, volume = {136}, number = {5}, pages = {947-956}, pmid = {26829039}, issn = {1523-1747}, support = {R01 AR066663/AR/NIAMS NIH HHS/United States ; R01 NR015639/NR/NINR NIH HHS/United States ; T32 AR007465/AR/NIAMS NIH HHS/United States ; T32 HG000046/HG/NHGRI NIH HHS/United States ; R00 AR060873/AR/NIAMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Quality Control ; RNA, Messenger/genetics ; Research Design ; Sequence Analysis, DNA/*methods ; Skin/*microbiology ; Staphylococcus/genetics ; Surveys and Questionnaires ; Tissue Culture Techniques ; }, abstract = {Culture-independent studies to characterize skin microbiota are increasingly common, due in part to affordable and accessible sequencing and analysis platforms. Compared to culture-based techniques, DNA sequencing of the bacterial 16S ribosomal RNA (rRNA) gene or whole metagenome shotgun (WMS) sequencing provides more precise microbial community characterizations. Most widely used protocols were developed to characterize microbiota of other habitats (i.e., gastrointestinal) and have not been systematically compared for their utility in skin microbiome surveys. Here we establish a resource for the cutaneous research community to guide experimental design in characterizing skin microbiota. We compare two widely sequenced regions of the 16S rRNA gene to WMS sequencing for recapitulating skin microbiome community composition, diversity, and genetic functional enrichment. We show that WMS sequencing most accurately recapitulates microbial communities, but sequencing of hypervariable regions 1-3 of the 16S rRNA gene provides highly similar results. Sequencing of hypervariable region 4 poorly captures skin commensal microbiota, especially Propionibacterium. WMS sequencing, which is resource and cost intensive, provides evidence of a community's functional potential; however, metagenome predictions based on 16S rRNA sequence tags closely approximate WMS genetic functional profiles. This study highlights the importance of experimental design for downstream results in skin microbiome surveys.}, } @article {pmid26828871, year = {2017}, author = {Angelakis, E and Lagier, JC}, title = {Samples and techniques highlighting the links between obesity and microbiota.}, journal = {Microbial pathogenesis}, volume = {106}, number = {}, pages = {119-126}, doi = {10.1016/j.micpath.2016.01.024}, pmid = {26828871}, issn = {1096-1208}, mesh = {Bacteria/classification/metabolism ; Food ; *Gastrointestinal Microbiome/genetics/physiology ; Gastrointestinal Tract/*microbiology/surgery ; High-Throughput Screening Assays ; Humans ; Metagenomics/methods ; *Obesity ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {The composition of gut microbiota and its relationship to human health, particularly its links with obesity remain an ongoing challenge for scientists. The current gold standard for exploring human gut microbiota consists of using stool samples and only applying next generations sequencing techniques, which sometimes generate contradictory results. Here, we comprehensively describe nutrient absorption, fat digestion, carbohydrate and protein absorption, demonstrating that absorption of these diverse nutrients occurs mainly in the stomach and small intestine. Indeed, bariatric surgery, including Roux-en-Y, removes part of the upper intestine, resulting in weight loss, while colonic surgery is associated with a stable weight. However, most studies only use stool samples rather than small intestine samples because of the easy with which this can be accessed. Metagenomics studies are associated with several biases such as extraction and primer biases and depth bias, including the more modern platforms. High-throughput culture-dependent techniques, such as culturomics, which uses rapid identification methods such as MALDI-TOF, remain time-consuming, but have demonstrated their complementarity with molecular techniques. In conclusion, we believe that a comprehensive analysis of the relationships between obesity and gut microbiota requires large-scale studies coupling metagenomics and culture-dependent research, in order to analyse both small intestine and stool samples.}, } @article {pmid26828196, year = {2016}, author = {Dominguez-Bello, MG and De Jesus-Laboy, KM and Shen, N and Cox, LM and Amir, A and Gonzalez, A and Bokulich, NA and Song, SJ and Hoashi, M and Rivera-Vinas, JI and Mendez, K and Knight, R and Clemente, JC}, title = {Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer.}, journal = {Nature medicine}, volume = {22}, number = {3}, pages = {250-253}, pmid = {26828196}, issn = {1546-170X}, support = {P30 CA016087/CA/NCI NIH HHS/United States ; P30 CA023100/CA/NCI NIH HHS/United States ; R01 DK090989/DK/NIDDK NIH HHS/United States ; P30CA016087/CA/NCI NIH HHS/United States ; }, mesh = {Bacteroides/genetics ; Cesarean Section/*methods ; Delivery, Obstetric ; Female ; Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Lactobacillus/genetics ; Longitudinal Studies ; Male ; Metagenome ; *Microbiota ; Mouth/*microbiology ; Pilot Projects ; Pregnancy ; Skin/*microbiology ; Vagina/*microbiology ; }, abstract = {Exposure of newborns to the maternal vaginal microbiota is interrupted with cesarean birthing. Babies delivered by cesarean section (C-section) acquire a microbiota that differs from that of vaginally delivered infants, and C-section delivery has been associated with increased risk for immune and metabolic disorders. Here we conducted a pilot study in which infants delivered by C-section were exposed to maternal vaginal fluids at birth. Similarly to vaginally delivered babies, the gut, oral and skin bacterial communities of these newborns during the first 30 d of life was enriched in vaginal bacteria--which were underrepresented in unexposed C-section-delivered infants--and the microbiome similarity to those of vaginally delivered infants was greater in oral and skin samples than in anal samples. Although the long-term health consequences of restoring the microbiota of C-section-delivered infants remain unclear, our results demonstrate that vaginal microbes can be partially restored at birth in C-section-delivered babies.}, } @article {pmid26824357, year = {2016}, author = {Gloux, K and Anba-Mondoloni, J}, title = {Unique β-Glucuronidase Locus in Gut Microbiomes of Crohn's Disease Patients and Unaffected First-Degree Relatives.}, journal = {PloS one}, volume = {11}, number = {1}, pages = {e0148291}, pmid = {26824357}, issn = {1932-6203}, mesh = {Adult ; Amino Acid Motifs ; Bacterial Proteins/chemistry/*genetics/metabolism ; Case-Control Studies ; Crohn Disease/complications/*microbiology/pathology ; Dysbiosis/complications/*microbiology/pathology ; Escherichia coli/classification/genetics/metabolism ; Eubacterium/classification/genetics/metabolism ; Family ; Female ; Firmicutes/classification/genetics/metabolism ; Gastrointestinal Microbiome/*genetics ; Genetic Loci ; Glucuronic Acid/metabolism ; Glucuronidase/chemistry/*genetics/metabolism ; Glucuronides/metabolism ; Humans ; Male ; Membrane Transport Proteins/chemistry/*genetics/metabolism ; Molecular Sequence Data ; *Phylogeny ; Plasmids/chemistry/metabolism ; Risk Factors ; Sequence Alignment ; }, abstract = {Crohn's disease, an incurable chronic inflammatory bowel disease, has been attributed to both genetic predisposition and environmental factors. A dysbiosis of the gut microbiota, observed in numerous patients but also in at least one hundred unaffected first-degree relatives, was proposed to have a causal role. Gut microbiota β-D-glucuronidases (EC 3.2.1.33) hydrolyse β-D-glucuronate from glucuronidated compounds. They include a GUS group, that is homologous to the Escherichia coli GusA, and a BG group, that is homologous to metagenomically identified H11G11 BG and has unidentified natural substrates. H11G11 BG is part of the functional core of the human gut microbiota whereas GusA, known to regenerate various toxic products, is variably found in human subjects. We investigated potential risk markers for Crohn's disease using DNA-sequence-based exploration of the β-D-glucuronidase loci (GUS or Firmicute H11G11-BG and the respective co-encoded glucuronide transporters). Crohn's disease-related microbiomes revealed a higher frequency of a C7D2 glucuronide transporter (12/13) compared to unrelated healthy subjects (8/32). This transporter was in synteny with the potential harmful GUS β-D-glucuronidase as only observed in a Eubacterium eligens plasmid. A conserved NH2-terminal sequence in the transporter (FGDFGND motif) was found in 83% of the disease-related subjects and only in 12% of controls. We propose a microbiota-pathology hypothesis in which the presence of this unique β-glucuronidase locus may contribute to an increase risk for Crohn's disease.}, } @article {pmid26822997, year = {2016}, author = {Bryanskaya, AV and Malup, TK and Lazareva, EV and Taran, OP and Rozanov, AS and Efimov, VM and Peltek, SE}, title = {The role of environmental factors for the composition of microbial communities of saline lakes in the Novosibirsk region (Russia).}, journal = {BMC microbiology}, volume = {16 Suppl 1}, number = {Suppl 1}, pages = {4}, pmid = {26822997}, issn = {1471-2180}, mesh = {Archaea/classification/genetics/*isolation & purification/metabolism ; Bacteria/classification/genetics/*isolation & purification/metabolism ; *Biodiversity ; Lakes/chemistry/*microbiology ; Phylogeny ; Russia ; Sodium Chloride/*analysis/metabolism ; }, abstract = {BACKGROUND: Nothing is currently known about microbial composition of saline lakes of the Novosibirsk region and its dependence on physical-chemical parameters of waters. We studied the structure of microbial communities of saline lakes of the Novosibirsk region and the effect of physical-chemical parameters of waters on microbial communities of these lakes.

RESULTS: According to the ion content, the lakes were classified either as chloride or chloride-sulfate types. Water salinity ranges from 4.3 to 290 g L(-1). Many diverse microbial communities were found. Filamentous and colonial Cyanobacteria of the genera Scytonema, Aphanocapsa, and/or filamentous Algae dominated in littoral communities. Spatial and temporal organization of planktonic microbial communities and the quantities of Archaea and Bacteria were investigated using fluorescent in situ hybridization. We have found that the dominant planktonic component is represented by Archaea, or, less frequently, by Bacteria. Various phylogenetic groups (Bacteria, Archaea, Algae, and Cyanobacteria) are nonuniformly distributed. The principal component analysis was used to detect environmental factors that affect microorganism abundance. We found the principal components responsible for 71.1 % of the observed variation. It was demonstrated that two-block partial least squares was a better method than principal component analysis for analysis of the data. We observed general relationships between microbial abundance and water salinity.

CONCLUSIONS: We have performed the first-ever study of the structure of the microbial communities of eleven saline lakes in the Novosibirsk region along with their physical-chemical parameters of waters. Our study demonstrates that saline lakes in the Novosibirsk region contain a unique microbial communities that may become a prolific source of microorganisms for fundamental and applied studies in various fields of ecology, microbiology, geochemistry, and biotechnology, and deserve further metagenomic investigation.}, } @article {pmid26822785, year = {2016}, author = {Maruthamuthu, M and Jiménez, DJ and Stevens, P and van Elsas, JD}, title = {A multi-substrate approach for functional metagenomics-based screening for (hemi)cellulases in two wheat straw-degrading microbial consortia unveils novel thermoalkaliphilic enzymes.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {86}, pmid = {26822785}, issn = {1471-2164}, mesh = {Carbohydrate Metabolism/genetics ; Cellulases/chemistry/*genetics/metabolism ; Gene Library ; Gene Order ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; *Microbial Consortia/genetics ; Triticum/*microbiology ; Xylosidases/genetics ; alpha-Galactosidase/genetics ; beta-Galactosidase/genetics ; }, abstract = {BACKGROUND: Functional metagenomics is a promising strategy for the exploration of the biocatalytic potential of microbiomes in order to uncover novel enzymes for industrial processes (e.g. biorefining or bleaching pulp). Most current methodologies used to screen for enzymes involved in plant biomass degradation are based on the use of single substrates. Moreover, highly diverse environments are used as metagenomic sources. However, such methods suffer from low hit rates of positive clones and hence the discovery of novel enzymatic activities from metagenomes has been hampered.

RESULTS: Here, we constructed fosmid libraries from two wheat straw-degrading microbial consortia, denoted RWS (bred on untreated wheat straw) and TWS (bred on heat-treated wheat straw). Approximately 22,000 clones from each library were screened for (hemi)cellulose-degrading enzymes using a multi-chromogenic substrate approach. The screens yielded 71 positive clones for both libraries, giving hit rates of 1:440 and 1:1,047 for RWS and TWS, respectively. Seven clones (NT2-2, T5-5, NT18-17, T4-1, 10BT, NT18-21 and T17-2) were selected for sequence analyses. Their inserts revealed the presence of 18 genes encoding enzymes belonging to twelve different glycosyl hydrolase families (GH2, GH3, GH13, GH17, GH20, GH27, GH32, GH39, GH53, GH58, GH65 and GH109). These encompassed several carbohydrate-active gene clusters traceable mainly to Klebsiella related species. Detailed functional analyses showed that clone NT2-2 (containing a beta-galactosidase of ~116 kDa) had highest enzymatic activity at 55 °C and pH 9.0. Additionally, clone T5-5 (containing a beta-xylosidase of ~86 kDa) showed > 90% of enzymatic activity at 55 °C and pH 10.0.

CONCLUSIONS: This study employed a high-throughput method for rapid screening of fosmid metagenomic libraries for (hemi)cellulose-degrading enzymes. The approach, consisting of screens on multi-substrates coupled to further analyses, revealed high hit rates, as compared with recent other studies. Two clones, 10BT and T4-1, required the presence of multiple substrates for detectable activity, indicating a new avenue in library activity screening. Finally, clones NT2-2, T5-5 and NT18-17 were found to encode putative novel thermo-alkaline enzymes, which could represent a starting point for further biotechnological applications.}, } @article {pmid26820746, year = {2016}, author = {Al-Ghalith, GA and Montassier, E and Ward, HN and Knights, D}, title = {NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes.}, journal = {PLoS computational biology}, volume = {12}, number = {1}, pages = {e1004658}, pmid = {26820746}, issn = {1553-7358}, support = {R01 AI121383/AI/NIAID NIH HHS/United States ; UL1 TR000114/TR/NCATS NIH HHS/United States ; R01AI121383/AI/NIAID NIH HHS/United States ; }, mesh = {Chromosome Mapping/*methods ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome/genetics ; Microbiota ; Ribosomes/*genetics ; *Software ; }, abstract = {The explosion of bioinformatics technologies in the form of next generation sequencing (NGS) has facilitated a massive influx of genomics data in the form of short reads. Short read mapping is therefore a fundamental component of next generation sequencing pipelines which routinely match these short reads against reference genomes for contig assembly. However, such techniques have seldom been applied to microbial marker gene sequencing studies, which have mostly relied on novel heuristic approaches. We propose NINJA Is Not Just Another OTU-Picking Solution (NINJA-OPS, or NINJA for short), a fast and highly accurate novel method enabling reference-based marker gene matching (picking Operational Taxonomic Units, or OTUs). NINJA takes advantage of the Burrows-Wheeler (BW) alignment using an artificial reference chromosome composed of concatenated reference sequences, the "concatesome," as the BW input. Other features include automatic support for paired-end reads with arbitrary insert sizes. NINJA is also free and open source and implements several pre-filtering methods that elicit substantial speedup when coupled with existing tools. We applied NINJA to several published microbiome studies, obtaining accuracy similar to or better than previous reference-based OTU-picking methods while achieving an order of magnitude or more speedup and using a fraction of the memory footprint. NINJA is a complete pipeline that takes a FASTA-formatted input file and outputs a QIIME-formatted taxonomy-annotated BIOM file for an entire MiSeq run of human gut microbiome 16S genes in under 10 minutes on a dual-core laptop.}, } @article {pmid26818725, year = {2016}, author = {Mangericao, TC and Peng, Z and Zhang, X}, title = {Computational prediction of CRISPR cassettes in gut metagenome samples from Chinese type-2 diabetic patients and healthy controls.}, journal = {BMC systems biology}, volume = {10 Suppl 1}, number = {Suppl 1}, pages = {5}, pmid = {26818725}, issn = {1752-0509}, mesh = {Algorithms ; China ; Cluster Analysis ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Computational Biology ; Databases, Genetic ; Diabetes Mellitus, Type 2/*genetics ; Gastrointestinal Microbiome/*genetics ; Genome, Microbial ; Humans ; *Metagenome ; Software ; }, abstract = {BACKGROUND: CRISPR has been becoming a hot topic as a powerful technique for genome editing for human and other higher organisms. The original CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats coupled with CRISPR-associated proteins) is an important adaptive defence system for prokaryotes that provides resistance against invading elements such as viruses and plasmids. A CRISPR cassette contains short nucleotide sequences called spacers. These unique regions retain a history of the interactions between prokaryotes and their invaders in individual strains and ecosystems. One important ecosystem in the human body is the human gut, a rich habitat populated by a great diversity of microorganisms. Gut microbiomes are important for human physiology and health. Metagenome sequencing has been widely applied for studying the gut microbiomes. Most efforts in metagenome study has been focused on profiling taxa compositions and gene catalogues and identifying their associations with human health. Less attention has been paid to the analysis of the ecosystems of microbiomes themselves especially their CRISPR composition.

RESULTS: We conducted a preliminary analysis of CRISPR sequences in a human gut metagenomic data set of Chinese individuals of type-2 diabetes patients and healthy controls. Applying an available CRISPR-identification algorithm, PILER-CR, we identified 3169 CRISPR cassettes in the data, from which we constructed a set of 1302 unique repeat sequences and 36,709 spacers. A more extensive analysis was made for the CRISPR repeats: these repeats were submitted to a more comprehensive clustering and classification using the web server tool CRISPRmap. All repeats were compared with known CRISPRs in the database CRISPRdb. A total of 784 repeats had matches in the database, and the remaining 518 repeats from our set are potentially novel ones.

CONCLUSIONS: The computational analysis of CRISPR composition based contigs of metagenome sequencing data is feasible. It provides an efficient approach for finding potential novel CRISPR arrays and for analysing the ecosystem and history of human microbiomes.}, } @article {pmid26817720, year = {2016}, author = {Chan, XY and Hong, KW and Yin, WF and Chan, KG}, title = {Microbiome and Biocatalytic Bacteria in Monkey Cup (Nepenthes Pitcher) Digestive Fluid.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {20016}, pmid = {26817720}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics/metabolism ; Biocatalysis ; Genome, Bacterial ; Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; Tracheophyta/*microbiology ; }, abstract = {Tropical carnivorous plant, Nepenthes, locally known as "monkey cup", utilises its pitcher as a passive trap to capture insects. It then secretes enzymes into the pitcher fluid to digest the insects for nutrients acquisition. However, little is known about the microbiota and their activity in its pitcher fluid. Eighteen bacteria phyla were detected from the metagenome study in the Nepenthes pitcher fluid. Proteobacteria, Bacteroidetes and Actinobacteria are the dominant phyla in the Nepenthes pitcher fluid. We also performed culturomics approach by isolating 18 bacteria from the Nepenthes pitcher fluid. Most of the bacterial isolates possess chitinolytic, proteolytic, amylolytic, and cellulolytic and xylanolytic activities. Fifteen putative chitinase genes were identified from the whole genome analysis on the genomes of the 18 bacteria isolated from Nepenthes pitcher fluid and expressed for chitinase assay. Of these, six clones possessed chitinase activity. In conclusion, our metagenome result shows that the Nepenthes pitcher fluid contains vast bacterial diversity and the culturomic studies confirmed the presence of biocatalytic bacteria within the Nepenthes pitcher juice which may act in symbiosis for the turn over of insects trapped in the Nepenthes pitcher fluid.}, } @article {pmid26817477, year = {2015}, author = {Singh, B and Qin, N and Reid, G}, title = {Microbiome Regulation of Autoimmune, Gut and Liver Associated Diseases.}, journal = {Inflammation & allergy drug targets}, volume = {14}, number = {2}, pages = {84-93}, doi = {10.2174/1871528114666160128150747}, pmid = {26817477}, issn = {2212-4055}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Anti-Bacterial Agents/therapeutic use ; Autoimmune Diseases/epidemiology/immunology/*microbiology/therapy ; Bacteria/drug effects/genetics/*growth & development/immunology ; Fecal Microbiota Transplantation ; Feces/microbiology ; Gastrointestinal Diseases/epidemiology/immunology/*microbiology/therapy ; *Gastrointestinal Microbiome/drug effects ; Gastrointestinal Tract/drug effects/immunology/*microbiology ; Human Migration ; Humans ; Liver Diseases/epidemiology/immunology/*microbiology/therapy ; Protective Factors ; Risk Factors ; }, abstract = {Extensive analysis of the complexity and diversity of microbiota using metagenomics in the gut and other body sites has provided evidence that dysbiosis occurs in many disease states. With the application of next generation sequencing technology this research is starting to uncover the impact of microbiota on metabolic, physiological and immunological pathways and elucidate the cellular and molecular mechanisms involved. To highlight these advances we have focused on autoimmunity and gut and liver related diseases and discuss the opportunities and challenges of translating microbiome research towards its application in humans. Towards this goal we discuss the application of fecal microbiome transplantation (FMT) for the treatment of multiple chronic gut associated inflammatory diseases such as Clostridium difficile infection (CDI) and inflammatory bowel disease (IBD). The potential role of human migration across continents and cultures leading to alteration in their microbiome and its implication in health and disease is also discussed.}, } @article {pmid26814226, year = {2016}, author = {Larsen, PA and Hayes, CE and Williams, CV and Junge, RE and Razafindramanana, J and Mass, V and Rakotondrainibe, H and Yoder, AD}, title = {Blood transcriptomes reveal novel parasitic zoonoses circulating in Madagascar's lemurs.}, journal = {Biology letters}, volume = {12}, number = {1}, pages = {20150829}, pmid = {26814226}, issn = {1744-957X}, support = {S10 OD018164/OD/NIH HHS/United States ; }, mesh = {Animals ; Endangered Species ; Gram-Negative Bacterial Infections/blood/veterinary ; Lemur/blood/*microbiology/*parasitology ; Madagascar ; Protozoan Infections, Animal/blood ; *Transcriptome ; Zoonoses ; }, abstract = {Zoonotic diseases are a looming threat to global populations, and nearly 75% of emerging infectious diseases can spread among wildlife, domestic animals and humans. A 'One World, One Health' perspective offers us an ideal framework for understanding and potentially mitigating the spread of zoonoses, and the island of Madagascar serves as a natural laboratory for conducting these studies. Rapid habitat degradation and climate change on the island are contributing to more frequent contact among humans, livestock and wildlife, increasing the potential for pathogen spillover events. Given Madagascar's long geographical isolation, coupled with recent and repeated introduction of agricultural and invasive species, it is likely that a number of circulating pathogens remain uncharacterized in lemur populations. Thus, it is imperative that new approaches be implemented for de novo pathogen discovery. To this end, we used non-targeted deep sequencing of blood transcriptomes from two species of critically endangered wild lemurs (Indri indri and Propithecus diadema) to characterize blood-borne pathogens. Our results show several undescribed vector-borne parasites circulating within lemurs, some of which may cause disease in wildlife, livestock and humans. We anticipate that advanced methods for de novo identification of unknown pathogens will have broad utility for characterizing other complex disease transmission systems.}, } @article {pmid26811868, year = {2016}, author = {Korpela, K and Salonen, A and Virta, LJ and Kekkonen, RA and Forslund, K and Bork, P and de Vos, WM}, title = {Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {10410}, pmid = {26811868}, issn = {2041-1723}, support = {250172/ERC_/European Research Council/International ; }, mesh = {Anti-Bacterial Agents/adverse effects/*therapeutic use ; Bacteria/classification/genetics/*isolation & purification ; Bacterial Infections/*drug therapy ; Child ; Child, Preschool/statistics & numerical data ; Cohort Studies ; Day Care, Medical/statistics & numerical data ; Feces/microbiology ; Female ; Finland ; Gastrointestinal Microbiome/*drug effects ; Humans ; Macrolides/adverse effects/*therapeutic use ; Male ; }, abstract = {Early-life antibiotic use is associated with increased risk for metabolic and immunological diseases, and mouse studies indicate a causal role of the disrupted microbiome. However, little is known about the impacts of antibiotics on the developing microbiome of children. Here we use phylogenetics, metagenomics and individual antibiotic purchase records to show that macrolide use in 2-7 year-old Finnish children (N=142; sampled at two time points) is associated with a long-lasting shift in microbiota composition and metabolism. The shift includes depletion of Actinobacteria, increase in Bacteroidetes and Proteobacteria, decrease in bile-salt hydrolase and increase in macrolide resistance. Furthermore, macrolide use in early life is associated with increased risk of asthma and predisposes to antibiotic-associated weight gain. Overweight and asthmatic children have distinct microbiota compositions. Penicillins leave a weaker mark on the microbiota than macrolides. Our results support the idea that, without compromising clinical practice, the impact on the intestinal microbiota should be considered when prescribing antibiotics.}, } @article {pmid26811607, year = {2016}, author = {Nosho, K and Sukawa, Y and Adachi, Y and Ito, M and Mitsuhashi, K and Kurihara, H and Kanno, S and Yamamoto, I and Ishigami, K and Igarashi, H and Maruyama, R and Imai, K and Yamamoto, H and Shinomura, Y}, title = {Association of Fusobacterium nucleatum with immunity and molecular alterations in colorectal cancer.}, journal = {World journal of gastroenterology}, volume = {22}, number = {2}, pages = {557-566}, pmid = {26811607}, issn = {2219-2840}, mesh = {*Adaptive Immunity ; Animals ; Biomarkers, Tumor/*genetics/immunology/metabolism ; Colorectal Neoplasms/genetics/immunology/metabolism/*microbiology ; Fusobacterium Infections/genetics/immunology/metabolism/*microbiology ; Fusobacterium nucleatum/immunology/metabolism/*pathogenicity ; *Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Humans ; *Immunity, Innate ; Lymphocyte Activation ; Lymphocytes, Tumor-Infiltrating/immunology/microbiology ; Microsatellite Instability ; T-Lymphocyte Subsets/immunology/microbiology ; Tumor Escape ; Tumor Microenvironment ; }, abstract = {The human intestinal microbiome plays a major role in human health and diseases, including colorectal cancer. Colorectal carcinogenesis represents a heterogeneous process with a differing set of somatic molecular alterations, influenced by diet, environmental and microbial exposures, and host immunity. Fusobacterium species are part of the human oral and intestinal microbiota. Metagenomic analyses have shown an enrichment of Fusobacterium nucleatum (F. nucleatum) in colorectal carcinoma tissue. Using 511 colorectal carcinomas from Japanese patients, we assessed the presence of F. nucleatum. Our results showed that the frequency of F. nucleatum positivity in the Japanese colorectal cancer was 8.6% (44/511), which was lower than that in United States cohort studies (13%). Similar to the United States studies, F. nucleatum positivity in Japanese colorectal cancers was significantly associated with microsatellite instability (MSI)-high status. Regarding the immune response in colorectal cancer, high levels of infiltrating T-cell subsets (i.e., CD3+, CD8+, CD45RO+, and FOXP3+ cells) have been associated with better patient prognosis. There is also evidence to indicate that molecular features of colorectal cancer, especially MSI, influence T-cell-mediated adaptive immunity. Concerning the association between the gut microbiome and immunity, F. nucleatum has been shown to expand myeloid-derived immune cells, which inhibit T-cell proliferation and induce T-cell apoptosis in colorectal cancer. This finding indicates that F. nucleatum possesses immunosuppressive activities by inhibiting human T-cell responses. Certain microRNAs are induced during the macrophage inflammatory response and have the ability to regulate host-cell responses to pathogens. MicroRNA-21 increases the levels of IL-10 and prostaglandin E2, which suppress antitumor T-cell-mediated adaptive immunity through the inhibition of the antigen-presenting capacities of dendritic cells and T-cell proliferation in colorectal cancer cells. Thus, emerging evidence may provide insights for strategies to target microbiota, immune cells and tumor molecular alterations for colorectal cancer prevention and treatment. Further investigation is needed to clarify the association of Fusobacterium with T-cells and microRNA expressions in colorectal cancer.}, } @article {pmid26811460, year = {2016}, author = {Mark Welch, JL and Rossetti, BJ and Rieken, CW and Dewhirst, FE and Borisy, GG}, title = {Biogeography of a human oral microbiome at the micron scale.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {6}, pages = {E791-800}, pmid = {26811460}, issn = {1091-6490}, support = {R01 DE022586/DE/NIDCR NIH HHS/United States ; R13 GM085967/GM/NIGMS NIH HHS/United States ; R37 DE016937/DE/NIDCR NIH HHS/United States ; DE022586/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/*classification ; Dental Plaque/microbiology ; Gingiva/pathology ; Humans ; Metagenomics ; Microbial Consortia ; *Microbiota ; Models, Biological ; Mouth/*microbiology ; *Phylogeography ; Sequence Analysis, DNA ; }, abstract = {The spatial organization of complex natural microbiomes is critical to understanding the interactions of the individual taxa that comprise a community. Although the revolution in DNA sequencing has provided an abundance of genomic-level information, the biogeography of microbiomes is almost entirely uncharted at the micron scale. Using spectral imaging fluorescence in situ hybridization as guided by metagenomic sequence analysis, we have discovered a distinctive, multigenus consortium in the microbiome of supragingival dental plaque. The consortium consists of a radially arranged, nine-taxon structure organized around cells of filamentous corynebacteria. The consortium ranges in size from a few tens to a few hundreds of microns in radius and is spatially differentiated. Within the structure, individual taxa are localized at the micron scale in ways suggestive of their functional niche in the consortium. For example, anaerobic taxa tend to be in the interior, whereas facultative or obligate aerobes tend to be at the periphery of the consortium. Consumers and producers of certain metabolites, such as lactate, tend to be near each other. Based on our observations and the literature, we propose a model for plaque microbiome development and maintenance consistent with known metabolic, adherence, and environmental considerations. The consortium illustrates how complex structural organization can emerge from the micron-scale interactions of its constituent organisms. The understanding that plaque community organization is an emergent phenomenon offers a perspective that is general in nature and applicable to other microbiomes.}, } @article {pmid26809473, year = {2016}, author = {Weir, W and Capewell, P and Foth, B and Clucas, C and Pountain, A and Steketee, P and Veitch, N and Koffi, M and De Meeûs, T and Kaboré, J and Camara, M and Cooper, A and Tait, A and Jamonneau, V and Bucheton, B and Berriman, M and MacLeod, A}, title = {Population genomics reveals the origin and asexual evolution of human infective trypanosomes.}, journal = {eLife}, volume = {5}, number = {}, pages = {e11473}, pmid = {26809473}, issn = {2050-084X}, support = {085349/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Evolution, Molecular ; Humans ; Metagenomics ; Mutation ; *Reproduction, Asexual ; Trypanosoma brucei gambiense/*genetics ; Trypanosomiasis/parasitology ; }, abstract = {Evolutionary theory predicts that the lack of recombination and chromosomal re-assortment in strictly asexual organisms results in homologous chromosomes irreversibly accumulating mutations and thus evolving independently of each other, a phenomenon termed the Meselson effect. We apply a population genomics approach to examine this effect in an important human pathogen, Trypanosoma brucei gambiense. We determine that T.b. gambiense is evolving strictly asexually and is derived from a single progenitor, which emerged within the last 10,000 years. We demonstrate the Meselson effect for the first time at the genome-wide level in any organism and show large regions of loss of heterozygosity, which we hypothesise to be a short-term compensatory mechanism for counteracting deleterious mutations. Our study sheds new light on the genomic and evolutionary consequences of strict asexuality, which this pathogen uses as it exploits a new biological niche, the human population.}, } @article {pmid26807926, year = {2016}, author = {Groah, SL and Pérez-Losada, M and Caldovic, L and Ljungberg, IH and Sprague, BM and Castro-Nallar, E and Chandel, NJ and Hsieh, MH and Pohl, HG}, title = {Redefining Healthy Urine: A Cross-Sectional Exploratory Metagenomic Study of People With and Without Bladder Dysfunction.}, journal = {The Journal of urology}, volume = {196}, number = {2}, pages = {579-587}, doi = {10.1016/j.juro.2016.01.088}, pmid = {26807926}, issn = {1527-3792}, mesh = {Adult ; Biomarkers/urine ; Case-Control Studies ; Cross-Sectional Studies ; Female ; Humans ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Phenotype ; Urinary Bladder, Neurogenic/diagnosis/*microbiology/physiopathology/urine ; Urine/*microbiology ; }, abstract = {PURPOSE: We used the PathoScope platform to perform species level analyses of publicly available, 16S rRNA pyrosequenced, asymptomatic urine data to determine relationships between microbiomes, and clinical and functional phenotypes.

MATERIALS AND METHODS: We reanalyzed previously reported, cross-sectionally acquired urine samples from 47 asymptomatic subjects, including 23 controls and 24 subjects with neuropathic bladder. Urine was originally collected by the usual method of bladder drainage and analyzed by urinalysis, culture and pyrosequencing. Urinalysis and culture values were stratified as leukocyte esterase (0, or 1 or greater), nitrite (positive or negative), pyuria (fewer than 5, or 5 or greater white blood cells per high power field), cloudy urine (positive or negative) and urine culture bacterial growth (less than 50,000, or 50,000 or greater cfu/ml). PathoScope was used for next generation sequencing alignment, bacterial classification and microbial diversity characterization.

RESULTS: Subjects with neuropathic bladder were significantly more likely to have positive leukocyte esterase and pyuria, cloudy urine and bacterial growth. Of 47 samples 23 showed bacterial growth on culture and in all samples bacteria were identified by pyrosequencing. Nonneuropathic bladder urine microbiomes included greater proportions of Lactobacillus crispatus in females and Staphylococcus haemolyticus in males. The Lactobacillus community differed significantly among females depending on bladder function. Irrespective of gender the subjects with neuropathic bladder had greater proportions of Enterococcus faecalis, Proteus mirabilis and Klebsiella pneumonia. In 4 subjects with neuropathic bladder Actinobaculum sp. was detected by sequencing and by PathoScope but not by cultivation and in all cases it was associated with pyuria.

CONCLUSIONS: Using PathoScope plus 16S pyrosequencing we were able to identify unique, phenotype dependent, species level microbes. Novel findings included absent L. crispatus in the urine of females with neuropathic bladder and the presence of Actinobaculum only in subjects with neuropathic bladder.}, } @article {pmid26806545, year = {2016}, author = {Lokesh, J and Kiron, V}, title = {Transition from freshwater to seawater reshapes the skin-associated microbiota of Atlantic salmon.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {19707}, pmid = {26806545}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; *Fresh Water ; Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salmo salar/*microbiology ; *Seawater ; Skin/*microbiology ; }, abstract = {Knowledge concerning shifts in microbiota is important in order to elucidate the perturbations in the mucosal barrier during the transitional life stages of the host. In the present study, a 16S rRNA gene sequencing technique was employed to examine the compositional changes and presumptive functions of the skin-associated bacterial communities of Atlantic salmon reared under controlled laboratory conditions and transferred from freshwater to seawater. Proteobacteria was the dominant phylum in salmon from both freshwater (45%) and seawater (above 89%). Bacteroidetes, Actinobacteria, Firmicutes, Cyanobacteria and Verrucomicrobia were the most abundant phyla in salmon from freshwater. The transition to seawater influenced the OTU richness and evenness. The high abundance (~62%) of the genus Oleispira made Proteobacteria the most significantly abundant phylum in salmon from seawater. The predictive functional profile suggested that the communities had the ability to extract energy from amino acids in order to maintain their metabolism and scavenge and biosynthesise compounds to make structural changes and carry out signalling for their survival. These findings need to be further explored in relation to metabolic processes, the fish genotype, and the environment.}, } @article {pmid26803795, year = {2016}, author = {Dias, MF and Colturato, LF and de Oliveira, JP and Leite, LR and Oliveira, G and Chernicharo, CA and de Araújo, JC}, title = {Metagenomic analysis of a desulphurisation system used to treat biogas from vinasse methanisation.}, journal = {Bioresource technology}, volume = {205}, number = {}, pages = {58-66}, doi = {10.1016/j.biortech.2016.01.007}, pmid = {26803795}, issn = {1873-2976}, mesh = {Bacteria ; *Biofuels ; Biomass ; Bioreactors/*microbiology ; Hydrogen Sulfide/chemistry ; Metagenomics ; *Microbial Consortia ; Saccharum/*metabolism ; Sulfides/*metabolism ; }, abstract = {We investigated the response of microbial community to changes in H2S loading rate in a microaerated desulphurisation system treating biogas from vinasse methanisation. H2S removal efficiency was high, and both COD and DO seemed to be important parameters to biomass activity. DGGE analysis retrieved sequences of sulphide-oxidising bacteria (SOB), such as Thioalkalimicrobium sp. Deep sequencing analysis revealed that the microbial community was complex and remained constant throughout the experiment. Most sequences belonged to Firmicutes and Proteobacteria, and, to a lesser extent, Bacteroidetes, Chloroflexi, and Synergistetes. Despite the high sulphide removal efficiency, the abundance of the taxa of SOB was low, and was negatively affected by the high sulphide loading rate.}, } @article {pmid26802086, year = {2016}, author = {Valles-Colomer, M and Darzi, Y and Vieira-Silva, S and Falony, G and Raes, J and Joossens, M}, title = {Meta-omics in Inflammatory Bowel Disease Research: Applications, Challenges, and Guidelines.}, journal = {Journal of Crohn's & colitis}, volume = {10}, number = {6}, pages = {735-746}, doi = {10.1093/ecco-jcc/jjw024}, pmid = {26802086}, issn = {1876-4479}, mesh = {Bacterial Proteins/genetics/metabolism ; DNA, Bacterial/analysis ; Gastrointestinal Microbiome/*genetics ; Genome ; Humans ; Inflammatory Bowel Diseases/*microbiology ; *Metagenomics ; Proteome ; *Proteomics ; RNA, Bacterial/analysis ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; Transcriptome ; }, abstract = {Meta-omics [metagenomics, metatranscriptomics, and metaproteomics] are rapidly expanding our knowledge of the gut microbiota in health and disease. These technologies are increasingly used in inflammatory bowel disease [IBD] research. Yet, meta-omics data analysis, interpretation, and among-study comparison remain challenging. In this review we discuss the role these techniques are playing in IBD research, highlighting their strengths and limitations. We give guidelines on proper sample collection and preparation methods, and on performing the analyses and interpreting the results, reporting available user-friendly tools and pipelines.}, } @article {pmid26791505, year = {2016}, author = {Schöler, A and de Vries, M and Vestergaard, G and Schloter, M}, title = {Reconstruction of Transformation Processes Catalyzed by the Soil Microbiome Using Metagenomic Approaches.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1399}, number = {}, pages = {197-206}, doi = {10.1007/978-1-4939-3369-3_12}, pmid = {26791505}, issn = {1940-6029}, mesh = {High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; Microbiota/genetics ; Plants/genetics/microbiology ; *Soil Microbiology ; Transformation, Bacterial/*genetics ; }, abstract = {Microorganisms are central players in the turnover of nutrients in soil and drive the decomposition of complex organic materials into simpler forms that can be utilized by other biota. Therefore microbes strongly drive soil quality and ecosystem services provided by soils, including plant yield and quality. Thus it is one of the major goals of soil sciences to describe the most relevant enzymes that are involved in nutrient mobilization and to understand the regulation of gene expression of the corresponding genes. This task is however impeded by the enormous microbial diversity in soils. Indeed, we are far to appreciate the number of species present in 1 g of soil, as well as the major functional traits they carry. Here, also most next-generation sequencing (NGS) approaches fail as immense sequencing efforts are needed to fully uncover the functional diversity of soils. Thus even if a gene of interest can be identified by BLAST similarity analysis, the obtained number of reads by NGS is too low for a quantitative assessment of the gene or for a description of its taxonomic diversity. Here we present an integrated approach, which we termed the second-generation full cycle approach, to quantify the abundance and diversity of key enzymes involved in nutrient mobilization. This approach involves the functional annotation of metagenomic data with a relative low coverage (5 Gbases or less) and the design of highly targeted primer systems to assess the abundance or diversity of enzyme-coding genes that are drivers for a particular transformation step in nutrient turnover.}, } @article {pmid26791496, year = {2016}, author = {Dequiedt, S and Maron, PA and Ranjard, L}, title = {GenoSol Platform: A Logistic and Technical Platform for Conserving and Exploring Soil Microbial Diversity.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1399}, number = {}, pages = {55-60}, doi = {10.1007/978-1-4939-3369-3_3}, pmid = {26791496}, issn = {1940-6029}, mesh = {Bacteria/*genetics/isolation & purification ; Ecology ; Ecosystem ; *Genetic Variation ; *Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {In 2008, the platform "GenoSol" (http://www.dijon.inra.fr/plateforme_genosol) was created at the INRA (French National Institute for Agronomic Research) of Dijon. This platform was launched by several soil microbial ecologist senior scientists to provide a logistics and technical structure dedicated to the acquisition, conservation, characterization, and supply of genetic resources (DNA) of soils from very large-scale samplings (several hundred to several thousand corresponding to large spatial and/or temporal scales). Thanks to this structure metagenomic analysis of soil microbial communities has been standardized as well as a reliable reference system for analysis of the microbial genetic resources of the collected soils (more than 10,000 soil samples to date). This platform also illustrates the usefulness of existing soil archives in providing a readily available source of ecological information that is relevant to microbial ecology, probably more than we can currently fathom.}, } @article {pmid26791101, year = {2016}, author = {Fujimura, R and Kim, SW and Sato, Y and Oshima, K and Hattori, M and Kamijo, T and Ohta, H}, title = {Unique pioneer microbial communities exposed to volcanic sulfur dioxide.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {19687}, pmid = {26791101}, issn = {2045-2322}, mesh = {Carbon/chemistry ; Japan ; Metagenomics ; *Microbiota ; Nitrogen/chemistry ; RNA, Ribosomal, 16S ; *Soil Microbiology ; Sulfur Dioxide/*analysis ; Volcanic Eruptions/*analysis ; }, abstract = {Newly exposed volcanic substrates contain negligible amounts of organic materials. Heterotrophic organisms in newly formed ecosystems require bioavailable carbon and nitrogen that are provided from CO2 and N2 fixation by pioneer microbes. However, the knowledge of initial ecosystem developmental mechanisms, especially the association between microbial succession and environmental change, is still limited. This study reports the unique process of microbial succession in fresh basaltic ash, which was affected by long-term exposure to volcanic sulfur dioxide (SO2). Here we compared the microbial ecosystems among deposits affected by SO2 exposure at different levels. The results of metagenomic analysis suggested the importance of autotrophic iron-oxidizing bacteria, particularly those involved in CO2 and N2 fixation, in the heavily SO2 affected site. Changes in the chemical properties of the deposits after the decline of the SO2 impact led to an apparent decrease in the iron-oxidizer abundance and a possible shift in the microbial community structure. Furthermore, the community structure of the deposits that had experienced lower SO2 gas levels showed higher similarity with that of the control forest soil. Our results implied that the effect of SO2 exposure exerted a selective pressure on the pioneer community structure by changing the surrounding environment of the microbes.}, } @article {pmid26790627, year = {2017}, author = {Rashamuse, K and Sanyika Tendai, W and Mathiba, K and Ngcobo, T and Mtimka, S and Brady, D}, title = {Metagenomic mining of glycoside hydrolases from the hindgut bacterial symbionts of a termite (Trinervitermes trinervoides) and the characterization of a multimodular β-1,4-xylanase (GH11).}, journal = {Biotechnology and applied biochemistry}, volume = {64}, number = {2}, pages = {174-186}, doi = {10.1002/bab.1480}, pmid = {26790627}, issn = {1470-8744}, mesh = {Animals ; Cellulases/chemistry/classification/genetics/isolation & purification ; Gastrointestinal Microbiome/*genetics ; Glycoside Hydrolases/chemistry/classification/*genetics/isolation & purification ; Hydrolysis ; Isoptera/enzymology/genetics/*microbiology ; *Metagenomics ; Protein Conformation ; Structure-Activity Relationship ; Substrate Specificity ; Symbiosis/genetics ; }, abstract = {In recent years, there have been particular emphases worldwide on the development and optimization of bioprocesses for the utilization of biomass. An essential component of the biomass processing conduit has been the need for robust biocatalysts as high-performance tools for both the depolymerization of lignocellulosic biomass and synthesis of new high-value bio-based chemical entities. Through functional screening of the metagenome of the hindgut bacterial symbionts of a termite, Trinervitermes trinervoides, we discovered open reading frames for 25 cellulases and hemicellulases. These were classified into 14 different glycoside hydrolase (GH) families: eight GH family 5; four GH9, two GH13, and one each in GH2, GH10, GH11, GH26, GH29, GH43, GH44, GH45, GH67, and GH94 families. Of these, eight were overexpressed and partially characterized to be shown to be endocellulases (GH5C, GH5E, GH5F, and GH5G), an exocellulase (GH5D), endoxylanases (GH5H and GH11), and an α-fucosidase (GH29). The GH11 (Xyl1) was of particular interest as it was discovered to be a multimodular β-1,4-xylanase, consisting of a catalytic domain and two carbohydrate-binding modules (CBMs). The CBM functions to selectively bind insoluble xylan and increases the rate of hydrolysis. The primary structure of GH11 showed a classical catalytic dyad of glutamic acid residues that generally forms part of the active site in GH11 enzyme family. This endoxylanase was optimal at pH 6 and 50 °C, and generated xylobiose and xylotriose from various xylan sources, including beechwood, birchwood, and wheat arabinoxylan. The catalytic ability of GH11 against natural substrate (e.g., wheat arabinoxylan) renders GH11 as a potential useful biocatalyst in the effective dismantling of complex plant biomass architecture.}, } @article {pmid26787827, year = {2016}, author = {Hu, P and Tom, L and Singh, A and Thomas, BC and Baker, BJ and Piceno, YM and Andersen, GL and Banfield, JF}, title = {Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs.}, journal = {mBio}, volume = {7}, number = {1}, pages = {e01669-15}, pmid = {26787827}, issn = {2150-7511}, mesh = {Alaska ; Anaerobiosis ; Archaea/*classification/genetics/metabolism ; Bacteria/*classification/genetics/metabolism ; *Biota ; Biotransformation ; Fermentation ; Hydrocarbons/metabolism ; *Metagenome ; Metagenomics ; Oil and Gas Fields/*microbiology ; Temperature ; }, abstract = {UNLABELLED: Oil reservoirs are major sites of methane production and carbon turnover, processes with significant impacts on energy resources and global biogeochemical cycles. We applied a cultivation-independent genomic approach to define microbial community membership and predict roles for specific organisms in biogeochemical transformations in Alaska North Slope oil fields. Produced water samples were collected from six locations between 1,128 m (24 to 27°C) and 2,743 m (80 to 83°C) below the surface. Microbial community complexity decreased with increasing temperature, and the potential to degrade hydrocarbon compounds was most prevalent in the lower-temperature reservoirs. Sulfate availability, rather than sulfate reduction potential, seems to be the limiting factor for sulfide production in some of the reservoirs under investigation. Most microorganisms in the intermediate- and higher-temperature samples were related to previously studied methanogenic and nonmethanogenic archaea and thermophilic bacteria, but one candidate phylum bacterium, a member of the Acetothermia (OP1), was present in Kuparuk sample K3. The greatest numbers of candidate phyla were recovered from the mesothermic reservoir samples SB1 and SB2. We reconstructed a nearly complete genome for an organism from the candidate phylum Parcubacteria (OD1) that was abundant in sample SB1. Consistent with prior findings for members of this lineage, the OD1 genome is small, and metabolic predictions support an obligately anaerobic, fermentation-based lifestyle. At moderate abundance in samples SB1 and SB2 were members of bacteria from other candidate phyla, including Microgenomates (OP11), Atribacteria (OP9), candidate phyla TA06 and WS6, and Marinimicrobia (SAR406). The results presented here elucidate potential roles of organisms in oil reservoir biological processes.

IMPORTANCE: The activities of microorganisms in oil reservoirs impact petroleum resource quality and the global carbon cycle. We show that bacteria belonging to candidate phyla are present in some oil reservoirs and provide the first insights into their potential roles in biogeochemical processes based on several nearly complete genomes.}, } @article {pmid26784367, year = {2016}, author = {Hino, A and Maruyama, H and Kikuchi, T}, title = {A novel method to assess the biodiversity of parasites using 18S rDNA Illumina sequencing; parasitome analysis method.}, journal = {Parasitology international}, volume = {65}, number = {5 Pt B}, pages = {572-575}, doi = {10.1016/j.parint.2016.01.009}, pmid = {26784367}, issn = {1873-0329}, abstract = {Understanding parasite diversity has important implications in several research fields, including ecology, evolutionary biology, and epidemiology. Here, we introduce a novel method to assess the biodiversity of parasites-especially those in the host alimentary tract-using an 18S rDNA-based metagenomic approach. The method is easy and quick compared to conventional methods, and does not require dissections of host bodies or identification skills for various parasite species. The use of a "next generation sequencer" in this method allows us to perform the assessment in a high throughput manner, which will increase our knowledge of parasite diversity.}, } @article {pmid26781463, year = {2016}, author = {Zhang, X and Niu, J and Liang, Y and Liu, X and Yin, H}, title = {Metagenome-scale analysis yields insights into the structure and function of microbial communities in a copper bioleaching heap.}, journal = {BMC genetics}, volume = {17}, number = {}, pages = {21}, pmid = {26781463}, issn = {1471-2156}, mesh = {Bacteria/*genetics/isolation & purification/metabolism ; Biodiversity ; Carbon Cycle ; China ; *Copper ; Environmental Microbiology ; Ferrous Compounds/metabolism ; Hydrogen-Ion Concentration ; Hydroxyl Radical/metabolism ; Industrial Microbiology/methods ; *Metagenome ; *Microbiota ; *Mining ; Nitrogen/metabolism ; Solvents ; Sulfur/metabolism ; }, abstract = {BACKGROUND: Metagenomics allows us to acquire the potential resources from both cultivatable and uncultivable microorganisms in the environment. Here, shotgun metagenome sequencing was used to investigate microbial communities from the surface layer of low grade copper tailings that were industrially bioleached at the Dexing Copper Mine, China. A bioinformatics analysis was further performed to elucidate structural and functional properties of the microbial communities in a copper bioleaching heap.

RESULTS: Taxonomic analysis revealed unexpectedly high microbial biodiversity of this extremely acidic environment, as most sequences were phylogenetically assigned to Proteobacteria, while Euryarchaeota-related sequences occupied little proportion in this system, assuming that Archaea probably played little role in the bioleaching systems. At the genus level, the microbial community in mineral surface-layer was dominated by the sulfur- and iron-oxidizing acidophiles such as Acidithiobacillus-like populations, most of which were A. ferrivorans-like and A. ferrooxidans-like groups. In addition, Caudovirales were the dominant viral type observed in this extremely environment. Functional analysis illustrated that the principal participants related to the key metabolic pathways (carbon fixation, nitrogen metabolism, Fe(II) oxidation and sulfur metabolism) were mainly identified to be Acidithiobacillus-like, Thiobacillus-like and Leptospirillum-like microorganisms, indicating their vital roles. Also, microbial community harbored certain adaptive mechanisms (heavy metal resistance, low pH adaption, organic solvents tolerance and detoxification of hydroxyl radicals) as they performed their functions in the bioleaching system.

CONCLUSION: Our study provides several valuable datasets for understanding the microbial community composition and function in the surface-layer of copper bioleaching heap.}, } @article {pmid26780037, year = {2016}, author = {Stefanini, I and Albanese, D and Cavazza, A and Franciosi, E and De Filippo, C and Donati, C and Cavalieri, D}, title = {Dynamic changes in microbiota and mycobiota during spontaneous 'Vino Santo Trentino' fermentation.}, journal = {Microbial biotechnology}, volume = {9}, number = {2}, pages = {195-208}, pmid = {26780037}, issn = {1751-7915}, mesh = {*Biota ; Fermentation ; Fungi/*classification/genetics/*isolation & purification ; Italy ; Metagenomics ; Wine/*microbiology ; }, abstract = {Vino Santo is a sweet wine produced from late harvesting and pressing of Nosiola grapes in a small, well-defined geographical area in the Italian Alps. We used metagenomics to characterize the dynamics of microbial communities in the products of three wineries, resulting from spontaneous fermentation with almost the same timing and procedure. Comparing fermentation dynamics and grape microbial composition, we show a rapid increase in a small number of wine yeast species, with a parallel decrease in complexity. Despite the application of similar protocols, slight changes in the procedures led to significant differences in the microbiota in the three cases of fermentation: (i) fungal content of the must varied significantly in the different wineries, (ii) Pichia membranifaciens persisted in only one of the wineries, (iii) one fermentation was characterized by the balanced presence of Saccharomyces cerevisiae and Hanseniaspora osmophila during the later phases. We suggest the existence of a highly winery-specific 'microbial-terroir' contributing significantly to the final product rather than a regional 'terroir'. Analysis of changes in abundance during fermentation showed evident correlations between different species, suggesting that fermentation is the result of a continuum of interaction between different species and physical-chemical parameters.}, } @article {pmid26778510, year = {2016}, author = {Lindgreen, S and Adair, KL and Gardner, PP}, title = {An evaluation of the accuracy and speed of metagenome analysis tools.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {19233}, pmid = {26778510}, issn = {2045-2322}, mesh = {Computational Biology/methods ; Ecosystem ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Skin/*microbiology ; *Software ; }, abstract = {Metagenome studies are becoming increasingly widespread, yielding important insights into microbial communities covering diverse environments from terrestrial and aquatic ecosystems to human skin and gut. With the advent of high-throughput sequencing platforms, the use of large scale shotgun sequencing approaches is now commonplace. However, a thorough independent benchmark comparing state-of-the-art metagenome analysis tools is lacking. Here, we present a benchmark where the most widely used tools are tested on complex, realistic data sets. Our results clearly show that the most widely used tools are not necessarily the most accurate, that the most accurate tool is not necessarily the most time consuming, and that there is a high degree of variability between available tools. These findings are important as the conclusions of any metagenomics study are affected by errors in the predicted community composition and functional capacity. Data sets and results are freely available from http://www.ucbioinformatics.org/metabenchmark.html.}, } @article {pmid26774270, year = {2016}, author = {Dubinkina, VB and Ischenko, DS and Ulyantsev, VI and Tyakht, AV and Alexeev, DG}, title = {Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis.}, journal = {BMC bioinformatics}, volume = {17}, number = {}, pages = {38}, pmid = {26774270}, issn = {1471-2105}, mesh = {Chromosome Mapping ; Cluster Analysis ; Computational Biology ; Computer Simulation ; Databases, Genetic ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Humans ; *Metagenome ; Metagenomics/*methods ; Models, Molecular ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates classification, clustering and model analysis for testing and refining biological hypotheses. "Shotgun" metagenome is an analytically challenging type of genomic data - containing sequences of all genes from the totality of a complex microbial community. Recently, researchers started to analyze metagenomes using reference-free methods based on the analysis of oligonucleotides (k-mers) frequency spectrum previously applied to isolated genomes. However, little is known about their correlation with the existing approaches for metagenomic feature extraction, as well as the limits of applicability. Here we evaluated a metagenomic pairwise dissimilarity measure based on short k-mer spectrum using the example of human gut microbiota, a biomedically significant object of study.

RESULTS: We developed a method for calculating pairwise dissimilarity (beta-diversity) of "shotgun" metagenomes based on short k-mer spectra (5 ≤ k ≤ 11). The method was validated on simulated metagenomes and further applied to a large collection of human gut metagenomes from the populations of the world (n=281). The k-mer spectrum-based measure was found to behave similarly to one based on mapping to a reference gene catalog, but different from one using a genome catalog. This difference turned out to be associated with a significant presence of viral reads in a number of metagenomes. Simulations showed limited impact of bacterial genetic variability as well as sequencing errors on k-mer spectra. Specific differences between the datasets from individual populations were identified.

CONCLUSIONS: Our approach allows rapid estimation of pairwise dissimilarity between metagenomes. Though we applied this technique to gut microbiota, it should be useful for arbitrary metagenomes, even metagenomes with novel microbiota. Dissimilarity measure based on k-mer spectrum provides a wider perspective in comparison with the ones based on the alignment against reference sequence sets. It helps not to miss possible outstanding features of metagenomic composition, particularly related to the presence of an unknown bacteria, virus or eukaryote, as well as to technical artifacts (sample contamination, reads of non-biological origin, etc.) at the early stages of bioinformatic analysis. Our method is complementary to reference-based approaches and can be easily integrated into metagenomic analysis pipelines.}, } @article {pmid26767716, year = {2017}, author = {Kaakoush, NO and Martire, SI and Raipuria, M and Mitchell, HM and Nielsen, S and Westbrook, RF and Morris, MJ}, title = {Alternating or continuous exposure to cafeteria diet leads to similar shifts in gut microbiota compared to chow diet.}, journal = {Molecular nutrition & food research}, volume = {61}, number = {1}, pages = {}, doi = {10.1002/mnfr.201500815}, pmid = {26767716}, issn = {1613-4133}, mesh = {Adipose Tissue ; Animals ; *Diet ; Diet, Western ; Eating ; Feeding Behavior ; *Gastrointestinal Microbiome/genetics ; Insulin/blood ; Leptin/blood ; Male ; Metagenomics/methods ; Obesity/etiology/*microbiology ; Rats, Sprague-Dawley ; }, abstract = {SCOPE: Overconsumption of energy-rich food is a major contributor to the obesity epidemic. The eating habits of many people are characterized by the cycling between overconsumption of energy-rich foods and dieting, the effects of which on the microbiota are currently unknown.

METHODS AND RESULTS: We compared the fecal microbiota of rats either continuously fed chow or palatable cafeteria diet to a "cycled" group switched between the two diets (chow for 4, cafeteria for 3 days/wk, n = 12/group) over 16 wk. Enriched bacterial metabolic pathways were predicted, and a range of metabolic parameters was correlated to microbial taxa and pathways. Cycled rats showed large excursions in food intake on each diet switch. When switched from chow to cafeteria, they overconsumed, and when switched back to chow they underconsumed relative to those maintained on the two diets. Metabolic parameters of cycled rats were intermediate between those of the other diet groups (p < 0.05). The microbiota of cycled rats was nearly indistinguishable from rats under constant cafeteria diet, and both groups were significantly different to the chow group. Correlation analyses identified microbial metabolic pathways associated with an obese phenotype.

CONCLUSION: These data suggest that continuous or intermittent exposure to palatable foods have similar effects on the gut microbiota.}, } @article {pmid26765226, year = {2016}, author = {Chang, CL and Chung, CY and Kuo, CH and Kuo, TF and Yang, CW and Yang, WC}, title = {Beneficial Effect of Bidens pilosa on Body Weight Gain, Food Conversion Ratio, Gut Bacteria and Coccidiosis in Chickens.}, journal = {PloS one}, volume = {11}, number = {1}, pages = {e0146141}, pmid = {26765226}, issn = {1932-6203}, mesh = {*Animal Feed ; Animals ; *Bidens ; Biodiversity ; Chickens ; Cluster Analysis ; Coccidiosis/*veterinary ; *Gastrointestinal Microbiome ; Poultry Diseases/*parasitology ; *Weight Gain ; }, abstract = {In the interests of food safety and public health, plants and their compounds are now re-emerging as an alternative approach to treat gastrointestinal diseases in chickens. Here, we studied the impact of the edible medicinal plant, B. pilosa, on growth performance, gut bacteria and coccidiosis in chickens. First, we found that B. pilosa significantly elevated body weight gain and lowered feed conversion ratio in chickens. Next, we showed that B. pilosa reduced cecal damage as evidenced by increased hemorrhage, villus destruction and decreased villus-to-crypt ratio in chicken ceca. We also performed pyrosequencing of the PCR ampilcons based on the 16S rRNA genes of gut bacteria in chickens. Metagenomic analysis indicated that the chicken gut bacteria belonged to 6 phyla, 6 classes, 6 orders, 9 families, and 8 genera. More importantly, we found that B. pilosa affected the composition of bacteria. This change in bacteria composition was correlated with body weight gain, feed conversion ratio and gut pathology in chickens. Collectively, this work suggests that B. pilosa has beneficial effects on growth performance and protozoan infection in chickens probably via modulation of gut bacteria.}, } @article {pmid26758568, year = {2016}, author = {Ganju, P and Nagpal, S and Mohammed, MH and Nishal Kumar, P and Pandey, R and Natarajan, VT and Mande, SS and Gokhale, RS}, title = {Microbial community profiling shows dysbiosis in the lesional skin of Vitiligo subjects.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {18761}, pmid = {26758568}, issn = {2045-2322}, mesh = {Adult ; Biodiversity ; *Dysbiosis ; Female ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Skin/*microbiology/pathology ; Vitiligo/*etiology ; Young Adult ; }, abstract = {Healthy human skin harbours a diverse array of microbes that comprise the skin microbiome. Commensal bacteria constitute an important component of resident microbiome and are intricately linked to skin health. Recent studies describe an association between altered skin microbial community and epidemiology of diseases, like psoriasis, atopic dermatitis etc. In this study, we compare the differences in bacterial community of lesional and non-lesional skin of vitiligo subjects. Our study reveals dysbiosis in the diversity of microbial community structure in lesional skin of vitiligo subjects. Although individual specific signature is dominant over the vitiligo-specific microbiota, a clear decrease in taxonomic richness and evenness can be noted in lesional patches. Investigation of community specific correlation networks reveals distinctive pattern of interactions between resident bacterial populations of the two sites (lesional and non-lesional). While Actinobacterial species constitute the central regulatory nodes (w.r.t. degree of interaction) in non-lesional skin, species belonging to Firmicutes dominate on lesional sites. We propose that the changes in taxonomic characteristics of vitiligo lesions, as revealed by our study, could play a crucial role in altering the maintenance and severity of disease. Future studies would elucidate mechanistic relevance of these microbial dynamics that can provide new avenues for therapeutic interventions.}, } @article {pmid26757840, year = {2016}, author = {Wallis, A and Butt, H and Ball, M and Lewis, DP and Bruck, D}, title = {Support for the Microgenderome: Associations in a Human Clinical Population.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {19171}, pmid = {26757840}, issn = {2045-2322}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacteria/classification ; Biodiversity ; Child ; Fatigue Syndrome, Chronic/diagnosis/microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Male ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; Sex Factors ; Young Adult ; }, abstract = {The 'microgenderome' provides a paradigm shift that highlights the role of sex differences in the host-microbiota interaction relevant for autoimmune and neuro-immune conditions. Analysis of cross-sectional self-report and faecal microbial data from 274 patients with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) suggests that commensal gut microorganisms may play both protective and deleterious roles in symptom expression. Results revealed significant sex-specific interactions between Firmicutes (Clostridium, Streptococcus, Lactobacillus and Enterococcus) and ME/CFS symptoms (including neurological, immune and mood symptoms), regardless of compositional similarity in microbial levels across the sexes. Extending animal studies, we provide support for the microgenderome in a human clinical population. Applied and mechanistic research needs to consider sex-interactions when examining the composition and function of human microbiota.}, } @article {pmid26757703, year = {2016}, author = {Jiang, Y and Xiong, X and Danska, J and Parkinson, J}, title = {Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.}, journal = {Microbiome}, volume = {4}, number = {}, pages = {2}, pmid = {26757703}, issn = {2049-2618}, support = {GET-101831//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Brassica/microbiology ; Cattle ; Fermentation ; Gene Ontology ; Hydrothermal Vents/microbiology ; Intestine, Large/microbiology ; Metabolic Networks and Pathways/*genetics ; *Metagenome ; Mice ; Microbiota/*genetics ; Molecular Sequence Annotation ; Permafrost/microbiology ; *Phylogeny ; RNA, Bacterial/*genetics ; RNA, Messenger/*genetics ; Raphanus/microbiology ; Rumen/microbiology ; Sequence Analysis, RNA ; }, abstract = {BACKGROUND: Metatranscriptomics is emerging as a powerful technology for the functional characterization of complex microbial communities (microbiomes). Use of unbiased RNA-sequencing can reveal both the taxonomic composition and active biochemical functions of a complex microbial community. However, the lack of established reference genomes, computational tools and pipelines make analysis and interpretation of these datasets challenging. Systematic studies that compare data across microbiomes are needed to demonstrate the ability of such pipelines to deliver biologically meaningful insights on microbiome function.

RESULTS: Here, we apply a standardized analytical pipeline to perform a comparative analysis of metatranscriptomic data from diverse microbial communities derived from mouse large intestine, cow rumen, kimchi culture, deep-sea thermal vent and permafrost. Sequence similarity searches allowed annotation of 19 to 76% of putative messenger RNA (mRNA) reads, with the highest frequency in the kimchi dataset due to its relatively low complexity and availability of closely related reference genomes. Metatranscriptomic datasets exhibited distinct taxonomic and functional signatures. From a metabolic perspective, we identified a common core of enzymes involved in amino acid, energy and nucleotide metabolism and also identified microbiome-specific pathways such as phosphonate metabolism (deep sea) and glycan degradation pathways (cow rumen). Integrating taxonomic and functional annotations within a novel visualization framework revealed the contribution of different taxa to metabolic pathways, allowing the identification of taxa that contribute unique functions.

CONCLUSIONS: The application of a single, standard pipeline confirms that the rich taxonomic and functional diversity observed across microbiomes is not simply an artefact of different analysis pipelines but instead reflects distinct environmental influences. At the same time, our findings show how microbiome complexity and availability of reference genomes can impact comprehensive annotation of metatranscriptomes. Consequently, beyond the application of standardized pipelines, additional caution must be taken when interpreting their output and performing downstream, microbiome-specific, analyses. The pipeline used in these analyses along with a tutorial has been made freely available for download from our project website: http://www.compsysbio.org/microbiome .}, } @article {pmid26754178, year = {2016}, author = {Bazett, M and Bergeron, ME and Haston, CK}, title = {Streptomycin treatment alters the intestinal microbiome, pulmonary T cell profile and airway hyperresponsiveness in a cystic fibrosis mouse model.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {19189}, pmid = {26754178}, issn = {2045-2322}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Load ; Bone and Bones/drug effects ; Cystic Fibrosis/*complications ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/*drug effects ; Immunomodulation/drug effects ; Immunophenotyping ; Metagenome ; Metagenomics ; Mice ; Mice, Inbred BALB C ; Mice, Transgenic ; Phenotype ; Respiratory Hypersensitivity/*complications/drug therapy/mortality/*pathology ; Streptomycin/*pharmacology ; T-Lymphocyte Subsets/*drug effects/immunology/metabolism/*pathology ; }, abstract = {Cystic fibrosis transmembrane conductance regulator deficient mouse models develop phenotypes of relevance to clinical cystic fibrosis (CF) including airway hyperresponsiveness, small intestinal bacterial overgrowth and an altered intestinal microbiome. As dysbiosis of the intestinal microbiota has been recognized as an important contributor to many systemic diseases, herein we investigated whether altering the intestinal microbiome of BALB/c Cftr(tm1UNC) mice and wild-type littermates, through treatment with the antibiotic streptomycin, affects the CF lung, intestinal and bone disease. We demonstrate that streptomycin treatment reduced the intestinal bacterial overgrowth in Cftr(tm1UNC) mice and altered the intestinal microbiome similarly in Cftr(tm1UNC) and wild-type mice, principally by affecting Lactobacillus levels. Airway hyperresponsiveness of Cftr(tm1UNC) mice was ameliorated with streptomycin, and correlated with Lactobacillus abundance in the intestine. Additionally, streptomycin treated Cftr(tm1UNC) and wild-type mice displayed an increased percentage of pulmonary and mesenteric lymph node Th17, CD8 + IL-17+ and CD8 + IFNγ+ lymphocytes, while the CF-specific increase in respiratory IL-17 producing γδ T cells was decreased in streptomycin treated Cftr(tm1UNC) mice. Bone disease and intestinal phenotypes were not affected by streptomycin treatment. The airway hyperresponsiveness and lymphocyte profile of BALB/c Cftr(tm1UNC) mice were affected by streptomycin treatment, revealing a potential intestinal microbiome influence on lung response in BALB/c Cftr(tm1UNC) mice.}, } @article {pmid26750872, year = {2016}, author = {Fiore-Donno, AM and Weinert, J and Wubet, T and Bonkowski, M}, title = {Metacommunity analysis of amoeboid protists in grassland soils.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {19068}, pmid = {26750872}, issn = {2045-2322}, mesh = {Amoeba/*genetics ; Cluster Analysis ; Genetic Variation ; *Grassland ; *Metagenomics ; Phylogeny ; Principal Component Analysis ; Soil/*parasitology ; }, abstract = {This study reveals the diversity and distribution of two major ubiquitous groups of soil amoebae, the genus Acanthamoeba and the Myxomycetes (plasmodial slime-moulds) that are rarely, if ever, recovered in environmental sampling studies. We analyzed 150 grassland soil samples from three Biodiversity Exploratories study regions in Germany. We developed specific primers targeting the V2 variable region in the first part of the small subunit of the ribosomal RNA gene for high-throughput pyrotag sequencing. From ca. 1 million reads, applying very stringent filtering and clustering parameters to avoid overestimation of the diversity, we obtained 273 acanthamoebal and 338 myxomycete operational taxonomic units (OTUs, 96% similarity threshold). This number is consistent with the genetic diversity known in the two investigated lineages, but unequalled to date by any environmental sampling study. Only very few OTUs were identical to already known sequences. Strikingly different OTUs assemblages were found between the three German regions (PerMANOVA p.value = 0.001) and even between sites of the same region (multiple-site Simpson-based similarity indices <0.4), showing steep biogeographical gradients.}, } @article {pmid26749561, year = {2016}, author = {Caputo, A and Lagier, JC and Azza, S and Robert, C and Mouelhi, D and Fournier, PE and Raoult, D}, title = {Microvirga massiliensis sp. nov., the human commensal with the largest genome.}, journal = {MicrobiologyOpen}, volume = {5}, number = {2}, pages = {307-322}, pmid = {26749561}, issn = {2045-8827}, mesh = {Adolescent ; Alphaproteobacteria/classification/*genetics ; Bacterial Typing Techniques ; Computational Biology/methods ; France ; Gastrointestinal Microbiome/genetics ; *Genome, Bacterial ; *Genomics/methods ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Molecular Sequence Annotation ; Phenotype ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Microvirga massiliensis sp. nov. strain JC119(T) is a bacteria isolated in Marseille from a stool sample collected in Senegal. The 16S rRNA (JF824802) of M. massiliensis JC119(T) revealed 95% sequence identity with Microvirga lotononidis WSM3557(T) (HM362432). This bacterium is aerobic, gram negative, catalase positive, and oxidase negative. The draft genome of M. massiliensis JC119(T) comprises a 9,207,211-bp-long genome that is the largest bacterial genome of an isolate in humans. The genome exhibits a G+C content of 63.28% and contains 8685 protein-coding genes and 77 RNA genes, including 21 rRNA genes. Here, we describe the features of M. massiliensis JC119(T), together with the genome sequence information and its annotation.}, } @article {pmid26749443, year = {2016}, author = {Zheng, J and Xiao, X and Zhang, Q and Yu, M and Xu, J and Qi, C and Wang, T}, title = {The programming effects of nutrition-induced catch-up growth on gut microbiota and metabolic diseases in adult mice.}, journal = {MicrobiologyOpen}, volume = {5}, number = {2}, pages = {296-306}, pmid = {26749443}, issn = {2045-8827}, mesh = {Animals ; Biodiversity ; Body Weight ; Cluster Analysis ; Diet, High-Fat ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Glucose Tolerance Test ; Insulin Resistance ; Lipids/blood ; Male ; Metabolic Diseases/*etiology/metabolism ; Metagenome ; Metagenomics ; Mice ; *Nutritive Value ; }, abstract = {Substantial evidence indicated that catch-up growth could increase the susceptibility to obesity, insulin resistance, and type 2 diabetes mellitus in adulthood. However, investigations into the "programming" effects of catch-up growth on gut microbiota in the offspring are limited. C57/BL6 mice were fed on either low protein (LP) or normal chow (NC) diet throughout gestation and lactation. Then, the offspring were randomly weaned to either NC or high fat (HF) diet until 32 weeks of age, generating four experimental groups: NC-NC, NC-HF, LP-NC, and LP-HF. Metabolic parameters and gut microbiota were examined in the offspring. It showed that the NC-HF and LP-HF offspring displayed higher body weight (P < 0.05), impaired glucose tolerance (P < 0.001), and elevated serum lipids (P < 0.05) at 32 weeks of age. Both the operational taxonomic units (OTUs) and the Shannon indexes (P < 0.05) showed significantly lower microbial diversity in NC-HF and LP-HF offspring. There were significant variations in the compositions of gut microbiota in the NC-HF and LP-HF offspring, compared with NC-NC offspring (P < 0.05). Furthermore, it indicated Lactobacillus percentage was negatively associated with blood glucose concentrations of intraperitoneal glucose tolerance test (r = -0.886, P = 0.019). In conclusion, catch-up growth predisposes the offspring to gut microbiota perturbation, obesity, impaired glucose tolerance, insulin resistance, and dyslipidemia. Our study is novel in showing the "programming" effects of nutrition-induced catch-up growth on gut microbiota and metabolic diseases in later life.}, } @article {pmid26746720, year = {2016}, author = {Heller, D and Helmerhorst, EJ and Gower, AC and Siqueira, WL and Paster, BJ and Oppenheim, FG}, title = {Microbial Diversity in the Early In Vivo-Formed Dental Biofilm.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {6}, pages = {1881-1888}, pmid = {26746720}, issn = {1098-5336}, support = {97577//Canadian Institutes of Health Research/Canada ; U54-TR001012/TR/NCATS NIH HHS/United States ; R37 DE005672/DE/NIDCR NIH HHS/United States ; R01 DE007652/DE/NIDCR NIH HHS/United States ; U54 TR001012/TR/NCATS NIH HHS/United States ; DE05672/DE/NIDCR NIH HHS/United States ; R01 DE021565/DE/NIDCR NIH HHS/United States ; 113166//Canadian Institutes of Health Research/Canada ; AI087803/AI/NIAID NIH HHS/United States ; DE021565/DE/NIDCR NIH HHS/United States ; F31 DE005672/DE/NIDCR NIH HHS/United States ; AI101067/AI/NIAID NIH HHS/United States ; K02 AI101067/AI/NIAID NIH HHS/United States ; 106657//Canadian Institutes of Health Research/Canada ; R01 DE005672/DE/NIDCR NIH HHS/United States ; R01 AI087803/AI/NIAID NIH HHS/United States ; DE07652/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics/*isolation & purification ; *Biodiversity ; Biofilms/*growth & development ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Healthy Volunteers ; Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tooth/*microbiology ; }, abstract = {Although the mature dental biofilm composition is well studied, there is very little information on the earliest phase of in vivo tooth colonization. Progress in dental biofilm collection methodologies and techniques of large-scale microbial identification have made new studies in this field of oral biology feasible. The aim of this study was to characterize the temporal changes and diversity of the cultivable and noncultivable microbes in the early dental biofilm. Samples of early dental biofilm were collected from 11 healthy subjects at 0, 2, 4, and 6 h after removal of plaque and pellicle from tooth surfaces. With the semiquantitative Human Oral Microbiome Identification Microarray (HOMIM) technique, which is based on 16S rRNA sequence hybridizations, plaque samples were analyzed with the currently available 407 HOMIM microbial probes. This led to the identification of at least 92 species, with streptococci being the most abundant bacteria across all time points in all subjects. High-frequency detection was also made with Haemophilus parainfluenzae, Gemella haemolysans, Slackia exigua, and Rothia species. Abundance changes over time were noted for Streptococcus anginosus and Streptococcus intermedius (P = 0.02), Streptococcus mitis bv. 2 (P = 0.0002), Streptococcus oralis (P = 0.0002), Streptococcus cluster I (P = 0.003), G. haemolysans (P = 0.0005), and Stenotrophomonas maltophilia (P = 0.02). Among the currently uncultivable microbiota, eight phylotypes were detected in the early stages of biofilm formation, one belonging to the candidate bacterial division TM7, which has attracted attention due to its potential association with periodontal disease.}, } @article {pmid26746718, year = {2016}, author = {Marquardt, M and Vader, A and Stübner, EI and Reigstad, M and Gabrielsen, TM}, title = {Strong Seasonality of Marine Microbial Eukaryotes in a High-Arctic Fjord (Isfjorden, in West Spitsbergen, Norway).}, journal = {Applied and environmental microbiology}, volume = {82}, number = {6}, pages = {1868-1880}, pmid = {26746718}, issn = {1098-5336}, mesh = {Aquatic Organisms/*classification/genetics/*isolation & purification ; Arctic Regions ; *Biota ; DNA, Ribosomal/chemistry/genetics ; Estuaries ; Eukaryota/*classification/genetics/*isolation & purification ; Metagenomics ; RNA, Ribosomal, 18S/genetics ; Seasons ; Sequence Analysis, DNA ; Svalbard ; }, abstract = {The Adventfjorden time series station (IsA) in Isfjorden, West Spitsbergen, Norway, was sampled frequently from December 2011 to December 2012. The community composition of microbial eukaryotes (size, 0.45 to 10 μm) from a depth of 25 m was determined using 454 sequencing of the 18S V4 region amplified from both DNA and RNA. The compositional changes throughout the year were assessed in relation to in situ fjord environmental conditions. Size fractionation analyses of chlorophyll a showed that the photosynthetic biomass was dominated by small cells (<10 μm) most of the year but that larger cells dominated during the spring and summer. The winter and early-spring communities were more diverse than the spring and summer/autumn communities. Dinophyceae were predominant throughout the year. The Arctic Micromonas ecotype was abundant mostly in the early-bloom and fall periods, whereas heterotrophs, such as marine stramenopiles (MASTs), Picozoa, and the parasitoid marine alveolates (MALVs), displayed higher relative abundance in the winter than in other seasons. Our results emphasize the extreme seasonality of Arctic microbial eukaryotic communities driven by the light regime and nutrient availability but point to the necessity of a thorough knowledge of hydrography for full understanding of their succession and variability.}, } @article {pmid26746713, year = {2016}, author = {Zhong, ZP and Liu, Y and Miao, LL and Wang, F and Chu, LM and Wang, JL and Liu, ZP}, title = {Prokaryotic Community Structure Driven by Salinity and Ionic Concentrations in Plateau Lakes of the Tibetan Plateau.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {6}, pages = {1846-1858}, pmid = {26746713}, issn = {1098-5336}, mesh = {Archaea/classification/genetics/*isolation & purification ; Bacteria/classification/genetics/*isolation & purification ; *Biota ; Chemical Phenomena ; Ions/analysis ; Lakes/*chemistry/*microbiology ; Metagenomics ; *Osmolar Concentration ; *Salinity ; Sequence Analysis, DNA ; Tibet ; }, abstract = {The prokaryotic community composition and diversity and the distribution patterns at various taxonomic levels across gradients of salinity and physiochemical properties in the surface waters of seven plateau lakes in the Qaidam Basin, Tibetan Plateau, were evaluated using Illumina MiSeq sequencing. These lakes included Lakes Keluke (salinity, <1 g/liter), Qing (salinity, 5.5 to 6.6 g/liter), Tuosu (salinity, 24 to 35 g/liter), Dasugan (salinity, 30 to 33 g/liter), Gahai (salinity, 92 to 96 g/liter), Xiaochaidan (salinity, 94 to 99 g/liter), and Gasikule (salinity, 317 to 344 g/liter). The communities were dominated by Bacteria in lakes with salinities of <100 g/liter and by Archaea in Lake Gasikule. The clades At12OctB3 and Salinibacter, previously reported only in hypersaline environments, were found in a hyposaline lake (salinity, 5.5 to 6.6 g/liter) at an abundance of ∼1.0%, indicating their ecological plasticity. Salinity and the concentrations of the chemical ions whose concentrations covary with salinity (Mg(2+), K(+), Cl(-), Na(+), SO4 (2-), and Ca(2+)) were found to be the primary environmental factors that directly or indirectly determined the composition and diversity at the level of individual clades as well as entire prokaryotic communities. The distribution patterns of two phyla, five classes, five orders, five families, and three genera were well predicted by salinity. The variation of the prokaryotic community structure also significantly correlated with the dissolved oxygen concentration, pH, the total nitrogen concentration, and the PO4 (3-) concentration. Such correlations varied depending on the taxonomic level, demonstrating the importance of comprehensive correlation analyses at various taxonomic levels in evaluating the effects of environmental variable factors on prokaryotic community structures. Our findings clarify the distribution patterns of the prokaryotic community composition in plateau lakes at the levels of individual clades as well as whole communities along gradients of salinity and ionic concentrations.}, } @article {pmid26745269, year = {2016}, author = {Lyte, M and Chapel, A and Lyte, JM and Ai, Y and Proctor, A and Jane, JL and Phillips, GJ}, title = {Resistant Starch Alters the Microbiota-Gut Brain Axis: Implications for Dietary Modulation of Behavior.}, journal = {PloS one}, volume = {11}, number = {1}, pages = {e0146406}, pmid = {26745269}, issn = {1932-6203}, support = {UL1 TR000427/TR/NCATS NIH HHS/United States ; P510D11106//PHS HHS/United States ; P51RR000167/RR/NCRR NIH HHS/United States ; R33 MH104198/MH/NIMH NIH HHS/United States ; UL1TR000427/TR/NCATS NIH HHS/United States ; P51 OD011106/OD/NIH HHS/United States ; R01 GM099537/GM/NIGMS NIH HHS/United States ; P51 RR000167/RR/NCRR NIH HHS/United States ; R01GM099537/GM/NIGMS NIH HHS/United States ; }, mesh = {Actinobacteria/classification/genetics/isolation & purification ; Animals ; Anxiety/chemically induced/physiopathology ; Bacillaceae/classification/genetics/isolation & purification ; Behavior, Animal/*drug effects ; Brain/drug effects/metabolism/physiopathology ; Diet ; Dietary Carbohydrates/metabolism/*pharmacology ; Exploratory Behavior/drug effects ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/genetics ; Gastrointestinal Tract/drug effects/metabolism/microbiology ; Humans ; Male ; Maze Learning/drug effects ; Metagenome/*drug effects/genetics ; Mice ; Proteobacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Starch/metabolism/*pharmacology ; Verrucomicrobia/classification/genetics/isolation & purification ; Weight Gain/drug effects ; }, abstract = {The increasing recognition that the gut microbiota plays a central role in behavior and cognition suggests that the manipulation of microbial taxa through diet may provide a means by which behavior may be altered in a reproducible and consistent manner in order to achieve a beneficial outcome for the host. Resistant starch continues to receive attention as a dietary intervention that can benefit the host through mechanisms that include altering the intestinal microbiota. Given the interest in dietary approaches to improve health, the aim of this study was to investigate whether the use of dietary resistant starch in mice to alter the gut microbiota also results in a change in behavior. Forty-eight 6 week-old male Swiss-Webster mice were randomly assigned to 3 treatment groups (n = 16 per group) and fed either a normal corn starch diet (NCS) or diets rich in resistant starches HA7 diet (HA7) or octenyl-succinate HA7 diet (OS-HA7) for 6 week and monitored for weight, behavior and fecal microbiota composition. Animals fed an HA7 diet displayed comparable weight gain over the feeding period to that recorded for NCS-fed animals while OS-HA7 displayed a lower weight gain as compared to either NCS or HA7 animals (ANOVA p = 0.0001; NCS:HA7 p = 0.244; HA7:OS-HA7 p<0.0001; NCS:OS-HA7 p<0.0001). Analysis of fecal microbiota using 16s rRNA gene taxonomic profiling revealed that each diet corresponded with a unique gut microbiota. The distribution of taxonomic classes was dynamic over the 6 week feeding period for each of the diets. At the end of the feeding periods, the distribution of taxa included statistically significant increases in members of the phylum Proteobacteria in OS-HA7 fed mice, while the Verrucomicrobia increased in HA7 fed mice over that of mice fed OS-HA7. At the class level, members of the class Bacilli decreased in the OS-HA7 fed group, and Actinobacteria, which includes the genus Bifidobacteria, was enriched in the HA7 fed group compared to the control diet. Behavioral analysis revealed that animals demonstrated profound anxiety-like behavior as observed by performance on the elevated-plus maze with time spent by the mice in the open arm (ANOVA p = 0.000; NCS:HA7 p = 0.004; NCS:OS-HA7 p = 1.000; HA7:OS-HA7 p = 0.0001) as well as entries in the open arm (ANOVA p = 0.039; NCS:HA7 p = 0.041; HA7:OS-HA7 p = 0.221; NCS:OS-HA7 p = 1.000). Open-field behavior, a measure of general locomotion and exploration, revealed statistically significant differences between groups in locomotion as a measure of transitions across quadrant boundaries. Additionally, the open-field assay revealed decreased exploration as well as decreased rearing in HA7 and OS-HA7 fed mice demonstrating a consistent pattern of increased anxiety-like behavior among these groups. Critically, behavior was not correlated with weight. These results indicate that diets based on resistant starch can be utilized to produce quantifiable changes in the gut microbiota and should be useful to "dial-in" a specific microbiome that is unique to a particular starch composition. However, undesirable effects can also be associated with resistant starch, including lack of weight gain and increased anxiety-like behaviors. These observations warrant careful consideration when developing diets rich in resistant starch in humans and animal models.}, } @article {pmid26739424, year = {2016}, author = {Liu, Y and Liu, Y and Zhou, H and Li, L and Zheng, J and Zhang, X and Zheng, J and Pan, G}, title = {Abundance, composition and activity of denitrifier communities in metal polluted paddy soils.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {19086}, pmid = {26739424}, issn = {2045-2322}, mesh = {China ; *Denitrification ; Metagenome ; Metagenomics/methods ; Metals, Heavy/*chemistry ; *Microbiota ; *Oryza ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants/*chemistry ; }, abstract = {Denitrification is one of the most important soil microbial processes leading to the production of nitrous oxide (N2O). The potential changes with metal pollution in soil microbial community for N2O production and reduction are not well addressed. In this study, topsoil samples were collected both from polluted and non-polluted rice paddy fields and denitrifier communities were characterized with molecular fingerprinting procedures. All the retrieved nirK sequences could be grouped into neither α- nor β- proteobacteria, while most of the nosZ sequences were affiliated with α-proteobacteria. The abundances of the nirK and nosZ genes were reduced significantly in the two polluted soils. Thus, metal pollution markedly affected composition of both nirK and nosZ denitrifiers. While the total denitrifying activity and N2O production rate were both reduced under heavy metal pollution of the two sites, the N2O reduction rate showed no significant change. These findings suggest that N2O production activity could be sensitive to heavy metal pollution, which could potentially lead to a decrease in N2O emission in polluted paddies. Therefore, metal pollution could have potential impacts on soil N transformation and thus on N2O emission from paddy soils.}, } @article {pmid26738556, year = {2016}, author = {Fitzpatrick, D and Walsh, F}, title = {Antibiotic resistance genes across a wide variety of metagenomes.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {2}, pages = {}, doi = {10.1093/femsec/fiv168}, pmid = {26738556}, issn = {1574-6941}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/*genetics ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenome/drug effects/*genetics ; Metagenomics ; Plants/microbiology ; Soil Microbiology ; Tetracycline Resistance/genetics ; beta-Lactamases/genetics ; }, abstract = {The distribution of potential clinically relevant antibiotic resistance (AR) genes across soil, water, animal, plant and human microbiomes is not well understood. We aimed to investigate if there were differences in the distribution and relative abundances of resistance genes across a variety of ecological niches. All sequence reads (human, animal, water, soil, plant and insect metagenomes) from the MG-RAST database were downloaded and assembled into a local sequence database. We show that there are many reservoirs of the basic form of resistance genes e.g. blaTEM, but the human and mammalian gut microbiomes contain the widest diversity of clinically relevant resistance genes using metagenomic analysis. The human microbiomes contained a high relative abundance of resistance genes, while the relative abundances varied greatly in the marine and soil metagenomes, when datasets with greater than one million genes were compared. While these results reflect a bias in the distribution of AR genes across the metagenomes, we note this interpretation with caution. Metagenomics analysis includes limits in terms of detection and identification of AR genes in complex and diverse microbiome population. Therefore, if we do not detect the AR gene is it in fact not there or just below the limits of our techniques?}, } @article {pmid26738553, year = {2016}, author = {Colombo, S and Arioli, S and Guglielmetti, S and Lunelli, F and Mora, D}, title = {Virome-associated antibiotic-resistance genes in an experimental aquaculture facility.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {3}, pages = {}, doi = {10.1093/femsec/fiw003}, pmid = {26738553}, issn = {1574-6941}, mesh = {Anti-Bacterial Agents/*pharmacology ; Aquaculture ; Bacteria/classification/*drug effects/*genetics/isolation & purification ; Bacterial Proteins/*genetics ; Bacteriophages/classification/genetics/*isolation & purification ; Drug Resistance, Microbial/genetics ; Metagenome/drug effects ; Metagenomics ; Microbiota ; Open Reading Frames ; Wastewater/microbiology/virology ; }, abstract = {We report the comprehensive characterization of viral and microbial communities within an aquaculture wastewater sample, by a shotgun sequencing and 16S rRNA gene profiling metagenomic approach. Caudovirales had the largest representation within the sample, with over 50% of the total taxonomic abundance, whereas approximately 30% of the total open reading frames (ORFs) identified were from eukaryotic viruses (Mimiviridae and Phycodnaviridae). Antibiotic resistance genes (ARGs) within the virome accounted for 0.85% of the total viral ORFs and showed a similar distribution both in virome and in microbiome. Among the ARGs, those encoding proteins involved in the modulation of antibiotic efflux pumps were the most abundant. Interestingly, the taxonomy of the bacterial ORFs identified in the viral metagenome did not reflect the microbial taxonomy as deduced by 16S rRNA gene profiling and shotgun metagenomic analysis. A limited number of ARGs appeared to be mobilized from bacteria to phages or vice versa, together with other bacterial genes encoding products involved in general metabolic functions, even in the absence of any antibiotic treatment within the aquaculture plant. Thus, these results confirm the presence of a complex phage-bacterial network in the aquaculture environment.}, } @article {pmid26731732, year = {2016}, author = {Porter, TM and Shokralla, S and Baird, D and Golding, GB and Hajibabaei, M}, title = {Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas.}, journal = {PloS one}, volume = {11}, number = {1}, pages = {e0142759}, pmid = {26731732}, issn = {1932-6203}, mesh = {Alberta ; *Biota ; Chloroplast Proteins/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Fungal/*analysis ; DNA, Plant/*analysis ; DNA, Ribosomal/*analysis ; DNA, Ribosomal Spacer/*analysis ; Fungi/classification/genetics ; Genetic Markers ; *High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Plant Proteins/*genetics ; Plastids/*chemistry ; Ribulose-Bisphosphate Carboxylase/*genetics ; Sequence Homology, Nucleic Acid ; Soil/*chemistry ; *Soil Microbiology ; Species Specificity ; *Wetlands ; }, abstract = {Though the use of metagenomic methods to sample below-ground fungal communities is common, the use of similar methods to sample plants from their underground structures is not. In this study we use high throughput sequencing of the ribulose-bisphosphate carboxylase large subunit (rbcL) plastid marker to study the plant community as well as the internal transcribed spacer and large subunit ribosomal DNA (rDNA) markers to investigate the fungal community from two wetland sites. Observed community richness and composition varied by marker. The two rDNA markers detected complementary sets of fungal taxa and total fungal composition clustered according to primer rather than by site. The composition of the most abundant plants, however, clustered according to sites as expected. We suggest that future studies consider using multiple genetic markers, ideally generated from different primer sets, to detect a more taxonomically diverse suite of taxa compared with what can be detected by any single marker alone. Conclusions drawn from the presence of even the most frequently observed taxa should be made with caution without corroborating lines of evidence.}, } @article {pmid26729718, year = {2016}, author = {Simmons, MP and Sudek, S and Monier, A and Limardo, AJ and Jimenez, V and Perle, CR and Elrod, VA and Pennington, JT and Worden, AZ}, title = {Abundance and Biogeography of Picoprasinophyte Ecotypes and Other Phytoplankton in the Eastern North Pacific Ocean.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {6}, pages = {1693-1705}, pmid = {26729718}, issn = {1098-5336}, mesh = {Chlorophyta/*classification/genetics ; DNA, Plant/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Ecotype ; Metagenomics ; Pacific Ocean ; Phylogeography ; Phytoplankton/*classification/genetics/*isolation & purification ; RNA, Ribosomal, 18S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Eukaryotic algae within the picoplankton size class (≤2 μm in diameter) are important marine primary producers, but their spatial and ecological distributions are not well characterized. Here, we studied three picoeukaryotic prasinophyte genera and their cyanobacterial counterparts, Prochlorococcus and Synechococcus, during two cruises along a North Pacific transect characterized by different ecological regimes. Picoeukaryotes and Synechococcus reached maximum abundances of 1.44 × 10(5) and 3.37 × 10(5) cells · ml(-1), respectively, in mesotrophic waters, while Prochlorococcus reached 1.95 × 10(5) cells · ml(-1) in the oligotrophic ocean. Of the picoeukaryotes, Bathycoccus was present at all stations in both cruises, reaching 21,368 ± 327 18S rRNA gene copies · ml(-1). Micromonas and Ostreococcus clade OI were detected only in mesotrophic and coastal waters and Ostreococcus clade OII only in the oligotrophic ocean. To resolve proposed Bathycoccus ecotypes, we established genetic distances for 1,104 marker genes using targeted metagenomes and the Bathycoccus prasinos genome. The analysis was anchored in comparative genome analysis of three Ostreococcus species for which physiological and environmental data are available to facilitate data interpretation. We established that two Bathycoccus ecotypes exist, named here BI (represented by coastal isolate Bathycoccus prasinos) and BII. These share 82% ± 6% nucleotide identity across homologs, while the Ostreococcus spp. share 75% ± 8%. We developed and applied an analysis of ecomarkers to metatranscriptomes sequenced here and published -omics data from the same region. The results indicated that the Bathycoccus ecotypes cooccur more often than Ostreococcus clades OI and OII do. Exploratory analyses of relative transcript abundances suggest that Bathycoccus NRT2.1 and AMT2.2 are high-affinity NO3 (-) and low-affinity NH4 (+) transporters, respectively, with close homologs in multiple picoprasinophytes. Additionally, in the open ocean, where dissolved iron concentrations were low (0.08 nM), there appeared to be a shift to the use of nickel superoxide dismutases (SODs) from Mn/Fe/Cu SODs closer inshore. Our study documents the distribution of picophytoplankton along a North Pacific ecological gradient and offers new concepts and techniques for investigating their biogeography.}, } @article {pmid26729711, year = {2016}, author = {Mehrshad, M and Amoozegar, MA and Ghai, R and Shahzadeh Fazeli, SA and Rodriguez-Valera, F}, title = {Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes in the Brackish Waters of the Caspian Sea.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {5}, pages = {1599-1612}, pmid = {26729711}, issn = {1098-5336}, mesh = {Archaea/classification/genetics/*isolation & purification ; Bacteria/classification/genetics/*isolation & purification ; *Biota ; Fresh Water/*microbiology ; Genome, Archaeal ; Genome, Bacterial ; *Metagenomics ; Molecular Sequence Data ; Phylogeny ; *Saline Waters ; Sequence Analysis, DNA ; }, abstract = {We present here the findings from a study of the microbiome of the southern basin of the Caspian Sea, the largest water body on Earth disconnected from any ocean and a brackish inland sea. By high-throughput metagenomics, we were able to reconstruct the genomes of representative microbes. The gross community structure (at the phylum level) was different from the structure of typical marine and freshwater communities in temperate open oceans, with the Caspian Sea having freshwater-like amounts of Actinobacteria and Alphaproteobacteria, while Gammaproteobacteria and Betaproteobacteria were present at intermediate levels. We assembled the genomes of several groups and provide detailed descriptions of partial genomes from Actinobacteria, Thaumarchaea, and Alphaproteobacteria. Most belonged to hitherto unknown groups, although they were related to either marine or freshwater groups. The phylogenetic placement of the Caspian genomes indicates that the organisms have multiple and separate phylogenetic origins and that they are related to organisms with both freshwater and marine lineages. Comparative recruitment from global aquatic metagenomes indicated that most Caspian microbes are endemic. However, some Caspian genomes were recruited significantly from either marine water (a member of the Alphaproteobacteria) or freshwater (a member of the Actinobacteria). Reciprocally, some genomes of other origins, such as the marine thaumarchaeon " Candidatus Nitrosopelagicus" or the actinobacterium "Candidatus Actinomarina," were recruited from the Caspian Sea, indicating some degree of overlap with the microbiota of other water bodies. Some of these microbes seem to have a remarkably widespread geographic and environmental distribution.}, } @article {pmid26729566, year = {2016}, author = {Yang, I and Woltemate, S and Piazuelo, MB and Bravo, LE and Yepez, MC and Romero-Gallo, J and Delgado, AG and Wilson, KT and Peek, RM and Correa, P and Josenhans, C and Fox, JG and Suerbaum, S}, title = {Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {18594}, pmid = {26729566}, issn = {2045-2322}, support = {R01 DK053620/DK/NIDDK NIH HHS/United States ; P01 CA028842/CA/NCI NIH HHS/United States ; R01 CA077955/CA/NCI NIH HHS/United States ; R01 CA190612/CA/NCI NIH HHS/United States ; P01 CA28842/CA/NCI NIH HHS/United States ; R01 CA77955/CA/NCI NIH HHS/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; R01 AT004821/AT/NCCIH NIH HHS/United States ; P30 ES002109/ES/NIEHS NIH HHS/United States ; P01 CA116087/CA/NCI NIH HHS/United States ; I01 BX001453/BX/BLRD VA/United States ; R01 DK058587/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Colombia/epidemiology ; Female ; Helicobacter Infections/complications/microbiology ; Helicobacter pylori/genetics ; Humans ; Male ; Metagenome ; Metagenomics ; *Microbiota ; Middle Aged ; Risk ; Stomach/*microbiology ; Stomach Neoplasms/diagnosis/*epidemiology/*etiology ; }, abstract = {Inhabitants of Túquerres in the Colombian Andes have a 25-fold higher risk of gastric cancer than inhabitants of the coastal town Tumaco, despite similar H. pylori prevalences. The gastric microbiota was recently shown in animal models to accelerate the development of H. pylori-induced precancerous lesions. 20 individuals from each town, matched for age and sex, were selected, and gastric microbiota analyses were performed by deep sequencing of amplified 16S rDNA. In parallel, analyses of H. pylori status, carriage of the cag pathogenicity island and assignment of H. pylori to phylogeographic groups were performed to test for correlations between H. pylori strain properties and microbiota composition. The gastric microbiota composition was highly variable between individuals, but showed a significant correlation with the town of origin. Multiple OTUs were detected exclusively in either Tumaco or Túquerres. Two operational taxonomic units (OTUs), Leptotrichia wadei and a Veillonella sp., were significantly more abundant in Túquerres, and 16 OTUs, including a Staphylococcus sp. were significantly more abundant in Tumaco. There was no significant correlation of H. pylori phylogeographic population or carriage of the cagPAI with microbiota composition. From these data, testable hypotheses can be generated and examined in suitable animal models and prospective clinical trials.}, } @article {pmid26728449, year = {2016}, author = {Gonzalez-Martinez, A and Rodriguez-Sanchez, A and Lotti, T and Garcia-Ruiz, MJ and Osorio, F and Gonzalez-Lopez, J and van Loosdrecht, MC}, title = {Comparison of bacterial communities of conventional and A-stage activated sludge systems.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {18786}, pmid = {26728449}, issn = {2045-2322}, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; Bioreactors ; Environment ; Metagenome ; *Microbiota ; Phylogeny ; Sewage/*microbiology ; Wastewater/microbiology ; }, abstract = {The bacterial community structure of 10 different wastewater treatment systems and their influents has been investigated through pyrosequencing, yielding a total of 283486 reads. These bioreactors had different technological configurations: conventional activated sludge (CAS) systems and very highly loaded A-stage systems. A-stage processes are proposed as the first step in an energy producing municipal wastewater treatment process. Pyrosequencing analysis indicated that bacterial community structure of all influents was similar. Also the bacterial community of all CAS bioreactors was similar. Bacterial community structure of A-stage bioreactors showed a more case-specific pattern. A core of genera was consistently found for all influents, all CAS bioreactors and all A-stage bioreactors, respectively, showing that different geographical locations in The Netherlands and Spain did not affect the functional bacterial communities in these technologies. The ecological roles of these bacteria were discussed. Influents and A-stage bioreactors shared several core genera, while none of these were shared with CAS bioreactors communities. This difference is thought to reside in the different operational conditions of the two technologies. This study shows that bacterial community structure of CAS and A-stage bioreactors are mostly driven by solids retention time (SRT) and hydraulic retention time (HRT), as suggested by multivariate redundancy analysis.}, } @article {pmid26727463, year = {2016}, author = {Liu, G and Weston, CQ and Pham, LK and Waltz, S and Barnes, H and King, P and Sphar, D and Yamamoto, RT and Forsyth, RA}, title = {Epigenetic Segregation of Microbial Genomes from Complex Samples Using Restriction Endonucleases HpaII and McrB.}, journal = {PloS one}, volume = {11}, number = {1}, pages = {e0146064}, pmid = {26727463}, issn = {1932-6203}, mesh = {5-Methylcytosine/*analysis ; CpG Islands/genetics ; DNA Methylation ; *DNA Restriction Enzymes/isolation & purification/metabolism ; DNA, Bacterial/genetics/*isolation & purification ; DNA, Fungal/genetics/*isolation & purification ; DNA, Plant/genetics/*isolation & purification ; DNA, Protozoan/genetics/*isolation & purification ; DNA, Viral/genetics/*isolation & purification ; *Deoxyribonuclease HpaII/isolation & purification/metabolism ; *Escherichia coli Proteins/isolation & purification/metabolism ; Gene Library ; Genetics, Microbial/*methods ; Genomics/*methods ; Humans ; *Metagenome ; Microbiota/genetics ; Sequence Analysis, DNA ; Sputum/microbiology ; Substrate Specificity ; }, abstract = {We describe continuing work to develop restriction endonucleases as tools to enrich targeted genomes of interest from diverse populations. Two approaches were developed in parallel to segregate genomic DNA based on cytosine methylation. First, the methyl-sensitive endonuclease HpaII was used to bind non-CG methylated DNA. Second, a truncated fragment of McrB was used to bind CpG methylated DNA. Enrichment levels of microbial genomes can exceed 100-fold with HpaII allowing improved genomic detection and coverage of otherwise trace microbial genomes from sputum. Additionally, we observe interesting enrichment results that correlate with the methylation states not only of bacteria, but of fungi, viruses, a protist and plants. The methods presented here offer promise for testing biological samples for pathogens and global analysis of population methylomes.}, } @article {pmid26721429, year = {2016}, author = {Wang, Y and Lei, X and Wang, S and Wang, Z and Song, N and Zeng, F and Chen, T}, title = {Effect of k-tuple length on sample-comparison with high-throughput sequencing data.}, journal = {Biochemical and biophysical research communications}, volume = {469}, number = {4}, pages = {1021-1027}, doi = {10.1016/j.bbrc.2015.11.094}, pmid = {26721429}, issn = {1090-2104}, mesh = {Algorithms ; Bacteria/classification/*genetics/isolation & purification ; Base Sequence ; Data Mining/*methods ; Databases, Genetic ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome/*genetics ; Microbiota/*genetics ; Molecular Sequence Data ; Natural Language Processing ; Pattern Recognition, Automated/methods ; Reproducibility of Results ; *Sample Size ; Sensitivity and Specificity ; Sequence Analysis, DNA/methods ; }, abstract = {The high-throughput metagenomic sequencing offers a powerful technique to compare the microbial communities. Without requiring extra reference sequences, alignment-free models with short k-tuple (k = 2-10 bp) yielded promising results. Short k-tuples describe the overall statistical distribution, but is hard to capture the specific characteristics inside one microbial community. Longer k-tuple contains more abundant information. However, because the frequency vector of long k-tuple(k ≥ 30 bp) is sparse, the statistical measures designed for short k-tuples are not applicable. In our study, we considered each tuple as a meaningful word and then each sequencing data as a document composed of the words. Therefore, the comparison between two sequencing data is processed as "topic analysis of documents" in text mining. We designed a pipeline with long k-tuple features to compare metagenomic samples combined using algorithms from text mining and pattern recognition. The pipeline is available at http://culotuple.codeplex.com/. Experiments show that our pipeline with long k-tuple features: ①separates genomes with high similarity; ②outperforms short k-tuple models in all experiments. When k ≥ 12, the short k-tuple measures are not applicable anymore. When k is between 20 and 40, long k-tuple pipeline obtains much better grouping results; ③is free from the effect of sequencing platforms/protocols. ③We obtained meaningful and supported biological results on the 40-tuples selected for comparison.}, } @article {pmid26719306, year = {2016}, author = {Kabeerdoss, J and Sandhya, P and Danda, D}, title = {Gut inflammation and microbiome in spondyloarthritis.}, journal = {Rheumatology international}, volume = {36}, number = {4}, pages = {457-468}, pmid = {26719306}, issn = {1437-160X}, mesh = {Animals ; Anti-Bacterial Agents/therapeutic use ; Bacteria/immunology/*pathogenicity ; Cytokines/immunology ; Disease Models, Animal ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Humans ; Inflammation Mediators/immunology ; Inflammatory Bowel Diseases/immunology/microbiology ; Intestines/*microbiology ; Prebiotics ; Probiotics/therapeutic use ; Signal Transduction ; Spondylarthritis/immunology/*microbiology/therapy ; }, abstract = {Spondyloarthritis (SpA) is chronic inflammatory disease involving joints and the spine. Bowel inflammation is common in SpA, which may be classified as acute or chronic. Chronic gut inflammation is most common in SpA patients with axial involvement as compared to those presenting with peripheral involvement alone. The pathogenesis of gut inflammation in SpA could be explained by two factors-over-activation of immunological cells and altered gut microbiome. This is exemplified by SpA animal models, namely HLA-B27-expressing transgenic animals and SKG mice models. Immunological mechanisms include homing of activated T cells from gut into synovium, excess pro-inflammatory cytokines secretion by immune cells such as IL-23 and genetic variations in immunological genes. The evidence for role of gut microbiome in SpA is gradually emerging. Recently, metagenomic study of gut microbiome by sequencing of microbial nucleic acids has enabled identification of new microbial taxa and their functions in gut of patients with SpA. In SpA, the gut microbiome could emerge as diagnostic and prognostic marker of disease. Modulation of gut microbiome is slated to have therapeutic potential as well.}, } @article {pmid26718942, year = {2016}, author = {Tejesvi, MV and Arvonen, M and Kangas, SM and Keskitalo, PL and Pirttilä, AM and Karttunen, TJ and Vähäsalo, P}, title = {Faecal microbiome in new-onset juvenile idiopathic arthritis.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {35}, number = {3}, pages = {363-370}, pmid = {26718942}, issn = {1435-4373}, mesh = {Anti-Inflammatory Agents, Non-Steroidal/therapeutic use ; Antibodies, Antinuclear/immunology ; Arthritis, Juvenile/diagnosis/drug therapy/*etiology ; Case-Control Studies ; Child ; Child, Preschool ; Computational Biology/methods ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome ; Genes, Bacterial ; Genes, rRNA ; HLA-B27 Antigen/immunology ; Humans ; Male ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Alterations in the intestinal microbial flora have been linked with autoimmune diseases. Our objective was to analyse the composition of the faecal microbiome of children with new-onset juvenile idiopathic arthritis (JIA) compared to healthy controls, and to identify specific gut bacteria associated with JIA. Stool samples from patients were taken at the time of diagnosis of JIA. The microbiome profiles of samples of 30 children with JIA (mean age 6.2 years, 22 girls) were analysed with 16S region-based sequencing profiling and compared to the stool samples of healthy controls (n = 27, mean age 5.4 years, 18 girls). The proportion of bacteria belonging to the phylum Firmicutes was significantly lower in children with JIA [21 % (95 % confident interval [CI]: 17-25 %)] compared to controls [33 % (95 % CI: 26-41 %), p = 0.009]. Bacteria belonging to Bacteroidetes were significantly more abundant in JIA [78 % (95 % CI: 74-82 %)] than in control samples [65 % (95 % CI: 57-73 %), p = 0.008]. Shared operational taxonomic units (OTUs) between the groups revealed that genera Actinobacteria and Fusobacteria were present only in JIA patients and Lentisphaerae only in controls. In summary, faecal flora in JIA is characterised by a low level of Firmicutes and an abundance of Bacteroidetes, resembling the aberration reported in type 1 diabetes. We suggest that alterations in the intestinal microbial flora may challenge the mucosal immune system of genetically susceptible subjects predisposing to local proinflammatory cascades, thus contributing to the development of JIA.}, } @article {pmid26718401, year = {2016}, author = {Ranjan, R and Rani, A and Metwally, A and McGee, HS and Perkins, DL}, title = {Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing.}, journal = {Biochemical and biophysical research communications}, volume = {469}, number = {4}, pages = {967-977}, pmid = {26718401}, issn = {1090-2104}, support = {R01 AI053878/AI/NIAID NIH HHS/United States ; R01 HL081663/HL/NHLBI NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/isolation & purification ; Base Sequence ; Chromosome Mapping/*methods ; DNA, Bacterial/*genetics ; Humans ; Metagenome/*genetics ; Microbiota/*genetics ; Molecular Sequence Data ; RNA, Ribosomal, 16S/*genetics ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods ; }, abstract = {The human microbiome has emerged as a major player in regulating human health and disease. Translational studies of the microbiome have the potential to indicate clinical applications such as fecal transplants and probiotics. However, one major issue is accurate identification of microbes constituting the microbiota. Studies of the microbiome have frequently utilized sequencing of the conserved 16S ribosomal RNA (rRNA) gene. We present a comparative study of an alternative approach using whole genome shotgun sequencing (WGS). In the present study, we analyzed the human fecal microbiome compiling a total of 194.1 × 10(6) reads from a single sample using multiple sequencing methods and platforms. Specifically, after establishing the reproducibility of our methods with extensive multiplexing, we compared: 1) The 16S rRNA amplicon versus the WGS method, 2) the Illumina HiSeq versus MiSeq platforms, 3) the analysis of reads versus de novo assembled contigs, and 4) the effect of shorter versus longer reads. Our study demonstrates that whole genome shotgun sequencing has multiple advantages compared with the 16S amplicon method including enhanced detection of bacterial species, increased detection of diversity and increased prediction of genes. In addition, increased length, either due to longer reads or the assembly of contigs, improved the accuracy of species detection.}, } @article {pmid26715502, year = {2016}, author = {Ojima, M and Motooka, D and Shimizu, K and Gotoh, K and Shintani, A and Yoshiya, K and Nakamura, S and Ogura, H and Iida, T and Shimazu, T}, title = {Metagenomic Analysis Reveals Dynamic Changes of Whole Gut Microbiota in the Acute Phase of Intensive Care Unit Patients.}, journal = {Digestive diseases and sciences}, volume = {61}, number = {6}, pages = {1628-1634}, pmid = {26715502}, issn = {1573-2568}, mesh = {Adult ; Aged ; Aged, 80 and over ; Gastrointestinal Tract/*microbiology ; Humans ; *Intensive Care Units ; *Metagenomics ; Microbiota/*genetics ; Middle Aged ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Metagenomic analysis targeting the 16S rRNA gene has made it possible to characterize the vast array of microorganisms contained in the gut.

AIM: The purpose of this study was to evaluate how gut microbiota change in intensive care unit (ICU) patients in the acute phase after admission.

METHODS: This prospective observational cohort study investigated 12 patients admitted to a single ICU of a large urban tertiary referral hospital. All patients were mechanically ventilated on admission. Fecal samples were collected from patients on days 1-2, 2-4, 5-8, and 7-10 after admission. DNA was extracted from fecal samples, and 16S rRNA deep sequencing was performed to monitor gut changes.

RESULTS: Bacteria belonging to the phyla Firmicutes or Bacteroidetes were predominant in each sample. We observed serial dynamic changes in the percentages of Bacteroidetes and Firmicutes that were significantly altered during study period (p < 0.05). A ratio of Bacteroidetes to Firmicutes (B/F ratio) of >10 was seen in four of the six patients who died, whereas a B/F ratio of <0.10 was seen in only one of the six deaths. None of the survivors had a B/F ratio of >10 or <0.10. There was a statistical difference in the B/F ratio between the dead patients and survivors (p = 0.022).

CONCLUSIONS: Dynamic changes in gut microbiota at the phylum level of ICU patients during the acute phase were identified by high-throughput DNA sequencing. An extreme imbalance in gut microbiota may be associated with prognosis in critically ill patients.}, } @article {pmid26715080, year = {2015}, author = {Wahlqvist, ML}, title = {Lactose nutrition in lactase nonpersisters.}, journal = {Asia Pacific journal of clinical nutrition}, volume = {24 Suppl 1}, number = {}, pages = {S21-5}, doi = {10.6133/apjcn.2015.24.s1.04}, pmid = {26715080}, issn = {0964-7058}, mesh = {Animals ; Culture ; Dairy Products ; Diet ; Fermentation ; Food ; Humans ; Intestinal Absorption ; Intestines/enzymology/microbiology ; Lactase/genetics/*metabolism ; Lactose/administration & dosage/*metabolism ; Lactose Intolerance ; Metagenomics ; Microbiota/physiology ; Milk ; *Nutritional Physiological Phenomena ; White People ; }, abstract = {Lactose handling by the human gut by most people, beyond being breast-fed, has been considered a disorder rather than physiological. A non-human mammalian milk source is novel for the majority. During the first 6 months of life, when neonates and infants are best breast-fed, lactose along with other macronutrients, provides energy, but may have other functions as well. At birth, babies are endowed with their mother's vaginal microbiome, but not if they are born by Caesarean section. How much maternal milk lactose survives the infant's small intestine and is processed by this unique gut microbiome and to what end is still uncertain, but no lactose or galactose appears in the faeces. Once intestinal lactase activity declines in most infants, lactose may enhance innate immunity through the cathelicidin antimicrobial peptide (CAMP), which is best achieved by lactose synergy with other colonic fermentation metabolites such as butyrate. It is of interest whether this lactose function or a variant of it persists. It might not be evident when lactase is persistent, as it is in most people of northern European ancestry. Population genomics indicate that lactase persistence became prevalent only about 3000-1000 BC, the Bronze Age of Eurasia. Gastrointestinal symptoms (GIS) in lactase nonpersisters who consume dairy foods are partly dose dependent and not usually evident with single lactose intakes≤25 g per day. Spreading intake across the day reduces the risk as can various dietary patterns. Nevertheless, individual differences in GIS lactose sensitivity may merit public health and clinical consideration.}, } @article {pmid26714477, year = {2015}, author = {Nathani, NM and Patel, AK and Mootapally, CS and Reddy, B and Shah, SV and Lunagaria, PM and Kothari, RK and Joshi, CG}, title = {Effect of roughage on rumen microbiota composition in the efficient feed converter and sturdy Indian Jaffrabadi buffalo (Bubalus bubalis).}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {1116}, pmid = {26714477}, issn = {1471-2164}, mesh = {Animals ; Buffaloes/genetics/*metabolism ; Dietary Fiber/*microbiology ; Glycoside Hydrolases/genetics ; Metagenome/genetics ; Metagenomics ; Microbiota/*genetics ; Rumen ; }, abstract = {BACKGROUND: The rumen microbiota functions as an effective system for conversion of dietary feed to microbial proteins and volatile fatty acids. In the present study, metagenomic approach was applied to elucidate the buffalo rumen microbiome of Jaffrabadi buffalo adapted to varied dietary treatments with the hypothesis that the microbial diversity and subsequent in the functional capacity will alter with diet change and enhance our knowledge of effect of microbe on host physiology. Eight adult animals were gradually adapted to an increasing roughage diet (4 animals each with green and dry roughage) containing 50:50 (J1), 75:25 (J2) and 100:0 (J3) roughage to concentrate proportion for 6 weeks. Metagenomic sequences of solid (fiber adherent microbiota) and liquid (fiber free microbiota) fractions obtained using Ion Torrent PGM platform were analyzed using MG-RAST server and CAZymes approach.

RESULTS: Taxonomic analysis revealed that Bacteroidetes was the most abundant phylum followed by Firmicutes, Fibrobacter and Proteobacteria. Functional analysis revealed protein (25-30 %) and carbohydrate (15-20 %) metabolism as the dominant categories. Principal component analysis demonstrated that roughage proportion, fraction of rumen and type of forage affected rumen microbiome at taxonomic as well as functional level. Rumen metabolite study revealed that rumen fluid nitrogen content reduced in high roughage diet fed animals and pathway analysis showed reduction in the genes coding enzymes involved in methanogenesis pathway. CAZyme annotation revealed the abundance of genes encoding glycoside hydrolases (GH), with the GH3 family most abundant followed by GH2 and GH13 in all samples.

CONCLUSIONS: Results reveals that high roughage diet feed improved microbial protein synthesis and reduces methane emission. CAZyme analysis indicated the importance of microbiome in feed component digestion for fulfilling energy requirements of the host. The findings help determine the role of rumen microbes in plant polysaccharide breakdown and in developing strategies to maximize productivity in ruminants.}, } @article {pmid26713550, year = {2016}, author = {Pii, Y and Borruso, L and Brusetti, L and Crecchio, C and Cesco, S and Mimmo, T}, title = {The interaction between iron nutrition, plant species and soil type shapes the rhizosphere microbiome.}, journal = {Plant physiology and biochemistry : PPB}, volume = {99}, number = {}, pages = {39-48}, doi = {10.1016/j.plaphy.2015.12.002}, pmid = {26713550}, issn = {1873-2690}, mesh = {Hordeum/metabolism/*microbiology ; Iron/*metabolism ; Solanum lycopersicum/metabolism/*microbiology ; Metagenome/genetics/physiology ; Microbiota/genetics/*physiology ; *Rhizosphere ; Soil/*chemistry ; }, abstract = {Plant-associated microorganisms can stimulate plants growth and influence both crops yield and quality by nutrient mobilization and transport. Therefore, rhizosphere microbiome appears to be one of the key determinants of plant health and productivity. The roots of plants have the ability to influence its surrounding microbiology, the rhizosphere microbiome, through the creation of specific chemical niches in the soil mediated by the release of phytochemicals (i.e. root exudates) that depends on several factors, such as plants genotype, soil properties, plant nutritional status, climatic conditions. In the present research, two different crop species, namely barley and tomato, characterized by different strategies for Fe acquisition, have been grown in the RHIZOtest system using either complete or Fe-free nutrient solution to induce Fe starvation. Afterward, plants were cultivated for 6 days on two different calcareous soils. Total DNA was extracted from rhizosphere and bulk soil and 454 pyrosequencing technology was applied to V1-V3 16S rRNA gene region. Approximately 5000 sequences were obtained for each sample. The analysis of the bacterial population confirmed that the two bulk soils showed a different microbial community. The presence of the two plant species, as well as the nutritional status (Fe-deficiency and Fe-sufficiency), could promote a differentiation of the rhizosphere microbiome, as highlighted by non-metric multidimensional scaling (NMDS) analysis. Alphaproteobacteria, Actinobacteria, Chloracidobacteria, Thermoleophilia, Betaproteobacteria, Saprospirae, Gemmatimonadetes, Gammaproteobacteria, Acidobacteria were the most represented classes in all the samples analyzed even though their relative abundance changed as a function of the soil, plant species and nutritional status. To our knowledge, this research demonstrate for the first time that different plants species with a diverse nutritional status can promote the development of a peculiar rhizosphere microbiome, depending on the growth substrate.}, } @article {pmid26711739, year = {2016}, author = {Durgan, DJ and Ganesh, BP and Cope, JL and Ajami, NJ and Phillips, SC and Petrosino, JF and Hollister, EB and Bryan, RM}, title = {Role of the Gut Microbiome in Obstructive Sleep Apnea-Induced Hypertension.}, journal = {Hypertension (Dallas, Tex. : 1979)}, volume = {67}, number = {2}, pages = {469-474}, pmid = {26711739}, issn = {1524-4563}, support = {R21 NS094806/NS/NINDS NIH HHS/United States ; R01 NS080531/NS/NINDS NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; DK56338/DK/NIDDK NIH HHS/United States ; R01NS080531/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Blood Pressure/*physiology ; Disease Models, Animal ; Dysbiosis/*complications/microbiology ; Gastrointestinal Microbiome/*physiology ; Hypertension/*etiology/physiopathology ; Male ; Polysomnography ; Rats ; Rats, Long-Evans ; Sleep/*physiology ; Sleep Apnea Syndromes/*complications/microbiology/physiopathology ; }, abstract = {Individuals suffering from obstructive sleep apnea (OSA) are at increased risk for systemic hypertension. The importance of a healthy gut microbiota, and detriment of a dysbiotic microbiota, on host physiology is becoming increasingly evident. We tested the hypothesis that gut dysbiosis contributes to hypertension observed with OSA. OSA was modeled in rats by inflating a tracheal balloon during the sleep cycle (10-s inflations, 60 per hour). On normal chow diet, OSA had no effect on blood pressure; however, in rats fed a high-fat diet, blood pressure increased 24 and 29 mm Hg after 7 and 14 days of OSA, respectively (P<0.05 each). Bacterial community characterization was performed on fecal pellets isolated before and after 14 days of OSA in chow and high-fat fed rats. High-fat diet and OSA led to significant alterations of the gut microbiota, including decreases in bacterial taxa known to produce the short chain fatty acid butyrate (P<0.05). Finally, transplant of dysbiotic cecal contents from hypertensive OSA rats on high-fat diet into OSA recipient rats on normal chow diet (shown to be normotensive) resulted in hypertension similar to that of the donor (increased 14 and 32 mm Hg after 7 and 14 days of OSA, respectively; P<0.05). These studies demonstrate a causal relationship between gut dysbiosis and hypertension, and suggest that manipulation of the microbiota may be a viable treatment for OSA-induced, and possibly other forms of, hypertension.}, } @article {pmid26711277, year = {2016}, author = {Prajapati, VS and Purohit, HJ and Raje, DV and Parmar, N and Patel, AB and Jones, OAH and Joshi, CG}, title = {The effect of a high-roughage diet on the metabolism of aromatic compounds by rumen microbes: a metagenomic study using Mehsani buffalo (Bubalus bubalis).}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {3}, pages = {1319-1331}, doi = {10.1007/s00253-015-7239-0}, pmid = {26711277}, issn = {1432-0614}, mesh = {Animal Feed/*analysis ; Animals ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Biodiversity ; Buffaloes/metabolism/*microbiology ; Dietary Fiber/*metabolism ; *Gastrointestinal Microbiome ; Metagenomics ; Phylogeny ; Rumen/metabolism/*microbiology ; Volatile Organic Compounds/*metabolism ; }, abstract = {In developing countries, livestock are often fed a high-lignin, low-nutrient diet that is rich in aromatic compounds. It is therefore important to understand the structure of the microbial community responsible for the metabolism of these substances. A metagenomic analysis was therefore carried out to assess the microbial communities associated with the liquid and solid fractions of rumen biomaterial from domestic Mehsani buffalo (Bubalus bubalis) fed with varying proportions of roughage. The experimental design consisted of three feeding regimes (50, 75 and 100 % roughage) and two roughage types (green and dry). Genes associated with aromatic compound degradation were assessed via high-throughput DNA sequencing. A total of 3914.94 Mb data were generated from all treatment groups. Genes coding for functional responses associated with aromatic compound metabolism were more prevalent in the liquid fraction of rumen samples than solid fractions. Statistically significant differences (p < 0.05) were also observed between treatment groups. These differences were dependent on the proportion of roughage fed to the animal, with the type of roughage having little effect. The genes present in the highest abundance in all treatment groups were those related to aromatic compound catabolism. At the phylum level, Bacteroidetes were dominant in all treatments closely followed by the Firmicutes. This study demonstrates the use of feed type to selectively enrich microbial communities capable of metabolizing aromatic compounds in the rumen of domestic buffalo. The results may help to improve nutrient utilization efficiency in livestock and are thus of interest to farming industries, particularly in developing countries, worldwide.}, } @article {pmid26709835, year = {2015}, author = {Rajpal, DK and Klein, JL and Mayhew, D and Boucheron, J and Spivak, AT and Kumar, V and Ingraham, K and Paulik, M and Chen, L and Van Horn, S and Thomas, E and Sathe, G and Livi, GP and Holmes, DJ and Brown, JR}, title = {Selective Spectrum Antibiotic Modulation of the Gut Microbiome in Obesity and Diabetes Rodent Models.}, journal = {PloS one}, volume = {10}, number = {12}, pages = {e0145499}, pmid = {26709835}, issn = {1932-6203}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Ceftazidime/pharmacology ; Diabetes Mellitus, Type 2/*microbiology ; Diet/adverse effects ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; Male ; Mice ; Obesity/etiology/*microbiology ; Phenotype ; Prebiotics ; Rats ; }, abstract = {The gastrointestinal tract microbiome has been suggested as a potential therapeutic target for metabolic diseases such as obesity and Type 2 diabetes mellitus (T2DM). However, the relationship between changes in microbial communities and metabolic disease-phenotypes are still poorly understood. In this study, we used antibiotics with markedly different antibacterial spectra to modulate the gut microbiome in a diet-induced obesity mouse model and then measured relevant biochemical, hormonal and phenotypic biomarkers of obesity and T2DM. Mice fed a high-fat diet were treated with either ceftazidime (a primarily anti-Gram negative bacteria antibiotic) or vancomycin (mainly anti-Gram positive bacteria activity) in an escalating three-dose regimen. We also dosed animals with a well-known prebiotic weight-loss supplement, 10% oligofructose saccharide (10% OFS). Vancomycin treated mice showed little weight change and no improvement in glycemic control while ceftazidime and 10% OFS treatments induced significant weight loss. However, only ceftazidime showed significant, dose dependent improvement in key metabolic variables including glucose, insulin, protein tyrosine tyrosine (PYY) and glucagon-like peptide-1 (GLP-1). Subsequently, we confirmed the positive hyperglycemic control effects of ceftazidime in the Zucker diabetic fatty (ZDF) rat model. Metagenomic DNA sequencing of bacterial 16S rRNA gene regions V1-V3 showed that the microbiomes of ceftazidime dosed mice and rats were enriched for the phylum Firmicutes while 10% OFS treated mice had a greater abundance of Bacteroidetes. We show that specific changes in microbial community composition are associated with obesity and glycemic control phenotypes. More broadly, our study suggests that in vivo modulation of the microbiome warrants further investigation as a potential therapeutic strategy for metabolic diseases.}, } @article {pmid26700882, year = {2016}, author = {Pitta, DW and Indugu, N and Kumar, S and Vecchiarelli, B and Sinha, R and Baker, LD and Bhukya, B and Ferguson, JD}, title = {Metagenomic assessment of the functional potential of the rumen microbiome in Holstein dairy cows.}, journal = {Anaerobe}, volume = {38}, number = {}, pages = {50-60}, doi = {10.1016/j.anaerobe.2015.12.003}, pmid = {26700882}, issn = {1095-8274}, mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Cattle ; Computational Biology/methods ; Lactation ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Phylogeny ; Rumen/*microbiology/physiology ; }, abstract = {The microbial ecology of the rumen microbiome is influenced by the diet and the physiological status of the dairy cow and can have tremendous influence on the yield and components of milk. There are significant differences in milk yields between first and subsequent lactations of dairy cows, but information on how the rumen microbiome changes as the dairy cow gets older has received little attention. We characterized the rumen microbiome of the dairy cow for phylogeny and functional pathways by lactation group and stage of lactation using a metagenomics approach. Our findings revealed that the rumen microbiome was dominated by Bacteroidetes (70%), Firmicutes (15-20%) and Proteobacteria (7%). The abundance of Firmicutes and Proteobacteria were independently influenced by diet and lactation. Bacteroidetes contributed to a majority of the metabolic functions in first lactation dairy cows while the contribution from Firmicutes and Proteobacteria increased incrementally in second and third lactation dairy cows. We found that nearly 70% of the CAZymes were oligosaccharide breaking enzymes which reflect the higher starch and fermentable sugars in the diet. The results of this study suggest that the rumen microbiome continues to evolve as the dairy cow advances in lactations and these changes may have a significant role in milk production.}, } @article {pmid26692900, year = {2015}, author = {Liu, Z and Lin, S and Piantadosi, S}, title = {Network construction and structure detection with metagenomic count data.}, journal = {BioData mining}, volume = {8}, number = {}, pages = {40}, pmid = {26692900}, issn = {1756-0381}, support = {UL1 TR000124/TR/NCATS NIH HHS/United States ; }, abstract = {BACKGROUND: The human microbiome plays a critical role in human health. Massive amounts of metagenomic data have been generated with advances in next-generation sequencing technologies that characterize microbial communities via direct isolation and sequencing. How to extract, analyze, and transform these vast amounts of data into useful knowledge is a great challenge to bioinformaticians. Microbial biodiversity research has focused primarily on taxa composition and abundance and less on the co-occurrences among different taxa. However, taxa co-occurrences and their relationships to environmental and clinical conditions are important because network structure may help to understand how microbial taxa function together.

RESULTS: We propose a systematic robust approach for bacteria network construction and structure detection using metagenomic count data. Pairwise similarity/distance measures between taxa are proposed by adapting distance measures for samples in ecology. We also extend the sparse inverse covariance approach to a sparse inverse of a similarity matrix from count data for network construction. Our approach is efficient for large metagenomic count data with thousands of bacterial taxa. We evaluate our method with real and simulated data. Our method identifies true and biologically significant network structures efficiently.

CONCLUSIONS: Network analysis is crucial for detecting subnetwork structures with metagenomic count data. We developed a software tool in MATLAB for network construction and biologically significant module detection. Software MetaNet can be downloaded from http://biostatistics.csmc.edu/MetaNet/.}, } @article {pmid26690305, year = {2016}, author = {Kim, MS and Bae, JW}, title = {Spatial disturbances in altered mucosal and luminal gut viromes of diet-induced obese mice.}, journal = {Environmental microbiology}, volume = {18}, number = {5}, pages = {1498-1510}, doi = {10.1111/1462-2920.13182}, pmid = {26690305}, issn = {1462-2920}, mesh = {Animals ; Bacteroidetes ; Diet, High-Fat/*adverse effects ; Gastrointestinal Microbiome ; Intestinal Mucosa/*microbiology ; Mice ; Mice, Obese ; Microbiota/*genetics ; Obesity/*virology ; Viruses/classification/*genetics ; }, abstract = {Gut microbial biogeography is a key feature of host-microbe relationships. In gut viral ecology, biogeography and responses to dietary intervention remain poorly understood. Here, we conducted a metagenomic study to determine the composition of the mucosal and luminal viromes of the gut and to evaluate the impact of a Western diet on gut viral ecology. We found that mucosal and luminal viral assemblages comprised predominantly temperate phages. The mucosal virome significantly differed from the luminal virome in low-fat diet-fed lean mice, where spatial variation correlated with bacterial microbiota from the mucosa and lumen. The mucosal and luminal viromes of high-fat, high-sucrose 'Western' diet-fed obese mice were significantly enriched with temperate phages of the Caudovirales order. Interestingly, this community alteration occurred to a greater extent in the mucosa than lumen, leading to loss of spatial differences; however, these changes recovered after switching to a low-fat diet. Temperate phages enriched in the Western diet-induced obese mice were associated with the Bacilli, Negativicutes and Bacteroidia classes and temperate phages from the Bacteroidia class particularly encoded stress and niche-specific functions advantageous to bacterial host adaptation. This study illustrates a biogeographic view of the gut virome and phage-bacterial host connections under the diet-induced microbial dysbiosis.}, } @article {pmid26686366, year = {2016}, author = {Moestedt, J and Müller, B and Westerholm, M and Schnürer, A}, title = {Ammonia threshold for inhibition of anaerobic digestion of thin stillage and the importance of organic loading rate.}, journal = {Microbial biotechnology}, volume = {9}, number = {2}, pages = {180-194}, pmid = {26686366}, issn = {1751-7915}, mesh = {Ammonia/*metabolism ; Anaerobiosis ; Archaea/classification/*drug effects/isolation & purification/*metabolism ; *Biofuels ; *Biota ; Cluster Analysis ; *Environmental Microbiology ; Fermentation ; Metagenomics ; Organic Chemicals/*metabolism ; Phylogeny ; }, abstract = {Biogas production from nitrogen-rich feedstock results in release of ammonia (NH3), causing inhibition of the microbial process. The reported threshold ammonia value for stable biogas production varies greatly between studies, probably because of differences in operating conditions. Moreover, it is often difficult to separate the effect of ammonia inhibition from that of organic loading rate (OLR), as these two factors are often interrelated. This study attempted to distinguish the effects of ammonia and OLR by analysis of two laboratory-scale biogas reactors operating with thin stillage and subjected to an increase in free ammonia (from 0.30 to 1.1 g L(-1)) either by addition of an external nitrogen source (urea) or by increasing the OLR (3.2-6.0 g volatile solids L(-1) d(-1)). The results showed that ammonia concentration was detrimental for process performance, with the threshold for stability in both processes identified as being about 1 g NH3-N L(-1), irrespective of OLR. Analysis of the methanogenic community showed limited differences between the two reactors on order level and a clear increase in the abundance of Methanomicrobiales, particularly Methanoculleus sp., in response to increasing ammonia concentration. Further comprehensive molecular analysis revealed that diverse Methanoculleus species dominated in the reactors at a given ammonia level at different OLR. The acetogenic community was clearly affected by both ammonia concentration and OLR, suggesting that the volatile fatty acid load in relation to the higher OLR was important for the dynamics of this community.}, } @article {pmid26684897, year = {2015}, author = {Rudney, JD and Jagtap, PD and Reilly, CS and Chen, R and Markowski, TW and Higgins, L and Johnson, JE and Griffin, TJ}, title = {Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {69}, pmid = {26684897}, issn = {2049-2618}, support = {R01 DE017734/DE/NIDCR NIH HHS/United States ; R01 DE021366/DE/NIDCR NIH HHS/United States ; 5R01DE17734/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacterial Proteins/*analysis ; Biofilms/drug effects/growth & development ; Biomarkers ; Dental Caries/etiology/*microbiology/prevention & control ; Dental Plaque/chemistry/*microbiology ; Dysbiosis/*chemically induced/metabolism/microbiology ; Glycolysis/drug effects ; Humans ; Microbial Consortia/drug effects/genetics/physiology ; Microbiota/drug effects/genetics/*physiology ; Proteins/*analysis ; Proteomics ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; Sucrose/administration & dosage/*pharmacology ; }, abstract = {BACKGROUND: The etiology of dental caries is multifactorial, but frequent consumption of free sugars, notably sucrose, appears to be a major factor driving the supragingival microbiota in the direction of dysbiosis. Recent 16S rRNA-based studies indicated that caries-associated communities were less diverse than healthy supragingival plaque but still displayed considerable taxonomic diversity between individuals. Metagenomic studies likewise have found that healthy oral sites from different people were broadly similar with respect to gene function, even though there was an extensive individual variation in their taxonomic profiles. That pattern may also extend to dysbiotic communities. In that case, shifts in community-wide protein relative abundance might provide better biomarkers of dysbiosis that can be achieved through taxonomy alone.

RESULTS: In this study, we used a paired oral microcosm biofilm model of dental caries to investigate differences in community composition and protein relative abundance in the presence and absence of sucrose. This approach provided large quantities of protein, which facilitated deep metaproteomic analysis. Community composition was evaluated using 16S rRNA sequencing and metaproteomic approaches. Although taxonomic diversity was reduced by sucrose pulsing, considerable inter-subject variation in community composition remained. By contrast, functional analysis using the SEED ontology found that sucrose induced changes in protein relative abundance patterns for pathways involving glycolysis, lactate production, aciduricity, and ammonia/glutamate metabolism that were conserved across taxonomically diverse dysbiotic oral microcosm biofilm communities.

CONCLUSIONS: Our findings support the concept of using function-based changes in protein relative abundance as indicators of dysbiosis. Our microcosm model cannot replicate all aspects of the oral environment, but the deep level of metaproteomic analysis it allows makes it suitable for discovering which proteins are most consistently abundant during dysbiosis. It then may be possible to define biomarkers that could be used to detect at-risk tooth surfaces before the development of overt carious lesions.}, } @article {pmid26684730, year = {2016}, author = {Mordret, S and Romac, S and Henry, N and Colin, S and Carmichael, M and Berney, C and Audic, S and Richter, DJ and Pochon, X and de Vargas, C and Decelle, J}, title = {The symbiotic life of Symbiodinium in the open ocean within a new species of calcifying ciliate (Tiarina sp.).}, journal = {The ISME journal}, volume = {10}, number = {6}, pages = {1424-1436}, pmid = {26684730}, issn = {1751-7370}, mesh = {Animals ; *Biodiversity ; Biological Evolution ; Ciliophora/*genetics/physiology ; DNA Barcoding, Taxonomic ; DNA, Ribosomal/chemistry/genetics ; Dinoflagellida/*genetics/physiology ; Ecology ; Ecosystem ; Genotype ; Geography ; Haplotypes ; Metagenomics ; Oceans and Seas ; Phylogeny ; *Symbiosis ; }, abstract = {Symbiotic partnerships between heterotrophic hosts and intracellular microalgae are common in tropical and subtropical oligotrophic waters of benthic and pelagic marine habitats. The iconic example is the photosynthetic dinoflagellate genus Symbiodinium that establishes mutualistic symbioses with a wide diversity of benthic hosts, sustaining highly biodiverse reef ecosystems worldwide. Paradoxically, although various species of photosynthetic dinoflagellates are prevalent eukaryotic symbionts in pelagic waters, Symbiodinium has not yet been reported in symbiosis within oceanic plankton, despite its high propensity for the symbiotic lifestyle. Here we report a new pelagic photosymbiosis between a calcifying ciliate host and the microalga Symbiodinium in surface ocean waters. Confocal and scanning electron microscopy, together with an 18S rDNA-based phylogeny, showed that the host is a new ciliate species closely related to Tiarina fusus (Colepidae). Phylogenetic analyses of the endosymbionts based on the 28S rDNA gene revealed multiple novel closely related Symbiodinium clade A genotypes. A haplotype network using the high-resolution internal transcribed spacer-2 marker showed that these genotypes form eight divergent, biogeographically structured, subclade types that do not seem to associate with any benthic hosts. Ecological analyses using the Tara Oceans metabarcoding data set (V9 region of the 18S rDNA) and contextual oceanographic parameters showed a global distribution of the symbiotic partnership in nutrient-poor surface waters. The discovery of the symbiotic life of Symbiodinium in the open ocean provides new insights into the ecology and evolution of this pivotal microalga and raises new hypotheses about coastal pelagic connectivity.}, } @article {pmid26682918, year = {2015}, author = {Kaminski, J and Gibson, MK and Franzosa, EA and Segata, N and Dantas, G and Huttenhower, C}, title = {High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED.}, journal = {PLoS computational biology}, volume = {11}, number = {12}, pages = {e1004557}, pmid = {26682918}, issn = {1553-7358}, support = {DP2 DK098089/DK/NIDDK NIH HHS/United States ; R01 GM099538/GM/NIGMS NIH HHS/United States ; DP2DK098089/DK/NIDDK NIH HHS/United States ; R01GM099538/GM/NIGMS NIH HHS/United States ; R01 HG005969/HG/NHGRI NIH HHS/United States ; R01HG005969/HG/NHGRI NIH HHS/United States ; }, mesh = {*Algorithms ; Bacterial Proteins/*classification/*genetics ; Genetic Markers/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Microbiota/*genetics ; Open Reading Frames/genetics ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Alignment/*methods ; Software ; }, abstract = {Profiling microbial community function from metagenomic sequencing data remains a computationally challenging problem. Mapping millions of DNA reads from such samples to reference protein databases requires long run-times, and short read lengths can result in spurious hits to unrelated proteins (loss of specificity). We developed ShortBRED (Short, Better Representative Extract Dataset) to address these challenges, facilitating fast, accurate functional profiling of metagenomic samples. ShortBRED consists of two components: (i) a method that reduces reference proteins of interest to short, highly representative amino acid sequences ("markers") and (ii) a search step that maps reads to these markers to quantify the relative abundance of their associated proteins. After evaluating ShortBRED on synthetic data, we applied it to profile antibiotic resistance protein families in the gut microbiomes of individuals from the United States, China, Malawi, and Venezuela. Our results support antibiotic resistance as a core function in the human gut microbiome, with tetracycline-resistant ribosomal protection proteins and Class A beta-lactamases being the most widely distributed resistance mechanisms worldwide. ShortBRED markers are applicable to other homology-based search tasks, which we demonstrate here by identifying phylogenetic signatures of antibiotic resistance across more than 3,000 microbial isolate genomes. ShortBRED can be applied to profile a wide variety of protein families of interest; the software, source code, and documentation are available for download at http://huttenhower.sph.harvard.edu/shortbred.}, } @article {pmid26681599, year = {2015}, author = {Ercolini, D and Francavilla, R and Vannini, L and De Filippis, F and Capriati, T and Di Cagno, R and Iacono, G and De Angelis, M and Gobbetti, M}, title = {From an imbalance to a new imbalance: Italian-style gluten-free diet alters the salivary microbiota and metabolome of African celiac children.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {18571}, pmid = {26681599}, issn = {2045-2322}, mesh = {Actinobacteria/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; Black People ; Celiac Disease/*diet therapy/metabolism/*microbiology/pathology ; Child ; Cluster Analysis ; *Diet, Gluten-Free ; Firmicutes/genetics/isolation & purification ; Gas Chromatography-Mass Spectrometry ; Humans ; *Metabolome ; *Microbiota ; Principal Component Analysis ; RNA, Ribosomal, 16S/analysis/genetics ; Salivary Glands/chemistry/metabolism/*microbiology ; Sequence Analysis, DNA ; Solid Phase Microextraction ; }, abstract = {Fourteen Saharawi celiac children following an African-style gluten-free diet for at least two years were subjected to a change of diet to an Italian-style gluten-free diet for 60 days. Significant differences were identified in the salivary microbiota and metabolome when Saharawi celiac children switched from African- to Italian-style dietary habits. An Italian-style gluten-free diet caused increases in the abundance of Granulicatella, Porphyromonas and Neisseria and decreases in Clostridium, Prevotella and Veillonella, altering the 'salivary type' of the individuals. Furthermore, operational taxonomic unit co-occurrence/exclusion patterns indicated that the initial equilibrium of co-occurring microbial species was perturbed by a change in diet: the microbial diversity was reduced, with a few species out-competing the previously established microbiota and becoming dominant. Analysis of predicted metagenomes revealed a remarkable change in the metabolic potential of the microbiota following the diet change, with increased potential for amino acid, vitamin and co-factor metabolism. High concentrations of acetone and 2-butanone during treatment with the Italian-style gluten-free diet suggested metabolic dysfunction in the Saharawi celiac children. The findings of this study support the need for a translational medicine pipeline to examine interactions between food and microbiota when evaluating human development, nutritional needs and the impact and consequences of westernisation.}, } @article {pmid26680320, year = {2016}, author = {Jakubovics, NS}, title = {A new association for the oral metagenome.}, journal = {Oral diseases}, volume = {22}, number = {2}, pages = {77-80}, doi = {10.1111/odi.12421}, pmid = {26680320}, issn = {1601-0825}, mesh = {Arthritis, Rheumatoid/*microbiology ; Humans ; Intestines/*microbiology ; *Microbiota ; Mouth/*microbiology ; }, } @article {pmid26679041, year = {2015}, author = {Daily, JW and Park, S and Lee, YE}, title = {Microbiome and Beyond: Non-Viable Food Microbes and Human Health.}, journal = {Journal of medicinal food}, volume = {18}, number = {12}, pages = {1289-1290}, doi = {10.1089/jmf.2015.28999.yel}, pmid = {26679041}, issn = {1557-7600}, mesh = {Food ; Humans ; *Metagenome ; *Microbiota ; }, } @article {pmid26676774, year = {2015}, author = {Nouri, S and Salem, N and Nigg, JC and Falk, BW}, title = {Diverse Array of New Viral Sequences Identified in Worldwide Populations of the Asian Citrus Psyllid (Diaphorina citri) Using Viral Metagenomics.}, journal = {Journal of virology}, volume = {90}, number = {5}, pages = {2434-2445}, pmid = {26676774}, issn = {1098-5514}, mesh = {Animals ; *Biodiversity ; Cluster Analysis ; Computational Biology ; Gene Expression Profiling ; Hemiptera/*virology ; Insect Viruses/*classification/genetics/*isolation & purification ; Metagenomics/*methods ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, RNA ; }, abstract = {UNLABELLED: The Asian citrus psyllid, Diaphorina citri, is the natural vector of the causal agent of Huanglongbing (HLB), or citrus greening disease. Together; HLB and D. citri represent a major threat to world citrus production. As there is no cure for HLB, insect vector management is considered one strategy to help control the disease, and D. citri viruses might be useful. In this study, we used a metagenomic approach to analyze viral sequences associated with the global population of D. citri. By sequencing small RNAs and the transcriptome coupled with bioinformatics analysis, we showed that the virus-like sequences of D. citri are diverse. We identified novel viral sequences belonging to the picornavirus superfamily, the Reoviridae, Parvoviridae, and Bunyaviridae families, and an unclassified positive-sense single-stranded RNA virus. Moreover, a Wolbachia prophage-related sequence was identified. This is the first comprehensive survey to assess the viral community from worldwide populations of an agricultural insect pest. Our results provide valuable information on new putative viruses, some of which may have the potential to be used as biocontrol agents.

IMPORTANCE: Insects have the most species of all animals, and are hosts to, and vectors of, a great variety of known and unknown viruses. Some of these most likely have the potential to be important fundamental and/or practical resources. In this study, we used high-throughput next-generation sequencing (NGS) technology and bioinformatics analysis to identify putative viruses associated with Diaphorina citri, the Asian citrus psyllid. D. citri is the vector of the bacterium causing Huanglongbing (HLB), currently the most serious threat to citrus worldwide. Here, we report several novel viral sequences associated with D. citri.}, } @article {pmid26676710, year = {2018}, author = {Barbian, HJ and Li, Y and Ramirez, M and Klase, Z and Lipende, I and Mjungu, D and Moeller, AH and Wilson, ML and Pusey, AE and Lonsdorf, EV and Bushman, FD and Hahn, BH}, title = {Destabilization of the gut microbiome marks the end-stage of simian immunodeficiency virus infection in wild chimpanzees.}, journal = {American journal of primatology}, volume = {80}, number = {1}, pages = {}, pmid = {26676710}, issn = {1098-2345}, support = {R37 AI050529/AI/NIAID NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; R01 AI120810/AI/NIAID NIH HHS/United States ; R01 AI050529/AI/NIAID NIH HHS/United States ; R01 AI058715/AI/NIAID NIH HHS/United States ; T32 AI055400/AI/NIAID NIH HHS/United States ; }, mesh = {Adenoviruses, Simian/genetics ; Animals ; Ape Diseases/*microbiology/virology ; Bacteria/*classification/genetics ; DNA Viruses/genetics ; Feces/microbiology/virology ; Female ; *Gastrointestinal Microbiome ; Male ; Metagenome ; *Pan troglodytes ; RNA, Ribosomal, 16S ; Simian Acquired Immunodeficiency Syndrome/*microbiology/pathology ; Simian Immunodeficiency Virus ; Tanzania ; }, abstract = {Enteric dysbiosis is a characteristic feature of progressive human immunodeficiency virus type 1 (HIV-1) infection but has not been observed in simian immunodeficiency virus (SIVmac)-infected macaques, including in animals with end-stage disease. This has raised questions concerning the mechanisms underlying the HIV-1 associated enteropathy, with factors other than virus infection, such as lifestyle and antibiotic use, implicated as playing possible causal roles. Simian immunodeficiency virus of chimpanzees (SIVcpz) is also associated with increased mortality in wild-living communities, and like HIV-1 and SIVmac, can cause CD4[+] T cell depletion and immunodeficiency in infected individuals. Given the central role of the intestinal microbiome in mammalian health, we asked whether gut microbial constituents could be identified that are indicative of SIVcpz status and/or disease progression. Here, we characterized the gut microbiome of SIVcpz-infected and -uninfected chimpanzees in Gombe National Park, Tanzania. Subjecting a small number of fecal samples (N = 9) to metagenomic (shotgun) sequencing, we found bacteria of the family Prevotellaceae to be enriched in SIVcpz-infected chimpanzees. However, 16S rRNA gene sequencing of a larger number of samples (N = 123) failed to show significant differences in both the composition and diversity (alpha and beta) of gut bacterial communities between infected (N = 24) and uninfected (N = 26) chimpanzees. Similarly, chimpanzee stool-associated circular virus (Chi-SCV) and chimpanzee adenovirus (ChAdV) identified by metagenomic sequencing were neither more prevalent nor more abundant in SIVcpz-infected individuals. However, fecal samples collected from SIVcpz-infected chimpanzees within 5 months before their AIDS-related death exhibited significant compositional changes in their gut bacteriome. These data indicate that SIVcpz-infected chimpanzees retain a stable gut microbiome throughout much of their natural infection course, with a significant destabilization of bacterial (but not viral) communities observed only in individuals with known immunodeficiency within the last several months before their death. Am. J. Primatol. 80:e22515, 2018. © 2015 Wiley Periodicals, Inc.}, } @article {pmid26669711, year = {2015}, author = {Mourembou, G and Yasir, M and Azhar, EI and Lagier, JC and Bibi, F and Jiman-Fatani, AA and Helmy, N and Robert, C and Rathored, J and Fournier, PE and Raoult, D and Million, M}, title = {Rise of Microbial Culturomics: Noncontiguous Finished Genome Sequence and Description of Beduini massiliensis gen. nov., sp. nov.}, journal = {Omics : a journal of integrative biology}, volume = {19}, number = {12}, pages = {766-776}, pmid = {26669711}, issn = {1557-8100}, mesh = {Adult ; Bacillus/*classification/drug effects/*genetics/ultrastructure ; Female ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Genomics ; Humans ; *Metagenome ; *Metagenomics/methods ; Phenotype ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbial culturomics is a new field of omics sciences that examines the bacterial diversity of human gut coupled with a taxono-genomic strategy. Using microbial culturomics, we report here for the first time a novel Gram negative, catalase- and oxidase-negative, strict anaerobic bacilli named Beduini massiliensis gen. nov., sp nov. strain GM1 (= CSUR P1440 = DSM 100188), isolated from the stools of a female nomadic Bedouin from Saudi Arabia. With a length of 2,850,586 bp, the Beduini massiliensis genome exhibits a G + C content of 35.9%, and contains 2819 genes (2744 protein-coding and 75 RNA genes including 57 tRNA and 18 rRNA genes). It is composed of 6 scaffolds (composed of 6 contigs). A total of 1859 genes (67.75%) were assigned a putative function (by COGs or by NR blast). At least 1457 (53%) orthologous proteins were not shared with the closest phylogenetic species. 274 genes (10.0%) were identified as ORFans. These results show that microbial culturomics can dramatically improve the characterization of the human microbiota repertoire, deciphering new bacterial species and new genes. Further studies will clarify the geographic specificity and the putative role of these new microbes and their related functional genetic content in health and disease. Microbial culturomics is an emerging frontier of omics systems sciences and integrative biology and thus, warrants further consideration as part of the postgenomics methodology toolbox.}, } @article {pmid26667648, year = {2015}, author = {Hugerth, LW and Larsson, J and Alneberg, J and Lindh, MV and Legrand, C and Pinhassi, J and Andersson, AF}, title = {Metagenome-assembled genomes uncover a global brackish microbiome.}, journal = {Genome biology}, volume = {16}, number = {}, pages = {279}, pmid = {26667648}, issn = {1474-760X}, mesh = {Bacteria/genetics ; *Genome, Bacterial ; *Metagenome ; Microbiota/*genetics ; Oceans and Seas ; Phylogeny ; Phylogeography ; Plankton/*genetics ; Seasons ; Seawater/*microbiology ; }, abstract = {BACKGROUND: Microbes are main drivers of biogeochemical cycles in oceans and lakes. Although the genome is a foundation for understanding the metabolism, ecology and evolution of an organism, few bacterioplankton genomes have been sequenced, partly due to difficulties in cultivating them.

RESULTS: We use automatic binning to reconstruct a large number of bacterioplankton genomes from a metagenomic time-series from the Baltic Sea, one of world's largest brackish water bodies. These genomes represent novel species within typical freshwater and marine clades, including clades not previously sequenced. The genomes' seasonal dynamics follow phylogenetic patterns, but with fine-grained lineage-specific variations, reflected in gene-content. Signs of streamlining are evident in most genomes, and estimated genome sizes correlate with abundance variation across filter size fractions. Comparing the genomes with globally distributed metagenomes reveals significant fragment recruitment at high sequence identity from brackish waters in North America, but little from lakes or oceans. This suggests the existence of a global brackish metacommunity whose populations diverged from freshwater and marine relatives over 100,000 years ago, long before the Baltic Sea was formed (8000 years ago). This markedly contrasts to most Baltic Sea multicellular organisms, which are locally adapted populations of freshwater or marine counterparts.

CONCLUSIONS: We describe the gene content, temporal dynamics and biogeography of a large set of new bacterioplankton genomes assembled from metagenomes. We propose that brackish environments exert such strong selection that lineages adapted to them flourish globally with limited influence from surrounding aquatic communities.}, } @article {pmid26663884, year = {2015}, author = {Koleva, PT and Kim, JS and Scott, JA and Kozyrskyj, AL}, title = {Microbial programming of health and disease starts during fetal life.}, journal = {Birth defects research. Part C, Embryo today : reviews}, volume = {105}, number = {4}, pages = {265-277}, doi = {10.1002/bdrc.21117}, pmid = {26663884}, issn = {1542-9768}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Fetus/*microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Immune System/*physiology ; Infant, Newborn ; Infant, Newborn, Diseases/*microbiology ; *Metagenome ; *Microbiota ; }, abstract = {The pioneer microbiota of the neonatal gut are essential for gut maturation, and metabolic and immunologic programming. Recent research has shown that early bacterial colonization may impact the occurrence of disease later in life (microbial programming). Despite early conflicting evidence, it has long been considered that the womb is a sterile environment and human microbial colonization begins at birth. In the last few years, several findings have reiterated the presence of microbes in infant first stool (meconium) and pointed to the existence of in utero microbial colonization of the infant gut. The dominant bacterial taxa detected in meconium specimens belong to the Enterobacteriaceae family (Escherichia genus) and lactic acid bacteria (notably members of the genera Leuconostoc, Enterococcus, and Lactococcus). Maternal atopy promotes dominance of Enterobacteriaceae in newborn meconium, which in turn may lead to respiratory problems in the infant. This microbial interaction with the host immune system may in fact, originate during fetal life. Our review evaluates the evidence for an intrauterine origin of meconium microbiota, their composition and influences, and potential clinical implications on infant health.}, } @article {pmid26663423, year = {2016}, author = {Reveillaud, J and Reddington, E and McDermott, J and Algar, C and Meyer, JL and Sylva, S and Seewald, J and German, CR and Huber, JA}, title = {Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise.}, journal = {Environmental microbiology}, volume = {18}, number = {6}, pages = {1970-1987}, pmid = {26663423}, issn = {1462-2920}, mesh = {Animals ; Biodiversity ; Hydrogen/*analysis ; Hydrothermal Vents/chemistry/*microbiology ; }, abstract = {Warm fluids emanating from hydrothermal vents can be used as windows into the rocky subseafloor habitat and its resident microbial community. Two new vent systems on the Mid-Cayman Rise each exhibits novel geologic settings and distinctively hydrogen-rich vent fluid compositions. We have determined and compared the chemistry, potential energy yielding reactions, abundance, community composition, diversity, and function of microbes in venting fluids from both sites: Piccard, the world's deepest vent site, hosted in mafic rocks; and Von Damm, an adjacent, ultramafic-influenced system. Von Damm hosted a wider diversity of lineages and metabolisms in comparison to Piccard, consistent with thermodynamic models that predict more numerous energy sources at ultramafic systems. There was little overlap in the phylotypes found at each site, although similar and dominant hydrogen-utilizing genera were present at both. Despite the differences in community structure, depth, geology, and fluid chemistry, energetic modelling and metagenomic analysis indicate near functional equivalence between Von Damm and Piccard, likely driven by the high hydrogen concentrations and elevated temperatures at both sites. Results are compared with hydrothermal sites worldwide to provide a global perspective on the distinctiveness of these newly discovered sites and the interplay among rocks, fluid composition and life in the subseafloor.}, } @article {pmid26663004, year = {2015}, author = {Gkolfakis, P and Dimitriadis, G and Triantafyllou, K}, title = {Gut microbiota and non-alcoholic fatty liver disease.}, journal = {Hepatobiliary & pancreatic diseases international : HBPD INT}, volume = {14}, number = {6}, pages = {572-581}, doi = {10.1016/s1499-3872(15)60026-1}, pmid = {26663004}, issn = {1499-3872}, mesh = {Bacteria/classification/genetics/*growth & development ; Bacterial Load ; Bacterial Translocation ; Breath Tests ; Dysbiosis ; *Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Humans ; Intestines/*microbiology ; Non-alcoholic Fatty Liver Disease/diagnosis/epidemiology/*microbiology/therapy ; Probiotics/therapeutic use ; Prognosis ; Ribotyping ; Risk Factors ; }, abstract = {BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) is a common disorder with poorly understood pathogenesis. Beyond environmental and genetic factors, cumulative data support the causative role of gut microbiota in disease development and progression.

DATA SOURCE: We performed a PubMed literature search with the following key words: "non-alcoholic fatty liver disease", "non-alcoholic steatohepatitis", "fatty liver", "gut microbiota" and "microbiome", to review the data implicating gut microbiota in NAFLD development and progression.

RESULTS: Recent metagenomic studies revealed differences in the phylum and genus levels between patients with fatty liver and healthy controls. While bacteroidetes and firmicutes remain the dominant phyla among NAFLD patients, their proportional abundance and genera detection vary among different studies. New techniques indicate a correlation between the methanogenic archaeon (methanobrevibacter smithii) and obesity, while the bacterium akkermanshia municiphila protects against metabolic syndrome. Among NAFLD patients, small intestinal bacterial overgrowth detected by breath tests might induce gut microbiota and host interactions, facilitating disease development.

CONCLUSIONS: There is evidence that gut microbiota participates in NAFLD development through, among others, obesity induction, endogenous ethanol production, inflammatory response triggering and alterations in choline metabolism. Further studies with emerging techniques are needed to further elucidate the microbiome and host crosstalk in NAFLD pathogenesis.}, } @article {pmid26660761, year = {2016}, author = {Althani, AA and Marei, HE and Hamdi, WS and Nasrallah, GK and El Zowalaty, ME and Al Khodor, S and Al-Asmakh, M and Abdel-Aziz, H and Cenciarelli, C}, title = {Human Microbiome and its Association With Health and Diseases.}, journal = {Journal of cellular physiology}, volume = {231}, number = {8}, pages = {1688-1694}, doi = {10.1002/jcp.25284}, pmid = {26660761}, issn = {1097-4652}, mesh = {*Bacteria/classification/genetics/growth & development/pathogenicity ; Digestive System Diseases/microbiology/virology ; Disease Susceptibility ; *Dysbiosis/microbiology/virology ; *Fungi/classification/genetics/growth & development/pathogenicity ; *Health Status ; Host-Pathogen Interactions ; Humans ; Metabolic Diseases/microbiology/virology ; *Microbiota ; Neurodegenerative Diseases/microbiology/virology ; Risk Factors ; *Viruses/classification/genetics/growth & development/pathogenicity ; }, abstract = {Human microbiota are distinct communities of microorganisms that resides at different body niches. Exploration of the human microbiome has become a reality due to the availability of powerful metagenomics and metatranscriptomic analysis technologies. Recent advances in sequencing and bioinformatics over the past decade help provide a deep insight into the nature of the host-microbial interactions and identification of potential deriver genes and pathways associated with human health, well-being, and predisposition to different diseases. In the present review, we outline recent studies devoted to elucidate the possible link between the microbiota and various type of diseases. The present review also highlights the potential utilization of microbiota as a potential therapeutic option to treat a wide array of human diseases. J. Cell. Physiol. 231: 1688-1694, 2016. © 2015 Wiley Periodicals, Inc.}, } @article {pmid26657581, year = {2015}, author = {Ma, Q and Qu, Y and Zhang, X and Liu, Z and Li, H and Zhang, Z and Wang, J and Shen, W and Zhou, J}, title = {Systematic investigation and microbial community profile of indole degradation processes in two aerobic activated sludge systems.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {17674}, pmid = {26657581}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics ; *Biodegradation, Environmental ; Bioreactors ; Carbon ; Glucose/metabolism ; Indoles/*metabolism ; Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; }, abstract = {Indole is widely spread in various environmental matrices. Indole degradation by bacteria has been reported previously, whereas its degradation processes driven by aerobic microbial community were as-yet unexplored. Herein, eight sequencing batch bioreactors fed with municipal and coking activated sludges were constructed for aerobic treatment of indole. The whole operation processes contained three stages, i.e. stage I, glucose and indole as carbon sources; stage II, indole as carbon source; and stage III, indole as carbon and nitrogen source. Indole could be completely removed in both systems. Illumina sequencing revealed that alpha diversity was reduced after indole treatment and microbial communities were significantly distinct among the three stages. At genus level, Azorcus and Thauera were dominant species in stage I in both systems, while Alcaligenes, Comamonas and Pseudomonas were the core genera in stage II and III in municipal sludge system, Alcaligenes and Burkholderia in coking sludge system. In addition, four strains belonged to genera Comamonas, Burkholderia and Xenophilus were isolated using indole as sole carbon source. Burkholderia sp. IDO3 could remove 100 mg/L indole completely within 14 h, the highest degradation rate to date. These findings provide novel information and enrich our understanding of indole aerobic degradation processes.}, } @article {pmid26657285, year = {2016}, author = {Metcalf, JL and Xu, ZZ and Weiss, S and Lax, S and Van Treuren, W and Hyde, ER and Song, SJ and Amir, A and Larsen, P and Sangwan, N and Haarmann, D and Humphrey, GC and Ackermann, G and Thompson, LR and Lauber, C and Bibat, A and Nicholas, C and Gebert, MJ and Petrosino, JF and Reed, SC and Gilbert, JA and Lynne, AM and Bucheli, SR and Carter, DO and Knight, R}, title = {Microbial community assembly and metabolic function during mammalian corpse decomposition.}, journal = {Science (New York, N.Y.)}, volume = {351}, number = {6269}, pages = {158-162}, doi = {10.1126/science.aad2646}, pmid = {26657285}, issn = {1095-9203}, support = {3 R01 HG004872-03S2/HG/NHGRI NIH HHS/United States ; 5 U01 HG004866-04/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/*metabolism ; Biodegradation, Environmental ; *Cadaver ; Ecosystem ; Fungi/classification/*metabolism ; Mice ; *Microbial Consortia ; Nitrogen Cycle ; Soil/chemistry/classification ; *Soil Microbiology ; }, abstract = {Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.}, } @article {pmid26655942, year = {2016}, author = {Neu, J}, title = {Intestinal Microbiota Studies in Preterm Infants.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {62}, number = {2}, pages = {193-194}, doi = {10.1097/MPG.0000000000001068}, pmid = {26655942}, issn = {1536-4801}, mesh = {Feces ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Infant, Premature ; Intestines ; Metagenome ; Microbiota ; }, } @article {pmid26655752, year = {2016}, author = {Jimenez-Infante, F and Ngugi, DK and Vinu, M and Alam, I and Kamau, AA and Blom, J and Bajic, VB and Stingl, U}, title = {Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {4}, pages = {1215-1226}, pmid = {26655752}, issn = {1098-5336}, mesh = {Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Ecotype ; Genomics ; Indian Ocean ; Methylophilaceae/*classification/*genetics ; Molecular Sequence Data ; *Phylogeny ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs that play important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (here designated MBRS-H7) from the ultraoligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species that forms a distinct cluster together with isolate KB13 from Hawaii (Hawaii-Red Sea [H-RS] cluster) that is separate from the cluster represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S-23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low-chlorophyll and/or high-temperature provinces for the H-RS cluster but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of the H-RS cluster include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely, the existence of the NADH:quinone oxidoreductase complex I (NUO) system in the H-RS cluster and the nonhomologous NADH:quinone oxidoreductase (NQR) system in the HTCC2181 cluster, which might have implications for their overall energetic yields.}, } @article {pmid26655498, year = {2016}, author = {Kuleshov, V and Jiang, C and Zhou, W and Jahanbani, F and Batzoglou, S and Snyder, M}, title = {Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome.}, journal = {Nature biotechnology}, volume = {34}, number = {1}, pages = {64-69}, pmid = {26655498}, issn = {1546-1696}, support = {P50 HG007735/HG/NHGRI NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; U54 DK102556/DK/NIDDK NIH HHS/United States ; }, mesh = {*High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota ; *Species Specificity ; }, abstract = {Identifying bacterial strains in metagenome and microbiome samples using computational analyses of short-read sequences remains a difficult problem. Here, we present an analysis of a human gut microbiome using TruSeq synthetic long reads combined with computational tools for metagenomic long-read assembly, variant calling and haplotyping (Nanoscope and Lens). Our analysis identifies 178 bacterial species, of which 51 were not found using shotgun reads alone. We recover bacterial contigs that comprise multiple operons, including 22 contigs of >1 Mbp. Furthermore, we observe extensive intraspecies variation within microbial strains in the form of haplotypes that span up to hundreds of Kbp. Incorporation of synthetic long-read sequencing technology with standard short-read approaches enables more precise and comprehensive analyses of metagenomic samples.}, } @article {pmid26648930, year = {2015}, author = {Setati, ME and Jacobson, D and Bauer, FF}, title = {Sequence-based Analysis of the Vitis vinifera L. cv Cabernet Sauvignon Grape Must Mycobiome in Three South African Vineyards Employing Distinct Agronomic Systems.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1358}, pmid = {26648930}, issn = {1664-302X}, abstract = {Recent microbiomic research of agricultural habitats has highlighted tremendous microbial biodiversity associated with such ecosystems. Data generated in vineyards have furthermore highlighted significant regional differences in vineyard biodiversity, hinting at the possibility that such differences might be responsible for regional differences in wine style and character, a hypothesis referred to as "microbial terroir." The current study further contributes to this body of work by comparing the mycobiome associated with South African (SA) Cabernet Sauvignon grapes in three neighboring vineyards that employ different agronomic approaches, and comparing the outcome with similar data sets from Californian vineyards. The aim of this study was to fully characterize the mycobiomes associated with the grapes from these vineyards. The data revealed approximately 10 times more fungal diversity than what is typically retrieved from culture-based studies. The Biodynamic vineyard was found to harbor a more diverse fungal community (H = 2.6) than the conventional (H = 2.1) and integrated (H = 1.8) vineyards. The data show that ascomycota are the most abundant phylum in the three vineyards, with Aureobasidium pullulans and its close relative Kabatiella microsticta being the most dominant fungi. This is the first report to reveal a high incidence of K. microsticta in the grape/wine ecosystem. Different common wine yeast species, such as Metschnikowia pulcherrima and Starmerella bacillaris dominated the mycobiome in the three vineyards. The data show that the filamentous fungi are the most abundant community in grape must although they are not regarded as relevant during wine fermentation. Comparison of metagenomic datasets from the three SA vineyards and previously published data from Californian vineyards revealed only 25% of the fungi in the SA dataset was also present in the Californian dataset, with greater variation evident amongst ubiquitous epiphytic fungi.}, } @article {pmid26645474, year = {2016}, author = {Bryant, JA and Aylward, FO and Eppley, JM and Karl, DM and Church, MJ and DeLong, EF}, title = {Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre.}, journal = {The ISME journal}, volume = {10}, number = {6}, pages = {1308-1322}, pmid = {26645474}, issn = {1751-7370}, mesh = {*Biodiversity ; Ecosystem ; Hawaii ; *Metagenomics ; *Microbial Consortia ; Pacific Ocean ; Phylogeny ; Plankton/*microbiology ; Seasons ; Seawater/*microbiology ; Sunlight ; Wind ; }, abstract = {Few microbial time-series studies have been conducted in open ocean habitats having low seasonal variability such as the North Pacific Subtropical Gyre (NPSG), where surface waters experience comparatively mild seasonal variation. To better describe microbial seasonal variability in this habitat, we analyzed rRNA amplicon and shotgun metagenomic data over two years at the Hawaii Ocean Time-series Station ALOHA. We postulated that this relatively stable habitat might reveal different environmental factors that influence planktonic microbial community diversity than those previously observed in more seasonally dynamic habitats. Unexpectedly, the data showed that microbial diversity at 25 m was positively correlated with average wind speed 3 to 10 days prior to sampling. In addition, microbial community composition at 25 m exhibited significant correlations with solar irradiance. Many bacterial groups whose relative abundances varied with solar radiation corresponded to taxa known to exhibit strong seasonality in other oceanic regions. Network co-correlation analysis of 25 m communities showed seasonal transitions in composition, and distinct successional cohorts of co-occurring phylogenetic groups. Similar network analyses of metagenomic data also indicated distinct seasonality in genes originating from cyanophage, and several bacterial clades including SAR116 and SAR324. At 500 m, microbial community diversity and composition did not vary significantly with any measured environmental parameters. The minimal seasonal variability in the NPSG facilitated detection of more subtle environmental influences, such as episodic wind variation, on surface water microbial diversity. Community composition in NPSG surface waters varied in response to solar irradiance, but less dramatically than reported in other ocean provinces.}, } @article {pmid26642878, year = {2015}, author = {Weinmaier, T and Probst, AJ and La Duc, MT and Ciobanu, D and Cheng, JF and Ivanova, N and Rattei, T and Vaishampayan, P}, title = {A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {62}, pmid = {26642878}, issn = {2049-2618}, mesh = {*Environment, Controlled ; *Environmental Microbiology ; Eukaryota/classification/genetics ; Humans ; *Metagenome ; *Metagenomics/methods ; Microbial Viability/*genetics ; Microbiota ; Prokaryotic Cells/classification ; RNA, Ribosomal, 16S/genetics ; Viruses/classification/genetics ; }, abstract = {BACKGROUND: Recent studies posit a reciprocal dependency between the microbiomes associated with humans and indoor environments. However, none of these metagenome surveys has considered the viability of constituent microorganisms when inferring impact on human health.

RESULTS: Reported here are the results of a viability-linked metagenomics assay, which (1) unveil a remarkably complex community profile for bacteria, fungi, and viruses and (2) bolster the detection of underrepresented taxa by eliminating biases resulting from extraneous DNA. This approach enabled, for the first time ever, the elucidation of viral genomes from a cleanroom environment. Upon comparing the viable biomes and distribution of phylotypes within a cleanroom and adjoining (uncontrolled) gowning enclosure, the rigorous cleaning and stringent control countermeasures of the former were observed to select for a greater presence of anaerobes and spore-forming microflora. Sequence abundance and correlation analyses suggest that the viable indoor microbiome is influenced by both the human microbiome and the surrounding ecosystem(s).

CONCLUSIONS: The findings of this investigation constitute the literature's first ever account of the indoor metagenome derived from DNA originating solely from the potential viable microbial population. Results presented in this study should prove valuable to the conceptualization and experimental design of future studies on indoor microbiomes aimed at inferring impact on human health.}, } @article {pmid26638243, year = {2015}, author = {Bel'kova, NL and Denikina, NN and Dzyuba, EV}, title = {[Study of the Microbiome of the Intestine of the Comephorus dybowski Korotneff, 1904].}, journal = {Izvestiia Akademii nauk. Seriia biologicheskaia}, volume = {}, number = {5}, pages = {544-551}, pmid = {26638243}, issn = {1026-3470}, mesh = {Animals ; *Bacteria/classification/genetics/growth & development ; Intestines/*microbiology ; *Metagenome ; Microbiota/*genetics ; Perciformes/*microbiology ; }, abstract = {Data on metagenomic analysis of the microbial community of the intestine of the Comephorus dybowski are presented for the first time. It was established that the bacterial community is characterized by a significant species diversity. In its composition 301 phylotypes (OTU) belonging to 23 phyla (out of which six are candidate, including the Thermobaculum, Gracilibacteria, Candidatus Saccharibacteria, TM6, Latescibacteria, and Parcubacteria) were detected. It was demonstrated that species richness estimated by means of the non-parametric ACE and Chao1 criteria was 568 and 504, respectively; and the species diversity by the Shannon index was 4.05. The analysis ofunique peculiarities of the C. dybowski ecology and biology allows us to explain some of the data obtained on the intestinal microbiome of this specie.}, } @article {pmid26637379, year = {2016}, author = {Zhou, Y and Wylie, KM and El Feghaly, RE and Mihindukulasuriya, KA and Elward, A and Haslam, DB and Storch, GA and Weinstock, GM}, title = {Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens.}, journal = {Journal of clinical microbiology}, volume = {54}, number = {2}, pages = {368-375}, pmid = {26637379}, issn = {1098-660X}, support = {U54 HG004968/HG/NHGRI NIH HHS/United States ; U54HG004968./HG/NHGRI NIH HHS/United States ; }, mesh = {Adolescent ; Child ; Child, Preschool ; Cluster Analysis ; Diarrhea/*diagnosis/*microbiology ; Drug Resistance, Microbial ; Feces/*microbiology/virology ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Infant, Newborn ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Reproducibility of Results ; }, abstract = {The potential to rapidly capture the entire microbial community structure and/or gene content makes metagenomic sequencing an attractive tool for pathogen identification and the detection of resistance/virulence genes in clinical settings. Here, we assessed the consistency between PCR from a diagnostic laboratory, quantitative PCR (qPCR) from a research laboratory, 16S rRNA gene sequencing, and metagenomic shotgun sequencing (MSS) for Clostridium difficile identification in diarrhea stool samples. Twenty-two C. difficile-positive diarrhea samples identified by PCR and qPCR and five C. difficile-negative diarrhea controls were studied. C. difficile was detected in 90.9% of C. difficile-positive samples using 16S rRNA gene sequencing, and C. difficile was detected in 86.3% of C. difficile-positive samples using MSS. CFU inferred from qPCR analysis were positively correlated with the relative abundance of C. difficile from 16S rRNA gene sequencing (r(2) = -0.60) and MSS (r(2) = -0.55). C. difficile was codetected with Clostridium perfringens, norovirus, sapovirus, parechovirus, and anellovirus in 3.7% to 27.3% of the samples. A high load of Candida spp. was found in a symptomatic control sample in which no causative agents for diarrhea were identified in routine clinical testing. Beta-lactamase and tetracycline resistance genes were the most prevalent (25.9%) antibiotic resistance genes in these samples. In summary, the proof-of-concept study demonstrated that next-generation sequencing (NGS) in pathogen detection is moderately correlated with laboratory testing and is advantageous in detecting pathogens without a priori knowledge.}, } @article {pmid26636484, year = {2016}, author = {Ponziani, FR and Gerardi, V and Gasbarrini, A}, title = {Diagnosis and treatment of small intestinal bacterial overgrowth.}, journal = {Expert review of gastroenterology & hepatology}, volume = {10}, number = {2}, pages = {215-227}, doi = {10.1586/17474124.2016.1110017}, pmid = {26636484}, issn = {1747-4132}, mesh = {Bacteria/*growth & development ; *Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Intestinal Diseases/*diagnosis/microbiology/*therapy ; Intestine, Small/*microbiology ; Predictive Value of Tests ; Risk Factors ; Treatment Outcome ; }, abstract = {A huge number of bacteria are hosted in the gastrointestinal tract, following a gradient increasing towards the colon. Gastric acid secretion and intestinal clearance provide the qualitative and quantitative partitioning of intestinal bacteria; small intestinal bacteria overgrowth (SIBO) occurs when these barrier mechanisms fail. Diagnosis of SIBO is challenging due to the low specificity of symptoms, the frequent association with other diseases of the gastrointestinal tract and the absence of optimal objective diagnostic tests. The therapeutic approach to SIBO is oriented towards resolving predisposing conditions, and is supported by antibiotic treatment to restore the normal small intestinal microflora and by modifications of dietary habits for symptomatic relief. In the near future, metagenomics and metabolomics will help to overcome the uncertainties of SIBO diagnosis and the pitfalls of therapeutic management, allowing the design of a personalized strategy based on the direct insight into the small intestinal microbial community.}, } @article {pmid26635759, year = {2015}, author = {López-López, O and Knapik, K and Cerdán, ME and González-Siso, MI}, title = {Metagenomics of an Alkaline Hot Spring in Galicia (Spain): Microbial Diversity Analysis and Screening for Novel Lipolytic Enzymes.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1291}, pmid = {26635759}, issn = {1664-302X}, abstract = {A fosmid library was constructed with the metagenomic DNA from the water of the Lobios hot spring (76°C, pH = 8.2) located in Ourense (Spain). Metagenomic sequencing of the fosmid library allowed the assembly of 9722 contigs ranging in size from 500 to 56,677 bp and spanning ~18 Mbp. 23,207 ORFs (Open Reading Frames) were predicted from the assembly. Biodiversity was explored by taxonomic classification and it revealed that bacteria were predominant, while the archaea were less abundant. The six most abundant bacterial phyla were Deinococcus-Thermus, Proteobacteria, Firmicutes, Acidobacteria, Aquificae, and Chloroflexi. Within the archaeal superkingdom, the phylum Thaumarchaeota was predominant with the dominant species "Candidatus Caldiarchaeum subterraneum." Functional classification revealed the genes associated to one-carbon metabolism as the most abundant. Both taxonomic and functional classifications showed a mixture of different microbial metabolic patterns: aerobic and anaerobic, chemoorganotrophic and chemolithotrophic, autotrophic and heterotrophic. Remarkably, the presence of genes encoding enzymes with potential biotechnological interest, such as xylanases, galactosidases, proteases, and lipases, was also revealed in the metagenomic library. Functional screening of this library was subsequently done looking for genes encoding lipolytic enzymes. Six genes conferring lipolytic activity were identified and one was cloned and characterized. This gene was named LOB4Est and it was expressed in a yeast mesophilic host. LOB4Est codes for a novel esterase of family VIII, with sequence similarity to β-lactamases, but with unusual wide substrate specificity. When the enzyme was purified from the mesophilic host it showed half-life of 1 h and 43 min at 50°C, and maximal activity at 40°C and pH 7.5 with p-nitrophenyl-laurate as substrate. Interestingly, the enzyme retained more than 80% of maximal activity in a broad range of pH from 6.5 to 8.}, } @article {pmid26634543, year = {2015}, author = {Silva Neta, MT and Maciel, BM and Lopes, AT and Marques, EL and Rezende, RP and Boehs, G}, title = {Microbiological quality and bacterial diversity of the tropical oyster Crassostrea rhizophorae in a monitored farming system and from natural stocks.}, journal = {Genetics and molecular research : GMR}, volume = {14}, number = {4}, pages = {15754-15768}, doi = {10.4238/2015.December.1.27}, pmid = {26634543}, issn = {1676-5680}, mesh = {*Agriculture ; Animals ; Bacteria/*classification/genetics ; *Biodiversity ; Brazil ; Crassostrea/*microbiology ; Environmental Microbiology ; Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; }, abstract = {Microbiological evaluation is one of the most important parameters for analyzing the viability of an oyster farming system, which addresses public health and ecological concerns. Here, the microbiological quality of the oyster Crassostrea rhizophorae cultivated in a monitored environment and from natural beds in Bahia, northeastern Brazil, was determined. Bacterial diversity in oysters was measured by polymerase chain reaction-denaturing gradient gel electrophoresis. Sequence analysis revealed that most bacterial species showed similarity with uncultured or unidentified bacteria from environmental samples, and were clustered into the phylum Proteobacteria. Diverse bacteria from cultivated (monitored) oyster samples were grouped in the same cluster with a high similarity index (above 79%). Microbiological analyses revealed that these oysters did not contain pathogens. These results reflect the natural balance of the microbial communities essential to the maintenance of health and in inhibiting pathogen colonization in the oyster. On the other hand, bacterial diversity of samples from native stocks in extractive areas displayed a similarity index varying between 55 and 77%, and all samples were clustered separately from each other and from the cluster of samples derived from the cultivation area. Microbiological analyses showed that oysters from the extractive area were not fit for human consumption. This reflected a different composition of the microbial community in this area, probably resulting from anthropic impact. Our study also demonstrated that low temperatures and high rainfall limits the bacterial concentration in tropical oysters. This is the first study analyzing the total bacterial community profiles of the oyster C. rhizophorae.}, } @article {pmid26633628, year = {2015}, author = {Forslund, K and Hildebrand, F and Nielsen, T and Falony, G and Le Chatelier, E and Sunagawa, S and Prifti, E and Vieira-Silva, S and Gudmundsdottir, V and Pedersen, HK and Arumugam, M and Kristiansen, K and Voigt, AY and Vestergaard, H and Hercog, R and Costea, PI and Kultima, JR and Li, J and Jørgensen, T and Levenez, F and Dore, J and , and Nielsen, HB and Brunak, S and Raes, J and Hansen, T and Wang, J and Ehrlich, SD and Bork, P and Pedersen, O}, title = {Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.}, journal = {Nature}, volume = {528}, number = {7581}, pages = {262-266}, pmid = {26633628}, issn = {1476-4687}, mesh = {Biodiversity ; Diabetes Mellitus, Type 2/drug therapy/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/genetics/*physiology ; Humans ; Hypoglycemic Agents/pharmacology/therapeutic use ; Male ; Metagenome/drug effects/physiology ; Metformin/*pharmacology/therapeutic use ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In recent years, several associations between common chronic human disorders and altered gut microbiome composition and function have been reported. In most of these reports, treatment regimens were not controlled for and conclusions could thus be confounded by the effects of various drugs on the microbiota, which may obscure microbial causes, protective factors or diagnostically relevant signals. Our study addresses disease and drug signatures in the human gut microbiome of type 2 diabetes mellitus (T2D). Two previous quantitative gut metagenomics studies of T2D patients that were unstratified for treatment yielded divergent conclusions regarding its associated gut microbial dysbiosis. Here we show, using 784 available human gut metagenomes, how antidiabetic medication confounds these results, and analyse in detail the effects of the most widely used antidiabetic drug metformin. We provide support for microbial mediation of the therapeutic effects of metformin through short-chain fatty acid production, as well as for potential microbiota-mediated mechanisms behind known intestinal adverse effects in the form of a relative increase in abundance of Escherichia species. Controlling for metformin treatment, we report a unified signature of gut microbiome shifts in T2D with a depletion of butyrate-producing taxa. These in turn cause functional microbiome shifts, in part alleviated by metformin-induced changes. Overall, the present study emphasizes the need to disentangle gut microbiota signatures of specific human diseases from those of medication.}, } @article {pmid26633360, year = {2015}, author = {Cuadrat, RR and Cury, JC and Dávila, AM}, title = {Metagenomic Analysis of Upwelling-Affected Brazilian Coastal Seawater Reveals Sequence Domains of Type I PKS and Modular NRPS.}, journal = {International journal of molecular sciences}, volume = {16}, number = {12}, pages = {28285-28295}, pmid = {26633360}, issn = {1422-0067}, mesh = {Computational Biology ; Datasets as Topic ; *Metagenomics ; Peptide Synthases/*genetics ; Phylogeny ; Polyketide Synthases/*genetics ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {Marine environments harbor a wide range of microorganisms from the three domains of life. These microorganisms have great potential to enable discovery of new enzymes and bioactive compounds for industrial use. However, only ~1% of microorganisms from the environment can currently be identified through cultured isolates, limiting the discovery of new compounds. To overcome this limitation, a metagenomics approach has been widely adopted for biodiversity studies on samples from marine environments. In this study, we screened metagenomes in order to estimate the potential for new natural compound synthesis mediated by diversity in the Polyketide Synthase (PKS) and Nonribosomal Peptide Synthetase (NRPS) genes. The samples were collected from the Praia dos Anjos (Angel's Beach) surface water-Arraial do Cabo (Rio de Janeiro state, Brazil), an environment affected by upwelling. In order to evaluate the potential for screening natural products in Arraial do Cabo samples, we used KS (keto-synthase) and C (condensation) domains (from PKS and NRPS, respectively) to build Hidden Markov Models (HMM) models. From both samples, a total of 84 KS and 46 C novel domain sequences were obtained, showing the potential of this environment for the discovery of new genes of biotechnological interest. These domains were classified by phylogenetic analysis and this was the first study conducted to screen PKS and NRPS genes in an upwelling affected sample.}, } @article {pmid26632844, year = {2015}, author = {Millares, L and Pérez-Brocal, V and Ferrari, R and Gallego, M and Pomares, X and García-Núñez, M and Montón, C and Capilla, S and Monsó, E and Moya, A}, title = {Functional Metagenomics of the Bronchial Microbiome in COPD.}, journal = {PloS one}, volume = {10}, number = {12}, pages = {e0144448}, pmid = {26632844}, issn = {1932-6203}, mesh = {Aged ; Disease Progression ; Female ; Humans ; Lung/*metabolism/pathology ; Male ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; Middle Aged ; Pulmonary Disease, Chronic Obstructive/genetics/*metabolism/pathology ; RNA, Ribosomal, 16S/genetics/*metabolism ; }, abstract = {The course of chronic obstructive pulmonary disease (COPD) is frequently aggravated by exacerbations, and changes in the composition and activity of the microbiome may be implicated in their appearance. The aim of this study was to analyse the composition and the gene content of the microbial community in bronchial secretions of COPD patients in both stability and exacerbation. Taxonomic data were obtained by 16S rRNA gene amplification and pyrosequencing, and metabolic information through shotgun metagenomics, using the Metagenomics RAST server (MG-RAST), and the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) programme, which predict metagenomes from 16S data. Eight severe COPD patients provided good quality sputum samples, and no significant differences in the relative abundance of any phyla and genera were found between stability and exacerbation. Bacterial biodiversity (Chao1 and Shannon indexes) did not show statistical differences and beta-diversity analysis (Bray-Curtis dissimilarity index) showed a similar microbial composition in the two clinical situations. Four functional categories showed statistically significant differences with MG-RAST at KEGG level 2: in exacerbation, Cell growth and Death and Transport and Catabolism decreased in abundance [1.6 (0.2-2.3) vs 3.6 (3.3-6.9), p = 0.012; and 1.8 (0-3.3) vs 3.6 (1.8-5.1), p = 0.025 respectively], while Cancer and Carbohydrate Metabolism increased [0.8 (0-1.5) vs 0 (0-0.5), p = 0.043; and 7 (6.4-9) vs 5.9 (6.3-6.1), p = 0.012 respectively]. In conclusion, the bronchial microbiome as a whole is not significantly modified when exacerbation symptoms appear in severe COPD patients, but its functional metabolic capabilities show significant changes in several pathways.}, } @article {pmid26630941, year = {2015}, author = {Lin, KH and Liao, BY and Chang, HW and Huang, SW and Chang, TY and Yang, CY and Wang, YB and Lin, YT and Wu, YW and Tang, SL and Yu, HT}, title = {Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {1029}, pmid = {26630941}, issn = {1471-2164}, mesh = {Biodiversity ; Carbon/metabolism ; Carbon Cycle ; Genome, Bacterial ; Genomics/methods ; Hot Springs/*microbiology ; *Metabolomics ; *Metagenomics ; Microbial Interactions ; *Microbiota ; Nitrogen/metabolism ; Nitrogen Cycle ; Phylogeny ; Polymorphism, Single Nucleotide ; RNA, Ribosomal, 16S/genetics ; Taiwan ; *Water Microbiology ; }, abstract = {BACKGROUND: Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited.

RESULTS: In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted other carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions.

CONCLUSIONS: Our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures.}, } @article {pmid26626101, year = {2016}, author = {Rothenberg, SE and Keiser, S and Ajami, NJ and Wong, MC and Gesell, J and Petrosino, JF and Johs, A}, title = {The role of gut microbiota in fetal methylmercury exposure: Insights from a pilot study.}, journal = {Toxicology letters}, volume = {242}, number = {}, pages = {60-67}, pmid = {26626101}, issn = {1879-3169}, support = {L30 ES023165/ES/NIEHS NIH HHS/United States ; R15 ES022409/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biotransformation ; Feces/chemistry ; Female ; Fetal Blood/*metabolism ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Gene Expression Profiling/methods ; Gestational Age ; Hair/chemistry ; Humans ; Lyases/genetics/metabolism ; Maternal Exposure ; *Maternal-Fetal Exchange ; Metagenome ; Metagenomics/methods ; Methylmercury Compounds/*blood ; Oxidoreductases/genetics/metabolism ; Pilot Projects ; Pregnancy ; Pregnancy Trimester, Third ; Ribotyping ; }, abstract = {PURPOSE: The mechanisms by which gut microbiota contribute to methylmercury metabolism remain unclear. Among a cohort of pregnant mothers, the objectives of our pilot study were to determine (1) associations between gut microbiota and mercury concentrations in biomarkers (stool, hair and cord blood) and (2) the contributions of gut microbial mercury methylation/demethylation to stool methylmercury.

METHODS: Pregnant women (36-39 weeks gestation, n=17) donated hair and stool specimens, and cord blood was collected for a subset (n=7). The diversity of gut microbiota was determined using 16S rRNA gene profiling (n=17). For 6 stool samples with highest/lowest methylmercury concentrations, metagenomic whole genome shotgun sequencing was employed to search for the mercury methylation gene (hgcA), and two mer operon genes involved in methylmercury detoxification (merA and merB).

RESULTS: Seventeen bacterial genera were significantly correlated (increasing or decreasing) with stool methylmercury, stool inorganic mercury, or hair total mercury; however, aside from one genus, there was no overlap between biomarkers. There were no definitive matches for hgcA or merB, while merA was detected at low concentrations in all six samples.

MAJOR CONCLUSIONS: Proportional differences in stool methylmercury were not likely attributed to gut microbiota through methylation/demethylation. Gut microbiota potentially altered methylmercury metabolism using indirect pathways.}, } @article {pmid26625708, year = {2015}, author = {Shen, H and Ye, F and Xie, L and Yang, J and Li, Z and Xu, P and Meng, F and Li, L and Chen, Y and Bo, X and Ni, M and Zhang, X}, title = {Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {17450}, pmid = {26625708}, issn = {2045-2322}, mesh = {Aged ; Aged, 80 and over ; Bacteria/classification/*genetics ; Bile/*microbiology ; Female ; Gallstones/*microbiology ; Humans ; Male ; *Metagenome ; Microbial Consortia/*genetics ; Middle Aged ; }, abstract = {Despite the high worldwide prevalence of gallstone disease, the role of the biliary microbiota in gallstone pathogenesis remains obscure. Next-generation sequencing offers advantages for systematically understanding the human microbiota; however, there have been few such investigations of the biliary microbiome. Here, we performed whole-metagenome shotgun (WMS) sequencing and 16S rRNA sequencing on bile samples from 15 Chinese patients with gallstone disease. Microbial communities of most individuals were clustered into two types, according to the relative enrichment of different intestinal bacterial species. In the bile samples, oral cavity/respiratory tract inhabitants were more prevalent than intestinal inhabitants and existed in both community types. Unexpectedly, the two types were not associated with fever status or surgical history, and many bacteria were patient-specific. We identified 13 novel biliary bacteria based on WMS sequencing, as well as genes encoding putative proteins related to gallstone formation and bile resistance (e.g., β-glucuronidase and multidrug efflux pumps). Bile samples from gallstone patients had reduced microbial diversity compared to healthy faecal samples. Patient samples were enriched in pathways related to oxidative stress and flagellar assembly, whereas carbohydrate metabolic pathways showed varying behaviours. As the first biliary WMS survey, our study reveals the complexity and specificity of biliary microecology.}, } @article {pmid26621789, year = {2016}, author = {Herbst, FA and Lünsmann, V and Kjeldal, H and Jehmlich, N and Tholey, A and von Bergen, M and Nielsen, JL and Hettich, RL and Seifert, J and Nielsen, PH}, title = {Enhancing metaproteomics--The value of models and defined environmental microbial systems.}, journal = {Proteomics}, volume = {16}, number = {5}, pages = {783-798}, doi = {10.1002/pmic.201500305}, pmid = {26621789}, issn = {1615-9861}, mesh = {Animals ; Bacteria/*genetics ; Caenorhabditis elegans/genetics ; Ecosystem ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/microbiology ; Humans ; Metagenomics/*methods ; Proteome/*analysis ; Proteomics/*methods ; Sewage/*microbiology ; }, abstract = {Metaproteomics--the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time--has provided new features to study complex microbial communities in order to unravel these "black boxes." New technical challenges arose that were not an issue for classical proteome analytics before that could be tackled by the application of different model systems. Here, we review different current and future model systems for metaproteome analysis. Following a short introduction to microbial communities and metaproteomics, we introduce model systems for clinical and biotechnological research questions including acid mine drainage, anaerobic digesters, and activated sludge. Model systems are useful to evaluate the challenges encountered within (but not limited to) metaproteomics, including species complexity and coverage, biomass availability, or reliable protein extraction. The implementation of model systems can be considered as a step forward to better understand microbial community responses and ecological functions of single member organisms. In the future, improvements are necessary to fully explore complex environmental systems by metaproteomics.}, } @article {pmid26620247, year = {2016}, author = {Solomon, KV and Henske, JK and Theodorou, MK and O'Malley, MA}, title = {Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi.}, journal = {Anaerobe}, volume = {38}, number = {}, pages = {39-46}, doi = {10.1016/j.anaerobe.2015.11.008}, pmid = {26620247}, issn = {1095-8274}, mesh = {Cryopreservation/*methods ; DNA, Fungal/*isolation & purification ; *Fungi ; *Gastrointestinal Microbiome ; Genome, Fungal ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Sequence Analysis, DNA ; }, abstract = {Cell storage and DNA isolation are essential to developing an expanded suite of microorganisms for biotechnology. However, many features of non-model microbes, such as an anaerobic lifestyle and rigid cell wall, present formidable challenges to creating strain repositories and extracting high quality genomic DNA. Here, we establish accessible, high efficiency, and robust techniques to store lignocellulolytic anaerobic gut fungi long term without specialized equipment. Using glycerol as a cryoprotectant, gut fungal isolates were preserved for a minimum of 23 months at -80 °C. Unlike previously reported approaches, this improved protocol is non-toxic and rapid, with samples surviving twice as long with negligible growth impact. Genomic DNA extraction for these isolates was optimized to yield samples compatible with next generation sequencing platforms (e.g. Illumina, PacBio). Popular DNA isolation kits and precipitation protocols yielded preps that were unsuitable for sequencing due to carbohydrate contaminants from the chitin-rich cell wall and extensive energy reserves of gut fungi. To address this, we identified a proprietary method optimized for hardy plant samples that rapidly yielded DNA fragments in excess of 10 kb with minimal RNA, protein or carbohydrate contamination. Collectively, these techniques serve as fundamental tools to manipulate powerful biomass-degrading gut fungi and improve their accessibility among researchers.}, } @article {pmid26617277, year = {2015}, author = {Bauer, E and Laczny, CC and Magnusdottir, S and Wilmes, P and Thiele, I}, title = {Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {55}, pmid = {26617277}, issn = {2049-2618}, mesh = {Biomarkers ; Cell Membrane/metabolism ; Cluster Analysis ; *Energy Metabolism ; Gastrointestinal Microbiome/*physiology ; Genotype ; Humans ; Metagenome ; Models, Biological ; *Phenotype ; Phylogeny ; }, abstract = {BACKGROUND: The human gastrointestinal tract harbors a diverse microbial community, in which metabolic phenotypes play important roles for the human host. Recent developments in meta-omics attempt to unravel metabolic roles of microbes by linking genotypic and phenotypic characteristics. This connection, however, still remains poorly understood with respect to its evolutionary and ecological context.

RESULTS: We generated automatically refined draft genome-scale metabolic models of 301 representative intestinal microbes in silico. We applied a combination of unsupervised machine-learning and systems biology techniques to study individual and global differences in genomic content and inferred metabolic capabilities. Based on the global metabolic differences, we found that energy metabolism and membrane synthesis play important roles in delineating different taxonomic groups. Furthermore, we found an exponential relationship between phylogeny and the reaction composition, meaning that closely related microbes of the same genus can exhibit pronounced differences with respect to their metabolic capabilities while at the family level only marginal metabolic differences can be observed. This finding was further substantiated by the metabolic divergence within different genera. In particular, we could distinguish three sub-type clusters based on membrane and energy metabolism within the Lactobacilli as well as two clusters within the Bifidobacteria and Bacteroides.

CONCLUSIONS: We demonstrate that phenotypic differentiation within closely related species could be explained by their metabolic repertoire rather than their phylogenetic relationships. These results have important implications in our understanding of the ecological and evolutionary complexity of the human gastrointestinal microbiome.}, } @article {pmid26614914, year = {2016}, author = {Zhang, W and Tian, R and Bo, Y and Cao, H and Cai, L and Chen, L and Zhou, G and Sun, J and Zhang, X and Al-Suwailem, A and Qian, PY}, title = {Environmental switching during biofilm development in a cold seep system and functional determinants of species sorting.}, journal = {Molecular ecology}, volume = {25}, number = {9}, pages = {1958-1971}, doi = {10.1111/mec.13501}, pmid = {26614914}, issn = {1365-294X}, mesh = {Bacteria/*classification ; Biofilms/*growth & development ; Cold Temperature ; DNA, Bacterial/genetics ; *Ecosystem ; *Metagenome ; Microbial Consortia ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salts ; Seawater/*microbiology ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {The functional basis for species sorting theory remains elusive, especially for microbial community assembly in deep-sea environments. Using artificial surface-based biofilm models, our recent work revealed taxonomic succession during biofilm development in a newly defined cold seep system, the Thuwal cold seeps II, which comprises a brine pool and the adjacent normal bottom water (NBW) to form a metacommunity via the potential immigration of organisms from one patch to another. Here, we designed an experiment to investigate the effects of environmental switching between the brine pool and the NBW on biofilm assembly, which could reflect environmental filtering effects during bacterial immigration to new environments. Analyses of 16S rRNA genes of 71 biofilm samples suggested that the microbial composition of biofilms established in new environments was determined by both the source community and the incubation conditions. Moreover, a comparison of 18 metagenomes provided evidence for biofilm community assembly that was based primarily on functional features rather than taxonomic identities; metal ion resistance and amino acid metabolism were the major species sorting determinants for the succession of biofilm communities. Genome binning and pathway reconstruction of two bacterial species (Marinobacter sp. and Oleispira sp.) further demonstrated metal ion resistance and amino acid metabolism as functional traits conferring the survival of habitat generalists in both the brine pool and NBW. The results of this study shed new light on microbial community assembly in special habitats and bridge a gap in species sorting theory.}, } @article {pmid26613748, year = {2016}, author = {Söllinger, A and Schwab, C and Weinmaier, T and Loy, A and Tveit, AT and Schleper, C and Urich, T}, title = {Phylogenetic and genomic analysis of Methanomassiliicoccales in wetlands and animal intestinal tracts reveals clade-specific habitat preferences.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {1}, pages = {}, doi = {10.1093/femsec/fiv149}, pmid = {26613748}, issn = {1574-6941}, support = {P 23117/FWF_/Austrian Science Fund FWF/Austria ; P 25369/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Air Pollutants/metabolism ; Animals ; Austria ; Base Sequence ; Cattle ; Ecosystem ; Euryarchaeota/*classification/*genetics/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Genomics ; Germany ; Humans ; Italy ; Metagenome ; Methane/biosynthesis/*metabolism ; Oxidoreductases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; Soil/chemistry ; Soil Microbiology ; Wetlands ; }, abstract = {Methanogenic Thermoplasmata of the novel order Methanomassiliicoccales were recently discovered in human and animal gastro-intestinal tracts (GITs). However, their distribution in other methanogenic environments has not been addressed systematically. Here, we surveyed Methanomassiliicoccales presence in wetland soils, a globally important source of methane emissions to the atmosphere, and in the GITs of different animals by PCR targeting their 16S rRNA and methyl:coenzyme M reductase (α-subunit) genes. We detected Methanomassiliicoccales in all 16 peat soils investigated, indicating their wide distribution in these habitats. Additionally, we detected their genes in various animal faeces. Methanomassiliicoccales were subdivided in two broad phylogenetic clades designated 'environmental' and 'GIT' clades based on differential, although non-exclusive, habitat preferences of their members. A well-supported cluster within the environmental clade comprised more than 80% of all wetland 16S rRNA gene sequences. Metagenome assembly from bovine rumen fluid enrichments resulted in two almost complete genomes of both Methanomassiliicoccales clades. Comparative genomics revealed that members of the environmental clade contain larger genomes and a higher number of genes encoding anti-oxidative enzymes than animal GIT clade representatives. This study highlights the wide distribution of Methanomassiliicoccales in wetlands, which suggests that they contribute to methane emissions from these climate-relevant ecosystems.}, } @article {pmid26613615, year = {2016}, author = {Manjula, A and Pushpanathan, M and Sathyavathi, S and Gunasekaran, P and Rajendhran, J}, title = {Comparative Analysis of Microbial Diversity in Termite Gut and Termite Nest Using Ion Sequencing.}, journal = {Current microbiology}, volume = {72}, number = {3}, pages = {267-275}, pmid = {26613615}, issn = {1432-0991}, mesh = {Animals ; *Biota ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Gastrointestinal Tract/microbiology ; *High-Throughput Nucleotide Sequencing ; Isoptera/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Termite gut and termite nest possess complex microbial communities. However, only limited information is available on the comparative investigation of termite gut- and nest-associated microbial communities. In the present study, we examined and compared the bacterial diversity of termite gut and their respective nest by high-throughput sequencing of V3 hypervariable region of 16S rDNA. A total of 14 barcoded libraries were generated from seven termite gut samples and their respective nest samples, and sequenced using Ion Torrent platform. The sequences of each group were pooled, which yielded 170,644 and 132,000 reads from termite gut and termite nest samples, respectively. Phylogenetic analysis revealed significant differences in the bacterial diversity and community structure between termite gut and termite nest samples. Phyla Verrucomicrobia and Acidobacteria were observed only in termite gut, whereas Synergistetes and Chlorobi were observed only in termite nest samples. These variations in microbial structure and composition could be attributed with the differences in physiological conditions prevailing in the termite gut (anoxic and alkaline) and termite nest (oxic, slightly acidic and rich in organic matter) environment. Overall, this study unmasked the complexity of bacterial population in the respective niche. Interestingly, majority of the sequence reads could be classified only up to the domain level indicating the presence of a huge number of uncultivable or unidentified novel bacterial species in both termite gut and nest samples. Whole metagenome sequencing and assessing the metabolic potential of these samples will be useful for biotechnological applications.}, } @article {pmid26607965, year = {2015}, author = {Rossmassler, K and Dietrich, C and Thompson, C and Mikaelyan, A and Nonoh, JO and Scheffrahn, RH and Sillam-Dussès, D and Brune, A}, title = {Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {56}, pmid = {26607965}, issn = {2049-2618}, mesh = {Animals ; Bacteria/classification/genetics ; *Gastrointestinal Microbiome ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Isoptera/*microbiology ; *Metagenome ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Termites are important contributors to carbon and nitrogen cycling in tropical ecosystems. Higher termites digest lignocellulose in various stages of humification with the help of an entirely prokaryotic microbiota housed in their compartmented intestinal tract. Previous studies revealed fundamental differences in community structure between compartments, but the functional roles of individual lineages in symbiotic digestion are mostly unknown.

RESULTS: Here, we conducted a highly resolved analysis of the gut microbiota in six species of higher termites that feed on plant material at different levels of humification. Combining amplicon sequencing and metagenomics, we assessed similarities in community structure and functional potential between the major hindgut compartments (P1, P3, and P4). Cluster analysis of the relative abundances of orthologous gene clusters (COGs) revealed high similarities among wood- and litter-feeding termites and strong differences to humivorous species. However, abundance estimates of bacterial phyla based on 16S rRNA genes greatly differed from those based on protein-coding genes.

CONCLUSION: Community structure and functional potential of the microbiota in individual gut compartments are clearly driven by the digestive strategy of the host. The metagenomics libraries obtained in this study provide the basis for future studies that elucidate the fundamental differences in the symbiont-mediated breakdown of lignocellulose and humus by termites of different feeding groups. The high proportion of uncultured bacterial lineages in all samples calls for a reference-independent approach for the correct taxonomic assignment of protein-coding genes.}, } @article {pmid26603211, year = {2015}, author = {Tian, BY and Cao, Y and Zhang, KQ}, title = {Metagenomic insights into communities, functions of endophytes, and their associates with infection by root-knot nematode, Meloidogyne incognita, in tomato roots.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {17087}, pmid = {26603211}, issn = {2045-2322}, mesh = {Animals ; Carbohydrate Metabolism/physiology ; Endophytes/*genetics/*metabolism ; Solanum lycopersicum/genetics/*microbiology/parasitology ; *Metagenomics ; Microbiota ; Nitrogen/metabolism ; Plant Proteins/metabolism ; Plant Roots/genetics/microbiology/parasitology ; Plant Tumors/genetics/microbiology ; Polysaccharides/metabolism ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Rhizosphere ; Sequence Analysis, DNA ; Tylenchoidea/genetics/*pathogenicity ; }, abstract = {Endophytes are known to play important roles in plant's health and productivity. In this study, we investigated the root microbiome of tomato in association with infection by root knot nematodes. Our objectives were to observe the effects and response of the bacterial endophytes before nematode attacks and to reveal the functional attributes of microbes in plant health and nematode pathogenesis. Community analysis of root-associated microbiomes in healthy and nematode-infected tomatoes indicated that nematode infections were associated with variation and differentiation of the endophyte and rhizosphere bacterial populations in plant roots. The community of the resident endophytes in tomato root was significantly affected by nemato-pathogenesis. Remarkably, some bacterial groups in the nematode feeding structure, the root gall, were specifically enriched, suggesting an association with nematode pathogenesis. Function-based metagenomic analysis indicated that the enriched bacterial populations in root gall harbored abundant genes related to degradation of plant polysaccharides, carbohydrate and protein metabolism, and biological nitrogen fixation. Our data indicated that some of the previously assumed beneficial endophytes or bacterial associates with nematode might be involved in nematode infections of the tomato roots.}, } @article {pmid26602877, year = {2016}, author = {Thomas, AC and Deagle, BE and Eveson, JP and Harsch, CH and Trites, AW}, title = {Quantitative DNA metabarcoding: improved estimates of species proportional biomass using correction factors derived from control material.}, journal = {Molecular ecology resources}, volume = {16}, number = {3}, pages = {714-726}, doi = {10.1111/1755-0998.12490}, pmid = {26602877}, issn = {1755-0998}, mesh = {Animals ; Biostatistics/*methods ; *Biota ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; }, abstract = {DNA metabarcoding is a powerful new tool allowing characterization of species assemblages using high-throughput amplicon sequencing. The utility of DNA metabarcoding for quantifying relative species abundances is currently limited by both biological and technical biases which influence sequence read counts. We tested the idea of sequencing 50/50 mixtures of target species and a control species in order to generate relative correction factors (RCFs) that account for multiple sources of bias and are applicable to field studies. RCFs will be most effective if they are not affected by input mass ratio or co-occurring species. In a model experiment involving three target fish species and a fixed control, we found RCFs did vary with input ratio but in a consistent fashion, and that 50/50 RCFs applied to DNA sequence counts from various mixtures of the target species still greatly improved relative abundance estimates (e.g. average per species error of 19 ± 8% for uncorrected vs. 3 ± 1% for corrected estimates). To demonstrate the use of correction factors in a field setting, we calculated 50/50 RCFs for 18 harbour seal (Phoca vitulina) prey species (RCFs ranging from 0.68 to 3.68). Applying these corrections to field-collected seal scats affected species percentages from individual samples (Δ 6.7 ± 6.6%) more than population-level species estimates (Δ 1.7 ± 1.2%). Our results indicate that the 50/50 RCF approach is an effective tool for evaluating and correcting biases in DNA metabarcoding studies. The decision to apply correction factors will be influenced by the feasibility of creating tissue mixtures for the target species, and the level of accuracy needed to meet research objectives.}, } @article {pmid26602872, year = {2015}, author = {d'Avila-Levy, CM and Boucinha, C and Kostygov, A and Santos, HL and Morelli, KA and Grybchuk-Ieremenko, A and Duval, L and Votýpka, J and Yurchenko, V and Grellier, P and Lukeš, J}, title = {Exploring the environmental diversity of kinetoplastid flagellates in the high-throughput DNA sequencing era.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {110}, number = {8}, pages = {956-965}, pmid = {26602872}, issn = {1678-8060}, mesh = {*Biodiversity ; Biomarkers ; Computational Biology ; DNA Barcoding, Taxonomic/trends ; DNA, Protozoan/*genetics ; Databases, Genetic ; Environment ; High-Throughput Nucleotide Sequencing/*methods ; Kinetoplastida/classification/cytology/*genetics ; Metagenomics/trends ; *Phylogeny ; RNA, Protozoan/*genetics ; RNA, Ribosomal, 18S/genetics ; }, abstract = {The class Kinetoplastea encompasses both free-living and parasitic species from a wide range of hosts. Several representatives of this group are responsible for severe human diseases and for economic losses in agriculture and livestock. While this group encompasses over 30 genera, most of the available information has been derived from the vertebrate pathogenic genera Leishmaniaand Trypanosoma. Recent studies of the previously neglected groups of Kinetoplastea indicated that the actual diversity is much higher than previously thought. This article discusses the known segment of kinetoplastid diversity and how gene-directed Sanger sequencing and next-generation sequencing methods can help to deepen our knowledge of these interesting protists.}, } @article {pmid26602791, year = {2016}, author = {Li, G and Xiong, J and Wong, PK and An, T}, title = {Enhancing tetrabromobisphenol A biodegradation in river sediment microcosms and understanding the corresponding microbial community.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {208}, number = {Pt B}, pages = {796-802}, doi = {10.1016/j.envpol.2015.11.001}, pmid = {26602791}, issn = {1873-6424}, mesh = {Bacillus/metabolism ; Benzhydryl Compounds/chemistry ; Biodegradation, Environmental/drug effects ; Biodiversity ; Electronic Waste/analysis ; Geologic Sediments/*chemistry/microbiology ; Ochrobactrum/metabolism ; Phenols/chemistry ; Polybrominated Biphenyls/analysis/chemistry/*metabolism ; RNA, Ribosomal, 16S ; Rivers/chemistry/*microbiology ; Sphingomonas ; }, abstract = {In situ remediation of contaminated sediment using microbes is a promising environmental treatment method. This study used bioaugmentation to investigate the biodegradation of tetrabromobisphenol A (TBBPA) in sediment microcosms collected from an electronic-waste recycling site. Treatments included adding possible biodegradation intermediates of TBBPA, including 2,4-dibromophenol (2,4-DBP), 2,4,6-tribromophenol (TBP), and bisphenol A (BPA) as co-substrates. Bioaugmentation was done with Ochrobactrum sp. T (TBBPA-degrader) and a mixed culture of Ochrobactrum sp. T, Bacillus sp. GZT (TBP-degrader) and Bacillus sp. GZB (BPA-degrader). Results showed that bioaugmentation with Ochrobactrum sp. T significantly improved TBBPA degradation efficiencies in sediment microcosms (P < 0.01); aerobic conditions increased the microbes' degradation activities. Co-substrates 2,4-DBP, TBP and BPA inhibited biodegradation of TBBPA. A metagenomic analysis of total 16S rRNA genes from the treated sediment microcosms showed that the following dominant genera: Ochrobactrum, Parasegetibacter, Thermithiobacillus, Phenylobacterium and Sphingomonas. The genus level of Ochrobactrum increased with increased degradation time, within 10-week of incubation. Microbes from genus Ochrobactrum are mainly linked to enhance the TBBPA biodegradation.}, } @article {pmid26601189, year = {2015}, author = {Aguirre de Cárcer, D and López-Bueno, A and Pearce, DA and Alcamí, A}, title = {Biodiversity and distribution of polar freshwater DNA viruses.}, journal = {Science advances}, volume = {1}, number = {5}, pages = {e1400127}, pmid = {26601189}, issn = {2375-2548}, abstract = {Viruses constitute the most abundant biological entities and a large reservoir of genetic diversity on Earth. Despite the recent surge in their study, our knowledge on their actual biodiversity and distribution remains sparse. We report the first metagenomic analysis of Arctic freshwater viral DNA communities and a comparative analysis with other freshwater environments. Arctic viromes are dominated by unknown and single-stranded DNA viruses with no close relatives in the database. These unique viral DNA communities mostly relate to each other and present some minor genetic overlap with other environments studied, including an Arctic Ocean virome. Despite common environmental conditions in polar ecosystems, the Arctic and Antarctic DNA viromes differ at the fine-grain genetic level while sharing a similar taxonomic composition. The study uncovers some viral lineages with a bipolar distribution, suggesting a global dispersal capacity for viruses, and seemingly indicates that viruses do not follow the latitudinal diversity gradient known for macroorganisms. Our study sheds light into the global biogeography and connectivity of viral communities.}, } @article {pmid26600078, year = {2016}, author = {Boursier, J and Mueller, O and Barret, M and Machado, M and Fizanne, L and Araujo-Perez, F and Guy, CD and Seed, PC and Rawls, JF and David, LA and Hunault, G and Oberti, F and Calès, P and Diehl, AM}, title = {The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota.}, journal = {Hepatology (Baltimore, Md.)}, volume = {63}, number = {3}, pages = {764-775}, pmid = {26600078}, issn = {1527-3350}, support = {R01 DK053792/DK/NIDDK NIH HHS/United States ; R56 DK106633/DK/NIDDK NIH HHS/United States ; R01-DK053792/DK/NIDDK NIH HHS/United States ; R01-DK106633/DK/NIDDK NIH HHS/United States ; }, mesh = {Aged ; Dysbiosis/*complications/*microbiology ; Feces/microbiology ; Female ; Fibrosis ; *Gastrointestinal Microbiome ; Humans ; Liver/pathology ; Male ; Metagenome ; Middle Aged ; Non-alcoholic Fatty Liver Disease/complications/*microbiology/pathology ; }, abstract = {UNLABELLED: Several animal studies have emphasized the role of gut microbiota in nonalcoholic fatty liver disease (NAFLD). However, data about gut dysbiosis in human NAFLD remain scarce in the literature, especially studies including the whole spectrum of NAFLD lesions. We aimed to evaluate the association between gut dysbiosis and severe NAFLD lesions, that is, nonalcoholic steatohepatitis (NASH) and fibrosis, in a well-characterized population of adult NAFLD. Fifty-seven patients with biopsy-proven NAFLD were enrolled. Taxonomic composition of gut microbiota was determined using 16S ribosomal RNA gene sequencing of stool samples. Thirty patients had F0/F1 fibrosis stage at liver biopsy (10 with NASH), and 27 patients had significant F≥2 fibrosis (25 with NASH). Bacteroides abundance was significantly increased in NASH and F≥2 patients, whereas Prevotella abundance was decreased. Ruminococcus abundance was significantly higher in F≥2 patients. By multivariate analysis, Bacteroides abundance was independently associated with NASH and Ruminococcus with F≥2 fibrosis. Stratification according to the abundance of these two bacteria generated three patient subgroups with increasing severity of NAFLD lesions. Based on imputed metagenomic profiles, Kyoto Encyclopedia of Genes and Genomes pathways significantly related to NASH and fibrosis F≥2 were mostly related to carbohydrate, lipid, and amino acid metabolism.

CONCLUSION: NAFLD severity associates with gut dysbiosis and a shift in metabolic function of the gut microbiota. We identified Bacteroides as independently associated with NASH and Ruminococcus with significant fibrosis. Thus, gut microbiota analysis adds information to classical predictors of NAFLD severity and suggests novel metabolic targets for pre-/probiotics therapies.}, } @article {pmid26599789, year = {2015}, author = {Laguardia-Nascimento, M and Branco, KM and Gasparini, MR and Giannattasio-Ferraz, S and Leite, LR and Araujo, FM and Salim, AC and Nicoli, JR and de Oliveira, GC and Barbosa-Stancioli, EF}, title = {Vaginal Microbiome Characterization of Nellore Cattle Using Metagenomic Analysis.}, journal = {PloS one}, volume = {10}, number = {11}, pages = {e0143294}, pmid = {26599789}, issn = {1932-6203}, mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Cattle ; Female ; Fungi/classification/genetics ; Gene Library ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Microbiota ; Phylogeny ; Vagina/*microbiology ; }, abstract = {Understanding of microbial communities inhabiting cattle vaginal tract may lead to a better comprehension of bovine physiology and reproductive health being of great economic interest. Up to date, studies involving cattle microbiota are focused on the gastrointestinal tract, and little is known about the vaginal microbiota. This study aimed to investigate the vaginal microbiome in Nellore cattle, heifers and cows, pregnant and non-pregnant, using a culture independent approach. The main bacterial phyla found were Firmicutes (~40-50%), Bacteroidetes (~15-25%) and Proteobacteria (~5-25%), in addition to ~10-20% of non-classified bacteria. 45-55% of the samples were represented by only ten OTUs: Aeribacillus, Bacteroides, Clostridium, Ruminococcus, Rikenella, Alistipes, Bacillus, Eubacterium, Prevotella and non-classified bacteria. Interestingly, microbiota from all 20 animals could be grouped according to the respiratory metabolism of the main OTUs found, creating three groups of vaginal microbiota in cattle. Archaeal samples were dominated by the Methanobrevibacter genus (Euryarchaeota, ~55-70%). Ascomycota was the main fungal phylum (~80-95%) and Mycosphaerella the most abundant genus (~70-85%). Hormonal influence was not clear, but a tendency for the reduction of bacterial and increase of archaeal populations in pregnant animals was observed. Eukaryotes did not vary significantly between pregnant and non-pregnant animals, but tended to be more abundant on cows than on heifers. The present work describes a great microbial variability in the vaginal community among the evaluated animals and groups (heifers and cows, pregnant and non-pregnant), which is significantly different from the findings previously reported using culture dependent methods, pointing out the need for further studies on this issue. The microbiome found also indicates that the vaginal colonization appears to be influenced by the gastrointestinal community.}, } @article {pmid26599606, year = {2015}, author = {Hart, ML and Meyer, A and Johnson, PJ and Ericsson, AC}, title = {Comparative Evaluation of DNA Extraction Methods from Feces of Multiple Host Species for Downstream Next-Generation Sequencing.}, journal = {PloS one}, volume = {10}, number = {11}, pages = {e0143334}, pmid = {26599606}, issn = {1932-6203}, support = {T32 OD011126/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; U42 OD010918-13/OD/NIH HHS/United States ; }, mesh = {Animals ; Biodiversity ; Cats ; Chemical Fractionation/*methods ; DNA/*isolation & purification ; Dogs ; Feces/*microbiology ; Gastrointestinal Microbiome ; *High-Throughput Nucleotide Sequencing/methods ; Horses ; *Metagenome ; Mice ; *Microbiota ; ROC Curve ; Zebrafish ; }, abstract = {The gastrointestinal tract contains a vast community of microbes that to this day remain largely unculturable, making studies in this area challenging. With the newly affordable advanced sequencing technology, important breakthroughs in this exciting field are now possible. However, standardized methods of sample collection, handling, and DNA extraction have yet to be determined. To help address this, we investigated the use of 5 common DNA extraction methods on fecal samples from 5 different species. Our data show that the method of DNA extraction impacts DNA concentration and purity, successful NGS amplification, and influences microbial communities seen in NGS output dependent on the species of fecal sample and the DNA extraction method used. These data highlight the importance of careful consideration of DNA extraction method used when designing and interpreting data from cross species studies.}, } @article {pmid26596573, year = {2016}, author = {Watts, MP and Moreau, JW}, title = {New insights into the genetic and metabolic diversity of thiocyanate-degrading microbial consortia.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {3}, pages = {1101-1108}, doi = {10.1007/s00253-015-7161-5}, pmid = {26596573}, issn = {1432-0614}, mesh = {Bacteria/classification/*genetics/isolation & purification/*metabolism ; Biodegradation, Environmental ; Biodiversity ; *Microbial Consortia ; Thiocyanates/*metabolism ; }, abstract = {Thiocyanate is a common contaminant of the gold mining and coal coking industries for which biological degradation generally represents the most viable approach to remediation. Recent studies of thiocyanate-degrading bioreactor systems have revealed new information on the structure and metabolic activity of thiocyanate-degrading microbial consortia. Previous knowledge was limited primarily to pure-culture or co-culture studies in which the effects of linked carbon, sulfur and nitrogen cycling could not be fully understood. High throughput sequencing, DNA fingerprinting and targeted gene amplification have now elucidated the genetic and metabolic diversity of these complex microbial consortia. Specifically, this has highlighted the roles of key consortium members involved in sulfur oxidation and nitrification. New insights into the biogeochemical cycling of sulfur and nitrogen in bioreactor systems allow tailoring of the microbial metabolism towards meeting effluent composition requirements. Here we review these rapidly advancing studies and synthesize a conceptual model to inform new biotechnologies for thiocyanate remediation.}, } @article {pmid26595736, year = {2015}, author = {Huang, YJ and Boushey, HA}, title = {The Sputum Microbiome in Chronic Obstructive Pulmonary Disease Exacerbations.}, journal = {Annals of the American Thoracic Society}, volume = {12 Suppl 2}, number = {Suppl 2}, pages = {S176-80}, pmid = {26595736}, issn = {2325-6621}, support = {K23 HL105572/HL/NHLBI NIH HHS/United States ; U10 HL098107/HL/NHLBI NIH HHS/United States ; HL098107/HL/NHLBI NIH HHS/United States ; }, mesh = {Adrenal Cortex Hormones/therapeutic use ; Anti-Bacterial Agents/therapeutic use ; Disease Progression ; Haemophilus influenzae/genetics ; Humans ; *Microbiota ; Pulmonary Disease, Chronic Obstructive/drug therapy/*microbiology/*physiopathology ; RNA, Ribosomal, 16S/genetics ; Sputum/*microbiology ; }, abstract = {Acute exacerbations of chronic obstructive pulmonary disease (COPD) are thought to be associated with--and perhaps to mediate--accelerated loss of lung function in COPD. Although the application of culture-independent methods for detection of bacteria have shown COPD to be associated with marked differences in the burden, diversity, and composition of the bronchial bacterial microbiome, few studies have examined the changes associated with community-acquired exacerbations of the disease. In a longitudinal cohort study of COPD, the availability of sputum samples from subjects obtained at the onset of an exacerbation and during periods of clinical stability before and after the event enabled us to recently address this gap in knowledge, using culture-independent, 16S rRNA-based analysis methods combined with in silico inference of metagenomic functions. We observed sputum bacterial composition to be generally stable over the preexacerbation period of clinical stability, but to change at the time of exacerbation, with specific enrichment in not only typical COPD-associated bacterial species (e.g., Haemophilus influenzae) but also other phylogenetically related species with pathogenic potential. Concurrently, we observed depleted abundance of other bacteria whose predicted metagenomes suggest functional capacities to produce a variety of antiinflammatory compounds. Most strikingly, we found that resolution of these exacerbation-related changes in sputum microbiota composition differed significantly, depending on the exacerbation treatments prescribed. Treatment with corticosteroids resulted in microbiome enrichment for a number of bacterial communities, mostly members of the Proteobacteria phylum, whereas prolonged suppression of microbiota was seen in those treated with antibiotics alone. Taken together, our findings suggest that exacerbations of COPD are associated with heterogeneous changes in the bronchial microbiome, with increases in the abundance of species related to typical COPD pathogens and decreases in microbiota members that contribute to compositional and functional homeostasis. The findings further suggest that exacerbation treatments may have very different impacts on the bronchial microbiome's rate of return toward baseline composition.}, } @article {pmid26594201, year = {2015}, author = {Zeldes, BM and Keller, MW and Loder, AJ and Straub, CT and Adams, MW and Kelly, RM}, title = {Extremely thermophilic microorganisms as metabolic engineering platforms for production of fuels and industrial chemicals.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1209}, pmid = {26594201}, issn = {1664-302X}, support = {T32 GM008776/GM/NIGMS NIH HHS/United States ; }, abstract = {Enzymes from extremely thermophilic microorganisms have been of technological interest for some time because of their ability to catalyze reactions of industrial significance at elevated temperatures. Thermophilic enzymes are now routinely produced in recombinant mesophilic hosts for use as discrete biocatalysts. Genome and metagenome sequence data for extreme thermophiles provide useful information for putative biocatalysts for a wide range of biotransformations, albeit involving at most a few enzymatic steps. However, in the past several years, unprecedented progress has been made in establishing molecular genetics tools for extreme thermophiles to the point that the use of these microorganisms as metabolic engineering platforms has become possible. While in its early days, complex metabolic pathways have been altered or engineered into recombinant extreme thermophiles, such that the production of fuels and chemicals at elevated temperatures has become possible. Not only does this expand the thermal range for industrial biotechnology, it also potentially provides biodiverse options for specific biotransformations unique to these microorganisms. The list of extreme thermophiles growing optimally between 70 and 100°C with genetic toolkits currently available includes archaea and bacteria, aerobes and anaerobes, coming from genera such as Caldicellulosiruptor, Sulfolobus, Thermotoga, Thermococcus, and Pyrococcus. These organisms exhibit unusual and potentially useful native metabolic capabilities, including cellulose degradation, metal solubilization, and RuBisCO-free carbon fixation. Those looking to design a thermal bioprocess now have a host of potential candidates to choose from, each with its own advantages and challenges that will influence its appropriateness for specific applications. Here, the issues and opportunities for extremely thermophilic metabolic engineering platforms are considered with an eye toward potential technological advantages for high temperature industrial biotechnology.}, } @article {pmid26590590, year = {2016}, author = {Assunção, A and Costa, MC and Carlier, JD}, title = {Application of urea-agarose gel electrophoresis to select non-redundant 16S rRNAs for taxonomic studies: palladium(II) removal bacteria.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {6}, pages = {2721-2735}, doi = {10.1007/s00253-015-7163-3}, pmid = {26590590}, issn = {1432-0614}, mesh = {Bacteria/classification/genetics/*metabolism ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrophoresis, Agar Gel/*methods ; Environmental Pollutants/*metabolism ; Metagenomics/*methods ; *Nucleic Acid Denaturation ; Palladium/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Urea ; }, abstract = {The 16S ribosomal RNA (rRNA) gene has been the most commonly used sequence to characterize bacterial communities. The classical approach to obtain gene sequences to study bacterial diversity implies cloning amplicons, selecting clones, and Sanger sequencing cloned fragments. A more recent approach is direct sequencing of millions of genes using massive parallel technologies, allowing a large-scale biodiversity analysis of many samples simultaneously. However, currently, this technique is still expensive when applied to few samples; therefore, the classical approach is still used. Recently, we found a community able to remove 50 mg/L Pd(II). In this work, aiming to identify the bacteria potentially involved in Pd(II) removal, the separation of urea/heat-denatured DNA fragments by urea-agarose gel electrophoresis was applied for the first time to select 16S rRNA-cloned amplicons for taxonomic studies. The major raise in the percentage of bacteria belonging to genus Clostridium sensu stricto from undetected to 21 and 41 %, respectively, for cultures without, with 5 and 50 mg/L Pd(II) accompanying Pd(II) removal point to this taxa as a potential key agent for the bio-recovery of this metal. Despite sulfate-reducing bacteria were not detected, the hypothesis of Pd(II) removal by activity of these bacteria cannot be ruled out because a slight decrease of sulfate concentration of the medium was verified and the formation of PbS precipitates seems to occur. This work also contributes with knowledge about suitable partial 16S rRNA gene regions for taxonomic studies and shows that unidirectional sequencing is enough when Sanger sequencing cloned 16S rRNA genes for taxonomic studies to genus level.}, } @article {pmid26589591, year = {2015}, author = {Levy, M and Thaiss, CA and Elinav, E}, title = {Metagenomic cross-talk: the regulatory interplay between immunogenomics and the microbiome.}, journal = {Genome medicine}, volume = {7}, number = {}, pages = {120}, pmid = {26589591}, issn = {1756-994X}, mesh = {Animals ; Gastrointestinal Tract/immunology/microbiology ; Gene Expression Regulation/immunology ; Genome, Microbial/genetics/immunology ; Humans ; Immune System/microbiology ; Immune System Diseases/immunology/microbiology ; Metagenomics/*methods ; Microbiota/*genetics/*immunology ; }, abstract = {The human microbiome, often referred to as the 'second genome', encompasses up to 100-fold more genes than the host genome. In contrast to the human genome, the microbial genome is flexible and amenable to change during the host's lifetime. As the composition of the microbial metagenome has been associated with the development of human disease, the mechanisms controlling the composition and function of the metagenome are of considerable interest and therapeutic potential. In the past few years, studies have revealed how the host immune system is involved in determining the microbial metagenome, and, in turn, how the microbiota regulates gene expression in the immune system. This species-specific bidirectional interaction is required for homeostatic health, whereas aberrations in the tightly controlled regulatory circuits that link the host immunogenome and the microbial metagenome drive susceptibility to common human diseases. Here, we summarize some of the major principles orchestrating this cross-talk between microbial and host genomes, with a special focus on the interaction between the intestinal immune system and the gut microbiome. Understanding the reciprocal genetic and epigenetic control between host and microbiota will be an important step towards the development of novel therapies against microbiome-driven diseases.}, } @article {pmid26588090, year = {2016}, author = {Putignani, L and Del Chierico, F and Vernocchi, P and Cicala, M and Cucchiara, S and Dallapiccola, B and , }, title = {Gut Microbiota Dysbiosis as Risk and Premorbid Factors of IBD and IBS Along the Childhood-Adulthood Transition.}, journal = {Inflammatory bowel diseases}, volume = {22}, number = {2}, pages = {487-504}, doi = {10.1097/MIB.0000000000000602}, pmid = {26588090}, issn = {1536-4844}, mesh = {Adult ; Child ; Dysbiosis/*complications/diagnosis ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*etiology ; Irritable Bowel Syndrome/*etiology ; Prognosis ; *Transition to Adult Care ; }, abstract = {Gastrointestinal disorders, although clinically heterogeneous, share pathogenic mechanisms, including genetic susceptibility, impaired gut barrier function, altered microbiota, and environmental triggers (infections, social and behavioral factors, epigenetic control, and diet). Gut microbiota has been studied for inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) in either children or adults, while modifiable gut microbiota features, acting as risk and premorbid factors along the childhood-adulthood transition, have not been thoroughly investigated so far. Indeed, the relationship between variations of the entire host/microbiota/environmental scenario and clinical phenotypes is still not fully understood. In this respect, tracking gut dysbiosis grading may help deciphering host phenotype-genotype associations and microbiota shifts in an integrated top-down omics-based approach within large-scale pediatric and adult case-control cohorts. Large-scale gut microbiota signatures and host inflammation patterns may be integrated with dietary habits, under genetic and epigenetic constraints, providing gut dysbiosis profiles acting as risk predictors of IBD or IBS in preclinical cases. Tracking dysbiosis supports new personalized/stratified IBD and IBS prevention programmes, generating Decision Support System tools. They include (1) high risk or flare-up recurrence -omics-based dysbiosis profiles; (2) microbial and molecular biomarkers of health and disease; (3) -omics-based pipelines for laboratory medicine diagnostics; (4) health apps for self-management of score-based dietary profiles, which can be shared with clinicians for nutritional habit and lifestyle amendment; (5) -omics profiling data warehousing and public repositories for IBD and IBS profile consultation. Dysbiosis-related indexes can represent novel laboratory and clinical medicine tools preventing or postponing the disease, finally interfering with its natural history.}, } @article {pmid26583008, year = {2015}, author = {Hemme, CL and Tu, Q and Shi, Z and Qin, Y and Gao, W and Deng, Y and Nostrand, JD and Wu, L and He, Z and Chain, PS and Tringe, SG and Fields, MW and Rubin, EM and Tiedje, JM and Hazen, TC and Arkin, AP and Zhou, J}, title = {Comparative metagenomics reveals impact of contaminants on groundwater microbiomes.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1205}, pmid = {26583008}, issn = {1664-302X}, abstract = {To understand patterns of geochemical cycling in pristine versus contaminated groundwater ecosystems, pristine shallow groundwater (FW301) and contaminated groundwater (FW106) samples from the Oak Ridge Integrated Field Research Center (OR-IFRC) were sequenced and compared to each other to determine phylogenetic and metabolic difference between the communities. Proteobacteria (e.g., Burkholderia, Pseudomonas) are the most abundant lineages in the pristine community, though a significant proportion (>55%) of the community is composed of poorly characterized low abundance (individually <1%) lineages. The phylogenetic diversity of the pristine community contributed to a broader diversity of metabolic networks than the contaminated community. In addition, the pristine community encodes redundant and mostly complete geochemical cycles distributed over multiple lineages and appears capable of a wide range of metabolic activities. In contrast, many geochemical cycles in the contaminated community appear truncated or minimized due to decreased biodiversity and dominance by Rhodanobacter populations capable of surviving the combination of stresses at the site. These results indicate that the pristine site contains more robust and encodes more functional redundancy than the stressed community, which contributes to more efficient nutrient cycling and adaptability than the stressed community.}, } @article {pmid26581409, year = {2015}, author = {Hevia, A and Delgado, S and Margolles, A and Sánchez, B}, title = {Application of density gradient for the isolation of the fecal microbial stool component and the potential use thereof.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {16807}, pmid = {26581409}, issn = {2045-2322}, mesh = {Bacteria/*isolation & purification ; Biodiversity ; Centrifugation, Density Gradient/*methods ; Feces/*microbiology ; Humans ; Microbiota ; Multivariate Analysis ; Phylogeny ; }, abstract = {The idea of considering the gut microbiota as a virtual human organ has led to the concept of fecal microbiota transplantation (FMT), which has recently been extremely successful in the treatment of cases of recurrent Clostridium difficile infection. Administration of safe, viable, and representative fecal microbiota is crucial for FMT. To our knowledge, suitable techniques and systematic conditions for separating the fecal microbiota from stool samples have not been thoroughly investigated. In this work we show the potential to separate stool microorganisms from the rest of fecal material using a procedure with a Nycodenz® density gradient, yielding 10(10) viable bacteria per two grams of feces. This procedure did not affect the original microbiota composition in terms of viability, distribution and proportions, as assessed by a phylogenetic metagenomic approach. Obtaining the fecal microbiota by concentration and separation of the microorganisms from the rest of the stool components would allow the standardization of its recovery and its long-term preservation. FMT or similar microbiota restoration therapies could be used for the treatment of several disorders, or even for aesthetic purposes, so the method described in our work may contribute to the setting of the basis for the development of safe and standardized products.}, } @article {pmid26579098, year = {2015}, author = {Sanli, K and Bengtsson-Palme, J and Nilsson, RH and Kristiansson, E and Alm Rosenblad, M and Blanck, H and Eriksson, KM}, title = {Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1192}, pmid = {26579098}, issn = {1664-302X}, abstract = {Periphyton communities are complex phototrophic, multispecies biofilms that develop on surfaces in aquatic environments. These communities harbor a large diversity of organisms comprising viruses, bacteria, algae, fungi, protozoans, and metazoans. However, thus far the total biodiversity of periphyton has not been described. In this study, we use metagenomics to characterize periphyton communities from the marine environment of the Swedish west coast. Although we found approximately ten times more eukaryotic rRNA marker gene sequences compared to prokaryotic, the whole metagenome-based similarity searches showed that bacteria constitute the most abundant phyla in these biofilms. We show that marine periphyton encompass a range of heterotrophic and phototrophic organisms. Heterotrophic bacteria, including the majority of proteobacterial clades and Bacteroidetes, and eukaryotic macro-invertebrates were found to dominate periphyton. The phototrophic groups comprise Cyanobacteria and the alpha-proteobacterial genus Roseobacter, followed by different micro- and macro-algae. We also assess the metabolic pathways that predispose these communities to an attached lifestyle. Functional indicators of the biofilm form of life in periphyton involve genes coding for enzymes that catalyze the production and degradation of extracellular polymeric substances, mainly in the form of complex sugars such as starch and glycogen-like meshes together with chitin. Genes for 278 different transporter proteins were detected in the metagenome, constituting the most abundant protein complexes. Finally, genes encoding enzymes that participate in anaerobic pathways, such as denitrification and methanogenesis, were detected suggesting the presence of anaerobic or low-oxygen micro-zones within the biofilms.}, } @article {pmid26578777, year = {2015}, author = {Low-Décarie, E and Kolber, M and Homme, P and Lofano, A and Dumbrell, A and Gonzalez, A and Bell, G}, title = {Community rescue in experimental metacommunities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {46}, pages = {14307-14312}, pmid = {26578777}, issn = {1091-6490}, mesh = {Base Sequence ; Biodegradation, Environmental ; *Biological Evolution ; Glucose/*metabolism ; Metagenome ; *Microbial Consortia ; *Models, Biological ; Molecular Sequence Data ; Propionates/*metabolism ; Soil ; *Soil Microbiology ; }, abstract = {The conditions that allow biodiversity to recover following severe environmental degradation are poorly understood. We studied community rescue, the recovery of a viable community through the evolutionary rescue of many populations within an evolving community, in metacommunities of soil microbes adapting to a herbicide. The metacommunities occupied a landscape of crossed spatial gradients of the herbicide (Dalapon) and a resource (glucose), whereas their constituent communities were either isolated or connected by dispersal. The spread of adapted communities across the landscape and the persistence of communities when that landscape was degraded were strongly promoted by dispersal, and the capacity to adapt to lethal stress was also related to community size and initial diversity. After abrupt and lethal stress, community rescue was most frequent in communities that had previously experienced sublethal levels of stress and had been connected by dispersal. Community rescue occurred through the evolutionary rescue of both initially common taxa, which remained common, and of initially rare taxa, which grew to dominate the evolved community. Community rescue may allow productivity and biodiversity to recover from severe environmental degradation.}, } @article {pmid26578596, year = {2016}, author = {Forster, SC and Browne, HP and Kumar, N and Hunt, M and Denise, H and Mitchell, A and Finn, RD and Lawley, TD}, title = {HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes.}, journal = {Nucleic acids research}, volume = {44}, number = {D1}, pages = {D604-9}, pmid = {26578596}, issn = {1362-4962}, support = {/WT_/Wellcome Trust/United Kingdom ; 1091097/MRC_/Medical Research Council/United Kingdom ; BB/M011755/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Databases, Nucleic Acid ; Disease ; Gastrointestinal Tract/microbiology/virology ; Genes, Microbial ; *Genome, Microbial ; Humans ; Internet ; *Metagenomics/standards ; Microbiota ; Molecular Sequence Annotation ; Reference Standards ; Sequence Analysis, DNA ; }, abstract = {The Human Pan-Microbe Communities (HPMC) database (http://www.hpmcd.org/) provides a manually curated, searchable, metagenomic resource to facilitate investigation of human gastrointestinal microbiota. Over the past decade, the application of metagenome sequencing to elucidate the microbial composition and functional capacity present in the human microbiome has revolutionized many concepts in our basic biology. When sufficient high quality reference genomes are available, whole genome metagenomic sequencing can provide direct biological insights and high-resolution classification. The HPMC database provides species level, standardized phylogenetic classification of over 1800 human gastrointestinal metagenomic samples. This is achieved by combining a manually curated list of bacterial genomes from human faecal samples with over 21000 additional reference genomes representing bacteria, viruses, archaea and fungi with manually curated species classification and enhanced sample metadata annotation. A user-friendly, web-based interface provides the ability to search for (i) microbial groups associated with health or disease state, (ii) health or disease states and community structure associated with a microbial group, (iii) the enrichment of a microbial gene or sequence and (iv) enrichment of a functional annotation. The HPMC database enables detailed analysis of human microbial communities and supports research from basic microbiology and immunology to therapeutic development in human health and disease.}, } @article {pmid26577924, year = {2015}, author = {Castro-Mejía, JL and Muhammed, MK and Kot, W and Neve, H and Franz, CM and Hansen, LH and Vogensen, FK and Nielsen, DS}, title = {Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {64}, pmid = {26577924}, issn = {2049-2618}, mesh = {Bacteriophages/*genetics/isolation & purification/ultrastructure ; Biodiversity ; Computational Biology/methods ; DNA, Viral ; Feces/microbiology/virology ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Metagenomics/methods ; }, abstract = {BACKGROUND: The human gut is densely populated with archaea, eukaryotes, bacteria, and their viruses, such as bacteriophages. Advances in high-throughput sequencing (HTS) as well as bioinformatics have opened new opportunities for characterizing the viral communities harbored in our gut. However, limited attention has been given to the efficiency of protocols dealing with extraction of phages from fecal communities prior to HTS and their impact on the metagenomic dataset.

RESULTS: We describe two optimized methods for extraction of phages from fecal samples based on tangential-flow filtration (TFF) and polyethylene glycol precipitation (PEG) approaches using an adapted method from a published protocol as control (literature-adapted protocol (LIT)). To quantify phage recovery, samples were spiked with low numbers of c2, ϕ29, and T4 phages (representatives of the Siphoviridae, Podoviridae, and Myoviridae families, respectively) and their concentration (plaque-forming units) followed at every step during the extraction procedure. Compared with LIT, TFF and PEG had higher recovery of all spiked phages, yielding up to 16 times more phage particles (PPs) and up to 68 times more phage DNA per volume, increasing thus the chances of extracting low abundant phages. TFF- and PEG-derived metaviromes showed 10% increase in relative abundance of Caudovirales and unclassified phages infecting gut-associated bacteria (>92% for TFF and PEG, 82.4% for LIT). Our methods obtained lower relative abundance of the Myoviridae family (<16%) as compared to the reference protocol (22%). This decline, however, was not considered a true loss of Myoviridae phages but rather a greater level of extraction of Siphoviridae phages (TFF and PEG >32.5%, LIT 22.6%), which was achieved with the enhanced conditions of our procedures (e.g., reduced filter clogging). A high degree of phage diversity in samples extracted using TFF and PEG was documented by transmission electron microscopy.

CONCLUSIONS: Two procedures (TFF and PEG) for extraction of bacteriophages from fecal samples were optimized using a set of spiked bacteriophages as process control. These protocols are highly efficient tools for extraction and purification of PPs prior to HTS in phage-metavirome studies. Our methods can be easily modified, being thus applicable and adjustable for in principle any solid environmental material in dissolution.}, } @article {pmid26576770, year = {2015}, author = {Fernandez, M and Riveros, JD and Campos, M and Mathee, K and Narasimhan, G}, title = {Microbial "social networks".}, journal = {BMC genomics}, volume = {16 Suppl 11}, number = {Suppl 11}, pages = {S6}, pmid = {26576770}, issn = {1471-2164}, mesh = {Bacteria/classification/*genetics ; *Bacterial Physiological Phenomena ; Female ; Humans ; Male ; Metagenomics/*methods ; Microbiota ; Middle Aged ; Smoking ; }, abstract = {BACKGROUND: It is well understood that distinct communities of bacteria are present at different sites of the body, and that changes in the structure of these communities have strong implications for human health. Yet, challenges remain in understanding the complex interconnections between the bacterial taxa within these microbial communities and how they change during the progression of diseases. Many recent studies attempt to analyze the human microbiome using traditional ecological measures and cataloging differences in bacterial community membership. In this paper, we show how to push metagenomic analyses beyond mundane questions related to the bacterial taxonomic profiles that differentiate one sample from another.

METHODS: We develop tools and techniques that help us to investigate the nature of social interactions in microbial communities, and demonstrate ways of compactly capturing extensive information about these networks and visually conveying them in an effective manner. We define the concept of bacterial "social clubs", which are groups of taxa that tend to appear together in many samples. More importantly, we define the concept of "rival clubs", entire groups that tend to avoid occurring together in many samples. We show how to efficiently compute social clubs and rival clubs and demonstrate their utility with the help of examples including a smokers' dataset and a dataset from the Human Microbiome Project (HMP).

RESULTS: The tools developed provide a framework for analyzing relationships between bacterial taxa modeled as bacterial co-occurrence networks. The computational techniques also provide a framework for identifying clubs and rival clubs and for studying differences in the microbiomes (and their interactions) of two or more collections of samples.

CONCLUSIONS: Microbial relationships are similar to those found in social networks. In this work, we assume that strong (positive or negative) tendencies to co-occur or co-infect is likely to have biological, physiological, or ecological significance, possibly as a result of cooperation or competition. As a consequence of the analysis, a variety of biological interpretations are conjectured. In the human microbiome context, the pattern of strength of interactions between bacterial taxa is unique to body site.}, } @article {pmid26575616, year = {2016}, author = {Li, YF and Shi, J and Nelson, MC and Chen, PH and Graf, J and Li, Y and Yu, Z}, title = {Impact of different ratios of feedstock to liquid anaerobic digestion effluent on the performance and microbiome of solid-state anaerobic digesters digesting corn stover.}, journal = {Bioresource technology}, volume = {200}, number = {}, pages = {744-752}, doi = {10.1016/j.biortech.2015.10.078}, pmid = {26575616}, issn = {1873-2976}, mesh = {Anaerobiosis ; Archaea/metabolism ; Bacteria/genetics/metabolism ; Biodiversity ; Biofuels/analysis ; Bioreactors/*microbiology ; Fatty Acids, Volatile/analysis ; Hydrogen-Ion Concentration ; Methane/biosynthesis ; *Microbiota ; Phylogeny ; Principal Component Analysis ; Refuse Disposal/*instrumentation/*methods ; Sequence Analysis, DNA ; *Waste Disposal, Fluid ; *Waste Products ; Zea mays/*chemistry ; }, abstract = {The objective of this study was to understand how the non-microbial factors of L-AD effluent affected the microbiome composition and successions in the SS-AD digesters using both Illumina sequencing and qPCR quantification of major genera of methanogens. The SS-AD digesters started with a feedstock/total effluent (F/Et) ratio 2.2 (half of the effluent was autoclaved) performed stably, while the SS-AD digesters started with a 4.4 F/Et ratio (no autoclaved effluent) suffered from digester acidification, accumulation of volatile fatty acids, and ceased biogas production two weeks after startup. Some bacteria and methanogens were affected by non-microbial factors of the L-AD fluent. Alkalinity, the main difference between the two F/Et ratios, may be the crucial factor when SS-AD digesters were started using L-AD effluent.}, } @article {pmid26569458, year = {2015}, author = {Glassing, A and Dowd, SE and Galandiuk, S and Davis, B and Jorden, JR and Chiodini, RJ}, title = {Changes in 16s RNA Gene Microbial Community Profiling by Concentration of Prokaryotic DNA.}, journal = {Journal of microbiological methods}, volume = {119}, number = {}, pages = {239-242}, doi = {10.1016/j.mimet.2015.11.001}, pmid = {26569458}, issn = {1872-8359}, mesh = {Bacteria/classification/genetics/*isolation & purification ; DNA, Bacterial/genetics ; Humans ; Ileum/*microbiology ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Microbial metagenomics are hindered in clinical tissue samples as a result of the large relative amount of human DNA in relation to microbial DNA acting as competitive inhibitors of downstream applications. We evaluated the LOOXSTER® Enrichment Kit to separate eukaryotic and prokaryotic DNA in submucosal intestinal tissue samples having a low microbial biomass and to determine the effects of enrichment on 16s rRNA microbiota sequencing. The enrichment kit reduced the amount of human DNA in the samples 40-70% resulting in a 3.5-fold increase in the number of 16s bacterial gene sequences detected on the Illumina MiSeq platform. This increase was accompanied by the detection of 41 additional bacterial genera and 94 tentative species. The additional bacterial taxa detected accounted for as much as 25% of the total bacterial population that significantly altered the relative prevalence and composition of the intestinal microbiota. The ability to reduce the competitive inhibition created by human DNA and the concentration of bacterial DNA may allow metagenomics to be performed on complex tissues containing a low bacterial biomass.}, } @article {pmid26569070, year = {2016}, author = {Li, H and He, J and Jia, W}, title = {The influence of gut microbiota on drug metabolism and toxicity.}, journal = {Expert opinion on drug metabolism & toxicology}, volume = {12}, number = {1}, pages = {31-40}, pmid = {26569070}, issn = {1744-7607}, support = {P30 CA071789/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Drug Design ; Drug-Related Side Effects and Adverse Reactions/*metabolism/microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Humans ; Metabolomics/methods ; Metagenomics/methods ; Pharmaceutical Preparations/administration & dosage/*metabolism ; }, abstract = {INTRODUCTION: Gut microbiota plays critical roles in drug metabolism. The variation of gut microbiota contributes to the interindividual differences toward drug therapy including drug-induced toxicity and efficacy. Accordingly, the investigation and elucidation of gut microbial impacts on drug metabolism and toxicity will not only facilitate the way of personalized medicine, but also improve rational drug design.

AREAS COVERED: This review provides an overview of the microbiota-host co-metabolism on drug metabolism and summarizes 30 clinical drugs that are co-metabolized by host and gut microbiota. Moreover, this review is specifically focused on elucidating the gut microbial modulation of some clinical drugs, in which the gut microbial influences on drug metabolism, drug-induced toxicity and efficacy are discussed.

EXPERT OPINION: The gut microbial contribution to drug metabolism and toxicity is increasingly recognized, but remains largely unexplored due to the extremely complex relationship between gut microbiota and host. The mechanistic elucidation of gut microbiota in drug metabolism is critical before any practical progress in drug design or personalized medicine could be made by modulating human gut microbiota. Analytical technique innovation is urgently required to strengthen our capability in recognizing microbial functions, including metagenomics, metabolomics and the integration of multidisciplinary knowledge.}, } @article {pmid26568626, year = {2016}, author = {Biggs, MB and Papin, JA}, title = {Metabolic network-guided binning of metagenomic sequence fragments.}, journal = {Bioinformatics (Oxford, England)}, volume = {32}, number = {6}, pages = {867-874}, pmid = {26568626}, issn = {1367-4811}, support = {R01 GM108501/GM/NIGMS NIH HHS/United States ; T32 GM008715/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Cluster Analysis ; Humans ; Metabolic Networks and Pathways ; *Metagenomics ; Microbiota ; }, abstract = {MOTIVATION: Most microbes on Earth have never been grown in a laboratory, and can only be studied through DNA sequences. Environmental DNA sequence samples are complex mixtures of fragments from many different species, often unknown. There is a pressing need for methods that can reliably reconstruct genomes from complex metagenomic samples in order to address questions in ecology, bioremediation, and human health.

RESULTS: We present the SOrting by NEtwork Completion (SONEC) approach for assigning reactions to incomplete metabolic networks based on a metabolite connectivity score. We successfully demonstrate proof of concept in a set of 100 genome-scale metabolic network reconstructions, and delineate the variables that impact reaction assignment accuracy. We further demonstrate the integration of SONEC with existing approaches (such as cross-sample scaffold abundance profile clustering) on a set of 94 metagenomic samples from the Human Microbiome Project. We show that not only does SONEC aid in reconstructing species-level genomes, but it also improves functional predictions made with the resulting metabolic networks.

The datasets and code presented in this work are available at: https://bitbucket.org/mattbiggs/sorting_by_network_completion/

CONTACT: papin@virginia.edu

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid26568202, year = {2016}, author = {Yurkov, AM and Röhl, O and Pontes, A and Carvalho, C and Maldonado, C and Sampaio, JP}, title = {Local climatic conditions constrain soil yeast diversity patterns in Mediterranean forests, woodlands and scrub biome.}, journal = {FEMS yeast research}, volume = {16}, number = {1}, pages = {fov103}, doi = {10.1093/femsyr/fov103}, pmid = {26568202}, issn = {1567-1364}, mesh = {*Biota ; *Climate ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; *Forests ; Mediterranean Region ; Metagenome ; Molecular Sequence Data ; Phylogeny ; Portugal ; Sequence Analysis, DNA ; *Soil Microbiology ; Yeasts/*classification/genetics/growth & development/*isolation & purification ; }, abstract = {Soil yeasts represent a poorly known fraction of the soil microbiome due to limited ecological surveys. Here, we provide the first comprehensive inventory of cultivable soil yeasts in a Mediterranean ecosystem, which is the leading biodiversity hotspot for vascular plants and vertebrates in Europe. We isolated and identified soil yeasts from forested sites of Serra da Arrábida Natural Park (Portugal), representing the Mediterranean forests, woodlands and scrub biome. Both cultivation experiments and the subsequent species richness estimations suggest the highest species richness values reported to date, resulting in a total of 57 and 80 yeast taxa, respectively. These values far exceed those reported for other forest soils in Europe. Furthermore, we assessed the response of yeast diversity to microclimatic environmental factors in biotopes composed of the same plant species but showing a gradual change from humid broadleaf forests to dry maquis. We observed that forest properties constrained by precipitation level had strong impact on yeast diversity and on community structure and lower precipitation resulted in an increased number of rare species and decreased evenness values. In conclusion, the structure of soil yeast communities mirrors the environmental factors that affect aboveground phytocenoses, aboveground biomass and plant projective cover.}, } @article {pmid26568112, year = {2015}, author = {Amato, KR and Yeoman, CJ and Cerda, G and Schmitt, CA and Cramer, JD and Miller, ME and Gomez, A and Turner, TR and Wilson, BA and Stumpf, RM and Nelson, KE and White, BA and Knight, R and Leigh, SR}, title = {Variable responses of human and non-human primate gut microbiomes to a Western diet.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {53}, pmid = {26568112}, issn = {2049-2618}, support = {P40 OD010965/OD/NIH HHS/United States ; P40 RR019963/RR/NCRR NIH HHS/United States ; P51 OD011132/OD/NIH HHS/United States ; R01 RR016300/RR/NCRR NIH HHS/United States ; 5R01RR016300/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Carbohydrate Metabolism ; Chlorocebus aethiops ; *Diet, High-Fat ; *Diet, Western ; Dietary Proteins/*administration & dosage ; Firmicutes/genetics/*isolation & purification ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/statistics & numerical data ; *Microbiota ; Models, Animal ; Prevotella/genetics/*isolation & purification ; }, abstract = {BACKGROUND: The human gut microbiota interacts closely with human diet and physiology. To better understand the mechanisms behind this relationship, gut microbiome research relies on complementing human studies with manipulations of animal models, including non-human primates. However, due to unique aspects of human diet and physiology, it is likely that host-gut microbe interactions operate differently in humans and non-human primates.

RESULTS: Here, we show that the human microbiome reacts differently to a high-protein, high-fat Western diet than that of a model primate, the African green monkey, or vervet (Chlorocebus aethiops sabaeus). Specifically, humans exhibit increased relative abundance of Firmicutes and reduced relative abundance of Prevotella on a Western diet while vervets show the opposite pattern. Predictive metagenomics demonstrate an increased relative abundance of genes associated with carbohydrate metabolism in the microbiome of only humans consuming a Western diet.

CONCLUSIONS: These results suggest that the human gut microbiota has unique properties that are a result of changes in human diet and physiology across evolution or that may have contributed to the evolution of human physiology. Therefore, the role of animal models for understanding the relationship between the human gut microbiota and host metabolism must be re-focused.}, } @article {pmid26565724, year = {2016}, author = {Sebastián, M and Smith, AF and González, JM and Fredricks, HF and Van Mooy, B and Koblížek, M and Brandsma, J and Koster, G and Mestre, M and Mostajir, B and Pitta, P and Postle, AD and Sánchez, P and Gasol, JM and Scanlan, DJ and Chen, Y}, title = {Lipid remodelling is a widespread strategy in marine heterotrophic bacteria upon phosphorus deficiency.}, journal = {The ISME journal}, volume = {10}, number = {4}, pages = {968-978}, pmid = {26565724}, issn = {1751-7370}, mesh = {Alphaproteobacteria/*metabolism ; Glycosyltransferases/metabolism ; Heterotrophic Processes ; Mediterranean Sea ; Oceans and Seas ; Phosphates/chemistry ; Phospholipases/metabolism ; Phospholipids/*chemistry ; Phosphorus/*chemistry ; Phylogeny ; Phytoplankton/*metabolism ; Seawater/*microbiology ; Water Microbiology ; }, abstract = {Upon phosphorus (P) deficiency, marine phytoplankton reduce their requirements for P by replacing membrane phospholipids with alternative non-phosphorus lipids. It was very recently demonstrated that a SAR11 isolate also shares this capability when phosphate starved in culture. Yet, the extent to which this process occurs in other marine heterotrophic bacteria and in the natural environment is unknown. Here, we demonstrate that the substitution of membrane phospholipids for a variety of non-phosphorus lipids is a conserved response to P deficiency among phylogenetically diverse marine heterotrophic bacteria, including members of the Alphaproteobacteria and Flavobacteria. By deletion mutagenesis and complementation in the model marine bacterium Phaeobacter sp. MED193 and heterologous expression in recombinant Escherichia coli, we confirm the roles of a phospholipase C (PlcP) and a glycosyltransferase in lipid remodelling. Analyses of the Global Ocean Sampling and Tara Oceans metagenome data sets demonstrate that PlcP is particularly abundant in areas characterized by low phosphate concentrations. Furthermore, we show that lipid remodelling occurs seasonally and responds to changing nutrient conditions in natural microbial communities from the Mediterranean Sea. Together, our results point to the key role of lipid substitution as an adaptive strategy enabling heterotrophic bacteria to thrive in the vast P-depleted areas of the ocean.}, } @article {pmid26565698, year = {2015}, author = {Hoy, YE and Bik, EM and Lawley, TD and Holmes, SP and Monack, DM and Theriot, JA and Relman, DA}, title = {Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time.}, journal = {PloS one}, volume = {10}, number = {11}, pages = {e0142825}, pmid = {26565698}, issn = {1932-6203}, support = {DP1 OD000964/OD/NIH HHS/United States ; P50 GM107615/GM/NIGMS NIH HHS/United States ; DP1OD000964/OD/NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Bacteria/*classification ; Diet ; Feces/*microbiology ; Female ; Genetic Variation ; Metagenome ; Mice ; Mice, Inbred Strains ; Microbiota/*genetics ; Models, Statistical ; Nucleotides/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Genetics, diet, and other environmental exposures are thought to be major factors in the development and composition of the intestinal microbiota of animals. However, the relative contributions of these factors in adult animals, as well as variation with time in a variety of important settings, are still not fully understood. We studied a population of inbred, female mice fed the same diet and housed under the same conditions. We collected fecal samples from 46 individual mice over two weeks, sampling four of these mice for periods as long as 236 days for a total of 190 samples, and determined the phylogenetic composition of their microbial communities after analyzing 1,849,990 high-quality pyrosequencing reads of the 16S rRNA gene V3 region. Even under these controlled conditions, we found significant inter-individual variation in community composition, as well as variation within an individual over time, including increases in alpha diversity during the first 2 months of co-habitation. Some variation was explained by mouse membership in different cage and vendor shipment groups. The differences among individual mice from the same shipment group and cage were still significant. Overall, we found that 23% of the variation in intestinal microbiota composition was explained by changes within the fecal microbiota of a mouse over time, 12% was explained by persistent differences among individual mice, 14% by cage, and 18% by shipment group. Our findings suggest that the microbiota of controlled populations of inbred laboratory animals may not be as uniform as previously thought, that animal rearing and handling may account for some variation, and that as yet unidentified factors may explain additional components of variation in the composition of the microbiota within populations and individuals over time. These findings have implications for the design and interpretation of experiments involving laboratory animals.}, } @article {pmid26565399, year = {2015}, author = {Nayfach, S and Bradley, PH and Wyman, SK and Laurent, TJ and Williams, A and Eisen, JA and Pollard, KS and Sharpton, TJ}, title = {Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes.}, journal = {PLoS computational biology}, volume = {11}, number = {11}, pages = {e1004573}, pmid = {26565399}, issn = {1553-7358}, support = {T32 EB009383/EB/NIBIB NIH HHS/United States ; T32 GM067547/GM/NIGMS NIH HHS/United States ; }, mesh = {Chromosome Mapping/*methods ; Computer Simulation ; Crohn Disease/microbiology ; Genetic Markers/genetics ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Models, Genetic ; }, abstract = {Shotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial communities. Several bioinformatic tools can be used to functionally annotate metagenomes, allowing researchers to draw inferences about the functional potential of the community and to identify putative functional biomarkers. However, little is known about how decisions made during annotation affect the reliability of the results. Here, we use statistical simulations to rigorously assess how to optimize annotation accuracy and speed, given parameters of the input data like read length and library size. We identify best practices in metagenome annotation and use them to guide the development of the Shotgun Metagenome Annotation Pipeline (ShotMAP). ShotMAP is an analytically flexible, end-to-end annotation pipeline that can be implemented either on a local computer or a cloud compute cluster. We use ShotMAP to assess how different annotation databases impact the interpretation of how marine metagenome and metatranscriptome functional capacity changes across seasons. We also apply ShotMAP to data obtained from a clinical microbiome investigation of inflammatory bowel disease. This analysis finds that gut microbiota collected from Crohn's disease patients are functionally distinct from gut microbiota collected from either ulcerative colitis patients or healthy controls, with differential abundance of metabolic pathways related to host-microbiome interactions that may serve as putative biomarkers of disease.}, } @article {pmid26563586, year = {2015}, author = {Ziesemer, KA and Mann, AE and Sankaranarayanan, K and Schroeder, H and Ozga, AT and Brandt, BW and Zaura, E and Waters-Rist, A and Hoogland, M and Salazar-García, DC and Aldenderfer, M and Speller, C and Hendy, J and Weston, DA and MacDonald, SJ and Thomas, GH and Collins, MJ and Lewis, CM and Hofman, C and Warinner, C}, title = {Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {16498}, pmid = {26563586}, issn = {2045-2322}, support = {//Wellcome Trust/United Kingdom ; R01 GM089886/GM/NIGMS NIH HHS/United States ; 097829//Wellcome Trust/United Kingdom ; }, mesh = {Archaeology ; Bacteria/classification/genetics ; Dental Calculus/microbiology ; Female ; Gastrointestinal Microbiome/genetics ; *Gene Amplification ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Metagenome/*genetics ; Metagenomics/*methods ; Methanobrevibacter/classification/genetics ; Microbiota/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/*genetics ; }, abstract = {To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.}, } @article {pmid26562935, year = {2015}, author = {Sébastien, A and Lester, PJ and Hall, RJ and Wang, J and Moore, NE and Gruber, MA}, title = {Invasive ants carry novel viruses in their new range and form reservoirs for a honeybee pathogen.}, journal = {Biology letters}, volume = {11}, number = {9}, pages = {20150610}, pmid = {26562935}, issn = {1744-957X}, mesh = {Animals ; Ants/*virology ; Argentina ; Australia ; Bees/virology ; Insect Viruses/classification/genetics/*isolation & purification ; *Introduced Species ; Metagenomics ; New Zealand ; Picornaviridae/classification/genetics/*isolation & purification ; RNA, Viral/classification/genetics/*isolation & purification ; }, abstract = {When exotic animal species invade new environments they also bring an often unknown microbial diversity, including pathogens. We describe a novel and widely distributed virus in one of the most globally widespread, abundant and damaging invasive ants (Argentine ants, Linepithema humile). The Linepithema humile virus 1 is a dicistrovirus, a viral family including species known to cause widespread arthropod disease. It was detected in samples from Argentina, Australia and New Zealand. Argentine ants in New Zealand were also infected with a strain of Deformed wing virus common to local hymenopteran species, which is a major pathogen widely associated with honeybee mortality. Evidence for active replication of viral RNA was apparent for both viruses. Our results suggest co-introduction and exchange of pathogens within local hymenopteran communities. These viral species may contribute to the collapse of Argentine ant populations and offer new options for the control of a globally widespread invader.}, } @article {pmid26558345, year = {2016}, author = {Lahoz-Monfort, JJ and Guillera-Arroita, G and Tingley, R}, title = {Statistical approaches to account for false-positive errors in environmental DNA samples.}, journal = {Molecular ecology resources}, volume = {16}, number = {3}, pages = {673-685}, doi = {10.1111/1755-0998.12486}, pmid = {26558345}, issn = {1755-0998}, mesh = {Biostatistics/*methods ; *Biota ; Computational Biology/methods ; DNA/chemistry/*genetics/*isolation & purification ; *Ecosystem ; *False Positive Reactions ; Metagenomics/*methods ; }, abstract = {Environmental DNA (eDNA) sampling is prone to both false-positive and false-negative errors. We review statistical methods to account for such errors in the analysis of eDNA data and use simulations to compare the performance of different modelling approaches. Our simulations illustrate that even low false-positive rates can produce biased estimates of occupancy and detectability. We further show that removing or classifying single PCR detections in an ad hoc manner under the suspicion that such records represent false positives, as sometimes advocated in the eDNA literature, also results in biased estimation of occupancy, detectability and false-positive rates. We advocate alternative approaches to account for false-positive errors that rely on prior information, or the collection of ancillary detection data at a subset of sites using a sampling method that is not prone to false-positive errors. We illustrate the advantages of these approaches over ad hoc classifications of detections and provide practical advice and code for fitting these models in maximum likelihood and Bayesian frameworks. Given the severe bias induced by false-negative and false-positive errors, the methods presented here should be more routinely adopted in eDNA studies.}, } @article {pmid26556279, year = {2015}, author = {Rasmussen, AL}, title = {Probing the Viromic Frontiers.}, journal = {mBio}, volume = {6}, number = {6}, pages = {e01767-15}, pmid = {26556279}, issn = {2150-7511}, mesh = {Humans ; Metagenomics/*methods ; *Microbiota ; Virology/*methods ; Viruses/*classification/genetics/*isolation & purification ; }, abstract = {Modern molecular technology, and particularly high-throughput sequencing (HTS), has revolutionized virus discovery and expanded the depth and breadth of the virome. Recent HTS was used to identify and discover a previously undescribed member of the family Flaviviridae that has genomic features characteristic of both hepaciviruses and pegiviruses. This virus, designated human hepegivirus-1 (HHpgV-1), may represent a previously undescribed new genus in the Flaviviridae family with implications for public health and blood supply safety. Detecting uncharacterized viruses such as HHpgV-1 in clinical samples requires an unbiased screening method that is as sensitive as PCR, while simultaneously detecting multiple rare viral sequences. The virome-capture-sequencing platform for vertebrate viruses (VirCapSeq-VERT) uses positive-selection oligonucleotide capture to sensitively detect sequences from every known vertebrate virus, even in high-background specimens with low-abundance viruses. VirCapSeq-VERT can also detect uncharacterized viruses with sequence homology to known viruses, enabling a new paradigm for virus detection.}, } @article {pmid26556275, year = {2015}, author = {Zaura, E and Brandt, BW and Teixeira de Mattos, MJ and Buijs, MJ and Caspers, MP and Rashid, MU and Weintraub, A and Nord, CE and Savell, A and Hu, Y and Coates, AR and Hubank, M and Spratt, DA and Wilson, M and Keijser, BJ and Crielaard, W}, title = {Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces.}, journal = {mBio}, volume = {6}, number = {6}, pages = {e01693-15}, pmid = {26556275}, issn = {2150-7511}, mesh = {Anti-Bacterial Agents/*administration & dosage/pharmacology ; DNA, Ribosomal/chemistry/genetics ; Feces/*microbiology ; Healthy Volunteers ; Humans ; Microbiota/*drug effects ; Placebos/administration & dosage ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; Sequence Analysis, DNA ; Sweden ; Time Factors ; United Kingdom ; }, abstract = {UNLABELLED: Due to the spread of resistance, antibiotic exposure receives increasing attention. Ecological consequences for the different niches of individual microbiomes are, however, largely ignored. Here, we report the effects of widely used antibiotics (clindamycin, ciprofloxacin, amoxicillin, and minocycline) with different modes of action on the ecology of both the gut and the oral microbiomes in 66 healthy adults from the United Kingdom and Sweden in a two-center randomized placebo-controlled clinical trial. Feces and saliva were collected at baseline, immediately after exposure, and 1, 2, 4, and 12 months after administration of antibiotics or placebo. Sequences of 16S rRNA gene amplicons from all samples and metagenomic shotgun sequences from selected baseline and post-antibiotic-treatment sample pairs were analyzed. Additionally, metagenomic predictions based on 16S rRNA gene amplicon data were performed using PICRUSt. The salivary microbiome was found to be significantly more robust, whereas the antibiotics negatively affected the fecal microbiome: in particular, health-associated butyrate-producing species became strongly underrepresented. Additionally, exposure to different antibiotics enriched genes associated with antibiotic resistance. In conclusion, healthy individuals, exposed to a single antibiotic treatment, undergo considerable microbial shifts and enrichment in antibiotic resistance in their feces, while their salivary microbiome composition remains unexpectedly stable. The health-related consequences for the gut microbiome should increase the awareness of the individual risks involved with antibiotic use, especially in a (diseased) population with an already dysregulated microbiome. On the other hand, understanding the mechanisms behind the resilience of the oral microbiome toward ecological collapse might prove useful in combating microbial dysbiosis elsewhere in the body.

IMPORTANCE: Many health care professionals use antibiotic prophylaxis strategies to prevent infection after surgery. This practice is under debate since it enhances the spread of antibiotic resistance. Another important reason to avoid nonessential use of antibiotics, the impact on our microbiome, has hardly received attention. In this study, we assessed the impact of antibiotics on the human microbial ecology at two niches. We followed the oral and gut microbiomes in 66 individuals from before, immediately after, and up to 12 months after exposure to different antibiotic classes. The salivary microbiome recovered quickly and was surprisingly robust toward antibiotic-induced disturbance. The fecal microbiome was severely affected by most antibiotics: for months, health-associated butyrate-producing species became strongly underrepresented. Additionally, there was an enrichment of genes associated with antibiotic resistance. Clearly, even a single antibiotic treatment in healthy individuals contributes to the risk of resistance development and leads to long-lasting detrimental shifts in the gut microbiome.}, } @article {pmid26556047, year = {2015}, author = {Shelburne, SA and Ajami, NJ and Chibucos, MC and Beird, HC and Tarrand, J and Galloway-Peña, J and Albert, N and Chemaly, RF and Ghantoji, SS and Marsh, L and Pemmaraju, N and Andreeff, M and Shpall, EJ and Wargo, JA and Rezvani, K and Alousi, A and Bruno, VM and Futreal, PA and Petrosino, JF and Kontoyiannis, DP}, title = {Implementation of a Pan-Genomic Approach to Investigate Holobiont-Infecting Microbe Interaction: A Case Report of a Leukemic Patient with Invasive Mucormycosis.}, journal = {PloS one}, volume = {10}, number = {11}, pages = {e0139851}, pmid = {26556047}, issn = {1932-6203}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; R01AI089891/AI/NIAID NIH HHS/United States ; R01 CA061508/CA/NCI NIH HHS/United States ; U19 AI110820/AI/NIAID NIH HHS/United States ; U19AI110820/AI/NIAID NIH HHS/United States ; HHSN272200900009C//PHS HHS/United States ; HHSN272200900009C/AI/NIAID NIH HHS/United States ; R01 AI089891/AI/NIAID NIH HHS/United States ; }, mesh = {Antifungal Agents/therapeutic use ; Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Chemotherapy-Induced Febrile Neutropenia ; Fungal Proteins/genetics ; Fungemia/microbiology ; Gastrointestinal Microbiome/*genetics ; *Genome, Fungal ; Host-Pathogen Interactions ; Humans ; Leukemia, Myeloid, Acute/*complications ; Male ; Middle Aged ; Mucor/*genetics/isolation & purification ; Mucormycosis/drug therapy/*microbiology ; Neoplasm Proteins/genetics ; Onychomycosis/complications ; Opportunistic Infections/drug therapy/*microbiology ; }, abstract = {Disease can be conceptualized as the result of interactions between infecting microbe and holobiont, the combination of a host and its microbial communities. It is likely that genomic variation in the host, infecting microbe, and commensal microbiota are key determinants of infectious disease clinical outcomes. However, until recently, simultaneous, multiomic investigation of infecting microbe and holobiont components has rarely been explored. Herein, we characterized the infecting microbe, host, micro- and mycobiomes leading up to infection onset in a leukemia patient that developed invasive mucormycosis. We discovered that the patient was infected with a strain of the recently described Mucor velutinosus species which we determined was hypervirulent in a Drosophila challenge model and has a predisposition for skin dissemination. After completing the infecting M. velutinosus genome and genomes from four other Mucor species, comparative pathogenomics was performed and assisted in identifying 66 M. velutinosus-specific putatively secreted proteins, including multiple novel secreted aspartyl proteinases which may contribute to the unique clinical presentation of skin dissemination. Whole exome sequencing of the patient revealed multiple non-synonymous polymorphisms in genes critical to control of fungal proliferation, such as TLR6 and PTX3. Moreover, the patient had a non-synonymous polymorphism in the NOD2 gene and a missense mutation in FUT2, which have been linked to microbial dysbiosis and microbiome diversity maintenance during physiologic stress, respectively. In concert with host genetic polymorphism data, the micro- and mycobiome analyses revealed that the infection developed amid a dysbiotic microbiome with low α-diversity, dominated by staphylococci. Additionally, longitudinal mycobiome data showed that M. velutinosus DNA was detectable in oral samples preceding disease onset. Our genome-level study of the host-infecting microbe-commensal triad extends the concept of personalized genomic medicine to the holobiont-infecting microbe interface thereby offering novel opportunities for using synergistic genetic methods to increase understanding of infectious diseases pathogenesis and clinical outcomes.}, } @article {pmid26555787, year = {2015}, author = {Burrough, ER and Arruda, BL and Patience, JF and Plummer, PJ}, title = {Alterations in the Colonic Microbiota of Pigs Associated with Feeding Distillers Dried Grains with Solubles.}, journal = {PloS one}, volume = {10}, number = {11}, pages = {e0141337}, pmid = {26555787}, issn = {1932-6203}, mesh = {Amino Acids ; *Animal Feed/analysis ; Animals ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Bacteroidetes/classification/isolation & purification ; Colon/*microbiology ; Dietary Fiber ; Dietary Proteins ; Firmicutes/classification/isolation & purification ; Fish Products ; Genes, Bacterial ; Metagenomics ; *Microbiota ; Ribotyping ; *Glycine max ; Sus scrofa/*microbiology ; Swine ; Whey ; *Zea mays ; }, abstract = {In an effort to reduce feed costs, many pork producers have increased their use of coproducts of biofuel production in commercial pig diets, including increased feeding of distiller's dried grains with solubles (DDGS). The inclusion of DDGS increases the insoluble fiber content in the ration, which has the potential to impact the colonic microbiota considerably as the large intestine contains a dynamic microenvironment with tremendous interplay between microorganisms. Any alteration to the physical or chemical properties of the colonic contents has the potential to impact the resident bacterial population and potentially favor or inhibit the establishment of pathogenic species. In the present study, colonic contents collected at necropsy from pigs fed either 30% or no DDGS were analyzed to examine the relative abundance of bacterial taxa associated with feeding this ingredient. No difference in alpha diversity (richness) was detected between diet groups. However, the beta diversity was significantly different between groups with feeding of DDGS being associated with a decreased Firmicutes:Bacteriodetes ratio (P = .004) and a significantly lower abundance of Lactobacillus spp. (P = .016). Predictive functional profiling of the microbiota revealed more predicted genes associated with carbohydrate metabolism, protein digestion, and degradation of glycans in the microbiota of pigs fed DDGS. Taken together, these findings confirm that alterations in dietary insoluble fiber significantly alter the colonic microbial profile of pigs and suggest the resultant microbiome may predispose to the development of colitis.}, } @article {pmid26553382, year = {2015}, author = {Yim, KJ and Kwon, J and Cha, IT and Oh, KS and Song, HS and Lee, HW and Rhee, JK and Song, EJ and Rho, JR and Seo, ML and Choi, JS and Choi, HJ and Lee, SJ and Nam, YD and Roh, SW}, title = {Occurrence of viable, red-pigmented haloarchaea in the plumage of captive flamingoes.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {16425}, pmid = {26553382}, issn = {2045-2322}, mesh = {Animals ; Archaea/*classification/genetics ; Birds/*microbiology ; Carotenoids/chemistry ; Chromatography, High Pressure Liquid ; Feathers/*microbiology ; Metagenome ; Metagenomics ; Microbiota ; Phylogeny ; *Pigmentation ; *Pigments, Biological/chemistry ; RNA, Ribosomal, 16S ; }, abstract = {Flamingoes (Phoenicopterus spp.) whose plumage displays elegant colors, inhabit warm regions close to the ocean throughout the world. The pink or reddish color of their plumage originates from carotenoids ingested from carotenoid-abundant food sources, since flamingoes are unable to synthesize these compounds de novo. In this study, viable red-colored archaeal strains classified as extremely halophilic archaea (i.e., haloarchaea) and belonging to the genera Halococcus and Halogeometricum were isolated from the plumage of flamingoes in captivity. Detailed analysis for haloarchaeal community structure in flamingo feathers based on metagenomic data identified several haloarchaeal genera and unclassified sequences of the class Halobacteria at the genus level. Carotenoid pigment analyses showed that a bacterioruberin precursor carotenoid in haloarchaea was identical to one of the pigments found in flamingo plumage. To the best of our knowledge, this is the first report of viable extremophilic archaea in avian plumage, thus contributing to our understanding of the ecology of haloarchaea. The potential influence of haloarchaea as an environmental factor determining avian plumage coloration should be investigated in further studies.}, } @article {pmid26552974, year = {2016}, author = {Gosalbes, MJ and Vázquez-Castellanos, JF and Angebault, C and Woerther, PL and Ruppé, E and Ferrús, ML and Latorre, A and Andremont, A and Moya, A}, title = {Carriage of Enterobacteria Producing Extended-Spectrum β-Lactamases and Composition of the Gut Microbiota in an Amerindian Community.}, journal = {Antimicrobial agents and chemotherapy}, volume = {60}, number = {1}, pages = {507-514}, pmid = {26552974}, issn = {1098-6596}, mesh = {Adult ; Aged ; Carrier State ; Desulfovibrio/genetics/isolation & purification ; Enterobacteriaceae/classification/enzymology/*genetics/isolation & purification ; Enterobacteriaceae Infections/*epidemiology/microbiology ; Feces/microbiology ; Female ; French Guiana/epidemiology ; Gastrointestinal Microbiome/*genetics ; Gene Expression ; *Genes, Bacterial ; Humans ; *Indians, North American ; Male ; Metagenome ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Transcriptome ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Epidemiological and individual risk factors for colonization by enterobacteria producing extended-spectrum beta-lactamases (E-ESBL) have been studied extensively, but whether such colonization is associated with significant changes in the composition of the rest of the microbiota is still unknown. To address this issue, we assessed in an isolated Amerindian Guianese community whether intestinal carriage of E-ESBL was associated with specificities in gut microbiota using metagenomic and metatranscriptomic approaches. While the richness of taxa of the active microbiota of carriers was similar to that of noncarriers, the taxa were less homogeneous. In addition, species of four genera, Desulfovibrio, Oscillospira, Parabacteroides, and Coprococcus, were significantly more abundant in the active microbiota of noncarriers than in the active microbiota of carriers, whereas such was the case only for species of Desulfovibrio and Oscillospira in the total microbiota. Differential genera in noncarrier microbiota could either be associated with resistance to colonization or be the consequence of the colonization by E-ESBL.}, } @article {pmid26552395, year = {2016}, author = {Llorens-Marès, T and Triadó-Margarit, X and Borrego, CM and Dupont, CL and Casamayor, EO}, title = {High Bacterial Diversity and Phylogenetic Novelty in Dark Euxinic Freshwaters Analyzed by 16S Tag Community Profiling.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {566-574}, pmid = {26552395}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation & purification/metabolism ; *Biodiversity ; DNA, Bacterial/genetics ; Lakes/*microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spain ; }, abstract = {Microbial communities growing under extreme low redox conditions are present in anoxic and sulfide-rich (euxinic) environments such as karstic lakes and experience limitation of electron acceptors. The fine natural chemical gradients and the large diversity of organic and inorganic compounds accumulated in bottom waters are impossible to mimic under laboratory conditions, and only a few groups have been cultured. We investigated the bacterial composition in the oxic-anoxic interface and in the deep waters of three sulfurous lakes from the Lake Banyoles karstic area (NE Spain) through 16S rRNA gene tag sequencing and identified the closest GenBank counterpart. High diversity indices were found in most of the samples with >15 phyla/classes and >45 bacterial orders. A higher proportion of operational taxonomic units (OTUs) of the "highest novelty" was found in the hypolimnia (38 % of total sequences) than in the metalimnia (17 %), whereas the percentage of OTUs closer to cultured counterparts (i.e., 97 % identity in the 16S rRNA gene) was 6 to 21 %, respectively. Elusimicrobia, Chloroflexi, Fibrobacteres, and Spirochaetes were the taxa with the highest proportion of novel sequences. Interestingly, tag sequencing results comparison with metagenomics data available from the same dataset, showed a systematic underestimation of sulfur-oxidizing Epsilonproteobacteria with the currently available 907R "universal" primer. Overall, despite the limitation of electron acceptors, a highly diverse and novel assemblage was present in dark and euxinic hypolimnetic freshwaters, unveiling a hotspot of microbial diversity with a remarkable gap with cultured counterparts.}, } @article {pmid26552373, year = {2015}, author = {Hanning, I and Diaz-Sanchez, S}, title = {The functionality of the gastrointestinal microbiome in non-human animals.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {51}, pmid = {26552373}, issn = {2049-2618}, mesh = {Adaptation, Biological ; Animals ; Bacteria ; Environment ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; }, abstract = {Due to the significance of the microbiome on human health, much of the current data available regarding microbiome functionality is centered on human medicine. For agriculturally important taxa, the functionality of gastrointestinal bacteria has been studied with the primary goals of improving animal health and production performance. With respect to cattle, the digestive functions of bacteria in cattle are unarguably critical to digestion and positively impact production performance. Conversely, some research suggests that the gastrointestinal microbiome in chickens competes with the host for nutrients and produces toxins that can harm the host resulting in decreased growth efficiency. Concerning many other species including reptiles and cetaceans, some cataloging of fecal bacteria has been conducted, but the functionality within the host remains ambiguous. These taxa could provide interesting gastrointestinal insight into functionality and symbiosis considering the extreme feeding regimes (snakes), highly specialized diets (vampire bats), and living environments (polar bears), which warrants further exploration.}, } @article {pmid26552345, year = {2015}, author = {Kovatcheva-Datchary, P and Nilsson, A and Akrami, R and Lee, YS and De Vadder, F and Arora, T and Hallen, A and Martens, E and Björck, I and Bäckhed, F}, title = {Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella.}, journal = {Cell metabolism}, volume = {22}, number = {6}, pages = {971-982}, doi = {10.1016/j.cmet.2015.10.001}, pmid = {26552345}, issn = {1932-7420}, mesh = {Aged ; Animals ; Bacteroides/genetics/growth & development/physiology ; Blood Glucose/analysis ; Cross-Over Studies ; Dietary Fiber/*pharmacology ; Feces/microbiology ; Female ; Glucose/*metabolism ; Glycogen/metabolism ; Humans ; Hydrogen/metabolism ; Insulin/blood ; Intestines/microbiology ; Liver/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Microbiota/*drug effects ; Middle Aged ; Prevotella/genetics/*growth & development/physiology ; RNA, Ribosomal, 16S/chemistry/metabolism ; }, abstract = {The gut microbiota plays an important role in human health by interacting with host diet, but there is substantial inter-individual variation in the response to diet. Here we compared the gut microbiota composition of healthy subjects who exhibited improved glucose metabolism following 3-day consumption of barley kernel-based bread (BKB) with those who responded least to this dietary intervention. The Prevotella/Bacteroides ratio was higher in responders than non-responders after BKB. Metagenomic analysis showed that the gut microbiota of responders was enriched in Prevotella copri and had increased potential to ferment complex polysaccharides after BKB. Finally, germ-free mice transplanted with microbiota from responder human donors exhibited improved glucose metabolism and increased abundance of Prevotella and liver glycogen content compared with germ-free mice that received non-responder microbiota. Our findings indicate that Prevotella plays a role in the BKB-induced improvement in glucose metabolism observed in certain individuals, potentially by promoting increased glycogen storage.}, } @article {pmid26551842, year = {2016}, author = {Ignacio, A and Fernandes, MR and Rodrigues, VA and Groppo, FC and Cardoso, AL and Avila-Campos, MJ and Nakano, V}, title = {Correlation between body mass index and faecal microbiota from children.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {22}, number = {3}, pages = {258.e1-8}, doi = {10.1016/j.cmi.2015.10.031}, pmid = {26551842}, issn = {1469-0691}, mesh = {*Body Mass Index ; Brazil/epidemiology ; Child ; Child, Preschool ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Microbiota ; Obesity/epidemiology/etiology ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; }, abstract = {Childhood obesity is an increasing problem at the global level and considered as a risk factor for obesity development and the associated co-morbidities in adult life. In this study, the occurrence of Bacteroides fragilis group, Clostridium spp., Bifidobacterium spp. and Escherichia coli in 84 faecal samples from 30 obese, 24 overweight and 30 lean children was verified by culture technique and quantitative determination by quantitative PCR. In addition, Lactobacillus spp. and Methanobrevibacter smithii were also analysed. A correlation between the body mass index (BMI) and these bacteria was sought. Bacteroides vulgatus, Clostridium perfringens and Bifidobacterium adolescentis were most prevalent in all samples evaluated by culture-method. The B. fragilis group were found at high concentrations in obese and overweight children when compared with the lean ones (p 0.015). The obese and overweight children harboured higher numbers of Lactobacillus spp. than lean children (p 0.022). The faecal concentrations of the B. fragilis group (r = 0.24; p 0.026) and Lactobacillus spp. (r = 0.44; p 0.002) were positively correlated with BMI. Bifidobacterium spp. were found in higher numbers in the lean group than the overweight and obese ones (p 0.042). Furthermore, a negative correlation between BMI and Bifidobacterium spp. copy number (r = -0.22; p 0.039) was observed. Our findings show some difference in the intestinal microbial ecosystem of obese children compared with the lean ones and a significant association between number of Lactobacillus spp. and B. fragilis group and BMI.}, } @article {pmid26551525, year = {2016}, author = {Wang, J and Sun, C and Liu, C and Yang, Y and Lu, W}, title = {Comparison of vaginal microbial community structure in healthy and endometritis dairy cows by PCR-DGGE and real-time PCR.}, journal = {Anaerobe}, volume = {38}, number = {}, pages = {1-6}, doi = {10.1016/j.anaerobe.2015.11.004}, pmid = {26551525}, issn = {1095-8274}, mesh = {Animals ; Cattle ; Cattle Diseases/*microbiology ; Cluster Analysis ; Denaturing Gradient Gel Electrophoresis ; Endometritis/*veterinary ; Female ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Vagina/*microbiology ; }, abstract = {The normal vaginal microflora provides protection against infections of the reproductive tract. Previous studies have focused on the isolation and screening of probiotic strains from the vagina of cows; however, the vaginal microflora of postpartum cows is poorly characterized. The present study was conducted to evaluate and characterize the vaginal microflora of healthy postpartum cows in relation to postpartum cows with endometritis by using PCR followed by denaturing gradient gel electrophoresis (PCR-DGGE) and Real-time PCR. The study population comprised 5 healthy cows and 5 cows with endometritis. The results indicated that the vaginal bacterial microflora of healthy postpartum cows was dominated by Lactobacillus sakei subsp. and Weissella koreensis, while there were no dominant bacterial species in the vaginal microflora of postpartum cows with endometritis. Common microorganisms such as Bacteroides spp., Fusobacterium spp., Enterococcus spp., Prevotella spp., Clostridium perfringens strains, and Escherichia coli were detected in both groups of cows by Real-time PCR. The bacterial diversity in the vagina of cows with endometritis was significantly higher than that in healthy cows. The results indicated that the vaginal microflora of cows with endometritis was more diverse and lacked dominant bacterial species as compared to that of the healthy cows, suggesting that disruption of the normal vaginal microflora may contribute to the onset of endometritis. This microbial community analysis provided information that might be used to develop probiotics to treat endometritis in cows; however, further investigation is needed.}, } @article {pmid26549842, year = {2015}, author = {Simões, MF and Antunes, A and Ottoni, CA and Amini, MS and Alam, I and Alzubaidy, H and Mokhtar, NA and Archer, JA and Bajic, VB}, title = {Soil and Rhizosphere Associated Fungi in Gray Mangroves (Avicennia marina) from the Red Sea--A Metagenomic Approach.}, journal = {Genomics, proteomics & bioinformatics}, volume = {13}, number = {5}, pages = {310-320}, pmid = {26549842}, issn = {2210-3244}, mesh = {Ascomycota/*genetics/isolation & purification ; Avicennia/*microbiology ; Basidiomycota/*genetics/isolation & purification ; Biodiversity ; Ecosystem ; Indian Ocean ; Metagenomics ; Plant Roots/*microbiology ; *Rhizosphere ; Soil ; Soil Microbiology ; }, abstract = {Covering a quarter of the world's tropical coastlines and being one of the most threatened ecosystems, mangroves are among the major sources of terrestrial organic matter to oceans and harbor a wide microbial diversity. In order to protect, restore, and better understand these ecosystems, researchers have extensively studied their microbiology, yet few surveys have focused on their fungal communities. Our lack of knowledge is even more pronounced for specific fungal populations, such as the ones associated with the rhizosphere. Likewise, the Red Sea gray mangroves (Avicennia marina) remain poorly characterized, and understanding of their fungal communities still relies on cultivation-dependent methods. In this study, we analyzed metagenomic datasets from gray mangrove rhizosphere and bulk soil samples collected in the Red Sea coast, to obtain a snapshot of their fungal communities. Our data indicated that Ascomycota was the dominant phylum (76%-85%), while Basidiomycota was less abundant (14%-24%), yet present in higher numbers than usually reported for such environments. Fungal communities were more stable within the rhizosphere than within the bulk soil, both at class and genus level. This finding is consistent with the intrinsic patchiness in soil sediments and with the selection of specific microbial communities by plant roots. Our study indicates the presence of several species on this mycobiome that were not previously reported as mangrove-associated. In particular, we detected representatives of several commercially-used fungi, e.g., producers of secreted cellulases and anaerobic producers of cellulosomes. These results represent additional insights into the fungal community of the gray mangroves of the Red Sea, and show that they are significantly richer than previously reported.}, } @article {pmid26549712, year = {2016}, author = {Luo, F and Devine, CE and Edwards, EA}, title = {Cultivating microbial dark matter in benzene-degrading methanogenic consortia.}, journal = {Environmental microbiology}, volume = {18}, number = {9}, pages = {2923-2936}, doi = {10.1111/1462-2920.13121}, pmid = {26549712}, issn = {1462-2920}, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; Benzene/*metabolism ; Biodegradation, Environmental ; Metagenome ; *Microbial Consortia ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The microbes responsible for anaerobic benzene biodegradation remain poorly characterized. In this study, we identified and quantified microbial populations in a series of 16 distinct methanogenic, benzene-degrading enrichment cultures using a combination of traditional 16S rRNA clone libraries (four cultures), pyrotag 16S rRNA amplicon sequencing (11 cultures), metagenome sequencing (1 culture) and quantitative polymerase chain reaction (qPCR; 12 cultures). An operational taxonomic unit (OTU) from the Deltaproteobacteria designated ORM2 that is only 84% to 86% similar to Syntrophus or Desulfobacterium spp. was consistently identified in all enrichment cultures, and typically comprised more than half of the bacterial sequences. In addition to ORM2, a sequence belonging to Parcubacteria (candidate division OD1) identified from the metagenome data was the only other OTU common to all the cultures surveyed. Culture transfers (1% and 0.1%) were made in the presence and absence of benzene, and the abundance of ORM2, OD1 and other OTUs was tracked over 415 days using qPCR. ORM2 sequence abundance increased only when benzene was present, while the abundance of OD1 and other OTUs increased even in the absence of benzene. Deltaproteobacterium ORM2 is unequivocally the benzene-metabolizing population. This study also hints at laboratory cultivation conditions for a member of the widely distributed yet uncultivated Parcubacteria (OD1).}, } @article {pmid26547806, year = {2015}, author = {Mundra, S and Bahram, M and Tedersoo, L and Kauserud, H and Halvorsen, R and Eidesen, PB}, title = {Temporal variation of Bistorta vivipara-associated ectomycorrhizal fungal communities in the High Arctic.}, journal = {Molecular ecology}, volume = {24}, number = {24}, pages = {6289-6302}, doi = {10.1111/mec.13458}, pmid = {26547806}, issn = {1365-294X}, mesh = {Arctic Regions ; *Biodiversity ; DNA, Fungal ; High-Throughput Nucleotide Sequencing ; Mycorrhizae/*classification/genetics ; Plant Roots/microbiology ; Polygonaceae/*microbiology ; *Seasons ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Ectomycorrhizal (ECM) fungi are important for efficient nutrient uptake of several widespread arctic plant species. Knowledge of temporal variation of ECM fungi, and the relationship of these patterns to environmental variables, is essential to understand energy and nutrient cycling in Arctic ecosystems. We sampled roots of Bistorta vivipara ten times over two years; three times during the growing-season (June, July and September) and twice during winter (November and April) of both years. We found 668 ECM OTUs belonging to 25 different ECM lineages, whereof 157 OTUs persisted throughout all sampling time-points. Overall, ECM fungal richness peaked in winter and species belonging to Cortinarius, Serendipita and Sebacina were more frequent in winter than during summer. Structure of ECM fungal communities was primarily affected by spatial factors. However, after accounting for spatial effects, significant seasonal variation was evident revealing correspondence with seasonal changes in environmental conditions. We demonstrate that arctic ECM richness and community structure differ between summer (growing-season) and winter, possibly due to reduced activity of the core community, and addition of fungi adapted for winter conditions forming a winter-active fungal community. Significant month × year interactions were observed both for fungal richness and community composition, indicating unpredictable between-year variation. Our study indicates that addressing seasonal changes requires replication over several years.}, } @article {pmid26547568, year = {2016}, author = {Guibert, LM and Loviso, CL and Borglin, S and Jansson, JK and Dionisi, HM and Lozada, M}, title = {Diverse Bacterial Groups Contribute to the Alkane Degradation Potential of Chronically Polluted Subantarctic Coastal Sediments.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {100-112}, pmid = {26547568}, issn = {1432-184X}, mesh = {Alkanes/*metabolism ; Bacteria/classification/genetics/*isolation & purification/*metabolism ; Biodegradation, Environmental ; Biodiversity ; Geologic Sediments/analysis/*microbiology ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Phylogeny ; Seawater/analysis/microbiology ; Water Pollutants, Chemical/analysis/*metabolism ; }, abstract = {We aimed to gain insight into the alkane degradation potential of microbial communities from chronically polluted sediments of a subantarctic coastal environment using a combination of metagenomic approaches. A total of 6178 sequences annotated as alkane-1-monooxygenases (EC 1.14.15.3) were retrieved from a shotgun metagenomic dataset that included two sites analyzed in triplicate. The majority of the sequences binned with AlkB described in Bacteroidetes (32 ± 13 %) or Proteobacteria (29 ± 7 %), although a large proportion remained unclassified at the phylum level. Operational taxonomic unit (OTU)-based analyses showed small differences in AlkB distribution among samples that could be correlated with alkane concentrations, as well as with site-specific variations in pH and salinity. A number of low-abundance OTUs, mostly affiliated with Actinobacterial sequences, were found to be only present in the most contaminated samples. On the other hand, the molecular screening of a large-insert metagenomic library of intertidal sediments from one of the sampling sites identified two genomic fragments containing novel alkB gene sequences, as well as various contiguous genes related to lipid metabolism. Both genomic fragments were affiliated with the phylum Planctomycetes, and one could be further assigned to the genus Rhodopirellula due to the presence of a partial sequence of the 23S ribosomal RNA (rRNA) gene. This work highlights the diversity of bacterial groups contributing to the alkane degradation potential and reveals patterns of functional diversity in relation with environmental stressors in a chronically polluted, high-latitude coastal environment. In addition, alkane biodegradation genes are described for the first time in members of Planctomycetes.}, } @article {pmid26547201, year = {2016}, author = {Franasiak, JM and Werner, MD and Juneau, CR and Tao, X and Landis, J and Zhan, Y and Treff, NR and Scott, RT}, title = {Endometrial microbiome at the time of embryo transfer: next-generation sequencing of the 16S ribosomal subunit.}, journal = {Journal of assisted reproduction and genetics}, volume = {33}, number = {1}, pages = {129-136}, pmid = {26547201}, issn = {1573-7330}, mesh = {Adult ; Bacteria/classification/*genetics ; Embryo Transfer/methods ; Endometrium/growth & development/*microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/genetics ; Microbiota/*genetics ; Pregnancy ; Pregnancy Outcome ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {PURPOSE: Characterization of the human microbiome has become more precise with the application of powerful molecular tools utilizing the unique 16S ribosomal subunit's hypervariable regions to greatly increase sensitivity. The microbiome of the lower genital tract can prognosticate obstetrical outcome while the upper reproductive tract remains poorly characterized. Here, the endometrial microbiome at the time of single embryo transfer (SET) is characterized by reproductive outcome.

METHODS: Consecutive patients undergoing euploid, SET was included in the analysis. After embryo transfer, performed as per routine, the most distal 5-mm portion of the transfer catheter was sterilely placed in a DNA free PCR tube. Next-generation sequencing of the bacteria specific 16S ribosome gene was performed, allowing genus and species calls for microorganisms.

RESULTS: Taxonomy assignments were made on 35 samples from 33 patients and 2 Escherichia coli controls. Of the 33 patients, 18 had ongoing pregnancies and 15 did not. There were a total of 278 different genus calls present across patient samples. The microbiome at time of transfer for those patients with ongoing pregnancy vs. those without ongoing pregnancy was characterized by top genera by sum fraction. Lactobacillus was the top species call for both outcomes.

CONCLUSIONS: The data presented here show the microbiome at the time of embryo transfer can successfully be characterized without altering standard clinical practice. This novel approach, both in specimen collection and analysis, is the first step toward the goal of determining physiologic from pathophysiologic microbiota. Further studies will help delineate if differences in the microbiome at the time of embryo transfer have a reliable impact on pregnancy outcome.}, } @article {pmid26546424, year = {2016}, author = {Ferrocino, I and Greppi, A and La Storia, A and Rantsiou, K and Ercolini, D and Cocolin, L}, title = {Impact of Nisin-Activated Packaging on Microbiota of Beef Burgers during Storage.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {2}, pages = {549-559}, pmid = {26546424}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification/drug effects/genetics/*isolation & purification ; Cattle ; Food Additives/*pharmacology ; Food Packaging ; Food Preservation ; Food Storage ; Meat Products/analysis/*microbiology ; Microbiota/*drug effects ; Nisin/*pharmacology ; }, abstract = {Beef burgers were stored at 4°C in a vacuum in nisin-activated antimicrobial packaging. Microbial ecology analyses were performed on samples collected between days 0 and 21 of storage to discover the population diversity. Two batches were analyzed using RNA-based denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. The active packaging retarded the growth of the total viable bacteria and lactic acid bacteria. Culture-independent analysis by pyrosequencing of RNA extracted directly from meat showed that Photobacterium phosphoreum, Lactococcus piscium, Lactobacillus sakei, and Leuconostoc carnosum were the major operational taxonomic units (OTUs) shared between control and treated samples. Beta diversity analysis of the 16S rRNA sequence data and RNA-DGGE showed a clear separation between two batches based on the microbiota. Control samples from batch B showed a significant high abundance of some taxa sensitive to nisin, such as Kocuria rhizophila, Staphylococcus xylosus, Leuconostoc carnosum, and Carnobacterium divergens, compared to control samples from batch A. However, only from batch B was it possible to find a significant difference between controls and treated samples during storage due to the active packaging. Predicted metagenomes confirmed differences between the two batches and indicated that the use of nisin-based antimicrobial packaging can determine a reduction in the abundance of specific metabolic pathways related to spoilage. The present study aimed to assess the viable bacterial communities in beef burgers stored in nisin-based antimicrobial packaging, and it highlights the efficacy of this strategy to prolong beef burger shelf life.}, } @article {pmid26544955, year = {2015}, author = {Lluch, J and Servant, F and Païssé, S and Valle, C and Valière, S and Kuchly, C and Vilchez, G and Donnadieu, C and Courtney, M and Burcelin, R and Amar, J and Bouchez, O and Lelouvier, B}, title = {The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline.}, journal = {PloS one}, volume = {10}, number = {11}, pages = {e0142334}, pmid = {26544955}, issn = {1932-6203}, mesh = {Animal Structures/*microbiology ; Animals ; Computational Biology ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; Mice ; Mice, Inbred C57BL ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Substantial progress in high-throughput metagenomic sequencing methodologies has enabled the characterisation of bacteria from various origins (for example gut and skin). However, the recently-discovered bacterial microbiota present within animal internal tissues has remained unexplored due to technical difficulties associated with these challenging samples.

RESULTS: We have optimized a specific 16S rDNA-targeted metagenomics sequencing (16S metabarcoding) pipeline based on the Illumina MiSeq technology for the analysis of bacterial DNA in human and animal tissues. This was successfully achieved in various mouse tissues despite the high abundance of eukaryotic DNA and PCR inhibitors in these samples. We extensively tested this pipeline on mock communities, negative controls, positive controls and tissues and demonstrated the presence of novel tissue specific bacterial DNA profiles in a variety of organs (including brain, muscle, adipose tissue, liver and heart).

CONCLUSION: The high throughput and excellent reproducibility of the method ensured exhaustive and precise coverage of the 16S rDNA bacterial variants present in mouse tissues. This optimized 16S metagenomic sequencing pipeline will allow the scientific community to catalogue the bacterial DNA profiles of different tissues and will provide a database to analyse host/bacterial interactions in relation to homeostasis and disease.}, } @article {pmid26544883, year = {2015}, author = {Bhattacharya, T and Ghosh, TS and Mande, SS}, title = {Global Profiling of Carbohydrate Active Enzymes in Human Gut Microbiome.}, journal = {PloS one}, volume = {10}, number = {11}, pages = {e0142038}, pmid = {26544883}, issn = {1932-6203}, mesh = {Adult ; Age Factors ; Carbohydrate Metabolism/*genetics ; Child ; Dietary Carbohydrates/metabolism ; Esterases/*genetics ; Gastrointestinal Microbiome/*genetics ; Glycoside Hydrolases/*genetics ; Humans ; Lyases/*genetics ; Microbiota/*genetics ; }, abstract = {MOTIVATION: Carbohydrate Active enzyme (CAZyme) families, encoded by human gut microflora, play a crucial role in breakdown of complex dietary carbohydrates into components that can be absorbed by our intestinal epithelium. Since nutritional wellbeing of an individual is dependent on the nutrient harvesting capability of the gut microbiome, it is important to understand how CAZyme repertoire in the gut is influenced by factors like age, geography and food habits.

RESULTS: This study reports a comprehensive in-silico analysis of CAZyme profiles in the gut microbiomes of 448 individuals belonging to different geographies, using similarity searches of the corresponding gut metagenomic contigs against the carbohydrate active enzymes database. The study identifies a core group of 89 CAZyme families that are present across 85% of the gut microbiomes. The study detects several geography/age-specific trends in gut CAZyme repertoires of the individuals. Notably, a group of CAZymes having a positive correlation with BMI has been identified. Further this group of BMI-associated CAZymes is observed to be specifically abundant in the Firmicutes phyla. One of the major findings from this study is identification of three distinct groups of individuals, referred to as 'CAZotypes', having similar CAZyme profiles. Distinct taxonomic drivers for these CAZotypes as well as the probable dietary basis for such trends have also been elucidated. The results of this study provide a global view of CAZyme profiles across individuals of various geographies and age-groups. These results reiterate the need of a more precise understanding of the role of carbohydrate active enzymes in human nutrition.}, } @article {pmid26542074, year = {2016}, author = {Huws, SA and Edwards, JE and Creevey, CJ and Rees Stevens, P and Lin, W and Girdwood, SE and Pachebat, JA and Kingston-Smith, AH}, title = {Temporal dynamics of the metabolically active rumen bacteria colonizing fresh perennial ryegrass.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {1}, pages = {}, doi = {10.1093/femsec/fiv137}, pmid = {26542074}, issn = {1574-6941}, support = {BB/E/W/10964A01//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Actinobacteria/genetics/isolation & purification/metabolism ; Animals ; Bacteria/genetics/isolation & purification/*metabolism ; Butyrivibrio/genetics/isolation & purification/metabolism ; Cattle ; Female ; Fibrobacter/genetics/isolation & purification/metabolism ; Gastrointestinal Microbiome/*genetics/physiology ; Lolium/*microbiology ; Prevotella/genetics/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Ruminococcus/genetics/isolation & purification/metabolism ; Succinivibrionaceae/genetics/isolation & purification/metabolism ; }, abstract = {This study investigated successional colonization of fresh perennial ryegrass (PRG) by the rumen microbiota over time. Fresh PRG was incubated in sacco in the rumens of three Holstein × Friesian cows over a period of 8 h, with samples recovered at various times. The diversity of attached bacteria was assessed using 454 pyrosequencing of 16S rRNA (cDNA). Results showed that plant epiphytic communities either decreased to low relative abundances or disappeared following rumen incubation, and that temporal colonization of the PRG by the rumen bacteria was biphasic with primary (1 and 2 h) and secondary (4-8 h) events evident with the transition period being with 2-4 h. A decrease in sequence reads pertaining to Succinivibrio spp. and increases in Pseudobutyrivibrio, Roseburia and Ruminococcus spp. (the latter all order Clostridiales) were evident during secondary colonization. Irrespective of temporal changes, the continually high abundances of Butyrivibrio, Fibrobacter, Olsenella and Prevotella suggest that they play a major role in the degradation of the plant. It is clear that a temporal understanding of the functional roles of these microbiota within the rumen is now required to unravel the role of these bacteria in the ruminal degradation of fresh PRG.}, } @article {pmid26542073, year = {2016}, author = {Bagnoud, A and de Bruijn, I and Andersson, AF and Diomidis, N and Leupin, OX and Schwyn, B and Bernier-Latmani, R}, title = {A minimalistic microbial food web in an excavated deep subsurface clay rock.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {1}, pages = {}, doi = {10.1093/femsec/fiv138}, pmid = {26542073}, issn = {1574-6941}, mesh = {Aluminum Silicates/*chemistry ; Clay ; Ecosystem ; *Food Chain ; Heterotrophic Processes ; Metabolic Networks and Pathways/genetics ; Metagenomics ; Microbiota/*genetics ; Peptococcaceae/genetics/isolation & purification/*metabolism ; Pseudomonas/genetics/isolation & purification/*metabolism ; RNA, Ribosomal, 16S/genetics ; Radioactive Waste ; Refuse Disposal ; Soil/chemistry ; Soil Microbiology ; Sulfates/metabolism ; Switzerland ; }, abstract = {Clay rocks are being considered for radioactive waste disposal, but relatively little is known about the impact of microbes on the long-term safety of geological repositories. Thus, a more complete understanding of microbial community structure and function in these environments would provide further detail for the evaluation of the safety of geological disposal of radioactive waste in clay rocks. It would also provide a unique glimpse into a poorly studied deep subsurface microbial ecosystem. Previous studies concluded that microorganisms were present in pristine Opalinus Clay, but inactive. In this work, we describe the microbial community and assess the metabolic activities taking place within borehole water. Metagenomic sequencing and genome-binning of a porewater sample containing suspended clay particles revealed a remarkably simple heterotrophic microbial community, fueled by sedimentary organic carbon, mainly composed of two organisms: a Pseudomonas sp. fermenting bacterium growing on organic macromolecules and releasing organic acids and H2, and a sulfate-reducing Peptococcaceae able to oxidize organic molecules to CO(2). In Opalinus Clay, this microbial system likely thrives where pore space allows it. In a repository, this may occur where the clay rock has been locally damaged by excavation or in engineered backfills.}, } @article {pmid26540050, year = {2015}, author = {Zhang, Y and Lun, CY and Tsui, SK}, title = {Metagenomics: A New Way to Illustrate the Crosstalk between Infectious Diseases and Host Microbiome.}, journal = {International journal of molecular sciences}, volume = {16}, number = {11}, pages = {26263-26279}, pmid = {26540050}, issn = {1422-0067}, mesh = {Acquired Immunodeficiency Syndrome/microbiology/virology ; Animals ; Communicable Diseases/*microbiology/*virology ; HIV Infections/microbiology/virology ; Hepatitis B/microbiology/virology ; High-Throughput Nucleotide Sequencing ; *Host-Pathogen Interactions ; Humans ; Influenza, Human/microbiology/virology ; *Metagenomics/methods ; *Microbial Interactions ; *Microbiota/genetics ; Tuberculosis/microbiology ; }, abstract = {Microbes have co-evolved with human beings for millions of years. They play a very important role in maintaining the health of the host. With the advancement in next generation sequencing technology, the microbiome profiling in the host can be obtained under different circumstances. This review focuses on the current knowledge of the alteration of complex microbial communities upon the infection of different pathogens, such as human immunodeficiency virus, hepatitis B virus, influenza virus, and Mycobacterium tuberculosis, at different body sites. It is believed that the increased understanding of the correlation between infectious disease and the alteration of the microbiome can contribute to better management of disease progression in the future. However, future studies may need to be more integrative so as to establish the exact causality of diseases by analyzing the correlation between microorganisms within the human host and the pathogenesis of infectious diseases.}, } @article {pmid26538306, year = {2015}, author = {Ditzler, G and Morrison, JC and Lan, Y and Rosen, GL}, title = {Fizzy: feature subset selection for metagenomics.}, journal = {BMC bioinformatics}, volume = {16}, number = {}, pages = {358}, pmid = {26538306}, issn = {1471-2105}, mesh = {Algorithms ; Computational Biology/*methods ; Databases, Genetic ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; *Software ; Vegetarians ; }, abstract = {BACKGROUND: Some of the current software tools for comparative metagenomics provide ecologists with the ability to investigate and explore bacterial communities using α- & β-diversity. Feature subset selection--a sub-field of machine learning--can also provide a unique insight into the differences between metagenomic or 16S phenotypes. In particular, feature subset selection methods can obtain the operational taxonomic units (OTUs), or functional features, that have a high-level of influence on the condition being studied. For example, in a previous study we have used information-theoretic feature selection to understand the differences between protein family abundances that best discriminate between age groups in the human gut microbiome.

RESULTS: We have developed a new Python command line tool, which is compatible with the widely adopted BIOM format, for microbial ecologists that implements information-theoretic subset selection methods for biological data formats. We demonstrate the software tools capabilities on publicly available datasets.

CONCLUSIONS: We have made the software implementation of Fizzy available to the public under the GNU GPL license. The standalone implementation can be found at http://github.com/EESI/Fizzy.}, } @article {pmid26536246, year = {2015}, author = {Fortunato, CS and Crump, BC}, title = {Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient.}, journal = {PloS one}, volume = {10}, number = {11}, pages = {e0140578}, pmid = {26536246}, issn = {1932-6203}, mesh = {Aquatic Organisms/*microbiology ; Ecosystem ; Energy Metabolism/*genetics ; Gene Expression Profiling ; Genes, Microbial ; Metagenome/genetics ; Microbial Consortia/*genetics ; Oxygen Consumption/*genetics ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Salinity ; *Water Microbiology ; }, abstract = {Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly influence bacterioplankton community structure, yet, a parallel change in functional diversity has not been described. Metagenomic and metatranscriptomic analyses were conducted on five water samples spanning the salinity gradient of the Columbia River coastal margin, including river, estuary, plume, and ocean, in August 2010. Samples were pre-filtered through 3 μm filters and collected on 0.2 μm filters, thus results were focused on changes among free-living microbial communities. Results from metagenomic 16S rRNA sequences showed taxonomically distinct bacterial communities in river, estuary, and coastal ocean. Despite the strong salinity gradient observed over sampling locations (0 to 33), the functional gene profiles in the metagenomes were very similar from river to ocean with an average similarity of 82%. The metatranscriptomes, however, had an average similarity of 31%. Although differences were few among the metagenomes, we observed a change from river to ocean in the abundance of genes encoding for catabolic pathways, osmoregulators, and metal transporters. Additionally, genes specifying both bacterial oxygenic and anoxygenic photosynthesis were abundant and expressed in the estuary and plume. Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary. Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1) the taxonomy of the community changed strongly with salinity, 2) metabolic potential was highly similar across samples, with few differences in functional gene abundance from river to ocean, and 3) gene expression was highly variable and generally was independent of changes in salinity.}, } @article {pmid26535711, year = {2015}, author = {Su, LJ and Liu, YQ and Liu, H and Wang, Y and Li, Y and Lin, HM and Wang, FQ and Song, AD}, title = {Linking lignocellulosic dietary patterns with gut microbial Enterotypes of Tsaitermes ampliceps and comparison with Mironasutitermes shangchengensis.}, journal = {Genetics and molecular research : GMR}, volume = {14}, number = {4}, pages = {13954-13967}, doi = {10.4238/2015.October.29.16}, pmid = {26535711}, issn = {1676-5680}, mesh = {*Animal Feed ; Animals ; Biodiversity ; Cluster Analysis ; *Gastrointestinal Microbiome ; Isoptera/*microbiology ; *Lignin ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Tsaitermes ampliceps (lower termites) and Mironasutitermes shangchengensis (higher termites) are highly eusocial insects that thrive on recalcitrant lignocellulosic diets through nutritional symbioses with gut dwelling prokaryotes and eukaryotes. We used denaturing gradient gel electrophoresis and a 16S rRNA clone library to investigate i) how microbial communities adapt to lignocellulosic diets with different cellulose and lignin content, ii) the differences in the dominant gut microbial communities of the 2 types of termites. The results indicated that gut microbiota composition in T. ampliceps was profoundly affected by 2-week diet shifts. Comparison of these changes indicated that Bacteroidetes and Spirochaetes act in cellulose degradation, while Firmicutes were responsible for lignin degradation. Additionally, Proteobacteria consistently participated in energy production and balanced the gut environment. Bacteroidetes may function without hindgut protozoans in higher termites. The diversity of enteric microorganisms in M. shangchengensis was higher than that in T. ampliceps, possibly because of the more complicated survival mechanisms of higher termites.}, } @article {pmid26527325, year = {2015}, author = {Mao, S and Zhang, M and Liu, J and Zhu, W}, title = {Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {16116}, pmid = {26527325}, issn = {2045-2322}, mesh = {Animals ; Bacteria/*genetics ; Bacteroidetes/genetics ; Carbohydrate Metabolism/genetics ; Cattle ; DNA, Bacterial/isolation & purification/metabolism ; Databases, Genetic ; Fatty Acids, Volatile/metabolism ; Female ; Firmicutes/genetics ; Gastrointestinal Tract/*microbiology ; Hydrogen-Ion Concentration ; Intestinal Mucosa/microbiology ; *Microbiota ; Principal Component Analysis ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/chemistry/genetics ; Rumen/microbiology ; Sequence Analysis, DNA ; }, abstract = {The bacterial community composition and function in the gastrointestinal tracts (GITs) of dairy cattle is very important, since it can influence milk production and host health. However, our understanding of bacterial communities in the GITs of dairy cattle is still very limited. This study analysed bacterial communities in ten distinct GIT sites (the digesta and mucosa of the rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon and rectum) in six dairy cattle. The study observed 542 genera belonging to 23 phyla distributed throughout the cattle GITs, with the Firmicutes, Bacteroidetes and Proteobacteria predominating. In addition, data revealed significant spatial heterogeneity in composition, diversity and species abundance distributions of GIT microbiota. Furthermore, the study inferred significant differences in the predicted metagenomic profiles among GIT regions. In particular, the relative abundances of the genes involved in carbohydrate metabolism were overrepresented in the digesta samples of forestomaches, and the genes related to amino acid metabolism were mainly enriched in the mucosal samples. In general, this study provides the first deep insights into the composition of GIT microbiota in dairy cattle, and it may serve as a foundation for future studies in this area.}, } @article {pmid26527161, year = {2015}, author = {Wang, M and Doak, TG and Ye, Y}, title = {Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes.}, journal = {Genome biology}, volume = {16}, number = {}, pages = {243}, pmid = {26527161}, issn = {1474-760X}, support = {R01 AI108888/AI/NIAID NIH HHS/United States ; 1R01AI108888-01A1/AI/NIAID NIH HHS/United States ; }, mesh = {Diabetes Mellitus, Type 2/*microbiology ; Gastrointestinal Tract/microbiology ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; }, abstract = {Comparative metagenomics remains challenging due to the size and complexity of metagenomic datasets. Here we introduce subtractive assembly, a de novo assembly approach for comparative metagenomics that directly assembles only the differential reads that distinguish between two groups of metagenomes. Using simulated datasets, we show it improves both the efficiency of the assembly and the assembly quality of the differential genomes and genes. Further, its application to type 2 diabetes (T2D) metagenomic datasets reveals clear signatures of the T2D gut microbiome, revealing new phylogenetic and functional features of the gut microbial communities associated with T2D.}, } @article {pmid26526170, year = {2016}, author = {Lee, YS and Seo, SH and Yoon, SH and Kim, SY and Hahn, BS and Sim, JS and Koo, BS and Lee, CM}, title = {Identification of a novel alkaline amylopullulanase from a gut metagenome of Hermetia illucens.}, journal = {International journal of biological macromolecules}, volume = {82}, number = {}, pages = {514-521}, doi = {10.1016/j.ijbiomac.2015.10.067}, pmid = {26526170}, issn = {1879-0003}, mesh = {Amino Acid Sequence ; Animals ; Diptera/*microbiology ; Enzyme Activation ; *Gastrointestinal Microbiome ; Genomic Library ; Glycoside Hydrolases/*chemistry/*genetics/isolation & purification/metabolism ; Hydrogen-Ion Concentration ; Hydrolysis ; *Metagenome ; Metagenomics ; Molecular Sequence Data ; Phylogeny ; Protein Interaction Domains and Motifs ; Recombinant Proteins ; Starch/chemistry ; Temperature ; }, abstract = {A novel pullulanase gene, PulSS4, was identified from the gut microflora of Hermetia illucens by a function-based metagenome screening. The PulSS4 gene had an open reading frame of 4455 base pairs, and encoded a mature protein of 1484 amino acids, with a signal peptide sequence of 44 amino acids. The deduced amino acid sequence of PulSS4 gene showed 51% identity with that of the amylopullulanase of Amphibacillus xylanus, exhibiting no significant sequence homology to already known pullulanases. A conserved domain analysis revealed it to be a pullulanase type II with respective active sites at the N-terminal pullulanase and C-terminal amylase domain. PulSS4 was active in the temperature range of 10-50°C, with an optimum activity at 40°C. It was active in the pH range of 6.5-10.5, with optimum pH at 9.0, and retained more than 80% of its original activity in a broad pH range of 5-11 for 24h at 30°C. Also, PulSS4 was highly stable against many different chemical reagents, including 10% polar organic solvents and 1% non-ionic detergents. Overall, PulSS4 is expected to have the strong potential for application in biotechnological industries that require high activity at moderate temperature and alkaline conditions.}, } @article {pmid26526132, year = {2016}, author = {Behzad, H and Ibarra, MA and Mineta, K and Gojobori, T}, title = {Metagenomic studies of the Red Sea.}, journal = {Gene}, volume = {576}, number = {2 Pt 1}, pages = {717-723}, doi = {10.1016/j.gene.2015.10.034}, pmid = {26526132}, issn = {1879-0038}, mesh = {Biotechnology ; Indian Ocean ; *Metagenomics ; Microbiota ; }, abstract = {Metagenomics has significantly advanced the field of marine microbial ecology, revealing the vast diversity of previously unknown microbial life forms in different marine niches. The tremendous amount of data generated has enabled identification of a large number of microbial genes (metagenomes), their community interactions, adaptation mechanisms, and their potential applications in pharmaceutical and biotechnology-based industries. Comparative metagenomics reveals that microbial diversity is a function of the local environment, meaning that unique or unusual environments typically harbor novel microbial species with unique genes and metabolic pathways. The Red Sea has an abundance of unique characteristics; however, its microbiota is one of the least studied among marine environments. The Red Sea harbors approximately 25 hot anoxic brine pools, plus a vibrant coral reef ecosystem. Physiochemical studies describe the Red Sea as an oligotrophic environment that contains one of the warmest and saltiest waters in the world with year-round high UV radiations. These characteristics are believed to have shaped the evolution of microbial communities in the Red Sea. Over-representation of genes involved in DNA repair, high-intensity light responses, and osmoregulation were found in the Red Sea metagenomic databases suggesting acquisition of specific environmental adaptation by the Red Sea microbiota. The Red Sea brine pools harbor a diverse range of halophilic and thermophilic bacterial and archaeal communities, which are potential sources of enzymes for pharmaceutical and biotechnology-based application. Understanding the mechanisms of these adaptations and their function within the larger ecosystem could also prove useful in light of predicted global warming scenarios where global ocean temperatures are expected to rise by 1-3°C in the next few decades. In this review, we provide an overview of the published metagenomic studies that were conducted in the Red Sea, and the bio-prospecting potential of the Red Sea microbiota. Furthermore, we discuss the limitations of the previous studies and the need for generating a large and representative metagenomic database of the Red Sea to help establish a dynamic model of the Red Sea microbiota.}, } @article {pmid26526081, year = {2015}, author = {Quince, C and Ijaz, UZ and Loman, N and Eren, AM and Saulnier, D and Russell, J and Haig, SJ and Calus, ST and Quick, J and Barclay, A and Bertz, M and Blaut, M and Hansen, R and McGrogan, P and Russell, RK and Edwards, CA and Gerasimidis, K}, title = {Extensive Modulation of the Fecal Metagenome in Children With Crohn's Disease During Exclusive Enteral Nutrition.}, journal = {The American journal of gastroenterology}, volume = {110}, number = {12}, pages = {1718-29; quiz 1730}, pmid = {26526081}, issn = {1572-0241}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; G0800675/MRC_/Medical Research Council/United Kingdom ; MR/M501621/1/MRC_/Medical Research Council/United Kingdom ; MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; G0600329/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adolescent ; Child ; Crohn Disease/blood/*genetics/metabolism/*microbiology ; *Enteral Nutrition ; *Feces/chemistry ; Female ; Humans ; Leukocyte L1 Antigen Complex/metabolism ; Linear Models ; Male ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S ; Sequence Analysis, RNA ; }, abstract = {OBJECTIVES: Exploring associations between the gut microbiota and colonic inflammation and assessing sequential changes during exclusive enteral nutrition (EEN) may offer clues into the microbial origins of Crohn's disease (CD).

METHODS: Fecal samples (n=117) were collected from 23 CD and 21 healthy children. From CD children fecal samples were collected before, during EEN, and when patients returned to their habitual diets. Microbiota composition and functional capacity were characterized using sequencing of the 16S rRNA gene and shotgun metagenomics.

RESULTS: Microbial diversity was lower in CD than controls before EEN (P=0.006); differences were observed in 36 genera, 141 operational taxonomic units (OTUs), and 44 oligotypes. During EEN, the microbial diversity of CD children further decreased, and the community structure became even more dissimilar than that of controls. Every 10 days on EEN, 0.6 genus diversity equivalents were lost; 34 genera decreased and one increased during EEN. Fecal calprotectin correlated with 35 OTUs, 14 of which accounted for 78% of its variation. OTUs that correlated positively or negatively with calprotectin decreased during EEN. The microbiota of CD patients had a broader functional capacity than healthy controls, but diversity decreased with EEN. Genes involved in membrane transport, sulfur reduction, and nutrient biosynthesis differed between patients and controls. The abundance of genes involved in biotin (P=0.005) and thiamine biosynthesis decreased (P=0.017), whereas those involved in spermidine/putrescine biosynthesis (P=0.031), or the shikimate pathway (P=0.058), increased during EEN.

CONCLUSIONS: Disease improvement following treatment with EEN is associated with extensive modulation of the gut microbiome.}, } @article {pmid26525290, year = {2015}, author = {Babickova, J and Gardlik, R}, title = {Pathological and therapeutic interactions between bacteriophages, microbes and the host in inflammatory bowel disease.}, journal = {World journal of gastroenterology}, volume = {21}, number = {40}, pages = {11321-11330}, pmid = {26525290}, issn = {2219-2840}, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacteria/drug effects/*virology ; *Bacteriophages ; Dysbiosis ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/drug effects ; Host-Pathogen Interactions ; Humans ; Inflammatory Bowel Diseases/diagnosis/immunology/*microbiology/therapy ; Intestines/drug effects/immunology/*microbiology ; Probiotics/therapeutic use ; }, abstract = {The intestinal microbiome is a dynamic system of interactions between the host and its microbes. Under physiological conditions, a fine balance and mutually beneficial relationship is present. Disruption of this balance is a hallmark of inflammatory bowel disease (IBD). Whether an altered microbiome is the consequence or the cause of IBD is currently not fully understood. The pathogenesis of IBD is believed to be a complex interaction between genetic predisposition, the immune system and environmental factors. In the recent years, metagenomic studies of the human microbiome have provided useful data that are helping to assemble the IBD puzzle. In this review, we summarize and discuss current knowledge on the composition of the intestinal microbiota in IBD, host-microbe interactions and therapeutic possibilities using bacteria in IBD. Moreover, an outlook on the possible contribution of bacteriophages in the pathogenesis and therapy of IBD is provided.}, } @article {pmid26521553, year = {2015}, author = {Devi, SG and Ramya, M}, title = {PCR- RFLP based bacterial diversity analysis of a municipal sewage treatment plant.}, journal = {Journal of environmental biology}, volume = {36}, number = {5}, pages = {1113-1118}, pmid = {26521553}, issn = {0254-8704}, mesh = {Bacteria/*classification/*genetics ; Biodiversity ; Cities ; Phylogeny ; Polymerase Chain Reaction/*methods ; Polymorphism, Restriction Fragment Length ; Sewage/*microbiology ; Soil Microbiology ; Waste Disposal Facilities ; }, abstract = {Bacterial diversity of sewage soil is an essential study to discover novel bacterial species involved in biodegradation. Restriction Fragment Length Polymorphism is one of the most useful molecular technique for diversity analysis in terms of cost effectiveness and reliability. The present study focuses on bacterial diversity of municipal sewage treatment plant in Chennai, Tamil Nadu, India through metagenomic approach. A 16S r DNA clone library was constructed from metagenomic DNA of sewage soil. 200 clones from the library were subjected to colony PCR and RFLP analysis. Upon RFLP analysis, 16 different Operational Taxonomic Units (OTU's) were obtained and a single clone from each OTU was subjected to sequencing. Phylogenetic analysis of sequences revealed the presence of five different groups of bacteria namely Proteobacteria (56%), Actinobacteria (7%), Firmicutes (5%), Bacteroidetes (17%) and Plancomycetes (7%). Three novel and uncultured groups of bacteria (8%) were also discovered. Most of the organisms identified through this study were reported to be efficient degraders of hydrocarbons, aromatic compounds and heavy metals, thereby promoting biodegradation of polluted environment.}, } @article {pmid26519142, year = {2015}, author = {Wang, X and Van Nostrand, JD and Deng, Y and Lü, X and Wang, C and Zhou, J and Han, X}, title = {Scale-dependent effects of climate and geographic distance on bacterial diversity patterns across northern China's grasslands.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {12}, pages = {}, doi = {10.1093/femsec/fiv133}, pmid = {26519142}, issn = {1574-6941}, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; China ; *Climate ; Geography ; *Grassland ; Microbial Consortia/*physiology ; Molecular Typing ; Plants/microbiology ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Patterns of variation in plant and animal diversity along precipitation gradients have been extensively studied, but much less is known about how and to what extent precipitation affects the biogeographic distribution of microbial diversity in arid areas across large spatial scales. Here we collected soils from 54 sites along a 3700 km transect covering a wide range of grassland ecosystems with distinct aridity gradients. We quantified the bacterial community diversity and the effects of climate, edaphic parameter and geographic distance on the bacterial community structure using high-throughput 16S rRNA gene sequencing. Of the 35 phyla detected, 6 were dominant: Actinobacteria, Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Bacteroidetes and Planctomycetes. Aridity was a major factor influencing bacterial diversity, community composition and taxon abundance. Although the pattern of bacterial species richness is markedly different from that of plant species richness, most soil bacteria were endemic to particular bioregions like macro-organisms. Community similarity significantly declined with environmental distance and geographic distance (r = -0.579 and -0.773, respectively). Geographic distance (historical contingencies) contributed more to bacterial community variation (36.02%) than combined environmental factors (24.06%). Overall, our results showed that geographic distance and climatic factors concurrently govern bacterial biogeographic patterns in arid and semi-arid grassland.}, } @article {pmid26518717, year = {2016}, author = {Mineta, K and Gojobori, T}, title = {Databases of the marine metagenomics.}, journal = {Gene}, volume = {576}, number = {2 Pt 1}, pages = {724-728}, doi = {10.1016/j.gene.2015.10.035}, pmid = {26518717}, issn = {1879-0038}, mesh = {*Databases, Genetic ; *Marine Biology ; *Metagenomics ; }, abstract = {The metagenomic data obtained from marine environments is significantly useful for understanding marine microbial communities. In comparison with the conventional amplicon-based approach of metagenomics, the recent shotgun sequencing-based approach has become a powerful tool that provides an efficient way of grasping a diversity of the entire microbial community at a sampling point in the sea. However, this approach accelerates accumulation of the metagenome data as well as increase of data complexity. Moreover, when metagenomic approach is used for monitoring a time change of marine environments at multiple locations of the seawater, accumulation of metagenomics data will become tremendous with an enormous speed. Because this kind of situation has started becoming of reality at many marine research institutions and stations all over the world, it looks obvious that the data management and analysis will be confronted by the so-called Big Data issues such as how the database can be constructed in an efficient way and how useful knowledge should be extracted from a vast amount of the data. In this review, we summarize the outline of all the major databases of marine metagenome that are currently publically available, noting that database exclusively on marine metagenome is none but the number of metagenome databases including marine metagenome data are six, unexpectedly still small. We also extend our explanation to the databases, as reference database we call, that will be useful for constructing a marine metagenome database as well as complementing important information with the database. Then, we would point out a number of challenges to be conquered in constructing the marine metagenome database.}, } @article {pmid26516089, year = {2015}, author = {Liu, Q and Zhou, YG and Xin, YH}, title = {High diversity and distinctive community structure of bacteria on glaciers in China revealed by 454 pyrosequencing.}, journal = {Systematic and applied microbiology}, volume = {38}, number = {8}, pages = {578-585}, doi = {10.1016/j.syapm.2015.09.005}, pmid = {26516089}, issn = {1618-0984}, mesh = {Bacteria/*classification/genetics/growth & development ; Biota ; China ; Climate ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Ice Cover/*microbiology ; Metagenome ; Molecular Sequence Data ; *Phylogeography ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The bacterial diversity, community structure and preliminary microbial biogeographic pattern were assessed on glacier surfaces, including three northern glaciers (cold glaciers) and three southern glaciers (temperate glaciers) in China that experienced distinct climatic conditions. Pyrosequencing revealed that bacterial diversities were surprisingly high. With respect to operational taxonomic units (OTUs), Proteobacteria was the most dominant phylum on the glacier surfaces, especially Betaproteobacteria. Significant differences of the bacterial communities were observed between northern and southern glacier surfaces. The rare and abundant populations showed similar clustering patterns to the whole community. The analysis of the culturable bacterial compositions from four glaciers supported this conclusion. Redundancy analysis (RDA) and partial Mantel tests indicated that annual mean temperature, as well as geographical distance, was significantly correlated with the bacterial communities on the glaciers. It was inferred that bacterial communities on northern and southern glacier surfaces experienced different climate, water and nutrient patterns, and consequently evolved different lifestyles.}, } @article {pmid26515509, year = {2015}, author = {Khurshid, M and Aslam, B and Nisar, MA and Akbar, R and Rahman, H and Khan, AA and Rasool, MH}, title = {Bacterial munch for infants: potential pediatric therapeutic interventions of probiotics.}, journal = {Future microbiology}, volume = {10}, number = {11}, pages = {1881-1895}, doi = {10.2217/fmb.15.102}, pmid = {26515509}, issn = {1746-0921}, mesh = {Administration, Oral ; Biological Therapy/*methods ; Clinical Trials as Topic ; Gastrointestinal Diseases/*therapy ; Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Microbiota ; Probiotics/*administration & dosage ; Reproducibility of Results ; Treatment Outcome ; }, abstract = {Probiotics are viable microorganisms with the capacity to alter the gastrointestinal microbiota of the host. The recent scientific advancements and development of probiotic formulations have rekindled the importance of these clinical interpretations, underlining the starring role of the gut flora in host metabolism, defense and immune regulation. Despite encouraging preliminary results from randomized clinical trials of probiotics for various clinical conditions including irritable bowel syndrome, necrotizing enterocolitis, gastroenteritis, antibiotic-associated diarrhea, infantile colic, and improvement of digestion and immune function, further evidence is needed to determine the reproducibility of the findings and elucidate the underlying mechanisms. In this review, we have considered the postnatal development of gut flora and appraised the role of probiotics in health and disease condition among infants.}, } @article {pmid26512813, year = {2016}, author = {Beale, DJ and Karpe, AV and McLeod, JD and Gondalia, SV and Muster, TH and Othman, MZ and Palombo, EA and Joshi, D}, title = {An 'omics' approach towards the characterisation of laboratory scale anaerobic digesters treating municipal sewage sludge.}, journal = {Water research}, volume = {88}, number = {}, pages = {346-357}, doi = {10.1016/j.watres.2015.10.029}, pmid = {26512813}, issn = {1879-2448}, mesh = {Anaerobiosis ; Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Biofuels ; Bioreactors/*microbiology ; High-Throughput Nucleotide Sequencing ; Metabolomics/*methods ; Metagenomics/*methods ; Methane/metabolism ; Microbial Consortia/*physiology ; Sulfates/metabolism ; Waste Disposal, Fluid/instrumentation/*methods ; }, abstract = {In this study, laboratory scale digesters were operated to simulate potential shocks to the Anaerobic Digestion (AD) process at a 350 ML/day wastewater treatment plant. The shocks included high (42 °C) and low (32 °C) temperature (either side of mesophilic 37 °C) and a 20% loading of fats, oil and grease (FOG; 20% w:v). These variables were explored at two sludge retention times (12 and 20 days) and two organic loading rates (2.0 and 2.5 kgTS/m(3)day OLR). Metagenomic and metabolomic approaches were then used to characterise the impact of operational shocks in regard to temperature and FOG addition, as determined through monitoring of biogas production, the microbial profile and their metabolism. Results showed that AD performance was not greatly affected by temperature shocks, with the biggest impact being a reduction in biogas production at 42 °C that persisted for 32 ± 1 days. The average biogas production across all digesters at the completion of the experiment was 264.1 ± 76.5 mL/day, with FOG addition observed to significantly promote biogas production (+87.8 mL/day). Metagenomic and metabolomic analyses of the digesters indicated that methanogens and methane oxidising bacteria (MOB) were low in relative abundance, and that the ratio of oxidising bacteria (methane, sulphide and sulphate) with respect to sulphate reducing bacteria (SRB) had a noticeable influence on biogas production. Furthermore, increased biogas production correlated with an increase in short chain fatty acids, a product of the addition of 20% FOG. This work demonstrates the application of metagenomics and metabolomics to characterise the microbiota and their metabolism in AD digesters, providing insight to the resilience of crucial microbial populations when exposed to operational shocks.}, } @article {pmid26512100, year = {2015}, author = {Jones, MB and Highlander, SK and Anderson, EL and Li, W and Dayrit, M and Klitgord, N and Fabani, MM and Seguritan, V and Green, J and Pride, DT and Yooseph, S and Biggs, W and Nelson, KE and Venter, JC}, title = {Library preparation methodology can influence genomic and functional predictions in human microbiome research.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {45}, pages = {14024-14029}, pmid = {26512100}, issn = {1091-6490}, mesh = {Analysis of Variance ; Base Composition ; Base Sequence ; Feces/chemistry ; *Gene Library ; Genome, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods/trends ; Microbiota/*genetics ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Observations from human microbiome studies are often conflicting or inconclusive. Many factors likely contribute to these issues including small cohort sizes, sample collection, and handling and processing differences. The field of microbiome research is moving from 16S rDNA gene sequencing to a more comprehensive genomic and functional representation through whole-genome sequencing (WGS) of complete communities. Here we performed quantitative and qualitative analyses comparing WGS metagenomic data from human stool specimens using the Illumina Nextera XT and Illumina TruSeq DNA PCR-free kits, and the KAPA Biosystems Hyper Prep PCR and PCR-free systems. Significant differences in taxonomy are observed among the four different next-generation sequencing library preparations using a DNA mock community and a cell control of known concentration. We also revealed biases in error profiles, duplication rates, and loss of reads representing organisms that have a high %G+C content that can significantly impact results. As with all methods, the use of benchmarking controls has revealed critical differences among methods that impact sequencing results and later would impact study interpretation. We recommend that the community adopt PCR-free-based approaches to reduce PCR bias that affects calculations of abundance and to improve assemblies for accurate taxonomic assignment. Furthermore, the inclusion of a known-input cell spike-in control provides accurate quantitation of organisms in clinical samples.}, } @article {pmid26511562, year = {2015}, author = {Dubilier, N and McFall-Ngai, M and Zhao, L}, title = {Microbiology: Create a global microbiome effort.}, journal = {Nature}, volume = {526}, number = {7575}, pages = {631-634}, pmid = {26511562}, issn = {1476-4687}, mesh = {Humans ; *International Cooperation ; Metagenome ; Microbiota/genetics/*physiology ; Research/economics/*organization & administration ; Research Personnel/organization & administration ; Workforce ; }, } @article {pmid26510185, year = {2015}, author = {Ying, S and Zeng, DN and Chi, L and Tan, Y and Galzote, C and Cardona, C and Lax, S and Gilbert, J and Quan, ZX}, title = {The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban and Rural Human Populations.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0141842}, pmid = {26510185}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Age Factors ; Bacteria/classification/genetics ; Biodiversity ; Child ; Cluster Analysis ; Computational Biology ; Female ; Humans ; Male ; Metagenome ; *Microbiota ; Middle Aged ; Public Health Surveillance ; *Rural Population ; Sex Factors ; Skin/*microbiology ; *Urban Population ; Young Adult ; }, abstract = {Differences in the bacterial community structure associated with 7 skin sites in 71 healthy people over five days showed significant correlations with age, gender, physical skin parameters, and whether participants lived in urban or rural locations in the same city. While body site explained the majority of the variance in bacterial community structure, the composition of the skin-associated bacterial communities were predominantly influenced by whether the participants were living in an urban or rural environment, with a significantly greater relative abundance of Trabulsiella in urban populations. Adults maintained greater overall microbial diversity than adolescents or the elderly, while the intragroup variation among the elderly and rural populations was significantly greater. Skin-associated bacterial community structure and composition could predict whether a sample came from an urban or a rural resident ~5x greater than random.}, } @article {pmid26510171, year = {2016}, author = {Mahdavinia, M and Keshavarzian, A and Tobin, MC and Landay, AL and Schleimer, RP}, title = {A comprehensive review of the nasal microbiome in chronic rhinosinusitis (CRS).}, journal = {Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology}, volume = {46}, number = {1}, pages = {21-41}, pmid = {26510171}, issn = {1365-2222}, support = {R01 HL078860/HL/NHLBI NIH HHS/United States ; R01 AT007143/AT/NCCIH NIH HHS/United States ; U19 AI106683/AI/NIAID NIH HHS/United States ; R01 AT007143-05/AT/NCCIH NIH HHS/United States ; R01 AA023417/AA/NIAAA NIH HHS/United States ; R01 AA020216-05/AA/NIAAA NIH HHS/United States ; R37 HL068546/HL/NHLBI NIH HHS/United States ; R01 AA020216/AA/NIAAA NIH HHS/United States ; R01 AA023417-02/AA/NIAAA NIH HHS/United States ; }, mesh = {Animals ; Asthma/genetics/immunology/metabolism/microbiology ; Bacteria/classification/genetics ; Biofilms ; Chronic Disease ; Disease Susceptibility ; Fungi/classification/genetics ; Genetic Predisposition to Disease ; Host-Pathogen Interactions ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Nasal Mucosa/immunology/metabolism/*microbiology ; Respiratory Mucosa/immunology/microbiology ; Rhinitis/genetics/immunology/metabolism/*microbiology/therapy ; Sinusitis/genetics/immunology/metabolism/*microbiology/therapy ; Staphylococcus aureus/physiology ; Viruses/classification/genetics ; }, abstract = {Chronic rhinosinusitis (CRS) has been known as a disease with strong infectious and inflammatory components for decades. The recent advancement in methods identifying microbes has helped implicate the airway microbiome in inflammatory respiratory diseases such as asthma and COPD. Such studies support a role of resident microbes in both health and disease of host tissue, especially in the case of inflammatory mucosal diseases. Identifying interactive events between microbes and elements of the immune system can help us to uncover the pathogenic mechanisms underlying CRS. Here we provide a review of the findings on the complex upper respiratory microbiome in CRS in comparison with healthy controls. Furthermore, we have reviewed the defects and alterations of the host immune system that interact with microbes and could be associated with dysbiosis in CRS.}, } @article {pmid26506368, year = {2015}, author = {Pereira da Fonseca, TA and Pessôa, R and Sanabani, SS}, title = {Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces.}, journal = {International journal of environmental research and public health}, volume = {12}, number = {10}, pages = {13276-13288}, pmid = {26506368}, issn = {1660-4601}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Brazil ; Manufactured Materials/*microbiology ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$) notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or "feiras" in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.}, } @article {pmid26502961, year = {2015}, author = {Kathiravan, MN and Gim, GH and Ryu, J and Kim, PI and Lee, CW and Kim, SW}, title = {Enhanced method for microbial community DNA extraction and purification from agricultural yellow loess soil.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {53}, number = {11}, pages = {767-775}, pmid = {26502961}, issn = {1976-3794}, mesh = {*Agriculture ; DNA, Bacterial/genetics/*isolation & purification ; Metagenomics/*methods ; Microbial Consortia/*genetics ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; *Soil Microbiology ; }, abstract = {In this study, novel DNA extraction and purification methods were developed to obtain high-quantity and reliable quality DNA from the microbial community of agricultural yellow loess soil samples. The efficiencies of five different soil DNAextraction protocols were evaluated on the basis of DNA yield, quality and DNA shearing. Our suggested extraction method, which used CTAB, EDTA and cell membrane lytic enzymes in the extraction followed by DNA precipitation using isopropanol, yielded a maximum DNA content of 42.28 ± 5.59 µg/g soil. In addition, among the five different purification protocols, the acid-treated polyvinyl polypyrrolidone (PVPP) spin column purification method yielded high-quality DNA and recovered 91% of DNA from the crude DNA. Spectrophotometry revealed that the ultraviolet A 260/A 230 and A 260/A 280 absorbance ratios of the purified DNA were 1.82 ± 0.03 and 1.94 ± 0.05, respectively. PCR-based 16S rRNA amplification showed clear bands at ~1.5 kb with acid-treated PVPP-purified DNA templates. In conclusion, our suggested extraction and purification protocols can be used to recover high concentration, high purity, and high-molecular-weight DNA from clay and silica-rich agricultural soil samples.}, } @article {pmid26502935, year = {2015}, author = {Lopez, P and Halary, S and Bapteste, E}, title = {Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life.}, journal = {Biology direct}, volume = {10}, number = {}, pages = {64}, pmid = {26502935}, issn = {1745-6150}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Evolution, Molecular ; *Gastrointestinal Microbiome ; *Genetic Variation ; Genomics ; Humans ; Phylogeny ; }, abstract = {BACKGROUND: Microbial genetic diversity is often investigated via the comparison of relatively similar 16S molecules through multiple alignments between reference sequences and novel environmental samples using phylogenetic trees, direct BLAST matches, or phylotypes counts. However, are we missing novel lineages in the microbial dark universe by relying on standard phylogenetic and BLAST methods? If so, how can we probe that universe using alternative approaches? We performed a novel type of multi-marker analysis of genetic diversity exploiting the topology of inclusive sequence similarity networks.

RESULTS: Our protocol identified 86 ancient gene families, well distributed and rarely transferred across the 3 domains of life, and retrieved their environmental homologs among 10 million predicted ORFs from human gut samples and other metagenomic projects. Numerous highly divergent environmental homologs were observed in gut samples, although the most divergent genes were over-represented in non-gut environments. In our networks, most divergent environmental genes grouped exclusively with uncultured relatives, in maximal cliques. Sequences within these groups were under strong purifying selection and presented a range of genetic variation comparable to that of a prokaryotic domain.

CONCLUSIONS: Many genes families included environmental homologs that were highly divergent from cultured homologs: in 79 gene families (including 18 ribosomal proteins), Bacteria and Archaea were less divergent than some groups of environmental sequences were to any cultured or viral homologs. Moreover, some groups of environmental homologs branched very deeply in phylogenetic trees of life, when they were not too divergent to be aligned. These results underline how limited our understanding of the most diverse elements of the microbial world remains, and encourage a deeper exploration of natural communities and their genetic resources, hinting at the possibility that still unknown yet major divisions of life have yet to be discovered.}, } @article {pmid26502721, year = {2015}, author = {Checinska, A and Probst, AJ and Vaishampayan, P and White, JR and Kumar, D and Stepanov, VG and Fox, GE and Nilsson, HR and Pierson, DL and Perry, J and Venkateswaran, K}, title = {Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {50}, pmid = {26502721}, issn = {2049-2618}, mesh = {*Air Microbiology ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Biodiversity ; Cluster Analysis ; *Dust ; Environment, Controlled ; Fungi/classification/genetics ; Humans ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Spacecraft ; }, abstract = {BACKGROUND: The International Space Station (ISS) is a unique built environment due to the effects of microgravity, space radiation, elevated carbon dioxide levels, and especially continuous human habitation. Understanding the composition of the ISS microbial community will facilitate further development of safety and maintenance practices. The primary goal of this study was to characterize the viable microbiome of the ISS-built environment. A second objective was to determine if the built environments of Earth-based cleanrooms associated with space exploration are an appropriate model of the ISS environment.

RESULTS: Samples collected from the ISS and two cleanrooms at the Jet Propulsion Laboratory (JPL, Pasadena, CA) were analyzed by traditional cultivation, adenosine triphosphate (ATP), and propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR) assays to estimate viable microbial populations. The 16S rRNA gene Illumina iTag sequencing was used to elucidate microbial diversity and explore differences between ISS and cleanroom microbiomes. Statistical analyses showed that members of the phyla Actinobacteria, Firmicutes, and Proteobacteria were dominant in the samples examined but varied in abundance. Actinobacteria were predominant in the ISS samples whereas Proteobacteria, least abundant in the ISS, dominated in the cleanroom samples. The viable bacterial populations seen by PMA treatment were greatly decreased. However, the treatment did not appear to have an effect on the bacterial composition (diversity) associated with each sampling site.

CONCLUSIONS: The results of this study provide strong evidence that specific human skin-associated microorganisms make a substantial contribution to the ISS microbiome, which is not the case in Earth-based cleanrooms. For example, Corynebacterium and Propionibacterium (Actinobacteria) but not Staphylococcus (Firmicutes) species are dominant on the ISS in terms of viable and total bacterial community composition. The results obtained will facilitate future studies to determine how stable the ISS environment is over time. The present results also demonstrate the value of measuring viable cell diversity and population size at any sampling site. This information can be used to identify sites that can be targeted for more stringent cleaning. Finally, the results will allow comparisons with other built sites and facilitate future improvements on the ISS that will ensure astronaut health.}, } @article {pmid26500226, year = {2016}, author = {Saint-Georges-Chaumet, Y and Edeas, M}, title = {Microbiota-mitochondria inter-talk: consequence for microbiota-host interaction.}, journal = {Pathogens and disease}, volume = {74}, number = {1}, pages = {ftv096}, doi = {10.1093/femspd/ftv096}, pmid = {26500226}, issn = {2049-632X}, mesh = {Animals ; *Ecosystem ; Gastrointestinal Microbiome/*immunology/*physiology ; Host-Pathogen Interactions ; Humans ; Intestinal Mucosa/*immunology/*microbiology ; Mitochondria/metabolism/*physiology ; Reactive Oxygen Species/*metabolism/toxicity ; Signal Transduction ; }, abstract = {New discoveries in metagenomics and clinical research have highlighted the importance of the gut microbiota for human health through the regulation of the host immune response and energetic metabolism. The microbiota interacts with host cells in particular by intermingling with the mitochondrial activities. This mitochondria-microbiota cross-talk is intriguing because mitochondria share many common structural and functional features with the prokaryotic world. Several studies reported a correlation between microbiota quality and diversity and mitochondrial function. The mitochondrial production of reactive oxygen species (ROS) plays an important role during the innate immune response and inflammation, and is often targeted by pathogenic bacteria. Data suggest that excessive mitochondrial ROS production may affect ROS signaling induced by the microbiota to regulate the gut epithelial barrier. Finally, the microbiota releases metabolites that can directly interfere with the mitochondrial respiratory chain and ATP production. Short chain fatty acids have beneficial effects on mitochondrial activity. All these data suggest that the microbiota targets mitochondria to regulate its interaction with the host. Imbalance of this targeting may result in a pathogenic state as observed in numerous studies. The challenge to find new treatments will be to find strategies to modulate the quality and diversity of the microbiota rather than acting on microbiota metabolites and microbiota-related factors.}, } @article {pmid26497477, year = {2015}, author = {Flowers, SA and Ellingrod, VL}, title = {The Microbiome in Mental Health: Potential Contribution of Gut Microbiota in Disease and Pharmacotherapy Management.}, journal = {Pharmacotherapy}, volume = {35}, number = {10}, pages = {910-916}, doi = {10.1002/phar.1640}, pmid = {26497477}, issn = {1875-9114}, mesh = {Affect/physiology ; Animals ; Bile Acids and Salts/metabolism ; Blood-Brain Barrier/metabolism ; Brain/metabolism ; Diet ; Fatty Acids/metabolism ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/metabolism ; Humans ; Inflammation/metabolism ; Inflammation Mediators/metabolism ; Mental Disorders/*physiopathology ; *Mental Health ; }, abstract = {The gut microbiome is composed of ~10(13) -10(14) microbial cells and viruses that exist in a symbiotic bidirectional communicative relationship with the host. Bacterial functions in the gut have an important role in healthy host metabolic function, and dysbiosis can contribute to the pathology of many medical conditions. Alterations in the relationship between gut microbiota and host have gained some attention in mental health because new evidence supports the association of gut bacteria to cognitive and emotional processes. Of interest, illnesses such as major depressive disorder are disproportionately prevalent in patients with gastrointestinal illnesses such as inflammatory bowel disease, which pathologically has been strongly linked to microbiome function. Not only is the microbiome associated with the disease itself, but it may also influence the effectiveness or adverse effects associated with pharmacologic agents used to treat these disorders. This field of study may also provide new insights on how dietary agents may help manage mental illness both directly as well as though their influence on the therapeutic and adverse effects of psychotropic agents.}, } @article {pmid26497460, year = {2016}, author = {Nelson, WC and Maezato, Y and Wu, YW and Romine, MF and Lindemann, SR}, title = {Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {1}, pages = {255-267}, pmid = {26497460}, issn = {1098-5336}, mesh = {Algorithms ; Chromosome Mapping ; Computational Biology ; *Genetic Variation ; Genome, Bacterial ; Halomonas/genetics/growth & development/isolation & purification ; *Metagenome ; Metagenomics/*methods ; Microbial Consortia/*genetics ; Molecular Sequence Data ; Phylogeny ; Rhodobacteraceae/genetics/isolation & purification ; Sequence Analysis, DNA ; }, abstract = {To gain a predictive understanding of the interspecies interactions within microbial communities that govern community function, the genomic complement of every member population must be determined. Although metagenomic sequencing has enabled the de novo reconstruction of some microbial genomes from environmental communities, microdiversity confounds current genome reconstruction techniques. To overcome this issue, we performed short-read metagenomic sequencing on parallel consortia, defined as consortia cultivated under the same conditions from the same natural community with overlapping species composition. The differences in species abundance between the two consortia allowed reconstruction of near-complete (at an estimated >85% of gene complement) genome sequences for 17 of the 20 detected member species. Two Halomonas spp. indistinguishable by amplicon analysis were found to be present within the community. In addition, comparison of metagenomic reads against the consensus scaffolds revealed within-species variation for one of the Halomonas populations, one of the Rhodobacteraceae populations, and the Rhizobiales population. Genomic comparison of these representative instances of inter- and intraspecies microdiversity suggests differences in functional potential that may result in the expression of distinct roles in the community. In addition, isolation and complete genome sequence determination of six member species allowed an investigation into the sensitivity and specificity of genome reconstruction processes, demonstrating robustness across a wide range of sequence coverage (9× to 2,700×) within the metagenomic data set.}, } @article {pmid26496746, year = {2015}, author = {Bowers, RM and Clum, A and Tice, H and Lim, J and Singh, K and Ciobanu, D and Ngan, CY and Cheng, JF and Tringe, SG and Woyke, T}, title = {Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {856}, pmid = {26496746}, issn = {1471-2164}, mesh = {Archaea/genetics ; Bacteria/genetics ; Base Composition ; Biomass ; Contig Mapping ; Gene Library ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The rapid development of sequencing technologies has provided access to environments that were either once thought inhospitable to life altogether or that contain too few cells to be analyzed using genomics approaches. While 16S rRNA gene microbial community sequencing has revolutionized our understanding of community composition and diversity over time and space, it only provides a crude estimate of microbial functional and metabolic potential. Alternatively, shotgun metagenomics allows comprehensive sampling of all genetic material in an environment, without any underlying primer biases. Until recently, one of the major bottlenecks of shotgun metagenomics has been the requirement for large initial DNA template quantities during library preparation.

RESULTS: Here, we investigate the effects of varying template concentrations across three low biomass library preparation protocols on their ability to accurately reconstruct a mock microbial community of known composition. We analyze the effects of input DNA quantity and library preparation method on library insert size, GC content, community composition, assembly quality and metagenomic binning. We found that library preparation method and the amount of starting material had significant impacts on the mock community metagenomes. In particular, GC content shifted towards more GC rich sequences at the lower input quantities regardless of library prep method, the number of low quality reads that could not be mapped to the reference genomes increased with decreasing input quantities, and the different library preparation methods had an impact on overall metagenomic community composition.

CONCLUSIONS: This benchmark study provides recommendations for library creation of representative and minimally biased metagenome shotgun sequencing, enabling insights into functional attributes of low biomass ecosystem microbial communities.}, } @article {pmid26496191, year = {2015}, author = {Koslicki, D and Chatterjee, S and Shahrivar, D and Walker, AW and Francis, SC and Fraser, LJ and Vehkaperä, M and Lan, Y and Corander, J}, title = {ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0140644}, pmid = {26496191}, issn = {1932-6203}, support = {/WT_/Wellcome Trust/United Kingdom ; G0701039/MRC_/Medical Research Council/United Kingdom ; MR/K012126/1/MRC_/Medical Research Council/United Kingdom ; G1002369/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Algorithms ; Bacteria/classification/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Feces/microbiology ; Humans ; Internet ; Metagenomics/*methods ; Microbiota/*genetics ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {MOTIVATION: Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of such large datasets is challenging.

RESULTS: There has been a recent surge of interest in using compressed sensing inspired and convex-optimization based methods to solve the estimation problem for bacterial community composition. These methods typically rely on summarizing the sequence data by frequencies of low-order k-mers and matching this information statistically with a taxonomically structured database. Here we show that the accuracy of the resulting community composition estimates can be substantially improved by aggregating the reads from a sample with an unsupervised machine learning approach prior to the estimation phase. The aggregation of reads is a pre-processing approach where we use a standard K-means clustering algorithm that partitions a large set of reads into subsets with reasonable computational cost to provide several vectors of first order statistics instead of only single statistical summarization in terms of k-mer frequencies. The output of the clustering is then processed further to obtain the final estimate for each sample. The resulting method is called Aggregation of Reads by K-means (ARK), and it is based on a statistical argument via mixture density formulation. ARK is found to improve the fidelity and robustness of several recently introduced methods, with only a modest increase in computational complexity.

AVAILABILITY: An open source, platform-independent implementation of the method in the Julia programming language is freely available at https://github.com/dkoslicki/ARK. A Matlab implementation is available at http://www.ee.kth.se/ctsoftware.}, } @article {pmid26494419, year = {2015}, author = {Kubinak, JL and Stephens, WZ and Soto, R and Petersen, C and Chiaro, T and Gogokhia, L and Bell, R and Ajami, NJ and Petrosino, JF and Morrison, L and Potts, WK and Jensen, PE and O'Connell, RM and Round, JL}, title = {MHC variation sculpts individualized microbial communities that control susceptibility to enteric infection.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {8642}, pmid = {26494419}, issn = {2041-1723}, support = {DP2 AT008746/AT/NCCIH NIH HHS/United States ; P40 OD010995/OD/NIH HHS/United States ; K22 AI95375/AI/NIAID NIH HHS/United States ; DP2 GM111099/GM/NIGMS NIH HHS/United States ; N01AI95375/AI/NIAID NIH HHS/United States ; R00 HL102228/HL/NHLBI NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; DP2AT008746-01/AT/NCCIH NIH HHS/United States ; T32 AI-055434/AI/NIAID NIH HHS/United States ; 1S10RR026802-01/RR/NCRR NIH HHS/United States ; S10 RR026802/RR/NCRR NIH HHS/United States ; 5-P39-DK034987/DK/NIDDK NIH HHS/United States ; T32 AI055434/AI/NIAID NIH HHS/United States ; AI109122/AI/NIAID NIH HHS/United States ; K22 AI095375/AI/NIAID NIH HHS/United States ; DP2GM111099-01/DP/NCCDPHP CDC HHS/United States ; R56 AI107090/AI/NIAID NIH HHS/United States ; AI107090/AI/NIAID NIH HHS/United States ; T32 GM007464/GM/NIGMS NIH HHS/United States ; R21 AI109122/AI/NIAID NIH HHS/United States ; 5-P40-OD010995/OD/NIH HHS/United States ; R00HL102228-05/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Disease Susceptibility ; Enteritis/*immunology ; Female ; *Gastrointestinal Microbiome ; Heterozygote ; Immunoglobulin A/genetics ; Intestinal Mucosa/*immunology ; Lactobacillus ; *Major Histocompatibility Complex ; Male ; Mice, Inbred BALB C ; Phenotype ; Polymorphism, Genetic ; Salmonella Infections, Animal/*immunology ; Salmonella enterica ; Symbiosis ; }, abstract = {The presentation of protein antigens on the cell surface by major histocompatibility complex (MHC) molecules coordinates vertebrate adaptive immune responses, thereby mediating susceptibility to a variety of autoimmune and infectious diseases. The composition of symbiotic microbial communities (the microbiota) is influenced by host immunity and can have a profound impact on host physiology. Here we use an MHC congenic mouse model to test the hypothesis that genetic variation at MHC genes among individuals mediates susceptibility to disease by controlling microbiota composition. We find that MHC genotype significantly influences antibody responses against commensals in the gut, and that these responses are correlated with the establishment of unique microbial communities. Transplantation experiments in germfree mice indicate that MHC-mediated differences in microbiota composition are sufficient to explain susceptibility to enteric infection. Our findings indicate that MHC polymorphisms contribute to defining an individual's unique microbial fingerprint that influences health.}, } @article {pmid26494241, year = {2015}, author = {Wallace, RJ and Rooke, JA and McKain, N and Duthie, CA and Hyslop, JJ and Ross, DW and Waterhouse, A and Watson, M and Roehe, R}, title = {The rumen microbial metagenome associated with high methane production in cattle.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {839}, pmid = {26494241}, issn = {1471-2164}, support = {BBS/E/D/20211553/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004243/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/K001744/1/MRC_/Medical Research Council/United Kingdom ; BB/J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; G0900740/MRC_/Medical Research Council/United Kingdom ; BBS/E/D/05191132/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Archaea/classification/genetics ; Australia ; Bacteria/classification/genetics ; Cattle ; Metagenome/*genetics ; Metagenomics ; Methane/*biosynthesis/metabolism ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Rumen/metabolism/*microbiology ; }, abstract = {BACKGROUND: Methane represents 16 % of total anthropogenic greenhouse gas emissions. It has been estimated that ruminant livestock produce ca. 29 % of this methane. As individual animals produce consistently different quantities of methane, understanding the basis for these differences may lead to new opportunities for mitigating ruminal methane emissions. Metagenomics is a powerful new tool for understanding the composition and function of complex microbial communities. Here we have applied metagenomics to the rumen microbial community to identify differences in the microbiota and metagenome that lead to high- and low-methane-emitting cattle phenotypes.

METHODS: Four pairs of beef cattle were selected for extreme high and low methane emissions from 72 animals, matched for breed (Aberdeen-Angus or Limousin cross) and diet (high or medium concentrate). Community analysis was carried out by qPCR of 16S and 18S rRNA genes and by alignment of Illumina HiSeq reads to the GREENGENES database. Total genomic reads were aligned to the KEGG genes databasefor functional analysis.

RESULTS: Deep sequencing produced on average 11.3 Gb per sample. 16S rRNA gene abundances indicated that archaea, predominantly Methanobrevibacter, were 2.5× more numerous (P = 0.026) in high emitters, whereas among bacteria Proteobacteria, predominantly Succinivibrionaceae, were 4-fold less abundant (2.7 vs. 11.2 %; P = 0.002). KEGG analysis revealed that archaeal genes leading directly or indirectly to methane production were 2.7-fold more abundant in high emitters. Genes less abundant in high emitters included acetate kinase, electron transport complex proteins RnfC and RnfD and glucose-6-phosphate isomerase. Sequence data were assembled de novo and over 1.5 million proteins were annotated on the subsequent metagenome scaffolds. Less than half of the predicted genes matched matched a domain within Pfam. Amongst 2774 identified proteins of the 20 KEGG orthologues that correlated with methane emissions, only 16 showed 100 % identity with a publicly available protein sequence.

CONCLUSIONS: The abundance of archaeal genes in ruminal digesta correlated strongly with differing methane emissions from individual animals, a finding useful for genetic screening purposes. Lower emissions were accompanied by higher Succinovibrionaceae abundance and changes in acetate and hydrogen production leading to less methanogenesis, as similarly postulated for Australian macropods. Large numbers of predicted protein sequences differed between high- and low-methane-emitting cattle. Ninety-nine percent were unknown, indicating a fertile area for future exploitation.}, } @article {pmid26493119, year = {2015}, author = {Fox, C and Eichelberger, K}, title = {Maternal microbiome and pregnancy outcomes.}, journal = {Fertility and sterility}, volume = {104}, number = {6}, pages = {1358-1363}, doi = {10.1016/j.fertnstert.2015.09.037}, pmid = {26493119}, issn = {1556-5653}, mesh = {Bacteria/*growth & development/pathogenicity ; Dysbiosis ; Female ; Gene-Environment Interaction ; Host-Pathogen Interactions ; Humans ; *Microbiota ; Placenta/*microbiology ; Pregnancy ; Pregnancy Complications, Infectious/genetics/*microbiology/physiopathology/prevention & control ; *Pregnancy Outcome ; Risk Factors ; Vagina/*microbiology ; Virulence ; }, abstract = {Alterations of the human microbiome are a known characteristic of various inflammatory disease states and have been linked to spontaneous preterm birth and other adverse pregnancy outcomes. Recent advances in metagenomic research have proven that the placenta harbors its own rich diverse microbiome, even in clinically healthy pregnancies, and preterm birth may be a result of hematogenous infection rather than exclusively ascending infection as previously hypothesized. In this review, we describe the microbiome in healthy nongravid and gravid women to contrast it with the alterations of the microbiome associated with spontaneous preterm birth. We also discuss the importance of host gene-environment interactions and the potential for microbiota-specific targeted therapies to reduce the risk of adverse pregnancy outcomes.}, } @article {pmid26490635, year = {2015}, author = {Qin, N and Zheng, B and Yao, J and Guo, L and Zuo, J and Wu, L and Zhou, J and Liu, L and Guo, J and Ni, S and Li, A and Zhu, Y and Liang, W and Xiao, Y and Ehrlich, SD and Li, L}, title = {Influence of H7N9 virus infection and associated treatment on human gut microbiota.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {14771}, pmid = {26490635}, issn = {2045-2322}, mesh = {Adult ; Aged ; Aged, 80 and over ; Clostridium/genetics/pathogenicity ; Enterococcus faecium/genetics/pathogenicity ; Escherichia coli/genetics/pathogenicity ; Female ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Influenza A Virus, H7N9 Subtype/*genetics/pathogenicity ; Influenza, Human/*genetics/microbiology/virology ; Male ; *Metagenomics ; Middle Aged ; }, abstract = {Between March and June, 2013, forty H7N9 patients were hospitalized in our hospital. Next-generation sequencing technologies have been used to sequence the fecal DNA samples of the patient, the within sample diversity analysis, enterotyping, functional gene and metagenomic species analysis have been carried on both the patients and healthy controls. The influence of associated treatment in H7N9 infected patients is dramatic and was firstly revealed in species level due to deep sequencing technology. We found that most of the MetaGenomic Species (MGS) enriched in the control samples were Roseburia inulinivorans DSM 16841, butyrate producing bacterium SS3/4 and most of MGS enriched in the H7N9 patients were Clostridium sp. 7 2 43FAA and Enterococcus faecium. It was concluded that H7N9 viral infection and antibiotic administration have a significant effect on the microbiota community with decreased diversity and overgrowth of the bacteria such as Escherichia coli and Enterococcus faecium. Enterotype analysis showed that the communities were unstable. Treatment including antivirals, probiotics and antibiotics helps to improve the microbiota diversity and the abundance of beneficial bacteria in the gut.}, } @article {pmid26489866, year = {2015}, author = {Hannigan, GD and Meisel, JS and Tyldsley, AS and Zheng, Q and Hodkinson, BP and SanMiguel, AJ and Minot, S and Bushman, FD and Grice, EA}, title = {The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome.}, journal = {mBio}, volume = {6}, number = {5}, pages = {e01578-15}, pmid = {26489866}, issn = {2150-7511}, support = {R00 AR060873/AR/NIAMS NIH HHS/United States ; T32 AR007465/AR/NIAMS NIH HHS/United States ; T32 HG000046/HG/NHGRI NIH HHS/United States ; AR060873/AR/NIAMS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics ; Bacteriophages/*classification/genetics/isolation & purification ; Computational Biology ; DNA/*genetics ; DNA Viruses/*classification/genetics/isolation & purification ; DNA, Viral/*genetics ; *Genetic Variation ; Humans ; Metagenomics ; *Microbiota ; Sequence Analysis, DNA ; Skin/*virology ; Spatio-Temporal Analysis ; }, abstract = {UNLABELLED: Viruses make up a major component of the human microbiota but are poorly understood in the skin, our primary barrier to the external environment. Viral communities have the potential to modulate states of cutaneous health and disease. Bacteriophages are known to influence the structure and function of microbial communities through predation and genetic exchange. Human viruses are associated with skin cancers and a multitude of cutaneous manifestations. Despite these important roles, little is known regarding the human skin virome and its interactions with the host microbiome. Here we evaluated the human cutaneous double-stranded DNA virome by metagenomic sequencing of DNA from purified virus-like particles (VLPs). In parallel, we employed metagenomic sequencing of the total skin microbiome to assess covariation and infer interactions with the virome. Samples were collected from 16 subjects at eight body sites over 1 month. In addition to the microenviroment, which is known to partition the bacterial and fungal microbiota, natural skin occlusion was strongly associated with skin virome community composition. Viral contigs were enriched for genes indicative of a temperate phage replication style and also maintained genes encoding potential antibiotic resistance and virulence factors. CRISPR spacers identified in the bacterial DNA sequences provided a record of phage predation and suggest a mechanism to explain spatial partitioning of skin phage communities. Finally, we modeled the structure of bacterial and phage communities together to reveal a complex microbial environment with a Corynebacterium hub. These results reveal the previously underappreciated diversity, encoded functions, and viral-microbial dynamic unique to the human skin virome.

IMPORTANCE: To date, most cutaneous microbiome studies have focused on bacterial and fungal communities. Skin viral communities and their relationships with their hosts remain poorly understood despite their potential to modulate states of cutaneous health and disease. Previous studies employing whole-metagenome sequencing without purification for virus-like particles (VLPs) have provided some insight into the viral component of the skin microbiome but have not completely characterized these communities or analyzed interactions with the host microbiome. Here we present an optimized virus purification technique and corresponding analysis tools for gaining novel insights into the skin virome, including viral "dark matter," and its potential interactions with the host microbiome. The work presented here establishes a baseline of the healthy human skin virome and is a necessary foundation for future studies examining viral perturbations in skin health and disease.}, } @article {pmid26485443, year = {2015}, author = {Brakstad, OG and Throne-Holst, M and Netzer, R and Stoeckel, DM and Atlas, RM}, title = {Microbial communities related to biodegradation of dispersed Macondo oil at low seawater temperature with Norwegian coastal seawater.}, journal = {Microbial biotechnology}, volume = {8}, number = {6}, pages = {989-998}, pmid = {26485443}, issn = {1751-7915}, mesh = {*Biota ; Biotransformation ; Cold Temperature ; Gulf of Mexico ; Norway ; Oils/*metabolism ; Seawater/chemistry/*microbiology ; Water Pollutants/*metabolism ; }, abstract = {The Deepwater Horizon (DWH) accident in 2010 created a deepwater plume of small oil droplets from a deepwater well in the Mississippi Canyon lease block 252 ('Macondo oil'). A novel laboratory system was used in the current study to investigate biodegradation of Macondo oil dispersions (10 μm or 30 μm median droplet sizes) at low oil concentrations (2 mg l(-1)) in coastal Norwegian seawater at a temperature of 4-5°C. Whole metagenome analyses showed that oil biodegradation was associated with the successive increased abundances of Gammaproteobacteria, while Alphaproteobacteria (Pelagibacter) became dominant at the end of the experiment. Colwellia and Oceanospirillales were related to n-alkane biodegradation, while particularly Cycloclasticus and Marinobacter were associated with degradation of aromatic hydrocarbons (HCs). The larger oil droplet dispersions resulted in delayed sequential changes of Oceanospirillales and Cycloclasticus, related with slower degradation of alkanes and aromatic HCs. The bacterial successions associated with oil biodegradation showed both similarities and differences when compared with the results from DWH field samples and laboratory studies performed with deepwater from the Gulf of Mexico.}, } @article {pmid26484735, year = {2016}, author = {Wu, X and Holmfeldt, K and Hubalek, V and Lundin, D and Åström, M and Bertilsson, S and Dopson, M}, title = {Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations.}, journal = {The ISME journal}, volume = {10}, number = {5}, pages = {1192-1203}, pmid = {26484735}, issn = {1751-7370}, mesh = {Bacteria/*genetics ; Biodiversity ; Biological Evolution ; Biomass ; Computational Biology ; Groundwater ; *Metagenome ; Microbiota ; Phylogeny ; Principal Component Analysis ; Proteobacteria/genetics ; Sequence Analysis, DNA ; Species Specificity ; Sweden ; *Water Microbiology ; }, abstract = {Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from <20 to several thousand years) and depth (171 to 448 m) revealed phylogenetically distinct microbial community subsets that either passed or were retained by a 0.22 μm filter. Such cells of <0.22 μm would have been overlooked in previous studies relying on membrane capture. Metagenomes from the three water types were used for reconstruction of 69 distinct microbial genomes, each with >86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the <0.22 μm populations were generally smaller than their phylogenetically closest relatives, suggesting that small dimensions along with a reduced genome size may be adaptations to oligotrophy. Shallow 'modern marine' water showed community members with a predominantly heterotrophic lifestyle. In contrast, the deeper, 'old saline' water adhered more closely to the current paradigm of a hydrogen-driven deep biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.}, } @article {pmid26484216, year = {2015}, author = {De Mandal, S and Zothansanga, and Lalremsanga, HT and Kumar, NS}, title = {Bacterial diversity of Murlen National Park located in Indo-Burman Biodiversity hotspot region: A metagenomic approach.}, journal = {Genomics data}, volume = {5}, number = {}, pages = {25-26}, pmid = {26484216}, issn = {2213-5960}, abstract = {Paired end Illumina Mi-Seq sequencing of 16S rRNA gene amplicon was carried out to study the bacterial community in the soil of Murlen National Park located in Indo-Burman Biodiversity hotspot region. Metagenome consisted of 302,416 reads with 151.81 Mb data and G + C content of 56.48%. More than 85% sequence was having a Phred score >=Q30 and individual sequence length was 251 bp. Metagenome sequence data are available at NCBI under the Bioproject database with accession no. SRP057136. Community metagenomics revealed a total of 1802 species belonging to 29 different phyla dominated by Acidobacteria (39.45%), Proteobacteria (26.95%) and Planctomycetes (7.81%). Our data detected a wide group of bacterial community which will be useful in further isolating and characterizing the economic importance of bacteria from this region.}, } @article {pmid26484212, year = {2015}, author = {De Mandal, S and Panda, AK and Lalnunmawii, E and Bisht, SS and Kumar, NS}, title = {Illumina-based analysis of bacterial community in Khuangcherapuk cave of Mizoram, Northeast India.}, journal = {Genomics data}, volume = {5}, number = {}, pages = {13-14}, pmid = {26484212}, issn = {2213-5960}, abstract = {Bacterial community of the Khuangcherapuk cave sediment was assessed by Illumina amplicon sequencing. The metagenome comprised of 533,120 raw reads with an average base quality (Phred score) 36.75 and G + C content is 57.61%. A total of 18 bacterial phyla were detected with following abundant genus - Mycobacterium (21.72%), Rhodococcus (7.09%), Alteromonas (1.42%), Holomonas (0.7%) and Salinisphaera (0.20%). Majority portion of the sequences (68%) is unclassified at the genus level indicating the possibilities for the presence of novel species in this cave. This study reports the cave bacterial diversity from the biodiversity hotspot region of Eastern Himalayas. Metagenome sequence data are available at NCBI under the Bioproject database with accession no. SRP056890.}, } @article {pmid26484083, year = {2014}, author = {Gao, Y and Wang, S and Xu, D and Yu, H and Wu, L and Lin, Q and Hu, Y and Li, X and He, Z and Deng, Y and Zhou, J and Yang, Y}, title = {GeoChip as a metagenomics tool to analyze the microbial gene diversity along an elevation gradient.}, journal = {Genomics data}, volume = {2}, number = {}, pages = {132-134}, pmid = {26484083}, issn = {2213-5960}, abstract = {To examine microbial responses to climate change, we used a microarray-based metagenomics tool named GeoChip 4.0 to profile soil microbial functional genes along four sites/elevations of a Tibetan mountainous grassland. We found that microbial communities differed among four elevations. Soil pH, temperature, NH4 (+)-N and vegetation diversity were four major attributes affecting soil microbial communities. Here we describe in details the experiment design, the data normalization process, soil and vegetation analyses associated with the study published on ISME Journal in 2014 [1], whose raw data have been uploaded to Gene Expression Omnibus (accession number GSM1185243).}, } @article {pmid26481089, year = {2015}, author = {Jeffries, TC and Ostrowski, M and Williams, RB and Xie, C and Jensen, RM and Grzymski, JJ and Senstius, SJ and Givskov, M and Hoeke, R and Philip, GK and Neches, RY and Drautz-Moses, DI and Chénard, C and Paulsen, IT and Lauro, FM}, title = {Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {15383}, pmid = {26481089}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; *Ecosystem ; Indian Ocean ; Metagenome ; Metagenomics/methods ; *Water Microbiology ; }, abstract = {Microorganisms act both as drivers and indicators of perturbations in the marine environment. In an effort to establish baselines to predict the response of marine habitats to environmental change, here we report a broad survey of microbial diversity across the Indian Ocean, including the first microbial samples collected in the pristine lagoon of Salomon Islands, Chagos Archipelago. This was the first large-scale ecogenomic survey aboard a private yacht employing a 'citizen oceanography' approach and tools and protocols easily adapted to ocean going sailboats. Our data highlighted biogeographic patterns in microbial community composition across the Indian Ocean. Samples from within the Salomon Islands lagoon contained a community which was different even from adjacent samples despite constant water exchange, driven by the dominance of the photosynthetic cyanobacterium Synechococcus. In the lagoon, Synechococcus was also responsible for driving shifts in the metatranscriptional profiles. Enrichment of transcripts related to photosynthesis and nutrient cycling indicated bottom-up controls of community structure. However a five-fold increase in viral transcripts within the lagoon during the day, suggested a concomitant top-down control by bacteriophages. Indeed, genome recruitment against Synechococcus reference genomes suggested a role of viruses in providing the ecological filter for determining the β-diversity patterns in this system.}, } @article {pmid26479726, year = {2015}, author = {Cai, L and Wu, H and Li, D and Zhou, K and Zou, F}, title = {Type 2 Diabetes Biomarkers of Human Gut Microbiota Selected via Iterative Sure Independent Screening Method.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0140827}, pmid = {26479726}, issn = {1932-6203}, mesh = {Aged ; Diabetes Mellitus, Type 2/*genetics/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Genetic Markers/*genetics ; Genome-Wide Association Study ; *Genomics ; Humans ; Male ; Middle Aged ; }, abstract = {Type 2 diabetes, which is a complex metabolic disease influenced by genetic and environment, has become a worldwide problem. Previous published results focused on genetic components through genome-wide association studies that just interpret this disease to some extent. Recently, two research groups published metagenome-wide association studies (MGWAS) result that found meta-biomarkers related with type 2 diabetes. However, One key problem of analyzing genomic data is that how to deal with the ultra-high dimensionality of features. From a statistical viewpoint it is challenging to filter true factors in high dimensional data. Various methods and techniques have been proposed on this issue, which can only achieve limited prediction performance and poor interpretability. New statistical procedure with higher performance and clear interpretability is appealing in analyzing high dimensional data. To address this problem, we apply an excellent statistical variable selection procedure called iterative sure independence screening to gene profiles that obtained from metagenome sequencing, and 48/24 meta-markers were selected in Chinese/European cohorts as predictors with 0.97/0.99 accuracy in AUC (area under the curve), which showed a better performance than other model selection methods, respectively. These results demonstrate the power and utility of data mining technologies within the large-scale and ultra-high dimensional genomic-related dataset for diagnostic and predictive markers identifying.}, } @article {pmid26479188, year = {2016}, author = {Bharwani, A and Mian, MF and Foster, JA and Surette, MG and Bienenstock, J and Forsythe, P}, title = {Structural & functional consequences of chronic psychosocial stress on the microbiome & host.}, journal = {Psychoneuroendocrinology}, volume = {63}, number = {}, pages = {217-227}, doi = {10.1016/j.psyneuen.2015.10.001}, pmid = {26479188}, issn = {1873-3360}, support = {GSM-136180//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Behavior, Animal/physiology ; Cells, Cultured ; Chronic Disease ; Dominance-Subordination ; Exploratory Behavior/physiology ; Gastrointestinal Microbiome/*physiology ; Host-Pathogen Interactions/*physiology ; Interleukin-10/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Social Behavior ; Stress, Psychological/immunology/*microbiology/*psychology ; }, abstract = {INTRODUCTION: Given the lasting impact of psychological distress on behavior, along with the role of the microbiome in neurobehavioral development, we sought to examine the relationship between the microbiota and stress-induced behavioral deficits.

METHODS: Male C57BL/6 mice exposed to chronic social defeat were subjected to behavioral analysis and profiling of the intestinal microbiome. Mice were also analyzed for phenotypic and functional immune changes. A computational approach on 16S rRNA marker gene sequences was used to predict functional changes in the metagenome as a consequence of structural shifts in the microbiota.

RESULTS: Chronic social defeat induced behavioral changes that were associated with reduced richness and diversity of the gut microbial community, along with distinct shifts at the level of operational taxonomic units (OTU) across phyla. The degree of deficits in social, but not exploratory behavior was correlated with group differences between the microbial community profile. In silico analysis predicted a shift in the functional profile of the microbiome: defeated mice exhibited reduced functional diversity and a lower prevalence of pathways involved in the synthesis and metabolism of neurotransmitter precursors and short-chain fatty acids. Defeated mice also exhibited sustained alterations in dendritic cell activation, and transiently elevated levels of IL-10+ T regulatory cells that were suppressed over time.

CONCLUSIONS: This study indicates that stress-induced disruptions in neurologic function are associated with altered immunoregulatory responses and complex OTU-level shifts in the microbiota. It is thus suggested that a dysbiotic state, along with specific changes in microbial markers, may predict the onset of adverse neurocognitive deficits commonly observed following exposure to severe stressors. The data also predict novel pathways that might underlie microbiota-mediated effects on brain and behavior, thus presenting targets for investigations into mechanisms and potential therapy.}, } @article {pmid26476293, year = {2016}, author = {Nagai, S and Hida, K and Urusizaki, S and Takano, Y and Hongo, Y and Kameda, T and Abe, K}, title = {Massively parallel sequencing-based survey of eukaryotic community structures in Hiroshima Bay and Ishigaki Island.}, journal = {Gene}, volume = {576}, number = {2 Pt 1}, pages = {681-689}, doi = {10.1016/j.gene.2015.10.026}, pmid = {26476293}, issn = {1879-0038}, mesh = {*Biodiversity ; DNA, Plant/genetics ; Eukaryotic Cells/*classification ; High-Throughput Nucleotide Sequencing/*methods ; Japan ; Phytoplankton/classification/genetics ; Surveys and Questionnaires ; }, abstract = {In this study, we compared the eukaryote biodiversity between Hiroshima Bay and Ishigaki Island in Japanese coastal waters by using the massively parallel sequencing (MPS)-based technique to collect preliminary data. The relative abundance of Alveolata was highest in both localities, and the second highest groups were Stramenopiles, Opisthokonta, or Hacrobia, which varied depending on the samples considered. For microalgal phyla, the relative abundance of operational taxonomic units (OTUs) and the number of MPS were highest for Dinophyceae in both localities, followed by Bacillariophyceae in Hiroshima Bay, and by Bacillariophyceae or Chlorophyceae in Ishigaki Island. The number of detected OTUs in Hiroshima Bay and Ishigaki Island was 645 and 791, respectively, and 15.3% and 12.5% of the OTUs were common between the two localities. In the non-metric multidimensional scaling analysis, the samples from the two localities were plotted in different positions. In the dendrogram developed using similarity indices, the samples were clustered into different nodes based on localities with high multiscale bootstrap values, reflecting geographic differences in biodiversity. Thus, we succeeded in demonstrating biodiversity differences between the two localities, although the read numbers of the MPSs were not high enough. The corresponding analysis showed a clear seasonal change in the biodiversity of Hiroshima Bay but it was not clear in Ishigaki Island. Thus, the MPS-based technique shows a great advantage of high performance by detecting several hundreds of OTUs from a single sample, strongly suggesting the effectiveness to apply this technique to routine monitoring programs.}, } @article {pmid26475937, year = {2016}, author = {Nagai, S and Hida, K and Urushizaki, S and Onitsuka, G and Yasuike, M and Nakamura, Y and Fujiwara, A and Tajimi, S and Kimoto, K and Kobayashi, T and Gojobori, T and Ototake, M}, title = {Influences of diurnal sampling bias on fixed-point monitoring of plankton biodiversity determined using a massively parallel sequencing-based technique.}, journal = {Gene}, volume = {576}, number = {2 Pt 1}, pages = {667-675}, doi = {10.1016/j.gene.2015.10.025}, pmid = {26475937}, issn = {1879-0038}, mesh = {*Biodiversity ; *Circadian Rhythm ; *Genes, Plant ; Phytoplankton/*classification/genetics ; RNA, Ribosomal, 18S/genetics ; Seawater ; }, abstract = {In this study, we investigated the influence of diurnal sampling bias on the community structure of plankton by comparing the biodiversity among seawater samples (n=9) obtained every 3h for 24h by using massively parallel sequencing (MPS)-based plankton monitoring at a fixed point conducted at Himedo seaport in Yatsushiro Sea, Japan. The number of raw operational taxonomy units (OTUs) and OTUs after re-sampling was 507-658 (558 ± 104, mean ± standard deviation) and 448-544 (467 ± 81), respectively, indicating high plankton biodiversity at the sampling location. The relative abundance of the top 20 OTUs in the samples from Himedo seaport was 48.8-67.7% (58.0 ± 5.8%), and the highest-ranked OTU was Pseudo-nitzschia species (Bacillariophyta) with a relative abundance of 17.3-39.2%, followed by Oithona sp. 1 and Oithona sp. 2 (Arthropoda). During seawater sampling, the semidiurnal tidal current having an amplitude of 0.3ms(-1) was dominant, and the westward residual current driven by the northeasterly wind was continuously observed during the 24-h monitoring. Therefore, the relative abundance of plankton species apparently fluctuated among the samples, but no significant difference was noted according to G-test (p>0.05). Significant differences were observed between the samples obtained from a different locality (Kusuura in Yatsushiro Sea) and at different dates, suggesting that the influence of diurnal sampling bias on plankton diversity, determined using the MPS-based survey, was not significant and acceptable.}, } @article {pmid26475934, year = {2016}, author = {Alzubaidy, H and Essack, M and Malas, TB and Bokhari, A and Motwalli, O and Kamanu, FK and Jamhor, SA and Mokhtar, NA and Antunes, A and Simões, MF and Alam, I and Bougouffa, S and Lafi, FF and Bajic, VB and Archer, JA}, title = {Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea.}, journal = {Gene}, volume = {576}, number = {2 Pt 1}, pages = {626-636}, doi = {10.1016/j.gene.2015.10.032}, pmid = {26475934}, issn = {1879-0038}, mesh = {Avicennia/genetics/metabolism/*microbiology ; Indian Ocean ; *Metagenomics ; *Microbiota ; *Rhizosphere ; Saudi Arabia ; }, abstract = {Mangroves are unique, and endangered, coastal ecosystems that play a vital role in the tropical and subtropical environments. A comprehensive description of the microbial communities in these ecosystems is currently lacking, and additional studies are required to have a complete understanding of the functioning and resilience of mangroves worldwide. In this work, we carried out a metagenomic study by comparing the microbial community of mangrove sediment with the rhizosphere microbiome of Avicennia marina, in northern Red Sea mangroves, along the coast of Saudi Arabia. Our results revealed that rhizosphere samples presented similar profiles at the taxonomic and functional levels and differentiated from the microbiome of bulk soil controls. Overall, samples showed predominance by Proteobacteria, Bacteroidetes and Firmicutes, with high abundance of sulfate reducers and methanogens, although specific groups were selectively enriched in the rhizosphere. Functional analysis showed significant enrichment in 'metabolism of aromatic compounds', 'mobile genetic elements', 'potassium metabolism' and 'pathways that utilize osmolytes' in the rhizosphere microbiomes. To our knowledge, this is the first metagenomic study on the microbiome of mangroves in the Red Sea, and the first application of unbiased 454-pyrosequencing to study the rhizosphere microbiome associated with A. marina. Our results provide the first insights into the range of functions and microbial diversity in the rhizosphere and soil sediments of gray mangrove (A. marina) in the Red Sea.}, } @article {pmid26475244, year = {2015}, author = {Carlson, JM and Hyde, ER and Petrosino, JF and Manage, ABW and Primm, TP}, title = {The host effects of Gambusia affinis with an antibiotic-disrupted microbiome.}, journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP}, volume = {178}, number = {}, pages = {163-168}, doi = {10.1016/j.cbpc.2015.10.004}, pmid = {26475244}, issn = {1532-0456}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Cyprinodontiformes/*microbiology ; Feces/microbiology ; Fish Diseases/drug therapy/microbiology ; Microbiota/*drug effects ; }, abstract = {While serving as critical tools against bacterial infections, antimicrobial therapies can also result in serious side effects, such as antibiotic-associated entercolitis. Recent studies utilizing next generation sequencing to generate community 16S gene profiles have shown that antibiotics can strongly alter community composition and deplete diversity. However, how these community changes in the microbiota are related to the host side effects is still unclear. We have used the freshwater Western mosquitofish (Gambusia affinis) as a tractable vertebrate model system to study host effects following exposure to a broad spectrum antibiotic, rifampicin. After 3days of exposure, the bacterial communities of the mucosal skin and gut microbiomes lost diversity and shifted composition. Compared to unexposed controls, treated fish were more susceptible to a specific pathogen, Edwardsiella ictaluri, yet displayed no survival differences when subjected to a polymicrobial water challenge of soil or feces. Treated fish were more susceptible to osmotic stress from NaCl, but not to the toxin nitrate. Treated fish failed to gain weight as well as controls over one month when fed a matched diet. Because of small sample sizes, pathogen susceptibility and weight gain differences were not statistically significant. This study provides supporting evidence in an experimental laboratory system that an antibiotic can have significant and persistent negative host effects, and provides for future study into the mechanisms of these effects.}, } @article {pmid26474376, year = {2016}, author = {Kao, CM and Liao, HY and Chien, CC and Tseng, YK and Tang, P and Lin, CE and Chen, SC}, title = {The change of microbial community from chlorinated solvent-contaminated groundwater after biostimulation using the metagenome analysis.}, journal = {Journal of hazardous materials}, volume = {302}, number = {}, pages = {144-150}, doi = {10.1016/j.jhazmat.2015.09.047}, pmid = {26474376}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; Groundwater/*microbiology ; Metagenomics ; Microbiota/*drug effects ; Trichloroethylene/*toxicity ; }, abstract = {The compositions of bacterial community in one site contaminated with PCE/TCE after the slow polycolloid-releasing substrate (SPRS) (contained vegetable oil, cane molasses, and surfactants) addition were analyzed. Results show that SPRS caused a rapid enhancement of reductive dechlorination of TCE. The transformation of PCE/TCE into ethene was observed after 20 days of operation. To compare the change of bacterial communities before and after SPRS addition, 16S rRNA amplicon sequencing using the metagenome analysis was performed. Results demonstrated the detection of the increased amounts of Dehalogenimonas by 2.2-fold, Pseudomonas by 3.4-fold and Sulfuricurvum by 4-fold with the analysis of the ribosomal database project (RDP). Metagenomic DNA was extracted from PCE/TCE-contaminated groundwater after SPRS addition, and subjected to sequencing. Results obtained from metagenomic sequencing indicate that genes from Dehalococcoides mccartyi was ranked as the second abundant bacteria among all of the detected bacteria via the analysis of the lowest common ancestor (LCA). Abundance of these bacterial groups, as shown above suggests their role in TCE biodegradation. Functional analysis of the metagenome, with the specific reference to chloroalkane and chloroalkene degradation, revealed the presence of some genes responsible for TCE biodegradation. Overall, results of this study provided new insights for a better understanding of the potential of biostimulation on TCE-contaminated sites.}, } @article {pmid26473721, year = {2016}, author = {Howe, A and Ringus, DL and Williams, RJ and Choo, ZN and Greenwald, SM and Owens, SM and Coleman, ML and Meyer, F and Chang, EB}, title = {Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice.}, journal = {The ISME journal}, volume = {10}, number = {5}, pages = {1217-1227}, pmid = {26473721}, issn = {1751-7370}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; T32 DK007074/DK/NIDDK NIH HHS/United States ; DK07074/DK/NIDDK NIH HHS/United States ; DK097268/DK/NIDDK NIH HHS/United States ; R01 DK097268/DK/NIDDK NIH HHS/United States ; P30 DK42086/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification ; Contig Mapping ; *Diet ; Dietary Fats ; Dietary Fiber ; Dietary Sucrose ; Female ; Gastrointestinal Diseases/*microbiology/*virology ; *Gastrointestinal Microbiome ; Intestines/microbiology ; Metagenome ; Mice ; Mice, Inbred C57BL ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Viruses/classification ; }, abstract = {To improve our understanding of the stability of mammalian intestinal communities, we characterized the responses of both bacterial and viral communities in murine fecal samples to dietary changes between high- and low-fat (LF) diets. Targeted DNA extraction methods for bacteria, virus-like particles and induced prophages were used to generate bacterial and viral metagenomes as well as 16S ribosomal RNA amplicons. Gut microbiome communities from two cohorts of C57BL/6 mice were characterized in a 6-week diet perturbation study in response to high fiber, LF and high-refined sugar, milkfat (MF) diets. The resulting metagenomes from induced bacterial prophages and extracellular viruses showed significant overlap, supporting a largely temperate viral lifestyle within these gut microbiomes. The resistance of baseline communities to dietary disturbances was evaluated, and we observed contrasting responses of baseline LF and MF bacterial and viral communities. In contrast to baseline LF viral communities and bacterial communities in both diet treatments, baseline MF viral communities were sensitive to dietary disturbances as reflected in their non-recovery during the washout period. The contrasting responses of bacterial and viral communities suggest that these communities can respond to perturbations independently of each other and highlight the potentially unique role of viruses in gut health.}, } @article {pmid26472517, year = {2016}, author = {Roux, S and Enault, F and Ravet, V and Colombet, J and Bettarel, Y and Auguet, JC and Bouvier, T and Lucas-Staat, S and Vellet, A and Prangishvili, D and Forterre, P and Debroas, D and Sime-Ngando, T}, title = {Analysis of metagenomic data reveals common features of halophilic viral communities across continents.}, journal = {Environmental microbiology}, volume = {18}, number = {3}, pages = {889-903}, doi = {10.1111/1462-2920.13084}, pmid = {26472517}, issn = {1462-2920}, mesh = {Australia ; Caudovirales/*genetics/isolation & purification ; Chromosome Mapping ; Genetic Variation ; Genome, Viral/*genetics ; Metagenomics ; Ponds/*virology ; *Salinity ; Senegal ; Spain ; }, abstract = {Microbial communities from hypersaline ponds, dominated by halophilic archaea, are considered specific of such extreme conditions. The associated viral communities have accordingly been shown to display specific features, such as similar morphologies among different sites. However, little is known about the genetic diversity of these halophilic viral communities across the Earth. Here, we studied viral communities in hypersaline ponds sampled on the coast of Senegal (8-36% of salinity) using metagenomics approach, and compared them with hypersaline viromes from Australia and Spain. The specificity of hyperhalophilic viruses could first be demonstrated at a community scale, salinity being a strong discriminating factor between communities. For the major viral group detected in all samples (Caudovirales), only a limited number of halophilic Caudovirales clades were highlighted. These clades gather viruses from different continents and display consistent genetic composition, indicating that they represent related lineages with a worldwide distribution. Non-tailed hyperhalophilic viruses display a greater rate of gene transfer and recombination, with uncharacterized genes conserved across different kind of viruses and plasmids. Thus, hypersaline viral communities around the world appear to form a genetically consistent community that are likely to harbour new genes coding for enzymes specifically adapted to these environments.}, } @article {pmid26471960, year = {2015}, author = {Delafont, V and Samba-Louaka, A and Bouchon, D and Moulin, L and Héchard, Y}, title = {Shedding light on microbial dark matter: a TM6 bacterium as natural endosymbiont of a free-living amoeba.}, journal = {Environmental microbiology reports}, volume = {7}, number = {6}, pages = {970-978}, doi = {10.1111/1758-2229.12343}, pmid = {26471960}, issn = {1758-2229}, mesh = {Amoeba/*microbiology ; *Bacteria/classification/genetics ; Metagenome ; Metagenomics ; Microbiota ; Phylogeny ; RNA, Ribosomal/genetics ; *Symbiosis ; }, abstract = {The TM6 phylum belongs to the so-called microbial dark matter that gathers uncultivated bacteria detected only via DNA sequencing. Recently, the genome sequence of a TM6 bacterium (TM6SC1) has led to suggest that this bacterium would adopt an endosymbiotic life. In the present paper, free-living amoebae bearing a TM6 strain were isolated from a water network. The amoebae were identified as Vermamoeba vermiformis and the presence of a TM6 strain was detected by polymerase chain reaction and microscopy. The partial sequence of its 16S rRNA gene showed this strain to be closely related to the sequenced TM6SC1 strain. These bacteria displayed a pyriform shape and were found within V. vermiformis. Therefore, these bacteria were named Vermiphilus pyriformis. Interactions studies showed that V. pyriformis was highly infectious and that its relation with V. vermiformis was specific and highly stable. Finally, it was found that V. pyriformis inhibited the encystment of V. vermiformis. Overall, this study describes for the first time an endosymbiotic relationship between a TM6 bacterium and a free-living amoeba in the environment. It suggests that other bacteria of the TM6 phylum might also be endosymbiotic bacteria and may be found in other free-living amoebae or other organisms.}, } @article {pmid26471001, year = {2016}, author = {Casaburi, G and Duscher, AA and Reid, RP and Foster, JS}, title = {Characterization of the stromatolite microbiome from Little Darby Island, The Bahamas using predictive and whole shotgun metagenomic analysis.}, journal = {Environmental microbiology}, volume = {18}, number = {5}, pages = {1452-1469}, pmid = {26471001}, issn = {1462-2920}, support = {NNX14AK14G//NASA/United States ; }, mesh = {Bahamas ; Biological Evolution ; Geologic Sediments/*microbiology ; Islands ; Metagenomics/*methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Modern stromatolites represent ideal ecosystems to understand the biological processes required for the precipitation of carbonate due to their long evolutionary history and occurrence in a wide range of habitats. However, most of the prior molecular work on stromatolites has focused on understanding the taxonomic complexity and not fully elucidating the functional capabilities of these systems. Here, we begin to characterize the microbiome associated with stromatolites of Little Darby Island, The Bahamas using predictive metagenomics of the 16S rRNA gene coupled with direct whole shotgun sequencing. The metagenomic analysis of the Little Darby stromatolites revealed many shared taxa and core pathways associated with biologically induced carbonate precipitation, suggesting functional convergence within Bahamian stromatolites. A comparison of the Little Darby stromatolites with other lithifying microbial ecosystems also revealed that although factors, such as geographic location and salinity, do drive some differences within the population, there are extensive similarities within the microbial populations. These results suggest that for stromatolite formation, 'who' is in the community is not as critical as metabolic activities and environmental interactions. Together, these analyses help improve our understanding of the similarities among lithifying ecosystems and provide an important first step in characterizing the shared microbiome of modern stromatolites.}, } @article {pmid26468751, year = {2015}, author = {Lewis, JD and Chen, EZ and Baldassano, RN and Otley, AR and Griffiths, AM and Lee, D and Bittinger, K and Bailey, A and Friedman, ES and Hoffmann, C and Albenberg, L and Sinha, R and Compher, C and Gilroy, E and Nessel, L and Grant, A and Chehoud, C and Li, H and Wu, GD and Bushman, FD}, title = {Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease.}, journal = {Cell host & microbe}, volume = {18}, number = {4}, pages = {489-500}, pmid = {26468751}, issn = {1934-6069}, support = {UH2 DK083981/DK/NIDDK NIH HHS/United States ; K24 DK078228/DK/NIDDK NIH HHS/United States ; P30 DK050306/DK/NIDDK NIH HHS/United States ; S10 RR024525/RR/NCRR NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; UL1RR024134/RR/NCRR NIH HHS/United States ; R01 GM103591/GM/NIGMS NIH HHS/United States ; T32 AI007632/AI/NIAID NIH HHS/United States ; UH3 DK083981/DK/NIDDK NIH HHS/United States ; UH3DK083981/DK/NIDDK NIH HHS/United States ; P30 AI 045008/AI/NIAID NIH HHS/United States ; K24-DK078228/DK/NIDDK NIH HHS/United States ; S10RR024525/RR/NCRR NIH HHS/United States ; UL1 RR024134/RR/NCRR NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*administration & dosage/adverse effects ; Archaea/classification/isolation & purification ; Bacteria/classification/isolation & purification ; Crohn Disease/*pathology/*therapy ; Diet/adverse effects/*methods ; Dysbiosis/*etiology ; Fungi/classification/isolation & purification ; Gastrointestinal Microbiome/*drug effects ; Humans ; Inflammation/*pathology ; Prospective Studies ; Viruses/classification/isolation & purification ; }, abstract = {Abnormal composition of intestinal bacteria--"dysbiosis"-is characteristic of Crohn's disease. Disease treatments include dietary changes and immunosuppressive anti-TNFα antibodies as well as ancillary antibiotic therapy, but their effects on microbiota composition are undetermined. Using shotgun metagenomic sequencing, we analyzed fecal samples from a prospective cohort of pediatric Crohn's disease patients starting therapy with enteral nutrition or anti-TNFα antibodies and reveal the full complement and dynamics of bacteria, fungi, archaea, and viruses during treatment. Bacterial community membership was associated independently with intestinal inflammation, antibiotic use, and therapy. Antibiotic exposure was associated with increased dysbiosis, whereas dysbiosis decreased with reduced intestinal inflammation. Fungal proportions increased with disease and antibiotic use. Dietary therapy had independent and rapid effects on microbiota composition distinct from other stressor-induced changes and effectively reduced inflammation. These findings reveal that dysbiosis results from independent effects of inflammation, diet, and antibiotics and shed light on Crohn disease treatments.}, } @article {pmid26468738, year = {2015}, author = {Hill, AA and Diehl, GE}, title = {The Infectious Cause of the Chronic Effect.}, journal = {Cell host & microbe}, volume = {18}, number = {4}, pages = {383-385}, doi = {10.1016/j.chom.2015.09.011}, pmid = {26468738}, issn = {1934-6069}, mesh = {Female ; *Gastrointestinal Microbiome ; Humans ; Immune System Diseases/*microbiology/*pathology ; Lymphatic Diseases/*pathology ; Male ; Yersinia pseudotuberculosis/*physiology ; Yersinia pseudotuberculosis Infections/*immunology ; }, abstract = {While acute infections cause short-term tissue damage, their long-term impact remains unknown. In a recent publication in Cell, Morais da Fonseca et al. (2015) demonstrate disruption of mesenteric lymph nodes and associated lymphatics after Yersinia pseudotuberculosis infection and clearance. This leads to chronic inflammation and an inability to initiate subsequent intestinal immune responses.}, } @article {pmid26458227, year = {2016}, author = {Jousselin, E and Clamens, AL and Galan, M and Bernard, M and Maman, S and Gschloessl, B and Duport, G and Meseguer, AS and Calevro, F and Coeur d'acier, A}, title = {Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus.}, journal = {Molecular ecology resources}, volume = {16}, number = {3}, pages = {628-640}, doi = {10.1111/1755-0998.12478}, pmid = {26458227}, issn = {1755-0998}, mesh = {Animals ; Aphids/*microbiology ; Bacteria/*classification/genetics/*isolation & purification ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; *Microbiota ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/methods ; Symbiosis ; }, abstract = {The bacterial communities inhabiting arthropods are generally dominated by a few endosymbionts that play an important role in the ecology of their hosts. Rather than comparing bacterial species richness across samples, ecological studies on arthropod endosymbionts often seek to identify the main bacterial strains associated with each specimen studied. The filtering out of contaminants from the results and the accurate taxonomic assignment of sequences are therefore crucial in arthropod microbiome studies. We aimed here to validate an Illumina 16S rRNA gene sequencing protocol and analytical pipeline for investigating endosymbiotic bacteria associated with aphids. Using replicate DNA samples from 12 species (Aphididae: Lachninae, Cinara) and several controls, we removed individual sequences not meeting a minimum threshold number of reads in each sample and carried out taxonomic assignment for the remaining sequences. With this approach, we show that (i) contaminants accounted for a negligible proportion of the bacteria identified in our samples; (ii) the taxonomic composition of our samples and the relative abundance of reads assigned to a taxon were very similar across PCR and DNA replicates for each aphid sample; in particular, bacterial DNA concentration had no impact on the results. Furthermore, by analysing the distribution of unique sequences across samples rather than aggregating them into operational taxonomic units (OTUs), we gained insight into the specificity of endosymbionts for their hosts. Our results confirm that Serratia symbiotica is often present in Cinara species, in addition to the primary symbiont, Buchnera aphidicola. Furthermore, our findings reveal new symbiotic associations with Erwinia- and Sodalis-related bacteria. We conclude with suggestions for generating and analysing 16S rRNA gene sequences for arthropod-endosymbiont studies.}, } @article {pmid26458130, year = {2015}, author = {Henschel, A and Anwar, MZ and Manohar, V}, title = {Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities.}, journal = {PLoS computational biology}, volume = {11}, number = {10}, pages = {e1004468}, pmid = {26458130}, issn = {1553-7358}, mesh = {Chromosome Mapping/methods ; Data Mining/methods ; Databases, Genetic ; *Ecosystem ; Genetic Variation/*genetics ; Genome, Bacterial/*genetics ; Metagenome/*genetics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Comprehensive mapping of environmental microbiomes in terms of their compositional features remains a great challenge in understanding the microbial biosphere of the Earth. It bears promise to identify the driving forces behind the observed community patterns and whether community assembly happens deterministically. Advances in Next Generation Sequencing allow large community profiling studies, exceeding sequencing data output of conventional methods in scale by orders of magnitude. However, appropriate collection systems are still in a nascent state. We here present a database of 20,427 diverse environmental 16S rRNA profiles from 2,426 independent studies, which forms the foundation of our meta-analysis. We conducted a sample size adaptive all-against-all beta diversity comparison while also respecting phylogenetic relationships of Operational Taxonomic Units(OTUs). After conventional hierarchical clustering we systematically test for enrichment of Environmental Ontology terms and their abstractions in all possible clusters. This post-hoc algorithm provides a novel formalism that quantifies to what extend compositional and semantic similarity of microbial community samples coincide. We automatically visualize significantly enriched subclusters on a comprehensive dendrogram of microbial communities. As a result we obtain the hitherto most differentiated and comprehensive view on global patterns of microbial community diversity. We observe strong clusterability of microbial communities in ecosystems such as human/mammal-associated, geothermal, fresh water, plant-associated, soils and rhizosphere microbiomes, whereas hypersaline and anthropogenic samples are less homogeneous. Moreover, saline samples appear less cohesive in terms of compositional properties than previously reported.}, } @article {pmid26452390, year = {2015}, author = {Serban, DE}, title = {Microbiota in Inflammatory Bowel Disease Pathogenesis and Therapy: Is It All About Diet?.}, journal = {Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition}, volume = {30}, number = {6}, pages = {760-779}, doi = {10.1177/0884533615606898}, pmid = {26452390}, issn = {1941-2452}, mesh = {*Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*microbiology/*therapy ; *Prebiotics ; Probiotics/*therapeutic use ; }, abstract = {Inflammatory bowel disease (IBD), including ulcerative colitis, Crohn's disease, and unclassified IBD, continues to cause significant morbidity. While its incidence is increasing, no clear etiology and no cure have yet been discovered. Recent findings suggest that IBD may have a multifactorial etiology, where complex interactions between genetics, epigenetics, environmental factors (including diet but also infections, antibiotics, and sanitation), and host immune system lead to abnormal immune responses and chronic inflammation. Over the past years, the role of altered gut microbiota (in both composition and function) in IBD pathogenesis has emerged as an outstanding area of interest. According to new findings, gut dysbiosis may appear as a key element in initiation of inflammation in IBD and its complications. Moreover, complex metagenomic studies provide possibilities to distinguish between IBD types and appreciate severity and prognosis of the disease, as well as response to therapy. This review provides an updated knowledge of recent findings linking altered bacterial composition and functions, viruses, and fungi to IBD pathogenesis. It also highlights the complex genetic, epigenetic, immune, and microbial interactions in relation to environmental factors (including diet). We overview the actual options to manipulate the altered microbiota, such as modified diet, probiotics, prebiotics, synbiotics, antibiotics, and fecal transplantation. Future possible therapies are also included. Targeting altered microbiota could be the next therapeutic personalized approach, but more research and well-designed comparative prospective studies are required to formulate adequate directions for prevention and therapy.}, } @article {pmid26451823, year = {2015}, author = {Qiu, YQ and Tian, X and Zhang, S}, title = {Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {12}, number = {5}, pages = {1112-1122}, doi = {10.1109/TCBB.2015.2415814}, pmid = {26451823}, issn = {1557-9964}, mesh = {Algorithms ; Base Sequence ; Chromosome Mapping/*methods ; Computer Simulation ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome/*genetics ; Metagenomics/*methods ; Models, Genetic ; Models, Statistical ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Metagenomic research uses sequencing technologies to investigate the genetic biodiversity of microbiomes presented in various ecosystems or animal tissues. The composition of a microbial community is highly associated with the environment in which the organisms exist. As large amount of sequencing short reads of microorganism genomes obtained, accurately estimating the abundance of microorganisms within a metagenomic sample is becoming an increasing challenge in bioinformatics. In this paper, we describe a hierarchical taxonomy tree-based mixture model (HTTMM) for estimating the abundance of taxon within a microbial community by incorporating the structure of the taxonomy tree. In this model, genome-specific short reads and homologous short reads among genomes can be distinguished and represented by leaf and intermediate nodes in the taxonomy tree, respectively. We adopt an expectation-maximization algorithm to solve this model. Using simulated and real-world data, we demonstrate that the proposed method is superior to both flat mixture model and lowest common ancestry-based methods. Moreover, this model can reveal previously unaddressed homologous genomes.}, } @article {pmid26451629, year = {2015}, author = {Ju, F and Zhang, T}, title = {Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology.}, journal = {Environmental science & technology}, volume = {49}, number = {21}, pages = {12628-12640}, doi = {10.1021/acs.est.5b03719}, pmid = {26451629}, issn = {1520-5851}, mesh = {Biodegradation, Environmental ; Biofuels ; Biotechnology/*methods ; Computational Biology/*methods ; Ecology/*methods ; Genome ; Metagenomics/*methods ; Microbial Consortia/genetics ; Microbial Interactions ; Research Design ; Sequence Analysis, DNA ; Waste Disposal, Fluid/methods ; }, abstract = {Recent advances in DNA sequencing technologies have prompted the widespread application of metagenomics for the investigation of novel bioresources (e.g., industrial enzymes and bioactive molecules) and unknown biohazards (e.g., pathogens and antibiotic resistance genes) in natural and engineered microbial systems across multiple disciplines. This review discusses the rigorous experimental design and sample preparation in the context of applying metagenomics in environmental sciences and biotechnology. Moreover, this review summarizes the principles, methodologies, and state-of-the-art bioinformatics procedures, tools and database resources for metagenomics applications and discusses two popular strategies (analysis of unassembled reads versus assembled contigs/draft genomes) for quantitative or qualitative insights of microbial community structure and functions. Overall, this review aims to facilitate more extensive application of metagenomics in the investigation of uncultured microorganisms, novel enzymes, microbe-environment interactions, and biohazards in biotechnological applications where microbial communities are engineered for bioenergy production, wastewater treatment, and bioremediation.}, } @article {pmid26451501, year = {2016}, author = {Pernice, MC and Giner, CR and Logares, R and Perera-Bel, J and Acinas, SG and Duarte, CM and Gasol, JM and Massana, R}, title = {Large variability of bathypelagic microbial eukaryotic communities across the world's oceans.}, journal = {The ISME journal}, volume = {10}, number = {4}, pages = {945-958}, pmid = {26451501}, issn = {1751-7370}, mesh = {*Biodiversity ; DNA, Ribosomal/*genetics ; Ecosystem ; Eukaryota/*genetics ; Geography ; Metagenomics ; Oceans and Seas ; Polymerase Chain Reaction ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {In this work, we study the diversity of bathypelagic microbial eukaryotes (0.8-20 μm) in the global ocean. Seawater samples from 3000 to 4000 m depth from 27 stations in the Atlantic, Pacific and Indian Oceans were analyzed by pyrosequencing the V4 region of the 18S ribosomal DNA. The relative abundance of the most abundant operational taxonomic units agreed with the results of a parallel metagenomic analysis, suggesting limited PCR biases in the tag approach. Although rarefaction curves for single stations were seldom saturated, the global analysis of all sequences together suggested an adequate recovery of bathypelagic diversity. Community composition presented a large variability among samples, which was poorly explained by linear geographic distance. In fact, the similarity between communities was better explained by water mass composition (26% of the variability) and the ratio in cell abundance between prokaryotes and microbial eukaryotes (21%). Deep diversity appeared dominated by four taxonomic groups (Collodaria, Chrysophytes, Basidiomycota and MALV-II) appearing in different proportions in each sample. Novel diversity amounted to 1% of the pyrotags and was lower than expected. Our study represents an essential step in the investigation of bathypelagic microbial eukaryotes, indicating dominating taxonomic groups and suggesting idiosyncratic assemblages in distinct oceanic regions.}, } @article {pmid26448087, year = {2015}, author = {Brown, CT}, title = {Strain recovery from metagenomes.}, journal = {Nature biotechnology}, volume = {33}, number = {10}, pages = {1041-1043}, pmid = {26448087}, issn = {1546-1696}, mesh = {Bacteria/*genetics ; Epigenesis, Genetic/*genetics ; Genome, Bacterial/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; }, } @article {pmid26443005, year = {2015}, author = {Li, L and Zhao, X}, title = {Comparative analyses of fecal microbiota in Tibetan and Chinese Han living at low or high altitude by barcoded 454 pyrosequencing.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {14682}, pmid = {26443005}, issn = {2045-2322}, mesh = {Adolescent ; Adult ; *Altitude ; China ; *DNA Barcoding, Taxonomic ; DNA, Bacterial/*genetics ; Feces/*microbiology ; Female ; Humans ; Male ; Metagenomics ; Microbiota/*genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA/methods ; Tibet ; Young Adult ; }, abstract = {Knowledge about the impact of altitude and ethnicity on human gut microbiota is currently limited. In this study, fecal microbiota from 12 Tibetans (T group), 11 Chinese Han living in Tibet (HH group) and 12 Chinese Han living in Shaanxi province (LH group) were profiled by 454 pyrosequencing. Analysis of UniFrac principal coordinates showed significant structural changes in fecal microbiota among the three groups. There were significant differences in the composition of fecal microbiota among the three groups at phylum and genus levels. At the phylum level, the fecal samples of HH and T groups had higher relative abundances of Firmicutes, whereas the LH group had a higher relative abundance of Bacteroidetes. These changes at the phylum level reflected different dominant genus compositions. Compared with the LH group, changes of Firmicutes and Bacteroidetes were mainly due to a significant decrease of Prevotella in the HH group and were primarily attributable to significant decreases of Bacteroides and Prevotella as well as a significant increase of Catenibacterium in the T group. In conclusion, our results suggest that high altitude may contribute to shaping human gut microbiota. Genetic and dietary factors may also explain the different microbiota compositions between Tibetan and Chinese Han.}, } @article {pmid26440540, year = {2015}, author = {Bahr, SM and Tyler, BC and Wooldridge, N and Butcher, BD and Burns, TL and Teesch, LM and Oltman, CL and Azcarate-Peril, MA and Kirby, JR and Calarge, CA}, title = {Use of the second-generation antipsychotic, risperidone, and secondary weight gain are associated with an altered gut microbiota in children.}, journal = {Translational psychiatry}, volume = {5}, number = {10}, pages = {e652}, pmid = {26440540}, issn = {2158-3188}, support = {K23 MH085005/MH/NIMH NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; K23MH085005/MH/NIMH NIH HHS/United States ; 2UL1TR000442-06/TR/NCATS NIH HHS/United States ; UL1 TR000442/TR/NCATS NIH HHS/United States ; U24 DK100469/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Antipsychotic Agents/administration & dosage/adverse effects ; *Bacteroidetes/drug effects/isolation & purification ; Child ; Cross-Sectional Studies ; Female ; *Firmicutes/drug effects/isolation & purification ; Gastrointestinal Microbiome/*drug effects ; Humans ; Male ; *Mental Disorders/drug therapy/microbiology ; *Risperidone/administration & dosage/adverse effects ; Weight Gain/*drug effects ; }, abstract = {The atypical antipsychotic risperidone (RSP) is often associated with weight gain and cardiometabolic side effects. The mechanisms for these adverse events are poorly understood and, undoubtedly, multifactorial in etiology. In light of growing evidence implicating the gut microbiome in the host's energy regulation and in xenobiotic metabolism, we hypothesized that RSP treatment would be associated with changes in the gut microbiome in children and adolescents. Thus, the impact of chronic (>12 months) and short-term use of RSP on the gut microbiome of pediatric psychiatrically ill male participants was examined in a cross-sectional and prospective (up to 10 months) design, respectively. Chronic treatment with RSP was associated with an increase in body mass index (BMI) and a significantly lower ratio of Bacteroidetes:Firmicutes as compared with antipsychotic-naïve psychiatric controls (ratio=0.15 vs 1.24, respectively; P<0.05). Furthermore, a longitudinal observation, beginning shortly after onset of RSP treatment, revealed a gradual decrease in the Bacteroidetes:Firmicutes ratio over the ensuing months of treatment, in association with BMI gain. Lastly, metagenomic analyses were performed based on extrapolation from 16S ribosomal RNA data using the software package, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Those data indicate that gut microbiota dominating the RSP-treated participants are enriched for pathways that have been implicated in weight gain, such as short-chain fatty acid production.}, } @article {pmid26439881, year = {2016}, author = {Gudbergsdóttir, SR and Menzel, P and Krogh, A and Young, M and Peng, X}, title = {Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs.}, journal = {Environmental microbiology}, volume = {18}, number = {3}, pages = {863-874}, doi = {10.1111/1462-2920.13079}, pmid = {26439881}, issn = {1462-2920}, mesh = {Archaeal Viruses/*genetics ; Biodiversity ; *Genome, Viral ; Hot Springs/*microbiology ; *Metagenome ; }, abstract = {Limited by culture-dependent methods the number of viruses identified from thermophilic Archaea and Bacteria is still very small. In this study we retrieved viral sequences from six hot spring metagenomes isolated worldwide, revealing a wide distribution of four archaeal viral families, Ampullaviridae, Bicaudaviridae, Lipothrixviridae and Rudiviridae. Importantly, we identified 10 complete or near complete viral genomes allowing, for the first time, an assessment of genome conservation and evolution of the Ampullaviridae family as well as Sulfolobus Monocaudavirus 1 (SMV1)-related viruses. Among the novel genomes, one belongs to a putative thermophilic virus infecting the bacterium Hydrogenobaculum, for which no virus has been reported in the literature. Moreover, a high viral diversity was observed in the metagenomes, especially among the Lipothrixviridae, as indicated by the large number of unique contigs and the lack of a completely assembled genome for this family. This is further supported by the large number of novel genes in the complete and partial genomes showing no sequence similarities to public databases. CRISPR analysis revealed hundreds of novel CRISPR loci and thousands of novel CRISPR spacers from each metagenome, reinforcing the notion of high viral diversity in the thermal environment.}, } @article {pmid26437943, year = {2015}, author = {Ning, J and Beiko, RG}, title = {Phylogenetic approaches to microbial community classification.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {47}, pmid = {26437943}, issn = {2049-2618}, mesh = {Biodiversity ; Dental Plaque/microbiology ; Humans ; *Metagenome ; *Microbiota ; Mouth/microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Supervised Machine Learning ; }, abstract = {BACKGROUND: The microbiota from different body sites are dominated by different major groups of microbes, but the variations within a body site such as the mouth can be more subtle. Accurate predictive models can serve as useful tools for distinguishing sub-sites and understanding key organisms and their roles and can highlight deviations from expected distributions of microbes. Good classification depends on choosing the right combination of classifier, feature representation, and learning model. Machine-learning procedures have been used in the past for supervised classification, but increased attention to feature representation and selection may produce better models and predictions.

RESULTS: We focused our attention on the classification of nine oral sites and dental plaque in particular, using data collected from the Human Microbiome Project. A key focus of our representations was the use of phylogenetic information, both as the basis for custom kernels and as a way to represent sets of microbes to the classifier. We also used the PICRUSt software, which draws on phylogenetic relationships to predict molecular functions and to generate additional features for the classifier. Custom kernels based on the UniFrac measure of community dissimilarity did not improve performance. However, feature representation was vital to classification accuracy, with microbial clade and function representations providing useful information to the classifier; combining the two types of features did not yield increased prediction accuracy. Many of the best-performing clades and functions had clear associations with oral microflora.

CONCLUSIONS: The classification of oral microbiota remains a challenging problem; our best accuracy on the plaque dataset was approximately 81 %. Perfect accuracy may be unattainable due to the close proximity of the sites and intra-individual variation. However, further exploration of the space of both classifiers and feature representations is likely to increase the accuracy of predictive models.}, } @article {pmid26437933, year = {2015}, author = {Zheng, W and Tsompana, M and Ruscitto, A and Sharma, A and Genco, R and Sun, Y and Buck, MJ}, title = {An accurate and efficient experimental approach for characterization of the complex oral microbiota.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {48}, pmid = {26437933}, issn = {2049-2618}, support = {T32 DE023526/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Microbiota ; Mouth/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Currently, taxonomic interrogation of microbiota is based on amplification of 16S rRNA gene sequences in clinical and scientific settings. Accurate evaluation of the microbiota depends heavily on the primers used, and genus/species resolution bias can arise with amplification of non-representative genomic regions. The latest Illumina MiSeq sequencing chemistry has extended the read length to 300 bp, enabling deep profiling of large number of samples in a single paired-end reaction at a fraction of the cost. An increasingly large number of researchers have adopted this technology for various microbiome studies targeting the 16S rRNA V3-V4 hypervariable region.

RESULTS: To expand the applicability of this powerful platform for further descriptive and functional microbiome studies, we standardized and tested an efficient, reliable, and straightforward workflow for the amplification, library construction, and sequencing of the 16S V1-V3 hypervariable region using the new 2 × 300 MiSeq platform. Our analysis involved 11 subgingival plaque samples from diabetic and non-diabetic human subjects suffering from periodontitis. The efficiency and reliability of our experimental protocol was compared to 16S V3-V4 sequencing data from the same samples. Comparisons were based on measures of observed taxonomic richness and species evenness, along with Procrustes analyses using beta(β)-diversity distance metrics. As an experimental control, we also analyzed a total of eight technical replicates for the V1-V3 and V3-V4 regions from a synthetic community with known bacterial species operon counts. We show that our experimental protocol accurately measures true bacterial community composition. Procrustes analyses based on unweighted UniFrac β-diversity metrics depicted significant correlation between oral bacterial composition for the V1-V3 and V3-V4 regions. However, measures of phylotype richness were higher for the V1-V3 region, suggesting that V1-V3 offers a deeper assessment of population diversity and community ecology for the complex oral microbiota.

CONCLUSION: This study provides researchers with valuable experimental evidence for the selection of appropriate 16S amplicons for future human oral microbiome studies. We expect that the tested 16S V1-V3 framework will be widely applicable to other types of microbiota, allowing robust, time-efficient, and inexpensive examination of thousands of samples for population, phylogenetic, and functional crossectional and longitutidal studies.}, } @article {pmid26436511, year = {2015}, author = {Bezerra, RA and Giné, GA and Marques, EL and Abreu-Tarazi, MF and Rezende, RP and Gaiotto, FA}, title = {Short Communication: Elucidation of bacterial community structure on thin-spined porcupine (Chaetomys subspinosus) spines by denaturing.}, journal = {Genetics and molecular research : GMR}, volume = {14}, number = {4}, pages = {11867-11875}, doi = {10.4238/2015.October.2.20}, pmid = {26436511}, issn = {1676-5680}, mesh = {Animals ; Bacillus/classification/genetics ; Bacillus anthracis/classification/genetics ; Bacillus cereus/classification/genetics ; Bacillus thuringiensis/classification/genetics ; Bacteria/classification/*genetics ; DNA, Bacterial/*genetics ; Denaturing Gradient Gel Electrophoresis ; Endangered Species ; *Metagenome ; Microbial Consortia/genetics ; *Phylogeny ; Polymerase Chain Reaction ; Porcupines/*microbiology ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Thin-spined porcupines (Chaetomys subspinosus) are threatened with extinction and are categorized as vulnerable. This is because of alteration to and loss of their habitat and possible hunting activities in their distribution area. Their spines constitute one of their defense mechanisms, which can be fomites for pathogens to humans. However, little is known about such pathogens. The present study aimed to detect bacteria on spines of C. subspinosus, from the Una Biological Reserve, South of Bahia, northeastern Brazil, by analyzing metagenomic DNA, isolating bacterial culture, using the denaturing gradient gel electrophoresis (DGGE) technique, and sequencing. Six anatomical points were selected for withdrawing spine samples from an individual C. subspinosus. At all sample points, bacteria were detected by bacteriological culture and/or DGGE and sequencing of excised bands. When all samples were combined, standard PCR-DGGE analysis of bacteria present in the spines identified 15 distinct bands, thereby revealing a distinct bacterial community. The main pathogens identified through sequencing were Bacillus cereus, B. thuringiensis, B. anthracis, and B. pumilus. The present study demonstrated the isolation and identification of non-pathogenic and pathogenic bacteria on the spines of C. subspinosus.}, } @article {pmid26436508, year = {2015}, author = {Gonçalves, AC and dos Santos, AC and dos Santos, TF and Pessoa, TB and Dias, JC and Rezende, RP}, title = {High yield of functional metagenomic library from mangroves constructed in fosmid vector.}, journal = {Genetics and molecular research : GMR}, volume = {14}, number = {4}, pages = {11841-11847}, doi = {10.4238/2015.October.2.17}, pmid = {26436508}, issn = {1676-5680}, mesh = {Aminohydrolases/genetics ; Amylases/genetics ; Bacteria/*enzymology/genetics ; Bacterial Proteins/*genetics/metabolism ; Cellulases/genetics ; Culture Media/chemistry ; Esterases/genetics ; *Gene Library ; Genetic Vectors/*chemistry ; *Metagenome ; Microbial Consortia/genetics ; Peptide Hydrolases/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; *Wetlands ; }, abstract = {In the present study, metagenomic technique and fosmid vectors were used to construct a library of clones for exploring the biotechnological potential of mangrove soils by isolation of functional genes encoding hydrolytic enzymes. The library was built with genomic DNA from the soil samples of mangrove sediments and the functional screening of 1824 clones (~64 Mbp) was performed to detect the hydrolytic activity specific for cellulases, amylases (at acidic, neutral and basic pH), lipases/esterases, proteases, and nitrilases. Significant numbers of clones, positive for the tested enzyme activities were obtained. Our results indicate the importance and biotechnological potential of mangrove soils especially when compared to those obtained using other soil metagenomic libraries.}, } @article {pmid26434770, year = {2015}, author = {Barry Roche, D and Brüls, T}, title = {An assessment of the amount of untapped fold level novelty in under-sampled areas of the tree of life.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {14717}, pmid = {26434770}, issn = {2045-2322}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry ; Humans ; Microbiota ; Models, Molecular ; Protein Conformation ; *Protein Folding ; Proteome/chemistry ; }, abstract = {Previous studies of protein fold space suggest that fold coverage is plateauing. However, sequence sampling has been -and remains to a large extent- heavily biased, focusing on culturable phyla. Sustained technological developments have fuelled the advent of metagenomics and single-cell sequencing, which might correct the current sequencing bias. The extent to which these efforts affect structural diversity remains unclear, although preliminary results suggest that uncultured organisms could constitute a source of new folds. We investigate to what extent genomes from uncultured and under-sampled phyla accessed through single cell sequencing, metagenomics and high-throughput culturing efforts have the potential to increase protein fold space, and conclude that i) genomes from under-sampled phyla appear enriched in sequences not covered by current protein family and fold profile libraries, ii) this enrichment is linked to an excess of short (and possibly partly spurious) sequences in some of the datasets, iii) the discovery rate of novel folds among sequences uncovered by current fold and family profile libraries may be as high as 36%, but would ultimately translate into a marginal increase in global discovery of novel folds. Thus, genomes from under-sampled phyla should have a rather limited impact on increasing coarse grained tertiary structure level novelty.}, } @article {pmid26434730, year = {2015}, author = {Franzén, O and Hu, J and Bao, X and Itzkowitz, SH and Peter, I and Bashir, A}, title = {Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {43}, pmid = {26434730}, issn = {2049-2618}, support = {K01 DK094986/DK/NIDDK NIH HHS/United States ; 1K01DK094986-01/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics ; Cluster Analysis ; Computational Biology/methods ; *High-Throughput Nucleotide Sequencing ; *Metagenome ; Microbiota ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Reproducibility of Results ; }, abstract = {BACKGROUND: High-throughput bacterial 16S rRNA gene sequencing followed by clustering of short sequences into operational taxonomic units (OTUs) is widely used for microbiome profiling. However, clustering of short 16S rRNA gene reads into biologically meaningful OTUs is challenging, in part because nucleotide variation along the 16S rRNA gene is only partially captured by short reads. The recent emergence of long-read platforms, such as single-molecule real-time (SMRT) sequencing from Pacific Biosciences, offers the potential for improved taxonomic and phylogenetic profiling. Here, we evaluate the performance of long- and short-read 16S rRNA gene sequencing using simulated and experimental data, followed by OTU inference using computational pipelines based on heuristic and complete-linkage hierarchical clustering.

RESULTS: In simulated data, long-read sequencing was shown to improve OTU quality and decrease variance. We then profiled 40 human gut microbiome samples using a combination of Illumina MiSeq and Blautia-specific SMRT sequencing, further supporting the notion that long reads can identify additional OTUs. We implemented a complete-linkage hierarchical clustering strategy using a flexible computational pipeline, tailored specifically for PacBio circular consensus sequencing (CCS) data that outperforms heuristic methods in most settings: https://github.com/oscar-franzen/oclust/ .

CONCLUSION: Our data demonstrate that long reads can improve OTU inference; however, the choice of clustering algorithm and associated clustering thresholds has significant impact on performance.}, } @article {pmid26433967, year = {2016}, author = {Yan, X and Luo, X and Zhao, M}, title = {Metagenomic analysis of microbial community in uranium-contaminated soil.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {1}, pages = {299-310}, doi = {10.1007/s00253-015-7003-5}, pmid = {26433967}, issn = {1432-0614}, mesh = {Bacteria/*classification/genetics/*metabolism ; *Biota ; China ; *Metagenome ; Metagenomics ; *Soil Microbiology ; Soil Pollutants/*metabolism ; Uranium/*metabolism ; }, abstract = {Uranium tailing is a serious pollution challenge for the environment. Based on metagenomic sequencing analysis, we explored the functional and structural diversity of the microbial community in six soil samples taken at different soil depths from uranium-contaminated and uncontaminated areas. Kyoto Encyclopedia of Genes and Genomes Orthology (KO) groups were obtained using a Basic Local Alignment Search Tool search based on the universal protein resource database. The KO-pathway network was then constructed using the selected KOs. Finally, alpha and beta diversity analyses were performed to explore the differences in soil bacterial diversity between the radioactive soil and uncontaminated soil. In total, 30-68 million high-quality reads were obtained. Sequence assembly yielded 286,615 contigs; and these contigs mostly annotated to 1699 KOs. The KO distributions were similar among the six soil samples. Moreover, the proportion of the metabolism of other amino acids (e.g., beta-alanine, taurine, and hypotaurine) and signal transduction was significantly lower in radioactive soil than in uncontaminated soil, whereas the proportion of membrane transport and carbohydrate metabolism was higher. Additionally, KOs were mostly enriched in ATP-binding cassette transporters and two-component systems. According to diversity analyses, Actinobacteria and Proteobacteria were the dominant phyla in radioactive and uncontaminated soil, and Robiginitalea, Microlunatus, and Alicyclobacillus were the dominant genera in radioactive soil. Taken together, these results demonstrate that soil microbial community, structure, and functions show significant changes in uranium-contaminated soil. The dominant categories such as Actinobacteria and Proteobacteria may be applied in environmental governance for uranium-contaminated soil in southern China.}, } @article {pmid26432095, year = {2015}, author = {Tong, Y}, title = {Metagenome-wide Association Studies Potentiate Precision Medicine for Rheumatoid Arthritis.}, journal = {Genomics, proteomics & bioinformatics}, volume = {13}, number = {4}, pages = {208-209}, pmid = {26432095}, issn = {2210-3244}, mesh = {Arthritis, Rheumatoid/*microbiology ; Humans ; Intestines/*microbiology ; *Microbiota ; Mouth/*microbiology ; }, } @article {pmid26431583, year = {2016}, author = {Song, H and Yoo, Y and Hwang, J and Na, YC and Kim, HS}, title = {Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis.}, journal = {The Journal of allergy and clinical immunology}, volume = {137}, number = {3}, pages = {852-860}, doi = {10.1016/j.jaci.2015.08.021}, pmid = {26431583}, issn = {1097-6825}, mesh = {*Clostridiales/classification/genetics/metabolism ; Cluster Analysis ; Computational Biology/methods ; Dermatitis, Atopic/*etiology ; *Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics ; Models, Biological ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Atopic dermatitis (AD) is a serious global epidemic associated with a modern lifestyle.

OBJECTIVE: Although aberrant interactions between gut microbes and the intestinal immune system have been implicated in this skin disease, the nature of the microbiome dysfunction underlying the disease remains unclear.

METHODS: The gut microbiome from 132 subjects, including 90 patients with AD, was analyzed by using 16S rRNA gene and metagenome sequence analyses. Reference genomes from the Human Microbiome Project and the KEGG Orthology database were used for metagenome analyses. Short-chain fatty acids in fecal samples were compared by using gas chromatographic-mass spectrometric analyses.

RESULTS: We show that enrichment of a subspecies of the major gut species Faecalibacterium prausnitzii is strongly associated with AD. In addition, the AD microbiome was enriched in genes encoding the use of various nutrients that could be released from damaged gut epithelium, reflecting a bloom of auxotrophic bacteria. Fecal samples from patients with AD showed decreased levels of butyrate and propionate, which have anti-inflammatory effects. This is likely a consequence of an intraspecies compositional change in F prausnitzii that reduces the number of high butyrate and propionate producers, including those related to the strain A2-165, a lack of which has been implicated in patients with Crohn disease.

CONCLUSIONS: The data suggest that feedback interactions between dysbiosis in F prausnitzii and dysregulation of gut epithelial inflammation might underlie the chronic progression of AD by resulting in impairment of the gut epithelial barrier, which ultimately leads to aberrant TH2-type immune responses to allergens in the skin.}, } @article {pmid26430162, year = {2015}, author = {Grice, EA}, title = {The intersection of microbiome and host at the skin interface: genomic- and metagenomic-based insights.}, journal = {Genome research}, volume = {25}, number = {10}, pages = {1514-1520}, pmid = {26430162}, issn = {1549-5469}, mesh = {Animals ; Forecasting ; *Genomics ; Humans ; *Metagenomics ; *Microbiota ; Skin/*microbiology/virology ; Skin Diseases, Bacterial/microbiology ; }, abstract = {The past two decades have been marked by a surge in research to understand the microbial communities that live in association with the human body, in part stimulated by affordable, high-throughput DNA sequencing technology. In the context of the skin, this Perspective focuses on the current state of genomic- and metagenomic-based host-microbe research and future challenges and opportunities to move the field forward. These include elucidating nonbacterial components of the skin microbiome (i.e., viruses); systematic studies to address common perturbations to the skin microbiome (e.g., antimicrobial drugs, topical cosmetic/hygienic products); improved approaches for identifying potential microbial triggers for skin diseases, including species- and strain-level resolution; and improved, clinically relevant models for studying the functional and mechanistic roles of the skin microbiome. In the next 20 years, we can realistically expect that our knowledge of the skin microbiome will inform the clinical management and treatment of skin disorders through diagnostic tests to stratify patient subsets and predict best treatment modality and outcomes and through treatment strategies such as targeted manipulation or reconstitution of microbial communities.}, } @article {pmid26426811, year = {2016}, author = {Derakhshani, H and Tun, HM and Khafipour, E}, title = {An extended single-index multiplexed 16S rRNA sequencing for microbial community analysis on MiSeq illumina platforms.}, journal = {Journal of basic microbiology}, volume = {56}, number = {3}, pages = {321-326}, doi = {10.1002/jobm.201500420}, pmid = {26426811}, issn = {1521-4028}, mesh = {Base Sequence ; Cluster Analysis ; Computational Biology/methods ; DNA Barcoding, Taxonomic/methods ; DNA Primers ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome ; Microbiota/*genetics ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; Sensitivity and Specificity ; Sequence Alignment/methods ; Sequence Analysis, RNA/*methods ; }, abstract = {The primary 16S rRNA sequencing protocol for microbial community analysis using Illumina platforms includes a single-indexing approach that allows pooling of hundreds of samples in each sequencing run. The protocol targets the V4 hypervariable region (HVR) of 16S rRNA using 150 bp paired-end (PE) sequencing. However, the latest improvement in Illumina chemistry has increased the read length up to 600 bp using 300 bp PE sequencing. To take advantage of the longer read length, a dual-indexing approach was previously developed for targeting different HVRs. However, due to simple working protocols, the single-index 150 bp PE approach still continues to be attractive to many researchers. Here, we described an extended single-indexing protocol for 300 bp PE illumina sequencing that targets the V3-V4 HVRs of 16S rRNA. The new primer set led to increased read length and alignment resolution, as well as increased richness and diversity of resulting microbial profile compared to that obtained from150 bp PE protocol for V4 sequencing. The β-diversity profile also differed qualitatively and quantitatively between the two approaches. Both primer sets had high coverage rates and specificity to detect dominant phyla; however, their coverage rate with regards to the rare biosphere varied. Our data further confirms that the choice of primer is the most deterministic factor in sequencing coverage and specificity.}, } @article {pmid26425705, year = {2015}, author = {Zhang, C and Yin, A and Li, H and Wang, R and Wu, G and Shen, J and Zhang, M and Wang, L and Hou, Y and Ouyang, H and Zhang, Y and Zheng, Y and Wang, J and Lv, X and Wang, Y and Zhang, F and Zeng, B and Li, W and Yan, F and Zhao, Y and Pang, X and Zhang, X and Fu, H and Chen, F and Zhao, N and Hamaker, BR and Bridgewater, LC and Weinkove, D and Clement, K and Dore, J and Holmes, E and Xiao, H and Zhao, G and Yang, S and Bork, P and Nicholson, JK and Wei, H and Tang, H and Zhang, X and Zhao, L}, title = {Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children.}, journal = {EBioMedicine}, volume = {2}, number = {8}, pages = {968-984}, pmid = {26425705}, issn = {2352-3964}, mesh = {Adolescent ; Animals ; Antigens, Bacterial/blood ; Child ; Child, Preschool ; Dietary Carbohydrates/*administration & dosage ; Dysbiosis/blood/*diet therapy/genetics/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Mice ; Prader-Willi Syndrome/blood/*diet therapy/genetics/*microbiology ; }, abstract = {UNLABELLED: Gut microbiota has been implicated as a pivotal contributing factor in diet-related obesity; however, its role in development of disease phenotypes in human genetic obesity such as Prader-Willi syndrome (PWS) remains elusive. In this hospitalized intervention trial with PWS (n = 17) and simple obesity (n = 21) children, a diet rich in non-digestible carbohydrates induced significant weight loss and concomitant structural changes of the gut microbiota together with reduction of serum antigen load and alleviation of inflammation. Co-abundance network analysis of 161 prevalent bacterial draft genomes assembled directly from metagenomic datasets showed relative increase of functional genome groups for acetate production from carbohydrates fermentation. NMR-based metabolomic profiling of urine showed diet-induced overall changes of host metabotypes and identified significantly reduced trimethylamine N-oxide and indoxyl sulfate, host-bacteria co-metabolites known to induce metabolic deteriorations. Specific bacterial genomes that were correlated with urine levels of these detrimental co-metabolites were found to encode enzyme genes for production of their precursors by fermentation of choline or tryptophan in the gut. When transplanted into germ-free mice, the pre-intervention gut microbiota induced higher inflammation and larger adipocytes compared with the post-intervention microbiota from the same volunteer. Our multi-omics-based systems analysis indicates a significant etiological contribution of dysbiotic gut microbiota to both genetic and simple obesity in children, implicating a potentially effective target for alleviation.

RESEARCH IN CONTEXT: Poorly managed diet and genetic mutations are the two primary driving forces behind the devastating epidemic of obesity-related diseases. Lack of understanding of the molecular chain of causation between the driving forces and the disease endpoints retards progress in prevention and treatment of the diseases. We found that children genetically obese with Prader-Willi syndrome shared a similar dysbiosis in their gut microbiota with those having diet-related obesity. A diet rich in non-digestible but fermentable carbohydrates significantly promoted beneficial groups of bacteria and reduced toxin-producers, which contributes to the alleviation of metabolic deteriorations in obesity regardless of the primary driving forces.}, } @article {pmid26423395, year = {2015}, author = {Yin, J and Zhang, XX and Wu, B and Xian, Q}, title = {Metagenomic insights into tetracycline effects on microbial community and antibiotic resistance of mouse gut.}, journal = {Ecotoxicology (London, England)}, volume = {24}, number = {10}, pages = {2125-2132}, pmid = {26423395}, issn = {1573-3017}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Microbial ; Gastrointestinal Microbiome/*drug effects ; High-Throughput Nucleotide Sequencing ; Male ; Metagenome/*drug effects ; Mice/*metabolism/*microbiology ; Sequence Analysis, DNA ; Tetracycline/*pharmacology ; }, abstract = {Antibiotics have been widely used for disease prevention and treatment of the human and animals, and for growth promotion in animal husbandry. Antibiotics can disturb the intestinal microbial community, which play a fundamental role in animals' health. Misuse or overuse of antibiotics can result in increase and spread of microbial antibiotic resistance, threatening human health and ecological safety. In this study, we used Illumina Hiseq sequencing, (1)H nuclear magnetic resonance spectroscopy and metagenomics approaches to investigate intestinal microbial community shift and antibiotic resistance alteration of the mice drinking the water containing tetracycline hydrochloride (TET). Two-week TET administration caused reduction of gut microbial diversity (from 194 to 89 genera), increase in Firmicutes abundance (from 24.9 to 39.8%) and decrease in Bacteroidetes abundance (from 69.8 to 51.2%). Metagenomic analysis showed that TET treatment affected the intestinal microbial functions of carbohydrate, ribosomal, cell wall/membrane/envelope and signal transduction, which is evidenced by the alteration in the metabolites of mouse serum. Meanwhile, in the mouse intestinal microbiota, TET treatment enhanced the abundance of antibiotic resistance genes (ARGs) (from 307.3 to 1492.7 ppm), plasmids (from 425.4 to 3235.1 ppm) and integrons (from 0.8 to 179.6 ppm) in mouse gut. Our results indicated that TET administration can disturb gut microbial community and physiological metabolism of mice, and increase the opportunity of ARGs and mobile genetic elements entering into the environment with feces discharge.}, } @article {pmid26422376, year = {2015}, author = {Santiago-Rodriguez, TM and Fornaciari, G and Luciani, S and Dowd, SE and Toranzos, GA and Marota, I and Cano, RJ}, title = {Gut Microbiome of an 11th Century A.D. Pre-Columbian Andean Mummy.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0138135}, pmid = {26422376}, issn = {1932-6203}, mesh = {Clostridium/*genetics ; Drug Resistance, Bacterial/*genetics ; *Gastrointestinal Microbiome ; Humans ; Mummies/*microbiology ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The process of natural mummification is a rare and unique process from which little is known about the resulting microbial community structure. In the present study, we characterized the microbiome of paleofeces, and ascending, transverse and descending colon of an 11th century A.D. pre-Columbian Andean mummy by 16S rRNA gene high-throughput sequencing and metagenomics. Firmicutes were the most abundant bacterial group, with Clostridium spp. comprising up to 96.2% of the mummified gut, while Turicibacter spp. represented 89.2% of the bacteria identified in the paleofeces. Microbiome profile of the paleofeces was unique when compared to previously characterized coprolites that did not undergo natural mummification. We identified DNA sequences homologous to Clostridium botulinum, Trypanosoma cruzi and human papillomaviruses (HPVs). Unexpectedly, putative antibiotic-resistance genes including beta-lactamases, penicillin-binding proteins, resistance to fosfomycin, chloramphenicol, aminoglycosides, macrolides, sulfa, quinolones, tetracycline and vancomycin, and multi-drug transporters, were also identified. The presence of putative antibiotic-resistance genes suggests that resistance may not necessarily be associated with a selective pressure of antibiotics or contact with European cultures. Identification of pathogens and antibiotic-resistance genes in ancient human specimens will aid in the understanding of the evolution of pathogens as a way to treat and prevent diseases caused by bacteria, microbial eukaryotes and viruses.}, } @article {pmid26420832, year = {2015}, author = {Taxis, TM and Wolff, S and Gregg, SJ and Minton, NO and Zhang, C and Dai, J and Schnabel, RD and Taylor, JF and Kerley, MS and Pires, JC and Lamberson, WR and Conant, GC}, title = {The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity.}, journal = {Nucleic acids research}, volume = {43}, number = {20}, pages = {9600-9612}, pmid = {26420832}, issn = {1362-4962}, mesh = {Animals ; Cattle ; DNA, Ribosomal/chemistry ; Enzymes/genetics ; Fatty Acids, Volatile/metabolism ; Male ; Metabolic Networks and Pathways ; Metagenome ; Metagenomics ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rumen/metabolism/*microbiology ; }, abstract = {By mapping translated metagenomic reads to a microbial metabolic network, we show that ruminal ecosystems that are rather dissimilar in their taxonomy can be considerably more similar at the metabolic network level. Using a new network bi-partition approach for linking the microbial network to a bovine metabolic network, we observe that these ruminal metabolic networks exhibit properties consistent with distinct metabolic communities producing similar outputs from common inputs. For instance, the closer in network space that a microbial reaction is to a reaction found in the host, the lower will be the variability of its enzyme copy number across hosts. Similarly, these microbial enzymes that are nearby to host nodes are also higher in copy number than are more distant enzymes. Collectively, these results demonstrate a widely expected pattern that, to our knowledge, has not been explicitly demonstrated in microbial communities: namely that there can exist different community metabolic networks that have the same metabolic inputs and outputs but differ in their internal structure.}, } @article {pmid26420038, year = {2015}, author = {Yu, DH and Gadkari, M and Zhou, Q and Yu, S and Gao, N and Guan, Y and Schady, D and Roshan, TN and Chen, MH and Laritsky, E and Ge, Z and Wang, H and Chen, R and Westwater, C and Bry, L and Waterland, RA and Moriarty, C and Hwang, C and Swennes, AG and Moore, SR and Shen, L}, title = {Postnatal epigenetic regulation of intestinal stem cells requires DNA methylation and is guided by the microbiome.}, journal = {Genome biology}, volume = {16}, number = {}, pages = {211}, pmid = {26420038}, issn = {1474-760X}, support = {R01 DK081557/DK/NIDDK NIH HHS/United States ; P30GM103331/GM/NIGMS NIH HHS/United States ; K02 TW008767/TW/FIC NIH HHS/United States ; P30 DK56338/DK/NIDDK NIH HHS/United States ; 1R01DK081557/DK/NIDDK NIH HHS/United States ; P30 GM103331/GM/NIGMS NIH HHS/United States ; K02TW008767/TW/FIC NIH HHS/United States ; R01 HD061916/HD/NICHD NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 DK102934/DK/NIDDK NIH HHS/United States ; R21 CA137689/CA/NCI NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01HD061916/HD/NICHD NIH HHS/United States ; 1R21CA137689/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Animals, Suckling/genetics ; Cell Differentiation/*genetics ; CpG Islands/genetics ; DNA (Cytosine-5-)-Methyltransferase 1 ; DNA (Cytosine-5-)-Methyltransferases/genetics ; DNA Methylation/*genetics ; DNA Methyltransferase 3A ; *Epigenesis, Genetic ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Mice ; Microbiota/genetics ; Stem Cells/cytology/*metabolism ; }, abstract = {BACKGROUND: DNA methylation is an epigenetic mechanism central to development and maintenance of complex mammalian tissues, but our understanding of its role in intestinal development is limited.

RESULTS: We use whole genome bisulfite sequencing, and find that differentiation of mouse colonic intestinal stem cells to intestinal epithelium is not associated with major changes in DNA methylation. However, we detect extensive dynamic epigenetic changes in intestinal stem cells and their progeny during the suckling period, suggesting postnatal epigenetic development in this stem cell population. We find that postnatal DNA methylation increases at 3' CpG islands (CGIs) correlate with transcriptional activation of glycosylation genes responsible for intestinal maturation. To directly test whether 3' CGI methylation regulates transcription, we conditionally disrupted two major DNA methyltransferases, Dnmt1 or Dnmt3a, in fetal and adult intestine. Deficiency of Dnmt1 causes severe intestinal abnormalities in neonates and disrupts crypt homeostasis in adults, whereas Dnmt3a loss was compatible with intestinal development. These studies reveal that 3' CGI methylation is functionally involved in the regulation of transcriptional activation in vivo, and that Dnmt1 is a critical regulator of postnatal epigenetic changes in intestinal stem cells. Finally, we show that postnatal 3' CGI methylation and associated gene activation in intestinal epithelial cells are significantly altered by germ-free conditions.

CONCLUSIONS: Our results demonstrate that the suckling period is critical for epigenetic development of intestinal stem cells, with potential important implications for lifelong gut health, and that the gut microbiome guides and/or facilitates these postnatal epigenetic processes.}, } @article {pmid26419531, year = {2015}, author = {Auchtung, JM and Robinson, CD and Britton, RA}, title = {Cultivation of stable, reproducible microbial communities from different fecal donors using minibioreactor arrays (MBRAs).}, journal = {Microbiome}, volume = {3}, number = {}, pages = {42}, pmid = {26419531}, issn = {2049-2618}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; U19 AI090872/AI/NIAID NIH HHS/United States ; 5U19AI090872-02/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Biodiversity ; *Bioreactors ; Cluster Analysis ; Feces/*microbiology ; Gastrointestinal Microbiome ; Humans ; Mice ; *Microbiota ; Reproducibility of Results ; }, abstract = {BACKGROUND: Continuous-flow culture models are one tool for studying complex interactions between members of human fecal microbiotas because they allow studies to be completed during an extended period of time under conditions where pH, nutrient availability, and washout of waste products and dead cells can be controlled. Because many of the existing well-validated continuous-flow models are large and complex, we were interested in developing a simpler continuous-flow system that would allow microbial community dynamics to be examined in higher throughput while still maintaining complex microbial communities. To this end, we developed minibioreactor arrays (MBRAs), small volume bioreactors (15 ml) that allow simultaneous cultivation of up to 48 microbial communities in a single anaerobic chamber.

RESULTS: We used MBRA to characterize the microbial community dynamics of replicate reactors inoculated from three different human fecal donors and reactors seeded with feces pooled from these three donors. We found that MBRA could be used to efficiently cultivate complex microbial communities that were a subset of the initial fecal inoculum (15-25 % of fecal OTUs initially observed). After an initial acclimation period of approximately 1 week, communities in each reactor stabilized and exhibited day-to-day variation similar to that observed in stable mouse fecal communities. Replicate reactors were predominately populated by shared core microbial communities; variation between replicate reactors was primarily driven by shifts in abundance of shared operational taxonomic units (OTUs). Consistent with differences between fecal donors, MBRA communities present in reactors seeded with different fecal samples had distinct composition and structure.

CONCLUSIONS: From these analyses, we conclude that MBRAs can be used to cultivate communities that recapitulate key features of human fecal communities and are a useful tool to facilitate higher-throughput studies of the dynamics of these communities.}, } @article {pmid26419466, year = {2015}, author = {McCabe, L and Britton, RA and Parameswaran, N}, title = {Prebiotic and Probiotic Regulation of Bone Health: Role of the Intestine and its Microbiome.}, journal = {Current osteoporosis reports}, volume = {13}, number = {6}, pages = {363-371}, pmid = {26419466}, issn = {1544-2241}, support = {R01 DK101050/DK/NIDDK NIH HHS/United States ; R01DK101050/DK/NIDDK NIH HHS/United States ; R01 AT007695/AT/NCCIH NIH HHS/United States ; R01AT007695/AT/NCCIH NIH HHS/United States ; R21 AT005472/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; Bone Density/*physiology ; Bone and Bones/*physiology ; Calcium/metabolism ; Dysbiosis/drug therapy/*metabolism/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Intestinal Mucosa/metabolism ; Intestines/microbiology ; Osteoporosis/drug therapy/*metabolism/microbiology ; *Prebiotics ; Probiotics/*therapeutic use ; }, abstract = {Recent advances in our understanding of how the intestinal microbiome contributes to health and disease have generated great interest in developing strategies for modulating the abundance of microbes and/or their activity to improve overall human health and prevent pathologies such as osteoporosis. Bone is an organ that the gut has long been known to regulate through absorption of calcium, the key bone mineral. However, it is clear that modulation of the gut and its microbiome can affect bone density and strength in a variety of animal models (zebrafish, rodents, chicken) and humans. This is demonstrated in studies ablating the microbiome through antibiotic treatment or using germ-free mouse conditions as well as in studies modulating the microbiome activity and composition through prebiotic and/or probiotic treatment. This review will discuss recent developments in this new and exciting area.}, } @article {pmid26417678, year = {2016}, author = {Raymond, JA}, title = {Dependence on epiphytic bacteria for freezing protection in an Antarctic moss, Bryum argenteum.}, journal = {Environmental microbiology reports}, volume = {8}, number = {1}, pages = {14-19}, doi = {10.1111/1758-2229.12337}, pmid = {26417678}, issn = {1758-2229}, mesh = {Antarctic Regions ; Bacteria/*classification/genetics/*metabolism ; Bacterial Proteins/genetics/*metabolism ; *Biota ; Bryopsida/*microbiology/radiation effects ; *Freezing ; Metagenomics ; Plant Leaves/*microbiology/radiation effects ; Sequence Analysis, DNA ; Survival Analysis ; }, abstract = {Mosses are the dominant flora of Antarctica, but their mechanisms of survival in the face of extreme low temperatures are poorly understood. A variety of Bryum argenteum from 77° S was previously shown to have strong ice-pitting activity, a sign of the presence of ice-binding proteins (IBPs) that mitigate freezing damage. Here, using samples that had been stored at -25(o) C for 10 years, it is shown that much if not all of the activity is due to bacterial ice-binding proteins secreted on the leaves of the moss. Sequencing of the leaf metagenome revealed the presence of hundreds of genes from a variety of bacteria (mostly Actinobacteria and Bacteroidetes) that encode a domain (DUF3494) that is associated with ice binding. The frequency of occurrence of this domain is one to two orders of magnitude higher than it is in representative mesophilic bacterial metagenomes. Genes encoding 42 bacterial IBPs with N-terminal secretion signals were assembled. There appears to be a commensal relationship in which the moss provides sustenance to the bacteria in return for freezing protection.}, } @article {pmid26416191, year = {2015}, author = {Macnaughtan, J and Jalan, R}, title = {Clinical and pathophysiological consequences of alterations in the microbiome in cirrhosis.}, journal = {The American journal of gastroenterology}, volume = {110}, number = {10}, pages = {1399-410; quiz 1411}, pmid = {26416191}, issn = {1572-0241}, mesh = {Biodiversity ; Dysbiosis/etiology/*microbiology/physiopathology ; Gastrointestinal Microbiome/genetics/*physiology ; Genetic Variation ; Humans ; Liver Cirrhosis/complications/*microbiology/physiopathology ; Metagenomics ; Phylogeny ; }, abstract = {Cirrhosis is a major cause of mortality worldwide. Exponential rises in prevalence have been observed secondary to increases in obesity and alcohol consumption. Multiple lines of evidence implicate gut-derived bacteria and bacterial ligands as a central driver of pathogenesis. Recent developments in culture-independent techniques have facilitated a more accurate description of microbiome composition in cirrhosis and led to the description of measures of dysbiosis shown to be associated with disease. More importantly, metagenomic studies are adding to an understanding of the functional contribution of the microbiota and may prove to be a more clinically relevant biomarker than phylogenetic studies. Much like other dysbiotic states such as inflammatory bowel disease, the microbiota in cirrhosis is characterized by a low microbial and genetic diversity. Therapeutic strategies to diminish this process are currently limited to selective intestinal decontamination with antibiotics. This review summarizes the available data and develops a framework for the use of current and future treatment strategies to diminish the consequences of dysbiosis in cirrhosis. Interventional strategies to bind bacterial products in the gut lumen and blood, and modulate the magnitude of host sensing mechanisms remain an unmet clinical need. A greater understanding of the host-microbiota interaction in cirrhosis is of key importance to inform future interventional strategies to diminish the currently escalating burden of the disease.}, } @article {pmid26416167, year = {2015}, author = {Zanvit, P and Konkel, JE and Jiao, X and Kasagi, S and Zhang, D and Wu, R and Chia, C and Ajami, NJ and Smith, DP and Petrosino, JF and Abbatiello, B and Nakatsukasa, H and Chen, Q and Belkaid, Y and Chen, ZJ and Chen, W}, title = {Antibiotics in neonatal life increase murine susceptibility to experimental psoriasis.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {8424}, pmid = {26416167}, issn = {2041-1723}, support = {//Intramural NIH HHS/United States ; }, mesh = {Aminoquinolines ; Animals ; Animals, Newborn ; Anti-Bacterial Agents/*adverse effects ; Disease Susceptibility ; Drug Interactions ; Imiquimod ; Interleukin-17/metabolism ; Interleukins/metabolism ; Mice ; Mice, Inbred C57BL ; Microbiota/*drug effects ; Polymyxin B/*adverse effects ; Psoriasis/*chemically induced/drug therapy/metabolism ; Skin/immunology ; T-Lymphocytes/metabolism ; Vancomycin/*adverse effects ; Interleukin-22 ; }, abstract = {Psoriasis is an inflammatory skin disease affecting ∼2% of the world's population, but the aetiology remains incompletely understood. Recently, microbiota have been shown to differentially regulate the development of autoimmune diseases, but their influence on psoriasis is incompletely understood. We show here that adult mice treated with antibiotics that target Gram-negative and Gram-positive bacteria develop ameliorated psoriasiform dermatitis induced by imiquimod, with decreased pro-inflammatory IL-17- and IL-22-producing T cells. Surprisingly, mice treated neonatally with these antibiotics develop exacerbated psoriasis induced by imiquimod or recombinant IL-23 injection when challenged as adults, with increased IL-22-producing γδ(+) T cells. 16S rRNA gene compositional analysis reveals that neonatal antibiotic-treatment dysregulates gut and skin microbiota in adults, which is associated with increased susceptibility to experimental psoriasis. This link between neonatal antibiotic-mediated imbalance in microbiota and development of experimental psoriasis provides precedence for further investigation of its specific aetiology as it relates to human psoriasis.}, } @article {pmid26414350, year = {2015}, author = {Xiao, L and Feng, Q and Liang, S and Sonne, SB and Xia, Z and Qiu, X and Li, X and Long, H and Zhang, J and Zhang, D and Liu, C and Fang, Z and Chou, J and Glanville, J and Hao, Q and Kotowska, D and Colding, C and Licht, TR and Wu, D and Yu, J and Sung, JJ and Liang, Q and Li, J and Jia, H and Lan, Z and Tremaroli, V and Dworzynski, P and Nielsen, HB and Bäckhed, F and Doré, J and Le Chatelier, E and Ehrlich, SD and Lin, JC and Arumugam, M and Wang, J and Madsen, L and Kristiansen, K}, title = {A catalog of the mouse gut metagenome.}, journal = {Nature biotechnology}, volume = {33}, number = {10}, pages = {1103-1108}, pmid = {26414350}, issn = {1546-1696}, mesh = {Animals ; Bacteria/*genetics ; Bacterial Proteins/genetics ; Catalogs as Topic ; Chromosome Mapping/*methods ; *Databases, Genetic ; Genome, Bacterial/*genetics ; Humans ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Microbiota/*genetics ; Species Specificity ; }, abstract = {We established a catalog of the mouse gut metagenome comprising ∼2.6 million nonredundant genes by sequencing DNA from fecal samples of 184 mice. To secure high microbiome diversity, we used mouse strains of diverse genetic backgrounds, from different providers, kept in different housing laboratories and fed either a low-fat or high-fat diet. Similar to the human gut microbiome, >99% of the cataloged genes are bacterial. We identified 541 metagenomic species and defined a core set of 26 metagenomic species found in 95% of the mice. The mouse gut microbiome is functionally similar to its human counterpart, with 95.2% of its Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologous groups in common. However, only 4.0% of the mouse gut microbial genes were shared (95% identity, 90% coverage) with those of the human gut microbiome. This catalog provides a useful reference for future studies.}, } @article {pmid26414193, year = {2015}, author = {Kergourlay, G and Taminiau, B and Daube, G and Champomier Vergès, MC}, title = {Metagenomic insights into the dynamics of microbial communities in food.}, journal = {International journal of food microbiology}, volume = {213}, number = {}, pages = {31-39}, doi = {10.1016/j.ijfoodmicro.2015.09.010}, pmid = {26414193}, issn = {1879-3460}, mesh = {Base Sequence ; *Food Handling ; *Food Microbiology ; *Food Storage ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Plants/microbiology ; Sequence Analysis, DNA/methods ; Soil ; }, abstract = {Metagenomics has proven to be a powerful tool in exploring a large diversity of natural environments such as air, soil, water, and plants, as well as various human microbiota (e.g. digestive tract, lungs, skin). DNA sequencing techniques are becoming increasingly popular and less and less expensive. Given that high-throughput DNA sequencing approaches have only recently started to be used to decipher food microbial ecosystems, there is a significant growth potential for such technologies in the field of food microbiology. The aim of this review is to present a survey of recent food investigations via metagenomics and to illustrate how this approach can be a valuable tool in the better characterization of foods and their transformation, storage and safety. Traditional food in particular has been thoroughly explored by global approaches in order to provide information on multi-species and multi-organism communities.}, } @article {pmid26408641, year = {2017}, author = {Yu, J and Feng, Q and Wong, SH and Zhang, D and Liang, QY and Qin, Y and Tang, L and Zhao, H and Stenvang, J and Li, Y and Wang, X and Xu, X and Chen, N and Wu, WK and Al-Aama, J and Nielsen, HJ and Kiilerich, P and Jensen, BA and Yau, TO and Lan, Z and Jia, H and Li, J and Xiao, L and Lam, TY and Ng, SC and Cheng, AS and Wong, VW and Chan, FK and Xu, X and Yang, H and Madsen, L and Datz, C and Tilg, H and Wang, J and Brünner, N and Kristiansen, K and Arumugam, M and Sung, JJ and Wang, J}, title = {Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer.}, journal = {Gut}, volume = {66}, number = {1}, pages = {70-78}, doi = {10.1136/gutjnl-2015-309800}, pmid = {26408641}, issn = {1468-3288}, mesh = {Aged ; Area Under Curve ; Austria ; *Biomarkers, Tumor ; Case-Control Studies ; China ; Cohort Studies ; Colorectal Neoplasms/complications/*diagnosis ; Denmark ; Dysbiosis/complications/*microbiology ; Feces/*microbiology ; Female ; Firmicutes/isolation & purification ; France ; Fusobacterium nucleatum/isolation & purification ; Gastrointestinal Microbiome/*genetics ; Genome-Wide Association Study ; Humans ; Male ; Metagenomics ; Middle Aged ; Peptostreptococcus/isolation & purification ; ROC Curve ; }, abstract = {OBJECTIVE: To evaluate the potential for diagnosing colorectal cancer (CRC) from faecal metagenomes.

DESIGN: We performed metagenome-wide association studies on faecal samples from 74 patients with CRC and 54 controls from China, and validated the results in 16 patients and 24 controls from Denmark. We further validated the biomarkers in two published cohorts from France and Austria. Finally, we employed targeted quantitative PCR (qPCR) assays to evaluate diagnostic potential of selected biomarkers in an independent Chinese cohort of 47 patients and 109 controls.

RESULTS: Besides confirming known associations of Fusobacterium nucleatum and Peptostreptococcus stomatis with CRC, we found significant associations with several species, including Parvimonas micra and Solobacterium moorei. We identified 20 microbial gene markers that differentiated CRC and control microbiomes, and validated 4 markers in the Danish cohort. In the French and Austrian cohorts, these four genes distinguished CRC metagenomes from controls with areas under the receiver-operating curve (AUC) of 0.72 and 0.77, respectively. qPCR measurements of two of these genes accurately classified patients with CRC in the independent Chinese cohort with AUC=0.84 and OR of 23. These genes were enriched in early-stage (I-II) patient microbiomes, highlighting the potential for using faecal metagenomic biomarkers for early diagnosis of CRC.

CONCLUSIONS: We present the first metagenomic profiling study of CRC faecal microbiomes to discover and validate microbial biomarkers in ethnically different cohorts, and to independently validate selected biomarkers using an affordable clinically relevant technology. Our study thus takes a step further towards affordable non-invasive early diagnostic biomarkers for CRC from faecal samples.}, } @article {pmid26407883, year = {2015}, author = {Thompson, H and Rybalka, A and Moazzez, R and Dewhirst, FE and Wade, WG}, title = {In vitro culture of previously uncultured oral bacterial phylotypes.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {24}, pages = {8307-8314}, pmid = {26407883}, issn = {1098-5336}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R37 DE016937/DE/NIDCR NIH HHS/United States ; U01 DE016937/DE/NIDCR NIH HHS/United States ; DE016937/DE/NIDCR NIH HHS/United States ; }, mesh = {Actinomyces/growth & development/metabolism ; Bacteriological Techniques ; Bacteroidetes/growth & development/metabolism ; Biofilms/growth & development ; Clostridiales/growth & development/metabolism ; Culture Media/*chemical synthesis ; Dental Plaque/*microbiology ; Humans ; In Situ Hybridization, Fluorescence ; Microbiota/genetics ; Molecular Sequence Data ; Mouth/*microbiology ; Periodontitis/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Around a third of oral bacteria cannot be grown using conventional bacteriological culture media. Community profiling targeting 16S rRNA and shotgun metagenomics methods have proved valuable in revealing the complexity of the oral bacterial community. Studies investigating the role of oral bacteria in health and disease require phenotypic characterizations that are possible only with live cultures. The aim of this study was to develop novel culture media and use an in vitro biofilm model to culture previously uncultured oral bacteria. Subgingival plaque samples collected from subjects with periodontitis were cultured on complex mucin-containing agar plates supplemented with proteose peptone (PPA), beef extract (BEA), or Gelysate (GA) as well as on fastidious anaerobe agar plus 5% horse blood (FAA). In vitro biofilms inoculated with the subgingival plaque samples and proteose peptone broth (PPB) as the growth medium were established using the Calgary biofilm device. Specific PCR primers were designed and validated for the previously uncultivated oral taxa Bacteroidetes bacteria HOT 365 and HOT 281, Lachnospiraceae bacteria HOT 100 and HOT 500, and Clostridiales bacterium HOT 093. All agar media were able to support the growth of 10 reference strains of oral bacteria. One previously uncultivated phylotype, Actinomyces sp. HOT 525, was cultivated on FAA. Of 93 previously uncultivated phylotypes found in the inocula, 26 were detected in in vitro-cultivated biofilms. Lachnospiraceae bacterium HOT 500 was successfully cultured from biofilm material harvested from PPA plates in coculture with Parvimonas micra or Veillonella dispar/parvula after colony hybridization-directed enrichment. The establishment of in vitro biofilms from oral inocula enables the cultivation of previously uncultured oral bacteria and provides source material for isolation in coculture.}, } @article {pmid26403720, year = {2016}, author = {Li, D and Sharp, JO and Drewes, JE}, title = {Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {78-86}, pmid = {26403720}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation & purification/*metabolism ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Geologic Sediments/chemistry/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers/chemistry/*microbiology ; Wastewater/chemistry/*microbiology ; }, abstract = {To reveal the variation of microbial community functions during water filtration process in river sediments, which has been utilized widely in natural water treatment systems, this study investigates the influence of municipal wastewater discharge to streams on the phylotype and metabolic potential of the microbiome in upstream and particularly various depths of downstream river sediments. Cluster analyses based on both microbial phylogenetic and functional data collectively revealed that shallow upstream sediments grouped with those from deeper subsurface downstream regions. These sediment samples were distinct from those found in shallow downstream sediments. Functional genes associated with carbohydrate, xenobiotic, and certain amino acid metabolisms were overrepresented in upstream and deep downstream samples. In contrast, the more immediate contact with wastewater discharge in shallow downstream samples resulted in an increase in the relative abundance of genes associated with nitrogen, sulfur, purine and pyrimidine metabolisms, as well as restriction-modification systems. More diverse bacterial phyla were associated with upstream and deep downstream sediments, mainly including Actinobacteria, Planctomycetes, and Firmicutes. In contrast, in shallow downstream sediments, genera affiliated with Betaproteobacteria and Gammaproteobacteria were enriched with putative functions that included ammonia and sulfur oxidation, polyphosphate accumulation, and methylotrophic bacteria. Collectively, these results highlight the enhanced capabilities of microbial communities residing in deeper stream sediments for the transformation of water contaminants and thus provide a foundation for better design of natural water treatment systems to further improve the removal of contaminants.}, } @article {pmid26401902, year = {2015}, author = {Sommer, MO}, title = {Advancing gut microbiome research using cultivation.}, journal = {Current opinion in microbiology}, volume = {27}, number = {}, pages = {127-132}, doi = {10.1016/j.mib.2015.08.004}, pmid = {26401902}, issn = {1879-0364}, mesh = {Bacteria/classification/genetics/*growth & development/isolation & purification ; Colony Count, Microbial/*methods ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Phenotype ; Phylogeny ; Probiotics/isolation & purification ; }, abstract = {Culture-independent approaches have driven the field of microbiome research and illuminated intricate relationships between the gut microbiota and human health. However, definitively associating phenotypes to specific strains or elucidating physiological interactions is challenging for metagenomic approaches. Recently a number of new approaches to gut microbiota cultivation have emerged through the integration of high-throughput phylogenetic mapping and new simplified cultivation methods. These methodologies are described along with their potential use within microbiome research. Deployment of novel cultivation approaches should enable improved studies of xenobiotic tolerance and modification phenotypes and allow a drastic expansion of the gut microbiota reference genome catalogues. Furthermore, the new cultivation methods should facilitate systematic studies of the causal relationship between constituents of the microbiota and human health accelerating new probiotic development.}, } @article {pmid26399409, year = {2015}, author = {Praveen, P and Jordan, F and Priami, C and Morine, MJ}, title = {The role of breast-feeding in infant immune system: a systems perspective on the intestinal microbiome.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {41}, pmid = {26399409}, issn = {2049-2618}, mesh = {Biodiversity ; *Breast Feeding ; Cluster Analysis ; Gastrointestinal Microbiome/physiology ; Gene Expression Regulation ; Gene Regulatory Networks ; Humans ; Immune System/*physiology ; Infant ; Metagenome ; Milk, Human/*immunology ; Transcriptome ; }, abstract = {BACKGROUND: The human intestinal microbiota changes from being sparsely populated and variable to possessing a mature, adult-like stable microbiome during the first 2 years of life. This assembly process of the microbiota can lead to either negative or positive effects on health, depending on the colonization sequence and diet. An integrative study on the diet, the microbiota, and genomic activity at the transcriptomic level may give an insight into the role of diet in shaping the human/microbiome relationship. This study aims at better understanding the effects of microbial community and feeding mode (breast-fed and formula-fed) on the immune system, by comparing intestinal metagenomic and transcriptomic data from breast-fed and formula-fed babies.

RESULTS: We re-analyzed a published metagenomics and host gene expression dataset from a systems biology perspective. Our results show that breast-fed samples co-express genes associated with immunological, metabolic, and biosynthetic activities. The diversity of the microbiota is higher in formula-fed than breast-fed infants, potentially reflecting the weaker dependence of infants on maternal microbiome. We mapped the microbial composition and the expression patterns for host systems and studied their relationship from a systems biology perspective, focusing on the differences.

CONCLUSIONS: Our findings revealed that there is co-expression of more genes in breast-fed samples but lower microbial diversity compared to formula-fed. Applying network-based systems biology approach via enrichment of microbial species with host genes revealed the novel key relationships of the microbiota with immune and metabolic activity. This was supported statistically by data and literature.}, } @article {pmid26395244, year = {2015}, author = {Singh, P and Teal, TK and Marsh, TL and Tiedje, JM and Mosci, R and Jernigan, K and Zell, A and Newton, DW and Salimnia, H and Lephart, P and Sundin, D and Khalife, W and Britton, RA and Rudrik, JT and Manning, SD}, title = {Intestinal microbial communities associated with acute enteric infections and disease recovery.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {45}, pmid = {26395244}, issn = {2049-2618}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; U19 AI090872/AI/NIAID NIH HHS/United States ; U19AI090872/AI/NIAID NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Bacteria/classification/genetics ; Biodiversity ; Case-Control Studies ; Child ; Child, Preschool ; Cluster Analysis ; Enteritis/epidemiology/*microbiology/*rehabilitation ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenome ; Michigan/epidemiology ; Middle Aged ; Public Health Surveillance ; RNA, Ribosomal, 16S/genetics ; Time Factors ; Young Adult ; }, abstract = {BACKGROUND: The intestinal microbiome represents a complex network of microbes that are important for human health and preventing pathogen invasion. Studies that examine differences in intestinal microbial communities across individuals with and without enteric infections are useful for identifying microbes that support or impede intestinal health.

RESULTS: 16S rRNA gene sequencing was conducted on stool DNA from patients with enteric infections (n = 200) and 75 healthy family members to identify differences in intestinal community composition. Stools from 13 patients were also examined post-infection to better understand how intestinal communities recover. Patient communities had lower species richness, evenness, and diversity versus uninfected communities, while principle coordinate analysis demonstrated close clustering of uninfected communities, but not the patient communities, irrespective of age, gender, and race. Differences in community composition between patients and family members were mostly due to variation in the abundance of phyla Proteobacteria, Bacteroidetes, and Firmicutes. Patient communities had significantly more Proteobacteria representing genus Escherichia relative to uninfected communities, which were dominated by Bacteroides. Intestinal communities from patients with bloody diarrhea clustered together in the neighbor-joining phylogeny, while communities from 13 patients' post-infection had a significant increase in Bacteroidetes and Firmicutes and clustered together with uninfected communities.

CONCLUSIONS: These data demonstrate that the intestinal communities in patients with enteric bacterial infections get altered in similar ways. Furthermore, preventing an increase in Escherichia abundance may be an important consideration for future prevention strategies.}, } @article {pmid26393325, year = {2015}, author = {Sanders, JG and Beichman, AC and Roman, J and Scott, JJ and Emerson, D and McCarthy, JJ and Girguis, PR}, title = {Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {8285}, pmid = {26393325}, issn = {2041-1723}, support = {T32 HG002536/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Carnivory ; Feces/microbiology ; Fermentation ; *Gastrointestinal Microbiome ; Genes, Bacterial ; Herbivory ; Metagenomics ; RNA, Ribosomal, 16S/*chemistry ; Whales/*microbiology ; }, abstract = {Mammals host gut microbiomes of immense physiological consequence, but the determinants of diversity in these communities remain poorly understood. Diet appears to be the dominant factor, but host phylogeny also seems to be an important, if unpredictable, correlate. Here we show that baleen whales, which prey on animals (fish and crustaceans), harbor unique gut microbiomes with surprising parallels in functional capacity and higher level taxonomy to those of terrestrial herbivores. These similarities likely reflect a shared role for fermentative metabolisms despite a shift in primary carbon sources from plant-derived to animal-derived polysaccharides, such as chitin. In contrast, protein catabolism and essential amino acid synthesis pathways in baleen whale microbiomes more closely resemble those of terrestrial carnivores. Our results demonstrate that functional attributes of the microbiome can vary independently even given an animal-derived diet, illustrating how diet and evolutionary history combine to shape microbial diversity in the mammalian gut.}, } @article {pmid26391875, year = {2015}, author = {Yin, H and Niu, J and Ren, Y and Cong, J and Zhang, X and Fan, F and Xiao, Y and Zhang, X and Deng, J and Xie, M and He, Z and Zhou, J and Liang, Y and Liu, X}, title = {An integrated insight into the response of sedimentary microbial communities to heavy metal contamination.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {14266}, pmid = {26391875}, issn = {2045-2322}, mesh = {*Biodiversity ; *Environmental Pollution ; Geologic Sediments/*chemistry/*microbiology ; Metagenome ; Metagenomics ; Metals, Heavy/*chemistry ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Response of biological communities to environmental stresses is a critical issue in ecology, but how microbial communities shift across heavy metal gradients remain unclear. To explore the microbial response to heavy metal contamination (e.g., Cr, Mn, Zn), the composition, structure and functional potential of sedimentary microbial community were investigated by sequencing of 16S rRNA gene amplicons and a functional gene microarray. Analysis of 16S rRNA sequences revealed that the composition and structure of sedimentary microbial communities changed significantly across a gradient of heavy metal contamination, and the relative abundances were higher for Firmicutes, Chloroflexi and Crenarchaeota, but lower for Proteobacteria and Actinobacteria in highly contaminated samples. Also, molecular ecological network analysis of sequencing data indicated that their possible interactions might be enhanced in highly contaminated communities. Correspondently, key functional genes involved in metal homeostasis (e.g., chrR, metC, merB), carbon metabolism, and organic remediation showed a higher abundance in highly contaminated samples, indicating that bacterial communities in contaminated areas may modulate their energy consumption and organic remediation ability. This study indicated that the sedimentary indigenous microbial community may shift the composition and structure as well as function priority and interaction network to increase their adaptability and/or resistance to environmental contamination.}, } @article {pmid26388969, year = {2015}, author = {Brown, BL and LePrell, RV and Franklin, RB and Rivera, MC and Cabral, FM and Eaves, HL and Gardiakos, V and Keegan, KP and King, TL}, title = {Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River.}, journal = {Standards in genomic sciences}, volume = {10}, number = {}, pages = {65}, pmid = {26388969}, issn = {1944-3277}, abstract = {Knowledge of the diversity and ecological function of the microbial consortia of James River in Virginia, USA, is essential to developing a more complete understanding of the ecology of this model river system. Metagenomic analysis of James River's planktonic microbial community was performed for the first time using an unamplified genomic library and a 16S rDNA amplicon library prepared and sequenced by Ion PGM and MiSeq, respectively. From the 0.46-Gb WGS library (GenBank:SRR1146621; MG-RAST:4532156.3), 4 × 10(6) reads revealed >3 × 10(6) genes, 240 families of prokaryotes, and 155 families of eukaryotes. From the 0.68-Gb 16S library (GenBank:SRR2124995; MG-RAST:4631271.3; EMB:2184), 4 × 10(6) reads revealed 259 families of eubacteria. Results of the WGS and 16S analyses were highly consistent and indicated that more than half of the bacterial sequences were Proteobacteria, predominantly Comamonadaceae. The most numerous genera in this group were Acidovorax (including iron oxidizers, nitrotolulene degraders, and plant pathogens), which accounted for 10 % of assigned bacterial reads. Polaromonas were another 6 % of all bacterial reads, with many assignments to groups capable of degrading polycyclic aromatic hydrocarbons. Albidiferax (iron reducers) and Variovorax (biodegraders of a variety of natural biogenic compounds as well as anthropogenic contaminants such as polycyclic aromatic hydrocarbons and endocrine disruptors) each accounted for an additional 3 % of bacterial reads. Comparison of these data to other publically-available aquatic metagenomes revealed that this stretch of James River is highly similar to the upper Mississippi River, and that these river systems are more similar to aquaculture and sludge ecosystems than they are to lakes or to a pristine section of the upper Amazon River. Taken together, these analyses exposed previously unknown aspects of microbial biodiversity, documented the ecological responses of microbes to urban effects, and revealed the noteworthy presence of 22 human-pathogenic bacterial genera (e.g., Enterobacteriaceae, pathogenic Pseudomonadaceae, and 'Vibrionales') and 6 pathogenic eukaryotic genera (e.g., Trypanosomatidae and Vahlkampfiidae). This information about pathogen diversity may be used to promote human epidemiological studies, enhance existing water quality monitoring efforts, and increase awareness of the possible health risks associated with recreational use of James River.}, } @article {pmid26388852, year = {2015}, author = {Pinto, C and Pinho, D and Cardoso, R and Custódio, V and Fernandes, J and Sousa, S and Pinheiro, M and Egas, C and Gomes, AC}, title = {Wine fermentation microbiome: a landscape from different Portuguese wine appellations.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {905}, pmid = {26388852}, issn = {1664-302X}, abstract = {Grapes and wine musts harbor a complex microbiome, which plays a crucial role in wine fermentation as it impacts on wine flavour and, consequently, on its final quality and value. Unveiling the microbiome and its dynamics, and understanding the ecological factors that explain such biodiversity, has been a challenge to oenology. In this work, we tackle this using a metagenomics approach to describe the natural microbial communities, both fungal and bacterial microorganisms, associated with spontaneous wine fermentations. For this, the wine microbiome, from six Portuguese wine appellations, was fully characterized as regards to three stages of fermentation - Initial Musts (IM), and Start and End of alcoholic fermentations (SF and EF, respectively). The wine fermentation process revealed a higher impact on fungal populations when compared with bacterial communities, and the fermentation evolution clearly caused a loss of the environmental microorganisms. Furthermore, significant differences (p < 0.05) were found in the fungal populations between IM, SF, and EF, and in the bacterial population between IM and SF. Fungal communities were characterized by either the presence of environmental microorganisms and phytopathogens in the IM, or yeasts associated with alcoholic fermentations in wine must samples as Saccharomyces and non-Saccharomyces yeasts (as Lachancea, Metschnikowia, Hanseniaspora, Hyphopichia, Sporothrix, Candida, and Schizosaccharomyces). Among bacterial communities, the most abundant family was Enterobacteriaceae; though families of species associated with the production of lactic acid (Lactobacillaceae, Leuconostocaceae) and acetic acid (Acetobacteriaceae) were also detected. Interestingly, a biogeographical correlation for both fungal and bacterial communities was identified between wine appellations at IM suggesting that each wine region contains specific and embedded microbial communities which may contribute to the uniqueness of regional wines.}, } @article {pmid26388143, year = {2015}, author = {Coelho, ED and Santiago, AM and Arrais, JP and Oliveira, JL}, title = {Computational methodology for predicting the landscape of the human-microbial interactome region level influence.}, journal = {Journal of bioinformatics and computational biology}, volume = {13}, number = {5}, pages = {1550023}, doi = {10.1142/S0219720015500237}, pmid = {26388143}, issn = {1757-6334}, mesh = {*Algorithms ; Computational Biology/*methods ; Computing Methodologies ; Databases, Protein ; Female ; Genetic Variation ; Host-Pathogen Interactions ; Humans ; Male ; Metagenomics/statistics & numerical data ; *Microbiota ; Organ Specificity ; Phylogeny ; Protein Interaction Mapping/*statistics & numerical data ; }, abstract = {Microbial communities thrive in close association among themselves and with the host, establishing protein-protein interactions (PPIs) with the latter, and thus being able to benefit (positively impact) or disturb (negatively impact) biological events in the host. Despite major collaborative efforts to sequence the Human microbiome, there is still a great lack of understanding their impact. We propose a computational methodology to predict the impact of microbial proteins in human biological events, taking into account the abundance of each microbial protein and its relation to all other microbial and human proteins. This alternative methodology is centered on an improved impact estimation algorithm that integrates PPIs between human and microbial proteins with Reactome pathway data. This methodology was applied to study the impact of 24 microbial phyla over different cellular events, within 10 different human microbiomes. The results obtained confirm findings already described in the literature and explore new ones. We believe the Human microbiome can no longer be ignored as not only is there enough evidence correlating microbiome alterations and disease states, but also the return to healthy states once these alterations are reversed.}, } @article {pmid26381989, year = {2015}, author = {Qin, N and Le Chatelier, E and Guo, J and Prifti, E and Li, L and Ehrlich, SD}, title = {Qin et al. reply.}, journal = {Nature}, volume = {525}, number = {7569}, pages = {E2-3}, pmid = {26381989}, issn = {1476-4687}, mesh = {Gastrointestinal Tract/*microbiology ; Humans ; Liver Cirrhosis/*diagnosis/*microbiology ; *Metagenomics ; Microbiota/*genetics/*physiology ; }, } @article {pmid26381988, year = {2015}, author = {Bajaj, JS and Betrapally, NS and Gillevet, PM}, title = {Decompensated cirrhosis and microbiome interpretation.}, journal = {Nature}, volume = {525}, number = {7569}, pages = {E1-2}, pmid = {26381988}, issn = {1476-4687}, support = {I01 CX001076/CX/CSRD VA/United States ; R01 DK087913/DK/NIDDK NIH HHS/United States ; }, mesh = {Gastrointestinal Tract/*microbiology ; Humans ; Liver Cirrhosis/*diagnosis/*microbiology ; *Metagenomics ; Microbiota/*genetics/*physiology ; }, } @article {pmid26381211, year = {2015}, author = {Giacomin, P and Zakrzewski, M and Croese, J and Su, X and Sotillo, J and McCann, L and Navarro, S and Mitreva, M and Krause, L and Loukas, A and Cantacessi, C}, title = {Experimental hookworm infection and escalating gluten challenges are associated with increased microbial richness in celiac subjects.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {13797}, pmid = {26381211}, issn = {2045-2322}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Ancylostomatoidea/immunology ; Animals ; *Biodiversity ; Case-Control Studies ; Celiac Disease/*etiology/therapy ; Feces/microbiology ; *Gastrointestinal Microbiome/immunology ; Glutens/*metabolism ; High-Throughput Nucleotide Sequencing ; *Hookworm Infections/immunology ; Humans ; Immunomodulation ; Metagenome ; Metagenomics/methods ; }, abstract = {The intestinal microbiota plays a critical role in the development of the immune system. Recent investigations have highlighted the potential of helminth therapy for treating a range of inflammatory disorders, including celiac disease (CeD); however, the mechanisms by which helminths modulate the immune response of the human host and ameliorate CeD pathology are unknown. In this study, we investigated the potential role of alterations in the human gut microbiota in helminth-mediated suppression of an inflammatory disease. We assessed the qualitative and quantitative changes in the microbiota of human volunteers with CeD prior to and following infection with human hookworms, and following challenge with escalating doses of dietary gluten. Experimental hookworm infection of the trial subjects resulted in maintenance of the composition of the intestinal flora, even after a moderate gluten challenge. Notably, we observed a significant increase in microbial species richness over the course of the trial, which could represent a potential mechanism by which hookworms can regulate gluten-induced inflammation and maintain intestinal immune homeostasis.}, } @article {pmid26380076, year = {2015}, author = {Larsen, PE and Dai, Y}, title = {Metabolome of human gut microbiome is predictive of host dysbiosis.}, journal = {GigaScience}, volume = {4}, number = {}, pages = {42}, pmid = {26380076}, issn = {2047-217X}, mesh = {Humans ; Intestines/*microbiology ; *Metabolome ; *Microbiota ; Support Vector Machine ; }, abstract = {BACKGROUND: Humans live in constant and vital symbiosis with a closely linked bacterial ecosystem called the microbiome, which influences many aspects of human health. When this microbial ecosystem becomes disrupted, the health of the human host can suffer; a condition called dysbiosis. However, the community compositions of human microbiomes also vary dramatically from individual to individual, and over time, making it difficult to uncover the underlying mechanisms linking the microbiome to human health. We propose that a microbiome's interaction with its human host is not necessarily dependent upon the presence or absence of particular bacterial species, but instead is dependent on its community metabolome; an emergent property of the microbiome.

RESULTS: Using data from a previously published, longitudinal study of microbiome populations of the human gut, we extrapolated information about microbiome community enzyme profiles and metabolome models. Using machine learning techniques, we demonstrated that the aggregate predicted community enzyme function profiles and modeled metabolomes of a microbiome are more predictive of dysbiosis than either observed microbiome community composition or predicted enzyme function profiles.

CONCLUSIONS: Specific enzyme functions and metabolites predictive of dysbiosis provide insights into the molecular mechanisms of microbiome-host interactions. The ability to use machine learning to predict dysbiosis from microbiome community interaction data provides a potentially powerful tool for understanding the links between the human microbiome and human health, pointing to potential microbiome-based diagnostics and therapeutic interventions.}, } @article {pmid26379658, year = {2015}, author = {Trindade, M and van Zyl, LJ and Navarro-Fernández, J and Abd Elrazak, A}, title = {Targeted metagenomics as a tool to tap into marine natural product diversity for the discovery and production of drug candidates.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {890}, pmid = {26379658}, issn = {1664-302X}, abstract = {Microbial natural products exhibit immense structural diversity and complexity and have captured the attention of researchers for several decades. They have been explored for a wide spectrum of applications, most noteworthy being their prominent role in medicine, and their versatility expands to application as drugs for many diseases. Accessing unexplored environments harboring unique microorganisms is expected to yield novel bioactive metabolites with distinguishing functionalities, which can be supplied to the starved pharmaceutical market. For this purpose the oceans have turned out to be an attractive and productive field. Owing to the enormous biodiversity of marine microorganisms, as well as the growing evidence that many metabolites previously isolated from marine invertebrates and algae are actually produced by their associated bacteria, the interest in marine microorganisms has intensified. Since the majority of the microorganisms are uncultured, metagenomic tools are required to exploit the untapped biochemistry. However, after years of employing metagenomics for marine drug discovery, new drugs are vastly under-represented. While a plethora of natural product biosynthetic genes and clusters are reported, only a minor number of potential therapeutic compounds have resulted through functional metagenomic screening. This review explores specific obstacles that have led to the low success rate. In addition to the typical problems encountered with traditional functional metagenomic-based screens for novel biocatalysts, there are enormous limitations which are particular to drug-like metabolites. We also present how targeted and function-guided strategies, employing modern, and multi-disciplinary approaches have yielded some of the most exciting discoveries attributed to uncultured marine bacteria. These discoveries set the stage for progressing the production of drug candidates from uncultured bacteria for pre-clinical and clinical development.}, } @article {pmid26378926, year = {2015}, author = {Rutten, NB and Gorissen, DM and Eck, A and Niers, LE and Vlieger, AM and Besseling-van der Vaart, I and Budding, AE and Savelkoul, PH and van der Ent, CK and Rijkers, GT}, title = {Long Term Development of Gut Microbiota Composition in Atopic Children: Impact of Probiotics.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0137681}, pmid = {26378926}, issn = {1932-6203}, mesh = {Bacterial Typing Techniques ; Bifidobacterium ; Biodiversity ; Child ; Child, Preschool ; Dietary Supplements ; Double-Blind Method ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Humans ; Hypersensitivity/immunology ; Infant ; Infant, Newborn ; Lactobacillus ; Male ; Metagenome/*genetics ; Placebos/therapeutic use ; Pregnancy ; Probiotics/*therapeutic use ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; }, abstract = {INTRODUCTION: Imbalance of the human gut microbiota in early childhood is suggested as a risk factor for immune-mediated disorders such as allergies. With the objective to modulate the intestinal microbiota, probiotic supplementation during infancy has been used for prevention of allergic diseases in infants, with variable success. However, not much is known about the long-term consequences of neonatal use of probiotics on the microbiota composition. The aim of this study was to assess the composition and microbial diversity in stool samples of infants at high-risk for atopic disease, from birth onwards to six years of age, who were treated with probiotics or placebo during the first year of life.

METHODS: In a double-blind, randomized, placebo-controlled trial, a probiotic mixture consisting of B. bifidum W23, B. lactis W52 and Lc. Lactis W58 (Ecologic® Panda) was administered to pregnant women during the last 6 weeks of pregnancy and to their offspring during the first year of life. During follow-up, faecal samples were collected from 99 children over a 6-year period with the following time points: first week, second week, first month, three months, first year, eighteen months, two years and six years. Bacterial profiling was performed by IS-pro. Differences in bacterial abundance and diversity were assessed by conventional statistics.

RESULTS: The presence of the supplemented probiotic strains in faecal samples was confirmed, and the probiotic strains had a higher abundance and prevalence in the probiotic group during supplementation. Only minor and short term differences in composition of microbiota were found between the probiotic and placebo group and between children with or without atopy. The diversity of Bacteroidetes was significantly higher after two weeks in the placebo group, and at the age of two years atopic children had a significantly higher Proteobacteria diversity (p < 0.05). Gut microbiota development continued between two and six years, whereby microbiota composition at phylum level evolved more and more towards an adult-like configuration.

CONCLUSION: Perinatal supplementation with Ecologic® Panda, to children at high-risk for atopic disease, had minor effects on gut microbiota composition during the supplementation period. No long lasting differences were identified. Regardless of intervention or atopic disease status, children had a shared microbiota development over time determined by age that continued to develop between two and six years.}, } @article {pmid26378041, year = {2015}, author = {Ericsson, AC and Akter, S and Hanson, MM and Busi, SB and Parker, TW and Schehr, RJ and Hankins, MA and Ahner, CE and Davis, JW and Franklin, CL and Amos-Landgraf, JM and Bryda, EC}, title = {Differential susceptibility to colorectal cancer due to naturally occurring gut microbiota.}, journal = {Oncotarget}, volume = {6}, number = {32}, pages = {33689-33704}, pmid = {26378041}, issn = {1949-2553}, support = {P40 OD011062/OD/NIH HHS/United States ; T32 OD011126/OD/NIH HHS/United States ; }, mesh = {Animals ; Colorectal Neoplasms/*microbiology/pathology ; Disease Models, Animal ; Disease Susceptibility ; Female ; Gastrointestinal Microbiome ; Humans ; Male ; Rats ; Rats, Inbred F344 ; Rats, Sprague-Dawley ; }, abstract = {Recent studies investigating the human microbiome have identified particular bacterial species that correlate with the presence of colorectal cancer. To evaluate the role of qualitatively different but naturally occurring gut microbiota and the relationship with colorectal cancer development, genetically identical embryos from the Polyposis in Rat Colon (Pirc) rat model of colorectal cancer were transferred into recipients of three different genetic backgrounds (F344/NHsd, LEW/SsNHsd, and Crl:SD). Tumor development in the pups was tracked longitudinally via colonoscopy, and end-stage tumor burden was determined. To confirm vertical transmission and identify associations between the gut microbiota and disease phenotype, the fecal microbiota was characterized in recipient dams 24 hours pre-partum, and in Pirc rat offspring prior to and during disease progression. Our data show that the gut microbiota varies between rat strains, with LEW/SsNHsd having a greater relative abundance of the bacteria Prevotella copri. The mature gut microbiota of pups resembled the profile of their dams, indicating that the dam is the primary determinant of the developing microbiota. Both male and female F344-Pirc rats harboring the Lewis microbiota had decreased tumor burden relative to genetically identical rats harboring F344 or SD microbiota. Significant negative correlations were detected between tumor burden and the relative abundance of specific taxa from samples taken at weaning and shortly thereafter, prior to observable adenoma development. Notably, this naturally occurring variation in the gut microbiota is associated with a significant difference in severity of colorectal cancer, and the abundance of certain taxa is associated with decreased tumor burden.}, } @article {pmid26374288, year = {2015}, author = {Blekhman, R and Goodrich, JK and Huang, K and Sun, Q and Bukowski, R and Bell, JT and Spector, TD and Keinan, A and Ley, RE and Gevers, D and Clark, AG}, title = {Host genetic variation impacts microbiome composition across human body sites.}, journal = {Genome biology}, volume = {16}, number = {1}, pages = {191}, pmid = {26374288}, issn = {1474-760X}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 DK093595/DK/NIDDK NIH HHS/United States ; T32 GM007617/GM/NIGMS NIH HHS/United States ; U54 HG004969/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteria/classification/isolation & purification ; *Genetic Variation ; Genome, Human ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {BACKGROUND: The composition of bacteria in and on the human body varies widely across human individuals, and has been associated with multiple health conditions. While microbial communities are influenced by environmental factors, some degree of genetic influence of the host on the microbiome is also expected. This study is part of an expanding effort to comprehensively profile the interactions between human genetic variation and the composition of this microbial ecosystem on a genome- and microbiome-wide scale.

RESULTS: Here, we jointly analyze the composition of the human microbiome and host genetic variation. By mining the shotgun metagenomic data from the Human Microbiome Project for host DNA reads, we gathered information on host genetic variation for 93 individuals for whom bacterial abundance data are also available. Using this dataset, we identify significant associations between host genetic variation and microbiome composition in 10 of the 15 body sites tested. These associations are driven by host genetic variation in immunity-related pathways, and are especially enriched in host genes that have been previously associated with microbiome-related complex diseases, such as inflammatory bowel disease and obesity-related disorders. Lastly, we show that host genomic regions associated with the microbiome have high levels of genetic differentiation among human populations, possibly indicating host genomic adaptation to environment-specific microbiomes.

CONCLUSIONS: Our results highlight the role of host genetic variation in shaping the composition of the human microbiome, and provide a starting point toward understanding the complex interaction between human genetics and the microbiome in the context of human evolution and disease.}, } @article {pmid26373611, year = {2015}, author = {Boers, SA and Hays, JP and Jansen, R}, title = {Micelle PCR reduces chimera formation in 16S rRNA profiling of complex microbial DNA mixtures.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {14181}, pmid = {26373611}, issn = {2045-2322}, mesh = {High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/*genetics ; Reproducibility of Results ; }, abstract = {16S rRNA gene profiling has revolutionized the field of microbial ecology. Many researchers in various fields have embraced this technology to investigate bacterial compositions of samples derived from many different ecosystems. However, it is important to acknowledge the current limitations and drawbacks of 16S rRNA gene profiling. Although sample handling, DNA extraction methods and the choice of universal 16S rRNA gene PCR primers are well known factors that could seriously affect the final results of microbiota profiling studies, inevitable amplification artifacts, such as chimera formation and PCR competition, are seldom appreciated. Here we report on a novel micelle based amplification strategy, which overcomes these limitations via the clonal amplification of targeted DNA molecules. Our results show that micelle PCR drastically reduces chimera formation by a factor of 38 (1.5% vs. 56.9%) compared with traditional PCR, resulting in improved microbial diversity estimates. In addition, compartmentalization during micelle PCR prevents PCR competition due to unequal amplification rates of different 16S template molecules, generating robust and accurate 16S microbiota profiles required for comparative studies (e.g. longitudinal surveys).}, } @article {pmid26372576, year = {2015}, author = {Relman, DA}, title = {The Human Microbiome and the Future Practice of Medicine.}, journal = {JAMA}, volume = {314}, number = {11}, pages = {1127-1128}, doi = {10.1001/jama.2015.10700}, pmid = {26372576}, issn = {1538-3598}, mesh = {Forecasting ; Humans ; Metagenome ; Microbiota/*physiology ; Organ Specificity ; Species Specificity ; }, } @article {pmid26369961, year = {2015}, author = {Willmann, M and El-Hadidi, M and Huson, DH and Schütz, M and Weidenmaier, C and Autenrieth, IB and Peter, S}, title = {Antibiotic Selection Pressure Determination through Sequence-Based Metagenomics.}, journal = {Antimicrobial agents and chemotherapy}, volume = {59}, number = {12}, pages = {7335-7345}, pmid = {26369961}, issn = {1098-6596}, mesh = {Adult ; Algorithms ; Anti-Bacterial Agents/*pharmacology ; Biodiversity ; Ciprofloxacin/pharmacology ; Drug Resistance, Microbial/*drug effects/*genetics ; Gastrointestinal Microbiome/*drug effects/genetics ; Humans ; Male ; Metagenomics/*methods ; Real-Time Polymerase Chain Reaction/methods ; Selection, Genetic/drug effects ; beta-Lactamases/genetics ; }, abstract = {The human gut forms a dynamic reservoir of antibiotic resistance genes (ARGs). Treatment with antimicrobial agents has a significant impact on the intestinal resistome and leads to enhanced horizontal transfer and selection of resistance. We have monitored the development of intestinal ARGs over a 6-day course of ciprofloxacin (Cp) treatment in two healthy individuals by using sequenced-based metagenomics and different ARG quantification methods. Fixed- and random-effect models were applied to determine the change in ARG abundance per defined daily dose of Cp as an expression of the respective selection pressure. Among various shifts in the composition of the intestinal resistome, we found in one individual a strong positive selection for class D beta-lactamases which were partly located on a mobile genetic element. Furthermore, a trend to a negative selection has been observed with class A beta-lactamases (-2.66 hits per million sample reads/defined daily dose; P = 0.06). By 4 weeks after the end of treatment, the composition of ARGs returned toward their initial state but to a different degree in both subjects. We present here a novel analysis algorithm for the determination of antibiotic selection pressure which can be applied in clinical settings to compare therapeutic regimens regarding their effect on the intestinal resistome. This information is of critical importance for clinicians to choose antimicrobial agents with a low selective force on their patients' intestinal ARGs, likely resulting in a diminished spread of resistance and a reduced burden of hospital-acquired infections with multidrug-resistant pathogens.}, } @article {pmid26368049, year = {2015}, author = {Cleary, B and Brito, IL and Huang, K and Gevers, D and Shea, T and Young, S and Alm, EJ}, title = {Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning.}, journal = {Nature biotechnology}, volume = {33}, number = {10}, pages = {1053-1060}, pmid = {26368049}, issn = {1546-1696}, support = {T32 GM087237/GM/NIGMS NIH HHS/United States ; U54HG003067/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/classification/*genetics ; Chromosome Mapping/methods ; Databases, Genetic ; Datasets as Topic ; Epigenesis, Genetic/*genetics ; Genome, Bacterial/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; Species Specificity ; }, abstract = {Analyses of metagenomic datasets that are sequenced to a depth of billions or trillions of bases can uncover hundreds of microbial genomes, but naive assembly of these data is computationally intensive, requiring hundreds of gigabytes to terabytes of RAM. We present latent strain analysis (LSA), a scalable, de novo pre-assembly method that separates reads into biologically informed partitions and thereby enables assembly of individual genomes. LSA is implemented with a streaming calculation of unobserved variables that we call eigengenomes. Eigengenomes reflect covariance in the abundance of short, fixed-length sequences, or k-mers. As the abundance of each genome in a sample is reflected in the abundance of each k-mer in that genome, eigengenome analysis can be used to partition reads from different genomes. This partitioning can be done in fixed memory using tens of gigabytes of RAM, which makes assembly and downstream analyses of terabytes of data feasible on commodity hardware. Using LSA, we assemble partial and near-complete genomes of bacterial taxa present at relative abundances as low as 0.00001%. We also show that LSA is sensitive enough to separate reads from several strains of the same species.}, } @article {pmid26366561, year = {2015}, author = {Seksik, P and Landman, C}, title = {Understanding Microbiome Data: A Primer for Clinicians.}, journal = {Digestive diseases (Basel, Switzerland)}, volume = {33 Suppl 1}, number = {}, pages = {11-16}, doi = {10.1159/000437034}, pmid = {26366561}, issn = {1421-9875}, abstract = {The human gut contains 1014 bacteria and many other micro-organisms such as Archaea, viruses and fungi. This gut microbiota has co-evolved with host determinants through symbiotic and co-dependent relationships. Bacteria, which represent 10 times the number of human cells, form the most depicted part of this black box owing to new tools. Re-evaluating the gut microbiota showed how this entity participates in gut physiology and beyond this in human health. Studying and handling this real 'hidden organ' remains a challenge for clinicians. In this review, we aimed to bring information about gut microbiota, its structure, its roles and the way to capture and measure it. After bacterial colonization in infant, intestinal microbial composition is unique for each individual although more than 95% can be assigned to 4 major phyla. Besides its biodiversity, the major characteristics of gut microbiota are stability over time and resilience after perturbation. In pathological situations, dysbiosis (i.e. imbalance in gut microbiota composition) is observed with a loss in overall diversity. Dysbiosis associated with inflammatory bowel disease was specified with the reduction in biodiversity, the decreased representation of different taxa in the Firmicutes phylum and an increase in Gammaproteobacteria. Beyond depicting gut microbial composition, metagenomics allows the description of the combined genomes of the microorganisms present in the gut, giving access to their potential functions. In fact, each individual overall microbial metagenome outnumbers the size of human genome by a factor of 150. Besides a functional core in which there is redundancy for mandatory functions assuring the robustness of the ecosystem, human gut contains an important diversity and high number of non-redundant bacterial genes. Clinical data, treatment and all the factors able to influence microbiome should enter integrated big data sets to put in light pathways of interplay within the supra organism composed of gut microbiome and host. A better understanding of dynamics within human gut microbiota and microbes-host interaction will allow new insight into gut pathophysiology especially regarding resilience mechanisms and dysbiosis onset and maintenance. This will lead to description of biomarkers of diseases, development of new probiotics/prebiotics and new therapies.}, } @article {pmid26362264, year = {2015}, author = {Fransen, F and Zagato, E and Mazzini, E and Fosso, B and Manzari, C and El Aidy, S and Chiavelli, A and D'Erchia, AM and Sethi, MK and Pabst, O and Marzano, M and Moretti, S and Romani, L and Penna, G and Pesole, G and Rescigno, M}, title = {BALB/c and C57BL/6 Mice Differ in Polyreactive IgA Abundance, which Impacts the Generation of Antigen-Specific IgA and Microbiota Diversity.}, journal = {Immunity}, volume = {43}, number = {3}, pages = {527-540}, doi = {10.1016/j.immuni.2015.08.011}, pmid = {26362264}, issn = {1097-4180}, mesh = {Animals ; Antigens, Bacterial/*immunology ; Bacteria/classification/genetics/immunology ; DNA, Bacterial/chemistry/genetics ; Feces/microbiology ; Flow Cytometry ; Genetic Variation/*immunology ; Host-Pathogen Interactions/immunology ; Immunization ; Immunoglobulin A/blood/*immunology/metabolism ; Metagenomics/methods ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Microbiota/genetics/*immunology ; Peyer's Patches/immunology/metabolism/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salmonella typhimurium/genetics/immunology/physiology ; Species Specificity ; }, abstract = {The interrelationship between IgAs and microbiota diversity is still unclear. Here we show that BALB/c mice had higher abundance and diversity of IgAs than C57BL/6 mice and that this correlated with increased microbiota diversity. We show that polyreactive IgAs mediated the entrance of non-invasive bacteria to Peyer's patches, independently of CX3CR1(+) phagocytes. This allowed the induction of bacteria-specific IgA and the establishment of a positive feedback loop of IgA production. Cohousing of mice or fecal transplantation had little or no influence on IgA production and had only partial impact on microbiota composition. Germ-free BALB/c, but not C57BL/6, mice already had polyreactive IgAs that influenced microbiota diversity and selection after colonization. Together, these data suggest that genetic predisposition to produce polyreactive IgAs has a strong impact on the generation of antigen-specific IgAs and the selection and maintenance of microbiota diversity.}, } @article {pmid26360776, year = {2015}, author = {Kreisinger, J and Čížková, D and Kropáčková, L and Albrecht, T}, title = {Cloacal Microbiome Structure in a Long-Distance Migratory Bird Assessed Using Deep 16sRNA Pyrosequencing.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0137401}, pmid = {26360776}, issn = {1932-6203}, mesh = {*Animal Migration ; Animals ; Biodiversity ; Birds/*microbiology ; Breeding ; Cloaca/*microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Male ; Metagenome ; *Microbiota ; RNA, Bacterial ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Effects of vertebrate-associated microbiota on physiology and health are of significant interest in current biological research. Most previous studies have focused on host-microbiota interactions in captive-bred mammalian models. These interactions and their outcomes are still relatively understudied, however, in wild populations and non-mammalian taxa. Using deep pyrosequencing, we described the cloacal microbiome (CM) composition in free living barn swallows Hirundo rustica, a long-distance migratory passerine bird. Barn swallow CM was dominated by bacteria of the Actinobacteria, Proteobacteria and Firmicutes phyla. Bacteroidetes, which represent an important proportion of the digestive tract microbiome in many vertebrate species, was relatively rare in barn swallow CM (< 5%). CM composition did not differ between males and females. A significant correlation of CM within breeding pair members is consistent with the hypothesis that cloacal contact during within-pair copulation may promote transfer of bacterial assemblages. This effect on CM composition had a relatively low effect size, however, possibly due to the species' high level of sexual promiscuity.}, } @article {pmid26359913, year = {2016}, author = {Raymond, F and Ouameur, AA and Déraspe, M and Iqbal, N and Gingras, H and Dridi, B and Leprohon, P and Plante, PL and Giroux, R and Bérubé, È and Frenette, J and Boudreau, DK and Simard, JL and Chabot, I and Domingo, MC and Trottier, S and Boissinot, M and Huletsky, A and Roy, PH and Ouellette, M and Bergeron, MG and Corbeil, J}, title = {The initial state of the human gut microbiome determines its reshaping by antibiotics.}, journal = {The ISME journal}, volume = {10}, number = {3}, pages = {707-720}, pmid = {26359913}, issn = {1751-7370}, mesh = {Adult ; Anti-Bacterial Agents/*administration & dosage ; Bacteria/classification/*drug effects/genetics/*isolation & purification ; Bacterial Proteins/genetics/metabolism ; Cephalosporins/administration & dosage ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Healthy Volunteers ; Humans ; Male ; Metagenomics ; Young Adult ; Cefprozil ; }, abstract = {Microbiome studies have demonstrated the high inter-individual diversity of the gut microbiota. However, how the initial composition of the microbiome affects the impact of antibiotics on microbial communities is relatively unexplored. To specifically address this question, we administered a second-generation cephalosporin, cefprozil, to healthy volunteers. Stool samples gathered before antibiotic exposure, at the end of the treatment and 3 months later were analysed using shotgun metagenomic sequencing. On average, 15 billion nucleotides were sequenced for each sample. We show that standard antibiotic treatment can alter the gut microbiome in a specific, reproducible and predictable manner. The most consistent effect of the antibiotic was the increase of Lachnoclostridium bolteae in 16 out of the 18 cefprozil-exposed participants. Strikingly, we identified a subgroup of participants who were enriched in the opportunistic pathogen Enterobacter cloacae after exposure to the antibiotic, an effect linked to lower initial microbiome diversity and to a Bacteroides enterotype. Although the resistance gene content of participants' microbiomes was altered by the antibiotic, the impact of cefprozil remained specific to individual participants. Resistance genes that were not detectable prior to treatment were observed after a 7-day course of antibiotic administration. Specifically, point mutations in beta-lactamase blaCfxA-6 were enriched after antibiotic treatment in several participants. This suggests that monitoring the initial composition of the microbiome before treatment could assist in the prevention of some of the adverse effects associated with antibiotics or other treatments.}, } @article {pmid26359182, year = {2015}, author = {Wang, Y and Xia, Y and Ju, F and Zhang, T}, title = {Metagenome approaches revealed a biological prospect for improvement on mesophilic cellulose degradation.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {24}, pages = {10871-10879}, doi = {10.1007/s00253-015-6945-y}, pmid = {26359182}, issn = {1432-0614}, mesh = {Acetates/metabolism ; Biotransformation ; Butyrates/metabolism ; Cellulose/*metabolism ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Methane/metabolism ; Methanobacteriaceae/genetics/isolation & purification ; Methanosarcinales/genetics/isolation & purification ; *Microbial Consortia ; Propionates/metabolism ; Temperature ; }, abstract = {Improvement on the bioconversion of cellulosic biomass depends much on the expanded knowledge on the underlying microbial structure and the relevant genetic information. In this study, metagenomic analysis was applied to characterize an enriched mesophilic cellulose-converting consortium, to explore its cellulose-hydrolyzing genes, and to discern genes involved in methanogenesis. Cellulose conversion efficiency of the mesophilic consortium enriched in this study was around 70 %. Apart from methane, acetate was the major fermentation product in the liquid phase, while propionate and butyrate were also detected at relatively high concentrations. With the intention to uncover the biological factors that might shape the varying cellulose conversion efficiency at different temperatures, results of this mesophilic consortium were then compared with that of a previously reported thermophilic cellulose-converting consortium. It was found that the mesophilic consortium harbored a larger pool of putative carbohydrate-active genes, with 813 of them in 54 GH modules and 607 genes in 13 CBM modules. Methanobacteriaceae and Methanosaetaceae were the two methanogen families identified, with a preponderance of the hydrogenotrophic Methanobacteriaceae. In contrast to its relatively high diversity and high abundance of carbohydrate-active genes, the abundance of genes involved in the methane metabolism was comparatively lower in the mesophilic consortium. A biological enhancement on the methanogenic process might serve as an effective option for the improvement of the cellulose bioconversion at mesophilic temperature.}, } @article {pmid26357214, year = {2015}, author = {Jiang, X and Hu, X and Xu, W and Park, EK}, title = {Predicting Microbial Interactions Using Vector Autoregressive Model with Graph Regularization.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {12}, number = {2}, pages = {254-261}, doi = {10.1109/TCBB.2014.2338298}, pmid = {26357214}, issn = {1557-9964}, mesh = {Computational Biology/*methods ; Databases, Factual ; Humans ; *Microbial Interactions ; Microbiota ; *Models, Biological ; Models, Statistical ; }, abstract = {Microbial interactions play important roles on the structure and function of complex microbial communities. With the rapid accumulation of high-throughput metagenomic or 16S rRNA sequencing data, it is possible to infer complex microbial interactions. Co-occurrence patterns of microbial species among multiple samples are often utilized to infer interactions. There are few methods to consider the temporally interacting patterns among microbial species. In this paper, we present a Graph-regularized Vector Autoregressive (GVAR) model to infer causal relationships among microbial entities. The new model has advantage comparing to the original vector autoregressive (VAR) model. Specifically, GVAR can incorporate similarity information for microbial interaction inference--i.e., GVAR assumed that if two species are similar in the previous stage, they tend to have similar influence on the other species in the next stage. We apply the model on a time series dataset of human gut microbiome which was treated with repeated antibiotics. The experimental results indicate that the new approach has better performance than several other VAR-based models and demonstrate its capability of extracting relevant microbial interactions.}, } @article {pmid26356733, year = {2015}, author = {Angelakis, E and Armougom, F and Carrière, F and Bachar, D and Laugier, R and Lagier, JC and Robert, C and Michelle, C and Henrissat, B and Raoult, D}, title = {A Metagenomic Investigation of the Duodenal Microbiota Reveals Links with Obesity.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0137784}, pmid = {26356733}, issn = {1932-6203}, mesh = {Adult ; Biodiversity ; Cluster Analysis ; DNA Barcoding, Taxonomic ; Duodenum/*microbiology ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metagenome ; Middle Aged ; Obesity/*epidemiology/*etiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Few studies have tested the small intestine microbiota in humans, where most nutrient digestion and absorption occur. Here, our objective was to examine the duodenal microbiota between obese and normal volunteers using metagenomic techniques.

We tested duodenal samples from five obese and five normal volunteers using 16S rDNA V6 pyrosequencing and Illumina MiSeq deep sequencing. The predominant phyla of the duodenal microbiota were Firmicutes and Actinobacteria, whereas Bacteroidetes were absent. Obese individuals had a significant increase in anaerobic genera (p < 0.001) and a higher abundance of genes encoding Acyl-CoA dehydrogenase (p = 0.0018) compared to the control group. Obese individuals also had a reduced abundance of genes encoding sucrose phosphorylase (p = 0.015) and 1,4-alpha-glucan branching enzyme (p = 0.05). Normal weight people had significantly increased FabK (p = 0.027), and the glycerophospholipid metabolism pathway revealed the presence of phospholipase A1 only in the control group (p = 0.05).

CONCLUSIONS/SIGNIFICANCE: The duodenal microbiota of obese individuals exhibit alterations in the fatty acid and sucrose breakdown pathways, probably induced by diet imbalance.}, } @article {pmid26354707, year = {2015}, author = {Tian, M and Zhao, F and Shen, X and Chu, K and Wang, J and Chen, S and Guo, Y and Liu, H}, title = {The first metagenome of activated sludge from full-scale anaerobic/anoxic/oxic (A2O) nitrogen and phosphorus removal reactor using Illumina sequencing.}, journal = {Journal of environmental sciences (China)}, volume = {35}, number = {}, pages = {181-190}, doi = {10.1016/j.jes.2014.12.027}, pmid = {26354707}, issn = {1001-0742}, mesh = {Bacteria/classification/*genetics/metabolism ; Biodegradation, Environmental ; Bioreactors/*microbiology ; *Metagenome ; Nitrogen/metabolism ; Phosphorus/metabolism ; Sewage/*microbiology ; Waste Disposal, Fluid ; }, abstract = {The anaerobic/anoxic/oxic (A2O) process is globally one of the widely used biological sewage treatment processes. This is the first report of a metagenomic analysis using Illumina sequencing of full-scale A2O sludge from a municipal sewage treatment plant. With more than 530,000 clean reads from different taxa and metabolic categories, the metagenome results allow us to gain insight into the functioning of the biological community of the A2O sludge. There are 51 phyla and nearly 900 genera identified from the A2O activated sludge ecosystem. Proteobacteria, Bacteroidetes, Nitrospirae and Chloroflexi are predominant phyla in the activated sludge, suggesting that these organisms play key roles in the biodegradation processes in the A2O sewage treatment system. Nitrospira, Thauera, Dechloromonas and Ignavibacterium, which have abilities to metabolize nitrogen and aromatic compounds, are most prevalent genera. The percent of nitrogen and phosphorus metabolism in the A2O sludge is 2.72% and 1.48%, respectively. In the current A2O sludge, the proportion of Candidatus Accumulibacter is 1.37%, which is several times more than that reported in a recent study of A2O sludge. Among the four processes of nitrogen metabolism, denitrification related genes had the highest number of sequences (76.74%), followed by ammonification (15.77%), nitrogen fixation (3.88%) and nitrification (3.61%). In phylum Planctomycetes, four genera (Planctomyces, Pirellula, Gemmata and Singulisphaera) are included in the top 30 abundant genera, suggesting the key role of ANAMMOX in nitrogen metabolism in the A2O sludge.}, } @article {pmid26353777, year = {2015}, author = {Satinsky, BM and Fortunato, CS and Doherty, M and Smith, CB and Sharma, S and Ward, ND and Krusche, AV and Yager, PL and Richey, JE and Moran, MA and Crump, BC}, title = {Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {39}, pmid = {26353777}, issn = {2049-2618}, mesh = {*Metagenome ; *Metagenomics ; Microbiota ; Rivers/*microbiology ; *Seasons ; *Transcriptome ; }, abstract = {BACKGROUND: The Amazon River runs nearly 6500 km across the South American continent before emptying into the western tropical North Atlantic Ocean. In terms of both volume and watershed area, it is the world's largest riverine system, affecting elemental cycling on a global scale.

RESULTS: A quantitative inventory of genes and transcripts benchmarked with internal standards was obtained at five stations in the lower Amazon River during May 2011. At each station, metagenomes and metatranscriptomes were obtained in duplicate for two microbial size fractions (free-living, 0.2 to 2.0 μm; particle-associated, 2.0 to 297 μm) using 150 × 150 paired-end Illumina sequencing. Forty eight sample datasets were obtained, averaging 15 × 10(6) potential protein-encoding reads each (730 × 10(6) total). Prokaryotic metagenomes and metatranscriptomes were dominated by members of the phyla Actinobacteria, Planctomycetes, Betaproteobacteria, Verrucomicrobia, Nitrospirae, and Acidobacteria. The actinobacterium SCGC AAA027-L06 reference genome recruited the greatest number of reads overall, with this single bin contributing an average of 50 billion genes and 500 million transcripts per liter of river water. Several dominant taxa were unevenly distributed between the free-living and particle-associated size fractions, such as a particle-associated bias for reads binning to planctomycete Schlesneria paludicola and a free-living bias for actinobacterium SCGC AAA027-L06. Gene expression ratios (transcripts to gene copy ratio) increased downstream from Óbidos to Macapá and Belém, indicating higher per cell activity of Amazon River bacteria and archaea as river water approached the ocean.

CONCLUSION: This inventory of riverine microbial genes and transcripts, benchmarked with internal standards for full quantitation, provides an unparalleled window into microbial taxa and functions in the globally important Amazon River ecosystem.}, } @article {pmid26347019, year = {2015}, author = {Thomas, V and Clark, J and Doré, J}, title = {Fecal microbiota analysis: an overview of sample collection methods and sequencing strategies.}, journal = {Future microbiology}, volume = {10}, number = {9}, pages = {1485-1504}, doi = {10.2217/fmb.15.87}, pmid = {26347019}, issn = {1746-0921}, mesh = {Biomedical Research ; DNA, Bacterial/genetics ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Specimen Handling ; }, abstract = {Despite huge interest, there are still no universally accepted standards to conduct clinical studies in the field of gut microbiota analysis. Stool material is frequently used as a proxy of gut microbiota, but many different protocols can be used for collection and DNA extraction. Whereas 16S rRNA encoding gene amplification and sequencing has been widely used to study the composition of bacterial populations, it is now being challenged by the random, shotgun approach that brings far more information, although at a higher cost. In this review we give an overview of existing methods and important points to consider when conducting gut microbiota studies, with the objective to provide recommendations to those who would like to conduct such research.}, } @article {pmid26345272, year = {2016}, author = {Greshake, B and Zehr, S and Dal Grande, F and Meiser, A and Schmitt, I and Ebersberger, I}, title = {Potential and pitfalls of eukaryotic metagenome skimming: a test case for lichens.}, journal = {Molecular ecology resources}, volume = {16}, number = {2}, pages = {511-523}, doi = {10.1111/1755-0998.12463}, pmid = {26345272}, issn = {1755-0998}, mesh = {Ascomycota/classification/genetics ; *Biota ; Chlorophyta/classification/genetics ; Computational Biology/*methods ; Computer Simulation ; Lichens/classification/*genetics ; *Metagenome ; Metagenomics/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {Whole-genome shotgun sequencing of multispecies communities using only a single library layout is commonly used to assess taxonomic and functional diversity of microbial assemblages. Here, we investigate to what extent such metagenome skimming approaches are applicable for in-depth genomic characterizations of eukaryotic communities, for example lichens. We address how to best assemble a particular eukaryotic metagenome skimming data, what pitfalls can occur, and what genome quality can be expected from these data. To facilitate a project-specific benchmarking, we introduce the concept of twin sets, simulated data resembling the outcome of a particular metagenome sequencing study. We show that the quality of genome reconstructions depends essentially on assembler choice. Individual tools, including the metagenome assemblers Omega and MetaVelvet, are surprisingly sensitive to low and uneven coverages. In combination with the routine of assembly parameter choice to optimize the assembly N50 size, these tools can preclude an entire genome from the assembly. In contrast, MIRA, an all-purpose overlap assembler, and SPAdes, a multisized de Bruijn graph assembler, facilitate a comprehensive view on the individual genomes across a wide range of coverage ratios. Testing assemblers on a real-world metagenome skimming data from the lichen Lasallia pustulata demonstrates the applicability of twin sets for guiding method selection. Furthermore, it reveals that the assembly outcome for the photobiont Trebouxia sp. falls behind the a priori expectation given the simulations. Although the underlying reasons remain still unclear, this highlights that further studies on this organism require special attention during sequence data generation and downstream analysis.}, } @article {pmid26344799, year = {2015}, author = {Brandon-Mong, GJ and Gan, HM and Sing, KW and Lee, PS and Lim, PE and Wilson, JJ}, title = {DNA metabarcoding of insects and allies: an evaluation of primers and pipelines.}, journal = {Bulletin of entomological research}, volume = {105}, number = {6}, pages = {717-727}, doi = {10.1017/S0007485315000681}, pmid = {26344799}, issn = {1475-2670}, mesh = {Animals ; Arthropods/*genetics ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; *DNA Primers ; DNA, Mitochondrial/chemistry ; Electron Transport Complex IV/chemistry/genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Nucleic Acid Amplification Techniques ; Polymerase Chain Reaction ; }, abstract = {Metabarcoding, the coupling of DNA-based species identification and high-throughput sequencing, offers enormous promise for arthropod biodiversity studies but factors such as cost, speed and ease-of-use of bioinformatic pipelines, crucial for making the leapt from demonstration studies to a real-world application, have not yet been adequately addressed. Here, four published and one newly designed primer sets were tested across a diverse set of 80 arthropod species, representing 11 orders, to establish optimal protocols for Illumina-based metabarcoding of tropical Malaise trap samples. Two primer sets which showed the highest amplification success with individual specimen polymerase chain reaction (PCR, 98%) were used for bulk PCR and Illumina MiSeq sequencing. The sequencing outputs were subjected to both manual and simple metagenomics quality control and filtering pipelines. We obtained acceptable detection rates after bulk PCR and high-throughput sequencing (80-90% of input species) but analyses were complicated by putative heteroplasmic sequences and contamination. The manual pipeline produced similar or better outputs to the simple metagenomics pipeline (1.4 compared with 0.5 expected:unexpected Operational Taxonomic Units). Our study suggests that metabarcoding is slowly becoming as cheap, fast and easy as conventional DNA barcoding, and that Malaise trap metabarcoding may soon fulfill its potential, providing a thermometer for biodiversity.}, } @article {pmid26344404, year = {2015}, author = {Luo, C and Knight, R and Siljander, H and Knip, M and Xavier, RJ and Gevers, D}, title = {ConStrains identifies microbial strains in metagenomic datasets.}, journal = {Nature biotechnology}, volume = {33}, number = {10}, pages = {1045-1052}, pmid = {26344404}, issn = {1546-1696}, support = {U54 DK102557/DK/NIDDK NIH HHS/United States ; P01 DK078669/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 DK092405/DK/NIDDK NIH HHS/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; }, mesh = {*Algorithms ; Bacteria/classification/*genetics ; Chromosome Mapping/methods ; Databases, Genetic ; Datasets as Topic ; Genome, Bacterial/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; Species Specificity ; }, abstract = {An important fraction of microbial diversity is harbored in strain individuality, so identification of conspecific bacterial strains is imperative for improved understanding of microbial community functions. Limitations in bioinformatics and sequencing technologies have to date precluded strain identification owing to difficulties in phasing short reads to faithfully recover the original strain-level genotypes, which have highly similar sequences. We present ConStrains, an open-source algorithm that identifies conspecific strains from metagenomic sequence data and reconstructs the phylogeny of these strains in microbial communities. The algorithm uses single-nucleotide polymorphism (SNP) patterns in a set of universal genes to infer within-species structures that represent strains. Applying ConStrains to simulated and host-derived datasets provides insights into microbial community dynamics.}, } @article {pmid26343383, year = {2015}, author = {Jiménez, DJ and Chaves-Moreno, D and van Elsas, JD}, title = {Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {13845}, pmid = {26343383}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics/metabolism ; Biomass ; Computational Biology ; Energy Metabolism/genetics ; Gene Order ; Metagenome ; Metagenomics ; *Microbial Consortia/genetics ; Molecular Sequence Annotation ; Open Reading Frames/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Triticum/*microbiology ; }, abstract = {Based on the premise that plant biomass can be efficiently degraded by mixed microbial cultures and/or enzymes, we here applied a targeted metagenomics-based approach to explore the metabolic potential of two forest soil-derived lignocellulolytic microbial consortia, denoted RWS and TWS (bred on wheat straw). Using the metagenomes of three selected batches of two experimental systems, about 1.2 Gb of sequence was generated. Comparative analyses revealed an overrepresentation of predicted carbohydrate transporters (ABC, TonB and phosphotransferases), two-component sensing systems and β-glucosidases/galactosidases in the two consortia as compared to the forest soil inoculum. Additionally, "profiling" of carbohydrate-active enzymes showed significant enrichments of several genes encoding glycosyl hydrolases of families GH2, GH43, GH92 and GH95. Sequence analyses revealed these to be most strongly affiliated to genes present on the genomes of Sphingobacterium, Bacteroides, Flavobacterium and Pedobacter spp. Assembly of the RWS and TWS metagenomes generated 16,536 and 15,902 contigs of ≥10 Kb, respectively. Thirteen contigs, containing 39 glycosyl hydrolase genes, constitute novel (hemi)cellulose utilization loci with affiliation to sequences primarily found in the Bacteroidetes. Overall, this study provides deep insight in the plant polysaccharide degrading capabilities of microbial consortia bred from forest soil, highlighting their biotechnological potential.}, } @article {pmid26341384, year = {2016}, author = {Ellebrecht, CT and Srinivas, G and Bieber, K and Banczyk, D and Kalies, K and Künzel, S and Hammers, CM and Baines, JF and Zillikens, D and Ludwig, RJ and Westermann, J}, title = {Skin microbiota-associated inflammation precedes autoantibody induced tissue damage in experimental epidermolysis bullosa acquisita.}, journal = {Journal of autoimmunity}, volume = {68}, number = {}, pages = {14-22}, doi = {10.1016/j.jaut.2015.08.007}, pmid = {26341384}, issn = {1095-9157}, mesh = {Animals ; Autoantibodies/*immunology ; Disease Models, Animal ; Disease Susceptibility ; Epidermolysis Bullosa Acquisita/*etiology/*pathology ; Female ; Host-Pathogen Interactions ; Immunity, Innate ; Immunization ; Metagenomics ; Mice ; *Microbiota ; ROC Curve ; Skin/immunology/microbiology/pathology ; }, abstract = {Epidermolysis bullosa acquisita (EBA) is a chronic autoimmune blistering skin disease characterized by autoantibodies against type VII collagen (COL7). Immunization of SJL/J mice with recombinant murine COL7 results in break of tolerance and skin blisters. Strikingly, despite circulating autoantibodies, the same genetic background and identical environmental conditions, 20% of mice remain healthy. To elucidate the regulation of the transition from the presence of autoantibodies to overt autoimmune disease, we characterized the innate and adaptive immune response of mice that remain healthy after immunization and compared it to mice that developed skin disease. Both clinically healthy and diseased SJL/J mice showed circulating autoantibodies and deposition of complement-fixing IgG2c autoantibodies and C3 at the dermal-epidermal junction. However, only in diseased animals significant neutrophil infiltration and increase in FcgRIV expression were observed in the skin. In contrast, the expression of T cell signature cytokines in the T cell zone of the draining lymph node was comparable between clinically healthy and diseased animals after immunization. Surprisingly, health was associated with a decreased expression of CD11c, TNFA and KC (CXCL1) in the skin prior to immunization and could be predicted with a negative predictive value of >80%. Furthermore, mice that did not develop clinical disease showed a significantly higher richness and distinctly clustered diversity of their skin microbiota before immunization. Our data indicate that the decision whether blisters develop in the presence of autoantibodies is governed in the skin rather than in the lymph node, and that a greater richness of cutaneous bacterial species appears to be protective.}, } @article {pmid26341209, year = {2015}, author = {Stellato, G and De Filippis, F and La Storia, A and Ercolini, D}, title = {Coexistence of Lactic Acid Bacteria and Potential Spoilage Microbiota in a Dairy Processing Environment.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {22}, pages = {7893-7904}, pmid = {26341209}, issn = {1098-5336}, mesh = {Bacteria/classification/*genetics/isolation & purification/metabolism ; Cheese/microbiology ; DNA, Bacterial/genetics/metabolism ; Food Handling ; *Food Microbiology ; Lactic Acid/metabolism ; Metagenome ; Microbiota/*physiology ; Phylogeny ; RNA, Ribosomal/genetics/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {Microbial contamination in food processing plants can play a fundamental role in food quality and safety. In this study, the microbiota in a dairy plant was studied by both 16S rRNA- and 26S rRNA-based culture-independent high-throughput amplicon sequencing. Environmental samples from surfaces and tools were studied along with the different types of cheese produced in the same plant. The microbiota of environmental swabs was very complex, including more than 200 operational taxonomic units with extremely variable relative abundances (0.01 to 99%) depending on the species and sample. A core microbiota shared by 70% of the samples indicated a coexistence of lactic acid bacteria with a remarkable level of Streptococcus thermophilus and possible spoilage-associated bacteria, including Pseudomonas, Acinetobacter, and Psychrobacter, with a relative abundance above 50%. The most abundant yeasts were Kluyveromyces marxianus, Yamadazyma triangularis, Trichosporon faecale, and Debaryomyces hansenii. Beta-diversity analyses showed a clear separation of environmental and cheese samples based on both yeast and bacterial community structure. In addition, predicted metagenomes also indicated differential distribution of metabolic pathways between the two categories of samples. Cooccurrence and coexclusion pattern analyses indicated that the occurrence of potential spoilers was excluded by lactic acid bacteria. In addition, their persistence in the environment can be helpful to counter the development of potential spoilers that may contaminate the cheeses, with possible negative effects on their microbiological quality.}, } @article {pmid26340501, year = {2016}, author = {Zhang, X and Johnston, ER and Liu, W and Li, L and Han, X}, title = {Environmental changes affect the assembly of soil bacterial community primarily by mediating stochastic processes.}, journal = {Global change biology}, volume = {22}, number = {1}, pages = {198-207}, doi = {10.1111/gcb.13080}, pmid = {26340501}, issn = {1365-2486}, mesh = {Bacteria/genetics ; *Bacterial Physiological Phenomena ; China ; *Environment ; *Grassland ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Stochastic Processes ; }, abstract = {Both 'species fitness difference'-based deterministic processes, such as competitive exclusion and environmental filtering, and 'species fitness difference'-independent stochastic processes, such as birth/death and dispersal/colonization, can influence the assembly of soil microbial communities. However, how both types of processes are mediated by anthropogenic environmental changes has rarely been explored. Here we report a novel and general pattern that almost all anthropogenic environmental changes that took place in a grassland ecosystem affected soil bacterial community assembly primarily through promoting or restraining stochastic processes. We performed four experiments mimicking 16 types of environmental changes and separated the compositional variation of soil bacterial communities caused by each environmental change into deterministic and stochastic components, with a recently developed method. Briefly, because the difference between control and treatment communities is primarily caused by deterministic processes, the deterministic change was quantified as (mean compositional variation between treatment and control) - (mean compositional variation within control). The difference among replicate treatment communities is primarily caused by stochastic processes, so the stochastic change was estimated as (mean compositional variation within treatment) - (mean compositional variation within control). The absolute of the stochastic change was greater than that of the deterministic change across almost all environmental changes, which was robust for both taxonomic and functional-based criterion. Although the deterministic change may become more important as environmental changes last longer, our findings showed that changes usually occurred through mediating stochastic processes over 5 years, challenging the traditional determinism-dominated view.}, } @article {pmid26335953, year = {2015}, author = {Caverly, LJ and Zhao, J and LiPuma, JJ}, title = {Cystic fibrosis lung microbiome: opportunities to reconsider management of airway infection.}, journal = {Pediatric pulmonology}, volume = {50 Suppl 40}, number = {}, pages = {S31-8}, doi = {10.1002/ppul.23243}, pmid = {26335953}, issn = {1099-0496}, support = {K12 HD028820/HD/NICHD NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacteria ; Cystic Fibrosis/*drug therapy/*microbiology ; Drug Resistance, Bacterial ; Humans ; Lung/*microbiology ; Metagenome ; *Microbiota ; Respiratory Tract Infections/*drug therapy/etiology/*microbiology ; }, abstract = {The importance of infection in the pathogenesis of cystic fibrosis (CF) lung disease has been long recognized, and the use of antibiotics targeting bacteria identified in cultures of respiratory specimens has played a critical role in improving outcomes for individuals with CF. Over the past ∼15 years, the use of culture-independent methods to assess airway microbiology in CF has revealed complex and dynamic CF airway bacterial communities. Recent areas of investigation of the CF lung microbiome have included exploring how bacterial community structures change over time, particularly with respect to disease progression or pulmonary exacerbation, and in response to antibiotic therapies. This review will discuss what has been learned from these studies as well as how these findings offer opportunities to further refine management of CF airway infection.}, } @article {pmid26334878, year = {2015}, author = {Ordiz, MI and May, TD and Mihindukulasuriya, K and Martin, J and Crowley, J and Tarr, PI and Ryan, K and Mortimer, E and Gopalsamy, G and Maleta, K and Mitreva, M and Young, G and Manary, MJ}, title = {The effect of dietary resistant starch type 2 on the microbiota and markers of gut inflammation in rural Malawi children.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {37}, pmid = {26334878}, issn = {2049-2618}, support = {P30DK052574/DK/NIDDK NIH HHS/United States ; T32 HD071839/HD/NICHD NIH HHS/United States ; P30 DK056341/DK/NIDDK NIH HHS/United States ; P41 GM103422/GM/NIGMS NIH HHS/United States ; P30 DK020579/DK/NIDDK NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; }, mesh = {Age Factors ; Biomarkers ; Child ; *Dietary Carbohydrates ; Feces/microbiology ; Female ; Gastroenteritis/epidemiology/genetics/*metabolism/*microbiology ; Humans ; Malawi/epidemiology ; Male ; Metagenome ; *Microbiota ; RNA, Messenger/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; *Rural Population ; *Starch ; }, abstract = {BACKGROUND: Resistant starch (RS) decreases intestinal inflammation in some settings. We tested the hypothesis that gut inflammation will be reduced with dietary supplementation with RS in rural Malawian children. Eighteen stunted 3-5-year-old children were supplemented with 8.5 g/day of RS type 2 for 4 weeks. The fecal samples were analyzed for the microbiota, the microbiome, short chain fatty acids, metabolome, and proteins indicative of inflammation before and after the intervention. Subjects served as their own controls.

RESULTS: The consumption of RS changed the composition of the microbiota; at the phylum level Actinobacteria increased, while Firmicutes decreased. Among the most prevalent genera, Lactobacillus was increased and Roseburia, Blautia, and Lachnospiracea incertae sedis were decreased. The Shannon H index at the genus level decreased from 2.02 on the habitual diet and 1.76 after the introduction of RS (P < 0.01). Fecal acetate concentration decreased, and fecal propionate concentration increased after RS administration (-5.2 and 2.0 μmol/g, respectively). Fecal calprotectin increased from 29 ± 69 to 89 ± 49 μg/g (P = 0.003) after RS was given. The lipopolysaccharide biosynthesis pathway was upregulated.

CONCLUSIONS: Our findings do not support the hypothesis that RS reduces gut inflammation in rural Malawian children.}, } @article {pmid26334731, year = {2015}, author = {Mitra, S and Drautz-Moses, DI and Alhede, M and Maw, MT and Liu, Y and Purbojati, RW and Yap, ZH and Kushwaha, KK and Gheorghe, AG and Bjarnsholt, T and Hansen, GM and Sillesen, HH and Hougen, HP and Hansen, PR and Yang, L and Tolker-Nielsen, T and Schuster, SC and Givskov, M}, title = {In silico analyses of metagenomes from human atherosclerotic plaque samples.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {38}, pmid = {26334731}, issn = {2049-2618}, mesh = {Atherosclerosis/*microbiology/*pathology ; Biodiversity ; Cluster Analysis ; DNA Barcoding, Taxonomic ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; In Situ Hybridization, Fluorescence ; Male ; *Metagenome ; *Microbiota ; Plaque, Atherosclerotic/*microbiology ; }, abstract = {BACKGROUND: Through several observational and mechanistic studies, microbial infection is known to promote cardiovascular disease. Direct infection of the vessel wall, along with the cardiovascular risk factors, is hypothesized to play a key role in the atherogenesis by promoting an inflammatory response leading to endothelial dysfunction and generating a proatherogenic and prothrombotic environment ultimately leading to clinical manifestations of cardiovascular disease, e.g., acute myocardial infarction or stroke. There are many reports of microbial DNA isolation and even a few studies of viable microbes isolated from human atherosclerotic vessels. However, high-resolution investigation of microbial infectious agents from human vessels that may contribute to atherosclerosis is very limited. In spite of the progress in recent sequencing technologies, analyzing host-associated metagenomes remain a challenge.

RESULTS: To investigate microbiome diversity within human atherosclerotic tissue samples, we employed high-throughput metagenomic analysis on: (1) atherosclerotic plaques obtained from a group of patients who underwent endarterectomy due to recent transient cerebral ischemia or stroke. (2) Presumed stabile atherosclerotic plaques obtained from autopsy from a control group of patients who all died from causes not related to cardiovascular disease. Our data provides evidence that suggest a wide range of microbial agents in atherosclerotic plaques, and an intriguing new observation that shows these microbiota displayed differences between symptomatic and asymptomatic plaques as judged from the taxonomic profiles in these two groups of patients. Additionally, functional annotations reveal significant differences in basic metabolic and disease pathway signatures between these groups.

CONCLUSIONS: We demonstrate the feasibility of novel high-resolution techniques aimed at identification and characterization of microbial genomes in human atherosclerotic tissue samples. Our analysis suggests that distinct groups of microbial agents might play different roles during the development of atherosclerotic plaques. These findings may serve as a reference point for future studies in this area of research.}, } @article {pmid26333424, year = {2015}, author = {Feng, XJ and Jiang, GF and Fan, Z}, title = {Identification of outliers in a genomic scan for selection along environmental gradients in the bamboo locust, Ceracris kiangsu.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {13758}, pmid = {26333424}, issn = {2045-2322}, mesh = {Algorithms ; Amplified Fragment Length Polymorphism Analysis/*methods ; Animals ; Biological Evolution ; Chromosome Mapping/*methods ; Grasshoppers/*genetics ; Metagenomics/*methods ; Polymorphism, Restriction Fragment Length/*genetics ; Quantitative Trait Loci/*genetics ; Selection, Genetic/genetics ; }, abstract = {Identification of loci under divergent selection is a key step in understanding the evolutionary process because those loci are responsible for the genetic variations that affect fitness in different environments. Understanding how environmental forces give rise to adaptive genetic variation is a challenge in pest control. Here, we performed an amplified fragment length polymorphism (AFLP) genome scan in populations of the bamboo locust, Ceracris kiangsu, to search for candidate loci that are influenced by selection along an environmental gradient in southern China. In outlier locus detection, loci that demonstrate significantly higher or lower among-population genetic differentiation than expected under neutrality are identified as outliers. We used several outlier detection methods to study the features of C. kiangsu, including method DFDIST, BayeScan, and logistic regression. A total of 97 outlier loci were detected in the C. kiangsu genome with very high statistical supports. Moreover, the results suggested that divergent selection arising from environmental variation has been driven by differences in temperature, precipitation, humidity and sunshine. These findings illustrate that divergent selection and potential local adaptation are prevalent in locusts despite seemingly high levels of gene flow. Thus, we propose that native environments in each population may induce divergent natural selection.}, } @article {pmid26332837, year = {2015}, author = {Del Chierico, F and Vernocchi, P and Petrucca, A and Paci, P and Fuentes, S and Praticò, G and Capuani, G and Masotti, A and Reddel, S and Russo, A and Vallone, C and Salvatori, G and Buffone, E and Signore, F and Rigon, G and Dotta, A and Miccheli, A and de Vos, WM and Dallapiccola, B and Putignani, L}, title = {Phylogenetic and Metabolic Tracking of Gut Microbiota during Perinatal Development.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0137347}, pmid = {26332837}, issn = {1932-6203}, mesh = {Humans ; Infant, Newborn ; Intestines/*microbiology ; Magnetic Resonance Spectroscopy ; *Microbiota ; *Phylogeny ; }, abstract = {The colonization and development of gut microbiota immediately after birth is highly variable and depends on several factors, such as delivery mode and modality of feeding during the first months of life. A cohort of 31 mother and neonate pairs, including 25 at-term caesarean (CS) and 6 vaginally (V) delivered neonates (DNs), were included in this study and 121 meconium/faecal samples were collected at days 1 through 30 following birth. Operational taxonomic units (OTUs) were assessed in 69 stool samples by phylogenetic microarray HITChip and inter- and intra-individual distributions were established by inter-OTUs correlation matrices and OTUs co-occurrence or co-exclusion networks. 1H-NMR metabolites were determined in 70 stool samples, PCA analysis was performed on 55 CS DNs samples, and metabolome/OTUs co-correlations were assessed in 45 CS samples, providing an integrated map of the early microbiota OTUs-metabolome. A microbiota "core" of OTUs was identified that was independent of delivery mode and lactation stage, suggesting highly specialized communities that act as seminal colonizers of microbial networks. Correlations among OTUs, metabolites, and OTUs-metabolites revealed metabolic profiles associated with early microbial ecological dynamics, maturation of milk components, and host physiology.}, } @article {pmid26324853, year = {2015}, author = {Ramachandran, A and Walsh, DA}, title = {Investigation of XoxF methanol dehydrogenases reveals new methylotrophic bacteria in pelagic marine and freshwater ecosystems.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {10}, pages = {}, doi = {10.1093/femsec/fiv105}, pmid = {26324853}, issn = {1574-6941}, mesh = {Alcohol Oxidoreductases/*metabolism ; Betaproteobacteria/*classification/enzymology/genetics ; Ecosystem ; *Estuaries ; Genetic Markers/genetics ; Lakes/*microbiology ; Methanol/*metabolism ; North America ; Phytoplankton/*classification/enzymology/genetics ; }, abstract = {The diversity and distribution of methylotrophic bacteria have been investigated in the oceans and lakes using the methanol dehydrogenase mxaF gene as a functional marker. However, pelagic marine (OM43) and freshwater (LD28 and PRD01a001B) methylotrophs within the Betaproteobacteria lack mxaF, instead possessing a related xoxF4-encoded methanol dehydrogenase. Here, we developed and employed xoxF4 as a complementary functional gene marker to mxaF for studying methylotrophs in aquatic environment. Using xoxF4, we detected OM43-related and LD28-related methylotrophs in the ocean and freshwaters of North America, respectively, and showed the coexistence of these two lineages in a large estuarine system (St Lawrence Estuary). Gene expression patterns of xoxF4 supported a positive relationship between xoxF4-containing methylotroph activity and spring time productivity, suggesting phytoplankton blooms are a source of methylotrophic substrates. Further investigation of methanol dehydrogenase diversity in pelagic ecosystems using comparative metagenomics provided strong support for a widespread distribution of xoxF4 (as well as several distinct xoxF5) containing methylotrophs in marine and freshwater surface waters. In total, these results demonstrate a geographical distribution of OM43/LD28-related methylotrophs that includes marine and freshwaters and suggest that methylotrophy occurring in the water column is an important component of lake and estuary carbon cycling and biogeochemistry.}, } @article {pmid26323632, year = {2015}, author = {Hiergeist, A and Gläsner, J and Reischl, U and Gessner, A}, title = {Analyses of Intestinal Microbiota: Culture versus Sequencing.}, journal = {ILAR journal}, volume = {56}, number = {2}, pages = {228-240}, doi = {10.1093/ilar/ilv017}, pmid = {26323632}, issn = {1930-6180}, mesh = {Animals ; Computational Biology/methods ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Analyzing human as well as animal microbiota composition has gained growing interest because structural components and metabolites of microorganisms fundamentally influence all aspects of host physiology. Originally dominated by culture-dependent methods for exploring these ecosystems, the development of molecular techniques such as high throughput sequencing has dramatically increased our knowledge. Because many studies of the microbiota are based on the bacterial 16S ribosomal RNA (rRNA) gene targets, they can, at least in principle, be compared to determine the role of the microbiome composition for developmental processes, host metabolism, and physiology as well as different diseases. In our review, we will summarize differences and pitfalls in current experimental protocols, including all steps from nucleic acid extraction to bioinformatical analysis which may produce variation that outweighs subtle biological differences. Future developments, such as integration of metabolomic, transcriptomic, and metagenomic data sets and standardization of the procedures, will be discussed.}, } @article {pmid26323630, year = {2015}, author = {Ericsson, AC and Franklin, CL}, title = {Manipulating the Gut Microbiota: Methods and Challenges.}, journal = {ILAR journal}, volume = {56}, number = {2}, pages = {205-217}, pmid = {26323630}, issn = {1930-6180}, support = {P40 OD011062/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; P40OD011062/OD/NIH HHS/United States ; U42OD010918/OD/NIH HHS/United States ; }, mesh = {Animals ; Gastrointestinal Microbiome/genetics/*physiology ; Metagenomics ; Mice ; Models, Animal ; Rats ; }, abstract = {Eukaryotic organisms are colonized by rich and dynamic communities of microbes, both internally (e.g., in the gastrointestinal and respiratory tracts) and externally (e.g., on skin and external mucosal surfaces). The vast majority of bacterial microbes reside in the lower gastrointestinal (GI) tract, and it is estimated that the gut of a healthy human is home to some 100 trillion bacteria, roughly an order of magnitude greater than the number of host somatic cells. The development of culture-independent methods to characterize the gut microbiota (GM) has spurred a renewed interest in its role in host health and disease. Indeed, associations have been identified between various changes in the composition of the GM and an extensive list of diseases, both enteric and systemic. Animal models provide a means whereby causal relationships between characteristic differences in the GM and diseases or conditions can be formally tested using genetically identical animals in highly controlled environments. Clearly, the GM and its interactions with the host and myriad environmental factors are exceedingly complex, and it is rare that a single microbial taxon associates with, much less causes, a phenotype with perfect sensitivity and specificity. Moreover, while the exact numbers are the subject of debate, it is well recognized that only a minority of gut bacteria can be successfully cultured ex vivo. Thus, to perform studies investigating causal roles of the GM in animal model phenotypes, researchers need clever techniques to experimentally manipulate the GM of animals, and several ingenious methods of doing so have been developed, each providing its own type of information and with its own set of advantages and drawbacks. The current review will focus on the various means of experimentally manipulating the GM of research animals, drawing attention to the factors that would aid a researcher in selecting an experimental approach, and with an emphasis on mice and rats, the primary model species used to evaluate the contribution of the GM to a disease phenotype.}, } @article {pmid26323626, year = {2015}, author = {Nelson, KE}, title = {An Update on the Status of Current Research on the Mammalian Microbiome.}, journal = {ILAR journal}, volume = {56}, number = {2}, pages = {163-168}, doi = {10.1093/ilar/ilv033}, pmid = {26323626}, issn = {1930-6180}, mesh = {Animals ; Bacteria/metabolism ; Humans ; Mammals/*microbiology ; Microbiota/genetics/*physiology ; Models, Animal ; }, abstract = {The microbiome refers to the thousands of microbial species that inhabit a specific host or environment. Extensive microbiome surveys have been conducted for soils, the built environment, and our oceans. In addition, extensive studies of the human microbiome have revealed significant microbial diversity across all body sites and have hinted at new opportunities for diagnostic and therapeutic approaches to addressing human health and disease. Mammals in general are known to hold a complicated mix of species within their gastrointestinal tracts, including virus, archaea, bacteria, and fungi. These microbial species present beneficial aspects to the host species through the production of vitamins, metabolism of plant structural compounds and sugars, and education of the immune system. In addition to a vast number of studies on humans, studies of the mammalian microbiome have been performed, with several publications on a variety of animal species currently available. These have included studies on the microbiome of companion animals, animals used for research, and animals used for agricultural and food purposes, and various human/animal models.}, } @article {pmid26322695, year = {2015}, author = {Vasilakis, N and Tesh, RB}, title = {Insect-specific viruses and their potential impact on arbovirus transmission.}, journal = {Current opinion in virology}, volume = {15}, number = {}, pages = {69-74}, pmid = {26322695}, issn = {1879-6265}, support = {HHSN272201000040I/AI/NIAID NIH HHS/United States ; HHSN272201000040I/HHSN27200004/D04//PHS HHS/United States ; }, mesh = {Animals ; Arbovirus Infections/*transmission/*virology ; Arboviruses/*physiology ; Biodiversity ; Culicidae/virology ; Humans ; Insect Vectors/*virology ; Insect Viruses/classification/*physiology ; RNA Viruses/classification/physiology ; }, abstract = {Arthropod-borne viruses (arboviruses) are the causative agents of significant morbidity and mortality among humans and animals globally. In the past few years, the widespread adoption of next generation sequencing and metagenomics has led to a new era of virus discovery, where many novel viruses have been documented, exhibiting a restricted host-range in mosquitoes. They represent a wide-range of insect-specific viruses within the families of Bunyaviridae, Flaviviridae, Mesoniviridae, Reoviridae, Rhabdoviridae, Togaviridae, and the newly recognized taxon of Negeviruses. Collectively, their discovery has opened new vistas about the extent of viral diversity and evolution, their influence on vector competence and ability of their insect hosts to transmit human pathogens (e.g. arboviruses), and their potential development as biological control agents or novel vaccine platforms.}, } @article {pmid26321425, year = {2015}, author = {Shi, LL and Li, Y and Wang, Y and Feng, Y}, title = {MDG-1, an Ophiopogon polysaccharide, regulate gut microbiota in high-fat diet-induced obese C57BL/6 mice.}, journal = {International journal of biological macromolecules}, volume = {81}, number = {}, pages = {576-583}, doi = {10.1016/j.ijbiomac.2015.08.057}, pmid = {26321425}, issn = {1879-0003}, mesh = {Animals ; Diet, High-Fat ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; Lactobacillus/classification/drug effects/genetics/metabolism ; Male ; Metabolome ; Metabolomics/methods ; Metagenome ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Molecular Structure ; Obesity/*etiology/metabolism ; Polysaccharides/administration & dosage/chemistry/*pharmacology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Most plant polysaccharides cannot be digested and utilized by host enzymes, and must be subjected to microbial fermentation before being assimilated by the host. MDG-1, a water-soluble β-d-fructan extracted from the roots of Ophiopogon japonicus, has potent anti-obesity and hypoglycemic effects. Interestingly, we found that MDG-1 is hardly absorbed into the blood. We presumed that MDG-1 might exhibit its potent efficacy via regulating the gut microbiota of the host. However, the overall microbiota structure variation of obese mice treated with MDG-1 and the direct metabolic consequences of MDG-1 on specific microbiota phyla remain poorly understood. Here, obese male C57BL/6 mice induced by a high-fat diet were given either vehicle or MDG-1 at a dose of 300mg/kg for 12 weeks and the overall fecal gut microbiota structure change was analyzed via pyrosequencing. On this basis, we further separated and identified the dominant bacteria of the feces from the MDG-1 treated mice. These bacteria were then cultured with MDG-1 in vitro and their metabolic profiles were analyzed via a metabonomic approach. The results showed that MDG-1 could decrease the ratio of Firmicutes/Bacteroidetes, adjust the abnormal gut microbiota to the normal state and alter their metabolic profiles. In addition, we identified that the indigestible MDG-1 could be degraded and utilized by gut microbiota that could, in turn, be assimilated and used by the host, where it exerted weight loss effects, energy metabolism promotion and boosted the immune system effectiveness.}, } @article {pmid26320104, year = {2015}, author = {Dingemanse, C and Belzer, C and van Hijum, SA and Günthel, M and Salvatori, D and den Dunnen, JT and Kuijper, EJ and Devilee, P and de Vos, WM and van Ommen, GB and Robanus-Maandag, EC}, title = {Akkermansia muciniphila and Helicobacter typhlonius modulate intestinal tumor development in mice.}, journal = {Carcinogenesis}, volume = {36}, number = {11}, pages = {1388-1396}, doi = {10.1093/carcin/bgv120}, pmid = {26320104}, issn = {1460-2180}, mesh = {Amoxicillin/pharmacology ; Animals ; Anti-Bacterial Agents/*pharmacology ; Carcinogenesis ; Clarithromycin/pharmacology ; Drug Therapy, Combination ; Female ; Gastrointestinal Microbiome ; Goblet Cells/microbiology ; Helicobacter/*drug effects ; Helicobacter Infections/*complications/drug therapy ; Intestinal Neoplasms/*microbiology/prevention & control ; Intestines/microbiology/pathology ; Male ; Metronidazole/pharmacology ; Mice, Inbred C57BL ; Omeprazole/pharmacology ; Verrucomicrobia/*drug effects ; }, abstract = {Gastrointestinal tumor growth is thought to be promoted by gastrointestinal bacteria and their inflammatory products. We observed that intestine-specific conditional Apc mutant mice (FabplCre;Apc (15lox/+)) developed many more colorectal tumors under conventional than under pathogen-low housing conditions. Shotgun metagenomic sequencing plus quantitative PCR analysis of feces DNA revealed the presence of two bacterial species in conventional mice, absent from pathogen-low mice. One, Helicobacter typhlonius, has not been associated with cancer in man, nor in immune-competent mice. The other species, mucin-degrading Akkermansia muciniphila, is abundantly present in healthy humans, but reduced in patients with inflammatory gastrointestinal diseases and in obese and type 2 diabetic mice. Eradication of H.typhlonius in young conventional mice by antibiotics decreased the number of intestinal tumors. Additional presence of A.muciniphila prior to the antibiotic treatment reduced the tumor number even further. Colonization of pathogen-low FabplCre;Apc (15lox/+) mice with H.typhlonius or A.muciniphila increased the number of intestinal tumors, the thickness of the intestinal mucus layer and A.muciniphila colonization without H.typhlonius increased the density of mucin-producing goblet cells. However, dual colonization with H.typhlonius and A.muciniphila significantly reduced the number of intestinal tumors, the mucus layer thickness and goblet cell density to that of control mice. By global microbiota composition analysis, we found a positive association of A.muciniphila, and of H.typhlonius, and a negative association of unclassified Clostridiales with increased tumor burden. We conclude that A.muciniphila and H.typhlonius can modulate gut microbiota composition and intestinal tumor development in mice.}, } @article {pmid26319658, year = {2015}, author = {Liu, S and Zhao, L and Zhai, Z and Zhao, W and Ding, J and Dai, R and Sun, T and Meng, H}, title = {Porcine Epidemic Diarrhea Virus Infection Induced the Unbalance of Gut Microbiota in Piglets.}, journal = {Current microbiology}, volume = {71}, number = {6}, pages = {643-649}, pmid = {26319658}, issn = {1432-0991}, mesh = {Animals ; Animals, Newborn ; Coronavirus Infections/microbiology/*veterinary/virology ; Diarrhea/microbiology/*veterinary/virology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; Porcine epidemic diarrhea virus/*growth & development ; Swine ; Swine Diseases/*microbiology/*virology ; }, abstract = {Porcine epidemic diarrhea (PED) is a devastating disease in livestock industry. Most of the previous studies related to the PED were focused on the pathology and etiology of porcine epidemic diarrhea virus (PEDV). A little was known regarding the status of gut microbiota after piglets infected by PEDV. In this study, aided by metagenome sequencing technology, gut microbiota profiles in feces of viral diarrhea (VD) and viral control (VC) piglets were investigated. The results showed that the abundance of four dominant phyla (Fusobacteria, Actinobacteria, Verrucomicrobia, and Proteobacteria) in feces was affected greatly by porcine epidemic diarrhea. Especially, the abundance of Fusobacteria was higher in VD piglets (36%) than in VC piglets (5%). On the contrary, the Verrucomicrobia was detected in lower distribution proportion in VD piglets (around 0%) than in VC piglets (20%). Furthermore, 25 genera were significantly different between VC and VD piglets at the genus level. Among the 25 genera, Leptotrichia belonging to Fusobacteria was remarkably lower in VC piglets than in VD piglets. Akkermansia belonging to Verrucomicrobia was higher in VC piglets than in VD piglets. Our findings implicated that the gut microbiota associated with PED significantly provided an insight into the pathology and physiology of PED.}, } @article {pmid26316341, year = {2015}, author = {Walugembe, M and Hsieh, JC and Koszewski, NJ and Lamont, SJ and Persia, ME and Rothschild, MF}, title = {Effects of dietary fiber on cecal short-chain fatty acid and cecal microbiota of broiler and laying-hen chicks.}, journal = {Poultry science}, volume = {94}, number = {10}, pages = {2351-2359}, doi = {10.3382/ps/pev242}, pmid = {26316341}, issn = {0032-5791}, mesh = {Animal Feed/analysis ; *Animal Nutritional Physiological Phenomena ; Animals ; Cecum ; Chickens/*microbiology/*physiology ; Diet/*veterinary ; Dietary Fiber/administration & dosage/*metabolism ; Digestion/physiology ; Edible Grain/chemistry ; Fatty Acids, Volatile/*metabolism ; Female ; Microbiota/*physiology ; Polymerase Chain Reaction/veterinary ; Polymorphism, Restriction Fragment Length ; Random Allocation ; }, abstract = {This experiment was conducted to evaluate the effects of feeding dietary fiber on cecal short-chain fatty acid (SCFA) concentration and cecal microbiota of broiler and laying-hen chicks. The lower fiber diet was based on corn-soybean meal (SBM) and the higher fiber diet was formulated using corn-SBM-dried distillers grains with solubles (DDGS) and wheat bran to contain 60.0 g/kg of both DDGS and wheat bran from 1 to 12 d and 80.0 g/kg of both DDGS and wheat bran from 13 to 21 d. Diets were formulated to meet or exceed NRC nutrient requirements. Broiler and laying-hen chicks were randomly assigned to the high and low fiber diets with 11 replicates of 8 chicks for each of the 4 treatments. One cecum from 3 chicks was collected from each replicate: one cecum underwent SCFA concentration analysis, one underwent bacterial DNA isolation for terminal restriction fragment length polymorphism (TRFLP), and the third cecum was used for metagenomics analyses. There were interactions between bird line and dietary fiber for acetic acid (P = 0.04) and total SCFA (P = 0.04) concentration. There was higher concentration of acetic acid (P = 0.02) and propionic acid (P < 0.01) in broiler chicks compared to laying-hen chicks. TRFLP analysis showed that cecal microbiota varied due to diet (P = 0.02) and chicken line (P = 0.03). Metagenomics analyses identified differences in the relative abundance of Helicobacter pullorum and Megamonas hypermegale and the genera Enterobacteriaceae, Campylobacter, Faecalibacterium, and Bacteroides in different treatment groups. These results provide insights into the effect of dietary fiber on SCFA concentration and modulation of cecal microbiota in broiler and laying-hen chicks.}, } @article {pmid26316190, year = {2015}, author = {Ditzler, G and Polikar, R and Rosen, G}, title = {Multi-Layer and Recursive Neural Networks for Metagenomic Classification.}, journal = {IEEE transactions on nanobioscience}, volume = {14}, number = {6}, pages = {608-616}, doi = {10.1109/TNB.2015.2461219}, pmid = {26316190}, issn = {1558-2639}, mesh = {Algorithms ; Metagenomics/*methods ; Microbiota ; *Neural Networks, Computer ; }, abstract = {Recent advances in machine learning, specifically in deep learning with neural networks, has made a profound impact on fields such as natural language processing, image classification, and language modeling; however, feasibility and potential benefits of the approaches to metagenomic data analysis has been largely under-explored. Deep learning exploits many layers of learning nonlinear feature representations, typically in an unsupervised fashion, and recent results have shown outstanding generalization performance on previously unseen data. Furthermore, some deep learning methods can also represent the structure in a data set. Consequently, deep learning and neural networks may prove to be an appropriate approach for metagenomic data. To determine whether such approaches are indeed appropriate for metagenomics, we experiment with two deep learning methods: i) a deep belief network, and ii) a recursive neural network, the latter of which provides a tree representing the structure of the data. We compare these approaches to the standard multi-layer perceptron, which has been well-established in the machine learning community as a powerful prediction algorithm, though its presence is largely missing in metagenomics literature. We find that traditional neural networks can be quite powerful classifiers on metagenomic data compared to baseline methods, such as random forests. On the other hand, while the deep learning approaches did not result in improvements to the classification accuracy, they do provide the ability to learn hierarchical representations of a data set that standard classification methods do not allow. Our goal in this effort is not to determine the best algorithm in terms accuracy-as that depends on the specific application-but rather to highlight the benefits and drawbacks of each of the approach we discuss and provide insight on how they can be improved for predictive metagenomic analysis.}, } @article {pmid26315673, year = {2015}, author = {Hurez, V and Dao, V and Liu, A and Pandeswara, S and Gelfond, J and Sun, L and Bergman, M and Orihuela, CJ and Galvan, V and Padrón, Á and Drerup, J and Liu, Y and Hasty, P and Sharp, ZD and Curiel, TJ}, title = {Chronic mTOR inhibition in mice with rapamycin alters T, B, myeloid, and innate lymphoid cells and gut flora and prolongs life of immune-deficient mice.}, journal = {Aging cell}, volume = {14}, number = {6}, pages = {945-956}, pmid = {26315673}, issn = {1474-9726}, support = {F30 CA180377/CA/NCI NIH HHS/United States ; I01 BX002211/BX/BLRD VA/United States ; AG013319/AG/NIA NIH HHS/United States ; KL2 TR001118/TR/NCATS NIH HHS/United States ; T35 AG038048/AG/NIA NIH HHS/United States ; P30 AG044271/AG/NIA NIH HHS/United States ; R21 CA170491/CA/NCI NIH HHS/United States ; AG038048/AG/NIA NIH HHS/United States ; TL1 TR001119/TR/NCATS NIH HHS/United States ; CA180377/CA/NCI NIH HHS/United States ; AG036613/AG/NIA NIH HHS/United States ; CA54174/CA/NCI NIH HHS/United States ; R01 CA193835/CA/NCI NIH HHS/United States ; CA170491/CA/NCI NIH HHS/United States ; KL2 TR000118/TR/NCATS NIH HHS/United States ; P30 AG013319/AG/NIA NIH HHS/United States ; P30 CA054174/CA/NCI NIH HHS/United States ; UL1 TR001120/TR/NCATS NIH HHS/United States ; TR000118/TR/NCATS NIH HHS/United States ; TR001119/TR/NCATS NIH HHS/United States ; RC2 AG036613/AG/NIA NIH HHS/United States ; R01 AI114800/AI/NIAID NIH HHS/United States ; AI114800/AI/NIAID NIH HHS/United States ; }, mesh = {Aging/drug effects ; Animals ; Antibiotics, Antineoplastic/*pharmacology ; B-Lymphocytes/*immunology ; CD8-Positive T-Lymphocytes/*immunology ; Cell Differentiation/drug effects ; Dendritic Cells/*immunology ; Female ; Flagellin/immunology ; Gastrointestinal Microbiome ; Gene Expression Profiling ; Immunologic Memory/immunology ; Interleukins/metabolism ; Longevity/*drug effects/immunology ; Male ; Melanoma, Experimental ; Mice ; Mice, Inbred C57BL ; Myeloid Cells/*immunology ; Programmed Cell Death 1 Receptor/biosynthesis ; Sirolimus/*pharmacology ; Spleen/cytology/immunology ; T-Lymphocytes, Regulatory/cytology/*immunology ; TOR Serine-Threonine Kinases/*antagonists & inhibitors/immunology ; Interleukin-22 ; }, abstract = {The mammalian (mechanistic) target of rapamycin (mTOR) regulates critical immune processes that remain incompletely defined. Interest in mTOR inhibitor drugs is heightened by recent demonstrations that the mTOR inhibitor rapamycin extends lifespan and healthspan in mice. Rapamycin or related analogues (rapalogues) also mitigate age-related debilities including increasing antigen-specific immunity, improving vaccine responses in elderly humans, and treating cancers and autoimmunity, suggesting important new clinical applications. Nonetheless, immune toxicity concerns for long-term mTOR inhibition, particularly immunosuppression, persist. Although mTOR is pivotal to fundamental, important immune pathways, little is reported on immune effects of mTOR inhibition in lifespan or healthspan extension, or with chronic mTOR inhibitor use. We comprehensively analyzed immune effects of rapamycin as used in lifespan extension studies. Gene expression profiling found many and novel changes in genes affecting differentiation, function, homeostasis, exhaustion, cell death, and inflammation in distinct T- and B-lymphocyte and myeloid cell subpopulations. Immune functions relevant to aging and inflammation, and to cancer and infections, and innate lymphoid cell effects were validated in vitro and in vivo. Rapamycin markedly prolonged lifespan and healthspan in cancer- and infection-prone mice supporting disease mitigation as a mechanism for mTOR suppression-mediated longevity extension. It modestly altered gut metagenomes, and some metagenomic effects were linked to immune outcomes. Our data show novel mTOR inhibitor immune effects meriting further studies in relation to longevity and healthspan extension.}, } @article {pmid26315488, year = {2016}, author = {Ushida, K and Tsuchida, S and Ogura, Y and Toyoda, A and Maruyama, F}, title = {Domestication and cereal feeding developed domestic pig-type intestinal microbiota in animals of suidae.}, journal = {Animal science journal = Nihon chikusan Gakkaiho}, volume = {87}, number = {6}, pages = {835-841}, doi = {10.1111/asj.12492}, pmid = {26315488}, issn = {1740-0929}, mesh = {*Animal Feed ; Animals ; Animals, Domestic/*microbiology ; Animals, Wild/microbiology ; Bifidobacterium/genetics ; Datasets as Topic ; *Domestication ; *Edible Grain ; Enterobacteriaceae/genetics ; Evolution, Molecular ; Female ; *Gastrointestinal Microbiome/genetics ; Intestines/*microbiology ; Lactobacillus/genetics ; Male ; Metagenome ; Phylogeny ; Swine/*microbiology ; }, abstract = {Intestinal microbiota are characterized by host-specific microorganisms, which have been selected through host-microbe interactions under phylogenetic evolution and transition of feeding behavior by the host. Although many studies have focused on disease-related intestinal microbiota, the origin and evolution of host-specific intestinal microbiota have not been well elucidated. Pig is the ideal mammal model to reveal the origin and evolution of host-specific intestinal microbiota because their direct wild ancestor and close phylogenetic neighbors are available for comparison. The pig has been recognized as a Lactobacillus-type animal. We analyzed the intestinal microbiota of various animals in Suidae: domestic pigs, wild boars and Red river hogs to survey the origin and evolution of Lactobacillus-dominated intestinal microbiota by metagenomic approach and following quantitative PCR confirmation. The metagenomic datasets were separated in two clusters; the wild animal cluster being characterized by a high abundance of Bifidobacterium, whereas the domesticated (or captured) animal cluster by Lactobacillus. In addition, Enterobacteriaceae were harbored as the major family only in domestic Sus scrofa. We conclude that domestication may have induced a larger Enterobacteriaceae population in pigs, and the introduction of modern feeding system further caused the development of Lactobacillus-dominated intestinal microbiota, with genetic and geographical factors possibly having a minor impact.}, } @article {pmid26314125, year = {2015}, author = {Tian, M and Liu, HH and Shen, X and Zhao, FQ and Chen, S and Yao, YJ}, title = {[Biodiversity and Function Analyses of BIOLAK Activated Sludge Metagenome].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {36}, number = {5}, pages = {1739-1748}, pmid = {26314125}, issn = {0250-3301}, mesh = {Archaea ; Bacteria ; *Biodiversity ; *Metagenome ; Nitrification ; Nitrogen ; Phosphorus ; Sewage/*microbiology ; Wastewater ; }, abstract = {The BIOLAK is a multi-stage activated sludge process, which has been successfully promoted worldwide. However, the biological community and function of the BIOLAK activated sludge (the core component in the process) have not been reported so far. In this study, taking Lianyungang Dapu Industrial Zone WWTP as an example, a large-scale metagenomic data (428 588 high-quality DNA sequences) of the BIOLAK activated sludge were obtained by means of a new generation of high-throughput sequencing technology. Amazing biodiversity was revealed in the BIOLAK activated sludge, which included 47 phyla, 872 genera and 1351 species. There were 33 phyla identified in the Bacteria domain (289 933 sequences). Proteohacteria was the most abundant phylum (62.54%), followed by Bacteroidetes (11.29%), Nitrospirae (5. 65%) and Planctomycetes (4.79%), suggesting that these groups played a key role in the BIOLAK wastewater treatment system. Among the 748 bacterial genera, Nitrospira (5.60%) was the most prevalent genus, which was a key group in the nitrogen cycle. Followed by Gemmatimonas (2.45%), which was an important genus in the biological phosphorus removal process. In Archaea domain (1019 sequences), three phyla and 39 genera were detected. In Eukaryota domain (1055 sequences), 60 genera and 10 phyla were identified, among which Ciliophora was the largest phylum (257 sequences). Meanwhile, 448 viral sequences were detected in the BIOLAK sludge metagenome, which were dominated by bacteriophages. The proportions of nitrogen, aromatic compounds and phosphorus metabolism in the BIOLAK sludge were 2.50%, 2.28% and 1.56%, respectively, which were higher than those in the sludge of United States and Australia. Among four processes of nitrogen metabolism, denitrification-related genes were most abundant (80.81%), followed by ammonification (12.78%), nitrification,(4.38%) and nitrogen fixation (2.04%). In conclusion, the BIOLAK activated sludge had amazing biodiversity, meanwhile, functional genes involved in nitrogen, aromatic compounds and phosphorus metabolism were very abundant.}, } @article {pmid26313691, year = {2015}, author = {Pérez-Brocal, V and García-López, R and Nos, P and Beltrán, B and Moret, I and Moya, A}, title = {Metagenomic Analysis of Crohn's Disease Patients Identifies Changes in the Virome and Microbiome Related to Disease Status and Therapy, and Detects Potential Interactions and Biomarkers.}, journal = {Inflammatory bowel diseases}, volume = {21}, number = {11}, pages = {2515-2532}, doi = {10.1097/MIB.0000000000000549}, pmid = {26313691}, issn = {1536-4844}, mesh = {Adolescent ; Adult ; Case-Control Studies ; Crohn Disease/*microbiology/*virology ; DNA, Bacterial/genetics ; DNA, Viral/genetics ; Feces/*microbiology ; Female ; Humans ; Male ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Middle Aged ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {BACKGROUND: The aim of this study was to survey the bacterial and viral communities in different types of samples from patients with Crohn's disease (CD) at different stages of the disease to relate their distribution with the origin and progression of this disorder.

METHODS: A total of 42 fecal samples and 15 biopsies from 20 patients with CD and 20 healthy control individuals were collected for bacterial 16S rRNA gene profiling and DNA/RNA virome metagenomic analysis through 454 pyrosequencing. Their composition, abundance, and diversity were analyzed, and comparisons of disease status, patient status, and sample origin were used to determine statistical differences between the groups.

RESULTS: Bacterial composition and relative abundance in new-onset patients with CD differed markedly from control individuals. Individual variability and sample origin had a stronger impact on viral communities than the disease, contrary to what was observed for bacterial populations although increased numbers of overrepresented viruses were observed in feces from patients with CD. Correlation-based networks were constructed to show potential relations between bacteria and between those and viruses.

CONCLUSIONS: The bacterial community reflects the disease status of individuals more accurately than their viral counterparts. However, numerous viral biomarkers specifically associated with CD disease were identified. Because viruses can modulate bacterial communities, the correlation networks between both communities constitute a step forward in unraveling their interactions under normal and CD disease conditions.}, } @article {pmid26313376, year = {2016}, author = {Gorham, J and Gleeson, M}, title = {Cirrhosis and dysbiosis: New insights from next-generation sequencing.}, journal = {Hepatology (Baltimore, Md.)}, volume = {63}, number = {1}, pages = {336-338}, doi = {10.1002/hep.28133}, pmid = {26313376}, issn = {1527-3350}, mesh = {Gastrointestinal Tract/*microbiology ; Humans ; Liver Cirrhosis/*diagnosis/*microbiology ; *Metagenomics ; Microbiota/*genetics/*physiology ; }, } @article {pmid26308318, year = {2016}, author = {Fofanova, TY and Petrosino, JF and Kellermayer, R}, title = {Microbiome-Epigenome Interactions and the Environmental Origins of Inflammatory Bowel Diseases.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {62}, number = {2}, pages = {208-219}, pmid = {26308318}, issn = {1536-4801}, support = {T32 GM088129/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteria ; DNA Methylation ; *Diet ; *Environment ; *Epigenesis, Genetic ; *Genome ; Humans ; Inflammatory Bowel Diseases/*etiology/genetics/microbiology ; *Microbiota ; }, abstract = {The incidence of pediatric inflammatory bowel disease (IBD), which includes Crohn disease and ulcerative colitis, has risen alarmingly in the Western and developing world in recent decades. Epidemiologic (including monozygotic twin and migrant) studies highlight the substantial role of environment and nutrition in IBD etiology. Here we review the literature supporting the developmental and environmental origins hypothesis of IBD. We also provide a detailed exploration of how the human microbiome and epigenome (primarily through DNA methylation) may be important elements in the developmental origins of IBD in both children and adults.}, } @article {pmid26307935, year = {2016}, author = {Uchii, K and Doi, H and Minamoto, T}, title = {A novel environmental DNA approach to quantify the cryptic invasion of non-native genotypes.}, journal = {Molecular ecology resources}, volume = {16}, number = {2}, pages = {415-422}, doi = {10.1111/1755-0998.12460}, pmid = {26307935}, issn = {1755-0998}, mesh = {*Biota ; DNA/*analysis/chemistry/*genetics/isolation & purification ; Genotype ; Humans ; *Introduced Species ; Japan ; Metagenomics/*methods ; Polymorphism, Single Nucleotide ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA/methods ; Water/*chemistry ; }, abstract = {The invasion of non-native species that are closely related to native species can lead to competitive elimination of the native species and/or genomic extinction through hybridization. Such invasions often become serious before they are detected, posing unprecedented threats to biodiversity. A Japanese native strain of common carp (Cyprinus carpio) has become endangered owing to the invasion of non-native strains introduced from the Eurasian continent. Here, we propose a rapid environmental DNA-based approach to quantitatively monitor the invasion of non-native genotypes. Using this system, we developed a method to quantify the relative proportion of native and non-native DNA based on a single-nucleotide polymorphism using cycling probe technology in real-time PCR. The efficiency of this method was confirmed in aquarium experiments, where the quantified proportion of native and non-native DNA in the water was well correlated to the biomass ratio of native and non-native genotypes. This method provided quantitative estimates for the proportion of native and non-native DNA in natural rivers and reservoirs, which allowed us to estimate the degree of invasion of non-native genotypes without catching and analysing individual fish. Our approach would dramatically facilitate the process of quantitatively monitoring the invasion of non-native conspecifics in aquatic ecosystems, thus revealing a promising method for risk assessment and management in biodiversity conservation.}, } @article {pmid26306992, year = {2015}, author = {Chaves-Moreno, D and Plumeier, I and Kahl, S and Krismer, B and Peschel, A and Oxley, AP and Jauregui, R and Pieper, DH}, title = {The microbial community structure of the cotton rat nose.}, journal = {Environmental microbiology reports}, volume = {7}, number = {6}, pages = {929-935}, doi = {10.1111/1758-2229.12334}, pmid = {26306992}, issn = {1758-2229}, mesh = {Animals ; Bacteria/classification/genetics ; *Biodiversity ; Metagenome ; Metagenomics ; *Microbiota ; Nose/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sigmodontinae/*microbiology ; }, abstract = {The cotton rat nose is commonly used as a model for Staphylococcus aureus colonization, as it is both physiologically and anatomically comparable to the human nares and can be easily colonized by this organism. However, while the colonization of the human anterior nares has been extensively studied, the microbial community structure of cotton rat noses has not been reported so far. We describe here the microbial community structure of the cotton rat (Sigmodon hispidus) nose through next-generation sequencing of 16S rRNA gene amplicons covering the V1-V2 region and the analysis of nearly full length 16S rRNA genes of the major phylotypes. Roughly half of the microbial community was composed of two undescribed species of the genus Campylobacter, with phylotypes belonging to the genera Catonella, Acholeplasma, Streptobacillus and Capnocytophaga constituting the predominant community members. Thus, the nasal community of the cotton rat is uniquely composed of several novel bacterial species and may not reflect the complex interactions that occur in human anterior nares. Mammalian airway microbiota may, however, be a rich source of hitherto unknown microbes.}, } @article {pmid26306392, year = {2015}, author = {Hollister, EB and Riehle, K and Luna, RA and Weidler, EM and Rubio-Gonzales, M and Mistretta, TA and Raza, S and Doddapaneni, HV and Metcalf, GA and Muzny, DM and Gibbs, RA and Petrosino, JF and Shulman, RJ and Versalovic, J}, title = {Structure and function of the healthy pre-adolescent pediatric gut microbiome.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {36}, pmid = {26306392}, issn = {2049-2618}, support = {U01 CA170930/CA/NCI NIH HHS/United States ; U54 HG004973/HG/NHGRI NIH HHS/United States ; R01 NR05337/NR/NINR NIH HHS/United States ; R01 NR013497/NR/NINR NIH HHS/United States ; UH3 DK083990/DK/NIDDK NIH HHS/United States ; UH2 DK093990/DK/NIDDK NIH HHS/United States ; R01 NR005337/NR/NINR NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 AT004326/AT/NCCIH NIH HHS/United States ; UH2 DK083990/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Age Factors ; *Biodiversity ; Child ; Cluster Analysis ; DNA Barcoding, Taxonomic ; Female ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Male ; Metagenome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The gut microbiome influences myriad host functions, including nutrient acquisition, immune modulation, brain development, and behavior. Although human gut microbiota are recognized to change as we age, information regarding the structure and function of the gut microbiome during childhood is limited. Using 16S rRNA gene and shotgun metagenomic sequencing, we characterized the structure, function, and variation of the healthy pediatric gut microbiome in a cohort of school-aged, pre-adolescent children (ages 7-12 years). We compared the healthy pediatric gut microbiome with that of healthy adults previously recruited from the same region (Houston, TX, USA).

RESULTS: Although healthy children and adults harbored similar numbers of taxa and functional genes, their composition and functional potential differed significantly. Children were enriched in Bifidobacterium spp., Faecalibacterium spp., and members of the Lachnospiraceae, while adults harbored greater abundances of Bacteroides spp. From a functional perspective, significant differences were detected with respect to the relative abundances of genes involved in vitamin synthesis, amino acid degradation, oxidative phosphorylation, and triggering mucosal inflammation. Children's gut communities were enriched in functions which may support ongoing development, while adult communities were enriched in functions associated with inflammation, obesity, and increased risk of adiposity.

CONCLUSIONS: Previous studies suggest that the human gut microbiome is relatively stable and adult-like after the first 1 to 3 years of life. Our results suggest that the healthy pediatric gut microbiome harbors compositional and functional qualities that differ from those of healthy adults and that the gut microbiome may undergo a more prolonged development than previously suspected.}, } @article {pmid26305682, year = {2015}, author = {Whitfield-Cargile, CM and Cohen, ND and Suchodolski, J and Chaffin, MK and McQueen, CM and Arnold, CE and Dowd, SE and Blodgett, GP}, title = {Composition and Diversity of the Fecal Microbiome and Inferred Fecal Metagenome Does Not Predict Subsequent Pneumonia Caused by Rhodococcus equi in Foals.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0136586}, pmid = {26305682}, issn = {1932-6203}, mesh = {Animals ; Disease Susceptibility ; Feces/microbiology ; Horse Diseases/genetics/*microbiology ; Horses/genetics/microbiology ; *Metagenome ; Microbiota/*genetics ; Pneumonia/microbiology/veterinary ; Rhodococcus equi/*genetics/pathogenicity ; }, abstract = {In equids, susceptibility to disease caused by Rhodococcus equi occurs almost exclusively in foals. This distribution might be attributable to the age-dependent maturation of immunity following birth undergone by mammalian neonates that renders them especially susceptible to infectious diseases. Expansion and diversification of the neonatal microbiome contribute to development of immunity in the gut. Moreover, diminished diversity of the gastrointestinal microbiome has been associated with risk of infections and immune dysregulation. We thus hypothesized that varying composition or reduced diversity of the intestinal microbiome of neonatal foals would contribute to increased susceptibility of their developing R. equi pneumonia. The composition and diversity indices of the fecal microbiota at 3 and 5 weeks of age were compared among 3 groups of foals: 1) foals that subsequently developed R. equi pneumonia after sampling; 2) foals that subsequently developed ultrasonographic evidence of pulmonary abscess formation or consolidation but not clinical signs (subclinical group); and, 3) foals that developed neither clinical signs nor ultrasonographic evidence of pulmonary abscess formation or consolidation. No significant differences were found among groups at either sampling time, indicating absence of evidence of an influence of composition or diversity of the fecal microbiome, or predicted fecal metagenome, on susceptibility to subsequent R. equi pneumonia. A marked and significant difference identified between a relatively short interval of time appeared to reflect ongoing adaptation to transition from a milk diet to a diet including available forage (including hay) and access to concentrate fed to the mare.}, } @article {pmid26304839, year = {2015}, author = {Nathani, NM and Kothari, RK and Patel, AK and Joshi, CG}, title = {Functional Characterization Reveals Novel Putative Coding Sequences in Prevotella ruminicola Genome Extracted from Rumen Metagenomic Studies.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {25}, number = {4}, pages = {292-299}, doi = {10.1159/000437265}, pmid = {26304839}, issn = {1660-2412}, mesh = {Animals ; Bacteria/classification/enzymology/genetics/isolation & purification ; Bacterial Proteins/genetics ; Buffaloes ; Cattle ; Gastrointestinal Microbiome ; Genome, Bacterial ; Metagenomics ; Open Reading Frames ; Phylogeny ; Prevotella ruminicola/classification/enzymology/*genetics/isolation & purification ; Rumen/*microbiology ; }, abstract = {AIM: To reassemble Prevotella ruminicola genome from rumen metagenomic data of cattle and buffalo and compare with the published reference genome.

METHOD: Rumen microbial communities from Mehsani buffaloes (n = 8) and Kankrej cattle (n = 8), each adapted to different proportions of a dry or green roughage diet, were subjected to metagenomic sequencing by Ion Torrent PGM, and subsequent reads were analyzed by MG-RAST. Using reference-guided assembly of the sequences against the published P. ruminicola strain 23, draft genomes of 2.56 and 2.46 Mb were reconstructed from Mehsani buffalo and Kankrej cows, respectively. The genomes were annotated using the RAST Server and carbohydrate active enzyme (CAZyme) analysis.

RESULTS: Taxonomic analysis by MG-RAST revealed P. ruminicola to be the most abundant species present among the rumen microflora. Functional annotation of reconstructed genomes using the RAST Server depicted the maximum assignment of coding sequences involved in the subsystems amino acid and derivatives and carbohydrate metabolism. CAZyme profiling revealed the glycoside hydrolases (GH) family to be the most abundant. GH family subclassification revealed that the extracted genomes had more sequence hits for GH2, GH3, GH92 and GH97 as compared to the reference.

CONCLUSION: The results reflect the metabolic significance of rumen-adapted P. ruminicola in utilizing a coarse diet for animals based on acquisition of novel genetic elements.}, } @article {pmid26304302, year = {2015}, author = {Wieland, A and Frank, DN and Harnke, B and Bambha, K}, title = {Systematic review: microbial dysbiosis and nonalcoholic fatty liver disease.}, journal = {Alimentary pharmacology & therapeutics}, volume = {42}, number = {9}, pages = {1051-1063}, doi = {10.1111/apt.13376}, pmid = {26304302}, issn = {1365-2036}, mesh = {Animals ; Dysbiosis/*microbiology ; Humans ; Intestines/*microbiology ; Metagenome ; *Microbiota ; Models, Animal ; Non-alcoholic Fatty Liver Disease/*microbiology/*physiopathology ; }, abstract = {BACKGROUND: The human intestinal microbiota is a key regulator of host metabolic and immune functions and alterations in the microbiome ('dysbiosis') have been implicated in several human diseases. Because of the anatomical links between the intestines and the liver, dysbiosis may also disrupt hepatic function and thereby contribute to the pathogenesis of nonalcoholic fatty liver disease (NAFLD).

AIM: To perform a comprehensive review of the medical literature investigating associations between intestinal dysbiosis and NAFLD, with a particular emphasis on studies that characterise the microbiome in NAFLD.

METHODS: We conducted a search of PubMed, Embase, and Web of Science using multiple search terms including: 'NAFLD, NASH, fatty liver, steatohepatitis' combined with 'metagenome, microbiom*, microbiota*, fecal flora, intestinal flora, gut bacteria'. Results were manually reviewed and studies selected based on relevance to intestinal microbiota and NAFLD. We also included studies that addressed potential mechanistic models of pathways linking the dysbiosis to NAFLD.

RESULTS: Nine studies (five human and four animal models) were identified in our search that assessed associations between specific intestinal microbiota composition and NAFLD. We reviewed and summarised the results of additional investigations that more broadly addressed the mechanisms by which the microbiome may impact NAFLD pathogenesis.

CONCLUSIONS: Investigations in humans and animals demonstrate associations between intestinal dysbiosis and NAFLD; however, causality has not been proven and mechanistic links require further delineation. As the field of microbiome research matures in techniques and study design, more detailed insights into NAFLD pathogenesis and its associations with the intestinal microbiota will be elucidated.}, } @article {pmid26299977, year = {2015}, author = {Shu, D and He, Y and Yue, H and Zhu, L and Wang, Q}, title = {Metagenomic insights into the effects of volatile fatty acids on microbial community structures and functional genes in organotrophic anammox process.}, journal = {Bioresource technology}, volume = {196}, number = {}, pages = {621-633}, doi = {10.1016/j.biortech.2015.07.107}, pmid = {26299977}, issn = {1873-2976}, mesh = {Ammonia/*metabolism ; *Fatty Acids, Volatile/chemistry/metabolism ; Metagenome/*genetics ; Metagenomics ; Microbial Consortia/*genetics ; Nitrates/*metabolism ; }, abstract = {To explore the metabolic versatility of "Candidatus Brocadia sinica" in the presence of VFAs, the impacts of VFAs on anammox activity and nitrogen removal were investigated in this study. Results found that low VFAs concentrations has no affect on anammox activity and the removal efficiencies of NH4(+)-N and NO2(-)-N. However, "Ca. Brocadia sinica" showed higher adaptability to some VFAs stresses. Furthermore, Illumina MiSeq pyrosequencing results indicated that the microbial community structures varied significantly and the phyla Chloroflexi, Proteobacteria, Bacteroidetes and Chlorobi were dominated. Finally, qPCR was performed to validate the growth of anammox bacteria and gain the quantitative insights into the correlation between nitrogen transformation rates and the key functional genes in the organotrophic anammox system. Combined analysis clearly demonstrated that the coupling of the anammox, denitrification and DNRA were the noteworthy pathway for the simultaneous removal of nitrogen and organic carbon.}, } @article {pmid26299453, year = {2015}, author = {Ussar, S and Griffin, NW and Bezy, O and Fujisaka, S and Vienberg, S and Softic, S and Deng, L and Bry, L and Gordon, JI and Kahn, CR}, title = {Interactions between Gut Microbiota, Host Genetics and Diet Modulate the Predisposition to Obesity and Metabolic Syndrome.}, journal = {Cell metabolism}, volume = {22}, number = {3}, pages = {516-530}, pmid = {26299453}, issn = {1932-7420}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; R01 DK030292/DK/NIDDK NIH HHS/United States ; P30 DK036836/DK/NIDDK NIH HHS/United States ; DK31036/DK/NIDDK NIH HHS/United States ; T32 DK007120/DK/NIDDK NIH HHS/United States ; P30DK036836/DK/NIDDK NIH HHS/United States ; R01 DK031036/DK/NIDDK NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; R01 DK082659/DK/NIDDK NIH HHS/United States ; DK78669/DK/NIDDK NIH HHS/United States ; DK007120/DK/NIDDK NIH HHS/United States ; R01 DK070977/DK/NIDDK NIH HHS/United States ; P30DK034854/DK/NIDDK NIH HHS/United States ; K12 HD000850/HD/NICHD NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; DK30292/DK/NIDDK NIH HHS/United States ; R01 DK033201/DK/NIDDK NIH HHS/United States ; DK70977/DK/NIDDK NIH HHS/United States ; DK33201/DK/NIDDK NIH HHS/United States ; DK82659/DK/NIDDK NIH HHS/United States ; R37 DK031036/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Diabetes Mellitus/*genetics/*microbiology/pathology ; Diet ; *Gastrointestinal Microbiome ; Gene-Environment Interaction ; Genotype ; Insulin Resistance ; Male ; Metabolic Syndrome/*genetics/*microbiology/pathology ; Mice, Inbred C57BL ; Mice, Inbred Strains ; Obesity/*genetics/*microbiology/pathology ; Phenotype ; Weight Gain ; }, abstract = {Obesity, diabetes, and metabolic syndrome result from complex interactions between genetic and environmental factors, including the gut microbiota. To dissect these interactions, we utilized three commonly used inbred strains of mice-obesity/diabetes-prone C57Bl/6J mice, obesity/diabetes-resistant 129S1/SvImJ from Jackson Laboratory, and obesity-prone but diabetes-resistant 129S6/SvEvTac from Taconic-plus three derivative lines generated by breeding these strains in a new, common environment. Analysis of metabolic parameters and gut microbiota in all strains and their environmentally normalized derivatives revealed strong interactions between microbiota, diet, breeding site, and metabolic phenotype. Strain-dependent and strain-independent correlations were found between specific microbiota and phenotypes, some of which could be transferred to germ-free recipient animals by fecal transplantation. Environmental reprogramming of microbiota resulted in 129S6/SvEvTac becoming obesity resistant. Thus, development of obesity/metabolic syndrome is the result of interactions between gut microbiota, host genetics, and diet. In permissive genetic backgrounds, environmental reprograming of microbiota can ameliorate development of metabolic syndrome.}, } @article {pmid26293474, year = {2015}, author = {Cuív, PÓ and Smith, WJ and Pottenger, S and Burman, S and Shanahan, ER and Morrison, M}, title = {Isolation of Genetically Tractable Most-Wanted Bacteria by Metaparental Mating.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {13282}, pmid = {26293474}, issn = {2045-2322}, mesh = {Aerobiosis ; Anaerobiosis ; Biodiversity ; Clostridium/*genetics/*isolation & purification ; *Conjugation, Genetic ; Fluorescent Dyes/metabolism ; Genetic Vectors/metabolism ; Metagenomics/*methods ; Microscopy, Fluorescence ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {Metagenomics has rapidly advanced our inventory and appreciation of the genetic potential inherent to the gut microbiome. However it is widely accepted that two key constraints to further genetic dissection of the gut microbiota and host-microbe interactions have been our inability to recover new isolates from the human gut, and the paucity of genetically tractable gut microbes. To address this challenge we developed a modular RP4 mobilisable recombinant vector system and an approach termed metaparental mating to support the rapid and directed isolation of genetically tractable fastidious gut bacteria. Using this approach we isolated transconjugants affiliated with Clostridium cluster IV (Faecalibacterium and Oscillibacter spp.), Clostridium cluster XI (Anaerococcus) and Clostridium XIVa (Blautia spp.) and group 2 ruminococci amongst others, and demonstrated that the recombinant vectors were stably maintained in their recipient hosts. By a similar approach we constructed fluorescently labelled bacterial transconjugants affiliated with Clostridium cluster IV (including Flavonifractor and Pseudoflavonifractor spp.), Clostridium XIVa (Blautia spp.) and Clostridium cluster XVIII (Clostridium ramosum) that expressed a flavin mononucleotide-based reporter gene (evoglow-C-Bs2). Our approach will advance the integration of bacterial genetics with metagenomics and realize new directions to support a more mechanistic dissection of host-microbe associations relevant to human health and disease.}, } @article {pmid26292041, year = {2016}, author = {Barnett, C and Nazzal, L and Goldfarb, DS and Blaser, MJ}, title = {The Presence of Oxalobacter formigenes in the Microbiome of Healthy Young Adults.}, journal = {The Journal of urology}, volume = {195}, number = {2}, pages = {499-506}, pmid = {26292041}, issn = {1527-3792}, support = {U54 DK083908/DK/NIDDK NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; UH2 AR057506/AR/NIAMS NIH HHS/United States ; U54 DK 083908/DK/NIDDK NIH HHS/United States ; R01 DK090989/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Feces/microbiology ; Female ; Healthy Volunteers ; Humans ; Male ; Metagenome/genetics ; *Microbiota ; Oxalobacter formigenes/classification/genetics/*isolation & purification ; United States ; }, abstract = {PURPOSE: Oxalobacter formigenes, a member of the human colonic microbiota with a major role in net colonic oxalate transport and secretion, is protective against the formation of calcium oxalate kidney stones. We describe the prevalence, relative abundance and stability of O. formigenes in healthy young adults in the United States.

MATERIALS AND METHODS: We used HMP (Human Microbiome Project) data on fecal samples from 242 healthy young adults who had 1 to 3 study visits. Samples underwent whole genomic shotgun sequencing and/or 16S rRNA sequencing. Three data sets available from the processed sequence data were studied, including whole genomic shotgun metagenomic analysis by alignment to reference genomes using shotgun community profiling, or MetaPhlAn (http://huttenhower.sph.harvard.edu/metaphlan) or QIIME (http://qiime.org/) analysis of the V1-3 or V3-5 16S sequences.

RESULTS: O. formigenes was detected in fecal samples using whole genomic shotgun and 16S rRNA data. Analysis of the whole genomic shotgun data set using shotgun community profiling showed that 29 of 94 subjects (31%) were O. formigenes positive. V1-3 and V3-5 analyses were less sensitive for O. formigenes detection. When present, O. formigenes relative abundance varied over 3 log10 and was normally distributed. All assays agreed in 58 of 66 samples (88%) studied by all 3 methods. Of 14 subjects who were O. formigenes positive at baseline 13 (93%) were positive at the followup visit, indicating the stability of colonization.

CONCLUSIONS: O. formigenes appears to be stably present in fewer than half of healthy young adults in the United States. It is most sensitively detected by whole genomic shotgun.}, } @article {pmid26290472, year = {2015}, author = {Chong, CW and Ahmad, AF and Lim, YA and Teh, CS and Yap, IK and Lee, SC and Chin, YT and Loke, P and Chua, KH}, title = {Effect of ethnicity and socioeconomic variation to the gut microbiota composition among pre-adolescent in Malaysia.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {13338}, pmid = {26290472}, issn = {2045-2322}, mesh = {Adolescent ; Biodiversity ; Child ; DNA, Ribosomal/genetics ; *Ethnicity ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Hygiene ; Linear Models ; Malaysia ; Male ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Principal Component Analysis ; Socioeconomic Factors ; }, abstract = {Gut microbiota plays an important role in mammalian host metabolism and physiological functions. The functions are particularly important in young children where rapid mental and physical developments are taking place. Nevertheless, little is known about the gut microbiome and the factors that contribute to microbial variation in the gut of South East Asian children. Here, we compared the gut bacterial richness and composition of pre-adolescence in Northern Malaysia. Our subjects covered three distinct ethnic groups with relatively narrow range of socioeconomic discrepancy. These included the Malays (n = 24), Chinese (n = 17) and the Orang Asli (indigenous) (n = 20). Our results suggested a strong ethnicity and socioeconomic-linked bacterial diversity. Highest bacterial diversity was detected from the economically deprived indigenous children while the lowest diversity was recorded from the relatively wealthy Chinese children. In addition, predicted functional metagenome profiling suggested an over-representation of pathways pertinent to bacterial colonisation and chemotaxis in the former while the latter exhibited enriched gene pathways related to sugar metabolism.}, } @article {pmid26289776, year = {2015}, author = {Collins, J and Auchtung, JM and Schaefer, L and Eaton, KA and Britton, RA}, title = {Humanized microbiota mice as a model of recurrent Clostridium difficile disease.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {35}, pmid = {26289776}, issn = {2049-2618}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; U19 AI090872/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/administration & dosage/pharmacology ; Bacteria/classification/genetics ; Biodiversity ; *Clostridioides difficile ; Disease Models, Animal ; Drug Therapy, Combination ; Enterocolitis, Pseudomembranous/drug therapy/*microbiology ; Feces/microbiology ; Humans ; Mice ; *Microbiota/drug effects ; Recurrence ; }, abstract = {BACKGROUND: Clostridium difficile disease is the leading antibiotic-associated cause of diarrhea and nosocomial acquired infection in the western world. The per annum burden in the USA alone amounts to 250,000 cases with 14,000 ascribed deaths and medical costs in excess of a billion dollars. Novel models for the study of C. difficile infection are therefore pertinent.

RESULTS: Germ free C57BL/6 mice gavaged with a healthy human fecal microbiota maintained a stable "humanized" microbiota over multiple generations when housed under specific pathogen-free (SPF) conditions. As with mice containing a conventional microbiota, treatment with a five-antibiotic cocktail followed by a single dose of clindamycin renders the animals susceptible to C. difficile infection (CDI). Interestingly, after recovery from the initial CDI infection, a single intraperitoneal injection of clindamycin is sufficient to induce CDI relapse. Relapse of CDI can be induced up to 35 days postinfection after recovery from the initial infection, and multiple episodes of relapse can be induced.

CONCLUSIONS: This model enables the study of recurrent C. difficile disease in a host containing a human-derived microbiota. Probiotic treatments using human-derived microbes, either prophylactic or curative, can be tested within the model. The identification and testing of human-derived microbial communities within a humanized microbiota mouse model may enable a higher rate of successful transfer of bacteria-based treatments from the lab to human patients due to the microbes involved initiating from, and being adapted to, the human GI tract.}, } @article {pmid26289044, year = {2015}, author = {Cong, J and Liu, X and Lu, H and Xu, H and Li, Y and Deng, Y and Li, D and Zhang, Y}, title = {Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest.}, journal = {BMC microbiology}, volume = {15}, number = {}, pages = {167}, pmid = {26289044}, issn = {1471-2180}, mesh = {*Biota ; Carbon/metabolism ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Microarray Analysis ; Molecular Sequence Data ; Nitrogen/*analysis/metabolism ; Phosphorus/metabolism ; *Rainforest ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {BACKGROUND: Tropical rainforests cover over 50% of all known plant and animal species and provide a variety of key resources and ecosystem services to humans, largely mediated by metabolic activities of soil microbial communities. A deep analysis of soil microbial communities and their roles in ecological processes would improve our understanding on biogeochemical elemental cycles. However, soil microbial functional gene diversity in tropical rainforests and causative factors remain unclear. GeoChip, contained almost all of the key functional genes related to biogeochemical cycles, could be used as a specific and sensitive tool for studying microbial gene diversity and metabolic potential. In this study, soil microbial functional gene diversity in tropical rainforest was analyzed by using GeoChip technology.

RESULTS: Gene categories detected in the tropical rainforest soils were related to different biogeochemical processes, such as carbon (C), nitrogen (N) and phosphorus (P) cycling. The relative abundance of genes related to C and P cycling detected mostly derived from the cultured bacteria. C degradation gene categories for substrates ranging from labile C to recalcitrant C were all detected, and gene abundances involved in many recalcitrant C degradation gene categories were significantly (P < 0.05) different among three sampling sites. The relative abundance of genes related to N cycling detected was significantly (P < 0.05) different, mostly derived from the uncultured bacteria. The gene categories related to ammonification had a high relative abundance. Both canonical correspondence analysis and multivariate regression tree analysis showed that soil available N was the most correlated with soil microbial functional gene structure.

CONCLUSIONS: Overall high microbial functional gene diversity and different soil microbial metabolic potential for different biogeochemical processes were considered to exist in tropical rainforest. Soil available N could be the key factor in shaping the soil microbial functional gene structure and metabolic potential.}, } @article {pmid26288277, year = {2015}, author = {Damman, CJ and Brittnacher, MJ and Westerhoff, M and Hayden, HS and Radey, M and Hager, KR and Marquis, SR and Miller, SI and Zisman, TL}, title = {Low Level Engraftment and Improvement following a Single Colonoscopic Administration of Fecal Microbiota to Patients with Ulcerative Colitis.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0133925}, pmid = {26288277}, issn = {1932-6203}, support = {P30 DK089507/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Colitis, Ulcerative/*microbiology/pathology/*therapy ; Colon/*microbiology/*pathology ; Colonoscopy/methods ; Feces/*microbiology ; Female ; Humans ; Male ; *Microbiota ; Middle Aged ; Prospective Studies ; Treatment Outcome ; }, abstract = {OBJECTIVE: Fecal microbiota transplantation (FMT) is an investigational treatment for diseases thought to involve alterations in the intestinal microbiota including ulcerative colitis (UC). Case reports have described therapeutic benefit of FMT in patients with UC, possibly due to changes in the microbiota. We measured the degree to which the transplanted microbiota engraft following FMT in patients with UC using a donor similarity index (DSI).

METHODS: Seven patients with mild to moderate UC (UC disease activity index scores 3-10) received a single colonoscopic administration of FMT. Metagenomic sequence data from stool were analyzed using an alignment-free comparison tool, to measure the DSI, and a phylogenetic analysis tool, to characterize taxonomic changes. Clinical, endoscopic, histologic, and fecal calprotectin outcome measures were also collected.

RESULTS: One of 5 patients from whom sequencing data were available achieved the primary endpoint of 50% donor similarity at week 4; an additional 2 patients achieved 40% donor similarity. One patient with 40% donor similarity achieved clinical and histologic remission 1 month after FMT. However, these were lost by 2-3 months, and loss correlated with a decrease in DSI. The remaining patients did not demonstrate clinical response or remission. Histology scores improved in all but 1 patient. No patients remained in remission at 3 months after FMT.

CONCLUSIONS: Following a single colonoscopic fecal transplant, a DSI of 40-50% is achieved in about two-thirds of recipients. This level of engraftment correlated with a temporary clinical improvement in only 1/5 patients. Larger sample sizes could further validate this method for measuring engraftment, and changes in transplant frequency or method might improve microbiota engraftment and efficacy.

TRIAL REGISTRATION: ClinicalTrials.gov NCT01742754.}, } @article {pmid26287723, year = {2016}, author = {Větrovský, T and Kolařík, M and Žifčáková, L and Zelenka, T and Baldrian, P}, title = {The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities.}, journal = {Molecular ecology resources}, volume = {16}, number = {2}, pages = {388-401}, doi = {10.1111/1755-0998.12456}, pmid = {26287723}, issn = {1755-0998}, mesh = {*Biota ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Forests ; Fungi/*classification/enzymology/*genetics ; *Genetic Variation ; Metagenomics/*methods ; Phylogeny ; Picea/growth & development ; Protein Subunits/genetics ; RNA Polymerase II/*genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Although the commonly used internal transcribed spacer region of rDNA (ITS) is well suited for taxonomic identification of fungi, the information on the relative abundance of taxa and diversity is negatively affected by the multicopy nature of rDNA and the existence of ITS paralogues. Moreover, due to high variability, ITS sequences cannot be used for phylogenetic analyses of unrelated taxa. The part of single-copy gene encoding the second largest subunit of RNA polymerase II (rpb2) was thus compared with first spacer of ITS as an alternative marker for the analysis of fungal communities in spruce forest topsoil, and their applicability was tested on a comprehensive mock community. In soil, rpb2 exhibited broad taxonomic coverage of the entire fungal tree of life including basal fungal lineages. The gene exhibited sufficient variation for the use in phylogenetic analyses and taxonomic assignments, although it amplifies also paralogues. The fungal taxon spectra obtained with rbp2 region and ITS1 corresponded, but sequence abundance differed widely, especially in the basal lineages. The proportions of OTU counts and read counts of major fungal groups were close to the reality when rpb2 was used as a molecular marker while they were strongly biased towards the Basidiomycota when using the ITS primers ITS1/ITS4. Although the taxonomic placement of rbp2 sequences is currently more difficult than that of the ITS sequences, its discriminative power, quantitative representation of community composition and suitability for phylogenetic analyses represent significant advantages.}, } @article {pmid26285202, year = {2015}, author = {Bowman, JS and Ducklow, HW}, title = {Microbial Communities Can Be Described by Metabolic Structure: A General Framework and Application to a Seasonally Variable, Depth-Stratified Microbial Community from the Coastal West Antarctic Peninsula.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0135868}, pmid = {26285202}, issn = {1932-6203}, mesh = {Antarctic Regions ; Archaea/*classification/genetics/*metabolism ; Bacteria/*classification/genetics/*metabolism ; Biodiversity ; Metabolic Networks and Pathways ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Seasons ; }, abstract = {Taxonomic marker gene studies, such as the 16S rRNA gene, have been used to successfully explore microbial diversity in a variety of marine, terrestrial, and host environments. For some of these environments long term sampling programs are beginning to build a historical record of microbial community structure. Although these 16S rRNA gene datasets do not intrinsically provide information on microbial metabolism or ecosystem function, this information can be developed by identifying metabolisms associated with related, phenotyped strains. Here we introduce the concept of metabolic inference; the systematic prediction of metabolism from phylogeny, and describe a complete pipeline for predicting the metabolic pathways likely to be found in a collection of 16S rRNA gene phylotypes. This framework includes a mechanism for assigning confidence to each metabolic inference that is based on a novel method for evaluating genomic plasticity. We applied this framework to 16S rRNA gene libraries from the West Antarctic Peninsula marine environment, including surface and deep summer samples and surface winter samples. Using statistical methods commonly applied to community ecology data we found that metabolic structure differed between summer surface and winter and deep samples, comparable to an analysis of community structure by 16S rRNA gene phylotypes. While taxonomic variance between samples was primarily driven by low abundance taxa, metabolic variance was attributable to both high and low abundance pathways. This suggests that clades with a high degree of functional redundancy can occupy distinct adjacent niches. Overall our findings demonstrate that inferred metabolism can be used in place of taxonomy to describe the structure of microbial communities. Coupling metabolic inference with targeted metagenomics and an improved collection of completed genomes could be a powerful way to analyze microbial communities in a high-throughput manner that provides direct access to metabolic and ecosystem function.}, } @article {pmid26284777, year = {2015}, author = {Bordenstein, SR and Theis, KR}, title = {Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes.}, journal = {PLoS biology}, volume = {13}, number = {8}, pages = {e1002226}, pmid = {26284777}, issn = {1545-7885}, support = {P30 DK058404/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Humans ; *Metagenome ; Microbiota/*genetics ; Mutation ; Plants/genetics ; Selection, Genetic ; Symbiosis/*genetics ; }, abstract = {Groundbreaking research on the universality and diversity of microorganisms is now challenging the life sciences to upgrade fundamental theories that once seemed untouchable. To fully appreciate the change that the field is now undergoing, one has to place the epochs and foundational principles of Darwin, Mendel, and the modern synthesis in light of the current advances that are enabling a new vision for the central importance of microbiology. Animals and plants are no longer heralded as autonomous entities but rather as biomolecular networks composed of the host plus its associated microbes, i.e., "holobionts." As such, their collective genomes forge a "hologenome," and models of animal and plant biology that do not account for these intergenomic associations are incomplete. Here, we integrate these concepts into historical and contemporary visions of biology and summarize a predictive and refutable framework for their evaluation. Specifically, we present ten principles that clarify and append what these concepts are and are not, explain how they both support and extend existing theory in the life sciences, and discuss their potential ramifications for the multifaceted approaches of zoology and botany. We anticipate that the conceptual and evidence-based foundation provided in this essay will serve as a roadmap for hypothesis-driven, experimentally validated research on holobionts and their hologenomes, thereby catalyzing the continued fusion of biology's subdisciplines. At a time when symbiotic microbes are recognized as fundamental to all aspects of animal and plant biology, the holobiont and hologenome concepts afford a holistic view of biological complexity that is consistent with the generally reductionist approaches of biology.}, } @article {pmid26283367, year = {2015}, author = {Cohen, LJ and Kang, HS and Chu, J and Huang, YH and Gordon, EA and Reddy, BV and Ternei, MA and Craig, JW and Brady, SF}, title = {Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {35}, pages = {E4825-34}, pmid = {26283367}, issn = {1091-6490}, support = {UL1 TR000043/TR/NCATS NIH HHS/United States ; GM077516/GM/NIGMS NIH HHS/United States ; T32GM07739/GM/NIGMS NIH HHS/United States ; T32 DK007792/DK/NIDDK NIH HHS/United States ; R01 GM077516/GM/NIGMS NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; T32 GM007739/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA/genetics ; Glycine/*analogs & derivatives/pharmacology ; HEK293 Cells ; Humans ; *Metagenomics ; *Microbiota ; Microscopy, Fluorescence ; Molecular Sequence Data ; Palmitates/*pharmacology ; Phylogeny ; Receptors, G-Protein-Coupled/*agonists ; }, abstract = {The trillions of bacteria that make up the human microbiome are believed to encode functions that are important to human health; however, little is known about the specific effectors that commensal bacteria use to interact with the human host. Functional metagenomics provides a systematic means of surveying commensal DNA for genes that encode effector functions. Here, we examine 3,000 Mb of metagenomic DNA cloned from three phenotypically distinct patients for effectors that activate NF-κB, a transcription factor known to play a central role in mediating responses to environmental stimuli. This screen led to the identification of 26 unique commensal bacteria effector genes (Cbegs) that are predicted to encode proteins with diverse catabolic, anabolic, and ligand-binding functions and most frequently interact with either glycans or lipids. Detailed analysis of one effector gene family (Cbeg12) recovered from all three patient libraries found that it encodes for the production of N-acyl-3-hydroxypalmitoyl-glycine (commendamide). This metabolite was also found in culture broth from the commensal bacterium Bacteroides vulgatus, which harbors a gene highly similar to Cbeg12. Commendamide resembles long-chain N-acyl-amides that function as mammalian signaling molecules through activation of G-protein-coupled receptors (GPCRs), which led us to the observation that commendamide activates the GPCR G2A/GPR132. G2A has been implicated in disease models of autoimmunity and atherosclerosis. This study shows the utility of functional metagenomics for identifying potential mechanisms used by commensal bacteria for host interactions and outlines a functional metagenomics-based pipeline for the systematic identification of diverse commensal bacteria effectors that impact host cellular functions.}, } @article {pmid26283343, year = {2015}, author = {Leff, JW and Jones, SE and Prober, SM and Barberán, A and Borer, ET and Firn, JL and Harpole, WS and Hobbie, SE and Hofmockel, KS and Knops, JM and McCulley, RL and La Pierre, K and Risch, AC and Seabloom, EW and Schütz, M and Steenbock, C and Stevens, CJ and Fierer, N}, title = {Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {35}, pages = {10967-10972}, pmid = {26283343}, issn = {1091-6490}, mesh = {Archaea/physiology ; Bacterial Physiological Phenomena ; *Ecosystem ; Fungi/physiology ; Nitrogen/metabolism ; Phosphorus/metabolism ; Poaceae/*physiology ; *Soil Microbiology ; }, abstract = {Soil microorganisms are critical to ecosystem functioning and the maintenance of soil fertility. However, despite global increases in the inputs of nitrogen (N) and phosphorus (P) to ecosystems due to human activities, we lack a predictive understanding of how microbial communities respond to elevated nutrient inputs across environmental gradients. Here we used high-throughput sequencing of marker genes to elucidate the responses of soil fungal, archaeal, and bacterial communities using an N and P addition experiment replicated at 25 globally distributed grassland sites. We also sequenced metagenomes from a subset of the sites to determine how the functional attributes of bacterial communities change in response to elevated nutrients. Despite strong compositional differences across sites, microbial communities shifted in a consistent manner with N or P additions, and the magnitude of these shifts was related to the magnitude of plant community responses to nutrient inputs. Mycorrhizal fungi and methanogenic archaea decreased in relative abundance with nutrient additions, as did the relative abundances of oligotrophic bacterial taxa. The metagenomic data provided additional evidence for this shift in bacterial life history strategies because nutrient additions decreased the average genome sizes of the bacterial community members and elicited changes in the relative abundances of representative functional genes. Our results suggest that elevated N and P inputs lead to predictable shifts in the taxonomic and functional traits of soil microbial communities, including increases in the relative abundances of faster-growing, copiotrophic bacterial taxa, with these shifts likely to impact belowground ecosystems worldwide.}, } @article {pmid26280746, year = {2016}, author = {Tu, Q and Zhou, X and He, Z and Xue, K and Wu, L and Reich, P and Hobbie, S and Zhou, J}, title = {The Diversity and Co-occurrence Patterns of N2-Fixing Communities in a CO2-Enriched Grassland Ecosystem.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {604-615}, pmid = {26280746}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; *Biodiversity ; Carbon Dioxide/*metabolism ; Ecosystem ; Grassland ; Nitrogen/*metabolism ; Nitrogen Fixation ; Phylogeny ; *Soil Microbiology ; }, abstract = {Diazotrophs are the major organismal group responsible for atmospheric nitrogen (N2) fixation in natural ecosystems. The extensive diversity and structure of N2-fixing communities in grassland ecosystems and their responses to increasing atmospheric CO2 remain to be further explored. Through pyrosequencing of nifH gene amplicons and extraction of nifH genes from shotgun metagenomes, coupled with co-occurrence ecological network analysis approaches, we comprehensively analyzed the diazotrophic community in a grassland ecosystem exposed to elevated CO2 (eCO2) for 12 years. Long-term eCO2 increased the abundance of nifH genes but did not change the overall nifH diversity and diazotrophic community structure. Taxonomic and phylogenetic analysis of amplified nifH sequences suggested a high diversity of nifH genes in the soil ecosystem, the majority belonging to nifH clusters I and II. Co-occurrence ecological network analysis identified different co-occurrence patterns for different groups of diazotrophs, such as Azospirillum/Actinobacteria, Mesorhizobium/Conexibacter, and Bradyrhizobium/Acidobacteria. This indicated a potential attraction of non-N2-fixers by diazotrophs in the soil ecosystem. Interestingly, more complex co-occurrence patterns were found for free-living diazotrophs than commonly known symbiotic diazotrophs, which is consistent with the physical isolation nature of symbiotic diazotrophs from the environment by root nodules. The study provides novel insights into our understanding of the microbial ecology of soil diazotrophs in natural ecosystems.}, } @article {pmid26278534, year = {2015}, author = {Kunkel, SA and Pagilla, KR and Stark, BC}, title = {Directed evolution to produce sludge communities with improved oxygen uptake abilities.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {24}, pages = {10725-10734}, doi = {10.1007/s00253-015-6891-8}, pmid = {26278534}, issn = {1432-0614}, mesh = {Aerobiosis ; *Biological Evolution ; *Biota ; Hemoglobins/genetics ; Metagenome ; Oxygen/*metabolism ; Sewage/*microbiology ; }, abstract = {Two activated sludge cultures, seeded with activated sludge from the same source, were cultivated for 370 days in synthetic wastewater. Both cultures were transferred weekly to fresh medium; one culture was operated at high dissolved oxygen (DO) (near saturation) and the other at low DO (0.25 mg O2/L). There were significant changes in the abundances of bacterial species and phyla present in each culture throughout the 370-day operational period. In the low DO culture, over time, there was a continuously increasing proportion of cells of species known to encode truncated hemoglobins (Hbs). These are the types of Hbs which may enhance delivery of oxygen to the respiratory chain, to enhance ATP production, especially under low aeration conditions. The levels of heme b, the heme found in Vitreoscilla hemoglobin, increased in parallel to the increase in Hb-encoding species, to much higher levels in the low DO culture than in the high DO culture. Specific oxygen uptake rates increased by 3 % for the high DO culture near the end of the 370-day period, while those for the low DO culture increased steadily to a level 28 % higher than that of the starting culture. Thus, imposition of low DO conditions may, due to selection for Hb-expressing species, be useful in developing bacterial communities with enhanced ability to function efficiently in aerobic wastewater treatment, especially under low aeration conditions.}, } @article {pmid26277095, year = {2015}, author = {Castro-Nallar, E and Shen, Y and Freishtat, RJ and Pérez-Losada, M and Manimaran, S and Liu, G and Johnson, WE and Crandall, KA}, title = {Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities.}, journal = {BMC medical genomics}, volume = {8}, number = {}, pages = {50}, pmid = {26277095}, issn = {1755-8794}, support = {K12 HL119994/HL/NHLBI NIH HHS/United States ; R01 MD007075/MD/NIMHD NIH HHS/United States ; 5 K12 HL119994/HL/NHLBI NIH HHS/United States ; }, mesh = {Adolescent ; Asthma/*genetics/immunology/*microbiology/virology ; Child ; Female ; *Gene Expression Profiling ; Host-Pathogen Interactions/*genetics ; Humans ; Male ; Metagenomics ; Microbiota/*genetics ; Sequence Analysis, RNA ; Young Adult ; }, abstract = {BACKGROUND: The relationships between infections in early life and asthma are not completely understood. Likewise, the clinical relevance of microbial communities present in the respiratory tract is only partially known. A number of microbiome studies analyzing respiratory tract samples have found increased proportions of gamma-Proteobacteria including Haemophilus influenzae, Moraxella catarrhalis, and Firmicutes such as Streptococcus pneumoniae. The aim of this study was to present a new approach that combines RNA microbial identification with host gene expression to characterize and validate metagenomic taxonomic profiling in individuals with asthma.

METHODS: Using whole metagenomic shotgun RNA sequencing, we characterized and compared the microbial communities of individuals, children and adolescents, with asthma and controls. The resulting data were analyzed by partitioning human and microbial reads. Microbial reads were then used to characterize the microbial diversity of each patient, and potential differences between asthmatic and healthy groups. Human reads were used to assess the expression of known genes involved in the host immune response to specific pathogens and detect potential differences between those with asthma and controls.

RESULTS: Microbial communities in the nasal cavities of children differed significantly between asthmatics and controls. After read count normalization, some bacterial species were significantly overrepresented in asthma patients (Wald test, p-value < 0.05), including Escherichia coli and Psychrobacter. Among these, Moraxella catarrhalis exhibited ~14-fold over abundance in asthmatics versus controls. Differential host gene expression analysis confirms that the presence of Moraxella catarrhalis is associated to a specific M. catarrhalis core gene signature expressed by the host.

CONCLUSIONS: For the first time, we show the power of combining RNA taxonomic profiling and host gene expression signatures for microbial identification. Our approach not only identifies microbes from metagenomic data, but also adds support to these inferences by determining if the host is mounting a response against specific infectious agents. In particular, we show that M. catarrhalis is abundant in asthma patients but not in controls, and that its presence is associated with a specific host gene expression signature.}, } @article {pmid26276111, year = {2015}, author = {Steven, B and Kuske, CR and Gallegos-Graves, LV and Reed, SC and Belnap, J}, title = {Climate change and physical disturbance manipulations result in distinct biological soil crust communities.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {21}, pages = {7448-7459}, pmid = {26276111}, issn = {1098-5336}, mesh = {Biomass ; *Biota ; *Climate Change ; *Hydrostatic Pressure ; Rain ; *Soil Microbiology ; Temperature ; }, abstract = {Biological soil crusts (biocrusts) colonize plant interspaces in many drylands and are critical to soil nutrient cycling. Multiple climate change and land use factors have been shown to detrimentally impact biocrusts on a macroscopic (i.e., visual) scale. However, the impact of these perturbations on the bacterial components of the biocrusts remains poorly understood. We employed multiple long-term field experiments to assess the impacts of chronic physical (foot trampling) and climatic changes (2°C soil warming, altered summer precipitation [wetting], and combined warming and wetting) on biocrust bacterial biomass, composition, and metabolic profile. The biocrust bacterial communities adopted distinct states based on the mechanism of disturbance. Chronic trampling decreased biomass and caused small community compositional changes. Soil warming had little effect on biocrust biomass or composition, while wetting resulted in an increase in the cyanobacterial biomass and altered bacterial composition. Warming combined with wetting dramatically altered bacterial composition and decreased Cyanobacteria abundance. Shotgun metagenomic sequencing identified four functional gene categories that differed in relative abundance among the manipulations, suggesting that climate and land use changes affected soil bacterial functional potential. This study illustrates that different types of biocrust disturbance damage biocrusts in macroscopically similar ways, but they differentially impact the resident soil bacterial communities, and the communities' functional profiles can differ depending on the disturbance type. Therefore, the nature of the perturbation and the microbial response are important considerations for management and restoration of drylands.}, } @article {pmid26276109, year = {2015}, author = {Kittelmann, S and Kirk, MR and Jonker, A and McCulloch, A and Janssen, PH}, title = {Buccal swabbing as a noninvasive method to determine bacterial, archaeal, and eukaryotic microbial community structures in the rumen.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {21}, pages = {7470-7483}, pmid = {26276109}, issn = {1098-5336}, mesh = {Animals ; Archaea/classification/*isolation & purification ; Bacteria/classification/*isolation & purification ; *Biota ; Eukaryota/classification/*isolation & purification ; Molecular Sequence Data ; Mouth Mucosa/*microbiology ; Rumen/*microbiology ; Sequence Analysis, DNA ; Sheep ; }, abstract = {Analysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (R = 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (R = 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants.}, } @article {pmid26274050, year = {2016}, author = {Brown, K and Godovannyi, A and Ma, C and Zhang, Y and Ahmadi-Vand, Z and Dai, C and Gorzelak, MA and Chan, Y and Chan, JM and Lochner, A and Dutz, JP and Vallance, BA and Gibson, DL}, title = {Prolonged antibiotic treatment induces a diabetogenic intestinal microbiome that accelerates diabetes in NOD mice.}, journal = {The ISME journal}, volume = {10}, number = {2}, pages = {321-332}, pmid = {26274050}, issn = {1751-7370}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Anti-Bacterial Agents/adverse effects/*therapeutic use ; Diabetes Mellitus, Type 1/drug therapy/immunology/*microbiology ; Disease Progression ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestines/drug effects/immunology/*microbiology ; Male ; Mice ; Mice, Inbred NOD ; Th17 Cells/drug effects/immunology ; }, abstract = {Accumulating evidence supports that the intestinal microbiome is involved in Type 1 diabetes (T1D) pathogenesis through the gut-pancreas nexus. Our aim was to determine whether the intestinal microbiota in the non-obese diabetic (NOD) mouse model played a role in T1D through the gut. To examine the effect of the intestinal microbiota on T1D onset, we manipulated gut microbes by: (1) the fecal transplantation between non-obese diabetic (NOD) and resistant (NOR) mice and (2) the oral antibiotic and probiotic treatment of NOD mice. We monitored diabetes onset, quantified CD4+T cells in the Peyer's patches, profiled the microbiome and measured fecal short-chain fatty acids (SCFA). The gut microbiota from NOD mice harbored more pathobionts and fewer beneficial microbes in comparison with NOR mice. Fecal transplantation of NOD microbes induced insulitis in NOR hosts suggesting that the NOD microbiome is diabetogenic. Moreover, antibiotic exposure accelerated diabetes onset in NOD mice accompanied by increased T-helper type 1 (Th1) and reduced Th17 cells in the intestinal lymphoid tissues. The diabetogenic microbiome was characterized by a metagenome altered in several metabolic gene clusters. Furthermore, diabetes susceptibility correlated with reduced fecal SCFAs. In an attempt to correct the diabetogenic microbiome, we administered VLS#3 probiotics to NOD mice but found that VSL#3 colonized the intestine poorly and did not delay diabetes. We conclude that NOD mice harbor gut microbes that induce diabetes and that their diabetogenic microbiome can be amplified early in life through antibiotic exposure. Protective microbes like VSL#3 are insufficient to overcome the effects of a diabetogenic microbiome.}, } @article {pmid26274026, year = {2015}, author = {Falony, G and Vieira-Silva, S and Raes, J}, title = {Microbiology Meets Big Data: The Case of Gut Microbiota-Derived Trimethylamine.}, journal = {Annual review of microbiology}, volume = {69}, number = {}, pages = {305-321}, doi = {10.1146/annurev-micro-091014-104422}, pmid = {26274026}, issn = {1545-3251}, mesh = {Animals ; Atherosclerosis/*metabolism/pathology ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; *Metagenomics ; Methylamines/*metabolism ; }, abstract = {During the past decade, meta-omics approaches have revolutionized microbiology, allowing for a cultivation-free assessment of the composition and functional properties of entire microbial ecosystems. On the one hand, a phylogenetic and functional interpretation of such data relies on accumulated genetic, biochemical, metabolic, and phenotypic characterization of microbial variation. On the other hand, the increasing availability of extensive microbiome data sets and corresponding metadata provides a vast, underused resource for the microbiology field as a whole. To demonstrate the potential for integrating big data into a functional microbiology workflow, we review literature on trimethylamine (TMA), a microbiota-generated metabolite linked to atherosclerosis development. Translating recently elucidated microbial pathways resulting in TMA production into genomic orthologs, we demonstrate how to mine for their presence in public (meta-) genomic databases and link findings to associated metadata. Reviewing pathway abundance in public data sets shows that TMA production potential is associated with symptomatic atherosclerosis and allows identification of currently uncharacterized TMA-producing bacteria.}, } @article {pmid26273600, year = {2015}, author = {Merlino, G and Balloi, A and Marzorati, M and Mapelli, F and Rizzi, A and Lavazza, D and de Ferra, F and Carpani, G and Daffonchio, D}, title = {Diverse Reductive Dehalogenases Are Associated with Clostridiales-Enriched Microcosms Dechlorinating 1,2-Dichloroethane.}, journal = {BioMed research international}, volume = {2015}, number = {}, pages = {242856}, pmid = {26273600}, issn = {2314-6141}, mesh = {Biodegradation, Environmental ; Chlorine/chemistry/isolation & purification/metabolism ; Clostridiales/*classification/*enzymology/genetics ; Ethylene Dichlorides/chemistry/isolation & purification/*metabolism ; Groundwater/*microbiology ; Halogenation ; Hydrolases/*metabolism ; Microbiota/physiology ; Oxidation-Reduction ; Species Specificity ; Water Pollutants, Chemical/isolation & purification/*metabolism ; Water Purification/methods ; }, abstract = {The achievement of successful biostimulation of active microbiomes for the cleanup of a polluted site is strictly dependent on the knowledge of the key microorganisms equipped with the relevant catabolic genes responsible for the degradation process. In this work, we present the characterization of the bacterial community developed in anaerobic microcosms after biostimulation with the electron donor lactate of groundwater polluted with 1,2-dichloroethane (1,2-DCA). Through a multilevel analysis, we have assessed (i) the structural analysis of the bacterial community; (ii) the identification of putative dehalorespiring bacteria; (iii) the characterization of functional genes encoding for putative 1,2-DCA reductive dehalogenases (RDs). Following the biostimulation treatment, the structure of the bacterial community underwent a notable change of the main phylotypes, with the enrichment of representatives of the order Clostridiales. Through PCR targeting conserved regions within known RD genes, four novel variants of RDs previously associated with the reductive dechlorination of 1,2-DCA were identified in the metagenome of the Clostridiales-dominated bacterial community.}, } @article {pmid26269741, year = {2015}, author = {Flores, R and Shi, J and Yu, G and Ma, B and Ravel, J and Goedert, JJ and Sinha, R}, title = {Collection media and delayed freezing effects on microbial composition of human stool.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {33}, pmid = {26269741}, issn = {2049-2618}, support = {//Intramural NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics ; Biodiversity ; Feces/*microbiology ; Female ; Freezing ; Humans ; Male ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Specimen Handling/methods ; }, abstract = {BACKGROUND: Different bacteria in stool have markedly varied growth and survival when stored at ambient temperature. It is paramount to develop optimal biostabilization of stool samples during collection and assess long-term storage for clinical specimens and epidemiological microbiome studies. We evaluated the effect of collection media and delayed freezing up to 7 days on microbial composition. Ten participants collected triplicate stool samples each into no media as well as RNAlater® with and without kanamycin or ciprofloxacin. For each set of conditions, triplicate samples were frozen on dry ice immediately (time = 0) or frozen at -80 °C after 3-days and 7-days incubation at 25 °C. Microbiota metrics were estimated from Illumina MiSeq sequences of 16S rRNA gene fragments (V3-V4 region). Intraclass correlation coefficients (ICC) across triplicates, collection media, and incubation time were estimated for taxonomy and alpha and beta diversity metrics.

RESULTS: RNAlater® alone yielded the highest ICCs for diversity metrics at time = 0 [ICC median 0.935 (range 0.89-0.97)], but ICCs varied greatly (range 0.44-1.0) for taxa with relative abundances <1%. The 3- and 7-day freezing delays were generally associated with stable beta diversity for all three media conditions. Freezing delay caused increased variance for Shannon index (median ICC 0.77) and especially for observed species abundance (median ICC 0.47). Variance in observed species abundance and in phylogenetic distance whole tree was similarly increased with a 7-day delay. Antibiotics did not mitigate variance. No media had inferior ICCs at time 0 and differed markedly from any media in microbiome composition (e.g., P =0.01 for relative abundance of Bacteroidetes).

CONCLUSION: Bacterial community composition was stable for 7 days at room temperature in RNAlater® alone. RNAlater® provides some stability for beta diversity analyses, but analyses of rare taxa will be inaccurate if specimens are not frozen immediately. RNAlater® could be used as collection media with minimal change in the microbiota composition.}, } @article {pmid26268374, year = {2015}, author = {Sarno, M and Discepolo, V and Troncone, R and Auricchio, R}, title = {Risk factors for celiac disease.}, journal = {Italian journal of pediatrics}, volume = {41}, number = {}, pages = {57}, pmid = {26268374}, issn = {1824-7288}, mesh = {Celiac Disease/*etiology/immunology/*prevention & control ; Genetic Predisposition to Disease ; Humans ; Metagenome/immunology ; Microbiota/immunology ; Risk Factors ; }, abstract = {Celiac Disease (CD) is an immune-mediated systemic disorder elicited by gluten and related prolamines in genetically susceptible individuals and it is the result of the interaction between genetic and environmental factors. Among genetic risk factors, the strongest association is with the HLA class II DQ region; nevertheless at least 39 non-HLA loci are associated with CD. Gluten is the main environmental trigger of the disease. In addition, infant feeding and weaning practices as well as timing of gluten introduction in the diet have been suggested to contribute to CD risk. Furthermore a role for infectious agents and microbiota composition in disease development has also been proposed.Aim of this short review is to discuss the current knowledge on both genetic and environmental risk factors for the development of CD; moreover we will provide a brief overview of the possible strategies that could be envisaged to prevent this condition, at least in the population at-risk.}, } @article {pmid26264196, year = {2015}, author = {Kirschner, R and Hsu, T and Tuan, NN and Chen, CL and Huang, SL}, title = {Characterization of fungal and bacterial components in gut/fecal microbiome.}, journal = {Current drug metabolism}, volume = {16}, number = {4}, pages = {272-283}, doi = {10.2174/1389200216666150812124625}, pmid = {26264196}, issn = {1875-5453}, mesh = {Animals ; Archaea ; Bacteria ; Feces/*microbiology ; Fungi ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; }, abstract = {The gut microbiota is a complex ecosystem that affects the development, nutritional status and immunological responses of the host. Prokaryotes and fungi in the community have the abilities to withstand the adverse conditions of high temperature, low oxygen etc. and to decompose complex organic molecules. The novel approaches of metagenomics and metaproteomics provide data that allow the detection of patterns of constancy or changes in time or under different conditions, such as different diets, disease condition and antibiotic therapy. These large-scale patterns can be correlated with certain health or disease conditions. From the organismic point of view, however, the species identity of the organisms and their interactions in the gut and how these interactions influence the prevention or development of disease are poorly known. The diversity and roles of fungi in animal feces appear to be better known than in human gut/feces. A combined compilation of the diverse methods applied towards prokaryotes and fungi in the gut/feces microbiome serves as a base for meeting the challenges of masses of large-scale datasets on the one hand and lack of substantial organismic understanding on the other. Starting from long-term monitoring and large-scale characterization of the composition of microbiome from systematic higher groups down to the genus level, microbial genomes and proteomes, particular key components with antimicrobial or immune functions can be selected and investigated in detail with respect to understanding of host-microbiota interaction, disease pathogenesis and developing diagnostic and therapeutic tools.}, } @article {pmid26264139, year = {2015}, author = {Leyva-Díaz, JC and González-Martínez, A and Muñío, MM and Poyatos, JM}, title = {Two-step nitrification in a pure moving bed biofilm reactor-membrane bioreactor for wastewater treatment: nitrifying and denitrifying microbial populations and kinetic modeling.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {23}, pages = {10333-10343}, doi = {10.1007/s00253-015-6894-5}, pmid = {26264139}, issn = {1432-0614}, mesh = {Ammonium Compounds/metabolism ; Bacteria/classification/*metabolism ; Biofilms/*growth & development ; Bioreactors/*microbiology ; *Biota ; Membranes/*microbiology ; Metagenomics ; *Nitrification ; Nitrites/metabolism ; Oxidation-Reduction ; Wastewater/*microbiology ; Water Purification ; }, abstract = {The moving bed biofilm reactor-membrane bioreactor (MBBR-MBR) is a novel solution to conventional activated sludge processes and membrane bioreactors. In this study, a pure MBBR-MBR was studied. The pure MBBR-MBR mainly had attached biomass. The bioreactor operated with a hydraulic retention time (HRT) of 9.5 h. The kinetic parameters for heterotrophic and autotrophic biomasses, mainly nitrite-oxidizing bacteria (NOB), were evaluated. The analysis of the bacterial community structure of the ammonium-oxidizing bacteria (AOB), NOB, and denitrifying bacteria (DeNB) from the pure MBBR-MBR was carried out by means of pyrosequencing to detect and quantify the contribution of the nitrifying and denitrifying bacteria in the total bacterial community. The relative abundance of AOB, NOB, and DeNB were 5, 1, and 3%, respectively, in the mixed liquor suspended solids (MLSS), and these percentages were 18, 5, and 2%, respectively, in the biofilm density (BD) attached to carriers. The pure MBBR-MBR had a high efficiency of total nitrogen (TN) removal of 71.81±16.04%, which could reside in the different bacterial assemblages in the fixed biofilm on the carriers. In this regard, the kinetic parameters for autotrophic biomass had values of YA=2.3465 mg O2 mg N(-1), μm, A=0.7169 h(-1), and KNH=2.0748 mg NL(-1).}, } @article {pmid26264042, year = {2015}, author = {Jarvis, KG and White, JR and Grim, CJ and Ewing, L and Ottesen, AR and Beaubrun, JJ and Pettengill, JB and Brown, E and Hanes, DE}, title = {Cilantro microbiome before and after nonselective pre-enrichment for Salmonella using 16S rRNA and metagenomic sequencing.}, journal = {BMC microbiology}, volume = {15}, number = {}, pages = {160}, pmid = {26264042}, issn = {1471-2180}, mesh = {Cluster Analysis ; Coriandrum/*microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Microbiological Techniques ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salmonella enterica/genetics/*isolation & purification ; Sequence Analysis, DNA ; United States ; }, abstract = {BACKGROUND: Salmonella enterica is a common cause of foodborne gastroenteritis in the United States and is associated with outbreaks in fresh produce such as cilantro. Salmonella culture-based detection methods are complex and time consuming, and improvments to increase detection sensitivity will benefit consumers. In this study, we used 16S rRNA sequencing to determine the microbiome of cilantro. We also investigated changes to the microbial community prior to and after a 24-hour nonselective pre-enrichment culture step commonly used by laboratory analysts to resuscitate microorganisms in foods suspected of contamination with pathogens. Cilantro samples were processed for Salmonella detection according to the method in the United States Food and Drug Administration Bacteriological Analytical Manual. Genomic DNA was extracted from culture supernatants prior to and after a 24-hour nonselective pre-enrichment step and 454 pyrosequencing was performed on 16S rRNA amplicon libraries. A database of Enterobacteriaceae 16S rRNA sequences was created, and used to screen the libraries for Salmonella, as some samples were known to be culture positive. Additionally, culture positive cilantro samples were examined for the presence of Salmonella using shotgun metagenomics on the Illumina MiSeq.

RESULTS: Time zero uncultured samples had an abundance of Proteobacteria while the 24-hour enriched samples were composed mostly of Gram-positive Firmicutes. Shotgun metagenomic sequencing of Salmonella culture positive cilantro samples revealed variable degrees of Salmonella contamination among the sequenced samples.

CONCLUSIONS: Our cilantro study demonstrates the use of high-throughput sequencing to reveal the microbiome of cilantro, and how the microbiome changes during the culture-based protocols employed by food safety laboratories to detect foodborne pathogens. Finding that culturing the cilantro shifts the microbiome to a predominance of Firmicutes suggests that changing our culture-based methods will improve detection sensitivity for foodborne enteric pathogens.}, } @article {pmid26260905, year = {2015}, author = {Leary, DH and Hervey, WJ and Malanoski, AP and Wang, Z and Eddie, BJ and Tender, GS and Vora, GJ and Tender, LM and Lin, B and Strycharz-Glaven, SM}, title = {Metaproteomic evidence of changes in protein expression following a change in electrode potential in a robust biocathode microbiome.}, journal = {Proteomics}, volume = {15}, number = {20}, pages = {3486-3496}, doi = {10.1002/pmic.201400585}, pmid = {26260905}, issn = {1615-9861}, mesh = {Biofilms/growth & development ; Bioreactors ; Marinobacter/genetics ; Microbiota/*genetics ; Protein Biosynthesis/*genetics ; *Proteomics ; RNA, Ribosomal, 16S/*genetics ; Transcriptome ; }, abstract = {Microorganisms that respire electrodes may be exploited for biotechnology applications if key pathways for extracellular electron transfer can be identified and manipulated through bioengineering. To determine whether expression of proposed Biocathode-MCL extracellular electron transfer proteins are changed by modulating electrode potential without disrupting the relative distribution of microbial constituents, metaproteomic and 16S rRNA gene expression analyses were performed after switching from an optimal to suboptimal potential based on an expected decrease in electrode respiration. Five hundred and seventy-nine unique proteins were identified across both potentials, the majority of which were assigned to three previously defined Biocathode-MCL metagenomic clusters: a Marinobacter sp., a member of the family Chromatiaceae, and a Labrenzia sp (abbreviated as MCL). Statistical analysis of spectral counts using the Fisher's exact test identified 16 proteins associated with the optimal potential, five of which are predicted electron transfer proteins. The majority of proteins associated with the suboptimal potential were involved in protein turnover/synthesis, motility, and membrane transport. Unipept and 16S rRNA gene expression analyses indicated that the taxonomic profile of the microbiome did not change after 52 h at the suboptimal potential. These findings show that protein expression is sensitive to the electrode potential without inducing shifts in community composition, a feature that may be exploited for engineering Biocathode-MCL. All MS data have been deposited in the ProteomeXchange with identifier PXD001590 (http://proteomecentral.proteomexchange.org/dataset/PXD001590).}, } @article {pmid26259788, year = {2015}, author = {Bengtsson-Palme, J and Angelin, M and Huss, M and Kjellqvist, S and Kristiansson, E and Palmgren, H and Larsson, DG and Johansson, A}, title = {The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents.}, journal = {Antimicrobial agents and chemotherapy}, volume = {59}, number = {10}, pages = {6551-6560}, pmid = {26259788}, issn = {1098-6596}, mesh = {Adult ; Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Microbial/*genetics ; Escherichia coli/drug effects ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metagenomics ; Microbial Sensitivity Tests ; Proteobacteria/drug effects/genetics ; Sulfonamides/pharmacology ; Trimethoprim/pharmacology ; Young Adult ; beta-Lactams/pharmacology ; }, abstract = {Previous studies of antibiotic resistance dissemination by travel have, by targeting only a select number of cultivable bacterial species, omitted most of the human microbiome. Here, we used explorative shotgun metagenomic sequencing to address the abundance of >300 antibiotic resistance genes in fecal specimens from 35 Swedish students taken before and after exchange programs on the Indian peninsula or in Central Africa. All specimens were additionally cultured for extended-spectrum beta-lactamase (ESBL)-producing enterobacteria, and the isolates obtained were genome sequenced. The overall taxonomic diversity and composition of the gut microbiome remained stable before and after travel, but there was an increasing abundance of Proteobacteria in 25/35 students. The relative abundance of antibiotic resistance genes increased, most prominently for genes encoding resistance to sulfonamide (2.6-fold increase), trimethoprim (7.7-fold), and beta-lactams (2.6-fold). Importantly, the increase observed occurred without any antibiotic intake. Of 18 students visiting the Indian peninsula, 12 acquired ESBL-producing Escherichia coli, while none returning from Africa were positive. Despite deep sequencing efforts, the sensitivity of metagenomics was not sufficient to detect acquisition of the low-abundant genes responsible for the observed ESBL phenotype. In conclusion, metagenomic sequencing of the intestinal microbiome of Swedish students returning from exchange programs in Central Africa or the Indian peninsula showed increased abundance of genes encoding resistance to widely used antibiotics.}, } @article {pmid26258924, year = {2015}, author = {Vernocchi, P and Del Chierico, F and Fiocchi, AG and El Hachem, M and Dallapiccola, B and Rossi, P and Putignani, L}, title = {Understanding probiotics' role in allergic children: the clue of gut microbiota profiling.}, journal = {Current opinion in allergy and clinical immunology}, volume = {15}, number = {5}, pages = {495-503}, doi = {10.1097/ACI.0000000000000203}, pmid = {26258924}, issn = {1473-6322}, mesh = {Animals ; Child ; Gastrointestinal Microbiome/*immunology ; Gene Expression Profiling ; Host-Pathogen Interactions ; Humans ; Hypersensitivity/*diet therapy/microbiology ; Precision Medicine ; Probiotics/*therapeutic use ; Transcriptome ; }, abstract = {PURPOSE OF REVIEW: To investigate the functional role of gut microbiota in diet-modulated diseases, evaluating probiotic administration effects by systems biology-driven approaches. Understanding the role of host-gut microbial and gut microbe-microbe interactions in either allergic and healthy children may assist in selecting effective and targeted probiotics for personalized therapies.

RECENT FINDINGS: Food allergy shows a significant increase, especially in Western countries where growing epidemiological data indicate prevalence of small family groups, limited rate of infections in childhood compared with low-income countries, high consumption of sterile foods, hence stimulating a poor trigger of the gut immune system. Therefore, new therapeutic strategies to treat food allergy consist of probiotic administration since early life, thus modulating gut microbiota through immune system stimulation at the mucosal level.

SUMMARY: Currently, new insights for probiotic selection should take into consideration both phenotyping and genotyping bacterial features and host-microbial cross-talk at gut level, by employing multicomponent systems biology approaches to unveil gut ecosystem dynamics in terms of bacteria phylotypes and their metabolic activities. Moreover, new food processes need to be considered to assess the actual performance of probiotic strains administered to allergic patients. The advent of high-performance platforms employing genomic- and mass spectrometry-based techniques has opened new perspectives on the gut microbiota field, and may now serve as advanced tool to dynamically investigate the interplay between probiotics and gut microbiota ecology under allergic conditions.}, } @article {pmid26257129, year = {2015}, author = {Scarpellini, E and Ianiro, G and Attili, F and Bassanelli, C and De Santis, A and Gasbarrini, A}, title = {The human gut microbiota and virome: Potential therapeutic implications.}, journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver}, volume = {47}, number = {12}, pages = {1007-1012}, pmid = {26257129}, issn = {1878-3562}, mesh = {Bacteriophages/isolation & purification ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/*virology ; *Genome, Viral ; Humans ; Viruses/classification/*isolation & purification ; }, abstract = {Human gut microbiota is a complex ecosystem with several functions integrated in the host organism (metabolic, immune, nutrients absorption, etc.). Human microbiota is composed by bacteria, yeasts, fungi and, last but not least, viruses, whose composition has not been completely described. According to previous evidence on pathogenic viruses, the human gut harbours plant-derived viruses, giant viruses and, only recently, abundant bacteriophages. New metagenomic methods have allowed to reconstitute entire viral genomes from the genetic material spread in the human gut, opening new perspectives on the understanding of the gut virome composition, the importance of gut microbiome, and potential clinical applications. This review reports the latest evidence on human gut "virome" composition and its function, possible future therapeutic applications in human health in the context of the gut microbiota, and attempts to clarify the role of the gut "virome" in the larger microbial ecosystem.}, } @article {pmid26254872, year = {2015}, author = {Garza, DR and Dutilh, BE}, title = {From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {72}, number = {22}, pages = {4287-4308}, pmid = {26254872}, issn = {1420-9071}, mesh = {Computer Simulation ; Ecosystem ; Genome, Microbial/*genetics ; Genome, Viral/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; Microbial Consortia/genetics ; Microbiological Techniques/*methods ; Models, Theoretical ; Viruses/genetics ; }, abstract = {Microorganisms and the viruses that infect them are the most numerous biological entities on Earth and enclose its greatest biodiversity and genetic reservoir. With strength in their numbers, these microscopic organisms are major players in the cycles of energy and matter that sustain all life. Scientists have only scratched the surface of this vast microbial world through culture-dependent methods. Recent developments in generating metagenomes, large random samples of nucleic acid sequences isolated directly from the environment, are providing comprehensive portraits of the composition, structure, and functioning of microbial communities. Moreover, advances in metagenomic analysis have created the possibility of obtaining complete or nearly complete genome sequences from uncultured microorganisms, providing important means to study their biology, ecology, and evolution. Here we review some of the recent developments in the field of metagenomics, focusing on the discovery of genetic novelty and on methods for obtaining uncultured genome sequences, including through the recycling of previously published datasets. Moreover we discuss how metagenomics has become a core scientific tool to characterize eco-evolutionary patterns of microbial ecosystems, thus allowing us to simultaneously discover new microbes and study their natural communities. We conclude by discussing general guidelines and challenges for modeling the interactions between uncultured microorganisms and viruses based on the information contained in their genome sequences. These models will significantly advance our understanding of the functioning of microbial ecosystems and the roles of microbes in the environment.}, } @article {pmid26252189, year = {2015}, author = {Li, B and Ju, F and Cai, L and Zhang, T}, title = {Profile and Fate of Bacterial Pathogens in Sewage Treatment Plants Revealed by High-Throughput Metagenomic Approach.}, journal = {Environmental science & technology}, volume = {49}, number = {17}, pages = {10492-10502}, doi = {10.1021/acs.est.5b02345}, pmid = {26252189}, issn = {1520-5851}, mesh = {Anaerobiosis ; Bacteria/*genetics ; Biodiversity ; Biofilms ; Cluster Analysis ; High-Throughput Nucleotide Sequencing/*methods ; Hong Kong ; Metagenomics/*methods ; Principal Component Analysis ; Sewage/*microbiology ; Species Specificity ; Waste Disposal, Fluid ; *Water Purification ; }, abstract = {The broad-spectrum profile of bacterial pathogens and their fate in sewage treatment plants (STPs) were investigated using high-throughput sequencing based metagenomic approach. This novel approach could provide a united platform to standardize bacterial pathogen detection and realize direct comparison among different samples. Totally, 113 bacterial pathogen species were detected in eight samples including influent, effluent, activated sludge (AS), biofilm, and anaerobic digestion sludge with the abundances ranging from 0.000095% to 4.89%. Among these 113 bacterial pathogens, 79 species were reported in STPs for the first time. Specially, compared to AS in bulk mixed liquor, more pathogen species and higher total abundance were detected in upper foaming layer of AS. This suggests that the foaming layer of AS might impose more threat to onsite workers and citizens in the surrounding areas of STPs because pathogens in foaming layer are easily transferred into air and cause possible infections. The high removal efficiency (98.0%) of total bacterial pathogens suggests that AS treatment process is effective to remove most bacterial pathogens. Remarkable similarities of bacterial pathogen compositions between influent and human gut indicated that bacterial pathogen profiles in influents could well reflect the average bacterial pathogen communities of urban resident guts within the STP catchment area.}, } @article {pmid26251177, year = {2016}, author = {Ferguson, LR and Laing, B and Marlow, G and Bishop, K}, title = {The role of vitamin D in reducing gastrointestinal disease risk and assessment of individual dietary intake needs: Focus on genetic and genomic technologies.}, journal = {Molecular nutrition & food research}, volume = {60}, number = {1}, pages = {119-133}, doi = {10.1002/mnfr.201500243}, pmid = {26251177}, issn = {1613-4133}, mesh = {Cost-Benefit Analysis ; Diet ; Dietary Supplements ; *Food, Fortified ; Gastrointestinal Diseases/blood/complications/*prevention & control ; Gastrointestinal Microbiome/drug effects ; Gastrointestinal Tract/drug effects/metabolism/microbiology ; Genomics ; Humans ; Nutrition Assessment ; Nutritional Requirements ; Randomized Controlled Trials as Topic ; Risk Factors ; Vitamin D/*administration & dosage/blood ; Vitamin D Deficiency/blood/complications/drug therapy ; }, abstract = {With the endogenous formation of vitamin D being significantly curtailed because of public awareness of skin cancer dangers, attention is turning to dietary sources. Cumulative evidence has implicated vitamin D deficiency in increasing susceptibility to various gastrointestinal disorders, including colorectal cancer, inflammatory bowel diseases, diverticulitis, and irritable bowel syndrome. There is also reason to suggest adjunct vitamin D therapy for such diseases. Although there is justification for increasing vitamin D intake overall, optimal intakes will vary among individuals. Genomic technologies have revealed several hundreds of genes associated with vitamin D actions. The nature of these genes emphasizes the potentially negative implications of modulating vitamin D intakes in the absence of complementary human genetic and genomic data, including information on the gut microbiome. However, we are not yet in a position to apply this information. Genomic data (transcriptomics, metabolomics, proteomics, and metagenomics) could provide evidence that vitamin D sufficiency has been achieved. We suggest that there is an increasingly strong case for considering the more widespread use of vitamin D fortified foods and/or dietary supplements to benefit gastrointestinal health. However, intake levels might beneficially be informed by personalized genetic and genomic information, for optimal disease prevention and maintenance of remission.}, } @article {pmid26242906, year = {2015}, author = {Fang, L and Chen, L and Liu, Y and Tao, W and Zhang, Z and Liu, H and Tang, Y}, title = {Planktonic and sedimentary bacterial diversity of Lake Sayram in summer.}, journal = {MicrobiologyOpen}, volume = {4}, number = {5}, pages = {814-825}, pmid = {26242906}, issn = {2045-8827}, mesh = {Bacteria/*classification/*genetics ; *Biota ; China ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Lake Sayram is an ancient cold water lake locating at a mountain basin in Xinjiang, China. The lake water is brackish, alkaline, unpolluted, and abundant in SO4(2-) and Mg(2+). The lacustrine ecosystem of Lake Sayram has been intensely investigated. However, profiles of the microbial communities in the lake remain largely unknown. In this study, taxonomic compositions of the planktonic and sedimentary bacterial communities in Lake Sayram were investigated using 16S rRNA metagenomics. The lacustrine bacterial communities were generally structured by environmental conditions, including the hydrological and physicochemical parameters. Proteobacteria was the dominating phylum. In the lake water, the genera Acinetobacter and Ilumatobacter held an absolute predominance, implying their metabolic significance. In the bottom sediment, biogeochemically significant bacteria and thermophilic or acidothermophilic extremophiles were recovered. In contrast to the planktonic bacteria, an appreciable portion of the sedimentary bacteria could not be classified into any known taxonomic unit, indicating the largely unknown bacteriosphere hiding in the bottom sediment of Lake Sayram.}, } @article {pmid26241507, year = {2015}, author = {Gibson, MK and Crofts, TS and Dantas, G}, title = {Antibiotics and the developing infant gut microbiota and resistome.}, journal = {Current opinion in microbiology}, volume = {27}, number = {}, pages = {51-56}, pmid = {26241507}, issn = {1879-0364}, support = {DP2 DK098089/DK/NIDDK NIH HHS/United States ; R01 GM099538/GM/NIGMS NIH HHS/United States ; DP2-DK-098089/DK/NIDDK NIH HHS/United States ; T32 HD049305/HD/NICHD NIH HHS/United States ; R01-GM099538/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Anti-Bacterial Agents/administration & dosage/*pharmacology/therapeutic use ; Drug Resistance, Microbial/*genetics ; Gastrointestinal Microbiome/*drug effects/physiology ; Genes, Bacterial ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Infant, Very Low Birth Weight ; Metagenomics ; }, abstract = {The microbial communities colonizing the human gut are tremendously diverse and highly personal. The composition and function of the microbiota play important roles in human health and disease, and considerable research has focused on understanding the ecological forces shaping these communities. While it is clear that factors such as diet, genotype of the host, and environment influence the adult gut microbiota community composition, recent work has emphasized the importance of early-life assembly dynamics in both the immediate and long-term personalized nature of the gut microbiota. While the mature adult gut microbiota is believed to be relatively stable, the developing infant gut microbiota (IGM) is highly dynamic and prone to disruption by external factors, including antibiotic exposure. Studies have revealed both transient and persistent alterations to the adult gut microbiota community resulting from antibiotic treatment later in life. As antibiotics are routinely prescribed at a greater rate in the first years of life, the impact of these interventions on the developing IGM is emerging as a key research priority. In addition to understanding the impact of these disruptions on the infant gut microbial architecture and related host diseases, we need to understand the contribution of early life antibiotics to the selection of antibiotic resistance gene reservoirs in the microbiota, and their threat to successful treatment of infectious disease. Here we review the current understanding of the developmental progression of the IGM and the impact of antibiotic therapies on its composition and encoded reservoir of antibiotic resistance genes.}, } @article {pmid26234684, year = {2016}, author = {Welte, CU and de Graaf, RM and van den Bosch, TJ and Op den Camp, HJ and van Dam, NM and Jetten, MS}, title = {Plasmids from the gut microbiome of cabbage root fly larvae encode SaxA that catalyses the conversion of the plant toxin 2-phenylethyl isothiocyanate.}, journal = {Environmental microbiology}, volume = {18}, number = {5}, pages = {1379-1390}, doi = {10.1111/1462-2920.12997}, pmid = {26234684}, issn = {1462-2920}, mesh = {Animals ; Bacteria/classification/*enzymology/*genetics/isolation & purification ; Bacterial Proteins/genetics/metabolism ; Biocatalysis ; Brassica ; Diptera/growth & development/*microbiology ; Escherichia coli/genetics ; Gastrointestinal Microbiome/*genetics ; Genes, Bacterial ; Isothiocyanates/*metabolism ; Larva/microbiology ; Metagenome ; Phylogeny ; Plasmids/*genetics ; }, abstract = {Cabbage root fly larvae (Delia radicum) cause severe crop losses (≥ 50%) of rapeseed/ canola and cabbages used in the food and biofuel industries. These losses occur despite the fact that cabbages produce insecticidal toxins such as isothiocyanates. Here we describe the cabbage root fly larval gut microbiome as a source of isothiocyanate degrading enzymes. We sequenced the microbial gut community of the larvae and analysed phylogenetic markers and functional genes. We combined this with the isolation of several microbial strains representing the phylogenetic distribution of the metagenome. Eleven of those isolates were highly resistant towards 2-phenylethyl isothiocyanate, a subset also metabolized 2-phenylethyl isothiocyanate. Several plasmids appeared to be shared between those isolates that metabolized the toxin. One of the plasmids harboured a saxA gene that upon transformation gave resistance and enabled the degradation of 2-phenylethyl isothiocyanate in Escherichia coli. Taken together, the results showed that the cabbage root fly larval gut microbiome is capable of isothiocyanate degradation, a characteristic that has not been observed before, and may help us understand and design new pest control strategies.}, } @article {pmid26231653, year = {2015}, author = {Milani, C and Mancabelli, L and Lugli, GA and Duranti, S and Turroni, F and Ferrario, C and Mangifesta, M and Viappiani, A and Ferretti, P and Gorfer, V and Tett, A and Segata, N and van Sinderen, D and Ventura, M}, title = {Exploring Vertical Transmission of Bifidobacteria from Mother to Child.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {20}, pages = {7078-7087}, pmid = {26231653}, issn = {1098-5336}, mesh = {Bifidobacteriales Infections/*transmission ; Bifidobacterium/*classification/genetics/*isolation & purification ; DNA, Bacterial/chemistry/genetics ; Feces/microbiology ; Genome, Bacterial ; Humans ; *Infectious Disease Transmission, Vertical ; Microbiota ; Milk, Human/microbiology ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Passage through the birth canal and consequent exposure to the mother's microbiota is considered to represent the initiating event for microbial colonization of the gastrointestinal tract of the newborn. However, a precise evaluation of such suspected vertical microbiota transmission has yet to be performed. Here, we evaluated the microbiomes of four sample sets, each consisting of a mother's fecal and milk samples and the corresponding infant's fecal sample, by means of amplicon-based profiling supported by shotgun metagenomics data for two key samples. Notably, targeted genome reconstruction from microbiome data revealed vertical transmission of a Bifidobacterium breve strain and a Bifidobacterium longum subsp. longum strain from mother to infant, a notion confirmed by strain isolation and genome sequencing. Furthermore, PCR analyses targeting unique genes from these two strains highlighted their persistence in the infant gut at 6 months. Thus, this study demonstrates the existence of specific bifidobacterial strains that are common to mother and child and thus indicative of vertical transmission and that are maintained in the infant for at least relatively short time spans.}, } @article {pmid26229116, year = {2015}, author = {Korem, T and Zeevi, D and Suez, J and Weinberger, A and Avnit-Sagi, T and Pompan-Lotan, M and Matot, E and Jona, G and Harmelin, A and Cohen, N and Sirota-Madi, A and Thaiss, CA and Pevsner-Fischer, M and Sorek, R and Xavier, R and Elinav, E and Segal, E}, title = {Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples.}, journal = {Science (New York, N.Y.)}, volume = {349}, number = {6252}, pages = {1101-1106}, pmid = {26229116}, issn = {1095-9203}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/*growth & development ; Diabetes Mellitus, Type 2/*microbiology ; Gastrointestinal Tract/*microbiology ; Genome, Bacterial ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Metagenome ; Metagenomics ; Microbiota/genetics/*physiology ; }, abstract = {Metagenomic sequencing increased our understanding of the role of the microbiome in health and disease, yet it only provides a snapshot of a highly dynamic ecosystem. Here, we show that the pattern of metagenomic sequencing read coverage for different microbial genomes contains a single trough and a single peak, the latter coinciding with the bacterial origin of replication. Furthermore, the ratio of sequencing coverage between the peak and trough provides a quantitative measure of a species' growth rate. We demonstrate this in vitro and in vivo, under different growth conditions, and in complex bacterial communities. For several bacterial species, peak-to-trough coverage ratios, but not relative abundances, correlated with the manifestation of inflammatory bowel disease and type II diabetes.}, } @article {pmid26227909, year = {2015}, author = {Nam, YJ and Kim, H and Lee, JH and Yoon, H and Kim, JG}, title = {Metagenomic analysis of soil fungal communities on Ulleungdo and Dokdo Islands.}, journal = {The Journal of general and applied microbiology}, volume = {61}, number = {3}, pages = {67-74}, doi = {10.2323/jgam.61.67}, pmid = {26227909}, issn = {1349-8037}, mesh = {Ascomycota/classification/genetics/*isolation & purification ; Basidiomycota/classification/genetics/*isolation & purification ; Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Islands ; *Metagenomics ; Mycorrhizae/genetics/isolation & purification ; Phylogeny ; Plants/microbiology ; Republic of Korea ; *Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; Volcanic Eruptions ; }, abstract = {Ulleungdo and Dokdo are volcanic islands that experience a characteristic marine climate, influenced by warm currents. The richness and diversity of the plant species, particularly vascular plants, are higher on Ulleungdo than on Dokdo. In contrast to the native plant life, little is known about the diversity of soil fungi living in the rhizosphere of these two islands. In this study, we utilized the barcoded pyrosequencing method to analyze rhizosphere soil fungi on Ulleungdo and Dokdo. In total, 768 operational taxonomic units (OTUs) were analyzed from the Ulleungdo samples, while 640 OTUs and 382 OTUs were analyzed from the Dongdo and Seodo (islets of Dokdo) samples, respectively. Species richness was considerably higher in the Ulleungdo samples than in the Dongdo and Seodo samples, while there was little difference in species diversity between the samples. The taxonomic composition analyses demonstrated that members of the phylum Basidiomycota dominated the Ulleungdo samples, whereas members of the phylum Ascomycota were predominant in the Dokdo samples. Ectomycorrhizal fungi belonging to the phylum Basidiomycota, in particular, were more abundant in the Ulleungdo samples. This finding suggests that the difference in the abundance of the ectomycorrhizal fungi in the rhizospheres of Ulleungdo and Dokdo may have been affected by species richness and diversity of the vascular plants. Our study is the first detailed report of the composition of soil fungal communities on the Ulleungdo and Dokdo islands. In addition, our findings provide a basis for understanding the ecological interactions between plants and fungi.}, } @article {pmid26226335, year = {2015}, author = {Zhong, X and Guidoni, B and Jacas, L and Jacquet, S}, title = {Structure and diversity of ssDNA Microviridae viruses in two peri-alpine lakes (Annecy and Bourget, France).}, journal = {Research in microbiology}, volume = {166}, number = {8}, pages = {644-654}, doi = {10.1016/j.resmic.2015.07.003}, pmid = {26226335}, issn = {1769-7123}, mesh = {Bacteroidetes/virology ; Capsid Proteins/genetics ; Ecosystem ; France ; Genetic Variation ; Lakes/*virology ; *Microbial Consortia ; Microviridae/*classification/*genetics/growth & development ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Time Factors ; *Water Microbiology ; }, abstract = {Microviridae is a subset of single-stranded DNA (ssDNA) viruses infecting bacteria. This group of phages has been previously observed to be very abundant (representing >90% of the total known viral metagenomic sequences) in Lake Bourget. However, this observation was made only during one period (in summer) and from a single sample collected at a single depth (near surface). This result suggests the importance of these viruses, poorly examined thus far, especially in fresh waters. In this study, performed on the two largest natural lakes in France (e.g. Lakes Annecy and Bourget), Microviridae structure was determined each month throughout the year (2011) using PCR-DGGE, with primers that target the major-capsid-protein-encoding gene VP1; cloning/sequencing was used to investigate their diversity. Our results confirm that Microviridae are diverse in peri-alpine lakes and are mainly represented by gokushoviruses. We also found for the first time ssDNA viruses belonging to Alpavirinae, another subfamily within Microviridae recently proposed by Krupovic and Forterre (2011), generally prophages infecting members of the Phylum Bacteroidetes. Our data also support highly variable community composition and dynamics of individual components whose patterns were different between lakes, suggesting distinct host communities and/or abiotic influences between the two ecosystems. We point out that most of the major observed ssDNA Microviridae viruses display boom-bust patterns (with a sharp increase/decline) in their dynamics, with high relative abundances, suggesting brutal control of hosts and rapid regulation of the host community structure.}, } @article {pmid26223650, year = {2015}, author = {Ma, KL and Li, XK and Wang, K and Zhou, HX and Meng, LW and Zhang, J}, title = {454-Pyrosequencing Reveals Microbial Community Structure and Composition in a Mesophilic UAFB System Treating PTA Wastewater.}, journal = {Current microbiology}, volume = {71}, number = {5}, pages = {551-558}, pmid = {26223650}, issn = {1432-0991}, mesh = {Anaerobiosis ; Bacteria/classification/genetics ; Bioreactors/*microbiology ; *High-Throughput Nucleotide Sequencing ; In Situ Hybridization, Fluorescence ; *Metagenome ; *Microbiota ; Phylogeny ; Sewage/microbiology ; Temperature ; Wastewater/*microbiology ; }, abstract = {To well understand the community structure and composition of mesophilic microorganisms in anaerobic system fed with PTA wastewater, an up-flow anaerobic fixed bed reactor was continuously run at 33 and 37 °C for 75 and 60 days, respectively. Both fluorescence in situ hybridization analysis and 454-pyrosequencing were applied to investigate the microbial distinction within mesophilic ranges. A preferable performance was achieved at 37 than 33 °C. The taxonomic complexities of two samples were further compared at phylum, class, and genus levels. Notably, microbial diversity differed a lot and the change of populations was observed mainly in the shared OTUs. Genus level analysis showed that when temperature was increased to 37 °C, the abundance of Thauera and Hydrogenophaga (β-Proteobacteria) decreased by 93.75 and 61.47 %, respectively, whereas that of Syntrophorhabdus (δ-Proteobacteria) increased from 4.93 to 16.01 %. Furthermore, the dominant archaeal Methanobacterium at both temperatures indicated the prevailing contribution of hydrogenotrophic methanogens in mesophilic anaerobic system.}, } @article {pmid26223443, year = {2015}, author = {Colatriano, D and Ramachandran, A and Yergeau, E and Maranger, R and Gélinas, Y and Walsh, DA}, title = {Metaproteomics of aquatic microbial communities in a deep and stratified estuary.}, journal = {Proteomics}, volume = {15}, number = {20}, pages = {3566-3579}, doi = {10.1002/pmic.201500079}, pmid = {26223443}, issn = {1615-9861}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Canada ; Carbon/metabolism ; Membrane Transport Proteins/biosynthesis/*genetics ; Metagenomics ; Nitrification/genetics ; Nitrogen/metabolism ; *Proteomics ; Water Microbiology ; }, abstract = {Here we harnessed the power of metaproteomics to assess the metabolic diversity and function of stratified aquatic microbial communities in the deep and expansive Lower St. Lawrence Estuary, located in eastern Canada. Vertical profiling of the microbial communities through the stratified water column revealed differences in metabolic lifestyles and in carbon and nitrogen processing pathways. In productive surface waters, we identified heterotrophic populations involved in the processing of high and low molecular weight organic matter from both terrestrial (e.g. cellulose and xylose) and marine (e.g. organic compatible osmolytes) sources. In the less productive deep waters, chemosynthetic production coupled to nitrification by MG-I Thaumarchaeota and Nitrospina appeared to be a dominant metabolic strategy. Similar to other studies of the coastal ocean, we identified methanol oxidation proteins originating from the common OM43 marine clade. However, we also identified a novel lineage of methanol-oxidizers specifically in the particle-rich bottom (i.e. nepheloid) layer. Membrane transport proteins assigned to the uncultivated MG-II Euryarchaeota were also specifically detected in the nepheloid layer. In total, these results revealed strong vertical structure of microbial taxa and metabolic activities, as well as the presence of specific "nepheloid" taxa that may contribute significantly to coastal ocean nutrient cycling.}, } @article {pmid26223320, year = {2015}, author = {Denesvre, C and Dumarest, M and Rémy, S and Gourichon, D and Eloit, M}, title = {Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin.}, journal = {Virus genes}, volume = {51}, number = {2}, pages = {209-216}, pmid = {26223320}, issn = {1572-994X}, mesh = {Animals ; *Biodiversity ; Chickens ; DNA Viruses/*classification/*isolation & purification ; High-Throughput Nucleotide Sequencing ; Skin/*virology ; }, abstract = {Recent studies show that human skin at homeostasis is a complex ecosystem whose virome include circular DNA viruses, especially papillomaviruses and polyomaviruses. To determine the chicken skin virome in comparison with human skin virome, a chicken swabs pool sample from fifteen indoor healthy chickens of five genetic backgrounds was examined for the presence of DNA viruses by high-throughput sequencing (HTS). The results indicate a predominance of herpesviruses from the Mardivirus genus, coming from either vaccinal origin or presumably asymptomatic infection. Despite the high sensitivity of the HTS method used herein to detect small circular DNA viruses, we did not detect any papillomaviruses, polyomaviruses, or circoviruses, indicating that these viruses may not be resident of the chicken skin. The results suggest that the turkey herpesvirus is a resident of chicken skin in vaccinated chickens. This study indicates major differences between the skin viromes of chickens and humans. The origin of this difference remains to be further studied in relation with skin physiology, environment, or virus population dynamics.}, } @article {pmid26217325, year = {2015}, author = {Dziewit, L and Pyzik, A and Romaniuk, K and Sobczak, A and Szczesny, P and Lipinski, L and Bartosik, D and Drewniak, L}, title = {Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {694}, pmid = {26217325}, issn = {1664-302X}, abstract = {Methanogenic Archaea produce approximately one billion tons of methane annually, but their biology remains largely unknown. This is partially due to the large phylogenetic and phenotypic diversity of this group of organisms, which inhabit various anoxic environments including peatlands, freshwater sediments, landfills, anaerobic digesters and the intestinal tracts of ruminants. Research is also hampered by the inability to cultivate methanogenic Archaea. Therefore, biodiversity studies have relied on the use of 16S rRNA and mcrA [encoding the α subunit of the methyl coenzyme M (methyl-CoM) reductase] genes as molecular markers for the detection and phylogenetic analysis of methanogens. Here, we describe four novel molecular markers that should prove useful in the detailed analysis of methanogenic consortia, with a special focus on methylotrophic methanogens. We have developed and validated sets of degenerate PCR primers for the amplification of genes encoding key enzymes involved in methanogenesis: mcrB and mcrG (encoding β and γ subunits of the methyl-CoM reductase, involved in the conversion of methyl-CoM to methane), mtaB (encoding methanol-5-hydroxybenzimidazolylcobamide Co-methyltransferase, catalyzing the conversion of methanol to methyl-CoM) and mtbA (encoding methylated [methylamine-specific corrinoid protein]:coenzyme M methyltransferase, involved in the conversion of mono-, di- and trimethylamine into methyl-CoM). The sensitivity of these primers was verified by high-throughput sequencing of PCR products amplified from DNA isolated from microorganisms present in anaerobic digesters. The selectivity of the markers was analyzed using phylogenetic methods. Our results indicate that the selected markers and the PCR primer sets can be used as specific tools for in-depth diversity analyses of methanogenic consortia.}, } @article {pmid26214846, year = {2015}, author = {Pereira, MR and Mercaldi, GF and Maester, TC and Balan, A and Lemos, EG}, title = {Est16, a New Esterase Isolated from a Metagenomic Library of a Microbial Consortium Specializing in Diesel Oil Degradation.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0133723}, pmid = {26214846}, issn = {1932-6203}, mesh = {*Biodegradation, Environmental ; Enzyme Stability ; Esterases/chemistry/classification/genetics/*metabolism ; *Gasoline ; Gene Library ; Hydrogen-Ion Concentration ; Kinetics ; Lipase/genetics/metabolism ; Lipolysis ; *Metagenomics ; *Microbial Consortia/genetics ; Models, Molecular ; Phylogeny ; Protein Conformation ; Substrate Specificity ; Thermodynamics ; }, abstract = {Lipolytic enzymes have attracted attention from a global market because they show enormous biotechnological potential for applications such as detergent production, leather processing, cosmetics production, and use in perfumes and biodiesel. Due to the intense demand for biocatalysts, a metagenomic approach provides methods of identifying new enzymes. In this study, an esterase designated as Est16 was selected from 4224 clones of a fosmid metagenomic library, revealing an 87% amino acid identity with an esterase/lipase (accession number ADM63076.1) from an uncultured bacterium. Phylogenetic studies showed that the enzyme belongs to family V of bacterial lipolytic enzymes and has sequence and structural similarities with an aryl-esterase from Pseudomonas fluorescens and a patented Anti-Kazlauskas lipase (patent number US20050153404). The protein was expressed and purified as a highly soluble, thermally stable enzyme that showed a preference for basic pH. Est16 exhibited activity toward a wide range of substrates and the highest catalytic efficiency against p-nitrophenyl butyrate and p-nitrophenyl valerate. Est16 also showed tolerance to the presence of organic solvents, detergents and metals. Based on molecular modeling, we showed that the large alpha-beta domain is conserved in the patented enzymes but not the substrate pocket. Here, it was demonstrated that a metagenomic approach is suitable for discovering the lipolytic enzyme diversity and that Est16 has the biotechnological potential for use in industrial processes.}, } @article {pmid26214836, year = {2015}, author = {Zhang, X and Zhang, D and Jia, H and Feng, Q and Wang, D and Liang, D and Wu, X and Li, J and Tang, L and Li, Y and Lan, Z and Chen, B and Li, Y and Zhong, H and Xie, H and Jie, Z and Chen, W and Tang, S and Xu, X and Wang, X and Cai, X and Liu, S and Xia, Y and Li, J and Qiao, X and Al-Aama, JY and Chen, H and Wang, L and Wu, QJ and Zhang, F and Zheng, W and Li, Y and Zhang, M and Luo, G and Xue, W and Xiao, L and Li, J and Chen, W and Xu, X and Yin, Y and Yang, H and Wang, J and Kristiansen, K and Liu, L and Li, T and Huang, Q and Li, Y and Wang, J}, title = {The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment.}, journal = {Nature medicine}, volume = {21}, number = {8}, pages = {895-905}, pmid = {26214836}, issn = {1546-170X}, mesh = {Antirheumatic Agents/therapeutic use ; Arthritis, Rheumatoid/drug therapy/*microbiology ; C-Reactive Protein/analysis ; Humans ; Intestines/*microbiology ; Metagenome ; *Microbiota ; Mouth/*microbiology ; Saliva/microbiology ; }, abstract = {We carried out metagenomic shotgun sequencing and a metagenome-wide association study (MGWAS) of fecal, dental and salivary samples from a cohort of individuals with rheumatoid arthritis (RA) and healthy controls. Concordance was observed between the gut and oral microbiomes, suggesting overlap in the abundance and function of species at different body sites. Dysbiosis was detected in the gut and oral microbiomes of RA patients, but it was partially resolved after RA treatment. Alterations in the gut, dental or saliva microbiome distinguished individuals with RA from healthy controls, were correlated with clinical measures and could be used to stratify individuals on the basis of their response to therapy. In particular, Haemophilus spp. were depleted in individuals with RA at all three sites and negatively correlated with levels of serum autoantibodies, whereas Lactobacillus salivarius was over-represented in individuals with RA at all three sites and was present in increased amounts in cases of very active RA. Functionally, the redox environment, transport and metabolism of iron, sulfur, zinc and arginine were altered in the microbiota of individuals with RA. Molecular mimicry of human antigens related to RA was also detectable. Our results establish specific alterations in the gut and oral microbiomes in individuals with RA and suggest potential ways of using microbiome composition for prognosis and diagnosis.}, } @article {pmid26209669, year = {2015}, author = {Wong, ML and An, D and Caffrey, SM and Soh, J and Dong, X and Sensen, CW and Oldenburg, TB and Larter, SR and Voordouw, G}, title = {Roles of Thermophiles and Fungi in Bitumen Degradation in Mostly Cold Oil Sands Outcrops.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {19}, pages = {6825-6838}, pmid = {26209669}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Biodegradation, Environmental ; Cold Temperature ; Fungi/classification/genetics/*isolation & purification ; Hydrocarbons/*metabolism ; Microbial Consortia ; Molecular Sequence Data ; Oil and Gas Fields/*microbiology ; Phylogeny ; Rivers/chemistry/microbiology ; Temperature ; }, abstract = {Oil sands are surface exposed in river valley outcrops in northeastern Alberta, where flat slabs (tablets) of weathered, bitumen-saturated sandstone can be retrieved from outcrop cliffs or from riverbeds. Although the average yearly surface temperature of this region is low (0.7°C), we found that the temperatures of the exposed surfaces of outcrop cliffs reached 55 to 60°C on sunny summer days, with daily maxima being 27 to 31°C. Analysis of the cooccurrence of taxa derived from pyrosequencing of 16S/18S rRNA genes indicated that an aerobic microbial network of fungi and hydrocarbon-, methane-, or acetate-oxidizing heterotrophic bacteria was present in all cliff tablets. Metagenomic analyses indicated an elevated presence of fungal cytochrome P450 monooxygenases in these samples. This network was distinct from the heterotrophic community found in riverbeds, which included fewer fungi. A subset of cliff tablets had a network of anaerobic and/or thermophilic taxa, including methanogens, Firmicutes, and Thermotogae, in the center. Long-term aerobic incubation of outcrop samples at 55°C gave a thermophilic microbial community. Analysis of residual bitumen with a Fourier transform ion cyclotron resonance mass spectrometer indicated that aerobic degradation proceeded at 55°C but not at 4°C. Little anaerobic degradation was observed. These results indicate that bitumen degradation on outcrop surfaces is a largely aerobic process with a minor anaerobic contribution and is catalyzed by a consortium of bacteria and fungi. Bitumen degradation is stimulated by periodic high temperatures on outcrop cliffs, which cause significant decreases in bitumen viscosity.}, } @article {pmid26207681, year = {2015}, author = {Ponomarova, O and Patil, KR}, title = {Metabolic interactions in microbial communities: untangling the Gordian knot.}, journal = {Current opinion in microbiology}, volume = {27}, number = {}, pages = {37-44}, doi = {10.1016/j.mib.2015.06.014}, pmid = {26207681}, issn = {1879-0364}, mesh = {Archaea/metabolism ; Bacteria/*metabolism ; Ecosystem ; Mass Spectrometry/methods ; *Metabolic Networks and Pathways ; Metabolomics ; Metagenomics ; Microbial Consortia/*physiology ; *Microbial Interactions ; }, abstract = {Metabolic exchanges are ubiquitous in microbial communities. However, detecting metabolite cross-feedings is difficult due to their intrinsically dynamic nature and the complexity of communities. Thus, while exhaustive description of metabolic networks operating in natural systems is a task for the future, the battle of today is divided between detailed characterizations of small, reduced complexity microbial consortia, and focusing on particular metabolic aspects of natural ecosystems. Detecting metabolic interactions requires methodological blend able to capture species identity, dependencies and the nature of exchanged metabolites. Multiple combinations of diverse techniques, from metagenomics to imaging mass spectrometry, offer solutions to this challenge, each combination being tailored to the community at hand.}, } @article {pmid26207384, year = {2015}, author = {Hov, JR and Zhong, H and Qin, B and Anmarkrud, JA and Holm, K and Franke, A and Lie, BA and Karlsen, TH}, title = {The Influence of the Autoimmunity-Associated Ancestral HLA Haplotype AH8.1 on the Human Gut Microbiota: A Cross-Sectional Study.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0133804}, pmid = {26207384}, issn = {1932-6203}, mesh = {Adult ; *Autoimmunity ; Bacteria/classification/genetics ; Cross-Sectional Studies ; Female ; Gastrointestinal Microbiome/*immunology ; Genotype ; HLA-DRB1 Chains/genetics/immunology ; *Haplotypes ; Histocompatibility Antigens/*genetics ; Humans ; Male ; Metagenome ; Middle Aged ; Phylogeny ; }, abstract = {Multiple immune-related genes are encoded in the HLA complex on chromosome 6p21. The 8.1 ancestral haplotype (AH8.1) include the classical HLA alleles HLA-B*08:01 and HLA-DRB1*03:01, and has been associated with a large number of autoimmune diseases, but the underlying mechanisms for this association are largely unknown. Given the recently established links between the gut microbiota and inflammatory diseases, we hypothesized that the AH8.1 influences the host gut microbial community composition. To study this further, healthy individuals were selected from the Norwegian Bone Marrow Donor Registry and categorized as either I. AH8.1 homozygote (n=34), II. AH8.1 heterozygote (n=38), III. Non AH8.1 heterozygote or IV. HLA-DRB1 homozygote but non AH8.1 (n=15). Bacterial DNA from stool samples were subjected to sequencing of the V3-V5 region of the 16S rRNA gene on the 454 Life Sciences platform and data analyzed using Mothur and QIIME. The results showed that the abundances of different taxa were highly variable within all pre-defined AH8.1 genotype groups. Using univariate non-parametric statistics, there were no differences regarding alpha or beta diversity between AH8.1 carriers (categories I and II) and non-carriers (categories III and IV), however four different taxa (Prevotellaceae, Clostridium XVIII, Coprococcus, Enterorhabdus) had nominally significant lower abundances in AH8.1 carriers than non-carriers. After including possible confounders in a multivariate linear regression, only the two latter genera remained significantly associated. In conclusion, the overall contribution of the AH8.1 haplotype to the variation in gut microbiota profile of stool in the present study was small.}, } @article {pmid26207044, year = {2015}, author = {Cameron, SJ and Huws, SA and Hegarty, MJ and Smith, DP and Mur, LA}, title = {The human salivary microbiome exhibits temporal stability in bacterial diversity.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {9}, pages = {fiv091}, doi = {10.1093/femsec/fiv091}, pmid = {26207044}, issn = {1574-6941}, mesh = {Actinobacteria/genetics/physiology ; Adult ; Bacteroidetes/genetics/physiology ; Base Sequence ; Biodiversity ; DNA, Bacterial/genetics ; Female ; Fusobacteria/genetics/physiology ; Gene Dosage/*genetics ; Humans ; Male ; Metagenome/genetics ; Microbiota/genetics/*physiology ; Proteobacteria/genetics/physiology ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The temporal variability of the human microbiome may be an important factor in determining its relationship with health and disease. In this study, the saliva of 40 participants was collected every 2 months over a one-year period to determine the temporal variability of the human salivary microbiome. Salivary pH and 16S rRNA gene copy number were measured for all participants, with the microbiome of 10 participants assessed through 16S rRNA amplicon sequencing. In February 2013, 16S rRNA gene copy number was significantly (P < 0.001) higher, with individual changes between time points significant (P = 0.003). Salivary pH levels were significantly (P < 0.001) higher in December 2012 than in October 2012 and February 2013, with significant (P < 0.001) individual variations seen throughout. Bacterial α-diversity showed significant differences between participants (P < 0.001), but not sampling periods (P = 0.801), and a significant positive correlation with salivary pH (R(2) = 7.8%; P = 0.019). At the phylum level, significant differences were evident between participants in the Actinobacteria (P < 0.001), Bacteroidetes (P < 0.001), Firmicutes (P = 0.008), Fusobacteria (P < 0.001), Proteobacteria (P < 0.001), Synergistetes (P < 0.001) and Spirochaetes (P = 0.003) phyla. This study charted the temporal variability of the salivary microbiome, suggesting that bacterial diversity is stable, but that 16S rRNA gene copy number may be subject to seasonal flux.}, } @article {pmid26204808, year = {2015}, author = {Kodzius, R and Gojobori, T}, title = {Marine metagenomics as a source for bioprospecting.}, journal = {Marine genomics}, volume = {24 Pt 1}, number = {}, pages = {21-30}, doi = {10.1016/j.margen.2015.07.001}, pmid = {26204808}, issn = {1876-7478}, mesh = {Animals ; Aquatic Organisms/chemistry/*genetics/metabolism ; Biodiversity ; Biological Evolution ; Drug Discovery ; Food ; *Metagenomics ; }, abstract = {This review summarizes usage of genome-editing technologies for metagenomic studies; these studies are used to retrieve and modify valuable microorganisms for production, particularly in marine metagenomics. Organisms may be cultivable or uncultivable. Metagenomics is providing especially valuable information for uncultivable samples. The novel genes, pathways and genomes can be deducted. Therefore, metagenomics, particularly genome engineering and system biology, allows for the enhancement of biological and chemical producers and the creation of novel bioresources. With natural resources rapidly depleting, genomics may be an effective way to efficiently produce quantities of known and novel foods, livestock feed, fuels, pharmaceuticals and fine or bulk chemicals.}, } @article {pmid26203332, year = {2015}, author = {Ten Hoopen, P and Pesant, S and Kottmann, R and Kopf, A and Bicak, M and Claus, S and Deneudt, K and Borremans, C and Thijsse, P and Dekeyzer, S and Schaap, DM and Bowler, C and Glöckner, FO and Cochrane, G}, title = {Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards.}, journal = {Standards in genomic sciences}, volume = {10}, number = {}, pages = {20}, pmid = {26203332}, issn = {1944-3277}, abstract = {Contextual data collected concurrently with molecular samples are critical to the use of metagenomics in the fields of marine biodiversity, bioinformatics and biotechnology. We present here Marine Microbial Biodiversity, Bioinformatics and Biotechnology (M2B3) standards for "Reporting" and "Serving" data. The M2B3 Reporting Standard (1) describes minimal mandatory and recommended contextual information for a marine microbial sample obtained in the epipelagic zone, (2) includes meaningful information for researchers in the oceanographic, biodiversity and molecular disciplines, and (3) can easily be adopted by any marine laboratory with minimum sampling resources. The M2B3 Service Standard defines a software interface through which these data can be discovered and explored in data repositories. The M2B3 Standards were developed by the European project Micro B3, funded under 7(th) Framework Programme "Ocean of Tomorrow", and were first used with the Ocean Sampling Day initiative. We believe that these standards have value in broader marine science.}, } @article {pmid26202196, year = {2015}, author = {Ajami, NJ and Hutchinson, DS and Petrosino, JF}, title = {Promise and Pragmatism in Clinical Microbiome Research.}, journal = {Mini reviews in medicinal chemistry}, volume = {16}, number = {3}, pages = {222-224}, doi = {10.2174/1389557515666150722103457}, pmid = {26202196}, issn = {1875-5607}, mesh = {High-Throughput Nucleotide Sequencing/trends ; Humans ; *Microbiota ; Research/*trends ; }, abstract = {The evolution of human microbiome research has lead to a systems biology approach that encompasses multidisciplinary investigations. The implementation of next generation sequencing technologies has allowed researchers to study unculturable organisms, discover novel ones, and provide insights into the role of the human microbiome in health and disease. When these approaches are applied to large-scale longitudinal studies designed to interrogate the association of the microbiome with specific clinical outcomes, the development of new therapeutics and diagnostics intended to modulate or detect changes in microbiome composition to improve human health are born. We are just starting to unravel the role of the microbiome in a wide-variety of diseases, and while some of it appears to be related to causation and provide opportunities for intervention, a good dose of pragmatism is warranted as the field is still in its infancy.}, } @article {pmid26198938, year = {2015}, author = {Sheng, HF and Zhou, HW}, title = {[Methods, challenges and opportunities for big data analyses of microbiome].}, journal = {Nan fang yi ke da xue xue bao = Journal of Southern Medical University}, volume = {35}, number = {7}, pages = {931-934}, pmid = {26198938}, issn = {1673-4254}, mesh = {Bacteria/classification ; Humans ; *Metagenome ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {Microbiome is a novel research field related with a variety of chronic inflamatory diseases. Technically, there are two major approaches to analysis of microbiome: metataxonome by sequencing the 16S rRNA variable tags, and metagenome by shot-gun sequencing of the total microbial (mainly bacterial) genome mixture. The 16S rRNA sequencing analyses pipeline includes sequence quality control, diversity analyses, taxonomy and statistics; metagenome analyses further includes gene annotation and functional analyses. With the development of the sequencing techniques, the cost of sequencing will decrease, and big data analyses will become the central task. Data standardization, accumulation, modeling and disease prediction are crucial for future exploit of these data. Meanwhile, the information property in these data, and the functional verification with culture-dependent and culture-independent experiments remain the focus in future research. Studies of human microbiome will bring a better understanding of the relations between the human body and the microbiome, especially in the context of disease diagnosis and therapy, which promise rich research opportunities.}, } @article {pmid26196489, year = {2015}, author = {Segata, N}, title = {Gut Microbiome: Westernization and the Disappearance of Intestinal Diversity.}, journal = {Current biology : CB}, volume = {25}, number = {14}, pages = {R611-3}, doi = {10.1016/j.cub.2015.05.040}, pmid = {26196489}, issn = {1879-0445}, mesh = {*Biological Evolution ; *Diet, Paleolithic ; Ethnicity/*genetics ; Gastrointestinal Microbiome/*genetics/*physiology ; Humans ; Metagenome/*genetics ; White People/*genetics ; }, abstract = {The environment shapes our intestinal microbiome. By contrasting the gut microbiomes of African hunter-gatherer and European subjects, a new study reveals that urbanization is associated with a loss of microbial organisms and genes. What will be the consequences of the lost biodiversity in the sanitized, western-diet world?}, } @article {pmid26193110, year = {2015}, author = {Zinicola, M and Higgins, H and Lima, S and Machado, V and Guard, C and Bicalho, R}, title = {Shotgun Metagenomic Sequencing Reveals Functional Genes and Microbiome Associated with Bovine Digital Dermatitis.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0133674}, pmid = {26193110}, issn = {1932-6203}, mesh = {Animals ; Biopsy ; Cattle ; Cattle Diseases/*genetics/*microbiology ; Chemotaxis ; Copper/chemistry ; Digital Dermatitis/*genetics/*microbiology/pathology ; Drug Resistance, Bacterial ; Female ; Flagella/genetics ; Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Treponema/genetics ; Zinc/chemistry ; }, abstract = {Metagenomic methods amplifying 16S ribosomal RNA genes have been used to describe the microbial diversity of healthy skin and lesion stages of bovine digital dermatitis (DD) and to detect critical pathogens involved with disease pathogenesis. In this study, we characterized the microbiome and for the first time, the composition of functional genes of healthy skin (HS), active (ADD) and inactive (IDD) lesion stages using a whole-genome shotgun approach. Metagenomic sequences were annotated using MG-RAST pipeline. Six phyla were identified as the most abundant. Firmicutes and Actinobacteria were the predominant bacterial phyla in the microbiome of HS, while Spirochetes, Bacteroidetes and Proteobacteria were highly abundant in ADD and IDD. T. denticola-like, T. vincentii-like and T. phagedenis-like constituted the most abundant species in ADD and IDD. Recruitment plots comparing sequences from HS, ADD and IDD samples to the genomes of specific Treponema spp., supported the presence of T. denticola and T. vincentii in ADD and IDD. Comparison of the functional composition of HS to ADD and IDD identified a significant difference in genes associated with motility/chemotaxis and iron acquisition/metabolism. We also provide evidence that the microbiome of ADD and IDD compared to that of HS had significantly higher abundance of genes associated with resistance to copper and zinc, which are commonly used in footbaths to prevent and control DD. In conclusion, the results from this study provide new insights into the HS, ADD and IDD microbiomes, improve our understanding of the disease pathogenesis and generate unprecedented knowledge regarding the functional genetic composition of the digital dermatitis microbiome.}, } @article {pmid26189342, year = {2015}, author = {Kashinskaya, EN and Belkova, NL and Izvekova, GI and Simonov, EP and Andree, KB and Glupov, VV and Baturina, OA and Kabilov, MR and Solovyev, MM}, title = {A comparative study on microbiota from the intestine of Prussian carp (Carassius gibelio) and their aquatic environmental compartments, using different molecular methods.}, journal = {Journal of applied microbiology}, volume = {119}, number = {4}, pages = {948-961}, doi = {10.1111/jam.12904}, pmid = {26189342}, issn = {1365-2672}, mesh = {Animals ; Aquaculture ; Bacteria/classification/genetics/*isolation & purification ; Bacterial Typing Techniques/*methods ; Carps/*microbiology ; Ecosystem ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/*methods ; Intestines/*microbiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {AIMS: The aim of this study was to evaluate, via various molecular methods, the possible correlations between microbial community structure of Prussian carp and the environmental compartments of their habitat.

METHODS AND RESULTS: Microbial communities in the intestine and environmental compartments were studied using PCR-screening, cloning and next-generation high-throughput sequencing of the 16S ribosomal RNA genes. The 16S rDNA metagenomic sequencing showed higher bacterial diversity in comparison with clone libraries, while group-specific PCR showed positive detection of nine bacteria phyla. Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria and Actinobacteria were most abundant both in the intestine and habitat environments. The comparative analyses reveal that the bacterial community in the Prussian carp intestine is most similar to that identified from the chironomid.

CONCLUSIONS: This study demonstrated some differences between molecular methods and showed advantages and limitations associated with them. These differences have the potential to reduce bias in results obtained from analysis of the community structure. The advantages of each molecular technique can be used for a better understanding of microbial diversity. The microbiota of Prussian carp intestine is most similar to those from the chironomids.

We investigated the diversity of the intestinal microbiota in an economically important aquaculture species, the Prussian carp (Carassius gibelio). The results provide significant information to discuss possible functions of these bacteria for further understanding of Prussian carp health.}, } @article {pmid26186976, year = {2015}, author = {Pandit, AS and Joshi, MN and Bhargava, P and Shaikh, I and Ayachit, GN and Raj, SR and Saxena, AK and Bagatharia, SB}, title = {A snapshot of microbial communities from the Kutch: one of the largest salt deserts in the World.}, journal = {Extremophiles : life under extreme conditions}, volume = {19}, number = {5}, pages = {973-987}, pmid = {26186976}, issn = {1433-4909}, mesh = {Biomass ; *Desert Climate ; Genome, Archaeal ; Genome, Bacterial ; India ; *Microbiota ; Phylogeny ; *Salt Tolerance ; Seasons ; *Soil Microbiology ; }, abstract = {Here we present the first report on the taxonomic diversity of the microbial communities of the saline desert of the Great Rann of Kutch, Gujarat, India, using a metagenomic approach. Seven samples, differing in salinity levels and covering different seasons, were analysed to investigate the dynamics of microbial communities in relation to salinity and season. Metagenomic data generated using whole metagenome sequencing revealed that despite its very high salinity (4.11-30.79 %), the saline desert's microbiota had a rich microbial diversity that included all major phyla. Notably, 67 archaeal genera, representing more than 60 % of all known archaeal genera, were present in this ecosystem. A strong positive correlation (0.85) was observed between the presence of the extremely halophilic bacterium Salinibacter and salinity level. Taxonomic and functional comparisons of the saline desert metagenome with those of other publicly available metagenomes (i.e. sea, hypersaline lagoon, solar saltern, brine, hot desert) was carried out. The microbial community of the Kutch was found to be unique yet more similar to the sea biomes followed by hypersaline lagoon.}, } @article {pmid26184859, year = {2015}, author = {Mandal, RS and Saha, S and Das, S}, title = {Metagenomic surveys of gut microbiota.}, journal = {Genomics, proteomics & bioinformatics}, volume = {13}, number = {3}, pages = {148-158}, pmid = {26184859}, issn = {2210-3244}, mesh = {Animals ; Base Sequence ; Biodiversity ; DNA, Bacterial/*genetics ; Diabetes Mellitus, Type 2/microbiology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Genome, Bacterial/*genetics ; Humans ; Metagenomics/*methods ; Microbial Interactions/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Gut microbiota of higher vertebrates is host-specific. The number and diversity of the organisms residing within the gut ecosystem are defined by physiological and environmental factors, such as host genotype, habitat, and diet. Recently, culture-independent sequencing techniques have added a new dimension to the study of gut microbiota and the challenge to analyze the large volume of sequencing data is increasingly addressed by the development of novel computational tools and methods. Interestingly, gut microbiota maintains a constant relative abundance at operational taxonomic unit (OTU) levels and altered bacterial abundance has been associated with complex diseases such as symptomatic atherosclerosis, type 2 diabetes, obesity, and colorectal cancer. Therefore, the study of gut microbial population has emerged as an important field of research in order to ultimately achieve better health. In addition, there is a spontaneous, non-linear, and dynamic interaction among different bacterial species residing in the gut. Thus, predicting the influence of perturbed microbe-microbe interaction network on health can aid in developing novel therapeutics. Here, we summarize the population abundance of gut microbiota and its variation in different clinical states, computational tools available to analyze the pyrosequencing data, and gut microbe-microbe interaction networks.}, } @article {pmid26182345, year = {2015}, author = {Albertsen, M and Karst, SM and Ziegler, AS and Kirkegaard, RH and Nielsen, PH}, title = {Back to Basics--The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0132783}, pmid = {26182345}, issn = {1932-6203}, mesh = {DNA Primers/genetics ; DNA, Bacterial/*genetics/isolation & purification ; Gram-Negative Bacteria/classification/*genetics ; Gram-Positive Bacteria/classification/*genetics ; In Situ Hybridization, Fluorescence ; Metagenomics ; Microbial Consortia/genetics ; *Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; Solid Phase Extraction/*methods ; }, abstract = {DNA extraction and primer choice have a large effect on the observed community structure in all microbial amplicon sequencing analyses. Although the biases are well known, no comprehensive analysis has been conducted in activated sludge communities. In this study we systematically explored the impact of a number of parameters on the observed microbial community: bead beating intensity, primer choice, extracellular DNA removal, and various PCR settings. In total, 176 samples were subjected to 16S rRNA amplicon sequencing, and selected samples were investigated through metagenomics and metatranscriptomics. Quantitative fluorescence in situ hybridization was used as a DNA extraction-independent method for qualitative comparison. In general, an effect on the observed community was found on all parameters tested, although bead beating and primer choice had the largest effect. The effect of bead beating intensity correlated with cell-wall strength as seen by a large increase in DNA from Gram-positive bacteria (up to 400%). However, significant differences were present at lower phylogenetic levels within the same phylum, suggesting that additional factors are at play. The best primer set based on in silico analysis was found to underestimate a number of important bacterial groups. For 16S rRNA gene analysis in activated sludge we recommend using the FastDNA SPIN Kit for Soil with four times the normal bead beating and V1-3 primers.}, } @article {pmid26179741, year = {2015}, author = {Garcia, SL and Buck, M and McMahon, KD and Grossart, HP and Eiler, A and Warnecke, F}, title = {Auxotrophy and intrapopulation complementary in the 'interactome' of a cultivated freshwater model community.}, journal = {Molecular ecology}, volume = {24}, number = {17}, pages = {4449-4459}, doi = {10.1111/mec.13319}, pmid = {26179741}, issn = {1365-294X}, mesh = {Bacteria/classification/*metabolism ; Crenarchaeota/genetics/*metabolism ; Fresh Water/*microbiology ; Genome, Archaeal ; Genome, Bacterial ; Heterotrophic Processes ; Lakes/microbiology ; *Metabolome ; *Metagenome ; *Microbial Consortia ; Phylogeny ; Plankton/classification/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vitamin B 12/biosynthesis ; }, abstract = {Microorganisms are usually studied either in highly complex natural communities or in isolation as monoclonal model populations that we manage to grow in the laboratory. Here, we uncover the biology of some of the most common and yet-uncultured bacteria in freshwater environments using a mixed culture from Lake Grosse Fuchskuhle. From a single shotgun metagenome of a freshwater mixed culture of low complexity, we recovered four high-quality metagenome-assembled genomes (MAGs) for metabolic reconstruction. This analysis revealed the metabolic interconnectedness and niche partitioning of these naturally dominant bacteria. In particular, vitamin- and amino acid biosynthetic pathways were distributed unequally with a member of Crenarchaeota most likely being the sole producer of vitamin B12 in the mixed culture. Using coverage-based partitioning of the genes recovered from a single MAG intrapopulation metabolic complementarity was revealed pointing to 'social' interactions for the common good of populations dominating freshwater plankton. As such, our MAGs highlight the power of mixed cultures to extract naturally occurring 'interactomes' and to overcome our inability to isolate and grow the microbes dominating in nature.}, } @article {pmid26179554, year = {2015}, author = {Keshavarzian, A and Green, SJ and Engen, PA and Voigt, RM and Naqib, A and Forsyth, CB and Mutlu, E and Shannon, KM}, title = {Colonic bacterial composition in Parkinson's disease.}, journal = {Movement disorders : official journal of the Movement Disorder Society}, volume = {30}, number = {10}, pages = {1351-1360}, doi = {10.1002/mds.26307}, pmid = {26179554}, issn = {1531-8257}, mesh = {Adult ; Aged ; Colon, Sigmoid/*microbiology ; Dysbiosis/*complications ; Feces/*microbiology ; Female ; Humans ; Intestinal Mucosa/*microbiology ; Male ; *Microbiota ; Middle Aged ; Parkinson Disease/*etiology ; Protein Folding ; alpha-Synuclein/*chemistry ; }, abstract = {INTRODUCTION: We showed that Parkinson's disease (PD) patients have alpha-synuclein (α-Syn) aggregation in their colon with evidence of colonic inflammation. If PD patients have altered colonic microbiota, dysbiosis might be the mechanism of neuroinflammation that leads to α-Syn misfolding and PD pathology.

METHODS: Sixty-six sigmoid mucosal biopsies and 65 fecal samples were collected from 38 PD patients and 34 healthy controls. Mucosal-associated and feces microbiota compositions were characterized using high-throughput ribosomal RNA gene amplicon sequencing. Data were correlated with clinical measures of PD, and a predictive assessment of microbial community functional potential was used to identify microbial functions.

RESULTS: The mucosal and fecal microbial community of PD patients was significantly different than control subjects, with the fecal samples showing more marked differences than the sigmoid mucosa. At the taxonomic level of genus, putative, "anti-inflammatory" butyrate-producing bacteria from the genera Blautia, Coprococcus, and Roseburia were significantly more abundant in feces of controls than PD patients. Bacteria from the genus Faecalibacterium were significantly more abundant in the mucosa of controls than PD. Putative, "proinflammatory" Proteobacteria of the genus Ralstonia were significantly more abundant in mucosa of PD than controls. Predictive metagenomics indicated that a large number of genes involved in metabolism were significantly lower in the PD fecal microbiome, whereas genes involved in lipopolysaccharide biosynthesis and type III bacterial secretion systems were significantly higher in PD patients.

CONCLUSION: This report provides evidence that proinflammatory dysbiosis is present in PD patients and could trigger inflammation-induced misfolding of α-Syn and development of PD pathology.}, } @article {pmid26175748, year = {2015}, author = {Monteiro, F and Romeiras, MM and Figueiredo, A and Sebastiana, M and Baldé, A and Catarino, L and Batista, D}, title = {Tracking cashew economically important diseases in the West African region using metagenomics.}, journal = {Frontiers in plant science}, volume = {6}, number = {}, pages = {482}, pmid = {26175748}, issn = {1664-462X}, abstract = {During the last decades, agricultural land-uses in West Africa were marked by dramatic shifts in the coverage of individual crops. Nowadays, cashew (Anacardium occidentale L.) is one of the most export-oriented horticulture crops, notably in Guinea-Bissau. Relying heavily on agriculture to increase their income, developing countries have been following a strong trend of moving on from traditional farming systems toward commercial production. Emerging infectious diseases, driven either by adaptation to local conditions or inadvertent importation of plant pathogens, are able to cause tremendous cashew production losses, with economic and social impact of which, in developing countries is often underestimated. Presently, plant genomics with metagenomics as an emergent tool, presents an enormous potential to better characterize diseases by providing extensive knowledge on plant pathogens at a large scale. In this perspective, we address metagenomics as a promising genomic tool to identify cashew fungal associated diseases as well as to discriminate the causal pathogens, aiming at obtaining tools to help design effective strategies for disease control and thus promote the sustainable production of cashew in West African Region.}, } @article {pmid26174127, year = {2015}, author = {Papadopoulou, A and Taberlet, P and Zinger, L}, title = {Metagenome skimming for phylogenetic community ecology: a new era in biodiversity research.}, journal = {Molecular ecology}, volume = {24}, number = {14}, pages = {3515-3517}, doi = {10.1111/mec.13263}, pmid = {26174127}, issn = {1365-294X}, mesh = {Animals ; *Biodiversity ; *Biota ; DNA, Mitochondrial/*genetics ; *Metagenomics ; *Phylogeny ; }, abstract = {It is now well recognized that considering species evolutionary history is crucial for understanding the processes driving community assembly (Cavender-Bares et al.). Considerable efforts have been made to integrate phylogenetics and community ecology into a single theoretical framework. Yet, assessing phylogenetic structure at the community scale remains a great challenge, in particular for poorly known organisms. While DNA metabarcoding is increasingly used for assessing taxonomic composition of complex communities from environmental samples, biases and limitations of this technique can preclude the retrieval of information on phylogenetic community structure. In this issue of Molecular Ecology, Andújar et al. (2015) demonstrate that shotgun sequencing of bulk samples of soil beetles and subsequent reconstruction of mitochondrial genomes can provide a solid phylogenetic framework to estimate species diversity and gain insights into the mechanisms underlying the spatial turnover of soil mesofaunal assemblages. This work highlights the enormous potential of 'metagenome skimming' not only for improving the current standards of DNA-based biodiversity assessment but also for opening up the application of phylogenetic community ecology to hyperdiverse and poorly known biota, which was heretofore inconceivable.}, } @article {pmid26169485, year = {2015}, author = {Lin, R and Lin, X and Guo, T and Wu, L and Zhang, W and Lin, W}, title = {Metaproteomic analysis of bacterial communities in marine mudflat aquaculture sediment.}, journal = {World journal of microbiology & biotechnology}, volume = {31}, number = {9}, pages = {1397-1408}, pmid = {26169485}, issn = {1573-0972}, mesh = {Animals ; Bacteria/chemistry/classification/genetics/*metabolism ; Bacterial Proteins/chemistry/genetics/*isolation & purification/metabolism ; Bivalvia/microbiology ; Geologic Sediments/*microbiology ; Metagenome ; Protein Folding ; Proteomics/*methods ; Water Microbiology ; }, abstract = {Bacteria living in marine sediment play crucial roles in the benthic-pelagic interface coupling process. However, the complexity of the marine environment and the abundance of interfering materials hamper metaproteomic research of the marine mudflat environment. In this study, a modified sequential protein extraction method was used for marine mudflat sediment metaproteomic investigation. For marine sediment samples in cultured clam mudflat, more than 1000 protein spots were visualized in a two-dimensional gel electrophoresis map and 78 % of 194 randomly selected spots were successfully identified by mass spectrometry. We further applied this method to compare long-term clam aquaculture and natural mudflat sediment and identified 53 altered proteins from different microbe resources, which belonged to different functional categories or metabolic pathways. We found that proteins involved in stress/defense response process, ATP regeneration and protein folding more inclined to increase abundance while arginine biosynthesis and signal transduction process related proteins preferred to decrease in clam cultured mudflat sediment. Meanwhile, proteins were abundant in pathogens of bivalves, such as Vibrio and Photobacterium, and decreased in Acinetobacter, after about 8 months clam cultured. Furthermore, the terminal restriction fragment length polymorphism assay was performed to compare microbial community composition between sediments mentioned above. Results showed that the top three enrich genera in natural sediment were Cytophaga, Butyrivibrio and Spirochaeta, while Cytophaga, Spirochaeta and Azoarcus were found enrichment in long-term mudflat aquaculture sediment.}, } @article {pmid26168244, year = {2015}, author = {Tzeng, TD and Pao, YY and Chen, PC and Weng, FC and Jean, WD and Wang, D}, title = {Effects of Host Phylogeny and Habitats on Gut Microbiomes of Oriental River Prawn (Macrobrachium nipponense).}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0132860}, pmid = {26168244}, issn = {1932-6203}, mesh = {Animals ; Crustacea/*microbiology ; *Ecosystem ; Intestines/*microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The gut microbial community is one of the richest and most complex ecosystems on earth, and the intestinal microbes play an important role in host development and health. Next generation sequencing approaches, which rapidly produce millions of short reads that enable the investigation on a culture independent basis, are now popular for exploring microbial community. Currently, the gut microbiome in fresh water shrimp is unexplored. To explore gut microbiomes of the oriental river prawn (Macrobrachium nipponense) and investigate the effects of host genetics and habitats on the microbial composition, 454 pyrosequencing based on the 16S rRNA gene were performed. We collected six groups of samples, including M. nipponense shrimp from two populations, rivers and lakes, and one sister species (M. asperulum) as an out group. We found that Proteobacteria is the major phylum in oriental river prawn, followed by Firmicutes and Actinobacteria. Compositional analysis showed microbial divergence between the two shrimp species is higher than that between the two populations of one shrimp species collected from river and lake. Hierarchical clustering also showed that host genetics had a greater impact on the divergence of gut microbiome than host habitats. This finding was also congruent with the functional prediction from the metagenomic data implying that the two shrimp species still shared the same type of biological functions, reflecting a similar metabolic profile in their gut environments. In conclusion, this study provides the first investigation of the gut microbiome of fresh water shrimp, and supports the hypothesis of host species-specific signatures of bacterial community composition.}, } @article {pmid26162884, year = {2015}, author = {Shaw, JL and Monis, P and Weyrich, LS and Sawade, E and Drikas, M and Cooper, AJ}, title = {Using Amplicon Sequencing To Characterize and Monitor Bacterial Diversity in Drinking Water Distribution Systems.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {18}, pages = {6463-6473}, pmid = {26162884}, issn = {1098-5336}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Biota ; Chloramines ; Disinfection/methods/standards ; Drinking Water/*microbiology ; Genes, rRNA ; Metagenome ; Microbial Interactions ; *Microbiota ; Nitrification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; *Water Microbiology/standards ; Water Purification/standards ; Water Quality ; }, abstract = {Drinking water assessments use a variety of microbial, physical, and chemical indicators to evaluate water treatment efficiency and product water quality. However, these indicators do not allow the complex biological communities, which can adversely impact the performance of drinking water distribution systems (DWDSs), to be characterized. Entire bacterial communities can be studied quickly and inexpensively using targeted metagenomic amplicon sequencing. Here, amplicon sequencing of the 16S rRNA gene region was performed alongside traditional water quality measures to assess the health, quality, and efficiency of two distinct, full-scale DWDSs: (i) a linear DWDS supplied with unfiltered water subjected to basic disinfection before distribution and (ii) a complex, branching DWDS treated by a four-stage water treatment plant (WTP) prior to disinfection and distribution. In both DWDSs bacterial communities differed significantly after disinfection, demonstrating the effectiveness of both treatment regimes. However, bacterial repopulation occurred further along in the DWDSs, and some end-user samples were more similar to the source water than to the postdisinfection water. Three sample locations appeared to be nitrified, displaying elevated nitrate levels and decreased ammonia levels, and nitrifying bacterial species, such as Nitrospira, were detected. Burkholderiales were abundant in samples containing large amounts of monochloramine, indicating resistance to disinfection. Genera known to contain pathogenic and fecal-associated species were also identified in several locations. From this study, we conclude that metagenomic amplicon sequencing is an informative method to support current compliance-based methods and can be used to reveal bacterial community interactions with the chemical and physical properties of DWDSs.}, } @article {pmid26156216, year = {2015}, author = {Verbeke, KA and Boobis, AR and Chiodini, A and Edwards, CA and Franck, A and Kleerebezem, M and Nauta, A and Raes, J and van Tol, EA and Tuohy, KM}, title = {Towards microbial fermentation metabolites as markers for health benefits of prebiotics.}, journal = {Nutrition research reviews}, volume = {28}, number = {1}, pages = {42-66}, pmid = {26156216}, issn = {1475-2700}, mesh = {Bacteria/metabolism ; Carbohydrates ; Colon/physiology ; Fatty Acids/metabolism ; Fatty Acids, Volatile/analysis/metabolism ; Feces/chemistry/microbiology ; Fermentation/*physiology ; Gastrointestinal Microbiome/drug effects ; *Health Promotion ; Humans ; Intestines/*microbiology ; Metabolomics ; Metagenomics ; Plants/chemistry ; Polyphenols/metabolism ; *Prebiotics ; Proteins/metabolism ; }, abstract = {Available evidence on the bioactive, nutritional and putative detrimental properties of gut microbial metabolites has been evaluated to support a more integrated view of how prebiotics might affect host health throughout life. The present literature inventory targeted evidence for the physiological and nutritional effects of metabolites, for example, SCFA, the potential toxicity of other metabolites and attempted to determine normal concentration ranges. Furthermore, the biological relevance of more holistic approaches like faecal water toxicity assays and metabolomics and the limitations of faecal measurements were addressed. Existing literature indicates that protein fermentation metabolites (phenol, p-cresol, indole, ammonia), typically considered as potentially harmful, occur at concentration ranges in the colon such that no toxic effects are expected either locally or following systemic absorption. The endproducts of saccharolytic fermentation, SCFA, may have effects on colonic health, host physiology, immunity, lipid and protein metabolism and appetite control. However, measuring SCFA concentrations in faeces is insufficient to assess the dynamic processes of their nutrikinetics. Existing literature on the usefulness of faecal water toxicity measures as indicators of cancer risk seems limited. In conclusion, at present there is insufficient evidence to use changes in faecal bacterial metabolite concentrations as markers of prebiotic effectiveness. Integration of results from metabolomics and metagenomics holds promise for understanding the health implications of prebiotic microbiome modulation but adequate tools for data integration and interpretation are currently lacking. Similarly, studies measuring metabolite fluxes in different body compartments to provide a more accurate picture of their nutrikinetics are needed.}, } @article {pmid26154405, year = {2015}, author = {Zheng, W and Zhang, Z and Liu, C and Qiao, Y and Zhou, D and Qu, J and An, H and Xiong, M and Zhu, Z and Zhao, X}, title = {Metagenomic sequencing reveals altered metabolic pathways in the oral microbiota of sailors during a long sea voyage.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {9131}, pmid = {26154405}, issn = {2045-2322}, mesh = {Biodiversity ; Folic Acid/blood/metabolism ; Homocysteine/blood ; Humans ; *Metabolic Networks and Pathways ; Metagenome ; *Metagenomics ; *Microbiota ; Mouth/*microbiology ; Mouth Mucosa/microbiology ; RNA, Ribosomal, 16S/genetics ; Vitamin B 12/blood ; }, abstract = {Seafaring is a difficult occupation, and sailors face higher health risks than individuals on land. Commensal microbiota participates in the host immune system and metabolism, reflecting the host's health condition. However, the interaction mechanisms between the microbiota and the host's health condition remain unclear. This study reports the influence of long sea voyages on human health by utilising a metagenomic analysis of variation in the microbiota of the buccal mucosa. Paired samples collected before and after a sea-voyage were analysed. After more than 120 days of ocean sailing, the oral microbial diversity of sailors was reduced by approximately 5 fold, and the levels of several pathogens (e.g., Streptococcus pneumonia) increased. Moreover, 69.46% of the identified microbial sequences were unclassified microbiota. Notably, several metabolic pathways were dramatically decreased, including folate biosynthesis, carbohydrate, lipid and amino acid pathways. Clinical examination of the hosts confirmed the identified metabolic changes, as demonstrated by decreased serum levels of haemoglobin and folic acid, a decreased neutrophil-to-lymphocyte ratio, and increased levels of triglycerides, cholesterol and homocysteine, which are consistent with the observed microbial variation. Our study suggests that oral mucosal bacteria may reflect host health conditions and could provide approaches for improving the health of sailors.}, } @article {pmid26154300, year = {2015}, author = {Kurilshikov, A and Livanova, NN and Fomenko, NV and Tupikin, AE and Rar, VA and Kabilov, MR and Livanov, SG and Tikunova, NV}, title = {Comparative Metagenomic Profiling of Symbiotic Bacterial Communities Associated with Ixodes persulcatus, Ixodes pavlovskyi and Dermacentor reticulatus Ticks.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0131413}, pmid = {26154300}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/*genetics ; Biodiversity ; Dermacentor/*microbiology ; Female ; Ixodes/*microbiology ; Male ; *Metagenomics ; Symbiosis/*genetics ; }, abstract = {Ixodes persulcatus, Ixodes pavlovskyi, and Dermacentor reticulatus ticks inhabiting Western Siberia are responsible for the transmission of a number of etiological agents that cause human and animal tick-borne diseases. Because these ticks are abundant in the suburbs of large cities, agricultural areas, and popular tourist sites and frequently attack people and livestock, data regarding the microbiomes of these organisms are required. Using metagenomic 16S profiling, we evaluate bacterial communities associated with I. persulcatus, I. pavlovskyi, and D. reticulatus ticks collected from the Novosibirsk region of Russia. A total of 1214 ticks were used for this study. DNA extracted from the ticks was pooled according to tick species and sex. Sequencing of the V3-V5 domains of 16S rRNA genes was performed using the Illumina Miseq platform. The following bacterial genera were prevalent in the examined communities: Acinetobacter (all three tick species), Rickettsia (I. persulcatus and D. reticulatus) and Francisella (D. reticulatus). B. burgdorferi sensu lato and B. miyamotoi sequences were detected in I. persulcatus and I. pavlovskyi but not in D. reticulatus ticks. The pooled samples of all tick species studied contained bacteria from the Anaplasmataceae family, although their occurrence was low. DNA from A. phagocytophilum and Candidatus Neoehrlichia mikurensis was first observed in I. pavlovskyi ticks. Significant inter-species differences in the number of bacterial taxa as well as intra-species diversity related to tick sex were observed. The bacterial communities associated with the I. pavlovskyi ticks displayed a higher biodiversity compared with those of the I. persulcatus and D. reticulatus ticks. Bacterial community structure was also diverse across the studied tick species, as shown by permutational analysis of variance using the Bray-Curtis dissimilarity metric (p = 0.002). Between-sex variation was confirmed by PERMANOVA testing in I. persulcatus (p = 0.042) and I. pavlovskyi (p = 0.042) ticks. Our study indicated that 16S metagenomic profiling could be used for rapid assessment of the occurrence of medically important bacteria in tick populations inhabiting different natural biotopes and therefore the epidemic danger of studied foci.}, } @article {pmid26152743, year = {2015}, author = {Pal, SK and Li, SM and Wu, X and Qin, H and Kortylewski, M and Hsu, J and Carmichael, C and Frankel, P}, title = {Stool Bacteriomic Profiling in Patients with Metastatic Renal Cell Carcinoma Receiving Vascular Endothelial Growth Factor-Tyrosine Kinase Inhibitors.}, journal = {Clinical cancer research : an official journal of the American Association for Cancer Research}, volume = {21}, number = {23}, pages = {5286-5293}, doi = {10.1158/1078-0432.CCR-15-0724}, pmid = {26152743}, issn = {1557-3265}, mesh = {Adult ; Aged ; Antineoplastic Agents/adverse effects/therapeutic use ; Bacteria/*classification/*genetics ; Biodiversity ; Carcinoma, Renal Cell/*complications/drug therapy/pathology ; Cluster Analysis ; Diarrhea/*etiology/microbiology ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Kidney Neoplasms/*complications/drug therapy/pathology ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Protein Kinase Inhibitors/adverse effects/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Vascular Endothelial Growth Factor A/antagonists & inhibitors ; }, abstract = {PURPOSE: Diarrhea occurs in approximately half of patients with metastatic renal cell carcinoma (mRCC) receiving vascular endothelial growth factor-tyrosine kinase inhibitors (VEGF-TKI). We evaluated the relationship between VEGF-TKI-related diarrhea and stool microbiota.

EXPERIMENTAL DESIGN: Stool samples were collected from 20 mRCC patients receiving VEGF-TKIs. 16S rRNA sequencing was used to characterize the stool bacteriomic profiling of patients. Assay validation with Salmonella typhimurium spike-in experiments suggested greatest speciation with use of the V5 region.

RESULTS: Higher levels of Bacteroides spp. and lower levels of Prevotella spp. were found in patients with diarrhea. In addition, patients receiving VEGF-TKIs with mRCC appeared to have less relative abundance of Bifidobacterium spp. as compared with previous reports based on healthy subjects.

CONCLUSIONS: We have thus demonstrated interplay between microbiota and VEGF-TKI-induced diarrhea. Further studies are warranted to evaluate the potential causative role of preexisting dysbiosis in VEGF-TKI-related diarrhea.}, } @article {pmid26150661, year = {2015}, author = {Kreisinger, J and Bastien, G and Hauffe, HC and Marchesi, J and Perkins, SE}, title = {Interactions between multiple helminths and the gut microbiota in wild rodents.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1675}, pages = {}, pmid = {26150661}, issn = {1471-2970}, mesh = {Animals ; Female ; *Gastrointestinal Microbiome/genetics ; Genetic Variation ; Helminths/genetics/isolation & purification/*pathogenicity ; *Host-Parasite Interactions/genetics ; Host-Pathogen Interactions/genetics ; Male ; Murinae/*microbiology/*parasitology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The gut microbiota is vital to host health and, as such, it is important to elucidate the mechanisms altering its composition and diversity. Intestinal helminths are host immunomodulators and have evolved both temporally and spatially in close association with the gut microbiota, resulting in potential mechanistic interplay. Host-helminth and host-microbiota interactions are comparatively well-examined, unlike microbiota-helminth relationships, which typically focus on experimental infection with a single helminth species in laboratory animals. Here, in addition to a review of the literature on helminth-microbiota interactions, we examined empirically the association between microbiota diversity and composition and natural infection of multiple helminth species in wild mice (Apodemus flavicollis), using 16S rRNA gene catalogues (metataxonomics). In general, helminth presence is linked with high microbiota diversity, which may confer health benefits to the host. Within our wild rodent system variation in the composition and abundance of gut microbial taxa associated with helminths was specific to each helminth species and occurred both up- and downstream of a given helminth's niche (gut position). The most pronounced helminth-microbiota association was between the presence of tapeworms in the small intestine and increased S24-7 (Bacteroidetes) family in the stomach. Helminths clearly have the potential to alter gut homeostasis. Free-living rodents with a diverse helminth community offer a useful model system that enables both correlative (this study) and manipulative inference to elucidate helminth-microbiota interactions.}, } @article {pmid26150453, year = {2015}, author = {Jeon, SJ and Vieira-Neto, A and Gobikrushanth, M and Daetz, R and Mingoti, RD and Parize, AC and de Freitas, SL and da Costa, AN and Bicalho, RC and Lima, S and Jeong, KC and Galvão, KN}, title = {Uterine Microbiota Progression from Calving until Establishment of Metritis in Dairy Cows.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {18}, pages = {6324-6332}, pmid = {26150453}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification/isolation & purification ; Bacteroidetes/isolation & purification ; Cattle/*microbiology ; Cattle Diseases/*microbiology ; Endometritis/microbiology/*veterinary ; Female ; Fusobacteria/isolation & purification ; High-Throughput Nucleotide Sequencing ; Microbial Interactions ; *Microbiota ; *Postpartum Period ; Proteobacteria/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Time Factors ; Uterus/*microbiology ; }, abstract = {The objective of this study was to evaluate the progression of the uterine microbiota from calving until establishment of metritis. Uterine swabs (n = 72) collected at 0, 2, and 6 ± 2 days postpartum (dpp) from 12 metritic and 12 healthy cows were used for metagenomic sequencing of the 16S rRNA gene on the Illumina MiSeq platform. A heat map showed that uterine microbiota was established at calving. The microbiota changed rapidly from 0 to 6 ± 2 dpp, with a decrease in the abundance of Proteobacteria and an increase in the abundance of Bacteroidetes and Fusobacteria, which were dominant in metritic cows. Uterine microbiota composition was shared; however, metritic and healthy cows could be discriminated using relative abundance of bacterial genera at 0, 2, and 6 ± 2 dpp. Bacteroides was the main genus associated with metritis because it was the only genus that showed significantly greater abundance in cows with metritis. As the abundance of Bacteroides organisms increased, the uterine discharge score, a measure of uterine health, worsened. Fusobacterium was also an important genus associated with metritis because Fusobacterium abundance increased as Bacteroides abundance increased and the uterine discharge score worsened as the abundance increased. The correlation with uterine discharge score and the correlation with Bacteroides or Fusobacterium showed that other bacteria, such as Helcoccocus, Filifactor, and Porphyromonas, were also associated with metritis. There were also bacteria associated with uterine health, such as "Candidatus Blochmannia," Escherichia, Sneathia, and Pedobacter.}, } @article {pmid26147095, year = {2015}, author = {Frank, DN and Bales, ES and Monks, J and Jackman, MJ and MacLean, PS and Ir, D and Robertson, CE and Orlicky, DJ and McManaman, JL}, title = {Perilipin-2 Modulates Lipid Absorption and Microbiome Responses in the Mouse Intestine.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0131944}, pmid = {26147095}, issn = {1932-6203}, support = {P30 DK048520/DK/NIDDK NIH HHS/United States ; P30CA046934/CA/NCI NIH HHS/United States ; R01 HD075285/HD/NICHD NIH HHS/United States ; 2R01HD045962/HD/NICHD NIH HHS/United States ; DK48520/DK/NIDDK NIH HHS/United States ; P30 CA046934/CA/NCI NIH HHS/United States ; U10 HD045962/HD/NICHD NIH HHS/United States ; UL1 TR001082/TR/NCATS NIH HHS/United States ; }, mesh = {Adiposity/physiology ; Animals ; Body Weight ; Diet, Fat-Restricted ; Diet, High-Fat ; Fatty Liver/*metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Intestinal Mucosa/*metabolism ; Intestines/microbiology ; Lipid Metabolism/*physiology ; Liver/*metabolism ; Male ; Membrane Proteins/genetics/*metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Perilipin-2 ; RNA, Ribosomal, 16S ; }, abstract = {Obesity and its co-morbidities, such as fatty liver disease, are increasingly prevalent worldwide health problems. Intestinal microorganisms have emerged as critical factors linking diet to host physiology and metabolic function, particularly in the context of lipid homeostasis. We previously demonstrated that deletion of the cytoplasmic lipid drop (CLD) protein Perilipin-2 (Plin2) in mice largely abrogates long-term deleterious effects of a high fat (HF) diet. Here we test the hypotheses that Plin2 function impacts the earliest steps of HF diet-mediated pathogenesis as well as the dynamics of diet-associated changes in gut microbiome diversity and function. WT and perilipin-2 null mice raised on a standard chow diet were randomized to either low fat (LF) or HF diets. After four days, animals were assessed for changes in physiological (body weight, energy balance, and fecal triglyceride levels), histochemical (enterocyte CLD content), and fecal microbiome parameters. Plin2-null mice had significantly lower respiratory exchange ratios, diminished frequencies of enterocyte CLDs, and increased fecal triglyceride levels compared with WT mice. Microbiome analyses, employing both 16S rRNA profiling and metagenomic deep sequencing, indicated that dietary fat content and Plin2 genotype were significantly and independently associated with gut microbiome composition, diversity, and functional differences. These data demonstrate that Plin2 modulates rapid effects of diet on fecal lipid levels, enterocyte CLD contents, and fuel utilization properties of mice that correlate with structural and functional differences in their gut microbial communities. Collectively, the data provide evidence of Plin2 regulated intestinal lipid uptake, which contributes to rapid changes in the gut microbial communities implicated in diet-induced obesity.}, } @article {pmid26145983, year = {2015}, author = {Holt, PG}, title = {The mechanism or mechanisms driving atopic asthma initiation: The infant respiratory microbiome moves to center stage.}, journal = {The Journal of allergy and clinical immunology}, volume = {136}, number = {1}, pages = {15-22}, doi = {10.1016/j.jaci.2015.05.011}, pmid = {26145983}, issn = {1097-6825}, mesh = {Animals ; Asthma/*immunology/*microbiology ; Child ; Host-Pathogen Interactions ; Humans ; Hypersensitivity, Immediate/*immunology/*microbiology ; *Immunocompetence ; Infant ; *Microbiota ; Respiratory System/immunology/*microbiology ; }, abstract = {Developments over the last 5 to 10 years, principally from studies on comprehensively phenotyped prospective birth cohorts, have highlighted the important role of viral respiratory tract infections during infancy and early childhood, particularly those occurring against a background of pre-existing sensitization to perennial aeroallergens, in driving the development of early-onset atopic asthma. Although debate surrounding the mechanism or mechanisms governing this causal pathway remains intense, demonstration of the capacity of pretreatment with anti-IgE antibody to blunt seasonal virus-associated asthma exacerbations in children provides strong support for the underlying concept. However, emerging data appear set to further complicate this picture. Notably, a combination of culture-based studies and complementary population-wide bacterial metagenomic data suggests that parallel host-bacteria interactions during infancy might play an additional role in modulating this causal pathway, as well as contributing independently to pathogenesis. These and related issues surrounding development of immune competence during the crucial early postnatal period, when these pathways are maximally active, are discussed below.}, } @article {pmid26143242, year = {2015}, author = {Wei, F and Wang, X and Wu, Q}, title = {The giant panda gut microbiome.}, journal = {Trends in microbiology}, volume = {23}, number = {8}, pages = {450-452}, doi = {10.1016/j.tim.2015.06.004}, pmid = {26143242}, issn = {1878-4380}, mesh = {Animals ; Cellulose/metabolism ; Feeding Behavior ; *Gastrointestinal Microbiome ; Ursidae/*microbiology ; }, abstract = {Giant pandas (Ailuropoda melanoleuca) are bamboo specialists that evolved from carnivores. Their gut microbiota probably aids in the digestion of cellulose and this is considered an example of gut microbiota adaptation to a bamboo diet. However, this issue remains unresolved and further functional and compositional studies are needed.}, } @article {pmid26139332, year = {2015}, author = {Steinmeyer, S and Lee, K and Jayaraman, A and Alaniz, RC}, title = {Microbiota metabolite regulation of host immune homeostasis: a mechanistic missing link.}, journal = {Current allergy and asthma reports}, volume = {15}, number = {5}, pages = {24}, pmid = {26139332}, issn = {1534-6315}, support = {R01 AI110642/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Tract/*microbiology ; *Homeostasis/immunology ; Humans ; *Microbiota ; Tryptophan/metabolism ; }, abstract = {Metazoans predominantly co-exist with symbiotic microorganisms called the microbiota. Metagenomic surveys of the microbiota reveal a diverse ecosystem of microbes particularly in the gastrointestinal (GI) tract. Perturbations in the GI microbiota in higher mammals (i.e., humans) are linked to diseases with variegated symptomology including inflammatory bowel disease, asthma, and auto-inflammatory disorders. Indeed, studies using germ-free mice (lacking a microbiota) confirm that host development and homeostasis are dependent on the microbiota. A long-known key feature of the GI tract microbiota is metabolizing host indigestible dietary matter for maximum energy extraction; however, host signaling pathways are greatly influenced by the microbiota as well. In line with these observations, recent research has revealed that metabolites produced strictly by select microbiota members are mechanistic regulators of host cell functions. In this review, we discuss two major classes of microbiota-produced metabolites: short-chain fatty acids and tryptophan metabolites. We describe the known important roles for these metabolites in shaping host immunity and comment on the current status and future directions for microbiota metabolomics research.}, } @article {pmid26137633, year = {2015}, author = {Ravin, NV and Mardanova, AV and Skryabin, KG}, title = {[Metagenomics as a Tool for the Investigation of Uncultured Microorganisms].}, journal = {Genetika}, volume = {51}, number = {5}, pages = {519-528}, pmid = {26137633}, issn = {0016-6758}, mesh = {*Genome, Bacterial ; *Metagenome ; Metagenomics/*methods ; Microbial Consortia/*genetics ; }, abstract = {Uncultured microorganisms represent a significant part of the Earth's biodiversity. Natural ecosystems contain less than 0.1-1% of the microorganisms that can be cultured in the laboratory. Therefore, new methodological approaches are required for the identification and description of uncultured microorganisms, for studies of their genetic diversity and the structure of microbial associations, and for an understanding of their ecological importance in the biosphere. Metagenomics, a method of analyzing the collective genome.of a microbial community without cultivation, makes it possible to unravel fundamental matters of the microbiology and ecology of microorganisms. Another efficient method of analysis of uncultured forms of microorganisms is "single cell genomics," which involves the isolation of single cells from microbial communities and the sequencing of their genomes. Developed in the last decade, the high throughput technologies of next-generation sequencing provide important input into the investigation of genome reconstruction for all of the microorganisms residing and interacting within ecosystems. This review describes the major methodological approaches used in metagenomic analysis of microbial communities, as well as accomplishments in the search for new uncultured microorganism, the unraveling of their genomes, and an elucidation of their role in ecosystems.}, } @article {pmid26130132, year = {2015}, author = {Fosso, B and Santamaria, M and Marzano, M and Alonso-Alemany, D and Valiente, G and Donvito, G and Monaco, A and Notarangelo, P and Pesole, G}, title = {BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS.}, journal = {BMC bioinformatics}, volume = {16}, number = {}, pages = {203}, pmid = {26130132}, issn = {1471-2105}, mesh = {Bacteria/*genetics ; Biodiversity ; Computational Biology/*methods ; Fungi/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; *Metagenomics ; *Software ; }, abstract = {BACKGROUND: Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects.

RESULTS: BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data).

CONCLUSION: BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent the currently known bacterial and fungal world, showed that BioMaS outperforms QIIME and MOTHUR in terms of extent and accuracy of deep taxonomic sequence assignments.}, } @article {pmid26130576, year = {2015}, author = {Manter, DK and Bakker, MG}, title = {Estimating beta diversity for under-sampled communities using the variably weighted Odum dissimilarity index and OTUshuff.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {21}, pages = {3451-3459}, doi = {10.1093/bioinformatics/btv394}, pmid = {26130576}, issn = {1367-4811}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Computer Simulation ; DNA, Bacterial/genetics ; Humans ; *Metagenomics ; *Models, Theoretical ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Selection Bias ; *Soil Microbiology ; }, abstract = {MOTIVATION: In profiling the composition and structure of complex microbial communities via high throughput amplicon sequencing, a very low proportion of community members are typically sampled. As a result of this incomplete sampling, estimates of dissimilarity between communities are often inflated, an issue we term pseudo β-diversity.

RESULTS: We present a set of tools to identify and correct for the presence of pseudo β-diversity in contrasts between microbial communities. The variably weighted Odum dissimilarity (DwOdum) allows for down-weighting the influence of either abundant or rare taxa in calculating a measure of similarity between two communities. We show that down-weighting the influence of rare taxa can be used to minimize pseudo β-diversity arising from incomplete sampling. Down-weighting the influence of abundant taxa can increase the sensitivity of hypothesis testing. OTUshuff is an associated test for identifying the presence of pseudo β-diversity in pairwise community contrasts.

A Perl script for calculating the DwOdum score from a taxon abundance table and performing pairwise contrasts with OTUshuff can be obtained at http://www.ars.usda.gov/services/software/software.htm?modecode=30-12-10-00.

CONTACT: daniel.manter@ars.usda.gov

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid26125856, year = {2015}, author = {Rodrigues, NF and Kästle, J and Coutinho, TJ and Amorim, AT and Campos, GB and Santos, VM and Marques, LM and Timenetsky, J and de Farias, ST}, title = {Qualitative analysis of the vaginal microbiota of healthy cattle and cattle with genital-tract disease.}, journal = {Genetics and molecular research : GMR}, volume = {14}, number = {2}, pages = {6518-6528}, doi = {10.4238/2015.June.12.4}, pmid = {26125856}, issn = {1676-5680}, mesh = {Animals ; Bacteria/classification/*genetics/pathogenicity ; Cattle ; Female ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reproductive Tract Infections/*microbiology/veterinary ; Vagina/*microbiology ; }, abstract = {The microbial community of the reproductive appara-tus, when known, can provide information about the health of the host. Metagenomics has been used to characterize and obtain genetic infor-mation about microbial communities in various environments and can relate certain diseases with changes in this community composition. In this study, samples of vaginal surface mucosal secretions were col-lected from five healthy cows and five cows that showed symptoms of reproductive disorders. Following high-throughput sequencing of the isolated microbial DNA, data were processed using the Mothur soft-ware to remove low-quality sequences and chimeras, and released to the Ribosomal Database Project for classification of operational taxo-nomic units (OTUs). Local BLASTn was performed and results were loaded into the MEGAN program for viewing profiles and taxonomic microbial attributes. The control profile comprised a total of 15 taxa, with Bacteroides, Enterobacteriaceae, and Victivallis comprising the highest representation of OTUs; the reproductive disorder-positive profile comprised 68 taxa, with Bacteroides, Enterobacteriaceae, His-tophilus, Victivallis, Alistipes, and Coriobacteriaceae being the taxa with the most OTU representation. A change was observed in both the community composition as well as in the microbial attributes of the profiles, suggesting that a relationship might exist between the patho-gen and representative taxa, reflecting the production of metabolites to disease progression.}, } @article {pmid26121551, year = {2015}, author = {Sato, Y and Yamagishi, J and Yamashita, R and Shinozaki, N and Ye, B and Yamada, T and Yamamoto, M and Nagasaki, M and Tsuboi, A}, title = {Inter-Individual Differences in the Oral Bacteriome Are Greater than Intra-Day Fluctuations in Individuals.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0131607}, pmid = {26121551}, issn = {1932-6203}, mesh = {Adult ; Bacteria/*classification/*genetics ; Biodiversity ; Cluster Analysis ; DNA Barcoding, Taxonomic ; Dental Plaque/microbiology ; Humans ; Male ; *Metagenome ; *Microbiota ; Mouth/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Time Factors ; }, abstract = {Given the advent of massively parallel DNA sequencing, human microbiome is analyzed comprehensively by metagenomic approaches. However, the inter- and intra-individual variability and stability of the human microbiome remain poorly characterized, particularly at the intra-day level. This issue is of crucial importance for studies examining the effects of microbiome on human health. Here, we focused on bacteriome of oral plaques, for which repeated, time-controlled sampling is feasible. Eighty-one supragingival plaque subjects were collected from healthy individuals, examining multiple sites within the mouth at three time points (forenoon, evening, and night) over the course of 3 days. Bacterial composition was estimated by 16S rRNA sequencing and species-level profiling, resulting in identification of a total of 162 known bacterial species. We found that species compositions and their relative abundances were similar within individuals, and not between sampling time or tooth type. This suggests that species-level oral bacterial composition differs significantly between individuals, although the number of subjects is limited and the intra-individual variation also occurs. The majority of detected bacterial species (98.2%; 159/162), however, did not fluctuate over the course of the day, implying a largely stable oral microbiome on an intra-day time scale. In fact, the stability of this data set enabled us to estimate potential interactions between rare bacteria, with 40 co-occurrences supported by the existing literature. In summary, the present study provides a valuable basis for studies of the human microbiome, with significant implications in terms of biological and clinical outcomes.}, } @article {pmid26117598, year = {2015}, author = {Hu, Q and Guo, X and Liang, Y and Hao, X and Ma, L and Yin, H and Liu, X}, title = {Comparative metagenomics reveals microbial community differentiation in a biological heap leaching system.}, journal = {Research in microbiology}, volume = {166}, number = {6}, pages = {525-534}, doi = {10.1016/j.resmic.2015.06.005}, pmid = {26117598}, issn = {1769-7123}, mesh = {Acidiphilium/genetics/*isolation & purification ; Acidithiobacillus/genetics/*isolation & purification ; Copper/metabolism ; DNA Repair/genetics ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Microbial Consortia/*genetics/physiology ; Mining ; Phylogeny ; }, abstract = {The microbial community in a biological heap leaching (BHL) system is crucial for the decomposition of ores. However, the microbial community structure and functional differentiation in different parts of a biological heap leaching system are still unknown. In this study, metagenomic sequencing was used to fully illuminate the microbial community differentiation in the pregnant leach solution (PLS) and leaching heap (LH) of a BHL system. Long-read sequences (1.3 million) were obtained for the two samples, and the MG_RAST server was used to perform further analysis. The taxa analysis results indicated that the dominant genera of PLS is autotrophic bacterium Acidithiobacillus, but heterotrophic bacterium Acidiphilium is predominant in LH. Furthermore, functional annotation and hierarchical comparison with different reference samples showed that the abundant presence of genes was involved in transposition, DNA repair and heavy metal transport. The sequences related to transposase, which is important for the survival of the organism in the hostile environment, were both mainly classified into Acidiphilium for PLS and LH. These results indicated that not only autotrophic bacteria such as Acidithiobacillus, but also heterotrophic bacteria such as Acidiphilium, were essential participants in the bioleaching process. This new meta-view research will further facilitate the effective application of bioleaching.}, } @article {pmid26114888, year = {2016}, author = {Dittami, SM and Duboscq-Bidot, L and Perennou, M and Gobet, A and Corre, E and Boyen, C and Tonon, T}, title = {Host-microbe interactions as a driver of acclimation to salinity gradients in brown algal cultures.}, journal = {The ISME journal}, volume = {10}, number = {1}, pages = {51-63}, pmid = {26114888}, issn = {1751-7370}, mesh = {Acclimatization/*physiology ; Bacteria/genetics ; Fresh Water/*microbiology ; Metagenome ; Microbial Interactions/genetics/*physiology ; Microbiota/genetics ; Phaeophyceae/*microbiology/physiology ; Salt Tolerance/genetics/physiology ; Seawater/*microbiology ; }, abstract = {Like most eukaryotes, brown algae live in association with bacterial communities that frequently have beneficial effects on their development. Ectocarpus is a genus of small filamentous brown algae, which comprises a strain that has recently colonized freshwater, a rare transition in this lineage. We generated an inventory of bacteria in Ectocarpus cultures and examined the effect they have on acclimation to an environmental change, that is, the transition from seawater to freshwater medium. Our results demonstrate that Ectocarpus depends on bacteria for this transition: cultures that have been deprived of their associated microbiome do not survive a transfer to freshwater, but restoring their microflora also restores the capacity to acclimate to this change. Furthermore, the transition between the two culture media strongly affects the bacterial community composition. Examining a range of other closely related algal strains, we observed that the presence of two bacterial operational taxonomic units correlated significantly with an increase in low salinity tolerance of the algal culture. Despite differences in the community composition, no indications were found for functional differences in the bacterial metagenomes predicted to be associated with algae in the salinities tested, suggesting functional redundancy in the associated bacterial community. Our study provides an example of how microbial communities may impact the acclimation and physiological response of algae to different environments, and thus possibly act as facilitators of speciation. It paves the way for functional examinations of the underlying host-microbe interactions, both in controlled laboratory and natural conditions.}, } @article {pmid26113243, year = {2015}, author = {Hedlund, BP and Murugapiran, SK and Alba, TW and Levy, A and Dodsworth, JA and Goertz, GB and Ivanova, N and Woyke, T}, title = {Uncultivated thermophiles: current status and spotlight on 'Aigarchaeota'.}, journal = {Current opinion in microbiology}, volume = {25}, number = {}, pages = {136-145}, doi = {10.1016/j.mib.2015.06.008}, pmid = {26113243}, issn = {1879-0364}, mesh = {Archaea/*classification/genetics/growth & development/*physiology ; Bacteria/classification/genetics/growth & development ; *Biodiversity ; Hot Springs/*microbiology ; Hot Temperature ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S ; *Water Microbiology ; }, abstract = {Meta-analysis of cultivation-independent sequence data shows that geothermal systems host an abundance of novel organisms, representing a vast unexplored phylogenetic and functional diversity among yet-uncultivated thermophiles. A number of thermophiles have recently been interrogated using metagenomic and/or single-cell genomic approaches, including members of taxonomic groups that inhabit both thermal and non-thermal environments, such as 'Acetothermia' (OP1) and 'Atribacteria' (OP9/JS1), as well as the exclusively thermophilic lineages 'Korarchaeota', 'Calescamantes' (EM19), 'Fervidibacteria' (OctSpA1-106), and 'Aigarchaeota' (HWCG-I). The 'Aigarchaeota', a sister lineage to the Thaumarchaeota, likely includes both hyperthermophiles and moderate thermophiles. They inhabit terrestrial, marine, and subsurface thermal environments and comprise at least nine genus-level lineages, several of which are globally distributed.}, } @article {pmid26112912, year = {2015}, author = {Nasir, A and Kim, KM and Caetano-Anollés, G}, title = {Lokiarchaeota: eukaryote-like missing links from microbial dark matter?.}, journal = {Trends in microbiology}, volume = {23}, number = {8}, pages = {448-450}, doi = {10.1016/j.tim.2015.06.001}, pmid = {26112912}, issn = {1878-4380}, mesh = {Archaea/classification/*genetics ; *Evolution, Molecular ; *Genome, Archaeal ; }, abstract = {Identification and genome sequencing of novel organismal groups can reduce the gap between the sequenced minority and the unexplored majority. The recent discovery of phylum Lokiarchaeota promises understanding of biological history. Here we inquire if Lokiarchaeota truly represent ancient eukaryotic ancestors or just microbial dark matter of expanding archaeal diversity.}, } @article {pmid26111733, year = {2015}, author = {Roterman, YR and Benayahu, Y and Reshef, L and Gophna, U}, title = {The gill microbiota of invasive and indigenous Spondylus oysters from the Mediterranean Sea and northern Red Sea.}, journal = {Environmental microbiology reports}, volume = {7}, number = {6}, pages = {860-867}, doi = {10.1111/1758-2229.12315}, pmid = {26111733}, issn = {1758-2229}, mesh = {Animals ; Bacteria/classification/genetics ; Biodiversity ; Gills/*microbiology ; Indian Ocean ; Mediterranean Sea ; Metagenome ; Metagenomics ; *Microbiota ; Ostreidae/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; }, abstract = {The gill tissue of bivalve mollusks hosts rich symbiotic microbial communities that may contribute to the animal's metabolism. Spondylus spinosus is an invasive oyster that has become highly abundant along the eastern Mediterranean Sea (EMS) coastline, but is scarce in the northern Red Sea (NRS), its indigenous region. The composition and seasonal dynamics of the gill microbial communities of S. spinosus were examined in both regions, using 16S rRNA gene amplicon sequencing. Additionally, two Red Sea Spondylus species, S. avramsingeri and S. pickeringae, were investigated using the same approach. Significant differences were found between microbial communities of the EMS S. spinosus and the three NRS species. Bacteria from the family Hahellaceae dominated the communities of the EMS S. spinosus and the NRS S. avramsingeri, oysters that are dominant in their habitat, yet were rare in the NRS S. spinosus and S. pickeringae, which are only seldom encountered. Bacterial communities of EMS S. spinosus were more similar to those of NRS S. spinosus than to those of other NRS Spondylus species, indicating that either part of the microbiota had co-invaded with their host into the Mediterranean Sea, or that there are species-specific selective constraints on microbial composition.}, } @article {pmid26109514, year = {2015}, author = {Engelhardt, T and Orsi, WD and Jørgensen, BB}, title = {Viral activities and life cycles in deep subseafloor sediments.}, journal = {Environmental microbiology reports}, volume = {7}, number = {6}, pages = {868-873}, doi = {10.1111/1758-2229.12316}, pmid = {26109514}, issn = {1758-2229}, mesh = {Biodiversity ; Clustered Regularly Interspaced Short Palindromic Repeats ; DNA, Viral ; *Environmental Microbiology ; Gene Expression Regulation, Viral ; Geologic Sediments/*virology ; Metagenome ; Metagenomics ; RNA, Viral ; *Viruses/classification/genetics ; }, abstract = {Viruses are highly abundant in marine subsurface sediments and can even exceed the number of prokaryotes. However, their activity and quantitative impact on microbial populations are still poorly understood. Here, we use gene expression data from published continental margin subseafloor metatranscriptomes to qualitatively assess viral diversity and activity in sediments up to 159 metres below seafloor (mbsf). Mining of the metatranscriptomic data revealed 4651 representative viral homologues (RVHs), representing 2.2% of all metatranscriptome sequence reads, which have close translated homology (average 77%, range 60-97% amino acid identity) to viral proteins. Archaea-infecting RVHs are exclusively detected in the upper 30 mbsf, whereas RVHs for filamentous inoviruses predominate in the deepest sediment layers. RVHs indicative of lysogenic phage-host interactions and lytic activity, notably cell lysis, are detected at all analysed depths and suggest a dynamic virus-host association in the marine deep biosphere studied here. Ongoing lytic viral activity is further indicated by the expression of clustered, regularly interspaced, short palindromic repeat-associated cascade genes involved in cellular defence against viral attacks. The data indicate the activity of viruses in subsurface sediment of the Peruvian margin and suggest that viruses indeed cause cell mortality and may play an important role in the turnover of subseafloor microbial biomass.}, } @article {pmid26108827, year = {2015}, author = {Ehrenberg, R}, title = {Urban microbes come out of the shadows.}, journal = {Nature}, volume = {522}, number = {7557}, pages = {399-400}, doi = {10.1038/522399a}, pmid = {26108827}, issn = {1476-4687}, mesh = {Animals ; Bacteria/genetics/isolation & purification/pathogenicity ; *Cities/epidemiology ; *Environmental Microbiology ; Humans ; Metagenome/genetics ; Microbiota/genetics ; Sewage/microbiology ; Viruses/genetics/isolation & purification/pathogenicity ; }, } @article {pmid26104745, year = {2015}, author = {Nayfach, S and Fischbach, MA and Pollard, KS}, title = {MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {20}, pages = {3368-3370}, pmid = {26104745}, issn = {1367-4811}, support = {T32 EB009383/EB/NIBIB NIH HHS/United States ; T32 GM067547/GM/NIGMS NIH HHS/United States ; }, mesh = {Diabetes Mellitus/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Genes, Bacterial ; Humans ; Inflammatory Bowel Diseases/microbiology ; Internet ; Metagenomics/*methods ; Molecular Sequence Annotation ; *Software ; }, abstract = {UNLABELLED: Microbiome researchers frequently want to know how abundant a particular microbial gene or pathway is across different human hosts, including its association with disease and its co-occurrence with other genes or microbial taxa. With thousands of publicly available metagenomes, these questions should be easy to answer. However, computational barriers prevent most researchers from conducting such analyses. We address this problem with MetaQuery, a web application for rapid and quantitative analysis of specific genes in the human gut microbiome. The user inputs one or more query genes, and our software returns the estimated abundance of these genes across 1267 publicly available fecal metagenomes from American, European and Chinese individuals. In addition, our application performs downstream statistical analyses to identify features that are associated with gene variation, including other query genes (i.e. gene co-variation), taxa, clinical variables (e.g. inflammatory bowel disease and diabetes) and average genome size. The speed and accessibility of MetaQuery are a step toward democratizing metagenomics research, which should allow many researchers to query the abundance and variation of specific genes in the human gut microbiome.

http://metaquery.docpollard.org.

CONTACT: snayfach@gmail.comS UPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid26104013, year = {2015}, author = {Chumpitazi, BP and Cope, JL and Hollister, EB and Tsai, CM and McMeans, AR and Luna, RA and Versalovic, J and Shulman, RJ}, title = {Randomised clinical trial: gut microbiome biomarkers are associated with clinical response to a low FODMAP diet in children with the irritable bowel syndrome.}, journal = {Alimentary pharmacology & therapeutics}, volume = {42}, number = {4}, pages = {418-427}, pmid = {26104013}, issn = {1365-2036}, support = {R01 NR05337/NR/NINR NIH HHS/United States ; K23 DK101688/DK/NIDDK NIH HHS/United States ; UH3 DK083990/DK/NIDDK NIH HHS/United States ; P30 DK56338/DK/NIDDK NIH HHS/United States ; R01 NR005337/NR/NINR NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; }, mesh = {Abdominal Pain/*etiology ; Adolescent ; Biomarkers/metabolism ; Child ; Cross-Over Studies ; Disaccharides/administration & dosage ; Double-Blind Method ; Female ; Fermentation ; *Gastrointestinal Microbiome ; Humans ; Irritable Bowel Syndrome/*diet therapy/microbiology ; Male ; Monosaccharides/administration & dosage ; Oligosaccharides/administration & dosage ; Polymers/administration & dosage ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: A low fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAP) diet can ameliorate symptoms in adult irritable bowel syndrome (IBS) within 48 h.

AIM: To determine the efficacy of a low FODMAP diet in childhood IBS and whether gut microbial composition and/or metabolic capacity are associated with its efficacy.

METHODS: In a double-blind, crossover trial, children with Rome III IBS completed a 1-week baseline period. They then were randomised to a low FODMAP diet or typical American childhood diet (TACD), followed by a 5-day washout period before crossing over to the other diet. GI symptoms were assessed with abdominal pain frequency being the primary outcome. Baseline gut microbial composition (16S rRNA sequencing) and metabolic capacity (PICRUSt) were determined. Metagenomic biomarker discovery (LEfSe) compared Responders (≥50% decrease in abdominal pain frequency on low FODMAP diet only) vs. Nonresponders (no improvement during either intervention).

RESULTS: Thirty-three children completed the study. Less abdominal pain occurred during the low FODMAP diet vs. TACD [1.1 ± 0.2 (SEM) episodes/day vs. 1.7 ± 0.4, P < 0.05]. Compared to baseline (1.4 ± 0.2), children had fewer daily abdominal pain episodes during the low FODMAP diet (P < 0.01) but more episodes during the TACD (P < 0.01). Responders were enriched at baseline in taxa with known greater saccharolytic metabolic capacity (e.g. Bacteroides, Ruminococcaceae, Faecalibacterium prausnitzii) and three Kyoto Encyclopedia of Genes and Genomes orthologues, of which two relate to carbohydrate metabolism.

CONCLUSIONS: In childhood IBS, a low FODMAP diet decreases abdominal pain frequency. Gut microbiome biomarkers may be associated with low FODMAP diet efficacy. ClinicalTrials.gov identifier: NCT01339117.}, } @article {pmid26102287, year = {2015}, author = {Steinway, SN and Biggs, MB and Loughran, TP and Papin, JA and Albert, R}, title = {Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome.}, journal = {PLoS computational biology}, volume = {11}, number = {5}, pages = {e1004338}, pmid = {26102287}, issn = {1553-7358}, support = {F30 DK093234/DK/NIDDK NIH HHS/United States ; R01 GM108501/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Anti-Bacterial Agents/chemistry/therapeutic use ; Clindamycin/chemistry ; *Clostridioides difficile ; Clostridium Infections/*microbiology ; Coculture Techniques ; Computer Simulation ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology ; Metabolic Networks and Pathways ; Mice ; Microbiota ; }, abstract = {We present a novel methodology to construct a Boolean dynamic model from time series metagenomic information and integrate this modeling with genome-scale metabolic network reconstructions to identify metabolic underpinnings for microbial interactions. We apply this in the context of a critical health issue: clindamycin antibiotic treatment and opportunistic Clostridium difficile infection. Our model recapitulates known dynamics of clindamycin antibiotic treatment and C. difficile infection and predicts therapeutic probiotic interventions to suppress C. difficile infection. Genome-scale metabolic network reconstructions reveal metabolic differences between community members and are used to explore the role of metabolism in the observed microbial interactions. In vitro experimental data validate a key result of our computational model, that B. intestinihominis can in fact slow C. difficile growth.}, } @article {pmid26099921, year = {2015}, author = {Mohammed, A and Guda, C}, title = {Application of a hierarchical enzyme classification method reveals the role of gut microbiome in human metabolism.}, journal = {BMC genomics}, volume = {16 Suppl 7}, number = {Suppl 7}, pages = {S16}, pmid = {26099921}, issn = {1471-2164}, support = {R01 GM086533/GM/NIGMS NIH HHS/United States ; 1R01GM086533-01A1/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*enzymology ; Bacterial Proteins/*classification ; Computational Biology/*methods ; Gastrointestinal Microbiome/*genetics ; Genome, Human ; Humans ; Machine Learning ; Metabolic Networks and Pathways ; Proteomics/methods ; }, abstract = {BACKGROUND: Enzymes are known as the molecular machines that drive the metabolism of an organism; hence identification of the full enzyme complement of an organism is essential to build the metabolic blueprint of that species as well as to understand the interplay of multiple species in an ecosystem. Experimental characterization of the enzymatic reactions of all enzymes in a genome is a tedious and expensive task. The problem is more pronounced in the metagenomic samples where even the species are not adequately cultured or characterized. Enzymes encoded by the gut microbiota play an essential role in the host metabolism; thus, warranting the need to accurately identify and annotate the full enzyme complements of species in the genomic and metagenomic projects. To fulfill this need, we develop and apply a method called ECemble, an ensemble approach to identify enzymes and enzyme classes and study the human gut metabolic pathways.

RESULTS: ECemble method uses an ensemble of machine-learning methods to accurately model and predict enzymes from protein sequences and also identifies the enzyme classes and subclasses at the finest resolution. A tenfold cross-validation result shows accuracy between 97 and 99% at different levels in the hierarchy of enzyme classification, which is superior to comparable methods. We applied ECemble to predict the entire complements of enzymes from ten sequenced proteomes including the human proteome. We also applied this method to predict enzymes encoded by the human gut microbiome from gut metagenomic samples, and to study the role played by the microbe-derived enzymes in the human metabolism. After mapping the known and predicted enzymes to canonical human pathways, we identified 48 pathways that have at least one bacteria-encoded enzyme, which demonstrates the complementary role of gut microbiome in human gut metabolism. These pathways are primarily involved in metabolizing dietary nutrients such as carbohydrates, amino acids, lipids, cofactors and vitamins.

CONCLUSIONS: The ECemble method is able to hierarchically assign high quality enzyme annotations to genomic and metagenomic data. This study demonstrated the real application of ECemble to understand the indispensable role played by microbe-encoded enzymes in the healthy functioning of human metabolic systems.}, } @article {pmid26099498, year = {2015}, author = {Hohlfeld, R and Wekerle, H}, title = {[Multiple sclerosis and microbiota. From genome to metagenome?].}, journal = {Der Nervenarzt}, volume = {86}, number = {8}, pages = {925-933}, pmid = {26099498}, issn = {1433-0407}, mesh = {Gastrointestinal Microbiome/genetics/*immunology ; Humans ; Immunity, Innate/immunology ; Lymphoid Tissue/*immunology/*microbiology ; Metagenome/genetics ; *Models, Immunological ; Multiple Sclerosis/genetics/*immunology/*microbiology ; }, abstract = {The individual risk of contracting multiple sclerosis (MS) is determined by genetic predisposition as well as environmental factors. In monozygotic twins the concordance rate for MS is approximately 30 % indicating that environmental factors are even more important than genetic factors. Observations in a T-cell receptor-transgenic, spontaneous mouse model strongly point to an important contribution of the individual gut microbiome (microbiota). Mice maintained in a germ-free environment are completely protected from experimental autoimmune encephalomyelitis (EAE) in this model, whereas mice that are kept under normal conditions spontaneously develop a relapsing-remitting central nervous system (CNS) disease which is astoundingly similar to human MS. It appears that the autoimmune reaction against CNS tissue is "remotely controlled" by the gut microbiota. This may be explained by the facts that the microbiota influences the gut-associated lymphoid tissue (GALT) and, vice versa, the GALT regulates systemic immunity. The precise role of the microbiota in MS remains to be clarified. New methods of DNA sequencing and bioinformatics allow the analysis of very complex bacterial metagenomes. If individual microbial risk profiles can be identified this would provide completely new perspectives for the prophylaxis and therapy of MS.}, } @article {pmid26097697, year = {2015}, author = {Kopf, A and Bicak, M and Kottmann, R and Schnetzer, J and Kostadinov, I and Lehmann, K and Fernandez-Guerra, A and Jeanthon, C and Rahav, E and Ullrich, M and Wichels, A and Gerdts, G and Polymenakou, P and Kotoulas, G and Siam, R and Abdallah, RZ and Sonnenschein, EC and Cariou, T and O'Gara, F and Jackson, S and Orlic, S and Steinke, M and Busch, J and Duarte, B and Caçador, I and Canning-Clode, J and Bobrova, O and Marteinsson, V and Reynisson, E and Loureiro, CM and Luna, GM and Quero, GM and Löscher, CR and Kremp, A and DeLorenzo, ME and Øvreås, L and Tolman, J and LaRoche, J and Penna, A and Frischer, M and Davis, T and Katherine, B and Meyer, CP and Ramos, S and Magalhães, C and Jude-Lemeilleur, F and Aguirre-Macedo, ML and Wang, S and Poulton, N and Jones, S and Collin, R and Fuhrman, JA and Conan, P and Alonso, C and Stambler, N and Goodwin, K and Yakimov, MM and Baltar, F and Bodrossy, L and Van De Kamp, J and Frampton, DM and Ostrowski, M and Van Ruth, P and Malthouse, P and Claus, S and Deneudt, K and Mortelmans, J and Pitois, S and Wallom, D and Salter, I and Costa, R and Schroeder, DC and Kandil, MM and Amaral, V and Biancalana, F and Santana, R and Pedrotti, ML and Yoshida, T and Ogata, H and Ingleton, T and Munnik, K and Rodriguez-Ezpeleta, N and Berteaux-Lecellier, V and Wecker, P and Cancio, I and Vaulot, D and Bienhold, C and Ghazal, H and Chaouni, B and Essayeh, S and Ettamimi, S and Zaid, el H and Boukhatem, N and Bouali, A and Chahboune, R and Barrijal, S and Timinouni, M and El Otmani, F and Bennani, M and Mea, M and Todorova, N and Karamfilov, V and Ten Hoopen, P and Cochrane, G and L'Haridon, S and Bizsel, KC and Vezzi, A and Lauro, FM and Martin, P and Jensen, RM and Hinks, J and Gebbels, S and Rosselli, R and De Pascale, F and Schiavon, R and Dos Santos, A and Villar, E and Pesant, S and Cataletto, B and Malfatti, F and Edirisinghe, R and Silveira, JA and Barbier, M and Turk, V and Tinta, T and Fuller, WJ and Salihoglu, I and Serakinci, N and Ergoren, MC and Bresnan, E and Iriberri, J and Nyhus, PA and Bente, E and Karlsen, HE and Golyshin, PN and Gasol, JM and Moncheva, S and Dzhembekova, N and Johnson, Z and Sinigalliano, CD and Gidley, ML and Zingone, A and Danovaro, R and Tsiamis, G and Clark, MS and Costa, AC and El Bour, M and Martins, AM and Collins, RE and Ducluzeau, AL and Martinez, J and Costello, MJ and Amaral-Zettler, LA and Gilbert, JA and Davies, N and Field, D and Glöckner, FO}, title = {The ocean sampling day consortium.}, journal = {GigaScience}, volume = {4}, number = {}, pages = {27}, pmid = {26097697}, issn = {2047-217X}, mesh = {Biodiversity ; Database Management Systems ; *Marine Biology ; Metagenomics ; Oceans and Seas ; }, abstract = {Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.}, } @article {pmid26092554, year = {2015}, author = {Praveckova, M and Brennerova, MV and Cvancarova, M and De Alencastro, LF and Holliger, C and Rossi, P}, title = {Divergent PCB organohalide-respiring consortia enriched from the efflux channel of a former Delor manufacturer in Eastern Europe.}, journal = {Ecotoxicology and environmental safety}, volume = {120}, number = {}, pages = {223-234}, doi = {10.1016/j.ecoenv.2015.05.038}, pmid = {26092554}, issn = {1090-2414}, mesh = {Bacteria, Anaerobic/classification/*isolation & purification/metabolism ; Biodegradation, Environmental ; Chloroflexi/*isolation & purification/metabolism ; Cloning, Molecular ; DNA, Bacterial/genetics ; Environmental Monitoring ; Geologic Sediments/chemistry/microbiology ; Halogenation ; Hydrogen-Ion Concentration ; *Microbial Consortia ; Multivariate Analysis ; Phylogeny ; Polychlorinated Biphenyls/*analysis ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Slovakia ; Water Pollutants, Chemical/analysis ; }, abstract = {Polychlorinated biphenyl (PCB) organohalide-respiring communities from the efflux channel of a former Delor manufacturer in Eastern Slovakia were assessed using metagenomic, statistical and cultivation-adapted approaches. Multivariate analysis of environmental factors together with terminal restriction fragment length polymorphisms of the bacterial communities in the primary sediments revealed both temporal and spatial heterogeneity in the distribution of microbial populations, which reflects the dynamic pattern of contamination and altered conditions for biodegradation activity along the channel. Anaerobic microcosms were developed from eight sediments sampled along the channel, where high concentrations of PCBs - from 6.6 to 136mg/kg dry weight, were measured. PCB dehalorespiring activity, congruent with changes in the microbial composition in all microcosms, was detected. After 10 months of cultivation, the divergently evolved consortia achieved up to 35.9 percent reduction of the total PCB concentration. Phylogenetic-analysis of the active Chloroflexi-related organohalide-respiring bacteria by partial sequencing of 16S rRNA genes in cDNA from microcosms with the highest PCB dechlorination activity revealed diverse and unique complexity of the populations. The predominant organohalide respirers were either affiliated with Dehalococcoides sp. and Dehalococcoides-like group (DLG) organisms or were composed of currently unknown distant clades of DLG bacteria. The present study should encourage researchers to explore the full potential of the indigenous PCB dechlorinating populations to develop effective bioremediation approaches that can perform the complete mineralization of PCBs in polluted environments.}, } @article {pmid26092461, year = {2015}, author = {Yergeau, E and Maynard, C and Sanschagrin, S and Champagne, J and Juck, D and Lee, K and Greer, CW}, title = {Microbial Community Composition, Functions, and Activities in the Gulf of Mexico 1 Year after the Deepwater Horizon Accident.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {17}, pages = {5855-5866}, pmid = {26092461}, issn = {1098-5336}, mesh = {Archaea/classification/genetics/*isolation & purification ; Bacteria/*classification/genetics/*isolation & purification ; *Biodiversity ; Geologic Sediments/chemistry/microbiology ; Gulf of Mexico ; Mexico ; Petroleum Pollution/*analysis ; Seawater/chemistry/*microbiology ; }, abstract = {Several studies have assessed the effects of the released oil on microbes, either during or immediately after the Deepwater Horizon accident. However, little is known about the potential longer-term persistent effects on microbial communities and their functions. In this study, one water column station near the wellhead (3.78 km southwest of the wellhead), one water column reference station outside the affected area (37.77 km southeast of the wellhead), and deep-sea sediments near the wellhead (3.66 km southeast of the wellhead) were sampled 1 year after the capping of the well. In order to analyze microbial community composition, function, and activity, we used metagenomics, metatranscriptomics, and mineralization assays. Mineralization of hexadecane was significantly higher at the wellhead station at a depth of ∼1,200 m than at the reference station. Community composition based on taxonomical or functional data showed that the samples taken at a depth of ∼1,200 m were significantly more dissimilar between the stations than at other depths (surface, 100 m, 750 m, and >1,500 m). Both Bacteria and Archaea showed reduced activity at depths of ∼1,200 m when the wellhead station was compared to the reference station, and their activity was significantly higher in surficial sediments than in 10-cm sediments. Surficial sediments also harbored significantly different active genera than did 5- and 10-cm sediments. For the remaining microbial parameters assessed, no significant differences could be observed between the wellhead and reference stations and between surface and 5- to 10-cm-deep sediments.}, } @article {pmid26091682, year = {2015}, author = {Kanengoni, AT and Chimonyo, M and Tasara, T and Cormican, P and Chapwanya, A and Ndimba, BK and Dzama, K}, title = {A comparison of faecal microbial populations of South African Windsnyer-type indigenous pigs (SAWIPs) and Large White × Landrace (LW × LR) crosses fed diets containing ensiled maize cobs.}, journal = {FEMS microbiology letters}, volume = {362}, number = {13}, pages = {fnv100}, doi = {10.1093/femsle/fnv100}, pmid = {26091682}, issn = {1574-6968}, mesh = {*Animal Feed ; Animals ; Bacteroides/genetics/isolation & purification ; Clostridium/genetics/isolation & purification ; Desulfovibrio/genetics/isolation & purification ; Diet/standards/veterinary ; Dietary Fiber/metabolism ; Feces/*microbiology ; Fermentation ; High-Throughput Nucleotide Sequencing ; Intestines/*microbiology ; Metagenomics ; *Microbial Consortia ; Peptococcus/genetics/isolation & purification ; South Africa ; Sus scrofa/*classification/*microbiology/physiology ; Swine ; *Zea mays ; }, abstract = {Faecal microbial communities in South African Windsnyer-type indigenous pigs (SAWIPs) and Large White × Landrace (LW × LR) crosses were investigated using high-throughput sequencing of the 16S rDNA genes. The faecal microbial communities in LW × LR crosses and SAWIPs fed control (CON) and high maize cob (HMC) diets were evaluated through parallel sequencing of 16S rDNA genes. Butrivibrio, Faecalibacterium and Desulfovibrio, although present in LW × LR pigs, were absent from the SAWIP microbial community. Bacteroides, Succiniclasticum, Peptococcus and Akkermansia were found in SAWIPs but not in LW × LR crosses. The ratios of Bacteroidia to Clostridia on the CON and HMC diets were similar (0.37 versus 0.39) in SAWIPs but different (0.24 versus 0.1) in LW × LR crosses. The faecal microbial profiles determined were different between the LW × LR and SAWIP breeds but not between pigs fed the CON and HMC diets. The composition of faecal bacterial communities in SAWIPs was determined for the first time. The differences in microbial communities detected may explain the enhanced ability of SAWIPs to digest fibrous diets compared with the LW × LR crosses.}, } @article {pmid26090804, year = {2015}, author = {Meirelles, PM and Amado-Filho, GM and Pereira-Filho, GH and Pinheiro, HT and de Moura, RL and Joyeux, JC and Mazzei, EF and Bastos, AC and Edwards, RA and Dinsdale, E and Paranhos, R and Santos, EO and Iida, T and Gotoh, K and Nakamura, S and Sawabe, T and Rezende, CE and Gadelha, LM and Francini-Filho, RB and Thompson, C and Thompson, FL}, title = {Baseline Assessment of Mesophotic Reefs of the Vitória-Trindade Seamount Chain Based on Water Quality, Microbial Diversity, Benthic Cover and Fish Biomass Data.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0130084}, pmid = {26090804}, issn = {1932-6203}, mesh = {Animals ; Atlantic Ocean ; *Biodiversity ; *Biomass ; Brazil ; *Coral Reefs ; *Ecosystem ; *Fishes ; Metagenomics ; *Water Microbiology ; *Water Quality ; }, abstract = {Seamounts are considered important sources of biodiversity and minerals. However, their biodiversity and health status are not well understood; therefore, potential conservation problems are unknown. The mesophotic reefs of the Vitória-Trindade Seamount Chain (VTC) were investigated via benthic community and fish surveys, metagenomic and water chemistry analyses, and water microbial abundance estimations. The VTC is a mosaic of reef systems and includes fleshy algae dominated rhodolith beds, crustose coralline algae (CCA) reefs, and turf algae dominated rocky reefs of varying health levels. Macro-carnivores and larger fish presented higher biomass at the CCA reefs (4.4 kg per frame) than in the rhodolith beds and rocky reefs (0.0 to 0.1 kg per frame). A larger number of metagenomic sequences identified as primary producers (e.g., Chlorophyta and Streptophyta) were found at the CCA reefs. However, the rocky reefs contained more diseased corals (>90%) than the CCA reefs (~40%) and rhodolith beds (~10%). Metagenomic analyses indicated a heterotrophic and fast-growing microbiome in rocky reef corals that may possibly lead to unhealthy conditions possibly enhanced by environmental features (e.g. light stress and high loads of labile dissolved organic carbon). VTC mounts represent important hotspots of biodiversity that deserve further conservation actions.}, } @article {pmid26088524, year = {2015}, author = {Brandl, K and Schnabl, B}, title = {Is intestinal inflammation linking dysbiosis to gut barrier dysfunction during liver disease?.}, journal = {Expert review of gastroenterology & hepatology}, volume = {9}, number = {8}, pages = {1069-1076}, pmid = {26088524}, issn = {1747-4132}, support = {I01 BX002213/BX/BLRD VA/United States ; K08 DK081830/DK/NIDDK NIH HHS/United States ; R01 AA020703/AA/NIAAA NIH HHS/United States ; U01 AA021856/AA/NIAAA NIH HHS/United States ; }, mesh = {Animals ; Dysbiosis/*physiopathology ; Enteritis/microbiology/*physiopathology ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/*metabolism ; Liver Diseases/microbiology/*physiopathology ; Permeability ; }, abstract = {Changes in the intestinal microbiota composition contribute to the pathogenesis of many disorders including gastrointestinal and liver diseases. Recent studies have broadened our understanding of the "gut-liver" axis. Dietary changes, other environmental and genetic factors can lead to alterations in the microbiota. Dysbiosis can further disrupt the integrity of the intestinal barrier leading to pathological bacterial translocation and the initiation of an inflammatory response in the liver. In this article, the authors dissect the different steps involved in disease pathogenesis to further refine approaches for the medical management of liver diseases. The authors will specifically discuss the role of dysbiosis in inducing intestinal inflammation and increasing intestinal permeability.}, } @article {pmid26088176, year = {2015}, author = {Chaudhary, PP and Gaci, N and Borrel, G and O'Toole, PW and Brugère, JF}, title = {Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {14}, pages = {5801-5815}, doi = {10.1007/s00253-015-6739-2}, pmid = {26088176}, issn = {1432-0614}, mesh = {Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenomics/*methods ; Methane/*metabolism ; *Microbiota ; }, abstract = {Until recently, human gut microbiota was believed to be colonized by few methanogenic archaeal species. Much higher microbial diversity within the human gut was revealed by the use of molecular approaches as compared to routine microbiological techniques, but still, a lot remains unknown. Molecular techniques has the advantage of being rapid, reproducible, and can be highly discriminative as compared to conventional culturing methods. Some of them provide both qualitative and quantitative information. However, the choice of method should be taken with care to avoid biases. The advent of next-generation sequencing gives much deeper information from which functional and ecological hypotheses can be drawn. In this review, molecular techniques that are currently used together with their possible future developments to study gut methanogenic communities are indicated along with their limitations and difficulties that are encountered during their implementation. Moreover, the high amount of metagenomics data from the human gut microbiome indicate that this environment could be a paradigm for new directions in methanogen diversity studies and help to develop new approaches for other environments as well. Concerning humans, this should help us to better understand the possible association of methanogens with some of the diseased conditions and their peculiar distribution among age groups in human.}, } @article {pmid26087428, year = {2015}, author = {Tilg, H and Adolph, TE}, title = {Influence of the human intestinal microbiome on obesity and metabolic dysfunction.}, journal = {Current opinion in pediatrics}, volume = {27}, number = {4}, pages = {496-501}, doi = {10.1097/MOP.0000000000000234}, pmid = {26087428}, issn = {1531-698X}, mesh = {Cesarean Section/*adverse effects ; Delivery, Obstetric ; Diet ; Feeding Behavior ; Female ; Gastrointestinal Microbiome/immunology/*physiology ; Gastrointestinal Tract/*immunology ; Humans ; Immunity, Innate/*physiology ; Male ; Metabolic Syndrome/etiology/*immunology/physiopathology ; Obesity/complications/*immunology/physiopathology ; Pregnancy ; Pregnant Women ; }, abstract = {PURPOSE OF REVIEW: Recent studies have suggested that there may be a strong link between the gut microbiota, energy extraction and body metabolism.

RECENT FINDINGS: Evidence is accumulating that the intestinal microbiota, in addition to other major factors such as diet and host genetics, contributes to obesity, metabolic dysfunction and diabetes. Both preclinical experimental and human studies have shown that obesity and metabolic dysfunction are characterized by a profound dysbiosis. Several human metagenome-wide association studies have demonstrated highly significant correlations of certain members of intestinal microbiota with obesity and type 2 diabetes. In addition dietary factors that substantially affect microbial composition, microbiota disruption, and the consequence of early-life antibiotic use, may contribute to childhood obesity and metabolic dysfunction. Further evidence for an association between microbiota and metabolic dysfunction has been derived from studies in pregnancy demonstrating that major gut microbial shifts occur during pregnancy thereby affecting host metabolism. In particular, the high rate of obesity following caesarean section could be partially explained by functional alterations in the intestinal microbiota.

SUMMARY: Obesity and associated metabolic dysfunction emerge from disturbed interactions between the intestinal microbiota, dietary changes and host immune functions. A better understanding of this relationship might lead to better therapies for human metabolic and inflammatory diseases in the future.}, } @article {pmid26086670, year = {2015}, author = {Liu, Q and Tang, J and Bai, Z and Hecker, M and Giesy, JP}, title = {Distribution of petroleum degrading genes and factor analysis of petroleum contaminated soil from the Dagang Oilfield, China.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {11068}, pmid = {26086670}, issn = {2045-2322}, mesh = {China ; *Factor Analysis, Statistical ; *Metagenome ; *Microbiota ; *Petroleum ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants/*chemistry ; }, abstract = {Genes that encode for enzymes that can degrade petroleum hydrocarbons (PHs) are critical for the ability of microorganisms to bioremediate soils contaminated with PHs. Distributions of two petroleum-degrading genes AlkB and Nah in soils collected from three zones of the Dagang Oilfield, Tianjin, China were investigated. Numbers of copies of AlkB ranged between 9.1 × 10(5) and 1.9 × 10(7) copies/g dry mass (dm) soil, and were positively correlated with total concentrations of PHs (TPH) (R(2) = 0.573, p = 0.032) and alkanes (C33 ~ C40) (R(2) = 0.914, p < 0.01). The Nah gene was distributed relatively evenly among sampling zones, ranging between 1.9 × 10(7) and 1.1 × 10(8) copies/g dm soil, and was negatively correlated with concentrations of total aromatic hydrocarbons (TAH) (R(2) = -0.567, p = 0.035) and ∑16 PAHs (R(2) = -0.599, p = 0.023). Results of a factor analysis showed that individual samples of soils were not ordinated as a function of the zones.}, } @article {pmid26083617, year = {2015}, author = {Chehoud, C and Albenberg, LG and Judge, C and Hoffmann, C and Grunberg, S and Bittinger, K and Baldassano, RN and Lewis, JD and Bushman, FD and Wu, GD}, title = {Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease.}, journal = {Inflammatory bowel diseases}, volume = {21}, number = {8}, pages = {1948-1956}, pmid = {26083617}, issn = {1536-4844}, support = {UH2 DK083981/DK/NIDDK NIH HHS/United States ; UH3 DK083981/DK/NIDDK NIH HHS/United States ; K24 DK078228/DK/NIDDK NIH HHS/United States ; UH2DK083981/DK/NIDDK NIH HHS/United States ; P30 DK050306/DK/NIDDK NIH HHS/United States ; S10 RR024525/RR/NCRR NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; UL1RR024134/RR/NCRR NIH HHS/United States ; R01 GM103591/GM/NIGMS NIH HHS/United States ; P30 AI 045008/AI/NIAID NIH HHS/United States ; K24-DK078228/DK/NIDDK NIH HHS/United States ; S10RR024525/RR/NCRR NIH HHS/United States ; UL1 RR024134/RR/NCRR NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Archaea/*genetics ; Case-Control Studies ; Child ; Child, Preschool ; Cohort Studies ; Cross-Sectional Studies ; Feces/microbiology ; Female ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*genetics/*microbiology ; Male ; *Metagenome ; Microbiota/*genetics ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) involves dysregulation of mucosal immunity in response to environmental factors such as the gut microbiota. The bacterial microbiota is often altered in IBD, but the connection to disease is not fully clarified and gut fungi have recently been suggested to play a role as well. In this study, we compared microbes from all 3 domains of life-bacteria, archaea, and eukaryota-in pediatric patients with IBD and healthy controls.

METHODS: A stool sample was collected from patients with IBD (n = 32) or healthy control subjects (n = 90), and bacterial, archaeal, and fungal communities were characterized by deep sequencing of rRNA gene segments specific to each domain.

RESULTS: Patients with IBD (Crohn's disease or ulcerative colitis) had lower bacterial diversity and distinctive fungal communities. Two lineages annotating as Candida were significantly more abundant in patients with IBD (P = 0.0034 and P = 0.00038, respectively), whereas a lineage annotating as Cladosporium was more abundant in healthy subjects (P = 0.0025). There were no statistically significant differences in archaea, which were rare in pediatric samples compared with those from adults.

CONCLUSIONS: Pediatric IBD is associated with reduced diversity in both fungal and bacterial gut microbiota. Specific Candida taxa were found to be increased in abundance in the IBD samples. These data emphasize the potential importance of fungal microbiota signatures as biomarkers of pediatric IBD, supporting their possible role in disease pathogenesis.}, } @article {pmid26077811, year = {2015}, author = {Young, JC and Pan, C and Adams, RM and Brooks, B and Banfield, JF and Morowitz, MJ and Hettich, RL}, title = {Metaproteomics reveals functional shifts in microbial and human proteins during a preterm infant gut colonization case.}, journal = {Proteomics}, volume = {15}, number = {20}, pages = {3463-3473}, pmid = {26077811}, issn = {1615-9861}, support = {R01 GM103600/GM/NIGMS NIH HHS/United States ; 1R01-GM-103600/GM/NIGMS NIH HHS/United States ; }, mesh = {Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; *Metagenomics ; Microbiota/*genetics ; *Proteomics ; }, abstract = {Microbial colonization of the human gastrointestinal tract plays an important role in establishing health and homeostasis. However, the time-dependent functional signatures of microbial and human proteins during early colonization of the gut have yet to be determined. To this end, we employed shotgun proteomics to simultaneously monitor microbial and human proteins in fecal samples from a preterm infant during the first month of life. Microbial community complexity increased over time, with compositional changes that were consistent with previous metagenomic and rRNA gene data. More specifically, the function of the microbial community initially involved biomass growth, protein production, and lipid metabolism, and then switched to more complex metabolic functions, such as carbohydrate metabolism, once the community stabilized and matured. Human proteins detected included those responsible for epithelial barrier function and antimicrobial activity. Some neutrophil-derived proteins increased in abundance early in the study period, suggesting activation of the innate immune system. Likewise, abundances of cytoskeletal and mucin proteins increased later in the time course, suggestive of subsequent adjustment to the increased microbial load. This study provides the first snapshot of coordinated human and microbial protein expression in a preterm infant's gut during early development.}, } @article {pmid26077158, year = {2015}, author = {Gao, X and Gao, W and Cui, Z and Han, B and Yang, P and Sun, C and Zheng, L}, title = {Biodiversity and degradation potential of oil-degrading bacteria isolated from deep-sea sediments of South Mid-Atlantic Ridge.}, journal = {Marine pollution bulletin}, volume = {97}, number = {1-2}, pages = {373-380}, doi = {10.1016/j.marpolbul.2015.05.065}, pmid = {26077158}, issn = {1879-3363}, mesh = {Atlantic Ocean ; Bacteria/*genetics/metabolism ; Biodegradation, Environmental ; *Biodiversity ; Geologic Sediments/microbiology ; Microbial Consortia/genetics/*physiology ; Petroleum/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; }, abstract = {The indigenous oil-degrading bacterial consortia MARA and MARB were enriched from the deep-sea sediments of South Mid-Atlantic Ridge (MAR) with crude oil as sole carbon and energy sources. Biodiversity and community analyses showed that members of α-Proteobacteria were the key players in consortium MARA, whereas those of γ-Proteobacteria were the key players in consortium MARB, which were studied by MiSeq sequencing method. Gravimetric method estimated the oil degradation rates of MARA and MARB to be 63.4% and 85.8%, respectively, after 20d. Eleven cultivable oil degraders with different morphologies were isolated. These strains were identified as Alcanivorax, Bacillus, Dietzia, Erythrobacter, Marinobacter, Nitratireductor, and Oceanicola based on 16S rRNA gene sequences. Three strains belonging to Dietzia exhibited the highest oil degradation capability. Results indicated that the intrinsic biodegradation capacity of oil contaminants by indigenous microbial communities exists in South MAR sediments.}, } @article {pmid26076489, year = {2015}, author = {Gall, A and Fero, J and McCoy, C and Claywell, BC and Sanchez, CA and Blount, PL and Li, X and Vaughan, TL and Matsen, FA and Reid, BJ and Salama, NR}, title = {Bacterial Composition of the Human Upper Gastrointestinal Tract Microbiome Is Dynamic and Associated with Genomic Instability in a Barrett's Esophagus Cohort.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0129055}, pmid = {26076489}, issn = {1932-6203}, support = {K05 CA124911/CA/NCI NIH HHS/United States ; R01 HG005966/HG/NHGRI NIH HHS/United States ; R01 CA179949/CA/NCI NIH HHS/United States ; P30 CA015704/CA/NCI NIH HHS/United States ; P01 CA091955/CA/NCI NIH HHS/United States ; R01 CA136725/CA/NCI NIH HHS/United States ; P01 CA 91955/CA/NCI NIH HHS/United States ; T32 AI055396/AI/NIAID NIH HHS/United States ; S10 OD020069/OD/NIH HHS/United States ; T32 GM007266/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenocarcinoma/epidemiology/etiology ; Aged ; Aged, 80 and over ; *Bacteria/classification/genetics ; Barrett Esophagus/complications/*genetics/*microbiology/pathology ; Biodiversity ; Disease Susceptibility ; Esophageal Neoplasms/epidemiology/etiology ; Female ; Gastric Mucosa/metabolism ; *Genomic Instability ; Humans ; Incidence ; Male ; Metagenome ; *Microbiota ; Microvilli/microbiology ; Middle Aged ; Mucous Membrane/metabolism/microbiology/pathology ; Phylogeny ; Quantitative Trait, Heritable ; Risk Factors ; Stomach/microbiology ; Upper Gastrointestinal Tract/*microbiology ; Waist-Hip Ratio ; }, abstract = {BACKGROUND: The incidence of esophageal adenocarcinoma (EAC) has increased nearly five-fold over the last four decades in the United States. Barrett's esophagus, the replacement of the normal squamous epithelial lining with a mucus-secreting columnar epithelium, is the only known precursor to EAC. Like other parts of the gastrointestinal (GI) tract, the esophagus hosts a variety of bacteria and comparisons among published studies suggest bacterial communities in the stomach and esophagus differ. Chronic infection with Helicobacter pylori in the stomach has been inversely associated with development of EAC, but the mechanisms underlying this association remain unclear.

METHODOLOGY: The bacterial composition in the upper GI tract was characterized in a subset of participants (n=12) of the Seattle Barrett's Esophagus Research cohort using broad-range 16S PCR and pyrosequencing of biopsy and brush samples collected from squamous esophagus, Barrett's esophagus, stomach corpus and stomach antrum. Three of the individuals were sampled at two separate time points. Prevalence of H. pylori infection and subsequent development of aneuploidy (n=339) and EAC (n=433) was examined in a larger subset of this cohort.

RESULTS/SIGNIFICANCE: Within individuals, bacterial communities of the stomach and esophagus showed overlapping community membership. Despite closer proximity, the stomach antrum and corpus communities were less similar than the antrum and esophageal samples. Re-sampling of study participants revealed similar upper GI community membership in two of three cases. In this Barrett's esophagus cohort, Streptococcus and Prevotella species dominate the upper GI and the ratio of these two species is associated with waist-to-hip ratio and hiatal hernia length, two known EAC risk factors in Barrett's esophagus. H. pylori-positive individuals had a significantly decreased incidence of aneuploidy and a non-significant trend toward lower incidence of EAC.}, } @article {pmid26072503, year = {2015}, author = {Yuan, C and Lei, J and Cole, J and Sun, Y}, title = {Reconstructing 16S rRNA genes in metagenomic data.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {12}, pages = {i35-43}, pmid = {26072503}, issn = {1367-4811}, mesh = {Computational Biology/*methods ; Databases, Nucleic Acid ; Genes, rRNA/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA ; }, abstract = {UNLABELLED: Metagenomic data, which contains sequenced DNA reads of uncultured microbial species from environmental samples, provide a unique opportunity to thoroughly analyze microbial species that have never been identified before. Reconstructing 16S ribosomal RNA, a phylogenetic marker gene, is usually required to analyze the composition of the metagenomic data. However, massive volume of dataset, high sequence similarity between related species, skewed microbial abundance and lack of reference genes make 16S rRNA reconstruction difficult. Generic de novo assembly tools are not optimized for assembling 16S rRNA genes. In this work, we introduce a targeted rRNA assembly tool, REAGO (REconstruct 16S ribosomal RNA Genes from metagenOmic data). It addresses the above challenges by combining secondary structure-aware homology search, zproperties of rRNA genes and de novo assembly. Our experimental results show that our tool can correctly recover more rRNA genes than several popular generic metagenomic assembly tools and specially designed rRNA construction tools.

The source code of REAGO is freely available at https://github.com/chengyuan/reago.}, } @article {pmid26072397, year = {2015}, author = {Cleary, DF and de Voogd, NJ and Polónia, AR and Freitas, R and Gomes, NC}, title = {Composition and Predictive Functional Analysis of Bacterial Communities in Seawater, Sediment and Sponges in the Spermonde Archipelago, Indonesia.}, journal = {Microbial ecology}, volume = {70}, number = {4}, pages = {889-903}, pmid = {26072397}, issn = {1432-184X}, mesh = {Animals ; Bacteria/genetics ; Biodiversity ; Coral Reefs ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; Ecosystem ; Geologic Sediments/*microbiology ; Indonesia ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; Xestospongia/microbiology ; }, abstract = {In this study, we used a 16S rRNA gene barcoded pyrosequencing approach to sample bacterial communities from six biotopes, namely, seawater, sediment and four sponge species (Stylissa carteri, Stylissa massa, Xestospongia testudinaria and Hyrtios erectus) inhabiting coral reefs of the Spermonde Archipelago, South Sulawesi, Indonesia. Samples were collected along a pronounced onshore to offshore environmental gradient. Our goals were to (1) compare higher taxon abundance among biotopes, (2) test to what extent variation in bacterial composition can be explained by the biotope versus environment, (3) identify dominant (>300 sequences) bacterial operational taxonomic units (OTUs) and their closest known relatives and (4) assign putative functions to the sponge bacterial communities using a recently developed predictive metagenomic approach. We observed marked differences in bacterial composition and the relative abundance of the most abundant phyla, classes and orders among sponge species, seawater and sediment. Although all biotopes housed compositionally distinct bacterial communities, there were three prominent clusters. These included (1) both Stylissa species and seawater, (2) X. testudinaria and H. erectus and (3) sediment. Bacterial communities sampled from the same biotope, but different environments (based on proximity to the coast) were much more similar than bacterial communities from different biotopes in the same environment. The biotope thus appears to be a much more important structuring force than the surrounding environment. There were concomitant differences in the predicted counts of KEGG orthologs (KOs) suggesting that bacterial communities housed in different sponge species, sediment and seawater perform distinct functions. In particular, the bacterial communities of both Stylissa species were predicted to be enriched for KOs related to chemotaxis, nitrification and denitrification whereas bacterial communities in X. testudinaria and H. erectus were predicted to be enriched for KOs related to the toxin-antitoxin (TA) system, nutrient starvation and heavy metal export.}, } @article {pmid26070414, year = {2015}, author = {Preidis, GA and Ajami, NJ and Wong, MC and Bessard, BC and Conner, ME and Petrosino, JF}, title = {Composition and function of the undernourished neonatal mouse intestinal microbiome.}, journal = {The Journal of nutritional biochemistry}, volume = {26}, number = {10}, pages = {1050-1057}, doi = {10.1016/j.jnutbio.2015.04.010}, pmid = {26070414}, issn = {1873-4847}, mesh = {Animals ; Animals, Newborn/*microbiology ; Bacteria/classification/genetics ; DNA, Bacterial/analysis ; Gastrointestinal Microbiome/*physiology ; Malnutrition/*microbiology ; Mice ; Protein-Energy Malnutrition/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Undernutrition remains one of the key global health challenges facing children today. Distinct microbial profiles have been associated with obesity and undernutrition, although mechanisms behind these associations are unknown. We sought to understand how protein-energy undernutrition alters the microbiome and to propose mechanisms by which these alterations influence the malnourished phenotype. Outbred CD1 neonatal mice were undernourished by timed separation from lactating dams, while control animals nursed ad libitum. 16S rRNA gene sequencing and compositional analysis identified microbes from luminal contents of ileum, cecum and colon, while whole metagenome shotgun sequencing identified microbial gene content. Our results suggest that the most important determinant of microbiome composition is body compartment; communities derived from ileum are distinct from those from cecum and colon as observed by phylogenetic clustering analysis. However, within each compartment, microbiota from undernourished and control mice cluster separately. At the phylum level, undernourished mice harbor more Verrucomicrobia and less Bacteroidetes in the distal intestine; these changes are driven by an increase in Akkermansia muciniphila and decreases in Bacteroides and Alistipes. Undernourished mice have an overall loss of microbial community richness and diversity and are deficient in multiple microbial genetic pathways including N-glycan, inositol phosphate and one-carbon metabolism. Losses in these microbial genes may confer less efficient extraction of energy from nondigestible dietary components including glycans and phytates, whereas epigenetic alterations provide a means of persistently altering metabolism even after adequate nutrition is restored. Thus, the microbiome of an undernourished host may perpetuate states of poor nutrition via multiple mechanisms.}, } @article {pmid26070087, year = {2015}, author = {Wei, Y and Zhou, H and Zhang, J and Zhang, L and Geng, A and Liu, F and Zhao, G and Wang, S and Zhou, Z and Yan, X}, title = {Insight into Dominant Cellulolytic Bacteria from Two Biogas Digesters and Their Glycoside Hydrolase Genes.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0129921}, pmid = {26070087}, issn = {1932-6203}, mesh = {Bacteria/classification/*genetics/*metabolism ; Biodiversity ; Biofuels/*microbiology ; *Biotransformation ; Computational Biology ; Gene Expression ; Genomics ; Glycoside Hydrolases/*genetics/metabolism ; Lignin/metabolism ; Metagenomics ; Multigene Family ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Diverse cellulolytic bacteria are essential for maintaining high lignocellulose degradation ability in biogas digesters. However, little was known about functional genes and gene clusters of dominant cellulolytic bacteria in biogas digesters. This is the foundation to understand lignocellulose degradation mechanisms of biogas digesters and apply these gene resource for optimizing biofuel production. A combination of metagenomic and 16S rRNA gene clone library methods was used to investigate the dominant cellulolytic bacteria and their glycoside hydrolase (GH) genes in two biogas digesters. The 16S rRNA gene analysis revealed that the dominant cellulolytic bacteria were strains closely related to Clostridium straminisolvens and an uncultured cellulolytic bacterium designated BG-1. To recover GH genes from cellulolytic bacteria in general, and BG-1 in particular, a refined assembly approach developed in this study was used to assemble GH genes from metagenomic reads; 163 GH-containing contigs ≥ 1 kb in length were obtained. Six recovered GH5 genes that were expressed in E. coli demonstrated multiple lignocellulase activities and one had high mannanase activity (1255 U/mg). Eleven fosmid clones harboring the recovered GH-containing contigs were sequenced and assembled into 10 fosmid contigs. The composition of GH genes in the 163 assembled metagenomic contigs and 10 fosmid contigs indicated that diverse GHs and lignocellulose degradation mechanisms were present in the biogas digesters. In particular, a small portion of BG-1 genome information was recovered by PhyloPythiaS analysis. The lignocellulase gene clusters in BG-1 suggested that it might use a possible novel lignocellulose degradation mechanism to efficiently degrade lignocellulose. Dominant cellulolytic bacteria of biogas digester possess diverse GH genes, not only in sequences but also in their functions, which may be applied for production of biofuel in the future.}, } @article {pmid26069274, year = {2016}, author = {Vandeputte, D and Falony, G and Vieira-Silva, S and Tito, RY and Joossens, M and Raes, J}, title = {Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates.}, journal = {Gut}, volume = {65}, number = {1}, pages = {57-62}, pmid = {26069274}, issn = {1468-3288}, mesh = {Adult ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; *Gastrointestinal Transit ; Healthy Volunteers ; Humans ; Middle Aged ; Self Report ; }, abstract = {OBJECTIVE: The assessment of potentially confounding factors affecting colon microbiota composition is essential to the identification of robust microbiome based disease markers. Here, we investigate the link between gut microbiota variation and stool consistency using Bristol Stool Scale classification, which reflects faecal water content and activity, and is considered a proxy for intestinal colon transit time.

DESIGN: Through 16S rDNA Illumina profiling of faecal samples of 53 healthy women, we evaluated associations between microbiome richness, Bacteroidetes:Firmicutes ratio, enterotypes, and genus abundance with self-reported, Bristol Stool Scale-based stool consistency. Each sample's microbiota growth potential was calculated to test whether transit time acts as a selective force on gut bacterial growth rates.

RESULTS: Stool consistency strongly correlates with all known major microbiome markers. It is negatively correlated with species richness, positively associated to the Bacteroidetes:Firmicutes ratio, and linked to Akkermansia and Methanobrevibacter abundance. Enterotypes are distinctly distributed over the BSS-scores. Based on the correlations between microbiota growth potential and stool consistency scores within both enterotypes, we hypothesise that accelerated transit contributes to colon ecosystem differentiation. While shorter transit times can be linked to increased abundance of fast growing species in Ruminococcaceae-Bacteroides samples, hinting to a washout avoidance strategy of faster replication, this trend is absent in Prevotella-enterotyped individuals. Within this enterotype adherence to host tissue therefore appears to be a more likely bacterial strategy to cope with washout.

CONCLUSIONS: The strength of the associations between stool consistency and species richness, enterotypes and community composition emphasises the crucial importance of stool consistency assessment in gut metagenome-wide association studies.}, } @article {pmid26067958, year = {2015}, author = {De Mandal, S and Sanga, Z and Senthil Kumar, N}, title = {Metagenome Sequencing Reveals Rhodococcus Dominance in Farpuk Cave, Mizoram, India, an Eastern Himalayan Biodiversity Hot Spot Region.}, journal = {Genome announcements}, volume = {3}, number = {3}, pages = {}, pmid = {26067958}, issn = {2169-8287}, abstract = {The present study employed 16S rRNA amplicon sequencing to survey the prokaryotic microbiota on Farpuk Cave, revealing a diverse bacterial community with 4,021 operational taxonomical units (OTUs), mainly dominated by the genus Rhodococcus. Moreover, 18.17% of the OTUs were unclassified at the phylum level, suggesting the existence of novel bacterial species.}, } @article {pmid26067561, year = {2015}, author = {Chao, Y and Mao, Y and Wang, Z and Zhang, T}, title = {Diversity and functions of bacterial community in drinking water biofilms revealed by high-throughput sequencing.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {10044}, pmid = {26067561}, issn = {2045-2322}, mesh = {*Biofilms ; *Bradyrhizobiaceae/classification/physiology ; Drinking Water/*microbiology ; *High-Throughput Nucleotide Sequencing ; Microbial Consortia/*physiology ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; }, abstract = {The development of biofilms in drinking water (DW) systems may cause various problems to water quality. To investigate the community structure of biofilms on different pipe materials and the global/specific metabolic functions of DW biofilms, PCR-based 454 pyrosequencing data for 16S rRNA genes and Illumina metagenomic data were generated and analysed. Considerable differences in bacterial diversity and taxonomic structure were identified between biofilms formed on stainless steel and biofilms formed on plastics, indicating that the metallic materials facilitate the formation of higher diversity biofilms. Moreover, variations in several dominant genera were observed during biofilm formation. Based on PCA analysis, the global functions in the DW biofilms were similar to other DW metagenomes. Beyond the global functions, the occurrences and abundances of specific protective genes involved in the glutathione metabolism, the SoxRS system, the OxyR system, RpoS regulated genes, and the production/degradation of extracellular polymeric substances were also evaluated. A near-complete and low-contamination draft genome was constructed from the metagenome of the DW biofilm, based on the coverage and tetranucleotide frequencies, and identified as a Bradyrhizobiaceae-like bacterium according to a phylogenetic analysis. Our findings provide new insight into DW biofilms, especially in terms of their metabolic functions.}, } @article {pmid26066038, year = {2015}, author = {Kumbhare, SV and Dhotre, DP and Dhar, SK and Jani, K and Apte, DA and Shouche, YS and Sharma, A}, title = {Insights into Diversity and Imputed Metabolic Potential of Bacterial Communities in the Continental Shelf of Agatti Island.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0129864}, pmid = {26066038}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics/*metabolism ; *Biodiversity ; DNA, Bacterial/genetics ; *Ecosystem ; *Genes, Bacterial ; Geologic Sediments/*microbiology ; Islands ; Metagenomics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Marine microbes play a key role and contribute largely to the global biogeochemical cycles. This study aims to explore microbial diversity from one such ecological hotspot, the continental shelf of Agatti Island. Sediment samples from various depths of the continental shelf were analyzed for bacterial diversity using deep sequencing technology along with the culturable approach. Additionally, imputed metagenomic approach was carried out to understand the functional aspects of microbial community especially for microbial genes important in nutrient uptake, survival and biogeochemical cycling in the marine environment. Using culturable approach, 28 bacterial strains representing 9 genera were isolated from various depths of continental shelf. The microbial community structure throughout the samples was dominated by phylum Proteobacteria and harbored various bacterioplanktons as well. Significant differences were observed in bacterial diversity within a short region of the continental shelf (1-40 meters) i.e. between upper continental shelf samples (UCS) with lesser depths (i.e. 1-20 meters) and lower continental shelf samples (LCS) with greater depths (i.e. 25-40 meters). By using imputed metagenomic approach, this study also discusses several adaptive mechanisms which enable microbes to survive in nutritionally deprived conditions, and also help to understand the influence of nutrition availability on bacterial diversity.}, } @article {pmid26059898, year = {2016}, author = {Davidovics, ZH and Carter, BA and Luna, RA and Hollister, EB and Shulman, RJ and Versalovic, J}, title = {The Fecal Microbiome in Pediatric Patients With Short Bowel Syndrome.}, journal = {JPEN. Journal of parenteral and enteral nutrition}, volume = {40}, number = {8}, pages = {1106-1113}, pmid = {26059898}, issn = {1941-2444}, support = {U01 CA170930/CA/NCI NIH HHS/United States ; UH3 DK083990/DK/NIDDK NIH HHS/United States ; R01 DK065075/DK/NIDDK NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 AT004326/AT/NCCIH NIH HHS/United States ; UH2 DK083990/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacillus/isolation & purification ; Bacterial Translocation ; Case-Control Studies ; Child ; Child, Preschool ; DNA, Bacterial/isolation & purification ; Feces/*microbiology ; Female ; Gammaproteobacteria/isolation & purification ; *Gastrointestinal Microbiome ; Humans ; Infant ; Intestines/microbiology ; Lactobacillus/isolation & purification ; Male ; RNA, Ribosomal, 16S/isolation & purification ; Ruminococcus/isolation & purification ; Sequence Analysis, DNA ; Short Bowel Syndrome/*microbiology/therapy ; Specimen Handling ; }, abstract = {BACKGROUND: Changes in the intestinal microbiome of patients with short bowel syndrome (SBS) are thought to significantly affect clinical outcome. These changes may not only delay enteral diet advancement but may also predispose patients to bacterial translocation, bacteremia, and liver disease. Patients with SBS are thought to be more susceptible to changes in gut microbial communities due to intestinal dysmotility and/or lack of anatomic safeguards such as the ileocecal valve.

MATERIALS AND METHODS: We analyzed the bacterial composition of 21 fecal specimens from 9 children with SBS and 8 healthy children ages 4 months to 8 years by 16S ribosomal RNA gene sequencing. The sequences were quality filtered and analyzed using QIIME, the Ribosomal Database Project Classifier, and the randomForest supervised learning algorithm.

RESULTS: The fecal microbiome of patients with SBS is different from that of healthy controls. Stool from patients with SBS had a significantly greater abundance of the bacterial classes Gammaproteobacteria and Bacilli. Stool from patients with SBS who experienced increased stool frequency tended to have increased abundance of Lactobacillus (P = .057) and decreased abundance of Ruminococcus.

CONCLUSION: This study shows that the fecal microbiome of patients with SBS is significantly different from that of healthy controls when analyzed by 16S metagenomics. Differences in the composition and function of gut microbiomes in children with SBS may affect bowel physiology, and these findings may provide new opportunities for intestinal rehabilitation and clinical management.}, } @article {pmid26058415, year = {2016}, author = {Bolaños, LM and Rosenblueth, M and Castillo-Ramírez, S and Figuier-Huttin, G and Martínez-Romero, E}, title = {Species-specific diversity of novel bacterial lineages and differential abundance of predicted pathways for toxic compound degradation in scorpion gut microbiota.}, journal = {Environmental microbiology}, volume = {18}, number = {5}, pages = {1364-1378}, doi = {10.1111/1462-2920.12939}, pmid = {26058415}, issn = {1462-2920}, mesh = {Animals ; Bacteria/*classification/genetics/isolation & purification/metabolism ; Biodiversity ; Food Deprivation ; *Gastrointestinal Microbiome/genetics ; Inactivation, Metabolic ; Metabolic Networks and Pathways ; Metagenome ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Scorpions/*microbiology ; Species Specificity ; }, abstract = {Scorpions are considered 'living fossils' that have conserved ancestral anatomical features and have adapted to numerous habitats. However, their gut microbiota diversity has not been studied. Here, we characterized the gut microbiota of two scorpion species, Vaejovis smithi and Centruroides limpidus. Our results indicate that scorpion gut microbiota is species-specific and that food deprivation reduces bacterial diversity. 16S rRNA gene phylogenetic analysis revealed novel bacterial lineages showing a low level of sequence identity to any known bacteria. Furthermore, these novel bacterial lineages were each restricted to a different scorpion species. Additionally, our results of the predicted metagenomic profiles revealed a core set of pathways that were highly abundant in both species, and mostly related to amino acid, carbohydrate, vitamin and cofactor metabolism. Notably, the food-deprived V. smithi shotgun metagenome matched almost completely the metabolic features of the prediction. Finally, comparisons among predicted metagenomic profiles showed that toxic compound degradation pathways were more abundant in recently captured C. limpidus scorpions. This study gives a first insight into the scorpion gut microbiota and provides a reference for future studies on the gut microbiota from other arachnid species.}, } @article {pmid26056847, year = {2015}, author = {Roossinck, MJ and Martin, DP and Roumagnac, P}, title = {Plant Virus Metagenomics: Advances in Virus Discovery.}, journal = {Phytopathology}, volume = {105}, number = {6}, pages = {716-727}, doi = {10.1094/PHYTO-12-14-0356-RVW}, pmid = {26056847}, issn = {0031-949X}, mesh = {Animals ; Biodiversity ; Computational Biology ; DNA, Viral/genetics ; Feces/virology ; High-Throughput Nucleotide Sequencing ; Insecta/virology ; *Metagenomics ; Plant Diseases/*virology ; Plant Viruses/*genetics ; Plants/*virology ; RNA, Viral/genetics ; Sequence Analysis, DNA ; }, abstract = {In recent years plant viruses have been detected from many environments, including domestic and wild plants and interfaces between these systems-aquatic sources, feces of various animals, and insects. A variety of methods have been employed to study plant virus biodiversity, including enrichment for virus-like particles or virus-specific RNA or DNA, or the extraction of total nucleic acids, followed by next-generation deep sequencing and bioinformatic analyses. All of the methods have some shortcomings, but taken together these studies reveal our surprising lack of knowledge about plant viruses and point to the need for more comprehensive studies. In addition, many new viruses have been discovered, with most virus infections in wild plants appearing asymptomatic, suggesting that virus disease may be a byproduct of domestication. For plant pathologists these studies are providing useful tools to detect viruses, and perhaps to predict future problems that could threaten cultivated plants.}, } @article {pmid26056770, year = {2015}, author = {Ventosa, A and de la Haba, RR and Sánchez-Porro, C and Papke, RT}, title = {Microbial diversity of hypersaline environments: a metagenomic approach.}, journal = {Current opinion in microbiology}, volume = {25}, number = {}, pages = {80-87}, doi = {10.1016/j.mib.2015.05.002}, pmid = {26056770}, issn = {1879-0364}, mesh = {Archaea/classification/genetics/metabolism/*physiology ; Bacteria/classification/genetics/metabolism ; *Bacterial Physiological Phenomena ; *Biodiversity ; Ecosystem ; Metagenome ; *Metagenomics ; Microbiota/genetics/*physiology ; Phylogeny ; *Salinity ; Salt Tolerance ; Sodium Chloride/metabolism ; *Water Microbiology ; }, abstract = {Recent studies based on metagenomics and other molecular techniques have permitted a detailed knowledge of the microbial diversity and metabolic activities of microorganisms in hypersaline environments. The current accepted model of community structure in hypersaline environments is that the square archaeon Haloquadratum waslbyi, the bacteroidete Salinibacter ruber and nanohaloarchaea are predominant members at higher salt concentrations, while more diverse archaeal and bacterial taxa are observed in habitats with intermediate salinities. Additionally, metagenomic studies may provide insight into the isolation and characterization of the principal microbes in these habitats, such as the recently described gammaproteobacterium Spiribacter salinus.}, } @article {pmid26056565, year = {2015}, author = {Lam, KN and Charles, TC}, title = {Strong spurious transcription likely contributes to DNA insert bias in typical metagenomic clone libraries.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {22}, pmid = {26056565}, issn = {2049-2618}, abstract = {BACKGROUND: Clone libraries provide researchers with a powerful resource to study nucleic acid from diverse sources. Metagenomic clone libraries in particular have aided in studies of microbial biodiversity and function, and allowed the mining of novel enzymes. Libraries are often constructed by cloning large inserts into cosmid or fosmid vectors. Recently, there have been reports of GC bias in fosmid metagenomic libraries, and it was speculated to be a result of fragmentation and loss of AT-rich sequences during cloning. However, evidence in the literature suggests that transcriptional activity or gene product toxicity may play a role.

RESULTS: To explore possible mechanisms responsible for sequence bias in clone libraries, we constructed a cosmid library from a human microbiome sample and sequenced DNA from different steps during library construction: crude extract DNA, size-selected DNA, and cosmid library DNA. We confirmed a GC bias in the final cosmid library, and we provide evidence that the bias is not due to fragmentation and loss of AT-rich sequences but is likely occurring after DNA is introduced into Escherichia coli. To investigate the influence of strong constitutive transcription, we searched the sequence data for promoters and found that rpoD/σ(70) promoter sequences were underrepresented in the cosmid library. Furthermore, when we examined the genomes of taxa that were differentially abundant in the cosmid library relative to the original sample, we found the bias to be more correlated with the number of rpoD/σ(70) consensus sequences in the genome than with simple GC content.

CONCLUSIONS: The GC bias of metagenomic libraries does not appear to be due to DNA fragmentation. Rather, analysis of promoter sequences provides support for the hypothesis that strong constitutive transcription from sequences recognized as rpoD/σ(70) consensus-like in E. coli may lead to instability, causing loss of the plasmid or loss of the insert DNA that gives rise to the transcription. Despite widespread use of E. coli to propagate foreign DNA in metagenomic libraries, the effects of in vivo transcriptional activity on clone stability are not well understood. Further work is required to tease apart the effects of transcription from those of gene product toxicity.}, } @article {pmid26051673, year = {2015}, author = {Chistoserdova, L}, title = {Methylotrophs in natural habitats: current insights through metagenomics.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {14}, pages = {5763-5779}, doi = {10.1007/s00253-015-6713-z}, pmid = {26051673}, issn = {1432-0614}, mesh = {Aerobiosis ; Anaerobiosis ; Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; *Environmental Microbiology ; *Metagenomics ; Methane/*metabolism ; Methanol/*metabolism ; Microbial Consortia ; }, abstract = {The focus of this review is on the recent data from the omics approaches, measuring the presence of methylotrophs in natural environments. Both Bacteria and Archaea are considered. The data are discussed in the context of the current knowledge on the biochemistry of methylotrophy and the physiology of cultivated methylotrophs. One major issue discussed is the recent metagenomic data pointing toward the activity of "aerobic" methanotrophs, such as Methylobacter, in microoxic or hypoxic conditions. A related issue of the metabolic distinction between aerobic and "anaerobic" methylotrophy is addressed in the light of the genomic and metagenomic data for respective organisms. The role of communities, as opposed to single-organism activities in environmental cycling of single-carbon compounds, such as methane, is also discussed. In addition, the emerging issue of the role of non-traditional methylotrophs in global metabolism of single-carbon compounds and the role of methylotrophy pathways in non-methylotrophs is briefly mentioned.}, } @article {pmid26048598, year = {2015}, author = {Fang, H and Huang, C and Zhao, H and Deng, M}, title = {CCLasso: correlation inference for compositional data through Lasso.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {19}, pages = {3172-3180}, pmid = {26048598}, issn = {1367-4811}, support = {GM59507/GM/NIGMS NIH HHS/United States ; }, mesh = {*Algorithms ; Bacteria/*classification/genetics ; Computational Biology/*methods ; Computer Simulation ; Genomics/methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {MOTIVATION: Direct analysis of microbial communities in the environment and human body has become more convenient and reliable owing to the advancements of high-throughput sequencing techniques for 16S rRNA gene profiling. Inferring the correlation relationship among members of microbial communities is of fundamental importance for genomic survey study. Traditional Pearson correlation analysis treating the observed data as absolute abundances of the microbes may lead to spurious results because the data only represent relative abundances. Special care and appropriate methods are required prior to correlation analysis for these compositional data.

RESULTS: In this article, we first discuss the correlation definition of latent variables for compositional data. We then propose a novel method called CCLasso based on least squares with [Formula: see text] penalty to infer the correlation network for latent variables of compositional data from metagenomic data. An effective alternating direction algorithm from augmented Lagrangian method is used to solve the optimization problem. The simulation results show that CCLasso outperforms existing methods, e.g. SparCC, in edge recovery for compositional data. It also compares well with SparCC in estimating correlation network of microbe species from the Human Microbiome Project.

CCLasso is open source and freely available from https://github.com/huayingfang/CCLasso under GNU LGPL v3.

CONTACT: dengmh@pku.edu.cn

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid26048203, year = {2015}, author = {Horwitz, D and McCue, T and Mapes, AC and Ajami, NJ and Petrosino, JF and Ramig, RF and Trautner, BW}, title = {Decreased microbiota diversity associated with urinary tract infection in a trial of bacterial interference.}, journal = {The Journal of infection}, volume = {71}, number = {3}, pages = {358-367}, pmid = {26048203}, issn = {1532-2742}, support = {R21 AI121545/AI/NIAID NIH HHS/United States ; R21 DK092293/DK/NIDDK NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; *Antibiosis ; Bacteremia/microbiology ; *Biodiversity ; Catheters, Indwelling/microbiology ; Escherichia coli/genetics/*growth & development/physiology ; Female ; Humans ; Male ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Urinary Bladder/*microbiology ; Urinary Catheterization ; Urinary Catheters/*microbiology ; Urinary Tract Infections/drug therapy/etiology/*microbiology ; Urine/microbiology ; }, abstract = {BACKGROUND: Patients with long-term indwelling catheters are at high risk of catheter-associated urinary tract infection (CAUTI). We hypothesized that colonizing the bladder with a benign Escherichia coli strain (E. coli HU2117, a derivative of E. coli 83972) would prevent CAUTI in older, catheterized adults.

MATERIALS AND METHODS: Adults with chronic, indwelling urinary catheters received study catheters that had been pre-coated with E. coli HU2117. We monitored the cultivatable organisms in the bladder for 28 days or until loss of E. coli HU2117. Urine from 4 subjects was collected longitudinally for 16S rRNA gene profiling.

RESULTS: Eight of the ten subjects (average age 70.9 years) became colonized with E. coli HU2117, with a mean duration of 57.7 days (median: 28.5, range 0-266). All subjects also remained colonized by uropathogens. Five subjects suffered invasive UTI, 3 febrile UTI and 2 urosepsis/bacteremia, all associated with overgrowth of a urinary pathogen. Colonization with E. coli HU2117 did not impact bacterial bladder diversity, but subjects who developed infections had less diverse bladder microbiota.

CONCLUSIONS: Colonization with E. coli HU2117 did not prevent bladder colonization or subsequent invasive disease by uropathogens. Microbial diversity may play a protective role against invasive infection of the catheterized bladder.

TRIAL REGISTRATION: ClinicalTrials.gov, NCT00554996 http://clinicaltrials.gov/ct2/show/NCT00554996.}, } @article {pmid26048196, year = {2015}, author = {Cowan, DA and Ramond, JB and Makhalanyane, TP and De Maayer, P}, title = {Metagenomics of extreme environments.}, journal = {Current opinion in microbiology}, volume = {25}, number = {}, pages = {97-102}, doi = {10.1016/j.mib.2015.05.005}, pmid = {26048196}, issn = {1879-0364}, mesh = {Archaea/*genetics/*physiology ; Bacteria/classification/*genetics ; *Bacterial Physiological Phenomena ; Ecosystem ; Environment ; *Metagenomics ; Microbial Consortia/genetics/*physiology ; }, abstract = {Whether they are exposed to extremes of heat or cold, or buried deep beneath the Earth's surface, microorganisms have an uncanny ability to survive under these conditions. This ability to survive has fascinated scientists for nearly a century, but the recent development of metagenomics and 'omics' tools has allowed us to make huge leaps in understanding the remarkable complexity and versatility of extremophile communities. Here, in the context of the recently developed metagenomic tools, we discuss recent research on the community composition, adaptive strategies and biological functions of extremophiles.}, } @article {pmid26047662, year = {2016}, author = {Stilling, RM and Dinan, TG and Cryan, JF}, title = {The brain's Geppetto-microbes as puppeteers of neural function and behaviour?.}, journal = {Journal of neurovirology}, volume = {22}, number = {1}, pages = {14-21}, pmid = {26047662}, issn = {1538-2443}, mesh = {Animals ; *Behavior ; Behavior, Animal ; Biological Evolution ; Brain/*microbiology/parasitology/physiopathology/virology ; Diet ; Feeding Behavior ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology/parasitology/physiopathology/virology ; *Host-Pathogen Interactions ; Humans ; Symbiosis/physiology ; }, abstract = {Research on the microbiome and its interaction with various host organs, including the brain, is increasingly gaining momentum. With more evidence establishing a comprehensive microbiota-gut-brain axis, questions have been raised as to the extent to which microbes influence brain physiology and behaviour. In parallel, there is a growing literature showing active behavioural manipulation in favour of the microbe for certain parasites. However, it seems unclear where the hidden majority of microbes are localised on the parasitism-mutualism spectrum. A long evolutionary history intimately connects host and microbiota, which complicates this classification. In this conceptual minireview, we discuss current hypotheses on host-microbe interaction and argue that novel experimental approaches and theoretical concepts, such as the hologenome theory, are necessary to incorporate transgenerational epigenetic inheritance of the microbiome into evolutionary theories.}, } @article {pmid26046242, year = {2015}, author = {Jin, D and Wu, S and Zhang, YG and Lu, R and Xia, Y and Dong, H and Sun, J}, title = {Lack of Vitamin D Receptor Causes Dysbiosis and Changes the Functions of the Murine Intestinal Microbiome.}, journal = {Clinical therapeutics}, volume = {37}, number = {5}, pages = {996-1009.e7}, doi = {10.1016/j.clinthera.2015.04.004}, pmid = {26046242}, issn = {1879-114X}, mesh = {Animals ; Cecum/microbiology ; Down-Regulation ; Dysbiosis/*physiopathology ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Intestines/microbiology ; Male ; Mice, Knockout ; Phylogeny ; Receptors, Calcitriol/*deficiency/physiology ; Signal Transduction/genetics ; }, abstract = {PURPOSE: The microbiome modulates numerous aspects of human physiology and is a crucial factor in the development of various human diseases. Vitamin D deficiency and downregulation of the vitamin D receptor (VDR) are also associated with the pathogenesis of diseases such as inflammatory bowel disease, cancers, obesity, diabetes, and asthma. VDR is a nuclear receptor that regulates the expression of antimicrobial peptides and autophagy regulator ATG16L1. Vitamin D may promote a balanced intestinal microbiome and improve glucose homeostasis in diabetes. However, how VDR regulates microbiome is not well known. In the current study, we hypothesize that VDR status regulates the composition and functions of the intestinal bacterial community.

METHODS: Fecal and cecal stool samples were harvested from Vdr knockout (Vdr(-/-)) and wild-type mice for bacterial DNA and then sequenced with 454 pyrosequencing. The sequences were denoised and clustered into operational taxonomic units, then queried against the National Center for Biotechnology Information database. Metagenomics were analyzed, and the abundances of genes involved in metabolic pathways were compared by reference to the Kyoto Encyclopedia of Genes and Genomes and Clusters of Orthologous Groups databases.

FINDINGS: In the Vdr(-/-) mice, Lactobacillus was depleted in the fecal stool, whereas Clostridium and Bacteroides were enriched. Bacterial taxa along the Sphingobacteria-to-Sphingobacteriaceae lineage were enriched, but no genera reached statistical significance. In the cecal stool, Alistipes and Odoribacter were depleted, and Eggerthella was enriched. Notably, all of the taxa upstream of Eggerthella remained unchanged. A comparison of Vdr(-/-) and wild-type samples revealed 40 (26 enriched, 14 depleted) and 72 (41 enriched, 31 depleted) functional modules that were significantly altered in the cecal and fecal microbiomes, respectively (both, P < 0.05), due to the loss of Vdr. In addition to phylogenetic differences in gut microbiome with different intestinal origins, we identify several important pathways, such as nucleotide-binding oligomerization domain-like receptor, affected by Vdr status, including amino acid, carbohydrate, and fatty acid synthesis and metabolism, detoxification, infections, signal transduction, and cancer and other diseases.

IMPLICATIONS: Our study fills knowledge gaps by having investigated the microbial profile affected by VDR. Insights from our findings can be exploited to develop novel strategies to treat or prevent various diseases by restoring VDR function and healthy microbe-host interactions.}, } @article {pmid26040274, year = {2015}, author = {Mongui, A and Pérez-Llanos, FJ and Yamamoto, MM and Lozano, M and Zambrano, MM and Del Portillo, P and Fernández-Becerra, C and Restrepo, S and Del Portillo, HA and Junca, H}, title = {Development of a genetic tool for functional screening of anti-malarial bioactive extracts in metagenomic libraries.}, journal = {Malaria journal}, volume = {14}, number = {}, pages = {233}, pmid = {26040274}, issn = {1475-2875}, mesh = {Antimalarials/*pharmacology ; Biodiversity ; *Genomic Library ; Malaria, Falciparum/drug therapy ; Metagenome ; *Parasitic Sensitivity Tests ; Plant Extracts/*pharmacology ; Plants/*chemistry ; Plasmodium falciparum/*drug effects/genetics ; }, abstract = {BACKGROUND: The chemical treatment of Plasmodium falciparum for human infections is losing efficacy each year due to the rise of resistance. One possible strategy to find novel anti-malarial drugs is to access the largest reservoir of genomic biodiversity source on earth present in metagenomes of environmental microbial communities.

METHODS: A bioluminescent P. falciparum parasite was used to quickly detect shifts in viability of microcultures grown in 96-well plates. A synthetic gene encoding the Dermaseptin 4 peptide was designed and cloned under tight transcriptional control in a large metagenomic insert context (30 kb) to serve as proof-of-principle for the screening platform.

RESULTS: Decrease in parasite viability consistently correlated with bioluminescence emitted from parasite microcultures, after their exposure to bacterial extracts containing a plasmid or fosmid engineered to encode the Dermaseptin 4 anti-malarial peptide.

CONCLUSIONS: Here, a new technical platform to access the anti-malarial potential in microbial environmental metagenomes has been developed.}, } @article {pmid26040234, year = {2015}, author = {He, B and Nohara, K and Ajami, NJ and Michalek, RD and Tian, X and Wong, M and Losee-Olson, SH and Petrosino, JF and Yoo, SH and Shimomura, K and Chen, Z}, title = {Transmissible microbial and metabolomic remodeling by soluble dietary fiber improves metabolic homeostasis.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {10604}, pmid = {26040234}, issn = {2045-2322}, support = {R01 GM114424/GM/NIGMS NIH HHS/United States ; 2P30-DK056338/DK/NIDDK NIH HHS/United States ; R01 AG045828/AG/NIA NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01, AG045828/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Biomarkers ; Blood Glucose ; Cluster Analysis ; *Dietary Fiber ; Disease Models, Animal ; *Gastrointestinal Microbiome ; *Homeostasis ; Metabolic Diseases/metabolism/microbiology ; *Metabolome ; *Metabolomics ; Mice ; Polysaccharides/metabolism ; }, abstract = {Dietary fibers are increasingly appreciated as beneficial nutritional components. However, a requisite role of gut microbiota in fiber function and the overall impact of fibers on metabolomic flux remain unclear. We herein showed enhancing effects of a soluble resistant maltodextrin (RM) on glucose homeostasis in mouse metabolic disease models. Remarkably, fecal microbiota transplantation (FMT) caused pronounced and time-dependent improvement in glucose tolerance in RM recipient mice, indicating a causal relationship between microbial remodeling and metabolic efficacy. Microbial 16S sequencing revealed transmissible taxonomic changes correlated with improved metabolism, notably enrichment of probiotics and reduction of Alistipes and Bacteroides known to associate with high fat/protein diets. Metabolomic profiling further illustrated broad changes, including enrichment of phenylpropionates and decreases in key intermediates of glucose utilization, cholesterol biosynthesis and amino acid fermentation. These studies elucidate beneficial roles of RM-dependent microbial remodeling in metabolic homeostasis, and showcase prevalent health-promoting potentials of dietary fibers.}, } @article {pmid26038180, year = {2015}, author = {Pible, O and Armengaud, J}, title = {Improving the quality of genome, protein sequence, and taxonomy databases: a prerequisite for microbiome meta-omics 2.0.}, journal = {Proteomics}, volume = {15}, number = {20}, pages = {3418-3423}, doi = {10.1002/pmic.201500104}, pmid = {26038180}, issn = {1615-9861}, mesh = {Amino Acid Sequence/*genetics ; Classification ; Computational Biology ; Databases, Genetic ; *Genomics ; Metagenome/genetics ; Microbiota/*genetics ; Molecular Sequence Annotation ; *Proteomics ; Tandem Mass Spectrometry ; Transcriptome/genetics ; }, abstract = {High-throughput shotgun metaproteomic approaches on environmental or medical microbiomes are producing huge amounts of tandem mass spectrometry data. These can be interpreted either with a general protein sequence database comprising tens of thousands of sequenced genomes or with a more customized database such as those obtained after metagenome sequencing of the DNA extracted from the same sample. However, not all entries in a nucleotide or protein sequence database are of equal quality and this can critically impact metaproteomic data interpretation. In this viewpoint article, we exemplify several key issues. First, either genome or transcriptome data interpretation due to inaccurate contig assembly and gene prediction may be erroneous, for its mitigation the metaproteogenomic strategies could have an interesting perspective. Errors in sample handling and taxonomical characterization may also be problematic. Cross-contamination of genome sequences is also underestimated while frequent. As a consequence of these structural errors regarding protein sequences and additional problems due to homology-based functional annotation of proteins, specific efforts for better interpretation of metaproteomic data are required. We propose the development of new bioinformatic pipelines devoted to detection and correction of errors and contaminations to improve the overall quality of sequence and taxonomy databases for metaproteomics.}, } @article {pmid26036920, year = {2016}, author = {Wang, J and Gao, Y and Zhao, F}, title = {Phage-bacteria interaction network in human oral microbiome.}, journal = {Environmental microbiology}, volume = {18}, number = {7}, pages = {2143-2158}, doi = {10.1111/1462-2920.12923}, pmid = {26036920}, issn = {1462-2920}, mesh = {Bacteria/classification/genetics/isolation & purification/*virology ; Bacteriophages/classification/genetics/*isolation & purification/physiology ; Humans ; Microbiota ; Mouth/*microbiology/*virology ; Phylogeny ; }, abstract = {Although increasing knowledge suggests that bacteriophages play important roles in regulating microbial ecosystems, phage-bacteria interaction in human oral cavities remains less understood. Here we performed a metagenomic analysis to explore the composition and variation of oral dsDNA phage populations and potential phage-bacteria interaction. A total of 1,711 contigs assembled with more than 100 Gb shotgun sequencing data were annotated to 104 phages based on their best BLAST matches against the NR database. Bray-Curtis dissimilarities demonstrated that both phage and bacterial composition are highly diverse between periodontally healthy samples but show a trend towards homogenization in diseased gingivae samples. Significantly, according to the CRISPR arrays that record infection relationship between bacteria and phage, we found certain oral phages were able to invade other bacteria besides their putative bacterial hosts. These cross-infective phages were positively correlated with commensal bacteria while were negatively correlated with major periodontal pathogens, suggesting possible connection between these phages and microbial community structure in oral cavities. By characterizing phage-bacteria interaction as networks rather than exclusively pairwise predator-prey relationships, our study provides the first insight into the participation of cross-infective phages in forming human oral microbiota.}, } @article {pmid26035208, year = {2015}, author = {Jalali, S and Kohli, S and Latka, C and Bhatia, S and Vellarikal, SK and Sivasubbu, S and Scaria, V and Ramachandran, S}, title = {Screening currency notes for microbial pathogens and antibiotic resistance genes using a shotgun metagenomic approach.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0128711}, pmid = {26035208}, issn = {1932-6203}, mesh = {Drug Resistance, Microbial/*genetics ; Fomites/*microbiology ; India ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA ; }, abstract = {Fomites are a well-known source of microbial infections and previous studies have provided insights into the sojourning microbiome of fomites from various sources. Paper currency notes are one of the most commonly exchanged objects and its potential to transmit pathogenic organisms has been well recognized. Approaches to identify the microbiome associated with paper currency notes have been largely limited to culture dependent approaches. Subsequent studies portrayed the use of 16S ribosomal RNA based approaches which provided insights into the taxonomical distribution of the microbiome. However, recent techniques including shotgun sequencing provides resolution at gene level and enable estimation of their copy numbers in the metagenome. We investigated the microbiome of Indian paper currency notes using a shotgun metagenome sequencing approach. Metagenomic DNA isolated from samples of frequently circulated denominations of Indian currency notes were sequenced using Illumina Hiseq sequencer. Analysis of the data revealed presence of species belonging to both eukaryotic and prokaryotic genera. The taxonomic distribution at kingdom level revealed contigs mapping to eukaryota (70%), bacteria (9%), viruses and archae (~1%). We identified 78 pathogens including Staphylococcus aureus, Corynebacterium glutamicum, Enterococcus faecalis, and 75 cellulose degrading organisms including Acidothermus cellulolyticus, Cellulomonas flavigena and Ruminococcus albus. Additionally, 78 antibiotic resistance genes were identified and 18 of these were found in all the samples. Furthermore, six out of 78 pathogens harbored at least one of the 18 common antibiotic resistance genes. To the best of our knowledge, this is the first report of shotgun metagenome sequence dataset of paper currency notes, which can be useful for future applications including as bio-surveillance of exchangeable fomites for infectious agents.}, } @article {pmid26033481, year = {2015}, author = {Hwang, J and Zhao, Q and Yang, ZL and Wang, Z and Townsend, JP}, title = {Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples - an example of saddle fungi.}, journal = {Environmental microbiology reports}, volume = {7}, number = {4}, pages = {658-667}, doi = {10.1111/1758-2229.12303}, pmid = {26033481}, issn = {1758-2229}, mesh = {Ascomycota/*classification/*genetics/isolation & purification ; *Biodiversity ; Biological Evolution ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Ecosystem ; Mycorrhizae/*classification/*genetics/isolation & purification ; Phylogeny ; Plants/microbiology ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {The relation between ecological and genetic divergence of Helvella species (saddle fungi) has been perplexing. While a few species have been clearly demonstrated to be ectomycorrhizal fungi, ecological roles of many other species have been controversial, alternately considered as either saprotrophic or mycorrhizal. We applied SATé to build an inclusive deoxyribonucleic acid sequence alignment for the internal transcribed spacers (ITS) of annotated Helvella species and related environmental sequences. Phylogenetic informativeness of ITS and its regions were assessed using PhyDesign. Mycorrhizal lineages present a diversity of ecology, host type and geographic distribution. In two Helvella clades, no Helvella ITS sequences were recovered from root tips. Inclusion of environmental sequences in the ITS phylogeny from these sequences has the potential to link these data and reveal Helvella ecology. This study can serve as a model for revealing the diversity of relationships between unculturable fungi and their potential plant hosts. How non-mycorrhizal life styles within Helvella evolved will require expanded metagenomic investigation of soil and other environmental samples along with study of Helvella genomes.}, } @article {pmid26030271, year = {2015}, author = {Shi, C and Liu, Y and Hu, X and Xiong, J and Zhang, B and Yuan, Z}, title = {A metagenomic survey of viral abundance and diversity in mosquitoes from Hubei province.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0129845}, pmid = {26030271}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Biodiversity ; China ; Culicidae/*virology ; Dicistroviridae/genetics ; Genome, Viral/genetics ; Metagenomics/methods ; Parvovirus, Porcine/genetics ; Phylogeny ; Rhabdoviridae/genetics ; Sequence Alignment ; Surveys and Questionnaires ; Swine/virology ; }, abstract = {Mosquitoes as one of the most common but important vectors have the potential to transmit or acquire a lot of viruses through biting, however viral flora in mosquitoes and its impact on mosquito-borne disease transmission has not been well investigated and evaluated. In this study, the metagenomic techniquehas been successfully employed in analyzing the abundance and diversity of viral community in three mosquito samples from Hubei, China. Among 92,304 reads produced through a run with 454 GS FLX system, 39% have high similarities with viral sequences belonging to identified bacterial, fungal, animal, plant and insect viruses, and 0.02% were classed into unidentified viral sequences, demonstrating high abundance and diversity of viruses in mosquitoes. Furthermore, two novel viruses in subfamily Densovirinae and family Dicistroviridae were identified, and six torque tenosus virus1 in family Anelloviridae, three porcine parvoviruses in subfamily Parvovirinae and a Culex tritaeniorhynchus rhabdovirus in Family Rhabdoviridae were preliminarily characterized. The viral metagenomic analysis offered us a deep insight into the viral population of mosquito which played an important role in viral initiative or passive transmission and evolution during the process.}, } @article {pmid26027543, year = {2015}, author = {Lee, J and Lee, HT and Hong, WY and Jang, E and Kim, J}, title = {FCMM: A comparative metagenomic approach for functional characterization of multiple metagenome samples.}, journal = {Journal of microbiological methods}, volume = {115}, number = {}, pages = {121-128}, doi = {10.1016/j.mimet.2015.05.023}, pmid = {26027543}, issn = {1872-8359}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Geologic Sediments/*microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; Metagenomics/*methods ; Microbiota ; Soil Microbiology ; Water Microbiology ; }, abstract = {Next-generation sequencing (NGS) technologies make it possible to obtain the entire genomic content of microorganisms in metagenome samples. Thus, many studies have developed methods for the processing and analysis of metagenomic NGS reads, including analyses for predicting functions and their enrichments in environmental metagenome samples. Especially, comparative functional studies by using multi-metagenome samples are essential for identifying and comparing different characteristics of multiple environmental samples. In this paper, we introduce a pipeline for functional characterization of multiple metagenome samples to infer major functions as well as their quantitative scores in a comparative metagenomics manner. The pipeline performs the annotation of functions related to expected proteins in the metagenome samples, calculates their enrichment scores based on the reads per kilobase per million reads (RPKM) measure, and predicts the relative abundance of associated functions by a statistical test. The results from single sample analysis are then used to find common and sample-specific major functions. By applying the pipeline to six different environmental metagenome samples, including two ocean (Antarctica aquatic and Baltic Sea) and four terrestrial (Acid mine drainage, human gut microbiome, Amazon River, and Wasca soil) samples, we were able to predict common functions as well as environment-specific functions. Our pipeline is available at http://bioinfo.konkuk.ac.kr/FCMM/.}, } @article {pmid26025238, year = {2015}, author = {Foxman, B and Martin, ET}, title = {Use of the Microbiome in the Practice of Epidemiology: A Primer on -Omic Technologies.}, journal = {American journal of epidemiology}, volume = {182}, number = {1}, pages = {1-8}, pmid = {26025238}, issn = {1476-6256}, support = {K01 AI099006/AI/NIAID NIH HHS/United States ; K01AI099006/AI/NIAID NIH HHS/United States ; }, mesh = {*Computational Biology ; Epidemiology/*trends ; Humans ; *Microbiota ; }, abstract = {The term microbiome refers to the collective genome of the microbes living in and on our bodies, but it has colloquially come to mean the bacteria, viruses, archaea, and fungi that make up the microbiota (previously known as microflora). We can identify the microbes present in the human body (membership) and their relative abundance using genomics, characterize their genetic potential (or gene pool) using metagenomics, and describe their ongoing functions using transcriptomics, proteomics, and metabolomics. Epidemiologists can make a major contribution to this emerging field by performing well-designed, well-conducted, and appropriately powered studies and by including measures of microbiota in current and future cohort studies to characterize natural variation in microbiota composition and function, identify important confounders and effect modifiers, and generate and test hypotheses about the role of microbiota in health and disease. In this review, we provide an overview of the rapidly growing literature on the microbiome, describe which aspects of the microbiome can be measured and how, and discuss the challenges of including the microbiome as either an exposure or an outcome in epidemiologic studies.}, } @article {pmid26023875, year = {2016}, author = {Chapelle, E and Mendes, R and Bakker, PA and Raaijmakers, JM}, title = {Fungal invasion of the rhizosphere microbiome.}, journal = {The ISME journal}, volume = {10}, number = {1}, pages = {265-268}, pmid = {26023875}, issn = {1751-7370}, mesh = {*Antibiosis ; Bacteria/classification/genetics/*isolation & purification ; Bacterial Physiological Phenomena ; Metagenomics ; *Microbiota ; Plant Roots/microbiology ; Plants/microbiology ; Rhizoctonia/*physiology ; Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The rhizosphere is the infection court where soil-borne pathogens establish a parasitic relationship with the plant. To infect root tissue, pathogens have to compete with members of the rhizosphere microbiome for available nutrients and microsites. In disease-suppressive soils, pathogens are strongly restricted in growth by the activities of specific rhizosphere microorganisms. Here, we sequenced metagenomic DNA and RNA of the rhizosphere microbiome of sugar beet seedlings grown in a soil suppressive to the fungal pathogen Rhizoctonia solani. rRNA-based analyses showed that Oxalobacteraceae, Burkholderiaceae, Sphingobacteriaceae and Sphingomonadaceae were significantly more abundant in the rhizosphere upon fungal invasion. Metatranscriptomics revealed that stress-related genes (ppGpp metabolism and oxidative stress) were upregulated in these bacterial families. We postulate that the invading pathogenic fungus induces, directly or via the plant, stress responses in the rhizobacterial community that lead to shifts in microbiome composition and to activation of antagonistic traits that restrict pathogen infection.}, } @article {pmid26022326, year = {2015}, author = {Ininbergs, K and Bergman, B and Larsson, J and Ekman, M}, title = {Microbial metagenomics in the Baltic Sea: Recent advancements and prospects for environmental monitoring.}, journal = {Ambio}, volume = {44 Suppl 3}, number = {Suppl 3}, pages = {439-450}, pmid = {26022326}, issn = {1654-7209}, mesh = {Biodiversity ; Ecosystem ; Environmental Monitoring/*methods ; Metagenomics/*methods ; Oceans and Seas ; Seawater/microbiology ; }, abstract = {Metagenomics refers to the analysis of DNA from a whole community. Metagenomic sequencing of environmental DNA has greatly improved our knowledge of the identity and function of microorganisms in aquatic, terrestrial, and human biomes. Although open oceans have been the primary focus of studies on aquatic microbes, coastal and brackish ecosystems are now being surveyed. Here, we review so far published studies on microbes in the Baltic Sea, one of the world's largest brackish water bodies, using high throughput sequencing of environmental DNA and RNA. Collectively the data illustrate that Baltic Sea microbes are unique and highly diverse, and well adapted to this brackish-water ecosystem, findings that represent a novel base-line knowledge necessary for monitoring purposes and a sustainable management. More specifically, the data relate to environmental drivers for microbial community composition and function, assessments of the microbial biodiversity, adaptations and role of microbes in the nitrogen cycle, and microbial genome assembly from metagenomic sequences. With these discoveries as background, prospects of using metagenomics for Baltic Sea environmental monitoring are discussed.}, } @article {pmid26020167, year = {2015}, author = {Firkins, JL and Yu, Z}, title = {RUMINANT NUTRITION SYMPOSIUM: How to use data on the rumen microbiome to improve our understanding of ruminant nutrition.}, journal = {Journal of animal science}, volume = {93}, number = {4}, pages = {1450-1470}, doi = {10.2527/jas.2014-8754}, pmid = {26020167}, issn = {1525-3163}, mesh = {*Animal Nutritional Physiological Phenomena ; Animals ; *Biodiversity ; Dietary Fiber/metabolism ; Metagenomics/*methods/trends ; Methane/biosynthesis ; *Microbiota ; Nitrogen/metabolism ; Rumen/*microbiology ; Ruminants/*microbiology/*physiology ; }, abstract = {Metagenomics and high-throughput sequencing have greatly expanded our knowledge of the rumen microbiome. Surveys of all 4 cellular microbial groups (bacteria, archaea, protozoa, and fungi) reveal profound diversity. Even so, evidence exists for core members to perform key degradative or fermentative roles for the host. Some core members are functionally similar yet taxonomically diverse, and noncore members are particularly diverse and probably vary among diets, animals, and over time after feeding. Gains in functional knowledge are being made and offer much potential not only to improve fiber digestibility, decrease methane emissions, and improve efficiency of nitrogen usage but also to help explain the differences in nutrient digestibility or feed efficiency among animals fed the same diet. Integrated research using metagenomics, bioinformatics, traditional ruminant nutrition, and statistical inferences have provided opportunities for ruminant nutritionists and rumen microbiologists to work synergistically to improve nutrient utilization efficiency while minimizing output of wastes and emissions of methane and ammonia. Examples we highlight include residual feed intake, rumen biohydrogenation of unsaturated fatty acids, and dietary inclusion of ionophores. However, there are still some quantitative limitations in approaches being used. This review addresses knowledge gained and current limitations and challenges that remain.}, } @article {pmid26020166, year = {2015}, author = {McAllister, TA and Meale, SJ and Valle, E and Guan, LL and Zhou, M and Kelly, WJ and Henderson, G and Attwood, GT and Janssen, PH}, title = {RUMINANT NUTRITION SYMPOSIUM: Use of genomics and transcriptomics to identify strategies to lower ruminal methanogenesis.}, journal = {Journal of animal science}, volume = {93}, number = {4}, pages = {1431-1449}, doi = {10.2527/jas.2014-8329}, pmid = {26020166}, issn = {1525-3163}, mesh = {Animals ; Euryarchaeota/genetics/*metabolism ; Fermentation ; *Gastrointestinal Microbiome ; Livestock/metabolism/*microbiology ; Metagenomics/*methods/trends ; Methane/*biosynthesis ; Rumen/*microbiology ; Ruminants/metabolism/*microbiology ; }, abstract = {Globally, methane (CH4) emissions account for 40% to 45% of greenhouse gas emissions from ruminant livestock, with over 90% of these emissions arising from enteric fermentation. Reduction of carbon dioxide to CH4 is critical for efficient ruminal fermentation because it prevents the accumulation of reducing equivalents in the rumen. Methanogens exist in a symbiotic relationship with rumen protozoa and fungi and within biofilms associated with feed and the rumen wall. Genomics and transcriptomics are playing an increasingly important role in defining the ecology of ruminal methanogenesis and identifying avenues for its mitigation. Metagenomic approaches have provided information on changes in abundances as well as the species composition of the methanogen community among ruminants that vary naturally in their CH4 emissions, their feed efficiency, and their response to CH4 mitigators. Sequencing the genomes of rumen methanogens has provided insight into surface proteins that may prove useful in the development of vaccines and has allowed assembly of biochemical pathways for use in chemogenomic approaches to lowering ruminal CH4 emissions. Metagenomics and metatranscriptomic analysis of entire rumen microbial communities are providing new perspectives on how methanogens interact with other members of this ecosystem and how these relationships may be altered to reduce methanogenesis. Identification of community members that produce antimethanogen agents that either inhibit or kill methanogens could lead to the identification of new mitigation approaches. Discovery of a lytic archaeophage that specifically lyses methanogens is 1 such example. Efforts in using genomic data to alter methanogenesis have been hampered by a lack of sequence information that is specific to the microbial community of the rumen. Programs such as Hungate1000 and the Global Rumen Census are increasing the breadth and depth of our understanding of global ruminal microbial communities, steps that are key to using these tools to further define the science of ruminal methanogenesis.}, } @article {pmid26019163, year = {2015}, author = {Field, W and Hershberg, R}, title = {Alarmingly High Segregation Frequencies of Quinolone Resistance Alleles within Human and Animal Microbiomes Are Not Explained by Direct Clinical Antibiotic Exposure.}, journal = {Genome biology and evolution}, volume = {7}, number = {6}, pages = {1743-1757}, pmid = {26019163}, issn = {1759-6653}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/genetics ; DNA Gyrase/genetics ; DNA Topoisomerase IV/genetics ; Drug Resistance, Bacterial/*genetics ; Female ; Gastrointestinal Tract/microbiology ; *Gene Frequency ; Humans ; Infant ; Microbiota/*genetics ; Quinolones/pharmacology ; Rifamycins/pharmacology ; Streptomycin/pharmacology ; }, abstract = {Antibiotic resistance poses a major threat to human health. It is therefore important to characterize the frequency of resistance within natural bacterial environments. Many studies have focused on characterizing the frequencies with which horizontally acquired resistance genes segregate within natural bacterial populations. Yet, very little is currently understood regarding the frequency of segregation of resistance alleles occurring within the housekeeping targets of antibiotics. We surveyed a large number of metagenomic datasets extracted from a large variety of host-associated and non host-associated environments for such alleles conferring resistance to three groups of broad spectrum antibiotics: streptomycin, rifamycins, and quinolones. We find notable segregation frequencies of resistance alleles occurring within the target genes of each of the three antibiotics, with quinolone resistance alleles being the most frequent and rifamycin resistance alleles being the least frequent. Resistance allele frequencies varied greatly between different phyla and as a function of environment. The frequency of quinolone resistance alleles was especially high within host-associated environments, where it averaged an alarming ∼ 40%. Within host-associated environments, resistance to quinolones was most often conferred by a specific resistance allele. High frequencies of quinolone resistance alleles were also found within hosts that were not directly treated with antibiotics. Therefore, the high segregation frequency of quinolone resistance alleles occurring within the housekeeping targets of antibiotics in host-associated environments does not seem to be the sole result of clinical antibiotic usage.}, } @article {pmid26018867, year = {2015}, author = {Pierre Louis, AM and Yu, H and Shumlas, SL and Van Aken, B and Schoonen, MA and Strongin, DR}, title = {Effect of Phospholipid on Pyrite Oxidation and Microbial Communities under Simulated Acid Mine Drainage (AMD) Conditions.}, journal = {Environmental science & technology}, volume = {49}, number = {13}, pages = {7701-7708}, doi = {10.1021/es505374g}, pmid = {26018867}, issn = {1520-5851}, mesh = {Acids/*chemistry ; Bacteria/metabolism ; Biodegradation, Environmental ; Geologic Sediments/chemistry ; Hydrogen-Ion Concentration ; Iron/*chemistry ; Metagenomics ; *Microbiota ; *Mining ; Oxidation-Reduction ; Phospholipids/*chemistry ; Phylogeny ; Sulfates/analysis ; Sulfides/*chemistry ; *Waste Disposal, Fluid ; X-Ray Diffraction ; }, abstract = {The effect of phospholipid on the biogeochemistry of pyrite oxidation, which leads to acid mine drainage (AMD) chemistry in the environment, was investigated. Metagenomic analyses were carried out to understand how the microbial community structure, which developed during the oxidation of pyrite-containing coal mining overburden/waste rock (OWR), was affected by the presence of adsorbed phospholipid. Using columns packed with OWR (with and without lipid adsorption), the release of sulfate (SO4(2-)) and soluble iron (FeTot) was investigated. Exposure of lipid-free OWR to flowing pH-neutral water resulted in an acidic effluent with a pH range of 2-4.5 over a 3-year period. The average concentration of FeTot and SO4(2-) in the effluent was ≥20 and ≥30 mg/L, respectively. In contrast, in packed-column experiments where OWR was first treated with phospholipid, the effluent pH remained at ∼6.5 and the average concentrations of FeTot and SO4(2-) were ≤2 and l.6 mg/L, respectively. 16S rDNA metagenomic pyrosequencing analysis of the microbial communities associated with OWR samples revealed the development of AMD-like communities dominated by acidophilic sulfide-oxidizing bacteria on untreated OWR samples, but not on refuse pretreated with phospholipid.}, } @article {pmid26015565, year = {2015}, author = {Byrd, AL and Segre, JA}, title = {Elucidating microbial codes to distinguish individuals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {22}, pages = {6778-6779}, pmid = {26015565}, issn = {1091-6490}, mesh = {Genetic Markers/*genetics ; *Genetic Variation ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Precision Medicine/*methods ; }, } @article {pmid26012569, year = {2015}, author = {Manzo, VE and Bhatt, AS}, title = {The human microbiome in hematopoiesis and hematologic disorders.}, journal = {Blood}, volume = {126}, number = {3}, pages = {311-318}, pmid = {26012569}, issn = {1528-0020}, support = {K08 CA184420/CA/NCI NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/*isolation & purification ; Fungi/classification/genetics/*isolation & purification ; Hematologic Diseases/genetics/*microbiology ; Hematopoiesis/*physiology ; Humans ; *Microbiota ; }, abstract = {Humans are now understood to be in complex symbiosis with a diverse ecosystem of microbial organisms, including bacteria, viruses, and fungi. Efforts to characterize the role of these microorganisms, commonly referred as the microbiota, in human health have sought to answer the fundamental questions of what organisms are present, how are they functioning to interact with human cells, and by what mechanism are these interactions occurring. In this review, we describe recent efforts to describe the microbiota in healthy and diseased individuals, summarize the role of various molecular technologies (ranging from 16S ribosomal RNA to shotgun metagenomic sequencing) in enumerating the community structure of the microbiota, and explore known interactions between the microbiota and humans, with a focus on the microbiota's role in hematopoiesis and hematologic diseases.}, } @article {pmid26010362, year = {2015}, author = {Probst, AJ and Weinmaier, T and DeSantis, TZ and Santo Domingo, JW and Ashbolt, N}, title = {New perspectives on microbial community distortion after whole-genome amplification.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0124158}, pmid = {26010362}, issn = {1932-6203}, mesh = {Bacteria/classification/genetics ; Base Composition/genetics ; Biofilms ; Ecosystem ; Genome Size ; *Genome, Bacterial ; Microbiota/*genetics ; Nitrogen/metabolism ; Nucleic Acid Amplification Techniques/*methods ; Sewage/microbiology ; }, abstract = {Whole-genome amplification (WGA) has become an important tool to explore the genomic information of microorganisms in an environmental sample with limited biomass, however potential selective biases during the amplification processes are poorly understood. Here, we describe the effects of WGA on 31 different microbial communities from five biotopes that also included low-biomass samples from drinking water and groundwater. Our findings provide evidence that microbiome segregation by biotope was possible despite WGA treatment. Nevertheless, samples from different biotopes revealed different levels of distortion, with genomic GC content significantly correlated with WGA perturbation. Certain phylogenetic clades revealed a homogenous trend across various sample types, for instance Alpha- and Betaproteobacteria showed a decrease in their abundance after WGA treatment. On the other hand, Enterobacteriaceae, an important biomarker group for fecal contamination in groundwater and drinking water, were strongly affected by WGA treatment without a predictable pattern. These novel results describe the impact of WGA on low-biomass samples and may highlight issues to be aware of when designing future metagenomic studies that necessitate preceding WGA treatment.}, } @article {pmid26005845, year = {2015}, author = {Faust, K and Lahti, L and Gonze, D and de Vos, WM and Raes, J}, title = {Metagenomics meets time series analysis: unraveling microbial community dynamics.}, journal = {Current opinion in microbiology}, volume = {25}, number = {}, pages = {56-66}, doi = {10.1016/j.mib.2015.04.004}, pmid = {26005845}, issn = {1879-0364}, mesh = {Humans ; *Metagenomics ; Microbial Consortia/*genetics/*physiology ; Microbial Interactions ; Microbiota/genetics/*physiology ; Models, Statistical ; Time Factors ; }, abstract = {The recent increase in the number of microbial time series studies offers new insights into the stability and dynamics of microbial communities, from the world's oceans to human microbiota. Dedicated time series analysis tools allow taking full advantage of these data. Such tools can reveal periodic patterns, help to build predictive models or, on the contrary, quantify irregularities that make community behavior unpredictable. Microbial communities can change abruptly in response to small perturbations, linked to changing conditions or the presence of multiple stable states. With sufficient samples or time points, such alternative states can be detected. In addition, temporal variation of microbial interactions can be captured with time-varying networks. Here, we apply these techniques on multiple longitudinal datasets to illustrate their potential for microbiome research.}, } @article {pmid25999515, year = {2015}, author = {Brum, JR and Ignacio-Espinoza, JC and Roux, S and Doulcier, G and Acinas, SG and Alberti, A and Chaffron, S and Cruaud, C and de Vargas, C and Gasol, JM and Gorsky, G and Gregory, AC and Guidi, L and Hingamp, P and Iudicone, D and Not, F and Ogata, H and Pesant, S and Poulos, BT and Schwenck, SM and Speich, S and Dimier, C and Kandels-Lewis, S and Picheral, M and Searson, S and , and Bork, P and Bowler, C and Sunagawa, S and Wincker, P and Karsenti, E and Sullivan, MB}, title = {Ocean plankton. Patterns and ecological drivers of ocean viral communities.}, journal = {Science (New York, N.Y.)}, volume = {348}, number = {6237}, pages = {1261498}, doi = {10.1126/science.1261498}, pmid = {25999515}, issn = {1095-9203}, support = {294823/ERC_/European Research Council/International ; }, mesh = {Biodiversity ; DNA, Viral/genetics ; Ecological and Environmental Phenomena ; *Ecosystem ; Metagenome/genetics ; Microbiota/genetics ; Oceans and Seas ; Plankton/*classification/genetics ; Seawater/*virology ; Viral Proteins/genetics ; Viruses/*classification/genetics ; }, abstract = {Viruses influence ecosystems by modulating microbial population size, diversity, metabolic outputs, and gene flow. Here, we use quantitative double-stranded DNA (dsDNA) viral-fraction metagenomes (viromes) and whole viral community morphological data sets from 43 Tara Oceans expedition samples to assess viral community patterns and structure in the upper ocean. Protein cluster cataloging defined pelagic upper-ocean viral community pan and core gene sets and suggested that this sequence space is well-sampled. Analyses of viral protein clusters, populations, and morphology revealed biogeographic patterns whereby viral communities were passively transported on oceanic currents and locally structured by environmental conditions that affect host community structure. Together, these investigations establish a global ocean dsDNA viromic data set with analyses supporting the seed-bank hypothesis to explain how oceanic viral communities maintain high local diversity.}, } @article {pmid25999513, year = {2015}, author = {Sunagawa, S and Coelho, LP and Chaffron, S and Kultima, JR and Labadie, K and Salazar, G and Djahanschiri, B and Zeller, G and Mende, DR and Alberti, A and Cornejo-Castillo, FM and Costea, PI and Cruaud, C and d'Ovidio, F and Engelen, S and Ferrera, I and Gasol, JM and Guidi, L and Hildebrand, F and Kokoszka, F and Lepoivre, C and Lima-Mendez, G and Poulain, J and Poulos, BT and Royo-Llonch, M and Sarmento, H and Vieira-Silva, S and Dimier, C and Picheral, M and Searson, S and Kandels-Lewis, S and , and Bowler, C and de Vargas, C and Gorsky, G and Grimsley, N and Hingamp, P and Iudicone, D and Jaillon, O and Not, F and Ogata, H and Pesant, S and Speich, S and Stemmann, L and Sullivan, MB and Weissenbach, J and Wincker, P and Karsenti, E and Raes, J and Acinas, SG and Bork, P}, title = {Ocean plankton. Structure and function of the global ocean microbiome.}, journal = {Science (New York, N.Y.)}, volume = {348}, number = {6237}, pages = {1261359}, doi = {10.1126/science.1261359}, pmid = {25999513}, issn = {1095-9203}, support = {294823/ERC_/European Research Council/International ; }, mesh = {Databases, Genetic ; Ecosystem ; Gastrointestinal Tract/microbiology ; Genetic Variation ; Humans ; Metagenome ; Microbiota/*genetics ; Oceans and Seas ; Plankton/*classification/genetics/isolation & purification ; Seawater/*microbiology ; }, abstract = {Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.}, } @article {pmid25998815, year = {2015}, author = {Illeghems, K and Weckx, S and De Vuyst, L}, title = {Applying meta-pathway analyses through metagenomics to identify the functional properties of the major bacterial communities of a single spontaneous cocoa bean fermentation process sample.}, journal = {Food microbiology}, volume = {50}, number = {}, pages = {54-63}, doi = {10.1016/j.fm.2015.03.005}, pmid = {25998815}, issn = {1095-9998}, mesh = {Bacteria/genetics/*metabolism ; Bacteriocins ; Brazil ; Cacao/*microbiology ; Citrates/metabolism ; Clustered Regularly Interspaced Short Palindromic Repeats ; Enterobacteriaceae/genetics/metabolism ; *Fermentation ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Lactobacillus/genetics/metabolism ; *Metabolic Networks and Pathways ; *Metagenome ; Metagenomics/methods ; Microbial Consortia/*physiology ; Pyruvaldehyde/metabolism ; }, abstract = {A high-resolution functional metagenomic analysis of a representative single sample of a Brazilian spontaneous cocoa bean fermentation process was carried out to gain insight into its bacterial community functioning. By reconstruction of microbial meta-pathways based on metagenomic data, the current knowledge about the metabolic capabilities of bacterial members involved in the cocoa bean fermentation ecosystem was extended. Functional meta-pathway analysis revealed the distribution of the metabolic pathways between the bacterial members involved. The metabolic capabilities of the lactic acid bacteria present were most associated with the heterolactic fermentation and citrate assimilation pathways. The role of Enterobacteriaceae in the conversion of substrates was shown through the use of the mixed-acid fermentation and methylglyoxal detoxification pathways. Furthermore, several other potential functional roles for Enterobacteriaceae were indicated, such as pectinolysis and citrate assimilation. Concerning acetic acid bacteria, metabolic pathways were partially reconstructed, in particular those related to responses toward stress, explaining their metabolic activities during cocoa bean fermentation processes. Further, the in-depth metagenomic analysis unveiled functionalities involved in bacterial competitiveness, such as the occurrence of CRISPRs and potential bacteriocin production. Finally, comparative analysis of the metagenomic data with bacterial genomes of cocoa bean fermentation isolates revealed the applicability of the selected strains as functional starter cultures.}, } @article {pmid25998521, year = {2015}, author = {Simmons, MP and Bachy, C and Sudek, S and van Baren, MJ and Sudek, L and Ares, M and Worden, AZ}, title = {Intron Invasions Trace Algal Speciation and Reveal Nearly Identical Arctic and Antarctic Micromonas Populations.}, journal = {Molecular biology and evolution}, volume = {32}, number = {9}, pages = {2219-2235}, pmid = {25998521}, issn = {1537-1719}, support = {R01 GM040478/GM/NIGMS NIH HHS/United States ; GM040478/GM/NIGMS NIH HHS/United States ; }, mesh = {Antarctic Regions ; Arctic Regions ; Base Sequence ; Chlorophyta/*genetics ; Genes, Plant ; Genetic Speciation ; Introns ; Inverted Repeat Sequences ; Molecular Sequence Data ; Phylogeography ; Phytoplankton/genetics ; RNA, Plant/genetics ; RNA, Ribosomal, 18S ; Sequence Analysis, RNA ; }, abstract = {Spliceosomal introns are a hallmark of eukaryotic genes that are hypothesized to play important roles in genome evolution but have poorly understood origins. Although most introns lack sequence homology to each other, new families of spliceosomal introns that are repeated hundreds of times in individual genomes have recently been discovered in a few organisms. The prevalence and conservation of these introner elements (IEs) or introner-like elements in other taxa, as well as their evolutionary relationships to regular spliceosomal introns, are still unknown. Here, we systematically investigate introns in the widespread marine green alga Micromonas and report new families of IEs, numerous intron presence-absence polymorphisms, and potential intron insertion hot-spots. The new families enabled identification of conserved IE secondary structure features and establishment of a novel general model for repetitive intron proliferation across genomes. Despite shared secondary structure, the IE families from each Micromonas lineage bear no obvious sequence similarity to those in the other lineages, suggesting that their appearance is intimately linked with the process of speciation. Two of the new IE families come from an Arctic culture (Micromonas Clade E2) isolated from a polar region where abundance of this alga is increasing due to climate induced changes. The same two families were detected in metagenomic data from Antarctica--a system where Micromonas has never before been reported. Strikingly high identity between the Arctic isolate and Antarctic coding sequences that flank the IEs suggests connectivity between populations in the two polar systems that we postulate occurs through deep-sea currents. Recovery of Clade E2 sequences in North Atlantic Deep Waters beneath the Gulf Stream supports this hypothesis. Our research illuminates the dynamic relationships between an unusual class of repetitive introns, genome evolution, speciation, and global distribution of this sentinel marine alga.}, } @article {pmid25992554, year = {2015}, author = {Lecomte, V and Kaakoush, NO and Maloney, CA and Raipuria, M and Huinao, KD and Mitchell, HM and Morris, MJ}, title = {Changes in gut microbiota in rats fed a high fat diet correlate with obesity-associated metabolic parameters.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0126931}, pmid = {25992554}, issn = {1932-6203}, support = {//Medical Research Council/United Kingdom ; }, mesh = {Animals ; Biodiversity ; Biomarkers ; Body Weight ; Diet ; *Diet, High-Fat ; *Energy Metabolism ; *Gastrointestinal Microbiome ; Glucose/metabolism ; Insulin/metabolism ; Male ; Metagenome ; Obesity/blood/*etiology/*metabolism ; Rats ; }, abstract = {The gut microbiota is emerging as a new factor in the development of obesity. Many studies have described changes in microbiota composition in response to obesity and high fat diet (HFD) at the phylum level. In this study we used 16s RNA high throughput sequencing on faecal samples from rats chronically fed HFD or control chow (n = 10 per group, 16 weeks) to investigate changes in gut microbiota composition at the species level. 53.17% dissimilarity between groups was observed at the species level. Lactobacillus intestinalis dominated the microbiota in rats under the chow diet. However this species was considerably less abundant in rats fed HFD (P<0.0001), this being compensated by an increase in abundance of propionate/acetate producing species. To further understand the influence of these species on the development of the obese phenotype, we correlated their abundance with metabolic parameters associated with obesity. Of the taxa contributing the most to dissimilarity between groups, 10 presented significant correlations with at least one of the tested parameters, three of them correlated positively with all metabolic parameters: Phascolarctobacterium, Proteus mirabilis and Veillonellaceae, all propionate/acetate producers. Lactobacillus intestinalis was the only species whose abundance was negatively correlated with change in body weight and fat mass. This species decreased drastically in response to HFD, favouring propionate/acetate producing bacterial species whose abundance was strongly correlated with adiposity and deterioration of metabolic factors. Our observations suggest that these species may play a key role in the development of obesity in response to a HFD.}, } @article {pmid25991682, year = {2015}, author = {David, LA and Weil, A and Ryan, ET and Calderwood, SB and Harris, JB and Chowdhury, F and Begum, Y and Qadri, F and LaRocque, RC and Turnbaugh, PJ}, title = {Gut microbial succession follows acute secretory diarrhea in humans.}, journal = {mBio}, volume = {6}, number = {3}, pages = {e00381-15}, pmid = {25991682}, issn = {2150-7511}, support = {T32 AI007061/AI/NIAID NIH HHS/United States ; P50 GM068763/GM/NIGMS NIH HHS/United States ; R01 AI03055/AI/NIAID NIH HHS/United States ; K08 AI123494/AI/NIAID NIH HHS/United States ; R01 AI106878/AI/NIAID NIH HHS/United States ; U01 AI106878/AI/NIAID NIH HHS/United States ; U01 AI058935/AI/NIAID NIH HHS/United States ; T32 AI070611976/AI/NIAID NIH HHS/United States ; R01 AI103055/AI/NIAID NIH HHS/United States ; R56 AI106878/AI/NIAID NIH HHS/United States ; R37 AI106878/AI/NIAID NIH HHS/United States ; }, mesh = {Cholera/*microbiology ; Diarrhea/*microbiology ; Enterotoxigenic Escherichia coli ; Escherichia coli Infections/*microbiology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenomics ; Vibrio cholerae/pathogenicity ; }, abstract = {UNLABELLED: Disability after childhood diarrhea is an important burden on global productivity. Recent studies suggest that gut bacterial communities influence how humans recover from infectious diarrhea, but we still lack extensive data and mechanistic hypotheses for how these bacterial communities respond to diarrheal disease and its treatment. Here, we report that after Vibrio cholerae infection, the human gut microbiota undergoes an orderly and reproducible succession that features transient reversals in relative levels of enteric Bacteroides and Prevotella. Elements of this succession may be a common feature in microbiota recovery from acute secretory diarrhea, as we observed similar successional dynamics after enterotoxigenic Escherichia coli (ETEC) infection. Our metagenomic analyses suggest that multiple mechanisms drive microbial succession after cholera, including bacterial dispersal properties, changing enteric oxygen and carbohydrate levels, and phage dynamics. Thus, gut microbiota recovery after cholera may be predictable at the level of community structure but is driven by a complex set of temporally varying ecological processes. Our findings suggest opportunities for diagnostics and therapies targeting the gut microbiota in humans recovering from infectious diarrhea.

IMPORTANCE: Disability after diarrhea is a major burden on public health in the developing world. Gut bacteria may affect this recovery, but it remains incompletely understood how resident microbes in the digestive tract respond to diarrheal illness. Here, we observed an orderly and reproducible succession of gut bacterial groups after cholera in humans. Genomic analyses associated the succession with bacterial dispersal in food, an altered microbial environment, and changing phage levels. Our findings suggest that it may one day be feasible to manage resident bacterial populations in the gut after infectious diarrhea.}, } @article {pmid25991679, year = {2015}, author = {He, S and Malfatti, SA and McFarland, JW and Anderson, FE and Pati, A and Huntemann, M and Tremblay, J and Glavina del Rio, T and Waldrop, MP and Windham-Myers, L and Tringe, SG}, title = {Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions.}, journal = {mBio}, volume = {6}, number = {3}, pages = {e00066-15}, pmid = {25991679}, issn = {2150-7511}, mesh = {Archaea/classification/genetics/metabolism ; Bacteria/classification/genetics/metabolism ; *Biota ; California ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Genes, rRNA ; Metabolic Networks and Pathways/*genetics ; *Metagenome ; Methane/*metabolism ; Molecular Sequence Data ; Phylogeography ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; *Wetlands ; }, abstract = {UNLABELLED: Wetland restoration on peat islands previously drained for agriculture has potential to reverse land subsidence and sequester atmospheric carbon dioxide as peat accretes. However, the emission of methane could potentially offset the greenhouse gas benefits of captured carbon. As microbial communities play a key role in governing wetland greenhouse gas fluxes, we are interested in how microbial community composition and functions are associated with wetland hydrology, biogeochemistry, and methane emission, which is critical to modeling the microbial component in wetland methane fluxes and to managing restoration projects for maximal carbon sequestration. Here, we couple sequence-based methods with biogeochemical and greenhouse gas measurements to interrogate microbial communities from a pilot-scale restored wetland in the Sacramento-San Joaquin Delta of California, revealing considerable spatial heterogeneity even within this relatively small site. A number of microbial populations and functions showed strong correlations with electron acceptor availability and methane production; some also showed a preference for association with plant roots. Marker gene phylogenies revealed a diversity of major methane-producing and -consuming populations and suggested novel diversity within methanotrophs. Methanogenic archaea were observed in all samples, as were nitrate-, sulfate-, and metal-reducing bacteria, indicating that no single terminal electron acceptor was preferred despite differences in energetic favorability and suggesting spatial microheterogeneity and microniches. Notably, methanogens were negatively correlated with nitrate-, sulfate-, and metal-reducing bacteria and were most abundant at sampling sites with high peat accretion and low electron acceptor availability, where methane production was highest.

IMPORTANCE: Wetlands are the largest nonanthropogenic source of atmospheric methane but also a key global carbon reservoir. Characterizing belowground microbial communities that mediate carbon cycling in wetlands is critical to accurately predicting their responses to changes in land management and climate. Here, we studied a restored wetland and revealed substantial spatial heterogeneity in biogeochemistry, methane production, and microbial communities, largely associated with the wetland hydraulic design. We observed patterns in microbial community composition and functions correlated with biogeochemistry and methane production, including diverse microorganisms involved in methane production and consumption. We found that methanogenesis gene abundance is inversely correlated with genes from pathways exploiting other electron acceptors, yet the ubiquitous presence of genes from all these pathways suggests that diverse electron acceptors contribute to the energetic balance of the ecosystem. These investigations represent an important step toward effective management of wetlands to reduce methane flux to the atmosphere and enhance belowground carbon storage.}, } @article {pmid25990300, year = {2015}, author = {Velichko, N and Chernyaeva, E and Averina, S and Gavrilova, O and Lapidus, A and Pinevich, A}, title = {Consortium of the 'bichlorophyllous' cyanobacterium Prochlorothrix hollandica and chemoheterotrophic partner bacteria: culture and metagenome-based description.}, journal = {Environmental microbiology reports}, volume = {7}, number = {4}, pages = {623-633}, doi = {10.1111/1758-2229.12298}, pmid = {25990300}, issn = {1758-2229}, mesh = {Bacteroidetes/*classification/genetics/growth & development/isolation & purification ; *Biota ; Cluster Analysis ; In Situ Hybridization, Fluorescence ; *Metagenome ; *Microbial Consortia ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; Phylogeny ; Prochlorothrix/genetics/*growth & development ; Proteobacteria/*classification/genetics/growth & development/isolation & purification ; Sequence Analysis, DNA ; }, abstract = {'Bacterial consortium' sensu lato applies to mutualism or syntrophy-based systems consisting of unrelated bacteria. Consortia of cyanobacteria have been preferentially studied on Anabaena epibioses; non-photosynthetic satellites of other filamentous or unicellular cyanobacteria were also considered although structure-functional data are few. At the same time, information about consortia of cyanobacteria which have light-harvesting antennae distinct from standard phycobilisome was missing. In this study, we characterized first, via a polyphasic approach, the cultivable consortium of Prochlorothrix hollandica CCAP 1490/1 (filamentous cyanobacterium which contains chlorophylls a, b/carotenoid/protein complex in the absence of phycobilisome) and non-photosynthetic heterotrophic bacteria. The strains of most abundant satellites were isolated and identified. Consortium metagenome reconstructed via 454-pyro and Illumina sequencing was shown to include, except for P. hollandica, several phylotypes of Proteobacteria and Bacteroidetes. The ratio of consortium members was essentially stable irrespective of culture age, and restored after artificially imposed imbalance. The consortium had a complex spatial arrangement as demonstrated by FISH and SEM images of the association, epibiosis, and biofilm type. Preliminary data of metagenome annotation agreed with the hypothesis that satellite bacteria contribute to P. hollandica protection from reactive oxygen species (ROS).}, } @article {pmid25988396, year = {2015}, author = {Albanese, D and Fontana, P and De Filippo, C and Cavalieri, D and Donati, C}, title = {MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {9743}, pmid = {25988396}, issn = {2045-2322}, mesh = {Algorithms ; Biodiversity ; Computational Biology/methods ; DNA Barcoding, Taxonomic/*methods ; Datasets as Topic ; Metagenomics/*methods ; Microbiota/genetics ; *Software ; }, abstract = {The introduction of high throughput sequencing technologies has triggered an increase of the number of studies in which the microbiota of environmental and human samples is characterized through the sequencing of selected marker genes. While experimental protocols have undergone a process of standardization that makes them accessible to a large community of scientist, standard and robust data analysis pipelines are still lacking. Here we introduce MICCA, a software pipeline for the processing of amplicon metagenomic datasets that efficiently combines quality filtering, clustering of Operational Taxonomic Units (OTUs), taxonomy assignment and phylogenetic tree inference. MICCA provides accurate results reaching a good compromise among modularity and usability. Moreover, we introduce a de-novo clustering algorithm specifically designed for the inference of Operational Taxonomic Units (OTUs). Tests on real and synthetic datasets shows that thanks to the optimized reads filtering process and to the new clustering algorithm, MICCA provides estimates of the number of OTUs and of other common ecological indices that are more accurate and robust than currently available pipelines. Analysis of public metagenomic datasets shows that the higher consistency of results improves our understanding of the structure of environmental and human associated microbial communities. MICCA is an open source project.}, } @article {pmid25985413, year = {2015}, author = {Li, Y and Guo, W and Han, S and Kong, F and Wang, C and Li, D and Zhang, H and Yang, M and Xu, H and Zeng, B and Zhao, J}, title = {The evolution of the gut microbiota in the giant and the red pandas.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {10185}, pmid = {25985413}, issn = {2045-2322}, mesh = {Animals ; Bacteria/classification/genetics ; *Biological Evolution ; *Carnivora ; *Gastrointestinal Microbiome ; Metagenome ; *Ursidae ; }, abstract = {The independent dietary shift from carnivore to herbivore with over 90% being bamboo in the giant and the red pandas is of great interests to biologists. Although previous studies have shown convergent evolution of the giant and the red pandas at both morphological and molecular level, the evolution of the gut microbiota in these pandas remains largely unknown. The goal of this study was to determine whether the gut microbiota of the pandas converged due to the same diet, or diverged. We characterized the fecal microbiota from these two species by pyrosequencing the 16S V1-V3 hypervariable regions using the 454 GS FLX Titanium platform. We also included fecal samples from Asian black bears, a species phylogenetically closer to the giant panda, in our analyses. By analyzing the microbiota from these 3 species and those from other carnivores reported previously, we found the gut microbiotas of the giant pandas are distinct from those of the red pandas and clustered closer to those of the black bears. Our data suggests the divergent evolution of the gut microbiota in the pandas.}, } @article {pmid25983555, year = {2015}, author = {Oulas, A and Pavloudi, C and Polymenakou, P and Pavlopoulos, GA and Papanikolaou, N and Kotoulas, G and Arvanitidis, C and Iliopoulos, I}, title = {Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies.}, journal = {Bioinformatics and biology insights}, volume = {9}, number = {}, pages = {75-88}, pmid = {25983555}, issn = {1177-9322}, abstract = {Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field and the establishment of "metagenomics", often defined as the analysis of DNA from microbial communities in environmental samples without prior need for culturing. Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies. We focus on the currently available bioinformatics techniques, tools, and methodologies for performing each individual step of a typical metagenomic dataset analysis. We also provide future trends in the field with respect to tools and technologies currently under development. Moreover, we discuss data management, distribution, and integration tools that are capable of performing comparative metagenomic analyses of multiple datasets using well-established databases, as well as commonly used annotation standards.}, } @article {pmid25981789, year = {2015}, author = {Rampelli, S and Schnorr, SL and Consolandi, C and Turroni, S and Severgnini, M and Peano, C and Brigidi, P and Crittenden, AN and Henry, AG and Candela, M}, title = {Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota.}, journal = {Current biology : CB}, volume = {25}, number = {13}, pages = {1682-1693}, doi = {10.1016/j.cub.2015.04.055}, pmid = {25981789}, issn = {1879-0445}, mesh = {Amino Acid Sequence ; Amino Acids/biosynthesis/metabolism ; Base Sequence ; *Biological Evolution ; *Diet, Paleolithic ; Drug Resistance, Microbial/genetics ; Ethnicity/*genetics ; Gastrointestinal Microbiome/*genetics/*physiology ; High-Throughput Nucleotide Sequencing ; Humans ; Italy ; Metagenome/*genetics ; Molecular Sequence Data ; Principal Component Analysis ; Statistics, Nonparametric ; Tanzania ; White People/*genetics ; }, abstract = {Through human microbiome sequencing, we can better understand how host evolutionary and ontogenetic history is reflected in the microbial function. However, there has been no information on the gut metagenome configuration in hunter-gatherer populations, posing a gap in our knowledge of gut microbiota (GM)-host mutualism arising from a lifestyle that describes over 90% of human evolutionary history. Here, we present the first metagenomic analysis of GM from Hadza hunter-gatherers of Tanzania, showing a unique enrichment in metabolic pathways that aligns with the dietary and environmental factors characteristic of their foraging lifestyle. We found that the Hadza GM is adapted for broad-spectrum carbohydrate metabolism, reflecting the complex polysaccharides in their diet. Furthermore, the Hadza GM is equipped for branched-chain amino acid degradation and aromatic amino acid biosynthesis. Resistome functionality demonstrates the existence of antibiotic resistance genes in a population with little antibiotic exposure, indicating the ubiquitous presence of environmentally derived resistances. Our results demonstrate how the functional specificity of the GM correlates with certain environment and lifestyle factors and how complexity from the exogenous environment can be balanced by endogenous homeostasis. The Hadza gut metagenome structure allows us to appreciate the co-adaptive functional role of the GM in complementing the human physiology, providing a better understanding of the versatility of human life and subsistence.}, } @article {pmid25974306, year = {2015}, author = {Bäckhed, F and Roswall, J and Peng, Y and Feng, Q and Jia, H and Kovatcheva-Datchary, P and Li, Y and Xia, Y and Xie, H and Zhong, H and Khan, MT and Zhang, J and Li, J and Xiao, L and Al-Aama, J and Zhang, D and Lee, YS and Kotowska, D and Colding, C and Tremaroli, V and Yin, Y and Bergman, S and Xu, X and Madsen, L and Kristiansen, K and Dahlgren, J and Wang, J}, title = {Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life.}, journal = {Cell host & microbe}, volume = {17}, number = {5}, pages = {690-703}, doi = {10.1016/j.chom.2015.04.004}, pmid = {25974306}, issn = {1934-6069}, mesh = {Adult ; Breast Feeding ; Delivery, Obstetric/methods ; Feces/microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Infant ; Infant, Newborn ; Metagenomics ; *Microbiota ; Molecular Sequence Data ; Sequence Analysis, DNA ; Sweden ; }, abstract = {The gut microbiota is central to human health, but its establishment in early life has not been quantitatively and functionally examined. Applying metagenomic analysis on fecal samples from a large cohort of Swedish infants and their mothers, we characterized the gut microbiome during the first year of life and assessed the impact of mode of delivery and feeding on its establishment. In contrast to vaginally delivered infants, the gut microbiota of infants delivered by C-section showed significantly less resemblance to their mothers. Nutrition had a major impact on early microbiota composition and function, with cessation of breast-feeding, rather than introduction of solid food, being required for maturation into an adult-like microbiota. Microbiota composition and ecological network had distinctive features at each sampled stage, in accordance with functional maturation of the microbiome. Our findings establish a framework for understanding the interplay between the gut microbiome and the human body in early life.}, } @article {pmid25974302, year = {2015}, author = {Hacquard, S and Garrido-Oter, R and González, A and Spaepen, S and Ackermann, G and Lebeis, S and McHardy, AC and Dangl, JL and Knight, R and Ley, R and Schulze-Lefert, P}, title = {Microbiota and Host Nutrition across Plant and Animal Kingdoms.}, journal = {Cell host & microbe}, volume = {17}, number = {5}, pages = {603-616}, doi = {10.1016/j.chom.2015.04.009}, pmid = {25974302}, issn = {1934-6069}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Adaptation, Biological ; Animals ; Gastrointestinal Tract/*microbiology ; Mammals ; *Metabolism ; Metagenome ; *Microbiota ; Plant Roots/*microbiology ; }, abstract = {Plants and animals each have evolved specialized organs dedicated to nutrient acquisition, and these harbor specific bacterial communities that extend the host's metabolic repertoire. Similar forces driving microbial community establishment in the gut and plant roots include diet/soil-type, host genotype, and immune system as well as microbe-microbe interactions. Here we show that there is no overlap of abundant bacterial taxa between the microbiotas of the mammalian gut and plant roots, whereas taxa overlap does exist between fish gut and plant root communities. A comparison of root and gut microbiota composition in multiple host species belonging to the same evolutionary lineage reveals host phylogenetic signals in both eukaryotic kingdoms. The reasons underlying striking differences in microbiota composition in independently evolved, yet functionally related, organs in plants and animals remain unclear but might include differences in start inoculum and niche-specific factors such as oxygen levels, temperature, pH, and organic carbon availability.}, } @article {pmid25974221, year = {2015}, author = {Zhao, M and Zhang, DL and Su, XQ and Duan, SM and Wan, JQ and Yuan, WX and Liu, BY and Ma, Y and Pan, YH}, title = {An Integrated Metagenomics/Metaproteomics Investigation of the Microbial Communities and Enzymes in Solid-state Fermentation of Pu-erh tea.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {10117}, pmid = {25974221}, issn = {2045-2322}, mesh = {Aspergillus/*genetics/metabolism ; Camellia sinensis/metabolism/*microbiology ; Catalase/metabolism ; Fermentation/physiology ; Metagenomics ; Microbial Consortia/genetics ; Peroxidases/metabolism ; Peroxiredoxins/metabolism ; Plant Leaves/metabolism/microbiology ; Proteobacteria/*genetics/metabolism ; Proteomics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Solid-Phase Synthesis Techniques/*methods ; Tea/*metabolism/microbiology ; }, abstract = {Microbial enzymes during solid-state fermentation (SSF), which play important roles in the food, chemical, pharmaceutical and environmental fields, remain relatively unknown. In this work, the microbial communities and enzymes in SSF of Pu-erh tea, a well-known traditional Chinese tea, were investigated by integrated metagenomics/metaproteomics approach. The dominant bacteria and fungi were identified as Proteobacteria (48.42%) and Aspergillus (94.98%), through pyrosequencing-based analyses of the bacterial 16S and fungal 18S rRNA genes, respectively. In total, 335 proteins with at least two unique peptides were identified and classified into 28 Biological Processes and 35 Molecular Function categories using a metaproteomics analysis. The integration of metagenomics and metaproteomics data demonstrated that Aspergillus was dominant fungus and major host of identified proteins (50.45%). Enzymes involved in the degradation of the plant cell wall were identified and associated with the soft-rotting of tea leaves. Peroxiredoxins, catalase and peroxidases were associated with the oxidation of catechins. In conclusion, this work greatly advances our understanding of the SSF of Pu-erh tea and provides a powerful tool for studying SSF mechanisms, especially in relation to the microbial communities present.}, } @article {pmid25971745, year = {2015}, author = {Gilbert, JA}, title = {Our unique microbial identity.}, journal = {Genome biology}, volume = {16}, number = {1}, pages = {97}, pmid = {25971745}, issn = {1474-760X}, mesh = {Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; *Genome, Bacterial ; Humans ; *Metagenome ; }, abstract = {A recent article examines the extent of individual variation in microbial identities and how this might determine disease susceptibility, therapeutic responses and recovery from clinical interventions.}, } @article {pmid25970451, year = {2015}, author = {DeWeerdt, S}, title = {Microbiome: Microbial mystery.}, journal = {Nature}, volume = {521}, number = {7551}, pages = {S10-1}, pmid = {25970451}, issn = {1476-4687}, mesh = {Adenoma/microbiology ; Animals ; Anti-Bacterial Agents/pharmacology ; Anti-Inflammatory Agents/metabolism/pharmacology ; Bacterial Toxins/genetics/isolation & purification ; Bacteroides fragilis/drug effects/isolation & purification/pathogenicity/physiology ; Butyrates/metabolism/pharmacology ; Case-Control Studies ; Cell Proliferation/drug effects ; Colorectal Neoplasms/*etiology/genetics/*microbiology/pathology ; Diet/adverse effects ; Disease Models, Animal ; Escherichia coli/drug effects/isolation & purification/pathogenicity/physiology ; Fusobacterium/drug effects/isolation & purification/physiology ; Germ-Free Life ; Healthy Volunteers ; Humans ; Inflammatory Bowel Diseases/microbiology/pathology ; Interleukin-17/adverse effects/immunology ; Metagenome/genetics/physiology ; Metalloendopeptidases/genetics/isolation & purification ; Mice ; Microbiota/genetics/*physiology ; Mutagens/pharmacology ; Probiotics/pharmacology/therapeutic use ; }, } @article {pmid25964341, year = {2015}, author = {Franzosa, EA and Huang, K and Meadow, JF and Gevers, D and Lemon, KP and Bohannan, BJ and Huttenhower, C}, title = {Identifying personal microbiomes using metagenomic codes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {22}, pages = {E2930-8}, pmid = {25964341}, issn = {1091-6490}, support = {R01 AI101018/AI/NIAID NIH HHS/United States ; U54HG004969/HG/NHGRI NIH HHS/United States ; HHSN272200900018C/AI/NIAID NIH HHS/United States ; P50 GM098911/GM/NIGMS NIH HHS/United States ; HHSN272200900018C//PHS HHS/United States ; R01 HG005969/HG/NHGRI NIH HHS/United States ; U54 HG004969/HG/NHGRI NIH HHS/United States ; R01HG005969/HG/NHGRI NIH HHS/United States ; P50GM098911/GM/NIGMS NIH HHS/United States ; }, mesh = {Confidentiality/standards/trends ; Genetic Markers/*genetics ; *Genetic Variation ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Models, Genetic ; Precision Medicine/*methods ; }, abstract = {Community composition within the human microbiome varies across individuals, but it remains unknown if this variation is sufficient to uniquely identify individuals within large populations or stable enough to identify them over time. We investigated this by developing a hitting set-based coding algorithm and applying it to the Human Microbiome Project population. Our approach defined body site-specific metagenomic codes: sets of microbial taxa or genes prioritized to uniquely and stably identify individuals. Codes capturing strain variation in clade-specific marker genes were able to distinguish among 100s of individuals at an initial sampling time point. In comparisons with follow-up samples collected 30-300 d later, ∼30% of individuals could still be uniquely pinpointed using metagenomic codes from a typical body site; coincidental (false positive) matches were rare. Codes based on the gut microbiome were exceptionally stable and pinpointed >80% of individuals. The failure of a code to match its owner at a later time point was largely explained by the loss of specific microbial strains (at current limits of detection) and was only weakly associated with the length of the sampling interval. In addition to highlighting patterns of temporal variation in the ecology of the human microbiome, this work demonstrates the feasibility of microbiome-based identifiability-a result with important ethical implications for microbiome study design. The datasets and code used in this work are available for download from huttenhower.sph.harvard.edu/idability.}, } @article {pmid25960327, year = {2015}, author = {Alfano, N and Courtiol, A and Vielgrader, H and Timms, P and Roca, AL and Greenwood, AD}, title = {Variation in koala microbiomes within and between individuals: effect of body region and captivity status.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {10189}, pmid = {25960327}, issn = {2045-2322}, support = {R01 GM092706/GM/NIGMS NIH HHS/United States ; R01GM092706/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; Eye/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome ; *Genetic Variation ; Male ; Microbiota/*genetics ; Mouth/microbiology ; *Organ Specificity ; Phascolarctidae/*microbiology ; Phylogeny ; Principal Component Analysis ; Rectum/microbiology ; }, abstract = {Metagenomic analysis of 16S ribosomal RNA has been used to profile microbial communities at high resolution, and to examine their association with host diet or diseases. We examined the oral and gut microbiome composition of two captive koalas to determine whether bacterial communities are unusual in this species, given that their diet consists almost exclusively of Eucalyptus leaves. Despite a highly specialized diet, koala oral and gut microbiomes were similar in composition to the microbiomes from the same body regions of other mammals. Rectal swabs contained all of the diversity present in faecal samples, along with additional taxa, suggesting that faecal bacterial communities may merely subsample the gut bacterial diversity. Furthermore, the faecal microbiomes of the captive koalas were similar to those reported for wild koalas, suggesting that captivity may not compromise koala microbial health. Since koalas frequently suffer from ocular diseases caused by Chlamydia infection, we also examined the eye microbiome composition of two captive koalas, establishing the healthy baseline for this body part. The eye microbial community was very diverse, similar to other mammalian ocular microbiomes but with an unusually high representation of bacteria from the family Phyllobacteriaceae.}, } @article {pmid25957694, year = {2015}, author = {Carugati, L and Corinaldesi, C and Dell'Anno, A and Danovaro, R}, title = {Metagenetic tools for the census of marine meiofaunal biodiversity: An overview.}, journal = {Marine genomics}, volume = {24 Pt 1}, number = {}, pages = {11-20}, doi = {10.1016/j.margen.2015.04.010}, pmid = {25957694}, issn = {1876-7478}, mesh = {Animals ; Aquatic Organisms/*genetics ; *Biodiversity ; Genome ; Invertebrates/*genetics ; Metagenomics/*methods ; }, abstract = {Marine organisms belonging to meiofauna (size range: 20-500 μm) are amongst the most abundant and highly diversified metazoans on Earth including 22 over 35 known animal Phyla and accounting for more than 2/3 of the abundance of metazoan organisms. In any marine system, meiofauna play a key role in the functioning of the food webs and sustain important ecological processes. Estimates of meiofaunal biodiversity have been so far almost exclusively based on morphological analyses, but the very small size of these organisms and, in some cases, the insufficient morphological distinctive features limit considerably the census of the biodiversity of this component. Molecular approaches recently applied also to small invertebrates (including meiofauna) can offer a new momentum for the census of meiofaunal biodiversity. Here, we provide an overview on the application of metagenetic approaches based on the use of next generation sequencing platforms to study meiofaunal biodiversity, with a special focus on marine nematodes. Our overview shows that, although such approaches can represent a useful tool for the census of meiofaunal biodiversity, there are still different shortcomings and pitfalls that prevent their extensive use without the support of the classical taxonomic identification. Future investigations are needed to address these problems and to provide a good match between the contrasting findings emerging from classical taxonomic and molecular/bioinformatic tools.}, } @article {pmid25957318, year = {2015}, author = {Crampton-Platt, A and Timmermans, MJ and Gimmel, ML and Kutty, SN and Cockerill, TD and Vun Khen, C and Vogler, AP}, title = {Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample.}, journal = {Molecular biology and evolution}, volume = {32}, number = {9}, pages = {2302-2316}, pmid = {25957318}, issn = {1537-1719}, mesh = {Animals ; Borneo ; Coleoptera/*genetics ; Contig Mapping ; Gene Frequency ; Genes, Insect ; Genetic Variation ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Metagenome ; Mitochondria/*genetics ; Phylogeny ; Rainforest ; Sequence Analysis, DNA ; }, abstract = {In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to accelerate this process if all specimens obtained through mass-trapping, many of which will be new species, could be incorporated routinely into phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial genomes are assembled from complex ecological mixtures through mitochondrial metagenomics, and demonstrate how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from approximately 500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of major lineages of Coleoptera. When all sequences were combined only minor topological changes were induced against this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, while the ecological sample expanded the tip-level representation of several lineages. Robust trees generated from ecological samples now enable an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic tree, constitute novel DNA "superbarcodes" for testing hypotheses regarding global patterns of diversity.}, } @article {pmid25956022, year = {2015}, author = {Staley, C and Gould, TJ and Wang, P and Phillips, J and Cotner, JB and Sadowsky, MJ}, title = {Evaluation of water sampling methodologies for amplicon-based characterization of bacterial community structure.}, journal = {Journal of microbiological methods}, volume = {114}, number = {}, pages = {43-50}, doi = {10.1016/j.mimet.2015.05.003}, pmid = {25956022}, issn = {1872-8359}, mesh = {Bacteria/*classification/*genetics ; Bacteriological Techniques/*methods ; *Biota ; Metagenomics/*methods ; Reproducibility of Results ; Rivers/*microbiology ; }, abstract = {Reduction in costs of next-generation sequencing technologies has allowed unprecedented characterization of bacterial communities from environmental samples including aquatic ecosystems. However, the extent to which extrinsic factors including sampling volume, sample replication, DNA extraction kits, and sequencing target affect the community structure inferred are poorly explored. Here, triplicate 1, 2, and 6L volume water samples from the Upper Mississippi River were processed to determine variation among replicates and sample volumes. Replicate variability significantly influenced differences in the community α-diversity (P=0.046), while volume significantly changed β-diversity (P=0.037). Differences in phylogenetic and taxonomic community structure differed both among triplicate samples and among the volumes filtered. Communities from 2L and 6L water samples showed similar clustering via discriminant analysis. To assess variation due to DNA extraction method, DNA was extracted from triplicate cell pellets from four sites along the Upper Mississippi River using the Epicentre Metagenomic DNA Isolation Kit for Water and MoBio PowerSoil kit. Operational taxonomic units representing ≤14% of sequence reads differed significantly among all sites and extraction kits used, although differences in diversity and community coverage were not significant (P≥0.057). Samples characterized using only the V6 region had significantly higher coverage and lower richness and α-diversity than those characterized using V4-V6 regions (P<0.001). Triplicate sampling of at least 2L of water provides robust representation of community variability, and these results indicate that DNA extraction kit and sequencing target displayed taxonomic biases that did not affect the overall biological conclusions drawn.}, } @article {pmid25954902, year = {2015}, author = {Kalmokoff, M and Franklin, J and Petronella, N and Green, J and Brooks, SP}, title = {Phylum level change in the cecal and fecal gut communities of rats fed diets containing different fermentable substrates supports a role for nitrogen as a factor contributing to community structure.}, journal = {Nutrients}, volume = {7}, number = {5}, pages = {3279-3299}, pmid = {25954902}, issn = {2072-6643}, mesh = {Ammonia/metabolism ; Animals ; Bacteria/genetics/*growth & development/metabolism ; Bacteroidetes/genetics/growth & development ; Cecum/metabolism/*microbiology ; Colon, Sigmoid/metabolism/*microbiology ; DNA, Bacterial/analysis ; *Diet ; Dietary Proteins/metabolism ; Feces/*microbiology ; Fermentation ; Firmicutes/genetics/growth & development ; Gastrointestinal Microbiome/*genetics ; Male ; Metagenome ; Nitrogen/*metabolism ; RNA, Ribosomal, 16S/genetics ; Rats ; }, abstract = {Fermentation differs between the proximal and distal gut but little is known regarding how the bacterial communities differ or how they are influenced by diet. In order to investigate this, we compared community diversity in the cecum and feces of rats by 16S rRNA gene content and DNA shot gun metagenomics after feeding purified diets containing different fermentable substrates. Gut community composition was dependent on the source of fermentable substrate included in the diet. Cecal communities were dominated by Firmicutes, and contained a higher abundance of Lachnospiraceae compared to feces. In feces, community structure was shifted by varying degrees depending on diet towards the Bacteroidetes, although this change was not always evident from 16S rRNA gene data. Multi-dimensional scaling analysis (PCoA) comparing cecal and fecal metagenomes grouped by location within the gut rather than by diet, suggesting that factors in addition to substrate were important for community change in the distal gut. Differentially abundant genes in each environment supported this shift away from the Firmicutes in the cecum (e.g., motility) towards the Bacteroidetes in feces (e.g., Bacteroidales transposons). We suggest that this phylum level change reflects a shift to ammonia as the primary source of nitrogen used to support continued microbial growth in the distal gut.}, } @article {pmid25953766, year = {2015}, author = {Behzad, H and Gojobori, T and Mineta, K}, title = {Challenges and opportunities of airborne metagenomics.}, journal = {Genome biology and evolution}, volume = {7}, number = {5}, pages = {1216-1226}, pmid = {25953766}, issn = {1759-6653}, mesh = {*Air Microbiology ; Bacteria/genetics/isolation & purification ; Biodiversity ; Fungi/genetics/isolation & purification ; Genes, rRNA ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods/*trends ; Sequence Analysis, DNA ; Viruses/isolation & purification ; }, abstract = {Recent metagenomic studies of environments, such as marine and soil, have significantly enhanced our understanding of the diverse microbial communities living in these habitats and their essential roles in sustaining vast ecosystems. The increase in the number of publications related to soil and marine metagenomics is in sharp contrast to those of air, yet airborne microbes are thought to have significant impacts on many aspects of our lives from their potential roles in atmospheric events such as cloud formation, precipitation, and atmospheric chemistry to their major impact on human health. In this review, we will discuss the current progress in airborne metagenomics, with a special focus on exploring the challenges and opportunities of undertaking such studies. The main challenges of conducting metagenomic studies of airborne microbes are as follows: 1) Low density of microorganisms in the air, 2) efficient retrieval of microorganisms from the air, 3) variability in airborne microbial community composition, 4) the lack of standardized protocols and methodologies, and 5) DNA sequencing and bioinformatics-related challenges. Overcoming these challenges could provide the groundwork for comprehensive analysis of airborne microbes and their potential impact on the atmosphere, global climate, and our health. Metagenomic studies offer a unique opportunity to examine viral and bacterial diversity in the air and monitor their spread locally or across the globe, including threats from pathogenic microorganisms. Airborne metagenomic studies could also lead to discoveries of novel genes and metabolic pathways relevant to meteorological and industrial applications, environmental bioremediation, and biogeochemical cycles.}, } @article {pmid25953741, year = {2015}, author = {Sangwan, N and Lambert, C and Sharma, A and Gupta, V and Khurana, P and Khurana, JP and Sockett, RE and Gilbert, JA and Lal, R}, title = {Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator-prey genotypes.}, journal = {Environmental microbiology reports}, volume = {7}, number = {6}, pages = {812-823}, doi = {10.1111/1758-2229.12297}, pmid = {25953741}, issn = {1758-2229}, mesh = {Adaptation, Biological/genetics ; Arsenic/*analysis/toxicity ; *Genotype ; Hot Springs/*chemistry/*microbiology ; *Metagenome ; *Metagenomics ; *Microbiota ; Phylogeny ; Stress, Physiological ; *Water Microbiology ; }, abstract = {Bdellovibrio bacteriovorus are small Deltaproteobacteria that invade, kill and assimilate their prey. Metagenomic assembly analysis of the microbial mats of an arsenic rich, hot spring was performed to describe the genotypes of the predator Bdellovibrio and the ecogenetically adapted taxa Enterobacter. The microbial mats were enriched with Bdellovibrio (1.3%) and several Gram-negative bacteria including Bordetella (16%), Enterobacter (6.8%), Burkholderia (4.8%), Acinetobacter (2.3%) and Yersinia (1%). A high-quality (47 contigs, 25X coverage; 3.5 Mbp) draft genome of Bdellovibrio (strain ArHS; Arsenic Hot Spring) was reassembled, which lacked the marker gene Bd0108 associated with the usual method of prey interaction and invasion for this genus, while maintaining genes coding for the hydrolytic enzymes necessary for prey assimilation. By filtering microbial mat samples (< 0.45 μm) to enrich for small predatory cell sizes, we observed Bdellovibrio-like cells attached side-on to E. coli through electron microscopy. Furthermore, a draft pan-genome of the dominant potential host taxon, Enterobacter cloacae ArHS (4.8 Mb), along with three of its viral genotypes (n = 3; 42 kb, 49 kb and 50 kb), was assembled. These data were further used to analyse the population level evolutionary dynamics (taxonomical and functional) of reconstructed genotypes.}, } @article {pmid25950956, year = {2015}, author = {Kurtz, ZD and Müller, CL and Miraldi, ER and Littman, DR and Blaser, MJ and Bonneau, RA}, title = {Sparse and compositionally robust inference of microbial ecological networks.}, journal = {PLoS computational biology}, volume = {11}, number = {5}, pages = {e1004226}, pmid = {25950956}, issn = {1553-7358}, support = {R01 DK103358-01/DK/NIDDK NIH HHS/United States ; R01 GM063270/GM/NIGMS NIH HHS/United States ; R01 GM63270/GM/NIGMS NIH HHS/United States ; R01 DK103358/DK/NIDDK NIH HHS/United States ; T32 AI007180/AI/NIAID NIH HHS/United States ; T32AI007180-30/AI/NIAID NIH HHS/United States ; R01 DK090989/DK/NIDDK NIH HHS/United States ; }, mesh = {Algorithms ; *Biota ; Computational Biology/methods ; Gastrointestinal Microbiome ; Humans ; Metagenomics/methods ; Microbiota/genetics/*physiology ; *Models, Biological ; RNA, Ribosomal, 16S/genetics ; }, abstract = {16S ribosomal RNA (rRNA) gene and other environmental sequencing techniques provide snapshots of microbial communities, revealing phylogeny and the abundances of microbial populations across diverse ecosystems. While changes in microbial community structure are demonstrably associated with certain environmental conditions (from metabolic and immunological health in mammals to ecological stability in soils and oceans), identification of underlying mechanisms requires new statistical tools, as these datasets present several technical challenges. First, the abundances of microbial operational taxonomic units (OTUs) from amplicon-based datasets are compositional. Counts are normalized to the total number of counts in the sample. Thus, microbial abundances are not independent, and traditional statistical metrics (e.g., correlation) for the detection of OTU-OTU relationships can lead to spurious results. Secondly, microbial sequencing-based studies typically measure hundreds of OTUs on only tens to hundreds of samples; thus, inference of OTU-OTU association networks is severely under-powered, and additional information (or assumptions) are required for accurate inference. Here, we present SPIEC-EASI (SParse InversE Covariance Estimation for Ecological Association Inference), a statistical method for the inference of microbial ecological networks from amplicon sequencing datasets that addresses both of these issues. SPIEC-EASI combines data transformations developed for compositional data analysis with a graphical model inference framework that assumes the underlying ecological association network is sparse. To reconstruct the network, SPIEC-EASI relies on algorithms for sparse neighborhood and inverse covariance selection. To provide a synthetic benchmark in the absence of an experimentally validated gold-standard network, SPIEC-EASI is accompanied by a set of computational tools to generate OTU count data from a set of diverse underlying network topologies. SPIEC-EASI outperforms state-of-the-art methods to recover edges and network properties on synthetic data under a variety of scenarios. SPIEC-EASI also reproducibly predicts previously unknown microbial associations using data from the American Gut project.}, } @article {pmid25948578, year = {2015}, author = {Jiménez, E and de Andrés, J and Manrique, M and Pareja-Tobes, P and Tobes, R and Martínez-Blanch, JF and Codoñer, FM and Ramón, D and Fernández, L and Rodríguez, JM}, title = {Metagenomic Analysis of Milk of Healthy and Mastitis-Suffering Women.}, journal = {Journal of human lactation : official journal of International Lactation Consultant Association}, volume = {31}, number = {3}, pages = {406-415}, doi = {10.1177/0890334415585078}, pmid = {25948578}, issn = {1552-5732}, mesh = {Case-Control Studies ; Female ; Humans ; Mastitis/*microbiology ; *Metagenome ; Microbiota/*genetics ; Milk, Human/*microbiology ; }, abstract = {BACKGROUND: Some studies have been conducted to assess the composition of the bacterial communities inhabiting human milk, but they did not evaluate the presence of other microorganisms, such as fungi, archaea, protozoa, or viruses.

OBJECTIVE: This study aimed to compare the metagenome of human milk samples provided by healthy and mastitis-suffering women.

METHODS: DNA was isolated from human milk samples collected from 10 healthy women and 10 women with symptoms of lactational mastitis. Shotgun libraries from total extracted DNA were constructed and the libraries were sequenced by 454 pyrosequencing.

RESULTS: The amount of human DNA sequences was ≥ 90% in all the samples. Among the bacterial sequences, the predominant phyla were Proteobacteria, Firmicutes, and Bacteroidetes. The healthy core microbiome included the genera Staphylococcus, Streptococcus, Bacteroides, Faecalibacterium, Ruminococcus, Lactobacillus, and Propionibacterium. At the species level, a high degree of inter-individual variability was observed among healthy women. In contrast, Staphylococcus aureus clearly dominated the microbiome in the samples from the women with acute mastitis whereas high increases in Staphylococcus epidermidis-related reads were observed in the milk of those suffering from subacute mastitis. Fungal and protozoa-related reads were identified in most of the samples, whereas Archaea reads were absent in samples from women with mastitis. Some viral-related sequence reads were also detected.

CONCLUSION: Human milk contains a complex microbial metagenome constituted by the genomes of bacteria, archaea, viruses, fungi, and protozoa. In mastitis cases, the milk microbiome reflects a loss of bacterial diversity and a high increase of the sequences related to the presumptive etiological agents.}, } @article {pmid25942317, year = {2015}, author = {Jiang, WX and Hu, YJ and Gao, L and He, ZY and Zhu, CL and Ma, R and Huang, ZW}, title = {The impact of various time intervals on the supragingival plaque dynamic core microbiome.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0124631}, pmid = {25942317}, issn = {1932-6203}, mesh = {Adult ; Biodiversity ; Cluster Analysis ; Computational Biology ; Dental Plaque/*microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Time Factors ; }, abstract = {OBJECTIVE: The aim of this study was to examine the influence of various time intervals on the composition of the supragingival plaque microbiome, especially the dynamic core microbiome, and to find a suitable observation interval for further studies on oral microbiota.

METHODS AND MATERIALS: Eight qualified volunteers whose respective age ranges from 25 to 28 years participated in the present study. The supragingival plaque was collected from the buccogingival surface of the maxillary first molar at eight time slots with different intervals (day 0, 1 day, 3 days, 1 week, 2 weeks, 3 weeks, 1 month, and 3 months). Bioinformatic analyses was performed based on 16S rDNA pyrosequencing (454 sequencing platform) targeting at the hypervariable V4-V5 region, in order to assess the diversity and variation of the supragingival plaque microbiome.

RESULTS: A total of 359,565 qualified reads for 64 samples were generated for subsequent analyses, which represents 8,452 operational taxonomic units identified at 3% dissimilarity. The dynamic core microbiome detected in the current study included five phyla, 12 genera and 13 species. At the genus level, the relative abundance of bacterial communities under the "1 day," "1 month," and "3 months" intervals was clustered into sub-category. At the species level, the number of overlapping species remained stable between the "1 month" and "3 months" intervals, whereas the number of dynamic core species became stable within only 1 week.

CONCLUSIONS: This study emphasized the impact of different time intervals (days, weeks and months) on the composition, commonality and diversity of the supragingival microbiome. The analyses found that for various types of studies, the time interval of a month is more suitable for observing the general composition of the supragingival microbiome, and that a week is better for observing the dynamic core microbiome.}, } @article {pmid25939040, year = {2015}, author = {Wang, W and Jovel, J and Halloran, B and Wine, E and Patterson, J and Ford, G and OʼKeefe, S and Meng, B and Song, D and Zhang, Y and Tian, Z and Wasilenko, ST and Rahbari, M and Reza, S and Mitchell, T and Jordan, T and Carpenter, E and Madsen, K and Fedorak, R and Dielemann, LA and Ka-Shu Wong, G and Mason, AL}, title = {Metagenomic analysis of microbiome in colon tissue from subjects with inflammatory bowel diseases reveals interplay of viruses and bacteria.}, journal = {Inflammatory bowel diseases}, volume = {21}, number = {6}, pages = {1419-1427}, pmid = {25939040}, issn = {1536-4844}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacteriophages ; Child ; Colon/*microbiology ; Colonoscopy ; Female ; Gastrointestinal Microbiome/*genetics ; Herpesviridae/genetics ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Male ; *Metagenomics ; Middle Aged ; RNA, Viral ; Retroviridae Proteins/genetics ; Young Adult ; }, abstract = {Inflammatory bowel diseases (IBD), Crohn's disease and ulcerative colitis, are poorly understood disorders affecting the intestinal tract. The current model for disease suggests that genetically susceptible patients develop intolerance to gut microflora, and chronic inflammation develops as a result of environmental insults. Although interest has mainly focused on studying genetic variants and gut bacterial flora, little is known about the potential of viral infection to contribute to disease. Accordingly, we conducted a metagenomic analysis to document the baseline virome in colonic biopsy samples from patients with IBD in order to assess the contribution of viral infection to IBD. Libraries were generated from colon RNA to create approximately 2 GB sequence data per library. Using a bioinformatic pipeline designed to detect viral sequences, more than 1000 viral reads were derived directly from tissue without any coculture or isolation procedure. Herein, we describe the complexity and abundance of viruses, bacteria/bacteriophage, and human endogenous retroviral sequences from 10 patients with IBD and 5 healthy subjects undergoing surveillance colonoscopy. Differences in gut microflora and the abundance of mammalian viruses and human endogenous retroviruses were readily detected in the metagenomic analyses. Specifically, patients with herpesviridae sequences in their colon demonstrated increased expression of human endogenous viral sequences and differences in the diversity of their microbiome. This study provides a promising metagenomic approach to describe the colonic microbiome that can be used to better understand virus-host and phage-bacteria interactions in IBD.}, } @article {pmid25938477, year = {2015}, author = {Houlden, A and Hayes, KS and Bancroft, AJ and Worthington, JJ and Wang, P and Grencis, RK and Roberts, IS}, title = {Chronic Trichuris muris Infection in C57BL/6 Mice Causes Significant Changes in Host Microbiota and Metabolome: Effects Reversed by Pathogen Clearance.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0125945}, pmid = {25938477}, issn = {1932-6203}, support = {/WT_/Wellcome Trust/United Kingdom ; 100290/WT_/Wellcome Trust/United Kingdom ; WT 100290MA/WT_/Wellcome Trust/United Kingdom ; G1100076/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Anthelmintics/administration & dosage/pharmacokinetics ; Bacteria/classification/genetics ; Biodiversity ; Chronic Disease ; Disease Models, Animal ; *Host-Parasite Interactions ; *Metabolome ; Metabolomics/methods ; Metagenome ; Mice ; Mice, Inbred C57BL ; *Microbiota ; Time Factors ; Trichuriasis/drug therapy/*metabolism/*microbiology/*parasitology ; *Trichuris/drug effects/immunology ; }, abstract = {Trichuris species are a globally important and prevalent group of intestinal helminth parasites, in which Trichuris muris (mouse whipworm) is an ideal model for this disease. This paper describes the first ever highly controlled and comprehensive investigation into the effects of T. muris infection on the faecal microbiota of mice and the effects on the microbiota following successful clearance of the infection. Communities were profiled using DGGE, 454 pyrosequencing, and metabolomics. Changes in microbial composition occurred between 14 and 28 days post infection, resulting in significant changes in α and β- diversity. This impact was dominated by a reduction in the diversity and abundance of Bacteroidetes, specifically Prevotella and Parabacteroides. Metabolomic analysis of stool samples of infected mice at day 41 showed significant differences to uninfected controls with a significant increase in the levels of a number of essential amino acids and a reduction in breakdown of dietary plant derived carbohydrates. The significant reduction in weight gain by infected mice probably reflects these metabolic changes and the incomplete digestion of dietary polysaccharides. Following clearance of infection the intestinal microbiota underwent additional changes gradually transitioning by day 91 towards a microbiota of an uninfected animal. These data indicate that the changes in microbiota as a consequence of infection were transitory requiring the presence of the pathogen for maintenance. Interestingly this was not observed for all of the key immune cell populations associated with chronic T. muris infection. This reflects the highly regulated chronic response and potential lasting immunological consequences of dysbiosis in the microbiota. Thus infection of T. muris causes a significant and substantial impact on intestinal microbiota and digestive function of mice with affects in long term immune regulation.}, } @article {pmid25938416, year = {2015}, author = {Lu, X and Zhang, XX and Wang, Z and Huang, K and Wang, Y and Liang, W and Tan, Y and Liu, B and Tang, J}, title = {Bacterial pathogens and community composition in advanced sewage treatment systems revealed by metagenomics analysis based on high-throughput sequencing.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0125549}, pmid = {25938416}, issn = {1932-6203}, mesh = {Bacteria/*classification/*genetics ; Biodiversity ; *High-Throughput Nucleotide Sequencing ; *Metagenomics ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Virulence Factors/genetics ; }, abstract = {This study used 454 pyrosequencing, Illumina high-throughput sequencing and metagenomic analysis to investigate bacterial pathogens and their potential virulence in a sewage treatment plant (STP) applying both conventional and advanced treatment processes. Pyrosequencing and Illumina sequencing consistently demonstrated that Arcobacter genus occupied over 43.42% of total abundance of potential pathogens in the STP. At species level, potential pathogens Arcobacter butzleri, Aeromonas hydrophila and Klebsiella pneumonia dominated in raw sewage, which was also confirmed by quantitative real time PCR. Illumina sequencing also revealed prevalence of various types of pathogenicity islands and virulence proteins in the STP. Most of the potential pathogens and virulence factors were eliminated in the STP, and the removal efficiency mainly depended on oxidation ditch. Compared with sand filtration, magnetic resin seemed to have higher removals in most of the potential pathogens and virulence factors. However, presence of the residual A. butzleri in the final effluent still deserves more concerns. The findings indicate that sewage acts as an important source of environmental pathogens, but STPs can effectively control their spread in the environment. Joint use of the high-throughput sequencing technologies is considered a reliable method for deep and comprehensive overview of environmental bacterial virulence.}, } @article {pmid25935300, year = {2015}, author = {Tan, J and Zuniga, C and Zengler, K}, title = {Unraveling interactions in microbial communities - from co-cultures to microbiomes.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {53}, number = {5}, pages = {295-305}, pmid = {25935300}, issn = {1976-3794}, mesh = {Bacteria/*genetics/metabolism ; Biodiversity ; Ecosystem ; Humans ; Metagenome ; *Microbial Consortia ; Microbiota/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microorganisms do not exist in isolation in the environment. Instead, they form complex communities among themselves as well as with their hosts. Different forms of interactions not only shape the composition of these communities but also define how these communities are established and maintained. The kinds of interaction a bacterium can employ are largely encoded in its genome. This allows us to deploy a genomescale modeling approach to understand, and ultimately predict, the complex and intertwined relationships in which microorganisms engage. So far, most studies on microbial communities have been focused on synthetic co-cultures and simple communities. However, recent advances in molecular and computational biology now enable bottom up methods to be deployed for complex microbial communities from the environment to provide insight into the intricate and dynamic interactions in which microorganisms are engaged. These methods will be applicable for a wide range of microbial communities involved in industrial processes, as well as understanding, preserving and reconditioning natural microbial communities present in soil, water, and the human microbiome.}, } @article {pmid25933115, year = {2015}, author = {Wintermans, B and Brandt, B and Vandenbroucke-Grauls, C and Budding, A}, title = {TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0123851}, pmid = {25933115}, issn = {1932-6203}, mesh = {Feces/microbiology ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Klebsiella/genetics ; Metagenomics/*methods ; Microbiota/genetics ; Phenotype ; *Software ; }, abstract = {Next-generation sequencing is not yet commonly used in clinical laboratories because of a lack of simple and intuitive tools. We developed a software tool (TreeSeq) with a quaternary tree search structure for the analysis of sequence data. This permits rapid searches for sequences of interest in large datasets. We used TreeSeq to screen a gut microbiota metagenomic dataset and a whole genome sequencing (WGS) dataset of a strain of Klebsiella pneumoniae for antibiotic resistance genes and compared the results with BLAST and phenotypic resistance determination. TreeSeq was more than thirty times faster than BLAST and accurately detected resistance gene sequences in complex metagenomic data and resistance genes corresponding with the phenotypic resistance pattern of the Klebsiella strain. Resistance genes found by TreeSeq were visualized as a gene coverage heat map, aiding in the interpretation of results. TreeSeq brings analysis of metagenomic and WGS data within reach of clinical diagnostics.}, } @article {pmid25930203, year = {2015}, author = {Sengupta, A and Dick, WA}, title = {Bacterial Community Diversity in Soil Under two Tillage Practices as Determined by Pyrosequencing.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {853-859}, pmid = {25930203}, issn = {1432-184X}, mesh = {Agriculture/*methods ; Bacteria/*classification ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Ohio ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The ability of soil to provide ecosystem services is dependent on microbial diversity, with 80-90 % of the processes in soil being mediated by microbes. There still exists a knowledge gap in the types of microorganisms present in soil and how soil management affects them. However, identification of microorganisms is severely limited by classical culturing techniques that have been traditionally used in laboratories. Metagenomic approaches are increasingly becoming common, with current high-throughput sequencing approaches allowing for more in-depth analysis. We conducted a preliminary analysis of bacterial diversity in soils from the longest continuously maintained no-till (NT) plots in the world (52 years) and in adjacent plow-till (PT) plots in Ohio, USA managed similarly except for tillage. Bacterial diversity was determined using a culture-independent approach of high-throughput pyrosequencing of the 16S rRNA gene. Proteobacteria and Acidobacteria were predominant in both samples but the NT soil had a higher number of reads, bacterial richness, and five unique phyla. Four unique phyla were observed in PT and 99 % of the community had relative abundance of <1 %. Plowing and secondary tillage tend to homogenize the soil and reduces the unique (i.e., diverse) microenvironments where microbial populations can reside. We conclude that tillage leads to fewer dominant species being present in soil and that these species contribute to a higher percentage of the total community.}, } @article {pmid25926546, year = {2015}, author = {Ames, SK and Gardner, SN and Marti, JM and Slezak, TR and Gokhale, MB and Allen, JE}, title = {Using populations of human and microbial genomes for organism detection in metagenomes.}, journal = {Genome research}, volume = {25}, number = {7}, pages = {1056-1067}, pmid = {25926546}, issn = {1549-5469}, mesh = {Computational Biology/methods ; Databases, Nucleic Acid ; *Genome, Microbial ; Humans ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; ROC Curve ; }, abstract = {Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-free human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. Left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected.}, } @article {pmid25921438, year = {2015}, author = {Hedlund, BP and Dodsworth, JA and Staley, JT}, title = {The changing landscape of microbial biodiversity exploration and its implications for systematics.}, journal = {Systematic and applied microbiology}, volume = {38}, number = {4}, pages = {231-236}, doi = {10.1016/j.syapm.2015.03.003}, pmid = {25921438}, issn = {1618-0984}, mesh = {*Archaea/classification/genetics ; *Bacteria/classification/genetics ; *Metagenomics ; *Single-Cell Analysis ; }, abstract = {A vast diversity of Bacteria and Archaea exists in nature that has evaded axenic culture. Advancements in single-cell genomics, metagenomics, and molecular microbial ecology approaches provide ever-improving insight into the biology of this so-called "microbial dark matter"; however, due to the International Code of Nomenclature of Prokaryotes, yet-uncultivated microorganisms are not accommodated in formal taxonomy regardless of the quantity or quality of data. Meanwhile, efforts to calibrate the existing taxonomy with phylogenetic anchors and genomic data are increasingly robust. The current climate provides an exciting opportunity to leverage rapidly expanding single-cell genomics and metagenomics datasets to improve the taxonomy of Bacteria and Archaea. However, this opportunity must be weighted carefully in light of the strengths and limitations of these approaches. We propose to expand the definition of the Candidatus taxonomy to include taxa, from the phylum level to the species level, that are described genomically, particularly when genomic work is coupled with advanced molecular ecology approaches to probe metabolic functions in situ. This system would preserve the rigor and value of traditional microbial systematics while enabling growth of a provisional taxonomic structure to facilitate communication about "dark" lineages on the tree of life.}, } @article {pmid25918444, year = {2015}, author = {van Schaik, W}, title = {The human gut resistome.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1670}, pages = {20140087}, pmid = {25918444}, issn = {1471-2970}, mesh = {Disease Reservoirs/*microbiology ; Drug Resistance, Microbial/*genetics ; Gastrointestinal Microbiome/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Humans ; Metagenomics/*methods/trends ; }, abstract = {In recent decades, the emergence and spread of antibiotic resistance among bacterial pathogens has become a major threat to public health. Bacteria can acquire antibiotic resistance genes by the mobilization and transfer of resistance genes from a donor strain. The human gut contains a densely populated microbial ecosystem, termed the gut microbiota, which offers ample opportunities for the horizontal transfer of genetic material, including antibiotic resistance genes. Recent technological advances allow microbiota-wide studies into the diversity and dynamics of the antibiotic resistance genes that are harboured by the gut microbiota ('the gut resistome'). Genes conferring resistance to antibiotics are ubiquitously present among the gut microbiota of humans and most resistance genes are harboured by strictly anaerobic gut commensals. The horizontal transfer of genetic material, including antibiotic resistance genes, through conjugation and transduction is a frequent event in the gut microbiota, but mostly involves non-pathogenic gut commensals as these dominate the microbiota of healthy individuals. Resistance gene transfer from commensals to gut-dwelling opportunistic pathogens appears to be a relatively rare event but may contribute to the emergence of multi-drug resistant strains, as is illustrated by the vancomycin resistance determinants that are shared by anaerobic gut commensals and the nosocomial pathogen Enterococcus faecium.}, } @article {pmid25918393, year = {2015}, author = {Tveit, AT and Urich, T and Frenzel, P and Svenning, MM}, title = {Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {19}, pages = {E2507-16}, pmid = {25918393}, issn = {1091-6490}, mesh = {Archaea/genetics/*metabolism ; Arctic Regions ; Carbon/chemistry ; Carbon Dioxide/chemistry ; Chromatography, Gas ; Chromatography, High Pressure Liquid ; Ecosystem ; Environment ; Fermentation ; Gene Expression Profiling ; *Global Warming ; Hydrogen/chemistry ; Hydrolysis ; Linear Models ; Methane/*biosynthesis ; Microbiota ; Polysaccharides/chemistry ; RNA, Ribosomal/metabolism ; Soil/chemistry ; *Soil Microbiology ; Sphagnopsida ; Temperature ; }, abstract = {Arctic permafrost soils store large amounts of soil organic carbon (SOC) that could be released into the atmosphere as methane (CH4) in a future warmer climate. How warming affects the complex microbial network decomposing SOC is not understood. We studied CH4 production of Arctic peat soil microbiota in anoxic microcosms over a temperature gradient from 1 to 30 °C, combining metatranscriptomic, metagenomic, and targeted metabolic profiling. The CH4 production rate at 4 °C was 25% of that at 25 °C and increased rapidly with temperature, driven by fast adaptations of microbial community structure, metabolic network of SOC decomposition, and trophic interactions. Below 7 °C, syntrophic propionate oxidation was the rate-limiting step for CH4 production; above this threshold temperature, polysaccharide hydrolysis became rate limiting. This change was associated with a shift within the functional guild for syntrophic propionate oxidation, with Firmicutes being replaced by Bacteroidetes. Correspondingly, there was a shift from the formate- and H2-using Methanobacteriales to Methanomicrobiales and from the acetotrophic Methanosarcinaceae to Methanosaetaceae. Methanogenesis from methylamines, probably stemming from degradation of bacterial cells, became more important with increasing temperature and corresponded with an increased relative abundance of predatory protists of the phylum Cercozoa. We concluded that Arctic peat microbiota responds rapidly to increased temperatures by modulating metabolic and trophic interactions so that CH4 is always highly produced: The microbial community adapts through taxonomic shifts, and cascade effects of substrate availability cause replacement of functional guilds and functional changes within taxa.}, } @article {pmid25917564, year = {2015}, author = {Lu, CY and Ni, YH}, title = {Gut microbiota and the development of pediatric diseases.}, journal = {Journal of gastroenterology}, volume = {50}, number = {7}, pages = {720-726}, pmid = {25917564}, issn = {1435-5922}, mesh = {Child ; Dysbiosis/*etiology/microbiology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology ; Humans ; }, abstract = {The human gut harbors a huge number of microbes, which are collectively named "microbiota." The dynamic composition of the human gut microbiota is determined by multiple factors, including mode of delivery, diet, environment, and antibiotics. A healthy gut microbiota is helpful to the host in many aspects, including providing nutrients, protection from pathogens, and maturation of immune responses. Dysbiosis plays important roles in various diseases in infancy and later life: necrotizing enterocolitis, inflammatory bowel disease, obesity, and atopic diseases are some examples. Studies of functional metagenomics by newly developed techniques, such as next-generation sequencing, will not only elucidate the molecular mechanisms underlying gut microbiota-host interactions but will also provide new possibilities for disease prevention and treatment.}, } @article {pmid25917520, year = {2015}, author = {Hajela, N and Ramakrishna, BS and Nair, GB and Abraham, P and Gopalan, S and Ganguly, NK}, title = {Gut microbiome, gut function, and probiotics: Implications for health.}, journal = {Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology}, volume = {34}, number = {2}, pages = {93-107}, pmid = {25917520}, issn = {0975-0711}, mesh = {Digestive System Diseases/etiology/prevention & control/therapy ; Endocrine System Diseases/etiology/prevention & control/therapy ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/physiology ; Humans ; Immune System Diseases/etiology/prevention & control/therapy ; Metabolic Diseases/etiology/prevention & control/therapy ; Metagenomics ; Nervous System Diseases/etiology/prevention & control/therapy ; Probiotics/*therapeutic use ; }, abstract = {New insights from a rapidly developing field of research have ushered in a new era of understanding of the complexity of host-microbe interactions within the human body. The paradigm shift from culturing to metagenomics has provided an insight into the complex diversity of the microbial species that we harbor, revealing the fact that we are in fact more microbes than human cells. The largest consortium of these microbes resides in the gut and is called the gut microbiota. This new science has expanded the ability to document shifts in microbial populations to an unparalleled degree. It is now understood that signals from the microbiota provide trophic, nutritional, metabolic, and protective effects for the development and maintenance of the host digestive, immune, and neuroendocrine system. Evidence linking changes in the gut microbiota to gastrointestinal and extraintestinal disorders like irritable bowel syndrome, inflammatory bowel disease, obesity, diabetes, and celiac disease have begun to emerge recently. Probiotics act through diverse mechanisms positively affecting the composition and/or function of the commensal microbiota and alter host immunological responses. Well-controlled intervention trials, systematic reviews, and meta-analysis provide convincing evidence for the benefit of probiotics in prevention and treatment of gastrointestinal as well as extraintestinal disorders.}, } @article {pmid25915636, year = {2015}, author = {Franzosa, EA and Hsu, T and Sirota-Madi, A and Shafquat, A and Abu-Ali, G and Morgan, XC and Huttenhower, C}, title = {Sequencing and beyond: integrating molecular 'omics' for microbial community profiling.}, journal = {Nature reviews. Microbiology}, volume = {13}, number = {6}, pages = {360-372}, pmid = {25915636}, issn = {1740-1534}, support = {R01 HG005969/HG/NHGRI NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; R01HG005969/HG/NHGRI NIH HHS/United States ; U54DK102557/DK/NIDDK NIH HHS/United States ; }, mesh = {Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; Metabolomics/*methods ; Metagenomics/*methods ; Microbiota/genetics/*physiology ; Proteomics/*methods ; Systems Biology/*methods ; }, abstract = {High-throughput DNA sequencing has proven invaluable for investigating diverse environmental and host-associated microbial communities. In this Review, we discuss emerging strategies for microbial community analysis that complement and expand traditional metagenomic profiling. These include novel DNA sequencing strategies for identifying strain-level microbial variation and community temporal dynamics; measuring multiple 'omic' data types that better capture community functional activity, such as transcriptomics, proteomics and metabolomics; and combining multiple forms of omic data in an integrated framework. We highlight studies in which the 'multi-omics' approach has led to improved mechanistic models of microbial community structure and function.}, } @article {pmid25914678, year = {2015}, author = {Chow, CE and Winget, DM and White, RA and Hallam, SJ and Suttle, CA}, title = {Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {265}, pmid = {25914678}, issn = {1664-302X}, abstract = {Viral diversity and virus-host interactions in oxygen-starved regions of the ocean, also known as oxygen minimum zones (OMZs), remain relatively unexplored. Microbial community metabolism in OMZs alters nutrient and energy flow through marine food webs, resulting in biological nitrogen loss and greenhouse gas production. Thus, viruses infecting OMZ microbes have the potential to modulate community metabolism with resulting feedback on ecosystem function. Here, we describe viral communities inhabiting oxic surface (10 m) and oxygen-starved basin (200 m) waters of Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia using viral metagenomics and complete viral fosmid sequencing on samples collected between April 2007 and April 2010. Of 6459 open reading frames (ORFs) predicted across all 34 viral fosmids, 77.6% (n = 5010) had no homology to reference viral genomes. These fosmids recruited a higher proportion of viral metagenomic sequences from Saanich Inlet than from nearby northeastern subarctic Pacific Ocean (Line P) waters, indicating differences in the viral communities between coastal and open ocean locations. While functional annotations of fosmid ORFs were limited, recruitment to NCBI's non-redundant "nr" database and publicly available single-cell genomes identified putative viruses infecting marine thaumarchaeal and SUP05 proteobacteria to provide potential host linkages with relevance to coupled biogeochemical cycling processes in OMZ waters. Taken together, these results highlight the power of coupled analyses of multiple sequence data types, such as viral metagenomic and fosmid sequence data with prokaryotic single cell genomes, to chart viral diversity, elucidate genomic and ecological contexts for previously unclassifiable viral sequences, and identify novel host interactions in natural and engineered ecosystems.}, } @article {pmid25914197, year = {2015}, author = {Xiong, W and Abraham, PE and Li, Z and Pan, C and Hettich, RL}, title = {Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota.}, journal = {Proteomics}, volume = {15}, number = {20}, pages = {3424-3438}, pmid = {25914197}, issn = {1615-9861}, support = {R01 GM103600/GM/NIGMS NIH HHS/United States ; 1R01-GM-103600/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Animals ; Gastrointestinal Microbiome/*genetics ; Genomics ; Humans ; Infant, Newborn ; Metagenome/*genetics ; Mice ; Microbiota/genetics ; *Proteomics ; RNA, Messenger/genetics ; }, abstract = {The human gastrointestinal tract is a complex, dynamic ecosystem that consists of a carefully tuned balance of human host and microbiota membership. The microbiome is not merely a collection of opportunistic parasites, but rather provides important functions to the host that are absolutely critical to many aspects of health, including nutrient transformation and absorption, drug metabolism, pathogen defense, and immune system development. Microbial metaproteomics provides the ability to characterize the human gut microbiota functions and metabolic activities at a remarkably deep level, revealing information about microbiome development and stability as well as their interactions with their human host. Generally, microbial and human proteins can be extracted and then measured by high performance MS-based proteomics technology. Here, we review the field of human gut microbiome metaproteomics, with a focus on the experimental and informatics considerations involved in characterizing systems ranging from low-complexity model gut microbiota in gnotobiotic mice, to the emerging gut microbiome in the GI tract of newborn human infants, and finally to an established gut microbiota in human adults.}, } @article {pmid25913376, year = {2015}, author = {Heberling, C and Dhurjati, P}, title = {Novel systems modeling methodology in comparative microbial metabolomics: identifying key enzymes and metabolites implicated in autism spectrum disorders.}, journal = {International journal of molecular sciences}, volume = {16}, number = {4}, pages = {8949-8967}, pmid = {25913376}, issn = {1422-0067}, mesh = {Autism Spectrum Disorder/*microbiology ; Bacterial Proteins/*genetics ; Computational Biology ; Data Mining ; Gastrointestinal Microbiome ; Glutamate Synthase/genetics ; Humans ; Ketone Oxidoreductases/genetics ; Metabolomics ; Transaminases/genetics ; }, abstract = {Autism spectrum disorders are a group of mental illnesses highly correlated with gastrointestinal dysfunction. Recent studies have shown that there may be one or more microbial "fingerprints" in terms of the composition characterizing individuals with autism, which could be used for diagnostic purposes. This paper proposes a computational approach whereby metagenomes characteristic of "healthy" and autistic individuals are artificially constructed via genomic information, analyzed for the enzymes coded within, and then these enzymes are compared in detail. This is a text mining application. A custom-designed online application was built and used for the comparative metabolomics study and made publically available. Several of the enzyme-catalyzing reactions involved with the amino acid glutamate were curiously missing from the "autism" microbiome and were coded within almost every organism included in the "control" microbiome. Interestingly, there exists a leading hypothesis regarding autism and glutamate involving a neurological excitation/inhibition imbalance; but the association with this study is unclear. The results included data on the transsulfuration and transmethylation pathways, involved with oxidative stress, also of importance to autism. The results from this study are in alignment with leading hypotheses in the field, which is impressive, considering the purely in silico nature of this study. The present study provides new insight into the complex metabolic interactions underlying autism, and this novel methodology has potential to be useful for developing new hypotheses. However, limitations include sparse genome data availability and conflicting literature experimental data. We believe our software tool and methodology has potential for having great utility as data become more available, comprehensive and reliable.}, } @article {pmid25913208, year = {2015}, author = {Charlop-Powers, Z and Brady, SF}, title = {phylogeo: an R package for geographic analysis and visualization of microbiome data.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {17}, pages = {2909-2911}, pmid = {25913208}, issn = {1367-4811}, support = {F32 AI110029/AI/NIAID NIH HHS/United States ; U01 GM110714/GM/NIGMS NIH HHS/United States ; AI110029/AI/NIAID NIH HHS/United States ; GM077516/GM/NIGMS NIH HHS/United States ; }, mesh = {*Computer Graphics ; Data Interpretation, Statistical ; Humans ; *Metagenome ; Microbiota/*genetics ; *Phylogeny ; *Programming Languages ; Sequence Analysis, DNA/*methods ; *Software ; Web Browser ; }, abstract = {MOTIVATION: We have created an R package named phylogeo that provides a set of geographic utilities for sequencing-based microbial ecology studies. Although the geographic location of samples is an important aspect of environmental microbiology, none of the major software packages used in processing microbiome data include utilities that allow users to map and explore the spatial dimension of their data. phylogeo solves this problem by providing a set of plotting and mapping functions that can be used to visualize the geographic distribution of samples, to look at the relatedness of microbiomes using ecological distance, and to map the geographic distribution of particular sequences. By extending the popular phyloseq package and using the same data structures and command formats, phylogeo allows users to easily map and explore the geographic dimensions of their data from the R programming language.

phylogeo is documented and freely available http://zachcp.github.io/phylogeo

CONTACT: : zcharlop@rockefeller.edu.}, } @article {pmid25912934, year = {2015}, author = {Wei, ZG and Zhang, SW}, title = {MtHc: a motif-based hierarchical method for clustering massive 16S rRNA sequences into OTUs.}, journal = {Molecular bioSystems}, volume = {11}, number = {7}, pages = {1907-1913}, doi = {10.1039/c5mb00089k}, pmid = {25912934}, issn = {1742-2051}, mesh = {Algorithms ; Cluster Analysis ; Gastrointestinal Microbiome/*genetics ; Humans ; Molecular Typing/*methods ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA ; }, abstract = {The recent sequencing revolution driven by high-throughput technologies has led to rapid accumulation of 16S rRNA sequences for microbial communities. Clustering short sequences into operational taxonomic units (OTUs) is an initial crucial process in analyzing metagenomic data. Although many methods have been proposed for OTU inferences, a major challenge is the balance between inference accuracy and computational efficiency. To address these challenges, we present a novel motif-based hierarchical method (namely MtHc) for clustering massive 16S rRNA sequences into OTUs with high clustering accuracy and low memory usage. Suppose all the 16S rRNA sequences can be used to construct a complete weighted network, where sequences are viewed as nodes, each pair of sequences is connected by an imaginary edge, and the distance of a pair of sequences represents the weight of the edge. MtHc consists of three main phrases. First, heuristically search the motif that is defined as n-node sub-graph (in the present study, n = 3, 4, 5), in which the distance between any two nodes is less than a threshold. Second, use the motif as a seed to form candidate clusters by computing the distances of other sequences with the motif. Finally, hierarchically merge the candidate clusters to generate the OTUs by only calculating the distances of motifs between two clusters. Compared with the existing methods on several simulated and real-life metagenomic datasets, we demonstrate that MtHc has higher clustering performance, less memory usage and robustness for setting parameters, and that it is more effective to handle the large-scale metagenomic datasets. The MtHC software can be freely download from for academic users.}, } @article {pmid25911946, year = {2015}, author = {Urbieta, MS and Donati, ER and Chan, KG and Shahar, S and Sin, LL and Goh, KM}, title = {Thermophiles in the genomic era: Biodiversity, science, and applications.}, journal = {Biotechnology advances}, volume = {33}, number = {6 Pt 1}, pages = {633-647}, doi = {10.1016/j.biotechadv.2015.04.007}, pmid = {25911946}, issn = {1873-1899}, mesh = {*Archaea/chemistry/enzymology ; Archaeal Proteins ; *Bacteria/chemistry/enzymology ; Bacterial Proteins ; *Biodegradation, Environmental ; *Biofuels ; Enzymes ; *Hot Temperature ; *Industrial Microbiology ; Metagenome ; Sulfolobus solfataricus ; }, abstract = {Thermophiles and hyperthermophiles are present in various regions of the Earth, including volcanic environments, hot springs, mud pots, fumaroles, geysers, coastal thermal springs, and even deep-sea hydrothermal vents. They are also found in man-made environments, such as heated compost facilities, reactors, and spray dryers. Thermophiles, hyperthermophiles, and their bioproducts facilitate various industrial, agricultural, and medicinal applications and offer potential solutions to environmental damages and the demand for biofuels. Intensified efforts to sequence the entire genome of hyperthermophiles and thermophiles are increasing rapidly, as evidenced by the fact that over 120 complete genome sequences of the hyperthermophiles Aquificae, Thermotogae, Crenarchaeota, and Euryarchaeota are now available. In this review, we summarise the major current applications of thermophiles and thermozymes. In addition, emphasis is placed on recent progress in understanding the biodiversity, genomes, transcriptomes, metagenomes, and single-cell sequencing of thermophiles in the genomic era.}, } @article {pmid25908654, year = {2015}, author = {Tkacz, A and Poole, P}, title = {Role of root microbiota in plant productivity.}, journal = {Journal of experimental botany}, volume = {66}, number = {8}, pages = {2167-2175}, pmid = {25908654}, issn = {1460-2431}, mesh = {Metagenomics ; *Microbiota ; Mycorrhizae/*physiology ; *Plant Development ; Plant Root Nodulation ; Plant Roots/*microbiology ; }, abstract = {The growing human population requires increasing amounts of food, but modern agriculture has limited possibilities for increasing yields. New crop varieties may be bred to have increased yields and be more resistant to environmental stress and pests. However, they still require fertilization to supplement essential nutrients that are normally limited in the soil. Soil microorganisms present an opportunity to reduce the requirement for inorganic fertilization in agriculture. Microorganisms, due to their enormous genetic pool, are also a potential source of biochemical reactions that recycle essential nutrients for plant growth. Microbes that associate with plants can be considered to be part of the plant's pan-genome. Therefore, it is essential for us to understand microbial community structure and their 'metagenome' and how it is influenced by different soil types and crop varieties. In the future we may be able to modify and better utilize the soil microbiota potential for promoting plant growth.}, } @article {pmid25907678, year = {2015}, author = {Lax, S and Gilbert, JA}, title = {Hospital-associated microbiota and implications for nosocomial infections.}, journal = {Trends in molecular medicine}, volume = {21}, number = {7}, pages = {427-432}, doi = {10.1016/j.molmed.2015.03.005}, pmid = {25907678}, issn = {1471-499X}, mesh = {Cross Infection/epidemiology ; Environmental Microbiology ; Hospitals/*statistics & numerical data ; Humans ; Microbiota/*physiology ; }, abstract = {The rise of high-throughput sequencing technologies and culture-independent microbial surveys has the potential to revolutionize our understanding of how microbes colonize, move about, and evolve in hospital environments. Genome analysis of individual organisms, characterization of population dynamics, and microbial community ecology are facilitating the identification of novel pathogens, the tracking of disease outbreaks, and the study of the evolution of antibiotic resistance. Here we review the recent applications of these methods to microbial ecology studies in hospitals and discuss their potential to influence hospital management policy and practice and to reduce nosocomial infections and the spread of antibiotic resistance.}, } @article {pmid25906115, year = {2015}, author = {Jiang, W and Liang, P and Wang, B and Fang, J and Lang, J and Tian, G and Jiang, J and Zhu, TF}, title = {Optimized DNA extraction and metagenomic sequencing of airborne microbial communities.}, journal = {Nature protocols}, volume = {10}, number = {5}, pages = {768-779}, pmid = {25906115}, issn = {1750-2799}, mesh = {*Air Microbiology ; Biochemistry/instrumentation/*methods ; China ; DNA/*isolation & purification ; Environmental Monitoring/instrumentation/*methods ; Equipment Design ; Metagenome ; Microbial Consortia/*genetics ; Particulate Matter ; Quality Control ; Sequence Analysis, DNA ; Workflow ; }, abstract = {Metagenomic sequencing has been widely used for the study of microbial communities from various environments such as soil, ocean, sediment and fresh water. Nonetheless, metagenomic sequencing of microbial communities in the air remains technically challenging, partly owing to the limited mass of collectable atmospheric particulate matter and the low biological content it contains. Here we present an optimized protocol for extracting up to tens of nanograms of airborne microbial genomic DNA from collected particulate matter. With an improved sequencing library preparation protocol, this quantity is sufficient for downstream applications, such as metagenomic sequencing for sampling various genes from the airborne microbial community. The described protocol takes ∼12 h of bench time over 2-3 d, and it can be performed with standard molecular biology equipment in the laboratory. A modified version of this protocol may also be used for genomic DNA extraction from other environmental samples of limited mass or low biological content.}, } @article {pmid25900454, year = {2015}, author = {Lopes, LD and de Souza Lima, AO and Taketani, RG and Darias, P and da Silva, LR and Romagnoli, EM and Louvandini, H and Abdalla, AL and Mendes, R}, title = {Exploring the sheep rumen microbiome for carbohydrate-active enzymes.}, journal = {Antonie van Leeuwenhoek}, volume = {108}, number = {1}, pages = {15-30}, doi = {10.1007/s10482-015-0459-6}, pmid = {25900454}, issn = {1572-9699}, mesh = {Animals ; Bacteria/*classification/*enzymology ; *Carbohydrate Metabolism ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Glycoside Hydrolases/genetics/*metabolism ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; *Sheep ; }, abstract = {The rumen is a complex ecosystem enriched for microorganisms able to degrade biomass during the animal's digestion process. The recovery of new enzymes from naturally evolved biomass-degrading microbial communities is a promising strategy to overcome the inefficient enzymatic plant destruction in industrial production of biofuels. In this context, this study aimed to describe the bacterial composition and functions in the sheep rumen microbiome, focusing on carbohydrate-active enzymes (CAE). Here, we used phylogenetic profiling analysis (inventory of 16S rRNA genes) combined with metagenomics to access the rumen microbiome of four sheep and explore its potential to identify fibrolytic enzymes. The bacterial community was dominated by Bacteroidetes and Firmicutes, followed by Proteobacteria. As observed for other ruminants, Prevotella was the dominant genus in the microbiome, comprising more than 30 % of the total bacterial community. Multivariate analysis of the phylogenetic profiling data and chemical parameters showed a positive correlation between the abundance of Prevotellaceae (Bacteroidetes phylum) and organic matter degradability. A negative correlation was observed between Succinivibrionaceae (Proteobacteria phylum) and methane production. An average of 2 % of the shotgun metagenomic reads was assigned to putative CAE when considering nine protein databases. In addition, assembled contigs allowed recognition of 67 putative partial CAE (NCBI-Refseq) representing 12 glycosyl hydrolase families (Pfam database). Overall, we identified a total of 28 lignocellulases, 22 amylases and 9 other putative CAE, showing the sheep rumen microbiome as a promising source of new fibrolytic enzymes.}, } @article {pmid25900137, year = {2015}, author = {Wang, J and Moore, NE and Murray, ZL and McInnes, K and White, DJ and Tompkins, DM and Hall, RJ}, title = {Discovery of novel virus sequences in an isolated and threatened bat species, the New Zealand lesser short-tailed bat (Mystacina tuberculata).}, journal = {The Journal of general virology}, volume = {96}, number = {8}, pages = {2442-2452}, pmid = {25900137}, issn = {1465-2099}, mesh = {Animals ; Chiroptera/*virology ; Endangered Species ; Genome, Viral ; Metagenomics ; Molecular Sequence Data ; New Zealand ; Phylogeny ; Viral Proteins/genetics ; Viruses/classification/genetics/*isolation & purification ; }, abstract = {Bats harbour a diverse array of viruses, including significant human pathogens. Extensive metagenomic studies of material from bats, in particular guano, have revealed a large number of novel or divergent viral taxa that were previously unknown. New Zealand has only two extant indigenous terrestrial mammals, which are both bats, Mystacina tuberculata (the lesser short-tailed bat) and Chalinolobus tuberculatus (the long-tailed bat). Until the human introduction of exotic mammals, these species had been isolated from all other terrestrial mammals for over 1 million years (potentially over 16 million years for M. tuberculata). Four bat guano samples were collected from M. tuberculata roosts on the isolated offshore island of Whenua hou (Codfish Island) in New Zealand. Metagenomic analysis revealed that this species still hosts a plethora of divergent viruses. Whilst the majority of viruses detected were likely to be of dietary origin, some putative vertebrate virus sequences were identified. Papillomavirus, polyomavirus, calicivirus and hepevirus were found in the metagenomic data and subsequently confirmed using independent PCR assays and sequencing. The new hepevirus and calicivirus sequences may represent new genera within these viral families. Our findings may provide an insight into the origins of viral families, given their detection in an isolated host species.}, } @article {pmid25898829, year = {2015}, author = {Sharma, A and Sangwan, N and Negi, V and Kohli, P and Khurana, JP and Rao, DL and Lal, R}, title = {Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {313}, pmid = {25898829}, issn = {1471-2164}, mesh = {Base Sequence ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genotype ; Hexachlorocyclohexane/chemistry/*metabolism ; Integrons/genetics ; Metagenomics ; Phylogeny ; Pseudomonas/classification/*genetics/isolation & purification ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA ; Soil Microbiology ; Water Microbiology ; Water Pollutants, Chemical/chemistry/metabolism ; }, abstract = {BACKGROUND: Phylogenetic heterogeneity across Pseudomonas genus is complemented by its diverse genome architecture enriched by accessory genetic elements (plasmids, transposons, and integrons) conferring resistance across this genus. Here, we sequenced a stress tolerant genotype i.e. Pseudomonas sp. strain RL isolated from a hexachlorocyclohexane (HCH) contaminated pond (45 mg of total HCH g(-1) sediment) and further compared its gene repertoire with 17 reference ecotypes belonging to P. stutzeri, P. mendocina, P. aeruginosa, P. psychrotolerans and P. denitrificans, representing metabolically diverse ecosystems (i.e. marine, clinical, and soil/sludge). Metagenomic data from HCH contaminated pond sediment and similar HCH contaminated sites were further used to analyze the pan-genome dynamics of Pseudomonas genotypes enriched across increasing HCH gradient.

RESULTS: Although strain RL demonstrated clear species demarcation (ANI ≤ 80.03%) from the rest of its phylogenetic relatives, it was found to be closest to P. stutzeri clade which was further complemented functionally. Comparative functional analysis elucidated strain specific enrichment of metabolic pathways like α-linoleic acid degradation and carbazole degradation in Pseudomonas sp. strain RL and P. stutzeri XLDN-R, respectively. Composition based methods (%codon bias and %G + C difference) further highlighted the significance of horizontal gene transfer (HGT) in evolution of nitrogen metabolism, two-component system (TCS) and methionine metabolism across the Pseudomonas genomes used in this study. An intact mobile class-I integron (3,552 bp) with a captured gene cassette encoding for dihydrofolate reductase (dhfra1) was detected in strain RL, distinctly demarcated from other integron harboring species (i.e. P. aeruginosa, P. stutzeri, and P. putida). Mobility of this integron was confirmed by its association with Tnp21-like transposon (95% identity) suggesting stress specific mobilization across HCH contaminated sites. Metagenomics data from pond sediment and recently surveyed HCH adulterated soils revealed the in situ enrichment of integron associated transposase gene (TnpA6100) across increasing HCH contamination (0.7 to 450 mg HCH g(-1) of soil).

CONCLUSIONS: Unlocking the potential of comparative genomics supplemented with metagenomics, we have attempted to resolve the environment and strain specific demarcations across 18 Pseudomonas gene complements. Pan-genome analyses of these strains indicate at astoundingly diverse metabolic strategies and provide genetic basis for the cosmopolitan existence of this taxon.}, } @article {pmid25898122, year = {2015}, author = {Niu, Q and Li, P and Hao, S and Zhang, Y and Kim, SW and Li, H and Ma, X and Gao, S and He, L and Wu, W and Huang, X and Hua, J and Zhou, B and Huang, R}, title = {Dynamic distribution of the gut microbiota and the relationship with apparent crude fiber digestibility and growth stages in pigs.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {9938}, pmid = {25898122}, issn = {2045-2322}, mesh = {*Animal Feed ; Animals ; Bacteria ; Biodiversity ; *Dietary Fiber ; *Digestion ; *Gastrointestinal Microbiome ; *Growth and Development ; Metagenome ; Swine ; }, abstract = {The gut microbiota plays an important role in nutrient digestibility in animals. To examine changes in the pig gut microbiota across growth stages and its effects on nutrient digestion, the gut microbiota population in pigs at 28 days (before weaning), and 60, 90, and 150 days of age was assessed by 16S rDNA gene sequencing. The apparent digestibility of crude fiber (CF), neutral detergent fiber (NDF), acid detergent fiber (ADF), crude protein (CP) and ether extract (EE) was also assessed in these pigs. A total of 19,875 operational taxonomic units (OTUs) were identified from all samples. Both bacterial abundance and diversity increased with age. A total of 22 phyla and 249 genera were identified from all fecal samples; Firmicutes and Bacteroidetes were the most dominant phyla in all samples. With increasing age, the proportion of TM7 and Tenericutes increased, whereas the proportion of Lentisphaerae and Synergistetes decreased. The abundance of 36 genera varied with age, and the apparent digestibility of CF increased with age. Three phyla, Proteobacteria, Tenericutes and TM7, and 11 genera, including Anaeroplasma, Campylobacter, and Clostridium, were correlated with apparent CF digestibility.}, } @article {pmid25896518, year = {2015}, author = {Zhu, A and Sunagawa, S and Mende, DR and Bork, P}, title = {Inter-individual differences in the gene content of human gut bacterial species.}, journal = {Genome biology}, volume = {16}, number = {1}, pages = {82}, pmid = {25896518}, issn = {1474-760X}, support = {268985/ERC_/European Research Council/International ; }, mesh = {Chromosome Mapping ; Databases, Genetic ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Gene Deletion ; Genetic Loci ; Genetic Variation ; Genome Size ; *Genome, Bacterial ; Humans ; *Metagenome ; Phylogeny ; Polysaccharides/metabolism ; Selection, Genetic ; }, abstract = {BACKGROUND: Gene content differences in human gut microbes can lead to inter-individual phenotypic variations such as digestive capacity. It is unclear whether gene content variation is caused by differences in microbial species composition or by the presence of different strains of the same species; the extent of gene content variation in the latter is unknown. Unlike pan-genome studies of cultivable strains, the use of metagenomic data can provide an unbiased view of structural variation of gut bacterial strains by measuring them in their natural habitats, the gut of each individual in this case, representing native boundaries between gut bacterial populations. We analyzed publicly available metagenomic data from fecal samples to characterize inter-individual variation in gut bacterial species.

RESULTS: A comparison of 11 abundant gut bacterial species showed that the gene content of strains from the same species differed, on average, by 13% between individuals. This number is based on gene deletions only and represents a lower limit, yet the variation is already in a similar range as observed between completely sequenced strains of cultivable species. We show that accessory genes that differ considerably between individuals can encode important functions, such as polysaccharide utilization and capsular polysaccharide synthesis loci.

CONCLUSION: Metagenomics can yield insights into gene content variation of strains in complex communities, which cannot be predicted by phylogenetic marker genes alone. The large degree of inter-individual variability in gene content implies that strain resolution must be considered in order to fully assess the functional potential of an individual's human gut microbiome.}, } @article {pmid25895091, year = {2015}, author = {Krustok, I and Truu, J and Odlare, M and Truu, M and Ligi, T and Tiirik, K and Nehrenheim, E}, title = {Effect of lake water on algal biomass and microbial community structure in municipal wastewater-based lab-scale photobioreactors.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {15}, pages = {6537-6549}, doi = {10.1007/s00253-015-6580-7}, pmid = {25895091}, issn = {1432-0614}, mesh = {Bacteria/classification/genetics/*growth & development ; Biomass ; *Biota ; Cluster Analysis ; Lakes/*microbiology ; Metagenome ; Microalgae/classification/genetics/*growth & development ; Molecular Sequence Data ; Photobioreactors/*microbiology ; Sequence Analysis, DNA ; Wastewater/*microbiology ; Water Pollutants, Chemical/metabolism ; }, abstract = {Photobioreactors are a novel environmental technology that can produce biofuels with the simultaneous removal of nutrients and pollutants from wastewaters. The aim of this study was to evaluate the effect of lake water inoculation on the production of algal biomass and phylogenetic and functional structure of the algal and bacterial communities in municipal wastewater-treating lab-scale photobioreactors. Inoculating the reactors with lake water had a significant benefit to the overall algal biomass growth and nutrient reduction in the reactors with wastewater and lake water (ratio 70/30 v/v). The metagenome-based survey showed that the most abundant algal phylum in these reactors was Chlorophyta with Scenedesmus being the most prominent genus. The most abundant bacterial phyla were Proteobacteria and Bacteroidetes with most dominant families being Sphingobacteriaceae, Cytophagaceae, Flavobacteriaceae, Comamonadaceae, Planctomycetaceae, Nocardiaceae and Nostocaceae. These photobioreactors were also effective in reducing the overall amount of pathogens in wastewater compared to reactors with wastewater/tap water mixture. Functional analysis of the photobioreactor metagenomes revealed an increase in relative abundance genes related to photosynthesis, synthesis of vitamins important for auxotrophic algae and decrease in virulence and nitrogen metabolism subsystems in lake water reactors. The results of the study indicate that adding lake water to the wastewater-based photobioreactor leads to an altered bacterial community phylogenetic and functional structure that could be linked to higher algal biomass production, as well as to enhanced nutrient and pathogen reduction in these reactors.}, } @article {pmid25888405, year = {2015}, author = {Mysara, M and Leys, N and Raes, J and Monsieurs, P}, title = {NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads.}, journal = {BMC bioinformatics}, volume = {16}, number = {1}, pages = {88}, pmid = {25888405}, issn = {1471-2105}, mesh = {*Algorithms ; Bacteria/classification/genetics ; Cluster Analysis ; Metagenomics/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: The popularity of new sequencing technologies has led to an explosion of possible applications, including new approaches in biodiversity studies. However each of these sequencing technologies suffers from sequencing errors originating from different factors. For 16S rRNA metagenomics studies, the 454 pyrosequencing technology is one of the most frequently used platforms, but sequencing errors still lead to important data analysis issues (e.g. in clustering in taxonomic units and biodiversity estimation). Moreover, retaining a higher portion of the sequencing data by preserving as much of the read length as possible while maintaining the error rate within an acceptable range, will have important consequences at the level of taxonomic precision.

RESULTS: The new error correction algorithm proposed in this work - NoDe (Noise Detector) - is trained to identify those positions in 454 sequencing reads that are likely to have an error, and subsequently clusters those error-prone reads with correct reads resulting in error-free representative read. A benchmarking study with other denoising algorithms shows that NoDe can detect up to 75% more errors in a large scale mock community dataset, and this with a low computational cost compared to the second best algorithm considered in this study. The positive effect of NoDe in 16S rRNA studies was confirmed by the beneficial effect on the precision of the clustering of pyrosequencing reads in operational taxonomic units.

CONCLUSIONS: NoDe was shown to be a computational efficient denoising algorithm for pyrosequencing reads, producing the lowest error rates in an extensive benchmarking study with other denoising algorithms.}, } @article {pmid25888310, year = {2015}, author = {Yasir, M and Azhar, EI and Khan, I and Bibi, F and Baabdullah, R and Al-Zahrani, IA and Al-Ghamdi, AK}, title = {Composition of soil microbiome along elevation gradients in southwestern highlands of Saudi Arabia.}, journal = {BMC microbiology}, volume = {15}, number = {}, pages = {65}, pmid = {25888310}, issn = {1471-2180}, mesh = {*Altitude ; Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Metagenome ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saudi Arabia ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {BACKGROUND: Saudi Arabia is mostly barren except the southwestern highlands that are susceptible to environmental changes, a hotspot for biodiversity, but poorly studied for microbial diversity and composition. In this study, 454-pyrosequencing of 16S rRNA gene hypervariable region V6 was used to analyze soil bacterial community along elevation gradients of the southwestern highlands.

RESULTS: In general, lower percentage of total soil organic matter (SOM) and nitrogen were detected in the analyzed soil samples. Total 33 different phyla were identified across the samples, including dominant phyla Proteobacteria, Actinobacteria and Acidobacteria. Representative OTUs were grouped into 329 and 508 different taxa at family and genus level taxonomic classification, respectively. The identified OTUs unique to each sample were very low irrespective of the altitude. Jackknifed principal coordinates analysis (PCoA) revealed, overall differences in the bacterial community were more related to the quantity of specific OTUs than to their diversity among the studied samples.

CONCLUSIONS: Bacterial diversity and soil physicochemical properties did not show consistent changes along the elevation gradients. The large number of OTUs shared between the studied samples suggest the presence of a core soil bacterial community in the southwestern highlands of Saudi Arabia.}, } @article {pmid25888298, year = {2015}, author = {Caputo, A and Dubourg, G and Croce, O and Gupta, S and Robert, C and Papazian, L and Rolain, JM and Raoult, D}, title = {Whole-genome assembly of Akkermansia muciniphila sequenced directly from human stool.}, journal = {Biology direct}, volume = {10}, number = {}, pages = {5}, doi = {10.1186/s13062-015-0041-1}, pmid = {25888298}, issn = {1745-6150}, mesh = {Anti-Bacterial Agents/chemistry ; Base Sequence ; Chromosome Mapping ; Cluster Analysis ; DNA, Bacterial/genetics ; Enterococcus/genetics ; Feces/microbiology ; *Genome, Bacterial ; Humans ; Intestines/microbiology ; Male ; Metagenome ; Metagenomics ; Microbiota/genetics ; Middle Aged ; Verrucomicrobia/*genetics ; }, abstract = {BACKGROUND: Alterations in gut microbiota composition under antibiotic pressure have been widely studied, revealing a restricted diversity of gut flora, including colonization by organisms such as Enterococci, while their impact on bacterial load is variable. High-level colonization by Akkermansia muciniphila, ranging from 39% to 84% of the total bacterial population, has been recently reported in two patients being treated with broad-spectrum antibiotics, although attempts to cultivate this microorganism have been unsuccessful.

RESULTS: Here, we propose an original approach of genome sequencing for Akkermansia muciniphila directly from the stool sample collected from one of these patients. We performed and assembly using metagenomic data obtained from the stool sample. We used a mapping method consisting of aligning metagenomic sequencing reads against the reference genome of the Akkermansia muciniphila Muc(T) strain, and a De novo assembly to support this mapping method. We obtained draft genome of the Akkermansia muciniphila strain Urmite with only 56 gaps. The absence of particular metabolic requirement as possible explanation of our inability to culture this microorganism, suggests that the bacterium was dead before the inoculation of the stool sample. Additional antibiotic resistance genes were found following comparison with the reference genome, providing some clues pertaining to its survival and colonization in the gut of a patient treated with broad-spectrum antimicrobial agents. However, no gene coding for imipenem resistance was detected, although this antibiotic was a part of the patient's antibiotic regimen.

CONCLUSIONS: This work highlights the potential of metagenomics to facilitate the assembly of genomes directly from human stool.}, } @article {pmid25888008, year = {2015}, author = {Voigt, AY and Costea, PI and Kultima, JR and Li, SS and Zeller, G and Sunagawa, S and Bork, P}, title = {Temporal and technical variability of human gut metagenomes.}, journal = {Genome biology}, volume = {16}, number = {1}, pages = {73}, pmid = {25888008}, issn = {1474-760X}, support = {268985/ERC_/European Research Council/International ; }, mesh = {Adult ; Cluster Analysis ; DNA, Bacterial/genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/metabolism/*microbiology ; *Genome, Human ; Humans ; Male ; Metagenome/*genetics ; Metagenomics/methods ; *Time Factors ; }, abstract = {BACKGROUND: Metagenomics has become a prominent approach for exploring the role of the gut microbiota in human health. However, the temporal variability of the healthy gut microbiome has not yet been studied in depth using metagenomics and little is known about the effects of different sampling and preservation approaches. We performed metagenomic analysis on fecal samples from seven subjects collected over a period of up to two years to investigate temporal variability and assess preservation-induced variation, specifically, fresh frozen compared to RNALater. We also monitored short-term disturbances caused by antibiotic treatment and bowel cleansing in one subject.

RESULTS: We find that the human gut microbiome is temporally stable and highly personalized at both taxonomic and functional levels. Over multiple time points, samples from the same subject clustered together, even in the context of a large dataset of 888 European and American fecal metagenomes. One exception was observed in an antibiotic intervention case where, more than one year after the treatment, samples did not resemble the pre-treatment state. Clustering was not affected by the preservation method. No species differed significantly in abundance, and only 0.36% of gene families were differentially abundant between preservation methods.

CONCLUSIONS: Technical variability is small compared to the temporal variability of an unperturbed gut microbiome, which in turn is much smaller than the observed between-subject variability. Thus, short-term preservation of fecal samples in RNALater is an appropriate and cost-effective alternative to freezing of fecal samples for metagenomic studies.}, } @article {pmid25887946, year = {2015}, author = {Gupta, VK and Chaudhari, NM and Iskepalli, S and Dutta, C}, title = {Divergences in gene repertoire among the reference Prevotella genomes derived from distinct body sites of human.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {153}, pmid = {25887946}, issn = {1471-2164}, mesh = {Gastrointestinal Tract/microbiology ; *Genome, Bacterial ; Humans ; Metagenome ; Microbiota/*genetics ; Mouth/microbiology ; *Phylogeny ; Prevotella/*genetics ; Skin/microbiology ; Tissue Distribution ; Urogenital System/microbiology ; }, abstract = {BACKGROUND: The community composition of the human microbiome is known to vary at distinct anatomical niches. But little is known about the nature of variations, if any, at the genome/sub-genome levels of a specific microbial community across different niches. The present report aims to explore, as a case study, the variations in gene repertoire of 28 Prevotella reference genomes derived from different body-sites of human, as reported earlier by the Human Microbiome Consortium.

RESULTS: The pan-genome for Prevotella remains "open". On an average, 17% of predicted protein-coding genes of any particular Prevotella genome represent the conserved core genes, while the remaining 83% contribute to the flexible and singletons. The study reveals exclusive presence of 11798, 3673, 3348 and 934 gene families and exclusive absence of 17, 221, 115 and 645 gene families in Prevotella genomes derived from human oral cavity, gastro-intestinal tracts (GIT), urogenital tract (UGT) and skin, respectively. Distribution of various functional COG categories differs significantly among the habitat-specific genes. No niche-specific variations could be observed in distribution of KEGG pathways.

CONCLUSIONS: Prevotella genomes derived from different body sites differ appreciably in gene repertoire, suggesting that these microbiome components might have developed distinct genetic strategies for niche adaptation within the host. Each individual microbe might also have a component of its own genetic machinery for host adaptation, as appeared from the huge number of singletons.}, } @article {pmid25887914, year = {2015}, author = {Plaza Onate, F and Batto, JM and Juste, C and Fadlallah, J and Fougeroux, C and Gouas, D and Pons, N and Kennedy, S and Levenez, F and Dore, J and Ehrlich, SD and Gorochov, G and Larsen, M}, title = {Quality control of microbiota metagenomics by k-mer analysis.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {183}, pmid = {25887914}, issn = {1471-2164}, mesh = {Bacteria/classification/genetics ; Cluster Analysis ; Feces/microbiology ; Gastrointestinal Tract/microbiology ; Genome, Bacterial ; Humans ; *Metagenome ; Metagenomics/*methods/standards ; *Microbiota ; Quality Control ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: The biological and clinical consequences of the tight interactions between host and microbiota are rapidly being unraveled by next generation sequencing technologies and sophisticated bioinformatics, also referred to as microbiota metagenomics. The recent success of metagenomics has created a demand to rapidly apply the technology to large case-control cohort studies and to studies of microbiota from various habitats, including habitats relatively poor in microbes. It is therefore of foremost importance to enable a robust and rapid quality assessment of metagenomic data from samples that challenge present technological limits (sample numbers and size). Here we demonstrate that the distribution of overlapping k-mers of metagenome sequence data predicts sequence quality as defined by gene distribution and efficiency of sequence mapping to a reference gene catalogue.

RESULTS: We used serial dilutions of gut microbiota metagenomic datasets to generate well-defined high to low quality metagenomes. We also analyzed a collection of 52 microbiota-derived metagenomes. We demonstrate that k-mer distributions of metagenomic sequence data identify sequence contaminations, such as sequences derived from "empty" ligation products. Of note, k-mer distributions were also able to predict the frequency of sequences mapping to a reference gene catalogue not only for the well-defined serial dilution datasets, but also for 52 human gut microbiota derived metagenomic datasets.

CONCLUSIONS: We propose that k-mer analysis of raw metagenome sequence reads should be implemented as a first quality assessment prior to more extensive bioinformatics analysis, such as sequence filtering and gene mapping. With the rising demand for metagenomic analysis of microbiota it is crucial to provide tools for rapid and efficient decision making. This will eventually lead to a faster turn-around time, improved analytical quality including sample quality metrics and a significant cost reduction. Finally, improved quality assessment will have a major impact on the robustness of biological and clinical conclusions drawn from metagenomic studies.}, } @article {pmid25887697, year = {2015}, author = {Xu, B and Xu, W and Li, J and Dai, L and Xiong, C and Tang, X and Yang, Y and Mu, Y and Zhou, J and Ding, J and Wu, Q and Huang, Z}, title = {Metagenomic analysis of the Rhinopithecus bieti fecal microbiome reveals a broad diversity of bacterial and glycoside hydrolase profiles related to lignocellulose degradation.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {174}, pmid = {25887697}, issn = {1471-2164}, mesh = {Animals ; Archaea/classification/genetics/isolation & purification ; Bacteria/*classification/genetics/isolation & purification ; Biodiversity ; Cattle ; Colobinae/*microbiology ; Dogs ; Eukaryota/classification/genetics/isolation & purification ; Feces/microbiology/virology ; Glycoside Hydrolases/*genetics ; Humans ; Lignin/*metabolism ; *Metagenome ; Metagenomics ; Mice ; *Microbiota ; Phylogeny ; Viruses/classification/genetics/isolation & purification ; }, abstract = {BACKGROUND: The animal gastrointestinal tract contains a complex community of microbes, whose composition ultimately reflects the co-evolution of microorganisms with their animal host and the diet adopted by the host. Although the importance of gut microbiota of humans has been well demonstrated, there is a paucity of research regarding non-human primates (NHPs), especially herbivorous NHPs.

RESULTS: In this study, an analysis of 97,942 pyrosequencing reads generated from Rhinopithecus bieti fecal DNA extracts was performed to help better understanding of the microbial diversity and functional capacity of the R. bieti gut microbiome. The taxonomic analysis of the metagenomic reads indicated that R. bieti fecal microbiomes were dominated by Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria phyla. The comparative analysis of taxonomic classification revealed that the metagenome of R. bieti was characterized by an overrepresentation of bacteria of phylum Fibrobacteres and Spirochaetes as compared with other animals. Primary functional categories were associated mainly with protein, carbohydrates, amino acids, DNA and RNA metabolism, cofactors, cell wall and capsule and membrane transport. Comparing glycoside hydrolase profiles of R. bieti with those of other animal revealed that the R. bieti microbiome was most closely related to cow rumen.

CONCLUSIONS: Metagenomic and functional analysis demonstrated that R. bieti possesses a broad diversity of bacteria and numerous glycoside hydrolases responsible for lignocellulosic biomass degradation which might reflect the adaptations associated with a diet rich in fibrous matter. These results would contribute to the limited body of NHPs metagenome studies and provide a unique genetic resource of plant cell wall degrading microbial enzymes. However, future studies on the metagenome sequencing of R. bieti regarding the effects of age, genetics, diet and environment on the composition and activity of the metagenomes are required.}, } @article {pmid25887483, year = {2015}, author = {Park, SH and Kim, KA and Ahn, YT and Jeong, JJ and Huh, CS and Kim, DH}, title = {Comparative analysis of gut microbiota in elderly people of urbanized towns and longevity villages.}, journal = {BMC microbiology}, volume = {15}, number = {}, pages = {49}, pmid = {25887483}, issn = {1471-2180}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/*classification/*genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; *Longevity ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Republic of Korea ; Rural Population ; Sequence Analysis, DNA ; Urban Population ; }, abstract = {BACKGROUND: To understand differences in the gut microbiota between elderly people of urbanized town communities (UTC) and longevity village communities (LVC), we analyzed fecal microbiota collected from individuals living in 2 UTC (Seoul and Chuncheon) and 3 LVC (Gurye, Damyang, and Soonchang) selected on the basis of indices for superlongevity (the ratio of centenarians to the total population) and longevity (the ratio of those aged 85 years or greater to those aged 65 years or greater) in South Korea by 454 pyrosequencing.

RESULTS: Taxonomy-based analysis showed that The relative abundance of Firmicutes, Tenericutes, and Actinobacteria was significantly lower in LVC than in UTC. Due to an increase of Firmicutes and a reduction of Bacteroidetes, the ratio of Firmicutes to Bacteroidetes in the gut microbiota was greater in UTC adults than in UTC children or LVC adults. The population levels of Bacteroides, Prevotella, and Lachnospira were significantly higher in LVC than in UTC, but the levels of Dialister, Subdoligranulum, Megamonas, EF401882_g, and AM275436_g were lower in LVC than in UTC. Although most of the species detected in LVC were detected in UTC, some Bacteroides spp. and Faecalibacterium spp. were detected only in LVC. Among Bacteroides spp., ACWH_s, EF403317_s, and EF403722_s were detected in children and LVC samples only but FJ363527_s, 4P000677_s, and 4P000015_s were detected in UTC samples. EF402172_s and EF404388_s, members of Faecalibacterium spp., which are known to have anti-inflammatory properties, were detected in LVC and children only (>3.9% of total sequence). In addition, the fecal lipopolysaccharides (LPS) content was significantly higher in UTC than in LVC.

CONCLUSIONS: These findings suggest that maintaining gut microbiota, including Faecalibacterium spp. EF402172_s and EF404388_s, as well as low LPS levels may play an important role in preserving residents' health in LVC.}, } @article {pmid25885687, year = {2015}, author = {Manor, O and Borenstein, E}, title = {MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome.}, journal = {Genome biology}, volume = {16}, number = {1}, pages = {53}, pmid = {25885687}, issn = {1474-760X}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; P30 DK089507/DK/NIDDK NIH HHS/United States ; }, mesh = {Algorithms ; Cell Proliferation/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Machine Learning ; *Metagenomics ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Functional metagenomic analyses commonly involve a normalization step, where measured levels of genes or pathways are converted into relative abundances. Here, we demonstrate that this normalization scheme introduces marked biases both across and within human microbiome samples, and identify sample- and gene-specific properties that contribute to these biases. We introduce an alternative normalization paradigm, MUSiCC, which combines universal single-copy genes with machine learning methods to correct these biases and to obtain an accurate and biologically meaningful measure of gene abundances. Finally, we demonstrate that MUSiCC significantly improves downstream discovery of functional shifts in the microbiome.MUSiCC is available at http://elbo.gs.washington.edu/software.html .}, } @article {pmid25880314, year = {2015}, author = {Guo, J and Peng, Y and Ni, BJ and Han, X and Fan, L and Yuan, Z}, title = {Dissecting microbial community structure and methane-producing pathways of a full-scale anaerobic reactor digesting activated sludge from wastewater treatment by metagenomic sequencing.}, journal = {Microbial cell factories}, volume = {14}, number = {}, pages = {33}, pmid = {25880314}, issn = {1475-2859}, mesh = {Anaerobiosis ; Archaea/classification/genetics/metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/classification/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Bioreactors/*microbiology ; Biosynthetic Pathways/genetics ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenome/*genetics ; Metagenomics/methods ; Methane/*biosynthesis ; Methanosarcina/genetics/metabolism ; Methanosarcinales/genetics/metabolism ; Microbial Consortia/*genetics ; Sewage/chemistry/*microbiology ; Waste Disposal, Fluid ; Wastewater/chemistry/*microbiology ; }, abstract = {BACKGROUND: Anaerobic digestion has been widely applied to treat the waste activated sludge from biological wastewater treatment and produce methane for biofuel, which has been one of the most efficient solutions to both energy crisis and environmental pollution challenges. Anaerobic digestion sludge contains highly complex microbial communities, which play crucial roles in sludge treatment. However, traditional approaches based on 16S rRNA amplification or fluorescent in situ hybridization cannot completely reveal the whole microbial community structure due to the extremely high complexity of the involved communities. In this sense, the next-generation high-throughput sequencing provides a powerful tool for dissecting microbial community structure and methane-producing pathways in anaerobic digestion.

RESULTS: In this work, the metagenomic sequencing was used to characterize microbial community structure of the anaerobic digestion sludge from a full-scale municipal wastewater treatment plant. Over 3.0 gigabases of metagenomic sequence data were generated with the Illumina HiSeq 2000 platform. Taxonomic analysis by MG-RAST server indicated that overall bacteria were dominant (~93%) whereas a considerable abundance of archaea (~6%) were also detected in the anaerobic digestion sludge. The most abundant bacterial populations were found to be Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Key microorganisms and related pathways involved in methanogenesis were further revealed. The dominant proliferation of Methanosaeta and Methanosarcina, together with the functional affiliation of enzymes-encoding genes (acetate kinase (AckA), phosphate acetyltransferase (PTA), and acetyl-CoA synthetase (ACSS)), suggested that the acetoclastic methanogenesis is the dominant methanogenesis pathway in the full-scale anaerobic digester.

CONCLUSIONS: In short, the metagenomic sequencing study of this work successfully dissected the detail microbial community structure and the dominated methane-producing pathways of a full-scale anaerobic digester. The knowledge garnered would facilitate to develop more efficient full-scale anaerobic digestion systems to achieve high-rate waste sludge treatment and methane production.}, } @article {pmid25880246, year = {2015}, author = {Brooks, JP and Edwards, DJ and Harwich, MD and Rivera, MC and Fettweis, JM and Serrano, MG and Reris, RA and Sheth, NU and Huang, B and Girerd, P and , and Strauss, JF and Jefferson, KK and Buck, GA}, title = {The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies.}, journal = {BMC microbiology}, volume = {15}, number = {}, pages = {66}, pmid = {25880246}, issn = {1471-2180}, support = {P60 MD002256/MD/NIMHD NIH HHS/United States ; 2P60MD002256-06/MD/NIMHD NIH HHS/United States ; UH3AI08326-01/AI/NIAID NIH HHS/United States ; U54 HD080784/HD/NICHD NIH HHS/United States ; 8U54HD080784/HD/NICHD NIH HHS/United States ; }, mesh = {*Artifacts ; Bacteria/classification/*genetics/isolation & purification ; Bias ; DNA, Bacterial/*genetics/isolation & purification ; Female ; *Genes, rRNA ; High-Throughput Nucleotide Sequencing/standards ; Humans ; Metagenomics/instrumentation/methods/standards ; Microbial Consortia/genetics ; Microbiota/genetics ; Models, Biological ; Phylogeny ; Polymerase Chain Reaction/standards ; RNA, Ribosomal, 16S/*genetics/isolation & purification ; Specimen Handling/*standards ; Vagina/microbiology ; }, abstract = {BACKGROUND: Characterizing microbial communities via next-generation sequencing is subject to a number of pitfalls involving sample processing. The observed community composition can be a severe distortion of the quantities of bacteria actually present in the microbiome, hampering analysis and threatening the validity of conclusions from metagenomic studies. We introduce an experimental protocol using mock communities for quantifying and characterizing bias introduced in the sample processing pipeline. We used 80 bacterial mock communities comprised of prescribed proportions of cells from seven vaginally-relevant bacterial strains to assess the bias introduced in the sample processing pipeline. We created two additional sets of 80 mock communities by mixing prescribed quantities of DNA and PCR product to quantify the relative contribution to bias of (1) DNA extraction, (2) PCR amplification, and (3) sequencing and taxonomic classification for particular choices of protocols for each step. We developed models to predict the "true" composition of environmental samples based on the observed proportions, and applied them to a set of clinical vaginal samples from a single subject during four visits.

RESULTS: We observed that using different DNA extraction kits can produce dramatically different results but bias is introduced regardless of the choice of kit. We observed error rates from bias of over 85% in some samples, while technical variation was very low at less than 5% for most bacteria. The effects of DNA extraction and PCR amplification for our protocols were much larger than those due to sequencing and classification. The processing steps affected different bacteria in different ways, resulting in amplified and suppressed observed proportions of a community. When predictive models were applied to clinical samples from a subject, the predicted microbiome profiles were better reflections of the physiology and diagnosis of the subject at the visits than the observed community compositions.

CONCLUSIONS: Bias in 16S studies due to DNA extraction and PCR amplification will continue to require attention despite further advances in sequencing technology. Analysis of mock communities can help assess bias and facilitate the interpretation of results from environmental samples.}, } @article {pmid25879764, year = {2015}, author = {Tseng, CH and Chiang, PW and Lai, HC and Shiah, FK and Hsu, TC and Chen, YL and Wen, LS and Tseng, CM and Shieh, WY and Saeed, I and Halgamuge, S and Tang, SL}, title = {Prokaryotic assemblages and metagenomes in pelagic zones of the South China Sea.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {219}, pmid = {25879764}, issn = {1471-2164}, mesh = {Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; China ; Cluster Analysis ; Computational Biology ; Exonucleases/genetics/metabolism ; Genome, Archaeal ; Genome, Bacterial ; Membrane Transport Proteins/genetics/metabolism ; *Metagenomics ; RNA, Ribosomal, 16S/analysis/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Urease/genetics/metabolism ; Vitamin B 12/biosynthesis ; }, abstract = {BACKGROUND: Prokaryotic microbes, the most abundant organisms in the ocean, are remarkably diverse. Despite numerous studies of marine prokaryotes, the zonation of their communities in pelagic zones has been poorly delineated. By exploiting the persistent stratification of the South China Sea (SCS), we performed a 2-year, large spatial scale (10, 100, 1000, and 3000 m) survey, which included a pilot study in 2006 and comprehensive sampling in 2007, to investigate the biological zonation of bacteria and archaea using 16S rRNA tag and shotgun metagenome sequencing.

RESULTS: Alphaproteobacteria dominated the bacterial community in the surface SCS, where the abundance of Betaproteobacteria was seemingly associated with climatic activity. Gammaproteobacteria thrived in the deep SCS, where a noticeable amount of Cyanobacteria were also detected. Marine Groups II and III Euryarchaeota were predominant in the archaeal communities in the surface and deep SCS, respectively. Bacterial diversity was higher than archaeal diversity at all sampling depths in the SCS, and peaked at mid-depths, agreeing with the diversity pattern found in global water columns. Metagenomic analysis not only showed differential %GC values and genome sizes between the surface and deep SCS, but also demonstrated depth-dependent metabolic potentials, such as cobalamin biosynthesis at 10 m, osmoregulation at 100 m, signal transduction at 1000 m, and plasmid and phage replication at 3000 m. When compared with other oceans, urease at 10 m and both exonuclease and permease at 3000 m were more abundant in the SCS. Finally, enriched genes associated with nutrient assimilation in the sea surface and transposase in the deep-sea metagenomes exemplified the functional zonation in global oceans.

CONCLUSIONS: Prokaryotic communities in the SCS stratified with depth, with maximal bacterial diversity at mid-depth, in accordance with global water columns. The SCS had functional zonation among depths and endemically enriched metabolic potentials at the study site, in contrast to other oceans.}, } @article {pmid25879181, year = {2015}, author = {Kinet, R and Destain, J and Hiligsmann, S and Thonart, P and Delhalle, L and Taminiau, B and Daube, G and Delvigne, F}, title = {Thermophilic and cellulolytic consortium isolated from composting plants improves anaerobic digestion of cellulosic biomass: Toward a microbial resource management approach.}, journal = {Bioresource technology}, volume = {189}, number = {}, pages = {138-144}, doi = {10.1016/j.biortech.2015.04.010}, pmid = {25879181}, issn = {1873-2976}, mesh = {Anaerobiosis ; Biofuels ; *Biomass ; Cellulose/*metabolism ; Fatty Acids, Volatile/analysis ; Hydrogen-Ion Concentration ; Kinetics ; Methane/biosynthesis ; *Microbial Consortia ; Plants/*microbiology ; Refuse Disposal/*methods ; *Soil ; *Temperature ; }, abstract = {A cellulolytic consortium was isolated from a composting plant in order to boost the initial hydrolysis step encountered in anaerobic digestion. Improvement of the cellulose degradation, as well as biogas production, was observed for the cultures inoculated with the exogenous consortium. Metagenomics analyses pointed out a weak richness (related to the number of OTUs) of the exogenous consortium induced by the selective pressure (cellulose as sole carbon source) met during the initial isolation steps. Main microbial strains determined were strictly anaerobic and belong to the Clostridia class. During cellulose anaerobic degradation, pH drop induced a strong modification of the microbial population. Despite the fact that richness and evenness were very weak, the exogenous consortium was able to adapt and to maintain the cellulolytic degradation potential. This important result point out the fact that simplified microbial communities could be used in order to increase the robustness of mixed cultures involved in environmental biotechnology.}, } @article {pmid25875449, year = {2015}, author = {Chen, X and Di, P and Wang, H and Li, B and Pan, Y and Yan, S and Wang, Y}, title = {Bacterial community associated with the intestinal tract of Chinese mitten crab (Eriocheir sinensis) farmed in Lake Tai, China.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0123990}, pmid = {25875449}, issn = {1932-6203}, mesh = {Animals ; Bacteria/genetics/*growth & development ; Brachyura/*microbiology ; China ; Clone Cells ; Cloning, Molecular ; Colony Count, Microbial ; Denaturing Gradient Gel Electrophoresis ; Female ; Fluorescent Dyes/metabolism ; In Situ Hybridization, Fluorescence ; Intestines/*microbiology ; *Lakes ; Metagenome ; *Microbiota ; Microvilli/microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Chinese mitten crab (CMC, Eriocheir sinensis) is an economically valuable species in South-East Asia that has been widely farmed in China. Characterization of the intestinal bacterial diversity of CMC will provide insights into the aquaculturing of CMCs. Based on the analysis of cloned 16S rRNA genes from culture-independent CMC gut bacteria, 124 out of 128 different clones reveal ＞95% nucleotide similarity to the species belonging to the four phyla of Tenericutes, Bacteroidetes, Firmicutes and Proteobacteria; one clone shows 91% sequence similarity to the member of TM7 (a candidate phylum without cultured representatives). Fluorescent in situ hybridization also reveals the abundance of Bacteroidetes in crab intestine. Electron micrographs show that spherical and filamentous bacteria are closely associated with the microvillus brush border of the midgut epithelium and are often inserted into the space between the microvilli using a stalk-like cell appendage. In contrast, the predominant rod-shaped bacteria in the hindgut are tightly attached to the epithelium surface by an unusual pili-like structure. Both 16S rRNA gene denaturing gel gradient electrophoresis and metagenome library indicate that the CMC Mollicutes group 2 appears to be present in both the midgut and hindgut with no significant difference in abundance. The CMC Mollicutes group 1, however, was found mostly in the midgut of CMCs. The CMC gut Mollicutes phylotypes appear to be most closely related to Mollicutes symbionts detected in the gut of isopods (Crustacea: Isopoda). Overall, the results suggest that CMCs harbor diverse, novel and specific gut bacteria, which are likely to live in close relationships with the CMC host.}, } @article {pmid25875428, year = {2015}, author = {Allali, I and Delgado, S and Marron, PI and Astudillo, A and Yeh, JJ and Ghazal, H and Amzazi, S and Keku, T and Azcarate-Peril, MA}, title = {Gut microbiome compositional and functional differences between tumor and non-tumor adjacent tissues from cohorts from the US and Spain.}, journal = {Gut microbes}, volume = {6}, number = {3}, pages = {161-172}, pmid = {25875428}, issn = {1949-0984}, support = {P30 DK034987/DK/NIDDK NIH HHS/United States ; P30 DK34987/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/*classification/genetics/*isolation & purification ; Colorectal Neoplasms/*microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spain ; United States ; }, abstract = {Colorectal cancer (CRC) is the third most common cancer in the world and the second leading cause of cancer deaths in the US and Spain. The molecular mechanisms involved in the etiology of CRC are not yet elucidated due in part to the complexity of the human gut microbiota. In this study, we compared the microbiome composition of 90 tumor and matching adjacent tissue (adjacent) from cohorts from the US and Spain by 16S rRNA amplicon sequencing in order to determine the impact of the geographic origin on the CRC microbiome. Data showed a significantly (P < 0.05) higher Phylogenetic Diversity (PD) for the US (PD Adjacent = 26.3 ± 5.3, PD Tumor = 23.3 ± 6.2) compared to the Spanish cohort (PD Adjacent = 18.9 ± 5.9, PD Tumor = 18.7 ± 6.6) while no significant differences in bacterial diversity were observed between tumor and adjacent tissues for individuals from the same country. Adjacent tissues from the Spanish cohort were enriched in Firmicutes (SP = 43.9% and US = 22.2%, P = 0.0001) and Actinobacteria (SP = 1.6% and US = 0.5%, P = 0.0018) compared to US adjacent tissues, while adjacent tissues from the US had significantly higher abundances of Fusobacteria (US = 8.1% and SP = 1.5%, P = 0.0023) and Sinergistetes (US = 0.3% and SP = 0.1%, P = 0.0097). Comparisons between tumor and adjacent tissues in each cohort identified the genus Eikenella significantly over represented in US tumors (T = 0.024% and A = 0%, P = 0.03), and the genera Fusobacterium (T = 10.4% and A = 1.5%, P = <0.0001), Bulleida (T = 0.36% and A = 0.09%, P = 0.02), Gemella (T = 1.46% and A = 0.19%, P = 0.03), Parvimonas (T = 3.14% and A = 0.86%, P = 0.03), Campylobacter (T = 0.15% and A = 0.008%, P = 0.047), and Streptococcus (T = 2.84% and A = 2.19%, P = 0.05) significantly over represented in Spanish tumors. Predicted metagenome functional content from 16S rRNA surveys showed that bacterial motility proteins and proteins involved in flagellar assembly were over represented in adjacent tissues of both cohorts, while pathways involved in fatty acid biosynthesis, the MAPK signaling pathway, and bacterial toxins were over represented in tumors. Our study suggests that microbiome compositional and functional dissimilarities by geographic location should be taken in consideration when approaching CRC therapeutic options.}, } @article {pmid25874630, year = {2015}, author = {Hunter, ME and Oyler-McCance, SJ and Dorazio, RM and Fike, JA and Smith, BJ and Hunter, CT and Reed, RN and Hart, KM}, title = {Environmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive burmese pythons.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0121655}, pmid = {25874630}, issn = {1932-6203}, mesh = {Animals ; Boidae/*genetics ; DNA/*genetics/isolation & purification ; *Ecology ; Florida ; Introduced Species ; *Metagenomics ; Species Specificity ; }, abstract = {Environmental DNA (eDNA) methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence probabilities while not considering the effects of imperfect detection. Low detection of invasive giant constrictors using visual surveys and traps has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida, USA. Giant constrictor snakes pose a threat to native species and the ecological restoration of the Florida Everglades. To assist with detection, we developed species-specific eDNA assays using quantitative PCR (qPCR) for the Burmese python (Python molurus bivittatus), Northern African python (P. sebae), boa constrictor (Boa constrictor), and the green (Eunectes murinus) and yellow anaconda (E. notaeus). Burmese pythons, Northern African pythons, and boa constrictors are established and reproducing, while the green and yellow anaconda have the potential to become established. We validated the python and boa constrictor assays using laboratory trials and tested all species in 21 field locations distributed in eight southern Florida regions. Burmese python eDNA was detected in 37 of 63 field sampling events; however, the other species were not detected. Although eDNA was heterogeneously distributed in the environment, occupancy models were able to provide the first estimates of detection probabilities, which were greater than 91%. Burmese python eDNA was detected along the leading northern edge of the known population boundary. The development of informative detection tools and eDNA occupancy models can improve conservation efforts in southern Florida and support more extensive studies of invasive constrictors. Generic sampling design and terminology are proposed to standardize and clarify interpretations of eDNA-based occupancy models.}, } @article {pmid25874504, year = {2015}, author = {Guo, Y and Xu, J and Yuan, Z and Li, X and Zhou, W and Xu, H and Liang, C and Zhang, Y and Zhuang, X}, title = {Metagenomic analysis for the microbial consortium of anaerobic CO oxidizers.}, journal = {Microbial biotechnology}, volume = {8}, number = {5}, pages = {846-852}, pmid = {25874504}, issn = {1751-7915}, mesh = {Anaerobiosis ; Bacteria/*classification/genetics ; Carbon Dioxide/*metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Metagenomics ; *Microbial Consortia ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/microbiology ; }, abstract = {Metagenomics analysis has been applied to identify the dominant anaerobic microbial consortium of the carbon monoxide (CO) oxidizers in anaerobic sludge. Reads from the hypervariable V6 region in the bacterial 16s rDNA were aligned and finally clustered into operational taxonomic units (OTUs). The OTUs from different stages in anaerobic CO condition were classified. Alphaproteobacteria, clostridia, betaproteobacteria and actinobacteria were the most abundant groups, while alphaproteobacteria, betaproteobacteria and actinobacteria were variable groups. CO consumption and production efficiency of the microbial consortium were studied. Semi-continuous trials showed that these anaerobic CO oxidizers formed a stable microbial community, and the CO conversion rate was at over 84%, with the highest CO consumption activity of 28.9 mmol CO/g VSS●day and methane production activity at 7.6 mmol CH4 /g VSS●day during six cycles.}, } @article {pmid25874383, year = {2015}, author = {Heyer, R and Kohrs, F and Reichl, U and Benndorf, D}, title = {Metaproteomics of complex microbial communities in biogas plants.}, journal = {Microbial biotechnology}, volume = {8}, number = {5}, pages = {749-763}, pmid = {25874383}, issn = {1751-7915}, mesh = {*Biofuels ; Bioreactors/*microbiology ; Biotechnology/methods/trends ; Ecosystem ; Gene Expression Profiling/methods ; Germany ; Metabolomics/methods ; Metagenomics/methods ; *Microbial Consortia ; Proteomics/*methods ; }, abstract = {Production of biogas from agricultural biomass or organic wastes is an important source of renewable energy. Although thousands of biogas plants (BGPs) are operating in Germany, there is still a significant potential to improve yields, e.g. from fibrous substrates. In addition, process stability should be optimized. Besides evaluating technical measures, improving our understanding of microbial communities involved into the biogas process is considered as key issue to achieve both goals. Microscopic and genetic approaches to analyse community composition provide valuable experimental data, but fail to detect presence of enzymes and overall metabolic activity of microbial communities. Therefore, metaproteomics can significantly contribute to elucidate critical steps in the conversion of biomass to methane as it delivers combined functional and phylogenetic data. Although metaproteomics analyses are challenged by sample impurities, sample complexity and redundant protein identification, and are still limited by the availability of genome sequences, recent studies have shown promising results. In the following, the workflow and potential pitfalls for metaproteomics of samples from full-scale BGP are discussed. In addition, the value of metaproteomics to contribute to the further advancement of microbial ecology is evaluated. Finally, synergistic effects expected when metaproteomics is combined with advanced imaging techniques, metagenomics, metatranscriptomics and metabolomics are addressed.}, } @article {pmid25873456, year = {2015}, author = {Rua, CP and Gregoracci, GB and Santos, EO and Soares, AC and Francini-Filho, RB and Thompson, F}, title = {Potential metabolic strategies of widely distributed holobionts in the oceanic archipelago of St Peter and St Paul (Brazil).}, journal = {FEMS microbiology ecology}, volume = {91}, number = {6}, pages = {}, doi = {10.1093/femsec/fiv043}, pmid = {25873456}, issn = {1574-6941}, mesh = {Animals ; Bacteriophages/genetics/isolation & purification ; Base Sequence ; Brazil ; Carbon/metabolism ; Hydrocarbons, Aromatic/metabolism ; Metagenomics ; Microbiota/*genetics ; Nitrogen/metabolism ; Phylogeny ; Porifera/*microbiology ; Principal Component Analysis ; Sequence Analysis, DNA ; Sulfur/metabolism ; Symbiosis/physiology ; }, abstract = {Sponges are one of the most complex symbiotic communities and while the taxonomic composition of associated microbes has been determined, the biggest challenge now is to uncover their functional role in symbiosis. We investigated the microbiota of two widely distributed sponge species, regarding both their taxonomic composition and their functional roles. Samples of Didiscus oxeata and Scopalina ruetzleri were collected in the oceanic archipelago of St Peter and St Paul and analysed through metagenomics. Sequences generated by 454 pyrosequencing and Ion Torrent were taxonomically and functionally annotated on the MG-RAST server using the GenBank and SEED databases, respectively. Both communities exhibit equivalence in core functions, interestingly played by the most abundant taxa in each community. Conversely, the microbial communities differ in composition, taxonomic diversity and potential metabolic strategies. Functional annotation indirectly suggests differences in preferential pathways of carbon, nitrogen and sulphur metabolisms, which may indicate different metabolic strategies.}, } @article {pmid25870877, year = {2015}, author = {Taketani, RG and Kavamura, VN and Mendes, R and Melo, IS}, title = {Functional congruence of rhizosphere microbial communities associated to leguminous tree from Brazilian semiarid region.}, journal = {Environmental microbiology reports}, volume = {7}, number = {1}, pages = {95-101}, doi = {10.1111/1758-2229.12187}, pmid = {25870877}, issn = {1758-2229}, mesh = {Bacteria/classification/genetics/growth & development/*isolation & purification ; Biodiversity ; Brazil ; Fabaceae/*microbiology ; Metagenome ; Phylogeny ; *Rhizosphere ; Seasons ; *Soil Microbiology ; Trees/*microbiology ; }, abstract = {Semiarid environments are characterized by the uneven spread of rain throughout the year. This leads to the establishment of a biota that can go through long periods without rain. In order to understand the dynamics of rhizosphere microbial communities across these contrasting seasons in Caatinga, we used the Ion Torrent platform to sequence the metagenome of the rhizosphere of a native leguminous plant (Mimosa tenuiflora). The annotation indicated that most abundant groups detected were the Actinobacteria and Proteobacteria, and the dominant functional groups were carbohydrate and protein metabolisms, and that in the wet season, the communities carried carbohydrate and amino acid metabolisms.The major differences observed between seasons were higher abundance of genes related to carbohydrate and amino acid metabolisms in the rainy season, indicating that the populations present might be better adapted to a higher abundance of organic matter. Besides, no clear separation of samples was detected based on their taxonomic composition whereas the functional composition indicates that samples from the rain season are more related. Altogether, our results indicate that there is al arge functional stability in these communities mostly due to the selection of features that aid the biota to endure the dry season and blossom during rain.}, } @article {pmid25867897, year = {2015}, author = {Dugat-Bony, E and Straub, C and Teissandier, A and Onésime, D and Loux, V and Monnet, C and Irlinger, F and Landaud, S and Leclercq-Perlat, MN and Bento, P and Fraud, S and Gibrat, JF and Aubert, J and Fer, F and Guédon, E and Pons, N and Kennedy, S and Beckerich, JM and Swennen, D and Bonnarme, P}, title = {Overview of a surface-ripened cheese community functioning by meta-omics analyses.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0124360}, pmid = {25867897}, issn = {1932-6203}, mesh = {*Cheese ; Metagenomics ; *Microbiota ; Transcriptome ; }, abstract = {Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-ripened cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a long time on surface-ripened cheeses, but only limited knowledge has been acquired about its in situ metabolic activities. We applied metagenomic, metatranscriptomic and biochemical analyses to an experimental surface-ripened cheese composed of nine microbial species during four weeks of ripening. By combining all of the data, we were able to obtain an overview of the cheese maturation process and to better understand the metabolic activities of the different community members and their possible interactions. Furthermore, differential expression analysis was used to select a set of biomarker genes, providing a valuable tool that can be used to monitor the cheese-making process.}, } @article {pmid25866080, year = {2015}, author = {Orr, CH and Stewart, CJ and Leifert, C and Cooper, JM and Cummings, SP}, title = {Effect of crop management and sample year on abundance of soil bacterial communities in organic and conventional cropping systems.}, journal = {Journal of applied microbiology}, volume = {119}, number = {1}, pages = {208-214}, doi = {10.1111/jam.12822}, pmid = {25866080}, issn = {1365-2672}, mesh = {Agriculture/*methods ; Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; Crops, Agricultural/*growth & development ; Molecular Sequence Data ; Nitrogen/analysis/metabolism ; RNA, Ribosomal, 16S ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {AIMS: To identify changes in the bacterial community, at the phylum level brought about by varied crop management.

METHODS AND RESULTS: Next-generation sequencing methods were used to compare the taxonomic structure of the bacterial community within 24 agricultural soils managed with either organic or conventional methods, over a 3-year period. Relative abundance of the proportionately larger phyla (e.g. Acidobacteria and Actinobacteria) was primarily affected by sample year rather than crop management. Changes of abundance in these phyla were correlated with changes in pH, organic nitrogen and soil basal respiration. Crop management affected some of the less dominant phyla (Chloroflexi, Nitrospirae, Gemmatimonadetes) which also correlated with pH and organic N.

CONCLUSION: Soil diversity can vary with changing environmental variables and soil chemistry. If these factors remain constant, soil diversity can also remain constant even under changing land use.

The impact of crop management on environmental variables must be considered when interpreting bacterial diversity studies in agricultural soils. Impact of land use change should always be monitored across different sampling time points. Further studies at the functional group level are necessary to assess whether management-induced changes in bacterial community structure are of biological and agronomic relevance.}, } @article {pmid25865150, year = {2015}, author = {Andújar, C and Arribas, P and Ruzicka, F and Crampton-Platt, A and Timmermans, MJ and Vogler, AP}, title = {Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics.}, journal = {Molecular ecology}, volume = {24}, number = {14}, pages = {3603-3617}, doi = {10.1111/mec.13195}, pmid = {25865150}, issn = {1365-294X}, mesh = {Animals ; Bayes Theorem ; *Biodiversity ; *Biota ; Coleoptera/classification ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; *Phylogeny ; Sequence Analysis, DNA ; Spain ; }, abstract = {High-throughput DNA methods hold great promise for the study of taxonomically intractable mesofauna of the soil. Here, we assess species diversity and community structure in a phylogenetic framework, by sequencing total DNA from bulk specimen samples and assembly of mitochondrial genomes. The combination of mitochondrial metagenomics and DNA barcode sequencing of 1494 specimens in 69 soil samples from three geographic regions in southern Iberia revealed >300 species of soil Coleoptera (beetles) from a broad spectrum of phylogenetic lineages. A set of 214 mitochondrial sequences longer than 3000 bp was generated and used to estimate a well-supported phylogenetic tree of the order Coleoptera. Shorter sequences, including cox1 barcodes, were placed on this mitogenomic tree. Raw Illumina reads were mapped against all available sequences to test for species present in local samples. This approach simultaneously established the species richness, phylogenetic composition and community turnover at species and phylogenetic levels. We find a strong signature of vertical structuring in soil fauna that shows high local community differentiation between deep soil and superficial horizons at phylogenetic levels. Within the two vertical layers, turnover among regions was primarily at the tip (species) level and was stronger in the deep soil than leaf litter communities, pointing to layer-mediated drivers determining species diversification, spatial structure and evolutionary assembly of soil communities. This integrated phylogenetic framework opens the application of phylogenetic community ecology to the mesofauna of the soil, among the most diverse and least well-understood ecosystems, and will propel both theoretical and applied soil science.}, } @article {pmid25864640, year = {2015}, author = {Sankar, SA and Lagier, JC and Pontarotti, P and Raoult, D and Fournier, PE}, title = {The human gut microbiome, a taxonomic conundrum.}, journal = {Systematic and applied microbiology}, volume = {38}, number = {4}, pages = {276-286}, doi = {10.1016/j.syapm.2015.03.004}, pmid = {25864640}, issn = {1618-0984}, mesh = {*Bacteria/classification/genetics ; Humans ; *Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; }, abstract = {From culture to metagenomics, within only 130 years, our knowledge of the human microbiome has considerably improved. With >1000 microbial species identified to date, the gastro-intestinal microbiota is the most complex of human biotas. It is composed of a majority of Bacteroidetes and Firmicutes and, although exhibiting great inter-individual variations according to age, geographic origin, disease or antibiotic uptake, it is stable over time. Metagenomic studies have suggested associations between specific gut microbiota compositions and a variety of diseases, including irritable bowel syndrome, Crohn's disease, colon cancer, type 2 diabetes and obesity. However, these data remain method-dependent, as no consensus strategy has been defined to decipher the complexity of the gut microbiota. High-throughput culture-independent techniques have highlighted the limitations of culture by showing the importance of uncultured species, whereas modern culture methods have demonstrated that metagenomics underestimates the microbial diversity by ignoring minor populations. In this review, we highlight the progress and challenges that pave the way to a complete understanding of the human gastrointestinal microbiota and its influence on human health.}, } @article {pmid25862077, year = {2015}, author = {Duran-Pinedo, AE and Frias-Lopez, J}, title = {Beyond microbial community composition: functional activities of the oral microbiome in health and disease.}, journal = {Microbes and infection}, volume = {17}, number = {7}, pages = {505-516}, pmid = {25862077}, issn = {1769-714X}, support = {R01 DE021553/DE/NIDCR NIH HHS/United States ; U01 DE021127/DE/NIDCR NIH HHS/United States ; DE021553/DE/NIDCR NIH HHS/United States ; DE021127/DE/NIDCR NIH HHS/United States ; }, mesh = {Dental Caries/*etiology/pathology ; Gastrointestinal Microbiome/*immunology ; *Health Status ; Host-Pathogen Interactions/*immunology ; Humans ; Metagenome ; *Oral Health ; }, abstract = {The oral microbiome plays a relevant role in the health status of the host and is a key element in a variety of oral and non-oral diseases. Despite advances in our knowledge of changes in microbial composition associated with different health conditions the functional aspects of the oral microbiome that lead to dysbiosis remain for the most part unknown. In this review, we discuss the progress made towards understanding the functional role of the oral microbiome in health and disease and how novel technologies are expanding our knowledge on this subject.}, } @article {pmid25861819, year = {2015}, author = {Reichenberger, ER and Rosen, G and Hershberg, U and Hershberg, R}, title = {Prokaryotic nucleotide composition is shaped by both phylogeny and the environment.}, journal = {Genome biology and evolution}, volume = {7}, number = {5}, pages = {1380-1389}, pmid = {25861819}, issn = {1759-6653}, support = {P01 AI106697/AI/NIAID NIH HHS/United States ; P01AI106697./AI/NIAID NIH HHS/United States ; }, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Base Composition ; DNA, Archaeal/*chemistry ; DNA, Bacterial/*chemistry ; Environment ; Gastrointestinal Tract/microbiology ; *Gene-Environment Interaction ; Genetic Variation ; Humans ; Microbiota ; Nucleotides/analysis ; *Phylogeny ; }, abstract = {The causes of the great variation in nucleotide composition of prokaryotic genomes have long been disputed. Here, we use extensive metagenomic and whole-genome data to demonstrate that both phylogeny and the environment shape prokaryotic nucleotide content. We show that across environments, various phyla are characterized by different mean guanine and cytosine (GC) values as well as by the extent of variation on that mean value. At the same time, we show that GC-content varies greatly as a function of environment, in a manner that cannot be entirely explained by disparities in phylogenetic composition. We find environmentally driven differences in nucleotide content not only between highly diverged environments (e.g., soil, vs. aquatic vs. human gut) but also within a single type of environment. More specifically, we demonstrate that some human guts are associated with a microbiome that is consistently more GC-rich across phyla, whereas others are associated with a more AT-rich microbiome. These differences appear to be driven both by variations in phylogenetic composition and by environmental differences-which are independent of these phylogenetic composition differences. Combined, our results demonstrate that both phylogeny and the environment significantly affect nucleotide composition and that the environmental differences affecting nucleotide composition are far subtler than previously appreciated.}, } @article {pmid25860481, year = {2015}, author = {Zhang, J and Liu, H and Liang, X and Zhang, M and Wang, R and Peng, G and Li, J}, title = {Investigation of salivary function and oral microbiota of radiation caries-free people with nasopharyngeal carcinoma.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0123137}, pmid = {25860481}, issn = {1932-6203}, mesh = {Adult ; Aged ; Carcinoma ; Case-Control Studies ; Dental Caries ; Female ; Humans ; Male ; Metagenome ; *Microbiota ; Middle Aged ; Mouth/*microbiology ; Nasopharyngeal Carcinoma ; Nasopharyngeal Neoplasms/*microbiology/*physiopathology/radiotherapy ; Oral Hygiene ; Saliva/chemistry/microbiology ; Salivary Glands/*physiopathology/radiation effects ; Young Adult ; }, abstract = {Radiation caries have been reported to be correlated with radiotherapy-induced destruction of salivary function and changes in oral microbiota. There have been no published reports detailing patients who have remained radiation caries-free following radiotherapy for nasopharyngeal carcinoma. The aim of this study was to investigate the relationship between salivary function, oral microbiota and the absence of radiation caries. Twelve radiation caries-free patients and nine patients exhibiting radiation caries following irradiated nasopharyngeal carcinoma were selected. V40, the dose at which the volume of the contralateral parotid gland receives more than 40 Gy, was recorded. Stimulated saliva flow rate, pH values and buffering capacity were examined to assess salivary function. Stimulated saliva was used for molecular profiling by Denaturing Gradient Gel Electrophoresis. Mutans streptococci and Lactobacilli in saliva were also cultivated. There were no significant differences in V40 between radiation caries-free individuals and those with radiation caries. Compared with normal values, the radiation caries-free group had significantly decreased simulated saliva flow rate, while there were no significant differences in the saliva pH value and buffering capacity. Similar results were observed in the radiation caries group. There was no statistical difference in microbial diversity, composition and log CFU counts in cultivation from the radiation caries-free group and the radiation caries group. Eleven genera were detected in these two groups, among which Streptococcus spp. and Neisseria spp. had the highest distribution. Our results suggest that changes in salivary function and in salivary microbiota do not explain the absence of radiation caries in radiation caries-free individuals.}, } @article {pmid25859745, year = {2015}, author = {Zhang, R and Cheng, Z and Guan, J and Zhou, S}, title = {Exploiting topic modeling to boost metagenomic reads binning.}, journal = {BMC bioinformatics}, volume = {16 Suppl 5}, number = {Suppl 5}, pages = {S2}, pmid = {25859745}, issn = {1471-2105}, mesh = {*Algorithms ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Molecular Sequence Annotation/*methods ; Phylogeny ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {BACKGROUND: With the rapid development of high-throughput technologies, researchers can sequence the whole metagenome of a microbial community sampled directly from the environment. The assignment of these metagenomic reads into different species or taxonomical classes is a vital step for metagenomic analysis, which is referred to as binning of metagenomic data.

RESULTS: In this paper, we propose a new method TM-MCluster for binning metagenomic reads. First, we represent each metagenomic read as a set of "k-mers" with their frequencies occurring in the read. Then, we employ a probabilistic topic model -- the Latent Dirichlet Allocation (LDA) model to the reads, which generates a number of hidden "topics" such that each read can be represented by a distribution vector of the generated topics. Finally, as in the MCluster method, we apply SKWIC -- a variant of the classical K-means algorithm with automatic feature weighting mechanism to cluster these reads represented by topic distributions.

CONCLUSIONS: Experiments show that the new method TM-MCluster outperforms major existing methods, including AbundanceBin, MetaCluster 3.0/5.0 and MCluster. This result indicates that the exploitation of topic modeling can effectively improve the binning performance of metagenomic reads.}, } @article {pmid25859244, year = {2015}, author = {Hall, RJ and Draper, JL and Nielsen, FG and Dutilh, BE}, title = {Beyond research: a primer for considerations on using viral metagenomics in the field and clinic.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {224}, pmid = {25859244}, issn = {1664-302X}, abstract = {Powered by recent advances in next-generation sequencing technologies, metagenomics has already unveiled vast microbial biodiversity in a range of environments, and is increasingly being applied in clinics for difficult-to-diagnose cases. It can be tempting to suggest that metagenomics could be used as a "universal test" for all pathogens without the need to conduct lengthy serial testing using specific assays. While this is an exciting prospect, there are issues that need to be addressed before metagenomic methods can be applied with rigor as a diagnostic tool, including the potential for incidental findings, unforeseen consequences for trade and regulatory authorities, privacy and cultural issues, data sharing, and appropriate reporting of results to end-users. These issues will require consideration and discussion across a range of disciplines, with inclusion of scientists, ethicists, clinicians, diagnosticians, health practitioners, and ultimately the public. Here, we provide a primer for consideration on some of these issues.}, } @article {pmid25858184, year = {2015}, author = {Aguirre, E and Galiana, A and Mira, A and Guardiola, R and Sánchez-Guillén, L and Garcia-Pachon, E and Santibañez, M and Royo, G and Rodríguez, JC}, title = {Analysis of microbiota in stable patients with chronic obstructive pulmonary disease.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {123}, number = {5}, pages = {427-432}, doi = {10.1111/apm.12363}, pmid = {25858184}, issn = {1600-0463}, mesh = {Aged ; Aged, 80 and over ; Bacteria/classification/genetics/isolation & purification ; Bacterial Typing Techniques/methods ; DNA, Bacterial/genetics/isolation & purification ; Female ; Humans ; Male ; Metagenome/genetics ; *Microbiota/genetics ; Middle Aged ; Molecular Typing/methods ; Polymerase Chain Reaction/methods ; Prospective Studies ; Pulmonary Disease, Chronic Obstructive/*microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sputum/microbiology ; }, abstract = {To identify the bacterial diversity (microbiota) in expectorated sputum, a pyrosequencing method that investigates complex microbial communities of expectorated sputum was done in 19 stable chronic obstructive pulmonary disease patients (mean (SD) FEV1: 47 (18%) of predicted value). Using conventional culture, 3 phyla and 20 bacterial genera were identified, whereas the pyrosequencing approach detected 9 phyla and 43 genera (p < 0.001). In sputum the prevalent genera with pyrosequencing approach were Streptococcus, Actinomyces, Neisseria, Haemophilus, Rothia, Fusobacterium, Gemella, Granulicatella, Porphyromonas, Prevotella and Veillonella. Enterobacteriaceae, detected frequently in conventional culture, were not significantly detected with pyrosequencing methods. In addition, we found that important pathogens such as Haemophilus and Moraxella were detected more frequently with the new genetic procedures. The presence of Enterobacteriaceae is probably overestimated with conventional culture, whereas other difficult cultivable pathogens are underestimated. These studies open a new perspective for evaluating the role of bacterial colonization in chronic obstructive pulmonary disease pathogenesis and progression.}, } @article {pmid25857928, year = {2015}, author = {Jerde, CL and Mahon, AR}, title = {Improving confidence in environmental DNA species detection.}, journal = {Molecular ecology resources}, volume = {15}, number = {3}, pages = {461-463}, doi = {10.1111/1755-0998.12377}, pmid = {25857928}, issn = {1755-0998}, mesh = {*Biodiversity ; *Ecosystem ; Environmental Monitoring ; Genotyping Techniques/*methods ; Metagenomics/*methods ; *Phylogeography ; }, abstract = {Will we catch fish today? Our grandfathers' responses were usually something along the lines of, 'Probably. I've caught them here before'. One of the foundations of ecology is identifying which species are present, and where. This informs our understanding of species richness patterns, spread of invasive species, and loss of threatened and endangered species due to environmental change. However, our understanding is often lacking, particularly in aquatic environments where biodiversity remains hidden below the water's surface. The emerging field of metagenetic species surveillance is aiding our ability to rapidly determine which aquatic species are present, and where. In this issue of Molecular Ecology Resources, Ficetola et al. () provide a framework for metagenetic environmental DNA surveillance to foster the confidence of our grandfathers' fishing prowess by more rigorously evaluating the replication levels necessary to quantify detection errors and ultimately improving our confidence in aquatic species presence.}, } @article {pmid25853934, year = {2015}, author = {Nayfach, S and Pollard, KS}, title = {Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome.}, journal = {Genome biology}, volume = {16}, number = {1}, pages = {51}, pmid = {25853934}, issn = {1474-760X}, support = {T32 EB009383/EB/NIBIB NIH HHS/United States ; T32 GM067547/GM/NIGMS NIH HHS/United States ; }, mesh = {*Genome Size ; Genome, Bacterial ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; Sequence Analysis, DNA ; }, abstract = {Average genome size is an important, yet often overlooked, property of microbial communities. We developed MicrobeCensus to rapidly and accurately estimate average genome size from shotgun metagenomic data and applied our tool to 1,352 human microbiome samples. We found that average genome size differs significantly within and between body sites and tracks with major functional and taxonomic differences. In the gut, average genome size is positively correlated with the abundance of Bacteroides and genes related to carbohydrate metabolism. Importantly, we found that average genome size variation can bias comparative analyses, and that normalization improves detection of differentially abundant genes.}, } @article {pmid25852170, year = {2015}, author = {Ericsson, AC and Davis, DJ and Franklin, CL and Hagan, CE}, title = {Exoelectrogenic capacity of host microbiota predicts lymphocyte recruitment to the gut.}, journal = {Physiological genomics}, volume = {47}, number = {7}, pages = {243-252}, pmid = {25852170}, issn = {1531-2267}, support = {U42 OD010918/OD/NIH HHS/United States ; 5U42OD-010918-15/OD/NIH HHS/United States ; }, mesh = {Adoptive Transfer ; Animals ; Base Sequence ; Cell Movement/*physiology ; Computational Biology ; Electrolysis ; Electrophysiological Phenomena/*physiology ; Enzyme-Linked Immunosorbent Assay ; Feces/chemistry ; Fluorometry ; Gastric Mucosa/*physiology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/cytology/microbiology/*physiology ; Gene Expression Regulation/*physiology ; Gene Library ; Immunohistochemistry ; Lymphocytes/*physiology ; Mice ; Mice, Inbred C57BL ; Microscopy, Confocal ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Proteobacteria/metabolism ; Real-Time Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Statistics, Nonparametric ; }, abstract = {Electrotaxis, directional cell movement in response to an electric potential, has been demonstrated in a wide range of cell types including lymphocytes. Exoelectrogens, microorganisms capable of generating electrical currents, have been identified in microbial fuel cells. However, no studies have investigated exoelectrogenic microbes in fresh feces or the effects of an exoelectrogenic microbiota on the host organism. Here we show that commensal gut microbial populations differ in their capacity for electrical current production by exoelectrogens and that those differences are predictive of increased lymphocyte trafficking to the gut in vivo, despite the lack of increased production of canonical lymphocyte-specific chemokines. Additionally, we demonstrate that the difference in current production between mice purchased from different commercial sources correlates reproducibly with the presence or absence of segmented filamentous bacteria, and while our data do not support a direct role for segmented filamentous bacteria in ex vivo current production, an exoelectrogenic microbiota can be transferred in vivo via mucosa-associated bacteria present in the ileum. Moreover, we detect upregulation of microbial genes associated with extracellular electron transfer in feces of mice colonized with exoelectrogenic microbiota containing segmented filamentous bacteria. While still correlative, these results suggest a novel means by which the gut microbiota modulates the recruitment of cells of the immune system to the gut.}, } @article {pmid25851097, year = {2015}, author = {Hoppe, B and Krger, K and Kahl, T and Arnstadt, T and Buscot, F and Bauhus, J and Wubet, T}, title = {A pyrosequencing insight into sprawling bacterial diversity and community dynamics in decaying deadwood logs of Fagus sylvatica and Picea abies.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {9456}, pmid = {25851097}, issn = {2045-2322}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; *Fagus ; Metagenome ; *Microbiota ; Phylogeny ; *Picea ; RNA, Ribosomal, 16S/genetics ; *Trees ; Wood/*microbiology ; }, abstract = {Deadwood is an important biodiversity hotspot in forest ecosystems. While saproxylic insects and wood-inhabiting fungi have been studied extensively, little is known about deadwood-inhabiting bacteria. The study we present is among the first to compare bacterial diversity and community structure of deadwood under field conditions. We therefore compared deadwood logs of two temperate forest tree species Fagus sylvatica and Picea abies using 16S rDNA pyrosequencing to identify changes in bacterial diversity and community structure at different stages of decay in forest plots under different management regimes. Alphaproteobacteria, Acidobacteria and Actinobacteria were the dominant taxonomic groups in both tree species. There were no differences in bacterial OTU richness between deadwood of Fagus sylvatica and Picea abies. Bacteria from the order Rhizobiales became more abundant during the intermediate and advanced stages of decay, accounting for up to 25% of the entire bacterial community in such logs. The most dominant OTU was taxonomically assigned to the genus Methylovirgula, which was recently described in a woodblock experiment of Fagus sylvatica. Besides tree species we were able to demonstrate that deadwood physico-chemical properties, in particular remaining mass, relative wood moisture, pH, and C/N ratio serve as drivers of community composition of deadwood-inhabiting bacteria.}, } @article {pmid25848871, year = {2015}, author = {Liu, J and Yan, R and Zhong, Q and Ngo, S and Bangayan, NJ and Nguyen, L and Lui, T and Liu, M and Erfe, MC and Craft, N and Tomida, S and Li, H}, title = {The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin.}, journal = {The ISME journal}, volume = {9}, number = {9}, pages = {2078-2093}, pmid = {25848871}, issn = {1751-7370}, support = {T32AI07323/AI/NIAID NIH HHS/United States ; UH2AR057503/AR/NIAMS NIH HHS/United States ; T32 AI007323/AI/NIAID NIH HHS/United States ; R01GM099530/GM/NIGMS NIH HHS/United States ; R01 GM099530/GM/NIGMS NIH HHS/United States ; UH2 AR057503/AR/NIAMS NIH HHS/United States ; }, mesh = {Acne Vulgaris/*microbiology ; Bacteriophages/*genetics ; Base Sequence ; Biodiversity ; Clustered Regularly Interspaced Short Palindromic Repeats ; Genome, Viral ; *Host-Pathogen Interactions ; Humans ; Metagenome ; Microscopy, Electron ; Phylogeny ; Polymorphism, Single Nucleotide ; Propionibacterium acnes/*genetics/*pathogenicity/virology ; Skin/*microbiology ; }, abstract = {The viral population, including bacteriophages, is an important component of the human microbiota, yet is poorly understood. We aim to determine whether bacteriophages modulate the composition of the bacterial populations, thus potentially playing a role in health or disease. We investigated the diversity and host interactions of the bacteriophages of Propionibacterium acnes, a major human skin commensal implicated in acne pathogenesis. By sequencing 48 P. acnes phages isolated from acne patients and healthy individuals and by analyzing the P. acnes phage populations in healthy skin metagenomes, we revealed that P. acnes phage populations in the skin microbial community are often dominated by one strain. We also found phage strains shared among both related and unrelated individuals, suggesting that a pool of common phages exists in the human population and that transmission of phages may occur between individuals. To better understand the bacterium-phage interactions in the skin microbiota, we determined the outcomes of 74 genetically defined Propionibacterium strains challenged by 15 sequenced phages. Depending on the Propionibacterium lineage, phage infection can result in lysis, pseudolysogeny, or resistance. In type II P. acnes strains, we found that encoding matching clustered regularly interspaced short palindromic repeat spacers is insufficient to confer phage resistance. Overall, our findings suggest that the prey-predator relationship between bacteria and phages may have a role in modulating the composition of the microbiota. Our study also suggests that the microbiome structure of an individual may be an important factor in the design of phage-based therapy.}, } @article {pmid25847866, year = {2015}, author = {Neumann, AM and Balmonte, JP and Berger, M and Giebel, HA and Arnosti, C and Voget, S and Simon, M and Brinkhoff, T and Wietz, M}, title = {Different utilization of alginate and other algal polysaccharides by marine Alteromonas macleodii ecotypes.}, journal = {Environmental microbiology}, volume = {17}, number = {10}, pages = {3857-3868}, doi = {10.1111/1462-2920.12862}, pmid = {25847866}, issn = {1462-2920}, mesh = {Alginates/*metabolism ; Alteromonas/genetics/isolation & purification/*metabolism ; Aquatic Organisms/genetics/*metabolism ; Atlantic Ocean ; Bacterial Proteins/genetics ; Ecotype ; Energy Metabolism/*physiology ; Genome, Bacterial/genetics ; Genomic Islands/genetics ; Glucans/metabolism ; Glucuronic Acid/metabolism ; Hexuronic Acids/metabolism ; Membrane Proteins/genetics ; Metagenome/genetics ; Polysaccharide-Lyases/*genetics/metabolism ; Seawater/microbiology ; Xylans/metabolism ; }, abstract = {The marine bacterium Alteromonas macleodii is a copiotrophic r-strategist, but little is known about its potential to degrade polysaccharides. Here, we studied the degradation of alginate and other algal polysaccharides by A. macleodii strain 83-1 in comparison to other A. macleodii strains. Cell densities of strain 83-1 with alginate as sole carbon source were comparable to those with glucose, but the exponential phase was delayed. The genome of 83-1 was found to harbour an alginolytic system comprising five alginate lyases, whose expression was induced by alginate. The alginolytic system contains additional CAZymes, including two TonB-dependent receptors, and is part of a 24 kb genomic island unique to the A. macleodii 'surface clade' ecotype. In contrast, strains of the 'deep clade' ecotype contain only a single alginate lyase in a separate 7 kb island. This difference was reflected in an eightfold greater efficiency of surface clade strains to grow on alginate. Strain 83-1 furthermore hydrolysed laminarin, pullulan and xylan, and corresponding polysaccharide utilization loci were detected in the genome. Alteromonas macleodii alginate lyases were predominantly detected in Atlantic Ocean metagenomes. The demonstrated hydrolytic capacities are likely of ecological relevance and represent another level of adaptation among A. macleodii ecotypes.}, } @article {pmid25842038, year = {2015}, author = {Nasanit, R and Krataithong, K and Tantirungkij, M and Limtong, S}, title = {Assessment of epiphytic yeast diversity in rice (Oryza sativa) phyllosphere in Thailand by a culture-independent approach.}, journal = {Antonie van Leeuwenhoek}, volume = {107}, number = {6}, pages = {1475-1490}, doi = {10.1007/s10482-015-0442-2}, pmid = {25842038}, issn = {1572-9699}, mesh = {*Biodiversity ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Metagenomics ; Molecular Sequence Data ; Oryza/*microbiology ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; Thailand ; Yeasts/*classification/genetics/*isolation & purification ; }, abstract = {The epiphytic yeast diversity in rice phyllosphere in Thailand was investigated by a culture-independent technique based on the RFLP pattern and the sequence of the D1/D2 domain of the large subunit rRNA gene. Forty-four samples of rice leaf were collected randomly from six provinces. The DNA was extracted from leaf washing samples and the D1/D2 domain was amplified using PCR technique. The PCR products were cloned and then screened by colony PCR. Of total 1121 clones, 451 clones (40.2 %) revealed the D1/D2 domain sequences closely related to sequences of yeasts in GenBank, and they were clustered into 45 operational taxonomic units (OTUs) at 99 % homology. Of total yeast related clones, 329 clones (72.9 %) were identified as nine known yeast species, which consisted of 314 clones (8 OTUs) in the phylum Basidiomycota including Bullera japonica, Pseudozyma antarctica, Pseudozyma aphidis, Sporobolomyces blumeae, Sporobolomyces carnicolor and Sporobolomyces oryzicola and 15 clones (6 OTUs) in the phylum Ascomycota including Metschnikowia koreensis, Meyerozyma guilliermondii and Wickerhamomyces anomalus. The D1/D2 sequences (122 clones) that could not be identified as known yeast species were closest to 3 and 14 species in Ascomycota and Basidiomycota, respectively, some of which may be new yeast species. The most predominant species detected was P. antarctica (42.6 %) followed by B. japonica (25.9 %) with 63.6 and 22.7 % frequency of occurrence, respectively. The results of OTU richness of each sampling location revealed that climate condition and sampling location could affect epiphytic yeast diversity in rice phyllosphere.}, } @article {pmid25842007, year = {2015}, author = {Imangaliyev, S and Keijser, B and Crielaard, W and Tsivtsivadze, E}, title = {Personalized microbial network inference via co-regularized spectral clustering.}, journal = {Methods (San Diego, Calif.)}, volume = {83}, number = {}, pages = {28-35}, doi = {10.1016/j.ymeth.2015.03.017}, pmid = {25842007}, issn = {1095-9130}, mesh = {Algorithms ; *Cluster Analysis ; Computational Biology/*methods ; Humans ; *Microbial Consortia ; Microbiota/*genetics ; }, abstract = {We use Human Microbiome Project (HMP) cohort (Peterson et al., 2009) to infer personalized oral microbial networks of healthy individuals. To determine clustering of individuals with similar microbial profiles, co-regularized spectral clustering algorithm is applied to the dataset. For each cluster we discovered, we compute co-occurrence relationships among the microbial species that determine microbial network per cluster of individuals. The results of our study suggest that there are several differences in microbial interactions on personalized network level in healthy oral samples acquired from various niches. Based on the results of co-regularized spectral clustering we discover two groups of individuals with different topology of their microbial interaction network. The results of microbial network inference suggest that niche-wise interactions are different in these two groups. Our study shows that healthy individuals have different microbial clusters according to their oral microbiota. Such personalized microbial networks open a better understanding of the microbial ecology of healthy oral cavities and new possibilities for future targeted medication. The scripts written in scientific Python and in Matlab, which were used for network visualization, are provided for download on the website http://learning-machines.com/.}, } @article {pmid25841004, year = {2015}, author = {Reavy, B and Swanson, MM and Cock, PJ and Dawson, L and Freitag, TE and Singh, BK and Torrance, L and Mushegian, AR and Taliansky, M}, title = {Distinct circular single-stranded DNA viruses exist in different soil types.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {12}, pages = {3934-3945}, pmid = {25841004}, issn = {1098-5336}, mesh = {Base Sequence ; Biodiversity ; Capsid Proteins/genetics ; Circoviridae/classification/genetics/*isolation & purification ; DNA Viruses/*classification/genetics/*isolation & purification ; DNA, Single-Stranded/genetics ; DNA, Viral/genetics ; Genome, Viral ; Ireland ; Metagenomics ; Microviridae/classification/genetics/*isolation & purification ; Phylogeny ; Scotland ; Sequence Analysis, DNA ; Soil/*classification ; *Soil Microbiology ; Virion/classification/isolation & purification ; }, abstract = {The potential dependence of virus populations on soil types was examined by electron microscopy, and the total abundance of virus particles in four soil types was similar to that previously observed in soil samples. The four soil types examined differed in the relative abundances of four morphological groups of viruses. Machair, a unique type of coastal soil in western Scotland and Ireland, differed from the others tested in having a higher proportion of tailed bacteriophages. The other soils examined contained predominantly spherical and thin filamentous virus particles, but the Machair soil had a more even distribution of the virus types. As the first step in looking at differences in populations in detail, virus sequences from Machair and brown earth (agricultural pasture) soils were examined by metagenomic sequencing after enriching for circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) virus genomes. Sequences from the family Microviridae (icosahedral viruses mainly infecting bacteria) of CRESS-DNA viruses were predominant in both soils. Phylogenetic analysis of Microviridae major coat protein sequences from the Machair viruses showed that they spanned most of the diversity of the subfamily Gokushovirinae, whose members mainly infect obligate intracellular parasites. The brown earth soil had a higher proportion of sequences that matched the morphologically similar family Circoviridae in BLAST searches. However, analysis of putative replicase proteins that were similar to those of viruses in the Circoviridae showed that they are a novel clade of Circoviridae-related CRESS-DNA viruses distinct from known Circoviridae genera. Different soils have substantially different taxonomic biodiversities even within ssDNA viruses, which may be driven by physicochemical factors.}, } @article {pmid25833886, year = {2015}, author = {Duffy, LC and Raiten, DJ and Hubbard, VS and Starke-Reed, P}, title = {Progress and challenges in developing metabolic footprints from diet in human gut microbial cometabolism.}, journal = {The Journal of nutrition}, volume = {145}, number = {5}, pages = {1123S-1130S}, pmid = {25833886}, issn = {1541-6100}, mesh = {Animals ; *Biomedical Research/trends ; Congresses as Topic ; Diet/*adverse effects ; *Global Health ; Humans ; Intestinal Mucosa/metabolism/*microbiology ; *Metabolomics/trends ; *Microbiology/trends ; *Microbiota ; Prebiotics/adverse effects ; Probiotics/adverse effects ; }, abstract = {Homo sapiens harbor trillions of microbes, whose microbial metagenome (collective genome of a microbial community) using omic validation interrogation tools is estimated to be at least 100-fold that of human cells, which comprise 23,000 genes. This article highlights some of the current progress and open questions in nutrition-related areas of microbiome research. It also underscores the metabolic capabilities of microbial fermentation on nutritional substrates that require further mechanistic understanding and systems biology approaches of studying functional interactions between diet composition, gut microbiota, and host metabolism. Questions surrounding bacterial fermentation and degradation of dietary constituents (particularly by Firmicutes and Bacteroidetes) and deciphering how microbial encoding of enzymes and derived metabolites affect recovery of dietary energy by the host are more complex than previously thought. Moreover, it is essential to understand to what extent the intestinal microbiota is subject to dietary control and to integrate these data with functional metabolic signatures and biomarkers. Many lines of research have demonstrated the significant role of the gut microbiota in human physiology and disease. Probiotic and prebiotic products are proliferating in the market in response to consumer demand, and the science and technology around these products are progressing rapidly. With high-throughput molecular technologies driving the science, studying the bidirectional interactions of host-microbial cometabolism, epithelial cell maturation, shaping of innate immune development, normal vs. dysfunctional nutrient absorption and processing, and the complex signaling pathways involved is now possible. Substantiating the safety and mechanisms of action of probiotic/prebiotic formulations is critical. Beneficial modulation of the human microbiota by using these nutritional and biotherapeutic strategies holds considerable promise as next-generation drugs, vaccinomics, and metabolic agents and in novel food discovery.}, } @article {pmid25826451, year = {2015}, author = {Gilbert, JA}, title = {Social behavior and the microbiome.}, journal = {eLife}, volume = {4}, number = {}, pages = {}, pmid = {25826451}, issn = {2050-084X}, mesh = {Animals ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metagenomics/*methods ; Papio/*microbiology ; *Social Behavior ; *Social Environment ; }, abstract = {Social interactions influence the communities of microbes that live in wild baboons.}, } @article {pmid25822599, year = {2015}, author = {Andongma, AA and Wan, L and Dong, YC and Li, P and Desneux, N and White, JA and Niu, CY}, title = {Pyrosequencing reveals a shift in symbiotic bacteria populations across life stages of Bactrocera dorsalis.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {9470}, pmid = {25822599}, issn = {2045-2322}, mesh = {Animals ; Bacteria/*classification/*genetics ; Biodiversity ; Cluster Analysis ; Life Cycle Stages ; *Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; Tephritidae/growth & development/*microbiology ; }, abstract = {Bactrocera dorsalis is one of the most economically important fruit flies around the world. In this study, 454 pyrosequencing was used to identify the bacteria associated with different developmental stages of B. dorsalis. At ≥ 97% nucleotide similarity, total reads could be assigned to 172 Operational Taxonomic Units belonging to six phyla. Proteobacteria dominated in immature stages while Firmicutes dominated in adult stages. The most abundant families were Enterococcaceae and Comamondaceae. The genus Comamonas was most abundant in pupae whereas completely absent in adults. Some identified species had low sequence similarity to reported species indicating the possibility of novel taxa. However, a majority sequence reads were similar to sequences previously identified to be associated with Bactrocera correcta, suggesting a characteristic microbial fauna for this insect genus. The type and abundance of different bacterial groups varied across the life stages of B. dorsalis. Selection pressure exerted by the host insect as a result of its habitat and diet choices could be the reason for the observed shift in the bacteria groups. These findings increase our understanding of the intricate symbiotic relationships between bacteria and B. dorsalis and provide clues to develop potential biocontrol techniques against this fruit fly.}, } @article {pmid25822072, year = {2015}, author = {Falcinelli, S and Picchietti, S and Rodiles, A and Cossignani, L and Merrifield, DL and Taddei, AR and Maradonna, F and Olivotto, I and Gioacchini, G and Carnevali, O}, title = {Lactobacillus rhamnosus lowers zebrafish lipid content by changing gut microbiota and host transcription of genes involved in lipid metabolism.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {9336}, pmid = {25822072}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Cholesterol/metabolism ; *Gastrointestinal Microbiome ; Gene Expression Regulation ; Intestinal Mucosa/metabolism/microbiology/ultrastructure ; *Lacticaseibacillus rhamnosus ; Lipid Metabolism/*genetics ; Metagenome ; Probiotics ; *Transcription, Genetic ; Triglycerides/metabolism ; Zebrafish/*genetics/growth & development/*metabolism ; }, abstract = {The microbiome plays an important role in lipid metabolism but how the introduction of probiotic communities affects host lipid metabolism is poorly understood. Using a multidisciplinary approach we addressed this knowledge gap using the zebrafish model by coupling high-throughput sequencing with biochemical, molecular and morphological analysis to evaluate the changes in the intestine. Analysis of bacterial 16S libraries revealed that Lactobacillus rhamnosus was able to modulate the gut microbiome of zebrafish larvae, elevating the abundance of Firmicutes sequences and reducing the abundance of Actinobacteria. The gut microbiome changes modulated host lipid processing by inducing transcriptional down-regulation of genes involved in cholesterol and triglycerides metabolism (fit2, agpat4, dgat2, mgll, hnf4α, scap, and cck) concomitantly decreasing total body cholesterol and triglyceride content and increasing fatty acid levels. L. rhamnosus treatment also increased microvilli and enterocyte lengths and decreased lipid droplet size in the intestinal epithelium. These changes resulted in elevated zebrafish larval growth. This integrated system investigation demonstrates probiotic modulation of the gut microbiome, highlights a novel gene network involved in lipid metabolism, provides an insight into how the microbiome regulates molecules involved in lipid metabolism, and reveals a new potential role for L. rhamnosus in the treatment of lipid disorders.}, } @article {pmid25816749, year = {2015}, author = {Plé, C and Breton, J and Daniel, C and Foligné, B}, title = {Maintaining gut ecosystems for health: Are transitory food bugs stowaways or part of the crew?.}, journal = {International journal of food microbiology}, volume = {213}, number = {}, pages = {139-143}, doi = {10.1016/j.ijfoodmicro.2015.03.015}, pmid = {25816749}, issn = {1879-3460}, mesh = {Cheese/microbiology ; Colitis/*microbiology ; *Food Microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Homeostasis ; Humans ; Metagenomics ; Probiotics/therapeutic use ; }, abstract = {Do food ecosystems feed gut ecosystems? And if so… fuel the immune system? Recent developments in metagenomics have provided researchers tools to open the "black box" of microbiome science. These novel technologies have enabled the establishment of correlations between dysbiotic microbial communities and many diseases. The complex interaction of the commensal microbiota with the immune system is a topic of substantial interest due to its relevance to health. The human gastrointestinal tract is composed of an immense number of resident and transient microorganisms. Both may play a direct and vital role in the maintenance of human health and well-being. An understanding of the interactions and mechanisms through which commensal and food-derived microbes shape host immunity and metabolism may yield new insights into the pathogenesis of many immune-mediated diseases. Consequently, by manipulating the contribution of food microbiota to the functionality of the gut ecosystem, there is great hope for development of new prophylactic and therapeutic interventions. This paper presents some insights and comments on the possible impact of exogenous fermented food microbes on the gut homeostasis. We shed light on the similar features shared by both fermented food microbes and probiotics. In particular, the key role of microbial strains as part of food ecosystems for health and diseases is discussed through the prism of fermented dairy products and gut inflammation.}, } @article {pmid25815895, year = {2015}, author = {Albanese, D and De Filippo, C and Cavalieri, D and Donati, C}, title = {Explaining diversity in metagenomic datasets by phylogenetic-based feature weighting.}, journal = {PLoS computational biology}, volume = {11}, number = {3}, pages = {e1004186}, pmid = {25815895}, issn = {1553-7358}, mesh = {Algorithms ; *Databases, Genetic ; Gastrointestinal Microbiome/genetics ; Genetic Variation/*genetics ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Phylogeny ; }, abstract = {Metagenomics is revolutionizing our understanding of microbial communities, showing that their structure and composition have profound effects on the ecosystem and in a variety of health and disease conditions. Despite the flourishing of new analysis methods, current approaches based on statistical comparisons between high-level taxonomic classes often fail to identify the microbial taxa that are differentially distributed between sets of samples, since in many cases the taxonomic schema do not allow an adequate description of the structure of the microbiota. This constitutes a severe limitation to the use of metagenomic data in therapeutic and diagnostic applications. To provide a more robust statistical framework, we introduce a class of feature-weighting algorithms that discriminate the taxa responsible for the classification of metagenomic samples. The method unambiguously groups the relevant taxa into clades without relying on pre-defined taxonomic categories, thus including in the analysis also those sequences for which a taxonomic classification is difficult. The phylogenetic clades are weighted and ranked according to their abundance measuring their contribution to the differentiation of the classes of samples, and a criterion is provided to define a reduced set of most relevant clades. Applying the method to public datasets, we show that the data-driven definition of relevant phylogenetic clades accomplished by our ranking strategy identifies features in the samples that are lost if phylogenetic relationships are not considered, improving our ability to mine metagenomic datasets. Comparison with supervised classification methods currently used in metagenomic data analysis highlights the advantages of using phylogenetic information.}, } @article {pmid25813857, year = {2015}, author = {Singh, A and Singh, DP and Tiwari, R and Kumar, K and Singh, RV and Singh, S and Prasanna, R and Saxena, AK and Nain, L}, title = {Taxonomic and functional annotation of gut bacterial communities of Eisenia foetida and Perionyx excavatus.}, journal = {Microbiological research}, volume = {175}, number = {}, pages = {48-56}, doi = {10.1016/j.micres.2015.03.003}, pmid = {25813857}, issn = {1618-0623}, mesh = {Animals ; Bacteria/*classification/*genetics/growth & development/isolation & purification ; *Biota ; Cluster Analysis ; Culture Media/chemistry ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Gastrointestinal Microbiome ; Lignin/metabolism ; Metagenome ; Molecular Sequence Data ; Oligochaeta/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Epigeic earthworms can significantly hasten the decomposition of organic matter, which is known to be mediated by gut associated microflora. However, there is scanty information on the abundance and diversity of the gut bacterial flora in different earthworm genera fed with a similar diet, particularly Eisenia foetida and Perionyx excavatus. In this context, 16S rDNA based clonal survey of gut metagenomic DNA was assessed after growth of these two earthworms on lignocellulosic biomass. A set of 67 clonal sequences belonging to E. foetida and 75 to P. excavatus were taxonomically annotated using MG-RAST and RDP pipeline servers. Highest number of sequences were annotated to Proteobacteria (38-44%), followed by unclassified bacteria (14-18%) and Firmicutes (9.3-11%). Comparative analyses revealed significantly higher abundance of Actinobacteria and Firmicutes in the gut of P. excavatus. The functional annotation for the 16S rDNA clonal libraries of both the metagenomes revealed a high abundance of xylan degraders (12.1-24.1%). However, chitin degraders (16.7%), ammonia oxidizers (24.1%) and nitrogen fixers (7.4%) were relatively higher in E. foetida, while in P. excavatus; sulphate reducers and sulphate oxidizers (12.1-29.6%) were more abundant. Lignin degradation was detected in 3.7% clones of E. foetida, while cellulose degraders represented 1.7%. The gut microbiomes showed relative abundance of dehalogenators (17.2-22.2%) and aromatic hydrocarbon degraders (1.7-5.6%), illustrating their role in bioremediation. This study highlights the significance of differences in the inherent microbiome of these two earthworms in shaping the metagenome for effective degradation of different types of biomass under tropical conditions.}, } @article {pmid25809788, year = {2015}, author = {Navarrete, AA and Tsai, SM and Mendes, LW and Faust, K and de Hollander, M and Cassman, NA and Raes, J and van Veen, JA and Kuramae, EE}, title = {Soil microbiome responses to the short-term effects of Amazonian deforestation.}, journal = {Molecular ecology}, volume = {24}, number = {10}, pages = {2433-2448}, doi = {10.1111/mec.13172}, pmid = {25809788}, issn = {1365-294X}, mesh = {Agriculture/methods ; Bacteria/*classification ; *Conservation of Natural Resources ; DNA, Bacterial/genetics ; Forests ; High-Throughput Nucleotide Sequencing ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Slash-and-burn clearing of forest typically results in increase in soil nutrient availability. However, the impact of these nutrients on the soil microbiome is not known. Using next generation sequencing of 16S rRNA gene and shotgun metagenomic DNA, we compared the structure and the potential functions of bacterial community in forest soils to deforested soils in the Amazon region and related the differences to soil chemical factors. Deforestation decreased soil organic matter content and factors linked to soil acidity and raised soil pH, base saturation and exchangeable bases. Concomitant to expected changes in soil chemical factors, we observed an increase in the alpha diversity of the bacterial microbiota and relative abundances of putative copiotrophic bacteria such as Actinomycetales and a decrease in the relative abundances of bacterial taxa such as Chlamydiae, Planctomycetes and Verrucomicrobia in the deforested soils. We did not observe an increase in genes related to microbial nutrient metabolism in deforested soils. However, we did observe changes in community functions such as increases in DNA repair, protein processing, modification, degradation and folding functions, and these functions might reflect adaptation to changes in soil characteristics due to forest clear-cutting and burning. In addition, there were changes in the composition of the bacterial groups associated with metabolism-related functions. Co-occurrence microbial network analysis identified distinct phylogenetic patterns for forest and deforested soils and suggested relationships between Planctomycetes and aluminium content, and Actinobacteria and nitrogen sources in Amazon soils. The results support taxonomic and functional adaptations in the soil bacterial community following deforestation. We hypothesize that these microbial adaptations may serve as a buffer to drastic changes in soil fertility after slash-and-burning deforestation in the Amazon region.}, } @article {pmid25807110, year = {2015}, author = {Obregon-Tito, AJ and Tito, RY and Metcalf, J and Sankaranarayanan, K and Clemente, JC and Ursell, LK and Zech Xu, Z and Van Treuren, W and Knight, R and Gaffney, PM and Spicer, P and Lawson, P and Marin-Reyes, L and Trujillo-Villarroel, O and Foster, M and Guija-Poma, E and Troncoso-Corzo, L and Warinner, C and Ozga, AT and Lewis, CM}, title = {Subsistence strategies in traditional societies distinguish gut microbiomes.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {6505}, pmid = {25807110}, issn = {2041-1723}, support = {R25 CA085771/CA/NCI NIH HHS/United States ; U54 GM104938/GM/NIGMS NIH HHS/United States ; R01 GM089886/GM/NIGMS NIH HHS/United States ; U54GM104938/GM/NIGMS NIH HHS/United States ; R01 HG005172/HG/NHGRI NIH HHS/United States ; }, mesh = {Actinobacteria/genetics/isolation & purification ; Adolescent ; Adult ; *Agriculture ; Bacteroidetes/genetics/isolation & purification ; Biodiversity ; Child ; Child, Preschool ; Classification ; Diet ; *Diet, Paleolithic ; Female ; Firmicutes/genetics/isolation & purification ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Industrial Development ; Infant ; Male ; Metagenome/genetics ; Middle Aged ; Oklahoma ; Peru ; RNA, Ribosomal, 16S/*genetics ; Treponema/genetics/isolation & purification ; Young Adult ; }, abstract = {Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. Here we examine the relationship between lifeways and gut microbiota through taxonomic and functional potential characterization of faecal samples from hunter-gatherer and traditional agriculturalist communities in Peru and an urban-industrialized community from the US. We find that in addition to taxonomic and metabolic differences between urban and traditional lifestyles, hunter-gatherers form a distinct sub-group among traditional peoples. As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2-2.5 MB, coverage depth × 26-513) and functional potential characterization, we discover these Treponema are diverse, fall outside of pathogenic clades and are similar to Treponema succinifaciens, a known carbohydrate metabolizer in swine. Gut Treponema are found in non-human primates and all traditional peoples studied to date, suggesting they are symbionts lost in urban-industrialized societies.}, } @article {pmid25803243, year = {2015}, author = {Dickson, RP and Erb-Downward, JR and Freeman, CM and McCloskey, L and Beck, JM and Huffnagle, GB and Curtis, JL}, title = {Spatial Variation in the Healthy Human Lung Microbiome and the Adapted Island Model of Lung Biogeography.}, journal = {Annals of the American Thoracic Society}, volume = {12}, number = {6}, pages = {821-830}, pmid = {25803243}, issn = {2325-6621}, support = {T32 HL007749/HL/NHLBI NIH HHS/United States ; R01HL114447/HL/NHLBI NIH HHS/United States ; I01 BX001389/BX/BLRD VA/United States ; R01 HL114447/HL/NHLBI NIH HHS/United States ; T32HL00774921/HL/NHLBI NIH HHS/United States ; U01 HL098961/HL/NHLBI NIH HHS/United States ; U01HL098961/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Bronchoalveolar Lavage/methods ; Bronchoalveolar Lavage Fluid/*microbiology ; Bronchoscopy/methods ; DNA, Bacterial/analysis ; Female ; Healthy Volunteers ; Humans ; *Lung/microbiology/pathology ; Male ; Metagenome/*physiology ; Microbiota/*physiology ; Middle Aged ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA ; Spatial Analysis ; }, abstract = {RATIONALE: The lung microbiome is spatially heterogeneous in advanced airway diseases, but whether it varies spatially in health is unknown. We postulated that the primary determinant of lung microbiome constitution in health is the balance of immigration and elimination of communities from the upper respiratory tract (URT; "adapted island model of lung biogeography"), rather than differences in regional bacterial growth conditions.

OBJECTIVES: To determine if the lung microbiome is spatially varied in healthy adults.

METHODS: Bronchoscopy was performed on 15 healthy subjects. Specimens were sequentially collected in the lingula and right middle lobe (by bronchoalveolar lavage [BAL]), then in the right upper lobe, left upper lobe, and supraglottic space (by protected-specimen brush). Bacterial 16S ribosmal RNA-encoding genes were sequenced using MiSeq (Illumina, San Diego, CA).

MEASUREMENTS AND MAIN RESULTS: There were no significant differences between specimens collected by BAL and protected-specimen brush. Spatially separated intrapulmonary sites, when compared with each other, did not contain consistently distinct microbiota. On average, intrasubject variation was significantly less than intersubject variation (P = 0.00003). By multiple ecologic parameters (community richness, community composition, intersubject variability, and similarity to source community), right upper lobe microbiota more closely resembled those of the URT than did microbiota from more distal sites. As predicted by the adapted island model, community richness decreased with increasing distance from the source community of the URT (P < 0.05).

CONCLUSIONS: In healthy lungs, spatial variation in microbiota within an individual is significantly less than variation across individuals. The lung microbiome in health is more influenced by microbial immigration and elimination (the adapted island model) than by the effects of local growth conditions on bacterial reproduction rates, which are more determinant in advanced lung diseases. BAL of a single lung segment is an acceptable method of sampling the healthy lung microbiome. Clinical trial registered with www.clinicaltrials.gov (NCT02392182).}, } @article {pmid25798135, year = {2015}, author = {Chan, CS and Chan, KG and Tay, YL and Chua, YH and Goh, KM}, title = {Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {177}, pmid = {25798135}, issn = {1664-302X}, abstract = {The Sungai Klah (SK) hot spring is the second hottest geothermal spring in Malaysia. This hot spring is a shallow, 150-m-long, fast-flowing stream, with temperatures varying from 50 to 110°C and a pH range of 7.0-9.0. Hidden within a wooded area, the SK hot spring is continually fed by plant litter, resulting in a relatively high degree of total organic content (TOC). In this study, a sample taken from the middle of the stream was analyzed at the 16S rRNA V3-V4 region by amplicon metagenome sequencing. Over 35 phyla were detected by analyzing the 16S rRNA data. Firmicutes and Proteobacteria represented approximately 57% of the microbiome. Approximately 70% of the detected thermophiles were strict anaerobes; however, Hydrogenobacter spp., obligate chemolithotrophic thermophiles, represented one of the major taxa. Several thermophilic photosynthetic microorganisms and acidothermophiles were also detected. Most of the phyla identified by 16S rRNA were also found using the shotgun metagenome approaches. The carbon, sulfur, and nitrogen metabolism within the SK hot spring community were evaluated by shotgun metagenome sequencing, and the data revealed diversity in terms of metabolic activity and dynamics. This hot spring has a rich diversified phylogenetic community partly due to its natural environment (plant litter, high TOC, and a shallow stream) and geochemical parameters (broad temperature and pH range). It is speculated that symbiotic relationships occur between the members of the community.}, } @article {pmid25792433, year = {2015}, author = {Miao, Y and Liao, R and Zhang, XX and Wang, Y and Wang, Z and Shi, P and Liu, B and Li, A}, title = {Metagenomic insights into Cr(VI) effect on microbial communities and functional genes of an expanded granular sludge bed reactor treating high-nitrate wastewater.}, journal = {Water research}, volume = {76}, number = {}, pages = {43-52}, doi = {10.1016/j.watres.2015.02.042}, pmid = {25792433}, issn = {1879-2448}, mesh = {Bacteria/*drug effects/metabolism ; Biodiversity ; *Bioreactors ; Chromium/*pharmacology ; Denitrification ; Genes, Bacterial ; Metagenomics ; Microbial Consortia ; Nitrates/*metabolism ; Sewage/*microbiology ; Waste Disposal, Fluid/*methods ; Water Purification/*methods ; }, abstract = {In this study, a lab-scale expanded granular sludge bed reactor was continuously operated to treat high-nitrate wastewater containing different concentrations of hexavalent chromium (Cr(VI)). Nearly complete nitrate removal was achieved even at 120 mg/L influent Cr(VI). Pyrosequencing of 16S rRNA gene showed that Cr(VI) decreased the biodiversity of the bacterial community and potential denitrifiers. Proteobacteria dominated in the bioreactor, and Betaproteobacteria had increased abundance after Cr(VI) feeding. Thauera and Halomonas were the two predominant genera in the bioreactor fed with Cr(VI), demonstrating opposite responses to the Cr(VI) stress. Metagenomic analysis indicated that Cr(VI) feeding posed no obvious effect on the overall function of the bacterial community, but altered the abundance of specific denitrifying genes, which was evidenced by quantitative real time PCR. This study revealed that Halomonas mainly contributed to the denitrification under no or low Cr(VI) stress, while Thauera played a more important role under high Cr(VI) stress.}, } @article {pmid25790045, year = {2015}, author = {Kapgate, SS and Barbuddhe, SB and Kumanan, K}, title = {Next generation sequencing technologies: tool to study avian virus diversity.}, journal = {Acta virologica}, volume = {59}, number = {1}, pages = {3-13}, doi = {10.4149/av_2015_01_3}, pmid = {25790045}, issn = {0001-723X}, mesh = {Animals ; Bird Diseases/*virology ; Birds ; *Genetic Variation ; High-Throughput Nucleotide Sequencing/*methods ; Host-Pathogen Interactions ; Virus Diseases/*veterinary/virology ; Viruses/*classification/*genetics/isolation & purification ; }, abstract = {Increased globalisation, climatic changes and wildlife-livestock interface led to emergence of novel viral pathogens or zoonoses that have become serious concern to avian, animal and human health. High biodiversity and bird migration facilitate spread of the pathogen and provide reservoirs for emerging infectious diseases. Current classical diagnostic methods designed to be virus-specific or aim to be limited to group of viral agents, hinder identifying of novel viruses or viral variants. Recently developed approaches of next-generation sequencing (NGS) provide culture-independent methods that are useful for understanding viral diversity and discovery of novel virus, thereby enabling a better diagnosis and disease control. This review discusses the different possible steps of a NGS study utilizing sequence-independent amplification, high-throughput sequencing and bioinformatics approaches to identify novel avian viruses and their diversity. NGS lead to the identification of a wide range of new viruses such as picobirnavirus, picornavirus, orthoreovirus and avian gamma coronavirus associated with fulminating disease in guinea fowl and is also used in describing viral diversity among avian species. The review also briefly discusses areas of viral-host interaction and disease associated causalities with newly identified avian viruses.}, } @article {pmid25786308, year = {2014}, author = {Provorov, NA and Tikhonovich, IA}, title = {[Super-species genetic systems].}, journal = {Zhurnal obshchei biologii}, volume = {75}, number = {4}, pages = {247-260}, pmid = {25786308}, issn = {0044-4596}, mesh = {Gene Transfer, Horizontal/*physiology ; Metagenome/*physiology ; Microbial Consortia/*physiology ; *Models, Biological ; Quorum Sensing/physiology ; Symbiosis/physiology ; }, abstract = {Genetic integration of diverse organisms results in generation of three types of the super-species systems of heredity: metagenome (set of genetic factors of the microbial community which occupies a certain ecological niche), symbiogenome (functionally integrated system of the partners' symbiotic genes) and hologenome (entire hereditary system of a symbiotically originated organism). The integrity of metagenome is based on the cross-regulation and horizontal transfer of genes in co-evolving organisms which in the soil microbial communities are accompanied by maintenance of the stable extracellular DNA pool. Formation of symbiogenome is related to the highly specific partners' signaling interactions which are responsible for development of the joint metabolic pathways based on the specialized cellular and tissue structures. Transitions of symbiogenome into hologenome are due to the endosymbiotic gene transfer from microsymbionts to their hosts. In symbiotic bacteria, these transitions are coupled with establishments of multi-component, reduced and rudimentary genomes revealed for the ecologically obligatory symbionts, genetically obligatory symbionts, and cellular organelles, respectively. Their evolution is related to the stringency of transmission of microsymbionts by hosts increased from pseudo-vertical (via environment) to the trans-embryonic (via embryos and the surrounding tissues) and trans-ovarian transmission (via germ cells) which are culminated in the cytoplasmic inheritance of cellular organelles. We suggest the hypothesis about generation of endophytic plant symbiogenome on the basis of soil metagenome subjected to the control of host by its involvement into the quorum sensing auto-regulation of microbial community.}, } @article {pmid25781343, year = {2015}, author = {Eaton, K and Yang, W and , }, title = {Registered report: Intestinal inflammation targets cancer-inducing activity of the microbiota.}, journal = {eLife}, volume = {4}, number = {}, pages = {}, pmid = {25781343}, issn = {2050-084X}, mesh = {Animals ; Azoxymethane/toxicity ; Carcinogens/toxicity ; Cell Transformation, Neoplastic/drug effects/genetics ; Colitis/*microbiology ; Colorectal Neoplasms/chemically induced/*microbiology ; Escherichia coli/genetics/pathogenicity ; Genomic Islands/genetics ; Interleukin-10/genetics ; Intestines/*microbiology/pathology ; Metagenome/genetics ; Mice, Knockout ; Microbiota/genetics/*physiology ; Mutation ; Polyketide Synthases/genetics ; Sequence Deletion ; Virulence/genetics ; }, abstract = {The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of 50 papers in the field of cancer biology published between 2010 and 2012. This Registered report describes the proposed replication plan of key experiments from ‘Intestinal Inflammation Targets Cancer-Inducing Activity of the Microbiota’ by Arthur et al. (2012), published in Science in 2012. Arthur and colleagues identified a genotoxic island in Escherichia coli NC101 that appeared to be responsible for causing neoplastic lesions in inflammation-induced IL10-/- mice treated with azoxymethane. The experiments that will be replicated are those reported in Figure 4 (Arthur et al., 2012). Arthur and colleagues inoculated IL10-/- mice with a mutated strain of E. coli NC101 lacking the genotoxic island, and showed that those mice suffered from fewer neoplastic lesions than mice inoculated with the wild type form of E. coli NC101 (Figure 4). The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Science and Science Exchange, and the results of the replications will be published by eLife.}, } @article {pmid25778463, year = {2015}, author = {Moissl-Eichinger, C and Auerbach, AK and Probst, AJ and Mahnert, A and Tom, L and Piceno, Y and Andersen, GL and Venkateswaran, K and Rettberg, P and Barczyk, S and Pukall, R and Berg, G}, title = {Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {9156}, pmid = {25778463}, issn = {2045-2322}, mesh = {*Air Microbiology ; *Air Pollution, Indoor ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Biodiversity ; Cluster Analysis ; *Environment, Controlled ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Space agencies maintain highly controlled cleanrooms to ensure the demands of planetary protection. To study potential effects of microbiome control, we analyzed microbial communities in two particulate-controlled cleanrooms (ISO 5 and ISO 8) and two vicinal uncontrolled areas (office, changing room) by cultivation and 16S rRNA gene amplicon analysis (cloning, pyrotagsequencing, and PhyloChip G3 analysis). Maintenance procedures affected the microbiome on total abundance and microbial community structure concerning richness, diversity and relative abundance of certain taxa. Cleanroom areas were found to be mainly predominated by potentially human-associated bacteria; archaeal signatures were detected in every area. Results indicate that microorganisms were mainly spread from the changing room (68%) into the cleanrooms, potentially carried along with human activity. The numbers of colony forming units were reduced by up to ~400 fold from the uncontrolled areas towards the ISO 5 cleanroom, accompanied with a reduction of the living portion of microorganisms from 45% (changing area) to 1% of total 16S rRNA gene signatures as revealed via propidium monoazide treatment of the samples. Our results demonstrate the strong effects of cleanroom maintenance on microbial communities in indoor environments and can be used to improve the design and operation of biologically controlled cleanrooms.}, } @article {pmid25775938, year = {2015}, author = {Maropola, MK and Ramond, JB and Trindade, M}, title = {Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench).}, journal = {Journal of microbiological methods}, volume = {112}, number = {}, pages = {104-117}, doi = {10.1016/j.mimet.2015.03.012}, pmid = {25775938}, issn = {1872-8359}, mesh = {Bacteria/classification/genetics/*isolation & purification ; *Biodiversity ; DNA/genetics/*isolation & purification ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Endophytes/classification/genetics/*isolation & purification ; Genes, rRNA ; Metagenomics/*methods ; Plant Roots/microbiology ; Plant Stems/microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; Sorghum/*microbiology ; }, abstract = {Culture-independent studies rely on the quantity and quality of the extracted environmental metagenomic DNA (mDNA). To fully access the plant tissue microbiome, the extracted plant mDNA should allow optimal PCR applications and the genetic content must be representative of the total microbial diversity. In this study, we evaluated the endophytic bacterial diversity retrieved using different mDNA extraction procedures. Metagenomic DNA from sorghum (Sorghum bicolor L. Moench) stem and root tissues were extracted using two classical DNA extraction protocols (CTAB- and SDS-based) and five commercial kits. The mDNA yields and quality as well as the reproducibility were compared. 16S rRNA gene terminal restriction fragment length polymorphism (t-RFLP) was used to assess the impact on endophytic bacterial community structures observed. Generally, the classical protocols obtained high mDNA yields from sorghum tissues; however, they were less reproducible than the commercial kits. Commercial kits retrieved higher quality mDNA, but with lower endophytic bacterial diversities compared to classical protocols. The SDS-based protocol enabled access to the highest sorghum endophytic diversities. Therefore, "SDS-extracted" sorghum root and stem microbiome diversities were analysed via 454 pyrosequencing, and this revealed that the two tissues harbour significantly different endophytic communities. Nevertheless, both communities are dominated by agriculturally important genera such as Microbacterium, Agrobacterium, Sphingobacterium, Herbaspirillum, Erwinia, Pseudomonas and Stenotrophomonas; which have previously been shown to play a role in plant growth promotion. This study shows that DNA extraction protocols introduce biases in culture-independent studies of environmental microbial communities by influencing the mDNA quality, which impacts the microbial diversity analyses and evaluation. Using the broad-spectrum SDS-based DNA extraction protocol allows the recovery of the most diverse endophytic communities associated with sorghum tissues and, as such, establishes a reliable basis for future study of endophytic communities.}, } @article {pmid25775922, year = {2015}, author = {Prince, AL and Chu, DM and Seferovic, MD and Antony, KM and Ma, J and Aagaard, KM}, title = {The perinatal microbiome and pregnancy: moving beyond the vaginal microbiome.}, journal = {Cold Spring Harbor perspectives in medicine}, volume = {5}, number = {6}, pages = {}, pmid = {25775922}, issn = {2157-1422}, support = {DP2 DP21DP2OD001500/OD/NIH HHS/United States ; T32GM007330/GM/NIGMS NIH HHS/United States ; DP2 OD001500/OD/NIH HHS/United States ; T32GM088129/GM/NIGMS NIH HHS/United States ; R01NR014792/NR/NINR NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; R01 DK089201/DK/NIDDK NIH HHS/United States ; T32 GM007330/GM/NIGMS NIH HHS/United States ; R01 NR014792/NR/NINR NIH HHS/United States ; T32 GM088129/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Bacterial/genetics ; Female ; Genome-Wide Association Study ; Humans ; Infant, Newborn ; Infectious Disease Transmission, Vertical ; Metagenomics/*methods ; Mice ; Microbiota/genetics/*physiology ; Placenta/microbiology ; Pregnancy ; Pregnancy Complications, Infectious/*microbiology ; Reproductive Health ; Vagina/*microbiology ; }, abstract = {The human microbiome, the collective genome of the microbial community that is on and within us, has recently been mapped. The initial characterization of healthy subjects has provided investigators with a reference population for interrogating the microbiome in metabolic, intestinal, and reproductive health and disease states. Although it is known that bacteria can colonize the vagina, recent metagenomic studies have shown that the vaginal microbiome varies among reproductive age women. Similarly, the richness and diversity of intestinal microbiota also naturally fluctuate among gravidae in both human and nonhuman primates, as well as mice. Moreover, recent evidence suggests that microbiome niches in pregnancy are not limited to maternal body sites, as the placenta appears to harbor a low biomass microbiome that is presumptively established in early pregnancy and varies in association with a remote history of maternal antenatal infection as well as preterm birth. In this article, we will provide a brief overview on metagenomics science as a means to investigate the microbiome, observations pertaining to both variation and the presumptive potential role of a varied microbiome during pregnancy, and how future studies of the microbiome in pregnancy may lend to a better understanding of human biology, reproductive health, and parturition.}, } @article {pmid25774601, year = {2015}, author = {Tung, J and Barreiro, LB and Burns, MB and Grenier, JC and Lynch, J and Grieneisen, LE and Altmann, J and Alberts, SC and Blekhman, R and Archie, EA}, title = {Social networks predict gut microbiome composition in wild baboons.}, journal = {eLife}, volume = {4}, number = {}, pages = {}, pmid = {25774601}, issn = {2050-084X}, support = {P2C HD065563/HD/NICHD NIH HHS/United States ; P30 AG034424/AG/NIA NIH HHS/United States ; R01 AG034513/AG/NIA NIH HHS/United States ; P2C HD047879/HD/NICHD NIH HHS/United States ; P01 AG031719/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics ; DNA, Bacterial/chemistry/genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Grooming ; Humans ; Male ; Metagenomics/*methods ; Papio/*microbiology ; Sequence Analysis, DNA ; *Social Behavior ; *Social Environment ; Species Specificity ; }, abstract = {Social relationships have profound effects on health in humans and other primates, but the mechanisms that explain this relationship are not well understood. Using shotgun metagenomic data from wild baboons, we found that social group membership and social network relationships predicted both the taxonomic structure of the gut microbiome and the structure of genes encoded by gut microbial species. Rates of interaction directly explained variation in the gut microbiome, even after controlling for diet, kinship, and shared environments. They therefore strongly implicate direct physical contact among social partners in the transmission of gut microbial species. We identified 51 socially structured taxa, which were significantly enriched for anaerobic and non-spore-forming lifestyles. Our results argue that social interactions are an important determinant of gut microbiome composition in natural animal populations-a relationship with important ramifications for understanding how social relationships influence health, as well as the evolution of group living.}, } @article {pmid25766736, year = {2015}, author = {Vervoort, J and Xavier, BB and Stewardson, A and Coenen, S and Godycki-Cwirko, M and Adriaenssens, N and Kowalczyk, A and Lammens, C and Harbarth, S and Goossens, H and Malhotra-Kumar, S}, title = {Metagenomic analysis of the impact of nitrofurantoin treatment on the human faecal microbiota.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {70}, number = {7}, pages = {1989-1992}, doi = {10.1093/jac/dkv062}, pmid = {25766736}, issn = {1460-2091}, mesh = {Anti-Infective Agents/administration & dosage/*pharmacology ; Bacteria/*classification/isolation & purification ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Longitudinal Studies ; *Metagenomics ; Microbiota/*drug effects ; Molecular Sequence Data ; Nitrofurantoin/administration & dosage/*pharmacology ; Phylogeny ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Urinary Tract Infections/drug therapy ; }, abstract = {OBJECTIVES: The objective was to study changes in the faecal microbiota of patients with uncomplicated urinary tract infections (UTIs) treated with nitrofurantoin and of non-treated healthy controls using 16S rRNA analysis.

METHODS: Serial stool samples were collected from patients receiving nitrofurantoin treatment at different timepoints [before treatment (day 1; T1), within 48 h of end of treatment (days 5-15; T2) and 28 days after treatment (days 31-43; T3)], as well as from healthy controls. Direct DNA extraction (PowerSoil DNA Isolation Kit, MoBio Laboratories, Carlsbad, CA, USA) from stool samples was followed by pyrosequencing (454 GS FLX Titanium) of the V3-V5 region of the bacterial 16S rRNA gene.

RESULTS: Among UTI patients, mean proportions of the Actinobacteria phylum increased by 19.6% in the first follow-up sample (T2) in comparison with the pretreatment baseline stool sample (T1) (P = 0.026). However, proportions of Actinobacteria reversed to 'normal' pre-antibiotic levels, with a mean difference of 1.0% compared with baseline proportions, in the second follow-up sample (T3). The increase in Actinobacteria was specifically due to an increase in the Bifidobacteriaceae family (Bifidobacterium genus), which constituted 81.0% (95% CI ±7.4%) of this phylum.

CONCLUSIONS: No significant impact was observed other than a temporary increase in the beneficial Bifidobacterium genus following nitrofurantoin treatment, which supports its reintroduction into clinical use.}, } @article {pmid25766684, year = {2015}, author = {Heath, AC}, title = {Metagenomics: a new frontier for translational research and personalized therapeutics in psychiatry?.}, journal = {Biological psychiatry}, volume = {77}, number = {7}, pages = {600-601}, doi = {10.1016/j.biopsych.2015.01.013}, pmid = {25766684}, issn = {1873-2402}, support = {K05 AA017688/AA/NIAAA NIH HHS/United States ; P01 DK078669/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Gastrointestinal Tract/*microbiology ; Male ; *Microbiota ; Obesity/*microbiology/*physiopathology ; }, } @article {pmid25764541, year = {2015}, author = {Michail, S and Lin, M and Frey, MR and Fanter, R and Paliy, O and Hilbush, B and Reo, NV}, title = {Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {2}, pages = {1-9}, pmid = {25764541}, issn = {1574-6941}, support = {R21 AT003400/AT/NCCIH NIH HHS/United States ; AT003423/AT/NCCIH NIH HHS/United States ; R01 HD081197/HD/NICHD NIH HHS/United States ; HD065575/HD/NICHD NIH HHS/United States ; R01 DK095004/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Child ; Energy Metabolism/*physiology ; Ethanol/metabolism ; Feces/microbiology ; Gammaproteobacteria/genetics ; Humans ; Intestines/*microbiology ; Male ; Metagenome/genetics ; Microbiota/*genetics ; Non-alcoholic Fatty Liver Disease/*metabolism ; Obesity/*metabolism ; Phylogeny ; Prevotella/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Obesity is becoming the new pediatric epidemic. Non-alcoholic fatty liver disease (NAFLD) is frequently associated with obesity and has become the most common cause of pediatric liver disease. The gut microbiome is the major metabolic organ and determines how calories are processed, serving as a caloric gate and contributing towards the pathogenesis of NAFLD. The goal of this study is to examine gut microbial profiles in children with NAFLD using phylogenetic, metabolomic, metagenomic and proteomic approaches. Fecal samples were obtained from obese children with or without NAFLD and healthy lean children. Stool specimens were subjected to 16S rRNA gene microarray, shotgun sequencing, mass spectroscopy for proteomics and NMR spectroscopy for metabolite analysis. Children with NAFLD had more abundant Gammaproteobacteria and Prevotella and significantly higher levels of ethanol, with differential effects on short chain fatty acids. This group also had increased genomic and protein abundance for energy production with a reduction in carbohydrate and amino acid metabolism and urea cycle and urea transport systems. The metaproteome and metagenome showed similar findings. The gut microbiome in pediatric NAFLD is distinct from lean healthy children with more alcohol production and pathways allocated to energy metabolism over carbohydrate and amino acid metabolism, which would contribute to development of disease.}, } @article {pmid25764467, year = {2015}, author = {de Voogd, NJ and Cleary, DF and Polónia, AR and Gomes, NC}, title = {Bacterial community composition and predicted functional ecology of sponges, sediment and seawater from the thousand islands reef complex, West Java, Indonesia.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {4}, pages = {}, doi = {10.1093/femsec/fiv019}, pmid = {25764467}, issn = {1574-6941}, mesh = {Actinobacteria/classification/genetics ; Animals ; Base Sequence ; Biodiversity ; Coral Reefs ; DNA, Bacterial/genetics ; Deltaproteobacteria/classification/genetics ; Ecosystem ; Geologic Sediments/*microbiology ; Indonesia ; Metagenome/genetics ; Microbial Consortia/*genetics ; Nitrogen Cycle/genetics ; Phylogeny ; Proteobacteria/classification/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Xestospongia/*microbiology ; }, abstract = {In the present study, we assessed the composition of Bacteria in four biotopes namely sediment, seawater and two sponge species (Stylissa massa and Xestospongia testudinaria) at four different reef sites in a coral reef ecosystem in West Java, Indonesia. In addition to this, we used a predictive metagenomic approach to estimate to what extent nitrogen metabolic pathways differed among bacterial communities from different biotopes. We observed marked differences in bacterial composition of the most abundant bacterial phyla, classes and orders among sponge species, water and sediment. Proteobacteria were by far the most abundant phylum in terms of both sequences and Operational Taxonomic Units (OTUs). Predicted counts for genes associated with the nitrogen metabolism suggested that several genes involved in the nitrogen cycle were enriched in sponge samples, including nosZ, nifD, nirK, norB and nrfA genes. Our data show that a combined barcoded pyrosequencing and predictive metagenomic approach can provide novel insights into the potential ecological functions of the microbial communities. Not only is this approach useful for our understanding of the vast microbial diversity found in sponges but also to understand the potential response of microbial communities to environmental change.}, } @article {pmid25764459, year = {2015}, author = {Liljeqvist, M and Ossandon, FJ and González, C and Rajan, S and Stell, A and Valdes, J and Holmes, DS and Dopson, M}, title = {Metagenomic analysis reveals adaptations to a cold-adapted lifestyle in a low-temperature acid mine drainage stream.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {4}, pages = {}, doi = {10.1093/femsec/fiv011}, pmid = {25764459}, issn = {1574-6941}, mesh = {Acclimatization/genetics ; Acidithiobacillus/classification/*genetics/isolation & purification ; Amino Acid Sequence ; Antifreeze Proteins/genetics ; Base Sequence ; Biofilms/growth & development ; Chemoautotrophic Growth ; Cold Temperature ; Cold-Shock Response/genetics ; DNA, Bacterial/genetics ; Gallionellaceae/classification/*genetics/isolation & purification ; Hydrogen-Ion Concentration ; Iron/metabolism ; Metagenome/*genetics ; Microbial Consortia ; Nitrogen Fixation/genetics ; Oxidation-Reduction ; Oxidative Stress/genetics ; Phylogeny ; Plankton/classification/*genetics ; Rivers ; Sequence Analysis, DNA ; Sweden ; Wastewater/*microbiology ; }, abstract = {An acid mine drainage (pH 2.5-2.7) stream biofilm situated 250 m below ground in the low-temperature (6-10°C) Kristineberg mine, northern Sweden, contained a microbial community equipped for growth at low temperature and acidic pH. Metagenomic sequencing of the biofilm and planktonic fractions identified the most abundant microorganism to be similar to the psychrotolerant acidophile, Acidithiobacillus ferrivorans. In addition, metagenome contigs were most similar to other Acidithiobacillus species, an Acidobacteria-like species, and a Gallionellaceae-like species. Analyses of the metagenomes indicated functional characteristics previously characterized as related to growth at low temperature including cold-shock proteins, several pathways for the production of compatible solutes and an anti-freeze protein. In addition, genes were predicted to encode functions related to pH homeostasis and metal resistance related to growth in the acidic metal-containing mine water. Metagenome analyses identified microorganisms capable of nitrogen fixation and exhibiting a primarily autotrophic lifestyle driven by the oxidation of the ferrous iron and inorganic sulfur compounds contained in the sulfidic mine waters. The study identified a low diversity of abundant microorganisms adapted to a low-temperature acidic environment as well as identifying some of the strategies the microorganisms employ to grow in this extreme environment.}, } @article {pmid25761675, year = {2015}, author = {Chen, H and Liu, Y and Zhang, M and Wang, G and Qi, Z and Bridgewater, L and Zhao, L and Tang, Z and Pang, X}, title = {A Filifactor alocis-centered co-occurrence group associates with periodontitis across different oral habitats.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {9053}, pmid = {25761675}, issn = {2045-2322}, mesh = {Adult ; Aged ; Case-Control Studies ; *Gram-Positive Cocci/classification/genetics ; Humans ; Metagenome ; Microbiota ; Middle Aged ; *Oral Hygiene ; Periodontitis/diagnosis/*epidemiology/*etiology ; Phylogeny ; ROC Curve ; Young Adult ; }, abstract = {Periodontitis is a highly prevalent polymicrobial disease worldwide, yet the synergistic pattern of the multiple oral pathogens involved is still poorly characterized. Here, saliva, supragingival and subgingival plaque samples from periodontitis patients and periodontally healthy volunteers were collected and profiled with 16S rRNA gene pyrosequencing. Different oral habitats harbored significantly different microbiota, and segregation of microbiota composition between periodontitis and health was observed as well. Two-step redundancy analysis identified twenty-one OTUs, including Porphyromonas gingivalis, Tannerella forsythia and Filifactor alocis, as potential pathogens that were significantly associated with periodontitis and with two periodontitis diagnostic parameters (pocket depth and attachment loss) in both saliva and supragingival plaque habitats. Interestingly, pairwise correlation analysis among the 21 OTUs revealed that Filifactor alocis was positively correlated with seven other putative pathogens (R > 0.6, P < 0.05), forming a co-occurrence group that was remarkably enriched in all three habitats of periodontitis patients. This bacterial cluster showed a higher diagnostic value for periodontitis than did any individual potential pathogens, especially in saliva. Thus, our study identified a potential synergistic ecological pattern involving eight co-infecting pathogens across various oral habitats, providing a new framework for understanding the etiology of periodontitis and developing new diagnoses and therapies.}, } @article {pmid25758642, year = {2015}, author = {Feng, Q and Liang, S and Jia, H and Stadlmayr, A and Tang, L and Lan, Z and Zhang, D and Xia, H and Xu, X and Jie, Z and Su, L and Li, X and Li, X and Li, J and Xiao, L and Huber-Schönauer, U and Niederseer, D and Xu, X and Al-Aama, JY and Yang, H and Wang, J and Kristiansen, K and Arumugam, M and Tilg, H and Datz, C and Wang, J}, title = {Gut microbiome development along the colorectal adenoma-carcinoma sequence.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {6528}, doi = {10.1038/ncomms7528}, pmid = {25758642}, issn = {2041-1723}, mesh = {Actinobacteria/classification/genetics/isolation & purification ; Adenomatous Polyps/etiology/metabolism/*microbiology/pathology ; Aged ; Aged, 80 and over ; Bacteroidetes/classification/genetics/isolation & purification ; Case-Control Studies ; Colorectal Neoplasms/etiology/metabolism/*microbiology/pathology ; Diet ; Disease Progression ; Feces/microbiology ; Female ; Firmicutes/classification/genetics/isolation & purification ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; *Metagenome ; Middle Aged ; Proteobacteria/classification/genetics/isolation & purification ; Red Meat/adverse effects ; Risk Factors ; Vegetables/chemistry ; }, abstract = {Colorectal cancer, a commonly diagnosed cancer in the elderly, often develops slowly from benign polyps called adenoma. The gut microbiota is believed to be directly involved in colorectal carcinogenesis. The identity and functional capacity of the adenoma- or carcinoma-related gut microbe(s), however, have not been surveyed in a comprehensive manner. Here we perform a metagenome-wide association study (MGWAS) on stools from advanced adenoma and carcinoma patients and from healthy subjects, revealing microbial genes, strains and functions enriched in each group. An analysis of potential risk factors indicates that high intake of red meat relative to fruits and vegetables appears to associate with outgrowth of bacteria that might contribute to a more hostile gut environment. These findings suggest that faecal microbiome-based strategies may be useful for early diagnosis and treatment of colorectal adenoma or carcinoma.}, } @article {pmid25758319, year = {2015}, author = {MacIntyre, DA and Chandiramani, M and Lee, YS and Kindinger, L and Smith, A and Angelopoulos, N and Lehne, B and Arulkumaran, S and Brown, R and Teoh, TG and Holmes, E and Nicoholson, JK and Marchesi, JR and Bennett, PR}, title = {The vaginal microbiome during pregnancy and the postpartum period in a European population.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {8988}, pmid = {25758319}, issn = {2045-2322}, support = {MR/L009226/1//Medical Research Council/United Kingdom ; }, mesh = {Adult ; Bacteria/classification/genetics ; Biodiversity ; Ethnicity ; Female ; Gestational Age ; Humans ; Metagenome ; *Microbiota ; *Postpartum Period ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; United Kingdom ; Vagina/*microbiology ; *White People ; }, abstract = {The composition and structure of the pregnancy vaginal microbiome may influence susceptibility to adverse pregnancy outcomes. Studies on the pregnant vaginal microbiome have largely been limited to Northern American populations. Using MiSeq sequencing of 16S rRNA gene amplicons, we characterised the vaginal microbiota of a mixed British cohort of women (n = 42) who experienced uncomplicated term delivery and who were sampled longitudinally throughout pregnancy (8-12, 20-22, 28-30 and 34-36 weeks gestation) and 6 weeks postpartum. We show that vaginal microbiome composition dramatically changes postpartum to become less Lactobacillus spp. dominant with increased alpha-diversity irrespective of the community structure during pregnancy and independent of ethnicity. While the pregnancy vaginal microbiome was characteristically dominated by Lactobacillus spp. and low alpha-diversity, unlike Northern American populations, a significant number of pregnant women this British population had a L. jensenii-dominated microbiome characterised by low alpha-diversity. L. jensenii was predominantly observed in women of Asian and Caucasian ethnicity whereas L. gasseri was absent in samples from Black women. This study reveals new insights into biogeographical and ethnic effects upon the pregnancy and postpartum vaginal microbiome and has important implications for future studies exploring relationships between the vaginal microbiome, host health and pregnancy outcomes.}, } @article {pmid25758166, year = {2015}, author = {Ansari, MI and Harb, M and Jones, B and Hong, PY}, title = {Molecular-based approaches to characterize coastal microbial community and their potential relation to the trophic state of Red Sea.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {9001}, pmid = {25758166}, issn = {2045-2322}, mesh = {Geography ; Humans ; Indian Ocean ; Metagenome ; Microbiota ; Molecular Sequence Data ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {Molecular-based approaches were used to characterize the coastal microbiota and to elucidate the trophic state of Red Sea. Nutrient content and enterococci numbers were monitored, and used to correlate with the abundance of microbial markers. Microbial source tracking revealed the presence of >1 human-associated Bacteroides spp. at some of the near-shore sampling sites and at a heavily frequented beach. Water samples collected from the beaches had occasional exceedances in enterococci numbers, higher total organic carbon (TOC, 1.48-2.18 mg/L) and nitrogen (TN, 0.15-0.27 mg/L) than that detected in the near-shore waters. Enterococci abundances obtained from next-generation sequencing did not correlate well with the cultured enterococci numbers. The abundance of certain genera, for example Arcobacter, Pseudomonas and unclassified Campylobacterales, was observed to exhibit slight correlation with TOC and TN. Low abundance of functional genes accounting for up to 41 copies/L of each Pseudomonas aeruginosa and Campylobacter coli were detected. Arcobacter butzleri was also detected in abundance ranging from 111 to 238 copies/L. Operational taxonomic units (OTUs) associated with cyanobacteria, Prochlorococcus, Ostreococcus spp. and Gramella were more prevalent in waters that were likely impacted by urban runoffs and recreational activities. These OTUs could potentially serve as quantifiable markers indicative of the water quality.}, } @article {pmid25756118, year = {2014}, author = {Tsementzi, D and Poretsky, R and Rodriguez-R, LM and Luo, C and Konstantinidis, KT}, title = {Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities.}, journal = {Environmental microbiology reports}, volume = {6}, number = {6}, pages = {640-655}, doi = {10.1111/1758-2229.12180}, pmid = {25756118}, issn = {1758-2229}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; DNA, Bacterial/genetics ; Ecosystem ; Fresh Water/*microbiology ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Metatranscriptomics of environmental samples enables the identification of community activities without a priori knowledge of taxonomic or functional composition. However, several technical challenges associated with the RNA preparation protocols can affect the relative representation of transcripts and data interpretation. Here, seven replicate metatranscriptomes from planktonic freshwater samples (Lake Lanier, USA) were sequenced to evaluate technical and biological reproducibility of different RNA extraction protocols. Organic versus bead-beating extraction showed significant enrichment for low versus high G + C% mRNA populations respectively. The sequencing data were best modelled by a negative binomial distribution to account for the large technical and biological variation observed. Despite the variation, the transcriptional activities of populations that persisted in year-round metagenomes from the same site consistently showed distinct expression patterns, reflecting different ecologic strategies and allowing us to test prevailing models on the contribution of both rare biosphere and abundant members to community activity. For instance, abundant members of the Verrucomicrobia phylum systematically showed low transcriptional activity compared with other abundant taxa. Our results provide a practical guide to the analysis of metatranscriptomes and advance understanding of the activity and ecology of abundant and rare members of temperate freshwater microbial communities.}, } @article {pmid25754179, year = {2015}, author = {Lax, S and Nagler, CR and Gilbert, JA}, title = {Our interface with the built environment: immunity and the indoor microbiota.}, journal = {Trends in immunology}, volume = {36}, number = {3}, pages = {121-123}, pmid = {25754179}, issn = {1471-4981}, support = {R01 AI106302/AI/NIAID NIH HHS/United States ; }, mesh = {Ecological Systems, Closed ; Environment ; Environment Design/trends ; Humans ; *Immunity ; Information Dissemination ; Metagenome/*immunology ; Microbiota/*immunology ; Social Media ; Symbiosis/*immunology ; Urbanization/trends ; }, abstract = {The rise of urbanization and an increasingly indoor lifestyle has affected human interactions with our microbiota in unprecedented ways. We discuss how this lifestyle may influence immune development and function, and argue that it is time that we examined ways to manipulate the indoor environment to increase our exposure to a wider phylogeny of microorganisms. An important step is to continue to engage citizen scientists in the efforts to characterize our interactions with the diverse microbial environments that we inhabit.}, } @article {pmid25753751, year = {2015}, author = {Quandt, CA and Kohler, A and Hesse, CN and Sharpton, TJ and Martin, F and Spatafora, JW}, title = {Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome.}, journal = {Environmental microbiology}, volume = {17}, number = {8}, pages = {2952-2968}, doi = {10.1111/1462-2920.12840}, pmid = {25753751}, issn = {1462-2920}, mesh = {Base Sequence ; Bradyrhizobiaceae/classification/*genetics ; DNA Transposable Elements/genetics ; DNA, Fungal/*genetics ; Eurotiales/classification/*genetics ; Fruiting Bodies, Fungal/*genetics ; Genome, Fungal/*genetics ; *Metagenome ; Metagenomics ; Microbiota/genetics ; Mycorrhizae/genetics ; Phylogeny ; Sequence Analysis, DNA ; Talaromyces/genetics ; }, abstract = {Many obligate symbiotic fungi are difficult to maintain in culture, and there is a growing need for alternative approaches to obtaining tissue and subsequent genomic assemblies from such species. In this study, the genome of Elaphomyces granulatus was sequenced from sporocarp tissue. The genome assembly remains on many contigs, but gene space is estimated to be mostly complete. Phylogenetic analyses revealed that the Elaphomyces lineage is most closely related to Talaromyces and Trichocomaceae s.s. The genome of E. granulatus is reduced in carbohydrate-active enzymes, despite a large expansion in genome size, both of which are consistent with what is seen in Tuber melanosporum, the other sequenced ectomycorrhizal ascomycete. A large number of transposable elements are predicted in the E. granulatus genome, especially Gypsy-like long terminal repeats, and there has also been an expansion in helicases. The metagenome is a complex community dominated by bacteria in Bradyrhizobiaceae, and there is evidence to suggest that the community may be reduced in functional capacity as estimated by KEGG pathways. Through the sequencing of sporocarp tissue, this study has provided insights into Elaphomyces phylogenetics, genomics, metagenomics and the evolution of the ectomycorrhizal association.}, } @article {pmid25749835, year = {2015}, author = {Hacard, F and Nosbaum, A and Huynh, VA and Nicolas, JF and Bérard, F}, title = {[Diversity of cutaneous bacteria decreases inflammation].}, journal = {Annales de dermatologie et de venereologie}, volume = {142 Suppl 1}, number = {}, pages = {S13-7}, doi = {10.1016/S0151-9638(15)30002-8}, pmid = {25749835}, issn = {0151-9638}, mesh = {Humans ; Inflammation/*immunology ; *Microbiota ; Skin/*microbiology ; }, abstract = {Human microbiota includes all microorganisms, saprophytes and pathogens that colonize our bodies. Recent advances in metagenomic analysis techniques have expanded our knowledge of the microbiota and fundamentally changed our view of its relationships with the immune system. The commensal flora appears to be essential to the development of the immune system, and the diversity of the microbiota is correlated with good health status of individuals. These findings open up new conceptual and therapeutic approaches in chronic inflammatory diseases.}, } @article {pmid25748152, year = {2015}, author = {Ohno, H}, title = {[Impact of gut microbiota on host physiology and pathology].}, journal = {Nihon Shokakibyo Gakkai zasshi = The Japanese journal of gastro-enterology}, volume = {112}, number = {2}, pages = {264-269}, doi = {10.11405/nisshoshi.112.264}, pmid = {25748152}, issn = {0446-6586}, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Mice ; T-Lymphocytes, Regulatory/physiology ; }, } @article {pmid25745868, year = {2015}, author = {Agga, GE and Scott, HM and Vinasco, J and Nagaraja, TG and Amachawadi, RG and Bai, J and Norby, B and Renter, DG and Dritz, SS and Nelssen, JL and Tokach, MD}, title = {Effects of chlortetracycline and copper supplementation on the prevalence, distribution, and quantity of antimicrobial resistance genes in the fecal metagenome of weaned pigs.}, journal = {Preventive veterinary medicine}, volume = {119}, number = {3-4}, pages = {179-189}, doi = {10.1016/j.prevetmed.2015.02.008}, pmid = {25745868}, issn = {1873-1716}, mesh = {Animal Feed/analysis ; Animals ; Anti-Bacterial Agents/administration & dosage/*pharmacology ; Cephalosporins/pharmacology ; Chlortetracycline/administration & dosage/*pharmacology ; Copper/administration & dosage/*pharmacology ; Diet/veterinary ; Dietary Supplements/analysis ; *Drug Resistance, Bacterial ; Gastrointestinal Microbiome/*drug effects ; Male ; Polymerase Chain Reaction/veterinary ; Random Allocation ; *Selection, Genetic ; Sus scrofa/*microbiology ; }, abstract = {Use of in-feed antibiotics such as chlortetracycline (CTC) in food animals is fiercely debated as a cause of antimicrobial resistance in human pathogens; as a result, alternatives to antibiotics such as heavy metals have been proposed. We used a total community DNA approach to experimentally investigate the effects of CTC and copper supplementation on the presence and quantity of antimicrobial resistance elements in the gut microbial ecology of pigs. Total community DNA was extracted from 569 fecal samples collected weekly over a 6-week period from groups of 5 pigs housed in 32 pens that were randomized to receive either control, CTC, copper, or copper plus CTC regimens. Qualitative and quantitative PCR were used to detect the presence of 14 tetracycline resistance (tet) genes and to quantify gene copies of tetA, tetB, blaCMY-2 (a 3rd generation cephalosporin resistance gene), and pcoD (a copper resistance gene), respectively. The detection of tetA and tetB decreased over the subsequent sampling periods, whereas the prevalence of tetC and tetP increased. CTC and copper plus CTC supplementation increased both the prevalence and gene copy numbers of tetA, while decreasing both the prevalence and gene copies of tetB. In summary, tet gene presence was initially very diverse in the gut bacterial community of weaned pigs; thereafter, copper and CTC supplementation differentially impacted the prevalence and quantity of the various tetracycline, ceftiofur and copper resistance genes resulting in a less diverse gene population.}, } @article {pmid25743945, year = {2015}, author = {Nasrollahzadeh, D and Malekzadeh, R and Ploner, A and Shakeri, R and Sotoudeh, M and Fahimi, S and Nasseri-Moghaddam, S and Kamangar, F and Abnet, CC and Winckler, B and Islami, F and Boffetta, P and Brennan, P and Dawsey, SM and Ye, W}, title = {Variations of gastric corpus microbiota are associated with early esophageal squamous cell carcinoma and squamous dysplasia.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {8820}, pmid = {25743945}, issn = {2045-2322}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Aged ; Biodiversity ; Carcinoma, Squamous Cell/*etiology/*pathology ; Case-Control Studies ; Esophageal Neoplasms/*etiology/*pathology ; Esophageal Squamous Cell Carcinoma ; Female ; Gastric Mucosa/*microbiology/pathology ; Humans ; Male ; Metagenome ; *Microbiota ; Middle Aged ; Neoplasm Staging ; *Precancerous Conditions ; }, abstract = {Observational studies revealed a relationship between changes in gastric mucosa and risk of esophageal squamous cell carcinoma (ESCC) which suggested a possible role for gastric microbiota in ESCC carcinogenesis. In this study we aimed to compare pattern of gastric corpus microbiota in ESCC with normal esophagus. Cases were included subjects with early ESCC (stage I-II) and esophageal squamous dysplasia (ESD) as the cancer precursor. Control groups included age and sex-matched subjects with mid-esophagus esophagitis (diseased-control), and histologically normal esophagus (healthy-control). DNA was extracted from snap-frozen gastric corpus tissues and 16S rRNA was sequenced on GS-FLX Titanium. After noise removal, an average of 3004 reads per sample was obtained from 93 subjects. We applied principal coordinate analysis to ordinate distances from beta diversity data. Pattern of gastric microbiota using Unifrac (p = 0.004) and weighted Unifrac distances (p = 0.018) statistically varied between cases and healthy controls. Sequences were aligned to SILVA database and Clostridiales and Erysipelotrichales orders were more abundant among cases after controling for multiple testing (p = 0.011). No such difference was observed between mid-esophagitis and healthy controls. This study is the first to show that composition of gastric corpus mucosal microbiota differs in early ESCC and ESD from healthy esophagus.}, } @article {pmid25740652, year = {2015}, author = {Schnell, IB and Bohmann, K and Gilbert, MT}, title = {Tag jumps illuminated--reducing sequence-to-sample misidentifications in metabarcoding studies.}, journal = {Molecular ecology resources}, volume = {15}, number = {6}, pages = {1289-1303}, doi = {10.1111/1755-0998.12402}, pmid = {25740652}, issn = {1755-0998}, mesh = {Animals ; Chiroptera/microbiology ; DNA Barcoding, Taxonomic/*methods ; *Diagnostic Errors ; *Environmental Microbiology ; Feces/microbiology ; Gastrointestinal Microbiome ; Leeches/microbiology ; Metagenomics/*methods ; }, abstract = {Metabarcoding of environmental samples on second-generation sequencing platforms has rapidly become a valuable tool for ecological studies. A fundamental assumption of this approach is the reliance on being able to track tagged amplicons back to the samples from which they originated. In this study, we address the problem of sequences in metabarcoding sequencing outputs with false combinations of used tags (tag jumps). Unless these sequences can be identified and excluded from downstream analyses, tag jumps creating sequences with false, but already used tag combinations, can cause incorrect assignment of sequences to samples and artificially inflate diversity. In this study, we document and investigate tag jumping in metabarcoding studies on Illumina sequencing platforms by amplifying mixed-template extracts obtained from bat droppings and leech gut contents with tagged generic arthropod and mammal primers, respectively. We found that an average of 2.6% and 2.1% of sequences had tag combinations, which could be explained by tag jumping in the leech and bat diet study, respectively. We suggest that tag jumping can happen during blunt-ending of pools of tagged amplicons during library build and as a consequence of chimera formation during bulk amplification of tagged amplicons during library index PCR. We argue that tag jumping and contamination between libraries represents a considerable challenge for Illumina-based metabarcoding studies, and suggest measures to avoid false assignment of tag jumping-derived sequences to samples.}, } @article {pmid25740621, year = {2015}, author = {Tsurumaru, H and Okubo, T and Okazaki, K and Hashimoto, M and Kakizaki, K and Hanzawa, E and Takahashi, H and Asanome, N and Tanaka, F and Sekiyama, Y and Ikeda, S and Minamisawa, K}, title = {Metagenomic analysis of the bacterial community associated with the taproot of sugar beet.}, journal = {Microbes and environments}, volume = {30}, number = {1}, pages = {63-69}, pmid = {25740621}, issn = {1347-4405}, mesh = {Bacteria/*classification/*genetics ; Beta vulgaris/*microbiology ; *Biodiversity ; DNA, Bacterial/chemistry/genetics ; Metabolic Networks and Pathways/*genetics ; Metagenomics ; Molecular Sequence Data ; Plant Roots/*microbiology ; Sequence Analysis, DNA ; }, abstract = {We analyzed a metagenome of the bacterial community associated with the taproot of sugar beet (Beta vulgaris L.) in order to investigate the genes involved in plant growth-promoting traits (PGPTs), namely 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, indole acetic acid (IAA), N2 fixation, phosphate solubilization, pyrroloquinoline quinone, siderophores, and plant disease suppression as well as methanol, sucrose, and betaine utilization. The most frequently detected gene among the PGPT categories encoded β-1,3-glucanase (18 per 10(5) reads), which plays a role in the suppression of plant diseases. Genes involved in phosphate solubilization (e.g., for quinoprotein glucose dehydrogenase), methanol utilization (e.g., for methanol dehydrogenase), siderophore production (e.g. isochorismate pyruvate lyase), and ACC deaminase were also abundant. These results suggested that such PGPTs are crucially involved in supporting the growth of sugar beet. In contrast, genes for IAA production (iaaM and ipdC) were less abundant (~1 per 10(5) reads). N2 fixation genes (nifHDK) were not detected; bacterial N2 -fixing activity was not observed in the (15)N2 -feeding experiment. An analysis of nitrogen metabolism suggested that the sugar beet microbiome mainly utilized ammonium and nitroalkane as nitrogen sources. Thus, N2 fixation and IAA production did not appear to contribute to sugar beet growth. Taxonomic assignment of this metagenome revealed the high abundance of Mesorhizobium, Bradyrhizobium, and Streptomyces, suggesting that these genera have ecologically important roles in the taproot of sugar beet. Bradyrhizobium-assigned reads in particular were found in almost all categories of dominant PGPTs with high abundance. The present study revealed the characteristic functional genes in the taproot-associated microbiome of sugar beet, and suggest the opportunity to select sugar beet growth-promoting bacteria.}, } @article {pmid25739499, year = {2015}, author = {Hultman, J and Waldrop, MP and Mackelprang, R and David, MM and McFarland, J and Blazewicz, SJ and Harden, J and Turetsky, MR and McGuire, AD and Shah, MB and VerBerkmoes, NC and Lee, LH and Mavrommatis, K and Jansson, JK}, title = {Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes.}, journal = {Nature}, volume = {521}, number = {7551}, pages = {208-212}, pmid = {25739499}, issn = {1476-4687}, mesh = {Alaska ; Atmosphere/chemistry ; Carbon Cycle ; Climate ; Denitrification ; Freezing ; Genome, Bacterial/*genetics ; Iron/metabolism ; Metagenome/*genetics ; Methane/metabolism ; Microbiota/genetics/*physiology ; Nitrates/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Permafrost/*microbiology ; Phylogeny ; Seasons ; *Soil Microbiology ; Sulfur/metabolism ; Time Factors ; *Wetlands ; }, abstract = {Over 20% of Earth's terrestrial surface is underlain by permafrost with vast stores of carbon that, once thawed, may represent the largest future transfer of carbon from the biosphere to the atmosphere. This process is largely dependent on microbial responses, but we know little about microbial activity in intact, let alone in thawing, permafrost. Molecular approaches have recently revealed the identities and functional gene composition of microorganisms in some permafrost soils and a rapid shift in functional gene composition during short-term thaw experiments. However, the fate of permafrost carbon depends on climatic, hydrological and microbial responses to thaw at decadal scales. Here we use the combination of several molecular 'omics' approaches to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog. The multi-omics strategy reveals a good correlation of process rates to omics data for dominant processes, such as methanogenesis in the bog, as well as novel survival strategies for potentially active microbes in permafrost.}, } @article {pmid25736916, year = {2015}, author = {Faure, D and Joly, D}, title = {Next-generation sequencing as a powerful motor for advances in the biological and environmental sciences.}, journal = {Genetica}, volume = {143}, number = {2}, pages = {129-132}, pmid = {25736916}, issn = {1573-6857}, mesh = {Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Ecology/methods ; Gene Expression Profiling ; Genomics ; High-Throughput Nucleotide Sequencing/*methods ; }, abstract = {Next-generation sequencing (NGS) provides unprecedented insight into (meta)genomes, (meta)transcriptomes (cDNA) and (meta)barcodes of individuals, populations and communities of Archaea, Bacteria and Eukarya, as well as viruses. This special issue combines reviews and original papers reporting technical and scientific advances in genomics and transcriptomics of non-model species, as well as quantification and functional analyses of biodiversity using NGS technologies of the second and third generations. In addition, certain papers also exemplify the transition from Sanger to NGS barcodes in molecular taxonomy.}, } @article {pmid25733079, year = {2015}, author = {Ushio, M and Yamasaki, E and Takasu, H and Nagano, AJ and Fujinaga, S and Honjo, MN and Ikemoto, M and Sakai, S and Kudoh, H}, title = {Microbial communities on flower surfaces act as signatures of pollinator visitation.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {8695}, pmid = {25733079}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Environmental Microbiology ; Flowers/*microbiology ; Insecta/microbiology ; Metagenome ; *Microbiota ; *Pollination ; }, abstract = {Microbes are easily dispersed from one place to another, and immigrant microbes might contain information about the environments from which they came. We hypothesized that part of the microbial community on a flower's surface is transferred there from insect body surfaces and that this community can provide information to identify potential pollinator insects of that plant. We collected insect samples from the field, and found that an insect individual harbored an average of 12.2 × 10(5) microbial cells on its surface. A laboratory experiment showed that the microbial community composition on a flower surface changed after contact with an insect, suggesting that microbes are transferred from the insect to the flower. Comparison of the microbial fingerprint approach and direct visual observation under field condition suggested that the microbial community on a flower surface could to some extent indicate the structure of plant-pollinator interactions. In conclusion, species-specific insect microbial communities specific to insect species can be transferred from an insect body to a flower surface, and these microbes can serve as a "fingerprint" of the insect species, especially for large-bodied insects. Dispersal of microbes is a ubiquitous phenomenon that has unexpected and novel applications in many fields and disciplines.}, } @article {pmid25732610, year = {2015}, author = {Bahcall, OG}, title = {Metagenomics: Urban microbiome.}, journal = {Nature reviews. Genetics}, volume = {16}, number = {4}, pages = {194}, doi = {10.1038/nrg3921}, pmid = {25732610}, issn = {1471-0064}, mesh = {Humans ; Metagenome ; *Metagenomics ; Microbiota ; }, } @article {pmid25732259, year = {2015}, author = {Cobo-Díaz, JF and Fernández-González, AJ and Villadas, PJ and Robles, AB and Toro, N and Fernández-López, M}, title = {Metagenomic assessment of the potential microbial nitrogen pathways in the rhizosphere of a mediterranean forest after a wildfire.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {895-904}, pmid = {25732259}, issn = {1432-184X}, mesh = {*Fires ; *Forests ; *Metagenome ; Microbiota/*genetics ; Nitrogen/*metabolism ; Quercus/metabolism/microbiology ; Rhizosphere ; *Soil Microbiology ; Spain ; }, abstract = {Wildfires are frequent in the forests of the Mediterranean Basin and have greatly influenced this ecosystem. Changes to the physical and chemical properties of the soil, due to fire and post-fire conditions, result in alterations of both the bacterial communities and the nitrogen cycle. We explored the effects of a holm oak forest wildfire on the rhizospheric bacterial communities involved in the nitrogen cycle. Metagenomic data of the genes involved in the nitrogen cycle showed that both the undisturbed and burned rhizospheres had a conservative nitrogen cycle with a larger number of sequences related to the nitrogen incorporation pathways and a lower number for nitrogen output. However, the burned rhizosphere showed a statistically significant increase in the number of sequences for nitrogen incorporation (allantoin utilization and nitrogen fixation) and a significantly lower number of sequences for denitrification and dissimilatory nitrite reductase subsystems, possibly in order to compensate for nitrogen loss from the soil after burning. The genetic potential for nitrogen incorporation into the ecosystem was assessed through the diversity of the nitrogenase reductase enzyme, which is encoded by the nifH gene. We found that nifH gene diversity and richness were lower in burned than in undisturbed rhizospheric soils. The structure of the bacterial communities involved in the nitrogen cycle showed a statistically significant increase of Actinobacteria and Firmicutes phyla after the wildfire. Both approaches showed the important role of gram-positive bacteria in the ecosystem after a wildfire.}, } @article {pmid25732064, year = {2015}, author = {Bulgarelli, D and Garrido-Oter, R and Münch, PC and Weiman, A and Dröge, J and Pan, Y and McHardy, AC and Schulze-Lefert, P}, title = {Structure and function of the bacterial root microbiota in wild and domesticated barley.}, journal = {Cell host & microbe}, volume = {17}, number = {3}, pages = {392-403}, pmid = {25732064}, issn = {1934-6069}, support = {323094/ERC_/European Research Council/International ; }, mesh = {Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Hordeum/*microbiology ; Metagenomics ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The microbial communities inhabiting the root interior of healthy plants, as well as the rhizosphere, which consists of soil particles firmly attached to roots, engage in symbiotic associations with their host. To investigate the structural and functional diversification among these communities, we employed a combination of 16S rRNA gene profiling and shotgun metagenome analysis of the microbiota associated with wild and domesticated accessions of barley (Hordeum vulgare). Bacterial families Comamonadaceae, Flavobacteriaceae, and Rhizobiaceae dominate the barley root-enriched microbiota. Host genotype has a small, but significant, effect on the diversity of root-associated bacterial communities, possibly representing a footprint of barley domestication. Traits related to pathogenesis, secretion, phage interactions, and nutrient mobilization are enriched in the barley root-associated microbiota. Strikingly, protein families assigned to these same traits showed evidence of positive selection. Our results indicate that the combined action of microbe-microbe and host-microbe interactions drives microbiota differentiation at the root-soil interface.}, } @article {pmid25731033, year = {2014}, author = {Kadnikov, VV and Mardanov, AV and Beleckiĭ, AV and Karnachuk, OV and Ravin, NV}, title = {[Characteristics of the new plasmid, pMTB1, from the metagenome of the microbial community of underground thermal waters of Western Siberia].}, journal = {Izvestiia Akademii nauk. Seriia biologicheskaia}, volume = {}, number = {3}, pages = {236-240}, pmid = {25731033}, issn = {1026-3470}, mesh = {Archaea/genetics ; Base Sequence ; DNA Replication ; Groundwater/*microbiology ; Metagenome ; Microbiota/*genetics ; Plasmids/genetics/*isolation & purification ; Siberia ; }, abstract = {A new circular 4935-bp long plasmid pMTB1 has been identified in sequences of the metagenome. The nucleotide sequence of pMTB1 is highly similar to that of plasmids, pME2001 and pME2200, from the methanogenic archaeon Methanothermobacter marburgensis. One of six putative protein-coding genes encodes a protein containing helix-turn-helix and ATP/GTP-binding motifs and, probably, functioning as a replication initiator protein. Homologs of other genes have been found only in the plasmids of M. marburgensis, but their functions are unknown. Comparison of the complete nucleotide sequences of the plasmids pMTB1, pME2001, and pME2200 has revealed that they have a common origin but differ from each other by the presence of several inserts flanked by nearly perfect direct repeats within regions not essential for replication.}, } @article {pmid25727367, year = {2016}, author = {Emerson, JB and Thomas, BC and Alvarez, W and Banfield, JF}, title = {Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla.}, journal = {Environmental microbiology}, volume = {18}, number = {6}, pages = {1686-1703}, doi = {10.1111/1462-2920.12817}, pmid = {25727367}, issn = {1462-2920}, mesh = {Archaea/classification/*genetics/isolation & purification/metabolism ; Bacteria/classification/*genetics/isolation & purification/metabolism ; Biodiversity ; Carbon Cycle ; Carbon Dioxide/*metabolism ; Chemoautotrophic Growth ; Metagenome ; Metagenomics ; Phylogeny ; Sulfur/metabolism ; }, abstract = {Research on geologic carbon sequestration raises questions about potential impacts of subsurface microbiota on carbon cycling and biogeochemistry. Subsurface, high-CO2 systems are poorly biologically characterized, partly because of difficulty accessing high-volume, uncontaminated samples. CO2 -driven Crystal Geyser (CG, Utah, USA), an established geologic carbon sequestration analogue, provides high volumes of deep (∼ 200-500 m) subsurface fluids. We explored microbial diversity and metabolic potential in this high-CO2 environment by assembly and analysis of metagenomes recovered from geyser water filtrate. The system is dominated by neutrophilic, iron-oxidizing bacteria, including 'marine' Mariprofundus (Zetaproteobacteria) and 'freshwater' Gallionellales, sulfur-oxidizing Thiomicrospira crunogena and Thiobacillus-like Hydrogenophilales. Near-complete genomes were reconstructed for these bacteria. CG is notably populated by a wide diversity of bacteria and archaea from phyla lacking isolated representatives (candidate phyla) and from as-yet undefined lineages. Many bacteria affiliate with OD1, OP3, OP9, PER, ACD58, WWE3, BD1-5, OP11, TM7 and ZB2. The recovery of nearly 100 genes encoding ribulose-1,5 bisphosphate carboxylase-oxygenase subunit proteins of the Calvin cycle and AMP salvage pathways suggests a strong biological role in high-CO2 subsurface carbon cycling. Overall, we predict microbial impacts on subsurface biogeochemistry via iron, sulfur, and complex carbon oxidation, carbon and nitrogen fixation, fermentation, hydrogen metabolism, and aerobic and anaerobic respiration.}, } @article {pmid25722081, year = {2015}, author = {Young, JM and Weyrich, LS and Clarke, LJ and Cooper, A}, title = {Residual soil DNA extraction increases the discriminatory power between samples.}, journal = {Forensic science, medicine, and pathology}, volume = {11}, number = {2}, pages = {268-272}, pmid = {25722081}, issn = {1556-2891}, mesh = {DNA, Bacterial/*isolation & purification ; DNA, Fungal/*isolation & purification ; DNA, Ribosomal Spacer/genetics ; Forensic Sciences/methods ; High-Throughput Nucleotide Sequencing ; Humans ; Hydrogen-Ion Concentration ; Metagenomics ; Polymerase Chain Reaction ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Forensic soil analysis relies on capturing an accurate and reproducible representation of the diversity from limited quantities of soil; however, inefficient DNA extraction can markedly alter the taxonomic abundance. The performance of a standard commercial DNA extraction kit (MOBIO PowerSoil DNA Isolation kit) and three modified protocols of this kit: soil pellet re-extraction (RE); an additional 24-h lysis incubation step at room temperature (RT); and 24-h lysis incubation step at 55°C (55) were compared using high-throughput sequencing of the internal transcribed spacer I ribosomal DNA. DNA yield was not correlated with fungal diversity and the four DNA extraction methods displayed distinct fungal community profiles for individual samples, with some phyla detected exclusively using the modified methods. Application of a 24 h lysis step will provide a more complete inventory of fungal biodiversity, and re-extraction of the residual soil pellet offers a novel tool for increasing discriminatory power between forensic soil samples.}, } @article {pmid25721729, year = {2015}, author = {Ramond, JB and Lako, JD and Stafford, WH and Tuffin, MI and Cowan, DA}, title = {Evidence of novel plant-species specific ammonia oxidizing bacterial clades in acidic South African fynbos soils.}, journal = {Journal of basic microbiology}, volume = {55}, number = {8}, pages = {1040-1047}, doi = {10.1002/jobm.201400933}, pmid = {25721729}, issn = {1521-4028}, mesh = {Ammonia/*metabolism ; Betaproteobacteria/*classification/genetics/*isolation & purification ; Biodiversity ; Gene Library ; Nitrification ; Nitrogen/metabolism ; Oxidation-Reduction ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; Proteaceae/*microbiology ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; South Africa ; }, abstract = {Ammonia-oxidizing bacteria (AOB) are essential in the biogeochemical cycling of nitrogen as they catalyze the rate-limiting oxidation of ammonia into nitrite. Since their first isolation in the late 19th century, chemolithoautotrophic AOBs have been identified in a wide range of natural (e.g., soils, sediments, estuarine, and freshwaters) and man created or impacted habitats (e.g., wastewater treatment plants and agricultural soils). However, little is known on the plant-species association of AOBs, particularly in the nutrient-starved fynbos terrestrial biome. In this study, we evaluated the diversity of AOBs in the plant canopy of three South African fynbos-specific plant species, namely Leucadendron xanthoconus, Leucospermum truncatulum and Leucadendron microcephalum, through the construction of amoA-gene clone libraries. Our results clearly demonstrate that plant-species specific and monophyletic AOB clades are present in fynbos canopy soils.}, } @article {pmid25721682, year = {2015}, author = {Luef, B and Frischkorn, KR and Wrighton, KC and Holman, HY and Birarda, G and Thomas, BC and Singh, A and Williams, KH and Siegerist, CE and Tringe, SG and Downing, KH and Comolli, LR and Banfield, JF}, title = {Diverse uncultivated ultra-small bacterial cells in groundwater.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {6372}, doi = {10.1038/ncomms7372}, pmid = {25721682}, issn = {2041-1723}, mesh = {Bacteria/*genetics/*ultrastructure ; Base Sequence ; Cryoelectron Microscopy ; Filtration ; Genome Size/genetics ; Groundwater/*microbiology ; Microbiota/*genetics ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; *Water Microbiology ; }, abstract = {Bacteria from phyla lacking cultivated representatives are widespread in natural systems and some have very small genomes. Here we test the hypothesis that these cells are small and thus might be enriched by filtration for coupled genomic and ultrastructural characterization. Metagenomic analysis of groundwater that passed through a ~0.2-μm filter reveals a wide diversity of bacteria from the WWE3, OP11 and OD1 candidate phyla. Cryogenic transmission electron microscopy demonstrates that, despite morphological variation, cells consistently have small cell size (0.009±0.002 μm(3)). Ultrastructural features potentially related to cell and genome size minimization include tightly packed spirals inferred to be DNA, few densely packed ribosomes and a variety of pili-like structures that might enable inter-organism interactions that compensate for biosynthetic capacities inferred to be missing from genomic data. The results suggest that extremely small cell size is associated with these relatively common, yet little known organisms.}, } @article {pmid25721383, year = {2015}, author = {Yan, Q and Bi, Y and Deng, Y and He, Z and Wu, L and Van Nostrand, JD and Shi, Z and Li, J and Wang, X and Hu, Z and Yu, Y and Zhou, J}, title = {Impacts of the Three Gorges Dam on microbial structure and potential function.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {8605}, pmid = {25721383}, issn = {2045-2322}, mesh = {Biodiversity ; China ; Genes, Bacterial ; Genetic Variation ; Phytoplankton/physiology ; Proteobacteria/physiology ; Rivers/*microbiology ; Sequence Analysis, DNA ; *Water Microbiology ; Water Quality ; }, abstract = {The Three Gorges Dam has significantly altered ecological and environmental conditions within the reservoir region, but how these changes affect bacterioplankton structure and function is unknown. Here, three widely accepted metagenomic tools were employed to study the impact of damming on the bacterioplankton community in the Xiangxi River. Our results indicated that bacterioplankton communities were both taxonomically and functionally different between backwater and riverine sites, which represent communities with and without direct dam effects, respectively. There were many more nitrogen cycling Betaproteobacteria (e.g., Limnohabitans), and a higher abundance of functional genes and KEGG orthology (KO) groups involved in nitrogen cycling in the riverine sites, suggesting a higher level of bacterial activity involved in generating more nitrogenous nutrients for the growth of phytoplankton. Additionally, the KO categories involved in carbon and sulfur metabolism, as well as most of the detected functional genes also showed clear backwater and riverine patterns. As expected, these diversity patterns all significantly correlated with environmental characteristics, confirming that the bacterioplankton communities in the Xiangxi River were really affected by environmental changes from the Three Gorges Dam. This study provides a first comparative metagenomic insight for evaluating the impacts of the large dam on microbial function.}, } @article {pmid25715277, year = {2015}, author = {Grogan, D}, title = {The microbes within.}, journal = {Nature}, volume = {518}, number = {7540}, pages = {S2}, doi = {10.1038/518S2a}, pmid = {25715277}, issn = {1476-4687}, mesh = {Health ; Humans ; Intestines/immunology/microbiology/physiology ; Metagenome/genetics ; Microbiota/genetics/immunology/*physiology ; Symbiosis ; }, } @article {pmid25714833, year = {2015}, author = {Erlacher, A and Cardinale, M and Grube, M and Berg, G}, title = {Biotic stress shifted structure and abundance of Enterobacteriaceae in the lettuce microbiome.}, journal = {PloS one}, volume = {10}, number = {2}, pages = {e0118068}, pmid = {25714833}, issn = {1932-6203}, mesh = {Animals ; *Antibiosis ; Enterobacteriaceae/*classification/genetics ; Gastropoda ; Lactuca/*microbiology/parasitology ; Metagenome ; *Microbiota ; Plant Leaves/microbiology/parasitology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil Microbiology ; }, abstract = {Lettuce cultivars are not only amongst the most popular vegetables eaten raw, they are also involved in severe pathogen outbreaks world-wide. While outbreaks caused by Enterobacteriaceae species are well-studied, less is known about their occurrence in natural environments as well as the impact of biotic stress. Here, we studied the ecology of the human health-relevant bacterial family Enterobacteriaceae and assessed the impact of biotic disturbances by a soil-borne phytopathogenic fungus and Gastropoda on their structure and abundance in mesocosm and pot experiments. Using a polyphasic approach including network analyses of 16S rRNA gene amplicon libraries, quantitative PCR and complementary fluorescence in situ hybridization (FISH) microscopy we found substantial yet divergent Enterobacteriaceae communities. A similar spectrum of 14 genera was identified from rhizo- and phyllospheres but the abundance of Enterobacteriaceae was on average 3fold higher in phyllosphere samples. Both stress factors shifted the bacterial community of the leaf habitat, characterized by increases of species abundance and diversity. For the rhizosphere, we observed significant structural shifts of Enterobacteriaceae communities but also a high degree of resilience. These results could be confirmed by FISH microscopy but it was difficult to visualize phyllosphere communities. Additional inoculation experiments with Escherichia coli as model revealed their presence below the wax layer as well as in the endosphere of leaves. The observed presence influenced by stress factors and the endophytic life style of Enterobacteriaceae on lettuce can be an important aspect in relation to human health.}, } @article {pmid25714355, year = {2015}, author = {Bézy, VS and Valverde, RA and Plante, CJ}, title = {Olive ridley sea turtle hatching success as a function of the microbial abundance in nest sand at Ostional, Costa Rica.}, journal = {PloS one}, volume = {10}, number = {2}, pages = {e0118579}, pmid = {25714355}, issn = {1932-6203}, mesh = {Animals ; Costa Rica ; Metagenome ; *Microbiota ; *Nesting Behavior ; Temperature ; *Turtles ; }, abstract = {Several studies have suggested that significant embryo mortality is caused by microbes, while high microbial loads are generated by the decomposition of eggs broken by later nesting turtles. This occurs commonly when nesting density is high, especially during mass nesting events (arribadas). However, no previous research has directly quantified microbial abundance and the associated effects on sea turtle hatching success at a nesting beach. The aim of this study was to test the hypothesis that the microbial abundance in olive ridley sea turtle nest sand affects the hatching success at Ostional, Costa Rica. We applied experimental treatments to alter the microbial abundance within the sand into which nests were relocated. We monitored temperature, oxygen, and organic matter content throughout the incubation period and quantified the microbial abundance within the nest sand using a quantitative polymerase chain reaction (qPCR) molecular analysis. The most successful treatment in increasing hatching success was the removal and replacement of nest sand. We found a negative correlation between hatching success and fungal abundance (fungal 18S rRNA gene copies g(-1) nest sand). Of secondary importance in determining hatching success was the abundance of bacteria (bacterial 16S rRNA gene copies g(-1) g(-1) nest sand). Our data are consistent with the hypothesis that high microbial activity is responsible for the lower hatching success observed at Ostional beach. Furthermore, the underlying mechanism appears to be the deprivation of oxygen and exposure to higher temperatures resulting from microbial decomposition in the nest.}, } @article {pmid25712554, year = {2015}, author = {Menzel, P and Gudbergsdóttir, SR and Rike, AG and Lin, L and Zhang, Q and Contursi, P and Moracci, M and Kristjansson, JK and Bolduc, B and Gavrilov, S and Ravin, N and Mardanov, A and Bonch-Osmolovskaya, E and Young, M and Krogh, A and Peng, X}, title = {Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {411-424}, pmid = {25712554}, issn = {1432-184X}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; China ; Ecosystem ; Hot Springs/*microbiology ; Iceland ; Italy ; Metagenomics/*methods ; Russia ; Sequence Analysis, DNA ; Temperature ; United States ; }, abstract = {Hot springs are natural habitats for thermophilic Archaea and Bacteria. In this paper, we present the metagenomic analysis of eight globally distributed terrestrial hot springs from China, Iceland, Italy, Russia, and the USA with a temperature range between 61 and 92 (∘)C and pH between 1.8 and 7. A comparison of the biodiversity and community composition generally showed a decrease in biodiversity with increasing temperature and decreasing pH. Another important factor shaping microbial diversity of the studied sites was the abundance of organic substrates. Several species of the Crenarchaeal order Thermoprotei were detected, whereas no single bacterial species was found in all samples, suggesting a better adaptation of certain archaeal species to different thermophilic environments. Two hot springs show high abundance of Acidithiobacillus, supporting the idea of a true thermophilic Acidithiobacillus species that can thrive in hyperthermophilic environments. Depending on the sample, up to 58 % of sequencing reads could not be assigned to a known phylum, reinforcing the fact that a large number of microorganisms in nature, including those thriving in hot environments remain to be isolated and characterized.}, } @article {pmid25709557, year = {2015}, author = {Tully, BJ and Emerson, JB and Andrade, K and Brocks, JJ and Allen, EE and Banfield, JF and Heidelberg, KB}, title = {De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2015}, number = {}, pages = {875784}, pmid = {25709557}, issn = {1472-3654}, mesh = {*Biodiversity ; Euryarchaeota/*classification/*genetics/isolation & purification ; Gene Order ; Genes, Archaeal ; Lakes/*microbiology ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Metagenomics ; Sequence Analysis, DNA ; Synteny ; Victoria ; }, abstract = {Hypersaline systems near salt saturation levels represent an extreme environment, in which organisms grow and survive near the limits of life. One of the abundant members of the microbial communities in hypersaline systems is the square archaeon, Haloquadratum walsbyi. Utilizing a short-read metagenome from Lake Tyrrell, a hypersaline ecosystem in Victoria, Australia, we performed a comparative genomic analysis of H. walsbyi to better understand the extent of variation between strains/subspecies. Results revealed that previously isolated strains/subspecies do not fully describe the complete repertoire of the genomic landscape present in H. walsbyi. Rearrangements, insertions, and deletions were observed for the Lake Tyrrell derived Haloquadratum genomes and were supported by environmental de novo sequences, including shifts in the dominant genomic landscape of the two most abundant strains. Analysis pertaining to halomucins indicated that homologs for this large protein are not a feature common for all species of Haloquadratum. Further, we analyzed ATP-binding cassette transporters (ABC-type transporters) for evidence of niche partitioning between different strains/subspecies. We were able to identify unique and variable transporter subunits from all five genomes analyzed and the de novo environmental sequences, suggesting that differences in nutrient and carbon source acquisition may play a role in maintaining distinct strains/subspecies.}, } @article {pmid25708646, year = {2015}, author = {Wood-Charlson, EM and Weynberg, KD and Suttle, CA and Roux, S and van Oppen, MJ}, title = {Metagenomic characterization of viral communities in corals: mining biological signal from methodological noise.}, journal = {Environmental microbiology}, volume = {17}, number = {10}, pages = {3440-3449}, doi = {10.1111/1462-2920.12803}, pmid = {25708646}, issn = {1462-2920}, mesh = {Animals ; Anthozoa/*virology ; *Coral Reefs ; DNA/genetics ; DNA Viruses/*genetics/isolation & purification ; DNA, Single-Stranded/genetics ; Dinoflagellida/virology ; Eukaryotic Cells/virology ; Genome, Viral/*genetics ; Metagenomics ; Microbial Consortia/*genetics ; RNA Viruses/*genetics/isolation & purification ; Symbiosis/genetics ; Transcriptome ; }, abstract = {Reef-building corals form close associations with organisms from all three domains of life and therefore have many potential viral hosts. Yet knowledge of viral communities associated with corals is barely explored. This complexity presents a number of challenges in terms of the metagenomic assessments of coral viral communities and requires specialized methods for purification and amplification of viral nucleic acids, as well as virome annotation. In this minireview, we conduct a meta-analysis of the limited number of existing coral virome studies, as well as available coral transcriptome and metagenome data, to identify trends and potential complications inherent in different methods. The analysis shows that the method used for viral nucleic acid isolation drastically affects the observed viral assemblage and interpretation of the results. Further, the small number of viral reference genomes available, coupled with short sequence read lengths might cause errors in virus identification. Despite these limitations and potential biases, the data show that viral communities associated with corals are diverse, with double- and single-stranded DNA and RNA viruses. The identified viruses are dominated by double-stranded DNA-tailed bacteriophages, but there are also viruses that infect eukaryote hosts, likely the endosymbiotic dinoflagellates, Symbiodinium spp., host coral and other eukaryotes in close association.}, } @article {pmid25706044, year = {2015}, author = {Kowallik, V and Miller, E and Greig, D}, title = {The interaction of Saccharomyces paradoxus with its natural competitors on oak bark.}, journal = {Molecular ecology}, volume = {24}, number = {7}, pages = {1596-1610}, pmid = {25706044}, issn = {1365-294X}, mesh = {Antibiosis ; Bacteroidetes/growth & development ; Biota ; DNA, Fungal/genetics/isolation & purification ; *Ecosystem ; High-Throughput Nucleotide Sequencing ; Metagenome ; Plant Bark/*microbiology ; Pseudomonas/growth & development ; Quercus/*microbiology ; Saccharomyces/*growth & development/isolation & purification ; Sequence Analysis, DNA ; }, abstract = {The natural history of the model yeast Saccharomyces cerevisiae is poorly understood and confounded by domestication. In nature, S. cerevisiae and its undomesticated relative S. paradoxus are usually found on the bark of oak trees, a habitat very different from wine or other human fermentations. It is unclear whether the oak trees are really the primary habitat for wild yeast, or whether this apparent association is due to biased sampling. We use culturing and high-throughput environmental sequencing to show that S. paradoxus is a very rare member of the oak bark microbial community. We find that S. paradoxus can grow well on sterile medium made from oak bark, but that its growth is strongly suppressed when the other members of the community are present. We purified a set of twelve common fungal and bacterial species from the oak bark community and tested how each affected the growth of S. paradoxus in direct competition on oak bark medium at summer and winter temperatures, identifying both positive and negative interactions. One Pseudomonas species produces a diffusible toxin that suppresses S. paradoxus as effectively as either the whole set of twelve species together or the complete community present in nonsterilized oak medium. Conversely, one of the twelve species, Mucilaginibacter sp., had the opposite effect and promoted S. paradoxus growth at low temperatures. We conclude that, in its natural oak tree habitat, S. paradoxus is a rare species whose success depends on the much more abundant microbial species surrounding it.}, } @article {pmid25705611, year = {2015}, author = {Thompson, AL and Monteagudo-Mera, A and Cadenas, MB and Lampl, ML and Azcarate-Peril, MA}, title = {Milk- and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {5}, number = {}, pages = {3}, pmid = {25705611}, issn = {2235-2988}, support = {P30 DK034987/DK/NIDDK NIH HHS/United States ; K01 HD071948-01/HD/NICHD NIH HHS/United States ; K01 HD071948/HD/NICHD NIH HHS/United States ; R24 HD050924/HD/NICHD NIH HHS/United States ; 5 R24 HD050924/HD/NICHD NIH HHS/United States ; P30 DK34987/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; Breast Feeding ; Child Day Care Centers/statistics & numerical data ; Cohort Studies ; Feces/microbiology ; *Feeding Methods ; Female ; Gastrointestinal Tract/metabolism/*microbiology ; Humans ; Infant ; Male ; *Microbiota ; Milk, Human/metabolism ; Phylogeny ; }, abstract = {The development of the infant intestinal microbiome in response to dietary and other exposures may shape long-term metabolic and immune function. We examined differences in the community structure and function of the intestinal microbiome between four feeding groups, exclusively breastfed infants before introduction of solid foods (EBF), non-exclusively breastfed infants before introduction of solid foods (non-EBF), EBF infants after introduction of solid foods (EBF+S), and non-EBF infants after introduction of solid foods (non-EBF+S), and tested whether out-of-home daycare attendance was associated with differences in relative abundance of gut bacteria. Bacterial 16S rRNA amplicon sequencing was performed on 49 stool samples collected longitudinally from a cohort of 9 infants (5 male, 4 female). PICRUSt metabolic inference analysis was used to identify metabolic impacts of feeding practices on the infant gut microbiome. Sequencing data identified significant differences across groups defined by feeding and daycare attendance. Non-EBF and daycare-attending infants had higher diversity and species richness than EBF and non-daycare attending infants. The gut microbiome of EBF infants showed increased proportions of Bifidobacterium and lower abundance of Bacteroidetes and Clostridiales than non-EBF infants. PICRUSt analysis indicated that introduction of solid foods had a marginal impact on the microbiome of EBF infants (24 enzymes overrepresented in EBF+S infants). In contrast, over 200 bacterial gene categories were overrepresented in non-EBF+S compared to non-EBF infants including several bacterial methyl-accepting chemotaxis proteins (MCP) involved in signal transduction. The identified differences between EBF and non-EBF infants suggest that breast milk may provide the gut microbiome with a greater plasticity (despite having a lower phylogenetic diversity) that eases the transition into solid foods.}, } @article {pmid25703686, year = {2015}, author = {Nakayama, J and Watanabe, K and Jiang, J and Matsuda, K and Chao, SH and Haryono, P and La-Ongkham, O and Sarwoko, MA and Sujaya, IN and Zhao, L and Chen, KT and Chen, YP and Chiu, HH and Hidaka, T and Huang, NX and Kiyohara, C and Kurakawa, T and Sakamoto, N and Sonomoto, K and Tashiro, K and Tsuji, H and Chen, MJ and Leelavatcharamas, V and Liao, CC and Nitisinprasert, S and Rahayu, ES and Ren, FZ and Tsai, YC and Lee, YK}, title = {Diversity in gut bacterial community of school-age children in Asia.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {8397}, pmid = {25703686}, issn = {2045-2322}, mesh = {Asia ; Bacteroides/classification/genetics/*isolation & purification ; Bifidobacterium/classification/genetics/*isolation & purification ; Bile Acids and Salts/biosynthesis ; *Biodiversity ; Carbohydrate Metabolism ; Child ; Cluster Analysis ; DNA, Bacterial/analysis ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenome ; Phylogeny ; Prevotella/classification/genetics/*isolation & purification ; Principal Component Analysis ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Asia differs substantially among and within its regions populated by diverse ethnic groups, which maintain their own respective cultures and dietary habits. To address the diversity in their gut microbiota, we characterized the bacterial community in fecal samples obtained from 303 school-age children living in urban or rural regions in five countries spanning temperate and tropical areas of Asia. The microbiota profiled for the 303 subjects were classified into two enterotype-like clusters, each driven by Prevotella (P-type) or Bifidobacterium/Bacteroides (BB-type), respectively. Majority in China, Japan and Taiwan harbored BB-type, whereas those from Indonesia and Khon Kaen in Thailand mainly harbored P-type. The P-type microbiota was characterized by a more conserved bacterial community sharing a greater number of type-specific phylotypes. Predictive metagenomics suggests higher and lower activity of carbohydrate digestion and bile acid biosynthesis, respectively, in P-type subjects, reflecting their high intake of diets rich in resistant starch. Random-forest analysis classified their fecal species community as mirroring location of resident country, suggesting eco-geographical factors shaping gut microbiota. In particular, children living in Japan harbored a less diversified microbiota with high abundance of Bifidobacterium and less number of potentially pathogenic bacteria, which may reflect their living environment and unique diet.}, } @article {pmid25702727, year = {2015}, author = {Walker, B and Kassim, K and Stokes, LD}, title = {The microbiome: a contributor to health and disease.}, journal = {Journal of health care for the poor and underserved}, volume = {26}, number = {1}, pages = {62-72}, doi = {10.1353/hpu.2015.0025}, pmid = {25702727}, issn = {1548-6869}, mesh = {Cardiovascular Diseases/microbiology ; Human Genome Project ; Humans ; Intestines/microbiology ; Irritable Bowel Syndrome/microbiology ; *Metagenome ; *Microbiota ; Neoplasms/microbiology ; Obesity/microbiology ; Renal Insufficiency, Chronic/microbiology ; }, abstract = {As the 21st century unfolds there is substantial evidence that biological research is experiencing extraordinary scientific and technological advances. Prominent among these advances are the completion of the Human Genome Project, which laid the foundation for the second advance, the Human Microbiome Project. Emerging from these advances are two overarching conclusions: a) genomics is no longer the sole domain of the geneticist, and b) we each are hosts to trillions of microorganisms. Genomics and other technologies have enhanced efforts to characterize the structure, composition, and functions of the microbiome. This characterization has fueled progress in understanding the role of the microbiome in health and disease. In this review, we highlight developments that have helped illuminate the microbiome-health connection. This information can improve an understanding of connections and relationships among multiple factors (or determinants) of health.}, } @article {pmid25702576, year = {2015}, author = {Castelle, CJ and Wrighton, KC and Thomas, BC and Hug, LA and Brown, CT and Wilkins, MJ and Frischkorn, KR and Tringe, SG and Singh, A and Markillie, LM and Taylor, RC and Williams, KH and Banfield, JF}, title = {Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling.}, journal = {Current biology : CB}, volume = {25}, number = {6}, pages = {690-701}, doi = {10.1016/j.cub.2015.01.014}, pmid = {25702576}, issn = {1879-0445}, mesh = {Anaerobiosis/genetics ; Archaea/classification/*genetics/*metabolism ; Biodiversity ; Carbon Cycle/*genetics ; *Genome, Archaeal ; Metagenomics ; Models, Biological ; Models, Genetic ; Phylogeny ; }, abstract = {BACKGROUND: Archaea represent a significant fraction of Earth's biodiversity, yet they remain much less well understood than Bacteria. Gene surveys, a few metagenomic studies, and some single-cell sequencing projects have revealed numerous little-studied archaeal phyla. Certain lineages appear to branch deeply and may be part of a major phylum radiation. The structure of this radiation and the physiology of the organisms remain almost unknown.

RESULTS: We used genome-resolved metagenomic analyses to investigate the diversity, genomes sizes, metabolic capacities, and potential roles of Archaea in terrestrial subsurface biogeochemical cycles. We sequenced DNA from complex sediment and planktonic consortia from an aquifer adjacent to the Colorado River (USA) and reconstructed the first complete genomes for Archaea using cultivation-independent methods. To provide taxonomic context, we analyzed an additional 151 newly sampled archaeal sequences. We resolved two new phyla within a major, apparently deep-branching group of phyla (a superphylum). The organisms have small genomes, and metabolic predictions indicate that their primary contributions to Earth's biogeochemical cycles involve carbon and hydrogen metabolism, probably associated with symbiotic and/or fermentation-based lifestyles.

CONCLUSIONS: The results dramatically expand genomic sampling of the domain Archaea and clarify taxonomic designations within a major superphylum. This study, in combination with recently published work on bacterial phyla lacking cultivated representatives, reveals a fascinating phenomenon of major radiations of organisms with small genomes, novel proteome composition, and strong interdependence in both domains.}, } @article {pmid25700157, year = {2015}, author = {Han, X and Yang, Y and Yan, H and Wang, X and Qu, L and Chen, Y}, title = {Rumen bacterial diversity of 80 to 110-day-old goats using 16S rRNA sequencing.}, journal = {PloS one}, volume = {10}, number = {2}, pages = {e0117811}, pmid = {25700157}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/*genetics ; *Biodiversity ; Computational Biology ; Goats/*microbiology ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The ability of rumen microorganisms to use fibrous plant matter plays an important role in ruminant animals; however, little information about rumen colonization by microbial populations after weaning has been reported. In this study, high-throughput sequencing was used to investigate the establishment of this microbial population in 80 to 110-day-old goats. Illumina sequencing of goat rumen samples yielded 101,356,610 nucleotides that were assembled into 256,868 reads with an average read length of 394 nucleotides. Taxonomic analysis of metagenomic reads indicated that the predominant phyla were distinct at different growth stages. The phyla Firmicutes and Synergistetes were predominant in samples taken from 80 to 100-day-old goats, but Bacteroidetes and Firmicutes became the most abundant phyla in samples from 110-day-old animals. There was a remarkable variation in the microbial populations with age; Firmicutes and Synergistetes decreased after weaning, but Bacteroidetes and Proteobacteria increased from 80 to 110 day of age. These findings suggested that colonization of the rumen by microorganisms is related to their function in the rumen digestive system. These results give a better understanding of the role of rumen microbes and the establishment of the microbial population, which help to maintain the host's health and improve animal performance.}, } @article {pmid25691586, year = {2015}, author = {Shi, B and Chang, M and Martin, J and Mitreva, M and Lux, R and Klokkevold, P and Sodergren, E and Weinstock, GM and Haake, SK and Li, H}, title = {Dynamic changes in the subgingival microbiome and their potential for diagnosis and prognosis of periodontitis.}, journal = {mBio}, volume = {6}, number = {1}, pages = {e01926-14}, pmid = {25691586}, issn = {2150-7511}, support = {R01 DE021574/DE/NIDCR NIH HHS/United States ; RC1 DE020298/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; *Biota ; Gingiva/*microbiology ; Humans ; Longitudinal Studies ; Metagenomics ; Middle Aged ; Periodontitis/*diagnosis/*microbiology ; Predictive Value of Tests ; Sequence Analysis, DNA ; Tooth Root/*microbiology ; }, abstract = {UNLABELLED: The human microbiome influences and reflects the health or disease state of the host. Periodontitis, a disease affecting about half of American adults, is associated with alterations in the subgingival microbiome of individual tooth sites. Although it can be treated, the disease can reoccur and may progress without symptoms. Without prognostic markers, follow-up examinations are required to assess reoccurrence and disease progression and to determine the need for additional treatments. To better identify and predict the disease progression, we aim to determine whether the subgingival microbiome can serve as a diagnosis and prognosis indicator. Using metagenomic shotgun sequencing, we characterized the dynamic changes in the subgingival microbiome in periodontitis patients before and after treatment at the same tooth sites. At the taxonomic composition level, the periodontitis-associated microorganisms were significantly shifted from highly correlated in the diseased state to poorly correlated after treatment, suggesting that coordinated interactions among the pathogenic microorganisms are essential to disease pathogenesis. At the functional level, we identified disease-associated pathways that were significantly altered in relative abundance in the two states. Furthermore, using the subgingival microbiome profile, we were able to classify the samples to their clinical states with an accuracy of 81.1%. Follow-up clinical examination of the sampled sites supported the predictive power of the microbiome profile on disease progression. Our study revealed the dynamic changes in the subgingival microbiome contributing to periodontitis and suggested potential clinical applications of monitoring the subgingival microbiome as an indicator in disease diagnosis and prognosis.

IMPORTANCE: Periodontitis is a common oral disease. Although it can be treated, the disease may reoccur without obvious symptoms. Current clinical examination parameters are useful in disease diagnosis but cannot adequately predict the outcome of individual tooth sites after treatment. A link between the subgingival microbiota and periodontitis was identified previously; however, it remains to be investigated whether the microbiome can serve as a diagnostic and prognostic indicator. In this study, for the first time, we characterized the subgingival microbiome of individual tooth sites before and after treatment using a large-scale metagenomic analysis. Our longitudinal study revealed changes in the microbiota in taxonomic composition, cooccurrence of subgingival microorganisms, and functional composition. Using the microbiome profiles, we were able to classify the clinical states of subgingival plaque samples with a high accuracy. Follow-up clinical examination of sampled sites indicates that the subgingival microbiome profile shows promise for the development of diagnostic and prognostic tools.}, } @article {pmid25689026, year = {2015}, author = {Rodriguez-R, LM and Overholt, WA and Hagan, C and Huettel, M and Kostka, JE and Konstantinidis, KT}, title = {Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill.}, journal = {The ISME journal}, volume = {9}, number = {9}, pages = {1928-1940}, pmid = {25689026}, issn = {1751-7370}, mesh = {Alphaproteobacteria/classification ; Biodiversity ; Ecosystem ; Environmental Monitoring/methods ; Environmental Pollutants/*analysis ; Florida ; Gammaproteobacteria/classification ; Gulf of Mexico ; Hydrocarbons/analysis ; Metagenomics ; Petroleum/*analysis ; Petroleum Pollution/*analysis ; RNA, Ribosomal, 16S/genetics ; Seasons ; *Water Microbiology ; }, abstract = {Although petroleum hydrocarbons discharged from the Deepwater Horizon (DWH) blowout were shown to have a pronounced impact on indigenous microbial communities in the Gulf of Mexico, effects on nearshore or coastal ecosystems remain understudied. This study investigated the successional patterns of functional and taxonomic diversity for over 1 year after the DWH oil was deposited on Pensacola Beach sands (FL, USA), using metagenomic and 16S rRNA gene amplicon techniques. Gamma- and Alphaproteobacteria were enriched in oiled sediments, in corroboration of previous studies. In contrast to previous studies, we observed an increase in the functional diversity of the community in response to oil contamination and a functional transition from generalist populations within 4 months after oil came ashore to specialists a year later, when oil was undetectable. At the latter time point, a typical beach community had reestablished that showed little to no evidence of oil hydrocarbon degradation potential, was enriched in archaeal taxa known to be sensitive to xenobiotics, but differed significantly from the community before the oil spill. Further, a clear succession pattern was observed, where early responders to oil contamination, likely degrading aliphatic hydrocarbons, were replaced after 3 months by populations capable of aromatic hydrocarbon decomposition. Collectively, our results advance the understanding of how natural benthic microbial communities respond to crude oil perturbation, supporting the specialization-disturbance hypothesis; that is, the expectation that disturbance favors generalists, while providing (microbial) indicator species and genes for the chemical evolution of oil hydrocarbons during degradation and weathering.}, } @article {pmid25688558, year = {2015}, author = {Zhao, W and Wang, Y and Liu, S and Huang, J and Zhai, Z and He, C and Ding, J and Wang, J and Wang, H and Fan, W and Zhao, J and Meng, H}, title = {The dynamic distribution of porcine microbiota across different ages and gastrointestinal tract segments.}, journal = {PloS one}, volume = {10}, number = {2}, pages = {e0117441}, pmid = {25688558}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/*genetics/isolation & purification ; Bacteroidetes/classification/genetics/isolation & purification ; Feces/microbiology ; Female ; Firmicutes/classification/genetics/isolation & purification ; Gastrointestinal Tract/*microbiology ; Intestine, Large/microbiology ; Intestine, Small/microbiology ; Male ; *Microbiota ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/analysis/genetics ; Swine ; }, abstract = {Metagenome of gut microbes has been implicated in metabolism, immunity, and health maintenance of its host. However, in most of previous studies, the microbiota was sampled from feces instead of gastrointestinal (GI) tract. In this study, we compared the microbial populations from feces at four different developmental stages and contents of four intestinal segments at maturity to examine the dynamic shift of microbiota in pigs and investigated whether adult porcine fecal samples could be used to represent samples of the GI tract. Analysis results revealed that the ratio of Firmicutes to Bacteroidetes from the feces of the older pigs (2-, 3-, 6- month) were 10 times higher compared to those from piglets (1-month). As the pigs matured, so did it seem that the composition of microbiome became more stable in feces. In adult pigs, there were significant differences in microbial profiles between the contents of the small intestine and large intestine. The dominant genera in the small intestine belonged to aerobe or facultative anaerobe categories, whereas the main genera in the large intestine were all anaerobes. Compared to the GI tract, the composition of microbiome was quite different in feces. The microbial profile in large intestine was more similar to feces than those in the small intestine, with the similarity of 0.75 and 0.38 on average, respectively. Microbial functions, predicted by metagenome profiles, showed the enrichment associated with metabolism pathway and metabolic disease in large intestine and feces while higher abundance of infectious disease, immune function disease, and cancer in small intestine. Fecal microbes also showed enriched function in metabolic pathways compared to microbes from pooled gut contents. Our study extended the understanding of dynamic shift of gut microbes during pig growth and also characterized the profiles of bacterial communities across GI tracts of mature pigs.}, } @article {pmid25687743, year = {2015}, author = {Dlugosz, A and Winckler, B and Lundin, E and Zakikhany, K and Sandström, G and Ye, W and Engstrand, L and Lindberg, G}, title = {No difference in small bowel microbiota between patients with irritable bowel syndrome and healthy controls.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {8508}, pmid = {25687743}, issn = {2045-2322}, mesh = {Adolescent ; Adult ; Biodiversity ; Case-Control Studies ; Cluster Analysis ; Female ; Humans ; Intestine, Small/*microbiology ; Irritable Bowel Syndrome/*etiology ; Male ; Metagenome ; *Microbiota ; Middle Aged ; Principal Component Analysis ; Young Adult ; }, abstract = {Several studies have indicated that colonic microbiota may exhibit important differences between patients with irritable bowel syndrome (IBS) and healthy controls. Less is known about the microbiota of the small bowel. We used massive parallel sequencing to explore the composition of small bowel mucosa-associated microbiota in patients with IBS and healthy controls. We analysed capsule biopsies from the jejunum of 35 patients (26 females) with IBS aged 18-(36)-57 years and 16 healthy volunteers (11 females) aged 20-(32)-48 years. Sequences were analysed based on taxonomic classification. The phyla with the highest total abundance across all samples were: Firmicutes (43%), Proteobacteria (23%), Bacteroidetes (15%), Actinobacteria (9.3%) and Fusobacteria (7.0%). The most abundant genera were: Streptococcus (19%), Veillonella (13%), Prevotella (12%), Rothia (6.4%), Haemophilus (5.7%), Actinobacillus (5.5%), Escherichia (4.6%) and Fusobacterium (4.3%). We found no difference among major phyla or genera between patients with IBS and controls. We identified a cluster of samples in the small bowel microbiota dominated by Prevotella, which may represent a common enterotype of the upper small intestine. The remaining samples formed a gradient, dominated by Streptococcus at one end and Escherichia at the other.}, } @article {pmid25680374, year = {2015}, author = {Felczykowska, A and Krajewska, A and Zielińska, S and Łoś, JM and Bloch, SK and Nejman-Faleńczyk, B}, title = {The most widespread problems in the function-based microbial metagenomics.}, journal = {Acta biochimica Polonica}, volume = {62}, number = {1}, pages = {161-166}, doi = {10.18388/abp.2014_917}, pmid = {25680374}, issn = {1734-154X}, mesh = {Codon ; *Metagenomics ; *Microbiota ; }, abstract = {Metagenomics is a powerful tool to better understand the microbial niches, especially these from extreme habitats like oceans and seas, hot springs or deserts. However, one who is going to face the metagenomic studies should realize the challenges which might occur in the course of experiments. This manuscript indicates common problems in function-driven metagenomics, especially factors that influence gene expression are taken into account. Codon usage bias, internal cell accumulation, correct protein folding or presence of proper initiation factors are discussed and possible ways to overcome these problems are proposed. Finally, the annotation process is described, including possible limitations that one should take under consideration. What is more, the most popular databases for metagenomic data are mentioned and discussed.}, } @article {pmid25680373, year = {2015}, author = {Felczykowska, A and Krajewska, A and Zielińska, S and Łoś, JM}, title = {Sampling, metadata and DNA extraction - important steps in metagenomic studies.}, journal = {Acta biochimica Polonica}, volume = {62}, number = {1}, pages = {151-160}, doi = {10.18388/abp.2014_916}, pmid = {25680373}, issn = {1734-154X}, mesh = {DNA/*isolation & purification ; Ecosystem ; *Metagenomics ; Sewage ; }, abstract = {Metagenomic studies have become increasingly popular. They allow for the estimation of biodiversity in complex populations. This diversity presents an enormous but largely unexpected genetic and biological pool and can be exploited for the recovery of novel genes, entire metabolic pathways and their products. Generally metagenomic study is a genomic analysis of organisms by direct extraction and cloning of DNA from their natural environment. The most common problems of modern metagenomics are as follows: majority of the microorganisms present in the environment cannot be cultivated by standard techniques, DNA extraction methods are not very effective, isolated DNA is contaminated with various compounds, a choice for a screening method is not obvious.}, } @article {pmid25678254, year = {2015}, author = {Narayanasamy, S and Muller, EE and Sheik, AR and Wilmes, P}, title = {Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities.}, journal = {Microbial biotechnology}, volume = {8}, number = {3}, pages = {363-368}, pmid = {25678254}, issn = {1751-7915}, mesh = {*Ecosystem ; Gene Expression Profiling/*methods ; Metabolomics/*methods ; Metagenomics/*methods ; *Microbial Consortia ; Proteomics/*methods ; Systems Biology ; Wastewater/*microbiology ; Water Purification ; }, abstract = {Biological wastewater treatment plants harbour diverse and complex microbial communities which prominently serve as models for microbial ecology and mixed culture biotechnological processes. Integrated omic analyses (combined metagenomics, metatranscriptomics, metaproteomics and metabolomics) are currently gaining momentum towards providing enhanced understanding of community structure, function and dynamics in situ as well as offering the potential to discover novel biological functionalities within the framework of Eco-Systems Biology. The integration of information from genome to metabolome allows the establishment of associations between genetic potential and final phenotype, a feature not realizable by only considering single 'omes'. Therefore, in our opinion, integrated omics will become the future standard for large-scale characterization of microbial consortia including those underpinning biological wastewater treatment processes. Systematically obtained time and space-resolved omic datasets will allow deconvolution of structure-function relationships by identifying key members and functions. Such knowledge will form the foundation for discovering novel genes on a much larger scale compared with previous efforts. In general, these insights will allow us to optimize microbial biotechnological processes either through better control of mixed culture processes or by use of more efficient enzymes in bioengineering applications.}, } @article {pmid25676781, year = {2015}, author = {Uchihashi, M and Bergin, IL and Bassis, CM and Hashway, SA and Chai, D and Bell, JD}, title = {Influence of age, reproductive cycling status, and menstruation on the vaginal microbiome in baboons (Papio anubis).}, journal = {American journal of primatology}, volume = {77}, number = {5}, pages = {563-578}, pmid = {25676781}, issn = {1098-2345}, support = {K12 HD065257/HD/NICHD NIH HHS/United States ; UL1 TR000433/TR/NCATS NIH HHS/United States ; UL1TR000433/TR/NCATS NIH HHS/United States ; K12 HD 065257-01/HD/NICHD NIH HHS/United States ; }, mesh = {Age Factors ; Animals ; Female ; Genome, Bacterial ; Menstruation/*physiology ; Metagenome ; *Microbiota ; Ovulation/physiology ; Papio anubis/*microbiology/physiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Vagina/*microbiology ; }, abstract = {The vaginal microbiome is believed to influence host health by providing protection from pathogens and influencing reproductive outcomes such as fertility and gestational length. In humans, age-associated declines in diversity of the vaginal microbiome occur in puberty and persist into adulthood. Additionally, menstruation has been associated with decreased microbial community stability. Adult female baboons, like other non-human primates (NHPs), have a different and highly diverse vaginal microbiome compared to that of humans, which is most commonly dominated by Lactobacillus spp. We evaluated the influence of age, reproductive cycling status (cycling vs. non-cycling) and menstruation on the vaginal microbiome of 38 wild-caught, captive female olive baboons (Papio anubis) by culture-independent sequencing of the V3-V5 region of the bacterial 16S rRNA gene. All baboons had highly diverse vaginal microbial communities. Adult baboons had significantly lower microbial diversity in comparison to subadult baboons, which was attributable to decreased relative abundance of minor taxa. No significant differences were detected based on cycling state or menstruation. Predictive metagenomic analysis showed uniformity in relative abundance of metabolic pathways regardless of age, cycle stage, or menstruation, indicating conservation of microbial community functions. This study suggests that selection of an optimal vaginal microbial community occurs at puberty. Since decreased diversity occurs in both baboons and humans at puberty, this may reflect a general strategy for selection of adult vaginal microbial communities. Comparative evaluation of vaginal microbial community development and composition may elucidate mechanisms of community formation and function that are conserved across host species or across microbial community types. These findings have implications for host health, evolutionary biology, and microbe-host ecosystems.}, } @article {pmid25675346, year = {2015}, author = {Mehta, SD and Donovan, B and Weber, KM and Cohen, M and Ravel, J and Gajer, P and Gilbert, D and Burgad, D and Spear, GT}, title = {The vaginal microbiota over an 8- to 10-year period in a cohort of HIV-infected and HIV-uninfected women.}, journal = {PloS one}, volume = {10}, number = {2}, pages = {e0116894}, pmid = {25675346}, issn = {1932-6203}, support = {U01 AI034994/AI/NIAID NIH HHS/United States ; UO1-AI-34994/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Cluster Analysis ; Cohort Studies ; Coinfection ; Female ; Follow-Up Studies ; HIV Infections/immunology/*microbiology/virology ; Humans ; Lactobacillus/classification/genetics ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S ; Risk Factors ; Sequence Analysis, DNA ; Time Factors ; Vagina/*microbiology ; Young Adult ; }, abstract = {BACKGROUND: We identified predominant vaginal microbiota communities, changes over time, and how this varied by HIV status and other factors in a cohort of 64 women.

METHODS: Bacterial DNA was extracted from reposited cervicovaginal lavage samples collected annually over an 8-10 year period from Chicago Women's Interagency HIV Study participants: 22 HIV-negative, 22 HIV-positive with stable infection, 20 HIV-positive with progressive infection. The vaginal microbiota was defined by pyrosequencing of the V1/V2 region of the 16S rRNA gene. Scheduled visits included Bacterial vaginsosis (BV) screening; clinically detected cases were referred for treatment. Hierarchical clustering identified bacterial community state types (CST). Multinomial mixed effects modeling determined trends over time in CST, by HIV status and other factors.

RESULTS: The median follow-up time was 8.1 years (range 5.5-15.3). Six CSTs were identified. The mean relative abundance (RA) of Lactobacillus spp. by CST (with median number of bacterial taxa) was: CST-1-25.7% (10), CST-2-27.1% (11), CST-3-34.6% (9), CST-4-46.8% (9), CST-5-57.9% (4), CST-6-69.4% (2). The two CSTs representing the highest RA of Lactobacillus and lowest diversity increased with each additional year of follow-up (CST-5, adjusted odds ratio (aOR) = 1.62 [95% CI: 1.34-1.94]; CST-6, aOR = 1.57 [95 CI: 1.31-1.89]), while the two CSTs representing lowest RA of Lactobacillus and higher diversity decreased with each additional year (CST-1, aOR = 0.89 [95% CI: 0.80-1.00]; CST-2, aOR = 0.86 [95% CI: 0.75-0.99]). There was no association between HIV status and CST at baseline or over time. CSTs representing lower RA of Lactobacillus were associated with current cigarette smoking.

CONCLUSIONS: The vaginal microbial community significantly improved over time in this cohort of women with HIV and at high risk for HIV who had regular detection and treatment referral for BV.}, } @article {pmid25675094, year = {2015}, author = {Ericsson, AC and Davis, JW and Spollen, W and Bivens, N and Givan, S and Hagan, CE and McIntosh, M and Franklin, CL}, title = {Effects of vendor and genetic background on the composition of the fecal microbiota of inbred mice.}, journal = {PloS one}, volume = {10}, number = {2}, pages = {e0116704}, pmid = {25675094}, issn = {1932-6203}, support = {U42 OD010918/OD/NIH HHS/United States ; U42 OD010918-13/OD/NIH HHS/United States ; }, mesh = {Animals ; *Animals, Laboratory ; Biodiversity ; Cluster Analysis ; Feces/*microbiology ; Female ; Gastrointestinal Tract/microbiology ; Metagenome ; Mice ; Mice, Inbred Strains/*genetics/*microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The commensal gut microbiota has been implicated as a determinant in several human diseases and conditions. There is mounting evidence that the gut microbiota of laboratory mice (Mus musculus) similarly modulates the phenotype of mouse models used to study human disease and development. While differing model phenotypes have been reported using mice purchased from different vendors, the composition and uniformity of the fecal microbiota in mice of various genetic backgrounds from different vendors is unclear. Using culture-independent methods and robust statistical analysis, we demonstrate significant differences in the richness and diversity of fecal microbial populations in mice purchased from two large commercial vendors. Moreover, the abundance of many operational taxonomic units, often identified to the species level, as well as several higher taxa, differed in vendor- and strain-dependent manners. Such differences were evident in the fecal microbiota of weanling mice and persisted throughout the study, to twenty-four weeks of age. These data provide the first in-depth analysis of the developmental trajectory of the fecal microbiota in mice from different vendors, and a starting point from which researchers may be able to refine animal models affected by differences in the gut microbiota and thus possibly reduce the number of animals required to perform studies with sufficient statistical power.}, } @article {pmid25673657, year = {2015}, author = {Rozman Grinberg, I and Yin, G and Borovok, I and Berg Miller, ME and Yeoman, CJ and Dassa, B and Yu, Z and Mizrahi, I and Flint, HJ and Bayer, EA and White, BA and Lamed, R}, title = {Functional phylotyping approach for assessing intraspecific diversity of Ruminococcus albus within the rumen microbiome.}, journal = {FEMS microbiology letters}, volume = {362}, number = {3}, pages = {1-10}, doi = {10.1093/femsle/fnu047}, pmid = {25673657}, issn = {1574-6968}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/chemistry/genetics ; Cattle ; Cellulases/chemistry/*genetics ; Cellulose/metabolism ; Genetic Variation ; *Microbiota ; Molecular Sequence Data ; *Molecular Typing ; Phylogeny ; Rumen/*microbiology ; Ruminococcus/*classification/enzymology/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Ruminococcus albus, a cellulolytic bacterium, is a critical member of the rumen community. Ruminococcus albus lacks a classical cellulosome complex, but it possesses a unique family 37 carbohydrate-binding module (CBM37), which is integrated into a variety of carbohydrate-active enzymes. We developed a potential molecular tool for functional phylotyping of the R. albus population in the rumen, based on a variable region in the cel48A gene. cel48A encodes a single copy of the CBM37-associated family 48 glycoside hydrolase in all known strains of this bacterium. A segment of the cel48A gene was amplified from rumen metagenomic samples of four bovines, and its abundance and diversity were evaluated. Analysis of the obtained sequences revealed the co-existence of multiple functional phylotypes of cel48A in all four animals. These included sequences identical or similar to those of R. albus isolates (reference strains), as well as several novel sequences. The dominant cel48A type varied among animals. This method can be used for detection of intraspecific diversity of R. albus in metagenomic samples. Together with scaC, a previously reported gene marker for R. flavefaciens, we present a set of two species-specific markers for phylotyping of Ruminococci in the herbivore rumen.}, } @article {pmid25667601, year = {2015}, author = {Chown, SL and Hodgins, KA and Griffin, PC and Oakeshott, JG and Byrne, M and Hoffmann, AA}, title = {Biological invasions, climate change and genomics.}, journal = {Evolutionary applications}, volume = {8}, number = {1}, pages = {23-46}, pmid = {25667601}, issn = {1752-4571}, abstract = {The rate of biological invasions is expected to increase as the effects of climate change on biological communities become widespread. Climate change enhances habitat disturbance which facilitates the establishment of invasive species, which in turn provides opportunities for hybridization and introgression. These effects influence local biodiversity that can be tracked through genetic and genomic approaches. Metabarcoding and metagenomic approaches provide a way of monitoring some types of communities under climate change for the appearance of invasives. Introgression and hybridization can be followed by the analysis of entire genomes so that rapidly changing areas of the genome are identified and instances of genetic pollution monitored. Genomic markers enable accurate tracking of invasive species' geographic origin well beyond what was previously possible. New genomic tools are promoting fresh insights into classic questions about invading organisms under climate change, such as the role of genetic variation, local adaptation and climate pre-adaptation in successful invasions. These tools are providing managers with often more effective means to identify potential threats, improve surveillance and assess impacts on communities. We provide a framework for the application of genomic techniques within a management context and also indicate some important limitations in what can be achieved.}, } @article {pmid25666826, year = {2015}, author = {Yolken, RH and Severance, EG and Sabunciyan, S and Gressitt, KL and Chen, O and Stallings, C and Origoni, A and Katsafanas, E and Schweinfurth, LA and Savage, CL and Banis, M and Khushalani, S and Dickerson, FB}, title = {Metagenomic Sequencing Indicates That the Oropharyngeal Phageome of Individuals With Schizophrenia Differs From That of Controls.}, journal = {Schizophrenia bulletin}, volume = {41}, number = {5}, pages = {1153-1161}, pmid = {25666826}, issn = {1745-1701}, support = {P50 MH094268/MH/NIMH NIH HHS/United States ; MH-94268/MH/NIMH NIH HHS/United States ; }, mesh = {Adult ; Bacteriophages/*genetics ; Female ; Humans ; Lactobacillus/*virology ; Male ; *Metagenome ; *Microbiota ; Middle Aged ; Oropharynx/*virology ; Schizophrenia/*virology ; Sequence Analysis, DNA ; }, abstract = {Mucosal sites such as the oropharynx contain a wide range of microorganisms, collectively designated as the microbiome. The microbiome can affect behavior through a number of neurobiological and immunological mechanisms. Most previous studies have focused on the bacterial components of the microbiome. However, the microbiome also includes viruses such as bacteriophages, which are viruses that infect bacteria and alter their metabolism and replication. We employed metagenomic analysis to characterize bacteriophage genomes in the oral pharynx of 41 individuals with schizophrenia and 33 control individuals without a psychiatric disorder. This analysis was performed by the generation of more than 100,000,000 sequence reads from each sample and the mapping of these reads to databases. We identified 79 distinct bacteriophage sequences in the oropharyngeal samples. Of these, one bacteriophage genome, Lactobacillus phage phiadh, was found to be significantly different in individuals with schizophrenia (P < .00037, q < 0.03 adjusted for multiple comparisons). The differential levels of Lactobacillus phage phiadh remained significant when controlling for age, gender, race, socioeconomic status, or cigarette smoking (P < .006). Within the group of individuals with schizophrenia, the level of Lactobacillus phage phiadh correlated with the prevalence of immunological disorders as well as with the administration of valproate, which has been shown in animal models to alter the microbiome. The bacteriophage composition of the oropharynx in individuals with schizophrenia differs from that of controls. The biological consequences of this difference and the potential effects of altering bacteriophage levels through therapeutic interventions are worthy of further investigation.}, } @article {pmid25665577, year = {2015}, author = {Sharon, I and Kertesz, M and Hug, LA and Pushkarev, D and Blauwkamp, TA and Castelle, CJ and Amirebrahimi, M and Thomas, BC and Burstein, D and Tringe, SG and Williams, KH and Banfield, JF}, title = {Accurate, multi-kb reads resolve complex populations and detect rare microorganisms.}, journal = {Genome research}, volume = {25}, number = {4}, pages = {534-543}, pmid = {25665577}, issn = {1549-5469}, mesh = {Bacterial Proteins/*genetics ; Base Sequence ; Biodiversity ; Chloroflexi/genetics/isolation & purification ; DNA, Bacterial/genetics ; Deltaproteobacteria/*genetics/isolation & purification ; Genome, Bacterial ; Geologic Sediments/analysis/*microbiology ; Glucose/metabolism ; Hydrolases/*genetics ; Metagenomics/methods ; Microbial Consortia/*genetics ; Sequence Analysis, DNA ; }, abstract = {Accurate evaluation of microbial communities is essential for understanding global biogeochemical processes and can guide bioremediation and medical treatments. Metagenomics is most commonly used to analyze microbial diversity and metabolic potential, but assemblies of the short reads generated by current sequencing platforms may fail to recover heterogeneous strain populations and rare organisms. Here we used short (150-bp) and long (multi-kb) synthetic reads to evaluate strain heterogeneity and study microorganisms at low abundance in complex microbial communities from terrestrial sediments. The long-read data revealed multiple (probably dozens of) closely related species and strains from previously undescribed Deltaproteobacteria and Aminicenantes (candidate phylum OP8). Notably, these are the most abundant organisms in the communities, yet short-read assemblies achieved only partial genome coverage, mostly in the form of short scaffolds (N50 = ∼ 2200 bp). Genome architecture and metabolic potential for these lineages were reconstructed using a new synteny-based method. Analysis of long-read data also revealed thousands of species whose abundances were <0.1% in all samples. Most of the organisms in this "long tail" of rare organisms belong to phyla that are also represented by abundant organisms. Genes encoding glycosyl hydrolases are significantly more abundant than expected in rare genomes, suggesting that rare species may augment the capability for carbon turnover and confer resilience to changing environmental conditions. Overall, the study showed that a diversity of closely related strains and rare organisms account for a major portion of the communities. These are probably common features of many microbial communities and can be effectively studied using a combination of long and short reads.}, } @article {pmid25663664, year = {2015}, author = {Singh, KM and Patel, AK and Shah, RK and Reddy, B and Joshi, CG}, title = {Potential functional gene diversity involved in methanogenesis and methanogenic community structure in Indian buffalo (Bubalus bubalis) rumen.}, journal = {Journal of applied genetics}, volume = {56}, number = {3}, pages = {411-426}, pmid = {25663664}, issn = {2190-3883}, mesh = {Animals ; Buffaloes/*microbiology ; DNA, Archaeal/genetics ; Genetic Variation ; Metabolome ; *Metagenome ; Methane/*biosynthesis ; Methanobacteriaceae/classification ; Methanococcus/classification ; Methanosarcina/classification ; Microbiota ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Understanding the methanogen community structure and methanogenesis from Bubalus bubalis in India may be beneficial to methane mitigation. Our current understanding of the microbial processes leading to methane production is incomplete, and further advancement in the knowledge of methanogenesis pathways would provide means to manipulate its emission in the future. In the present study, we evaluated the methanogenic community structure in the rumen as well as their potential genes involved in methanogenesis. The taxonomic and metabolic profiles of methanogens were assessed by shotgun sequencing of rumen metagenome by Ion Torrent semiconductor sequencing. The buffalo rumen contained representative genera of all the families of methanogens. Members of Methanobacteriaceae were found to be dominant, followed by Methanosarcinaceae, Methanococcaceae, Methanocorpusculaceae, and Thermococcaceae. A total of 60 methanogenic genera were detected in buffalo rumen. Methanogens related to the genera Methanobrevibacter, Methanosarcina, Methanococcus, Methanocorpusculum, Methanothermobacter, and Methanosphaera were predominant, representing >70 % of total archaeal sequences. The metagenomic dataset indicated the presence of genes involved in the methanogenesis and acetogenesis pathways, and the main functional genes were those of key enzymes in the methanogenesis. Sequences related to CoB--CoM heterodisulfide reductase, methyl coenzyme M reductase, f420-dependent methylenetetrahydromethanopterin reductase, and formylmethanofuran dehydrogenase were predominant in rumen. In addition, methenyltetrahydrofolate cyclohydrolase, methylenetetrahydrofolate dehydrogenase, 5,10-methylenetetrahydrofolate reductase, and acetyl-coenzyme A synthetase were also recovered.}, } @article {pmid25663091, year = {2015}, author = {McLaughlin, RW and Cochran, PA and Dowd, SE}, title = {Metagenomic analysis of the gut microbiota of the Timber Rattlesnake, Crotalus horridus.}, journal = {Molecular biology reports}, volume = {42}, number = {7}, pages = {1187-1195}, pmid = {25663091}, issn = {1573-4978}, mesh = {Actinobacteria/classification/genetics/metabolism ; Animals ; Bacteroides/classification/genetics/metabolism ; Carbohydrate Metabolism ; Colon/microbiology/parasitology/virology ; Crotalus/*microbiology/parasitology/virology ; Eukaryota/classification/genetics/metabolism ; Firmicutes/classification/genetics/metabolism ; Gastrointestinal Microbiome/genetics ; Gene Library ; High-Throughput Nucleotide Sequencing ; Intestine, Small/microbiology/parasitology/virology ; *Metagenome ; *Phylogeny ; Proteobacteria/classification/*genetics/metabolism ; RNA, Ribosomal, 16S/*genetics/isolation & purification ; Stomach/microbiology/parasitology/virology ; Viruses/classification/genetics/metabolism ; }, abstract = {Snakes are capable of surviving long periods without food. In this study we characterized the microbiota of a Timber Rattlesnake (Crotalus horridus), devoid of digesta, living in the wild. Pyrosequencing-based metagenomics were used to analyze phylogenetic and metabolic profiles with the aid of the MG-RAST server. Pyrosequencing of samples taken from the stomach, small intestine and colon yielded 691696, 957756 and 700419 high quality sequence reads. Taxonomic analysis of metagenomic reads indicated Eukarya was the most predominant domain, followed by bacteria and then viruses, for all three tissues. The most predominant phylum in the domain Bacteria was Proteobacteria for the tissues examined. Functional classifications by the subsystem database showed cluster-based subsystems were most predominant (10-15 %). Almost equally predominant (10-13 %) was carbohydrate metabolism. To identify bacteria in the colon at a finer taxonomic resolution, a 16S rRNA gene clone library was created. Proteobacteria was again found to be the most predominant phylum. The present study provides a baseline for understanding the microbial ecology of snakes living in the wild.}, } @article {pmid25662977, year = {2015}, author = {Steffen, MM and Belisle, BS and Watson, SB and Boyer, GL and Bourbonniere, RA and Wilhelm, SW}, title = {Metatranscriptomic evidence for co-occurring top-down and bottom-up controls on toxic cyanobacterial communities.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {9}, pages = {3268-3276}, pmid = {25662977}, issn = {1098-5336}, mesh = {Bacteriophages/growth & development ; *Biota ; Cyanobacteria/*growth & development/virology ; Eutrophication ; Fresh Water/*microbiology ; Gene Expression Profiling ; Lakes/microbiology ; Metagenomics ; Molecular Sequence Data ; Sequence Analysis, DNA ; United States ; }, abstract = {Little is known about the molecular and physiological function of co-occurring microbes within freshwater cyanobacterial harmful algal blooms (cHABs). To address this, community metatranscriptomes collected from the western basin of Lake Erie during August 2012 were examined. Using sequence data, we tested the hypothesis that the activity of the microbial community members is independent of community structure. Predicted metabolic and physiological functional profiles from spatially distinct metatranscriptomes were determined to be ≥90% similar between sites. Targeted analysis of Microcystis aeruginosa, the historical causative agent of cyanobacterial harmful algal blooms over the past ∼20 years, as well as analysis of Planktothrix agardhii and Anabaena cylindrica, revealed ongoing transcription of genes involved in microcystin toxin synthesis as well as the acquisition of both nitrogen and phosphorus, nutrients often implicated as independent bottom-up drivers of eutrophication in aquatic systems. Transcription of genes involved in carbon dioxide (CO2) concentration and metabolism also provided support for the alternate hypothesis that high-pH conditions and dense algal biomass result in CO2-limiting conditions that further favor cyanobacterial dominance. Additionally, the presence of Microcystis-specific cyanophage sequences provided preliminary evidence of possible top-down virus-mediated control of cHAB populations. Overall, these data provide insight into the complex series of constraints associated with Microcystis blooms that dominate the western basin of Lake Erie during summer months, demonstrating that multiple environmental factors work to shape the microbial community.}, } @article {pmid25661279, year = {2017}, author = {Yang, CW and Huang, HW and Chang, BV}, title = {Microbial communities associated with anaerobic degradation of polybrominated diphenyl ethers in river sediment.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {50}, number = {1}, pages = {32-39}, doi = {10.1016/j.jmii.2014.12.009}, pmid = {25661279}, issn = {1995-9133}, mesh = {*Anaerobiosis ; Archaea/*classification/genetics/metabolism ; Bacteria/*classification/genetics/metabolism ; *Biota ; Biotransformation ; Chromatography, Gas ; Geologic Sediments/*microbiology ; Halogenated Diphenyl Ethers/*metabolism ; Iron/metabolism ; Metagenomics ; Rivers/*microbiology ; Sequence Analysis, DNA ; Taiwan ; }, abstract = {BACKGROUND/PURPOSE: Polybrominated diphenyl ethers (PBDEs) are extensively used as a class of flame retardants and have become ubiquitous environmental pollutants. We aimed to uncover the changes in microbial community with PBDE anaerobic degradation with and without zero-valent iron in sediment from the Erren River, considered one of the most heavily contaminated rivers in Taiwan.

METHODS: PBDE anaerobic degradation in sediment was analyzed by gas chromatography with an electron capture detector. Microbial community composition was analyzed by a pyrosequencing-based metagenomic approach.

RESULTS: The anaerobic degradation rate of BDE-209 was higher than BDE-28 in sediment; the addition of zero-valent iron enhanced the degradation rates of both. In total, 19 known bacterial genera (4 major genera: Clostridium, Lysinibacillus, Rummeliibacillus, and Brevundimonas) were considered PBDE degradation-associated bacteria (sequence frequency negatively correlated with PBDE remaining percentage) as were four known archaea genera (Methanobacterium, Methanosarcina, Methanocorpusculum, and Halalkalicoccus; sequence frequency positively correlated with PBDE remaining percentage).

CONCLUSION: The composition of bacteria and that of archaea affected the anaerobic degradation of BDE-28 and BDE-209. The addition of zero-valent iron further decreased the archaea content to undetectable levels.}, } @article {pmid25658053, year = {2015}, author = {Reed, DC and Breier, JA and Jiang, H and Anantharaman, K and Klausmeier, CA and Toner, BM and Hancock, C and Speer, K and Thurnherr, AM and Dick, GJ}, title = {Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents.}, journal = {The ISME journal}, volume = {9}, number = {8}, pages = {1857-1869}, pmid = {25658053}, issn = {1751-7370}, mesh = {Autotrophic Processes/physiology ; Bacteria/*isolation & purification ; Hydrothermal Vents/*microbiology ; Metagenomics ; *Microbiota ; Models, Theoretical ; Oceans and Seas ; Seawater/chemistry/*microbiology ; Thermodynamics ; }, abstract = {Submarine hydrothermal vents perturb the deep-ocean microbiome by injecting reduced chemical species into the water column that act as an energy source for chemosynthetic organisms. These systems thus provide excellent natural laboratories for studying the response of microbial communities to shifts in marine geochemistry. The present study explores the processes that regulate coupled microbial-geochemical dynamics in hydrothermal plumes by means of a novel mathematical model, which combines thermodynamics, growth and reaction kinetics, and transport processes derived from a fluid dynamics model. Simulations of a plume located in the ABE vent field of the Lau basin were able to reproduce metagenomic observations well and demonstrated that the magnitude of primary production and rate of autotrophic growth are largely regulated by the energetics of metabolisms and the availability of electron donors, as opposed to kinetic parameters. Ambient seawater was the dominant source of microbes to the plume and sulphur oxidisers constituted almost 90% of the modelled community in the neutrally-buoyant plume. Data from drifters deployed in the region allowed the different time scales of metabolisms to be cast in a spatial context, which demonstrated spatial succession in the microbial community. While growth was shown to occur over distances of tens of kilometers, microbes persisted over hundreds of kilometers. Given that high-temperature hydrothermal systems are found less than 100 km apart on average, plumes may act as important vectors between different vent fields and other environments that are hospitable to similar organisms, such as oil spills and oxygen minimum zones.}, } @article {pmid25656071, year = {2015}, author = {Nurdiani, D and Ito, M and Maruyama, T and Terahara, T and Mori, T and Ugawa, S and Takeyama, H}, title = {Analysis of bacterial xylose isomerase gene diversity using gene-targeted metagenomics.}, journal = {Journal of bioscience and bioengineering}, volume = {120}, number = {2}, pages = {174-180}, doi = {10.1016/j.jbiosc.2014.12.022}, pmid = {25656071}, issn = {1347-4421}, mesh = {Aldose-Ketose Isomerases/classification/*genetics ; Amino Acid Sequence ; Base Sequence ; Biofuels/supply & distribution ; DNA Primers/genetics ; DNA, Bacterial/genetics ; Databases, Nucleic Acid ; Genes, Bacterial/*genetics ; Genetic Variation/*genetics ; Lignin/metabolism ; Metagenome/*genetics ; *Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil Microbiology ; Xylose/metabolism ; }, abstract = {Bacterial xylose isomerases (XI) are promising resources for efficient biofuel production from xylose in lignocellulosic biomass. Here, we investigated xylose isomerase gene (xylA) diversity in three soil metagenomes differing in plant vegetation and geographical location, using an amplicon pyrosequencing approach and two newly-designed primer sets. A total of 158,555 reads from three metagenomic DNA replicates for each soil sample were classified into 1127 phylotypes, detected in triplicate and defined by 90% amino acid identity. The phylotype coverage was estimated to be within the range of 84.0-92.7%. The xylA gene phylotypes obtained were phylogenetically distributed across the two known xylA groups. They shared 49-100% identities with their closest-related XI sequences in GenBank. Phylotypes demonstrating <90% identity with known XIs in the database accounted for 89% of the total xylA phylotypes. The differences among xylA members and compositions within each soil sample were significantly smaller than they were between different soils based on a UniFrac distance analysis, suggesting soil-specific xylA genotypes and taxonomic compositions. The differences among xylA members and their compositions in the soil were strongly correlated with 16S rRNA variation between soil samples, also assessed by amplicon pyrosequencing. This is the first report of xylA diversity in environmental samples assessed by amplicon pyrosequencing. Our data provide information regarding xylA diversity in nature, and can be a basis for the screening of novel xylA genotypes for practical applications.}, } @article {pmid25654499, year = {2015}, author = {Charalampakis, G and Belibasakis, GN}, title = {Microbiome of peri-implant infections: lessons from conventional, molecular and metagenomic analyses.}, journal = {Virulence}, volume = {6}, number = {3}, pages = {183-187}, pmid = {25654499}, issn = {2150-5608}, mesh = {Biofilms/growth & development ; Dental Implants/*microbiology ; Humans ; Metagenomics/methods ; *Microbiota ; Molecular Typing ; Peri-Implantitis/complications/*microbiology ; }, abstract = {Osseointegrated dental implants are now a well-established treatment option in the armament of restorative dentistry. These technologically advanced devices are designed to functionally and esthetically replace missing teeth. Despite the revolutionary advances that implants have incurred, they have also provided the oral cavity with new artificial surfaces prone to the formation of oral biofilms, similarly to the hard tissue surfaces of natural teeth. Biofilm formation on the implant surface can trigger the inflammatory destruction of the peri-implant tissue, in what is known as peri-implantitis. The mixed microbial flora of peri-implant infections resembles that of periodontal infections, with some notable differences. These are likely to expand with the ever increasing application of metagenomics and metatrascriptomics in the analysis of oral ecology. This review presents the wealth of knowledge we have gained from microbiological methods used in the characterization of peri-implant microflora and sheds light over potential new benefits, as well as limitations, of the new sequencing technology in our understanding of peri-implant disease pathogenesis.}, } @article {pmid25654162, year = {2015}, author = {Zehnder, M and Belibasakis, GN}, title = {On the dynamics of root canal infections-what we understand and what we don't.}, journal = {Virulence}, volume = {6}, number = {3}, pages = {216-222}, pmid = {25654162}, issn = {2150-5608}, mesh = {Bacterial Infections/*microbiology ; Dental Pulp Cavity/immunology/*microbiology/physiopathology ; Dental Pulp Necrosis/etiology ; Humans ; Metagenomics ; Microbiota ; Root Canal Therapy ; }, abstract = {Infections of the root canal space and their sequelae can be extremely painful and potentially dangerous, yet they do not necessarily have to be. Chronic, asymptomatic inflammatory lesions around the apex of a tooth with a necrotic dental pulp or an insufficient root canal treatment can develop unnoticed by the patient, and remain so for years. The course of disease is modulated by both the virulence of the microbiota established in the root canal space and the capacity of the immune system to curb the infection. To both ends, highly convincing investigations to help us understand when and why the tissues around an endodontically involved tooth become acutely inflamed are missing. We will discuss how recent advances in molecular identification of microorganisms have altered our understanding of root canal infections, and which information is currently missing to link clinical experience with observations from experimental research.}, } @article {pmid25652653, year = {2015}, author = {Pajarillo, EA and Chae, JP and Kim, HB and Kim, IH and Kang, DK}, title = {Barcoded pyrosequencing-based metagenomic analysis of the faecal microbiome of three purebred pig lines after cohabitation.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {13}, pages = {5647-5656}, doi = {10.1007/s00253-015-6408-5}, pmid = {25652653}, issn = {1432-0614}, mesh = {Animals ; Cluster Analysis ; DNA Barcoding, Taxonomic ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Swine ; }, abstract = {The microbial communities in the pig gut perform a variety of beneficial functions. Along with host genetics and diet, farm management practices are an important aspect of agricultural animal production that could influence gut microbial diversity. In this study, we used barcoded pyrosequencing of the V1-V3 regions of the 16S ribosomal RNA (rRNA) genes to characterise the faecal microbiome of three common commercial purebred pig lines (Duroc, Landrace and Yorkshire) before and after cohabitation. The diversity of faecal microbiota was characterised by employing phylogenetic, distance-based and multivariate-clustering approaches. Bacterial diversity tended to become more uniform after mixing of the litters. Age-related shifts were also observed at various taxonomic levels, with an increase in the proportion of the phylum Firmicutes and a decrease in Bacteroidetes over time, regardless of the purebred group. Cohabitation had a detectable effect on the microbial shift among purebred pigs. We identified the bacterial genus Parasutterella as having utility in discriminating pigs according to time. Similarly, Dialister and Bacteroides can be used to differentiate the purebred lines used. The microbial communities of the three purebred pigs became more similar after cohabitation, but retained a certain degree of breed specificity, with the microbiota of Landrace and Yorkshire remaining distinct from that of their distant relative, Duroc.}, } @article {pmid25649202, year = {2015}, author = {van den Brand, TP and Roest, K and Chen, GH and Brdjanovic, D and van Loosdrecht, MC}, title = {Occurrence and activity of sulphate reducing bacteria in aerobic activated sludge systems.}, journal = {World journal of microbiology & biotechnology}, volume = {31}, number = {3}, pages = {507-516}, pmid = {25649202}, issn = {1573-0972}, mesh = {Aerobiosis ; *Biota ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Deltaproteobacteria/*classification/genetics/*metabolism ; Metagenome ; Molecular Sequence Data ; Netherlands ; Oxidation-Reduction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; Sewage/*microbiology ; Sulfates/*metabolism ; Temperature ; Water Purification ; }, abstract = {In the sewage or wastewater treatment plant, biological sulphate reduction can occur spontaneously or be applied beneficially for its treatment. The results of this study can be applied to control SRB in the sewage and WWTP. Therefore, population diversity analyses of SRB for nine activated sludge wastewater treatment plants (WWTP) in the Netherlands and the effect of long-term (months) oxygen exposures on the SRB activity were carried out. T-RFLP and clone sequencing analyses of winter and summer samples revealed that (1) all WWTP have a similar SRB population, (2) there is no seasonal impact (10-20 °C) on the SRB population present in the WWTP and (3) Desulfobacter postgatei, Desulfovibrio desulfuricans and Desulfovibrio intestinalis were the most common and dominant SRB species observed in these samples, and origin from the sewage. Short term activity tests demonstrated that SRB were not active in the aerobic WWTP, but while flushed with N2-gas SRB became slightly active after 3 h. In a laboratory reactor at a dissolved oxygen concentration of <2 %, sulphate reduction occurred and 89 % COD removal was achieved. SRB grew in granules, in order to protect themselves for oxygen exposures. SRB are naturally present in aerobic WWTP, which is due to the formation of granules.}, } @article {pmid25647155, year = {2015}, author = {Suskind, DL and Brittnacher, MJ and Wahbeh, G and Shaffer, ML and Hayden, HS and Qin, X and Singh, N and Damman, CJ and Hager, KR and Nielson, H and Miller, SI}, title = {Fecal microbial transplant effect on clinical outcomes and fecal microbiome in active Crohn's disease.}, journal = {Inflammatory bowel diseases}, volume = {21}, number = {3}, pages = {556-563}, pmid = {25647155}, issn = {1536-4844}, support = {KL2 TR000421/TR/NCATS NIH HHS/United States ; P30 DK089507/DK/NIDDK NIH HHS/United States ; UL1 TR000423/TR/NCATS NIH HHS/United States ; UL1TR000423/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; *Biological Therapy ; Child ; Computational Biology ; Crohn Disease/microbiology/physiopathology/*therapy ; Feces/*microbiology ; Female ; Humans ; Male ; Metagenome ; *Microbiota ; Prognosis ; Young Adult ; }, abstract = {BACKGROUND: Crohn's disease (CD) is a chronic idiopathic inflammatory intestinal disorder associated with fecal dysbiosis. Fecal microbial transplant (FMT) is a potential therapeutic option for individuals with CD based on the hypothesis that changing the fecal dysbiosis could promote less intestinal inflammation.

METHODS: Nine patients, aged 12 to 19 years, with mild-to-moderate symptoms defined by Pediatric Crohn's Disease Activity Index (PCDAI of 10-29) were enrolled into a prospective open-label study of FMT in CD (FDA IND 14942). Patients received FMT by nasogastric tube with follow-up evaluations at 2, 6, and 12 weeks. PCDAI, C-reactive protein, and fecal calprotectin were evaluated at each study visit.

RESULTS: All reported adverse events were graded as mild except for 1 individual who reported moderate abdominal pain after FMT. All adverse events were self-limiting. Metagenomic evaluation of stool microbiome indicated evidence of FMT engraftment in 7 of 9 patients. The mean PCDAI score improved with patients having a baseline of 19.7 ± 7.2, with improvement at 2 weeks to 6.4 ± 6.6 and at 6 weeks to 8.6 ± 4.9. Based on PCDAI, 7 of 9 patients were in remission at 2 weeks and 5 of 9 patients who did not receive additional medical therapy were in remission at 6 and 12 weeks. No or modest improvement was seen in patients who did not engraft or whose microbiome was most similar to their donor.

CONCLUSIONS: This is the first study to demonstrate that FMT for CD may be a possible therapeutic option for CD. Further prospective studies are required to fully assess the safety and efficacy of the FMT in patients with CD.}, } @article {pmid25644956, year = {2015}, author = {Priya, H and Prasanna, R and Ramakrishnan, B and Bidyarani, N and Babu, S and Thapa, S and Renuka, N}, title = {Influence of cyanobacterial inoculation on the culturable microbiome and growth of rice.}, journal = {Microbiological research}, volume = {171}, number = {}, pages = {78-89}, doi = {10.1016/j.micres.2014.12.011}, pmid = {25644956}, issn = {1618-0623}, mesh = {Biodiversity ; Biological Evolution ; Chlorophyll/metabolism ; Cyanobacteria/classification/*genetics/metabolism/ultrastructure ; DNA Fingerprinting ; Fatty Acids/metabolism ; Indoleacetic Acids/metabolism ; *Metagenome ; *Microbiota ; Nitrogenase/metabolism ; Oryza/growth & development/metabolism/*microbiology ; Phylogeny ; Plant Roots/microbiology ; Plant Shoots/microbiology ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Rice plants are selective with their associations with bacteria that are beneficial for growth, nutrient uptake, exhibit induced resistance or antagonism towards pathogens. Cyanobacteria as bioinoculants are known to promote the growth and health of rice plants. The present investigation was aimed at understanding whether and how cyanobacterial (Calothrix elenkinii) inoculation influenced the rice plant growth and the culturable bacterial populations and identifying the dominant culturable "microbiome" members. The plant tissue extracts were used to enumerate populations of the culturable microbiome members using selected enrichment media with different nutrient levels. About 10-fold increases in population densities of culturable microbiome members in different media were recorded, with some isolates having metabolic potential for nitrogen fixation and phosphorus solubilization. Fatty acid methyl ester (FAME) analysis and 16S rRNA sequencing of selected microbial morphotypes suggested the predominance of the members of Bacillaceae. Significant increases in plant growth attributes, nitrogenase activity and indole acetic acid production, and activities of hydrolytic and defense enzymes were recorded in the Calothrix inoculated plants. The PCR-based analysis and scanning electron microscopic (SEM) observations confirmed the presence of inoculated cyanobacterium inside the plant tissues. This investigation illustrated that cyanobacterial inoculation can play significant roles in improving growth and metabolism of rice directly and interact with the beneficial members from the endophytic microbiome of rice seedlings synergistically.}, } @article {pmid25644890, year = {2015}, author = {Pérez-Chaparro, PJ and Duarte, PM and Pannuti, CM and Figueiredo, LC and Mestnik, MJ and Gonçalves, CP and Faveri, M and Feres, M}, title = {Evaluation of human and microbial DNA content in subgingival plaque samples collected by paper points or curette.}, journal = {Journal of microbiological methods}, volume = {111}, number = {}, pages = {19-20}, doi = {10.1016/j.mimet.2015.01.023}, pmid = {25644890}, issn = {1872-8359}, mesh = {Chronic Periodontitis/microbiology ; DNA/*isolation & purification ; DNA, Bacterial/*isolation & purification ; Dental Plaque/*microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; Microbiota ; Paper ; *Real-Time Polymerase Chain Reaction ; Specimen Handling/methods ; }, abstract = {Host DNA may adversely affect metagenomic studies focusing on the prokaryotic microbiota. This study compared the levels of host DNA in subgingival plaque collected by paper points and curette, using quantitative PCR. Lower proportions of host DNA and higher proportions of bacterial DNA were recovered from samples collected with curettes.}, } @article {pmid25640238, year = {2015}, author = {Greenblum, S and Carr, R and Borenstein, E}, title = {Extensive strain-level copy-number variation across human gut microbiome species.}, journal = {Cell}, volume = {160}, number = {4}, pages = {583-594}, pmid = {25640238}, issn = {1097-4172}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; DP2 AT 007802-01/AT/NCCIH NIH HHS/United States ; }, mesh = {Bacteroidaceae/classification/*genetics ; Bacteroidetes/classification/*genetics ; Enterobacteriaceae/classification/*genetics ; Gastrointestinal Tract/*microbiology ; *Gene Dosage ; Gram-Positive Bacteria/classification/*genetics ; Humans ; Inflammatory Bowel Diseases/microbiology ; *Microbiota ; Obesity/microbiology ; Principal Component Analysis ; }, abstract = {Within each bacterial species, different strains may vary in the set of genes they encode or in the copy number of these genes. Yet, taxonomic characterization of the human microbiota is often limited to the species level or to previously sequenced strains, and accordingly, the prevalence of intra-species variation, its functional role, and its relation to host health remain unclear. Here, we present a comprehensive large-scale analysis of intra-species copy-number variation in the gut microbiome, introducing a rigorous computational pipeline for detecting such variation directly from shotgun metagenomic data. We uncover a large set of variable genes in numerous species and demonstrate that this variation has significant functional and clinically relevant implications. We additionally infer intra-species compositional profiles, identifying population structure shifts and the presence of yet uncharacterized variants. Our results highlight the complex relationship between microbiome composition and functional capacity, linking metagenome-level compositional shifts to strain-level variation.}, } @article {pmid25639680, year = {2015}, author = {Brum, JR and Sullivan, MB}, title = {Rising to the challenge: accelerated pace of discovery transforms marine virology.}, journal = {Nature reviews. Microbiology}, volume = {13}, number = {3}, pages = {147-159}, pmid = {25639680}, issn = {1740-1534}, mesh = {*Biota ; Metagenomics/methods/trends ; Seawater/*virology ; Virology/methods/trends ; }, abstract = {Marine viruses have important roles in microbial mortality, gene transfer, metabolic reprogramming and biogeochemical cycling. In this Review, we discuss recent technological advances in marine virology including the use of near-quantitative, reproducible metagenomics for large-scale investigation of viral communities and the emergence of gene-based viral ecology. We also describe the reprogramming of microbially driven processes by viral metabolic genes, the identification of novel viruses using cultivation-dependent and cultivation-independent tools, and the potential for modelling studies to provide a framework for studying virus-host interactions. These transformative advances have set a rapid pace in exploring and predicting how marine viruses manipulate and respond to their environment.}, } @article {pmid25636948, year = {2015}, author = {Mika, M and Mack, I and Korten, I and Qi, W and Aebi, S and Frey, U and Latzin, P and Hilty, M}, title = {Dynamics of the nasal microbiota in infancy: a prospective cohort study.}, journal = {The Journal of allergy and clinical immunology}, volume = {135}, number = {4}, pages = {905-912.e11}, doi = {10.1016/j.jaci.2014.12.1909}, pmid = {25636948}, issn = {1097-6825}, mesh = {Bacteria/classification/genetics ; Bacterial Load ; Biodiversity ; DNA, Bacterial ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenome ; *Microbiota ; Nose/*microbiology ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Seasons ; }, abstract = {BACKGROUND: Understanding the composition and dynamics of the upper respiratory tract microbiota in healthy infants is a prerequisite to investigate the role of the microbiota in patients with respiratory diseases. This is especially true in early life, when the immune system is in development.

OBJECTIVE: We sought to describe the dynamics of the upper respiratory tract microbiota in healthy infants within the first year of life.

METHODS: After exclusion of low-quality samples, microbiota characterization was performed by using 16S rDNA pyrosequencing of 872 nasal swabs collected biweekly from 47 unselected infants.

RESULTS: Bacterial density increased and diversity decreased within the first year of life (R(2) = 0.95 and 0.73, respectively). A distinct profile for the first 3 months of life was found with increased relative abundances of Staphlyococcaceae and Corynebacteriaceae (exponential decay: R(2) = 0.94 and 0.96, respectively). In addition, relative bacterial abundance and composition differed significantly from summer to winter months. The individual composition of the microbiota changed with increasing time intervals between samples and was best modeled by an exponential function (R(2) = 0.97). Within-subject dissimilarity in a 2-week time interval was consistently lower than that between subjects, indicating a personalized microbiota.

CONCLUSION: This study reveals age and seasonality as major factors driving the composition of the nasal microbiota within the first year of life. A subject's microbiota is personalized but dynamic throughout the first year. These data are indispensable to interpretation of cross-sectional studies and investigation of the role of the microbiota in both healthy subjects and patients with respiratory diseases. They might also serve as a baseline for future intervention studies.}, } @article {pmid25635690, year = {2015}, author = {Day, JM and Oakley, BB and Seal, BS and Zsak, L}, title = {Comparative analysis of the intestinal bacterial and RNA viral communities from sentinel birds placed on selected broiler chicken farms.}, journal = {PloS one}, volume = {10}, number = {1}, pages = {e0117210}, pmid = {25635690}, issn = {1932-6203}, mesh = {*Animal Husbandry ; Animals ; Chickens/*microbiology/*virology ; Cluster Analysis ; Intestines/*microbiology/*virology ; Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Viral/*genetics ; Sequence Analysis, RNA ; }, abstract = {There is a great deal of interest in characterizing the complex microbial communities in the poultry gut, and in understanding the effects of these dynamic communities on poultry performance, disease status, animal welfare, and microbes with human health significance. Investigations characterizing the poultry enteric virome have identified novel poultry viruses, but the roles these viruses play in disease and performance problems have yet to be fully characterized. The complex bacterial community present in the poultry gut influences gut development, immune status, and animal health, each of which can be an indicator of overall performance. The present metagenomic investigation was undertaken to provide insight into the colonization of specific pathogen free chickens by enteric microorganisms under field conditions and to compare the pre-contact intestinal microbiome with the altered microbiome following contact with poultry raised in the field. Analysis of the intestinal virome from contact birds ("sentinels") placed on farms revealed colonization by members of the Picornaviridae, Picobirnaviridae, Reoviridae, and Astroviridae that were not present in pre-contact birds or present in proportionally lower numbers. Analysis of the sentinel gut bacterial community revealed an altered community in the post-contact birds, notably by members of the Lachnospiracea/Clostridium and Lactobacillus families and genera. Members of the avian enteric Reoviridae and Astroviridae have been well-characterized and have historically been implicated in poultry enteric disease; members of the Picobirnaviridae and Picornaviridae have only relatively recently been described in the poultry and avian gut, and their roles in the recognized disease syndromes and in poultry performance in general have not been determined. This metagenomic analysis has provided insight into the colonization of the poultry gut by enteric microbes circulating in commercial broiler flocks, and has identified enteric viruses and virus communities that warrant further study in order to understand their role(s) in avian gut health and disease.}, } @article {pmid25632945, year = {2015}, author = {Rocca-Serra, P and Walls, R and Parnell, J and Gallery, R and Zheng, J and Sansone, SA and Gonzalez-Beltran, A}, title = {Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach.}, journal = {Database : the journal of biological databases and curation}, volume = {2015}, number = {}, pages = {}, pmid = {25632945}, issn = {1758-0463}, support = {BB/I025840/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; EU COSMOS EC312941/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/E025080/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/I000771/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J020265/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biodiversity ; Gene Ontology ; *Genes, Bacterial ; *Genes, rRNA ; Microbial Consortia/*physiology ; *Models, Biological ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The advent of affordable sequencing technology provides for a new generation of explorers who probe the world's microbial diversity. Projects such as Tara Oceans, Moorea Biocode Project and Gut Microbiome rely on sequencing technologies to probe community diversity. Either targeted gene surveys (also known as community surveys) or complete metagenomes are evaluated. The former, being the less costly of the two methods, relies on the identification of specific genomic regions, which can be used as a proxy to estimate genetic distance between related species in a Phylum. For instance, 16 S ribosomal RNA gene surveys are used to probe bacterial communities while internal transcribed spacer surveys, for example, can be used for probing fungal communities. With the explosion of projects and frenzy to explore new domains of life, scientists in the field have issued guidelines to report minimal information (following a checklist), ensuring that information is contextualized in a meaningful way. Yet the semantics of a checklist are not explicit. We demonstrate here how a tabular template can be used to collect information on microbial diversity using an explicit representation in the Resource Description Framework that is consistent with community agreed-upon knowledge representation patterns found in the Ontology for Biomedical Investigations.}, } @article {pmid25630378, year = {2015}, author = {Zhbannikov, IY and Foster, JA}, title = {MetAmp: combining amplicon data from multiple markers for OTU analysis.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {11}, pages = {1830-1832}, pmid = {25630378}, issn = {1367-4811}, support = {F31 GM016448/GM/NIGMS NIH HHS/United States ; P20 GM103408/GM/NIGMS NIH HHS/United States ; P20GM016454/GM/NIGMS NIH HHS/United States ; P20GM16448/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Classification/methods ; Genetic Markers ; Humans ; Metagenomics/*methods ; Microbiota ; RNA, Ribosomal, 16S/genetics ; *Software ; }, abstract = {MOTIVATION: We present a novel method and corresponding application, MetAmp, to combine amplicon data from multiple genomic markers into Operational Taxonomic Units (OTUs) for microbial community analysis, calibrating the markers using data from known microbial genomes. When amplicons for multiple markers such as the 16S rRNA gene hypervariable regions are available, MetAmp improves the accuracy of OTU-based methods for characterizing bacterial composition and community structure. MetAmp works best with at least three markers, and is applicable to non-bacterial analyses and to non 16S markers. Our application and testing have been limited to 16S analysis of microbial communities.

RESULTS: We clustered standard test sequences derived from the Human Microbiome Mock Community test sets and compared MetAmp and other tools with respect to their ability to recover OTUs for these benchmark bacterial communities. MetAmp compared favorably to QIIME, UPARSE and Mothur using amplicons from one, two, and three markers.

MetAmp is available at http://izhbannikov.github.io/MetAmp/.}, } @article {pmid25629612, year = {2015}, author = {Boutin, S and Graeber, SY and Weitnauer, M and Panitz, J and Stahl, M and Clausznitzer, D and Kaderali, L and Einarsson, G and Tunney, MM and Elborn, JS and Mall, MA and Dalpke, AH}, title = {Comparison of microbiomes from different niches of upper and lower airways in children and adolescents with cystic fibrosis.}, journal = {PloS one}, volume = {10}, number = {1}, pages = {e0116029}, pmid = {25629612}, issn = {1932-6203}, mesh = {Adolescent ; Biodiversity ; Child ; Computational Biology ; Cross-Sectional Studies ; Cystic Fibrosis/*complications ; Datasets as Topic ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenome ; *Microbiota ; Prospective Studies ; Respiratory Tract Infections/*etiology/*microbiology ; Risk Factors ; Young Adult ; }, abstract = {Changes in the airway microbiome may be important in the pathophysiology of chronic lung disease in patients with cystic fibrosis. However, little is known about the microbiome in early cystic fibrosis lung disease and the relationship between the microbiomes from different niches in the upper and lower airways. Therefore, in this cross-sectional study, we examined the relationship between the microbiome in the upper (nose and throat) and lower (sputum) airways from children with cystic fibrosis using next generation sequencing. Our results demonstrate a significant difference in both α and β-diversity between the nose and the two other sampling sites. The nasal microbiome was characterized by a polymicrobial community while the throat and sputum communities were less diverse and dominated by a few operational taxonomic units. Moreover, sputum and throat microbiomes were closely related especially in patients with clinically stable lung disease. There was a high inter-individual variability in sputum samples primarily due to a decrease in evenness linked to increased abundance of potential respiratory pathogens such as Pseudomonas aeruginosa. Patients with chronic Pseudomonas aeruginosa infection exhibited a less diverse sputum microbiome. A high concordance was found between pediatric and adult sputum microbiomes except that Burkholderia was only observed in the adult cohort. These results indicate that an adult-like lower airways microbiome is established early in life and that throat swabs may be a good surrogate in clinically stable children with cystic fibrosis without chronic Pseudomonas aeruginosa infection in whom sputum sampling is often not feasible.}, } @article {pmid25629401, year = {2015}, author = {Lim, SW and Tran, TM and Abate, AR}, title = {PCR-activated cell sorting for cultivation-free enrichment and sequencing of rare microbes.}, journal = {PloS one}, volume = {10}, number = {1}, pages = {e0113549}, pmid = {25629401}, issn = {1932-6203}, mesh = {Escherichia coli/classification/genetics ; Escherichia coli Proteins/genetics ; *Flow Cytometry/methods ; Genome, Bacterial ; *Metagenomics ; Microbiota/genetics ; *Polymerase Chain Reaction/methods ; Real-Time Polymerase Chain Reaction ; Reproducibility of Results ; Single-Cell Analysis/methods ; }, abstract = {Microbial systems often exhibit staggering diversity, making the study of rare, interesting species challenging. For example, metagenomic analyses of mixed-cell populations are often dominated by the sequences of the most abundant organisms, while those of rare microbes are detected only at low levels, if at all. To overcome this, selective cultivation or fluorescence-activated cell sorting (FACS) can be used to enrich for the target species prior to sequence analysis; however, since most microbes cannot be grown in the lab, cultivation strategies often fail, while cell sorting requires techniques to uniquely label the cell type of interest, which is often not possible with uncultivable microbes. Here, we introduce a culture-independent strategy for sorting microbial cells based on genomic content, which we term PCR-activated cell sorting (PACS). This technology, which utilizes the power of droplet-based microfluidics, is similar to FACS in that it uses a fluorescent signal to uniquely identify and sort target species. However, PACS differs importantly from FACS in that the signal is generated by performing PCR assays on the cells in microfluidic droplets, allowing target cells to be identified with high specificity with suitable design of PCR primers and TaqMan probes. The PACS assay is general, requires minimal optimization and, unlike antibody methods, can be developed without access to microbial antigens. Compared to non-specific methods in which cells are sorted based on size, granularity, or the ability to take up dye, PACS enables genetic sequence-specific sorting and recovery of the cell genomes. In addition to sorting microbes, PACS can be applied to eukaryotic cells, viruses, and naked nucleic acids.}, } @article {pmid25627938, year = {2015}, author = {Berg, G}, title = {Beyond borders: investigating microbiome interactivity and diversity for advanced biocontrol technologies.}, journal = {Microbial biotechnology}, volume = {8}, number = {1}, pages = {5-7}, pmid = {25627938}, issn = {1751-7915}, mesh = {Bacteria/genetics/growth & development/isolation & purification ; Bacterial Infections/microbiology/*prevention & control ; *Bacterial Physiological Phenomena ; *Biodiversity ; Humans ; Metagenome ; *Microbiota ; Plant Diseases/microbiology/*prevention & control ; }, } @article {pmid25625766, year = {2015}, author = {Lindsay, B and Oundo, J and Hossain, MA and Antonio, M and Tamboura, B and Walker, AW and Paulson, JN and Parkhill, J and Omore, R and Faruque, AS and Das, SK and Ikumapayi, UN and Adeyemi, M and Sanogo, D and Saha, D and Sow, S and Farag, TH and Nasrin, D and Li, S and Panchalingam, S and Levine, MM and Kotloff, K and Magder, LS and Hungerford, L and Sommerfelt, H and Pop, M and Nataro, JP and Stine, OC}, title = {Microbiota that affect risk for shigellosis in children in low-income countries.}, journal = {Emerging infectious diseases}, volume = {21}, number = {2}, pages = {242-250}, pmid = {25625766}, issn = {1080-6059}, support = {MC_U190074190/MRC_/Medical Research Council/United Kingdom ; MC_U190081991/MRC_/Medical Research Council/United Kingdom ; U19 AI090873/AI/NIAID NIH HHS/United States ; U19 090873//PHS HHS/United States ; }, mesh = {Age Factors ; Biodiversity ; Case-Control Studies ; Child, Preschool ; Developing Countries ; Diarrhea/diagnosis/epidemiology/microbiology ; Dysentery, Bacillary/diagnosis/*epidemiology/*microbiology ; Feces/microbiology/virology ; Gastrointestinal Tract/microbiology/virology ; Genes, Bacterial ; Humans ; Infant ; Infant, Newborn ; Metagenome ; *Microbiota ; Odds Ratio ; RNA, Ribosomal, 16S/genetics ; Risk ; Severity of Illness Index ; Shigella/classification/*genetics ; }, abstract = {Pathogens in the gastrointestinal tract exist within a vast population of microbes. We examined associations between pathogens and composition of gut microbiota as they relate to Shigella spp./enteroinvasive Escherichia coli infection. We analyzed 3,035 stool specimens (1,735 nondiarrheal and 1,300 moderate-to-severe diarrheal) from the Global Enteric Multicenter Study for 9 enteropathogens. Diarrheal specimens had a higher number of enteropathogens (diarrheal mean 1.4, nondiarrheal mean 0.95; p<0.0001). Rotavirus showed a negative association with Shigella spp. in cases of diarrhea (odds ratio 0.31, 95% CI 0.17-0.55) and had a large combined effect on moderate-to-severe diarrhea (odds ratio 29, 95% CI 3.8-220). In 4 Lactobacillus taxa identified by 16S rRNA gene sequencing, the association between pathogen and disease was decreased, which is consistent with the possibility that Lactobacillus spp. are protective against Shigella spp.-induced diarrhea. Bacterial diversity of gut microbiota was associated with diarrhea status, not high levels of the Shigella spp. ipaH gene.}, } @article {pmid25625313, year = {2015}, author = {Yoon, SS and Kim, EK and Lee, WJ}, title = {Functional genomic and metagenomic approaches to understanding gut microbiota-animal mutualism.}, journal = {Current opinion in microbiology}, volume = {24}, number = {}, pages = {38-46}, doi = {10.1016/j.mib.2015.01.007}, pmid = {25625313}, issn = {1879-0364}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Metagenomics ; Symbiosis ; }, abstract = {Accumulating data sets of gut microbiome by next-generation sequencing allow us to gain a comprehensive view of the functional diversity of the gut-associated metagenome. However, many microbiome functions are unknown and/or have only been predicted, and may not necessarily reflect the in vivo function within a gut niche. Functional genomic and metagenomic approaches have been successfully applied to broaden the understanding of invertebrate and vertebrate gut microbiome involved in diverse functions, including colonization ability, nutritional processing, antibiotic resistance, microbial physiology and metabolism, and the modulation of the host physiology. In this review, we discuss the recent knowledge obtained from the study of functional genomics and metagenomics of the animal intestine and its potential values for understanding gut microbiota-animal mutualism.}, } @article {pmid25624713, year = {2015}, author = {Wang, WL and Xu, SY and Ren, ZG and Tao, L and Jiang, JW and Zheng, SS}, title = {Application of metagenomics in the human gut microbiome.}, journal = {World journal of gastroenterology}, volume = {21}, number = {3}, pages = {803-814}, pmid = {25624713}, issn = {2219-2840}, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacteria/drug effects/*genetics ; Drug Resistance, Bacterial/genetics ; Dysbiosis ; Gene Expression Regulation, Bacterial ; Host-Pathogen Interactions ; Humans ; Intestines/*microbiology ; *Metagenome/drug effects ; *Metagenomics/methods ; Microbiota/*genetics ; }, abstract = {There are more than 1000 microbial species living in the complex human intestine. The gut microbial community plays an important role in protecting the host against pathogenic microbes, modulating immunity, regulating metabolic processes, and is even regarded as an endocrine organ. However, traditional culture methods are very limited for identifying microbes. With the application of molecular biologic technology in the field of the intestinal microbiome, especially metagenomic sequencing of the next-generation sequencing technology, progress has been made in the study of the human intestinal microbiome. Metagenomics can be used to study intestinal microbiome diversity and dysbiosis, as well as its relationship to health and disease. Moreover, functional metagenomics can identify novel functional genes, microbial pathways, antibiotic resistance genes, functional dysbiosis of the intestinal microbiome, and determine interactions and co-evolution between microbiota and host, though there are still some limitations. Metatranscriptomics, metaproteomics and metabolomics represent enormous complements to the understanding of the human gut microbiome. This review aims to demonstrate that metagenomics can be a powerful tool in studying the human gut microbiome with encouraging prospects. The limitations of metagenomics to be overcome are also discussed. Metatranscriptomics, metaproteomics and metabolomics in relation to the study of the human gut microbiome are also briefly discussed.}, } @article {pmid25622869, year = {2015}, author = {Treven, P and Mrak, V and Bogovič Matijašić, B and Horvat, S and Rogelj, I}, title = {Administration of probiotics Lactobacillus rhamnosus GG and Lactobacillus gasseri K7 during pregnancy and lactation changes mouse mesenteric lymph nodes and mammary gland microbiota.}, journal = {Journal of dairy science}, volume = {98}, number = {4}, pages = {2114-2128}, doi = {10.3168/jds.2014-8519}, pmid = {25622869}, issn = {1525-3198}, mesh = {Animals ; Bacterial Load ; Bifidobacterium/metabolism ; DNA, Bacterial/genetics/*isolation & purification ; Feces/microbiology ; Female ; Lactation ; Lactobacillus/metabolism ; Lacticaseibacillus rhamnosus/metabolism ; Lymph Nodes/metabolism/*microbiology ; Male ; Mammary Glands, Animal/metabolism/*microbiology ; Metagenomics/methods ; Mice ; Mice, Inbred Strains ; *Microbiota ; Milk/microbiology ; Pregnancy ; Probiotics/*administration & dosage ; RNA, Ribosomal, 16S/*isolation & purification ; Sequence Analysis, DNA ; }, abstract = {The milk and mammary gland (MG) microbiome can be influenced by several factors, such as mode of delivery, breastfeeding, maternal lifestyle, health status, and diet. An increasing number of studies show a variety of positive effects of consumption of probiotics during pregnancy and breastfeeding on the mother and the newborn. The aim of this study was to investigate the effect of oral administration of probiotics Lactobacillus gasseri K7 (LK7) and Lactobacillus rhamnosus GG (LGG) during pregnancy and lactation on microbiota of the mouse mesenteric lymph nodes (MLN), MG, and milk. Pregnant FVB/N mice were fed skim milk or probiotics LGG or LK7 resuspended in skim milk during gestation and lactation. On d 3 and 8 postpartum, blood, feces, MLN, MG, and milk were analyzed for the presence of LGG or LK7. The effects of probiotics on MLN, MG, and milk microbiota was evaluated by real-time PCR and by 16S ribosomal DNA 454-pyrosequencing. In 5 of 8 fecal samples from the LGG group and in 5 of 8 fecal samples from the LK7 group, more than 1 × 10(3) of live LGG or LK7 bacterial cells were detected, respectively, whereas no viable LGG or LK7 cells were detected in the control group. Live lactic acid bacteria but no LGG or LK7 were detected in blood, MLN, and MG. Both probiotics significantly increased the total bacterial load as assessed by copies of 16S ribosomal DNA in MLN, and a similar trend was observed in MG. Metagenomic sequencing revealed that both probiotics increased the abundance of Firmicutes in MG, especially the abundance of lactic acid bacteria. The Lactobacillus genus appeared exclusively in MG from probiotic groups. Both probiotics influenced MLN microbiota by decreasing diversity (Chao1) and increasing the distribution of species (Shannon index). The LGG probiotic also affected the MG microbiota as it increased diversity and distribution of species and proportions of the genera Lactobacillus and Bifidobacterium. These results provide evidence that probiotics can modulate the bacterial composition of MLN and MG microbiota in ways that could improve the health of the MG and, ultimately, the health of the newborn.}, } @article {pmid25619480, year = {2015}, author = {Tai, N and Wong, FS and Wen, L}, title = {The role of gut microbiota in the development of type 1, type 2 diabetes mellitus and obesity.}, journal = {Reviews in endocrine & metabolic disorders}, volume = {16}, number = {1}, pages = {55-65}, pmid = {25619480}, issn = {1573-2606}, support = {DK09882/DK/NIDDK NIH HHS/United States ; UL1 RR024139/RR/NCRR NIH HHS/United States ; F32 DK009882/DK/NIDDK NIH HHS/United States ; UL1 RR 024139/RR/NCRR NIH HHS/United States ; R01 DK088181/DK/NIDDK NIH HHS/United States ; P30 DK045735/DK/NIDDK NIH HHS/United States ; DK088181/DK/NIDDK NIH HHS/United States ; UL1 TR000142/TR/NCATS NIH HHS/United States ; R01 DK092882/DK/NIDDK NIH HHS/United States ; DK100500/DK/NIDDK NIH HHS/United States ; R01 DK100500/DK/NIDDK NIH HHS/United States ; }, mesh = {Diabetes Mellitus, Type 1/metabolism/*microbiology ; Diabetes Mellitus, Type 2/metabolism/*microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Microbiota/*physiology ; Obesity/metabolism/*microbiology ; }, abstract = {Diabetes is a group of metabolic disorders characterized by persistent hyperglycemia and has become a major public health concern. Autoimmune type 1 diabetes (T1D) and insulin resistant type 2 diabetes (T2D) are the two main types. A combination of genetic and environmental factors contributes to the development of these diseases. Gut microbiota have emerged recently as an essential player in the development of T1D, T2D and obesity. Altered gut microbiota have been strongly linked to disease in both rodent models and humans. Both classic 16S rRNA sequencing and shot-gun metagenomic pyrosequencing analysis have been successfully applied to explore the gut microbiota composition and functionality. This review focuses on the association between gut microbiota and diabetes and discusses the potential mechanisms by which gut microbiota regulate disease development in T1D, T2D and obesity.}, } @article {pmid25617726, year = {2015}, author = {Kang, DW and DiBaise, JK and Ilhan, ZE and Crowell, MD and Rideout, JR and Caporaso, JG and Rittmann, BE and Krajmalnik-Brown, R}, title = {Gut microbial and short-chain fatty acid profiles in adults with chronic constipation before and after treatment with lubiprostone.}, journal = {Anaerobe}, volume = {33}, number = {}, pages = {33-41}, doi = {10.1016/j.anaerobe.2015.01.005}, pmid = {25617726}, issn = {1095-8274}, mesh = {Adult ; Aged ; Biodiversity ; Case-Control Studies ; Chloride Channel Agonists/therapeutic use ; Chronic Disease ; Constipation/drug therapy/*metabolism/*microbiology ; Fatty Acids, Volatile/*metabolism ; Female ; *Gastrointestinal Microbiome ; Gene Dosage ; Humans ; Lubiprostone/therapeutic use ; Male ; Metagenome ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; }, abstract = {Identifying specific gut microorganisms associated with chronic constipation may be useful for diagnostic and therapeutic purposes. The objective of this study was to evaluate whether or not the gut microbial community of constipated subjects had specific microbial signatures and to assess the effects of lubiprostone treatment on the gut microbial community. Stool diaries, breath H2 and CH4 levels, and stool samples were collected from ten healthy subjects and nine patients meeting the Rome III criteria for chronic functional constipation. Constipated subjects received lubiprostone for four weeks, during which stool diaries were maintained. Stool samples were evaluated for gut microbial communities using pyrosequencing and quantitative real-time PCR (qPCR) targeting 16S-rRNA gene, along with concentrations of short-chain fatty acids (SCFAs) using high-performance liquid chromatography. Prior to treatment, gut microbial profiles were similar between constipated subjects and healthy subjects, while iso-butyrate levels were significantly higher in constipated subjects compared with healthy subjects. Despite increases in stool frequency and improvements in consistency after lubiprostone treatment, gut microbial profiles and community diversity after treatment showed no significant change compared to before treatment. While we did not observe a significant difference in either breath methane or archaeal abundance between the stool samples of healthy and constipated subjects, we confirmed a strong correlation between archaeal abundance measured by qPCR and the amount of methane gas exhaled in the fasting breath. Butyrate levels, however, were significantly higher in the stool samples of constipated subjects after lubiprostone treatment, suggesting that lubiprostone treatment had an effect on the net accumulation of SCFAs in the gut. In conclusion, lubiprostone treatment improved constipation symptoms and increased levels of butyrate without substantial modification of the gut microbial structure.}, } @article {pmid25615931, year = {2015}, author = {Doré, J and Blottière, H}, title = {The influence of diet on the gut microbiota and its consequences for health.}, journal = {Current opinion in biotechnology}, volume = {32}, number = {}, pages = {195-199}, doi = {10.1016/j.copbio.2015.01.002}, pmid = {25615931}, issn = {1879-0429}, mesh = {Animals ; *Diet ; Feeding Behavior ; Humans ; Intestines/*microbiology ; Life Style ; Metagenome ; *Microbiota ; }, abstract = {Man is an intimate symbiosis between 10 trillion human cells and some 100 trillion bacteria, most of which inhabit the intestine where they constitute an extremely dense and diverse microbiota. This symbiotic balance that has to be established within each newborn is key to the maintenance of health and well being. Its development is markedly influenced by microbial exposure encountered very early in life. Mode of infant feeding, and the post-weaning transition to habitual diet will further shape the microbiota. Recent studies support the concept that diet should be viewed as a means to prevent potentially durable alterations of symbiosis observed in immune-mediated metabolic and inflammatory diseases. Non-digestible dietary fiber will play a major role in this context.}, } @article {pmid25615436, year = {2015}, author = {Orsi, WD and Smith, JM and Wilcox, HM and Swalwell, JE and Carini, P and Worden, AZ and Santoro, AE}, title = {Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter.}, journal = {The ISME journal}, volume = {9}, number = {8}, pages = {1747-1763}, pmid = {25615436}, issn = {1751-7370}, mesh = {California ; DNA, Bacterial/analysis ; Euryarchaeota/genetics/*physiology ; Geologic Sediments ; In Situ Hybridization, Fluorescence ; Metagenome ; Organic Chemicals/*analysis ; *Particulate Matter ; Phylogeny ; Phytoplankton/genetics ; RNA, Ribosomal, 16S/analysis ; Seawater/chemistry/*microbiology ; }, abstract = {Particles in aquatic environments host distinct communities of microbes, yet the evolution of particle-specialized taxa and the extent to which specialized microbial metabolism is associated with particles is largely unexplored. Here, we investigate the hypothesis that a widely distributed and uncultivated microbial group--the marine group II euryarchaea (MGII)--interacts with living and detrital particulate organic matter (POM) in the euphotic zone of the central California Current System. Using fluorescent in situ hybridization, we verified the association of euryarchaea with POM. We further quantified the abundance and distribution of MGII 16 S ribosomal RNA genes in size-fractionated seawater samples and compared MGII functional capacity in metagenomes from the same fractions. The abundance of MGII in free-living and >3 μm fractions decreased with increasing distance from the coast, whereas MGII abundance in the 0.8-3 μm fraction remained constant. At several offshore sites, MGII abundance was highest in particle fractions, indicating that particle-attached MGII can outnumber free-living MGII under oligotrophic conditions. Compared with free-living MGII, the genome content of MGII in particle-associated fractions exhibits an increased capacity for surface adhesion, transcriptional regulation and catabolism of high molecular weight substrates. Moreover, MGII populations in POM fractions are phylogenetically distinct from and more diverse than free-living MGII. Eukaryotic phytoplankton additions stimulated MGII growth in bottle incubations, providing the first MGII net growth rate measurements. These ranged from 0.47 to 0.54 d(-1). However, MGII were not recovered in whole-genome amplifications of flow-sorted picoeukaryotic phytoplankton and heterotrophic nanoflagellates, suggesting that MGII in particle fractions are not physically attached to living POM. Collectively, our results support a linkage between MGII ecophysiology and POM, implying that marine archaea have a role in elemental cycling through interactions with particles.}, } @article {pmid25614621, year = {2015}, author = {Morgun, A and Dzutsev, A and Dong, X and Greer, RL and Sexton, DJ and Ravel, J and Schuster, M and Hsiao, W and Matzinger, P and Shulzhenko, N}, title = {Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks.}, journal = {Gut}, volume = {64}, number = {11}, pages = {1732-1743}, pmid = {25614621}, issn = {1468-3288}, support = {Z01 AI000581-19/ImNIH/Intramural NIH HHS/United States ; Z01 AI000581/ImNIH/Intramural NIH HHS/United States ; P40 RR018603/RR/NCRR NIH HHS/United States ; P40RR018603/RR/NCRR NIH HHS/United States ; U01 AI109695/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Gastrointestinal Microbiome/*drug effects/*genetics ; *Gene Regulatory Networks ; Mice ; Mice, Inbred C57BL ; }, abstract = {OBJECTIVE: Despite widespread use of antibiotics for the treatment of life-threatening infections and for research on the role of commensal microbiota, our understanding of their effects on the host is still very limited.

DESIGN: Using a popular mouse model of microbiota depletion by a cocktail of antibiotics, we analysed the effects of antibiotics by combining intestinal transcriptome together with metagenomic analysis of the gut microbiota. In order to identify specific microbes and microbial genes that influence the host phenotype in antibiotic-treated mice, we developed and applied analysis of the transkingdom network.

RESULTS: We found that most antibiotic-induced alterations in the gut can be explained by three factors: depletion of the microbiota; direct effects of antibiotics on host tissues and the effects of remaining antibiotic-resistant microbes. Normal microbiota depletion mostly led to downregulation of different aspects of immunity. The two other factors (antibiotic direct effects on host tissues and antibiotic-resistant microbes) primarily inhibited mitochondrial gene expression and amounts of active mitochondria, increasing epithelial cell death. By reconstructing and analysing the transkingdom network, we discovered that these toxic effects were mediated by virulence/quorum sensing in antibiotic-resistant bacteria, a finding further validated using in vitro experiments.

CONCLUSIONS: In addition to revealing mechanisms of antibiotic-induced alterations, this study also describes a new bioinformatics approach that predicts microbial components that regulate host functions and establishes a comprehensive resource on what, why and how antibiotics affect the gut in a widely used mouse model of microbiota depletion by antibiotics.}, } @article {pmid25613225, year = {2015}, author = {Ding, J and Zhang, Y and Deng, Y and Cong, J and Lu, H and Sun, X and Yang, C and Yuan, T and Van Nostrand, JD and Li, D and Zhou, J and Yang, Y}, title = {Integrated metagenomics and network analysis of soil microbial community of the forest timberline.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {7994}, pmid = {25613225}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics ; *Biodiversity ; Carbon Cycle/genetics ; Ecosystem ; Environment ; *Forests ; Gene Regulatory Networks ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Nitrogen Cycle/genetics ; Phosphorus/chemistry ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The forest timberline responds quickly and markedly to climate changes, rendering it a ready indicator. Climate warming has caused an upshift of the timberline worldwide. However, the impact on belowground ecosystem and biogeochemical cycles remain elusive. To understand soil microbial ecology of the timberline, we analyzed microbial communities via 16s rRNA Illumina sequencing, a microarray-based tool named GeoChip 4.0 and a random matrix theory-based association network approach. We selected 24 sampling sites at two vegetation belts forming the timberline of Shennongjia Mountain in Hubei Province of China, a region with extraordinarily rich biodiversity. We found that temperature, among all of measured environmental parameters, showed the most significant and extensive linkages with microbial biomass, microbial diversity and composition at both taxonomic and functional gene levels, and microbial association network. Therefore, temperature was the best predictor for microbial community variations in the timberline. Furthermore, abundances of nitrogen cycle and phosphorus cycle genes were concomitant with NH4(+)-N, NO3(-)-N and total phosphorus, offering tangible clues to the underlying mechanisms of soil biogeochemical cycles. As the first glimpse at both taxonomic and functional compositions of soil microbial community of the timberline, our findings have major implications for predicting consequences of future timberline upshift.}, } @article {pmid25609144, year = {2015}, author = {Zhang, Y and Zhao, F and Deng, Y and Zhao, Y and Ren, H}, title = {Metagenomic and metabolomic analysis of the toxic effects of trichloroacetamide-induced gut microbiome and urine metabolome perturbations in mice.}, journal = {Journal of proteome research}, volume = {14}, number = {4}, pages = {1752-1761}, doi = {10.1021/pr5011263}, pmid = {25609144}, issn = {1535-3907}, mesh = {Acetamides/*toxicity ; Animals ; Base Sequence ; Chloroacetates/*toxicity ; Disinfectants/*toxicity ; Gastrointestinal Microbiome/*drug effects ; High-Throughput Nucleotide Sequencing ; Magnetic Resonance Spectroscopy ; Metabolome/*drug effects/physiology ; Metabolomics/methods ; Mice ; Molecular Sequence Data ; Risk Assessment/methods ; Urine/*physiology ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Disinfection byproducts (DBPs) in drinking water have been linked to various diseases, including colon, colorectal, rectal, and bladder cancer. Trichloroacetamide (TCAcAm) is an emerging nitrogenous DBP, and our previous study found that TCAcAm could induce some changes associated with host-gut microbiota co-metabolism. In this study, we used an integrated approach combining metagenomics, based on high-throughput sequencing, and metabolomics, based on nuclear magnetic resonance (NMR), to evaluate the toxic effects of TCAcAm exposure on the gut microbiome and urine metabolome. High-throughput sequencing revealed that the gut microbiome's composition and function were significantly altered after TCAcAm exposure for 90 days in Mus musculus mice. In addition, metabolomic analysis showed that a number of gut microbiota-related metabolites were dramatically perturbed in the urine of the mice. These results may provide novel insight into evaluating the health risk of environmental pollutants as well as revealing the potential mechanism of TCAcAm's toxic effects.}, } @article {pmid25603154, year = {2015}, author = {Ma, J and Deng, Y and Yuan, T and Zhou, J and Alvarez, PJ}, title = {Succession of microbial functional communities in response to a pilot-scale ethanol-blended fuel release throughout the plume life cycle.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {198}, number = {}, pages = {154-160}, doi = {10.1016/j.envpol.2015.01.005}, pmid = {25603154}, issn = {1873-6424}, mesh = {Biodegradation, Environmental ; Chemical Hazard Release ; Environmental Pollutants/*metabolism ; Ethanol/*metabolism ; *Genes, Microbial ; Life Cycle Stages ; *Microbial Consortia ; Oxidation-Reduction ; Pilot Projects ; Protein Array Analysis ; }, abstract = {GeoChip, a comprehensive gene microarray, was used to examine changes in microbial functional gene structure throughout the 4-year life cycle of a pilot-scale ethanol blend plume, including 2-year continuous released followed by plume disappearance after source removal. Canonical correlation analysis (CCA) and Mantel tests showed that dissolved O2 (which was depleted within 5 days of initiating the release and rebounded 194 days after source removal) was the most influential environmental factor on community structure. Initially, the abundance of anaerobic BTEX degradation genes increased significantly while that of aerobic BTEX degradation genes decreased. Gene abundance for N fixation, nitrification, P utilization, sulfate reduction and S oxidation also increased, potentially changing associated biogeochemical cycle dynamics. After plume disappearance, most genes returned to pre-release abundance levels, but the final functional structure significantly differed from pre-release conditions. Overall, observed successions of functional structure reflected adaptive responses that were conducive to biodegradation of ethanol-blend releases.}, } @article {pmid25602283, year = {2015}, author = {Waldor, MK and Tyson, G and Borenstein, E and Ochman, H and Moeller, A and Finlay, BB and Kong, HH and Gordon, JI and Nelson, KE and Dabbagh, K and Smith, H}, title = {Where next for microbiome research?.}, journal = {PLoS biology}, volume = {13}, number = {1}, pages = {e1002050}, pmid = {25602283}, issn = {1545-7885}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; R37 AI042347/AI/NIAID NIH HHS/United States ; }, mesh = {Biological Evolution ; Biomedical Research/*trends ; Gastrointestinal Tract/microbiology ; Humans ; *Microbiota ; Skin/microbiology ; Synthetic Biology ; Systems Biology ; }, abstract = {The development of high-throughput sequencing technologies has transformed our capacity to investigate the composition and dynamics of the microbial communities that populate diverse habitats. Over the past decade, these advances have yielded an avalanche of metagenomic data. The current stage of "van Leeuwenhoek"-like cataloguing, as well as functional analyses, will likely accelerate as DNA and RNA sequencing, plus protein and metabolic profiling capacities and computational tools, continue to improve. However, it is time to consider: what's next for microbiome research? The short pieces included here briefly consider the challenges and opportunities awaiting microbiome research.}, } @article {pmid25600706, year = {2015}, author = {Kim, YS and Kim, J and Park, SJ}, title = {High-throughput 16S rRNA gene sequencing reveals alterations of mouse intestinal microbiota after radiotherapy.}, journal = {Anaerobe}, volume = {33}, number = {}, pages = {1-7}, doi = {10.1016/j.anaerobe.2015.01.004}, pmid = {25600706}, issn = {1095-8274}, mesh = {Animals ; Biodiversity ; Cluster Analysis ; Computational Biology ; Gamma Rays ; Gastrointestinal Microbiome/*radiation effects ; Gastrointestinal Tract/microbiology/radiation effects ; High-Throughput Nucleotide Sequencing ; Intestinal Mucosa/microbiology/radiation effects ; Male ; *Metagenome ; Mice ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The mammalian gastrointestinal tract harbors a highly complex microbial community that comprises hundreds of different types of bacterial cells. The gastrointestinal microbiota plays an important role in the function of the host intestine. Most cancer patients undergoing pelvic irradiation experience side effects such as diarrhea; however, little is currently known about the effects of irradiation on the microorganisms colonizing the mucosal surfaces of the gastrointestinal tract. The aim of this study was to investigate the effects of gamma irradiation on the compositions of the large and small intestinal microbiotas. The gut microbiotas in control mice and mice receiving irradiation treatment were characterized by high-throughput sequencing of the bacterial 16S rRNA gene. Irradiation treatment induced significant alterations in the bacterial compositions of the large and small intestines at the genus level. Unexpectedly, irradiation treatment increased the number of operational taxonomic units in the small intestine but not the large intestine. In particular, irradiation treatment increased the level of the genera Alistipes in the large intestine and increased the level of the genus Corynebacterium in the small intestine. By contrast, compared with that in the corresponding control group, the level of the genera Prevotella was lower in the irradiated large intestine, and the level of the genera Alistipes was lower in the irradiated small intestine. Overall, the data presented here reveal the potential microbiological effects of pelvic irradiation on the gastrointestinal tracts of cancer patients.}, } @article {pmid25599982, year = {2015}, author = {Azad, MB and Konya, T and Guttman, DS and Field, CJ and Sears, MR and HayGlass, KT and Mandhane, PJ and Turvey, SE and Subbarao, P and Becker, AB and Scott, JA and Kozyrskyj, AL and , }, title = {Infant gut microbiota and food sensitization: associations in the first year of life.}, journal = {Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology}, volume = {45}, number = {3}, pages = {632-643}, doi = {10.1111/cea.12487}, pmid = {25599982}, issn = {1365-2222}, support = {100714//Wellcome Trust/United Kingdom ; 227312//Canadian Institutes of Health Research/Canada ; }, mesh = {Age Factors ; Biodiversity ; Canada/epidemiology ; Female ; Food Hypersensitivity/epidemiology/*etiology ; Gastrointestinal Tract/*immunology/*microbiology ; Humans ; Infant ; Infant Food/*adverse effects ; Infant, Newborn ; Male ; Metagenome ; *Microbiota ; Population Surveillance ; RNA, Ribosomal, 16S ; Skin Tests ; }, abstract = {BACKGROUND: The gut microbiota is established during infancy and plays a fundamental role in shaping host immunity. Colonization patterns may influence the development of atopic disease, but existing evidence is limited and conflicting.

OBJECTIVE: To explore associations of infant gut microbiota and food sensitization.

METHODS: Food sensitization at 1 year was determined by skin prick testing in 166 infants from the population-based Canadian Healthy Infant Longitudinal Development (CHILD) study. Faecal samples were collected at 3 and 12 months, and microbiota was characterized by Illumina 16S rRNA sequencing.

RESULTS: Twelve infants (7.2%) were sensitized to ≥ 1 common food allergen at 1 year. Enterobacteriaceae were overrepresented and Bacteroidaceae were underrepresented in the gut microbiota of food-sensitized infants at 3 months and 1 year, whereas lower microbiota richness was evident only at 3 months. Each quartile increase in richness at 3 months was associated with a 55% reduction in risk for food sensitization by 1 year (adjusted odds ratio 0.45, 95% confidence interval 0.23-0.87). Independently, each quartile increase in Enterobacteriaceae/Bacteroidaceae ratio was associated with a twofold increase in risk (2.02, 1.07-3.80). These associations were upheld in a sensitivity analysis among infants who were vaginally delivered, exclusively breastfed and unexposed to antibiotics. At 1 year, the Enterobacteriaceae/Bacteroidaceae ratio remained elevated among sensitized infants, who also tended to have decreased abundance of Ruminococcaceae.

Low gut microbiota richness and an elevated Enterobacteriaceae/Bacteroidaceae ratio in early infancy are associated with subsequent food sensitization, suggesting that early gut colonization may contribute to the development of atopic disease, including food allergy.}, } @article {pmid25599565, year = {2015}, author = {Charlop-Powers, Z and Owen, JG and Reddy, BV and Ternei, MA and Guimarães, DO and de Frias, UA and Pupo, MT and Seepe, P and Feng, Z and Brady, SF}, title = {Global biogeographic sampling of bacterial secondary metabolism.}, journal = {eLife}, volume = {4}, number = {}, pages = {e05048}, pmid = {25599565}, issn = {2050-084X}, support = {F32 AI110029/AI/NIAID NIH HHS/United States ; R01 GM077516/GM/NIGMS NIH HHS/United States ; GM077516/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/enzymology/*metabolism ; Base Sequence ; Biodiversity ; Biological Products/metabolism ; *Phylogeography ; Polyketide Synthases/chemistry/metabolism ; Protein Structure, Tertiary ; *Secondary Metabolism ; }, abstract = {Recent bacterial (meta)genome sequencing efforts suggest the existence of an enormous untapped reservoir of natural-product-encoding biosynthetic gene clusters in the environment. Here we use the pyro-sequencing of PCR amplicons derived from both nonribosomal peptide adenylation domains and polyketide ketosynthase domains to compare biosynthetic diversity in soil microbiomes from around the globe. We see large differences in domain populations from all except the most proximal and biome-similar samples, suggesting that most microbiomes will encode largely distinct collections of bacterial secondary metabolites. Our data indicate a correlation between two factors, geographic distance and biome-type, and the biosynthetic diversity found in soil environments. By assigning reads to known gene clusters we identify hotspots of biomedically relevant biosynthetic diversity. These observations not only provide new insights into the natural world, they also provide a road map for guiding future natural products discovery efforts.}, } @article {pmid25598242, year = {2015}, author = {Mao, B and Li, D and Zhao, J and Liu, X and Gu, Z and Chen, YQ and Zhang, H and Chen, W}, title = {Metagenomic insights into the effects of fructo-oligosaccharides (FOS) on the composition of fecal microbiota in mice.}, journal = {Journal of agricultural and food chemistry}, volume = {63}, number = {3}, pages = {856-863}, doi = {10.1021/jf505156h}, pmid = {25598242}, issn = {1520-5118}, mesh = {Actinobacteria/drug effects/growth & development ; Animals ; Bacteria/classification/isolation & purification ; Bifidobacterium/drug effects/growth & development ; DNA, Bacterial/analysis ; Feces/*microbiology ; Lactobacillus/drug effects/growth & development ; Male ; *Metagenomics ; Mice ; Mice, Inbred C57BL ; Microbiota/*drug effects ; Oligosaccharides/*pharmacology ; *Prebiotics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Fructo-oligosaccharides (FOS) are usually regarded as a type of prebiotic, favorably stimulating the growth of bifidobacteria and lactobacilli. However, they are not the specific substrates for these target species, and other bacteria, such as Streptococcus, Escherichia, and Clostridium, have been shown to be able to utilize FOS. Previous studies have mainly investigated only a few bacteria groups, and few reports analyzed the global effects of FOS on intestinal microbial communities. In this study the effects of FOS on gut bacteria in mice were investigated through a 16S rRNA metagenomic analysis. In the FOS-low group, the abundance of Actinobacteria significantly increased and that of Bacteroidetes decreased after FOS diet (5%) for 3 weeks. In the FOS-high group, Enterococcus was promoted and levels of Bifidobacterium and Olsenella both notably increased after FOS diet (25%) and the microbiota tended to revert to initial structure 2 weeks after FOS treatment ceased. The most striking observation was that Olsenella became a dominant genus comparable with Bifidobacterium after FOS treatment, and one strain of Olsenella, isolated from mice feces, was confirmed, for the first time, to be capable of using FOS. The results indicated that metagenomic analysis was helpful to reveal the FOS effects on the global composition of gut communities and new target for future studies.}, } @article {pmid25595762, year = {2015}, author = {Alcaide, M and Tchigvintsev, A and Martínez-Martínez, M and Popovic, A and Reva, ON and Lafraya, Á and Bargiela, R and Nechitaylo, TY and Matesanz, R and Cambon-Bonavita, MA and Jebbar, M and Yakimov, MM and Savchenko, A and Golyshina, OV and Yakunin, AF and Golyshin, PN and Ferrer, M and , }, title = {Identification and characterization of carboxyl esterases of gill chamber-associated microbiota in the deep-sea shrimp Rimicaris exoculata by using functional metagenomics.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {6}, pages = {2125-2136}, pmid = {25595762}, issn = {1098-5336}, support = {U54 GM074942/GM/NIGMS NIH HHS/United States ; U54 GM094585/GM/NIGMS NIH HHS/United States ; GM074942/GM/NIGMS NIH HHS/United States ; GM094585/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Atlantic Ocean ; Carboxylic Ester Hydrolases/genetics/*isolation & purification/metabolism ; Decapoda/*microbiology ; Enzyme Activators/metabolism ; Enzyme Inhibitors/metabolism ; Enzyme Stability ; Gills/*microbiology ; Hydrothermal Vents ; *Metagenome ; Metagenomics ; *Microbiota ; Molecular Sequence Data ; Salts/metabolism ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Substrate Specificity ; Temperature ; }, abstract = {The shrimp Rimicaris exoculata dominates the fauna in deep-sea hydrothermal vent sites along the Mid-Atlantic Ridge (depth, 2,320 m). Here, we identified and biochemically characterized three carboxyl esterases from microbial communities inhabiting the R. exoculata gill that were isolated by naive screens of a gill chamber metagenomic library. These proteins exhibit low to moderate identity to known esterase sequences (≤52%) and to each other (11.9 to 63.7%) and appear to have originated from unknown species or from genera of Proteobacteria related to Thiothrix/Leucothrix (MGS-RG1/RG2) and to the Rhodobacteraceae group (MGS-RG3). A library of 131 esters and 31 additional esterase/lipase preparations was used to evaluate the activity profiles of these enzymes. All 3 of these enzymes had greater esterase than lipase activity and exhibited specific activities with ester substrates (≤356 U mg(-1)) in the range of similar enzymes. MGS-RG3 was inhibited by salts and pressure and had a low optimal temperature (30°C), and its substrate profile clustered within a group of low-activity and substrate-restricted marine enzymes. In contrast, MGS-RG1 and MGS-RG2 were most active at 45 to 50°C and were salt activated and barotolerant. They also exhibited wider substrate profiles that were close to those of highly active promiscuous enzymes from a marine hydrothermal vent (MGS-RG2) and from a cold brackish lake (MGS-RG1). The data presented are discussed in the context of promoting the examination of enzyme activities of taxa found in habitats that have been neglected for enzyme prospecting; the enzymes found in these taxa may reflect distinct habitat-specific adaptations and may constitute new sources of rare reaction specificities.}, } @article {pmid25589730, year = {2015}, author = {Friedland, RP}, title = {Mechanisms of molecular mimicry involving the microbiota in neurodegeneration.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {45}, number = {2}, pages = {349-362}, doi = {10.3233/JAD-142841}, pmid = {25589730}, issn = {1875-8908}, mesh = {Animals ; Cytokines/metabolism ; Humans ; *Microbiota ; *Molecular Mimicry ; Neurodegenerative Diseases/*metabolism/*physiopathology ; }, abstract = {The concept of molecular mimicry was established to explain commonalities of structure which developed in response to evolutionary pressures. Most examples of molecular mimicry in medicine have involved homologies of primary protein structure which cause disease. Molecular mimicry can be expanded beyond amino acid sequence to include microRNA and proteomic effects which are either pathogenic or salutogenic (beneficial) in regard to Parkinson's disease, Alzheimer's disease, and related disorders. Viruses of animal or plant origin may mimic nucleotide sequences of microRNAs and influence protein expression. Both Parkinson's and Alzheimer's diseases involve the formation of transmissible self-propagating prion-like proteins. However, the initiating factors responsible for creation of these misfolded nucleating factors are unknown. Amyloid patterns of protein folding are highly conserved through evolution and are widely distributed in the world. Similarities of tertiary protein structure may be involved in the creation of these prion-like agents through molecular mimicry. Cross-seeding of amyloid misfolding, altered proteostasis, and oxidative stress may be induced by amyloid proteins residing in bacteria in our microbiota in the gut and in the diet. Pathways of molecular mimicry induced processes induced by bacterial amyloid in neurodegeneration may involve TLR 2/1, CD14, and NFκB, among others. Furthermore, priming of the innate immune system by the microbiota may enhance the inflammatory response to cerebral amyloids (such as amyloid-β and α-synuclein). This paper describes the specific molecular pathways of these cross-seeding and neuroinflammatory processes. Evolutionary conservation of proteins provides the opportunity for conserved sequences and structures to influence neurological disease through molecular mimicry.}, } @article {pmid25586384, year = {2015}, author = {Mendes, LW and Tsai, SM and Navarrete, AA and de Hollander, M and van Veen, JA and Kuramae, EE}, title = {Soil-borne microbiome: linking diversity to function.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {255-265}, pmid = {25586384}, issn = {1432-184X}, mesh = {Agriculture/*methods ; Base Sequence ; Brazil ; Conservation of Natural Resources/methods ; Forests ; Genetic Variation/*physiology ; Metagenomics/*methods ; Microbiota/*genetics/physiology ; Models, Theoretical ; Molecular Sequence Data ; Sequence Analysis, DNA ; *Soil Microbiology ; Glycine max/*growth & development ; Time Factors ; Tropical Climate ; }, abstract = {Soil microorganisms are sensitive to environment disturbances, and such alterations have consequences on microbial diversity and functions. Our hypothesis is that alpha diversity of microbial communities and functional diversity decrease from undisturbed to disturbed soils, with consequences for functional redundancy in the soil ecosystem. To test this hypothesis, we used soil DNA shotgun metagenomics approach to assess the soil microbiome in a chronosequence of land-use from a native tropical forest, followed by deforestation and cultivation of soybean croplands and pasture in different seasons. Agriculture and pasture soils were among the most diverse and presented higher functional redundancy, which is important to maintain the ecosystem functioning after the forest conversion. On the other hand, the ecosystem equilibrium in forest is maintained based on a lower alpha diversity but higher abundance of microorganisms. Our results indicate that land-use change alters the structure and composition of microbial communities; however, ecosystem functionality is overcome by different strategies based on the abundance and diversity of the communities.}, } @article {pmid25584460, year = {2015}, author = {D'Argenio, V and Salvatore, F}, title = {The role of the gut microbiome in the healthy adult status.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {451}, number = {Pt A}, pages = {97-102}, doi = {10.1016/j.cca.2015.01.003}, pmid = {25584460}, issn = {1873-3492}, mesh = {Adult ; Bacteria/*metabolism ; Gastrointestinal Microbiome/genetics/*physiology ; *Health ; Health Status ; Humans ; }, abstract = {The gut microbiome, which hosts up to 1000 bacterial species that encode about 5 million genes, perform many of the functions required for host physiology and survival. Consequently, it is also known as "our forgotten organ". The recent development of next-generation sequencing technologies has greatly improved metagenomic research. In particular, it has increased our knowledge about the microbiome and its mutually beneficial relationships with the human host. Microbial colonization begins immediately at birth. Although influenced by a variety of stimuli, namely, diet, physical activity, travel, illness, hormonal cycles and therapies, the microbiome is practically stable in healthy adults. This suggests that the microbiome plays a role in the maintenance of a healthy state in adulthood. Quantitative and qualitative alterations in the composition of the gut microbiome could lead to pathological dysbiosis, and have been related to an increasing number of intestinal and extra-intestinal diseases. With the increase in knowledge about gut microbiome functions, it is becoming increasingly more possible to develop novel diagnostic, prognostic and, most important, therapeutic strategies based on microbiome manipulation.}, } @article {pmid25583170, year = {2015}, author = {Horton, JM and Gao, Z and Sullivan, DM and Shopsin, B and Perez-Perez, GI and Blaser, MJ}, title = {The cutaneous microbiome in outpatients presenting with acute skin abscesses.}, journal = {The Journal of infectious diseases}, volume = {211}, number = {12}, pages = {1895-1904}, pmid = {25583170}, issn = {1537-6613}, support = {P30 CA016087/CA/NCI NIH HHS/United States ; R01 AI103268/AI/NIAID NIH HHS/United States ; UH2 AR057506/AR/NIAMS NIH HHS/United States ; }, mesh = {Abscess/*diagnosis ; Adolescent ; Adult ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Microbiota ; *Outpatients ; Real-Time Polymerase Chain Reaction ; Skin/*microbiology ; Skin Diseases, Bacterial/*diagnosis ; Surveys and Questionnaires ; Young Adult ; }, abstract = {BACKGROUND: Previous studies have demonstrated an association between antibiotic use and the development of skin abscesses. We tested the hypothesis that alterations in the composition of the cutaneous microbiota may predispose individuals to skin abscesses.

METHODS: We studied 25 patients with skin abscesses and 25 age-matched controls, who each completed a questionnaire. Skin swab samples were obtained for DNA analysis from 4 sites around the abscess site (hereafter, "peri-abscess specimens") and from similar sites on the patient's contralateral side and on healthy control subjects. DNA was extracted and analyzed by quantitative polymerase chain reaction (qPCR) and high-throughput sequencing. The purulent abscess drainage was sent for culture.

RESULTS: Fifteen patients with abscess were infected with Staphylococcus aureus. Use of nuc qPCR to quantitate S. aureus revealed a significantly greater frequency of positive results for peri-abscess and contralateral skin samples, compared with control skin specimens. Analysis of community structure showed greater heterogeneity in the control samples than in the peri-abscess and contralateral samples. Metagenomic analysis detected significantly more predicted genes related to metabolic activity in the peri-abscess specimens than in the control samples.

CONCLUSIONS: The peri-abscess microbiome was similar to the contralateral microbiome, but both microbiomes differed from that for control patients. Host characteristics affecting microbial populations might be important determinants of abscess risk.}, } @article {pmid25579666, year = {2015}, author = {Yohda, M and Yagi, O and Takechi, A and Kitajima, M and Matsuda, H and Miyamura, N and Aizawa, T and Nakajima, M and Sunairi, M and Daiba, A and Miyajima, T and Teruya, M and Teruya, K and Shiroma, A and Shimoji, M and Tamotsu, H and Juan, A and Nakano, K and Aoyama, M and Terabayashi, Y and Satou, K and Hirano, T}, title = {Genome sequence determination and metagenomic characterization of a Dehalococcoides mixed culture grown on cis-1,2-dichloroethene.}, journal = {Journal of bioscience and bioengineering}, volume = {120}, number = {1}, pages = {69-77}, doi = {10.1016/j.jbiosc.2014.12.001}, pmid = {25579666}, issn = {1347-4421}, mesh = {Base Sequence ; Biodegradation, Environmental ; Chlorine/metabolism ; Chloroflexi/*genetics/growth & development/isolation & purification/*metabolism ; Dichloroethylenes/*metabolism ; Ethylenes/metabolism ; Genes, rRNA/genetics ; Genome, Bacterial/*genetics ; Halogenation ; *Metagenomics ; Microbial Consortia/*genetics/physiology ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {A Dehalococcoides-containing bacterial consortium that performed dechlorination of 0.20 mM cis-1,2-dichloroethene to ethene in 14 days was obtained from the sediment mud of the lotus field. To obtain detailed information of the consortium, the metagenome was analyzed using the short-read next-generation sequencer SOLiD 3. Matching the obtained sequence tags with the reference genome sequences indicated that the Dehalococcoides sp. in the consortium was highly homologous to Dehalococcoides mccartyi CBDB1 and BAV1. Sequence comparison with the reference sequence constructed from 16S rRNA gene sequences in a public database showed the presence of Sedimentibacter, Sulfurospirillum, Clostridium, Desulfovibrio, Parabacteroides, Alistipes, Eubacterium, Peptostreptococcus and Proteocatella in addition to Dehalococcoides sp. After further enrichment, the members of the consortium were narrowed down to almost three species. Finally, the full-length circular genome sequence of the Dehalococcoides sp. in the consortium, D. mccartyi IBARAKI, was determined by analyzing the metagenome with the single-molecule DNA sequencer PacBio RS. The accuracy of the sequence was confirmed by matching it to the tag sequences obtained by SOLiD 3. The genome is 1,451,062 nt and the number of CDS is 1566, which includes 3 rRNA genes and 47 tRNA genes. There exist twenty-eight RDase genes that are accompanied by the genes for anchor proteins. The genome exhibits significant sequence identity with other Dehalococcoides spp. throughout the genome, but there exists significant difference in the distribution RDase genes. The combination of a short-read next-generation DNA sequencer and a long-read single-molecule DNA sequencer gives detailed information of a bacterial consortium.}, } @article {pmid25575311, year = {2015}, author = {Sullam, KE and Rubin, BE and Dalton, CM and Kilham, SS and Flecker, AS and Russell, JA}, title = {Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies.}, journal = {The ISME journal}, volume = {9}, number = {7}, pages = {1508-1522}, pmid = {25575311}, issn = {1751-7370}, mesh = {Adaptation, Physiological/genetics ; Animal Distribution ; Animals ; *Biological Evolution ; Diet ; Ecosystem ; Ecotype ; Gastrointestinal Microbiome/*genetics ; Poecilia/*genetics/*microbiology ; RNA, Ribosomal, 16S/genetics ; Trinidad and Tobago ; }, abstract = {Diverse microbial consortia profoundly influence animal biology, necessitating an understanding of microbiome variation in studies of animal adaptation. Yet, little is known about such variability among fish, in spite of their importance in aquatic ecosystems. The Trinidadian guppy, Poecilia reticulata, is an intriguing candidate to test microbiome-related hypotheses on the drivers and consequences of animal adaptation, given the recent parallel origins of a similar ecotype across streams. To assess the relationships between the microbiome and host adaptation, we used 16S rRNA amplicon sequencing to characterize gut bacteria of two guppy ecotypes with known divergence in diet, life history, physiology and morphology collected from low-predation (LP) and high-predation (HP) habitats in four Trinidadian streams. Guts were populated by several recurring, core bacteria that are related to other fish associates and rarely detected in the environment. Although gut communities of lab-reared guppies differed from those in the wild, microbiome divergence between ecotypes from the same stream was evident under identical rearing conditions, suggesting host genetic divergence can affect associations with gut bacteria. In the field, gut communities varied over time, across streams and between ecotypes in a stream-specific manner. This latter finding, along with PICRUSt predictions of metagenome function, argues against strong parallelism of the gut microbiome in association with LP ecotype evolution. Thus, bacteria cannot be invoked in facilitating the heightened reliance of LP guppies on lower-quality diets. We argue that the macroevolutionary microbiome convergence seen across animals with similar diets may be a signature of secondary microbial shifts arising some time after host-driven adaptation.}, } @article {pmid25575307, year = {2015}, author = {Llorens-Marès, T and Yooseph, S and Goll, J and Hoffman, J and Vila-Costa, M and Borrego, CM and Dupont, CL and Casamayor, EO}, title = {Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics.}, journal = {The ISME journal}, volume = {9}, number = {7}, pages = {1648-1661}, pmid = {25575307}, issn = {1751-7370}, mesh = {Ammonia/metabolism ; Archaea/genetics ; Bacteria/*genetics ; *Biodiversity ; Carbon/metabolism ; Carbon Cycle/genetics ; Denitrification/genetics ; Lakes/chemistry/*microbiology ; Metagenomics/*methods ; Nitrates/metabolism ; Nitrification ; Nitrogen/metabolism ; Nitrogen Fixation/genetics ; Oxidation-Reduction ; Spain ; Sulfur/metabolism ; *Water Microbiology ; }, abstract = {Stratified sulfurous lakes are appropriate environments for studying the links between composition and functionality in microbial communities and are potentially modern analogs of anoxic conditions prevailing in the ancient ocean. We explored these aspects in the Lake Banyoles karstic area (NE Spain) through metagenomics and in silico reconstruction of carbon, nitrogen and sulfur metabolic pathways that were tightly coupled through a few bacterial groups. The potential for nitrogen fixation and denitrification was detected in both autotrophs and heterotrophs, with a major role for nitrogen and carbon fixations in Chlorobiaceae. Campylobacterales accounted for a large percentage of denitrification genes, while Gallionellales were putatively involved in denitrification, iron oxidation and carbon fixation and may have a major role in the biogeochemistry of the iron cycle. Bacteroidales were also abundant and showed potential for dissimilatory nitrate reduction to ammonium. The very low abundance of genes for nitrification, the minor presence of anammox genes, the high potential for nitrogen fixation and mineralization and the potential for chemotrophic CO2 fixation and CO oxidation all provide potential clues on the anoxic zones functioning. We observed higher gene abundance of ammonia-oxidizing bacteria than ammonia-oxidizing archaea that may have a geochemical and evolutionary link related to the dominance of Fe in these environments. Overall, these results offer a more detailed perspective on the microbial ecology of anoxic environments and may help to develop new geochemical proxies to infer biology and chemistry interactions in ancient ecosystems.}, } @article {pmid25563637, year = {2015}, author = {Cleary, DF and Becking, LE and Polónia, AR and Freitas, RM and Gomes, NC}, title = {Composition and predicted functional ecology of mussel-associated bacteria in Indonesian marine lakes.}, journal = {Antonie van Leeuwenhoek}, volume = {107}, number = {3}, pages = {821-834}, doi = {10.1007/s10482-014-0375-1}, pmid = {25563637}, issn = {1572-9699}, mesh = {Animals ; Aquatic Organisms/microbiology ; Bacteria/*classification/*genetics ; *Biota ; Bivalvia/*microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Indonesia ; Lakes ; *Metagenome ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {In the present study, we sampled bacterial communities associated with mussels inhabiting two distinct coastal marine ecosystems in Kalimantan, Indonesia, namely, marine lakes and coastal mangroves. We used 16S rRNA gene pyrosequencing and predicted metagenomic analysis to compare microbial composition and function. Marine lakes are small landlocked bodies of seawater isolated to varying degrees from the open sea environment. They contain numerous endemic taxa and represent natural laboratories of speciation. Our primary goals were to (1) use BLAST search to identify closely related organisms to dominant bacterial OTUs in our mussel dataset and (2) to compare bacterial communities and enrichment in the predicted bacterial metagenome among lakes. Our sequencing effort yielded 3553 OTUs belonging to 44 phyla, 99 classes and 121 orders. Mussels in the largest marine lake (Kakaban) and the coastal mangrove habitat were dominated by bacteria belonging to the phylum Proteobacteria whereas smaller lakes, located on the island of Maratua, were dominated by bacteria belonging to the phyla Firmicutes and Tenericutes. The single most abundant OTU overall was assigned to the genus Mycoplasma. There were several significant differences among locations with respect to metabolic pathways. These included enrichment of xenobiotic biodegradation pathways in the largest marine lake and coastal mangrove. These locations were also the most enriched with respect to nitrogen metabolism. The presence of genes related to isoquinoline alkaloids, polyketides, hydrolases, mono and dioxygenases in the predicted analysis of functional pathways is an indication that the bacterial communities of Brachidontes mussels may be potentially important sources of new marine medicines and enzymes of industrial interest. Future work should focus on measuring how mussel microbial communities influence nutrient dynamics within the marine lake environment and isolating microbes with potential biotechnological applications.}, } @article {pmid25561343, year = {2015}, author = {Cammarota, G and Ianiro, G and Cianci, R and Bibbò, S and Gasbarrini, A and Currò, D}, title = {The involvement of gut microbiota in inflammatory bowel disease pathogenesis: potential for therapy.}, journal = {Pharmacology & therapeutics}, volume = {149}, number = {}, pages = {191-212}, doi = {10.1016/j.pharmthera.2014.12.006}, pmid = {25561343}, issn = {1879-016X}, mesh = {Animals ; Anti-Bacterial Agents/*therapeutic use ; *Dietary Supplements ; *Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/*drug effects/immunology ; Humans ; Inflammatory Bowel Diseases/*diet therapy/*drug therapy/immunology ; Models, Immunological ; Prebiotics ; Probiotics/pharmacology/therapeutic use ; Synbiotics ; }, abstract = {Over the past recent years, a great number of studies have been directed toward the evaluation of the human host-gut microbiota interaction, with the goal to progress the understanding of the etiology of several complex diseases. Alterations in the intestinal microbiota associated with inflammatory bowel disease are well supported by literature data and have been widely accepted by the research community. The concomitant implementation of high-throughput sequencing techniques to analyze and characterize the composition of the intestinal microbiota has reinforced the view that inflammatory bowel disease results from altered interactions between gut microbes and the mucosal immune system and has raised the possibility that some form of modulation of the intestinal microbiota may constitute a potential therapeutic basis for the disease. The aim of this review is to describe the changes of gut microbiota in inflammatory bowel disease, focusing the attention on its involvement in the pathogenesis of the disease, and to review and discuss the therapeutic potential to modify the intestinal microbial population with antibiotics, probiotics, prebiotics, synbiotics and fecal microbiota transplantation.}, } @article {pmid25559298, year = {2015}, author = {Warinner, C and Speller, C and Collins, MJ and Lewis, CM}, title = {Ancient human microbiomes.}, journal = {Journal of human evolution}, volume = {79}, number = {}, pages = {125-136}, pmid = {25559298}, issn = {1095-8606}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 GM089886/GM/NIGMS NIH HHS/United States ; R01 GM089886)/GM/NIGMS NIH HHS/United States ; }, mesh = {Dental Calculus/microbiology ; Diet ; Feces/microbiology ; Health/history ; High-Throughput Nucleotide Sequencing ; History, Ancient ; Humans ; Metagenomics ; *Microbiota ; *Paleontology ; }, abstract = {Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today.}, } @article {pmid25559083, year = {2015}, author = {Tang, MS and Poles, J and Leung, JM and Wolff, MJ and Davenport, M and Lee, SC and Lim, YA and Chua, KH and Loke, P and Cho, I}, title = {Inferred metagenomic comparison of mucosal and fecal microbiota from individuals undergoing routine screening colonoscopy reveals similar differences observed during active inflammation.}, journal = {Gut microbes}, volume = {6}, number = {1}, pages = {48-56}, pmid = {25559083}, issn = {1949-0984}, support = {P30 CA016087/CA/NCI NIH HHS/United States ; AI093811/AI/NIAID NIH HHS/United States ; AI094166/AI/NIAID NIH HHS/United States ; }, mesh = {*Biota ; Colitis/*microbiology ; Feces/*microbiology ; Humans ; Intestinal Mucosa/*microbiology ; Male ; Metabolic Networks and Pathways/*genetics ; Middle Aged ; }, abstract = {The mucosal microbiota lives in close proximity with the intestinal epithelium and may interact more directly with the host immune system than the luminal/fecal bacteria. The availability of nutrients in the mucus layer of the epithelium is also very different from the gut lumen environment. Inferred metagenomic analysis for microbial function of the mucosal microbiota is possible by PICRUSt. We recently found that by using this approach, actively inflamed tissue of ulcerative colitis (UC) patients have mucosal communities enriched for genes involved in lipid and amino acid metabolism, and reduced for carbohydrate and nucleotide metabolism. Here, we find that the same bacterial taxa (e.g. Acinetobacter) and predicted microbial pathways enriched in actively inflamed colitis tissue are also enriched in the mucosa of subjects undergoing routine screening colonoscopies, when compared with paired samples of luminal/fecal bacteria. These results suggest that the mucosa of healthy individuals may be a reservoir of aerotolerant microbial communities expanded during colitis.}, } @article {pmid25557210, year = {2015}, author = {Antony, KM and Ma, J and Mitchell, KB and Racusin, DA and Versalovic, J and Aagaard, K}, title = {The preterm placental microbiome varies in association with excess maternal gestational weight gain.}, journal = {American journal of obstetrics and gynecology}, volume = {212}, number = {5}, pages = {653.e1-16}, pmid = {25557210}, issn = {1097-6868}, support = {U54 HG004973/HG/NHGRI NIH HHS/United States ; U54HG004973/HG/NHGRI NIH HHS/United States ; DP2 OD001500/OD/NIH HHS/United States ; DP21DP2OD001500/OD/NIH HHS/United States ; R01NR014792/NR/NINR NIH HHS/United States ; R01 DK089201/DK/NIDDK NIH HHS/United States ; R01 NR014792/NR/NINR NIH HHS/United States ; }, mesh = {Actinobacteria/genetics/isolation & purification ; Adult ; Bacteroidetes/genetics/isolation & purification ; Body Mass Index ; Case-Control Studies ; Chloroflexi/genetics/isolation & purification ; Cyanobacteria/genetics/isolation & purification ; Female ; Humans ; Metagenome/*genetics ; Microbiota/*genetics ; Molecular Typing ; Obesity/*microbiology ; Placenta/*microbiology ; Pregnancy ; Pregnancy Complications/*microbiology ; Premature Birth/*microbiology ; Proteobacteria/genetics/isolation & purification ; RNA, Ribosomal, 16S/*analysis ; Streptococcus agalactiae/genetics/isolation & purification ; Thinness/microbiology ; Verrucomicrobia/genetics/isolation & purification ; *Weight Gain ; Young Adult ; }, abstract = {OBJECTIVE: Although a higher maternal body mass index is associated with preterm birth, it is unclear whether excess gestational weight gain (GWG) or obesity drives increased risk. We and others have shown that the placenta harbors microbiota, which is significantly different among preterm births. Our aim in this study was to investigate whether the preterm placental microbiome varies by virtue of obesity or alternately by excess GWG.

STUDY DESIGN: Placentas (n=320) were collected from term and preterm pregnancies. Genomic DNA was extracted and subjected to metagenomic sequencing. Data were analyzed by clinical covariates that included the 2009 Institute of Medicine's GWG guideline and obesity.

RESULTS: Analysis of 16S recombinant RNA-based metagenomics revealed no clustering of the microbiome by virtue of obesity (P=.161). Among women who spontaneously delivered preterm, there was again no clustering by obesity (P=.480), but there was significant clustering by excess GWG (P=.022). Moreover, among preterm births, detailed analysis identified microbial genera (family and genus level) and bacterial metabolic gene pathways that varied among pregnancies with excess GWG. Notably, excess GWG was associated with decreased microbial folate biosynthesis pathways and decreased butanoate metabolism (linear discriminate analysis, >3.0-fold).

CONCLUSION: Although there were no significant alterations in the microbiome by virtue of obesity per se, excess GWG was associated with an altered microbiome and its metabolic profile among those women who experienced a preterm birth.}, } @article {pmid25556404, year = {2015}, author = {Barkovskii, AL and Babb, CM and Hurley, D and Shin, E}, title = {Origins and environmental mobility of antibiotic resistance genes, virulence factors and bacteria in a tidal creek's watershed.}, journal = {Journal of applied microbiology}, volume = {118}, number = {3}, pages = {764-776}, doi = {10.1111/jam.12735}, pmid = {25556404}, issn = {1365-2672}, mesh = {Bacteria/*classification/genetics/isolation & purification/pathogenicity ; Biodiversity ; Integrases/genetics ; Tetracycline Resistance/*genetics ; Virulence Factors/*genetics ; *Water Microbiology ; Wetlands ; }, abstract = {AIMS: To compare bacterial compositions of watershed run-offs released by a human settlement and a forested area, and to evaluate their role as carriers of antibiotic resistance and virulence genes.

METHODS AND RESULTS: Run-offs from a forested area and a small settlement in a tidal creek' s watershed were compared for bacterial composition and profiles of 16 tetracycline resistance (TRG), eight virulence (VG) and integrase1 and 2 genes. Integrase 1 gene was detected only once. No integrase 2 gene was observed. VGs were detected only in settlement's run-offs, and TRG incidence frequency there was twice as high as in the forest's run-offs. Gene incidences revealed a positive correspondence to the rainfall, and weak correlations to water parameters. Metagenomic, Principle Coordinates and Shannon analyses together revealed distinctive bacterial compositions of the forest's and settlement's run-offs. Passage of the latter through a salt marsh resulted in the elimination of TRGs and three-fold decrease in VG incidence, and their bacterial composition was shifted towards that of the tidal creek.

CONCLUSIONS: The settlement was a major source of TRGs and VGs in the watershed, but these contaminants were mitigated by a salt marsh system.

Our data revealed the role of small settlements in biological contamination of the coastal waters. They also indicated that salt marshes are capable of reducing not only chemical but also biological contamination of run-offs.}, } @article {pmid25552511, year = {2014}, author = {Kostriukova, ES and Karpova, IY and Larin, AK and Popenko, AC and Tiakht, AV and Il'ina, EN}, title = {[Variability in the relative quantity of human DNA resulted from metagenomic analysis of gut microbiota].}, journal = {Biomeditsinskaia khimiia}, volume = {60}, number = {6}, pages = {695-701}, doi = {10.18097/pbmc20146006695}, pmid = {25552511}, issn = {2310-6972}, mesh = {Adult ; DNA/*genetics/isolation & purification ; Feces/*chemistry/microbiology ; Female ; Humans ; Intestines/*microbiology ; *Metagenome ; Microbiota/*genetics ; }, abstract = {We conducted the comparative study of seven different methods of total DNA extraction from human feces. All these methods are recommended in protocols for metagenomic analysis of human gut microbiota. We studied the relative quantity of human DNA calculated from shotgun sequencing on a SOLiD 4 genetic analyzer of metagenomic samples. It was shown that either initial amount of feces or a method applied for total DNA extraction do not affect on final relative human DNA abundance, which is less than 1% in healthy people. Invariance of this parameter allows to consider increased abundance of human DNA in metagenomic samples as a potential marker of inflammatory bowel diseases.}, } @article {pmid26978420, year = {2015}, author = {Shalikiani, NV and Bakulin, IG and Dubinkina, VB and Ishchenko, DS and Alexeev, DG and Tyakht, AV and Pavlenko, AV and Ilyina, EN and Kostryukova, ES and Taraskina, AE and Skorodumova, LO and Maev, IV and Govorun, VM}, title = {[Specific features of the enteric microbiota composition in patients with alcoholic liver cirrhosis].}, journal = {Terapevticheskii arkhiv}, volume = {87}, number = {12}, pages = {59-65}, doi = {10.17116/terarkh2015871259-65}, pmid = {26978420}, issn = {0040-3660}, mesh = {Adult ; Dysbiosis/*etiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Liver Cirrhosis, Alcoholic/*complications ; Male ; Metagenome/*genetics ; Middle Aged ; }, abstract = {AIM: To establish the specific features of the taxonomic and functional composition of the enteric microbiota in patients with alcoholic liver cirrhosis (LC).

SUBJECTS AND METHODS: Metagenomic analysis was used to study the taxonomic composition and functional potential of the enteric microbiota in 20 patients with alcoholic LC. Total DNA was isolated from the patients' fecal samples; thereafter full genome sequencing was carried out. The metagenomic analysis yielded the results of the relative taxonomic and functional abundance of microbial species in the test samples. These were comparatively analyzed with the previously published metagenomic datasets of healthy population cohorts in the Russian Federation, as well as in Denmark, China, and the USA.

RESULTS: In the majority of patients, the dominant part of the intestinal community represented bacterial species constituting the normal human intestinal flora. At the same time, abnormal gut microbiota composition, which was suggestive of marked dysbacteriosis, was identified in a number of patients. In addition, pooled analysis of the data could identify a number of species with a statistically significantly increase and decrease in the relative abundance as compared to the control groups. Thus, the enteric microbiota of the patients with alcoholic LC showed a high proportion of bacteria characteristic of the oral cavity. Analysis of the pooled metabolic potential of the microbiota in these patients demonstrated the higher abundance of enzyme genes involved in alcohol metabolism.

CONCLUSION: In the patients with alcoholic LC, the microbiota composition changes identified in individual bacterial species may be associated with gastrointestinal comorbidities, such as chronic erosive gastritis, chronic pancreatitis, and gastric ulcer. The alterations occurring in alcoholic cirrhosis promote the penetration and generation of oral cavity-specific microorganisms in the human intestine. This may a potential biomarker for the diagnosis of liver diseases. The bacterial enzyme genes involved in alcohol metabolism have an increased abundance in patients with alcoholic LC and healthy volunteers from the Russian Federation.}, } @article {pmid25549184, year = {2014}, author = {Lim, YW and Haynes, M and Furlan, M and Robertson, CE and Harris, JK and Rohwer, F}, title = {Purifying the impure: sequencing metagenomes and metatranscriptomes from complex animal-associated samples.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {94}, pages = {}, pmid = {25549184}, issn = {1940-087X}, support = {R01 GM095384/GM/NIGMS NIH HHS/United States ; 1 R01 GM095384-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cystic Fibrosis/*microbiology ; DNA/analysis/genetics/isolation & purification ; DNA, Bacterial/analysis/genetics/isolation & purification ; DNA, Viral/analysis/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; Sputum/microbiology ; }, abstract = {The accessibility of high-throughput sequencing has revolutionized many fields of biology. In order to better understand host-associated viral and microbial communities, a comprehensive workflow for DNA and RNA extraction was developed. The workflow concurrently generates viral and microbial metagenomes, as well as metatranscriptomes, from a single sample for next-generation sequencing. The coupling of these approaches provides an overview of both the taxonomical characteristics and the community encoded functions. The presented methods use Cystic Fibrosis (CF) sputum, a problematic sample type, because it is exceptionally viscous and contains high amount of mucins, free neutrophil DNA, and other unknown contaminants. The protocols described here target these problems and successfully recover viral and microbial DNA with minimal human DNA contamination. To complement the metagenomics studies, a metatranscriptomics protocol was optimized to recover both microbial and host mRNA that contains relatively few ribosomal RNA (rRNA) sequences. An overview of the data characteristics is presented to serve as a reference for assessing the success of the methods. Additional CF sputum samples were also collected to (i) evaluate the consistency of the microbiome profiles across seven consecutive days within a single patient, and (ii) compare the consistency of metagenomic approach to a 16S ribosomal RNA gene-based sequencing. The results showed that daily fluctuation of microbial profiles without antibiotic perturbation was minimal and the taxonomy profiles of the common CF-associated bacteria were highly similar between the 16S rDNA libraries and metagenomes generated from the hypotonic lysis (HL)-derived DNA. However, the differences between 16S rDNA taxonomical profiles generated from total DNA and HL-derived DNA suggest that hypotonic lysis and the washing steps benefit in not only removing the human-derived DNA, but also microbial-derived extracellular DNA that may misrepresent the actual microbial profiles.}, } @article {pmid25546169, year = {2015}, author = {Hu, KT and Zheng, JX and Yu, ZJ and Chen, Z and Cheng, H and Pan, WG and Yang, WZ and Wang, HY and Deng, QW and Zeng, ZM}, title = {Directed shift of vaginal microbiota induced by vaginal application of sucrose gel in rhesus macaques.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {33}, number = {}, pages = {32-36}, doi = {10.1016/j.ijid.2014.12.040}, pmid = {25546169}, issn = {1878-3511}, mesh = {Administration, Topical ; Animals ; Female ; Gram-Negative Bacteria/genetics/isolation & purification ; Humans ; Lactobacillus/genetics/isolation & purification ; Macaca mulatta ; *Microbiota ; Sucrose/*administration & dosage/therapeutic use ; Vagina/*microbiology ; Vaginosis, Bacterial/drug therapy/*microbiology ; }, abstract = {OBJECTIVES: Sucrose gel was used to treat bacterial vaginosis in a phase III clinical trial. However, the changes of vaginal flora after treatment were only examined by Nugent score in that clinical trial, While the vaginal microbiota of rhesus macaques is characterized by anaerobic, Gram-negative bacteria, few lactobacilli, and pH levels above 4.6, similar to the microbiota of patients with bacterial vaginosis. This study is aimed to investigate the change of the vaginal microbiota of rehsus macaques after topical use of sucrose gel to reveal more precisely the bacterial population shift after the topical application of sucrose gel.

METHODS: Sixteen rhesus macaques were treated with 0.5 g sucrose gel vaginally and three with 0.5 g of placebo gel. Vaginal swabs were collected daily following treatment. Vaginal pH levels and Nugent scores were recorded. The composition of the vaginal micotbiota was tested by V3∼V4 16S rDNA metagenomic sequencing. Dynamic changes in the Lactobacillus genus were analyzed by qPCR.

RESULTS: The vaginal microbiota of rhesus macaques are dominated by anaerobic Gram-negative bacteria, with few lactobacilli and high pH levels above 4.6. After five days' treatment with topical sucrose gel, the component percentage of Lactobacillus in vaginal microbiota increased from 1.31% to 81.59%, while the component percentage of Porphyromonas decreased from 18.60% to 0.43%, Sneathia decreased from 15.09% to 0.89%, Mobiluncus decreased from 8.23% to 0.12%, etc.. The average vaginal pH values of 16 rhesus macaques of the sucrose gel group decreased from 5.4 to 3.89. There were no significant changes in microbiota and vaginal pH observed in the placebo group.

CONCLUSIONS: Rhesus macaques can be used as animal models of bacterial vaginosis to develop drugs and test treatment efficacy. Furthermore, the topical application of sucrose gel induced the shifting of vaginal flora of rhesus macaques from a BV kind of flora to a lactobacilli-dominating flora.}, } @article {pmid25544325, year = {2014}, author = {Schneider, GW and Winslow, R}, title = {Parts and wholes: the human microbiome, ecological ontology, and the challenges of community.}, journal = {Perspectives in biology and medicine}, volume = {57}, number = {2}, pages = {208-223}, doi = {10.1353/pbm.2014.0016}, pmid = {25544325}, issn = {1529-8795}, mesh = {Ethics, Research ; Humans ; *Metagenome ; *Microbiota ; National Institutes of Health (U.S.) ; Politics ; United States ; }, abstract = {The early results of the Human Microbiome Project, released in June 2012, add to the overwhelming data that show that there are literally trillions of microbes that live in and on each human individual. This research raises profound questions about what it means to be an individual organism, human or otherwise. In this paper, we ask two broad questions: (1) how might we conceive of an individual organism, given these results? and (2) in light of this emerging conception of the individual organism, what are the implications for how humans conceive of their own self-sufficiency and interact with other members of the living world? We highlight the ontological and political presuppositions animating this research and return to Aristotle for insights into how to conceive of and how to behave towards and within a diverse community of interdependent living parts that function together as one.}, } @article {pmid25540374, year = {2015}, author = {Sullivan, MB}, title = {Viromes, not gene markers, for studying double-stranded DNA virus communities.}, journal = {Journal of virology}, volume = {89}, number = {5}, pages = {2459-2461}, pmid = {25540374}, issn = {1098-5514}, mesh = {Biota ; DNA/*genetics ; DNA Viruses/*classification/genetics/*isolation & purification ; Metagenomics/*methods ; }, abstract = {Microbes have recently been recognized as dominant forces in nature, with studies benefiting from gene markers that can be quickly, informatively, and universally surveyed. Viruses, where explored, have proven to be powerful modulators of locally and globally important microbes through mortality, horizontal gene transfer, and metabolic reprogramming. However, community-wide virus studies have been challenged by the lack of a universal marker. Here, I propose that viral metagenomics has advanced to largely take over study of double-stranded DNA viruses.}, } @article {pmid25535937, year = {2015}, author = {Chen, LX and Hu, M and Huang, LN and Hua, ZS and Kuang, JL and Li, SJ and Shu, WS}, title = {Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage.}, journal = {The ISME journal}, volume = {9}, number = {7}, pages = {1579-1592}, pmid = {25535937}, issn = {1751-7370}, mesh = {Acidithiobacillus ; Acids/metabolism ; Bacteria/*genetics ; Biodiversity ; Environmental Microbiology ; Hydrogen-Ion Concentration ; Metagenomics/*methods ; *Mining ; }, abstract = {The microbial communities in acid mine drainage have been extensively studied to reveal their roles in acid generation and adaption to this environment. Lacking, however, are integrated community- and organism-wide comparative gene transcriptional analyses that could reveal the response and adaptation mechanisms of these extraordinary microorganisms to different environmental conditions. In this study, comparative metagenomics and metatranscriptomics were performed on microbial assemblages collected from four geochemically distinct acid mine drainage (AMD) sites. Taxonomic analysis uncovered unexpectedly high microbial biodiversity of these extremely acidophilic communities, and the abundant taxa of Acidithiobacillus, Leptospirillum and Acidiphilium exhibited high transcriptional activities. Community-wide comparative analyses clearly showed that the AMD microorganisms adapted to the different environmental conditions via regulating the expression of genes involved in multiple in situ functional activities, including low-pH adaptation, carbon, nitrogen and phosphate assimilation, energy generation, environmental stress resistance, and other functions. Organism-wide comparative analyses of the active taxa revealed environment-dependent gene transcriptional profiles, especially the distinct strategies used by Acidithiobacillus ferrivorans and Leptospirillum ferrodiazotrophum in nutrients assimilation and energy generation for survival under different conditions. Overall, these findings demonstrate that the gene transcriptional profiles of AMD microorganisms are closely related to the site physiochemical characteristics, providing clues into the microbial response and adaptation mechanisms in the oligotrophic, extremely acidic environments.}, } @article {pmid25535824, year = {2015}, author = {Leung, HC and Yiu, SM and Chin, FY}, title = {IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {22}, number = {5}, pages = {367-376}, doi = {10.1089/cmb.2014.0139}, pmid = {25535824}, issn = {1557-8666}, mesh = {Algorithms ; Bacterial Proteins/*chemistry/genetics ; Contig Mapping/methods/*statistics & numerical data ; Data Mining ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods/statistics & numerical data ; Microbial Consortia/*genetics ; Proteome/chemistry/genetics ; RNA, Bacterial/chemistry/genetics ; RNA, Messenger/*chemistry/genetics ; Sequence Analysis, DNA ; *Software ; *Transcriptome ; }, abstract = {Metatranscriptomic analysis provides information on how a microbial community reacts to environmental changes. Using next-generation sequencing (NGS) technology, biologists can study the microbe community by sampling short reads from a mixture of mRNAs (metatranscriptomic data). As most microbial genome sequences are unknown, it would seem that de novo assembly of the mRNAs is needed. However, NGS reads are short and mRNAs share many similar regions and differ tremendously in abundance levels, making de novo assembly challenging. The existing assembler, IDBA-MT, designed specifically for the assembly of metatranscriptomic data and performs well only on high-expressed mRNAs. This article introduces IDBA-MTP, which adopts a novel approach to metatranscriptomic assembly that makes use of the fact that there is a database of millions of known protein sequences associated with mRNAs. How to effectively use the protein information is nontrivial given the size of the database and given that different mRNAs might lead to proteins with similar functions (because different amino acids might have similar characteristics). IDBA-MTP employs a similarity measure between mRNAs and protein sequences, dynamic programming techniques, and seed-and-extend heuristics to tackle the problem effectively and efficiently. Experimental results show that IDBA-MTP outperforms existing assemblers by reconstructing 14% more mRNAs.}, } @article {pmid25532804, year = {2015}, author = {Carmody, RN and Gerber, GK and Luevano, JM and Gatti, DM and Somes, L and Svenson, KL and Turnbaugh, PJ}, title = {Diet dominates host genotype in shaping the murine gut microbiota.}, journal = {Cell host & microbe}, volume = {17}, number = {1}, pages = {72-84}, pmid = {25532804}, issn = {1934-6069}, support = {P50 GM068763/GM/NIGMS NIH HHS/United States ; P30 DK063720/DK/NIDDK NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; P50GM068763/GM/NIGMS NIH HHS/United States ; P50 GM076468/GM/NIGMS NIH HHS/United States ; F32 DK101154/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Diet ; *Feeding Behavior ; Gastrointestinal Tract/*microbiology ; Mice ; *Microbiota ; }, abstract = {Mammals exhibit marked interindividual variations in their gut microbiota, but it remains unclear if this is primarily driven by host genetics or by extrinsic factors like dietary intake. To address this, we examined the effect of dietary perturbations on the gut microbiota of five inbred mouse strains, mice deficient for genes relevant to host-microbial interactions (MyD88(-/-), NOD2(-/-), ob/ob, and Rag1(-/-)), and >200 outbred mice. In each experiment, consumption of a high-fat, high-sugar diet reproducibly altered the gut microbiota despite differences in host genotype. The gut microbiota exhibited a linear dose response to dietary perturbations, taking an average of 3.5 days for each diet-responsive bacterial group to reach a new steady state. Repeated dietary shifts demonstrated that most changes to the gut microbiota are reversible, while also uncovering bacteria whose abundance depends on prior consumption. These results emphasize the dominant role that diet plays in shaping interindividual variations in host-associated microbial communities.}, } @article {pmid25531678, year = {2015}, author = {Minamoto, Y and Otoni, CC and Steelman, SM and Büyükleblebici, O and Steiner, JM and Jergens, AE and Suchodolski, JS}, title = {Alteration of the fecal microbiota and serum metabolite profiles in dogs with idiopathic inflammatory bowel disease.}, journal = {Gut microbes}, volume = {6}, number = {1}, pages = {33-47}, pmid = {25531678}, issn = {1949-0984}, mesh = {Animals ; *Biota ; Dog Diseases/*pathology/therapy ; Dogs ; Feces/*microbiology ; Inflammatory Bowel Diseases/pathology/therapy/*veterinary ; Metabolome ; Metabolomics ; Metagenomics ; Sequence Analysis, DNA ; Serum/*chemistry ; }, abstract = {Idiopathic inflammatory bowel disease (IBD) is a common cause of chronic gastrointestinal (GI) disease in dogs. The combination of an underlying host genetic susceptibility, an intestinal dysbiosis, and dietary/environmental factors are suspected as main contributing factors in the pathogenesis of canine IBD. However, actual mechanisms of the host-microbe interactions remain elusive. The aim of this study was to compare the fecal microbiota and serum metabolite profiles between healthy dogs (n = 10) and dogs with IBD before and after 3 weeks of medical therapy (n = 12). Fecal microbiota and metabolite profiles were characterized by 454-pyrosequencing of 16 S rRNA genes and by an untargeted metabolomics approach, respectively. Significantly lower bacterial diversity and distinct microbial communities were observed in dogs with IBD compared to the healthy control dogs. While Gammaproteobacteria were overrepresented, Erysipelotrichia, Clostridia, and Bacteroidia were underrepresented in dogs with IBD. The functional gene content was predicted from the 16 S rRNA gene data using PICRUSt, and revealed overrepresented bacterial secretion system and transcription factors, and underrepresented amino acid metabolism in dogs with IBD. The serum metabolites 3-hydroxybutyrate, hexuronic acid, ribose, and gluconic acid lactone were significantly more abundant in dogs with IBD. Although a clinical improvement was observed after medical therapy in all dogs with IBD, this was not accompanied by significant changes in the fecal microbiota or in serum metabolite profiles. These results suggest the presence of oxidative stress and a functional alteration of the GI microbiota in dogs with IBD, which persisted even in the face of a clinical response to medical therapy.}, } @article {pmid25527750, year = {2015}, author = {Holscher, HD and Caporaso, JG and Hooda, S and Brulc, JM and Fahey, GC and Swanson, KS}, title = {Fiber supplementation influences phylogenetic structure and functional capacity of the human intestinal microbiome: follow-up of a randomized controlled trial.}, journal = {The American journal of clinical nutrition}, volume = {101}, number = {1}, pages = {55-64}, doi = {10.3945/ajcn.114.092064}, pmid = {25527750}, issn = {1938-3207}, mesh = {Adult ; Bacteroidetes/classification/*growth & development/isolation & purification/metabolism ; Cross-Over Studies ; Digestive System Physiological Phenomena ; Double-Blind Method ; Feces/microbiology ; Fermentation ; Follow-Up Studies ; Glucans/administration & dosage/adverse effects/chemistry ; Gram-Positive Bacteria/classification/*growth & development/isolation & purification/metabolism ; Humans ; Illinois ; Intestines/*microbiology/physiology ; Male ; *Microbiota ; Molecular Typing ; Phylogeny ; *Prebiotics/adverse effects ; Principal Component Analysis ; Solubility ; Young Adult ; Zea mays/adverse effects/chemistry ; }, abstract = {BACKGROUND: In our published randomized, double-blind, placebo-controlled, 3-period crossover trial, healthy adult men (n = 21) consumed bars containing no supplemental fiber (placebo; NFC), polydextrose (21 g/d), and soluble corn fiber (SCF; 21 g/d) for 21 d each. Fecal specimens were collected between days 16 and 21 for fermentative end-product analysis and 16S ribosomal RNA bacterial gene amplification for bacterial taxa identification. Fiber supplementation decreased fecal putrefaction compounds and shifted abundances of several bacterial taxa.

OBJECTIVE: The objective was to perform whole-genome shotgun 454 pyrosequencing on the same fecal specimens collected in that clinical trial to obtain comprehensive fecal bacterial genome sequencing coverage and explore the full range of bacterial genetic information in the fecal microbiome, thereby using a systematic approach to study the impact of dietary fiber supplementation on fecal metabolites, bacterial taxa, and bacterial metagenomes.

DESIGN: Fecal samples were subjected to whole-genome shotgun 454 pyrosequencing to identify both fecal bacterial populations present and their functional genetic capacity.

RESULTS: Whole-genome shotgun sequencing results revealed that fiber consumption shifted the Bacteroidetes:Firmicutes ratio, increasing the relative abundance of Bacteroidetes 12 ± 2% and 13 ± 2% with polydextrose and SCF, respectively, compared with NFC. Bivariate correlations showed a positive correlation between the Bacteroidetes:Firmicutes ratio and total dietary fiber intake but not body mass index. Principal coordinates analysis of Bray-Curtis distances indicated that bacterial gene composition was more similar in participants consuming fibers (polydextrose and SCF combined) in comparison with NFC. Shifts in bacterial gene abundances after polydextrose and SCF supplementation included genes associated with carbohydrate, amino acid, and lipid metabolism, as well as metabolism of cofactors and vitamins.

CONCLUSION: This study conveys novel information about the impact of dietary fiber supplementation on the phylogenetic structure and functional capacity of the fecal microbiome of healthy adults.}, } @article {pmid25525206, year = {2015}, author = {Nami, Y and Haghshenas, B and Abdullah, N and Barzegari, A and Radiah, D and Rosli, R and Yari Khosroushahi, A}, title = {Probiotics or antibiotics: future challenges in medicine.}, journal = {Journal of medical microbiology}, volume = {64}, number = {Pt 2}, pages = {137-146}, doi = {10.1099/jmm.0.078923-0}, pmid = {25525206}, issn = {1473-5644}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Drug Therapy/*trends ; Gastrointestinal Tract/microbiology ; Humans ; Medicine/*trends ; Microbiota ; Probiotics/*therapeutic use ; }, abstract = {Genetic and environmental factors can affect the intestinal microbiome and microbial metabolome. Among these environmental factors, the consumption of antibiotics can significantly change the intestinal microbiome of individuals and consequently affect the corresponding metagenome. The term 'probiotics' is related to preventive medicine rather than therapeutic procedures and is, thus, considered the opposite of antibiotics. This review discusses the challenges between these opposing treatments in terms of the following points: (i) antibiotic resistance, the relationship between antibiotic consumption and microbiome diversity reduction, antibiotic effect on the metagenome, and disease associated with antibiotics; and (ii) probiotics as living drugs, probiotic effect on epigenetic alterations, and gut microbiome relevance to hygiene indulgence. The intestinal microbiome is more specific for individuals and may be affected by environmental alterations and the occurrence of diseases.}, } @article {pmid25524569, year = {2015}, author = {Hong, PY and Mao, Y and Ortiz-Kofoed, S and Shah, R and Cann, I and Mackie, RI}, title = {Metagenomic-based study of the phylogenetic and functional gene diversity in Galápagos land and marine iguanas.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {444-456}, pmid = {25524569}, issn = {1432-184X}, mesh = {Animals ; Archaea/*classification/genetics/isolation & purification ; Bacteria/*classification/genetics/isolation & purification ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Ecuador ; Fatty Acids, Volatile/analysis ; Feces/microbiology ; Host-Pathogen Interactions ; Iguanas/*microbiology ; Islands ; *Metagenome ; Metagenomics ; Microbiota ; Multigene Family ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {In this study, a metagenome-based analysis of the fecal samples from the macrophytic algae-consuming marine iguana (MI; Amblyrhynchus cristatus) and terrestrial biomass-consuming land iguanas (LI; Conolophus spp.) was conducted. Phylogenetic affiliations of the fecal microbiome were more similar between both iguanas than to other mammalian herbivorous hosts. However, functional gene diversities in both MI and LI iguana hosts differed in relation to the diet, where the MI fecal microbiota had a functional diversity that clustered apart from the other terrestrial-biomass consuming reptilian and mammalian hosts. A further examination of the carbohydrate-degrading genes revealed that several of the prevalent glycosyl hydrolases (GH), glycosyl transferases (GT), carbohydrate binding modules (CBM), and carbohydrate esterases (CE) gene classes were conserved among all examined herbivorous hosts, reiterating the important roles these genes play in the breakdown and metabolism of herbivorous diets. Genes encoding some classes of carbohydrate-degrading families, including GH2, GH13, GT2, GT4, CBM50, CBM48, CE4, and CE11, as well as genes associated with sulfur metabolism and dehalogenation, were highly enriched or unique to the MI. In contrast, gene sequences that relate to archaeal methanogenesis were detected only in LI fecal microbiome, and genes coding for GH13, GH66, GT2, GT4, CBM50, CBM13, CE4, and CE8 carbohydrate active enzymes were highly abundant in the LI. Bacterial populations were enriched on various carbohydrates substrates (e.g., glucose, arabinose, xylose). The majority of the enriched bacterial populations belong to genera Clostridium spp. and Enterococcus spp. that likely accounted for the high prevalence of GH13 and GH2, as well as the GT families (e.g., GT2, GT4, GT28, GT35, and GT51) that were ubiquitously present in the fecal microbiota of all herbivorous hosts.}, } @article {pmid25523018, year = {2015}, author = {Duranti, S and Milani, C and Lugli, GA and Turroni, F and Mancabelli, L and Sanchez, B and Ferrario, C and Viappiani, A and Mangifesta, M and Mancino, W and Gueimonde, M and Margolles, A and van Sinderen, D and Ventura, M}, title = {Insights from genomes of representatives of the human gut commensal Bifidobacterium bifidum.}, journal = {Environmental microbiology}, volume = {17}, number = {7}, pages = {2515-2531}, doi = {10.1111/1462-2920.12743}, pmid = {25523018}, issn = {1462-2920}, mesh = {Animals ; Bifidobacterium/*genetics/growth & development/*metabolism ; Biological Evolution ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Genome, Bacterial ; Humans ; Infant ; Infant, Newborn ; Molecular Sequence Data ; Mucins/metabolism ; Polysaccharides/*metabolism ; }, abstract = {Bifidobacteria are bacterial gut commensals of mammals, birds and social insects that are perceived to influence the metabolism/physiology of their host. In this context, members of the Bifidobacterium bifidum species are believed to significantly contribute to the overall microbiota of the human gut at infant stage. However, the molecular reasons for their adaptation to this environment are poorly understood. In this study, we analysed the pan-genome of B. bifidum species by decoding genomes of 15 B. bifidum strains, which highlighted the existence of a conserved gene uniquely present in this bifidobacterial taxon, underscoring a nutrient acquisition strategy that targets host-derived glycans, such as those present in mucin. Growth experiments and corresponding transcriptomic analyses confirmed the in silico data and supported these intriguing and unique host glycan-specific saccharolytic features. The ubiquity of the genetic features of B. bifidum for the breakdown of host glycans was confirmed by interrogating metagenomic datasets, thereby supporting the notion that metabolic access to host-derived glycans is a potent evolutionary force that has shaped B. bifidum genomes and consequently the ecology of the infant intestinal microbiota.}, } @article {pmid25517115, year = {2014}, author = {Labbé, A and Ganopolsky, JG and Martoni, CJ and Prakash, S and Jones, ML}, title = {Bacterial bile metabolising gene abundance in Crohn's, ulcerative colitis and type 2 diabetes metagenomes.}, journal = {PloS one}, volume = {9}, number = {12}, pages = {e115175}, pmid = {25517115}, issn = {1932-6203}, mesh = {Amidohydrolases/genetics ; Animals ; Bacteria/enzymology ; Bile Acids and Salts/*metabolism ; Colitis, Ulcerative/*enzymology/genetics/microbiology ; Crohn Disease/*enzymology/genetics/microbiology ; Databases, Factual ; Diabetes Mellitus, Type 2/*enzymology/genetics/microbiology ; Feces/enzymology/microbiology ; Gastrointestinal Tract/*enzymology/microbiology ; Genes, Bacterial/*genetics ; Humans ; Hydroxysteroid Dehydrogenases/genetics ; *Metagenome ; Metagenomics ; Mice ; Microbiota ; Phylogeny ; }, abstract = {We performed an analysis to determine the importance of bile acid modification genes in the gut microbiome of inflammatory bowel disease and type 2 diabetic patients. We used publicly available metagenomic datasets from the Human Microbiome Project and the MetaHIT consortium, and determined the abundance of bile salt hydrolase gene (bsh), 7 alpha-dehydroxylase gene (adh) and 7-alpha hydroxysteroid dehydrogenase gene (hsdh) in fecal bacteria in diseased populations of Crohn's disease (CD), Ulcerative Colitis (UC) and Type 2 diabetes mellitus (T2DM). Phylum level abundance analysis showed a significant reduction in Firmicute-derived bsh in UC and T2DM patients but not in CD patients, relative to healthy controls. Reduction of adh and hsdh genes was also seen in UC and T2DM patients, while an increase was observed in the CD population as compared to healthy controls. A further analysis of the bsh genes showed significant differences in the correlations of certain Firmicutes families with disease or healthy populations. From this observation we proceeded to analyse BSH protein sequences and identified BSH proteins clusters representing the most abundant strains in our analysis of Firmicute bsh genes. The abundance of the bsh genes corresponding to one of these protein clusters was significantly reduced in all disease states relative to healthy controls. This cluster includes bsh genes derived from Lachospiraceae, Clostridiaceae, Erysipelotrichaceae and Ruminococcaceae families. This metagenomic analysis provides evidence of the importance of bile acid modifying enzymes in health and disease. It further highlights the importance of identifying gene and protein clusters, as the same gene may be associated with health or disease, depending on the strains expressing the enzyme, and differences in the enzymes themselves.}, } @article {pmid25515303, year = {2015}, author = {Jo, Y and Cho, JK and Choi, H and Chu, H and Lian, S and Cho, WK}, title = {Bacterial communities in the phylloplane of Prunus species.}, journal = {Journal of basic microbiology}, volume = {55}, number = {4}, pages = {504-508}, doi = {10.1002/jobm.201400651}, pmid = {25515303}, issn = {1521-4028}, mesh = {Bacteria/genetics/*isolation & purification ; Biodiversity ; Computational Biology ; DNA, Bacterial/*analysis ; Methylobacterium/genetics/*isolation & purification ; Phylogeny ; Prunus/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sphingomonas/genetics/*isolation & purification ; }, abstract = {Bacterial populations in the phylloplane of four different Prunus species were investigated by 16 S rRNA pyrosequencing. Bioinformatic analysis identified an average of 510 operational taxonomic units belonging to 159 genera in 76 families. The two genera, Sphingomonas and Methylobacterium, were dominant in the phylloplane of four Prunus species. Twenty three genera were commonly identified in the four Prunus species, indicating a high level of bacterial diversity dependent on the plant species. Our study based on 16 S rRNA sequencing reveals the complexity of bacterial diversity in the phylloplane of Prunus species in detail.}, } @article {pmid25515234, year = {2014}, author = {Li, J and Quinque, D and Horz, HP and Li, M and Rzhetskaya, M and Raff, JA and Hayes, MG and Stoneking, M}, title = {Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa.}, journal = {BMC microbiology}, volume = {14}, number = {}, pages = {316}, pmid = {25515234}, issn = {1471-2180}, mesh = {Adult ; Africa ; Alaska ; Animals ; Bacteria/*classification/genetics ; Climate ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Germany ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metagenome ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {BACKGROUND: Although the importance of the human oral microbiome for health and disease is increasingly recognized, variation in the composition of the oral microbiome across different climates and geographic regions is largely unexplored.

RESULTS: Here we analyze the saliva microbiome from native Alaskans (76 individuals from 4 populations), Germans (10 individuals from 1 population), and Africans (66 individuals from 3 populations) based on next-generation sequencing of partial 16S rRNA gene sequences. After quality filtering, a total of 67,916 analyzed sequences resulted in 5,592 OTUs (defined at ≥97% identity) and 123 genera. The three human groups differed significantly by the degree of diversity between and within individuals (e.g. beta diversity: Africans > Alaskans > Germans; alpha diversity: Germans > Alaskans > Africans). UniFrac, network, ANOSIM, and correlation analyses all indicated more similarities in the saliva microbiome of native Alaskans and Germans than between either group and Africans. The native Alaskans and Germans also had the highest number of shared bacterial interactions. At the level of shared OTUs, only limited support for a core microbiome shared across all three continental regions was provided, although partial correlation analysis did highlight interactions involving several pairs of genera as conserved across all human groups. Subsampling strategies for compensating for the unequal number of individuals per group or unequal sequence reads confirmed the above observations.

CONCLUSION: Overall, this study illustrates the distinctiveness of the saliva microbiome of human groups living under very different climatic conditions.}, } @article {pmid25502374, year = {2015}, author = {Larsen, P and Dai, Y and Collart, FR}, title = {Predicting bacterial community assemblages using an artificial neural network approach.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1260}, number = {}, pages = {33-43}, doi = {10.1007/978-1-4939-2239-0_3}, pmid = {25502374}, issn = {1940-6029}, mesh = {Environment ; Metagenomics/*methods ; *Microbial Consortia ; *Neural Networks, Computer ; Software ; }, abstract = {Microbial communities are found in nearly all environments and play a critical role in defining ecosystem service. Understanding the relationship between these microbial communities and their environment is essential for prediction of community structure, robustness, and response to ecosystem changes. Microbial Assemblage Prediction (MAP) describes microbial community structure as an artificial neural network (ANN) that models the microbial community as functions of environmental parameters and community intra-microbial interactions. MAP models can be used to predict community assemblages over a wide range of possible environmental parameters, extrapolate the results of point observations across spatial scales, and make predictions about how microbial communities may fluctuate as the result of changes in their environment.}, } @article {pmid25501572, year = {2014}, author = {Mosca, S and Li Destri Nicosia, MG and Cacciola, SO and Schena, L}, title = {Molecular analysis of Colletotrichum species in the carposphere and phyllosphere of olive.}, journal = {PloS one}, volume = {9}, number = {12}, pages = {e114031}, pmid = {25501572}, issn = {1932-6203}, mesh = {Biodiversity ; Colletotrichum/genetics/*isolation & purification/physiology ; DNA Primers/genetics ; DNA, Fungal/genetics/isolation & purification ; Diffusion ; Olea/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {A metagenomic approach based on the use of genus specific primers was developed and utilized to characterize Colletotrichum species associated with the olive phyllosphere and carposphere. Selected markers enabled the specific amplification of almost the entire ITS1-5.8S-ITS2 region of the rDNA and its use as barcode gene. The analysis of different olive samples (green and senescent leaves, floral residues, symptomatic and asymptomatic fruits, and litter leaves and mummies) in three different phenological phases (June, October and December) enabled the detection of 12 genotypes associated with 4 phylotypes identified as C. godetiae, C. acutatum s.s., C. gloeosporioides s.s. and C. kahawae. Another three genotypes were not identified at the level of species but were associated with the species complexes of C. acutatum, C. gloeosporioides and C. boninense sensu lato. Colletotrichum godetiae and C. acutatum s.s. were by far the most abundant while C. gloeosporioides s.s. was detected in a limited number of samples whereas ther phylotypes were rarely found. The high incidence of C. acutatum s.s. represents a novelty for Italy and more generally for the Mediterranean basin since it had been previously reported only in Portugal. As regards to the phenological phase, Colletotrichum species were found in a few samples in June and were diffused on all assessed samples in December. According to data new infections on olive tissues mainly occur in the late fall. Furthermore, Colletotrichum species seem to have a saprophytic behavior on floral olive residues. The method developed in the present study proved to be valuable and its future application may contribute to the study of cycle and aetiology of diseases caused by Colletotrichum species in many different pathosystems.}, } @article {pmid25501481, year = {2015}, author = {Lima, FS and Oikonomou, G and Lima, SF and Bicalho, ML and Ganda, EK and Filho, JC and Lorenzo, G and Trojacanec, P and Bicalhoa, RC}, title = {Prepartum and postpartum rumen fluid microbiomes: characterization and correlation with production traits in dairy cows.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {4}, pages = {1327-1337}, pmid = {25501481}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Cattle/metabolism/*microbiology ; Female ; Fungi/classification/genetics/*isolation & purification ; Lactation ; *Microbiota ; Milk/metabolism ; Postpartum Period/metabolism ; Pregnancy ; Rumen/metabolism/*microbiology ; }, abstract = {Microbes present in the rumen of dairy cows are essential for degradation of cellulosic and nonstructural carbohydrates of plant origin. The prepartum and postpartum diets of high-producing dairy cows are substantially different, but in what ways the rumen microbiome changes in response and how those changes may influence production traits are not well elucidated. Here, we sequenced the 16S and 18S rRNA genes using the MiSeq platform to characterize the prepartum and postpartum rumen fluid microbiomes in 115 high-producing dairy cows, including both primiparous and multiparous animals. Discriminant analysis identified differences between the microbiomes of prepartum and postpartum samples and between primiparous and multiparous cows. 18S rRNA sequencing revealed an overwhelming dominance of the protozoan class Litostomatea, with over 90% of the eukaryotic microbial population belonging to that group. Additionally, fungi were relatively more prevalent and Litostomatea relatively less prevalent in prepartum samples than in postpartum ones. The core rumen microbiome (common to all samples) consisted of 64 bacterial taxa, of which members of the genus Prevotella were the most prevalent. The Chao1 richness index was greater for prepartum multiparous cows than for postpartum multiparous cows. Multivariable models identified bacterial taxa associated with increased or reduced milk production, and general linear models revealed that a metagenomically based prediction of productivity is highly associated with production of actual milk and milk components. In conclusion, the structure of the rumen fluid microbiome shifts between the prepartum and first-week postpartum periods, and its profile within the context of this study could be used to accurately predict production traits.}, } @article {pmid25500524, year = {2015}, author = {Estrela, S and Whiteley, M and Brown, SP}, title = {The demographic determinants of human microbiome health.}, journal = {Trends in microbiology}, volume = {23}, number = {3}, pages = {134-141}, pmid = {25500524}, issn = {1878-4380}, support = {095831//Wellcome Trust/United Kingdom ; R01 DE020100/DE/NIDCR NIH HHS/United States ; R01 DE023193/DE/NIDCR NIH HHS/United States ; 1R01DE020100/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/genetics/*metabolism ; Demography ; Health ; Humans ; Metagenome ; Microbial Consortia ; *Microbiota ; Phylogeny ; Symbiosis ; }, abstract = {The human microbiome is a vast reservoir of microbial diversity and increasingly recognized to have a fundamental role in human health. In polymicrobial communities, the presence of one species can modulate the demography (i.e., growth and distribution) of other species. These demographic impacts generate feedbacks in multispecies interactions, which can be magnified in spatially structured populations (e.g., host-associated communities). Here, we argue that demographic feedbacks between species are central to microbiome development, shaping whether and how potential metabolic interactions come to be realized between expanding lineages of bacteria. Understanding how demographic feedbacks tune metabolic interactions and in turn shape microbiome structure and function is now a key challenge to our abilities to better manage microbiome health.}, } @article {pmid25496341, year = {2014}, author = {Almeida, M and Hébert, A and Abraham, AL and Rasmussen, S and Monnet, C and Pons, N and Delbès, C and Loux, V and Batto, JM and Leonard, P and Kennedy, S and Ehrlich, SD and Pop, M and Montel, MC and Irlinger, F and Renault, P}, title = {Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {1101}, pmid = {25496341}, issn = {1471-2164}, support = {R01 AI100947/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*genetics/*metabolism ; Cheese/microbiology ; Dairy Products/*microbiology ; *Databases, Genetic ; *Fermentation ; Genome, Bacterial/genetics ; Metagenomics/*methods ; Microbiota ; Sequence Analysis ; }, abstract = {BACKGROUND: Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety and functional role in cheese making of these microbial communities are still not well understood. Metagenomic analysis of these communities by high throughput shotgun sequencing is a promising approach to characterize their genomic and functional profiles. Such analyses, however, critically depend on the availability of appropriate reference genome databases against which the sequencing reads can be aligned.

RESULTS: We built a reference genome catalog suitable for short read metagenomic analysis using a low-cost sequencing strategy. We selected 142 bacteria isolated from dairy products belonging to 137 different species and 67 genera, and succeeded to reconstruct the draft genome of 117 of them at a standard or high quality level, including isolates from the genera Kluyvera, Luteococcus and Marinilactibacillus, still missing from public database. To demonstrate the potential of this catalog, we analysed the microbial composition of the surface of two smear cheeses and one blue-veined cheese, and showed that a significant part of the microbiota of these traditional cheeses was composed of microorganisms newly sequenced in our study.

CONCLUSIONS: Our study provides data, which combined with publicly available genome references, represents the most expansive catalog to date of cheese-associated bacteria. Using this extended dairy catalog, we revealed the presence in traditional cheese of dominant microorganisms not deliberately inoculated, mainly Gram-negative genera such as Pseudoalteromonas haloplanktis or Psychrobacter immobilis, that may contribute to the characteristics of cheese produced through traditional methods.}, } @article {pmid25495929, year = {2015}, author = {Ramond, JB and Makhalanyane, TP and Tuffin, MI and Cowan, DA}, title = {Normalization of environmental metagenomic DNA enhances the discovery of under-represented microbial community members.}, journal = {Letters in applied microbiology}, volume = {60}, number = {4}, pages = {359-366}, doi = {10.1111/lam.12380}, pmid = {25495929}, issn = {1472-765X}, mesh = {Bacteria/classification/*genetics ; Base Sequence ; DNA, Bacterial/*genetics ; Ecosystem ; Gene Library ; Metagenomics/*methods ; Microbial Consortia/*genetics ; Molecular Sequence Data ; Molecular Typing/*methods ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {UNLABELLED: Normalization is a procedure classically employed to detect rare sequences in cellular expression profiles (i.e. cDNA libraries). Here, we present a normalization protocol involving the direct treatment of extracted environmental metagenomic DNA with S1 nuclease, referred to as normalization of metagenomic DNA: NmDNA. We demonstrate that NmDNA, prior to post hoc PCR-based experiments (16S rRNA gene T-RFLP fingerprinting and clone library), increased the diversity of sequences retrieved from environmental microbial communities by detection of rarer sequences. This approach could be used to enhance the resolution of detection of ecologically relevant rare members in environmental microbial assemblages and therefore is promising in enabling a better understanding of ecosystem functioning.

This study is the first testing 'normalization' on environmental metagenomic DNA (mDNA). The aim of this procedure was to improve the identification of rare phylotypes in environmental communities. Using hypoliths as model systems, we present evidence that this post-mDNA extraction molecular procedure substantially enhances the detection of less common phylotypes and could even lead to the discovery of novel microbial genotypes within a given environment.}, } @article {pmid25495900, year = {2014}, author = {Scully, ED and Geib, SM and Carlson, JE and Tien, M and McKenna, D and Hoover, K}, title = {Functional genomics and microbiome profiling of the Asian longhorned beetle (Anoplophora glabripennis) reveal insights into the digestive physiology and nutritional ecology of wood feeding beetles.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {1096}, pmid = {25495900}, issn = {1471-2164}, mesh = {*Animal Feed ; *Animal Nutritional Physiological Phenomena ; Animals ; Bacteria/classification/genetics/metabolism ; Biodiversity ; Coleoptera/*microbiology/*physiology ; Computational Biology ; DNA, Intergenic ; *Digestive System Physiological Phenomena ; Fungi/classification/genetics/metabolism ; Gastrointestinal Tract/microbiology/physiology ; Metabolic Networks and Pathways ; *Metagenome ; *Microbiota ; Molecular Sequence Annotation ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Wood-feeding beetles harbor an ecologically rich and taxonomically diverse assemblage of gut microbes that appear to promote survival in woody tissue, which is devoid of nitrogen and essential nutrients. Nevertheless, the contributions of these apparent symbionts to digestive physiology and nutritional ecology remain uncharacterized in most beetle lineages.

RESULTS: Through parallel transcriptome profiling of beetle- and microbial- derived mRNAs, we demonstrate that the midgut microbiome of the Asian longhorned beetle (Anoplophora glabripennis), a member of the beetle family Cerambycidae, is enriched in biosynthetic pathways for the synthesis of essential amino acids, vitamins, and sterols. Consequently, the midgut microbiome of A. glabripennis can provide essential nutrients that the beetle cannot obtain from its woody diet or synthesize itself. The beetle gut microbiota also produce their own suite of transcripts that can enhance lignin degradation, degrade hemicellulose, and ferment xylose and wood sugars. An abundance of cellulases from several glycoside hydrolase families are expressed endogenously by A. glabripennis, as well as transcripts that allow the beetle to convert microbe-synthesized essential amino acids into non-essential amino acids. A. glabripennis and its gut microbes likely collaborate to digest carbohydrates and convert released sugars and amino acid intermediates into essential nutrients otherwise lacking from their woody host plants.

CONCLUSIONS: The nutritional provisioning capabilities of the A. glabripennis gut microbiome may contribute to the beetles' unusually broad host range. The presence of some of the same microbes in the guts of other Cerambycidae and other wood-feeding beetles suggests that partnerships with microbes may be a facilitator of evolutionary radiations in beetles, as in certain other groups of insects, allowing access to novel food sources through enhanced nutritional provisioning.}, } @article {pmid25492981, year = {2014}, author = {Visagie, CM and Hirooka, Y and Tanney, JB and Whitfield, E and Mwange, K and Meijer, M and Amend, AS and Seifert, KA and Samson, RA}, title = {Aspergillus, Penicillium and Talaromyces isolated from house dust samples collected around the world.}, journal = {Studies in mycology}, volume = {78}, number = {}, pages = {63-139}, pmid = {25492981}, issn = {0166-0616}, abstract = {As part of a worldwide survey of the indoor mycobiota, dust was collected from nine countries. Analyses of dust samples included the culture-dependent dilution-to-extinction method and the culture-independent 454-pyrosequencing. Of the 7 904 isolates, 2 717 isolates were identified as belonging to Aspergillus, Penicillium and Talaromyces. The aim of this study was to identify isolates to species level and describe the new species found. Secondly, we wanted to create a reliable reference sequence database to be used for next-generation sequencing projects. Isolates represented 59 Aspergillus species, including eight undescribed species, 49 Penicillium species of which seven were undescribed and 18 Talaromyces species including three described here as new. In total, 568 ITS barcodes were generated, and 391 β-tubulin and 507 calmodulin sequences, which serve as alternative identification markers.}, } @article {pmid25491920, year = {2014}, author = {Ang, L and Arboleya, S and Lihua, G and Chuihui, Y and Nan, Q and Suarez, M and Solís, G and de los Reyes-Gavilán, CG and Gueimonde, M}, title = {The establishment of the infant intestinal microbiome is not affected by rotavirus vaccination.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {7417}, pmid = {25491920}, issn = {2045-2322}, mesh = {Humans ; Infant ; Intestines/*microbiology ; Male ; Metagenomics/*methods ; Microbiota/*physiology ; Rotavirus Vaccines/*administration & dosage/adverse effects ; *Vaccination ; }, abstract = {The microbial colonization of the intestine during the first months of life constitutes the most important process for the microbiota-induced host-homeostasis. Alterations in this process may entail a high-risk for disease in later life. However, the potential factors affecting this process in the infant are not well known. Moreover, the potential impact of orally administered vaccines upon the establishing microbiome remains unknown. Here we assessed the intestinal microbiome establishment process and evaluated the impact of rotavirus vaccination upon this process. Metagenomic, PCR-DGGE and faecal short chain fatty acids analyses were performed on faecal samples obtained from three infants before and after the administration of each dose of vaccine. We found a high inter-individual variability in the early life gut microbiota at microbial composition level, but a large similarity between the infants' microbiomes at functional level. Rotavirus vaccination did not show any major effects upon the infant gut microbiota. Thus, the individual microbiome establishment and development process seems to occur in a defined manner during the first stages of life and rotavirus vaccination appears to be inconsequential for this process.}, } @article {pmid25487334, year = {2015}, author = {Pedersen, MW and Overballe-Petersen, S and Ermini, L and Sarkissian, CD and Haile, J and Hellstrom, M and Spens, J and Thomsen, PF and Bohmann, K and Cappellini, E and Schnell, IB and Wales, NA and Carøe, C and Campos, PF and Schmidt, AM and Gilbert, MT and Hansen, AJ and Orlando, L and Willerslev, E}, title = {Ancient and modern environmental DNA.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130383}, pmid = {25487334}, issn = {1471-2970}, mesh = {*Biodiversity ; DNA/*genetics/history ; Geologic Sediments/*chemistry ; History, Ancient ; Metagenomics/*methods/trends ; Water/*chemistry ; }, abstract = {DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene/Holocene transition, with implications for the extinction of megafauna. Furthermore, eDNA can reflect the biodiversity of extant flora and fauna, both qualitatively and quantitatively, allowing detection of rare species. As such, trace studies of plant and vertebrate DNA in the environment have revolutionized our knowledge of biogeography. However, the approach remains marred by biases related to DNA behaviour in environmental settings, incomplete reference databases and false positive results due to contamination. We provide a review of the field.}, } @article {pmid25487328, year = {2015}, author = {Warinner, C and Speller, C and Collins, MJ}, title = {A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130376}, pmid = {25487328}, issn = {1471-2970}, support = {097829/Z/11/A//Wellcome Trust/United Kingdom ; }, mesh = {Archaeology/*methods/trends ; Dental Calculus/*microbiology ; *Fossils ; High-Throughput Nucleotide Sequencing/methods/trends ; Humans ; Microbiological Techniques/*methods/trends ; Microbiota/*genetics ; Paleodontology/*methods/trends ; }, abstract = {The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes.}, } @article {pmid25486254, year = {2014}, author = {He, Y and Chen, Z and Liu, X and Wang, C and Lu, W}, title = {Influence of trace elements mixture on bacterial diversity and fermentation characteristics of liquid diet fermented with probiotics under air-tight condition.}, journal = {PloS one}, volume = {9}, number = {12}, pages = {e114218}, pmid = {25486254}, issn = {1932-6203}, mesh = {*Animal Feed ; Bacteria/classification/genetics/growth & development/*metabolism ; *Biodiversity ; Cluster Analysis ; *Fermentation ; Hydrogen-Ion Concentration ; Lactic Acid/biosynthesis ; Metagenomics ; Microbiota ; Phylogeny ; *Probiotics ; *Trace Elements ; }, abstract = {Cu2+, Zn2+, Fe2+ and I- are often supplemented to the diet of suckling and early weaning piglets, but little information is available regarding the effects of different Cu2+, Zn2+, Fe2+ and I- mixtures on bacteria growth, diversity and fermentation characteristics of fermented liquid diet for piglets. Pyrosequencing was performed to investigate the effect of Cu2+, Zn2+, Fe2+ and I- mixtures on the diversity, growth and fermentation characteristics of bacteria in the liquid diet fermented with Bacillus subtilis and Enterococcus faecalis under air-tight condition. Results showed that the mixtures of Cu2+, Zn2+, Fe2+ and I- at different concentrations promoted Bacillus growth, increased bacterial diversity and lactic acid production and lowered pH to about 5. The importance of Cu2+, Zn2+, Fe2+ and I- is different for Bacillus growth with the order Zn2+> Fe2+>Cu2+> I- in a 21-d fermentation and Cu2+>I->Fe2+>Zn2+ in a 42-d fermentation. Cu2+, Zn2+, Fe2+ and I- is recommended at a level of 150, 60, 150 and 0.6 mg/kg respectively for the production of fermented liquid diet with Bacillus subtilis. The findings improve our understanding of the influence of trace elements on liquid diet fermentation with probiotics and support the proper use of trace elements in the production of fermented liquid diet for piglets.}, } @article {pmid25482875, year = {2014}, author = {Lim, MY and Rho, M and Song, YM and Lee, K and Sung, J and Ko, G}, title = {Stability of gut enterotypes in Korean monozygotic twins and their association with biomarkers and diet.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {7348}, pmid = {25482875}, issn = {2045-2322}, mesh = {Asian People ; Biodiversity ; Biomarkers/metabolism ; Cluster Analysis ; *Diet ; Feces/microbiology ; Gastrointestinal Tract/*metabolism/*microbiology ; Humans ; Metagenome ; *Microbiota ; Republic of Korea ; *Twins, Monozygotic ; }, abstract = {Studies on the human gut microbiota have suggested that human individuals could be categorized into enterotypes based on the compositions of their gut microbial communities. Here, we report that the gut microbiota of healthy Koreans are clustered into two enterotypes, dominated by either Bacteroides (enterotype 1) or Prevotella (enterotype 2). More than 72% of the paired fecal samples from monozygotic twin pairs were assigned to the same enterotype. Our longitudinal analysis of these twins indicated that more than 80% of the individuals belonged to the same enterotype after about a 2-year interval. Microbial functions based on KEGG pathways were also divided into two clusters. For enterotype 2, 100% of the samples belonged to the same functional cluster, while for enterotype 1, approximately half of the samples belonged to each functional cluster. Enterotype 2 was significantly associated with long-term dietary habits that were high in dietary fiber, various vitamins, and minerals. Among anthropometrical and biochemical traits, the level of serum uric acid was associated with enterotype. These results suggest that host genetics as well as host properties such as long-term dietary patterns and a particular clinical biomarker could be important contributors to the enterotype of an individual.}, } @article {pmid25477242, year = {2015}, author = {Mesuere, B and Debyser, G and Aerts, M and Devreese, B and Vandamme, P and Dawyndt, P}, title = {The Unipept metaproteomics analysis pipeline.}, journal = {Proteomics}, volume = {15}, number = {8}, pages = {1437-1442}, doi = {10.1002/pmic.201400361}, pmid = {25477242}, issn = {1615-9861}, mesh = {Computer Graphics ; Humans ; Metagenome ; Microbiota ; Molecular Sequence Annotation ; Peptide Fragments/chemistry ; Phylogeny ; *Proteomics ; *User-Computer Interface ; }, abstract = {Unipept (http://unipept.ugent.be) is a web application that offers a user-friendly way to explore the biodiversity of complex metaproteome samples by providing interactive visualizations. In this article, the updates and changes to Unipept since its initial release are presented. This includes the addition of interactive sunburst and treeview visualizations to the multipeptide analysis, the foundations of an application programming interface (API) and a command line interface, updated data sources, and the open-sourcing of the entire application under the MIT license.}, } @article {pmid25477209, year = {2015}, author = {Colman, DR and Thomas, R and Maas, KR and Takacs-Vesbach, CD}, title = {Detection and analysis of elusive members of a novel and diverse archaeal community within a thermal spring streamer consortium.}, journal = {Extremophiles : life under extreme conditions}, volume = {19}, number = {2}, pages = {307-313}, pmid = {25477209}, issn = {1433-4909}, support = {P20GM103452/GM/NIGMS NIH HHS/United States ; R25 GM075149/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaea/classification/*genetics/isolation & purification ; Genes, Archaeal ; Hot Springs/*microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recent metagenomic analyses of Yellowstone National Park (YNP) thermal spring communities suggested the presence of minor archaeal populations that simultaneous PCR-based assays using traditional 'universal' 16S rRNA gene primers failed to detect. Here we use metagenomics to identify PCR primers effective at detecting elusive members of the Archaea, assess their efficacy, and describe the diverse and novel archaeal community from a circum-neutral thermal spring from the Bechler region of YNP. We determined that a less commonly used PCR primer, Arch349F, captured more diversity in this spring than the widely used A21F primer. A search of the PCR primers against the RDP 16S rRNA gene database indicated that Arch349F also captured the largest percentage of Archaea, including 41 % more than A21F. Pyrosequencing using the Arch349F primer recovered all of the phylotypes present in the clone-based portion of the study and the metagenome of this spring in addition to several other populations of Archaea, some of which are phylogenetically novel. In contrast to the lack of amplification with traditional 16S rRNA gene primers, our comprehensive analyses suggested a diverse archaeal community in the Bechler spring, with implications for recently discovered groups such as the Geoarchaeota and other undescribed archaeal groups.}, } @article {pmid25475614, year = {2015}, author = {Arsène-Ploetze, F and Bertin, PN and Carapito, C}, title = {Proteomic tools to decipher microbial community structure and functioning.}, journal = {Environmental science and pollution research international}, volume = {22}, number = {18}, pages = {13599-13612}, pmid = {25475614}, issn = {1614-7499}, mesh = {Animals ; Bacterial Proteins/metabolism ; *Environmental Microbiology ; Humans ; Metagenomics ; Microbial Interactions ; Microbiota ; Proteome/metabolism ; Proteomics ; }, abstract = {Recent advances in microbial ecology allow studying microorganisms in their environment, without laboratory cultivation, in order to get access to the large uncultivable microbial community. With this aim, environmental proteomics has emerged as an appropriate complementary approach to metagenomics providing information on key players that carry out main metabolic functions and addressing the adaptation capacities of living organisms in situ. In this review, a wide range of proteomic approaches applied to investigate the structure and functioning of microbial communities as well as recent examples of such studies are presented.}, } @article {pmid25474574, year = {2014}, author = {Chain, FJ and Feulner, PG and Panchal, M and Eizaguirre, C and Samonte, IE and Kalbe, M and Lenz, TL and Stoll, M and Bornberg-Bauer, E and Milinski, M and Reusch, TB}, title = {Extensive copy-number variation of young genes across stickleback populations.}, journal = {PLoS genetics}, volume = {10}, number = {12}, pages = {e1004830}, pmid = {25474574}, issn = {1553-7404}, mesh = {Adaptation, Biological/genetics ; Animals ; *DNA Copy Number Variations ; Evolution, Molecular ; Female ; Gene Deletion ; Gene Dosage ; Gene Duplication ; Genes, Duplicate/*genetics ; *Genetic Variation ; Male ; Metagenomics ; Phylogeny ; Smegmamorpha/*genetics ; }, abstract = {Duplicate genes emerge as copy-number variations (CNVs) at the population level, and remain copy-number polymorphic until they are fixed or lost. The successful establishment of such structural polymorphisms in the genome plays an important role in evolution by promoting genetic diversity, complexity and innovation. To characterize the early evolutionary stages of duplicate genes and their potential adaptive benefits, we combine comparative genomics with population genomics analyses to evaluate the distribution and impact of CNVs across natural populations of an eco-genomic model, the three-spined stickleback. With whole genome sequences of 66 individuals from populations inhabiting three distinct habitats, we find that CNVs generally occur at low frequencies and are often only found in one of the 11 populations surveyed. A subset of CNVs, however, displays copy-number differentiation between populations, showing elevated within-population frequencies consistent with local adaptation. By comparing teleost genomes to identify lineage-specific genes and duplications in sticklebacks, we highlight rampant gene content differences among individuals in which over 30% of young duplicate genes are CNVs. These CNV genes are evolving rapidly at the molecular level and are enriched with functional categories associated with environmental interactions, depicting the dynamic early copy-number polymorphic stage of genes during population differentiation.}, } @article {pmid25474207, year = {2014}, author = {Turner, CR and Miller, DJ and Coyne, KJ and Corush, J}, title = {Improved methods for capture, extraction, and quantitative assay of environmental DNA from Asian bigheaded carp (Hypophthalmichthys spp.).}, journal = {PloS one}, volume = {9}, number = {12}, pages = {e114329}, pmid = {25474207}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Carps/*genetics ; DNA/genetics/*isolation & purification ; *Ecosystem ; *Metagenomics ; }, abstract = {Indirect, non-invasive detection of rare aquatic macrofauna using aqueous environmental DNA (eDNA) is a relatively new approach to population and biodiversity monitoring. As such, the sensitivity of monitoring results to different methods of eDNA capture, extraction, and detection is being investigated in many ecosystems and species. One of the first and largest conservation programs with eDNA-based monitoring as a central instrument focuses on Asian bigheaded carp (Hypophthalmichthys spp.), an invasive fish spreading toward the Laurentian Great Lakes. However, the standard eDNA methods of this program have not advanced since their development in 2010. We developed new, quantitative, and more cost-effective methods and tested them against the standard protocols. In laboratory testing, our new quantitative PCR (qPCR) assay for bigheaded carp eDNA was one to two orders of magnitude more sensitive than the existing endpoint PCR assays. When applied to eDNA samples from an experimental pond containing bigheaded carp, the qPCR assay produced a detection probability of 94.8% compared to 4.2% for the endpoint PCR assays. Also, the eDNA capture and extraction method we adapted from aquatic microbiology yielded five times more bigheaded carp eDNA from the experimental pond than the standard method, at a per sample cost over forty times lower. Our new, more sensitive assay provides a quantitative tool for eDNA-based monitoring of bigheaded carp, and the higher-yielding eDNA capture and extraction method we describe can be used for eDNA-based monitoring of any aquatic species.}, } @article {pmid25468489, year = {2015}, author = {Fond, G and Boukouaci, W and Chevalier, G and Regnault, A and Eberl, G and Hamdani, N and Dickerson, F and Macgregor, A and Boyer, L and Dargel, A and Oliveira, J and Tamouza, R and Leboyer, M}, title = {The "psychomicrobiotic": Targeting microbiota in major psychiatric disorders: A systematic review.}, journal = {Pathologie-biologie}, volume = {63}, number = {1}, pages = {35-42}, doi = {10.1016/j.patbio.2014.10.003}, pmid = {25468489}, issn = {1768-3114}, mesh = {Animals ; Dietary Supplements ; Drug Delivery Systems/methods ; Dysbiosis/complications/*diet therapy/microbiology ; Humans ; Mental Disorders/complications/*diet therapy/microbiology ; Microbiota/*drug effects ; *Prebiotics/administration & dosage ; Probiotics/*therapeutic use ; }, abstract = {The gut microbiota is increasingly considered as a symbiotic partner in the maintenance of good health. Metagenomic approaches could help to discover how the complex gut microbial ecosystem participates in the control of the host's brain development and function, and could be relevant for future therapeutic developments, such as probiotics, prebiotics and nutritional approaches for psychiatric disorders. Previous reviews focused on the effects of microbiota on the central nervous system in in vitro and animal studies. The aim of the present review is to synthetize the current data on the association between microbiota dysbiosis and onset and/or maintenance of major psychiatric disorders, and to explore potential therapeutic opportunities targeting microbiota dysbiosis in psychiatric patients.}, } @article {pmid25467553, year = {2015}, author = {Gharechahi, J and Zahiri, HS and Noghabi, KA and Salekdeh, GH}, title = {In-depth diversity analysis of the bacterial community resident in the camel rumen.}, journal = {Systematic and applied microbiology}, volume = {38}, number = {1}, pages = {67-76}, doi = {10.1016/j.syapm.2014.09.004}, pmid = {25467553}, issn = {1618-0984}, mesh = {Animals ; Bacteroidetes/genetics ; Camelus/*microbiology ; Female ; Firmicutes/genetics ; Gastrointestinal Microbiome/*genetics ; Metagenome ; Molecular Typing ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The rumen compartment of the ruminant digestive tract is an enlarged fermentation chamber which houses a diverse collection of symbiotic microorganisms that provide the host animal with a remarkable ability to digest plant lignocellulosic materials. Characterization of the ruminal microbial community provides opportunities to improve animal food digestion efficiency, mitigate methane emission, and develop efficient fermentation systems to convert plant biomasses into biofuels. In this study, 16S rRNA gene amplicon pyrosequencing was applied in order to explore the structure of the bacterial community inhabiting the camel rumen. Using 76,333 quality-checked, chimera- and singleton-filtered reads, 4954 operational taxonomic units (OTUs) were identified at a 97% species level sequence identity. At the phylum level, more than 96% of the reads were affiliated to OTUs belonging to Bacteroidetes (51%), Firmicutes (31%), Proteobacteria (4.8%), Spirochaetes (3.5%), Fibrobacteres (3.1%), Verrucomicrobia (2.7%), and Tenericutes (0.95%). A total of 15% of the OTUs (746) that contained representative sequences from all major taxa were shared by all animals and they were considered as candidate members of the core camel rumen microbiome. Analysis of microbial composition through the solid and liquid fractions of rumen digesta revealed differential enrichment of members of Fibrobacter, Clostridium, Ruminococcus, and Treponema in the solid fraction, as well as members of Prevotella, Verrucomicrobia, Cyanobacteria, and Succinivibrio in the liquid fraction. The results clearly showed that the camel rumen microbiome was structurally similar but compositionally distinct from that of other ruminants, such as the cow. The unique characteristic of the camel rumen microbiome that differentiated it from those of other ruminants was the significant enrichment for cellulolytic bacteria.}, } @article {pmid25464142, year = {2015}, author = {Araújo, C and Muñoz-Atienza, E and Nahuelquín, Y and Poeta, P and Igrejas, G and Hernández, PE and Herranz, C and Cintas, LM}, title = {Inhibition of fish pathogens by the microbiota from rainbow trout (Oncorhynchus mykiss, Walbaum) and rearing environment.}, journal = {Anaerobe}, volume = {32}, number = {}, pages = {7-14}, doi = {10.1016/j.anaerobe.2014.11.001}, pmid = {25464142}, issn = {1095-8274}, mesh = {Animals ; *Antibiosis ; DNA Barcoding, Taxonomic ; Fishes/*microbiology ; *Host-Pathogen Interactions ; Lactobacillales/classification/genetics/metabolism ; Metagenome ; *Microbiota ; }, abstract = {This work reports the isolation and taxonomic identification of the cultivable total microbiota (TM) and Lactic Acid Bacteria (LAB) from rainbow trout (Oncorhynchus mykiss, Walbaum) and rearing environment from selected stages of the life-cycle, and the evaluation of the LAB antimicrobial activity against the main fish pathogens. TM and LAB isolates were randomly selected and identified by 16S rRNA and/or superoxide dismutase gene sequencing. Although a great diversity in the TM was observed, Enterobacteriaceae and Aeromonadaceae were clearly prevalent, while the genus Lactococcus was the predominant LAB. From a total of 1620 randomly selected LAB, 1159 isolates (71.5%) showed antimicrobial activity. From these, 248 isolates (21.4%) selected for their activity against, at least, four fish pathogens, were taxonomically identified, being Lactococcus lactis the most common species (164 isolates, 66.1%). Interestingly, 88 isolates (35.5%), including 55 L. lactis isolates, exerted activity against four strains of the rainbow trout pathogen Lactococcus garvieae. Our results demonstrate that rainbow trout and rearing environment are potential sources for the isolation of LAB, mainly lactococci, active against L. garvieae and other fish pathogens. Moreover, this is the first study describing the cultivable TM and LAB from rainbow trout intestine and rearing environment along the fish life-cycle. The host-derived LAB active against fish pathogens comprise potential candidates as probiotics in rainbow trout farming as an alternative or complementary strategy to antibiotics and vaccines for disease prevention.}, } @article {pmid25459223, year = {2014}, author = {Zhao, J and Zuo, J and Wang, X and Lin, J and Yang, Y and Zhou, J and Chu, H and Li, P}, title = {GeoChip-based analysis of microbial community of a combined nitritation-anammox reactor treating anaerobic digestion supernatant.}, journal = {Water research}, volume = {67}, number = {}, pages = {345-354}, doi = {10.1016/j.watres.2014.09.029}, pmid = {25459223}, issn = {1879-2448}, mesh = {Ammonia/*metabolism ; Bacteria, Anaerobic/*genetics ; Bioreactors/*microbiology ; Carbon/analysis ; *Cellular Microenvironment ; Genes, Bacterial/genetics ; Hydrogen-Ion Concentration ; Microbiota/*genetics ; Nitrogen/analysis ; Oligonucleotide Array Sequence Analysis/methods ; Species Specificity ; Temperature ; }, abstract = {A combined nitritation-anammox reactor was established to treat anaerobic digestion supernatant. The reactor achieved a nitrogen loading rate of 0.5 kg N/(m(3)·d) and total nitrogen removal efficiency of 85% after 140 days' operation. To examine the microbial community responsible for the process, GeoChip 4.0, a high-throughput, microarray-based metagenomic tool, was adopted to measure microbial functional potential under different percentages of digestion supernatant. Intriguingly, our results showed that microbial community composition in a stably functioning bioreactor were significantly different under varying environmental conditions. Functional gene diversities decreased with increasing percentages of digestion supernatant. Genes involved in organic remediation and metal resistance were highly abundant, revealing new metabolic potentials in addition to nitrogen and carbon removal. Compared to the significant decrease of genes involved in denitrification and nitrification caused by inhibition of the digestion supernatant, relative abundances of genes for anammox remained relatively stable. This could be partially attributed to the protection of biofilm, which was vital for the stable performance of nitrogen removal. In addition, nitrogen compounds, C/N ratio and the operation parameters (pH and temperature) were the key variables shaping the microbial community, contributing to a total of 76.64% of the variance of the reactor.}, } @article {pmid25458215, year = {2014}, author = {Kolisko, M and Boscaro, V and Burki, F and Lynn, DH and Keeling, PJ}, title = {Single-cell transcriptomics for microbial eukaryotes.}, journal = {Current biology : CB}, volume = {24}, number = {22}, pages = {R1081-2}, doi = {10.1016/j.cub.2014.10.026}, pmid = {25458215}, issn = {1879-0445}, mesh = {Biodiversity ; Cell Size ; Eukaryota/cytology/*genetics ; Gene Expression Profiling/methods ; *Single-Cell Analysis ; *Transcriptome ; }, abstract = {One of the greatest hindrances to a comprehensive understanding of microbial genomics, cell biology, ecology, and evolution is that most microbial life is not in culture. Solutions to this problem have mainly focused on whole-community surveys like metagenomics, but these analyses inevitably loose information and present particular challenges for eukaryotes, which are relatively rare and possess large, gene-sparse genomes. Single-cell analyses present an alternative solution that allows for specific species to be targeted, while retaining information on cellular identity, morphology, and partitioning of activities within microbial communities. Single-cell transcriptomics, pioneered in medical research, offers particular potential advantages for uncultivated eukaryotes, but the efficiency and biases have not been tested. Here we describe a simple and reproducible method for single-cell transcriptomics using manually isolated cells from five model ciliate species; we examine impacts of amplification bias and contamination, and compare the efficacy of gene discovery to traditional culture-based transcriptomics. Gene discovery using single-cell transcriptomes was found to be comparable to mass-culture methods, suggesting single-cell transcriptomics is an efficient entry point into genomic data from the vast majority of eukaryotic biodiversity.}, } @article {pmid25457810, year = {2014}, author = {Dellagnezze, BM and de Sousa, GV and Martins, LL and Domingos, DF and Limache, EEG and de Vasconcellos, SP and da Cruz, GF and de Oliveira, VM}, title = {Bioremediation potential of microorganisms derived from petroleum reservoirs.}, journal = {Marine pollution bulletin}, volume = {89}, number = {1-2}, pages = {191-200}, doi = {10.1016/j.marpolbul.2014.10.003}, pmid = {25457810}, issn = {1879-3363}, mesh = {Alkanes/metabolism ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Brazil ; Chromatography, Gas ; Cytochrome P-450 CYP4A/genetics ; Gas Chromatography-Mass Spectrometry ; Hydrocarbons, Aromatic/metabolism ; Microbial Consortia/genetics/*physiology ; Micrococcus/metabolism ; Oil and Gas Fields/*microbiology ; Petroleum/analysis/*metabolism ; Phenanthrenes/metabolism ; Seawater/microbiology ; }, abstract = {Bacterial strains and metagenomic clones, both obtained from petroleum reservoirs, were evaluated for petroleum degradation abilities either individually or in pools using seawater microcosms for 21 days. Gas Chromatography-Flame Ionization Detector (GC-FID) and Gas Chromatography-Mass Spectrometry (GC-MS) analyses were carried out to evaluate crude oil degradation. The results showed that metagenomic clones 1A and 2B were able to biodegrade n-alkanes (C14 to C33) and isoprenoids (phytane and pristane), with rates ranging from 31% to 47%, respectively. The bacteria Dietzia maris CBMAI 705 and Micrococcus sp. CBMAI 636 showed higher rates reaching 99% after 21 days. The metagenomic clone pool biodegraded these compounds at rates ranging from 11% to 45%. Regarding aromatic compound biodegradation, metagenomic clones 2B and 10A were able to biodegrade up to 94% of phenanthrene and methylphenanthrenes (3-MP, 2-MP, 9-MP and 1-MP) with rates ranging from 55% to 70% after 21 days, while the bacteria Dietzia maris CBMAI 705 and Micrococcus sp. CBMAI 636 were able to biodegrade 63% and up to 99% of phenanthrene, respectively, and methylphenanthrenes (3-MP, 2-MP, 9-MP and 1-MP) with rates ranging from 23% to 99% after 21 days. In this work, isolated strains as well as metagenomic clones were capable of degrading several petroleum compounds, revealing an innovative strategy and a great potential for further biotechnological and bioremediation applications.}, } @article {pmid25450165, year = {2015}, author = {Steglich, C and Stazic, D and Lott, SC and Voigt, K and Greengrass, E and Lindell, D and Hess, WR}, title = {Dataset for metatranscriptome analysis of Prochlorococcus-rich marine picoplankton communities in the Gulf of Aqaba, Red Sea.}, journal = {Marine genomics}, volume = {19}, number = {}, pages = {5-7}, doi = {10.1016/j.margen.2014.10.009}, pmid = {25450165}, issn = {1876-7478}, support = {203406/ERC_/European Research Council/International ; }, mesh = {*Biota ; Indian Ocean ; Metagenomics/methods ; Plankton/*genetics/metabolism ; Prochlorococcus/*genetics/metabolism ; Regulatory Sequences, Ribonucleic Acid/*genetics ; Transcriptome/*genetics ; }, abstract = {Regulatory RNAs play a central role in the regulation of gene expression and can act on several regulatory levels from transcriptional initiation and RNA processing to the control of initiation of translation and RNA stability. One class of these molecules is non-coding (nc)RNAs in bacteria that typically lack protein-coding potential, range in size between 50 and 500nt and originate from intergenic regions. Common methods for the identification of these RNAs are either based on computational predictions, or on transcriptomic analyses of laboratory cultures, whereas very little is known about ncRNAs in environmental microbial populations. Here, we have combined a metatranscriptomics approach with a selective enrichment protocol for ncRNAs. The primary objective of this study was the identification of novel, environmentally relevant ncRNAs focusing on the cyanobacterium Prochlorococcus, which was one of the dominant microorganisms of the marine community of the Gulf of Aqaba when samples were taken.}, } @article {pmid25448477, year = {2015}, author = {Kim, Y and Koh, I and Rho, M}, title = {Deciphering the human microbiome using next-generation sequencing data and bioinformatics approaches.}, journal = {Methods (San Diego, Calif.)}, volume = {79-80}, number = {}, pages = {52-59}, doi = {10.1016/j.ymeth.2014.10.022}, pmid = {25448477}, issn = {1095-9130}, mesh = {Computational Biology/*methods ; DNA, Bacterial/chemistry ; Humans ; Microbiota/*genetics ; }, abstract = {The human microbiome is one of the key factors affecting the host immune system and metabolic functions that are not encoded in the human genome. Culture-independent analysis of the human microbiome using metagenomics approach allows us to investigate the compositions and functions of the human microbiome. Computational methods analyze the microbial community by using specific marker genes or by using shotgun sequencing of the entire microbial community. Taxonomy profiling is conducted by using the reference sequences or by de novo clustering of the specific region of sequences. Functional profiling, which is mainly based on the sequence similarity, is more challenging since about half of ORFs predicted in the metagenomic data could not find homology with known protein families. This review examines computational methods that are valuable for the analysis of human microbiome, and highlights the results of several large-scale human microbiome studies. It is becoming increasingly evident that dysbiosis of the gut microbiome is strongly associated with the development of immune disorder and metabolic dysfunction.}, } @article {pmid25446611, year = {2015}, author = {Tomazetto, G and Wibberg, D and Schlüter, A and Oliveira, VM}, title = {New FeFe-hydrogenase genes identified in a metagenomic fosmid library from a municipal wastewater treatment plant as revealed by high-throughput sequencing.}, journal = {Research in microbiology}, volume = {166}, number = {1}, pages = {9-19}, doi = {10.1016/j.resmic.2014.11.002}, pmid = {25446611}, issn = {1769-7123}, mesh = {Algorithms ; Archaea/classification/enzymology/*genetics ; Bacteria/classification/enzymology/*genetics ; Base Sequence ; Brazil ; Clostridium/genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Genetic Variation ; *Genomic Library ; High-Throughput Nucleotide Sequencing/methods ; Hydrogen/metabolism ; Hydrogenase/*genetics ; Iron-Sulfur Proteins/*genetics ; *Metagenome ; Microbial Consortia/*genetics ; Phylogeny ; Sewage/*microbiology ; }, abstract = {A fosmid metagenomic library was constructed with total community DNA obtained from a municipal wastewater treatment plant (MWWTP), with the aim of identifying new FeFe-hydrogenase genes encoding the enzymes most important for hydrogen metabolism. The dataset generated by pyrosequencing of a fosmid library was mined to identify environmental gene tags (EGTs) assigned to FeFe-hydrogenase. The majority of EGTs representing FeFe-hydrogenase genes were affiliated with the class Clostridia, suggesting that this group is the main hydrogen producer in the MWWTP analyzed. Based on assembled sequences, three FeFe-hydrogenase genes were predicted based on detection of the L2 motif (MPCxxKxxE) in the encoded gene product, confirming true FeFe-hydrogenase sequences. These sequences were used to design specific primers to detect fosmids encoding FeFe-hydrogenase genes predicted from the dataset. Three identified fosmids were completely sequenced. The cloned genomic fragments within these fosmids are closely related to members of the Spirochaetaceae, Bacteroidales and Firmicutes, and their FeFe-hydrogenase sequences are characterized by the structure type M3, which is common to clostridial enzymes. FeFe-hydrogenase sequences found in this study represent hitherto undetected sequences, indicating the high genetic diversity regarding these enzymes in MWWTP. Results suggest that MWWTP have to be considered as reservoirs for new FeFe-hydrogenase genes.}, } @article {pmid25445830, year = {2015}, author = {Chan, TF and Ji, KM and Yim, AK and Liu, XY and Zhou, JW and Li, RQ and Yang, KY and Li, J and Li, M and Law, PT and Wu, YL and Cai, ZL and Qin, H and Bao, Y and Leung, RK and Ng, PK and Zou, J and Zhong, XJ and Ran, PX and Zhong, NS and Liu, ZG and Tsui, SK}, title = {The draft genome, transcriptome, and microbiome of Dermatophagoides farinae reveal a broad spectrum of dust mite allergens.}, journal = {The Journal of allergy and clinical immunology}, volume = {135}, number = {2}, pages = {539-548}, doi = {10.1016/j.jaci.2014.09.031}, pmid = {25445830}, issn = {1097-6825}, mesh = {Allergens/*genetics/immunology ; Animals ; Antigens, Dermatophagoides/*genetics/immunology ; Dermatophagoides farinae/anatomy & histology/classification/*genetics/*immunology/microbiology ; Female ; *Genome ; Genomics ; High-Throughput Nucleotide Sequencing ; Metagenome ; Microbiota ; Phylogeny ; Proteomics ; *Transcriptome ; }, abstract = {BACKGROUND: A sequenced house dust mite (HDM) genome would advance our understanding of HDM allergens, a common cause of human allergies.

OBJECTIVE: We sought to produce an annotated Dermatophagoides farinae draft genome and develop a combined genomic-transcriptomic-proteomic approach for elucidation of HDM allergens.

METHODS: A D farinae draft genome and transcriptome were assembled with high-throughput sequencing, accommodating microbiome sequences. The allergen gene structures were validated by means of Sanger sequencing. The mite's microbiome composition was determined, and the predominant genus was validated immunohistochemically. The allergenicity of a ubiquinol-cytochrome c reductase binding protein homologue was evaluated with immunoblotting, immunosorbent assays, and skin prick tests.

RESULTS: The full gene structures of 20 canonical allergens and 7 noncanonical allergen homologues were produced. A novel major allergen, ubiquinol-cytochrome c reductase binding protein-like protein, was found and designated Der f 24. All 40 sera samples from patients with mite allergy had IgE antibodies against rDer f 24. Of 10 patients tested, 5 had positive skin reactions. The predominant bacterial genus among 100 identified species was Enterobacter (63.4%). An intron was found in the 13.8-kDa D farinae bacteriolytic enzyme gene, indicating that it is of HDM origin. The Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed a phototransduction pathway in D farinae, as well as thiamine and amino acid synthesis pathways, which is suggestive of an endosymbiotic relationship between D farinae and its microbiome.

CONCLUSION: An HDM genome draft produced from genomic, transcriptomic, and proteomic experiments revealed allergen genes and a diverse endosymbiotic microbiome, providing a tool for further identification and characterization of HDM allergens and development of diagnostics and immunotherapeutic vaccines.}, } @article {pmid25443179, year = {2015}, author = {Rogers, GB}, title = {The human microbiome: opportunities and challenges for clinical care.}, journal = {Internal medicine journal}, volume = {45}, number = {9}, pages = {889-898}, doi = {10.1111/imj.12650}, pmid = {25443179}, issn = {1445-5994}, mesh = {Adaptive Immunity ; Anti-Infective Agents/administration & dosage/adverse effects ; Dysbiosis/complications/*immunology ; Host-Pathogen Interactions/*immunology ; Humans ; Immunity, Innate ; Metagenomics/*trends ; *Microbiota/drug effects ; }, abstract = {There is a growing appreciation of the importance of the human microbiome to our normal physiology. This complex microbial ecosystem plays a range of roles, including influencing the development and function of our immune systems, providing essential nutrients, regulating metabolism and protecting us from opportunistic infections. Our increasing understanding of these processes is due, to a large extent, to the development of high-throughput sequencing technologies, providing for the first time a means by which complex microbial dynamics can be detailed. There is also a growing recognition that disruption of commensal microbiota, a phenomenon known as dysbiosis, is associated with several common disorders, including inflammatory bowel disease, type 2 diabetes and oncogenesis. Further, where innate immunity fails to protect us, the microbial communities that colonise the external surfaces of our bodies represent a ready source of infection. This review discusses the mechanisms that govern our interaction with our resident microbiota, both in health and disease, the technological advances that allow us to gain insight into these relationships, and the way in which our growing understanding can inform clinical practice.}, } @article {pmid25440116, year = {2014}, author = {Defazio, J and Fleming, ID and Shakhsheer, B and Zaborina, O and Alverdy, JC}, title = {The opposing forces of the intestinal microbiome and the emerging pathobiome.}, journal = {The Surgical clinics of North America}, volume = {94}, number = {6}, pages = {1151-1161}, pmid = {25440116}, issn = {1558-3171}, support = {UL1 TR000430/TR/NCATS NIH HHS/United States ; P30 DK042086/DK/NIDDK NIH HHS/United States ; R01 GM062344/GM/NIGMS NIH HHS/United States ; T32 GM099697/GM/NIGMS NIH HHS/United States ; 5R01 GM062344-11/GM/NIGMS NIH HHS/United States ; P30 DK42086/DK/NIDDK NIH HHS/United States ; }, mesh = {Anastomotic Leak/microbiology/prevention & control ; Antibiotic Prophylaxis ; Cathartics/adverse effects ; Drug Resistance, Bacterial ; Humans ; Intestines/*microbiology/surgery ; Metagenomics ; *Microbiota/drug effects/genetics ; Postoperative Complications/microbiology/prevention & control ; Preoperative Care/adverse effects/methods ; Proteomics ; Sepsis/etiology/microbiology/prevention & control ; Surgical Wound Infection/*microbiology/prevention & control ; }, abstract = {This article summarizes emerging concepts on the role of the intestinal microbiome in surgical patients. Revolutionary research over the past decade has shown that human beings live in close and constant contact with boundless communities of microbes. Recent innovations in the study of the human microbiome are reviewed. To demonstrate the applicability of these studies to surgical disease, the authors discuss what is known about the role of microbes in the pathogenesis of perioperative complications. Enhanced awareness of the human microbiome will empower clinicians to adopt novel practices in the prevention and treatment of a variety of surgical conditions.}, } @article {pmid25440055, year = {2014}, author = {Joice, R and Yasuda, K and Shafquat, A and Morgan, XC and Huttenhower, C}, title = {Determining microbial products and identifying molecular targets in the human microbiome.}, journal = {Cell metabolism}, volume = {20}, number = {5}, pages = {731-741}, pmid = {25440055}, issn = {1932-7420}, support = {R01 HG005969/HG/NHGRI NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; R01HG005969/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteria/genetics/metabolism ; Fungi/genetics/metabolism ; Humans ; Metabolic Networks and Pathways ; Metabolomics/methods ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; }, abstract = {Human-associated microbes are the source of many bioactive microbial products (proteins and metabolites) that play key functions both in human host pathways and in microbe-microbe interactions. Culture-independent studies now provide an accelerated means of exploring novel bioactives in the human microbiome; however, intriguingly, a substantial fraction of the microbial metagenome cannot be mapped to annotated genes or isolate genomes and is thus of unknown function. Meta'omic approaches, including metagenomic sequencing, metatranscriptomics, metabolomics, and integration of multiple assay types, represent an opportunity to efficiently explore this large pool of potential therapeutics. In combination with appropriate follow-up validation, high-throughput culture-independent assays can be combined with computational approaches to identify and characterize novel and biologically interesting microbial products. Here we briefly review the state of microbial product identification and characterization and discuss possible next steps to catalog and leverage the large uncharted fraction of the microbial metagenome.}, } @article {pmid25440054, year = {2014}, author = {Sharon, G and Garg, N and Debelius, J and Knight, R and Dorrestein, PC and Mazmanian, SK}, title = {Specialized metabolites from the microbiome in health and disease.}, journal = {Cell metabolism}, volume = {20}, number = {5}, pages = {719-730}, pmid = {25440054}, issn = {1932-7420}, support = {R01 MH100556/MH/NIMH NIH HHS/United States ; GM099535/GM/NIGMS NIH HHS/United States ; MH100556/MH/NIMH NIH HHS/United States ; AI095125/AI/NIAID NIH HHS/United States ; GM095384/GM/NIGMS NIH HHS/United States ; R01 GM095384/GM/NIGMS NIH HHS/United States ; UL1 TR000100/TR/NCATS NIH HHS/United States ; DK078938/DK/NIDDK NIH HHS/United States ; UL1TR000100/TR/NCATS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 GM099535/GM/NIGMS NIH HHS/United States ; R01 NS085910/NS/NINDS NIH HHS/United States ; R01 AI095125/AI/NIAID NIH HHS/United States ; R01 DK078938/DK/NIDDK NIH HHS/United States ; R56 DK078938/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/genetics/*metabolism ; Cardiovascular Diseases/microbiology ; Cystic Fibrosis/microbiology ; Gastrointestinal Tract/*microbiology ; Health ; Humans ; Metagenome ; *Microbiota ; Neoplasms/microbiology ; }, abstract = {The microbiota, and the genes that comprise its microbiome, play key roles in human health. Host-microbe interactions affect immunity, metabolism, development, and behavior, and dysbiosis of gut bacteria contributes to disease. Despite advances in correlating changes in the microbiota with various conditions, specific mechanisms of host-microbiota signaling remain largely elusive. We discuss the synthesis of microbial metabolites, their absorption, and potential physiological effects on the host. We propose that the effects of specialized metabolites may explain present knowledge gaps in linking the gut microbiota to biological host mechanisms during initial colonization, and in health and disease.}, } @article {pmid25439274, year = {2014}, author = {Huang, B and Fettweis, JM and Brooks, JP and Jefferson, KK and Buck, GA}, title = {The changing landscape of the vaginal microbiome.}, journal = {Clinics in laboratory medicine}, volume = {34}, number = {4}, pages = {747-761}, pmid = {25439274}, issn = {1557-9832}, support = {U54 HD080784/HD/NICHD NIH HHS/United States ; UH3 AI083263/AI/NIAID NIH HHS/United States ; 4UH3AI083263/AI/NIAID NIH HHS/United States ; 8U54HD080784/HD/NICHD NIH HHS/United States ; }, mesh = {Female ; Female Urogenital Diseases/microbiology/pathology/prevention & control ; Humans ; Lactobacillus/physiology ; *Microbiota ; Pregnancy ; Premature Birth/microbiology ; Vagina/*microbiology ; Vaginosis, Bacterial/microbiology ; }, abstract = {Deep sequence analysis of the vaginal microbiome is revealing an unexpected complexity that was not anticipated as recently as several years ago. The lack of clarity in the definition of a healthy vaginal microbiome, much less an unhealthy vaginal microbiome, underscores the need for more investigation of these phenomena. Some clarity may be gained by the careful analysis of the genomes of the specific bacteria in these women. Ongoing studies will clarify this process and offer relief for women with recurring vaginal maladies and hope for pregnant women to avoid the experience of preterm birth.}, } @article {pmid25432777, year = {2014}, author = {Zeller, G and Tap, J and Voigt, AY and Sunagawa, S and Kultima, JR and Costea, PI and Amiot, A and Böhm, J and Brunetti, F and Habermann, N and Hercog, R and Koch, M and Luciani, A and Mende, DR and Schneider, MA and Schrotz-King, P and Tournigand, C and Tran Van Nhieu, J and Yamada, T and Zimmermann, J and Benes, V and Kloor, M and Ulrich, CM and von Knebel Doeberitz, M and Sobhani, I and Bork, P}, title = {Potential of fecal microbiota for early-stage detection of colorectal cancer.}, journal = {Molecular systems biology}, volume = {10}, number = {11}, pages = {766}, pmid = {25432777}, issn = {1744-4292}, support = {268985/ERC_/European Research Council/International ; U01 CA206110/CA/NCI NIH HHS/United States ; }, mesh = {Case-Control Studies ; Colorectal Neoplasms/*diagnosis/*microbiology ; Early Detection of Cancer/*methods ; Feces/*microbiology ; Humans ; Metagenomics/methods ; Microbiota ; Molecular Typing ; Occult Blood ; Sensitivity and Specificity ; }, abstract = {Several bacterial species have been implicated in the development of colorectal carcinoma (CRC), but CRC-associated changes of fecal microbiota and their potential for cancer screening remain to be explored. Here, we used metagenomic sequencing of fecal samples to identify taxonomic markers that distinguished CRC patients from tumor-free controls in a study population of 156 participants. Accuracy of metagenomic CRC detection was similar to the standard fecal occult blood test (FOBT) and when both approaches were combined, sensitivity improved > 45% relative to the FOBT, while maintaining its specificity. Accuracy of metagenomic CRC detection did not differ significantly between early- and late-stage cancer and could be validated in independent patient and control populations (N = 335) from different countries. CRC-associated changes in the fecal microbiome at least partially reflected microbial community composition at the tumor itself, indicating that observed gene pool differences may reveal tumor-related host-microbe interactions. Indeed, we deduced a metabolic shift from fiber degradation in controls to utilization of host carbohydrates and amino acids in CRC patients, accompanied by an increase of lipopolysaccharide metabolism.}, } @article {pmid25431780, year = {2014}, author = {Kim, H and Lee, JY and Lee, KK}, title = {Thermal characteristics and bacterial diversity of forest soil in the Haean basin of Korea.}, journal = {TheScientificWorldJournal}, volume = {2014}, number = {}, pages = {247401}, pmid = {25431780}, issn = {1537-744X}, mesh = {*Biodiversity ; *Forests ; *Hot Temperature ; Republic of Korea ; *Soil ; *Soil Microbiology ; }, abstract = {To predict biotic responses to disturbances in forest environments, it is important to examine both the thermophysical properties of forest soils and the diversity of microorganisms that these soils contain. To predict the effects of climate change on forests, in particular, it is essential to understand the interactions between the soil surface, the air, and the biological diversity in the soil. In this study, the temperature and thermal properties of forest soil at three depths at a site in the Haean basin of Korea were measured over a period of four months. Metagenomic analyses were also carried out to ascertain the diversity of microorganisms inhabiting the soil. The thermal diffusivity of the soil at the study site was 5.9 × 10(-8) m(2) · s(-1). The heat flow through the soil resulted from the cooling and heating processes acting on the surface layers of the soils. The heat productivity in the soil varied through time. The phylum Proteobacteria predominated at all three soil depths, with members of Proteobacteria forming a substantial fraction (25.64 to 39.29%). The diversity and richness of microorganisms in the soil were both highest at the deepest depth, 90 cm, where the soil temperature fluctuation was the minimum.}, } @article {pmid25429361, year = {2014}, author = {Schulze-Schweifing, K and Banerjee, A and Wade, WG}, title = {Comparison of bacterial culture and 16S rRNA community profiling by clonal analysis and pyrosequencing for the characterization of the dentine caries-associated microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {4}, number = {}, pages = {164}, pmid = {25429361}, issn = {2235-2988}, mesh = {Adult ; Dental Caries/*microbiology ; Dentin/*microbiology/pathology ; Female ; Humans ; Male ; *Metagenome ; *Microbiota ; Phylogeny ; *RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Streptococcus/classification/genetics ; Young Adult ; }, abstract = {Culture-independent analyses have greatly expanded knowledge regarding the composition of complex bacterial communities including those associated with oral diseases. A consistent finding from such studies, however, has been the under-reporting of members of the phylum Actinobacteria. In this study, five pairs of broad range primers targeting 16S rRNA genes were used in clonal analysis of 6 samples collected from tooth lesions involving dentine in subjects with active caries. Samples were also subjected to cultural analysis and pyrosequencing by means of the 454 platform. A diverse bacterial community of 229 species-level taxa was revealed by culture and clonal analysis, dominated by representatives of the genera Prevotella, Lactobacillus, Selenomonas, and Streptococcus. The five most abundant species were: Lactobacillus gasseri, Prevotella denticola, Alloprevotella tannerae, S. mutans and Streptococcus sp. HOT 070, which together made up 31.6 % of the sequences. Two samples were dominated by lactobacilli, while the remaining samples had low numbers of lactobacilli but significantly higher numbers of Prevotella species. The different primer pairs produced broadly similar data but proportions of the phylum Bacteroidetes were significantly higher when primer 1387R was used. All of the primer sets underestimated the proportion of Actinobacteria compared to culture. Pyrosequencing analysis of the samples was performed to a depth of sequencing of 4293 sequences per sample which were identified to 264 species-level taxa, and resulted in significantly higher coverage estimates than the clonal analysis. Pyrosequencing, however, also underestimated the relative abundance of Actinobacteria compared to culture.}, } @article {pmid25423727, year = {2014}, author = {Kochkina, GA and Ozerskaia, SM and Ivanushkina, NE and Chigineva, NE and Vasilenko, OV and Spirina, EV and Gilichinskiĭ, DA}, title = {[Fungal diversity in the Antarctic active layer].}, journal = {Mikrobiologiia}, volume = {83}, number = {2}, pages = {236-244}, pmid = {25423727}, issn = {0026-3656}, mesh = {Adaptation, Physiological ; Antarctic Regions ; Biodiversity ; DNA, Fungal ; Fungi/classification/genetics/*isolation & purification ; Geologic Sediments/*microbiology ; Metagenome ; Molecular Sequence Data ; }, abstract = {Taxonomic diversity of fungi in the samples of the active layer of Antarctica was investigated using conventional microbiological techniques and metagenomic analysis of total DNA extracted from environmental samples. The list of Antarctic microscopic fungi was expanded, including detection of the species representing a portion of the fungal complex, which is nonculturable or sterile on conventional nutrient media.}, } @article {pmid25423494, year = {2014}, author = {Roggenbuck, M and Bærholm Schnell, I and Blom, N and Bælum, J and Bertelsen, MF and Sicheritz-Pontén, T and Sørensen, SJ and Gilbert, MT and Graves, GR and Hansen, LH}, title = {The microbiome of New World vultures.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {5498}, doi = {10.1038/ncomms6498}, pmid = {25423494}, issn = {2041-1723}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Birds/*microbiology ; Ecosystem ; Feces/microbiology ; Gastrointestinal Tract/microbiology ; *Metagenomics ; *Microbiota ; Phylogeny ; Skin/microbiology ; }, abstract = {Vultures are scavengers that fill a key ecosystem niche, in which they have evolved a remarkable tolerance to bacterial toxins in decaying meat. Here we report the first deep metagenomic analysis of the vulture microbiome. Through face and gut comparisons of 50 vultures representing two species, we demonstrate a remarkably conserved low diversity of gut microbial flora. The gut samples contained an average of 76 operational taxonomic units (OTUs) per specimen, compared with 528 OTUs on the facial skin. Clostridia and Fusobacteria, widely pathogenic to other vertebrates, dominate the vulture's gut microbiota. We reveal a likely faecal-oral-gut route for their origin. DNA of prey species detectable on facial swabs was completely degraded in the gut samples from most vultures, suggesting that the gastrointestinal tracts of vultures are extremely selective. Our findings show a strong adaption of vultures and their bacteria to their food source, exemplifying a specialized host-microbial alliance.}, } @article {pmid25420093, year = {2014}, author = {Wang, Z and Zhang, XX and Lu, X and Liu, B and Li, Y and Long, C and Li, A}, title = {Abundance and diversity of bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants revealed by high-throughput sequencing.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e113603}, pmid = {25420093}, issn = {1932-6203}, mesh = {Aerobiosis ; Ammonia/metabolism ; Anaerobiosis ; Archaea/classification/genetics/growth & development ; Bacteria/classification/*genetics/*growth & development ; Biodiversity ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Denitrification/genetics ; Ecosystem ; Genetic Variation ; High-Throughput Nucleotide Sequencing/*methods ; Molecular Sequence Data ; Nitrification/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; *Tanning ; Waste Disposal, Fluid/methods ; Wastewater/*microbiology ; }, abstract = {Biological nitrification/denitrification is frequently used to remove nitrogen from tannery wastewater containing high concentrations of ammonia. However, information is limited about the bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants (WWTPs) due to the low-throughput of the previously used methods. In this study, 454 pyrosequencing and Illumina high-throughput sequencing, combined with molecular methods, were used to comprehensively characterize structures and functions of nitrification and denitrification bacterial communities in aerobic and anaerobic sludge of two full-scale tannery WWTPs. Pyrosequencing of 16S rRNA genes showed that Proteobacteria and Synergistetes dominated in the aerobic and anaerobic sludge, respectively. Ammonia-oxidizing bacteria (AOB) amoA gene cloning revealed that Nitrosomonas europaea dominated the ammonia-oxidizing community in the WWTPs. Metagenomic analysis showed that the denitrifiers mainly included the genera of Thauera, Paracoccus, Hyphomicrobium, Comamonas and Azoarcus, which may greatly contribute to the nitrogen removal in the two WWTPs. It is interesting that AOB and ammonia-oxidizing archaea had low abundance although both WWTPs demonstrated high ammonium removal efficiency. Good correlation between the qPCR and metagenomic analysis is observed for the quantification of functional genes amoA, nirK, nirS and nosZ, indicating that the metagenomic approach may be a promising method used to comprehensively investigate the abundance of functional genes of nitrifiers and denitrifiers in the environment.}, } @article {pmid25418454, year = {2014}, author = {Guet-Revillet, H and Coignard-Biehler, H and Jais, JP and Quesne, G and Frapy, E and Poirée, S and Le Guern, AS and Le Flèche-Matéos, A and Hovnanian, A and Consigny, PH and Lortholary, O and Nassif, X and Nassif, A and Join-Lambert, O}, title = {Bacterial pathogens associated with hidradenitis suppurativa, France.}, journal = {Emerging infectious diseases}, volume = {20}, number = {12}, pages = {1990-1998}, pmid = {25418454}, issn = {1080-6059}, mesh = {Bacteria, Anaerobic/classification/genetics/isolation & purification ; Biodiversity ; France/epidemiology ; Hidradenitis Suppurativa/*epidemiology/*microbiology ; Humans ; Metagenomics ; }, abstract = {Hidradenitis suppurativa (HS) is a skin disease characterized by recurrent nodules or abscesses and chronic suppurating lesions. In the absence of clear pathophysiology, HS is considered to be an inflammatory disease and has no satisfactory medical treatment. Recently, prolonged antimicrobial treatments were shown to improve or resolve HS lesions. We prospectively studied the microbiology of 102 HS lesions sampled from 82 patients using prolonged bacterial cultures and bacterial metagenomics on 6 samples. Staphylococcus lugdunensis was cultured as a unique or predominant isolate from 58% of HS nodules and abscesses, and a polymicrobial anaerobic microflora comprising strict anaerobes, milleri group streptococci, and actinomycetes was found in 24% of abscesses or nodules and in 87% of chronic suppurating lesions. These data show that bacteria known to cause soft tissue and skin infections are associated with HS lesions. Whether these pathogens are the cause of the lesions or are secondary infectious agents, these findings support targeted antimicrobial treatment of HS.}, } @article {pmid25417646, year = {2015}, author = {Larraufie, P and de Wouters, T and Potocki-Veronese, G and Blottière, HM and Doré, J}, title = {Functional metagenomics to decipher food-microbe-host crosstalk.}, journal = {The Proceedings of the Nutrition Society}, volume = {74}, number = {1}, pages = {1-4}, doi = {10.1017/S0029665114001566}, pmid = {25417646}, issn = {1475-2719}, mesh = {*Food ; Humans ; Intestines/*microbiology ; Metagenomics/*methods ; Microbiota/*physiology ; }, abstract = {The recent developments of metagenomics permit an extremely high-resolution molecular scan of the intestinal microbiota giving new insights and opening perspectives for clinical applications. Beyond the unprecedented vision of the intestinal microbiota given by large-scale quantitative metagenomics studies, such as the EU MetaHIT project, functional metagenomics tools allow the exploration of fine interactions between food constituents, microbiota and host, leading to the identification of signals and intimate mechanisms of crosstalk, especially between bacteria and human cells. Cloning of large genome fragments, either from complex intestinal communities or from selected bacteria, allows the screening of these biological resources for bioactivity towards complex plant polymers or functional food such as prebiotics. This permitted identification of novel carbohydrate-active enzyme families involved in dietary fibre and host glycan breakdown, and highlighted unsuspected bacterial players at the top of the intestinal microbial food chain. Similarly, exposure of fractions from genomic and metagenomic clones onto human cells engineered with reporter systems to track modulation of immune response, cell proliferation or cell metabolism has allowed the identification of bioactive clones modulating key cell signalling pathways or the induction of specific genes. This opens the possibility to decipher mechanisms by which commensal bacteria or candidate probiotics can modulate the activity of cells in the intestinal epithelium or even in distal organs such as the liver, adipose tissue or the brain. Hence, in spite of our inability to culture many of the dominant microbes of the human intestine, functional metagenomics open a new window for the exploration of food-microbe-host crosstalk.}, } @article {pmid25412107, year = {2014}, author = {Shafiei, M and Dunn, KA and Chipman, H and Gu, H and Bielawski, JP}, title = {BiomeNet: a Bayesian model for inference of metabolic divergence among microbial communities.}, journal = {PLoS computational biology}, volume = {10}, number = {11}, pages = {e1003918}, pmid = {25412107}, issn = {1553-7358}, support = {CMF-108026//Canadian Institutes of Health Research/Canada ; }, mesh = {Algorithms ; Animals ; Bayes Theorem ; Carnivory/physiology ; Computational Biology/*methods ; Herbivory/physiology ; Humans ; Inflammatory Bowel Diseases/metabolism/microbiology ; Metagenome ; Microbiota/genetics/*physiology ; *Models, Biological ; Reproducibility of Results ; }, abstract = {Metagenomics yields enormous numbers of microbial sequences that can be assigned a metabolic function. Using such data to infer community-level metabolic divergence is hindered by the lack of a suitable statistical framework. Here, we describe a novel hierarchical Bayesian model, called BiomeNet (Bayesian inference of metabolic networks), for inferring differential prevalence of metabolic subnetworks among microbial communities. To infer the structure of community-level metabolic interactions, BiomeNet applies a mixed-membership modelling framework to enzyme abundance information. The basic idea is that the mixture components of the model (metabolic reactions, subnetworks, and networks) are shared across all groups (microbiome samples), but the mixture proportions vary from group to group. Through this framework, the model can capture nested structures within the data. BiomeNet is unique in modeling each metagenome sample as a mixture of complex metabolic systems (metabosystems). The metabosystems are composed of mixtures of tightly connected metabolic subnetworks. BiomeNet differs from other unsupervised methods by allowing researchers to discriminate groups of samples through the metabolic patterns it discovers in the data, and by providing a framework for interpreting them. We describe a collapsed Gibbs sampler for inference of the mixture weights under BiomeNet, and we use simulation to validate the inference algorithm. Application of BiomeNet to human gut metagenomes revealed a metabosystem with greater prevalence among inflammatory bowel disease (IBD) patients. Based on the discriminatory subnetworks for this metabosystem, we inferred that the community is likely to be closely associated with the human gut epithelium, resistant to dietary interventions, and interfere with human uptake of an antioxidant connected to IBD. Because this metabosystem has a greater capacity to exploit host-associated glycans, we speculate that IBD-associated communities might arise from opportunist growth of bacteria that can circumvent the host's nutrient-based mechanism for bacterial partner selection.}, } @article {pmid25411373, year = {2014}, author = {Schweyen, H and Rozenberg, A and Leese, F}, title = {Detection and removal of PCR duplicates in population genomic ddRAD studies by addition of a degenerate base region (DBR) in sequencing adapters.}, journal = {The Biological bulletin}, volume = {227}, number = {2}, pages = {146-160}, doi = {10.1086/BBLv227n2p146}, pmid = {25411373}, issn = {1939-8697}, mesh = {Animals ; DNA Restriction Enzymes/metabolism ; Invertebrates/genetics ; Metagenomics/*methods ; Polymerase Chain Reaction/*standards ; Polymorphism, Genetic/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Restriction-site associated DNA sequencing (RAD) has emerged as a powerful marker system for studying genome-wide DNA polymorphisms using next-generation sequencing. A recent technical facilitation of RAD is double-digest RAD (ddRAD), which utilizes two restriction enzymes for library preparation. The more flexible and balanced ddRAD allows analysis of genomic loci in hundreds of individuals. However, in contrast to paired-end sequencing of traditional RAD libraries, PCR duplicates cannot be detected with ddRAD. This is a concern because duplicates can contribute substantially to read coverage data and erroneously inflate the proportion of homozygous loci (allele dropout). Allele dropout can bias population genetic parameter inference and complicate the detection of outlier loci under selection. Here we outline a simple and straightforward approach to detecting PCR duplicates from ddRAD libraries. Our approach introduces a degenerate base region (DBR, 12,288 unique combinations) in the sequencing adapter. We demonstrate the high efficiency and low rate of false positives in simulations. In addition, a pilot study was performed to test this approach on six aquatic invertebrates, sequenced on a HiSeq 2500 sequencer. The reads of the ddRAD libraries consisted of 33.48% PCR duplicates distributed on 19.40% of the loci. A disproportionate number of PCR duplicates were detected in only 4.66% of the loci. While this should not be a concern for general parameter inference, outlier loci detection in particular would be improved by the DBR technique. Given the easy and straightforward application of the technique in other RAD protocols as well, we suggest that DBR regions should generally be included in PCR-based RAD studies.}, } @article {pmid25411370, year = {2014}, author = {Bik, HM}, title = {Deciphering diversity and ecological function from marine metagenomes.}, journal = {The Biological bulletin}, volume = {227}, number = {2}, pages = {107-116}, doi = {10.1086/BBLv227n2p107}, pmid = {25411370}, issn = {1939-8697}, mesh = {Aquatic Organisms/*genetics ; *Biodiversity ; Computational Biology/trends ; Ecosystem ; Metagenome/*genetics ; Petroleum Pollution ; Research/trends ; Viruses/genetics ; }, abstract = {Metagenomic sequencing now represents a common, powerful approach for investigating diversity and functional relationships in marine ecosystems. High-throughput datasets generated from random fragments of environmental DNA can provide a less biased view of organismal abundance (versus PCR-based amplicon sequencing) and enable novel exploration of microbial genomes by recovering genome assemblies from uncultured species, identifying ecological functions, and reconstructing metabolic pathways. This review highlights the current state of knowledge in marine metagenomics, focusing on biological insights gained from recent environmental studies and detailing commonly employed methods for data collection and analysis.}, } @article {pmid25409177, year = {2014}, author = {Galley, JD and Bailey, M and Kamp Dush, C and Schoppe-Sullivan, S and Christian, LM}, title = {Maternal obesity is associated with alterations in the gut microbiome in toddlers.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e113026}, pmid = {25409177}, issn = {1932-6203}, support = {R21HD067670/HD/NICHD NIH HHS/United States ; R01 AT006552/AT/NCCIH NIH HHS/United States ; R21 HD067670/HD/NICHD NIH HHS/United States ; R01AT006552/AT/NCCIH NIH HHS/United States ; T32 DE014320/DE/NIDCR NIH HHS/United States ; R01NR01366/NR/NINR NIH HHS/United States ; }, mesh = {Body Mass Index ; *Breast Feeding ; Child, Preschool ; Feces/*microbiology ; Female ; Humans ; Infant ; Male ; Metagenome ; *Microbiota ; Obesity/complications/epidemiology/*microbiology ; *Pregnancy ; Self Report ; Socioeconomic Factors ; }, abstract = {Children born to obese mothers are at increased risk for obesity, but the mechanisms behind this association are not fully delineated. A novel possible pathway linking maternal and child weight is the transmission of obesogenic microbes from mother to child. The current study examined whether maternal obesity was associated with differences in the composition of the gut microbiome in children in early life. Fecal samples from children 18-27 months of age (n = 77) were analyzed by pyro-tag 16S sequencing. Significant effects of maternal obesity on the composition of the gut microbiome of offspring were observed among dyads of higher socioeconomic status (SES). In the higher SES group (n = 47), children of obese (BMI≥30) versus non-obese mothers clustered on a principle coordinate analysis (PCoA) and exhibited greater homogeneity in the composition of their gut microbiomes as well as greater alpha diversity as indicated by the Shannon Diversity Index, and measures of richness and evenness. Also in the higher SES group, children born to obese versus non-obese mothers had differences in abundances of Faecalibacterium spp., Eubacterium spp., Oscillibacter spp., and Blautia spp. Prior studies have linked some of these bacterial groups to differences in weight and diet. This study provides novel evidence that maternal obesity is associated with differences in the gut microbiome in children in early life, particularly among those of higher SES. Among obese adults, the relative contribution of genetic versus behavioral factors may differ based on SES. Consequently, the extent to which maternal obesity confers measureable changes to the gut microbiome of offspring may differ based on the etiology of maternal obesity. Continued research is needed to examine this question as well as the relevance of the observed differences in gut microbiome composition for weight trajectory over the life course.}, } @article {pmid25408171, year = {2014}, author = {Colombo, RP and Fernández Bidondo, L and Silvani, VA and Carbonetto, MB and Rascovan, N and Bompadre, MJ and Pérgola, M and Cuenca, G and Godeas, AM}, title = {Diversity of arbuscular mycorrhizal fungi in soil from the Pampa Ondulada, Argentina, assessed by pyrosequencing and morphological techniques.}, journal = {Canadian journal of microbiology}, volume = {60}, number = {12}, pages = {819-827}, doi = {10.1139/cjm-2014-0364}, pmid = {25408171}, issn = {1480-3275}, mesh = {Agriculture ; Argentina ; *Biodiversity ; Genome, Fungal ; Metagenome ; Mycorrhizae/*classification/cytology/genetics/isolation & purification ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The aim of this study was to assess the effects of agronomic practices on the arbuscular mycorrhizal (AM) fungal community in soils from the Pampa Ondulada region (Argentina), and to compare conclusions reached when using pyrosequencing or a morphological approach. The AM fungal diversity of 3 agricultural exploitations located in the Pampa Ondulada region (Argentina) was assessed by using 454 amplicon pyrosequencing and morphological (based on spore traits) approaches. Two kinds of soil managements are found in these sites: agronomic and non-agronomic. A total of 188 molecular operational taxonomic units and 29 morphological species of AM fungi were identified. No effect of soil management on AM richness was detected. AM fungal communities were more diverse and equitable in the absence of agronomic management. In contrast, the results on β-diversity varied according to the methodology used. We concluded that agronomic management of soil has a negative effect on AM fungal community biodiversity in the Pampa Ondulada region. We also conclude that both methodologies complement each other in the study of AM fungal ecology. This study greatly improved the knowledge about AM fungi in South America where the molecular diversity of AM fungi was practically unknown.}, } @article {pmid25407519, year = {2015}, author = {Vázquez-Castellanos, JF and Serrano-Villar, S and Latorre, A and Artacho, A and Ferrús, ML and Madrid, N and Vallejo, A and Sainz, T and Martínez-Botas, J and Ferrando-Martínez, S and Vera, M and Dronda, F and Leal, M and Del Romero, J and Moreno, S and Estrada, V and Gosalbes, MJ and Moya, A}, title = {Altered metabolism of gut microbiota contributes to chronic immune activation in HIV-infected individuals.}, journal = {Mucosal immunology}, volume = {8}, number = {4}, pages = {760-772}, pmid = {25407519}, issn = {1935-3456}, mesh = {Adaptive Immunity ; Antiretroviral Therapy, Highly Active ; Bayes Theorem ; Biodiversity ; Case-Control Studies ; Cluster Analysis ; Disease Progression ; *Gastrointestinal Microbiome ; HIV Infections/drug therapy/*immunology/metabolism/*microbiology ; HIV-1/*immunology ; Humans ; Immunity, Innate ; Markov Chains ; Metabolome ; Metabolomics ; Metagenome ; RNA, Ribosomal, 16S ; }, abstract = {Altered interplay between gut mucosa and microbiota during treated HIV infection may possibly contribute to increased bacterial translocation and chronic immune activation, both of which are predictors of morbidity and mortality. Although a dysbiotic gut microbiota has recently been reported in HIV+ individuals, the metagenome gene pool associated with HIV infection remains unknown. The aim of this study is to characterize the functional gene content of gut microbiota in HIV+ patients and to define the metabolic pathways of this bacterial community, which is potentially associated with immune dysfunction. We determined systemic markers of innate and adaptive immunity in a cohort of HIV-infected individuals on successful antiretroviral therapy without comorbidities and in healthy non-HIV-infected subjects. Metagenome sequencing revealed an altered functional profile, with enrichment of the genes involved in various pathogenic processes, lipopolysaccharide biosynthesis, bacterial translocation, and other inflammatory pathways. In contrast, we observed depletion of genes involved in amino acid metabolism and energy processes. Bayesian networks showed significant interactions between the bacterial community, their altered metabolic pathways, and systemic markers of immune dysfunction. This study reveals altered metabolic activity of microbiota and provides novel insight into the potential host-microbiota interactions driving the sustained inflammatory state in successfully treated HIV-infected patients.}, } @article {pmid25405856, year = {2014}, author = {Della Sala, G and Hochmuth, T and Teta, R and Costantino, V and Mangoni, A}, title = {Polyketide synthases in the microbiome of the marine sponge Plakortis halichondrioides: a metagenomic update.}, journal = {Marine drugs}, volume = {12}, number = {11}, pages = {5425-5440}, pmid = {25405856}, issn = {1660-3397}, mesh = {Animals ; Caribbean Region ; *Metagenomics ; *Microbiota ; Plakortis/*genetics/metabolism/microbiology ; Polyketide Synthases/*genetics ; Polyketides/metabolism ; Polymerase Chain Reaction ; Secondary Metabolism ; }, abstract = {Sponge-associated microorganisms are able to assemble the complex machinery for the production of secondary metabolites such as polyketides, the most important class of marine natural products from a drug discovery perspective. A comprehensive overview of polyketide biosynthetic genes of the sponge Plakortis halichondrioides and its symbionts was obtained in the present study by massively parallel 454 pyrosequencing of complex and heterogeneous PCR (Polymerase Chain Reaction) products amplified from the metagenomic DNA of a specimen of P. halichondrioides collected in the Caribbean Sea. This was accompanied by a survey of the bacterial diversity within the sponge. In line with previous studies, sequences belonging to supA and swfA, two widespread sponge-specific groups of polyketide synthase (PKS) genes were dominant. While they have been previously reported as belonging to Poribacteria (a novel bacterial phylum found exclusively in sponges), re-examination of current genomic sequencing data showed supA and swfA not to be present in the poribacterial genome. Several non-supA, non-swfA type-I PKS fragments were also identified. A significant portion of these fragments resembled type-I PKSs from protists, suggesting that bacteria may not be the only source of polyketides from P. halichondrioides, and that protistan PKSs should receive further investigation as a source of novel polyketides.}, } @article {pmid25404119, year = {2015}, author = {Romani, L and Zelante, T and Palmieri, M and Napolioni, V and Picciolini, M and Velardi, A and Aversa, F and Puccetti, P}, title = {The cross-talk between opportunistic fungi and the mammalian host via microbiota's metabolism.}, journal = {Seminars in immunopathology}, volume = {37}, number = {2}, pages = {163-171}, pmid = {25404119}, issn = {1863-2300}, mesh = {Animals ; Fungi/*immunology/*metabolism ; Gastrointestinal Tract/immunology/metabolism/microbiology ; Homeostasis ; *Host-Pathogen Interactions/immunology ; Humans ; Immune Tolerance ; Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism ; Metabolome ; *Microbiota ; Mycoses/*immunology/*metabolism/microbiology ; Receptors, Aryl Hydrocarbon/metabolism ; *Symbiosis ; }, abstract = {An increased understanding of the importance of microbiota in shaping the host's immune and metabolic activities has rendered fungal interactions with their hosts more complex than previously appreciated. It is now clear that a three-way interaction between host, fungi, and microbiota dictates the types of host-fungus relationship. Indeed, microbial dysbiosis predisposes to a variety of chronic fungal infections and diseases at local and distant sites. By correlating changes in metabolite profiles with microbiota metagenomic composition, we have defined a functional node whereby certain bacteria species contribute to host-fungal symbiosis and mucosal homeostasis. A tryptophan catabolic pathway is exploited by commensal lactobacilli and the mammalian host to increase fitness in response to Candida albicans by inducing resistance and tolerance mechanisms of antifungal immunity. Much like lactobacilli in the gut, Firmicutes change significantly in the airways during aspergillosis. The aryl hydrocarbon receptor has a pivotal role in connecting tryptophan catabolism by microbial communities and the host's own pathway of tryptophan degradation through the enzyme indoleamine 2,3-dioxygenase 1. These data suggest that the study of the human microbiota in the trans-omics era, with a focus on metagenomics and metabonomics, is providing novel insights into the regulation of host immune responsiveness to fungi.}, } @article {pmid25404113, year = {2015}, author = {Koch, L}, title = {Metagenomics: Shaping the gut microbiome.}, journal = {Nature reviews. Genetics}, volume = {16}, number = {1}, pages = {2}, doi = {10.1038/nrg3869}, pmid = {25404113}, issn = {1471-0064}, mesh = {Animals ; Bacteria/*classification/*isolation & purification ; Feces/*microbiology ; Female ; Humans ; Male ; *Microbiota ; }, } @article {pmid25402007, year = {2015}, author = {Buchfink, B and Xie, C and Huson, DH}, title = {Fast and sensitive protein alignment using DIAMOND.}, journal = {Nature methods}, volume = {12}, number = {1}, pages = {59-60}, pmid = {25402007}, issn = {1548-7105}, mesh = {Algorithms ; Base Sequence ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Sensitivity and Specificity ; Sequence Alignment/*methods ; Sequence Analysis, DNA ; *Software ; }, abstract = {The alignment of sequencing reads against a protein reference database is a major computational bottleneck in metagenomics and data-intensive evolutionary projects. Although recent tools offer improved performance over the gold standard BLASTX, they exhibit only a modest speedup or low sensitivity. We introduce DIAMOND, an open-source algorithm based on double indexing that is 20,000 times faster than BLASTX on short reads and has a similar degree of sensitivity.}, } @article {pmid25400621, year = {2014}, author = {Lau, MC and Cameron, C and Magnabosco, C and Brown, CT and Schilkey, F and Grim, S and Hendrickson, S and Pullin, M and Sherwood Lollar, B and van Heerden, E and Kieft, TL and Onstott, TC}, title = {Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {531}, pmid = {25400621}, issn = {1664-302X}, support = {R01 HG007513/HG/NHGRI NIH HHS/United States ; }, abstract = {Comparative studies on community phylogenetics and phylogeography of microorganisms living in extreme environments are rare. Terrestrial subsurface habitats are valuable for studying microbial biogeographical patterns due to their isolation and the restricted dispersal mechanisms. Since the taxonomic identity of a microorganism does not always correspond well with its functional role in a particular community, the use of taxonomic assignments or patterns may give limited inference on how microbial functions are affected by historical, geographical and environmental factors. With seven metagenomic libraries generated from fracture water samples collected from five South African mines, this study was carried out to (1) screen for ubiquitous functions or pathways of biogeochemical cycling of CH4, S, and N; (2) to characterize the biodiversity represented by the common functional genes; (3) to investigate the subsurface biogeography as revealed by this subset of genes; and (4) to explore the possibility of using metagenomic data for evolutionary study. The ubiquitous functional genes are NarV, NPD, PAPS reductase, NifH, NifD, NifK, NifE, and NifN genes. Although these eight common functional genes were taxonomically and phylogenetically diverse and distinct from each other, the dissimilarity between samples did not correlate strongly with geographical or environmental parameters or residence time of the water. Por genes homologous to those of Thermodesulfovibrio yellowstonii detected in all metagenomes were deep lineages of Nitrospirae, suggesting that subsurface habitats have preserved ancestral genetic signatures that inform the study of the origin and evolution of prokaryotes.}, } @article {pmid25398855, year = {2015}, author = {Wang, Z and Leary, DH and Malanoski, AP and Li, RW and Hervey, WJ and Eddie, BJ and Tender, GS and Yanosky, SG and Vora, GJ and Tender, LM and Lin, B and Strycharz-Glaven, SM}, title = {A previously uncharacterized, nonphotosynthetic member of the Chromatiaceae is the primary CO2-fixing constituent in a self-regenerating biocathode.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {2}, pages = {699-712}, pmid = {25398855}, issn = {1098-5336}, mesh = {*Bioelectric Energy Sources ; Biota ; Carbon Dioxide/*metabolism ; Chromatiaceae/genetics/*isolation & purification/*metabolism ; DNA, Bacterial/chemistry/genetics ; Electrodes/*microbiology ; Metagenome ; Microbial Consortia ; Molecular Sequence Data ; Proteome ; Sequence Analysis, DNA ; }, abstract = {Biocathode extracellular electron transfer (EET) may be exploited for biotechnology applications, including microbially mediated O2 reduction in microbial fuel cells and microbial electrosynthesis. However, biocathode mechanistic studies needed to improve or engineer functionality have been limited to a few select species that form sparse, homogeneous biofilms characterized by little or no growth. Attempts to cultivate isolates from biocathode environmental enrichments often fail due to a lack of some advantage provided by life in a consortium, highlighting the need to study and understand biocathode consortia in situ. Here, we present metagenomic and metaproteomic characterization of a previously described biocathode biofilm (+310 mV versus a standard hydrogen electrode [SHE]) enriched from seawater, reducing O2, and presumably fixing CO2 for biomass generation. Metagenomics identified 16 distinct cluster genomes, 15 of which could be assigned at the family or genus level and whose abundance was roughly divided between Alpha- and Gammaproteobacteria. A total of 644 proteins were identified from shotgun metaproteomics and have been deposited in the the ProteomeXchange with identifier PXD001045. Cluster genomes were used to assign the taxonomic identities of 599 proteins, with Marinobacter, Chromatiaceae, and Labrenzia the most represented. RubisCO and phosphoribulokinase, along with 9 other Calvin-Benson-Bassham cycle proteins, were identified from Chromatiaceae. In addition, proteins similar to those predicted for iron oxidation pathways of known iron-oxidizing bacteria were observed for Chromatiaceae. These findings represent the first description of putative EET and CO2 fixation mechanisms for a self-regenerating, self-sustaining multispecies biocathode, providing potential targets for functional engineering, as well as new insights into biocathode EET pathways using proteomics.}, } @article {pmid25392361, year = {2015}, author = {Stokell, JR and Gharaibeh, RZ and Hamp, TJ and Zapata, MJ and Fodor, AA and Steck, TR}, title = {Analysis of changes in diversity and abundance of the microbial community in a cystic fibrosis patient over a multiyear period.}, journal = {Journal of clinical microbiology}, volume = {53}, number = {1}, pages = {237-247}, pmid = {25392361}, issn = {1098-660X}, mesh = {Adult ; Anti-Bacterial Agents/therapeutic use ; Bacterial Load ; *Biodiversity ; Chronic Disease ; Cystic Fibrosis/*complications/genetics/therapy ; Disease Progression ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenome ; *Microbiota ; Pneumonia, Bacterial/drug therapy/*microbiology ; RNA, Bacterial ; RNA, Ribosomal, 16S/genetics ; Sputum/microbiology ; Treatment Outcome ; }, abstract = {The evolution of pulmonary disease in cystic fibrosis (CF) usually begins when bacteria get trapped in mucus in the lungs and become established as a chronic infection. While most CF patients experience periods of stability, pulmonary exacerbations (PEs) can occur multiple times per year and result in permanent damage to the lungs. Little is known of the shift from a period of stability to a PE, but this shift is likely to be attributed to changes in the bacterial community. Here, we identified changes in the lung microbiota to determine if they reflect patient health, indicate the onset of exacerbations, or are related to antibiotic treatment. In contrast to most bacterial studies on CF, we collected weekly samples from an adult CF patient over a period of 3 years and performed quantitative PCR (qPCR) and Illumina sequencing on those samples. While many DNA-based studies have shown the CF microbiota to be relatively stable, we observed an increase in the total bacterial abundance over time (P < 0.001), while the number of different taxa (bacterial richness) and the number of different taxa and their abundances (diversity) significantly decreased over time (P < 0.03), which was likely due to repeated antibiotic exposure. Using genus-specific primers with qPCR, we observed an increase in the abundance of Burkholderia multivorans, a CF-associated pathogen, prior to the occurrence of a PE (P = 0.006). Combining these DNA-based techniques with frequent sampling identified a potential initiator for exacerbations and described a response of the CF microbiota to time and antibiotic treatment not observed in previous CF microbiota studies.}, } @article {pmid25387460, year = {2014}, author = {Salter, SJ and Cox, MJ and Turek, EM and Calus, ST and Cookson, WO and Moffatt, MF and Turner, P and Parkhill, J and Loman, NJ and Walker, AW}, title = {Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.}, journal = {BMC biology}, volume = {12}, number = {}, pages = {87}, pmid = {25387460}, issn = {1741-7007}, support = {/WT_/Wellcome Trust/United Kingdom ; 097117/WT_/Wellcome Trust/United Kingdom ; MR/J014370/1/MRC_/Medical Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*DNA Contamination ; Indicators and Reagents/*analysis ; *Laboratories ; *Metagenomics ; *Microbiota ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/analysis ; Salmonella/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents.

RESULTS: In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits and other laboratory reagents, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. Contamination impacts both PCR-based 16S rRNA gene surveys and shotgun metagenomics. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination.

CONCLUSIONS: These results suggest that caution should be advised when applying sequence-based techniques to the study of microbiota present in low biomass environments. Concurrent sequencing of negative control samples is strongly advised.}, } @article {pmid25387109, year = {2015}, author = {Denman, SE and McSweeney, CS}, title = {The early impact of genomics and metagenomics on ruminal microbiology.}, journal = {Annual review of animal biosciences}, volume = {3}, number = {}, pages = {447-465}, doi = {10.1146/annurev-animal-022114-110705}, pmid = {25387109}, issn = {2165-8110}, mesh = {Animals ; Dietary Fiber/metabolism ; Genomics ; Methane/biosynthesis ; Microbiota/*genetics ; Phylogeny ; Rumen/*microbiology ; Ruminants/*microbiology ; }, abstract = {Knowledge gained from early and recent studies that define the functions of microbial populations within the rumen microbiome is essential to allow for directed rumen manipulation strategies. A large number of omic studies have focused on carbohydrate active enzymes either for improved fiber digestion within the animal or for use in industries such as biofuels. Studies of the rumen microbiome with respect to methane production and abatement strategies have led to initiatives for defining the microbiome of low- and high-methane-emitting animals while ensuring optimal feed conversion. With advances in omic technologies, the ability to link host genetics and the rumen microbiome by studying all the biological components (holobiont) through the use of hologenomics has begun. However, a program to culture and isolate microbial species for the purpose of standard microbial characterization to aid in assigning function to genomic data remains critical, especially for genes of unknown function.}, } @article {pmid25384884, year = {2014}, author = {Takeshita, T and Matsuo, K and Furuta, M and Shibata, Y and Fukami, K and Shimazaki, Y and Akifusa, S and Han, DH and Kim, HD and Yokoyama, T and Ninomiya, T and Kiyohara, Y and Yamashita, Y}, title = {Distinct composition of the oral indigenous microbiota in South Korean and Japanese adults.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {6990}, pmid = {25384884}, issn = {2045-2322}, mesh = {Adult ; Aged ; DNA, Bacterial/*genetics ; Female ; Fusobacterium/genetics/isolation & purification ; Haemophilus/genetics/isolation & purification ; Humans ; Japan/epidemiology ; Male ; *Metagenome ; Microbiota/*genetics ; Middle Aged ; Mouth/*microbiology ; Neisseria/genetics/isolation & purification ; Oral Health/ethnology ; Oral Hygiene ; Periodontitis/epidemiology/ethnology ; Prevotella/genetics/isolation & purification ; RNA, Ribosomal, 16S/*genetics ; Republic of Korea/epidemiology ; Saliva/*microbiology ; Sequence Analysis, DNA ; Veillonella/genetics/isolation & purification ; }, abstract = {A comparison of national surveys on oral health suggested that the population of South Korea has a better periodontal health status than that of Japan, despite their similar inherent backgrounds. Here, we investigated differences in oral bacterial assemblages between individuals from those two countries. To exclude potential effects of oral health condition on the microbiota, we selected 52 Korean and 88 Japanese orally healthy adults (aged 40-79 years) from the participants of two cohort studies, the Yangpyeong study in South Korea and the Hisayama study in Japan, and compared the salivary microbiomes. The microbiota of the Japanese individuals comprised a more diverse community, with greater proportions of 17 bacterial genera, including Veillonella, Prevotella, and Fusobacterium, compared to the microbiota of the Korean individuals. Conversely, Neisseria and Haemophilus species were present in much lower proportions in the microbiota of the Japanese individuals than the Korean individuals. Because higher proportions of Prevotella and Veillonella and lower proportions of Neisseria and Haemophilus in the salivary microbiome were implicated in periodontitis, the results of this study suggest that the greater proportion of dysbiotic oral microbiota in the Japanese individuals is associated with their higher susceptibility to periodontitis compared to the Korean individuals.}, } @article {pmid25383623, year = {2014}, author = {Li, RW and Giarrizzo, JG and Wu, S and Li, W and Duringer, JM and Craig, AM}, title = {Metagenomic insights into the RDX-degrading potential of the ovine rumen microbiome.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e110505}, pmid = {25383623}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Biodegradation, Environmental ; Cloning, Molecular ; Genes, Bacterial/genetics ; Male ; Metagenomics/*methods ; Microbiota/*genetics/physiology ; Molecular Sequence Annotation ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; Sheep/*microbiology ; Triazines/*metabolism ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The manufacturing processes of royal demolition explosive (RDX), or hexahydro-1,3,5-trinitro-1,3,5-triazine, have resulted in serious water contamination. As a potential carcinogen, RDX can cause a broad range of harmful effects to humans and animals. The ovine rumen is capable of rapid degradation of nitroaromatic compounds, including RDX. While ruminal RDX-degrading bacteria have been identified, the genes and pathways responsible for RDX degradation in the rumen have yet to be characterized. In this study, we characterized the metabolic potential of the ovine rumen using metagenomic approaches. Sequences homologous to at least five RDX-degrading genes cloned from environmental samples (diaA, xenA, xenB, xplA, and xplB) were present in the ovine rumen microbiome. Among them, diaA was the most abundant, likely reflective of the predominance of the genus Clostridium in the ovine rumen. At least ten genera known to harbor RDX-degrading microorganisms were detectable. Metagenomic sequences were also annotated using public databases, such as Pfam, COG, and KEGG. Five of the six Pfam protein families known to be responsible for RDX degradation in environmental samples were identified in the ovine rumen. However, increased substrate availability did not appear to enhance the proliferation of RDX-degrading bacteria and alter the microbial composition of the ovine rumen. This implies that the RDX-degrading capacity of the ovine rumen microbiome is likely regulated at the transcription level. Our results provide metagenomic insights into the RDX-degrading potential of the ovine rumen, and they will facilitate the development of novel and economic bioremediation strategies.}, } @article {pmid25382376, year = {2015}, author = {Yap, IK and Kho, MT and Lim, SH and Ismail, NH and Yam, WK and Chong, CW}, title = {Acclimatisation-induced stress influenced host metabolic and gut microbial composition change.}, journal = {Molecular bioSystems}, volume = {11}, number = {1}, pages = {297-306}, doi = {10.1039/c4mb00463a}, pmid = {25382376}, issn = {1742-2051}, mesh = {*Acclimatization ; Animals ; Corticosterone/metabolism ; Feces/chemistry/microbiology ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*metabolism/*microbiology ; Male ; Metabolomics/methods ; Metagenome ; Mice ; RNA, Ribosomal, 16S/genetics ; *Stress, Physiological ; }, abstract = {Understanding the basal gut bacterial community structure and the host metabolic composition is pivotal for the interpretation of laboratory treatments designed to answer questions pertinent to host-microbe interactions. In this study, we report for the first time the underlying gut microbiota and systemic metabolic composition in BALB/c mice during the acclimatisation period. Our results showed that stress levels were reduced in the first three days of the study when the animals were subjected to repetitive handling daily but the stress levels were increased when handling was carried out at lower frequencies (weekly). We also observed a strong influence of stress on the host metabolism and commensal compositional variability. In addition, temporal biological compartmental variations in the responses were observed. Based on these results, we suggest that consistency in the frequency and duration of laboratory handling is crucial in murine models to minimise the impact of stress levels on the commensal and host metabolism dynamics. Furthermore, caution is advised in consideration of the temporal delay effect when integrating metagenomics and metabonomics data across different biological matrices (i.e. faeces and urine).}, } @article {pmid25381053, year = {2015}, author = {Sasaki, M and Orba, Y and Ueno, K and Ishii, A and Moonga, L and Hang'ombe, BM and Mweene, AS and Ito, K and Sawa, H}, title = {Metagenomic analysis of the shrew enteric virome reveals novel viruses related to human stool-associated viruses.}, journal = {The Journal of general virology}, volume = {96}, number = {Pt 2}, pages = {440-452}, doi = {10.1099/vir.0.071209-0}, pmid = {25381053}, issn = {1465-2099}, mesh = {Animals ; *Biota ; Cluster Analysis ; Intestines/*virology ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Shrews/*virology ; Viruses/*classification/*genetics ; }, abstract = {Shrews are small insectivorous mammals that are distributed worldwide. Similar to rodents, shrews live on the ground and are commonly found near human residences. In this study, we investigated the enteric virome of wild shrews in the genus Crocidura using a sequence-independent viral metagenomics approach. A large portion of the shrew enteric virome was composed of insect viruses, whilst novel viruses including cyclovirus, picornavirus and picorna-like virus were also identified. Several cycloviruses, including variants of human cycloviruses detected in cerebrospinal fluid and stools, were detected in wild shrews at a high prevalence rate. The identified picornavirus was distantly related to human parechovirus, inferring the presence of a new genus in this family. The identified picorna-like viruses were characterized as different species of calhevirus 1, which was discovered previously in human stools. Complete or nearly complete genome sequences of these novel viruses were determined in this study and then were subjected to further genetic characterization. Our study provides an initial view of the diversity and distinctiveness of the shrew enteric virome and highlights unique novel viruses related to human stool-associated viruses.}, } @article {pmid25372390, year = {2014}, author = {Shiozaki, A and Yoneda, S and Yoneda, N and Yonezawa, R and Matsubayashi, T and Seo, G and Saito, S}, title = {Intestinal microbiota is different in women with preterm birth: results from terminal restriction fragment length polymorphism analysis.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e111374}, pmid = {25372390}, issn = {1932-6203}, mesh = {Adult ; Bacteria/classification/genetics ; Cross-Sectional Studies ; Female ; Humans ; Infant, Newborn ; Intestines/*microbiology ; Metagenome ; *Microbiota ; Polymorphism, Restriction Fragment Length ; Pregnancy ; Premature Birth/*etiology ; Prospective Studies ; Risk Factors ; Vagina/microbiology ; }, abstract = {Preterm birth is a leading cause of perinatal morbidity and mortality. Studies using a cultivation method or molecular identification have shown that bacterial vaginosis is one of the risk factors for preterm birth. However, an association between preterm birth and intestinal microbiota has not been reported using molecular techniques, although the vaginal microbiota changes during pregnancy. Our aim here was to clarify the difference in intestinal and vaginal microbiota between women with preterm birth and women without preterm labor. 16S ribosomal ribonucleic acid genes were amplified from fecal and vaginal DNA by polymerase chain reaction. Using terminal restriction fragment length polymorphism (T-RFLP), we compared the levels of operational taxonomic units of both intestinal and vaginal flora among three groups: pregnant women who delivered term babies without preterm labor (non-PTL group) (n = 20), those who had preterm labor but delivered term babies (PTL group) (n = 11), and those who had preterm birth (PTB group) (n = 10). Significantly low levels of Clostridium subcluster XVIII, Clostridium cluster IV, Clostridium subcluster XIVa, and Bacteroides, and a significantly high level of Lactobacillales were observed in the intestinal microbiota in the PTB group compared with those in the non-PTL group. The levels of Clostridium subcluster XVIII and Clostridium subcluster XIVa in the PTB group were significantly lower than those in the PTL group, and these levels in the PTL group were significantly lower than those in non-PTL group. However, there were no significant differences in vaginal microbiota among the three groups. Intestinal microbiota in the PTB group was found to differ from that in the non-PTL group using the T-RFLP method.}, } @article {pmid25370749, year = {2015}, author = {Patterson, E and Marques, TM and O'Sullivan, O and Fitzgerald, P and Fitzgerald, GF and Cotter, PD and Dinan, TG and Cryan, JF and Stanton, C and Ross, RP}, title = {Streptozotocin-induced type-1-diabetes disease onset in Sprague-Dawley rats is associated with an altered intestinal microbiota composition and decreased diversity.}, journal = {Microbiology (Reading, England)}, volume = {161}, number = {Pt 1}, pages = {182-193}, doi = {10.1099/mic.0.082610-0}, pmid = {25370749}, issn = {1465-2080}, mesh = {Animals ; Antibiotics, Antineoplastic/administration & dosage/adverse effects ; *Biodiversity ; Diabetes Mellitus, Experimental/*etiology ; Diabetes Mellitus, Type 1/*etiology ; Disease Models, Animal ; Disease Progression ; Fatty Acids, Volatile/metabolism ; Intestines/*microbiology ; Lactic Acid/biosynthesis ; Male ; Metagenome ; *Microbiota ; Rats ; Rats, Sprague-Dawley ; Streptozocin/administration & dosage/adverse effects ; }, abstract = {There is a growing appreciation that microbiota composition can significantly affect host health and play a role in disease onset and progression. This study assessed the impact of streptozotocin (STZ)-induced type-1-diabetes (T1D) on intestinal microbiota composition and diversity in Sprague-Dawley rats, compared with healthy controls over time. T1D was induced by injection of a single dose (60 mg STZ kg(-1)) of STZ, administered via the intraperitoneal cavity. Total DNA was isolated from faecal pellets at weeks 0 (pre-STZ injection), 1, 2 and 4 and from caecal content at week 5 from both healthy and T1D groups. High-throughput 16S rRNA sequencing was employed to investigate intestinal microbiota composition. The data revealed that although intestinal microbiota composition between the groups was similar at week 0, a dramatic impact of T1D development on the microbiota was apparent post-STZ injection and for up to 5 weeks. Most notably, T1D onset was associated with a shift in the Bacteroidetes : Firmicutes ratio (P<0.05), while at the genus level, increased proportions of lactic acid producing bacteria such as Lactobacillus and Bifidobacterium were associated with the later stages of T1D progression (P<0.05). Coincidently, T1D increased caecal lactate levels (P<0.05). Microbial diversity was also reduced following T1D (P<0.05). Principle co-ordinate analyses demonstrated temporal clustering in T1D and control groups with distinct separation between groups. The results provide a comprehensive account of how T1D is associated with an altered intestinal microbiota composition and reduced microbial diversity over time.}, } @article {pmid25370726, year = {2015}, author = {Unno, T and Kim, JM and Guevarra, RB and Nguyen, SG}, title = {Effects of antibiotic growth promoter and characterization of ecological succession in Swine gut microbiota.}, journal = {Journal of microbiology and biotechnology}, volume = {25}, number = {4}, pages = {431-438}, doi = {10.4014/jmb.1408.08063}, pmid = {25370726}, issn = {1738-8872}, mesh = {*Animal Feed ; Animals ; Anti-Bacterial Agents/*pharmacology ; Biodiversity ; Body Weight ; Cluster Analysis ; Gastrointestinal Microbiome/*drug effects ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Swine ; }, abstract = {Ever since the ban on antibiotic growth promoters (AGPs), the livestock death rate has increased owing to pathogenic bacterial infections. There is a need of developing AGP alternatives; however, the mechanisms by which AGP enhances livestock growth performance are not clearly understood. In this study, we fed 3-week-old swine for 9 weeks with and without AGPs containing chlortetracycline, sulfathiazole, and penicillin to investigate the effects of AGPs on swine gut microbiota. Microbial community analysis was done based on bacterial 16S rRNA genes using MiSeq. The use of AGP showed no growth promoting effect, but inhibited the growth of potential pathogens during the early growth stage. Our results showed the significant increase in species richness after the stabilization of gut microbiota during the post-weaning period (4-week-old). Moreover, the swine gut microbiota was divided into four clusters based on the distribution of operational taxonomic units, which was significantly correlated to the swine weight regardless of AGP treatments. Taxonomic abundance analysis indicated a negative correlation between host weight and the abundance of the family Prevotellaceae species, but showed positive correlation to the abundance of the family Spirochaetaceae, Clostridiaceae_1, and Peptostreptococcaeae species. Although no growth performance enhancement was observed, the use of AGP inhibited the potential pathogens in the early growth stage of swine. In addition, our results indicated the ecological succession of swine gut microbiota according to swine weight. Here, we present a characterization of swine gut microbiota with respect to the effects of AGPs on growth performance.}, } @article {pmid25370493, year = {2014}, author = {Tian, RM and Wang, Y and Bougouffa, S and Gao, ZM and Cai, L and Zhang, WP and Bajic, V and Qian, PY}, title = {Effect of copper treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis.}, journal = {mBio}, volume = {5}, number = {6}, pages = {e01980}, pmid = {25370493}, issn = {2150-7511}, mesh = {Animals ; Bacteria/*classification/*drug effects/genetics ; Bacteriophages/*classification/genetics ; Biota/*drug effects ; Cluster Analysis ; Copper/*toxicity ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Haliclona/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {UNLABELLED: Marine sponges are the most primitive metazoan and host symbiotic microorganisms. They are crucial components of the marine ecological system and play an essential role in pelagic processes. Copper pollution is currently a widespread problem and poses a threat to marine organisms. Here, we examined the effects of copper treatment on the composition of the sponge-associated bacterial community and the genetic features that facilitate the survival of enriched bacteria under copper stress. The 16S rRNA gene sequencing results showed that the sponge Haliclona cymaeformis harbored symbiotic sulfur-oxidizing Ectothiorhodospiraceae and photosynthetic Cyanobacteria as dominant species. However, these autotrophic bacteria decreased substantially after treatment with a high copper concentration, which enriched for a heterotrophic-bacterium-dominated community. Metagenomic comparison revealed a varied profile of functional genes and enriched functions, including bacterial motility and chemotaxis, extracellular polysaccharide and capsule synthesis, virulence-associated genes, and genes involved in cell signaling and regulation, suggesting short-period mechanisms of the enriched bacterial community for surviving copper stress in the microenvironment of the sponge. Microscopic observation and comparison revealed dynamic bacterial aggregation within the matrix and lysis of sponge cells. The bacteriophage community was also enriched, and the complete genome of a dominant phage was determined, implying that a lytic phage cycle was stimulated by the high copper concentration. This study demonstrated a copper-induced shift in the composition of functional genes of the sponge-associated bacterial community, revealing the selective effect of copper treatment on the functions of the bacterial community in the microenvironment of the sponge.

IMPORTANCE: This study determined the bacterial community structure of the common sponge Haliclona cymaeformis and examined the effect of copper treatment on the community structure and functional gene composition, revealing that copper treatment had a selective effect on the functions of the bacterial community in the sponge. These findings suggest that copper pollution has an ecological impact on the sponge symbiont. The analysis showed that the untreated sponges hosted symbiotic autotrophic bacteria as dominant species, and the high-concentration copper treatment enriched for a heterotrophic bacterial community with enrichment for genes important for bacterial motility, supplementary cellular components, signaling and regulation, and virulence. Microscopic observation showed obvious bacterial aggregation and a reduction of sponge cell numbers in treated sponges, which suggested the formation of aggregates to reduce the copper concentration. The enrichment for functions of directional bacterial movement and supplementary cellular components and the formation of bacterial aggregates and phage enrichment are novel findings in sponge studies.}, } @article {pmid25365331, year = {2014}, author = {Huang, Q and Briggs, BR and Dong, H and Jiang, H and Wu, G and Edwardson, C and De Vlaminck, I and Quake, S}, title = {Taxonomic and functional diversity provides insight into microbial pathways and stress responses in the saline Qinghai Lake, China.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e111681}, pmid = {25365331}, issn = {1932-6203}, mesh = {*Biodiversity ; China ; Cyanobacteria/*classification/*physiology ; Lakes/*microbiology ; Stress, Physiological/*physiology ; *Water Microbiology ; }, abstract = {Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change.}, } @article {pmid25365329, year = {2014}, author = {Rawat, A and Engelthaler, DM and Driebe, EM and Keim, P and Foster, JT}, title = {MetaGeniE: characterizing human clinical samples using deep metagenomic sequencing.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e110915}, pmid = {25365329}, issn = {1932-6203}, mesh = {Biodiversity ; Databases, Nucleic Acid ; Datasets as Topic ; Genotype ; *High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Metagenomics/methods ; Microbiota ; Polymorphism, Single Nucleotide ; Reproducibility of Results ; *Software ; }, abstract = {With the decreasing cost of next-generation sequencing, deep sequencing of clinical samples provides unique opportunities to understand host-associated microbial communities. Among the primary challenges of clinical metagenomic sequencing is the rapid filtering of human reads to survey for pathogens with high specificity and sensitivity. Metagenomes are inherently variable due to different microbes in the samples and their relative abundance, the size and architecture of genomes, and factors such as target DNA amounts in tissue samples (i.e. human DNA versus pathogen DNA concentration). This variation in metagenomes typically manifests in sequencing datasets as low pathogen abundance, a high number of host reads, and the presence of close relatives and complex microbial communities. In addition to these challenges posed by the composition of metagenomes, high numbers of reads generated from high-throughput deep sequencing pose immense computational challenges. Accurate identification of pathogens is confounded by individual reads mapping to multiple different reference genomes due to gene similarity in different taxa present in the community or close relatives in the reference database. Available global and local sequence aligners also vary in sensitivity, specificity, and speed of detection. The efficiency of detection of pathogens in clinical samples is largely dependent on the desired taxonomic resolution of the organisms. We have developed an efficient strategy that identifies "all against all" relationships between sequencing reads and reference genomes. Our approach allows for scaling to large reference databases and then genome reconstruction by aggregating global and local alignments, thus allowing genetic characterization of pathogens at higher taxonomic resolution. These results were consistent with strain level SNP genotyping and bacterial identification from laboratory culture.}, } @article {pmid25362486, year = {2014}, author = {Zhou, X and Wang, B and Pan, Q and Zhang, J and Kumar, S and Sun, X and Liu, Z and Pan, H and Lin, Y and Liu, G and Zhan, W and Li, M and Ren, B and Ma, X and Ruan, H and Cheng, C and Wang, D and Shi, F and Hui, Y and Tao, Y and Zhang, C and Zhu, P and Xiang, Z and Jiang, W and Chang, J and Wang, H and Cao, Z and Jiang, Z and Li, B and Yang, G and Roos, C and Garber, PA and Bruford, MW and Li, R and Li, M}, title = {Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history.}, journal = {Nature genetics}, volume = {46}, number = {12}, pages = {1303-1310}, pmid = {25362486}, issn = {1546-1718}, support = {R01 HG002096/HG/NHGRI NIH HHS/United States ; HG002096-12/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Cellulose/chemistry ; Colobinae/*genetics ; *Diet ; Fatty Acids/chemistry ; Genetic Variation ; Genome ; Geography ; Herbivory/*genetics ; Heterozygote ; Humans ; Male ; Metagenome ; Mutation ; Phylogeny ; Polymorphism, Single Nucleotide ; Ribonucleases/*genetics ; Sequence Analysis, DNA ; Species Specificity ; Xenobiotics/chemistry ; }, abstract = {Colobines are a unique group of Old World monkeys that principally eat leaves and seeds rather than fruits and insects. We report the sequencing at 146× coverage, de novo assembly and analyses of the genome of a male golden snub-nosed monkey (Rhinopithecus roxellana) and resequencing at 30× coverage of three related species (Rhinopithecus bieti, Rhinopithecus brelichi and Rhinopithecus strykeri). Comparative analyses showed that Asian colobines have an enhanced ability to derive energy from fatty acids and to degrade xenobiotics. We found evidence for functional evolution in the colobine RNASE1 gene, encoding a key secretory RNase that digests the high concentrations of bacterial RNA derived from symbiotic microflora. Demographic reconstructions indicated that the profile of ancient effective population sizes for R. roxellana more closely resembles that of giant panda rather than its congeners. These findings offer new insights into the dietary adaptations and evolutionary history of colobine primates.}, } @article {pmid25361395, year = {2015}, author = {Hua, ZS and Han, YJ and Chen, LX and Liu, J and Hu, M and Li, SJ and Kuang, JL and Chain, PS and Huang, LN and Shu, WS}, title = {Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics.}, journal = {The ISME journal}, volume = {9}, number = {6}, pages = {1280-1294}, pmid = {25361395}, issn = {1751-7370}, mesh = {Acids ; Betaproteobacteria/*genetics ; Carbon ; *Ecology ; Environmental Pollutants/*chemistry ; Gene Expression Profiling ; Gene Expression Regulation ; Genome ; High-Throughput Nucleotide Sequencing ; Hydrogen-Ion Concentration ; Metagenomics ; Metals, Heavy/chemistry ; *Mining ; Nitrogen Fixation ; Oxidative Stress ; Sulfur/chemistry ; Transcriptome ; }, abstract = {High-throughput sequencing is expanding our knowledge of microbial diversity in the environment. Still, understanding the metabolic potentials and ecological roles of rare and uncultured microbes in natural communities remains a major challenge. To this end, we applied a 'divide and conquer' strategy that partitioned a massive metagenomic data set (>100 Gbp) into subsets based on K-mer frequency in sequence assembly to a low-diversity acid mine drainage (AMD) microbial community and, by integrating with an additional metatranscriptomic assembly, successfully obtained 11 draft genomes most of which represent yet uncultured and/or rare taxa (relative abundance <1%). We report the first genome of a naturally occurring Ferrovum population (relative abundance >90%) and its metabolic potentials and gene expression profile, providing initial molecular insights into the ecological role of these lesser known, but potentially important, microorganisms in the AMD environment. Gene transcriptional analysis of the active taxa revealed major metabolic capabilities executed in situ, including carbon- and nitrogen-related metabolisms associated with syntrophic interactions, iron and sulfur oxidation, which are key in energy conservation and AMD generation, and the mechanisms of adaptation and response to the environmental stresses (heavy metals, low pH and oxidative stress). Remarkably, nitrogen fixation and sulfur oxidation were performed by the rare taxa, indicating their critical roles in the overall functioning and assembly of the AMD community. Our study demonstrates the potential of the 'divide and conquer' strategy in high-throughput sequencing data assembly for genome reconstruction and functional partitioning analysis of both dominant and rare species in natural microbial assemblages.}, } @article {pmid25359473, year = {2014}, author = {Noguera, DR and Wright, ES and Camejo, P and Yilmaz, LS}, title = {Mathematical tools to optimize the design of oligonucleotide probes and primers.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {23}, pages = {9595-9608}, doi = {10.1007/s00253-014-6165-x}, pmid = {25359473}, issn = {1432-0614}, mesh = {*Biota ; Computer-Aided Design ; DNA Primers/*chemistry/*genetics ; In Situ Hybridization, Fluorescence/methods ; Metagenomics/*methods ; Microarray Analysis/methods ; Models, Theoretical ; Oligonucleotide Probes/*chemistry/*genetics ; Polymerase Chain Reaction/methods ; Software ; }, abstract = {The identification and quantification of specific organisms in mixed microbial communities often relies on the ability to design oligonucleotide probes and primers with high specificity and sensitivity. The design of these oligonucleotides (or "oligos" for short) shares many of the same principles in spite of their widely divergent applications. Three common molecular biology technologies that require oligonucleotide design are polymerase chain reaction (PCR), fluorescence in situ hybridization (FISH), and DNA microarrays. This article reviews techniques and software available for the design and optimization of oligos with the goal of targeting a specific group of organisms within mixed microbial communities. Strategies for enhancing specificity without compromising sensitivity are described, as well as design tools well suited for this purpose.}, } @article {pmid25359471, year = {2014}, author = {Patel, V and Patel, AK and Parmar, NR and Patel, AB and Reddy, B and Joshi, CG}, title = {Characterization of the rumen microbiome of Indian Kankrej cattle (Bos indicus) adapted to different forage diet.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {23}, pages = {9749-9761}, doi = {10.1007/s00253-014-6153-1}, pmid = {25359471}, issn = {1432-0614}, mesh = {*Animal Feed ; Animals ; Bacteria/*classification/*genetics ; *Biota ; Cattle ; DNA, Bacterial/chemistry/genetics ; Diet/*methods ; Metabolic Networks and Pathways/genetics ; Metagenomics ; Molecular Sequence Data ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Present study described rumen microbiome of Indian cattle (Kankrej breed) to better understand the microbial diversity and largely unknown functional capacity of the rumen microbiome under different dietary treatments. Kankrej cattle were gradually adapted to a high-forage diet (four animals with dry forage and four with green forage) containing 50 % (K1), 75 % (K2) to 100 % (K3) forage, and remaining concentrate diet, each for 6 weeks followed by analysis of rumen fiber adherent and fiber-free metagenomic community by shotgun sequencing using ion torrent PGM platform and EBI-metagenomics annotation pipeline. Taxonomic analysis indicated that rumen microbiome was dominated by Bacteroidetes followed by Firmicutes, Fibrobacter, Proteobacteria, and Tenericutes. Functional analysis based on gene ontology classified all reads in total 157 categories based on their functional role in biological, molecular, and cellular component with abundance of genes associated with hydrolase activity, membrane, transport, transferase, and different metabolism (such as carbohydrate and protein). Statistical analysis using STAMP revealed significant differences (P < 0.05) between solid and liquid fraction of rumen (in 65 categories), between all three treatments (in 56 categories), and between green and dry roughage (17 categories). Diet treatment also exerted significant difference in environmental gene tags (EGTs) involved in metabolic pathways for production of volatile fatty acids. EGTs for butyrate production were abundant in K2, whereas EGTs for propionate production was abundant during K1. Principal component analysis also demonstrated that diet proportion, fraction of rumen, and type of forage affected rumen microbiome at taxonomic as well as functional level.}, } @article {pmid25359376, year = {2014}, author = {Nunes-Alves, C}, title = {Antimicrobials: Commensally sourced antibiotics.}, journal = {Nature reviews. Drug discovery}, volume = {13}, number = {11}, pages = {812}, pmid = {25359376}, issn = {1474-1784}, mesh = {Bacteria/*chemistry/*genetics ; Humans ; Metagenomics/*methods ; *Microbiota ; }, } @article {pmid25356041, year = {2014}, author = {Wang, ZK and Yang, YS and Chen, Y and Yuan, J and Sun, G and Peng, LH}, title = {Intestinal microbiota pathogenesis and fecal microbiota transplantation for inflammatory bowel disease.}, journal = {World journal of gastroenterology}, volume = {20}, number = {40}, pages = {14805-14820}, pmid = {25356041}, issn = {2219-2840}, mesh = {Animals ; Biological Therapy/*methods ; Feces/*microbiology ; Host-Pathogen Interactions ; Humans ; Immunity, Mucosal ; Inflammatory Bowel Diseases/diagnosis/immunology/microbiology/*therapy ; Intestines/immunology/*microbiology ; *Microbiota ; Probiotics/therapeutic use ; Treatment Outcome ; }, abstract = {The intestinal microbiota plays an important role in inflammatory bowel disease (IBD). The pathogenesis of IBD involves inappropriate ongoing activation of the mucosal immune system driven by abnormal intestinal microbiota in genetically predisposed individuals. However, there are still no definitive microbial pathogens linked to the onset of IBD. The composition and function of the intestinal microbiota and their metabolites are indeed disturbed in IBD patients. The special alterations of gut microbiota associated with IBD remain to be evaluated. The microbial interactions and host-microbe immune interactions are still not clarified. Limitations of present probiotic products in IBD are mainly due to modest clinical efficacy, few available strains and no standardized administration. Fecal microbiota transplantation (FMT) may restore intestinal microbial homeostasis, and preliminary data have shown the clinical efficacy of FMT on refractory IBD or IBD combined with Clostridium difficile infection. Additionally, synthetic microbiota transplantation with the defined composition of fecal microbiota is also a promising therapeutic approach for IBD. However, FMT-related barriers, including the mechanism of restoring gut microbiota, standardized donor screening, fecal material preparation and administration, and long-term safety should be resolved. The role of intestinal microbiota and FMT in IBD should be further investigated by metagenomic and metatranscriptomic analyses combined with germ-free/human flora-associated animals and chemostat gut models.}, } @article {pmid25346017, year = {2015}, author = {Zheng, J and Gänzle, MG and Lin, XB and Ruan, L and Sun, M}, title = {Diversity and dynamics of bacteriocins from human microbiome.}, journal = {Environmental microbiology}, volume = {17}, number = {6}, pages = {2133-2143}, doi = {10.1111/1462-2920.12662}, pmid = {25346017}, issn = {1462-2920}, mesh = {Bacteria/genetics/metabolism ; Bacteriocins/genetics/*metabolism ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenomics ; *Microbiota ; Mouth/*microbiology ; Respiratory System/*microbiology ; Symbiosis ; Vagina/*microbiology ; }, abstract = {Human commensal microbiota are an important determinant of health and disease of the host. Different human body sites harbour different bacterial microbiota, bacterial communities that maintain a stable balance. However, many of the factors influencing the stabilities of bacterial communities associated with humans remain unknown. In this study, we identified putative bacteriocins produced by human commensal microbiota. Bacteriocins are peptides or proteins with antimicrobial activity that contribute to the stability and dynamics of microbial communities. We employed bioinformatic analyses to identify putative bacteriocin sequences in metagenomic sequences obtained from different human body sites. Prevailing bacterial taxa of the putative bacteriocins producers matched the most abundant organisms in each human body site. Remarkably, we found that samples from different body sites contain different density of putative bacteriocin genes, with the highest in samples from the vagina, the airway, and the oral cavity and the lowest in those from gut. Inherent differences of different body sites thus influence the density and types of bacteriocins produced by commensal bacteria. Our results suggest that bacteriocins play important roles to allow different bacteria to occupy several human body sites, and to establish a long-term commensal relationship with human hosts.}, } @article {pmid25345349, year = {2015}, author = {Egan, F and Reen, FJ and O'Gara, F}, title = {Tle distribution and diversity in metagenomic datasets reveal niche specialization.}, journal = {Environmental microbiology reports}, volume = {7}, number = {2}, pages = {194-203}, doi = {10.1111/1758-2229.12222}, pmid = {25345349}, issn = {1758-2229}, mesh = {Bacterial Secretion Systems ; *Biota ; Environmental Microbiology ; *Metagenome ; *Microbial Interactions ; }, abstract = {The existence of microbial communities and the complex interactions that govern their dynamics have received considerable attention in recent years. Advances in genomic sequencing technologies have greatly enhanced our understanding of 'what is there'. However, the question as to 'what are they doing' remains less well defined. The continual development of the genomic and metagenomic sequence databases provides an exciting opportunity to interrogate the distribution and prevalence of key microbial systems across a diverse set of ecosystems. The widely distributed type VI secretion system (T6SS) has been shown to play a significant role in bacterial-bacterial and bacterial-host interactions. While several T6SS effectors have been shown to target the cell wall and membrane of competing cells, little is known about the roles these proteins play in different ecosystems. Therefore, the prevalence of a key T6SS effector superfamily known as type six lipase effectors (Tle) was studied in over 2000 metagenomic datasets representing diverse ecosystems and host niches. Increased Tle representation in environmental categories strongly supports the hypothesis of niche specialization and suggests that these effectors may play important niche-specific roles.}, } @article {pmid25344237, year = {2015}, author = {Pjevac, P and Korlević, M and Berg, JS and Bura-Nakić, E and Ciglenečki, I and Amann, R and Orlić, S}, title = {Community shift from phototrophic to chemotrophic sulfide oxidation following anoxic holomixis in a stratified seawater lake.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {1}, pages = {298-308}, pmid = {25344237}, issn = {1098-5336}, mesh = {Anaerobiosis ; Bacteria/*classification/*isolation & purification ; Biota/*drug effects ; DNA, Bacterial/chemistry/genetics ; Metagenomics ; Molecular Sequence Data ; Oxidation-Reduction ; Phototrophic Processes ; Seawater/*chemistry/*microbiology ; Sequence Analysis, DNA ; Sulfides/*metabolism ; }, abstract = {Most stratified sulfidic holomictic lakes become oxygenated after annual turnover. In contrast, Lake Rogoznica, on the eastern Adriatic coast, has been observed to undergo a period of water column anoxia after water layer mixing and establishment of holomictic conditions. Although Lake Rogoznica's chemistry and hydrography have been studied extensively, it is unclear how the microbial communities typically inhabiting the oxic epilimnion and a sulfidic hypolimnion respond to such a drastic shift in redox conditions. We investigated the impact of anoxic holomixis on microbial diversity and microbially mediated sulfur cycling in Lake Rogoznica with an array of culture-independent microbiological methods. Our data suggest a tight coupling between the lake's chemistry and occurring microorganisms. During stratification, anoxygenic phototrophic sulfur bacteria were dominant at the chemocline and in the hypolimnion. After an anoxic mixing event, the anoxygenic phototrophic sulfur bacteria entirely disappeared, and the homogeneous, anoxic water column was dominated by a bloom of gammaproteobacterial sulfur oxidizers related to the GSO/SUP05 clade. This study is the first report of a community shift from phototrophic to chemotrophic sulfide oxidizers as a response to anoxic holomictic conditions in a seasonally stratified seawater lake.}, } @article {pmid25343979, year = {2015}, author = {Auffret, MD and Yergeau, E and Labbé, D and Fayolle-Guichard, F and Greer, CW}, title = {Importance of Rhodococcus strains in a bacterial consortium degrading a mixture of hydrocarbons, gasoline, and diesel oil additives revealed by metatranscriptomic analysis.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {5}, pages = {2419-2430}, doi = {10.1007/s00253-014-6159-8}, pmid = {25343979}, issn = {1432-0614}, mesh = {Actinobacteria/classification/isolation & purification/*metabolism ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; Gene Expression Profiling ; Hydrocarbons/*metabolism ; Metagenomics/methods ; *Microbial Consortia ; Molecular Sequence Data ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {A bacterial consortium (Mix3) composed of microorganisms originating from different environments (soils and wastewater) was obtained after enrichment in the presence of a mixture of 16 hydrocarbons, gasoline, and diesel oil additives. After addition of the mixture, the development of the microbial composition of Mix3 was monitored at three different times (35, 113, and 222 days) using fingerprinting method and dominant bacterial species were identified. In parallel, 14 bacteria were isolated after 113 days and identified. Degradation capacities for Mix3 and the isolated bacterial strains were characterized and compared. At day 113, we induced the expression of catabolic genes in Mix3 by adding the substrate mixture to resting cells and the metatranscriptome was analyzed. After addition of the substrate mixture, the relative abundance of Actinobacteria increased at day 222 while a shift between Rhodococcus and Mycobacterium was observed after 113 days. Mix3 was able to degrade 13 compounds completely, with partial degradation of isooctane and 2-ethylhexyl nitrate, but tert-butyl alcohol was not degraded. Rhodococcus wratislaviensis strain IFP 2016 isolated from Mix3 showed almost the same degradation capacities as Mix3: these results were not observed with the other isolated strains. Transcriptomic results revealed that Actinobacteria and in particular, Rhodococcus species, were major contributors in terms of total and catabolic gene transcripts while other species were involved in cyclohexane degradation. Not all the microorganisms identified at day 113 were active except R. wratislaviensis IFP 2016 that appeared to be a major player in the degradation activity observed in Mix3.}, } @article {pmid25340824, year = {2014}, author = {Tanaka, R and Hino, A and Tsai, IJ and Palomares-Rius, JE and Yoshida, A and Ogura, Y and Hayashi, T and Maruyama, H and Kikuchi, T}, title = {Assessment of helminth biodiversity in wild rats using 18S rDNA based metagenomics.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e110769}, pmid = {25340824}, issn = {1932-6203}, mesh = {Animals ; Animals, Wild/*parasitology ; *Biodiversity ; Databases, Genetic ; Helminths/*genetics/isolation & purification ; Intestines/parasitology ; *Metagenomics ; Parasites/genetics/isolation & purification ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Rats ; Sequence Analysis, DNA ; Software ; Species Specificity ; }, abstract = {Parasite diversity has important implications in several research fields including ecology, evolutionary biology and epidemiology. Wide-ranging analysis has been restricted because of the difficult, highly specialised and time-consuming processes involved in parasite identification. In this study, we assessed parasite diversity in wild rats using 18S rDNA-based metagenomics. 18S rDNA PCR products were sequenced using an Illumina MiSeq sequencer and the analysis of the sequences using the QIIME software successfully classified them into several parasite groups. The comparison of the results with those obtained using standard methods including microscopic observation of helminth parasites in the rat intestines and PCR amplification/sequencing of 18S rDNA from isolated single worms suggests that this new technique is reliable and useful to investigate parasite diversity.}, } @article {pmid25340531, year = {2014}, author = {Weng, SL and Chiu, CM and Lin, FM and Huang, WC and Liang, C and Yang, T and Yang, TL and Liu, CY and Wu, WY and Chang, YA and Chang, TH and Huang, HD}, title = {Bacterial communities in semen from men of infertile couples: metagenomic sequencing reveals relationships of seminal microbiota to semen quality.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e110152}, pmid = {25340531}, issn = {1932-6203}, mesh = {Adult ; Bacteria/genetics ; Biodiversity ; Biomarkers/metabolism ; Case-Control Studies ; Cluster Analysis ; Demography ; Humans ; Infertility, Male/*microbiology ; Male ; *Metagenomics ; Microbiota/*genetics ; Middle Aged ; Principal Component Analysis ; Semen/*microbiology ; *Semen Analysis ; *Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Some previous studies have identified bacteria in semen as being a potential factor in male infertility. However, only few types of bacteria were taken into consideration while using PCR-based or culturing methods. Here we present an analysis approach using next-generation sequencing technology and bioinformatics analysis to investigate the associations between bacterial communities and semen quality. Ninety-six semen samples collected were examined for bacterial communities, measuring seven clinical criteria for semen quality (semen volume, sperm concentration, motility, Kruger's strict morphology, antisperm antibody (IgA), Atypical, and leukocytes). Computer-assisted semen analysis (CASA) was also performed. Results showed that the most abundant genera among all samples were Lactobacillus (19.9%), Pseudomonas (9.85%), Prevotella (8.51%) and Gardnerella (4.21%). The proportion of Lactobacillus and Gardnerella was significantly higher in the normal samples, while that of Prevotella was significantly higher in the low quality samples. Unsupervised clustering analysis demonstrated that the seminal bacterial communities were clustered into three main groups: Lactobacillus, Pseudomonas, and Prevotella predominant group. Remarkably, most normal samples (80.6%) were clustered in Lactobacillus predominant group. The analysis results showed seminal bacteria community types were highly associated with semen health. Lactobacillus might not only be a potential probiotic for semen quality maintenance, but also might be helpful in countering the negative influence of Prevotella and Pseudomonas. In this study, we investigated whole seminal bacterial communities and provided the most comprehensive analysis of the association between bacterial community and semen quality. The study significantly contributes to the current understanding of the etiology of male fertility.}, } @article {pmid25339401, year = {2015}, author = {Moore, NE and Wang, J and Hewitt, J and Croucher, D and Williamson, DA and Paine, S and Yen, S and Greening, GE and Hall, RJ}, title = {Metagenomic analysis of viruses in feces from unsolved outbreaks of gastroenteritis in humans.}, journal = {Journal of clinical microbiology}, volume = {53}, number = {1}, pages = {15-21}, pmid = {25339401}, issn = {1098-660X}, mesh = {Computational Biology ; *Disease Outbreaks ; Feces/*virology ; Gastroenteritis/*epidemiology/*virology ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Microbiota ; New Zealand/epidemiology ; Phylogeny ; Viruses/*classification/*genetics ; }, abstract = {The etiology of an outbreak of gastroenteritis in humans cannot always be determined, and ∼25% of outbreaks remain unsolved in New Zealand. It is hypothesized that novel viruses may account for a proportion of unsolved cases, and new unbiased high-throughput sequencing methods hold promise for their detection. Analysis of the fecal metagenome can reveal the presence of viruses, bacteria, and parasites which may have evaded routine diagnostic testing. Thirty-one fecal samples from 26 gastroenteritis outbreaks of unknown etiology occurring in New Zealand between 2011 and 2012 were selected for de novo metagenomic analysis. A total data set of 193 million sequence reads of 150 bp in length was produced on an Illumina MiSeq. The metagenomic data set was searched for virus and parasite sequences, with no evidence of novel pathogens found. Eight viruses and one parasite were detected, each already known to be associated with gastroenteritis, including adenovirus, rotavirus, sapovirus, and Dientamoeba fragilis. In addition, we also describe the first detection of human parechovirus 3 (HPeV3) in Australasia. Metagenomics may thus provide a useful audit tool when applied retrospectively to determine where routine diagnostic processes may have failed to detect a pathogen.}, } @article {pmid25338280, year = {2015}, author = {Aw, W and Fukuda, S}, title = {Toward the comprehensive understanding of the gut ecosystem via metabolomics-based integrated omics approach.}, journal = {Seminars in immunopathology}, volume = {37}, number = {1}, pages = {5-16}, pmid = {25338280}, issn = {1863-2300}, mesh = {Humans ; Intestines/*microbiology ; *Metabolomics ; *Microbiota ; }, abstract = {Recent advances in DNA sequencing and mass spectrometry technologies have allowed us to collect more data on microbiome and metabolome to assess the influence of the gut microbiota on human health at a whole-systems level. Major advances in metagenomics and metabolomics technologies have shown that the gut microbiota contributes to host overall health status to a large extent. As such, the gut microbiota is often likened to a measurable and functional organ consisting of prokaryotic cells, which creates the unique gut ecosystem together with the host eukaryotic cells. In this review, we discuss in detail the relationship between gut microbiota and its metabolites like choline, bile acids, phenols, and short-chain fatty acids in the host health and etiopathogenesis of various pathological states such as multiple sclerosis, autism, obesity, diabetes, and chronic kidney disease. By integrating metagenomic and metabolomic information on a systems biology-wide approach, we would be better able to understand this interplay between gut microbiome and host metabolism. Integration of the microbiome, metatranscriptome, and metabolome information will pave the way toward an improved holistic understanding of the complex mammalian superorganism. Through the modeling of metabolic interactions between lifestyle, diet, and microbiota, integrated omics-based understanding of the gut ecosystem is the new avenue, providing exciting novel therapeutic approaches for optimal host health.}, } @article {pmid25337874, year = {2015}, author = {Buffie, CG and Bucci, V and Stein, RR and McKenney, PT and Ling, L and Gobourne, A and No, D and Liu, H and Kinnebrew, M and Viale, A and Littmann, E and van den Brink, MR and Jenq, RR and Taur, Y and Sander, C and Cross, JR and Toussaint, NC and Xavier, JB and Pamer, EG}, title = {Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile.}, journal = {Nature}, volume = {517}, number = {7533}, pages = {205-208}, pmid = {25337874}, issn = {1476-4687}, support = {P01 CA023766/CA/NCI NIH HHS/United States ; T32GM07739/GM/NIGMS NIH HHS/United States ; R01 AI42135/AI/NIAID NIH HHS/United States ; DP2 OD008440/OD/NIH HHS/United States ; R37 AI039031/AI/NIAID NIH HHS/United States ; U54 CA148967/CA/NCI NIH HHS/United States ; DP2OD008440/OD/NIH HHS/United States ; K23 AI095398/AI/NIAID NIH HHS/United States ; T32 CA009149/CA/NCI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; AI95706/AI/NIAID NIH HHS/United States ; R01 AI095706/AI/NIAID NIH HHS/United States ; R01 AI042135/AI/NIAID NIH HHS/United States ; T32 GM007739/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bile Acids and Salts/*metabolism ; Biological Evolution ; Clostridioides difficile/drug effects/*physiology ; Clostridium/metabolism ; Colitis/metabolism/microbiology/prevention & control/therapy ; Disease Susceptibility/*microbiology ; Feces/microbiology ; Female ; Humans ; Intestinal Mucosa/*metabolism ; Intestines/drug effects/*microbiology ; Metagenome/genetics ; Mice ; Mice, Inbred C57BL ; Microbiota/drug effects/genetics/*physiology ; Symbiosis ; }, abstract = {The gastrointestinal tracts of mammals are colonized by hundreds of microbial species that contribute to health, including colonization resistance against intestinal pathogens. Many antibiotics destroy intestinal microbial communities and increase susceptibility to intestinal pathogens. Among these, Clostridium difficile, a major cause of antibiotic-induced diarrhoea, greatly increases morbidity and mortality in hospitalized patients. Which intestinal bacteria provide resistance to C. difficile infection and their in vivo inhibitory mechanisms remain unclear. Here we correlate loss of specific bacterial taxa with development of infection, by treating mice with different antibiotics that result in distinct microbiota changes and lead to varied susceptibility to C. difficile. Mathematical modelling augmented by analyses of the microbiota of hospitalized patients identifies resistance-associated bacteria common to mice and humans. Using these platforms, we determine that Clostridium scindens, a bile acid 7α-dehydroxylating intestinal bacterium, is associated with resistance to C. difficile infection and, upon administration, enhances resistance to infection in a secondary bile acid dependent fashion. Using a workflow involving mouse models, clinical studies, metagenomic analyses, and mathematical modelling, we identify a probiotic candidate that corrects a clinically relevant microbiome deficiency. These findings have implications for the rational design of targeted antimicrobials as well as microbiome-based diagnostics and therapeutics for individuals at risk of C. difficile infection.}, } @article {pmid25336203, year = {2014}, author = {Shamsaddini, A and Pan, Y and Johnson, WE and Krampis, K and Shcheglovitova, M and Simonyan, V and Zanne, A and Mazumder, R}, title = {Census-based rapid and accurate metagenome taxonomic profiling.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {918}, pmid = {25336203}, issn = {1471-2164}, mesh = {Biodiversity ; Classification/*methods ; Databases, Genetic ; Genome, Fungal/genetics ; Humans ; Intestines/microbiology ; *Metagenome ; Microbiota/genetics ; Respiratory Tract Infections/microbiology ; Time Factors ; }, abstract = {BACKGROUND: Understanding the taxonomic composition of a sample, whether from patient, food or environment, is important to several types of studies including pathogen diagnostics, epidemiological studies, biodiversity analysis and food quality regulation. With the decreasing costs of sequencing, metagenomic data is quickly becoming the preferred typed of data for such analysis.

RESULTS: Rapidly defining the taxonomic composition (both taxonomic profile and relative frequency) in a metagenomic sequence dataset is challenging because the task of mapping millions of sequence reads from a metagenomic study to a non-redundant nucleotide database such as the NCBI non-redundant nucleotide database (nt) is a computationally intensive task. We have developed a robust subsampling-based algorithm implemented in a tool called CensuScope meant to take a 'sneak peak' into the population distribution and estimate taxonomic composition as if a census was taken of the metagenomic landscape. CensuScope is a rapid and accurate metagenome taxonomic profiling tool that randomly extracts a small number of reads (based on user input) and maps them to NCBI's nt database. This process is repeated multiple times to ascertain the taxonomic composition that is found in majority of the iterations, thereby providing a robust estimate of the population and measures of the accuracy for the results.

CONCLUSION: CensuScope can be run on a laptop or on a high-performance computer. Based on our analysis we are able to provide some recommendations in terms of the number of sequence reads to analyze and the number of iterations to use. For example, to quantify taxonomic groups present in the sample at a level of 1% or higher a subsampling size of 250 random reads with 50 iterations yields a statistical power of >99%. Windows and UNIX versions of CensuScope are available for download at https://hive.biochemistry.gwu.edu/dna.cgi?cmd=censuscope. CensuScope is also available through the High-performance Integrated Virtual Environment (HIVE) and can be used in conjunction with other HIVE analysis and visualization tools.}, } @article {pmid25334059, year = {2014}, author = {Dudek, M and Adams, J and Swain, M and Hegarty, M and Huws, S and Gallagher, J}, title = {Metaphylogenomic and potential functionality of the limpet Patella pellucida's gastrointestinal tract microbiome.}, journal = {International journal of molecular sciences}, volume = {15}, number = {10}, pages = {18819-18839}, pmid = {25334059}, issn = {1422-0067}, mesh = {Animals ; Bacteria/*genetics/*isolation & purification ; Bacteroides/genetics/isolation & purification ; DNA, Bacterial/genetics/isolation & purification ; Gastrointestinal Tract/microbiology ; Gastropoda/*microbiology ; Metagenome ; Metagenomics ; Microbiota ; Phylogeny ; Proteobacteria/genetics/isolation & purification ; }, abstract = {This study investigated the microbial diversity associated with the digestive tract of the seaweed grazing marine limpet Patella pellucida. Using a modified indirect DNA extraction protocol and performing metagenomic profiling based on specific prokaryotic marker genes, the abundance of bacterial groups was identified from the analyzed metagenome. The members of three significantly abundant phyla of Proteobacteria, Firmicutes and Bacteroidetes were characterized through the literature and their predicted functions towards the host, as well as potential applications in the industrial environment assessed.}, } @article {pmid25330259, year = {2014}, author = {Ogawa, DM and Moriya, S and Tsuboi, Y and Date, Y and Prieto-da-Silva, ÁR and Rádis-Baptista, G and Yamane, T and Kikuchi, J}, title = {Biogeochemical typing of paddy field by a data-driven approach revealing sub-systems within a complex environment--a pipeline to filtrate, organize and frame massive dataset from multi-omics analyses.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e110723}, pmid = {25330259}, issn = {1932-6203}, mesh = {*Databases, Genetic ; *Ecosystem ; *Metagenome ; }, abstract = {We propose the technique of biogeochemical typing (BGC typing) as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. Given the intricate characteristic of both organismal and chemical consortia inherent to the nature, many environmental studies employ the holistic approach of multi-omics analyses undermining as much information as possible. Due to the massive amount of data produced applying multi-omics analyses, the results are hard to visualize and to process. The BGC typing analysis is a pipeline built using integrative statistical analysis that can treat such huge datasets filtering, organizing and framing the information based on the strength of the various mutual trends of the organismal and chemical fluctuations occurring simultaneously in the environment. To test our technique of BGC typing, we choose a rich environment abounding in chemical nutrients and organismal diversity: the surficial freshwater from Japanese paddy fields and surrounding waters. To identify the community consortia profile we employed metagenomics as high throughput sequencing (HTS) for the fragments amplified from Archaea rRNA, universal 16S rRNA and 18S rRNA; to assess the elemental content we employed ionomics by inductively coupled plasma optical emission spectroscopy (ICP-OES); and for the organic chemical profile, metabolomics employing both Fourier transformed infrared (FT-IR) spectroscopy and proton nuclear magnetic resonance (1H-NMR) all these analyses comprised our multi-omics dataset. The similar trends between the community consortia against the chemical profiles were connected through correlation. The result was then filtered, organized and framed according to correlation strengths and peculiarities. The output gave us four BGC types displaying uniqueness in community and chemical distribution, diversity and richness. We conclude therefore that the BGC typing is a successful technique for elucidating the sub-systems of organismal communities with associated chemical profiles in complex ecosystems.}, } @article {pmid25330000, year = {2014}, author = {Kong, LC and Holmes, BA and Cotillard, A and Habi-Rachedi, F and Brazeilles, R and Gougis, S and Gausserès, N and Cani, PD and Fellahi, S and Bastard, JP and Kennedy, SP and Doré, J and Ehrlich, SD and Zucker, JD and Rizkalla, SW and Clément, K}, title = {Dietary patterns differently associate with inflammation and gut microbiota in overweight and obese subjects.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e109434}, pmid = {25330000}, issn = {1932-6203}, mesh = {Adipose Tissue/pathology ; Adult ; Aged ; Biomarkers/metabolism ; Case-Control Studies ; Cohort Studies ; *Diet ; Eating ; Feces/microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Inflammation/metabolism ; Intestines/*microbiology ; Male ; *Microbiota ; Middle Aged ; Obesity/genetics/metabolism/*microbiology/pathology ; Polymerase Chain Reaction ; }, abstract = {BACKGROUND: Associations between dietary patterns, metabolic and inflammatory markers and gut microbiota are yet to be elucidated.

OBJECTIVES: We aimed to characterize dietary patterns in overweight and obese subjects and evaluate the different dietary patterns in relation to metabolic and inflammatory variables as well as gut microbiota.

DESIGN: Dietary patterns, plasma and adipose tissue markers, and gut microbiota were evaluated in a group of 45 overweight and obese subjects (6 men and 39 women). A group of 14 lean subjects were also evaluated as a reference group.

RESULTS: Three clusters of dietary patterns were identified in overweight/obese subjects. Cluster 1 had the least healthy eating behavior (highest consumption of potatoes, confectionary and sugary drinks, and the lowest consumption of fruits that was associated also with low consumption of yogurt, and water). This dietary pattern was associated with the highest LDL cholesterol, plasma soluble CD14 (p = 0.01) a marker of systemic inflammation but the lowest accumulation of CD163+ macrophages with anti-inflammatory profile in adipose tissue (p = 0.05). Cluster 3 had the healthiest eating behavior (lower consumption of confectionary and sugary drinks, and highest consumption of fruits but also yogurts and soups). Subjects in this Cluster had the lowest inflammatory markers (sCD14) and the highest anti-inflammatory adipose tissue CD163+ macrophages. Dietary intakes, insulin sensitivity and some inflammatory markers (plasma IL6) in Cluster 3 were close to those of lean subjects. Cluster 2 was in-between clusters 1 and 3 in terms of healthfulness. The 7 gut microbiota groups measured by qPCR were similar across the clusters. However, the healthiest dietary cluster had the highest microbial gene richness, as evaluated by quantitative metagenomics.

CONCLUSION: A healthier dietary pattern was associated with lower inflammatory markers as well as greater gut microbiota richness in overweight and obese subjects.

TRIAL REGISTRATION: ClinicalTrials.gov NCT01314690.}, } @article {pmid25329041, year = {2015}, author = {Chafee, M and Maignien, L and Simmons, SL}, title = {The effects of variable sample biomass on comparative metagenomics.}, journal = {Environmental microbiology}, volume = {17}, number = {7}, pages = {2239-2253}, doi = {10.1111/1462-2920.12668}, pmid = {25329041}, issn = {1462-2920}, mesh = {Arabidopsis/*microbiology ; *Biomass ; DNA/*genetics ; Gene Library ; Genomics ; Metagenomics/*methods ; Microbial Consortia/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA/methods ; }, abstract = {Longitudinal studies that integrate samples with variable biomass are essential to understand microbial community dynamics across space or time. Shotgun metagenomics is widely used to investigate these communities at the functional level, but little is known about the effects of combining low and high biomass samples on downstream analysis. We investigated the interacting effects of DNA input and library amplification by polymerase chain reaction on comparative metagenomic analysis using dilutions of a single complex template from an Arabidopsis thaliana-associated microbial community. We modified the Illumina Nextera kit to generate high-quality large-insert (680 bp) paired-end libraries using a range of 50 pg to 50 ng of input DNA. Using assembly-based metagenomic analysis, we demonstrate that DNA input level has a significant impact on community structure due to overrepresentation of low-GC genomic regions following library amplification. In our system, these differences were largely superseded by variations between biological replicates, but our results advocate verifying the influence of library amplification on a case-by-case basis. Overall, this study provides recommendations for quality filtering and de-replication prior to analysis, as well as a practical framework to address the issue of low biomass or biomass heterogeneity in longitudinal metagenomic surveys.}, } @article {pmid25328099, year = {2015}, author = {Dzutsev, A and Goldszmid, RS and Viaud, S and Zitvogel, L and Trinchieri, G}, title = {The role of the microbiota in inflammation, carcinogenesis, and cancer therapy.}, journal = {European journal of immunology}, volume = {45}, number = {1}, pages = {17-31}, doi = {10.1002/eji.201444972}, pmid = {25328099}, issn = {1521-4141}, support = {HHSN26120080001E//PHS HHS/United States ; //Intramural NIH HHS/United States ; }, mesh = {Adaptive Immunity ; Animals ; Antineoplastic Agents/therapeutic use ; Autoimmune Diseases/drug therapy/*microbiology/pathology ; Biological Evolution ; Carcinogenesis/*immunology/pathology ; Humans ; Immunity, Innate ; Immunomodulation ; Inflammation/drug therapy/immunology/microbiology/pathology ; Metagenome/immunology ; Mice ; Microbiota/*immunology ; Neoplasms/drug therapy/immunology/*microbiology/pathology ; Symbiosis/immunology ; Tumor Escape ; }, abstract = {Commensal microorganisms colonize barrier surfaces of all multicellular organisms, including those of humans. For more than 500 million years, commensal microorganisms and their hosts have coevolved and adapted to each other. As a result, the commensal microbiota affects many immune and nonimmune functions of their hosts, and de facto the two together comprise one metaorganism. The commensal microbiota communicates with the host via biologically active molecules. Recently, it has been reported that microbial imbalance may play a critical role in the development of multiple diseases, such as cancer, autoimmune conditions, and increased susceptibility to infection. In this review, we focus on the role of the commensal microbiota in the development, progression, and immune evasion of cancer, as well as some modulatory effects on the treatment of cancer. In particular, we discuss the mechanisms of microbiota-mediated regulation of innate and adaptive immune responses to tumors, and the consequences on cancer progression and whether tumors subsequently become resistant or susceptible to different anticancer therapeutic regiments.}, } @article {pmid25327646, year = {2015}, author = {Ficetola, GF and Pansu, J and Bonin, A and Coissac, E and Giguet-Covex, C and De Barba, M and Gielly, L and Lopes, CM and Boyer, F and Pompanon, F and Rayé, G and Taberlet, P}, title = {Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data.}, journal = {Molecular ecology resources}, volume = {15}, number = {3}, pages = {543-556}, doi = {10.1111/1755-0998.12338}, pmid = {25327646}, issn = {1755-0998}, mesh = {DNA Barcoding, Taxonomic/*methods/*standards ; *Diagnostic Errors ; *Environmental Microbiology ; Metagenomics/*methods/*standards ; }, abstract = {Environmental DNA (eDNA) metabarcoding is increasingly used to study the present and past biodiversity. eDNA analyses often rely on amplification of very small quantities or degraded DNA. To avoid missing detection of taxa that are actually present (false negatives), multiple extractions and amplifications of the same samples are often performed. However, the level of replication needed for reliable estimates of the presence/absence patterns remains an unaddressed topic. Furthermore, degraded DNA and PCR/sequencing errors might produce false positives. We used simulations and empirical data to evaluate the level of replication required for accurate detection of targeted taxa in different contexts and to assess the performance of methods used to reduce the risk of false detections. Furthermore, we evaluated whether statistical approaches developed to estimate occupancy in the presence of observational errors can successfully estimate true prevalence, detection probability and false-positive rates. Replications reduced the rate of false negatives; the optimal level of replication was strongly dependent on the detection probability of taxa. Occupancy models successfully estimated true prevalence, detection probability and false-positive rates, but their performance increased with the number of replicates. At least eight PCR replicates should be performed if detection probability is not high, such as in ancient DNA studies. Multiple DNA extractions from the same sample yielded consistent results; in some cases, collecting multiple samples from the same locality allowed detecting more species. The optimal level of replication for accurate species detection strongly varies among studies and could be explicitly estimated to improve the reliability of results.}, } @article {pmid25326827, year = {2014}, author = {Jiang, X and Hu, X}, title = {Inferring microbial interaction networks based on consensus similarity network fusion.}, journal = {Science China. Life sciences}, volume = {57}, number = {11}, pages = {1115-1120}, doi = {10.1007/s11427-014-4735-x}, pmid = {25326827}, issn = {1869-1889}, mesh = {Algorithms ; Cluster Analysis ; Computational Biology/*methods ; Computer Simulation ; Databases, Genetic ; Gene Regulatory Networks ; *Genes, Bacterial ; Genomics ; Humans ; Microbiota/*physiology ; Models, Biological ; Oxygen/chemistry ; }, abstract = {With the rapid accumulation of high-throughput metagenomic sequencing data, it is possible to infer microbial species relations in a microbial community systematically. In recent years, some approaches have been proposed for identifying microbial interaction network. These methods often focus on one dataset without considering the advantage of data integration. In this study, we propose to use a similarity network fusion (SNF) method to infer microbial relations. The SNF efficiently integrates the similarities of species derived from different datasets by a cross-network diffusion process. We also introduce consensus k-nearest neighborhood (Ck-NN) method instead of k-NN in the original SNF (we call the approach CSNF). The final network represents the augmented species relationships with aggregated evidence from various datasets, taking advantage of complementarity in the data. We apply the method on genus profiles derived from three microbiome datasets and we find that CSNF can discover the modular structure of microbial interaction network which cannot be identified by analyzing a single dataset.}, } @article {pmid25313075, year = {2014}, author = {Sakowski, EG and Munsell, EV and Hyatt, M and Kress, W and Williamson, SJ and Nasko, DJ and Polson, SW and Wommack, KE}, title = {Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {44}, pages = {15786-15791}, pmid = {25313075}, issn = {1091-6490}, support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; T32 GM008550/GM/NIGMS NIH HHS/United States ; }, mesh = {Aquatic Organisms/*genetics ; Base Sequence ; Biodiversity ; DNA Viruses/*genetics ; DNA, Single-Stranded/genetics ; DNA, Viral/genetics ; *Genome, Viral ; *Metagenome ; Molecular Sequence Data ; Ribonucleotide Reductases/*genetics ; Viral Proteins/*genetics ; }, abstract = {Virioplankton play a crucial role in aquatic ecosystems as top-down regulators of bacterial populations and agents of horizontal gene transfer and nutrient cycling. However, the biology and ecology of virioplankton populations in the environment remain poorly understood. Ribonucleotide reductases (RNRs) are ancient enzymes that reduce ribonucleotides to deoxyribonucleotides and thus prime DNA synthesis. Composed of three classes according to O2 reactivity, RNRs can be predictive of the physiological conditions surrounding DNA synthesis. RNRs are universal among cellular life, common within viral genomes and virioplankton shotgun metagenomes (viromes), and estimated to occur within >90% of the dsDNA virioplankton sampled in this study. RNRs occur across diverse viral groups, including all three morphological families of tailed phages, making these genes attractive for studies of viral diversity. Differing patterns in virioplankton diversity were clear from RNRs sampled across a broad oceanic transect. The most abundant RNRs belonged to novel lineages of podoviruses infecting α-proteobacteria, a bacterial class critical to oceanic carbon cycling. RNR class was predictive of phage morphology among cyanophages and RNR distribution frequencies among cyanophages were largely consistent with the predictions of the "kill the winner-cost of resistance" model. RNRs were also identified for the first time to our knowledge within ssDNA viromes. These data indicate that RNR polymorphism provides a means of connecting the biological and ecological features of virioplankton populations.}, } @article {pmid25311577, year = {2015}, author = {Mao, L and Franke, J}, title = {Symbiosis, dysbiosis, and rebiosis-the value of metaproteomics in human microbiome monitoring.}, journal = {Proteomics}, volume = {15}, number = {5-6}, pages = {1142-1151}, doi = {10.1002/pmic.201400329}, pmid = {25311577}, issn = {1615-9861}, mesh = {Biomarkers/analysis ; *Dysbiosis ; Humans ; Metagenomics/*methods ; *Microbiota ; Proteomics/*methods ; *Symbiosis ; Systems Biology ; }, abstract = {As just one species in the larger ecosystem, the health and disease status of human beings is highly dependent on other biological species in their environment, both inside and outside of the human body. Since proteins are the major functional building blocks of the biological world, most homeostasis regulations are realized at the protein level. Diagnosis-oriented monitoring of cross-species proteostasis will constitute a solid basis for next-generation preventive medicine. After a brief review of the history and state-of-the-art of metaproteomics in the field of environmental health research, focus of this perspective article will be put on the role of cross-species joint efforts in symbiosis, dysbiosis, and rebiosis of the human gut during human development, pathogenesis, and aging. The distinctive merit of metaproteomics on health state monitoring will be given special attention. Questions to be addressed include: How this microbial ecosystems in and around humans beings coevolve and stabilize during human development and aging? How the grade of microbial virulence is controlled at the community level? What happens upon temporary or ultimate homeostasis breakdown? How metaproteomics will affect next-generation diagnostics and preventive medicine? As an increasing amount of data becomes available, researchers need to become ever more hypothesis-oriented, so as not to be lost in sea of data, but instead efficiently extract the insights from "Big data." Future directions of metaproteomic research and its integration with other "omics" will be suggested, including the sophisticated use of systems biological approaches such as predictive modeling and simulations, in order to truly serve next-generation medicine.}, } @article {pmid25310759, year = {2015}, author = {Romano-Keeler, J and Weitkamp, JH}, title = {Maternal influences on fetal microbial colonization and immune development.}, journal = {Pediatric research}, volume = {77}, number = {1-2}, pages = {189-195}, pmid = {25310759}, issn = {1530-0447}, support = {T32HD068256/HD/NICHD NIH HHS/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; K08HD061607/HD/NICHD NIH HHS/United States ; K08 HD061607/HD/NICHD NIH HHS/United States ; P30DK058404/DK/NIDDK NIH HHS/United States ; UL1 RR024975/RR/NCRR NIH HHS/United States ; RR024975-01/RR/NCRR NIH HHS/United States ; T32 HD068256/HD/NICHD NIH HHS/United States ; }, mesh = {Female ; Fetus/*immunology/*microbiology ; Humans ; Immune System/*embryology/growth & development ; Maternal-Fetal Exchange/*immunology ; Microbiota/*immunology ; *Models, Immunological ; Placenta/*microbiology ; Pregnancy ; }, abstract = {While critical for normal development, the exact timing of establishment of the intestinal microbiome is unknown. For example, although preterm labor and birth have been associated with bacterial colonization of the amniotic cavity and fetal membranes for many years, the prevailing dogma of a sterile intrauterine environment during normal term pregnancies has been challenged more recently. While found to be a key contributor of evolution in the animal kingdom, maternal transmission of commensal bacteria may also constitute a critical process during healthy pregnancies in humans with yet unclear developmental importance. Metagenomic sequencing has elucidated a rich placental microbiome in normal term pregnancies likely providing important metabolic and immune contributions to the growing fetus. Conversely, an altered microbial composition during pregnancy may produce aberrant metabolites impairing fetal brain development and life-long neurological outcomes. Here we review the current understanding of microbial colonization at the feto-maternal interface and explain how normal gut colonization drives a balanced neonatal mucosal immune system, while dysbiosis contributes to aberrant immune function early in life and beyond. We discuss how maternal genetics, diet, medications, and probiotics inform the fetal microbiome in preparation for perinatal and postnatal bacterial colonization.}, } @article {pmid25309932, year = {2014}, author = {Ferreira, CM and Vieira, AT and Vinolo, MA and Oliveira, FA and Curi, R and Martins, Fdos S}, title = {The central role of the gut microbiota in chronic inflammatory diseases.}, journal = {Journal of immunology research}, volume = {2014}, number = {}, pages = {689492}, pmid = {25309932}, issn = {2314-7156}, mesh = {Chronic Disease ; Gastrointestinal Tract/*immunology/microbiology ; Humans ; Immune System/*immunology/microbiology ; Inflammatory Bowel Diseases/*immunology/microbiology/therapy ; Intestinal Mucosa/immunology/microbiology ; Microbiota/*immunology ; Models, Immunological ; }, abstract = {The commensal microbiota is in constant interaction with the immune system, teaching immune cells to respond to antigens. Studies in mice have demonstrated that manipulation of the intestinal microbiota alters host immune cell homeostasis. Additionally, metagenomic-sequencing analysis has revealed alterations in intestinal microbiota in patients suffering from inflammatory bowel disease, asthma, and obesity. Perturbations in the microbiota composition result in a deficient immune response and impaired tolerance to commensal microorganisms. Due to altered microbiota composition which is associated to some inflammatory diseases, several strategies, such as the administration of probiotics, diet, and antibiotic usage, have been utilized to prevent or ameliorate chronic inflammatory diseases. The purpose of this review is to present and discuss recent evidence showing that the gut microbiota controls immune system function and onset, development, and resolution of some common inflammatory diseases.}, } @article {pmid25306399, year = {2015}, author = {Magasin, JD and Gerloff, DL}, title = {Pooled assembly of marine metagenomic datasets: enriching annotation through chimerism.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {3}, pages = {311-317}, doi = {10.1093/bioinformatics/btu546}, pmid = {25306399}, issn = {1367-4811}, mesh = {Archaeal Proteins/*genetics ; Bacterial Proteins/*genetics ; *Chimerism ; *Datasets as Topic ; *Genome, Archaeal ; Genome, Bacterial ; *Metagenomics ; Molecular Sequence Annotation/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {MOTIVATION: Despite advances in high-throughput sequencing, marine metagenomic samples remain largely opaque. A typical sample contains billions of microbial organisms from thousands of genomes and quadrillions of DNA base pairs. Its derived metagenomic dataset underrepresents this complexity by orders of magnitude because of the sparseness and shortness of sequencing reads. Read shortness and sequencing errors pose a major challenge to accurate species and functional annotation. This includes distinguishing known from novel species. Often the majority of reads cannot be annotated and thus cannot help our interpretation of the sample.

RESULTS: Here, we demonstrate quantitatively how careful assembly of marine metagenomic reads within, but also across, datasets can alleviate this problem. For 10 simulated datasets, each with species complexity modeled on a real counterpart, chimerism remained within the same species for most contigs (97%). For 42 real pyrosequencing ('454') datasets, assembly increased the proportion of annotated reads, and even more so when datasets were pooled, by on average 1.6% (max 6.6%) for species, 9.0% (max 28.7%) for Pfam protein domains and 9.4% (max 22.9%) for PANTHER gene families. Our results outline exciting prospects for data sharing in the metagenomics community. While chimeric sequences should be avoided in other areas of metagenomics (e.g. biodiversity analyses), conservative pooled assembly is advantageous for annotation specificity and sensitivity. Intriguingly, our experiment also found potential prospects for (low-cost) discovery of new species in 'old' data.

CONTACT: dgerloff@ffame.org

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid25305639, year = {2014}, author = {Hyde, ER and Luk, B and Cron, S and Kusic, L and McCue, T and Bauch, T and Kaplan, H and Tribble, G and Petrosino, JF and Bryan, NS}, title = {Characterization of the rat oral microbiome and the effects of dietary nitrate.}, journal = {Free radical biology & medicine}, volume = {77}, number = {}, pages = {249-257}, doi = {10.1016/j.freeradbiomed.2014.09.017}, pmid = {25305639}, issn = {1873-4596}, support = {T32 GM008231/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Diet ; Humans ; Male ; Microbiota/*genetics ; Molecular Typing ; Nitrates/administration & dosage/*metabolism ; Nitrogen Oxides/blood ; RNA, Ribosomal, 16S/genetics ; Rats, Wistar ; Tongue/*microbiology ; }, abstract = {The nitrate-nitrite-NO pathway to nitric oxide (NO) production is a symbiotic pathway in mammals that is dependent on nitrate reducing oral commensal bacteria. Studies suggest that by contributing NO to the mammalian host, the oral microbiome helps maintain cardiovascular health. To begin to understand how changes in oral microbiota affect physiological functions such as blood pressure, we have characterized the Wistar rat nitrate reducing oral microbiome. Using 16S rRNA gene sequencing and analysis we compare the native Wistar rat tongue microbiome to that of healthy humans and to that of rats with sodium nitrate and chlorhexidine mouthwash treatments. We demonstrate that the rat tongue microbiome is less diverse than the human tongue microbiome, but that the physiological activity is comparable, as sodium nitrate supplementation significantly lowered diastolic blood pressure in Wistar rats and also lowers blood pressure (diastolic and systolic) in humans. We also show for the first time that sodium nitrate supplementation alters the abundance of specific bacterial species on the tongue. Our results suggest that the changes in oral nitrate reducing bacteria may affect nitric oxide availability and physiological functions such as blood pressure. Understanding individual changes in human oral microbiome may offer novel dietary approaches to restore NO availability and blood pressure.}, } @article {pmid25303278, year = {2015}, author = {Sherman, MP and Zaghouani, H and Niklas, V}, title = {Gut microbiota, the immune system, and diet influence the neonatal gut-brain axis.}, journal = {Pediatric research}, volume = {77}, number = {1-2}, pages = {127-135}, doi = {10.1038/pr.2014.161}, pmid = {25303278}, issn = {1530-0447}, mesh = {Brain/*physiology ; Dysbiosis/microbiology ; Enterocolitis, Necrotizing/microbiology ; Gastrointestinal Tract/*microbiology/*physiology ; Humans ; Infant, Newborn ; Infant, Newborn, Diseases/*microbiology ; Infant, Very Low Birth Weight ; Microbiota/*physiology ; *Models, Biological ; Sepsis/microbiology ; Signal Transduction/*physiology ; }, abstract = {The conceptual framework for a gut-brain axis has existed for decades. The Human Microbiome Project is responsible for establishing intestinal dysbiosis as a mediator of inflammatory bowel disease, obesity, and neurodevelopmental disorders in adults. Recent advances in metagenomics implicate gut microbiota and diet as key modulators of the bidirectional signaling pathways between the gut and brain that underlie neurodevelopmental and psychiatric disorders in adults. Evidence linking intestinal dysbiosis to neurodevelopmental disease outcomes in preterm infants is emerging. Recent clinical studies show that intestinal dysbiosis precedes late-onset neonatal sepsis and necrotizing enterocolitis in intensive care nurseries. Moreover, strong epidemiologic evidence links late-onset neonatal sepsis and necrotizing enterocolitis in long-term psychomotor disabilities of very-low-birth-weight infants. The notion of the gut-brain axis thereby supports that intestinal microbiota can indirectly harm the brain of preterm infants. In this review, we highlight the anatomy and physiology of the gut-brain axis and describe transmission of stress signals caused by immune-microbial dysfunction in the gut. These messengers initiate neurologic disease in preterm infants. Understanding neural and humoral signaling through the gut-brain axis will offer insight into therapeutic and dietary approaches that may improve the outcomes of very-low-birth-weight infants.}, } @article {pmid25299329, year = {2014}, author = {Knights, D and Ward, TL and McKinlay, CE and Miller, H and Gonzalez, A and McDonald, D and Knight, R}, title = {Rethinking "enterotypes".}, journal = {Cell host & microbe}, volume = {16}, number = {4}, pages = {433-437}, pmid = {25299329}, issn = {1934-6069}, support = {UL1 TR000114/TR/NCATS NIH HHS/United States ; }, mesh = {Bacteria/*classification/*genetics ; *Biota ; Cluster Analysis ; Gastrointestinal Tract/*microbiology ; Genetic Variation ; Genotype ; Humans ; *Metagenome ; }, abstract = {Classification of the human gut microbiome into distinct types, or "enterotypes," provides an attractive framework for understanding microbial variation in health and disease. However, as discussed here, several different methods of collapsing enterotype variation into a few discrete clusters suggest that enterotype distribution is continuous and can vary widely within an individual.}, } @article {pmid25294837, year = {2014}, author = {Tang, M and Tan, M and Meng, G and Yang, S and Su, X and Liu, S and Song, W and Li, Y and Wu, Q and Zhang, A and Zhou, X}, title = {Multiplex sequencing of pooled mitochondrial genomes-a crucial step toward biodiversity analysis using mito-metagenomics.}, journal = {Nucleic acids research}, volume = {42}, number = {22}, pages = {e166}, pmid = {25294837}, issn = {1362-4962}, mesh = {Animals ; Biodiversity ; Computer Simulation ; Drosophila/genetics ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; Molecular Sequence Data ; Sequence Analysis, DNA/*methods ; }, abstract = {The advent in high-throughput-sequencing (HTS) technologies has revolutionized conventional biodiversity research by enabling parallel capture of DNA sequences possessing species-level diagnosis. However, polymerase chain reaction (PCR)-based implementation is biased by the efficiency of primer binding across lineages of organisms. A PCR-free HTS approach will alleviate this artefact and significantly improve upon the multi-locus method utilizing full mitogenomes. Here we developed a novel multiplex sequencing and assembly pipeline allowing for simultaneous acquisition of full mitogenomes from pooled animals without DNA enrichment or amplification. By concatenating assemblies from three de novo assemblers, we obtained high-quality mitogenomes for all 49 pooled taxa, with 36 species >15 kb and the remaining >10 kb, including 20 complete mitogenomes and nearly all protein coding genes (99.6%). The assembly quality was carefully validated with Sanger sequences, reference genomes and conservativeness of protein coding genes across taxa. The new method was effective even for closely related taxa, e.g. three Drosophila spp., demonstrating its broad utility for biodiversity research and mito-phylogenomics. Finally, the in silico simulation showed that by recruiting multiple mito-loci, taxon detection was improved at a fixed sequencing depth. Combined, these results demonstrate the plausibility of a multi-locus mito-metagenomics approach as the next phase of the current single-locus metabarcoding method.}, } @article {pmid25293992, year = {2014}, author = {Gutiérrez-Escobar, AJ and Bayona-Rojas, M and Barragan-Vidal, C and Rojas-Lara, S and Oliveros, R}, title = {Metagenomic analysis of the gastric microbiota cultivable from a patient with gastritis concomitant with Barrett's esophagus.}, journal = {Revista de gastroenterologia del Peru : organo oficial de la Sociedad de Gastroenterologia del Peru}, volume = {34}, number = {3}, pages = {229-235}, pmid = {25293992}, issn = {1609-722X}, mesh = {Barrett Esophagus/complications/*microbiology ; Female ; Gastritis/complications/*microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenomics ; Middle Aged ; Stomach/*microbiology ; }, abstract = {Barrett's esophagus is a distal metaplasia characterized by the transformation of squamous mucosa into columnar mucosa. This esophageal phenotype is a product not only of the chronic reflux of gastric acids, but also by microorganisms that colonize the oral cavity and stomach. Two classes of microbiota can be identified in Barrett's esophagus; microbiota type I is associated with the normal esophagus and type II with an inflamed esophagus. The present study describes the gastric microbiota of a patient with antral gastritis concomitant with Barrett's esophagus absent infection with Helicobacter pylori. Gastric biopsies were obtained following the protocol of Sydney and following ethical practices. The isolates were cultivated under microaerophilic conditions on Columbia Agar supplemented with IsoVitaleX™ and 7% sterile blood. Extracted DNA was sequenced using 454-GS and the results analyzed on the MG-RAST server. Gram negative isolates were found and bacteria resistant to levofloxacin, amoxicillin, tetracycline, erythromycin, and clarithromycin. The phyla Bacteroidetes, Firmicutes, Fusobacteria and Proteobacteria, the genus Bacteroides and the species group Bacteroides fragilis were most abundant. Functionally, the metabolism of carbohydrates, amino acids, and to a lesser extent, the metabolism of cofactors and vitamins were most dominant, and of which the enzymes β-glucosidase (EC 3.2.1.21), β-galactosidase (EC 3.2.1.23) and β-N-acetylhexosaminidase (EC 3.2.1.52) were most dominant. The findings of this study, because they are of only one case may probably suggest a possible pathogenic role, previously undescribed for Bacteroides fragilis, associated with human gastritis when concomitant esophageal pathology exists.}, } @article {pmid25293875, year = {2015}, author = {Terrat, S and Dequiedt, S and Horrigue, W and Lelievre, M and Cruaud, C and Saby, NP and Jolivet, C and Arrouays, D and Maron, PA and Ranjard, L and Chemidlin Prévost-Bouré, N}, title = {Improving soil bacterial taxa-area relationships assessment using DNA meta-barcoding.}, journal = {Heredity}, volume = {114}, number = {5}, pages = {468-475}, pmid = {25293875}, issn = {1365-2540}, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA Fingerprinting ; DNA, Bacterial/genetics ; France ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {The evaluation of the taxa-area relationship (TAR) with molecular fingerprinting data demonstrated the spatial structuration of soil microorganisms and provided insights into the processes shaping their diversity. The increasing use of massive sequencing technologies in biodiversity investigations has now raised the question of the advantages of such technologies over the fingerprinting approach for elucidation of the determinism of soil microbial community assembly in broad-scale biogeographic studies. Our objectives in this study were to compare DNA fingerprinting and meta-barcoding approaches for evaluating soil bacterial TAR and the determinism of soil bacterial community assembly on a broad scale. This comparison was performed on 392 soil samples from four French geographic regions with different levels of environmental heterogeneity. Both molecular approaches demonstrated a TAR with a significant slope but, because of its more sensitive description of soil bacterial community richness, meta-barcoding provided significantly higher and more accurate estimates of turnover rates. Both approaches were useful in evidencing the processes shaping bacterial diversity variations on a broad scale. When different taxonomic resolutions were considered for meta-barcoding data, they significantly influenced the estimation of turnover rates but not the relative importance of each component process. Altogether, DNA meta-barcoding provides a more accurate evaluation of the TAR and may lead to re-examination of the processes shaping soil bacterial community assembly. This should provide new insights into soil microbial ecology in the context of sustainable use of soil resources.}, } @article {pmid25291122, year = {2014}, author = {Robles-Alonso, V and Guarner, F}, title = {From basic to applied research: lessons from the human microbiome projects.}, journal = {Journal of clinical gastroenterology}, volume = {48 Suppl 1}, number = {}, pages = {S3-4}, doi = {10.1097/MCG.0000000000000242}, pmid = {25291122}, issn = {1539-2031}, mesh = {Bacteria/*classification/genetics ; DNA, Bacterial/genetics ; Dysbiosis ; Host-Pathogen Interactions ; Humans ; Intestines/*microbiology ; Metagenome ; Metagenomics/methods ; *Microbiota ; Ribotyping ; }, abstract = {Two large-scale initiatives of major funding agencies aimed at deciphering the structure and function of the human gut microbiota, namely the NIH's Human Microbiome project and the European MetaHIT project, finalized their research program in 2012.}, } @article {pmid25291121, year = {2014}, author = {Patrignani, P and Tacconelli, S and Bruno, A}, title = {Gut microbiota, host gene expression, and aging.}, journal = {Journal of clinical gastroenterology}, volume = {48 Suppl 1}, number = {}, pages = {S28-31}, doi = {10.1097/MCG.0000000000000229}, pmid = {25291121}, issn = {1539-2031}, mesh = {Age Factors ; Aging/*genetics/metabolism ; Animals ; Bacteria/classification/*genetics ; *Gene Expression Regulation ; *Genome, Human ; Genomics/methods ; Host-Pathogen Interactions ; Humans ; Intestines/*microbiology ; Metabolomics/methods ; Metagenome ; MicroRNAs/genetics/metabolism ; *Microbiota ; Oxidative Stress ; }, abstract = {Novel concepts of disease susceptibility and development suggest an important role of gastrointestinal microbiota and microbial pathogens. They can contribute to physiological systems and disease processes, even outside of the gastrointestinal tract. There is increasing evidence that genetics of the host influence and interact with gut microbiota. Moreover, aging-associated oxidative stress may cause morphologic alterations of bacterial cells, thus influencing the aggressive potential and virulence markers of an anaerobic bacterium and finally the type of interaction with the host. At the same time, microbiota may influence host gene expression and it is becoming apparent that it may occur through the regulation of microRNAs. They are short single-stranded noncoding RNAs that regulate posttranscriptional gene expression by affecting mRNA stability and/or translational repression of their target mRNAs. The introduction of -omics approaches (such as metagenomics, metaproteomics, and metatranscriptomics) in microbiota research will certainly advance our knowledge of this area. This will lead to greatly deepen our understanding of the molecular targets in the homeostatic interaction between the gut microbiota and the host and, thereby, promises to reveal new ways to treat diseases and maintain health.}, } @article {pmid25288655, year = {2014}, author = {Vey, G and Charles, TC}, title = {MetaProx: the database of metagenomic proximons.}, journal = {Database : the journal of biological databases and curation}, volume = {2014}, number = {}, pages = {}, pmid = {25288655}, issn = {1758-0463}, mesh = {Animals ; *Databases, Genetic ; Humans ; Internet ; Metabolic Networks and Pathways/genetics ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Software ; User-Computer Interface ; }, abstract = {MetaProx is the database of metagenomic proximons: a searchable repository of proximon objects conceived with two specific goals. The first objective is to accelerate research involving metagenomic functional interactions by providing a database of metagenomic operon candidates. Proximons represent a special subset of directons (series of contiguous co-directional genes) where each member gene is in close proximity to its neighbours with respect to intergenic distance. As a result, proximons represent significant operon candidates where some subset of proximons is the set of true metagenomic operons. Proximons are well suited for the inference of metagenomic functional networks because predicted functional linkages do not rely on homology-dependent information that is frequently unavailable in metagenomic scenarios. The second objective is to explore representations for semistructured biological data that can offer an alternative to the traditional relational database approach. In particular, we use a serialized object implementation and advocate a Data as Data policy where the same serialized objects can be used at all levels (database, search tool and saved user file) without conversion or the use of human-readable markups. MetaProx currently includes 4,210,818 proximons consisting of 8 \,926,993 total member genes. Database URL: http://metaprox.uwaterloo.ca.}, } @article {pmid25286745, year = {2015}, author = {Nesme, J and Simonet, P}, title = {The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria.}, journal = {Environmental microbiology}, volume = {17}, number = {4}, pages = {913-930}, doi = {10.1111/1462-2920.12631}, pmid = {25286745}, issn = {1462-2920}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Ecology ; Fungi/metabolism ; Gene Transfer, Horizontal/*genetics ; Genetic Variation/genetics ; Humans ; Microbiota/drug effects/*genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Soil is a large reservoir of microbial diversity and the majority of antimicrobial compounds used today in human and veterinary health care have been isolated from soil microorganisms. The Darwinian hypothesis of an 'arms-shields race' between antibiotic producers and resistant strains is often cited to explain antibiotic resistance gene determinants (ARGD) origins and diversity. ARGD abundance and antibiotic molecule exposure are, however, not systematically linked, and many other factors can contribute to resistance gene emergence, selection and dissemination in the environment. Soil is a heterogeneous habitat and represents a broad spectrum of different ecological niches. Soil harbours a large genetic diversity at small spatial scale, favouring exchange of genetic materials by means of horizontal gene transfer (HGT) that will contribute to ARGD dissemination between bacteria and eventually acquisition by pathogen genomes, therefore threatening antibiotic therapies. Our current knowledge on the extent of the soil resistome abundance and diversity has been greatly enhanced since the metagenomic revolution and help of high-throughput sequencing technologies. Different ecological hypotheses explaining their high prevalence in soil and questioning their transfer rate to pathogens, in respect to these recent experimental results, will be discussed in the present review.}, } @article {pmid25284610, year = {2014}, author = {Leifer, CA and McConkey, C and Li, S and Chassaing, B and Gewirtz, AT and Ley, RE}, title = {Linking genetic variation in human Toll-like receptor 5 genes to the gut microbiome's potential to cause inflammation.}, journal = {Immunology letters}, volume = {162}, number = {2 Pt A}, pages = {3-9}, pmid = {25284610}, issn = {1879-0542}, support = {R01 AI076588/AI/NIAID NIH HHS/United States ; R03 AI097671/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptive Immunity ; Animals ; Antibody Formation/genetics ; Flagellin/genetics/immunology/*metabolism ; Gene Expression Regulation, Bacterial/genetics ; Genetic Predisposition to Disease ; Genetic Variation ; Humans ; Immunity, Innate ; Inflammation/genetics/*immunology/microbiology ; Intestinal Mucosa/*immunology/microbiology ; Mice ; Mice, Knockout ; *Microbiota ; Toll-Like Receptor 5/genetics/*metabolism ; }, abstract = {Immunodeficiencies can lead to alterations of the gut microbiome that render it pathogenic and capable of transmitting disease to naïve hosts. Here, we review the role of Toll-like receptor (TLR) 5, the innate receptor for bacterial flagellin, in immune responses to the normal gut microbiota with a focus its role on adaptive immunity. Loss of TLR5 has profound effects on the microbiota that include greater temporal instability of major lineages and upregulation of flagellar motility genes that may be linked to the reduced levels of anti-flagellin antibodies in the TLR5(-/-) host. A variety of human TLR5 gene alleles exist that also associated with inflammatory conditions and may do so via effects on the gut microbiome and altered host-microbial crosstalk.}, } @article {pmid25283802, year = {2014}, author = {Gimonneau, G and Tchioffo, MT and Abate, L and Boissière, A and Awono-Ambéné, PH and Nsango, SE and Christen, R and Morlais, I}, title = {Composition of Anopheles coluzzii and Anopheles gambiae microbiota from larval to adult stages.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {28}, number = {}, pages = {715-724}, doi = {10.1016/j.meegid.2014.09.029}, pmid = {25283802}, issn = {1567-7257}, mesh = {Animals ; Anopheles/*growth & development/*microbiology ; Bacteria/classification/genetics ; Biodiversity ; Larva ; *Life Cycle Stages ; Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {During their immature life stages, malaria mosquitoes are exposed to a wide array of microbes and contaminants from the aquatic habitats. Although prior studies have suggested that environmental exposure shapes the microbial community structure in the adult mosquito, most reports have focused on laboratory-based experiments and on a single mosquito epithelium, the gut. In this study, we investigated the influence of the breeding site on the development of the Anopheles coluzzii and Anopheles gambiae microbiota in natural conditions. We characterized bacterial communities from aquatic habitats, at surface microlayer and subsurface water levels, to freshly emerge adult mosquitoes using multiplexed 16S rRNA gene pyrosequencing and we separately analyzed the microbiota associated with the different epithelia of adult individual, midguts, ovaries and salivary glands. We found that the distribution of bacterial communities in the aquatic habitats differed according to the depth of water collections. Inter-individual variation of bacterial composition was large in larvae guts but adult mosquitoes from a same breeding site shared quite similar microbiota. Although some differences in bacterial abundances were highlighted between the different epithelia of freshly emerged An. coluzzii and An. gambiae, an intriguing feature from our study is the particular similarity of the overall bacterial communities. Our results call for further investigations on the bacterial population dynamics in the different tissues to determine the distinctive characteristics of each microbiota during the mosquito lifespan and to identify specific interactions between certain key phyla or species and the insect life history traits.}, } @article {pmid25279790, year = {2014}, author = {Sarma, RK and Gogoi, A and Dehury, B and Debnath, R and Bora, TC and Saikia, R}, title = {Community profiling of culturable fluorescent pseudomonads in the rhizosphere of green gram (Vigna radiata L.).}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e108378}, pmid = {25279790}, issn = {1932-6203}, mesh = {Biodiversity ; DNA Fingerprinting ; Genes, Fungal ; Metagenome ; Microbial Sensitivity Tests ; Osmotic Pressure ; Phenotype ; Phylogeny ; Pseudomonas/classification/drug effects/*genetics/isolation & purification/*metabolism ; Quantitative Trait, Heritable ; *Rhizosphere ; Soil Microbiology ; Stress, Physiological/genetics ; }, abstract = {Study on microbial diversity in the unexplored rhizosphere is important to understand their community structure, biology and ecological interaction with the host plant. This research assessed the genetic and functional diversity of fluorescent pseudomonads [FP] in the green gram rhizophere. One hundred and twenty types of morphologically distinct fluorescent pseudomonads were isolated during vegetative as well as reproductive growth phase of green gram. Rep PCR, ARDRA and RISA revealed two distinct clusters in each case at 75, 61 and 70% similarity coefficient index respectively. 16S rRNA partial sequencing analysis of 85 distantly related fluorescent pseudomonads depicted Pseudomonas aeruginosa as the dominant group. Out of 120 isolates, 23 (19%) showed antagonistic activity towards phytopathogenic fungi. These bacterial isolates showed varied production of salicylic acid, HCN and chitinase, 2, 4-diacetylphloroglucinol (DAPG), phenazine-1-carboxylic acid (PCA) and pyoluteorin (PLT). Production efficiency of inherent level of plant growth promoting (PGP) traits among the 120 isolates demonstrated that 10 (8%) solubilised inorganic phosphates, 25 (20%) produced indoles and 5 (4%) retained ACC deaminase activity. Pseudomonas aeruginosa GGRJ21 showed the highest production of all antagonistic and plant growth promoting (PGP) traits. In a greenhouse experiment, GGRJ21 suppressed root rot disease of green gram by 28-93% (p = 0.05). Consistent up regulation of three important stress responsive genes, i.e., acdS, KatA and gbsA and elevated production efficiency of different PGP traits could promote GGRJ21 as a potent plant growth regulator.}, } @article {pmid25274358, year = {2014}, author = {Bradley, JA and Singarayer, JS and Anesio, AM}, title = {Microbial community dynamics in the forefield of glaciers.}, journal = {Proceedings. Biological sciences}, volume = {281}, number = {1795}, pages = {}, pmid = {25274358}, issn = {1471-2954}, mesh = {*Ice Cover ; *Microbiota ; Models, Biological ; *Soil Microbiology ; }, abstract = {Retreating ice fronts (as a result of a warming climate) expose large expanses of deglaciated forefield, which become colonized by microbes and plants. There has been increasing interest in characterizing the biogeochemical development of these ecosystems using a chronosequence approach. Prior to the establishment of plants, microbes use autochthonously produced and allochthonously delivered nutrients for growth. The microbial community composition is largely made up of heterotrophic microbes (both bacteria and fungi), autotrophic microbes and nitrogen-fixing diazotrophs. Microbial activity is thought to be responsible for the initial build-up of labile nutrient pools, facilitating the growth of higher order plant life in developed soils. However, it is unclear to what extent these ecosystems rely on external sources of nutrients such as ancient carbon pools and periodic nitrogen deposition. Furthermore, the seasonal variation of chronosequence dynamics and the effect of winter are largely unexplored. Modelling this ecosystem will provide a quantitative evaluation of the key processes and could guide the focus of future research. Year-round datasets combined with novel metagenomic techniques will help answer some of the pressing questions in this relatively new but rapidly expanding field, which is of growing interest in the context of future large-scale ice retreat.}, } @article {pmid25271286, year = {2014}, author = {Chaston, JM and Newell, PD and Douglas, AE}, title = {Metagenome-wide association of microbial determinants of host phenotype in Drosophila melanogaster.}, journal = {mBio}, volume = {5}, number = {5}, pages = {e01631-14}, pmid = {25271286}, issn = {2150-7511}, support = {F32 GM099374/GM/NIGMS NIH HHS/United States ; R01 GM095372/GM/NIGMS NIH HHS/United States ; 1F32GM099374-01/GM/NIGMS NIH HHS/United States ; 1R01GM095372/GM/NIGMS NIH HHS/United States ; }, mesh = {Acetobacteraceae/genetics/isolation & purification ; Animals ; Bacteria/*genetics/isolation & purification ; Cloning, Molecular ; DNA, Bacterial/genetics ; Drosophila melanogaster/*microbiology ; Female ; Gene Expression Regulation, Bacterial ; *Genes, Bacterial ; Genetic Variation ; Host-Pathogen Interactions ; Lactobacillus/genetics/isolation & purification ; *Metagenome ; Microbiota ; Phenotype ; Phylogeny ; Proteobacteria/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Triglycerides/metabolism ; }, abstract = {UNLABELLED: Animal-associated bacteria (microbiota) affect host behaviors and physiological traits. To identify bacterial genetic determinants of microbiota-responsive host traits, we employed a metagenome-wide association (MGWA) approach in two steps. First, we measured two microbiota-responsive host traits, development time and triglyceride (TAG) content, in Drosophila melanogaster flies monoassociated with each of 41 bacterial strains. The effects of monoassociation on host traits were not confined to particular taxonomic groups. Second, we clustered protein-coding sequences of the bacteria by sequence similarity de novo and statistically associated the magnitude of the host trait with the bacterial gene contents. The animals had been monoassociated with genome-sequenced bacteria, so the metagenome content was unambiguous. This analysis showed significant effects of pyrroloquinoline quinone biosynthesis genes on development time, confirming the results of a published transposon mutagenesis screen, thereby validating the MGWA; it also identified multiple genes predicted to affect host TAG content, including extracellular glucose oxidation pathway components. To test the validity of the statistical associations, we expressed candidate genes in a strain that lacks them. Monoassociation with bacteria that ectopically expressed a predicted oxidoreductase or gluconate dehydrogenase conferred reduced Drosophila TAG contents relative to the TAG contents in empty vector controls. Consistent with the prediction that glucose oxidation pathway gene expression increased bacterial glucose utilization, the glucose content of the host diet was reduced when flies were exposed to these strains. Our findings indicate that microbiota affect host nutritional status through modulation of nutrient acquisition. Together, these findings demonstrate the utility of MGWA for identifying bacterial determinants of host traits and provide mechanistic insight into how gut microbiota modulate the nutritional status of a model host.

IMPORTANCE: To understand how certain gut bacteria promote the health of their animal hosts, we need to identify the bacterial genes that drive these beneficial relationships. This task is challenging because the bacterial communities can vary widely among different host individuals. To overcome this difficulty, we quantified how well each of 41 bacterial species protected Drosophila fruit flies from high fat content. The genomes of the chosen bacterial strains were previously sequenced, so we could statistically associate specific bacterial genes with bacterially mediated reduction in host fat content. Bacterial genes that promote glucose utilization were strongly represented in the association, and introducing these genes into the gut bacteria was sufficient to lower the animal's fat content. Our method is applicable to the study of many other host-microbe interactions as a way to uncover microbial genes important for host health.}, } @article {pmid25269839, year = {2015}, author = {Yang, CW and Huang, HW and Chao, WL and Chang, BV}, title = {Bacterial communities associated with aerobic degradation of polybrominated diphenyl ethers from river sediments.}, journal = {Environmental science and pollution research international}, volume = {22}, number = {5}, pages = {3810-3819}, pmid = {25269839}, issn = {1614-7499}, mesh = {Aerobiosis ; Bacteria/genetics/*metabolism ; Base Sequence ; Biodegradation, Environmental ; DNA Primers/genetics ; Geologic Sediments/*chemistry/*microbiology ; Halogenated Diphenyl Ethers/*metabolism ; Metagenomics ; Microbial Consortia ; Molecular Sequence Data ; Polybrominated Biphenyls ; RNA, Ribosomal, 16S/genetics ; *Rivers ; Sequence Analysis, DNA ; Taiwan ; Water Pollutants, Chemical/analysis/*metabolism ; }, abstract = {Polybrominated diphenyl ethers (PBDEs) are persistent organic pollutants and have therefore drawn much environmental concern. We aimed to compare aerobic degradation of different PBDE congeners under various treatments and reveal the bacterial community associated with PBDE degradation in sediment. Results of this study indicate that degradation rates of BDE-15 were enhanced 45.1 and 81.3 % with the addition of suspended and microencapsulated Pseudomonas sp., respectively. However, the degradation rates of BDE-28, BDE-47, BDE-99, and BDE-100 did not differ among experimental treatments. Degradation rates of PBDE congeners were in the order of BDE-15 > BDE-28 > BDE-47 > BDE-99 > BDE-100. Using a pyrosequencing-based metagenomic approach, we found that addition of various treatments altered the microbial community composition in the sediment. Twenty-four bacterial genera associated with degradation of PBDEs; six are the core bacterial genera common among PBDE degraders. The diverse bacterial composition among different PBDE congener degradation indicates different combinations of bacteria involved in degradation of different PBDE congeners.}, } @article {pmid25263745, year = {2014}, author = {Oakley, BB and Lillehoj, HS and Kogut, MH and Kim, WK and Maurer, JJ and Pedroso, A and Lee, MD and Collett, SR and Johnson, TJ and Cox, NA}, title = {The chicken gastrointestinal microbiome.}, journal = {FEMS microbiology letters}, volume = {360}, number = {2}, pages = {100-112}, doi = {10.1111/1574-6968.12608}, pmid = {25263745}, issn = {1574-6968}, mesh = {Animals ; *Chickens ; Gastrointestinal Tract/*microbiology ; *Microbiota ; Spatio-Temporal Analysis ; }, abstract = {The domestic chicken is a common model organism for human biological research and of course also forms the basis of a global protein industry. Recent methodological advances have spurred the recognition of microbiomes as complex communities with important influences on the health and disease status of the host. In this minireview, we provide an overview of the current state of knowledge of the chicken gastrointestinal microbiome focusing on spatial and temporal variability, the presence and importance of human pathogens, the influence of the microbiota on the immune system, and the importance of the microbiome for poultry nutrition. Review and meta-analysis of public data showed cecal communities dominated by Firmicutes and Bacteroides at the phylum level, while at finer levels of taxonomic resolution, a phylogenetically diverse assemblage of microorganisms appears to have similar metabolic functions that provide important benefits to the host as inferred from metagenomic data. This observation of functional redundancy may have important implications for management of the microbiome. We foresee advances in strategies to improve gut health in commercial operations through management of the intestinal microbiota as an alternative to in-feed subtherapeutic antibiotics, improvements in pre- and probiotics, improved management of polymicrobial poultry diseases, and better control of human pathogens via colonization reduction or competitive exclusion strategies.}, } @article {pmid25263219, year = {2014}, author = {Williams, BB and Van Benschoten, AH and Cimermancic, P and Donia, MS and Zimmermann, M and Taketani, M and Ishihara, A and Kashyap, PC and Fraser, JS and Fischbach, MA}, title = {Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine.}, journal = {Cell host & microbe}, volume = {16}, number = {4}, pages = {495-503}, pmid = {25263219}, issn = {1934-6069}, support = {DP2 OD007290/OD/NIH HHS/United States ; GM081879/GM/NIGMS NIH HHS/United States ; T32 EB009383/EB/NIBIB NIH HHS/United States ; K08 DK100638/DK/NIDDK NIH HHS/United States ; OD009180/OD/NIH HHS/United States ; DP5 OD009180/OD/NIH HHS/United States ; K08DK100638/DK/NIDDK NIH HHS/United States ; T32 GM064337/GM/NIGMS NIH HHS/United States ; P30 DK084567/DK/NIDDK NIH HHS/United States ; T32 GM008284/GM/NIGMS NIH HHS/United States ; T32 GM067547/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; P50 GM081879/GM/NIGMS NIH HHS/United States ; OD007290/OD/NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacteria/enzymology/genetics ; Biotransformation ; Carboxy-Lyases/chemistry/*genetics/metabolism ; Crystallography, X-Ray ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; *Microbiota ; Models, Molecular ; Molecular Sequence Data ; Neurotransmitter Agents/*metabolism ; Phylogeny ; Protein Conformation ; Sequence Homology ; Tryptamines/*metabolism ; Tryptophan/metabolism ; }, abstract = {Several recent studies describe the influence of the gut microbiota on host brain and behavior. However, the mechanisms responsible for microbiota-nervous system interactions are largely unknown. Using a combination of genetics, biochemistry, and crystallography, we identify and characterize two phylogenetically distinct enzymes found in the human microbiome that decarboxylate tryptophan to form the β-arylamine neurotransmitter tryptamine. Although this enzymatic activity is exceedingly rare among bacteria more broadly, analysis of the Human Microbiome Project data demonstrate that at least 10% of the human population harbors at least one bacterium encoding a tryptophan decarboxylase in their gut community. Our results uncover a previously unrecognized enzymatic activity that can give rise to host-modulatory compounds and suggests a potential direct mechanism by which gut microbiota can influence host physiology, including behavior.}, } @article {pmid25261516, year = {2014}, author = {Zhang, H and Liao, X and Sparks, JB and Luo, XM}, title = {Dynamics of gut microbiota in autoimmune lupus.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {24}, pages = {7551-7560}, pmid = {25261516}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification ; *Biodiversity ; Disease Models, Animal ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Lupus Erythematosus, Systemic/*microbiology ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; *Microbiota ; }, abstract = {Gut microbiota has been recognized as an important environmental factor in health, as well as in metabolic and immunological diseases, in which perturbation of the host gut microbiota is often observed in the diseased state. However, little is known on the role of gut microbiota in systemic lupus erythematosus. We investigated the effects of host genetics, sex, age, and dietary intervention on the gut microbiome in a murine lupus model. In young, female lupus-prone mice resembling women at childbearing age, a population with the highest risk for lupus, we found marked depletion of lactobacilli, and increases in Lachnospiraceae and overall diversity compared to age-matched healthy controls. The predicted metagenomic profile in lupus-prone mice showed a significant enrichment of bacterial motility- and sporulation-related pathways. Retinoic acid as a dietary intervention restored lactobacilli that were downregulated in lupus-prone mice, and this correlated with improved symptoms. The predicted metagenomes also showed that retinoic acid reversed many lupus-associated changes in microbial functions that deviated from the control. In addition, gut microbiota of lupus-prone mice were different between sexes, and an overrepresentation of Lachnospiraceae in females was associated with an earlier onset of and/or more severe lupus symptoms. Clostridiaceae and Lachnospiraceae, both harboring butyrate-producing genera, were more abundant in the gut of lupus-prone mice at specific time points during lupus progression. Together, our results demonstrate the dynamics of gut microbiota in murine lupus and provide evidence to suggest the use of probiotic lactobacilli and retinoic acid as dietary supplements to relieve inflammatory flares in lupus patients.}, } @article {pmid25257052, year = {2014}, author = {Rizzetto, L and De Filippo, C and Cavalieri, D}, title = {Richness and diversity of mammalian fungal communities shape innate and adaptive immunity in health and disease.}, journal = {European journal of immunology}, volume = {44}, number = {11}, pages = {3166-3181}, doi = {10.1002/eji.201344403}, pmid = {25257052}, issn = {1521-4141}, mesh = {*Adaptive Immunity ; Bacteria/*immunology ; Dysbiosis/*immunology/microbiology ; Fungi/*immunology/pathogenicity ; Host-Pathogen Interactions ; Humans ; *Immunity, Innate ; Lung/immunology ; Microbiota/*immunology ; Mouth/immunology ; Skin/microbiology ; }, abstract = {Human holobiomes are networks of mutualistic interactions between human cells and complex communities of bacteria and fungi that colonize the human body. The immune system must tolerate colonization with commensal bacteria and fungi but defend against invasion by either organism. Molecular ecological surveys of the human prokaryotic microbiota performed to date have revealed a remarkable degree of bacterial diversity and functionality. However, there is a dearth of information regarding the eukaryotic composition of the microbiota. In this review, we describe the ecology and the human niches of our fungal "fellow travelers" in both health and disease, discriminating between passengers, colonizers, and pathogens based on the interaction of these fungi with the human immune system. We conclude by highlighting the need to reconsider the etiology of many fungal and immune-related diseases in the context of the crosstalk between the human system and its resident microbial communities.}, } @article {pmid25251272, year = {2015}, author = {Johnson, ZI and Martiny, AC}, title = {Techniques for quantifying phytoplankton biodiversity.}, journal = {Annual review of marine science}, volume = {7}, number = {}, pages = {299-324}, doi = {10.1146/annurev-marine-010814-015902}, pmid = {25251272}, issn = {1941-0611}, mesh = {Biodiversity ; Chromatography, High Pressure Liquid ; DNA Fingerprinting ; Ecosystem ; Environmental Monitoring/*methods ; Flow Cytometry ; Gene Expression Profiling ; In Situ Hybridization, Fluorescence ; *Metagenomics ; Phylogeny ; *Phytoplankton/cytology/genetics/metabolism ; *Proteomics ; RNA, Ribosomal/genetics ; }, abstract = {The biodiversity of phytoplankton is a core measurement of the state and activity of marine ecosystems. In the context of historical approaches, we review recent major advances in the technologies that have enabled deeper characterization of the biodiversity of phytoplankton. In particular, high-throughput sequencing of single loci/genes, genomes, and communities (metagenomics) has revealed exceptional phylogenetic and genomic diversity whose breadth is not fully constrained. Other molecular tools-such as fingerprinting, quantitative polymerase chain reaction, and fluorescence in situ hybridization-have provided additional insight into the dynamics of this diversity in the context of environmental variability. Techniques for characterizing the functional diversity of community structure through targeted or untargeted approaches based on RNA or protein have also greatly advanced. A wide range of techniques is now available for characterizing phytoplankton communities, and these tools will continue to advance through ongoing improvements in both technology and data interpretation.}, } @article {pmid25250654, year = {2014}, author = {Snelling, TJ and Genç, B and McKain, N and Watson, M and Waters, SM and Creevey, CJ and Wallace, RJ}, title = {Diversity and community composition of methanogenic archaea in the rumen of Scottish upland sheep assessed by different methods.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e106491}, pmid = {25250654}, issn = {1932-6203}, support = {BBS/E/D/20211551/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004413/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004243/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/D/20211553/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Biodiversity ; DNA, Archaeal/chemistry/genetics ; Euryarchaeota/genetics/growth & development ; *Genetic Variation ; Geography ; Metagenome/genetics ; Methanobacteriaceae/growth & development ; Methanobacteriales/classification/*genetics/growth & development ; Methanobrevibacter/genetics/growth & development ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Rumen/*microbiology ; Scotland ; Sequence Analysis, DNA ; Sheep ; }, abstract = {Ruminal archaeomes of two mature sheep grazing in the Scottish uplands were analysed by different sequencing and analysis methods in order to compare the apparent archaeal communities. All methods revealed that the majority of methanogens belonged to the Methanobacteriales order containing the Methanobrevibacter, Methanosphaera and Methanobacteria genera. Sanger sequenced 1.3 kb 16S rRNA gene amplicons identified the main species of Methanobrevibacter present to be a SGMT Clade member Mbb. millerae (≥ 91% of OTUs); Methanosphaera comprised the remainder of the OTUs. The primers did not amplify ruminal Thermoplasmatales-related 16S rRNA genes. Illumina sequenced V6-V8 16S rRNA gene amplicons identified similar Methanobrevibacter spp. and Methanosphaera clades and also identified the Thermoplasmatales-related order as 13% of total archaea. Unusually, both methods concluded that Mbb. ruminantium and relatives from the same clade (RO) were almost absent. Sequences mapping to rumen 16S rRNA and mcrA gene references were extracted from Illumina metagenome data. Mapping of the metagenome data to 16S rRNA gene references produced taxonomic identification to Order level including 2-3% Thermoplasmatales, but was unable to discriminate to species level. Mapping of the metagenome data to mcrA gene references resolved 69% to unclassified Methanobacteriales. Only 30% of sequences were assigned to species level clades: of the sequences assigned to Methanobrevibacter, most mapped to SGMT (16%) and RO (10%) clades. The Sanger 16S amplicon and Illumina metagenome mcrA analyses showed similar species richness (Chao1 Index 19-35), while Illumina metagenome and amplicon 16S rRNA analysis gave lower richness estimates (10-18). The values of the Shannon Index were low in all methods, indicating low richness and uneven species distribution. Thus, although much information may be extracted from the other methods, Illumina amplicon sequencing of the V6-V8 16S rRNA gene would be the method of choice for studying rumen archaeal communities.}, } @article {pmid25250243, year = {2014}, author = {Roberts, AP and Kreth, J}, title = {The impact of horizontal gene transfer on the adaptive ability of the human oral microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {4}, number = {}, pages = {124}, pmid = {25250243}, issn = {2235-2988}, support = {R01 DE021726/DE/NIDCR NIH HHS/United States ; R01DE021726/DE/NIDCR NIH HHS/United States ; }, mesh = {*Adaptation, Biological ; Bacteria/genetics/metabolism ; Bacterial Adhesion ; Bacterial Physiological Phenomena ; Biofilms ; DNA Transposable Elements ; Drug Resistance, Bacterial ; Extracellular Space/metabolism ; *Gene Transfer, Horizontal ; Humans ; *Microbiota ; Mouth/*microbiology ; }, abstract = {The oral microbiome is composed of a multitude of different species of bacteria, each capable of occupying one or more of the many different niches found within the human oral cavity. This community exhibits many types of complex interactions which enable it to colonize and rapidly respond to changes in the environment in which they live. One of these interactions is the transfer, or acquisition, of DNA within this environment, either from co-resident bacterial species or from exogenous sources. Horizontal gene transfer in the oral cavity gives some of the resident bacteria the opportunity to sample a truly enormous metagenome affording them considerable adaptive potential which may be key to survival in such a varying environment. In this review the underlying mechanisms of HGT are discussed in relation to the oral microbiome with numerous examples described where the direct acquisition of exogenous DNA has contributed to the fitness of the bacterial host within the human oral cavity.}, } @article {pmid25249310, year = {2015}, author = {Song, LY and Wang, YQ}, title = {Investigation of microbial community structure of a shallow lake after one season copper sulfate algaecide treatment.}, journal = {Microbiological research}, volume = {170}, number = {}, pages = {105-113}, doi = {10.1016/j.micres.2014.08.008}, pmid = {25249310}, issn = {1618-0623}, mesh = {Anti-Infective Agents/*administration & dosage ; *Biodiversity ; Cluster Analysis ; Copper Sulfate/*administration & dosage ; Geography ; Lakes/chemistry/*microbiology ; Metagenome ; Michigan ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; *Seasons ; *Water Microbiology ; }, abstract = {In present work we described, for the first time, the phylogenic structure of the microbial community in a shallow freshwater lake (Hawk Island Lake, located in the Lower Peninsula of the State of Michigan, U.S.A.) after one season (four times during May to August 2007) of CuSO4 treatment for algae growth control. The microbial community structure was characterized by terminal restriction fragment length polymorphism (TRFLP), clone library and 454 pyrosequencing. The similar structure of water chemistry measured across three sampling sites suggested that the lake was well mixed. The concentration of chlorophyll a (chl-a) and turbidity was low, 3.35 ± 1.62 μg/L and 2.5 ± 1.9 NTU, respectively, implying that photosynthesis was suppressed. TRFLP profiles showed that the lake was dominated by 16 terminal fragments (TFs), accounting for 85.5-92.6% abundance. Analysis of similarity (ANOSIM) showed that the difference in microbial community structure between upper and lower depths of the water column was not significant (P=0.101). These results suggested that the microbial community structure within the lake was similar. Clone library and 454 pyrosequencing indicated that the lake was dominated by freshwater phyla, Proteobacteria, Bacteroides, and Actinobacteria. Moreover, the large number of unclassified bacteria (27.4% of total 2090,454 sequences) suggested a complex microbial community structure in the lake.}, } @article {pmid25248921, year = {2015}, author = {Francis, SS and Riley, LW}, title = {Metagenomic epidemiology: a new frontier.}, journal = {Journal of epidemiology and community health}, volume = {69}, number = {4}, pages = {306-308}, doi = {10.1136/jech-2014-203997}, pmid = {25248921}, issn = {1470-2738}, mesh = {Communicable Diseases/*epidemiology/genetics ; Genome, Human ; Humans ; *Metagenomics ; Microbiota/drug effects/*genetics ; *Molecular Epidemiology ; }, } @article {pmid25248007, year = {2015}, author = {Li, J and Butcher, J and Mack, D and Stintzi, A}, title = {Functional impacts of the intestinal microbiome in the pathogenesis of inflammatory bowel disease.}, journal = {Inflammatory bowel diseases}, volume = {21}, number = {1}, pages = {139-153}, doi = {10.1097/MIB.0000000000000215}, pmid = {25248007}, issn = {1536-4844}, mesh = {Animals ; Humans ; Inflammatory Bowel Diseases/immunology/*microbiology/*pathology ; Intestines/immunology/*microbiology ; Microbiota/*immunology ; }, abstract = {: The human intestinal microbiome plays a critical role in human health and disease, including the pathogenesis of inflammatory bowel disease (IBD). Numerous studies have identified altered bacterial diversity and abundance at varying taxonomic levels through biopsies and fecal samples of patients with IBD and diseased model animals. However, inconsistent observations regarding the microbial compositions of such patients have hindered the efforts in assessing the etiological role of specific bacterial species in the pathophysiology of IBD. These observations highlight the importance of minimizing the confounding factors associated with IBD and the need for a standardized methodology to analyze well-defined microbial sampling sources in early IBD diagnosis. Furthermore, establishing the linkage between microbiota compositions with their function within the host system can provide new insights on the pathogenesis of IBD. Such research has been greatly facilitated by technological advances that include functional metagenomics coupled with proteomic and metabolomic profiling. This review provides updates on the composition of the microbiome in IBD and emphasizes microbiota dysbiosis-involved mechanisms. We highlight functional roles of specific bacterial groups in the development and management of IBD. Functional analyses of the microbiome may be the key to understanding the role of microbiota in the development and chronicity of IBD and reveal new strategies for therapeutic intervention.}, } @article {pmid25247417, year = {2014}, author = {Fouhy, F and Ogilvie, LA and Jones, BV and Ross, RP and Ryan, AC and Dempsey, EM and Fitzgerald, GF and Stanton, C and Cotter, PD}, title = {Identification of aminoglycoside and β-lactam resistance genes from within an infant gut functional metagenomic library.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e108016}, pmid = {25247417}, issn = {1932-6203}, support = {G0901553//Medical Research Council/United Kingdom ; }, mesh = {Aminoglycosides/*pharmacology ; Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Microbial/genetics ; Feces/microbiology ; Gastrointestinal Tract/*drug effects/microbiology ; Humans ; Infant ; Metagenomics ; Microbiota/*drug effects/genetics ; beta-Lactam Resistance/*genetics ; beta-Lactams/*pharmacology ; }, abstract = {The infant gut microbiota develops rapidly during the first 2 years of life, acquiring microorganisms from diverse sources. During this time, significant opportunities exist for the infant to acquire antibiotic resistant bacteria, which can become established and constitute the infant gut resistome. With increased antibiotic resistance limiting our ability to treat bacterial infections, investigations into resistance reservoirs are highly pertinent. This study aimed to explore the nascent resistome in antibiotically-naïve infant gut microbiomes, using a combination of metagenomic approaches. Faecal samples from 22 six-month-old infants without previous antibiotic exposure were used to construct a pooled metagenomic library, which was functionally screened for ampicillin and gentamicin resistance. Our library of ∼220Mb contained 0.45 ampicillin resistant hits/Mb and 0.059 gentamicin resistant hits/Mb. PCR-based analysis of fosmid clones and uncloned metagenomic DNA, revealed a diverse and abundant aminoglycoside and β-lactam resistance reservoir within the infant gut, with resistance determinants exhibiting homology to those found in common gut inhabitants, including Escherichia coli, Enterococcus sp., and Clostridium difficile, as well as to genes from cryptic environmental bacteria. Notably, the genes identified differed from those revealed when a sequence-driven PCR-based screen of metagenomic DNA was employed. Carriage of these antibiotic resistance determinants conferred substantial, but varied (2-512x), increases in antibiotic resistance to their bacterial host. These data provide insights into the infant gut resistome, revealing the presence of a varied aminoglycoside and β-lactam resistance reservoir even in the absence of selective pressure, confirming the infant resistome establishes early in life, perhaps even at birth.}, } @article {pmid25246537, year = {2014}, author = {Poulsen, M and Hu, H and Li, C and Chen, Z and Xu, L and Otani, S and Nygaard, S and Nobre, T and Klaubauf, S and Schindler, PM and Hauser, F and Pan, H and Yang, Z and Sonnenberg, AS and de Beer, ZW and Zhang, Y and Wingfield, MJ and Grimmelikhuijzen, CJ and de Vries, RP and Korb, J and Aanen, DK and Wang, J and Boomsma, JJ and Zhang, G}, title = {Complementary symbiont contributions to plant decomposition in a fungus-farming termite.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {40}, pages = {14500-14505}, pmid = {25246537}, issn = {1091-6490}, mesh = {Animals ; Bacteria/classification/genetics/metabolism ; Carbohydrate Metabolism ; Digestive System/metabolism/microbiology ; Female ; Fungal Proteins/metabolism ; Glycoside Hydrolases/metabolism ; Host-Pathogen Interactions ; Isoptera/genetics/*metabolism/microbiology ; Male ; Metagenome/genetics ; Microbial Consortia/genetics/physiology ; Oligosaccharides/metabolism ; Plants/*metabolism ; Polysaccharides/metabolism ; Sequence Analysis, DNA ; *Symbiosis ; Termitomyces/genetics/*metabolism/physiology ; }, abstract = {Termites normally rely on gut symbionts to decompose organic matter but the Macrotermitinae domesticated Termitomyces fungi to produce their own food. This transition was accompanied by a shift in the composition of the gut microbiota, but the complementary roles of these bacteria in the symbiosis have remained enigmatic. We obtained high-quality annotated draft genomes of the termite Macrotermes natalensis, its Termitomyces symbiont, and gut metagenomes from workers, soldiers, and a queen. We show that members from 111 of the 128 known glycoside hydrolase families are represented in the symbiosis, that Termitomyces has the genomic capacity to handle complex carbohydrates, and that worker gut microbes primarily contribute enzymes for final digestion of oligosaccharides. This apparent division of labor is consistent with the Macrotermes gut microbes being most important during the second passage of comb material through the termite gut, after a first gut passage where the crude plant substrate is inoculated with Termitomyces asexual spores so that initial fungal growth and polysaccharide decomposition can proceed with high efficiency. Complex conversion of biomass in termite mounds thus appears to be mainly accomplished by complementary cooperation between a domesticated fungal monoculture and a specialized bacterial community. In sharp contrast, the gut microbiota of the queen had highly reduced plant decomposition potential, suggesting that mature reproductives digest fungal material provided by workers rather than plant substrate.}, } @article {pmid25245398, year = {2015}, author = {Gonzalez-Martinez, A and Rodriguez-Sanchez, A and Muñoz-Palazon, B and Garcia-Ruiz, MJ and Osorio, F and van Loosdrecht, MC and Gonzalez-Lopez, J}, title = {Microbial community analysis of a full-scale DEMON bioreactor.}, journal = {Bioprocess and biosystems engineering}, volume = {38}, number = {3}, pages = {499-508}, doi = {10.1007/s00449-014-1289-z}, pmid = {25245398}, issn = {1615-7605}, mesh = {Bioreactors/*microbiology ; *Denitrification ; *Microbiota ; Wastewater/*microbiology ; *Water Purification ; }, abstract = {Full-scale applications of autotrophic nitrogen removal technologies for the treatment of digested sludge liquor have proliferated during the last decade. Among these technologies, the aerobic/anoxic deammonification process (DEMON) is one of the major applied processes. This technology achieves nitrogen removal from wastewater through anammox metabolism inside a single bioreactor due to alternating cycles of aeration. To date, microbial community composition of full-scale DEMON bioreactors have never been reported. In this study, bacterial community structure of a full-scale DEMON bioreactor located at the Apeldoorn wastewater treatment plant was analyzed using pyrosequencing. This technique provided a higher-resolution study of the bacterial assemblage of the system compared to other techniques used in lab-scale DEMON bioreactors. Results showed that the DEMON bioreactor was a complex ecosystem where ammonium oxidizing bacteria, anammox bacteria and many other bacterial phylotypes coexist. The potential ecological role of all phylotypes found was discussed. Thus, metagenomic analysis through pyrosequencing offered new perspectives over the functioning of the DEMON bioreactor by exhaustive identification of microorganisms, which play a key role in the performance of bioreactors. In this way, pyrosequencing has been proven as a helpful tool for the in-depth investigation of the functioning of bioreactors at microbiological scale.}, } @article {pmid25244083, year = {2014}, author = {Nunes-Alves, C}, title = {Microbiome: Commensally sourced antibiotics.}, journal = {Nature reviews. Microbiology}, volume = {12}, number = {11}, pages = {726}, pmid = {25244083}, issn = {1740-1534}, mesh = {Bacteria/*chemistry/*genetics ; Humans ; Metagenomics/*methods ; *Microbiota ; }, } @article {pmid25243126, year = {2014}, author = {Devirgiliis, C and Zinno, P and Stirpe, M and Barile, S and Perozzi, G}, title = {Functional screening of antibiotic resistance genes from a representative metagenomic library of food fermenting microbiota.}, journal = {BioMed research international}, volume = {2014}, number = {}, pages = {290967}, pmid = {25243126}, issn = {2314-6141}, mesh = {Cheese/microbiology ; Dairy Products/microbiology ; Drug Resistance, Microbial/*genetics ; Fermentation/*genetics ; *Food Microbiology ; *Gene Library ; *Genetic Testing ; Genome, Bacterial ; Metagenome/*genetics ; Microbiota/*genetics ; }, abstract = {Lactic acid bacteria (LAB) represent the predominant microbiota in fermented foods. Foodborne LAB have received increasing attention as potential reservoir of antibiotic resistance (AR) determinants, which may be horizontally transferred to opportunistic pathogens. We have previously reported isolation of AR LAB from the raw ingredients of a fermented cheese, while AR genes could be detected in the final, marketed product only by PCR amplification, thus pointing at the need for more sensitive microbial isolation techniques. We turned therefore to construction of a metagenomic library containing microbial DNA extracted directly from the food matrix. To maximize yield and purity and to ensure that genomic complexity of the library was representative of the original bacterial population, we defined a suitable protocol for total DNA extraction from cheese which can also be applied to other lipid-rich foods. Functional library screening on different antibiotics allowed recovery of ampicillin and kanamycin resistant clones originating from Streptococcus salivarius subsp. thermophilus and Lactobacillus helveticus genomes. We report molecular characterization of the cloned inserts, which were fully sequenced and shown to confer AR phenotype to recipient bacteria. We also show that metagenomics can be applied to food microbiota to identify underrepresented species carrying specific genes of interest.}, } @article {pmid25239570, year = {2015}, author = {Quiroz, M and Triadó-Margarit, X and Casamayor, EO and Gajardo, G}, title = {Comparison of Artemia-bacteria associations in brines, laboratory cultures and the gut environment: a study based on Chilean hypersaline environments.}, journal = {Extremophiles : life under extreme conditions}, volume = {19}, number = {1}, pages = {135-147}, pmid = {25239570}, issn = {1433-4909}, mesh = {Animals ; Artemia/*microbiology/physiology ; Bacteria/*classification/isolation & purification ; Biodiversity ; Chile ; DNA, Bacterial/genetics ; Ecosystem ; Electrophoresis ; Intestines/*microbiology ; Metagenome ; *Microbiota ; Phylogeny ; Polymerase Chain Reaction ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {The brine shrimp Artemia (Crustacea) and a diversity of halophilic microorganisms coexist in natural brines, salterns and laboratory cultures; part of such environmental microbial diversity is represented in the gut of Artemia individuals. Bacterial diversity in these environments was assessed by 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) fingerprinting. Eight natural locations in Chile, where A. franciscana or A. persimilis occur, were sampled for analysis of free-living and gut-associated bacteria in water from nature and laboratory cultures. The highest ecological diversity (Shannon's index, H') was found in brines, it decreased in the gut of wild and laboratory animals, and in laboratory water. Significant differences in H' existed between brines and laboratory water, and between brines and gut of wild animals. The greatest similarity of bacterial community composition was between brines and the gut of field animals, suggesting a transient state of the gut microbiota. Sequences retrieved from DGGE patterns (n = 83) exhibited an average of 97.8% identity with 41 bacterial genera from the phyla Proteobacteria (55.4% of sequences match), Bacteroidetes (22.9%), Actinobacteria (16.9%) and Firmicutes (4.8%). Environment-exclusive genera distribution was seen in Sphingomonas and Paenibacillus (gut of field animals), Amaricoccus and Ornithinimicrobium (gut of laboratory animals), and Hydrogenophaga (water of laboratory cultures). The reported ecological and physiological capabilities of such bacteria can help to understand Artemia adaptation to natural and laboratory conditions.}, } @article {pmid25232735, year = {2014}, author = {Lees, H and Swann, J and Poucher, SM and Nicholson, JK and Holmes, E and Wilson, ID and Marchesi, JR}, title = {Age and microenvironment outweigh genetic influence on the Zucker rat microbiome.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e100916}, pmid = {25232735}, issn = {1932-6203}, mesh = {*Aging ; Animals ; Bacteria/classification/genetics ; Bacterial Typing Techniques ; Base Sequence ; Biodiversity ; Disease Models, Animal ; Environment ; Feces/microbiology ; Intestines/*microbiology ; Microbiota/*genetics ; Obesity/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Zucker ; Sequence Analysis, DNA ; }, abstract = {Animal models are invaluable tools which allow us to investigate the microbiome-host dialogue. However, experimental design introduces biases in the data that we collect, also potentially leading to biased conclusions. With obesity at pandemic levels animal models of this disease have been developed; we investigated the role of experimental design on one such rodent model. We used 454 pyrosequencing to profile the faecal bacteria of obese (n = 6) and lean (homozygous n = 6; heterozygous n = 6) Zucker rats over a 10 week period, maintained in mixed-genotype cages, to further understand the relationships between the composition of the intestinal bacteria and age, obesity progression, genetic background and cage environment. Phylogenetic and taxon-based univariate and multivariate analyses (non-metric multidimensional scaling, principal component analysis) showed that age was the most significant source of variation in the composition of the faecal microbiota. Second to this, cage environment was found to clearly impact the composition of the faecal microbiota, with samples from animals from within the same cage showing high community structure concordance, but large differences seen between cages. Importantly, the genetically induced obese phenotype was not found to impact the faecal bacterial profiles. These findings demonstrate that the age and local environmental cage variables were driving the composition of the faecal bacteria and were more deterministically important than the host genotype. These findings have major implications for understanding the significance of functional metagenomic data in experimental studies and beg the question; what is being measured in animal experiments in which different strains are housed separately, nature or nurture?}, } @article {pmid25232638, year = {2014}, author = {Ofek-Lalzar, M and Sela, N and Goldman-Voronov, M and Green, SJ and Hadar, Y and Minz, D}, title = {Niche and host-associated functional signatures of the root surface microbiome.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {4950}, doi = {10.1038/ncomms5950}, pmid = {25232638}, issn = {2041-1723}, mesh = {Crops, Agricultural/*microbiology ; Cucumis/microbiology ; DNA/chemistry ; Environment ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Gene Library ; Genetic Techniques ; Genomics ; Genotype ; Metagenomics ; *Microbiota ; Phylogeny ; Plant Roots/*microbiology ; Plants/microbiology ; Sequence Analysis, DNA ; Soil ; Soil Microbiology ; Triticum/microbiology ; }, abstract = {Plant microbiomes are critical to host adaptation and impact plant productivity and health. Root-associated microbiomes vary by soil and host genotype, but the contribution of these factors to community structure and metabolic potential has not been fully addressed. Here we characterize root microbial communities of two disparate agricultural crops grown in the same natural soil in a controlled and replicated experimental system. Metagenomic (genetic potential) analysis identifies a core set of functional genes associated with root colonization in both plant hosts, and metatranscriptomic (functional expression) analysis revealed that most genes enriched in the root zones are expressed. Root colonization requires multiple functional capabilities, and these capabilities are enriched at the community level. Differences between the root-associated microbial communities from different plants are observed at the genus or species level, and are related to root-zone environmental factors.}, } @article {pmid25231861, year = {2014}, author = {Hsiao, A and Ahmed, AM and Subramanian, S and Griffin, NW and Drewry, LL and Petri, WA and Haque, R and Ahmed, T and Gordon, JI}, title = {Members of the human gut microbiota involved in recovery from Vibrio cholerae infection.}, journal = {Nature}, volume = {515}, number = {7527}, pages = {423-426}, pmid = {25231861}, issn = {1476-4687}, support = {AI 43596/AI/NIAID NIH HHS/United States ; R01 AI043596/AI/NIAID NIH HHS/United States ; T32DK077653/DK/NIDDK NIH HHS/United States ; T32AI007172/AI/NIAID NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bangladesh ; Child ; Cholera/*microbiology ; Cohort Studies ; Diarrhea/microbiology ; Feces/microbiology ; Gene Expression Regulation, Bacterial ; Germ-Free Life ; Health ; Humans ; Intestines/*microbiology ; Male ; Metagenome/genetics ; Mice ; Microbiota/genetics/*physiology ; Quorum Sensing/physiology ; Ruminococcus/isolation & purification/*physiology ; Vibrio cholerae/genetics/isolation & purification/*pathogenicity/*physiology ; Virulence/genetics ; Virulence Factors/genetics/metabolism ; }, abstract = {Given the global burden of diarrhoeal diseases, it is important to understand how members of the gut microbiota affect the risk for, course of, and recovery from disease in children and adults. The acute, voluminous diarrhoea caused by Vibrio cholerae represents a dramatic example of enteropathogen invasion and gut microbial community disruption. Here we conduct a detailed time-series metagenomic study of faecal microbiota collected during the acute diarrhoeal and recovery phases of cholera in a cohort of Bangladeshi adults living in an area with a high burden of disease. We find that recovery is characterized by a pattern of accumulation of bacterial taxa that shows similarities to the pattern of assembly/maturation of the gut microbiota in healthy Bangladeshi children. To define the underlying mechanisms, we introduce into gnotobiotic mice an artificial community composed of human gut bacterial species that directly correlate with recovery from cholera in adults and are indicative of normal microbiota maturation in healthy Bangladeshi children. One of the species, Ruminococcus obeum, exhibits consistent increases in its relative abundance upon V. cholerae infection of the mice. Follow-up analyses, including mono- and co-colonization studies, establish that R. obeum restricts V. cholerae colonization, that R. obeum luxS (autoinducer-2 (AI-2) synthase) expression and AI-2 production increase significantly with V. cholerae invasion, and that R. obeum AI-2 causes quorum-sensing-mediated repression of several V. cholerae colonization factors. Co-colonization with V. cholerae mutants discloses that R. obeum AI-2 reduces Vibrio colonization/pathogenicity through a novel pathway that does not depend on the V. cholerae AI-2 sensor, LuxP. The approach described can be used to mine the gut microbiota of Bangladeshi or other populations for members that use autoinducers and/or other mechanisms to limit colonization with V. cholerae, or conceivably other enteropathogens.}, } @article {pmid25228469, year = {2014}, author = {Parmar, NR and Solanki, JV and Patel, AB and Shah, TM and Patel, AK and Parnerkar, S and Kumar, JI and Joshi, CG}, title = {Metagenome of Mehsani buffalo rumen microbiota: an assessment of variation in feed-dependent phylogenetic and functional classification.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {24}, number = {4}, pages = {249-261}, doi = {10.1159/000365054}, pmid = {25228469}, issn = {1660-2412}, mesh = {Animals ; Bacteria/*classification/*genetics ; Buffaloes ; Diet/*methods ; *Metagenome ; *Microbiota ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {AIM: To gain a greater understanding of the ecology and metabolic potential of the rumen microbiome with the changes in the animal diet.

METHODS: Diet composed of varying proportion of green and dry roughages along with grains was given to 8 Mehsani buffaloes, and rumen metagenome was sketched using shotgun semiconductor sequencing.

RESULTS: In the present study, the Bacteroidetes were found to be dominant at the phyla level and Prevotella at the genus level. The ratio of Firmicutes to Bacteroidetes was found to be higher in the solid fraction as compared to the liquid fraction. In the solid fraction of the dry roughage group, the significant increment (p < 0.05) in Bacteroidetes abundance was observed with increment of roughage concentration. At the genus level, Clostridium significantly increased with the increment in roughage concentration. A comparison of glycoside hydrolase and cellulosome functional genes revealed more glycoside hydrolase 3 encoding genes with higher fiber diet and significant difference in carbohydrate-active enzymes family composition between green and dry roughage groups of the liquid fraction.

CONCLUSION: The present study provides a base to understand the modulating behavior of microbiota which can be manipulated to improve livestock nutrient utilization efficiency and for targeting the efficient catabolism of complex carbohydrate molecules as well.}, } @article {pmid25227089, year = {2014}, author = {Lee, MS and Oh, S and Tang, H}, title = {Characterization of microbial associations in human oral microbiome.}, journal = {Bio-medical materials and engineering}, volume = {24}, number = {6}, pages = {3737-3744}, doi = {10.3233/BME-141202}, pmid = {25227089}, issn = {1878-3619}, mesh = {Bacteria/genetics ; Genetic Association Studies/*methods ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Mouth/*microbiology ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA ; }, abstract = {Microorganisms interact with each other within a community. Within the same community, some microorganisms tend to co-exist, whereas some others tend to avoid each other. The association among microorganisms can be revealed by computing the correlation between their abundance patterns that are measured through metagenomic sequencing across multiple communities. In this paper, we built an association network among microorganisms from the human oral microbiome. To improve its accuracy, we adopted a network deconvolution algorithm to filter out indirect associations, and we used an ensemble of three correlation measures to filter out the false-positive associations. When applying on the metagenomic data from human oral samples, experimental results showed that phylogenetically close microorganisms formed highly correlated network clusters. Additionally, most of the identified mutually exclusive associations were related to the order Lactobacillales.}, } @article {pmid25225969, year = {2014}, author = {Yousuf, B and Kumar, R and Mishra, A and Jha, B}, title = {Unravelling the carbon and sulphur metabolism in coastal soil ecosystems using comparative cultivation-independent genome-level characterisation of microbial communities.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e107025}, pmid = {25225969}, issn = {1932-6203}, mesh = {Bacteria/classification/genetics/metabolism ; Biodiversity ; Carbon/*metabolism ; *Ecosystem ; Genes, Bacterial ; *Metagenome ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S ; Soil/*chemistry ; *Soil Microbiology ; Sulfur/*metabolism ; }, abstract = {Bacterial autotrophy contributes significantly to the overall carbon balance, which stabilises atmospheric CO2 concentration and decelerates global warming. Little attention has been paid to different modes of carbon/sulphur metabolism mediated by autotrophic bacterial communities in terrestrial soil ecosystems. We studied these pathways by analysing the distribution and abundance of the diagnostic metabolic marker genes cbbM, apsA and soxB, which encode for ribulose-1,5-bisphosphate carboxylase/oxygenase, adenosine phosphosulphate reductase and sulphate thiohydrolase, respectively, among different contrasting soil types. Additionally, the abundance of community members was assessed by quantifying the gene copy numbers for 16S rRNA, cbbL, cbbM, apsA and soxB. Distinct compositional differences were observed among the clone libraries, which revealed a dominance of phylotypes associated with carbon and sulphur cycling, such as Gammaproteobacteria (Thiohalomonas, Allochromatium, Chromatium, Thiomicrospira) and Alphaproteobacteria (Rhodopseudomonas, Rhodovulum, Paracoccus). The rhizosphere soil was devoid of sulphur metabolism, as the soxB and apsA genes were not observed in the rhizosphere metagenome, which suggests the absence or inadequate representation of sulphur-oxidising bacteria. We hypothesise that the novel Gammaproteobacteria sulphur oxidisers might be actively involved in sulphur oxidation and inorganic carbon fixation, particularly in barren saline soil ecosystems, suggesting their significant putative ecological role and contribution to the soil carbon pool.}, } @article {pmid25223851, year = {2014}, author = {Zhi, W and Ge, Z and He, Z and Zhang, H}, title = {Methods for understanding microbial community structures and functions in microbial fuel cells: a review.}, journal = {Bioresource technology}, volume = {171}, number = {}, pages = {461-468}, doi = {10.1016/j.biortech.2014.08.096}, pmid = {25223851}, issn = {1873-2976}, mesh = {Bioelectric Energy Sources/*microbiology ; Electrochemical Techniques/*methods ; Electrodes/microbiology ; Genomics/*methods ; Microbiota/*genetics/*physiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbial fuel cells (MFCs) employ microorganisms to recover electric energy from organic matter. However, fundamental knowledge of electrochemically active bacteria is still required to maximize MFCs power output for practical applications. This review presents microbiological and electrochemical techniques to help researchers choose the appropriate methods for the MFCs study. Pre-genomic and genomic techniques such as 16S rRNA based phylogeny and metagenomics have provided important information in the structure and genetic potential of electrode-colonizing microbial communities. Post-genomic techniques such as metatranscriptomics allow functional characterizations of electrode biofilm communities by quantifying gene expression levels. Isotope-assisted phylogenetic analysis can further link taxonomic information to microbial metabolisms. A combination of electrochemical, phylogenetic, metagenomic, and post-metagenomic techniques offers opportunities to a better understanding of the extracellular electron transfer process, which in turn can lead to process optimization for power output.}, } @article {pmid25223021, year = {2014}, author = {Wang, SJ and Liu, JA and He, YH and Zhou, GY and Tan, YM and Zhou, JC}, title = {[Soil microfauna diversity among Cunninghamia lanceolata plantations based on pyrosequencing].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {25}, number = {6}, pages = {1661-1668}, pmid = {25223021}, issn = {1001-9332}, mesh = {Animals ; Annelida ; Arthropods ; *Biodiversity ; China ; *Cunninghamia ; *Forests ; *Invertebrates ; Nematoda ; Platyhelminths ; Rotifera ; *Soil ; Trees ; }, abstract = {In order to study the function of soil microfauna and its responses to environmental changes, we used metagenome analyses of the 18S rDNA gene region to identify differences in microfauna diversity and community structure among fifteen soil samples belonging to five different Cunninghamia lanceolate plantations. The plantations were located in Youxian County, Hunan Province in central China. The trees in these plantations were of different ages (3, 13, and 26 years) and belonged to different ecological successions (first, second, and third successions). The total dataset comprised 94922 high quality sequences with an average length of 436 bp. The dominant taxonomic groups across all samples were Chordata, Annelida, Arthropoda, Nematoda, Rotifera and Platyhelminthes with each accounting for 60.8%, 24.0%, 7.4%, 3.6%, 1.5% and 1.2% of the sequences, respectively. There were significant differences in ACE index and Shannon index among the five plantations. The lowest diversity of soil microfauna was in the 13-year old plantation of the first ecological succession. The correlation analysis showed that both ACE and available potassium concentration were negatively correlated to the Chaol index. However, there were no significant correlations between the Shannon, Simpson indices and the physical-chemical properties of soil. Overall, the Jaccard's similarity coefficient was less than 0.4 among samples at each site, and significant differences were found among plantations.}, } @article {pmid25222254, year = {2014}, author = {Wang, ZH and Yang, JQ and Zhang, DJ and Zhou, J and Zhang, CD and Su, XR and Li, TW}, title = {Composition and structure of microbial communities associated with different domestic sewage outfalls.}, journal = {Genetics and molecular research : GMR}, volume = {13}, number = {3}, pages = {7542-7552}, doi = {10.4238/2014.September.12.21}, pmid = {25222254}, issn = {1676-5680}, mesh = {Bacteria/classification/genetics ; Biodiversity ; China ; Cluster Analysis ; *Environmental Microbiology ; Geography ; Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Sewage/*microbiology ; }, abstract = {The diversity of microbiota in waste waters has not been thoroughly examined, despite the potential impact of microbes on effluent quality. Wastewater microbial communities harbor pathogenic bacteria, viruses, and parasites. To study microbial communities in domestic sewage outfalls, 454 pyrosequencing technology was used to investigate the composition of microbial communities associated with municipal wastewater during different seasons sampled over the course of one year. A total of 195,103 16S rRNA gene sequences were obtained from 20 samples. The R software was used to calculate the number of indices describing the alpha diversity associated with each bacterial assemblage. In this study, the a-diversity index (H', D, J), in which higher numbers represent more diversity, was found to change with seasonal cycle. The diversity of bacterial assemblages was high in all samples, indicating that species diversity was also very high. The taxonomic composition of the assemblages varied considerably among samples, with some dominated by Proteobacteria, while others were dominated by Bacteroidetes or Firmicutes. In 2 samples, the relative prevalence of Proteobacteria exceeded 90%. α-Proteobacteria, b-proteobacteria, and g-proteobacteria represented 90% or more of all Proteobacteria. The present characterization of wastewater from five sewage outfalls indicated the presence of some pathogenic bacteria. The g-Proteobacteria in sewage wastefalls identified in this study included Enterobacteriaceae, Vibrionaceae, Pseudomonadaceae, Salmonella, Yersinia, Vibrio, and Pseudomonas aeruginosa.}, } @article {pmid25218180, year = {2014}, author = {Alneberg, J and Bjarnason, BS and de Bruijn, I and Schirmer, M and Quick, J and Ijaz, UZ and Lahti, L and Loman, NJ and Andersson, AF and Quince, C}, title = {Binning metagenomic contigs by coverage and composition.}, journal = {Nature methods}, volume = {11}, number = {11}, pages = {1144-1146}, pmid = {25218180}, issn = {1548-7105}, support = {MR/J014370/1/MRC_/Medical Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Algorithms ; Bifidobacterium/genetics ; Contig Mapping/*methods ; Escherichia coli K12/genetics ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Genome, Bacterial/*genetics ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; Shiga-Toxigenic Escherichia coli/genetics ; *Software ; }, abstract = {Shotgun sequencing enables the reconstruction of genomes from complex microbial communities, but because assembly does not reconstruct entire genomes, it is necessary to bin genome fragments. Here we present CONCOCT, a new algorithm that combines sequence composition and coverage across multiple samples, to automatically cluster contigs into genomes. We demonstrate high recall and precision on artificial as well as real human gut metagenome data sets.}, } @article {pmid25217724, year = {2014}, author = {Henriet, O and Fourmentin, J and Delincé, B and Mahillon, J}, title = {Exploring the diversity of extremely halophilic archaea in food-grade salts.}, journal = {International journal of food microbiology}, volume = {191}, number = {}, pages = {36-44}, doi = {10.1016/j.ijfoodmicro.2014.08.019}, pmid = {25217724}, issn = {1879-3460}, mesh = {*Biodiversity ; *Food Microbiology ; Halobacteriaceae/*classification/genetics/*isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Salts ; }, abstract = {Salting is one of the oldest means of food preservation: adding salt decreases water activity and inhibits microbial development. However, salt is also a source of living bacteria and archaea. The occurrence and diversity of viable archaea in this extreme environment were assessed in 26 food-grade salts from worldwide origin by cultivation on four culture media. Additionally, metagenomic analysis of 16S rRNA gene was performed on nine salts. Viable archaea were observed in 14 salts and colony counts reached more than 10(5)CFU per gram in three salts. All archaeal isolates identified by 16S rRNA gene sequencing belonged to the Halobacteriaceae family and were related to 17 distinct genera among which Haloarcula, Halobacterium and Halorubrum were the most represented. High-throughput sequencing generated extremely different profiles for each salt. Four of them contained a single major genus (Halorubrum, Halonotius or Haloarcula) while the others had three or more genera of similar occurrence. The number of distinct genera per salt ranged from 21 to 27. Halorubrum had a significant contribution to the archaeal diversity in seven salts; this correlates with its frequent occurrence in crystallization ponds. On the contrary, Haloquadratum walsbyi, the halophilic archaea most commonly found in solar salterns, was a minor actor of the food-grade salt diversity. Our results indicate that the occurrence and diversity of viable halophilic archaea in salt can be important, while their fate in the gastrointestinal tract after ingestion remains largely unknown.}, } @article {pmid25215495, year = {2014}, author = {Donia, MS and Cimermancic, P and Schulze, CJ and Wieland Brown, LC and Martin, J and Mitreva, M and Clardy, J and Linington, RG and Fischbach, MA}, title = {A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics.}, journal = {Cell}, volume = {158}, number = {6}, pages = {1402-1414}, pmid = {25215495}, issn = {1097-4172}, support = {R01 AI101018/AI/NIAID NIH HHS/United States ; DP2 OD007290/OD/NIH HHS/United States ; R01 DK101674/DK/NIDDK NIH HHS/United States ; T32 GM067547/GM/NIGMS NIH HHS/United States ; R21 AI101722/AI/NIAID NIH HHS/United States ; P50 GM081879/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacteria/*chemistry/classification/*genetics/metabolism ; Biosynthetic Pathways ; Gastrointestinal Tract/microbiology ; Humans ; Metagenomics/*methods ; *Microbiota ; Molecular Sequence Data ; Mouth/microbiology ; Multigene Family ; Peptide Biosynthesis, Nucleic Acid-Independent ; Polyketides/analysis ; }, abstract = {In complex biological systems, small molecules often mediate microbe-microbe and microbe-host interactions. Using a systematic approach, we identified 3,118 small-molecule biosynthetic gene clusters (BGCs) in genomes of human-associated bacteria and studied their representation in 752 metagenomic samples from the NIH Human Microbiome Project. Remarkably, we discovered that BGCs for a class of antibiotics in clinical trials, thiopeptides, are widely distributed in genomes and metagenomes of the human microbiota. We purified and solved the structure of a thiopeptide antibiotic, lactocillin, from a prominent member of the vaginal microbiota. We demonstrate that lactocillin has potent antibacterial activity against a range of Gram-positive vaginal pathogens, and we show that lactocillin and other thiopeptide BGCs are expressed in vivo by analyzing human metatranscriptomic sequencing data. Our findings illustrate the widespread distribution of small-molecule-encoding BGCs in the human microbiome, and they demonstrate the bacterial production of drug-like molecules in humans. PAPERCLIP:}, } @article {pmid25213854, year = {2014}, author = {Zhu, J and Zheng, WM}, title = {Self-organizing approach for meta-genomes.}, journal = {Computational biology and chemistry}, volume = {53 Pt A}, number = {}, pages = {118-124}, doi = {10.1016/j.compbiolchem.2014.08.016}, pmid = {25213854}, issn = {1476-928X}, mesh = {Chromosome Mapping/methods/*statistics & numerical data ; *Codon ; Feces/chemistry/microbiology ; Gastrointestinal Tract/microbiology ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; Microbiota/genetics ; Molecular Sequence Annotation ; Sequence Analysis, DNA/*statistics & numerical data ; }, abstract = {We extend the self-organizing approach for annotation of a bacterial genome to analyze the raw sequencing data of the human gut metagenome without sequence assembling. The original approach divides the genomic sequence of a bacterium into non-overlapping segments of equal length and assigns to each segment one of seven 'phases', among which one is for the noncoding regions, three for the direct coding regions to indicate the three possible codon positions of the segment starting site, and three for the reverse coding regions. The noncoding phase and the six coding phases are described by two frequency tables of the 64 triplet types or 'codon usages'. A set of codon usages can be used to update the phase assignment and vice versa. An iteration after an initialization leads to a convergent phase assignment to give an annotation of the genome. In the extension of the approach to a metagenome, we consider a mixture model of a number of categories described by different codon usages. The Illumina Genome Analyzer sequencing data of the total DNA from faecal samples are then examined to understand the diversity of the human gut microbiome.}, } @article {pmid25213620, year = {2014}, author = {Perry, JA and Wright, GD}, title = {Forces shaping the antibiotic resistome.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {36}, number = {12}, pages = {1179-1184}, doi = {10.1002/bies.201400128}, pmid = {25213620}, issn = {1521-1878}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics ; Drug Resistance, Bacterial/drug effects/*genetics ; Environmental Monitoring ; Environmental Pollution/prevention & control ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Metagenomics ; Microbiota/genetics ; Mutation ; Selection, Genetic ; *Soil Microbiology ; }, abstract = {Antibiotic resistance has become a problem of global scale. Resistance arises through mutation or through the acquisition of resistance gene(s) from other bacteria in a process called horizontal gene transfer (HGT). While HGT is recognized as an important factor in the dissemination of resistance genes in clinical pathogens, its role in the environment has been called into question by a recent study published in Nature. The authors found little evidence of HGT in soil using a culture-independent functional metagenomics approach, which is in contrast to previous work from the same lab showing HGT between the environment and human microbiome. While surprising at face value, these results may be explained by the lack of selective pressure in the environment studied. Importantly, this work suggests the need for careful monitoring of environmental antibiotic pollution and stringent antibiotic stewardship in the fight against resistance.}, } @article {pmid25210772, year = {2014}, author = {Engel, P and Stepanauskas, R and Moran, NA}, title = {Hidden diversity in honey bee gut symbionts detected by single-cell genomics.}, journal = {PLoS genetics}, volume = {10}, number = {9}, pages = {e1004596}, pmid = {25210772}, issn = {1553-7404}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bacteria/*genetics ; Bees/*genetics/*microbiology ; Biodiversity ; Gastrointestinal Tract/*microbiology ; Genomics/methods ; Metagenome/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Symbiosis/*genetics ; }, abstract = {Microbial communities in animal guts are composed of diverse, specialized bacterial species, but little is known about how gut bacteria diversify to produce genetically and ecologically distinct entities. The gut microbiota of the honey bee, Apis mellifera, presents a useful model, because it consists of a small number of characteristic bacterial species, each showing signs of diversification. Here, we used single-cell genomics to study the variation within two species of the bee gut microbiota: Gilliamella apicola and Snodgrassella alvi. For both species, our analyses revealed extensive variation in intraspecific divergence of protein-coding genes but uniformly high levels of 16S rRNA similarity. In both species, the divergence of 16S rRNA loci appears to have been curtailed by frequent recombination within populations, while other genomic regions have continuously diverged. Furthermore, gene repertoires differ markedly among strains in both species, implying distinct metabolic capabilities. Our results show that, despite minimal divergence at 16S rRNA genes, in situ diversification occurs within gut communities and generates bacterial lineages with distinct ecological niches. Therefore, important dimensions of microbial diversity are not evident from analyses of 16S rRNA, and single cell genomics has potential to elucidate processes of bacterial diversification.}, } @article {pmid25209713, year = {2014}, author = {Veiga, P and Pons, N and Agrawal, A and Oozeer, R and Guyonnet, D and Brazeilles, R and Faurie, JM and van Hylckama Vlieg, JE and Houghton, LA and Whorwell, PJ and Ehrlich, SD and Kennedy, SP}, title = {Changes of the human gut microbiome induced by a fermented milk product.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {6328}, pmid = {25209713}, issn = {2045-2322}, mesh = {Bifidobacterium/growth & development ; Bilophila/growth & development ; Butyrates/metabolism ; *Cultured Milk Products ; Diet ; Feces/microbiology ; Food Microbiology ; Humans ; Irritable Bowel Syndrome/*microbiology ; Lactobacillus delbrueckii/growth & development ; Lactococcus lactis/growth & development ; Microbiota/*genetics ; *Probiotics ; RNA, Ribosomal, 16S/genetics ; Stomach/*microbiology ; Streptococcus thermophilus/growth & development ; }, abstract = {The gut microbiota (GM) consists of resident commensals and transient microbes conveyed by the diet but little is known about the role of the latter on GM homeostasis. Here we show, by a conjunction of quantitative metagenomics, in silico genome reconstruction and metabolic modeling, that consumption of a fermented milk product containing dairy starters and Bifidobacterium animalis potentiates colonic short chain fatty acids production and decreases abundance of a pathobiont Bilophila wadsworthia compared to a milk product in subjects with irritable bowel syndrome (IBS, n = 28). The GM changes parallel improvement of IBS state, suggesting a role of the fermented milk bacteria in gut homeostasis. Our data challenge the view that microbes ingested with food have little impact on the human GM functioning and rather provide support for beneficial health effects.}, } @article {pmid25208077, year = {2014}, author = {Ilmberger, N and Güllert, S and Dannenberg, J and Rabausch, U and Torres, J and Wemheuer, B and Alawi, M and Poehlein, A and Chow, J and Turaev, D and Rattei, T and Schmeisser, C and Salomon, J and Olsen, PB and Daniel, R and Grundhoff, A and Borchert, MS and Streit, WR}, title = {A comparative metagenome survey of the fecal microbiota of a breast- and a plant-fed Asian elephant reveals an unexpectedly high diversity of glycoside hydrolase family enzymes.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e106707}, pmid = {25208077}, issn = {1932-6203}, mesh = {Animals ; Biomass ; *Breast Feeding ; Data Collection ; Elephants/*microbiology ; Feces/*microbiology ; Female ; Glycoside Hydrolases/genetics/*metabolism ; Male ; *Metagenomics ; *Microbiota ; Phylogeny ; *Plants ; }, abstract = {A phylogenetic and metagenomic study of elephant feces samples (derived from a three-weeks-old and a six-years-old Asian elephant) was conducted in order to describe the microbiota inhabiting this large land-living animal. The microbial diversity was examined via 16S rRNA gene analysis. We generated more than 44,000 GS-FLX+454 reads for each animal. For the baby elephant, 380 operational taxonomic units (OTUs) were identified at 97% sequence identity level; in the six-years-old animal, close to 3,000 OTUs were identified, suggesting high microbial diversity in the older animal. In both animals most OTUs belonged to Bacteroidetes and Firmicutes. Additionally, for the baby elephant a high number of Proteobacteria was detected. A metagenomic sequencing approach using Illumina technology resulted in the generation of 1.1 Gbp assembled DNA in contigs with a maximum size of 0.6 Mbp. A KEGG pathway analysis suggested high metabolic diversity regarding the use of polymers and aromatic and non-aromatic compounds. In line with the high phylogenetic diversity, a surprising and not previously described biodiversity of glycoside hydrolase (GH) genes was found. Enzymes of 84 GH families were detected. Polysaccharide utilization loci (PULs), which are found in Bacteroidetes, were highly abundant in the dataset; some of these comprised cellulase genes. Furthermore the highest coverage for GH5 and GH9 family enzymes was detected for Bacteroidetes, suggesting that bacteria of this phylum are mainly responsible for the degradation of cellulose in the Asian elephant. Altogether, this study delivers insight into the biomass conversion by one of the largest plant-fed and land-living animals.}, } @article {pmid25207979, year = {2014}, author = {Cano, RJ and Rivera-Perez, J and Toranzos, GA and Santiago-Rodriguez, TM and Narganes-Storde, YM and Chanlatte-Baik, L and García-Roldán, E and Bunkley-Williams, L and Massey, SE}, title = {Paleomicrobiology: revealing fecal microbiomes of ancient indigenous cultures.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e106833}, pmid = {25207979}, issn = {1932-6203}, support = {R25 GM061151/GM/NIGMS NIH HHS/United States ; 5R25GM061151-12/GM/NIGMS NIH HHS/United States ; }, mesh = {Diet ; Feces/*microbiology/parasitology ; Humans ; *Microbiology ; *Microbiota ; *Paleontology ; *Population Groups ; Puerto Rico/ethnology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Coprolites are fossilized feces that can be used to provide information on the composition of the intestinal microbiota and, as we show, possibly on diet. We analyzed human coprolites from the Huecoid and Saladoid cultures from a settlement on Vieques Island, Puerto Rico. While more is known about the Saladoid culture, it is believed that both societies co-existed on this island approximately from 5 to 1170 AD. By extracting DNA from the coprolites, followed by metagenomic characterization, we show that both cultures can be distinguished from each other on the basis of their bacterial and fungal gut microbiomes. In addition, we show that parasite loads were heavy and also culturally distinct. Huecoid coprolites were characterized by maize and Basidiomycetes sequences, suggesting that these were important components of their diet. Saladoid coprolite samples harbored sequences associated with fish parasites, suggesting that raw fish was a substantial component of their diet. The present study shows that ancient DNA is not entirely degraded in humid, tropical environments, and that dietary and/or host genetic differences in ancient populations may be reflected in the composition of their gut microbiome. This further supports the hypothesis that the two ancient cultures studied were distinct, and that they retained distinct technological/cultural differences during an extended period of close proximity and peaceful co-existence. The two populations seemed to form the later-day Taínos, the Amerindians present at the point of Columbian contact. Importantly, our data suggest that paleomicrobiomics can be a powerful tool to assess cultural differences between ancient populations.}, } @article {pmid25205599, year = {2014}, author = {Koo, H and Mojib, N and Thacker, RW and Bej, AK}, title = {Comparative analysis of bacterial community-metagenomics in coastal Gulf of Mexico sediment microcosms following exposure to Macondo oil (MC252).}, journal = {Antonie van Leeuwenhoek}, volume = {106}, number = {5}, pages = {993-1009}, doi = {10.1007/s10482-014-0268-3}, pmid = {25205599}, issn = {1572-9699}, support = {P30AU027767//PHS HHS/United States ; }, mesh = {Biota/*drug effects ; Biotransformation ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/*microbiology ; Gulf of Mexico ; Metabolic Networks and Pathways/genetics ; Metagenomics ; Molecular Sequence Data ; Oils/metabolism ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/metabolism ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The indigenous bacterial communities in sediment microcosms from Dauphin Island (DI), Petit Bois Island (PB) and Perdido Pass (PP) of the coastal Gulf of Mexico were compared following treatment with Macondo oil (MC252) using pyrosequencing and culture-based approaches. After quality-based trimming, 28,991 partial 16S rRNA sequence reads were analyzed by rarefaction, confirming that analyses of bacterial communities were saturated with respect to species diversity. Changes in the relative abundances of Proteobacteria, Bacteroidetes and Firmicutes played an important role in structuring bacterial communities in oil-treated sediments. Proteobacteria were dominant in oil-treated samples, whereas Firmicutes and Bacteroidetes were either the second or the third most abundant taxa. Tenericutes, members of which are known for oil biodegradation, were detected shortly after treatment, and continued to increase in DI and PP sediments. Multivariate statistical analyses (ADONIS) revealed significant dissimilarity of bacterial communities between oil-treated and untreated samples and among locations. In addition, a similarity percentage analysis showed the contribution of each species to the contrast between untreated and oil-treated samples. PCR amplification using DNA from pure cultures of Exiguobacterium, Pseudoalteromonas, Halomonas and Dyadobacter, isolated from oil-treated microcosm sediments, produced amplicons similar to polycyclic aromatic hydrocarbon-degrading genes. In the context of the 2010 Macondo blowout, the results from our study demonstrated that the indigenous bacterial communities in coastal Gulf of Mexico sediment microcosms responded to the MC252 oil with altered community structure and species composition. The rapid proliferation of hydrocarbonoclastic bacteria suggests their involvement in the degradation of the spilt oil in the Gulf of Mexico ecosystem.}, } @article {pmid25205422, year = {2015}, author = {Alves Junior, N and Meirelles, PM and de Oliveira Santos, E and Dutilh, B and Silva, GG and Paranhos, R and Cabral, AS and Rezende, C and Iida, T and de Moura, RL and Kruger, RH and Pereira, RC and Valle, R and Sawabe, T and Thompson, C and Thompson, F}, title = {Microbial community diversity and physical-chemical features of the Southwestern Atlantic Ocean.}, journal = {Archives of microbiology}, volume = {197}, number = {2}, pages = {165-179}, doi = {10.1007/s00203-014-1035-6}, pmid = {25205422}, issn = {1432-072X}, mesh = {Antarctic Regions ; Atlantic Ocean ; *Biodiversity ; Metagenome/*genetics ; Microbiota/*genetics ; Seawater/*chemistry/*microbiology ; Temperature ; }, abstract = {Microbial oceanography studies have demonstrated the central role of microbes in functioning and nutrient cycling of the global ocean. Most of these former studies including at Southwestern Atlantic Ocean (SAO) focused on surface seawater and benthic organisms (e.g., coral reefs and sponges). This is the first metagenomic study of the SAO. The SAO harbors a great microbial diversity and marine life (e.g., coral reefs and rhodolith beds). The aim of this study was to characterize the microbial community diversity of the SAO along the depth continuum and different water masses by means of metagenomic, physical-chemical and biological analyses. The microbial community abundance and diversity appear to be strongly influenced by the temperature, dissolved organic carbon, and depth, and three groups were defined [1. surface waters; 2. sub-superficial chlorophyll maximum (SCM) (48-82 m) and 3. deep waters (236-1,200 m)] according to the microbial composition. The microbial communities of deep water masses [South Atlantic Central water, Antarctic Intermediate water and Upper Circumpolar Deep water] are highly similar. Of the 421,418 predicted genes for SAO metagenomes, 36.7 % had no homologous hits against 17,451,486 sequences from the North Atlantic, South Atlantic, North Pacific, South Pacific and Indian Oceans. From these unique genes from the SAO, only 6.64 % had hits against the NCBI non-redundant protein database. SAO microbial communities share genes with the global ocean in at least 70 cellular functions; however, more than a third of predicted SAO genes represent a unique gene pool in global ocean. This study was the first attempt to characterize the taxonomic and functional community diversity of different water masses at SAO and compare it with the microbial community diversity of the global ocean, and SAO had a significant portion of endemic gene diversity. Microbial communities of deep water masses (236-1,200 m) are highly similar, suggesting that these water masses have very similar microbiological attributes, despite the common knowledge that water masses determine prokaryotic community and are barriers to microbial dispersal. The present study also shows that SCM is a clearly differentiated layer within Tropical waters with higher abundance of phototrophic microbes and microbial diversity.}, } @article {pmid25204516, year = {2014}, author = {Kreisinger, J and Cížková, D and Vohánka, J and Piálek, J}, title = {Gastrointestinal microbiota of wild and inbred individuals of two house mouse subspecies assessed using high-throughput parallel pyrosequencing.}, journal = {Molecular ecology}, volume = {23}, number = {20}, pages = {5048-5060}, doi = {10.1111/mec.12909}, pmid = {25204516}, issn = {1365-294X}, mesh = {Animals ; Animals, Wild/microbiology ; Bacteria/classification ; DNA Barcoding, Taxonomic ; Gastrointestinal Tract/*microbiology ; *Genetic Variation ; Metagenome ; Mice ; Mice, Inbred Strains/*microbiology ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The effects of gastrointestinal tract microbiota (GTM) on host physiology and health have been the subject of considerable interest in recent years. While a variety of captive bred species have been used in experiments, the extent to which GTM of captive and/or inbred individuals resembles natural composition and variation in wild populations is poorly understood. Using 454 pyrosequencing, we performed 16S rDNA GTM barcoding for 30 wild house mice (Mus musculus) and wild-derived inbred strain mice belonging to two subspecies (M. m. musculus and M. m. domesticus). Sequenced individuals were selected according to a 2 × 2 experimental design: wild (14) vs. inbred origin (16) and M. m. musculus (15) vs. M. m. domesticus (15). We compared alpha diversity (i.e. number of operational taxonomic units - OTUs), beta diversity (i.e. interindividual variability) and microbiota composition across the four groups. We found no difference between M. m. musculus and M. m. domesticus subspecies, suggesting low effect of genetic differentiation between these two subspecies on GTM structure. Both inbred and wild populations showed the same level of microbial alpha and beta diversity; however, we found strong differentiation in microbiota composition between wild and inbred populations. Relative abundance of ~ 16% of OTUs differed significantly between wild and inbred individuals. As laboratory mice represent the most abundant model for studying the effects of gut microbiota on host metabolism, immunity and neurology, we suggest that the distinctness of laboratory-kept mouse microbiota, which differs from wild mouse microbiota, needs to be considered in future biomedical research.}, } @article {pmid25204351, year = {2014}, author = {Oliveira, V and Gomes, NC and Cleary, DF and Almeida, A and Silva, AM and Simões, MM and Silva, H and Cunha, Â}, title = {Halophyte plant colonization as a driver of the composition of bacterial communities in salt marshes chronically exposed to oil hydrocarbons.}, journal = {FEMS microbiology ecology}, volume = {90}, number = {3}, pages = {647-662}, doi = {10.1111/1574-6941.12425}, pmid = {25204351}, issn = {1574-6941}, mesh = {Alphaproteobacteria/classification/metabolism ; Amaranthaceae/microbiology/physiology ; Bacteria/*classification/genetics/isolation & purification ; Base Sequence ; Biodegradation, Environmental ; Denaturing Gradient Gel Electrophoresis ; Geologic Sediments/microbiology ; Hydrocarbons/*metabolism ; Metagenome/genetics ; Microbial Consortia/genetics ; *Petroleum Pollution ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Salt-Tolerant Plants/microbiology/*physiology ; Sequence Analysis, DNA ; *Wetlands ; }, abstract = {In this study, two molecular techniques [denaturing gradient gel electrophoresis (DGGE) and barcoded pyrosequencing] were used to evaluate the composition of bacterial communities in salt marsh microhabitats [bulk sediment and sediment surrounding the roots (rhizosphere) of Halimione portulacoides and Sarcocornia perennis ssp. perennis] that have been differentially affected by oil hydrocarbon (OH) pollution. Both DGGE and pyrosequencing revealed that bacterial composition is structured by microhabitat. Rhizosphere sediment from both plant species revealed enrichment of operational taxonomic units closely related to Acidimicrobiales, Myxococcales and Sphingomonadales. The in silico metagenome analyses suggest that homologous genes related to OH degradation appeared to be more frequent in both plant rhizospheres than in bulk sediment. In summary, this study suggests that halophyte plant colonization is an important driver of hydrocarbonoclastic bacterial community composition in estuarine environments, which can be exploited for in situ phytoremediation of OH in salt marsh environments.}, } @article {pmid25194233, year = {2014}, author = {Aguirre, M and Ramiro-Garcia, J and Koenen, ME and Venema, K}, title = {To pool or not to pool? Impact of the use of individual and pooled fecal samples for in vitro fermentation studies.}, journal = {Journal of microbiological methods}, volume = {107}, number = {}, pages = {1-7}, doi = {10.1016/j.mimet.2014.08.022}, pmid = {25194233}, issn = {1872-8359}, mesh = {Acetates/metabolism ; Adult ; Biodiversity ; Butyrates/metabolism ; Feces/*microbiology ; Female ; *Fermentation ; Humans ; *In Vitro Techniques ; Male ; Metagenome ; *Microbiota ; Middle Aged ; Phylogeny ; Propionates/metabolism ; Time Factors ; }, abstract = {This study investigated the stability and the activity of the microbiota from a single and a pool of donors in the TNO in vitro model of the colon (TIM-2 system). Our findings demonstrate the suitability of the preparation of a pool of fecal sample to be used for fermentation experiments.}, } @article {pmid25185007, year = {2014}, author = {Villegas, LM and Pimenta, PF}, title = {Metagenomics, paratransgenesis and the Anopheles microbiome: a portrait of the geographical distribution of the anopheline microbiota based on a meta-analysis of reported taxa.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {109}, number = {5}, pages = {672-684}, pmid = {25185007}, issn = {1678-8060}, mesh = {Animals ; Anopheles/*genetics/*microbiology ; Geography, Medical ; Insect Vectors/*genetics ; *Metagenomics ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Anophelines harbour a diverse microbial consortium that may represent an extended gene pool for the host. The proposed effects of the insect microbiota span physiological, metabolic and immune processes. Here we synthesise how current metagenomic tools combined with classical culture-dependent techniques provide new insights in the elucidation of the role of the Anopheles-associated microbiota. Many proposed malaria control strategies have been based upon the immunomodulating effects that the bacterial components of the microbiota appear to exert and their ability to express anti-Plasmodium peptides. The number of identified bacterial taxa has increased in the current "omics" era and the available data are mostly scattered or in "tables" that are difficult to exploit. Published microbiota reports for multiple anopheline species were compiled in an Excel® spreadsheet. We then filtered the microbiota data using a continent-oriented criterion and generated a visual correlation showing the exclusive and shared bacterial genera among four continents. The data suggested the existence of a core group of bacteria associated in a stable manner with their anopheline hosts. However, the lack of data from Neotropical vectors may reduce the possibility of defining the core microbiota and understanding the mosquito-bacteria interactive consortium.}, } @article {pmid25181646, year = {2014}, author = {Shah, JD and Baller, J and Zhang, Y and Silverstein, K and Xing, Z and Cardona, CJ}, title = {Comparison of tissue sample processing methods for harvesting the viral metagenome and a snapshot of the RNA viral community in a turkey gut.}, journal = {Journal of virological methods}, volume = {209}, number = {}, pages = {15-24}, pmid = {25181646}, issn = {1879-0984}, mesh = {Animals ; *Biota ; Gastrointestinal Tract/*virology ; Metagenomics/*methods ; RNA Viruses/genetics/*isolation & purification ; RNA, Viral/genetics/*isolation & purification ; Specimen Handling/*methods ; Turkeys ; }, abstract = {RNA viruses have been associated with enteritis in poultry and have been isolated from diseased birds. The same viral agents have also been detected in healthy flocks bringing into question their role in health and disease. In order to understand better eukaryotic viruses in the gut, this project focused on evaluating alternative methods to purify and concentrate viral particles, which do not involve the use of density gradients, for generating viral metagenome data. In this study, the sequence outcomes of three tissue processing methods have been evaluated and a data analysis pipeline has been established for RNA viruses from the gastrointestinal tract. In addition, with the use of the best method and increased sequencing depth, a glimpse of the RNA viral community in the gastrointestinal tract of a clinically normal 5-week old turkey is presented. The viruses from the Reoviridae and Astroviridae families together accounted for 76.3% of total viruses identified. The rarefaction curve at the species level further indicated that majority of the species diversity was included with the increased sequencing depth, implying that viruses from other viral families were present in very low abundance.}, } @article {pmid25179593, year = {2014}, author = {Chen, Y and Qin, N and Guo, J and Qian, G and Fang, D and Shi, D and Xu, M and Yang, F and He, Z and Van Nostrand, JD and Yuan, T and Deng, Y and Zhou, J and Li, L}, title = {Functional gene arrays-based analysis of fecal microbiomes in patients with liver cirrhosis.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {753}, pmid = {25179593}, issn = {1471-2164}, mesh = {Adult ; Aged ; Alcohols/adverse effects ; Biodiversity ; Cluster Analysis ; Feces/*microbiology ; Female ; Gene-Environment Interaction ; Genetic Variation ; Humans ; *Liver Cirrhosis/etiology ; Male ; *Metagenome/drug effects ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; }, abstract = {BACKGROUND: Human gut microbiota plays an important role in the pathogenesis of cirrhosis complications. Although the phylogenetic diversity of intestinal microbiota in patients with liver cirrhosis has been examined in several studies, little is known about their functional composition and structure.

RESULTS: To characterize the functional gene diversity of the gut microbiome in cirrhotic patients, we recruited a total of 42 individuals, 12 alcoholic cirrhosis patients, 18 hepatitis B virus (HBV)-related cirrhosis patients, and 12 normal controls. We determined the functional structure of these samples using a specific functional gene array, which is a combination of GeoChip for monitoring biogeochemical processes and HuMiChip specifically designed for analyzing human microbiomes. Our experimental data showed that the microbial community functional composition and structure were dramatically distinctive in the alcoholic cirrhosis. Various microbial functional genes involved in organic remediation, stress response, antibiotic resistance, metal resistance, and virulence were highly enriched in the alcoholic cirrhosis group compared to the control group and HBV-related cirrhosis group. Cirrhosis may have distinct influences on metabolic potential of fecal microbial communities. The abundance of functional genes relevant to nutrient metabolism, including amino acid metabolism, lipid metabolism, nucleotide metabolism, and isoprenoid biosynthesis, were significantly decreased in both alcoholic cirrhosis group and HBV-related cirrhosis group. Significant correlations were observed between functional gene abundances and Child-Pugh scores, such as those encoding aspartate-ammonia ligase, transaldolase, adenylosuccinate synthetase and IMP dehydrogenase.

CONCLUSIONS: Functional gene array was utilized to study the gut microbiome in alcoholic and HBV-related cirrhosis patients and controls in this study. Our array data indicated that the functional composition of fecal microbiomes was heavily influenced by cirrhosis, especially by alcoholic cirrhosis. This study provides new insights into the functional potentials and activity of gut microbiota in cirrhotic patients with different etiologies.}, } @article {pmid25177549, year = {2014}, author = {Peterson, SN and Meissner, T and Su, AI and Snesrud, E and Ong, AC and Schork, NJ and Bretz, WA}, title = {Functional expression of dental plaque microbiota.}, journal = {Frontiers in cellular and infection microbiology}, volume = {4}, number = {}, pages = {108}, pmid = {25177549}, issn = {2235-2988}, support = {UL1TR001114/TR/NCATS NIH HHS/United States ; UL1 TR001114/TR/NCATS NIH HHS/United States ; R01 GM089820/GM/NIGMS NIH HHS/United States ; N01AI15447/AI/NIAID NIH HHS/United States ; R01GM089820/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics/metabolism ; Biofilms ; Child ; Child, Preschool ; Cluster Analysis ; Dental Caries/etiology/pathology ; Dental Plaque/etiology/*microbiology ; Drug Resistance, Bacterial ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Expression Regulation, Bacterial ; Gene Regulatory Networks ; Gene-Environment Interaction ; Genetic Predisposition to Disease ; Humans ; Metagenome ; *Microbiota ; Oxidative Stress ; Phenotype ; Transcription, Genetic ; }, abstract = {Dental caries remains a significant public health problem and is considered pandemic worldwide. The prediction of dental caries based on profiling of microbial species involved in disease and equally important, the identification of species conferring dental health has proven more difficult than anticipated due to high interpersonal and geographical variability of dental plaque microbiota. We have used RNA-Seq to perform global gene expression analysis of dental plaque microbiota derived from 19 twin pairs that were either concordant (caries-active or caries-free) or discordant for dental caries. The transcription profiling allowed us to define a functional core microbiota consisting of nearly 60 species. Similarities in gene expression patterns allowed a preliminary assessment of the relative contribution of human genetics, environmental factors and caries phenotype on the microbiota's transcriptome. Correlation analysis of transcription allowed the identification of numerous functional networks, suggesting that inter-personal environmental variables may co-select for groups of genera and species. Analysis of functional role categories allowed the identification of dominant functions expressed by dental plaque biofilm communities, that highlight the biochemical priorities of dental plaque microbes to metabolize diverse sugars and cope with the acid and oxidative stress resulting from sugar fermentation. The wealth of data generated by deep sequencing of expressed transcripts enables a greatly expanded perspective concerning the functional expression of dental plaque microbiota.}, } @article {pmid25177534, year = {2014}, author = {Lim, YW and Cuevas, DA and Silva, GG and Aguinaldo, K and Dinsdale, EA and Haas, AF and Hatay, M and Sanchez, SE and Wegley-Kelly, L and Dutilh, BE and Harkins, TT and Lee, CC and Tom, W and Sandin, SA and Smith, JE and Zgliczynski, B and Vermeij, MJ and Rohwer, F and Edwards, RA}, title = {Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition.}, journal = {PeerJ}, volume = {2}, number = {}, pages = {e520}, pmid = {25177534}, issn = {2167-8359}, abstract = {Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phosphonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines.}, } @article {pmid25176148, year = {2014}, author = {Manor, O and Levy, R and Borenstein, E}, title = {Mapping the inner workings of the microbiome: genomic- and metagenomic-based study of metabolism and metabolic interactions in the human microbiome.}, journal = {Cell metabolism}, volume = {20}, number = {5}, pages = {742-752}, pmid = {25176148}, issn = {1932-7420}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; }, mesh = {Bacteria/genetics/metabolism ; Computer Simulation ; Fungi/genetics/metabolism ; Humans ; Metabolic Networks and Pathways ; Metabolome ; *Metabolomics/methods ; Metagenome ; *Metagenomics/methods ; Microbial Interactions ; *Microbiota ; Models, Biological ; }, abstract = {The human gut microbiome is a major contributor to human metabolism and health, yet the metabolic processes that are carried out by various community members, the way these members interact with each other and with the host, and the impact of such interactions on the overall metabolic machinery of the microbiome have not yet been mapped. Here, we discuss recent efforts to study the metabolic inner workings of this complex ecosystem. We will specifically highlight two interrelated lines of work, the first aiming to deconvolve the microbiome and to characterize the metabolic capacity of various microbiome species and the second aiming to utilize computational modeling to infer and study metabolic interactions between these species.}, } @article {pmid25172856, year = {2014}, author = {Zablocki, O and van Zyl, L and Adriaenssens, EM and Rubagotti, E and Tuffin, M and Cary, SC and Cowan, D}, title = {High-level diversity of tailed phages, eukaryote-associated viruses, and virophage-like elements in the metaviromes of antarctic soils.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {22}, pages = {6888-6897}, pmid = {25172856}, issn = {1098-5336}, mesh = {Antarctic Regions ; Bacteriophages/classification/genetics/*isolation & purification ; *Biodiversity ; Ecosystem ; Eukaryota/*virology ; Molecular Sequence Data ; Phylogeny ; Satellite Viruses/classification/genetics/*isolation & purification ; *Soil Microbiology ; }, abstract = {The metaviromes of two distinct Antarctic hyperarid desert soil communities have been characterized. Hypolithic communities, cyanobacterium-dominated assemblages situated on the ventral surfaces of quartz pebbles embedded in the desert pavement, showed higher virus diversity than surface soils, which correlated with previous bacterial community studies. Prokaryotic viruses (i.e., phages) represented the largest viral component (particularly Mycobacterium phages) in both habitats, with an identical hierarchical sequence abundance of families of tailed phages (Siphoviridae > Myoviridae > Podoviridae). No archaeal viruses were found. Unexpectedly, cyanophages were poorly represented in both metaviromes and were phylogenetically distant from currently characterized cyanophages. Putative phage genomes were assembled and showed a high level of unaffiliated genes, mostly from hypolithic viruses. Moreover, unusual gene arrangements in which eukaryotic and prokaryotic virus-derived genes were found within identical genome segments were observed. Phycodnaviridae and Mimiviridae viruses were the second-most-abundant taxa and more numerous within open soil. Novel virophage-like sequences (within the Sputnik clade) were identified. These findings highlight high-level virus diversity and novel species discovery potential within Antarctic hyperarid soils and may serve as a starting point for future studies targeting specific viral groups.}, } @article {pmid25172853, year = {2014}, author = {Gies, EA and Konwar, KM and Beatty, JT and Hallam, SJ}, title = {Illuminating microbial dark matter in meromictic Sakinaw Lake.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {21}, pages = {6807-6818}, pmid = {25172853}, issn = {1098-5336}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biota ; British Columbia ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Eukaryota/*classification/genetics ; Lakes/*microbiology ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Despite recent advances in metagenomic and single-cell genomic sequencing to investigate uncultivated microbial diversity and metabolic potential, fundamental questions related to population structure, interactions, and biogeochemical roles of candidate divisions remain. Numerous molecular surveys suggest that stratified ecosystems manifesting anoxic, sulfidic, and/or methane-rich conditions are enriched in these enigmatic microbes. Here we describe diversity, abundance, and cooccurrence patterns of uncultivated microbial communities inhabiting the permanently stratified waters of meromictic Sakinaw Lake, British Columbia, Canada, using 454 sequencing of the small-subunit rRNA gene with three-domain resolution. Operational taxonomic units (OTUs) were affiliated with 64 phyla, including more than 25 candidate divisions. Pronounced trends in community structure were observed for all three domains with eukaryotic sequences vanishing almost completely below the mixolimnion, followed by a rapid and sustained increase in methanogen-affiliated (∼10%) and unassigned (∼60%) archaeal sequences as well as bacterial OTUs affiliated with Chloroflexi (∼22%) and candidate divisions (∼28%). Network analysis revealed highly correlated, depth-dependent cooccurrence patterns between Chloroflexi, candidate divisions WWE1, OP9/JS1, OP8, and OD1, methanogens, and unassigned archaeal OTUs indicating niche partitioning and putative syntrophic growth modes. Indeed, pathway reconstruction using recently published Sakinaw Lake single-cell genomes affiliated with OP9/JS1 and OP8 revealed complete coverage of the Wood-Ljungdahl pathway with potential to drive syntrophic acetate oxidation to hydrogen and carbon dioxide under methanogenic conditions. Taken together, these observations point to previously unrecognized syntrophic networks in meromictic lake ecosystems with the potential to inform design and operation of anaerobic methanogenic bioreactors.}, } @article {pmid25171437, year = {2015}, author = {Jiménez, DJ and Dini-Andreote, F and Ottoni, JR and de Oliveira, VM and van Elsas, JD and Andreote, FD}, title = {Compositional profile of α / β-hydrolase fold proteins in mangrove soil metagenomes: prevalence of epoxide hydrolases and haloalkane dehalogenases in oil-contaminated sites.}, journal = {Microbial biotechnology}, volume = {8}, number = {3}, pages = {604-613}, pmid = {25171437}, issn = {1751-7915}, mesh = {Biodiversity ; Brazil ; Epoxide Hydrolases/*genetics ; *Genetic Variation ; Hydrolases/*genetics ; *Metagenome ; Oils/*analysis ; Phylogeny ; Sequence Homology, Amino Acid ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants/analysis ; Wetlands ; }, abstract = {The occurrence of genes encoding biotechnologically relevant α/β-hydrolases in mangrove soil microbial communities was assessed using data obtained by whole-metagenome sequencing of four mangroves areas, denoted BrMgv01 to BrMgv04, in São Paulo, Brazil. The sequences (215 Mb in total) were filtered based on local amino acid alignments against the Lipase Engineering Database. In total, 5923 unassembled sequences were affiliated with 30 different α/β-hydrolase fold superfamilies. The most abundant predicted proteins encompassed cytosolic hydrolases (abH08; ∼ 23%), microsomal hydrolases (abH09; ∼ 12%) and Moraxella lipase-like proteins (abH04 and abH01; < 5%). Detailed analysis of the genes predicted to encode proteins of the abH08 superfamily revealed a high proportion related to epoxide hydrolases and haloalkane dehalogenases in polluted mangroves BrMgv01-02-03. This suggested selection and putative involvement in local degradation/detoxification of the pollutants. Seven sequences that were annotated as genes for putative epoxide hydrolases and five for putative haloalkane dehalogenases were found in a fosmid library generated from BrMgv02 DNA. The latter enzymes were predicted to belong to Actinobacteria, Deinococcus-Thermus, Planctomycetes and Proteobacteria. Our integrated approach thus identified 12 genes (complete and/or partial) that may encode hitherto undescribed enzymes. The low amino acid identity (< 60%) with already-described genes opens perspectives for both production in an expression host and genetic screening of metagenomes.}, } @article {pmid25170151, year = {2014}, author = {Lax, S and Smith, DP and Hampton-Marcell, J and Owens, SM and Handley, KM and Scott, NM and Gibbons, SM and Larsen, P and Shogan, BD and Weiss, S and Metcalf, JL and Ursell, LK and Vázquez-Baeza, Y and Van Treuren, W and Hasan, NA and Gibson, MK and Colwell, R and Dantas, G and Knight, R and Gilbert, JA}, title = {Longitudinal analysis of microbial interaction between humans and the indoor environment.}, journal = {Science (New York, N.Y.)}, volume = {345}, number = {6200}, pages = {1048-1052}, pmid = {25170151}, issn = {1095-9203}, support = {DP2 DK098089/DK/NIDDK NIH HHS/United States ; P01 DK078669/DK/NIDDK NIH HHS/United States ; T32 GM008759/GM/NIGMS NIH HHS/United States ; DP2-DK-098089/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; U01 HG004866/HG/NHGRI NIH HHS/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; T32 EB009412/EB/NIBIB NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification/genetics/pathogenicity ; Beds/microbiology ; *Family ; Floors and Floorcoverings ; Foot/microbiology ; Hand/microbiology ; *Host-Pathogen Interactions ; *Household Articles ; Humans ; Metagenome ; Microbiota/genetics/*physiology ; Nose/microbiology ; Pets/microbiology ; Surface Properties ; }, abstract = {The bacteria that colonize humans and our built environments have the potential to influence our health. Microbial communities associated with seven families and their homes over 6 weeks were assessed, including three families that moved their home. Microbial communities differed substantially among homes, and the home microbiome was largely sourced from humans. The microbiota in each home were identifiable by family. Network analysis identified humans as the primary bacterial vector, and a Bayesian method significantly matched individuals to their dwellings. Draft genomes of potential human pathogens observed on a kitchen counter could be matched to the hands of occupants. After a house move, the microbial community in the new house rapidly converged on the microbial community of the occupants' former house, suggesting rapid colonization by the family's microbiota.}, } @article {pmid25168749, year = {2015}, author = {Cui, B and Feng, Q and Wang, H and Wang, M and Peng, Z and Li, P and Huang, G and Liu, Z and Wu, P and Fan, Z and Ji, G and Wang, X and Wu, K and Fan, D and Zhang, F}, title = {Fecal microbiota transplantation through mid-gut for refractory Crohn's disease: safety, feasibility, and efficacy trial results.}, journal = {Journal of gastroenterology and hepatology}, volume = {30}, number = {1}, pages = {51-58}, doi = {10.1111/jgh.12727}, pmid = {25168749}, issn = {1440-1746}, mesh = {Adolescent ; Adult ; Aged ; Biological Therapy/*methods ; Child ; Colon/*microbiology ; Crohn Disease/*microbiology/*therapy ; Feasibility Studies ; Feces/*microbiology ; Female ; Humans ; Male ; Metagenome ; *Microbiota/genetics ; Middle Aged ; Pilot Projects ; Treatment Outcome ; Young Adult ; }, abstract = {BACKGROUND AND AIM: The gut microbiota plays a pivotal role in the intestinal diseases. Fecal microbiota transplantation (FMT) might be a rescue therapy for refractory inflammatory bowel disease. This study aimed to evaluate the safety, feasibility, and efficacy of FMT through mid-gut for refractory Crohn's disease (CD).

METHODS: We established standardized laboratory protocol and clinical work flow for FMT. Only refractory CD patients with Harvey-Bradshaw Index (HBI) score ≥ 7 were enrolled for this study. All included patients were treated with single FMT through mid-gut and assessed during follow-up.

RESULTS: Metagenomics analysis showed a high concordance between feces sample and purified fecal microbiota from same donors. Standardized fecal microbiota preparation and clinical flow significantly simplified the practical aspects of FMT. Totally, 30 patients were qualified for the present analysis. The rate of clinical improvement and remission based on clinical activity at the first month was 86.7% (26/30) and 76.7% (23/30), respectively, which was higher than other assessment points within 15-month follow-up. Patients' body weight increased after FMT, and the lipid profile improved as well. FMT also showed a fast and continuous significant effect in relieving the sustaining abdominal pain associated with sustaining CD.

CONCLUSION: This is a pilot study with the largest sample of patients with refractory CD who underwent single FMT. The results demonstrated that FMT through mid-gut might be a safe, feasible, and efficient rescue therapy for refractory CD.}, } @article {pmid25168269, year = {2014}, author = {Sekar, S and Zintchem, AA and Keshri, J and Kamika, I and Momba, MN}, title = {Bacterial profiling in brine samples of the Emalahleni Water Reclamation Plant, South Africa, using 454-pyrosequencing method.}, journal = {FEMS microbiology letters}, volume = {359}, number = {1}, pages = {55-63}, doi = {10.1111/1574-6968.12557}, pmid = {25168269}, issn = {1574-6968}, mesh = {Bacteria/*classification/*genetics ; *Biota ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing ; Hydrogen-Ion Concentration ; Metagenomics ; Salinity ; Salts/chemistry ; Sequence Analysis, DNA ; South Africa ; Water Purification ; }, abstract = {A metagenomic approach was applied using 454-pyrosequencing data analysis for the profiling of bacterial communities in the brine samples of the water reclamation plant. Some physicochemical characteristics of brine samples were also determined using standard methods. Samples ranged from being lightly alkaline to highly alkaline (pH 7.40-10.91) throughout the various treatment stages, with the salinity ranging from 1.62 to 4.53 g L(-1) and dissolved oxygen concentrations ranging from 7.47 to 9.12 mg L(-1). Phenotypic switching was found to occur due to these physicochemical parameters. Microbial diversities increased from those present in Stage I reactor (six taxonomic groups) to those in Reverse Osmosis (RO) stage I (17 taxonomic groups), whereas in the second phase of the treatment, it increased in Stage II clarifier (14 taxonomic groups) followed by a decrease in RO stage II (seven taxonomic groups). Overall, seven phyla were detected, apart from many bacterial sequences that were unclassified at the phylum level. The most dominant phylum found was Proteobacteria accounting for 59% of the total sequences. A blastn sequence similarity search showed that the majority of the sequences (56%) were homologous to the uncultured bacterial species, underlining the vast untapped bacterial diversity.}, } @article {pmid25159704, year = {2015}, author = {Gagic, D and Maclean, PH and Li, D and Attwood, GT and Moon, CD}, title = {Improving the genetic representation of rare taxa within complex microbial communities using DNA normalization methods.}, journal = {Molecular ecology resources}, volume = {15}, number = {3}, pages = {464-476}, doi = {10.1111/1755-0998.12321}, pmid = {25159704}, issn = {1755-0998}, mesh = {*Biodiversity ; *Genetic Variation ; Genotyping Techniques/*methods/*standards ; Metagenomics/*methods/*standards ; *Microbial Consortia ; Sensitivity and Specificity ; }, abstract = {Complex microbial communities typically contain a large number of low abundance species, which collectively, comprise a considerable proportion of the community. This 'rare biosphere' has been speculated to contain keystone species and act as a repository of genomic diversity to facilitate community adaptation. Many environmental microbes are currently resistant to cultivation, and can only be accessed via culture-independent approaches. To enhance our understanding of the role of the rare biosphere, we aimed to improve their metagenomic representation using DNA normalization methods, and assess normalization success via shotgun DNA sequencing. A synthetic metagenome was constructed from the genomic DNA of five bacterial species, pooled in a defined ratio spanning three orders of magnitude. The synthetic metagenome was fractionated and thermally renatured, allowing the most abundant sequences to hybridize. Double-stranded DNA was removed either by hydroxyapatite chromatography, or by a duplex-specific nuclease (DSN). The chromatographic method failed to enrich for the genomes present in low starting abundance, whereas the DSN method resulted in all genomes reaching near equimolar abundance. The representation of the rarest member was increased by approximately 450-fold. De novo assembly of the normalized metagenome enabled up to 18.0% of genes from the rarest organism to be assembled, in contrast to the un-normalized sample, where genes were not able to be assembled at the same sequencing depth. This study has demonstrated that the application of normalization methods to metagenomic samples is a powerful tool to enrich for sequences from rare taxa, which will shed further light on their ecological niches.}, } @article {pmid25158668, year = {2014}, author = {Li, SJ and Hua, ZS and Huang, LN and Li, J and Shi, SH and Chen, LX and Kuang, JL and Liu, J and Hu, M and Shu, WS}, title = {Microbial communities evolve faster in extreme environments.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {6205}, pmid = {25158668}, issn = {2045-2322}, mesh = {Archaea/genetics ; Bacteria/genetics ; Cluster Analysis ; Ecosystem ; *Evolution, Molecular ; *Gene-Environment Interaction ; Genes, Archaeal ; Genes, Bacterial ; Hot Springs/microbiology ; Microbial Consortia/*genetics ; Microbial Interactions ; Mutation Rate ; Phylogeny ; *Water Microbiology ; }, abstract = {Evolutionary analysis of microbes at the community level represents a new research avenue linking ecological patterns to evolutionary processes, but remains insufficiently studied. Here we report a relative evolutionary rates (rERs) analysis of microbial communities from six diverse natural environments based on 40 metagenomic samples. We show that the rERs of microbial communities are mainly shaped by environmental conditions, and the microbes inhabiting extreme habitats (acid mine drainage, saline lake and hot spring) evolve faster than those populating benign environments (surface ocean, fresh water and soil). These findings were supported by the observation of more relaxed purifying selection and potentially frequent horizontal gene transfers in communities from extreme habitats. The mechanism of high rERs was proposed as high mutation rates imposed by stressful conditions during the evolutionary processes. This study brings us one stage closer to an understanding of the evolutionary mechanisms underlying the adaptation of microbes to extreme environments.}, } @article {pmid25156802, year = {2014}, author = {Bozinovski, D and Taubert, M and Kleinsteuber, S and Richnow, HH and von Bergen, M and Vogt, C and Seifert, J}, title = {Metaproteogenomic analysis of a sulfate-reducing enrichment culture reveals genomic organization of key enzymes in the m-xylene degradation pathway and metabolic activity of proteobacteria.}, journal = {Systematic and applied microbiology}, volume = {37}, number = {7}, pages = {488-501}, doi = {10.1016/j.syapm.2014.07.005}, pmid = {25156802}, issn = {1618-0984}, mesh = {Carbon Isotopes/metabolism ; Chromatography, Liquid ; DNA, Bacterial/chemistry/genetics ; Environmental Microbiology ; Isotope Labeling ; Metabolic Networks and Pathways/*genetics ; *Metagenome ; *Microbial Consortia ; Molecular Sequence Data ; Proteobacteria/chemistry/genetics/*metabolism ; *Proteome ; Sequence Analysis, DNA ; Tandem Mass Spectrometry ; Xylenes/*metabolism ; }, abstract = {This study aimed to ascertain the functional and phylogenetic relationships within an m-xylene degrading sulfate-reducing enrichment culture, which had been maintained for several years in the laboratory with m-xylene as the sole source of carbon and energy. Previous studies indicated that a phylotype affiliated to the Desulfobacteraceae was the main m-xylene assimilating organism. In the present study, genes and gene products were identified by a metaproteogenomic approach using LC-MS/MS analysis of the microbial community, and 2426 peptides were identified from 576 proteins. In the metagenome of the community, gene clusters encoding enzymes involved in fumarate addition to a methyl moiety of m-xylene (nms, bss), as well as gene clusters coding for enzymes involved in modified beta-oxidation to (3-methyl)benzoyl-CoA (bns), were identified in two separate contigs. Additionally, gene clusters containing homologues to bam genes encoding benzoyl-CoA reductase (Bcr) class II, catalyzing the dearomatization of (3-methyl)benzoyl-CoA, were identified. Time-resolved protein stable isotope probing (protein-SIP) experiments using (13)C-labeled m-xylene showed that the respective gene products were highly (13)C-labeled. The present data suggested the identification of gene products that were similar to those involved in methylnaphthalene degradation even though the consortium was not capable of growing in the presence of naphthalene, methylnaphthalene or toluene as substrates. Thus, a novel branch of enzymes was found that was probably specific for anaerobic m-xylene degradation.}, } @article {pmid25156377, year = {2014}, author = {Muniesa, M and Jofre, J}, title = {Identifying and analyzing bacteriophages in human fecal samples: what could we discover?.}, journal = {Future microbiology}, volume = {9}, number = {7}, pages = {879-886}, doi = {10.2217/fmb.14.47}, pmid = {25156377}, issn = {1746-0921}, mesh = {Bacteria/chemistry/cytology/isolation & purification ; Bacteriophages/classification/genetics/*isolation & purification ; Feces/microbiology/*virology ; Humans ; Intestines/microbiology/virology ; Microbiota ; }, abstract = {The human gut is a complex ecosystem, densely populated with microbes including enormous amounts of phages. Metagenomic studies indicate a great diversity of bacteriophages, and because of the variety of gut bacterial species, the human or animal gut is probably a perfect ecological niche for phages that can infect and propagate in their bacterial communities. In addition, some phages have the capacity to mobilize genes, as demonstrated by the enormous fraction of phage particles in feces that contain bacterial DNA. All these facts indicate that, through predation and horizontal gene transfer, bacteriophages play a key role in shaping the size, structure and function of intestinal microbiomes, although our understanding of their effects on gut bacterial populations is only just beginning.}, } @article {pmid25154801, year = {2015}, author = {Parahitiyawa, NB and Chu, FC and Leung, WK and Yam, WC and Jin, LJ and Samaranayake, LP}, title = {Clonality of bacterial consortia in root canals and subjacent gingival crevices.}, journal = {Journal of investigative and clinical dentistry}, volume = {6}, number = {1}, pages = {32-39}, doi = {10.1111/jicd.12070}, pmid = {25154801}, issn = {2041-1626}, mesh = {Adult ; Bacteria/*classification/genetics ; Biodiversity ; DNA, Bacterial/analysis ; Dental Plaque/*microbiology ; Dental Pulp Cavity/*microbiology ; Dental Pulp Exposure/microbiology ; Genome, Microbial/genetics ; Gingiva/*microbiology ; Humans ; Incisor/injuries ; Male ; Metagenome/genetics ; Microbial Consortia/*physiology ; Periapical Diseases/microbiology ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tooth Fractures/microbiology ; }, abstract = {AIM: No oral niche can be considered to be segregated from the subjacent milieu because of the complex community behavior and nature of the oral biofilms. The aim of this study was to address the paucity of information on how these species are clonally related to the subjacent gingival crevice bacteria.

METHODS: We utilized a metagenomic approach of amplifying 16S rDNA from genomic DNA, cloning, sequencing and analysis using LIBSHUFF software to assess the genetic homogeneity of the bacterial species from two infected root canals and subjacent gingival crevices.

RESULTS: The four niches studied yielded 186 clones representing 54 phylotypes. Clone library comparisons using LIBSHUFF software indicated that each niche was inhabited by a unique flora. Further, 42% of the clones were of hitherto unknown phylotypes indicating the extent of bacterial diversity, especially in infected root canals and subjacent gingival crevices.

CONCLUSIONS: We believe data generated through this novel analytical tool shed new light on understanding oral microbial ecosystems.}, } @article {pmid25148512, year = {2014}, author = {Carr, R and Borenstein, E}, title = {Comparative analysis of functional metagenomic annotation and the mappability of short reads.}, journal = {PloS one}, volume = {9}, number = {8}, pages = {e105776}, pmid = {25148512}, issn = {1932-6203}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; P30 DK089507/DK/NIDDK NIH HHS/United States ; DP2 AT007802-01/AT/NCCIH NIH HHS/United States ; }, mesh = {Algorithms ; Computational Biology/methods ; Genome, Archaeal ; Genome, Bacterial ; Humans ; Metagenomics/*methods ; Microbial Consortia/*genetics ; Microbiota/genetics ; Molecular Sequence Annotation/*methods ; Phylogeny ; Sequence Analysis, DNA/methods ; Software ; Streptococcus/genetics ; }, abstract = {To assess the functional capacities of microbial communities, including those inhabiting the human body, shotgun metagenomic reads are often aligned to a database of known genes. Such homology-based annotation practices critically rely on the assumption that short reads can map to orthologous genes of similar function. This assumption, however, and the various factors that impact short read annotation, have not been systematically evaluated. To address this challenge, we generated an extremely large database of simulated reads (totaling 15.9 Gb), spanning over 500,000 microbial genes and 170 curated genomes and including, for many genomes, every possible read of a given length. We annotated each read using common metagenomic protocols, fully characterizing the effect of read length, sequencing error, phylogeny, database coverage, and mapping parameters. We additionally rigorously quantified gene-, genome-, and protocol-specific annotation biases. Overall, our findings provide a first comprehensive evaluation of the capabilities and limitations of functional metagenomic annotation, providing crucial goal-specific best-practice guidelines to inform future metagenomic research.}, } @article {pmid25145207, year = {2014}, author = {Bai, Y and Liang, J and Liu, R and Hu, C and Qu, J}, title = {Metagenomic analysis reveals microbial diversity and function in the rhizosphere soil of a constructed wetland.}, journal = {Environmental technology}, volume = {35}, number = {17-20}, pages = {2521-2527}, doi = {10.1080/09593330.2014.911361}, pmid = {25145207}, issn = {0959-3330}, mesh = {Biodegradation, Environmental ; Metagenomics/*methods ; Microbial Consortia/*genetics ; *Rhizosphere ; *Soil Microbiology ; Water Pollutants, Chemical ; *Water Purification ; *Wetlands ; }, abstract = {Microbial communities play a critical role in the degradation of effluent contaminants in constructed wetlands. Many questions remain, however, regarding the role ofmicrobial communities in rhizospheric soil. In this study, we used metagenomic analysis to assess microbial community composition and function in a constructed wetland receiving surface water. The diversity of the microbial community of rhizosphere soil was found to be significantly greater than that of the wetland influent water. This enhancement is likely due to the availability of diverse habitats and nutrients provided by the wetland plants. From function annotation of metagenomic data, a number of biodegradation pathways associated with 14 xenobiotic compounds were identified in soil. Nitrogen fixation, nitrification and denitrification genes were semi-quantitatively analysed. By screening of manganese transformation genes, we found that the biological oxidation of Mn2+ (mainly catalysed by multicopper oxidase) in the influent water yielded insoluble Mn4+, which subsequently precipitated and were incorporated into the wetland soil. These data show that the use of metagenomic analysis can provide important new insights for the study of wetland ecosystems and, in particular, how biologically mediated transformation or degradation can be used to reduce contamination of point and non-point source wastewater.}, } @article {pmid25141006, year = {2014}, author = {de Wouters, T and Ledue, F and Nepelska, M and Doré, J and Blottière, HM and Lapaque, N}, title = {A robust and adaptable high throughput screening method to study host-microbiota interactions in the human intestine.}, journal = {PloS one}, volume = {9}, number = {8}, pages = {e105598}, pmid = {25141006}, issn = {1932-6203}, mesh = {HT29 Cells ; High-Throughput Screening Assays/*methods ; Host-Pathogen Interactions ; Humans ; Intestines/*microbiology ; Metagenome ; *Microbiota ; }, abstract = {The intestinal microbiota has many beneficial roles for its host. However, the precise mechanisms developed by the microbiota to influence the host intestinal cell responses are only partially known. The complexity of the ecosystem and our inability to culture most of these micro-organisms have led to the development of molecular approaches such as functional metagenomics, i.e. the heterologous expression of a metagenome in order to identify functions. This elegant strategy coupled to high throughput screening allowed to identify novel enzymes from different ecosystems where culture methods have not yet been adapted to isolate the candidate microorganisms. We have proposed to use this functional metagenomic approach in order to model the microbiota's interaction with the host by combining this heterologous expression with intestinal reporter cell lines. The addition of the cellular component to this functional metagenomic approach introduced a second important source of variability resulting in a novel challenge for high throughput screening. First attempts of high throughput screening with various reporter cell-lines showed a high distribution of the response and consequent difficulties to reproduce the response, impairing an easy and clear identification of confirmed hits. In this study, we developed a robust and reproducible methodology to combine these two biological systems for high throughput application. We optimized experimental setups and completed them by appropriate statistical analysis tools allowing the use this innovative approach in a high throughput manner and on a broad range of reporter assays. We herewith present a methodology allowing a high throughput screening combining two biological systems. Therefore ideal conditions for homogeneity, sensitivity and reproducibility of both metagenomic clones as well as reporter cell lines have been identified and validated. We believe that this innovative method will allow the identification of new bioactive microbial molecules and, subsequently, will promote understanding of host-microbiota interactions.}, } @article {pmid25136572, year = {2014}, author = {Singh, KM and Reddy, B and Patel, D and Patel, AK and Parmar, N and Patel, A and Patel, JB and Joshi, CG}, title = {High potential source for biomass degradation enzyme discovery and environmental aspects revealed through metagenomics of Indian buffalo rumen.}, journal = {BioMed research international}, volume = {2014}, number = {}, pages = {267189}, pmid = {25136572}, issn = {2314-6141}, mesh = {Animals ; *Bacterial Proteins/genetics/metabolism ; *Biomass ; Buffaloes/*microbiology ; Metagenome/*physiology ; Microbiota/*physiology ; *Rumen/enzymology/microbiology ; }, abstract = {The complex microbiomes of the rumen functions as an effective system for plant cell wall degradation, and biomass utilization provide genetic resource for degrading microbial enzymes that could be used in the production of biofuel. Therefore the buffalo rumen microbiota was surveyed using shot gun sequencing. This metagenomic sequencing generated 3.9 GB of sequences and data were assembled into 137270 contiguous sequences (contigs). We identified potential 2614 contigs encoding biomass degrading enzymes including glycoside hydrolases (GH: 1943 contigs), carbohydrate binding module (CBM: 23 contigs), glycosyl transferase (GT: 373 contigs), carbohydrate esterases (CE: 259 contigs), and polysaccharide lyases (PE: 16 contigs). The hierarchical clustering of buffalo metagenomes demonstrated the similarities and dissimilarity in microbial community structures and functional capacity. This demonstrates that buffalo rumen microbiome was considerably enriched in functional genes involved in polysaccharide degradation with great prospects to obtain new molecules that may be applied in the biofuel industry.}, } @article {pmid25135363, year = {2014}, author = {Kiran Kumar Reddy, G and Nancharaiah, YV and Venugopalan, VP}, title = {Aerobic granular sludge mediated biodegradation of an organophosphorous ester, dibutyl phosphite.}, journal = {FEMS microbiology letters}, volume = {359}, number = {1}, pages = {110-115}, doi = {10.1111/1574-6968.12581}, pmid = {25135363}, issn = {1574-6968}, mesh = {Acetates/metabolism ; Aerobiosis ; Bacteria/classification/genetics ; Bioreactors/microbiology ; Biota ; Biotransformation ; Esters/*metabolism ; Metagenomics ; Organophosphates/*metabolism ; Phosphites/*metabolism ; Polymorphism, Restriction Fragment Length ; Sewage/*microbiology ; }, abstract = {Dibutyl phosphite, an organophosphorous compound, finds applications in different chemical industries and processes. Here, we report an efficient approach of biodegradation to be eventually used in bioremediation of dibutyl phosphite. Aerobic granules capable of dibutyl phosphite biodegradation were cultivated in a sequencing batch reactor (SBR). The SBR was operated with a 24-h cycle by feeding with dibutyl phosphite as a cosubstrate along with acetate. During the course of the SBR operation, aerobic granules of 0.9 ± 0.3 mm size were developed. Complete biodegradation of 1.4, 2 and 3 mM of dibutyl phosphite was achieved in 4, 5 and 8 h, respectively, accompanied by stoichiometric release of phosphite (H3 PO3). Phosphatase activity in the dibutyl phosphite-degrading granular biomass was 3- and 1.5-fold higher as compared to the activated sludge (seed biomass) and acetate-fed aerobic granules, respectively, indicating involvement in the hydrolysis of dibutyl phosphite. Microbial community analysis by t-RFLP showed the presence of 12 different bacterial types. Two bacterial strains capable of growth on dibutyl phosphite as sole carbon source were isolated and characterized as Acidovorax sp. and Sphingobium sp. The results show that aerobic microbial granules based process is suitable for the treatment of dibutyl phosphite contaminated water.}, } @article {pmid25131220, year = {2014}, author = {Huang, H and Vangay, P and McKinlay, CE and Knights, D}, title = {Multi-omics analysis of inflammatory bowel disease.}, journal = {Immunology letters}, volume = {162}, number = {2 Pt A}, pages = {62-68}, doi = {10.1016/j.imlet.2014.07.014}, pmid = {25131220}, issn = {1879-0542}, mesh = {Animals ; *Computational Biology ; Gene Expression Profiling ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Host-Pathogen Interactions ; Humans ; Immunity, Mucosal ; Inflammatory Bowel Diseases/*diagnosis/genetics/microbiology ; Intestinal Mucosa/microbiology/*physiology ; *Microbiota/genetics/immunology ; }, abstract = {Crohn's disease and ulcerative colitis, known together as inflammatory bowel disease (IBD), are severe autoimmune disorders now causing gut inflammation and ulceration, among other symptoms, in up to 1 in 250 people worldwide. Incidence and prevalence of IBD have been increasing dramatically over the past several decades, although the causes for this increase are still unknown. IBD has both a complex genotype and a complex phenotype, and although it has received substantial attention from the medical research community over recent years, much of the etiology remains unexplained. Genome-wide association studies have identified a rich genetic signature of disease risk in patients with IBD, consisting of at least 163 genetic loci. Many of these loci contain genes directly involved in microbial handling, indicating that the genetic architecture of the disease has been driven by host-microbe interactions. In addition, systematic shifts in gut microbiome structure (enterotype) and function have been observed in patients with IBD. Furthermore, both the host genotype and enterotype are associated with aspects of the disease phenotype, including location of the disease. This provides strong evidence of interactions between host genotype and enterotype; however, there is a lack of published multi-omics data from IBD patients, and a lack of bioinformatics tools for modeling such systems. In this article we discuss, from a computational biologist's point of view, the potential benefits of and the challenges involved in designing and analyzing such multi-omics studies of IBD.}, } @article {pmid25130883, year = {2014}, author = {Okubo, T and Ikeda, S and Sasaki, K and Ohshima, K and Hattori, M and Sato, T and Minamisawa, K}, title = {Phylogeny and functions of bacterial communities associated with field-grown rice shoots.}, journal = {Microbes and environments}, volume = {29}, number = {3}, pages = {329-332}, pmid = {25130883}, issn = {1347-4405}, mesh = {Bacteria/*classification/genetics/*isolation & purification ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Molecular Sequence Data ; Oryza/classification/growth & development/*microbiology ; *Phylogeny ; Plant Roots/growth & development/microbiology ; Plant Shoots/growth & development/*microbiology ; Rhizosphere ; Soil Microbiology ; }, abstract = {Metagenomic analysis was applied to bacterial communities associated with the shoots of two field-grown rice cultivars, Nipponbare and Kasalath. In both cultivars, shoot microbiomes were dominated by Alphaproteobacteria (51-52%), Actinobacteria (11-15%), Gammaproteobacteria (9-10%), and Betaproteobacteria (4-10%). Compared with other rice microbiomes (root, rhizosphere, and phyllosphere) in public databases, the shoot microbiomes harbored abundant genes for C1 compound metabolism and 1-aminocyclopropane-1-carboxylate catabolism, but fewer genes for indole-3-acetic acid production and nitrogen fixation. Salicylate hydroxylase was detected in all microbiomes, except the rhizosphere. These genomic features facilitate understanding of plant-microbe interactions and biogeochemical metabolism in rice shoots.}, } @article {pmid25129545, year = {2014}, author = {Ventosa, A and Fernández, AB and León, MJ and Sánchez-Porro, C and Rodriguez-Valera, F}, title = {The Santa Pola saltern as a model for studying the microbiota of hypersaline environments.}, journal = {Extremophiles : life under extreme conditions}, volume = {18}, number = {5}, pages = {811-824}, pmid = {25129545}, issn = {1433-4909}, mesh = {*Metagenome ; *Microbiota ; Ponds/chemistry/*microbiology/virology ; *Salinity ; *Salt Tolerance ; }, abstract = {Multi-pond salterns constitute an excellent model for the study of the microbial diversity and ecology of hypersaline environments, showing a wide range of salt concentrations, from seawater to salt saturation. Accumulated studies on the Santa Pola (Alicante, Spain) multi-pond solar saltern during the last 35 years include culture-dependent and culture-independent molecular methods and metagenomics more recently. These approaches have permitted to determine in depth the microbial diversity of the ponds with intermediate salinities (from 10% salts) up to salt saturation, with haloarchaea and bacteria as the two main dominant groups. In this review, we describe the main results obtained using the different methodologies, the most relevant contributions for understanding the ecology of these extreme environments and the future perspectives for such studies.}, } @article {pmid25129502, year = {2014}, author = {Sun, Z and Liu, W and Bao, Q and Zhang, J and Hou, Q and Kwok, L and Sun, T and Zhang, H}, title = {Investigation of bacterial and fungal diversity in tarag using high-throughput sequencing.}, journal = {Journal of dairy science}, volume = {97}, number = {10}, pages = {6085-6096}, doi = {10.3168/jds.2014-8360}, pmid = {25129502}, issn = {1525-3198}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Cattle ; Computational Biology ; DNA, Bacterial/chemistry/genetics/isolation & purification ; DNA, Fungal/chemistry/genetics/isolation & purification ; Female ; Fermentation ; Fungi/classification/genetics/*isolation & purification ; High-Throughput Nucleotide Sequencing/*veterinary ; Microbiota ; Polymerase Chain Reaction/veterinary ; Sequence Analysis, DNA/veterinary ; Yogurt/*microbiology ; }, abstract = {This is the first study on the bacterial and fungal community diversity in 17 tarag samples (naturally fermented dairy products) through a metagenomic approach involving high-throughput pyrosequencing. Our results revealed the presence of a total of 47 bacterial and 43 fungal genera in all tarag samples, in which Lactobacillus and Galactomyces were the predominant genera of bacteria and fungi, respectively. The number of some microbial genera, such as Lactococcus, Acetobacter, Saccharomyces, Trichosporon, and Kluyveromyces, among others, was found to vary between different samples. Altogether, our results showed that the microbial flora in different samples may be stratified by geographic region.}, } @article {pmid25128740, year = {2014}, author = {Jadhav, A and Shanmugham, B and Rajendiran, A and Pan, A}, title = {Unraveling novel broad-spectrum antibacterial targets in food and waterborne pathogens using comparative genomics and protein interaction network analysis.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {27}, number = {}, pages = {300-308}, doi = {10.1016/j.meegid.2014.08.007}, pmid = {25128740}, issn = {1567-7257}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics/metabolism ; Bacterial Secretion Systems ; Food Microbiology ; Foodborne Diseases/*microbiology ; Gastrointestinal Tract/microbiology ; Humans ; Metabolic Networks and Pathways ; *Metagenomics ; Microbiota ; Peptidoglycan/biosynthesis ; *Protein Interaction Mapping ; *Proteomics ; Water Microbiology ; }, abstract = {Food and waterborne diseases are a growing concern in terms of human morbidity and mortality worldwide, even in the 21st century, emphasizing the need for new therapeutic interventions for these diseases. The current study aims at prioritizing broad-spectrum antibacterial targets, present in multiple food and waterborne bacterial pathogens, through a comparative genomics strategy coupled with a protein interaction network analysis. The pathways unique and common to all the pathogens under study (viz., methane metabolism, d-alanine metabolism, peptidoglycan biosynthesis, bacterial secretion system, two-component system, C5-branched dibasic acid metabolism), identified by comparative metabolic pathway analysis, were considered for the analysis. The proteins/enzymes involved in these pathways were prioritized following host non-homology analysis, essentiality analysis, gut flora non-homology analysis and protein interaction network analysis. The analyses revealed a set of promising broad-spectrum antibacterial targets, present in multiple food and waterborne pathogens, which are essential for bacterial survival, non-homologous to host and gut flora, and functionally important in the metabolic network. The identified broad-spectrum candidates, namely, integral membrane protein/virulence factor (MviN), preprotein translocase subunits SecB and SecG, carbon storage regulator (CsrA), and nitrogen regulatory protein P-II 1 (GlnB), contributed by the peptidoglycan pathway, bacterial secretion systems and two-component systems, were also found to be present in a wide range of other disease-causing bacteria. Cytoplasmic proteins SecG, CsrA and GlnB were considered as drug targets, while membrane proteins MviN and SecB were classified as vaccine targets. The identified broad-spectrum targets can aid in the design and development of antibacterial agents not only against food and waterborne pathogens but also against other pathogens.}, } @article {pmid25122209, year = {2014}, author = {Zhang, Y and Sun, Y and Cole, JR}, title = {A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data.}, journal = {PLoS computational biology}, volume = {10}, number = {8}, pages = {e1003737}, pmid = {25122209}, issn = {1553-7358}, mesh = {Chromosome Mapping/*methods ; Databases, Genetic ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {Gene assembly, which recovers gene segments from short reads, is an important step in functional analysis of next-generation sequencing data. Lacking quality reference genomes, de novo assembly is commonly used for RNA-Seq data of non-model organisms and metagenomic data. However, heterogeneous sequence coverage caused by heterogeneous expression or species abundance, similarity between isoforms or homologous genes, and large data size all pose challenges to de novo assembly. As a result, existing assembly tools tend to output fragmented contigs or chimeric contigs, or have high memory footprint. In this work, we introduce a targeted gene assembly program SAT-Assembler, which aims to recover gene families of particular interest to biologists. It addresses the above challenges by conducting family-specific homology search, homology-guided overlap graph construction, and careful graph traversal. It can be applied to both RNA-Seq and metagenomic data. Our experimental results on an Arabidopsis RNA-Seq data set and two metagenomic data sets show that SAT-Assembler has smaller memory usage, comparable or better gene coverage, and lower chimera rate for assembling a set of genes from one or multiple pathways compared with other assembly tools. Moreover, the family-specific design and rapid homology search allow SAT-Assembler to be naturally compatible with parallel computing platforms. The source code of SAT-Assembler is available at https://sourceforge.net/projects/sat-assembler/. The data sets and experimental settings can be found in supplementary material.}, } @article {pmid25120959, year = {2014}, author = {Diaz, PI and Strausbaugh, LD and Dongari-Bagtzoglou, A}, title = {Fungal-bacterial interactions and their relevance to oral health: linking the clinic and the bench.}, journal = {Frontiers in cellular and infection microbiology}, volume = {4}, number = {}, pages = {101}, pmid = {25120959}, issn = {2235-2988}, support = {R01 DE013986/DE/NIDCR NIH HHS/United States ; R01 DE021578/DE/NIDCR NIH HHS/United States ; R01DE021578/DE/NIDCR NIH HHS/United States ; R01DE013986/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; Bacteria ; *Bacterial Physiological Phenomena ; Fungi/*physiology ; Humans ; Metagenome ; Metagenomics ; *Microbial Interactions ; *Microbiota ; Mouth/*microbiology ; *Oral Health ; Translational Research, Biomedical ; }, abstract = {High throughput sequencing has accelerated knowledge on the oral microbiome. While the bacterial component of oral communities has been extensively characterized, the role of the fungal microbiota in the oral cavity is largely unknown. Interactions among fungi and bacteria are likely to influence oral health as exemplified by the synergistic relationship between Candida albicans and oral streptococci. In this perspective, we discuss the current state of the field of fungal-bacterial interactions in the context of the oral cavity. We highlight the need to conduct longitudinal clinical studies to simultaneously characterize the bacterial and fungal components of the human oral microbiome in health and during disease progression. Such studies need to be coupled with investigations using disease-relevant models to mechanistically test the associations observed in humans and eventually identify fungal-bacterial interactions that could serve as preventive or therapeutic targets for oral diseases.}, } @article {pmid25120956, year = {2014}, author = {McLean, JS}, title = {Advancements toward a systems level understanding of the human oral microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {4}, number = {}, pages = {98}, pmid = {25120956}, issn = {2235-2988}, support = {R01 DE020102/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/metabolism ; Bacterial Physiological Phenomena ; Biofilms ; Datasets as Topic ; Dental Plaque/microbiology ; Host-Pathogen Interactions ; Humans ; Hydrogen-Ion Concentration ; *Metagenome ; Metagenomics ; Microbial Interactions ; *Microbiota ; Mouth/*microbiology ; Phylogeny ; Tooth Demineralization/etiology ; }, abstract = {Oral microbes represent one of the most well studied microbial communities owing to the fact that they are a fundamental part of human development influencing health and disease, an easily accessible human microbiome, a highly structured and remarkably resilient biofilm as well as a model of bacteria-bacteria and bacteria-host interactions. In the last 80 years since oral plaque was first characterized for its functionally stable physiological properties such as the highly repeatable rapid pH decrease upon carbohydrate addition and subsequent recovery phase, the fundamental approaches to study the oral microbiome have cycled back and forth between community level investigations and characterizing individual model isolates. Since that time, many individual species have been well characterized and the development of the early plaque community, which involves many cell-cell binding interactions, has been carefully described. With high throughput sequencing enabling the enormous diversity of the oral cavity to be realized, a number of new challenges to progress were revealed. The large number of uncultivated oral species, the high interpersonal variability of taxonomic carriage and the possibility of multiple pathways to dysbiosis pose as major hurdles to obtain a systems level understanding from the community to the gene level. It is now possible however to start connecting the insights gained from single species with community wide approaches. This review will discuss some of the recent insights into the oral microbiome at a fundamental level, existing knowledge gaps, as well as challenges that have surfaced and the approaches to address them.}, } @article {pmid25118239, year = {2014}, author = {Eilam, O and Zarecki, R and Oberhardt, M and Ursell, LK and Kupiec, M and Knight, R and Gophna, U and Ruppin, E}, title = {Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptations.}, journal = {mBio}, volume = {5}, number = {4}, pages = {}, pmid = {25118239}, issn = {2150-7511}, support = {T32 GM008759/GM/NIGMS NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*metabolism ; *Diet ; Gastrointestinal Tract/*microbiology ; Genomics ; Humans ; Linear Models ; Metagenomics ; *Microbiota ; Polysaccharides/*metabolism ; Prebiotics ; }, abstract = {UNLABELLED: Glycans form the primary nutritional source for microbes in the human gut, and understanding their metabolism is a critical yet understudied aspect of microbiome research. Here, we present a novel computational pipeline for modeling glycan degradation (GlyDeR) which predicts the glycan degradation potency of 10,000 reference glycans based on either genomic or metagenomic data. We first validated GlyDeR by comparing degradation profiles for genomes in the Human Microbiome Project against KEGG reaction annotations. Next, we applied GlyDeR to the analysis of human and mammalian gut microbial communities, which revealed that the glycan degradation potential of a community is strongly linked to host diet and can be used to predict diet with higher accuracy than sequence data alone. Finally, we show that a microbe's glycan degradation potential is significantly correlated (R = 0.46) with its abundance, with even higher correlations for potential pathogens such as the class Clostridia (R = 0.76). GlyDeR therefore represents an important tool for advancing our understanding of bacterial metabolism in the gut and for the future development of more effective prebiotics for microbial community manipulation.

IMPORTANCE: The increased availability of high-throughput sequencing data has positioned the gut microbiota as a major new focal point for biomedical research. However, despite the expenditure of huge efforts and resources, sequencing-based analysis of the microbiome has uncovered mostly associative relationships between human health and diet, rather than a causal, mechanistic one. In order to utilize the full potential of systems biology approaches, one must first characterize the metabolic requirements of gut bacteria, specifically, the degradation of glycans, which are their primary nutritional source. We developed a computational framework called GlyDeR for integrating expert knowledge along with high-throughput data to uncover important new relationships within glycan metabolism. GlyDeR analyzes particular bacterial (meta)genomes and predicts the potency by which they degrade a variety of different glycans. Based on GlyDeR, we found a clear connection between microbial glycan degradation and human diet, and we suggest a method for the rational design of novel prebiotics.}, } @article {pmid25118069, year = {2014}, author = {Alele, PO and Sheil, D and Surget-Groba, Y and Lingling, S and Cannon, CH}, title = {How does conversion of natural tropical rainforest ecosystems affect soil bacterial and fungal communities in the Nile river watershed of Uganda?.}, journal = {PloS one}, volume = {9}, number = {8}, pages = {e104818}, pmid = {25118069}, issn = {1932-6203}, mesh = {Bacteria/classification/isolation & purification ; Biodiversity ; Calcium/analysis ; Carbon/analysis ; Conservation of Natural Resources/*methods ; DNA, Bacterial/genetics ; Fungi/classification/isolation & purification ; Humans ; Hydrogen-Ion Concentration ; Nitrogen/analysis ; RNA, Ribosomal, 16S/genetics ; Rainforest ; Rivers/microbiology ; Soil/*chemistry ; *Soil Microbiology ; Uganda ; }, abstract = {Uganda's forests are globally important for their conservation values but are under pressure from increasing human population and consumption. In this study, we examine how conversion of natural forest affects soil bacterial and fungal communities. Comparisons in paired natural forest and human-converted sites among four locations indicated that natural forest soils consistently had higher pH, organic carbon, nitrogen, and calcium, although variation among sites was large. Despite these differences, no effect on the diversity of dominant taxa for either bacterial or fungal communities was detected, using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Composition of fungal communities did generally appear different in converted sites, but surprisingly, we did not observe a consistent pattern among sites. The spatial distribution of some taxa and community composition was associated with soil pH, organic carbon, phosphorus and sodium, suggesting that changes in soil communities were nuanced and require more robust metagenomic methods to understand the various components of the community. Given the close geographic proximity of the paired sampling sites, the similarity between natural and converted sites might be due to continued dispersal between treatments. Fungal communities showed greater environmental differentiation than bacterial communities, particularly according to soil pH. We detected biotic homogenization in converted ecosystems and substantial contribution of β-diversity to total diversity, indicating considerable geographic structure in soil biota in these forest communities. Overall, our results suggest that soil microbial communities are relatively resilient to forest conversion and despite a substantial and consistent change in the soil environment, the effects of conversion differed widely among sites. The substantial difference in soil chemistry, with generally lower nutrient quantity in converted sites, does bring into question, how long this resilience will last.}, } @article {pmid25113821, year = {2014}, author = {Hedlund, BP and Dodsworth, JA and Murugapiran, SK and Rinke, C and Woyke, T}, title = {Impact of single-cell genomics and metagenomics on the emerging view of extremophile "microbial dark matter".}, journal = {Extremophiles : life under extreme conditions}, volume = {18}, number = {5}, pages = {865-875}, pmid = {25113821}, issn = {1433-4909}, mesh = {*Adaptation, Physiological ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Single-Cell Analysis ; }, abstract = {Despite >130 years of microbial cultivation studies, many microorganisms remain resistant to traditional cultivation approaches, including numerous candidate phyla of bacteria and archaea. Unraveling the mysteries of these candidate phyla is a grand challenge in microbiology and is especially important in habitats where they are abundant, including some extreme environments and low-energy ecosystems. Over the past decade, parallel advances in DNA amplification, DNA sequencing and computing have enabled rapid progress on this problem, particularly through metagenomics and single-cell genomics. Although each approach suffers limitations, metagenomics and single-cell genomics are particularly powerful when combined synergistically. Studies focused on extreme environments have revealed the first substantial genomic information for several candidate phyla, encompassing putative acidophiles (Parvarchaeota), halophiles (Nanohaloarchaeota), thermophiles (Acetothermia, Aigarchaeota, Atribacteria, Calescamantes, Korarchaeota, and Fervidibacteria), and piezophiles (Gracilibacteria). These data have enabled insights into the biology of these organisms, including catabolic and anabolic potential, molecular adaptations to life in extreme environments, unique genomic features such as stop codon reassignments, and predictions about cell ultrastructure. In addition, the rapid expansion of genomic coverage enabled by these studies continues to yield insights into the early diversification of microbial lineages and the relationships within and between the phyla of Bacteria and Archaea. In the next 5 years, the genomic foliage within the tree of life will continue to grow and the study of yet-uncultivated candidate phyla will firmly transition into the post-genomic era.}, } @article {pmid25113243, year = {2014}, author = {Bragina, A and Oberauner-Wappis, L and Zachow, C and Halwachs, B and Thallinger, GG and Müller, H and Berg, G}, title = {The Sphagnum microbiome supports bog ecosystem functioning under extreme conditions.}, journal = {Molecular ecology}, volume = {23}, number = {18}, pages = {4498-4510}, doi = {10.1111/mec.12885}, pmid = {25113243}, issn = {1365-294X}, mesh = {Bacteria/*genetics ; *Metagenome ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Sphagnopsida/genetics/*microbiology ; *Wetlands ; }, abstract = {Sphagnum-dominated bogs represent a unique yet widely distributed type of terrestrial ecosystem and strongly contribute to global biosphere functioning. Sphagnum is colonized by highly diverse microbial communities, but less is known about their function. We identified a high functional diversity within the Sphagnum microbiome applying an Illumina-based metagenomic approach followed by de novo assembly and MG-RAST annotation. An interenvironmental comparison revealed that the Sphagnum microbiome harbours specific genetic features that distinguish it significantly from microbiomes of higher plants and peat soils. The differential traits especially support ecosystem functioning by a symbiotic lifestyle under poikilohydric and ombrotrophic conditions. To realise a plasticity-stability balance, we found abundant subsystems responsible to cope with oxidative and drought stresses, to exchange (mobile) genetic elements, and genes that encode for resistance to detrimental environmental factors, repair and self-controlling mechanisms. Multiple microbe-microbe and plant-microbe interactions were also found to play a crucial role as indicated by diverse genes necessary for biofilm formation, interaction via quorum sensing and nutrient exchange. A high proportion of genes involved in nitrogen cycle and recycling of organic material supported the role of bacteria for nutrient supply. 16S rDNA analysis indicated a higher structural diversity than that which had been previously detected using PCR-dependent techniques. Altogether, the diverse Sphagnum microbiome has the ability to support the life of the host plant and the entire ecosystem under changing environmental conditions. Beyond this, the moss microbiome presents a promising bio-resource for environmental biotechnology - with respect to novel enzymes or stress-protecting bacteria.}, } @article {pmid25111794, year = {2014}, author = {Scholz, CF and Jensen, A and Lomholt, HB and Brüggemann, H and Kilian, M}, title = {A novel high-resolution single locus sequence typing scheme for mixed populations of Propionibacterium acnes in vivo.}, journal = {PloS one}, volume = {9}, number = {8}, pages = {e104199}, pmid = {25111794}, issn = {1932-6203}, mesh = {Bacterial Typing Techniques/*methods ; Genetic Loci/*genetics ; Genomics ; Humans ; Microbiota/genetics ; Propionibacterium acnes/*classification/*genetics ; Sequence Analysis ; Species Specificity ; }, abstract = {The Gram-positive anaerobic bacterium Propionibacterium acnes is a prevalent member of the normal skin microbiota of human adults. In addition to its suspected role in acne vulgaris it is involved in a variety of opportunistic infections. Multi-locus sequence-typing (MLST) schemes identified distinct phylotypes associated with health and disease. Being based on 8 to 9 house-keeping genes these MLST schemes have a high discriminatory power, but their application is time- and cost-intensive. Here we describe a single-locus sequence typing (SLST) scheme for P. acnes. The target locus was identified with a genome mining approach that took advantage of the availability of representative genome sequences of all known phylotypes of P. acnes. We applied this SLST on a collection of 188 P. acnes strains and demonstrated a resolution comparable to that of existing MLST schemes. Phylogenetic analysis applied to the SLST locus resulted in clustering patterns identical to a reference tree based on core genome sequences. We further demonstrate that SLST can be applied to detect multiple phylotypes in complex microbial communities by a metagenomic pyrosequencing approach. The described SLST strategy may be applied to any bacterial species with a basically clonal population structure to achieve easy typing and mapping of multiple phylotypes in complex microbiotas. The P. acnes SLST database can be found at http://medbac.dk/slst/pacnes.}, } @article {pmid25105904, year = {2015}, author = {Kamanda Ngugi, D and Blom, J and Alam, I and Rashid, M and Ba-Alawi, W and Zhang, G and Hikmawan, T and Guan, Y and Antunes, A and Siam, R and El Dorry, H and Bajic, V and Stingl, U}, title = {Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea.}, journal = {The ISME journal}, volume = {9}, number = {2}, pages = {396-411}, pmid = {25105904}, issn = {1751-7370}, mesh = {Acclimatization ; Archaea/*classification/*genetics/isolation & purification/metabolism ; Bacteria/classification/isolation & purification ; Biodiversity ; Ecosystem ; Genome, Archaeal ; Genomics ; Indian Ocean ; Metagenomics ; Molecular Sequence Data ; Osmotic Pressure ; Phylogeny ; Salinity ; Seawater/chemistry/*microbiology ; }, abstract = {The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares ∼54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate 'switch' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA.}, } @article {pmid25102857, year = {2015}, author = {Matsen, FA}, title = {Phylogenetics and the human microbiome.}, journal = {Systematic biology}, volume = {64}, number = {1}, pages = {e26-41}, pmid = {25102857}, issn = {1076-836X}, support = {R01 HG005966/HG/NHGRI NIH HHS/United States ; R01-HG005966-01/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Humans ; Microbiota/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of sequencing and genetic analysis of microbiome samples. Much of the analytical work for these sequences involves phylogenetics, at least indirectly, but methodology has developed in a somewhat different direction than for other applications of phylogenetics. In this article, I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work.}, } @article {pmid25101744, year = {2014}, author = {Mick, E and Sorek, R}, title = {High-resolution metagenomics.}, journal = {Nature biotechnology}, volume = {32}, number = {8}, pages = {750-751}, pmid = {25101744}, issn = {1546-1696}, mesh = {*Metagenomics ; Microbiota ; }, } @article {pmid25101249, year = {2014}, author = {Fernandez y Mostajo, M and van der Reijden, WA and Buijs, MJ and Beertsen, W and Van der Weijden, F and Crielaard, W and Zaura, E}, title = {Effect of an oxygenating agent on oral bacteria in vitro and on dental plaque composition in healthy young adults.}, journal = {Frontiers in cellular and infection microbiology}, volume = {4}, number = {}, pages = {95}, pmid = {25101249}, issn = {2235-2988}, mesh = {Adult ; Anti-Infective Agents/*pharmacology/therapeutic use ; Bacteria/classification/drug effects/genetics ; Dental Plaque/drug therapy/*microbiology ; Female ; Healthy Volunteers ; Humans ; Male ; Metagenome ; Microbial Sensitivity Tests ; Microbiota ; Mouth/*drug effects/*microbiology ; Mouthwashes/*pharmacology/therapeutic use ; Oral Hygiene ; Oxidants/*pharmacology/therapeutic use ; Pilot Projects ; Young Adult ; }, abstract = {UNLABELLED: Oral bacteria live in symbiosis with the host. Therefore, when mouthwashes are indicated, selective inhibition of taxa contributing to disease is preferred instead of broad-spectrum antimicrobials. The potential selectivity of an oxygenating mouthwash, Ardox-X® (AX), has not been assessed. The aim of this study was to determine the antimicrobial potential of AX and the effects of a twice-daily oral rinse on dental plaque composition.

MATERIAL AND METHODS: In vitro, 16 oral bacterial strains were tested using agar diffusion susceptibility, minimum inhibitory and minimum bactericidal concentration tests. A pilot clinical study was performed with 25 healthy volunteers. Clinical assessments and microbiological sampling of supragingival plaque were performed at 1 month before the experiment (Pre-exp), at the start of the experiment (Baseline) and after the one-week experimental period (Post-exp). During the experiment individuals used AX mouthwash twice daily in absence of other oral hygiene measures. The microbiological composition of plaque was assessed by 16S rRNA gene amplicon sequencing.

RESULTS: AX showed high inter-species variation in microbial growth inhibition. The tested Prevotella strains and Fusobacterium nucleatum showed the highest sensitivity, while streptococci and Lactobacillus acidophilus were most resistant to AX. Plaque scores at Pre-exp and Baseline visits did not differ significantly (p = 0.193), nor did the microbial composition of plaque. During a period of 7-days non-brushing but twice daily rinsing plaque scores increased from 2.21 (0.31) at Baseline to 2.43 (0.39) Post-exp. A significant microbial shift in composition was observed: genus Streptococcus and Veillonella increased while Corynebacterium, Haemophilus, Leptotrichia, Cardiobacterium and Capnocytophaga decreased (p ≤ 0.001).

CONCLUSION: AX has the potential for selective inhibition of oral bacteria. The shift in oral microbiome after 1 week of rinsing deserves further research.}, } @article {pmid25089898, year = {2014}, author = {Qiu, Y and Nakao, R and Ohnuma, A and Kawamori, F and Sugimoto, C}, title = {Microbial population analysis of the salivary glands of ticks; a possible strategy for the surveillance of bacterial pathogens.}, journal = {PloS one}, volume = {9}, number = {8}, pages = {e103961}, pmid = {25089898}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/genetics/*growth & development ; DNA, Ribosomal/genetics ; Female ; Likelihood Functions ; Male ; Microbiota ; Molecular Sequence Data ; Phylogeny ; Principal Component Analysis ; Salivary Glands/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; Ticks/*microbiology ; }, abstract = {Ticks are one of the most important blood-sucking vectors for infectious microorganisms in humans and animals. When feeding they inject saliva, containing microbes, into the host to facilitate the uptake of blood. An understanding of the microbial populations within their salivary glands would provide a valuable insight when evaluating the vectorial capacity of ticks. Three tick species (Ixodes ovatus, I. persulcatus and Haemaphysalis flava) were collected in Shizuoka Prefecture of Japan between 2008 and 2011. Each tick was dissected and the salivary glands removed. Bacterial communities in each salivary gland were characterized by 16S amplicon pyrosequencing using a 454 GS-Junior Next Generation Sequencer. The Ribosomal Database Project (RDP) Classifier was used to classify sequence reads at the genus level. The composition of the microbial populations of each tick species were assessed by principal component analysis (PCA) using the Metagenomics RAST (MG-RAST) metagenomic analysis tool. Rickettsia-specific PCR was used for the characterization of rickettsial species. Almost full length of 16S rDNA was amplified in order to characterize unclassified bacterial sequences obtained in I. persulcatus female samples. The numbers of bacterial genera identified for the tick species were 71 (I. ovatus), 127 (I. persulcatus) and 59 (H. flava). Eighteen bacterial genera were commonly detected in all tick species. The predominant bacterial genus observed in all tick species was Coxiella. Spiroplasma was detected in Ixodes, and not in H. flava. PCA revealed that microbial populations in tick salivary glands were different between tick species, indicating that host specificities may play an important role in determining the microbial complement. Four female I. persulcatus samples contained a high abundance of several sequences belonging to Alphaproteobacteria symbionts. This study revealed the microbial populations within the salivary glands of three species of ticks, and the results will contribute to the knowledge and prediction of emerging tick-borne diseases.}, } @article {pmid25089581, year = {2014}, author = {Mao, Y and Yu, K and Xia, Y and Chao, Y and Zhang, T}, title = {Genome reconstruction and gene expression of "Candidatus Accumulibacter phosphatis" Clade IB performing biological phosphorus removal.}, journal = {Environmental science & technology}, volume = {48}, number = {17}, pages = {10363-10371}, doi = {10.1021/es502642b}, pmid = {25089581}, issn = {1520-5851}, mesh = {Base Sequence ; Betaproteobacteria/*genetics ; Biodegradation, Environmental ; Contig Mapping ; *Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Genome, Bacterial/*genetics ; Metabolic Networks and Pathways/genetics ; Metagenome/genetics ; Metagenomics ; Microbiota/genetics ; Models, Biological ; Phosphorus/*isolation & purification ; *Phylogeny ; Sequence Analysis, DNA ; Transcriptome/genetics ; }, abstract = {We report the first integrated metatranscriptomic and metagenomic analysis of enhanced biological phosphorus removal (EBPR) sludge. A draft genome of Candidatus Accumulibacter spp. strain HKU-1, a member of Clade IB, was retrieved. It was estimated to be ∼90% complete and shared average nucleotide identities of 83% and 88% with the finished genome CAP IIA UW-1 and the draft genome CAP IA UW-2, respectively. Different from CAP IIA UW-1, the phosphotransferase (pap) in polyphosphate metabolism and V-ATPase in orthophosphate transport were absent from CAP IB HKU-1. Additionally, unlike CAP IA UW-2, CAP IB HKU-1 carried the genes for carbon fixation and nitrogen fixation. Despite these differences, the key genes required for acetate uptake, glycolysis and polyhydroxyalkanoate (PHA) synthesis were conserved in all these Accumulibacter genomes. The preliminary metatranscriptomic results revealed that the most significantly up-regulated genes of CAP IB HKU-1 from the anaerobic to the aerobic phase were responsible for assimilatory sulfate reduction, genetic information processing and phosphorus absorption, while the down-regulated genes were related to N2O reduction, PHA synthesis and acetyl-CoA formation. This study yielded another important Accumulibacter genome, revealed the functional difference within the Accumulibacter Type I, and uncovered the genetic responses to EBPR stimuli at a higher resolution.}, } @article {pmid25087692, year = {2015}, author = {De Cruz, P and Kang, S and Wagner, J and Buckley, M and Sim, WH and Prideaux, L and Lockett, T and McSweeney, C and Morrison, M and Kirkwood, CD and Kamm, MA}, title = {Association between specific mucosa-associated microbiota in Crohn's disease at the time of resection and subsequent disease recurrence: a pilot study.}, journal = {Journal of gastroenterology and hepatology}, volume = {30}, number = {2}, pages = {268-278}, doi = {10.1111/jgh.12694}, pmid = {25087692}, issn = {1440-1746}, mesh = {Adalimumab/administration & dosage ; Adult ; Aged ; Biopsy ; Cecum/microbiology/surgery ; Colonoscopy ; Crohn Disease/drug therapy/*microbiology/*surgery ; Cross-Sectional Studies ; Drug Therapy, Combination ; Female ; Forecasting ; *Gastrointestinal Microbiome ; Humans ; Ileum/microbiology/surgery ; Intestinal Mucosa/*microbiology ; Longitudinal Studies ; Male ; Methyltransferases/administration & dosage ; Metronidazole/administration & dosage ; Middle Aged ; *Pilot Projects ; Postoperative Care ; Prognosis ; Recurrence ; Risk ; Time Factors ; Young Adult ; }, abstract = {BACKGROUND AND AIM: Crohn's disease pathogenesis involves alterations in the gut microbiota. We characterized the mucosa-associated microbiota at the time of surgical resection and 6 months later to identify bacterial profiles associated with recurrence and remission.

METHODS: Tissue samples were collected from surgical resection specimens in 12 Crohn's disease patients, and at 6 months postoperative colonoscopy from the neoterminal ileum and anastomosis. Endoscopic recurrence was assessed using the Rutgeerts score. Microbiota was characterized using microarray and 454 pyrosequencing. Longitudinal comparisons were made within patients, and cross-sectional comparisons made with colonoscopic biopsies from the terminal ileum and cecum of 10 healthy subjects.

RESULTS: Microbiota of healthy subjects had high diversity and was dominated by the Firmicutes, Bacteroidetes, and Proteobacteria phyla. Biodiversity was lower in Crohn's disease patients at the time of surgery, increased after surgery, but still differed from healthy subjects. Crohn's disease patients with recurrent disease retained a microbiota favoring proteolytic-fueled fermentation and lactic acid-producing bacteria, including Enterococcus and Veillonella spp., while those maintaining remission demonstrated predominant saccharolytic Bacteroides, Prevotella, and Parabacteroides spp., and saccharolytic, butyrate-producing Firmicutes.

CONCLUSION: In Crohn's disease, the mucosa-associated microbiota diversity is reduced at the time of surgery, but also differs between patients with different clinical outcomes at 6 months. These findings may provide prognostic information at the time of surgery, allowing identification of patients at increased risk of recurrence, and provide basis for a more targeted approach for therapeutic interventions after surgery.}, } @article {pmid25084126, year = {2014}, author = {Keller, A and Horn, H and Förster, F and Schultz, J}, title = {Computational integration of genomic traits into 16S rDNA microbiota sequencing studies.}, journal = {Gene}, volume = {549}, number = {1}, pages = {186-191}, doi = {10.1016/j.gene.2014.07.066}, pmid = {25084126}, issn = {1879-0038}, mesh = {Bacteria/classification/*genetics ; Computational Biology/*methods ; DNA Barcoding, Taxonomic ; DNA, Bacterial/*genetics ; DNA, Ribosomal/*genetics ; Genetic Markers ; Genome, Bacterial ; Genomics ; Metagenomics ; Microbiota/*genetics ; Multigene Family ; RNA, Ribosomal, 16S/*genetics ; Reproducibility of Results ; }, abstract = {Molecular sequencing techniques help to understand microbial biodiversity with regard to species richness, assembly structure and function. In this context, available methods are barcoding, metabarcoding, genomics and metagenomics. The first two are restricted to taxonomic assignments, whilst genomics only refers to functional capabilities of a single organism. Metagenomics by contrast yields information about organismal and functional diversity of a community. However currently it is very demanding regarding labour and costs and thus not applicable to most laboratories. Here, we show in a proof-of-concept that computational approaches are able to retain functional information about microbial communities assessed through 16S rDNA (meta)barcoding by referring to reference genomes. We developed an automatic pipeline to show that such integration may infer preliminary or supplementary genomic content of a community. We applied it to two biological datasets and delineated significantly overrepresented protein families between communities. The script alongside supporting data is available at http://bioapps.biozentrum.uni-wuerzburg.de.}, } @article {pmid25083986, year = {2014}, author = {Dalal, SR and Chang, EB}, title = {The microbial basis of inflammatory bowel diseases.}, journal = {The Journal of clinical investigation}, volume = {124}, number = {10}, pages = {4190-4196}, pmid = {25083986}, issn = {1558-8238}, support = {T32 DK07074/DK/NIDDK NIH HHS/United States ; R37 DK47722/DK/NIDDK NIH HHS/United States ; P30 DK042086/DK/NIDDK NIH HHS/United States ; F32 DK09025/DK/NIDDK NIH HHS/United States ; T32 DK007074/DK/NIDDK NIH HHS/United States ; R37 DK047722/DK/NIDDK NIH HHS/United States ; F32 DK009025/DK/NIDDK NIH HHS/United States ; R01 DK047722/DK/NIDDK NIH HHS/United States ; R01 DK097268/DK/NIDDK NIH HHS/United States ; P30 DK42086/DK/NIDDK NIH HHS/United States ; }, mesh = {Disease Progression ; Dysbiosis/*microbiology ; Gastrointestinal Tract ; Genetic Predisposition to Disease ; Genome ; Humans ; Immune System ; Inflammation ; Inflammatory Bowel Diseases/*microbiology ; Intestines/*microbiology ; Metagenome ; *Microbiota ; Treatment Outcome ; }, abstract = {Inflammatory bowel diseases (IBD) are chronic, progressive diseases characterized by aberrant immune responses to environmental and gut microbial triggers in genetically susceptible hosts. Clinical, genetic, and experimental data support the role of gut microbes in causing and sustaining these diseases. Our understanding of IBD has changed dramatically as the result of advances in cultivation-independent approaches and computational platforms for the analysis of large data sets. However, investigations relevant to clinical observations and the natural history of the diseases will be essential for the development of microbial, genetic, and biological metrics that may be used to individualize assessment of risk and improve clinical outcomes in IBD.}, } @article {pmid25081552, year = {2014}, author = {Li, LG and Cai, L and Zhang, XX and Zhang, T}, title = {Potentially novel copper resistance genes in copper-enriched activated sludge revealed by metagenomic analysis.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {24}, pages = {10255-10266}, doi = {10.1007/s00253-014-5939-5}, pmid = {25081552}, issn = {1432-0614}, mesh = {Archaea/*drug effects/genetics ; Bacteria/*drug effects/genetics ; Biota/drug effects ; Cluster Analysis ; Copper/*toxicity ; DNA, Ribosomal/chemistry/genetics ; *Drug Resistance, Microbial ; Eukaryota/*drug effects/genetics ; Metagenomics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Sewage/chemistry/*microbiology ; }, abstract = {In this study, we utilized the Illumina high-throughput metagenomic approach to investigate diversity and abundance of both microbial community and copper resistance genes (CuRGs) in activated sludge (AS) which was enriched under copper selective stress up to 800 mg/L. The raw datasets (~3.5 Gb for each sample, i.e., the copper-enriched AS and the control AS) were merged and normalized for the BLAST analyses against the SILVA SSU rRNA gene database and self-constructed copper resistance protein database (CuRD). Also, the raw metagenomic sequences were assembled into contigs and analyzed based on Open Reading Frames (ORFs) to identify potentially novel copper resistance genes. Among the different resistance systems for copper detoxification under the high copper stress condition, the Cus system was the most enriched system. The results also indicated that genes encoding multi-copper oxidase played a more important role than those encoding efflux proteins. More significantly, several potentially novel copper resistance ORFs were identified by Pfam search and phylogenic analysis. This study demonstrated a new understanding of microbial-mediated copper resistance under high copper stress using high-throughput shotgun sequencing technique.}, } @article {pmid25080446, year = {2015}, author = {Anhê, FF and Roy, D and Pilon, G and Dudonné, S and Matamoros, S and Varin, TV and Garofalo, C and Moine, Q and Desjardins, Y and Levy, E and Marette, A}, title = {A polyphenol-rich cranberry extract protects from diet-induced obesity, insulin resistance and intestinal inflammation in association with increased Akkermansia spp. population in the gut microbiota of mice.}, journal = {Gut}, volume = {64}, number = {6}, pages = {872-883}, doi = {10.1136/gutjnl-2014-307142}, pmid = {25080446}, issn = {1468-3288}, mesh = {Animals ; Diet, High-Fat/adverse effects ; Endotoxemia/etiology/prevention & control ; Enteritis/*drug therapy/*microbiology ; Hepatitis/prevention & control ; Homeostasis/drug effects ; *Insulin Resistance ; Intestines/microbiology ; Lipid Metabolism/drug effects ; Lipids/blood ; Lipopolysaccharides/blood ; Liver/drug effects/metabolism/pathology ; Male ; Mice ; Mice, Inbred C57BL ; Microbiota/drug effects ; Obesity, Abdominal/etiology/*prevention & control ; Organ Size/drug effects ; Plant Extracts/*pharmacology ; Polyphenols/analysis/pharmacology ; Triglycerides/metabolism ; Vaccinium macrocarpon/*chemistry ; Verrucomicrobia/*drug effects/isolation & purification ; }, abstract = {OBJECTIVE: The increasing prevalence of obesity and type 2 diabetes (T2D) demonstrates the failure of conventional treatments to curb these diseases. The gut microbiota has been put forward as a key player in the pathophysiology of diet-induced T2D. Importantly, cranberry (Vaccinium macrocarpon Aiton) is associated with a number of beneficial health effects. We aimed to investigate the metabolic impact of a cranberry extract (CE) on high fat/high sucrose (HFHS)-fed mice and to determine whether its consequent antidiabetic effects are related to modulations in the gut microbiota.

DESIGN: C57BL/6J mice were fed either a chow or a HFHS diet. HFHS-fed mice were gavaged daily either with vehicle (water) or CE (200 mg/kg) for 8 weeks. The composition of the gut microbiota was assessed by analysing 16S rRNA gene sequences with 454 pyrosequencing.

RESULTS: CE treatment was found to reduce HFHS-induced weight gain and visceral obesity. CE treatment also decreased liver weight and triglyceride accumulation in association with blunted hepatic oxidative stress and inflammation. CE administration improved insulin sensitivity, as revealed by improved insulin tolerance, lower homeostasis model assessment of insulin resistance and decreased glucose-induced hyperinsulinaemia during an oral glucose tolerance test. CE treatment was found to lower intestinal triglyceride content and to alleviate intestinal inflammation and oxidative stress. Interestingly, CE treatment markedly increased the proportion of the mucin-degrading bacterium Akkermansia in our metagenomic samples.

CONCLUSIONS: CE exerts beneficial metabolic effects through improving HFHS diet-induced features of the metabolic syndrome, which is associated with a proportional increase in Akkermansia spp.}, } @article {pmid25079328, year = {2014}, author = {Qin, N and Yang, F and Li, A and Prifti, E and Chen, Y and Shao, L and Guo, J and Le Chatelier, E and Yao, J and Wu, L and Zhou, J and Ni, S and Liu, L and Pons, N and Batto, JM and Kennedy, SP and Leonard, P and Yuan, C and Ding, W and Chen, Y and Hu, X and Zheng, B and Qian, G and Xu, W and Ehrlich, SD and Zheng, S and Li, L}, title = {Alterations of the human gut microbiome in liver cirrhosis.}, journal = {Nature}, volume = {513}, number = {7516}, pages = {59-64}, pmid = {25079328}, issn = {1476-4687}, mesh = {Case-Control Studies ; Chronic Disease ; Diabetes Mellitus, Type 2/microbiology ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Genetic Markers/genetics ; Health ; Humans ; Inflammatory Bowel Diseases/microbiology ; Liver Cirrhosis/*diagnosis/*microbiology ; *Metagenomics ; Microbiota/*genetics/*physiology ; Mouth/microbiology ; Phylogeny ; Reproducibility of Results ; }, abstract = {Liver cirrhosis occurs as a consequence of many chronic liver diseases that are prevalent worldwide. Here we characterize the gut microbiome in liver cirrhosis by comparing 98 patients and 83 healthy control individuals. We build a reference gene set for the cohort containing 2.69 million genes, 36.1% of which are novel. Quantitative metagenomics reveals 75,245 genes that differ in abundance between the patients and healthy individuals (false discovery rate < 0.0001) and can be grouped into 66 clusters representing cognate bacterial species; 28 are enriched in patients and 38 in control individuals. Most (54%) of the patient-enriched, taxonomically assigned species are of buccal origin, suggesting an invasion of the gut from the mouth in liver cirrhosis. Biomarkers specific to liver cirrhosis at gene and function levels are revealed by a comparison with those for type 2 diabetes and inflammatory bowel disease. On the basis of only 15 biomarkers, a highly accurate patient discrimination index is created and validated on an independent cohort. Thus microbiota-targeted biomarkers may be a powerful tool for diagnosis of different diseases.}, } @article {pmid25077800, year = {2014}, author = {Pongor, LS and Vera, R and Ligeti, B}, title = {Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e103441}, pmid = {25077800}, issn = {1932-6203}, mesh = {Computer Graphics ; *Datasets as Topic ; *Metagenome ; Microbiota/*genetics ; User-Computer Interface ; }, abstract = {Next generation sequencing (NGS) of metagenomic samples is becoming a standard approach to detect individual species or pathogenic strains of microorganisms. Computer programs used in the NGS community have to balance between speed and sensitivity and as a result, species or strain level identification is often inaccurate and low abundance pathogens can sometimes be missed. We have developed Taxoner, an open source, taxon assignment pipeline that includes a fast aligner (e.g. Bowtie2) and a comprehensive DNA sequence database. We tested the program on simulated datasets as well as experimental data from Illumina, IonTorrent, and Roche 454 sequencing platforms. We found that Taxoner performs as well as, and often better than BLAST, but requires two orders of magnitude less running time meaning that it can be run on desktop or laptop computers. Taxoner is slower than the approaches that use small marker databases but is more sensitive due the comprehensive reference database. In addition, it can be easily tuned to specific applications using small tailored databases. When applied to metagenomic datasets, Taxoner can provide a functional summary of the genes mapped and can provide strain level identification. Taxoner is written in C for Linux operating systems. The code and documentation are available for research applications at http://code.google.com/p/taxoner.}, } @article {pmid25072413, year = {2015}, author = {Grube, M and Cernava, T and Soh, J and Fuchs, S and Aschenbrenner, I and Lassek, C and Wegner, U and Becher, D and Riedel, K and Sensen, CW and Berg, G}, title = {Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics.}, journal = {The ISME journal}, volume = {9}, number = {2}, pages = {412-424}, pmid = {25072413}, issn = {1751-7370}, support = {I 882/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Ascomycota/genetics/*physiology ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Bacterial Physiological Phenomena ; Chlorophyta/genetics ; Lichens/*microbiology ; Metagenome ; Metagenomics ; *Microbiota ; Photosynthesis ; Proteome ; Proteomics ; *Symbiosis/genetics ; }, abstract = {Symbioses represent a frequent and successful lifestyle on earth and lichens are one of their classic examples. Recently, bacterial communities were identified as stable, specific and structurally integrated partners of the lichen symbiosis, but their role has remained largely elusive in comparison to the well-known functions of the fungal and algal partners. We have explored the metabolic potentials of the microbiome using the lung lichen Lobaria pulmonaria as the model. Metagenomic and proteomic data were comparatively assessed and visualized by Voronoi treemaps. The study was complemented with molecular, microscopic and physiological assays. We have found that more than 800 bacterial species have the ability to contribute multiple aspects to the symbiotic system, including essential functions such as (i) nutrient supply, especially nitrogen, phosphorous and sulfur, (ii) resistance against biotic stress factors (that is, pathogen defense), (iii) resistance against abiotic factors, (iv) support of photosynthesis by provision of vitamin B12, (v) fungal and algal growth support by provision of hormones, (vi) detoxification of metabolites, and (vii) degradation of older parts of the lichen thallus. Our findings showed the potential of lichen-associated bacteria to interact with the fungal as well as algal partner to support health, growth and fitness of their hosts. We developed a model of the symbiosis depicting the functional multi-player network of the participants, and argue that the strategy of functional diversification in lichens supports the longevity and persistence of lichens under extreme and changing ecological conditions.}, } @article {pmid25064656, year = {2014}, author = {Delcenserie, V and Taminiau, B and Delhalle, L and Nezer, C and Doyen, P and Crevecoeur, S and Roussey, D and Korsak, N and Daube, G}, title = {Microbiota characterization of a Belgian protected designation of origin cheese, Herve cheese, using metagenomic analysis.}, journal = {Journal of dairy science}, volume = {97}, number = {10}, pages = {6046-6056}, doi = {10.3168/jds.2014-8225}, pmid = {25064656}, issn = {1525-3198}, mesh = {Animals ; Bacteria/genetics/*isolation & purification ; Bacterial Load/veterinary ; Belgium ; Cheese/*microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Gene Library ; High-Throughput Nucleotide Sequencing/veterinary ; Metagenomics/*methods ; Microbiota/*genetics ; Milk/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/veterinary ; }, abstract = {Herve cheese is a Belgian soft cheese with a washed rind, and is made from raw or pasteurized milk. The specific microbiota of this cheese has never previously been fully explored and the use of raw or pasteurized milk in addition to starters is assumed to affect the microbiota of the rind and the heart. The aim of the study was to analyze the bacterial microbiota of Herve cheese using classical microbiology and a metagenomic approach based on 16S ribosomal DNA pyrosequencing. Using classical microbiology, the total counts of bacteria were comparable for the 11 samples of tested raw and pasteurized milk cheeses, reaching almost 8 log cfu/g. Using the metagenomic approach, 207 different phylotypes were identified. The rind of both the raw and pasteurized milk cheeses was found to be highly diversified. However, 96.3 and 97.9% of the total microbiota of the raw milk and pasteurized cheese rind, respectively, were composed of species present in both types of cheese, such as Corynebacterium casei, Psychrobacter spp., Lactococcus lactis ssp. cremoris, Staphylococcus equorum, Vagococcus salmoninarum, and other species present at levels below 5%. Brevibacterium linens were present at low levels (0.5 and 1.6%, respectively) on the rind of both the raw and the pasteurized milk cheeses, even though this bacterium had been inoculated during the manufacturing process. Interestingly, Psychroflexus casei, also described as giving a red smear to Raclette-type cheese, was identified in small proportions in the composition of the rind of both the raw and pasteurized milk cheeses (0.17 and 0.5%, respectively). In the heart of the cheeses, the common species of bacteria reached more than 99%. The main species identified were Lactococcus lactis ssp. cremoris, Psychrobacter spp., and Staphylococcus equorum ssp. equorum. Interestingly, 93 phylotypes were present only in the raw milk cheeses and 29 only in the pasteurized milk cheeses, showing the high diversity of the microbiota. Corynebacterium casei and Enterococcus faecalis were more prevalent in the raw milk cheeses, whereas Psychrobacter celer was present in the pasteurized milk cheeses. However, this specific microbiota represented a low proportion of the cheese microbiota. This study demonstrated that Herve cheese microbiota is rich and that pasteurized milk cheeses are microbiologically very close to raw milk cheeses, probably due to the similar manufacturing process. The characterization of the microbiota of this particular protected designation of origin cheese was useful in enabling us to gain a better knowledge of the bacteria responsible for the character of this cheese.}, } @article {pmid25056226, year = {2014}, author = {Enomoto, T and Sowa, M and Nishimori, K and Shimazu, S and Yoshida, A and Yamada, K and Furukawa, F and Nakagawa, T and Yanagisawa, N and Iwabuchi, N and Odamaki, T and Abe, F and Nakayama, J and Xiao, JZ}, title = {Effects of bifidobacterial supplementation to pregnant women and infants in the prevention of allergy development in infants and on fecal microbiota.}, journal = {Allergology international : official journal of the Japanese Society of Allergology}, volume = {63}, number = {4}, pages = {575-585}, doi = {10.2332/allergolint.13-OA-0683}, pmid = {25056226}, issn = {1440-1592}, mesh = {Adult ; Bifidobacterium/*immunology ; Biodiversity ; Feces/*microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Hypersensitivity/epidemiology/*microbiology/*prevention & control ; Infant ; Male ; Metagenomics ; *Microbiota ; Odds Ratio ; Patient Compliance ; Pregnancy ; Prevalence ; Probiotics/*administration & dosage ; Young Adult ; }, abstract = {BACKGROUND: Probiotic administration may be a useful method for preventing allergies in infants; however, there have been controversial results about the efficacy. We investigated the effects of bifidobacterial supplementation on the risk of developing allergic diseases in the Japanese population.

METHODS: In an open trial, we gave Bifidobacterium breve M-16V and Bifidobacterium longum BB536 prenatally to 130 mothers beginning 1 month prior to delivery and postnatally to their infants for 6 months. Another 36 mother-infant pairs served as controls and did not receive the bifidobacterial supplementation. Development of allergic symptoms in the infants was assessed at 4, 10 and 18 months of age. Fecal samples were collected from the mothers and infants.

RESULTS: The risk of developing eczema/atopic dermatitis (AD) during the first 18 months of life was significantly reduced in infants in the probiotic group (OR: 0.231 [95% CI: 0.084-0.628] and 0.304 [0.105-0.892] at 10 and 18 months of age, respectively). Pyrosequencing analyses indicated an altered composition of the fecal microbiota at 4 months for infants who developed eczema/AD at 4 and 10 months of age. The proportion of Proteobacteria was significantly lower (P = 0.007) in mothers at the time of delivery who received the supplementation when compared with the control group and was positively correlated (r = 0.283, P = 0.024) with that of infants at 4 months of age. No adverse effects were related to the use of probiotics.

CONCLUSIONS: These data suggest that the prenatal and postnatal supplementation of bifidobacteria is effective in primary preventing allergic diseases. Some limited changes in the composition of fecal microbiota by the bifidobacterial supplementation were observed.}, } @article {pmid25054627, year = {2014}, author = {Fisher, CK and Mehta, P}, title = {Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e102451}, pmid = {25054627}, issn = {1932-6203}, support = {K25 GM086909/GM/NIGMS NIH HHS/United States ; K25GM086909/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Bacteroides/*genetics ; Bacteroides fragilis/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; *Linear Models ; Metagenomics/*methods ; Microbial Interactions ; Microbiota/*genetics ; Time Factors ; }, abstract = {Human associated microbial communities exert tremendous influence over human health and disease. With modern metagenomic sequencing methods it is now possible to follow the relative abundance of microbes in a community over time. These microbial communities exhibit rich ecological dynamics and an important goal of microbial ecology is to infer the ecological interactions between species directly from sequence data. Any algorithm for inferring ecological interactions must overcome three major obstacles: 1) a correlation between the abundances of two species does not imply that those species are interacting, 2) the sum constraint on the relative abundances obtained from metagenomic studies makes it difficult to infer the parameters in timeseries models, and 3) errors due to experimental uncertainty, or mis-assignment of sequencing reads into operational taxonomic units, bias inferences of species interactions due to a statistical problem called "errors-in-variables". Here we introduce an approach, Learning Interactions from MIcrobial Time Series (LIMITS), that overcomes these obstacles. LIMITS uses sparse linear regression with boostrap aggregation to infer a discrete-time Lotka-Volterra model for microbial dynamics. We tested LIMITS on synthetic data and showed that it could reliably infer the topology of the inter-species ecological interactions. We then used LIMITS to characterize the species interactions in the gut microbiomes of two individuals and found that the interaction networks varied significantly between individuals. Furthermore, we found that the interaction networks of the two individuals are dominated by distinct "keystone species", Bacteroides fragilis and Bacteroided stercosis, that have a disproportionate influence on the structure of the gut microbiome even though they are only found in moderate abundance. Based on our results, we hypothesize that the abundances of certain keystone species may be responsible for individuality in the human gut microbiome.}, } @article {pmid25048881, year = {2014}, author = {Guo, X and Liu, S and Wang, Z and Zhang, XX and Li, M and Wu, B}, title = {Metagenomic profiles and antibiotic resistance genes in gut microbiota of mice exposed to arsenic and iron.}, journal = {Chemosphere}, volume = {112}, number = {}, pages = {1-8}, doi = {10.1016/j.chemosphere.2014.03.068}, pmid = {25048881}, issn = {1879-1298}, mesh = {Animals ; Arsenic/*pharmacology ; Drug Resistance, Microbial/*genetics ; Intestinal Mucosa/metabolism ; Intestines/*drug effects/*microbiology ; Iron/*pharmacology ; Male ; Metagenome/*drug effects/*genetics ; Metagenomics ; Mice ; Microbiota/drug effects/*genetics ; }, abstract = {Iron (Fe) has been widely applied to treat arsenic (As)-contaminated water, and Fe could influence bioavailability and toxicity of As. However, little is known about the impact of As and/or Fe on gut microbiota, which plays important roles in host health. In this study, high-throughput sequencing and quantitative real time PCR were applied to analyze the impact of As and Fe on mouse gut microbiota. Co-exposure of As and Fe mitigated effects on microbial community to a certain extent. Correlation analysis showed the shifts in gut microbiota caused by As and/or Fe exposure might be important reason of changes in metabolic profiles of mouse. For antibiotic resistance genes (ARGs), co-exposure of As and Fe increased types and abundance of ARGs. But for high abundance ARGs, such as tetQ, tetO and tetM, co-exposure of As and Fe mitigated effects on their abundances compared to exposure to As and Fe alone. No obvious relationship between ARGs and mobile genetic elements were found. The changes in ARGs caused by metal exposure might be due to the alteration of gut microbial diversity. Our results show that changes of gut microbial community caused by As and/or Fe can influence host metabolisms and abundances of ARGs in gut, indicating that changes of gut microbiota should be considered during the risk assessment of As and/or Fe.}, } @article {pmid25048741, year = {2014}, author = {Bulgari, D and Casati, P and Quaglino, F and Bianco, PA}, title = {Endophytic bacterial community of grapevine leaves influenced by sampling date and phytoplasma infection process.}, journal = {BMC microbiology}, volume = {14}, number = {}, pages = {198}, pmid = {25048741}, issn = {1471-2180}, mesh = {*Biota ; Endophytes/*classification/*isolation & purification ; Italy ; Metagenomics ; Phytoplasma/*growth & development ; Plant Diseases/microbiology ; Plant Leaves/*microbiology ; Polymerase Chain Reaction ; Seasons ; Vitis/*microbiology ; }, abstract = {BACKGROUND: Endophytic bacteria benefit host plant directly or indirectly, e.g. by biocontrol of the pathogens. Up to now, their interactions with the host and with other microorganisms are poorly understood. Consequently, a crucial step for improving the knowledge of those relationships is to determine if pathogens or plant growing season influence endophytic bacterial diversity and dynamic.

RESULTS: Four healthy, four phytoplasma diseased and four recovered (symptomatic plants that spontaneously regain a healthy condition) grapevine plants were sampled monthly from June to October 2010 in a vineyard in north-western Italy. Metagenomic DNA was extracted from sterilized leaves and the endophytic bacterial community dynamic and diversity were analyzed by taxon specific real-time PCR, Length-Heterogeneity PCR and genus-specific PCR. These analyses revealed that both sampling date and phytoplasma infection influenced the endophytic bacterial composition. Interestingly, in June, when the plants are symptomless and the pathogen is undetectable (i) the endophytic bacterial community associated with diseased grapevines was different from those in the other sampling dates, when the phytoplasmas are detectable inside samples; (ii) the microbial community associated with recovered plants differs from that living inside healthy and diseased plants. Interestingly, LH-PCR database identified bacteria previously reported as biocontrol agents in the examined grapevines. Of these, Burkholderia, Methylobacterium and Pantoea dynamic was influenced by the phytoplasma infection process and seasonality.

CONCLUSION: Results indicated that endophytic bacterial community composition in grapevine is correlated to both phytoplasma infection and sampling date. For the first time, data underlined that, in diseased plants, the pathogen infection process can decrease the impact of seasonality on community dynamic. Moreover, based on experimental evidences, it was reasonable to hypothesize that after recovery the restructured microbial community could maintain the main structure between seasons.}, } @article {pmid25046331, year = {2014}, author = {Walia, R and Kunde, S and Mahajan, L}, title = {Fecal microbiota transplantation in the treatment of refractory Clostridium difficile infection in children: an update.}, journal = {Current opinion in pediatrics}, volume = {26}, number = {5}, pages = {573-578}, doi = {10.1097/MOP.0000000000000127}, pmid = {25046331}, issn = {1531-698X}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Biological Therapy/*methods ; Child ; Child, Preschool ; Clostridioides difficile/*drug effects ; Clostridium Infections/immunology/microbiology/*therapy ; Enterocolitis, Pseudomembranous/immunology/microbiology/*therapy ; Feces/*microbiology ; Humans ; Immunocompromised Host ; Infant ; Intubation, Gastrointestinal ; Metagenome ; Microbiota/*immunology ; Treatment Outcome ; }, abstract = {PURPOSE OF REVIEW: The use of transplanted fecal material for the treatment of diarrheal illness dates back to the fourth-century China. While fecal microbiota transplant has gained increasing popularity over the past 50 years for the treatment of refractory Clostridium difficile infections (RCDIs) in adults, it has only been recently utilized in children. The purpose of this article is to review the use of fecal microbiota transplant (FMT) in the treatment of pediatric RCDIs.

RECENT FINDINGS: Minimal pediatric data, including few case reports and series, document the successful use of FMT for treatment of RCDI in the past 2 years. Patients in these reports included otherwise healthy children, those with inflammatory bowel disease as well as significantly immunocompromised children. Donor fecal infusion via nasogastric tube, gastroscope or colonoscope in children aged 16 months and older demonstrated a high rate of symptom resolution and organism eradication. No complications to date have been reported in children who have undergone FMT.

SUMMARY: FMT is emerging as a well-tolerated and effective treatment for RCDI in not only adults but also children.}, } @article {pmid25043051, year = {2014}, author = {Deng, L and Ignacio-Espinoza, JC and Gregory, AC and Poulos, BT and Weitz, JS and Hugenholtz, P and Sullivan, MB}, title = {Viral tagging reveals discrete populations in Synechococcus viral genome sequence space.}, journal = {Nature}, volume = {513}, number = {7517}, pages = {242-245}, pmid = {25043051}, issn = {1476-4687}, mesh = {Biodiversity ; *Environmental Microbiology ; Genome, Viral/*genetics ; Host-Pathogen Interactions ; Metagenome ; Molecular Sequence Data ; Pacific Ocean ; Seawater/*virology ; Species Specificity ; Synechococcus/*virology ; }, abstract = {Microbes and their viruses drive myriad processes across ecosystems ranging from oceans and soils to bioreactors and humans. Despite this importance, microbial diversity is only now being mapped at scales relevant to nature, while the viral diversity associated with any particular host remains little researched. Here we quantify host-associated viral diversity using viral-tagged metagenomics, which links viruses to specific host cells for high-throughput screening and sequencing. In a single experiment, we screened 10(7) Pacific Ocean viruses against a single strain of Synechococcus and found that naturally occurring cyanophage genome sequence space is statistically clustered into discrete populations. These population-based, host-linked viral ecological data suggest that, for this single host and seawater sample alone, there are at least 26 double-stranded DNA viral populations with estimated relative abundances ranging from 0.06 to 18.2%. These populations include previously cultivated cyanophage and new viral types missed by decades of isolate-based studies. Nucleotide identities of homologous genes mostly varied by less than 1% within populations, even in hypervariable genome regions, and by 42-71% between populations, which provides benchmarks for viral metagenomics and genome-based viral species definitions. Together these findings showcase a new approach to viral ecology that quantitatively links objectively defined environmental viral populations, and their genomes, to their hosts.}, } @article {pmid25039472, year = {2015}, author = {Soffer, N and Zaneveld, J and Vega Thurber, R}, title = {Phage-bacteria network analysis and its implication for the understanding of coral disease.}, journal = {Environmental microbiology}, volume = {17}, number = {4}, pages = {1203-1218}, doi = {10.1111/1462-2920.12553}, pmid = {25039472}, issn = {1462-2920}, mesh = {Animals ; Anthozoa/*microbiology/virology ; Bacteriophages/*genetics ; Campylobacter/genetics/growth & development/*virology ; Humans ; Microbial Consortia ; Microbial Interactions/physiology ; RNA, Ribosomal, 16S/genetics ; Rhodobacteraceae/genetics/growth & development/*virology ; }, abstract = {Multiple studies have explored microbial shifts in diseased or stressed corals; however, little is known about bacteriophage interactions with microbes in this context. This study characterized microbial 16S rRNA amplicons and phage metagenomes associated with Montastraea annularis corals during a concurrent white plague disease outbreak and bleaching event. Phage consortia differed between bleached and diseased tissues. Phages in the family Inoviridae were elevated in diseased or healthy tissues compared with bleached portions of diseased tissues. Microbial communities also differed between diseased and bleached corals. Bacteria in the orders Rhodobacterales and Campylobacterales were increased while Kiloniellales was decreased in diseased compared with other tissues. A network of phage-bacteria interactions was constructed of all phage strains and 11 bacterial genera that differed across health states. Phage-bacteria interactions varied in specificity: phages interacted with one to eight bacterial hosts while bacteria interacted with up to 59 phages. Six phages were identified that interacted exclusively with Rhodobacterales and Campylobacterales. These results suggest that phages have a role in controlling stress-associated bacteria, and that networks can be utilized to select potential phages for mitigating detrimental bacterial growth in phage therapy applications.}, } @article {pmid26082117, year = {2014}, author = {Casas, V and Maloy, S}, title = {Genomic and Metagenomic Approaches for Predicting Pathogen Evolution.}, journal = {Microbiology spectrum}, volume = {2}, number = {1}, pages = {OH-0019-2013}, doi = {10.1128/microbiolspec.OH-0019-2013}, pmid = {26082117}, issn = {2165-0497}, support = {R01 GM098736/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biota ; Climate Change ; Communicable Disease Control/*methods ; Communicable Diseases, Emerging/*epidemiology ; Computational Biology/methods ; Humans ; Metagenomics/*methods ; }, abstract = {Global climate change can alter the distribution of microbial pathogens and vectors that transmit infectious diseases, exposing humans to newly emerging or reemerging diseases. Early detection of potential pathogens and vectors in the environment can facilitate upstream interventions that limit the spread of infectious disease. Metagenomics is the analysis of DNA sequences from a population of microorganisms in a particular environment, followed by the computational reconstruction of the data to determine what organisms are present and predict their role in the environment. Defining the microbial populations associated with humans, animals, and their environment provides insight into the structure of microbial communities in any particular niche, including the abundance, diversity, and composition of the microbes and viruses present. It can also reveal the distribution of virulence genes within that niche. These data can be used to identify reservoirs of pathogens in an environment and predict environments with a high probability for evolution of new pathogens or outbreaks caused by known pathogens, thereby facilitating approaches to prevent infections of animals or humans before serious outbreaks of infectious disease.}, } @article {pmid26742302, year = {2014}, author = {Perez, HJ and Menezes, ME and d'Acâmpora, AJ}, title = {[Intestinal microbiota].}, journal = {Acta gastroenterologica Latinoamericana}, volume = {44}, number = {3}, pages = {265-272}, pmid = {26742302}, issn = {0300-9033}, mesh = {Animals ; Dysbiosis/microbiology/pathology ; Gastrointestinal Microbiome/*physiology ; Homeostasis/physiology ; Humans ; Metagenome ; Molecular Diagnostic Techniques ; Translational Research, Biomedical/methods ; }, abstract = {There is accumulative evidence on the multiple functions of the intestinal microflora in relation to the homeostasis of the host. At first considered as a simple mutualism, today this relationship proves to be essential to the health and to pathologic processes, particularly metabolic (eg, obesity) and gastrointestinal (eg, inflammatory bowel disease and functional disorders). The first studies were conducted on the microbiota from fecal material cultured anaerobically. With the advent of molecular biology, it has become possible to determine qualitative and quantitatively the dominant, subdominant and transients species. In recent years, there were advances in the understanding of the relationship betwen the microbiota and the host, as well as among the microorganisms in their respective niches. These advances result from translational integration of microbiology with specialities such as molecular biology, cell phisiology, immunology and ecology. There are few studies on the spatial distribution of the microflora in the gut. Unravelling the topography of the microflora in mammals is a way to validate new animal models for the study of microflora.}, } @article {pmid26355506, year = {2014}, author = {Liao, R and Zhang, R and Guan, J and Zhou, S}, title = {A New Unsupervised Binning Approach for Metagenomic Sequences Based on N-grams and Automatic Feature Weighting.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {11}, number = {1}, pages = {42-54}, doi = {10.1109/TCBB.2013.137}, pmid = {26355506}, issn = {1557-9964}, mesh = {Algorithms ; Cluster Analysis ; Computer Simulation ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Microbial Consortia/*genetics ; }, abstract = {The rapid development of high-throughput technologies enables researchers to sequence the whole metagenome of a microbial community sampled directly from the environment. The assignment of these sequence reads into different species or taxonomical classes is a crucial step for metagenomic analysis, which is referred to as binning of metagenomic data. Most traditional binning methods rely on known reference genomes for accurate assignment of the sequence reads, therefore cannot classify reads from unknown species without the help of close references. To overcome this drawback, unsupervised learning based approaches have been proposed, which need not any known species' reference genome for help. In this paper, we introduce a novel unsupervised method called MCluster for binning metagenomic sequences. This method uses N-grams to extract sequence features and utilizes automatic feature weighting to improve the performance of the basic K-means clustering algorithm. We evaluate MCluster on a variety of simulated data sets and a real data set, and compare it with three latest binning methods: AbundanceBin, MetaCluster 3.0, and MetaCluster 5.0. Experimental results show that MCluster achieves obviously better overall performance (F-measure) than AbundanceBin and MetaCluster 3.0 on long metagenomic reads (≥800 bp); while compared with MetaCluster 5.0, MCluster obtains a larger sensitivity, and a comparable yet more stable F-measure on short metagenomic reads (<300 bp). This suggests that MCluster can serve as a promising tool for effectively binning metagenomic sequences.}, } @article {pmid26260088, year = {2015}, author = {Ericsson, AC and Turner, G and Montoya, L and Wolfe, A and Meeker, S and Hsu, C and Maggio-Price, L and Franklin, CL}, title = {Isolation of segmented filamentous bacteria from complex gut microbiota.}, journal = {BioTechniques}, volume = {59}, number = {2}, pages = {94-98}, doi = {10.2144/000114319}, pmid = {26260088}, issn = {1940-9818}, mesh = {Animals ; *Bacteriological Techniques ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Gram-Negative Bacteria/*isolation & purification ; Mice ; }, abstract = {Segmented filamentous bacteria (SFB) modulate the ontogeny of the immune system, and their presence can significantly affect mouse models of disease. Until recently, the inability to successfully culture SFB has made controlled studies on the mechanisms by which these bacteria exert their influence problematic. Here, we report a new method for selecting SFB from complex microbial mixtures, providing researchers a simple and cost-effective means to prepare pure infective inocula for prospective studies and also to compare individual SFB isolates.}, } @article {pmid25842410, year = {2014}, author = {Vakhitov, TIa and Sitkin, SI}, title = {[The superorganism concept in biology and medicine].}, journal = {Eksperimental'naia i klinicheskaia gastroenterologiia = Experimental & clinical gastroenterology}, volume = {}, number = {7}, pages = {72-85}, pmid = {25842410}, issn = {1682-8658}, mesh = {Animals ; Biological Evolution ; *Clinical Medicine ; Gastrointestinal Tract/*microbiology ; *Host-Pathogen Interactions/genetics ; Humans ; Metagenome ; *Microbiology ; *Microbiota/genetics ; *Symbiosis/genetics ; }, abstract = {The paper discusses the concept of the superorganism of man and his microbiota. A unique and little-known details regarding mutualistic relationship of the host and its microbiome are represented. The main metabolic effects of the gut microbiota of the intestine are described. The use of microbial metabolites as autoregulatory substances in experiments and in clinical practice is discussed. Authors propose an innovative concept of controlled microbiocenosis as a main goal and a priority task of the development of clinically effective probiotics and metabolite preparations (metabiotics).}, } @article {pmid25744641, year = {2014}, author = {Hattori, M}, title = {[Advanced technologies for the human gut microbiome analysis].}, journal = {Nihon Rinsho Men'eki Gakkai kaishi = Japanese journal of clinical immunology}, volume = {37}, number = {5}, pages = {412-422}, doi = {10.2177/jsci.37.412}, pmid = {25744641}, issn = {1349-7413}, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Intestines/*microbiology ; Metagenomics/*methods/trends ; Microbiota/*genetics ; Polymerase Chain Reaction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Analysis of the human gut microbiome, collective genomes of over 100 trillion cells of intestinal microbes which form the complex bacterial community, has recently become more practical due to remarkable advances in next-generation sequencing technologies (NGS). Several studies using NGS-based metagenomic approaches have been conducted to comprehensively analyze genes/functions and species composition in the human gut microbiome. These NGS-based approaches have demonstrated that their ecological and biological features that have been rather difficult to pursue can now be characterized with relative ease and high-throughput. There have also been several analytical developments and improvements to accurately evaluate the microbiome data from viewpoint of biology and ecology. In addition to the impact of external factors such as diet, these NGS-based studies have strongly suggested that the human gut microbiome has profound influences on various host physiologies including disease, of which the gut microbiome exhibited ecologically and functionally aberrant structure as compared with that of healthy control. On the other hand, the detailed assessment of the effect of experimental protocols including sample storage and delivery, DNA preparation, and sequencers used on the gut microbiome structure is also necessary. I herein present the NGS-based methodology for the human gut microbiome analysis.}, } @article {pmid25036636, year = {2014}, author = {Wolfe, BE and Button, JE and Santarelli, M and Dutton, RJ}, title = {Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity.}, journal = {Cell}, volume = {158}, number = {2}, pages = {422-433}, pmid = {25036636}, issn = {1097-4172}, support = {P50 GM068763/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacteria/*classification/metabolism ; Bacterial Physiological Phenomena ; Biodiversity ; Biofilms ; Cheese/*microbiology ; Fungi/classification/metabolism ; *Metagenomics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; }, abstract = {Tractable microbial communities are needed to bridge the gap between observations of patterns of microbial diversity and mechanisms that can explain these patterns. We developed cheese rinds as model microbial communities by characterizing in situ patterns of diversity and by developing an in vitro system for community reconstruction. Sequencing of 137 different rind communities across 10 countries revealed 24 widely distributed and culturable genera of bacteria and fungi as dominant community members. Reproducible community types formed independent of geographic location of production. Intensive temporal sampling demonstrated that assembly of these communities is highly reproducible. Patterns of community composition and succession observed in situ can be recapitulated in a simple in vitro system. Widespread positive and negative interactions were identified between bacterial and fungal community members. Cheese rind microbial communities represent an experimentally tractable system for defining mechanisms that influence microbial community assembly and function.}, } @article {pmid25036299, year = {2014}, author = {}, title = {Microbiota meet big data.}, journal = {Nature chemical biology}, volume = {10}, number = {8}, pages = {605}, pmid = {25036299}, issn = {1552-4469}, mesh = {Child ; Child Nutrition Disorders/microbiology ; Data Mining ; Genomics/*methods/trends ; Humans ; Intestines/microbiology ; Metagenome ; *Microbiota ; }, } @article {pmid25026370, year = {2014}, author = {Welz, PJ and Palmer, Z and Isaacs, S and Kirby, B and le Roes-Hill, M}, title = {Analysis of substrate degradation, metabolite formation and microbial community responses in sand bioreactors treating winery wastewater: a comparative study.}, journal = {Journal of environmental management}, volume = {145}, number = {}, pages = {147-156}, doi = {10.1016/j.jenvman.2014.06.025}, pmid = {25026370}, issn = {1095-8630}, mesh = {Biodegradation, Environmental ; Bioreactors ; Industrial Waste/*analysis ; *Microbial Consortia ; Silicon Dioxide/*chemistry ; Waste Disposal, Fluid/*methods ; Wastewater/*analysis ; *Wine ; }, abstract = {There is a global need for the implementation of more cost-effective green technologies for the treatment of effluent from wineries. However, systems reliant on microbial biodegradation may be adversely affected by the highly seasonal character of cellar waste. In this study, the biodegradation of two different formulations of winery effluent in sand bioreactors was compared. The degradation of organic substrates and formation of metabolites was monitored by physicochemical analyses of pore water and final effluent samples. Changes in the bacterial community structures were detected using molecular fingerprinting. In wastewater with an overall COD of 2027 mg/L, a formulation with a high concentration of acetate (800 mg COD/L) was more recalcitrant to degradation than a formulation with a high concentration of glucose (800 mg COD/L). Ethanol, glucose and phenolics were degraded preferentially in the deeper layers of the sand bioreactors (average Eh 25 mV) than in the superficial layers (average Eh 102 mV). The redox status also played a pivotal role on the bacterial community composition. The study yielded valuable insight that can be utilized in the design (configuration and operation) of full scale sand bioreactors.}, } @article {pmid25026170, year = {2014}, author = {Aßhauer, KP and Klingenberg, H and Lingner, T and Meinicke, P}, title = {Exploring neighborhoods in the metagenome universe.}, journal = {International journal of molecular sciences}, volume = {15}, number = {7}, pages = {12364-12378}, pmid = {25026170}, issn = {1422-0067}, mesh = {Genome, Human ; Genomics/*methods ; Humans ; *Metagenome ; Microbiota/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The variety of metagenomes in current databases provides a rapidly growing source of information for comparative studies. However, the quantity and quality of supplementary metadata is still lagging behind. It is therefore important to be able to identify related metagenomes by means of the available sequence data alone. We have studied efficient sequence-based methods for large-scale identification of similar metagenomes within a database retrieval context. In a broad comparison of different profiling methods we found that vector-based distance measures are well-suitable for the detection of metagenomic neighbors. Our evaluation on more than 1700 publicly available metagenomes indicates that for a query metagenome from a particular habitat on average nine out of ten nearest neighbors represent the same habitat category independent of the utilized profiling method or distance measure. While for well-defined labels a neighborhood accuracy of 100% can be achieved, in general the neighbor detection is severely affected by a natural overlap of manually annotated categories. In addition, we present results of a novel visualization method that is able to reflect the similarity of metagenomes in a 2D scatter plot. The visualization method shows a similarly high accuracy in the reduced space as compared with the high-dimensional profile space. Our study suggests that for inspection of metagenome neighborhoods the profiling methods and distance measures can be chosen to provide a convenient interpretation of results in terms of the underlying features. Furthermore, supplementary metadata of metagenome samples in the future needs to comply with readily available ontologies for fine-grained and standardized annotation. To make profile-based k-nearest-neighbor search and the 2D-visualization of the metagenome universe available to the research community, we included the proposed methods in our CoMet-Universe server for comparative metagenome analysis.}, } @article {pmid25025462, year = {2014}, author = {Wang, Y and Xue, J and Zhou, X and You, M and Du, Q and Yang, X and He, J and Zou, J and Cheng, L and Li, M and Li, Y and Zhu, Y and Li, J and Shi, W and Xu, X}, title = {Oral microbiota distinguishes acute lymphoblastic leukemia pediatric hosts from healthy populations.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e102116}, pmid = {25025462}, issn = {1932-6203}, mesh = {Biodiversity ; Case-Control Studies ; Child ; Child, Preschool ; Cluster Analysis ; Female ; Healthy Volunteers ; Humans ; Male ; Metagenome ; *Microbiota ; Mouth/*microbiology ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma ; Risk Factors ; }, abstract = {In leukemia, oral manifestations indicate aberrations in oral microbiota. Microbiota structure is determined by both host and environmental factors. In human hosts, how health status shapes the composition of oral microbiota is largely unknown. Taking advantage of advances in high-throughput sequencing, we compared the composition of supragingival plaque microbiota of acute lymphoblastic leukemia (ALL) pediatric patients with healthy controls. The oral microbiota of leukemia patients had lower richness and less diversity compared to healthy controls. Microbial samples clustered into two major groups, one of ALL patients and another of healthy children, with different structure and composition. Abundance changes of certain taxa including the Phylum Firmicutes, the Class Bacilli, the Order Lactobacillales, the Family Aerococcaceae and Carnobacteriaceae, as well as the Genus Abiotrophia and Granulicatella were associated with leukemia status. ALL patients demonstrated a structural imbalance of the oral microbiota, characterized by reduced diversity and abundance alterations, possibly involved in systemic infections, indicating the importance of immune status in shaping the structure of oral microbiota.}, } @article {pmid25020228, year = {2014}, author = {Abeles, SR and Pride, DT}, title = {Molecular bases and role of viruses in the human microbiome.}, journal = {Journal of molecular biology}, volume = {426}, number = {23}, pages = {3892-3906}, pmid = {25020228}, issn = {1089-8638}, support = {K08 AI085028/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteriophages/*growth & development ; *Ecosystem ; Humans ; *Microbiota ; }, abstract = {Viruses are dependent biological entities that interact with the genetic material of most cells on the planet, including the trillions within the human microbiome. Their tremendous diversity renders analysis of human viral communities ("viromes") to be highly complex. Because many of the viruses in humans are bacteriophage, their dynamic interactions with their cellular hosts add greatly to the complexities observed in examining human microbial ecosystems. We are only beginning to be able to study human viral communities on a large scale, mostly as a result of recent and continued advancements in sequencing and bioinformatic technologies. Bacteriophage community diversity in humans not only is inexorably linked to the diversity of their cellular hosts but also is due to their rapid evolution, horizontal gene transfers, and intimate interactions with host nucleic acids. There are vast numbers of observed viral genotypes on many body surfaces studied, including the oral, gastrointestinal, and respiratory tracts, and even in the human bloodstream, which previously was considered a purely sterile environment. The presence of viruses in blood suggests that virome members can traverse mucosal barriers, as indeed these communities are substantially altered when mucosal defenses are weakened. Perhaps the most interesting aspect of human viral communities is the extent to which they can carry gene functions involved in the pathogenesis of their hosts, particularly antibiotic resistance. Persons in close contact with each other have been shown to share a fraction of oral virobiota, which could potentially have important implications for the spread of antibiotic resistance to healthy individuals. Because viruses can have a large impact on ecosystem dynamics through mechanisms such as the transfers of beneficial gene functions or the lysis of certain populations of cellular hosts, they may have both beneficial and detrimental roles that affect human health, including improvements in microbial resilience to disturbances, immune evasion, maintenance of physiologic processes, and altering the microbial community in ways that promote or prevent pathogen colonization.}, } @article {pmid25015892, year = {2014}, author = {Tveit, AT and Urich, T and Svenning, MM}, title = {Metatranscriptomic analysis of arctic peat soil microbiota.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {18}, pages = {5761-5772}, pmid = {25015892}, issn = {1098-5336}, mesh = {Archaea/*classification/genetics/metabolism ; Bacteria/*classification/genetics/metabolism ; *Biota ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Molecular Sequence Data ; Polysaccharides/metabolism ; RNA, Messenger/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; *Soil Microbiology ; Svalbard ; }, abstract = {Recent advances in meta-omics and particularly metatranscriptomic approaches have enabled detailed studies of the structure and function of microbial communities in many ecosystems. Molecular analyses of peat soils, ecosystems important to the global carbon balance, are still challenging due to the presence of coextracted substances that inhibit enzymes used in downstream applications. We sampled layers at different depths from two high-Arctic peat soils in Svalbard for metatranscriptome preparation. Here we show that enzyme inhibition in the preparation of metatranscriptomic libraries can be circumvented by linear amplification of diluted template RNA. A comparative analysis of mRNA-enriched and nonenriched metatranscriptomes showed that mRNA enrichment resulted in a 2-fold increase in the relative abundance of mRNA but biased the relative distribution of mRNA. The relative abundance of transcripts for cellulose degradation decreased with depth, while the transcripts for hemicellulose debranching increased, indicating that the polysaccharide composition of the peat was different in the deeper and older layers. Taxonomic annotation revealed that Actinobacteria and Bacteroidetes were the dominating polysaccharide decomposers. The relative abundances of 16S rRNA and mRNA transcripts of methanogenic Archaea increased substantially with depth. Acetoclastic methanogenesis was the dominating pathway, followed by methanogenesis from formate. The relative abundances of 16S rRNA and mRNA assigned to the methanotrophic Methylococcaceae, primarily Methylobacter, increased with depth. In conclusion, linear amplification of total RNA and deep sequencing constituted the preferred method for metatranscriptomic preparation to enable high-resolution functional and taxonomic analyses of the active microbiota in Arctic peat soil.}, } @article {pmid25014551, year = {2014}, author = {Belzer, C and Gerber, GK and Roeselers, G and Delaney, M and DuBois, A and Liu, Q and Belavusava, V and Yeliseyev, V and Houseman, A and Onderdonk, A and Cavanaugh, C and Bry, L}, title = {Dynamics of the microbiota in response to host infection.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e95534}, pmid = {25014551}, issn = {1932-6203}, support = {R01-HD061916/HD/NICHD NIH HHS/United States ; R01 HD061916/HD/NICHD NIH HHS/United States ; #P30-DK034854/DK/NIDDK NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; UL1 RR025758/RR/NCRR NIH HHS/United States ; #UL1 RR 025758/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Bacterial Load ; Citrobacter rodentium/*genetics/growth & development ; Colitis/*microbiology ; Enterobacter/genetics/isolation & purification ; Enterobacteriaceae Infections/*microbiology ; *Genes, Bacterial ; Host-Pathogen Interactions ; Intestinal Mucosa/microbiology ; Intestines/microbiology ; Lactobacillus/genetics/isolation & purification ; Metagenome ; Mice ; Microbiota/*genetics ; Molecular Sequence Annotation ; Phylogeny ; Proteus vulgaris/genetics/isolation & purification ; RNA, Ribosomal, 16S/classification/*genetics ; }, abstract = {Longitudinal studies of the microbiota are important for discovering changes in microbial communities that affect the host. The complexity of these ecosystems requires rigorous integrated experimental and computational methods to identify temporal signatures that promote physiologic or pathophysiologic responses in vivo. Employing a murine model of infectious colitis with the pathogen Citrobacter rodentium, we generated a 2-month time-series of 16S rDNA gene profiles, and quantitatively cultured commensals, from multiple intestinal sites in infected and uninfected mice. We developed a computational framework to discover time-varying signatures for individual taxa, and to automatically group signatures to identify microbial sub-communities within the larger gut ecosystem that demonstrate common behaviors. Application of this model to the 16S rDNA dataset revealed dynamic alterations in the microbiota at multiple levels of resolution, from effects on systems-level metrics to changes across anatomic sites for individual taxa and species. These analyses revealed unique, time-dependent microbial signatures associated with host responses at different stages of colitis. Signatures included a Mucispirillum OTU associated with early disruption of the colonic surface mucus layer, prior to the onset of symptomatic colitis, and members of the Clostridiales and Lactobacillales that increased with successful resolution of inflammation, after clearance of the pathogen. Quantitative culture data validated findings for predominant species, further refining and strengthening model predictions. These findings provide new insights into the complex behaviors found within host ecosystems, and define several time-dependent microbial signatures that may be leveraged in studies of other infectious or inflammatory conditions.}, } @article {pmid25013912, year = {2014}, author = {Jones, ML and Ganopolsky, JG and Martoni, CJ and Labbé, A and Prakash, S}, title = {Emerging science of the human microbiome.}, journal = {Gut microbes}, volume = {5}, number = {4}, pages = {446-457}, doi = {10.4161/gmic.29810}, pmid = {25013912}, issn = {1949-0984}, mesh = {Communicable Diseases/*microbiology ; *Health ; *Host-Pathogen Interactions ; Humans ; Metagenomics/*trends ; Microbiology/*trends ; *Microbiota ; }, abstract = {The human gastrointestinal tract hosts a large number of microbial cells which exceed their mammalian counterparts by approximately 3-fold. The genes expressed by these microorganisms constitute the gut microbiome and may participate in diverse functions that are essential to the host, including digestion, regulation of energy metabolism, and modulation of inflammation and immunity. The gut microbiome can be modulated by dietary changes, antibiotic use, or disease. Different ailments have distinct associated microbiomes in which certain species or genes are present in different relative quantities. Thus, identifying specific disease-associated signatures in the microbiome as well as the factors that alter microbial populations and gene expression will lead to the development of new products such as prebiotics, probiotics, antimicrobials, live biotherapeutic products, or more traditional drugs to treat these disorders. Gained knowledge on the microbiome may result in molecular lab tests that may serve as personalized tools to guide the use of the aforementioned products and monitor interventional progress.}, } @article {pmid25008839, year = {2014}, author = {Nema, V and Nair, R}, title = {Metagenomic analysis of diarrheal stool samples of HIV infected individual and HIV-uninfected individual using 16SrDNA sequencing.}, journal = {Indian journal of medical microbiology}, volume = {32}, number = {3}, pages = {347-348}, doi = {10.4103/0255-0857.136606}, pmid = {25008839}, issn = {1998-3646}, mesh = {Adult ; Bacteria/*classification/*genetics ; *Biota ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Diarrhea/*microbiology ; Feces/*microbiology ; HIV Infections/complications ; Humans ; Male ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, } @article {pmid25006989, year = {2014}, author = {Pallav, K and Dowd, SE and Villafuerte, J and Yang, X and Kabbani, T and Hansen, J and Dennis, M and Leffler, DA and Newburg, DS and Kelly, CP}, title = {Effects of polysaccharopeptide from Trametes versicolor and amoxicillin on the gut microbiome of healthy volunteers: a randomized clinical trial.}, journal = {Gut microbes}, volume = {5}, number = {4}, pages = {458-467}, doi = {10.4161/gmic.29558}, pmid = {25006989}, issn = {1949-0984}, support = {8UL1TR000170-05/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Amoxicillin/*administration & dosage ; Anti-Bacterial Agents/*administration & dosage ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Healthy Volunteers ; Humans ; Male ; Metagenomics ; Microbiota/*drug effects ; Middle Aged ; *Prebiotics ; Proteoglycans/*administration & dosage/isolation & purification ; Trametes/*chemistry ; Young Adult ; }, abstract = {BACKGROUND: Interactions between the microbial flora of the intestine and the human host play a critical role inmaintaining intestinal health and in the pathophysiology of a wide variety of disorders such as antibiotic associated diarrhea, Clostridium difficile infection, and inflammatory bowel disease. Prebiotics can confer health benefits by beneficial effects on the intestinal microbiome, whereas antibiotics can disrupt the microbiome leading to diarrhea andother side effects.

AIM: To compare the effects of the prebiotic, polysaccharopeptide from Trametes versicolor, to those of the antibiotic,amoxicillin, on the human gut microbiome

METHODS: Twenty-four healthy volunteers were randomized to receive PSP, amoxicillin, or no treatment (control).Stool specimens were analyzed using bTEFAP microbial ecology methods on seven occasions over 8 weeks from each participant in the active treatment groups and on three occasions for the controls.

RESULTS: Twenty-two of 24 participants completed the protocol. PSP led to clear and consistent microbiome changes consistent with its activity as a prebiotic. Despite the diversity of the human microbiome we noted strong microbiome clustering among subjects. Baseline microbiomes tended to remain stable and to overshadow the treatment effects.Amoxicillin treatment caused substantial microbiome changes most notably an increase in Escherichia/Shigella. Antibiotic associated changes persisted to the end of the study, 42 days after antibiotic therapy ended.

CONCLUSIONS: The microbiomes of healthy individuals show substantial diversity but remain stable over time.The antibiotic amoxicillin alters the microbiome and recovery from this disruption can take several weeks. PSP from T. versicolor acts as a prebiotic to modulate human intestinal microbiome composition.}, } @article {pmid25003508, year = {2014}, author = {Boschker, HT and Vasquez-Cardenas, D and Bolhuis, H and Moerdijk-Poortvliet, TW and Moodley, L}, title = {Chemoautotrophic carbon fixation rates and active bacterial communities in intertidal marine sediments.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e101443}, pmid = {25003508}, issn = {1932-6203}, mesh = {*Bacteria/classification/genetics ; Biodiversity ; Carbon/*chemistry ; Geologic Sediments/*chemistry/*microbiology ; Metagenome ; *Microbiota ; Netherlands ; Oxygen/chemistry ; Phylogeny ; }, abstract = {Chemoautotrophy has been little studied in typical coastal marine sediments, but may be an important component of carbon recycling as intense anaerobic mineralization processes in these sediments lead to accumulation of high amounts of reduced compounds, such as sulfides and ammonium. We studied chemoautotrophy by measuring dark-fixation of 13C-bicarbonate into phospholipid derived fatty acid (PLFA) biomarkers at two coastal sediment sites with contrasting sulfur chemistry in the Eastern Scheldt estuary, The Netherlands. At one site where free sulfide accumulated in the pore water right to the top of the sediment, PLFA labeling was restricted to compounds typically found in sulfur and ammonium oxidizing bacteria. At the other site, with no detectable free sulfide in the pore water, a very different PLFA labeling pattern was found with high amounts of label in branched i- and a-PLFA besides the typical compounds for sulfur and ammonium oxidizing bacteria. This suggests that other types of chemoautotrophic bacteria were also active, most likely Deltaproteobacteria related to sulfate reducers. Maximum rates of chemoautotrophy were detected in first 1 to 2 centimeters of both sediments and chemosynthetic biomass production was high ranging from 3 to 36 mmol C m(-2) d(-1). Average dark carbon fixation to sediment oxygen uptake ratios were 0.22±0.07 mol C (mol O2)(-1), which is in the range of the maximum growth yields reported for sulfur oxidizing bacteria indicating highly efficient growth. Chemoautotrophic biomass production was similar to carbon mineralization rates in the top of the free sulfide site, suggesting that chemoautotrophic bacteria could play a crucial role in the microbial food web and labeling in eukaryotic poly-unsaturated PLFA was indeed detectable. Our study shows that dark carbon fixation by chemoautotrophic bacteria is a major process in the carbon cycle of coastal sediments, and should therefore receive more attention in future studies on sediment biogeochemistry and microbial ecology.}, } @article {pmid25002514, year = {2014}, author = {Hurwitz, BL and Westveld, AH and Brum, JR and Sullivan, MB}, title = {Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {29}, pages = {10714-10719}, pmid = {25002514}, issn = {1091-6490}, mesh = {Bayes Theorem ; *Gene Regulatory Networks ; Genes, Viral ; *Marine Biology ; *Metagenomics ; Microbiota/*genetics ; *Models, Biological ; *Oceans and Seas ; Pacific Ocean ; Seasons ; Viruses/*genetics ; }, abstract = {Long-standing questions in marine viral ecology are centered on understanding how viral assemblages change along gradients in space and time. However, investigating these fundamental ecological questions has been challenging due to incomplete representation of naturally occurring viral diversity in single gene- or morphology-based studies and an inability to identify up to 90% of reads in viral metagenomes (viromes). Although protein clustering techniques provide a significant advance by helping organize this unknown metagenomic sequence space, they typically use only ∼75% of the data and rely on assembly methods not yet tuned for naturally occurring sequence variation. Here, we introduce an annotation- and assembly-free strategy for comparative metagenomics that combines shared k-mer and social network analyses (regression modeling). This robust statistical framework enables visualization of complex sample networks and determination of ecological factors driving community structure. Application to 32 viromes from the Pacific Ocean Virome dataset identified clusters of samples broadly delineated by photic zone and revealed that geographic region, depth, and proximity to shore were significant predictors of community structure. Within subsets of this dataset, depth, season, and oxygen concentration were significant drivers of viral community structure at a single open ocean station, whereas variability along onshore-offshore transects was driven by oxygen concentration in an area with an oxygen minimum zone and not depth or proximity to shore, as might be expected. Together these results demonstrate that this highly scalable approach using complete metagenomic network-based comparisons can both test and generate hypotheses for ecological investigation of viral and microbial communities in nature.}, } @article {pmid24997786, year = {2014}, author = {Li, J and Jia, H and Cai, X and Zhong, H and Feng, Q and Sunagawa, S and Arumugam, M and Kultima, JR and Prifti, E and Nielsen, T and Juncker, AS and Manichanh, C and Chen, B and Zhang, W and Levenez, F and Wang, J and Xu, X and Xiao, L and Liang, S and Zhang, D and Zhang, Z and Chen, W and Zhao, H and Al-Aama, JY and Edris, S and Yang, H and Wang, J and Hansen, T and Nielsen, HB and Brunak, S and Kristiansen, K and Guarner, F and Pedersen, O and Doré, J and Ehrlich, SD and , and Bork, P and Wang, J and , }, title = {An integrated catalog of reference genes in the human gut microbiome.}, journal = {Nature biotechnology}, volume = {32}, number = {8}, pages = {834-841}, pmid = {24997786}, issn = {1546-1696}, mesh = {Catalogs as Topic ; Humans ; Intestines/*microbiology ; Metagenomics ; *Microbiota ; }, abstract = {Many analyses of the human gut microbiome depend on a catalog of reference genes. Existing catalogs for the human gut microbiome are based on samples from single cohorts or on reference genomes or protein sequences, which limits coverage of global microbiome diversity. Here we combined 249 newly sequenced samples of the Metagenomics of the Human Intestinal Tract (MetaHit) project with 1,018 previously sequenced samples to create a cohort from three continents that is at least threefold larger than cohorts used for previous gene catalogs. From this we established the integrated gene catalog (IGC) comprising 9,879,896 genes. The catalog includes close-to-complete sets of genes for most gut microbes, which are also of considerably higher quality than in previous catalogs. Analyses of a group of samples from Chinese and Danish individuals using the catalog revealed country-specific gut microbial signatures. This expanded catalog should facilitate quantitative characterization of metagenomic, metatranscriptomic and metaproteomic data from the gut microbiome to understand its variation across populations in human health and disease.}, } @article {pmid24997028, year = {2014}, author = {Fodor, A}, title = {Utilizing "omics" tools to study the complex gut ecosystem.}, journal = {Advances in experimental medicine and biology}, volume = {817}, number = {}, pages = {25-38}, doi = {10.1007/978-1-4939-0897-4_2}, pmid = {24997028}, issn = {0065-2598}, mesh = {Animals ; *Ecosystem ; Host-Pathogen Interactions/*physiology ; Humans ; Intestines/*microbiology ; Metagenome/*physiology ; Microbiota/*physiology ; RNA, Ribosomal, 16S/chemistry ; }, abstract = {In a healthy gut, the immune system tolerates a diverse microbial commensal community avoiding inappropriate inflammation responses and minimizing the presence of pathogens. When the balance between host and microbes is disrupted, risk for disease increases. There is mounting evidence that microbial dysbiosis is a substantial risk factor for common gut diseases including IBS, IBD and colorectal cancer. Understanding this dysbiosis is challenging because of the extraordinary complexity of the gut ecosystem and the tremendous variability between healthy individuals in the taxa that make up the human microbiome. Advances in technology, especially sequencing technology, are beginning to allow for a full description of this complexity. In this review, we consider how new "omics" technology can be applied to the study of the gut ecosystem in human and animal models with special consideration given to factors that should be considered in the design of experiments and clinical trials.}, } @article {pmid24994863, year = {2015}, author = {Kumar Singh, P and Shukla, P}, title = {Systems biology as an approach for deciphering microbial interactions.}, journal = {Briefings in functional genomics}, volume = {14}, number = {2}, pages = {166-168}, doi = {10.1093/bfgp/elu023}, pmid = {24994863}, issn = {2041-2657}, mesh = {Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Microbial Interactions ; Software ; Systems Biology/*methods ; }, abstract = {Different systems biology approaches may have a significant consequence in deciphering microbial interactions. Here, we endeavor to summarize, epigrammatic description of sophisticated techniques and software that provides an enhanced understanding of metagenomics data analysis. Apparently, such techniques are helpful to catalog various analysis categories and components that add appraisal to understand this approach. In addition, the constructions of metabolic networks of various genes present in human gut microbiome also give significant directions for determining the topological features of target enzymes.}, } @article {pmid24989676, year = {2014}, author = {Pacton, M and Wacey, D and Corinaldesi, C and Tangherlini, M and Kilburn, MR and Gorin, GE and Danovaro, R and Vasconcelos, C}, title = {Viruses as new agents of organomineralization in the geological record.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {4298}, doi = {10.1038/ncomms5298}, pmid = {24989676}, issn = {2041-1723}, mesh = {*Geologic Sediments ; Metagenomics ; *Microbial Consortia ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; *Minerals ; *Viruses ; }, abstract = {Viruses are the most abundant biological entities throughout marine and terrestrial ecosystems, but little is known about virus-mineral interactions or the potential for virus preservation in the geological record. Here we use contextual metagenomic data and microscopic analyses to show that viruses occur in high diversity within a modern lacustrine microbial mat, and vastly outnumber prokaryotes and other components of the microbial mat. Experimental data reveal that mineral precipitation takes place directly on free viruses and, as a result of viral infections, on cell debris resulting from cell lysis. Viruses are initially permineralized by amorphous magnesium silicates, which then alter to magnesium carbonate nanospheres of ~80-200 nm in diameter during diagenesis. Our findings open up the possibility to investigate the evolution and geological history of viruses and their role in organomineralization, as well as providing an alternative explanation for enigmatic carbonate nanospheres previously observed in the geological record.}, } @article {pmid24987952, year = {2014}, author = {Del Chierico, F and Vernocchi, P and Dallapiccola, B and Putignani, L}, title = {Mediterranean diet and health: food effects on gut microbiota and disease control.}, journal = {International journal of molecular sciences}, volume = {15}, number = {7}, pages = {11678-11699}, pmid = {24987952}, issn = {1422-0067}, mesh = {Cardiovascular Diseases/*prevention & control ; Diabetes Mellitus/*prevention & control ; *Diet, Mediterranean ; Humans ; Intestines/*microbiology ; *Microbiota ; }, abstract = {The Mediterranean diet (MD) is considered one of the healthiest dietary models. Many of the characteristic components of the MD have functional features with positive effects on health and wellness. The MD adherence, calculated through various computational scores, can lead to a reduction of the incidence of major diseases (e.g., cancers, metabolic and cardiovascular syndromes, neurodegenerative diseases, type 2 diabetes and allergy). Furthermore, eating habits are the main significant determinants of the microbial multiplicity of the gut, and dietary components influence both microbial populations and their metabolic activities from the early stages of life. For this purpose, we present a study proposal relying on the generation of individual gut microbiota maps from MD-aware children/adolescents. The maps, based on meta-omics approaches, may be considered as new tools, acting as a systems biology-based proof of evidence to evaluate MD effects on gut microbiota homeostasis. Data integration of food metabotypes and gut microbiota "enterotypes" may allow one to interpret MD adherence and its effects on health in a new way, employable for the design of targeted diets and nutraceutical interventions in childcare and clinical management of food-related diseases, whose onset has been significantly shifted early in life.}, } @article {pmid24985977, year = {2014}, author = {Reddy, B and Singh, KM and Patel, AK and Antony, A and Panchasara, HJ and Joshi, CG}, title = {Insights into resistome and stress responses genes in Bubalus bubalis rumen through metagenomic analysis.}, journal = {Molecular biology reports}, volume = {41}, number = {10}, pages = {6405-6417}, pmid = {24985977}, issn = {1573-4978}, mesh = {Animals ; Anti-Infective Agents/pharmacology ; Biodiversity ; *Buffaloes ; Cluster Analysis ; Computational Biology/methods ; Databases, Factual ; Drug Resistance, Microbial ; *Metagenome ; *Metagenomics/methods ; Microbial Sensitivity Tests ; *Microbiota/drug effects/genetics ; Phylogeny ; Rumen/*microbiology ; *Stress, Physiological ; }, abstract = {Buffalo rumen microbiota experience variety of diets and represents a huge reservoir of mobilome, resistome and stress responses. However, knowledge of metagenomic responses to such conditions is still rudimentary. We analyzed the metagenomes of buffalo rumen in the liquid and solid phase of the rumen biomaterial from river buffalo adapted to varying proportion of concentrate to green or dry roughages, using high-throughput sequencing to know the occurrence of antibiotics resistance genes, genetic exchange between bacterial population and environmental reservoirs. A total of 3914.94 MB data were generated from all three treatments group. The data were analysed with Metagenome rapid annotation system tools. At phyla level, Bacteroidetes were dominant in all the treatments followed by Firmicutes. Genes coding for functional responses to stress (oxidative stress and heat shock proteins) and resistome genes (resistance to antibiotics and toxic compounds, phages, transposable elements and pathogenicity islands) were prevalent in similar proportion in liquid and solid fraction of rumen metagenomes. The fluoroquinolone resistance, MDR efflux pumps and Methicillin resistance genes were broadly distributed across 11, 9, and 14 bacterial classes, respectively. Bacteria responsible for phages replication and prophages and phage packaging and rlt-like streptococcal phage genes were mostly assigned to phyla Bacteroides, Firmicutes and proteaobacteria. Also, more reads matching the sigma B genes were identified in the buffalo rumen. This study underscores the presence of diverse mechanisms of adaptation to different diet, antibiotics and other stresses in buffalo rumen, reflecting the proportional representation of major bacterial groups.}, } @article {pmid24983534, year = {2014}, author = {Mao, Y and Li, X and Smyth, EM and Yannarell, AC and Mackie, RI}, title = {Enrichment of specific bacterial and eukaryotic microbes in the rhizosphere of switchgrass (Panicum virgatum L.) through root exudates.}, journal = {Environmental microbiology reports}, volume = {6}, number = {3}, pages = {293-306}, doi = {10.1111/1758-2229.12152}, pmid = {24983534}, issn = {1758-2229}, mesh = {Bacteria/metabolism ; Carbon Dioxide/metabolism ; Carbon Isotopes/metabolism ; Cluster Analysis ; Genes, rRNA ; Metagenome ; Microbiota ; Panicum/*microbiology/*physiology ; Plant Roots/metabolism/*microbiology ; *Rhizosphere ; }, abstract = {Identification of microbes that actively utilize root exudates is essential to understand plant-microbe interactions. To identify active root exudate-utilizing microorganisms associated with switchgrass - a potential bioenergy crop - plants were labelled in situ with (13) CO2 , and 16S and 18S rRNA genes in the (13) C-labelled rhizosphere DNA were pyrosequenced. Multi-pulse labelling for 5 days produced detectable (13) C-DNA, which was well separated from unlabelled DNA. Methylibium from the order Burkholderiales were the most heavily labelled bacteria. Pythium, Auricularia and Galerina were the most heavily labelled eukaryotic microbes. We also identified a Glomus intraradices-like species; Glomus members are arbuscular mycorrhizal fungi that are able to colonize the switchgrass root. All of these heavily labelled microorganisms were also among the most abundant species in the rhizosphere. Species belonging to Methylibium and Pythium were the most heavily labelled and the most abundant bacteria and eukaryotes in the rhizosphere of switchgrass. Our results revealed that nearly all of the dominant rhizosphere bacterial and eukaryotic microbes were able to utilize root exudates. The enrichment of microbial species in the rhizosphere is selective and mostly due to root exudation, which functions as a nutrition source, promoting the growth of these microbes.}, } @article {pmid24982662, year = {2014}, author = {Sharpton, TJ}, title = {An introduction to the analysis of shotgun metagenomic data.}, journal = {Frontiers in plant science}, volume = {5}, number = {}, pages = {209}, pmid = {24982662}, issn = {1664-462X}, abstract = {Environmental DNA sequencing has revealed the expansive biodiversity of microorganisms and clarified the relationship between host-associated microbial communities and host phenotype. Shotgun metagenomic DNA sequencing is a relatively new and powerful environmental sequencing approach that provides insight into community biodiversity and function. But, the analysis of metagenomic sequences is complicated due to the complex structure of the data. Fortunately, new tools and data resources have been developed to circumvent these complexities and allow researchers to determine which microbes are present in the community and what they might be doing. This review describes the analytical strategies and specific tools that can be applied to metagenomic data and the considerations and caveats associated with their use. Specifically, it documents how metagenomes can be analyzed to quantify community structure and diversity, assemble novel genomes, identify new taxa and genes, and determine which metabolic pathways are encoded in the community. It also discusses several methods that can be used compare metagenomes to identify taxa and functions that differentiate communities.}, } @article {pmid24982315, year = {2014}, author = {Achermann, Y and Goldstein, EJ and Coenye, T and Shirtliff, ME}, title = {Propionibacterium acnes: from commensal to opportunistic biofilm-associated implant pathogen.}, journal = {Clinical microbiology reviews}, volume = {27}, number = {3}, pages = {419-440}, pmid = {24982315}, issn = {1098-6618}, support = {R01 AI069568/AI/NIAID NIH HHS/United States ; R01 AI69568-01A2/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Biofilms ; Gram-Positive Bacterial Infections/diagnosis/*microbiology/prevention & control/therapy ; Host-Pathogen Interactions/immunology ; Humans ; Metagenome ; Microbiota ; Propionibacterium acnes/classification/pathogenicity/*physiology ; Prostheses and Implants/microbiology ; Prosthesis-Related Infections/diagnosis/*microbiology/prevention & control/therapy ; Virulence ; }, abstract = {Propionibacterium acnes is known primarily as a skin commensal. However, it can present as an opportunistic pathogen via bacterial seeding to cause invasive infections such as implant-associated infections. These infections have gained more attention due to improved diagnostic procedures, such as sonication of explanted foreign materials and prolonged cultivation time of up to 14 days for periprosthetic biopsy specimens, and improved molecular methods, such as broad-range 16S rRNA gene PCR. Implant-associated infections caused by P. acnes are most often described for shoulder prosthetic joint infections as well as cerebrovascular shunt infections, fibrosis of breast implants, and infections of cardiovascular devices. P. acnes causes disease through a number of virulence factors, such as biofilm formation. P. acnes is highly susceptible to a wide range of antibiotics, including beta-lactams, quinolones, clindamycin, and rifampin, although resistance to clindamycin is increasing. Treatment requires a combination of surgery and a prolonged antibiotic treatment regimen to successfully eliminate the remaining bacteria. Most authors suggest a course of 3 to 6 months of antibiotic treatment, including 2 to 6 weeks of intravenous treatment with a beta-lactam. While recently reported data showed a good efficacy of rifampin against P. acnes biofilms, prospective, randomized, controlled studies are needed to confirm evidence for combination treatment with rifampin, as has been performed for staphylococcal implant-associated infections.}, } @article {pmid24982156, year = {2014}, author = {Kelly, LW and Williams, GJ and Barott, KL and Carlson, CA and Dinsdale, EA and Edwards, RA and Haas, AF and Haynes, M and Lim, YW and McDole, T and Nelson, CE and Sala, E and Sandin, SA and Smith, JE and Vermeij, MJ and Youle, M and Rohwer, F}, title = {Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {28}, pages = {10227-10232}, pmid = {24982156}, issn = {1091-6490}, mesh = {*Adaptation, Physiological ; *Bacteria/genetics/metabolism ; *Coral Reefs ; *Gene Transfer, Horizontal ; *Metagenome ; *Microbiota ; Pacific Ocean ; *Water Pollution ; }, abstract = {Holobionts are species-specific associations between macro- and microorganisms. On coral reefs, the benthic coverage of coral and algal holobionts varies due to natural and anthropogenic forcings. Different benthic macroorganisms are predicted to have specific microbiomes. In contrast, local environmental factors are predicted to select for specific metabolic pathways in microbes. To reconcile these two predictions, we hypothesized that adaptation of microbiomes to local conditions is facilitated by the horizontal transfer of genes responsible for specific metabolic capabilities. To test this hypothesis, microbial metagenomes were sequenced from 22 coral reefs at 11 Line Islands in the central Pacific that together span a wide range of biogeochemical and anthropogenic influences. Consistent with our hypothesis, the percent cover of major benthic functional groups significantly correlated with particular microbial taxa. Reefs with higher coral cover had a coral microbiome with higher abundances of Alphaproteobacteria (such as Rhodobacterales and Sphingomonadales), whereas microbiomes of algae-dominated reefs had higher abundances of Gammaproteobacteria (such as Alteromonadales, Pseudomonadales, and Vibrionales), Betaproteobacteria, and Bacteriodetes. In contrast to taxa, geography was the strongest predictor of microbial community metabolism. Microbial communities on reefs with higher nutrient availability (e.g., equatorial upwelling zones) were enriched in genes involved in nutrient-related metabolisms (e.g., nitrate and nitrite ammonification, Ton/Tol transport, etc.). On reefs further from the equator, microbes had more genes encoding chlorophyll biosynthesis and photosystems I/II. These results support the hypothesis that core microbiomes are determined by holobiont macroorganisms, and that those core taxa adapt to local conditions by selecting for advantageous metabolic genes.}, } @article {pmid24973096, year = {2014}, author = {Guo, M and Huang, K and Chen, S and Qi, X and He, X and Cheng, WH and Luo, Y and Xia, K and Xu, W}, title = {Combination of metagenomics and culture-based methods to study the interaction between ochratoxin a and gut microbiota.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {141}, number = {1}, pages = {314-323}, pmid = {24973096}, issn = {1096-0929}, mesh = {Animals ; Chromatography, Thin Layer ; Dose-Response Relationship, Drug ; Feces/microbiology ; Intestines/*drug effects/microbiology ; Lactobacillus/*drug effects/genetics/isolation & purification ; Male ; Metagenomics/*methods ; Microbiota/*drug effects/*genetics ; Ochratoxins/*toxicity ; RNA, Ribosomal, 16S/genetics ; Rats, Inbred F344 ; }, abstract = {Gut microbiota represent an important bridge between environmental substances and host metabolism. Here we reported a comprehensive study of gut microbiota interaction with ochratoxin A (OTA), a major food-contaminating mycotoxin, using the combination of metagenomics and culture-based methods. Rats were given OTA (0, 70, or 210 μg/kg body weight) by gavage and fecal samples were collected at day 0 and day 28. Bacterial genomic DNA was extracted from the fecal samples and both 16S rRNA and shotgun sequencing (two main methods of metagenomics) were performed. The results indicated OTA treatment decreased the within-subject diversity of the gut microbiota, and the relative abundance of Lactobacillus increased considerably. Changes in functional genes of gut microbiota including signal transduction, carbohydrate transport, transposase, amino acid transport system, and mismatch repair were observed. To further understand the biological sense of increased Lactobacillus, Lactobacillus selective medium was used to isolate Lactobacillus species from fecal samples, and a strain with 99.8% 16S rRNA similarity with Lactobacillus plantarum strain PFK2 was obtained. Thin-layer chromatography showed that this strain could absorb but not degrade OTA, which was in agreement with the result in metagenomics that no genes related to OTA degradation increased. In conclusion, combination of metagenomics and culture-based methods can be a new strategy to study intestinal toxicity of toxins and find applicable bacterial strains for detoxification. When it comes to OTA, this kind of mycotoxin can cause compositional and functional changes of gut microbiota, and Lactobacillus are key genus to detoxify OTA in vivo.}, } @article {pmid24971452, year = {2014}, author = {Probst, AJ and Birarda, G and Holman, HY and DeSantis, TZ and Wanner, G and Andersen, GL and Perras, AK and Meck, S and Völkel, J and Bechtel, HA and Wirth, R and Moissl-Eichinger, C}, title = {Coupling genetic and chemical microbiome profiling reveals heterogeneity of archaeome and bacteriome in subsurface biofilms that are dominated by the same archaeal species.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e99801}, pmid = {24971452}, issn = {1932-6203}, mesh = {Archaea/genetics/*isolation & purification/physiology/ultrastructure ; Bacteria/genetics/*isolation & purification/ultrastructure ; Bacterial Physiological Phenomena ; *Biofilms ; Hot Springs/*microbiology ; *Microbiota ; }, abstract = {Earth harbors an enormous portion of subsurface microbial life, whose microbiome flux across geographical locations remains mainly unexplored due to difficult access to samples. Here, we investigated the microbiome relatedness of subsurface biofilms of two sulfidic springs in southeast Germany that have similar physical and chemical parameters and are fed by one deep groundwater current. Due to their unique hydrogeological setting these springs provide accessible windows to subsurface biofilms dominated by the same uncultivated archaeal species, called SM1 Euryarchaeon. Comparative analysis of infrared imaging spectra demonstrated great variations in archaeal membrane composition between biofilms of the two springs, suggesting different SM1 euryarchaeal strains of the same species at both aquifer outlets. This strain variation was supported by ultrastructural and metagenomic analyses of the archaeal biofilms, which included intergenic spacer region sequencing of the rRNA gene operon. At 16S rRNA gene level, PhyloChip G3 DNA microarray detected similar biofilm communities for archaea, but site-specific communities for bacteria. Both biofilms showed an enrichment of different deltaproteobacterial operational taxonomic units, whose families were, however, congruent as were their lipid spectra. Consequently, the function of the major proportion of the bacteriome appeared to be conserved across the geographic locations studied, which was confirmed by dsrB-directed quantitative PCR. Consequently, microbiome differences of these subsurface biofilms exist at subtle nuances for archaea (strain level variation) and at higher taxonomic levels for predominant bacteria without a substantial perturbation in bacteriome function. The results of this communication provide deep insight into the dynamics of subsurface microbial life and warrant its future investigation with regard to metabolic and genomic analyses.}, } @article {pmid24969751, year = {2014}, author = {Dias, R and Xavier, MG and Rossi, FD and Neves, MV and Lange, TA and Giongo, A and De Rose, CA and Triplett, EW}, title = {MPI-blastn and NCBI-TaxCollector: improving metagenomic analysis with high performance classification and wide taxonomic attachment.}, journal = {Journal of bioinformatics and computational biology}, volume = {12}, number = {3}, pages = {1450013}, doi = {10.1142/S0219720014500139}, pmid = {24969751}, issn = {1757-6334}, mesh = {Algorithms ; Classification/methods ; Computational Biology ; High-Throughput Nucleotide Sequencing/statistics & numerical data ; Humans ; Metagenomics/methods/*statistics & numerical data ; Microbiota/genetics ; *Software ; }, abstract = {Metagenomic sequencing technologies are advancing rapidly and the size of output data from high-throughput genetic sequencing has increased substantially over the years. This brings us to a scenario where advanced computational optimizations are requested to perform a metagenomic analysis. In this paper, we describe a new parallel implementation of nucleotide BLAST (MPI-blastn) and a new tool for taxonomic attachment of Basic Local Alignment Search Tool (BLAST) results that supports the NCBI taxonomy (NCBI-TaxCollector). MPI-blastn obtained a high performance when compared to the mpiBLAST and ScalaBLAST. In our best case, MPI-blastn was able to run 408 times faster in 384 cores. Our evaluations demonstrated that NCBI-TaxCollector is able to perform taxonomic attachments 125 times faster and needs 120 times less RAM than the previous TaxCollector. Through our optimizations, a multiple sequence search that currently takes 37 hours can be performed in less than 6 min and a post processing with NCBI taxonomic data attachment, which takes 48 hours, now is able to run in 23 min.}, } @article {pmid24969288, year = {2014}, author = {Wine, E}, title = {Should we be treating the bugs instead of cytokines and T cells?.}, journal = {Digestive diseases (Basel, Switzerland)}, volume = {32}, number = {4}, pages = {403-409}, doi = {10.1159/000358146}, pmid = {24969288}, issn = {1421-9875}, mesh = {Animals ; Cytokines/*metabolism ; Humans ; Inflammatory Bowel Diseases/microbiology ; *Microbiota ; Models, Biological ; T-Lymphocytes/*metabolism ; Translational Research, Biomedical ; }, abstract = {BACKGROUND/AIM: It is now clear that intestinal microbes are involved in many aspects of inflammatory bowel diseases (IBD) and that understanding how microbes lead to disease could present novel opportunities for diagnosis and treatment. Microbes are linked to most disease-associated genetic polymorphisms and are critical mediators of environmental effects (through food, hygiene, and infection). This paper reviews recent findings and future implications for targeting microbes in IBD.

METHODS: A comprehensive review of the literature is presented, with specific focus on how treating microbes could alter patient care in the future.

RESULTS: Human and animal-based research supports the central role of microbes in IBD pathogenesis at multiple levels. Antibiotics, probiotics, diet, and potentially fecal transplantation are all potential treatments for IBD. Animal models of IBD only develop in the presence of microbes and co-housing mice genetically susceptible to gut inflammation with normal mice can lead to the development of bowel injury. Key papers have used microbial sequencing and metagenomics to study the role of microbes in IBD and we are now on the cusp of expanding into clinically relevant fields, such as diagnosis and therapeutics. However, many challenges still remain in understanding how microbes can be manipulated to prevent or treat disease.

CONCLUSIONS: In the future, we may be able to predict risk of disease, define biological subtypes, establish tools for prevention, and even cure IBD using microbes or their products. A broad spectrum of therapeutic tools, spanning from fecal transplantation, probiotics, prebiotics, microbial products to microbe-tailored diets, may replace current IBD treatments.}, } @article {pmid24965364, year = {2014}, author = {Ma, L and Kim, J and Hatzenpichler, R and Karymov, MA and Hubert, N and Hanan, IM and Chang, EB and Ismagilov, RF}, title = {Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {27}, pages = {9768-9773}, pmid = {24965364}, issn = {1091-6490}, support = {UL1 TR000430/TR/NCATS NIH HHS/United States ; R01HG005826/HG/NHGRI NIH HHS/United States ; R01 HG005826/HG/NHGRI NIH HHS/United States ; R37 DK047722/DK/NIDDK NIH HHS/United States ; R01 DK047722/DK/NIDDK NIH HHS/United States ; }, mesh = {*Gene Targeting ; Humans ; Intestines/*microbiology ; *Microbiota ; *Microfluidic Analytical Techniques ; Molecular Sequence Data ; }, abstract = {This paper describes a microfluidics-based workflow for genetically targeted isolation and cultivation of microorganisms from complex clinical samples. Data sets from high-throughput sequencing suggest the existence of previously unidentified bacterial taxa and functional genes with high biomedical importance. Obtaining isolates of these targets, preferably in pure cultures, is crucial for advancing understanding of microbial genetics and physiology and enabling physical access to microbes for further applications. However, the majority of microbes have not been cultured, due in part to the difficulties of both identifying proper growth conditions and characterizing and isolating each species. We describe a method that enables genetically targeted cultivation of microorganisms through a combination of microfluidics and on- and off-chip assays. This method involves (i) identification of cultivation conditions for microbes using growth substrates available only in small quantities as well as the correction of sampling bias using a "chip wash" technique; and (ii) performing on-chip genetic assays while also preserving live bacterial cells for subsequent scale-up cultivation of desired microbes, by applying recently developed technology to create arrays of individually addressable replica microbial cultures. We validated this targeted approach by cultivating a bacterium, here referred to as isolate microfluidicus 1, from a human cecal biopsy. Isolate microfluidicus 1 is, to our knowledge, the first successful example of targeted cultivation of a microorganism from the high-priority group of the Human Microbiome Project's "Most Wanted" list, and, to our knowledge, the first cultured representative of a previously unidentified genus of the Ruminococcaceae family.}, } @article {pmid24959907, year = {2014}, author = {Winter, C and Garcia, JA and Weinbauer, MG and DuBow, MS and Herndl, GJ}, title = {Comparison of deep-water viromes from the atlantic ocean and the mediterranean sea.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e100600}, pmid = {24959907}, issn = {1932-6203}, support = {P 24413/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Atlantic Ocean ; Base Composition ; *Biodiversity ; Ecosystem ; Genome, Viral/genetics ; Mediterranean Sea ; Metagenomics ; Seawater/*microbiology ; Viruses/*classification/genetics ; }, abstract = {The aim of this study was to compare the composition of two deep-sea viral communities obtained from the Romanche Fracture Zone in the Atlantic Ocean (collected at 5200 m depth) and the southwest Mediterranean Sea (from 2400 m depth) using a pyro-sequencing approach. The results are based on 18.7% and 6.9% of the sequences obtained from the Atlantic Ocean and the Mediterranean Sea, respectively, with hits to genomes in the non-redundant viral RefSeq database. The identifiable richness and relative abundance in both viromes were dominated by archaeal and bacterial viruses accounting for 92.3% of the relative abundance in the Atlantic Ocean and for 83.6% in the Mediterranean Sea. Despite characteristic differences in hydrographic features between the sampling sites in the Atlantic Ocean and the Mediterranean Sea, 440 virus genomes were found in both viromes. An additional 431 virus genomes were identified in the Atlantic Ocean and 75 virus genomes were only found in the Mediterranean Sea. The results indicate that the rather contrasting deep-sea environments of the Atlantic Ocean and the Mediterranean Sea share a common core set of virus types constituting the majority of both virus communities in terms of relative abundance (Atlantic Ocean: 81.4%; Mediterranean Sea: 88.7%).}, } @article {pmid24958360, year = {2014}, author = {Hawley, ER and Malfatti, SA and Pagani, I and Huntemann, M and Chen, A and Foster, B and Copeland, A and del Rio, TG and Pati, A and Jansson, JR and Gilbert, JA and Tringe, SG and Lorenson, TD and Hess, M}, title = {Metagenomes from two microbial consortia associated with Santa Barbara seep oil.}, journal = {Marine genomics}, volume = {18 Pt B}, number = {}, pages = {97-99}, doi = {10.1016/j.margen.2014.06.003}, pmid = {24958360}, issn = {1876-7478}, mesh = {Base Sequence ; California ; DNA Primers/genetics ; Gene Library ; Metagenome/*genetics ; Microbial Consortia/*genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; Pacific Ocean ; *Petroleum Pollution ; Sequence Analysis, DNA ; }, abstract = {The metagenomes from two microbial consortia associated with natural oils seeping into the Pacific Ocean offshore the coast of Santa Barbara (California, USA) were determined to complement already existing metagenomes generated from microbial communities associated with hydrocarbons that pollute the marine ecosystem. This genomics resource article is the first of two publications reporting a total of four new metagenomes from oils that seep into the Santa Barbara Channel.}, } @article {pmid24953670, year = {2014}, author = {Thomas, LV and Ockhuizen, T and Suzuki, K}, title = {Exploring the influence of the gut microbiota and probiotics on health: a symposium report.}, journal = {The British journal of nutrition}, volume = {112 Suppl 1}, number = {Suppl 1}, pages = {S1-18}, pmid = {24953670}, issn = {1475-2662}, mesh = {Animals ; Congresses as Topic ; Humans ; Immunity, Mucosal ; Intestinal Diseases/immunology/microbiology/*prevention & control ; Intestinal Mucosa/immunology/*microbiology ; Metabolic Diseases/immunology/microbiology/prevention & control ; Microbiota ; Nutrition Disorders/immunology/microbiology/prevention & control ; Probiotics/*therapeutic use ; }, abstract = {The present report describes the presentations delivered at the 7th International Yakult Symposium, 'The Intestinal Microbiota and Probiotics: Exploiting Their Influence on Health', in London on 22-23 April 2013. The following two themes associated with health risks were covered: (1) the impact of age and diet on the gut microbiota and (2) the gut microbiota's interaction with the host. The strong influence of the maternal gut microbiota on neonatal colonisation was reported, as well as rapid changes in the gut microbiome of older people who move from community living to residential care. The effects of dietary changes on gut metabolism were described and the potential influence of inter-individual microbiota differences was noted, in particular the presence/absence of keystone species involved in butyrate metabolism. Several speakers highlighted the association between certain metabolic disorders and imbalanced or less diverse microbiota. Data from metagenomic analyses and novel techniques (including an ex vivo human mucosa model) provided new insights into the microbiota's influence on coeliac, obesity-related and inflammatory diseases, as well as the potential of probiotics. Akkermansia muciniphila and Faecalibacterium prausnitzii were suggested as targets for intervention. Host-microbiota interactions were explored in the context of gut barrier function, pathogenic bacteria recognition, and the ability of the immune system to induce either tolerogenic or inflammatory responses. There was speculation that the gut microbiota should be considered a separate organ, and whether analysis of an individual's microbiota could be useful in identifying their disease risk and/or therapy; however, more research is needed into specific diseases, different population groups and microbial interventions including probiotics.}, } @article {pmid24950204, year = {2014}, author = {Huttenhower, C and Kostic, AD and Xavier, RJ}, title = {Inflammatory bowel disease as a model for translating the microbiome.}, journal = {Immunity}, volume = {40}, number = {6}, pages = {843-854}, pmid = {24950204}, issn = {1097-4180}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 DK092405/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Colitis, Ulcerative/*immunology/*microbiology ; Crohn Disease/*immunology/*microbiology ; *Disease Models, Animal ; Gastrointestinal Tract/immunology/microbiology ; Humans ; Metagenome ; Mice ; Microbiota/*immunology ; *Translational Research, Biomedical ; }, abstract = {The inflammatory bowel diseases (IBDs) are among the most closely studied chronic inflammatory disorders that involve environmental, host genetic, and commensal microbial factors. This combination of features has made IBD both an appropriate and a high-priority platform for translatable research in host-microbiome interactions. Decades of epidemiology have identified environmental risk factors, although most mechanisms of action remain unexplained. The genetic architecture of IBD has been carefully dissected in multiple large populations, identifying several responsible host epithelial and immune pathways but without yet a complete systems-level explanation. Most recently, the commensal gut microbiota have been found to be both ecologically and functionally perturbed during the disease, but with as-yet-unexplained heterogeneity among IBD subtypes and individual patients. IBD thus represents perhaps the most comprehensive current model for understanding the human microbiome's role in complex inflammatory disease. Here, we review the influences of the microbiota on IBD and its potential for translational medicine.}, } @article {pmid24950202, year = {2014}, author = {Dorrestein, PC and Mazmanian, SK and Knight, R}, title = {Finding the missing links among metabolites, microbes, and the host.}, journal = {Immunity}, volume = {40}, number = {6}, pages = {824-832}, pmid = {24950202}, issn = {1097-4180}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; R01 MH100556/MH/NIMH NIH HHS/United States ; U01 HG004866/HG/NHGRI NIH HHS/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; R01 NS085910/NS/NINDS NIH HHS/United States ; /HHMI_/Howard Hughes Medical Institute/United States ; R01 DK078938/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacterial Proteins/immunology ; Gastrointestinal Tract/immunology/microbiology ; Humans ; *Metabolome ; *Metagenome ; Microbiota/*genetics/*immunology ; }, abstract = {The unexpected diversity of the human microbiome and metabolome far exceeds the complexity of the human genome. Although we now understand microbial taxonomic and genetic repertoires in some populations, we are just beginning to assemble the necessary computational and experimental tools to understand the metabolome in comparable detail. However, even with the limited current state of knowledge, individual connections between microbes and metabolites, between microbes and immune function, and between metabolites and immune function are being established. Here, we provide our perspective on these connections and outline a systematic research program that could turn these individual links into a broader network that allows us to understand how these components interact. This program will enable us to exploit connections among the microbiome, metabolome, and host immune system to maintain health and perhaps help us understand how to reverse the processes that lead to a wide range of immune and other diseases.}, } @article {pmid24943724, year = {2014}, author = {Brotman, RM and Shardell, MD and Gajer, P and Tracy, JK and Zenilman, JM and Ravel, J and Gravitt, PE}, title = {Interplay between the temporal dynamics of the vaginal microbiota and human papillomavirus detection.}, journal = {The Journal of infectious diseases}, volume = {210}, number = {11}, pages = {1723-1733}, pmid = {24943724}, issn = {1537-6613}, support = {UH2 AI083264/AI/NIAID NIH HHS/United States ; R01 CA123467/CA/NCI NIH HHS/United States ; UH2-AI083264/AI/NIAID NIH HHS/United States ; K01-AI080974/AI/NIAID NIH HHS/United States ; K25 AG034216/AG/NIA NIH HHS/United States ; K25-AG034216/AG/NIA NIH HHS/United States ; K01 AI080974/AI/NIAID NIH HHS/United States ; R03-AI061131/AI/NIAID NIH HHS/United States ; R03 AI061131/AI/NIAID NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Alphapapillomavirus/classification/genetics/*isolation & purification ; Cluster Analysis ; Female ; Humans ; Markov Chains ; Metagenome ; Microbiota ; Middle Aged ; Papillomavirus Infections/*virology ; Risk Factors ; Vagina/*microbiology/*virology ; Vaginosis, Bacterial/microbiology/virology ; Young Adult ; }, abstract = {BACKGROUND: We sought to describe the temporal relationship between vaginal microbiota and human papillomavirus (HPV) detection.

METHODS: Thirty-two reproductive-age women self-collected midvaginal swabs twice weekly for 16 weeks (937 samples). Vaginal bacterial communities were characterized by pyrosequencing of barcoded 16S rRNA genes and clustered into 6 community state types (CSTs). Each swab was tested for 37 HPV types. The effects of CSTs on the rate of transition between HPV-negative and HPV-positive states were assessed using continuous-time Markov models.

RESULTS: Participants had an average of 29 samples, with HPV point prevalence between 58%-77%. CST was associated with changes in HPV status (P<.001). Lactobacillus gasseri-dominated CSTs had the fastest HPV remission rate, and a low Lactobacillus community with high proportions of the genera Atopobium (CST IV-B) had the slowest rate compared to L. crispatus-dominated CSTs (adjusted transition rate ratio [aTRR], 4.43, 95% confidence interval [CI], 1.11-17.7; aTRR, 0.33, 95% CI, .12-1.19, respectively). The rate ratio of incident HPV for low Lactobacillus CST IV-A was 1.86 (95% CI, .52-6.74).

CONCLUSIONS: Vaginal microbiota dominated by L. gasseri was associated with increased clearance of detectable HPV. Frequent longitudinal sampling is necessary for evaluation of the association between HPV detection and dynamic microbiota.}, } @article {pmid24943089, year = {2015}, author = {Hirai, J and Kuriyama, M and Ichikawa, T and Hidaka, K and Tsuda, A}, title = {A metagenetic approach for revealing community structure of marine planktonic copepods.}, journal = {Molecular ecology resources}, volume = {15}, number = {1}, pages = {68-80}, doi = {10.1111/1755-0998.12294}, pmid = {24943089}, issn = {1755-0998}, mesh = {Animals ; *Biota ; Cluster Analysis ; Copepoda/anatomy & histology/*classification/*genetics ; DNA, Ribosomal/chemistry/genetics ; *Metagenomics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/genetics ; Seawater ; Sequence Analysis, DNA ; }, abstract = {Marine planktonic copepods are an ecologically important group with high species richness and abundance. Here, we propose a new metagenetic approach for revealing the community structure of marine planktonic copepods using 454 pyrosequencing of nuclear large subunit ribosomal DNA. We determined an appropriate similarity threshold for clustering pyrosequencing data into molecular operational taxonomic units (MOTUs) using an artificial community containing 33 morphologically identified species. The 99% similarity threshold had high species-level resolution for MOTU clustering but overestimated species richness. The artificial community was appropriately clustered into MOTUs at 97% similarity, with little inflation in MOTU numbers and with relatively high species-level resolution. The number of sequence reads of each MOTU was correlated with dry weight of that taxon, suggesting that sequence reads could be used as a proxy for biomass. Next, we applied the method to field-collected samples, and the results corresponded reasonably well with morphological analysis of these communities. Numbers of MOTUs were well correlated with species richness at 97% similarity, and large numbers of sequence reads were generally observed in MOTUs derived from species with large biomass. Further, MOTUs were successfully classified into taxonomic groups at the family level at 97% similarity; similar patterns of species richness and biomass were revealed within families with metagenetic and morphological analyses. At the 99% similarity threshold, MOTUs with high proportions of sequence reads were identified as biomass-dominant species in each field-collected sample. The metagenetic approach reported here can be an effective tool for rapid and comprehensive assessment of copepod community structure.}, } @article {pmid24939885, year = {2014}, author = {Seekatz, AM and Aas, J and Gessert, CE and Rubin, TA and Saman, DM and Bakken, JS and Young, VB}, title = {Recovery of the gut microbiome following fecal microbiota transplantation.}, journal = {mBio}, volume = {5}, number = {3}, pages = {e00893-14}, pmid = {24939885}, issn = {2150-7511}, support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; U19 AI090871/AI/NIAID NIH HHS/United States ; U19AI090871/AI/NIAID NIH HHS/United States ; P30DK034933/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/genetics/*isolation & purification ; *Biological Therapy ; Clostridioides difficile/*physiology ; Clostridium Infections/microbiology/*therapy ; Feces/*microbiology ; Female ; Gastrointestinal Tract/microbiology ; Humans ; Male ; *Microbiota ; Middle Aged ; Molecular Sequence Data ; Phylogeny ; }, abstract = {UNLABELLED: Clostridium difficile infection is one of the most common health care-associated infections, and up to 40% of patients suffer from recurrence of disease following standard antibiotic therapy. Recently, fecal microbiota transplantation (FMT) has been successfully used to treat recurrent C. difficile infection. It is hypothesized that FMT aids in recovery of a microbiota capable of colonization resistance to C. difficile. However, it is not fully understood how this occurs. Here we investigated changes in the fecal microbiota structure following FMT in patients with recurrent C. difficile infection, and imputed a hypothetical functional profile based on the 16S rRNA profile using a predictive metagenomic tool. Increased relative abundance of Bacteroidetes and decreased abundance of Proteobacteria were observed following FMT. The fecal microbiota of recipients following transplantation was more diverse and more similar to the donor profile than the microbiota prior to transplantation. Additionally, we observed differences in the imputed metagenomic profile. In particular, amino acid transport systems were overrepresented in samples collected prior to transplantation. These results suggest that functional changes accompany microbial structural changes following this therapy. Further identification of the specific community members and functions that promote colonization resistance may aid in the development of improved treatment methods for C. difficile infection.

IMPORTANCE: Within the last decade, Clostridium difficile infection has surpassed other bacterial infections to become the leading cause of nosocomial infections. Antibiotic use, which disrupts the gut microbiota and its capability in providing colonization resistance against C. difficile, is a known risk factor in C. difficile infection. In particular, recurrent C. difficile remains difficult to treat with standard antibiotic therapy. Fecal microbiota transplantation (FMT) has provided a successful treatment method for some patients with recurrent C. difficile infection, but its mechanism and long-term effects remain unknown. Our results provide insight into the structural and potential metabolic changes that occur following FMT, which may aid in the development of new treatment methods for C. difficile infection.}, } @article {pmid24939130, year = {2014}, author = {Abraham, PE and Giannone, RJ and Xiong, W and Hettich, RL}, title = {Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities.}, journal = {Current protocols in bioinformatics}, volume = {46}, number = {}, pages = {13.26.1-13.26.14}, doi = {10.1002/0471250953.bi1326s46}, pmid = {24939130}, issn = {1934-340X}, mesh = {Databases, Protein ; Information Storage and Retrieval ; *Microbiota ; Peptides/chemistry ; Proteins/chemistry ; *Proteomics ; }, abstract = {Contemporary microbial ecology studies usually employ one or more "omics" approaches to investigate the structure and function of microbial communities. Among these, metaproteomics aims to characterize the metabolic activities of the microbial membership, providing a direct link between the genetic potential and functional metabolism. The successful deployment of metaproteomics research depends on the integration of high-quality experimental and bioinformatic techniques for uncovering the metabolic activities of a microbial community in a way that is complementary to other "meta-omic" approaches. The essential, quality-defining informatics steps in metaproteomics investigations are: (1) construction of the metagenome, (2) functional annotation of predicted protein-coding genes, (3) protein database searching, (4) protein inference, and (5) extraction of metabolic information. In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool.}, } @article {pmid24930037, year = {2014}, author = {de Goffau, MC and Fuentes, S and van den Bogert, B and Honkanen, H and de Vos, WM and Welling, GW and Hyöty, H and Harmsen, HJ}, title = {Aberrant gut microbiota composition at the onset of type 1 diabetes in young children.}, journal = {Diabetologia}, volume = {57}, number = {8}, pages = {1569-1577}, pmid = {24930037}, issn = {1432-0428}, mesh = {Child, Preschool ; Clostridium/isolation & purification ; Diabetes Mellitus, Type 1/*microbiology ; Feces/*microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Infant ; Male ; Metagenome ; *Microbiota ; }, abstract = {AIMS/HYPOTHESIS: Recent studies indicate that an aberrant gut microbiota is associated with the development of type 1 diabetes, yet little is known about the microbiota in children who have diabetes at an early age. To this end, the microbiota of children aged 1-5 years with new-onset type 1 diabetes was compared with the microbiota of age-matched healthy controls.

METHODS: A deep global analysis of the gut microbiota composition was established by phylogenetic microarray analysis using a Human Intestinal Tract Chip (HITChip).

RESULTS: Principal component analyses highlighted the importance of age when comparing age-matched pairs. In pairs younger than 2.9 years, the combined abundance of the class Bacilli (notably streptococci) and the phylum Bacteroidetes was higher in diabetic children, whereas the combined abundance of members of Clostridium clusters IV and XIVa was higher in the healthy controls. Controls older than 2.9 years were characterised by a higher fraction of butyrate-producing species within Clostridium clusters IV and XIVa than was seen in the corresponding diabetic children or in children from the younger age groups, while the diabetic children older than 2.9 years could be differentiated by having an increased microbial diversity.

CONCLUSIONS/INTERPRETATION: The results from both age groups suggest that non-diabetic children have a more balanced microbiota in which butyrate-producing species appear to hold a pivotal position.}, } @article {pmid24927237, year = {2014}, author = {Otlewska, A and Adamiak, J and Gutarowska, B}, title = {Application of molecular techniques for the assessment of microorganism diversity on cultural heritage objects.}, journal = {Acta biochimica Polonica}, volume = {61}, number = {2}, pages = {217-225}, pmid = {24927237}, issn = {1734-154X}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Bacterial Typing Techniques ; Biodegradation, Environmental ; *Biodiversity ; DNA Fingerprinting ; *Environmental Restoration and Remediation ; Gene Library ; Metagenome ; Microbial Consortia/*genetics ; }, abstract = {As a result of their unpredictable ability to adapt to varying environmental conditions, microorganisms inhabit different types of biological niches on Earth. Owing to the key role of microorganisms in many biogeochemical processes, trends in modern microbiology emphasize the need to know and understand the structure and function of complex microbial communities. This is particularly important if the strategy relates to microbial communities that cause biodeterioration of materials that constitute our cultural heritage. Until recently, the detection and identification of microorganisms inhabiting objects of cultural value was based only on cultivation-dependent methods. In spite of many advantages, these methods provide limited information because they identify only viable organisms capable of growth under standard laboratory conditions. However, in order to carry out proper conservation and renovation, it is necessary to know the complete composition of microbial communities and their activity. This paper presents and characterizes modern techniques such as genetic fingerprinting and clone library construction for the assessment of microbial diversity based on molecular biology. Molecular methods represent a favourable alternative to culture-dependent methods and make it possible to assess the biodiversity of microorganisms inhabiting technical materials and cultural heritage objects.}, } @article {pmid24926861, year = {2015}, author = {Gomariz, M and Martínez-García, M and Santos, F and Rodriguez, F and Capella-Gutiérrez, S and Gabaldón, T and Rosselló-Móra, R and Meseguer, I and Antón, J}, title = {From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists.}, journal = {The ISME journal}, volume = {9}, number = {1}, pages = {16-31}, pmid = {24926861}, issn = {1751-7370}, support = {310325/ERC_/European Research Council/International ; }, mesh = {Actinobacteria/isolation & purification ; Archaea/classification/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; Bacteroidetes/*classification/genetics/isolation & purification ; Biodiversity ; Genome, Bacterial ; Halobacteriaceae/isolation & purification ; Metagenomics ; *Microbiota ; Ponds/*microbiology ; Salinity ; }, abstract = {The microbiota of multi-pond solar salterns around the world has been analyzed using a variety of culture-dependent and molecular techniques. However, studies addressing the dynamic nature of these systems are very scarce. Here we have characterized the temporal variation during 1 year of the microbiota of five ponds with increasing salinity (from 18% to >40%), by means of CARD-FISH and DGGE. Microbial community structure was statistically correlated with several environmental parameters, including ionic composition and meteorological factors, indicating that the microbial community was dynamic as specific phylotypes appeared only at certain times of the year. In addition to total salinity, microbial composition was strongly influenced by temperature and specific ionic composition. Remarkably, DGGE analyses unveiled the presence of most phylotypes previously detected in hypersaline systems using metagenomics and other molecular techniques, such as the very abundant Haloquadratum and Salinibacter representatives or the recently described low GC Actinobacteria and Nanohaloarchaeota. In addition, an uncultured group of Bacteroidetes was present along the whole range of salinity. Database searches indicated a previously unrecognized widespread distribution of this phylotype. Single-cell genome analysis of five members of this group suggested a set of metabolic characteristics that could provide competitive advantages in hypersaline environments, such as polymer degradation capabilities, the presence of retinal-binding light-activated proton pumps and arsenate reduction potential. In addition, the fairly high metagenomic fragment recruitment obtained for these single cells in both the intermediate and hypersaline ponds further confirm the DGGE data and point to the generalist lifestyle of this new Bacteroidetes group.}, } @article {pmid24925896, year = {2014}, author = {Vande Voorde, J and Balzarini, J and Liekens, S}, title = {An emerging understanding of the Janus face of the human microbiome: enhancement versus impairment of cancer therapy.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {10}, pages = {2878-2880}, doi = {10.1093/jac/dku201}, pmid = {24925896}, issn = {1460-2091}, mesh = {Animals ; Humans ; *Metagenome ; *Microbiota ; Neoplasms/etiology/pathology/therapy ; }, } @article {pmid24923965, year = {2014}, author = {Carbonetto, B and Rascovan, N and Álvarez, R and Mentaberry, A and Vázquez, MP}, title = {Structure, composition and metagenomic profile of soil microbiomes associated to agricultural land use and tillage systems in Argentine Pampas.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e99949}, pmid = {24923965}, issn = {1932-6203}, mesh = {*Agriculture/methods ; Argentina ; Bacteria/classification/genetics ; Crops, Agricultural ; Ecosystem ; Herbicides/pharmacology ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; Microbiota/*genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Agriculture is facing a major challenge nowadays: to increase crop production for food and energy while preserving ecosystem functioning and soil quality. Argentine Pampas is one of the main world producers of crops and one of the main adopters of conservation agriculture. Changes in soil chemical and physical properties of Pampas soils due to different tillage systems have been deeply studied. Still, not much evidence has been reported on the effects of agricultural practices on Pampas soil microbiomes. The aim of our study was to investigate the effects of agricultural land use on community structure, composition and metabolic profiles on soil microbiomes of Argentine Pampas. We also compared the effects associated to conventional practices with the effects of no-tillage systems. Our results confirmed the impact on microbiome structure and composition due to agricultural practices. The phyla Verrucomicrobia, Plactomycetes, Actinobacteria, and Chloroflexi were more abundant in non cultivated soils while Gemmatimonadetes, Nitrospirae and WS3 were more abundant in cultivated soils. Effects on metabolic metagenomic profiles were also observed. The relative abundance of genes assigned to transcription, protein modification, nucleotide transport and metabolism, wall and membrane biogenesis and intracellular trafficking and secretion were higher in cultivated fertilized soils than in non cultivated soils. We also observed significant differences in microbiome structure and taxonomic composition between soils under conventional and no-tillage systems. Overall, our results suggest that agronomical land use and the type of tillage system have induced microbiomes to shift their life-history strategies. Microbiomes of cultivated fertilized soils (i.e. higher nutrient amendment) presented tendencies to copiotrophy while microbiomes of non cultivated homogenous soils appeared to have a more oligotrophic life-style. Additionally, we propose that conventional tillage systems may promote copiotrophy more than no-tillage systems by decreasing soil organic matter stability and therefore increasing nutrient availability.}, } @article {pmid24922569, year = {2014}, author = {Thaiss, CA and Elinav, E}, title = {Exploring new horizons in microbiome research.}, journal = {Cell host & microbe}, volume = {15}, number = {6}, pages = {662-667}, doi = {10.1016/j.chom.2014.05.016}, pmid = {24922569}, issn = {1934-6069}, mesh = {*Biomedical Research ; Host-Pathogen Interactions/*immunology ; Humans ; Inflammatory Bowel Diseases/microbiology ; *Metagenome ; *Microbiota ; }, abstract = {Leading scientists in microbiome research met at Lake Titisee, Germany, in April 2014 to discuss the current state of the field, the most urgent and unresolved questions, state-of-the-art technological advances, and new avenues of future research. We summarize some of the concepts and themes discussed at this meeting.}, } @article {pmid24922184, year = {2014}, author = {Kim, M and Yoon, H and Kim, YE and Kim, YJ and Kong, WS and Kim, JG}, title = {Comparative analysis of bacterial diversity and communities inhabiting the fairy ring of Tricholoma matsutake by barcoded pyrosequencing.}, journal = {Journal of applied microbiology}, volume = {117}, number = {3}, pages = {699-710}, doi = {10.1111/jam.12572}, pmid = {24922184}, issn = {1365-2672}, mesh = {Acidobacteria/isolation & purification ; Actinobacteria/isolation & purification ; Bacteria/*classification/genetics/isolation & purification ; Biodiversity ; DNA Barcoding, Taxonomic ; Proteobacteria/isolation & purification ; Soil/chemistry ; *Soil Microbiology ; *Tricholoma ; }, abstract = {AIMS: Comparative analysis of the soil bacterial communities inhabiting the fairy ring of Tricholoma matsutake.

METHODS AND RESULTS: The bacterial communities in soil samples collected from inside, beneath and outside the T. matsutake fairy ring were investigated using barcoded pyrosequencing. A total of 15 129 reads were obtained, and 500-536 operational taxonomic units were observed at a 97% similarity level. Taxonomic analysis showed similar taxa distribution patterns inside and beneath the fairy ring. Three bacterial phyla, Proteobacteria, Acidobacteria and Actinobacteria, were dominant in all sampling sites. A heat-map analysis of the bacterial genera showed that the uncultured bacterium EU445199 was remarkably abundant outside the fairy ring, and the uncultured bacteria GU727715 and DQ451510 were more and less abundant, respectively, beneath the fairy ring than inside and outside the fairy ring.

CONCLUSIONS: The results indicated that there was no significant difference in bacterial diversity inside, beneath and outside the fairy ring even though T. matsutake is predominant beneath the fairy ring.

This study is the first report on the numerous culturable, unculturable and unclassified bacteria in the fairy ring of T. matsutake using the pyrosequencing method.}, } @article {pmid24921648, year = {2014}, author = {Ferreira, AJ and Siam, R and Setubal, JC and Moustafa, A and Sayed, A and Chambergo, FS and Dawe, AS and Ghazy, MA and Sharaf, H and Ouf, A and Alam, I and Abdel-Haleem, AM and Lehvaslaiho, H and Ramadan, E and Antunes, A and Stingl, U and Archer, JA and Jankovic, BR and Sogin, M and Bajic, VB and El-Dorry, H}, title = {Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e97338}, pmid = {24921648}, issn = {1932-6203}, mesh = {Adaptation, Physiological ; Light ; *Metagenome ; Microbiota/*genetics/physiology ; Multigene Family ; Phylogeny ; Seawater/*microbiology ; }, abstract = {Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.}, } @article {pmid24921207, year = {2014}, author = {Bustos Fernandez, LM and Lasa, JS and Man, F}, title = {Intestinal microbiota: its role in digestive diseases.}, journal = {Journal of clinical gastroenterology}, volume = {48}, number = {8}, pages = {657-666}, doi = {10.1097/MCG.0000000000000153}, pmid = {24921207}, issn = {1539-2031}, mesh = {Animals ; Digestive System Diseases/*microbiology/physiopathology ; Humans ; Intestines/*microbiology/physiopathology ; Metagenomics/methods ; *Microbiota ; }, abstract = {It is now well known that intestinal microbiota exerts not only several physiological functions, but has also been implied in the mechanisms of many conditions, both intestinal and extraintestinal. These advances, to the best of our knowledge, have been made possible by the development of new ways of studying gut flora. Metagenomics, the study of genetic material taken directly from environmental samples, avoiding individual culture, has become an excellent tool to study the human microbiota. Therefore, it has demonstrated an association between an altered intestinal microbiota and inflammatory bowel disease or irritable bowel syndrome, perhaps the most extensively studied conditions associated with this particular subject. However, microbiota has a potential role in the development of other diseases; their manifestations are not confined to the intestine only. In this article, an extensive updated review is conducted on the role intestinal microbiota has in health and in different diseases. Focus is made on the following conditions: inflammatory bowel disease, irritable bowel syndrome, celiac disease, hepatic encephalopathy, and obesity.}, } @article {pmid24920529, year = {2014}, author = {Moitinho-Silva, L and Seridi, L and Ryu, T and Voolstra, CR and Ravasi, T and Hentschel, U}, title = {Revealing microbial functional activities in the Red Sea sponge Stylissa carteri by metatranscriptomics.}, journal = {Environmental microbiology}, volume = {16}, number = {12}, pages = {3683-3698}, doi = {10.1111/1462-2920.12533}, pmid = {24920529}, issn = {1462-2920}, mesh = {Ammonia/metabolism ; Animals ; Archaea/*genetics/*physiology ; Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Coral Reefs ; Indian Ocean ; Membrane Transport Proteins/genetics/metabolism ; Metagenomics ; *Microbiota ; Molecular Sequence Annotation ; Oxidation-Reduction ; Photosynthesis ; Phylogeny ; Porifera/*microbiology ; *Symbiosis ; Synechococcus/genetics/physiology ; Transcriptome ; }, abstract = {Sponges are important components of marine benthic environments and are associated with microbial symbionts that carry out ecologically relevant functions. Stylissa carteri is an abundant, low-microbial abundance species in the Red Sea. We aimed to achieve the functional and taxonomic characterization of the most actively expressed prokaryotic genes in S. carteri. Prokaryotic mRNA was enriched from sponge total RNA, sequenced using Illumina HiSeq technology and annotated using the metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) pipeline. We detected high expression of archaeal ammonia oxidation and photosynthetic carbon fixation by members of the genus Synechococcus. Functions related to stress response and membrane transporters were among the most highly expressed by S. carteri symbionts. Unexpectedly, gene functions related to methylotrophy were highly expressed by gammaproteobacterial symbionts. The presence of seawater-derived microbes is indicated by the phylogenetic proximity of organic carbon transporters to orthologues of members from the SAR11 clade. In summary, we revealed the most expressed functions of the S. carteri-associated microbial community and linked them to the dominant taxonomic members of the microbiome. This work demonstrates the applicability of metatranscriptomics to explore poorly characterized symbiotic consortia and expands our knowledge of the ecologically relevant functions carried out by coral reef sponge symbionts.}, } @article {pmid24912178, year = {2014}, author = {Wang, J and Linnenbrink, M and Künzel, S and Fernandes, R and Nadeau, MJ and Rosenstiel, P and Baines, JF}, title = {Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {26}, pages = {E2703-10}, pmid = {24912178}, issn = {1091-6490}, mesh = {Analysis of Variance ; Animal Feed/*analysis ; Animals ; Bacteria/*genetics ; Base Sequence ; Carbon Isotopes/analysis ; Cluster Analysis ; DNA Primers/genetics ; *Diet ; Feces/microbiology ; France ; Germany ; Intestines/*microbiology ; Liver/chemistry ; Metagenomics/methods ; Mice/*microbiology ; Microbiota/*genetics ; Molecular Sequence Data ; Muscle, Skeletal/chemistry ; Nitrogen Isotopes/analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Understanding the origins of gut microbial community structure is critical for the identification and interpretation of potential fitness-related traits for the host. The presence of community clusters characterized by differences in the abundance of signature taxa, referred to as enterotypes, is a debated concept first reported in humans and later extended to other mammalian hosts. In this study, we provide a thorough assessment of their existence in wild house mice using a panel of evaluation criteria. We identify support for two clusters that are compositionally similar to clusters identified in humans, chimpanzees, and laboratory mice, characterized by differences in Bacteroides, Robinsoniella, and unclassified genera belonging to the family Lachnospiraceae. To further evaluate these clusters, we (i) monitored community changes associated with moving mice from the natural to a laboratory environment, (ii) performed functional metagenomic sequencing, and (iii) subjected wild-caught samples to stable isotope analysis to reconstruct dietary patterns. This process reveals differences in the proportions of genes involved in carbohydrate versus protein metabolism in the functional metagenome, as well as differences in plant- versus meat-derived food sources between clusters. In conjunction with wild-caught mice quickly changing their enterotype classification upon transfer to a standard laboratory chow diet, these results provide strong evidence that dietary history contributes to the presence of enterotype-like clustering in wild mice.}, } @article {pmid24911191, year = {2014}, author = {Ge, Y and Schimel, JP and Holden, PA}, title = {Analysis of run-to-run variation of bar-coded pyrosequencing for evaluating bacterial community shifts and individual taxa dynamics.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e99414}, pmid = {24911191}, issn = {1932-6203}, mesh = {Analysis of Variance ; Bacteria/*classification/*genetics ; Biodiversity ; *DNA Barcoding, Taxonomic ; *High-Throughput Nucleotide Sequencing/methods/standards ; *Metagenome ; Reproducibility of Results ; Soil Microbiology ; }, abstract = {Bar-coded pyrosequencing has been increasingly used due to its fine taxonomic resolution and high throughput. Yet, concerns arise regarding the reproducibility of bar-coded pyrosequencing. We evaluated the run-to-run variation of bar-coded pyrosequencing in detecting bacterial community shifts and taxa dynamics. Our results demonstrate that pyrosequencing is reproducible in evaluating community shifts within a run, but not between runs. Also, the reproducibility of pyrosequencing in detecting individual taxa increased as a function of taxa abundance. Based on our findings: (1) for studies with modest sequencing depth, it is doubtful that data from different pyrosequencing runs can be considered comparable; (2) if multiple pyrosequencing runs are needed to increase the sequencing depth, additional sequencing efforts should be applied to all samples, rather than to selected samples; (3) if pyrosequencing is used for estimating bacterial population dynamics, only the abundant taxa should be considered; (4) for less-abundant taxa, the sequencing depth should be increased to ensure an accurate evaluation of taxon variation trends across samples.}, } @article {pmid24908633, year = {2014}, author = {Mozar, M and Claverie, JM}, title = {Expanding the Mimiviridae family using asparagine synthase as a sequence bait.}, journal = {Virology}, volume = {466-467}, number = {}, pages = {112-122}, doi = {10.1016/j.virol.2014.05.013}, pmid = {24908633}, issn = {1096-0341}, mesh = {Aspartate-Ammonia Ligase/*genetics ; Biodiversity ; Databases, Nucleic Acid ; Genome, Viral/*genetics ; *Metagenome ; Metagenomics/*methods ; Mimiviridae/classification/enzymology/genetics/*isolation & purification ; Phylogeny ; Viral Proteins/genetics ; }, abstract = {Since the pioneering Global Ocean Sampling project, large-scale sequencing of environmental DNA has become a common approach to assess the biodiversity of diverse environments, with an emphasis on microbial populations: unicellular eukaryotes ("protists"), bacteria, archaea, and their innumerous associated viruses and phages. However, the global analysis of the viral diversity ("the virome") from sequence data is fundamentally hampered by the lack of a universal gene that would allow their unambiguous identification and reliable separation from cellular microorganisms. The problem has been made even more difficult with the discovery of micron-sized giant viruses for which the usual fractionation protocol on a "sterilizing" filter is no longer an option. In the present proof-of-principle work we used actual metagenomic data to show that glutamine-hydrolysing asparagine synthase is a reliable sequence probe to discover new members of the Mimiviridae family, hint at the existence of a new family of large DNA viruses, and point out misidentified database entries.}, } @article {pmid24907332, year = {2014}, author = {Martin, M and Biver, S and Steels, S and Barbeyron, T and Jam, M and Portetelle, D and Michel, G and Vandenbol, M}, title = {Identification and characterization of a halotolerant, cold-active marine endo-β-1,4-glucanase by using functional metagenomics of seaweed-associated microbiota.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {16}, pages = {4958-4967}, pmid = {24907332}, issn = {1098-5336}, mesh = {Bacteria/classification/*enzymology/genetics/isolation & purification ; Bacterial Proteins/*chemistry/*genetics/metabolism ; Cold Temperature ; Enzyme Stability ; Glycoside Hydrolases/*chemistry/*genetics/metabolism ; Metagenomics ; *Microbiota ; Molecular Sequence Data ; Phaeophyceae/*microbiology ; Phylogeny ; Seaweed/*microbiology ; Sodium Chloride/metabolism ; }, abstract = {A metagenomic library was constructed from microorganisms associated with the brown alga Ascophyllum nodosum. Functional screening of this library revealed 13 novel putative esterase loci and two glycoside hydrolase loci. Sequence and gene cluster analysis showed the wide diversity of the identified enzymes and gave an idea of the microbial populations present during the sample collection period. Lastly, an endo-β-1,4-glucanase having less than 50% identity to sequences of known cellulases was purified and partially characterized, showing activity at low temperature and after prolonged incubation in concentrated salt solutions.}, } @article {pmid24907284, year = {2014}, author = {Shi, W and Moon, CD and Leahy, SC and Kang, D and Froula, J and Kittelmann, S and Fan, C and Deutsch, S and Gagic, D and Seedorf, H and Kelly, WJ and Atua, R and Sang, C and Soni, P and Li, D and Pinares-Patiño, CS and McEwan, JC and Janssen, PH and Chen, F and Visel, A and Wang, Z and Attwood, GT and Rubin, EM}, title = {Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome.}, journal = {Genome research}, volume = {24}, number = {9}, pages = {1517-1525}, pmid = {24907284}, issn = {1549-5469}, mesh = {Animals ; Archaea/genetics/metabolism ; Archaeal Proteins/*genetics/metabolism ; Base Sequence ; *Metagenome ; Methane/*biosynthesis ; *Microbiota ; Molecular Sequence Data ; Phenotype ; Quantitative Trait, Heritable ; Rumen/metabolism/*microbiology ; Sheep/metabolism/*microbiology ; Transcriptome ; }, abstract = {Ruminant livestock represent the single largest anthropogenic source of the potent greenhouse gas methane, which is generated by methanogenic archaea residing in ruminant digestive tracts. While differences between individual animals of the same breed in the amount of methane produced have been observed, the basis for this variation remains to be elucidated. To explore the mechanistic basis of this methane production, we measured methane yields from 22 sheep, which revealed that methane yields are a reproducible, quantitative trait. Deep metagenomic and metatranscriptomic sequencing demonstrated a similar abundance of methanogens and methanogenesis pathway genes in high and low methane emitters. However, transcription of methanogenesis pathway genes was substantially increased in sheep with high methane yields. These results identify a discrete set of rumen methanogens whose methanogenesis pathway transcription profiles correlate with methane yields and provide new targets for CH4 mitigation at the levels of microbiota composition and transcriptional regulation.}, } @article {pmid24902956, year = {2015}, author = {Hermes, GD and Zoetendal, EG and Smidt, H}, title = {Molecular ecological tools to decipher the role of our microbial mass in obesity.}, journal = {Beneficial microbes}, volume = {6}, number = {1}, pages = {61-81}, doi = {10.3920/BM2014.0016}, pmid = {24902956}, issn = {1876-2891}, mesh = {*Biota ; Fatty Acids/metabolism ; Gastrointestinal Tract/*microbiology ; Gene Expression Profiling/*methods ; Humans ; Metabolomics/*methods ; Metagenomics/*methods ; Microbiota ; Obesity/*microbiology ; Proteomics/*methods ; }, abstract = {After birth, our gastrointestinal (GI) tract is colonised by a highly complex assemblage of microbes, collectively termed the GI microbiota, that develops intimate interactions with our body. Recent evidence indicates that the GI microbiota and its products may contribute to the development of obesity and related diseases. This, coupled with the current worldwide epidemic of obesity, has moved microbiome research into the spotlight of attention. Although the main cause of obesity and its associated metabolic complications is excess caloric intake compared with expenditure, differences in GI tract microbial ecology between individuals might be an important biomarker, mediator or new therapeutic target. This can be investigated using a diverse set of complementary so called -omics technologies, such as 16S ribosomal RNA gene-targeted composition profiling, metabolomics, metagenomics, metatranscriptomics and metaproteomics. This review aims to describe the different molecular approaches and their contributions to our understanding of the role of the GI microbiota in host energy homeostasis. Correspondingly, we highlight their respective strengths, but also try to create awareness for their specific limitations. However, it is currently still unclear which bacterial groups play a role in the development of obesity in humans. This might partly be explained by the heterogeneity in genotype, lifestyle, diet and the complex ethology of obesity and its associated metabolic disorders (OAMD). Nevertheless, recent research on this matter has shown a conceptual shift by focusing on more homogenous subpopulations, through the use of both anthropometric (weight, total body fat) as well as biochemical variables (insulin resistance, hyperlipidaemia) to define categories. Combined with technological advances, recent data suggests that an OAMD associated microbiota can be characterised by a potential pro-inflammatory composition, with less potential for the production of short chain fatty acids and butyrate in particular.}, } @article {pmid24899389, year = {2014}, author = {Wopereis, H and Oozeer, R and Knipping, K and Belzer, C and Knol, J}, title = {The first thousand days - intestinal microbiology of early life: establishing a symbiosis.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {25}, number = {5}, pages = {428-438}, doi = {10.1111/pai.12232}, pmid = {24899389}, issn = {1399-3038}, mesh = {Child, Preschool ; Humans ; Hypersensitivity/immunology/microbiology ; Infant ; Infant, Newborn ; Intestines/*microbiology ; Metagenome/*immunology ; Microbiota/*immunology ; Symbiosis/*immunology ; }, abstract = {The development of the intestinal microbiota in the first years of life is a dynamic process significantly influenced by early-life nutrition. Pioneer bacteria colonizing the infant intestinal tract and the gradual diversification to a stable climax ecosystem plays a crucial role in establishing host-microbe interactions essential for optimal symbiosis. This colonization process and establishment of symbiosis may profoundly influence health throughout life. Recent developments in microbiologic cultivation-independent methods allow a detailed view of the key players and factors involved in this process and may further elucidate their roles in a healthy gut and immune maturation. Aberrant patterns may lead to identifying key microbial signatures involved in developing immunologic diseases into adulthood, such as asthma and atopic diseases. The central role of early-life nutrition in the developmental human microbiota, immunity, and metabolism offers promising strategies for prevention and treatment of such diseases. This review provides an overview of the development of the intestinal microbiota, its bidirectional relationship with the immune system, and its role in impacting health and disease, with emphasis on allergy, in early life.}, } @article {pmid24894538, year = {2014}, author = {Cheng, W and Chen, H and Yan, S and Su, J}, title = {Illumina sequencing-based analyses of bacterial communities during short-chain fatty-acid production from food waste and sewage sludge fermentation at different pH values.}, journal = {World journal of microbiology & biotechnology}, volume = {30}, number = {9}, pages = {2387-2395}, pmid = {24894538}, issn = {1573-0972}, mesh = {Anaerobiosis ; Bacteria/*classification/*genetics ; *Biota ; Fatty Acids, Volatile/*metabolism ; Fermentation ; *Food Microbiology ; Hydrogen-Ion Concentration ; *Industrial Waste ; Metagenomics ; Sequence Analysis, DNA ; Sewage/chemistry/*microbiology ; }, abstract = {Short-chain fatty acids (SCFAs) can be produced by primary and waste activated sludge anaerobic fermentation. The yield and product spectrum distribution of SCFAs can be significantly affected by different initial pH values. However, most studies have focused on the physical and chemical aspects of SCFA production by waste activated sludge fermentation at different pH values. Information on the bacterial community structures during acidogenic fermentation is limited. In this study, comparisons of the bacterial communities during the co-substrate fermentation of food wastes and sewage sludge at different pH values were performed using the barcoded Illumina paired-end sequencing method. The results showed that different pH environments harbored a characteristic bacterial community, including sequences related to Lactobacillus, Prevotella, Mitsuokella, Treponema, Clostridium, and Ureibacillus. The most abundant bacterial operational taxonomic units in the different pH environments were those related to carbohydrate-degrading bacteria, which are associated with constituents of co-substrate fermentation. Further analyses showed that during organic matter fermentation, a core microbiota composed of Firmicutes, Proteobacteria, and Bacteroidetes existed. Comparison analyses revealed that the bacterial community during fermentation was significantly affected by the pH, and that the diverse product distribution was related to the shift in bacterial communities.}, } @article {pmid24888892, year = {2014}, author = {Lentendu, G and Wubet, T and Chatzinotas, A and Wilhelm, C and Buscot, F and Schlegel, M}, title = {Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach.}, journal = {Molecular ecology}, volume = {23}, number = {13}, pages = {3341-3355}, doi = {10.1111/mec.12819}, pmid = {24888892}, issn = {1365-294X}, mesh = {*Biodiversity ; Cercozoa/classification/genetics ; Chrysophyta/classification/genetics ; DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; *Fertilizers ; Fungi/classification/genetics ; Kinetoplastida/classification/genetics ; Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 23S/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {To understand the fine-scale effects of changes in nutrient availability on eukaryotic soil microorganisms communities, a multiple barcoding approach was used to analyse soil samples from four different treatments in a long-term fertilization experiment. We performed PCR amplification on soil DNA with primer pairs specifically targeting the 18S rRNA genes of all eukaryotes and three protist groups (Cercozoa, Chrysophyceae-Synurophyceae and Kinetoplastida) as well as the ITS gene of fungi and the 23S plastid rRNA gene of photoautotrophic microorganisms. Amplicons were pyrosequenced, and a total of 88,706 quality filtered reads were clustered into 1232 operational taxonomic units (OTU) across the six data sets. Comparisons of the taxonomic coverage achieved based on overlapping assignment of OTUs revealed that half of the eukaryotic taxa identified were missed by the universal eukaryotic barcoding marker. There were only little differences in OTU richness observed between organic- (farmyard manure), mineral- and nonfertilized soils. However, the community compositions appeared to be strongly structured by organic fertilization in all data sets other than that generated using the universal eukaryotic 18S rRNA gene primers, whereas mineral fertilization had only a minor effect. In addition, a co-occurrence based network analysis revealed complex potential interaction patterns between OTUs from different trophic levels, for example between fungivorous flagellates and fungi. Our results demonstrate that changes in pH, moisture and organic nutrients availability caused shifts in the composition of eukaryotic microbial communities at multiple trophic levels.}, } @article {pmid24886836, year = {2014}, author = {Das, S and Dash, HR and Mangwani, N and Chakraborty, J and Kumari, S}, title = {Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms.}, journal = {Journal of microbiological methods}, volume = {103}, number = {}, pages = {80-100}, doi = {10.1016/j.mimet.2014.05.013}, pmid = {24886836}, issn = {1872-8359}, mesh = {Bacteria/classification/genetics/metabolism ; Bacterial Typing Techniques ; Biodiversity ; Fungi/classification/genetics/metabolism ; Genes, Essential ; *Metagenome ; Molecular Typing/methods ; *Phylogeny ; Proteome ; Proteomics ; }, abstract = {The major proportion of earth's biological diversity is inhabited by microorganisms and they play a useful role in diversified environments. However, taxonomy of microorganisms is progressing at a snail's pace, thus less than 1% of the microbial population has been identified so far. The major problem associated with this is due to a lack of uniform, reliable, advanced, and common to all practices for microbial identification and systematic studies. However, recent advances have developed many useful techniques taking into account the house-keeping genes as well as targeting other gene catalogues (16S rRNA, rpoA, rpoB, gyrA, gyrB etc. in case of bacteria and 26S, 28S, β-tubulin gene in case of fungi). Some uncultivable approaches using much advanced techniques like flow cytometry and gel based techniques have also been used to decipher microbial diversity. However, all these techniques have their corresponding pros and cons. In this regard, a polyphasic taxonomic approach is advantageous because it exploits simultaneously both conventional as well as molecular identification techniques. In this review, certain aspects of the merits and limitations of different methods for molecular identification and systematics of microorganisms have been discussed. The major advantages of the polyphasic approach have also been described taking into account certain groups of bacteria as case studies to arrive at a consensus approach to microbial identification.}, } @article {pmid24886397, year = {2014}, author = {Alsop, EB and Boyd, ES and Raymond, J}, title = {Merging metagenomics and geochemistry reveals environmental controls on biological diversity and evolution.}, journal = {BMC ecology}, volume = {14}, number = {}, pages = {16}, pmid = {24886397}, issn = {1472-6785}, mesh = {Algorithms ; Bacteria/classification/genetics ; *Biodiversity ; *Biological Evolution ; Cluster Analysis ; *Environment ; Hot Springs/chemistry/microbiology ; Markov Chains ; *Metagenomics ; Principal Component Analysis ; Seawater/chemistry/microbiology ; Water Microbiology ; }, abstract = {BACKGROUND: The metabolic strategies employed by microbes inhabiting natural systems are, in large part, dictated by the physical and geochemical properties of the environment. This study sheds light onto the complex relationship between biology and environmental geochemistry using forty-three metagenomes collected from geochemically diverse and globally distributed natural systems. It is widely hypothesized that many uncommonly measured geochemical parameters affect community dynamics and this study leverages the development and application of multidimensional biogeochemical metrics to study correlations between geochemistry and microbial ecology. Analysis techniques such as a Markov cluster-based measure of the evolutionary distance between whole communities and a principal component analysis (PCA) of the geochemical gradients between environments allows for the determination of correlations between microbial community dynamics and environmental geochemistry and provides insight into which geochemical parameters most strongly influence microbial biodiversity.

RESULTS: By progressively building from samples taken along well defined geochemical gradients to samples widely dispersed in geochemical space this study reveals strong links between the extent of taxonomic and functional diversification of resident communities and environmental geochemistry and reveals temperature and pH as the primary factors that have shaped the evolution of these communities. Moreover, the inclusion of extensive geochemical data into analyses reveals new links between geochemical parameters (e.g. oxygen and trace element availability) and the distribution and taxonomic diversification of communities at the functional level. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial taxonomic and functional composition.

CONCLUSIONS: Clustering based on the frequency in which orthologous proteins occur among metagenomes facilitated accurate prediction of the ordering of community functional composition along geochemical gradients, despite a lack of geochemical input. The consistency in the results obtained from the application of Markov clustering and multivariate methods to distinct natural systems underscore their utility in predicting the functional potential of microbial communities within a natural system based on system geochemistry alone, allowing geochemical measurements to be used to predict purely biological metrics such as microbial community composition and metabolism.}, } @article {pmid24886057, year = {2014}, author = {Bodewes, R and Ruiz-Gonzalez, A and Schapendonk, CM and van den Brand, JM and Osterhaus, AD and Smits, SL}, title = {Viral metagenomic analysis of feces of wild small carnivores.}, journal = {Virology journal}, volume = {11}, number = {}, pages = {89}, pmid = {24886057}, issn = {1743-422X}, mesh = {Animals ; *Biodiversity ; Carnivora/*virology ; Feces/*virology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Molecular Sequence Data ; Polymerase Chain Reaction ; Spain ; Viruses/*classification/genetics/*isolation & purification ; }, abstract = {BACKGROUND: Recent studies have clearly demonstrated the enormous virus diversity that exists among wild animals. This exemplifies the required expansion of our knowledge of the virus diversity present in wildlife, as well as the potential transmission of these viruses to domestic animals or humans.

METHODS: In the present study we evaluated the viral diversity of fecal samples (n = 42) collected from 10 different species of wild small carnivores inhabiting the northern part of Spain using random PCR in combination with next-generation sequencing. Samples were collected from American mink (Neovison vison), European mink (Mustela lutreola), European polecat (Mustela putorius), European pine marten (Martes martes), stone marten (Martes foina), Eurasian otter (Lutra lutra) and Eurasian badger (Meles meles) of the family of Mustelidae; common genet (Genetta genetta) of the family of Viverridae; red fox (Vulpes vulpes) of the family of Canidae and European wild cat (Felis silvestris) of the family of Felidae.

RESULTS: A number of sequences of possible novel viruses or virus variants were detected, including a theilovirus, phleboviruses, an amdovirus, a kobuvirus and picobirnaviruses.

CONCLUSIONS: Using random PCR in combination with next generation sequencing, sequences of various novel viruses or virus variants were detected in fecal samples collected from Spanish carnivores. Detected novel viruses highlight the viral diversity that is present in fecal material of wild carnivores.}, } @article {pmid24882717, year = {2014}, author = {Proal, AD and Albert, PJ and Marshall, TG}, title = {Inflammatory disease and the human microbiome.}, journal = {Discovery medicine}, volume = {17}, number = {95}, pages = {257-265}, pmid = {24882717}, issn = {1944-7930}, mesh = {Gene Expression Regulation, Bacterial ; Genome, Human ; Genomics ; Humans ; Immunity, Innate ; Inflammation/*microbiology/*physiopathology ; Metagenome ; *Microbiota ; }, abstract = {The human body is a superorganism in which thousands of microbial genomes continually interact with the human genome. A range of physical and neurological inflammatory diseases are now associated with shifts in microbiome composition. Seemingly disparate inflammatory conditions may arise from similar disruption of microbiome homeostasis. Intracellular pathogens long associated with inflammatory disease are able to slow the innate immune response by dysregulating activity of the VDR nuclear receptor. This facilitates the ability of other species to gradually accumulate in tissue and blood, where they generate proteins and metabolites that significantly interfere with the body's metabolic processes. The microbes that contribute to this dysfunction are often inherited from family members. Immunosuppressive therapies for inflammatory disease allow pathogens driving these processes to spread with greater ease. In contrast to immunosuppression, treatments that stimulate the immune system seem to allow for reversal of this pathogen-induced genomic dysregulation.}, } @article {pmid24879347, year = {2014}, author = {Shin, S and Lee, TK and Han, JM and Park, J}, title = {Regional effects on chimera formation in 454 pyrosequenced amplicons from a mock community.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {52}, number = {7}, pages = {566-573}, pmid = {24879347}, issn = {1976-3794}, mesh = {*Biodiversity ; *Environmental Microbiology ; Metagenomics/*methods ; Nucleic Acid Amplification Techniques/methods ; Oxidoreductases/genetics ; RNA, Ribosomal, 16S/genetics ; *Recombination, Genetic ; Sequence Analysis, DNA/methods ; }, abstract = {Chimeras are a frequent artifact in polymerase chain reaction and could be the underlying causes of erroneous taxonomic identifications, overestimated microbial diversity, and spurious sequences. However, little is known about the regional effects on chimera formation. Therefore, we investigated the chimera formation rates in different regions of phylogenetically important biomarker genes to test the regional effects on chimera formation. An empirical study of chimera formation rates was performed using the Roche GSFLX™ system with sequences of the V1/V2/V3 and V4/V5 regions of the 16S rRNA gene and sequences of the nifH gene from a mock microbial community. The chimera formation rates for the 16S V1/V2/V3 region, V4/V5 region, and nifH gene were 22.1-38.5%, 3.68-3.88%, and 0.31-0.98%, respectively. Some amplicons from the V1/V2/V3 regions were shorter than the typical length (∼7-31%), reflecting incomplete extension. In the V1/V2/V3 and V4/V5 regions, conserved and hypervariable regions were identified. Chimeric hot spots were located in parts of conserved regions near the ends of the amplicons. The 16S V1/V2/V3 region had the highest chimera formation rate, likely because of long template lengths and incomplete extension. The amplicons of the nifH gene had the lowest frequency of chimera formation most likely because of variations in their wobble positions in triplet codons. Our results suggest that the main reasons for chimera formation are sequence similarity and premature termination of DNA extension near primer regions. Other housekeeping genes can be a good substitute for 16S rRNA genes in molecular microbial studies to reduce the effects of chimera formation.}, } @article {pmid24871104, year = {2015}, author = {Montagna, M and Gómez-Zurita, J and Giorgi, A and Epis, S and Lozzia, G and Bandi, C}, title = {Metamicrobiomics in herbivore beetles of the genus Cryptocephalus (Chrysomelidae): toward the understanding of ecological determinants in insect symbiosis.}, journal = {Insect science}, volume = {22}, number = {3}, pages = {340-352}, doi = {10.1111/1744-7917.12143}, pmid = {24871104}, issn = {1744-7917}, mesh = {Animals ; Bacteria/classification/*genetics ; Coleoptera/*microbiology ; Metagenomics ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {The Cryptocephalus marginellus (Coleoptera: Chrysomelidae) complex is composed by six species that are supposed to have originated by events of allo- or parapatric speciation. In the present study we investigated the alternative hypotheses that the bacterial communities associated with six populations of this species complex are shaped by environmental factors, or reflect the proposed pattern of speciation. The microbiota associated with the six populations, from five species of the complex, have been characterized through 16S rRNA pyrotag sequencing. Based on a 97% sequence similarity threshold, data were clustered into 381 OTUs, which were analyzed using a variety of diversity indices. The microbiota of C. acquitanus and C. marginellus (Calanques) were the most diverse (over 100 OTUs), while that from C. zoiai yielded less bacterial diversity (45 OTUs). Taxonomic assignment revealed Proteobacteria, Tenericutes and Firmicutes as the dominant components of these beetles' microbiota. The most abundant genera were Ralstonia, Sphingomonas, Rickettsia, and Pseudomonas. Different strains of Rickettsia were detected in C. eridani and C. renatae. The analysis of β-diversity revealed high OTU turnover among the populations of C. marginellus complex, with only few shared species. Hierarchical clustering taking into account relative abundances of OTUs does not match the phylogeny of the beetles, therefore we hypothesize that factors other than phylogenetic constraints play a role in shaping the insects' microbiota. Environmental factors that could potentially affect the composition of bacterial communities were tested by fitting them on the results of a multi-dimensional scaling analysis. No significant correlations were observed towards the geographic distances or the host plants, while the composition of the microbiota appeared associated with altitude. The metabolic profiles of the microbiotas associated with each population were inferred from bacterial taxonomy, and interestingly, the obtained clustering pattern was consistent with the host phylogeny.}, } @article {pmid24866801, year = {2014}, author = {Krull, AC and Shearer, JK and Gorden, PJ and Cooper, VL and Phillips, GJ and Plummer, PJ}, title = {Deep sequencing analysis reveals temporal microbiota changes associated with development of bovine digital dermatitis.}, journal = {Infection and immunity}, volume = {82}, number = {8}, pages = {3359-3373}, pmid = {24866801}, issn = {1098-5522}, mesh = {Animals ; Biopsy ; Cattle ; Digital Dermatitis/*microbiology ; High-Throughput Nucleotide Sequencing ; Longitudinal Studies ; Metagenomics ; *Microbiota ; Skin/microbiology ; }, abstract = {Bovine digital dermatitis (DD) is a leading cause of lameness in dairy cattle throughout the world. Despite 35 years of research, the definitive etiologic agent associated with the disease process is still unknown. Previous studies have demonstrated that multiple bacterial species are associated with lesions, with spirochetes being the most reliably identified organism. This study details the deep sequencing-based metagenomic evaluation of 48 staged DD biopsy specimens collected during a 3-year longitudinal study of disease progression. Over 175 million sequences were evaluated by utilizing both shotgun and 16S metagenomic techniques. Based on the shotgun sequencing results, there was no evidence of a fungal or DNA viral etiology. The bacterial microbiota of biopsy specimens progresses through a systematic series of changes that correlate with the novel morphological lesion scoring system developed as part of this project. This scoring system was validated, as the microbiota of each stage was statistically significantly different from those of other stages (P < 0.001). The microbiota of control biopsy specimens were the most diverse and became less diverse as lesions developed. Although Treponema spp. predominated in the advanced lesions, they were in relatively low abundance in the newly described early lesions that are associated with the initiation of the disease process. The consortium of Treponema spp. identified at the onset of disease changes considerably as the lesions progress through the morphological stages identified. The results of this study support the hypothesis that DD is a polybacterial disease process and provide unique insights into the temporal changes in bacterial populations throughout lesion development.}, } @article {pmid24861948, year = {2014}, author = {Rajilić-Stojanović, M and de Vos, WM}, title = {The first 1000 cultured species of the human gastrointestinal microbiota.}, journal = {FEMS microbiology reviews}, volume = {38}, number = {5}, pages = {996-1047}, pmid = {24861948}, issn = {1574-6976}, mesh = {Archaea/classification/genetics/isolation & purification/*physiology ; Bacteria/classification/genetics/isolation & purification ; *Bacterial Physiological Phenomena ; *Biodiversity ; Eukaryota/classification/genetics/isolation & purification/*physiology ; Gastrointestinal Tract/*microbiology/*parasitology ; Humans ; }, abstract = {The microorganisms that inhabit the human gastrointestinal tract comprise a complex ecosystem with functions that significantly contribute to our systemic metabolism and have an impact on health and disease. In line with its importance, the human gastrointestinal microbiota has been extensively studied. Despite the fact that a significant part of the intestinal microorganisms has not yet been cultured, presently over 1000 different microbial species that can reside in the human gastrointestinal tract have been identified. This review provides a systematic overview and detailed references of the total of 1057 intestinal species of Eukarya (92), Archaea (8) and Bacteria (957), based on the phylogenetic framework of their small subunit ribosomal RNA gene sequences. Moreover, it unifies knowledge about the prevalence, abundance, stability, physiology, genetics and the association with human health of these gastrointestinal microorganisms, which is currently scattered over a vast amount of literature published in the last 150 years. This detailed physiological and genetic information is expected to be instrumental in advancing our knowledge of the gastrointestinal microbiota. Moreover, it opens avenues for future comparative and functional metagenomic and other high-throughput approaches that need a systematic and physiological basis to have an impact.}, } @article {pmid24859864, year = {2014}, author = {Kim, YE and Yoon, H and Kim, M and Nam, YJ and Kim, H and Seo, Y and Lee, GM and Ja Kim, Y and Kong, WS and Kim, JG and Seu, YB}, title = {Metagenomic analysis of bacterial communities on Dokdo Island.}, journal = {The Journal of general and applied microbiology}, volume = {60}, number = {2}, pages = {65-74}, doi = {10.2323/jgam.60.65}, pmid = {24859864}, issn = {1349-8037}, mesh = {Bacteria/*classification/*genetics ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geography ; Islands ; Metagenomics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Dokdo, located east of the mainland of South Korea, is a volcanic island designated as a natural monument of South Korea due to its ecological value. Dokdo is divided into Dongdo and Seodo, islands with geological differences. The soil bacterial communities on Dokdo (Dongdo and Seodo) were analyzed using the pyrosequencing method. There were 1,693 and 1,408 operational taxonomic units (OTU) from Dongdo and Seodo, respectively. The statistical analyses (rarefaction curves as well as Chao1, Shannon, and Simpson indices) showed that bacterial diversity was slightly higher in Dongdo than Seodo. From results of a BLASTN search against the EzTaxon-e database, the validated reads (obtained after sequence preprocessing) were almost all classified at the phylum level. From the phylum level down to the species level, the number of classified reads considerably decreased due to the absence of information concerning unculturable or unidentified bacteria to date. Among the 36 phyla identified, three phyla (Proteobacteria, Actinobacteria and Acidobacteria) accounted for around 74.64%. The taxonomic composition was similar at the higher ranks (family and above) between Dongdo and Seodo, but a little different at the genus level. There were also various differences in the relative abundance of taxonomic ranks between Dongdo and Seodo. In particular, the proportion of the genus Acidobacterium (of the phylum Acidobacteria) was about six times higher in Seodo than Dongdo. In addition, the percentage of the genus Mycobacterium (of the phylum Actinobacteria) was nearly three times higher in Seodo than Dongdo, and the proportion of the genus Gaiella was about 3.7 times higher in Dongdo than Seodo. Overall, through the metagenomic analysis, the number of species identified in Dongdo and Seodo was 1,239 and 1,055, respectively. This information on the numerous culturable and unculturable bacteria is expected to help in the screening of new species in Dokdo.}, } @article {pmid24859309, year = {2014}, author = {Narihiro, T and Suzuki, A and Yoshimune, K and Hori, T and Hoshino, T and Yumoto, I and Yokota, A and Kimura, N and Kamagata, Y}, title = {The combination of functional metagenomics and an oil-fed enrichment strategy revealed the phylogenetic diversity of lipolytic bacteria overlooked by the cultivation-based method.}, journal = {Microbes and environments}, volume = {29}, number = {2}, pages = {154-161}, pmid = {24859309}, issn = {1347-4405}, mesh = {Actinobacteria/classification/*genetics/isolation & purification ; Alphaproteobacteria/classification/genetics/isolation & purification ; Bacterial Load ; Base Sequence ; Betaproteobacteria/classification/genetics/isolation & purification ; Biodiversity ; DNA, Bacterial/chemistry/genetics ; Firmicutes/classification/*genetics/isolation & purification ; Forests ; Gammaproteobacteria/classification/genetics/isolation & purification ; Lipase/chemistry/metabolism ; Lipolysis ; *Metagenomics ; Mutagenesis ; Oils/metabolism ; Phylogeny ; Proteobacteria/classification/*genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Metagenomic screening and conventional cultivation have been used to exploit microbial lipolytic enzymes in nature. We used an indigenous forest soil (NS) and oil-fed enriched soil (OS) as microbial and genetic resources. Thirty-four strains (17 each) of lipolytic bacteria were isolated from the NS and OS microcosms. These isolates were classified into the (sub)phyla Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria, all of which are known to be the main microbial resources of commercially available lipolytic enzymes. Seven and 39 lipolytic enzymes were successfully retrieved from the metagenomic libraries of the NS and OS microcosms, respectively. The screening efficiency (a ratio of positive lipolytic clones to the total number of environmental clones) was markedly higher in the OS microcosm than in the NS microcosm. Moreover, metagenomic clones encoding the lipolytic enzymes associated with Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Armatimonadetes, and Planctomycetes and hitherto-uncultivated microbes were recovered from these libraries. The results of the present study indicate that functional metagenomics can be effectively used to capture as yet undiscovered lipolytic enzymes that have eluded the cultivation-based method, and these combined approaches may be able to provide an overview of lipolytic organisms potentially present in nature.}, } @article {pmid24859088, year = {2014}, author = {Zawar-Reza, P and Argüello-Astorga, GR and Kraberger, S and Julian, L and Stainton, D and Broady, PA and Varsani, A}, title = {Diverse small circular single-stranded DNA viruses identified in a freshwater pond on the McMurdo Ice Shelf (Antarctica).}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {26}, number = {}, pages = {132-138}, doi = {10.1016/j.meegid.2014.05.018}, pmid = {24859088}, issn = {1567-7257}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Antarctic Regions ; *Biodiversity ; Cloning, Molecular ; Conserved Sequence ; *DNA, Circular ; DNA, Single-Stranded/*classification/*physiology ; *DNA, Viral ; Genome, Viral ; Molecular Sequence Data ; Phylogeny ; Ponds/*virology ; Sequence Analysis, DNA ; Virus Replication ; *Water Microbiology ; }, abstract = {Antarctica has some of the harshest environmental conditions for existence of life on Earth. In this pilot study we recovered eight diverse circular single-stranded DNA (ssDNA) viral genome sequences (1904-3120 nts) from benthic mats dominated by filamentous cyanobacteria in a freshwater pond on the McMurdo Ice Shelf sampled in 1988. All genomes contain two to three major open reading frames (ORFs) that are uni- or bi-directionally transcribed and all have an ORF encoding a replication-associated protein (Rep). In one genome, the second ORF has similarity to a capsid protein (CP) of Nepavirus which is most closely related to geminiviruses. Additionally, all genomes have two intergenic regions that contain putative stem loop structures, six genomes have NANTATTAC as the nonanucleotide motif, while one has CCTTATTAC, and another has a non-canonical stem loop. In the large intergenic region, we identified iterative sequences flanking the putative stem-loop elements which are a hallmark of most circular ssDNA viruses encoding rolling circle replication (RCR) initiators of the HUH endonuclease superfamily. The Reps encoded by ssDNA viral genomes recovered in this study shared <38% pairwise identity to all other Reps of known ssDNA viruses. A previous study on Lake Limnopolar (Livingston Island, South Shetland Islands), using next-generation sequencing identified circular ssDNA viruses and their putative Reps share <35% pairwise identity to those from the viral genomes removed in this study. It is evident from our pilot study that the global diversity of ssDNA viruses is grossly underestimated and there is limited knowledge on ssDNA viruses in Antarctica.}, } @article {pmid24858451, year = {2014}, author = {Callewaert, C and Buysschaert, B and Vossen, E and Fievez, V and Van de Wiele, T and Boon, N}, title = {Artificial sweat composition to grow and sustain a mixed human axillary microbiome.}, journal = {Journal of microbiological methods}, volume = {103}, number = {}, pages = {6-8}, doi = {10.1016/j.mimet.2014.05.005}, pmid = {24858451}, issn = {1872-8359}, mesh = {Axilla/*microbiology ; Humans ; Mass Spectrometry ; Metagenome ; *Microbiota ; Odorants/analysis ; Phylogeny ; Sweat/*chemistry/*microbiology ; }, abstract = {A novel artificial sweat composition, Skin Community Interaction simulation, designed to mimic the human axillary sweat, was compared to other artificial sweat compositions. Axillary microbiota grown in the novel composition closely resembled the original community. Volatile organic compound analysis showed good correlations with in vivo axillary (mal)odor components.}, } @article {pmid24855011, year = {2014}, author = {Tlaskalova-Hogenova, H and Vannucci, L and Klimesova, K and Stepankova, R and Krizan, J and Kverka, M}, title = {Microbiome and colorectal carcinoma: insights from germ-free and conventional animal models.}, journal = {Cancer journal (Sudbury, Mass.)}, volume = {20}, number = {3}, pages = {217-224}, doi = {10.1097/PPO.0000000000000052}, pmid = {24855011}, issn = {1540-336X}, mesh = {Animals ; Colorectal Neoplasms/*microbiology ; *Disease Models, Animal ; *Germ-Free Life ; Humans ; Inflammation/microbiology ; *Microbiota ; Tumor Microenvironment ; }, abstract = {The mammalian microbiota plays a crucial role in the pathogenesis of many diseases. Thanks to recent advances in metagenomics, proteomics, and metabolomics, microbiome composition and metabolic activity can now be studied in detail. Results obtained by such fascinating and provocative studies would be meaningless without considering the perspective of the whole organism. Our work using gnotobiology as the major tool to unravel the mechanisms of host-microbe interaction has demonstrated the crucial role of microbiota in the initiation and progression of inflammation-associated colorectal neoplasia. Carcinogenesis in the gut is driven by the presence of potentially harmful microbes or by lack of protective ones, by the production of carcinogens generated by microbes, and by the induction of inflammation and modulation of the immune system. Here, we review these mechanisms with special emphasis on those where gnotobiology has yielded important insights.}, } @article {pmid24851867, year = {2014}, author = {Lee, SC and Tang, MS and Lim, YA and Choy, SH and Kurtz, ZD and Cox, LM and Gundra, UM and Cho, I and Bonneau, R and Blaser, MJ and Chua, KH and Loke, P}, title = {Helminth colonization is associated with increased diversity of the gut microbiota.}, journal = {PLoS neglected tropical diseases}, volume = {8}, number = {5}, pages = {e2880}, pmid = {24851867}, issn = {1935-2735}, support = {R01 AI093811/AI/NIAID NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; AI094166/AI/NIAID NIH HHS/United States ; AI093811/AI/NIAID NIH HHS/United States ; R01 DK090989/DK/NIDDK NIH HHS/United States ; R21 AI094166/AI/NIAID NIH HHS/United States ; T32 AI007180/AI/NIAID NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Animals ; Bacteria/classification/genetics/isolation & purification ; Child ; Child, Preschool ; Feces/microbiology/parasitology ; Female ; Helminthiasis/epidemiology/*microbiology/*parasitology ; Helminths/classification/genetics/isolation & purification ; Humans ; Infant ; Malaysia/epidemiology ; Male ; Metagenome/genetics ; Microbiota/*physiology ; New York City/epidemiology ; Young Adult ; }, abstract = {Soil-transmitted helminths colonize more than 1.5 billion people worldwide, yet little is known about how they interact with bacterial communities in the gut microbiota. Differences in the gut microbiota between individuals living in developed and developing countries may be partly due to the presence of helminths, since they predominantly infect individuals from developing countries, such as the indigenous communities in Malaysia we examine in this work. We compared the composition and diversity of bacterial communities from the fecal microbiota of 51 people from two villages in Malaysia, of which 36 (70.6%) were infected by helminths. The 16S rRNA V4 region was sequenced at an average of nineteen thousand sequences per samples. Helminth-colonized individuals had greater species richness and number of observed OTUs with enrichment of Paraprevotellaceae, especially with Trichuris infection. We developed a new approach of combining centered log-ratio (clr) transformation for OTU relative abundances with sparse Partial Least Squares Discriminant Analysis (sPLS-DA) to enable more robust predictions of OTU interrelationships. These results suggest that helminths may have an impact on the diversity, bacterial community structure and function of the gut microbiota.}, } @article {pmid24850358, year = {2014}, author = {Huang, YJ and Sethi, S and Murphy, T and Nariya, S and Boushey, HA and Lynch, SV}, title = {Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease.}, journal = {Journal of clinical microbiology}, volume = {52}, number = {8}, pages = {2813-2823}, pmid = {24850358}, issn = {1098-660X}, support = {K23 HL105572/HL/NHLBI NIH HHS/United States ; HL105572/HL/NHLBI NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Humans ; Longitudinal Studies ; Male ; *Microbiota ; Middle Aged ; Phylogeny ; Proteobacteria/*classification/genetics ; Pulmonary Disease, Chronic Obstructive/*microbiology ; RNA, Ribosomal, 16S/genetics ; Respiratory System/*microbiology ; Sequence Analysis, DNA ; Sputum/microbiology ; }, abstract = {Specific bacterial species are implicated in the pathogenesis of exacerbations of chronic obstructive pulmonary disease (COPD). However, recent studies of clinically stable COPD patients have demonstrated a greater diversity of airway microbiota, whose role in acute exacerbations is unclear. In this study, temporal changes in the airway microbiome before, at the onset of, and after an acute exacerbation were examined in 60 sputum samples collected from subjects enrolled in a longitudinal study of bacterial infection in COPD. Microbiome composition and predicted functions were examined using 16S rRNA-based culture-independent profiling methods. Shifts in the abundance (≥ 2-fold, P < 0.05) of many taxa at exacerbation and after treatment were observed. Microbiota members that were increased at exacerbation were primarily of the Proteobacteria phylum, including nontypical COPD pathogens. Changes in the bacterial composition after treatment for an exacerbation differed significantly among the therapy regimens clinically prescribed (antibiotics only, oral corticosteroids only, or both). Treatment with antibiotics alone primarily decreased the abundance of Proteobacteria, with the prolonged suppression of some microbiota members being observed. In contrast, treatment with corticosteroids alone led to enrichment for Proteobacteria and members of other phyla. Predicted metagenomes of particular microbiota members involved in these compositional shifts indicated exacerbation-associated loss of functions involved in the synthesis of antimicrobial and anti-inflammatory products, alongside enrichment in functions related to pathogen-elicited inflammation. These trends reversed upon clinical recovery. Further larger studies will be necessary to determine whether specific compositional or functional changes detected in the airway microbiome could be useful indicators of exacerbation development or outcome.}, } @article {pmid24848255, year = {2014}, author = {Aagaard, K and Ma, J and Antony, KM and Ganu, R and Petrosino, J and Versalovic, J}, title = {The placenta harbors a unique microbiome.}, journal = {Science translational medicine}, volume = {6}, number = {237}, pages = {237ra65}, pmid = {24848255}, issn = {1946-6242}, support = {U54 HG004973/HG/NHGRI NIH HHS/United States ; DP2 DP21DP2OD001500/OD/NIH HHS/United States ; U54HG004973/HG/NHGRI NIH HHS/United States ; DP2 OD001500/OD/NIH HHS/United States ; R01 NR014792/NR/NINR NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics/isolation & purification ; Case-Control Studies ; Chi-Square Distribution ; Classification ; DNA, Bacterial/*genetics ; Female ; Humans ; Metagenomics ; Microbiota/*genetics ; Multivariate Analysis ; Placenta/*microbiology ; Pregnancy ; Pregnancy Complications, Infectious/microbiology ; Pregnancy Trimester, First ; Premature Birth/microbiology ; RNA, Ribosomal, 16S/*genetics ; Ribotyping ; Risk Factors ; Urinary Tract Infections/microbiology ; }, abstract = {Humans and their microbiomes have coevolved as a physiologic community composed of distinct body site niches with metabolic and antigenic diversity. The placental microbiome has not been robustly interrogated, despite recent demonstrations of intracellular bacteria with diverse metabolic and immune regulatory functions. A population-based cohort of placental specimens collected under sterile conditions from 320 subjects with extensive clinical data was established for comparative 16S ribosomal DNA-based and whole-genome shotgun (WGS) metagenomic studies. Identified taxa and their gene carriage patterns were compared to other human body site niches, including the oral, skin, airway (nasal), vaginal, and gut microbiomes from nonpregnant controls. We characterized a unique placental microbiome niche, composed of nonpathogenic commensal microbiota from the Firmicutes, Tenericutes, Proteobacteria, Bacteroidetes, and Fusobacteria phyla. In aggregate, the placental microbiome profiles were most akin (Bray-Curtis dissimilarity <0.3) to the human oral microbiome. 16S-based operational taxonomic unit analyses revealed associations of the placental microbiome with a remote history of antenatal infection (permutational multivariate analysis of variance, P = 0.006), such as urinary tract infection in the first trimester, as well as with preterm birth <37 weeks (P = 0.001).}, } @article {pmid24846382, year = {2014}, author = {Ly, M and Abeles, SR and Boehm, TK and Robles-Sikisaka, R and Naidu, M and Santiago-Rodriguez, T and Pride, DT}, title = {Altered oral viral ecology in association with periodontal disease.}, journal = {mBio}, volume = {5}, number = {3}, pages = {e01133-14}, pmid = {24846382}, issn = {2150-7511}, support = {K08 AI085028/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; 1K08AI085028/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Aged ; Bacteria/classification/genetics ; Biodiversity ; Biofilms ; Comorbidity ; Female ; Humans ; Male ; Metagenome ; Middle Aged ; Mouth/microbiology/*virology ; Periodontal Diseases/diagnosis/*virology ; RNA, Ribosomal, 16S ; RNA, Viral ; Risk Factors ; Saliva/virology ; Viruses/classification/genetics/isolation & purification ; }, abstract = {UNLABELLED: The human oral cavity is home to a large and diverse community of viruses that have yet to be characterized in patients with periodontal disease. We recruited and sampled saliva and oral biofilm from a cohort of humans either periodontally healthy or with mild or significant periodontal disease to discern whether there are differences in viral communities that reflect their oral health status. We found communities of viruses inhabiting saliva and the subgingival and supragingival biofilms of each subject that were composed largely of bacteriophage. While there were homologous viruses common to different subjects and biogeographic sites, for most of the subjects, virome compositions were significantly associated with the oral sites from which they were derived. The largest distinctions between virome compositions were found when comparing the subgingival and supragingival biofilms to those of planktonic saliva. Differences in virome composition were significantly associated with oral health status for both subgingival and supragingival biofilm viruses but not for salivary viruses. Among the differences identified in virome compositions was a significant expansion of myoviruses in subgingival biofilm, suggesting that periodontal disease favors lytic phage. We also characterized the bacterial communities in each subject at each biogeographic site by using the V3 hypervariable segment of the 16S rRNA and did not identify distinctions between oral health and disease similar to those found in viral communities. The significantly altered ecology of viruses of oral biofilm in subjects with periodontal disease compared to that of relatively periodontally healthy ones suggests that viruses may serve as useful indicators of oral health status.

IMPORTANCE: Little is known about the role or the constituents of viruses as members of the human microbiome. We investigated the composition of human oral viral communities in a group of relatively periodontally healthy subjects or significant periodontitis to determine whether health status may be associated with differences in viruses. We found that most of the viruses present were predators of bacteria. The viruses inhabiting dental plaque were significantly different on the basis of oral health status, while those present in saliva were not. Dental plaque viruses in periodontitis were predicted to be significantly more likely to kill their bacterial hosts than those found in healthy mouths. Because oral diseases such as periodontitis have been shown to have altered bacterial communities, we believe that viruses and their role as drivers of ecosystem diversity are important contributors to the human oral microbiome in health and disease states.}, } @article {pmid24846174, year = {2014}, author = {Hasan, NA and Young, BA and Minard-Smith, AT and Saeed, K and Li, H and Heizer, EM and McMillan, NJ and Isom, R and Abdullah, AS and Bornman, DM and Faith, SA and Choi, SY and Dickens, ML and Cebula, TA and Colwell, RR}, title = {Microbial community profiling of human saliva using shotgun metagenomic sequencing.}, journal = {PloS one}, volume = {9}, number = {5}, pages = {e97699}, pmid = {24846174}, issn = {1932-6203}, support = {1R01A139129-01//PHS HHS/United States ; 2R01A1039129-11A2//PHS HHS/United States ; }, mesh = {Adult ; Female ; Humans ; Male ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Saliva/*microbiology ; Sequence Analysis, DNA/*methods ; }, abstract = {Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify bacterial species using unassembled short NGS reads was used to identify the bacterial species comprising the microbiomes of the saliva samples and datasets. Results, achieved within minutes and at greater than 90% accuracy, showed more than 175 bacterial species comprised the bacterial flora of human saliva, including bacteria known to be commensal human flora but also Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn) analysis in parallel, reported ca. five times more species than those actually comprising the in silico sample. Both GENIUS and BLAST analyses of saliva samples identified major genera comprising the bacterial flora of saliva, but GENIUS provided a more precise description of species composition, identifying to strain in most cases and delivered results at least 10,000 times faster. Therefore, GENIUS offers a facile and accurate system for identification and quantification of bacterial species and/or strains in metagenomic samples.}, } @article {pmid24845653, year = {2014}, author = {Seth, S and Välimäki, N and Kaski, S and Honkela, A}, title = {Exploration and retrieval of whole-metagenome sequencing samples.}, journal = {Bioinformatics (Oxford, England)}, volume = {30}, number = {17}, pages = {2471-2479}, pmid = {24845653}, issn = {1367-4811}, mesh = {Algorithms ; Data Mining ; Diabetes Mellitus, Type 2/microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Inflammatory Bowel Diseases/microbiology ; Metagenomics/*methods ; Microbiota ; Sequence Analysis, DNA ; }, abstract = {MOTIVATION: Over the recent years, the field of whole-metagenome shotgun sequencing has witnessed significant growth owing to the high-throughput sequencing technologies that allow sequencing genomic samples cheaper, faster and with better coverage than before. This technical advancement has initiated the trend of sequencing multiple samples in different conditions or environments to explore the similarities and dissimilarities of the microbial communities. Examples include the human microbiome project and various studies of the human intestinal tract. With the availability of ever larger databases of such measurements, finding samples similar to a given query sample is becoming a central operation.

RESULTS: In this article, we develop a content-based exploration and retrieval method for whole-metagenome sequencing samples. We apply a distributed string mining framework to efficiently extract all informative sequence k-mers from a pool of metagenomic samples and use them to measure the dissimilarity between two samples. We evaluate the performance of the proposed approach on two human gut metagenome datasets as well as human microbiome project metagenomic samples. We observe significant enrichment for diseased gut samples in results of queries with another diseased sample and high accuracy in discriminating between different body sites even though the method is unsupervised.

A software implementation of the DSM framework is available at https://github.com/HIITMetagenomics/dsm-framework.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid24843156, year = {2014}, author = {Franzosa, EA and Morgan, XC and Segata, N and Waldron, L and Reyes, J and Earl, AM and Giannoukos, G and Boylan, MR and Ciulla, D and Gevers, D and Izard, J and Garrett, WS and Chan, AT and Huttenhower, C}, title = {Relating the metatranscriptome and metagenome of the human gut.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {22}, pages = {E2329-38}, pmid = {24843156}, issn = {1091-6490}, support = {R01 CA166150/CA/NCI NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 CA137178/CA/NCI NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 HG005969/HG/NHGRI NIH HHS/United States ; CA166150/CA/NCI NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; HHSN272200900018C/AI/NIAID NIH HHS/United States ; P50 CA127003/CA/NCI NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; }, mesh = {DNA, Bacterial/analysis ; Feces/microbiology ; Gastrointestinal Tract/*microbiology/physiology ; Gene Expression Regulation, Bacterial ; Genomics/*methods ; Humans ; Metagenome/*genetics ; Microbiota/*genetics ; Mouth/microbiology ; RNA, Bacterial/analysis ; Saliva/microbiology ; Specimen Handling/methods ; Transcriptome/*genetics ; }, abstract = {Although the composition of the human microbiome is now well-studied, the microbiota's >8 million genes and their regulation remain largely uncharacterized. This knowledge gap is in part because of the difficulty of acquiring large numbers of samples amenable to functional studies of the microbiota. We conducted what is, to our knowledge, one of the first human microbiome studies in a well-phenotyped prospective cohort incorporating taxonomic, metagenomic, and metatranscriptomic profiling at multiple body sites using self-collected samples. Stool and saliva were provided by eight healthy subjects, with the former preserved by three different methods (freezing, ethanol, and RNAlater) to validate self-collection. Within-subject microbial species, gene, and transcript abundances were highly concordant across sampling methods, with only a small fraction of transcripts (<5%) displaying between-method variation. Next, we investigated relationships between the oral and gut microbial communities, identifying a subset of abundant oral microbes that routinely survive transit to the gut, but with minimal transcriptional activity there. Finally, systematic comparison of the gut metagenome and metatranscriptome revealed that a substantial fraction (41%) of microbial transcripts were not differentially regulated relative to their genomic abundances. Of the remainder, consistently underexpressed pathways included sporulation and amino acid biosynthesis, whereas up-regulated pathways included ribosome biogenesis and methanogenesis. Across subjects, metatranscriptional profiles were significantly more individualized than DNA-level functional profiles, but less variable than microbial composition, indicative of subject-specific whole-community regulation. The results thus detail relationships between community genomic potential and gene expression in the gut, and establish the feasibility of metatranscriptomic investigations in subject-collected and shipped samples.}, } @article {pmid24841417, year = {2014}, author = {Gibbons, SM and Jones, E and Bearquiver, A and Blackwolf, F and Roundstone, W and Scott, N and Hooker, J and Madsen, R and Coleman, ML and Gilbert, JA}, title = {Human and environmental impacts on river sediment microbial communities.}, journal = {PloS one}, volume = {9}, number = {5}, pages = {e97435}, pmid = {24841417}, issn = {1932-6203}, support = {T32 EB009412/EB/NIBIB NIH HHS/United States ; }, mesh = {Biodiversity ; Geologic Sediments/*microbiology ; Humans ; RNA, Ribosomal, 16S/genetics ; Rivers ; }, abstract = {Sediment microbial communities are responsible for a majority of the metabolic activity in river and stream ecosystems. Understanding the dynamics in community structure and function across freshwater environments will help us to predict how these ecosystems will change in response to human land-use practices. Here we present a spatiotemporal study of sediments in the Tongue River (Montana, USA), comprising six sites along 134 km of river sampled in both spring and fall for two years. Sequencing of 16S rRNA amplicons and shotgun metagenomes revealed that these sediments are the richest (∼ 65,000 microbial 'species' identified) and most novel (93% of OTUs do not match known microbial diversity) ecosystems analyzed by the Earth Microbiome Project to date, and display more functional diversity than was detected in a recent review of global soil metagenomes. Community structure and functional potential have been significantly altered by anthropogenic drivers, including increased pathogenicity and antibiotic metabolism markers near towns and metabolic signatures of coal and coalbed methane extraction byproducts. The core (OTUs shared across all samples) and the overall microbial community exhibited highly similar structure, and phylogeny was weakly coupled with functional potential. Together, these results suggest that microbial community structure is shaped by environmental drivers and niche filtering, though stochastic assembly processes likely play a role as well. These results indicate that sediment microbial communities are highly complex and sensitive to changes in land use practices.}, } @article {pmid24841227, year = {2014}, author = {Bedaiwi, MK and Inman, RD}, title = {Microbiome and probiotics: link to arthritis.}, journal = {Current opinion in rheumatology}, volume = {26}, number = {4}, pages = {410-415}, doi = {10.1097/BOR.0000000000000075}, pmid = {24841227}, issn = {1531-6963}, mesh = {Arthritis, Rheumatoid/drug therapy/*microbiology ; Humans ; Metagenome ; *Microbiota ; Probiotics/*therapeutic use ; Spondylitis, Ankylosing/drug therapy/*microbiology ; }, abstract = {PURPOSE OF REVIEW: The gut microbiome plays an integral role in the development and maintenance of the host immune system. Expanding knowledge about this microbial microenvironment has raised the possibility of new treatments based on this knowledge. In this review, we describe the recent evidence of the impact of the gut microbiome on arthritis and possible novel therapeutic approaches to alter the gut flora.

RECENT FINDINGS: Recent studies support the growing evidence of microbiome as a causative agent underlying certain rheumatic diseases like ankylosing spondylitis and rheumatoid arthritis. There is intriguing yet still inconclusive evidence to support the use of probiotics as a treatment for these diseases.

SUMMARY: There is recently a new level of understanding how the microbiome interacts with the immune system. Gene-environment interaction is another important element that sets the stage for initiation of autoimmune disease, which calls for further investigation. Probiotics could be an appealing therapeutic strategy, but further interventional studies exploring the dynamic interaction of microbiome and probiotics are still needed.}, } @article {pmid24838875, year = {2014}, author = {Yaung, SJ and Church, GM and Wang, HH}, title = {Recent progress in engineering human-associated microbiomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1151}, number = {}, pages = {3-25}, doi = {10.1007/978-1-4939-0554-6_1}, pmid = {24838875}, issn = {1940-6029}, support = {1DP5OD009172-01/OD/NIH HHS/United States ; }, mesh = {Animals ; Genetic Engineering/*methods ; Host-Pathogen Interactions ; Humans ; Metagenomics/methods ; *Microbiota ; Models, Animal ; Synthetic Biology/methods ; }, abstract = {Recent progress in molecular biology and genetics opens up the possibility of engineering a variety of biological systems, from single-cellular to multicellular organisms. The consortia of microbes that reside on the human body, the human-associated microbiota, are particularly interesting as targets for forward engineering and manipulation due to their relevance in health and disease. New technologies in analysis and perturbation of the human microbiota will lead to better diagnostic and therapeutic strategies against diseases of microbial origin or pathogenesis. Here, we discuss recent advances that are bringing us closer to realizing the true potential of an engineered human-associated microbial community.}, } @article {pmid24838250, year = {2014}, author = {Joshi, MN and Dhebar, SV and Dhebar, SV and Bhargava, P and Pandit, A and Patel, RP and Saxena, A and Bagatharia, SB}, title = {Metagenomics of petroleum muck: revealing microbial diversity and depicting microbial syntrophy.}, journal = {Archives of microbiology}, volume = {196}, number = {8}, pages = {531-544}, doi = {10.1007/s00203-014-0992-0}, pmid = {24838250}, issn = {1432-072X}, mesh = {Biodiversity ; Gammaproteobacteria/*genetics/isolation & purification ; Genes, Bacterial ; Hydrocarbons/metabolism ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Metagenomics ; Microbial Interactions ; Microbial Viability ; Petroleum/*microbiology ; Pseudomonas stutzeri/*genetics/isolation & purification ; Sequence Analysis, DNA ; }, abstract = {Present study attempts in revealing taxonomic and functional diversity of microorganism from petroleum muck using metagenomics approach. Using Ion Torrent Personal Genome Machine, total of 249 Mb raw data were obtained which was analysed using MG-RAST platform. The taxonomic analysis revealed predominance of Proteobacteria with Gammaproteobacteria as major class and Pseudomonas stutzeri as most abundant organism. Several enzymes involved in aliphatic and aromatic hydrocarbon degradation through both aerobic and anaerobic routes and proteins related to stress response were also present. Comparison of our metagenome with the existing metagenomes from oil-contaminated sites and wastewater treatment plant indicated uniqueness of this metagenome taxonomically and functionally. Based on these results a hypothetical community model showing survival and syntrophy of microorganisms in hydrocarbon-rich environment is proposed. Validation of the metagenome data was done in three tiers by validating major OTUs by isolating oil-degrading microbes, confirmation of key genes responsible for hydrocarbon degradation by Sanger sequencing and studying functional dynamics for degradation of the hydrocarbons by the muck meta-community using GC-MS.}, } @article {pmid24837716, year = {2014}, author = {Laurence, M and Hatzis, C and Brash, DE}, title = {Common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes.}, journal = {PloS one}, volume = {9}, number = {5}, pages = {e97876}, pmid = {24837716}, issn = {1932-6203}, support = {P50 CA121974/CA/NCI NIH HHS/United States ; 5P50CA121974/CA/NCI NIH HHS/United States ; }, mesh = {Base Sequence ; Bradyrhizobium/genetics/isolation & purification ; *DNA Contamination ; DNA, Bacterial/*chemistry/isolation & purification ; High-Throughput Nucleotide Sequencing/*methods/standards ; Microbiota ; Molecular Sequence Data ; Sequence Alignment ; Sequence Analysis, DNA/*methods/standards ; }, abstract = {Unbiased high-throughput sequencing of whole metagenome shotgun DNA libraries is a promising new approach to identifying microbes in clinical specimens, which, unlike other techniques, is not limited to known sequences. Unlike most sequencing applications, it is highly sensitive to laboratory contaminants as these will appear to originate from the clinical specimens. To assess the extent and diversity of sequence contaminants, we aligned 57 "1000 Genomes Project" sequencing runs from six centers against the four largest NCBI BLAST databases, detecting reads of diverse contaminant species in all runs and identifying the most common of these contaminant genera (Bradyrhizobium) in assembled genomes from the NCBI Genome database. Many of these microorganisms have been reported as contaminants of ultrapure water systems. Studies aiming to identify novel microbes in clinical specimens will greatly benefit from not only preventive measures such as extensive UV irradiation of water and cross-validation using independent techniques, but also a concerted effort to sequence the complete genomes of common contaminants so that they may be subtracted computationally.}, } @article {pmid24833634, year = {2014}, author = {Tilg, H and Moschen, AR}, title = {Microbiota and diabetes: an evolving relationship.}, journal = {Gut}, volume = {63}, number = {9}, pages = {1513-1521}, doi = {10.1136/gutjnl-2014-306928}, pmid = {24833634}, issn = {1468-3288}, mesh = {Diabetes Mellitus, Type 2/immunology/metabolism/*microbiology/therapy ; Diet Therapy ; Feces/microbiology ; Humans ; Hypoglycemic Agents/adverse effects ; Immunity, Innate ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Metabolic Syndrome/immunology/metabolism/microbiology/therapy ; Metagenome ; Metformin/adverse effects ; *Microbiota/drug effects/physiology ; Obesity/immunology/metabolism/microbiology/therapy ; }, abstract = {The gut microbiota affects numerous biological functions throughout the body and its characterisation has become a major research area in biomedicine. Recent studies have suggested that gut bacteria play a fundamental role in diseases such as obesity, diabetes and cardiovascular disease. Data are accumulating in animal models and humans suggesting that obesity and type 2 diabetes (T2D) are associated with a profound dysbiosis. First human metagenome-wide association studies demonstrated highly significant correlations of specific intestinal bacteria, certain bacterial genes and respective metabolic pathways with T2D. Importantly, especially butyrate-producing bacteria such as Roseburia intestinalis and Faecalibacterium prausnitzii concentrations were lower in T2D subjects. This supports the increasing evidence, that butyrate and other short-chain fatty acids are able to exert profound immunometabolic effects. Endotoxaemia, most likely gut-derived has also been observed in patients with metabolic syndrome and T2D and might play a key role in metabolic inflammation. A further hint towards an association between microbiota and T2D has been derived from studies in pregnancy showing that major gut microbial shifts occurring during pregnancy affect host metabolism. Interestingly, certain antidiabetic drugs such as metformin also interfere with the intestinal microbiota. Specific members of the microbiota such as Akkermansia muciniphila might be decreased in diabetes and when administered to murines exerted antidiabetic effects. Therefore, as a 'gut signature' becomes more evident in T2D, a better understanding of the role of the microbiota in diabetes might provide new aspects regarding its pathophysiological relevance and pave the way for new therapeutic principles.}, } @article {pmid24831911, year = {2013}, author = {Smith, S}, title = {Intestinal microbiota transplantation: a case of Crohn's colitis with superimposed Clostridium difficile infection.}, journal = {The West Indian medical journal}, volume = {62}, number = {7}, pages = {675-677}, doi = {10.7727/wimj.2012.231}, pmid = {24831911}, issn = {0043-3144}, mesh = {Addison Disease/complications ; Adult ; Anti-Infective Agents/therapeutic use ; Clostridioides difficile/pathogenicity ; Crohn Disease/*complications/immunology/therapy ; Enterocolitis, Pseudomembranous/complications/immunology/*therapy ; Fatal Outcome ; Feces/*microbiology ; Female ; Humans ; Intestines/*microbiology ; Metagenome ; Metronidazole/therapeutic use ; Microbiota ; Superinfection ; Vancomycin/therapeutic use ; }, } @article {pmid24831027, year = {2014}, author = {Campanaro, S and Treu, L and Vendramin, V and Bovo, B and Giacomini, A and Corich, V}, title = {Metagenomic analysis of the microbial community in fermented grape marc reveals that Lactobacillus fabifermentans is one of the dominant species: insights into its genome structure.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {13}, pages = {6015-6037}, doi = {10.1007/s00253-014-5795-3}, pmid = {24831027}, issn = {1432-0614}, mesh = {Alcoholic Beverages/*microbiology ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genome, Bacterial ; Lactobacillus/*genetics/isolation & purification ; Metagenomics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vitis/microbiology ; }, abstract = {Grape marc used for the production of distilled beverages undergoes prolonged storage which allows alcoholic fermentation to occur. Harsh conditions including low pH, limited oxygen and nutrients, temperature fluctuations, and high ethanol concentrations imposed by that environment create a strong selective pressure on microorganisms. A detailed characterization of the bacterial community during two time points of the fermentation process was performed using high-throughput sequencing of the V3-V6 16S rDNA hypervariable regions. The results revealed a marked reduction in the number of bacterial species after 30 days of incubation and made it possible to identify those species that are able to grow in that extreme environment. The genome sequence of Lactobacillus fabifermentans, one of the dominant species identified, was then analyzed using shotgun sequencing and comparative genomics. The results revealed that it is one of the largest genomes among the Lactobacillus sequenced and is characterized by a large number of genes involved in carbohydrate utilization and in the regulation of gene expression. The genome was shaped through a large number of gene duplication events, while lateral gene transfer contributed to a lesser extent with respect to other Lactobacillus species. According to genomic analysis, its carbohydrate utilization pattern and ability to form biofilm are the main genetic traits linked to the adaptation the species underwent permitting it to grow in fermenting grape marc.}, } @article {pmid24829242, year = {2014}, author = {Be, NA and Allen, JE and Brown, TS and Gardner, SN and McLoughlin, KS and Forsberg, JA and Kirkup, BC and Chromy, BA and Luciw, PA and Elster, EA and Jaing, CJ}, title = {Microbial profiling of combat wound infection through detection microarray and next-generation sequencing.}, journal = {Journal of clinical microbiology}, volume = {52}, number = {7}, pages = {2583-2594}, pmid = {24829242}, issn = {1098-660X}, mesh = {Adult ; Bacteria/*classification/genetics/*isolation & purification ; Bacterial Load ; *Biota ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Microarray Analysis/*methods ; Military Personnel ; Wound Healing ; Wound Infection/*microbiology ; Young Adult ; }, abstract = {Combat wound healing and resolution are highly affected by the resident microbial flora. We therefore sought to achieve comprehensive detection of microbial populations in wounds using novel genomic technologies and bioinformatics analyses. We employed a microarray capable of detecting all sequenced pathogens for interrogation of 124 wound samples from extremity injuries in combat-injured U.S. service members. A subset of samples was also processed via next-generation sequencing and metagenomic analysis. Array analysis detected microbial targets in 51% of all wound samples, with Acinetobacter baumannii being the most frequently detected species. Multiple Pseudomonas species were also detected in tissue biopsy specimens. Detection of the Acinetobacter plasmid pRAY correlated significantly with wound failure, while detection of enteric-associated bacteria was associated significantly with successful healing. Whole-genome sequencing revealed broad microbial biodiversity between samples. The total wound bioburden did not associate significantly with wound outcome, although temporal shifts were observed over the course of treatment. Given that standard microbiological methods do not detect the full range of microbes in each wound, these data emphasize the importance of supplementation with molecular techniques for thorough characterization of wound-associated microbes. Future application of genomic protocols for assessing microbial content could allow application of specialized care through early and rapid identification and management of critical patterns in wound bioburden.}, } @article {pmid24827833, year = {2014}, author = {Kraal, L and Abubucker, S and Kota, K and Fischbach, MA and Mitreva, M}, title = {The prevalence of species and strains in the human microbiome: a resource for experimental efforts.}, journal = {PloS one}, volume = {9}, number = {5}, pages = {e97279}, pmid = {24827833}, issn = {1932-6203}, support = {DP2 OD007290/OD/NIH HHS/United States ; T32 GM067547/GM/NIGMS NIH HHS/United States ; P50 GM081879/GM/NIGMS NIH HHS/United States ; T32 EB009383/EB/NIBIB NIH HHS/United States ; U54 HG004968/HG/NHGRI NIH HHS/United States ; U54 HG003079/HG/NHGRI NIH HHS/United States ; U54HG004968/HG/NHGRI NIH HHS/United States ; }, mesh = {Genome, Bacterial/*genetics ; Humans ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/*genetics ; Phylogeny ; Prevalence ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Experimental efforts to characterize the human microbiota often use bacterial strains that were chosen for historical rather than biological reasons. Here, we report an analysis of 380 whole-genome shotgun samples from 100 subjects from the NIH Human Microbiome Project. By mapping their reads to 1,751 reference genome sequences and analyzing the resulting relative strain abundance in each sample we present metrics and visualizations that can help identify strains of interest for experimentalists. We also show that approximately 14 strains of 10 species account for 80% of the mapped reads from a typical stool sample, indicating that the function of a community may not be irreducibly complex. Some of these strains account for >20% of the sequence reads in a subset of samples but are absent in others, a dichotomy that could underlie biological differences among subjects. These data should serve as an important strain selection resource for the community of researchers who take experimental approaches to studying the human microbiota.}, } @article {pmid24824669, year = {2014}, author = {Rodriguez-R, LM and Konstantinidis, KT}, title = {Estimating coverage in metagenomic data sets and why it matters.}, journal = {The ISME journal}, volume = {8}, number = {11}, pages = {2349-2351}, pmid = {24824669}, issn = {1751-7370}, mesh = {Data Interpretation, Statistical ; Humans ; Metagenomics/*methods ; Microbiota ; }, } @article {pmid24824449, year = {2014}, author = {O'Connor, EM and O'Herlihy, EA and O'Toole, PW}, title = {Gut microbiota in older subjects: variation, health consequences and dietary intervention prospects.}, journal = {The Proceedings of the Nutrition Society}, volume = {73}, number = {4}, pages = {441-451}, doi = {10.1017/S0029665114000597}, pmid = {24824449}, issn = {1475-2719}, mesh = {Adipogenesis/physiology ; Aged ; Diabetes Mellitus/microbiology ; Diet ; Dietary Supplements ; Gastrointestinal Diseases/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Lipid Metabolism/physiology ; *Microbiota ; Obesity/microbiology ; Prebiotics ; }, abstract = {Alterations in intestinal microbiota composition and function have been linked to conditions including functional gastrointestinal disorders, obesity and diabetes. The gut microbiome encodes metabolic capability in excess of that encoded by the human genome, and bacterially produced enzymes are important for releasing nutrients from complex dietary ingredients. Previous culture-based studies had indicated that the gut microbiota of older people was different from that of younger adults, but the detailed findings were contradictory. Small-scale studies had also shown that the microbiota composition could be altered by dietary intervention or supplementation. We showed that the core microbiota and aggregate composition in 161 seniors was distinct from that of younger persons. To further investigate the reasons for this variation, we analysed the microbiota composition of 178 elderly subjects for whom the dietary intake data were available. The data revealed distinct microbiota composition groups, which overlapped with distinct dietary patterns that were governed by where people lived: at home, in rehabilitation or in long-term residential care. These diet-microbiota separations correlated with cluster analysis of NMR-derived faecal metabolites and shotgun metagenomic data. Major separations in the microbiota correlated with selected clinical measurements. It should thus be possible to programme the microbiota to enrich bacterial species and activities that promote healthier ageing. A number of other studies have investigated the effect of certain dietary components and their ability to modulate the microbiota composition to promote health. This review will discuss dietary interventions conducted thus far, especially those in elderly populations and highlight their impact on the intestinal microbiota.}, } @article {pmid24824442, year = {2014}, author = {Jung, SP and Kang, H}, title = {Assessment of microbial diversity bias associated with soil heterogeneity and sequencing resolution in pyrosequencing analyses.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {52}, number = {7}, pages = {574-580}, pmid = {24824442}, issn = {1976-3794}, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; Metagenomics/*methods ; Nucleic Acid Amplification Techniques/methods ; Oxidoreductases/genetics ; RNA, Ribosomal, 16S/genetics ; *Recombination, Genetic ; Sequence Analysis, DNA/methods ; *Soil Microbiology ; }, abstract = {It is important to estimate the true microbial diversities accurately for a comparative microbial diversity analysis among various ecological settings in ecological models. Despite drastically increasing amounts of 16S rRNA gene targeting pyrosequencing data, sampling and data interpretation for comparative analysis have not yet been standardized. For more accurate bacterial diversity analyses, the influences of soil heterogeneity and sequence resolution on bacterial diversity estimates were investigated using pyrosequencing data of oak and pine forest soils with focus on the bacterial 16SrRNA gene. Soil bacterial community sets were phylogenetically clustered into two separate groups by forest type. Rarefaction curves showed that bacterial communities sequenced from the DNA mixtures and the DNAs of the soil mixtures had midsize richness compared with other samples. Richness and diversity estimates were highly variable depending on the sequence read numbers. Bacterial richness estimates (ACE, Chao 1 and Jack) of the forest soils had positive linear relationships with the sequence read number. Bacterial diversity estimates (NPShannon, Shannon and the inverse Simpson) of the forest soils were also positively correlated with the sequence read number. One-way ANOVA shows that sequence resolution significantly affected the α-diversity indices (P<0.05), but the soil heterogeneity did not (P>0.05). For an unbiased evaluation, richness and diversity estimates should be calculated and compared from subsets of the same size.}, } @article {pmid24821515, year = {2014}, author = {Bohmann, K and Evans, A and Gilbert, MT and Carvalho, GR and Creer, S and Knapp, M and Yu, DW and de Bruyn, M}, title = {Environmental DNA for wildlife biology and biodiversity monitoring.}, journal = {Trends in ecology & evolution}, volume = {29}, number = {6}, pages = {358-367}, doi = {10.1016/j.tree.2014.04.003}, pmid = {24821515}, issn = {1872-8383}, mesh = {Animals ; Animals, Wild/*genetics ; Bacteria/*genetics ; *Biodiversity ; DNA/*analysis ; *Ecosystem ; Environmental Monitoring/methods ; Fungi/*genetics ; Metagenomics/*methods ; Plants/*genetics ; }, abstract = {Extraction and identification of DNA from an environmental sample has proven noteworthy recently in detecting and monitoring not only common species, but also those that are endangered, invasive, or elusive. Particular attributes of so-called environmental DNA (eDNA) analysis render it a potent tool for elucidating mechanistic insights in ecological and evolutionary processes. Foremost among these is an improved ability to explore ecosystem-level processes, the generation of quantitative indices for analyses of species, community diversity, and dynamics, and novel opportunities through the use of time-serial samples and unprecedented sensitivity for detecting rare or difficult-to-sample taxa. Although technical challenges remain, here we examine the current frontiers of eDNA, outline key aspects requiring improvement, and suggest future developments and innovations for research.}, } @article {pmid24820193, year = {2014}, author = {Tian, P and Xu, B and Sun, H and Li, X and Li, Z and Wei, P}, title = {Isolation and gut microbiota modulation of antibiotic-resistant probiotics from human feces.}, journal = {Diagnostic microbiology and infectious disease}, volume = {79}, number = {4}, pages = {405-412}, doi = {10.1016/j.diagmicrobio.2014.04.002}, pmid = {24820193}, issn = {1879-0070}, mesh = {Adult ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics ; Conjugation, Genetic ; Disk Diffusion Antimicrobial Tests ; *Drug Resistance, Bacterial/genetics ; Feces/*microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Infant ; Infant, Newborn ; Metagenome ; Mice ; Microbial Sensitivity Tests ; *Microbiota ; *Probiotics ; RNA, Bacterial ; RNA, Ribosomal, 16S ; }, abstract = {Antibiotic-resistant probiotics may be advantageous for antibiotic-induced gut microbiota imbalance. In this article, we aimed to isolate antibiotic-resistant bacteria as potential probiotics. Feces from 3 healthy adults and 2 infants were used to isolate the antibiotic-resistant bacteria. Then we established gut microbiota imbalance mice model by antibiotics treatment and used it to assess the effect of the probiotics. Finally, we identified 8 isolates, and 6 of them were used as probiotics cocktail. Number of anaerobe, lactobacilli, and Bifidobacterium in feces were higher in the probiotic group (9.47±0.35 log10CFU/g, 8.74±0.18 log10CFU/g, 7.24±0.38 log10CFU/g, respectively) compared with model group (P<0.05). Richness and diversity index of probiotic group (19.79±0.29 and 2.95±0.06, respectively) were larger than model group (P<0.05). Diarrhea and mucosal edema had been alleviated during probiotic treatment. Our results validated that bacteriotherapy was available to treat gut microbiota imbalance.}, } @article {pmid24808136, year = {2014}, author = {Gibson, J and Shokralla, S and Porter, TM and King, I and van Konynenburg, S and Janzen, DH and Hallwachs, W and Hajibabaei, M}, title = {Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {22}, pages = {8007-8012}, pmid = {24808136}, issn = {1091-6490}, mesh = {Animals ; Arthropods/*chemistry ; *Biodiversity ; Costa Rica ; DNA Barcoding, Taxonomic/methods ; Ecological Parameter Monitoring/*methods ; Ecosystem ; Electron Transport Complex IV/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Conventional assessments of ecosystem sample composition are based on morphology-based or DNA barcode identification of individuals. Both approaches are costly and time-consuming, especially when applied to the large number of specimens and taxa commonly included in ecological investigations. Next-generation sequencing approaches can overcome the bottleneck of individual specimen isolation and identification by simultaneously sequencing specimens of all taxa in a bulk mixture. Here we apply multiple parallel amplification primers, multiple DNA barcode markers, 454-pyrosequencing, and Illumina MiSeq sequencing to the same sample to maximize recovery of the arthropod macrobiome and the bacterial and other microbial microbiome of a bulk arthropod sample. We validate this method with a complex sample containing 1,066 morphologically distinguishable arthropods from a tropical terrestrial ecosystem with high taxonomic diversity. Multiamplicon next-generation DNA barcoding was able to recover sequences corresponding to 91% of the distinguishable individuals in a bulk environmental sample, as well as many species present as undistinguishable tissue. 454-pyrosequencing was able to recover 10 more families of arthropods and 30 more species than did conventional Sanger sequencing of each individual specimen. The use of other loci (16S and 18S ribosomal DNA gene regions) also added the detection of species of microbes associated with these terrestrial arthropods. This method greatly decreases the time and money necessary to perform DNA-based comparisons of biodiversity among ecosystem samples. This methodology opens the door to much cheaper and increased capacity for ecological and evolutionary studies applicable to a wide range of socio-economic issues, as well as a basic understanding of how the world works.}, } @article {pmid24803806, year = {2014}, author = {Wang, LL and Yu, XJ and Zhan, SH and Jia, SJ and Tian, ZB and Dong, QJ}, title = {Participation of microbiota in the development of gastric cancer.}, journal = {World journal of gastroenterology}, volume = {20}, number = {17}, pages = {4948-4952}, pmid = {24803806}, issn = {2219-2840}, mesh = {Bacteria/classification/metabolism/*pathogenicity ; *Cell Transformation, Neoplastic/metabolism/pathology ; Gastric Mucosa/metabolism ; Helicobacter pylori/pathogenicity ; Humans ; *Microbiota ; Nitroso Compounds/metabolism ; Prognosis ; Risk Factors ; Stomach/*microbiology/pathology ; Stomach Neoplasms/metabolism/*microbiology/pathology ; }, abstract = {There are a large number of bacteria inhabiting the human body, which provide benefits for the health. Alterations of microbiota participate in the pathogenesis of diseases. The gastric microbiota consists of bacteria from seven to eleven phyla, predominantly Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria. Intrusion by Helicobacter pylori (H. pylori) does not remarkably interrupt the composition and structure of the gastric microbiota. Absence of bacterial commensal from the stomach delays the onset of H. pylori-induced gastric cancer, while presence of artificial microbiota accelerates the carcinogenesis. Altered gastric microbiota may increase the production of N-nitroso compounds, promoting the development of gastric cancer. Further investigation of the carcinogenic mechanisms of microbiota would benefit for the prevention and management of gastric cancer.}, } @article {pmid24803517, year = {2014}, author = {Schubert, AM and Rogers, MA and Ring, C and Mogle, J and Petrosino, JP and Young, VB and Aronoff, DM and Schloss, PD}, title = {Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls.}, journal = {mBio}, volume = {5}, number = {3}, pages = {e01021-14}, pmid = {24803517}, issn = {2150-7511}, support = {U19 AI090871/AI/NIAID NIH HHS/United States ; 1R01GM099514/GM/NIGMS NIH HHS/United States ; R01 HG005975/HG/NHGRI NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; R01HG005975/HG/NHGRI NIH HHS/United States ; U19AI090871/AI/NIAID NIH HHS/United States ; T32 AI007528/AI/NIAID NIH HHS/United States ; P30DK034933/DK/NIDDK NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacterial Infections/diagnosis/drug therapy/*microbiology ; Biodiversity ; Clostridioides difficile/*genetics ; Cluster Analysis ; Diagnosis, Differential ; Diarrhea/diagnosis/drug therapy/*microbiology ; Feces/microbiology ; Female ; Humans ; Male ; Metagenome ; Microbiota/*genetics ; Middle Aged ; RNA, Bacterial ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Antibiotic usage is the most commonly cited risk factor for hospital-acquired Clostridium difficile infections (CDI). The increased risk is due to disruption of the indigenous microbiome and a subsequent decrease in colonization resistance by the perturbed bacterial community; however, the specific changes in the microbiome that lead to increased risk are poorly understood. We developed statistical models that incorporated microbiome data with clinical and demographic data to better understand why individuals develop CDI. The 16S rRNA genes were sequenced from the feces of 338 individuals, including cases, diarrheal controls, and nondiarrheal controls. We modeled CDI and diarrheal status using multiple clinical variables, including age, antibiotic use, antacid use, and other known risk factors using logit regression. This base model was compared to models that incorporated microbiome data, using diversity metrics, community types, or specific bacterial populations, to identify characteristics of the microbiome associated with CDI susceptibility or resistance. The addition of microbiome data significantly improved our ability to distinguish CDI status when comparing cases or diarrheal controls to nondiarrheal controls. However, only when we assigned samples to community types was it possible to differentiate cases from diarrheal controls. Several bacterial species within the Ruminococcaceae, Lachnospiraceae, Bacteroides, and Porphyromonadaceae were largely absent in cases and highly associated with nondiarrheal controls. The improved discriminatory ability of our microbiome-based models confirms the theory that factors affecting the microbiome influence CDI. IMPORTANCE The gut microbiome, composed of the trillions of bacteria residing in the gastrointestinal tract, is responsible for a number of critical functions within the host. These include digestion, immune system stimulation, and colonization resistance. The microbiome's role in colonization resistance, which is the ability to prevent and limit pathogen colonization and growth, is key for protection against Clostridium difficile infections. However, the bacteria that are important for colonization resistance have not yet been elucidated. Using statistical modeling techniques and different representations of the microbiome, we demonstrated that several community types and the loss of several bacterial populations, including Bacteroides, Lachnospiraceae, and Ruminococcaceae, are associated with CDI. Our results emphasize the importance of considering the microbiome in mediating colonization resistance and may also direct the design of future multispecies probiotic therapies.}, } @article {pmid24801164, year = {2015}, author = {Morgante, V and Mirete, S and de Figueras, CG and Postigo Cacho, M and González-Pastor, JE}, title = {Exploring the diversity of arsenic resistance genes from acid mine drainage microorganisms.}, journal = {Environmental microbiology}, volume = {17}, number = {6}, pages = {1910-1925}, doi = {10.1111/1462-2920.12505}, pmid = {24801164}, issn = {1462-2920}, mesh = {Arsenates/metabolism ; Arsenic/*metabolism/pharmacology ; Biodiversity ; Drainage, Sanitary ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/genetics/*metabolism ; Metagenomics ; Molecular Sequence Data ; RNA Processing, Post-Transcriptional/physiology ; Rivers/*microbiology ; }, abstract = {The microbial communities from the Tinto River, a natural acid mine drainage environment, were explored to search for novel genes involved in arsenic resistance using a functional metagenomic approach. Seven pentavalent arsenate resistance clones were selected and analysed to find the genes responsible for this phenotype. Insights about their possible mechanisms of resistance were obtained from sequence similarities and cellular arsenic concentration. A total of 19 individual open reading frames were analysed, and each one was individually cloned and assayed for its ability to confer arsenic resistance in Escherichia coli cells. A total of 13 functionally active genes involved in arsenic resistance were identified, and they could be classified into different global processes: transport, stress response, DNA damage repair, phospholipids biosynthesis, amino acid biosynthesis and RNA-modifying enzymes. Most genes (11) encode proteins not previously related to heavy metal resistance or hypothetical or unknown proteins. On the other hand, two genes were previously related to heavy metal resistance in microorganisms. In addition, the ClpB chaperone and the RNA-modifying enzymes retrieved in this work were shown to increase the cell survival under different stress conditions (heat shock, acid pH and UV radiation). Thus, these results reveal novel insights about unidentified mechanisms of arsenic resistance.}, } @article {pmid24800728, year = {2015}, author = {Xu, X and He, J and Xue, J and Wang, Y and Li, K and Zhang, K and Guo, Q and Liu, X and Zhou, Y and Cheng, L and Li, M and Li, Y and Li, Y and Shi, W and Zhou, X}, title = {Oral cavity contains distinct niches with dynamic microbial communities.}, journal = {Environmental microbiology}, volume = {17}, number = {3}, pages = {699-710}, doi = {10.1111/1462-2920.12502}, pmid = {24800728}, issn = {1462-2920}, mesh = {Actinobacteria/classification/genetics/isolation & purification ; Adolescent ; Adult ; Aged ; Bacterial Typing Techniques ; Bacteroidetes/classification/genetics/isolation & purification ; Base Sequence ; Child ; Child, Preschool ; Dental Plaque/*microbiology ; Female ; Fusobacteria/classification/genetics/isolation & purification ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenome ; Microbiota/*genetics ; Middle Aged ; Mouth/*microbiology ; Phylogeny ; Proteobacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; Sequence Analysis, DNA ; Spirochaetales/classification/genetics/isolation & purification ; Young Adult ; }, abstract = {Microbes colonize human oral surfaces within hours after delivery. During postnatal development, physiological changes, such as the eruption of primary teeth and replacement of the primary dentition with permanent dentition, greatly alter the microbial habitats, which, in return, may lead to community composition shifts at different phases in people's lives. By profiling saliva, supragingival and mucosal plaque samples from healthy volunteers at different ages and dentition stages, we observed that the oral cavity is a highly heterogeneous ecological system containing distinct niches with significantly different microbial communities. More importantly, the phylogenetic microbial structure varies with ageing. In addition, only a few taxa were present across the whole populations, indicating a core oral microbiome should be defined based on age and oral niches.}, } @article {pmid24797613, year = {2014}, author = {Patel, DD and Patel, AK and Parmar, NR and Shah, TM and Patel, JB and Pandya, PR and Joshi, CG}, title = {Microbial and Carbohydrate Active Enzyme profile of buffalo rumen metagenome and their alteration in response to variation in the diet.}, journal = {Gene}, volume = {545}, number = {1}, pages = {88-94}, doi = {10.1016/j.gene.2014.05.003}, pmid = {24797613}, issn = {1879-0038}, mesh = {*Animal Feed ; Animals ; Bacteroidetes/enzymology/genetics ; Buffaloes/*genetics/*microbiology ; Carbohydrate Metabolism ; Diet ; *Metagenome ; Microbiota ; Phylogeny ; Rumen/*enzymology/*microbiology ; }, abstract = {Rumen microbiome represents rich source of enzymes degrading complex plant polysaccharides. We describe here analysis of Carbohydrate Active Enzymes (CAZymes) from 3.5 gigabase sequences of metagenomic data from rumen samples of Mehsani buffaloes fed on different proportions of green or dry roughages to concentrate ration. A total of 2597 contigs encoding putative CAZymes were identified by CAZyme Analysis Toolkit (CAT). The phylogenetic analysis of these contigs by MG-RAST revealed predominance of Bacteroidetes, followed by Firmicutes, Proteobacteria, and Actinobacteria phyla. Moreover, a higher abundance of oligosaccharide degrading and debranching enzymes in buffalo rumen metagenome and that of cellulases and hemicellulases in termite hindgut was observed when we compared glycoside hydrolase (GH) profile of buffalo rumen metagenome with cow rumen, termite hindgut and chicken caecum metagenome. Further, comparison of microbial profile of green or dry roughage fed animals showed significantly higher abundance (p-value<0.05) of various polysaccharide degrading bacterial genera like Fibrobacter, Prevotella, Bacteroides, Clostridium and Ruminococcus in green roughage fed animals. In addition, we found a significantly higher abundance (p-value<0.05) of enzymes associated with pectin digestion such as pectin lyase (PL) 1, PL10 and GH28 in green roughage fed animals. Our study outlines CAZyme profile of buffalo rumen metagenome and provides a scope to study the role of abundant enzyme families (oligosaccharide degrading and debranching enzymes) in digestion of coarse feed.}, } @article {pmid24797416, year = {2014}, author = {Arimatsu, K and Yamada, H and Miyazawa, H and Minagawa, T and Nakajima, M and Ryder, MI and Gotoh, K and Motooka, D and Nakamura, S and Iida, T and Yamazaki, K}, title = {Oral pathobiont induces systemic inflammation and metabolic changes associated with alteration of gut microbiota.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {4828}, pmid = {24797416}, issn = {2045-2322}, mesh = {Animals ; Cytokines/metabolism ; Dental Plaque/microbiology ; Diabetes Mellitus, Type 2/metabolism/microbiology/pathology ; Disease Models, Animal ; Endotoxemia/metabolism/microbiology/pathology ; Gingiva/metabolism/microbiology/pathology ; Glucose Intolerance/metabolism/microbiology/pathology ; Ileum/*metabolism/*microbiology/pathology ; Inflammation/*metabolism/*microbiology/pathology ; Insulin/metabolism ; Insulin Resistance/physiology ; Male ; Metabolic Diseases/*metabolism/*microbiology/pathology ; Mice ; Mice, Inbred C57BL ; Microbiota ; Periodontitis/metabolism/microbiology/pathology ; Porphyromonas gingivalis ; Tight Junction Proteins/metabolism ; }, abstract = {Periodontitis has been implicated as a risk factor for metabolic disorders such as type 2 diabetes, atherosclerotic vascular diseases, and non-alcoholic fatty liver disease. Although bacteremias from dental plaque and/or elevated circulating inflammatory cytokines emanating from the inflamed gingiva are suspected mechanisms linking periodontitis and these diseases, direct evidence is lacking. We hypothesize that disturbances of the gut microbiota by swallowed bacteria induce a metabolic endotoxemia leading metabolic disorders. To investigate this hypothesis, changes in the gut microbiota, insulin and glucose intolerance, and levels of tissue inflammation were analysed in mice after oral administration of Porphyromonas gingivalis, a representative periodontopathogens. Pyrosequencing revealed that the population belonging to Bacteroidales was significantly elevated in P. gingivalis-administered mice which coincided with increases in insulin resistance and systemic inflammation. In P. gingivalis-administered mice blood endotoxin levels tended to be higher, whereas gene expression of tight junction proteins in the ileum was significantly decreased. These results provide a new paradigm for the interrelationship between periodontitis and systemic diseases.}, } @article {pmid24795737, year = {2014}, author = {Stobbe, AH and Roossinck, MJ}, title = {Plant virus metagenomics: what we know and why we need to know more.}, journal = {Frontiers in plant science}, volume = {5}, number = {}, pages = {150}, pmid = {24795737}, issn = {1664-462X}, } @article {pmid24793619, year = {2014}, author = {Prince, AL and Antony, KM and Chu, DM and Aagaard, KM}, title = {The microbiome, parturition, and timing of birth: more questions than answers.}, journal = {Journal of reproductive immunology}, volume = {104-105}, number = {}, pages = {12-19}, pmid = {24793619}, issn = {1872-7603}, support = {DP2 OD001500/OD/NIH HHS/United States ; R01 NR014792/NR/NINR NIH HHS/United States ; }, mesh = {Animals ; Female ; Humans ; Microbiota/*immunology ; Parturition/*immunology ; Pregnancy ; *Pregnancy Complications, Infectious/immunology/microbiology ; *Premature Birth/immunology/microbiology ; Reproductive Tract Infections/*immunology ; }, abstract = {The causes of preterm birth are multifactorial, but its association with infection has been well-established. The predominant paradigm describes an ascending infection from the lower genital tract through the cervix and into the presumably sterile fetal membranes and placenta. Thus, an evaluation of the role of the vaginal microbiome in preterm birth is implicated. However, emerging fields of data described in this review suggest that the placenta might not be sterile, even in the absence of clinical infection. We thus propose an additional mechanism for placental colonization and infection: hematogenous spread. When considered in the context of decades of evidence demonstrating a strong risk of recurrence for preterm birth, studies on parturition are ideal for applying the rapidly expanding field of metagenomics and analytic pipelines. The translational implications toward identification of innovative treatments for the prevention of preterm birth are further discussed. In sum, exciting advances in understanding the role of both host and microbiota in parturition and preterm birth are on the horizon.}, } @article {pmid24785449, year = {2014}, author = {ElRakaiby, M and Dutilh, BE and Rizkallah, MR and Boleij, A and Cole, JN and Aziz, RK}, title = {Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics.}, journal = {Omics : a journal of integrative biology}, volume = {18}, number = {7}, pages = {402-414}, pmid = {24785449}, issn = {1557-8100}, mesh = {Animals ; Anti-Infective Agents/pharmacology/therapeutic use ; Biodiversity ; Genomics ; Humans ; *Metagenome ; Microbiology/trends ; *Microbiota ; *Pharmacogenetics ; *Precision Medicine ; }, abstract = {The Human Microbiome Project (HMP) is a global initiative undertaken to identify and characterize the collection of human-associated microorganisms at multiple anatomic sites (skin, mouth, nose, colon, vagina), and to determine how intra-individual and inter-individual alterations in the microbiome influence human health, immunity, and different disease states. In this review article, we summarize the key findings and applications of the HMP that may impact pharmacology and personalized therapeutics. We propose a microbiome cloud model, reflecting the temporal and spatial uncertainty of defining an individual's microbiome composition, with examples of how intra-individual variations (such as age and mode of delivery) shape the microbiome structure. Additionally, we discuss how this microbiome cloud concept explains the difficulty to define a core human microbiome and to classify individuals according to their biome types. Detailed examples are presented on microbiome changes related to colorectal cancer, antibiotic administration, and pharmacomicrobiomics, or drug-microbiome interactions, highlighting how an improved understanding of the human microbiome, and alterations thereof, may lead to the development of novel therapeutic agents, the modification of antibiotic policies and implementation, and improved health outcomes. Finally, the prospects of a collaborative computational microbiome research initiative in Africa are discussed.}, } @article {pmid24785351, year = {2014}, author = {Lebuhn, M and Hanreich, A and Klocke, M and Schlüter, A and Bauer, C and Pérez, CM}, title = {Towards molecular biomarkers for biogas production from lignocellulose-rich substrates.}, journal = {Anaerobe}, volume = {29}, number = {}, pages = {10-21}, doi = {10.1016/j.anaerobe.2014.04.006}, pmid = {24785351}, issn = {1095-8274}, mesh = {Archaea/classification/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Biofuels ; Biomarkers/metabolism ; Bioreactors ; Crops, Agricultural ; Genetic Variation ; Hydrogen-Ion Concentration ; Hydrolysis ; Lignin/*metabolism ; Metagenome ; Methane/*biosynthesis ; Microbial Consortia/*genetics ; Phylogeny ; Pressure ; RNA, Ribosomal, 16S/*genetics ; Real-Time Polymerase Chain Reaction ; Temperature ; Waste Products ; }, abstract = {Biogas production from lignocellulose-rich agricultural residues is gaining increasingly importance in sustainable energy production. Hydrolysis/acidogenesis (H/A) of lignocellulose as the initial rate-limiting step deserves particular optimization. A mixture of straw/hay was methanized applying two-phase digester systems with an initial H/A reactor and a one-stage system at different, meso- and thermophilic temperatures. H/A was intensified with increasing pH values and increasing temperature. H/A fermenters, however, were prone to switch to methanogenic systems at these conditions. Substrate turnover was accelerated in the bi-phasic process but did not reach the methanation efficiency of the single-stage digestion. There was no indication that two different cellulolytic inocula could establish in the given process. Bacterial communities were analyzed applying conventional amplicon clone sequencing targeting the hypervariable 16S rRNA gene region V6-V8 and by metagenome analyses applying direct DNA pyrosequencing without a PCR step. Corresponding results suggested that PCR did not introduce a bias but offered better phylogenetic resolution. Certain Clostridium IV and Prevotella members were most abundant in the H/A system operated at 38 °C, certain Clostridium III and Lachnospiraceae bacteria in the 45 °C, and certain Clostridium IV and Thermohydrogenium/Thermoanaerobacterium members in the 55 °C H/A system. Clostridium III representatives, Lachnospiraceae and Thermotogae dominated in the thermophilic single-stage system, in which also a higher portion of known syntrophic acetate oxidizers was found. Specific (RT-)qPCR systems were designed and applied for the most significant and abundant populations to assess their activity in the different digestion systems. The RT-qPCR results agreed with the DNA based community profiles obtained at the different temperatures. Up to 10(12) 16S rRNA copies mL(-1) were determined in H/A fermenters with prevalence of rRNA of a Ruminococcaceae subgroup. Besides, Thermohydrogenium/Thermoanaerobacterium rRNA prevailed at thermophilic and Prevotellaceae rRNA at mesophilic conditions. The developed (RT)-qPCR systems can be used as biomarkers to optimize biogas production from straw/hay and possibly other lignocellulosic substrates.}, } @article {pmid24781901, year = {2014}, author = {Tong, M and McHardy, I and Ruegger, P and Goudarzi, M and Kashyap, PC and Haritunians, T and Li, X and Graeber, TG and Schwager, E and Huttenhower, C and Fornace, AJ and Sonnenburg, JL and McGovern, DP and Borneman, J and Braun, J}, title = {Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism.}, journal = {The ISME journal}, volume = {8}, number = {11}, pages = {2193-2206}, pmid = {24781901}, issn = {1751-7370}, support = {UL1 RR033176/RR/NCRR NIH HHS/United States ; U01 DK062413/DK/NIDDK NIH HHS/United States ; P30-CA051008/CA/NCI NIH HHS/United States ; UL1 TR000124/TR/NCATS NIH HHS/United States ; T32 GM074897/GM/NIGMS NIH HHS/United States ; P30 CA051008/CA/NCI NIH HHS/United States ; R01 DK085691/DK/NIDDK NIH HHS/United States ; R01 AI078885/AI/NIAID NIH HHS/United States ; P01 DK046763/DK/NIDDK NIH HHS/United States ; DK046763/DK/NIDDK NIH HHS/United States ; AI078885/AI/NIAID NIH HHS/United States ; UL1TR000124/TR/NCATS NIH HHS/United States ; R35 CA197449/CA/NCI NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; P30 CA016042/CA/NCI NIH HHS/United States ; DK062413/DK/NIDDK NIH HHS/United States ; DK08569/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Aged ; Animals ; Bacteria/metabolism ; Crohn Disease/*genetics ; Energy Metabolism/genetics ; Female ; Fucosyltransferases/*genetics ; Humans ; Intestinal Mucosa/*microbiology ; Male ; Metabolome ; Metagenome ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; *Microbiota ; Middle Aged ; *Polymorphism, Genetic ; Proteome/metabolism ; Risk Factors ; Galactoside 2-alpha-L-fucosyltransferase ; }, abstract = {Fucosyltransferase 2 (FUT2) is an enzyme that is responsible for the synthesis of the H antigen in body fluids and on the intestinal mucosa. The H antigen is an oligosaccharide moiety that acts as both an attachment site and carbon source for intestinal bacteria. Non-secretors, who are homozygous for the loss-of-function alleles of FUT2 gene (sese), have increased susceptibility to Crohn's disease (CD). To characterize the effect of FUT2 polymorphism on the mucosal ecosystem, we profiled the microbiome, meta-proteome and meta-metabolome of 75 endoscopic lavage samples from the cecum and sigmoid of 39 healthy subjects (12 SeSe, 18 Sese and 9 sese). Imputed metagenomic analysis revealed perturbations of energy metabolism in the microbiome of non-secretor and heterozygote individuals, notably the enrichment of carbohydrate and lipid metabolism, cofactor and vitamin metabolism and glycan biosynthesis and metabolism-related pathways, and the depletion of amino-acid biosynthesis and metabolism. Similar changes were observed in mice bearing the FUT2(-/-) genotype. Metabolomic analysis of human specimens revealed concordant as well as novel changes in the levels of several metabolites. Human metaproteomic analysis indicated that these functional changes were accompanied by sub-clinical levels of inflammation in the local intestinal mucosa. Therefore, the colonic microbiota of non-secretors is altered at both the compositional and functional levels, affecting the host mucosal state and potentially explaining the association of FUT2 genotype and CD susceptibility.}, } @article {pmid24769905, year = {2014}, author = {Mao, Y and Xia, Y and Wang, Z and Zhang, T}, title = {Reconstructing a Thauera genome from a hydrogenotrophic-denitrifying consortium using metagenomic sequence data.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {15}, pages = {6885-6895}, doi = {10.1007/s00253-014-5756-x}, pmid = {24769905}, issn = {1432-0614}, mesh = {Bacterial Proteins/genetics/metabolism ; Bioreactors/microbiology ; Denitrification ; *Genome, Bacterial ; Hydrogen/*metabolism ; Hydrogenase/genetics/metabolism ; Metagenomics ; *Microbial Consortia ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Thauera/classification/*genetics/isolation & purification/metabolism ; }, abstract = {Here, shotgun metagenomic sequencing was conducted to reveal the hydrogen-oxidizing autotrophic-denitrifying metabolism in an enriched Thauera-dominated consortium. A draft genome named Thauera R4 of over 90 % completeness (3.8 Mb) was retrieved mainly by a coverage-defined binning method from 3.5 Gb paired-end Illumina reads. We identified 1,263 genes (accounting for 33 % of total genes in the finished genome of Thauera aminoaromatica MZ1T) with average nucleotide identity of 87.6 % shared between Thauera R4 and T. aminoaromatica MZ1T. Although Thauera R4 and T. aminoaromatica shared quite similar nitrogen metabolism and a high nucleotide similarity (98.8 %) in their 16S ribosomal RNA genes, they showed different functional potentials in several important environmentally relevant processes. Unlike T. aminoaromatica MZ1T, Thauera R4 carries an operon of [NiFe]-hydrogenase (EC 1.12.99.6) catalyzing molecular hydrogen oxidation in nitrate-rich solution. Moreover, Thauera R4 is a mixtrophic bacterium possessing key enzymes for autotrophic CO2-fixation and heterotrophic acetate assimilation metabolism. This Thauera R4 bin provides another genetic reference to better understand the niches of Thauera and demonstrates a model pipeline to reveal functional profiles and reconstruct novel and dominant genomes from a simplified mixed culture in environmental studies.}, } @article {pmid24767457, year = {2014}, author = {Benítez-Páez, A and Belda-Ferre, P and Simón-Soro, A and Mira, A}, title = {Microbiota diversity and gene expression dynamics in human oral biofilms.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {311}, pmid = {24767457}, issn = {1471-2164}, mesh = {*Biofilms ; *Gene Expression ; Humans ; Metagenome ; Microbiota/*genetics ; Mouth/*microbiology ; }, abstract = {BACKGROUND: Micro-organisms inhabiting teeth surfaces grow on biofilms where a specific and complex succession of bacteria has been described by co-aggregation tests and DNA-based studies. Although the composition of oral biofilms is well established, the active portion of the bacterial community and the patterns of gene expression in vivo have not been studied.

RESULTS: Using RNA-sequencing technologies, we present the first metatranscriptomic study of human dental plaque, performed by two different approaches: (1) A short-reads, high-coverage approach by Illumina sequencing to characterize the gene activity repertoire of the microbial community during biofilm development; (2) A long-reads, lower-coverage approach by pyrosequencing to determine the taxonomic identity of the active microbiome before and after a meal ingestion. The high-coverage approach allowed us to analyze over 398 million reads, revealing that microbial communities are individual-specific and no bacterial species was detected as key player at any time during biofilm formation. We could identify some gene expression patterns characteristic for early and mature oral biofilms. The transcriptomic profile of several adhesion genes was confirmed through qPCR by measuring expression of fimbriae-associated genes. In addition to the specific set of gene functions overexpressed in early and mature oral biofilms, as detected through the short-reads dataset, the long-reads approach detected specific changes when comparing the metatranscriptome of the same individual before and after a meal, which can narrow down the list of organisms responsible for acid production and therefore potentially involved in dental caries.

CONCLUSIONS: The bacteria changing activity during biofilm formation and after meal ingestion were person-specific. Interestingly, some individuals showed extreme homeostasis with virtually no changes in the active bacterial population after food ingestion, suggesting the presence of a microbial community which could be associated to dental health.}, } @article {pmid24763225, year = {2014}, author = {Ghosh, TS and Gupta, SS and Bhattacharya, T and Yadav, D and Barik, A and Chowdhury, A and Das, B and Mande, SS and Nair, GB}, title = {Gut microbiomes of Indian children of varying nutritional status.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e95547}, pmid = {24763225}, issn = {1932-6203}, mesh = {Bacteria/genetics ; Child ; Child Nutrition Disorders/*microbiology ; Gastrointestinal Tract/*microbiology ; Genes, Bacterial ; Humans ; India ; Microbiota/*genetics ; Molecular Typing ; Nutritional Status ; Sequence Analysis, DNA ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Malnutrition is a global health problem affecting more than 300 million pre-school children worldwide. It is one of the major health concerns in India since around 50% of children below the age of two suffer from various forms of malnutrition. The gut microbiome plays an important role in nutrient pre-processing, assimilation and energy harvest from food. Consequently, dysbiosis of the gut microbiota has been implicated in malnutrition.

Metagenomics approach was adopted to investigate the gut microbiome sampled from 20 rural Indian children with varying nutritional status. The changes in the abundances of various taxonomic and functional groups were investigated across these gut microbiomes. A core set of 23 genera were observed across samples, with some showing differential abundances with varying nutritional status. One of the findings of the current study is the positive/negative associations of specific taxonomic and functional groups with the nutritional status of the children. Notable alterations in the architecture of the inter-microbial co-occurrence networks were also observed with changes in nutritional status. A key example is the clustering of potentially pathogenic groups into a distinct hub in severely malnourished gut. Our data does not demonstrate causality with the microbiome patterns that we observed, rather a description of some interesting patterns, whose underlying mechanism remains to be uncovered.

CONCLUSIONS: The present study envisioned interrelationships between the pattern of gut microbiome and the nutritional status of children. The cause of this pattern needs to be explored. However, insights obtained from the present study form the basis for further metagenomic investigations on larger population of children. Results of such studies will be useful in identifying the key microbial groups that can be utilized for targeted therapeutic interventions for managing severe acute malnutrition.}, } @article {pmid24758293, year = {2014}, author = {Dominianni, C and Wu, J and Hayes, RB and Ahn, J}, title = {Comparison of methods for fecal microbiome biospecimen collection.}, journal = {BMC microbiology}, volume = {14}, number = {}, pages = {103}, pmid = {24758293}, issn = {1471-2180}, support = {R01 CA164964/CA/NCI NIH HHS/United States ; R03 CA159414/CA/NCI NIH HHS/United States ; R21 CA183887/CA/NCI NIH HHS/United States ; R01 CA159036/CA/NCI NIH HHS/United States ; }, mesh = {Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Feces/*microbiology ; Female ; Healthy Volunteers ; Humans ; Male ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Specimen Handling/*methods ; }, abstract = {BACKGROUND: Effective means are needed to efficiently collect fecal samples for microbiome analysis in large-scale epidemiological studies. Using twenty-four fecal aliquots prepared from three healthy individuals, we compared the following four fecal sample collection methods for assessment of human gut microbiome: 1) fecal occult blood test cards, held at room temperature for three days, 2) Eppendorf tubes, at room temperature for three days, 3) Eppendorf tubes with RNAlater, at room temperature, and 4) as controls, samples immediately frozen at -80°C. The 24 samples were assayed by 16S rRNA gene sequencing to compare overall microbiome structure and taxon distributions according to collection method.

RESULTS: Storing fecal occult blood test card samples at room temperature for three days did not affect total DNA purity and relative 16S rRNA bacterial gene contents, compared with fresh frozen collection. Overall microbiome structure, based on phylogenetic UniFrac index, differed significantly by subject (p = 0.001), but microbiome structure (p = 0.497) and relative abundance of major microbial taxa (phyla) (p > 0.05) did not differ significantly by collection method.

CONCLUSIONS: Our findings suggest that low-cost fecal occult blood test card collection may be a feasible means of sample collection for fecal microbiome assessment in large-scale population-based studies.}, } @article {pmid24757212, year = {2014}, author = {Vital, M and Howe, AC and Tiedje, JM}, title = {Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data.}, journal = {mBio}, volume = {5}, number = {2}, pages = {e00889}, pmid = {24757212}, issn = {2150-7511}, support = {UH3 DK083993/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/*genetics/*metabolism ; Butyrates/*metabolism ; Feces/*microbiology ; Healthy Volunteers ; Humans ; Metabolic Networks and Pathways/*genetics ; *Metagenomics ; *Microbiota ; }, abstract = {Butyrate-producing bacteria have recently gained attention, since they are important for a healthy colon and when altered contribute to emerging diseases, such as ulcerative colitis and type II diabetes. This guild is polyphyletic and cannot be accurately detected by 16S rRNA gene sequencing. Consequently, approaches targeting the terminal genes of the main butyrate-producing pathway have been developed. However, since additional pathways exist and alternative, newly recognized enzymes catalyzing the terminal reaction have been described, previous investigations are often incomplete. We undertook a broad analysis of butyrate-producing pathways and individual genes by screening 3,184 sequenced bacterial genomes from the Integrated Microbial Genome database. Genomes of 225 bacteria with a potential to produce butyrate were identified, including many previously unknown candidates. The majority of candidates belong to distinct families within the Firmicutes, but members of nine other phyla, especially from Actinobacteria, Bacteroidetes, Fusobacteria, Proteobacteria, Spirochaetes, and Thermotogae, were also identified as potential butyrate producers. The established gene catalogue (3,055 entries) was used to screen for butyrate synthesis pathways in 15 metagenomes derived from stool samples of healthy individuals provided by the HMP (Human Microbiome Project) consortium. A high percentage of total genomes exhibited a butyrate-producing pathway (mean, 19.1%; range, 3.2% to 39.4%), where the acetyl-coenzyme A (CoA) pathway was the most prevalent (mean, 79.7% of all pathways), followed by the lysine pathway (mean, 11.2%). Diversity analysis for the acetyl-CoA pathway showed that the same few firmicute groups associated with several Lachnospiraceae and Ruminococcaceae were dominating in most individuals, whereas the other pathways were associated primarily with Bacteroidetes. IMPORTANCE Microbiome research has revealed new, important roles of our gut microbiota for maintaining health, but an understanding of effects of specific microbial functions on the host is in its infancy, partly because in-depth functional microbial analyses are rare and publicly available databases are often incomplete/misannotated. In this study, we focused on production of butyrate, the main energy source for colonocytes, which plays a critical role in health and disease. We have provided a complete database of genes from major known butyrate-producing pathways, using in-depth genomic analysis of publicly available genomes, filling an important gap to accurately assess the butyrate-producing potential of complex microbial communities from "-omics"-derived data. Furthermore, a reference data set containing the abundance and diversity of butyrate synthesis pathways from the healthy gut microbiota was established through a metagenomics-based assessment. This study will help in understanding the role of butyrate producers in health and disease and may assist the development of treatments for functional dysbiosis.}, } @article {pmid24755769, year = {2014}, author = {Juhász, J and Kertész-Farkas, A and Szabó, D and Pongor, S}, title = {Emergence of collective territorial defense in bacterial communities: horizontal gene transfer can stabilize microbiomes.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e95511}, pmid = {24755769}, issn = {1932-6203}, mesh = {Bacteria/*genetics/*immunology ; Computer Simulation ; *Gene Transfer, Horizontal ; Genetic Variation ; Genotype ; Microbiota/*genetics ; Models, Biological ; }, abstract = {Multispecies bacterial communities such as the microbiota of the gastrointestinal tract can be remarkably stable and resilient even though they consist of cells and species that compete for resources and also produce a large number of antimicrobial agents. Computational modeling suggests that horizontal transfer of resistance genes may greatly contribute to the formation of stable and diverse communities capable of protecting themselves with a battery of antimicrobial agents while preserving a varied metabolic repertoire of the constituent species. In other words horizontal transfer of resistance genes makes a community compatible in terms of exoproducts and capable to maintain a varied and mature metagenome. The same property may allow microbiota to protect a host organism, or if used as a microbial therapy, to purge pathogens and restore a protective environment.}, } @article {pmid24752365, year = {2014}, author = {Iwai, S and Huang, D and Fong, S and Jarlsberg, LG and Worodria, W and Yoo, S and Cattamanchi, A and Davis, JL and Kaswabuli, S and Segal, M and Huang, L and Lynch, SV}, title = {The lung microbiome of Ugandan HIV-infected pneumonia patients is compositionally and functionally distinct from that of San Franciscan patients.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e95726}, pmid = {24752365}, issn = {1932-6203}, support = {U01 AI075410/AI/NIAID NIH HHS/United States ; HL087713/HL/NHLBI NIH HHS/United States ; U01 HL098964/HL/NHLBI NIH HHS/United States ; K24 HL087713/HL/NHLBI NIH HHS/United States ; P30 AI027763/AI/NIAID NIH HHS/United States ; R01 HL090335/HL/NHLBI NIH HHS/United States ; HL090335-02S109/HL/NHLBI NIH HHS/United States ; HL098964/HL/NHLBI NIH HHS/United States ; AI075410/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Female ; HIV Infections/*microbiology ; Humans ; Lung/*microbiology ; Male ; Microbiota/genetics/*physiology ; Middle Aged ; Pneumonia/*microbiology ; Pseudomonas aeruginosa/pathogenicity ; San Francisco ; Uganda ; Young Adult ; }, abstract = {Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome was significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population.}, } @article {pmid24751628, year = {2014}, author = {Neu, J}, title = {The developing intestinal microbiome: probiotics and prebiotics.}, journal = {World review of nutrition and dietetics}, volume = {110}, number = {}, pages = {167-176}, doi = {10.1159/000358465}, pmid = {24751628}, issn = {1662-3975}, mesh = {Enterocolitis, Necrotizing/microbiology/prevention & control ; High-Throughput Nucleotide Sequencing ; Humans ; Infant, Newborn ; Infant, Premature/growth & development ; Intestines/*microbiology ; Metagenomics ; Microbiota/*physiology ; *Prebiotics ; *Probiotics ; Randomized Controlled Trials as Topic ; }, abstract = {The microbes in the human intestinal tract interact with the host to form a 'superorganism'. The functional aspects of the host microbe interactions are being increasingly scrutinized and it is becoming evident that this interaction in early life is critical for development of the immune system and metabolic function and aberrations may result in life-long health consequences. Evidence is suggesting that such interactions occur even before birth, where the microbes may be either beneficial or harmful, and possibly even triggering preterm birth. Mode of delivery, use of antibiotics, and other perturbations may have life-long consequences in terms of health and disease. Manipulating the microbiota by use of pro- and prebiotics may offer a means for maintenance of 'healthy' host microbe interactions, but over-exuberance in their use also has the potential to cause harm. Considerable controversy exists concerning the routine use of probiotics in the prevention of necrotizing enterocolitis. This chapter will provide a brief overview of the developing intestinal microbiome and discuss the use of pro- and prebiotics in preterm infants.}, } @article {pmid24751579, year = {2014}, author = {Tyler, AD and Smith, MI and Silverberg, MS}, title = {Analyzing the human microbiome: a "how to" guide for physicians.}, journal = {The American journal of gastroenterology}, volume = {109}, number = {7}, pages = {983-993}, doi = {10.1038/ajg.2014.73}, pmid = {24751579}, issn = {1572-0241}, mesh = {Computational Biology/*methods ; Gastrointestinal Tract/*microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; }, abstract = {The application of high-throughput next-generation sequencing to the analysis of the human microbiome has led to a shift in our understanding of the etiology of complex diseases. In consequence, a great deal of literature can now be found exploring this complex system, and reviewing recent findings. Observations of alterations in the intestinal microbiome associating with inflammatory bowel disease and other chronic conditions are well supported and have been widely accepted by the research community. Yet, it can be difficult to objectively evaluate the importance of these results, given the wide variety of methodologies applied by different groups in the field. The aim of this review is to focus attention on the basic principles involved in microbiome analyses, and to describe factors that may have an impact on the accurate interpretation of results.}, } @article {pmid24748167, year = {2014}, author = {Panda, S and El khader, I and Casellas, F and López Vivancos, J and García Cors, M and Santiago, A and Cuenca, S and Guarner, F and Manichanh, C}, title = {Short-term effect of antibiotics on human gut microbiota.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e95476}, pmid = {24748167}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/genetics ; Biodiversity ; Biomass ; Feces/microbiology ; Female ; Gastrointestinal Tract/*drug effects/*microbiology ; Humans ; Male ; Metagenome ; Microbiota/*drug effects ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S ; Young Adult ; }, abstract = {From birth onwards, the human gut microbiota rapidly increases in diversity and reaches an adult-like stage at three years of age. After this age, the composition may fluctuate in response to external factors such as antibiotics. Previous studies have shown that resilience is not complete months after cessation of the antibiotic intake. However, little is known about the short-term effects of antibiotic intake on the gut microbial community. Here we examined the load and composition of the fecal microbiota immediately after treatment in 21 patients, who received broad-spectrum antibiotics such as fluoroquinolones and β-lactams. A fecal sample was collected from all participants before treatment and one week after for microbial load and community composition analyses by quantitative PCR and pyrosequencing of the 16S rRNA gene, respectively. Fluoroquinolones and β-lactams significantly decreased microbial diversity by 25% and reduced the core phylogenetic microbiota from 29 to 12 taxa. However, at the phylum level, these antibiotics increased the Bacteroidetes/Firmicutes ratio (p = 0.0007, FDR = 0.002). At the species level, our findings unexpectedly revealed that both antibiotic types increased the proportion of several unknown taxa belonging to the Bacteroides genus, a Gram-negative group of bacteria (p = 0.0003, FDR<0.016). Furthermore, the average microbial load was affected by the treatment. Indeed, the β-lactams increased it significantly by two-fold (p = 0.04). The maintenance of or possible increase detected in microbial load and the selection of Gram-negative over Gram-positive bacteria breaks the idea generally held about the effect of broad-spectrum antibiotics on gut microbiota.}, } @article {pmid24748147, year = {2014}, author = {Boissy, RJ and Romberger, DJ and Roughead, WA and Weissenburger-Moser, L and Poole, JA and LeVan, TD}, title = {Shotgun pyrosequencing metagenomic analyses of dusts from swine confinement and grain facilities.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e95578}, pmid = {24748147}, issn = {1932-6203}, support = {R01 OH008539/OH/NIOSH CDC HHS/United States ; R01 ES019325/ES/NIEHS NIH HHS/United States ; 2R01OH008539/OH/NIOSH CDC HHS/United States ; U54 OH010162/OH/NIOSH CDC HHS/United States ; U54OH010162//ACL HHS/United States ; ES019325/ES/NIEHS NIH HHS/United States ; I01 CX000434/CX/CSRD VA/United States ; 1U54OH010162-01/OH/NIOSH CDC HHS/United States ; }, mesh = {*Agriculture ; Animals ; Bacteria/classification/genetics ; Biomarkers ; Datasets as Topic ; Dust/*analysis ; Edible Grain/*microbiology ; *Environmental Microbiology ; Genome ; Humans ; *Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Swine/*microbiology ; }, abstract = {Inhalation of agricultural dusts causes inflammatory reactions and symptoms such as headache, fever, and malaise, which can progress to chronic airway inflammation and associated diseases, e.g. asthma, chronic bronchitis, chronic obstructive pulmonary disease, and hypersensitivity pneumonitis. Although in many agricultural environments feed particles are the major constituent of these dusts, the inflammatory responses that they provoke are likely attributable to particle-associated bacteria, archaebacteria, fungi, and viruses. In this study, we performed shotgun pyrosequencing metagenomic analyses of DNA from dusts from swine confinement facilities or grain elevators, with comparisons to dusts from pet-free households. DNA sequence alignment showed that 19% or 62% of shotgun pyrosequencing metagenomic DNA sequence reads from swine facility or household dusts, respectively, were of swine or human origin, respectively. In contrast only 2% of such reads from grain elevator dust were of mammalian origin. These metagenomic shotgun reads of mammalian origin were excluded from our analyses of agricultural dust microbiota. The ten most prevalent bacterial taxa identified in swine facility compared to grain elevator or household dust were comprised of 75%, 16%, and 42% gram-positive organisms, respectively. Four of the top five swine facility dust genera were assignable (Clostridium, Lactobacillus, Ruminococcus, and Eubacterium, ranging from 4% to 19% relative abundance). The relative abundances of these four genera were lower in dust from grain elevators or pet-free households. These analyses also highlighted the predominance in swine facility dust of Firmicutes (70%) at the phylum level, Clostridia (44%) at the Class level, and Clostridiales at the Order level (41%). In summary, shotgun pyrosequencing metagenomic analyses of agricultural dusts show that they differ qualitatively and quantitatively at the level of microbial taxa present, and that the bioinformatic analyses used for such studies must be carefully designed to avoid the potential contribution of non-microbial DNA, e.g. from resident mammals.}, } @article {pmid24747819, year = {2014}, author = {Munk, B and Lebuhn, M}, title = {Process diagnosis using methanogenic Archaea in maize-fed, trace element depleted fermenters.}, journal = {Anaerobe}, volume = {29}, number = {}, pages = {22-28}, doi = {10.1016/j.anaerobe.2014.04.002}, pmid = {24747819}, issn = {1095-8274}, mesh = {Biofuels ; Bioreactors ; Cobalt/metabolism/pharmacology ; DNA, Archaeal/*genetics ; Fermentation/drug effects ; Genetic Variation ; Hydrogen-Ion Concentration ; Metagenome ; Methane/*biosynthesis ; Methanobacteriaceae/drug effects/*genetics/metabolism ; Microbial Consortia/drug effects/*genetics ; Pressure ; RNA, Ribosomal, 16S/*genetics ; Real-Time Polymerase Chain Reaction ; Selenium/metabolism/pharmacology ; Temperature ; Trace Elements/metabolism/pharmacology ; Zea mays/*metabolism ; }, abstract = {A mesophilic maize-fed pilot-scale fermenter was severely acidified due to trace element (TE) deficiency. Mainly cobalt (0.07 mg * kg(-1) fresh mass (FM)), selenium (0.007 mg * kg(-1) FM) and sodium (13 mg * kg(-1) FM) were depleted. From this inoculum, three lab-scale flow-through fermenters were operated to analyse micronutrient deficiencies and population dynamics in more detail. One fermenter was supplemented with selenium, one with cobalt, and one served as control. After starvation and recovery of the fermenters, the organic loading rate (OLR) was increased. In parallel, the concentration (Real-Time PCR) of methanogens and their population composition (amplicon sequencing) was determined at the DNA and mRNA level. The parameters Metabolic Quotient (MQ) and cDNA/DNA were calculated to assess the activity of the methanogens. The control without TE supplementation acidified first at an OLR of 4.0 kg volatile solids (VS) * m(-3) * d(-1) while the singular addition of selenium and of cobalt positively influenced the fermenter stability up to an OLR of 4.5 or 5.0 kg VS * m(-3) * d(-1), respectively. In the stable process, the methanogenic populations were dominated by probably residual hydrogenotrophic Methanoculleus sp. (DNA-level), but representatives of versatile Methanosarcina sp. were most active (cDNA-level). When the TE supplemented fermenters began to acidify, Methanosarcina spp. were dominant in the whole (DNA-level) and the active (cDNA-level) community. The acidified control fermenter was dominated by Methanobacteriaceae genus IV. Until acidification, the concentration of methanogens increased with higher OLRs. The MQ indicated stress metabolism approximately one month before the TVA/TIC ratio reached a critical level of 0.7, demonstrating its suitability as early warning parameter of process acidification. The development of the cDNA/DNA ratio also reflected the increasing methanogenic activity with higher OLRs. Highest cDNA/DNA values (ca. 2) were obtained at metabolic strain of the methanogens, at the onset of acidification.}, } @article {pmid24743166, year = {2014}, author = {Sarmiento-Ramírez, JM and van der Voort, M and Raaijmakers, JM and Diéguez-Uribeondo, J}, title = {Unravelling the microbiome of eggs of the endangered sea turtle Eretmochelys imbricata identifies bacteria with activity against the emerging pathogen Fusarium falciforme.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e95206}, pmid = {24743166}, issn = {1932-6203}, mesh = {Animals ; Bacteria ; *Endangered Species ; *Fusarium ; Microbiota/*physiology ; Ovum ; Turtles/*microbiology ; }, abstract = {Habitat bioaugmentation and introduction of protective microbiota have been proposed as potential conservation strategies to rescue endangered mammals and amphibians from emerging diseases. For both strategies, insight into the microbiomes of the endangered species and their habitats is essential. Here, we sampled nests of the endangered sea turtle species Eretmochelys imbricata that were infected with the fungal pathogen Fusarium falciforme. Metagenomic analysis of the bacterial communities associated with the shells of the sea turtle eggs revealed approximately 16,664 operational taxonomic units, with Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes as the most dominant phyla. Subsequent isolation of Actinobacteria from the eggshells led to the identification of several genera (Streptomyces, Amycolaptosis, Micromomospora Plantactinospora and Solwaraspora) that inhibit hyphal growth of the pathogen F. falciforme. These bacterial genera constitute a first set of microbial indicators to evaluate the potential role of microbiota in conservation of endangered sea turtle species.}, } @article {pmid24740130, year = {2014}, author = {DeWeerdt, S}, title = {Microbiome: A complicated relationship status.}, journal = {Nature}, volume = {508}, number = {7496}, pages = {S61-3}, pmid = {24740130}, issn = {1476-4687}, mesh = {Animals ; Bacteroidetes/isolation & purification ; Body Mass Index ; Body Weight ; Case-Control Studies ; Diet/adverse effects ; Enterobacter/isolation & purification ; Feces/microbiology ; Gastrointestinal Transit ; Germ-Free Life/physiology ; Gram-Positive Bacteria/isolation & purification ; Humans ; Intestines/*microbiology ; Leptin/genetics/metabolism ; Male ; Metagenome/genetics ; Mice ; Microbiota/genetics/*physiology ; Obesity/etiology/*microbiology ; Prebiotics ; Species Specificity ; Verrucomicrobia/isolation & purification ; }, } @article {pmid24739969, year = {2014}, author = {Ding, T and Schloss, PD}, title = {Dynamics and associations of microbial community types across the human body.}, journal = {Nature}, volume = {509}, number = {7500}, pages = {357-360}, pmid = {24739969}, issn = {1476-4687}, support = {R01 HG005975/HG/NHGRI NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; R01HG005975/HG/NHGRI NIH HHS/United States ; R01GM099514/GM/NIGMS NIH HHS/United States ; P30DK034933/DK/NIDDK NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; }, mesh = {Breast Feeding ; Disease Susceptibility ; Educational Status ; Feces/microbiology ; Female ; Gastrointestinal Tract/microbiology ; Health ; *Human Body ; Humans ; Life Style ; Male ; Metagenome/genetics ; *Microbiota/genetics ; Mouth/microbiology ; *Organ Specificity ; Precision Medicine ; RNA, Ribosomal, 16S/genetics ; Sex Characteristics ; Time Factors ; Vagina/microbiology ; }, abstract = {A primary goal of the Human Microbiome Project (HMP) was to provide a reference collection of 16S ribosomal RNA gene sequences collected from sites across the human body that would allow microbiologists to better associate changes in the microbiome with changes in health. The HMP Consortium has reported the structure and function of the human microbiome in 300 healthy adults at 18 body sites from a single time point. Using additional data collected over the course of 12-18 months, we used Dirichlet multinomial mixture models to partition the data into community types for each body site and made three important observations. First, there were strong associations between whether individuals had been breastfed as an infant, their gender, and their level of education with their community types at several body sites. Second, although the specific taxonomic compositions of the oral and gut microbiomes were different, the community types observed at these sites were predictive of each other. Finally, over the course of the sampling period, the community types from sites within the oral cavity were the least stable, whereas those in the vagina and gut were the most stable. Our results demonstrate that even with the considerable intra- and interpersonal variation in the human microbiome, this variation can be partitioned into community types that are predictive of each other and are probably the result of life-history characteristics. Understanding the diversity of community types and the mechanisms that result in an individual having a particular type or changing types, will allow us to use their community types to assess disease risk and to personalize therapies.}, } @article {pmid24737430, year = {2014}, author = {Santos, AC and Rezende, RP and Brendel, M and Souza, SS and Gonçalves, AC and Dias, JC}, title = {Evaluation of the biodegradability of petroleum in microcosm systems by using mangrove sediments from Camamu Bay, Bahia, Brazil.}, journal = {Genetics and molecular research : GMR}, volume = {13}, number = {1}, pages = {2048-2059}, doi = {10.4238/2014.March.24.9}, pmid = {24737430}, issn = {1676-5680}, mesh = {Bacteria/classification/genetics ; Bays ; *Biodegradation, Environmental ; Brazil ; Carbon Dioxide/analysis/chemistry ; Cluster Analysis ; Environmental Pollutants/analysis/*metabolism ; Geologic Sediments/chemistry/*microbiology ; Metagenome ; Microbiota/*physiology ; Petroleum/analysis/*metabolism ; RNA, Ribosomal, 16S ; Rhizophoraceae/*microbiology ; }, abstract = {We investigated the biodegradability of oil in mangrove sediment from Camamu Bay and measured its effect on the bacterial community. Microcosms of mangrove sediment were contaminated with 0.1, 0.5, 1, 2, and 5% (w/v) oil, and the microbial activity was compared to that in uncontaminated sediment. The evolution of CO2 and gas chromatography showed the mineralization of oil compounds, which could reach 100%. Bacterial diversity was determined by polymerase chain reaction using a set of primers for the V3 and V6-V8 regions of 16S rDNA. The band profile obtained by denaturing gradient gel electrophoresis of the amplicons that were obtained for the V3 region showed a negative correlation between band number and oil concentration, whereas that of the V6-V8 region showed a positive correlation between band numbers and oil concentration. The latter also gave similar results for microcosms that were contaminated with 2 and 5% oil. These results demonstrate the mangrove sediment's capacity to recover from oil contamination (in vitro) and suggest that native mangrove microorganisms contain enzymes necessary for the catabolism of oil.}, } @article {pmid24736271, year = {2014}, author = {Klymiuk, I and Högenauer, C and Halwachs, B and Thallinger, GG and Fricke, WF and Steininger, C}, title = {A physicians' wish list for the clinical application of intestinal metagenomics.}, journal = {PLoS medicine}, volume = {11}, number = {4}, pages = {e1001627}, pmid = {24736271}, issn = {1549-1676}, mesh = {Humans ; Intestines/*microbiology ; *Metagenomics ; *Microbiota ; }, abstract = {Christoph Steininger and colleagues explore how multiple infectious, autoimmune, metabolic, and neoplastic diseases have been associated with changes in the intestinal microbiome, although a cause-effect relationship is often difficult to establish. Integration of metagenomics into clinical medicine is a challenge, and the authors highlight clinical approaches that are of high priority for the useful medical application of metagenomics. Please see later in the article for the Editors' Summary.}, } @article {pmid24735678, year = {2014}, author = {Bell, TH and Joly, S and Pitre, FE and Yergeau, E}, title = {Increasing phytoremediation efficiency and reliability using novel omics approaches.}, journal = {Trends in biotechnology}, volume = {32}, number = {5}, pages = {271-280}, doi = {10.1016/j.tibtech.2014.02.008}, pmid = {24735678}, issn = {1879-3096}, mesh = {*Biodegradation, Environmental ; Computational Biology/*methods ; Genomics/*methods ; Microbiota ; Plants/*chemistry/*genetics/metabolism/microbiology ; Proteomics/*methods ; Soil/chemistry ; Soil Pollutants/metabolism ; }, abstract = {Phytoremediation is a cost-effective green alternative to traditional soil remediation technologies, but has experienced varied success in practice. The recent omics revolution has led to leaps in our understanding of soil microbial communities and plant metabolism, and some of the conditions that promote predictable activity in contaminated soils and heterogeneous environments. Combinations of omics tools and new bioinformatics approaches will allow us to understand integrated activity patterns between plants and microbes, and determine how this metaorganism can be modified to maximize growth, appropriate assembly of microbial communities, and, ultimately, phytoremediation activity. Here we provide an overview of how new omics-mediated discoveries can potentially be translated into an effective and reliable environmental technology.}, } @article {pmid24734220, year = {2014}, author = {De Paepe, M and Leclerc, M and Tinsley, CR and Petit, MA}, title = {Bacteriophages: an underestimated role in human and animal health?.}, journal = {Frontiers in cellular and infection microbiology}, volume = {4}, number = {}, pages = {39}, pmid = {24734220}, issn = {2235-2988}, mesh = {Animals ; Bacteriophages/growth & development/*physiology ; Dysbiosis ; *Ecosystem ; *Health ; Homeostasis ; Humans ; *Microbiota ; }, abstract = {Metagenomic approaches applied to viruses have highlighted their prevalence in almost all microbial ecosystems investigated. In all ecosystems, notably those associated with humans or animals, the viral fraction is dominated by bacteriophages. Whether they contribute to dysbiosis, i.e., the departure from microbiota composition in symbiosis at equilibrium and entry into a state favoring human or animal disease is unknown at present. This review summarizes what has been learnt on phages associated with human and animal microbiota, and focuses on examples illustrating the several ways by which phages may contribute to a shift to pathogenesis, either by modifying population equilibrium, by horizontal transfer, or by modulating immunity.}, } @article {pmid24732106, year = {2014}, author = {Putignani, L and Del Chierico, F and Petrucca, A and Vernocchi, P and Dallapiccola, B}, title = {The human gut microbiota: a dynamic interplay with the host from birth to senescence settled during childhood.}, journal = {Pediatric research}, volume = {76}, number = {1}, pages = {2-10}, doi = {10.1038/pr.2014.49}, pmid = {24732106}, issn = {1530-0447}, mesh = {Bacteria ; Breast Feeding ; Child ; Female ; Gastrointestinal Tract/immunology/*microbiology ; Genomics ; Humans ; Immune System ; Infant ; Infant, Newborn ; Maternal-Fetal Exchange ; Metabolomics ; *Microbiota ; Phenotype ; Pregnancy ; Probiotics ; Proteomics ; Systems Biology ; }, abstract = {The microbiota "organ" is the central bioreactor of the gastrointestinal tract, populated by a total of 10(14) bacteria and characterized by a genomic content (microbiome), which represents more than 100 times the human genome. The microbiota plays an important role in child health by acting as a barrier against pathogens and their invasion with a highly dynamic modality, exerting metabolic multistep functions and stimulating the development of the host immune system, through well-organized programming, which influences all of the growth and aging processes. The advent of "omics" technologies (genomics, proteomics, metabolomics), characterized by complex technological platforms and advanced analytical and computational procedures, has opened new avenues to the knowledge of the gut microbiota ecosystem, clarifying some aspects on the establishment of microbial communities that constitute it, their modulation and active interaction with external stimuli as well as food, within the host genetic variability. With a huge interdisciplinary effort and an interface work between basic, translational, and clinical research, microbiologists, specialists in "-omics" disciplines, and clinicians are now clarifying the role of the microbiota in the programming process of several gut-related diseases, from the physiological symbiosis to the microbial dysbiosis stage, through an integrated systems biology approach.}, } @article {pmid24730667, year = {2014}, author = {Pawłowska, J and Lejzerowicz, F and Esling, P and Szczuciński, W and Zajączkowski, M and Pawlowski, J}, title = {Ancient DNA sheds new light on the Svalbard foraminiferal fossil record of the last millennium.}, journal = {Geobiology}, volume = {12}, number = {4}, pages = {277-288}, doi = {10.1111/gbi.12087}, pmid = {24730667}, issn = {1472-4669}, mesh = {Biodiversity ; DNA/analysis ; Foraminifera/*genetics ; *Fossils ; Metagenomics ; }, abstract = {Recent palaeogenetic studies have demonstrated the occurrence of preserved ancient DNA (aDNA) in various types of fossilised material. Environmental aDNA sequences assigned to modern species have been recovered from marine sediments dating to the Pleistocene. However, the match between the aDNA and the fossil record still needs to be evaluated for the environmental DNA approaches to be fully exploited. Here, we focus on foraminifera in sediments up to one thousand years old retrieved from the Hornsund fjord (Svalbard). We compared the diversity of foraminiferal microfossil assemblages with the diversity of aDNA sequenced from subsurface sediment samples using both cloning and high-throughput sequencing (HTS). Our study shows that 57% of the species archived in the fossil record were also detected in the aDNA data. However, the relative abundance of aDNA sequence reads and fossil specimens differed considerably. We also found a limited match between the stratigraphic occurrence of some fossil species and their aDNA sequences, especially in the case of rare taxa. The aDNA data comprised a high proportion of non-fossilised monothalamous species, which are known to dominate in modern foraminiferal communities of the Svalbard region. Our results confirm the relevance of HTS for studying past micro-eukaryotic diversity and provide insight into its ability to reflect fossil assemblages. Palaeogenetic studies including aDNA analyses of non-fossilised groups expand the range of palaeoceanographical proxies and therefore may increase the accuracy of palaeoenvironmental reconstructions.}, } @article {pmid24727777, year = {2014}, author = {Brüssow, H and Parkinson, SJ}, title = {You are what you eat.}, journal = {Nature biotechnology}, volume = {32}, number = {3}, pages = {243-245}, pmid = {24727777}, issn = {1546-1696}, mesh = {Animals ; Bacteria/*genetics/*isolation & purification ; *Diet ; Female ; Gastrointestinal Tract/*microbiology ; *Gluconeogenesis ; Humans ; Intestinal Mucosa/*metabolism ; Intestines/*innervation ; Male ; *Metagenome ; *Microbiota ; }, } @article {pmid24727280, year = {2014}, author = {Wagner, AO and Malin, C and Lins, P and Gstraunthaler, G and Illmer, P}, title = {Reactor performance of a 750 m(3) anaerobic digestion plant: varied substrate input conditions impacting methanogenic community.}, journal = {Anaerobe}, volume = {29}, number = {}, pages = {29-33}, doi = {10.1016/j.anaerobe.2014.03.012}, pmid = {24727280}, issn = {1095-8274}, mesh = {Ammonia/metabolism ; Anaerobiosis ; Biofuels ; Bioreactors ; Carbon/metabolism ; DNA, Archaeal/*genetics ; Fatty Acids, Volatile/metabolism ; Fermentation ; Food ; Genetic Variation ; Hydrogen-Ion Concentration ; Metagenome ; Methane/*biosynthesis ; Methanobacteriaceae/*genetics/metabolism ; Microbial Consortia/*genetics ; Nitrogen/metabolism ; Pressure ; RNA, Ribosomal, 16S/*genetics ; Real-Time Polymerase Chain Reaction ; Temperature ; Waste Products ; }, abstract = {A 750 m(3) anaerobic digester was studied over a half year period including a shift from good reactor performance to a reduced one. Various abiotic parameters like volatile fatty acids (VFA) (formic-, acetic-, propionic-, (iso-)butyric-, (iso-)valeric-, lactic acid), total C, total N, NH4 -N, and total proteins, as well as the organic matter content and dry mass were determined. In addition several process parameters such as temperature, pH, retention time and input of substrate and the concentrations of CH4, H2, CO2 and H2S within the reactor were monitored continuously. The present study aimed at the investigation of the abundance of acetogens and total cell numbers and the microbial methanogenic community as derived from PCR-dHPLC analysis in order to put it into context with the determined abiotic parameters. An influence of substrate quantity on the efficiency of the anaerobic digestion process was found as well as a shift from a hydrogenotrophic in times of good reactor performance towards an acetoclastic dominated methanogenic community in times of reduced reactor performance. After the change in substrate conditions it took the methano-archaeal community about 5-6 weeks to be affected but then changes occurred quickly.}, } @article {pmid24727124, year = {2014}, author = {Bucci, V and Xavier, JB}, title = {Towards predictive models of the human gut microbiome.}, journal = {Journal of molecular biology}, volume = {426}, number = {23}, pages = {3907-3916}, pmid = {24727124}, issn = {1089-8638}, support = {DP2 OD008440/OD/NIH HHS/United States ; U54 CA14896704/CA/NCI NIH HHS/United States ; DP2OD008440/OD/NIH HHS/United States ; }, mesh = {*Biota ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenomics ; *Microbiota ; *Models, Theoretical ; }, abstract = {The intestinal microbiota is an ecosystem susceptible to external perturbations such as dietary changes and antibiotic therapies. Mathematical models of microbial communities could be of great value in the rational design of microbiota-tailoring diets and therapies. Here, we discuss how advances in another field, engineering of microbial communities for wastewater treatment bioreactors, could inspire development of mechanistic mathematical models of the gut microbiota. We review the state of the art in bioreactor modeling and current efforts in modeling the intestinal microbiota. Mathematical modeling could benefit greatly from the deluge of data emerging from metagenomic studies, but data-driven approaches such as network inference that aim to predict microbiome dynamics without explicit mechanistic knowledge seem better suited to model these data. Finally, we discuss how the integration of microbiome shotgun sequencing and metabolic modeling approaches such as flux balance analysis may fulfill the promise of a mechanistic model.}, } @article {pmid24722629, year = {2014}, author = {Taş, N and Prestat, E and McFarland, JW and Wickland, KP and Knight, R and Berhe, AA and Jorgenson, T and Waldrop, MP and Jansson, JK}, title = {Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest.}, journal = {The ISME journal}, volume = {8}, number = {9}, pages = {1904-1919}, pmid = {24722629}, issn = {1751-7370}, mesh = {Alaska ; Biodiversity ; Carbon/*analysis ; *Fires ; *Metagenome ; Permafrost/chemistry/*microbiology ; Soil Microbiology ; *Taiga ; }, abstract = {Permafrost soils are large reservoirs of potentially labile carbon (C). Understanding the dynamics of C release from these soils requires us to account for the impact of wildfires, which are increasing in frequency as the climate changes. Boreal wildfires contribute to global emission of greenhouse gases (GHG-CO2, CH4 and N2O) and indirectly result in the thawing of near-surface permafrost. In this study, we aimed to define the impact of fire on soil microbial communities and metabolic potential for GHG fluxes in samples collected up to 1 m depth from an upland black spruce forest near Nome Creek, Alaska. We measured geochemistry, GHG fluxes, potential soil enzyme activities and microbial community structure via 16SrRNA gene and metagenome sequencing. We found that soil moisture, C content and the potential for respiration were reduced by fire, as were microbial community diversity and metabolic potential. There were shifts in dominance of several microbial community members, including a higher abundance of candidate phylum AD3 after fire. The metagenome data showed that fire had a pervasive impact on genes involved in carbohydrate metabolism, methanogenesis and the nitrogen cycle. Although fire resulted in an immediate release of CO2 from surface soils, our results suggest that the potential for emission of GHG was ultimately reduced at all soil depths over the longer term. Because of the size of the permafrost C reservoir, these results are crucial for understanding whether fire produces a positive or negative feedback loop contributing to the global C cycle.}, } @article {pmid24722376, year = {2014}, author = {Ku, HJ and Lee, JH}, title = {Development of a novel long-range 16S rRNA universal primer set for metagenomic analysis of gastrointestinal microbiota in newborn infants.}, journal = {Journal of microbiology and biotechnology}, volume = {24}, number = {6}, pages = {812-822}, doi = {10.4014/jmb.1403.03032}, pmid = {24722376}, issn = {1738-8872}, mesh = {Adult ; Bacteria/classification/genetics/*isolation & purification ; DNA Primers/*genetics ; DNA, Bacterial/genetics ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Infant, Newborn ; Male ; *Metagenomics ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/*genetics ; Young Adult ; }, abstract = {Metagenomic analysis of the human intestinal microbiota has extended our understanding of the role of these bacteria in improving human intestinal health; however, a number of reports have shown that current total fecal DNA extraction methods and 16S rRNA universal primer sets could affect the species coverage and resolution of these analyses. Here, we improved the extraction method for total DNA from human fecal samples by optimization of the lysis buffer, boiling time (10 min), and bead-beating time (0 min). In addition, we developed a new longrange 16S rRNA universal PCR primer set targeting the V6 to V9 regions with a 580 bp DNA product length. This new 16S rRNA primer set was evaluated by comparison with two previously developed 16S rRNA universal primer sets and showed high species coverage and resolution. The optimized total fecal DNA extraction method and newly designed long-range 16S rRNA universal primer set will be useful for the highly accurate metagenomic analysis of adult and infant intestinal microbiota with minimization of any bias.}, } @article {pmid24719854, year = {2014}, author = {D'Argenio, V and Casaburi, G and Precone, V and Salvatore, F}, title = {Comparative metagenomic analysis of human gut microbiome composition using two different bioinformatic pipelines.}, journal = {BioMed research international}, volume = {2014}, number = {}, pages = {325340}, pmid = {24719854}, issn = {2314-6141}, mesh = {Bacteria/classification/*genetics ; Computational Biology/*methods ; Gastrointestinal Tract/microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Technological advances in next-generation sequencing-based approaches have greatly impacted the analysis of microbial community composition. In particular, 16S rRNA-based methods have been widely used to analyze the whole set of bacteria present in a target environment. As a consequence, several specific bioinformatic pipelines have been developed to manage these data. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology (QIIME) are two freely available tools for metagenomic analyses that have been used in a wide range of studies. Here, we report the comparative analysis of the same dataset with both QIIME and MG-RAST in order to evaluate their accuracy in taxonomic assignment and in diversity analysis. We found that taxonomic assignment was more accurate with QIIME which, at family level, assigned a significantly higher number of reads. Thus, QIIME generated a more accurate BIOM file, which in turn improved the diversity analysis output. Finally, although informatics skills are needed to install QIIME, it offers a wide range of metrics that are useful for downstream applications and, not less important, it is not dependent on server times.}, } @article {pmid24718324, year = {2014}, author = {Masahata, K and Umemoto, E and Kayama, H and Kotani, M and Nakamura, S and Kurakawa, T and Kikuta, J and Gotoh, K and Motooka, D and Sato, S and Higuchi, T and Baba, Y and Kurosaki, T and Kinoshita, M and Shimada, Y and Kimura, T and Okumura, R and Takeda, A and Tajima, M and Yoshie, O and Fukuzawa, M and Kiyono, H and Fagarasan, S and Iida, T and Ishii, M and Takeda, K}, title = {Generation of colonic IgA-secreting cells in the caecal patch.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {3704}, doi = {10.1038/ncomms4704}, pmid = {24718324}, issn = {2041-1723}, mesh = {Adoptive Transfer ; Animals ; Appendix/*cytology/*immunology ; Base Sequence ; Cell Movement/*immunology ; Colon/*cytology ; DNA Primers/genetics ; Dendritic Cells/immunology ; Feces/microbiology ; Flow Cytometry ; Immunoglobulin A/*immunology/metabolism ; Immunohistochemistry ; Luminescent Proteins/metabolism ; Lymphoid Tissue/*immunology/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Microbiota/*genetics ; Molecular Sequence Data ; Peyer's Patches/cytology ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Statistics, Nonparametric ; }, abstract = {Gut-associated lymphoid tissues are responsible for the generation of IgA-secreting cells. However, the function of the caecal patch, a lymphoid tissue in the appendix, remains unknown. Here we analyse the role of the caecal patch using germ-free mice colonized with intestinal bacteria after appendectomy. Appendectomized mice show delayed accumulation of IgA(+) cells in the large intestine, but not the small intestine, after colonization. Decreased colonic IgA(+) cells correlate with altered faecal microbiota composition. Experiments using photoconvertible Kaede-expressing mice or adoptive transfer show that the caecal patch IgA(+) cells migrate to the large and small intestines, whereas Peyer's patch cells are preferentially recruited to the small intestine. IgA(+) cells in the caecal patch express higher levels of CCR10. Dendritic cells in the caecal patch, but not Peyer's patches, induce CCR10 on cocultured B cells. Thus, the caecal patch is a major site for generation of IgA-secreting cells that migrate to the large intestine.}, } @article {pmid24714329, year = {2014}, author = {Botta, C and Langerholc, T and Cencič, A and Cocolin, L}, title = {In vitro selection and characterization of new probiotic candidates from table olive microbiota.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e94457}, pmid = {24714329}, issn = {1932-6203}, mesh = {Bacterial Adhesion ; Drug Resistance, Bacterial/genetics ; *Food Microbiology ; Humans ; Intestinal Mucosa/metabolism/microbiology ; Lactobacillus/classification/drug effects/genetics/metabolism ; Metagenome ; Microbial Sensitivity Tests ; *Microbiota ; Olea/*microbiology ; Phylogeny ; *Probiotics ; }, abstract = {To date, only a few studies have investigated the complex microbiota of table olives in order to identify new probiotic microorganisms, even though this food matrix has been shown to be a suitable source of beneficial lactic acid bacteria (LAB). Two hundred and thirty eight LAB, belonging to Lactobacillus plantarum, Lactobacillus pentosus and Leuconostoc mesenteroides species, and isolated from Nocellara Etnea table olives, have been screened in this survey through an in vitro approach. A simulation of transit tolerance in the upper human gastrointestinal tract, together with autoaggregation and hydrophobicity, have been decisive in reducing the number of LAB to 17 promising probiotics. None of the selected strains showed intrinsic resistances towards a broad spectrum of antibiotics and were therefore accurately characterized on an undifferentiated and 3D functional model of the human intestinal tract made up of H4-1 epithelial cells. As far as the potential colonization of the intestinal tract is concerned, a high adhesion ratio was observed for Lb. plantarum O2T60C (over 9%) when tested in the 3D functional model, which closely mimics real intestinal conditions. The stimulation properties towards the epithelial barrier integrity and the in vitro inhibition of L. monocytogenes adhesion and invasion have also been assessed. Lb. plantarum S1T10A and S11T3E enhanced trans-epithelial electrical resistance (TEER) and therefore the integrity of the polarized epithelium in the 3D model. Moreover, S11T3E showed the ability to inhibit L. monocytogenes invasion in the undifferentiated epithelial model. The reduction in L. monocytogenes infection, together with the potential enhancement of barrier integrity and an adhesion ratio that was above the average in the 3D functional model (6.9%) would seem to suggest the Lb. plantarum S11T3E strain as the most interesting candidate for possible in vivo animal and human trials.}, } @article {pmid24712530, year = {2014}, author = {Choudhari, S and Lohia, R and Grigoriev, A}, title = {Comparative metagenome analysis of an Alaskan glacier.}, journal = {Journal of bioinformatics and computational biology}, volume = {12}, number = {2}, pages = {1441003}, doi = {10.1142/S0219720014410030}, pmid = {24712530}, issn = {1757-6334}, mesh = {Alaska ; Bacteria/classification/*genetics/*isolation & purification ; Base Sequence ; Ice Cover/*microbiology ; Metagenome/*genetics ; Microbial Consortia/*genetics ; Molecular Sequence Data ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The temperature in the Arctic region has been increasing in the recent past accompanied by melting of its glaciers. We took a snapshot of the current microbial inhabitation of an Alaskan glacier (which can be considered as one of the simplest possible ecosystems) by using metagenomic sequencing of 16S rRNA recovered from ice/snow samples. Somewhat contrary to our expectations and earlier estimates, a rich and diverse microbial population of more than 2,500 species was revealed including several species of Archaea that has been identified for the first time in the glaciers of the Northern hemisphere. The most prominent bacterial groups found were Proteobacteria, Bacteroidetes, and Firmicutes. Firmicutes were not reported in large numbers in a previously studied Alpine glacier but were dominant in an Antarctic subglacial lake. Representatives of Cyanobacteria, Actinobacteria and Planctomycetes were among the most numerous, likely reflecting the dependence of the ecosystem on the energy obtained through photosynthesis and close links with the microbial community of the soil. Principal component analysis (PCA) of nucleotide word frequency revealed distinct sequence clusters for different taxonomic groups in the Alaskan glacier community and separate clusters for the glacial communities from other regions of the world. Comparative analysis of the community composition and bacterial diversity present in the Byron glacier in Alaska with other environments showed larger overlap with an Arctic soil than with a high Arctic lake, indicating patterns of community exchange and suggesting that these bacteria may play an important role in soil development during glacial retreat.}, } @article {pmid24710024, year = {2014}, author = {Buelow, E and Gonzalez, TB and Versluis, D and Oostdijk, EA and Ogilvie, LA and van Mourik, MS and Oosterink, E and van Passel, MW and Smidt, H and D'Andrea, MM and de Been, M and Jones, BV and Willems, RJ and Bonten, MJ and van Schaik, W}, title = {Effects of selective digestive decontamination (SDD) on the gut resistome.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {8}, pages = {2215-2223}, doi = {10.1093/jac/dku092}, pmid = {24710024}, issn = {1460-2091}, support = {G0901553/MRC_/Medical Research Council/United Kingdom ; G090553/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/administration & dosage/*therapeutic use ; Bacterial Typing Techniques ; Base Sequence ; Clostridium/drug effects/isolation & purification ; Critical Care ; DNA, Bacterial/genetics ; Decontamination/*methods ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Humans ; Intestines/*microbiology ; Male ; Microbiota/drug effects/genetics ; Molecular Sequence Data ; Oropharynx/*microbiology ; Phosphotransferases (Alcohol Group Acceptor)/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {OBJECTIVES: Selective digestive decontamination (SDD) is an infection prevention measure for critically ill patients in intensive care units (ICUs) that aims to eradicate opportunistic pathogens from the oropharynx and intestines, while sparing the anaerobic flora, by the application of non-absorbable antibiotics. Selection for antibiotic-resistant bacteria is still a major concern for SDD. We therefore studied the impact of SDD on the reservoir of antibiotic resistance genes (i.e. the resistome) by culture-independent approaches.

METHODS: We evaluated the impact of SDD on the gut microbiota and resistome in a single ICU patient during and after an ICU stay by several metagenomic approaches. We also determined by quantitative PCR the relative abundance of two common aminoglycoside resistance genes in longitudinally collected samples from 12 additional ICU patients who received SDD.

RESULTS: The patient microbiota was highly dynamic during the hospital stay. The abundance of antibiotic resistance genes more than doubled during SDD use, mainly due to a 6.7-fold increase in aminoglycoside resistance genes, in particular aph(2″)-Ib and an aadE-like gene. We show that aph(2″)-Ib is harboured by anaerobic gut commensals and is associated with mobile genetic elements. In longitudinal samples of 12 ICU patients, the dynamics of these two genes ranged from a ∼10(4) fold increase to a ∼10(-10) fold decrease in relative abundance during SDD.

CONCLUSIONS: ICU hospitalization and the simultaneous application of SDD has large, but highly individualized, effects on the gut resistome of ICU patients. Selection for transferable antibiotic resistance genes in anaerobic commensal bacteria could impact the risk of transfer of antibiotic resistance genes to opportunistic pathogens.}, } @article {pmid24710002, year = {2014}, author = {Somboonna, N and Wilantho, A and Jankaew, K and Assawamakin, A and Sangsrakru, D and Tangphatsornruang, S and Tongsima, S}, title = {Microbial ecology of Thailand tsunami and non-tsunami affected terrestrials.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e94236}, pmid = {24710002}, issn = {1932-6203}, mesh = {Biodiversity ; *Ecological and Environmental Phenomena ; Ecosystem ; Metagenomics ; *Microbiota ; Thailand ; *Tsunamis ; }, abstract = {The effects of tsunamis on microbial ecologies have been ill-defined, especially in Phang Nga province, Thailand. This ecosystem was catastrophically impacted by the 2004 Indian Ocean tsunami as well as the 600 year-old tsunami in Phra Thong island, Phang Nga province. No study has been conducted to elucidate their effects on microbial ecology. This study represents the first to elucidate their effects on microbial ecology. We utilized metagenomics with 16S and 18S rDNA-barcoded pyrosequencing to obtain prokaryotic and eukaryotic profiles for this terrestrial site, tsunami affected (S1), as well as a parallel unaffected terrestrial site, non-tsunami affected (S2). S1 demonstrated unique microbial community patterns than S2. The dendrogram constructed using the prokaryotic profiles supported the unique S1 microbial communities. S1 contained more proportions of archaea and bacteria domains, specifically species belonging to Bacteroidetes became more frequent, in replacing of the other typical floras like Proteobacteria, Acidobacteria and Basidiomycota. Pathogenic microbes, including Acinetobacter haemolyticus, Flavobacterium spp. and Photobacterium spp., were also found frequently in S1. Furthermore, different metabolic potentials highlighted this microbial community change could impact the functional ecology of the site. Moreover, the habitat prediction based on percent of species indicators for marine, brackish, freshwater and terrestrial niches pointed the S1 to largely comprise marine habitat indicating-species.}, } @article {pmid24708260, year = {2014}, author = {Xia, JH and Lin, G and Fu, GH and Wan, ZY and Lee, M and Wang, L and Liu, XJ and Yue, GH}, title = {The intestinal microbiome of fish under starvation.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {266}, pmid = {24708260}, issn = {1471-2164}, mesh = {Animals ; Biodiversity ; Cluster Analysis ; Computational Biology ; Fishes/*microbiology ; Gene Expression Profiling ; Gene-Environment Interaction ; Intestines/*microbiology ; *Metagenome ; *Microbiota ; Molecular Sequence Data ; Nutritional Status ; Phylogeny ; RNA, Ribosomal, 16S ; *Starvation ; }, abstract = {BACKGROUND: Starvation not only affects the nutritional and health status of the animals, but also the microbial composition in the host's intestine. Next-generation sequencing provides a unique opportunity to explore gut microbial communities and their interactions with hosts. However, studies on gut microbiomes have been conducted predominantly in humans and land animals. Not much is known on gut microbiomes of aquatic animals and their changes under changing environmental conditions. To address this shortcoming, we determined the microbial gene catalogue, and investigated changes in the microbial composition and host-microbe interactions in the intestine of Asian seabass in response to starvation.

RESULTS: We found 33 phyla, 66 classes, 130 orders and 278 families in the intestinal microbiome. Proteobacteria (48.8%), Firmicutes (15.3%) and Bacteroidetes (8.2%) were the three most abundant bacteria taxa. Comparative analyses of the microbiome revealed shifts in bacteria communities, with dramatic enrichment of Bacteroidetes, but significant depletion of Betaproteobacteria in starved intestines. In addition, significant differences in clusters of orthologous groups (COG) functional categories and orthologous groups were observed. Genes related to antibiotic activity in the microbiome were significantly enriched in response to starvation, and host genes related to the immune response were generally up-regulated.

CONCLUSIONS: This study provides the first insights into the fish intestinal microbiome and its changes under starvation. Further detailed study on interactions between intestinal microbiomes and hosts under dynamic conditions will shed new light on how the hosts and microbes respond to the changing environment.}, } @article {pmid24708091, year = {2014}, author = {Kidd, JM and Sharpton, TJ and Bobo, D and Norman, PJ and Martin, AR and Carpenter, ML and Sikora, M and Gignoux, CR and Nemat-Gorgani, N and Adams, A and Guadalupe, M and Guo, X and Feng, Q and Li, Y and Liu, X and Parham, P and Hoal, EG and Feldman, MW and Pollard, KS and Wall, JD and Bustamante, CD and Henn, BM}, title = {Exome capture from saliva produces high quality genomic and metagenomic data.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {262}, pmid = {24708091}, issn = {1471-2164}, support = {R01HG003229/HG/NHGRI NIH HHS/United States ; T32HG000044/HG/NHGRI NIH HHS/United States ; GM007790/GM/NIGMS NIH HHS/United States ; R01 AI017892/AI/NIAID NIH HHS/United States ; T32GM007175/GM/NIGMS NIH HHS/United States ; R01HG400409/HG/NHGRI NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; T32 GM007790/GM/NIGMS NIH HHS/United States ; DP5 OD009154/OD/NIH HHS/United States ; AI17892/AI/NIAID NIH HHS/United States ; 1DP5OD009154/OD/NIH HHS/United States ; }, mesh = {*Exome ; Genome, Human ; *Genomics ; Genotype ; HLA Antigens/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenomics ; Microbiota ; Molecular Sequence Data ; Mouth/microbiology ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Receptors, KIR/genetics ; Saliva/*chemistry/*microbiology ; }, abstract = {BACKGROUND: Targeted capture of genomic regions reduces sequencing cost while generating higher coverage by allowing biomedical researchers to focus on specific loci of interest, such as exons. Targeted capture also has the potential to facilitate the generation of genomic data from DNA collected via saliva or buccal cells. DNA samples derived from these cell types tend to have a lower human DNA yield, may be degraded from age and/or have contamination from bacteria or other ambient oral microbiota. However, thousands of samples have been previously collected from these cell types, and saliva collection has the advantage that it is a non-invasive and appropriate for a wide variety of research.

RESULTS: We demonstrate successful enrichment and sequencing of 15 South African KhoeSan exomes and 2 full genomes with samples initially derived from saliva. The expanded exome dataset enables us to characterize genetic diversity free from ascertainment bias for multiple KhoeSan populations, including new exome data from six HGDP Namibian San, revealing substantial population structure across the Kalahari Desert region. Additionally, we discover and independently verify thirty-one previously unknown KIR alleles using methods we developed to accurately map and call the highly polymorphic HLA and KIR loci from exome capture data. Finally, we show that exome capture of saliva-derived DNA yields sufficient non-human sequences to characterize oral microbial communities, including detection of bacteria linked to oral disease (e.g. Prevotella melaninogenica). For comparison, two samples were sequenced using standard full genome library preparation without exome capture and we found no systematic bias of metagenomic information between exome-captured and non-captured data.

CONCLUSIONS: DNA from human saliva samples, collected and extracted using standard procedures, can be used to successfully sequence high quality human exomes, and metagenomic data can be derived from non-human reads. We find that individuals from the Kalahari carry a higher oral pathogenic microbial load than samples surveyed in the Human Microbiome Project. Additionally, rare variants present in the exomes suggest strong population structure across different KhoeSan populations.}, } @article {pmid24706600, year = {2014}, author = {Pacchioni, RG and Carvalho, FM and Thompson, CE and Faustino, AL and Nicolini, F and Pereira, TS and Silva, RC and Cantão, ME and Gerber, A and Vasconcelos, AT and Agnez-Lima, LF}, title = {Taxonomic and functional profiles of soil samples from Atlantic forest and Caatinga biomes in northeastern Brazil.}, journal = {MicrobiologyOpen}, volume = {3}, number = {3}, pages = {299-315}, pmid = {24706600}, issn = {2045-8827}, mesh = {Bacteria/*classification/*genetics ; Brazil ; DNA, Bacterial/chemistry/genetics ; Forests ; Metagenomics ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Although microorganisms play crucial roles in ecosystems, metagenomic analyses of soil samples are quite scarce, especially in the Southern Hemisphere. In this work, the microbial diversity of soil samples from an Atlantic Forest and Caatinga was analyzed using a metagenomic approach. Proteobacteria and Actinobacteria were the dominant phyla in both samples. Among which, a significant proportion of stress-resistant bacteria associated to organic matter degradation was found. Sequences related to metabolism of amino acids, nitrogen, and DNA and stress resistance were more frequent in Caatinga soil, while the forest sample showed the highest occurrence of hits annotated in phosphorous metabolism, defense mechanisms, and aromatic compound degradation subsystems. The principal component analysis (PCA) showed that our samples are close to the desert metagenomes in relation to taxonomy, but are more similar to rhizosphere microbiota in relation to the functional profiles. The data indicate that soil characteristics affect the taxonomic and functional distribution; these characteristics include low nutrient content, high drainage (both are sandy soils), vegetation, and exposure to stress. In both samples, a rapid turnover of organic matter with low greenhouse gas emission was suggested by the functional profiles obtained, reinforcing the importance of preserving natural areas.}, } @article {pmid24698744, year = {2014}, author = {Walker, AW and Duncan, SH and Louis, P and Flint, HJ}, title = {Phylogeny, culturing, and metagenomics of the human gut microbiota.}, journal = {Trends in microbiology}, volume = {22}, number = {5}, pages = {267-274}, doi = {10.1016/j.tim.2014.03.001}, pmid = {24698744}, issn = {1878-4380}, mesh = {Gastrointestinal Tract/*microbiology ; Humans ; Metagenomics/*methods ; Microbiological Techniques/*methods ; *Microbiota ; *Phylogeny ; }, abstract = {The human intestinal tract is colonised by a complex community of microbes, which can have major impacts on host health. Recent research on the gut microbiota has largely been driven by the advent of modern sequence-based techniques, such as metagenomics. Although these are powerful and valuable tools, they have limitations. Traditional culturing and phylogeny can mitigate some of these limitations, either by expanding reference databases or by assigning functionality to specific microbial lineages. As such, culture and phylogeny will continue to have crucially important roles in human microbiota research, and will be required for the development of novel therapeutics.}, } @article {pmid24695826, year = {2014}, author = {Venkateswaran, K and Vaishampayan, P and Cisneros, J and Pierson, DL and Rogers, SO and Perry, J}, title = {International Space Station environmental microbiome - microbial inventories of ISS filter debris.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {14}, pages = {6453-6466}, doi = {10.1007/s00253-014-5650-6}, pmid = {24695826}, issn = {1432-0614}, mesh = {Azides/metabolism ; Bacteria/*classification/genetics ; *Environmental Microbiology ; Enzyme Inhibitors/metabolism ; Fungi/*classification/genetics ; Metagenomics/methods ; *Microbial Viability ; *Microbiota ; Propidium/analogs & derivatives/metabolism ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Spacecraft ; }, abstract = {Despite an expanding array of molecular approaches for detecting microorganisms in a given sample, rapid and robust means of assessing the differential viability of the microbial cells, as a function of phylogenetic lineage, remain elusive. A propidium monoazide (PMA) treatment coupled with downstream quantitative polymerase chain reaction (qPCR) and pyrosequencing analyses was carried out to better understand the frequency, diversity, and distribution of viable microorganisms associated with debris collected from the crew quarters of the International Space Station (ISS). The cultured bacterial counts were more in the ISS samples than cultured fungal population. The rapid molecular analyses targeted to estimate viable population exhibited 5-fold increase in bacterial (qPCR-PMA assay) and 25-fold increase in microbial (adenosine triphosphate assay) burden than the cultured bacterial population. The ribosomal nucleic acid-based identification of cultivated strains revealed the presence of only four to eight bacterial species in the ISS samples, however, the viable bacterial diversity detected by the PMA-pyrosequencing method was far more diverse (12 to 23 bacterial taxa) with the majority consisting of members of actinobacterial genera (Propionibacterium, Corynebacterium) and Staphylococcus. Sample fractions not treated with PMA (inclusive of both live and dead cells) yielded a great abundance of highly diverse bacterial (94 to 118 taxa) and fungal lineages (41 taxa). Even though deep sequencing capability of the molecular analysis widened the understanding about the microbial diversity, the cultivation assay also proved to be essential since some of the spore-forming microorganisms were detected only by the culture-based method. Presented here are the findings of the first comprehensive effort to assess the viability of microbial cells associated with ISS surfaces, and correlate differential viability with phylogenetic affiliation.}, } @article {pmid24695540, year = {2014}, author = {Dishaw, LJ and Flores-Torres, J and Lax, S and Gemayel, K and Leigh, B and Melillo, D and Mueller, MG and Natale, L and Zucchetti, I and De Santis, R and Pinto, MR and Litman, GW and Gilbert, JA}, title = {The gut of geographically disparate Ciona intestinalis harbors a core microbiota.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e93386}, pmid = {24695540}, issn = {1932-6203}, support = {R01 AI023338/AI/NIAID NIH HHS/United States ; R37 AI023338/AI/NIAID NIH HHS/United States ; R56 AI023338/AI/NIAID NIH HHS/United States ; AI23338/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; Ciona intestinalis/*microbiology ; Ecosystem ; Gastrointestinal Tract/*microbiology ; Larva/microbiology ; Metagenome/genetics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {It is now widely understood that all animals engage in complex interactions with bacteria (or microbes) throughout their various life stages. This ancient exchange can involve cooperation and has resulted in a wide range of evolved host-microbial interdependencies, including those observed in the gut. Ciona intestinalis, a filter-feeding basal chordate and classic developmental model that can be experimentally manipulated, is being employed to help define these relationships. Ciona larvae are first exposed internally to microbes upon the initiation of feeding in metamorphosed individuals; however, whether or not these microbes subsequently colonize the gut and whether or not Ciona forms relationships with specific bacteria in the gut remains unknown. In this report, we show that the Ciona gut not only is colonized by a complex community of bacteria, but also that samples from three geographically isolated populations reveal striking similarity in abundant operational taxonomic units (OTUs) consistent with the selection of a core community by the gut ecosystem.}, } @article {pmid24694712, year = {2014}, author = {Everard, A and Lazarevic, V and Gaïa, N and Johansson, M and Ståhlman, M and Backhed, F and Delzenne, NM and Schrenzel, J and François, P and Cani, PD}, title = {Microbiome of prebiotic-treated mice reveals novel targets involved in host response during obesity.}, journal = {The ISME journal}, volume = {8}, number = {10}, pages = {2116-2130}, pmid = {24694712}, issn = {1751-7370}, support = {336452/ERC_/European Research Council/International ; }, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification ; Cecum/microbiology ; Diet, High-Fat ; Gastrointestinal Tract/*microbiology ; Inflammation/etiology ; Intestinal Mucosa/metabolism ; Membrane Glycoproteins/metabolism ; Metagenome ; Mice ; Mice, Inbred C57BL ; *Microbiota ; Obesity/etiology/*microbiology ; Peptides/metabolism ; *Prebiotics ; }, abstract = {The gut microbiota is involved in metabolic and immune disorders associated with obesity and type 2 diabetes. We previously demonstrated that prebiotic treatment may significantly improve host health by modulating bacterial species related to the improvement of gut endocrine, barrier and immune functions. An analysis of the gut metagenome is needed to determine which bacterial functions and taxa are responsible for beneficial microbiota-host interactions upon nutritional intervention. We subjected mice to prebiotic (Pre) treatment under physiological (control diet: CT) and pathological conditions (high-fat diet: HFD) for 8 weeks and investigated the production of intestinal antimicrobial peptides and the gut microbiome. HFD feeding significantly decreased the expression of regenerating islet-derived 3-gamma (Reg3g) and phospholipase A2 group-II (PLA2g2) in the jejunum. Prebiotic treatment increased Reg3g expression (by ∼50-fold) and improved intestinal homeostasis as suggested by the increase in the expression of intectin, a key protein involved in intestinal epithelial cell turnover. Deep metagenomic sequencing analysis revealed that HFD and prebiotic treatment significantly affected the gut microbiome at different taxonomic levels. Functional analyses based on the occurrence of clusters of orthologous groups (COGs) of proteins also revealed distinct profiles for the HFD, Pre, HFD-Pre and CT groups. Finally, the gut microbiota modulations induced by prebiotics counteracted HFD-induced inflammation and related metabolic disorders. Thus, we identified novel putative taxa and metabolic functions that may contribute to the development of or protection against the metabolic alterations observed during HFD feeding and HFD-Pre feeding.}, } @article {pmid24694711, year = {2014}, author = {Hopkins, M and Kailasan, S and Cohen, A and Roux, S and Tucker, KP and Shevenell, A and Agbandje-McKenna, M and Breitbart, M}, title = {Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein.}, journal = {The ISME journal}, volume = {8}, number = {10}, pages = {2093-2103}, pmid = {24694711}, issn = {1751-7370}, mesh = {Biodiversity ; Capsid Proteins/classification/*genetics ; DNA, Single-Stranded/chemistry ; DNA, Viral/chemistry ; Environmental Microbiology ; Microviridae/classification/*genetics ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {The small single-stranded DNA (ssDNA) bacteriophages of the subfamily Gokushovirinae were traditionally perceived as narrowly targeted, niche-specific viruses infecting obligate parasitic bacteria, such as Chlamydia. The advent of metagenomics revealed gokushoviruses to be widespread in global environmental samples. This study expands knowledge of gokushovirus diversity in the environment by developing a degenerate PCR assay to amplify a portion of the major capsid protein (MCP) gene of gokushoviruses. Over 500 amplicons were sequenced from 10 environmental samples (sediments, sewage, seawater and freshwater), revealing the ubiquity and high diversity of this understudied phage group. Residue-level conservation data generated from multiple alignments was combined with a predicted 3D structure, revealing a tendency for structurally internal residues to be more highly conserved than surface-presenting protein-protein or viral-host interaction domains. Aggregating this data set into a phylogenetic framework, many gokushovirus MCP clades contained samples from multiple environments, although distinct clades dominated the different samples. Antarctic sediment samples contained the most diverse gokushovirus communities, whereas freshwater springs from Florida were the least diverse. Whether the observed diversity is being driven by environmental factors or host-binding interactions remains an open question. The high environmental diversity of this previously overlooked ssDNA viral group necessitates further research elucidating their natural hosts and exploring their ecological roles.}, } @article {pmid24692635, year = {2014}, author = {Jorth, P and Turner, KH and Gumus, P and Nizam, N and Buduneli, N and Whiteley, M}, title = {Metatranscriptomics of the human oral microbiome during health and disease.}, journal = {mBio}, volume = {5}, number = {2}, pages = {e01012-14}, pmid = {24692635}, issn = {2150-7511}, support = {F31 DE021633/DE/NIDCR NIH HHS/United States ; R01 DE023193/DE/NIDCR NIH HHS/United States ; 5F31DE021633-02/DE/NIDCR NIH HHS/United States ; 1R01DE020100/DE/NIDCR NIH HHS/United States ; R01 DE020100/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Dysbiosis ; Female ; Humans ; Male ; *Metagenome ; *Microbiota ; Mouth/*microbiology ; Periodontitis/microbiology ; *Transcriptome ; }, abstract = {The human microbiome plays important roles in health, but when disrupted, these same indigenous microbes can cause disease. The composition of the microbiome changes during the transition from health to disease; however, these changes are often not conserved among patients. Since microbiome-associated diseases like periodontitis cause similar patient symptoms despite interpatient variability in microbial community composition, we hypothesized that human-associated microbial communities undergo conserved changes in metabolism during disease. Here, we used patient-matched healthy and diseased samples to compare gene expression of 160,000 genes in healthy and diseased periodontal communities. We show that health- and disease-associated communities exhibit defined differences in metabolism that are conserved between patients. In contrast, the metabolic gene expression of individual species was highly variable between patients. These results demonstrate that despite high interpatient variability in microbial composition, disease-associated communities display conserved metabolic profiles that are generally accomplished by a patient-specific cohort of microbes. IMPORTANCE The human microbiome project has shown that shifts in our microbiota are associated with many diseases, including obesity, Crohn's disease, diabetes, and periodontitis. While changes in microbial populations are apparent during these diseases, the species associated with each disease can vary from patient to patient. Taking into account this interpatient variability, we hypothesized that specific microbiota-associated diseases would be marked by conserved microbial community behaviors. Here, we use gene expression analyses of patient-matched healthy and diseased human periodontal plaque to show that microbial communities have highly conserved metabolic gene expression profiles, whereas individual species within the community do not. Furthermore, disease-associated communities exhibit conserved changes in metabolic and virulence gene expression.}, } @article {pmid24692253, year = {2014}, author = {Crowther, TW and Maynard, DS and Leff, JW and Oldfield, EE and McCulley, RL and Fierer, N and Bradford, MA}, title = {Predicting the responsiveness of soil biodiversity to deforestation: a cross-biome study.}, journal = {Global change biology}, volume = {20}, number = {9}, pages = {2983-2994}, doi = {10.1111/gcb.12565}, pmid = {24692253}, issn = {1365-2486}, mesh = {Analysis of Variance ; Base Sequence ; *Biodiversity ; Carbon Dioxide/metabolism ; Conservation of Natural Resources/*statistics & numerical data ; Fatty Acids/metabolism ; *Forests ; High-Throughput Nucleotide Sequencing ; Linear Models ; Microbiota/*genetics ; Molecular Sequence Data ; Puerto Rico ; Soil/*chemistry ; *Soil Microbiology ; Species Specificity ; United States ; }, abstract = {The consequences of deforestation for aboveground biodiversity have been a scientific and political concern for decades. In contrast, despite being a dominant component of biodiversity that is essential to the functioning of ecosystems, the responses of belowground biodiversity to forest removal have received less attention. Single-site studies suggest that soil microbes can be highly responsive to forest removal, but responses are highly variable, with negligible effects in some regions. Using high throughput sequencing, we characterize the effects of deforestation on microbial communities across multiple biomes and explore what determines the vulnerability of microbial communities to this vegetative change. We reveal consistent directional trends in the microbial community response, yet the magnitude of this vegetation effect varied between sites, and was explained strongly by soil texture. In sandy sites, the difference in vegetation type caused shifts in a suite of edaphic characteristics, driving substantial differences in microbial community composition. In contrast, fine-textured soil buffered microbes against these effects and there were minimal differences between communities in forest and grassland soil. These microbial community changes were associated with distinct changes in the microbial catabolic profile, placing community changes in an ecosystem functioning context. The universal nature of these patterns allows us to predict where deforestation will have the strongest effects on soil biodiversity, and how these effects could be mitigated.}, } @article {pmid24691166, year = {2014}, author = {Xu, Z and Hansen, MA and Hansen, LH and Jacquiod, S and Sørensen, SJ}, title = {Bioinformatic approaches reveal metagenomic characterization of soil microbial community.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e93445}, pmid = {24691166}, issn = {1932-6203}, mesh = {*Biodiversity ; Biomarkers ; Computational Biology/*methods ; Ecosystem ; Metabolomics/methods ; Metagenome ; Metagenomics/*methods ; Microbial Interactions ; Phylogeny ; *Soil Microbiology ; }, abstract = {As is well known, soil is a complex ecosystem harboring the most prokaryotic biodiversity on the Earth. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated the progress of soil ecological studies. However, how to effectively understand the underlying biological features of large-scale sequencing data is a new challenge. In the present study, we used 33 publicly available metagenomes from diverse soil sites (i.e. grassland, forest soil, desert, Arctic soil, and mangrove sediment) and integrated some state-of-the-art computational tools to explore the phylogenetic and functional characterizations of the microbial communities in soil. Microbial composition and metabolic potential in soils were comprehensively illustrated at the metagenomic level. A spectrum of metagenomic biomarkers containing 46 taxa and 33 metabolic modules were detected to be significantly differential that could be used as indicators to distinguish at least one of five soil communities. The co-occurrence associations between complex microbial compositions and functions were inferred by network-based approaches. Our results together with the established bioinformatic pipelines should provide a foundation for future research into the relation between soil biodiversity and ecosystem function.}, } @article {pmid24691073, year = {2014}, author = {Tyakht, AV and Alexeev, DG and Popenko, AS and Kostryukova, ES and Govorun, VM}, title = {Rural and urban microbiota: To be or not to be?.}, journal = {Gut microbes}, volume = {5}, number = {3}, pages = {351-356}, pmid = {24691073}, issn = {1949-0984}, mesh = {*Biota ; Cohort Studies ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenomics ; *Microbiota ; Rural Population ; Russia ; Urban Population ; }, abstract = {A multitude of metagenomic studies has brought to light an enormous richness of human gut microbiota compositions. In this space of possible configurations, clinical specialists are trying to mine the markers of healthy microbiota via case-control and longitudinal studies. We have discovered potentially beneficial communities while examining the microbial diversity in rural Russians in comparison with the urban dwellers. In this addendum, we further examine the data by elaborating on some of the less common types and suggesting the possible co-metabolism of their drivers. In the light of the first validated clinically effective bacterial transplantation, we discuss the concept of a reference healthy microbiota, outline the problems encountered on the way to its restoration in the developed world, and speculate if rural communities can serve as a source for its prototype.}, } @article {pmid24690147, year = {2014}, author = {Li, YF and Chen, PH and Yu, Z}, title = {Spatial and temporal variations of microbial community in a mixed plug-flow loop reactor fed with dairy manure.}, journal = {Microbial biotechnology}, volume = {7}, number = {4}, pages = {332-346}, pmid = {24690147}, issn = {1751-7915}, mesh = {Animals ; Bioreactors/*microbiology ; *Biota ; Cattle ; Fatty Acids/analysis ; Hydrogen-Ion Concentration ; Industrial Microbiology ; Manure/*microbiology ; Metagenomics ; Spatio-Temporal Analysis ; }, abstract = {Mixed plug-flow loop reactor (MPFLR) has been widely adopted by the US dairy farms to convert cattle manure to biogas. However, the microbiome in MPFLR digesters remains unexplored. In this study, the microbiome in a MPFLR digester operated on a mega-dairy farm was examined thrice over a 2 month period. Within 23 days of retention time, 55-70% of total manure solid was digested. Except for a few minor volatile fatty acids (VFAs), total VFA concentration and pH remained similar along the course of the digester and over time. Metagenomic analysis showed that although with some temporal variations, the bacterial community was rather stable spatially in the digester. The methanogenic community was also stable both spatially and temporally in the digester. Among methanogens, genus Methanosaeta dominated in the digester. Quantitative polymerase chain reaction (qPCR) analysis and metagenomic analysis yielded different relative abundance of individual genera of methanogens, especially for Methanobacterium, which was predominant based on qPCR analysis but undetectable by metagenomics. Collectively, the results showed that only small microbial and chemical gradients existed within the digester, and the digestion process occurred similarly throughout the MPFLR digester. The findings of this study may help improve the operation and design of this type of manure digesters.}, } @article {pmid24685216, year = {2014}, author = {El Kaoutari, A and Armougom, F and Raoult, D and Henrissat, B}, title = {[Gut microbiota and digestion of polysaccharides].}, journal = {Medecine sciences : M/S}, volume = {30}, number = {3}, pages = {259-265}, doi = {10.1051/medsci/20143003013}, pmid = {24685216}, issn = {0767-0974}, mesh = {Animals ; Bacteria/metabolism ; Digestion/*physiology ; Fermentation/physiology ; Gastrointestinal Tract/metabolism/*microbiology ; Humans ; Hydrolysis ; Intestinal Mucosa/metabolism ; Intestines/microbiology ; Microbiota/*physiology ; Polysaccharides/*metabolism ; }, abstract = {The distal gut microbiota corresponds to all the microorganisms, essentially bacteria, that reside commonly in the colon. The microbial population is characterized by a large taxonomical diversity, counting approximately a thousand distinct bacterial species for a single individual. The pace of investigations of this microbial system has greatly accelerated these last few years, fuelled by the advent of metagenomics techniques, which do not rely on bacterial cultivation, but utilize high throughput DNA sequencing. In just a few years studies of the intestinal microbiota have become fashionable, albeit with often contradictory results when attempting to correlate changes in microbial composition to diverse pathologies. The article focuses on one of the essential functions of the distal gut microbiota: the digestion of the immense variety of polysaccharides from our diet that enzymes of the host cannot breakdown.}, } @article {pmid24682299, year = {2014}, author = {Lin, X and Tfaily, MM and Green, SJ and Steinweg, JM and Chanton, P and Imvittaya, A and Chanton, JP and Cooper, W and Schadt, C and Kostka, JE}, title = {Microbial metabolic potential for carbon degradation and nutrient (nitrogen and phosphorus) acquisition in an ombrotrophic peatland.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {11}, pages = {3531-3540}, pmid = {24682299}, issn = {1098-5336}, mesh = {Bacteria/classification/*metabolism ; Biota ; Carbon/*metabolism ; Magnetic Resonance Spectroscopy ; Metagenomics ; Minnesota ; Nitrogen/*metabolism ; Organic Chemicals/*metabolism ; Phosphorus/*metabolism ; *Soil Microbiology ; }, abstract = {This study integrated metagenomic and nuclear magnetic resonance (NMR) spectroscopic approaches to investigate microbial metabolic potential for organic matter decomposition and nitrogen (N) and phosphorus (P) acquisition in soils of an ombrotrophic peatland in the Marcell Experimental Forest (MEF), Minnesota, USA. This analysis revealed vertical stratification in key enzymatic pathways and taxa containing these pathways. Metagenomic analyses revealed that genes encoding laccases and dioxygenases, involved in aromatic compound degradation, declined in relative abundance with depth, while the relative abundance of genes encoding metabolism of amino sugars and all four saccharide groups increased with depth in parallel with a 50% reduction in carbohydrate content. Most Cu-oxidases were closely related to genes from Proteobacteria and Acidobacteria, and type 4 laccase-like Cu-oxidase genes were >8 times more abundant than type 3 genes, suggesting an important and overlooked role for type 4 Cu-oxidase in phenolic compound degradation. Genes associated with sulfate reduction and methanogenesis were the most abundant anaerobic respiration genes in these systems, with low levels of detection observed for genes of denitrification and Fe(III) reduction. Fermentation genes increased in relative abundance with depth and were largely affiliated with Syntrophobacter. Methylocystaceae-like small-subunit (SSU) rRNA genes, pmoA, and mmoX genes were more abundant among methanotrophs. Genes encoding N2 fixation, P uptake, and P regulons were significantly enriched in the surface peat and in comparison to other ecosystems, indicating N and P limitation. Persistence of inorganic orthophosphate throughout the peat profile in this P-limiting environment indicates that P may be bound to recalcitrant organic compounds, thus limiting P bioavailability in the subsurface. Comparative metagenomic analysis revealed a high metabolic potential for P transport and starvation, N2 fixation, and oligosaccharide degradation at MEF relative to other wetland and soil environments, consistent with the nutrient-poor and carbohydrate-rich conditions found in this Sphagnum-dominated boreal peatland.}, } @article {pmid24681719, year = {2014}, author = {Costea, PI and Zeller, G and Sunagawa, S and Bork, P}, title = {A fair comparison.}, journal = {Nature methods}, volume = {11}, number = {4}, pages = {359}, pmid = {24681719}, issn = {1548-7105}, mesh = {Animals ; *Genetic Markers ; Humans ; Metagenomics/*methods ; *Microbiota ; RNA, Ribosomal, 16S/*genetics ; }, } @article {pmid24681718, year = {2014}, author = {Paulson, JN and Bravo, HC and Pop, M}, title = {Reply to: "a fair comparison".}, journal = {Nature methods}, volume = {11}, number = {4}, pages = {359-360}, pmid = {24681718}, issn = {1548-7105}, mesh = {Animals ; *Genetic Markers ; Humans ; Metagenomics/*methods ; *Microbiota ; RNA, Ribosomal, 16S/*genetics ; }, } @article {pmid24679105, year = {2014}, author = {Imirzalioglu, C and Sethi, S and Schneider, C and Hain, T and Chakraborty, T and Mayser, P and Domann, E}, title = {Distinct polymicrobial populations in a chronic foot ulcer with implications for diagnostics and anti-infective therapy.}, journal = {BMC research notes}, volume = {7}, number = {}, pages = {196}, pmid = {24679105}, issn = {1756-0500}, mesh = {Anti-Bacterial Agents/therapeutic use ; Chromatography, High Pressure Liquid/methods ; Chronic Disease ; Drug Resistance, Multiple, Bacterial ; Female ; Foot Ulcer/complications/diagnosis/drug therapy/*microbiology ; Gram-Negative Bacterial Infections/complications/diagnosis/drug therapy/*microbiology ; Gram-Positive Bacterial Infections/complications/diagnosis/drug therapy/*microbiology ; Humans ; Microbiota/genetics ; Middle Aged ; Osteomyelitis/complications/diagnosis/drug therapy/*microbiology ; Treatment Failure ; }, abstract = {BACKGROUND: Polymicrobial infections caused by combinations of different bacteria are being detected with an increasing frequency. The evidence of such complex infections is being revealed through the use of novel molecular and culture-independent methods. Considerable progress has been made in the last decade regarding the diagnostic application of such molecular techniques. In particular, 16S rDNA-based sequencing and even metagenomic analyses have been successfully used to study the microbial diversity in ecosystems and human microbiota. Here, we utilized denaturing high-performance liquid chromatography (DHPLC) as a diagnostic tool for identifying different bacterial species in complex clinical samples of a patient with a chronic foot ulcer.

CASE PRESENTATION: A 45-year-old female suffered from a chronic 5x5cm large plantar ulcer located in the posterior calcaneal area with subcutaneous tissue infection and osteomyelitis. The chronic ulcer developed over a period of 8 years. Culture and DHPLC revealed a distinct and location-dependent polymicrobial infection of the ulcer. The analysis of a superficial biopsy revealed a mixture of Staphylococcus aureus, Proteus vulgaris, and Fusobacterium nucleatum, whereas the tissue-deep biopsy harbored a mixture of four different bacterial species, namely Gemella morbillorum, Porphyromonas asaccharolytica, Bacteroides fragilis, and Arcanobacterium haemolyticum.

CONCLUSIONS: This clinical case highlights the difficulties in assessing polymicrobial infections where a mixture of fastidious, rapid and slow growing bacteria as well as anaerobes exists as structured communities within the tissue architecture of chronic wound infections. The diagnosis of this multilayered polymicrobial infection led to a microbe-adapted antibiotic therapy, targeting the polymicrobial nature of this infection in addition to a standard local wound treatment. However, a complete wound closure could not be achieved due to the long-lasting extensive destruction of tissue.}, } @article {pmid24675997, year = {2014}, author = {Kianoush, N and Adler, CJ and Nguyen, KA and Browne, GV and Simonian, M and Hunter, N}, title = {Bacterial profile of dentine caries and the impact of pH on bacterial population diversity.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e92940}, pmid = {24675997}, issn = {1932-6203}, support = {R01 DE015272/DE/NIDCR NIH HHS/United States ; R01 DEO15272-07//PHS HHS/United States ; }, mesh = {*Bacteria ; *Biodiversity ; Computational Biology ; DNA, Bacterial ; Dental Caries/*microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; *Hydrogen-Ion Concentration ; Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Dental caries is caused by the release of organic acids from fermentative bacteria, which results in the dissolution of hydroxyapatite matrices of enamel and dentine. While low environmental pH is proposed to cause a shift in the consortium of oral bacteria, favouring the development of caries, the impact of this variable has been overlooked in microbial population studies. This study aimed to detail the zonal composition of the microbiota associated with carious dentine lesions with reference to pH. We used 454 sequencing of the 16S rRNA gene (V3-V4 region) to compare microbial communities in layers ranging in pH from 4.5-7.8 from 25 teeth with advanced dentine caries. Pyrosequencing of the amplicons yielded 449,762 sequences. Nine phyla, 97 genera and 409 species were identified from the quality-filtered, de-noised and chimera-free sequences. Among the microbiota associated with dentinal caries, the most abundant taxa included Lactobacillus sp., Prevotella sp., Atopobium sp., Olsenella sp. and Actinomyces sp. We found a disparity between microbial communities localised at acidic versus neutral pH strata. Acidic conditions were associated with low diversity microbial populations, with Lactobacillus species including L. fermentum, L. rhamnosus and L. crispatus, being prominent. In comparison, the distinctive species of a more diverse flora associated with neutral pH regions of carious lesions included Alloprevotella tanerrae, Leptothrix sp., Sphingomonas sp. and Streptococcus anginosus. While certain bacteria were affected by the pH gradient, we also found that ∼ 60% of the taxa associated with caries were present across the investigated pH range, representing a substantial core. We demonstrated that some bacterial species implicated in caries progression show selective clustering with respect to pH gradient, providing a basis for specific therapeutic strategies.}, } @article {pmid24672398, year = {2014}, author = {Kumar, G and Lin, CY}, title = {Biogenic hydrogen conversion of de-oiled jatropha waste via anaerobic sequencing batch reactor operation: process performance, microbial insights, and CO2 reduction efficiency.}, journal = {TheScientificWorldJournal}, volume = {2014}, number = {}, pages = {946503}, pmid = {24672398}, issn = {1537-744X}, mesh = {Anaerobiosis ; Animals ; *Biodegradation, Environmental ; Biofuels ; *Bioreactors ; *Fermentation ; Hydrogen/*metabolism ; Jatropha/*metabolism/*microbiology ; Metabolomics ; Metagenome ; Microbiota ; Molecular Sequence Data ; *Refuse Disposal ; }, abstract = {We report the semicontinuous, direct (anaerobic sequencing batch reactor operation) hydrogen fermentation of de-oiled jatropha waste (DJW). The effect of hydraulic retention time (HRT) was studied and results show that the stable and peak hydrogen production rate of 1.48 L/L ∗ d and hydrogen yield of 8.7 mL H2/g volatile solid added were attained when the reactor was operated at HRT 2 days (d) with a DJW concentration of 200 g/L, temperature 55 °C, and pH 6.5. Reduced HRT enhanced the production performance until 1.75 d. Further reduction has lowered the process efficiency in terms of biogas production and hydrogen gas content. The effluent from hydrogen fermentor was utilized for methane fermentation in batch reactors using pig slurry and cow dung as seed sources. The results revealed that pig slurry was a feasible seed source for methane generation. Peak methane production rate of 0.43 L CH4/L ∗ d and methane yield of 20.5 mL CH4/g COD were observed at substrate concentration of 10 g COD/L, temperature 30 °C, and pH 7.0. PCR-DGGE analysis revealed that combination of cellulolytic and fermentative bacteria were present in the hydrogen producing ASBR.}, } @article {pmid24670812, year = {2014}, author = {Hyde, ER and Andrade, F and Vaksman, Z and Parthasarathy, K and Jiang, H and Parthasarathy, DK and Torregrossa, AC and Tribble, G and Kaplan, HB and Petrosino, JF and Bryan, NS}, title = {Metagenomic analysis of nitrate-reducing bacteria in the oral cavity: implications for nitric oxide homeostasis.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e88645}, pmid = {24670812}, issn = {1932-6203}, support = {R01 DE021394/DE/NIDCR NIH HHS/United States ; T32 GM008231/GM/NIGMS NIH HHS/United States ; U54 HG004973/HG/NHGRI NIH HHS/United States ; }, mesh = {Anaerobiosis ; Bacteria/classification/*genetics ; Biodiversity ; Biofilms/growth & development ; *Homeostasis ; Humans ; Metabolic Networks and Pathways/genetics ; Metagenomics/*methods ; Microbial Consortia ; Microbiota/genetics ; Mouth/*microbiology ; Nitrates/*metabolism ; Nitric Oxide/*metabolism ; Nitrites/metabolism ; Oxidation-Reduction ; Principal Component Analysis ; Sequence Analysis, DNA ; Species Specificity ; Time Factors ; }, abstract = {The microbiota of the human lower intestinal tract helps maintain healthy host physiology, for example through nutrient acquisition and bile acid recycling, but specific positive contributions of the oral microbiota to host health are not well established. Nitric oxide (NO) homeostasis is crucial to mammalian physiology. The recently described entero-salivary nitrate-nitrite-nitric oxide pathway has been shown to provide bioactive NO from dietary nitrate sources. Interestingly, this pathway is dependent upon oral nitrate-reducing bacteria, since humans lack this enzyme activity. This pathway appears to represent a newly recognized symbiosis between oral nitrate-reducing bacteria and their human hosts in which the bacteria provide nitrite and nitric oxide from nitrate reduction. Here we measure the nitrate-reducing capacity of tongue-scraping samples from six healthy human volunteers, and analyze metagenomes of the bacterial communities to identify bacteria contributing to nitrate reduction. We identified 14 candidate species, seven of which were not previously believed to contribute to nitrate reduction. We cultivated isolates of four candidate species in single- and mixed-species biofilms, revealing that they have substantial nitrate- and nitrite-reduction capabilities. Colonization by specific oral bacteria may thus contribute to host NO homeostasis by providing nitrite and nitric oxide. Conversely, the lack of specific nitrate-reducing communities may disrupt the nitrate-nitrite-nitric oxide pathway and lead to a state of NO insufficiency. These findings may also provide mechanistic evidence for the oral systemic link. Our results provide a possible new therapeutic target and paradigm for NO restoration in humans by specific oral bacteria.}, } @article {pmid24670254, year = {2014}, author = {Dassi, E and Ballarini, A and Covello, G and , and Quattrone, A and Jousson, O and De Sanctis, V and Bertorelli, R and Denti, MA and Segata, N}, title = {Enhanced microbial diversity in the saliva microbiome induced by short-term probiotic intake revealed by 16S rRNA sequencing on the IonTorrent PGM platform.}, journal = {Journal of biotechnology}, volume = {190}, number = {}, pages = {30-39}, doi = {10.1016/j.jbiotec.2014.03.024}, pmid = {24670254}, issn = {1873-4863}, mesh = {Adult ; Bacteria/classification/genetics ; DNA, Bacterial/*chemistry ; Female ; *High-Throughput Nucleotide Sequencing ; Humans ; Male ; Microbiota/*genetics ; Probiotics/*administration & dosage ; RNA, Ribosomal, 16S/*genetics ; Saliva/*microbiology ; Sequence Analysis, DNA/methods ; }, abstract = {Microbial communities populating several human body habitats are important determinants of human health. Cultivation-free community-wide approaches like bacterial 16S rRNA sequencing recently revolutionized the study of such human-associated microbial diversity, and the continuously decreasing cost/throughput ratio of current sequencing platforms is further enhancing the availability and effectiveness of microbiome research. The IonTorrent PGM platform is among the latest available commercial high-throughput sequencing tools, but it is just starting to be used for 16S rRNA surveys with only episodic assessments of its performance. We present here the first IonTorrent profiling of the human saliva microbiome collected from 12 healthy individuals. In this cohort, a subset of the volunteers was asked to assume a probiotic product, in order to investigate its impact on the composition and the structure of the saliva microbiome. Analysis of the generated dataset suggests the suitability of the IonTorrent platform for 16S rRNA surveys, even though some platform-specific choices are required to optimize the consistency of the obtained bacterial profiles. Interestingly, we found a marked and statistically significant increase of the overall bacterial diversity in the saliva of individuals who received the probiotic product compared to the control group, suggesting a short-term effect of probiotic product administration on oral microbiome composition.}, } @article {pmid24664844, year = {2014}, author = {Gomez-Alvarez, V}, title = {Biofilm-growing bacteria involved in the corrosion of concrete wastewater pipes: protocols for comparative metagenomic analyses.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1147}, number = {}, pages = {323-340}, doi = {10.1007/978-1-4939-0467-9_23}, pmid = {24664844}, issn = {1940-6029}, mesh = {Bacteria/*classification/*genetics ; *Bacterial Physiological Phenomena ; Biofilms/*growth & development ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Metagenomics/methods ; Microbiota ; Wastewater/*microbiology ; *Water Microbiology ; }, abstract = {Advances in high-throughput next-generation sequencing (NGS) technology for direct sequencing of environmental DNA (i.e., shotgun metagenomics) are transforming the field of microbiology. NGS technologies are now regularly being applied in comparative metagenomic studies, which provide the data for functional annotations, taxonomic comparisons, community profile, and metabolic reconstructions. For example, comparative metagenomic analysis of corroded pipes unveiled novel insights on the bacterial populations associated with the sulfur and nitrogen cycle, which may be directly or indirectly implicated in concrete wastewater pipe corrosion. The objective of this chapter is to describe the steps involved in the taxonomic and functional analysis of metagenome datasets from biofilm involved in microbial-induced concrete corrosion (MICC).}, } @article {pmid24657972, year = {2014}, author = {Sergeant, MJ and Constantinidou, C and Cogan, TA and Bedford, MR and Penn, CW and Pallen, MJ}, title = {Extensive microbial and functional diversity within the chicken cecal microbiome.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e91941}, pmid = {24657972}, issn = {1932-6203}, support = {BB/H019340/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Biodiversity ; Cecum/*microbiology ; Chickens/*microbiology ; Hydrogen/metabolism ; *Microbiota ; }, abstract = {Chickens are major source of food and protein worldwide. Feed conversion and the health of chickens relies on the largely unexplored complex microbial community that inhabits the chicken gut, including the ceca. We have carried out deep microbial community profiling of the microbiota in twenty cecal samples via 16S rRNA gene sequences and an in-depth metagenomics analysis of a single cecal microbiota. We recovered 699 phylotypes, over half of which appear to represent previously unknown species. We obtained 648,251 environmental gene tags (EGTs), the majority of which represent new species. These were binned into over two-dozen draft genomes, which included Campylobacter jejuni and Helicobacter pullorum. We found numerous polysaccharide- and oligosaccharide-degrading enzymes encoding within the metagenome, some of which appeared to be part of polysaccharide utilization systems with genetic evidence for the co-ordination of polysaccharide degradation with sugar transport and utilization. The cecal metagenome encodes several fermentation pathways leading to the production of short-chain fatty acids, including some with novel features. We found a dozen uptake hydrogenases encoded in the metagenome and speculate that these provide major hydrogen sinks within this microbial community and might explain the high abundance of several genera within this microbiome, including Campylobacter, Helicobacter and Megamonas.}, } @article {pmid24643867, year = {2014}, author = {Quinn, RA and Lim, YW and Maughan, H and Conrad, D and Rohwer, F and Whiteson, KL}, title = {Biogeochemical forces shape the composition and physiology of polymicrobial communities in the cystic fibrosis lung.}, journal = {mBio}, volume = {5}, number = {2}, pages = {e00956-13}, pmid = {24643867}, issn = {2150-7511}, support = {R01 GM095384/GM/NIGMS NIH HHS/United States ; R01 GM095384-01/GM/NIGMS NIH HHS/United States ; R01GM095384-01S1/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Infections/*microbiology ; *Biota ; Cystic Fibrosis/*complications ; High-Throughput Nucleotide Sequencing ; Humans ; Lung/*microbiology ; Metabolic Networks and Pathways/genetics ; Metagenome ; Sputum/microbiology ; Transcriptome ; }, abstract = {The cystic fibrosis (CF) lung contains thick mucus colonized by opportunistic pathogens which adapt to the CF lung environment over decades. The difficulty associated with sampling airways has impeded a thorough examination of the biochemical microhabitats these pathogens are exposed to. An indirect approach is to study the responses of microbial communities to these microhabitats, facilitated by high-throughput sequencing of microbial DNA and RNA from sputum samples. Microbial metagenomes and metatranscriptomes were sequenced from multiple CF patients, and the reads were assigned taxonomy and function through sequence homology to NCBI and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database hierarchies. For a comparison, saliva microbial metagenomes from the Human Microbiome Project (HMP) were also analyzed. These analyses identified that functions encoded and expressed by CF microbes were significantly enriched for amino acid catabolism, folate biosynthesis, and lipoic acid biosynthesis. The data indicate that the community uses oxidative phosphorylation as a major energy source but that terminal electron acceptors were diverse. Nitrate reduction was the most abundant anaerobic respiratory pathway, and genes for nitrate reductase were largely assigned to Pseudomonas and Rothia. Although many reductive pathways of the nitrogen cycle were present, the cycle was incomplete, because the oxidative pathways were absent. Due to the abundant amino acid catabolism and incomplete nitrogen cycle, the CF microbial community appears to accumulate ammonia. This finding was verified experimentally using a CF bronchiole culture model system. The data also revealed abundant sensing and transport of iron, ammonium, zinc, and other metals along with a low-oxygen environment. This study reveals the core biochemistry and physiology of the CF microbiome. IMPORTANCE The cystic fibrosis (CF) microbial community is complex and adapts to the environmental conditions of the lung over the lifetime of a CF patient. This analysis illustrates the core functions of the CF microbial community in the context of CF lung biochemistry. There are many studies of the metabolism and physiology of individual microbes within the CF lung, but none that collectively analyze data from the whole microbiome. Understanding the core metabolism of microbes that inhabit the CF lung can provide new targets for novel therapies. The fundamental processes that CF pathogens rely on for survival may represent an Achilles heel for this pathogenic community. Novel therapies that are designed to disrupt understudied survival strategies of the CF microbial community may succeed against otherwise untreatable or antibiotic-resistant microbes.}, } @article {pmid24642836, year = {2014}, author = {Henrich, B and Rumming, M and Sczyrba, A and Velleuer, E and Dietrich, R and Gerlach, W and Gombert, M and Rahn, S and Stoye, J and Borkhardt, A and Fischer, U}, title = {Mycoplasma salivarium as a dominant coloniser of Fanconi anaemia associated oral carcinoma.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e92297}, pmid = {24642836}, issn = {1932-6203}, mesh = {Adult ; Carcinoma, Squamous Cell/*microbiology ; Case-Control Studies ; Fanconi Anemia/*complications ; Genes, Bacterial ; Humans ; Male ; Microbiota/genetics ; Molecular Typing ; Mouth/microbiology ; Mycoplasma Infections/*microbiology ; Mycoplasma salivarium/*genetics ; RNA, Ribosomal, 16S/genetics ; Retrospective Studies ; Tongue Neoplasms/*microbiology ; }, abstract = {Mycoplasma salivarium belongs to the class of the smallest self-replicating Tenericutes and is predominantly found in the oral cavity of humans. In general it is considered as a non-pathogenic commensal. However, some reports point to an association with human diseases. M. salivarium was found e.g. as causative agent of a submasseteric abscess, in necrotic dental pulp, in brain abscess and clogged biliary stent. Here we describe the detection of M. salivarium on the surface of a squamous cell carcinoma of the tongue of a patient with Fanconi anaemia (FA). FA is an inherited bone marrow failure syndrome based on defective DNA-repair that increases the risk of carcinomas especially oral squamous cell carcinoma. Employing high coverage, massive parallel Roche/454-next-generation-sequencing of 16S rRNA gene amplicons we analysed the oral microbiome of this FA patient in comparison to that of an FA patient with a benign leukoplakia and five healthy individuals. The microbiota of the FA patient with leukoplakia correlated well with that of the healthy controls. A dominance of Streptococcus, Veillonella and Neisseria species was typically observed. In contrast, the microbiome of the cancer bearing FA patient was dominated by Pseudomonas aeruginosa at the healthy sites, which changed to a predominance of 98% M. salivarium on the tumour surface. Quantification of the mycoplasma load in five healthy, two tumour- and two leukoplakia-FA patients by TaqMan-PCR confirmed the prevalence of M. salivarium at the tumour sites. These new findings suggest that this mycoplasma species with its reduced coding capacity found ideal breeding grounds at the tumour sites. Interestingly, the oral cavity of all FA patients and especially samples at the tumour sites were in addition positive for Candida albicans. It remains to be elucidated in further studies whether M. salivarium can be used as a predictive biomarker for tumour development in these patients.}, } @article {pmid24642489, year = {2014}, author = {Xu, P and Gunsolley, J}, title = {Application of metagenomics in understanding oral health and disease.}, journal = {Virulence}, volume = {5}, number = {3}, pages = {424-432}, pmid = {24642489}, issn = {2150-5608}, support = {R01 DE018138/DE/NIDCR NIH HHS/United States ; R01 DE023078/DE/NIDCR NIH HHS/United States ; R01DE018138/DE/NIDCR NIH HHS/United States ; R01DE023078/DE/NIDCR NIH HHS/United States ; }, mesh = {Host-Pathogen Interactions ; Humans ; *Metagenomics ; *Microbiota ; Mouth Diseases/*microbiology ; *Oral Health ; Symbiosis ; }, abstract = {Oral diseases including periodontal disease and caries are some of the most prevalent infectious diseases in humans. Different microbial species cohabitate and form a polymicrobial biofilm called dental plaque in the oral cavity. Metagenomics using next generation sequencing technologies has produced bacterial profiles and genomic profiles to study the relationships between microbial diversity, genetic variation, and oral diseases. Several oral metagenomic studies have examined the oral microbiome of periodontal disease and caries. Gene annotations in these studies support the association of specific genes or metabolic pathways with oral health and with specific diseases. The roles of pathogenic species and functions of specific genes in oral disease development have been recognized by metagenomic analysis. A model is proposed in which three levels of interactions occur in the oral microbiome that determines oral health or disease.}, } @article {pmid24637798, year = {2014}, author = {Hu, Y and Yang, X and Lu, N and Zhu, B}, title = {The abundance of antibiotic resistance genes in human guts has correlation to the consumption of antibiotics in animal.}, journal = {Gut microbes}, volume = {5}, number = {2}, pages = {245-249}, pmid = {24637798}, issn = {1949-0984}, mesh = {Animals ; Anti-Bacterial Agents ; Drug Resistance, Bacterial/*physiology ; Gastrointestinal Tract/*microbiology ; Humans ; Microbiota/physiology ; Tetracycline ; }, abstract = {Increasing evidence has accumulated to support that the human gut is a reservoir for antibiotic resistance genes. We previously identified more than 1000 genes displaying high similarity with known antibiotic resistance genes in the human gut gene set generated from the Chinese, Danish, and Spanish populations. Here, first, we add our new understanding of antibiotic resistance genes in the US and the Japanese populations; next, we describe the structure of a vancomycin-resistant operon in a Danish sample; and finally, we provide discussions on the correlation of the abundance of resistance genes in human gut with the antibiotic consumption in human medicine and in animal husbandry. These results, combined with those we published previously, provide comprehensive insights into the antibiotic resistance genes in the human gut microbiota at a population level.}, } @article {pmid24637600, year = {2014}, author = {Levy, R and Borenstein, E}, title = {Metagenomic systems biology and metabolic modeling of the human microbiome: from species composition to community assembly rules.}, journal = {Gut microbes}, volume = {5}, number = {2}, pages = {265-270}, pmid = {24637600}, issn = {1949-0984}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; DP2 AT007802-01/AT/NCCIH NIH HHS/United States ; }, mesh = {Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Systems Biology/*methods ; }, abstract = {The human microbiome is a key contributor to health and development. Yet little is known about the ecological forces that are at play in defining the composition of such host-associated communities. Metagenomics-based studies have uncovered clear patterns of community structure but are often incapable of distinguishing alternative structuring paradigms. In a recent study, we integrated metagenomic analysis with a systems biology approach, using a reverse ecology framework to model numerous human microbiota species and to infer metabolic interactions between species. Comparing predicted interactions with species composition data revealed that the assembly of the human microbiome is dominated at the community level by habitat filtering. Furthermore, we demonstrated that this habitat filtering cannot be accounted for by known host phenotypes or by the metabolic versatility of the various species. Here we provide a summary of our findings and offer a brief perspective on related studies and on future approaches utilizing this metagenomic systems biology framework.}, } @article {pmid24636808, year = {2014}, author = {del Campo, R and Garriga, M and Pérez-Aragón, A and Guallarte, P and Lamas, A and Máiz, L and Bayón, C and Roy, G and Cantón, R and Zamora, J and Baquero, F and Suárez, L}, title = {Improvement of digestive health and reduction in proteobacterial populations in the gut microbiota of cystic fibrosis patients using a Lactobacillus reuteri probiotic preparation: a double blind prospective study.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {13}, number = {6}, pages = {716-722}, doi = {10.1016/j.jcf.2014.02.007}, pmid = {24636808}, issn = {1873-5010}, mesh = {Adolescent ; Adult ; Child ; Cross-Over Studies ; Cystic Fibrosis/*complications/*microbiology ; Double-Blind Method ; Feces/microbiology ; Female ; Humans ; Intestines/*microbiology ; *Limosilactobacillus reuteri ; Male ; Metagenomics ; Microbiota ; Probiotics/*therapeutic use ; Prospective Studies ; Proteobacteria/isolation & purification ; Young Adult ; }, abstract = {BACKGROUND: Although scientific knowledge about the benefits of probiotic use in cystis fibrosis (CF) is scarce, their expectative is promising. The aim of this work was to analyze the effect of a Lactobacillus reuteri probiotic preparation versus placebo in CF patients.

METHODS: A prospective, double blind, crossover and with placebo study was carried out in 30 CF patients from two Spanish hospitals. Patients were randomized in Group A (6 months of probiotic followed by 6 months of placebo) and Group B (6 months of placebo followed by 6 months of probiotic). GIQLI (gastrointestinal) and SF-12 (general) health tests were performed after probiotic and placebo intakes. Fat absorption coefficient, calprotectin, and inflammatory interleukin quantification were determined in fecal samples. Total fecal DNA was obtained and metagenomic 454-pyrosequencing was applied to analyze the microbiome composition. STATA v12 MP software was used for statistical analyses.

RESULTS: Statistically significant improvement in the gastrointestinal health and decrease of the calprotectin levels were demonstrated in patients after probiotic exposure, in comparison with placebo. All CF subjects reported good tolerance to L. reuteri without secondary effects. Metagenomic analysis showed an important dysbiosis in CF gut microbiota associated with a high concentration of Proteobacteria. Probiotic intake was followed by a reduction in the total bacterial density, mostly due to a considerable reduction in the γ-Proteobacteria phylum; and an important increase of the microbial diversity with a higher representation of Firmicutes.

CONCLUSIONS: Probiotics might ameliorate the dysbiosis of CF gut microbiota, characterized by a high density of Proteobacterial organisms. L. reuteri significantly decrease intestinal inflammation and increase digestive comfort.}, } @article {pmid24634890, year = {2014}, author = {Vayssier-Taussat, M and Albina, E and Citti, C and Cosson, JF and Jacques, MA and Lebrun, MH and Le Loir, Y and Ogliastro, M and Petit, MA and Roumagnac, P and Candresse, T}, title = {Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {4}, number = {}, pages = {29}, pmid = {24634890}, issn = {2235-2988}, mesh = {Animals ; *Host-Pathogen Interactions ; Humans ; *Microbiota ; Virulence Factors/*metabolism ; }, abstract = {The concept of pathogenesis has evolved considerably over recent years, and the scenario "a microbe + virulence factors = disease" is probably far from reality in a number of cases. Actual pathogens have extremely broad biological diversity and are found in all major groups of microorganisms (viruses, bacteria, fungi, protozoa…). Their pathogenicity results from strong and often highly specific interactions they have with either their microbial environment, hosts and/or arthropod vectors. In this review, we explore the contribution of metagenomic approaches toward understanding pathogens within the context of microbial communities. With this broader view, we discussed the concept of "pathobiome" and the research questions that this raises.}, } @article {pmid24634228, year = {2014}, author = {Kodama, CS and Cuadros-Orellana, S and Bandeira, CH and Graças, DA and Santos, AS and Silva, A}, title = {Use of PCR-DHPLC with fluorescence detection for the characterization of the bacterial diversity during cassava (Manihot esculenta Crantz) fermentation.}, journal = {Genetics and molecular research : GMR}, volume = {13}, number = {1}, pages = {1304-1313}, doi = {10.4238/2014.February.28.2}, pmid = {24634228}, issn = {1676-5680}, mesh = {Bacteria/*classification/genetics/*isolation & purification ; Chromatography, High Pressure Liquid ; Cloning, Molecular ; Colony Count, Microbial ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Fermentation ; Manihot/classification/*microbiology ; *Metagenome ; Microbiota ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Denaturing high-performance liquid chromatography (DHPLC) has been described as a suitable method to study DNA polymorphisms. Here, cassava (Manihot esculenta Crantz) fermentation liquor was examined using DHPLC analysis to characterize the bacterial diversity during the fermentation process. GC-clamped amplicons corresponding to a variable region of the bacterial community 16S rDNA were synthesized using polymerase chain reaction (PCR) and then resolved on a base-composition basis using preparative DHPLC. Eluate fractions were collected at random and used as a source of whole community DNA that could be used to determine the bacterial diversity. As a first approach, GC-clamps were removed from the eluted DNA fragments using PCR to avoid the possible bias these clamps could cause during the construction of clone libraries. As a second approach, a clone library of each eluate sample was constructed, preserving the GC-clamps of the DNA fragments. The first approach generated 132 bacterial rDNA sequences with an average size of 200 bp, 45% of which had similarity to unculturable or non-classified bacteria. The second approach produced 194 sequences identified as Proteobacteria (48%), uncultured or non-classified environmental bacteria (40%) and Firmicutes (12%). We detected a remarkably greater bacterial diversity using the first approach than the second approach. The DHPLC-PCR method allowed for the fast and non-laborious detection of a vast bacterial diversity that was associated with cassava fermentation, and we conclude that it is a promising alternative for the characterization of the overall microbial diversity in complex samples.}, } @article {pmid24633414, year = {2014}, author = {Yang, Y and Yu, K and Xia, Y and Lau, FT and Tang, DT and Fung, WC and Fang, HH and Zhang, T}, title = {Metagenomic analysis of sludge from full-scale anaerobic digesters operated in municipal wastewater treatment plants.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {12}, pages = {5709-5718}, doi = {10.1007/s00253-014-5648-0}, pmid = {24633414}, issn = {1432-0614}, mesh = {Anaerobiosis ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biota ; Cluster Analysis ; Computational Biology ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Humans ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; *Water Purification ; }, abstract = {This study applied Illumina high-throughput sequencing to explore the microbial communities and functions in anaerobic digestion sludge (ADS) from two wastewater treatment plants based on a metagenomic view. Taxonomic analysis using SILVA SSU database indicated that Proteobacteria (9.52-13.50 %), Bacteroidetes (7.18 %-10.65 %) and Firmicutes (7.53 %-9.46 %) were the most abundant phyla in the ADS. Differences of microbial communities between the two types of ADS were identified. Genera of Methanosaeta and Methanosarcina were the major methanogens. Functional analysis by SEED subsystems showed that the basic metabolic functions of metagenomes in the four ADS samples had no significant difference among them, but they were different from other microbial communities from activated sludge, human faeces, ocean and soil. Abundances of genes in methanogenesis pathway were also quantified using a methanogenesis genes database extracted from KEGG. Results showed that acetotrophic was the major methanogenic pathway in the anaerobic sludge digestion.}, } @article {pmid24633337, year = {2014}, author = {Ju, F and Zhang, T}, title = {Novel microbial populations in ambient and mesophilic biogas-producing and phenol-degrading consortia unraveled by high-throughput sequencing.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {235-246}, pmid = {24633337}, issn = {1432-184X}, mesh = {Archaea/*classification/genetics/growth & development ; Bacteria/*classification/genetics/growth & development ; Biofuels/microbiology ; Bioreactors/microbiology ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Metagenome ; Methane/*biosynthesis ; *Microbial Consortia ; Phenols/*metabolism ; Sequence Analysis, DNA ; }, abstract = {Methanogenesis from wastewater-borne organics and organic solid wastes (e.g., food residues) can be severely suppressed by the presence of toxic phenols. In this work, ambient (20 °C) and mesophilic (37 °C) methane-producing and phenol-degrading consortia were enriched and characterized using high-throughput sequencing (HTS). 454 Pyrosequencing indicated novel W22 (25.0 % of bacterial sequences) in the WWE1 and Sulfurovum-resembled species (32.0 %) in the family Campylobacterales were the most abundant in mesophilic and ambient reactors, respectively, which challenges previous knowledge that Syntrophorhabdus was the most predominant. Previous findings may underestimate bacterial diversity and low-abundance bacteria, but overestimate abundance of Syntrophorhabdus. Illumina HTS revealed that archaeal populations were doubled in ambient reactor and tripled in mesophilic reactor, respectively, compared to the ∼4.9 % (of the bacteria and archaea sequences) in the seed sludge. Moreover, unlike the dominance of Methanosarcina in seed sludge, acetotrophic Methanosaeta predominated both (71.4-76.5 % of archaeal sequences) ambient and mesophilic enrichments. Noteworthy, this study, for the first time, discovered the co-occurrence of green sulfur bacteria Chlorobia, sulfur-reducing Desulfovibrio, and Sulfurovum-resembling species under ambient condition, which could presumably establish mutualistic relationships to compete with syntrophic bacteria and methanogens, leading to the deterioration of methanogenic activity. Taken together, this HTS-based study unravels the high microbial diversity and complicated bacterial interactions within the biogas-producing and phenol-degrading bioreactors, and the identification of novel bacterial species and dominant methanogens involved in the phenol degradation provides novel insights into the operation of full-scale bioreactors for maximizing biogas generation.}, } @article {pmid24632729, year = {2014}, author = {Howe, AC and Jansson, JK and Malfatti, SA and Tringe, SG and Tiedje, JM and Brown, CT}, title = {Tackling soil diversity with the assembly of large, complex metagenomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {13}, pages = {4904-4909}, pmid = {24632729}, issn = {1091-6490}, support = {R01 HG007513/HG/NHGRI NIH HHS/United States ; }, mesh = {*Biodiversity ; Gastrointestinal Tract/microbiology ; Humans ; Iowa ; Metagenome/*genetics ; *Soil ; *Soil Microbiology ; Species Specificity ; Zea mays/genetics ; }, abstract = {The large volumes of sequencing data required to sample deeply the microbial communities of complex environments pose new challenges to sequence analysis. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires substantial computational resources. We combine two preassembly filtering approaches--digital normalization and partitioning--to generate previously intractable large metagenome assemblies. Using a human-gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes totaling 398 billion bp (equivalent to 88,000 Escherichia coli genomes) from matched Iowa corn and native prairie soils. The resulting assembled contigs could be used to identify molecular interactions and reaction networks of known metabolic pathways using the Kyoto Encyclopedia of Genes and Genomes Orthology database. Nonetheless, more than 60% of predicted proteins in assemblies could not be annotated against known databases. Many of these unknown proteins were abundant in both corn and prairie soils, highlighting the benefits of assembly for the discovery and characterization of novelty in soil biodiversity. Moreover, 80% of the sequencing data could not be assembled because of low coverage, suggesting that considerably more sequencing data are needed to characterize the functional content of soil.}, } @article {pmid24630527, year = {2014}, author = {Shapiro, BJ and Polz, MF}, title = {Ordering microbial diversity into ecologically and genetically cohesive units.}, journal = {Trends in microbiology}, volume = {22}, number = {5}, pages = {235-247}, pmid = {24630527}, issn = {1878-4380}, support = {P30 ES002109/ES/NIEHS NIH HHS/United States ; P30-ES002109/ES/NIEHS NIH HHS/United States ; }, mesh = {*Biota ; Gene Transfer, Horizontal ; *Genetic Variation ; Mutation ; Phylogeography ; Recombination, Genetic ; Selection, Genetic ; }, abstract = {We propose that microbial diversity must be viewed in light of gene flow and selection, which define units of genetic similarity, and of phenotype and ecological function, respectively. We discuss to what extent ecological and genetic units overlap to form cohesive populations in the wild, based on recent evolutionary modeling and on evidence from some of the first microbial populations studied with genomics. These show that if recombination is frequent and selection moderate, ecologically adaptive mutations or genes can spread within populations independently of their original genomic background (gene-specific sweeps). Alternatively, if the effect of recombination is smaller than selection, genome-wide selective sweeps should occur. In both cases, however, distinct units of overlapping ecological and genotypic similarity will form if microgeographic separation, likely involving ecological tradeoffs, induces barriers to gene flow. These predictions are supported by (meta)genomic data, which suggest that a 'reverse ecology' approach, in which genomic and gene flow information is used to make predictions about the nature of ecological units, is a powerful approach to ordering microbial diversity.}, } @article {pmid24629524, year = {2014}, author = {Tuan, NN and Chang, YC and Yu, CP and Huang, SL}, title = {Multiple approaches to characterize the microbial community in a thermophilic anaerobic digester running on swine manure: a case study.}, journal = {Microbiological research}, volume = {169}, number = {9-10}, pages = {717-724}, doi = {10.1016/j.micres.2014.02.003}, pmid = {24629524}, issn = {1618-0623}, mesh = {Anaerobiosis ; Animals ; Archaea/*classification/*metabolism ; Bacteria/*classification/*metabolism ; *Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; Hot Temperature ; Manure/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Swine ; }, abstract = {In this study, the first survey of microbial community in thermophilic anaerobic digester using swine manure as sole feedstock was performed by multiple approaches including denaturing gradient gel electrophoresis (DGGE), clone library and pyrosequencing techniques. The integrated analysis of 21 DGGE bands, 126 clones and 8506 pyrosequencing read sequences revealed that Clostridia from the phylum Firmicutes account for the most dominant Bacteria. In addition, our analysis also identified additional taxa that were missed by the previous researches, including members of the bacterial phyla Synergistetes, Planctomycetes, Armatimonadetes, Chloroflexi and Nitrospira which might also play a role in thermophilic anaerobic digester. Most archaeal 16S rRNA sequences could be assigned to the order Methanobacteriales instead of Methanomicrobiales comparing to previous studies. In addition, this study reported that the member of Methanothermobacter genus was firstly found in thermophilic anaerobic digester.}, } @article {pmid24629344, year = {2014}, author = {Gevers, D and Kugathasan, S and Denson, LA and Vázquez-Baeza, Y and Van Treuren, W and Ren, B and Schwager, E and Knights, D and Song, SJ and Yassour, M and Morgan, XC and Kostic, AD and Luo, C and González, A and McDonald, D and Haberman, Y and Walters, T and Baker, S and Rosh, J and Stephens, M and Heyman, M and Markowitz, J and Baldassano, R and Griffiths, A and Sylvester, F and Mack, D and Kim, S and Crandall, W and Hyams, J and Huttenhower, C and Knight, R and Xavier, RJ}, title = {The treatment-naive microbiome in new-onset Crohn's disease.}, journal = {Cell host & microbe}, volume = {15}, number = {3}, pages = {382-392}, pmid = {24629344}, issn = {1934-6069}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 DK092405/DK/NIDDK NIH HHS/United States ; R01DK092405/DK/NIDDK NIH HHS/United States ; T32 GM074897/GM/NIGMS NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; R01 HG005969/HG/NHGRI NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; R35 CA197449/CA/NCI NIH HHS/United States ; }, mesh = {Adolescent ; Bacteria/*classification/isolation & purification ; Child ; Child, Preschool ; Cohort Studies ; Crohn Disease/*complications/*microbiology ; *Dysbiosis ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenome ; *Microbiota ; }, abstract = {Inflammatory bowel diseases (IBDs), including Crohn's disease (CD), are genetically linked to host pathways that implicate an underlying role for aberrant immune responses to intestinal microbiota. However, patterns of gut microbiome dysbiosis in IBD patients are inconsistent among published studies. Using samples from multiple gastrointestinal locations collected prior to treatment in new-onset cases, we studied the microbiome in the largest pediatric CD cohort to date. An axis defined by an increased abundance in bacteria which include Enterobacteriaceae, Pasteurellacaea, Veillonellaceae, and Fusobacteriaceae, and decreased abundance in Erysipelotrichales, Bacteroidales, and Clostridiales, correlates strongly with disease status. Microbiome comparison between CD patients with and without antibiotic exposure indicates that antibiotic use amplifies the microbial dysbiosis associated with CD. Comparing the microbial signatures between the ileum, the rectum, and fecal samples indicates that at this early stage of disease, assessing the rectal mucosal-associated microbiome offers unique potential for convenient and early diagnosis of CD.}, } @article {pmid24628983, year = {2014}, author = {Gogleva, AA and Gelfand, MS and Artamonova, II}, title = {Comparative analysis of CRISPR cassettes from the human gut metagenomic contigs.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {202}, pmid = {24628983}, issn = {1471-2164}, mesh = {Amino Acid Sequence ; Bacteriophages/genetics ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Computational Biology/methods ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; *Metagenomics ; *Microbiota ; Molecular Sequence Data ; Sequence Alignment ; Viral Proteins/chemistry/genetics ; }, abstract = {BACKGROUND: CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a prokaryotic adaptive defence system that provides resistance against alien replicons such as viruses and plasmids. Spacers in a CRISPR cassette confer immunity against viruses and plasmids containing regions complementary to the spacers and hence they retain a footprint of interactions between prokaryotes and their viruses in individual strains and ecosystems. The human gut is a rich habitat populated by numerous microorganisms, but a large fraction of these are unculturable and little is known about them in general and their CRISPR systems in particular.

RESULTS: We used human gut metagenomic data from three open projects in order to characterize the composition and dynamics of CRISPR cassettes in the human-associated microbiota. Applying available CRISPR-identification algorithms and a previously designed filtering procedure to the assembled human gut metagenomic contigs, we found 388 CRISPR cassettes, 373 of which had repeats not observed previously in complete genomes or other datasets. Only 171 of 3,545 identified spacers were coupled with protospacers from the human gut metagenomic contigs. The number of matches to GenBank sequences was negligible, providing protospacers for 26 spacers.Reconstruction of CRISPR cassettes allowed us to track the dynamics of spacer content. In agreement with other published observations we show that spacers shared by different cassettes (and hence likely older ones) tend to the trailer ends, whereas spacers with matches in the metagenomes are distributed unevenly across cassettes, demonstrating a preference to form clusters closer to the active end of a CRISPR cassette, adjacent to the leader, and hence suggesting dynamical interactions between prokaryotes and viruses in the human gut. Remarkably, spacers match protospacers in the metagenome of the same individual with frequency comparable to a random control, but may match protospacers from metagenomes of other individuals.

CONCLUSIONS: The analysis of assembled contigs is complementary to the approach based on the analysis of original reads and hence provides additional data about composition and evolution of CRISPR cassettes, revealing the dynamics of CRISPR-phage interactions in metagenomes.}, } @article {pmid24628935, year = {2014}, author = {Russell, JA and Dubilier, N and Rudgers, JA}, title = {Nature's microbiome: introduction.}, journal = {Molecular ecology}, volume = {23}, number = {6}, pages = {1225-1237}, doi = {10.1111/mec.12676}, pmid = {24628935}, issn = {1365-294X}, mesh = {Animals ; Biodiversity ; Biological Evolution ; Environment ; Metagenome ; Metagenomics ; *Microbiota ; *Symbiosis ; }, } @article {pmid24618913, year = {2014}, author = {Davenport, ER and Mizrahi-Man, O and Michelini, K and Barreiro, LB and Ober, C and Gilad, Y}, title = {Seasonal variation in human gut microbiome composition.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e90731}, pmid = {24618913}, issn = {1932-6203}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; R01 HL085197/HL/NHLBI NIH HHS/United States ; R01 HG006123/HG/NHGRI NIH HHS/United States ; P30-DK42086/DK/NIDDK NIH HHS/United States ; HG006123/HG/NHGRI NIH HHS/United States ; HL085197/HL/NHLBI NIH HHS/United States ; }, mesh = {Age Factors ; Biodiversity ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; *Metagenome ; *Microbiota ; *Seasons ; }, abstract = {The composition of the human gut microbiome is influenced by many environmental factors. Diet is thought to be one of the most important determinants, though we have limited understanding of the extent to which dietary fluctuations alter variation in the gut microbiome between individuals. In this study, we examined variation in gut microbiome composition between winter and summer over the course of one year in 60 members of a founder population, the Hutterites. Because of their communal lifestyle, Hutterite diets are similar across individuals and remarkably stable throughout the year, with the exception that fresh produce is primarily served during the summer and autumn months. Our data indicate that despite overall gut microbiome stability within individuals over time, there are consistent and significant population-wide shifts in microbiome composition across seasons. We found seasonal differences in both (i) the abundance of particular taxa (false discovery rate <0.05), including highly abundant phyla Bacteroidetes and Firmicutes, and (ii) overall gut microbiome diversity (by Shannon diversity; P = 0.001). It is likely that the dietary fluctuations between seasons with respect to produce availability explain, at least in part, these differences in microbiome composition. For example, high levels of produce containing complex carbohydrates consumed during the summer months might explain increased abundance of Bacteroidetes, which contain complex carbohydrate digesters, and decreased levels of Actinobacteria, which have been negatively correlated to fiber content in food questionnaires. Our observations demonstrate the plastic nature of the human gut microbiome in response to variation in diet.}, } @article {pmid24618773, year = {2014}, author = {Montalvo, NF and Davis, J and Vicente, J and Pittiglio, R and Ravel, J and Hill, RT}, title = {Integration of culture-based and molecular analysis of a complex sponge-associated bacterial community.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e90517}, pmid = {24618773}, issn = {1932-6203}, mesh = {Animals ; Bacteria/*classification/*genetics/isolation & purification ; Biodiversity ; *Metagenome ; *Microbiota ; Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {The bacterial communities of sponges have been studied using molecular techniques as well as culture-based techniques, but the communities described by these two methods are remarkably distinct. Culture-based methods describe communities dominated by Proteobacteria, and Actinomycetes while molecular methods describe communities dominated by predominantly uncultivated groups such as the Chloroflexi, Acidobacteria, and Acidimicrobidae. In this study, we used a wide range of culture media to increase the diversity of cultivable bacteria from the closely related giant barrel sponges, Xestospongia muta collected from the Florida Keys, Atlantic Ocean and Xestospongia testudinaria, collected from Indonesia, Pacific Ocean. Over 400 pure cultures were isolated and identified from X. muta and X. testudinaria and over 90 bacterial species were represented. Over 16,000 pyrosequences were analyzed and assigned to 976 OTUs. We employed both cultured-based methods and pyrosequencing to look for patterns of overlap between the culturable and molecular communities. Only one OTU was found in both the molecular and culturable communities, revealing limitations inherent in both approaches.}, } @article {pmid24618772, year = {2014}, author = {Lu, N and Hu, Y and Zhu, L and Yang, X and Yin, Y and Lei, F and Zhu, Y and Du, Q and Wang, X and Meng, Z and Zhu, B}, title = {DNA microarray analysis reveals that antibiotic resistance-gene diversity in human gut microbiota is age related.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {4302}, pmid = {24618772}, issn = {2045-2322}, mesh = {Adult ; Age Factors ; Child ; Child, Preschool ; DNA, Bacterial/classification/*genetics ; Drug Resistance, Microbial/*genetics ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Genetic Variation ; Humans ; Male ; *Metagenome ; Microarray Analysis ; Microbiota/drug effects/*genetics ; Multigene Family ; Oligonucleotide Array Sequence Analysis ; *Phylogeny ; }, abstract = {The human gut is a reservoir for antibiotic resistance genes. In this report, we used a DNA microarray chip covering 369 resistance types to investigate the relationship between antibiotic resistance-gene diversity and human age. Metagenomic DNA from fecal samples from 124 healthy volunteers of four different age groups (pre-school-aged children (CH), school-aged children (SC), high school students (HSS) and adults (AD)) were hybridized to the microarray chip. The results showed that 80 different gene types were recovered from the gut microbiota of the 124 individuals: 25 from CH, 37 from SC, 58 from HSS and 72 from AD. Further analysis indicated that the antibiotic resistance genes in the CH, SC and AD groups clustered independently, whereas the gene types in the HSS group were more divergent. Our results indicated that antibiotic resistance genes in the human gut microbiota accumulate from childhood to adulthood and become more complex with age.}, } @article {pmid24618403, year = {2014}, author = {Shafquat, A and Joice, R and Simmons, SL and Huttenhower, C}, title = {Functional and phylogenetic assembly of microbial communities in the human microbiome.}, journal = {Trends in microbiology}, volume = {22}, number = {5}, pages = {261-266}, pmid = {24618403}, issn = {1878-4380}, support = {R01 HG005969/HG/NHGRI NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; R01HG005969/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; Microbiota/*physiology ; *Phylogeny ; }, abstract = {Microbial communities associated with the human body, that is, the human microbiome, are complex ecologies critical for normal development and health. The taxonomic and phylogenetic composition of these communities tends to significantly differ among individuals, precluding the definition of a simple, shared set of 'core' microbes. Here, we review recent evidence and ecological theory supporting the assembly of host-associated microbial communities in terms of functional traits rather than specific organisms. That is, distinct microbial species may be responsible for specific host-associated functions and phenotypes in distinct hosts. We discuss how ecological processes (selective and stochastic forces) governing the assembly of metazoan communities can be adapted to describe microbial ecologies in host-associated environments, resulting in both niche-specific and 'core' metabolic and other pathways maintained throughout the human microbiome. The extent to which phylogeny and functional traits are linked in host-associated microbes, as opposed to unlinked by mechanisms, such as lateral transfer, remains to be determined. However, the definition of these functional assembly rules within microbial communities using controlled model systems and integrative 'omics' represents a fruitful opportunity for molecular systems ecology.}, } @article {pmid24614401, year = {2014}, author = {Zhao, J and Murray, S and Lipuma, JJ}, title = {Modeling the impact of antibiotic exposure on human microbiota.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {4345}, pmid = {24614401}, issn = {2045-2322}, support = {RC1 HL100809/HL/NHLBI NIH HHS/United States ; UL1 RR024986/RR/NCRR NIH HHS/United States ; UL1RR024986/RR/NCRR NIH HHS/United States ; 1RC1HL100809-01/HL/NHLBI NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Anti-Bacterial Agents/*therapeutic use ; Biodiversity ; Cystic Fibrosis/*drug therapy/genetics/microbiology ; Cystic Fibrosis Transmembrane Conductance Regulator/genetics ; DNA, Bacterial/classification/*genetics/isolation & purification ; Dose-Response Relationship, Drug ; Drug Administration Routes ; Drug Administration Schedule ; Female ; Humans ; Linear Models ; Lung/*drug effects/microbiology ; Male ; Metagenome/*drug effects ; Microbiota/*drug effects/genetics ; Multivariate Analysis ; Mutation ; Sex Factors ; Sputum/microbiology ; }, abstract = {Human-associated microbial communities play important roles in health and disease. Antibiotic administration is arguably one of the most important modifiable determinants of the composition of the human microbiota. However, quantitatively modeling antibiotic use to account for its impact on microbial community dynamics presents a challenge. We used antibiotic therapy of chronic lung infection in persons with cystic fibrosis as a model system to assess the influence of key variables of therapy on measures of microbial community perturbation. We constructed multivariate linear mixed models with bacterial community diversity as the outcome measure and various scales of antibiotic weighting as predictors, while controlling for other variables. Antibiotic weighting consisted of three components: (i) dosing duration; (ii) timing of administration relative to sample collection; and (iii) antibiotic type and route of administration. Antibiotic weighting based on total dose and proximity to the time of sampling was most predictive of bacterial community change. Using this model to control for antibiotic use enabled the identification of other significant independent predictors of microbial community diversity such as dominant taxon, disease stage, and gender. Quantitative modeling of antibiotic use is critical in understanding the relationships between human microbiota and disease treatment and progression.}, } @article {pmid24612332, year = {2014}, author = {Wang, ZK and Yang, YS and Stefka, AT and Sun, G and Peng, LH}, title = {Review article: fungal microbiota and digestive diseases.}, journal = {Alimentary pharmacology & therapeutics}, volume = {39}, number = {8}, pages = {751-766}, doi = {10.1111/apt.12665}, pmid = {24612332}, issn = {1365-2036}, mesh = {Bacteria/isolation & purification ; Feces/microbiology ; Fungi/isolation & purification ; Gastrointestinal Diseases/*microbiology/physiopathology ; Humans ; Inflammation/*microbiology/physiopathology ; Inflammatory Bowel Diseases/*microbiology/physiopathology ; Microbiota ; }, abstract = {BACKGROUND: The role of the fungal microbiota in digestive diseases is poorly defined, but is becoming better understood due to advances in metagenomics.

AIM: To review the gastrointestinal fungal microbiota and its relationship with digestive diseases.

METHODS: Search of the literature using PubMed and MEDLINE databases. Subject headings including 'fungal-bacterial interactions', 'mycotoxins', 'immunity to fungi', 'fungal infection', 'fungal microbiota', 'mycobiome' and 'digestive diseases' were used.

RESULTS: The fungal microbiota is an integral part of the gastrointestinal microecosystem with up to 10(6) microorganisms per gram of faeces. Next-generation sequencing of the fungal 18S rRNA gene has allowed better characterisation of the gastrointestinal mycobiome. Numerous interactions between fungi and bacteria and the complex immune response to gastrointestinal commensal or pathogenic fungi all impact on the pathophysiology of inflammatory bowel disease and other gastrointestinal inflammatory entities such as peptic ulcers. Mycotoxins generated as fungal metabolites contribute to disturbances of gastrointestinal barrier and immune functions and are associated with chronic intestinal inflammatory conditions as well as hepatocellular and oesophagogastric cancer. Systemic and gastrointestinal disease can also lead to secondary fungal infections. Fungal genomic databases and methodologies need to be further developed and will allow a much better understanding of the diversity and function of the mycobiome in gastrointestinal inflammation, tumourigenesis, liver cirrhosis and transplantation, and its alteration as a consequence of antibiotic therapy and chemotherapy.

CONCLUSIONS: The fungal microbiota and its metabolites impact gastrointestinal function and contribute to the pathogenesis of digestive diseases. Further metagenomic analyses of the gastrointestinal mycobiome in health and disease is needed.}, } @article {pmid24612293, year = {2014}, author = {Der Sarkissian, C and Ermini, L and Jónsson, H and Alekseev, AN and Crubezy, E and Shapiro, B and Orlando, L}, title = {Shotgun microbial profiling of fossil remains.}, journal = {Molecular ecology}, volume = {23}, number = {7}, pages = {1780-1798}, doi = {10.1111/mec.12690}, pmid = {24612293}, issn = {1365-294X}, mesh = {Animals ; DNA/isolation & purification ; DNA Damage ; *Fossils ; Horses/genetics/*microbiology ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; Siberia ; }, abstract = {Millions to billions of DNA sequences can now be generated from ancient skeletal remains thanks to the massive throughput of next-generation sequencing platforms. Except in cases of exceptional endogenous DNA preservation, most of the sequences isolated from fossil material do not originate from the specimen of interest, but instead reflect environmental organisms that colonized the specimen after death. Here, we characterize the microbial diversity recovered from seven c. 200- to 13 000-year-old horse bones collected from northern Siberia. We use a robust, taxonomy-based assignment approach to identify the microorganisms present in ancient DNA extracts and quantify their relative abundance. Our results suggest that molecular preservation niches exist within ancient samples that can potentially be used to characterize the environments from which the remains are recovered. In addition, microbial community profiling of the seven specimens revealed site-specific environmental signatures. These microbial communities appear to comprise mainly organisms that colonized the fossils recently. Our approach significantly extends the amount of useful data that can be recovered from ancient specimens using a shotgun sequencing approach. In future, it may be possible to correlate, for example, the accumulation of postmortem DNA damage with the presence and/or abundance of particular microbes.}, } @article {pmid24611950, year = {2014}, author = {Choi, EB and Hong, SW and Kim, DK and Jeon, SG and Kim, KR and Cho, SH and Gho, YS and Jee, YK and Kim, YK}, title = {Decreased diversity of nasal microbiota and their secreted extracellular vesicles in patients with chronic rhinosinusitis based on a metagenomic analysis.}, journal = {Allergy}, volume = {69}, number = {4}, pages = {517-526}, doi = {10.1111/all.12374}, pmid = {24611950}, issn = {1398-9995}, mesh = {Adult ; Aged ; Bacteria/classification/genetics ; Biodiversity ; Exosomes ; Female ; Humans ; Male ; Metagenome ; *Microbiota ; Middle Aged ; Nasal Mucosa/*microbiology/pathology ; Phylogeny ; RNA, Ribosomal, 16S ; Rhinitis/*microbiology/pathology ; Sinusitis/*microbiology/pathology ; Young Adult ; }, abstract = {BACKGROUND: Chronic rhinosinusitis (CRS) is an inflammatory process in the nasal cavity and paranasal sinuses, and bacteria have been considered to be a cause. Indeed, recent evidence indicates that bacteria-derived extracellular vesicles (EV) appear to be an important causative agent of inflammatory diseases. Here, we aimed to evaluate the diversity of nasal microbiota and their secreted EV in patients with CRS.

METHODS: Nasal lavage (NAL) fluid samples were obtained from five patients with CRS with polyposis, three patients with CRS without polyposis, and three non-CRS controls. After preparation of bacteria and EV from samples using differential centrifugation, genomic DNA was extracted and 16S-rDNA amplicons were subjected to high-throughput pyrosequencing on a Roche 454 GS-FLX platform.

RESULTS: Metagenomics showed that bacteria composition was positively correlated with EV composition. Samples from patients with CRS had greater bacterial abundance and lower diversity, both from bacteria and the EV portion of samples, compared with non-CRS samples. At each phylogenetic level, Bacteroidetes decreased while Proteobacteria increased in the CRS group at the phylum level. At the genus level, Prevotella spp. decreased in the CRS group, while Staphylococcus spp. increased from both bacteria and EV. Moreover, Staphylococcus aureus and its secreting EV compositions were higher in samples from CRS with polyps compared with CRS without polyps.

CONCLUSIONS: These results suggest that patients with CRS have altered nasal microbiota and decreased diversity in bacterial compositions as well as increased S. aureus abundance in those patients with polyps.}, } @article {pmid24599149, year = {2014}, author = {Hauser, PM and Bernard, T and Greub, G and Jaton, K and Pagni, M and Hafen, GM}, title = {Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e90934}, pmid = {24599149}, issn = {1932-6203}, mesh = {Adolescent ; Bacteria/genetics ; Cystic Fibrosis/*microbiology ; Female ; Fungi/genetics ; Genome, Human/*genetics ; Humans ; Lung/*microbiology ; *Microbiota/genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Species Specificity ; Sputum/microbiology ; }, abstract = {Determination of the precise composition and variation of microbiota in cystic fibrosis lungs is crucial since chronic inflammation due to microorganisms leads to lung damage and ultimately, death. However, this constitutes a major technical challenge. Culturing of microorganisms does not provide a complete representation of a microbiota, even when using culturomics (high-throughput culture). So far, only PCR-based metagenomics have been investigated. However, these methods are biased towards certain microbial groups, and suffer from uncertain quantification of the different microbial domains. We have explored whole genome sequencing (WGS) using the Illumina high-throughput technology applied directly to DNA extracted from sputa obtained from two cystic fibrosis patients. To detect all microorganism groups, we used four procedures for DNA extraction, each with a different lysis protocol. We avoided biases due to whole DNA amplification thanks to the high efficiency of current Illumina technology. Phylogenomic classification of the reads by three different methods produced similar results. Our results suggest that WGS provides, in a single analysis, a better qualitative and quantitative assessment of microbiota compositions than cultures and PCRs. WGS identified a high quantity of Haemophilus spp. (patient 1) or Staphylococcus spp. plus Streptococcus spp. (patient 2) together with low amounts of anaerobic (Veillonella, Prevotella, Fusobacterium) and aerobic bacteria (Gemella, Moraxella, Granulicatella). WGS suggested that fungal members represented very low proportions of the microbiota, which were detected by cultures and PCRs because of their selectivity. The future increase of reads' sizes and decrease in cost should ensure the usefulness of WGS for the characterisation of microbiota.}, } @article {pmid24599074, year = {2014}, author = {Duran-Pinedo, AE and Chen, T and Teles, R and Starr, JR and Wang, X and Krishnan, K and Frias-Lopez, J}, title = {Community-wide transcriptome of the oral microbiome in subjects with and without periodontitis.}, journal = {The ISME journal}, volume = {8}, number = {8}, pages = {1659-1672}, pmid = {24599074}, issn = {1751-7370}, support = {R01 DE021553/DE/NIDCR NIH HHS/United States ; U01 DE021127/DE/NIDCR NIH HHS/United States ; DE021553/DE/NIDCR NIH HHS/United States ; DE021127/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Bacteria/*genetics/isolation & purification/metabolism ; Humans ; Metagenome ; Microbiota/*genetics ; Periodontitis/*microbiology ; Phylogeny ; *Transcriptome ; Virulence Factors/genetics ; }, abstract = {Despite increasing knowledge on phylogenetic composition of the human microbiome, our understanding of the in situ activities of the organisms in the community and their interactions with each other and with the environment remains limited. Characterizing gene expression profiles of the human microbiome is essential for linking the role of different members of the bacterial communities in health and disease. The oral microbiome is one of the most complex microbial communities in the human body and under certain circumstances, not completely understood, the healthy microbial community undergoes a transformation toward a pathogenic state that gives rise to periodontitis, a polymicrobial inflammatory disease. We report here the in situ genome-wide transcriptome of the subgingival microbiome in six periodontally healthy individuals and seven individuals with periodontitis. The overall picture of metabolic activities showed that iron acquisition, lipopolysaccharide synthesis and flagellar synthesis were major activities defining disease. Unexpectedly, the vast majority of virulence factors upregulated in subjects with periodontitis came from organisms that are not considered major periodontal pathogens. One of the organisms whose gene expression profile was characterized was the uncultured candidate division TM7, showing an upregulation of putative virulence factors in the diseased community. These data enhance understanding of the core activities that are characteristic of periodontal disease as well as the role that individual organisms in the subgingival community play in periodontitis.}, } @article {pmid24596265, year = {2014}, author = {Ju, F and Guo, F and Ye, L and Xia, Y and Zhang, T}, title = {Metagenomic analysis on seasonal microbial variations of activated sludge from a full-scale wastewater treatment plant over 4 years.}, journal = {Environmental microbiology reports}, volume = {6}, number = {1}, pages = {80-89}, doi = {10.1111/1758-2229.12110}, pmid = {24596265}, issn = {1758-2229}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; *Metagenomics ; Phylogeny ; Seasons ; Sewage/*microbiology ; Wastewater/*microbiology ; Water Purification/*instrumentation ; }, abstract = {Metagenomic technique was employed to characterize the seasonal dynamics of activated sludge (AS) communities in a municipal wastewater treatment plant (WWTP) over 4 years. The results indicated that contrary to Eukaryota (mainly Rotifera and Nematoda), abundances of Bacteria and Archaea (mainly Euryarchaeota) were significantly higher in winter than summer. Two-way analysis of variance and canonical correspondence analysis revealed that many functionally important genera followed strong seasonal variation patterns driven by temperature and salinity gradients; among them, two nitrifying bacteria, Nitrospira and Nitrosomonas, displayed much higher abundances in summer, whereas phosphate-removing genus Tetrasphaera, denitrifier Paracoccus and potential human faecal bacteria, i.e. Bifidobacterium, Dorea and Ruminococcus, showed significantly higher abundances in winter. Particularly, occurrence of dual variation patterns beyond explanation merely by seasonality indicated that multivariables (e.g. dissolved oxygen, sludge retention time, nutrients) participated in shaping AS community structure. However, SEED subsystems annotation showed that functional categories in AS showed no significant difference between summer and winter, indicating that compared with its microbial components, the functional profiles of AS were much more stable. Taken together, our study provides novel insights into the microbial community variations in AS and discloses their correlations with influential factors in WWTPs.}, } @article {pmid24595026, year = {2014}, author = {Tu, Q and He, Z and Li, Y and Chen, Y and Deng, Y and Lin, L and Hemme, CL and Yuan, T and Van Nostrand, JD and Wu, L and Zhou, X and Shi, W and Li, L and Xu, J and Zhou, J}, title = {Development of HuMiChip for functional profiling of human microbiomes.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e90546}, pmid = {24595026}, issn = {1932-6203}, mesh = {Gastrointestinal Tract/*microbiology ; High-Throughput Nucleotide Sequencing/instrumentation ; Humans ; Metagenome ; *Microbiota ; Mouth/*microbiology ; Oligonucleotide Array Sequence Analysis/*instrumentation ; }, abstract = {Understanding the diversity, composition, structure, function, and dynamics of human microbiomes in individual human hosts is crucial to reveal human-microbial interactions, especially for patients with microbially mediated disorders, but challenging due to the high diversity of the human microbiome. Here we have developed a functional gene-based microarray for profiling human microbiomes (HuMiChip) with 36,802 probes targeting 50,007 protein coding sequences for 139 key functional gene families. Computational evaluation suggested all probes included are highly specific to their target sequences. HuMiChip was used to analyze human oral and gut microbiomes, showing significantly different functional gene profiles between oral and gut microbiome. Obvious shifts of microbial functional structure and composition were observed for both patients with dental caries and periodontitis from moderate to advanced stages, suggesting a progressive change of microbial communities in response to the diseases. Consistent gene family profiles were observed by both HuMiChip and next generation sequencing technologies. Additionally, HuMiChip was able to detect gene families at as low as 0.001% relative abundance. The results indicate that the developed HuMiChip is a useful and effective tool for functional profiling of human microbiomes.}, } @article {pmid24589583, year = {2014}, author = {Luo, C and Rodriguez-R, LM and Konstantinidis, KT}, title = {MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences.}, journal = {Nucleic acids research}, volume = {42}, number = {8}, pages = {e73}, pmid = {24589583}, issn = {1362-4962}, mesh = {Algorithms ; Classification/methods ; Genes ; Genomics/*methods ; Humans ; Metagenomics/*methods ; Microbiota ; *Phylogeny ; Software ; }, abstract = {Determining the taxonomic affiliation of sequences assembled from metagenomes remains a major bottleneck that affects research across the fields of environmental, clinical and evolutionary microbiology. Here, we introduce MyTaxa, a homology-based bioinformatics framework to classify metagenomic and genomic sequences with unprecedented accuracy. The distinguishing aspect of MyTaxa is that it employs all genes present in an unknown sequence as classifiers, weighting each gene based on its (predetermined) classifying power at a given taxonomic level and frequency of horizontal gene transfer. MyTaxa also implements a novel classification scheme based on the genome-aggregate average amino acid identity concept to determine the degree of novelty of sequences representing uncharacterized taxa, i.e. whether they represent novel species, genera or phyla. Application of MyTaxa on in silico generated (mock) and real metagenomes of varied read length (100-2000 bp) revealed that it correctly classified at least 5% more sequences than any other tool. The analysis also showed that ∼10% of the assembled sequences from human gut metagenomes represent novel species with no sequenced representatives, several of which were highly abundant in situ such as members of the Prevotella genus. Thus, MyTaxa can find several important applications in microbial identification and diversity studies.}, } @article {pmid24586961, year = {2014}, author = {Gruninger, RJ and Sensen, CW and McAllister, TA and Forster, RJ}, title = {Diversity of rumen bacteria in canadian cervids.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e89682}, pmid = {24586961}, issn = {1932-6203}, mesh = {Animals ; Bacteria/*classification/genetics ; *Biodiversity ; Canada ; DNA, Bacterial ; Deer ; Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Rumen/*microbiology ; Ruminants ; Sequence Analysis, DNA ; }, abstract = {Interest in the bacteria responsible for the breakdown of lignocellulosic feedstuffs within the rumen has increased due to their potential utility in industrial applications. To date, most studies have focused on bacteria from domesticated ruminants. We have expanded the knowledge of the microbial ecology of ruminants by examining the bacterial populations found in the rumen of non-domesticated ruminants found in Canada. Next-generation sequencing of 16S rDNA was employed to characterize the liquid and solid-associated bacterial communities in the rumen of elk (Cervus canadensis), and white tailed deer (Odocoileus virginianus). Despite variability in the microbial populations between animals, principle component and weighted UniFrac analysis indicated that bacterial communities in the rumen of elk and white tail deer are distinct. Populations clustered according to individual host animal and not the association with liquid or solid phase of the rumen contents. In all instances, Bacteroidetes and Firmicutes were the dominant bacterial phyla, although the relative abundance of these differed among ruminant species and between phases of rumen digesta, respectively. In the elk samples Bacteroidetes were more predominant in the liquid phase whereas Firmicutes was the most prevalent phyla in the solid digesta (P = 1×10(-5)). There were also statistically significant differences in the abundance of OTUs classified as Fibrobacteres (P = 5×10(-3)) and Spirochaetes (P = 3×10(-4)) in the solid digesta of the elk samples. We identified a number of OTUs that were classified as phylotypes not previously observed in the rumen environment. Our results suggest that although the bacterial diversity in wild North American ruminants shows overall similarities to domesticated ruminants, we observed a number of OTUs not previously described. Previous studies primarily focusing on domesticated ruminants do not fully represent the microbial diversity of the rumen and studies focusing on non-domesticated ruminants should be expanded.}, } @article {pmid24586863, year = {2014}, author = {Dupont, CL and Larsson, J and Yooseph, S and Ininbergs, K and Goll, J and Asplund-Samuelsson, J and McCrow, JP and Celepli, N and Allen, LZ and Ekman, M and Lucas, AJ and Hagström, Å and Thiagarajan, M and Brindefalk, B and Richter, AR and Andersson, AF and Tenney, A and Lundin, D and Tovchigrechko, A and Nylander, JA and Brami, D and Badger, JH and Allen, AE and Rusch, DB and Hoffman, J and Norrby, E and Friedman, R and Pinhassi, J and Venter, JC and Bergman, B}, title = {Functional tradeoffs underpin salinity-driven divergence in microbial community composition.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e89549}, pmid = {24586863}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics ; Baltic States ; Ecosystem ; *Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; *Salinity ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.}, } @article {pmid24586319, year = {2014}, author = {Appelt, S and Armougom, F and Le Bailly, M and Robert, C and Drancourt, M}, title = {Polyphasic analysis of a middle ages coprolite microbiota, Belgium.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e88376}, pmid = {24586319}, issn = {1932-6203}, mesh = {Actinobacteria/genetics ; Belgium ; Chlamydia/genetics ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/*physiology ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Paleomicrobiological investigations of a 14(th)-century coprolite found inside a barrel in Namur, Belgium were done using microscopy, a culture-dependent approach and metagenomics. Results were confirmed by ad hoc PCR--sequencing. Investigations yielded evidence for flora from ancient environment preserved inside the coprolite, indicated by microscopic observation of amoebal cysts, plant fibers, seeds, pollens and mold remains. Seventeen different bacterial species were cultured from the coprolite, mixing organisms known to originate from the environment and organisms known to be gut inhabitants. Metagenomic analyses yielded 107,470 reads, of which known sequences (31.9%) comprised 98.98% bacterial, 0.52% eukaryotic, 0.44% archaeal and 0.06% viral assigned reads. Most abundant bacterial phyla were Proteobacteria, Gemmatimonadetes, Actinobacteria and Bacteroidetes. The 16 S rRNA gene dataset yielded 132,000 trimmed reads and 673 Operational Taxonomic Units. Most abundant bacterial phyla observed in the 16 S rRNA gene dataset belonged to Proteobacteria, Firmicutes, Actinobacteria and Chlamydia. The Namur coprolite yielded typical gut microbiota inhabitants, intestinal parasites Trichuris and Ascaris and systemic pathogens Bartonella and Bordetella. This study adds knowledge to gut microbiota in medieval times.}, } @article {pmid24584416, year = {2014}, author = {Zhang, M and Liu, N and Qian, C and Wang, Q and Wang, Q and Long, Y and Huang, Y and Zhou, Z and Yan, X}, title = {Phylogenetic and functional analysis of gut microbiota of a fungus-growing higher termite: Bacteroidetes from higher termites are a rich source of β-glucosidase genes.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {416-425}, pmid = {24584416}, issn = {1432-184X}, mesh = {Animals ; Bacteroidetes/enzymology/*genetics ; DNA, Bacterial/genetics ; Digestive System/microbiology ; Genes, Bacterial ; Isoptera/*microbiology ; *Microbiota ; Molecular Sequence Annotation ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; beta-Glucosidase/*genetics/metabolism ; }, abstract = {Fungus-growing termites, their symbiotic fungi, and microbiota inhibiting their intestinal tract comprise a highly efficient cellulose-hydrolyzing system; however, little is known about the role of gut microbiota in this system. Twelve fosmid clones with β-glucosidase activity were previously obtained by functionally screening a metagenomic library of a fungus-growing termite, Macrotermes annandalei. Ten contigs containing putative β-glucosidase genes (bgl1-10) were assembled by sequencing data of these fosmid clones. All these contigs were binned to Bacteroidetes, and all these β-glucosidase genes were phylogenetically closed to those from Bacteroides or Dysgonomonas. Six out of 10 β-glucosidase genes had predicted signal peptides, indicating a transmembrane capability of these enzymes to mediate cellulose hydrolysis within the gut of the termites. To confirm the activities of these β-glucosidase genes, three genes (bgl5, bgl7, and bgl9) were successfully expressed and purified. The optimal temperature and pH of these enzymes largely resembled the environment of the host's gut. The gut microbiota composition of the fungus-growing termite was also determined by 454 pyrosequencing, showing that Bacteroidetes was the most dominant phylum. The diversity and the enzyme properties of β-glucosidases revealed in this study suggested that Bacteroidetes as the major member in fungus-growing termites contributed to cello-oligomer degradation in cellulose-hydrolyzing process and represented a rich source for β-glucosidase genes.}, } @article {pmid24583833, year = {2014}, author = {Potera, C}, title = {Clues to arsenic's toxicity: microbiome alterations in the mouse gut.}, journal = {Environmental health perspectives}, volume = {122}, number = {3}, pages = {A82}, pmid = {24583833}, issn = {1552-9924}, mesh = {Animals ; Arsenic/*toxicity ; Female ; Gastrointestinal Tract/*microbiology ; Metagenome/*drug effects ; Microbiota/*drug effects ; }, } @article {pmid24583479, year = {2014}, author = {Davenport, M and Poles, J and Leung, JM and Wolff, MJ and Abidi, WM and Ullman, T and Mayer, L and Cho, I and Loke, P}, title = {Metabolic alterations to the mucosal microbiota in inflammatory bowel disease.}, journal = {Inflammatory bowel diseases}, volume = {20}, number = {4}, pages = {723-731}, pmid = {24583479}, issn = {1536-4844}, support = {R01 AI093811/AI/NIAID NIH HHS/United States ; P01 DK072201/DK/NIDDK NIH HHS/United States ; R21 AI094166/AI/NIAID NIH HHS/United States ; 5R01AI093811/AI/NIAID NIH HHS/United States ; 3R21AI094166/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acids/*metabolism ; CD4 Lymphocyte Count ; Carbohydrate Metabolism/*physiology ; *Colitis, Ulcerative/microbiology ; Colon/microbiology ; *Crohn Disease/microbiology ; Humans ; Inflammation/microbiology ; Intestinal Mucosa/microbiology ; Lipid Metabolism/*physiology ; Metabolic Networks and Pathways ; Metagenomics ; Microbiota/*physiology ; Nucleotides/*metabolism ; T-Lymphocytes, Regulatory ; }, abstract = {BACKGROUND: Inflammation during inflammatory bowel disease may alter nutrient availability to adherent mucosal bacteria and impact their metabolic function. Microbial metabolites may regulate intestinal CD4 T-cell homeostasis. We investigated the relationship between inflammation and microbial function by inferred metagenomics of the mucosal microbiota from colonic pinch biopsies of patients with inflammatory bowel disease.

METHODS: Paired pinch biopsy samples of known inflammation states were analyzed from ulcerative colitis (UC) (23), Crohn's disease (CD) (21), and control (24) subjects by 16S ribosomal sequencing, histopathologic assessment, and flow cytometry. PICRUSt was used to generate metagenomic data and derive relative Kyoto Encyclopedia of Genes and Genomes Pathway abundance information. Leukocytes were isolated from paired biopsy samples and analyzed by multicolor flow cytometry. Active inflammation was defined by neutrophil infiltration into the epithelium.

RESULTS: Carriage of metabolic pathways in the mucosal microbiota was relatively stable among patients with inflammatory bowel disease, despite large variations in individual bacterial community structures. However, microbial function was significantly altered in inflamed tissue of UC patients, with a reduction in carbohydrate and nucleotide metabolism in favor of increased lipid and amino acid metabolism. These differences were not observed in samples from CD patients. In CD, microbial lipid, carbohydrate, and amino acid metabolism tightly correlated with the frequency of CD4Foxp3 Tregs, whereas in UC, these pathways correlated with the frequency of CD4IL-22 (TH22) cells.

CONCLUSIONS: Metabolic pathways of the mucosal microbiota in CD do not vary as much as UC with inflammation state, indicating a more systemic perturbation of host-bacteria interactions in CD compared with more localized dysfunction in UC.}, } @article {pmid24583074, year = {2014}, author = {Gerber, GK}, title = {The dynamic microbiome.}, journal = {FEBS letters}, volume = {588}, number = {22}, pages = {4131-4139}, doi = {10.1016/j.febslet.2014.02.037}, pmid = {24583074}, issn = {1873-3468}, mesh = {Aging ; Animals ; Computational Biology ; Disease ; Environment ; Humans ; *Microbiota/drug effects ; Models, Biological ; }, abstract = {While our genomes are essentially static, our microbiomes are inherently dynamic. The microbial communities we harbor in our bodies change throughout our lives due to many factors, including maturation during childhood, alterations in our diets, travel, illnesses, and medical treatments. Moreover, there is mounting evidence that our microbiomes change us, by promoting health through their beneficial actions or by increasing our susceptibility to diseases through a process termed dysbiosis. Recent technological advances are enabling unprecedentedly detailed studies of the dynamics of the microbiota in animal models and human populations. This review will highlight key areas of investigation in the field, including establishment of the microbiota during early childhood, temporal variability of the microbiome in healthy adults, responses of the microbiota to intentional perturbations such as antibiotics and dietary changes, and prospective analyses linking changes in the microbiota to host disease status. Given the importance of computational methods in the field, this review will also discuss issues and pitfalls in the analysis of microbiome time-series data, and explore several promising new directions for mathematical model and algorithm development.}, } @article {pmid24582508, year = {2014}, author = {Johansen, P and Vindeløv, J and Arneborg, N and Brockmann, E}, title = {Development of quantitative PCR and metagenomics-based approaches for strain quantification of a defined mixed-strain starter culture.}, journal = {Systematic and applied microbiology}, volume = {37}, number = {3}, pages = {186-193}, doi = {10.1016/j.syapm.2013.12.006}, pmid = {24582508}, issn = {1618-0984}, mesh = {Bacterial Load/*methods ; *Food Industry ; Industrial Microbiology/*methods ; Lactococcus lactis/genetics/*isolation & purification ; Metagenomics/*methods ; *Microbial Consortia ; Real-Time Polymerase Chain Reaction/*methods ; Reproducibility of Results ; }, abstract = {Although the strain composition of mixed cultures may hugely affect production of various fermented foods, such as e.g. cheese, tools for investigating it have so far been limited. In this study, two new approaches for quantification of seven Lactococcus lactis subsp. cremoris strains (S1-S7) in a defined mixed-strain starter culture were developed and verified. By mapping NGS reads from 47 sequenced L. lactis strains to de novo assembly contigs of the seven strains, two strain-specific sequence regions (SEQ1 and SEQ2) were identified for each strain for qPCR primer design (A1 and A2). The qPCR assays amplified their strain-specific sequence region target efficiently. Additionally, high reproducibility was obtained in a validation sample containing equal amounts of the seven strains, and assay-to-assay coefficients of variance (CVs) for six (i.e. S1, S2, S4-S7) of the seven strains correlated to the inter-plate CVs. Hence, at least for six strains, the qPCR assay design approach was successful. The metagenomics-based approach quantified the seven strains based on average coverage of SEQ1 and SEQ2 by mapping sequencing reads from the validation sample to the strain-specific sequence regions. Average coverages of the SEQ1 and SEQ2 in the metagenomics data showed CVs of ≤17.3% for six strains (i.e. S1-S4, S6, S7). Thus, the metagenomics-based quantification approach was considered successful for six strains, regardless of the strain-specific sequence region used. When comparing qPCR- and metagenomics-based quantifications of the validation sample, the identified strain-specific sequence regions were considered suitable and applicable for quantification at a strain level of defined mixed-strain starter cultures.}, } @article {pmid24565031, year = {2013}, author = {Rasheed, Z and Rangwala, H and Barbará, D}, title = {16S rRNA metagenome clustering and diversity estimation using locality sensitive hashing.}, journal = {BMC systems biology}, volume = {7 Suppl 4}, number = {Suppl 4}, pages = {S11}, pmid = {24565031}, issn = {1752-0509}, mesh = {Algorithms ; *Biodiversity ; Cluster Analysis ; Environment ; Humans ; Metagenomics/*methods ; RNA, Ribosomal, 16S/*genetics ; Time Factors ; }, abstract = {BACKGROUND: Advances in biotechnology have changed the manner of characterizing large populations of microbial communities that are ubiquitous across several environments."Metagenome" sequencing involves decoding the DNA of organisms co-existing within ecosystems ranging from ocean, soil and human body. Several researchers are interested in metagenomics because it provides an insight into the complex biodiversity across several environments. Clinicians are using metagenomics to determine the role played by collection of microbial organisms within human body with respect to human health wellness and disease.

RESULTS: We have developed an efficient and scalable, species richness estimation algorithm that uses locality sensitive hashing (LSH). Our algorithm achieves efficiency by approximating the pairwise sequence comparison operations using hashing and also incorporates matching of fixed-length, gapless subsequences criterion to improve the quality of sequence comparisons. We use LSH-based similarity function to cluster similar sequences and make individual groups, called operational taxonomic units (OTUs). We also compute different species diversity/richness metrics by utilizing OTU assignment results to further extend our analysis.

CONCLUSION: The algorithm is evaluated on synthetic samples and eight targeted 16S rRNA metagenome samples taken from seawater. We compare the performance of our algorithm with several competing diversity estimation algorithms. We show the benefits of our approach with respect to computational runtime and meaningful OTU assignments. We also demonstrate practical significance of the developed algorithm by comparing bacterial diversity and structure across different skin locations.

WEBSITE: http://www.cs.gmu.edu/~mlbio/LSH-DIV.}, } @article {pmid24564472, year = {2013}, author = {Mitra, S and Förster-Fromme, K and Damms-Machado, A and Scheurenbrand, T and Biskup, S and Huson, DH and Bischoff, SC}, title = {Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing.}, journal = {BMC genomics}, volume = {14 Suppl 5}, number = {Suppl 5}, pages = {S16}, pmid = {24564472}, issn = {1471-2164}, mesh = {Feces/*microbiology ; Humans ; Metagenome ; Metagenomics ; Microbiota/*genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Metagenomics seeks to understand microbial communities and assemblages by DNA sequencing. Technological advances in next generation sequencing technologies are fuelling a rapid growth in the number and scope of projects aiming to analyze complex microbial environments such as marine, soil or the gut. Recent improvements in longer read lengths and paired-sequencing allow better resolution in profiling microbial communities. While both 454 sequencing and Illumina sequencing have been used in numerous metagenomic studies, SOLiD sequencing is not commonly used in this area, as it is believed to be more suitable in the context of reference-guided projects.

RESULTS: To investigate the performance of SOLiD sequencing in a metagenomic context, we compared taxonomic profiles of SOLiD mate-pair sequencing reads with Sanger paired reads and 454 single reads. All sequences were obtained from the bacterial 16S rRNA gene, which was amplified from microbial DNA extracted from a human fecal sample. Additionally, from the same fecal sample, complete genomic microbial DNA was extracted and shotgun sequenced using SOLiD sequencing to study the composition of the intestinal microbiota and the existing microbial metabolism. We found that the microbiota composition of 16S rRNA gene sequences obtained using Sanger, 454 and SOLiD sequencing provide results comparable to the result based on shotgun sequencing. Moreover, with SOLiD sequences we obtained more resolution down to the species level. In addition, the shotgun data allowed us to determine a functional profile using the databases SEED and KEGG.

CONCLUSIONS: This study shows that SOLiD mate-pair sequencing is a viable and cost-efficient option for analyzing a complex microbiome. To the best of our knowledge, this is the first time that SOLiD sequencing has been used in a human sample.}, } @article {pmid24564377, year = {2014}, author = {Wang, Y and Leung, H and Yiu, S and Chin, F}, title = {MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning.}, journal = {BMC genomics}, volume = {15 Suppl 1}, number = {Suppl 1}, pages = {S12}, pmid = {24564377}, issn = {1471-2164}, mesh = {Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; Metagenome ; Metagenomics/methods ; Microbiota/*genetics ; Molecular Sequence Annotation/*methods ; Phylogeny ; Sequence Analysis, DNA ; Software ; }, abstract = {BACKGROUND: Taxonomic annotation of reads is an important problem in metagenomic analysis. Existing annotation tools, which rely on the approach of aligning each read to the taxonomic structure, are unable to annotate many reads efficiently and accurately as reads (~100 bp) are short and most of them come from unknown genomes. Previous work has suggested assembling the reads to make longer contigs before annotation. More reads/contigs can be annotated as a longer contig (in Kbp) can be aligned to a taxon even if it is from an unknown species as long as it contains a conserved region of that taxon. Unfortunately existing metagenomic assembly tools are not mature enough to produce long enough contigs. Binning tries to group reads/contigs of similar species together. Intuitively, reads in the same group (cluster) should be annotated to the same taxon and these reads altogether should cover a significant portion of the genome alleviating the problem of short contigs if the quality of binning is high. However, no existing work has tried to use binning results to help solve the annotation problem. This work explores this direction.

RESULTS: In this paper, we describe MetaCluster-TA, an assembly-assisted binning-based annotation tool which relies on an innovative idea of annotating binned reads instead of aligning each read or contig to the taxonomic structure separately. We propose the novel concept of the 'virtual contig' (which can be up to 10 Kb in length) to represent a set of reads and then represent each cluster as a set of 'virtual contigs' (which together can be total up to 1 Mb in length) for annotation. MetaCluster-TA can outperform widely-used MEGAN4 and can annotate (1) more reads since the virtual contigs are much longer; (2) more accurately since each cluster of long virtual contigs contains global information of the sampled genome which tends to be more accurate than short reads or assembled contigs which contain only local information of the genome; and (3) more efficiently since there are much fewer long virtual contigs to align than short reads. MetaCluster-TA outperforms MetaCluster 5.0 as a binning tool since binning itself can be more sensitive and precise given long virtual contigs and the binning results can be improved using the reference taxonomic database.

CONCLUSIONS: MetaCluster-TA can outperform widely-used MEGAN4 and can annotate more reads with higher accuracy and higher efficiency. It also outperforms MetaCluster 5.0 as a binning tool.}, } @article {pmid24563833, year = {2013}, author = {Tanney, JB and Seifert, KA}, title = {Rasamsonia pulvericola sp. nov., isolated from house dust.}, journal = {IMA fungus}, volume = {4}, number = {2}, pages = {205-212}, pmid = {24563833}, issn = {2210-6340}, abstract = {In the course of a global survey of the indoor mycobiota, we sampled and analysed settled dust from 87 buildings from 14 countries, using both a modified dilution-to-extinction method and 454-pyrosequencing. Rasamsonia is a recently established genus including thermotolerant or thermophilic species, five of which have been isolated from humans, including the emerging pathogen R. argillacea. A new species, R. pulvericola, was recovered from one residence in Songkhla, Thailand, and is morphologically characterised and compared phylogenetically with other members of the genus. Rasamsonia pulvericola forms a clade with R. brevistipitata and shares morphological characters such as usually biverticillate and never terverticillate conidiophores, and subglobose to ellipsoidal conidia. It has a lower maximum growth temperature and is the first mesophilic species added to the genus. The ITS sequence of R. pulvericola was not detected in the 454-pyrosequencing data for Thailand or other countries, but a similar ITS sequence was detected in Micronesia, probably representing another undescribed Rasamsonia species.}, } @article {pmid24561721, year = {2014}, author = {Ai, B and Li, J and Chi, X and Meng, J and Liu, C and Shi, E}, title = {Butyric acid fermentation of sodium hydroxide pretreated rice straw with undefined mixed culture.}, journal = {Journal of microbiology and biotechnology}, volume = {24}, number = {5}, pages = {629-638}, doi = {10.4014/jmb.1309.09078}, pmid = {24561721}, issn = {1738-8872}, mesh = {Biodegradation, Environmental ; Biotransformation ; Butyric Acid/*metabolism ; *Fermentation ; Metagenome ; Microbiota ; Molecular Sequence Data ; Oryza/chemistry/*metabolism/microbiology ; Phylogeny ; Sodium Hydroxide/chemistry ; Temperature ; }, abstract = {This study describes an alternative mixed culture fermentation technology to anaerobically convert lignocellulosic biomass into butyric acid, a valuable product with wide application, without supplementary cellulolytic enzymes. Rice straw was soaked in 1% NaOH solution to increase digestibility. Among the tested pretreatment conditions, soaking rice straw at 50°C for 72 h removed ~66% of the lignin, but retained ~84% of the cellulose and ~71% of the hemicellulose. By using an undefined cellulose-degrading butyrate-producing microbial community as butyric acid producer in batch fermentation, about 6 g/l of butyric acid was produced from the pretreated rice straw, which accounted for ~76% of the total volatile fatty acids. In the repeated-batch operation, the butyric acid production declined batch by batch, which was most possibly caused by the shift of microbial community structure monitored by denaturing gradient gel electrophoresis. In this study, batch operation was observed to be more suitable for butyric acid production.}, } @article {pmid24560869, year = {2014}, author = {Kostic, AD and Xavier, RJ and Gevers, D}, title = {The microbiome in inflammatory bowel disease: current status and the future ahead.}, journal = {Gastroenterology}, volume = {146}, number = {6}, pages = {1489-1499}, pmid = {24560869}, issn = {1528-0012}, support = {R01 DK092405/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; Anti-Inflammatory Agents/therapeutic use ; Bacteria/*classification/drug effects/genetics ; Humans ; *Immunity, Mucosal ; Inflammatory Bowel Diseases/drug therapy/immunology/*microbiology ; Intestines/drug effects/immunology/*microbiology ; Metagenome ; Metagenomics/methods ; *Microbiota/immunology ; Probiotics/therapeutic use ; Risk Factors ; }, abstract = {Studies of the roles of microbial communities in the development of inflammatory bowel disease (IBD) have reached an important milestone. A decade of genome-wide association studies and other genetic analyses have linked IBD with loci that implicate an aberrant immune response to the intestinal microbiota. More recently, profiling studies of the intestinal microbiome have associated the pathogenesis of IBD with characteristic shifts in the composition of the intestinal microbiota, reinforcing the view that IBD results from altered interactions between intestinal microbes and the mucosal immune system. Enhanced technologies can increase our understanding of the interactions between the host and its resident microbiota and their respective roles in IBD from both a large-scale pathway view and at the metabolic level. We review important microbiome studies of patients with IBD and describe what we have learned about the mechanisms of intestinal microbiota dysfunction. We describe the recent progress in microbiome research from exploratory 16S-based studies, reporting associations of specific organisms with a disease, to more recent studies that have taken a more nuanced view, addressing the function of the microbiota by metagenomic and metabolomic methods. Finally, we propose study designs and methodologies for future investigations of the microbiome in patients with inflammatory gut and autoimmune diseases in general.}, } @article {pmid24553467, year = {2014}, author = {Reichardt, N and Duncan, SH and Young, P and Belenguer, A and McWilliam Leitch, C and Scott, KP and Flint, HJ and Louis, P}, title = {Phylogenetic distribution of three pathways for propionate production within the human gut microbiota.}, journal = {The ISME journal}, volume = {8}, number = {6}, pages = {1323-1335}, pmid = {24553467}, issn = {1751-7370}, mesh = {Acrylates/metabolism ; Bacteria/classification/isolation & purification/*metabolism ; Fermentation ; Gastrointestinal Tract/*microbiology ; Gram-Positive Bacteria/classification/isolation & purification/metabolism ; Humans ; *Microbiota ; Phylogeny ; Propionates/*metabolism ; Propylene Glycols/metabolism ; Succinates/metabolism ; }, abstract = {Propionate is produced in the human large intestine by microbial fermentation and may help maintain human health. We have examined the distribution of three different pathways used by bacteria for propionate formation using genomic and metagenomic analysis of the human gut microbiota and by designing degenerate primer sets for the detection of diagnostic genes for these pathways. Degenerate primers for the acrylate pathway (detecting the lcdA gene, encoding lactoyl-CoA dehydratase) together with metagenomic mining revealed that this pathway is restricted to only a few human colonic species within the Lachnospiraceae and Negativicutes. The operation of this pathway for lactate utilisation in Coprococcus catus (Lachnospiraceae) was confirmed using stable isotope labelling. The propanediol pathway that processes deoxy sugars such as fucose and rhamnose was more abundant within the Lachnospiraceae (based on the pduP gene, which encodes propionaldehyde dehydrogenase), occurring in relatives of Ruminococcus obeum and in Roseburia inulinivorans. The dominant source of propionate from hexose sugars, however, was concluded to be the succinate pathway, as indicated by the widespread distribution of the mmdA gene that encodes methylmalonyl-CoA decarboxylase in the Bacteroidetes and in many Negativicutes. In general, the capacity to produce propionate or butyrate from hexose sugars resided in different species, although two species of Lachnospiraceae (C. catus and R. inulinivorans) are now known to be able to switch from butyrate to propionate production on different substrates. A better understanding of the microbial ecology of short-chain fatty acid formation may allow modulation of propionate formation by the human gut microbiota.}, } @article {pmid24552737, year = {2014}, author = {Drewes, JE and Li, D and Regnery, J and Alidina, M and Wing, A and Hoppe-Jones, C}, title = {Tuning the performance of a natural treatment process using metagenomics for improved trace organic chemical attenuation.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {69}, number = {3}, pages = {628-633}, doi = {10.2166/wst.2013.750}, pmid = {24552737}, issn = {0273-1223}, mesh = {Metagenomics ; *Microbial Consortia ; Organic Chemicals/*isolation & purification ; *Water Purification ; }, abstract = {By utilizing high-throughput sequencing and metagenomics, this study revealed how the microbial community characteristics including composition, diversity, as well as functional genes in managed aquifer recharge (MAR) systems can be tuned to enhance removal of trace organic chemicals of emerging concern (CECs). Increasing the humic content of the primary substrate resulted in higher microbial diversity. Lower concentrations and a higher humic content of the primary substrate promoted the attenuation of biodegradable CECs in laboratory and field MAR systems. Metagenomic results indicated that the metabolic capabilities of xenobiotic biodegradation were significantly promoted for the microbiome under carbon-starving conditions.}, } @article {pmid24550501, year = {2014}, author = {Zhou, J and Deng, Y and Zhang, P and Xue, K and Liang, Y and Van Nostrand, JD and Yang, Y and He, Z and Wu, L and Stahl, DA and Hazen, TC and Tiedje, JM and Arkin, AP}, title = {Stochasticity, succession, and environmental perturbations in a fluidic ecosystem.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {9}, pages = {E836-45}, pmid = {24550501}, issn = {1091-6490}, mesh = {*Ecosystem ; Groundwater/*microbiology ; Microbiota/drug effects/*genetics ; Models, Biological ; Plant Oils/*pharmacology ; Population Dynamics ; Species Specificity ; Stochastic Processes ; Time Factors ; *Water Microbiology ; }, abstract = {Unraveling the drivers of community structure and succession in response to environmental change is a central goal in ecology. Although the mechanisms shaping community structure have been intensively examined, those controlling ecological succession remain elusive. To understand the relative importance of stochastic and deterministic processes in mediating microbial community succession, a unique framework composed of four different cases was developed for fluidic and nonfluidic ecosystems. The framework was then tested for one fluidic ecosystem: a groundwater system perturbed by adding emulsified vegetable oil (EVO) for uranium immobilization. Our results revealed that groundwater microbial community diverged substantially away from the initial community after EVO amendment and eventually converged to a new community state, which was closely clustered with its initial state. However, their composition and structure were significantly different from each other. Null model analysis indicated that both deterministic and stochastic processes played important roles in controlling the assembly and succession of the groundwater microbial community, but their relative importance was time dependent. Additionally, consistent with the proposed conceptual framework but contradictory to conventional wisdom, the community succession responding to EVO amendment was primarily controlled by stochastic rather than deterministic processes. During the middle phase of the succession, the roles of stochastic processes in controlling community composition increased substantially, ranging from 81.3% to 92.0%. Finally, there are limited successional studies available to support different cases in the conceptual framework, but further well-replicated explicit time-series experiments are needed to understand the relative importance of deterministic and stochastic processes in controlling community succession.}, } @article {pmid24550451, year = {2014}, author = {Charlop-Powers, Z and Owen, JG and Reddy, BV and Ternei, MA and Brady, SF}, title = {Chemical-biogeographic survey of secondary metabolism in soil.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {10}, pages = {3757-3762}, pmid = {24550451}, issn = {1091-6490}, support = {R01 GM077516/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; GM077516/GM/NIGMS NIH HHS/United States ; }, mesh = {Cluster Analysis ; *Genetic Variation ; Geographic Mapping ; Metabolome/*genetics ; Microbiota/*genetics ; Multigene Family/genetics ; New England ; Phylogeography ; Secondary Metabolism/genetics ; Soil/*chemistry ; *Soil Microbiology ; Southwestern United States ; }, abstract = {In this study, we compare biosynthetic gene richness and diversity of 96 soil microbiomes from diverse environments found throughout the southwestern and northeastern regions of the United States. The 454-pyroseqencing of nonribosomal peptide adenylation (AD) and polyketide ketosynthase (KS) domain fragments amplified from these microbiomes provide a means to evaluate the variation of secondary metabolite biosynthetic diversity in different soil environments. Through soil composition and AD- and KS-amplicon richness analysis, we identify soil types with elevated biosynthetic potential. In general, arid soils show the richest observed biosynthetic diversity, whereas brackish sediments and pine forest soils show the least. By mapping individual environmental amplicon sequences to sequences derived from functionally characterized biosynthetic gene clusters, we identified conserved soil type-specific secondary metabolome enrichment patterns despite significant sample-to-sample sequence variation. These data are used to create chemical biogeographic distribution maps for biomedically valuable families of natural products in the environment that should prove useful for directing the discovery of bioactive natural products in the future.}, } @article {pmid24531274, year = {2014}, author = {Li, XR and Lv, Y and Meng, H and Gu, JD and Quan, ZX}, title = {Analysis of microbial diversity by pyrosequencing the small-subunit ribosomal RNA without PCR amplification.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {8}, pages = {3777-3789}, doi = {10.1007/s00253-014-5583-0}, pmid = {24531274}, issn = {1432-0614}, mesh = {*Biota ; DNA, Ribosomal/*chemistry/*genetics ; Metagenomics/*methods ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Sewage/microbiology ; }, abstract = {To avoid the biases associated with PCR amplification in analysis of microbial communities, a new method has been tested for direct sequencing of the cDNA of full-length Small-subunit Ribosomal RNA withOut specific PCR amplification (SROP). In silico analysis of the SROP method demonstrated that more than 99 % of the SROP sequences could be correctly annotated. Two environmental samples (activated sludge and anaerobic sludge) with complex microbial communities were used for comparison in this study. The SROP results demonstrated that the families Rhodocyclaceae and Nitrosomonadaceae in activated sludge and the phyla Synergistetes and Spirochaetes in anaerobic sludge were underestimated by PCR-based detection. One third of the 16S ribosomal RNA (rRNA) sequences obtained by the SROP method covered the V3 amplicon region, and they are suitable for phylogenetic and diversity index analyses. The microbial diversity index calculated from the rRNA sequences by the SROP was much higher than that calculated by conventional PCR, particularly for the anaerobic sludge. The metatranscriptome-based SROP method will contribute to our better understanding of the diversity of complex microbial communities.}, } @article {pmid24529988, year = {2014}, author = {Klünemann, M and Schmid, M and Patil, KR}, title = {Computational tools for modeling xenometabolism of the human gut microbiota.}, journal = {Trends in biotechnology}, volume = {32}, number = {3}, pages = {157-165}, doi = {10.1016/j.tibtech.2014.01.005}, pmid = {24529988}, issn = {1879-3096}, mesh = {Biotransformation ; Databases, Factual ; Humans ; *Microbiota ; *Models, Biological ; *Software ; Xenobiotics/*metabolism ; }, abstract = {The gut microbiota is increasingly being recognized as a key site of metabolism for drugs and other xenobiotic compounds that are relevant to human health. The molecular complexity of the gut microbiota revealed by recent metagenomics studies has highlighted the need as well as the challenges for system-level modeling of xenobiotic metabolism in the gut. Here, we outline the possible pathways through which the gut microbiota can modify xenobiotics and review the available computational tools towards modeling complex xenometabolic processes. We put these diverse computational tools and relevant experimental findings into a unified perspective towards building holistic models of xenobiotic metabolism in the gut.}, } @article {pmid24526077, year = {2014}, author = {Mondav, R and Woodcroft, BJ and Kim, EH and McCalley, CK and Hodgkins, SB and Crill, PM and Chanton, J and Hurst, GB and VerBerkmoes, NC and Saleska, SR and Hugenholtz, P and Rich, VI and Tyson, GW}, title = {Discovery of a novel methanogen prevalent in thawing permafrost.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {3212}, doi = {10.1038/ncomms4212}, pmid = {24526077}, issn = {2041-1723}, mesh = {Archaea/*isolation & purification ; Arctic Regions ; Climate Change ; Methane/*metabolism ; *Microbial Consortia ; Permafrost/*microbiology ; }, abstract = {Thawing permafrost promotes microbial degradation of cryo-sequestered and new carbon leading to the biogenic production of methane, creating a positive feedback to climate change. Here we determine microbial community composition along a permafrost thaw gradient in northern Sweden. Partially thawed sites were frequently dominated by a single archaeal phylotype, Candidatus 'Methanoflorens stordalenmirensis' gen. nov. sp. nov., belonging to the uncultivated lineage 'Rice Cluster II' (Candidatus 'Methanoflorentaceae' fam. nov.). Metagenomic sequencing led to the recovery of its near-complete genome, revealing the genes necessary for hydrogenotrophic methanogenesis. These genes are highly expressed and methane carbon isotope data are consistent with hydrogenotrophic production of methane in the partially thawed site. In addition to permafrost wetlands, 'Methanoflorentaceae' are widespread in high methane-flux habitats suggesting that this lineage is both prevalent and a major contributor to global methane production. In thawing permafrost, Candidatus 'M. stordalenmirensis' appears to be a key mediator of methane-based positive feedback to climate warming.}, } @article {pmid24525698, year = {2014}, author = {Russell, JA and Boyd, JH}, title = {Metagenomics and innate immunity - a unique partnership or a battlefield?.}, journal = {Journal of innate immunity}, volume = {6}, number = {3}, pages = {251-252}, pmid = {24525698}, issn = {1662-8128}, mesh = {Host-Pathogen Interactions ; Humans ; *Immunity, Innate ; *Metagenomics ; Microbiota ; }, } @article {pmid24525633, year = {2014}, author = {Boyd, JH and Russell, JA and Fjell, CD}, title = {The meta-genome of sepsis: host genetics, pathogens and the acute immune response.}, journal = {Journal of innate immunity}, volume = {6}, number = {3}, pages = {272-283}, pmid = {24525633}, issn = {1662-8128}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Acute Disease ; Bacterial Infections/diagnosis/genetics/*immunology ; Biodiversity ; Genetic Predisposition to Disease ; High-Throughput Screening Assays ; Humans ; Immunity/genetics ; Metagenome/genetics/*immunology ; Microbiota/genetics/*immunology ; Pathology, Molecular ; Sepsis/diagnosis/genetics/*immunology ; }, abstract = {Severe infection and the patient response constitute sepsis. Here, we review the meta-genome (patient genetics, pathogen communities and host response) and its impact upon the outcome of severe sepsis. Patient genetics, both predisposition for infection and the subsequent response to infection are reviewed. The pathogen is discussed with particular emphasis upon the modern era of microbiome analysis and nucleic acid diagnostics. Finally, we discuss the host clinical and immune responses and present new data to suggest that the immune response is the key to understanding sepsis and improving a death rate of nearly 30%.}, } @article {pmid24525127, year = {2014}, author = {Yan, Z and Poroyko, V and Gu, S and Zhang, Z and Pan, L and Wang, J and Bao, N and Hong, L}, title = {Characterization of the intestinal microbiome of Hirschsprung's disease with and without enterocolitis.}, journal = {Biochemical and biophysical research communications}, volume = {445}, number = {2}, pages = {269-274}, doi = {10.1016/j.bbrc.2014.01.104}, pmid = {24525127}, issn = {1090-2104}, mesh = {Child ; Child, Preschool ; Enterocolitis/*complications/*microbiology ; Female ; Hirschsprung Disease/*complications/*microbiology ; Humans ; Intestines/*microbiology ; Male ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Hirschsprung's disease (HD) is a congenital malformation of the gastrointestinal tract characterized by the absence of the distal enteric nervous system. Hirschsprung-associated enterocolitis (HAEC) is severe life threatening complication of HD. The disease pathogenesis is still unclear, but evidences suggest that the intestinal microbiota may play important role in the development of HD and HAEC. Because microbial abundance and diversity might differ in HD patients with enterocolitis, we sought to generate comparative metagenomic signatures to characterize the structure of the microbiome in HD patients with and without enterocolitis. Our experimental design is to enroll four HD patients (two with enterocolitis and two without enterocolitis). The microbiome was characterized by 16S rRNA gene, and the data obtained will be used to taxonomically classify and compare community structure among different samples. We found that the structure of the microbiome within HAEC patients are differ from those without enterocolitis. This study helps us to understand microbial contributions to the etiology of Hirschsprung-associated enterocolitis.}, } @article {pmid24524278, year = {2014}, author = {Sandri, M and Manfrin, C and Pallavicini, A and Stefanon, B}, title = {Microbial biodiversity of the liquid fraction of rumen content from lactating cows.}, journal = {Animal : an international journal of animal bioscience}, volume = {8}, number = {4}, pages = {572-579}, doi = {10.1017/S1751731114000056}, pmid = {24524278}, issn = {1751-732X}, mesh = {Animal Husbandry/*methods ; Animals ; Biodiversity ; Cattle ; Dairying ; Diet/veterinary ; Fatty Acids, Volatile/metabolism ; Female ; Gram-Positive Endospore-Forming Rods/genetics/isolation & purification ; Lactation/*physiology ; Milk/physiology ; RNA, Ribosomal, 16S/metabolism ; Rumen/*microbiology ; }, abstract = {Host and dietary interactions with the rumen microbiome can affect the efficacy of supplements, and their effect on the composition of the bacterial population is still unknown. A 16S rRNA metagenomic approach and Next-Generation Sequencing (NGS) technology were used to investigate the bacterial microbiome composition in the liquid fraction of the rumen content collected via stomach tubing. To investigate biodiversity, samples were taken from three groups of four lactating dairy cows given a supplement of either 50 g of potato protein (Ctrl group), or 50 g of lyophilized Saccharomyces cerevisiae (LY group) or 50 g of dried S. cerevisiae (DY group) in a potato protein support. Rumen samples were collected after 15 days of dietary treatments and milk production was similar between the three groups. Taxonomic distribution analysis revealed a prevalence of the Firmicutes phylum in all cows (79.76%) and a significantly (P<0.05) higher presence of the genus Bacillus in the DY group. Volatile fatty-acid concentration was not significantly different between groups, possibly because of relatively high inter-animal variability or limited effect of the treatments or both, and the correlation analysis with bacterial taxa showed significant associations, in particular between many Firmicutes genera and butyrate. Limited differences were observed between dietary treatments, but the lack of microbiome data before yeast administration does not allow to draw firm conclusions on the effect of dietary treatments.}, } @article {pmid24522917, year = {2014}, author = {Ma, Y and Madupu, R and Karaoz, U and Nossa, CW and Yang, L and Yooseph, S and Yachimski, PS and Brodie, EL and Nelson, KE and Pei, Z}, title = {Human papillomavirus community in healthy persons, defined by metagenomics analysis of human microbiome project shotgun sequencing data sets.}, journal = {Journal of virology}, volume = {88}, number = {9}, pages = {4786-4797}, pmid = {24522917}, issn = {1098-5514}, support = {UH3 CA140233/CA/NCI NIH HHS/United States ; U01 CA182370/CA/NCI NIH HHS/United States ; UH3CA140233/CA/NCI NIH HHS/United States ; R01 CA159036/CA/NCI NIH HHS/United States ; U01CA18237/CA/NCI NIH HHS/United States ; }, mesh = {Coinfection/epidemiology/virology ; Female ; *Healthy Volunteers ; Humans ; Metagenomics ; *Microbiota ; Papillomaviridae/*classification/genetics/*isolation & purification ; Papillomavirus Infections/epidemiology/*virology ; Prevalence ; Sequence Analysis, DNA ; }, abstract = {UNLABELLED: Human papillomavirus (HPV) causes a number of neoplastic diseases in humans. Here, we show a complex normal HPV community in a cohort of 103 healthy human subjects, by metagenomics analysis of the shotgun sequencing data generated from the NIH Human Microbiome Project. The overall HPV prevalence was 68.9% and was highest in the skin (61.3%), followed by the vagina (41.5%), mouth (30%), and gut (17.3%). Of the 109 HPV types as well as additional unclassified types detected, most were undetectable by the widely used commercial kits targeting the vaginal/cervical HPV types. These HPVs likely represent true HPV infections rather than transitory exposure because of strong organ tropism and persistence of the same HPV types in repeat samples. Coexistence of multiple HPV types was found in 48.1% of the HPV-positive samples. Networking between HPV types, cooccurrence or exclusion, was detected in vaginal and skin samples. Large contigs assembled from short HPV reads were obtained from several samples, confirming their genuine HPV origin. This first large-scale survey of HPV using a shotgun sequencing approach yielded a comprehensive map of HPV infections among different body sites of healthy human subjects.

IMPORTANCE: This nonbiased survey indicates that the HPV community in healthy humans is much more complex than previously defined by widely used kits that are target selective for only a few high- and low-risk HPV types for cervical cancer. The importance of nononcogenic viruses in a mixed HPV infection could be for stimulating or inhibiting a coexisting oncogenic virus via viral interference or immune cross-reaction. Knowledge gained from this study will be helpful to guide the designing of epidemiological and clinical studies in the future to determine the impact of nononcogenic HPV types on the outcome of HPV infections.}, } @article {pmid24522263, year = {2014}, author = {Looft, T and Allen, HK and Cantarel, BL and Levine, UY and Bayles, DO and Alt, DP and Henrissat, B and Stanton, TB}, title = {Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations.}, journal = {The ISME journal}, volume = {8}, number = {8}, pages = {1566-1576}, pmid = {24522263}, issn = {1751-7370}, mesh = {*Animal Feed ; Animals ; Anti-Bacterial Agents/administration & dosage/*pharmacology ; Bacteria/*classification/genetics/isolation & purification ; Bacteriophages/genetics/isolation & purification ; Female ; Intestine, Large/microbiology ; Intestine, Small/microbiology ; Intestines/*microbiology ; Male ; Microbiota/*drug effects ; Swine/*microbiology ; }, abstract = {Disturbance of the beneficial gut microbial community is a potential collateral effect of antibiotics, which have many uses in animal agriculture (disease treatment or prevention and feed efficiency improvement). Understanding antibiotic effects on bacterial communities at different intestinal locations is essential to realize the full benefits and consequences of in-feed antibiotics. In this study, we defined the lumenal and mucosal bacterial communities from the small intestine (ileum) and large intestine (cecum and colon) plus feces, and characterized the effects of in-feed antibiotics (chlortetracycline, sulfamethazine and penicillin (ASP250)) on these communities. 16S rRNA gene sequence and metagenomic analyses of bacterial membership and functions revealed dramatic differences between small and large intestinal locations, including enrichment of Firmicutes and phage-encoding genes in the ileum. The large intestinal microbiota encoded numerous genes to degrade plant cell wall components, and these genes were lacking in the ileum. The mucosa-associated ileal microbiota harbored greater bacterial diversity than the lumen but similar membership to the mucosa of the large intestine, suggesting that most gut microbes can associate with the mucosa and might serve as an inoculum for the lumen. The collateral effects on the microbiota of antibiotic-fed animals caused divergence from that of control animals, with notable changes being increases in Escherichia coli populations in the ileum, Lachnobacterium spp. in all gut locations, and resistance genes to antibiotics not administered. Characterizing the differential metabolic capacities and response to perturbation at distinct intestinal locations will inform strategies to improve gut health and food safety.}, } @article {pmid24521706, year = {2014}, author = {Allan, E}, title = {Metagenomics: unrestricted access to microbial communities.}, journal = {Virulence}, volume = {5}, number = {3}, pages = {397-398}, pmid = {24521706}, issn = {2150-5608}, mesh = {*Biota ; *Ecosystem ; Metagenomics/*methods ; }, } @article {pmid24521415, year = {2014}, author = {Dhal, PK and Sar, P}, title = {Microbial communities in uranium mine tailings and mine water sediment from Jaduguda U mine, India: A culture independent analysis.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering}, volume = {49}, number = {6}, pages = {694-709}, doi = {10.1080/10934529.2014.865458}, pmid = {24521415}, issn = {1532-4117}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Biodegradation, Environmental ; Carbon/analysis ; Cluster Analysis ; Computational Biology ; Hydrogen-Ion Concentration ; India ; Metals, Heavy/analysis ; *Microbiota ; *Mining ; Nitrogen/analysis ; Phosphorus/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Stem Cells ; *Uranium ; Waste Products/*analysis ; Wastewater/*microbiology ; }, abstract = {Microbial diversity within uranium mine tailings and mine water sediment from the Jaduguda uranium mine, India was characterized by metagenome-derived 16S rRNA gene clone libraries. Samples from fresh tailings (JFT244), abandoned (vegetated) tailings (JOT245) and mine water sediment (J1-5) having wide ranges of pH (5.7 to 10.4), nitrogen, phosphorus and organic carbon [150-5700 ppm, 800-9100 ppm and 0.18-6.5% (w/w)] and elevated metals (Ni, Cu, Zn and U) were used to explore the inhabitant bacterial and archaeal community structures. Consistent to the sample's physicochemical properties, up to four orders of magnitude variation in bacterial CFU counts was observed. The data showed that with increasing metal and decreasing nutrient (organic C, N, P, etc.) contents, microbial diversity indices decrease within the samples. Culture-independent analyses revealed predominance of phyla Proteobacteria and/or Acidobacteria within the samples along with members of Actinobacteria, Cyanobacteria, Chloroflexi, Genera incertae sedis OP10, Firmicutes and Planctomycete as relatively minor groups. Abundance of Crenarchaeota in tailings samples and Euryachaeota in mine water sediment was noted. Diversity of dissimilatory sulfate reductase gene (dsr) was studied. Putative metabolic properties as derived from taxonomy and phylogenetic lineages indicated presence of chemolithotrophic and heteotrophic aerobic and anaerobic organisms capable of nitrogen fixation, nitrate reduction and biogeochemical cycling of metals, sulfur and methane. The data indicated that indigenous microbial populations are capable of maintaining self-sustenance in these highly hazardous environments and possess catalytic potential for their use in in situ bioremediation.}, } @article {pmid24519380, year = {2014}, author = {Yu, P and Shaw, CA}, title = {An efficient algorithm for accurate computation of the Dirichlet-multinomial log-likelihood function.}, journal = {Bioinformatics (Oxford, England)}, volume = {30}, number = {11}, pages = {1547-1554}, pmid = {24519380}, issn = {1367-4811}, support = {U54CA149196/CA/NCI NIH HHS/United States ; }, mesh = {*Algorithms ; Humans ; Likelihood Functions ; Metagenomics/*methods ; Microbiota ; }, abstract = {The Dirichlet-multinomial (DMN) distribution is a fundamental model for multicategory count data with overdispersion. This distribution has many uses in bioinformatics including applications to metagenomics data, transctriptomics and alternative splicing. The DMN distribution reduces to the multinomial distribution when the overdispersion parameter ψ is 0. Unfortunately, numerical computation of the DMN log-likelihood function by conventional methods results in instability in the neighborhood of [Formula: see text]. An alternative formulation circumvents this instability, but it leads to long runtimes that make it impractical for large count data common in bioinformatics. We have developed a new method for computation of the DMN log-likelihood to solve the instability problem without incurring long runtimes. The new approach is composed of a novel formula and an algorithm to extend its applicability. Our numerical experiments show that this new method both improves the accuracy of log-likelihood evaluation and the runtime by several orders of magnitude, especially in high-count data situations that are common in deep sequencing data. Using real metagenomic data, our method achieves manyfold runtime improvement. Our method increases the feasibility of using the DMN distribution to model many high-throughput problems in bioinformatics. We have included in our work an R package giving access to this method and a vingette applying this approach to metagenomic data.}, } @article {pmid24516926, year = {2013}, author = {Shen, F and Fan, JG}, title = {[Current status of gut microbiota and metagenome with nonalcoholic fatty liver disease].}, journal = {Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology}, volume = {21}, number = {11}, pages = {811-814}, pmid = {24516926}, issn = {1007-3418}, mesh = {Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; *Microbiota ; Non-alcoholic Fatty Liver Disease/*microbiology ; }, } @article {pmid24513652, year = {2014}, author = {Reitschuler, C and Lins, P and Wagner, AO and Illmer, P}, title = {Cultivation of moonmilk-born non-extremophilic Thaum and Euryarchaeota in mixed culture.}, journal = {Anaerobe}, volume = {29}, number = {}, pages = {73-79}, doi = {10.1016/j.anaerobe.2013.10.002}, pmid = {24513652}, issn = {1095-8274}, mesh = {Aerobiosis ; Anaerobiosis ; Austria ; Biodiversity ; Calcium Carbonate ; Caves/microbiology ; Cold Temperature ; DNA, Archaeal/*genetics ; Euryarchaeota/classification/*genetics/isolation & purification/metabolism ; *Metagenome ; Methane/biosynthesis ; Microbial Consortia/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {PCR-DGGE, qPCR and sequencing highlighted a quite homogenous archaeal community prevailing in secondary calcite deposits, so-called moonmilk, within the cold alpine Hundalm cave in Tyrol (Austria). Furthermore, the depth profile of this moonmilk could prove that the Archaea are located in oxygen-rich near- and oxygen-depleted sub-surface layers. To gather these communities we therefore applied an aerobic and anaerobic cultivation approach in oligotrophic and methanotrophic media. The mixed moonmilk community was analyzed with a combination of molecular methods using qPCR, PCR-DGGE and sequencing. Anaerobic and aerobic cultures were additionally investigated with GC and HPLC analyses. It was possible to initially cultivate and enrich the supposed aerobic/microaerophilic and anaerobic archaeal fraction, representing the natural archaeal community. While the naturally less abundant near-surface Archaea are closely related to members of the Thaumarchaeota (Nitrosopumilus maritimus), the highly abundant anaerobic Archaea are more distantly related to members within the Euryarchaeota. It is possible that these cultivable moonmilk-born Archaea represent new ecotypes or are so far undescribed. Based on the sequencing results and the production of very low amounts of methane, a corresponding methanogenic community is thought to represent only a minor abundant archaeal fraction. On a physiological level the cultivated moonmilk community is cold-adapted and basically of oligotrophic and organotrophic character.}, } @article {pmid24510138, year = {2013}, author = {Huete-Pérez, JA and Quezada, F}, title = {Genomic approaches in marine biodiversity and aquaculture.}, journal = {Biological research}, volume = {46}, number = {4}, pages = {353-361}, doi = {10.4067/S0716-97602013000400007}, pmid = {24510138}, issn = {0717-6287}, mesh = {Animals ; *Aquaculture ; Aquatic Organisms/*classification/*genetics ; *Biodiversity ; *Biotechnology ; *Genomics ; }, abstract = {Recent advances in genomic and post-genomic technologies have now established the new standard in medical and biotechnological research. The introduction of next-generation sequencing, NGS,has resulted in the generation of thousands of genomes from all domains of life, including the genomes of complex uncultured microbial communities revealed through metagenomics. Although the application of genomics to marine biodiversity remains poorly developed overall, some noteworthy progress has been made in recent years. The genomes of various model marine organisms have been published and a few more are underway. In addition, the recent large-scale analysis of marine microbes, along with transcriptomic and proteomic approaches to the study of teleost fishes, mollusks and crustaceans, to mention a few, has provided a better understanding of phenotypic variability and functional genomics. The past few years have also seen advances in applications relevant to marine aquaculture and fisheries. In this review we introduce several examples of recent discoveries and progress made towards engendering genomic resources aimed at enhancing our understanding of marine biodiversity and promoting the development of aquaculture. Finally, we discuss the need for auspicious science policies to address challenges confronting smaller nations in the appropriate oversight of this growing domain as they strive to guarantee food security and conservation of their natural resources.}, } @article {pmid24509925, year = {2014}, author = {Appelt, S and Fancello, L and Le Bailly, M and Raoult, D and Drancourt, M and Desnues, C}, title = {Viruses in a 14th-century coprolite.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {9}, pages = {2648-2655}, pmid = {24509925}, issn = {1098-5336}, mesh = {Bacteriophages/classification/genetics/isolation & purification/ultrastructure ; Belgium ; Feces/*virology ; Fossils/history/*virology ; History, Medieval ; Humans ; Metagenomics/history ; Microbiota ; Molecular Sequence Data ; Phylogeny ; Viruses/classification/genetics/*isolation & purification/ultrastructure ; }, abstract = {Coprolites are fossilized fecal material that can reveal information about ancient intestinal and environmental microbiota. Viral metagenomics has allowed systematic characterization of viral diversity in environmental and human-associated specimens, but little is known about the viral diversity in fossil remains. Here, we analyzed the viral community of a 14th-century coprolite from a closed barrel in a Middle Ages site in Belgium using electron microscopy and metagenomics. Viruses that infect eukaryotes, bacteria, and archaea were detected, and we confirmed the presence of some of them by ad hoc suicide PCR. The coprolite DNA viral metagenome was dominated by sequences showing homologies to phages commonly found in modern stools and soil. Although their phylogenetic compositions differed, the metabolic functions of the viral communities have remained conserved across centuries. Antibiotic resistance was one of the reconstructed metabolic functions detected.}, } @article {pmid24508599, year = {2014}, author = {Norman, JM and Handley, SA and Virgin, HW}, title = {Kingdom-agnostic metagenomics and the importance of complete characterization of enteric microbial communities.}, journal = {Gastroenterology}, volume = {146}, number = {6}, pages = {1459-1469}, pmid = {24508599}, issn = {1528-0012}, support = {R01 AI084887/AI/NIAID NIH HHS/United States ; R01 OD011170/OD/NIH HHS/United States ; T32 AI007163/AI/NIAID NIH HHS/United States ; 5T32AI007163-35/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Disease Susceptibility ; Fungi/classification/*genetics ; Gastrointestinal Diseases/microbiology/virology ; Gene Expression Regulation, Fungal ; Gene Expression Regulation, Viral ; Humans ; Intestines/*microbiology/*virology ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Viruses/classification/*genetics ; }, abstract = {Advanced sequencing techniques have shown that bacteria are not the only complex and important microbes in the human intestine. Nonbacterial organisms, particularly the virome and the mycobiome, are important regulators of intestinal immunity and inflammation. The virome is mucosal and systemic; it can alter the host response to bacteria and interact with host genes and bacteria to contribute to disease pathogenesis. The human mycobiome is also complex and can contribute to intestinal inflammation. We review what has recently been learned about the nonbacterial and nonarchaeal microbes in the gastrointestinal tract, discussing their potential effects on health and disease and analytical approaches for their study. Studies of associations between the microbiome and intestinal pathology should incorporate kingdom-agnostic approaches if we are to fully understand intestinal health and disease.}, } @article {pmid24498390, year = {2014}, author = {Kong, F and Zhao, J and Han, S and Zeng, B and Yang, J and Si, X and Yang, B and Yang, M and Xu, H and Li, Y}, title = {Characterization of the gut microbiota in the red panda (Ailurus fulgens).}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e87885}, pmid = {24498390}, issn = {1932-6203}, mesh = {Ailuridae/genetics/*microbiology ; Animals ; Cellulose/metabolism ; Feces/*microbiology ; Gastrointestinal Tract/*microbiology ; *Metagenome ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {The red panda is the only living species of the genus Ailurus. Like giant pandas, red pandas are also highly specialized to feed mainly on highly fibrous bamboo. Although several studies have focused on the gut microbiota in the giant panda, little is known about the gut microbiota of the red panda. In this study, we characterized the fecal microbiota from both wild (n = 16) and captive (n = 6) red pandas using a pyrosequecing based approach targeting the V1-V3 hypervariable regions of the 16S rRNA gene. Distinct bacterial communities were observed between the two groups based on both membership and structure. Wild red pandas maintained significantly higher community diversity, richness and evenness than captive red pandas, the communities of which were skewed and dominated by taxa associated with Firmicutes. Phylogenetic analysis of the top 50 OTUs revealed that 10 of them were related to known cellulose degraders. To the best of our knowledge, this is the first study of the gut microbiota of the red panda. Our data suggest that, similar to the giant panda, the gut microbiota in the red panda might also play important roles in the digestion of bamboo.}, } @article {pmid24492144, year = {2014}, author = {Holler, E and Butzhammer, P and Schmid, K and Hundsrucker, C and Koestler, J and Peter, K and Zhu, W and Sporrer, D and Hehlgans, T and Kreutz, M and Holler, B and Wolff, D and Edinger, M and Andreesen, R and Levine, JE and Ferrara, JL and Gessner, A and Spang, R and Oefner, PJ}, title = {Metagenomic analysis of the stool microbiome in patients receiving allogeneic stem cell transplantation: loss of diversity is associated with use of systemic antibiotics and more pronounced in gastrointestinal graft-versus-host disease.}, journal = {Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation}, volume = {20}, number = {5}, pages = {640-645}, pmid = {24492144}, issn = {1523-6536}, support = {P01 CA039542/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Anti-Bacterial Agents/therapeutic use ; Biodiversity ; Enterococcus faecalis/drug effects/genetics ; Enterococcus faecium/drug effects/genetics ; Feces/microbiology ; Female ; Gastrointestinal Tract/drug effects/immunology/*microbiology ; Graft vs Host Disease/drug therapy/immunology/*microbiology ; *Hematopoietic Stem Cell Transplantation ; Humans ; Indican/urine ; Male ; *Metagenome ; Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Transplantation, Homologous ; }, abstract = {Next-generation sequencing of the hypervariable V3 region of the 16s rRNA gene isolated from serial stool specimens collected from 31 patients receiving allogeneic stem cell transplantation (SCT) was performed to elucidate variations in the composition of the intestinal microbiome in the course of allogeneic SCT. Metagenomic analysis was complemented by strain-specific enterococcal PCR and indirect assessment of bacterial load by liquid chromatography-tandem mass spectrometry of urinary indoxyl sulfate. At the time of admission, patients showed a predominance of commensal bacteria. After transplantation, a relative shift toward enterococci was observed, which was more pronounced under antibiotic prophylaxis and treatment of neutropenic infections. The shift was particularly prominent in patients that developed subsequently or suffered from active gastrointestinal (GI) graft-versus-host disease (GVHD). The mean proportion of enterococci in post-transplant stool specimens was 21% in patients who did not develop GI GVHD as compared with 46% in those that subsequently developed GI GVHD and 74% at the time of active GVHD. Enterococcal PCR confirmed predominance of Enterococcus faecium or both E. faecium and Enterococcus faecalis in these specimens. As a consequence of the loss of bacterial diversity, mean urinary indoxyl sulfate levels dropped from 42.5 ± 11 μmol/L to 11.8 ± 2.8 μmol/L in all post-transplant samples and to 3.5 ± 3 μmol/L in samples from patients with active GVHD. Our study reveals major microbiome shifts in the course of allogeneic SCT that occur in the period of antibiotic treatment but are more prominent in association with GI GVHD. Our data indicate early microbiome shifts and a loss of diversity of the intestinal microbiome that may affect intestinal inflammation in the setting of allogeneic SCT.}, } @article {pmid24489768, year = {2014}, author = {Zhu, L and Xu, Y and Ferretti, JJ and Kreth, J}, title = {Probing oral microbial functionality--expression of spxB in plaque samples.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e86685}, pmid = {24489768}, issn = {1932-6203}, support = {R01 DE021726/DE/NIDCR NIH HHS/United States ; R03 DE022601/DE/NIDCR NIH HHS/United States ; DE022601/DE/NIDCR NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics/metabolism ; Biofilms/growth & development ; Conserved Sequence ; Databases, Factual ; Dental Plaque/*microbiology ; *Gene Expression Regulation, Bacterial ; Humans ; Hydrogen Peroxide/metabolism ; Microbiota/*genetics ; Molecular Sequence Data ; Pyruvate Oxidase/*genetics/metabolism ; Real-Time Polymerase Chain Reaction ; Streptococcus/classification/*genetics/isolation & purification/metabolism ; }, abstract = {The Human Oral Microbiome Database (HOMD) provides an extensive collection of genome sequences from oral bacteria. The sequence information is a static snapshot of the microbial potential of the so far sequenced species. A major challenge is to connect the microbial potential encoded in the metagenome to an actual function in the in vivo oral biofilm. In the present study we took a reductionist approach and identified a considerably conserved metabolic gene, spxB to be encoded by a majority of oral streptococci using the HOMD metagenome information. spxB encodes the pyruvate oxidase responsible for the production of growth inhibiting amounts of hydrogen peroxide (H2O2) and has previously been shown as important in the interspecies competition in the oral biofilm. Here we demonstrate a strong correlation of H2O2 production and the presence of the spxB gene in dental plaque. Using Real-Time RT PCR we show that spxB is expressed in freshly isolated human plaque samples from several donors and that the expression is relative constant when followed over time in one individual. This is the first demonstration of an oral community encoded gene expressed in vivo suggesting a functional role of spxB in oral biofilm physiology. This also demonstrates a possible strategy to connect the microbial potential of the metagenome to its functionality in future studies by identifying similar highly conserved genes in the oral microbial community.}, } @article {pmid24486053, year = {2014}, author = {Morgan, XC and Huttenhower, C}, title = {Meta'omic analytic techniques for studying the intestinal microbiome.}, journal = {Gastroenterology}, volume = {146}, number = {6}, pages = {1437-1448.e1}, doi = {10.1053/j.gastro.2014.01.049}, pmid = {24486053}, issn = {1528-0012}, support = {R01HG005969/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/*genetics ; DNA, Bacterial/analysis ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Genotype ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions ; Humans ; Inflammatory Bowel Diseases/microbiology ; Intestines/*microbiology ; *Metagenome ; *Metagenomics/methods ; Microbiota/*genetics ; Models, Statistical ; Phenotype ; Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Ribotyping ; Transcriptome ; }, abstract = {Nucleotide sequencing has become increasingly common and affordable, and is now a vital tool for studies of the human microbiome. Comprehensive microbial community surveys such as MetaHit and the Human Microbiome Project have described the composition and molecular functional profile of the healthy (normal) intestinal microbiome. This knowledge will increase our ability to analyze host and microbial DNA (genome) and RNA (transcriptome) sequences. Bioinformatic and statistical tools then can be used to identify dysbioses that might cause disease, and potential treatments. Analyses that identify perturbations in specific molecules can leverage thousands of culture-based isolate genomes to contextualize culture-independent sequences, or may integrate sequence data with whole-community functional assays such as metaproteomic or metabolomic analyses. We review the state of available systems-level models for studies of the intestinal microbiome, along with analytic techniques and tools that can be used to determine its functional capabilities in healthy and unhealthy individuals.}, } @article {pmid24486050, year = {2014}, author = {Hollister, EB and Gao, C and Versalovic, J}, title = {Compositional and functional features of the gastrointestinal microbiome and their effects on human health.}, journal = {Gastroenterology}, volume = {146}, number = {6}, pages = {1449-1458}, pmid = {24486050}, issn = {1528-0012}, support = {U01 CA170930/CA/NCI NIH HHS/United States ; UH3 DK083990/DK/NIDDK NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; DK56338/DK/NIDDK NIH HHS/United States ; R01 AT004326/AT/NCCIH NIH HHS/United States ; }, mesh = {Age Factors ; Aging ; Bacteria/*classification/genetics/metabolism ; Disease Susceptibility ; Gastrointestinal Diseases/metabolism/*microbiology ; Gastrointestinal Tract/metabolism/*microbiology ; Gene Expression Regulation, Bacterial ; Health Status ; Humans ; Metagenomics ; *Microbiota/genetics ; Risk Factors ; }, abstract = {The human gastrointestinal tract contains distinct microbial communities that differ in composition and function based on their location, as well as age, sex, race/ethnicity, and diet of their host. We describe the bacterial taxa present in different locations of the GI tract, and their specific metabolic features. The distinct features of these specific microbial communities might affect human health and disease. Several bacterial taxa and metabolic modules (biochemical functions) have been associated with human health and the absence of disease. Core features of the healthy microbiome might be defined and targeted to prevent disease and optimize human health.}, } @article {pmid24485451, year = {2014}, author = {Heintz, C and Mair, W}, title = {You are what you host: microbiome modulation of the aging process.}, journal = {Cell}, volume = {156}, number = {3}, pages = {408-411}, pmid = {24485451}, issn = {1097-4172}, support = {R01 AG044346/AG/NIA NIH HHS/United States ; }, mesh = {*Aging ; Animals ; Humans ; Longevity ; Metagenome ; *Microbiota ; Models, Animal ; }, abstract = {The critical impact that microbiota have on health and disease makes the interaction between host and microbiome increasingly important as we evaluate therapeutics. Here, we highlight growing evidence that, beyond disease, microbes also affect the most fundamental of host physiological phenotypes, the rate of aging itself.}, } @article {pmid24479734, year = {2014}, author = {Jones, ML and Martoni, CJ and Ganopolsky, JG and Labbé, A and Prakash, S}, title = {The human microbiome and bile acid metabolism: dysbiosis, dysmetabolism, disease and intervention.}, journal = {Expert opinion on biological therapy}, volume = {14}, number = {4}, pages = {467-482}, doi = {10.1517/14712598.2014.880420}, pmid = {24479734}, issn = {1744-7682}, mesh = {Animals ; Atherosclerosis/metabolism ; Bile Acids and Salts/*metabolism ; Diabetes Mellitus, Type 2/metabolism ; Dysbiosis/*metabolism ; Female ; Gastrointestinal Diseases/metabolism ; Health Status ; Humans ; Male ; Metabolic Diseases/*metabolism ; Microbiota/*physiology ; Obesity/metabolism/microbiology ; Osteoporosis/metabolism ; Probiotics ; }, abstract = {INTRODUCTION: Recent evidence indicates that the human gut microbiome plays a significant role in health and disease. Dysbiosis, defined as a pathological imbalance in a microbial community, is becoming increasingly appreciated as a 'central environmental factor' that is both associated with complex phenotypes and affected by host genetics, diet and antibiotic use. More recently, a link has been established between the dysmetabolism of bile acids (BAs) in the gut to dysbiosis.

AREAS COVERED: BAs, which are transformed by the gut microbiota, have been shown to regulate intestinal homeostasis and are recognized as signaling molecules in a wide range of metabolic processes. This review will examine the connection between BA metabolism as it relates to the gut microbiome and its implication in health and disease.

EXPERT OPINION: A disrupted gut microbiome, including a reduction of bile salt hydrolase (BSH)-active bacteria, can significantly impair the metabolism of BAs and may result in an inability to maintain glucose homeostasis as well as normal cholesterol breakdown and excretion. To better understand the link between dysbiosis, BA dysmetabolism and chronic degenerative disease, large-scale metagenomic sequencing studies, metatranscriptomics, metaproteomics and metabolomics should continue to catalog functional diversity in the gastrointestinal tract of both healthy and diseased populations. Further, BSH-active probiotics should continue to be explored as treatment options to help restore metabolic levels.}, } @article {pmid24478471, year = {2014}, author = {Lim, YW and Evangelista, JS and Schmieder, R and Bailey, B and Haynes, M and Furlan, M and Maughan, H and Edwards, R and Rohwer, F and Conrad, D}, title = {Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis.}, journal = {Journal of clinical microbiology}, volume = {52}, number = {2}, pages = {425-437}, pmid = {24478471}, issn = {1098-660X}, mesh = {Adult ; Bacteria/*classification/genetics ; Cystic Fibrosis/*microbiology ; Female ; Fungi/*classification/genetics ; Humans ; Male ; *Metagenome ; *Microbiota ; Sputum/*microbiology ; Viruses/*classification/genetics ; }, abstract = {As DNA sequencing becomes faster and cheaper, genomics-based approaches are being explored for their use in personalized diagnoses and treatments. Here, we provide a proof of principle for disease monitoring using personal metagenomic sequencing and traditional clinical microbiology by focusing on three adults with cystic fibrosis (CF). The CF lung is a dynamic environment that hosts a complex ecosystem composed of bacteria, viruses, and fungi that can vary in space and time. Not surprisingly, the microbiome data from the induced sputum samples we collected revealed a significant amount of species diversity not seen in routine clinical laboratory cultures. The relative abundances of several species changed as clinical treatment was altered, enabling the identification of the climax and attack communities that were proposed in an earlier work. All patient microbiomes encoded a diversity of mechanisms to resist antibiotics, consistent with the characteristics of multidrug-resistant microbial communities that are commonly observed in CF patients. The metabolic potentials of these communities differed by the health status and recovery route of each patient. Thus, this pilot study provides an example of how metagenomic data might be used with clinical assessments for the development of treatments tailored to individual patients.}, } @article {pmid24477921, year = {2014}, author = {Tout, J and Jeffries, TC and Webster, NS and Stocker, R and Ralph, PJ and Seymour, JR}, title = {Variability in microbial community composition and function between different niches within a coral reef.}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {540-552}, pmid = {24477921}, issn = {1432-184X}, mesh = {Archaea/classification/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; *Biodiversity ; *Coral Reefs ; *Environment ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Queensland ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {To explore how microbial community composition and function varies within a coral reef ecosystem, we performed metagenomic sequencing of seawater from four niches across Heron Island Reef, within the Great Barrier Reef. Metagenomes were sequenced from seawater samples associated with (1) the surface of the coral species Acropora palifera, (2) the surface of the coral species Acropora aspera, (3) the sandy substrate within the reef lagoon and (4) open water, outside of the reef crest. Microbial composition and metabolic function differed substantially between the four niches. The taxonomic profile showed a clear shift from an oligotroph-dominated community (e.g. SAR11, Prochlorococcus, Synechococcus) in the open water and sandy substrate niches, to a community characterised by an increased frequency of copiotrophic bacteria (e.g. Vibrio, Pseudoalteromonas, Alteromonas) in the coral seawater niches. The metabolic potential of the four microbial assemblages also displayed significant differences, with the open water and sandy substrate niches dominated by genes associated with core house-keeping processes such as amino acid, carbohydrate and protein metabolism as well as DNA and RNA synthesis and metabolism. In contrast, the coral surface seawater metagenomes had an enhanced frequency of genes associated with dynamic processes including motility and chemotaxis, regulation and cell signalling. These findings demonstrate that the composition and function of microbial communities are highly variable between niches within coral reef ecosystems and that coral reefs host heterogeneous microbial communities that are likely shaped by habitat structure, presence of animal hosts and local biogeochemical conditions.}, } @article {pmid24477198, year = {2014}, author = {Shilova, IN and Robidart, JC and James Tripp, H and Turk-Kubo, K and Wawrik, B and Post, AF and Thompson, AW and Ward, B and Hollibaugh, JT and Millard, A and Ostrowski, M and Scanlan, DJ and Paerl, RW and Stuart, R and Zehr, JP}, title = {A microarray for assessing transcription from pelagic marine microbial taxa.}, journal = {The ISME journal}, volume = {8}, number = {7}, pages = {1476-1491}, pmid = {24477198}, issn = {1751-7370}, mesh = {Alphaproteobacteria/classification/*genetics ; Aquatic Organisms ; Archaea/classification/*genetics ; Genetic Markers ; Genetic Variation ; Iron/metabolism ; Metagenome ; Microbial Consortia ; Oceans and Seas ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Prochlorococcus/classification/*genetics ; Synechococcus/classification/*genetics ; *Transcription, Genetic ; Viruses/classification/*genetics ; }, abstract = {Metagenomic approaches have revealed unprecedented genetic diversity within microbial communities across vast expanses of the world's oceans. Linking this genetic diversity with key metabolic and cellular activities of microbial assemblages is a fundamental challenge. Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. MicroTOOLs integrates nucleotide sequence information from disparate data types: genomes, PCR-amplicons, metagenomes, and metatranscriptomes. It targets 19 400 unique sequences over 145 different genes that are relevant to stress responses and microbial metabolism across the three domains of life and viruses. MicroTOOLs was used in a proof-of-concept experiment that compared the functional responses of microbial communities following Fe and P enrichments of surface water samples from the North Pacific Subtropical Gyre. We detected transcription of 68% of the gene targets across major taxonomic groups, and the pattern of transcription indicated relief from Fe limitation and transition to N limitation in some taxa. Prochlorococcus (eHLI), Synechococcus (sub-cluster 5.3) and Alphaproteobacteria SAR11 clade (HIMB59) showed the strongest responses to the Fe enrichment. In addition, members of uncharacterized lineages also responded. The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions.}, } @article {pmid24475077, year = {2014}, author = {Wang, JH and Bose, S and Kim, GC and Hong, SU and Kim, JH and Kim, JE and Kim, H}, title = {Flos Lonicera ameliorates obesity and associated endotoxemia in rats through modulation of gut permeability and intestinal microbiota.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e86117}, pmid = {24475077}, issn = {1932-6203}, mesh = {Adiposity/drug effects ; Animals ; Body Weight/drug effects ; Cell Line ; Cytokines/metabolism ; Diet, High-Fat ; Endotoxemia/*complications/drug therapy/*metabolism/microbiology ; Gastrointestinal Tract/drug effects/*metabolism/*microbiology ; Gene Expression Regulation/drug effects ; Humans ; Inflammation Mediators/metabolism ; Intestinal Mucosa/drug effects/immunology/metabolism/pathology ; Lipids/blood ; Lipopolysaccharides/immunology ; Liver/drug effects/immunology/metabolism/pathology ; Lonicera/*chemistry ; Macrophages/immunology/metabolism ; Male ; Metagenome ; Mice ; Microbiota ; Nitric Oxide/biosynthesis ; Obesity/*complications/drug therapy/*metabolism/microbiology ; Permeability/drug effects ; Plant Extracts/administration & dosage/*pharmacology ; Rats ; }, abstract = {BACKGROUND AND AIM: Increasing evidence has indicated a close association of host-gut flora metabolic interaction with obesity. Flos Lonicera, a traditional herbal medicine, is used widely in eastern Asia for the treatment of various disorders. The aim of this study was to evaluate whether unfermented or fermented formulations of Flos Lonicera could exert a beneficial impact to combat obesity and related metabolic endotoxemia.

METHODS: Obesity and metabolic endotoxemia were induced separately or together in rats through feeding a eight-week high fat diet either alone (HFD control group) or in combination with a single LPS stimulation (intraperitoneal injection, 0.75 mg/kg) (LPS control group). While, the mechanism of action of the Lonicera formulations was explored in vitro using RAW 264.7 and HCT 116 cell lines as models.

RESULTS: In cell-based studies, treatment with both unfermented Flos Lonicera (UFL) and fermented Flos Lonicera (FFL) formulations resulted in suppression of LPS-induced NO production and gene expression of vital proinflammatory cytokines (TNF-α, COX-2, and IL-6) in RAW 264.7 cells, reduced the gene expression of zonula occludens (ZO)-1 and claudin-1, and normalized trans epithelial electric resistance (TEER) and horseradish peroxidase (HRP) flux in LPS-treated HCT-116 cells. In an animal study, treatment of HFD as well as HFD+LPS groups with UFL or FFL resulted in a notable decrease in body and adipose tissue weights, ameliorated total cholesterol, HDL, triglyceride, aspartate transaminase and endotoxin levels in serum, reduced the urinary lactulose/mannitol ratio, and markedly alleviated lipid accumulation in liver. In addition, exposure of HFD as well as HFD+LPS groups with UFL or FFL resulted in significant alteration of the distribution of intestinal flora, especially affecting the population of Akkermansia spp. and ratio of Bacteroidetes and Firmicutes.

CONCLUSION: This evidence collectively demonstrates that Flos Lonicera ameliorates obesity and related metabolic endotoxemia via regulating distribution of gut flora and gut permeability.}, } @article {pmid24475066, year = {2014}, author = {Haverkamp, TH and Hammer, Ø and Jakobsen, KS}, title = {Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e85990}, pmid = {24475066}, issn = {1932-6203}, mesh = {Biodiversity ; *Environmental Microbiology ; Geography ; Geologic Sediments/*chemistry/*microbiology ; *Geology ; Metagenome ; Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment.}, } @article {pmid24475017, year = {2014}, author = {Tun, HM and Mauroo, NF and Yuen, CS and Ho, JC and Wong, MT and Leung, FC}, title = {Microbial diversity and evidence of novel homoacetogens in the gut of both geriatric and adult giant pandas (Ailuropoda melanoleuca).}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e79902}, pmid = {24475017}, issn = {1932-6203}, mesh = {Age Factors ; Animals ; Bacteria/classification/genetics ; *Biodiversity ; DNA, Ribosomal Spacer ; Formate-Tetrahydrofolate Ligase/genetics ; Fungi/classification/genetics ; Gastrointestinal Tract/*microbiology ; Metagenome ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S ; Ursidae/*microbiology ; }, abstract = {Recent studies have described the bacterial community residing in the guts of giant pandas, together with the presence of lignocellulolytic enzymes. However, a more comprehensive understanding of the intestinal microbial composition and its functional capacity in giant pandas remains a major goal. Here, we conducted a comparison of bacterial, fungal and homoacetogenic microbial communities from fecal samples taken from two geriatric and two adult captive giant pandas. 16S rDNA amplicon pyrosequencing revealed that Firmicutes and Proteobacteria are the most abundant microbiota in both geriatric and adult giant pandas. However, members of phylum Actinobacteria found in adult giant pandas were absent in their geriatric counterparts. Similarly, ITS1 amplicon pyrosequencing identified developmental changes in the most abundant fungal classes from Sordariomycetes in adult pandas to Saccharomycetes in geriatric pandas. Geriatric pandas exhibited significantly higher abundance of a potential probiotic fungus (Candida tropicalis) as compared to adult pandas, indicating their importance in the normal digestive physiology of aged pandas. Our study also reported the presence of a lignocellulolytic white-rot fungus, Perenniporia medulla-panis, and the evidence of novel homoacetogens residing in the guts of giant pandas.}, } @article {pmid24473752, year = {2014}, author = {Druart, C and Dewulf, EM and Cani, PD and Neyrinck, AM and Thissen, JP and Delzenne, NM}, title = {Gut microbial metabolites of polyunsaturated fatty acids correlate with specific fecal bacteria and serum markers of metabolic syndrome in obese women.}, journal = {Lipids}, volume = {49}, number = {4}, pages = {397-402}, pmid = {24473752}, issn = {1558-9307}, mesh = {Adult ; Aged ; Bifidobacterium/metabolism ; Fatty Acids, Unsaturated/*blood/isolation & purification ; Feces/microbiology ; Female ; Gastrointestinal Tract/metabolism/microbiology ; Humans ; Metabolic Syndrome/*blood/microbiology/pathology ; Metagenome ; *Microbiota ; Obesity/*blood/microbiology/pathology ; Phylogeny ; Prebiotics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The aim of this human study was to assess the influence of prebiotic-induced gut microbiota modulation on PUFA-derived bacterial metabolites production. Therefore, we analyzed the circulating fatty acid profile including CLA/CLnA in obese women treated during 3 months with inulin-type fructan prebiotics. In these patients, we had already determined gut microbiota composition by phylogenetic microarray and qPCR analysis of 16S rDNA. Some PUFA-derived bacterial metabolites were detected in the serum of obese patients. Despite the prebiotic-induced modulation of gut microbiota, including changes in CLA/CLnA-producing bacteria, the treatment did not impact significantly on the circulating level of these metabolites. However, some PUFA-derived bacterial metabolites were positively correlated with specific fecal bacteria (Bifidobacterium spp., Eubacterium ventriosum and Lactobacillus spp.) and inversely correlated with serum cholesterol (total, LDL, HDL). These correlations suggest a potential beneficial effect of some of these metabolites but this remains to be confirmed by further investigation.}, } @article {pmid24473131, year = {2014}, author = {Cao, H and Wang, Y and Lee, OO and Zeng, X and Shao, Z and Qian, PY}, title = {Microbial sulfur cycle in two hydrothermal chimneys on the Southwest Indian Ridge.}, journal = {mBio}, volume = {5}, number = {1}, pages = {e00980-13}, pmid = {24473131}, issn = {2150-7511}, mesh = {*Biota ; Hydrothermal Vents/*microbiology ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Molecular Sequence Data ; Oxidation-Reduction ; Sequence Analysis, DNA ; Sulfur/*metabolism ; }, abstract = {UNLABELLED: Sulfur is an important element in sustaining microbial communities present in hydrothermal vents. Sulfur oxidation has been extensively studied due to its importance in chemosynthetic pathways in hydrothermal fields; however, less is known about sulfate reduction. Here, the metagenomes of hydrothermal chimneys located on the ultraslow-spreading Southwest Indian Ridge (SWIR) were pyrosequenced to elucidate the associated microbial sulfur cycle. A taxonomic summary of known genes revealed a few dominant bacteria that participated in the microbial sulfur cycle, particularly sulfate-reducing Deltaproteobacteria. The metagenomes studied contained highly abundant genes related to sulfur oxidation and reduction. Several carbon metabolic pathways, in particular the Calvin-Benson-Bassham pathway and the reductive tricarboxylic acid cycles for CO2 fixation, were identified in sulfur-oxidizing autotrophic bacteria. In contrast, highly abundant genes related to the oxidation of short-chain alkanes were grouped with sulfate-reducing bacteria, suggesting an important role for short-chain alkanes in the sulfur cycle. Furthermore, sulfur-oxidizing bacteria were associated with enrichment for genes involved in the denitrification pathway, while sulfate-reducing bacteria displayed enrichment for genes responsible for hydrogen utilization. In conclusion, this study provides insights regarding major microbial metabolic activities that are driven by the sulfur cycle in low-temperature hydrothermal chimneys present on an ultraslow midocean ridge.

IMPORTANCE: There have been limited studies on chimney sulfides located at ultraslow-spreading ridges. The analysis of metagenomes of hydrothermal chimneys on the ultraslow-spreading Southwest Indian Ridge suggests the presence of a microbial sulfur cycle. The sulfur cycle should be centralized within a microbial community that displays enrichment for sulfur metabolism-related genes. The present study elucidated a significant role of the microbial sulfur cycle in sustaining an entire microbial community in low-temperature hydrothermal chimneys on an ultraslow spreading midocean ridge, which has characteristics distinct from those of other types of hydrothermal fields.}, } @article {pmid24466089, year = {2014}, author = {Card, RM and Warburton, PJ and MacLaren, N and Mullany, P and Allan, E and Anjum, MF}, title = {Application of microarray and functional-based screening methods for the detection of antimicrobial resistance genes in the microbiomes of healthy humans.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e86428}, pmid = {24466089}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Anti-Infective Agents/pharmacology ; Dihydropteroate Synthase/chemistry/genetics ; Drug Resistance, Microbial/*genetics ; Feces/microbiology ; Healthy Volunteers ; Humans ; *Metagenome ; Microarray Analysis/methods ; Microbial Sensitivity Tests ; *Microbiota ; Molecular Sequence Data ; Saliva/microbiology ; Sequence Alignment ; }, abstract = {The aim of this study was to screen for the presence of antimicrobial resistance genes within the saliva and faecal microbiomes of healthy adult human volunteers from five European countries. Two non-culture based approaches were employed to obviate potential bias associated with difficult to culture members of the microbiota. In a gene target-based approach, a microarray was employed to screen for the presence of over 70 clinically important resistance genes in the saliva and faecal microbiomes. A total of 14 different resistance genes were detected encoding resistances to six antibiotic classes (aminoglycosides, β-lactams, macrolides, sulphonamides, tetracyclines and trimethoprim). The most commonly detected genes were erm(B), blaTEM, and sul2. In a functional-based approach, DNA prepared from pooled saliva samples was cloned into Escherichia coli and screened for expression of resistance to ampicillin or sulphonamide, two of the most common resistances found by array. The functional ampicillin resistance screen recovered genes encoding components of a predicted AcrRAB efflux pump. In the functional sulphonamide resistance screen, folP genes were recovered encoding mutant dihydropteroate synthase, the target of sulphonamide action. The genes recovered from the functional screens were from the chromosomes of commensal species that are opportunistically pathogenic and capable of exchanging DNA with related pathogenic species. Genes identified by microarray were not recovered in the activity-based screen, indicating that these two methods can be complementary in facilitating the identification of a range of resistance mechanisms present within the human microbiome. It also provides further evidence of the diverse reservoir of resistance mechanisms present in bacterial populations in the human gut and saliva. In future the methods described in this study can be used to monitor changes in the resistome in response to antibiotic therapy.}, } @article {pmid24465951, year = {2014}, author = {Kamika, I and Momba, MN}, title = {Microbial diversity of Emalahleni mine water in South Africa and tolerance ability of the predominant organism to vanadium and nickel.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e86189}, pmid = {24465951}, issn = {1932-6203}, mesh = {*Adaptation, Biological ; Biodiversity ; Humans ; Hydrogen-Ion Concentration ; *Industrial Waste ; Metagenome ; *Microbiota ; Molecular Sequence Data ; *Nickel/toxicity ; Phylogeny ; RNA, Ribosomal, 16S ; South Africa ; *Vanadium/toxicity ; Wastewater/*microbiology ; *Water Microbiology ; }, abstract = {The present study aims firstly at determining the microbial diversity of mine-water collected in Emalahleni, South Africa and secondly isolating and characterizing the most dominant bacterial species found in the mine water in terms of its resistance to both V(5+) and Ni(2+) in a modified wastewater liquid media. The results revealed a microbial diversity of 17 orders, 27 families and 33 genera were found in the mine-water samples with Marinobacteria (47.02%) and Anabaena (17.66%) being the most abundant genera. Considering their abundance in the mine-water samples, a species of the Marinobacter genera was isolated, identified, and characterised for metal tolerance and removal ability. The MWI-1 isolate (Marinobacter sp. MWI-1 [AB793286]) was found to be closely related to Marinobacter goseongensis at 97% of similarity. The isolate was exposed to various concentrations of Ni(2+) and V(5+) in wastewater liquid media and its tolerance to metals was also assessed. The MWI-1 isolate could tolerate V(5+) and Ni(2+) separately at concentrations (in terms of MIC) up to 13.41 ± 0.56 mM and 5.39 ± 0.5 mM at pH 7, whereas at pH 3, the tolerance limit decrease to 11.45 ± 0.57 mM and 2.67 ± 0.1 mM, respectively. The removal of V(5+) and Ni(2+) in liquid media was noted to gradually decrease with a gradual increase of the test metals. A significant difference (p<0.05) between V(5+) and Ni(2+) removal was noted. Marinobacter sp. MWI-1 achieved the maximum permissible limit of 0.1 mg-V(5+)/L prescribed by UN-FAO at 100 mg/L, while at 200 mg/L only V(5+) was removed at approximately 95% and Ni(2+) at 47%. This study suggests that mine-water indigenous microorganisms are the best solution for the remediation of polluted mine water.}, } @article {pmid24463575, year = {2014}, author = {Ikeda, S and Sasaki, K and Okubo, T and Yamashita, A and Terasawa, K and Bao, Z and Liu, D and Watanabe, T and Murase, J and Asakawa, S and Eda, S and Mitsui, H and Sato, T and Minamisawa, K}, title = {Low nitrogen fertilization adapts rice root microbiome to low nutrient environment by changing biogeochemical functions.}, journal = {Microbes and environments}, volume = {29}, number = {1}, pages = {50-59}, pmid = {24463575}, issn = {1347-4405}, mesh = {Archaea/classification/genetics/*isolation & purification/metabolism ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Biodiversity ; Fertilizers/*analysis ; *Microbiota ; Molecular Sequence Data ; Nitrogen/analysis/*metabolism ; Oryza/*microbiology ; Phylogeny ; Plant Roots/microbiology ; Soil Microbiology ; }, abstract = {Reduced fertilizer usage is one of the objectives of field management in the pursuit of sustainable agriculture. Here, we report on shifts of bacterial communities in paddy rice ecosystems with low (LN), standard (SN), and high (HN) levels of N fertilizer application (0, 30, and 300 kg N ha(-1), respectively). The LN field had received no N fertilizer for 5 years prior to the experiment. The LN and HN plants showed a 50% decrease and a 60% increase in biomass compared with the SN plant biomass, respectively. Analyses of 16S rRNA genes suggested shifts of bacterial communities between the LN and SN root microbiomes, which were statistically confirmed by metagenome analyses. The relative abundances of Burkholderia, Bradyrhizobium and Methylosinus were significantly increased in root microbiome of the LN field relative to the SN field. Conversely, the abundance of methanogenic archaea was reduced in the LN field relative to the SN field. The functional genes for methane oxidation (pmo and mmo) and plant association (acdS and iaaMH) were significantly abundant in the LN root microbiome. Quantitative PCR of pmoA/mcrA genes and a (13)C methane experiment provided evidence of more active methane oxidation in the rice roots of the LN field. In addition, functional genes for the metabolism of N, S, Fe, and aromatic compounds were more abundant in the LN root microbiome. These results suggest that low-N-fertilizer management is an important factor in shaping the microbial community structure containing key microbes for plant associations and biogeochemical processes in paddy rice ecosystems.}, } @article {pmid24462268, year = {2014}, author = {Lekunberri, I and Gasol, JM and Acinas, SG and Gómez-Consarnau, L and Crespo, BG and Casamayor, EO and Massana, R and Pedrós-Alió, C and Pinhassi, J}, title = {The phylogenetic and ecological context of cultured and whole genome-sequenced planktonic bacteria from the coastal NW Mediterranean Sea.}, journal = {Systematic and applied microbiology}, volume = {37}, number = {3}, pages = {216-228}, doi = {10.1016/j.syapm.2013.11.005}, pmid = {24462268}, issn = {1618-0984}, mesh = {Alphaproteobacteria/*classification/genetics/isolation & purification ; Bacteroidetes/*classification/genetics/isolation & purification ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gammaproteobacteria/*classification/genetics/isolation & purification ; Genome, Bacterial ; Mediterranean Sea ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Microbial isolates are useful models for physiological and ecological studies and can also be used to reassemble genomes from metagenomic analyses. However, the phylogenetic diversity that can be found among cultured marine bacteria may vary significantly depending on the isolation. Therefore, this study describes a set of 136 bacterial isolates obtained by traditional isolation techniques from the Blanes Bay Microbial Observatory, of which seven strains have had the whole genome sequenced. The complete set was compared to a series of environmental sequences obtained by culture-independent techniques (60 DGGE sequences and 303 clone library sequences) previously obtained by molecular methods. In this way, each isolate was placed in both its "ecological" (time of year, nutrient limitation, chlorophyll and temperature values) context or setting, and its "phylogenetic" landscape (i.e. similar organisms that were found by culture-independent techniques, when they were relevant, and when they appeared). Nearly all isolates belonged to the Gammaproteobacteria, Alphaproteobacteria, or the Bacteroidetes (70, 40 and 20 isolates, respectively). Rarefaction analyses showed similar diversity patterns for sequences from isolates and molecular approaches, except for Alphaproteobacteria where cultivation retrieved a higher diversity per unit effort. Approximately 30% of the environmental clones and isolates formed microdiversity clusters constrained at 99% 16S rRNA gene sequence identity, but the pattern was different in Bacteroidetes (less microdiversity) than in the other main groups. Seventeen cases (12.5%) of nearly complete (98-100%) rRNA sequence identity between isolates and environmental sequences were found: nine in the Alphaproteobacteria, five in the Gammaproteobacteria, and three in the Bacteroidetes, indicating that cultivation could be used to obtain at least some organisms representative of the various taxa detected by molecular methods. Collectively, these results illustrated the largely unexplored potential of culturing on standard media for complementing the study of microbial diversity by culture-independent techniques and for obtaining phylogenetically distinct model organisms from natural seawater.}, } @article {pmid24460444, year = {2014}, author = {Segal, LN and Rom, WN and Weiden, MD}, title = {Lung microbiome for clinicians. New discoveries about bugs in healthy and diseased lungs.}, journal = {Annals of the American Thoracic Society}, volume = {11}, number = {1}, pages = {108-116}, pmid = {24460444}, issn = {2325-6621}, support = {K24 AI080298/AI/NIAID NIH HHS/United States ; K23 AI102970/AI/NIAID NIH HHS/United States ; K24 AI080298A/AI/NIAID NIH HHS/United States ; 5 U01CA086137-14/CA/NCI NIH HHS/United States ; UL1 TR000038/TR/NCATS NIH HHS/United States ; U01 CA086137/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Inflammation ; Lung/immunology/*microbiology ; Lung Diseases/immunology/*microbiology ; Metagenome ; *Microbiota ; }, abstract = {Microbes are readily cultured from epithelial surfaces of the skin, mouth, and colon. In the last 10 years, culture-independent DNA-based techniques demonstrated that much more complex microbial communities reside on most epithelial surfaces; this includes the lower airways, where bacterial culture had failed to reliably demonstrate resident bacteria. Exposure to a diverse bacterial environment is important for adequate immunological development. The most common microbes found in the lower airways are also found in the upper airways. Increasing abundance of oral characteristic taxa is associated with increased inflammatory cells and exhaled nitric oxide, suggesting that the airway microbiome induces an immunological response in the lung. Furthermore, rhinovirus infection leads to outgrowth of Haemophilus in patients with chronic obstructive pulmonary disease, and human immunodeficiency virus-infected subjects have more Tropheryma whipplei in the lower airway, suggesting a bidirectional interaction in which the host immune defenses also influence the microbial niche. Quantitative and/or qualitative changes in the lung microbiome may be relevant for disease progression and exacerbations in a number of pulmonary diseases. Future investigations with longitudinal follow-up to understand the dynamics of the lung microbiome may lead to the development of new therapeutic targets.}, } @article {pmid24454903, year = {2014}, author = {Pinto, C and Pinho, D and Sousa, S and Pinheiro, M and Egas, C and Gomes, AC}, title = {Unravelling the diversity of grapevine microbiome.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e85622}, pmid = {24454903}, issn = {1932-6203}, mesh = {Ascomycota/genetics ; Basidiomycota/genetics ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Enterobacteriaceae/genetics ; Microbiota/*genetics ; Molecular Typing ; Mycological Typing Techniques ; Pseudomonadaceae/genetics ; Seasons ; Sphingomonadaceae/genetics ; Streptococcaceae/genetics ; Vitis/growth & development/*microbiology ; }, abstract = {Vitis vinifera is one of the most widely cultivated fruit crops with a great economic impact on the global industry. As a plant, it is naturally colonised by a wide variety of both prokaryotic and eukaryotic microorganisms that interact with grapevine, having either beneficial or phytopathogenic effects, who play a major role in fruit yield, grape quality and, ultimately, in the evolution of grape fermentation and wine production. Therefore, the objective of this study was to extensively characterize the natural microbiome of grapevine. Considering that the majority of microorganisms are uncultivable, we have deeply studied the microflora of grapevine leaves using massive parallel rDNA sequencing, along its vegetative cycle. Among eukaryotic population the most abundant microorganisms belonged to the early diverging fungi lineages and Ascomycota phylum, whereas the Basidiomycota were the least abundant. Regarding prokaryotes, a high diversity of Proteobacteria, Firmicutes and Actinobacteria was unveiled. Indeed, the microbial communities present in the vineyard during its vegetative cycle were shown to be highly structured and dynamic. In all cases, the major abundant microorganisms were the yeast-like fungus Aureobasidium and the prokaryotic Enterobacteriaceae. Herein, we report the first complete microbiome landscape of the vineyard, through a metagenomic approach, and highlight the analysis of the microbial interactions within the vineyard and its importance for the equilibrium of the microecosystem of grapevines.}, } @article {pmid24454771, year = {2014}, author = {Xie, G and Lo, CC and Scholz, M and Chain, PS}, title = {Recruiting human microbiome shotgun data to site-specific reference genomes.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e84963}, pmid = {24454771}, issn = {1932-6203}, support = {Y01 DE006006/DE/NIDCR NIH HHS/United States ; Y1-DE-6006-02/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Metagenome ; *Microbiota ; }, abstract = {The human body consists of innumerable multifaceted environments that predispose colonization by a number of distinct microbial communities, which play fundamental roles in human health and disease. In addition to community surveys and shotgun metagenomes that seek to explore the composition and diversity of these microbiomes, there are significant efforts to sequence reference microbial genomes from many body sites of healthy adults. To illustrate the utility of reference genomes when studying more complex metagenomes, we present a reference-based analysis of sequence reads generated from 55 shotgun metagenomes, selected from 5 major body sites, including 16 sub-sites. Interestingly, between 13% and 92% (62.3% average) of these shotgun reads were aligned to a then-complete list of 2780 reference genomes, including 1583 references for the human microbiome. However, no reference genome was universally found in all body sites. For any given metagenome, the body site-specific reference genomes, derived from the same body site as the sample, accounted for an average of 58.8% of the mapped reads. While different body sites did differ in abundant genera, proximal or symmetrical body sites were found to be most similar to one another. The extent of variation observed, both between individuals sampled within the same microenvironment, or at the same site within the same individual over time, calls into question comparative studies across individuals even if sampled at the same body site. This study illustrates the high utility of reference genomes and the need for further site-specific reference microbial genome sequencing, even within the already well-sampled human microbiome.}, } @article {pmid24452263, year = {2014}, author = {Faith, JJ and Ahern, PP and Ridaura, VK and Cheng, J and Gordon, JI}, title = {Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice.}, journal = {Science translational medicine}, volume = {6}, number = {220}, pages = {220ra11}, pmid = {24452263}, issn = {1946-6242}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; R01 DK030292/DK/NIDDK NIH HHS/United States ; R01 DK070977/DK/NIDDK NIH HHS/United States ; DK30292/DK/NIDDK NIH HHS/United States ; DK078669/DK/NIDDK NIH HHS/United States ; DK70977/DK/NIDDK NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; 096100/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adiposity ; Algorithms ; Animals ; Antigens, CD/metabolism ; Cecum/microbiology ; Fatty Acids/chemistry ; Feces/microbiology ; Female ; Forkhead Transcription Factors/genetics ; Gastrointestinal Tract/microbiology ; *Germ-Free Life ; Humans ; Immune System ; Integrin alpha Chains/metabolism ; Intestines/*microbiology ; Male ; Metagenome ; Mice ; Mice, Inbred C57BL ; Microbiota/*physiology ; Neuropilin-1/genetics ; Phenotype ; Systems Biology ; T-Lymphocytes, Regulatory/immunology ; }, abstract = {Identifying a scalable, unbiased method for discovering which members of the human gut microbiota influence specific physiologic, metabolic, and immunologic phenotypes remains a challenge. We describe a method in which a clonally arrayed collection of cultured, sequenced bacteria was generated from one of several human fecal microbiota samples found to transmit a particular phenotype to recipient germ-free mice. Ninety-four bacterial consortia of diverse size, randomly drawn from the culture collection, were introduced into germ-free animals. We identified an unanticipated range of bacterial strains that promoted accumulation of colonic regulatory T cells (T(regs)) and expansion of Nrp1(lo/-) peripheral T(regs), as well as strains that modulated mouse adiposity and cecal metabolite concentrations, using feature selection algorithms and follow-up monocolonizations. This combinatorial approach enables a systems-level understanding of microbial contributions to human biology.}, } @article {pmid24451205, year = {2014}, author = {Thrash, JC and Temperton, B and Swan, BK and Landry, ZC and Woyke, T and DeLong, EF and Stepanauskas, R and Giovannoni, SJ}, title = {Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype.}, journal = {The ISME journal}, volume = {8}, number = {7}, pages = {1440-1451}, pmid = {24451205}, issn = {1751-7370}, mesh = {Alphaproteobacteria/classification/*genetics ; DNA, Intergenic/classification ; Ecotype ; *Genes, rRNA ; Genomics ; Metagenome ; *Phylogeny ; RNA, Ribosomal, 16S/classification/*genetics ; Seawater/*microbiology ; Single-Cell Analysis ; Synteny ; }, abstract = {Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems, usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be specific to deep water. Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%-86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets. Subclade Ic genomes dominated metagenomic fragment recruitment below the euphotic zone. They had similar COG distributions, high local synteny and shared a large number (69%) of orthologous clusters with SAR11 surface genomes, yet were distinct at the 16S rRNA gene and amino-acid level, and formed a separate, monophyletic group in phylogenetic trees. Subclade Ic genomes were enriched in genes associated with membrane/cell wall/envelope biosynthesis and showed evidence of unique phage defenses. The majority of subclade Ic-specfic genes were hypothetical, and some were highly abundant in deep ocean metagenomic data, potentially masking mechanisms for niche differentiation. However, the evidence suggests these organisms have a similar metabolism to their surface counterparts, and that subclade Ic adaptations to the deep ocean do not involve large variations in gene content, but rather more subtle differences previously observed deep ocean genomic data, like preferential amino-acid substitutions, larger coding regions among SAR11 clade orthologs, larger intergenic regions and larger estimated average genome size.}, } @article {pmid24448980, year = {2014}, author = {Rosewarne, CP and Pope, PB and Cheung, JL and Morrison, M}, title = {Analysis of the bovine rumen microbiome reveals a diversity of Sus-like polysaccharide utilization loci from the bacterial phylum Bacteroidetes.}, journal = {Journal of industrial microbiology & biotechnology}, volume = {41}, number = {3}, pages = {601-606}, pmid = {24448980}, issn = {1476-5535}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; *Cattle ; DNA, Bacterial/genetics ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; Polysaccharides/metabolism ; Prevotella/genetics/*isolation & purification ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Swine ; }, abstract = {Several unique Sus-like polysaccharide utilization loci (PULs) were identified from bacteria resident in bovine rumen microbiomes through functional screening of a fosmid library. The loci were phylogenetically assigned to the genus Prevotella within the phylum Bacteroidetes. These findings were augmented by a bioinformatic re-evaluation of ruminal Prevotella genomes, revealing additional loci not previously reported in the literature. Analysis of Bacteroidales-affiliated genomes reconstructed from a bovine rumen metagenome in a previous study further expanded the diversity of Sus-like PULs resident in this microbiome. Our findings suggest that Sus-like systems represent an important mechanism for degradation of a range of plant-derived glycans in ruminants.}, } @article {pmid24448554, year = {2014}, author = {Mejía-León, ME and Petrosino, JF and Ajami, NJ and Domínguez-Bello, MG and de la Barca, AM}, title = {Fecal microbiota imbalance in Mexican children with type 1 diabetes.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {3814}, pmid = {24448554}, issn = {2045-2322}, mesh = {Adolescent ; Bacteria/*classification/*genetics ; Case-Control Studies ; Child ; Computational Biology ; Cross-Sectional Studies ; DNA, Bacterial/genetics ; Diabetes Mellitus, Type 1/*microbiology ; Feces/*microbiology ; Female ; Follow-Up Studies ; Gastrointestinal Tract/microbiology ; Humans ; Male ; Mexico ; *Microbiota ; Prognosis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Dysbiosis of the intestinal microbiota affecting the gut barrier could be triggering Type 1 Diabetes (T1D), the second most frequent autoimmune disease in childhood. This study compared the structure of the fecal microbiota in 29 mestizo children aged 7-18 years, including 8 T1D at onset, 13 T1D after 2 years treatment, and 8 healthy controls. Clinical information was collected, predisposing haplotypes were determined; the fecal DNA was extracted, the V4 region of the 16S rRNA gene amplified and 454-pyrosequenced. The newly diagnosed T1D cases had high levels of the genus Bacteroides (p < 0.004), whereas the control group had a gut microbiota dominated by Prevotella. Children with T1D treated for ≥2 years had levels of Bacteroides and Prevotella compared to those of the control group. The gut microbiota of newly diagnosed T1D cases is altered, but whether it is involved in disease causation or is a consequence of host selection remains unclear.}, } @article {pmid24440491, year = {2014}, author = {Patra, AK and Yu, Z}, title = {Combinations of nitrate, saponin, and sulfate additively reduce methane production by rumen cultures in vitro while not adversely affecting feed digestion, fermentation or microbial communities.}, journal = {Bioresource technology}, volume = {155}, number = {}, pages = {129-135}, doi = {10.1016/j.biortech.2013.12.099}, pmid = {24440491}, issn = {1873-2976}, mesh = {Analysis of Variance ; Animals ; Archaea/drug effects/*metabolism ; Bacteria/drug effects/*metabolism ; Denaturing Gradient Gel Electrophoresis ; Digestion/drug effects/physiology ; Fermentation/drug effects ; Metagenome/genetics ; Methane/*biosynthesis ; Microbiota/drug effects/*physiology ; Nitrates/pharmacology ; Polymerase Chain Reaction ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Saponins/pharmacology ; Sulfates/pharmacology ; }, abstract = {This study investigated the effects of saponin (0.6g/L), nitrate (5mM) and sulfate (5mM), alone and in combinations, on methanogenesis, rumen fermentation, microbial community, and abundances of select microbial populations using in vitro rumen culture. Combinations of nitrate with saponin and/or sulfate additively suppressed methane production, with the lowest reduction (nearly 46%) observed for the combination of all the three inhibitors. None of the treatments adversely affected feed digestion or rumen fermentation. All the inhibitors, either alone or in combinations, did not alter the abundances of total bacteria, Ruminococcus albus, or archaea. However, saponin, alone and together with nitrate and/or sulfate, increased the abundance of Fibrobacter succinogenes and Ruminococcus flavefaciens, but decreased that of protozoa. DGGE analyses revealed limited changes in both bacterial and archaeal communities by the treatments. The nitrate-saponin-sulfate combination may be an effective and practical strategy to mitigate methane emission from ruminants.}, } @article {pmid24439897, year = {2014}, author = {Degnan, PH and Barry, NA and Mok, KC and Taga, ME and Goodman, AL}, title = {Human gut microbes use multiple transporters to distinguish vitamin B12 analogs and compete in the gut.}, journal = {Cell host & microbe}, volume = {15}, number = {1}, pages = {47-57}, pmid = {24439897}, issn = {1934-6069}, support = {R00 GM083343/GM/NIGMS NIH HHS/United States ; GM103574/GM/NIGMS NIH HHS/United States ; R01 GM103574/GM/NIGMS NIH HHS/United States ; R01 GM083303/GM/NIGMS NIH HHS/United States ; GM083343/GM/NIGMS NIH HHS/United States ; K01 DK089121/DK/NIDDK NIH HHS/United States ; DK089121/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Antibiosis/physiology ; Bacterial Outer Membrane Proteins/classification/*genetics/metabolism ; Bacteroides/genetics/metabolism ; Biological Transport ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/classification/*genetics/metabolism ; Gastrointestinal Tract/*microbiology ; *Gene Expression Regulation, Bacterial ; *Genome, Bacterial ; Humans ; Membrane Transport Proteins/classification/*genetics/metabolism ; Mice ; *Microbiota ; Phylogeny ; Species Specificity ; Symbiosis/physiology ; Vitamin B 12/analogs & derivatives/*metabolism ; }, abstract = {Genomic and metagenomic sequencing efforts, including human microbiome projects, reveal that microbes often encode multiple systems that appear to accomplish the same task. Whether these predictions reflect actual functional redundancies is unclear. We report that the prominent human gut symbiont Bacteroides thetaiotaomicron employs three functional, homologous vitamin B12 transporters that in at least two cases confer a competitive advantage in the presence of distinct B12 analogs (corrinoids). In the mammalian gut, microbial fitness can be determined by the presence or absence of a single transporter. The total number of distinct corrinoid transporter families in the human gut microbiome likely exceeds those observed in B. thetaiotaomicron by an order of magnitude. These results demonstrate that human gut microbes use elaborate mechanisms to capture and differentiate corrinoids in vivo and that apparent redundancies observed in these genomes can instead reflect hidden specificities that determine whether a microbe will colonize its host.}, } @article {pmid24438664, year = {2014}, author = {Bourlioux, P}, title = {[Current view on gut microbiota].}, journal = {Annales pharmaceutiques francaises}, volume = {72}, number = {1}, pages = {15-21}, doi = {10.1016/j.pharma.2013.09.001}, pmid = {24438664}, issn = {0003-4509}, mesh = {Animals ; Bacterial Translocation ; Complementary Therapies ; Environmental Pollutants/pharmacokinetics ; Feces/microbiology ; Humans ; Inflammation/microbiology/therapy ; Intestines/embryology/growth & development/*microbiology ; Mammals/microbiology ; *Microbiota ; Probiotics/therapeutic use ; Symbiosis ; Xenobiotics/pharmacokinetics ; }, abstract = {Gut microbiota is more and more important since metagenomic research have brought new knowledge on this topic especially for human health. Firstly, gut microbiota is a key element for our organism he lives in symbiosis with. Secondly, it interacts favorably with many physiological functions of our organism. Thirdly, at the opposite, it can be an active participant in intestinal pathologies linked to a dysbiosis mainly in chronic inflammatory bowel diseases like Crohn disease or ulcerative colitis but also in obesity, metabolic syndrome, and more prudently in autism and behavioral disorders. In order to keep a good health, it is essential to protect our gut microbiota as soon as our young age and maintain it healthy. Face to a more and more important number of publications for treating certain digestive diseases with fecal microbial transplantation, it needs to be very careful and recommend further studies in order to assess risks and define standardized protocols. Gut microbiota metabolic capacities towards xenobiotics need to be developed, and we must take an interest in the modifications they induce on medicinal molecules. On the other hand, it is essential to study the potent effects of pesticides and other pollutants on microbiota functions.}, } @article {pmid24437411, year = {2014}, author = {Martinez, FD}, title = {The human microbiome. Early life determinant of health outcomes.}, journal = {Annals of the American Thoracic Society}, volume = {11 Suppl 1}, number = {Suppl 1}, pages = {S7-12}, pmid = {24437411}, issn = {2325-6621}, support = {R01 HL056177/HL/NHLBI NIH HHS/United States ; HL-56177/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Asthma/immunology/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; *Hygiene Hypothesis ; Inflammation/immunology/microbiology ; Lung/*microbiology ; Mice ; Microbiota/*immunology ; Mucous Membrane/*microbiology ; Obesity/immunology/microbiology ; }, abstract = {The development of new technologies to isolate and identify microbial genomes has markedly increased our understanding of the role of microbiomes in health and disease. The idea, first proposed as part of the hygiene hypothesis, that environmental microbes influence the developmental trajectories of the immune system in early life, has now been considerably extended and refined. The abundant microbiota present in mucosal surfaces, especially the gut, is actively selected by the host through complex receptor systems that respond differentially depending on the molecular patterns presented to mucosal cells. Germ-free mice are more likely to develop allergic airway inflammation and show alterations in normal motor control and anxiety. These effects can be reversed by neonatal microbial recolonization but remain unchanged if recolonization occurs in adults. What emerges from these recent studies is the discovery of a complex, major early environmental determinant of lifetime human phenotypes. To change the natural course of asthma, obesity, and other chronic inflammatory conditions, active manipulation of the extensive bacterial, phage, and fungal metagenomes present in mucosal surfaces may be required, specifically during the developing years. Domesticating the human microbiome and adapting it to our health needs may be a challenge akin to, but far more complex than, the one faced by humanity when a few dozen species of plants and animals were domesticated during the transition between hunter-gatherer and sedentary societies after the end of the Pleistocene era.}, } @article {pmid24437410, year = {2014}, author = {Kiley, JP and Caler, EV}, title = {The lung microbiome. A new frontier in pulmonary medicine.}, journal = {Annals of the American Thoracic Society}, volume = {11 Suppl 1}, number = {Suppl 1}, pages = {S66-70}, pmid = {24437410}, issn = {2325-6621}, mesh = {Congresses as Topic ; Humans ; Lung/*microbiology ; *Metagenome ; *Microbiota ; Pulmonary Medicine/*trends ; }, } @article {pmid24437402, year = {2014}, author = {Beck, JM}, title = {ABCs of the lung microbiome.}, journal = {Annals of the American Thoracic Society}, volume = {11 Suppl 1}, number = {Suppl 1}, pages = {S3-6}, pmid = {24437402}, issn = {2325-6621}, support = {U01 HL098961/HL/NHLBI NIH HHS/United States ; HL98961/HL/NHLBI NIH HHS/United States ; }, mesh = {Bronchoalveolar Lavage Fluid/microbiology ; Humans ; Lung/*microbiology ; *Metagenome ; Microbiota/*genetics ; }, abstract = {The lungs of healthy humans have traditionally been considered to be sterile when examined by culture-based techniques. However, molecular identification techniques are now being used to explore the lung microbiome in ways that mirror study of other body sites and organ systems. Familiarity with population definitions and indices of diversity will lead to better understanding of the literature now coming to publication. Differences in methodology and sampling may contribute significantly to experimental variability, and the field has not coalesced around standard ways to present data or to perform statistical comparisons. This emerging and exciting field of investigation is leading to new ways of thinking about the lung and about lung disease.}, } @article {pmid24437400, year = {2014}, author = {Segal, LN and Blaser, MJ}, title = {A brave new world: the lung microbiota in an era of change.}, journal = {Annals of the American Thoracic Society}, volume = {11 Suppl 1}, number = {Suppl 1}, pages = {S21-7}, pmid = {24437400}, issn = {2325-6621}, support = {UH2 AR57506/AR/NIAMS NIH HHS/United States ; UH2 AR057506/AR/NIAMS NIH HHS/United States ; K23 AI102970/AI/NIAID NIH HHS/United States ; UL1 TR000038/TR/NCATS NIH HHS/United States ; R01 DK090989/DK/NIDDK NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*therapeutic use ; Gastrointestinal Tract/*microbiology ; Humans ; Immunity, Mucosal/immunology ; Inflammation ; Lung/immunology/*microbiology ; Metagenome ; *Microbiota ; Respiratory Mucosa/immunology/*microbiology ; }, abstract = {The development of culture-independent techniques has revolutionized our understanding of how our human cells interact with the even greater number of microbial inhabitants of our bodies. As part of this revolution, data are increasingly challenging the old dogma that in health, the lung mucosa is sterile. To understand how the lung microbiome may play a role in human health, we identified five major questions for lung microbiome research: (1) Is the lung sterile? (2) Is there a unique core microbiome in the lung? (3) How dynamic are the microbial populations? (4) How do pulmonary immune responses affect microbiome composition? and (5) Are the lungs influenced by the intestinal immune responses to the gut microbiome? From birth, we are exposed to continuous microbial challenges that shape our microbiome. In our changing environment, perturbation of the gut microbiome affects both human health and disease. With widespread antibiotic use, the ancient microbes that formerly resided within us are being lost, for example, Helicobacter pylori in the stomach. Animal models show that antibiotic exposure in early life has developmental consequences. Considering the potential effects of this altered microbiome on pulmonary responses will be critical for future investigations.}, } @article {pmid24437399, year = {2014}, author = {Walters, WA and Knight, R}, title = {Technology and techniques for microbial ecology via DNA sequencing.}, journal = {Annals of the American Thoracic Society}, volume = {11 Suppl 1}, number = {Suppl 1}, pages = {S16-20}, pmid = {24437399}, issn = {2325-6621}, support = {T32 GM008759/GM/NIGMS NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA, Bacterial/*analysis ; DNA, Ribosomal/*analysis ; Humans ; Metagenome/*genetics ; Microbiota/*genetics ; *Phylogeny ; Sequence Analysis, DNA/instrumentation/*methods ; Software ; }, abstract = {High-throughput sequencing technology, coupled with the use of conserved marker genes, has allowed for the understanding of communities of microbes (both culturable and unculturable) as well as their phylogenetic placement. The recent explosion of sequencing data prompted the development of software that could process the vast amount of data generated and phylogenetically differentiate groups of samples. Host-associated microbial studies have revealed that microbes are highly varied between individuals and fluctuate within an individual. Large-scale studies are being undertaken that include collection of extensive environmental data to help uncover the forces that shape microbial communities.}, } @article {pmid24429972, year = {2014}, author = {Martín, R and Miquel, S and Langella, P and Bermúdez-Humarán, LG}, title = {The role of metagenomics in understanding the human microbiome in health and disease.}, journal = {Virulence}, volume = {5}, number = {3}, pages = {413-423}, pmid = {24429972}, issn = {2150-5608}, mesh = {*Disease ; *Health ; Host-Pathogen Interactions ; Humans ; Metagenomics/*methods ; *Microbiota ; Symbiosis ; }, abstract = {The term microbiome refers to the genetic material of the catalog of microbial taxa associated with humans. As in all ecosystems, the microbiota reaches a dynamic equilibrium in the human body, which can be altered by environmental factors and external stimuli. Metagenomics is a relatively new field of study of microbial genomes within diverse environmental samples, which is of increasing importance in microbiology. The introduction of this ecological perception of microbiology is the key to achieving real knowledge about the influence of the microbiota in human health and disease. The aim of this review is to summarize the link between the human microbiota (focusing on the intestinal, vaginal, skin, and airway body sites) and health from this ecological point of view, highlighting the contribution of metagenomics in the advance of this field.}, } @article {pmid24429899, year = {2014}, author = {Kimura, N}, title = {Metagenomic approaches to understanding phylogenetic diversity in quorum sensing.}, journal = {Virulence}, volume = {5}, number = {3}, pages = {433-442}, pmid = {24429899}, issn = {2150-5608}, mesh = {Archaea/classification/genetics/*physiology ; Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; Biodiversity ; Metabolic Networks and Pathways ; Metagenomics/*methods ; *Microbial Interactions ; Phylogeny ; *Quorum Sensing ; }, abstract = {Quorum sensing, a form of cell-cell communication among bacteria, allows bacteria to synchronize their behaviors at the population level in order to control behaviors such as luminescence, biofilm formation, signal turnover, pigment production, antibiotics production, swarming, and virulence. A better understanding of quorum-sensing systems will provide us with greater insight into the complex interaction mechanisms used widely in the Bacteria and even the Archaea domain in the environment. Metagenomics, the use of culture-independent sequencing to study the genomic material of microorganisms, has the potential to provide direct information about the quorum-sensing systems in uncultured bacteria. This article provides an overview of the current knowledge of quorum sensing focused on phylogenetic diversity, and presents examples of studies that have used metagenomic techniques. Future technologies potentially related to quorum-sensing systems are also discussed.}, } @article {pmid24428801, year = {2014}, author = {Wilbanks, EG and Jaekel, U and Salman, V and Humphrey, PT and Eisen, JA and Facciotti, MT and Buckley, DH and Zinder, SH and Druschel, GK and Fike, DA and Orphan, VJ}, title = {Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh.}, journal = {Environmental microbiology}, volume = {16}, number = {11}, pages = {3398-3415}, pmid = {24428801}, issn = {1462-2920}, mesh = {Bacteria/genetics/*metabolism ; Chromatiaceae/genetics/*metabolism ; Metagenome ; *Microbial Consortia ; Oxidation-Reduction ; Photosynthesis ; Phylogeny ; Sulfates/metabolism ; Sulfides/metabolism ; Sulfur/*metabolism ; *Wetlands ; }, abstract = {Microbial metabolism is the engine that drives global biogeochemical cycles, yet many key transformations are carried out by microbial consortia over short spatiotemporal scales that elude detection by traditional analytical approaches. We investigate syntrophic sulfur cycling in the 'pink berry' consortia of the Sippewissett Salt Marsh through an integrative study at the microbial scale. The pink berries are macroscopic, photosynthetic microbial aggregates composed primarily of two closely associated species: sulfide-oxidizing purple sulfur bacteria (PB-PSB1) and sulfate-reducing bacteria (PB-SRB1). Using metagenomic sequencing and (34) S-enriched sulfate stable isotope probing coupled with nanoSIMS, we demonstrate interspecies transfer of reduced sulfur metabolites from PB-SRB1 to PB-PSB1. The pink berries catalyse net sulfide oxidation and maintain internal sulfide concentrations of 0-500 μm. Sulfide within the berries, captured on silver wires and analysed using secondary ion mass spectrometer, increased in abundance towards the berry interior, while δ(34) S-sulfide decreased from 6‰ to -31‰ from the exterior to interior of the berry. These values correspond to sulfate-sulfide isotopic fractionations (15-53‰) consistent with either sulfate reduction or a mixture of reductive and oxidative metabolisms. Together this combined metagenomic and high-resolution isotopic analysis demonstrates active sulfur cycling at the microscale within well-structured macroscopic consortia consisting of sulfide-oxidizing anoxygenic phototrophs and sulfate-reducing bacteria.}, } @article {pmid24422665, year = {2014}, author = {Beebe, K and Sampey, B and Watkins, SM and Milburn, M and Eckhart, AD}, title = {Understanding the apothecaries within: the necessity of a systematic approach for defining the chemical output of the human microbiome.}, journal = {Clinical and translational science}, volume = {7}, number = {1}, pages = {74-81}, pmid = {24422665}, issn = {1752-8062}, mesh = {Biotransformation ; Homeostasis ; Humans ; Metabolome ; Metagenome ; Microbial Interactions ; Microbiota/*physiology ; Quorum Sensing ; Xenobiotics/metabolism ; }, abstract = {The human microbiome harbors a massive diversity of microbes that effectively form an "organ" that strongly influences metabolism and immune function and hence, human health. Although the growing interest in the microbiome has chiefly arisen due to its impact on human physiology, the probable rules of operation are embedded in the roots of microbiology where chemical communication (i.e., with metabolites) is a dominant feature of coexistence. Indeed, recent examples in microbiome research offer the impression that the collective microbiome operates as an "apothecary," creating chemical concoctions that influence health and alter drug response. Although these principles are not unappreciated, the majority of emphasis is on metagenomics and research efforts often omit systematic efforts to interrogate the chemical component of the complex equation between microbial community and host phenotype. One of the reasons for this omission may be due to the inaccessibility to high-breadth, high-throughput, and scalable technologies. Since these technologies are now available, we propose that a more systematic effort to survey the host-microbiota chemical output be embedded into microbiome research as there is strong likelihood, and growing precedence, that this component may often be integral to developing our understanding of these ultimate apothecaries and how they impact human health.}, } @article {pmid24422656, year = {2014}, author = {Singh, BK and Quince, C and Macdonald, CA and Khachane, A and Thomas, N and Al-Soud, WA and Sørensen, SJ and He, Z and White, D and Sinclair, A and Crooks, B and Zhou, J and Campbell, CD}, title = {Loss of microbial diversity in soils is coincident with reductions in some specialized functions.}, journal = {Environmental microbiology}, volume = {16}, number = {8}, pages = {2408-2420}, doi = {10.1111/1462-2920.12353}, pmid = {24422656}, issn = {1462-2920}, mesh = {Biodiversity ; Ecosystem ; Genes, rRNA ; Metagenomics ; Metals, Heavy/*toxicity ; Microbial Consortia/*drug effects/physiology ; *Phylogeny ; RNA, Ribosomal, 16S/*classification/genetics ; *Soil Microbiology ; Soil Pollutants/*toxicity ; }, abstract = {Loss of microbial diversity is considered a major threat because of its importance for ecosystem functions, but there is a lack of conclusive evidence that diversity itself is reduced under anthropogenic stress, and about the consequences of diversity loss. Heavy metals are one of the largest, widespread pollutant types globally, and these represent a significant environmental stressor for terrestrial microbial communities. Using combined metagenomics and functional assays, we show that the compositional and functional response of microbial communities to long-term heavy metal stress results in a significant loss of diversity. Our results indicate that even at a moderate loss of diversity, some key specialized functions (carried out by specific groups) may be compromised. Together with previous work, our data suggest disproportionate impact of contamination on microbes that carry out specialized, but essential, ecosystem functions. Based on these findings, we propose a conceptual framework to explicitly consider diversity of functions and microbial functional groups to test the relationship between biodiversity and soil functions.}, } @article {pmid24421406, year = {2014}, author = {Passos da Silva, D and Castañeda-Ojeda, MP and Moretti, C and Buonaurio, R and Ramos, C and Venturi, V}, title = {Bacterial multispecies studies and microbiome analysis of a plant disease.}, journal = {Microbiology (Reading, England)}, volume = {160}, number = {Pt 3}, pages = {556-566}, doi = {10.1099/mic.0.074468-0}, pmid = {24421406}, issn = {1465-2080}, mesh = {Bacteria/*classification/genetics/metabolism ; Bacterial Infections/*microbiology ; Metabolic Networks and Pathways ; Metagenome ; *Microbiota ; Olea/microbiology ; Plant Diseases/*microbiology ; Pseudomonas/genetics/metabolism ; }, abstract = {Although the great majority of bacteria found in nature live in multispecies communities, microbiological studies have focused historically on single species or competition and antagonism experiments between different species. Future directions need to focus much more on microbial communities in order to better understand what is happening in the wild. We are using olive knot disease as a model to study the role and interaction of multispecies bacterial communities in disease establishment/development. In the olive knot, non-pathogenic bacterial species (e.g. Erwinia toletana) co-exist with the pathogen (Pseudomonas savastanoi pv. savastanoi); we have demonstrated cooperation among these two species via quorum sensing (QS) signal sharing. The outcome of this interaction is a more aggressive disease when co-inoculations are made compared with single inoculations. In planta experiments show that these two species co-localize in the olive knot, and this close proximity most probably facilitates exchange of QS signals and metabolites. In silico recreation of their metabolic pathways showed that they could have complementing pathways also implicating sharing of metabolites. Our microbiome studies of nine olive knot samples have shown that the olive knot community possesses great bacterial diversity; however. the presence of five genera (i.e. Pseudomonas, Pantoea, Curtobacterium, Pectobacterium and Erwinia) can be found in almost all samples.}, } @article {pmid24418972, year = {2014}, author = {Ferrer, M and Martins dos Santos, VA and Ott, SJ and Moya, A}, title = {Gut microbiota disturbance during antibiotic therapy: a multi-omic approach.}, journal = {Gut microbes}, volume = {5}, number = {1}, pages = {64-70}, pmid = {24418972}, issn = {1949-0984}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; Microbiota/*drug effects ; beta-Lactams/*pharmacology ; }, abstract = {It is known that the gastrointestinal tract (GIT) microbiota responds to different antibiotics in different ways and that while some antibiotics do not induce disturbances of the community, others drastically influence the richness, diversity, and prevalence of bacterial taxa. However, the metabolic consequences thereof, independent of the degree of the community shifts, are not clearly understood. In a recent article, we used an integrative OMICS approach to provide new insights into the metabolic shifts caused by antibiotic disturbance. The study presented here further suggests that specific bacterial lineage blooms occurring at defined stages of antibiotic intervention are mostly associated with organisms that possess improved survival and colonization mechanisms, such as those of the Enterococcus, Blautia, Faecalibacterium, and Akkermansia genera. The study also provides an overview of the most variable metabolic functions affected as a consequence of a β-lactam antibiotic intervention. Thus, we observed that anabolic sugar metabolism, the production of acetyl donors and the synthesis and degradation of intestinal/colonic epithelium components were among the most variable functions during the intervention. We are aware that these results have been established with a single patient and will require further confirmation with a larger group of individuals and with other antibiotics. Future directions for exploration of the effects of antibiotic interventions are discussed.}, } @article {pmid24413919, year = {2014}, author = {Wang, LY and Ke, WJ and Sun, XB and Liu, JF and Gu, JD and Mu, BZ}, title = {Comparison of bacterial community in aqueous and oil phases of water-flooded petroleum reservoirs using pyrosequencing and clone library approaches.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {9}, pages = {4209-4221}, doi = {10.1007/s00253-013-5472-y}, pmid = {24413919}, issn = {1432-0614}, mesh = {Bacteria/*classification/genetics ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Metagenomics ; Molecular Sequence Data ; Petroleum ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Water ; }, abstract = {Bacterial communities in both aqueous and oil phases of water-flooded petroleum reservoirs were characterized by molecular analysis of bacterial 16S rRNA genes obtained from Shengli Oil Field using DNA pyrosequencing and gene clone library approaches. Metagenomic DNA was extracted from the aqueous and oil phases and subjected to polymerase chain reaction amplification with primers targeting the bacterial 16S rRNA genes. The analysis by these two methods showed that there was a large difference in bacterial diversity between the aqueous and oil phases of the reservoir fluids, especially in the reservoirs with lower water cut. At a high phylogenetic level, the predominant bacteria detected by these two approaches were identical. However, pyrosequencing allowed the detection of more rare bacterial species than the clone library method. Statistical analysis showed that the diversity of the bacterial community of the aqueous phase was lower than that of the oil phase. Phylogenetic analysis indicated that the vast majority of sequences detected in the water phase were from members of the genus Arcobacter within the Epsilonproteobacteria, which is capable of degrading the intermediates of hydrocarbon degradation such as acetate. The oil phase of reservoir fluid samples was dominated by members of the genus Pseudomonas within the Gammaproteobacteria and the genus Sphingomonas within the Alphaproteobacteria, which have the ability to degrade crude oil through adherence to hydrocarbons under aerobic conditions. In addition, many anaerobes that could degrade the component of crude oil were also found in the oil phase of reservoir fluids, mainly in the reservoir with lower water cut. These were represented by Desulfovibrio spp., Thermodesulfovibrio spp., Thermodesulforhabdus spp., Thermotoga spp., and Thermoanaerobacterium spp. This research suggested that simultaneous analysis of DNA extracted from both aqueous and oil phases can facilitate a better understanding of the bacterial communities in water-flooded petroleum reservoirs.}, } @article {pmid24413286, year = {2014}, author = {Lu, K and Abo, RP and Schlieper, KA and Graffam, ME and Levine, S and Wishnok, JS and Swenberg, JA and Tannenbaum, SR and Fox, JG}, title = {Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis.}, journal = {Environmental health perspectives}, volume = {122}, number = {3}, pages = {284-291}, pmid = {24413286}, issn = {1552-9924}, support = {P30 ES002109/ES/NIEHS NIH HHS/United States ; P30 ES010126/ES/NIEHS NIH HHS/United States ; P42 ES005948/ES/NIEHS NIH HHS/United States ; R01 OD011141/OD/NIH HHS/United States ; }, mesh = {Animals ; Arsenic/*toxicity ; Chromatography, Liquid ; DNA Barcoding, Taxonomic ; Female ; Gastrointestinal Tract/drug effects/*microbiology ; Mass Spectrometry ; Metabolome ; Metagenome/*drug effects ; Mice, Inbred C57BL ; Microbiota/*drug effects ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics/metabolism ; Sequence Analysis, DNA ; Specific Pathogen-Free Organisms ; }, abstract = {BACKGROUND: The human intestine is host to an enormously complex, diverse, and vast microbial community-the gut microbiota. The gut microbiome plays a profound role in metabolic processing, energy production, immune and cognitive development, epithelial homeostasis, and so forth. However, the composition and diversity of the gut microbiome can be readily affected by external factors, which raises the possibility that exposure to toxic environmental chemicals leads to gut microbiome alteration, or dysbiosis. Arsenic exposure affects large human populations worldwide and has been linked to a number of diseases, including cancer, diabetes, and cardiovascular disorders.

OBJECTIVES: We investigated the impact of arsenic exposure on the gut microbiome composition and its metabolic profiles.

METHODS: We used an integrated approach combining 16S rRNA gene sequencing and mass spectrometry-based metabolomics profiling to examine the functional impact of arsenic exposure on the gut microbiome.

RESULTS: 16S rRNA gene sequencing revealed that arsenic significantly perturbed the gut microbiome composition in C57BL/6 mice after exposure to 10 ppm arsenic for 4 weeks in drinking water. Moreover, metabolomics profiling revealed a concurrent effect, with a number of gut microflora-related metabolites being perturbed in multiple biological matrices.

CONCLUSIONS: Arsenic exposure not only alters the gut microbiome community at the abundance level but also substantially disturbs its metabolic profiles at the function level. These findings may provide novel insights regarding perturbations of the gut microbiome and its functions as a potential new mechanism by which arsenic exposure leads to or exacerbates human diseases.

CITATION: Lu K, Abo RP, Schlieper KA, Graffam ME, Levine S, Wishnok JS, Swenberg JA, Tannenbaum SR, Fox JG. 2014. Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis. Environ Health Perspect 122:284-291; http://dx.doi.org/10.1289/ehp.1307429.}, } @article {pmid24407225, year = {2014}, author = {Cornish, JP and Sanchez-Alberola, N and O'Neill, PK and O'Keefe, R and Gheba, J and Erill, I}, title = {Characterization of the SOS meta-regulon in the human gut microbiome.}, journal = {Bioinformatics (Oxford, England)}, volume = {30}, number = {9}, pages = {1193-1197}, pmid = {24407225}, issn = {1367-4811}, mesh = {Bacterial Proteins/genetics/metabolism ; Bacteriophages/genetics ; Base Sequence ; Binding Sites ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenome ; Metagenomics/*methods ; *Microbiota ; *Regulon ; *SOS Response, Genetics ; Serine Endopeptidases/genetics/metabolism ; }, abstract = {MOTIVATION: Data from metagenomics projects remain largely untapped for the analysis of transcriptional regulatory networks. Here, we provide proof-of-concept that metagenomic data can be effectively leveraged to analyze regulatory networks by characterizing the SOS meta-regulon in the human gut microbiome.

RESULTS: We combine well-established in silico and in vitro techniques to mine the human gut microbiome data and determine the relative composition of the SOS network in a natural setting. Our analysis highlights the importance of translesion synthesis as a primary function of the SOS response. We predict the association of this network with three novel protein clusters involved in cell wall biogenesis, chromosome partitioning and restriction modification, and we confirm binding of the SOS response transcriptional repressor to sites in the promoter of a cell wall biogenesis enzyme, a phage integrase and a death-on-curing protein. We discuss the implications of these findings and the potential for this approach for metagenome analysis.}, } @article {pmid24402126, year = {2014}, author = {Del Chierico, F and Gnani, D and Vernocchi, P and Petrucca, A and Alisi, A and Dallapiccola, B and Nobili, V and Lorenza, P}, title = {Meta-omic platforms to assist in the understanding of NAFLD gut microbiota alterations: tools and applications.}, journal = {International journal of molecular sciences}, volume = {15}, number = {1}, pages = {684-711}, pmid = {24402126}, issn = {1422-0067}, mesh = {Animals ; Gastrointestinal Tract/microbiology ; Humans ; Metabolomics ; Metagenomics ; *Microbiota ; Non-alcoholic Fatty Liver Disease/metabolism/*microbiology/pathology ; Peptide Mapping ; Proteomics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD) is the most common cause of chronic liver disease worldwide as a result of the increasing prevalence of obesity, starting from early life stages. It is characterized by a spectrum of liver diseases ranging from simple fatty liver (NAFL) to steatohepatitis (NASH), with a possible progression to fibrosis, thus increasing liver-related morbidity and mortality. NAFLD development is driven by the co-action of several risk factors, including obesity and metabolic syndrome, which may be both genetically induced and diet-related. Recently, particular attention has been paid to the gut-liver axis, which may play a physio-pathological role in the onset and progression of the disease. The gut microbiota is intended to act as a bioreactor that can guarantee autonomous metabolic and immunological functions and that can drive functional strategies within the environment of the body in response to external stimuli. The complexity of the gut microbiota suggests that it behaves as an organ. Therefore, the concept of the gut-liver axis must be complemented with the gut-microbiota-liver network due to the high intricacy of the microbiota components and metabolic activities; these activities form the active diet-driven power plant of the host. Such complexity can only be revealed using systems biology, which can integrate clinical phenomics and gut microbiota data.}, } @article {pmid24392128, year = {2014}, author = {Wang, Y and Liu, L and Chen, L and Chen, T and Sun, F}, title = {Comparison of metatranscriptomic samples based on k-tuple frequencies.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e84348}, pmid = {24392128}, issn = {1932-6203}, support = {R21 HG006199/HG/NHGRI NIH HHS/United States ; R21HG006199/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Cluster Analysis ; Computational Biology/methods ; Databases, Nucleic Acid ; Internet ; *Metagenomics/methods ; Microbiota ; Seawater/microbiology ; Software ; *Transcriptome ; Water Microbiology ; }, abstract = {BACKGROUND: The comparison of samples, or beta diversity, is one of the essential problems in ecological studies. Next generation sequencing (NGS) technologies make it possible to obtain large amounts of metagenomic and metatranscriptomic short read sequences across many microbial communities. De novo assembly of the short reads can be especially challenging because the number of genomes and their sequences are generally unknown and the coverage of each genome can be very low, where the traditional alignment-based sequence comparison methods cannot be used. Alignment-free approaches based on k-tuple frequencies, on the other hand, have yielded promising results for the comparison of metagenomic samples. However, it is not known if these approaches can be used for the comparison of metatranscriptome datasets and which dissimilarity measures perform the best.

RESULTS: We applied several beta diversity measures based on k-tuple frequencies to real metatranscriptomic datasets from pyrosequencing 454 and Illumina sequencing platforms to evaluate their effectiveness for the clustering of metatranscriptomic samples, including three d2-type dissimilarity measures, one dissimilarity measure in CVTree, one relative entropy based measure S2 and three classical 1p-norm distances. Results showed that the measure d2(S) can achieve superior performance on clustering metatranscriptomic samples into different groups under different sequencing depths for both 454 and Illumina datasets, recovering environmental gradients affecting microbial samples, classifying coexisting metagenomic and metatranscriptomic datasets, and being robust to sequencing errors. We also investigated the effects of tuple size and order of the background Markov model. A software pipeline to implement all the steps of analysis is built and is available at http://code.google.com/p/d2-tools/.

CONCLUSIONS: The k-tuple based sequence signature measures can effectively reveal major groups and gradient variation among metatranscriptomic samples from NGS reads. The d2(S) dissimilarity measure performs well in all application scenarios and its performance is robust with respect to tuple size and order of the Markov model.}, } @article {pmid24391833, year = {2013}, author = {Ghosh, TS and Gupta, SS and Nair, GB and Mande, SS}, title = {In silico analysis of antibiotic resistance genes in the gut microflora of individuals from diverse geographies and age-groups.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e83823}, pmid = {24391833}, issn = {1932-6203}, mesh = {Adult ; Age Factors ; Anti-Bacterial Agents/*pharmacology ; Biomarkers/metabolism ; Child ; Computational Biology ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Multiple/genetics ; Gastrointestinal Tract/*drug effects/metabolism/microbiology ; *Gene Expression Profiling ; Genes, Bacterial/*genetics ; Geography ; Humans ; Metagenome/*genetics ; Microbiota/drug effects/*genetics ; Oligonucleotide Array Sequence Analysis ; }, abstract = {The spread of antibiotic resistance, originating from the rampant and unrestrictive use of antibiotics in humans and livestock over the past few decades has emerged as a global health problem. This problem has been further compounded by recent reports implicating the gut microbial communities to act as reservoirs of antibiotic resistance. We have profiled the presence of probable antibiotic resistance genes in the gut flora of 275 individuals from eight different nationalities. For this purpose, available metagenomic data sets corresponding to 275 gut microbiomes were analyzed. Sequence similarity searches of the genomic fragments constituting each of these metagenomes were performed against genes conferring resistance to around 240 antibiotics. Potential antibiotic resistance genes conferring resistance against 53 different antibiotics were detected in the human gut microflora analysed in this study. In addition to several geography/country-specific patterns, four distinct clusters of gut microbiomes, referred to as 'Resistotypes', exhibiting similarities in their antibiotic resistance profiles, were identified. Groups of antibiotics having similarities in their resistance patterns within each of these clusters were also detected. Apart from this, mobile multi-drug resistance gene operons were detected in certain gut microbiomes. The study highlighted an alarmingly high abundance of antibiotic resistance genes in two infant gut microbiomes. The results obtained in the present study presents a holistic 'big picture' on the spectra of antibiotic resistance within our gut microbiota across different geographies. Such insights may help in implementation of new regulations and stringency on the existing ones.}, } @article {pmid24391809, year = {2013}, author = {Siddharth, J and Holway, N and Parkinson, SJ}, title = {A Western diet ecological module identified from the 'humanized' mouse microbiota predicts diet in adults and formula feeding in children.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e83689}, pmid = {24391809}, issn = {1932-6203}, mesh = {Adult ; Animals ; Bacteria/classification/genetics/*growth & development ; *Bottle Feeding ; Breast Feeding ; Child, Preschool ; *Diet ; Feces/*microbiology ; *Feeding Behavior ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenome ; Mice ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The interplay between diet and the microbiota has been implicated in the growing frequency of chronic diseases associated with the Western lifestyle. However, the complexity and variability of microbial ecology in humans and preclinical models has hampered identification of the molecular mechanisms underlying the association of the microbiota in this context. We sought to address two key questions. Can the microbial ecology of preclinical models predict human populations? And can we identify underlying principles that surpass the plasticity of microbial ecology in humans? To do this, we focused our study on diet; perhaps the most influential factor determining the composition of the gut microbiota. Beginning with a study in 'humanized' mice we identified an interactive module of 9 genera allied with Western diet intake. This module was applied to a controlled dietary study in humans. The abundance of the Western ecological module correctly predicted the dietary intake of 19/21 top and 21/21 of the bottom quartile samples inclusive of all 5 Western and 'low-fat' diet subjects, respectively. In 98 volunteers the abundance of the Western module correlated appropriately with dietary intake of saturated fatty acids, fat-soluble vitamins and fiber. Furthermore, it correlated with the geographical location and dietary habits of healthy adults from the Western, developing and third world. The module was also coupled to dietary intake in children (and piglets) correlating with formula (vs breast) feeding and associated with a precipitous development of the ecological module in young children. Our study provides a conceptual platform to translate microbial ecology from preclinical models to humans and identifies an ecological network module underlying the association of the gut microbiota with Western dietary habits.}, } @article {pmid24390919, year = {2014}, author = {Sirota, I and Zarek, SM and Segars, JH}, title = {Potential influence of the microbiome on infertility and assisted reproductive technology.}, journal = {Seminars in reproductive medicine}, volume = {32}, number = {1}, pages = {35-42}, pmid = {24390919}, issn = {1526-4564}, support = {ZIE HD008737-12//Intramural NIH HHS/United States ; }, mesh = {Adult ; Anti-Bacterial Agents/therapeutic use ; Cytokines/physiology ; Embryo Implantation ; Embryo Transfer ; Estrogens/blood ; Female ; Humans ; Infertility, Female/*microbiology ; Lactobacillus ; Microbiota/*physiology ; Pregnancy ; Progesterone/blood ; *Reproductive Techniques, Assisted ; Vagina/microbiology ; Vaginosis, Bacterial/microbiology ; }, abstract = {Although an altered vaginal microbiota has been demonstrated to affect parturition, its role in assisted reproductive technologies is uncertain. Nevertheless, the effect of known pathogens such as Mycoplasma tuberculosis, Chlamydia trachomatis, and Neisseria gonorrhoeae is clear, causing subclinical changes thought to be risk factors in subfertility. The Human Microbiome Project (HMP) has allowed for metagenomic studies to aid in characterizing normal vaginal flora. Recent findings from the HMP demonstrate that many different species of Lactobacillus are present in the vaginal tract, with a few that predominate. Studies that characterize the vaginal microbiome in assisted reproductive technology support the hypothesis that colonizing the transfer-catheter tip with Lactobacillus crispatus at the time of embryo transfer may increase the rates of implantation and live birth rate while decreasing the rate of infection. In addition, there is some evidence that a progesterone-resistant endometrium might increase the risk of an abnormal vaginal microbiome.}, } @article {pmid24390915, year = {2014}, author = {Ma, J and Prince, A and Aagaard, KM}, title = {Use of whole genome shotgun metagenomics: a practical guide for the microbiome-minded physician scientist.}, journal = {Seminars in reproductive medicine}, volume = {32}, number = {1}, pages = {5-13}, doi = {10.1055/s-0033-1361817}, pmid = {24390915}, issn = {1526-4564}, mesh = {Bacteria/classification ; Computational Biology/methods ; Databases, Genetic ; Female ; Gene Expression/genetics/physiology ; Genome, Human/*genetics ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics/*physiology ; Pregnancy ; Reproductive Medicine ; }, abstract = {Whole genome shotgun sequencing (WGS) has been increasingly recognized as the most comprehensive and robust approach for metagenomics research. When compared with 16S-based metagenomics, it offers the advantage of identification of species level taxonomy and the estimation of metabolic pathway activities from human and environmental samples. Several large-scale metagenomic projects have been recently conducted or are currently underway utilizing WGS. With the generation of vast amounts of data, the bioinformatics and computational analysis of WGS results become vital for the success of a metagenomics study. However, each step in the WGS data analysis, including metagenome assembly, gene prediction, taxonomy identification, function annotation, and pathway analysis, is complicated by the shear amount of data. Algorithms and tools have been developed specifically to handle WGS-generated metagenomics data with the hope of reducing the requirement on computational time and storage space. Here, we present an overview of the current state of metagenomics through WGS sequencing, challenges frequently encountered, and up-to-date solutions. Several applications that are uniquely applicable to microbiome studies in reproductive and perinatal medicine are also discussed.}, } @article {pmid24386245, year = {2013}, author = {Nelson, TM and Rogers, TL and Brown, MV}, title = {The gut bacterial community of mammals from marine and terrestrial habitats.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e83655}, pmid = {24386245}, issn = {1932-6203}, mesh = {Animals ; Bacteria/*classification/genetics ; Biodiversity ; Diet ; Ecosystem ; Gastrointestinal Tract/*microbiology ; Mammals ; Metagenome ; *Microbiota ; Phylogeny ; }, abstract = {After birth, mammals acquire a community of bacteria in their gastro-intestinal tract, which harvests energy and provides nutrients for the host. Comparative studies of numerous terrestrial mammal hosts have identified host phylogeny, diet and gut morphology as primary drivers of the gut bacterial community composition. To date, marine mammals have been excluded from these comparative studies, yet they represent distinct examples of evolutionary history, diet and lifestyle traits. To provide an updated understanding of the gut bacterial community of mammals, we compared bacterial 16S rRNA gene sequence data generated from faecal material of 151 marine and terrestrial mammal hosts. This included 42 hosts from a marine habitat. When compared to terrestrial mammals, marine mammals clustered separately and displayed a significantly greater average relative abundance of the phylum Fusobacteria. The marine carnivores (Antarctic and Arctic seals) and the marine herbivore (dugong) possessed significantly richer gut bacterial community than terrestrial carnivores and terrestrial herbivores, respectively. This suggests that evolutionary history and dietary items specific to the marine environment may have resulted in a gut bacterial community distinct to that identified in terrestrial mammals. Finally we hypothesize that reduced marine trophic webs, whereby marine carnivores (and herbivores) feed directly on lower trophic levels, may expose this group to high levels of secondary metabolites and influence gut microbial community richness.}, } @article {pmid24386174, year = {2013}, author = {Torrazza, RM and Ukhanova, M and Wang, X and Sharma, R and Hudak, ML and Neu, J and Mai, V}, title = {Intestinal microbial ecology and environmental factors affecting necrotizing enterocolitis.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e83304}, pmid = {24386174}, issn = {1932-6203}, support = {R01 HD059143/HD/NICHD NIH HHS/United States ; R01 HD 059143/HD/NICHD NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Bifidobacterium/classification/genetics ; Biodiversity ; Case-Control Studies ; Cluster Analysis ; Enterocolitis, Necrotizing/drug therapy/*etiology/microbiology ; *Environment ; Female ; Humans ; Infant, Newborn ; Infant, Premature ; Infant, Premature, Diseases/drug therapy/*etiology/microbiology ; Intestines/drug effects/*microbiology/*pathology ; Male ; Metagenome ; Microbiota ; RNA, Ribosomal, 16S ; Risk Factors ; }, abstract = {Necrotizing enterocolitis (NEC) is the most devastating intestinal disease affecting preterm infants. In addition to being associated with short term mortality and morbidity, survivors are left with significant long term sequelae. The cost of caring for these infants is high. Epidemiologic evidence suggests that use of antibiotics and type of feeding may cause an intestinal dysbiosis important in the pathogenesis of NEC, but the contribution of specific infectious agents is poorly understood. Fecal samples from preterm infants ≤ 32 weeks gestation were analyzed using 16S rRNA based methods at 2, 1, and 0 weeks, prior to diagnosis of NEC in 18 NEC cases and 35 controls. Environmental factors such as antibiotic usage, feeding type (human milk versus formula) and location of neonatal intensive care unit (NICU) were also evaluated. Microbiota composition differed between the three neonatal units where we observed differences in antibiotic usage. In NEC cases we observed a higher proportion of Proteobacteria (61%) two weeks and of Actinobacteria (3%) 1 week before diagnosis of NEC compared to controls (19% and 0.4%, respectively) and lower numbers of Bifidobacteria counts and Bacteroidetes proportions in the weeks before NEC diagnosis. In the first fecal samples obtained during week one of life we detected a novel signature sequence, distinct from but matching closest to Klebsiella pneumoniae, that was strongly associated with NEC development later in life. Infants who develop NEC exhibit a different pattern of microbial colonization compared to controls. Antibiotic usage correlated with these differences and combined with type of feeding likely plays a critical role in the development of NEC.}, } @article {pmid24385352, year = {2013}, author = {Sorokovikova, EG and Belykh, OI and Gladkikh, AS and Kotsar, OV and Tikhonova, IV and Timoshkin, OA and Parfenova, VV}, title = {Diversity of cyanobacterial species and phylotypes in biofilms from the littoral zone of Lake Baikal.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {51}, number = {6}, pages = {757-765}, pmid = {24385352}, issn = {1976-3794}, mesh = {*Biodiversity ; *Biofilms ; Cyanobacteria/classification/genetics/isolation & purification/*physiology ; Ecosystem ; Geologic Sediments/*microbiology ; Lakes/analysis ; Molecular Sequence Data ; Phylogeny ; Siberia ; }, abstract = {The majority of naturally occurring biofilms contain numerous microorganisms that have not yet been cultured. Additionally, there is little information available regarding the genetic structure and species diversity of these communities. Therefore, we characterised the species diversity, structure and metagenome of biofilms grown on stones and steel plates in the littoral zone of Lake Baikal (East Siberia, Russia) by applying three different approaches. First, light microscopy enabled identification of the species diversity of biofilm-forming cyanobacteria on different substrates with the dominance of Rivularia rufescens, Tolypothrix limbata, Chamaesiphon fuscus, Ch. subglobosus, and Heteroleibleinia pusilla. Additionally, scanning electron microscopy was used to show the spatial structure of biofilms. Finally, sequence analysis of 30,660 16S rRNA clones indicated a high diversity within the biofilm communities, with the majority of the microbes being closely related to Cyanobacteria (8-46% sequences), Proteobacteria (14-43%), and Bacteroidetes (10-41%). Rivularia sp., Pseudanabaena sp., and Chamaesiphon spp. were the dominant cyanobacterial phylotypes.}, } @article {pmid24385351, year = {2013}, author = {Aslam, Z and Yasir, M and Yoon, HS and Jeon, CO and Chung, YR}, title = {Diversity of the bacterial community in the rice rhizosphere managed under conventional and no-tillage practices.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {51}, number = {6}, pages = {747-756}, pmid = {24385351}, issn = {1976-3794}, mesh = {Agriculture/*methods ; Bacteria/classification/genetics/*isolation & purification ; *Biodiversity ; Molecular Sequence Data ; Oryza/growth & development/*microbiology ; Phylogeny ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Bacterial diversity in the rice rhizosphere at different rice growth stages, managed under conventional and no-tillage practices, was explored using a culture-based approach. Actinobacteria are among the bacterial phyla abundant in the rice rhizosphere. Their diversity was further examined by constructing metagenomic libraries based on the 16S rRNA gene, using actinobacterial- and streptomycete-specific polymerase chain reaction (PCR) primers. The study included 132 culturable strains and 125 clones from the 16S rRNA gene libraries. In conventional tillage, there were 38% Proteobacteria, 22% Actinobacteria, 33% Firmicutes, 5% Bacteroidetes, and 2% Acidobacteria, whereas with no-tillage management there were 63% Proteobacteria, 24% Actinobacteria, 6% Firmicutes, and 8% Bacteroidetes as estimated using the culture-dependent method during the four stages of rice cultivation. Principal coordinates analysis was used to cluster the bacterial communities along axes of maximal variance. The different growth stages of rice appeared to influence the rhizosphere bacterial profile for both cultivation practices. Novel clones with low similarities (89-97%) to Actinobacteria and Streptomyces were retrieved from both rice fields by screening the 16S rRNA gene libraries using actinobacterial- and streptomycete-specific primers. By comparing the actinobacterial community retrieved by culture-dependent and molecular methods, it was clear that a more comprehensive assessment of microbial diversity in the rice rhizosphere can be obtained using a combination of both techniques than by using either method alone. We also succeeded in culturing a number of bacteria that were previously described as unculturable. These were in a phylogenetically deep lineage when compared with related cultivable genera.}, } @article {pmid24376500, year = {2013}, author = {Brim, H and Yooseph, S and Zoetendal, EG and Lee, E and Torralbo, M and Laiyemo, AO and Shokrani, B and Nelson, K and Ashktorab, H}, title = {Microbiome analysis of stool samples from African Americans with colon polyps.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e81352}, pmid = {24376500}, issn = {1932-6203}, support = {UL1 RR031975/RR/NCRR NIH HHS/United States ; UL1 TR000101/TR/NCATS NIH HHS/United States ; UL1RR031975/RR/NCRR NIH HHS/United States ; UL1TR000101/TR/NCATS NIH HHS/United States ; G12 MD007597/MD/NIMHD NIH HHS/United States ; G12MD007597/MD/NIMHD NIH HHS/United States ; }, mesh = {*Black or African American ; Bacteria/classification ; Colonic Polyps/*microbiology ; Feces/*microbiology ; Humans ; Metagenomics ; *Microbiota/genetics ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Colonic polyps are common tumors occurring in ~50% of Western populations with ~10% risk of malignant progression. Dietary agents have been considered the primary environmental exposure to promote colorectal cancer (CRC) development. However, the colonic mucosa is permanently in contact with the microbiota and its metabolic products including toxins that also have the potential to trigger oncogenic transformation.

AIM: To analyze fecal DNA for microbiota composition and functional potential in African Americans with pre-neoplastic lesions.

MATERIALS & METHODS: We analyzed the bacterial composition of stool samples from 6 healthy individuals and 6 patients with colon polyps using 16S ribosomal RNA-based phylogenetic microarray; the Human intestinal Tract Chip (HITChip) and 16S rRNA gene barcoded 454 pyrosequencing. The functional potential was determined by sequence-based metagenomics using 454 pyrosequencing.

RESULTS: Fecal microbiota profiling of samples from the healthy and polyp patients using both a phylogenetic microarraying (HITChip) and barcoded 454 pyrosequencing generated similar results. A distinction between both sets of samples was only obtained when the analysis was performed at the sub-genus level. Most of the species leading to the dissociation were from the Bacteroides group. The metagenomic analysis did not reveal major differences in bacterial gene prevalence/abundances between the two groups even when the analysis and comparisons were restricted to available Bacteroides genomes.

CONCLUSION: This study reveals that at the pre-neoplastic stages, there is a trend showing microbiota changes between healthy and colon polyp patients at the sub-genus level. These differences were not reflected at the genome/functions levels. Bacteria and associated functions within the Bacteroides group need to be further analyzed and dissected to pinpoint potential actors in the early colon oncogenic transformation in a large sample size.}, } @article {pmid24375144, year = {2014}, author = {Luo, C and Rodriguez-R, LM and Johnston, ER and Wu, L and Cheng, L and Xue, K and Tu, Q and Deng, Y and He, Z and Shi, JZ and Yuan, MM and Sherry, RA and Li, D and Luo, Y and Schuur, EA and Chain, P and Tiedje, JM and Zhou, J and Konstantinidis, KT}, title = {Soil microbial community responses to a decade of warming as revealed by comparative metagenomics.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {5}, pages = {1777-1786}, pmid = {24375144}, issn = {1098-5336}, mesh = {Biota/*radiation effects ; Carbon/metabolism ; *Global Warming ; Humans ; Metabolic Networks and Pathways ; *Metagenomics ; Midwestern United States ; Nitrogen/metabolism ; *Soil Microbiology ; }, abstract = {Soil microbial communities are extremely complex, being composed of thousands of low-abundance species (<0.1% of total). How such complex communities respond to natural or human-induced fluctuations, including major perturbations such as global climate change, remains poorly understood, severely limiting our predictive ability for soil ecosystem functioning and resilience. In this study, we compared 12 whole-community shotgun metagenomic data sets from a grassland soil in the Midwestern United States, half representing soil that had undergone infrared warming by 2°C for 10 years, which simulated the effects of climate change, and the other half representing the adjacent soil that received no warming and thus, served as controls. Our analyses revealed that the heated communities showed significant shifts in composition and predicted metabolism, and these shifts were community wide as opposed to being attributable to a few taxa. Key metabolic pathways related to carbon turnover, such as cellulose degradation (∼13%) and CO2 production (∼10%), and to nitrogen cycling, including denitrification (∼12%), were enriched under warming, which was consistent with independent physicochemical measurements. These community shifts were interlinked, in part, with higher primary productivity of the aboveground plant communities stimulated by warming, revealing that most of the additional, plant-derived soil carbon was likely respired by microbial activity. Warming also enriched for a higher abundance of sporulation genes and genomes with higher G+C content. Collectively, our results indicate that microbial communities of temperate grassland soils play important roles in mediating feedback responses to climate change and advance the understanding of the molecular mechanisms of community adaptation to environmental perturbations.}, } @article {pmid24373613, year = {2013}, author = {Barfod, KK and Roggenbuck, M and Hansen, LH and Schjørring, S and Larsen, ST and Sørensen, SJ and Krogfelt, KA}, title = {The murine lung microbiome in relation to the intestinal and vaginal bacterial communities.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {303}, pmid = {24373613}, issn = {1471-2180}, mesh = {Animals ; Bacteria/*classification/*genetics ; Bronchoalveolar Lavage Fluid/microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Lung/*microbiology ; Metagenome ; Mice ; Mice, Inbred BALB C ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vagina/*microbiology ; Vaginal Douching ; }, abstract = {BACKGROUND: This work provides the first description of the bacterial population of the lung microbiota in mice. The aim of this study was to examine the lung microbiome in mice, the most used animal model for inflammatory lung diseases such as COPD, cystic fibrosis and asthma.Bacterial communities from broncho-alveolar lavage fluids and lung tissue were compared to samples taken from fecal matter (caecum) and vaginal lavage fluid from female BALB/cJ mice.

RESULTS: Using a customized 16S rRNA sequencing protocol amplifying the V3-V4 region our study shows that the mice have a lung microbiome that cluster separately from mouse intestinal microbiome (caecum). The mouse lung microbiome is dominated by Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Cyanobacteria overlapping the vaginal microbiome. We also show that removal of host tissue or cells from lung fluid during the DNA extraction step has an impact on the resulting bacterial community profile. Sample preparation needs to be considered when choosing an extraction method and interpreting data.

CONCLUSIONS: We have consistently amplified bacterial DNA from mouse lungs that is distinct from the intestinal microbiome in these mice. The gut microbiome has been extensively studied for its links to development of disease. Here we suggest that also the lung microbiome could be important in relation to inflammatory lung diseases. Further research is needed to understand the contribution of the lung microbiome and the gut-lung axis to the development of lung diseases such as COPD and asthma.}, } @article {pmid24369878, year = {2013}, author = {Wei, X and Yan, X and Zou, D and Yang, Z and Wang, X and Liu, W and Wang, S and Li, X and Han, J and Huang, L and Yuan, J}, title = {Abnormal fecal microbiota community and functions in patients with hepatitis B liver cirrhosis as revealed by a metagenomic approach.}, journal = {BMC gastroenterology}, volume = {13}, number = {}, pages = {175}, pmid = {24369878}, issn = {1471-230X}, mesh = {Adult ; Case-Control Studies ; Colon/*microbiology ; DNA, Bacterial/*analysis ; Feces/microbiology ; Female ; Hepatitis B/complications/*microbiology ; Humans ; Liver Cirrhosis/etiology/*microbiology ; Male ; *Metagenome ; Microbiota/*genetics/physiology ; Middle Aged ; }, abstract = {BACKGROUND: Assessment and characterization of human colon microbiota is now a major research area in human diseases, including in patients with hepatitis B liver cirrhosis (HBLC).

METHODS: We recruited 120 patients with HBLC and 120 healthy controls. The fecal microbial community and functions in the two groups were analyzed using high-throughput Solexa sequencing of the complete metagenomic DNA and bioinformatics methods.

RESULTS: Community and metabolism-wide changes of the fecal microbiota in 20 HBLC patients and 20 healthy controls were observed and compared. A negative correlation was observed between the Child-Turcotte-Pugh scores and Bacteroidetes (P < 0.01), whereas a positive correlation was observed between the scores and Enterobacteriaceae and Veillonella (P < 0.01). Analysis of the additional 200 fecal microbiota samples demonstrated that these intestinal microbial markers might be useful for distinguishing liver cirrhosis microbiota samples from normal ones. The functional diversity was significantly reduced in the fecal microbiota of cirrhotic patients compared with in the controls. At the module or pathway levels, the fecal microbiota of the HBLC patients showed enrichment in the metabolism of glutathione, gluconeogenesis, branched-chain amino acid, nitrogen, and lipid (P < 0.05), whereas there was a decrease in the level of aromatic amino acid, bile acid and cell cycle related metabolism (P < 0.05).

CONCLUSIONS: Extensive differences in the microbiota community and metabolic potential were detected in the fecal microbiota of cirrhotic patients. The intestinal microbial community may act as an independent organ to regulate the body's metabolic balance, which may affect the prognosis for HBLC patients.}, } @article {pmid24369151, year = {2014}, author = {Tanaseichuk, O and Borneman, J and Jiang, T}, title = {Phylogeny-based classification of microbial communities.}, journal = {Bioinformatics (Oxford, England)}, volume = {30}, number = {4}, pages = {449-456}, doi = {10.1093/bioinformatics/btt700}, pmid = {24369151}, issn = {1367-4811}, mesh = {Algorithms ; Bacteria/*classification/genetics ; Computational Biology/*methods ; Computer Simulation ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Microbiota/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {MOTIVATION: Next-generation sequencing coupled with metagenomics has led to the rapid growth of sequence databases and enabled a new branch of microbiology called comparative metagenomics. Comparative metagenomic analysis studies compositional patterns within and between different environments providing a deep insight into the structure and function of complex microbial communities. It is a fast growing field that requires the development of novel supervised learning techniques for addressing challenges associated with metagenomic data, e.g. sensitivity to the choice of sequence similarity cutoff used to define operational taxonomic units (OTUs), high dimensionality and sparsity of the data and so forth. On the other hand, the natural properties of microbial community data may provide useful information about the structure of the data. For example, similarity between species encoded by a phylogenetic tree captures the relationship between OTUs and may be useful for the analysis of complex microbial datasets where the diversity patterns comprise features at multiple taxonomic levels. Even though some of the challenges have been addressed by learning algorithms in the literature, none of the available methods take advantage of the inherent properties of metagenomic data.

RESULTS: We proposed a novel supervised classification method for microbial community samples, where each sample is represented as a set of OTU frequencies, which takes advantage of the natural structure in microbial community data encoded by a phylogenetic tree. This model allows us to take advantage of environment-specific compositional patterns that may contain features at multiple granularity levels. Our method is based on the multinomial logistic regression model with a tree-guided penalty function. Additionally, we proposed a new simulation framework for generating 16S ribosomal RNA gene read counts that may be useful in comparative metagenomics research. Our experimental results on simulated and real data show that the phylogenetic information used in our method improves the classification accuracy.

http://www.cs.ucr.edu/~tanaseio/metaphyl.htm.}, } @article {pmid24361423, year = {2014}, author = {Mathieu, A and Vogel, TM and Simonet, P}, title = {The future of skin metagenomics.}, journal = {Research in microbiology}, volume = {165}, number = {2}, pages = {69-76}, doi = {10.1016/j.resmic.2013.12.002}, pmid = {24361423}, issn = {1769-7123}, mesh = {Humans ; Metagenomics/*methods/trends ; *Microbiota ; Skin/*microbiology ; }, abstract = {Metagenomics, the direct exploitation of environmental microbial DNA, is complementary to traditional culture-based approaches for deciphering taxonomic and functional microbial diversity in a plethora of ecosystems, including those related to the human body such as the mouth, saliva, teeth, gut or skin. DNA extracted from human skin analyzed by sequencing the PCR-amplified rrs gene has already revealed the taxonomic diversity of microbial communities colonizing the human skin ("skin microbiome"). Each individual possesses his/her own skin microbial community structure, with marked taxonomic differences between different parts of the body and temporal evolution depending on physical and chemical conditions (sweat, washing etc.). However, technical limitations due to the low bacterial density at the surface of the human skin or contamination by human DNA still has inhibited extended use of the metagenomic approach for investigating the skin microbiome at a functional level. These difficulties have been overcome in part by the new generation of sequencing platforms that now provide sequences describing the genes and functions carried out by skin bacteria. These methodological advances should help us understand the mechanisms by which these microorganisms adapt to the specific chemical composition of each skin and thereby lead to a better understanding of bacteria/human host interdependence. This knowledge will pave the way for more systemic and individualized pharmaceutical and cosmetic applications.}, } @article {pmid24358302, year = {2013}, author = {Alvarez, TM and Paiva, JH and Ruiz, DM and Cairo, JP and Pereira, IO and Paixão, DA and de Almeida, RF and Tonoli, CC and Ruller, R and Santos, CR and Squina, FM and Murakami, MT}, title = {Structure and function of a novel cellulase 5 from sugarcane soil metagenome.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e83635}, pmid = {24358302}, issn = {1932-6203}, mesh = {Catalysis ; Cellulase/*chemistry/genetics/isolation & purification/*metabolism ; Cellulose/metabolism ; Cloning, Molecular ; Hydrogen-Ion Concentration ; *Metagenome ; Microbiota/genetics ; Models, Molecular ; Protein Structure, Tertiary ; *Saccharum/microbiology ; Soil/chemistry ; Soil Microbiology ; Structure-Activity Relationship ; }, abstract = {Cellulases play a key role in enzymatic routes for degradation of plant cell-wall polysaccharides into simple and economically-relevant sugars. However, their low performance on complex substrates and reduced stability under industrial conditions remain the main obstacle for the large-scale production of cellulose-derived products and biofuels. Thus, in this study a novel cellulase with unusual catalytic properties from sugarcane soil metagenome (CelE1) was isolated and characterized. The polypeptide deduced from the celE1 gene encodes a unique glycoside hydrolase domain belonging to GH5 family. The recombinant enzyme was active on both carboxymethyl cellulose and β-glucan with an endo-acting mode according to capillary electrophoretic analysis of cleavage products. CelE1 showed optimum hydrolytic activity at pH 7.0 and 50 °C with remarkable activity at alkaline conditions that is attractive for industrial applications in which conventional acidic cellulases are not suitable. Moreover, its three-dimensional structure was determined at 1.8 Å resolution that allowed the identification of an insertion of eight residues in the β8-α8 loop of the catalytic domain of CelE1, which is not conserved in its psychrophilic orthologs. This 8-residue-long segment is a prominent and distinguishing feature of thermotolerant cellulases 5 suggesting that it might be involved with thermal stability. Based on its unconventional characteristics, CelE1 could be potentially employed in biotechnological processes that require thermotolerant and alkaline cellulases.}, } @article {pmid24358183, year = {2013}, author = {Twomey, KB and Alston, M and An, SQ and O'Connell, OJ and McCarthy, Y and Swarbreck, D and Febrer, M and Dow, JM and Plant, BJ and Ryan, RP}, title = {Microbiota and metabolite profiling reveal specific alterations in bacterial community structure and environment in the cystic fibrosis airway during exacerbation.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e82432}, pmid = {24358183}, issn = {1932-6203}, support = {100204//Wellcome Trust/United Kingdom ; }, mesh = {Adult ; Cystic Fibrosis/*microbiology ; DNA, Bacterial/genetics ; Female ; Humans ; Male ; Metagenome ; Microbiota/*genetics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Respiratory System/*microbiology ; Sputum/*microbiology ; Young Adult ; }, abstract = {Chronic polymicrobial infections of the lung are the foremost cause of morbidity and mortality in cystic fibrosis (CF) patients. The composition of the microbial flora of the airway alters considerably during infection, particularly during patient exacerbation. An understanding of which organisms are growing, their environment and their behaviour in the airway is of importance for designing antibiotic treatment regimes and for patient prognosis. To this end, we have analysed sputum samples taken from separate cohorts of CF and non-CF subjects for metabolites and in parallel, and we have examined both isolated DNA and RNA for the presence of 16S rRNA genes and transcripts by high-throughput sequencing of amplicon or cDNA libraries. This analysis revealed that although the population size of all dominant orders of bacteria as measured by DNA- and RNA- based methods are similar, greater discrepancies are seen with less prevalent organisms, some of which we associated with CF for the first time. Additionally, we identified a strong relationship between the abundance of specific anaerobes and fluctuations in several metabolites including lactate and putrescine during patient exacerbation. This study has hence identified organisms whose occurrence within the CF microbiome has been hitherto unreported and has revealed potential metabolic biomarkers for exacerbation.}, } @article {pmid24355533, year = {2014}, author = {Moreau, MM and Eades, SC and Reinemeyer, CR and Fugaro, MN and Onishi, JC}, title = {Illumina sequencing of the V4 hypervariable region 16S rRNA gene reveals extensive changes in bacterial communities in the cecum following carbohydrate oral infusion and development of early-stage acute laminitis in the horse.}, journal = {Veterinary microbiology}, volume = {168}, number = {2-4}, pages = {436-441}, doi = {10.1016/j.vetmic.2013.11.017}, pmid = {24355533}, issn = {1873-2542}, mesh = {Acute Disease ; Animals ; Bacterial Infections/pathology/*veterinary ; Cecum/*microbiology/pathology ; Dietary Carbohydrates/pharmacology ; Foot Diseases/etiology/pathology/*veterinary ; Genes, rRNA ; Horse Diseases/etiology/*microbiology/pathology ; Horses ; Lactobacillus/genetics ; Lameness, Animal/etiology/microbiology/pathology ; *Microbiota ; RNA, Ribosomal, 16S/*genetics ; Serratia/genetics ; Streptococcus/classification/genetics ; Veillonella/genetics ; }, abstract = {In the equine carbohydrate overload model of acute laminitis, disease progression is associated with changes in bacteria found in the cecum. To date, research has focused on changes in specific Gram-positive bacteria in this portion of the intestinal tract. Metagenomic methods are now available making it possible to interrogate microbial communities using animal protocols that sufficiently power a study. In this study, the microbiota in cecal fluid collected from control, non-laminitic horses (n=8) and from horses with early-stage acute laminitis induced with either oligofructan (n=6) or cornstarch (n=6) were profiled. The microbiota were identified based on sequencing the V4 hypervariable region of the 16S rRNA gene. The results of the study show that the relative abundance of Lactobacillus sp. and Streptococcus sp. increased significantly (p<0.05) following OF and CS infusion. Other significant changes included an increase (p<0.05) in relative abundance of Veillonella sp. and Serratia sp., two potentially pathogenic, Gram-negative bacteria. Significant decreases in the relative abundance of presumptive normal flora were detected as well. Although changes in cecal microbiota described in this communication are from a pilot study, it is hypothesized that an overgrowth of pathogenic Gram-negative bacteria develops and contributes to enterocolitis, pyrexia and lameness in the carbohydrate overload model of acute laminitis.}, } @article {pmid24355504, year = {2014}, author = {More, RP and Mitra, S and Raju, SC and Kapley, A and Purohit, HJ}, title = {Mining and assessment of catabolic pathways in the metagenome of a common effluent treatment plant to induce the degradative capacity of biomass.}, journal = {Bioresource technology}, volume = {153}, number = {}, pages = {137-146}, doi = {10.1016/j.biortech.2013.11.065}, pmid = {24355504}, issn = {1873-2976}, mesh = {Bacteria/classification/*genetics ; Biodegradation, Environmental ; Biodiversity ; *Biomass ; *Data Mining ; Metabolic Networks and Pathways/*genetics ; *Metagenome ; Oxygen/metabolism ; Phylogeny ; Pilot Projects ; Sewage/microbiology ; Species Specificity ; *Waste Disposal, Fluid ; Wastewater/microbiology ; Water Purification/*methods ; }, abstract = {Metagenome analysis was used to understand the microbial community in activated sludge treating industrial wastewaters at a Common Effluent Treatment Plant (CETP) in South India. The taxonomic profile mapped onto National Center for Biotechnology Information (NCBI) taxonomy using MEtaGenome ANalyzer (MEGAN), demonstrated that the most abundant domain belonged to prokaryotes, dominated by bacteria. Bacteria representing nine phyla were identified from the sequence data including representatives from two new phyla, Synergistetes and Elusimicrobia. Functional analysis of the metagenome, with specific reference to the metabolism of aromatic compounds, revealed the dominance of genes of the central meta-cleavage pathway. This information was used to improve the degradative efficiency in the wastewater treatment plant. A pilot scale plant was set up with 200L of activated sludge using salicylate induced sludge and results demonstrated 52% removal in chemical oxygen demand (COD) against non-induced biomass.}, } @article {pmid24352003, year = {2013}, author = {Chao, Y and Ma, L and Yang, Y and Ju, F and Zhang, XX and Wu, WM and Zhang, T}, title = {Metagenomic analysis reveals significant changes of microbial compositions and protective functions during drinking water treatment.}, journal = {Scientific reports}, volume = {3}, number = {}, pages = {3550}, pmid = {24352003}, issn = {2045-2322}, mesh = {Alphaproteobacteria/drug effects/genetics/isolation & purification ; Bacterial Typing Techniques ; Base Sequence ; Betaproteobacteria/drug effects/genetics/isolation & purification ; Biodiversity ; Biofilms/*growth & development ; Chlorine/pharmacology ; DNA, Bacterial/genetics ; Drinking Water/*microbiology ; Drug Resistance, Microbial ; *Ecosystem ; Gammaproteobacteria/drug effects/genetics/isolation & purification ; Glutathione/genetics/metabolism ; Halogenation ; Metagenomics ; Oxidative Stress/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Water Microbiology ; Water Purification/*methods ; }, abstract = {The metagenomic approach was applied to characterize variations of microbial structure and functions in raw (RW) and treated water (TW) in a drinking water treatment plant (DWTP) at Pearl River Delta, China. Microbial structure was significantly influenced by the treatment processes, shifting from Gammaproteobacteria and Betaproteobacteria in RW to Alphaproteobacteria in TW. Further functional analysis indicated the basic metabolic functions of microorganisms in TW did not vary considerably. However, protective functions, i.e. glutathione synthesis genes in 'oxidative stress' and 'detoxification' subsystems, significantly increased, revealing the surviving bacteria may have higher chlorine resistance. Similar results were also found in glutathione metabolism pathway, which identified the major reaction for glutathione synthesis and supported more genes for glutathione metabolism existed in TW. This metagenomic study largely enhanced our knowledge about the influences of treatment processes, especially chlorination, on bacterial community structure and protective functions (e.g. glutathione metabolism) in ecosystems of DWTPs.}, } @article {pmid24349412, year = {2013}, author = {Culligan, EP and Sleator, RD and Marchesi, JR and Hill, C}, title = {Functional environmental screening of a metagenomic library identifies stlA; a unique salt tolerance locus from the human gut microbiome.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e82985}, pmid = {24349412}, issn = {1932-6203}, mesh = {Adult ; Bacterial Proteins/*genetics ; Datasets as Topic ; *Genes, Bacterial ; *Genetic Loci ; Humans ; Intestines/*microbiology ; Male ; Metagenomics/methods ; Microbiota/*genetics ; Salt Tolerance/*genetics ; }, abstract = {Functional environmental screening of metagenomic libraries is a powerful means to identify and assign function to novel genes and their encoded proteins without any prior sequence knowledge. In the current study we describe the identification and subsequent analysis of a salt-tolerant clone from a human gut metagenomic library. Following transposon mutagenesis we identified an unknown gene (stlA, for "salt tolerance locus A") with no current known homologues in the databases. Subsequent cloning and expression in Escherichia coli MKH13 revealed that stlA confers a salt tolerance phenotype in its surrogate host. Furthermore, a detailed in silico analysis was also conducted to gain additional information on the properties of the encoded StlA protein. The stlA gene is rare when searched against human metagenome datasets such as MetaHit and the Human Microbiome Project and represents a novel and unique salt tolerance determinant which appears to be found exclusively in the human gut environment.}, } @article {pmid24349410, year = {2013}, author = {Tanca, A and Palomba, A and Deligios, M and Cubeddu, T and Fraumene, C and Biosa, G and Pagnozzi, D and Addis, MF and Uzzau, S}, title = {Evaluating the impact of different sequence databases on metaproteome analysis: insights from a lab-assembled microbial mixture.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e82981}, pmid = {24349410}, issn = {1932-6203}, mesh = {Bacteria/*genetics ; Bacterial Proteins/*genetics ; *Databases, Protein ; Metalloproteins/*genetics ; Microbial Consortia/*genetics ; Proteome/*genetics ; Sequence Analysis, Protein/*methods ; }, abstract = {Metaproteomics enables the investigation of the protein repertoire expressed by complex microbial communities. However, to unleash its full potential, refinements in bioinformatic approaches for data analysis are still needed. In this context, sequence databases selection represents a major challenge. This work assessed the impact of different databases in metaproteomic investigations by using a mock microbial mixture including nine diverse bacterial and eukaryotic species, which was subjected to shotgun metaproteomic analysis. Then, both the microbial mixture and the single microorganisms were subjected to next generation sequencing to obtain experimental metagenomic- and genomic-derived databases, which were used along with public databases (namely, NCBI, UniProtKB/SwissProt and UniProtKB/TrEMBL, parsed at different taxonomic levels) to analyze the metaproteomic dataset. First, a quantitative comparison in terms of number and overlap of peptide identifications was carried out among all databases. As a result, only 35% of peptides were common to all database classes; moreover, genus/species-specific databases provided up to 17% more identifications compared to databases with generic taxonomy, while the metagenomic database enabled a slight increment in respect to public databases. Then, database behavior in terms of false discovery rate and peptide degeneracy was critically evaluated. Public databases with generic taxonomy exhibited a markedly different trend compared to the counterparts. Finally, the reliability of taxonomic attribution according to the lowest common ancestor approach (using MEGAN and Unipept software) was assessed. The level of misassignments varied among the different databases, and specific thresholds based on the number of taxon-specific peptides were established to minimize false positives. This study confirms that database selection has a significant impact in metaproteomics, and provides critical indications for improving depth and reliability of metaproteomic results. Specifically, the use of iterative searches and of suitable filters for taxonomic assignments is proposed with the aim of increasing coverage and trustworthiness of metaproteomic data.}, } @article {pmid24349140, year = {2013}, author = {Yooseph, S and Andrews-Pfannkoch, C and Tenney, A and McQuaid, J and Williamson, S and Thiagarajan, M and Brami, D and Zeigler-Allen, L and Hoffman, J and Goll, JB and Fadrosh, D and Glass, J and Adams, MD and Friedman, R and Venter, JC}, title = {A metagenomic framework for the study of airborne microbial communities.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e81862}, pmid = {24349140}, issn = {1932-6203}, mesh = {*Air Microbiology ; Bacteria/classification/*genetics ; Biodiversity ; DNA, Bacterial/classification/*genetics ; Environmental Monitoring ; Genes, rRNA ; Metagenomics ; *Nucleic Acid Amplification Techniques ; *Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/classification/*genetics ; }, abstract = {Understanding the microbial content of the air has important scientific, health, and economic implications. While studies have primarily characterized the taxonomic content of air samples by sequencing the 16S or 18S ribosomal RNA gene, direct analysis of the genomic content of airborne microorganisms has not been possible due to the extremely low density of biological material in airborne environments. We developed sampling and amplification methods to enable adequate DNA recovery to allow metagenomic profiling of air samples collected from indoor and outdoor environments. Air samples were collected from a large urban building, a medical center, a house, and a pier. Analyses of metagenomic data generated from these samples reveal airborne communities with a high degree of diversity and different genera abundance profiles. The identities of many of the taxonomic groups and protein families also allows for the identification of the likely sources of the sampled airborne bacteria.}, } @article {pmid24343271, year = {2013}, author = {D'Auria, G and Peris-Bondia, F and Džunková, M and Mira, A and Collado, MC and Latorre, A and Moya, A}, title = {Active and secreted IgA-coated bacterial fractions from the human gut reveal an under-represented microbiota core.}, journal = {Scientific reports}, volume = {3}, number = {}, pages = {3515}, pmid = {24343271}, issn = {2045-2322}, mesh = {Adult ; Bacteria/*classification/genetics/*immunology ; Biodiversity ; Computational Biology ; DNA Barcoding, Taxonomic ; Female ; Gastrointestinal Tract/*immunology/*microbiology ; Humans ; Immunoglobulin A/*immunology ; Male ; Metagenome ; *Microbiota ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Host-associated microbiota varies in distribution depending on the body area inhabited. Gut microbes are known to interact with the human immune system, maintaining gut homoeostasis. Thus, we studied whether secreted-IgA (S-IgA) coat specific microbial taxa without inducing strong immune responses. To do so, we fractionated gut microbiota by flow cytometry. We found that active and S-IgA-coated bacterial fractions were characterized by a higher diversity than those observed in raw faecal suspensions. A long-tail effect was observed in family distribution, revealing that rare bacteria represent up to 20% of total diversity. While Firmicutes was the most abundant phylum, the majority of its sequences were not assigned at the genus level. Finally, the single-cell-based approach enabled us to focus on active and S-IgA-coated bacteria. Thus, we revealed a microbiota core common to the healthy volunteers participating in the study. Interestingly, this core was composed mainly of low frequency taxa (e.g. Sphingomonadaceae).}, } @article {pmid24342523, year = {2013}, author = {Loire, E and Chiari, Y and Bernard, A and Cahais, V and Romiguier, J and Nabholz, B and Lourenço, JM and Galtier, N}, title = {Population genomics of the endangered giant Galápagos tortoise.}, journal = {Genome biology}, volume = {14}, number = {12}, pages = {R136}, pmid = {24342523}, issn = {1474-760X}, mesh = {Animals ; DNA, Mitochondrial/analysis ; Ecuador ; *Endangered Species ; Evolution, Molecular ; Gene Expression Profiling ; Genetic Drift ; *Genome ; Metagenomics/*methods ; Phylogeny ; Polymorphism, Single Nucleotide ; Population Density ; Selection, Genetic ; Stress, Physiological ; Turtles/classification/*genetics ; }, abstract = {BACKGROUND: The giant Galápagos tortoise, Chelonoidis nigra, is a large-sized terrestrial chelonian of high patrimonial interest. The species recently colonized a small continental archipelago, the Galápagos Islands, where it has been facing novel environmental conditions and limited resource availability. To explore the genomic consequences of this ecological shift, we analyze the transcriptomic variability of five individuals of C. nigra, and compare it to similar data obtained from several continental species of turtles.

RESULTS: Having clarified the timing of divergence in the Chelonoidis genus, we report in C. nigra a very low level of genetic polymorphism, signatures of a weakened efficacy of purifying selection, and an elevated mutation load in coding and regulatory sequences. These results are consistent with the hypothesis of an extremely low long-term effective population size in this insular species. Functional evolutionary analyses reveal a reduced diversity of immunity genes in C. nigra, in line with the hypothesis of attenuated pathogen diversity in islands, and an increased selective pressure on genes involved in response to stress, potentially related to the climatic instability of its environment and its elongated lifespan. Finally, we detect no population structure or homozygosity excess in our five-individual sample.

CONCLUSIONS: These results enlighten the molecular evolution of an endangered taxon in a stressful environment and point to island endemic species as a promising model for the study of the deleterious effects on genome evolution of a reduced long-term population size.}, } @article {pmid24339168, year = {2014}, author = {Lee, HS and Burkhardt, BR and McLeod, W and Smith, S and Eberhard, C and Lynch, K and Hadley, D and Rewers, M and Simell, O and She, JX and Hagopian, B and Lernmark, A and Akolkar, B and Ziegler, AG and Krischer, JP and , }, title = {Biomarker discovery study design for type 1 diabetes in The Environmental Determinants of Diabetes in the Young (TEDDY) study.}, journal = {Diabetes/metabolism research and reviews}, volume = {30}, number = {5}, pages = {424-434}, pmid = {24339168}, issn = {1520-7560}, support = {U01 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK95300/DK/NIDDK NIH HHS/United States ; U01 DK63861/DK/NIDDK NIH HHS/United States ; UC4 DK63863/DK/NIDDK NIH HHS/United States ; U01 DK63821/DK/NIDDK NIH HHS/United States ; UC4 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK063836/DK/NIDDK NIH HHS/United States ; HHSN267200700014C/DK/NIDDK NIH HHS/United States ; UC4 DK63865/DK/NIDDK NIH HHS/United States ; U01 DK063861/DK/NIDDK NIH HHS/United States ; U01 DK063790/DK/NIDDK NIH HHS/United States ; UC4 DK100238/DK/NIDDK NIH HHS/United States ; U01 DK63829/DK/NIDDK NIH HHS/United States ; UC4 DK63829/DK/NIDDK NIH HHS/United States ; U01 DK63836/DK/NIDDK NIH HHS/United States ; UC4 DK63821/DK/NIDDK NIH HHS/United States ; UC4 DK063863/DK/NIDDK NIH HHS/United States ; U01 DK063836/DK/NIDDK NIH HHS/United States ; HHSN267200700014C/LM/NLM NIH HHS/United States ; UC4 DK63836/DK/NIDDK NIH HHS/United States ; U01 DK063829/DK/NIDDK NIH HHS/United States ; U01 DK063865/DK/NIDDK NIH HHS/United States ; UC4 DK095300/DK/NIDDK NIH HHS/United States ; UC4 DK063861/DK/NIDDK NIH HHS/United States ; U01 DK63865/DK/NIDDK NIH HHS/United States ; UC4 DK063829/DK/NIDDK NIH HHS/United States ; U01 DK063863/DK/NIDDK NIH HHS/United States ; U01 DK63790/DK/NIDDK NIH HHS/United States ; UC4 DK063865/DK/NIDDK NIH HHS/United States ; U01 DK63863/DK/NIDDK NIH HHS/United States ; UC4 DK63861/DK/NIDDK NIH HHS/United States ; }, mesh = {Autoantibodies/*analysis/immunology ; Biomarkers/*analysis ; Case-Control Studies ; Diabetes Mellitus, Type 1/*immunology ; Diet ; *Epidemiologic Methods ; Gene Expression ; Humans ; Islets of Langerhans/immunology ; Metabolomics ; Metagenomics ; Microbiota ; }, abstract = {AIMS: The Environmental Determinants of Diabetes in the Young planned biomarker discovery studies on longitudinal samples for persistent confirmed islet cell autoantibodies and type 1 diabetes using dietary biomarkers, metabolomics, microbiome/viral metagenomics and gene expression.

METHODS: This article describes the details of planning The Environmental Determinants of Diabetes in the Young biomarker discovery studies using a nested case-control design that was chosen as an alternative to the full cohort analysis. In the frame of a nested case-control design, it guides the choice of matching factors, selection of controls, preparation of external quality control samples and reduction of batch effects along with proper sample allocation.

RESULTS AND CONCLUSION: Our design is to reduce potential bias and retain study power while reducing the costs by limiting the numbers of samples requiring laboratory analyses. It also covers two primary end points (the occurrence of diabetes-related autoantibodies and the diagnosis of type 1 diabetes). The resulting list of case-control matched samples for each laboratory was augmented with external quality control samples.}, } @article {pmid24336217, year = {2014}, author = {David, LA and Maurice, CF and Carmody, RN and Gootenberg, DB and Button, JE and Wolfe, BE and Ling, AV and Devlin, AS and Varma, Y and Fischbach, MA and Biddinger, SB and Dutton, RJ and Turnbaugh, PJ}, title = {Diet rapidly and reproducibly alters the human gut microbiome.}, journal = {Nature}, volume = {505}, number = {7484}, pages = {559-563}, pmid = {24336217}, issn = {1476-4687}, support = {P50 GM068763/GM/NIGMS NIH HHS/United States ; DK0046200/DK/NIDDK NIH HHS/United States ; P30 DK046200/DK/NIDDK NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 DK094162/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Bacteria/drug effects/*genetics/*isolation & purification ; Bacteroides/drug effects/genetics/isolation & purification ; Bile Acids and Salts/analysis/metabolism ; Bilophila/drug effects/genetics/isolation & purification ; Carnivory ; *Diet/adverse effects ; Diet, Vegetarian ; Dietary Fats/adverse effects/pharmacology ; Feces/chemistry/microbiology ; Female ; Fermentation/drug effects ; Food Microbiology ; Gastrointestinal Tract/drug effects/*microbiology/virology ; Gene Expression Regulation, Bacterial/drug effects ; Herbivory ; Humans ; Inflammatory Bowel Diseases/microbiology ; Male ; *Metagenome/drug effects/genetics ; *Microbiota/drug effects/genetics ; Time Factors ; Young Adult ; }, abstract = {Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.}, } @article {pmid24335204, year = {2013}, author = {Broecker, F and Kube, M and Klumpp, J and Schuppler, M and Biedermann, L and Hecht, J and Hombach, M and Keller, PM and Rogler, G and Moelling, K}, title = {Analysis of the intestinal microbiome of a recovered Clostridium difficile patient after fecal transplantation.}, journal = {Digestion}, volume = {88}, number = {4}, pages = {243-251}, doi = {10.1159/000355955}, pmid = {24335204}, issn = {1421-9867}, mesh = {Biological Therapy ; *Clostridioides difficile ; DNA, Bacterial/*analysis ; Enterocolitis, Pseudomembranous/*therapy ; Feces/*microbiology ; Female ; Humans ; Intestines/*microbiology ; Metagenomics ; *Microbiota ; Middle Aged ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Clostridium difficile infections upon antibiotic disruption of the gut microbiota are potentially lethal. Fecal microbiota transplantation (FMT) is a promising treatment option for recurrent C. difficile-associated disease (CDAD). Here, we present a patient with recurrent CDAD that received FMT, leading to full recovery for what has now been 3 years. We performed metagenomic sequencing on stool samples to assess if there are indications for recolonization with C. difficile and changes in the gut microbiota after FMT.

METHODS: DNA from the stool of the donor and recipient was subjected to illumina sequencing. Obtained read sets were assembled to contiguous sequences and open reading frames were predicted. Deduced proteins were taxonomically assigned.

RESULTS: We detected complex and apparently healthy microbiomes in the donor's and recipient's intestines after FMT, but no indications for C. difficile colonization.

CONCLUSIONS: Metagenomic analysis proved suitable to analyze the intestinal microbiome after FMT. Discussion of our evaluation procedure and data management may be helpful for future studies. We demonstrated restoration of a healthy and diverse gut microbiome with chimeric composition from donor and recipient, and long-lasting clearance of C. difficile. The procedure is simple, cheap, caused no side effects, and was stable over 3 years.}, } @article {pmid24330256, year = {2014}, author = {Abrahamsson, TR and Jakobsson, HE and Andersson, AF and Björkstén, B and Engstrand, L and Jenmalm, MC}, title = {Low gut microbiota diversity in early infancy precedes asthma at school age.}, journal = {Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology}, volume = {44}, number = {6}, pages = {842-850}, doi = {10.1111/cea.12253}, pmid = {24330256}, issn = {1365-2222}, mesh = {Age Factors ; Asthma/diagnosis/*etiology ; *Biodiversity ; Case-Control Studies ; Child ; Child, Preschool ; *Disease Susceptibility ; Feces/microbiology ; Female ; Follow-Up Studies ; Gastrointestinal Tract/*microbiology ; Humans ; Hypersensitivity/diagnosis/etiology ; Infant ; Infant, Newborn ; Male ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S ; Risk Factors ; }, abstract = {BACKGROUND: Low total diversity of the gut microbiota during the first year of life is associated with allergic diseases in infancy, but little is known how early microbial diversity is related to allergic disease later in school age.

OBJECTIVE: To assess microbial diversity and characterize the dominant bacteria in stool during the first year of life in relation to the prevalence of different allergic diseases in school age, such as asthma, allergic rhinoconjunctivitis (ARC) and eczema.

METHODS: The microbial diversity and composition was analysed with barcoded 16S rDNA 454 pyrosequencing in stool samples at 1 week, 1 month and 12 months of age in 47 infants which were subsequently assessed for allergic disease and skin prick test reactivity at 7 years of age (ClinicalTrials.gov ID NCT01285830).

RESULTS: Children developing asthma (n = 8) had a lower diversity of the total microbiota than non-asthmatic children at 1 week (P = 0.04) and 1 month (P = 0.003) of age, whereas allergic rhinoconjunctivitis (n = 13), eczema (n = 12) and positive skin prick reactivity (n = 14) at 7 years of age did not associate with the gut microbiota diversity. Neither was asthma associated with the microbiota composition later in infancy (at 12 months). Children having IgE-associated eczema in infancy and subsequently developing asthma had lower microbial diversity than those that did not. There were no significant differences, however, in relative abundance of bacterial phyla and genera between children with or without allergic disease.

Low total diversity of the gut microbiota during the first month of life was associated with asthma but not ARC in children at 7 years of age. Measures affecting microbial colonization of the infant during the first month of life may impact asthma development in childhood.}, } @article {pmid24319142, year = {2014}, author = {Zhang, Q and Doak, TG and Ye, Y}, title = {Expanding the catalog of cas genes with metagenomes.}, journal = {Nucleic acids research}, volume = {42}, number = {4}, pages = {2448-2459}, pmid = {24319142}, issn = {1362-4962}, mesh = {CRISPR-Associated Proteins/classification/*genetics ; CRISPR-Cas Systems ; Feces/microbiology ; Genes, Bacterial ; Genome, Bacterial ; Humans ; *Metagenome ; Metagenomics/methods ; Microbiota ; Mouth/microbiology ; }, abstract = {The CRISPR (clusters of regularly interspaced short palindromic repeats)-Cas adaptive immune system is an important defense system in bacteria, providing targeted defense against invasions of foreign nucleic acids. CRISPR-Cas systems consist of CRISPR loci and cas (CRISPR-associated) genes: sequence segments of invaders are incorporated into host genomes at CRISPR loci to generate specificity, while adjacent cas genes encode proteins that mediate the defense process. We pursued an integrated approach to identifying putative cas genes from genomes and metagenomes, combining similarity searches with genomic neighborhood analysis. Application of our approach to bacterial genomes and human microbiome datasets allowed us to significantly expand the collection of cas genes: the sequence space of the Cas9 family, the key player in the recently engineered RNA-guided platforms for genome editing in eukaryotes, is expanded by at least two-fold with metagenomic datasets. We found genes in cas loci encoding other functions, for example, toxins and antitoxins, confirming the recently discovered potential of coupling between adaptive immunity and the dormancy/suicide systems. We further identified 24 novel Cas families; one novel family contains 20 proteins, all identified from the human microbiome datasets, illustrating the importance of metagenomics projects in expanding the diversity of cas genes.}, } @article {pmid24315484, year = {2013}, author = {Hsiao, EY and McBride, SW and Hsien, S and Sharon, G and Hyde, ER and McCue, T and Codelli, JA and Chow, J and Reisman, SE and Petrosino, JF and Patterson, PH and Mazmanian, SK}, title = {Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders.}, journal = {Cell}, volume = {155}, number = {7}, pages = {1451-1463}, pmid = {24315484}, issn = {1097-4172}, support = {F31 MH090749/MH/NIMH NIH HHS/United States ; R01 MH100556/MH/NIMH NIH HHS/United States ; MH100556/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Anxiety/metabolism/microbiology ; Bacteroides fragilis ; Behavior, Animal ; Brain/physiology ; Child ; Child Development Disorders, Pervasive/metabolism/*microbiology ; Disease Models, Animal ; Female ; Gastrointestinal Tract/metabolism/*microbiology ; Humans ; Mice ; Mice, Inbred C57BL ; Microbiota ; Probiotics/administration & dosage ; }, abstract = {Neurodevelopmental disorders, including autism spectrum disorder (ASD), are defined by core behavioral impairments; however, subsets of individuals display a spectrum of gastrointestinal (GI) abnormalities. We demonstrate GI barrier defects and microbiota alterations in the maternal immune activation (MIA) mouse model that is known to display features of ASD. Oral treatment of MIA offspring with the human commensal Bacteroides fragilis corrects gut permeability, alters microbial composition, and ameliorates defects in communicative, stereotypic, anxiety-like and sensorimotor behaviors. MIA offspring display an altered serum metabolomic profile, and B. fragilis modulates levels of several metabolites. Treating naive mice with a metabolite that is increased by MIA and restored by B. fragilis causes certain behavioral abnormalities, suggesting that gut bacterial effects on the host metabolome impact behavior. Taken together, these findings support a gut-microbiome-brain connection in a mouse model of ASD and identify a potential probiotic therapy for GI and particular behavioral symptoms in human neurodevelopmental disorders.}, } @article {pmid24312248, year = {2013}, author = {Ocon, S and Murphy, C and Dang, AT and Sankaran-Walters, S and Li, CS and Tarara, R and Borujerdpur, N and Dandekar, S and Paster, BJ and George, MD}, title = {Transcription profiling reveals potential mechanisms of dysbiosis in the oral microbiome of rhesus macaques with chronic untreated SIV infection.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e80863}, pmid = {24312248}, issn = {1932-6203}, support = {P51 OD011107/OD/NIH HHS/United States ; R21 DE020025/DE/NIDCR NIH HHS/United States ; K12 HD051958/HD/NICHD NIH HHS/United States ; UL1 TR000002/TR/NCATS NIH HHS/United States ; 1R21DE020025/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; Cluster Analysis ; *Dysbiosis ; *Gene Expression Profiling ; Gene Expression Regulation ; Interferon-gamma/metabolism ; Macaca mulatta ; Male ; *Metagenome ; *Microbiota ; Mouth/*microbiology ; Mouth Mucosa/immunology/metabolism/microbiology/pathology ; Phylogeny ; Simian Acquired Immunodeficiency Syndrome/*genetics/immunology/virology ; *Simian Immunodeficiency Virus ; }, abstract = {A majority of individuals infected with human immunodeficiency virus (HIV) have inadequate access to antiretroviral therapy and ultimately develop debilitating oral infections that often correlate with disease progression. Due to the impracticalities of conducting host-microbe systems-based studies in HIV infected patients, we have evaluated the potential of simian immunodeficiency virus (SIV) infected rhesus macaques to serve as a non-human primate model for oral manifestations of HIV disease. We present the first description of the rhesus macaque oral microbiota and show that a mixture of human commensal bacteria and "macaque versions" of human commensals colonize the tongue dorsum and dental plaque. Our findings indicate that SIV infection results in chronic activation of antiviral and inflammatory responses in the tongue mucosa that may collectively lead to repression of epithelial development and impact the microbiome. In addition, we show that dysbiosis of the lingual microbiome in SIV infection is characterized by outgrowth of Gemella morbillorum that may result from impaired macrophage function. Finally, we provide evidence that the increased capacity of opportunistic pathogens (e.g. E. coli) to colonize the microbiome is associated with reduced production of antimicrobial peptides.}, } @article {pmid24312223, year = {2013}, author = {Chandel, K and Mendki, MJ and Parikh, RY and Kulkarni, G and Tikar, SN and Sukumaran, D and Prakash, S and Parashar, BD and Shouche, YS and Veer, V}, title = {Midgut microbial community of Culex quinquefasciatus mosquito populations from India.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e80453}, pmid = {24312223}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Culex/*microbiology ; Digestive System/*microbiology ; Female ; India ; Metagenome ; *Microbiota ; Molecular Sequence Data ; }, abstract = {The mosquito Culex quinquefasciatus is a ubiquitous species that serves as a major vector for west nile virus and lymphatic filariasis. Ingestion of bloodmeal by females triggers a series of physiological processes in the midgut and also exposes them to infection by these pathogens. The bacteria normally harbored in the midgut are known to influence physiology and can also alter the response to various pathogens. The midgut bacteria in female Cx. quinquefasciatus mosquitoes collected over a large geographical area from India was studied. Examination of 16S ribosomal DNA amplicons from culturable microflora revealed the presence of 83 bacterial species belonging to 31 bacterial genera. All of these species belong to three phyla i.e. Proteobacteria, Firmicutes and Actinobacteria. Phylum Proteobacteria was the most dominant phylum (37 species), followed by Firmicutes (33 species) and Actinobacteria (13 species). Phylum Proteobacteria, was dominated by members of γ-proteobacteria class. The genus Staphylococcus was the largest genus represented by 11 species whereas Enterobacter was the most prevalent genus and recovered from all the field stations except Leh. Highest bacterial prevalence was observed from Bhuj (22 species) followed by Nagrota (18 species), Masimpur (18 species) and Hathigarh (16 species). Whereas, least species were observed from Leh (8 species). It has been observed that individual mosquito harbor extremely diverse gut bacteria and have very small overlap bacterial taxa in their gut. This variation in midgut microbiota may be one of the factors responsible for variation in disease transmission rates or vector competence within mosquito population. The present data strongly encourage further investigations to verify the potential role of the detected bacteria in mosquito for the transmission of lymphatic filariasis and west nile virus. To the best of our knowledge this is the first study on midgut microbiota of wild Cx. quinquefasciatus from over a large geographical area.}, } @article {pmid24312203, year = {2013}, author = {López-Miras, Mdel M and Martín-Sánchez, I and Yebra-Rodríguez, A and Romero-Noguera, J and Bolívar-Galiano, F and Ettenauer, J and Sterflinger, K and Piñar, G}, title = {Contribution of the microbial communities detected on an oil painting on canvas to its biodeterioration.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e80198}, pmid = {24312203}, issn = {1932-6203}, mesh = {Biodiversity ; Metagenome ; *Microbiota ; *Paintings ; }, abstract = {In this study, we investigated the microbial community (bacteria and fungi) colonising an oil painting on canvas, which showed visible signs of biodeterioration. A combined strategy, comprising culture-dependent and -independent techniques, was selected. The results derived from the two techniques were disparate. Most of the isolated bacterial strains belonged to related species of the phylum Firmicutes, as Bacillus sp. and Paenisporosarcina sp., whereas the majority of the non-cultivable members of the bacterial community were shown to be related to species of the phylum Proteobacteria, as Stenotrophomonas sp. Fungal communities also showed discrepancies: the isolated fungal strains belonged to different genera of the order Eurotiales, as Penicillium and Eurotium, and the non-cultivable belonged to species of the order Pleosporales and Saccharomycetales. The cultivable microorganisms, which exhibited enzymatic activities related to the deterioration processes, were selected to evaluate their biodeteriorative potential on canvas paintings; namely Arthrobacter sp. as the representative bacterium and Penicillium sp. as the representative fungus. With this aim, a sample taken from the painting studied in this work was examined to determine the stratigraphic sequence of its cross-section. From this information, "mock paintings," simulating the structure of the original painting, were prepared, inoculated with the selected bacterial and fungal strains, and subsequently examined by micro-Fourier Transform Infrared spectroscopy, in order to determine their potential susceptibility to microbial degradation. The FTIR-spectra revealed that neither Arthrobacter sp. nor Penicillium sp. alone, were able to induce chemical changes on the various materials used to prepare "mock paintings." Only when inoculated together, could a synergistic effect on the FTIR-spectra be observed, in the form of a variation in band position on the spectrum.}, } @article {pmid24309213, year = {2014}, author = {Kohrs, F and Heyer, R and Magnussen, A and Benndorf, D and Muth, T and Behne, A and Rapp, E and Kausmann, R and Heiermann, M and Klocke, M and Reichl, U}, title = {Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants.}, journal = {Anaerobe}, volume = {29}, number = {}, pages = {59-67}, doi = {10.1016/j.anaerobe.2013.11.009}, pmid = {24309213}, issn = {1095-8274}, mesh = {Archaeal Proteins/*isolation & purification ; Bacterial Proteins/*isolation & purification ; Biofuels ; Bioreactors ; Electrophoresis, Polyacrylamide Gel/methods ; Fungal Proteins/*isolation & purification ; Isoelectric Focusing/methods ; Metagenome ; Methane/*biosynthesis ; Methanomicrobiales/chemistry/genetics/*metabolism ; Methanosarcinales/chemistry/genetics/*metabolism ; Microbial Consortia/physiology ; Plants/metabolism ; Proteolysis ; Proteome/*analysis ; Tandem Mass Spectrometry ; Temperature ; Waste Products ; }, abstract = {Biogas production from energy crops and biodegradable waste is one of the major sources for renewable energies in Germany. Within a biogas plant (BGP) a complex microbial community converts biomass to biogas. Unfortunately, disturbances of the biogas process occur occasionally and cause economic losses of varying extent. Besides technical failures the microbial community itself is commonly assumed as a reason for process instability. To improve the performance and efficiency of BGP, a deeper knowledge of the composition and the metabolic state of the microbial community is required and biomarkers for monitoring of process deviations or even the prediction of process failures have to be identified. Previous work based on 2D-electrophoresis demonstrated that the analysis of the metaproteome is well suited to provide insights into the apparent metabolism of the microbial communities. Using SDS-PAGE with subsequent mass spectrometry, stable protein patterns were evaluated for a number of anaerobic digesters. Furthermore, it was shown that severe changes in process parameters such as acidification resulted in significant modifications of the metaproteome. Monitoring of changing protein patterns derived from anaerobic digesters, however, is still a challenge due to the high complexity of the metaproteome. In this study, different combinations of separation techniques to reduce the complexity of proteomic BGP samples were compared with respect to the subsequent identification of proteins by tandem mass spectrometry (MS/MS): (i) 1D: proteins were tryptically digested and the resulting peptides were separated by reversed phase chromatography prior to MS/MS. (ii) 2D: proteins were separated by GeLC-MS/MS according to proteins molecular weights before tryptic digestion, (iii) 3D: proteins were separated by gel-free fractionation using isoelectric focusing (IEF) conducted before GeLC-MS/MS. For this study, a comparison of two anaerobic digesters operated at mesophilic and at thermophilic conditions was conducted. The addition of further separation dimensions before protein identification increased the number of identified proteins. On the other hand additional fractionation steps increased the experimental work load and the time required for LC-MS/MS measurement. The high resolution of the 3D-approach enabled the detection of approximately 750 to 1650 proteins covering the main pathways of hydrolysis, acidogenesis, acetogenesis and methanogenesis. Methanosarcinales dominated in the mesophilic BGP, whereas Methanomicrobiales were highly abundant in the thermophilic BGP. Pathway analysis confirmed the taxonomic results and revealed that the acetoclastic methanogenesis occurred preferentially at mesophilic conditions, whereas exclusively hydrogenotrophic methanogenesis was detected in thermophilic BGP. However, for the identification of process biomarkers by comprehensive screening of BGP it will be indispensable to find a balance between the experimental efforts and analytical resolution.}, } @article {pmid24305737, year = {2014}, author = {Cai, L and Ju, F and Zhang, T}, title = {Tracking human sewage microbiome in a municipal wastewater treatment plant.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {7}, pages = {3317-3326}, doi = {10.1007/s00253-013-5402-z}, pmid = {24305737}, issn = {1432-0614}, mesh = {Bacteria/*classification/genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Hong Kong ; Humans ; *Metagenome ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; Water Purification/*methods ; }, abstract = {Human sewage pollution is a major threat to public health because sewage always comes with pathogens. Human sewage is usually received and treated by wastewater treatment plants (WWTPs) to control pathogenic risks and ameliorate environmental health. However, untreated sewage that flows into water environments may cause serious waterborne diseases, as reported in India and Bangladesh. To examine the fate of the human sewage microbiome in a local municipal WWTP of Hong Kong, we used massively parallel sequencing of 16S rRNA gene to systematically profile microbial communities in samples from three sections (i.e., influent, activated sludge, and effluent) obtained monthly throughout 1 year. The results indicated that: (1) influent sewage bacterial profile reflected the human microbiome; (2) human gut bacterial community was the dominant force shaping influent sewage bacterial profile; (3) most human sewage bacteria could be effectively removed by the WWTP; (4) a total of 75 genera were profiled as potentially pathogenic bacteria, most of which were still present in the effluent although at a very low level; (5) a grouped pattern of bacterial community was observed among the same section samples but a dispersed pattern was found among the different section samples; and (6) activated sludge was less affected by the influent sewage bacteria, but it showed a significant impact on the effluent bacteria. All of these findings provide novel insights toward a mechanistic understanding of the fate of human sewage microbiome in the WWTP.}, } @article {pmid24303069, year = {2013}, author = {Centanni, M and Turroni, S and Consolandi, C and Rampelli, S and Peano, C and Severgnini, M and Biagi, E and Caredda, G and De Bellis, G and Brigidi, P and Candela, M}, title = {The enterocyte-associated intestinal microbiota of breast-fed infants and adults responds differently to a TNF-α-mediated pro-inflammatory stimulus.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e81762}, pmid = {24303069}, issn = {1932-6203}, mesh = {Adult ; *Breast Feeding ; Cell Line ; Cluster Analysis ; Enterocytes/*metabolism/*microbiology ; Feces/microbiology ; Humans ; Infant ; Intestinal Mucosa/metabolism/microbiology ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S ; Tumor Necrosis Factor-alpha/*metabolism ; }, abstract = {Co-evolved as an integral component of our immune system, the gut microbiota provides specific immunological services at different ages, supporting the immune education during our infancy and sustaining a well-balanced immunological homeostasis during the course of our life. In order to figure out whether this involves differences in the microbial groups primarily interacting with the host immune system, we developed a non-invasive HT29 cell-based minimal model to fingerprint the enterocyte-associated microbiota fraction in infants and adults. After depicting the fecal microbial community of 12 breast-fed infants and 6 adults by 16S rDNA amplicon pools 454 pyrosequencing, their respective HT29 cell-associated gut microbiota fractions were characterized by the universal phylogenetic array platform HTF-Microbi.Array, both in the presence and absence of a tumor necrosis factor-alpha (TNF-α)-mediated pro-inflammatory stimulus. Our data revealed remarkable differences between the enterocyte-associated microbiota fractions in breast-fed infants and adults, being dominated by Bifidobacterium and Enterobacteriaceae the first and Bacteroides-Prevotella and Clostridium clusters IV and XIVa the second. While in adults TNF-α resulted in a profound impairment of the structure of the enterocyte-associated microbiota fraction, in infants it remained unaffected. Differently from the adult-type gut microbial community, the infant-type microbiota is structured to cope with inflammation, being co-evolved to prime the early immune response by means of transient inflammatory signals from gut microorganisms.}, } @article {pmid24303043, year = {2013}, author = {Song, Y and Garg, S and Girotra, M and Maddox, C and von Rosenvinge, EC and Dutta, A and Dutta, S and Fricke, WF}, title = {Microbiota dynamics in patients treated with fecal microbiota transplantation for recurrent Clostridium difficile infection.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e81330}, pmid = {24303043}, issn = {1932-6203}, mesh = {Aged ; Anti-Bacterial Agents/pharmacology ; Biodiversity ; Biological Therapy/*methods ; *Clostridioides difficile ; Enterocolitis, Pseudomembranous/*microbiology/*therapy ; Feces/*microbiology ; Female ; Follow-Up Studies ; Humans ; Male ; Metagenome ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S ; Treatment Outcome ; }, abstract = {Clostridium difficile causes antibiotic-associated diarrhea and pseudomembraneous colitis and is responsible for a large and increasing fraction of hospital-acquired infections. Fecal microbiota transplantation (FMT) is an alternate treatment option for recurrent C. difficile infection (RCDI) refractory to antibiotic therapy. It has recently been discussed favorably in the clinical and scientific communities and is receiving increasing public attention. However, short- and long-term health consequences of FMT remain a concern, as the effects of the transplanted microbiota on the patient remain unknown. To shed light on microbial events associated with RCDI and treatment by FMT, we performed fecal microbiota analysis by 16S rRNA gene amplicon pyrosequencing of 14 pairs of healthy donors and RCDI patients treated successfully by FMT. Post-FMT patient and healthy donor samples collected up to one year after FMT were studied longitudinally, including one post-FMT patient with antibiotic-associated relapse three months after FMT. This analysis allowed us not only to confirm prior reports that RCDI is associated with reduced diversity and compositional changes in the fecal microbiota, but also to characterize previously undocumented post-FMT microbiota dynamics. Members of the Streptococcaceae, Enterococcaceae, or Enterobacteriaceae were significantly increased and putative butyrate producers, such as Lachnospiraceae and Ruminococcaceae were significantly reduced in samples from RCDI patients before FMT as compared to post-FMT patient and healthy donor samples. RCDI patient samples showed more case-specific variations than post-FMT patient and healthy donor samples. However, none of the bacterial groups were invariably associated with RCDI or successful treatment by FMT. Overall microbiota compositions in post-FMT patients, specifically abundances of the above-mentioned Firmicutes, continued to change for at least 16 weeks after FMT, suggesting that full microbiota recovery from RCDI may take much longer than expected based on the disappearance of diarrheal symptoms immediately after FMT.}, } @article {pmid24296462, year = {2014}, author = {Major, G and Spiller, R}, title = {Irritable bowel syndrome, inflammatory bowel disease and the microbiome.}, journal = {Current opinion in endocrinology, diabetes, and obesity}, volume = {21}, number = {1}, pages = {15-21}, pmid = {24296462}, issn = {1752-2978}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Dietary Carbohydrates/*adverse effects ; Female ; Humans ; Inflammatory Bowel Diseases/*diet therapy/immunology/microbiology ; Intestinal Mucosa/immunology/*microbiology ; Irritable Bowel Syndrome/*diet therapy/immunology/microbiology ; Male ; Metagenome ; *Microbiota ; Prebiotics ; Probiotics ; }, abstract = {PURPOSE OF REVIEW: The review aims to update the reader on current developments in our understanding of how the gut microbiota impact on inflammatory bowel disease and the irritable bowel syndrome. It will also consider current efforts to modulate the microbiota for therapeutic effect.

RECENT FINDINGS: Gene polymorphisms associated with inflammatory bowel disease increasingly suggest that interaction with the microbiota drives pathogenesis. This may be through modulation of the immune response, mucosal permeability or the products of microbial metabolism. Similar findings in irritable bowel syndrome have reinforced the role of gut-specific factors in this 'functional' disorder. Metagenomic analysis has identified alterations in pathways and interactions with the ecosystem of the microbiome that may not be recognized by taxonomic description alone, particularly in carbohydrate metabolism. Treatments targeted at the microbial stimulus with antibiotics, probiotics or prebiotics have all progressed in the past year. Studies on the long-term effects of treatment on the microbiome suggest that dietary intervention may be needed for prolonged efficacy.

SUMMARY: The microbiome represents 'the other genome', and to appreciate its role in health and disease will be as challenging as with our own genome. Intestinal diseases occur at the front line of our interaction with the microbiome and their future treatment will be shaped as we unravel our relationship with it.}, } @article {pmid24296350, year = {2013}, author = {Hannigan, GD and Grice, EA}, title = {Microbial ecology of the skin in the era of metagenomics and molecular microbiology.}, journal = {Cold Spring Harbor perspectives in medicine}, volume = {3}, number = {12}, pages = {a015362}, pmid = {24296350}, issn = {2157-1422}, support = {P30 AR057217/AR/NIAMS NIH HHS/United States ; R00 AR060873/AR/NIAMS NIH HHS/United States ; AR060873/AR/NIAMS NIH HHS/United States ; AR057217/AR/NIAMS NIH HHS/United States ; }, mesh = {Alphapapillomavirus/physiology ; Biodiversity ; Fungi/physiology ; Humans ; Malassezia/physiology ; Metagenomics/trends ; Microbiology/trends ; Microbiota/physiology ; Skin/*microbiology ; Skin Diseases, Infectious/diagnosis/*microbiology ; }, abstract = {The skin is the primary physical barrier between the body and the external environment and is also a substrate for the colonization of numerous microbes. Previously, dermatological microbiology research was dominated by culture-based techniques, but significant advances in genomic technologies have enabled the development of less-biased, culture-independent approaches to characterize skin microbial communities. These molecular microbiology approaches illustrate the great diversity of microbiota colonizing the skin and highlight unique features such as site specificity, temporal dynamics, and interpersonal variation. Disruptions in skin commensal microbiota are associated with the progression of many dermatological diseases. A greater understanding of how skin microbes interact with each other and with their host, and how we can therapeutically manipulate those interactions, will provide powerful tools for treating and preventing dermatological disease.}, } @article {pmid24293637, year = {2014}, author = {Wang, H and Du, P and Li, J and Zhang, Y and Zhang, W and Han, N and Woo, PCY and Chen, C}, title = {Comparative analysis of microbiome between accurately identified 16S rDNA and quantified bacteria in simulated samples.}, journal = {Journal of medical microbiology}, volume = {63}, number = {Pt 3}, pages = {433-440}, doi = {10.1099/jmm.0.060616-0}, pmid = {24293637}, issn = {1473-5644}, mesh = {Aeromonas/*classification/genetics ; Base Sequence ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Enterobacteriaceae/*classification/genetics ; Humans ; Metagenome ; *Microbiota ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/chemistry/*genetics ; Sequence Analysis, DNA ; Species Specificity ; Staphylococcus aureus/*classification/genetics ; }, abstract = {Although 16S rRNA gene (rDNA) sequencing is the gold standard for categorizing bacteria or characterizing microbial communities its clinical utility is limited by bias in metagenomic studies, in either the experiments or the data analyses. To evaluate the efficiency of current metagenomic methods, we sequenced seven simulated samples of ten bacterial species mixed at different concentrations. The V3 region of 16S rDNA was targeted and used to determine the distribution of bacterial species. The number of target sequences in individual simulated samples was in the range 1-1000 to provide a better reflection of natural microbial communities. However, for a given bacterial species present in the same proportion but at different concentrations, the observed percentage of 16S rDNAs was similar, except at very low concentrations that cannot be detected by real-time PCR. These results confirmed that the comparative microbiome in a sample characterized by 16S rDNA sequencing is sufficient to detect not only potential infectious pathogens, but also the relative proportion of 16S rDNA in the sample.}, } @article {pmid24286763, year = {2014}, author = {Aliouat-Denis, CM and Chabé, M and Delhaes, L and Dei-Cas, E}, title = {Aerially transmitted human fungal pathogens: what can we learn from metagenomics and comparative genomics?.}, journal = {Revista iberoamericana de micologia}, volume = {31}, number = {1}, pages = {54-61}, doi = {10.1016/j.riam.2013.10.006}, pmid = {24286763}, issn = {2173-9188}, mesh = {*Air Microbiology ; Comparative Genomic Hybridization ; Cystic Fibrosis/complications/microbiology ; Evolution, Molecular ; Fungi/*genetics/pathogenicity ; *Genome, Fungal ; Humans ; Lung/microbiology ; *Metagenomics ; Microbiota ; Molecular Diagnostic Techniques ; Mycology/methods ; Mycoses/microbiology/*transmission ; Pulmonary Disease, Chronic Obstructive/microbiology ; Respiratory Hypersensitivity/microbiology ; Respiratory Tract Infections/microbiology/transmission ; Species Specificity ; Sputum/microbiology ; Virulence ; }, abstract = {In the last few decades, aerially transmitted human fungal pathogens have been increasingly recognized to impact the clinical course of chronic pulmonary diseases, such as asthma, cystic fibrosis or chronic obstructive pulmonary disease. Thanks to recent development of culture-free high-throughput sequencing methods, the metagenomic approaches are now appropriate to detect, identify and even quantify prokaryotic or eukaryotic microorganism communities inhabiting human respiratory tract and to access the complexity of even low-burden microbe communities that are likely to play a role in chronic pulmonary diseases. In this review, we explore how metagenomics and comparative genomics studies can alleviate fungal culture bottlenecks, improve our knowledge about fungal biology, lift the veil on cross-talks between host lung and fungal microbiota, and gain insights into the pathogenic impact of these aerially transmitted fungi that affect human beings. We reviewed metagenomic studies and comparative genomic analyses of carefully chosen microorganisms, and confirmed the usefulness of such approaches to better delineate biology and pathogenesis of aerially transmitted human fungal pathogens. Efforts to generate and efficiently analyze the enormous amount of data produced by such novel approaches have to be pursued, and will potentially provide the patients suffering from chronic pulmonary diseases with a better management. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012).}, } @article {pmid24285146, year = {2013}, author = {Mohamed, YM and Ghazy, MA and Sayed, A and Ouf, A and El-Dorry, H and Siam, R}, title = {Isolation and characterization of a heavy metal-resistant, thermophilic esterase from a Red Sea brine pool.}, journal = {Scientific reports}, volume = {3}, number = {}, pages = {3358}, pmid = {24285146}, issn = {2045-2322}, mesh = {Amino Acid Sequence ; Bacteria/*enzymology ; Esterases/*isolation & purification/metabolism ; Hot Temperature ; Indian Ocean ; Metagenome ; Metals, Heavy/chemistry ; Microbial Consortia/physiology ; Molecular Sequence Data ; Salinity ; Seawater/*microbiology ; Sequence Alignment ; Sodium Chloride ; }, abstract = {The Red Sea Atlantis II brine pool is an extreme environment that displays multiple harsh conditions such as high temperature, high salinity and high concentrations of multiple, toxic heavy metals. The survival of microbes in such an environment by utilizing resistant enzymes makes them an excellent source of extremophilic enzymes. We constructed a fosmid metagenomic library using DNA isolated from the deepest and most secluded layer of this pool. We report the isolation and biochemical characterization of an unusual esterase: EstATII. EstATII is thermophilic (optimum temperature, 65°C), halotolerant (maintains its activity in up to 4.5 M NaCl) and maintains at least 60% of its activity in the presence of a wide spectrum of heavy metals. The combination of biochemical characteristics of the Red Sea Atlantis II brine pool esterase, i.e., halotolerance, thermophilicity and resistance to heavy metals, makes it a potentially useful biocatalyst.}, } @article {pmid24282523, year = {2013}, author = {Pérez-Cobas, AE and Artacho, A and Knecht, H and Ferrús, ML and Friedrichs, A and Ott, SJ and Moya, A and Latorre, A and Gosalbes, MJ}, title = {Differential effects of antibiotic therapy on the structure and function of human gut microbiota.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e80201}, pmid = {24282523}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/*pharmacology ; Biodiversity ; Drug Resistance, Bacterial/drug effects ; Follow-Up Studies ; Gastrointestinal Tract/drug effects/microbiology ; Humans ; Metagenome ; Microbiota/*drug effects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The human intestinal microbiota performs many essential functions for the host. Antimicrobial agents, such as antibiotics (AB), are also known to disturb microbial community equilibrium, thereby having an impact on human physiology. While an increasing number of studies investigate the effects of AB usage on changes in human gut microbiota biodiversity, its functional effects are still poorly understood. We performed a follow-up study to explore the effect of ABs with different modes of action on human gut microbiota composition and function. Four individuals were treated with different antibiotics and samples were taken before, during and after the AB course for all of them. Changes in the total and in the active (growing) microbiota as well as the functional changes were addressed by 16S rRNA gene and metagenomic 454-based pyrosequencing approaches. We have found that the class of antibiotic, particularly its antimicrobial effect and mode of action, played an important role in modulating the gut microbiota composition and function. Furthermore, analysis of the resistome suggested that oscillatory dynamics are not only due to antibiotic-target resistance, but also to fluctuations in the surviving bacterial community. Our results indicated that the effect of AB on the human gut microbiota relates to the interaction of several factors, principally the properties of the antimicrobial agent, and the structure, functions and resistance genes of the microbial community.}, } @article {pmid24277822, year = {2014}, author = {Bokulich, NA and Thorngate, JH and Richardson, PM and Mills, DA}, title = {Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {1}, pages = {E139-48}, pmid = {24277822}, issn = {1091-6490}, support = {T32 GM008799/GM/NIGMS NIH HHS/United States ; T32-GM008799/GM/NIGMS NIH HHS/United States ; }, mesh = {Agriculture/methods ; Biodiversity ; *Climate ; Environment ; Fermentation ; Food Microbiology ; Genomics ; Geography ; Phylogeny ; Saccharomyces/genetics ; Saccharomyces cerevisiae/genetics ; Sequence Analysis, DNA ; Species Specificity ; Vitis/*microbiology/*physiology ; Wine/*microbiology ; }, abstract = {Wine grapes present a unique biogeography model, wherein microbial biodiversity patterns across viticultural zones not only answer questions of dispersal and community maintenance, they are also an inherent component of the quality, consumer acceptance, and economic appreciation of a culturally important food product. On their journey from the vineyard to the wine bottle, grapes are transformed to wine through microbial activity, with indisputable consequences for wine quality parameters. Wine grapes harbor a wide range of microbes originating from the surrounding environment, many of which are recognized for their role in grapevine health and wine quality. However, determinants of regional wine characteristics have not been identified, but are frequently assumed to stem from viticultural or geological factors alone. This study used a high-throughput, short-amplicon sequencing approach to demonstrate that regional, site-specific, and grape-variety factors shape the fungal and bacterial consortia inhabiting wine-grape surfaces. Furthermore, these microbial assemblages are correlated to specific climatic features, suggesting a link between vineyard environmental conditions and microbial inhabitation patterns. Taken together, these factors shape the unique microbial inputs to regional wine fermentations, posing the existence of nonrandom "microbial terroir" as a determining factor in regional variation among wine grapes.}, } @article {pmid24277308, year = {2014}, author = {Shapiro, BJ}, title = {Signatures of natural selection and ecological differentiation in microbial genomes.}, journal = {Advances in experimental medicine and biology}, volume = {781}, number = {}, pages = {339-359}, doi = {10.1007/978-94-007-7347-9_17}, pmid = {24277308}, issn = {0065-2598}, mesh = {*Evolution, Molecular ; Metagenome/*physiology ; Microbiota/*physiology ; Recombination, Genetic/*physiology ; Selection, Genetic/*physiology ; }, abstract = {We live in a microbial world. Most of the genetic and metabolic diversity that exists on earth - and has existed for billions of years - is microbial. Making sense of this vast diversity is a daunting task, but one that can be approached systematically by analyzing microbial genome sequences. This chapter explores how the evolutionary forces of recombination and selection act to shape microbial genome sequences, leaving signatures that can be detected using comparative genomics and population-genetic tests for selection. I describe the major classes of tests, paying special attention to their relative strengths and weaknesses when applied to microbes. Specifically, I apply a suite of tests for selection to a set of closely-related bacterial genomes with different microhabitat preferences within the marine water column, shedding light on the genomic mechanisms of ecological differentiation in the wild. I will focus on the joint problem of simultaneously inferring the boundaries between microbial populations, and the selective forces operating within and between populations.}, } @article {pmid24265786, year = {2013}, author = {Liu, MB and Xu, SR and He, Y and Deng, GH and Sheng, HF and Huang, XM and Ouyang, CY and Zhou, HW}, title = {Diverse vaginal microbiomes in reproductive-age women with vulvovaginal candidiasis.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e79812}, pmid = {24265786}, issn = {1932-6203}, mesh = {Adult ; Anti-Infective Agents/administration & dosage/therapeutic use ; Biodiversity ; Candidiasis, Vulvovaginal/drug therapy/*microbiology ; Cluster Analysis ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Microbiota/drug effects ; Middle Aged ; Vagina/*microbiology ; Young Adult ; }, abstract = {Vulvovaginal candidiasis (VVC) is one of the most prevalent vaginal infectious diseases, and there are controversial reports regarding the diversity of the associated vaginal microbiota. We determined the vaginal microbial community in patients with VVC, bacterial vaginosis (BV), and mixed infection of VVC and BV using Illumina sequencing of 16S rRNA tags. Our results revealed for the first time the highly variable patterns of the vaginal microbiome from VVC patients. In general, the alpha-diversity results of species richness and evenness showed the following order: normal control < VVC only < mixed BV and VVC infection < BV only. The beta-diversity comparison of community structures also showed an intermediate composition of VVC between the control and BV samples. A detailed comparison showed that, although the control and BV communities had typical patterns, the vaginal microbiota of VVC is complex. The mixed BV and VVC infection group showed a unique pattern, with a relatively higher abundance of Lactobacillus than the BV group and higher abundance of Prevotella, Gardnerella, and Atopobium than the normal control. In contrast, the VVC-only group could not be described by any single profile, ranging from a community structure similar to the normal control (predominated with Lactobacillus) to BV-like community structures (abundant with Gardnerella and Atopobium). Treatment of VVC resulted in inconsistent changes of the vaginal microbiota, with four BV/VVC samples recovering to a higher Lactobacillus level, whereas many VVC-only patients did not. These results will be useful for future studies on the role of vaginal microbiota in VVC and related infectious diseases.}, } @article {pmid24262515, year = {2014}, author = {Jakobsdottir, G and Nyman, M and Fåk, F}, title = {Designing future prebiotic fiber to target metabolic syndrome.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {30}, number = {5}, pages = {497-502}, doi = {10.1016/j.nut.2013.08.013}, pmid = {24262515}, issn = {1873-1244}, mesh = {Bacteria/*metabolism ; Dietary Fiber/pharmacology/*therapeutic use ; Fatty Acids, Volatile/*metabolism ; Gastrointestinal Tract/*drug effects/metabolism/microbiology ; Humans ; Metabolic Syndrome/*drug therapy/metabolism/microbiology ; *Microbiota ; *Prebiotics ; }, abstract = {The metabolic syndrome (MetS), characterized by obesity, hyperlipidemia, hypertension, and insulin resistance, is a growing epidemic worldwide, requiring new prevention strategies and therapeutics. The concept of prebiotics refers to selective stimulation of growth and/or activity(ies) of one or a limited number of microbial genus(era)/species in the gut microbiota that confer(s) health benefits to the host. Sequencing the gut microbiome and performing metagenomics has provided new knowledge of the significance of the composition and activity of the gut microbiota in metabolic disease. As knowledge of how a healthy gut microbiota is composed and which bacterial metabolites are beneficial increases, tailor-made dietary interventions using prebiotic fibers could be developed for individuals with MetS. In this review, we describe how dietary fibers alter short-chain fatty acid (SCFA) profiles and the intrinsic and extrinsic effects of prebiotics on host metabolism. We focus on several key aspects in prebiotic research in relation to MetS and provide mechanistic data that support the use of prebiotic fibers in order to alter the gut microbiota composition and SCFA profiles. Further studies in the field should provide reliable mechanistic and clinical evidence for how prebiotics can be used to alleviate MetS and its complications. Additionally, it will be important to clarify the effect of individual differences in the gut microbiome on responsiveness to prebiotic interventions.}, } @article {pmid24260553, year = {2013}, author = {Couch, RD and Navarro, K and Sikaroodi, M and Gillevet, P and Forsyth, CB and Mutlu, E and Engen, PA and Keshavarzian, A}, title = {The approach to sample acquisition and its impact on the derived human fecal microbiome and VOC metabolome.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e81163}, pmid = {24260553}, issn = {1932-6203}, support = {RC2 AA019405/AA/NIAAA NIH HHS/United States ; 1RC2AA019405/AA/NIAAA NIH HHS/United States ; }, mesh = {Adult ; *Artifacts ; Feces/chemistry/microbiology ; Female ; Gas Chromatography-Mass Spectrometry ; Humans ; Male ; *Metabolome ; Microbiota/*physiology ; Middle Aged ; Principal Component Analysis ; Solid Phase Microextraction/methods/*standards ; Specimen Handling/methods/*standards ; Time Factors ; Volatile Organic Compounds/*isolation & purification ; }, abstract = {Recent studies have illustrated the importance of the microbiota in maintaining a healthy state, as well as promoting disease states. The intestinal microbiota exerts its effects primarily through its metabolites, and metabolomics investigations have begun to evaluate the diagnostic and health implications of volatile organic compounds (VOCs) isolated from human feces, enabled by specialized sampling methods such as headspace solid-phase microextraction (hSPME). The approach to stool sample collection is an important consideration that could potentially introduce bias and affect the outcome of a fecal metagenomic and metabolomic investigation. To address this concern, a comparison of endoscopically collected (in vivo) and home collected (ex vivo) fecal samples was performed, revealing slight variability in the derived microbiomes. In contrast, the VOC metabolomes differ widely between the home collected and endoscopy collected samples. Additionally, as the VOC extraction profile is hyperbolic, with short extraction durations more vulnerable to variation than extractions continued to equilibrium, a second goal of our investigation was to ascertain if hSPME-based fecal metabolomics studies might be biased by the extraction duration employed. As anticipated, prolonged extraction (18 hours) results in the identification of considerably more metabolites than short (20 minute) extractions. A comparison of the metabolomes reveals several analytes deemed unique to a cohort with the 20 minute extraction, but found common to both cohorts when the VOC extraction was performed for 18 hours. Moreover, numerous analytes perceived to have significant fold change with a 20 minute extraction were found insignificant in fold change with the prolonged extraction, underscoring the potential for bias associated with a 20 minute hSPME.}, } @article {pmid24260458, year = {2013}, author = {Tong, M and Li, X and Wegener Parfrey, L and Roth, B and Ippoliti, A and Wei, B and Borneman, J and McGovern, DP and Frank, DN and Li, E and Horvath, S and Knight, R and Braun, J}, title = {A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e80702}, pmid = {24260458}, issn = {1932-6203}, support = {UL1TR000124/TR/NCATS NIH HHS/United States ; U01 DK062413/DK/NIDDK NIH HHS/United States ; HG005964/HG/NHGRI NIH HHS/United States ; R21 DK084554/DK/NIDDK NIH HHS/United States ; UL1 TR000124/TR/NCATS NIH HHS/United States ; P01DK046763/DK/NIDDK NIH HHS/United States ; DK46763/DK/NIDDK NIH HHS/United States ; R21 HG005964/HG/NHGRI NIH HHS/United States ; R01 AI078885/AI/NIAID NIH HHS/United States ; P01 DK046763/DK/NIDDK NIH HHS/United States ; AI078885/AI/NIAID NIH HHS/United States ; DK062413/DK/NIDDK NIH HHS/United States ; DK084554/DK/NIDDK NIH HHS/United States ; }, mesh = {Cluster Analysis ; Cohort Studies ; Humans ; Inflammatory Bowel Diseases/etiology/*microbiology ; Intestinal Mucosa/*microbiology/pathology ; Metagenome ; *Microbiota ; Phenotype ; RNA, Ribosomal, 16S ; }, abstract = {Abnormalities of the intestinal microbiota are implicated in the pathogenesis of Crohn's disease (CD) and ulcerative colitis (UC), two spectra of inflammatory bowel disease (IBD). However, the high complexity and low inter-individual overlap of intestinal microbial composition are formidable barriers to identifying microbial taxa representing this dysbiosis. These difficulties might be overcome by an ecologic analytic strategy to identify modules of interacting bacteria (rather than individual bacteria) as quantitative reproducible features of microbial composition in normal and IBD mucosa. We sequenced 16S ribosomal RNA genes from 179 endoscopic lavage samples from different intestinal regions in 64 subjects (32 controls, 16 CD and 16 UC patients in clinical remission). CD and UC patients showed a reduction in phylogenetic diversity and shifts in microbial composition, comparable to previous studies using conventional mucosal biopsies. Analysis of weighted co-occurrence network revealed 5 microbial modules. These modules were unprecedented, as they were detectable in all individuals, and their composition and abundance was recapitulated in an independent, biopsy-based mucosal dataset 2 modules were associated with healthy, CD, or UC disease states. Imputed metagenome analysis indicated that these modules displayed distinct metabolic functionality, specifically the enrichment of oxidative response and glycan metabolism pathways relevant to host-pathogen interaction in the disease-associated modules. The highly preserved microbial modules accurately classified IBD status of individual patients during disease quiescence, suggesting that microbial dysbiosis in IBD may be an underlying disorder independent of disease activity. Microbial modules thus provide an integrative view of microbial ecology relevant to IBD.}, } @article {pmid24260424, year = {2013}, author = {Saint-Cyr, MJ and Perrin-Guyomard, A and Houée, P and Rolland, JG and Laurentie, M}, title = {Evaluation of an oral subchronic exposure of deoxynivalenol on the composition of human gut microbiota in a model of human microbiota-associated rats.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e80578}, pmid = {24260424}, issn = {1932-6203}, mesh = {Administration, Oral ; Adult ; Animals ; Feces/chemistry/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; Metagenome ; Microbiota/*drug effects ; Models, Animal ; Mycotoxins/*administration & dosage/chemistry ; Rats ; Time Factors ; Trichothecenes/*administration & dosage/chemistry ; }, abstract = {BACKGROUND: Deoxynivalenol (DON), a mycotoxin produced by Fusarium species, is one of the most prevalent mycotoxins present in cereal crops worldwide. Due to its toxic properties, high stability and prevalence, the presence of DON in the food chain represents a health risk for both humans and animals. The gastrointestinal microbiota represents potentially the first target for these food contaminants. Thus, the effects of mycotoxins on the human gut microbiota is clearly an issue that needs to be addressed in further detail. Using a human microbiota-associated rat model, the aim of the present study was to evaluate the impact of a chronic exposure of DON on the composition of human gut microbiota.

Four groups of 5 germ free male rats each, housed in 4 sterile isolators, were inoculated with a different fresh human fecal flora. Rats were then fed daily by gavage with a solution of DON at 100 µg/kg bw for 4 weeks. Fecal samples were collected at day 0 before the beginning of the treatment; days 7, 16, 21, and 27 during the treatment; and 10 days after the end of the treatment at day 37. DON effect was assessed by real-time PCR quantification of dominant and subdominant bacterial groups in feces. Despite a different intestinal microbiota in each isolator, similar trends were generally observed. During oral DON exposure, a significant increase of 0.5 log10 was observed for the Bacteroides/Prevotella group during the first 3 weeks of administration. Concentration levels for Escherichia coli decreased at day 27. This significant decrease (0.9 log10 CFU/g) remained stable until the end of the experiment.

CONCLUSIONS/SIGNIFICANCE: We have demonstrated an impact of oral DON exposure on the human gut microbiota composition. These findings can serve as a template for risk assessment studies of food contaminants on the human gut microbiota.}, } @article {pmid24256454, year = {2014}, author = {Ni, J and Yan, Q and Yu, Y and Zhang, T}, title = {Factors influencing the grass carp gut microbiome and its effect on metabolism.}, journal = {FEMS microbiology ecology}, volume = {87}, number = {3}, pages = {704-714}, doi = {10.1111/1574-6941.12256}, pmid = {24256454}, issn = {1574-6941}, mesh = {Amino Acids/metabolism ; Animal Feed ; Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Carbohydrate Metabolism ; Carps/*metabolism/*microbiology ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Feeding Behavior ; Gastrointestinal Tract/*microbiology ; Metagenome ; *Microbiota ; Open Reading Frames ; Phylogeny ; }, abstract = {Gut microbiota have attracted extensive attention recently because of their important role in host metabolism, immunity and health maintenance. The present study focused on factors affecting the gut microbiome of grass carp (Ctenopharyngodon idella) and further explored the potential effect of the gut microbiome on metabolism. Totally, 43.39 Gb of screened metagenomic sequences obtained from 24 gut samples were fully analysed. We detected 1228 phylotypes (116 Archaea and 1112 Bacteria), most of which belonged to the phyla Firmicutes, Proteobacteria and Fusobacteria. Totally, 41335 of the detected open reading frames (ORFs) were matched to Kyoto Encyclopedia of Genes and Genomes pathways, and carbohydrate and amino acid metabolism was the main matched pathway deduced from the annotated ORFs. Redundancy analysis based on the phylogenetic composition and gene composition of the gut microbiome indicated that gut fullness and feeding (i.e. ryegrass vs. commercial feed, and pond-cultured vs. wild) were significantly related to the gut microbiome. Moreover, many biosynthesis and metabolism pathways of carbohydrates, amino acids and lipids were significantly enhanced by the gut microbiome in ryegrass-fed grass carp. These findings suggest that the metabolic role played by the gut microbiome in grass carp can be affected by feeding. These findings contribute to the field of fish gut microbial ecology and also provide a basis for follow-up functional studies.}, } @article {pmid24251832, year = {2014}, author = {Ramond, JB and Welz, PJ and Le Roes-Hill, M and Tuffin, MI and Burton, SG and Cowan, DA}, title = {Selection of Clostridium spp. in biological sand filters neutralizing synthetic acid mine drainage.}, journal = {FEMS microbiology ecology}, volume = {87}, number = {3}, pages = {678-690}, doi = {10.1111/1574-6941.12255}, pmid = {24251832}, issn = {1574-6941}, mesh = {Acids/*metabolism ; Biodegradation, Environmental ; Clostridium/genetics/*isolation & purification ; Ferric Compounds/metabolism ; Ferrous Compounds/metabolism ; Filtration ; Microbial Consortia ; *Mining ; Oxidation-Reduction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Silicon Dioxide ; Sulfates/metabolism ; }, abstract = {In this study, three biological sand filter (BSF) were contaminated with a synthetic iron- [1500 mg L[-1] Fe(II), 500 mg L[-1] Fe(III)] and sulphate-rich (6000 mg L[-1] SO4[2-]) acid mine drainage (AMD) (pH = 2), for 24 days, to assess the remediation capacity and the evolution of autochthonous bacterial communities (monitored by T-RFLP and 16S rRNA gene clone libraries). To stimulate BSF bioremediation involving sulphate-reducing bacteria, a readily degradable carbon source (glucose, 8000 mg L[-1]) was incorporated into the influent AMD. Complete neutralization and average removal efficiencies of 81.5 (±5.6)%, 95.8 (±1.2)% and 32.8 (±14.0)% for Fe(II), Fe(III) and sulphate were observed, respectively. Our results suggest that microbial iron reduction and sulphate reduction associated with iron precipitation were the main processes contributing to AMD neutralization. The effect of AMD on BSF sediment bacterial communities was highly reproducible. There was a decrease in diversity, and notably a single dominant operational taxonomic unit (OTU), closely related to Clostridium beijerinckii, which represented up to 65% of the total community at the end of the study period.}, } @article {pmid24250784, year = {2013}, author = {Zhang, M and Powell, CA and Benyon, LS and Zhou, H and Duan, Y}, title = {Deciphering the bacterial microbiome of citrus plants in response to 'Candidatus Liberibacter asiaticus'-infection and antibiotic treatments.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e76331}, pmid = {24250784}, issn = {1932-6203}, mesh = {Ampicillin/pharmacology ; Bacteria/classification/*isolation & purification ; Citrus/genetics/*microbiology ; Gentamicins/pharmacology ; Microbiota/genetics ; Plant Diseases/genetics/*microbiology/prevention & control ; Plant Leaves/*microbiology ; }, abstract = {The bacterial microbiomes of citrus plants were characterized in response to 'Candidatus Liberibacter asiaticus' (Las)-infection and treatments with ampicillin (Amp) and gentamicin (Gm) by Phylochip-based metagenomics. The results revealed that 7,407 of over 50,000 known Operational Taxonomic Units (OTUs) in 53 phyla were detected in citrus leaf midribs using the PhyloChip™ G3 array, of which five phyla were dominant, Proteobacteria (38.7%), Firmicutes (29.0%), Actinobacteria (16.1%), Bacteroidetes (6.2%) and Cyanobacteria (2.3%). The OTU62806, representing 'Candidatus Liberibacter', was present with a high titer in the plants graft-inoculated with Las-infected scions treated with Gm at 100 mg/L and in the water-treated control (CK1). However, the Las bacterium was not detected in the plants graft-inoculated with Las-infected scions treated with Amp at 1.0 g/L or in plants graft-inoculated with Las-free scions (CK2). The PhyloChip array demonstrated that more OTUs, at a higher abundance, were detected in the Gm-treated plants than in the other treatment and the controls. Pairwise comparisons indicated that 23 OTUs from the Achromobacter spp. and 12 OTUs from the Methylobacterium spp. were more abundant in CK2 and CK1, respectively. Ten abundant OTUs from the Stenotrophomonas spp. were detected only in the Amp-treatment. These results provide new insights into microbial communities that may be associated with the progression of citrus huanglongbing (HLB) and the potential effects of antibiotics on the disease and microbial ecology.}, } @article {pmid24246975, year = {2013}, author = {Mondot, S and de Wouters, T and Doré, J and Lepage, P}, title = {The human gut microbiome and its dysfunctions.}, journal = {Digestive diseases (Basel, Switzerland)}, volume = {31}, number = {3-4}, pages = {278-285}, doi = {10.1159/000354678}, pmid = {24246975}, issn = {1421-9875}, mesh = {Biodiversity ; Gastrointestinal Tract/*microbiology/*pathology ; Humans ; Microbiota/*physiology ; Obesity/microbiology/pathology ; }, abstract = {The human gastrointestinal tract hosts more than 100 trillion bacteria and archaea, which together make up the gut microbiota. The amount of bacteria in the human gut outnumbers human cells by a factor of 10, but some finely tuned mechanisms allow these microorganisms to colonize and survive within the host in a mutual relationship. The human gut microbiota co-evolved with humans to achieve a symbiotic relationship leading to physiological homeostasis. The microbiota provides crucial functions that human cannot exert themselves while the human host provides a nutrient-rich environment. Chaotic in the early stages of life, the assembly of the human gut microbiota remains globally stable over time in healthy conditions and absence of perturbation. Following perturbation, such as antibiotic treatment, bacteria will recolonize the niches with a composition and diversity similar to the basal level since the ecosystem is highly resilient. Yet, recurrent perturbations lead to a decrease in resilience capacity of the gut microbiome. Shifts in the bacterial composition and diversity of the human gut microbiota have been associated with intestinal dysfunctions such as inflammatory bowel disease and obesity. More than specific bacteria, a general destructuration of the ecosystem seems to be involved in these pathologies. Application of metagenomics to this environment may help in deciphering key functions and correlation networks specifically involved in health maintenance. In term, fecal transplant and synthetic microbiome transplant might be promising therapies for dysbiosis-associated diseases.}, } @article {pmid24238986, year = {2014}, author = {Woo, HL and Hazen, TC and Simmons, BA and DeAngelis, KM}, title = {Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils.}, journal = {Systematic and applied microbiology}, volume = {37}, number = {1}, pages = {60-67}, doi = {10.1016/j.syapm.2013.10.001}, pmid = {24238986}, issn = {1618-0984}, mesh = {Aerobiosis ; Bacteria/classification/*enzymology/isolation & purification/*metabolism ; Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Enzymes/*analysis ; Lignin/*metabolism ; Molecular Sequence Data ; Phylogeny ; Puerto Rico ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Trees ; }, abstract = {Lignocellulolytic bacteria have promised to be a fruitful source of new enzymes for next-generation lignocellulosic biofuel production. Puerto Rican tropical forest soils were targeted because the resident microbes decompose biomass quickly and to near-completion. Isolates were initially screened based on growth on cellulose or lignin in minimal media. 75 Isolates were further tested for the following lignocellulolytic enzyme activities: phenol oxidase, peroxidase, β-d-glucosidase, cellobiohydrolase, β-xylopyranosidase, chitinase, CMCase, and xylanase. Cellulose-derived isolates possessed elevated β-d-glucosidase, CMCase, and cellobiohydrolase activity but depressed phenol oxidase and peroxidase activity, while the contrary was true of lignin isolates, suggesting that these bacteria are specialized to subsist on cellulose or lignin. Cellobiohydrolase and phenol oxidase activity rates could classify lignin and cellulose isolates with 61% accuracy, which demonstrates the utility of model degradation assays. Based on 16S rRNA gene sequencing, all isolates belonged to phyla dominant in the Puerto Rican soils, Proteobacteria, Firmicutes, and Actinobacteria, suggesting that many dominant taxa are capable of the rapid lignocellulose degradation characteristic of these soils. The isolated genera Aquitalea, Bacillus, Burkholderia, Cupriavidus, Gordonia, and Paenibacillus represent rarely or never before studied lignolytic or cellulolytic species and were undetected by metagenomic analysis of the soils. The study revealed a relationship between phylogeny and lignocellulose-degrading potential, supported by Kruskal-Wallis statistics which showed that enzyme activities of cultivated phyla and genera were different enough to be considered representatives of distinct populations. This can better inform future experiments and enzyme discovery efforts.}, } @article {pmid24238218, year = {2014}, author = {Dong, Y and Kumar, CG and Chia, N and Kim, PJ and Miller, PA and Price, ND and Cann, IK and Flynn, TM and Sanford, RA and Krapac, IG and Locke, RA and Hong, PY and Tamaki, H and Liu, WT and Mackie, RI and Hernandez, AG and Wright, CL and Mikel, MA and Walker, JL and Sivaguru, M and Fried, G and Yannarell, AC and Fouke, BW}, title = {Halomonas sulfidaeris-dominated microbial community inhabits a 1.8 km-deep subsurface Cambrian Sandstone reservoir.}, journal = {Environmental microbiology}, volume = {16}, number = {6}, pages = {1695-1708}, doi = {10.1111/1462-2920.12325}, pmid = {24238218}, issn = {1462-2920}, mesh = {Genes, Bacterial ; Halomonas/*genetics ; Illinois ; Metabolic Networks and Pathways/genetics ; Metagenome ; Microbiota/genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; Phylogeny ; Quartz ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {A low-diversity microbial community, dominated by the γ-proteobacterium Halomonas sulfidaeris, was detected in samples of warm saline formation porewater collected from the Cambrian Mt. Simon Sandstone in the Illinois Basin of the North American Midcontinent (1.8 km/5872 ft burial depth, 50°C, pH 8, 181 bars pressure). These highly porous and permeable quartz arenite sandstones are directly analogous to reservoirs around the world targeted for large-scale hydrocarbon extraction, as well as subsurface gas and carbon storage. A new downhole low-contamination subsurface sampling probe was used to collect in situ formation water samples for microbial environmental metagenomic analyses. Multiple lines of evidence suggest that this H. sulfidaeris-dominated subsurface microbial community is indigenous and not derived from drilling mud microbial contamination. Data to support this includes V1-V3 pyrosequencing of formation water and drilling mud, as well as comparison with previously published microbial analyses of drilling muds in other sites. Metabolic pathway reconstruction, constrained by the geology, geochemistry and present-day environmental conditions of the Mt. Simon Sandstone, implies that H. sulfidaeris-dominated subsurface microbial community may utilize iron and nitrogen metabolisms and extensively recycle indigenous nutrients and substrates. The presence of aromatic compound metabolic pathways suggests this microbial community can readily adapt to and survive subsurface hydrocarbon migration.}, } @article {pmid24236175, year = {2013}, author = {Muzny, CA and Sunesara, IR and Kumar, R and Mena, LA and Griswold, ME and Martin, DH and Lefkowitz, EJ and Schwebke, JR and Swiatlo, E}, title = {Characterization of the vaginal microbiota among sexual risk behavior groups of women with bacterial vaginosis.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e80254}, pmid = {24236175}, issn = {1932-6203}, support = {UL1 TR000165/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Bacteria/classification/genetics ; Cluster Analysis ; Cross-Sectional Studies ; Female ; Humans ; Male ; Metagenome ; *Microbiota ; Mississippi ; Phylogeny ; RNA, Ribosomal, 16S ; Risk-Taking ; Sexual Behavior ; Vagina/*microbiology ; Vaginosis, Bacterial/*microbiology ; Young Adult ; }, abstract = {BACKGROUND: The pathogenesis of bacterial vaginosis (BV) remains elusive. BV may be more common among women who have sex with women (WSW). The objective of this study was to use 454 pyrosequencing to investigate the vaginal microbiome of WSW, women who have sex with women and men (WSWM), and women who have sex with men (WSM) with BV to determine if there are differences in organism composition between groups that may inform new hypotheses regarding the pathogenesis of BV.

METHODS: Vaginal swab specimens from eligible women with BV at the Mississippi State Department of Health STD Clinic were used. After DNA extraction, 454 pyrosequencing of PCR-amplified 16S rRNA gene sequences was performed. Sequence data was classified using the Ribosomal Database Program classifer. Complete linkage clustering analysis was performed to compare bacterial community composition among samples. Differences in operational taxonomic units with an abundance of ≥ 2% between risk behavior groups were determined. Alpha and beta diversity were measured using Shannon's Index implemented in QIIME and Unifrac analysis, respectively.

RESULTS: 33 WSW, 35 WSWM, and 44 WSM were included. The vaginal bacterial communities of all women clustered into four taxonomic groups with the dominant taxonomic group in each being Lactobacillus, Lachnospiraceae, Prevotella, and Sneathia. Regarding differences in organism composition between risk behavior groups, the abundance of Atopobium (relative ratio (RR)=0.24; 95%CI 0.11-0.54) and Parvimonas (RR=0.33; 95%CI 0.11-0.93) were significantly lower in WSW than WSM, the abundance of Prevotella was significantly higher in WSW than WSWM (RR=1.77; 95%CI 1.10-2.86), and the abundance of Atopobium (RR=0.41; 95%CI 0.18-0.88) was significantly lower in WSWM than WSM. Overall, WSM had the highest diversity of bacterial taxa.

CONCLUSION: The microbiology of BV among women in different risk behavior groups is heterogeneous. WSM in this study had the highest diversity of bacterial taxa. Additional studies are needed to better understand these differences.}, } @article {pmid24236132, year = {2013}, author = {Jing, H and Xia, X and Suzuki, K and Liu, H}, title = {Vertical profiles of bacteria in the tropical and subarctic oceans revealed by pyrosequencing.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e79423}, pmid = {24236132}, issn = {1932-6203}, mesh = {Bacteria/*classification/*genetics ; Biodiversity ; Metagenome ; Pacific Ocean ; Phylogeny ; Phylogeography ; RNA, Ribosomal, 16S ; Seawater/*microbiology ; }, abstract = {Community composition of Bacteria in the surface and deep water layers were examined at three oceanic sites in the Pacific Ocean separated by great distance, i.e., the South China Sea (SCS) in the western tropical Pacific, the Costa Rica Dome (CRD) in the eastern tropical Pacific and the western subarctic North Pacific (SNP), using high throughput DNA pyrosequencing of the 16S rRNA gene. Bioinformatic analysis rendered a total of 143600 high quality sequences with an average 11967 sequences per sample and mean read length of 449 bp. Phylogenetic analysis showed that Proteobacteria dominated in all shallow and deep waters, with Alphaproteobacteria and Gammaproteobacteria the two most abundant components, and SAR11 the most abundant group at family level in all regions. Cyanobacteria occurred mainly in the surface euphotic layer, and the majority of them in the tropical waters belonged to the GpIIa family including Prochlorococcus and Synechococcus, whilst those associated with Cryptophytes and diatoms were common in the subarctic waters. In general, species richness (Chao1) and diversity (Shannon index H') were higher for the bacterial communities in the intermediate water layers than for those in surface and deep waters. Both NMDS plot and UPGMA clustering demonstrated that bacterial community composition in the deep waters (500 m ~2000 m) of the three oceanic regions shared a high similarity and were distinct from those in the upper waters (5 m ~100 m). Our study indicates that bacterial community composition in the DOC-poor deep water in both tropical and subarctic regions were rather stable, contrasting to those in the surface water layers, which could be strongly affected by the fluctuations of environmental factors.}, } @article {pmid24236055, year = {2013}, author = {Moore, AM and Patel, S and Forsberg, KJ and Wang, B and Bentley, G and Razia, Y and Qin, X and Tarr, PI and Dantas, G}, title = {Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e78822}, pmid = {24236055}, issn = {1932-6203}, support = {A14799-S01//PHS HHS/United States ; 5P30 DK052574/DK/NIDDK NIH HHS/United States ; T32 GM007067/GM/NIGMS NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; T32 HD043010/HD/NICHD NIH HHS/United States ; T32 HD043010-08/HD/NICHD NIH HHS/United States ; }, mesh = {Adolescent ; Anti-Bacterial Agents/pharmacology ; Bacteroides/genetics ; Child ; Child, Preschool ; Clostridium/genetics ; Drug Resistance, Bacterial/*genetics ; Enterobacter/genetics ; Feces/microbiology ; Female ; Genes, Bacterial ; Humans ; Infant ; Likelihood Functions ; Male ; Microbiota/*genetics ; Molecular Sequence Annotation ; Phylogeny ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Emerging antibiotic resistance threatens human health. Gut microbes are an epidemiologically important reservoir of resistance genes (resistome), yet prior studies indicate that the true diversity of gut-associated resistomes has been underestimated. To deeply characterize the pediatric gut-associated resistome, we created metagenomic recombinant libraries in an Escherichia coli host using fecal DNA from 22 healthy infants and children (most without recent antibiotic exposure), and performed functional selections for resistance to 18 antibiotics from eight drug classes. Resistance-conferring DNA fragments were sequenced (Illumina HiSeq 2000), and reads assembled and annotated with the PARFuMS computational pipeline. Resistance to 14 of the 18 antibiotics was found in stools of infants and children. Recovered genes included chloramphenicol acetyltransferases, drug-resistant dihydrofolate reductases, rRNA methyltransferases, transcriptional regulators, multidrug efflux pumps, and every major class of beta-lactamase, aminoglycoside-modifying enzyme, and tetracycline resistance protein. Many resistance-conferring sequences were mobilizable; some had low identity to any known organism, emphasizing cryptic organisms as potentially important resistance reservoirs. We functionally confirmed three novel resistance genes, including a 16S rRNA methylase conferring aminoglycoside resistance, and two tetracycline-resistance proteins nearly identical to a bifidobacterial MFS transporter (B. longum s. longum JDM301). We provide the first report to our knowledge of resistance to folate-synthesis inhibitors conferred by a predicted Nudix hydrolase (part of the folate synthesis pathway). This functional metagenomic survey of gut-associated resistomes, the largest of its kind to date, demonstrates that fecal resistomes of healthy children are far more diverse than previously suspected, that clinically relevant resistance genes are present even without recent selective antibiotic pressure in the human host, and that cryptic gut microbes are an important resistance reservoir. The observed transferability of gut-associated resistance genes to a gram-negative (E. coli) host also suggests that the potential for gut-associated resistomes to threaten human health by mediating antibiotic resistance in pathogens warrants further investigation.}, } @article {pmid24231160, year = {2014}, author = {Zheng, B and Wang, L and Liu, L}, title = {Bacterial community structure and its regulating factors in the intertidal sediment along the Liaodong Bay of Bohai Sea, China.}, journal = {Microbiological research}, volume = {169}, number = {7-8}, pages = {585-592}, doi = {10.1016/j.micres.2013.09.019}, pmid = {24231160}, issn = {1618-0623}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Bays/*microbiology ; *Biodiversity ; China ; Ecosystem ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Phylogeny ; Seawater/*microbiology ; }, abstract = {Investigating the entire species composition of the microorganisms is crucial to understand their roles in the biogeochemical cycles. Metagenomic DNA was extracted from six intertidal sediment samples along the Liaodong Bay of Bohai Sea, China, and was sequenced which yielded a total of 64,496 high-quality sequences from 83,485 reads, with an average read length of 463 bp. The sequences were assigned to 20,718 operational taxonomic units (OTUs) which belong to 42 phyla, 90 classes and 376 genera. At the different taxonomic levels, both the dominants and their abundances varied significantly among the six sites. Phylum Proteobacteria predominated in all the six samples, however, not only the abundance of this phylum varied significantly but also the proportions of Alpha-, Beta-, Gamma-, and delta- and epsilon-Proteobacteria varied greatly. The site sediment median grain size and dissolved oxygen (DO) revealed to be key factors regulating the observed significant differences in the bacterial community between sampling sites. In addition, the bacterial composition might be more sensitive than the richness and diversity to the studied environmental conditions.}, } @article {pmid24225369, year = {2013}, author = {Jang, JK and Kan, J and Bretschger, O and Gorby, YA and Hsu, L and Kim, BH and Nealson, KH}, title = {Electricity generation by microbial fuel cell using microorganisms as catalyst in cathode.}, journal = {Journal of microbiology and biotechnology}, volume = {23}, number = {12}, pages = {1765-1773}, doi = {10.4014/jmb.1310.10117}, pmid = {24225369}, issn = {1738-8872}, mesh = {Azides/metabolism ; Bacteria/*growth & development/isolation & purification/*metabolism/ultrastructure ; *Bacterial Physiological Phenomena ; Biodiversity ; *Bioelectric Energy Sources ; Biofilms/growth & development ; Cluster Analysis ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; *Electricity ; Electrodes/*microbiology ; Graphite ; Metagenome ; Microscopy, Electron ; Oxygen/metabolism ; Phylogeny ; Platinum ; Sequence Analysis, DNA ; }, abstract = {The cathode reaction is one of the most seriously limiting factors in a microbial fuel cell (MFC). The critical dissolved oxygen (DO) concentration of a platinum-loaded graphite electrode was reported as 2.2 mg/l, about 10-fold higher than an aerobic bacterium. A series of MFCs were run with the cathode compartment inoculated with activated sludge (biotic) or not (abiotic) on platinum-loaded or bare graphite electrodes. At the beginning of the operation, the current values from MFCs with a biocathode and abiotic cathode were 2.3 ± 0.1 and 2.6 ± 0.2 mA, respectively, at the air-saturated water supply in the cathode. The current from MFCs with an abiotic cathode did not change, but that of MFCs with a biotic cathode increased to 3.0 mA after 8 weeks. The coulomb efficiency was 59.6% in the MFCs with a biotic cathode, much higher than the value of 15.6% of the abiotic cathode. When the DO supply was reduced, the current from MFCs with an abiotic cathode decreased more sharply than in those with a biotic cathode. When the respiratory inhibitor azide was added to the catholyte, the current decreased in MFCs with a biotic cathode but did not change in MFCs with an abiotic cathode. The power density was higher in MFCs with a biotic cathode (430 W/m(3) cathode compartment) than the abiotic cathode MFC (257 W/m(3) cathode compartment). Electron microscopic observation revealed nanowire structures in biofilms that developed on both the anode and on the biocathode. These results show that an electron consuming bacterial consortium can be used as a cathode catalyst to improve the cathode reaction.}, } @article {pmid24225361, year = {2013}, author = {Hermann-Bank, ML and Skovgaard, K and Stockmarr, A and Larsen, N and Mølbak, L}, title = {The Gut Microbiotassay: a high-throughput qPCR approach combinable with next generation sequencing to study gut microbial diversity.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {788}, pmid = {24225361}, issn = {1471-2164}, mesh = {Animals ; Bacteria/*classification/genetics/isolation & purification ; DNA Primers/genetics ; DNA, Bacterial/genetics ; Diarrhea/microbiology ; Gastrointestinal Tract/*microbiology ; Intestine, Large/microbiology ; Intestine, Small/microbiology ; Metagenome ; *Microbiota ; Polymerase Chain Reaction/*methods ; Streptococcus/genetics/isolation & purification ; Swine ; }, abstract = {BACKGROUND: The intestinal microbiota is a complex and diverse ecosystem that plays a significant role in maintaining the health and well-being of the mammalian host. During the last decade focus has increased on the importance of intestinal bacteria. Several molecular methods can be applied to describe the composition of the microbiota. This study used a new approach, the Gut Microbiotassay: an assembly of 24 primer sets targeting the main phyla and taxonomically related subgroups of the intestinal microbiota, to be used with the high-throughput qPCR chip 'Access Array 48.48', AA48.48, (Fluidigm®) followed by next generation sequencing. Primers were designed if necessary and all primer sets were screened against DNA extracted from pure cultures of 15 representative bacterial species. Subsequently the setup was tested on DNA extracted from small and large intestinal content from piglets with and without diarrhoea. The PCR amplicons from the 2304 reaction chambers were harvested from the AA48.48, purified, and sequenced using 454-technology.

RESULTS: The Gut Microbiotassay was able to detect significant differences in the quantity and composition of the microbiota according to gut sections and diarrhoeic status. 454-sequencing confirmed the specificity of the primer sets. Diarrhoea was associated with a reduced number of members from the genus Streptococcus, and in particular S. alactolyticus.

CONCLUSION: The Gut Microbiotassay provides fast and affordable high-throughput quantification of the bacterial composition in many samples and enables further descriptive taxonomic information if combined with 454-sequencing.}, } @article {pmid24225095, year = {2013}, author = {Albertsen, M and Saunders, AM and Nielsen, KL and Nielsen, PH}, title = {Metagenomes obtained by 'deep sequencing' - what do they tell about the enhanced biological phosphorus removal communities?.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {68}, number = {9}, pages = {1959-1968}, doi = {10.2166/wst.2013.441}, pmid = {24225095}, issn = {0273-1223}, mesh = {Bacteria/genetics/*metabolism ; Betaproteobacteria/classification/genetics/metabolism ; Biota ; DNA, Bacterial/analysis ; Denmark ; High-Throughput Nucleotide Sequencing ; In Situ Hybridization, Fluorescence ; *Metagenome ; Phosphorus/*metabolism ; Phylogeny ; Sequence Analysis, DNA ; *Waste Disposal, Fluid ; Wastewater/analysis/*microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Metagenomics enables studies of the genomic potential of complex microbial communities by sequencing bulk genomic DNA directly from the environment. Knowledge of the genetic potential of a community can be used to formulate and test ecological hypotheses about stability and performance. In this study deep metagenomics and fluorescence in situ hybridization (FISH) were used to study a full-scale wastewater treatment plant with enhanced biological phosphorus removal (EBPR), and the results were compared to an existing EBPR metagenome. EBPR is a widely used process that relies on a complex community of microorganisms to function properly. Insight into community and species level stability and dynamics is valuable for knowledge-driven optimization of the EBPR process. The metagenomes of the EBPR communities were distinct compared to metagenomes of communities from a wide range of other environments, which could be attributed to selection pressures of the EBPR process. The metabolic potential of one of the key microorganisms in the EPBR process, Accumulibacter, was investigated in more detail in the two plants, revealing a potential importance of phage predation on the dynamics of Accumulibacter populations. The results demonstrate that metagenomics can be used as a powerful tool for system wide characterization of the EBPR community as well as for a deeper understanding of the function of specific community members. Furthermore, we discuss and illustrate some of the general pitfalls in metagenomics and stress the need of additional DNA extraction independent information in metagenome studies.}, } @article {pmid24223817, year = {2013}, author = {Wang, L and Hatem, A and Catalyurek, UV and Morrison, M and Yu, Z}, title = {Metagenomic insights into the carbohydrate-active enzymes carried by the microorganisms adhering to solid digesta in the rumen of cows.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e78507}, pmid = {24223817}, issn = {1932-6203}, mesh = {Animals ; Bacterial Proteins/classification/*genetics/metabolism ; Cattle ; Cellulases/classification/*genetics/metabolism ; Cellulose/*metabolism ; Digestion/physiology ; Endo-1,4-beta Xylanases/classification/*genetics/metabolism ; Glycoside Hydrolases/classification/*genetics/metabolism ; *Metagenome ; Microbial Consortia/genetics ; Molecular Sequence Annotation ; Phylogeny ; Rumen/enzymology/microbiology ; Ruminants/microbiology/physiology ; Xylans/*metabolism ; }, abstract = {The ruminal microbial community is a unique source of enzymes that underpin the conversion of cellulosic biomass. In this study, the microbial consortia adherent on solid digesta in the rumen of Jersey cattle were subjected to an activity-based metagenomic study to explore the genetic diversity of carbohydrolytic enzymes in Jersey cows, with a particular focus on cellulases and xylanases. Pyrosequencing and bioinformatic analyses of 120 carbohydrate-active fosmids identified genes encoding 575 putative Carbohydrate-Active Enzymes (CAZymes) and proteins putatively related to transcriptional regulation, transporters, and signal transduction coupled with polysaccharide degradation and metabolism. Most of these genes shared little similarity to sequences archived in databases. Genes that were predicted to encode glycoside hydrolases (GH) involved in xylan and cellulose hydrolysis (e.g., GH3, 5, 9, 10, 39 and 43) were well represented. A new subfamily (S-8) of GH5 was identified from contigs assigned to Firmicutes. These subfamilies of GH5 proteins also showed significant phylum-dependent distribution. A number of polysaccharide utilization loci (PULs) were found, and two of them contained genes encoding Sus-like proteins and cellulases that have not been reported in previous metagenomic studies of samples from the rumens of cows or other herbivores. Comparison with the large metagenomic datasets previously reported of other ruminant species (or cattle breeds) and wallabies showed that the rumen microbiome of Jersey cows might contain differing CAZymes. Future studies are needed to further explore how host genetics and diets affect the diversity and distribution of CAZymes and utilization of plant cell wall materials.}, } @article {pmid24212578, year = {2014}, author = {Tang, Y and Underwood, A and Gielbert, A and Woodward, MJ and Petrovska, L}, title = {Metaproteomics analysis reveals the adaptation process for the chicken gut microbiota.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {2}, pages = {478-485}, pmid = {24212578}, issn = {1098-5336}, mesh = {*Adaptation, Physiological ; Animals ; Bacteria/genetics ; Bacterial Proteins/genetics/*metabolism ; Chaperonin 60/metabolism ; Chickens/*microbiology ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Gene Ontology ; Lactobacillus/genetics ; *Microbiota/genetics ; Proteomics/*methods ; RNA, Ribosomal, 16S ; }, abstract = {The animal gastrointestinal tract houses a large microbial community, the gut microbiota, that confers many benefits to its host, such as protection from pathogens and provision of essential metabolites. Metagenomic approaches have defined the chicken fecal microbiota in other studies, but here, we wished to assess the correlation between the metagenome and the bacterial proteome in order to better understand the healthy chicken gut microbiota. Here, we performed high-throughput sequencing of 16S rRNA gene amplicons and metaproteomics analysis of fecal samples to determine microbial gut composition and protein expression. 16 rRNA gene sequencing analysis identified Clostridiales, Bacteroidaceae, and Lactobacillaceae species as the most abundant species in the gut. For metaproteomics analysis, peptides were generated by using the Fasp method and subsequently fractionated by strong anion exchanges. Metaproteomics analysis identified 3,673 proteins. Among the most frequently identified proteins, 380 proteins belonged to Lactobacillus spp., 155 belonged to Clostridium spp., and 66 belonged to Streptococcus spp. The most frequently identified proteins were heat shock chaperones, including 349 GroEL proteins, from many bacterial species, whereas the most abundant enzymes were pyruvate kinases, as judged by the number of peptides identified per protein (spectral counting). Gene ontology and KEGG pathway analyses revealed the functions and locations of the identified proteins. The findings of both metaproteomics and 16S rRNA sequencing analyses are discussed.}, } @article {pmid24209636, year = {2013}, author = {Morrison, M}, title = {Looking large, to make more, out of gut metagenomics.}, journal = {Current opinion in microbiology}, volume = {16}, number = {5}, pages = {630-635}, doi = {10.1016/j.mib.2013.10.003}, pmid = {24209636}, issn = {1879-0364}, mesh = {Animals ; *Biota ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; Metagenomics/*methods ; }, abstract = {The fields of biomedicine and livestock agriculture share a need for advances in our understanding of microbiology, since the gastrointestinal tracts of all animals support a microbiota (microbial community) and their genomes (microbiome) that serves as a functional and dynamic interface between its genotype, environment, and lifestyle, with commensurate effects on host nutrition and health. Recently, small animal (especially rodent) models have been an invaluable resource with respect to exploring and establishing these relationships, and their relevance, to human health and well-being. By highlighting recent research studies, this review seeks to address how the functional and comparative analyses of the gut microbiome from 'large' animals by metagenomics and related 'metaomic' approaches can provide mutual benefits for livestock agriculture and biomedicine.}, } @article {pmid24204941, year = {2013}, author = {Hyde, ER and Haarmann, DP and Lynne, AM and Bucheli, SR and Petrosino, JF}, title = {The living dead: bacterial community structure of a cadaver at the onset and end of the bloat stage of decomposition.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e77733}, pmid = {24204941}, issn = {1932-6203}, mesh = {Bacteria/*classification/*genetics ; Cadaver ; Humans ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Texas ; }, abstract = {Human decomposition is a mosaic system with an intimate association between biotic and abiotic factors. Despite the integral role of bacteria in the decomposition process, few studies have catalogued bacterial biodiversity for terrestrial scenarios. To explore the microbiome of decomposition, two cadavers were placed at the Southeast Texas Applied Forensic Science facility and allowed to decompose under natural conditions. The bloat stage of decomposition, a stage easily identified in taphonomy and readily attributed to microbial physiology, was targeted. Each cadaver was sampled at two time points, at the onset and end of the bloat stage, from various body sites including internal locations. Bacterial samples were analyzed by pyrosequencing of the 16S rRNA gene. Our data show a shift from aerobic bacteria to anaerobic bacteria in all body sites sampled and demonstrate variation in community structure between bodies, between sample sites within a body, and between initial and end points of the bloat stage within a sample site. These data are best not viewed as points of comparison but rather additive data sets. While some species recovered are the same as those observed in culture-based studies, many are novel. Our results are preliminary and add to a larger emerging data set; a more comprehensive study is needed to further dissect the role of bacteria in human decomposition.}, } @article {pmid24204633, year = {2013}, author = {Kang, CS and Ban, M and Choi, EJ and Moon, HG and Jeon, JS and Kim, DK and Park, SK and Jeon, SG and Roh, TY and Myung, SJ and Gho, YS and Kim, JG and Kim, YK}, title = {Extracellular vesicles derived from gut microbiota, especially Akkermansia muciniphila, protect the progression of dextran sulfate sodium-induced colitis.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e76520}, pmid = {24204633}, issn = {1932-6203}, mesh = {Animals ; Bacterial Secretion Systems/*physiology ; Colitis/chemically induced/*microbiology/*prevention & control ; Dextran Sulfate/adverse effects ; Disease Models, Animal ; Disease Progression ; Female ; Inflammatory Bowel Diseases/etiology/microbiology/prevention & control ; Metagenome ; Mice ; *Microbiota ; Secretory Vesicles/metabolism/ultrastructure ; Verrucomicrobia/*metabolism ; }, abstract = {Gut microbiota play an important part in the pathogenesis of mucosal inflammation, such as inflammatory bowel disease (IBD). However, owing to the complexity of the gut microbiota, our understanding of the roles of commensal and pathogenic bacteria in the maintenance of immune homeostasis in the gut is evolving only slowly. Here, we evaluated the role of gut microbiota and their secreting extracellular vesicles (EV) in the development of mucosal inflammation in the gut. Experimental IBD model was established by oral application of dextran sulfate sodium (DSS) to C57BL/6 mice. The composition of gut microbiota and bacteria-derived EV in stools was evaluated by metagenome sequencing using bacterial common primer of 16S rDNA. Metagenomics in the IBD mouse model showed that the change in stool EV composition was more drastic, compared to the change of bacterial composition. Oral DSS application decreased the composition of EV from Akkermansia muciniphila and Bacteroides acidifaciens in stools, whereas increased EV from TM7 phylum, especially from species DQ777900_s and AJ400239_s. In vitro pretreatment of A. muciniphila-derived EV ameliorated the production of a pro-inflammatory cytokine IL-6 from colon epithelial cells induced by Escherichia coli EV. Additionally, oral application of A. muciniphila EV also protected DSS-induced IBD phenotypes, such as body weight loss, colon length, and inflammatory cell infiltration of colon wall. Our data provides insight into the role of gut microbiota-derived EV in regulation of intestinal immunity and homeostasis, and A. muciniphila-derived EV have protective effects in the development of DSS-induced colitis.}, } @article {pmid24203705, year = {2014}, author = {Huang, K and Brady, A and Mahurkar, A and White, O and Gevers, D and Huttenhower, C and Segata, N}, title = {MetaRef: a pan-genomic database for comparative and community microbial genomics.}, journal = {Nucleic acids research}, volume = {42}, number = {Database issue}, pages = {D617-24}, pmid = {24203705}, issn = {1362-4962}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; U54HG004969/HG/NHGRI NIH HHS/United States ; R01HG005969/HG/NHGRI NIH HHS/United States ; HHSN272200900018C/AI/NIAID NIH HHS/United States ; }, mesh = {Archaea/classification ; Bacteria/classification ; *Databases, Genetic ; *Genome, Archaeal ; *Genome, Bacterial ; Genomics ; Internet ; Metagenomics ; Microbiota ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; }, abstract = {Microbial genome sequencing is one of the longest-standing areas of biological database development, but high-throughput, low-cost technologies have increased its throughput to an unprecedented number of new genomes per year. Several thousand microbial genomes are now available, necessitating new approaches to organizing information on gene function, phylogeny and microbial taxonomy to facilitate downstream biological interpretation. MetaRef, available at http://metaref.org, is a novel online resource systematically cataloguing a comprehensive pan-genome of all microbial clades with sequenced isolates. It organizes currently available draft and finished bacterial and archaeal genomes into quality-controlled clades, reports all core and pan gene families at multiple levels in the resulting taxonomy, and it annotates families' conservation, phylogeny and consensus functional information. MetaRef also provides a comprehensive non-redundant reference gene catalogue for metagenomic studies, including the abundance and prevalence of all gene families in the >700 shotgun metagenomic samples of the Human Microbiome Project. This constitutes a systematic mapping of clade-specific microbial functions within the healthy human microbiome across multiple body sites and can be used as reference for identifying potential functional biomarkers in disease-associate microbiomes. MetaRef provides all information both as an online browsable resource and as downloadable sequences and tabular data files that can be used for subsequent offline studies.}, } @article {pmid24200009, year = {2013}, author = {Delafont, V and Brouke, A and Bouchon, D and Moulin, L and Héchard, Y}, title = {Microbiome of free-living amoebae isolated from drinking water.}, journal = {Water research}, volume = {47}, number = {19}, pages = {6958-6965}, doi = {10.1016/j.watres.2013.07.047}, pmid = {24200009}, issn = {1879-2448}, mesh = {Amoeba/*isolation & purification/*microbiology ; Drinking Water/*microbiology/*parasitology ; Hartmannella/isolation & purification ; Microbiological Techniques ; *Microbiota ; RNA, Ribosomal, 16S ; RNA, Ribosomal, 18S ; }, abstract = {Free-living amoebae (FLA) are protozoa that can be found in water networks where they prey on bacteria within biofilms. Most bacteria are digested rapidly by phagocytosis, however some are able to survive within amoebae and some are even able to multiply, as it is the case for Legionella pneumophila. These resisting bacteria are a potential health problem as they could also resist to macrophage phagocytosis. Several publications already reported intra-amoebal bacteria but the methods of identification did not allow metagenomic analysis and are partly based on co-culture with one selected amoebal strain. The aim of our study was to conduct a rRNA-targeted metagenomic analysis on amoebae and intra-amoebal bacteria found in drinking water network, to provide the first FLA microbiome in environmental strains. Three sites of a water network were sampled during four months. Culturable FLA were isolated and total DNA was prepared, allowing purification of both amoebal and bacterial DNA. Metagenomic studies were then conducted through 18S or 16S amplicons sequencing. Hartmannella was by far the most represented genus of FLA. Regarding intra-amoebal bacteria, 54 genera were identified, among which 21 were newly described intra-amoebal bacteria, underlying the power of our approach. There were high differences in bacterial diversity between the three sites. Several genera were highly represented and/or found at least in two sites, underlying that these bacteria could be able to multiply within FLA. Our method is therefore useful to identify FLA microbiome and could be applied to other networks to have a more comprehensive view of intra-amoebal diversity.}, } @article {pmid24199199, year = {2013}, author = {Ntougias, S and Bourtzis, K and Tsiamis, G}, title = {The microbiology of olive mill wastes.}, journal = {BioMed research international}, volume = {2013}, number = {}, pages = {784591}, pmid = {24199199}, issn = {2314-6141}, mesh = {Bacteria/genetics/*growth & development ; Biodegradation, Environmental ; *Ecosystem ; Humans ; Microbial Consortia/*physiology ; *Olea ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Refuse Disposal ; *Solid Waste ; }, abstract = {Olive mill wastes (OMWs) are high-strength organic effluents, which upon disposal can degrade soil and water quality, negatively affecting aquatic and terrestrial ecosystems. The main purpose of this review paper is to provide an up-to-date knowledge concerning the microbial communities identified over the past 20 years in olive mill wastes using both culture-dependent and independent approaches. A database survey of 16S rRNA gene sequences (585 records in total) obtained from olive mill waste environments revealed the dominance of members of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria. Independent studies confirmed that OMW microbial communities' structure is cultivar dependent. On the other hand, the detection of fecal bacteria and other potential human pathogens in OMWs is of major concern and deserves further examination. Despite the fact that the degradation and detoxification of the olive mill wastes have been mostly investigated through the application of known bacterial and fungal species originated from other environmental sources, the biotechnological potential of indigenous microbiota should be further exploited in respect to olive mill waste bioremediation and inactivation of plant and human pathogens. The implementation of omic and metagenomic approaches will further elucidate disposal issues of olive mill wastes.}, } @article {pmid24193200, year = {2014}, author = {Sherman, MP and Minnerly, J and Curtiss, W and Rangwala, S and Kelley, ST}, title = {Research on neonatal microbiomes: what neonatologists need to know.}, journal = {Neonatology}, volume = {105}, number = {1}, pages = {14-24}, pmid = {24193200}, issn = {1661-7819}, support = {R44 HD057744/HD/NICHD NIH HHS/United States ; HD057744/HD/NICHD NIH HHS/United States ; }, mesh = {Biomedical Research/*trends ; Humans ; Infant, Newborn ; Metagenomics/methods ; Microbiota/*genetics ; Neonatology/*education ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The aim of this article is to educate neonatal caregivers about metagenomics. This scientific field uses novel and ever changing molecular methods to identify how infants become colonized with microbes after birth. Publications using metagenomics appear infrequently in the neonatal literature because clinicians are unaccustomed to the analytical techniques, data interpretation, and illustration of the results. This review covers those areas. After a brief introduction of neonatal citations forthcoming from metagenomic studies, the following topics are covered: (1) the history of metagenomics, (2) a description of current and emerging instruments used to define microbial populations in human organs, and (3) how extensive databases generated by genome analyzers are examined and presented to readers. Clinicians may feel like they are learning a new language; however, they will appreciate this task is essential to understanding and practicing neonatal medicine in the future.}, } @article {pmid24180266, year = {2013}, author = {Ross, EM and Petrovski, S and Moate, PJ and Hayes, BJ}, title = {Metagenomics of rumen bacteriophage from thirteen lactating dairy cattle.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {242}, pmid = {24180266}, issn = {1471-2180}, mesh = {Animals ; Bacteriophages/*classification/*genetics/isolation & purification ; *Biota ; Cattle ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Rumen/*virology ; }, abstract = {BACKGROUND: The bovine rumen hosts a diverse and complex community of Eukarya, Bacteria, Archea and viruses (including bacteriophage). The rumen viral population (the rumen virome) has received little attention compared to the rumen microbial population (the rumen microbiome). We used massively parallel sequencing of virus like particles to investigate the diversity of the rumen virome in thirteen lactating Australian Holstein dairy cattle all housed in the same location, 12 of which were sampled on the same day.

RESULTS: Fourteen putative viral sequence fragments over 30 Kbp in length were assembled and annotated. Many of the putative genes in the assembled contigs showed no homology to previously annotated genes, highlighting the large amount of work still required to fully annotate the functions encoded in viral genomes. The abundance of the contig sequences varied widely between animals, even though the cattle were of the same age, stage of lactation and fed the same diets. Additionally the twelve animals which were co-habited shared a number of their dominant viral contigs. We compared the functional characteristics of our bovine viromes with that of other viromes, as well as rumen microbiomes. At the functional level, we found strong similarities between all of the viral samples, which were highly distinct from the rumen microbiome samples.

CONCLUSIONS: Our findings suggest a large amount of between animal variation in the bovine rumen virome and that co-habiting animals may have more similar viromes than non co-habited animals. We report the deepest sequencing to date of the rumen virome. This work highlights the enormous amount of novelty and variation present in the rumen virome.}, } @article {pmid24179225, year = {2013}, author = {Fierer, N and Ladau, J and Clemente, JC and Leff, JW and Owens, SM and Pollard, KS and Knight, R and Gilbert, JA and McCulley, RL}, title = {Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States.}, journal = {Science (New York, N.Y.)}, volume = {342}, number = {6158}, pages = {621-624}, doi = {10.1126/science.1243768}, pmid = {24179225}, issn = {1095-9203}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Agriculture ; Archaea/*classification/genetics/isolation & purification ; Bacteria/*classification/genetics/isolation & purification ; *Biodiversity ; *Endangered Species ; Metagenomics ; Poaceae ; *Soil ; *Soil Microbiology ; United States ; }, abstract = {Native tallgrass prairie once dominated much of the midwestern United States, but this biome and the soil microbial diversity that once sustained this highly productive system have been almost completely eradicated by decades of agricultural practices. We reconstructed the soil microbial diversity that once existed in this biome by analyzing relict prairie soils and found that the biogeographical patterns were largely driven by changes in the relative abundance of Verrucomicrobia, a poorly studied bacterial phylum that appears to dominate many prairie soils. Shotgun metagenomic data suggested that these spatial patterns were associated with strong shifts in carbon dynamics. We show that metagenomic approaches can be used to reconstruct below-ground biogeochemical and diversity gradients in endangered ecosystems; such information could be used to improve restoration efforts, given that even small changes in below-ground microbial diversity can have important impacts on ecosystem processes.}, } @article {pmid24177731, year = {2013}, author = {Han, P and Huang, YT and Lin, JG and Gu, JD}, title = {A comparison of two 16S rRNA gene-based PCR primer sets in unraveling anammox bacteria from different environmental samples.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {24}, pages = {10521-10529}, doi = {10.1007/s00253-013-5305-z}, pmid = {24177731}, issn = {1432-0614}, mesh = {Ammonium Compounds/*metabolism ; Bacteria/classification/genetics/*isolation & purification/metabolism ; *Biota ; China ; Cluster Analysis ; DNA Primers/*genetics ; *Environmental Microbiology ; Metagenomics/*methods ; Molecular Sequence Data ; Oxidation-Reduction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Wetlands ; }, abstract = {Two 16S rRNA gene-based PCR primer sets (Brod541F/Amx820R and A438f/A684r) for detecting anammox bacteria were compared using sediments from Mai Po wetlands (MP), the South China Sea (SCS), a freshwater reservoir (R2), and sludge granules from a wastewater treatment plant (A2). By comparing their ability in profiling anammox bacteria, the recovered diversity, community structure, and abundance of anammox bacteria among all these diverse samples indicated that A438f/A684r performed better than Brod541F/Amx820R in retrieving anammox bacteria from these different environmental samples. Five Scalindua subclusters (zhenghei-I, SCS-I, SCS-III, arabica, and brodae) dominated in SCS whereas two Scalindua subclusters (zhenghei-II and wagneri) and one cluster of Kuenenia dominated in MP. R2 showed a higher diversity of anammox bacteria with two new retrieved clusters (R2-New-1 and R2-New-2), which deserves further detailed study. The dominance of Brocadia in sample A2 was supported by both of the primer sets used. Results collectively indicate strongly niche-specific community structures of anammox bacteria in different environments, and A438f/A684r is highly recommended for screening anammox bacteria from various environments when dealing with a collection of samples with diverse physiochemical characteristics.}, } @article {pmid24177592, year = {2013}, author = {Sharmin, F and Wakelin, S and Huygens, F and Hargreaves, M}, title = {Firmicutes dominate the bacterial taxa within sugar-cane processing plants.}, journal = {Scientific reports}, volume = {3}, number = {}, pages = {3107}, pmid = {24177592}, issn = {2045-2322}, mesh = {Bacteria/*classification/genetics ; Biodiversity ; Computational Biology ; Ecosystem ; *Metagenome ; *Microbiota ; Phylogeny ; Saccharum/*microbiology ; }, abstract = {Sugar cane processing sites are characterised by high sugar/hemicellulose levels, available moisture and warm conditions, and are relatively unexplored unique microbial environments. The PhyloChip microarray was used to investigate bacterial diversity and community composition in three Australian sugar cane processing plants. These ecosystems were highly complex and dominated by four main Phyla, Firmicutes (the most dominant), followed by Proteobacteria, Bacteroidetes, and Chloroflexi. Significant variation (p < 0.05) in community structure occurred between samples collected from 'floor dump sediment', 'cooling tower water', and 'bagasse leachate'. Many bacterial Classes contributed to these differences, however most were of low numerical abundance. Separation in community composition was also linked to Classes of Firmicutes, particularly Bacillales, Lactobacillales and Clostridiales, whose dominance is likely to be linked to their physiology as 'lactic acid bacteria', capable of fermenting the sugars present. This process may help displace other bacterial taxa, providing a competitive advantage for Firmicutes bacteria.}, } @article {pmid24173537, year = {2014}, author = {Pylro, VS and Roesch, LF and Ortega, JM and do Amaral, AM and Tótola, MR and Hirsch, PR and Rosado, AS and Góes-Neto, A and da Costa da Silva, AL and Rosa, CA and Morais, DK and Andreote, FD and Duarte, GF and de Melo, IS and Seldin, L and Lambais, MR and Hungria, M and Peixoto, RS and Kruger, RH and Tsai, SM and Azevedo, V and , }, title = {Brazilian Microbiome Project: revealing the unexplored microbial diversity--challenges and prospects.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {237-241}, pmid = {24173537}, issn = {1432-184X}, mesh = {Advisory Committees/*organization & administration ; Animals ; *Biodiversity ; Brazil ; Databases, Factual ; *Metagenome ; *Microbiota ; Plants/microbiology ; Soil Microbiology ; }, abstract = {The Brazilian Microbiome Project (BMP) aims to assemble a Brazilian Metagenomic Consortium/Database. At present, many metagenomic projects underway in Brazil are widely known. Our goal in this initiative is to co-ordinate and standardize these together with new projects to come. It is estimated that Brazil hosts approximately 20 % of the entire world's macroorganism biological diversity. It is 1 of the 17 countries that share nearly 70 % of the world's catalogued animal and plant species, and is recognized as one of the most megadiverse countries. At the end of 2012, Brazil has joined GBIF (Global Biodiversity Information Facility), as associated member, to improve the access to the Brazilian biodiversity data in a free and open way. This was an important step toward increasing international collaboration and clearly shows the commitment of the Brazilian government in directing national policies toward sustainable development. Despite its importance, the Brazilian microbial diversity is still considered to be largely unknown, and it is clear that to maintain ecosystem dynamics and to sustainably manage land use, it is crucial to understand the biological and functional diversity of the system. This is the first attempt to collect and collate information about Brazilian microbial genetic and functional diversity in a systematic and holistic manner. The success of the BMP depends on a massive collaborative effort of both the Brazilian and international scientific communities, and therefore, we invite all colleagues to participate in this project.}, } @article {pmid24162577, year = {2014}, author = {Hewson, I and Eggleston, EM and Doherty, M and Lee, DY and Owens, M and Shapleigh, JP and Cornwell, JC and Crump, BC}, title = {Metatranscriptomic analyses of plankton communities inhabiting surface and subpycnocline waters of the Chesapeake Bay during oxic-anoxic-oxic transitions.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {1}, pages = {328-338}, pmid = {24162577}, issn = {1098-5336}, mesh = {Aerobiosis ; Anaerobiosis ; Biota ; Energy Metabolism ; Metagenomics/*methods ; Plankton/*classification/*isolation & purification ; Seasons ; *Transcriptome ; United States ; *Water Microbiology ; }, abstract = {We used metatranscriptomics to study the gene transcription patterns of microbial plankton (0.2 to 64 μm) at a mesohaline station in the Chesapeake Bay under transitions from oxic to anoxic waters in spring and from anoxic to oxic waters in autumn. Samples were collected from surface (i.e., above pycnocline) waters (3 m) and from waters beneath the pycnocline (16 to 22 m) in both 2010 and 2011. Metatranscriptome profiles based on function and potential phylogeny were different between 2010 and 2011 and strongly variable in 2011. This difference in variability corresponded with a highly variable ratio of eukaryotic to bacterial sequences (0.3 to 5.5), reflecting transient algal blooms in 2011 that were absent in 2010. The similarity between metatranscriptomes changed at a lower rate during the transition from oxic to anoxic waters than after the return to oxic conditions. Transcripts related to photosynthesis and low-affinity cytochrome oxidases were significantly higher in shallow than in deep waters, while in deep water genes involved in anaerobic metabolism, particularly sulfate reduction, succinyl coenzyme A (succinyl-CoA)-to-propionyl-CoA conversion, and menaquinone synthesis, were enriched relative to in shallow waters. Expected transitions in metabolism between oxic and anoxic deep waters were reflected in elevated levels of anaerobic respiratory reductases and utilization of propenediol and acetoin. The percentage of archaeal transcripts increased in both years in late summer (from 0.1 to 4.4% of all transcripts in 2010 and from 0.1 to 6.2% in 2011). Denitrification-related genes were expressed in a predicted pattern during the oxic-anoxic transition. Overall, our data suggest that Chesapeake Bay microbial assemblages express gene suites differently in shallow and deep waters and that differences in deep waters reflect variable redox states.}, } @article {pmid24148160, year = {2014}, author = {Glass, JB and Yu, H and Steele, JA and Dawson, KS and Sun, S and Chourey, K and Pan, C and Hettich, RL and Orphan, VJ}, title = {Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments.}, journal = {Environmental microbiology}, volume = {16}, number = {6}, pages = {1592-1611}, doi = {10.1111/1462-2920.12314}, pmid = {24148160}, issn = {1462-2920}, mesh = {Archaea/*genetics ; Archaeal Proteins/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Biological Transport ; California ; Genes, Archaeal ; Genes, Bacterial ; Geologic Sediments/chemistry/*microbiology ; Metagenome ; Methane/metabolism ; Microbial Consortia/*genetics ; Microbiological Phenomena ; Molybdenum/metabolism ; Nickel/metabolism ; Oregon ; Oxidation-Reduction ; Phylogeny ; Proteome/genetics/metabolism ; Sulfur-Reducing Bacteria/*genetics ; Tungsten/metabolism ; }, abstract = {Microbes have obligate requirements for trace metals in metalloenzymes that catalyse important biogeochemical reactions. In anoxic methane- and sulphide-rich environments, microbes may have unique adaptations for metal acquisition and utilization because of decreased bioavailability as a result of metal sulphide precipitation. However, micronutrient cycling is largely unexplored in cold (≤ 10°C) and sulphidic (> 1 mM ΣH(2)S) deep-sea methane seep ecosystems. We investigated trace metal geochemistry and microbial metal utilization in methane seeps offshore Oregon and California, USA, and report dissolved concentrations of nickel (0.5-270 nM), cobalt (0.5-6 nM), molybdenum (10-5600 nM) and tungsten (0.3-8 nM) in Hydrate Ridge sediment porewaters. Despite low levels of cobalt and tungsten, metagenomic and metaproteomic data suggest that microbial consortia catalysing anaerobic oxidation of methane (AOM) utilize both scarce micronutrients in addition to nickel and molybdenum. Genetic machinery for cobalt-containing vitamin B12 biosynthesis was present in both anaerobic methanotrophic archaea (ANME) and sulphate-reducing bacteria. Proteins affiliated with the tungsten-containing form of formylmethanofuran dehydrogenase were expressed in ANME from two seep ecosystems, the first evidence for expression of a tungstoenzyme in psychrophilic microorganisms. Overall, our data suggest that AOM consortia use specialized biochemical strategies to overcome the challenges of metal availability in sulphidic environments.}, } @article {pmid24148122, year = {2013}, author = {Maurice, CF}, title = {[Xenobiotics and the active gut microbiome: unknown effects unveiled].}, journal = {Medecine sciences : M/S}, volume = {29}, number = {10}, pages = {846-848}, doi = {10.1051/medsci/20132910011}, pmid = {24148122}, issn = {0767-0974}, mesh = {Female ; Gastrointestinal Tract/*drug effects/metabolism/*microbiology ; Gene Expression Regulation, Bacterial/drug effects ; Gene-Environment Interaction ; Humans ; Metagenome/drug effects/physiology ; Microbial Viability/drug effects/genetics ; Microbiota/*drug effects/genetics ; Models, Biological ; Xenobiotics/adverse effects/*pharmacology ; }, } @article {pmid24146974, year = {2013}, author = {Kovács, E and Wirth, R and Maróti, G and Bagi, Z and Rákhely, G and Kovács, KL}, title = {Biogas production from protein-rich biomass: fed-batch anaerobic fermentation of casein and of pig blood and associated changes in microbial community composition.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e77265}, pmid = {24146974}, issn = {1932-6203}, mesh = {Acetates/chemistry ; Ammonium Compounds/chemistry ; Animals ; *Biofuels ; *Biomass ; Bioreactors ; Biotransformation ; Blood/metabolism/microbiology ; Caseins/chemistry/metabolism ; Enzyme Activation ; Fatty Acids/chemistry ; Fermentation ; *Industrial Waste ; Microbiota ; Peptide Hydrolases/chemistry/metabolism ; Substrate Specificity ; Swine ; Time Factors ; }, abstract = {It is generally accepted as a fact in the biogas technology that protein-rich biomass substrates should be avoided due to inevitable process inhibition. Substrate compositions with a low C/N ratio are considered difficult to handle and may lead to process failure, though protein-rich industrial waste products have outstanding biogas generation potential. This common belief has been challenged by using protein-rich substrates, i.e. casein and precipitated pig blood protein in laboratory scale continuously stirred mesophilic fed-batch biogas fermenters. Both substrates proved suitable for sustained biogas production (0.447 L CH4/g protein oDM, i.e. organic total solids) in high yield without any additives, following a period of adaptation of the microbial community. The apparent key limiting factors in the anaerobic degradation of these proteinaceous materials were the accumulation of ammonia and hydrogen sulfide. Changes in time in the composition of the microbiological community were determined by next-generation sequencing-based metagenomic analyses. Characteristic rearrangements of the biogas-producing community upon protein feeding and specific differences due to the individual protein substrates were recognized. The results clearly demonstrate that sustained biogas production is readily achievable, provided the system is well-characterized, understood and controlled. Biogas yields (0.45 L CH4/g oDM) significantly exceeding those of the commonly used agricultural substrates (0.25-0.28 L CH4/g oDM) were routinely obtained. The results amply reveal that these high-energy-content waste products can be converted to biogas, a renewable energy carrier with flexible uses that can replace fossil natural gas in its applications. Process control, with appropriate acclimation of the microbial community to the unusual substrate, is necessary. Metagenomic analysis of the microbial community by next-generation sequencing allows a precise determination of the alterations in the community composition in the course of the process.}, } @article {pmid24146609, year = {2013}, author = {Carr, R and Shen-Orr, SS and Borenstein, E}, title = {Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution.}, journal = {PLoS computational biology}, volume = {9}, number = {10}, pages = {e1003292}, pmid = {24146609}, issn = {1553-7358}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; U19 AI057229/AI/NIAID NIH HHS/United States ; DP2AT00780201/AT/NCCIH NIH HHS/United States ; }, mesh = {Genome, Bacterial/*genetics ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Models, Genetic ; Sequence Analysis, DNA/*methods ; Tongue/microbiology ; }, abstract = {Metagenomics has transformed our understanding of the microbial world, allowing researchers to bypass the need to isolate and culture individual taxa and to directly characterize both the taxonomic and gene compositions of environmental samples. However, associating the genes found in a metagenomic sample with the specific taxa of origin remains a critical challenge. Existing binning methods, based on nucleotide composition or alignment to reference genomes allow only a coarse-grained classification and rely heavily on the availability of sequenced genomes from closely related taxa. Here, we introduce a novel computational framework, integrating variation in gene abundances across multiple samples with taxonomic abundance data to deconvolve metagenomic samples into taxa-specific gene profiles and to reconstruct the genomic content of community members. This assembly-free method is not bounded by various factors limiting previously described methods of metagenomic binning or metagenomic assembly and represents a fundamentally different approach to metagenomic-based genome reconstruction. An implementation of this framework is available at http://elbo.gs.washington.edu/software.html. We first describe the mathematical foundations of our framework and discuss considerations for implementing its various components. We demonstrate the ability of this framework to accurately deconvolve a set of metagenomic samples and to recover the gene content of individual taxa using synthetic metagenomic samples. We specifically characterize determinants of prediction accuracy and examine the impact of annotation errors on the reconstructed genomes. We finally apply metagenomic deconvolution to samples from the Human Microbiome Project, successfully reconstructing genus-level genomic content of various microbial genera, based solely on variation in gene count. These reconstructed genera are shown to correctly capture genus-specific properties. With the accumulation of metagenomic data, this deconvolution framework provides an essential tool for characterizing microbial taxa never before seen, laying the foundation for addressing fundamental questions concerning the taxa comprising diverse microbial communities.}, } @article {pmid24145144, year = {2014}, author = {Del Chierico, F and Petrucca, A and Vernocchi, P and Bracaglia, G and Fiscarelli, E and Bernaschi, P and Muraca, M and Urbani, A and Putignani, L}, title = {Proteomics boosts translational and clinical microbiology.}, journal = {Journal of proteomics}, volume = {97}, number = {}, pages = {69-87}, doi = {10.1016/j.jprot.2013.10.013}, pmid = {24145144}, issn = {1876-7737}, mesh = {Animals ; Bacteria/genetics/*metabolism ; Communicable Diseases, Emerging/drug therapy/genetics/*metabolism/microbiology ; *Drug Resistance, Bacterial ; *Drug Resistance, Fungal ; Fungi/genetics/*metabolism ; Humans ; *Microbiota ; Proteomics/*methods/trends ; }, abstract = {The application of proteomics to translational and clinical microbiology is one of the most advanced frontiers in the management and control of infectious diseases and in the understanding of complex microbial systems within human fluids and districts. This new approach aims at providing, by dedicated bioinformatic pipelines, a thorough description of pathogen proteomes and their interactions within the context of human host ecosystems, revolutionizing the vision of infectious diseases in biomedicine and approaching new viewpoints in both diagnostic and clinical management of the patient. Indeed, in the last few years, many laboratories have matured a series of advanced proteomic applications, aiming at providing individual proteome charts of pathogens, with respect to their morph and/or cell life stages, antimicrobial or antimycotic resistance profiling, epidemiological dispersion. Herein, we aim at reviewing the current state-of-the-art on proteomic protocols designed and set-up for translational and diagnostic microbiological purposes, from axenic pathogens' characterization to microbiota ecosystems' full description. The final goal is to describe applications of the most common MALDI-TOF MS platforms to advanced diagnostic issues related to emerging infections, increasing of fastidious bacteria, and generation of patient-tailored phylotypes. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.}, } @article {pmid24144111, year = {2013}, author = {Eskin, I and Hormozdiari, F and Conde, L and Riby, J and Skibola, CF and Eskin, E and Halperin, E}, title = {eALPS: estimating abundance levels in pooled sequencing using available genotyping data.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {20}, number = {11}, pages = {861-877}, pmid = {24144111}, issn = {1557-8666}, support = {R01 CA154643/CA/NCI NIH HHS/United States ; 1R01CA154643-01A1/CA/NCI NIH HHS/United States ; DA024417/DA/NIDA NIH HHS/United States ; HL080079/HL/NHLBI NIH HHS/United States ; }, mesh = {Algorithms ; Escherichia coli/genetics ; False Positive Reactions ; Genome, Bacterial ; Genome, Human ; *Genotyping Techniques ; Humans ; Lymphoma, Non-Hodgkin/genetics ; Metagenome ; Microbiota/genetics ; Models, Genetic ; Polymorphism, Single Nucleotide ; *Sequence Analysis, DNA ; }, abstract = {The recent advances in high-throughput sequencing technologies bring the potential of a better characterization of the genetic variation in humans and other organisms. In many occasions, either by design or by necessity, the sequencing procedure is performed on a pool of DNA samples with different abundances, where the abundance of each sample is unknown. Such a scenario is naturally occurring in the case of metagenomics analysis where a pool of bacteria is sequenced, or in the case of population studies involving DNA pools by design. Particularly, various pooling designs were recently suggested that can identify carriers of rare alleles in large cohorts, dramatically reducing the cost of such large-scale sequencing projects. A fundamental problem with such approaches for population studies is that the uncertainty of DNA proportions from different individuals in the pools might lead to spurious associations. Fortunately, it is often the case that the genotype data of at least some of the individuals in the pool is known. Here, we propose a method (eALPS) that uses the genotype data in conjunction with the pooled sequence data in order to accurately estimate the proportions of the samples in the pool, even in cases where not all individuals in the pool were genotyped (eALPS-LD). Using real data from a sequencing pooling study of non-Hodgkin's lymphoma, we demonstrate that the estimation of the proportions is crucial, since otherwise there is a risk for false discoveries. Additionally, we demonstrate that our approach is also applicable to the problem of quantification of species in metagenomics samples (eALPS-BCR) and is particularly suitable for metagenomic quantification of closely related species.}, } @article {pmid24141494, year = {2013}, author = {Sunagawa, S and Mende, DR and Zeller, G and Izquierdo-Carrasco, F and Berger, SA and Kultima, JR and Coelho, LP and Arumugam, M and Tap, J and Nielsen, HB and Rasmussen, S and Brunak, S and Pedersen, O and Guarner, F and de Vos, WM and Wang, J and Li, J and Doré, J and Ehrlich, SD and Stamatakis, A and Bork, P}, title = {Metagenomic species profiling using universal phylogenetic marker genes.}, journal = {Nature methods}, volume = {10}, number = {12}, pages = {1196-1199}, pmid = {24141494}, issn = {1548-7105}, mesh = {Algorithms ; Calibration ; Cluster Analysis ; Computational Biology/methods ; DNA, Ribosomal/genetics ; Genetic Linkage ; Genetic Markers ; Genome ; Humans ; Intestines/microbiology ; *Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment/*methods ; Sequence Analysis, DNA/methods ; }, abstract = {To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at http://www.bork.embl.de/software/mOTU/.}, } @article {pmid24136777, year = {2014}, author = {Singh, KM and Shah, TM and Reddy, B and Deshpande, S and Rank, DN and Joshi, CG}, title = {Taxonomic and gene-centric metagenomics of the fecal microbiome of low and high feed conversion ratio (FCR) broilers.}, journal = {Journal of applied genetics}, volume = {55}, number = {1}, pages = {145-154}, pmid = {24136777}, issn = {2190-3883}, mesh = {Animal Feed ; Animals ; Bacteria/classification/genetics/*isolation & purification ; Chickens/growth & development/*microbiology ; DNA, Ribosomal/chemistry/genetics ; Feces/*microbiology ; Female ; Gastrointestinal Tract/*microbiology ; High-Throughput Nucleotide Sequencing ; Male ; *Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Weight Gain ; }, abstract = {Individual weight gain in broiler growers appears to vary, which may in part be due to variation in their gut microbiota. In this paper we analyse the fecal microbiota of low and high feed conversion ratio (FCR) broilers. After shotgun sequencing of the fecal microbiome, we used the SEED database to identify the microbial diversity and metabolic potential in low and high FCR birds. The domain-level breakdown of our samples was bacteria (>95 %), eukaryotes (>2 %), archaea (>0.2 %), and viruses (>0.2 %). At the phylum level, Proteobacteria (78.83 % in low and 52.04 % in high FCR), Firmicutes (11.97 % in low and 27.53 % in high FCR) and Bacteroidetes (7.10 % in low FCR and 17.53 % in high FCR) predominated in the fecal microbial community. Poultry fecal metagenomes revealed the sequences related to 33 genera in both low and high FCR with significantly different proportion. Functional analysis revealed that genes for the metabolism of carbohydrates, amino acids and derivatives and protein metabolism were most abundant in SEED subsystem in both samples. Genes associated with stress, virulence, cell wall and cell capsule were also abundant. Indeed, genes associated with sulphur assimilation, flagellum and flagellar motility were over represented in low FCR birds. This information could help in developing strategies to improve feed efficiency and feed formulation for broiler chickens.}, } @article {pmid24132758, year = {2013}, author = {Ge, X and Wu, Y and Wang, M and Wang, J and Wu, L and Yang, X and Zhang, Y and Shi, Z}, title = {Viral metagenomics analysis of planktonic viruses in East Lake, Wuhan, China.}, journal = {Virologica Sinica}, volume = {28}, number = {5}, pages = {280-290}, pmid = {24132758}, issn = {1995-820X}, mesh = {*Biodiversity ; China ; Cluster Analysis ; High-Throughput Nucleotide Sequencing ; Lakes/*virology ; *Metagenomics ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Phylogeny ; Seasons ; Sequence Homology ; Viruses/*classification/*genetics ; }, abstract = {East Lake (Lake Donghu), located in Wuhan, China, is a typical city freshwater lake that has been experiencing eutrophic conditions and algal blooming during recent years. Marine and fresh water are considered to contain a large number of viruses. However, little is known about their genetic diversity because of the limited techniques for culturing viruses. In this study, we conducted a viral metagenomic analysis using a high-throughput sequencing technique with samples collected from East Lake in Spring, Summer, Autumn, and Winter. The libraries from four samples each generated 234,669, 71,837, 12,820, and 34,236 contigs (> 90 bp each), respectively. The genetic structure of the viral community revealed a high genetic diversity covering 23 viral families, with the majority of contigs homologous to DNA viruses, including members of Myoviridae, Podoviridae, Siphoviridae, Phycodnaviridae, and Microviridae, which infect bacteria or algae, and members of Circoviridae, which infect invertebrates and vertebrates. The highest viral genetic diversity occurred in samples collected in August, then December and June, and the least diversity in March. Most contigs have low-sequence identities with known viruses. PCR detection targeting the conserved sequences of genes (g20, psbA, psbD, and DNApol) of cyanophages further confirmed that there are novel cyanophages in the East Lake. Our viral metagenomic data provide the first preliminary understanding of the virome in one freshwater lake in China and would be helpful for novel virus discovery and the control of algal blooming in the future.}, } @article {pmid24123672, year = {2014}, author = {Rodriguez-R, LM and Konstantinidis, KT}, title = {Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets.}, journal = {Bioinformatics (Oxford, England)}, volume = {30}, number = {5}, pages = {629-635}, doi = {10.1093/bioinformatics/btt584}, pmid = {24123672}, issn = {1367-4811}, mesh = {Algorithms ; Metagenome ; Metagenomics/*methods ; Microbiota ; Soil Microbiology ; }, abstract = {MOTIVATION: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Owing to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed.

RESULTS: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, operational taxonomic unit calling or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that ∼200 Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.

Nonpareil is available at https://github.com/lmrodriguezr/nonpareil/ under the Artistic License 2.0.}, } @article {pmid24118574, year = {2014}, author = {Delsuc, F and Metcalf, JL and Wegener Parfrey, L and Song, SJ and González, A and Knight, R}, title = {Convergence of gut microbiomes in myrmecophagous mammals.}, journal = {Molecular ecology}, volume = {23}, number = {6}, pages = {1301-1317}, doi = {10.1111/mec.12501}, pmid = {24118574}, issn = {1365-294X}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; *Diet ; Gastrointestinal Tract/*microbiology ; Metagenomics ; *Microbiota ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Xenarthra/*microbiology ; }, abstract = {Mammals have diversified into many dietary niches. Specialized myrmecophagous (ant- and termite-eating) placental mammals represent a textbook example of evolutionary convergence driven by extreme diet specialization. Armadillos, anteaters, aardvarks, pangolins and aardwolves thus provide a model system for understanding the potential role of gut microbiota in the convergent adaptation to myrmecophagy. Here, we expand upon previous mammalian gut microbiome studies by using high-throughput barcoded Illumina sequencing of the 16S rRNA gene to characterize the composition of gut microbiota in 15 species representing all placental myrmecophagous lineages and their close relatives from zoo- and field-collected samples. We confirm that both diet and phylogeny drive the evolution of mammalian gut microbiota, with cases of convergence in global composition, but also examples of phylogenetic inertia. Our results reveal specialized placental myrmecophages as a spectacular case of large-scale convergence in gut microbiome composition. Indeed, neighbour-net networks and beta-diversity plots based on UniFrac distances show significant clustering of myrmecophagous species (anteaters, aardvarks and aardwolves), even though they belong to phylogenetically distant lineages representing different orders. The aardwolf, which diverged from carnivorous hyenas only in the last 10 million years, experienced a convergent shift in the composition of its gut microbiome to become more similar to other myrmecophages. These results confirm diet adaptation to be a major driving factor of convergence in gut microbiome composition over evolutionary timescales. This study sets the scene for future metagenomic studies aiming at evaluating potential convergence in functional gene content in the microbiomes of specialized mammalian myrmecophages.}, } @article {pmid24113822, year = {2014}, author = {Jiménez, DJ and Korenblum, E and van Elsas, JD}, title = {Novel multispecies microbial consortia involved in lignocellulose and 5-hydroxymethylfurfural bioconversion.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {6}, pages = {2789-2803}, doi = {10.1007/s00253-013-5253-7}, pmid = {24113822}, issn = {1432-0614}, mesh = {Aerobiosis ; Bacteria/*classification/isolation & purification/metabolism ; Bacterial Load ; Biodiversity ; Biotransformation ; Colony Count, Microbial ; Fungi/*classification/isolation & purification/metabolism ; Furaldehyde/*analogs & derivatives/metabolism ; Lignin/*metabolism ; *Microbial Consortia ; Molecular Sequence Data ; Plant Stems/metabolism ; Sequence Analysis, DNA ; Triticum/metabolism ; }, abstract = {To develop a targeted metagenomics approach for the analysis of novel multispecies microbial consortia involved in the bioconversion of lignocellulose and furanic compounds, we applied replicated sequential batch aerobic enrichment cultures with either pretreated or untreated wheat straw as the sources of carbon and energy. After each transfer, exponential growth of bacteria was detected using microscopic cell counts, indicating that the substrate was being utilized. In batch, the final bacterial abundances increased from an estimated 5 to 8.7-9.5 log 16S rRNA gene copy numbers/ml. The abundances of fungal propagules showed greater variation, i.e., between 5.4 and 8.0 log ITS1 copies/ml. Denaturing gradient gel electrophoresis analyses showed that the bacterial consortia in both treatments reached approximate structural stability after six transfers. Moreover, the structures of the fungal communities were strongly influenced by substrate treatment. A total of 124 bacterial strains were isolated from the two types of enrichment cultures. The most abundant strains were affiliated with the genera Raoultella/Klebsiella, Kluyvera, Citrobacter, Enterobacter, Pseudomonas, Acinetobacter, Flavobacterium and Arthrobacter. Totals of 43 and 11 strains obtained from the untreated and pretreated substrates, respectively, showed (hemi)cellulolytic activity (CMC-ase and xylanase), whereas 96 strains were capable of growth in 7.5 mM 5-hydroxymethylfurfural. About 50 % of the latter showed extracellular oxidoreductase activity as detected by a novel iodide oxidation method. Also, (hemi)cellulolytic fungal strains related to Coniochaeta, Plectosphaerella and Penicillium were isolated. One Trichosporon strain was isolated from pretreated wheat straw. The two novel bacterial-fungal consortia are starting points for lignocellulose degradation applications.}, } @article {pmid24107500, year = {2013}, author = {Szajewska, H}, title = {Microbiota modulation: can probiotics prevent/treat disease in pediatrics?.}, journal = {Nestle Nutrition Institute workshop series}, volume = {77}, number = {}, pages = {99-110}, doi = {10.1159/000351392}, pmid = {24107500}, issn = {1664-2155}, mesh = {*Bacteria ; Chronic Disease/*therapy ; Gastrointestinal Diseases/*therapy ; Humans ; *Microbiota ; *Pediatrics ; Probiotics/*therapeutic use ; Respiratory Tract Infections/*therapy ; }, abstract = {A number of metagenomic analyses providing knowledge of the human microbiome have yielded data on the differences between healthy and diseased individuals. Microbiota manipulation, such as through the administration of probiotics, may potentially contribute to improved health outcomes. The objective of this review was to summarize the most recent data on the use of probiotics to treat or prevent diseases in pediatrics. MEDLINE and The Cochrane Database of Systematic Reviews were searched in September 2012 for randomized controlled trials or their meta-analyses published in the last 3 years. To provide examples of current research interests, the focus of the search was on well-studied, common pediatric conditions as well as on some chronic diseases for which the benefits of gut microbiota manipulation are only in the early stages.}, } @article {pmid24101743, year = {2013}, author = {Yang, F and Huang, S and He, T and Catrenich, C and Teng, F and Bo, C and Chen, J and Liu, J and Li, J and Song, Y and Li, R and Xu, J}, title = {Microbial basis of oral malodor development in humans.}, journal = {Journal of dental research}, volume = {92}, number = {12}, pages = {1106-1112}, doi = {10.1177/0022034513507065}, pmid = {24101743}, issn = {1544-0591}, mesh = {Actinomyces/isolation & purification ; Adult ; Bacteria/*classification/isolation & purification ; Biodiversity ; Cross-Sectional Studies ; Dental Plaque/microbiology ; Female ; Follow-Up Studies ; Gemella/isolation & purification ; Haemophilus/isolation & purification ; Halitosis/metabolism/*microbiology ; Humans ; Hydrogen Sulfide/analysis ; Leptotrichia/isolation & purification ; Longitudinal Studies ; Male ; Microbial Consortia ; Middle Aged ; Prevotella/isolation & purification ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Streptococcus/isolation & purification ; Tongue/*microbiology ; Young Adult ; }, abstract = {To better understand the microbial basis of oral malodor development in humans, we used a cross-sectional and longitudinal study design and the pyrosequencing approach to track and compare the tongue microbiota associated with oral malodor in 29 Chinese adults who underwent a consecutive three-day evaluation for the amount of H2S excreted orally. Three levels of the oral malodor state (healthy, oral malodor, and severe oral malodor) were defined based on the H2S level. Community structure of the tongue plaques was more sensitive to changes of malodor state than to interpersonal variations or differences in sampling times. Within each individual, the structure of microbiota was relatively stable, while their variations were correlated with the change in the H2S level. Severe oral malodor microbiota were the most conserved in community structure, whereas the healthy ones were relatively varied. Oral-malodor-associated bacteria were identified. The relative abundance of Leptotrichia and Prevotella was positively correlated with oral malodor severity, whereas Hemophilus and Gemella exhibited a negative relationship with oral malodor severity. Our study provides one of the first landscapes of oral microbiota changes associated with oral malodor development and reveals microbes potentially useful to the evaluation and control of oral malodor.}, } @article {pmid24098498, year = {2013}, author = {Fredriksson, NJ and Hermansson, M and Wilén, BM}, title = {The choice of PCR primers has great impact on assessments of bacterial community diversity and dynamics in a wastewater treatment plant.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e76431}, pmid = {24098498}, issn = {1932-6203}, mesh = {Bacteria/classification/*genetics ; Biodiversity ; DNA Primers/genetics ; Gene Library ; Humans ; *Metagenome ; Microbiota ; Polymerase Chain Reaction/*methods ; RNA, Bacterial ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Sewage/microbiology ; Wastewater/*microbiology ; }, abstract = {Assessments of bacterial community diversity and dynamics are fundamental for the understanding of microbial ecology as well as biotechnological applications. We show that the choice of PCR primers has great impact on the results of analyses of diversity and dynamics using gene libraries and DNA fingerprinting. Two universal primer pairs targeting the 16S rRNA gene, 27F&1492R and 63F&M1387R, were compared and evaluated by analyzing the bacterial community in the activated sludge of a large-scale wastewater treatment plant. The two primer pairs targeted distinct parts of the bacterial community, none encompassing the other, both with similar richness. Had only one primer pair been used, very different conclusions had been drawn regarding dominant phylogenetic and putative functional groups. With 27F&1492R, Betaproteobacteria would have been determined to be the dominating taxa while 63F&M1387R would have described Alphaproteobacteria as the most common taxa. Microscopy and fluorescence in situ hybridization analysis showed that both Alphaproteobacteria and Betaproteobacteria were abundant in the activated sludge, confirming that the two primer pairs target two different fractions of the bacterial community. Furthermore, terminal restriction fragment polymorphism analyses of a series of four activated sludge samples showed that the two primer pairs would have resulted in different conclusions about community stability and the factors contributing to changes in community composition. In conclusion, different PCR primer pairs, although considered universal, target different ranges of bacteria and will thus show the diversity and dynamics of different fractions of the bacterial community in the analyzed sample. We also show that while a database search can serve as an indicator of how universal a primer pair is, an experimental assessment is necessary to evaluate the suitability for a specific environmental sample.}, } @article {pmid24098424, year = {2013}, author = {Wang, Z and Zhang, XX and Huang, K and Miao, Y and Shi, P and Liu, B and Long, C and Li, A}, title = {Metagenomic profiling of antibiotic resistance genes and mobile genetic elements in a tannery wastewater treatment plant.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e76079}, pmid = {24098424}, issn = {1932-6203}, mesh = {Biodiversity ; *DNA Transposable Elements ; Drug Resistance, Microbial/*genetics ; Genes, rRNA ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Sewage/*microbiology ; }, abstract = {Antibiotics are often used to prevent sickness and improve production in animal agriculture, and the residues in animal bodies may enter tannery wastewater during leather production. This study aimed to use Illumina high-throughput sequencing to investigate the occurrence, diversity and abundance of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in aerobic and anaerobic sludge of a full-scale tannery wastewater treatment plant (WWTP). Metagenomic analysis showed that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria dominated in the WWTP, but the relative abundance of archaea in anaerobic sludge was higher than in aerobic sludge. Sequencing reads from aerobic and anaerobic sludge revealed differences in the abundance of functional genes between both microbial communities. Genes coding for antibiotic resistance were identified in both communities. BLAST analysis against Antibiotic Resistance Genes Database (ARDB) further revealed that aerobic and anaerobic sludge contained various ARGs with high abundance, among which sulfonamide resistance gene sul1 had the highest abundance, occupying over 20% of the total ARGs reads. Tetracycline resistance genes (tet) were highly rich in the anaerobic sludge, among which tet33 had the highest abundance, but was absent in aerobic sludge. Over 70 types of insertion sequences were detected in each sludge sample, and class 1 integrase genes were prevalent in the WWTP. The results highlighted prevalence of ARGs and MGEs in tannery WWTPs, which may deserve more public health concerns.}, } @article {pmid24096086, year = {2014}, author = {Stark, L and Giersch, T and Wünschiers, R}, title = {Efficiency of RNA extraction from selected bacteria in the context of biogas production and metatranscriptomics.}, journal = {Anaerobe}, volume = {29}, number = {}, pages = {85-90}, doi = {10.1016/j.anaerobe.2013.09.007}, pmid = {24096086}, issn = {1095-8274}, mesh = {Biofuels ; Bioreactors ; Electrophoresis, Agar Gel ; Gram-Negative Bacteria/classification/*genetics/isolation & purification ; Gram-Positive Bacteria/classification/*genetics/isolation & purification ; Guanidines/chemistry ; Liquid Phase Microextraction/*methods ; Metagenome ; Microbial Consortia/genetics ; Phenols/chemistry ; Phylogeny ; RNA, Bacterial/*isolation & purification ; Sonication ; Specimen Handling/*methods ; Thiocyanates/chemistry ; }, abstract = {Understanding the microbial population in anaerobic digestion is an essential task to increase efficient substrate use and process stability. The metabolic state, represented e.g. by the transcriptome, of a fermenting system can help to find markers for monitoring industrial biogas production to prevent failures or to model the whole process. Advances in next-generation sequencing make transcriptomes accessible for large-scale analyses. In order to analyze the metatranscriptome of a mixed-species sample, isolation of high-quality RNA is the first step. However, different extraction methods may yield different efficiencies in different species. Especially in mixed-species environmental samples, unbiased isolation of transcripts is important for meaningful conclusions. We applied five different RNA-extraction protocols to nine taxonomic diverse bacterial species. Chosen methods are based on various lysis and extraction principles. We found that the extraction efficiency of different methods depends strongly on the target organism. RNA isolation of gram-positive bacteria was characterized by low yield whilst from gram-negative species higher concentrations can be obtained. Transferring our results to mixed-species investigations, such as metatranscriptomics with biofilms or biogas plants, leads to the conclusion that particular microorganisms might be over- or underrepresented depending on the method applied. Special care must be taken when using such metatranscriptomics data for, e.g. process modeling.}, } @article {pmid24085391, year = {2014}, author = {St-Pierre, B and Wright, AD}, title = {Comparative metagenomic analysis of bacterial populations in three full-scale mesophilic anaerobic manure digesters.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {6}, pages = {2709-2717}, doi = {10.1007/s00253-013-5220-3}, pmid = {24085391}, issn = {1432-0614}, mesh = {Anaerobiosis ; Animals ; Bacteria/*classification/*genetics ; *Biota ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Manure/*microbiology ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vermont ; }, abstract = {While the use of anaerobic digestion to generate methane as a source of bioenergy is increasing worldwide, our knowledge of the microbial communities that perform biomethanation is very limited. Using next-generation sequencing, bacterial population profiles were determined in three full-scale mesophilic anaerobic digesters operated on dairy farms in the state of Vermont (USA). To our knowledge, this is the first report of a metagenomic analysis on the bacterial population of anaerobic digesters using dairy manure as their main substrate. A total of 20,366 non-chimeric sequence reads, covering the V1-V2 hypervariable regions of the bacterial 16S rRNA gene, were assigned to 2,176 operational taxonomic units (OTUs) at a genetic distance cutoff value of 5 %. Based on their limited sequence identity to validly characterized species, the majority of OTUs identified in our study likely represented novel bacterial species. Using a naïve Bayesian classifier, 1,624 anaerobic digester OTUs could be assigned to 16 bacterial phyla, while 552 OTUs could not be classified and may belong to novel bacterial taxonomic groups that have yet to be described. Firmicutes, Bacteroidetes, and Chloroflexi were the most highly represented bacteria overall, with Bacteroidetes and Chloroflexi showing the least and the most variation in abundance between digesters, respectively. All digesters shared 132 OTUs, which as a "core" group represented 65.4 to 70.6 % of sequences in individual digesters. Our results show that bacterial populations from microbial communities of anaerobic manure digesters can display high levels of diversity despite sharing a common core substrate.}, } @article {pmid24083370, year = {2013}, author = {Wu, T and Zhang, Z and Liu, B and Hou, D and Liang, Y and Zhang, J and Shi, P}, title = {Gut microbiota dysbiosis and bacterial community assembly associated with cholesterol gallstones in large-scale study.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {669}, pmid = {24083370}, issn = {1471-2164}, mesh = {Bacteria/*metabolism ; Biliary Tract/microbiology ; Cholesterol/*metabolism ; Dysbiosis/*microbiology ; Female ; Gallstones/*microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; Metagenomics ; Microbiota/*physiology ; Middle Aged ; Phylogeny ; }, abstract = {BACKGROUND: Elucidating gut microbiota among gallstone patients as well as the complex bacterial colonization of cholesterol gallstones may help in both the prediction and subsequent lowered risk of cholelithiasis. To this end, we studied the composition of bacterial communities of gut, bile, and gallstones from 29 gallstone patients as well as the gut of 38 normal individuals, examining and analyzing some 299, 217 bacterial 16S rRNA gene sequences from 120 samples.

RESULTS: First, as compared with normal individuals, in gallstone patients there were significant (P < 0.001) increases of gut bacterial phylum Proteobacteria and decreases of three gut bacterial genera, Faecalibacterium, Lachnospira, and Roseburia. Second, about 70% of gut bacterial operational taxonomic units (OTUs) from gallstone patients were detectable in the biliary tract and bacteria diversity of biliary tract was significantly (P < 0.001) higher than that of gut. Third, analysis of the biliary tract core microbiome (represented by 106 bacteria OTUs) among gallstone patients showed that 33.96% (36/106) of constituents can be matched to known bacterial species (15 of which have publicly available genomes). A genome-wide search of MDR, BSH, bG, and phL genes purpotedly associated with the formation of cholesterol gallstones showed that all 15 species with known genomes (e.g., Propionibacterium acnes, Bacteroides vulgates, and Pseudomonas putida) contained at least contained one of the four genes. This finding could potentially provide underlying information needed to explain the association between biliary tract microbiota and the formation of cholesterol gallstones.

CONCLUSIONS: To the best of our knowledge, this is the first study to discover gut microbiota dysbiosis among gallstone patients, the presence of which may be a key contributor to the complex bacteria community assembly linked with the presence of cholesterol gallstones. Likewise, this study also provides the first large-scale glimpse of biliary tract microbiota potentially associated with cholesterol gallstones. Such a characterization of the biliary tract core microbiome has potentially important biological and medical implications regarding the role of bacteria in the formation cholesterol gallstones.}, } @article {pmid24077702, year = {2013}, author = {Kharbush, JJ and Ugalde, JA and Hogle, SL and Allen, EE and Aluwihare, LI}, title = {Composite bacterial hopanoids and their microbial producers across oxygen gradients in the water column of the California Current.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {23}, pages = {7491-7501}, pmid = {24077702}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; California ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Lyases/genetics ; *Metagenome ; Molecular Sequence Data ; Oxygen/analysis ; Phylogeny ; Seawater/chemistry/*microbiology ; Sequence Analysis, DNA ; Triterpenes/*metabolism ; }, abstract = {Hopanoids are pentacyclic triterpenoid lipids produced by many prokaryotes as cell membrane components. The structural variations of composite hopanoids, or bacteriohopanepolyols (BHPs), produced by various bacterial genera make them potentially useful molecular biomarkers of bacterial communities and metabolic processes in both modern and ancient environments. Building on previous work suggesting that organisms in low-oxygen environments are important contributors to BHP production in the marine water column and that there may be physiological roles for BHPs specific to these environments, this study investigated the relationship between trends in BHP structural diversity and abundance and the genetic diversity of BHP producers for the first time in a low-oxygen environment of the Eastern Tropical North Pacific. Amplification of the hopanoid biosynthesis gene for squalene hopene cyclase (sqhC) indicated far greater genetic diversity than would be predicted by examining BHP structural diversity alone and that greater sqhC genetic diversity exists in the marine environment than is represented by cultured representatives and most marine metagenomes. In addition, the genetic relationships in this data set suggest microaerophilic environments as potential "hot spots" of BHP production. Finally, structural analysis of BHPs showed that an isomer of the commonly observed BHP bacteriohopanetetrol may be linked to a producer that is more abundant in low-oxygen environments. Results of this study increase the known diversity of BHP producers and provide a detailed phylogeny with implications for the role of hopanoids in modern bacteria, as well as the evolutionary history of hopanoid biosynthesis, both of which are important considerations for future interpretations of the marine sedimentary record.}, } @article {pmid24076764, year = {2013}, author = {Paulson, JN and Stine, OC and Bravo, HC and Pop, M}, title = {Differential abundance analysis for microbial marker-gene surveys.}, journal = {Nature methods}, volume = {10}, number = {12}, pages = {1200-1202}, pmid = {24076764}, issn = {1548-7105}, support = {R01 HG004885/HG/NHGRI NIH HHS/United States ; R01 HG005220/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Area Under Curve ; Cluster Analysis ; Computer Simulation ; Databases, Genetic ; Gene Expression Profiling/methods ; *Genetic Markers ; Genetic Variation ; Humans ; Intestines/microbiology ; Metagenomics/*methods ; Mice ; *Microbiota ; Models, Genetic ; Models, Statistical ; Normal Distribution ; Phenotype ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Software ; }, abstract = {We introduce a methodology to assess differential abundance in sparse high-throughput microbial marker-gene survey data. Our approach, implemented in the metagenomeSeq Bioconductor package, relies on a novel normalization technique and a statistical model that accounts for undersampling-a common feature of large-scale marker-gene studies. Using simulated data and several published microbiota data sets, we show that metagenomeSeq outperforms the tools currently used in this field.}, } @article {pmid24073227, year = {2013}, author = {Garcia-Garcerà, M and Garcia-Etxebarria, K and Coscollà, M and Latorre, A and Calafell, F}, title = {A new method for extracting skin microbes allows metagenomic analysis of whole-deep skin.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e74914}, pmid = {24073227}, issn = {1932-6203}, mesh = {Animals ; Bacteria/*genetics/*isolation & purification ; DNA/genetics ; GTP Phosphohydrolases/genetics ; Humans ; Metagenomics/*methods ; Mice ; Mice, Inbred C57BL ; Microbiota/*genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Skin/chemistry/metabolism/*microbiology ; }, abstract = {In the last decade, an extensive effort has been made to characterize the human microbiota, due to its clinical and economic interests. However, a metagenomic approach to the skin microbiota is hampered by the high proportion of host DNA that is recovered. In contrast with the burgeoning field of gut metagenomics, skin metagenomics has been hindered by the absence of an efficient method to avoid sequencing the host DNA. We present here a method for recovering microbial DNA from skin samples, based on a combination of molecular techniques. We have applied this method to mouse skin, and have validated it by standard, quantitative PCR and amplicon sequencing of 16S rRNA. The taxonomic diversity recovered was not altered by this new method, as proved by comparing the phylogenetic structure revealed by 16S rRNA sequencing in untreated vs. treated samples. As proof of concept, we also present the first two mouse skin metagenomes, which allowed discovering new taxa (not only prokaryotes but also viruses and eukaryots) not reachable by 16S rRNA sequencing, as well as to characterize the skin microbiome functional landscape. Our method paves the way for the development of skin metagenomics, which will allow a much deeper knowledge of the skin microbiome and its relationship with the host, both in a healthy state and in relation to disease.}, } @article {pmid24069303, year = {2013}, author = {Egge, E and Bittner, L and Andersen, T and Audic, S and de Vargas, C and Edvardsen, B}, title = {454 pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e74371}, pmid = {24069303}, issn = {1932-6203}, mesh = {*Biodiversity ; DNA, Complementary ; DNA, Ribosomal ; Haptophyta/*classification/*genetics ; *High-Throughput Nucleotide Sequencing/methods/standards ; *Metagenome ; Phylogeny ; }, abstract = {Next generation sequencing of ribosomal DNA is increasingly used to assess the diversity and structure of microbial communities. Here we test the ability of 454 pyrosequencing to detect the number of species present, and assess the relative abundance in terms of cell numbers and biomass of protists in the phylum Haptophyta. We used a mock community consisting of equal number of cells of 11 haptophyte species and compared targeting DNA and RNA/cDNA, and two different V4 SSU rDNA haptophyte-biased primer pairs. Further, we tested four different bioinformatic filtering methods to reduce errors in the resulting sequence dataset. With sequencing depth of 11000-20000 reads and targeting cDNA with Haptophyta specific primers Hap454 we detected all 11 species. A rarefaction analysis of expected number of species recovered as a function of sampling depth suggested that minimum 1400 reads were required here to recover all species in the mock community. Relative read abundance did not correlate to relative cell numbers. Although the species represented with the largest biomass was also proportionally most abundant among the reads, there was generally a weak correlation between proportional read abundance and proportional biomass of the different species, both with DNA and cDNA as template. The 454 sequencing generated considerable spurious diversity, and more with cDNA than DNA as template. With initial filtering based only on match with barcode and primer we observed 100-fold more operational taxonomic units (OTUs) at 99% similarity than the number of species present in the mock community. Filtering based on quality scores, or denoising with PyroNoise resulted in ten times more OTU99% than the number of species. Denoising with AmpliconNoise reduced the number of OTU99% to match the number of species present in the mock community. Based on our analyses, we propose a strategy to more accurately depict haptophyte diversity using 454 pyrosequencing.}, } @article {pmid24068019, year = {2013}, author = {Rogers, GB and Carroll, MP and Zain, NM and Bruce, KD and Lock, K and Walker, W and Jones, G and Daniels, TW and Lucas, JS}, title = {Complexity, temporal stability, and clinical correlates of airway bacterial community composition in primary ciliary dyskinesia.}, journal = {Journal of clinical microbiology}, volume = {51}, number = {12}, pages = {4029-4035}, pmid = {24068019}, issn = {1098-660X}, mesh = {Adolescent ; Adult ; Aged ; Bacteria/*classification/*genetics ; Bacterial Load ; *Biota ; Child ; Child, Preschool ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Humans ; *Kartagener Syndrome ; Male ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Respiratory System/*microbiology ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Primary ciliary dyskinesia (PCD) is a genetic disease characterized by abnormalities in ciliary function, leading to compromised airway clearance and chronic bacterial infection of the upper and lower airways. The compositions of these infections and the relationships between their characteristics and disease presentation are poorly defined. We describe here the first systematic culture-independent evaluation of lower airway bacteriology in PCD. Thirty-three airway samples (26 from sputum, 7 from bronchoalveolar lavage [BAL] fluid) were collected from 24 PCD patients aged 4 to 73 years. 16S rRNA quantitative PCR and pyrosequencing were used to determine the bacterial loads and community compositions of the samples. Bacterial loads, which ranged from 1.3 × 10(4) to 5.2 × 10(9) CFU/ml, were positively correlated with age (P = 0.002) but not lung function. An analysis of ∼7,000 16S rRNA sequences per sample identified bacterial species belonging to 128 genera. The concurrently collected paired samples showed high bacterial community similarity. The mean relative abundance of the dominant genera was 64.5% (standard deviation [SD], 24.5), including taxa reported through standard diagnostic microbiology (members of the genera Pseudomonas, Haemophilus, and Streptococcus) and those requiring specific ex vivo growth conditions (members of the genera Prevotella and Porphyromonas). The significant correlations observed included a positive relationship between Pseudomonas aeruginosa relative abundance and age and a negative relationship between P. aeruginosa relative abundance and lung function. Members of the genus Ralstonia were also found to contribute substantially to the bacterial communities in a number of patients. Follow-up samples from a subset of patients revealed high levels of bacterial community temporal stability. The detailed microbiological characterization presented here provides a basis for the reassessment of the clinical management of PCD airway infections.}, } @article {pmid24067887, year = {2014}, author = {Castelino, M and Eyre, S and Upton, M and Ho, P and Barton, A}, title = {The bacterial skin microbiome in psoriatic arthritis, an unexplored link in pathogenesis: challenges and opportunities offered by recent technological advances.}, journal = {Rheumatology (Oxford, England)}, volume = {53}, number = {5}, pages = {777-784}, doi = {10.1093/rheumatology/ket319}, pmid = {24067887}, issn = {1462-0332}, mesh = {Arthritis, Psoriatic/*microbiology/physiopathology ; Gastrointestinal Tract/microbiology/physiopathology ; Humans ; Inflammatory Bowel Diseases/microbiology/physiopathology ; Metagenomics ; Microbiota/*physiology ; Skin/*microbiology ; }, abstract = {The resident microbial community, harboured by humans in sites such as the skin and gastrointestinal tract, is enormous, representing a candidate environmental factor affecting susceptibility to complex diseases, where both genetic and environmental risk factors are important. The potential of microorganisms to influence the human immune system is considerable, given their ubiquity. The impact of the host-gene-microbe interaction on the maintenance of health and the development of disease has not yet been assessed robustly in chronic inflammatory conditions. PsA represents a model inflammatory disease to explore the role of the microbiome because skin involvement and overlap with IBD implicates both the skin and gastrointestinal tract as sources of microbial triggers for PsA. In parallel with genetic studies, characterization of the host microbiota may benefit our understanding of the microbial contribution to disease pathogenesis-knowledge that may eventually inform the development of novel therapeutics.}, } @article {pmid24041049, year = {2013}, author = {Valdovinos-Díaz, MÁ}, title = {[Intestinal microbiota in digestive disorders. Probiotics, prebiotics and symbiotics].}, journal = {Revista de gastroenterologia de Mexico}, volume = {78 Suppl 1}, number = {}, pages = {25-27}, doi = {10.1016/j.rgmx.2013.06.008}, pmid = {24041049}, issn = {0375-0906}, mesh = {Digestive System Diseases/*microbiology/*therapy ; Feces/microbiology ; Gastrointestinal Neoplasms/microbiology/prevention & control ; Humans ; Intestines/microbiology ; Irritable Bowel Syndrome/microbiology/therapy ; Metagenome ; *Microbiota ; *Prebiotics ; *Probiotics ; }, } @article {pmid24060133, year = {2013}, author = {Huson, DH and Weber, N}, title = {Microbial community analysis using MEGAN.}, journal = {Methods in enzymology}, volume = {531}, number = {}, pages = {465-485}, doi = {10.1016/B978-0-12-407863-5.00021-6}, pmid = {24060133}, issn = {1557-7988}, mesh = {Algorithms ; Databases, Genetic ; Metagenomics ; Microbial Consortia/genetics ; RNA, Ribosomal, 16S/*genetics/*isolation & purification ; Sequence Analysis, DNA ; *Software ; }, abstract = {Metagenomics, the study of microbes in the environment using DNA sequencing, depends upon dedicated software tools for processing and analyzing very large sequencing datasets. One such tool is MEGAN (MEtaGenome ANalyzer), which can be used to interactively analyze and compare metagenomic and metatranscriptomic data, both taxonomically and functionally. To perform a taxonomic analysis, the program places the reads onto the NCBI taxonomy, while functional analysis is performed by mapping reads to the SEED, COG, and KEGG classifications. Samples can be compared taxonomically and functionally, using a wide range of different charting and visualization techniques. PCoA analysis and clustering methods allow high-level comparison of large numbers of samples. Different attributes of the samples can be captured and used within analysis. The program supports various input formats for loading data and can export analysis results in different text-based and graphical formats. The program is designed to work with very large samples containing many millions of reads. It is written in Java and installers for the three major computer operating systems are available from http://www-ab.informatik.uni-tuebingen.de.}, } @article {pmid24060130, year = {2013}, author = {Preheim, SP and Perrotta, AR and Friedman, J and Smilie, C and Brito, I and Smith, MB and Alm, E}, title = {Computational methods for high-throughput comparative analyses of natural microbial communities.}, journal = {Methods in enzymology}, volume = {531}, number = {}, pages = {353-370}, doi = {10.1016/B978-0-12-407863-5.00018-6}, pmid = {24060130}, issn = {1557-7988}, mesh = {Classification ; Computational Biology/*methods ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; Microbial Consortia/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {One of the most widely employed methods in metagenomics is the amplification and sequencing of the highly conserved ribosomal RNA (rRNA) genes from organisms in complex microbial communities. rRNA surveys, typically using the 16S rRNA gene for prokaryotic identification, provide information about the total diversity and taxonomic affiliation of organisms present in a sample. Greatly enhanced by high-throughput sequencing, these surveys have uncovered the remarkable diversity of uncultured organisms and revealed unappreciated ecological roles ranging from nutrient cycling to human health. This chapter outlines the best practices for comparative analyses of microbial community surveys. We explain how to transform raw data into meaningful units for further analysis and discuss how to calculate sample diversity and community distance metrics. Finally, we outline how to find associations of species with specific metadata and true correlations between species from compositional data. We focus on data generated by next-generation sequencing platforms, using the Illumina platform as a test case, because of its widespread use especially among researchers just entering the field.}, } @article {pmid24060127, year = {2013}, author = {Mueller, RS and Pan, C}, title = {Sample handling and mass spectrometry for microbial metaproteomic analyses.}, journal = {Methods in enzymology}, volume = {531}, number = {}, pages = {289-303}, doi = {10.1016/B978-0-12-407863-5.00015-0}, pmid = {24060127}, issn = {1557-7988}, mesh = {Bacteria/genetics ; Chromatography, Liquid/*methods ; Mass Spectrometry/*methods ; *Metagenome ; Microbial Consortia/genetics ; Proteome/genetics ; *Specimen Handling ; }, abstract = {Metaproteomic studies of whole microbial communities from environmental samples (e.g., soil, sediments, freshwater, seawater, etc.) have rapidly increased in recent years due to many technological advances in mass spectrometry (MS). A single 24-h liquid chromatograph-tandem mass spectrometry (LC-MS/MS) measurement can potentially detect and quantify thousands of proteins from many dominant and subdominant naturally occurring microbial populations. Importantly, amino acid sequences and relative abundance information for detected peptides are determined, which allows for the characterization of expressed protein functions within communities and specific matches to be made to microbial lineages, with potential subspecies resolution. Continued optimization of protein extraction and fractionation protocols, development of quantification methods, and advances in mass spectrometry instrumentation are enabling more accurate and comprehensive peptide detection within samples, leading to wider research applicability, greater ease of use, and overall accessibility. This chapter provides a brief overview of metaproteomics experimental options, including a general protocol for sample handling and LC-MS/MS measurement.}, } @article {pmid24060126, year = {2013}, author = {Morris, RM and Nunn, BL}, title = {Sample preparation and processing for planktonic microbial community proteomics.}, journal = {Methods in enzymology}, volume = {531}, number = {}, pages = {271-287}, doi = {10.1016/B978-0-12-407863-5.00014-9}, pmid = {24060126}, issn = {1557-7988}, mesh = {Archaea/metabolism ; Bacteria/metabolism ; High-Throughput Nucleotide Sequencing ; Microbial Consortia/*genetics ; Proteins/isolation & purification ; Proteomics/*methods ; *Specimen Handling ; Tandem Mass Spectrometry ; }, abstract = {Advances in tandem mass spectrometry (tandem MS) and sequencing have enabled the field of community proteomics, which seeks to identify expressed proteins, their sequence variability, and the physiological responses of organisms to variable environmental conditions. Bottom-up tandem MS-based community proteomic approaches generate fragmentation spectra from peptides. Fragmentation spectra are then searched against genomic or metagenomic databases to deduce the amino acid sequences of peptides, providing positive identifications for proteins. Marine community proteomic studies have verified the importance of nutrient transport, energy generation, and carbon fixation functions in bacteria and archaea and revealed spatial and temporal shifts in the expressed functions of communities. Here, we discuss sample collection, preparation, and processing methods for planktonic tandem MS-based community proteomics.}, } @article {pmid24060124, year = {2013}, author = {Satinsky, BM and Gifford, SM and Crump, BC and Moran, MA}, title = {Use of internal standards for quantitative metatranscriptome and metagenome analysis.}, journal = {Methods in enzymology}, volume = {531}, number = {}, pages = {237-250}, doi = {10.1016/B978-0-12-407863-5.00012-5}, pmid = {24060124}, issn = {1557-7988}, mesh = {DNA, Bacterial/genetics/*isolation & purification/standards ; Gene Expression Profiling/*standards ; High-Throughput Nucleotide Sequencing ; Metagenome/*genetics ; Microbial Consortia/genetics ; RNA, Messenger/isolation & purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Next generation sequencing-enabled metatranscriptomic and metagenomic datasets are providing unprecedented insights into the functional diversity of microbial communities, allowing detection of the genes present in a community as well as differentiation of those being actively transcribed. An emerging challenge of meta-omics approaches is how to quantitatively compare metagenomes and metatranscriptomes collected across spatial and temporal scales, or among treatments in experimental manipulations. Here, we describe the use of internal DNA and mRNA standards in meta-omics methodologies, and highlight how data collected in an absolute framework (per L or per cell) provides increased comparative power and insight into underlying causes of differences between samples.}, } @article {pmid24060122, year = {2013}, author = {Stewart, FJ}, title = {Preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton.}, journal = {Methods in enzymology}, volume = {531}, number = {}, pages = {187-218}, doi = {10.1016/B978-0-12-407863-5.00010-1}, pmid = {24060122}, issn = {1557-7988}, mesh = {Aquatic Organisms/genetics ; DNA, Complementary/genetics ; Gene Expression Profiling/methods ; Metagenomics/*methods ; Microbial Consortia/*genetics ; Plankton/*genetics ; }, abstract = {High-throughput sequencing and analysis of microbial community cDNA (metatranscriptomics) are providing valuable insight into in situ microbial activity and metabolism in the oceans. A critical first step in metatranscriptomic studies is the preparation of high-quality cDNA. At the minimum, preparing cDNA for sequencing involves steps of biomass collection, RNA preservation, total RNA extraction, and cDNA synthesis. Each of these steps may present unique challenges for marine microbial samples, particularly for deep-sea samples whose transcriptional profiles may change between water collection and RNA preservation. Because bacterioplankton community RNA yields may be relatively low (<500 ng), it is often necessary to amplify total RNA to obtain sufficient cDNA for downstream sequencing. Additionally, depending on the nature of the samples, budgetary considerations, and the choice of sequencing technology, steps may be required to deplete the amount of ribosomal RNA (rRNA) transcripts in a sample in order to maximize mRNA recovery. cDNA preparation may also involve the addition of internal RNA standards to biomass samples, thereby allowing for absolute quantification of transcript abundance following sequencing. This chapter describes a general protocol for cDNA preparation from planktonic microbial communities, from RNA preservation to final cDNA synthesis, with specific emphasis placed on topics of sampling bias and rRNA depletion. Consideration of these topics is critical for helping standardize metatranscriptomics methods as they become widespread in marine microbiology research.}, } @article {pmid24060121, year = {2013}, author = {Hampton-Marcell, JT and Moormann, SM and Owens, SM and Gilbert, JA}, title = {Preparation and metatranscriptomic analyses of host-microbe systems.}, journal = {Methods in enzymology}, volume = {531}, number = {}, pages = {169-185}, doi = {10.1016/B978-0-12-407863-5.00009-5}, pmid = {24060121}, issn = {1557-7988}, mesh = {Genome, Bacterial ; Host-Pathogen Interactions ; Metabolomics ; Metagenomics/*methods ; Microbial Consortia/*genetics ; Sequence Analysis, RNA/*methods ; Systems Biology ; Transcriptome ; }, abstract = {Metatranscriptomics has increased our working knowledge of the functional significance and genetic variability of microbial communities, yet there is still limited information concerning how gene expression and regulation in a microbiome influences interactions with a host organism. During a pathogenic infection, eukaryotic organisms are subject to invasion by bacteria and other agents, or these "pathogens" can switch from a commensal to pathogenic trophic relationship with the host. Understanding how these trophic relationships initiate and persist in the host requires deciphering the functional response of the host and the microbiome, so-called Dual RNA-Seq. This technique is both fast and relatively cheap compared to proteomics and metabolomics and provides information on the potential functional interactions that occur between microbes, and with the host. These metatranscriptomic analyses can also be coupled with metagenomic analyses and statistical models to provide an in-depth approach to systems biology. In this chapter, we detail a standardized method to process and analyze host-associated microbial metatranscriptomes independent of the associated host.}, } @article {pmid24060119, year = {2013}, author = {Martínez, A and Osburne, MS}, title = {Preparation of fosmid libraries and functional metagenomic analysis of microbial community DNA.}, journal = {Methods in enzymology}, volume = {531}, number = {}, pages = {123-142}, doi = {10.1016/B978-0-12-407863-5.00007-1}, pmid = {24060119}, issn = {1557-7988}, mesh = {DNA, Bacterial ; Genetic Vectors ; *Genomic Library ; Metagenomics/*methods ; Microbial Consortia/*genetics ; }, abstract = {One of the most important challenges in contemporary microbial ecology is to assign a functional role to the large number of novel genes discovered through large-scale sequencing of natural microbial communities that lack similarity to genes of known function. Functional screening of metagenomic libraries, that is, screening environmental DNA clones for the ability to confer an activity of interest to a heterologous bacterial host, is a promising approach for bridging the gap between metagenomic DNA sequencing and functional characterization. Here, we describe methods for isolating environmental DNA and constructing metagenomic fosmid libraries, as well as methods for designing and implementing successful functional screens of such libraries.}, } @article {pmid24060114, year = {2013}, author = {Trembath-Reichert, E and Green-Saxena, A and Orphan, VJ}, title = {Whole cell immunomagnetic enrichment of environmental microbial consortia using rRNA-targeted Magneto-FISH.}, journal = {Methods in enzymology}, volume = {531}, number = {}, pages = {21-44}, doi = {10.1016/B978-0-12-407863-5.00002-2}, pmid = {24060114}, issn = {1557-7988}, support = {5 T32 GM07616/GM/NIGMS NIH HHS/United States ; }, mesh = {Anaerobiosis ; Archaea/classification/genetics ; DNA, Archaeal/classification/*genetics ; In Situ Hybridization, Fluorescence/*methods ; Metagenomics ; Microbial Consortia/*genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Magneto-FISH, in combination with metagenomic techniques, explores the middle ground between single-cell analysis and complex community characterization in bulk samples to better understand microbial partnerships and their roles in ecosystems. The Magneto-FISH method combines the selectivity of catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) with immunomagnetic capture to provide targeted molecular and metagenomic analysis of co-associated microorganisms in the environment. This method was originally developed by Pernthaler et al. (Pernthaler et al., 2008; Pernthaler & Orphan, 2010). It led to the discovery of new bacterial groups associated with anaerobic methane-oxidizing (ANME-2) archaea in methane seeps, as well as provided insight into their physiological potential using metagenomics. Here, we demonstrate the utility of this method for capturing aggregated consortia using a series of nested oligonucleotide probes of differing specificity designed to target either the ANME archaea or their Deltaproteobacteria partner, combined with 16S rRNA and mcrA analysis. This chapter outlines a modified Magneto-FISH protocol for large- and small-volume samples and evaluates the strengths and limitations of this method predominantly focusing on (1) the relationship between FISH probe specificity and sample selectivity, (2) means of improving DNA yield from paraformaldehyde-fixed samples, and (3) suggestions for adapting the Magneto-FISH method for other microbial systems, including potential for single-cell recovery.}, } @article {pmid24055975, year = {2013}, author = {Nie, Z and Zheng, Y and Wang, M and Han, Y and Wang, Y and Luo, J and Niu, D}, title = {Exploring microbial succession and diversity during solid-state fermentation of Tianjin duliu mature vinegar.}, journal = {Bioresource technology}, volume = {148}, number = {}, pages = {325-333}, doi = {10.1016/j.biortech.2013.08.152}, pmid = {24055975}, issn = {1873-2976}, mesh = {Acetic Acid/*metabolism ; Amino Acids/analysis ; Bacteria/genetics/*growth & development ; Base Sequence ; *Biodiversity ; China ; *Fermentation ; Fungi/genetics/*growth & development ; Hydrogen-Ion Concentration ; Metagenomics ; Molecular Sequence Data ; Phylogeny ; Principal Component Analysis ; Sequence Analysis, DNA ; }, abstract = {Tianjin duliu mature vinegar was one of famous Chinese traditional vinegars. The unique flavor and taste of vinegar are mainly generated by the multitudinous microorganisms during fermentation. In this research, the composition and succession of microbial communities in the entire solid-state fermentation were investigated, including starter daqu and acetic acid fermentation (AAF). Molds and yeasts in daqu, including Aspergillus, Saccharomycopsis and Pichia, decreased in AAF. The bacterial compositions increased from four genera in daqu to more than 13 genera in AAF. Principal component analysis showed that Acetobacter, Gluconacetobacter, Lactobacillus and Nostoc were dominant bacteria that were correlated well with AAF process. In the early fermentation period, lactic acid bacteria (LAB) decreased while acetic acid bacteria and Nostoc increased rapidly with the accumulation of total acids. Then, the abundance and diversity of LAB increased (more than 80%), indicating that LAB had important influences on the flavor and taste of vinegar.}, } @article {pmid24003922, year = {2013}, author = {Burcelin, R and Serino, M and Chabo, C and Garidou, L and Pomié, C and Courtney, M and Amar, J and Bouloumié, A}, title = {Metagenome and metabolism: the tissue microbiota hypothesis.}, journal = {Diabetes, obesity & metabolism}, volume = {15 Suppl 3}, number = {}, pages = {61-70}, doi = {10.1111/dom.12157}, pmid = {24003922}, issn = {1463-1326}, mesh = {Animals ; Cell Communication/physiology ; Host Specificity/immunology ; Humans ; Intestines/immunology/microbiology ; Metabolic Diseases/microbiology ; Metabolism/*physiology ; Metagenome/*physiology ; Mice ; Microbiota/*physiology ; }, abstract = {Over the last decade, the research community has revealed the role of a new organ: the intestinal microbiota. It is considered as a symbiont that is part of our organism since, at birth, it educates the immune system and contributes to the development of the intestinal vasculature and most probably the nervous system. With the advent of new generation sequencing techniques, a catalogue of genes that belong to this microbiome has been established that lists more than 5 million non-redundant genes called the metagenome. Using germ free mice colonized with the microbiota from different origins, it has been formally demonstrated that the intestinal microbiota causes the onset of metabolic diseases. Further to the role of point mutations in our genome, the microbiota can explain the on-going worldwide pandemic of obesity and diabetes, its dissemination and family inheritance, as well as the diversity of the associated metabolic phenotypes. More recently, the discovery of bacterial DNA within host tissues, such as the liver, the adipose tissue and the blood, which establishes a tissue microbiota, introduces new opportunities to identify targets and predictive biomarkers based on the host to microbiota interaction, as well as to define new strategies for pharmacological, immunomodulatory vaccines and nutritional applications.}, } @article {pmid24038656, year = {2013}, author = {Kang, HS and Brady, SF}, title = {Arimetamycin A: improving clinically relevant families of natural products through sequence-guided screening of soil metagenomes.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {52}, number = {42}, pages = {11063-11067}, pmid = {24038656}, issn = {1521-3773}, support = {/HHMI_/Howard Hughes Medical Institute/United States ; R01 GM077516/GM/NIGMS NIH HHS/United States ; GM077516/GM/NIGMS NIH HHS/United States ; }, mesh = {Anthracyclines/chemistry/*metabolism/pharmacology ; Antineoplastic Agents/chemistry/metabolism/pharmacology ; Biological Products/chemistry/*metabolism/pharmacology ; Cell Line, Tumor ; DNA, Bacterial/genetics/isolation & purification/metabolism ; Drug Screening Assays, Antitumor ; Humans ; *Metagenome ; Microbiota/*genetics ; *Soil Microbiology ; Structure-Activity Relationship ; }, abstract = {Sequence-tag-guided screening of soil environmental DNA libraries can be used to guide the discovery of new compounds with improved properties. In heterologous expression experiments the eDNA-derived arm cluster encodes arimetamycin A, an anthracycline that is more potent than clinically used natural anthracyclines and retains activity against multidrug-resistant (MDR) cancer cells.}, } @article {pmid24037656, year = {2013}, author = {Khan, NH and Bondici, VF and Medihala, PG and Lawrence, JR and Wolfaardt, GM and Warner, J and Korber, DR}, title = {Bacterial diversity and composition of an alkaline uranium mine tailings-water interface.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {51}, number = {5}, pages = {558-569}, pmid = {24037656}, issn = {1976-3794}, mesh = {Bacteria/*classification/*genetics/isolation & purification ; Bacteriological Techniques ; *Biota ; Cluster Analysis ; Culture Media/chemistry ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Environmental Microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saskatchewan ; Sequence Analysis, DNA ; *Uranium ; *Water ; }, abstract = {The microbial diversity and biogeochemical potential associated with a northern Saskatchewan uranium mine water-tailings interface was examined using culture-dependent and -independent techniques. Morphologically-distinct colonies from uranium mine water-tailings and a reference lake (MC) obtained using selective and non-selective media were selected for 16S rRNA gene sequencing and identification, revealing that culturable organisms from the uranium tailings interface were dominated by Firmicutes and Betaproteobacteria; whereas, MC organisms mainly consisted of Bacteroidetes and Gammaproteobacteria. Ion Torrent (IT) 16S rRNA metagenomic analysis carried out on extracted DNA from tailings and MC interfaces demonstrated the dominance of Firmicutes in both of the systems. Overall, the tailings-water interface environment harbored a distinct bacterial community relative to the MC, reflective of the ambient conditions (i.e., total dissolved solids, pH, salinity, conductivity, heavy metals) dominating the uranium tailings system. Significant correlations among the physicochemical data and the major bacterial groups present in the tailings and MC were also observed. Presence of sulfate reducing bacteria demonstrated by culture-dependent analyses and the dominance of Desulfosporosinus spp. indicated by Ion Torrent analyses within the tailings-water interface suggests the existence of anaerobic microenvironments along with the potential for reductive metabolic processes.}, } @article {pmid24036685, year = {2013}, author = {Tyakht, AV and Kostryukova, ES and Popenko, AS and Belenikin, MS and Pavlenko, AV and Larin, AK and Karpova, IY and Selezneva, OV and Semashko, TA and Ospanova, EA and Babenko, VV and Maev, IV and Cheremushkin, SV and Kucheryavyy, YA and Shcherbakov, PL and Grinevich, VB and Efimov, OI and Sas, EI and Abdulkhakov, RA and Abdulkhakov, SR and Lyalyukova, EA and Livzan, MA and Vlassov, VV and Sagdeev, RZ and Tsukanov, VV and Osipenko, MF and Kozlova, IV and Tkachev, AV and Sergienko, VI and Alexeev, DG and Govorun, VM}, title = {Human gut microbiota community structures in urban and rural populations in Russia.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {2469}, pmid = {24036685}, issn = {2041-1723}, mesh = {Adult ; Cluster Analysis ; Denmark ; Female ; Gastrointestinal Tract/*microbiology ; Geography ; Humans ; Male ; Metabolism ; Metagenome/genetics ; *Microbiota/genetics ; *Rural Population ; Russia ; United States ; *Urban Population ; }, abstract = {The microbial community of the human gut has a crucial role in sustaining host homeostasis. High-throughput DNA sequencing has delineated the structural and functional configurations of gut metagenomes in world populations. The microbiota of the Russian population is of particular interest to researchers, because Russia encompasses a uniquely wide range of environmental conditions and ethnogeographical cohorts. Here we conduct a shotgun metagenomic analysis of gut microbiota samples from 96 healthy Russian adult subjects, which reveals novel microbial community structures. The communities from several rural regions display similarities within each region and are dominated by the bacterial taxa associated with the healthy gut. Functional analysis shows that the metabolic pathways exhibiting differential abundance in the novel types are primarily associated with the trade-off between the Bacteroidetes and Firmicutes phyla. The specific signatures of the Russian gut microbiota are likely linked to the host diet, cultural habits and socioeconomic status.}, } @article {pmid24034943, year = {2013}, author = {He, Y and Zhou, BJ and Deng, GH and Jiang, XT and Zhang, H and Zhou, HW}, title = {Comparison of microbial diversity determined with the same variable tag sequence extracted from two different PCR amplicons.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {208}, pmid = {24034943}, issn = {1471-2180}, mesh = {Animals ; *Biota ; DNA Primers/*genetics ; Feces/*microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {BACKGROUND: Deep sequencing of the variable region of 16S rRNA genes has become the predominant tool for studying microbial ecology. As sequencing datasets have accumulated, meta-analysis of sequences obtained with different variable 16S rRNA gene targets and by different sequencing methods has become an intriguing prospect that remains to be evaluated experimentally.

RESULTS: We amplified a group of fecal samples using both V4F-V6R and V6F-V6R primer sets, excised the same V6 fragment from the two sets of Illumina sequencing data, and compared the resulting data in terms of the α-diversity, β-diversity, and community structure. Principal component analysis (PCA) comparing the microbial community structures of different datasets, including those with simulated sequencing errors, was very reliable. Procrustes analysis showed a high degree of concordance between the different datasets for both abundance-weighted and binary Jaccard distances (P < 0.05), and a meta-analysis of individual datasets resulted in similar conclusions. The Shannon's diversity index was consistent as well, with comparable values obtained for the different datasets and for the meta-analysis of different datasets. In contrast, richness estimators (OTU and Chao) varied significantly, and the meta-analysis of richness estimators was also biased. The community structures of the two datasets were obviously different and led to significant changes in the biomarkers identified by the LEfSe statistical tool.

CONCLUSIONS: Our results suggest that beta-diversity analysis and Shannon's diversity are relatively reliable for meta-analysis, while community structures and biomarkers are less consistent. These results should be useful for future meta-analyses of microbiomes from different data sources.}, } @article {pmid24030599, year = {2014}, author = {Ganesh, S and Parris, DJ and DeLong, EF and Stewart, FJ}, title = {Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone.}, journal = {The ISME journal}, volume = {8}, number = {1}, pages = {187-211}, pmid = {24030599}, issn = {1751-7370}, mesh = {Bacteria/classification/*genetics/metabolism ; *Biodiversity ; Chile ; *Metagenome ; Metagenomics ; Oxidation-Reduction ; Oxygen/analysis/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; }, abstract = {Marine oxygen minimum zones (OMZs) support diverse microbial communities with roles in major elemental cycles. It is unclear how the taxonomic composition and metabolism of OMZ microorganisms vary between particle-associated and free-living size fractions. We used amplicon (16S rRNA gene) and shotgun metagenome sequencing to compare microbial communities from large (>1.6 μm) and small (0.2-1.6 μm) filter size fractions along a depth gradient in the OMZ off Chile. Despite steep vertical redox gradients, size fraction was a significantly stronger predictor of community composition compared to depth. Phylogenetic diversity showed contrasting patterns, decreasing towards the anoxic OMZ core in the small size fraction, but exhibiting maximal values at these depths within the larger size fraction. Fraction-specific distributions were evident for key OMZ taxa, including anammox planctomycetes, whose coding sequences were enriched up to threefold in the 0.2-1.6 μm community. Functional gene composition also differed between fractions, with the >1.6 μm community significantly enriched in genes mediating social interactions, including motility, adhesion, cell-to-cell transfer, antibiotic resistance and mobile element activity. Prokaryotic transposase genes were three to six fold more abundant in this fraction, comprising up to 2% of protein-coding sequences, suggesting that particle surfaces may act as hotbeds for transposition-based genome changes in marine microbes. Genes for nitric and nitrous oxide reduction were also more abundant (three to seven fold) in the larger size fraction, suggesting microniche partitioning of key denitrification steps. These results highlight an important role for surface attachment in shaping community metabolic potential and genome content in OMZ microorganisms.}, } @article {pmid24030597, year = {2014}, author = {Ortiz, M and Legatzki, A and Neilson, JW and Fryslie, B and Nelson, WM and Wing, RA and Soderlund, CA and Pryor, BM and Maier, RM}, title = {Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave.}, journal = {The ISME journal}, volume = {8}, number = {2}, pages = {478-491}, pmid = {24030597}, issn = {1751-7370}, mesh = {*Archaea/genetics/metabolism ; Arizona ; *Bacteria/genetics/metabolism ; *Biodiversity ; Carbon Cycle/genetics ; Caves/*microbiology ; Desert Climate ; *Metagenome ; Metagenomics ; Nitrogen/metabolism ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {Carbonate caves represent subterranean ecosystems that are largely devoid of phototrophic primary production. In semiarid and arid regions, allochthonous organic carbon inputs entering caves with vadose-zone drip water are minimal, creating highly oligotrophic conditions; however, past research indicates that carbonate speleothem surfaces in these caves support diverse, predominantly heterotrophic prokaryotic communities. The current study applied a metagenomic approach to elucidate the community structure and potential energy dynamics of microbial communities, colonizing speleothem surfaces in Kartchner Caverns, a carbonate cave in semiarid, southeastern Arizona, USA. Manual inspection of a speleothem metagenome revealed a community genetically adapted to low-nutrient conditions with indications that a nitrogen-based primary production strategy is probable, including contributions from both Archaea and Bacteria. Genes for all six known CO2-fixation pathways were detected in the metagenome and RuBisCo genes representative of the Calvin-Benson-Bassham cycle were over-represented in Kartchner speleothem metagenomes relative to bulk soil, rhizosphere soil and deep-ocean communities. Intriguingly, quantitative PCR found Archaea to be significantly more abundant in the cave communities than in soils above the cave. MEtaGenome ANalyzer (MEGAN) analysis of speleothem metagenome sequence reads found Thaumarchaeota to be the third most abundant phylum in the community, and identified taxonomic associations to this phylum for indicator genes representative of multiple CO2-fixation pathways. The results revealed that this oligotrophic subterranean environment supports a unique chemoautotrophic microbial community with potentially novel nutrient cycling strategies. These strategies may provide key insights into other ecosystems dominated by oligotrophy, including aphotic subsurface soils or aquifers and photic systems such as arid deserts.}, } @article {pmid24029734, year = {2013}, author = {Di Bella, JM and Bao, Y and Gloor, GB and Burton, JP and Reid, G}, title = {High throughput sequencing methods and analysis for microbiome research.}, journal = {Journal of microbiological methods}, volume = {95}, number = {3}, pages = {401-414}, doi = {10.1016/j.mimet.2013.08.011}, pmid = {24029734}, issn = {1872-8359}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Computational Biology/*methods ; DNA/chemistry/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; *Microbiota ; }, abstract = {High-throughput sequencing technology is rapidly improving in quality, speed and cost. It is therefore becoming more widely used to study whole communities of prokaryotes in many niches. This review discusses these techniques, including nucleic acid extraction from different environments, sample preparation and high-throughput sequencing platforms. We also discuss commonly used and recently developed bioinformatic tools applied to microbiomes, including analyzing amplicon sequences, metagenome shotgun sequences and metatranscriptome sequences. This field is relatively new and rapidly evolving, thus we hope that this review will provide a baseline for understanding these methods of microbiome analyses. Additionally, we seek to stimulate others to solve the many problems that still exist with the sensitivity, specificity and interpretation of high throughput microbiome sequence analysis.}, } @article {pmid24024637, year = {2013}, author = {Dantas, G and Sommer, MO and Degnan, PH and Goodman, AL}, title = {Experimental approaches for defining functional roles of microbes in the human gut.}, journal = {Annual review of microbiology}, volume = {67}, number = {}, pages = {459-475}, pmid = {24024637}, issn = {1545-3251}, support = {UL1 RR024139/RR/NCRR NIH HHS/United States ; DP2 DK098089/DK/NIDDK NIH HHS/United States ; DP2-DK-089121/DK/NIDDK NIH HHS/United States ; DP2 GM105456/GM/NIGMS NIH HHS/United States ; K01 DK089121/DK/NIDDK NIH HHS/United States ; R01 GM103574/GM/NIGMS NIH HHS/United States ; DP2-DK098089/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/*genetics/isolation & purification/metabolism ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenome ; *Metagenomics/methods ; *Microbiota ; }, abstract = {The complex and intimate relationship between humans and their gut microbial communities is becoming less obscure, due in part to large-scale gut microbial genome-sequencing projects and culture-independent surveys of the composition and gene content of these communities. These studies build upon, and are complemented by, experimental efforts to define underlying mechanisms of host-microbe interactions in simplified model systems. This review highlights the intersection of these approaches. Experimental studies now leverage the advances in high-throughput DNA sequencing that have driven the explosion of microbial genome and community profiling projects, and the loss-of-function and gain-of-function strategies long employed in model organisms are now being extended to microbial genes, species, and communities from the human gut. These developments promise to deepen our understanding of human gut host-microbiota relationships and are readily applicable to other host-associated and free-living microbial communities.}, } @article {pmid24023907, year = {2013}, author = {Scully, ED and Geib, SM and Hoover, K and Tien, M and Tringe, SG and Barry, KW and Glavina del Rio, T and Chovatia, M and Herr, JR and Carlson, JE}, title = {Metagenomic profiling reveals lignocellulose degrading system in a microbial community associated with a wood-feeding beetle.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e73827}, pmid = {24023907}, issn = {1932-6203}, mesh = {*Animal Feed ; Animals ; Bacteria/classification/enzymology/*genetics/isolation & purification ; Coleoptera/*microbiology ; Fungi/classification/enzymology/*genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Introduced Species ; Lignin/*metabolism ; *Metagenomics ; Microbiota/genetics ; Phylogeny ; Sequence Analysis, DNA ; *Wood ; }, abstract = {The Asian longhorned beetle (Anoplophoraglabripennis) is an invasive, wood-boring pest that thrives in the heartwood of deciduous tree species. A large impediment faced by A. glabripennis as it feeds on woody tissue is lignin, a highly recalcitrant biopolymer that reduces access to sugars and other nutrients locked in cellulose and hemicellulose. We previously demonstrated that lignin, cellulose, and hemicellulose are actively deconstructed in the beetle gut and that the gut harbors an assemblage of microbes hypothesized to make significant contributions to these processes. While lignin degrading mechanisms have been well characterized in pure cultures of white rot basidiomycetes, little is known about such processes in microbial communities associated with wood-feeding insects. The goals of this study were to develop a taxonomic and functional profile of a gut community derived from an invasive population of larval A. glabripennis collected from infested host trees and to identify genes that could be relevant for the digestion of woody tissue and nutrient acquisition. To accomplish this goal, we taxonomically and functionally characterized the A. glabripennis midgut microbiota through amplicon and shotgun metagenome sequencing and conducted a large-scale comparison with the metagenomes from a variety of other herbivore-associated communities. This analysis distinguished the A. glabripennis larval gut metagenome from the gut communities of other herbivores, including previously sequenced termite hindgut metagenomes. Genes encoding enzymes were identified in the A. glabripennis gut metagenome that could have key roles in woody tissue digestion including candidate lignin degrading genes (laccases, dye-decolorizing peroxidases, novel peroxidases and β-etherases), 36 families of glycoside hydrolases (such as cellulases and xylanases), and genes that could facilitate nutrient recovery, essential nutrient synthesis, and detoxification. This community could serve as a reservoir of novel enzymes to enhance industrial cellulosic biofuels production or targets for novel control methods for this invasive and highly destructive insect.}, } @article {pmid24023808, year = {2013}, author = {Ross, EM and Moate, PJ and Marett, LC and Cocks, BG and Hayes, BJ}, title = {Metagenomic predictions: from microbiome to complex health and environmental phenotypes in humans and cattle.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e73056}, pmid = {24023808}, issn = {1932-6203}, mesh = {Animals ; Cattle ; *Environment ; *Health ; Humans ; Inflammatory Bowel Diseases/genetics/microbiology ; *Metagenomics ; Methane/biosynthesis ; Microbiota/*genetics ; *Phenotype ; }, abstract = {Mammals have a large cohort of endo- and ecto- symbiotic microorganisms (the microbiome) that potentially influence host phenotypes. There have been numerous exploratory studies of these symbiotic organisms in humans and other animals, often with the aim of relating the microbiome to a complex phenotype such as body mass index (BMI) or disease state. Here, we describe an efficient methodology for predicting complex traits from quantitative microbiome profiles. The method was demonstrated by predicting inflammatory bowel disease (IBD) status and BMI from human microbiome data, and enteric greenhouse gas production from dairy cattle rumen microbiome profiles. The method uses unassembled massively parallel sequencing (MPS) data to form metagenomic relationship matrices (analogous to genomic relationship matrices used in genomic predictions) to predict IBD, BMI and methane production phenotypes with useful accuracies (r = 0.423, 0.422 and 0.466 respectively). Our results show that microbiome profiles derived from MPS can be used to predict complex phenotypes of the host. Although the number of biological replicates used here limits the accuracy that can be achieved, preliminary results suggest this approach may surpass current prediction accuracies that are based on the host genome. This is especially likely for traits that are largely influenced by the gut microbiota, for example digestive tract disorders or metabolic functions such as enteric methane production in cattle.}, } @article {pmid24021386, year = {2013}, author = {Robertson, CE and Harris, JK and Wagner, BD and Granger, D and Browne, K and Tatem, B and Feazel, LM and Park, K and Pace, NR and Frank, DN}, title = {Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data.}, journal = {Bioinformatics (Oxford, England)}, volume = {29}, number = {23}, pages = {3100-3101}, pmid = {24021386}, issn = {1367-4811}, support = {R21 HG005964/HG/NHGRI NIH HHS/United States ; HG005964/HG/NHGRI NIH HHS/United States ; }, mesh = {Computational Biology ; *Computer Graphics ; *Database Management Systems ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Microbiota/*genetics ; Sequence Analysis, DNA ; *Software ; *User-Computer Interface ; }, abstract = {Studies of the human microbiome, and microbial community ecology in general, have blossomed of late and are now a burgeoning source of exciting research findings. Along with the advent of next-generation sequencing platforms, which have dramatically increased the scope of microbiome-related projects, several high-performance sequence analysis pipelines (e.g. QIIME, MOTHUR, VAMPS) are now available to investigators for microbiome analysis. The subject of our manuscript, the graphical user interface-based Explicet software package, fills a previously unmet need for a robust, yet intuitive means of integrating the outputs of the software pipelines with user-specified metadata and then visualizing the combined data.}, } @article {pmid24019895, year = {2013}, author = {Bonfert, T and Csaba, G and Zimmer, R and Friedel, CC}, title = {Mining RNA-seq data for infections and contaminations.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e73071}, pmid = {24019895}, issn = {1932-6203}, mesh = {Colorectal Neoplasms/genetics/microbiology ; *Data Mining ; HeLa Cells ; Humans ; Infections/*genetics ; Microbiota ; *Sequence Analysis, RNA ; }, abstract = {RNA sequencing (RNA-seq) provides novel opportunities for transcriptomic studies at nucleotide resolution, including transcriptomics of viruses or microbes infecting a cell. However, standard approaches for mapping the resulting sequencing reads generally ignore alternative sources of expression other than the host cell and are little equipped to address the problems arising from redundancies and gaps among sequenced microbe and virus genomes. We show that screening of sequencing reads for contaminations and infections can be performed easily using ContextMap, our recently developed mapping software. Based on mapping-derived statistics, mapping confidence, similarities and misidentifications (e.g. due to missing genome sequences) of species/strains can be assessed. Performance of our approach is evaluated on three real-life sequencing data sets and compared to state-of-the-art metagenomics tools. In particular, ContextMap vastly outperformed GASiC and GRAMMy in terms of runtime. In contrast to MEGAN4, it was capable of providing individual read mappings to species and resolving non-unique mappings, thus allowing the identification of misalignments caused by sequence similarities between genomes and missing genome sequences. Our study illustrates the importance and potentials of routinely mining RNA-seq experiments for infections or contaminations by microbes and viruses. By using ContextMap, gene expression of infecting agents can be analyzed and novel insights in infection processes and tumorigenesis can be obtained.}, } @article {pmid24019288, year = {2013}, author = {Li, H}, title = {Systems biology approaches to epidemiological studies of complex diseases.}, journal = {Wiley interdisciplinary reviews. Systems biology and medicine}, volume = {5}, number = {6}, pages = {677-686}, pmid = {24019288}, issn = {1939-005X}, support = {P30 CA016520/CA/NCI NIH HHS/United States ; CA127334/CA/NCI NIH HHS/United States ; R01 CA127334/CA/NCI NIH HHS/United States ; R01 GM097505/GM/NIGMS NIH HHS/United States ; GM097505/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Disease Transmission, Infectious ; Epigenomics/methods ; *Genome, Human ; Genome-Wide Association Study/methods ; Humans ; Metagenomics/methods ; Microbiota ; *Models, Biological ; Systems Biology/*methods ; }, abstract = {Systems biology approaches to epidemiological studies of complex diseases include collection of genetic, genomic, epigenomic, and metagenomic data in large-scale epidemiological studies of complex phenotypes. Designs and analyses of such studies raise many statistical challenges. This article reviews some issues related to integrative analysis of such high dimensional and inter-related datasets and outline some possible solutions. I focus my review on integrative approaches for genome-wide genetic variants and gene expression data, methods for joint analysis of genetic and epigenetic variants, and methods for analysis of microbiome data. Statistical methods such as mediation analysis, high-dimensional instrumental variable regression, sparse signal recovery, and compositional data regression provide potential frameworks for integrative analysis of these high-dimensional genomic data.}, } @article {pmid24018484, year = {2013}, author = {Statnikov, A and Alekseyenko, AV and Li, Z and Henaff, M and Perez-Perez, GI and Blaser, MJ and Aliferis, CF}, title = {Microbiomic signatures of psoriasis: feasibility and methodology comparison.}, journal = {Scientific reports}, volume = {3}, number = {}, pages = {2620}, pmid = {24018484}, issn = {2045-2322}, support = {1UL1 RR029893/RR/NCRR NIH HHS/United States ; R01 LM011179/LM/NLM NIH HHS/United States ; R01 LM011179-01A1/LM/NLM NIH HHS/United States ; UH2 AR057506-01S1/AR/NIAMS NIH HHS/United States ; UL1 RR029893/RR/NCRR NIH HHS/United States ; UH2 AR057506/AR/NIAMS NIH HHS/United States ; }, mesh = {Bacteria/*classification/*genetics ; Case-Control Studies ; Humans ; *Metagenome ; *Microbiota ; Psoriasis/diagnosis/*microbiology ; RNA, Ribosomal, 16S ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {Psoriasis is a common chronic inflammatory disease of the skin. We sought to use bacterial community abundance data to assess the feasibility of developing multivariate molecular signatures for differentiation of cutaneous psoriatic lesions, clinically unaffected contralateral skin from psoriatic patients, and similar cutaneous loci in matched healthy control subjects. Using 16S rRNA high-throughput DNA sequencing, we assayed the cutaneous microbiome for 51 such matched specimen triplets including subjects of both genders, different age groups, ethnicities and multiple body sites. None of the subjects had recently received relevant treatments or antibiotics. We found that molecular signatures for the diagnosis of psoriasis result in significant accuracy ranging from 0.75 to 0.89 AUC, depending on the classification task. We also found a significant effect of DNA sequencing and downstream analysis protocols on the accuracy of molecular signatures. Our results demonstrate that it is feasible to develop accurate molecular signatures for the diagnosis of psoriasis from microbiomic data.}, } @article {pmid24015199, year = {2013}, author = {Ugalde, JA and Gallardo, MJ and Belmar, C and Muñoz, P and Ruiz-Tagle, N and Ferrada-Fuentes, S and Espinoza, C and Allen, EE and Gallardo, VA}, title = {Microbial life in a fjord: metagenomic analysis of a microbial mat in Chilean patagonia.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e71952}, pmid = {24015199}, issn = {1932-6203}, mesh = {Chile ; DNA, Bacterial/genetics ; Energy Metabolism/genetics ; Gammaproteobacteria/classification/genetics ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Microbial Consortia/*genetics ; Molecular Sequence Annotation ; Molecular Typing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {The current study describes the taxonomic and functional composition of metagenomic sequences obtained from a filamentous microbial mat isolated from the Comau fjord, located in the northernmost part of the Chilean Patagonia. The taxonomic composition of the microbial community showed a high proportion of members of the Gammaproteobacteria, including a high number of sequences that were recruited to the genomes of Moritella marina MP-1 and Colwelliapsycherythraea 34H, suggesting the presence of populations related to these two psychrophilic bacterial species. Functional analysis of the community indicated a high proportion of genes coding for the transport and metabolism of amino acids, as well as in energy production. Among the energy production functions, we found protein-coding genes for sulfate and nitrate reduction, both processes associated with Gammaproteobacteria-related sequences. This report provides the first examination of the taxonomic composition and genetic diversity associated with these conspicuous microbial mat communities and provides a framework for future microbial studies in the Comau fjord.}, } @article {pmid24013298, year = {2014}, author = {Said, HS and Suda, W and Nakagome, S and Chinen, H and Oshima, K and Kim, S and Kimura, R and Iraha, A and Ishida, H and Fujita, J and Mano, S and Morita, H and Dohi, T and Oota, H and Hattori, M}, title = {Dysbiosis of salivary microbiota in inflammatory bowel disease and its association with oral immunological biomarkers.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {21}, number = {1}, pages = {15-25}, pmid = {24013298}, issn = {1756-1663}, mesh = {Adult ; Biomarkers/analysis ; Dysbiosis/immunology/*microbiology ; Female ; Humans ; Inflammatory Bowel Diseases/immunology/*microbiology ; Male ; Metagenome/immunology ; Microbiota/genetics/*immunology ; Middle Aged ; RNA, Bacterial/metabolism ; RNA, Ribosomal, 16S/metabolism ; Saliva/immunology/*microbiology ; }, abstract = {Analysis of microbiota in various biological and environmental samples under a variety of conditions has recently become more practical due to remarkable advances in next-generation sequencing. Changes leading to specific biological states including some of the more complex diseases can now be characterized with relative ease. It is known that gut microbiota is involved in the pathogenesis of inflammatory bowel disease (IBD), mainly Crohn's disease and ulcerative colitis, exhibiting symptoms in the gastrointestinal tract. Recent studies also showed increased frequency of oral manifestations among IBD patients, indicating aberrations in the oral microbiota. Based on these observations, we analyzed the composition of salivary microbiota of 35 IBD patients by 454 pyrosequencing of the bacterial 16S rRNA gene and compared it with that of 24 healthy controls (HCs). The results showed that Bacteroidetes was significantly increased with a concurrent decrease in Proteobacteria in the salivary microbiota of IBD patients. The dominant genera, Streptococcus, Prevotella, Neisseria, Haemophilus, Veillonella, and Gemella, were found to largely contribute to dysbiosis (dysbacteriosis) observed in the salivary microbiota of IBD patients. Analysis of immunological biomarkers in the saliva of IBD patients showed elevated levels of many inflammatory cytokines and immunoglobulin A, and a lower lysozyme level. A strong correlation was shown between lysozyme and IL-1β levels and the relative abundance of Streptococcus, Prevotella, Haemophilus and Veillonella. Our data demonstrate that dysbiosis of salivary microbiota is associated with inflammatory responses in IBD patients, suggesting that it is possibly linked to dysbiosis of their gut microbiota.}, } @article {pmid24003156, year = {2013}, author = {Suzuki, S and Ishii, S and Wu, A and Cheung, A and Tenney, A and Wanger, G and Kuenen, JG and Nealson, KH}, title = {Microbial diversity in The Cedars, an ultrabasic, ultrareducing, and low salinity serpentinizing ecosystem.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {38}, pages = {15336-15341}, pmid = {24003156}, issn = {1091-6490}, mesh = {Asbestos, Serpentine/chemistry ; Base Sequence ; *Biodiversity ; California ; Chloroflexi/genetics ; Cyanobacteria/genetics ; *Ecosystem ; Euryarchaeota/genetics ; Gram-Positive Bacteria/genetics ; Hydrogen-Ion Concentration ; Metagenome/*genetics ; Molecular Sequence Data ; Natural Springs/*chemistry/*microbiology ; Oxidation-Reduction ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; }, abstract = {The Cedars, in coastal northern California, is an active site of peridotite serpentinization. The spring waters that emerge from this system feature very high pH, low redox potential, and low ionic concentrations, making it an exceptionally challenging environment for life. We report a multiyear, culture-independent geomicrobiological study of three springs at The Cedars that differ with respect to the nature of the groundwater feeding them. Within each spring, both geochemical properties and microbial diversity in all three domains of life remained stable over a 3-y period, with multiple samples each year. Between the three springs, however, the microbial communities showed considerable differences that were strongly correlated with the source of the serpentinizing groundwater. In the spring fed solely by deep groundwater, phylum Chloroflexi, class Clostridia, and candidate division OD1 were the major taxa with one phylotype in Euryarchaeota. Less-abundant phylotypes include several minor members from other candidate divisions and one phylotype that was an outlier of candidate division OP3. In the springs fed by the mixture of deep and shallow groundwater, organisms close to the Hydrogenophaga within Betaproteobacteria dominated and coexisted with the deep groundwater community members. The shallow groundwater community thus appears to be similar to those described in other terrestrial serpentinizing sites, whereas the deep community is distinctly different from any other previously described terrestrial serpentinizing community. These unique communities have the potential to yield important insights into the development and survival of life in these early-earth analog environments.}, } @article {pmid23995931, year = {2013}, author = {Emerson, JB and Thomas, BC and Andrade, K and Heidelberg, KB and Banfield, JF}, title = {New approaches indicate constant viral diversity despite shifts in assemblage structure in an Australian hypersaline lake.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {21}, pages = {6755-6764}, pmid = {23995931}, issn = {1098-5336}, mesh = {Base Sequence ; *Biodiversity ; Cluster Analysis ; Genes, Viral/genetics ; Lakes/*virology ; Metagenomics/methods ; Microbiota/*genetics ; Molecular Sequence Data ; *Salinity ; Sequence Analysis, DNA ; Species Specificity ; Victoria ; }, abstract = {It is widely stated that viruses represent the most significant source of biodiversity on Earth, yet characterizing the diversity of viral assemblages in natural systems remains difficult. Viral diversity studies are challenging because viruses lack universally present, phylogenetically informative genes. Here, we developed an approach to estimate viral diversity using a series of functional and novel conserved genes. This approach provides direct estimates of viral assemblage diversity while retaining resolution at the level of individual viral populations in a natural system. We characterized viral assemblages in eight samples from hypersaline Lake Tyrrell (LT), Victoria, Australia, using 39,636 viral contigs. We defined viral operational taxonomic units (OTUs) in two ways. First, we used genes with three different functional predictions that were abundantly represented in the data set. Second, we clustered proteins of unknown function based on sequence similarity, and we chose genes represented by three clusters with numerous members to define OTUs. In combination, diversity metrics indicated between 412 and 735 sampled populations, and the number of populations remained relatively constant across samples. We determined the relative representation of each viral OTU in each sample and found that viral assemblage structures correlate with salinity and solution chemistry. LT viral assemblages were near-replicates from the same site sampled a few days apart but differed significantly on other spatial and temporal scales. The OTU definition approach proposed here paves the way for metagenomics-based analyses of viral assemblages using ecological models previously applied to bacteria and archaea.}, } @article {pmid23990294, year = {2013}, author = {Singh, D and Shi, L and Adams, JM}, title = {Bacterial diversity in the mountains of South-West China: climate dominates over soil parameters.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {51}, number = {4}, pages = {439-447}, pmid = {23990294}, issn = {1976-3794}, mesh = {Bacteria/*classification ; *Biodiversity ; China ; Climate ; Geography ; Microbiota ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Certain patterns in soil bacterial diversity and community composition have become evident from metagenomics studies on a range of scales, from various parts of the world. For example, soil pH has generally been seen as dominating variation in bacterial diversity, above all other soil and climate parameters. It is important however to test the generality of these relationships by studying previously un-sampled areas. We compared soil bacterial diversity and community composition under a wide range of climatic and edaphic conditions in mountainous Yunnan Province, SW China. Soil samples were taken from a range of primary forest types and altitudes, reflecting the great variation of forest environments in this region. From each soil sample, DNA was extracted and pyrosequenced for bacterial 16S rRNA gene identification. In contrast to other recent studies from other parts of the world, pH was a weaker predictor of bacterial community composition and diversity than exchangeable Ca(2+) concentration, and also the more poorly defined environmental parameter of elevation. Samples from within each forest type clustered strongly, showing the distinctive pattern of their microbial communities on a regional scale. It is clear that on a regional scale in a very heterogeneous environment, additional factors beyond pH can emerge as more important in determining bacterial diversity.}, } @article {pmid23990071, year = {2014}, author = {Bhattacharyya, PN and Tanti, B and Barman, P and Jha, DK}, title = {Culture-independent metagenomic approach to characterize the surface and subsurface soil bacterial community in the Brahmaputra valley, Assam, North-East India, an Indo-Burma mega-biodiversity hotspot.}, journal = {World journal of microbiology & biotechnology}, volume = {30}, number = {2}, pages = {519-528}, pmid = {23990071}, issn = {1573-0972}, mesh = {*Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; India ; Phylogeny ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Soil bacterial communities, which contain the highest level of prokaryotic diversity of any natural environment, are important for ecosystem functioning. A culture-independent metagenomic approach was employed in the present investigation to characterize the diversity of soil bacterial community composition in five geochemically and hydrologically different surface and subsurface soil habitats of Brahmaputra valley, Assam, North-East India, an Indo-Burma mega-biodiversity hotspot. The diversity of soil bacterial community was determined through sequence analysis of 16S-23S intergenic spacer regions (ISR). Polymerase chain reaction (PCR) universal primers, 1406F (5'-TGYACACACCGCCCGT-3') and 155r (5'-GGGTTBCATTCRG-3') were used for amplification of 16S-23S ribosomal DNA intergenic spacers of bacteria. Amplification resulted in an intense array of PCR products approximately ranging in size from 200 to 900 bp. Clear banding patterns were observed in analysed samples using the primer set in combination. A clear change in microbial ISR profile was observed on visual analysis of gel electrophoresis profiles. Fast alignment database searches of PCR amplicons of 16S-23S ISR sequence data revealed that the isolated sequences resembled five major phylogenetic groups of bacteria, namely α-, β- and γ-subdivisions of Proteobacteria, Acidobacterium and Comamonadaceae.}, } @article {pmid23985749, year = {2014}, author = {Cavalcanti, GS and Gregoracci, GB and dos Santos, EO and Silveira, CB and Meirelles, PM and Longo, L and Gotoh, K and Nakamura, S and Iida, T and Sawabe, T and Rezende, CE and Francini-Filho, RB and Moura, RL and Amado-Filho, GM and Thompson, FL}, title = {Physiologic and metagenomic attributes of the rhodoliths forming the largest CaCO3 bed in the South Atlantic Ocean.}, journal = {The ISME journal}, volume = {8}, number = {1}, pages = {52-62}, pmid = {23985749}, issn = {1751-7370}, mesh = {Animals ; Archaea/classification/genetics/metabolism/*physiology ; Atlantic Ocean ; Bacteria/classification/genetics/metabolism ; *Bacterial Physiological Phenomena ; *Biodiversity ; Brazil ; Calcium Carbonate/*metabolism ; Carbon/metabolism ; *Ecosystem ; Invertebrates/physiology ; Metagenome/*genetics ; Photosynthesis/genetics ; Rhodophyta/*microbiology ; }, abstract = {Rhodoliths are free-living coralline algae (Rhodophyta, Corallinales) that are ecologically important for the functioning of marine environments. They form extensive beds distributed worldwide, providing a habitat and nursery for benthic organisms and space for fisheries, and are an important source of calcium carbonate. The Abrolhos Bank, off eastern Brazil, harbors the world's largest continuous rhodolith bed (of ∼21,000 km(2)) and has one of the largest marine CaCO3 deposits (producing 25 megatons of CaCO3 per year). Nevertheless, there is a lack of information about the microbial diversity, photosynthetic potential and ecological interactions within the rhodolith holobiont. Herein, we performed an ecophysiologic and metagenomic analysis of the Abrolhos rhodoliths to understand their microbial composition and functional components. Rhodoliths contained a specific microbiome that displayed a significant enrichment in aerobic ammonia-oxidizing betaproteobacteria and dissimilative sulfate-reducing deltaproteobacteria. We also observed a significant contribution of bacterial guilds (that is, photolithoautotrophs, anaerobic heterotrophs, sulfide oxidizers, anoxygenic phototrophs and methanogens) in the rhodolith metagenome, suggested to have important roles in biomineralization. The increased hits in aromatic compounds, fatty acid and secondary metabolism subsystems hint at an important chemically mediated interaction in which a functional job partition among eukaryal, archaeal and bacterial groups allows the rhodolith holobiont to thrive in the global ocean. High rates of photosynthesis were measured for Abrolhos rhodoliths (52.16 μmol carbon m(-2)s(-1)), allowing the entire Abrolhos rhodolith bed to produce 5.65 × 10(5) tons C per day. This estimate illustrates the great importance of the Abrolhos rhodolith beds for dissolved carbon production in the South Atlantic Ocean.}, } @article {pmid23985745, year = {2014}, author = {Yang, Y and Gao, Y and Wang, S and Xu, D and Yu, H and Wu, L and Lin, Q and Hu, Y and Li, X and He, Z and Deng, Y and Zhou, J}, title = {The microbial gene diversity along an elevation gradient of the Tibetan grassland.}, journal = {The ISME journal}, volume = {8}, number = {2}, pages = {430-440}, pmid = {23985745}, issn = {1751-7370}, mesh = {*Altitude ; Bacteria/*genetics/metabolism ; *Ecosystem ; Genes, Microbial/*genetics ; *Genetic Variation ; *Metagenome ; Metagenomics ; Poaceae/microbiology ; *Soil Microbiology ; Tibet ; }, abstract = {Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, along four sites/elevations of a Tibetan mountainous grassland, aiming to explore the potential microbial responses to climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities were distinct for most but not all of the sites. Substantial variations were apparent in stress, N and C-cycling genes, but they were in line with the functional roles of these genes. Cold shock genes were more abundant at higher elevations. Also, gdh converting ammonium into urea was more abundant at higher elevations, whereas ureC converting urea into ammonium was less abundant, which was consistent with soil ammonium contents. Significant correlations were observed between N-cycling genes (ureC, gdh and amoA) and nitrous oxide flux, suggesting that they contributed to community metabolism. Lastly, we found by Canonical correspondence analysis, Mantel tests and the similarity tests that soil pH, temperature, NH4(+)-N and vegetation diversity accounted for the majority (81.4%) of microbial community variations, suggesting that these four attributes were major factors affecting soil microbial communities. On the basis of these observations, we predict that climate changes in the Tibetan grasslands are very likely to change soil microbial community functional structure, with particular impacts on microbial N-cycling genes and consequently microbe-mediated soil N dynamics.}, } @article {pmid23982459, year = {2013}, author = {Shoaie, S and Karlsson, F and Mardinoglu, A and Nookaew, I and Bordel, S and Nielsen, J}, title = {Understanding the interactions between bacteria in the human gut through metabolic modeling.}, journal = {Scientific reports}, volume = {3}, number = {}, pages = {2532}, pmid = {23982459}, issn = {2045-2322}, mesh = {*Bacterial Physiological Phenomena ; Computer Simulation ; Gastrointestinal Tract/*microbiology ; Genome, Bacterial/*physiology ; Humans ; Metagenome/*physiology ; Microbiota/*physiology ; *Models, Biological ; }, abstract = {The human gut microbiome plays an influential role in maintaining human health, and it is a potential target for prevention and treatment of disease. Genome-scale metabolic models (GEMs) can provide an increased understanding of the mechanisms behind the effects of diet, the genotype-phenotype relationship and microbial robustness. Here we reconstructed GEMs for three key species, (Bacteroides thetaiotamicron, Eubacterium rectale and Methanobrevibacter smithii) as relevant representatives of three main phyla in the human gut (Bacteroidetes, Firmicutes and Euryarchaeota). We simulated the interactions between these three bacteria in different combinations of gut ecosystems and compared the predictions with the experimental results obtained from colonization of germ free mice. Furthermore, we used our GEMs for analyzing the contribution of each species to the overall metabolism of the gut microbiota based on transcriptome data and demonstrated that these models can be used as a scaffold for understanding bacterial interactions in the gut.}, } @article {pmid23981941, year = {2013}, author = {Ko, JS}, title = {[The intestinal microbiota and human disease].}, journal = {The Korean journal of gastroenterology = Taehan Sohwagi Hakhoe chi}, volume = {62}, number = {2}, pages = {85-91}, doi = {10.4166/kjg.2013.62.2.85}, pmid = {23981941}, issn = {2233-6869}, mesh = {Animals ; Anti-Bacterial Agents/therapeutic use ; Clostridioides difficile/isolation & purification/pathogenicity ; Enterocolitis, Pseudomembranous/drug therapy/microbiology/pathology ; Fatty Liver/etiology/microbiology ; Humans ; Inflammatory Bowel Diseases/etiology/microbiology ; Intestines/*microbiology ; *Microbiota ; Obesity/etiology/microbiology ; }, abstract = {Advances in sequencing technology and the development of metagenomics have opened up new ways to investigate the microorganisms inhabiting the human gut. The intestinal microbiota confer protection against pathogens, contribute to the maturation of the immune system, and regulate host metabolism. The composition of gut microbiota in early life is influenced by mode of birth, diet, and antibiotics. Decreased biodiversity and alterations in the composition of the intestinal microbiota have been observed in many diseases including obesity, neonatal necrotizing enterocolitis, inflammatory bowel disease, and recurrent Clostridium difficile infection. Therapeutic options for the diseases linked to imbalance in the microbiota include modifying the gut microbiota through diet, probiotics, and fecal transplants.}, } @article {pmid23979974, year = {2013}, author = {Orenstein, R and Griesbach, CL and DiBaise, JK}, title = {Moving fecal microbiota transplantation into the mainstream.}, journal = {Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition}, volume = {28}, number = {5}, pages = {589-598}, doi = {10.1177/0884533613497516}, pmid = {23979974}, issn = {1941-2452}, mesh = {Clostridioides difficile ; Clostridium Infections/*therapy ; Feces/*microbiology ; Humans ; *Microbiota ; Probiotics/*administration & dosage ; Recurrence ; Transplantation/*methods ; Treatment Outcome ; United States/epidemiology ; }, abstract = {In recent years, fecal microbiota transplantation (aka fecal transplantation, fecal bacteriotherapy, FMT) has become increasing utilized to treat recurrent and refractory Clostridium difficile infection (CDI). Almost 600,000 cases of CDI occur each year in the United States. Of these, an estimated 15,000 patients have a recurrence. The management of recurrent disease has been challenging for patients and clinicians. Increasingly, FMT has been recognized as an effective option for these patients. This article explores why FMT has reemerged as a practical therapeutic modality. In the process, the logistics by which the procedure is performed and the factors that may affect quality, safety, and patient outcomes will be described.}, } @article {pmid23978768, year = {2013}, author = {Kuntal, BK and Ghosh, TS and Mande, SS}, title = {Community-analyzer: a platform for visualizing and comparing microbial community structure across microbiomes.}, journal = {Genomics}, volume = {102}, number = {4}, pages = {409-418}, doi = {10.1016/j.ygeno.2013.08.004}, pmid = {23978768}, issn = {1089-8646}, mesh = {*Algorithms ; Animals ; Computational Biology/*methods ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Models, Genetic ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {A key goal in comparative metagenomics is to identify microbial group(s) which are responsible for conferring specific characteristics to a given environment. These characteristics are the result of the inter-microbial interactions between the resident microbial groups. We present a new GUI-based comparative metagenomic analysis application called Community-Analyzer which implements a correlation-based graph layout algorithm that not only facilitates a quick visualization of the differences in the analyzed microbial communities (in terms of their taxonomic composition), but also provides insights into the inherent inter-microbial interactions occurring therein. Notably, this layout algorithm also enables grouping of the metagenomes based on the probable inter-microbial interaction patterns rather than simply comparing abundance values of various taxonomic groups. In addition, the tool implements several interactive GUI-based functionalities that enable users to perform standard comparative analyses across microbiomes. For academic and non-profit users, the Community-Analyzer is currently available for download from: http://metagenomics.atc.tcs.com/Community_Analyzer/.}, } @article {pmid23975514, year = {2013}, author = {Umu, OC and Oostindjer, M and Pope, PB and Svihus, B and Egelandsdal, B and Nes, IF and Diep, DB}, title = {Potential applications of gut microbiota to control human physiology.}, journal = {Antonie van Leeuwenhoek}, volume = {104}, number = {5}, pages = {609-618}, doi = {10.1007/s10482-013-0008-0}, pmid = {23975514}, issn = {1572-9699}, mesh = {*Biota ; Diet/*methods ; Gastrointestinal Tract/*microbiology ; Humans ; }, abstract = {The microorganisms living in our gut have been a black box to us for a long time. However, with the recent advances in high throughput DNA sequencing technologies, it is now possible to assess virtually all microorganisms in our gut including non-culturable ones. With the use of powerful bioinformatics tools to deal with multivariate analyses of huge amounts of data from metagenomics, metatranscriptomics, metabolomics, we now start to gain some important insights into these tiny gut inhabitants. Our knowledge is increasing about who they are, to some extent, what they do and how they affect our health. Gut microbiota have a broad spectrum of possible effects on health, from preventing serious diseases, improving immune system and gut health to stimulating the brain centers responsible for appetite and food intake control. Further, we may be on the verge of being capable of manipulating the gut microbiota by diet control to possibly improve our health. Diets consisting of different components that are fermentable by microbiota are substrates for different kinds of microbes in the gut. Thus, diet control can be used to favor the growth of some selected gut inhabitants. Nowadays, the gut microbiota is taken into account as a separate organ in human body and their activities and metabolites in gut have many physiological and neurological effects. In this mini-review, we discuss the diversity of gut microbiota, the technologies used to assess them, factors that affect microbial composition and metabolites that affect human physiology, and their potential applications in satiety control via the gut-brain axis.}, } @article {pmid23975157, year = {2013}, author = {Langille, MG and Zaneveld, J and Caporaso, JG and McDonald, D and Knights, D and Reyes, JA and Clemente, JC and Burkepile, DE and Vega Thurber, RL and Knight, R and Beiko, RG and Huttenhower, C}, title = {Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.}, journal = {Nature biotechnology}, volume = {31}, number = {9}, pages = {814-821}, pmid = {23975157}, issn = {1546-1696}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; T32 GM008759/GM/NIGMS NIH HHS/United States ; R01HG004872/HG/NHGRI NIH HHS/United States ; /CAPMC/CIHR/Canada ; U01HG004866/HG/NHGRI NIH HHS/United States ; T32 GM080177/GM/NIGMS NIH HHS/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; 1R01HG005969/HG/NHGRI NIH HHS/United States ; R01 HG005969/HG/NHGRI NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; U01 HG004866/HG/NHGRI NIH HHS/United States ; P01DK078669/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics ; Genes, Bacterial/genetics/physiology ; Genetic Markers/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community's functional capabilities. Here we describe PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this 'predictive metagenomic' approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.}, } @article {pmid23967097, year = {2013}, author = {Staubach, F and Baines, JF and Künzel, S and Bik, EM and Petrov, DA}, title = {Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e70749}, pmid = {23967097}, issn = {1932-6203}, support = {R01 GM097415/GM/NIGMS NIH HHS/United States ; R01 GM100366/GM/NIGMS NIH HHS/United States ; R01GM097415/GM/NIGMS NIH HHS/United States ; R01GM100366/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/*genetics ; Biodiversity ; Drosophila/*microbiology ; *Environmental Microbiology ; Host-Pathogen Interactions ; Male ; Metagenome ; *Microbiota ; Phenotype ; RNA, Bacterial ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {The fruit fly Drosophila is a classic model organism to study adaptation as well as the relationship between genetic variation and phenotypes. Although associated bacterial communities might be important for many aspects of Drosophila biology, knowledge about their diversity, composition, and factors shaping them is limited. We used 454-based sequencing of a variable region of the bacterial 16S ribosomal RNA gene to characterize the bacterial communities associated with wild and laboratory Drosophila isolates. In order to specifically investigate effects of food source and host species on bacterial communities, we analyzed samples from wild Drosophila melanogaster and D. simulans collected from a variety of natural substrates, as well as from adults and larvae of nine laboratory-reared Drosophila species. We find no evidence for host species effects in lab-reared flies; instead, lab of origin and stochastic effects, which could influence studies of Drosophila phenotypes, are pronounced. In contrast, the natural Drosophila-associated microbiota appears to be predominantly shaped by food substrate with an additional but smaller effect of host species identity. We identify a core member of this natural microbiota that belongs to the genus Gluconobacter and is common to all wild-caught flies in this study, but absent from the laboratory. This makes it a strong candidate for being part of what could be a natural D. melanogaster and D. simulans core microbiome. Furthermore, we were able to identify candidate pathogens in natural fly isolates.}, } @article {pmid23963220, year = {2013}, author = {Thompson, CC and Silva, GG and Vieira, NM and Edwards, R and Vicente, AC and Thompson, FL}, title = {Genomic taxonomy of the genus prochlorococcus.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {752-762}, pmid = {23963220}, issn = {1432-184X}, mesh = {Biodiversity ; *Genome, Bacterial ; Genomics ; Molecular Sequence Data ; *Phylogeny ; Prochlorococcus/*classification/*genetics ; Seawater/*microbiology ; }, abstract = {The genus Prochlorococcus is globally abundant and dominates the total phytoplankton biomass and production in the oligotrophic ocean. The single species, Prochlorococcus marinus, comprises six named ecotypes. Our aim was to analyze the taxonomic structure of the genus Prochlorococcus. We analyzed the complete genomes of 13 cultured P. marinus type and reference strains by means of several genomic taxonomy tools (i.e., multilocus sequence analysis, amino acid identity, Karlin genomic signature, and genome to genome distance). In addition, we estimated the diversity of Prochlorococcus species in over 100 marine metagenomes from all the major oceanic provinces. According to our careful taxonomic analysis, the 13 strains corresponded, in fact, to ten different Prochlorococcus species. This analysis establishes a new taxonomic framework for the genus Prochlorococcus. Further, the analysis of the metagenomic data suggests that, in total, there may only be 35 Prochlorococcus species in the world's oceans. We propose that the dearth of species observed in this study is driven by high selective pressures that limit diversification in the global ocean.}, } @article {pmid23955772, year = {2013}, author = {Edgar, RC}, title = {UPARSE: highly accurate OTU sequences from microbial amplicon reads.}, journal = {Nature methods}, volume = {10}, number = {10}, pages = {996-998}, pmid = {23955772}, issn = {1548-7105}, mesh = {Algorithms ; Databases, Genetic ; Humans ; Metagenomics ; Microbiota/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Research Design ; Sensitivity and Specificity ; Software ; }, abstract = {Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.}, } @article {pmid23949663, year = {2014}, author = {Soffer, N and Brandt, ME and Correa, AM and Smith, TB and Thurber, RV}, title = {Potential role of viruses in white plague coral disease.}, journal = {The ISME journal}, volume = {8}, number = {2}, pages = {271-283}, pmid = {23949663}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/microbiology/ultrastructure/*virology ; Biodiversity ; Caribbean Region ; *Coral Reefs ; DNA Viruses/classification/genetics/*physiology/ultrastructure ; DNA, Satellite/genetics ; DNA, Single-Stranded/genetics ; Genome, Viral/genetics ; Intracellular Space/virology ; Microscopy, Electron, Transmission ; Seawater/virology ; }, abstract = {White plague (WP)-like diseases of tropical corals are implicated in reef decline worldwide, although their etiological cause is generally unknown. Studies thus far have focused on bacterial or eukaryotic pathogens as the source of these diseases; no studies have examined the role of viruses. Using a combination of transmission electron microscopy (TEM) and 454 pyrosequencing, we compared 24 viral metagenomes generated from Montastraea annularis corals showing signs of WP-like disease and/or bleaching, control conspecific corals, and adjacent seawater. TEM was used for visual inspection of diseased coral tissue. No bacteria were visually identified within diseased coral tissues, but viral particles and sequence similarities to eukaryotic circular Rep-encoding single-stranded DNA viruses and their associated satellites (SCSDVs) were abundant in WP diseased tissues. In contrast, sequence similarities to SCSDVs were not found in any healthy coral tissues, suggesting SCSDVs might have a role in WP disease. Furthermore, Herpesviridae gene signatures dominated healthy tissues, corroborating reports that herpes-like viruses infect all corals. Nucleocytoplasmic large DNA virus (NCLDV) sequences, similar to those recently identified in cultures of Symbiodinium (the algal symbionts of corals), were most common in bleached corals. This finding further implicates that these NCLDV viruses may have a role in bleaching, as suggested in previous studies. This study determined that a specific group of viruses is associated with diseased Caribbean corals and highlights the potential for viral disease in regional coral reef decline.}, } @article {pmid23949662, year = {2014}, author = {Nyyssönen, M and Hultman, J and Ahonen, L and Kukkonen, I and Paulin, L and Laine, P and Itävaara, M and Auvinen, P}, title = {Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield.}, journal = {The ISME journal}, volume = {8}, number = {1}, pages = {126-138}, pmid = {23949662}, issn = {1751-7370}, mesh = {Adaptation, Physiological/genetics ; Archaea/classification/genetics/*physiology ; Bacteria/classification/genetics/virology ; *Bacterial Physiological Phenomena ; Bacteriophages/genetics ; *Biodiversity ; Carbon Cycle ; Finland ; Geology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Water/chemistry ; }, abstract = {Microbial life in the nutrient-limited and low-permeability continental crystalline crust is abundant but remains relatively unexplored. Using high-throughput sequencing to assess the 16S rRNA gene diversity, we found diverse bacterial and archaeal communities along a 2516-m-deep drill hole in continental crystalline crust in Outokumpu, Finland. These communities varied at different sampling depths in response to prevailing lithology and hydrogeochemistry. Further analysis by shotgun metagenomic sequencing revealed variable carbon and nutrient utilization strategies as well as specific functional and physiological adaptations uniquely associated with specific environmental conditions. Altogether, our results show that predominant geological and hydrogeochemical conditions, including the existence and connectivity of fracture systems and the low amounts of available energy, have a key role in controlling microbial ecology and evolution in the nutrient and energy-poor deep crustal biosphere.}, } @article {pmid23949660, year = {2014}, author = {Lagkouvardos, I and Weinmaier, T and Lauro, FM and Cavicchioli, R and Rattei, T and Horn, M}, title = {Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae.}, journal = {The ISME journal}, volume = {8}, number = {1}, pages = {115-125}, pmid = {23949660}, issn = {1751-7370}, support = {281633/ERC_/European Research Council/International ; }, mesh = {Bacterial Proteins/genetics ; *Biodiversity ; Chlamydiaceae/*classification/*genetics ; Databases, Genetic ; Ecology ; Environmental Microbiology ; Metagenomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In the era of metagenomics and amplicon sequencing, comprehensive analyses of available sequence data remain a challenge. Here we describe an approach exploiting metagenomic and amplicon data sets from public databases to elucidate phylogenetic diversity of defined microbial taxa. We investigated the phylum Chlamydiae whose known members are obligate intracellular bacteria that represent important pathogens of humans and animals, as well as symbionts of protists. Despite their medical relevance, our knowledge about chlamydial diversity is still scarce. Most of the nine known families are represented by only a few isolates, while previous clone library-based surveys suggested the existence of yet uncharacterized members of this phylum. Here we identified more than 22,000 high quality, non-redundant chlamydial 16S rRNA gene sequences in diverse databases, as well as 1900 putative chlamydial protein-encoding genes. Even when applying the most conservative approach, clustering of chlamydial 16S rRNA gene sequences into operational taxonomic units revealed an unexpectedly high species, genus and family-level diversity within the Chlamydiae, including 181 putative families. These in silico findings were verified experimentally in one Antarctic sample, which contained a high diversity of novel Chlamydiae. In our analysis, the Rhabdochlamydiaceae, whose known members infect arthropods, represents the most diverse and species-rich chlamydial family, followed by the protist-associated Parachlamydiaceae, and a putative new family (PCF8) with unknown host specificity. Available information on the origin of metagenomic samples indicated that marine environments contain the majority of the newly discovered chlamydial lineages, highlighting this environment as an important chlamydial reservoir.}, } @article {pmid23949332, year = {2013}, author = {Kim, M and Yoon, H and You, YH and Kim, YE and Woo, JR and Seo, Y and Lee, GM and Kim, YJ and Kong, WS and Kim, JG}, title = {Metagenomic analysis of fungal communities inhabiting the fairy ring zone of Tricholoma matsutake.}, journal = {Journal of microbiology and biotechnology}, volume = {23}, number = {10}, pages = {1347-1356}, doi = {10.4014/jmb1306.06068}, pmid = {23949332}, issn = {1738-8872}, mesh = {Asia ; *Biota ; DNA, Fungal/chemistry/genetics ; *Metagenomics ; Molecular Sequence Data ; Mycorrhizae/*classification/*genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Tricholoma/*classification/*genetics ; }, abstract = {Tricholoma matsutake, an ectomycorrhiza that has mutual relationships with the rootlet of Pinus denisflora, forms a fruiting body that serves as a valuable food in Asia. However, the artificial culture of this fungus has not been successful. Soil fungi, including T. matsutake, coexist with many other microorganisms and plants; therefore, complex microbial communities have an influence on the fruiting body formation of T. matsutake. Here, we report on the structures of fungal communities associated with the fairy ring of T. matsutake through the pyrosequencing method. Soil samples were collected inside the fairy ring zone, in the fairy ring zone, and outside the fairy ring zone. A total of 37,125 sequencing reads were obtained and 728 to 1,962 operational taxonomic units (OTUs) were observed in the sampling zones. The fairy ring zone had the lowest OTUs and the lowest fungal diversity of all sampling zones. The number of OTUs and fungal taxa inside and outside the fairy ring zone was, respectively, about 2 times and 1.5 times higher than the fairy ring. Taxonomic analysis showed that each sampling zone has different fungal communities. In particular, out of 209 genera total, 6 genera in the fairy ring zone, such as Hemimycena, were uniquely present and 31 genera, such as Mycena, Boletopsis, and Repetophragma, were specifically absent. The results of metagenomic analysis based on the pyrosequencing indicate a decrease of fungal communities in the fairy ring zone and changes of fungal communities depending on the fairy ring growth of T. matsutake.}, } @article {pmid23945370, year = {2014}, author = {Chistoserdova, L}, title = {Is metagenomics resolving identification of functions in microbial communities?.}, journal = {Microbial biotechnology}, volume = {7}, number = {1}, pages = {1-4}, pmid = {23945370}, issn = {1751-7915}, mesh = {*Biota ; Computational Biology/methods/trends ; *Metagenome ; Metagenomics/*methods/trends ; }, abstract = {We are coming up on the tenth anniversary of the broad use of the method involving whole metagenome shotgun sequencing, referred to as metagenomics. The application of this approach has definitely revolutionized microbiology and the related fields, including the realization of the importance of the human microbiome. As such, metagenomics has already provided a novel outlook on the complexity and dynamics of microbial communities that are an important part of the biosphere of the planet. Accumulation of massive amounts of sequence data also caused a surge in the development of bioinformatics tools specially designed to provide pipelines for data analysis and visualization. However, a critical outlook into the field is required to appreciate what could be and what has currently been gained from the massive sequence databases that are being generated with ever-increasing speed.}, } @article {pmid23943792, year = {2013}, author = {Cox, MJ and Cookson, WO and Moffatt, MF}, title = {Sequencing the human microbiome in health and disease.}, journal = {Human molecular genetics}, volume = {22}, number = {R1}, pages = {R88-94}, doi = {10.1093/hmg/ddt398}, pmid = {23943792}, issn = {1460-2083}, support = {097117//Wellcome Trust/United Kingdom ; G1000758/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacteria/classification/genetics/growth & development ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing/*methods ; Host-Pathogen Interactions ; Humans ; Metagenomics ; Microbiota/*genetics/physiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Molecular techniques have revolutionized the practice of standard microbiology. In particular, 16S rRNA sequencing, whole microbial genome sequencing and metagenomics are revealing the extraordinary diversity of microorganisms on Earth and their vast genetic and metabolic repertoire. The increase in length, accuracy and number of reads generated by high-throughput sequencing has coincided with a surge of interest in the human microbiota, the totality of bacteria associated with the human body, in both health and disease. Traditional views of host/pathogen interactions are being challenged as the human microbiota are being revealed to be important in normal immune system function, to diseases not previously thought to have a microbial component and to infectious diseases with unknown aetiology. In this review, we introduce the nature of the human microbiota and application of these three key sequencing techniques for its study, highlighting both advances and challenges in the field. We go on to discuss how further adoption of additional techniques, also originally developed in environmental microbiology, will allow the establishment of disease causality against a background of numerous, complex and interacting microorganisms within the human host.}, } @article {pmid23940820, year = {2013}, author = {Tang, K and Liu, K and Jiao, N and Zhang, Y and Chen, CT}, title = {Functional metagenomic investigations of microbial communities in a shallow-sea hydrothermal system.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e72958}, pmid = {23940820}, issn = {1932-6203}, mesh = {Biodiversity ; Carbon Cycle ; Ecosystem ; Genes, Bacterial ; Hydrothermal Vents/microbiology ; Metabolome ; Metagenome/physiology ; Metagenomics/*methods ; *Microbial Consortia/genetics ; Oceans and Seas ; Seawater/*microbiology ; Sulfur/metabolism ; }, abstract = {Little is known about the functional capability of microbial communities in shallow-sea hydrothermal systems (water depth of <200 m). This study analyzed two high-throughput pyrosequencing metagenomic datasets from the vent and the surface water in the shallow-sea hydrothermal system offshore NE Taiwan. This system exhibited distinct geochemical parameters. Metagenomic data revealed that the vent and the surface water were predominated by Epsilonproteobacteria (Nautiliales-like organisms) and Gammaproteobacteria (Thiomicrospira-like organisms), respectively. A significant difference in microbial carbon fixation and sulfur metabolism was found between the vent and the surface water. The chemoautotrophic microorganisms in the vent and in the surface water might possess the reverse tricarboxylic acid cycle and the Calvin-Bassham-Benson cycle for carbon fixation in response to carbon dioxide highly enriched in the environment, which is possibly fueled by geochemical energy with sulfur and hydrogen. Comparative analyses of metagenomes showed that the shallow-sea metagenomes contained some genes similar to those present in other extreme environments. This study may serve as a basis for deeply understanding the genetic network and functional capability of the microbial members of shallow-sea hydrothermal systems.}, } @article {pmid23940763, year = {2013}, author = {Vey, G}, title = {Metagenomic guilt by association: an operonic perspective.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e71484}, pmid = {23940763}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Epistasis, Genetic/*physiology ; Genes/physiology ; Genetic Association Studies/*methods ; Humans ; Metagenomics/*methods ; Molecular Sequence Annotation ; Operon/*genetics ; Sequence Analysis, DNA ; }, abstract = {Next-generation sequencing projects continue to drive a vast accumulation of metagenomic sequence data. Given the growth rate of this data, automated approaches to functional annotation are indispensable and a cornerstone heuristic of many computational protocols is the concept of guilt by association. The guilt by association paradigm has been heavily exploited by genomic context methods that offer functional predictions that are complementary to homology-based annotations, thereby offering a means to extend functional annotation. In particular, operon methods that exploit co-directional intergenic distances can provide homology-free functional annotation through the transfer of functions among co-operonic genes, under the assumption that guilt by association is indeed applicable. Although guilt by association is a well-accepted annotative device, its applicability to metagenomic functional annotation has not been definitively demonstrated. Here a large-scale assessment of metagenomic guilt by association is undertaken where functional associations are predicted on the basis of co-directional intergenic distances. Specifically, functional annotations are compared within pairs of adjacent co-directional genes, as well as operons of various lengths (i.e. number of member genes), in order to reveal new information about annotative cohesion versus operon length. The results suggests that co-directional gene pairs offer reduced confidence for metagenomic guilt by association due to difficulty in resolving the existence of functional associations when intergenic distance is the sole predictor of pairwise gene interactions. However, metagenomic operons, particularly those with substantial lengths, appear to be capable of providing a superior basis for metagenomic guilt by association due to increased annotative stability. The need for improved recognition of metagenomic operons is discussed, as well as the limitations of the present work.}, } @article {pmid23935906, year = {2013}, author = {Neville, BA and Sheridan, PO and Harris, HM and Coughlan, S and Flint, HJ and Duncan, SH and Jeffery, IB and Claesson, MJ and Ross, RP and Scott, KP and O'Toole, PW}, title = {Pro-inflammatory flagellin proteins of prevalent motile commensal bacteria are variably abundant in the intestinal microbiome of elderly humans.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e68919}, pmid = {23935906}, issn = {1932-6203}, mesh = {Adult ; Aged ; Amino Acid Sequence ; Bacteria/genetics/*growth & development ; Binding Sites ; Computer Simulation ; Electrophoresis, Polyacrylamide Gel ; Feces/microbiology ; Flagellin/chemistry/genetics/isolation & purification/*metabolism ; Gene Order/genetics ; Genetic Loci/genetics ; Genome, Bacterial/genetics ; Genomics ; Humans ; Inflammation Mediators/*metabolism ; Interleukin-8/metabolism ; Intestines/*microbiology ; Metagenome ; *Microbiota ; Molecular Sequence Annotation ; Molecular Sequence Data ; Movement ; Promoter Regions, Genetic/genetics ; Ribosomes/metabolism ; Sequence Alignment ; }, abstract = {Some Eubacterium and Roseburia species are among the most prevalent motile bacteria present in the intestinal microbiota of healthy adults. These flagellate species contribute "cell motility" category genes to the intestinal microbiome and flagellin proteins to the intestinal proteome. We reviewed and revised the annotation of motility genes in the genomes of six Eubacterium and Roseburia species that occur in the human intestinal microbiota and examined their respective locus organization by comparative genomics. Motility gene order was generally conserved across these loci. Five of these species harbored multiple genes for predicted flagellins. Flagellin proteins were isolated from R. inulinivorans strain A2-194 and from E. rectale strains A1-86 and M104/1. The amino-termini sequences of the R. inulinivorans and E. rectale A1-86 proteins were almost identical. These protein preparations stimulated secretion of interleukin-8 (IL-8) from human intestinal epithelial cell lines, suggesting that these flagellins were pro-inflammatory. Flagellins from the other four species were predicted to be pro-inflammatory on the basis of alignment to the consensus sequence of pro-inflammatory flagellins from the β- and γ- proteobacteria. Many fliC genes were deduced to be under the control of σ(28). The relative abundance of the target Eubacterium and Roseburia species varied across shotgun metagenomes from 27 elderly individuals. Genes involved in the flagellum biogenesis pathways of these species were variably abundant in these metagenomes, suggesting that the current depth of coverage used for metagenomic sequencing (3.13-4.79 Gb total sequence in our study) insufficiently captures the functional diversity of genomes present at low (≤1%) relative abundance. E. rectale and R. inulinivorans thus appear to synthesize complex flagella composed of flagellin proteins that stimulate IL-8 production. A greater depth of sequencing, improved evenness of sequencing and improved metagenome assembly from short reads will be required to facilitate in silico analyses of complete complex biochemical pathways for low-abundance target species from shotgun metagenomes.}, } @article {pmid23933971, year = {2013}, author = {Li, H and Jia, W}, title = {Cometabolism of microbes and host: implications for drug metabolism and drug-induced toxicity.}, journal = {Clinical pharmacology and therapeutics}, volume = {94}, number = {5}, pages = {574-581}, doi = {10.1038/clpt.2013.157}, pmid = {23933971}, issn = {1532-6535}, mesh = {Drug-Related Side Effects and Adverse Reactions/metabolism/*microbiology ; Gastrointestinal Tract/microbiology ; *Host-Pathogen Interactions/drug effects/physiology ; Humans ; Metabolomics ; Microbiota/drug effects/physiology ; Pharmaceutical Preparations/*metabolism ; Pharmacogenetics ; }, abstract = {The recognition of the gut microbial-mammalian metabolic axis and its implications in human metabolic disease opens a new window to understanding the contribution of the gut microbiome to drug metabolism and drug-induced toxicity. The integrative omics approaches, including pharmacometabonomics and metagenomics, have demonstrated great promise for characterizing xenobiotic interventions that are associated with wide variation in efficacy or toxicity in humans, as well as for predicting individual response and susceptibility to toxicity.}, } @article {pmid23927049, year = {2013}, author = {Vicente, CS and Nascimento, FX and Espada, M and Barbosa, P and Hasegawa, K and Mota, M and Oliveira, S}, title = {Characterization of bacterial communities associated with the pine sawyer beetle Monochamus galloprovincialis, the insect vector of the pinewood nematode Bursaphelenchus xylophilus.}, journal = {FEMS microbiology letters}, volume = {347}, number = {2}, pages = {130-139}, doi = {10.1111/1574-6968.12232}, pmid = {23927049}, issn = {1574-6968}, mesh = {Animals ; Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; Coleoptera/*microbiology/parasitology ; Diet ; Ecosystem ; Insect Vectors/*microbiology/parasitology ; Molecular Sequence Data ; Nematoda/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Pine wilt disease (PWD) has a tremendous impact on worldwide forestlands, both from the environmental and economical viewpoints. Monochamus sp., a xylophagous insect from the Cerambycidae family, plays an important role in dissemination of the pinewood nematode, Bursaphelenchus xylophilus, the primary pathogenic agent of PWD. This study investigates, for the first time, the bacterial communities of Monochamus galloprovincialis collected from Portuguese Pinus pinaster trees and B. xylophilus free, using a metagenomics approach. Overall, our results show that natural bacterial communities of M. galloprovincialis are mainly composed by γ-proteobacteria, Firmicutes and Bacteroidetes, which may be a reflection of insects' feeding diet and habitat characteristics. We also report different bacterial communities' composition in the thorax and abdomen of M. galloprovincialis, with high abundance of Serratia sp. in both. Our results encourage further studies in the possible relationship between bacteria from the insect vector and B. xylophilus.}, } @article {pmid23913425, year = {2013}, author = {Krohn-Molt, I and Wemheuer, B and Alawi, M and Poehlein, A and Güllert, S and Schmeisser, C and Pommerening-Röser, A and Grundhoff, A and Daniel, R and Hanelt, D and Streit, WR}, title = {Metagenome survey of a multispecies and alga-associated biofilm revealed key elements of bacterial-algal interactions in photobioreactors.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {20}, pages = {6196-6206}, pmid = {23913425}, issn = {1098-5336}, mesh = {Bacteria/*classification/genetics/isolation & purification ; *Bacterial Physiological Phenomena ; *Biodiversity ; Biofilms/*growth & development ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Microalgae/growth & development/*physiology ; *Microbial Interactions ; Molecular Sequence Data ; Photobioreactors/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Photobioreactors (PBRs) are very attractive for sunlight-driven production of biofuels and capturing of anthropogenic CO2. One major problem associated with PBRs however, is that the bacteria usually associated with microalgae in nonaxenic cultures can lead to biofouling and thereby affect algal productivity. Here, we report on a phylogenetic, metagenome, and functional analysis of a mixed-species bacterial biofilm associated with the microalgae Chlorella vulgaris and Scenedesmus obliquus in a PBR. The biofilm diversity and population dynamics were examined through 16S rRNA phylogeny. Overall, the diversity was rather limited, with approximately 30 bacterial species associated with the algae. The majority of the observed microorganisms were affiliated with Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes. A combined approach of sequencing via GS FLX Titanium from Roche and HiSeq 2000 from Illumina resulted in the overall production of 350 Mbp of sequenced DNA, 165 Mbp of which was assembled in larger contigs with a maximum size of 0.2 Mbp. A KEGG pathway analysis suggested high metabolic diversity with respect to the use of polymers and aromatic and nonaromatic compounds. Genes associated with the biosynthesis of essential B vitamins were highly redundant and functional. Moreover, a relatively high number of predicted and functional lipase and esterase genes indicated that the alga-associated bacteria are possibly a major sink for lipids and fatty acids produced by the microalgae. This is the first metagenome study of microalga- and PBR-associated biofilm bacteria, and it gives new clues for improved biofuel production in PBRs.}, } @article {pmid23909933, year = {2014}, author = {Boon, E and Meehan, CJ and Whidden, C and Wong, DH and Langille, MG and Beiko, RG}, title = {Interactions in the microbiome: communities of organisms and communities of genes.}, journal = {FEMS microbiology reviews}, volume = {38}, number = {1}, pages = {90-118}, pmid = {23909933}, issn = {1574-6976}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Chromosome Mapping ; Evolution, Molecular ; Genes/*genetics ; Genome, Bacterial/genetics ; Humans ; Microbiota/genetics/*physiology ; }, abstract = {A central challenge in microbial community ecology is the delineation of appropriate units of biodiversity, which can be taxonomic, phylogenetic, or functional in nature. The term 'community' is applied ambiguously; in some cases, the term refers simply to a set of observed entities, while in other cases, it requires that these entities interact with one another. Microorganisms can rapidly gain and lose genes, potentially decoupling community roles from taxonomic and phylogenetic groupings. Trait-based approaches offer a useful alternative, but many traits can be defined based on gene functions, metabolic modules, and genomic properties, and the optimal set of traits to choose is often not obvious. An analysis that considers taxon assignment and traits in concert may be ideal, with the strengths of each approach offsetting the weaknesses of the other. Individual genes also merit consideration as entities in an ecological analysis, with characteristics such as diversity, turnover, and interactions modeled using genes rather than organisms as entities. We identify some promising avenues of research that are likely to yield a deeper understanding of microbial communities that shift from observation-based questions of 'Who is there?' and 'What are they doing?' to the mechanistically driven question of 'How will they respond?'}, } @article {pmid23906500, year = {2013}, author = {Lecuit, M and Eloit, M}, title = {The human virome: new tools and concepts.}, journal = {Trends in microbiology}, volume = {21}, number = {10}, pages = {510-515}, pmid = {23906500}, issn = {1878-4380}, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Microbiota/immunology ; Sequence Analysis, DNA ; *Virus Diseases/genetics/immunology/pathology ; *Viruses/genetics/immunology/pathogenicity ; }, abstract = {The human virome is the viral component of the microbiome. Its composition, and interindividual and temporal variability are not precisely known. Its impact on human health has received less attention than that of the bacterial microbiome, but is likely to be equally important, both in homeostasis and disease. Here we review the recent advances in this field and the questions that arise in the context of our rapidly increasing knowledge regarding the composition and function of the human virome. With the ever-extending use of next-generation sequencing (NGS) on a variety of clinical samples, rapid progress on the composition of the human virome and its impact upon human health are to be expected in the coming years.}, } @article {pmid23899773, year = {2013}, author = {Peng, X and Yu, KQ and Deng, GH and Jiang, YX and Wang, Y and Zhang, GX and Zhou, HW}, title = {Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by Illumina sequencing of 16S rRNA tags.}, journal = {Journal of microbiological methods}, volume = {95}, number = {3}, pages = {455-462}, doi = {10.1016/j.mimet.2013.07.015}, pmid = {23899773}, issn = {1872-8359}, mesh = {Animals ; Costs and Cost Analysis ; DNA/chemistry/genetics/*isolation & purification ; Feces/microbiology ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/economics/*methods ; Specimen Handling/economics/*methods ; Time Factors ; }, abstract = {Low cost and high throughput capacity are major advantages of using next generation sequencing (NGS) techniques to determine metagenomic 16S rRNA tag sequences. These methods have significantly changed our view of microorganisms in the fields of human health and environmental science. However, DNA extraction using commercial kits has shortcomings of high cost and time constraint. In the present study, we evaluated the determination of fecal microbiomes using a direct boiling method compared with 5 different commercial extraction methods, e.g., Qiagen and MO BIO kits. Principal coordinate analysis (PCoA) using UniFrac distances and clustering showed that direct boiling of a wide range of feces concentrations gave a similar pattern of bacterial communities as those obtained from most of the commercial kits, with the exception of the MO BIO method. Fecal concentration by boiling method affected the estimation of α-diversity indices, otherwise results were generally comparable between boiling and commercial methods. The operational taxonomic units (OTUs) determined through direct boiling showed highly consistent frequencies with those determined through most of the commercial methods. Even those for the MO BIO kit were also obtained by the direct boiling method with high confidence. The present study suggested that direct boiling could be used to determine the fecal microbiome and using this method would significantly reduce the cost and improve the efficiency of the sample preparation for studying gut microbiome diversity.}, } @article {pmid23899544, year = {2013}, author = {Kump, PK and Gröchenig, HP and Lackner, S and Trajanoski, S and Reicht, G and Hoffmann, KM and Deutschmann, A and Wenzl, HH and Petritsch, W and Krejs, GJ and Gorkiewicz, G and Högenauer, C}, title = {Alteration of intestinal dysbiosis by fecal microbiota transplantation does not induce remission in patients with chronic active ulcerative colitis.}, journal = {Inflammatory bowel diseases}, volume = {19}, number = {10}, pages = {2155-2165}, doi = {10.1097/MIB.0b013e31829ea325}, pmid = {23899544}, issn = {1536-4844}, mesh = {Adolescent ; Adult ; *Biological Therapy ; Chronic Disease ; Clostridium Infections/genetics/microbiology/*therapy ; Colitis, Ulcerative/genetics/microbiology/*therapy ; Dysbiosis/genetics/microbiology/*prevention & control ; Feces/*microbiology ; Female ; Follow-Up Studies ; Humans ; Intestines/microbiology ; Male ; Metagenome/*genetics ; *Microbiota ; Middle Aged ; Phylogeny ; Prognosis ; RNA, Ribosomal, 16S/analysis ; Remission Induction ; Transplantation ; }, abstract = {BACKGROUND: In patients with ulcerative colitis (UC), alterations of the intestinal microbiota, termed dysbiosis, have been postulated to contribute to intestinal inflammation. Fecal microbiota transplantation (FMT) has been used as effective therapy for recurrent Clostridium difficile colitis also caused by dysbiosis. The aims of the present study were to investigate if patients with UC benefit from FMT and if dysbiosis can be reversed.

METHODS: Six patients with chronic active UC nonresponsive to standard medical therapy were treated with FMT by colonoscopic administration. Changes in the colonic microbiota were assessed by 16S rDNA-based microbial community profiling using high-throughput pyrosequencing from mucosal and stool samples.

RESULTS: All patients experienced short-term clinical improvement within the first 2 weeks after FMT. However, none of the patients achieved clinical remission. Microbiota profiling showed differences in the modification of the intestinal microbiota between individual patients after FMT. In 3 patients, the colonic microbiota changed toward the donor microbiota; however, this did not correlate with clinical response. On phylum level, there was a significant reduction of Proteobacteria and an increase in Bacteroidetes after FMT.

CONCLUSIONS: FMT by a single colonoscopic donor stool application is not effective in inducing remission in chronic active therapy-refractory UC. Changes in the composition of the intestinal microbiota were significant and resulted in a partial improvement of UC-associated dysbiosis. The results suggest that dysbiosis in UC is at least in part a secondary phenomenon induced by inflammation and diarrhea rather than being causative for inflammation in this disease.}, } @article {pmid23895412, year = {2013}, author = {Rastogi, G and Coaker, GL and Leveau, JH}, title = {New insights into the structure and function of phyllosphere microbiota through high-throughput molecular approaches.}, journal = {FEMS microbiology letters}, volume = {348}, number = {1}, pages = {1-10}, doi = {10.1111/1574-6968.12225}, pmid = {23895412}, issn = {1574-6968}, mesh = {*Biodiversity ; *High-Throughput Nucleotide Sequencing ; *Microbiological Techniques ; *Microbiota ; Plant Leaves/*microbiology ; }, abstract = {The phyllosphere is an ecologically and economically important ecosystem that hosts a large and diverse microbial community. Phyllosphere microbiota play a critical role in protecting plants from diseases as well as promoting their growth by various mechanisms. There are serious gaps in our understanding of how and why microbiota composition varies across spatial and temporal scales, the ecology of leaf surface colonizers and their interactions with their host, and the genetic adaptations that enable phyllosphere survival of microorganisms. These gaps are due in large part to past technical limitations, as earlier studies were restricted to the study of culturable bacteria only and used low-throughput molecular techniques to describe community structure and function. The availability of high-throughput and cost-effective molecular technologies is changing the field of phyllosphere microbiology, enabling researchers to begin to address the dynamics and composition of the phyllosphere microbiota across a large number of samples with high, in-depth coverage. Here, we discuss and connect the most recent studies that have used next-generation molecular techniques such as metagenomics, proteogenomics, genome sequencing, and transcriptomics to gain new insights into the structure and function of phyllosphere microbiota and highlight important challenges for future research.}, } @article {pmid23894461, year = {2013}, author = {Marsh, AJ and O'Sullivan, O and Hill, C and Ross, RP and Cotter, PD}, title = {Sequencing-based analysis of the bacterial and fungal composition of kefir grains and milks from multiple sources.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e69371}, pmid = {23894461}, issn = {1932-6203}, mesh = {Animals ; Bacteria/*classification/*genetics ; Biodiversity ; Cultured Milk Products/*microbiology ; DNA, Intergenic/genetics ; Fungi/*classification/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Milk/*microbiology ; Phylogeny ; }, abstract = {Kefir is a fermented milk-based beverage to which a number of health-promoting properties have been attributed. The microbes responsible for the fermentation of milk to produce kefir consist of a complex association of bacteria and yeasts, bound within a polysaccharide matrix, known as the kefir grain. The consistency of this microbial population, and that present in the resultant beverage, has been the subject of a number of previous, almost exclusively culture-based, studies which have indicated differences depending on geographical location and culture conditions. However, culture-based identification studies are limited by virtue of only detecting species with the ability to grow on the specific medium used and thus culture-independent, molecular-based techniques offer the potential for a more comprehensive analysis of such communities. Here we describe a detailed investigation of the microbial population, both bacterial and fungal, of kefir, using high-throughput sequencing to analyse 25 kefir milks and associated grains sourced from 8 geographically distinct regions. This is the first occasion that this technology has been employed to investigate the fungal component of these populations or to reveal the microbial composition of such an extensive number of kefir grains or milks. As a result several genera and species not previously identified in kefir were revealed. Our analysis shows that the bacterial populations in kefir are dominated by 2 phyla, the Firmicutes and the Proteobacteria. It was also established that the fungal populations of kefir were dominated by the genera Kazachstania, Kluyveromyces and Naumovozyma, but that a variable sub-dominant population also exists.}, } @article {pmid23894355, year = {2013}, author = {Xia, X and Zheng, D and Zhong, H and Qin, B and Gurr, GM and Vasseur, L and Lin, H and Bai, J and He, W and You, M}, title = {DNA sequencing reveals the midgut microbiota of diamondback moth, Plutella xylostella (L.) and a possible relationship with insecticide resistance.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e68852}, pmid = {23894355}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Gastrointestinal Tract/*microbiology ; Insecticide Resistance/*genetics ; Insecticides/*pharmacology ; Larva/microbiology ; *Metagenome ; *Microbiota ; Moths/*drug effects/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Insect midgut microbiota is important in host nutrition, development and immune response. Recent studies indicate possible links between insect gut microbiota and resistance to biological and chemical toxins. Studies of this phenomenon and symbionts in general have been hampered by difficulties in culture-based approach. In the present study, DNA sequencing was used to examine the midgut microbiota of diamondback moth (DBM), Plutella xylostella (L.), a destructive pest that attacks cruciferous crops worldwide. Its ability to develop resistance to many types of synthetic insecticide and even Bacillus thuringiensis toxins makes it an important species to study.

Bacteria of the DBM larval midgut in a susceptible and two insecticide (chlorpyrifos and fipronil) resistant lines were examined by Illumina sequencing sampled from an insect generation that was not exposed to insecticide. This revealed that more than 97% of the bacteria were from three orders: Enterobacteriales, Vibrionales and Lactobacillales. Both insecticide-resistant lines had more Lactobacillales and the much scarcer taxa Pseudomonadales and Xanthomonadales with fewer Enterobacteriales compared with the susceptible strain. Consistent with this, a second study observed an increase in the proportion of Lactobacillales in the midgut of DBM individuals from a generation treated with insecticides.

CONCLUSIONS/SIGNIFICANCE: This is the first report of high-throughput DNA sequencing of the entire microbiota of DBM. It reveals differences related to inter- and intra-generational exposure to insecticides. Differences in the midgut microbiota among susceptible and insecticide-resistant lines are independent of insecticide exposure in the sampled generations. While this is consistent with the hypothesis that Lactobacillales or other scarcer taxa play a role in conferring DBM insecticide resistance, further studies are necessary to rule out other possibilities. Findings constitute the basis for future molecular work on the functions of insect midgut microbiota taxa and their possible role in conferring host resistance to toxins.}, } @article {pmid23891019, year = {2013}, author = {van Baarlen, P and Kleerebezem, M and Wells, JM}, title = {Omics approaches to study host-microbiota interactions.}, journal = {Current opinion in microbiology}, volume = {16}, number = {3}, pages = {270-277}, doi = {10.1016/j.mib.2013.07.001}, pmid = {23891019}, issn = {1879-0364}, mesh = {Animals ; Cell Line ; Gene Expression Profiling/*methods ; *Host-Pathogen Interactions ; Humans ; Metabolomics/*methods ; Metagenomics/*methods ; Mice ; Microbiota/*physiology ; Models, Animal ; Systems Biology/methods ; }, abstract = {The intestinal microbiota has profound effects on our physiology and immune system and disturbances in the equilibrium between microbiota and host have been observed in many disorders. Here we discuss the possibilities to further our understanding of how microbiota impacts on human health and disease through the use of large-scale quantifiable tools such as transcriptomics, metagenomics and metabolomics. Reductionist models, including gnotobiotic mouse models have their place in testing hypotheses and elucidating mechanisms by which specific communities or individual species impact on host biology. Network biology approaches can be combined with studies in animal models and cell lines to create iterative cycle of hypotheses and testing, possibly leading to testing in clinical and nutritional intervention studies.}, } @article {pmid23889584, year = {2013}, author = {O' Donnell, MM and Harris, HM and Jeffery, IB and Claesson, MJ and Younge, B and O' Toole, PW and Ross, RP}, title = {The core faecal bacterial microbiome of Irish Thoroughbred racehorses.}, journal = {Letters in applied microbiology}, volume = {57}, number = {6}, pages = {492-501}, doi = {10.1111/lam.12137}, pmid = {23889584}, issn = {1472-765X}, mesh = {Animals ; Bacteria/*classification/genetics/*isolation & purification ; Feces/*microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Horses/*microbiology ; Male ; Metagenome ; *Microbiota ; }, abstract = {UNLABELLED: In this study, we characterized the gut microbiota in six healthy Irish thoroughbred racehorses and showed it to be dominated by the phyla Firmicutes, Bacteroidetes, Proteobacteria, Verrucomicrobia, Actinobacteria, Euryarchaeota, Fibrobacteres and Spirochaetes. Moreover, all the horses harboured Clostridium, Fibrobacter, Faecalibacterium, Ruminococcus, Eubacterium, Oscillospira, Blautia Anaerotruncus, Coprococcus, Treponema and Lactobacillus spp. Notwithstanding the sample size, it was noteworthy that the core microbiota species assignments identified Fibrobacter succinogenes, Eubacterium coprostanoligenes, Eubacterium hallii, Eubacterium ruminantium, Oscillospira guillermondii, Sporobacter termiditis, Lactobacillus equicursoris, Treponema parvum and Treponema porcinum in all the horses. This is the first study of the faecal microbiota in the Irish thoroughbred racehorse, a significant competitor in the global bloodstock industry. The information gathered in this pilot study provides a foundation for veterinarians and other equine health-associated professionals to begin to analyse the microbiome of performance of racehorses. This study and subsequent work may lead to alternate dietary approaches aimed at minimizing the risk of microbiota-related dysbiosis in these performance animals.

Although Irish thoroughbreds are used nationally and internationally as performance animals, very little is known about the core faecal microbiota of these animals. This is the first study to characterize the bacterial microbiota present in the Irish thoroughbred racehorse faeces and elucidate a core microbiome irrespective of diet, animal management and geographical location.}, } @article {pmid23889283, year = {2013}, author = {Durbán, A and Abellán, JJ and Jiménez-Hernández, N and Artacho, A and Garrigues, V and Ortiz, V and Ponce, J and Latorre, A and Moya, A}, title = {Instability of the faecal microbiota in diarrhoea-predominant irritable bowel syndrome.}, journal = {FEMS microbiology ecology}, volume = {86}, number = {3}, pages = {581-589}, doi = {10.1111/1574-6941.12184}, pmid = {23889283}, issn = {1574-6941}, mesh = {Aged ; Bacteria/*classification/genetics/isolation & purification ; Colon/microbiology/physiopathology ; Diarrhea/microbiology ; Feces/*microbiology ; Female ; Humans ; Intestinal Mucosa/microbiology ; Irritable Bowel Syndrome/*microbiology/physiopathology ; Male ; *Microbiota ; Middle Aged ; Young Adult ; }, abstract = {The irritable bowel syndrome (IBS) is a functional gastrointestinal disorder with a largely unknown aetiology and a wide range of symptoms. Most cross-sectional studies carried out so far suggest subtle alterations in the structure of the intestinal microbiota that are barely reproduced, partly because of the high inter-subject variation in the community composition and disorder-specific features. We performed a longitudinal study to explore the within-subject variation in the faecal microbiota in two patients with IBS classified into the diarrhoea subtype and the healthy spouse of one of them. Faecal communities were monitored over 6-8 weeks and analysed through metagenomic and metatranscriptomic approaches. We found a higher temporal instability in the fraction of active microbiota related to the IBS condition and fluctuating symptoms. Strong and quick shifts in the distribution of the active microbiota and changes in the global pattern of gene expression were detected in association with acute diarrhoea, whereas microbial composition and encoded functions were more stable. The specific alterations in the microbiota were barely reproduced within and between patients. Further research is needed to assess whether these changes are a consequence of the abnormal gut function in acute diarrhoeic episodes and the potential usefulness of tackling them.}, } @article {pmid23889170, year = {2013}, author = {Zhou, A and He, Z and Qin, Y and Lu, Z and Deng, Y and Tu, Q and Hemme, CL and Van Nostrand, JD and Wu, L and Hazen, TC and Arkin, AP and Zhou, J}, title = {StressChip as a high-throughput tool for assessing microbial community responses to environmental stresses.}, journal = {Environmental science & technology}, volume = {47}, number = {17}, pages = {9841-9849}, doi = {10.1021/es4018656}, pmid = {23889170}, issn = {1520-5851}, mesh = {Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; Computational Biology/methods ; Environmental Monitoring/*methods ; Eukaryota/*genetics/metabolism ; Genes, Archaeal/drug effects ; Genes, Bacterial/drug effects ; Gulf of Mexico ; *Metagenome/drug effects ; Microarray Analysis/*methods ; *Microbiota/drug effects ; Nucleic Acid Probes/metabolism ; Seawater/microbiology ; Stress, Physiological ; }, abstract = {Microbial community responses to environmental stresses are critical for microbial growth, survival, and adaptation. To fill major gaps in our ability to discern the influence of environmental changes on microbial communities from engineered and natural environments, a functional gene-based microarray, termed StressChip, has been developed. First, 46 functional genes involved in microbial responses to environmental stresses such as changes to temperature, osmolarity, oxidative status, nutrient limitation, or general stress response were selected and curated. A total of 22,855 probes were designed, covering 79,628 coding sequences from 985 bacterial, 76 archaeal, and 59 eukaryotic species/strains. Probe specificity was computationally verified. Second, the usefulness of functional genes as indicators of stress response was examined by surveying their distribution in metagenome data sets. The abundance of individual stress response genes is consistent with expected distributions based on respective habitats. Third, the StressChip was used to analyze marine microbial communities from the Deepwater Horizon oil spill. That functional stress response genes were detected in higher abundance (p < 0.05) in oil plume compared to nonplume samples indicated shifts in community composition and structure, consistent with previous results. In summary, StressChip provides a new tool for accessing microbial community functional structure and responses to environmental changes.}, } @article {pmid23887171, year = {2013}, author = {Flowers, JJ and He, S and Malfatti, S and del Rio, TG and Tringe, SG and Hugenholtz, P and McMahon, KD}, title = {Comparative genomics of two 'Candidatus Accumulibacter' clades performing biological phosphorus removal.}, journal = {The ISME journal}, volume = {7}, number = {12}, pages = {2301-2314}, pmid = {23887171}, issn = {1751-7370}, mesh = {Biodiversity ; Bioreactors ; Clustered Regularly Interspaced Short Palindromic Repeats ; DNA, Bacterial/genetics ; Denitrification ; *Genome, Bacterial ; Metagenomics ; Phosphorus/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Homology, Nucleic Acid ; Sewage/microbiology ; Wastewater/*microbiology ; }, abstract = {Members of the genus Candidatus Accumulibacter are important in many wastewater treatment systems performing enhanced biological phosphorus removal (EBPR). The Accumulibacter lineage can be subdivided phylogenetically into multiple clades, and previous work showed that these clades are ecologically distinct. The complete genome of Candidatus Accumulibacter phosphatis strain UW-1, a member of Clade IIA, was previously sequenced. Here, we report a draft genome sequence of Candidatus Accumulibacter spp. strain UW-2, a member of Clade IA, assembled following shotgun metagenomic sequencing of laboratory-scale bioreactor sludge. We estimate the genome to be 80-90% complete. Although the two clades share 16S rRNA sequence identity of >98.0%, we observed a remarkable lack of synteny between the two genomes. We identified 2317 genes shared between the two genomes, with an average nucleotide identity (ANI) of 78.3%, and accounting for 49% of genes in the UW-1 genome. Unlike UW-1, the UW-2 genome seemed to lack genes for nitrogen fixation and carbon fixation. Despite these differences, metabolic genes essential for denitrification and EBPR, including carbon storage polymer and polyphosphate metabolism, were conserved in both genomes. The ANI from genes associated with EBPR was statistically higher than that from genes not associated with EBPR, indicating a high selective pressure in EBPR systems. Further, we identified genomic islands of foreign origins including a near-complete lysogenic phage in the Clade IA genome. Interestingly, Clade IA appeared to be more phage susceptible based on it containing only a single Clustered Regularly Interspaced Short Palindromic Repeats locus as compared with the two found in Clade IIA. Overall, the comparative analysis provided a genetic basis to understand physiological differences and ecological niches of Accumulibacter populations, and highlights the importance of diversity in maintaining system functional resilience.}, } @article {pmid23887030, year = {2013}, author = {Avershina, E and Rudi, K}, title = {Is it who you are or what you do that is important in the human gut?.}, journal = {Beneficial microbes}, volume = {4}, number = {3}, pages = {219-222}, doi = {10.3920/BM2013.0016}, pmid = {23887030}, issn = {1876-2891}, mesh = {*Biota ; Gastrointestinal Tract/*microbiology ; Humans ; *Life Style ; Metagenomics/methods ; }, abstract = {The current leading view is that functionality and not phylotype is the most important determinant for the services provided by the gut microbiota. Here we present an alternative opinion, advocating the importance of phylotype in addition to function. We believe the literature is misled by technical artifacts in defining operational taxonomic units (OTUs), which are binned groups of bacteria based on sequence homology. Furthermore, the current metagenomic approaches where the total DNA in a sample is mixed prior to sequencing and subsequently resolved by a bioinformatics approach, are highly error prone with respect to both functional and phylotype assignments. We argue that the directions of the OTU and metagenome errors are such that stable phylotypes are overlooked, while functional stability is overestimated. Taking these errors into account, we propose that phylotype represents an interface for functionality, and is for this reason an important determinant for the services provided by the gut microbiota to the host.}, } @article {pmid23885002, year = {2013}, author = {Hugon, P and Lagier, JC and Robert, C and Lepolard, C and Papazian, L and Musso, D and Vialettes, B and Raoult, D}, title = {Molecular studies neglect apparently gram-negative populations in the human gut microbiota.}, journal = {Journal of clinical microbiology}, volume = {51}, number = {10}, pages = {3286-3293}, pmid = {23885002}, issn = {1098-660X}, mesh = {Adult ; Aged ; Bacteria/*classification/*genetics/isolation & purification ; Bacteriological Techniques/*methods ; *Biota ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; Middle Aged ; Young Adult ; }, abstract = {Studying the relationships between gut microbiota, human health, and diseases is a major challenge that generates contradictory results. Most studies draw conclusions about the gut repertoire using a single biased metagenomics approach. We analyzed 16 different stool samples collected from healthy subjects who were from different areas, had metabolic disorders, were immunocompromised, or were treated with antibiotics at the time of the stool collection. The analyses performed included Gram staining, flow cytometry, transmission electron microscopy (TEM), quantitative real-time PCR (qPCR) of the Bacteroidetes and Firmicutes phyla, and pyrosequencing of the 16S rRNA gene amplicons targeting the V6 region. We quantified 10(10) prokaryotes per gram of feces, which is less than was previously described. The Mann-Whitney test revealed that Gram-negative proportions of the prokaryotes obtained by Gram staining, TEM, and pyrosequencing differed according to the analysis used, with Gram-negative prokaryotes yielding median percentages of 70.6%, 31.0%, and 16.4%, respectively. A comparison of TEM and pyrosequencing analyses highlighted a difference of 14.6% in the identification of Gram-negative prokaryotes, and a Spearman test showed a tendency toward correlation, albeit not significant, in the Gram-negative/Gram-positive prokaryote ratio (ρ = 0.3282, P = 0.2146). In contrast, when comparing the qPCR and pyrosequencing results, a significant correlation was found for the Bacteroidetes/Firmicutes ratio (ρ = 0.6057, P = 0.0130). Our study showed that the entire diversity of the human gut microbiota remains unknown because different techniques generate extremely different results. We found that to assess the overall composition of bacterial communities, multiple techniques must be combined. The biases that exist for each technique may be useful in exploring the major discrepancies in molecular studies.}, } @article {pmid23882709, year = {2013}, author = {DeLeon-Rodriguez, N and Lathem, TL and Rodriguez-R, LM and Barazesh, JM and Anderson, BE and Beyersdorf, AJ and Ziemba, LD and Bergin, M and Nenes, A and Konstantinidis, KT}, title = {Reply to Smith and Griffin: Methods, air flows, and conclusions are robust in the DeLeon-Rodriguez et al. study.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {23}, pages = {E2085}, pmid = {23882709}, issn = {1091-6490}, mesh = {*Air Microbiology ; *Atmosphere ; *Biodiversity ; *Cyclonic Storms ; Metagenome/*genetics ; }, } @article {pmid23880441, year = {2013}, author = {Eikmeyer, FG and Köfinger, P and Poschenel, A and Jünemann, S and Zakrzewski, M and Heinl, S and Mayrhuber, E and Grabherr, R and Pühler, A and Schwab, H and Schlüter, A}, title = {Metagenome analyses reveal the influence of the inoculant Lactobacillus buchneri CD034 on the microbial community involved in grass ensiling.}, journal = {Journal of biotechnology}, volume = {167}, number = {3}, pages = {334-343}, doi = {10.1016/j.jbiotec.2013.07.021}, pmid = {23880441}, issn = {1873-4863}, mesh = {Bacteria/*classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; Fermentation ; Lactobacillus/*classification/genetics/isolation & purification ; Metagenome/*genetics ; Microbial Consortia/*genetics ; Poaceae ; RNA, Ribosomal, 16S/genetics ; Silage/*microbiology ; }, abstract = {Silage is green fodder conserved by lactic acid fermentation performed by epiphytic lactic acid bacteria under anaerobic conditions. To improve the ensiling process and the quality of the resulting silage, starter cultures are added to the fresh forage. A detailed analysis of the microbial community playing a role in grass ensiling has been carried out by high throughput sequencing technologies. Moreover, the influence of the inoculant Lactobacillus buchneri CD034 on the microbial community composition was studied. For this purpose, grass was ensiled untreated or inoculated with L. buchneri CD034. The fresh forage as well as silages after 14 and 58 days of fermentation were characterized physico-chemically. Characteristic silage conditions such as increased titers of lactic acid bacteria and higher concentrations of acetic acid were observed in the inoculated silage in comparison to the untreated samples. Taxonomic community profiles deduced from 16S rDNA amplicon sequences indicated that the relative abundance of Lactococci diminished in the course of fermentations and that the proportion of bacteria belonging to the phyla Proteobacteria and Bacteroidetes increased during the fermentation of untreated silage. In the inoculated silage, members of these phyla were repressed due to an increased abundance of Lactobacilli. In addition, metagenome analyses of silage samples confirmed taxonomic profiles based on 16S rDNA amplicons. Moreover, Lactobacillus plantarum, Lactobacillus brevis and Lactococcus lactis were found to be dominant species within silages as analyzed by means of fragment recruitments of metagenomic sequence reads on complete reference genome sequences. Fragment recruitments also provided clear evidence for the competitiveness of the inoculant strain L. buchneri CD034 during the fermentation of the inoculated silage. The inoculation strain was able to outcompete other community members and also affected physico-chemical characteristics of the silage.}, } @article {pmid23877117, year = {2013}, author = {Hu, Y and Yang, X and Qin, J and Lu, N and Cheng, G and Wu, N and Pan, Y and Li, J and Zhu, L and Wang, X and Meng, Z and Zhao, F and Liu, D and Ma, J and Qin, N and Xiang, C and Xiao, Y and Li, L and Yang, H and Wang, J and Yang, R and Gao, GF and Wang, J and Zhu, B}, title = {Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {2151}, doi = {10.1038/ncomms3151}, pmid = {23877117}, issn = {2041-1723}, mesh = {Asian People ; Drug Resistance, Multiple, Bacterial/*genetics ; Gastrointestinal Tract/*microbiology ; *Genes, Bacterial ; Humans ; *Metagenome ; Microbiota/*genetics ; Multigene Family ; Phylogeny ; White People ; }, abstract = {The human gut microbiota is a reservoir of antibiotic resistance genes, but little is known about their diversity and richness within the gut. Here we analyse the antibiotic resistance genes of gut microbiota from 162 individuals. We identify a total of 1,093 antibiotic resistance genes and find that Chinese individuals harbour the highest number and abundance of antibiotic resistance genes, followed by Danish and Spanish individuals. Single-nucleotide polymorphism-based analysis indicates that antibiotic resistance genes from the two European populations are more closely related while the Chinese ones are clustered separately. We also confirm high abundance of tetracycline resistance genes with this large cohort study. Our study provides a broad view of antibiotic resistance genes in the human gut microbiota.}, } @article {pmid23871656, year = {2013}, author = {Soh, J and Dong, X and Caffrey, SM and Voordouw, G and Sensen, CW}, title = {Phoenix 2: a locally installable large-scale 16S rRNA gene sequence analysis pipeline with Web interface.}, journal = {Journal of biotechnology}, volume = {167}, number = {4}, pages = {393-403}, doi = {10.1016/j.jbiotec.2013.07.004}, pmid = {23871656}, issn = {1873-4863}, mesh = {Algorithms ; Biodiversity ; Cluster Analysis ; Computational Biology/*methods ; *Genes, rRNA ; *Internet ; Metagenomics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/classification/*genetics ; *Sequence Analysis ; Software ; }, abstract = {We have developed Phoenix 2, a ribosomal RNA gene sequence analysis pipeline, which can be used to process large-scale datasets consisting of more than one hundred environmental samples and containing more than one million reads collectively. Rapid handling of large datasets is made possible by the removal of redundant sequences, pre-partitioning of sequences, parallelized clustering per partition, and subsequent merging of clusters. To build the pipeline, we have used a combination of open-source software tools and custom-developed Perl scripts. For our project we utilize hardware-accelerated searches, but it is possible to reconfigure the analysis pipeline for use with generic computing infrastructure only, with a considerable reduction in speed. The set of analysis results produced by Phoenix 2 is comprehensive, including taxonomic annotations using multiple methods, alpha diversity indices, beta diversity measurements, and a number of visualizations. To date, the pipeline has been used to analyze more than 1500 environmental samples from a wide variety of microbial communities, which are part of our Hydrocarbon Metagenomics Project (http://www.hydrocarbonmetagenomics.com). The software package can be installed as a local software suite with a Web interface. Phoenix 2 is freely available from http://sourceforge.net/projects/phoenix2.}, } @article {pmid23871375, year = {2013}, author = {Ross, EM and Moate, PJ and Marett, L and Cocks, BG and Hayes, BJ}, title = {Investigating the effect of two methane-mitigating diets on the rumen microbiome using massively parallel sequencing.}, journal = {Journal of dairy science}, volume = {96}, number = {9}, pages = {6030-6046}, doi = {10.3168/jds.2013-6766}, pmid = {23871375}, issn = {1525-3198}, mesh = {Animals ; Cattle/microbiology ; Diet/*veterinary ; Feces/microbiology ; High-Throughput Nucleotide Sequencing/methods/*veterinary ; Metagenome/genetics ; Methane/*biosynthesis ; Microbiota/drug effects/*genetics ; Rumen/drug effects/*microbiology ; }, abstract = {Variation in the composition of microorganisms in the rumen (the rumen microbiome) of dairy cattle (Bos taurus) is of great interest because of possible links to methane emission levels. Feed additives are one method being investigated to reduce enteric methane production by dairy cattle. Here we report the effect of 2 methane-mitigating feed additives (grapemarc and a combination of lipids and tannin) on rumen microbiome profiles of Holstein dairy cattle. We used untargeted (shotgun) massively parallel sequencing of microbes present in rumen fluid to generate quantitative rumen microbiome profiles. We observed large effects of the feed additives on the rumen microbiome profiles using multiple approaches, including linear mixed modeling, hierarchical clustering, and metagenomic predictions. The effect on the fecal microbiome profiles was not detectable using hierarchical clustering, but was significant in the linear mixed model and when metagenomic predictions were used, suggesting a more subtle effect of the diets on the lower gastrointestinal microbiome. A differential representation analysis (analogous to differential expression in RNA sequencing) showed significant overlap in the contigs (which are genome fragments representing different microorganism species) that were differentially represented between experiments. These similarities suggest that, despite the different additives used, the 2 diets assessed in this investigation altered the microbiomes of the samples in similar ways. Contigs that were differentially represented in both experiments were tested for associations with methane production in an independent set of animals. These animals were not treated with a methane-mitigating diet, but did show substantial natural variation in methane emission levels. The contigs that were significantly differentially represented in response to both dietary additives showed a significant enrichment for associations with methane production. This suggests that these methane-mitigating diets have altered the rumen microbiome toward naturally low methane-emitting microbial profiles. The contig sequences are predominantly new and include Faecalibacterium spp. The contigs we have identified here are potential biomarkers for low-methane-emitting cattle.}, } @article {pmid23870802, year = {2013}, author = {Blottière, HM and de Vos, WM and Ehrlich, SD and Doré, J}, title = {Human intestinal metagenomics: state of the art and future.}, journal = {Current opinion in microbiology}, volume = {16}, number = {3}, pages = {232-239}, doi = {10.1016/j.mib.2013.06.006}, pmid = {23870802}, issn = {1879-0364}, mesh = {Gastrointestinal Tract/*microbiology ; Humans ; Metagenomics/*methods ; *Microbiota ; }, abstract = {Over the last few years our understanding of human biology has undergone profound transformation. The key role of the 'world inside us', namely the gut microbiota, once considered a forgotten organ, has been revealed, with strong impact on our health and well-being. The present review highlights the most important recent findings on the role of gut microbiota and its impact on the host and raises crucial questions to be considered in future studies.}, } @article {pmid23869970, year = {2013}, author = {Burke, KE and Lamont, JT}, title = {Fecal transplantation for recurrent Clostridium difficile infection in older adults: a review.}, journal = {Journal of the American Geriatrics Society}, volume = {61}, number = {8}, pages = {1394-1398}, doi = {10.1111/jgs.12378}, pmid = {23869970}, issn = {1532-5415}, mesh = {Aged ; Aged, 80 and over ; *Clostridioides difficile/genetics/pathogenicity ; Enterocolitis, Necrotizing/microbiology/*therapy ; Feces/*microbiology ; Female ; Follow-Up Studies ; Genotype ; Humans ; Male ; *Metagenome ; Middle Aged ; Randomized Controlled Trials as Topic ; Recurrence ; *Transplants ; Treatment Failure ; Virulence/genetics ; }, abstract = {Recurrent Clostridium difficile infection (CDI) is a common nosocomial infection that has a large effect on morbidity and quality of life in older adults in hospitals and long-term care facilities. Because antibiotics are often unsuccessful in curing this disease, fecal transplantation has emerged as a second-line therapy for treatment of recurrent CDI. A comprehensive literature search of PubMed, Embase, and Web of Science regarding fecal transplantation for CDI was performed to further evaluate the efficacy and side effects of this promising therapy in older adults. Data were extracted from 10 published articles from 1984 to the present that met inclusion criteria, including nine open-label reports and one randomized controlled trial. Baseline characteristics and outcomes of individuals undergoing fecal transplantation and effects of fecal transplantation on the fecal microflora were reviewed. Methods of fecal transplantation and donor selection were reviewed. Fecal transplantation was performed in 115 individuals aged 60 to 101, with a female predominance. CDI cure was achieved in 103 (89.6%) individuals over a follow-up period of 2 months to 5 years (mean 5.9 months). There was no significant difference in cure rate between older and younger participants in included studies. Most failed transplantation occurred in individuals infected with the aggressive NAP1/027 strain of C. difficile. Microbiological studies of fecal biodiversity before and after fecal transplantation demonstrated greater bacterial diversity and shift in flora species to resemble donor flora after transplantation that correlated with clinical remission. Fecal transplantation provides a safe and durable cure for older adults with recurrent CDI.}, } @article {pmid23868401, year = {2013}, author = {Mobberley, JM and Khodadad, CL and Foster, JS}, title = {Metabolic potential of lithifying cyanobacteria-dominated thrombolitic mats.}, journal = {Photosynthesis research}, volume = {118}, number = {1-2}, pages = {125-140}, pmid = {23868401}, issn = {1573-5079}, support = {NNX12AD64G/NASA/NASA/United States ; }, mesh = {Carbonates/*metabolism ; Cyanobacteria/genetics/*metabolism ; Ecosystem ; Genes, Bacterial ; *Metagenome ; Microarray Analysis ; *Microbial Consortia ; Sequence Analysis, DNA ; }, abstract = {Thrombolites are unlaminated carbonate deposits formed by the metabolic activities of microbial mats and can serve as potential models for understanding the molecular mechanisms underlying the formation of lithifying communities. To assess the metabolic complexity of these ecosystems, high throughput DNA sequencing of a thrombolitic mat metagenome was coupled with phenotypic microarray analysis. Functional protein analysis of the thrombolite community metagenome delineated several of the major metabolic pathways that influence carbonate mineralization including cyanobacterial photosynthesis, sulfate reduction, sulfide oxidation, and aerobic heterotrophy. Spatial profiling of metabolite utilization within the thrombolite-forming microbial mats suggested that the top 5 mm contained a more metabolically diverse and active community than the deeper within the mat. This study provides evidence that despite the lack of mineral layering within the clotted thrombolite structure there is a vertical gradient of metabolic activity within the thrombolitic mat community. This metagenomic profiling also serves as a foundation for examining the active role individual functional groups of microbes play in coordinating metabolisms that lead to mineralization.}, } @article {pmid23864575, year = {2013}, author = {Terpend, K and Possemiers, S and Daguet, D and Marzorati, M}, title = {Arabinogalactan and fructo-oligosaccharides have a different fermentation profile in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME ®).}, journal = {Environmental microbiology reports}, volume = {5}, number = {4}, pages = {595-603}, doi = {10.1111/1758-2229.12056}, pmid = {23864575}, issn = {1758-2229}, mesh = {Bacteria/*classification/*metabolism ; *Biota ; Butyrates/metabolism ; Chromatography, Gel ; Denaturing Gradient Gel Electrophoresis ; Enzymes/analysis ; Fermentation ; Galactans/*metabolism ; Gastrointestinal Tract/*microbiology ; Humans ; Hydrogen-Ion Concentration ; *Metagenome ; Models, Theoretical ; Oligosaccharides/*metabolism ; Propionates/metabolism ; Quaternary Ammonium Compounds/metabolism ; Real-Time Polymerase Chain Reaction ; }, abstract = {Current prebiotics, such as fructo-oligosaccharides (FOS), are limited in their persistence in the distal colon and are predominantly fermented in the proximal colon. In order to identify a potential alternative, the differences in the fermentation profile of arabinogalactan (AG) and FOS have been assessed in the Simulator of the Human Intestinal Microbial Ecosystem. The effect of each product on the composition and activity of the microbial community was analysed during a 3-week treatment period at a dose of 5 g day(-1). While FOS indeed was mainly fermented in the simulated proximal colon, AG was still available for fermentation in the simulated distal colon as shown by pH profiles, size exclusion chromatography and analyses of specific enzymatic activities. As a consequence, the main effect of the products (increase in propionate and butyrate and decrease in ammonium production) occurred in different intestinal areas. DGGE and qPCR analyses confirmed that the main modulation of the microbiota by the two products occurred in different areas of the gut. AG was associated with a statistically significant increase in the concentration of total bacteria, Bacteroidetes, Faecalibacterium prausnitzii, a delayed bifidogenic effect and a decrease of the pathogenic Clostridium perfringens. FOS led to a strong lactobacillogenic effect.}, } @article {pmid23864572, year = {2013}, author = {Bowman, JS and Larose, C and Vogel, TM and Deming, JW}, title = {Selective occurrence of Rhizobiales in frost flowers on the surface of young sea ice near Barrow, Alaska and distribution in the polar marine rare biosphere.}, journal = {Environmental microbiology reports}, volume = {5}, number = {4}, pages = {575-582}, doi = {10.1111/1758-2229.12047}, pmid = {23864572}, issn = {1758-2229}, mesh = {Alaska ; Alphaproteobacteria/*classification/*isolation & purification ; Arctic Regions ; *Biodiversity ; Cloning, Molecular ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics/isolation & purification ; DNA, Ribosomal/chemistry/genetics/isolation & purification ; Ice Cover/*microbiology ; Microarray Analysis ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Frost flowers are highly saline ice structures that grow on the surface of young sea ice, a spatially extensive environment of increasing importance in the Arctic Ocean. In a previous study, we reported organic components of frost flowers in the form of elevated levels of bacteria and exopolymers relative to underlying ice. Here, DNA was extracted from frost flowers and young sea ice, collected in springtime from a frozen lead offshore of Barrow, Alaska, to identify bacteria in these understudied environments. Evaluation of the distribution of 16S rRNA genes via four methods (microarray analysis, T-RFLP, clone library and shotgun metagenomic sequencing) indicated distinctive bacterial assemblages between the two environments, with frost flowers appearing to select for Rhizobiales. A phylogenetic placement approach, used to evaluate the distribution of similar Rhizobiales sequences in other polar marine studies, indicated that some of the observed strains represent widely distributed members of the marine rare biosphere in both the Arctic and Antarctic.}, } @article {pmid23864568, year = {2013}, author = {Bakke, I and Skjermo, J and Vo, TA and Vadstein, O}, title = {Live feed is not a major determinant of the microbiota associated with cod larvae (Gadus morhua).}, journal = {Environmental microbiology reports}, volume = {5}, number = {4}, pages = {537-548}, doi = {10.1111/1758-2229.12042}, pmid = {23864568}, issn = {1758-2229}, mesh = {Animal Feed/*microbiology ; Animals ; *Biodiversity ; Denaturing Gradient Gel Electrophoresis ; Diet/methods ; Gadus morhua/*microbiology ; Gastrointestinal Tract/*microbiology ; Larva/microbiology ; *Metagenome ; Polymerase Chain Reaction ; }, abstract = {The gastrointestinal (GI) tract of newly hatched fish is probably colonized by bacteria present in the water, but how environmental and internal factors affect the development of the GI microbiota is poorly understood. In this study, we investigated the effect of diet and of rearing in separate tanks on the cod larval microbiota. Cod larvae were fed three different live feed diets. For each diet, larvae were reared in three replicate tanks. The microbial communities were investigated for water, live feed and individual larvae using a PCR/DGGE (Denaturing Gradient Gel Electrophoresis) strategy. Statistical tests were applied to investigate differences in the larval microbiota between groups of individuals. We found no differences in the larval microbiota due to diet after 8 dph (days post hatching). Moreover, the larval microbiota was similar at 17 and 32 dph, despite a change in live feed at 18 dph. The larval microbiota was generally more similar to the water microbiota than to live feed microbiota. We further found that rearing of larvae in replicate tanks with identical diet could result in significant differences in larval microbiota. These findings indicate that diet does not entail major changes to the composition of cod larval microbiota.}, } @article {pmid23861384, year = {2013}, author = {Lozupone, CA and Stombaugh, J and Gonzalez, A and Ackermann, G and Wendel, D and Vázquez-Baeza, Y and Jansson, JK and Gordon, JI and Knight, R}, title = {Meta-analyses of studies of the human microbiota.}, journal = {Genome research}, volume = {23}, number = {10}, pages = {1704-1714}, pmid = {23861384}, issn = {1549-5469}, support = {K01 DK090285/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; K01DK090285/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Aging ; Bacteria/*classification/genetics ; Biodiversity ; Crohn Disease/epidemiology/genetics/microbiology ; DNA, Bacterial/*genetics ; Feces/*microbiology ; Female ; Humans ; Infant ; Metagenome ; Metagenomics/*methods ; *Microbiota ; Pregnancy ; Pregnancy Trimester, First ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {Our body habitat-associated microbial communities are of intense research interest because of their influence on human health. Because many studies of the microbiota are based on the same bacterial 16S ribosomal RNA (rRNA) gene target, they can, in principle, be compared to determine the relative importance of different disease/physiologic/developmental states. However, differences in experimental protocols used may produce variation that outweighs biological differences. By comparing 16S rRNA gene sequences generated from diverse studies of the human microbiota using the QIIME database, we found that variation in composition of the microbiota across different body sites was consistently larger than technical variability across studies. However, samples from different studies of the Western adult fecal microbiota generally clustered by study, and the 16S rRNA target region, DNA extraction technique, and sequencing platform produced systematic biases in observed diversity that could obscure biologically meaningful compositional differences. In contrast, systematic compositional differences in the fecal microbiota that occurred with age and between Western and more agrarian cultures were great enough to outweigh technical variation. Furthermore, individuals with ileal Crohn's disease and in their third trimester of pregnancy often resembled infants from different studies more than controls from the same study, indicating parallel compositional attributes of these distinct developmental/physiological/disease states. Together, these results show that cross-study comparisons of human microbiota are valuable when the studied parameter has a large effect size, but studies of more subtle effects on the human microbiota require carefully selected control populations and standardized protocols.}, } @article {pmid23860099, year = {2013}, author = {Zhang, C and Li, S and Yang, L and Huang, P and Li, W and Wang, S and Zhao, G and Zhang, M and Pang, X and Yan, Z and Liu, Y and Zhao, L}, title = {Structural modulation of gut microbiota in life-long calorie-restricted mice.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {2163}, pmid = {23860099}, issn = {2041-1723}, support = {R01 AR050429/AR/NIAMS NIH HHS/United States ; }, mesh = {Acute-Phase Proteins/genetics ; Age Factors ; Animals ; Caloric Restriction ; Carrier Proteins/*blood/genetics ; DNA, Bacterial/classification/*genetics/metabolism ; *Diet, Fat-Restricted ; Diet, High-Fat ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Lipopolysaccharides/blood ; Membrane Glycoproteins/*blood/genetics ; *Metagenome ; Mice ; Mice, Inbred C57BL ; Microbiota/*genetics ; Phylogeny ; }, abstract = {Calorie restriction has been regarded as the only experimental regimen that can effectively lengthen lifespan in various animal models, but the actual mechanism remains controversial. The gut microbiota has been shown to have a pivotal role in host health, and its structure is mostly shaped by diet. Here we show that life-long calorie restriction on both high-fat or low-fat diet, but not voluntary exercise, significantly changes the overall structure of the gut microbiota of C57BL/6 J mice. Calorie restriction enriches phylotypes positively correlated with lifespan, for example, the genus Lactobacillus on low-fat diet, and reduces phylotypes negatively correlated with lifespan. These calorie restriction-induced changes in the gut microbiota are concomitant with significantly reduced serum levels of lipopolysaccharide-binding protein, suggesting that animals under calorie restriction can establish a structurally balanced architecture of gut microbiota that may exert a health benefit to the host via reduction of antigen load from the gut.}, } @article {pmid23858463, year = {2013}, author = {Levy, R and Borenstein, E}, title = {Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {31}, pages = {12804-12809}, pmid = {23858463}, issn = {1091-6490}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; }, mesh = {Genome, Bacterial/*physiology ; Host-Parasite Interactions/*physiology ; Humans ; Microbiota/*physiology ; *Models, Biological ; }, abstract = {The human microbiome plays a key role in human health and is associated with numerous diseases. Metagenomic-based studies are now generating valuable information about the composition of the microbiome in health and in disease, demonstrating nonneutral assembly processes and complex co-occurrence patterns. However, the underlying ecological forces that structure the microbiome are still unclear. Specifically, compositional studies alone with no information about mechanisms of interaction, potential competition, or syntrophy, cannot clearly distinguish habitat-filtering and species assortment assembly processes. To address this challenge, we introduce a computational framework, integrating metagenomic-based compositional data with genome-scale metabolic modeling of species interaction. We use in silico metabolic network models to predict levels of competition and complementarity among 154 microbiome species and compare predicted interaction measures to species co-occurrence. Applying this approach to two large-scale datasets describing the composition of the gut microbiome, we find that species tend to co-occur across individuals more frequently with species with which they strongly compete, suggesting that microbiome assembly is dominated by habitat filtering. Moreover, species' partners and excluders exhibit distinct metabolic interaction levels. Importantly, we show that these trends cannot be explained by phylogeny alone and hold across multiple taxonomic levels. Interestingly, controlling for host health does not change the observed patterns, indicating that the axes along which species are filtered are not fully defined by macroecological host states. The approach presented here lays the foundation for a reverse-ecology framework for addressing key questions concerning the assembly of host-associated communities and for informing clinical efforts to manipulate the microbiome.}, } @article {pmid23853523, year = {2013}, author = {Emerson, JB and Andrade, K and Thomas, BC and Norman, A and Allen, EE and Heidelberg, KB and Banfield, JF}, title = {Virus-host and CRISPR dynamics in Archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2013}, number = {}, pages = {370871}, pmid = {23853523}, issn = {1472-3654}, mesh = {Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; DNA, Archaeal/analysis/genetics ; DNA, Bacterial/analysis/genetics ; DNA, Intergenic/analysis/genetics ; DNA, Viral/analysis/genetics ; *Inverted Repeat Sequences ; Lakes/*microbiology ; Metagenomics ; Microbial Consortia/*genetics ; Plankton ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Victoria ; Viruses/*genetics/metabolism ; }, abstract = {The study of natural archaeal assemblages requires community context, namely, a concurrent assessment of the dynamics of archaeal, bacterial, and viral populations. Here, we use filter size-resolved metagenomic analyses to report the dynamics of 101 archaeal and bacterial OTUs and 140 viral populations across 17 samples collected over different timescales from 2007-2010 from Australian hypersaline Lake Tyrrell (LT). All samples were dominated by Archaea (75-95%). Archaeal, bacterial, and viral populations were found to be dynamic on timescales of months to years, and different viral assemblages were present in planktonic, relative to host-associated (active and provirus) size fractions. Analyses of clustered regularly interspaced short palindromic repeat (CRISPR) regions indicate that both rare and abundant viruses were targeted, primarily by lower abundance hosts. Although very few spacers had hits to the NCBI nr database or to the 140 LT viral populations, 21% had hits to unassembled LT viral concentrate reads. This suggests local adaptation to LT-specific viruses and/or undersampling of haloviral assemblages in public databases, along with successful CRISPR-mediated maintenance of viral populations at abundances low enough to preclude genomic assembly. This is the first metagenomic report evaluating widespread archaeal dynamics at the population level on short timescales in a hypersaline system.}, } @article {pmid23852605, year = {2013}, author = {Elinav, E and Thaiss, CA and Flavell, RA}, title = {Analysis of microbiota alterations in inflammasome-deficient mice.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1040}, number = {}, pages = {185-194}, doi = {10.1007/978-1-62703-523-1_14}, pmid = {23852605}, issn = {1940-6029}, mesh = {Animals ; Inflammasomes/*deficiency ; Intestines/microbiology ; Metagenome ; Mice ; Mice, Knockout/*microbiology ; *Microbiota ; Mouth/microbiology ; }, abstract = {Inflammasomes have emerged as central regulators of intestinal infection, immunity, and inflammation. Inflammasome activity mediates intestinal epithelial integrity, antimicrobial responses, and initiates inflammation through generation of the cytokines interleukin (IL-)1 and IL-18. Recent studies have identified an additional layer of inflammasome function in the intestine, namely, the control of intestinal microflora composition. Inflammasome-deficient mice show an aberrant microbial community which is dominantly transmissible to healthy mice. This dysbiosis in inflammasome-deficient mice has a profound impact on their physiology and pathophysiology, both locally in the intestine and systemically. Therefore, it is essential to consider the influence of the composition of microbial communities on experiments performed with inflammasome-deficient and other innate molecule-deficient mice, and to conduct experiments to control for potential dominant effects of the microflora on host responses. In this chapter, we provide experimental procedures to monitor inflammasome-mediated modifications of the intestinal microflora composition in mice and to test the resultant functional consequences of these changes in microbial communities and their transmission to cohoused mice.}, } @article {pmid23852569, year = {2013}, author = {Borody, TJ and Paramsothy, S and Agrawal, G}, title = {Fecal microbiota transplantation: indications, methods, evidence, and future directions.}, journal = {Current gastroenterology reports}, volume = {15}, number = {8}, pages = {337}, pmid = {23852569}, issn = {1534-312X}, mesh = {Biological Therapy/*methods/trends ; Enterocolitis, Pseudomembranous/*therapy ; Evidence-Based Medicine/methods ; Feces/*microbiology ; Gastrointestinal Tract/microbiology ; Humans ; Inflammatory Bowel Diseases/*therapy ; Irritable Bowel Syndrome/therapy ; Microbiota ; }, abstract = {Fecal microbiota transplantation (FMT) has attracted great interest in recent years, largely due to the global Clostridium difficile infection (CDI) epidemic and major advances in metagenomic sequencing of the gastrointestinal (GI) microbiota, with growing understanding of its structure and function. FMT is now recommended as the most effective therapy for relapsing CDI and, with further refinement, may even be used in "first-time" CDI. There is interest also in other conditions related to GI dysbiosis--for example, inflammatory bowel disease, irritable bowel syndrome, obesity, and diabetes mellitus--although quality evidence is at present lacking. A few trials are now underway in FMT for ulcerative colitis. Many unanswered questions remain, including FMT methodology--for example, optimal route of administration, what makes a "good donor," safety issues, and long-term effects of FMT.}, } @article {pmid23848937, year = {2013}, author = {Geller, J and Meyer, C and Parker, M and Hawk, H}, title = {Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all-taxa biotic surveys.}, journal = {Molecular ecology resources}, volume = {13}, number = {5}, pages = {851-861}, doi = {10.1111/1755-0998.12138}, pmid = {23848937}, issn = {1755-0998}, mesh = {Animals ; Aquatic Organisms/*classification/genetics ; *Biota ; California ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Invertebrates/*classification/genetics ; Polymerase Chain Reaction/methods ; Polynesia ; United States ; }, abstract = {DNA barcoding is a powerful tool for species detection, identification and discovery. Metazoan DNA barcoding is primarily based upon a specific region of the cytochrome c oxidase subunit I gene that is PCR amplified by primers HCO2198 and LCO1490 ('Folmer primers') designed by Folmer et al. (Molecular Marine Biology and Biotechnology, 3, 1994, 294). Analysis of sequences published since 1994 has revealed mismatches in the Folmer primers to many metazoans. These sequences also show that an extremely high level of degeneracy would be necessary in updated Folmer primers to maintain broad taxonomic utility. In primers jgHCO2198 and jgLCO1490, we replaced most fully degenerated sites with inosine nucleotides that complement all four natural nucleotides and modified other sites to better match major marine invertebrate groups. The modified primers were used to amplify and sequence cytochrome c oxidase subunit I from 9105 specimens from Moorea, French Polynesia and San Francisco Bay, California, USA representing 23 phyla, 42 classes and 121 orders. The new primers, jgHCO2198 and jgLCO1490, are well suited for routine DNA barcoding, all-taxon surveys and metazoan metagenomics.}, } @article {pmid23848071, year = {2013}, author = {Robles-Alonso, V and Guarner, F}, title = {[Progress in the knowledge of the intestinal human microbiota].}, journal = {Nutricion hospitalaria}, volume = {28}, number = {3}, pages = {553-557}, doi = {10.3305/nh.2013.28.3.6601}, pmid = {23848071}, issn = {1699-5198}, mesh = {Gastrointestinal Tract/microbiology ; Humans ; Intestines/*microbiology ; *Microbiota ; }, abstract = {New sequencing technologies together with the development of bio-informatics allow a description of the full spectrum of the microbial communities that inhabit the human intestinal tract, as well as their functional contributions to host health. Most community members belong to the domain Bacteria, but Archaea, Eukaryotes (yeasts and protists), and Viruses are also present. Only 7 to 9 of the 55 known divisions or phyla of the domain Bacteria are detected in faecal or mucosal samples from the human gut. Most taxa belong to just two divisions: Bacteroidetes and Firmicutes, and the other divisions that have been consistently found are Proteobacteria, Actinobacteria, Fusobacteria, and Verrucomicrobia. Bacteroides, Faecalibacterium and Bifidobacterium are the most abundant genera but their relative proportion is highly variable across individuals. Full metagenomic analysis has identified more than 5 million non-redundant microbial genes encoding up to 20,000 biological functions related with life in the intestinal habitat. The overall structure of predominant genera in the human gut can be assigned into three robust clusters, which are known as "enterotypes". Each of the three enterotypes is identifiable by the levels of one of three genera: Bacteroides (enterotype 1), Prevotella (enterotype 2) and Ruminococcus (enterotype 3). This suggests that microbiota variations across individuals are stratified, not continuous. Next steps include the identification of changes that may play a role in certain disease states. A better knowledge of the contributions of microbial symbionts to host health will help in the design of interventions to improve symbiosis and combat disease.}, } @article {pmid23844187, year = {2013}, author = {Kang, DW and Park, JG and Ilhan, ZE and Wallstrom, G and Labaer, J and Adams, JB and Krajmalnik-Brown, R}, title = {Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e68322}, pmid = {23844187}, issn = {1932-6203}, mesh = {Adolescent ; Autistic Disorder/*complications/*epidemiology ; Bacteroidaceae Infections/*complications/*epidemiology ; Biodiversity ; Child ; Child, Preschool ; Cluster Analysis ; Female ; Gastrointestinal Diseases/complications/epidemiology/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Incidence ; Male ; Metagenome ; Microbiota ; Phylogeny ; Prevotella/classification/genetics/*isolation & purification ; ROC Curve ; }, abstract = {High proportions of autistic children suffer from gastrointestinal (GI) disorders, implying a link between autism and abnormalities in gut microbial functions. Increasing evidence from recent high-throughput sequencing analyses indicates that disturbances in composition and diversity of gut microbiome are associated with various disease conditions. However, microbiome-level studies on autism are limited and mostly focused on pathogenic bacteria. Therefore, here we aimed to define systemic changes in gut microbiome associated with autism and autism-related GI problems. We recruited 20 neurotypical and 20 autistic children accompanied by a survey of both autistic severity and GI symptoms. By pyrosequencing the V2/V3 regions in bacterial 16S rDNA from fecal DNA samples, we compared gut microbiomes of GI symptom-free neurotypical children with those of autistic children mostly presenting GI symptoms. Unexpectedly, the presence of autistic symptoms, rather than the severity of GI symptoms, was associated with less diverse gut microbiomes. Further, rigorous statistical tests with multiple testing corrections showed significantly lower abundances of the genera Prevotella, Coprococcus, and unclassified Veillonellaceae in autistic samples. These are intriguingly versatile carbohydrate-degrading and/or fermenting bacteria, suggesting a potential influence of unusual diet patterns observed in autistic children. However, multivariate analyses showed that autism-related changes in both overall diversity and individual genus abundances were correlated with the presence of autistic symptoms but not with their diet patterns. Taken together, autism and accompanying GI symptoms were characterized by distinct and less diverse gut microbial compositions with lower levels of Prevotella, Coprococcus, and unclassified Veillonellaceae.}, } @article {pmid23844136, year = {2013}, author = {Dias, AC and Dini-Andreote, F and Hannula, SE and Andreote, FD and Pereira E Silva, Mde C and Salles, JF and de Boer, W and van Veen, J and van Elsas, JD}, title = {Different selective effects on rhizosphere bacteria exerted by genetically modified versus conventional potato lines.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e67948}, pmid = {23844136}, issn = {1932-6203}, mesh = {Bacteria/classification/*genetics/*metabolism ; Biodiversity ; Biomarkers/metabolism ; Fatty Acids/chemistry/metabolism ; Metagenome ; Microbiota ; Phenotype ; Phospholipids/chemistry/metabolism ; Phylogeny ; Plant Roots/microbiology ; Plants, Genetically Modified ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil Microbiology ; Solanum tuberosum/genetics/growth & development/*microbiology ; }, abstract = {BACKGROUND: In this study, we assessed the actively metabolizing bacteria in the rhizosphere of potato using two potato cultivars, i.e. the genetically-modified (GM) cultivar Modena (having tubers with altered starch content) and the near-isogenic non-GM cultivar Karnico. To achieve our aims, we pulse-labelled plants at EC90 stage with (13)C-CO2 and analysed their rhizosphere microbial communities 24 h, 5 and 12 days following the pulse. In the analyses, phospholipid fatty acid/stable isotope probing (PLFA-SIP) as well as RNA-SIP followed by reverse transcription and PCR-DGGE and clone library analysis, were used to determine the bacterial groups that actively respond to the root-released (13)C labelled carbonaceous compounds.

The PLFA-SIP data revealed major roles of bacteria in the uptake of root-released (13)C carbon, which grossly increased with time. Gram-negative bacteria, including members of the genera Pseudomonas and Burkholderia, were strong accumulators of the (13)C-labeled compounds at the two cultivars, whereas Gram-positive bacteria were lesser responders. PCR-DGGE analysis of cDNA produced from the two cultivar types showed that these had selected different bacterial, alpha- and betaproteobacterial communities at all time points. Moreover, an effect of time was observed, indicating dynamism in the structure of the active bacterial communities. PCR-DGGE as well as clone library analyses revealed that the main bacterial responders at cultivar Karnico were taxonomically affiliated with the genus Pseudomonas, next to Gluconacetobacter and Paracoccus. Cultivar Modena mainly attracted Burkholderia, next to Moraxella-like (Moraxellaceae family) and Sphingomonas types.

CONCLUSIONS/SIGNIFICANCE: Based on the use of Pseudomonas and Burkholderia as proxies for differentially-selected bacterial genera, we conclude that the selective forces exerted by potato cultivar Modena on the active bacterial populations differed from those exerted by cultivar Karnico.}, } @article {pmid23844068, year = {2013}, author = {Lazarevic, V and Gaïa, N and Girard, M and François, P and Schrenzel, J}, title = {Comparison of DNA extraction methods in analysis of salivary bacterial communities.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e67699}, pmid = {23844068}, issn = {1932-6203}, mesh = {Adult ; Bacteria/*classification/*genetics/isolation & purification ; Biodiversity ; Cluster Analysis ; Computational Biology/methods ; DNA, Bacterial/genetics/isolation & purification ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Microbiota ; RNA, Ribosomal, 16S ; Saliva/*microbiology ; }, abstract = {Culture-independent high-throughput sequencing-based methods are widely used to study bacterial communities. Although these approaches are superior to traditional culture-based methods, they introduce bias at the experimental and bioinformatics levels. We assessed the diversity of the human salivary microbiome by pyrosequencing of the 16S rDNA V1-3 amplicons using metagenomic DNA extracted by two different protocols: a simple proteinase K digestion without a subsequent DNA clean-up step, and a bead-beating mechanical lysis protocol followed by column DNA purification. A high degree of congruence was found between the two extraction methods, most notably in regard to the microbial community composition. The results showed that for a given bioinformatics pipeline, all the taxa with an average proportion >0.12% in samples processed using one extraction method were also detected in samples extracted using the other method. The same taxa tended to be abundant and frequent for both extraction methods. The relative abundance of sequence reads assigned to the phyla Actinobacteria, Spirochaetes, TM7, Synergistetes, and Tenericutes was significantly higher in the mechanically-treated samples than in the enzymatically-treated samples, whereas the phylum Firmicutes showed the opposite pattern. No significant differences in diversity indices were found between the extraction methods, although the mechanical lysis method revealed higher operational taxonomic unit richness. Differences between the extraction procedures outweighed the variations due to the bioinformatics analysis pipelines used.}, } @article {pmid23842651, year = {2013}, author = {Tseng, CH and Chiang, PW and Shiah, FK and Chen, YL and Liou, JR and Hsu, TC and Maheswararajah, S and Saeed, I and Halgamuge, S and Tang, SL}, title = {Microbial and viral metagenomes of a subtropical freshwater reservoir subject to climatic disturbances.}, journal = {The ISME journal}, volume = {7}, number = {12}, pages = {2374-2386}, pmid = {23842651}, issn = {1751-7370}, mesh = {Bacteria/genetics ; *Bacterial Physiological Phenomena ; Biodiversity ; Climate ; *Cyclonic Storms ; *Ecosystem ; Fresh Water/*microbiology/*virology ; *Metagenome ; Metagenomics ; Seasons ; *Virus Physiological Phenomena ; Viruses/genetics/ultrastructure ; Water Microbiology ; }, abstract = {Extreme climatic activities, such as typhoons, are widely known to disrupt our natural environment. In particular, studies have revealed that typhoon-induced perturbations can result in several long-term effects on various ecosystems. In this study, we have conducted a 2-year metagenomic survey to investigate the microbial and viral community dynamics associated with environmental changes and seasonal variations in an enclosed freshwater reservoir subject to episodic typhoons. We found that the microbial community structure and the associated metagenomes continuously changed, where microbial richness increased after typhoon events and decreased during winter. Among the environmental factors that influenced changes in the microbial community, precipitation was considered to be the most significant. Similarly, the viral community regularly showed higher relative abundances and diversity during summer in comparison to winter, with major variations happening in several viral families including Siphoviridae, Myoviridae, Podoviridae and Microviridae. Interestingly, we also found that the precipitation level was associated with the terrestrial viral abundance in the reservoir. In contrast to the dynamic microbial community (L-divergence 0.73 ± 0.25), we found that microbial metabolic profiles were relatively less divergent (L-divergence 0.24 ± 0.04) at the finest metabolic resolution. This study provides for the first time a glimpse at the microbial and viral community dynamics of a subtropical freshwater ecosystem, adding a comprehensive set of new knowledge to aquatic environments.}, } @article {pmid23840722, year = {2013}, author = {Lacombe, A and Li, RW and Klimis-Zacas, D and Kristo, AS and Tadepalli, S and Krauss, E and Young, R and Wu, VC}, title = {Lowbush wild blueberries have the potential to modify gut microbiota and xenobiotic metabolism in the rat colon.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e67497}, pmid = {23840722}, issn = {1932-6203}, mesh = {Animals ; Blueberry Plants/*metabolism ; Colon/*metabolism/*microbiology ; Computational Biology/methods ; Diet ; Health Promotion ; Male ; Metagenome ; Microbiota/*genetics ; Rats ; Rats, Sprague-Dawley ; Xenobiotics/*metabolism ; }, abstract = {The gastrointestinal tract is populated by an array of microbial species that play an important role in metabolic and immune functions. The composition of microorganisms is influenced by the components of the host's diet and can impact health. In the present study, dietary enrichment of lowbush wild blueberries (LWB) was examined to determine their effect on colon microbial composition and their potential in promoting gut health. The microbial composition and functional potential of the colon microbiota from Sprague Dawley rats fed control diets (AIN93) and LWB-enriched diets (AIN93+8% LWB powder substituting for dextrose) for 6 weeks were assessed using Illumina shotgun sequencing and bioinformatics tools. Our analysis revealed an alteration in the relative abundance of 3 phyla and 22 genera as representing approximately 14 and 8% of all phyla and genera identified, respectively. The LWB-enriched diet resulted in a significant reduction in the relative abundance of the genera Lactobacillus and Enterococcus. In addition, hierarchal analysis revealed a significant increase in the relative abundance of the phylum Actinobacteria, the order Actinomycetales, and several novel genera under the family Bifidobacteriaceae and Coriobacteriaceae, in the LWB group. Functional annotation of the shotgun sequences suggested that approximately 9% of the 4709 Kyoto Encyclopaedia of Gene and Genome (KEGG) hits identified were impacted by the LWB-diet. Open Reading Frames (ORFs) assigned to KEGG category xenobiotics biodegradation and metabolism were significantly greater in the LWB-enriched diet compared to the control and included the pathway for benzoate degradation [PATH:ko00362] and glycosaminoglycan degradation [PATH:ko00531]. Moreover, the number of ORFs assigned to the bacterial invasion of epithelial cells [PATH:ko05100] pathway was approximately 8 fold lower in the LWB group compared to controls. This study demonstrated that LWBs have the potential to promote gut health and can aid in the development of optimal diets.}, } @article {pmid23836415, year = {2013}, author = {Ursell, LK and Van Treuren, W and Metcalf, JL and Pirrung, M and Gewirtz, A and Knight, R}, title = {Replenishing our defensive microbes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {35}, number = {9}, pages = {810-817}, pmid = {23836415}, issn = {1521-1878}, support = {/HHMI/Howard Hughes Medical Institute/United States ; T32 GM008759/GM/NIGMS NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Disease ; Ecosystem ; Gastrointestinal Tract/immunology/*microbiology ; Host-Pathogen Interactions/immunology ; Humans ; *Metagenome ; *Microbiota ; Probiotics/metabolism ; }, abstract = {Large-scale characterization of the human microbiota has largely focused on Western adults, yet these populations may be uncharacteristic because of their diets and lifestyles. In particular, the rise of "Western diseases" may in part stem from reduced exposure to, or even loss of, microbes with which humans have coevolved. Here, we review beneficial microbes associated with pathogen resistance, highlighting the emerging role of complex microbial communities in protecting against disease. We discuss ways in which modern lifestyles and practices may deplete physiologically important microbiota, and explore prospects for reintroducing or encouraging the growth of beneficial microbes to promote the restoration of healthy microbial ecosystems.}, } @article {pmid23828521, year = {2013}, author = {Ramond, JB and Welz, PJ and Tuffin, MI and Burton, SG and Cowan, DA}, title = {Selection of diazotrophic bacterial communities in biological sand filter mesocosms used for the treatment of phenolic-laden wastewater.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {563-570}, pmid = {23828521}, issn = {1432-184X}, mesh = {Bacteria/classification/*isolation & purification/*metabolism ; Biodegradation, Environmental ; Biodiversity ; Filtration ; Nitrogen/analysis/metabolism ; Phenols/*metabolism ; Phylogeny ; Silicon Dioxide/chemistry ; Wastewater/analysis/microbiology ; Water Pollutants, Chemical/*metabolism ; *Water Purification/instrumentation ; }, abstract = {Agri effluents such as winery or olive mill wastewaters are characterized by high phenolic concentrations. These compounds are highly toxic and generally refractory to biodegradation. Biological sand filters (BSFs) represent inexpensive, environmentally friendly, and sustainable wastewater treatment systems which rely vastly on microbial catabolic processes. Using denaturing gradient gel electrophoresis and terminal-restriction fragment length polymorphism, this study aimed to assess the impact of increasing concentrations of synthetic phenolic-rich wastewater, ranging from 96 mg L(-1) gallic acid and 138 mg L(-1) vanillin (i.e., a total chemical oxygen demand (COD) of 234 mg L(-1)) to 2,400 mg L(-1) gallic acid and 3,442 mg L(-1) vanillin (5,842 mg COD L(-1)), on bacterial communities and the specific functional diazotrophic community from BSF mesocosms. This amendment procedure instigated efficient BSF phenolic removal, significant modifications of the bacterial communities, and notably led to the selection of a phenolic-resistant and less diverse diazotrophic community. This suggests that bioavailable N is crucial in the functioning of biological treatment processes involving microbial communities, and thus that functional alterations in the bacterial communities in BSFs ensure provision of sufficient bioavailable nitrogen for the degradation of wastewater with a high C/N ratio.}, } @article {pmid23810533, year = {2013}, author = {Koskella, B}, title = {Phage-mediated selection on microbiota of a long-lived host.}, journal = {Current biology : CB}, volume = {23}, number = {13}, pages = {1256-1260}, doi = {10.1016/j.cub.2013.05.038}, pmid = {23810533}, issn = {1879-0445}, mesh = {Bacteria/genetics/*virology ; *Bacterial Physiological Phenomena ; Bacteriophages/*physiology ; Biological Evolution ; Colony Count, Microbial ; England ; Microbiota ; Plant Leaves/microbiology/virology ; Seasons ; *Selection, Genetic ; Species Specificity ; Trees/*microbiology/virology ; }, abstract = {It is increasingly apparent that the dynamic microbial communities of long-lived hosts affect their phenotype, including resistance to disease. The host microbiota will change over time due to immigration of new species, interaction with the host immune system, and selection by bacteriophage viruses (phages), but the relative roles of each process are unclear. Previous metagenomic approaches confirm the presence of phages infecting host microbiota, and experimental coevolution of bacteria and phage populations in the laboratory has demonstrated rapid reciprocal change over time. The key challenge is to determine whether phages influence host-associated bacterial communities in nature, in the face of other selection pressures. I use a tree-bacteria-phage system to measure reciprocal changes in phage infectivity and bacterial resistance within microbial communities of tree hosts over one season. An experimental time shift shows that bacterial isolates are most resistant to lytic phages from the prior month and least resistant to those from the future month, providing clear evidence for both phage-mediated selection on bacterial communities and bacterial-mediated selection on phage communities in nature. These reciprocal changes suggest that phages indeed play a key role in shaping the microbiota of their eukaryotic hosts.}, } @article {pmid23806673, year = {2013}, author = {Bourlat, SJ and Borja, A and Gilbert, J and Taylor, MI and Davies, N and Weisberg, SB and Griffith, JF and Lettieri, T and Field, D and Benzie, J and Glöckner, FO and Rodríguez-Ezpeleta, N and Faith, DP and Bean, TP and Obst, M}, title = {Genomics in marine monitoring: new opportunities for assessing marine health status.}, journal = {Marine pollution bulletin}, volume = {74}, number = {1}, pages = {19-31}, doi = {10.1016/j.marpolbul.2013.05.042}, pmid = {23806673}, issn = {1879-3363}, mesh = {Aquatic Organisms/*genetics ; Biodiversity ; Conservation of Natural Resources ; Ecosystem ; Environmental Monitoring/economics/*methods ; *Genomics ; }, abstract = {This viewpoint paper explores the potential of genomics technology to provide accurate, rapid, and cost efficient observations of the marine environment. The use of such approaches in next generation marine monitoring programs will help achieve the goals of marine legislation implemented world-wide. Genomic methods can yield faster results from monitoring, easier and more reliable taxonomic identification, as well as quicker and better assessment of the environmental status of marine waters. A summary of genomic methods that are ready or show high potential for integration into existing monitoring programs is provided (e.g. qPCR, SNP based methods, DNA barcoding, microarrays, metagenetics, metagenomics, transcriptomics). These approaches are mapped to existing indicators and descriptors and a series of case studies is presented to assess the cost and added value of these molecular techniques in comparison with traditional monitoring systems. Finally, guidelines and recommendations are suggested for how such methods can enter marine monitoring programs in a standardized manner.}, } @article {pmid23806346, year = {2013}, author = {Schaeverbeke, T and Truchetet, ME and Richez, C}, title = {Gut metagenome and spondyloarthritis.}, journal = {Joint bone spine}, volume = {80}, number = {4}, pages = {349-352}, doi = {10.1016/j.jbspin.2013.02.005}, pmid = {23806346}, issn = {1778-7254}, mesh = {Animals ; Colitis, Ulcerative/microbiology/physiopathology ; Crohn Disease/microbiology/physiopathology ; Disease Models, Animal ; Feces/microbiology ; Gastrointestinal Tract/*microbiology/physiopathology ; Humans ; Immune System/physiopathology ; Metagenome/*genetics ; Metagenomics/*trends ; Mice ; Microbiota/*genetics ; Rats ; Spondylarthritis/*microbiology/physiopathology ; }, } @article {pmid23805896, year = {2013}, author = {Turner, TR and James, EK and Poole, PS}, title = {The plant microbiome.}, journal = {Genome biology}, volume = {14}, number = {6}, pages = {209}, pmid = {23805896}, issn = {1474-760X}, mesh = {Endophytes/genetics/metabolism ; *Metagenome ; Microbiota/*genetics ; Nitrogen Fixation/genetics ; Plant Immunity/genetics ; Plant Root Nodulation/genetics ; Plant Roots/*genetics/immunology/microbiology ; Plants/*genetics/immunology/microbiology ; Rhizosphere ; Symbiosis/genetics ; }, abstract = {Plant genomes contribute to the structure and function of the plant microbiome, a key determinant of plant health and productivity. High-throughput technologies are revealing interactions between these complex communities and their hosts in unprecedented detail.}, } @article {pmid23804402, year = {2013}, author = {Moeller, AH and Peeters, M and Ndjango, JB and Li, Y and Hahn, BH and Ochman, H}, title = {Sympatric chimpanzees and gorillas harbor convergent gut microbial communities.}, journal = {Genome research}, volume = {23}, number = {10}, pages = {1715-1720}, pmid = {23804402}, issn = {1549-5469}, support = {R37 AI050529/AI/NIAID NIH HHS/United States ; R01 GM101209/GM/NIGMS NIH HHS/United States ; R01 AI058715/AI/NIAID NIH HHS/United States ; R01 AI50529/AI/NIAID NIH HHS/United States ; R01 AI58715/AI/NIAID NIH HHS/United States ; R01 AI050529/AI/NIAID NIH HHS/United States ; }, mesh = {Actinobacteria/classification/genetics ; Africa, Central ; Animals ; Bacteria/*classification/genetics ; Bacteroidetes/classification/genetics ; Environment ; Evolution, Molecular ; Feces/*microbiology ; Gastrointestinal Tract/*microbiology ; Genetic Speciation ; Genome, Mitochondrial ; Gorilla gorilla/classification/genetics/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenome ; *Microbiota ; Pan paniscus/classification/genetics/*microbiology ; Pan troglodytes/classification/genetics/*microbiology ; Phylogeny ; Proteobacteria/classification/genetics ; RNA, Ribosomal, 16S/*genetics ; *Sympatry ; }, abstract = {The gut microbial communities within great apes have been shown to reflect the phylogenetic history of their hosts, indicating codiversification between great apes and their gut microbiota over evolutionary timescales. But because the great apes examined to date represent geographically isolated populations whose diets derive from different sources, it is unclear whether this pattern of codiversification has resulted from a long history of coadaptation between microbes and hosts (heritable factors) or from the ecological and geographic separation among host species (environmental factors). To evaluate the relative influences of heritable and environmental factors on the evolution of the great ape gut microbiota, we assayed the gut communities of sympatric and allopatric populations of chimpanzees, bonobos, and gorillas residing throughout equatorial Africa. Comparisons of these populations revealed that the gut communities of different host species can always be distinguished from one another but that the gut communities of sympatric chimpanzees and gorillas have converged in terms of community composition, sharing on average 53% more bacterial phylotypes than the gut communities of allopatric hosts. Host environment, independent of host genetics and evolutionary history, shaped the distribution of bacterial phylotypes across the Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria, the four most common phyla of gut bacteria. Moreover, the specific patterns of phylotype sharing among hosts suggest that chimpanzees living in sympatry with gorillas have acquired bacteria from gorillas. These results indicate that geographic isolation between host species has promoted the evolutionary differentiation of great ape gut bacterial communities.}, } @article {pmid23804381, year = {2013}, author = {Antharam, VC and Li, EC and Ishmael, A and Sharma, A and Mai, V and Rand, KH and Wang, GP}, title = {Intestinal dysbiosis and depletion of butyrogenic bacteria in Clostridium difficile infection and nosocomial diarrhea.}, journal = {Journal of clinical microbiology}, volume = {51}, number = {9}, pages = {2884-2892}, pmid = {23804381}, issn = {1098-660X}, support = {K08 AI077713/AI/NIAID NIH HHS/United States ; UL1 RR029890/RR/NCRR NIH HHS/United States ; KO8-AI077713/AI/NIAID NIH HHS/United States ; 1UL1RR029890/RR/NCRR NIH HHS/United States ; }, mesh = {Adult ; Aged ; Bacteria/isolation & purification/*metabolism ; Biota ; Butyric Acid/*metabolism ; Clostridium Infections/*microbiology ; Cluster Analysis ; Cross Infection/*microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Diarrhea/*microbiology ; *Dysbiosis ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; Metagenomics ; Middle Aged ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; United States ; }, abstract = {Clostridium difficile infection (CDI) causes nearly half a million cases of diarrhea and colitis in the United States each year. Although the importance of the gut microbiota in C. difficile pathogenesis is well recognized, components of the human gut flora critical for colonization resistance are not known. Culture-independent high-density Roche 454 pyrosequencing was used to survey the distal gut microbiota for 39 individuals with CDI, 36 subjects with C. difficile-negative nosocomial diarrhea (CDN), and 40 healthy control subjects. A total of 526,071 partial 16S rRNA sequence reads of the V1 to V3 regions were aligned with 16S databases, identifying 3,531 bacterial phylotypes from 115 fecal samples. Genomic analysis revealed significant alterations of organism lineages in both the CDI and CDN groups, which were accompanied by marked decreases in microbial diversity and species richness driven primarily by a paucity of phylotypes within the Firmicutes phylum. Normally abundant gut commensal organisms, including the Ruminococcaceae and Lachnospiraceae families and butyrate-producing C2 to C4 anaerobic fermenters, were significantly depleted in the CDI and CDN groups. These data demonstrate associations between the depletion of Ruminococcaceae, Lachnospiraceae, and butyrogenic bacteria in the gut microbiota and nosocomial diarrhea, including C. difficile infection. Mechanistic studies focusing on the functional roles of these organisms in diarrheal diseases and resistance against C. difficile colonization are warranted.}, } @article {pmid23802730, year = {2013}, author = {Xing, M and Hou, Z and Yuan, J and Liu, Y and Qu, Y and Liu, B}, title = {Taxonomic and functional metagenomic profiling of gastrointestinal tract microbiome of the farmed adult turbot (Scophthalmus maximus).}, journal = {FEMS microbiology ecology}, volume = {86}, number = {3}, pages = {432-443}, doi = {10.1111/1574-6941.12174}, pmid = {23802730}, issn = {1574-6941}, mesh = {Animals ; Aquaculture ; Bacteria/*classification/genetics/*isolation & purification ; DNA, Bacterial/genetics ; Flatfishes/*microbiology ; Fungi/classification/genetics/isolation & purification ; Gastrointestinal Tract/*microbiology ; *Microbiota ; Proteobacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Vibrio/genetics ; }, abstract = {Metagenomics combined with 16S rRNA gene sequence analyses was applied to unveil the taxonomic composition and functional diversity of the farmed adult turbot gastrointestinal (GI) microbiome. Proteobacteria and Firmicutes which existed in both GI content and mucus were dominated in the turbot GI microbiome. 16S rRNA gene sequence analyses also indicated that the turbot GI tract may harbor some bacteria which originated from associated seawater. Functional analyses indicated that the clustering-based subsystem and many metabolic subsystems were dominant in the turbot GI metagenome. Compared with other gut metagenomes, quorum sensing and biofilm formation was overabundant in the turbot GI metagenome. Genes associated with quorum sensing and biofilm formation were found in species within Vibrio, including Vibrio vulnificus, Vibrio cholerae and Vibrio parahaemolyticus. In farmed fish gut metagenomes, the stress response and protein folding subsystems were over-represented and several genes concerning antibiotic and heavy metal resistance were also detected. These data suggested that the turbot GI microbiome may be affected by human factors in aquaculture. Additionally, iron acquisition and the metabolism subsystem were more abundant in the turbot GI metagenome when compared with freshwater fish gut metagenome, suggesting that unique metabolic potential may be observed in marine animal GI microbiomes.}, } @article {pmid23797103, year = {2013}, author = {Hale, MC and Thrower, FP and Berntson, EA and Miller, MR and Nichols, KM}, title = {Evaluating adaptive divergence between migratory and nonmigratory ecotypes of a salmonid fish, Oncorhynchus mykiss.}, journal = {G3 (Bethesda, Md.)}, volume = {3}, number = {8}, pages = {1273-1285}, pmid = {23797103}, issn = {2160-1836}, mesh = {Animals ; Chromosome Mapping ; *Ecotype ; Genome ; Genotype ; High-Throughput Nucleotide Sequencing ; Linkage Disequilibrium ; Metagenomics ; Oncorhynchus mykiss/*genetics ; Phenotype ; *Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; }, abstract = {Next-generation sequencing and the application of population genomic and association approaches have made it possible to detect selection and unravel the genetic basis to variable phenotypic traits. The use of these two approaches in parallel is especially attractive in nonmodel organisms that lack a sequenced and annotated genome, but only works well when population structure is not confounded with the phenotype of interest. Herein, we use population genomics in a nonmodel fish species, rainbow trout (Oncorhynchus mykiss), to better understand adaptive divergence between migratory and nonmigratory ecotypes and to further our understanding about the genetic basis of migration. Restriction site-associated DNA (RAD) tag sequencing was used to identify single-nucleotide polymorphisms (SNPs) in migrant and resident O. mykiss from two systems, one in Alaska and the other in Oregon. A total of 7920 and 6755 SNPs met filtering criteria in the Alaska and Oregon data sets, respectively. Population genetic tests determined that 1423 SNPs were candidates for selection when loci were compared between resident and migrant samples. Previous linkage mapping studies that used RAD DNA tag SNPs were available to determine the position of 1990 markers. Several significant SNPs are located in genome regions that contain quantitative trait loci for migratory-related traits, reinforcing the importance of these regions in the genetic basis of migration/residency. Annotation of genome regions linked to significant SNPs revealed genes involved in processes known to be important in migration (such as osmoregulatory function). This study adds to our growing knowledge on adaptive divergence between migratory and nonmigratory ecotypes of this species; across studies, this complex trait appears to be controlled by many loci of small effect, with some in common, but many loci not shared between populations studied.}, } @article {pmid23797046, year = {2013}, author = {Willcox, MD}, title = {Characterization of the normal microbiota of the ocular surface.}, journal = {Experimental eye research}, volume = {117}, number = {}, pages = {99-105}, doi = {10.1016/j.exer.2013.06.003}, pmid = {23797046}, issn = {1096-0007}, mesh = {Bacteria/genetics/growth & development/*isolation & purification ; Colony Count, Microbial ; Conjunctiva/*microbiology ; Humans ; Metagenome ; Microbiota/*physiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The ocular surface is continually exposed to the environment and as a consequence to different types of microbes, but whether there is a normal microbiota of the ocular surface remains unresolved. Using traditional microbial culture techniques has shown that <80% of swabs of the conjunctiva yield cultivable microbes. These usually belong to the bacterial types of the coagulase-negative staphylococci, Propionibacterium sp., with low frequency of isolation of bacteria such as Staphylococcus aureus, Micrococcus sp., Gram-negative bacteria or fungi. Even when these are grown, the numbers of colony forming units (cfu) per swab of the conjunctiva is usually much less than 100 cfu. Swabs of the lid more commonly result in microbial growth, of the same species as from the conjunctiva and slightly higher cfu. Contact lenses have also been cultured, and they yield similar microbial types. Microbes can be isolated from the ocular surface almost immediately after birth. The advent of molecular techniques for microbial identification based on 16S rRNA sequencing has opened up the possibility of determining whether there are non-cultivable microbes that can colonise the ocular surface. Additionally, use of these techniques with cross-sectional and longitudinal studies may help to understand whether the ocular surface harbours its own unique microbiota, or whether the microbiota are only transiently present.}, } @article {pmid23793630, year = {2013}, author = {Srinivasiah, S and Lovett, J and Polson, S and Bhavsar, J and Ghosh, D and Roy, K and Fuhrmann, JJ and Radosevich, M and Wommack, KE}, title = {Direct assessment of viral diversity in soils by random PCR amplification of polymorphic DNA.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {18}, pages = {5450-5457}, pmid = {23793630}, issn = {1098-5336}, mesh = {*Biodiversity ; Costs and Cost Analysis ; DNA Fingerprinting/economics/*methods ; High-Throughput Screening Assays/economics/methods ; Random Amplified Polymorphic DNA Technique/economics/*methods ; *Soil Microbiology ; Virology/economics/*methods ; Viruses/*classification/genetics/*isolation & purification ; }, abstract = {Viruses are the most abundant and diverse biological entities within soils, yet their ecological impact is largely unknown. Defining how soil viral communities change with perturbation or across environments will contribute to understanding the larger ecological significance of soil viruses. A new approach to examining the composition of soil viral communities based on random PCR amplification of polymorphic DNA (RAPD-PCR) was developed. A key methodological improvement was the use of viral metagenomic sequence data for the design of RAPD-PCR primers. This metagenomically informed approach to primer design enabled the optimization of RAPD-PCR sensitivity for examining changes in soil viral communities. Initial application of RAPD-PCR viral fingerprinting to soil viral communities demonstrated that the composition of autochthonous soil viral assemblages noticeably changed over a distance of meters along a transect of Antarctic soils and across soils subjected to different land uses. For Antarctic soils, viral assemblages segregated upslope from the edge of dry valley lakes. In the case of temperate soils at the Kellogg Biological Station, viral communities clustered according to land use treatment. In both environments, soil viral communities changed along with environmental factors known to shape the composition of bacterial host communities. Overall, this work demonstrates that RAPD-PCR fingerprinting is an inexpensive, high-throughput means for addressing first-order questions of viral community dynamics within environmental samples and thus fills a methodological gap between narrow single-gene approaches and comprehensive shotgun metagenomic sequencing for the analysis of viral community diversity.}, } @article {pmid23793624, year = {2013}, author = {Kozich, JJ and Westcott, SL and Baxter, NT and Highlander, SK and Schloss, PD}, title = {Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {17}, pages = {5112-5120}, pmid = {23793624}, issn = {1098-5336}, support = {R01 HG005975/HG/NHGRI NIH HHS/United States ; U54HG004973/HG/NHGRI NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; R01HG005975/HG/NHGRI NIH HHS/United States ; U54 HG004973/HG/NHGRI NIH HHS/United States ; 5R01GM099514/GM/NIGMS NIH HHS/United States ; P30DK034933/DK/NIDDK NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biota ; Computational Biology/*methods ; Feces/microbiology ; High-Throughput Nucleotide Sequencing/*methods/*standards ; Humans ; *Metagenome ; Mice ; Soil Microbiology ; }, abstract = {Rapid advances in sequencing technology have changed the experimental landscape of microbial ecology. In the last 10 years, the field has moved from sequencing hundreds of 16S rRNA gene fragments per study using clone libraries to the sequencing of millions of fragments per study using next-generation sequencing technologies from 454 and Illumina. As these technologies advance, it is critical to assess the strengths, weaknesses, and overall suitability of these platforms for the interrogation of microbial communities. Here, we present an improved method for sequencing variable regions within the 16S rRNA gene using Illumina's MiSeq platform, which is currently capable of producing paired 250-nucleotide reads. We evaluated three overlapping regions of the 16S rRNA gene that vary in length (i.e., V34, V4, and V45) by resequencing a mock community and natural samples from human feces, mouse feces, and soil. By titrating the concentration of 16S rRNA gene amplicons applied to the flow cell and using a quality score-based approach to correct discrepancies between reads used to construct contigs, we were able to reduce error rates by as much as two orders of magnitude. Finally, we reprocessed samples from a previous study to demonstrate that large numbers of samples could be multiplexed and sequenced in parallel with shotgun metagenomes. These analyses demonstrate that our approach can provide data that are at least as good as that generated by the 454 platform while providing considerably higher sequencing coverage for a fraction of the cost.}, } @article {pmid23790204, year = {2013}, author = {Mendes, R and Garbeva, P and Raaijmakers, JM}, title = {The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms.}, journal = {FEMS microbiology reviews}, volume = {37}, number = {5}, pages = {634-663}, doi = {10.1111/1574-6976.12028}, pmid = {23790204}, issn = {1574-6976}, mesh = {Bacterial Infections/microbiology ; Host-Pathogen Interactions ; Humans ; Metagenomics ; *Microbiota ; Plants/*microbiology ; *Rhizosphere ; *Soil Microbiology ; Symbiosis ; }, abstract = {Microbial communities play a pivotal role in the functioning of plants by influencing their physiology and development. While many members of the rhizosphere microbiome are beneficial to plant growth, also plant pathogenic microorganisms colonize the rhizosphere striving to break through the protective microbial shield and to overcome the innate plant defense mechanisms in order to cause disease. A third group of microorganisms that can be found in the rhizosphere are the true and opportunistic human pathogenic bacteria, which can be carried on or in plant tissue and may cause disease when introduced into debilitated humans. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, for the vast majority of rhizosphere microorganisms no knowledge exists. To enhance plant growth and health, it is essential to know which microorganism is present in the rhizosphere microbiome and what they are doing. Here, we review the main functions of rhizosphere microorganisms and how they impact on health and disease. We discuss the mechanisms involved in the multitrophic interactions and chemical dialogues that occur in the rhizosphere. Finally, we highlight several strategies to redirect or reshape the rhizosphere microbiome in favor of microorganisms that are beneficial to plant growth and health.}, } @article {pmid23789899, year = {2013}, author = {Stalder, T and Alrhmoun, M and Louvet, JN and Casellas, M and Maftah, C and Carrion, C and Pons, MN and Pahl, O and Ploy, MC and Dagot, C}, title = {Dynamic assessment of the floc morphology, bacterial diversity, and integron content of an activated sludge reactor processing hospital effluent.}, journal = {Environmental science & technology}, volume = {47}, number = {14}, pages = {7909-7917}, doi = {10.1021/es4008646}, pmid = {23789899}, issn = {1520-5851}, mesh = {Bacteria/*classification ; Biodiversity ; Biomass ; *Bioreactors ; *Integrons ; Polymerase Chain Reaction ; *Sewage ; }, abstract = {The treatment of hospital effluents (HE) is a major concern, as they are suspected of disseminating drugs and antibiotic resistance determinants in the environment. In order to assess HE influence on wastewater treatment plant biomass, lab-scale conventional activated sludge systems (CAS) were continuously fed with real HE or urban effluent as a control. To gain insights into the main hurdles linked to HE treatment, we conducted a multiparameter study using classical physicochemical characterization, phase contrast and confocal laser scaning microscopy, and molecular biology (i.e., pyrosequencing) tools. HE caused erosion of floc structure and the production of extracellular polymeric substances attributed to the development of floc-forming bacteria. Adaptation of the sludge bacterial community to the HE characteristics, thus maintaining the purification performance of the biomass, was observed. Finally, the comparative metagenomic analysis of the CAS showed that HE treatment resulted in an increase of class 1 resistance integrons (RIs) and the introduction of Pseudomonas spp. into the bacterial community. HE treatment did not reduce the CAS process performance; nevertheless it increases the risk of dissemination into the environment of bacterial species and genetic determinants (RIs) involved in antibiotic resistance acquisition.}, } @article {pmid23786768, year = {2013}, author = {Koslicki, D and Foucart, S and Rosen, G}, title = {Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing.}, journal = {Bioinformatics (Oxford, England)}, volume = {29}, number = {17}, pages = {2096-2102}, doi = {10.1093/bioinformatics/btt336}, pmid = {23786768}, issn = {1367-4811}, mesh = {Algorithms ; Bacteria/*classification/genetics/isolation & purification ; Bayes Theorem ; Classification/methods ; Metagenomics ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {MOTIVATION: Many metagenomic studies compare hundreds to thousands of environmental and health-related samples by extracting and sequencing their 16S rRNA amplicons and measuring their similarity using beta-diversity metrics. However, one of the first steps--to classify the operational taxonomic units within the sample--can be a computationally time-consuming task because most methods rely on computing the taxonomic assignment of each individual read out of tens to hundreds of thousands of reads.

RESULTS: We introduce Quikr: a QUadratic, K-mer-based, Iterative, Reconstruction method, which computes a vector of taxonomic assignments and their proportions in the sample using an optimization technique motivated from the mathematical theory of compressive sensing. On both simulated and actual biological data, we demonstrate that Quikr typically has less error and is typically orders of magnitude faster than the most commonly used taxonomic assignment technique (the Ribosomal Database Project's Naïve Bayesian Classifier). Furthermore, the technique is shown to be unaffected by the presence of chimeras, thereby allowing for the circumvention of the time-intensive step of chimera filtering.

AVAILABILITY: The Quikr computational package (in MATLAB, Octave, Python and C) for the Linux and Mac platforms is available at http://sourceforge.net/projects/quikr/.}, } @article {pmid23776466, year = {2013}, author = {Mathieu, A and Delmont, TO and Vogel, TM and Robe, P and Nalin, R and Simonet, P}, title = {Life on human surfaces: skin metagenomics.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e65288}, pmid = {23776466}, issn = {1932-6203}, mesh = {Adult ; Bacteria/*genetics ; Base Sequence ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Male ; Metagenomics/*methods ; Microbiota/*genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; Principal Component Analysis ; Skin/*microbiology ; }, abstract = {The human skin microbiome could provide another example, after the gut, of the strong positive or negative impact that human colonizing bacteria can have on health. Deciphering functional diversity and dynamics within human skin microbial communities is critical for understanding their involvement and for developing the appropriate substances for improving or correcting their action. We present a direct PCR-free high throughput sequencing approach to unravel the human skin microbiota specificities through metagenomic dataset analysis and inter-environmental comparison. The approach provided access to the functions carried out by dominant skin colonizing taxa, including Corynebacterium, Staphylococcus and Propionibacterium, revealing their specific capabilities to interact with and exploit compounds from the human skin. These functions, which clearly illustrate the unique life style of the skin microbial communities, stand as invaluable investigation targets for understanding and potentially modifying bacterial interactions with the human host with the objective of increasing health and well being.}, } @article {pmid23765099, year = {2013}, author = {Makhalanyane, TP and Valverde, A and Birkeland, NK and Cary, SC and Tuffin, IM and Cowan, DA}, title = {Evidence for successional development in Antarctic hypolithic bacterial communities.}, journal = {The ISME journal}, volume = {7}, number = {11}, pages = {2080-2090}, pmid = {23765099}, issn = {1751-7370}, mesh = {Antarctic Regions ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; Models, Biological ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Time Factors ; }, abstract = {Hypoliths (cryptic microbial assemblages that develop on the undersides of translucent rocks) are significant contributors to regional C and N budgets in both hot and cold deserts. Previous studies in the Dry Valleys of Eastern Antarctica have reported three morphologically distinct hypolithic community types: cyanobacteria dominated (type I), fungus dominated (type II) and moss dominated (type III). Here we present terminal-restriction fragment length polymorphism analyses to elucidate the bacterial community structure in hypolithons and the surrounding soils. We show clear and robust distinction in bacterial composition between bulk surface soils and hypolithons. Moreover, the bacterial assemblages were similar in types II and III hypolithons and clearly distinct from those found in type I. Through 16S rRNA gene 454 pyrosequencing, we show that Proteobacteria dominated all three types of hypolithic communities. As expected, Cyanobacteria were more abundant in type I hypolithons, whereas Actinobacteria were relatively more abundant in types II and III hypolithons, and were the dominant group in soils. Using a probabilistic dissimilarity metric and random sampling, we demonstrate that deterministic processes are more important in shaping the structure of the bacterial community found in types II and III hypolithons. Most notably, the data presented in this study suggest that hypolithic bacterial communities establish via a successional model, with the type I hypolithons acting as the basal development state.}, } @article {pmid23762380, year = {2013}, author = {Tannières, M and Beury-Cirou, A and Vigouroux, A and Mondy, S and Pellissier, F and Dessaux, Y and Faure, D}, title = {A metagenomic study highlights phylogenetic proximity of quorum-quenching and xenobiotic-degrading amidases of the AS-family.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e65473}, pmid = {23762380}, issn = {1932-6203}, mesh = {Acyl-Butyrolactones/metabolism ; Amidohydrolases/*metabolism ; Bacteria/drug effects/enzymology/genetics ; Biocatalysis/drug effects ; Biodegradation, Environmental ; Biodiversity ; Caproates/pharmacology ; Carboxylic Ester Hydrolases/metabolism ; Genes, Bacterial/genetics ; Lactones/pharmacology ; *Metagenomics ; Open Reading Frames/genetics ; *Phylogeny ; Physical Chromosome Mapping ; *Quorum Sensing/drug effects/genetics ; Xenobiotics/*metabolism ; }, abstract = {Quorum-sensing (QS) signals of the N-acylhomoserine lactone (NAHL) class are cleaved by quorum-quenching enzymes, collectively named NAHLases. Here, functional metagenomics allowed the discovery of a novel bacterial NAHLase in a rhizosphere that was treated with γ-caprolactone. As revealed by rrs-DGGE and rrs-pyrosequencing, this treatment increased the percentage of the NAHL-degrading bacteria and strongly biased the structure of the bacterial community, among which Azospirillum dominated. Among the 29 760 fosmids of the metagenomic library, a single one was detected that expressed the qsdB gene conferring NAHL-degradation upon E. coli and decreased QS-regulated virulence in Pectobacterium. Phylogenetic analysis of the 34 orfs of the fosmid suggested that it would belong to an unknown Proteobacterium - probably a γ-proteobacterium. qPCR quantification of the NAHLase-encoding genes attM, qsdA, and qsdB revealed their higher abundance in the γ-caprolactone-treated rhizosphere as compared to an untreated control. The purified QsdB enzyme exhibited amidase activity. QsdB is the first amidase signature (AS) family member exhibiting NAHLase-activity. Point mutations in the AS-family catalytic triad K-S-S abolished the NAHLase activity of QsdB. This study extends the diversity of NAHLases and highlights a common phylogenic origin of AS-family enzymes involved in the degradation of natural compounds, such as NAHLs, and xenobiotics, such as nylon and linuron.}, } @article {pmid23760464, year = {2013}, author = {Zhou, J and Jiang, YH and Deng, Y and Shi, Z and Zhou, BY and Xue, K and Wu, L and He, Z and Yang, Y}, title = {Random sampling process leads to overestimation of β-diversity of microbial communities.}, journal = {mBio}, volume = {4}, number = {3}, pages = {e00324-13}, pmid = {23760464}, issn = {2150-7511}, mesh = {*Biota ; *Environmental Microbiology ; Metagenomics/*methods ; Models, Theoretical ; Molecular Biology/*methods ; Reproducibility of Results ; Selection Bias ; }, abstract = {The site-to-site variability in species composition, known as β-diversity, is crucial to understanding spatiotemporal patterns of species diversity and the mechanisms controlling community composition and structure. However, quantifying β-diversity in microbial ecology using sequencing-based technologies is a great challenge because of a high number of sequencing errors, bias, and poor reproducibility and quantification. Herein, based on general sampling theory, a mathematical framework is first developed for simulating the effects of random sampling processes on quantifying β-diversity when the community size is known or unknown. Also, using an analogous ball example under Poisson sampling with limited sampling efforts, the developed mathematical framework can exactly predict the low reproducibility among technically replicate samples from the same community of a certain species abundance distribution, which provides explicit evidences of random sampling processes as the main factor causing high percentages of technical variations. In addition, the predicted values under Poisson random sampling were highly consistent with the observed low percentages of operational taxonomic unit (OTU) overlap (<30% and <20% for two and three tags, respectively, based on both Jaccard and Bray-Curtis dissimilarity indexes), further supporting the hypothesis that the poor reproducibility among technical replicates is due to the artifacts associated with random sampling processes. Finally, a mathematical framework was developed for predicting sampling efforts to achieve a desired overlap among replicate samples. Our modeling simulations predict that several orders of magnitude more sequencing efforts are needed to achieve desired high technical reproducibility. These results suggest that great caution needs to be taken in quantifying and interpreting β-diversity for microbial community analysis using next-generation sequencing technologies. IMPORTANCE Due to the vast diversity and uncultivated status of the majority of microorganisms, microbial detection, characterization, and quantitation are of great challenge. Although large-scale metagenome sequencing technology such as PCR-based amplicon sequencing has revolutionized the studies of microbial communities, it suffers from several inherent drawbacks, such as a high number of sequencing errors, biases, poor quantitation, and very high percentages of technical variations, which could greatly overestimate microbial biodiversity. Based on general sampling theory, this study provided the first explicit evidence to demonstrate the importance of random sampling processes in estimating microbial β-diversity, which has not been adequately recognized and addressed in microbial ecology. Since most ecological studies are involved in random sampling, the conclusions learned from this study should also be applicable to other ecological studies in general. In summary, the results presented in this study should have important implications for examining microbial biodiversity to address both basic theoretical and applied management questions.}, } @article {pmid23760301, year = {2013}, author = {Pérez-Brocal, V and García-López, R and Vázquez-Castellanos, JF and Nos, P and Beltrán, B and Latorre, A and Moya, A}, title = {Study of the viral and microbial communities associated with Crohn's disease: a metagenomic approach.}, journal = {Clinical and translational gastroenterology}, volume = {4}, number = {6}, pages = {e36}, pmid = {23760301}, issn = {2155-384X}, abstract = {OBJECTIVES: This study aimed to analyze and compare the diversity and structure of the viral and microbial communities in fecal samples from a control group of healthy volunteers and from patients affected by Crohn's disease (CD).

METHODS: Healthy adult controls (n=8) and patients affected by ileocolic CD (n=11) were examined for the viral and microbial communities in their feces and, in one additional case, in the intestinal tissue. Using two different approaches, we compared the viral and microbial communities in several ways: by group (patients vs. controls), entity (viruses vs. bacteria), read assembly (unassembled vs. assembled reads), and methodology (our approach vs. an existing pipeline). Differences in the viral and microbial composition, and abundance between the two groups were analyzed to identify taxa that are under- or over-represented.

RESULTS: A lower diversity but more variability between the CD samples in both virome and microbiome was found, with a clear distinction between groups based on the microbiome. Only ≈5% of the differential viral biomarkers are more represented in the CD group (Synechococcus phage S CBS1 and Retroviridae family viruses), compared with 95% in the control group. Unrelated patterns of bacteria and bacteriophages were observed.

CONCLUSIONS: Our use of an extensive database is critical to retrieve more viral hits than in previous approaches. Unrelated patterns of bacteria and bacteriophages may be due to uneven representation of certain viruses in databases, among other factors. Further characterization of Retroviridae viruses in the CD group could be of interest, given their links with immunodeficiency and the immune responses. To conclude, some methodological considerations underlying the analysis of the viral community composition and abundance are discussed.}, } @article {pmid23758874, year = {2013}, author = {Ling, Z and Liu, X and Luo, Y and Yuan, L and Nelson, KE and Wang, Y and Xiang, C and Li, L}, title = {Pyrosequencing analysis of the human microbiota of healthy Chinese undergraduates.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {390}, pmid = {23758874}, issn = {1471-2164}, mesh = {Adult ; *Asian People ; Bacteria/classification/genetics ; Biodiversity ; Ecosystem ; Female ; Genes, Bacterial/genetics ; *Health ; *High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenome/*genetics ; *Sequence Analysis, RNA ; *Universities ; Young Adult ; }, abstract = {BACKGROUND: Elucidating the biogeography of bacterial communities on the human body is critical for establishing healthy baselines from which to detect differences associated with disease; however, little is known about the baseline bacterial profiles from various human habitats of healthy Chinese undergraduates.

RESULTS: Using parallel barcoded 454 pyrosequencing targeting on the 16S rRNA gene V3 region, the bacterial diversity of the nasopharynx, saliva, dominant hands, and feces were investigated from 10 healthy Chinese junior boarding undergraduates at Zhejiang University. The participants were 21-24 years of age with a body mass index (BMI) < 24 kg/m(2). A total of 156,717 high-quality pyrosequencing reads were obtained for evaluating bacterial diversity, which represented 29,887 unique phylotypes. The overall taxonomic distribution of the 16S rRNA gene-based amplicons demonstrated that these 4 habitats of the human body harbored distinct microbiota and could be divided into different clusters according to anatomic site, while the established patterns of bacterial diversity followed the human body habitat (feces, hands, saliva, and nasopharynx). Although significant inter-individual variation was observed, the healthy microbiota still shared a large number of phylotypes in each habitat, but not among the four habitats, indicating that a core microbiome existed in each healthy habitat. The vast majority of sequences from these different habitats were classified into different taxonmies that became the predominant bacteria of the healthy microbiota.

CONCLUSIONS: We first established the framework of microbial communities from four healthy human habitats of the same participants with similar living environments for the Chinese undergraduates. Our data represent an important step for determining the diversity of Chinese healthy microbiota, and can be used for more large-scale studies that focus on the interactions between healthy and diseases states for young Chinese adults in the same age range.}, } @article {pmid23735199, year = {2013}, author = {Liu, Y and Guo, J and Hu, G and Zhu, H}, title = {Gene prediction in metagenomic fragments based on the SVM algorithm.}, journal = {BMC bioinformatics}, volume = {14 Suppl 5}, number = {Suppl 5}, pages = {S12}, pmid = {23735199}, issn = {1471-2105}, mesh = {Artificial Intelligence ; Gastrointestinal Tract/microbiology ; *Genes, Archaeal ; *Genes, Bacterial ; Humans ; Metagenomics/*methods ; Microbiota ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA ; *Support Vector Machine ; }, abstract = {BACKGROUND: Metagenomic sequencing is becoming a powerful technology for exploring micro-ogranisms from various environments, such as human body, without isolation and cultivation. Accurately identifying genes from metagenomic fragments is one of the most fundamental issues.

RESULTS: In this article, we present a novel gene prediction method named MetaGUN for metagenomic fragments based on a machine learning approach of SVM. It implements in a three-stage strategy to predict genes. Firstly, it classifies input fragments into phylogenetic groups by a k-mer based sequence binning method. Then, protein-coding sequences are identified for each group independently with SVM classifiers that integrate entropy density profiles (EDP) of codon usage, translation initiation site (TIS) scores and open reading frame (ORF) length as input patterns. Finally, the TISs are adjusted by employing a modified version of MetaTISA. To identify protein-coding sequences, MetaGun builds the universal module and the novel module. The former is based on a set of representative species, while the latter is designed to find potential functionary DNA sequences with conserved domains.

CONCLUSIONS: Comparisons on artificial shotgun fragments with multiple current metagenomic gene finders show that MetaGUN predicts better results on both 3' and 5' ends of genes with fragments of various lengths. Especially, it makes the most reliable predictions among these methods. As an application, MetaGUN was used to predict genes for two samples of human gut microbiome. It identifies thousands of additional genes with significant evidences. Further analysis indicates that MetaGUN tends to predict more potential novel genes than other current metagenomic gene finders.}, } @article {pmid23734710, year = {2013}, author = {Ander, C and Schulz-Trieglaff, OB and Stoye, J and Cox, AJ}, title = {metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences.}, journal = {BMC bioinformatics}, volume = {14 Suppl 5}, number = {Suppl 5}, pages = {S2}, pmid = {23734710}, issn = {1471-2105}, mesh = {Algorithms ; Environmental Microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {Environmental shotgun sequencing (ESS) has potential to give greater insight into microbial communities than targeted sequencing of 16S regions, but requires much higher sequence coverage. The advent of next-generation sequencing has made it feasible for the Human Microbiome Project and other initiatives to generate ESS data on a large scale, but computationally efficient methods for analysing such data sets are needed.Here we present metaBEETL, a fast taxonomic classifier for environmental shotgun sequences. It uses a Burrows-Wheeler Transform (BWT) index of the sequencing reads and an indexed database of microbial reference sequences. Unlike other BWT-based tools, our method has no upper limit on the number or the total size of the reference sequences in its database. By capturing sequence relationships between strains, our reference index also allows us to classify reads which are not unique to an individual strain but are nevertheless specific to some higher phylogenetic order.Tested on datasets with known taxonomic composition, metaBEETL gave results that are competitive with existing similarity-based tools: due to normalization steps which other classifiers lack, the taxonomic profile computed by metaBEETL closely matched the true environmental profile. At the same time, its moderate running time and low memory footprint allow metaBEETL to scale well to large data sets.Code to construct the BWT indexed database and for the taxonomic classification is part of the BEETL library, available as a github repository at git@github.com:BEETL/BEETL.git.}, } @article {pmid23757140, year = {2013}, author = {Barret, M and Egan, F and O'Gara, F}, title = {Distribution and diversity of bacterial secretion systems across metagenomic datasets.}, journal = {Environmental microbiology reports}, volume = {5}, number = {1}, pages = {117-126}, doi = {10.1111/j.1758-2229.2012.00394.x}, pmid = {23757140}, issn = {1758-2229}, mesh = {Bacteria/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; *Bacterial Secretion Systems ; *Databases, Genetic ; Metagenomics/*methods ; Microbiota ; Phylogeny ; }, abstract = {Bacteria can manipulate their surrounding environment through the secretion of proteins into other living organisms and into the extracellular milieu. In Gram stain negative bacteria this process is mediated by different types of secretion systems from type I through type VI secretion system (T1SS-T6SS). In this study the prevalence of these secretion systems in 312 publicly available microbiomes derived from a wide range of ecosystems was investigated by a gene-centric approach. Our analysis demonstrates that some secretion systems are over-represented in some specific samples. In addition, some T3SS and T6SS phylogenetic clusters were specifically enriched in particular ecological niches, which could indicate specific bacterial adaptation to these environments.}, } @article {pmid23757040, year = {2013}, author = {Delmont, TO and Simonet, P and Vogel, TM}, title = {Mastering methodological pitfalls for surviving the metagenomic jungle.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {35}, number = {8}, pages = {744-754}, doi = {10.1002/bies.201200155}, pmid = {23757040}, issn = {1521-1878}, mesh = {Biodiversity ; Biotechnology ; Computational Biology ; DNA/analysis ; Ecology ; Ecosystem ; Genes, Bacterial ; Genetic Variation ; Humans ; *Metagenome ; Microbiota/*genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {Metagenomics is a culture- and PCR-independent approach that is now widely exploited for directly studying microbial evolution, microbial ecology, and developing biotechnologies. Observations and discoveries are critically dependent on DNA extraction methods, sequencing technologies, and bioinformatics tools. The potential pitfalls need to be understood and, to some degree, mastered if the resulting data are to survive scrutiny. In particular, methodological variations appear to affect results from different ecosystems differently, thus increasing the risk of biological and ecological misinterpretation. Part of the difficulty is derived from the lack of knowledge concerning the true microbial diversity and because no approach can guarantee accessing microorganisms in the same proportion in which they exist in the environment. However, the variation between different approaches (e.g. DNA extraction techniques, sequence annotation systems) can be used to evaluate whether observations are meaningful. These methodological variations can be integrated into the error analysis before comparing microbial communities.}, } @article {pmid23754728, year = {2013}, author = {Philosof, A and Béjà, O}, title = {Bacterial, archaeal and viral-like rhodopsins from the Red Sea.}, journal = {Environmental microbiology reports}, volume = {5}, number = {3}, pages = {475-482}, doi = {10.1111/1758-2229.12037}, pmid = {23754728}, issn = {1758-2229}, mesh = {Amino Acid Sequence ; Archaea/*genetics/metabolism ; Archaeal Proteins/classification/*genetics/metabolism ; Bacteria/*genetics/metabolism ; Bacterial Proteins/classification/*genetics/metabolism ; Ecosystem ; High-Throughput Nucleotide Sequencing ; Indian Ocean ; Metagenome ; Microbial Consortia ; Molecular Sequence Data ; Phycodnaviridae/*genetics/metabolism ; RNA, Messenger/classification/genetics/metabolism ; Rhodopsin/classification/*genetics/metabolism ; Sequence Alignment ; Viral Proteins/classification/*genetics/metabolism ; }, abstract = {The Gulf of Aqaba, extending north to the Red Sea, is an oligotrophic basin with typical open ocean gyre characteristics. Here we report on the existence of diverse microbial rhodopsins in the Gulf of Aqaba, based on 454-pyrosequencing-generated metagenome and metatranscriptome data sets, obtained from the microbial fraction smaller than 1.6 μm. Bacterial SAR11, SAR86 and archaeal proteorhodopsins as well as viral-like rhodopsins were detected on the DNA level. On the RNA level, only SAR11 and SAR86 proteorhodopsin transcripts were detected. Our results add to the growing evidence that microbial rhodopsins are a diverse, abundant and widespread protein family.}, } @article {pmid23752679, year = {2013}, author = {Ni, J and Yan, Q and Yu, Y}, title = {How much metagenomic sequencing is enough to achieve a given goal?.}, journal = {Scientific reports}, volume = {3}, number = {}, pages = {1968}, pmid = {23752679}, issn = {2045-2322}, mesh = {DNA/genetics ; *Metagenomics ; }, abstract = {Metagenomic studies have dramatically expanded our knowledge of the microbial world. Furthermore, the amount of sample for sequencing has significantly increased with the development of high-throughput sequencing technologies. However, fully capturing all DNA sequences carried by every microorganism in the environment is still impossible. Therefore, estimating a reasonable and practical amount for sequencing to achieve the objectives is particularly necessary. In the present study, we introduce a novel method for estimating the required minimum amount for metagenomic sequencing for a given goal. We also calculated the genomic proportion of each operational taxonomic unit and the detection efficiency of a specific gene (we have used SSU rRNA gene as an example) based on a given amount for random metagenomic sequencing. The reasonable and practical estimated amount for sequencing in metagenomic studies will provide good reference information when applying high-throughput sequencing for a given goal.}, } @article {pmid23743600, year = {2013}, author = {Jeon, YS and Chun, J and Kim, BS}, title = {Identification of household bacterial community and analysis of species shared with human microbiome.}, journal = {Current microbiology}, volume = {67}, number = {5}, pages = {557-563}, pmid = {23743600}, issn = {1432-0991}, mesh = {Bacteria/*classification/*genetics ; Computational Biology/methods ; Environmental Microbiology ; *Family Characteristics ; Humans ; *Metagenome ; *Microbiota ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {Microbial populations in indoor environments, where we live and eat, are important for public health. Various bacterial species reside in the kitchen, and refrigerators, the major means of food storage within kitchens, can be a direct source of food borne illness. Therefore, the monitoring of microbiota in the refrigerator is important for food safety. We investigated and compared bacterial communities that reside in the vegetable compartment of the refrigerator and on the seat of the toilet, which is recognized as highly colonized by microorganisms, in ten houses using high-throughput sequencing. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were predominant in refrigerator and toilet samples. However, Proteobacteria was more abundant in the refrigerator, and Firmicutes was more abundant in the toilet. These household bacterial communities were compared with those of human skin and gut to identify potential sources of household bacteria. Bacterial communities from refrigerators and toilets shared more species in common with human skin than gut. Opportunistic pathogens, including Propionibacterium acnes, Bacteroides vulgatus, and Staphylococcus epidermidis, were identified as species shared with human skin and gut microbiota. This approach can provide a general background of the household microbiota and a potential method of source-tracking for public health purposes.}, } @article {pmid23743597, year = {2013}, author = {Jiang, W and Zhang, J and Chen, H}, title = {Pyrosequencing analysis of oral microbiota in children with severe early childhood dental caries.}, journal = {Current microbiology}, volume = {67}, number = {5}, pages = {537-542}, pmid = {23743597}, issn = {1432-0991}, mesh = {Bacteria/classification/genetics ; Child ; Child, Preschool ; Dental Caries/*microbiology ; Dental Plaque/microbiology ; Humans ; *Metagenome ; *Microbiota ; Sequence Analysis, DNA ; }, abstract = {Severe early childhood caries are a prevalent public health problem among preschool children throughout the world. However, little is known about the microbiota found in association with severe early childhood caries. Our study aimed to explore the bacterial microbiota of dental plaques to study the etiology of severe early childhood caries through pyrosequencing analysis based on 16S rRNA gene V1-V3 hypervariable regions. Forty participants were enrolled in the study, and we obtained twenty samples of supragingival plaque from caries-free subjects and twenty samples from subjects with severe early childhood caries. A total of 175,918 reads met the quality control standards, and the bacteria found belonged to fourteen phyla and sixty-three genera. Our results show the overall structure and microbial composition of oral bacterial communities, and they suggest that these bacteria may present a core microbiome in the dental plaque microbiota. Three genera, Streptococcus, Granulicatella, and Actinomyces, were increased significantly in children with severe dental cavities. These data may facilitate improvements in the prevention and treatment of severe early childhood caries.}, } @article {pmid23741344, year = {2013}, author = {Li, X and Yan, Q and Xie, S and Hu, W and Yu, Y and Hu, Z}, title = {Gut microbiota contributes to the growth of fast-growing transgenic common carp (Cyprinus carpio L.).}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e64577}, pmid = {23741344}, issn = {1932-6203}, mesh = {Animals ; Animals, Genetically Modified ; Bacteroidetes/classification/genetics ; Body Size ; Carbohydrate Metabolism ; Carps/genetics/*growth & development/metabolism/*microbiology ; Fusobacteria/classification/genetics ; Gastrointestinal Tract/*microbiology ; High-Throughput Nucleotide Sequencing ; Life Cycle Stages/physiology ; Lipid Metabolism ; *Metagenome ; Microbiota/*genetics ; Phylogeny ; Proteobacteria/classification/genetics ; RNA, Ribosomal, 16S/classification/*genetics ; }, abstract = {Gut microbiota has shown tight and coordinated connection with various functions of its host such as metabolism, immunity, energy utilization, and health maintenance. To gain insight into whether gut microbes affect the metabolism of fish, we employed fast-growing transgenic common carp (Cyprinus carpio L.) to study the connections between its large body feature and gut microbes. Metagenome-based fingerprinting and high-throughput sequencing on bacterial 16S rRNA genes indicated that fish gut was dominated by Proteobacteria, Fusobacteria, Bacteroidetes and Firmicutes, which displayed significant differences between transgenic fish and wild-type controls. Analyses to study the association of gut microbes with the fish metabolism discovered three major phyla having significant relationships with the host metabolic factors. Biochemical and histological analyses indicated transgenic fish had increased carbohydrate but decreased lipid metabolisms. Additionally, transgenic fish has a significantly lower Bacteroidetes:Firmicutes ratio than that of wild-type controls, which is similar to mammals between obese and lean individuals. These findings suggest that gut microbiotas are associated with the growth of fast growing transgenic fish, and the relative abundance of Firmicutes over Bacteroidetes could be one of the factors contributing to its fast growth. Since the large body size of transgenic fish displays a proportional body growth, which is unlike obesity in human, the results together with the findings from others also suggest that the link between obesity and gut microbiota is likely more complex than a simple Bacteroidetes:Firmicutes ratio change.}, } @article {pmid23734239, year = {2013}, author = {Salipante, SJ and Sengupta, DJ and Rosenthal, C and Costa, G and Spangler, J and Sims, EH and Jacobs, MA and Miller, SI and Hoogestraat, DR and Cookson, BT and McCoy, C and Matsen, FA and Shendure, J and Lee, CC and Harkins, TT and Hoffman, NG}, title = {Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e65226}, pmid = {23734239}, issn = {1932-6203}, mesh = {Bacteria/classification/*genetics ; Bacterial Infections/*microbiology ; Bacterial Typing Techniques/methods ; Cystic Fibrosis/genetics/microbiology ; DNA, Bacterial/chemistry/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome/*genetics ; Microbiota/genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/classification/*genetics ; Reproducibility of Results ; Species Specificity ; Sputum/microbiology ; }, abstract = {Classifying individual bacterial species comprising complex, polymicrobial patient specimens remains a challenge for culture-based and molecular microbiology techniques in common clinical use. We therefore adapted practices from metagenomics research to rapidly catalog the bacterial composition of clinical specimens directly from patients, without need for prior culture. We have combined a semiconductor deep sequencing protocol that produces reads spanning 16S ribosomal RNA gene variable regions 1 and 2 (∼360 bp) with a de-noising pipeline that significantly improves the fraction of error-free sequences. The resulting sequences can be used to perform accurate genus- or species-level taxonomic assignment. We explore the microbial composition of challenging, heterogeneous clinical specimens by deep sequencing, culture-based strain typing, and Sanger sequencing of bulk PCR product. We report that deep sequencing can catalog bacterial species in mixed specimens from which usable data cannot be obtained by conventional clinical methods. Deep sequencing a collection of sputum samples from cystic fibrosis (CF) patients reveals well-described CF pathogens in specimens where they were not detected by standard clinical culture methods, especially for low-prevalence or fastidious bacteria. We also found that sputa submitted for CF diagnostic workup can be divided into a limited number of groups based on the phylogenetic composition of the airway microbiota, suggesting that metagenomic profiling may prove useful as a clinical diagnostic strategy in the future. The described method is sufficiently rapid (theoretically compatible with same-day turnaround times) and inexpensive for routine clinical use.}, } @article {pmid23731340, year = {2013}, author = {Oh, S and Tandukar, M and Pavlostathis, SG and Chain, PS and Konstantinidis, KT}, title = {Microbial community adaptation to quaternary ammonium biocides as revealed by metagenomics.}, journal = {Environmental microbiology}, volume = {15}, number = {10}, pages = {2850-2864}, doi = {10.1111/1462-2920.12154}, pmid = {23731340}, issn = {1462-2920}, mesh = {*Adaptation, Physiological ; Bacteria/*drug effects ; Benzalkonium Compounds/*pharmacology ; *Biodiversity ; Disinfectants/pharmacology ; *Metagenomics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Quaternary ammonium compounds (QACs) represent widely used cationic biocides that persist in natural environments. Although microbial degradation, sensitivity and resistance to QACs have been extensively documented, a quantitative understanding of how whole communities adapt to QAC exposure remain elusive. To gain insights into these issues, we exposed a microbial community from a contaminated river sediment to varied levels of benzalkonium chlorides (BACs, a family of QACs) for 3 years. Comparative metagenomic analysis showed that the BAC-fed communities were dramatically decreased in phylogenetic diversity compared with the control (no BAC exposure), resulting presumably from BAC toxicity, and dominated by Pseudomonas species (> 50% of the total). Time-course metagenomics revealed that community adaptation occurred primarily via selective enrichment of BAC-degrading Pseudomonas populations, particularly P. nitroreducens, and secondarily via amino acid substitutions and horizontal transfer of a few selected genes in the Pseudomonas populations, including a gene encoding a PAS/PAC sensor protein and ring-hydroxylating dioxygenase genes. P. nitroreducens isolates were reproducibly recoverable from communities after prolonged periods of no-BAC exposure, suggesting that they are robust BAC-degraders. Our study provides new insights into the mechanisms and tempo of microbial community adaptation to QAC exposure and has implications for treating QACs in biological engineered systems.}, } @article {pmid23728738, year = {2013}, author = {Pfleiderer, A and Lagier, JC and Armougom, F and Robert, C and Vialettes, B and Raoult, D}, title = {Culturomics identified 11 new bacterial species from a single anorexia nervosa stool sample.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {32}, number = {11}, pages = {1471-1481}, pmid = {23728738}, issn = {1435-4373}, mesh = {Anorexia Nervosa/*microbiology ; Bacteria/*classification/genetics/*isolation & purification ; Bacteriological Techniques/*methods ; *Biodiversity ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Feces/*microbiology ; Female ; Humans ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {The rebirth of bacterial culture has been highlighted successively by environmental microbiologists, the design of axenic culture for intracellular bacteria in clinical microbiology, and, more recently, by human gut microbiota studies. Indeed, microbial culturomics (large scale of culture conditions with the identification of colonies by MALDI-TOF or 16S rRNA) allowed to culture 32 new bacterial species from only four stool samples studied. We performed culturomics in comparison with pyrosequencing 16S rRNA targeting the V6 region on an anorexia nervosa stool sample because this clinical condition has never been explored before by culture, while its composition has been observed to be atypical by metagenomics. We tested 88 culture conditions generating 12,700 different colonies identifying 133 bacterial species, with 19 bacterial species never isolated from the human gut before, including 11 new bacterial species for which the genome has been sequenced. These 11 new bacterial species isolated from a single stool sample allow to extend more significantly the repertoire in comparison to the bacterial species validated by the rest of the world during the last 2 years. Pyrosequencing indicated a dramatic discrepancy with the culturomics results, with only 23 OTUs assigned to the species level overlapping (17 % of the culturomics results). Most of the sequences assigned to bacteria detected only by pyrosequencing belonged to Ruminococcaceae, Lachnospiraceae, and Erysipelotrichaceae constituted by strictly anaerobic species, indicating the future route for culturomics. This study revealed new bacterial species participating significantly to the extension of the gut microbiota repertoire, which is the first step before being able to connect the bacterial composition with the geographic or clinical status.}, } @article {pmid23726530, year = {2013}, author = {Garn, H and Neves, JF and Blumberg, RS and Renz, H}, title = {Effect of barrier microbes on organ-based inflammation.}, journal = {The Journal of allergy and clinical immunology}, volume = {131}, number = {6}, pages = {1465-1478}, pmid = {23726530}, issn = {1097-6825}, support = {R37 DK044319/DK/NIDDK NIH HHS/United States ; R01 DK088199/DK/NIDDK NIH HHS/United States ; R01 DK051362/DK/NIDDK NIH HHS/United States ; DK0034854/DK/NIDDK NIH HHS/United States ; R01 DK053056/DK/NIDDK NIH HHS/United States ; DK051362/DK/NIDDK NIH HHS/United States ; DK088199/DK/NIDDK NIH HHS/United States ; R01 DK044319/DK/NIDDK NIH HHS/United States ; DK044319/DK/NIDDK NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; DK053056/DK/NIDDK NIH HHS/United States ; R56 DK053056/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Biodiversity ; Gastrointestinal Tract/immunology/microbiology ; Humans ; Hygiene Hypothesis ; Hypersensitivity/immunology/microbiology ; Inflammation/*immunology/*microbiology ; Inflammatory Bowel Diseases/immunology/microbiology ; *Metagenome ; }, abstract = {The prevalence and incidence of chronic inflammatory disorders, including allergies and asthma, as well as inflammatory bowel disease, remain on the increase. Microbes are among the environmental factors that play an important role in shaping normal and pathologic immune responses. Several concepts have been put forward to explain the effect of microbes on the development of these conditions, including the hygiene hypothesis and the microbiota hypothesis. Recently, the dynamics of the development of (intestinal) microbial colonization, its effect on innate and adaptive immune responses (homeostasis), and the role of environmental factors, such as nutrition and others, have been extensively investigated. Furthermore, there is now increasing evidence that a qualitative and quantitative disturbance in colonization (dysbiosis) is associated with dysfunction of immune responses and development of various chronic inflammatory disorders. In this article the recent epidemiologic, clinical, and experimental evidence for this interaction is discussed.}, } @article {pmid23718284, year = {2013}, author = {Xu, M and He, Z and Deng, Y and Wu, L and van Nostrand, JD and Hobbie, SE and Reich, PB and Zhou, J}, title = {Elevated CO2 influences microbial carbon and nitrogen cycling.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {124}, pmid = {23718284}, issn = {1471-2180}, mesh = {Bacteria/classification/*drug effects/genetics/*metabolism ; *Biota ; Carbon/*metabolism ; Carbon Dioxide/*metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Metagenomics ; Microarray Analysis ; Nitrogen/*metabolism ; Soil Microbiology ; }, abstract = {BACKGROUND: Elevated atmospheric CO2 (eCO2) has been shown to have significant effects on terrestrial ecosystems. However, little is known about its influence on the structure, composition, and functional potential of soil microbial communities, especially carbon (C) and nitrogen (N) cycling. A high-throughput functional gene array (GeoChip 3.0) was used to examine the composition, structure, and metabolic potential of soil microbial communities from a grassland field experiment after ten-year field exposure to ambient and elevated CO2 concentrations.

RESULTS: Distinct microbial communities were established under eCO₂. The abundance of three key C fixation genes encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), carbon monoxide dehydrogenase (CODH) and propionyl-CoA/acetyl-CoA carboxylase (PCC/ACC), significantly increased under eCO₂, and so did some C degrading genes involved in starch, cellulose, and hemicellulose. Also, nifH and nirS involved in N cycling were significantly stimulated. In addition, based on variation partitioning analysis (VPA), the soil microbial community structure was largely shaped by direct and indirect eCO₂-driven factors.

CONCLUSIONS: These findings suggest that the soil microbial community structure and their ecosystem functioning for C and N cycling were altered dramatically at eCO₂. This study provides new insights into our understanding of the feedback response of soil microbial communities to elevated CO₂ and global change.}, } @article {pmid23718053, year = {2013}, author = {Parfenova, VV and Gladkikh, AS and Belykh, OI}, title = {[Comparative study of planktonic and biofilm forms diversity in microbial communities of Lake Baĭkal (Russia)].}, journal = {Mikrobiologiia}, volume = {82}, number = {1}, pages = {94-105}, doi = {10.7868/s0026365613010126}, pmid = {23718053}, issn = {0026-3656}, mesh = {Bacteroidetes/classification/*genetics/growth & development/isolation & purification ; Biodiversity ; Biofilms/classification/*growth & development ; Cyanobacteria/classification/*genetics/growth & development/isolation & purification ; Lakes/microbiology ; Metagenome ; Microbial Consortia/genetics ; Phylogeny ; Plankton/classification/*genetics/growth & development/isolation & purification ; Proteobacteria/classification/*genetics/growth & development/isolation & purification ; RNA, Ribosomal, 16S/classification/*genetics ; Russia ; Sequence Analysis, DNA ; }, } @article {pmid23717627, year = {2013}, author = {Dimon, MT and Wood, HM and Rabbitts, PH and Arron, ST}, title = {IMSA: integrated metagenomic sequence analysis for identification of exogenous reads in a host genomic background.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e64546}, pmid = {23717627}, issn = {1932-6203}, support = {KL2 TR000143/TR/NCATS NIH HHS/United States ; }, mesh = {Algorithms ; Carcinoma, Squamous Cell/virology ; Female ; *Genes, Bacterial ; *Genes, Viral ; Genome, Human ; HeLa Cells ; High-Throughput Nucleotide Sequencing ; Human papillomavirus 16/genetics ; Human papillomavirus 18/genetics ; Humans ; *Metagenome ; Microbiota/*genetics ; Molecular Sequence Annotation ; Papillomavirus Infections/virology ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; Uterine Cervical Neoplasms/virology ; }, abstract = {Metagenomics, the study of microbial genomes within diverse environments, is a rapidly developing field. The identification of microbial sequences within a host organism enables the study of human intestinal, respiratory, and skin microbiota, and has allowed the identification of novel viruses in diseases such as Merkel cell carcinoma. There are few publicly available tools for metagenomic high throughput sequence analysis. We present Integrated Metagenomic Sequence Analysis (IMSA), a flexible, fast, and robust computational analysis pipeline that is available for public use. IMSA takes input sequence from high throughput datasets and uses a user-defined host database to filter out host sequence. IMSA then aligns the filtered reads to a user-defined universal database to characterize exogenous reads within the host background. IMSA assigns a score to each node of the taxonomy based on read frequency, and can output this as a taxonomy report suitable for cluster analysis or as a taxonomy map (TaxMap). IMSA also outputs the specific sequence reads assigned to a taxon of interest for downstream analysis. We demonstrate the use of IMSA to detect pathogens and normal flora within sequence data from a primary human cervical cancer carrying HPV16, a primary human cutaneous squamous cell carcinoma carrying HPV 16, the CaSki cell line carrying HPV16, and the HeLa cell line carrying HPV18.}, } @article {pmid23715799, year = {2014}, author = {Hyman, RW and Fukushima, M and Jiang, H and Fung, E and Rand, L and Johnson, B and Vo, KC and Caughey, AB and Hilton, JF and Davis, RW and Giudice, LC}, title = {Diversity of the vaginal microbiome correlates with preterm birth.}, journal = {Reproductive sciences (Thousand Oaks, Calif.)}, volume = {21}, number = {1}, pages = {32-40}, pmid = {23715799}, issn = {1933-7205}, mesh = {Adult ; Black or African American ; Asian ; Bacteria/*classification/genetics/isolation & purification ; Case-Control Studies ; DNA, Bacterial/isolation & purification ; Female ; Hispanic or Latino ; Humans ; *Infant, Premature ; Lactobacillus/classification/genetics/isolation & purification ; Metagenome ; Metagenomics ; *Microbiota ; Pregnancy ; Premature Birth/ethnology/*microbiology ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Ribotyping ; Risk Factors ; San Francisco/epidemiology ; Vagina/*microbiology ; White People ; }, abstract = {Reproductive tract infection is a major initiator of preterm birth (PTB). The objective of this prospective cohort study of 88 participants was to determine whether PTB correlates with the vaginal microbiome during pregnancy. Total DNA was purified from posterior vaginal fornix swabs during gestation. The 16S ribosomal RNA gene was amplified using polymerase chain reaction primers, followed by chain-termination sequencing. Bacteria were identified by comparing contig consensus sequences with the Ribosomal Database Project. Dichotomous responses were summarized via proportions and continuous variables via means ± standard deviation. Mean Shannon Diversity index differed by Welch t test (P = .00016) between caucasians with PTB and term gestation. Species diversity was greatest among African Americans (P = .0045). Change in microbiome/Lactobacillus content and presence of putative novel/noxious bacteria did not correlate with PTB. We conclude that uncultured vaginal bacteria play an important role in PTB and race/ethnicity and sampling location are important determinants of the vaginal microbiome.}, } @article {pmid23708551, year = {2013}, author = {Sahm, K and John, P and Nacke, H and Wemheuer, B and Grote, R and Daniel, R and Antranikian, G}, title = {High abundance of heterotrophic prokaryotes in hydrothermal springs of the Azores as revealed by a network of 16S rRNA gene-based methods.}, journal = {Extremophiles : life under extreme conditions}, volume = {17}, number = {4}, pages = {649-662}, pmid = {23708551}, issn = {1433-4909}, mesh = {Archaea/classification/genetics/*isolation & purification ; Azores ; Bacteria/classification/genetics/*isolation & purification ; *Biodiversity ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Hot Springs/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Two hydrothermal springs (AI: 51 °C, pH 3; AIV: 92 °C, pH 8) were analysed to determine prokaryotic community composition. Using pyrosequencing, 93,576 partial 16S rRNA gene sequences amplified with V2/V3-specific primers for Bacteria and Archaea were investigated and compared to 16S rRNA gene sequences from direct metagenome sequencing without prior amplification. The results were evaluated by fluorescence in situ hybridization (FISH). While in site AIV Bacteria and Archaea were detected in similar relative abundances (Bacteria 40 %, Archaea 35 %), the acidic spring AI was dominated by Bacteria (68 %). In spring AIV the combination of 16S rRNA gene sequence analysis and FISH revealed high abundance (>50 %) of heterotrophic bacterial genera like Caldicellulosiruptor, Dictyoglomus, and Fervidobacterium. In addition, chemolithoautotrophic Aquificales were detected in the bacterial community with Sulfurihydrogenibium being the dominant genus. Regarding Archaea, only Crenarchaeota, were detected, dominated by the family Desulfurococcaceae (>50 %). In addition, Thermoproteaceae made up almost 25 %. In the acidic spring (AI) prokaryotic diversity was lower than in the hot, slightly alkaline spring AIV. The bacterial community of site AI was dominated by organisms related to the chemolithoautotrophic genus Acidithiobacillus (43 %), to the heterotrophic Acidicaldus (38 %) and to Anoxybacillus (7.8 %). This study reveals differences in the relative abundance of heterotrophic versus autotrophic microorganisms as compared to other hydrothermal habitats. Furthermore, it shows how different methods to analyse prokaryotic communities in complex ecosystems can complement each other to obtain an in-depth picture of the taxonomic composition and diversity within these hydrothermal springs.}, } @article {pmid23707234, year = {2014}, author = {Kolmeder, CA and de Vos, WM}, title = {Metaproteomics of our microbiome - developing insight in function and activity in man and model systems.}, journal = {Journal of proteomics}, volume = {97}, number = {}, pages = {3-16}, doi = {10.1016/j.jprot.2013.05.018}, pmid = {23707234}, issn = {1876-7737}, support = {250172/ERC_/European Research Council/International ; }, mesh = {Animals ; Bacteria/genetics/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Humans ; Metagenome/physiology ; Mice ; Microbiota/*physiology ; Proteomics/*methods/trends ; }, abstract = {We are all colonized by a large microbiome, a complex set of microbes that have intimate associations with us. Culture-based approaches have provided insights in the complexity of the microbial communities living on surfaces inside and outside the body. However, the application of high-throughput sequencing technologies has identified large numbers of community members at both the phylogenetic and the (meta-)genome level. The latter allowed defining a reference set of several millions of mainly bacterial genes and provided the basis for developing approaches to target the activity and function of the human microbiome with proteomic techniques. Moreover, recent improvements in protein and peptide separation efficiencies and highly accurate mass spectrometers have promoted the field of metaproteomics, the study of the collective proteome of microbial communities. We here review the approaches that have been developed to study the human metaproteomes, focusing on intestinal tract and body fluids. Moreover, we complement these by considering metaproteomic studies in mouse and other model systems offering the option to study single species or simple consortia. Finally, we discuss present and future avenues that may be used to advance the application of metaproteomic approaches to further improve our understanding of the microbes inside and around our body. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.}, } @article {pmid23706630, year = {2013}, author = {Wilson, MC and Piel, J}, title = {Metagenomic approaches for exploiting uncultivated bacteria as a resource for novel biosynthetic enzymology.}, journal = {Chemistry & biology}, volume = {20}, number = {5}, pages = {636-647}, doi = {10.1016/j.chembiol.2013.04.011}, pmid = {23706630}, issn = {1879-1301}, mesh = {Amides/chemistry/metabolism ; Bacteria/chemistry/*enzymology/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Biological Products/chemistry/*metabolism ; *Biosynthetic Pathways ; Cyanides/chemistry/metabolism ; Metagenomics/*methods ; Peptides/chemistry/metabolism ; Polyketides/chemistry/metabolism ; }, abstract = {Most biologically active microbial natural products are known from strains that can be isolated and cultivated in the laboratory. However, the genomics era has revealed that cultured bacteria represent a mere fraction of total estimated bacterial biodiversity. With the development of community genomics, termed metagenomics, the uncultivated majority became accessible for functional analysis. Through metagenomic studies, novel biocatalysts and biosynthetic pathways are being discovered at a pace previously not possible using traditional molecular biology techniques. Additionally, the study of uncultivated bacteria has provided valuable insights into previously overlooked biocatalysts from cultured strains. This perspective highlights recent discoveries from metagenomics of uncultivated bacteria and discusses the impact of those findings on the field of natural products.}, } @article {pmid23705844, year = {2013}, author = {Ward, TL and Hosid, S and Ioshikhes, I and Altosaar, I}, title = {Human milk metagenome: a functional capacity analysis.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {116}, pmid = {23705844}, issn = {1471-2180}, support = {82826//Canadian Institutes of Health Research/Canada ; }, mesh = {Bacteria/*classification/*genetics/isolation & purification ; *Biota ; Breast Feeding ; Female ; Gene Expression Profiling ; Humans ; Infant ; Infant Formula ; *Metagenome ; Milk, Human/*microbiology ; Open Reading Frames ; }, abstract = {BACKGROUND: Human milk contains a diverse population of bacteria that likely influences colonization of the infant gastrointestinal tract. Recent studies, however, have been limited to characterization of this microbial community by 16S rRNA analysis. In the present study, a metagenomic approach using Illumina sequencing of a pooled milk sample (ten donors) was employed to determine the genera of bacteria and the types of bacterial open reading frames in human milk that may influence bacterial establishment and stability in this primal food matrix. The human milk metagenome was also compared to that of breast-fed and formula-fed infants' feces (n = 5, each) and mothers' feces (n = 3) at the phylum level and at a functional level using open reading frame abundance. Additionally, immune-modulatory bacterial-DNA motifs were also searched for within human milk.

RESULTS: The bacterial community in human milk contained over 360 prokaryotic genera, with sequences aligning predominantly to the phyla of Proteobacteria (65%) and Firmicutes (34%), and the genera of Pseudomonas (61.1%), Staphylococcus (33.4%) and Streptococcus (0.5%). From assembled human milk-derived contigs, 30,128 open reading frames were annotated and assigned to functional categories. When compared to the metagenome of infants' and mothers' feces, the human milk metagenome was less diverse at the phylum level, and contained more open reading frames associated with nitrogen metabolism, membrane transport and stress response (P < 0.05). The human milk metagenome also contained a similar occurrence of immune-modulatory DNA motifs to that of infants' and mothers' fecal metagenomes.

CONCLUSIONS: Our results further expand the complexity of the human milk metagenome and enforce the benefits of human milk ingestion on the microbial colonization of the infant gut and immunity. Discovery of immune-modulatory motifs in the metagenome of human milk indicates more exhaustive analyses of the functionality of the human milk metagenome are warranted.}, } @article {pmid23705801, year = {2013}, author = {Ottesen, AR and González Peña, A and White, JR and Pettengill, JB and Li, C and Allard, S and Rideout, S and Allard, M and Hill, T and Evans, P and Strain, E and Musser, S and Knight, R and Brown, E}, title = {Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato).}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {114}, pmid = {23705801}, issn = {1471-2180}, mesh = {Bacteria/*classification/*genetics/isolation & purification ; *Biota ; Fungi/*classification/*genetics/isolation & purification ; Solanum lycopersicum/*microbiology ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Research to understand and control microbiological risks associated with the consumption of fresh fruits and vegetables has examined many environments in the farm to fork continuum. An important data gap however, that remains poorly studied is the baseline description of microflora that may be associated with plant anatomy either endemically or in response to environmental pressures. Specific anatomical niches of plants may contribute to persistence of human pathogens in agricultural environments in ways we have yet to describe. Tomatoes have been implicated in outbreaks of Salmonella at least 17 times during the years spanning 1990 to 2010. Our research seeks to provide a baseline description of the tomato microbiome and possibly identify whether or not there is something distinctive about tomatoes or their growing ecology that contributes to persistence of Salmonella in this important food crop.

RESULTS: DNA was recovered from washes of epiphytic surfaces of tomato anatomical organs; leaves, stems, roots, flowers and fruits of Solanum lycopersicum (BHN602), grown at a site in close proximity to commercial farms previously implicated in tomato-Salmonella outbreaks. DNA was amplified for targeted 16S and 18S rRNA genes and sheared for shotgun metagenomic sequencing. Amplicons and metagenomes were used to describe "native" bacterial microflora for diverse anatomical parts of Virginia-grown tomatoes.

CONCLUSIONS: Distinct groupings of microbial communities were associated with different tomato plant organs and a gradient of compositional similarity could be correlated to the distance of a given plant part from the soil. Unique bacterial phylotypes (at 95% identity) were associated with fruits and flowers of tomato plants. These include Microvirga, Pseudomonas, Sphingomonas, Brachybacterium, Rhizobiales, Paracocccus, Chryseomonas and Microbacterium. The most frequently observed bacterial taxa across aerial plant regions were Pseudomonas and Xanthomonas. Dominant fungal taxa that could be identified to genus with 18S amplicons included Hypocrea, Aureobasidium and Cryptococcus. No definitive presence of Salmonella could be confirmed in any of the plant samples, although 16S sequences suggested that closely related genera were present on leaves, fruits and roots.}, } @article {pmid23702516, year = {2013}, author = {Baker, BJ and Sheik, CS and Taylor, CA and Jain, S and Bhasi, A and Cavalcoli, JD and Dick, GJ}, title = {Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling.}, journal = {The ISME journal}, volume = {7}, number = {10}, pages = {1962-1973}, pmid = {23702516}, issn = {1751-7370}, mesh = {Archaea/classification/enzymology/genetics/metabolism/*physiology ; Bacteria/classification/enzymology/genetics/metabolism ; Biodiversity ; California ; *Carbon Cycle ; Genes, rRNA/genetics ; Hydrothermal Vents/*microbiology ; Metagenome/genetics ; Nitrites/metabolism ; *Nitrogen Cycle ; Oceans and Seas ; Oxidoreductases/genetics/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Transcriptome ; }, abstract = {The deep ocean is an important component of global biogeochemical cycles because it contains one of the largest pools of reactive carbon and nitrogen on earth. However, the microbial communities that drive deep-sea geochemistry are vastly unexplored. Metatranscriptomics offers new windows into these communities, but it has been hampered by reliance on genome databases for interpretation. We reconstructed the transcriptomes of microbial populations from Guaymas Basin, in the deep Gulf of California, through shotgun sequencing and de novo assembly of total community RNA. Many of the resulting messenger RNA (mRNA) contiguous sequences contain multiple genes, reflecting co-transcription of operons, including those from dominant members. Also prevalent were transcripts with only limited representation (2.8 times coverage) in a corresponding metagenome, including a considerable portion (1.2 Mb total assembled mRNA sequence) with similarity (96%) to a marine heterotroph, Alteromonas macleodii. This Alteromonas and euryarchaeal marine group II populations displayed abundant transcripts from amino-acid transporters, suggesting recycling of organic carbon and nitrogen from amino acids. Also among the most abundant mRNAs were catalytic subunits of the nitrite oxidoreductase complex and electron transfer components involved in nitrite oxidation. These and other novel genes are related to novel Nitrospirae and have limited representation in accompanying metagenomic data. High throughput sequencing of 16S ribosomal RNA (rRNA) genes and rRNA read counts confirmed that Nitrospirae are minor yet widespread members of deep-sea communities. These results implicate a novel bacterial group in deep-sea nitrite oxidation, the second step of nitrification. This study highlights metatranscriptomic assembly as a valuable approach to study microbial communities.}, } @article {pmid23694815, year = {2013}, author = {Hanreich, A and Schimpf, U and Zakrzewski, M and Schlüter, A and Benndorf, D and Heyer, R and Rapp, E and Pühler, A and Reichl, U and Klocke, M}, title = {Metagenome and metaproteome analyses of microbial communities in mesophilic biogas-producing anaerobic batch fermentations indicate concerted plant carbohydrate degradation.}, journal = {Systematic and applied microbiology}, volume = {36}, number = {5}, pages = {330-338}, doi = {10.1016/j.syapm.2013.03.006}, pmid = {23694815}, issn = {1618-0984}, mesh = {Anaerobiosis ; *Biofuels ; Bioreactors/*microbiology ; *Biota ; Biotransformation ; *Carbohydrate Metabolism ; Fermentation ; *Metagenome ; Plants/*chemistry ; *Proteome ; }, abstract = {Microbial communities in biogas batch fermentations, using straw and hay as co-substrates, were analyzed at the gene and protein level by metagenomic and metaproteomic approaches. The analysis of metagenomic data revealed that the Clostridiales and Bacteroidales orders were prevalent in the community. However, the number of sequences assigned to the Clostridiales order decreased during fermentation, whereas the number of sequences assigned to the Bacteroidales order increased. In addition, changes at the functional level were monitored and the metaproteomic analyses detected transporter proteins and flagellins, which were expressed mainly by members of the Bacteroidetes and Firmicutes phyla. A high number of sugar transporters, expressed by members of the Bacteroidetes, proved their potential to take up various glycans efficiently. Metagenome data also showed that methanogenic organisms represented less than 4% of the community, while 20-30% of the identified proteins were of archeal origin. These data suggested that methanogens were disproportionally active. In conclusion, the community studied was capable of digesting the recalcitrant co-substrate. Members of the Firmicutes phylum seemed to be the main degraders of cellulose, even though expression of only a few glycoside hydrolases was detected. The Bacteroidetes phylum expressed a high number of sugar transporters and seemed to specialize in the digestion of other polysaccharides. Finally, it was found that key enzymes of methanogenesis were expressed in high quantities, indicating the high metabolic activity of methanogens, although they only represented a minor group within the microbial community.}, } @article {pmid23694698, year = {2013}, author = {Jiang, X and Hu, X and Xu, W and He, T and Park, EK}, title = {Comparison of dimensional reduction methods for detecting and visualizing novel patterns in human and marine microbiome.}, journal = {IEEE transactions on nanobioscience}, volume = {12}, number = {3}, pages = {199-205}, doi = {10.1109/TNB.2013.2263287}, pmid = {23694698}, issn = {1558-2639}, mesh = {Animals ; Databases, Genetic ; Feces/microbiology ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Nonlinear Dynamics ; Oceans and Seas ; Principal Component Analysis ; Proteins/genetics/metabolism ; Water Microbiology ; }, abstract = {Using metagenomics to detect the global structure of microbial community remains a significant challenge. The structure of a microbial community and its functions are complicated because of not only the complex interactions among microbes but also their interactions with confounding environmental factors. Recently dimension reduction methods have been employed extensively to investigate the complex structure embedded in metagenomic profiles which summarize the abundance of functional or taxonomic categorizations in metagenomic studies. However, metagenomic profiles are not necessary to meet the "Assumption of Linearity" behind these methods. Therefore it is worth to investigate whether nonlinear methods are appropriate methods which can be utilized in metagenomic analysis. In this paper, we compare the applications of several methods, including two linear methods (Principle component analysis and nonnegative matrix factorization) and a nonlinear manifold learning method--Isomap on visualizing and analyzing metagenomic profiles. These methods are applied and compared on a taxonomic profile from 33 human gut metagenomes and a large-scale Pfam profile which are derived from 45 metagenomes in Global Ocean Sampling expedition. We find that all three methods can discover interesting structures of the taxonomic profile from human gut. Furthermore, Isomap identified a novel nonlinear structure of protein families. The relationships among the identified nonlinear components and environmental factors of global ocean are explored. The results indicate that nonlinear methods could be a complementary technique to current linear methods in analyzing metagenomic dataset.}, } @article {pmid23690942, year = {2013}, author = {Tottey, W and Denonfoux, J and Jaziri, F and Parisot, N and Missaoui, M and Hill, D and Borrel, G and Peyretaillade, E and Alric, M and Harris, HM and Jeffery, IB and Claesson, MJ and O'Toole, PW and Peyret, P and Brugère, JF}, title = {The human gut chip "HuGChip", an explorative phylogenetic microarray for determining gut microbiome diversity at family level.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e62544}, pmid = {23690942}, issn = {1932-6203}, mesh = {Analysis of Variance ; Bacteria/classification/*genetics ; Base Sequence ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Microarray Analysis ; Microbiota/*genetics ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis/instrumentation/*methods ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Evaluating the composition of the human gut microbiota greatly facilitates studies on its role in human pathophysiology, and is heavily reliant on culture-independent molecular methods. A microarray designated the Human Gut Chip (HuGChip) was developed to analyze and compare human gut microbiota samples. The PhylArray software was used to design specific and sensitive probes. The DNA chip was composed of 4,441 probes (2,442 specific and 1,919 explorative probes) targeting 66 bacterial families. A mock community composed of 16S rRNA gene sequences from intestinal species was used to define the threshold criteria to be used to analyze complex samples. This was then experimentally verified with three human faecal samples and results were compared (i) with pyrosequencing of the V4 hypervariable region of the 16S rRNA gene, (ii) metagenomic data, and (iii) qPCR analysis of three phyla. When compared at both the phylum and the family level, high Pearson's correlation coefficients were obtained between data from all methods. The HuGChip development and validation showed that it is not only able to assess the known human gut microbiota but could also detect unknown species with the explorative probes to reveal the large number of bacterial sequences not yet described in the human gut microbiota, overcoming the main inconvenience encountered when developing microarrays.}, } @article {pmid23688194, year = {2013}, author = {Minard, G and Mavingui, P and Moro, CV}, title = {Diversity and function of bacterial microbiota in the mosquito holobiont.}, journal = {Parasites & vectors}, volume = {6}, number = {}, pages = {146}, pmid = {23688194}, issn = {1756-3305}, mesh = {Animals ; Bacteria/*classification/*genetics ; Bacterial Physiological Phenomena ; *Biodiversity ; Culicidae/*microbiology ; Female ; Male ; *Metagenome ; Mosquito Control/methods ; Symbiosis ; }, abstract = {Mosquitoes (Diptera: Culicidae) have been shown to host diverse bacterial communities that vary depending on the sex of the mosquito, the developmental stage, and ecological factors. Some studies have suggested a potential role of microbiota in the nutritional, developmental and reproductive biology of mosquitoes. Here, we present a review of the diversity and functions of mosquito-associated bacteria across multiple variation factors, emphasizing recent findings. Mosquito microbiota is considered in the context of possible extended phenotypes conferred on the insect hosts that allow niche diversification and rapid adaptive evolution in other insects. These kinds of observations have prompted the recent development of new mosquito control methods based on the use of symbiotically-modified mosquitoes to interfere with pathogen transmission or reduce the host life span and reproduction. New opportunities for exploiting bacterial function for vector control are highlighted.}, } @article {pmid23686846, year = {2013}, author = {Launer, J}, title = {Meet your microbiome.}, journal = {Postgraduate medical journal}, volume = {89}, number = {1052}, pages = {367-368}, doi = {10.1136/postgradmedj-2013-132066}, pmid = {23686846}, issn = {1469-0756}, mesh = {Biomedical Research/*trends ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; *Metagenome ; *Metagenomics ; *Microbiota ; }, } @article {pmid23681441, year = {2013}, author = {van Helden, PD and van Helden, LS and Hoal, EG}, title = {One world, one health. Humans, animals and the environment are inextricably linked--a fact that needs to be remembered and exploited in our modern approach to health.}, journal = {EMBO reports}, volume = {14}, number = {6}, pages = {497-501}, pmid = {23681441}, issn = {1469-3178}, mesh = {Animals ; *Biodiversity ; Birds ; Cats ; Cattle ; Disease Reservoirs/parasitology/virology ; Health ; Humans ; Influenza in Birds/*transmission ; Influenza, Human/*transmission ; Metagenome/physiology ; Toxoplasmosis/prevention & control/*transmission ; Toxoplasmosis, Animal/prevention & control/*transmission ; Tuberculosis, Pulmonary/transmission/*veterinary ; Zoonoses ; }, } @article {pmid23679065, year = {2013}, author = {Siering, PL and Wolfe, GV and Wilson, MS and Yip, AN and Carey, CM and Wardman, CD and Shapiro, RS and Stedman, KM and Kyle, J and Yuan, T and Van Nostrand, JD and He, Z and Zhou, J}, title = {Microbial biogeochemistry of Boiling Springs Lake: a physically dynamic, oligotrophic, low-pH geothermal ecosystem.}, journal = {Geobiology}, volume = {11}, number = {4}, pages = {356-376}, doi = {10.1111/gbi.12041}, pmid = {23679065}, issn = {1472-4669}, support = {52002680//Howard Hughes Medical Institute/United States ; }, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biota ; California ; *Ecosystem ; Heterotrophic Processes ; Hot Springs/*chemistry/*microbiology ; Hot Temperature ; Hydrogen-Ion Concentration ; Lakes/*chemistry/*microbiology ; Metabolic Networks and Pathways/genetics ; Metagenome ; Microarray Analysis ; }, abstract = {Boiling Springs Lake (BSL) in Lassen Volcanic National Park, California, is North America's largest hot spring, but little is known about the physical, chemical, and biological features of the system. Using a remotely operated vessel, we characterized the bathymetry and near-surface temperatures at sub-meter resolution. The majority of the 1.2 ha, pH 2.2 lake is 10 m deep and 50-52 °C, but temperatures reach 93 °C locally. We extracted DNA from water and sediments collected from warm (52 °C) and hot (73-83 °C) sites separated by 180 m. Gene clone libraries and functional gene microarray (GeoChip 3.0) were used to investigate the BSL community, and uptake of radiolabeled carbon sources was used to assess the relative importance of heterotrophic vs. autotrophic production. Microbial assemblages are similar in both sites despite the strong temperature differential, supporting observations of a dynamic, convectively mixed system. Bacteria in the Actinobacteria and Aquificales phyla are abundant in the water column, and Archaea distantly related to known taxa are abundant in sediments. The functional potential appears similar across a 5-year time span, indicating a stable community with little inter-annual variation, despite the documented seasonal temperature cycle. BSL water-derived DNA contains genes for complete C, N, and S cycles, and low hybridization to probes for N and S oxidation suggests that reductive processes dominate. Many of the detected genes for these processes were from uncultivated bacteria, suggesting novel organisms are responsible for key ecosystem services. Selection imposed by low nutrients, low pH, and high temperature appear to result in low diversity and evenness of genes for key functions involved in C, N, and S cycling. Conversely, organic degradation genes appear to be functionally redundant, and the rapid assimilation of radiolabeled organic carbon into BSL cells suggests the importance of allochthonous C fueling heterotrophic production in the BSL C cycle.}, } @article {pmid23677009, year = {2013}, author = {von Bergen, M and Jehmlich, N and Taubert, M and Vogt, C and Bastida, F and Herbst, FA and Schmidt, F and Richnow, HH and Seifert, J}, title = {Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology.}, journal = {The ISME journal}, volume = {7}, number = {10}, pages = {1877-1885}, pmid = {23677009}, issn = {1751-7370}, mesh = {Animals ; Bacterial Proteins/*metabolism ; Carbon Isotopes/metabolism ; Ecology/*methods ; Humans ; Isotope Labeling ; Microbiota/genetics/*physiology ; Nitrogen Isotopes/metabolism ; *Proteomics ; }, abstract = {The recent development of metaproteomics has enabled the direct identification and quantification of expressed proteins from microbial communities in situ, without the need for microbial enrichment. This became possible by (1) significant increases in quality and quantity of metagenome data and by improvements of (2) accuracy and (3) sensitivity of modern mass spectrometers (MS). The identification of physiologically relevant enzymes can help to understand the role of specific species within a community or an ecological niche. Beside identification, relative and absolute quantitation is also crucial. We will review label-free and label-based methods of quantitation in MS-based proteome analysis and the contribution of quantitative proteome data to microbial ecology. Additionally, approaches of protein-based stable isotope probing (protein-SIP) for deciphering community structures are reviewed. Information on the species-specific metabolic activity can be obtained when substrates or nutrients are labeled with stable isotopes in a protein-SIP approach. The stable isotopes ((13)C, (15)N, (36)S) are incorporated into proteins and the rate of incorporation can be used for assessing the metabolic activity of the corresponding species. We will focus on the relevance of the metabolic and phylogenetic information retrieved with protein-SIP studies and for detecting and quantifying the carbon flux within microbial consortia. Furthermore, the combination of protein-SIP with established tools in microbial ecology such as other stable isotope probing techniques are discussed.}, } @article {pmid23671121, year = {2013}, author = {Chan, Y and Van Nostrand, JD and Zhou, J and Pointing, SB and Farrell, RL}, title = {Functional ecology of an Antarctic Dry Valley.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {22}, pages = {8990-8995}, pmid = {23671121}, issn = {1091-6490}, mesh = {Analysis of Variance ; Antarctic Regions ; Base Sequence ; *Biological Evolution ; Carbon/metabolism ; DNA Probes ; Ecology ; *Ecosystem ; *Genetic Variation ; Geography ; Metagenomics/methods ; Microarray Analysis ; Molecular Sequence Data ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; Soil/*analysis ; *Soil Microbiology ; Stress, Physiological/genetics ; }, abstract = {The McMurdo Dry Valleys are the largest ice-free region in Antarctica and are critically at risk from climate change. The terrestrial landscape is dominated by oligotrophic mineral soils and extensive exposed rocky surfaces where biota are largely restricted to microbial communities, although their ability to perform the majority of geobiological processes has remained largely uncharacterized. Here, we identified functional traits that drive microbial survival and community assembly, using a metagenomic approach with GeoChip-based functional gene arrays to establish metabolic capabilities in communities inhabiting soil and rock surface niches in McKelvey Valley. Major pathways in primary metabolism were identified, indicating significant plasticity in autotrophic, heterotrophic, and diazotrophic strategies supporting microbial communities. This represents a major advance beyond biodiversity surveys in that we have now identified how putative functional ecology drives microbial community assembly. Significant differences were apparent between open soil, hypolithic, chasmoendolithic, and cryptoendolithic communities. A suite of previously unappreciated Antarctic microbial stress response pathways, thermal, osmotic, and nutrient limitation responses were identified and related to environmental stressors, offering tangible clues to the mechanisms behind the enduring success of microorganisms in this seemingly inhospitable terrain. Rocky substrates exposed to larger fluctuations in environmental stress supported greater functional diversity in stress-response pathways than soils. Soils comprised a unique reservoir of genes involved in transformation of organic hydrocarbons and lignin-like degradative pathways. This has major implications for the evolutionary origin of the organisms, turnover of recalcitrant substrates in Antarctic soils, and predicting future responses to anthropogenic pollution.}, } @article {pmid23670539, year = {2013}, author = {Segata, N and Boernigen, D and Tickle, TL and Morgan, XC and Garrett, WS and Huttenhower, C}, title = {Computational meta'omics for microbial community studies.}, journal = {Molecular systems biology}, volume = {9}, number = {}, pages = {666}, pmid = {23670539}, issn = {1744-4292}, support = {1R01CA154426/CA/NCI NIH HHS/United States ; K08 AI078942/AI/NIAID NIH HHS/United States ; R01 CA154426/CA/NCI NIH HHS/United States ; 1R01HG005969/HG/NHGRI NIH HHS/United States ; R01 HG005969/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/classification/*genetics ; Computer Simulation ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Humans ; *Metagenome ; Metagenomics/*methods ; Microbial Consortia/*genetics ; Models, Genetic ; Phylogeny ; *Software ; }, abstract = {Complex microbial communities are an integral part of the Earth's ecosystem and of our bodies in health and disease. In the last two decades, culture-independent approaches have provided new insights into their structure and function, with the exponentially decreasing cost of high-throughput sequencing resulting in broadly available tools for microbial surveys. However, the field remains far from reaching a technological plateau, as both computational techniques and nucleotide sequencing platforms for microbial genomic and transcriptional content continue to improve. Current microbiome analyses are thus starting to adopt multiple and complementary meta'omic approaches, leading to unprecedented opportunities to comprehensively and accurately characterize microbial communities and their interactions with their environments and hosts. This diversity of available assays, analysis methods, and public data is in turn beginning to enable microbiome-based predictive and modeling tools. We thus review here the technological and computational meta'omics approaches that are already available, those that are under active development, their success in biological discovery, and several outstanding challenges.}, } @article {pmid23664726, year = {2013}, author = {Colson, P and Fancello, L and Gimenez, G and Armougom, F and Desnues, C and Fournous, G and Yoosuf, N and Million, M and La Scola, B and Raoult, D}, title = {Evidence of the megavirome in humans.}, journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology}, volume = {57}, number = {3}, pages = {191-200}, doi = {10.1016/j.jcv.2013.03.018}, pmid = {23664726}, issn = {1873-5967}, mesh = {Amino Acid Sequence ; Cluster Analysis ; DNA Viruses/classification/*genetics/*isolation & purification ; DNA, Viral/chemistry/genetics ; Gastrointestinal Tract/*virology ; *Genome, Viral ; Humans ; Male ; Metagenomics/methods ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; Senegal ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Young Adult ; }, abstract = {BACKGROUND: Megavirales is a proposed new virus order composed of Mimivirus, Marseillevirus and closely related viruses, as well as members of the families Poxviridae, Iridoviridae, Ascoviridae, Phycodnaviridae and Asfarviridae. The Megavirales virome, which we refer to as the megavirome, has been largely neglected until now because of the use of technical procedures that have jeopardized the discovery of giant viruses, particularly the use of filters with pore sizes in the 0.2-0.45-μm range. Concurrently, there has been accumulating evidence supporting the role of Mimivirus, discovered while investigating a pneumonia outbreak using amoebal coculture, as a causative agent in pneumonia.

OBJECTIVES: In this paper, we describe the detection of sequences related to Mimivirus and Marseillevirus in the gut microbiota from a young Senegalese man. We also searched for sequences related to Megavirales in human metagenomes publicly available in sequence databases.

RESULTS: We serendipitously detected Mimivirus- and Marseillevirus-like sequences while using a new metagenomic approach targeting bacterial DNA that subsequently led to the isolation of a new member of the family Marseilleviridae, named Senegalvirus, from human stools. This discovery demonstrates the possibility of the presence of giant viruses of amoebae in humans. In addition, we detected sequences related to Megavirales members in several human metagenomes, which adds to previous findings by several groups.

CONCLUSIONS: Overall, we present convergent evidence of the presence of mimiviruses and marseilleviruses in humans. Our findings suggest that we should re-evaluate the human megavirome and investigate the prevalence, diversity and potential pathogenicity of giant viruses in humans.}, } @article {pmid23663440, year = {2013}, author = {Haahtela, T and Holgate, S and Pawankar, R and Akdis, CA and Benjaponpitak, S and Caraballo, L and Demain, J and Portnoy, J and von Hertzen, L and , }, title = {The biodiversity hypothesis and allergic disease: world allergy organization position statement.}, journal = {The World Allergy Organization journal}, volume = {6}, number = {1}, pages = {3}, pmid = {23663440}, issn = {1939-4551}, support = {G0800766/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Biodiversity loss and climate change secondary to human activities are now being associated with various adverse health effects. However, less attention is being paid to the effects of biodiversity loss on environmental and commensal (indigenous) microbiotas. Metagenomic and other studies of healthy and diseased individuals reveal that reduced biodiversity and alterations in the composition of the gut and skin microbiota are associated with various inflammatory conditions, including asthma, allergic and inflammatory bowel diseases (IBD), type1 diabetes, and obesity. Altered indigenous microbiota and the general microbial deprivation characterizing the lifestyle of urban people in affluent countries appear to be risk factors for immune dysregulation and impaired tolerance. The risk is further enhanced by physical inactivity and a western diet poor in fresh fruit and vegetables, which may act in synergy with dysbiosis of the gut flora. Studies of immigrants moving from non-affluent to affluent regions indicate that tolerance mechanisms can rapidly become impaired in microbe-poor environments. The data on microbial deprivation and immune dysfunction as they relate to biodiversity loss are evaluated in this Statement of World Allergy Organization (WAO). We propose that biodiversity, the variability among living organisms from all sources are closely related, at both the macro- and micro-levels. Loss of the macrodiversity is associated with shrinking of the microdiversity, which is associated with alterations of the indigenous microbiota. Data on behavioural means to induce tolerance are outlined and a proposal made for a Global Allergy Plan to prevent and reduce the global allergy burden for affected individuals and the societies in which they live.}, } @article {pmid23662775, year = {2013}, author = {Stecher, B and Berry, D and Loy, A}, title = {Colonization resistance and microbial ecophysiology: using gnotobiotic mouse models and single-cell technology to explore the intestinal jungle.}, journal = {FEMS microbiology reviews}, volume = {37}, number = {5}, pages = {793-829}, doi = {10.1111/1574-6976.12024}, pmid = {23662775}, issn = {1574-6976}, mesh = {Animals ; Computational Biology ; *Germ-Free Life ; Intestines/*microbiology ; Isotope Labeling ; Mice ; *Microbiota ; *Models, Animal ; Single-Cell Analysis/*methods ; Symbiosis ; }, abstract = {The highly diverse intestinal microbiota forms a structured community engaged in constant communication with itself and its host and is characterized by extensive ecological interactions. A key benefit that the microbiota affords its host is its ability to protect against infections in a process termed colonization resistance (CR), which remains insufficiently understood. In this review, we connect basic concepts of CR with new insights from recent years and highlight key technological advances in the field of microbial ecology. We present a selection of statistical and bioinformatics tools used to generate hypotheses about synergistic and antagonistic interactions in microbial ecosystems from metagenomic datasets. We emphasize the importance of experimentally testing these hypotheses and discuss the value of gnotobiotic mouse models for investigating specific aspects related to microbiota-host-pathogen interactions in a well-defined experimental system. We further introduce new developments in the area of single-cell analysis using fluorescence in situ hybridization in combination with metabolic stable isotope labeling technologies for studying the in vivo activities of complex community members. These approaches promise to yield novel insights into the mechanisms of CR and intestinal ecophysiology in general, and give researchers the means to experimentally test hypotheses in vivo at varying levels of biological and ecological complexity.}, } @article {pmid23656607, year = {2013}, author = {Boase, S and Foreman, A and Cleland, E and Tan, L and Melton-Kreft, R and Pant, H and Hu, FZ and Ehrlich, GD and Wormald, PJ}, title = {The microbiome of chronic rhinosinusitis: culture, molecular diagnostics and biofilm detection.}, journal = {BMC infectious diseases}, volume = {13}, number = {}, pages = {210}, pmid = {23656607}, issn = {1471-2334}, mesh = {Adult ; Bacteria/classification/genetics/*isolation & purification ; *Bacterial Physiological Phenomena ; Biodiversity ; Biofilms/*growth & development ; Chronic Disease ; Coinfection/microbiology ; Female ; Fungi/classification/genetics/*isolation & purification ; Humans ; Male ; *Metagenome ; Microbiological Techniques/methods ; Middle Aged ; Rhinitis/*microbiology ; Sinusitis/*microbiology ; }, abstract = {BACKGROUND: Bacteria and fungi are believed to influence mucosal inflammation in chronic rhinosinusitis (CRS). However their presence and relationship to disease is debated. This study used multiple detection methods to compare microbial diversity and microbial abundance in healthy and diseased sinonasal mucosa. The utility of contemporary detection methods is also examined.

METHODS: Sinonasal mucosa was analyzed from 38 CRS and 6 controls. Bacterial and fungal analysis was performed using conventional culture, molecular diagnostics (polymerase chain reaction coupled with electrospray ionization time-of-flight mass spectrometry) and fluorescence in situ hybridization.

RESULTS: Microbes were detected in all samples, including controls, and were often polymicrobial. 33 different bacterial species were detected in CRS, 5 in control patients, with frequent recovery of anaerobes. Staphylococcus aureus and Propionibacterium acnes were the most common organisms in CRS and controls, respectively. Using a model organism, FISH had a sensitivity of 78%, and a specificity of 93%. Many species were detected in both CRS and controls however, microbial abundance was associated with disease manifestation.

CONCLUSIONS: This study highlights some cornerstones of microbial variations in healthy and diseased paranasal sinuses. Whilst the healthy sinus is clearly not sterile, it appears prevalence and abundance of organisms is critical in determining disease. Evidence from high-sensitivity techniques, limits the role of fungi in CRS to a small group of patients. Comparison with molecular analysis suggests that the detection threshold of FISH and culture is related to organism abundance and, furthermore, culture tends to select for rapidly growing organisms.}, } @article {pmid23651955, year = {2013}, author = {Broaders, E and Gahan, CG and Marchesi, JR}, title = {Mobile genetic elements of the human gastrointestinal tract: potential for spread of antibiotic resistance genes.}, journal = {Gut microbes}, volume = {4}, number = {4}, pages = {271-280}, pmid = {23651955}, issn = {1949-0984}, mesh = {Drug Resistance, Bacterial ; Gastrointestinal Tract/*microbiology ; Gene Transfer, Horizontal ; Humans ; *Interspersed Repetitive Sequences ; *Microbiota ; }, abstract = {The human intestine is an important location for horizontal gene transfer (HGT) due to the presence of a densely populated community of microorganisms which are essential to the health of the human superorganism. HGT in this niche has the potential to influence the evolution of members of this microbial community and to mediate the spread of antibiotic resistance genes from commensal organisms to potential pathogens. Recent culture-independent techniques and metagenomic studies have provided an insight into the distribution of mobile genetic elements (MGEs) and the extent of HGT in the human gastrointestinal tract. In this mini-review, we explore the current knowledge of mobile genetic elements in the gastrointestinal tract, the progress of research into the distribution of antibiotic resistance genes in the gut and the potential role of MGEs in the spread of antibiotic resistance. In the face of reduced treatment options for many clinical infections, understanding environmental and commensal antibiotic resistance and spread is critical to the future development of meaningful and long lasting anti-microbial therapies.}, } @article {pmid23651561, year = {2013}, author = {Lemay, MA and Donnelly, DJ and Russello, MA}, title = {Transcriptome-wide comparison of sequence variation in divergent ecotypes of kokanee salmon.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {308}, pmid = {23651561}, issn = {1471-2164}, mesh = {Animals ; *Ecotype ; *Genetic Variation ; Lakes ; Metagenomics ; Molecular Sequence Annotation ; Polymorphism, Single Nucleotide ; Salmon/classification/*genetics ; Sequence Analysis, RNA ; *Transcriptome ; }, abstract = {BACKGROUND: High throughput next-generation sequencing technology has enabled the collection of genome-wide sequence data and revolutionized single nucleotide polymorphism (SNP) discovery in a broad range of species. When analyzed within a population genomics framework, SNP-based genotypic data may be used to investigate questions of evolutionary, ecological, and conservation significance in natural populations of non-model organisms. Kokanee salmon are recently diverged freshwater populations of sockeye salmon (Oncorhynchus nerka) that exhibit reproductive ecotypes (stream-spawning and shore-spawning) in lakes throughout western North America and northeast Asia. Current conservation and management strategies may treat these ecotypes as discrete stocks, however their recent divergence and low levels of gene flow make in-season genetic stock identification a challenge. The development of genome-wide SNP markers is an essential step towards fine-scale stock identification, and may enable a direct investigation of the genetic basis of ecotype divergence.

RESULTS: We used pooled cDNA samples from both ecotypes of kokanee to generate 750 million base pairs of transcriptome sequence data. These raw data were assembled into 11,074 high coverage contigs from which we identified 32,699 novel single nucleotide polymorphisms. A subset of these putative SNPs was validated using high-resolution melt analysis and Sanger resequencing to genotype independent samples of kokanee and anadromous sockeye salmon. We also identified a number of contigs that were composed entirely of reads from a single ecotype, which may indicate regions of differential gene expression between the two reproductive ecotypes. In addition, we found some evidence for greater pathogen load among the kokanee sampled in stream-spawning habitats, suggesting a possible evolutionary advantage to shore-spawning that warrants further study.

CONCLUSIONS: This study provides novel genomic resources to support population genetic and genomic studies of both kokanee and anadromous sockeye salmon, and has the potential to produce markers capable of fine-scale stock assessment. While this RNAseq approach was successful at identifying a large number of new SNP loci, we found that the frequency of alleles present in the pooled transcriptome data was not an accurate predictor of population allele frequencies.}, } @article {pmid23646192, year = {2013}, author = {Oikonomou, G and Teixeira, AG and Foditsch, C and Bicalho, ML and Machado, VS and Bicalho, RC}, title = {Fecal microbial diversity in pre-weaned dairy calves as described by pyrosequencing of metagenomic 16S rDNA. Associations of Faecalibacterium species with health and growth.}, journal = {PloS one}, volume = {8}, number = {4}, pages = {e63157}, pmid = {23646192}, issn = {1932-6203}, mesh = {Animals ; Animals, Newborn ; Body Weight ; Cattle ; DNA, Ribosomal ; Feces/*microbiology ; Gastrointestinal Tract/microbiology ; *Metagenomics ; *Microbiota ; Molecular Sequence Data ; *RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {In this study, we use barcoded pyrosequencing of the 16S rRNA gene to characterize the fecal microbiota of neonatal calves and identify possible relationships of certain microbiota profiles with health and weight gain. Fecal samples were obtained weekly from 61 calves from birth until weaning (seventh week of the calves' life). Firmicutes was the most prevalent phylum, with a prevalence ranging from 63.84% to 81.90%, followed by Bacteroidetes (8.36% to 23.93%), Proteobacteria (3.72% to 9.75%), Fusobacteria (0.76% to 5.67%), and Actinobacteria (1.02% to 2.35%). Chao1 index gradually increased from the first to the seventh postnatal week. Chao1 index was lower during the third, fourth, and fifth week of life in calves that suffered from pneumonia and were treated with antibiotics. Diarrhea incidence during the first four weeks of the calves' life was also associated with a reduction of microbial diversity during the third week of life. Increased fecal microbial diversity after the second week of life was associated with higher weight gain. Using discriminant analysis we were able to show differences in the microbiota profiles between different weeks of life, between high and low weight gain groups of calves, and between calves affected and not affected with diarrhea during the first four weeks life. The prevalence of Faecalibacterium spp. in the first week of life was associated with weight gain and the incidence of diarrhea, with higher prevalence being associated with higher weight gain and less diarrhea. Representative sequences from Faecalibacterium spp. were closely affiliated to Faecalibacterium prausnitzii. Results presented here provide new information regarding the intestinal microbiota of neonatal calves and its association with health and growth. Fecal microbial diversity was associated with calf age, disease status and growth rates. Results suggesting a possible beneficial effect of Faecalibacterium spp. on health and growth are promising.}, } @article {pmid23643636, year = {2013}, author = {Wu, GD and Lewis, JD}, title = {Analysis of the human gut microbiome and association with disease.}, journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association}, volume = {11}, number = {7}, pages = {774-777}, pmid = {23643636}, issn = {1542-7714}, support = {R01 DK089472/DK/NIDDK NIH HHS/United States ; UH2 DK083981/DK/NIDDK NIH HHS/United States ; UH3 DK083981/DK/NIDDK NIH HHS/United States ; UH2/3 DK083981/DK/NIDDK NIH HHS/United States ; R01 GM 103591/GM/NIGMS NIH HHS/United States ; R01 GM103591/GM/NIGMS NIH HHS/United States ; }, mesh = {Diagnostic Tests, Routine/*methods ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; *Microbiota ; }, } @article {pmid23642112, year = {2013}, author = {Martínez, I and Brown, AW and Walter, J}, title = {Does host cholesterol metabolism impact the gut microbiota and why does it matter?.}, journal = {Future microbiology}, volume = {8}, number = {5}, pages = {571-573}, doi = {10.2217/fmb.13.24}, pmid = {23642112}, issn = {1746-0921}, mesh = {*Biota ; Cholesterol/*metabolism ; Gastrointestinal Tract/*microbiology ; *Metagenome ; }, } @article {pmid23637931, year = {2013}, author = {Martins, LF and Antunes, LP and Pascon, RC and de Oliveira, JC and Digiampietri, LA and Barbosa, D and Peixoto, BM and Vallim, MA and Viana-Niero, C and Ostroski, EH and Telles, GP and Dias, Z and da Cruz, JB and Juliano, L and Verjovski-Almeida, S and da Silva, AM and Setubal, JC}, title = {Metagenomic analysis of a tropical composting operation at the são paulo zoo park reveals diversity of biomass degradation functions and organisms.}, journal = {PloS one}, volume = {8}, number = {4}, pages = {e61928}, pmid = {23637931}, issn = {1932-6203}, mesh = {Bacteria/classification/genetics ; Base Composition ; *Biodiversity ; *Biomass ; Brazil ; Cluster Analysis ; Gene Order ; Lactobacillus/classification/genetics/metabolism ; Lignin/metabolism ; *Metagenomics ; Molecular Sequence Annotation ; Pectins/metabolism ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Composting operations are a rich source for prospection of biomass degradation enzymes. We have analyzed the microbiomes of two composting samples collected in a facility inside the São Paulo Zoo Park, in Brazil. All organic waste produced in the park is processed in this facility, at a rate of four tons/day. Total DNA was extracted and sequenced with Roche/454 technology, generating about 3 million reads per sample. To our knowledge this work is the first report of a composting whole-microbial community using high-throughput sequencing and analysis. The phylogenetic profiles of the two microbiomes analyzed are quite different, with a clear dominance of members of the Lactobacillus genus in one of them. We found a general agreement of the distribution of functional categories in the Zoo compost metagenomes compared with seven selected public metagenomes of biomass deconstruction environments, indicating the potential for different bacterial communities to provide alternative mechanisms for the same functional purposes. Our results indicate that biomass degradation in this composting process, including deconstruction of recalcitrant lignocellulose, is fully performed by bacterial enzymes, most likely by members of the Clostridiales and Actinomycetales orders.}, } @article {pmid23635865, year = {2013}, author = {Monier, A and Sudek, S and Fast, NM and Worden, AZ}, title = {Gene invasion in distant eukaryotic lineages: discovery of mutually exclusive genetic elements reveals marine biodiversity.}, journal = {The ISME journal}, volume = {7}, number = {9}, pages = {1764-1774}, pmid = {23635865}, issn = {1751-7370}, mesh = {Aquatic Organisms/*genetics ; *Biodiversity ; Chlorophyta/*genetics ; DNA Transposable Elements/genetics ; Environment ; Eukaryota/*genetics/virology ; Inteins/*genetics ; Introns/genetics ; Phylogeny ; RNA-Binding Proteins/genetics ; Species Specificity ; }, abstract = {Inteins are rare, translated genetic parasites mainly found in bacteria and archaea, while spliceosomal introns are distinctly eukaryotic features abundant in most nuclear genomes. Using targeted metagenomics, we discovered an intein in an Atlantic population of the photosynthetic eukaryote, Bathycoccus, harbored by the essential spliceosomal protein PRP8 (processing factor 8 protein). Although previously thought exclusive to fungi, we also identified PRP8 inteins in parasitic (Capsaspora) and predatory (Salpingoeca) protists. Most new PRP8 inteins were at novel insertion sites that, surprisingly, were not in the most conserved regions of the gene. Evolutionarily, Dikarya fungal inteins at PRP8 insertion site a appeared more related to the Bathycoccus intein at a unique insertion site, than to other fungal and opisthokont inteins. Strikingly, independent analyses of Pacific and Atlantic samples revealed an intron at the same codon as the Bathycoccus PRP8 intein. The two elements are mutually exclusive and neither was found in cultured Bathycoccus or other picoprasinophyte genomes. Thus, wild Bathycoccus contain one of few non-fungal eukaryotic inteins known and a rare polymorphic intron. Our data indicate at least two Bathycoccus ecotypes exist, associated respectively with oceanic or mesotrophic environments. We hypothesize that intein propagation is facilitated by marine viruses; and, while intron gain is still poorly understood, presence of a spliceosomal intron where a locus lacks an intein raises the possibility of new, intein-primed mechanisms for intron gain. The discovery of nucleus-encoded inteins and associated sequence polymorphisms in uncultivated marine eukaryotes highlights their diversity and reveals potential sexual boundaries between populations indistinguishable by common marker genes.}, } @article {pmid23633574, year = {2013}, author = {Smith, DJ and Griffin, DW}, title = {Inadequate methods and questionable conclusions in atmospheric life study.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {23}, pages = {E2084}, pmid = {23633574}, issn = {1091-6490}, mesh = {*Air Microbiology ; *Atmosphere ; *Biodiversity ; *Cyclonic Storms ; Metagenome/*genetics ; }, } @article {pmid23632211, year = {2013}, author = {Choi, JJ and Eum, SY and Rampersaud, E and Daunert, S and Abreu, MT and Toborek, M}, title = {Exercise attenuates PCB-induced changes in the mouse gut microbiome.}, journal = {Environmental health perspectives}, volume = {121}, number = {6}, pages = {725-730}, pmid = {23632211}, issn = {1552-9924}, support = {R01 CA133257/CA/NCI NIH HHS/United States ; R01 MH063022/MH/NIMH NIH HHS/United States ; P42 ES07380/ES/NIEHS NIH HHS/United States ; DA027569/DA/NIDA NIH HHS/United States ; MH63022/MH/NIMH NIH HHS/United States ; P42 ES007380/ES/NIEHS NIH HHS/United States ; R01 DA027569/DA/NIDA NIH HHS/United States ; MH072567/MH/NIMH NIH HHS/United States ; R01 MH072567/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Cholic Acid/pharmacology ; Environmental Pollutants/*toxicity ; Fatty Acids, Volatile/pharmacology ; Humans ; Intestines/*microbiology ; Male ; Metagenome/*drug effects ; Mice ; Mice, Inbred C57BL ; *Physical Conditioning, Animal ; Polychlorinated Biphenyls/*toxicity ; }, abstract = {BACKGROUND: The gut microbiome, a dynamic bacterial community that interacts with the host, is integral to human health because it regulates energy metabolism and immune functions. The gut microbiome may also play a role in risks from environmental toxicants.

OBJECTIVES: We investigated the effects of polychlorinated biphenyls (PCBs) and exercise on the composition and structure of the gut microbiome in mice.

METHODS: After mice exercised voluntarily for 5 weeks, they were treated by oral gavage with a mixture of environmentally relevant PCB congeners (PCB153, PCB138, and PCB180; total PCB dose, 150 µmol/kg) for 2 days. We then assessed the microbiome by determination of 16S rRNA using microarray analysis.

RESULTS: Oral exposure to PCBs significantly altered the abundance of the gut microbiome in mice primarily by decreasing the levels of Proteobacteria. The activity level of the mice correlated with a substantial shift in abundance, biodiversity, and composition of the microbiome. Importantly, exercise attenuated PCB-induced changes in the gut microbiome.

CONCLUSIONS: Our results show that oral exposure to PCBs can induce substantial changes in the gut microbiome, which may then influence their systemic toxicity. These changes can be attenuated by behavioral factors, such as voluntary exercise.}, } @article {pmid23628424, year = {2013}, author = {Zhang, Q and Rho, M and Tang, H and Doak, TG and Ye, Y}, title = {CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes.}, journal = {Genome biology}, volume = {14}, number = {4}, pages = {R40}, pmid = {23628424}, issn = {1474-760X}, mesh = {Bacteria/genetics ; *CRISPR-Cas Systems ; Genes, Microbial ; Humans ; *Interspersed Repetitive Sequences ; Microbiota/*genetics ; Prophages/genetics ; }, abstract = {BACKGROUND: Bacteria and archaea develop immunity against invading genomes by incorporating pieces of the invaders' sequences, called spacers, into a clustered regularly interspaced short palindromic repeats (CRISPR) locus between repeats, forming arrays of repeat-spacer units. When spacers are expressed, they direct CRISPR-associated (Cas) proteins to silence complementary invading DNA. In order to characterize the invaders of human microbiomes, we use spacers from CRISPR arrays that we had previously assembled from shotgun metagenomic datasets, and identify contigs that contain these spacers' targets.

RESULTS: We discover 95,000 contigs that are putative invasive mobile genetic elements, some targeted by hundreds of CRISPR spacers. We find that oral sites in healthy human populations have a much greater variety of mobile genetic elements than stool samples. Mobile genetic elements carry genes encoding diverse functions: only 7% of the mobile genetic elements are similar to known phages or plasmids, although a much greater proportion contain phage- or plasmid-related genes. A small number of contigs share similarity with known integrative and conjugative elements, providing the first examples of CRISPR defenses against this class of element. We provide detailed analyses of a few large mobile genetic elements of various types, and a relative abundance analysis of mobile genetic elements and putative hosts, exploring the dynamic activities of mobile genetic elements in human microbiomes. A joint analysis of mobile genetic elements and CRISPRs shows that protospacer-adjacent motifs drive their interaction network; however, some CRISPR-Cas systems target mobile genetic elements lacking motifs.

CONCLUSIONS: We identify a large collection of invasive mobile genetic elements in human microbiomes, an important resource for further study of the interaction between the CRISPR-Cas immune system and invaders.}, } @article {pmid23626688, year = {2013}, author = {Gulino, LM and Ouwerkerk, D and Kang, AY and Maguire, AJ and Kienzle, M and Klieve, AV}, title = {Shedding light on the microbial community of the macropod foregut using 454-amplicon pyrosequencing.}, journal = {PloS one}, volume = {8}, number = {4}, pages = {e61463}, pmid = {23626688}, issn = {1932-6203}, mesh = {Animals ; Bacteria/*classification/genetics/isolation & purification ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Macropodidae/*microbiology ; Metagenome ; Microbial Consortia/*genetics ; *Phylogeny ; Queensland ; RNA, Ribosomal, 16S/*classification/genetics/isolation & purification ; Stomach/*microbiology ; }, abstract = {Twenty macropods from five locations in Queensland, Australia, grazing on a variety of native pastures were surveyed and the bacterial community of the foregut was examined using 454-amplicon pyrosequencing. Specifically, the V3/V4 region of 16S rRNA gene was examined. A total of 5040 OTUs were identified in the data set (post filtering). Thirty-two OTUs were identified as 'shared' OTUS (i.e. present in all samples) belonging to either Firmicutes or Bacteroidetes (Clostridiales/Bacteroidales). These phyla predominated the general microbial community in all macropods. Genera represented within the shared OTUs included: unclassified Ruminococcaceae, unclassified Lachnospiraceae, unclassified Clostridiales, Peptococcus sp. Coprococcus spp., Streptococcus spp., Blautia sp., Ruminoccocus sp., Eubacterium sp., Dorea sp., Oscillospira sp. and Butyrivibrio sp. The composition of the bacterial community of the foregut samples of each the host species (Macropus rufus, Macropus giganteus and Macropus robustus) was significantly different allowing differentiation between the host species based on alpha and beta diversity measures. Specifically, eleven dominant OTUs that separated the three host species were identified and classified as: unclassified Ruminococcaceae, unclassified Bacteroidales, Prevotella spp. and a Syntrophococcus sucromutans. Putative reductive acetogens and fibrolytic bacteria were also identified in samples. Future work will investigate the presence and role of fibrolytics and acetogens in these ecosystems. Ideally, the isolation and characterization of these organisms will be used for enhanced feed efficiency in cattle, methane mitigation and potentially for other industries such as the biofuel industry.}, } @article {pmid23625762, year = {2013}, author = {Seifert, J and Herbst, FA and Halkjaer Nielsen, P and Planes, FJ and Jehmlich, N and Ferrer, M and von Bergen, M}, title = {Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities.}, journal = {Proteomics}, volume = {13}, number = {18-19}, pages = {2786-2804}, doi = {10.1002/pmic.201200566}, pmid = {23625762}, issn = {1615-9861}, mesh = {Bacteria/genetics/*metabolism ; Base Sequence ; Computational Biology/*methods ; Metagenomics/*methods ; Microbiota/*genetics ; Proteomics/*methods ; }, abstract = {Metaproteomics of microbial communities promises to add functional information to the blueprint of genes derived from metagenomics. Right from its beginning, the achievements and developments in metaproteomics were closely interlinked with metagenomics. In addition, the evaluation, visualization, and interpretation of metaproteome data demanded for the developments in bioinformatics. This review will give an overview about recent strategies to use genomic data either from public databases or organismal specific genomes/metagenomes to increase the number of identified proteins obtained by mass spectrometric measurements. We will review different published metaproteogenomic approaches in respect to the used MS pipeline and to the used protein identification workflow. Furthermore, different approaches of data visualization and strategies for phylogenetic interpretation of metaproteome data are discussed as well as approaches for functional mapping of the results to the investigated biological systems. This information will in the end allow a comprehensive analysis of interactions and interdependencies within microbial communities.}, } @article {pmid23623853, year = {2013}, author = {Ni, J and Tokuda, G}, title = {Lignocellulose-degrading enzymes from termites and their symbiotic microbiota.}, journal = {Biotechnology advances}, volume = {31}, number = {6}, pages = {838-850}, doi = {10.1016/j.biotechadv.2013.04.005}, pmid = {23623853}, issn = {1873-1899}, mesh = {Animals ; Biofuels/microbiology ; Cellulases/chemistry/*genetics/isolation & purification ; Gastrointestinal Tract/microbiology ; Isoptera/*enzymology ; Laccase/chemistry/*genetics ; Lignin/*chemistry/metabolism ; Metagenomics ; Microbiota ; Symbiosis/genetics ; }, abstract = {Lignocellulose-the dry matter of plants, or "plant biomass"-digestion is of increasing interest in organismal metabolism research, specifically the conversion of biomass into biofuels. Termites efficiently decompose lignocelluloses, and studies on lignocellulolytic systems may elucidate mechanisms of efficient lignocellulose degradation in termites as well as offer novel enzyme sources, findings which have significant potential industrial applications. Recent progress in metagenomic and metatranscriptomic research has illuminated the diversity of lignocellulolytic enzymes within the termite gut. Here, we review state-of-the-art research on lignocellulose-degrading systems in termites, specifically cellulases, xylanases, and lignin modification enzymes produced by termites and their symbiotic microbiota. We also discuss recent investigations into heterologous overexpression of lignocellulolytic enzymes from termites and their symbionts.}, } @article {pmid23623295, year = {2013}, author = {Greenblum, S and Chiu, HC and Levy, R and Carr, R and Borenstein, E}, title = {Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities.}, journal = {Current opinion in biotechnology}, volume = {24}, number = {4}, pages = {810-820}, pmid = {23623295}, issn = {1879-0429}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; }, mesh = {Bacteria/metabolism ; Ecosystem ; Gastrointestinal Tract/microbiology ; Humans ; *Microbiota ; *Models, Biological ; }, abstract = {The human microbiome represents a vastly complex ecosystem that is tightly linked to our development, physiology, and health. Our increased capacity to generate multiple channels of omic data from this system, brought about by recent advances in high throughput molecular technologies, calls for the development of systems-level methods and models that take into account not only the composition of genes and species in a microbiome but also the interactions between these components. Such models should aim to study the microbiome as a community of species whose metabolisms are tightly intertwined with each other and with that of the host, and should be developed with a view towards an integrated, comprehensive, and predictive modeling framework. Here, we review recent work specifically in metabolic modeling of the human microbiome, highlighting both novel methodologies and pressing challenges. We discuss various modeling approaches that lay the foundation for a full-scale predictive model, focusing on models of interactions between microbial species, metagenome-scale models of community-level metabolism, and models of the interaction between the microbiome and the host. Continued development of such models and of their integration into a multi-scale model of the microbiome will lead to a deeper mechanistic understanding of how variation in the microbiome impacts the host, and will promote the discovery of clinically relevant and ecologically relevant insights from the rich trove of data now available.}, } @article {pmid23616470, year = {2013}, author = {Herbst, FA and Bahr, A and Duarte, M and Pieper, DH and Richnow, HH and von Bergen, M and Seifert, J and Bombach, P}, title = {Elucidation of in situ polycyclic aromatic hydrocarbon degradation by functional metaproteomics (protein-SIP).}, journal = {Proteomics}, volume = {13}, number = {18-19}, pages = {2910-2920}, doi = {10.1002/pmic.201200569}, pmid = {23616470}, issn = {1615-9861}, mesh = {Bacterial Proteins/metabolism ; Biodegradation, Environmental ; Fluorenes ; *Isotope Labeling ; *Metagenomics ; Microbiota ; Naphthalenes/chemistry/metabolism ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Proteomics/*methods ; }, abstract = {Current knowledge of the physiology and phylogeny of polycyclic aromatic hydrocarbon (PAH) degrading bacteria often relies on laboratory enrichments and isolations. In the present study, in situ microcosms consisting of activated carbon pellets (BACTRAP®s) were loaded with either (13) C-naphthalene or (13) C-fluorene and were subsequently exposed in the contaminant source and plume fringe region of a PAH-contaminated aquifer. Metaproteomic analysis and protein-stable isotope probing revealed Burkholderiales, Actinomycetales, and Rhizobiales as the most active microorganisms in the groundwater communities. Proteins identified of the naphthalene degradation pathway showed a relative (13) C isotope abundance of approximately 50 atom% demonstrating that the identified naphthalene-degrading bacteria gained at least 80% of their carbon by PAH degradation. Although the microbial community grown on the fluorene-BACTRAPs showed a structure similar to the naphthalene-BACTRAPs, the identification of fluorene degraders and degradation pathways failed in situ. In complementary laboratory microcosms, a clear enrichment in proteins related to Rhodococcus and possible fluorene degradation enzymes was observed. This result demonstrates the impact of laboratory conditions on microbial community structure and activity of certain species and underlines the need on in situ exploration of microbial community functions. In situ microcosms in combination with protein-stable isotope probing may be a significant tool for in situ identification of metabolic key players as well as degradation pathways.}, } @article {pmid23616410, year = {2013}, author = {Diaz, PI and Hong, BY and Frias-Lopez, J and Dupuy, AK and Angeloni, M and Abusleme, L and Terzi, E and Ioannidou, E and Strausbaugh, LD and Dongari-Bagtzoglou, A}, title = {Transplantation-associated long-term immunosuppression promotes oral colonization by potentially opportunistic pathogens without impacting other members of the salivary bacteriome.}, journal = {Clinical and vaccine immunology : CVI}, volume = {20}, number = {6}, pages = {920-930}, pmid = {23616410}, issn = {1556-679X}, support = {R01 DE021578/DE/NIDCR NIH HHS/United States ; R21 DE016466/DE/NIDCR NIH HHS/United States ; R21DE016466/DE/NIDCR NIH HHS/United States ; R01DE021578/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Aged ; Animals ; Bacteria/*classification/*genetics ; *Biota ; Female ; Humans ; Immunosuppression Therapy ; Immunosuppressive Agents/*therapeutic use ; Male ; *Metagenome ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; *Transplantation ; }, abstract = {Solid-organ transplant recipients rely on pharmacological immunosuppression to prevent allograft rejection. The effect of such chronic immunosuppression on the microflora at mucosal surfaces is not known. We evaluated the salivary bacterial microbiome of 20 transplant recipients and 19 nonimmunosuppressed controls via 454 pyrosequencing of 16S rRNA gene amplicons. Alpha-diversity and global community structure did not differ between transplant and control subjects. However, principal coordinate analysis showed differences in community membership. Taxa more prevalent in transplant subjects included operational taxonomic units (OTUs) of potentially opportunistic Gammaproteobacteria such as Klebsiella pneumoniae, Pseudomonas fluorescens, Acinetobacter species, Vibrio species, Enterobacteriaceae species, and the genera Acinetobacter and Klebsiella. Transplant subjects also had increased proportions of Pseudomonas aeruginosa, Acinetobacter species, Enterobacteriaceae species, and Enterococcus faecalis, among other OTUs, while genera with increased proportions included Klebsiella, Acinetobacter, Staphylococcus, and Enterococcus. Furthermore, in transplant subjects, the dose of the immunosuppressant prednisone positively correlated with bacterial richness, while prednisone and mycophenolate mofetil doses positively correlated with the prevalence and proportions of transplant-associated taxa. Correlation network analysis of OTU relative abundance revealed a cluster containing potentially opportunistic pathogens as transplant associated. This cluster positively correlated with serum levels of C-reactive protein, suggesting a link between the resident flora at mucosal compartments and systemic inflammation. Network connectivity analysis revealed opportunistic pathogens as highly connected to each other and to common oral commensals, pointing to bacterial interactions that may influence colonization. This work demonstrates that immunosuppression aimed at limiting T-cell-mediated responses creates a more permissive oral environment for potentially opportunistic pathogens without affecting other members of the salivary bacteriome.}, } @article {pmid23616309, year = {2013}, author = {Cani, PD}, title = {Gut microbiota and obesity: lessons from the microbiome.}, journal = {Briefings in functional genomics}, volume = {12}, number = {4}, pages = {381-387}, doi = {10.1093/bfgp/elt014}, pmid = {23616309}, issn = {2041-2657}, mesh = {Diabetes Mellitus, Type 2/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Microbiota/genetics ; Obesity/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The distal gut harbours microbial communities that outnumber our own eukaryotic cells. The contribution of the gut microbiota to the development of several diseases (e.g. obesity, type 2 diabetes, steatosis, cardiovascular diseases and inflammatory bowel diseases) is becoming clear, although the causality remains to be proven in humans. Global changes in the gut microbiota have been observed by a number of culture-dependent and culture-independent methods, and while the latter have mostly included 16S ribosomal RNA gene analyses, more recent studies have utilized DNA sequencing of whole-microbial communities. Altogether, these high-throughput methods have facilitated the identification of novel candidate bacteria and, most importantly, metabolic functions that might be associated with obesity and type 2 diabetes. This review discusses the association between specific taxa and obesity, together with the techniques that are used to characterize the gut microbiota in the context of obesity and type 2 diabetes. Recent results are discussed in the framework of the interactions between gut microbiota and host metabolism.}, } @article {pmid23614961, year = {2013}, author = {Bohm, M and Siwiec, RM and Wo, JM}, title = {Diagnosis and management of small intestinal bacterial overgrowth.}, journal = {Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition}, volume = {28}, number = {3}, pages = {289-299}, doi = {10.1177/0884533613485882}, pmid = {23614961}, issn = {1941-2452}, mesh = {Abdominal Pain/drug therapy/microbiology ; Anti-Bacterial Agents/therapeutic use ; Bacterial Infections/*diagnosis/drug therapy ; Breath Tests ; Diarrhea/drug therapy/microbiology ; Flatulence/drug therapy/microbiology ; Gastrointestinal Motility ; Gram-Negative Bacteria ; Humans ; Irritable Bowel Syndrome/*diagnosis/drug therapy/*microbiology ; Jejunum/*microbiology ; Microbiota ; }, abstract = {Small intestinal bacterial overgrowth (SIBO) can result from failure of the gastric acid barrier, failure of small intestinal motility, anatomic alterations, or impairment of systemic and local immunity. The current accepted criteria for the diagnosis of SIBO is the presence of coliform bacteria isolated from the proximal jejunum with >10(5) colony-forming units/mL. A major concern with luminal aspiration is that it is only one random sampling of the small intestine and may not always be representative of the underlying microbiota. A new approach to examine the underlying microbiota uses rapid molecular sequencing, but its clinical utilization is still under active investigation. Clinical manifestations of SIBO are variable and include bloating, flatulence, abdominal distention, abdominal pain, and diarrhea. Severe cases may present with nutrition deficiencies due to malabsorption of micro- and macronutrients. The current management strategies for SIBO center on identifying and correcting underlying causes, addressing nutrition deficiencies, and judicious utilization of antibiotics to treat symptomatic SIBO.}, } @article {pmid23613805, year = {2013}, author = {Schippa, S and Iebba, V and Santangelo, F and Gagliardi, A and De Biase, RV and Stamato, A and Bertasi, S and Lucarelli, M and Conte, MP and Quattrucci, S}, title = {Cystic fibrosis transmembrane conductance regulator (CFTR) allelic variants relate to shifts in faecal microbiota of cystic fibrosis patients.}, journal = {PloS one}, volume = {8}, number = {4}, pages = {e61176}, pmid = {23613805}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; *Alleles ; Child ; Child, Preschool ; Cystic Fibrosis/*genetics/*microbiology ; Cystic Fibrosis Transmembrane Conductance Regulator/*genetics ; Demography ; Discriminant Analysis ; Electrophoresis, Agar Gel ; Feces/*microbiology ; Female ; Genotyping Techniques ; Humans ; Least-Squares Analysis ; Male ; *Metagenome ; Middle Aged ; Mutation/*genetics ; Phenotype ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Species Specificity ; Young Adult ; }, abstract = {INTRODUCTION: In this study we investigated the effects of the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene variants on the composition of faecal microbiota, in patients affected by Cystic Fibrosis (CF). CFTR mutations (F508del is the most common) lead to a decreased secretion of chloride/water, and to mucus sticky secretions, in pancreas, respiratory and gastrointestinal tracts. Intestinal manifestations are underestimated in CF, leading to ileum meconium at birth, or small bowel bacterial overgrowth in adult age.

METHODS: Thirty-six CF patients, fasting and under no-antibiotic treatment, were CFTR genotyped on both alleles. Faecal samples were subjected to molecular microbial profiling through Temporal Temperature Gradient Electrophoresis and species-specific PCR. Ecological parameters and multivariate algorithms were employed to find out if CFTR variants could be related to the microbiota structure.

RESULTS: Patients were classified by two different criteria: 1) presence/absence of F508del mutation; 2) disease severity in heterozygous and homozygous F508del patients. We found that homozygous-F508del and severe CF patients exhibited an enhanced dysbiotic faecal microbiota composition, even within the CF cohort itself, with higher biodiversity and evenness. We also found, by species-specific PCR, that potentially harmful species (Escherichia coli and Eubacterium biforme) were abundant in homozygous-F508del and severe CF patients, while beneficial species (Faecalibacterium prausnitzii, Bifidobacterium spp., and Eubacterium limosum) were reduced.

CONCLUSIONS: This is the first report that establishes a link among CFTR variants and shifts in faecal microbiota, opening the way to studies that perceive CF as a 'systemic disease', linking the lung and the gut in a joined axis.}, } @article {pmid23607777, year = {2013}, author = {Larsen, A and Tao, Z and Bullard, SA and Arias, CR}, title = {Diversity of the skin microbiota of fishes: evidence for host species specificity.}, journal = {FEMS microbiology ecology}, volume = {85}, number = {3}, pages = {483-494}, doi = {10.1111/1574-6941.12136}, pmid = {23607777}, issn = {1574-6941}, mesh = {Animals ; Bacteria/*classification/genetics/isolation & purification ; Biodiversity ; Fishes/*microbiology ; Gulf of Mexico ; *Host Specificity ; Humans ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Skin/*microbiology ; Species Specificity ; }, abstract = {Skin microbiota of Gulf of Mexico fishes were investigated by ribosomal internal spacer analysis (RISA) and 16S rRNA gene sequencing. A total of 102 fish specimens representing six species (Mugil cephalus, Lutjanus campechanus, Cynoscion nebulosus, Cynoscion arenarius, Micropogonias undulatus, and Lagodon rhomboides) were sampled at regular intervals throughout a year. The skin microbiota from each individual fish was analyzed by RISA and produced complex profiles with 23 bands on average. Similarities between RISA profiles ranged from 97.5% to 4.0%. At 70% similarity, 11 clusters were defined, each grouping individuals from the same fish species. Multidimensional scaling and analysis of similarity correlated the RISA-defined clusters with geographic locality, date, and fish species. Global R values indicated that fish species was the most indicative variable for group separation. Analysis of 16S rRNA gene sequences (from pooled samples of 10 individual fish for each fish species) showed that the Proteobacteria was the predominant phylum in skin microbiota, followed by the Firmicutes and the Actinobacteria. The distribution and abundance of bacterial sequences were different among all species analyzed. Aeribacillus was found in all fish species representing 19% of all clones sequenced, while some genera were fish species-specific (Neorickettsia in M. cephalus and Microbacterium in L. campechanus). Our data provide evidence for the existence of specific skin microbiota associated with particular fish species.}, } @article {pmid23604562, year = {2013}, author = {Gandolfi, I and Bertolini, V and Ambrosini, R and Bestetti, G and Franzetti, A}, title = {Unravelling the bacterial diversity in the atmosphere.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {11}, pages = {4727-4736}, doi = {10.1007/s00253-013-4901-2}, pmid = {23604562}, issn = {1432-0614}, mesh = {*Air Microbiology ; Bacteria/*classification ; Bacteriological Techniques/methods ; *Biodiversity ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; }, abstract = {The study of airborne biological particles ('bioaerosols') has gained interest in recent years, due to an increasing amount of evidence suggesting that this fraction of airborne particulate matter may play a critical role in the negative effects of aerosols on biological systems. Pioneer investigations demonstrated that bacteria do exist in the atmosphere and can be metabolically active, although studies have not proved whether they actually form ecological communities or are merely assemblages of organisms passively transported from different sources. For a long time, cultivation-based methods have been the gold standard to describe and quantify airborne microorganisms. However, the use of culture-independent techniques and, more recently, of the next-generation sequencing-based methods, has improved the ability of the scientific community to investigate bioaerosols in detail and to address further research questions, such as the temporal and spatial variability of airborne bacterial assemblages, the environmental factors affecting this variability and the potential sources of atmospheric bacteria. This paper provides a systematic review of the state-of-the-art methodologies used in the study of airborne bacteria to achieve each of the aforementioned research objectives, as well as the main results obtained so far. Critical evaluations of the current state of the knowledge and suggestions for further researches are provided.}, } @article {pmid23604540, year = {2013}, author = {Zeng, B and Li, G and Yuan, J and Li, W and Tang, H and Wei, H}, title = {Effects of age and strain on the microbiota colonization in an infant human flora-associated mouse model.}, journal = {Current microbiology}, volume = {67}, number = {3}, pages = {313-321}, pmid = {23604540}, issn = {1432-0991}, mesh = {Animals ; Denaturing Gradient Gel Electrophoresis ; Germ-Free Life ; Humans ; Infant ; Metagenome ; Mice ; Mice, Inbred BALB C ; *Microbiota ; Models, Animal ; Real-Time Polymerase Chain Reaction ; }, abstract = {The establishment of human flora-associated animal models allows the in vivo manipulation of host, microbial, and environmental parameters to influence the gut microbial community. However, it is difficult to simulate infant gut microbiota in germ-free animals because of the variation and dynamic state of infant microbial communities. In this study, the effects of age and strain on intestinal microbiota were observed in an infant human flora-associated (IHFA) mouse model. To establish an IHFA model, postnatal day (PND) 1 germ-free mice (Kunming, n = 10; BALB/c, n = 10) were infected with feces from a breast-fed infant. Microbiota in the feces of BALB/c mice (at PND 7, 14, and 21), and Kunming mice (at PND 14) were analyzed by PCR-denaturing gradient gel electrophoresis. Bifidobacteria and lactobacilli levels in the feces of BALB/c and Kunming mice (PND 7/14/21) were detected by quantitative real-time PCR. The Dice similarity coefficient (Cs) for the fecal microbiota of IHFA mice in comparison with the HD donor sample was higher for BALB/c mice than for Kunming mice (P < 0.05). In addition, the DCs at PND 7 were lower than those at PND 14 and PND 21 in both mouse strains (P < 0.05). The Bifidobacteria and Lactobacillus species colonizing the BALB/c mice were similar to those in the Kunming mice (at PND 7/14/21). The bifidobacteria counts increased with age in both mouse strains, whereas the lactobacilli counts decreased with age in both strains. These results suggest that both age and strain influence microbiota patterns in the IHFA mouse model.}, } @article {pmid23601077, year = {2013}, author = {Kerekes, J and Kaspari, M and Stevenson, B and Nilsson, RH and Hartmann, M and Amend, A and Bruns, TD}, title = {Nutrient enrichment increased species richness of leaf litter fungal assemblages in a tropical forest.}, journal = {Molecular ecology}, volume = {22}, number = {10}, pages = {2827-2838}, doi = {10.1111/mec.12259}, pmid = {23601077}, issn = {1365-294X}, mesh = {Base Sequence ; *Biodiversity ; DNA, Ribosomal Spacer/genetics ; Fertilizers/*microbiology ; Fungi/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenome/*genetics ; Molecular Sequence Data ; Nitrogen ; Panama ; Phosphorus ; Plant Leaves/*microbiology ; Potassium ; Sequence Homology ; *Soil Microbiology ; *Trees ; Tropical Climate ; }, abstract = {Microbial communities play a major role in terrestrial ecosystem functioning, but the determinates of their diversity and functional interactions are not well known. In this study, we explored leaf litter fungal diversity in a diverse Panama lowland tropical forest in which a replicated factorial N, P, K and micronutrient fertilization experiment of 40 × 40 m plots had been ongoing for nine years. We extracted DNA from leaf litter samples and used fungal-specific amplification and a 454 pyrosequencing approach to sequence two loci, the nuclear ribosomal internal transcribed spacer (ITS) region and the nuclear ribosomal large subunit (LSU) D1 region. Using a 95% sequence similarity threshold for ITS1 spacer recovered a total of 2523 OTUs, and the number of unique ITS1 OTUs per 0.5-1.0 g leaf litter sample ranged from 55 to 177. Ascomycota were the dominant phylum among the leaf litter fungi (71% of the OTUs), followed by Basidiomycota (26% of the OTUs). In contrast to our expectations based on temperate ecosystems, long-term addition of nutrients increased, rather than decreased, species richness relative to controls. Effect of individual nutrients was more subtle and seen primarily as changes in community compositions especially at lower taxonomic levels, rather than as significant changes in species richness. For example, plots receiving P tended to show a greater similarity in community composition compared to the other nutrient treatments, the +PK, +NK and +NPK plots appeared to be more dominated by the Nectriaceae than other treatments, and indicator species for particular nutrient combinations were identified.}, } @article {pmid23599893, year = {2013}, author = {Song, SJ and Lauber, C and Costello, EK and Lozupone, CA and Humphrey, G and Berg-Lyons, D and Caporaso, JG and Knights, D and Clemente, JC and Nakielny, S and Gordon, JI and Fierer, N and Knight, R}, title = {Cohabiting family members share microbiota with one another and with their dogs.}, journal = {eLife}, volume = {2}, number = {}, pages = {e00458}, pmid = {23599893}, issn = {2050-084X}, support = {K01 DK090285/DK/NIDDK NIH HHS/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; U01 HG004866/HG/NHGRI NIH HHS/United States ; HG4872, HG4866/HG/NHGRI NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Aged, 80 and over ; Animals ; Child ; Child, Preschool ; Dogs ; *Family ; Family Characteristics ; Feces/microbiology ; *Housing ; Humans ; Infant ; Intestines/*microbiology ; *Microbiota ; Middle Aged ; Pets/*microbiology ; *Residence Characteristics ; Skin/*microbiology ; Tongue/*microbiology ; }, abstract = {Human-associated microbial communities vary across individuals: possible contributing factors include (genetic) relatedness, diet, and age. However, our surroundings, including individuals with whom we interact, also likely shape our microbial communities. To quantify this microbial exchange, we surveyed fecal, oral, and skin microbiota from 60 families (spousal units with children, dogs, both, or neither). Household members, particularly couples, shared more of their microbiota than individuals from different households, with stronger effects of co-habitation on skin than oral or fecal microbiota. Dog ownership significantly increased the shared skin microbiota in cohabiting adults, and dog-owning adults shared more 'skin' microbiota with their own dogs than with other dogs. Although the degree to which these shared microbes have a true niche on the human body, vs transient detection after direct contact, is unknown, these results suggest that direct and frequent contact with our cohabitants may significantly shape the composition of our microbial communities. DOI:http://dx.doi.org/10.7554/eLife.00458.001.}, } @article {pmid23598791, year = {2013}, author = {Woodhouse, JN and Fan, L and Brown, MV and Thomas, T and Neilan, BA}, title = {Deep sequencing of non-ribosomal peptide synthetases and polyketide synthases from the microbiomes of Australian marine sponges.}, journal = {The ISME journal}, volume = {7}, number = {9}, pages = {1842-1851}, pmid = {23598791}, issn = {1751-7370}, mesh = {Animals ; Australia ; Bacteria/classification/*enzymology/*genetics ; *Genetic Variation ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Microbiota/genetics ; Peptide Synthases/chemistry/*genetics/metabolism ; Phylogeny ; Polyketide Synthases/chemistry/*genetics/metabolism ; Porifera/*microbiology ; Protein Structure, Tertiary ; Reproducibility of Results ; }, abstract = {The biosynthesis of non-ribosomal peptide and polyketide natural products is facilitated by multimodular enzymes that contain domains responsible for the sequential condensation of amino and carboxylic subunits. These conserved domains provide molecular targets for the discovery of natural products from microbial metagenomes. This study demonstrates the application of tag-encoded FLX amplicon pyrosequencing (TEFAP) targeting non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) genes as a method for determining the identity and diversity of natural product biosynthesis genes. To validate this approach, we assessed the diversity of NRPS and PKS genes within the microbiomes of six Australian marine sponge species using both TEFAP and metagenomic whole-genome shotgun sequencing approaches. The TEFAP approach identified 100 novel ketosynthase (KS) domain sequences and 400 novel condensation domain sequences within the microbiomes of the six sponges. The diversity of KS domains within the microbiome of a single sponge species Scopalina sp. exceeded that of any previously surveyed marine sponge. Furthermore, this study represented the first to target the condensation domain from NRPS biosynthesis and resulted in the identification of a novel condensation domain lineage. This study highlights the untapped potential of Australian marine sponges for the isolation of novel bioactive natural products. Furthermore, this study demonstrates that TEFAP approaches can be applied to functional genes, involved in natural product biosynthesis, as a tool to aid natural product discovery. It is envisaged that this approach will be used across multiple environments, offering an insight into the biological processes that influence the production of secondary metabolites.}, } @article {pmid23597788, year = {2013}, author = {Khosravi, A and Mazmanian, SK}, title = {Disruption of the gut microbiome as a risk factor for microbial infections.}, journal = {Current opinion in microbiology}, volume = {16}, number = {2}, pages = {221-227}, pmid = {23597788}, issn = {1879-0364}, support = {R01 DK078938/DK/NIDDK NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; DK 078938/DK/NIDDK NIH HHS/United States ; }, mesh = {*Biota ; Gastrointestinal Diseases/*microbiology ; Gastrointestinal Tract/*microbiology ; Host-Pathogen Interactions ; Humans ; Metagenome/*drug effects ; Models, Biological ; Risk Factors ; Symbiosis ; }, abstract = {The discovery that microorganisms can be etiologic agents of disease has driven clinical, research and public health efforts to reduce exposure to bacteria. However, despite extensive campaigns to eradicate pathogens (via antibiotics, vaccinations, hygiene, sanitation, etc.), the incidence and/or severity of multiple immune-mediated diseases including, paradoxically, infectious disease have increased in recent decades. We now appreciate that most microbes in our environment are not pathogenic, and that many human-associated bacteria are symbiotic or beneficial. Notably, recent examples have emerged revealing that the microbiome augments immune system function. This review will focus on how commensal-derived signals enhance various aspects of the host response against pathogens. We suggest that modern lifestyle advances may be depleting specific microbes that enhance immunity against pathogens. Validation of the notion that absence of beneficial microbes is a risk factor for infectious disease may have broad implications for future medical practices.}, } @article {pmid23586739, year = {2013}, author = {Dadheech, PK and Glöckner, G and Casper, P and Kotut, K and Mazzoni, CJ and Mbedi, S and Krienitz, L}, title = {Cyanobacterial diversity in the hot spring, pelagic and benthic habitats of a tropical soda lake.}, journal = {FEMS microbiology ecology}, volume = {85}, number = {2}, pages = {389-401}, doi = {10.1111/1574-6941.12128}, pmid = {23586739}, issn = {1574-6941}, mesh = {Bacteria/genetics ; Biodiversity ; Cyanobacteria/*classification/genetics/isolation & purification ; Ecosystem ; Geologic Sediments/microbiology ; Hot Springs/*microbiology ; Kenya ; Lakes/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Synechococcus/classification/genetics ; Tropical Climate ; }, abstract = {Hot springs and saline-alkaline lakes of East Africa are extreme habitats regarding temperature, or salinity and pH, respectively. This study examines whether divergent habitats of Lake Bogoria, Kenya, impacts cyanobacterial community structure. Samples from the hot springs, pelagic zone and sediment were analysed by light microscopy, multilocus 454-amplicons sequencing and metagenomics to compare the cyanobacterial diversity. Most of the phylogenetic lineages of Cyanobacteria occurred exclusively in the Bogoria hot springs suggesting a high degree of endemism. The prevalent phylotypes were mainly members of the Oscillatoriales (Leptolyngbya, Spirulina, Oscillatoria-like and Planktothricoides). The Chroococcales were represented by different clades of Synechococcus but not a single phylotype clustered with any of the lineages described earlier from different continents. In contrast, we found that the pelagic zone and the sediments were inhabited by only a few taxa, dominated by Arthrospira and Anabaenopsis. Arthrospira, the main food base of Lesser Flamingo, was detected in all three habitats by amplicons pyrosequencing, indicating its resilience and key role as a primary producer. Despite the close connection between the three habitats studied, the cyanobacterial communities in the hot springs and lake differed considerably, suggesting that they are unable to adapt to the extreme conditions of the neighbouring habitat.}, } @article {pmid23584965, year = {2013}, author = {Makhalanyane, TP and Valverde, A and Lacap, DC and Pointing, SB and Tuffin, MI and Cowan, DA}, title = {Evidence of species recruitment and development of hot desert hypolithic communities.}, journal = {Environmental microbiology reports}, volume = {5}, number = {2}, pages = {219-224}, doi = {10.1111/1758-2229.12003}, pmid = {23584965}, issn = {1758-2229}, mesh = {Bacteria/classification/genetics/growth & development/*isolation & purification ; Biodiversity ; Desert Climate ; Ecosystem ; Hot Temperature ; *Soil Microbiology ; }, abstract = {Hypoliths, photosynthetic microbial assemblages found underneath translucent rocks, are widely distributed within the western region of the Namib Desert and other similar environments. Terminal restriction fragment length polymorphism (T-RFLP) analysis was used to assess the bacterial community structure of hypoliths and surrounding soil (below and adjacent to the hypolithic rock) at a fine scale (10 m radius). Multivariate analysis of T-RFs showed that hypolithic and soil communities were structurally distinct. T-RFLP-derived operational taxonomic units were linked to 16S rRNA gene clone libraries. Applying the ecological concept of 'indicator species', six and nine indicator lineages were identified for hypoliths and soil, respectively. Hypolithic communities were dominated by cyanobacteria affiliated to Pleurocapsales, whereas actinobacteria were prevalent in the soil. These results are consistent with the concept of species sorting and suggest that the bottom of the quartz rocks provides conditions suitable for the development of discrete and demonstrably different microbial assemblages. However, we found strong evidence for neutral assembly processes, as almost 90% of the taxa present in the hypoliths were also detected in the soil. These results suggest that hypolithons do not develop independently from microbial communities found in the surrounding soil, but selectively recruit from local populations.}, } @article {pmid23584963, year = {2013}, author = {Dimitriu, PA and Boyce, G and Samarakoon, A and Hartmann, M and Johnson, P and Mohn, WW}, title = {Temporal stability of the mouse gut microbiota in relation to innate and adaptive immunity.}, journal = {Environmental microbiology reports}, volume = {5}, number = {2}, pages = {200-210}, doi = {10.1111/j.1758-2229.2012.00393.x}, pmid = {23584963}, issn = {1758-2229}, support = {77712//Canadian Institutes of Health Research/Canada ; }, mesh = {Adaptive Immunity ; Animals ; Bacteria/classification/genetics/immunology/*isolation & purification ; Biodiversity ; Female ; Gastrointestinal Tract/*immunology/*microbiology ; Homeodomain Proteins/genetics/immunology ; Immunity, Innate ; Leukocyte Common Antigens/genetics/immunology ; Male ; *Metagenome ; Mice/genetics/immunology/*microbiology ; Mice, Inbred C57BL ; Mice, Knockout ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Gut microbial community properties of mammals are thought to be partly shaped by a combination of host immunity and environmental factors, but their relative importance is not firmly established. To address this gap, we first characterized the faecal bacteria of mice with a functioning immune system (wild-type, WT), mice with defective immune responses (CD45), mice lacking an adaptive immune system (RAG), and mice with both immune dysfunctions (45RAG). Using fingerprinting of 16S rRNA genes, we observed significant differences in gut microbiota composition across all mouse strains (P < 0.001) and identified several mouse strain-specific genera via pyrosequencing, including Turicibacter sp. (in WT mice) and Allobaculum sp. (in CD45-deficient animals). To define the role of the host immune system in constraining gut microbiota stability after perturbation, we cohoused CD45-deficient and WT mice and monitored gut bacterial community dynamics during 8 weeks. Cohousing caused the WT bacterial communities to become indistinguishable from those of CD45 mice (P > 0.05). Time-series analysis indicated that the communities of cohoused mice changed directionally as opposed to the relatively stable communities of non-cohoused controls. When we considered only taxonomic membership, it was the communities of CD45 non-cohoused mice that experienced the highest rate of change. Rather than be governed by fluctuations in the relative abundance of taxa, we suggest that CD45-regulated immune responses either are stimulated by the presence of bacteria per se or promote temporal stability by selecting for the occurrence of specific taxa.}, } @article {pmid23577216, year = {2013}, author = {Dang, H and Zhou, H and Zhang, Z and Yu, Z and Hua, E and Liu, X and Jiao, N}, title = {Molecular detection of Candidatus Scalindua pacifica and environmental responses of sediment anammox bacterial community in the Bohai Sea, China.}, journal = {PloS one}, volume = {8}, number = {4}, pages = {e61330}, pmid = {23577216}, issn = {1932-6203}, mesh = {Anaerobiosis ; Bacteria/*classification/drug effects/*genetics/metabolism ; Biodiversity ; China ; DNA, Bacterial/genetics ; Environmental Pollutants/toxicity ; Genes, Bacterial/genetics ; Geologic Sediments/*microbiology ; Metagenome/drug effects/genetics ; *Molecular Typing ; *Oceans and Seas ; Oxidation-Reduction ; Phylogeny ; Quaternary Ammonium Compounds/*metabolism ; RNA, Ribosomal, 16S/genetics ; Spatial Analysis ; }, abstract = {The Bohai Sea is a large semi-enclosed shallow water basin, which receives extensive river discharges of various terrestrial and anthropogenic materials such as sediments, nutrients and contaminants. How these terrigenous inputs may influence the diversity, community structure, biogeographical distribution, abundance and ecophysiology of the sediment anaerobic ammonium oxidation (anammox) bacteria was unknown. To answer this question, an investigation employing both 16S rRNA and hzo gene biomarkers was carried out. Ca. Scalindua bacteria were predominant in the surface sediments of the Bohai Sea, while non-Scalindua anammox bacteria were also detected in the Yellow River estuary and inner part of Liaodong Bay that received strong riverine and anthropogenic impacts. A novel 16S rRNA gene sequence clade was identified, putatively representing an anammox bacterial new candidate species tentatively named "Ca. Scalindua pacifica". Several groups of environmental factors, usually with distinct physicochemical or biogeochemical natures, including general marine and estuarine physicochemical properties, availability of anammox substrates (inorganic N compounds), alternative reductants and oxidants, environmental variations caused by river discharges and associated contaminants such as heavy metals, were identified to likely play important roles in influencing the ecology and biogeochemical functioning of the sediment anammox bacteria. In addition to inorganic N compounds that might play a key role in shaping the anammox microbiota, organic carbon, organic nitrogen, sulfate, sulfide and metals all showed the potentials to participate in the anammox process, releasing the strict dependence of the anammox bacteria upon the direct availability of inorganic N nutrients that might be limiting in certain areas of the Bohai Sea. The importance of inorganic N nutrients and certain other environmental factors to the sediment anammox microbiota suggests that these bacteria were active for the in situ N transforming process and maintained a versatile life style well adapted to the varying environmental conditions of the studied coastal ocean.}, } @article {pmid23576059, year = {2013}, author = {Proal, AD and Albert, PJ and Marshall, TG and Blaney, GP and Lindseth, IA}, title = {Immunostimulation in the treatment for chronic fatigue syndrome/myalgic encephalomyelitis.}, journal = {Immunologic research}, volume = {56}, number = {2-3}, pages = {398-412}, pmid = {23576059}, issn = {1559-0755}, mesh = {Coinfection/*immunology/microbiology/therapy ; Dysbiosis ; Fatigue Syndrome, Chronic/immunology/microbiology/*therapy ; Gene Expression Regulation/immunology ; Humans ; Immunity, Innate ; Immunization ; Immunosuppression Therapy ; Infections/*immunology/microbiology/therapy ; Metagenome/immunology ; Microbiota/immunology ; Models, Biological ; Receptors, Calcitriol/genetics/*metabolism ; }, abstract = {Chronic fatigue syndrome (CFS)/myalgic encephalomyelitis (ME) has long been associated with the presence of infectious agents, but no single pathogen has been reliably identified in all patients with the disease. Recent studies using metagenomic techniques have demonstrated the presence of thousands of microbes in the human body that were previously undetected and unknown to science. More importantly, such species interact together by sharing genes and genetic function within communities. It follows that searching for a singular pathogen may greatly underestimate the microbial complexity potentially driving a complex disease like CFS/ME. Intracellular microbes alter the expression of human genes in order to facilitate their survival. We have put forth a model describing how multiple species-bacterial, viral, and fungal-can cumulatively dysregulate expression by the VDR nuclear receptor in order to survive and thus drive a disease process. Based on this model, we have developed an immunostimulatory therapy that is showing promise inducing both subjective and objective improvement in patients suffering from CFS/ME.}, } @article {pmid23575371, year = {2013}, author = {Hingamp, P and Grimsley, N and Acinas, SG and Clerissi, C and Subirana, L and Poulain, J and Ferrera, I and Sarmento, H and Villar, E and Lima-Mendez, G and Faust, K and Sunagawa, S and Claverie, JM and Moreau, H and Desdevises, Y and Bork, P and Raes, J and de Vargas, C and Karsenti, E and Kandels-Lewis, S and Jaillon, O and Not, F and Pesant, S and Wincker, P and Ogata, H}, title = {Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.}, journal = {The ISME journal}, volume = {7}, number = {9}, pages = {1678-1695}, pmid = {23575371}, issn = {1751-7370}, mesh = {Animals ; *Biodiversity ; Cell Nucleus/virology ; Cytoplasm/virology ; DNA Viruses/*classification/genetics/*physiology ; Eukaryota/virology ; Gene Transfer, Horizontal ; Genes, Viral/genetics ; Genome, Viral/genetics ; Indian Ocean ; *Metagenome ; Oceans and Seas ; Oomycetes/virology ; Phycodnaviridae/classification/genetics/physiology ; Phylogeny ; Population Density ; Prokaryotic Cells/physiology ; }, abstract = {Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2-1.6 μm size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 10(4)-10(5) genomes ml(-1) for the samples from the photic zone and 10(2)-10(3) genomes ml(-1) for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts.}, } @article {pmid23574280, year = {2013}, author = {Chen, LX and Li, JT and Chen, YT and Huang, LN and Hua, ZS and Hu, M and Shu, WS}, title = {Shifts in microbial community composition and function in the acidification of a lead/zinc mine tailings.}, journal = {Environmental microbiology}, volume = {15}, number = {9}, pages = {2431-2444}, doi = {10.1111/1462-2920.12114}, pmid = {23574280}, issn = {1462-2920}, mesh = {Acids/*chemistry ; Bacteria/*classification/drug effects/*genetics/metabolism ; *Biodiversity ; Environmental Pollutants/toxicity ; Genes, Bacterial/genetics ; Lead/chemistry/metabolism ; *Mining ; RNA, Ribosomal, 16S/genetics ; Zinc/chemistry/metabolism ; }, abstract = {In an attempt to link the microbial community composition and function in mine tailings to the generation of acid mine drainage, we simultaneously explored the geochemistry and microbiology of six tailings collected from a lead/zinc mine, i.e. primary tailings (T1), slightly acidic tailings (T2), extremely acidic tailings (T3, T4 and T5) and orange-coloured oxidized tailings (T6). Geochemical results showed that the six tailings (from T1 to T6) likely represented sequential stages of the acidification process of the mine tailings. 16S rRNA pyrosequencing revealed a contrasting microbial composition between the six tailings: Proteobacteria-related sequences dominated T1-T3 with relative abundance ranging from 56 to 93%, whereas Ferroplasma-related sequences dominated T4-T6 with relative abundance ranging from 28 to 58%. Furthermore, metagenomic analysis of the microbial communities of T2 and T6 indicated that the genes encoding key enzymes for microbial carbon fixation, nitrogen fixation and sulfur oxidation in T2 were largely from Thiobacillus and Acidithiobacillus, Methylococcus capsulatus, and Thiobacillus denitrificans respectively; while those in T6 were mostly identified in Acidithiobacillus and Leptospirillum, Acidithiobacillus and Leptospirillum, and Acidithiobacillus respectively. The microbial communities in T2 and T6 harboured more genes suggesting diverse metabolic capacities for sulfur oxidation/heavy metal detoxification and tolerating low pH respectively.}, } @article {pmid23565884, year = {2013}, author = {Lazarevic, V and Manzano, S and Gaïa, N and Girard, M and Whiteson, K and Hibbs, J and François, P and Gervaix, A and Schrenzel, J}, title = {Effects of amoxicillin treatment on the salivary microbiota in children with acute otitis media.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {19}, number = {8}, pages = {E335-42}, doi = {10.1111/1469-0691.12213}, pmid = {23565884}, issn = {1469-0691}, mesh = {Amoxicillin/*therapeutic use ; Anti-Bacterial Agents/*therapeutic use ; Child ; Child, Preschool ; Cluster Analysis ; Cohort Studies ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Humans ; Infant ; Male ; Metagenome ; Microbiota/*drug effects ; Molecular Sequence Data ; Otitis Media/*drug therapy ; Phylogeny ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Amoxicillin is a first-line antibiotic treatment for acute otitis media in children and one of the most commonly used antibiotics for human bacterial infections. We investigated changes in salivary bacterial communities among children treated with amoxicillin for acute otitis media (n = 18), using a culture-independent approach based on pyrosequencing of the V3 region of the bacterial 16S rRNA gene. The control group consisted of children with acute otitis media who were not given antibiotics (n = 15). One species-level phylotype assigned to the genus Streptococcus was identified across all (n = 99) saliva samples. Two additional species-level phylotypes from the genera Gemella and Granulicatella were shared by all (n = 45) samples of control subjects. Amoxicillin treatment resulted in reduced species richness and diversity, and a significant shift in the relative abundance of 35 taxa at different ranks from phylum to species-level phylotype. At the phylum level, prevalence of TM7 and Actinobacteria decreased at the end of treatment, whereas Proteobacteria had a higher relative abundance post-treatment. Multivariate analysis showed that samples from the same control subject taken over time intervals tended to cluster together. Among antibiotic-treated subjects, samples taken before and at the end of amoxicillin treatment formed two relatively well-separated clusters both of which greatly overlapped with samples taken about 3 weeks post-treatment. Our results point to a substantial but incomplete recovery of the salivary bacterial community from the antibiotic about 3 weeks after the end of treatment.}, } @article {pmid23562481, year = {2013}, author = {Baker, KS and Leggett, RM and Bexfield, NH and Alston, M and Daly, G and Todd, S and Tachedjian, M and Holmes, CE and Crameri, S and Wang, LF and Heeney, JL and Suu-Ire, R and Kellam, P and Cunningham, AA and Wood, JL and Caccamo, M and Murcia, PR}, title = {Metagenomic study of the viruses of African straw-coloured fruit bats: detection of a chiropteran poxvirus and isolation of a novel adenovirus.}, journal = {Virology}, volume = {441}, number = {2}, pages = {95-106}, pmid = {23562481}, issn = {1096-0341}, support = {/WT_/Wellcome Trust/United Kingdom ; G0801822/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Africa ; Animals ; *Biodiversity ; Chiroptera/*virology ; Cluster Analysis ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Viruses/*classification/*genetics ; }, abstract = {Viral emergence as a result of zoonotic transmission constitutes a continuous public health threat. Emerging viruses such as SARS coronavirus, hantaviruses and henipaviruses have wildlife reservoirs. Characterising the viruses of candidate reservoir species in geographical hot spots for viral emergence is a sensible approach to develop tools to predict, prevent, or contain emergence events. Here, we explore the viruses of Eidolon helvum, an Old World fruit bat species widely distributed in Africa that lives in close proximity to humans. We identified a great abundance and diversity of novel herpes and papillomaviruses, described the isolation of a novel adenovirus, and detected, for the first time, sequences of a chiropteran poxvirus closely related with Molluscum contagiosum. In sum, E. helvum display a wide variety of mammalian viruses, some of them genetically similar to known human pathogens, highlighting the possibility of zoonotic transmission.}, } @article {pmid23560063, year = {2013}, author = {Zakharova, YR and Galachyants, YP and Kurilkina, MI and Likhoshvay, AV and Petrova, DP and Shishlyannikov, SM and Ravin, NV and Mardanov, AV and Beletsky, AV and Likhoshway, YV}, title = {The structure of microbial community and degradation of diatoms in the deep near-bottom layer of Lake Baikal.}, journal = {PloS one}, volume = {8}, number = {4}, pages = {e59977}, pmid = {23560063}, issn = {1932-6203}, mesh = {Acidobacteria/classification/genetics ; Actinobacteria/classification/genetics ; Bacteroidetes/classification/genetics ; Biodiversity ; Cyanobacteria/classification/genetics ; Diatoms/*metabolism/*microbiology ; Ecosystem ; Geologic Sediments/microbiology ; Lakes/*microbiology ; *Metagenome ; *Phylogeny ; Proteobacteria/classification/genetics ; RNA, Ribosomal, 16S/classification/*genetics ; Russia ; Silicon Dioxide/metabolism ; Verrucomicrobia/genetics ; }, abstract = {Insight into the role of bacteria in degradation of diatoms is important for understanding the factors and components of silica turnover in aquatic ecosystems. Using microscopic methods, it has been shown that the degree of diatom preservation and the numbers of diatom-associated bacteria in the surface layer of bottom sediments decrease with depth; in the near-bottom water layer, the majority of bacteria are associated with diatom cells, being located either on the cell surface or within the cell. The structure of microbial community in the near-bottom water layer has been characterized by pyrosequencing of the 16S rRNA gene, which has revealed 149 208 unique sequences. According to the results of metagenomic analysis, the community is dominated by representatives of Proteobacteria (41.9%), Actinobacteria (16%); then follow Acidobacteria (6.9%), Cyanobacteria (5%), Bacteroidetes (4.7%), Firmicutes (2.8%), Nitrospira (1.6%), and Verrucomicrobia (1%); other phylotypes account for less than 1% each. For 18.7% of the sequences, taxonomic identification has been possible only to the Bacteria domain level. Many bacteria identified to the genus level have close relatives occurring in other aquatic ecosystems and soils. The metagenome of the bacterial community from the near-bottom water layer also contains 16S rRNA gene sequences found in previously isolated bacterial strains possessing hydrolytic enzyme activity. These data show that potential degraders of diatoms occur among the vast variety of microorganisms in the near-bottom water of Lake Baikal.}, } @article {pmid23555678, year = {2013}, author = {Park, DY and Ahn, YT and Park, SH and Huh, CS and Yoo, SR and Yu, R and Sung, MK and McGregor, RA and Choi, MS}, title = {Supplementation of Lactobacillus curvatus HY7601 and Lactobacillus plantarum KY1032 in diet-induced obese mice is associated with gut microbial changes and reduction in obesity.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e59470}, pmid = {23555678}, issn = {1932-6203}, mesh = {Adipocytes/drug effects/metabolism ; Adipose Tissue/drug effects/metabolism/pathology ; Animals ; Biodiversity ; Body Weight/drug effects ; Cholesterol/blood ; Diet/*adverse effects ; Gene Expression Regulation/drug effects ; Hormones/blood ; Intestines/*drug effects/*microbiology ; Lactobacillus plantarum/*physiology ; Liver/drug effects/metabolism ; Male ; Metagenome/drug effects ; Mice ; Mice, Inbred C57BL ; Obesity/*diet therapy/etiology/metabolism/*microbiology ; Probiotics/*pharmacology/therapeutic use ; }, abstract = {OBJECTIVE: To investigate the functional effects of probiotic treatment on the gut microbiota, as well as liver and adipose gene expression in diet-induced obese mice.

DESIGN: Male C57BL/6J mice were fed a high-fat diet (HFD) for 8 weeks to induce obesity, and then randomized to receive HFD+probiotic (Lactobacillus curvatus HY7601 and Lactobacillus plantarum KY1032, n = 9) or HFD+placebo (n = 9) for another 10 weeks. Normal diet (ND) fed mice (n = 9) served as non-obese controls.

RESULTS: Diet-induced obese mice treated with probiotics showed reduced body weight gain and fat accumulation as well as lowered plasma insulin, leptin, total-cholesterol and liver toxicity biomarkers. A total of 151,061 pyrosequencing reads for fecal microbiota were analyzed with a mean of 6,564, 5,274 and 4,464 reads for the ND, HFD+placebo and HFD+probiotic groups, respectively. Gut microbiota species were shared among the experimental groups despite the different diets and treatments. The diversity of the gut microbiota and its composition were significantly altered in the diet-induced obese mice and after probiotic treatment. We observed concurrent transcriptional changes in adipose tissue and the liver. In adipose tissue, pro-inflammatory genes (TNFα, IL6, IL1β and MCP1) were down-regulated in mice receiving probiotic treatment. In the liver, fatty acid oxidation-related genes (PGC1α, CPT1, CPT2 and ACOX1) were up-regulated in mice receiving probiotic treatment.

CONCLUSIONS: The gut microbiota of diet-induced obese mice appears to be modulated in mice receiving probiotic treatment. Probiotic treatment might reduce diet-induced obesity and modulate genes associated with metabolism and inflammation in the liver and adipose tissue.}, } @article {pmid23555039, year = {2013}, author = {Gouba, N and Raoult, D and Drancourt, M}, title = {Plant and fungal diversity in gut microbiota as revealed by molecular and culture investigations.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e59474}, pmid = {23555039}, issn = {1932-6203}, mesh = {Adult ; *Biodiversity ; *Culture Techniques ; Feces/microbiology ; Female ; Fungi/*classification/genetics/growth & development/isolation & purification ; Humans ; Intestines/*microbiology ; *Metagenome ; Obesity/microbiology ; Plants/*classification/genetics ; Polymerase Chain Reaction ; }, abstract = {BACKGROUND: Few studies describing eukaryotic communities in the human gut microbiota have been published. The objective of this study was to investigate comprehensively the repertoire of plant and fungal species in the gut microbiota of an obese patient.

A stool specimen was collected from a 27-year-old Caucasian woman with a body mass index of 48.9 who was living in Marseille, France. Plant and fungal species were identified using a PCR-based method incorporating 25 primer pairs specific for each eukaryotic phylum and universal eukaryotic primers targeting 18S rRNA, internal transcribed spacer (ITS) and a chloroplast gene. The PCR products amplified using these primers were cloned and sequenced. Three different culture media were used to isolate fungi, and these cultured fungi were further identified by ITS sequencing. A total of 37 eukaryotic species were identified, including a Diatoms (Blastocystis sp.) species, 18 plant species from the Streptophyta phylum and 18 fungal species from the Ascomycota, Basidiomycota and Chytridiocomycota phyla. Cultures yielded 16 fungal species, while PCR-sequencing identified 7 fungal species. Of these 7 species of fungi, 5 were also identified by culture. Twenty-one eukaryotic species were discovered for the first time in human gut microbiota, including 8 fungi (Aspergillus flavipes, Beauveria bassiana, Isaria farinosa, Penicillium brevicompactum, Penicillium dipodomyicola, Penicillium camemberti, Climacocystis sp. and Malassezia restricta). Many fungal species apparently originated from food, as did 11 plant species. However, four plant species (Atractylodes japonica, Fibraurea tinctoria, Angelica anomala, Mitella nuda) are used as medicinal plants.

CONCLUSIONS/SIGNIFICANCE: Investigating the eukaryotic components of gut microbiota may help us to understand their role in human health.}, } @article {pmid23552257, year = {2013}, author = {Albertsen, M and Stensballe, A and Nielsen, KL and Nielsen, PH}, title = {Digging into the extracellular matrix of a complex microbial community using a combined metagenomic and metaproteomic approach.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {67}, number = {7}, pages = {1650-1656}, doi = {10.2166/wst.2013.030}, pmid = {23552257}, issn = {0273-1223}, mesh = {Alginates ; Amyloid/metabolism ; Bacterial Proteins/*genetics/metabolism ; Extracellular Matrix/metabolism ; Glucuronic Acid/biosynthesis ; Hexuronic Acids ; *Metagenome ; Microbial Consortia/*genetics ; Polysaccharides, Bacterial/*biosynthesis ; }, abstract = {Knowledge about identity and function of extracellular polymeric substances (EPS) in complex microbial communities is sparse, although these components have a large influence on the function of the microbial communities. We investigated the presence of selected genes potentially involved in EPS production in a 145 Mbp metagenome prepared by Illumina sequencing from a full-scale wastewater treatment plant carrying out enhanced biological phosphorus removal (EBPR). A range of genes involved in alginate production was identified and assigned mainly to bacteria from the phylum Bacteroidetes. Furthermore, several proteins in the EPS matrix were extracted, purified and identified by mass spectrometry. By using the metagenome as a reference for the metaproteomic analysis, more proteins were identified compared to using only publicly available databases. This illustrates the low degree of similarity between the bacteria in the EBPR community and the sequenced bacteria in the public databases. Hence, the combination of metagenomics and metaproteomics presented here is needed to investigate the identity of the proteins in the EPS matrix.}, } @article {pmid23551703, year = {2013}, author = {Daae, FL and Økland, I and Dahle, H and Jørgensen, SL and Thorseth, IH and Pedersen, RB}, title = {Microbial life associated with low-temperature alteration of ultramafic rocks in the Leka ophiolite complex.}, journal = {Geobiology}, volume = {11}, number = {4}, pages = {318-339}, doi = {10.1111/gbi.12035}, pmid = {23551703}, issn = {1472-4669}, mesh = {*Biota ; Cluster Analysis ; Geologic Sediments/*chemistry/*microbiology ; Metagenomics ; Microbiological Techniques ; Microscopy ; Minerals/analysis ; Molecular Sequence Data ; Norway ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Water-rock interactions in ultramafic lithosphere generate reduced chemical species such as hydrogen that can fuel subsurface microbial communities. Sampling of this environment is expensive and technically demanding. However, highly accessible, uplifted oceanic lithospheres emplaced onto continental margins (ophiolites) are potential model systems for studies of the subsurface biosphere in ultramafic rocks. Here, we describe a microbiological investigation of partially serpentinized dunite from the Leka ophiolite (Norway). We analysed samples of mineral coatings on subsurface fracture surfaces from different depths (10-160 cm) and groundwater from a 50-m-deep borehole that penetrates several major fracture zones in the rock. The samples are suggested to represent subsurface habitats ranging from highly anaerobic to aerobic conditions. Water from a surface pond was analysed for comparison. To explore the microbial diversity and to make assessments about potential metabolisms, the samples were analysed by microscopy, construction of small subunit ribosomal RNA gene clone libraries, culturing and quantitative-PCR. Different microbial communities were observed in the groundwater, the fracture-coating material and the surface water, indicating that distinct microbial ecosystems exist in the rock. Close relatives of hydrogen-oxidizing Hydrogenophaga dominated (30% of the bacterial clones) in the oxic groundwater, indicating that microbial communities in ultramafic rocks at Leka could partially be driven by H2 produced by low-temperature water-rock reactions. Heterotrophic organisms, including close relatives of hydrocarbon degraders possibly feeding on products from Fischer-Tropsch-type reactions, dominated in the fracture-coating material. Putative hydrogen-, ammonia-, manganese- and iron-oxidizers were also detected in fracture coatings and the groundwater. The microbial communities reflect the existence of different subsurface redox conditions generated by differences in fracture size and distribution, and mixing of fluids. The particularly dense microbial communities in the shallow fracture coatings seem to be fuelled by both photosynthesis and oxidation of reduced chemical species produced by water-rock reactions.}, } @article {pmid23551379, year = {2013}, author = {Arnold, B and Corbett-Detig, RB and Hartl, D and Bomblies, K}, title = {RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling.}, journal = {Molecular ecology}, volume = {22}, number = {11}, pages = {3179-3190}, doi = {10.1111/mec.12276}, pmid = {23551379}, issn = {1365-294X}, mesh = {Animals ; Biodiversity ; Chromosome Mapping ; Drosophila melanogaster/*genetics ; Genetic Variation ; Haplotypes/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome ; Metagenomics/*methods ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {Reduced representation genome-sequencing approaches based on restriction digestion are enabling large-scale marker generation and facilitating genomic studies in a wide range of model and nonmodel systems. However, sampling chromosomes based on restriction digestion may introduce a bias in allele frequency estimation due to polymorphisms in restriction sites. To explore the effects of this nonrandom sampling and its sensitivity to different evolutionary parameters, we developed a coalescent-simulation framework to mimic the biased recovery of chromosomes in restriction-based short-read sequencing experiments (RADseq). We analysed simulated DNA sequence datasets and compared known values from simulations with those that would be estimated using a RADseq approach from the same samples. We compare these 'true' and 'estimated' values of commonly used summary statistics, π, θ(w), Tajima's D and F(ST). We show that loci with missing haplotypes have estimated summary statistic values that can deviate dramatically from true values and are also enriched for particular genealogical histories. These biases are sensitive to nonequilibrium demography, such as bottlenecks and population expansion. In silico digests with 102 completely sequenced Drosophila melanogaster genomes yielded results similar to our findings from coalescent simulations. Though the potential of RADseq for marker discovery and trait mapping in nonmodel systems remains undisputed, our results urge caution when applying this technique to make population genetic inferences.}, } @article {pmid23550823, year = {2013}, author = {Maurice, CF and Turnbaugh, PJ}, title = {Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales.}, journal = {FEMS microbiology reviews}, volume = {37}, number = {5}, pages = {830-848}, pmid = {23550823}, issn = {1574-6976}, support = {P50 GM068763/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Ecosystem ; Humans ; Metabolomics/*methods ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; Single-Cell Analysis/methods ; }, abstract = {Humans are home to complex microbial communities, whose aggregate genomes and their encoded metabolic activities are referred to as the human microbiome. Recently, researchers have begun to appreciate that different human body habitats and the activities of their resident microorganisms can be better understood in ecological terms, as a range of spatial scales encompassing single cells, guilds of microorganisms responsive to a similar substrate, microbial communities, body habitats, and host populations. However, the bulk of the work to date has focused on studies of culturable microorganisms in isolation or on DNA sequencing-based surveys of microbial diversity in small-to-moderate-sized cohorts of individuals. Here, we discuss recent work that highlights the potential for assessing the human microbiome at a range of spatial scales, and for developing novel techniques that bridge multiple levels: for example, through the combination of single-cell methods and metagenomic sequencing. These studies promise to not only provide a much-needed epidemiological and ecological context for mechanistic studies of culturable and genetically tractable microorganisms, but may also lead to the discovery of fundamental rules that govern the assembly and function of host-associated microbial communities.}, } @article {pmid23549457, year = {2013}, author = {Hansen, CH and Metzdorff, SB and Hansen, AK}, title = {Customizing laboratory mice by modifying gut microbiota and host immunity in an early "window of opportunity".}, journal = {Gut microbes}, volume = {4}, number = {3}, pages = {241-245}, pmid = {23549457}, issn = {1949-0984}, mesh = {Animals ; *Biota ; Gastrointestinal Tract/*immunology/*microbiology ; Homeostasis ; Immune System/*physiology ; *Metagenome ; Mice ; *Models, Animal ; }, abstract = {We recently investigated how post-natal microbial gut colonization is important for the development of the immune system, especially in the systemic compartments. This addendum presents additional data which in accordance with our previous findings show that early life microbial colonization is critical for a fine-tuned immune homeostasis to develop also in the intestinal environment. A generalized reduction in the expression of immune signaling related genes in the small intestine may explain previously shown increased systemic adaptive immune reactivity, if the regulatory cross-talk between intra- and extra-intestinal immune cells is immature following a neonatal germ-free period. These findings are furthermore discussed in the context of recently published results on how lack of microbial exposure in the neonatal life modifies disease expression in rodents used as models mimicking human inflammatory diseases. In particular, with a focus on how these interesting findings could be used to optimize the use of rodent models.}, } @article {pmid23549377, year = {2013}, author = {Zhang, Q and Widmer, G and Tzipori, S}, title = {A pig model of the human gastrointestinal tract.}, journal = {Gut microbes}, volume = {4}, number = {3}, pages = {193-200}, pmid = {23549377}, issn = {1949-0984}, support = {R01 AI088748/AI/NIAID NIH HHS/United States ; R56 AI094459/AI/NIAID NIH HHS/United States ; AI094459/AI/NIAID NIH HHS/United States ; AI088748/AI/NIAID NIH HHS/United States ; }, mesh = {Aged ; Animals ; Biota ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Gastrointestinal Tract/*microbiology ; Germ-Free Life ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Male ; *Metagenome ; Middle Aged ; *Models, Animal ; RNA, Ribosomal, 16S/genetics ; Swine ; Time Factors ; }, abstract = {Easy access to next generation sequencing has enabled the rapid analysis of complex microbial populations. To take full advantage of these technologies, animal models enabling the manipulation of human microbiomes and the study of the impact of such perturbations on the host are needed. To this aim we are developing experimentally tractable and clinically relevant pig models of the human adult and infant gastro-intestinal tract. The intestine of germ-free piglets was populated with human adult or infant fecal microbial populations, and the piglets were maintained on solid or milk diet, respectively. Amplicons of 16S rRNA V6 region were deep-sequenced to monitor to what extent the transplanted human microbiomes changed in the pig. Within 24 h of transfer of human fecal microbiome to pigs, bacterial microbiomes rich in Proteobacteria emerged. These populations evolved toward a more diverse composition rich in Bacteroidetes and Firmicutes. In the experiment where infant microbiome was used, the phylogenetic composition of the transplanted bacterial population converged toward that of the human inoculum. A majority of sequences belonged to a relatively small number of operational taxonomic units, whereas at the other end of the abundance spectrum, a large number of rare and transient OTUs were detected. Analysis of fecal and colonic microbiomes originating from the same animal indicate that feces closely replicate the colonic microbiome. We conclude that the pig intestine can be colonized with human fecal microbiomes to generate a realistic model of the human GI tract.}, } @article {pmid23542623, year = {2013}, author = {Bougouffa, S and Yang, JK and Lee, OO and Wang, Y and Batang, Z and Al-Suwailem, A and Qian, PY}, title = {Distinctive microbial community structure in highly stratified deep-sea brine water columns.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {11}, pages = {3425-3437}, pmid = {23542623}, issn = {1098-5336}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Base Sequence ; *Biodiversity ; Cell Count ; Cluster Analysis ; DNA Primers/genetics ; Hydrothermal Vents/*microbiology ; Indian Ocean ; Metagenome/*genetics ; Molecular Sequence Data ; Multivariate Analysis ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Sequence Analysis, DNA ; Species Specificity ; *Water Microbiology ; }, abstract = {Atlantis II and Discovery are two hydrothermal and hypersaline deep-sea pools in the Red Sea rift that are characterized by strong thermohalo-stratification and temperatures steadily peaking near the bottom. We conducted comprehensive vertical profiling of the microbial populations in both pools and highlighted the influential environmental factors. Pyrosequencing of the 16S rRNA genes revealed shifts in community structures vis-à-vis depth. High diversity and low abundance were features of the deepest convective layers despite the low cell density. Surprisingly, the brine interfaces had significantly higher cell counts than the overlying deep-sea water, yet they were lowest in diversity. Vertical stratification of the bacterial populations was apparent as we moved from the Alphaproteobacteria-dominated deep sea to the Planctomycetaceae- or Deferribacteres-dominated interfaces to the Gammaproteobacteria-dominated brine layers. Archaeal marine group I was dominant in the deep-sea water and interfaces, while several euryarchaeotic groups increased in the brine. Across sites, microbial phylotypes and abundances varied substantially in the brine interface of Discovery compared with Atlantis II, despite the near-identical populations in the overlying deep-sea waters. The lowest convective layers harbored interestingly similar microbial communities, even though temperature and heavy metal concentrations were very different. Multivariate analysis indicated that temperature and salinity were the major influences shaping the communities. The harsh conditions and the low-abundance phylotypes could explain the observed correlation in the brine pools.}, } @article {pmid23537200, year = {2013}, author = {Zhang, Y and Lu, Z and Liu, S and Yang, Y and He, Z and Ren, Z and Zhou, J and Li, D}, title = {Geochip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {72}, pmid = {23537200}, issn = {1471-2180}, mesh = {*Biota ; Genetic Variation ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Microarray Analysis/*methods ; Oligonucleotide Array Sequence Analysis/*methods ; *Soil Microbiology ; Tibet ; }, abstract = {BACKGROUND: GeoChip 3.0, a microbial functional gene array, containing ~28,000 oligonucleotide probes and targeting ~57,000 sequences from 292 functional gene families, provided a powerful tool for researching microbial community structure in natural environments. The alpine meadow is a dominant plant community in the Qinghai-Tibetan plateau, hence it is important to profile the unique geographical flora and assess the response of the microbial communities to environmental variables. In this study, Geochip 3.0 was employed to understand the microbial functional gene diversity and structure, and metabolic potential and the major environmental factors in shaping microbial communities structure of alpine meadow soil in Qinghai-Tibetan Plateau.

RESULTS: A total of 6143 microbial functional genes involved in carbon degradation, carbon fixation, methane oxidation and production, nitrogen cycling, phosphorus utilization, sulphur cycling, organic remediation, metal resistance, energy process and other category were detected in six soil samples and high diversity was observed. Interestingly, most of the detected genes associated with carbon degradation were derived from cultivated organisms. To identify major environmental factors in shaping microbial communities, Mantel test and CCA Statistical analyses were performed. The results indicated that altitude, C/N, pH and soil organic carbon were significantly (P < 0.05) correlated with the microbial functional structure and a total of 80.97% of the variation was significantly explained by altitude, C/N and pH. The C/N contributed 38.2% to microbial functional gene variation, which is in accordance with the hierarchical clustering of overall microbial functional genes.

CONCLUSIONS: High overall functional genes and phylogenetic diversity of the alpine meadow soil microbial communities existed in the Qinghai-Tibetan Plateau. Most of the genes involved in carbon degradation were derived from characterized microbial groups. Microbial composition and structures variation were significantly impacted by local environmental conditions, and soil C/N is the most important factor to impact the microbial structure in alpine meadow in Qinghai-Tibetan plateau.}, } @article {pmid23533327, year = {2013}, author = {Wemheuer, B and Taube, R and Akyol, P and Wemheuer, F and Daniel, R}, title = {Microbial diversity and biochemical potential encoded by thermal spring metagenomes derived from the Kamchatka Peninsula.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2013}, number = {}, pages = {136714}, pmid = {23533327}, issn = {1472-3654}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; *Biodiversity ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Hot Springs/*microbiology ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Russia ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Volcanic regions contain a variety of environments suitable for extremophiles. This study was focused on assessing and exploiting the prokaryotic diversity of two microbial communities derived from different Kamchatkian thermal springs by metagenomic approaches. Samples were taken from a thermoacidophilic spring near the Mutnovsky Volcano and from a thermophilic spring in the Uzon Caldera. Environmental DNA for metagenomic analysis was isolated from collected sediment samples by direct cell lysis. The prokaryotic community composition was examined by analysis of archaeal and bacterial 16S rRNA genes. A total number of 1235 16S rRNA gene sequences were obtained and used for taxonomic classification. Most abundant in the samples were members of Thaumarchaeota, Thermotogae, and Proteobacteria. The Mutnovsky hot spring was dominated by the Terrestrial Hot Spring Group, Kosmotoga, and Acidithiobacillus. The Uzon Caldera was dominated by uncultured members of the Miscellaneous Crenarchaeotic Group and Enterobacteriaceae. The remaining 16S rRNA gene sequences belonged to the Aquificae, Dictyoglomi, Euryarchaeota, Korarchaeota, Thermodesulfobacteria, Firmicutes, and some potential new phyla. In addition, the recovered DNA was used for generation of metagenomic libraries, which were subsequently mined for genes encoding lipolytic and proteolytic enzymes. Three novel genes conferring lipolytic and one gene conferring proteolytic activity were identified.}, } @article {pmid23529681, year = {2014}, author = {Gao, ZM and Xu, X and Ruan, LW}, title = {Enrichment and characterization of an anaerobic cellulolytic microbial consortium SQD-1.1 from mangrove soil.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {1}, pages = {465-474}, doi = {10.1007/s00253-013-4857-2}, pmid = {23529681}, issn = {1432-0614}, mesh = {Anaerobiosis ; Cellulose/*metabolism ; China ; DNA, Bacterial/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; *Microbial Consortia ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Enrichment of microbial consortia provides an approach to simulate and investigate microbial communities in natural environments. In this study, a cellulolytic microbial consortium SQD-1.1 was enriched from mangrove soil of Qinglan port (Hainan, China) by 27 times continuous subcultivation under anaerobic static conditions. The consortium could completely degrade 0.2% (w/v) filter paper within 3 days and utilized it as the sole carbon source. PCR-denaturing gradient gel electrophoresis analysis revealed a stable microbial community structure in the incubation process of 10 days and in the procedure of subcultivation. Twenty-four operational taxonomic units belonging to seven phyla were obtained from the full-length 16S rRNA gene library. Five clones, closest related to the genera Alkaliflexus, Clostridium, Alistipes, Spirochaeta, and Trichococcus, were the predominant ones. Among them, M117, phylogeneticly showing high similarity (16S rRNA gene identity, 95.3%) with the cellulolytic anaerobic bacterium Clostridium straminisolvens CSK1(T), was the potential key cellulolytic bacterium. Using the plate cultivation method, 12 strains, including one potential new species and four potential new species of new genera, were isolated. The strain P2, corresponding to the most frequently detected clone (M05) in the 16S rRNA gene library, showed both CMCase and xylanase activity and may be another important cellulolytic bacterium. The findings of cellulase activity in cell pellet and cohesion and dockerin domains in metagenome data further suggested the potential of utilization of cellulosomes by the consortium to degrade cellulose. Consortium SQD-1.1 provides a candidate for investigating the mechanism of cellulose degradation under anoxic conditions in natural environments.}, } @article {pmid23527207, year = {2013}, author = {Ding, GC and Piceno, YM and Heuer, H and Weinert, N and Dohrmann, AB and Carrillo, A and Andersen, GL and Castellanos, T and Tebbe, CC and Smalla, K}, title = {Changes of soil bacterial diversity as a consequence of agricultural land use in a semi-arid ecosystem.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e59497}, pmid = {23527207}, issn = {1932-6203}, mesh = {*Agriculture ; Analysis of Variance ; Bacteria/*genetics ; *Biodiversity ; DNA Primers/genetics ; Denaturing Gradient Gel Electrophoresis ; Desert Climate ; Hydrogen-Ion Concentration ; Metagenome/*genetics ; Mexico ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; Soil/analysis ; *Soil Microbiology ; Species Specificity ; }, abstract = {Natural scrublands in semi-arid deserts are increasingly being converted into fields. This results in losses of characteristic flora and fauna, and may also affect microbial diversity. In the present study, the long-term effect (50 years) of such a transition on soil bacterial communities was explored at two sites typical of semi-arid deserts. Comparisons were made between soil samples from alfalfa fields and the adjacent scrublands by two complementary methods based on 16S rRNA gene fragments amplified from total community DNA. Denaturing gradient gel electrophoresis (DGGE) analyses revealed significant effects of the transition on community composition of Bacteria, Actinobacteria, Alpha- and Betaproteobacteria at both sites. PhyloChip hybridization analysis uncovered that the transition negatively affected taxa such as Acidobacteria, Chloroflexi, Acidimicrobiales, Rubrobacterales, Deltaproteobacteria and Clostridia, while Alpha-, Beta- and Gammaproteobacteria, Bacteroidetes and Actinobacteria increased in abundance. Redundancy analysis suggested that the community composition of phyla responding to agricultural use (except for Spirochaetes) correlated with soil parameters that were significantly different between the agricultural and scrubland soil. The arable soils were lower in organic matter and phosphate concentration, and higher in salinity. The variation in the bacterial community composition was higher in soils from scrubland than from agriculture, as revealed by DGGE and PhyloChip analyses, suggesting reduced beta diversity due to agricultural practices. The long-term use for agriculture resulted in profound changes in the bacterial community and physicochemical characteristics of former scrublands, which may irreversibly affect the natural soil ecosystem.}, } @article {pmid23526971, year = {2013}, author = {Miranda, LN and Hutchison, K and Grossman, AR and Brawley, SH}, title = {Diversity and abundance of the bacterial community of the red Macroalga Porphyra umbilicalis: did bacterial farmers produce macroalgae?.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e58269}, pmid = {23526971}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics/metabolism ; Biodiversity ; Biological Evolution ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Metagenome ; Porphyra/metabolism/*microbiology ; Symbiosis ; }, abstract = {Macroalgae harbor microbial communities whose bacterial biodiversity remains largely uncharacterized. The goals of this study were 1) to examine the composition of the bacterial community associated with Porphyra umbilicalis Kützing from Schoodic Point, ME, 2) determine whether there are seasonal trends in species diversity but a core group of bacteria that are always present, and 3) to determine how the microbial community associated with a laboratory strain (P.um.1) established in the presence of antibiotics has changed. P. umbilicalis blades (n = 5, fall 2010; n = 5, winter 2011; n = 2, clonal P.um.1) were analyzed by pyrosequencing over two variable regions of the 16 S rDNA (V5-V6 and V8; 147,880 total reads). The bacterial taxa present were classified at an 80% confidence threshold into eight phyla (Bacteroidetes, Proteobacteria, Planctomycetes, Chloroflexi, Actinobacteria, Deinococcus-Thermus, Firmicutes, and the candidate division TM7). The Bacteroidetes comprised the majority of bacterial sequences on both field and lab blades, but the Proteobacteria (Alphaproteobacteria, Gammaproteobacteria) were also abundant. Sphingobacteria (Bacteroidetes) and Flavobacteria (Bacteroidetes) had inverse abundances on natural versus P.um.1 blades. Bacterial communities were richer and more diverse on blades sampled in fall compared to winter. Significant differences were observed between microbial communities among all three groups of blades examined. Only two OTUs were found on all 12 blades, and only one of these, belonging to the Saprospiraceae (Bacteroidetes), was abundant. Lewinella (as 66 OTUs) was found on all field blades and was the most abundant genus. Bacteria from the Bacteroidetes, Proteobacteria and Planctomycetes that are known to digest the galactan sulfates of red algal cell walls were well-represented. Some of these taxa likely provide essential morphogenetic and beneficial nutritive factors to P. umbilicalis and may have had unexpected effects upon evolution of macroalgal form as well as function.}, } @article {pmid23505458, year = {2013}, author = {Valverde, JR and Mellado, RP}, title = {Analysis of metagenomic data containing high biodiversity levels.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e58118}, pmid = {23505458}, issn = {1932-6203}, mesh = {*Biodiversity ; Computational Biology ; Databases, Nucleic Acid ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In this paper we have addressed the problem of analysing Next Generation Sequencing samples with an expected large biodiversity content. We analysed several well-known 16S rRNA datasets from experimental samples, including both large and short sequences, in numbers of tens of thousands, in addition to carefully crafted synthetic datasets containing more than 7000 OTUs. From this data analysis several patterns were identified and used to develop new guidelines for experimentation in conditions of high biodiversity. We analysed the suitability of different clustering packages for these type of situations, the problem of even sampling, the relative effectiveness of Chao1 and ACE estimators as well as their effect on sampling size for a variety of population distributions. As regards practical analysis procedures, we advocated an approach that retains as much high-quality experimental data as possible. By carefully applying selection rules combining the taxonomic assignment with clustering strategies, we derived a set of recommendations for ultra-sequencing data analysis at high biodiversity levels.}, } @article {pmid23487761, year = {2013}, author = {Gibbons, SM and Caporaso, JG and Pirrung, M and Field, D and Knight, R and Gilbert, JA}, title = {Evidence for a persistent microbial seed bank throughout the global ocean.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {12}, pages = {4651-4655}, pmid = {23487761}, issn = {1091-6490}, support = {T32 EB009412/EB/NIBIB NIH HHS/United States ; 5T-32EB-009412/EB/NIBIB NIH HHS/United States ; }, mesh = {*Bacteria ; *Biodiversity ; *Metagenome ; *Oceans and Seas ; *Phylogeny ; *Water Microbiology ; }, abstract = {Do bacterial taxa demonstrate clear endemism, like macroorganisms, or can one site's bacterial community recapture the total phylogenetic diversity of the world's oceans? Here we compare a deep bacterial community characterization from one site in the English Channel (L4-DeepSeq) with 356 datasets from the International Census of Marine Microbes (ICoMM) taken from around the globe (ranging from marine pelagic and sediment samples to sponge-associated environments). At the L4-DeepSeq site, increasing sequencing depth uncovers greater phylogenetic overlap with the global ICoMM data. This site contained 31.7-66.2% of operational taxonomic units identified in a given ICoMM biome. Extrapolation of this overlap suggests that 1.93 × 10(11) sequences from the L4 site would capture all ICoMM bacterial phylogenetic diversity. Current technology trends suggest this limit may be attainable within 3 y. These results strongly suggest the marine biosphere maintains a previously undetected, persistent microbial seed bank.}, } @article {pmid23481336, year = {2013}, author = {Song, S and Jarvie, T and Hattori, M}, title = {Our second genome-human metagenome: how next-generation sequencer changes our life through microbiology.}, journal = {Advances in microbial physiology}, volume = {62}, number = {}, pages = {119-144}, doi = {10.1016/B978-0-12-410515-7.00003-2}, pmid = {23481336}, issn = {2162-5468}, mesh = {Biota ; Communicable Diseases ; Health ; High-Throughput Nucleotide Sequencing/methods ; Host-Pathogen Interactions ; *Metagenome ; *Metagenomics/methods ; Humans ; }, abstract = {Next-generation sequencing has greatly expanded our ability to query the identity and genetic composition of entire communities of microbial organisms. This area of research, known as metagenomics, does not rely upon culturing the individual organisms. Rather, the genetic material from the entire community is processed and sequenced simultaneously. From this sequence data, researchers are able to determine the relative population of organisms within the community as well as determine which genes and metabolic pathways are present and expressed in the microbial community. While these techniques have been applied to a wide range of environmental samples, metagenomics is also the focus of intensive research on human-associated microbial communities. The scope of these human metagenomics studies are quite varied, but all have a common goal of attempting to understand the important role that human commensal microbial communities play in health and disease. The early results from studying the human metagenome indicate a vital role that microbial communities play in immunity, health, and disease. Going forward, human metagenomics is a wide open field of research with many unanswered questions such as which factors are responsible for the variation of composition of an individual's microbiome, how does the microbiome respond to disturbance, and what beneficial functions are the microorganisms performing?}, } @article {pmid23479168, year = {2013}, author = {Santos, CD and Dias, AC and Amaral, IM and Bonetti, AM and Campos, TA}, title = {New efficient DNA extraction method to access the microbiome of Ricinus communis seeds.}, journal = {Genetics and molecular research : GMR}, volume = {12}, number = {3}, pages = {3128-3135}, doi = {10.4238/2013.February.28.23}, pmid = {23479168}, issn = {1676-5680}, mesh = {Bacteria/classification/*genetics ; Castor Oil ; DNA, Bacterial/classification/genetics ; Genetic Variation ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; Ricinus/genetics/*microbiology ; Seeds/genetics/microbiology ; }, abstract = {Ricinus communis (castor bean) seeds are used to produce an alcohol-soluble oil that is used in more than 400 industrial processes. Despite its economic importance, there has been little research on the endophytic microbiota of castor bean seeds. This microbiota is important for plant metabolic processes and may have considerable biotechnological potential, such as production of lipases and plant growth promoter agents. We evaluated several DNA extraction methodologies in order to access the microbial diversity of castor bean through a metagenomic approach. Based on our observations, we developed a new methodology that takes advantage of the low solubility of calcium phosphates and the high affinity of these phosphates for proteins and polysaccharides. The extracted DNA quality was evaluated by PCR, using a selective primer pair for bacterial and mitochondrial 16S rDNA genes (799F and 1492R). We found this methodology quantitatively and qualitatively more efficient than the other approaches. In evaluating this new extraction methodology, we found that the difficulties of DNA extraction from castor bean seeds, such as abundant oil, polysaccharides, phenolic compounds, and plant enzymes, could be overcome. The resulting extracts had high concentration and purity, and they were obtained faster than with previous methods. The samples contained virtually all of the DNA, including the microbial DNA; this was validated by PCR analysis.}, } @article {pmid23478804, year = {2013}, author = {Wacklin, P and Kaukinen, K and Tuovinen, E and Collin, P and Lindfors, K and Partanen, J and Mäki, M and Mättö, J}, title = {The duodenal microbiota composition of adult celiac disease patients is associated with the clinical manifestation of the disease.}, journal = {Inflammatory bowel diseases}, volume = {19}, number = {5}, pages = {934-941}, doi = {10.1097/MIB.0b013e31828029a9}, pmid = {23478804}, issn = {1536-4844}, mesh = {Adolescent ; Adult ; Aged ; Anemia/*etiology/pathology ; *Biodiversity ; Case-Control Studies ; Celiac Disease/complications/genetics/*microbiology ; Dermatitis Herpetiformis/*etiology/pathology ; Duodenum/*microbiology ; Female ; Gastrointestinal Diseases/*etiology/pathology ; Humans ; Male ; *Metagenome ; Middle Aged ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {BACKGROUND: Celiac disease is classically manifested in the gastrointestinal (GI) tract but extraintestinal symptoms, such as dermatitis herpetiformis (DH), are also common. Besides several well-known shared genetic risk factors and an environmental trigger, gliadin, factors determining the clinical outcome of the disease are not known. In this study, the role of duodenal microbiota in the celiac disease outcome was studied by analyzing mucosa-associated microbiota in celiac disease patients with a variety of intestinal and extraintestinal symptoms.

METHODS: Microbiota in duodenal biopsy samples obtained from 33 patients with celiac disease with GI, DH, anemia, or mixed symptoms, as well as screen-detected asymptomatic celiac disease and 18 control subjects were analyzed using PCR denaturing gradient gel electrophoresis and a subset of samples additionally by the 16S ribosomal RNA gene sequencing.

RESULTS: The composition and diversity of mucosal microbiota was associated with the manifestation of celiac disease when analyzed using PCR denaturing gradient gel electrophoresis and the 16S ribosomal RNA gene sequencing. The patients with celiac disease with GI symptoms or anemia had lower microbial diversity than those with DH. Moreover, the patients with GI symptoms had different intestinal microbiota composition and structure, dominated by Proteobacteria, in comparison to those with DH or control subjects (patients with dyspepsia). The relatively similar intestinal microbiota composition in the control subjects and those with DH was characterized by the high abundance of Firmicutes.

CONCLUSIONS: The two common outcomes of celiac disease, classical GI and extraintestinal manifestations, had marked differences on the diversity and composition of intestinal microbiota. This association suggested that intestinal microbiota may have a role in the manifestation of the disease.}, } @article {pmid23475615, year = {2013}, author = {Ercolini, D}, title = {High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {10}, pages = {3148-3155}, pmid = {23475615}, issn = {1098-5336}, mesh = {Bacteria/genetics/growth & development ; Biota ; Ecosystem ; Fermentation ; Food Contamination/*analysis ; *Food Microbiology ; *Genes, Bacterial ; *High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Microbiota ; RNA, Bacterial/analysis ; Sequence Analysis, RNA ; }, abstract = {Following recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described.}, } @article {pmid23470515, year = {2013}, author = {Eme, L and Reigstad, LJ and Spang, A and Lanzén, A and Weinmaier, T and Rattei, T and Schleper, C and Brochier-Armanet, C}, title = {Metagenomics of Kamchatkan hot spring filaments reveal two new major (hyper)thermophilic lineages related to Thaumarchaeota.}, journal = {Research in microbiology}, volume = {164}, number = {5}, pages = {425-438}, doi = {10.1016/j.resmic.2013.02.006}, pmid = {23470515}, issn = {1769-7123}, support = {P 23000/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Archaea/*classification/genetics/*isolation & purification ; *Biota ; Cluster Analysis ; Hot Springs/*microbiology ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Russia ; Sequence Analysis, DNA ; }, abstract = {Based on phylogenetic analyses and gene distribution patterns of a few complete genomes, a new distinct phylum within the Archaea, the Thaumarchaeota, has recently been proposed. Here we present analyses of six archaeal fosmid sequences derived from a microbial hot spring community in Kamchatka. The phylogenetic analysis of informational components (ribosomal RNAs and proteins) reveals two major (hyper-)thermophilic clades ("Hot Thaumarchaeota-related Clade" 1 and 2, HTC1 and HTC2) related to Thaumarchaeota, representing either deep branches of this phylum or a new archaeal phylum and provides information regarding the ancient evolution of Archaea and their evolutionary links with Eukaryotes.}, } @article {pmid23469240, year = {2013}, author = {Benítez-Páez, A and Álvarez, M and Belda-Ferre, P and Rubido, S and Mira, A and Tomás, I}, title = {Detection of transient bacteraemia following dental extractions by 16S rDNA pyrosequencing: a pilot study.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e57782}, pmid = {23469240}, issn = {1932-6203}, mesh = {Adult ; Bacteremia/diagnosis/*microbiology ; Biodiversity ; Colony Count, Microbial ; DNA, Ribosomal ; Female ; Gingiva/*microbiology ; Humans ; Male ; Metagenome ; Pilot Projects ; Sequence Analysis, DNA ; Streptococcal Infections/diagnosis/*microbiology ; *Tooth Extraction ; Viridans Streptococci/*genetics/isolation & purification ; }, abstract = {OBJECTIVE: The current manuscript aims to determine the prevalence, duration and bacterial diversity of bacteraemia following dental extractions using conventional culture-dependent methods and 16S rDNA pyrosequencing.

METHODS: The study group included 8 patients undergoing dental extractions under general anaesthesia. Peripheral venous blood samples were collected at baseline, 30 seconds and 15 minutes after the dental extractions. Blood samples were analysed for bacteraemia applying conventional microbiological cultures under aerobic and anaerobic conditions as well as pyrosequencing using universal bacterial primers that target the 16S ribosomal DNA gene.

RESULTS: Transient bacteremia was detected by culture-based methods in one sample at baseline time, in eight samples at 30 seconds, and in six samples at 15 minutes after surgical procedure; whereas bacteraemia was detected only in five blood samples at 30 seconds after dental extraction by using pyrosequencing. By applying conventional microbiological methods, a single microbial species was detected in six patients, and Streptococcus viridans was the most frequently cultured identified bacterium. By using pyrosequencing approaches however, the estimated blood microbial diversity after dental extractions was 13.4±1.7 bacterial families and 22.8±1.1 genera per sample.

CONCLUSION: The application of 16S rDNA pyrosequencing underestimated the prevalence and duration of bacteraemia following dental extractions, presumably due to not reaching the minimum DNA required for PCR amplification. However, this molecular technique, unlike conventional culture-dependent methods, revealed an extraordinarily high bacterial diversity of post-extraction bacteraemia. We propose that microorganisms recovered by culture may be only the tip of an iceberg of a really diverse microbiota whose viability and potential pathogenicity should be further studied.}, } @article {pmid23461380, year = {2013}, author = {Di Maiuta, N and Schwarzentruber, P and Schenker, M and Schoelkopf, J}, title = {Microbial population dynamics in the faeces of wood-eating loricariid catfishes.}, journal = {Letters in applied microbiology}, volume = {56}, number = {6}, pages = {401-407}, doi = {10.1111/lam.12061}, pmid = {23461380}, issn = {1472-765X}, mesh = {Animals ; Bacteria/*classification/*genetics/growth & development/metabolism ; Biodiversity ; Catfishes/*microbiology/physiology ; Cellulose/metabolism ; Diet ; Eating ; Feces/*microbiology ; Gastrointestinal Tract/*microbiology ; *Metagenome ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Wood ; }, abstract = {UNLABELLED: Catfishes of the genus Panaque are known for their ability to feed on wood and hence to process cellulose fibres in their digestive systems. The paper industry uses cellulose fibres and thus has an interest in exploiting this property biomimetically: it could be employed as a pretreatment to lessen the energy required by the mechanical production stage of manufacturing nanocellulose fibres. Here, we characterize the diet-associated in situ microbial diversity and population dynamic in the faeces of catfish (Panaque sp.) exposed to consecutive diets of pellet food and then wood. Fish faeces samples were collected and investigated by parallel DNA deep amplicon sequencing of the bacterial 16S rRNA SSU for both diet conditions. The most frequently occurring bacterium in the faeces was Cetobacterium sp. The dominant cellulolytic bacterial genera found in ascending relative abundance were as follows: Aeromonas sp., Flavobacterium sp., Bacteroides sp., Pseudomonas sp. and Cellvibrio sp. Diet-associated changes in the faeces microbiome were noted for Flavobacterium sp. Extensive microbial diversity was found in catfish faeces, evidenced using culture-independent molecular techniques. No significant diet-associated effects on the microbiome in terms of biodiversity were observed in the catfish faeces, but diet-associated changes in the microbial population structure were observed.

Although catfishes are not classified as true xylivores, inhabiting their faeces are bacteria that may provide a novel source of cellulolytic enzyme. Based on this first microbiology study, the faeces and thus the gastrointestinal microbiome of Panaque catfishes are an unexplored reservoir of microbial extracts with enhanced polysaccharide transforming enzyme activity. The biomimetical exploitation of this cellulolytic activity in the form of novel enzymes or by applying a mixture of cellulolytic micro-organisms could accomplish a pretreatment to the mechanical production process of nanocellulose fibres, thus could reduce the energy consumption costs significantly.}, } @article {pmid23454028, year = {2013}, author = {Raman, M and Ahmed, I and Gillevet, PM and Probert, CS and Ratcliffe, NM and Smith, S and Greenwood, R and Sikaroodi, M and Lam, V and Crotty, P and Bailey, J and Myers, RP and Rioux, KP}, title = {Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease.}, journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association}, volume = {11}, number = {7}, pages = {868-75.e1-3}, doi = {10.1016/j.cgh.2013.02.015}, pmid = {23454028}, issn = {1542-7714}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Adult ; Biota ; Case-Control Studies ; Fatty Liver/complications/*pathology ; Feces/*chemistry/*microbiology ; Female ; Gas Chromatography-Mass Spectrometry ; Humans ; Male ; *Metabolome ; *Microbiota ; Middle Aged ; Non-alcoholic Fatty Liver Disease ; Obesity/complications/*pathology ; Sequence Analysis, DNA ; Volatile Organic Compounds/*analysis ; }, abstract = {BACKGROUND & AIMS: The histopathology of nonalcoholic fatty liver disease (NAFLD) is similar to that of alcoholic liver disease. Colonic bacteria are a source of many metabolic products, including ethanol and other volatile organic compounds (VOC) that may have toxic effects on the human host after intestinal absorption and delivery to the liver via the portal vein. Recent data suggest that the composition of the gut microbiota in obese human beings is different from that of healthy-weight individuals. The aim of this study was to compare the colonic microbiome and VOC metabolome of obese NAFLD patients (n = 30) with healthy controls (n = 30).

METHODS: Multitag pyrosequencing was used to characterize the fecal microbiota. Fecal VOC profiles were measured by gas chromatography-mass spectrometry.

RESULTS: There were statistically significant differences in liver biochemistry and metabolic parameters in NAFLD. Deep sequencing of the fecal microbiome revealed over-representation of Lactobacillus species and selected members of phylum Firmicutes (Lachnospiraceae; genera, Dorea, Robinsoniella, and Roseburia) in NAFLD patients, which was statistically significant. One member of phylum Firmicutes was under-represented significantly in the fecal microbiome of NAFLD patients (Ruminococcaceae; genus, Oscillibacter). Fecal VOC profiles of the 2 patient groups were different, with a significant increase in fecal ester compounds observed in NAFLD patients.

CONCLUSIONS: A significant increase in fecal ester VOC is associated with compositional shifts in the microbiome of obese NAFLD patients. These novel bacterial metabolomic and metagenomic factors are implicated in the etiology and complications of obesity.}, } @article {pmid23451294, year = {2012}, author = {Robbins, RJ and Amaral-Zettler, L and Bik, H and Blum, S and Edwards, J and Field, D and Garrity, G and Gilbert, JA and Kottmann, R and Krishtalka, L and Lapp, H and Lawrence, C and Morrison, N and Tuama, EÓ and Parr, C and San Gil, I and Schindel, D and Schriml, L and Vieglas, D and Wooley, J}, title = {RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011.}, journal = {Standards in genomic sciences}, volume = {7}, number = {1}, pages = {159-165}, pmid = {23451294}, issn = {1944-3277}, abstract = {Building on the planning efforts of the RCN4GSC project, a workshop was convened in San Diego to bring together experts from genomics and metagenomics, biodiversity, ecology, and bioinformatics with the charge to identify potential for positive interactions and progress, especially building on successes at establishing data standards by the GSC and by the biodiversity and ecological communities. Until recently, the contribution of microbial life to the biomass and biodiversity of the biosphere was largely overlooked (because it was resistant to systematic study). Now, emerging genomic and metagenomic tools are making investigation possible. Initial research findings suggest that major advances are in the offing. Although different research communities share some overlapping concepts and traditions, they differ significantly in sampling approaches, vocabularies and workflows. Likewise, their definitions of 'fitness for use' for data differ significantly, as this concept stems from the specific research questions of most importance in the different fields. Nevertheless, there is little doubt that there is much to be gained from greater coordination and integration. As a first step toward interoperability of the information systems used by the different communities, participants agreed to conduct a case study on two of the leading data standards from the two formerly disparate fields: (a) GSC's standard checklists for genomics and metagenomics and (b) TDWG's Darwin Core standard, used primarily in taxonomy and systematic biology.}, } @article {pmid23451293, year = {2012}, author = {Robbins, RJ and Cochrane, G and Davies, N and Dawyndt, P and Kottmann, R and Krishtalka, LK and Morrison, N and Tuama, EÓ and San Gil, I and Wooley, J}, title = {RCN4GSC Workshop Report: Modeling a Testbed for Managing Data at the Interface of Biodiversity and (Meta)Genomics, April 2011.}, journal = {Standards in genomic sciences}, volume = {7}, number = {1}, pages = {153-158}, pmid = {23451293}, issn = {1944-3277}, abstract = {At the GSC11 meeting (4-6 April 2011, Hinxton, England, the GSC's genomic biodiversity working group (GBWG) developed an initial model for a data management testbed at the interface of biodiversity with genomics and metagenomics. With representatives of the Global Biodiversity Information Facility (GBIF) participating, it was agreed that the most useful course of action would be for GBIF to collaborate with the GSC in its ongoing GBWG workshops to achieve common goals around interoperability/data integration across (meta)-genomic and species level data. It was determined that a quick comparison should be made of the contents of the Darwin Core (DwC) and the GSC data checklists, with a goal of determining their degree of overlap and compatibility. An ad-hoc task group lead by Renzo Kottman and Peter Dawyndt undertook an initial comparison between the Darwin Core (DwC) standard used by the Global Biodiversity Information Facility (GBIF) and the MIxS checklists put forward by the Genomic Standards Consortium (GSC). A term-by-term comparison showed that DwC and GSC concepts complement each other far more than they compete with each other. Because the preliminary analysis done at this meeting was based on expertise with GSC standards, but not with DwC standards, the group recommended that a joint meeting of DwC and GSC experts be convened as soon as possible to continue this joint assessment and to propose additional work going forward.}, } @article {pmid23443006, year = {2013}, author = {Shade, A and McManus, PS and Handelsman, J}, title = {Unexpected diversity during community succession in the apple flower microbiome.}, journal = {mBio}, volume = {4}, number = {2}, pages = {}, pmid = {23443006}, issn = {2150-7511}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Flowers/*microbiology ; Malus/*microbiology ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {UNLABELLED: Despite its importance to the host, the flower microbiome is poorly understood. We report a culture-independent, community-level assessment of apple flower microbial diversity and dynamics. We collected flowers from six apple trees at five time points, starting before flowers opened and ending at petal fall. We applied streptomycin to half of the trees when flowers opened. Assessment of microbial diversity using tag pyrosequencing of 16S rRNA genes revealed that the apple flower communities were rich and diverse and dominated by members of TM7 and Deinococcus-Thermus, phyla about which relatively little is known. From thousands of taxa, we identified six successional groups with coherent dynamics whose abundances peaked at different times before and after bud opening. We designated the groups Pioneer, Early, Mid, Late, Climax, and Generalist communities. The successional pattern was attributed to a set of prevalent taxa that were persistent and gradually changing in abundance. These taxa had significant associations with other community members, as demonstrated with a cooccurrence network based on local similarity analysis. We also detected a set of less-abundant, transient taxa that contributed to general tree-to-tree variability but not to the successional pattern. Communities on trees sprayed with streptomycin had slightly lower phylogenetic diversity than those on unsprayed trees but did not differ in structure or succession. Our results suggest that changes in apple flower microbial community structure are predictable over the life of the flower, providing a basis for ecological understanding and disease management.

IMPORTANCE: Flowering plants (angiosperms) represent a diverse group of an estimated 400,000 species, and their successful cultivation is essential to agriculture. Yet fundamental knowledge of flower-associated microbiotas remains largely unknown. Even less well understood are the changes that flower microbial communities experience through time. Flowers are particularly conducive to comprehensive temporal studies because they are, by nature, ephemeral organs. Here, we present the first culture-independent time series of bacterial and archaeal communities associated with the flowers of apple, an economically important crop. We found unexpected diversity on apple flowers, including a preponderance of taxa affiliated with Deinococcus-Thermus and TM7, phyla that are understudied but thought to be tolerant to an array of environmental stresses. Our results also suggest that changes in microbial community structure on the apple flower may be predictable over the life of the flower, providing the basis for ecological understanding and disease management.}, } @article {pmid23441921, year = {2013}, author = {Tourlousse, DM and Kurisu, F and Tobino, T and Furumai, H}, title = {Sensitive and substrate-specific detection of metabolically active microorganisms in natural microbial consortia using community isotope arrays.}, journal = {FEMS microbiology letters}, volume = {342}, number = {1}, pages = {70-75}, doi = {10.1111/1574-6968.12112}, pmid = {23441921}, issn = {1574-6968}, mesh = {DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gammaproteobacteria/*classification/*genetics ; Isotopes/*metabolism ; Metagenomics/*methods ; *Microbial Consortia ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phenol/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/microbiology ; Staining and Labeling/methods ; Wastewater/microbiology ; }, abstract = {The goal of this study was to develop and validate a novel fosmid-clone-based metagenome isotope array approach - termed the community isotope array (CIArray) - for sensitive detection and identification of microorganisms assimilating a radiolabeled substrate within complex microbial communities. More specifically, a sample-specific CIArray was used to identify anoxic phenol-degrading microorganisms in activated sludge treating synthetic coke-oven wastewater in a single-sludge predenitrification-nitrification process. Hybridization of the CIArray with DNA from the (14) C-phenol-amended sample indicated that bacteria assimilating (14) C-atoms, presumably directly from phenol, under nitrate-reducing conditions were abundant in the reactor, and taxonomic assignment of the fosmid clone end sequences suggested that they belonged to the Gammaproteobacteria. The specificity of the CIArray was validated by quantification of fosmid-clone-specific DNA in density-resolved DNA fractions from samples incubated with (13) C-phenol, which verified that all CIArray-positive probes stemmed from microorganisms that assimilated isotopically labeled carbon. This also demonstrated that the CIArray was more sensitive than DNA-SIP, as the former enabled positive detection at a phenol concentration that failed to yield a 'heavy' DNA fraction. Finally, two operational taxonomic units distantly related to marine Gammaproteobacteria were identified to account for more than half of 16S rRNA gene clones in the 'heavy' DNA library, corroborating the CIArray-based identification.}, } @article {pmid23439321, year = {2013}, author = {Mick, E and Stern, A and Sorek, R}, title = {Holding a grudge: persisting anti-phage CRISPR immunity in multiple human gut microbiomes.}, journal = {RNA biology}, volume = {10}, number = {5}, pages = {900-906}, pmid = {23439321}, issn = {1555-8584}, mesh = {Adult ; Archaea/genetics ; Bacteria/*genetics/*virology ; Bacteriophages/*genetics/physiology ; CRISPR-Associated Proteins/genetics/*metabolism ; *Clustered Regularly Interspaced Short Palindromic Repeats ; DNA, Intergenic ; Female ; Gastrointestinal Tract/*microbiology ; Gene Targeting ; Humans ; Lysogeny ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; }, abstract = {The CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) system of bacteria and archaea constitutes a mechanism of acquired adaptive immunity against phages, which is based on genome-encoded markers of previously infecting phage sequences ("spacers"). As a repository of phage sequences, these spacers make the system particularly suitable for elucidating phage-bacteria interactions in metagenomic studies. Recent metagenomic analyses of CRISPRs associated with the human microbiome intriguingly revealed conserved "memory spacers" shared by bacteria in multiple unrelated, geographically separated individuals. Here, we discuss possible avenues for explaining this phenomenon by integrating insights from CRISPR biology and phage-bacteria ecology, with a special focus on the human gut. We further explore the growing body of evidence for the role of CRISPR/Cas in regulating the interplay between bacteria and lysogenic phages, which may be intimately related to the presence of memory spacers and sheds new light on the multifaceted biological and ecological modes of action of CRISPR/Cas.}, } @article {pmid23437177, year = {2013}, author = {Takahara, T and Minamoto, T and Doi, H}, title = {Using environmental DNA to estimate the distribution of an invasive fish species in ponds.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e56584}, pmid = {23437177}, issn = {1932-6203}, mesh = {Animals ; DNA/genetics/*isolation & purification ; Ecosystem ; *Introduced Species ; *Metagenomics ; Perciformes/classification/*genetics ; Ponds ; Species Specificity ; Water ; }, abstract = {Knowledge of the presence of an invasive species is critical to monitoring the sustainability of communities and ecosystems. Environmental DNA (eDNA), DNA fragments that are likely to be bound to organic matters in the water or in shed cells, has been used to monitor the presence of aquatic animals. Using an eDNA-based method, we estimated the presence of the invasive bluegill sunfish, Lepomis macrochirus, in 70 ponds located in seven locales on the Japanese mainland and on surrounding islands. We quantified the concentration of DNA copies in a 1 L water sample using quantitative real-time polymerase chain reaction (qPCR) with a primer/probe set. In addition, we visually observed the bluegill presence in the ponds from the shoreline. We detected bluegill eDNA in all the ponds where bluegills were observed visually and some where bluegills were not observed. Bluegills were also less prevalent on the islands than the mainland, likely owing to limited dispersal and introduction by humans. Our eDNA method simply and rapidly detects the presence of this invasive fish species with less disturbance to the environment during field surveys than traditional methods.}, } @article {pmid23437130, year = {2013}, author = {Jensen, A and Fagö-Olsen, H and Sørensen, CH and Kilian, M}, title = {Molecular mapping to species level of the tonsillar crypt microbiota associated with health and recurrent tonsillitis.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e56418}, pmid = {23437130}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Base Sequence ; Biodiversity ; Child, Preschool ; Female ; Genetic Variation ; *Health ; Humans ; Male ; Metagenome/*genetics ; Palatine Tonsil/*microbiology/*pathology ; Principal Component Analysis ; Recurrence ; Species Specificity ; Tonsillitis/*microbiology/*pathology ; Young Adult ; }, abstract = {The human palatine tonsils, which belong to the central antigen handling sites of the mucosal immune system, are frequently affected by acute and recurrent infections. This study compared the microbiota of the tonsillar crypts in children and adults affected by recurrent tonsillitis with that of healthy adults and children with tonsillar hyperplasia. An in-depth 16S rRNA gene based pyrosequencing approach combined with a novel strategy that included phylogenetic analysis and detection of species-specific sequence signatures enabled identification of the major part of the microbiota to species level. A complex microbiota consisting of between 42 and 110 taxa was demonstrated in both children and adults. This included a core microbiome of 12 abundant genera found in all samples regardless of age and health status. Yet, Haemophilus influenzae, Neisseria species, and Streptococcus pneumoniae were almost exclusively detected in children. In contrast, Streptococcus pseudopneumoniae was present in all samples. Obligate anaerobes like Porphyromonas, Prevotella, and Fusobacterium were abundantly present in children, but the species diversity of Porphyromonas and Prevotella was larger in adults and included species that are considered putative pathogens in periodontal diseases, i.e. Porphyromonas gingivalis, Porphyromonas endodontalis, and Tannerella forsythia. Unifrac analysis showed that recurrent tonsillitis is associated with a shift in the microbiota of the tonsillar crypts. Fusobacterium necrophorum, Streptococcus intermedius and Prevotella melaninogenica/histicola were associated with recurrent tonsillitis in adults, whereas species traditionally associated with acute tonsillitis like pyogenic streptococci and Staphylococcus aureus were scarce. The findings suggest that recurrent tonsillitis is a polymicrobial infection in which interactions within consortia of taxa play an etiologic role. The study contributes to the human microbiome data, to the understanding of the etiology of infections affecting the tonsils, and forms a basis for further insight into the consequences of the intense microbe-host interactions that take place in the tonsils.}, } @article {pmid23435754, year = {2013}, author = {Huggett, JF and Studholme, DJ and Laver, T and Foy, CA}, title = {Progress in metagenomics requires a balanced appraisal of the available technologies.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {32}, number = {8}, pages = {1097-1098}, pmid = {23435754}, issn = {1435-4373}, mesh = {Bacterial Infections/microbiology ; Bacteriological Techniques/*methods ; Humans ; Metagenomics/*methods ; Microbiota ; Molecular Typing ; Polymerase Chain Reaction ; }, } @article {pmid23433344, year = {2013}, author = {Murri, M and Leiva, I and Gomez-Zumaquero, JM and Tinahones, FJ and Cardona, F and Soriguer, F and Queipo-Ortuño, MI}, title = {Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study.}, journal = {BMC medicine}, volume = {11}, number = {}, pages = {46}, pmid = {23433344}, issn = {1741-7015}, mesh = {Bacteria/*classification/*genetics ; *Biota ; Case-Control Studies ; Child ; Denaturing Gradient Gel Electrophoresis ; *Diabetes Mellitus, Type 1 ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; Metagenome ; Real-Time Polymerase Chain Reaction ; }, abstract = {BACKGROUND: A recent study using a rat model found significant differences at the time of diabetes onset in the bacterial communities responsible for type 1 diabetes modulation. We hypothesized that type 1 diabetes in humans could also be linked to a specific gut microbiota. Our aim was to quantify and evaluate the difference in the composition of gut microbiota between children with type 1 diabetes and healthy children and to determine the possible relationship of the gut microbiota of children with type 1 diabetes with the glycemic level.

METHODS: A case-control study was carried out with 16 children with type 1 diabetes and 16 healthy children. The fecal bacteria composition was investigated by polymerase chain reaction-denaturing gradient gel electrophoresis and real-time quantitative polymerase chain reaction.

RESULTS: The mean similarity index was 47.39% for the healthy children and 37.56% for the children with diabetes, whereas the intergroup similarity index was 26.69%. In the children with diabetes, the bacterial number of Actinobacteria and Firmicutes, and the Firmicutes to Bacteroidetes ratio were all significantly decreased, with the quantity of Bacteroidetes significantly increased with respect to healthy children. At the genus level, we found a significant increase in the number of Clostridium, Bacteroides and Veillonella and a significant decrease in the number of Lactobacillus, Bifidobacterium, Blautia coccoides/Eubacterium rectale group and Prevotella in the children with diabetes. We also found that the number of Bifidobacterium and Lactobacillus, and the Firmicutes to Bacteroidetes ratio correlated negatively and significantly with the plasma glucose level while the quantity of Clostridium correlated positively and significantly with the plasma glucose level in the diabetes group.

CONCLUSIONS: This is the first study showing that type 1 diabetes is associated with compositional changes in gut microbiota. The significant differences in the number of Bifidobacterium, Lactobacillus and Clostridium and in the Firmicutes to Bacteroidetes ratio observed between the two groups could be related to the glycemic level in the group with diabetes. Moreover, the quantity of bacteria essential to maintain gut integrity was significantly lower in the children with diabetes than the healthy children. These findings could be useful for developing strategies to control the development of type 1 diabetes by modifying the gut microbiota.}, } @article {pmid23431991, year = {2013}, author = {Bakhtiar, SM and LeBlanc, JG and Salvucci, E and Ali, A and Martin, R and Langella, P and Chatel, JM and Miyoshi, A and Bermúdez-Humarán, LG and Azevedo, V}, title = {Implications of the human microbiome in inflammatory bowel diseases.}, journal = {FEMS microbiology letters}, volume = {342}, number = {1}, pages = {10-17}, doi = {10.1111/1574-6968.12111}, pmid = {23431991}, issn = {1574-6968}, mesh = {*Biota ; High-Throughput Nucleotide Sequencing ; Humans ; Inflammatory Bowel Diseases/*microbiology ; *Metagenome ; }, abstract = {The study of the human microbiome or community of microorganisms and collection of genomes found in the human body is one of the fastest growing research areas because many diseases are reported to be associated with microbiome imbalance or dysbiosis. With the improvement in novel sequencing techniques, researchers are now generating millions of sequences of different sites from the human body and evaluating specific differences in microbial communities. The importance of microbiome constituency is so relevant that several consortia like the Human Microbiome project (HMP) and Metagenomics of the Human Intestinal Tract (MetaHIT) project are focusing mainly on the human microbiome. The aim of this review is to highlight points of research in this field, mainly focusing on particular factors that modulate the microbiome and important insights into its potential impact on our health and well-being.}, } @article {pmid23430196, year = {2013}, author = {Dubourg, G and Lagier, JC and Armougom, F and Robert, C and Hamad, I and Brouqui, P and Raoult, D}, title = {The proof of concept that culturomics can be superior to metagenomics to study atypical stool samples.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {32}, number = {8}, pages = {1099}, pmid = {23430196}, issn = {1435-4373}, mesh = {Bacteriological Techniques/*methods ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenome/*physiology ; Microbiota/*physiology ; Tuberculosis, Multidrug-Resistant/*drug therapy/*microbiology ; }, } @article {pmid23424136, year = {2013}, author = {Brown, DG and Truszkowski, J}, title = {LSHPlace: fast phylogenetic placement using locality-sensitive hashing.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {}, number = {}, pages = {310-319}, pmid = {23424136}, issn = {2335-6936}, mesh = {*Algorithms ; Computational Biology ; Databases, Nucleic Acid/statistics & numerical data ; Evolution, Molecular ; Humans ; Metagenomics/statistics & numerical data ; Microbiota/genetics ; *Phylogeny ; Sequence Alignment/statistics & numerical data ; Software ; }, abstract = {We consider the problem of phylogenetic placement, in which large numbers of sequences (often next-generation sequencing reads) are placed onto an existing phylogenetic tree. We adapt our recent work on phylogenetic tree inference, which uses ancestral sequence reconstruction and locality-sensitive hashing, to this domain. With these ideas, new sequences can be placed onto trees with high fidelity in strikingly fast runtimes. Our results are two orders of magnitude faster than existing programs for this domain, and show a modest accuracy tradeoff. Our results offer the possibility of analyzing many more reads in a next-generation sequencing project than is currently possible.}, } @article {pmid23420462, year = {2013}, author = {Chiellini, C and Munz, G and Petroni, G and Lubello, C and Mori, G and Verni, F and Vannini, C}, title = {Characterization and comparison of bacterial communities selected in conventional activated sludge and membrane bioreactor pilot plants: a focus on Nitrospira and Planctomycetes bacterial phyla.}, journal = {Current microbiology}, volume = {67}, number = {1}, pages = {77-90}, pmid = {23420462}, issn = {1432-0991}, mesh = {Bacteria/*classification/*genetics ; Bioreactors/*microbiology ; *Biota ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Membranes ; Metagenome ; Nitrogen Compounds/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; }, abstract = {A pilot-scale membrane bioreactor (MBR) and a conventional activated sludge system (CAS) were in parallel operated to investigate the impact of the separation technology on the structure and functionality of the selected microbial community. Microbial communities as well as nitrogen removal efficiency of the biomass were characterized. Kinetics and microbial community structure turned out to be duly correlated. The impact of the separation technology on selective conditions and, in particular, the higher variability of solid separation efficiency in CAS with respect to MBR pilot plant possibly represented the main factor influencing the selection of bacterial communities. Concerning nitrifiers, bacteria of the genus Nitrospira were predominant in the MBR. This was in accordance with kinetics of nitrite-oxidizing bacteria that suggested the presence of k-strategists, while r-strategists were selected in the CAS plant, possibly because of the presence of transient higher concentrations of nitrite (in the range of 0.05-0.18 and of 0.05-4.4 mg [Formula: see text]-N L(-1) in the MBR and CAS effluents, respectively). An unexpectedly high presence of bacteria belonging to two specific phylogenetic clades of Planctomycetes was found in both reactors.}, } @article {pmid23418476, year = {2013}, author = {Uroz, S and Ioannidis, P and Lengelle, J and Cébron, A and Morin, E and Buée, M and Martin, F}, title = {Functional assays and metagenomic analyses reveals differences between the microbial communities inhabiting the soil horizons of a Norway spruce plantation.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e55929}, pmid = {23418476}, issn = {1932-6203}, mesh = {Bacteria/*genetics ; Biodiversity ; *Metagenome ; Metagenomics ; Phylogeny ; Picea/*microbiology ; Soil/*analysis ; Soil Microbiology ; Trees/*microbiology ; }, abstract = {In temperate ecosystems, acidic forest soils are among the most nutrient-poor terrestrial environments. In this context, the long-term differentiation of the forest soils into horizons may impact the assembly and the functions of the soil microbial communities. To gain a more comprehensive understanding of the ecology and functional potentials of these microbial communities, a suite of analyses including comparative metagenomics was applied on independent soil samples from a spruce plantation (Breuil-Chenue, France). The objectives were to assess whether the decreasing nutrient bioavailability and pH variations that naturally occurs between the organic and mineral horizons affects the soil microbial functional biodiversity. The 14 Gbp of pyrosequencing and Illumina sequences generated in this study revealed complex microbial communities dominated by bacteria. Detailed analyses showed that the organic soil horizon was significantly enriched in sequences related to Bacteria, Chordata, Arthropoda and Ascomycota. On the contrary the mineral horizon was significantly enriched in sequences related to Archaea. Our analyses also highlighted that the microbial communities inhabiting the two soil horizons differed significantly in their functional potentials according to functional assays and MG-RAST analyses, suggesting a functional specialisation of these microbial communities. Consistent with this specialisation, our shotgun metagenomic approach revealed a significant increase in the relative abundance of sequences related glycoside hydrolases in the organic horizon compared to the mineral horizon that was significantly enriched in glycoside transferases. This functional stratification according to the soil horizon was also confirmed by a significant correlation between the functional assays performed in this study and the functional metagenomic analyses. Together, our results suggest that the soil stratification and particularly the soil resource availability impact the functional diversity and to a lesser extent the taxonomic diversity of the bacterial communities.}, } @article {pmid23409219, year = {2012}, author = {Robbins, RJ and Beach, J and Blum, S and Dawyndt, P and Deck, J and Kottmann, R and Morrison, N and Tuama, EÓ and San Gil, I and Vieglas, D and Wieczorek, J and Wooley, J}, title = {RCN4GSC Meeting Report: Initiating a Testbed for Managing Data at the Interface of Biodiversity and Genomics/Metagenomics, May 2011.}, journal = {Standards in genomic sciences}, volume = {7}, number = {1}, pages = {171-174}, pmid = {23409219}, issn = {1944-3277}, abstract = {Following up on efforts from two earlier workshops, a meeting was convened in San Diego to (a) establish working connections between experts in the use of the Darwin Core and the GSC MIxS standards, (b) conduct mutual briefings to promote knowledge exchange and to increase the understanding of the two communities' approaches, constraints, community goals, subtleties, etc., (c) perform an element-by-element comparison of the two standards, assessing the compatibility and complementarity of the two approaches, (d) propose and consider possible use cases and test beds in which a joint annotation approach might be tried, to useful scientific effect, and (e) propose additional action items necessary to continue the development of this joint effort. Several focused working teams were identified to continue the work after the meeting ended.}, } @article {pmid23407494, year = {2013}, author = {Zhao, Y and Temperton, B and Thrash, JC and Schwalbach, MS and Vergin, KL and Landry, ZC and Ellisman, M and Deerinck, T and Sullivan, MB and Giovannoni, SJ}, title = {Abundant SAR11 viruses in the ocean.}, journal = {Nature}, volume = {494}, number = {7437}, pages = {357-360}, pmid = {23407494}, issn = {1476-4687}, support = {P41 RR004050/RR/NCRR NIH HHS/United States ; }, mesh = {Aquatic Organisms/genetics/*isolation & purification ; Bacteria/classification/isolation & purification/virology ; Bacteriophages/*classification/genetics/*isolation & purification/physiology ; Bermuda ; Biota ; Competitive Behavior ; Food Chain ; Genome, Viral/genetics ; Metagenome/genetics ; Models, Biological ; Molecular Sequence Data ; Oregon ; Pacific Ocean ; Plankton/physiology ; Seawater/microbiology/*virology ; }, abstract = {Several reports proposed that the extraordinary dominance of the SAR11 bacterial clade in ocean ecosystems could be a consequence of unusual mechanisms of resistance to bacteriophage infection, including 'cryptic escape' through reduced cell size and/or K-strategist defence specialism. Alternatively, the evolution of high surface-to-volume ratios coupled with minimal genomes containing high-affinity transporters enables unusually efficient metabolism for oxidizing dissolved organic matter in the world's oceans that could support vast population sizes despite phage susceptibility. These ideas are important for understanding plankton ecology because they emphasize the potentially important role of top-down mechanisms in predation, thus determining the size of SAR11 populations and their concomitant role in biogeochemical cycling. Here we report the isolation of diverse SAR11 viruses belonging to two virus families in culture, for which we propose the name 'pelagiphage', after their host. Notably, the pelagiphage genomes were highly represented in marine viral metagenomes, demonstrating their importance in nature. One of the new phages, HTVC010P, represents a new podovirus subfamily more abundant than any seen previously, in all data sets tested, and may represent one of the most abundant virus subfamilies in the biosphere. This discovery disproves the theory that SAR11 cells are immune to viral predation and is consistent with the interpretation that the success of this highly abundant microbial clade is the result of successfully evolved adaptation to resource competition.}, } @article {pmid23407313, year = {2013}, author = {Haegeman, B and Hamelin, J and Moriarty, J and Neal, P and Dushoff, J and Weitz, JS}, title = {Robust estimation of microbial diversity in theory and in practice.}, journal = {The ISME journal}, volume = {7}, number = {6}, pages = {1092-1101}, pmid = {23407313}, issn = {1751-7370}, mesh = {Archaea/classification ; Bacteria/*classification ; *Biodiversity ; Computer Simulation ; Metagenomics ; Regression Analysis ; Seawater/*microbiology ; *Soil Microbiology ; }, abstract = {Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao's estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics ('Hill diversities'), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao's estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.}, } @article {pmid23403424, year = {2013}, author = {Newton, DF and Macfarlane, S and Macfarlane, GT}, title = {Effects of antibiotics on bacterial species composition and metabolic activities in chemostats containing defined populations of human gut microorganisms.}, journal = {Antimicrobial agents and chemotherapy}, volume = {57}, number = {5}, pages = {2016-2025}, pmid = {23403424}, issn = {1098-6596}, mesh = {Ampicillin/*pharmacology ; Anaerobiosis ; Anti-Infective Agents/*pharmacology ; Bacteroides/drug effects/metabolism ; Bifidobacterium/drug effects/metabolism ; Bioreactors ; Clostridium/drug effects/metabolism ; Fermentation ; Humans ; Intestine, Large/microbiology ; Metagenome/*drug effects/physiology ; Metronidazole/*pharmacology ; Microbial Consortia/*drug effects/physiology ; Models, Biological ; }, abstract = {The composition and metabolic activities of the human colonic microbiota are modulated by a number of external factors, including diet and antibiotic therapy. Changes in the structure and metabolism of the gut microbiota may have long-term consequences for host health. The large intestine harbors a complex microbial ecosystem comprising several hundreds of different bacterial species, which complicates investigations on intestinal physiology and ecology. To facilitate such studies, a highly simplified microbiota consisting of 14 anaerobic and facultatively anaerobic organisms (Bacteroides thetaiotaomicron, Bacteroides vulgatus, Bifidobacterium longum, Bifidobacterium infantis, Bifidobacterium pseudolongum, Bifidobacterium adolescentis, Clostridium butyricum, C. perfringens, C. bifermentans, C. innocuum, Escherichia coli, Enterococcus faecalis, Enterococcus faecium, Lactobacillus acidophilus) was used in this investigation. Ampicillin [9.2 μg (ml culture)(-1)] was added to two chemostats operated at different dilution rates (D; 0.10 h(-1) and 0.21 h(-1)), and metronidazole [76.9 μg (ml culture)(-1)] was added to a third vessel (D = 0.21 h(-1)). Perturbations in bacterial physiology and metabolism were sampled over a 48-h period. Lactobacillus acidophilus and C. bifermentans populations did not establish in the fermentors under the imposed growth conditions. Ampicillin resulted in substantial reductions in bacteroides and C. perfringens populations at both dilution rates. Metronidazole strongly affected bacteroides communities but had no effect on bifidobacterial communities. The bacteriostatic effect of ampicillin on bifidobacterial species was growth rate dependent. Several metabolic activities were affected by antibiotic addition, including fermentation product formation and enzyme synthesis. The growth of antibiotic-resistant bifidobacteria in the large bowel may enable them to occupy ecological niches left vacant after antibiotic administration, preventing colonization by pathogenic species.}, } @article {pmid23397517, year = {2013}, author = {Stomeo, F and Valverde, A and Pointing, SB and McKay, CP and Warren-Rhodes, KA and Tuffin, MI and Seely, M and Cowan, DA}, title = {Hypolithic and soil microbial community assembly along an aridity gradient in the Namib Desert.}, journal = {Extremophiles : life under extreme conditions}, volume = {17}, number = {2}, pages = {329-337}, pmid = {23397517}, issn = {1433-4909}, mesh = {Bacteria/*isolation & purification ; *Biodiversity ; Desert Climate ; Models, Biological ; Namibia ; *Soil Microbiology ; Weather ; }, abstract = {The Namib Desert is considered the oldest desert in the world and hyperarid for the last 5 million years. However, the environmental buffering provided by quartz and other translucent rocks supports extensive hypolithic microbial communities. In this study, open soil and hypolithic microbial communities have been investigated along an East-West transect characterized by an inverse fog-rainfall gradient. Multivariate analysis showed that structurally different microbial communities occur in soil and in hypolithic zones. Using variation partitioning, we found that hypolithic communities exhibited a fog-related distribution as indicated by the significant East-West clustering. Sodium content was also an important environmental factor affecting the composition of both soil and hypolithic microbial communities. Finally, although null models for patterns in microbial communities were not supported by experimental data, the amount of unexplained variation (68-97 %) suggests that stochastic processes also play a role in the assembly of such communities in the Namib Desert.}, } @article {pmid23397369, year = {2013}, author = {Delgado, S and Cabrera-Rubio, R and Mira, A and Suárez, A and Mayo, B}, title = {Microbiological survey of the human gastric ecosystem using culturing and pyrosequencing methods.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {763-772}, pmid = {23397369}, issn = {1432-184X}, mesh = {Adult ; Aged ; Bacteria/classification/genetics/growth & development/*isolation & purification ; *Biodiversity ; Colony Count, Microbial/*methods ; Ecosystem ; Female ; Gastric Juice/*microbiology ; Humans ; Male ; Metagenome ; Middle Aged ; Phylogeny ; Sequence Analysis, DNA/*methods ; Stomach/*microbiology ; }, abstract = {Stomach mucosa biopsies and gastric juices samples of 12 healthy persons were analysed by culturing in selective- and non-selective-rich media. Microbial DNA from four mucosal samples was also amplified by nested PCR using universal bacterial primers, and the 16S rDNA amplicons pyrosequenced. The total number of cultivable microorganisms recovered from the samples ranged from 10(2) to 10(4) cfu/g or ml. The isolates were identified at the species level by PCR amplification and sequencing of the 16S rDNA. Isolates belonged mainly to four genera; Propionibacterium, Lactobacillus, Streptococcus and Staphylococcus. A total of 15,622 high-quality 16S rDNA sequence reads were obtained by pyrosequencing from the four mucosal samples. Sequence analysis grouped the reads into 59 families and 69 genera, revealing wide bacterial diversity. Considerable differences in the composition of the gastric microbiota were observed among the subjects, although in all samples the most abundant operational taxonomic units belonged to Streptococcus, Propionibacterium and Lactobacillus. Comparison of the stomach microbiota with that present in other parts of the human gastrointestinal tract revealed distinctive microbial communities. This is the first study in which a combination of culture and culture-independent techniques has been used to explore the bacterial diversity of the human stomach.}, } @article {pmid23397107, year = {2013}, author = {Jaranowska, P and Cydzik-Kwiatkowska, A and Zielińska, M}, title = {Configuration of biological wastewater treatment line and influent composition as the main factors driving bacterial community structure of activated sludge.}, journal = {World journal of microbiology & biotechnology}, volume = {29}, number = {7}, pages = {1145-1153}, pmid = {23397107}, issn = {1573-0972}, mesh = {Bacteria/*classification/*genetics ; *Biota ; Metagenome ; Molecular Sequence Data ; Poland ; Sequence Analysis, DNA ; Sewage/*microbiology ; Water Purification/*methods ; }, abstract = {The structure of microbial consortia in wastewater treatment facilities is a resultant of environmental conditions created by the operational parameters of the purification process. In the research, activated sludge from nine Polish wastewater treatment plants (WWTPs) was investigated at a molecular level to determine the impact of the complexity of biological treatment line and the influent composition on the species structure and the diversity of bacterial consortia. The community fingerprints and technological data were subjected to the canonical correspondence and correlation analyses. The number of separated biological processes realized in the treatment line and the presence of industrial wastewater in the influent were the key factors determining the species structure of total and ammonia-oxidizing bacteria in biomass. The N2O-reducers community composition depended significantly on the design of the facility; the highest species richness of denitrifiers was noted in the WWTPs with separated denitrification tanks. The contribution of industrial streams to the inflow affected the diversity of total and denitrifying bacterial consortia and diminished the diversity of ammonia oxidizers. The obtained data are valuable for engineers since they revealed the main factors, including the design of wastewater treatment plant, influencing the microbial groups critical for the stability of purification processes.}, } @article {pmid23396038, year = {2013}, author = {Poirel, J and Joulian, C and Leyval, C and Billard, P}, title = {Arsenite-induced changes in abundance and expression of arsenite transporter and arsenite oxidase genes of a soil microbial community.}, journal = {Research in microbiology}, volume = {164}, number = {5}, pages = {457-465}, doi = {10.1016/j.resmic.2013.01.012}, pmid = {23396038}, issn = {1769-7123}, mesh = {Arsenite Transporting ATPases/genetics/*metabolism ; Arsenites/*metabolism ; Bacteria/*enzymology/genetics/*metabolism ; Biota ; *Gene Expression Regulation, Bacterial ; Metagenome ; Molecular Sequence Data ; Oxidoreductases/genetics/*metabolism ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; Up-Regulation ; }, abstract = {We describe a real-time PCR assay for the quantitative detection of arsB and ACR3(1) arsenite transporter gene families, two ubiquitous and key determinants of arsenic resistance in prokaryotes. The assay was applied in batch growth experiments using a wasteland soil bacterial community as an inoculum to investigate the effect of increasing arsenite [As(III)] concentrations on genes and transcript abundances. The aioA gene encoding the large subunit of arsenite oxidase was monitored in parallel. Results showed that arsB and ACR3(1) gene abundances correlated positively with the As(III) concentration. Both genes showed similar transcription patterns and strong upregulation by arsenic. Microbial As(III) oxidation occurred in As(III) spiked cultures and was associated with expression of the aioA gene in most cases. However, aioA was also expressed in several non-amended culture replicates. Analysis of cDNA clone libraries revealed that Pseudomonas was the dominant metabolically active genus whatever the As(III) concentration. Expressed arsB and ACR3(1) gene sequences were also affiliated with those from Pseudomonas, while expressed aioA sequences were more taxonomically diverse. The study suggests that arsenite transporter genes are appropriate biomarkers of arsenic stress that may be suitable for further exploring the adaptive response of bacterial communities to arsenic in contaminated environments.}, } @article {pmid23390612, year = {2013}, author = {Dlugosch, KM and Lai, Z and Bonin, A and Hierro, J and Rieseberg, LH}, title = {Allele identification for transcriptome-based population genomics in the invasive plant Centaurea solstitialis.}, journal = {G3 (Bethesda, Md.)}, volume = {3}, number = {2}, pages = {359-367}, pmid = {23390612}, issn = {2160-1836}, mesh = {Alleles ; Centaurea/*genetics ; Cluster Analysis ; Databases, Factual ; Gene Library ; Genetic Loci ; *Genome, Plant ; Genotype ; High-Throughput Nucleotide Sequencing ; Introduced Species ; *Metagenomics ; Polymorphism, Single Nucleotide ; Software ; *Transcriptome ; }, abstract = {Transcriptome sequences are becoming more broadly available for multiple individuals of the same species, providing opportunities to derive population genomic information from these datasets. Using the 454 Life Science Genome Sequencer FLX and FLX-Titanium next-generation platforms, we generated 11-430 Mbp of sequence for normalized cDNA for 40 wild genotypes of the invasive plant Centaurea solstitialis, yellow starthistle, from across its worldwide distribution. We examined the impact of sequencing effort on transcriptome recovery and overlap among individuals. To do this, we developed two novel publicly available software pipelines: SnoWhite for read cleaning before assembly, and AllelePipe for clustering of loci and allele identification in assembled datasets with or without a reference genome. AllelePipe is designed specifically for cases in which read depth information is not appropriate or available to assist with disentangling closely related paralogs from allelic variation, as in transcriptome or previously assembled libraries. We find that modest applications of sequencing effort recover most of the novel sequences present in the transcriptome of this species, including single-copy loci and a representative distribution of functional groups. In contrast, the coverage of variable sites, observation of heterozygosity, and overlap among different libraries are all highly dependent on sequencing effort. Nevertheless, the information gained from overlapping regions was informative regarding coarse population structure and variation across our small number of population samples, providing the first genetic evidence in support of hypothesized invasion scenarios.}, } @article {pmid23387867, year = {2013}, author = {Shakya, M and Quince, C and Campbell, JH and Yang, ZK and Schadt, CW and Podar, M}, title = {Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities.}, journal = {Environmental microbiology}, volume = {15}, number = {6}, pages = {1882-1899}, pmid = {23387867}, issn = {1462-2920}, support = {R01 HG004857/HG/NHGRI NIH HHS/United States ; 1R01HG004857-01A1/HG/NHGRI NIH HHS/United States ; }, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; *Biodiversity ; DNA Primers/genetics ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Microbiological Techniques/*standards ; Phylogeny ; RNA, Ribosomal/genetics ; Reproducibility of Results ; }, abstract = {Next-generation sequencing has dramatically changed the landscape of microbial ecology, large-scale and in-depth diversity studies being now widely accessible. However, determining the accuracy of taxonomic and quantitative inferences and comparing results obtained with different approaches are complicated by incongruence of experimental and computational data types and also by lack of knowledge of the true ecological diversity. Here we used highly diverse bacterial and archaeal synthetic communities assembled from pure genomic DNAs to compare inferences from metagenomic and SSU rRNA amplicon sequencing. Both Illumina and 454 metagenomic data outperformed amplicon sequencing in quantifying the community composition, but the outcome was dependent on analysis parameters and platform. New approaches in processing and classifying amplicons can reconstruct the taxonomic composition of the community with high reproducibility within primer sets, but all tested primers sets lead to significant taxon-specific biases. Controlled synthetic communities assembled to broadly mimic the phylogenetic richness in target environments can provide important validation for fine-tuning experimental and computational parameters used to characterize natural communities.}, } @article {pmid23385952, year = {2013}, author = {Heinrichs, G and Hübner, I and Schmidt, CK and de Hoog, GS and Haase, G}, title = {Analysis of black fungal biofilms occurring at domestic water taps. I: compositional analysis using Tag-Encoded FLX Amplicon Pyrosequencing.}, journal = {Mycopathologia}, volume = {175}, number = {5-6}, pages = {387-397}, pmid = {23385952}, issn = {1573-0832}, mesh = {Biofilms/*growth & development ; *Biota ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Drinking Water/*microbiology ; *Environmental Microbiology ; Fungi/*classification/genetics/growth & development/*isolation & purification ; Germany ; Humans ; Metagenomics ; Mycology ; Sequence Analysis, DNA ; }, abstract = {Mass growth of dark fungal biofilms on water taps and associated habitats was observed in various German drinking water distribution systems recently. Customers of affected drinking water systems are anxious about potential and unknown health risks. These environments are known to harbour a fungal flora also comprising a variety of fungal opportunists that are well known to cause superficial mycoses in humans (Exophiala equina, Exophiala lecanii-corni) but are not known to establish dark biofilms so far. To gain profound insight on composition of respective biofilms, a metagenomic approach using Tag-Encoded FLX Amplicon Pyrosequencing (TEFAP) of the ribosomal internal transcribed spacer 2 region in comparison with a classical cultivation approach using Sabouraud agar with chloramphenicol and erythritol-chloramphenicol-agar was performed. E. lecanii-corni was found to be the major component in 10 of 13 biofilms analysed independently of the method used. Alternaria sp., E. equina, Fusarium spp. and Ochroconis spp. were also relatively abundant. As expected, TEFAP usually revealed a higher diversity than the cultivation approaches. For example, opportunistic species like Candida albicans or Exophiala dermatitidis were detected in very low amounts. In conclusion, TEFAP turned out to be a promising and powerful tool for the semi-quantitative analysis of fungal biofilms. Referring to relevant literature, potential biological hazards caused by fungi of the dark biofilms can be regarded as low.}, } @article {pmid23382835, year = {2013}, author = {Hand, D and Wallis, C and Colyer, A and Penn, CW}, title = {Pyrosequencing the canine faecal microbiota: breadth and depth of biodiversity.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e53115}, pmid = {23382835}, issn = {1932-6203}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacteria/*classification/*genetics/isolation & purification ; Biodiversity ; DNA, Bacterial ; Dogs ; Feces/*microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Male ; Metagenome/*genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Mammalian intestinal microbiota remain poorly understood despite decades of interest and investigation by culture-based and other long-established methodologies. Using high-throughput sequencing technology we now report a detailed analysis of canine faecal microbiota. The study group of animals comprised eleven healthy adult miniature Schnauzer dogs of mixed sex and age, some closely related and all housed in kennel and pen accommodation on the same premises with similar feeding and exercise regimes. DNA was extracted from faecal specimens and subjected to PCR amplification of 16S rDNA, followed by sequencing of the 5' region that included variable regions V1 and V2. Barcoded amplicons were sequenced by Roche-454 FLX high-throughput pyrosequencing. Sequences were assigned to taxa using the Ribosomal Database Project Bayesian classifier and revealed dominance of Fusobacterium and Bacteroidetes phyla. Differences between animals in the proportions of different taxa, among 10,000 reads per animal, were clear and not supportive of the concept of a "core microbiota". Despite this variability in prominent genera, littermates were shown to have a more similar faecal microbial composition than unrelated dogs. Diversity of the microbiota was also assessed by assignment of sequence reads into operational taxonomic units (OTUs) at the level of 97% sequence identity. The OTU data were then subjected to rarefaction analysis and determination of Chao1 richness estimates. The data indicated that faecal microbiota comprised possibly as many as 500 to 1500 OTUs.}, } @article {pmid23381385, year = {2013}, author = {Wongwilaiwalin, S and Laothanachareon, T and Mhuantong, W and Tangphatsornruang, S and Eurwilaichitr, L and Igarashi, Y and Champreda, V}, title = {Comparative metagenomic analysis of microcosm structures and lignocellulolytic enzyme systems of symbiotic biomass-degrading consortia.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {20}, pages = {8941-8954}, doi = {10.1007/s00253-013-4699-y}, pmid = {23381385}, issn = {1432-0614}, mesh = {Animals ; Bacteria/classification/enzymology/*genetics/isolation & purification ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/*metabolism ; Biomass ; Cattle ; Cellulases/genetics/*metabolism ; Cellulose/metabolism ; Industrial Waste/analysis ; Lignin/metabolism ; *Metagenomics ; *Microbial Consortia ; Rumen/*microbiology/physiology ; Saccharum/*microbiology/physiology ; Sewage/*microbiology ; Symbiosis ; }, abstract = {Decomposition of lignocelluloses by cooperative microbial actions is an essential process of carbon cycling in nature and provides a basis for biomass conversion to fuels and chemicals in biorefineries. In this study, structurally stable symbiotic aero-tolerant lignocellulose-degrading microbial consortia were obtained from biodiversified microflora present in industrial sugarcane bagasse pile (BGC-1), cow rumen fluid (CRC-1), and pulp mill activated sludge (ASC-1) by successive subcultivation on rice straw under facultative anoxic conditions. Tagged 16S rRNA gene pyrosequencing revealed that all isolated consortia originated from highly diverse environmental microflora shared similar composite phylum profiles comprising mainly Firmicutes, reflecting convergent adaptation of microcosm structures, however, with substantial differences at refined genus level. BGC-1 comprising cellulolytic Clostridium and Acetanaerobacterium in stable coexistence with ligninolytic Ureibacillus showed the highest capability on degradation of agricultural residues and industrial pulp waste with CMCase, xylanase, and β-glucanase activities in the supernatant. Shotgun pyrosequencing of the BGC-1 metagenome indicated a markedly high relative abundance of genes encoding for glycosyl hydrolases, particularly for lignocellulytic enzymes in 26 families. The enzyme system comprised a unique composition of main-chain degrading and side-chain processing hydrolases, dominated by GH2, 3, 5, 9, 10, and 43, reflecting adaptation of enzyme profiles to the specific substrate. Gene mapping showed metabolic potential of BGC-1 for conversion of biomass sugars to various fermentation products of industrial importance. The symbiotic consortium is a promising simplified model for study of multispecies mechanisms on consolidated bioprocessing and a platform for discovering efficient synergistic enzyme systems for biotechnological application.}, } @article {pmid23365674, year = {2013}, author = {Cheung, MK and Lam, WY and Fung, WY and Law, PT and Au, CH and Nong, W and Kam, KM and Kwan, HS and Tsui, SK}, title = {Sputum microbiota in tuberculosis as revealed by 16S rRNA pyrosequencing.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e54574}, pmid = {23365674}, issn = {1932-6203}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/*genetics/isolation & purification ; Biodiversity ; Case-Control Studies ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenome/*genetics ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/classification/*genetics ; Sequence Analysis, DNA ; Sputum/*microbiology ; Tuberculosis, Pulmonary/*microbiology ; }, abstract = {BACKGROUND: Tuberculosis (TB) remains a global threat in the 21st century. Traditional studies of the disease are focused on the single pathogen Mycobacterium tuberculosis. Recent studies have revealed associations of some diseases with an imbalance in the microbial community. Characterization of the TB microbiota could allow a better understanding of the disease.

Here, the sputum microbiota in TB infection was examined by using 16S rRNA pyrosequencing. A total of 829,873 high-quality sequencing reads were generated from 22 TB and 14 control sputum samples. Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria were the five major bacterial phyla recovered, which together composed over 98% of the microbial community. Proteobacteria and Bacteroidetes were more represented in the TB samples and Firmicutes was more predominant in the controls. Sixteen major bacterial genera were recovered. Streptococcus, Neisseria and Prevotella were the most predominant genera, which were dominated by several operational taxonomic units grouped at a 97% similarity level. Actinomyces, Fusobacterium, Leptotrichia, Prevotella, Streptococcus, and Veillonella were found in all TB samples, possibly representing the core genera in TB sputum microbiota. The less represented genera Mogibacterium, Moryella and Oribacterium were enriched statistically in the TB samples, while a genus belonging to the unclassified Lactobacillales was enriched in the controls. The diversity of microbiota was similar in the TB and control samples.

CONCLUSIONS/SIGNIFICANCE: The composition and diversity of sputum microbiota in TB infection was characterized for the first time by using high-throughput pyrosequencing. It lays the framework for examination of potential roles played by the diverse microbiota in TB pathogenesis and progression, and could ultimately facilitate advances in TB treatment.}, } @article {pmid23359712, year = {2013}, author = {DeLeon-Rodriguez, N and Lathem, TL and Rodriguez-R, LM and Barazesh, JM and Anderson, BE and Beyersdorf, AJ and Ziemba, LD and Bergin, M and Nenes, A and Konstantinidis, KT}, title = {Microbiome of the upper troposphere: species composition and prevalence, effects of tropical storms, and atmospheric implications.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {7}, pages = {2575-2580}, pmid = {23359712}, issn = {1091-6490}, mesh = {*Air Microbiology ; Altitude ; Analysis of Variance ; *Atmosphere ; *Biodiversity ; Caribbean Region ; *Cyclonic Storms ; Metagenome/*genetics ; Phylogeography ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The composition and prevalence of microorganisms in the middle-to-upper troposphere (8-15 km altitude) and their role in aerosol-cloud-precipitation interactions represent important, unresolved questions for biological and atmospheric science. In particular, airborne microorganisms above the oceans remain essentially uncharacterized, as most work to date is restricted to samples taken near the Earth's surface. Here we report on the microbiome of low- and high-altitude air masses sampled onboard the National Aeronautics and Space Administration DC-8 platform during the 2010 Genesis and Rapid Intensification Processes campaign in the Caribbean Sea. The samples were collected in cloudy and cloud-free air masses before, during, and after two major tropical hurricanes, Earl and Karl. Quantitative PCR and microscopy revealed that viable bacterial cells represented on average around 20% of the total particles in the 0.25- to 1-μm diameter range and were at least an order of magnitude more abundant than fungal cells, suggesting that bacteria represent an important and underestimated fraction of micrometer-sized atmospheric aerosols. The samples from the two hurricanes were characterized by significantly different bacterial communities, revealing that hurricanes aerosolize a large amount of new cells. Nonetheless, 17 bacterial taxa, including taxa that are known to use C1-C4 carbon compounds present in the atmosphere, were found in all samples, indicating that these organisms possess traits that allow survival in the troposphere. The findings presented here suggest that the microbiome is a dynamic and underappreciated aspect of the upper troposphere with potentially important impacts on the hydrological cycle, clouds, and climate.}, } @article {pmid23352736, year = {2013}, author = {López-López, A and Richter, M and Peña, A and Tamames, J and Rosselló-Móra, R}, title = {New insights into the archaeal diversity of a hypersaline microbial mat obtained by a metagenomic approach.}, journal = {Systematic and applied microbiology}, volume = {36}, number = {3}, pages = {205-214}, doi = {10.1016/j.syapm.2012.11.008}, pmid = {23352736}, issn = {1618-0984}, mesh = {Archaea/*classification/*genetics ; Bacteria/classification/genetics ; *Biodiversity ; *Biomass ; Chromosomes, Archaeal ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Gene Order ; Genome, Archaeal ; *Metagenomics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A metagenomic approach was carried out in order to study the genetic pool of a hypersaline microbial mat, paying more attention to the archaeal community and, specifically, to the putatively methanogenic members. The main aim of the work was to expand the knowledge of a likely ecologically important archaeal lineage, candidate division MSBL1, which is probably involved in methanogenesis at very high salinities. The results obtained in this study were in accordance with our previous report on the bacterial diversity encountered by using a number of molecular techniques, but remarkable differences were found in the archaeal diversity retrieval by each of the procedures used (metagenomics and 16S rRNA-based methods). The lack of synteny for most of the metagenomic fragments with known genomes, together with the low degree of similarity of the annotated open reading frames (ORFs) with the sequences in the databases, reflected the high degree of novelty in the mat community studied. Linking the sequenced clones with representatives of division MSBL1 was not possible because of the lack of additional information concerning this archaeal group in the public gene repositories. However, given the high abundance of representatives of this division in the 16S rRNA clone libraries and the low identity of the archaeal clones with known genomes, it was hypothesized that some of them could arise from MSBL1 genomes. In addition, other prokaryotic groups known to be relevant in organic matter mineralization at high salinities were detected.}, } @article {pmid23349750, year = {2013}, author = {Lin, A and Bik, EM and Costello, EK and Dethlefsen, L and Haque, R and Relman, DA and Singh, U}, title = {Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e53838}, pmid = {23349750}, issn = {1932-6203}, support = {5R01AI043596/AI/NIAID NIH HHS/United States ; DP1OD000964/OD/NIH HHS/United States ; 1UL1 RR025744/RR/NCRR NIH HHS/United States ; R01 AI053724/AI/NIAID NIH HHS/United States ; AI 53724/AI/NIAID NIH HHS/United States ; UL1 RR025744/RR/NCRR NIH HHS/United States ; UL1 TR001085/TR/NCATS NIH HHS/United States ; R21 AI069382/AI/NIAID NIH HHS/United States ; AI 069382/AI/NIAID NIH HHS/United States ; R01 AI043596/AI/NIAID NIH HHS/United States ; DP1 OD000964/OD/NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Bacteria/*classification/genetics ; Bangladesh ; *Biodiversity ; Child ; Feces/microbiology ; Female ; *Health ; Humans ; Intestines/*microbiology ; Male ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Time Factors ; United States ; }, abstract = {BACKGROUND: Our current understanding of the composition and stability of the human distal gut microbiota is based largely on studies of infants and adults living in developed countries. In contrast, little is known about the gut microbiota and its variation over time in older children and adolescents, especially in developing countries.

We compared the diversity, composition, and temporal stability of the fecal microbiota of healthy children, ages 9 to 14 years, living in an urban slum in Bangladesh with that of children of the same age range in an upper-middle class suburban community in the United States. We analyzed >8,000 near full-length 16S rRNA gene sequences and over 845,000 pyrosequencing reads of the 16S rRNA V1-V3 region. The distal gut of Bangladeshi children harbored significantly greater bacterial diversity than that of U.S. children, including novel lineages from several bacterial phyla. Bangladeshi and U.S. children had distinct fecal bacterial community membership and structure; the microbiota of Bangladeshi children was enriched in Prevotella, Butyrivibrio, and Oscillospira and depleted in Bacteroides relative to U.S. children (although similar to Bangladeshi adults). Furthermore, community membership and structure in Bangladeshi children was significantly less stable month-to-month than U.S. children.

CONCLUSIONS/SIGNIFICANCE: Together, these results suggest that differing environmental or genetic factors may shape the microbiota of healthy children in the two countries. Further investigation is necessary to understand the mechanisms and factors that underlie these differences, and to incorporate these findings into new strategies for the prevention and treatment of childhood and adolescent diseases.}, } @article {pmid23349094, year = {2013}, author = {Dewar, ML and Arnould, JP and Dann, P and Trathan, P and Groscolas, R and Smith, S}, title = {Interspecific variations in the gastrointestinal microbiota in penguins.}, journal = {MicrobiologyOpen}, volume = {2}, number = {1}, pages = {195-204}, pmid = {23349094}, issn = {2045-8827}, mesh = {Animals ; *Biota ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gastrointestinal Tract/*microbiology ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spheniscidae/*microbiology ; }, abstract = {Despite the enormous amount of data available on the importance of the gastrointestinal (GI) microbiota in vertebrate (especially mammals), information on the GI microbiota of seabirds remains incomplete. As with many seabirds, penguins have a unique digestive physiology that enables them to store large reserves of adipose tissue, protein, and lipids. This study used quantitative real-time polymerase chain reaction (qPCR) and 16S rRNA gene pyrosequencing to characterize the interspecific variations of the GI microbiota of four penguin species: the king, gentoo, macaroni, and little penguin. The qPCR results indicated that there were significant differences in the abundance of the major phyla Firmicutes, Bacteroides, Actinobacteria, and Proteobacteria. A total of 132,340, 18,336, 6324, and 4826 near full-length 16S rRNA gene sequences were amplified from fecal samples collected from king, gentoo, macaroni, and little penguins, respectively. A total of 13 phyla were identified with Firmicutes, Bacteroidetes, Proteobacteria, and Fusobacteria dominating the composition; however, there were major differences in the relative abundance of the phyla. In addition, this study documented the presence of known human pathogens, such as Campylobacter, Helicobacter, Prevotella, Veillonella, Erysipelotrichaceae, Neisseria, and Mycoplasma. However, their role in disease in penguins remains unknown. To our knowledge, this is the first study to provide an in-depth investigation of the GI microbiota of penguins.}, } @article {pmid23349073, year = {2013}, author = {Barrett, E and Guinane, CM and Ryan, CA and Dempsey, EM and Murphy, BP and O'Toole, PW and Fitzgerald, GF and Cotter, PD and Ross, RP and Stanton, C}, title = {Microbiota diversity and stability of the preterm neonatal ileum and colon of two infants.}, journal = {MicrobiologyOpen}, volume = {2}, number = {2}, pages = {215-225}, pmid = {23349073}, issn = {2045-8827}, mesh = {Actinobacteria/isolation & purification ; Anti-Bacterial Agents/therapeutic use ; Bacteroidetes/isolation & purification ; Bifidobacterium/isolation & purification ; Biodiversity ; Clostridium/isolation & purification ; Colon/*microbiology ; Colostomy/methods ; Computational Biology ; DNA, Bacterial/isolation & purification ; Enterobacteriaceae/isolation & purification ; Feces/microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Ileostomy/methods ; Ileum/*microbiology ; Infant, Newborn ; Lactobacillus/isolation & purification ; Male ; *Metagenome ; }, abstract = {The composition of the microbiota associated with the human ileum and colon in the early weeks of life of two preterm infants was examined, with particular emphasis on the Lactobacillus and Bifidobacterium members. Culturing work showed that bifidobacteria and lactobacilli in the ileostomy changed over time, compared with the colostomy effluent where there was far less variation. The colostomy infant was dominated by two phyla, Actinobacteria and Firmicutes, while in the ileostomy samples, Proteobacteria emerged at the expense of Actinobacteria. Bacteroidetes were only detected following the reversal of the ileostomy in the final fecal sample and were not detected in any colonic fluid samples. Clostridia levels were unstable in the colostomy fluid, suggesting that the ileostomy/colostomy itself influenced the gut microbiota, in particular the strict anaerobes. Pyrosequencing analysis of microbiota composition indicated that bifidobacteria and lactobacilli are among the dominant genera in both the ileal and colonic fluids. Bifidobacteria and lactobacilli levels were unstable in the ileostomy fluid, with large reductions in numbers and relative proportions of both observed. These decreases were characterized by an increase in proportions of Streptococcus and Enterobacteriaceae. Clostridium was detected only in the colonic effluent, with large changes in the relative proportions over time.}, } @article {pmid23345438, year = {2013}, author = {Ottesen, EA and Young, CR and Eppley, JM and Ryan, JP and Chavez, FP and Scholin, CA and DeLong, EF}, title = {Pattern and synchrony of gene expression among sympatric marine microbial populations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {6}, pages = {E488-97}, pmid = {23345438}, issn = {1091-6490}, mesh = {Archaea/classification/genetics/isolation & purification/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; Biodiversity ; California ; Circadian Rhythm/genetics ; *Ecosystem ; Gene Expression Profiling ; Metagenome/*genetics ; Phylogeny ; Phytoplankton/classification/genetics/isolation & purification ; Plankton/classification/*genetics/isolation & purification ; Seawater/microbiology ; Synechococcus/genetics/metabolism ; Transcriptome ; *Water Microbiology ; }, abstract = {Planktonic marine microbes live in dynamic habitats that demand rapid sensing and response to periodic as well as stochastic environmental change. The kinetics, regularity, and specificity of microbial responses in situ, however, are not well-described. We report here simultaneous multitaxon genome-wide transcriptome profiling in a naturally occurring picoplankton community. An in situ robotic sampler using a Lagrangian sampling strategy enabled continuous tracking and repeated sampling of coherent microbial populations over 2 d. Subsequent RNA sequencing analyses yielded genome-wide transcriptome profiles of eukaryotic (Ostreococcus) and bacterial (Synechococcus) photosynthetic picoplankton as well as proteorhodopsin-containing heterotrophs, including Pelagibacter, SAR86-cluster Gammaproteobacteria, and marine Euryarchaea. The photosynthetic picoplankton exhibited strong diel rhythms over thousands of gene transcripts that were remarkably consistent with diel cycling observed in laboratory pure cultures. In contrast, the heterotrophs did not cycle diurnally. Instead, heterotrophic picoplankton populations exhibited cross-species synchronous, tightly regulated, temporally variable patterns of gene expression for many genes, particularly those genes associated with growth and nutrient acquisition. This multitaxon, population-wide gene regulation seemed to reflect sporadic, short-term, reversible responses to high-frequency environmental variability. Although the timing of the environmental responses among different heterotrophic species seemed synchronous, the specific metabolic genes that were expressed varied from taxon to taxon. In aggregate, these results provide insights into the kinetics, diversity, and functional patterns of microbial community response to environmental change. Our results also suggest a means by which complex multispecies metabolic processes could be coordinated, facilitating the regulation of matter and energy processing in a dynamically changing environment.}, } @article {pmid23340384, year = {2013}, author = {Dolci, P and Zenato, S and Pramotton, R and Barmaz, A and Alessandria, V and Rantsiou, K and Cocolin, L}, title = {Cheese surface microbiota complexity: RT-PCR-DGGE, a tool for a detailed picture?.}, journal = {International journal of food microbiology}, volume = {162}, number = {1}, pages = {8-12}, doi = {10.1016/j.ijfoodmicro.2012.12.009}, pmid = {23340384}, issn = {1879-3460}, mesh = {*Bacteria/classification/genetics ; *Biodiversity ; Cheese/*microbiology ; Cluster Analysis ; DNA, Bacterial/genetics ; *Denaturing Gradient Gel Electrophoresis ; *Food Microbiology ; Metagenome/genetics ; *Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {In this work, a culture-independent approach, based on PCR-DGGE and RT-PCR-DGGE, has been used to study the succession of bacterial communities that are encountered in Fontina PDO cheese. As already found for other smear ripened cheeses, it appeared that coryneform bacteria were actively present and could therefore be considered determinant in rind formation. DGGE profiles, especially at the RNA level, have shown the presence of Brevibacterium, Corynebacterium and Arthrobacter genera. RT-PCR-DGGE gels have lead to a richer band profile than the one obtained on the basis of DNA analysis, thus indicating that RNA analysis can highlight bacterial species that DNA analysis is not able to show. Thus, the biodiversity of the Fontina PDO surface has been described better by means of RT-PCR-DGGE, and RNA molecules should be considered a more informative target than DNA.}, } @article {pmid23339708, year = {2013}, author = {Nylund, L and Satokari, R and Nikkilä, J and Rajilić-Stojanović, M and Kalliomäki, M and Isolauri, E and Salminen, S and de Vos, WM}, title = {Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {12}, pmid = {23339708}, issn = {1471-2180}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Dermatitis, Atopic/*microbiology ; Female ; Follow-Up Studies ; Gastrointestinal Tract/*microbiology ; Humans ; Infant ; Male ; *Metagenome ; *Microarray Analysis ; Placebos/administration & dosage ; Probiotics/administration & dosage ; Randomized Controlled Trials as Topic ; }, abstract = {BACKGROUND: Deviations in composition and diversity of intestinal microbiota in infancy have been associated with both the development and recurrence of atopic eczema. Thus, we decided to use a deep and global microarray-based method to characterize the diversity and temporal changes of the intestinal microbiota in infancy and to define specific bacterial signatures associated with eczema. Faecal microbiota at 6 and 18 months of age were analysed from 34 infants (15 with eczema and 19 healthy controls) selected from a prospective follow-up study based on the availability of faecal samples. The infants were originally randomized to receive either Lactobacillus rhamnosus GG or placebo.

RESULTS: Children with eczema harboured a more diverse total microbiota than control subjects as assessed by the Simpson's reciprocal diversity index of the microarray profiles. Composition of the microbiota did not differ between study groups at age of 6 months, but was significantly different at age of 18 months as assessed by MCPP (p=0.01). At this age healthy children harboured 3 -fold greater amount of members of the Bacteroidetes (p=0.01). Microbiota of children suffering from eczema had increased abundance of the Clostridium clusters IV and XIVa, which are typically abundant in adults. Probiotic Lactobacillus rhamnosus GG supplementation in early infancy was observed to have minor long-term effects on the microbiota composition.

CONCLUSION: A diverse and adult-type microbiota in early childhood is associated with eczema and it may contribute to the perpetuation of eczema.}, } @article {pmid23335759, year = {2013}, author = {Dang, H and Zhou, H and Yang, J and Ge, H and Jiao, N and Luan, X and Zhang, C and Klotz, MG}, title = {Thaumarchaeotal signature gene distribution in sediments of the northern South China Sea: an indicator of the metabolic intersection of the marine carbon, nitrogen, and phosphorus cycles?.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {7}, pages = {2137-2147}, pmid = {23335759}, issn = {1098-5336}, mesh = {Archaea/*metabolism ; Biota ; Carbon/*metabolism ; China ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments ; Metabolic Networks and Pathways/*genetics ; *Metagenome ; Molecular Sequence Data ; Nitrogen/*metabolism ; Oxidoreductases/genetics ; Phosphorus/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Thaumarchaeota are abundant and active in marine waters, where they contribute to aerobic ammonia oxidation and light-independent carbon fixation. The ecological function of thaumarchaeota in marine sediments, however, has rarely been investigated, even though marine sediments constitute the majority of the Earth's surface. Thaumarchaeota in the upper layer of sediments may contribute significantly to the reservoir of nitrogen oxides in ocean waters and thus to productivity, including the assimilation of carbon. We tested this hypothesis in the northern South China Sea (nSCS), a section of a large oligotrophic marginal sea with limited influx of nutrients, including nitrogen, by investigating the diversity, abundance, community structure, and spatial distribution of thaumarchaeotal signatures in surface sediments. Quantitative real-time PCR using primers designed to detect 16S rRNA and amoA genes in sediment community DNA revealed a significantly higher abundance of pertinent thaumarchaeotal than betaproteobacterial genes. This finding correlates with high levels of hcd genes, a signature of thaumarchaeotal autotrophic carbon fixation. Thaumarchaeol, a signature lipid biomarker for thaumarchaeota, constituted the majority of archaeal lipids in marine sediments. Sediment temperature and organic P and silt contents were identified as key environmental factors shaping the community structure and distribution of the monitored thaumarchaeotal amoA genes. When the pore water PO4(3-) concentration was controlled for via partial-correlation analysis, thaumarchaeotal amoA gene abundance significantly correlated with the sediment pore water NO2(-) concentration, suggesting that the amoA-bearing thaumarchaeota contribute to nitrite production. Statistical analyses also suggest that thaumarchaeotal metabolism could serve as a pivotal intersection of the carbon, nitrogen, and phosphorus cycles in marine sediments.}, } @article {pmid23326555, year = {2013}, author = {Bálint, M and Tiffin, P and Hallström, B and O'Hara, RB and Olson, MS and Fankhauser, JD and Piepenbring, M and Schmitt, I}, title = {Host genotype shapes the foliar fungal microbiome of balsam poplar (Populus balsamifera).}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e53987}, pmid = {23326555}, issn = {1932-6203}, mesh = {Fungi/genetics/*growth & development/pathogenicity ; Genetic Variation ; Genotype ; *Metagenome ; Plant Leaves/genetics/microbiology ; *Populus/genetics/microbiology ; }, abstract = {Foliar fungal communities of plants are diverse and ubiquitous. In grasses endophytes may increase host fitness; in trees, their ecological roles are poorly understood. We investigated whether the genotype of the host tree influences community structure of foliar fungi. We sampled leaves from genotyped balsam poplars from across the species' range, and applied 454 amplicon sequencing to characterize foliar fungal communities. At the time of the sampling the poplars had been growing in a common garden for two years. We found diverse fungal communities associated with the poplar leaves. Linear discriminant analysis and generalized linear models showed that host genotypes had a structuring effect on the composition of foliar fungal communities. The observed patterns may be explained by a filtering mechanism which allows the trees to selectively recruit fungal strains from the environment. Alternatively, host genotype-specific fungal communities may be present in the tree systemically, and persist in the host even after two clonal reproductions. Both scenarios are consistent with host tree adaptation to specific foliar fungal communities and suggest that there is a functional basis for the strong biotic interaction.}, } @article {pmid23326417, year = {2013}, author = {Hou, W and Wang, S and Dong, H and Jiang, H and Briggs, BR and Peacock, JP and Huang, Q and Huang, L and Wu, G and Zhi, X and Li, W and Dodsworth, JA and Hedlund, BP and Zhang, C and Hartnett, HE and Dijkstra, P and Hungate, BA}, title = {A comprehensive census of microbial diversity in hot springs of Tengchong, Yunnan Province China using 16S rRNA gene pyrosequencing.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e53350}, pmid = {23326417}, issn = {1932-6203}, mesh = {*Biodiversity ; China ; Geography ; Geologic Sediments/microbiology ; Hot Springs/*microbiology ; *Hot Temperature ; Hydrogen-Ion Concentration ; Metagenome/genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The Rehai and Ruidian geothermal fields, located in Tengchong County, Yunnan Province, China, host a variety of geochemically distinct hot springs. In this study, we report a comprehensive, cultivation-independent census of microbial communities in 37 samples collected from these geothermal fields, encompassing sites ranging in temperature from 55.1 to 93.6°C, in pH from 2.5 to 9.4, and in mineralogy from silicates in Rehai to carbonates in Ruidian. Richness was low in all samples, with 21-123 species-level OTUs detected. The bacterial phylum Aquificae or archaeal phylum Crenarchaeota were dominant in Rehai samples, yet the dominant taxa within those phyla depended on temperature, pH, and geochemistry. Rehai springs with low pH (2.5-2.6), high temperature (85.1-89.1°C), and high sulfur contents favored the crenarchaeal order Sulfolobales, whereas those with low pH (2.6-4.8) and cooler temperature (55.1-64.5°C) favored the Aquificae genus Hydrogenobaculum. Rehai springs with neutral-alkaline pH (7.2-9.4) and high temperature (>80°C) with high concentrations of silica and salt ions (Na, K, and Cl) favored the Aquificae genus Hydrogenobacter and crenarchaeal orders Desulfurococcales and Thermoproteales. Desulfurococcales and Thermoproteales became predominant in springs with pH much higher than the optimum and even the maximum pH known for these orders. Ruidian water samples harbored a single Aquificae genus Hydrogenobacter, whereas microbial communities in Ruidian sediment samples were more diverse at the phylum level and distinctly different from those in Rehai and Ruidian water samples, with a higher abundance of uncultivated lineages, close relatives of the ammonia-oxidizing archaeon "Candidatus Nitrosocaldus yellowstonii", and candidate division O1aA90 and OP1. These differences between Ruidian sediments and Rehai samples were likely caused by temperature, pH, and sediment mineralogy. The results of this study significantly expand the current understanding of the microbiology in Tengchong hot springs and provide a basis for comparison with other geothermal systems around the world.}, } @article {pmid23326376, year = {2013}, author = {Bull-Otterson, L and Feng, W and Kirpich, I and Wang, Y and Qin, X and Liu, Y and Gobejishvili, L and Joshi-Barve, S and Ayvaz, T and Petrosino, J and Kong, M and Barker, D and McClain, C and Barve, S}, title = {Metagenomic analyses of alcohol induced pathogenic alterations in the intestinal microbiome and the effect of Lactobacillus rhamnosus GG treatment.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e53028}, pmid = {23326376}, issn = {1932-6203}, support = {U01 AA021901/AA/NIAAA NIH HHS/United States ; R01 AA018869/AA/NIAAA NIH HHS/United States ; RC2AA019385/AA/NIAAA NIH HHS/United States ; P30 AA019360/AA/NIAAA NIH HHS/United States ; R01 AA015970/AA/NIAAA NIH HHS/United States ; R01 AAO14371//PHS HHS/United States ; R01 AA014371/AA/NIAAA NIH HHS/United States ; R01 AA0015970/AA/NIAAA NIH HHS/United States ; R37 AA010762/AA/NIAAA NIH HHS/United States ; P01 AA017103/AA/NIAAA NIH HHS/United States ; R21 AA020848/AA/NIAAA NIH HHS/United States ; R01 AA018016/AA/NIAAA NIH HHS/United States ; R21 AA020849/AA/NIAAA NIH HHS/United States ; R01 DK071765/DK/NIDDK NIH HHS/United States ; RC2 AA019385/AA/NIAAA NIH HHS/United States ; }, mesh = {Animals ; Anti-Infective Agents, Local/toxicity ; Bacteria/drug effects/genetics/growth & development ; Biodiversity ; Claudin-1/genetics ; Ethanol/toxicity ; Feces/chemistry/microbiology ; Gene Expression/drug effects ; Genetic Variation ; Hydrogen-Ion Concentration/drug effects ; Intestinal Mucosa/metabolism ; Intestines/drug effects/*microbiology ; Lacticaseibacillus rhamnosus/*physiology ; Liver Diseases, Alcoholic/etiology/*microbiology/therapy ; Male ; Metagenome/drug effects/genetics ; Metagenomics/*methods ; Mice ; Mice, Inbred C57BL ; Probiotics/pharmacology ; RNA, Ribosomal, 16S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; Zonula Occludens-1 Protein ; }, abstract = {Enteric dysbiosis plays an essential role in the pathogenesis of alcoholic liver disease (ALD). Detailed characterization of the alterations in the gut microbiome is needed for understanding their pathogenic role in ALD and developing effective therapeutic approaches using probiotic supplementation. Mice were fed liquid Lieber-DeCarli diet without or with alcohol (5% v/v) for 6 weeks. A subset of mice were administered the probiotic Lactobacillus rhamnosus GG (LGG) from 6 to 8 weeks. Indicators of intestinal permeability, hepatic steatosis, inflammation and injury were evaluated. Metagenomic analysis of the gut microbiome was performed by analyzing the fecal DNA by amplification of the V3-V5 regions of the 16S rRNA gene and large-scale parallel pyrosequencing on the 454 FLX Titanium platform. Chronic ethanol feeding caused a decline in the abundance of both Bacteriodetes and Firmicutes phyla, with a proportional increase in the gram negative Proteobacteria and gram positive Actinobacteria phyla; the bacterial genera that showed the biggest expansion were the gram negative alkaline tolerant Alcaligenes and gram positive Corynebacterium. Commensurate with the qualitative and quantitative alterations in the microbiome, ethanol caused an increase in plasma endotoxin, fecal pH, hepatic inflammation and injury. Notably, the ethanol-induced pathogenic changes in the microbiome and the liver were prevented by LGG supplementation. Overall, significant alterations in the gut microbiome over time occur in response to chronic alcohol exposure and correspond to increases in intestinal barrier dysfunction and development of ALD. Moreover, the altered bacterial communities of the gut may serve as significant therapeutic target for the prevention/treatment of chronic alcohol intake induced intestinal barrier dysfunction and liver disease.}, } @article {pmid23326225, year = {2013}, author = {Koren, O and Knights, D and Gonzalez, A and Waldron, L and Segata, N and Knight, R and Huttenhower, C and Ley, RE}, title = {A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets.}, journal = {PLoS computational biology}, volume = {9}, number = {1}, pages = {e1002863}, pmid = {23326225}, issn = {1553-7358}, support = {HG4872/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; U01 HG004866/HG/NHGRI NIH HHS/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; 1R01HG005969/HG/NHGRI NIH HHS/United States ; R01 HG005969/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics ; Biodiversity ; Humans ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recent analyses of human-associated bacterial diversity have categorized individuals into 'enterotypes' or clusters based on the abundances of key bacterial genera in the gut microbiota. There is a lack of consensus, however, on the analytical basis for enterotypes and on the interpretation of these results. We tested how the following factors influenced the detection of enterotypes: clustering methodology, distance metrics, OTU-picking approaches, sequencing depth, data type (whole genome shotgun (WGS) vs.16S rRNA gene sequence data), and 16S rRNA region. We included 16S rRNA gene sequences from the Human Microbiome Project (HMP) and from 16 additional studies and WGS sequences from the HMP and MetaHIT. In most body sites, we observed smooth abundance gradients of key genera without discrete clustering of samples. Some body habitats displayed bimodal (e.g., gut) or multimodal (e.g., vagina) distributions of sample abundances, but not all clustering methods and workflows accurately highlight such clusters. Because identifying enterotypes in datasets depends not only on the structure of the data but is also sensitive to the methods applied to identifying clustering strength, we recommend that multiple approaches be used and compared when testing for enterotypes.}, } @article {pmid23322636, year = {2013}, author = {Guinane, CM and Tadrous, A and Fouhy, F and Ryan, CA and Dempsey, EM and Murphy, B and Andrews, E and Cotter, PD and Stanton, C and Ross, RP}, title = {Microbial composition of human appendices from patients following appendectomy.}, journal = {mBio}, volume = {4}, number = {1}, pages = {}, pmid = {23322636}, issn = {2150-7511}, mesh = {Adolescent ; Adult ; Appendectomy ; Appendicitis/surgery ; Appendix/*microbiology ; Bacteria/*classification/*genetics ; *Biodiversity ; Child, Preschool ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Humans ; Male ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {UNLABELLED: The human appendix has historically been considered a vestige of evolutionary development with an unknown function. While limited data are available on the microbial composition of the appendix, it has been postulated that this organ could serve as a microbial reservoir for repopulating the gastrointestinal tract in times of necessity. We aimed to explore the microbial composition of the human appendix, using high-throughput sequencing of the 16S rRNA gene V4 region. Seven patients, 5 to 25 years of age, presenting with symptoms of acute appendicitis were included in this study. Results showed considerable diversity and interindividual variability among the microbial composition of the appendix samples. In general, however, Firmicutes was the dominant phylum, with the majority of additional sequences being assigned at various levels to Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria. Despite the large diversity in the microbiota found within the appendix, however, a few major families and genera were found to comprise the majority of the sequences present. Interestingly, also, certain taxa not generally associated with the human intestine, including the oral pathogens Gemella, Parvimonas, and Fusobacterium, were identified among the appendix samples. The prevalence of genera such as Fusobacterium could also be linked to the severity of inflammation of the organ. We conclude that the human appendix contains a robust and varied microbiota distinct from the microbiotas in other niches within the human microbiome. The microbial composition of the human appendix is subject to extreme variability and comprises a diversity of biota that may play an important, as-yet-unknown role in human health.

IMPORTANCE: There are currently limited data available on the microbial composition of the human appendix. It has been suggested, however, that it may serve as a "safe house" for commensal bacteria that can reinoculate the gut at need. The present study is the first comprehensive view of the microbial composition of the appendix as determined by high-throughput sequencing. We have determined that the human appendix contains a wealth of microbes, including members of 15 phyla. Important information regarding the associated bacterial diversity of the appendix which will help determine the role, if any, the appendix microbiota has in human health is presented.}, } @article {pmid23316946, year = {2013}, author = {Zhou, Y and Gao, H and Mihindukulasuriya, KA and La Rosa, PS and Wylie, KM and Vishnivetskaya, T and Podar, M and Warner, B and Tarr, PI and Nelson, DE and Fortenberry, JD and Holland, MJ and Burr, SE and Shannon, WD and Sodergren, E and Weinstock, GM}, title = {Biogeography of the ecosystems of the healthy human body.}, journal = {Genome biology}, volume = {14}, number = {1}, pages = {R1}, pmid = {23316946}, issn = {1474-760X}, support = {UH3 AI083265/AI/NIAID NIH HHS/United States ; U54 HG004968/HG/NHGRI NIH HHS/United States ; 5P30 DK052574/DK/NIDDK NIH HHS/United States ; U54HG004968/HG/NHGRI NIH HHS/United States ; UH3 AI094641/AI/NIAID NIH HHS/United States ; 1R01HG004857/HG/NHGRI NIH HHS/United States ; }, mesh = {Healthy Volunteers ; Humans ; *Microbiota ; Mouth/*microbiology ; Organ Specificity ; RNA, Ribosomal, 16S/genetics ; Skin/*microbiology ; Urogenital System/*microbiology ; }, abstract = {BACKGROUND: Characterizing the biogeography of the microbiome of healthy humans is essential for understanding microbial associated diseases. Previous studies mainly focused on a single body habitat from a limited set of subjects. Here, we analyzed one of the largest microbiome datasets to date and generated a biogeographical map that annotates the biodiversity, spatial relationships, and temporal stability of 22 habitats from 279 healthy humans.

RESULTS: We identified 929 genera from more than 24 million 16S rRNA gene sequences of 22 habitats, and we provide a baseline of inter-subject variation for healthy adults. The oral habitat has the most stable microbiota with the highest alpha diversity, while the skin and vaginal microbiota are less stable and show lower alpha diversity. The level of biodiversity in one habitat is independent of the biodiversity of other habitats in the same individual. The abundances of a given genus at a body site in which it dominates do not correlate with the abundances at body sites where it is not dominant. Additionally, we observed the human microbiota exhibit both cosmopolitan and endemic features. Finally, comparing datasets of different projects revealed a project-based clustering pattern, emphasizing the significance of standardization of metagenomic studies.

CONCLUSIONS: The data presented here extend the definition of the human microbiome by providing a more complete and accurate picture of human microbiome biogeography, addressing questions best answered by a large dataset of subjects and body sites that are deeply sampled by sequencing.}, } @article {pmid23314371, year = {2013}, author = {Hong, Y and Yang, HS and Chang, HC and Kim, HY}, title = {Comparison of bacterial community changes in fermenting kimchi at two different temperatures using a denaturing gradient gel electrophoresis analysis.}, journal = {Journal of microbiology and biotechnology}, volume = {23}, number = {1}, pages = {76-84}, doi = {10.4014/jmb.1210.10002}, pmid = {23314371}, issn = {1738-8872}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Brassica/*microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; Fermentation ; *Food Microbiology ; Hydrogen-Ion Concentration ; *Metagenome ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Temperature ; }, abstract = {A polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) technique followed by sequencing of the 16S rDNA fragments eluted from the bands of interest on denaturing gradient gels was used to monitor changes in the bacterial microflora of two commercial kimchi, salted cabbage, and ingredient mix samples during 30 days of fermentation at 4°C and 10°C. Leuconostoc (Lc.) was the dominant lactic acid bacteria (LAB) over Lactobacillus (Lb.) species at 4°C. Weissella confusa was detected in the ingredient mix and also in kimchi samples throughout fermentation in both samples at 4°C and 10°C. Lc. gelidum was detected as the dominant LAB at 4°C in both samples. The temperature affected the LAB profile of kimchi by varing the pH, which was primarily caused by the temperature-dependent competition among different LAB species in kimchi. At 4°C, the sample variations in pH and titratable acidity were more conspicuous owing to the delayed growth of LAB. Temperature affected only initial decreases in pH and initial increases in viable cell counts, but affected both the initial increases and final values of titratable acidity. The initial microflora in the kimchi sample was probably determined by the microflora of the ingredient mix, not by that of the salted cabbage. The microbial distributions in the samples used in this study resembled across the different kimchi samples and the different fermentation temperatures as the numbers of LAB increased and titratable acidity decreased.}, } @article {pmid23308385, year = {2013}, author = {Akondi, KB and Lakshmi, VV}, title = {Emerging trends in genomic approaches for microbial bioprospecting.}, journal = {Omics : a journal of integrative biology}, volume = {17}, number = {2}, pages = {61-70}, doi = {10.1089/omi.2012.0082}, pmid = {23308385}, issn = {1557-8100}, mesh = {Biodiversity ; Genomics/methods ; Metagenomics/methods/*trends ; Microbiology/*trends ; Oligonucleotide Array Sequence Analysis ; Real-Time Polymerase Chain Reaction ; }, abstract = {Microorganisms constitute two out of the three domains of life on earth. They exhibit vast biodiversity and metabolic versatility. This enables the microorganisms to inhabit and thrive in even the most extreme environmental conditions, making them all pervading. The magnitude of biodiversity observed among microorganisms substantially supersedes that exhibited by the eukaryotes. These characteristics make the microbial world a very lucrative and inexhaustible resource for prospecting novel bioactive molecules. Despite their vast potential, over 99% of the microbial world still remains to be explored. The primary reason for this is that the culture-dependent methods used in the laboratories are grossly insufficient, as they support the growth of under 1% of the microorganisms found in nature. This limitation necessitated the development of techniques to circumvent culture dependency and gain access to the outstanding majority of the microorganisms. The development of culture-independent techniques has essentially reshaped the study of microbial diversity and community dynamics. Application of genomic and metagenomic approaches is contributing substantially towards characterization of the real microbial diversity. The amenability of these techniques to high throughput has opened the doors to explore the vast number of "uncultivable" microbial forms in substantially lesser time. The present article provides an update on the recent technological advances and emerging trends in exploring microbial community.}, } @article {pmid23308262, year = {2013}, author = {Mizrahi-Man, O and Davenport, ER and Gilad, Y}, title = {Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e53608}, pmid = {23308262}, issn = {1932-6203}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; R01 HL092206/HL/NHLBI NIH HHS/United States ; HL092206/HL/NHLBI NIH HHS/United States ; P30DK42086/DK/NIDDK NIH HHS/United States ; }, mesh = {Bayes Theorem ; DNA Barcoding, Taxonomic/*methods/statistics & numerical data ; *Genes, Bacterial ; *Genes, rRNA ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Microbial Consortia/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*classification/genetics ; Research Design ; Sequence Analysis, DNA/*methods/statistics & numerical data ; }, abstract = {Massively parallel high throughput sequencing technologies allow us to interrogate the microbial composition of biological samples at unprecedented resolution. The typical approach is to perform high-throughout sequencing of 16S rRNA genes, which are then taxonomically classified based on similarity to known sequences in existing databases. Current technologies cause a predicament though, because although they enable deep coverage of samples, they are limited in the length of sequence they can produce. As a result, high-throughout studies of microbial communities often do not sequence the entire 16S rRNA gene. The challenge is to obtain reliable representation of bacterial communities through taxonomic classification of short 16S rRNA gene sequences. In this study we explored properties of different study designs and developed specific recommendations for effective use of short-read sequencing technologies for the purpose of interrogating bacterial communities, with a focus on classification using naïve Bayesian classifiers. To assess precision and coverage of each design, we used a collection of ∼8,500 manually curated 16S rRNA gene sequences from cultured bacteria and a set of over one million bacterial 16S rRNA gene sequences retrieved from environmental samples, respectively. We also tested different configurations of taxonomic classification approaches using short read sequencing data, and provide recommendations for optimal choice of the relevant parameters. We conclude that with a judicious selection of the sequenced region and the corresponding choice of a suitable training set for taxonomic classification, it is possible to explore bacterial communities at great depth using current technologies, with only a minimal loss of taxonomic resolution.}, } @article {pmid23308097, year = {2013}, author = {Stein, ED and White, BP and Mazor, RD and Miller, PE and Pilgrim, EM}, title = {Evaluating ethanol-based sample preservation to facilitate use of DNA barcoding in routine freshwater biomonitoring programs using benthic macroinvertebrates.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e51273}, pmid = {23308097}, issn = {1932-6203}, mesh = {Animals ; Aquatic Organisms/genetics ; Base Sequence ; Biodiversity ; DNA/*genetics/isolation & purification ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Electron Transport Complex IV/genetics ; Ethanol/*chemistry ; Gastropoda/*genetics ; Insect Proteins/genetics ; Insecta/*genetics ; Preservation, Biological/*methods ; }, abstract = {Molecular methods, such as DNA barcoding, have the potential to enhance biomonitoring programs worldwide. Altering routinely used sample preservation methods to protect DNA from degradation may pose a potential impediment to application of DNA barcoding and metagenomics for biomonitoring using benthic macroinvertebrates. Using higher volumes or concentrations of ethanol, requirements for shorter holding times, or the need to include additional filtering may increase cost and logistical constraints to existing biomonitoring programs. To address this issue we evaluated the efficacy of various ethanol-based sample preservation methods at maintaining DNA integrity. We evaluated a series of methods that were minimally modified from typical field protocols in order to identify an approach that can be readily incorporated into existing monitoring programs. Benthic macroinvertebrates were collected from a minimally disturbed stream in southern California, USA and subjected to one of six preservation treatments. Ten individuals from five taxa were selected from each treatment and processed to produce DNA barcodes from the mitochondrial gene cytochrome c oxidase I (COI). On average, we obtained successful COI sequences (i.e. either full or partial barcodes) for between 93-99% of all specimens across all six treatments. As long as samples were initially preserved in 95% ethanol, successful sequencing of COI barcodes was not affected by a low dilution ratio of 2∶1, transfer to 70% ethanol, presence of abundant organic matter, or holding times of up to six months. Barcoding success varied by taxa, with Leptohyphidae (Ephemeroptera) producing the lowest barcode success rate, most likely due to poor PCR primer efficiency. Differential barcoding success rates have the potential to introduce spurious results. However, routine preservation methods can largely be used without adverse effects on DNA integrity.}, } @article {pmid23303373, year = {2013}, author = {Nakao, R and Abe, T and Nijhof, AM and Yamamoto, S and Jongejan, F and Ikemura, T and Sugimoto, C}, title = {A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks.}, journal = {The ISME journal}, volume = {7}, number = {5}, pages = {1003-1015}, pmid = {23303373}, issn = {1751-7370}, mesh = {Animals ; Archaea/classification/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; Eukaryota/classification/genetics/isolation & purification ; Humans ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; Tick-Borne Diseases/microbiology/parasitology/virology ; Ticks/classification/*microbiology/*parasitology/virology ; Viruses/classification/genetics/isolation & purification ; }, abstract = {Ticks transmit a variety of viral, bacterial and protozoal pathogens, which are often zoonotic. The aim of this study was to identify diverse tick microbiomes, which may contain as-yet unidentified pathogens, using a metagenomic approach. DNA prepared from bacteria/archaea-enriched fractions obtained from seven tick species, namely Amblyomma testudinarium, Amblyomma variegatum, Haemaphysalis formosensis, Haemaphysalis longicornis, Ixodes ovatus, Ixodes persulcatus and Ixodes ricinus, was subjected to pyrosequencing after whole-genome amplification. The resulting sequence reads were phylotyped using a Batch Learning Self-Organizing Map (BLSOM) program, which allowed phylogenetic estimation based on similarity of oligonucleotide frequencies, and functional annotation by BLASTX similarity searches. In addition to bacteria previously associated with human/animal diseases, such as Anaplasma, Bartonella, Borrelia, Ehrlichia, Francisella and Rickettsia, BLSOM analysis detected microorganisms belonging to the phylum Chlamydiae in some tick species. This was confirmed by pan-Chlamydia PCR and sequencing analysis. Gene sequences associated with bacterial pathogenesis were also identified, some of which were suspected to originate from horizontal gene transfer. These efforts to construct a database of tick microbes may lead to the ability to predict emerging tick-borne diseases. Furthermore, a comprehensive understanding of tick microbiomes will be useful for understanding tick biology, including vector competency and interactions with pathogens and symbionts.}, } @article {pmid23300721, year = {2012}, author = {Setati, ME and Jacobson, D and Andong, UC and Bauer, FF}, title = {The vineyard yeast microbiome, a mixed model microbial map.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e52609}, pmid = {23300721}, issn = {1932-6203}, mesh = {Agriculture ; Biodiversity ; DNA, Fungal/genetics ; *Metagenome ; Models, Biological ; Molecular Typing ; Mycological Typing Techniques ; Principal Component Analysis ; Vitis/*microbiology ; Wine/microbiology ; Yeasts/genetics/*isolation & purification/metabolism ; }, abstract = {Vineyards harbour a wide variety of microorganisms that play a pivotal role in pre- and post-harvest grape quality and will contribute significantly to the final aromatic properties of wine. The aim of the current study was to investigate the spatial distribution of microbial communities within and between individual vineyard management units. For the first time in such a study, we applied the Theory of Sampling (TOS) to sample gapes from adjacent and well established commercial vineyards within the same terroir unit and from several sampling points within each individual vineyard. Cultivation-based and molecular data sets were generated to capture the spatial heterogeneity in microbial populations within and between vineyards and analysed with novel mixed-model networks, which combine sample correlations and microbial community distribution probabilities. The data demonstrate that farming systems have a significant impact on fungal diversity but more importantly that there is significant species heterogeneity between samples in the same vineyard. Cultivation-based methods confirmed that while the same oxidative yeast species dominated in all vineyards, the least treated vineyard displayed significantly higher species richness, including many yeasts with biocontrol potential. The cultivatable yeast population was not fully representative of the more complex populations seen with molecular methods, and only the molecular data allowed discrimination amongst farming practices with multivariate and network analysis methods. Importantly, yeast species distribution is subject to significant intra-vineyard spatial fluctuations and the frequently reported heterogeneity of tank samples of grapes harvested from single vineyards at the same stage of ripeness might therefore, at least in part, be due to the differing microbiota in different sections of the vineyard.}, } @article {pmid23297252, year = {2013}, author = {Bermingham, EN and Young, W and Kittelmann, S and Kerr, KR and Swanson, KS and Roy, NC and Thomas, DG}, title = {Dietary format alters fecal bacterial populations in the domestic cat (Felis catus).}, journal = {MicrobiologyOpen}, volume = {2}, number = {1}, pages = {173-181}, pmid = {23297252}, issn = {2045-8827}, mesh = {Animals ; Bacteria/*classification/*isolation & purification ; *Biota ; Cats ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Diet/*methods ; Feces/*microbiology ; Female ; Male ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The effects of short-term (5-week) exposure to wet or dry diets on fecal bacterial populations in the cat were investigated. Sixteen mixed-sex, neutered, domestic short-haired cats (mean age = 6 years; mean bodyweight = 3.4 kg) were randomly allocated to wet or dry diets in a crossover design. Fecal bacterial DNA was isolated and bacterial 16S rRNA gene amplicons generated and analyzed by 454 Titanium pyrosequencing. Cats fed dry diets had higher abundances (P < 0.05) of Actinobacteria (16.5% vs. 0.1%) and lower abundances of Fusobacteria (0.3% vs. 23.1%) and Proteobacteria (0.4% vs. 1.1%) compared with cats fed the wet diet. Of the 46 genera identified, 30 were affected (P < 0.05) by diet, with higher abundances of Lactobacillus (31.8% vs. 0.1%), Megasphaera (23.0% vs. 0.0%), and Olsenella (16.4% vs. 0.0%), and lower abundances of Bacteroides (0.6% vs. 5.7%) and Blautia (0.3% vs. 2.3%) in cats fed the dry diet compared with cats fed the wet diet. These results demonstrate that short-term dietary exposure to diet leads to large shifts in fecal bacterial populations that have the potential to affect the ability of the cat to process macronutrients in the diet.}, } @article {pmid23296358, year = {2013}, author = {Foxman, B and Rosenthal, M}, title = {Implications of the human microbiome project for epidemiology.}, journal = {American journal of epidemiology}, volume = {177}, number = {3}, pages = {197-201}, pmid = {23296358}, issn = {1476-6256}, support = {R01 DE014899/DE/NIDCR NIH HHS/United States ; T32 AI049816/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/genetics/isolation & purification ; Epidemiology/*organization & administration ; Fungi/genetics/isolation & purification ; Humans ; *Metagenome ; Microbial Consortia ; Polymerase Chain Reaction ; Risk Factors ; Time Factors ; Viruses/genetics/isolation & purification ; }, abstract = {The structure and function of microorganisms that live in and on us, the human microbiota, are a tremendous resource. Microbiota may help to explain individual variability in health outcomes and be a source of new biomarkers for environmental exposures and of novel prognostic and diagnostic indicators. The increase in availability of low-cost, high-throughput techniques makes it relatively straightforward to include microbiota assessments in epidemiologic studies. With the recent joint publications of the findings of the Human Microbiome Consortium and related studies, the consequent surge of interest in microbiome research, and remarkable media attention, the time is ripe for epidemiologists to contribute their expertise to and translate results of microbiota research for population health.}, } @article {pmid23291779, year = {2013}, author = {Dubourg, G and Lagier, JC and Armougom, F and Robert, C and Hamad, I and Brouqui, P and Raoult, D}, title = {The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {32}, number = {5}, pages = {637-645}, pmid = {23291779}, issn = {1435-4373}, mesh = {Antitubercular Agents/pharmacology/therapeutic use ; Bacteriological Techniques/*methods ; DNA, Bacterial/analysis/genetics/isolation & purification ; Fatal Outcome ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenome/drug effects/genetics/*physiology ; Metagenomics/methods ; Microbial Sensitivity Tests ; Microbiota/drug effects/*physiology ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 18S ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Tuberculosis, Multidrug-Resistant/*drug therapy/*microbiology ; }, abstract = {Gut microbiota consists of 10(10) bacteria per gram of stool. Many antibiotic regimens induce a reduction in both the diversity and the abundance of the gut flora. We analyzed one stool sample collected from a patient treated for drug-resistant Mycobacterium tuberculosis and who ultimately died from pneumonia due to a Streptococcus pneumoniae 10 months later. We performed microscopic observation, used 70 culture conditions (microbial culturomics) with identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) and 16S rRNA amplification and sequencing, pyrosequencing, and 18S rRNA amplification and clone sequencing. Electron and optical microscopic observations revealed the presence of yeast, but no bacterial species were observed. By culture, only 39 bacterial species were identified, including one new species, as well as three species that have not been previously observed in the human gut. The pyrosequencing showed only 18 phylotypes, detecting a lower number of bacterial species than the culture techniques. Only two phylotypes overlapped with culturomics. In contrast, an amount of chloroplasts was found. Additionally, specific molecular eukaryote detection found three fungal species. We recovered, for the first time, more cultivable than non-cultivable bacterial species in a patient with a low bacterial load in the gut, demonstrating the depth bias of pyrosequencing. We propose that the desertification of gut microbiota in this patient is a reflection of the total body microbiota and may have contributed to the invasive infection of S. pneumoniae. This finding suggests that caution should be applied when treating patients with broad-spectrum antibiotics, and preventive measures should be taken in order to avoid invasive infection.}, } @article {pmid23286938, year = {2013}, author = {Boyton, RJ and Reynolds, CJ and Quigley, KJ and Altmann, DM}, title = {Immune mechanisms and the impact of the disrupted lung microbiome in chronic bacterial lung infection and bronchiectasis.}, journal = {Clinical and experimental immunology}, volume = {171}, number = {2}, pages = {117-123}, pmid = {23286938}, issn = {1365-2249}, support = {BB/H005439/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Bacterial Infections/complications/*immunology ; Bronchiectasis/*immunology/microbiology/prevention & control ; CD4-Positive T-Lymphocytes/immunology ; Chronic Disease ; Genetic Predisposition to Disease ; HLA-C Antigens/genetics/immunology ; Humans ; Killer Cells, Natural/immunology ; Lung/immunology/*microbiology ; Lung Diseases/immunology/microbiology ; Metagenome/*immunology ; Microbial Consortia ; Polymorphism, Genetic ; Receptors, KIR/genetics/immunology ; }, abstract = {Recent studies analysing immunogenetics and immune mechanisms controlling susceptibility to chronic bacterial infection in bronchiectasis implicate dysregulated immunity in conjunction with chronic bacterial infection. Bronchiectasis is a structural pathological end-point with many causes and disease associations. In about half of cases it is termed idiopathic, because it is of unknown aetiology. Bronchiectasis is proposed to result from a 'vicious cycle' of chronic bacterial infection and dysregulated inflammation. Paradoxically, both immune deficiency and excess immunity, either in the form of autoimmunity or excessive inflammatory activation, can predispose to disease. It appears to be a part of the spectrum of inflammatory, autoimmune and atopic conditions that have increased in prevalence through the 20th century, attributed variously to the hygiene hypothesis or the 'missing microbiota'. Immunogenetic studies showing a strong association with human leucocyte antigen (HLA)-Cw*03 and HLA-C group 1 homozygosity and combinational analysis of HLA-C and killer immunoglobulin-like receptors (KIR) genes suggests a shift towards activation of natural killer (NK) cells leading to lung damage. The association with HLA-DR1, DQ5 implicates a role for CD4 T cells, possibly operating through influence on susceptibility to specific pathogens. We hypothesize that disruption of the lung microbial ecosystem, by infection, inflammation and/or antibiotic therapy, creates a disturbed, simplified, microbial community ('disrupted microbiota') with downstream consequences for immune function. These events, acting with excessive NK cell activation, create a highly inflammatory lung environment that, in turn, permits the further establishment and maintenance of chronic infection dominated by microbial pathogens. This review discusses the implication of these concepts for the development of therapeutic interventions.}, } @article {pmid23286760, year = {2013}, author = {Ding, T and Palmer, MW and Melcher, U}, title = {Community terminal restriction fragment length polymorphisms reveal insights into the diversity and dynamics of leaf endophytic bacteria.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {1}, pmid = {23286760}, issn = {1471-2180}, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; DNA Fingerprinting ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Endophytes/*classification/genetics ; *Metagenome ; Oklahoma ; Plant Leaves/*microbiology ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Plant endophytic bacteria play an important role benefiting plant growth or being pathogenic to plants or organisms that consume those plants. Multiple species of bacteria have been found co-inhabiting plants, both cultivated and wild, with viruses and fungi. For these reasons, a general understanding of plant endophytic microbial communities and their diversity is necessary. A key issue is how the distributions of these bacteria vary with location, with plant species, with individual plants and with plant growing season.

RESULTS: Five common plant species were collected monthly for four months in the summer of 2010, with replicates from four different sampling sites in the Tallgrass Prairie Preserve in Osage County, Oklahoma, USA. Metagenomic DNA was extracted from ground, washed plant leaf samples, and fragments of the bacterial 16S rDNA genes were amplified for analysis of terminal restriction fragment length polymorphism (T-RFLP). We performed mono-digestion T-RFLP with restriction endonuclease DdeI, to reveal the structures of leaf endophytic bacterial communities, to identify the differences between plant-associated bacterial communities in different plant species or environments, and to explore factors affecting the bacterial distribution. We tested the impacts of three major factors on the leaf endophytic bacterial communities, including host plant species, sampling dates and sampling locations.

CONCLUSIONS: Results indicated that all of the three factors were significantly related (α = 0.05) to the distribution of leaf endophytic bacteria, with host species being the most important, followed by sampling dates and sampling locations.}, } @article {pmid23284876, year = {2012}, author = {La Rosa, PS and Brooks, JP and Deych, E and Boone, EL and Edwards, DJ and Wang, Q and Sodergren, E and Weinstock, G and Shannon, WD}, title = {Hypothesis testing and power calculations for taxonomic-based human microbiome data.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e52078}, pmid = {23284876}, issn = {1932-6203}, support = {U54 HG004968/HG/NHGRI NIH HHS/United States ; UH2 AI083265/AI/NIAID NIH HHS/United States ; 1UH2AI083265/AI/NIAID NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Algorithms ; Bacteria/classification/genetics ; Biodiversity ; Computational Biology ; Female ; Gingiva/microbiology ; Humans ; Male ; *Metagenome ; *Models, Statistical ; Reproducibility of Results ; Young Adult ; }, abstract = {This paper presents new biostatistical methods for the analysis of microbiome data based on a fully parametric approach using all the data. The Dirichlet-multinomial distribution allows the analyst to calculate power and sample sizes for experimental design, perform tests of hypotheses (e.g., compare microbiomes across groups), and to estimate parameters describing microbiome properties. The use of a fully parametric model for these data has the benefit over alternative non-parametric approaches such as bootstrapping and permutation testing, in that this model is able to retain more information contained in the data. This paper details the statistical approaches for several tests of hypothesis and power/sample size calculations, and applies them for illustration to taxonomic abundance distribution and rank abundance distribution data using HMP Jumpstart data on 24 subjects for saliva, subgingival, and supragingival samples. Software for running these analyses is available.}, } @article {pmid23284833, year = {2012}, author = {Hallin, S and Welsh, A and Stenström, J and Hallet, S and Enwall, K and Bru, D and Philippot, L}, title = {Soil functional operating range linked to microbial biodiversity and community composition using denitrifiers as model guild.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e51962}, pmid = {23284833}, issn = {1932-6203}, mesh = {Bacteria/classification/genetics ; *Biodiversity ; *Ecosystem ; *Environment ; Genotype ; Metagenome/genetics ; *Models, Theoretical ; Phylogeny ; Salts/chemistry ; Soil/chemistry ; *Soil Microbiology ; Sweden ; Temperature ; }, abstract = {Soil microorganisms are key players in biogeochemical cycles. Yet, there is no consistent view on the significance of microbial biodiversity for soil ecosystem functioning. According to the insurance hypothesis, declines in ecosystem functioning due to reduced biodiversity are more likely to occur under fluctuating, extreme or rapidly changing environmental conditions. Here, we compare the functional operating range, a new concept defined as the complete range of environmental conditions under which soil microbial communities are able to maintain their functions, between four naturally assembled soil communities from a long-term fertilization experiment. A functional trait approach was adopted with denitrifiers involved in nitrogen cycling as our model soil community. Using short-term temperature and salt gradients, we show that the functional operating range was broader and process rates were higher when the soil community was phylogenetically more diverse. However, key bacterial genotypes played an important role for maintaining denitrification as an ecosystem functioning under certain conditions.}, } @article {pmid23279728, year = {2013}, author = {Aziz, Q and Doré, J and Emmanuel, A and Guarner, F and Quigley, EM}, title = {Gut microbiota and gastrointestinal health: current concepts and future directions.}, journal = {Neurogastroenterology and motility}, volume = {25}, number = {1}, pages = {4-15}, doi = {10.1111/nmo.12046}, pmid = {23279728}, issn = {1365-2982}, mesh = {Gastrointestinal Diseases/*microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenome ; }, abstract = {BACKGROUND: The microbial community of the human gut - the enteric microbiota - plays a critical role in functions that sustain health and is a positive asset in host defenses. In recent years, our understanding of this so-called human 'super organism' has advanced, following characterization of fecal metagenomes which identified three core bacterial enterotypes, and based on basic and clinical research into the impact and consequences of microbiota biodiversity and change on gastrointestinal disorders and diseases.

PURPOSE: This article considers current knowledge and future perspectives on the make-up and function of human gut microbiota, with a particular focus on altered microbiota and gastrointestinal disorders, nutritional influences on the gut microbiota, and the consequences for gastrointestinal health, as well as improved understanding of gut-microbiota-brain communication.}, } @article {pmid23276768, year = {2013}, author = {Sha, S and Xu, B and Wang, X and Zhang, Y and Wang, H and Kong, X and Zhu, H and Wu, K}, title = {The biodiversity and composition of the dominant fecal microbiota in patients with inflammatory bowel disease.}, journal = {Diagnostic microbiology and infectious disease}, volume = {75}, number = {3}, pages = {245-251}, doi = {10.1016/j.diagmicrobio.2012.11.022}, pmid = {23276768}, issn = {1879-0070}, mesh = {Adult ; Aged ; Case-Control Studies ; Colitis, Ulcerative/*microbiology ; Crohn Disease/*microbiology ; DNA, Bacterial/*analysis/genetics ; Denaturing Gradient Gel Electrophoresis ; Feces/*microbiology ; Female ; Gene Dosage ; *Genetic Variation ; Humans ; Male ; *Metagenome ; Middle Aged ; RNA, Ribosomal, 16S/analysis/genetics ; Real-Time Polymerase Chain Reaction ; Young Adult ; }, abstract = {Clinical and experimental observations in animal models indicate that intestinal commensal bacteria are involved in the initiation and amplification of inflammatory bowel disease (IBD). As the majority of colonic bacteria cannot be identified by culture techniques, the aim of this study was to use sequence-based methods to investigate and characterize the composition of the dominant fecal microbiota in both patients with inflammatory bowel disease and healthy subjects. Fecal microbiota was isolated and quantified using real-time quantitative polymerase chain reaction. Denaturing gradient gel electrophoresis (DGGE) of 16S rDNA was used to evaluate the diversity of the dominant species. Analysis of individual bacterial groups showed a greater change in the fecal microbiota of patients with IBD, especially in those with active ulcerative colitis and active Crohn's disease. DGGE demonstrated the diversity of microbial flora in ulcerative colitis and Crohn's disease was less than in healthy subjects. Our results provide a better understanding of changes in fecal microbiota among patients with inflammatory bowel disease.}, } @article {pmid24832664, year = {2013}, author = {Gokul, JK and Valverde, A and Tuffin, M and Cary, SC and Cowan, DA}, title = {Micro-eukaryotic diversity in hypolithons from miers valley, antarctica.}, journal = {Biology}, volume = {2}, number = {1}, pages = {331-340}, pmid = {24832664}, issn = {2079-7737}, abstract = {The discovery of extensive and complex hypolithic communities in both cold and hot deserts has raised many questions regarding their ecology, biodiversity and relevance in terms of regional productivity. However, most hypolithic research has focused on the bacterial elements of the community. This study represents the first investigation of micro-eukaryotic communities in all three hypolith types. Here we show that Antarctic hypoliths support extensive populations of novel uncharacterized bryophyta, fungi and protists and suggest that well known producer-decomposer-predator interactions may create the necessary conditions for hypolithic productivity in Antarctic deserts.}, } @article {pmid24672981, year = {2013}, author = {Burcelin, R}, title = {[New insights into adipose cell biology].}, journal = {Bulletin de l'Academie nationale de medecine}, volume = {197}, number = {1}, pages = {79-92}, pmid = {24672981}, issn = {0001-4079}, mesh = {Adipocytes/*physiology ; Adipose Tissue/physiology ; Animals ; Diabetes Mellitus, Type 2/etiology ; Humans ; Incretins/*physiology ; Intestinal Mucosa/*metabolism ; Intestines/microbiology ; Mice ; Microbiota/*physiology ; }, abstract = {Our research focuses on the molecular mechanisms controlling glycemia in healthy and diabetic individuals. Diabetes is now considered as a worldwide epidemic by WHO, and is predicted to affect several hundred million people in the near future. Current therapies have failed to prevent or control hyperglycemia, as well as the deleterious cardiovascular consequences of the disease have increased. New paradigms are thus needed to develop novel therapeutic strategies. Over the last 15 years, we have been studying the intestine as a major regulator of the integrated cross-talk between the brain, liver, pancreas, muscles and blood vessels required for glycemic control. As a first example, we identified that during a meal the glucose transporter GLUT2 and the intestinal hormone glucagon-like peptide-1 (GLP-1) are involved in glucose detection by the entero-portal system. This was done using highly innovative experimental techniques in the awake free moving mouse. We then found that the enteric-vagal nervous system transmits this nutritional information towards the brain stem and hypothalamus, where leptin, neuropeptide Y and GLP-1 relay the enteric signal to control the endocrine pancreas (insulin-glucagon secretion), the liver (glycogen metabolism), the vascular system (vasodilation, arterial flow), and muscle metabolism. This "anticipatory metabolic reflex " is altered during diabetes and might thus represent a new pharmacological target. Subsequently, while investigating the molecular mechanisms responsible for regulating this new physiological pathway, we discovered that a fat-rich diabetogenic diet alters the intestinal microbiota and permeability. This leads to an increase in the concentration of plasma lipopolysaccharides (LPS), which causes metabolic endotoxemia responsible for the induction of low-grade inflammation that characterizes type 2 diabetes, insulin resistance, adipose tissue development and hepatic lipid storage. We then showed that bacteria can be translocated from the intestine towards tissues and the bloodstream. Bacterial DNA present in blood was found to be predictive of diabetes, 6-9 years before disease onset (patent), presenting new molecular targets in the microbiota-host relationship. This should enable the scientific community to discover new functional relationships between the genome and metagenome and thus to develop original preventive and therapeutic strategies for metabolic diseases. Four biotechnology companies have already been created on the basis of our findings.}, } @article {pmid23274977, year = {2012}, author = {Han, J and Jung, J and Hyun, S and Park, H and Park, W}, title = {Effects of nutritional input and diesel contamination on soil enzyme activities and microbial communities in Antarctic soils.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {50}, number = {6}, pages = {916-924}, pmid = {23274977}, issn = {1976-3794}, mesh = {Alkaline Phosphatase/chemistry/genetics ; Antarctic Regions ; Bacteria/classification/genetics ; Biodiversity ; DNA ; Ecosystem ; Environment ; Enzymes/*chemistry ; *Gasoline/adverse effects ; Gene Dosage ; Metagenome/genetics ; Oxidoreductases/chemistry/genetics ; Phylogeny ; RNA, Ribosomal, 16S ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants/adverse effects ; }, abstract = {Pollution of Antarctic soils may be attributable to increased nutritional input and diesel contamination via anthropogenic activities. To investigate the effect of these environmental changes on the Antarctic terrestrial ecosystem, soil enzyme activities and microbial communities in 3 types of Antarctic soils were evaluated. The activities of alkaline phosphomonoesterase and dehydrogenase were dramatically increased, whereas the activities of β-glucosidase, urease, arylsulfatase, and fluorescein diacetate hydrolysis were negligible. Alkaline phosphomonoesterase and dehydrogenase activities in the 3 types of soils increased 3- to 10-fold in response to nutritional input, but did not increase in the presence of diesel contamination. Consistent with the enzymatic activity data, increased copy numbers of the phoA gene, encoding an alkaline phosphomonoesterase, and the 16S rRNA gene were verified using quantitative real-time polymerase chain reaction. Interestingly, dehydrogenase activity and 16S rRNA gene copy number increased slightly after 30 days, even under diesel contamination, probably because of adaptation of the bacterial population. Intact Antarctic soils showed a predominance of Actinobacteria phylum (mostly Pseudonorcarida species) and other phyla such as Proteobacteria, Chloroflexi, Planctomycetes, Firmicutes, and Verrucomicrobia were present in successively lower proportions. Nutrient addition might act as a selective pressure on the bacterial community, resulting in the prevalence of Actinobacteria phylum (mostly Arthrobacter species). Soils contaminated by diesel showed a predominance of Proteobacteria phylum (mostly Phyllobacterium species), and other phyla such as Actinobacteria, Bacteroidetes, Planctomycetes, and Gemmatimonadetes were present in successively lower proportions. Our data reveal that nutritional input has a dramatic impact on bacterial communities in Antarctic soils and that diesel contamination is likely toxic to enzymes in this population.}, } @article {pmid23271066, year = {2013}, author = {Jeurink, PV and van Bergenhenegouwen, J and Jiménez, E and Knippels, LM and Fernández, L and Garssen, J and Knol, J and Rodríguez, JM and Martín, R}, title = {Human milk: a source of more life than we imagine.}, journal = {Beneficial microbes}, volume = {4}, number = {1}, pages = {17-30}, doi = {10.3920/BM2012.0040}, pmid = {23271066}, issn = {1876-2891}, mesh = {*Biota ; Female ; Humans ; Infant, Newborn ; *Metagenome ; Milk, Human/*microbiology ; Pregnancy ; }, abstract = {The presence of bacteria in human milk has been acknowledged since the seventies. For a long time, microbiological analysis of human milk was only performed in case of infections and therefore the presence of non-pathogenic bacteria was yet unknown. During the last decades, the use of more sophisticated culture-dependent and -independent techniques, and the steady development of the -omic approaches are opening up the new concept of the 'milk microbiome', a complex ecosystem with a greater diversity than previously anticipated. In this review, possible mechanisms by which bacteria can reach the mammary gland (contamination versus active migration) are discussed. In addition, the potential roles of human milk for both infant and maternal health are summarised. A better understanding of the link between the milk microbiome and health benefit, the potential factors influencing this relationship and whether or not it can be influenced by nutrition is required to open new avenues in the field of pregnancy and lactation.}, } @article {pmid23271065, year = {2013}, author = {Jin, JS and Touyama, M and Kibe, R and Tanaka, Y and Benno, Y and Kobayashi, T and Shimakawa, M and Maruo, T and Toda, T and Matsuda, I and Tagami, H and Matsumoto, M and Seo, G and Chonan, O and Benno, Y}, title = {Analysis of the human intestinal microbiota from 92 volunteers after ingestion of identical meals.}, journal = {Beneficial microbes}, volume = {4}, number = {2}, pages = {187-193}, doi = {10.3920/BM2012.0045}, pmid = {23271065}, issn = {1876-2891}, mesh = {Adult ; *Biodiversity ; Cluster Analysis ; DNA Fingerprinting ; *Eating ; Feces/microbiology ; Human Experimentation ; Humans ; Japan ; Male ; *Meals ; Metagenome/*drug effects ; Middle Aged ; Polymorphism, Restriction Fragment Length ; Young Adult ; }, abstract = {The intestinal microbiota composition of 92 volunteers living in Japan was identified following the consumption of 'identical meals' (1,879 kcal/day) for 3 days. When faecal samples were analysed by terminal restriction fragment length polymorphism with several primer-restriction enzyme systems and then clustered, the patterns could be divided into 2 clusters. Contribution tests and partition modelling showed that OTU211 of the 35f-MspI system and OTU237 of the 35f-AluI system were key factors in the distribution of these groups. However, significant differences among these groups in terms of body mass index and age were not observed.}, } @article {pmid23270920, year = {2013}, author = {Satoh, T and Odamaki, T and Namura, M and Shimizu, T and Iwatsuki, K and Nishimoto, M and Kitaoka, M and Xiao, JZ}, title = {In vitro comparative evaluation of the impact of lacto-N-biose I, a major building block of human milk oligosaccharides, on the fecal microbiota of infants.}, journal = {Anaerobe}, volume = {19}, number = {}, pages = {50-57}, doi = {10.1016/j.anaerobe.2012.12.007}, pmid = {23270920}, issn = {1095-8274}, mesh = {Acetic Acid/metabolism ; Acetylglucosamine/*analogs & derivatives/metabolism ; *Biota ; Feces/*microbiology ; Humans ; Infant ; Lactic Acid/metabolism ; Metagenome/*physiology ; Milk, Human/chemistry ; }, abstract = {Lacto-N-biose I (LNB) is a potential factor for the selective growth of bifidobacteria. We previously reported that the species of bifidobacteria predominant in infant intestines might use LNB. We aimed to assess the prebiotic properties of LNB in comparison to other oligosaccharides using an in vitro fermentation system. Stool samples from formula-fed infants were inoculated with media containing a sole carbon source of 1% LNB, lactulose, raffinose, galactooligosaccharide, or mannanoligosaccharides. LNB significantly increased the total bifidobacterial population similarly to other oligosaccharides, but induced a significantly higher level of Bifidobacterium bifidum in comparison to other oligosaccharides. Furthermore, significantly lower concentrations of lactic acid and significantly higher concentrations of acetic acid were produced in cultures containing LNB in comparison to cultures that contained other oligosaccharides. In conclusion, LNB might have a beneficial effect on the fecal microbiota of infants and is a potential prebiotic for application in infant foods or supplements.}, } @article {pmid23269735, year = {2013}, author = {Fite, A and Macfarlane, S and Furrie, E and Bahrami, B and Cummings, JH and Steinke, DT and Macfarlane, GT}, title = {Longitudinal analyses of gut mucosal microbiotas in ulcerative colitis in relation to patient age and disease severity and duration.}, journal = {Journal of clinical microbiology}, volume = {51}, number = {3}, pages = {849-856}, pmid = {23269735}, issn = {1098-660X}, mesh = {Adult ; Age Factors ; Aged ; Aged, 80 and over ; *Biodiversity ; Biopsy ; Colitis, Ulcerative/*microbiology/*pathology ; Female ; Humans ; Intestinal Mucosa/*microbiology/*pathology ; Longitudinal Studies ; Male ; *Metagenome ; Middle Aged ; Severity of Illness Index ; Time Factors ; Young Adult ; }, abstract = {Bacteria belonging to the normal colonic microbiota are associated with the etiology of ulcerative colitis (UC). Although several mucosal species have been implicated in the disease process, the organisms and mechanisms involved are unknown. The aim of this investigation was to characterize mucosal biofilm communities over time and to determine the relationship of these bacteria to patient age and disease severity and duration. Multiple rectal biopsy specimens were taken from 33 patients with active UC over a period of 1 year. Real-time PCR was used to quantify mucosal bacteria in UC patients compared to 18 noninflammatory bowel disease controls, and the relationship between indicators of disease severity and bacterial colonization was evaluated by linear regression analysis. Significant differences were detected in bacterial populations on the UC mucosa and in the control group, which varied over the study period. High clinical activity indices (CAI) and sigmoidoscopy scores (SS) were associated with enterobacteria, desulfovibrios, type E Clostridium perfringens, and Enterococcus faecalis, whereas the reverse was true for Clostridium butyricum, Ruminococcus albus, and Eubacterium rectale. Lactobacillus and bifidobacterium numbers were linked with low CAI. Only E. rectale and Clostridium clostridioforme had a high age dependence. These findings demonstrated that longitudinal variations in mucosal bacterial populations occur in UC and that bacterial community structure is related to disease severity.}, } @article {pmid23269455, year = {2013}, author = {López-Pérez, M and Gonzaga, A and Martin-Cuadrado, AB and López-García, P and Rodriguez-Valera, F and Kimes, NE}, title = {Intra- and intergenomic variation of ribosomal RNA operons in concurrent Alteromonas macleodii strains.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {720-730}, pmid = {23269455}, issn = {1432-184X}, mesh = {Alteromonas/chemistry/classification/*genetics/isolation & purification ; Base Sequence ; Biodiversity ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/*genetics ; *Genetic Variation ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Operon ; Phylogeny ; RNA, Ribosomal/chemistry/*genetics ; Seawater/*microbiology ; }, abstract = {Biodiversity estimates based on ribosomal operon sequence diversity rely on the premise that a sequence is characteristic of a single specific taxon or operational taxonomic unit (OTU). Here, we have studied the sequence diversity of 14 ribosomal RNA operons (rrn) contained in the genomes of two isolates (five operons in each genome) and four metagenomic fosmids, all from the same seawater sample. Complete sequencing of the isolate genomes and the fosmids establish that they represent strains of the same species, Alteromonas macleodii, with average nucleotide identity (ANI) values >97 %. Nonetheless, we observed high levels of intragenomic heterogeneity (i.e., variability between operons of a single genome) affecting multiple regions of the 16S and 23S rRNA genes as well as the internally transcribed spacer 1 (ITS-1) region. Furthermore, the ribosomal operons exhibited intergenomic heterogeneity (i.e., variability between operons located in separate genomes) in each of these regions, compounding the variability. Our data reveal the extensive heterogeneity observed in natural populations of A. macleodii at a single point in time and support the idea that distinct lineages of A. macleodii exist in the deep Mediterranean. These findings highlight the potential of rRNA fingerprinting methods to misrepresent species diversity while simultaneously failing to recognize the ecological significance of individual strains.}, } @article {pmid23266580, year = {2013}, author = {Ladirat, SE and Schols, HA and Nauta, A and Schoterman, MH and Keijser, BJ and Montijn, RC and Gruppen, H and Schuren, FH}, title = {High-throughput analysis of the impact of antibiotics on the human intestinal microbiota composition.}, journal = {Journal of microbiological methods}, volume = {92}, number = {3}, pages = {387-397}, doi = {10.1016/j.mimet.2012.12.011}, pmid = {23266580}, issn = {1872-8359}, mesh = {Adult ; Anti-Bacterial Agents/*pharmacology ; Bacteriological Techniques/methods ; *Biota ; Feces/*microbiology ; Female ; High-Throughput Screening Assays/methods ; Humans ; Male ; Metagenome/*drug effects ; Microarray Analysis/methods ; Middle Aged ; Models, Theoretical ; Phylogeny ; }, abstract = {Antibiotic treatments can lead to a disruption of the human microbiota. In this in-vitro study, the impact of antibiotics on adult intestinal microbiota was monitored in a new high-throughput approach: a fermentation screening-platform was coupled with a phylogenetic microarray analysis (Intestinal-chip). Fecal inoculum from healthy adults was exposed in a fermentation screening-platform to seven widely-used antibiotics during 24h in-vitro fermentation and the microbiota composition was subsequently determined with the Intestinal-chip. Phylogenetic microarray analysis was first verified to be reliable with respect to variations in the total number of bacteria and presence of dead (or inactive) cells. Intestinal-chip analysis was then used to identify and compare shifts in the intestinal microbial composition after exposure to low and high dose (1μgml(-1) and 10μgml(-1)) antibiotics. Observed shifts on family, genus and species level were both antibiotic and dose dependent. Stronger changes in microbiota composition were observed with higher doses. Shifts mainly concerned the bacterial groups Bacteroides, Bifidobacterium, Clostridium, Enterobacteriaceae, and Lactobacillus. Within bacterial groups, specific antibiotics were shown to differentially impact related species. The combination of the in-vitro fermentation screening platform with the phylogenetic microarray read-outs has shown to be reliable to simultaneously analyze the effects of several antibiotics on intestinal microbiota.}, } @article {pmid23263952, year = {2013}, author = {Yarwood, S and Brewer, E and Yarwood, R and Lajtha, K and Myrold, D}, title = {Soil microbe active community composition and capability of responding to litter addition after 12 years of no inputs.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {4}, pages = {1385-1392}, pmid = {23263952}, issn = {1098-5336}, mesh = {Biomass ; *Biota ; DNA/genetics/isolation & purification ; Metagenome ; Plant Leaves/metabolism ; Pseudotsuga/metabolism ; RNA/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 28S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; Time Factors ; }, abstract = {One explanation given for the high microbial diversity found in soils is that they contain a large inactive biomass that is able to persist in soils for long periods of time. This persistent microbial fraction may help to buffer the functionality of the soil community during times of low nutrients by providing a reservoir of specialized functions that can be reactivated when conditions improve. A study was designed to test the hypothesis: in soils lacking fresh root or detrital inputs, microbial community composition may persist relatively unchanged. Upon addition of new inputs, this community will be stimulated to grow and break down litter similarly to control soils. Soils from two of the Detrital Input and Removal Treatments (DIRT) at the H. J. Andrews Experimental Forest, the no-input and control treatment plots, were used in a microcosm experiment where Douglas-fir needles were added to soils. After 3 and 151 days of incubation, soil microbial DNA and RNA was extracted and characterized using quantitative PCR (qPCR) and 454 pyrosequencing. The abundance of 16S and 28S gene copies and RNA copies did not vary with soil type or amendment; however, treatment differences were observed in the abundance of archaeal ammonia-oxidizing amoA gene abundance. Analysis of ∼110,000 bacterial sequences showed a significant change in the active (RNA-based) community between day 3 and day 151, but microbial composition was similar between soil types. These results show that even after 12 years of plant litter exclusion, the legacy of community composition was well buffered against a dramatic disturbance.}, } @article {pmid23259758, year = {2012}, author = {Flores, R and Shi, J and Fuhrman, B and Xu, X and Veenstra, TD and Gail, MH and Gajer, P and Ravel, J and Goedert, JJ}, title = {Fecal microbial determinants of fecal and systemic estrogens and estrogen metabolites: a cross-sectional study.}, journal = {Journal of translational medicine}, volume = {10}, number = {}, pages = {253}, pmid = {23259758}, issn = {1479-5876}, mesh = {Adolescent ; Adult ; Aged ; Bacteria/classification/enzymology/genetics ; Biodiversity ; Cross-Sectional Studies ; Estrogens/*metabolism/urine ; Feces/*microbiology ; Female ; Genetic Variation ; Humans ; Male ; Menopause/urine ; *Metagenome/genetics ; Middle Aged ; Young Adult ; }, abstract = {BACKGROUND: High systemic estrogen levels contribute to breast cancer risk for postmenopausal women, whereas low levels contribute to osteoporosis risk. Except for obesity, determinants of non-ovarian systemic estrogen levels are undefined. We sought to identify members and functions of the intestinal microbial community associated with estrogen levels via enterohepatic recirculation.

METHODS: Fifty-one epidemiologists at the National Institutes of Health, including 25 men, 7 postmenopausal women, and 19 premenopausal women, provided urine and aliquots of feces, using methods proven to yield accurate and reproducible results. Estradiol, estrone, 13 estrogen metabolites (EM), and their sum (total estrogens) were quantified in urine and feces by liquid chromatography/tandem mass spectrometry. In feces, β-glucuronidase and β-glucosidase activities were determined by realtime kinetics, and microbiome diversity and taxonomy were estimated by pyrosequencing 16S rRNA amplicons. Pearson correlations were computed for each loge estrogen level, loge enzymatic activity level, and microbiome alpha diversity estimate. For the 55 taxa with mean relative abundance of at least 0.1%, ordinal levels were created [zero, low (below median of detected sequences), high] and compared to loge estrogens, β-glucuronidase and β-glucosidase enzymatic activity levels by linear regression. Significance was based on two-sided tests with α=0.05.

RESULTS: In men and postmenopausal women, levels of total urinary estrogens (as well as most individual EM) were very strongly and directly associated with all measures of fecal microbiome richness and alpha diversity (R≥0.50, P≤0.003). These non-ovarian systemic estrogens also were strongly and significantly associated with fecal Clostridia taxa, including non-Clostridiales and three genera in the Ruminococcaceae family (R=0.57-0.70, P=0.03-0.002). Estrone, but not other EM, in urine correlated significantly with functional activity of fecal β-glucuronidase (R=0.36, P=0.04). In contrast, fecal β-glucuronidase correlated inversely with fecal total estrogens, both conjugated and deconjugated (R≤-0.47, P≤0.01). Premenopausal female estrogen levels, which were collected across menstrual cycles and thus highly variable, were completely unrelated to fecal microbiome and enzyme parameters (P≥0.6).

CONCLUSIONS: Intestinal microbial richness and functions, including but not limited to β-glucuronidase, influence levels of non-ovarian estrogens via enterohepatic circulation. Thus, the gut microbial community likely affects the risk for estrogen-related conditions in older adults. Understanding how Clostridia taxa relate to systemic estrogens may identify targets for interventions.}, } @article {pmid23257018, year = {2013}, author = {Petrof, EO and Claud, EC and Gloor, GB and Allen-Vercoe, E}, title = {Microbial ecosystems therapeutics: a new paradigm in medicine?.}, journal = {Beneficial microbes}, volume = {4}, number = {1}, pages = {53-65}, doi = {10.3920/BM2012.0039}, pmid = {23257018}, issn = {1876-2891}, mesh = {Biological Products/*therapeutic use ; *Biota ; Clostridioides difficile/pathogenicity ; Clostridium Infections/microbiology/therapy ; Gastrointestinal Tract/*microbiology/*physiology ; Humans ; *Metagenome ; }, abstract = {Increasing evidence indicates that the complex microbial ecosystem of the human intestine plays a critical role in protecting the host against disease. This review discusses gut dysbiosis (here defined as a state of imbalance in the gut microbial ecosystem, including overgrowth of some organisms and loss of others) as the foundation for several diseases, and the applicability of refined microbial ecosystem replacement therapies as a future treatment modality. Consistent with the concept of a 'core' microbiome encompassing key functions required for normal intestinal homeostasis, 'Microbial Ecosystem Therapeutics' (MET) would entail replacing a dysfunctional, damaged ecosystem with a fully developed and healthy ecosystem of 'native' intestinal bacteria. Its application in treating Clostridium difficile infection is discussed and possible applications to other diseases such as ulcerative colitis, obesity, necrotising enterocolitis, and regressive-type autism are reviewed. Unlike conventional probiotic therapies that are generally limited to a single strain or at most a few strains of bacteria 'Microbial Ecosystem Therapeutics' would utilise whole bacterial communities derived directly from the human gastrointestinal tract. By taking into account the intrinsic needs of the entire microbial ecosystem, MET would emphasise the rational design of healthy, resilient and robust microbial communities that could be used to maintain or restore human health. More than simply a new probiotic treatment, this emerging paradigm in medicine may lead to novel strategies in treating and managing a wide variety of human diseases.}, } @article {pmid23257016, year = {2013}, author = {Rothe, M and Blaut, M}, title = {Evolution of the gut microbiota and the influence of diet.}, journal = {Beneficial microbes}, volume = {4}, number = {1}, pages = {31-37}, doi = {10.3920/BM2012.0029}, pmid = {23257016}, issn = {1876-2891}, mesh = {Animals ; *Biota ; Diet/*methods ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; Models, Animal ; }, abstract = {Diet is a major force that shapes the composition and activity of the gut microbiota. This is evident from alterations in gut microbiota composition after weaning or drastic dietary changes. Owing to the complexity of the microbiota, interactions of intestinal bacteria with the host are difficult to study. Gnotobiotic animal models offer the opportunity to reduce the complexity and the interindividual variability of the intestinal microbiota. Germ-free animals were associated with a simplified microbial community consisting of eight bacterial species, that are found in the human gut. These microbes were selected because their genome sequences are available, and they mimic to some extent the metabolic activity of the human gut microbiota. The microbiota responded to dietary modifications by changes in the relative proportions of the community members. This model offers the chance to better define the role of intestinal bacteria in obesity development, but little is known on how diet affects intestinal bacteria at the cellular level. Mice monoassociated with Escherichia coli were used as a simplified model to investigate the influence of dietary factors on bacterial protein expression in the intestine. The mice were fed three different diets: a carbohydrate (lactose)-rich diet, a protein-rich diet and a diet rich in starch. The lactose-rich diet led to an induction of proteins involved in E. coli's oxidative stress response (Fur, AhpF, Dps). The corresponding genes are under control of the OxyR transcriptional regulator which is activated by oxidative stress. Further experiments demonstrated that osmotic stress exerted by various carbohydrates leads to an upregulation of proteins belonging to the oxyR regulon. The data suggest that the upregulated proteins enable intestinal E. coli to better cope with diet-induced osmotic stress. These examples demonstrate that gnotobiotic animal models are a valuable tool for studying diet-induced changes at the community and the cell level.}, } @article {pmid23251909, year = {2012}, author = {Felczykowska, A and Bloch, SK and Nejman-Faleńczyk, B and Barańska, S}, title = {Metagenomic approach in the investigation of new bioactive compounds in the marine environment.}, journal = {Acta biochimica Polonica}, volume = {59}, number = {4}, pages = {501-505}, pmid = {23251909}, issn = {1734-154X}, mesh = {*Aquatic Organisms/enzymology/genetics/microbiology ; Biodiversity ; DNA, Bacterial/genetics/isolation & purification ; Gene Library ; Marine Biology ; *Metagenomics ; Seawater/*microbiology ; }, abstract = {The marine environment is estimated to be one of the most significant sources of biological activity in the world. In the last few decades an increase in the research intensity conducted on marine microorganisms has been observed, which confirms the great potential of these organisms in the field of bioactive compounds' production. In order to efficiently use the natural resources of the marine environment, metagenomics can be applied. This powerful technique allows for efficient screening of microbial biodiversity for bioactive compounds. The primary aim of this review is to present some aspects of the construction of metagenomic libraries, and strategies of screening for novel bioactives in the marine surrounding. This paper also illustrates several examples of the application of metagenomic methods in the discovery of novel enzymes and drugs in various marine environments.}, } @article {pmid23251582, year = {2012}, author = {Horňák, K and Corno, G}, title = {Every coin has a back side: invasion by Limnohabitans planktonicus promotes the maintenance of species diversity in bacterial communities.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e51576}, pmid = {23251582}, issn = {1932-6203}, mesh = {*Biodiversity ; Comamonadaceae/*growth & development ; *Introduced Species ; *Metagenome ; Species Specificity ; }, abstract = {One of the earliest challenges for ecologists has been to study the impact of invasive species on microbial communities. Although bacteria are fundamental in biological processes, current knowledge on invasion effects by aquatic non-pathogenic bacteria is still limited. Using pure cultures of diverse planktonic bacteria as model organisms at two different carbon concentration levels, we tested the response of an assembled community to the invasion by Limnohabitans planktonicus, an opportunistic bacterium, successful in freshwaters. The invader, introduced at the early stationary growth phase of the resident community, caused a strong decrement of the abundance of the dominant species. This was due to competition for nutrients and a potential allelopathic interaction. Simultaneously, resident species formerly unable to successfully compete within the community, thus potentially exposed to competitive exclusion, increased their abundances. The overall result of the invasion was preservation of species diversity, the higher the lower was the substrate content available. Our study provides new insights into bacterial invasions, offering an alternative interpretation of invasions for community ecology.}, } @article {pmid23251564, year = {2012}, author = {Alcaide, M and Messina, E and Richter, M and Bargiela, R and Peplies, J and Huws, SA and Newbold, CJ and Golyshin, PN and Simón, MA and López, G and Yakimov, MM and Ferrer, M}, title = {Gene sets for utilization of primary and secondary nutrition supplies in the distal gut of endangered Iberian lynx.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e51521}, pmid = {23251564}, issn = {1932-6203}, mesh = {Animals ; Animals, Wild ; Bacteria/genetics ; *Endangered Species ; Feeding Behavior/*physiology ; Gastrointestinal Tract/*microbiology ; Genes, Bacterial/*genetics ; Genetic Variation ; Lynx/*microbiology ; Spain ; }, abstract = {Recent studies have indicated the existence of an extensive trans-genomic trans-mural co-metabolism between gut microbes and animal hosts that is diet-, host phylogeny- and provenance-influenced. Here, we analyzed the biodiversity at the level of small subunit rRNA gene sequence and the metabolic composition of 18 Mbp of consensus metagenome sequences and activity characteristics of bacterial intra-cellular extracts, in wild Iberian lynx (Lynx pardinus) fecal samples. Bacterial signatures (14.43% of all of the Firmicutes reads and 6.36% of total reads) related to the uncultured anaerobic commensals Anaeroplasma spp., which are typically found in ovine and bovine rumen, were first identified. The lynx gut was further characterized by an over-representation of 'presumptive' aquaporin aqpZ genes and genes encoding 'active' lysosomal-like digestive enzymes that are possibly needed to acquire glycerol, sugars and amino acids from glycoproteins, glyco(amino)lipids, glyco(amino)glycans and nucleoside diphosphate sugars. Lynx gut was highly enriched (28% of the total glycosidases) in genes encoding α-amylase and related enzymes, although it exhibited low rate of enzymatic activity indicative of starch degradation. The preponderance of β-xylosidase activity in protein extracts further suggests lynx gut microbes being most active for the metabolism of β-xylose containing plant N-glycans, although β-xylosidases sequences constituted only 1.5% of total glycosidases. These collective and unique bacterial, genetic and enzymatic activity signatures suggest that the wild lynx gut microbiota not only harbors gene sets underpinning sugar uptake from primary animal tissues (with the monotypic dietary profile of the wild lynx consisting of 80-100% wild rabbits) but also for the hydrolysis of prey-derived plant biomass. Although, the present investigation corresponds to a single sample and some of the statements should be considered qualitative, the data most likely suggests a tighter, more coordinated and complex evolutionary and nutritional ecology scenario of carnivore gut microbial communities than has been previously assumed.}, } @article {pmid23251474, year = {2012}, author = {Dettai, A and Gallut, C and Brouillet, S and Pothier, J and Lecointre, G and Debruyne, R}, title = {Conveniently pre-tagged and pre-packaged: extended molecular identification and metagenomics using complete metazoan mitochondrial genomes.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e51263}, pmid = {23251474}, issn = {1932-6203}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Metagenomics ; Quality Control ; }, abstract = {BACKGROUND: Researchers sorely need markers and approaches for biodiversity exploration (both specimen linked and metagenomics) using the full potential of next generation sequencing technologies (NGST). Currently, most studies rely on expensive multiple tagging, PCR primer universality and/or the use of few markers, sometimes with insufficient variability.

We propose a novel approach for the isolation and sequencing of a universal, useful and popular marker across distant, non-model metazoans: the complete mitochondrial genome. It relies on the properties of metazoan mitogenomes for enrichment, on careful choice of the organisms to multiplex, as well as on the wide collection of accumulated mitochondrial reference datasets for post-sequencing sorting and identification instead of individual tagging. Multiple divergent organisms can be sequenced simultaneously, and their complete mitogenome obtained at a very low cost. We provide in silico testing of dataset assembly for a selected set of example datasets.

CONCLUSIONS/SIGNIFICANCE: This approach generates large mitogenome datasets. These sequences are useful for phylogenetics, molecular identification and molecular ecology studies, and are compatible with all existing projects or available datasets based on mitochondrial sequences, such as the Barcode of Life project. Our method can yield sequences both from identified samples and metagenomic samples. The use of the same datasets for both kinds of studies makes for a powerful approach, especially since the datasets have a high variability even at species level, and would be a useful complement to the less variable 18S rDNA currently prevailing in metagenomic studies.}, } @article {pmid23251414, year = {2012}, author = {Wang, K and Li, H and Yuan, Y and Etheridge, A and Zhou, Y and Huang, D and Wilmes, P and Galas, D}, title = {The complex exogenous RNA spectra in human plasma: an interface with human gut biota?.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e51009}, pmid = {23251414}, issn = {1932-6203}, mesh = {*Biota ; Gastrointestinal Tract ; Humans ; Metagenome ; Plasma/*metabolism ; RNA/*blood ; RNA, Circular ; }, abstract = {Human plasma has long been a rich source for biomarker discovery. It has recently become clear that plasma RNA molecules, such as microRNA, in addition to proteins are common and can serve as biomarkers. Surveying human plasma for microRNA biomarkers using next generation sequencing technology, we observed that a significant fraction of the circulating RNA appear to originate from exogenous species. With careful analysis of sequence error statistics and other controls, we demonstrated that there is a wide range of RNA from many different organisms, including bacteria and fungi as well as from other species. These RNAs may be associated with protein, lipid or other molecules protecting them from RNase activity in plasma. Some of these RNAs are detected in intracellular complexes and may be able to influence cellular activities under in vitro conditions. These findings raise the possibility that plasma RNAs of exogenous origin may serve as signaling molecules mediating for example the human-microbiome interaction and may affect and/or indicate the state of human health.}, } @article {pmid23249810, year = {2012}, author = {Ravel, J and Gajer, P and Fu, L and Mauck, CK and Koenig, SS and Sakamoto, J and Motsinger-Reif, AA and Doncel, GF and Zeichner, SL}, title = {Twice-daily application of HIV microbicides alter the vaginal microbiota.}, journal = {mBio}, volume = {3}, number = {6}, pages = {}, pmid = {23249810}, issn = {2150-7511}, support = {P30 AI087714/AI/NIAID NIH HHS/United States ; P30AI087714/AI/NIAID NIH HHS/United States ; AI1079798/AI/NIAID NIH HHS/United States ; }, mesh = {Administration, Intravaginal ; Adolescent ; Adult ; Anti-Infective Agents/*administration & dosage ; *Biota ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; HIV Infections/prevention & control ; Human Experimentation ; Humans ; Metagenome/*drug effects ; Middle Aged ; Placebos/administration & dosage ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vagina/*microbiology ; Young Adult ; }, abstract = {UNLABELLED: Vaginal HIV microbicides offer great promise in preventing HIV transmission, but failures of phase 3 clinical trials, in which microbicide-treated subjects had an increased risk of HIV transmission, raised concerns about endpoints used to evaluate microbicide safety. A possible explanation for the increased transmission risk is that the agents shifted the vaginal bacterial community, resulting in loss of natural protection and enhanced HIV transmission susceptibility. We characterized vaginal microbiota, using pyrosequencing of bar-coded 16S rRNA gene fragments, in samples from 35 healthy, sexually abstinent female volunteer subjects (ages 18 to 50 years) with regular menses in a repeat phase 1 study of twice-daily application over 13.5 days of 1 of 3 gel products: a hydroxyethylcellulose (HEC)-based "universal" placebo (10 subjects), 6% cellulose sulfate (CS; 13 subjects), and 4% nonoxynol-9 (N-9; 12 subjects). We used mixed effects models inferred using Bayesian Markov chain Monte Carlo methods, which showed that treatment with active agents shifted the microbiota toward a community type lacking significant numbers of Lactobacillus spp. and dominated by strict anaerobes. This state of the vaginal microbiota was associated with a low or intermediate Nugent score and was not identical to bacterial vaginosis, an HIV transmission risk factor. The placebo arm contained a higher proportion of communities dominated by Lactobacillus spp., particularly L. crispatus, throughout treatment. The data suggest that molecular evaluation of microbicide effects on vaginal microbiota may be a critical endpoint that should be incorporated in early clinical assessment of microbicide candidates.

IMPORTANCE: Despite large prevention efforts, HIV transmission and acquisition rates remain unacceptably high. In developing countries, transmission mainly occurs through heterosexual intercourse, where women are significantly more vulnerable to infection than men. Vaginal microbicides are considered to be one of the most promising female-controlled products, in that women themselves insert the microbicides into the vagina to prevent HIV transmission during sexual intercourse. The failure of several microbicides in clinical trials has raised questions concerning the low in vivo efficacy of such anti-HIV molecules. This study was designed to gain insights into the failures of two microbicides by testing the hypothesis that the microbicides negatively affect a critical line of defense against HIV, the vaginal microbiota. The results suggest that in the early assessment of candidate microbicides, culture-independent evaluation of their effect on the vaginal microbiota should be considered and may constitute a critical endpoint.}, } @article {pmid23247148, year = {2013}, author = {Fang, H and Cai, L and Yu, Y and Zhang, T}, title = {Metagenomic analysis reveals the prevalence of biodegradation genes for organic pollutants in activated sludge.}, journal = {Bioresource technology}, volume = {129}, number = {}, pages = {209-218}, doi = {10.1016/j.biortech.2012.11.054}, pmid = {23247148}, issn = {1873-2976}, mesh = {Bacterial Proteins/*physiology ; Biodegradation, Environmental ; Metagenome/*genetics ; Metagenomics/*methods ; Microbial Consortia/*genetics ; Organic Chemicals/*metabolism ; Sewage/*microbiology ; Water Pollutants, Chemical/isolation & purification/*metabolism ; }, abstract = {The abundance, diversity, and distribution of biodegradation genes (BDGs) and phenol degradation genes (PDGs) in activated sludge (AS) from two wastewater treatment plants (WWTPs) at different sampling times were assessed by metagenomic analysis using a total of 15 datasets derived from Illumina high-throughput sequencing and BLAST comparisons to BDGs and PDGs databases. The results showed that the abundance (0.015-0.030%) and diversity of BDGs in AS varied with the WWTP and the sampling times. The p450 and pmo genes were the most abundant genes in the BDGs and PDGs subgroups, respectively. MG-RAST analysis revealed that 87 detected bacterial genera potentially capable of degrading pollutants were mostly affiliated with Proteobacteria (59.8%), Bacteroidetes (17.2%), and Actinobacteria (9.2%). Mycobacterium, belonging to Actinobacteria, was found to be the most abundant genus (23.4%). This method could be used to monitor an AS's biodegradation ability for organic pollutants and to evaluate its wastewater treatment efficiency.}, } @article {pmid23247126, year = {2013}, author = {Wang, F and Li, Q and He, Q and Geng, Y and Tang, C and Wang, C and Li, J}, title = {Temporal variations of the ileal microbiota in intestinal ischemia and reperfusion.}, journal = {Shock (Augusta, Ga.)}, volume = {39}, number = {1}, pages = {96-103}, doi = {10.1097/SHK.0b013e318279265f}, pmid = {23247126}, issn = {1540-0514}, mesh = {Animals ; Bacteria/classification/*isolation & purification ; Bacterial Typing Techniques/methods ; Biodiversity ; DNA Fingerprinting/methods ; DNA, Bacterial/analysis ; Ileum/*microbiology/pathology/physiology ; Intestinal Diseases/*microbiology/pathology ; Intestinal Mucosa/pathology ; Male ; *Metagenome ; Phylogeny ; Rats ; Rats, Sprague-Dawley ; Regeneration ; Reperfusion Injury/*microbiology/pathology ; Tight Junctions/pathology ; Time Factors ; }, abstract = {Gastrointestinal bacteria and epithelia contribute to systemic inflammation and infections in critically ill patients, but the gut microbiota in these diseases has not been analyzed dynamically by molecular fingerprinting methods. This study aimed to identify ileal flora dysbiosis pattern and bacterial species that changed significantly in a rat model of intestinal ischemia and reperfusion and illustrate time courses of both epithelial alterations and gut flora variations in the same injury. Forty-eight rats were randomized into eight groups (n = 6/group). Six groups underwent superior mesenteric artery occlusion for 30 min and were killed at 1, 3, 6, 12, 24, and 72 h following reperfusion, respectively; a group of rats were killed just after anesthesia (control), and a sham-operated group received 12-h reperfusion. Denaturing gradient gel electrophoresis of ileal microbiota showed that gut flora pattern changed early after intestinal ischemia and reperfusion, differed significantly at 12 h of reperfusion, and then started to recover toward normal pattern. The specific dysbiosis were characterized by Escherichia coli proliferation and Lachnospiraceae and Lactobacilli reduction. These bacteria that contributed most were identified by principal component analysis and sequencing and confirmed by real-time polymerase chain reaction. In addition, alterations of ileal microbiota followed epithelial changes in the time course of reperfusion.}, } @article {pmid23241975, year = {2013}, author = {Xue, K and Wu, L and Deng, Y and He, Z and Van Nostrand, J and Robertson, PG and Schmidt, TM and Zhou, J}, title = {Functional gene differences in soil microbial communities from conventional, low-input, and organic farmlands.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {4}, pages = {1284-1292}, pmid = {23241975}, issn = {1098-5336}, mesh = {Agriculture/methods ; *Biota ; Carbon/metabolism ; *Genes, Bacterial ; Metabolic Networks and Pathways/genetics ; Metagenome ; Michigan ; Microarray Analysis ; Nitrogen/metabolism ; Phosphorus/metabolism ; Soil/chemistry ; *Soil Microbiology ; Sulfur/metabolism ; }, abstract = {Various agriculture management practices may have distinct influences on soil microbial communities and their ecological functions. In this study, we utilized GeoChip, a high-throughput microarray-based technique containing approximately 28,000 probes for genes involved in nitrogen (N)/carbon (C)/sulfur (S)/phosphorus (P) cycles and other processes, to evaluate the potential functions of soil microbial communities under conventional (CT), low-input (LI), and organic (ORG) management systems at an agricultural research site in Michigan. Compared to CT, a high diversity of functional genes was observed in LI. The functional gene diversity in ORG did not differ significantly from that of either CT or LI. Abundances of genes encoding enzymes involved in C/N/P/S cycles were generally lower in CT than in LI or ORG, with the exceptions of genes in pathways for lignin degradation, methane generation/oxidation, and assimilatory N reduction, which all remained unchanged. Canonical correlation analysis showed that selected soil (bulk density, pH, cation exchange capacity, total C, C/N ratio, NO(3)(-), NH(4)(+), available phosphorus content, and available potassium content) and crop (seed and whole biomass) variables could explain 69.5% of the variation of soil microbial community composition. Also, significant correlations were observed between NO(3)(-) concentration and denitrification genes, NH(4)(+) concentration and ammonification genes, and N(2)O flux and denitrification genes, indicating a close linkage between soil N availability or process and associated functional genes.}, } @article {pmid23236140, year = {2012}, author = {Fierer, N and Leff, JW and Adams, BJ and Nielsen, UN and Bates, ST and Lauber, CL and Owens, S and Gilbert, JA and Wall, DH and Caporaso, JG}, title = {Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {52}, pages = {21390-21395}, pmid = {23236140}, issn = {1091-6490}, mesh = {Bacteria/*genetics ; Biodiversity ; Desert Climate ; *Ecosystem ; Genes, Bacterial/genetics ; Metagenome/*genetics ; Metagenomics/*methods ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.}, } @article {pmid23236009, year = {2013}, author = {Pérez-Cobas, AE and Gosalbes, MJ and Friedrichs, A and Knecht, H and Artacho, A and Eismann, K and Otto, W and Rojo, D and Bargiela, R and von Bergen, M and Neulinger, SC and Däumer, C and Heinsen, FA and Latorre, A and Barbas, C and Seifert, J and dos Santos, VM and Ott, SJ and Ferrer, M and Moya, A}, title = {Gut microbiota disturbance during antibiotic therapy: a multi-omic approach.}, journal = {Gut}, volume = {62}, number = {11}, pages = {1591-1601}, pmid = {23236009}, issn = {1468-3288}, mesh = {Aged ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/isolation & purification ; Bacterial Typing Techniques/methods ; Biodiversity ; DNA, Bacterial/analysis ; Feces/microbiology ; Gastrointestinal Tract/metabolism/*microbiology ; Gene Expression Profiling/methods ; Gene Expression Regulation/drug effects ; Humans ; Male ; Metabolome/drug effects ; Microbiota/*drug effects ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; beta-Lactams/*pharmacology ; }, abstract = {OBJECTIVE: Antibiotic (AB) usage strongly affects microbial intestinal metabolism and thereby impacts human health. Understanding this process and the underlying mechanisms remains a major research goal. Accordingly, we conducted the first comparative omic investigation of gut microbial communities in faecal samples taken at multiple time points from an individual subjected to β-lactam therapy.

METHODS: The total (16S rDNA) and active (16S rRNA) microbiota, metagenome, metatranscriptome (mRNAs), metametabolome (high-performance liquid chromatography coupled to electrospray ionisation and quadrupole time-of-flight mass spectrometry) and metaproteome (ultra high performing liquid chromatography coupled to an Orbitrap MS(2) instrument [UPLC-LTQ Orbitrap-MS/MS]) of a patient undergoing AB therapy for 14 days were evaluated.

RESULTS: Apparently oscillatory population dynamics were observed, with an early reduction in Gram-negative organisms (day 6) and an overall collapse in diversity and possible further colonisation by 'presumptive' naturally resistant bacteria (day 11), followed by the re-growth of Gram-positive species (day 14). During this process, the maximum imbalance in the active microbial fraction occurred later (day 14) than the greatest change in the total microbial fraction, which reached a minimum biodiversity and richness on day 11; additionally, major metabolic changes occurred at day 6. Gut bacteria respond to ABs early by activating systems to avoid the antimicrobial effects of the drugs, while 'presumptively' attenuating their overall energetic metabolic status and the capacity to transport and metabolise bile acid, cholesterol, hormones and vitamins; host-microbial interactions significantly improved after treatment cessation.

CONCLUSIONS: This proof-of-concept study provides an extensive description of gut microbiota responses to follow-up β-lactam therapy. The results demonstrate that ABs targeting specific pathogenic infections and diseases may alter gut microbial ecology and interactions with host metabolism at a much higher level than previously assumed.}, } @article {pmid23227023, year = {2012}, author = {Pearce, DA and Newsham, KK and Thorne, MA and Calvo-Bado, L and Krsek, M and Laskaris, P and Hodson, A and Wellington, EM}, title = {Metagenomic analysis of a southern maritime antarctic soil.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {403}, pmid = {23227023}, issn = {1664-302X}, abstract = {Our current understanding of Antarctic soils is derived from direct culture on selective media, biodiversity studies based on clone library construction and analysis, quantitative PCR amplification of specific gene sequences and the application of generic microarrays for microbial community analysis. Here, we investigated the biodiversity and functional potential of a soil community at Mars Oasis on Alexander Island in the southern Maritime Antarctic, by applying 454 pyrosequencing technology to a metagenomic library constructed from soil genomic DNA. The results suggest that the commonly cited range of phylotypes used in clone library construction and analysis of 78-730 OTUs (de-replicated to 30-140) provides low coverage of the major groups present (∼5%). The vast majority of functional genes (>77%) were for structure, carbohydrate metabolism, and DNA/RNA processing and modification. This study suggests that prokaryotic diversity in Antarctic terrestrial environments appears to be limited at the generic level, with Proteobacteria, Actinobacteria being common. Cyanobacteria were surprisingly under-represented at 3.4% of sequences, although ∼1% of the genes identified were involved in CO(2) fixation. At the sequence level there appeared to be much greater heterogeneity, and this might be due to high divergence within the relatively restricted lineages which have successfully colonized Antarctic terrestrial environments.}, } @article {pmid23224222, year = {2013}, author = {Gori, K and Ryssel, M and Arneborg, N and Jespersen, L}, title = {Isolation and identification of the microbiota of Danish farmhouse and industrially produced surface-ripened cheeses.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {602-615}, pmid = {23224222}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Biodiversity ; Cattle ; Cheese/analysis/*microbiology ; Denmark ; *Metagenome ; Milk/*microbiology ; Molecular Sequence Data ; Phylogeny ; Yeasts/classification/genetics/*isolation & purification/metabolism ; }, abstract = {For studying the microbiota of four Danish surface-ripened cheeses produced at three farmhouses and one industrial dairy, both a culture-dependent and culture-independent approach were used. After dereplication of the initial set of 433 isolates by (GTG)5-PCR fingerprinting, 217 bacterial and 25 yeast isolates were identified by sequencing of the 16S rRNA gene or the D1/D2 domain of the 26S rRNA gene, respectively. At the end of ripening, the cheese core microbiota of the farmhouse cheeses consisted of the mesophilic lactic acid bacteria (LAB) starter cultures Lactococcus lactis subsp. lactis and Leuconostoc mesenteorides as well as non-starter LAB including different Lactobacillus spp. The cheese from the industrial dairy was almost exclusively dominated by Lb. paracasei. The surface bacterial microbiota of all four cheeses were dominated by Corynebacterium spp. and/or Brachybacterium spp. Brevibacterium spp. was found to be subdominant compared to other bacteria on the farmhouse cheeses, and no Brevibacterium spp. was found on the cheese from the industrial dairy, even though B. linens was used as surface-ripening culture. Moreover, Gram-negative bacteria identified as Alcalignes faecalis and Proteus vulgaris were found on one of the farmhouse cheeses. The surface yeast microbiota consisted primarily of one dominating species for each cheese. For the farmhouse cheeses, the dominant yeast species were Yarrowia lipolytica, Geotrichum spp. and Debaryomyces hansenii, respectively, and for the cheese from the industrial dairy, D. hansenii was the dominant yeast species. Additionally, denaturing gradient gel electrophoresis (DGGE) analysis revealed that Streptococcus thermophilus was present in the farmhouse raw milk cheese analysed in this study. Furthermore, DGGE bands corresponding to Vagococcus carniphilus, Psychrobacter spp. and Lb. curvatus on the cheese surfaces indicated that these bacterial species may play a role in cheese ripening.}, } @article {pmid23221525, year = {2012}, author = {Weerachavangkul, C and Laothanachareon, T and Boonyapakron, K and Wongwilaiwalin, S and Nimchua, T and Eurwilaichitr, L and Pootanakit, K and Igarashi, Y and Champreda, V}, title = {Alkaliphilic endoxylanase from lignocellulolytic microbial consortium metagenome for biobleaching of eucalyptus pulp.}, journal = {Journal of microbiology and biotechnology}, volume = {22}, number = {12}, pages = {1636-1643}, doi = {10.4014/jmb.1206.06044}, pmid = {23221525}, issn = {1738-8872}, mesh = {Bacterial Proteins/chemistry/genetics/*metabolism ; Bleaching Agents/chemistry/*metabolism ; Cloning, Molecular ; Endo-1,4-beta Xylanases/chemistry/genetics/*metabolism ; Escherichia coli/genetics ; Eucalyptus ; Hydrogen-Ion Concentration ; Hydrolysis ; Lignin/*metabolism ; Metagenome ; Microbial Consortia ; Recombinant Proteins/chemistry/genetics/metabolism ; Temperature ; }, abstract = {Enzymatic pre-bleaching by modification of pulp fibers with xylanases is an attractive approach to reduce the consumption of toxic bleaching chemicals in the paper industry. In this study, an alkaliphilic endoxylanase gene was isolated from metagenomic DNA of a structurally stable thermophilic lignocellulose-degrading microbial consortium using amplification with conserved glycosyl hydrolase family 10 primers and subsequent genome walking. The full-length xylanase showed 78% sequence identity to an endo-beta-1,4-xylanase of Clostridium phytofermentans and was expressed in a mature form with an N-terminal His6 tag fusion in Escherichia coli. The recombinant xylanase Xyn3F was thermotolerant and alkaliphilic, working optimally at 65-70 degrees C with an optimal pH at 9- 10 and retaining >80% activity at pH 9, 60 degrees C for 1 h. Xyn3F showed a Vmax of 2,327 IU/mg and Km of 3.5 mg/ml on birchwood xylan. Pre-bleaching of industrial eucalyptus pulp with no prior pH adjustment (pH 9) using Xyn3F at 50 IU/g dried pulp led to 4.5-5.1% increase in final pulp brightness and 90.4-102.4% increase in whiteness after a single-step hypochlorite bleaching over the untreated pulp, which allowed at least 20% decrease in hypochlorite consumption to achieve the same final bleaching indices. The alkaliphilic xylanase is promising for application in an environmentally friendly bleaching step of kraft and soda pulps with no requirement for pH adjustment, leading to improved economic feasibility of the process.}, } @article {pmid23220959, year = {2013}, author = {Smith, DJ and Timonen, HJ and Jaffe, DA and Griffin, DW and Birmele, MN and Perry, KD and Ward, PD and Roberts, MS}, title = {Intercontinental dispersal of bacteria and archaea by transpacific winds.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {4}, pages = {1134-1139}, pmid = {23220959}, issn = {1098-5336}, mesh = {*Air Microbiology ; Archaea/classification/genetics/*isolation & purification ; Bacteria/classification/genetics/*isolation & purification ; *Biodiversity ; Metagenome ; Microarray Analysis ; North America ; *Phylogeography ; RNA, Ribosomal, 16S/genetics ; Wind ; }, abstract = {Microorganisms are abundant in the upper atmosphere, particularly downwind of arid regions, where winds can mobilize large amounts of topsoil and dust. However, the challenge of collecting samples from the upper atmosphere and reliance upon culture-based characterization methods have prevented a comprehensive understanding of globally dispersed airborne microbes. In spring 2011 at the Mt. Bachelor Observatory in North America (2.8 km above sea level), we captured enough microbial biomass in two transpacific air plumes to permit a microarray analysis using 16S rRNA genes. Thousands of distinct bacterial taxa spanning a wide range of phyla and surface environments were detected before, during, and after each Asian long-range transport event. Interestingly, the transpacific plumes delivered higher concentrations of taxa already in the background air (particularly Proteobacteria, Actinobacteria, and Firmicutes). While some bacterial families and a few marine archaea appeared for the first and only time during the plumes, the microbial community compositions were similar, despite the unique transport histories of the air masses. It seems plausible, when coupled with atmospheric modeling and chemical analysis, that microbial biogeography can be used to pinpoint the source of intercontinental dust plumes. Given the degree of richness measured in our study, the overall contribution of Asian aerosols to microbial species in North American air warrants additional investigation.}, } @article {pmid23220956, year = {2013}, author = {Inceoglu, Ö and van Overbeek, LS and Falcão Salles, J and van Elsas, JD}, title = {Normal operating range of bacterial communities in soil used for potato cropping.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {4}, pages = {1160-1170}, pmid = {23220956}, issn = {1098-5336}, mesh = {*Biota ; DNA, Bacterial/chemistry/genetics ; *Metagenome ; Molecular Sequence Data ; Polymerase Chain Reaction ; Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; Solanum tuberosum/*growth & development ; }, abstract = {In this study, the impacts of six potato (Solanum tuberosum) cultivars with different tuber starch allocations (including one genetically modified [GM] line) on the bacterial communities in field soil were investigated across two growth seasons interspersed with 1 year of barley cultivation, using quantitative PCR, clone library, and PCR-denaturing gradient gel electrophoresis (DGGE) analyses. It was hypothesized that the modifications in the tuber starch contents of these plants, yielding changed root growth rates and exudation patterns, might have elicited altered bacterial communities in the soil. The data showed that bacterial abundances in the bulk soil varied over about 2 orders of magnitude across the 3 years. As expected, across all cultivars, positive potato rhizosphere effects on bacterial abundances were noted in the two potato years. The bulk soil bacterial community structures revealed progressive shifts across time, and moving-window analysis revealed a 60% change over the total experiment. Consistent with previous findings, the community structures in the potato rhizosphere compartments were mainly affected by the growth stage of the plants and, to a lesser extent, by plant cultivar type. The data from the soil under the non-GM potato lines were then taken to define the normal operating range (NOR) of the microbiota under potatoes. Interestingly, the bacterial communities under the GM potato line remained within this NOR. In regard to the bacterial community compositions, particular bacterial species in the soil appeared to be specific to (i) the plant species under investigation (barley versus potato) or, with respect to potatoes, (ii) the plant growth stage. Members of the genera Arthrobacter, Streptomyces, Rhodanobacter, and Dokdonella were consistently found only at the flowering potato plants in both seasons, whereas Rhodoplanes and Sporosarcina were observed only in the soil planted to barley.}, } @article {pmid23220955, year = {2013}, author = {Headd, B and Engel, AS}, title = {Evidence for niche partitioning revealed by the distribution of sulfur oxidation genes collected from areas of a terrestrial sulfidic spring with differing geochemical conditions.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {4}, pages = {1171-1182}, pmid = {23220955}, issn = {1098-5336}, mesh = {*Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Hot Springs/*microbiology ; Metabolic Networks and Pathways/*genetics ; Metagenome ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Sequence Analysis, DNA ; Sulfur/*metabolism ; Water/*chemistry ; }, abstract = {The diversity and phylogenetic significance of bacterial genes in the environment has been well studied, but comparatively little attention has been devoted to understanding the functional significance of different variations of the same metabolic gene that occur in the same environment. We analyzed the geographic distribution of 16S rRNA pyrosequences and soxB genes along a geochemical gradient in a terrestrial sulfidic spring to identify how different taxonomic variations of the soxB gene were naturally distributed within the spring outflow channel and to identify possible evidence for altered SoxB enzyme function in nature. Distinct compositional differences between bacteria that utilize their SoxB enzyme in the Paracoccus sulfide oxidation pathway (e.g., Bradyrhizobium, Paracoccus, and Rhodovulum) and bacteria that utilize their SoxB enzyme in the branched pathway (e.g., Chlorobium, Thiothrix, Thiobacillus, Halothiobacillus, and Thiomonas) were identified. Different variations of the soxB genes were present at different locations within the spring outflow channel in a manner that significantly corresponded to geochemical conditions. The distribution of the different soxB gene sequence variations suggests that the enzymes encoded by these genes are functionally different and could be optimized to specific geochemical conditions that define niche space for bacteria capable of oxidizing reduced sulfur compounds.}, } @article {pmid23220059, year = {2013}, author = {Alhamlan, FS and Ederer, MM and Brown, CJ and Coats, ER and Crawford, RL}, title = {Metagenomics-based analysis of viral communities in dairy lagoon wastewater.}, journal = {Journal of microbiological methods}, volume = {92}, number = {2}, pages = {183-188}, doi = {10.1016/j.mimet.2012.11.016}, pmid = {23220059}, issn = {1872-8359}, support = {P20RR16448/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; *Biodiversity ; Computational Biology ; *Food Industry ; Metagenomics/*methods ; Microscopy, Electron, Transmission ; Viruses/*classification/*genetics/ultrastructure ; Wastewater/*virology ; }, abstract = {Microbial populations, especially those of viruses, are poorly studied in dairy wastewater treatment operations. Here we report signature nucleic acid metagenomic sequences obtained by pyrosequencing viromes of virus-like particles that were extracted from two dairy waste treatment lagoons. The lagoons are operated in series, with Lagoon I being used as the primary stage and Lagoon II as the secondary stage of wastewater treatment. An average of 2000 sequences was obtained from each lagoon. More than 300 signatures from each lagoon matched sequences in the virus database of the National Center for Biotechnology Information (NCBI). We utilized a bioinformatics approach and transmission electron microscopy (TEM) to characterize the viral diversity and presence of potential viral pathogens within the lagoons. Our results showed differences in viral community compositions between Lagoon I and Lagoon II, suggesting that the viral community changes significantly in the transition of water between the two lagoons. Furthermore, the diverse viral community in the lagoon samples contained signature sequences of a variety of bacterial, plant, and animal viruses. Bacteriophage sequences dominated the viral community metagenomes in both lagoons. Ultimately these results can be used to identify viral bioindicators to rapidly assess wastewater treatment quality and the potential impacts of dairy operations on watersheds. Our viral metagenomic sequences have been submitted to GenBank (GPID 65805) and can provide insight into the composition and structure of viral communities within wastewaters of dairy lagoon systems.}, } @article {pmid23212172, year = {2012}, author = {Gonzaga, A and Martin-Cuadrado, AB and López-Pérez, M and Megumi Mizuno, C and García-Heredia, I and Kimes, NE and Lopez-García, P and Moreira, D and Ussery, D and Zaballos, M and Ghai, R and Rodriguez-Valera, F}, title = {Polyclonality of concurrent natural populations of Alteromonas macleodii.}, journal = {Genome biology and evolution}, volume = {4}, number = {12}, pages = {1360-1374}, pmid = {23212172}, issn = {1759-6653}, mesh = {Alteromonas/*genetics/isolation & purification ; Bacterial Proteins/genetics ; Base Sequence ; *Ecotype ; *Genetic Variation ; *Genome, Bacterial ; Genomic Islands ; Genomic Library ; Molecular Sequence Data ; Receptors, Cell Surface/genetics ; Recombination, Genetic ; Seawater/microbiology ; }, abstract = {We have analyzed a natural population of the marine bacterium, Alteromonas macleodii, from a single sample of seawater to evaluate the genomic diversity present. We performed full genome sequencing of four isolates and 161 metagenomic fosmid clones, all of which were assigned to A. macleodii by sequence similarity. Out of the four strain genomes, A. macleodii deep ecotype (AltDE1) represented a different genome, whereas AltDE2 and AltDE3 were identical to the previously described AltDE. Although the core genome (~80%) had an average nucleotide identity of 98.51%, both AltDE and AltDE1 contained flexible genomic islands (fGIs), that is, genomic islands present in both genomes in the same genomic context but having different gene content. Some of the fGIs encode cell surface receptors known to be phage recognition targets, such as the O-chain of the lipopolysaccharide, whereas others have genes involved in physiological traits (e.g., nutrient transport, degradation, and metal resistance) denoting microniche specialization. The presence in metagenomic fosmids of genomic fragments differing from the sequenced strain genomes, together with the presence of new fGIs, indicates that there are at least two more A. macleodii clones present. The availability of three or more sequences overlapping the same genomic region also allowed us to estimate the frequency and distribution of recombination events among these different clones, indicating that these clustered near the genomic islands. The results indicate that this natural A. macleodii population has multiple clones with a potential for different phage susceptibility and exploitation of resources, within a seemingly unstructured habitat.}, } @article {pmid23199876, year = {2012}, author = {de Pascale, D and De Santi, C and Fu, J and Landfald, B}, title = {The microbial diversity of Polar environments is a fertile ground for bioprospecting.}, journal = {Marine genomics}, volume = {8}, number = {}, pages = {15-22}, doi = {10.1016/j.margen.2012.04.004}, pmid = {23199876}, issn = {1876-7478}, mesh = {Adaptation, Physiological ; Antarctic Regions ; Arctic Regions ; Bacteria/*classification/*genetics ; *Biodiversity ; Biological Products/chemistry/metabolism ; Genetic Variation ; Metagenomics ; Phylogeny ; }, abstract = {The term bioprospecting has been adopted for systematic searches in nature for new bioactive compounds, genes, proteins, microorganisms and other products with potential for commercial use. Much effort has been focused on microorganisms able to thrive under harsh conditions, including the Polar environments. Both the lipid and protein cellular building blocks of Polar microorganisms are shaped by their adaptation to the permanently low temperatures. In addition, strongly differing environments, such as permafrost, glaciers and sea ice, have contributed to additional functional diversity. Emerging massive-parallel sequencing technologies have revealed the existence of a huge, hitherto unseen diversity of low-abundance phylotypes--the rare biosphere--even in the Polar environments. This realization has further strengthened the need to employ cultivation-independent approaches, including metagenomics and single-cell genomic sequencing, to get comprehensive access to the genetic diversity of microbial communities for bioprospecting purposes. In this review, we present an updated snapshot of recent findings on the molecular basis for adaptation to the cold and the phylogenetic diversities of different Polar environments. Novel approaches in bioprospecting are presented and we conclude by showing recent bioprospecting outcomes in terms of new molecules patented or applied by some biotech companies.}, } @article {pmid23199136, year = {2013}, author = {Wilkins, D and Lauro, FM and Williams, TJ and Demaere, MZ and Brown, MV and Hoffman, JM and Andrews-Pfannkoch, C and McQuaid, JB and Riddle, MJ and Rintoul, SR and Cavicchioli, R}, title = {Biogeographic partitioning of Southern Ocean microorganisms revealed by metagenomics.}, journal = {Environmental microbiology}, volume = {15}, number = {5}, pages = {1318-1333}, doi = {10.1111/1462-2920.12035}, pmid = {23199136}, issn = {1462-2920}, mesh = {Amino Acids, Branched-Chain/genetics ; Bacteria/*classification/*genetics/metabolism ; *Biodiversity ; Cyanobacteria/classification/genetics ; Eukaryota/genetics/metabolism/physiology ; *Metagenomics ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; *Water Microbiology ; }, abstract = {We performed a metagenomic survey (6.6 Gbp of 454 sequence data) of Southern Ocean (SO) microorganisms during the austral summer of 2007-2008, examining the genomic signatures of communities across a latitudinal transect from Hobart (44°S) to the Mertz Glacier, Antarctica (67°S). Operational taxonomic units (OTUs) of the SAR11 and SAR116 clades and the cyanobacterial genera Prochlorococcus and Synechococcus were strongly overrepresented north of the Polar Front (PF). Conversely, OTUs of the Gammaproteobacterial Sulfur Oxidizer-EOSA-1 (GSO-EOSA-1) complex, the phyla Bacteroidetes and Verrucomicrobia and order Rhodobacterales were characteristic of waters south of the PF. Functions enriched south of the PF included a range of transporters, sulfur reduction and histidine degradation to glutamate, while branched-chain amino acid transport, nucleic acid biosynthesis and methionine salvage were overrepresented north of the PF. The taxonomic and functional characteristics suggested a shift of primary production from cyanobacteria in the north to eukaryotic phytoplankton in the south, and reflected the different trophic statuses of the two regions. The study provides a new level of understanding about SO microbial communities, describing the contrasting taxonomic and functional characteristics of microbial assemblages either side of the PF.}, } @article {pmid23197942, year = {2012}, author = {Siggins, A and Enright, AM and Abram, F and Botting, C and O'Flaherty, V}, title = {Impact of trichloroethylene exposure on the microbial diversity and protein expression in anaerobic granular biomass at 37°C and 15°C.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2012}, number = {}, pages = {940159}, pmid = {23197942}, issn = {1472-3654}, mesh = {Anaerobiosis ; Biomass ; Bioreactors/*microbiology ; *Biota ; Cluster Analysis ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Metagenome ; Molecular Sequence Data ; Phylogeny ; Proteins/*metabolism ; Proteobacteria/*classification/genetics/metabolism ; Proteome ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Temperature ; Trichloroethylene/*toxicity ; *Water Microbiology ; }, abstract = {Granular biomass from a laboratory-scale anaerobic bioreactor trial was analysed to identify changes in microbial community structure and function in response to temperature and trichloroethylene (TCE). Two bioreactors were operated at 37°C, while two were operated at 15°C. At the time of sampling, one of each temperature pair of bioreactors was exposed to process failure-inducing concentrations of TCE (60 mg L(-1)) while the other served as a TCE-free control. Bacterial community structure was investigated using denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library analysis. Temperature was identified as an important factor for bacterial community composition, while minor differences were associated with trichloroethylene supplementation. Proteobacteria was the dominant phylum in all bioreactors, while clone library analysis revealed a higher proportion of Bacteroidetes-, Chloroflexi-, and Firmicutes-like clones at 15°C than at 37°C. Comparative metaproteomics in the presence and absence of TCE was carried out by two-dimensional gel electrophoresis (2-DGE), and 28 protein spots were identified, with putative functions related to cellular processes, including methanogenesis, glycolysis, the glyoxylate cycle, and the methyl malonyl pathway. A good agreement between metaproteomic species assignment and phylogenetic information was observed, with 10 of the identified proteins associated with members of the phylum Proteobacteria.}, } @article {pmid23197941, year = {2012}, author = {Wemheuer, B and Wemheuer, F and Daniel, R}, title = {RNA-based assessment of diversity and composition of active archaeal communities in the German Bight.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2012}, number = {}, pages = {695826}, pmid = {23197941}, issn = {1472-3654}, mesh = {Archaea/*classification/*genetics/isolation & purification ; *Biodiversity ; Germany ; *Metagenome ; Molecular Sequence Data ; RNA, Archaeal/*genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Archaea play an important role in various biogeochemical cycles. They are known extremophiles inhabiting environments such as thermal springs or hydrothermal vents. Recent studies have revealed a significant abundance of Archaea in moderate environments, for example, temperate sea water. Nevertheless, the composition and ecosystem function of these marine archaeal communities is largely unknown. To assess diversity and composition of active archaeal communities in the German Bight, seven marine water samples were taken and studied by RNA-based analysis of ribosomal 16S rRNA. For this purpose, total RNA was extracted from the samples and converted to cDNA. Archaeal community structures were investigated by pyrosequencing-based analysis of 16S rRNA amplicons generated from cDNA. To our knowledge, this is the first study combining next-generation sequencing and metatranscriptomics to study archaeal communities in marine habitats. The pyrosequencing-derived dataset comprised 62,045 archaeal 16S rRNA sequences. We identified Halobacteria as the predominant archaeal group across all samples with increased abundance in algal blooms. Thermoplasmatales (Euryarchaeota) and the Marine Group I (Thaumarchaeota) were identified in minor abundances. It is indicated that archaeal community patterns were influenced by environmental conditions.}, } @article {pmid23190727, year = {2013}, author = {Hamdan, LJ and Coffin, RB and Sikaroodi, M and Greinert, J and Treude, T and Gillevet, PM}, title = {Ocean currents shape the microbiome of Arctic marine sediments.}, journal = {The ISME journal}, volume = {7}, number = {4}, pages = {685-696}, pmid = {23190727}, issn = {1751-7370}, mesh = {Alaska ; Archaea/*classification/genetics ; Arctic Regions ; Bacteria/*classification/genetics ; Biodiversity ; Euryarchaeota/classification/genetics ; Geologic Sediments/chemistry/*microbiology ; *Metagenome ; Pacific Ocean ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Prokaryote communities were investigated on the seasonally stratified Alaska Beaufort Shelf (ABS). Water and sediment directly underlying water with origin in the Arctic, Pacific or Atlantic oceans were analyzed by pyrosequencing and length heterogeneity-PCR in conjunction with physicochemical and geographic distance data to determine what features structure ABS microbiomes. Distinct bacterial communities were evident in all water masses. Alphaproteobacteria explained similarity in Arctic surface water and Pacific derived water. Deltaproteobacteria were abundant in Atlantic origin water and drove similarity among samples. Most archaeal sequences in water were related to unclassified marine Euryarchaeota. Sediment communities influenced by Pacific and Atlantic water were distinct from each other and pelagic communities. Firmicutes and Chloroflexi were abundant in sediment, although their distribution varied in Atlantic and Pacific influenced sites. Thermoprotei dominated archaea in Pacific influenced sediments and Methanomicrobia dominated in methane-containing Atlantic influenced sediments. Length heterogeneity-PCR data from this study were analyzed with data from methane-containing sediments in other regions. Pacific influenced ABS sediments clustered with Pacific sites from New Zealand and Chilean coastal margins. Atlantic influenced ABS sediments formed another distinct cluster. Density and salinity were significant structuring features on pelagic communities. Porosity co-varied with benthic community structure across sites and methane did not. This study indicates that the origin of water overlying sediments shapes benthic communities locally and globally and that hydrography exerts greater influence on microbial community structure than the availability of methane.}, } @article {pmid23189159, year = {2012}, author = {Links, MG and Dumonceaux, TJ and Hemmingsen, SM and Hill, JE}, title = {The chaperonin-60 universal target is a barcode for bacteria that enables de novo assembly of metagenomic sequence data.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e49755}, pmid = {23189159}, issn = {1932-6203}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Bacteria/classification/*genetics/*metabolism ; Chaperonin 60/genetics/*metabolism ; DNA Barcoding, Taxonomic ; Genes, Bacterial ; Genome, Bacterial ; *Metagenomics ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {Barcoding with molecular sequences is widely used to catalogue eukaryotic biodiversity. Studies investigating the community dynamics of microbes have relied heavily on gene-centric metagenomic profiling using two genes (16S rRNA and cpn60) to identify and track Bacteria. While there have been criteria formalized for barcoding of eukaryotes, these criteria have not been used to evaluate gene targets for other domains of life. Using the framework of the International Barcode of Life we evaluated DNA barcodes for Bacteria. Candidates from the 16S rRNA gene and the protein coding cpn60 gene were evaluated. Within complete bacterial genomes in the public domain representing 983 species from 21 phyla, the largest difference between median pairwise inter- and intra-specific distances ("barcode gap") was found from cpn60. Distribution of sequence diversity along the ∼555 bp cpn60 target region was remarkably uniform. The barcode gap of the cpn60 universal target facilitated the faithful de novo assembly of full-length operational taxonomic units from pyrosequencing data from a synthetic microbial community. Analysis supported the recognition of both 16S rRNA and cpn60 as DNA barcodes for Bacteria. The cpn60 universal target was found to have a much larger barcode gap than 16S rRNA suggesting cpn60 as a preferred barcode for Bacteria. A large barcode gap for cpn60 provided a robust target for species-level characterization of data. The assembly of consensus sequences for barcodes was shown to be a reliable method for the identification and tracking of novel microbes in metagenomic studies.}, } @article {pmid23188460, year = {2013}, author = {Liu, M and Zhang, Y and Ding, R and Gao, Y and Yang, M}, title = {Response of activated sludge to the treatment of oxytetracycline production waste stream.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {19}, pages = {8805-8812}, doi = {10.1007/s00253-012-4589-8}, pmid = {23188460}, issn = {1432-0614}, mesh = {Anti-Bacterial Agents/*metabolism ; Bacteria/*drug effects/growth & development/metabolism ; Biological Oxygen Demand Analysis ; *Biota ; Drug Resistance, Bacterial ; Eukaryota/growth & development ; Interspersed Repetitive Sequences ; Metagenome ; Molecular Sequence Data ; Oxytetracycline/*metabolism ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sewage/microbiology ; Wastewater/*chemistry/*microbiology ; Water Purification/*methods ; }, abstract = {To investigate how the microbial community in activated sludge responded to high antibiotic levels, a bench-scale aerobic wastewater treatment system was used to treat oxytetracycline (OTC) mother liquor (OTC-ML). Removal efficiency of chemical oxygen demand decreased from 64.9 to 51.0 % when the OTC level increased from 191.6 to 620.5 mg/L, respectively. According to the cloning results, Psychrobacter and Cryptophyta were the dominant bacterium and eukaryote in the inoculated sludge, respectively, both of which related to low temperature. After OTC exposure, Alphaproteobacteria and Betaproteobacteria became the dominant bacteria, with a small proportion of Firmicutes, Actinobacteria appeared, and fungi (mainly Saccharomycotina) became the dominant eukaryotes, indicating the possible functions of these microorganisms in the wastewater treatment of OTC-ML. The relative abundance of nine tetracycline resistance genes and four mobile elements (class 1 integron, class 2 integron, transposon Tn916/1545, and pattern 1 insertion sequence common region) significantly increased from undetectable to 2.1 × 10(-3) in the inoculated sludge to 1.7 × 10(-4)-9.8 × 10(-1) in sludge exposed to 620.5 mg/L OTC by using real-time PCR. The variety of gene cassette arrays of class 1 integron in the sludge samples increased with increasing OTC exposure concentration.}, } @article {pmid23185130, year = {2012}, author = {Schluter, J and Foster, KR}, title = {The evolution of mutualism in gut microbiota via host epithelial selection.}, journal = {PLoS biology}, volume = {10}, number = {11}, pages = {e1001424}, pmid = {23185130}, issn = {1545-7885}, mesh = {Bacteria/genetics/*growth & development ; *Biological Evolution ; Biota ; Computer Simulation ; Gastrointestinal Tract/metabolism/*microbiology ; Genetic Variation ; Humans ; Intestinal Mucosa/*metabolism/microbiology ; Intestinal Secretions/microbiology ; *Metagenome ; Models, Biological ; Selection, Genetic ; *Symbiosis ; }, abstract = {The human gut harbours a large and genetically diverse population of symbiotic microbes that both feed and protect the host. Evolutionary theory, however, predicts that such genetic diversity can destabilise mutualistic partnerships. How then can the mutualism of the human microbiota be explained? Here we develop an individual-based model of host-associated microbial communities. We first demonstrate the fundamental problem faced by a host: The presence of a genetically diverse microbiota leads to the dominance of the fastest growing microbes instead of the microbes that are most beneficial to the host. We next investigate the potential for host secretions to influence the microbiota. This reveals that the epithelium-microbiota interface acts as a selectivity amplifier: Modest amounts of moderately selective epithelial secretions cause a complete shift in the strains growing at the epithelial surface. This occurs because of the physical structure of the epithelium-microbiota interface: Epithelial secretions have effects that permeate upwards through the whole microbial community, while lumen compounds preferentially affect cells that are soon to slough off. Finally, our model predicts that while antimicrobial secretion can promote host epithelial selection, epithelial nutrient secretion will often be key to host selection. Our findings are consistent with a growing number of empirical papers that indicate an influence of host factors upon microbiota, including growth-promoting glycoconjugates. We argue that host selection is likely to be a key mechanism in the stabilisation of the mutualism between a host and its microbiota.}, } @article {pmid23183985, year = {2013}, author = {An, C and Kuda, T and Yazaki, T and Takahashi, H and Kimura, B}, title = {FLX pyrosequencing analysis of the effects of the brown-algal fermentable polysaccharides alginate and laminaran on rat cecal microbiotas.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {3}, pages = {860-866}, pmid = {23183985}, issn = {1098-5336}, mesh = {Alginates/*metabolism ; Animals ; *Biodiversity ; Carboxylic Acids/analysis ; Cecum/*microbiology ; DNA Barcoding, Taxonomic ; Diet/*methods ; Glucans ; Glucuronic Acid/metabolism ; Hexuronic Acids/metabolism ; *Metagenome ; Phaeophyceae/*chemistry ; Polysaccharides/*metabolism ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rats ; }, abstract = {Edible brown algae are used as major food material in Far East Asian countries, particularly in South Korea and Japan. They contain fermentable dietary fibers, alginic acid (uronic acid polymer) and laminaran (β-1,3-glucan), that are fermented into organic acids by intestinal bacteria. To clarify the effect of edible algae on the intestinal environment, the cecal microbiotas of rats fed diets containing no dietary fiber (control) or 2% (wt/wt) sodium alginate or laminaran for 2 weeks were analyzed using FLX amplicon pyrosequencing with bar-coded primers targeting the bacterial 16S rRNA gene. The most abundant phylum in all groups was Firmicutes. Specifically, Allobaculum was dominant in all diet groups. In addition, Bacteroides capillosus (37.1%) was abundant in the alginate group, while Clostridium ramosum (3.14%) and Parabacteroides distasonis (1.36%) were only detected in the laminaran group. Furthermore, rats fed alginate showed simplified microbiota phylotypes compared with others. With respect to cecal chemical compounds, laminaran increased cecal organic acid levels, particularly propionic acid. Alginate increased total cecal organic acids. Cecal putrefactive compounds, such as indole, H(2)S, and phenol, were decreased by both alginate and laminaran. These results indicate that edible brown algae can alter the intestinal environment, with fermentation by intestinal microbiota.}, } @article {pmid23183474, year = {2012}, author = {Ismail, F and Baetzner, C and Heuer, W and Stumpp, N and Eberhard, J and Winkel, A and Ismail, I and Haverich, A and Stiesch, M}, title = {16S rDNA-based metagenomic analysis of human oral plaque microbiota in patients with atherosclerosis and healthy controls.}, journal = {Indian journal of medical microbiology}, volume = {30}, number = {4}, pages = {462-466}, doi = {10.4103/0255-0857.103771}, pmid = {23183474}, issn = {1998-3646}, mesh = {Adult ; Aged ; Atherosclerosis/*complications ; Biodiversity ; Dental Plaque/*microbiology ; Female ; Humans ; Male ; *Metagenome ; Middle Aged ; Polymorphism, Single-Stranded Conformational ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {To address the question if an altered oral microbiota is associated with atherosclerosis. Twenty patients suffering from atherosclerosis and 10 controls were recruited. Clinical oral, medical and laboratory investigations were performed. Oral bacteria were collected and 16S rDNA was sequenced following Single strand conformation polymorphism.(SSCP) Probing pocket depths in patients were significantly elevated. The oral microbiota of patients and controls were dominated by Fusobacterium (16%/17%), Streptococcus (21%/14%), Prevotella (10%/12%), Enterococcus (12%/12%), Porphyromonas (8%/7%), TM7 (0%/7%) and Veillonella (6%/7%). Differences in diversity were not significant between groups. The pathology of atherosclerosis may not be related to significant qualitative changes of the oral microbiota.}, } @article {pmid23178379, year = {2013}, author = {He, Y and Xie, K and Xu, P and Huang, X and Gu, W and Zhang, F and Tang, S}, title = {Evolution of microbial community diversity and enzymatic activity during composting.}, journal = {Research in microbiology}, volume = {164}, number = {2}, pages = {189-198}, doi = {10.1016/j.resmic.2012.11.001}, pmid = {23178379}, issn = {1769-7123}, mesh = {Animals ; Bacteria/*classification/enzymology/genetics/growth & development ; *Biota ; Carbon/analysis ; Chickens ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; Hydrogen-Ion Concentration ; Manure/microbiology ; *Metagenome ; Molecular Sequence Data ; Nitrogen/analysis ; Peptide Hydrolases/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The composting of organic material is dependent on microbial activity. However, the dynamics of the microbial community during the composting process remain obscure. Here, denaturing gradient gel electrophoresis of 16S rDNA amplicons in a chicken manure-based compost was applied to characterize the components of the microbial community during the composting process. In addition, the activity of key microbial enzymes was monitored. Arcobacter spp. and Marinospirillum spp. were the dominant species prior to composting, whereas Thermotogae spp. became more strongly represented as the composting process proceeded. Bacillus and Cohnella spp. were featured at various phases. Correlation analysis showed that the diversity of the microbial community was positively correlated with the compost pH, its total nitrogen level, its carbon-to-nitrogen ratio and the activity of protease, and negatively correlated with its organic carbon content and seed germination indices.}, } @article {pmid23176508, year = {2012}, author = {Abrudan, MI and Brown, S and Rozen, DE}, title = {Killing as means of promoting biodiversity.}, journal = {Biochemical Society transactions}, volume = {40}, number = {6}, pages = {1512-1516}, doi = {10.1042/BST20120196}, pmid = {23176508}, issn = {1470-8752}, mesh = {Adaptation, Biological ; Antibiosis/genetics ; Bacteriocins/genetics/*metabolism ; Biodiversity ; Evolution, Molecular ; Gram-Negative Bacteria/genetics/metabolism ; Gram-Positive Bacteria/genetics/metabolism ; Humans ; Metagenome ; Models, Biological ; }, abstract = {Bacteriocins are usually viewed as the effective weapons of bacterial killers. However, killing competitors with bacteriocins may be not only a means of eliminating other strains, but also a crucial unappreciated mechanism promoting bacterial diversity. In the present short review, we summarize recent empirical and theoretical studies examining the role bacteriocins that may play in driving and maintaining diversity among microbes. We conclude by highlighting limitations of current models and suggest directions for future studies.}, } @article {pmid23176186, year = {2012}, author = {Cui, Z and Zhou, Y and Li, H and Zhang, Y and Zhang, S and Tang, S and Guo, X}, title = {Complex sputum microbial composition in patients with pulmonary tuberculosis.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {276}, pmid = {23176186}, issn = {1471-2180}, mesh = {Adult ; Aged ; Bacteria/*classification/*genetics ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Humans ; Male ; *Metagenome ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sputum/*microbiology ; Tuberculosis, Pulmonary/*microbiology ; Young Adult ; }, abstract = {BACKGROUND: An increasing number of studies have implicated the microbiome in certain diseases, especially chronic diseases. In this study, the bacterial communities in the sputum of pulmonary tuberculosis patients were explored. Total DNA was extracted from sputum samples from 31 pulmonary tuberculosis patients and respiratory secretions of 24 healthy participants. The 16S rRNA V3 hyper-variable regions were amplified using bar-coded primers and pyro-sequenced using Roche 454 FLX.

RESULTS: The results showed that the microbiota in the sputum of pulmonary tuberculosis patients were more diverse than those of healthy participants (p<0.05). The sequences were classified into 24 phyla, all of which were found in pulmonary tuberculosis patients and 17 of which were found in healthy participants. Furthermore, many foreign bacteria, such as Stenotrophomonas, Cupriavidus, Pseudomonas, Thermus, Sphingomonas, Methylobacterium, Diaphorobacter, Comamonas, and Mobilicoccus, were unique to pulmonary tuberculosis patients.

CONCLUSIONS: This study concluded that the microbial composition of the respiratory tract of pulmonary tuberculosis patients is more complicated than that of healthy participants, and many foreign bacteria were found in the sputum of pulmonary tuberculosis patients. The roles of these foreign bacteria in the onset or development of pulmonary tuberculosis should be considered by clinicians.}, } @article {pmid23173441, year = {2012}, author = {Ding, J and Zhang, Q and Liu, X and Wang, G and Tian, F and Zhang, H and Chen, W}, title = {[Quantity of Desulfovibrios and analysis of intestinal microbiota diversity in health and intestinal disease people in Wuxi, Jiangsu province].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {52}, number = {8}, pages = {1033-1039}, pmid = {23173441}, issn = {0001-6209}, mesh = {Adult ; Aged ; Bacteria/classification/genetics/*isolation & purification ; *Biodiversity ; China ; DNA, Bacterial/genetics ; Desulfovibrio/classification/genetics/isolation & purification ; Female ; Humans ; Intestinal Diseases/*microbiology ; Intestines/*microbiology ; Male ; *Metagenome ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVE: This paper provides an overview of Desulfovibrio (DSV) incidence and its effect on bacterial diversity in human gastrointestinal tract of four groups: ulcerative colitis (UC), colorectal cancer (CRC), polypus (PP) and the healthy control (H).

METHODS: Real time fluorescence quantitative PCR (RT-PCR) assays were used to enumerate DSV in gastrointestinal tract of 58 subjects. Diversity of gut microbiota was analyzed by PCR-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) and 16S rRNA V3 sequencing.

RESULTS: RT-PCR detected DSV in all samples. Significantly increased numbers of DSV were observed for UC and PP groups compared with CRC and H groups. No significant difference was observed for CRC and H groups with gene copy numbers of DSV. Alterations of DSV and gut microbiota were observed in disease groups.

CONCLUSION: We found that quantity and diversity of DSV are significantly increased in UC and PP compared to controls. The increased numbers of DSV in disease groups suggests a possible harmful role.}, } @article {pmid23161451, year = {2013}, author = {Luis-Villaseñor, IE and Castellanos-Cervantes, T and Gomez-Gil, B and Carrillo-García, AE and Campa-Córdova, AI and Ascencio, F}, title = {Probiotics in the intestinal tract of juvenile whiteleg shrimp Litopenaeus vannamei: modulation of the bacterial community.}, journal = {World journal of microbiology & biotechnology}, volume = {29}, number = {2}, pages = {257-265}, pmid = {23161451}, issn = {1573-0972}, mesh = {Animals ; Bacillus/*physiology ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Intestines/drug effects/growth & development/microbiology ; *Metagenome ; Penaeidae/*drug effects/growth & development/*microbiology ; Probiotics/*pharmacology ; Vibrio parahaemolyticus/physiology ; }, abstract = {Molecular analysis of the 16S rDNA of the intestinal microbiota of whiteleg shrimp Litopenaeus vannamei was examined to investigate the effect of a Bacillus mix (Bacillus endophyticus YC3-b, Bacillus endophyticus C2-2, Bacillus tequilensisYC5-2) and the commercial probiotic (Alibio(®)) on intestinal bacterial communities and resistance to Vibrio infection. PCR and single strain conformation polymorphism (SSCP) analyses were then performed on DNA extracted directly from guts. Injection of shrimp with V. parahaemolyticus at 2.5 × 10(5) CFU g(-1) per shrimp followed 168 h after inoculation with Bacillus mix or the Alibio probiotic or the positive control. Diversity analyses showed that the bacterial community resulting from the Bacillus mix had the highest diversity and evenness and the bacterial community of the control had the lowest diversity. The bacterial community treated with probiotics mainly consisted of α- and γ-proteobacteria, fusobacteria, sphingobacteria, and flavobacteria, while the control mainly consisted of α-proteobacteria and flavobacteria. Differences were grouped using principal component analyses of PCR-SSCP of the microbiota, according to the time of inoculation. In Vibrio parahaemolyticus-infected shrimp, the Bacillus mix (~33 %) induced a significant increase in survival compared to Alibio (~21 %) and the control (~9 %). We conclude that administration of the Bacillus mix induced modulation of the intestinal microbiota of L. vannamei and increased its resistance to V. parahaemolyticus.}, } @article {pmid23161352, year = {2013}, author = {Ganu, RS and Ma, J and Aagaard, KM}, title = {The role of microbial communities in parturition: is there evidence of association with preterm birth and perinatal morbidity and mortality?.}, journal = {American journal of perinatology}, volume = {30}, number = {8}, pages = {613-624}, doi = {10.1055/s-0032-1329693}, pmid = {23161352}, issn = {1098-8785}, mesh = {Adult ; Female ; Genetic Predisposition to Disease ; Humans ; Infant, Newborn ; Metagenomics/methods ; Microbiota/*physiology ; *Perinatal Mortality ; Pregnancy ; Pregnancy Complications, Infectious/genetics/*microbiology ; Premature Birth/*etiology/genetics/microbiology ; Uterus/*microbiology/pathology ; Vagina/*microbiology ; }, abstract = {In 2005, the World Health Organization estimated that 9.6% or 12.9 million births worldwide were born preterm at <37 weeks of gestation and were accompanied by a mortality rate as high as 42% (http://www.who.int/bulletin/volumes/88/1/08-062554). Significant data suggesting that intrauterine infection is an important modifier for the risk of preterm birth have emerged over the past four decades. However, causative microbial culprits have yet to be identified, and interventional trials with antimicrobials have uniformly failed to demonstrate a significant benefit. To the contrary, treatment for clinically asymptomatic, commonly associated polymicrobial communities (i.e., bacterial vaginosis) has resulted in an increase in the rate of preterm birth. This article discusses the importance of vaginal microbiome and the variance in its composition during normal pregnancy. We will expand this discussion to include possible mechanisms that might trigger preterm birth in at-risk subjects. Finally, we will review why preterm birth may be an ideal forum with which to apply our rapidly expanding metagenomic sequencing and analytic pipelines to discern the role of host and microbe in the relative continuum of health and disease.}, } @article {pmid23160129, year = {2013}, author = {Chandler, DP and Knickerbocker, C and Bryant, L and Golova, J and Wiles, C and Williams, KH and Peacock, AD and Long, PE}, title = {Profiling in situ microbial community structure with an amplification microarray.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {3}, pages = {799-807}, pmid = {23160129}, issn = {1098-5336}, mesh = {Acetates/metabolism ; Bacteria/*classification/*genetics ; *Biota ; DNA, Bacterial/genetics ; Groundwater/*microbiology ; Metagenomics/*methods ; Microarray Analysis/*methods ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; Sodium Bicarbonate/metabolism ; }, abstract = {The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an in situ field experiment designed to compare U(VI) mobility under conditions of various alkalinities (as HCO(3)(-)) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consistent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (Flexibacter, Geobacter, Rhodoferax, and Shewanella) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO(3), but at much lower signal intensities and with a much more rapid decline (to nondetection). Azoarcus, Thaurea, and Methylobacterium were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications.}, } @article {pmid23159051, year = {2012}, author = {Bäckhed, F and Fraser, CM and Ringel, Y and Sanders, ME and Sartor, RB and Sherman, PM and Versalovic, J and Young, V and Finlay, BB}, title = {Defining a healthy human gut microbiome: current concepts, future directions, and clinical applications.}, journal = {Cell host & microbe}, volume = {12}, number = {5}, pages = {611-622}, doi = {10.1016/j.chom.2012.10.012}, pmid = {23159051}, issn = {1934-6069}, mesh = {Anti-Bacterial Agents ; Gastrointestinal Tract/*microbiology ; Humans ; Intestinal Diseases/*microbiology ; *Metagenome ; Microbial Consortia ; Prebiotics ; Probiotics ; }, abstract = {Indigenous microbiota are an essential component in the modern concept of human health, but the composition and functional characteristics of a healthy microbiome remain to be precisely defined. Patterns of microbial colonization associated with disease states have been documented, but the health-associated microbial patterns and their functional characteristics are less clear. A healthy microbiome, considered in the context of body habitat or body site, could be described in terms of ecologic stability (i.e., ability to resist community structure change under stress or to rapidly return to baseline following a stress-related change), by an idealized (presumably health-associated) composition or by a desirable functional profile (including metabolic and trophic provisions to the host). Elucidation of the properties of healthy microbiota would provide a target for dietary interventions and/or microbial modifications aimed at sustaining health in generally healthy populations and improving the health of individuals exhibiting disrupted microbiota and associated diseases.}, } @article {pmid23157386, year = {2013}, author = {Egan, S and Harder, T and Burke, C and Steinberg, P and Kjelleberg, S and Thomas, T}, title = {The seaweed holobiont: understanding seaweed-bacteria interactions.}, journal = {FEMS microbiology reviews}, volume = {37}, number = {3}, pages = {462-476}, doi = {10.1111/1574-6976.12011}, pmid = {23157386}, issn = {1574-6976}, mesh = {Bacteria/metabolism/pathogenicity ; *Bacterial Physiological Phenomena ; *Biodiversity ; *Host-Pathogen Interactions ; *Metagenome ; Seaweed/*microbiology ; *Symbiosis ; }, abstract = {Seaweeds (macroalgae) form a diverse and ubiquitous group of photosynthetic organisms that play an essential role in aquatic ecosystems. These ecosystem engineers contribute significantly to global primary production and are the major habitat formers on rocky shores in temperate waters, providing food and shelter for aquatic life. Like other eukaryotic organisms, macroalgae harbor a rich diversity of associated microorganisms with functions related to host health and defense. In particular, epiphytic bacterial communities have been reported as essential for normal morphological development of the algal host, and bacteria with antifouling properties are thought to protect chemically undefended macroalgae from detrimental, secondary colonization by other microscopic and macroscopic epibiota. This tight relationship suggests that macroalgae and epiphytic bacteria interact as a unified functional entity or holobiont, analogous to the previously suggested relationship in corals. Moreover, given that the impact of diseases in marine ecosystems is apparently increasing, understanding the role of bacteria as saprophytes and pathogens in seaweed communities may have important implications for marine management strategies. This review reports on the recent advances in the understanding of macroalgal-bacterial interactions with reference to the diversity and functional role of epiphytic bacteria in maintaining algal health, highlighting the holobiont concept.}, } @article {pmid23154883, year = {2013}, author = {Cox, LM and Cho, I and Young, SA and Anderson, WH and Waters, BJ and Hung, SC and Gao, Z and Mahana, D and Bihan, M and Alekseyenko, AV and Methé, BA and Blaser, MJ}, title = {The nonfermentable dietary fiber hydroxypropyl methylcellulose modulates intestinal microbiota.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {27}, number = {2}, pages = {692-702}, pmid = {23154883}, issn = {1530-6860}, support = {R01 DK090989/DK/NIDDK NIH HHS/United States ; UL1 RR029893/RR/NCRR NIH HHS/United States ; R01DK098989/DK/NIDDK NIH HHS/United States ; 1UL1RR029893/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Body Weight ; Diet, Fat-Restricted ; Diet, High-Fat ; Dietary Fiber/*administration & dosage ; Hypromellose Derivatives ; Intestines/*microbiology ; Metabolome ; *Metagenome/genetics ; Methylcellulose/administration & dosage/*analogs & derivatives ; Mice ; Mice, Inbred C57BL ; Phylogeny ; Prebiotics ; RNA, Bacterial/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics/isolation & purification ; }, abstract = {Diet influences host metabolism and intestinal microbiota; however, detailed understanding of this tripartite interaction is limited. To determine whether the nonfermentable fiber hydroxypropyl methylcellulose (HPMC) could alter the intestinal microbiota and whether such changes correlated with metabolic improvements, C57B/L6 mice were normalized to a high-fat diet (HFD), then either maintained on HFD (control), or switched to HFD supplemented with 10% HPMC, or a low-fat diet (LFD). Compared to control treatment, both LFD and HPMC reduced weight gain (11.8 and 5.7 g, respectively), plasma cholesterol (23.1 and 19.6%), and liver triglycerides (73.1 and 44.6%), and, as revealed by 454-pyrosequencing of the microbial 16S rRNA gene, decreased microbial α-diversity and differentially altered intestinal microbiota. Both LFD and HPMC increased intestinal Erysipelotrichaceae (7.3- and 12.4-fold) and decreased Lachnospiraceae (2.0- and 2.7-fold), while only HPMC increased Peptostreptococcaceae (3.4-fold) and decreased Ruminococcaceae (2.7-fold). Specific microorganisms were directly linked with weight change and metabolic parameters in HPMC and HFD mice, but not in LFD mice, indicating that the intestinal microbiota may play differing roles during the two dietary modulations. This work indicates that HPMC is a potential prebiotic fiber that influences intestinal microbiota and improves host metabolism.}, } @article {pmid23153041, year = {2012}, author = {Zeeuwen, PL and Boekhorst, J and van den Bogaard, EH and de Koning, HD and van de Kerkhof, PM and Saulnier, DM and van Swam, II and van Hijum, SA and Kleerebezem, M and Schalkwijk, J and Timmerman, HM}, title = {Microbiome dynamics of human epidermis following skin barrier disruption.}, journal = {Genome biology}, volume = {13}, number = {11}, pages = {R101}, pmid = {23153041}, issn = {1474-760X}, mesh = {Adult ; Epidermis/immunology/injuries/*microbiology ; Female ; Humans ; Keratinocytes/metabolism/microbiology ; Male ; *Microbiota ; Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA ; Skin/immunology/*microbiology ; }, abstract = {BACKGROUND: Recent advances in sequencing technologies have enabled metagenomic analyses of many human body sites. Several studies have catalogued the composition of bacterial communities of the surface of human skin, mostly under static conditions in healthy volunteers. Skin injury will disturb the cutaneous homeostasis of the host tissue and its commensal microbiota, but the dynamics of this process have not been studied before. Here we analyzed the microbiota of the surface layer and the deeper layers of the stratum corneum of normal skin, and we investigated the dynamics of recolonization of skin microbiota following skin barrier disruption by tape stripping as a model of superficial injury.

RESULTS: We observed gender differences in microbiota composition and showed that bacteria are not uniformly distributed in the stratum corneum. Phylogenetic distance analysis was employed to follow microbiota development during recolonization of injured skin. Surprisingly, the developing neo-microbiome at day 14 was more similar to that of the deeper stratum corneum layers than to the initial surface microbiome. In addition, we also observed variation in the host response towards superficial injury as assessed by the induction of antimicrobial protein expression in epidermal keratinocytes.

CONCLUSIONS: We suggest that the microbiome of the deeper layers, rather than that of the superficial skin layer, may be regarded as the host indigenous microbiome. Characterization of the skin microbiome under dynamic conditions, and the ensuing response of the microbial community and host tissue, will shed further light on the complex interaction between resident bacteria and epidermis.}, } @article {pmid23152108, year = {2013}, author = {Carey, HV and Walters, WA and Knight, R}, title = {Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle.}, journal = {American journal of physiology. Regulatory, integrative and comparative physiology}, volume = {304}, number = {1}, pages = {R33-42}, pmid = {23152108}, issn = {1522-1490}, support = {T32 GM008759/GM/NIGMS NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Acetates/analysis ; Ammonia/analysis ; Animals ; Bacteria/genetics/isolation & purification ; Bacteroidetes/genetics/isolation & purification ; Biodiversity ; Butyrates/analysis ; Fatty Acids, Volatile/analysis ; Female ; Gastrointestinal Tract/*microbiology ; Genes, rRNA ; *Hibernation ; Metagenome/*genetics ; Phylogeny ; Sciuridae/*microbiology/*physiology ; *Seasons ; Verrucomicrobia/genetics/isolation & purification ; }, abstract = {Many hibernating mammals suspend food intake during winter, relying solely on stored lipids to fuel metabolism. Winter fasting in these species eliminates a major source of degradable substrates to support growth of gut microbes, which may affect microbial community structure and host-microbial interactions. We explored the effect of the annual hibernation cycle on gut microbiotas using deep sequencing of 16S rRNA genes from ground squirrel cecal contents. Squirrel microbiotas were dominated by members of the phyla Bacteroidetes, Firmicutes, and Verrucomicrobia. UniFrac analysis showed that microbiotas clustered strongly by season, and maternal influences, diet history, host age, and host body temperature had minimal effects. Phylogenetic diversity and numbers of operational taxonomic units were lowest in late winter and highest in the spring after a 2-wk period of refeeding. Hibernation increased relative abundance of Bacteroidetes and Verrucomicrobia, phyla that contain species capable of surviving on host-derived substrates such as mucins, and reduced relative abundance of Firmicutes, many of which prefer dietary polysaccharides. Hibernation reduced cecal short-chain fatty acid and ammonia concentrations, and increased and decreased concentrations of acetate and butyrate, respectively. These results indicate that the ground squirrel microbiota is restructured each year in a manner that reflects differences in microbial preferences for dietary vs. host-derived substrates, and thus the competitive abilities of different taxa to survive in the altered environment in the hibernator gut.}, } @article {pmid23151157, year = {2012}, author = {Ye, L and Zhang, T and Wang, T and Fang, Z}, title = {Microbial structures, functions, and metabolic pathways in wastewater treatment bioreactors revealed using high-throughput sequencing.}, journal = {Environmental science & technology}, volume = {46}, number = {24}, pages = {13244-13252}, doi = {10.1021/es303454k}, pmid = {23151157}, issn = {1520-5851}, mesh = {Ammonia/metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Biodiversity ; Bioreactors/*microbiology ; DNA, Archaeal/*genetics ; DNA, Bacterial/genetics ; Genes, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/*methods ; *Metabolic Networks and Pathways/genetics ; Phylogeny ; Reproducibility of Results ; Sequence Analysis, DNA ; Sewage/microbiology ; Wastewater/*microbiology ; Water Purification/*instrumentation ; }, abstract = {The objective of this study was to explore microbial community structures, functional profiles, and metabolic pathways in a lab-scale and a full-scale wastewater treatment bioreactors. In order to do this, over 12 gigabases of metagenomic sequence data and 600,000 paired-end sequences of bacterial 16S rRNA gene were generated with the Illumina HiSeq 2000 platform, using DNA extracted from activated sludge in the two bioreactors. Three kinds of sequences (16S rRNA gene amplicons, 16S rRNA gene sequences obtained from metagenomic sequencing, and predicted proteins) were used to conduct taxonomic assignments. Specially, relative abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were analyzed. Compared with quantitative real-time PCR (qPCR), metagenomic sequencing was demonstrated to be a better approach to quantify AOA and AOB in activated sludge samples. It was found that AOB were more abundant than AOA in both reactors. Furthermore, the analysis of the metabolic profiles indicated that the overall patterns of metabolic pathways in the two reactors were quite similar (73.3% of functions shared). However, for some pathways (such as carbohydrate metabolism and membrane transport), the two reactors differed in the number of pathway-specific genes.}, } @article {pmid23146837, year = {2013}, author = {Lewin, A and Wentzel, A and Valla, S}, title = {Metagenomics of microbial life in extreme temperature environments.}, journal = {Current opinion in biotechnology}, volume = {24}, number = {3}, pages = {516-525}, doi = {10.1016/j.copbio.2012.10.012}, pmid = {23146837}, issn = {1879-0429}, mesh = {*Biota ; *Cold Temperature ; *Ecosystem ; *Environmental Microbiology ; *Hot Temperature ; *Metagenomics ; }, abstract = {Microbial life in extreme environments is attracting broad scientific interest. Knowledge about it helps in defining the boundaries for life to exist, and organisms living under extreme conditions are also interesting sources for enzymes with unusual and desirable properties. The tremendous progress in DNA sequencing technologies now makes it relatively easy to gain a representative overview of the composition of such communities, and many community studies have in the last decade applied metagenomics to characterize habitats extreme in, for example, temperature, salt and acidity. The future challenges in the field are likely to become more and more related to the conversion of the expected massive amounts of sequence information into an understanding of the corresponding biological community functions.}, } @article {pmid23144861, year = {2012}, author = {Fouts, DE and Szpakowski, S and Purushe, J and Torralba, M and Waterman, RC and MacNeil, MD and Alexander, LJ and Nelson, KE}, title = {Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e48289}, pmid = {23144861}, issn = {1932-6203}, mesh = {Animals ; Archaea/classification/genetics ; Cattle ; Eubacterium/genetics ; Female ; Fungi/classification/genetics ; *High-Throughput Nucleotide Sequencing ; Metagenome ; Molecular Typing/methods ; Mycological Typing Techniques/methods ; Phylogeny ; Prevotella/classification/genetics ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Fungal/genetics ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 18S/genetics ; Rumen/*microbiology ; *Sequence Analysis, DNA ; }, abstract = {A combination of Sanger and 454 sequences of small subunit rRNA loci were used to interrogate microbial diversity in the bovine rumen of 12 cows consuming a forage diet. Observed bacterial species richness, based on the V1-V3 region of the 16S rRNA gene, was between 1,903 to 2,432 species-level operational taxonomic units (OTUs) when 5,520 reads were sampled per animal. Eighty percent of species-level OTUs were dominated by members of the order Clostridiales, Bacteroidales, Erysipelotrichales and unclassified TM7. Abundance of Prevotella species varied widely among the 12 animals. Archaeal species richness, also based on 16S rRNA, was between 8 and 13 OTUs, representing 5 genera. The majority of archaeal OTUs (84%) found in this study were previously observed in public databases with only two new OTUs discovered. Observed rumen fungal species richness, based on the 18S rRNA gene, was between 21 and 40 OTUs with 98.4-99.9% of OTUs represented by more than one read, using Good's coverage. Examination of the fungal community identified numerous novel groups. Prevotella and Tannerella were overrepresented in the liquid fraction of the rumen while Butyrivibrio and Blautia were significantly overrepresented in the solid fraction of the rumen. No statistical difference was observed between the liquid and solid fractions in biodiversity of archaea and fungi. The survey of microbial communities and analysis of cross-domain correlations suggested there is a far greater extent of microbial diversity in the bovine rumen than previously appreciated, and that next generation sequencing technologies promise to reveal novel species, interactions and pathways that can be studied further in order to better understand how rumen microbial community structure and function affects ruminant feed efficiency, biofuel production, and environmental impact.}, } @article {pmid23141757, year = {2013}, author = {Peyyala, R and Ebersole, JL}, title = {Multispecies biofilms and host responses: "discriminating the trees from the forest".}, journal = {Cytokine}, volume = {61}, number = {1}, pages = {15-25}, pmid = {23141757}, issn = {1096-0023}, support = {P20 GM103538/GM/NIGMS NIH HHS/United States ; R21 DE018177/DE/NIDCR NIH HHS/United States ; DE 018177/DE/NIDCR NIH HHS/United States ; }, mesh = {Biodiversity ; *Biofilms ; Host-Pathogen Interactions/*immunology/physiology ; Humans ; Metagenome/immunology ; Mouth/*microbiology/*pathology ; Periodontal Diseases/*microbiology ; }, abstract = {Periodontal diseases reflect a tissue destructive process of the hard and soft tissues of the periodontium that are initiated by the accumulation of multispecies bacterial biofilms in the subgingival sulcus. This accumulation, in both quantity and quality of bacteria, results in a chronic immunoinflammatory response of the host to control this noxious challenge, leading to collateral damage of the tissues. As knowledge of the characteristics of the host-bacterial interactions in the oral cavity has expanded, new knowledge has become available on the complexity of the microbial challenge and the repertoire of host responses to this challenge. Recent results from the Human Microbiome Project continue to extend the array of taxa, genera, and species of bacteria that inhabit the multiple niches in the oral cavity; however, there is rather sparse information regarding variations in how host cells discriminate commensal from pathogenic species, as well as how the host response is affected by the three-dimensional architecture and interbacterial interactions that occur in the oral biofilms. This review provides some insights into these processes by including existing literature on the biology of nonoral bacterial biofilms, and the more recent literature just beginning to document how the oral cavity responds to multispecies biofilms.}, } @article {pmid23140990, year = {2013}, author = {Morgan, XC and Segata, N and Huttenhower, C}, title = {Biodiversity and functional genomics in the human microbiome.}, journal = {Trends in genetics : TIG}, volume = {29}, number = {1}, pages = {51-58}, pmid = {23140990}, issn = {0168-9525}, support = {R01 HG005969/HG/NHGRI NIH HHS/United States ; 1R01HG005969-01/HG/NHGRI NIH HHS/United States ; }, mesh = {*Biodiversity ; Computational Biology ; Gastrointestinal Tract/metabolism/*microbiology ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; Microbiota/*genetics/physiology ; Phylogeny ; }, abstract = {Over the course of our lives, humans are colonized by a tremendous diversity of commensal microbes, which comprise the human microbiome. The collective genetic potential (metagenome) of the human microbiome is orders of magnitude more than the human genome, and it profoundly affects human health and disease in ways we are only beginning to understand. Advances in computing and high-throughput sequencing have enabled population-level surveys such as MetaHIT and the recently released Human Microbiome Project, detailed investigations of the microbiome in human disease, and mechanistic studies employing gnotobiotic model organisms. The resulting knowledge of human microbiome composition, function, and range of variation across multiple body sites has begun to assemble a rich picture of commensal host-microbe and microbe-microbe interactions as well as their roles in human health and disease and their potential as diagnostic and therapeutic tools.}, } @article {pmid23140640, year = {2012}, author = {Holmes, E and Li, JV and Marchesi, JR and Nicholson, JK}, title = {Gut microbiota composition and activity in relation to host metabolic phenotype and disease risk.}, journal = {Cell metabolism}, volume = {16}, number = {5}, pages = {559-564}, doi = {10.1016/j.cmet.2012.10.007}, pmid = {23140640}, issn = {1932-7420}, mesh = {Animals ; Bacteria/*metabolism ; *Bacterial Physiological Phenomena ; *Biodiversity ; Diet ; Gastrointestinal Diseases/prevention & control ; Gastrointestinal Tract/*metabolism/*microbiology ; Humans ; Metagenome ; Metagenomics ; Phenotype ; }, abstract = {The symbiotic gut microbiota modulate health and disease of the host through a series of transgenomic metabolic and immune regulatory axes. We explore connections between microbiome composition and function related to individual metabolic phenotypes and consider these interactions as possible targets for developing new personalized therapies and clinical management strategies.}, } @article {pmid23138712, year = {2013}, author = {Prakash, O and Shouche, Y and Jangid, K and Kostka, JE}, title = {Microbial cultivation and the role of microbial resource centers in the omics era.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {1}, pages = {51-62}, doi = {10.1007/s00253-012-4533-y}, pmid = {23138712}, issn = {1432-0614}, mesh = {Bacteria/classification/genetics/growth & development/*isolation & purification ; *Biodiversity ; *Environmental Microbiology ; Fungi/classification/genetics/growth & development/*isolation & purification ; Metagenomics/*methods ; Microbiological Techniques/*methods ; }, abstract = {Despite tremendous advances in microbial ecology over the past two decades, traditional cultivation methods have failed to grow ecologically more relevant microorganisms in the laboratory, leading to a predominance of weed-like species in the world's culture collections. In this review, we highlight the gap between culture-based and culture-independent methods of microbial diversity analysis, especially in investigations of slow growers, oligotrophs, and fastidious and recalcitrant microorganisms. Furthermore, we emphasize the importance of microbial cultivation and the acquisition of the cultivation-based phenotypic data for the testing of hypotheses arising from genomics and proteomics approaches. Technical difficulties in cultivating novel microorganisms and how modern approaches have helped to overcome these limitations are highlighted. After cultivation, adequate preservation without changes in genotypic and phenotypic features of these microorganisms is necessary for future research and training. Hence, the contribution of microbial resource centers in the handling, preservation, and distribution of this novel diversity is discussed. Finally, we explore the concept of microbial patenting and requisite guidelines of the "Budapest Treaty" for establishment of an International Depositary Authority.}, } @article {pmid23134566, year = {2012}, author = {Lusk, TS and Ottesen, AR and White, JR and Allard, MW and Brown, EW and Kase, JA}, title = {Characterization of microflora in Latin-style cheeses by next-generation sequencing technology.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {254}, pmid = {23134566}, issn = {1471-2180}, mesh = {*Biodiversity ; Cheese/*microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Cheese contamination can occur at numerous stages in the manufacturing process including the use of improperly pasteurized or raw milk. Of concern is the potential contamination by Listeria monocytogenes and other pathogenic bacteria that find the high moisture levels and moderate pH of popular Latin-style cheeses like queso fresco a hospitable environment. In the investigation of a foodborne outbreak, samples typically undergo enrichment in broth for 24 hours followed by selective agar plating to isolate bacterial colonies for confirmatory testing. The broth enrichment step may also enable background microflora to proliferate, which can confound subsequent analysis if not inhibited by effective broth or agar additives. We used 16S rRNA gene sequencing to provide a preliminary survey of bacterial species associated with three brands of Latin-style cheeses after 24-hour broth enrichment.

RESULTS: Brand A showed a greater diversity than the other two cheese brands (Brands B and C) at nearly every taxonomic level except phylum. Brand B showed the least diversity and was dominated by a single bacterial taxon, Exiguobacterium, not previously reported in cheese. This genus was also found in Brand C, although Lactococcus was prominent, an expected finding since this bacteria belongs to the group of lactic acid bacteria (LAB) commonly found in fermented foods.

CONCLUSIONS: The contrasting diversity observed in Latin-style cheese was surprising, demonstrating that despite similarity of cheese type, raw materials and cheese making conditions appear to play a critical role in the microflora composition of the final product. The high bacterial diversity associated with Brand A suggests it may have been prepared with raw materials of high bacterial diversity or influenced by the ecology of the processing environment. Additionally, the presence of Exiguobacterium in high proportions (96%) in Brand B and, to a lesser extent, Brand C (46%), may have been influenced by the enrichment process. This study is the first to define Latin-style cheese microflora using Next-Generation Sequencing. These valuable preliminary data will direct selective tailoring of agar formulations to improve culture-based detection of pathogens in Latin-style cheese.}, } @article {pmid23131830, year = {2012}, author = {Rogers, GB and Bruce, KD}, title = {Exploring the parallel development of microbial systems in neonates with cystic fibrosis.}, journal = {mBio}, volume = {3}, number = {6}, pages = {e00408-12}, pmid = {23131830}, issn = {2150-7511}, mesh = {*Biota ; Cystic Fibrosis/*microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; Respiratory System/*microbiology ; }, abstract = {Recent studies have greatly extended our understanding of the microbiota present in and on the human body. Here, advanced sequencing strategies have provided unprecedented analytical power. The important implications that the emerging data have for human health emphasize the need to intensify research in this area (D. A. Relman, Nature 486:194-195, 2012). It is already clear from these studies that the microbiotas characterized in different body locations of healthy individuals are both complex and diverse (The Human Microbiome Project Consortium, Nature 486:215-221). These studies also provide a point of contrast for investigations that aim to characterize the microbiota present in disease conditions. In this regard, Madan et al. (mBio 3(4):e00251-12, 2012) monitored the development over time of microbiota in the oropharynges and feces of neonates with cystic fibrosis and explored the potential for interactions between these complex microbial systems.}, } @article {pmid23130351, year = {2012}, author = {Lagier, JC and Million, M and Hugon, P and Armougom, F and Raoult, D}, title = {Human gut microbiota: repertoire and variations.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {136}, pmid = {23130351}, issn = {2235-2988}, mesh = {Archaea/classification/isolation & purification ; Bacteria/classification/isolation & purification ; *Biota ; Eukaryota/classification/isolation & purification ; Gastrointestinal Tract/*microbiology ; Genomics/methods ; Humans ; *Microbiota ; Proteomics/methods ; Viruses/classification/isolation & purification ; }, abstract = {The composition of human gut microbiota and their relationship with the host and, consequently, with human health and disease, presents several challenges to microbiologists. Originally dominated by culture-dependent methods for exploring this ecosystem, the advent of molecular tools has revolutionized our ability to investigate these relationships. However, many biases that have led to contradictory results have been identified. Microbial culturomics, a recent concept based on a use of several culture conditions with identification by MALDI-TOF followed by the genome sequencing of the new species cultured had allowed a complementarity with metagenomics. Culturomics allowed to isolate 31 new bacterial species, the largest human virus, the largest bacteria, and the largest Archaea from human. Moreover, some members of this ecosystem, such as Eukaryotes, giant viruses, Archaea, and Planctomycetes, have been neglected by the majority of studies. In addition, numerous factors, such as age, geographic provenance, dietary habits, antibiotics, or probiotics, can influence the composition of the microbiota. Finally, in addition to the countless biases associated with the study techniques, a considerable limitation to the interpretation of studies of human gut microbiota is associated with funding sources and transparency disclosures. In the future, studies independent of food industry funding and using complementary methods from a broad range of both culture-based and molecular tools will increase our knowledge of the repertoire of this complex ecosystem and host-microbiota mutualism.}, } @article {pmid23128418, year = {2013}, author = {Suzaki, H and Watanabe, S and Pawankar, R}, title = {Rhinosinusitis and asthma-microbiome and new perspectives.}, journal = {Current opinion in allergy and clinical immunology}, volume = {13}, number = {1}, pages = {45-49}, doi = {10.1097/ACI.0b013e32835b34f6}, pmid = {23128418}, issn = {1473-6322}, mesh = {Animals ; Asthma/etiology/*microbiology ; Chronic Disease ; Humans ; Hygiene Hypothesis ; Intestines/microbiology ; *Metagenome ; Rhinitis/etiology/*microbiology ; Sinusitis/etiology/*microbiology ; }, abstract = {PURPOSE OF REVIEW: Microbiome is one of the new perspectives in human health research, including airway diseases. There are several publications about the relationship of the microbiome and allergic diseases. Although pathogenesis of chronic rhinosinusitis (CRS) as well as its relationship with asthma has been widely investigated, the relationship of the microbiome and CRS is not yet well known.

RECENT FINDINGS: The relationship between the hygiene hypothesis and microorganisms inside the human body and in the environment around it has been clearly shown. Furthermore, several researchers have reported that the microorganisms in the gut play a major role in regulating the immune cells that are of relevance to asthma and allergic diseases, such as Th1, Th2, Th17, Treg and dendritic cells as well as Toll-like receptors. Reduced contact of people with natural environmental features and biodiversity may adversely affect the human commensal microbiota and its immunomodulatory capacity.Some studies have shown a close relationship between CRS and Staphylococcus aureus, anaerobes and so on in the nasal cavity or paranasal sinuses, although the relationship between CRS and microorganisms in the gut has not been demonstrated.

SUMMARY: In this review, we summarized about the microbiome, mainly in asthma and allergic diseases. The relationship between asthma and CRS has been clearly shown, and in particular, CRS with nasal polyps (CRSwNP) has been considered to be Th2-dominant. Studies examining environmental microbial exposure in populations at risk for CRS are necessary to improve our understanding of the role this factor plays in disease development.}, } @article {pmid23126454, year = {2013}, author = {Williams, TJ and Wilkins, D and Long, E and Evans, F and DeMaere, MZ and Raftery, MJ and Cavicchioli, R}, title = {The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics.}, journal = {Environmental microbiology}, volume = {15}, number = {5}, pages = {1302-1317}, doi = {10.1111/1462-2920.12017}, pmid = {23126454}, issn = {1462-2920}, mesh = {Antarctic Regions ; Archaea/classification/genetics/metabolism ; Bacteria/classification/genetics/metabolism ; Biodiversity ; Chlorophyll/analysis/metabolism ; Chlorophyll A ; Eukaryota/metabolism ; Flavobacteriaceae/classification/*genetics/*metabolism ; Heterotrophic Processes ; *Metagenomics ; Phylogeny ; Phytoplankton/metabolism ; Plankton/genetics/metabolism ; Proteobacteria/metabolism ; *Proteomics ; Seawater/microbiology ; }, abstract = {Heterotrophic marine bacteria play key roles in remineralizing organic matter generated from primary production. However, far more is known about which groups are dominant than about the cellular processes they perform in order to become dominant. In the Southern Ocean, eukaryotic phytoplankton are the dominant primary producers. In this study we used metagenomics and metaproteomics to determine how the dominant bacterial and archaeal plankton processed bloom material. We examined the microbial community composition in 14 metagenomes and found that the relative abundance of Flavobacteria (dominated by Polaribacter) was positively correlated with chlorophyll a fluorescence, and the relative abundance of SAR11 was inversely correlated with both fluorescence and Flavobacteria abundance. By performing metaproteomics on the sample with the highest relative abundance of Flavobacteria (Newcomb Bay, East Antarctica) we defined how Flavobacteria attach to and degrade diverse complex organic material, how they make labile compounds available to Alphaproteobacteria (especially SAR11) and Gammaproteobacteria, and how these heterotrophic Proteobacteria target and utilize these nutrients. The presence of methylotrophic proteins for archaea and bacteria also indicated the importance of metabolic specialists. Overall, the study provides functional data for the microbial mechanisms of nutrient cycling at the surface of the coastal Southern Ocean.}, } @article {pmid23124960, year = {2013}, author = {Cotta, SR and Dias, AC and Marriel, IE and Gomes, EA and van Elsas, JD and Seldin, L}, title = {Temporal dynamics of microbial communities in the rhizosphere of two genetically modified (GM) maize hybrids in tropical agrosystems.}, journal = {Antonie van Leeuwenhoek}, volume = {103}, number = {3}, pages = {589-601}, doi = {10.1007/s10482-012-9843-7}, pmid = {23124960}, issn = {1572-9699}, mesh = {Bacteria/*classification/genetics ; *Biota ; Cluster Analysis ; Denaturing Gradient Gel Electrophoresis ; Fungi/*classification/genetics ; Metagenome ; Plant Roots/*microbiology ; Plants, Genetically Modified/*microbiology ; Polymerase Chain Reaction ; *Rhizosphere ; Time Factors ; Zea mays/*microbiology ; }, abstract = {The use of genetically modified (GM) plants still raises concerns about their environmental impact. The present study aimed to evaluate the possible effects of GM maize, in comparison to the parental line, on the structure and abundance of microbial communities in the rhizosphere. Moreover, the effect of soil type was addressed. For this purpose, the bacterial and fungal communities associated with the rhizosphere of GM plants were compared by culture-independent methodologies to the near-isogenic parental line. Two different soils and three stages of plant development in two different periods of the year were included. As evidenced by principal components analysis (PCA) of the PCR-DGGE profiles of evaluated community, clear differences occurred in these rhizosphere communities between soils and the periods of the year that maize was cultivated. However, there were no discernible effects of the GM lines as compared to the parental line. For all microbial communities evaluated, soil type and the period of the year that the maize was cultivated were the main factors that influenced their structures. No differences were observed in the abundances of total bacteria between the rhizospheres of GM and parental plant lines.}, } @article {pmid23124239, year = {2013}, author = {Kautz, S and Rubin, BE and Russell, JA and Moreau, CS}, title = {Surveying the microbiome of ants: comparing 454 pyrosequencing with traditional methods to uncover bacterial diversity.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {2}, pages = {525-534}, pmid = {23124239}, issn = {1098-5336}, mesh = {Animal Structures/microbiology ; Animals ; Ants/*microbiology ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {We are only beginning to understand the depth and breadth of microbial associations across the eukaryotic tree of life. Reliably assessing bacterial diversity is a key challenge, and next-generation sequencing approaches are facilitating this endeavor. In this study, we used 16S rRNA amplicon pyrosequencing to survey microbial diversity in ants. We compared 454 libraries with Sanger-sequenced clone libraries as well as cultivation of live bacteria. Pyrosequencing yielded 95,656 bacterial 16S rRNA reads from 19 samples derived from four colonies of one ant species. The most dominant bacterial orders in the microbiome of the turtle ant Cephalotes varians were Rhizobiales, Burkholderiales, Opitutales, Xanthomonadales, and Campylobacterales, as revealed through both 454 sequencing and cloning. Even after stringent quality filtering, pyrosequencing recovered 445 microbe operational taxonomic units (OTUs) not detected with traditional techniques. In comparing bacterial communities associated with specific tissues, we found that gut tissues had significantly higher diversity than nongut tissues, and many of the OTUs identified from these groups clustered within ant-specific lineages, indicating a deep coevolutionary history of Cephalotes ants and their associated microbes. These lineages likely function as nutritional symbionts. One of four ant colonies investigated was infected with a Spiroplasma sp. (order Entomoplasmatales), a potential ant pathogen. Our work shows that the microbiome associated with Cephalotes varians is dominated by a few dozen bacterial lineages and that 454 sequencing is a cost-efficient tool to screen ant symbiont diversity.}, } @article {pmid23121191, year = {2013}, author = {Keller, I and Wagner, CE and Greuter, L and Mwaiko, S and Selz, OM and Sivasundar, A and Wittwer, S and Seehausen, O}, title = {Population genomic signatures of divergent adaptation, gene flow and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes.}, journal = {Molecular ecology}, volume = {22}, number = {11}, pages = {2848-2863}, doi = {10.1111/mec.12083}, pmid = {23121191}, issn = {1365-294X}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Biodiversity ; Biological Evolution ; Chimera ; Cichlids/*classification/*genetics ; Gene Flow ; Genetic Speciation ; Lakes ; *Metagenomics ; Phylogeny ; Polymorphism, Single Nucleotide ; Tanzania ; }, abstract = {Adaptive radiations are an important source of biodiversity and are often characterized by many speciation events in very short succession. It has been proposed that the high speciation rates in these radiations may be fuelled by novel genetic combinations produced in episodes of hybridization among the young species. The role of such hybridization events in the evolutionary history of a group can be investigated by comparing the genealogical relationships inferred from different subsets of loci, but such studies have thus far often been hampered by shallow genetic divergences, especially in young adaptive radiations, and the lack of genome-scale molecular data. Here, we use a genome-wide sampling of SNPs identified within restriction site-associated DNA (RAD) tags to investigate the genomic consistency of patterns of shared ancestry and adaptive divergence among five sympatric cichlid species of two genera, Pundamilia and Mbipia, which form part of the massive adaptive radiation of cichlids in the East African Lake Victoria. Species pairs differ along several axes: male nuptial colouration, feeding ecology, depth distribution, as well as the morphological traits that distinguish the two genera and more subtle morphological differences. Using outlier scan approaches, we identify signals of divergent selection between all species pairs with a number of loci showing parallel patterns in replicated contrasts either between genera or between male colour types. We then create SNP subsets that we expect to be characterized to different extents by selection history and neutral processes and describe phylogenetic and population genetic patterns across these subsets. These analyses reveal very different evolutionary histories for different regions of the genome. To explain these results, we propose at least two intergeneric hybridization events (between Mbipia spp. and Pundamilia spp.) in the evolutionary history of these five species that would have lead to the evolution of novel trait combinations and new species.}, } @article {pmid23116182, year = {2012}, author = {Steven, B and Gallegos-Graves, LV and Yeager, CM and Belnap, J and Evans, RD and Kuske, CR}, title = {Dryland biological soil crust cyanobacteria show unexpected decreases in abundance under long-term elevated CO2.}, journal = {Environmental microbiology}, volume = {14}, number = {12}, pages = {3247-3258}, doi = {10.1111/1462-2920.12011}, pmid = {23116182}, issn = {1462-2920}, mesh = {Adaptation, Biological/*genetics ; Biodiversity ; Biomass ; Carbon Dioxide/*metabolism ; Cyanobacteria/genetics/*growth & development/*metabolism ; Ecosystem ; Gene Library ; Metagenome ; Nevada ; Oxidative Stress ; *Soil Microbiology ; United States ; }, abstract = {Biological soil crusts (biocrusts) cover soil surfaces in many drylands globally. The impacts of 10 years of elevated atmospheric CO2 on the cyanobacteria in biocrusts of an arid shrubland were examined at a large manipulated experiment in Nevada, USA. Cyanobacteria-specific quantitative PCR surveys of cyanobacteria small-subunit (SSU) rRNA genes suggested a reduction in biocrust cyanobacterial biomass in the elevated CO2 treatment relative to the ambient controls. Additionally, SSU rRNA gene libraries and shotgun metagenomes showed reduced representation of cyanobacteria in the total microbial community. Taxonomic composition of the cyanobacteria was similar under ambient and elevated CO2 conditions, indicating the decline was manifest across multiple cyanobacterial lineages. Recruitment of cyanobacteria sequences from replicate shotgun metagenomes to cyanobacterial genomes representing major biocrust orders also suggested decreased abundance of cyanobacteria sequences across the majority of genomes tested. Functional assignment of cyanobacteria-related shotgun metagenome sequences indicated that four subsystem categories, three related to oxidative stress, were differentially abundant in relation to the elevated CO2 treatment. Taken together, these results suggest that elevated CO2 affected a generalized decrease in cyanobacteria in the biocrusts and may have favoured cyanobacteria with altered gene inventories for coping with oxidative stress.}, } @article {pmid23113966, year = {2013}, author = {Ren, T and Glatt, DU and Nguyen, TN and Allen, EK and Early, SV and Sale, M and Winther, B and Wu, M}, title = {16S rRNA survey revealed complex bacterial communities and evidence of bacterial interference on human adenoids.}, journal = {Environmental microbiology}, volume = {15}, number = {2}, pages = {535-547}, doi = {10.1111/1462-2920.12000}, pmid = {23113966}, issn = {1462-2920}, support = {DC003166-S1/DC/NIDCD NIH HHS/United States ; }, mesh = {Adenoids/*microbiology/surgery ; Antibiosis/*physiology ; Bacteria/*classification/*genetics ; Biodiversity ; Humans ; Metagenome/physiology ; Otitis Media/microbiology ; RNA, Ribosomal, 16S/*genetics ; Respiratory Tract Infections/microbiology ; Sinusitis/microbiology ; }, abstract = {Adenoid microbiota plays an important role in the development of various infectious and non-infectious diseases of the upper airways, such as otitis media, adenotonsillitis, rhinosinusitis and adenoid hypertrophy. Studies have suggested that adenoids could act as a potential reservoir of opportunistic pathogens. However, previous bacterial surveys of adenoids were mainly culture based and therefore might only provide an incomplete and potentially biased assessment of the microbial diversity. To develop an in-depth and comprehensive understanding of the adenoid microbial communities and test the 'pathogen reservoir hypothesis', we carried out a 16S rRNA based, culture-independent survey of bacterial communities on 67 human adenoids removed by surgery. Our survey revealed highly diverse adenoid bacterial communities distinct from those of other body habitats. Despite large interpersonal variations, adenoid microbiota shared a core set of taxa and can be classified into at least five major types based on its bacterial species composition. Our results support the 'pathogen reservoir hypothesis' as we found common pathogens of otitis media to be both prevalent and abundant. Co-occurrence analyses revealed evidence consistent with the bacterial interference theory in that multiple common pathogens showed 'non-coexistence' relationships with non-pathogenic members of the commensal microflora.}, } @article {pmid23112324, year = {2012}, author = {Bascom-Slack, CA and Arnold, AE and Strobel, SA}, title = {IBI series winner. Student-directed discovery of the plant microbiome and its products.}, journal = {Science (New York, N.Y.)}, volume = {338}, number = {6106}, pages = {485-486}, doi = {10.1126/science.1215227}, pmid = {23112324}, issn = {1095-9203}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Biodiversity ; Endophytes/*isolation & purification ; Fungi/isolation & purification ; *Metagenome ; Microbiology/*education ; Plants/*microbiology ; *Program Development ; Research/*education ; United States ; Universities ; }, } @article {pmid23106823, year = {2013}, author = {Kolinko, S and Wanner, G and Katzmann, E and Kiemer, F and Fuchs, BM and Schüler, D}, title = {Clone libraries and single cell genome amplification reveal extended diversity of uncultivated magnetotactic bacteria from marine and freshwater environments.}, journal = {Environmental microbiology}, volume = {15}, number = {5}, pages = {1290-1301}, doi = {10.1111/1462-2920.12004}, pmid = {23106823}, issn = {1462-2920}, mesh = {Bacteria/*classification/*genetics/ultrastructure ; *Biodiversity ; DNA, Bacterial/genetics ; Ecosystem ; Fresh Water/*microbiology ; Genome, Bacterial/genetics ; Genomic Library ; Geologic Sediments/*microbiology ; Magnetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Magnetotactic bacteria (MTB), which orient along the earth's magnetic field using magnetosomes, are ubiquitous and abundant in marine and freshwater environments. Previous phylogenetic analysis of diverse MTB has been limited to few cultured species and the most abundant and conspicuous members of natural populations, which were assigned to various lineages of the Proteobacteria, the Nitrospirae phylum as well as the candidate division OP3. However, their known phylogenetic diversity still not matches the large morphological and ultrastructural variability of uncultured MTB found in environmental communities. Here, we used analysis of 16S rRNA gene clone libraries in combination with microsorting and whole-genome amplification to systematically address the entire diversity of uncultured MTB from two different habitats. This approach revealed extensive and novel diversity of MTB within the freshwater and marine sediment samples. In total, single-cell analysis identified eight different phylotypes, which were only partly represented in the clone libraries, and which could be unambiguously assigned to their respective morphotypes. Identified MTB belonged to the Alphaproteobacteria (seven species) and the Nitrospirae phylum (two species). End-sequencing of a small insert library created from WGA-derived DNA of a novel conspicuous magnetotactic vibrio identified genes with highest similarity to two cultivated MTB as well as to other phylogenetic groups. In conclusion, the combination of metagenomic cloning and single cell sorting represents a powerful approach to recover maximum bacterial diversity including low-abundant magnetotactic phylotypes from environmental samples and also provides access to genomic analysis of uncultivated MTB.}, } @article {pmid23104688, year = {2013}, author = {Rao, S and Hyde, KD and Pointing, SB}, title = {Comparison of DNA and RNA, and cultivation approaches for the recovery of terrestrial and aquatic fungi from environmental samples.}, journal = {Current microbiology}, volume = {66}, number = {2}, pages = {185-191}, pmid = {23104688}, issn = {1432-0991}, mesh = {*Biodiversity ; DNA, Fungal/*genetics ; *Environmental Microbiology ; Fungi/classification/*isolation & purification ; Metagenomics/*methods ; Microbiological Techniques/*methods ; Molecular Sequence Data ; RNA, Fungal/*genetics ; Sequence Analysis, DNA ; }, abstract = {Estimates of fungal biodiversity from environmental samples are all subject to bias. Major issues are that the commonly adopted cultivation-based approaches are suitable for taxa which grow readily under laboratory conditions, while the DNA-based approaches provide more reliable estimates, but do not indicate whether taxa are metabolically active. In this study, we have evaluated these approaches to estimate the fungal diversity in soil and freshwater samples from a subtropical forest, and compared these to RNA-based culture-independent approach intended to indicate the metabolically active fungal assemblage. In both soil and freshwater samples, the dominant taxon recovered by all three approaches was the same (Anguillospora furtiva). This taxon was cultivable from all samples and comprised 85-86 % DNA libraries and 90-91 % RNA libraries. The remaining taxa were phylogenetically diverse and spanned the Ascomycota, Basidiomycota, and Fungi incertae sedis. Their recovery was not consistent among the three approaches used and suggests that less abundant members of the assemblage may be subjected to greater bias when diversity estimates employ a single approach.}, } @article {pmid23095164, year = {2013}, author = {Milucka, J and Widdel, F and Shima, S}, title = {Immunological detection of enzymes for sulfate reduction in anaerobic methane-oxidizing consortia.}, journal = {Environmental microbiology}, volume = {15}, number = {5}, pages = {1561-1571}, doi = {10.1111/1462-2920.12003}, pmid = {23095164}, issn = {1462-2920}, mesh = {Anaerobiosis ; Archaea/enzymology/genetics ; Bacteria/enzymology ; Black Sea ; Enzymes/isolation & purification/*metabolism ; Immune Sera/metabolism ; Immunohistochemistry ; Methane/metabolism ; *Microbial Consortia ; Oxidation-Reduction ; Seawater/*microbiology ; Sulfates/*metabolism ; }, abstract = {Anaerobic oxidation of methane (AOM) coupled to sulfate reduction (SR) at marine gas seeps is performed by archaeal-bacterial consortia that have so far not been cultivated in axenic binary or pure cultures. Knowledge about possible biochemical reactions in AOM consortia is based on metagenomic retrieval of genes related to those in archaeal methanogenesis and bacterial sulfate reduction, and identification of a few catabolic enzymes in protein extracts. Whereas the possible enzyme for methane activation (a variant of methyl-coenzyme M reductase, Mcr) was shown to be harboured by the archaea, enzymes for sulfate activation and reduction have not been localized so far. We adopted a novel approach of fluorescent immunolabelling on semi-thin (0.3-0.5 μm) cryosections to localize two enzymes of the SR pathway, adenylyl : sulfate transferase (Sat; ATP sulfurylase) and dissimilatory sulfite reductase (Dsr) in microbial consortia from Black Sea methane seeps. Both Sat and Dsr were exclusively found in an abundant microbial morphotype (c. 50% of all cells), which was tentatively identified as Desulfosarcina/Desulfococcus-related bacteria. These results show that ANME-2 archaea in the Black Sea AOM consortia did not express bacterial enzymes of the canonical sulfate reduction pathway and thus, in contrast to previous suggestions, most likely cannot perform canonical sulfate reduction. Moreover, our results show that fluorescent immunolabelling on semi-thin cryosections which to our knowledge has been so far only applied on cell tissues, is a powerful tool for intracellular protein detection in natural microbial associations.}, } @article {pmid23087041, year = {2013}, author = {Miyatake, T and Macgregor, BJ and Boschker, HT}, title = {Depth-related differences in organic substrate utilization by major microbial groups in intertidal marine sediment.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {1}, pages = {389-392}, pmid = {23087041}, issn = {1098-5336}, mesh = {*Biota ; Cell Survival ; Cyanobacteria/metabolism/physiology ; Darkness ; Diatoms/metabolism/physiology ; Geologic Sediments/*microbiology ; Glucose/metabolism ; Isotope Labeling ; Metagenome ; Molecular Sequence Data ; Organic Chemicals/*metabolism ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; }, abstract = {Stable isotope probing of magnetic-bead-captured rRNA (Mag-SIP) indicated clear differences in in situ organic substrate utilization by major microbial groups between the more oxidized (0 to 2 cm) and sulfate-reducing (2 to 5 cm) horizons of marine intertidal sediment. We also showed that cyanobacteria and diatoms may survive by glucose utilization under dark anoxic conditions.}, } @article {pmid23084423, year = {2012}, author = {Duhaime, MB and Sullivan, MB}, title = {Ocean viruses: rigorously evaluating the metagenomic sample-to-sequence pipeline.}, journal = {Virology}, volume = {434}, number = {2}, pages = {181-186}, doi = {10.1016/j.virol.2012.09.036}, pmid = {23084423}, issn = {1096-0341}, mesh = {*Biota ; *Metagenome ; Metagenomics/*methods ; *Oceans and Seas ; Seawater/*virology ; Viruses/*classification/*genetics ; }, abstract = {As new environments are studied, viruses consistently emerge as important and prominent players in natural and man-made ecosystems. However, much of what we know is built both upon the foundation of the culturable minority and using methods that are often insufficiently ground-truthed. Here, we review the modern culture-independent viral metagenomic sample-to-sequence pipeline and how next-generation sequencing techniques are drastically altering our ability to systematically and rigorously evaluate them. Together, a series of studies quantitatively evaluate existing and new methods that allow-even for ultra-low DNA samples-the generation of replicable, near-quantitative datasets that maximize inter-comparability and biological inference.}, } @article {pmid23083746, year = {2013}, author = {Keshri, J and Mishra, A and Jha, B}, title = {Microbial population index and community structure in saline-alkaline soil using gene targeted metagenomics.}, journal = {Microbiological research}, volume = {168}, number = {3}, pages = {165-173}, doi = {10.1016/j.micres.2012.09.005}, pmid = {23083746}, issn = {1618-0623}, mesh = {Archaea/*classification/genetics ; Archaeal Proteins/genetics ; Bacteria/*classification/genetics ; Bacterial Proteins/genetics ; *Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Hydrogen-Ion Concentration ; *Metagenomics ; Molecular Sequence Data ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Population indices of bacteria and archaea were investigated from saline-alkaline soil and a possible microbe-environment pattern was established using gene targeted metagenomics. Clone libraries were constructed using 16S rRNA and functional gene(s) involved in carbon fixation (cbbL), nitrogen fixation (nifH), ammonia oxidation (amoA) and sulfur metabolism (apsA). Molecular phylogeny revealed the dominance of Actinobacteria, Firmicutes and Proteobacteria along with archaeal members of Halobacteraceae. The library consisted of novel bacterial (20%) and archaeal (38%) genera showing ≤95% similarity to previously retrieved sequences. Phylogenetic analysis indicated ability of inhabitant to survive in stress condition. The 16S rRNA gene libraries contained novel gene sequences and were distantly homologous with cultured bacteria. Functional gene libraries were found unique and most of the clones were distantly related to Proteobacteria, while clones of nifH gene library also showed homology with Cyanobacteria and Firmicutes. Quantitative real-time PCR exhibited that bacterial abundance was two orders of magnitude higher than archaeal. The gene(s) quantification indicated the size of the functional guilds harboring relevant key genes. The study provides insights on microbial ecology and different metabolic interactions occurring in saline-alkaline soil, possessing phylogenetically diverse groups of bacteria and archaea, which may be explored further for gene cataloging and metabolic profiling.}, } @article {pmid23082192, year = {2012}, author = {Oikonomou, G and Machado, VS and Santisteban, C and Schukken, YH and Bicalho, RC}, title = {Microbial diversity of bovine mastitic milk as described by pyrosequencing of metagenomic 16s rDNA.}, journal = {PloS one}, volume = {7}, number = {10}, pages = {e47671}, pmid = {23082192}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; *Biodiversity ; Cattle ; DNA, Ribosomal/*genetics ; Discriminant Analysis ; Female ; Mastitis, Bovine/diagnosis/*microbiology ; Metagenome/genetics ; Metagenomics/*methods ; Milk/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; *Temperature ; }, abstract = {Dairy cow mastitis is an important disease in the dairy industry. Different microbial species have been identified as causative agents in mastitis, and are traditionally diagnosed by bacterial culture. The objective of this study was to use metagenomic pyrosequencing of bacterial 16S rRNA genes to investigate bacterial DNA diversity in milk samples of mastitic and healthy dairy cows and compare the results with those obtained by classical bacterial culture. One hundred and thirty-six milk samples were collected from cows showing signs of mastitis and used for microbiological culture. Additionally, 20 milk samples were collected from healthy quarters. Bacterial DNA was isolated from the same milk samples and the 16S rRNA genes were individually amplified and pyrosequenced. Discriminant analysis showed that the groups of samples that were most clearly different from the rest and thus easily discriminated were the normal milk samples from healthy cows and those characterised by culture as Trueperella pyogenes and Streptococcus spp. The mastitis pathogens identified by culture were generally among the most frequent organisms detected by pyrosequencing, and in some cases (Escherichia coli, Klebsiella spp. and Streptococcus uberis mastitis) the single most prevalent microorganism. Trueperella pyogenes sequences were the second most prevalent sequences in mastitis cases diagnosed as Trueperella pyogenes by culture, Streptococcus dysgalactiae sequences were the second most prevalent sequences in mastitis cases diagnosed as Streptococcus dysgalactiae by culture, and Staphyloccocus aureus sequences were the third most prevalent in mastitis cases diagnosed as Staphylococcus aureus by culture. In samples that were aerobic culture negative, pyrosequencing identified DNA of bacteria that are known to cause mastitis, DNA of bacteria that are known pathogens but have so far not been associated with mastitis, and DNA of bacteria that are currently not known to be pathogens. A possible role of anaerobic pathogens in bovine mastitis is also suggested.}, } @article {pmid23082187, year = {2012}, author = {Džunková, M and D'Auria, G and Pérez-Villarroya, D and Moya, A}, title = {Hybrid sequencing approach applied to human fecal metagenomic clone libraries revealed clones with potential biotechnological applications.}, journal = {PloS one}, volume = {7}, number = {10}, pages = {e47654}, pmid = {23082187}, issn = {1932-6203}, mesh = {Biotechnology/*methods ; Enzymes/metabolism ; Feces/*microbiology ; *Gene Library ; Humans ; Industry ; *Metagenomics ; Molecular Sequence Annotation ; Open Reading Frames/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Natural environments represent an incredible source of microbial genetic diversity. Discovery of novel biomolecules involves biotechnological methods that often require the design and implementation of biochemical assays to screen clone libraries. However, when an assay is applied to thousands of clones, one may eventually end up with very few positive clones which, in most of the cases, have to be "domesticated" for downstream characterization and application, and this makes screening both laborious and expensive. The negative clones, which are not considered by the selected assay, may also have biotechnological potential; however, unfortunately they would remain unexplored. Knowledge of the clone sequences provides important clues about potential biotechnological application of the clones in the library; however, the sequencing of clones one-by-one would be very time-consuming and expensive. In this study, we characterized the first metagenomic clone library from the feces of a healthy human volunteer, using a method based on 454 pyrosequencing coupled with a clone-by-clone Sanger end-sequencing. Instead of whole individual clone sequencing, we sequenced 358 clones in a pool. The medium-large insert (7-15 kb) cloning strategy allowed us to assemble these clones correctly, and to assign the clone ends to maintain the link between the position of a living clone in the library and the annotated contig from the 454 assembly. Finally, we found several open reading frames (ORFs) with previously described potential medical application. The proposed approach allows planning ad-hoc biochemical assays for the clones of interest, and the appropriate sub-cloning strategy for gene expression in suitable vectors/hosts.}, } @article {pmid23080246, year = {2012}, author = {Ellis, JT and Sims, RC and Miller, CD}, title = {Monitoring microbial diversity of bioreactors using metagenomic approaches.}, journal = {Sub-cellular biochemistry}, volume = {64}, number = {}, pages = {73-94}, doi = {10.1007/978-94-007-5055-5_4}, pmid = {23080246}, issn = {0306-0225}, mesh = {Biological Products/metabolism ; Bioreactors/*microbiology/standards ; Biota/genetics ; Ecological Parameter Monitoring/*methods/standards ; Ecosystem ; *Genetic Variation ; Industrial Microbiology/methods/standards ; Metagenomics/*methods/standards ; Microbial Interactions/genetics ; }, abstract = {With the rapid development of molecular techniques, particularly 'omics' technologies, the field of microbial ecology is growing rapidly. The applications of next generation sequencing have allowed researchers to produce massive amounts of genetic data on individual microbes, providing information about microbial communities and their interactions through in situ and in vitro measurements. The ability to identify novel microbes, functions, and enzymes, along with developing an understanding of microbial interactions and functions, is necessary for efficient production of useful and high value products in bioreactors. The ability to optimize bioreactors fully and understand microbial interactions and functions within these systems will establish highly efficient industrial processes for the production of bioproducts. This chapter will provide an overview of bioreactors and metagenomic technologies to help the reader understand microbial communities, interactions, and functions in bioreactors.}, } @article {pmid23078375, year = {2012}, author = {Vitali, B and Cruciani, F and Baldassarre, ME and Capursi, T and Spisni, E and Valerii, MC and Candela, M and Turroni, S and Brigidi, P}, title = {Dietary supplementation with probiotics during late pregnancy: outcome on vaginal microbiota and cytokine secretion.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {236}, pmid = {23078375}, issn = {1471-2180}, mesh = {Adult ; *Biota ; Cytokines/*metabolism ; Denaturing Gradient Gel Electrophoresis ; *Dietary Supplements ; Female ; Humans ; *Metagenome ; Pilot Projects ; Polymerase Chain Reaction ; Pregnancy ; Probiotics/*administration & dosage ; Vagina/*immunology/*microbiology ; Young Adult ; }, abstract = {BACKGROUND: The vaginal microbiota of healthy women consists of a wide variety of anaerobic and aerobic bacterial genera and species dominated by the genus Lactobacillus. The activity of lactobacilli helps to maintain the natural healthy balance of the vaginal microbiota. This role is particularly important during pregnancy because vaginal dismicrobism is one of the most important mechanisms for preterm birth and perinatal complications. In the present study, we characterized the impact of a dietary supplementation with the probiotic VSL#3, a mixture of Lactobacillus, Bifidobacterium and Streptococcus strains, on the vaginal microbiota and immunological profiles of healthy women during late pregnancy.

RESULTS: An association between the oral intake of the probiotic VSL#3 and changes in the composition of the vaginal microbiota of pregnant women was revealed by PCR-DGGE population profiling. Despite no significant changes were found in the amounts of the principal vaginal bacterial populations in women administered with VSL#3, qPCR results suggested a potential role of the probiotic product in counteracting the decrease of Bifidobacterium and the increase of Atopobium, that occurred in control women during late pregnancy. The modulation of the vaginal microbiota was associated with significant changes in some vaginal cytokines. In particular, the decrease of the anti-inflammatory cytokines IL-4 and IL-10 was observed only in control women but not in women supplemented with VSL#3. In addition, the probiotic consumption induced the decrease of the pro-inflammatory chemokine Eotaxin, suggesting a potential anti-inflammatory effect on the vaginal immunity.

CONCLUSION: Dietary supplementation with the probiotic VSL#3 during the last trimester of pregnancy was associated to a modulation of the vaginal microbiota and cytokine secretion, with potential implications in preventing preterm birth.

TRIAL REGISTRATION: ClinicalTrials.gov NCT01367470.}, } @article {pmid23072625, year = {2012}, author = {Rosendale, DI and Blatchford, PA and Sims, IM and Parkar, SG and Carnachan, SM and Hedderley, D and Ansell, J}, title = {Characterizing kiwifruit carbohydrate utilization in vitro and its consequences for human faecal microbiota.}, journal = {Journal of proteome research}, volume = {11}, number = {12}, pages = {5863-5875}, doi = {10.1021/pr300646m}, pmid = {23072625}, issn = {1535-3907}, mesh = {Actinidia/*metabolism ; Bacteria/genetics/growth & development/metabolism ; Bacterial Proteins/metabolism ; Biota ; *Carbohydrate Metabolism ; Cellulose/metabolism ; Culture Media/metabolism ; Dietary Carbohydrates/metabolism ; Enzyme Activation ; Enzyme Assays ; Feces/*microbiology ; Fermentation ; Fruit/*metabolism ; Gastrointestinal Tract/metabolism/microbiology ; Genes, rRNA ; Humans ; *Metagenome ; Polysaccharides/metabolism ; RNA, Ribosomal, 16S/metabolism ; Solubility ; }, abstract = {It is well accepted that our gut bacteria have coevolved with us in relation to our genetics, diet and lifestyle and are integrated metabolically with us to affect our gut health adversely or beneficially. "Who is there" may vary quite widely between individuals, as might "how they do it", but "what they make" may be less variable. Many different individual species of bacteria can perform the same saccharolytic functions and so the availability of substrate (host or diet-derived) along with the degradative enzymes they possess may be key drivers of gut ecology. In this case study, we discuss detailed microbial ecology and metabolism analysis for three individuals following 48 h of in vitro faecal fermentation, using green kiwifruit as the substrate. In parallel, we have analyzed the chemical changes to the kiwifruit carbohydrates present in the fermenta to close the circle on substrate usage/degradative enzymes possessed/microbes present/microbial byproducts produced. In the absence of host carbohydrate, we see that kiwifruit carbohydrates were differentially utilized to drive microbial diversity, yet resulted in similar byproduct production. The starting ecology of each individual influenced the quantitative and qualitative microbial changes; but not necessarily the metabolic byproduct production. Thus, we propose that it is the consistent functional changes that are relevant for assessment of gut health benefits of any food. We recommend that in this era of large scale genotype/-omics studies that hypothesis-driven, bottom-up research is best placed to interpret metagenomic data in parallel with functional, phenotypic data.}, } @article {pmid23071673, year = {2012}, author = {Carroll, IM and Ringel-Kulka, T and Siddle, JP and Klaenhammer, TR and Ringel, Y}, title = {Characterization of the fecal microbiota using high-throughput sequencing reveals a stable microbial community during storage.}, journal = {PloS one}, volume = {7}, number = {10}, pages = {e46953}, pmid = {23071673}, issn = {1932-6203}, support = {K01 DK092330/DK/NIDDK NIH HHS/United States ; UL1 RR025747/RR/NCRR NIH HHS/United States ; UL1RR025747/RR/NCRR NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/growth & development ; Biodiversity ; DNA, Bacterial/chemistry/genetics ; Feces/*microbiology ; Freezing ; Genetic Variation ; Humans ; Intestines/microbiology ; Irritable Bowel Syndrome/microbiology ; Metagenome/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Specimen Handling/*methods ; Time Factors ; }, abstract = {The handling and treatment of biological samples is critical when characterizing the composition of the intestinal microbiota between different ecological niches or diseases. Specifically, exposure of fecal samples to room temperature or long term storage in deep freezing conditions may alter the composition of the microbiota. Thus, we stored fecal samples at room temperature and monitored the stability of the microbiota over twenty four hours. We also investigated the stability of the microbiota in fecal samples during a six month storage period at -80°C. As the stability of the fecal microbiota may be affected by intestinal disease, we analyzed two healthy controls and two patients with irritable bowel syndrome (IBS). We used high-throughput pyrosequencing of the 16S rRNA gene to characterize the microbiota in fecal samples stored at room temperature or -80°C at six and seven time points, respectively. The composition of microbial communities in IBS patients and healthy controls were determined and compared using the Quantitative Insights Into Microbial Ecology (QIIME) pipeline. The composition of the microbiota in fecal samples stored for different lengths of time at room temperature or -80°C clustered strongly based on the host each sample originated from. Our data demonstrates that fecal samples exposed to room or deep freezing temperatures for up to twenty four hours and six months, respectively, exhibit a microbial composition and diversity that shares more identity with its host of origin than any other sample.}, } @article {pmid23069343, year = {2013}, author = {Schneegurt, MA}, title = {Colorimetric microbial diversity analysis and halotolerance along a soil salinity gradient at the Great Salt Plains of Oklahoma.}, journal = {Research in microbiology}, volume = {164}, number = {1}, pages = {83-89}, doi = {10.1016/j.resmic.2012.10.004}, pmid = {23069343}, issn = {1769-7123}, mesh = {*Biodiversity ; Colony Count, Microbial ; Ecosystem ; Geography ; *Metagenome ; Oklahoma ; Pigments, Biological ; RNA, Ribosomal, 16S ; *Salinity ; Salt Tolerance/*physiology ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Microbial diversity was measured along a salinity gradient at the Great Salt Plains of Oklahoma using colony color quantified as RGB components of microbial isolate streaks. Numerical taxonomy was performed using a UPGMA method to create trees of relatedness, define OTUs, and calculate diversity indices. Surface soil samples along a 6-m salinity gradient (from hypersaline soil with 7.5% salinity to oligohaline rangeland soil) at WP68 were dilution-plated on SP medium of various salinities and hundreds of random colonies were collected. The salinity tolerance of isolates along the gradient was determined. From the 1364 colonies examined, 338 OTUs were defined by colony color and their distribution statistically analyzed by soil type and the salinity of enrichment media. Most colonies were shades of cream that became distinguishable based on RGB color components. Diversity indices were high overall and it is likely that the OTUs defined by colony color are below the species level, at the strain level, where the greatest diversity lies in this environment. These results are complementary to previous molecular genetic analyses of 16S rRNA clone libraries from soils at the Great Salt Plains. Great diversity at lower taxonomic levels supports the suggestion that gene flow is not highly fragmented, a result of less specialization, as expected given the highly variable salinity observed at the salt flats with rain events.}, } @article {pmid23066529, year = {2012}, author = {Jeffery, IB and Claesson, MJ and O'Toole, PW and Shanahan, F}, title = {Categorization of the gut microbiota: enterotypes or gradients?.}, journal = {Nature reviews. Microbiology}, volume = {10}, number = {9}, pages = {591-592}, pmid = {23066529}, issn = {1740-1534}, mesh = {Bacteria/classification ; *Biota ; Cluster Analysis ; Gastrointestinal Diseases/microbiology ; Gastrointestinal Tract/*microbiology/physiology ; High-Throughput Nucleotide Sequencing/methods/statistics & numerical data ; Humans ; *Metagenome ; }, } @article {pmid23064482, year = {2013}, author = {Winkler, MK and Kleerebezem, R and de Bruin, LM and Verheijen, PJ and Abbas, B and Habermacher, J and van Loosdrecht, MC}, title = {Microbial diversity differences within aerobic granular sludge and activated sludge flocs.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {16}, pages = {7447-7458}, doi = {10.1007/s00253-012-4472-7}, pmid = {23064482}, issn = {1432-0614}, mesh = {Bacteria/*classification/growth & development ; *Biodiversity ; DNA Fingerprinting ; DNA, Ribosomal/genetics ; Denaturing Gradient Gel Electrophoresis ; *Metagenome ; Netherlands ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; }, abstract = {In this study, we investigated during 400 days the microbial community variations as observed from 16S DNA gene DGGE banding patterns from an aerobic granular sludge pilot plant as well as the from a full-scale activated sludge treatment plant in Epe, the Netherlands. Both plants obtained the same wastewater and had the same relative hydraulic variations and run stable over time. For the total bacterial population, a similarity analysis was conducted showing that the community composition of both sludge types was very dissimilar. Despite this difference, general bacterial population of both systems had on average comparable species richness, entropy, and evenness, suggesting that different bacteria were sharing the same functionality. Moreover, multi-dimensional scaling analysis revealed that the microbial populations of the flocculent sludge system moved closely around the initial population, whereas the bacterial population in the aerobic granular sludge moved away from its initial population representing a permanent change. In addition, the ammonium-oxidizing community of both sludge systems was studied in detail showing more unevenness than the general bacterial community. Nitrosomonas was the dominant AOB in flocculent sludge, whereas in granular sludge, Nitrosomonas and Nitrosospira were present in equal amounts. A correlation analysis of process data and microbial data from DGGE gels showed that the microbial diversity shift in ammonium-oxidizing bacteria clearly correlated with fluctuations in temperature.}, } @article {pmid23064334, year = {2013}, author = {Dang, H and Yang, J and Li, J and Luan, X and Zhang, Y and Gu, G and Xue, R and Zong, M and Klotz, MG}, title = {Environment-dependent distribution of the sediment nifH-harboring microbiota in the Northern South China Sea.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {1}, pages = {121-132}, pmid = {23064334}, issn = {1098-5336}, mesh = {*Biota ; China ; *Genetic Variation ; Geologic Sediments/*microbiology ; *Metagenome ; Molecular Sequence Data ; Nitrogen Fixation ; Oxidoreductases/*genetics ; Phylogeography ; Sequence Analysis, DNA ; Temperature ; }, abstract = {The South China Sea (SCS), the largest marginal sea in the Western Pacific Ocean, is a huge oligotrophic water body with very limited influx of nitrogenous nutrients. This suggests that sediment microbial N(2) fixation plays an important role in the production of bioavailable nitrogen. To test the molecular underpinning of this hypothesis, the diversity, abundance, biogeographical distribution, and community structure of the sediment diazotrophic microbiota were investigated at 12 sampling sites, including estuarine, coastal, offshore, deep-sea, and methane hydrate reservoirs or their prospective areas by targeting nifH and some other functional biomarker genes. Diverse and novel nifH sequences were obtained, significantly extending the evolutionary complexity of extant nifH genes. Statistical analyses indicate that sediment in situ temperature is the most significant environmental factor influencing the abundance, community structure, and spatial distribution of the sediment nifH-harboring microbial assemblages in the northern SCS (nSCS). The significantly positive correlation of the sediment pore water NH(4)(+) concentration with the nifH gene abundance suggests that the nSCS sediment nifH-harboring microbiota is active in N(2) fixation and NH(4)(+) production. Several other environmental factors, including sediment pore water PO(4)(3-) concentration, sediment organic carbon, nitrogen and phosphorus levels, etc., are also important in influencing the community structure, spatial distribution, or abundance of the nifH-harboring microbial assemblages. We also confirmed that the nifH genes encoded by archaeal diazotrophs in the ANME-2c subgroup occur exclusively in the deep-sea methane seep areas, providing for the possibility to develop ANME-2c nifH genes as a diagnostic tool for deep-sea methane hydrate reservoir discovery.}, } @article {pmid23064332, year = {2013}, author = {Wu, JH and Wu, FY and Chuang, HP and Chen, WY and Huang, HJ and Chen, SH and Liu, WT}, title = {Community and proteomic analysis of methanogenic consortia degrading terephthalate.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {1}, pages = {105-112}, pmid = {23064332}, issn = {1098-5336}, mesh = {Genomics ; Metabolic Networks and Pathways/genetics ; Metagenome ; Methane/metabolism ; Methanomicrobiales/chemistry/classification/genetics/*isolation & purification ; Methanosarcinales/chemistry/classification/genetics/*isolation & purification ; Microbial Consortia/*genetics ; Peptococcaceae/chemistry/classification/genetics/*isolation & purification ; Phthalic Acids/*metabolism ; Proteome/*analysis ; Proteomics ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Temperature ; }, abstract = {Degradation of terephthalate (TA) through microbial syntrophy under moderately thermophilic (46 to 50°C) methanogenic conditions was characterized by using a metagenomic approach (A. Lykidis et al., ISME J. 5:122-130, 2011). To further study the activities of key microorganisms responsible for the TA degradation, community analysis and shotgun proteomics were used. The results of hierarchical oligonucleotide primer extension analysis of PCR-amplified 16S rRNA genes indicated that Pelotomaculum, Methanosaeta, and Methanolinea were predominant in the TA-degrading biofilms. Metaproteomic analysis identified a total of 482 proteins and revealed a distinctive distribution pattern of microbial functions expressed in situ. The results confirmed that TA was degraded by Pelotomaculum spp. via the proposed decarboxylation and benzoyl-coenzyme A-dependent pathway. The intermediate by-products, including acetate, H(2)/CO(2), and butyrate, were produced to support the growth of methanogens, as well as other microbial populations that could further degrade butyrate. Proteins related to energy production and conservation, and signal transduction mechanisms (that is, chemotaxis, PAS/GGDEF regulators, and stress proteins) were highly expressed, and these mechanisms were important for growth in energy-limited syntrophic ecosystems.}, } @article {pmid23064328, year = {2012}, author = {Jamindar, S and Polson, SW and Srinivasiah, S and Waidner, L and Wommack, KE}, title = {Evaluation of two approaches for assessing the genetic similarity of virioplankton populations as defined by genome size.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {24}, pages = {8773-8783}, pmid = {23064328}, issn = {1098-5336}, mesh = {*Biota ; DNA, Viral/chemistry/genetics ; Metagenomics/*methods ; Molecular Sequence Data ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Viruses/*classification/*genetics ; *Water Microbiology ; }, abstract = {Viral production estimates show that virioplankton communities turn over rapidly in aquatic ecosystems. Thus, it is likely that the genetic identity of viral populations comprising the virioplankton also change over temporal and spatial scales, reflecting shifts in viral-host interactions. However, there are few approaches that can provide data on the genotypic identity of viral populations at low cost and with the sample throughput necessary to assess dynamic changes in the virioplankton. This study examined two of these approaches-T4-like major capsid protein (g23) gene polymorphism and randomly amplified polymorphic DNA-PCR (RAPD-PCR) fingerprinting-to ask how well each technique could track differences in virioplankton populations over time and geographic location. Seasonal changes in overall virioplankton composition were apparent from pulsed-field gel electrophoresis (PFGE) analysis. T4-like phages containing similar g23 proteins were found within both small- and large-genome populations, including populations from different geographic locations and times. The surprising occurrence of T4-like g23 within small genomic groups (23 to 64 kb) indicated that the genome size range of T4-like phages may be broader than previously believed. In contrast, RAPD-PCR fingerprinting detected high genotypic similarity within PFGE bands from the same location, time, and genome size class without the requirement for DNA sequencing. Unlike g23 polymorphism, RAPD-PCR fingerprints showed a greater temporal than geographic variation. Thus, while polymorphism in a viral signature gene, such as g23, can be a powerful tool for inferring evolutionary relationships, the degree to which this approach can capture fine-scale variability within virioplankton populations is less clear.}, } @article {pmid23062738, year = {2012}, author = {Fancello, L and Raoult, D and Desnues, C}, title = {Computational tools for viral metagenomics and their application in clinical research.}, journal = {Virology}, volume = {434}, number = {2}, pages = {162-174}, pmid = {23062738}, issn = {1096-0341}, mesh = {Biomedical Research/*methods ; *Biota ; Computational Biology/methods ; Environmental Microbiology ; Humans ; *Metagenome ; Metagenomics/*methods ; Viruses/*classification/*genetics ; }, abstract = {There are 100 times more virions than eukaryotic cells in a healthy human body. The characterization of human-associated viral communities in a non-pathological state and the detection of viral pathogens in cases of infection are essential for medical care and epidemic surveillance. Viral metagenomics, the sequenced-based analysis of the complete collection of viral genomes directly isolated from an organism or an ecosystem, bypasses the "single-organism-level" point of view of clinical diagnostics and thus the need to isolate and culture the targeted organism. The first part of this review is dedicated to a presentation of past research in viral metagenomics with an emphasis on human-associated viral communities (eukaryotic viruses and bacteriophages). In the second part, we review more precisely the computational challenges posed by the analysis of viral metagenomes, and we illustrate the problem of sequences that do not have homologs in public databases and the possible approaches to characterize them.}, } @article {pmid23062173, year = {2013}, author = {Wilkins, D and Yau, S and Williams, TJ and Allen, MA and Brown, MV and DeMaere, MZ and Lauro, FM and Cavicchioli, R}, title = {Key microbial drivers in Antarctic aquatic environments.}, journal = {FEMS microbiology reviews}, volume = {37}, number = {3}, pages = {303-335}, doi = {10.1111/1574-6976.12007}, pmid = {23062173}, issn = {1574-6976}, mesh = {Antarctic Regions ; Biodiversity ; Biomass ; Carbon Dioxide/metabolism ; *Metagenome ; *Water Microbiology ; }, abstract = {Antarctica is arguably the world's most important continent for influencing the Earth's climate and ocean ecosystem function. The unique physico-chemical properties of the Southern Ocean enable high levels of microbial primary production to occur. This not only forms the base of a significant fraction of the global oceanic food web, but leads to the sequestration of anthropogenic CO2 and its transport to marine sediments, thereby removing it from the atmosphere; the Southern Ocean accounts for ~ 30% of global ocean uptake of CO2 despite representing ~ 10% of the total surface area of the global ocean. The Antarctic continent itself harbors some liquid water, including a remarkably diverse range of surface and subglacial lakes. Being one of the remaining natural frontiers, Antarctica delivers the paradox of needing to be protected from disturbance while requiring scientific endeavor to discover what is indigenous and learn how best to protect it. Moreover, like many natural environments on Earth, in Antarctica, microorganisms dominate the genetic pool and biomass of the colonizable niches and play the key roles in maintaining proper ecosystem function. This review puts into perspective insight that has been and can be gained about Antarctica's aquatic microbiota using molecular biology, and in particular, metagenomic approaches.}, } @article {pmid23061148, year = {2012}, author = {Colehour, A}, title = {The ecology of childbirth.}, journal = {Midwifery today with international midwife}, volume = {}, number = {103}, pages = {32-34}, pmid = {23061148}, issn = {1551-8892}, mesh = {Bacteria/classification ; Bifidobacterium/*classification ; Biota ; Digestive System/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Infant, Newborn ; Intestines/microbiology ; *Metagenome ; Probiotics/*classification ; }, } @article {pmid23060052, year = {2013}, author = {Engel, P and Moran, NA}, title = {Functional and evolutionary insights into the simple yet specific gut microbiota of the honey bee from metagenomic analysis.}, journal = {Gut microbes}, volume = {4}, number = {1}, pages = {60-65}, pmid = {23060052}, issn = {1949-0984}, mesh = {Animals ; Bacteria/genetics ; Bacterial Physiological Phenomena ; Bees/*microbiology ; *Biota ; Gastrointestinal Tract/microbiology ; *Metagenome ; Symbiosis ; }, abstract = {The honey bee, Apis mellifera, harbors a characteristic gut microbiota composed of only a few species which seem to be specific to social bees. The maintenance of this stable and distinct microbial community depends on the social lifestyle of these insects. As in other animals, the bacteria in the gut of honey bees probably govern important functions critical to host health. We recently sequenced a metagenome of the gut microbiota of A. mellifera, assigned gene contents to bins corresponding to the major species present in the honey bee gut, and compared functional gene categories between these species, and between the complete metagenome and those of other animals. Gene contents could be linked to different symbiotic functions with the host. Further, we found a high degree of genetic diversity within each of these species. In the case of the gammaproteobacterial species Gilliamella apicola, we experimentally showed a link between genetic variation of isolates and functional differences suggesting that niche partitioning within this species has emerged during evolution with its bee hosts. The consistent presence of only a few species, combined with strain variation within each of these species, makes the gut microbiota of social bees an ideal model for studying functional, structural, and evolutionary aspects of host-associated microbial communities: many characteristics resemble the gut microbiota of humans and other mammals, but the complexity is considerably reduced. In this addendum, we summarize and discuss our major findings and provide a detailed perspective on future research.}, } @article {pmid23060017, year = {2012}, author = {Loh, G and Blaut, M}, title = {Role of commensal gut bacteria in inflammatory bowel diseases.}, journal = {Gut microbes}, volume = {3}, number = {6}, pages = {544-555}, pmid = {23060017}, issn = {1949-0984}, mesh = {Animals ; Bacteria/*immunology/*pathogenicity ; Biota ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Intestinal Mucosa/*immunology/*microbiology/pathology ; Metagenome ; Models, Animal ; }, abstract = {Aberrant immune responses toward commensal gut bacteria can result in the onset and perpetuation of inflammatory bowel diseases (IBD). Reduced microbiota diversity in conjunction with lower proportion of Gram positive and higher proportion of Gram negative bacteria than in healthy subjects is frequently reported in IBD patients. In a subset of IBD patients, E. coli strains with specific features trigger disease. Important molecular mechanisms underlying this effect have been identified. However, in the majority of patients the exact nature of host-microbe interactions that contribute to IBD development has so far not been defined. The application of metagenomic techniques may help to identify bacterial functions that are involved in the aggravation or alleviation of IBD. Subsequently, the relevance for disease development of bacterial candidate genes may be tested taking advantage of reductionist animal models of chronic gut inflammation. This approach may help to identify bacterial functions that can be targeted in future concepts of IBD therapy.}, } @article {pmid23060016, year = {2012}, author = {Araújo-Pérez, F and McCoy, AN and Okechukwu, C and Carroll, IM and Smith, KM and Jeremiah, K and Sandler, RS and Asher, GN and Keku, TO}, title = {Differences in microbial signatures between rectal mucosal biopsies and rectal swabs.}, journal = {Gut microbes}, volume = {3}, number = {6}, pages = {530-535}, pmid = {23060016}, issn = {1949-0984}, support = {U54 CA156733/CA/NCI NIH HHS/United States ; R01 CA044684/CA/NCI NIH HHS/United States ; P30 DK 034987/DK/NIDDK NIH HHS/United States ; R01CA44684/CA/NCI NIH HHS/United States ; P50 CA106991/CA/NCI NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; P50CA106991/CA/NCI NIH HHS/United States ; R01 CA136887/CA/NCI NIH HHS/United States ; UL1RR025747/RR/NCRR NIH HHS/United States ; UL1 RR025747/RR/NCRR NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Biopsy ; *Biota ; DNA Fingerprinting ; Feces/microbiology ; Female ; Genetic Variation ; Humans ; Male ; *Metagenome ; Middle Aged ; Polymorphism, Restriction Fragment Length ; Real-Time Polymerase Chain Reaction ; Rectum/*microbiology ; Specimen Handling/*methods ; }, abstract = {There is growing evidence the microbiota of the large bowel may influence the risk of developing colorectal cancer as well as other diseases including type-1 diabetes, inflammatory bowel diseases and irritable bowel syndrome. Current sampling methods to obtain microbial specimens, such as feces and mucosal biopsies, are inconvenient and unappealing to patients. Obtaining samples through rectal swabs could prove to be a quicker and relatively easier method, but it is unclear if swabs are an adequate substitute. We compared bacterial diversity and composition from rectal swabs and rectal mucosal biopsies in order to examine the viability of rectal swabs as an alternative to biopsies. Paired rectal swabs and mucosal biopsy samples were collected in un-prepped participants (n = 11) and microbial diversity was characterized by Terminal Restriction Fragment Length polymorphism (T-RFLP) analysis and quantitative polymerase chain reaction (qPCR) of the 16S rRNA gene. Microbial community composition from swab samples was different from rectal mucosal biopsies (p = 0.001). Overall the bacterial diversity was higher in swab samples than in biopsies as assessed by diversity indexes such as: richness (p = 0.01), evenness (p = 0.06) and Shannon's diversity (p = 0.04). Analysis of specific bacterial groups by qPCR showed higher copy number of Lactobacillus (p < 0.0001) and Eubacteria (p = 0.0003) in swab samples compared with biopsies. Our findings suggest that rectal swabs and rectal mucosal samples provide different views of the microbiota in the large intestine.}, } @article {pmid23058949, year = {2012}, author = {Cuvelier, D and de Busserolles, F and Lavaud, R and Floc'h, E and Fabri, MC and Sarradin, PM and Sarrazin, J}, title = {Biological data extraction from imagery - How far can we go? A case study from the Mid-Atlantic Ridge.}, journal = {Marine environmental research}, volume = {82}, number = {}, pages = {15-27}, doi = {10.1016/j.marenvres.2012.09.001}, pmid = {23058949}, issn = {1879-0291}, mesh = {Animals ; Biodiversity ; Biomass ; Bivalvia/physiology ; Body Size ; Ecology/*methods/standards ; *Ecosystem ; *Hydrothermal Vents ; Invertebrates/physiology ; Metagenome/physiology ; Mid-Atlantic Region ; Observer Variation ; Reproducibility of Results ; Video Recording/*standards ; }, abstract = {In the past few decades, hydrothermal vent research has progressed immensely, resulting in higher-quality samples and long-term studies. With time, scientists are becoming more aware of the impacts of sampling on the faunal communities and are looking for less invasive ways to investigate the vent ecosystems. In this perspective, imagery analysis plays a very important role. With this study, we test which factors can be quantitatively and accurately assessed based on imagery, through comparison with faunal sampling. Twelve instrumented chains were deployed on the Atlantic Eiffel Tower hydrothermal edifice and the corresponding study sites were subsequently sampled. Discrete, quantitative samples were compared to the imagery recorded during the experiment. An observer-effect was tested, by comparing imagery data gathered by different scientists. Most factors based on image analyses concerning Bathymodiolus azoricus mussels were shown to be valid representations of the corresponding samples. Additional ecological assets, based exclusively on imagery, were included.}, } @article {pmid23049741, year = {2012}, author = {Jiang, X and Langille, MG and Neches, RY and Elliot, M and Levin, SA and Eisen, JA and Weitz, JS and Dushoff, J}, title = {Functional biogeography of ocean microbes revealed through non-negative matrix factorization.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e43866}, pmid = {23049741}, issn = {1932-6203}, mesh = {*Algorithms ; Aquatic Organisms/*classification/genetics ; Archaea/*classification/genetics ; Atlantic Ocean ; Bacteria/*classification/genetics ; Eukaryotic Cells/*classification/metabolism ; Metagenomics ; Microbial Consortia/genetics ; Pacific Ocean ; Phylogeny ; Phylogeography ; Proteins/*classification/genetics ; Viruses/*classification/genetics ; }, abstract = {The direct "metagenomic" sequencing of genomic material from complex assemblages of bacteria, archaea, viruses and microeukaryotes has yielded new insights into the structure of microbial communities. For example, analysis of metagenomic data has revealed the existence of previously unknown microbial taxa whose spatial distributions are limited by environmental conditions, ecological competition, and dispersal mechanisms. However, differences in genotypes that might lead biologists to designate two microbes as taxonomically distinct need not necessarily imply differences in ecological function. Hence, there is a growing need for large-scale analysis of the distribution of microbial function across habitats. Here, we present a framework for investigating the biogeography of microbial function by analyzing the distribution of protein families inferred from environmental sequence data across a global collection of sites. We map over 6,000,000 protein sequences from unassembled reads from the Global Ocean Survey dataset to [Formula: see text] protein families, generating a protein family relative abundance matrix that describes the distribution of each protein family across sites. We then use non-negative matrix factorization (NMF) to approximate these protein family profiles as linear combinations of a small number of ecological components. Each component has a characteristic functional profile and site profile. Our approach identifies common functional signatures within several of the components. We use our method as a filter to estimate functional distance between sites, and find that an NMF-filtered measure of functional distance is more strongly correlated with environmental distance than a comparable PCA-filtered measure. We also find that functional distance is more strongly correlated with environmental distance than with geographic distance, in agreement with prior studies. We identify similar protein functions in several components and suggest that functional co-occurrence across metagenomic samples could lead to future methods for de-novo functional prediction. We conclude by discussing how NMF, and other dimension reduction methods, can help enable a macroscopic functional description of marine ecosystems.}, } @article {pmid23049264, year = {2012}, author = {Ricanek, P and Lothe, SM and Frye, SA and Rydning, A and Vatn, MH and Tønjum, T}, title = {Gut bacterial profile in patients newly diagnosed with treatment-naïve Crohn's disease.}, journal = {Clinical and experimental gastroenterology}, volume = {5}, number = {}, pages = {173-186}, pmid = {23049264}, issn = {1178-7023}, abstract = {OBJECTIVES: The aim of this study was to define the composition of the gut bacterial flora in Norwegian patients with early stage Crohn's disease (CD).

METHODS: By using a nonselective metagenomics approach, the general bacterial composition in mucosal biopsies from the ileum and the colon of five subjects, four patients with different phenotypes of CD, and one noninflammatory bowel disease control, was characterized. After partial 16S ribosomal RNA (rRNA) gene sequencing, BLAST homology searches for species identification and phylogenetic analysis were performed.

RESULTS: An overall biodiversity of 106 different bacterial operational taxonomic units (OTUs) was detected in the cloned libraries. Nearly all OTUs belonged to the phylae Bacteroidetes (42% in CD, 71% in the control) or Firmicutes (42% in CD, 28% in the control), except for some OTUs that belonged to the phylum Proteobacteria (15% in CD, 0% in the control) and a few OTUs that could not be assigned to a phylum (2% in CD, 1% in the control).

CONCLUSION: Based on the high incidence of inflammatory bowel disease (IBD) in Norway, this pilot study represents a relevant determination of the gut microbiota in Norwegian patients compared to previous findings in other countries. The bacterial profile of Norwegian CD patients was found to be similar to that of CD patients in other countries. The findings do not support a particular bacterial composition as a predominant causative factor for the high incidence of IBD that exists in some countries.}, } @article {pmid23047701, year = {2012}, author = {Teske, AP}, title = {Tracking microbial habitats in subseafloor sediments.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {42}, pages = {16756-16757}, pmid = {23047701}, issn = {1091-6490}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biota ; Geologic Sediments/*analysis/*microbiology ; Metagenome/*genetics ; }, } @article {pmid23039259, year = {2012}, author = {Cassman, N and Prieto-Davó, A and Walsh, K and Silva, GG and Angly, F and Akhter, S and Barott, K and Busch, J and McDole, T and Haggerty, JM and Willner, D and Alarcón, G and Ulloa, O and DeLong, EF and Dutilh, BE and Rohwer, F and Dinsdale, EA}, title = {Oxygen minimum zones harbour novel viral communities with low diversity.}, journal = {Environmental microbiology}, volume = {14}, number = {11}, pages = {3043-3065}, doi = {10.1111/j.1462-2920.2012.02891.x}, pmid = {23039259}, issn = {1462-2920}, mesh = {Anaerobiosis ; Bacteria/classification/genetics ; Bacteriophages/genetics/physiology ; *Biodiversity ; Chile ; Genotype ; Nitrogen/metabolism ; Oceans and Seas ; Oxidation-Reduction ; Oxygen/*metabolism ; Phylogeny ; Seawater/*virology ; Sulfur/metabolism ; *Virus Physiological Phenomena ; Viruses/genetics ; }, abstract = {Oxygen minimum zones (OMZs) are oceanographic features that affect ocean productivity and biodiversity, and contribute to ocean nitrogen loss and greenhouse gas emissions. Here we describe the viral communities associated with the Eastern Tropical South Pacific (ETSP) OMZ off Iquique, Chile for the first time through abundance estimates and viral metagenomic analysis. The viral-to-microbial ratio (VMR) in the ETSP OMZ fluctuated in the oxycline and declined in the anoxic core to below one on several occasions. The number of viral genotypes (unique genomes as defined by sequence assembly) ranged from 2040 at the surface to 98 in the oxycline, which is the lowest viral diversity recorded to date in the ocean. Within the ETSP OMZ viromes, only 4.95% of genotypes were shared between surface and anoxic core viromes using reciprocal BLASTn sequence comparison. ETSP virome comparison with surface marine viromes (Sargasso Sea, Gulf of Mexico, Kingman Reef, Chesapeake Bay) revealed a dissimilarity of ETSP OMZ viruses to those from other oceanic regions. From the 1.4 million non-redundant DNA sequences sampled within the altered oxygen conditions of the ETSP OMZ, more than 97.8% were novel. Of the average 3.2% of sequences that showed similarity to the SEED non-redundant database, phage sequences dominated the surface viromes, eukaryotic virus sequences dominated the oxycline viromes, and phage sequences dominated the anoxic core viromes. The viral community of the ETSP OMZ was characterized by fluctuations in abundance, taxa and diversity across the oxygen gradient. The ecological significance of these changes was difficult to predict; however, it appears that the reduction in oxygen coincides with an increased shedding of eukaryotic viruses in the oxycline, and a shift to unique viral genotypes in the anoxic core.}, } @article {pmid23038177, year = {2013}, author = {Fancello, L and Trape, S and Robert, C and Boyer, M and Popgeorgiev, N and Raoult, D and Desnues, C}, title = {Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara.}, journal = {The ISME journal}, volume = {7}, number = {2}, pages = {359-369}, pmid = {23038177}, issn = {1751-7370}, mesh = {Africa, Northern ; Bacteriophages/*classification/genetics ; Biodiversity ; Contig Mapping ; DNA Viruses/classification/genetics ; Mauritania ; *Metagenomics ; Myoviridae/*classification/genetics ; Phylogeny ; Ponds/*virology ; *Water Microbiology ; }, abstract = {Here, we present the first metagenomic study of viral communities from four perennial ponds (gueltas) located in the central Sahara (Mauritania). Three of the four gueltas (Ilij, Molomhar and Hamdoun) are located at the source of three different wadis belonging to the same hydrologic basin, whereas the fourth (El Berbera) belongs to a different basin. Overall, sequences belonging to tailed bacteriophages were the most abundant in all four metagenomes although electron microscopy and sequencing confirmed the presence of other viral groups, such as large DNA viruses. We observed a decrease in the local viral biodiversity in El Berbera, a guelta with sustained human activities, compared with the pristine Ilij and Molomhar, and sequences related to viruses infecting crop pests were also detected as a probable consequence of the agricultural use of the soil. However, the structure of the El Berbera viral community shared the common global characteristics of the pristine gueltas, that is, it was dominated by Myoviridae and, more particularly, by virulent phages infecting photosynthetic cyanobacteria, such as Prochlorococcus and Synechococcus spp. In contrast, the Hamdoun viral community was characterized by a larger proportion of phages with the potential for a temperate lifestyle and by dominant species related to phages infecting heterotrophic bacteria commonly found in terrestrial environments. We hypothesized that the differences observed in the structural and functional composition of the Hamdoun viral community resulted from the critically low water level experienced by the guelta.}, } @article {pmid23038174, year = {2013}, author = {Martínez, I and Lattimer, JM and Hubach, KL and Case, JA and Yang, J and Weber, CG and Louk, JA and Rose, DJ and Kyureghian, G and Peterson, DA and Haub, MD and Walter, J}, title = {Gut microbiome composition is linked to whole grain-induced immunological improvements.}, journal = {The ISME journal}, volume = {7}, number = {2}, pages = {269-280}, pmid = {23038174}, issn = {1751-7370}, mesh = {Adult ; Bacteroidetes/growth & development ; Bifidobacterium/growth & development ; Biodiversity ; Biomarkers/blood ; Blood Glucose/analysis ; Cross-Over Studies ; *Diet ; *Edible Grain ; Eubacterium/growth & development ; Feces/microbiology ; Female ; Gastrointestinal Tract/immunology/metabolism/*microbiology ; Hordeum ; Humans ; Inflammation/blood ; Insulin/blood ; Interleukin-6/blood ; Male ; *Metagenome ; Oryza ; Young Adult ; }, abstract = {The involvement of the gut microbiota in metabolic disorders, and the ability of whole grains to affect both host metabolism and gut microbial ecology, suggest that some benefits of whole grains are mediated through their effects on the gut microbiome. Nutritional studies that assess the effect of whole grains on both the gut microbiome and human physiology are needed. We conducted a randomized cross-over trial with four-week treatments in which 28 healthy humans consumed a daily dose of 60 g of whole-grain barley (WGB), brown rice (BR), or an equal mixture of the two (BR+WGB), and characterized their impact on fecal microbial ecology and blood markers of inflammation, glucose and lipid metabolism. All treatments increased microbial diversity, the Firmicutes/Bacteroidetes ratio, and the abundance of the genus Blautia in fecal samples. The inclusion of WGB enriched the genera Roseburia, Bifidobacterium and Dialister, and the species Eubacterium rectale, Roseburia faecis and Roseburia intestinalis. Whole grains, and especially the BR+WGB treatment, reduced plasma interleukin-6 (IL-6) and peak postprandial glucose. Shifts in the abundance of Eubacterium rectale were associated with changes in the glucose and insulin postprandial response. Interestingly, subjects with greater improvements in IL-6 levels harbored significantly higher proportions of Dialister and lower abundance of Coriobacteriaceae. In conclusion, this study revealed that a short-term intake of whole grains induced compositional alterations of the gut microbiota that coincided with improvements in host physiological measures related to metabolic dysfunctions in humans.}, } @article {pmid23033984, year = {2012}, author = {Lagier, JC and Armougom, F and Million, M and Hugon, P and Pagnier, I and Robert, C and Bittar, F and Fournous, G and Gimenez, G and Maraninchi, M and Trape, JF and Koonin, EV and La Scola, B and Raoult, D}, title = {Microbial culturomics: paradigm shift in the human gut microbiome study.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {18}, number = {12}, pages = {1185-1193}, doi = {10.1111/1469-0691.12023}, pmid = {23033984}, issn = {1469-0691}, mesh = {*Biodiversity ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; Mass Spectrometry/methods ; *Metagenome ; Metagenomics/methods ; Microbiological Techniques/methods ; Molecular Sequence Data ; Sequence Analysis, DNA/methods ; }, abstract = {Comprehensive determination of the microbial composition of the gut microbiota and the relationships with health and disease are major challenges in the 21st century. Metagenomic analysis of the human gut microbiota detects mostly uncultured bacteria. We studied stools from two lean Africans and one obese European, using 212 different culture conditions (microbial culturomics), and tested the colonies by using mass spectrometry and 16S rRNA amplification and sequencing. In parallel, we analysed the same three samples by pyrosequencing 16S rRNA amplicons targeting the V6 region. The 32 500 colonies obtained by culturomics have yielded 340 species of bacteria from seven phyla and 117 genera, including two species from rare phyla (Deinococcus-Thermus and Synergistetes, five fungi, and a giant virus (Senegalvirus). The microbiome identified by culturomics included 174 species never described previously in the human gut, including 31 new species and genera for which the genomes were sequenced, generating c. 10 000 new unknown genes (ORFans), which will help in future molecular studies. Among these, the new species Microvirga massiliensis has the largest bacterial genome so far obtained from a human, and Senegalvirus is the largest virus reported in the human gut. Concurrent metagenomic analysis of the same samples produced 698 phylotypes, including 282 known species, 51 of which overlapped with the microbiome identified by culturomics. Thus, culturomics complements metagenomics by overcoming the depth bias inherent in metagenomic approaches.}, } @article {pmid23032991, year = {2013}, author = {Graessler, J and Qin, Y and Zhong, H and Zhang, J and Licinio, J and Wong, ML and Xu, A and Chavakis, T and Bornstein, AB and Ehrhart-Bornstein, M and Lamounier-Zepter, V and Lohmann, T and Wolf, T and Bornstein, SR}, title = {Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters.}, journal = {The pharmacogenomics journal}, volume = {13}, number = {6}, pages = {514-522}, doi = {10.1038/tpj.2012.43}, pmid = {23032991}, issn = {1473-1150}, mesh = {Adult ; Diabetes Mellitus, Type 2/*complications/metabolism ; Female ; *Gastric Bypass ; Humans ; Inflammation/*complications ; Male ; *Metagenome ; *Microbiota ; Middle Aged ; Obesity/complications/metabolism/*surgery ; Postoperative Period ; }, abstract = {Roux-en-Y gastric bypass (RYGB) has become a prominent therapeutic option for long-term treatment of morbid obesity and type 2 diabetes mellitus (T2D). Cross talk and pathogenetic consequences of RYGB-induced profound effects on metabolism and gut microbiome are poorly understood. The aim of the present study therefore was to characterize intra-individual changes of gut microbial composition before and 3 months after RYGB by metagenomic sequencing in morbidly obese patients (body mass index (BMI)>40 kg m(-)(2)) with T2D. Subsequently, metagenomic data were correlated with clinical indices. Based on gene relative abundance profile, 1061 species, 729 genera, 44 phyla and 5127 KO (KEGG Orthology) were identified. Despite high diversity, bacteria could mostly be assigned to seven bacterial divisions. The overall metagenomic RYGB-induced shift was characterized by a reduction of Firmicutes and Bacteroidetes and an increase of Proteobacteria. Twenty-two microbial species and 11 genera were significantly altered by RYGB. Using principal component analysis, highly correlated species were assembled into two common components. Component 1 consisted of species that were mainly associated with BMI and C-reactive protein. This component was characterized by increased numbers of Proteobacterium Enterobacter cancerogenus and decreased Firmicutes Faecalibacterium prausnitzii and Coprococcus comes. Functional analysis of carbohydrate metabolism by KO revealed significant effects in 13 KOs assigned to phosphotransferase system. Spearmen's Rank correlation indicated an association of 10 species with plasma total- or low-density lipoprotein cholesterol, and 5 species with triglycerides. F. prausnitzii was directly correlated to fasting blood glucose. This is the first clinical demonstration of a profound and specific intra-individual modification of gut microbial composition by full metagenomic sequencing. A clear correlation exists of microbiome composition and gene function with an improvement in metabolic and inflammatory parameters. This will allow to develop new diagnostic and therapeutic strategies based on metagenomic sequencing of the human gut microbiome.}, } @article {pmid23029440, year = {2012}, author = {Sangwan, N and Lata, P and Dwivedi, V and Singh, A and Niharika, N and Kaur, J and Anand, S and Malhotra, J and Jindal, S and Nigam, A and Lal, D and Dua, A and Saxena, A and Garg, N and Verma, M and Kaur, J and Mukherjee, U and Gilbert, JA and Dowd, SE and Raman, R and Khurana, P and Khurana, JP and Lal, R}, title = {Comparative metagenomic analysis of soil microbial communities across three hexachlorocyclohexane contamination levels.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e46219}, pmid = {23029440}, issn = {1932-6203}, mesh = {Archaea/classification/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Bacterial Proteins/genetics ; Biodegradation, Environmental ; Chemotaxis/genetics ; Fusarium/*genetics/metabolism ; Gene Transfer, Horizontal ; Genes, Bacterial ; Hexachlorocyclohexane/*metabolism ; Lyases/genetics ; *Metagenomics ; Microbial Consortia/*genetics ; Plasmids/genetics ; RNA, Ribosomal, 16S/classification/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {This paper presents the characterization of the microbial community responsible for the in-situ bioremediation of hexachlorocyclohexane (HCH). Microbial community structure and function was analyzed using 16S rRNA amplicon and shotgun metagenomic sequencing methods for three sets of soil samples. The three samples were collected from a HCH-dumpsite (450 mg HCH/g soil) and comprised of a HCH/soil ratio of 0.45, 0.0007, and 0.00003, respectively. Certain bacterial; (Chromohalobacter, Marinimicrobium, Idiomarina, Salinosphaera, Halomonas, Sphingopyxis, Novosphingobium, Sphingomonas and Pseudomonas), archaeal; (Halobacterium, Haloarcula and Halorhabdus) and fungal (Fusarium) genera were found to be more abundant in the soil sample from the HCH-dumpsite. Consistent with the phylogenetic shift, the dumpsite also exhibited a relatively higher abundance of genes coding for chemotaxis/motility, chloroaromatic and HCH degradation (lin genes). Reassembly of a draft pangenome of Chromohalobacter salaxigenes sp. (∼8X coverage) and 3 plasmids (pISP3, pISP4 and pLB1; 13X coverage) containing lin genes/clusters also provides an evidence for the horizontal transfer of HCH catabolism genes.}, } @article {pmid23027979, year = {2012}, author = {Jorgensen, SL and Hannisdal, B and Lanzén, A and Baumberger, T and Flesland, K and Fonseca, R and Ovreås, L and Steen, IH and Thorseth, IH and Pedersen, RB and Schleper, C}, title = {Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {42}, pages = {E2846-55}, pmid = {23027979}, issn = {1091-6490}, mesh = {Archaea/*genetics ; Arctic Regions ; Bacteria/*genetics ; *Biota ; Chromatography, Ion Exchange ; Cluster Analysis ; DNA Primers/genetics ; Geologic Sediments/*analysis/*microbiology ; Metagenome/*genetics ; Oceans and Seas ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA/methods ; Species Specificity ; }, abstract = {Microbial communities and their associated metabolic activity in marine sediments have a profound impact on global biogeochemical cycles. Their composition and structure are attributed to geochemical and physical factors, but finding direct correlations has remained a challenge. Here we show a significant statistical relationship between variation in geochemical composition and prokaryotic community structure within deep-sea sediments. We obtained comprehensive geochemical data from two gravity cores near the hydrothermal vent field Loki's Castle at the Arctic Mid-Ocean Ridge, in the Norwegian-Greenland Sea. Geochemical properties in the rift valley sediments exhibited strong centimeter-scale stratigraphic variability. Microbial populations were profiled by pyrosequencing from 15 sediment horizons (59,364 16S rRNA gene tags), quantitatively assessed by qPCR, and phylogenetically analyzed. Although the same taxa were generally present in all samples, their relative abundances varied substantially among horizons and fluctuated between Bacteria- and Archaea-dominated communities. By independently summarizing covariance structures of the relative abundance data and geochemical data, using principal components analysis, we found a significant correlation between changes in geochemical composition and changes in community structure. Differences in organic carbon and mineralogy shaped the relative abundance of microbial taxa. We used correlations to build hypotheses about energy metabolisms, particularly of the Deep Sea Archaeal Group, specific Deltaproteobacteria, and sediment lineages of potentially anaerobic Marine Group I Archaea. We demonstrate that total prokaryotic community structure can be directly correlated to geochemistry within these sediments, thus enhancing our understanding of biogeochemical cycling and our ability to predict metabolisms of uncultured microbes in deep-sea sediments.}, } @article {pmid23015674, year = {2012}, author = {Xu, Y and Moser, C and Al-Soud, WA and Sørensen, S and Høiby, N and Nielsen, PH and Thomsen, TR}, title = {Culture-dependent and -independent investigations of microbial diversity on urinary catheters.}, journal = {Journal of clinical microbiology}, volume = {50}, number = {12}, pages = {3901-3908}, pmid = {23015674}, issn = {1098-660X}, mesh = {Bacteria/*classification/genetics/growth & development/*isolation & purification ; Bacteriological Techniques/*methods ; *Biodiversity ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Humans ; Metagenomics/*methods ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Urinary Catheters/*microbiology ; }, abstract = {Catheter-associated urinary tract infection is caused by bacteria, which ascend the catheter along its external or internal surface to the bladder and subsequently develop into biofilms on the catheter and uroepithelium. Antibiotic-treated bacteria and bacteria residing in biofilm can be difficult to culture. In this study we used culture-based and 16S rRNA gene-based culture-independent methods (fingerprinting, cloning, and pyrosequencing) to determine the microbial diversity of biofilms on 24 urinary catheters. Most of the patients were catheterized for <30 days and had undergone recent antibiotic treatment. In addition, the corresponding urine samples for 16 patients were cultured. We found that gene analyses of the catheters were consistent with cultures of the corresponding urine samples for the presence of bacteria but sometimes discordant for the identity of the species. Cultures of catheter tips detected bacteria more frequently than urine cultures and gene analyses; coagulase-negative staphylococci were, in particular, cultured much more often from catheter tips, indicating potential contamination of the catheter tips during sampling. The external and internal surfaces of 19 catheters were separately analyzed by molecular methods, and discordant results were found in six catheters, suggesting that bacterial colonization intra- and extraluminally may be different. Molecular analyses showed that most of the species identified in this study were known uropathogens, and infected catheters were generally colonized by one to two species, probably due to antibiotic usage and short-term catheterization. In conclusion, our data showed that culture-independent molecular methods did not detect bacteria from urinary catheters more frequently than culture-based methods.}, } @article {pmid23013113, year = {2012}, author = {Newton, IL and Roeselers, G}, title = {The effect of training set on the classification of honey bee gut microbiota using the Naïve Bayesian Classifier.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {221}, pmid = {23013113}, issn = {1471-2180}, mesh = {Animals ; Bacteria/classification/genetics ; Bees/*microbiology ; *Biodiversity ; DNA, Ribosomal/chemistry/genetics ; Gastrointestinal Tract/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Microbial ecologists now routinely utilize next-generation sequencing methods to assess microbial diversity in the environment. One tool heavily utilized by many groups is the Naïve Bayesian Classifier developed by the Ribosomal Database Project (RDP-NBC). However, the consistency and confidence of classifications provided by the RDP-NBC is dependent on the training set utilized.

RESULTS: We explored the stability of classification of honey bee gut microbiota sequences by the RDP-NBC utilizing three publically available ribosomal RNA sequence databases as training sets: ARB-SILVA, Greengenes and RDP. We found that the inclusion of previously published, high-quality, full-length sequences from 16S rRNA clone libraries improved the precision in classification of novel bee-associated sequences. Specifically, by including bee-specific 16S rRNA gene sequences a larger fraction of sequences were classified at a higher confidence by the RDP-NBC (based on bootstrap scores).

CONCLUSIONS: Results from the analysis of these bee-associated sequences have ramifications for other environments represented by few sequences in the public databases or few bacterial isolates. We conclude that for the exploration of relatively novel habitats, the inclusion of high-quality, full-length 16S rRNA gene sequences allows for a more confident taxonomic classification.}, } @article {pmid23001654, year = {2012}, author = {Wang, Y and Sheng, HF and He, Y and Wu, JY and Jiang, YX and Tam, NF and Zhou, HW}, title = {Comparison of the levels of bacterial diversity in freshwater, intertidal wetland, and marine sediments by using millions of illumina tags.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {23}, pages = {8264-8271}, pmid = {23001654}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; China ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fresh Water/*microbiology ; Geologic Sediments/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers ; Seawater/*microbiology ; Sequence Analysis, DNA ; *Wetlands ; }, abstract = {Sediment, a special realm in aquatic environments, has high microbial diversity. While there are numerous reports about the microbial community in marine sediment, freshwater and intertidal sediment communities have been overlooked. The present study determined millions of Illumina reads for a comparison of bacterial communities in freshwater, intertidal wetland, and marine sediments along Pearl River, China, using a technically consistent approach. Our results show that both taxon richness and evenness were the highest in freshwater sediment, medium in intertidal sediment, and lowest in marine sediment. The high number of sequences allowed the determination of a wide variety of bacterial lineages in all sediments for reliable statistical analyses. Principal component analysis showed that the three types of communities could be well separated from phylum to operational taxonomy unit (OTU) levels, and the OTUs from abundant to rare showed satisfactory resolutions. Statistical analysis (LEfSe) demonstrated that the freshwater sediment was enriched with Acidobacteria, Nitrospira, Verrucomicrobia, Alphaproteobacteria, and Betaproteobacteria. The intertidal sediment had a unique community with diverse primary producers (such as Chloroflexi, Bacillariophyta, Gammaproteobacteria, and Epsilonproteobacteria) as well as saprophytic microbes (such as Actinomycetales, Bacteroidetes, and Firmicutes). The marine sediment had a higher abundance of Gammaproteobacteria and Deltaproteobacteria, which were mainly involved in sulfate reduction in anaerobic conditions. These results are helpful for a systematic understanding of bacterial communities in natural sediment environments.}, } @article {pmid23001646, year = {2012}, author = {Justice, NB and Pan, C and Mueller, R and Spaulding, SE and Shah, V and Sun, CL and Yelton, AP and Miller, CS and Thomas, BC and Shah, M and VerBerkmoes, N and Hettich, R and Banfield, JF}, title = {Heterotrophic archaea contribute to carbon cycling in low-pH, suboxic biofilm communities.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {23}, pages = {8321-8330}, pmid = {23001646}, issn = {1098-5336}, mesh = {Aerobiosis ; Anaerobiosis ; Archaea/classification/genetics/*metabolism/*physiology ; Bacteria/classification/genetics/*metabolism ; *Bacterial Physiological Phenomena ; Biofilms/*growth & development ; *Biota ; Carbon/*metabolism ; Environmental Microbiology ; Genes, rRNA ; Heterotrophic Processes ; Hydrogen-Ion Concentration ; Metagenome ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Archaea are widely distributed and yet are most often not the most abundant members of microbial communities. Here, we document a transition from Bacteria- to Archaea-dominated communities in microbial biofilms sampled from the Richmond Mine acid mine drainage (AMD) system (∼pH 1.0, ∼38°C) and in laboratory-cultivated biofilms. This transition occurs when chemoautotrophic microbial communities that develop at the air-solution interface sink to the sediment-solution interface and degrade under microaerobic and anaerobic conditions. The archaea identified in these sunken biofilms are from the class Thermoplasmata, and in some cases, the highly divergent ARMAN nanoarchaeal lineage. In several of the sunken biofilms, nanoarchaea comprise 10 to 25% of the community, based on fluorescent in situ hybridization and metagenomic analyses. Comparative community proteomic analyses show a persistence of bacterial proteins in sunken biofilms, but there is clear evidence for amino acid modifications due to acid hydrolysis. Given the low representation of bacterial cells in sunken biofilms based on microscopy, we infer that hydrolysis reflects proteins derived from lysed cells. For archaea, we detected ∼2,400 distinct proteins, including a subset involved in proteolysis and peptide uptake. Laboratory cultivation experiments using complex carbon substrates demonstrated anaerobic enrichment of Ferroplasma and Aplasma coupled to the reduction of ferric iron. These findings indicate dominance of acidophilic archaea in degrading biofilms and suggest that they play roles in anaerobic nutrient cycling at low pH.}, } @article {pmid23000871, year = {2012}, author = {Méthot, PO}, title = {Understanding pathogens in the era of next generation sequencing.}, journal = {Journal of infection in developing countries}, volume = {6}, number = {9}, pages = {689-691}, doi = {10.3855/jidc.3012}, pmid = {23000871}, issn = {1972-2680}, mesh = {*Biota ; Communicable Diseases/*microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Metagenome ; }, abstract = {What is a pathogen? Medical textbooks usually define a pathogen as any microorganism that causes disease. However, this widespread definition is problematic on a number of counts [1, 11]. Moreover, a generally accepted definition is not forthcoming among medical microbiologists, immunologists, and physicians. Here it is argued that there is another, and more pressing question to be asked, namely: what makes some organisms pathogenic and others not? Asking these questions instead allows for distinguishing pathogens from non-pathogens in a more flexible way, while at the same time emphasizing the roles of ecological and evolutionary processes in determining pathogenicity in infectious diseases.}, } @article {pmid22992344, year = {2012}, author = {Ishaq, SL and Wright, AD}, title = {Insight into the bacterial gut microbiome of the North American moose (Alces alces).}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {212}, pmid = {22992344}, issn = {1471-2180}, mesh = {Animals ; Bacteria/*classification/genetics ; *Biodiversity ; Cluster Analysis ; Colon/*microbiology ; Female ; Male ; Metagenome ; Microarray Analysis ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Ruminants/*microbiology ; }, abstract = {BACKGROUND: The work presented here provides the first intensive insight into the bacterial populations in the digestive tract of the North American moose (Alces alces). Eight free-range moose on natural pasture were sampled, producing eight rumen samples and six colon samples. Second generation (G2) PhyloChips were used to determine the presence of hundreds of operational taxonomic units (OTUs), representing multiple closely related species/strains (>97% identity), found in the rumen and colon of the moose.

RESULTS: A total of 789 unique OTUs were used for analysis, which passed the fluorescence and the positive fraction thresholds. There were 73 OTUs, representing 21 bacterial families, which were found exclusively in the rumen samples: Lachnospiraceae, Prevotellaceae and several unclassified families, whereas there were 71 OTUs, representing 22 bacterial families, which were found exclusively in the colon samples: Clostridiaceae, Enterobacteriaceae and several unclassified families. Overall, there were 164 OTUs that were found in 100% of the samples. The Firmicutes were the most dominant bacteria phylum in both the rumen and the colon. Microarray data available at ArrayExpress, accession number E-MEXP-3721.

CONCLUSIONS: Using PhyloTrac and UniFrac computer software, samples clustered into two distinct groups: rumen and colon, confirming that the rumen and colon are distinct environments. There was an apparent correlation of age to cluster, which will be validated by a larger sample size in future studies, but there were no detectable trends based upon gender.}, } @article {pmid22988916, year = {2012}, author = {Osei-Poku, J and Mbogo, CM and Palmer, WJ and Jiggins, FM}, title = {Deep sequencing reveals extensive variation in the gut microbiota of wild mosquitoes from Kenya.}, journal = {Molecular ecology}, volume = {21}, number = {20}, pages = {5138-5150}, doi = {10.1111/j.1365-294X.2012.05759.x}, pmid = {22988916}, issn = {1365-294X}, support = {092654//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bacteria/*classification/genetics ; *Biodiversity ; Culicidae/*microbiology ; DNA, Bacterial/genetics ; Female ; Gastrointestinal Tract/*microbiology ; Kenya ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The mosquito midgut is a hostile environment that vector-borne parasites must survive to be transmitted. Commensal bacteria in the midgut can reduce the ability of mosquitoes to transmit disease, either by having direct anti-parasite effects or by stimulating basal immune responses of the insect host. As different bacteria have different effects on parasite development, the composition of the bacterial community in the mosquito gut is likely to affect the probability of disease transmission. We investigated the diversity of mosquito gut bacteria in the field using 454 pyrosequencing of 16S rRNA to build up a comprehensive picture of the diversity of gut bacteria in eight mosquito species in this population. We found that mosquito gut typically has a very simple gut microbiota that is dominated by a single bacterial taxon. Although different mosquito species share remarkably similar gut bacteria, individuals in a population are extremely variable and can have little overlap in the bacterial taxa present in their guts. This may be an important factor in causing differences in disease transmission rates within mosquito populations.}, } @article {pmid22988084, year = {2012}, author = {Tang, CQ and Leasi, F and Obertegger, U and Kieneke, A and Barraclough, TG and Fontaneto, D}, title = {The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {40}, pages = {16208-16212}, pmid = {22988084}, issn = {1091-6490}, support = {BB/G004250/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; B/G004250/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Base Sequence ; *Biodiversity ; DNA Primers/genetics ; Electron Transport Complex IV/genetics ; Genetic Markers/*genetics ; Genetic Variation/*genetics ; Likelihood Functions ; Metagenome/*genetics ; *Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques ; *Phylogeny ; Predictive Value of Tests ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA ; }, abstract = {Molecular tools have revolutionized the exploration of biodiversity, especially in organisms for which traditional taxonomy is difficult, such as for microscopic animals (meiofauna). Environmental (eDNA) metabarcode surveys of DNA extracted from sediment samples are increasingly popular for surveying biodiversity. Most eDNA surveys use the nuclear gene-encoding small-subunit rDNA gene (18S) as a marker; however, different markers and metrics used for delimiting species have not yet been evaluated against each other or against morphologically defined species (morphospecies). We assessed more than 12,000 meiofaunal sequences of 18S and of the main alternatively used marker [Cytochrome c oxidase subunit I (COI) mtDNA] belonging to 55 datasets covering three taxonomic ranks. Our results show that 18S reduced diversity estimates by a factor of 0.4 relative to morphospecies, whereas COI increased diversity estimates by a factor of 7.6. Moreover, estimates of species richness using COI were robust among three of four commonly used delimitation metrics, whereas estimates using 18S varied widely with the different metrics. We show that meiofaunal diversity has been greatly underestimated by 18S eDNA surveys and that the use of COI provides a better estimate of diversity. The suitability of COI is supported by cross-mating experiments in the literature and evolutionary analyses of discreteness in patterns of genetic variation. Furthermore its splitting of morphospecies is expected from documented levels of cryptic taxa in exemplar meiofauna. We recommend against using 18S as a marker for biodiversity surveys and suggest that use of COI for eDNA surveys could provide more accurate estimates of species richness in the future.}, } @article {pmid22983039, year = {2012}, author = {Devine, SP and Pelletreau, KN and Rumpho, ME}, title = {16S rDNA-based metagenomic analysis of bacterial diversity associated with two populations of the kleptoplastic sea slug Elysia chlorotica and its algal prey Vaucheria litorea.}, journal = {The Biological bulletin}, volume = {223}, number = {1}, pages = {138-154}, doi = {10.1086/BBLv223n1p138}, pmid = {22983039}, issn = {1939-8697}, mesh = {Animals ; Aquatic Organisms/microbiology ; Bacteria/*classification/*genetics ; *Biota ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gastropoda/*microbiology ; Massachusetts ; *Metagenome ; Molecular Sequence Data ; Nova Scotia ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Stramenopiles/*microbiology ; }, abstract = {The molluscan sea slug Elysia chlorotica is best known for its obligate endosymbiosis with chloroplasts (= kleptoplasty) from its algal prey Vaucheria litorea and its ability to sustain itself photoautotrophically for several months. This unusual photosynthetic sea slug also harbors an array of undescribed bacteria, which may contribute to the long-term success of the symbiosis. Here, we utilized 16S rDNA-based metagenomic analyses to characterize the microbial diversity associated with two populations of E. chlorotica from Halifax, Nova Scotia, Canada, and from Martha's Vineyard, Massachusetts, USA. Animals were examined immediately after collection from their native environments, after being starved of their algal prey for several months, and after being bred in the laboratory (second-generation sea slugs) to characterize the effect of varying environmental and culturing conditions on the associated bacteria. Additionally, the microbiome of the algal prey, laboratory-cultured V. litorea, was analyzed to determine whether the laboratory-bred sea slugs obtained bacteria from their algal food source during development. Bacterial profiles varied between populations and among all conditions except for the F2 laboratory-bred samples, which were similar in diversity and abundance, but not to the algal microbiome. Alpha-, beta-, and gamma-proteobacteria dominated all of the samples along with Actinobacteria, Bacilli, Flavobacteria, and Sphingobacteria. Bacteria capable of polysaccharide digestion and photosynthesis, as well as putative nitrogen fixation, vitamin B(12) production, and natural product biosynthesis were associated with the sea slug and algal samples.}, } @article {pmid22983038, year = {2012}, author = {Petersen, JM and Wentrup, C and Verna, C and Knittel, K and Dubilier, N}, title = {Origins and evolutionary flexibility of chemosynthetic symbionts from deep-sea animals.}, journal = {The Biological bulletin}, volume = {223}, number = {1}, pages = {123-137}, doi = {10.1086/BBLv223n1p123}, pmid = {22983038}, issn = {1939-8697}, mesh = {Adaptation, Biological ; Animals ; Aquatic Organisms/*microbiology/physiology ; Bacteria/*genetics/*metabolism ; *Bacterial Physiological Phenomena ; Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Evolution, Molecular ; Metabolic Networks and Pathways/*genetics ; Methane/metabolism ; Molecular Sequence Data ; Mytilidae/*microbiology/physiology ; Oceans and Seas ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfur/metabolism ; *Symbiosis ; }, abstract = {Bathymodiolin mussels dominate hydrothermal vent and cold seep communities worldwide. Symbiotic associations with chemosynthetic sulfur- and methane-oxidizing bacteria that provide for their nutrition are the key to their ecological and evolutionary success. The current paradigm is that these symbioses evolved from two free-living ancestors, one methane-oxidizing and one sulfur-oxidizing bacterium. In contrast to previous studies, our phylogenetic analyses of the bathymodiolin symbionts show that both the sulfur and the methane oxidizers fall into multiple clades interspersed with free-living bacteria, many of which were discovered recently in metagenomes from marine oxygen minimum zones. We therefore hypothesize that symbioses between bathymodiolin mussels and free-living sulfur- and methane-oxidizing bacteria evolved multiple times in convergent evolution. Furthermore, by 16S rRNA sequencing and fluorescence in situ hybridization, we show that close relatives of the bathymodiolin symbionts occur on hosts belonging to different animal phyla: Raricirrus beryli, a terebellid polychaete from a whale-fall, and a poecilosclerid sponge from a cold seep. The host range within the bathymodiolin symbionts is therefore greater than previously recognized, confirming the remarkable flexibility of these symbiotic associations.}, } @article {pmid22978611, year = {2012}, author = {Lebeis, SL and Rott, M and Dangl, JL and Schulze-Lefert, P}, title = {Culturing a plant microbiome community at the cross-Rhodes.}, journal = {The New phytologist}, volume = {196}, number = {2}, pages = {341-344}, doi = {10.1111/j.1469-8137.2012.04336.x}, pmid = {22978611}, issn = {1469-8137}, mesh = {*Biota ; Genomics ; Greece ; *Metagenome ; Plants/*microbiology ; Proteomics ; Statistics as Topic ; }, } @article {pmid22978555, year = {2012}, author = {Colman, DR and Toolson, EC and Takacs-Vesbach, CD}, title = {Do diet and taxonomy influence insect gut bacterial communities?.}, journal = {Molecular ecology}, volume = {21}, number = {20}, pages = {5124-5137}, doi = {10.1111/j.1365-294X.2012.05752.x}, pmid = {22978555}, issn = {1365-294X}, support = {1P20RR18754/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification/genetics ; Bees/classification/microbiology ; Biodiversity ; Coleoptera/classification/microbiology ; DNA, Bacterial/genetics ; *Diet ; Gastrointestinal Tract/*microbiology ; Genes, Bacterial ; Insecta/classification/*microbiology ; Isoptera/classification/microbiology ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Wasps/classification/microbiology ; }, abstract = {Many insects contain diverse gut microbial communities. While several studies have focused on a single or small group of species, comparative studies of phylogenetically diverse hosts can illuminate general patterns of host-microbiota associations. In this study, we tested the hypotheses that (i) host diet and (ii) host taxonomy structure intestinal bacterial community composition among insects. We used published 16S rRNA gene sequence data for 58 insect species in addition to four beetle species sampled from the Sevilleta National Wildlife Refuge to test these hypotheses. Overall, gut bacterial species richness in these insects was low. Decaying wood xylophagous insects harboured the richest bacterial gut flora (102.8 species level operational taxonomic units (OTUs)/sample ± 71.7, 11.8 ± 5.9 phylogenetic diversity (PD)/sample), while bees and wasps harboured the least rich bacterial communities (11.0 species level OTUs/sample ± 5.4, 2.6 ± 0.8 PD/sample). We found evidence to support our hypotheses that host diet and taxonomy structure insect gut bacterial communities (P < 0.001 for both). However, while host taxonomy was important in hymenopteran and termite gut community structure, diet was an important community structuring factor particularly for insect hosts that ingest lignocellulose-derived substances. Our analysis provides a baseline comparison of insect gut bacterial communities from which to test further hypotheses concerning proximate and ultimate causes of these associations.}, } @article {pmid22977920, year = {2012}, author = {}, title = {The hidden hordes.}, journal = {Nature reviews. Microbiology}, volume = {10}, number = {8}, pages = {517}, pmid = {22977920}, issn = {1740-1534}, mesh = {*Biota ; Humans ; *Metagenome ; }, abstract = {With funding for the HMP and Meta-HIT consortia now ending, what's next for these large-scale efforts to map the hidden microbial hordes associated with the human body?}, } @article {pmid22975469, year = {2012}, author = {Fujimura, KE and Rauch, M and Matsui, E and Iwai, S and Calatroni, A and Lynn, H and Mitchell, H and Johnson, CC and Gern, JE and Togias, A and Boushey, HA and Kennedy, S and Lynch, SV}, title = {Development of a standardized approach for environmental microbiota investigations related to asthma development in children.}, journal = {Journal of microbiological methods}, volume = {91}, number = {2}, pages = {231-239}, pmid = {22975469}, issn = {1872-8359}, support = {N01-AI-25482/AI/NIAID NIH HHS/United States ; HHSN272201000021C/AI/NIAID NIH HHS/United States ; M01 RR000533/RR/NCRR NIH HHS/United States ; M01 RR000071/RR/NCRR NIH HHS/United States ; UL1 TR000448/TR/NCATS NIH HHS/United States ; 1UL1RR024156/RR/NCRR NIH HHS/United States ; HHSN272200900052C/AI/NIAID NIH HHS/United States ; HHSN272201000052I/AI/NIAID NIH HHS/United States ; N01-AI-25496/AI/NIAID NIH HHS/United States ; 5UL1RR024992-02/RR/NCRR NIH HHS/United States ; M01RR00533/RR/NCRR NIH HHS/United States ; N01AI25496/AI/NIAID NIH HHS/United States ; UL1 RR024156/RR/NCRR NIH HHS/United States ; UL1 RR025771/RR/NCRR NIH HHS/United States ; HHSN272201000051C/AI/NIAID NIH HHS/United States ; UL1 RR024992/RR/NCRR NIH HHS/United States ; M01 RR000052/RR/NCRR NIH HHS/United States ; 1UL1RR025771/RR/NCRR NIH HHS/United States ; HHSN272201000021I/AI/NIAID NIH HHS/United States ; RR00052/RR/NCRR NIH HHS/United States ; N01AI25482/AI/NIAID NIH HHS/United States ; M01RR00071/RR/NCRR NIH HHS/United States ; }, mesh = {Asthma/*etiology ; *Biota ; Child ; *Dust ; *Environmental Microbiology ; Humans ; *Metagenome ; Metagenomics/*methods/*standards ; Microarray Analysis/methods/standards ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Standardized studies examining environmental microbial exposure in populations at risk for asthma are necessary to improve our understanding of the role this factor plays in disease development. Here we describe studies aimed at developing guidelines for high-resolution culture-independent microbiome profiling, using a phylogenetic microarray (PhyloChip), of house dust samples in a cohort collected as part of the NIH-funded Inner City Asthma Consortium (ICAC). We demonstrate that though extracted DNA concentrations varied across dust samples, the majority produced sufficient 16S rRNA to be profiled by the array. Comparison of array and 454-pyrosequencing performed in parallel on a subset of samples, illustrated that increasingly deeper sequencing efforts validated greater numbers of array-detected taxa. Community composition agreement across samples exhibited a hierarchy in concordance, with the highest level of agreement in replicate array profiles followed by samples collected from adjacent 1×1 m(2) sites in the same room, adjacent sites with different sized sampling quadrants (1×1 and 2×2 m(2)), different sites within homes (living and bedroom) to lowest in living room samples collected from different homes. The guidelines for sample collection and processing in this pilot study extend beyond PhyloChip based studies of house-associated microbiota, and bear relevance for other microbiome profiling approaches such as next-generation sequencing.}, } @article {pmid22974186, year = {2012}, author = {Siddiqui, H and Lagesen, K and Nederbragt, AJ and Jeansson, SL and Jakobsen, KS}, title = {Alterations of microbiota in urine from women with interstitial cystitis.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {205}, pmid = {22974186}, issn = {1471-2180}, mesh = {Adult ; Aged ; *Biodiversity ; Cluster Analysis ; Cystitis, Interstitial/*microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Urine/*microbiology ; }, abstract = {BACKGROUND: Interstitial Cystitis (IC) is a chronic inflammatory condition of the bladder with unknown etiology. The aim of this study was to characterize the microbial community present in the urine from IC female patients by 454 high throughput sequencing of the 16S variable regions V1V2 and V6. The taxonomical composition, richness and diversity of the IC microbiota were determined and compared to the microbial profile of asymptomatic healthy female (HF) urine.

RESULTS: The composition and distribution of bacterial sequences differed between the urine microbiota of IC patients and HFs. Reduced sequence richness and diversity were found in IC patient urine, and a significant difference in the community structure of IC urine in relation to HF urine was observed. More than 90% of the IC sequence reads were identified as belonging to the bacterial genus Lactobacillus, a marked increase compared to 60% in HF urine.

CONCLUSION: The 16S rDNA sequence data demonstrates a shift in the composition of the bacterial community in IC urine. The reduced microbial diversity and richness is accompanied by a higher abundance of the bacterial genus Lactobacillus, compared to HF urine. This study demonstrates that high throughput sequencing analysis of urine microbiota in IC patients is a powerful tool towards a better understanding of this enigmatic disease.}, } @article {pmid22972298, year = {2012}, author = {Weinstock, GM}, title = {Genomic approaches to studying the human microbiota.}, journal = {Nature}, volume = {489}, number = {7415}, pages = {250-256}, pmid = {22972298}, issn = {1476-4687}, support = {U54 HG004968/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteria/genetics/isolation & purification ; *Biodiversity ; Genome/genetics ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/*genetics ; }, abstract = {The human body is colonized by a vast array of microbes, which form communities of bacteria, viruses and microbial eukaryotes that are specific to each anatomical environment. Every community must be studied as a whole because many organisms have never been cultured independently, and this poses formidable challenges. The advent of next-generation DNA sequencing has allowed more sophisticated analysis and sampling of these complex systems by culture-independent methods. These methods are revealing differences in community structure between anatomical sites, between individuals, and between healthy and diseased states, and are transforming our view of human biology.}, } @article {pmid22972295, year = {2012}, author = {Lozupone, CA and Stombaugh, JI and Gordon, JI and Jansson, JK and Knight, R}, title = {Diversity, stability and resilience of the human gut microbiota.}, journal = {Nature}, volume = {489}, number = {7415}, pages = {220-230}, pmid = {22972295}, issn = {1476-4687}, support = {K01 DK090285/DK/NIDDK NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; }, mesh = {*Biodiversity ; Diet ; Environment ; Health ; Humans ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; *Metagenome/genetics ; }, abstract = {Trillions of microbes inhabit the human intestine, forming a complex ecological community that influences normal physiology and susceptibility to disease through its collective metabolic activities and host interactions. Understanding the factors that underlie changes in the composition and function of the gut microbiota will aid in the design of therapies that target it. This goal is formidable. The gut microbiota is immensely diverse, varies between individuals and can fluctuate over time - especially during disease and early development. Viewing the microbiota from an ecological perspective could provide insight into how to promote health by targeting this microbial community in clinical treatments.}, } @article {pmid22968328, year = {2013}, author = {Ling, Z and Liu, X and Wang, Y and Li, L and Xiang, C}, title = {Pyrosequencing analysis of the salivary microbiota of healthy Chinese children and adults.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {487-495}, pmid = {22968328}, issn = {1432-184X}, mesh = {Asian People ; Bacteria/*classification/genetics/isolation & purification ; Biodiversity ; Child ; Child, Preschool ; DNA, Bacterial/genetics ; Female ; Humans ; Male ; *Metagenome ; Saliva/*microbiology ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Describing the biogeography of bacterial communities within the human body is critical for establishing healthy baselines from which to detect differences associated with diseases. Little is known, however, about the baseline of normal salivary microbiota from healthy Chinese children and adults. With parallel barcoded 454 pyrosequencing, the bacterial diversity and richness of saliva were thoroughly investigated from ten healthy Chinese children and adults. The overall taxonomic distribution of our metagenomic data demonstrated that the diversity of salivary microbiota from children was more complex than adults, while the composition and richness of salivary microbiota were similar in children and adults, especially for predominant bacteria. A large number of bacterial phylotypes were shared by healthy children and adults, indicating the existence of a core salivary microbiome. In children and adults, the vast majority of sequences in salivary microbiota belonged to Streptococcus, Prevotella, Neisseria, Haemophilus, Porphyromonas, Gemella, Rothia, Granulicatella, Fusobacterium, Actinomyces, Veillonella, and Aggregatibacter, which constituted the major components of normal salivary microbiota. With the exception of Actinomyces, the other seven non-predominant bacteria including Moraxella, Leptotrichia, Peptostreptococcus, Eubacterium, and members of Neisseriaceae, Flavobacteriaceae, and SR1 showed significant differences between children and adults (p < 0.05). We first established the framework of normal salivary microbiota from healthy Chinese children and adults. Our data represent a critical step for determining the diversity of healthy microbiota in Chinese children and adults, and our data established a platform for additional large-scale studies focusing on the interactions between health and diseases in the future.}, } @article {pmid22967509, year = {2012}, author = {Ulloa, O and Canfield, DE and DeLong, EF and Letelier, RM and Stewart, FJ}, title = {Microbial oceanography of anoxic oxygen minimum zones.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {40}, pages = {15996-16003}, pmid = {22967509}, issn = {1091-6490}, mesh = {Anaerobiosis ; *Biota ; Environmental Monitoring/*statistics & numerical data ; Metagenome/*genetics ; Oceanography ; Oceans and Seas ; Oxygen/*analysis/chemistry ; Seawater/*chemistry ; *Water Microbiology ; }, abstract = {Vast expanses of oxygen-deficient and nitrite-rich water define the major oxygen minimum zones (OMZs) of the global ocean. They support diverse microbial communities that influence the nitrogen economy of the oceans, contributing to major losses of fixed nitrogen as dinitrogen (N(2)) and nitrous oxide (N(2)O) gases. Anaerobic microbial processes, including the two pathways of N(2) production, denitrification and anaerobic ammonium oxidation, are oxygen-sensitive, with some occurring only under strictly anoxic conditions. The detection limit of the usual method (Winkler titrations) for measuring dissolved oxygen in seawater, however, is much too high to distinguish low oxygen conditions from true anoxia. However, new analytical technologies are revealing vanishingly low oxygen concentrations in nitrite-rich OMZs, indicating that these OMZs are essentially anoxic marine zones (AMZs). Autonomous monitoring platforms also reveal previously unrecognized episodic intrusions of oxygen into the AMZ core, which could periodically support aerobic metabolisms in a typically anoxic environment. Although nitrogen cycling is considered to dominate the microbial ecology and biogeochemistry of AMZs, recent environmental genomics and geochemical studies show the presence of other relevant processes, particularly those associated with the sulfur and carbon cycles. AMZs correspond to an intermediate state between two "end points" represented by fully oxic systems and fully sulfidic systems. Modern and ancient AMZs and sulfidic basins are chemically and functionally related. Global change is affecting the magnitude of biogeochemical fluxes and ocean chemical inventories, leading to shifts in AMZ chemistry and biology that are likely to continue well into the future.}, } @article {pmid22966776, year = {2012}, author = {Håvelsrud, OE and Haverkamp, TH and Kristensen, T and Jakobsen, KS and Rike, AG}, title = {Metagenomic and geochemical characterization of pockmarked sediments overlaying the Troll petroleum reservoir in the North Sea.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {203}, pmid = {22966776}, issn = {1471-2180}, mesh = {*Biota ; Geologic Sediments/*chemistry/*microbiology ; Hydrocarbons/metabolism ; *Metagenome ; North Sea ; Prokaryotic Cells/*classification ; }, abstract = {BACKGROUND: Pockmarks (depressions in the seabed) have been discovered throughout the world's oceans and are often related to hydrocarbon seepage. Although high concentrations of pockmarks are present in the seabed overlaying the Troll oil and gas reservoir in the northern North Sea, geological surveys have not detected hydrocarbon seepage in this area at the present time. In this study we have used metagenomics to characterize the prokaryotic communities inhabiting the surface sediments in the Troll area in relation to geochemical parameters, particularly related to hydrocarbon presence. We also investigated the possibility of increased potential for methane oxidation related to the pockmarks. Five metagenomes from pockmarks and plain seabed sediments were sequenced by pyrosequencing (Roche/454) technology. In addition, two metagenomes from seabed sediments geologically unlikely to be influenced by hydrocarbon seepage (the Oslofjord) were included. The taxonomic distribution and metabolic potential of the metagenomes were analyzed by multivariate analysis and statistical comparisons to reveal variation within and between the two sampling areas.

RESULTS: The main difference identified between the two sampling areas was an overabundance of predominantly autotrophic nitrifiers, especially Nitrosopumilus, and oligotrophic marine Gammaproteobacteria in the Troll metagenomes compared to the Oslofjord. Increased potential for degradation of hydrocarbons, especially aromatic hydrocarbons, was detected in two of the Troll samples: one pockmark sample and one from the plain seabed. Although presence of methanotrophic organisms was indicated in all samples, no overabundance in pockmark samples compared to the Oslofjord samples supports no, or only low level, methane seepage in the Troll pockmarks at the present time.

CONCLUSIONS: Given the relatively low content of total organic carbon and great depths of hydrocarbon containing sediments in the Troll area, it is possible that at least part of the carbon source available for the predominantly autotrophic nitrifiers thriving in this area originates from sequential prokaryotic degradation and oxidation of hydrocarbons to CO2. By turning CO2 back into organic carbon this subcommunity could play an important environmental role in these dark oligotrophic sediments. The oxidation of ammonia to nitrite and nitrate in this process could further increase the supply of terminal electron acceptors for hydrocarbon degradation.}, } @article {pmid22966151, year = {2012}, author = {Teeling, H and Glöckner, FO}, title = {Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective.}, journal = {Briefings in bioinformatics}, volume = {13}, number = {6}, pages = {728-742}, pmid = {22966151}, issn = {1477-4054}, mesh = {Biodiversity ; Computational Biology ; *Genome, Archaeal ; *Genome, Bacterial ; Metagenome ; Metagenomics/*methods/*trends ; }, abstract = {Metagenomics has become an indispensable tool for studying the diversity and metabolic potential of environmental microbes, whose bulk is as yet non-cultivable. Continual progress in next-generation sequencing allows for generating increasingly large metagenomes and studying multiple metagenomes over time or space. Recently, a new type of holistic ecosystem study has emerged that seeks to combine metagenomics with biodiversity, meta-expression and contextual data. Such 'ecosystems biology' approaches bear the potential to not only advance our understanding of environmental microbes to a new level but also impose challenges due to increasing data complexities, in particular with respect to bioinformatic post-processing. This mini review aims to address selected opportunities and challenges of modern metagenomics from a bioinformatics perspective and hopefully will serve as a useful resource for microbial ecologists and bioinformaticians alike.}, } @article {pmid22963791, year = {2012}, author = {Carvalhais, LC and Dennis, PG and Tyson, GW and Schenk, PM}, title = {Application of metatranscriptomics to soil environments.}, journal = {Journal of microbiological methods}, volume = {91}, number = {2}, pages = {246-251}, doi = {10.1016/j.mimet.2012.08.011}, pmid = {22963791}, issn = {1872-8359}, mesh = {Biota ; Metagenomics/*methods ; *Soil Microbiology ; *Transcriptome ; }, abstract = {The activities of soil microbial communities are of critical importance to terrestrial ecosystem functioning. The mechanisms that determine the interactions between soil microorganisms, their environment and neighbouring organisms, however, are poorly understood. Due to advances in sequencing technologies, an increasing number of metagenomics studies are being conducted on samples from diverse environments including soils. This information has not only increased our awareness of the functional potential of soil microbial communities, but also constitutes powerful reference material for soil metatranscriptomics studies. Metatranscriptomics provides a snapshot of transcriptional profiles that correspond to discrete populations within a microbial community at the time of sampling. This information can indicate the potential activities of complex microbial communities and the mechanisms that regulate them. Here we summarise the technical challenges for metatranscriptomics applied to soil environments and discuss approaches for gaining biologically meaningful insight into these datasets.}, } @article {pmid22962617, year = {2012}, author = {Flores, GE and Henley, JB and Fierer, N}, title = {A direct PCR approach to accelerate analyses of human-associated microbial communities.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e44563}, pmid = {22962617}, issn = {1932-6203}, mesh = {Bacteria/classification/*genetics ; DNA, Bacterial/*analysis/genetics ; Feces/microbiology ; Humans ; Metagenome/*genetics ; Microbial Consortia/*genetics ; Mouth/microbiology ; Phylogeny ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/*analysis/genetics ; Reagent Kits, Diagnostic ; Skin/microbiology ; }, abstract = {Since the composition of the human microbiome is highly variable both within and between individuals, researchers are increasingly reliant on high-throughput molecular approaches to identify linkages between the composition of these communities and human health. While new sequencing technologies have made it increasingly feasible to analyze large numbers of human-associated samples, the extraction of DNA from samples often remains a bottleneck in the process. Here we tested a direct PCR approach using the Extract-N-Amp Plant PCR Kit to accelerate the 16S rRNA gene-based analyses of human-associated bacterial communities, directly comparing this method to a more commonly-used approach whereby DNA is first extracted and purified from samples using a series of steps prior to PCR amplification. We used both approaches on replicate samples collected from each of five body habitats (tongue surface, feces, forehead skin, underarm skin, and forearm skin) from four individuals. With the exception of the tongue samples, there were few significant differences in the estimates of taxon richness or phylogenetic diversity obtained using the two approaches. Perhaps more importantly, there were no significant differences between the methods in their ability resolve body habitat differences or inter-individual differences in bacterial community composition and the estimates of the relative abundances of individual taxa were nearly identical with the two methods. Overall, the two methods gave very similar results and the direct PCR approach is clearly advantageous for many studies exploring the diversity and composition of human-associated bacterial communities given that large numbers of samples can be processed far more quickly and efficiently.}, } @article {pmid22961006, year = {2013}, author = {Westerbeek, EA and Slump, RA and Lafeber, HN and Knol, J and Georgi, G and Fetter, WP and van Elburg, RM}, title = {The effect of enteral supplementation of specific neutral and acidic oligosaccharides on the faecal microbiota and intestinal microenvironment in preterm infants.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {32}, number = {2}, pages = {269-276}, pmid = {22961006}, issn = {1435-4373}, mesh = {*Biota ; Diet/*methods ; Fatty Acids/analysis ; Feces/*chemistry/*microbiology ; Humans ; Hydrogen-Ion Concentration ; Immunoglobulin A, Secretory/analysis ; Infant, Newborn ; *Infant, Premature ; *Metagenome ; Oligosaccharides/*administration & dosage ; Placebos/administration & dosage ; }, abstract = {We aimed to determine the effects of enteral supplementation of a prebiotic mixture of neutral and acidic oligosaccharides (scGOS/lcFOS/pAOS) on the faecal microbiota and microenvironment in preterm infants. Furthermore, we determined the influence of perinatal factors on the development of the faecal microbiota. In a randomised controlled trial, preterm infants with gestational age <32 weeks and/or birth weight <1,500 g received enteral supplementation of scGOS/lcFOS/pAOS or placebo (maltodextrin) between days 3 and 30 of life. Faecal microbiota, as measured with fluorescent in situ hybridisation (FISH), and microenvironment [short-chain fatty acids (SCFAs), pH, sIgA] were measured at four time points: before the start of the study and at days 7, 14 and 30 of life. In total, 113 preterm infants were included. Enteral supplementation of the prebiotic mixture increased the total bacteria count at day 14 (Exp 3.92; 95 % confidence interval [CI] 1.18-13.04, p = 0.03), but not at day 30 (Exp 1.73; 95 % CI 0.60-5.03, p = 0.31). There was a trend toward increased bifidobacteria counts. There was a delayed intestinal colonisation of all bacteria. Enteral supplementation of the prebiotic mixture decreased the faecal pH (Exp 0.71; 95 % CI 0.54-0.93, p = 0.01) and there was a trend toward increased acetic acid compared to the placebo group (Exp 1.09; 95 % CI 0.99-1.20, p = 0.10). There was no effect on sIgA (Exp 1.94; 95 % CI 0.28-13.27, p = 0.50). Antibiotics decreased the total bacteria count (Exp 0.13; 95 % CI 0.08-0.22, p < 0.001). Enteral supplementation of a prebiotic mixture of neutral and acidic oligosaccharides increases the postnatal intestinal colonisation. However, the extensive use of broad-spectrum antibiotics in preterm infants decreased the growth of all intestinal microbiota, thereby, delaying the normal microbiota development.}, } @article {pmid22957194, year = {2012}, author = {Danielsen, L and Thürmer, A and Meinicke, P and Buée, M and Morin, E and Martin, F and Pilate, G and Daniel, R and Polle, A and Reich, M}, title = {Fungal soil communities in a young transgenic poplar plantation form a rich reservoir for fungal root communities.}, journal = {Ecology and evolution}, volume = {2}, number = {8}, pages = {1935-1948}, pmid = {22957194}, issn = {2045-7758}, abstract = {Fungal communities play a key role in ecosystem functioning. However, only little is known about their composition in plant roots and the soil of biomass plantations. The goal of this study was to analyze fungal biodiversity in their belowground habitats and to gain information on the strategies by which ectomycorrhizal (ECM) fungi form colonies. In a 2-year-old plantation, fungal communities in the soil and roots of three different poplar genotypes (Populus × canescens, wildtype and two transgenic lines with suppressed cinnamyl alcohol dehydrogenase activity) were analyzed by 454 pyrosequencing targeting the rDNA internal transcribed spacer 1 (ITS) region. The results were compared with the dynamics of the root-associated ECM community studied by morphotyping/Sanger sequencing in two subsequent years. Fungal species and family richness in the soil were surprisingly high in this simple plantation ecosystem, with 5944 operational taxonomic units (OTUs) and 186 described fungal families. These findings indicate the importance that fungal species are already available for colonization of plant roots (2399 OTUs and 115 families). The transgenic modification of poplar plants had no influence on fungal root or soil communities. Fungal families and OTUs were more evenly distributed in the soil than in roots, probably as a result of soil plowing before the establishment of the plantation. Saprophytic, pathogenic, and endophytic fungi were the dominating groups in soil, whereas ECMs were dominant in roots (87%). Arbuscular mycorrhizal diversity was higher in soil than in roots. Species richness of the root-associated ECM community, which was low compared with ECM fungi detected by 454 analyses, increased after 1 year. This increase was mainly caused by ECM fungal species already traced in the preceding year in roots. This result supports the priority concept that ECMs present on roots have a competitive advantage over soil-localized ECM fungi.}, } @article {pmid22955886, year = {2012}, author = {Kim, HB and Borewicz, K and White, BA and Singer, RS and Sreevatsan, S and Tu, ZJ and Isaacson, RE}, title = {Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter, tylosin.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {38}, pages = {15485-15490}, pmid = {22955886}, issn = {1091-6490}, mesh = {Animals ; Anti-Infective Agents/*pharmacology ; Bacteria/drug effects ; Biodiversity ; Computational Biology/methods ; Gastrointestinal Tract/drug effects/microbiology ; Gene Library ; Intestines/*microbiology ; Metagenome ; Metagenomics ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Swine ; Tylosin/*pharmacology ; }, abstract = {Antimicrobials have been used extensively as growth promoters (AGPs) in agricultural animal production. However, the specific mechanism of action for AGPs has not yet been determined. The work presented here was to determine and characterize the microbiome of pigs receiving one AGP, tylosin, compared with untreated pigs. We hypothesized that AGPs exerted their growth promoting effect by altering gut microbial population composition. We determined the fecal microbiome of pigs receiving tylosin compared with untreated pigs using pyrosequencing of 16S rRNA gene libraries. The data showed microbial population shifts representing both microbial succession and changes in response to the use of tylosin. Quantitative and qualitative analyses of sequences showed that tylosin caused microbial population shifts in both abundant and less abundant species. Our results established a baseline upon which mechanisms of AGPs in regulation of health and growth of animals can be investigated. Furthermore, the data will aid in the identification of alternative strategies to improve animal health and consequently production.}, } @article {pmid22952724, year = {2012}, author = {Kisand, V and Valente, A and Lahm, A and Tanet, G and Lettieri, T}, title = {Phylogenetic and functional metagenomic profiling for assessing microbial biodiversity in environmental monitoring.}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e43630}, pmid = {22952724}, issn = {1932-6203}, mesh = {Bacteria/classification/genetics ; *Biodiversity ; *Environmental Monitoring ; *Metagenomics ; *Microbiology ; Molecular Sequence Annotation ; Oceans and Seas ; Open Reading Frames/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Stress, Physiological ; }, abstract = {Decisions guiding environmental management need to be based on a broad and comprehensive understanding of the biodiversity and functional capability within ecosystems. Microbes are of particular importance since they drive biogeochemical cycles, being both producers and decomposers. Their quick and direct responses to changes in environmental conditions modulate the ecosystem accordingly, thus providing a sensitive readout. Here we have used direct sequencing of total DNA from water samples to compare the microbial communities of two distinct coastal regions exposed to different anthropogenic pressures: the highly polluted Port of Genoa and the protected area of Montecristo Island in the Mediterranean Sea. Analysis of the metagenomes revealed significant differences in both microbial diversity and abundance between the two areas, reflecting their distinct ecological habitats and anthropogenic stress conditions. Our results indicate that the combination of next generation sequencing (NGS) technologies and bioinformatics tools presents a new approach to monitor the diversity and the ecological status of aquatic ecosystems. Integration of metagenomics into environmental monitoring campaigns should enable the impact of the anthropogenic pressure on microbial biodiversity in various ecosystems to be better assessed and also predicted.}, } @article {pmid22951208, year = {2013}, author = {Lim, YW and Schmieder, R and Haynes, M and Willner, D and Furlan, M and Youle, M and Abbott, K and Edwards, R and Evangelista, J and Conrad, D and Rohwer, F}, title = {Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {12}, number = {2}, pages = {154-164}, pmid = {22951208}, issn = {1873-5010}, support = {R01 GM095384/GM/NIGMS NIH HHS/United States ; 1 R01GM095384-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Bacterial Infections/genetics/*microbiology ; Biota ; Cystic Fibrosis/genetics/*microbiology/*virology ; Humans ; Lung/*microbiology ; Metabolic Networks and Pathways/*physiology ; Metagenome ; Sputum/microbiology ; Transcriptome ; Virus Diseases/genetics/*virology ; }, abstract = {BACKGROUND: Samples collected from CF patient airways often contain large amounts of host-derived nucleic acids that interfere with recovery and purification of microbial and viral nucleic acids. This study describes metagenomic and metatranscriptomic methods that address these issues.

METHODS: Microbial and viral metagenomes, and microbial metatranscriptomes, were successfully prepared from sputum samples from five adult CF patients.

RESULTS: Contaminating host DNA was dramatically reduced in the metagenomes. Each CF patient presented a unique microbiome; in some Pseudomonas aeruginosa was replaced by other opportunistic bacteria. Even though the taxonomic composition of the microbiomes is very different, the metabolic potentials encoded by the community are very similar. The viral communities were dominated by phages that infect major CF pathogens. The metatranscriptomes reveal differential expression of encoded metabolic potential with changing health status.

CONCLUSIONS: Microbial and viral metagenomics combined with microbial transcriptomics characterize the dynamic polymicrobial communities found in CF airways, revealing both the taxa present and their current metabolic activities. These approaches can facilitate the development of individualized treatment plans and novel therapeutic approaches.}, } @article {pmid22950603, year = {2012}, author = {Walter, A and Knapp, BA and Farbmacher, T and Ebner, C and Insam, H and Franke-Whittle, IH}, title = {Searching for links in the biotic characteristics and abiotic parameters of nine different biogas plants.}, journal = {Microbial biotechnology}, volume = {5}, number = {6}, pages = {717-730}, pmid = {22950603}, issn = {1751-7915}, support = {P 20001/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Acetates/analysis ; Anaerobiosis ; Austria ; Biofuels/*microbiology ; *Biota ; Denaturing Gradient Gel Electrophoresis ; *Industrial Microbiology ; Italy ; Metagenome ; Methanosarcina/genetics/isolation & purification ; Methanosarcinales/genetics/isolation & purification ; Microarray Analysis ; Real-Time Polymerase Chain Reaction ; Sewage/chemistry/*microbiology ; }, abstract = {To find links between the biotic characteristics and abiotic process parameters in anaerobic digestion systems, the microbial communities of nine full-scale biogas plants in South Tyrol (Italy) and Vorarlberg (Austria) were investigated using molecular techniques and the physical and chemical properties were monitored. DNA from sludge samples was subjected to microarray hybridization with the ANAEROCHIP microarray and results indicated that sludge samples grouped into two main clusters, dominated either by Methanosarcina or by Methanosaeta, both aceticlastic methanogens. Hydrogenotrophic methanogens were hardly detected or if detected, gave low hybridization signals. Results obtained using denaturing gradient gel electrophoresis (DGGE) supported the findings of microarray hybridization. Real-time PCR targeting Methanosarcina and Methanosaeta was conducted to provide quantitative data on the dominating methanogens. Correlation analysis to determine any links between the microbial communities found by microarray analysis, and the physicochemical parameters investigated was conducted. It was shown that the sludge samples dominated by the genus Methanosarcina were positively correlated with higher concentrations of acetate, whereas sludge samples dominated by representatives of the genus Methanosaeta had lower acetate concentrations. No other correlations between biotic characteristics and abiotic parameters were found. Methanogenic communities in each reactor were highly stable and resilient over the whole year.}, } @article {pmid22950448, year = {2012}, author = {Altimira, F and Yáñez, C and Bravo, G and González, M and Rojas, LA and Seeger, M}, title = {Characterization of copper-resistant bacteria and bacterial communities from copper-polluted agricultural soils of central Chile.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {193}, pmid = {22950448}, issn = {1471-2180}, mesh = {Bacteria/*classification/*drug effects/genetics/isolation & purification ; Bacterial Proteins/genetics ; *Biodiversity ; Chile ; Cluster Analysis ; Copper/*metabolism/toxicity ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; *Drug Resistance, Bacterial ; Molecular Sequence Data ; Phylogeny ; Plasmids ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Soil Pollutants/*metabolism/toxicity ; }, abstract = {BACKGROUND: Copper mining has led to Cu pollution in agricultural soils. In this report, the effects of Cu pollution on bacterial communities of agricultural soils from Valparaiso region, central Chile, were studied. Denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA genes was used for the characterization of bacterial communities from Cu-polluted and non-polluted soils. Cu-resistant bacterial strains were isolated from Cu-polluted soils and characterized.

RESULTS: DGGE showed a similar high number of bands and banding pattern of the bacterial communities from Cu-polluted and non-polluted soils. The presence of copA genes encoding the multi-copper oxidase that confers Cu-resistance in bacteria was detected by PCR in metagenomic DNA from the three Cu-polluted soils, but not in the non-polluted soil. The number of Cu-tolerant heterotrophic cultivable bacteria was significantly higher in Cu-polluted soils than in the non-polluted soil. Ninety two Cu-resistant bacterial strains were isolated from three Cu-polluted agricultural soils. Five isolated strains showed high resistance to copper (MIC ranged from 3.1 to 4.7 mM) and also resistance to other heavy metals. 16S rRNA gene sequence analyses indicate that these isolates belong to the genera Sphingomonas, Stenotrophomonas and Arthrobacter. The Sphingomonas sp. strains O12, A32 and A55 and Stenotrophomonas sp. C21 possess plasmids containing the Cu-resistance copA genes. Arthrobacter sp. O4 possesses the copA gene, but plasmids were not detected in this strain. The amino acid sequences of CopA from Sphingomonas isolates (O12, A32 and A55), Stenotrophomonas strain (C21) and Arthrobacter strain (O4) are closely related to CopA from Sphingomonas, Stenotrophomonas and Arthrobacter strains, respectively.

CONCLUSIONS: This study suggests that bacterial communities of agricultural soils from central Chile exposed to long-term Cu-pollution have been adapted by acquiring Cu genetic determinants. Five bacterial isolates showed high copper resistance and additional resistance to other heavy metals. Detection of copA gene in plasmids of four Cu-resistant isolates indicates that mobile genetic elements are involved in the spreading of Cu genetic determinants in polluted environments.}, } @article {pmid22941080, year = {2012}, author = {Ercolini, D and De Filippis, F and La Storia, A and Iacono, M}, title = {"Remake" by high-throughput sequencing of the microbiota involved in the production of water buffalo mozzarella cheese.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {22}, pages = {8142-8145}, pmid = {22941080}, issn = {1098-5336}, mesh = {Animals ; Bacteria/*classification/*genetics ; *Biota ; Buffaloes ; Cheese/*microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Milk/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Intermediates of production of two batches of traditional mozzarella cheese were analyzed by culture-independent pyrosequencing. The quantitative distribution of taxa within the samples suggested that thermophilic lactic acid bacteria from the natural starter were mainly responsible for the fermentation, while microorganisms found in raw milk did not develop during fermentation.}, } @article {pmid22936250, year = {2013}, author = {Sharon, I and Morowitz, MJ and Thomas, BC and Costello, EK and Relman, DA and Banfield, JF}, title = {Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization.}, journal = {Genome research}, volume = {23}, number = {1}, pages = {111-120}, pmid = {22936250}, issn = {1549-5469}, support = {DP1 OD000964/OD/NIH HHS/United States ; R01 AI092531/AI/NIAID NIH HHS/United States ; 1R01AI092531-01/AI/NIAID NIH HHS/United States ; DP1OD000964/OD/NIH HHS/United States ; }, mesh = {Biota ; Drug Resistance, Bacterial/genetics ; *Genome, Bacterial ; *Genome, Viral ; Humans ; Infant, Newborn ; Infant, Premature ; Inositol/genetics ; Intestines/*microbiology ; *Metagenome ; Metagenomics/methods ; N-Acetylneuraminic Acid/genetics ; Propionibacterium acnes/*genetics/virology ; Staphylococcus Phages/*genetics/pathogenicity ; Staphylococcus epidermidis/*genetics/virology ; }, abstract = {The gastrointestinal microbiome undergoes shifts in species and strain abundances, yet dynamics involving closely related microorganisms remain largely unknown because most methods cannot resolve them. We developed new metagenomic methods and utilized them to track species and strain level variations in microbial communities in 11 fecal samples collected from a premature infant during the first month of life. Ninety six percent of the sequencing reads were assembled into scaffolds of >500 bp in length that could be assigned to organisms at the strain level. Six essentially complete (∼99%) and two near-complete genomes were assembled for bacteria that comprised as little as 1% of the community, as well as nine partial genomes of bacteria representing as little as 0.05%. In addition, three viral genomes were assembled and assigned to their hosts. The relative abundance of three Staphylococcus epidermidis strains, as well as three phages that infect them, changed dramatically over time. Genes possibly related to these shifts include those for resistance to antibiotics, heavy metals, and phage. At the species level, we observed the decline of an early-colonizing Propionibacterium acnes strain similar to SK137 and the proliferation of novel Propionibacterium and Peptoniphilus species late in colonization. The Propionibacterium species differed in their ability to metabolize carbon compounds such as inositol and sialic acid, indicating that shifts in species composition likely impact the metabolic potential of the community. These results highlight the benefit of reconstructing complete genomes from metagenomic data and demonstrate methods for achieving this goal.}, } @article {pmid22934781, year = {2012}, author = {Pallmann, P and Schaarschmidt, F and Hothorn, LA and Fischer, C and Nacke, H and Priesnitz, KU and Schork, NJ}, title = {Assessing group differences in biodiversity by simultaneously testing a user-defined selection of diversity indices.}, journal = {Molecular ecology resources}, volume = {12}, number = {6}, pages = {1068-1078}, pmid = {22934781}, issn = {1755-0998}, support = {5 UL1 RR025774/RR/NCRR NIH HHS/United States ; 5 R01 AG035020/AG/NIA NIH HHS/United States ; R01 DA030976/DA/NIDA NIH HHS/United States ; U19 AG023122/AG/NIA NIH HHS/United States ; 5 P01 AG027734/AG/NIA NIH HHS/United States ; 5 R01 HL089655/HL/NHLBI NIH HHS/United States ; 2 U19 AI063603/AI/NIAID NIH HHS/United States ; U01 DA024417/DA/NIDA NIH HHS/United States ; 5 R01 DA030976/DA/NIDA NIH HHS/United States ; R01 MH093500/MH/NIMH NIH HHS/United States ; U19 AI063603/AI/NIAID NIH HHS/United States ; 2 U19 AG023122/AG/NIA NIH HHS/United States ; P01 AG027734/AG/NIA NIH HHS/United States ; 1 R01 MH093500/MH/NIMH NIH HHS/United States ; UL1 RR025774/RR/NCRR NIH HHS/United States ; R01 HL089655/HL/NHLBI NIH HHS/United States ; R01 AG035020/AG/NIA NIH HHS/United States ; 5 U01 DA024417/DA/NIDA NIH HHS/United States ; }, mesh = {*Biodiversity ; Biostatistics/*methods ; *Data Interpretation, Statistical ; Software ; }, abstract = {Comparing diversities between groups is a task biologists are frequently faced with, for example in ecological field trials or when dealing with metagenomics data. However, researchers often waver about which measure of diversity to choose as there is a multitude of approaches available. As Jost (2008, Molecular Ecology, 17, 4015) has pointed out, widely used measures such as the Shannon or Simpson index have undesirable properties which make them hard to compare and interpret. Many of the problems associated with the use of these 'raw' indices can be corrected by transforming them into 'true' diversity measures. We introduce a technique that allows the comparison of two or more groups of observations and simultaneously tests a user-defined selection of a number of 'true' diversity measures. This procedure yields multiplicity-adjusted P-values according to the method of Westfall and Young (1993, Resampling-Based Multiple Testing: Examples and Methods for p-Value Adjustment, 49, 941), which ensures that the rate of false positives (type I error) does not rise when the number of groups and/or diversity indices is extended. Software is available in the R package 'simboot'.}, } @article {pmid22934641, year = {2012}, author = {Roossinck, MJ}, title = {Plant virus metagenomics: biodiversity and ecology.}, journal = {Annual review of genetics}, volume = {46}, number = {}, pages = {359-369}, doi = {10.1146/annurev-genet-110711-155600}, pmid = {22934641}, issn = {1545-2948}, mesh = {Base Sequence ; Computational Biology ; *Ecosystem ; *Environmental Microbiology ; Evolution, Molecular ; *Genetic Variation ; *Genome, Viral ; Information Storage and Retrieval ; Metagenomics/methods ; Plant Diseases/virology ; Plant Viruses/*genetics ; Plants/virology ; RNA, Small Interfering/genetics ; }, abstract = {Viral metagenomics is the study of viruses in environmental samples, using next generation sequencing that produces very large data sets. For plant viruses, these studies are still relatively new, but are already indicating that our current knowledge grossly underestimates the diversity of these viruses. Some plant virus studies are using thousands of individual plants so that each sequence can be traced back to its precise host. These studies should allow for deeper ecological and evolutionary analyses. The finding of so many new plant viruses that do not cause any obvious symptoms in wild plant hosts certainly changes our perception of viruses and how they interact with their hosts. The major difficulty in these (as in all) metagenomic studies continues to be the need for better bioinformatics tools to decipher the large data sets. The implications of this new information on plant viruses for international agriculture remain to be addressed.}, } @article {pmid22933715, year = {2013}, author = {Klindworth, A and Pruesse, E and Schweer, T and Peplies, J and Quast, C and Horn, M and Glöckner, FO}, title = {Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies.}, journal = {Nucleic acids research}, volume = {41}, number = {1}, pages = {e1}, pmid = {22933715}, issn = {1362-4962}, support = {281633/ERC_/European Research Council/International ; }, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Biodiversity ; Computer Simulation ; *DNA Primers ; Genes, rRNA ; Genetic Variation ; *High-Throughput Nucleotide Sequencing ; Metagenome ; *Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; *Sequence Analysis, DNA ; }, abstract = {16S ribosomal RNA gene (rDNA) amplicon analysis remains the standard approach for the cultivation-independent investigation of microbial diversity. The accuracy of these analyses depends strongly on the choice of primers. The overall coverage and phylum spectrum of 175 primers and 512 primer pairs were evaluated in silico with respect to the SILVA 16S/18S rDNA non-redundant reference dataset (SSURef 108 NR). Based on this evaluation a selection of 'best available' primer pairs for Bacteria and Archaea for three amplicon size classes (100-400, 400-1000, ≥ 1000 bp) is provided. The most promising bacterial primer pair (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21), with an amplicon size of 464 bp, was experimentally evaluated by comparing the taxonomic distribution of the 16S rDNA amplicons with 16S rDNA fragments from directly sequenced metagenomes. The results of this study may be used as a guideline for selecting primer pairs with the best overall coverage and phylum spectrum for specific applications, therefore reducing the bias in PCR-based microbial diversity studies.}, } @article {pmid22925473, year = {2013}, author = {Wolcott, R and Costerton, JW and Raoult, D and Cutler, SJ}, title = {The polymicrobial nature of biofilm infection.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {19}, number = {2}, pages = {107-112}, doi = {10.1111/j.1469-0691.2012.04001.x}, pmid = {22925473}, issn = {1469-0691}, mesh = {Bacteria/classification/*isolation & purification ; *Bacterial Physiological Phenomena ; Biofilms/*growth & development ; *Biota ; Coinfection/*diagnosis/microbiology ; Fungi/classification/*isolation & purification ; Humans ; Microbiological Techniques/methods ; Molecular Diagnostic Techniques/methods ; }, abstract = {The model of biofilm infection was first proposed over a decade ago. Recent scientific advances have added much to our understanding of biofilms, usually polymicrobial communities, which are commonly associated with chronic infection. Metagenomics has demonstrated that bacteria pursuing a biofilm strategy possess many mechanisms for encouraging diversity. By including multiple bacterial and/or fungal species in a single community, biofilms obtain numerous advantages, such as passive resistance, metabolic cooperation, byproduct influence, quorum sensing systems, an enlarged gene pool with more efficient DNA sharing, and many other synergies, which give them a competitive advantage. Routine clinical cultures are ill-suited for evaluating polymicrobial infections. DNA methods utilizing PCR methods, PCR/mass spectroscopy and sequencing have demonstrated their ability to identify microorganisms and quantitate their contribution to biofilms in clinical infections. A more robust model of biofilm infection along with more accurate diagnosis is rapidly translating into improved clinical outcomes.}, } @article {pmid22923392, year = {2012}, author = {Tetlock, A and Yost, CK and Stavrinides, J and Manzon, RG}, title = {Changes in the gut microbiome of the sea lamprey during metamorphosis.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {21}, pages = {7638-7644}, pmid = {22923392}, issn = {1098-5336}, mesh = {Aeromonas/classification/genetics/isolation & purification ; Animals ; Biodiversity ; DNA Gyrase/genetics ; Gastrointestinal Tract/*microbiology ; *Metagenome ; Metamorphosis, Biological ; Microbial Consortia ; Molecular Sequence Data ; Petromyzon/*growth & development/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA ; }, abstract = {Vertebrate metamorphosis is often marked by dramatic morphological and physiological changes of the alimentary tract, along with major shifts in diet following development from larva to adult. Little is known about how these developmental changes impact the gut microbiome of the host organism. The metamorphosis of the sea lamprey (Petromyzon marinus) from a sedentary filter-feeding larva to a free-swimming sanguivorous parasite is characterized by major physiological and morphological changes to all organ systems. The transformation of the alimentary canal includes closure of the larval esophagus and the physical isolation of the pharynx from the remainder of the gut, which results in a nonfeeding period that can last up to 8 months. To determine how the gut microbiome is affected by metamorphosis, the microbial communities of feeding and nonfeeding larval and parasitic sea lamprey were surveyed using both culture-dependent and -independent methods. Our results show that the gut of the filter-feeding larva contains a greater diversity of bacteria than that of the blood-feeding parasite, with the parasite gut being dominated by Aeromonas and, to a lesser extent, Citrobacter and Shewanella. Phylogenetic analysis of the culturable Aeromonas from both the larval and parasitic gut revealed that at least five distinct species were represented. Phenotypic characterization of these isolates revealed that over half were capable of sheep red blood cell hemolysis, but all were capable of trout red blood cell hemolysis. This suggests that the enrichment of Aeromonas that accompanies metamorphosis is likely related to the sanguivorous lifestyle of the parasitic sea lamprey.}, } @article {pmid22922559, year = {2012}, author = {Arboleya, S and Solís, G and Fernández, N and de los Reyes-Gavilán, CG and Gueimonde, M}, title = {Facultative to strict anaerobes ratio in the preterm infant microbiota: a target for intervention?.}, journal = {Gut microbes}, volume = {3}, number = {6}, pages = {583-588}, pmid = {22922559}, issn = {1949-0984}, mesh = {Bacteria, Anaerobic/*isolation & purification ; *Biota ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Infant, Newborn ; *Infant, Premature ; *Metagenome ; }, abstract = {During recent years there has been an increasing interest on the development of strategies for modulating the process of microbiota establishment in preterm infants. For successfully developing of such strategies, a detailed knowledge of the microbiota establishment process in these infants is needed. In a previous study we evidenced clear alterations in the process of microbiota establishment in preterm newborns when compared with a control group of full-term breast-fed infants. Here we have analyzed these data more in depth, corroborating a reduced proportion of strict anaerobes with respect to facultatives in the fecal microbiota of preterm infants. The potential benefits, as well as the side effects, of strategies aimed at counterbalancing this alteration in the facultative to strict anaerobes ratio are discussed in this addendum.}, } @article {pmid22920516, year = {2012}, author = {Bonilla-Rosso, G and Peimbert, M and Alcaraz, LD and Hernández, I and Eguiarte, LE and Olmedo-Alvarez, G and Souza, V}, title = {Comparative metagenomics of two microbial mats at Cuatro Ciénegas Basin II: community structure and composition in oligotrophic environments.}, journal = {Astrobiology}, volume = {12}, number = {7}, pages = {659-673}, pmid = {22920516}, issn = {1557-8070}, mesh = {Bacteria/*genetics/*growth & development ; Bacterial Proteins/genetics/metabolism ; *Environment ; *Environmental Microbiology ; Gene Library ; Genes, Bacterial/genetics ; Genetic Markers ; Geography ; Likelihood Functions ; Metagenome/genetics ; Metagenomics/*methods ; Mexico ; Microbial Consortia/*genetics ; Phylogeny ; Principal Component Analysis ; Pseudomonas/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbial mats are self-sustained, functionally complex ecosystems that make good models for the understanding of past and present microbial ecosystems as well as putative extraterrestrial ecosystems. Ecological theory suggests that the composition of these communities might be affected by nutrient availability and disturbance frequency. We characterized two microbial mats from two contrasting environments in the oligotrophic Cuatro Ciénegas Basin: a permanent green pool and a red desiccation pond. We analyzed their taxonomic structure and composition by means of 16S rRNA clone libraries and metagenomics and inferred their metabolic role by the analysis of functional traits in the most abundant organisms. Both mats showed a high diversity with metabolically diverse members and strongly differed in structure and composition. The green mat had a higher species richness and evenness than the red mat, which was dominated by a lineage of Pseudomonas. Autotrophs were abundant in the green mat, and heterotrophs were abundant in the red mat. When comparing with other mats and stromatolites, we found that taxonomic composition was not shared at species level but at order level, which suggests environmental filtering for phylogenetically conserved functional traits with random selection of particular organisms. The highest diversity and composition similarity was observed among systems from stable environments, which suggests that disturbance regimes might affect diversity more strongly than nutrient availability, since oligotrophy does not appear to prevent the establishment of complex and diverse microbial mat communities. These results are discussed in light of the search for extraterrestrial life.}, } @article {pmid22919912, year = {2012}, author = {Bryant, JA and Stewart, FJ and Eppley, JM and DeLong, EF}, title = {Microbial community phylogenetic and trait diversity declines with depth in a marine oxygen minimum zone.}, journal = {Ecology}, volume = {93}, number = {7}, pages = {1659-1673}, doi = {10.1890/11-1204.1}, pmid = {22919912}, issn = {0012-9658}, mesh = {Bacteria/*classification/genetics/*metabolism ; *Biodiversity ; DNA, Bacterial/classification/genetics ; Gene Expression Regulation, Bacterial/physiology ; Genomics ; Oceans and Seas ; Oxygen/*chemistry ; *Phylogeny ; Water/*chemistry ; }, abstract = {Oxygen minimum zones (OMZs) are natural physical features of the world's oceans. They create steep physiochemical gradients in the water column, which most notably include a dramatic draw down in oxygen concentrations over small vertical distances (<100 m). Microbial communities within OMZs play central roles in ocean and global biogeochemical cycles, yet we still lack a fundamental understanding of how microbial biodiversity is distributed across OMZs. Here, we used metagenomic sequencing to investigate microbial diversity across a vertical gradient in the water column during three seasons in the Eastern Tropical South Pacific (ETSP) OMZ. Based on analysis of small subunit ribosomal RNA (SSU rRNA) gene fragments, we found that both taxonomic and phylogenetic diversity declined steeply along the transition from oxygen-rich surface water to the permanent OMZ. We observed similar declines in the diversity of protein-coding gene categories, suggesting a decrease in functional (trait) diversity with depth. Metrics of functional and trait dispersion indicated that microbial communities are phylogenetically and functionally more overdispersed in oxic waters, but clustered within the OMZ. These dispersion patterns suggest that community assembly drivers (e.g., competition, environmental filtering) vary strikingly across the oxygen gradient. To understand the generality of our findings, we compared OMZ results to two marine depth gradients in subtropical oligotrophic sites and found that the oligotrophic sites did not display similar patterns, likely reflecting unique features found in the OMZ. Finally, we discuss how our results may relate to niche theory, diversity-energy relationships and stress gradients.}, } @article {pmid22919693, year = {2012}, author = {Ottman, N and Smidt, H and de Vos, WM and Belzer, C}, title = {The function of our microbiota: who is out there and what do they do?.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {104}, pmid = {22919693}, issn = {2235-2988}, mesh = {*Biota ; Europe ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenomics/methods ; Microbiota/*genetics/*physiology ; Proteomics/methods ; }, abstract = {Current meta-omics developments provide a portal into the functional potential and activity of the intestinal microbiota. The comparative and functional meta-omics approaches have made it possible to get a molecular snap shot of microbial function at a certain time and place. To this end, metagenomics is a DNA-based approach, metatranscriptomics studies the total transcribed RNA, metaproteomics focuses on protein levels and metabolomics describes metabolic profiles. Notably, the metagenomic toolbox is rapidly expanding and has been instrumental in the generation of draft genome sequences of over 1000 human associated microorganisms as well as an astonishing 3.3 million unique microbial genes derived from the intestinal tract of over 100 European adults. Remarkably, it appeared that there are at least 3 clusters of co-occurring microbial species, termed enterotypes, that characterize the intestinal microbiota throughout various continents. The human intestinal microbial metagenome further revealed unique functions carried out in the intestinal environment and provided the basis for newly discovered mechanisms for signaling, vitamin production and glycan, amino-acid and xenobiotic metabolism. The activity and composition of the microbiota is affected by genetic background, age, diet, and health status of the host. In its turn the microbiota composition and activity influence host metabolism and disease development. Exemplified by the differences in microbiota composition and activity between breast- as compared to formula-fed babies, healthy and malnourished infants, elderly and centenarians as compared to youngsters, humans that are either lean or obese and healthy or suffering of inflammatory bowel diseases (IBD). In this review we will focus on our current understanding of the functionality of the human intestinal microbiota based on all available metagenome, metatranscriptome, and metaproteome results.}, } @article {pmid22915614, year = {2012}, author = {Cabrera-Rubio, R and Garcia-Núñez, M and Setó, L and Antó, JM and Moya, A and Monsó, E and Mira, A}, title = {Microbiome diversity in the bronchial tracts of patients with chronic obstructive pulmonary disease.}, journal = {Journal of clinical microbiology}, volume = {50}, number = {11}, pages = {3562-3568}, pmid = {22915614}, issn = {1098-660X}, mesh = {Aged ; Bacteria/*classification/*genetics ; *Biota ; Bronchi/*microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Humans ; Male ; *Metagenome ; Molecular Sequence Data ; Pulmonary Disease, Chronic Obstructive/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sputum/microbiology ; }, abstract = {Culture of bacteria from bronchial secretions in respiratory patients has low sensitivity and does not allow for complete assessment of microbial diversity across different bronchial compartments. In addition, a significant number of clinical studies are based on sputum samples, and it is not known to what extent they describe the real diversity of the mucosa. In order to identify previously unrecognized lower airway bacteria and to investigate the complexity and distribution of microbiota in patients with chronic obstructive pulmonary disease (COPD), we performed PCR amplification and pyrosequencing of the 16S rRNA gene in patients not showing signs or symptoms of infection. Four types of respiratory samples (sputum, bronchial aspirate, bronchoalveolar lavage, and bronchial mucosa) were taken from each individual, obtaining on average >1,000 16S rRNA sequences per sample. The total number of genera per patient was >100, showing a high diversity, with Streptococcus, Prevotella, Moraxella, Haemophilus, Acinetobacter, Fusobacterium, and Neisseria being the most commonly identified. Sputum samples showed significantly lower diversity than the other three sample types. Lower-bronchial-tree samples, i.e., bronchoalveolar lavage and bronchial mucosa, showed a very similar bacterial compositions in contrast to sputum and bronchial aspirate samples. Thus, sputum and bronchial aspirate samples are upper bronchial tree samples that are not representative of the lower bronchial mucosa flora, and bronchoalveolar lavage samples showed the results closest to those for the bronchial mucosa. Our data confirm that the bronchial tree is not sterile in COPD patients and support the existence a different microbiota in the upper and lower compartments.}, } @article {pmid22911969, year = {2012}, author = {Madan, JC and Koestler, DC and Stanton, BA and Davidson, L and Moulton, LA and Housman, ML and Moore, JH and Guill, MF and Morrison, HG and Sogin, ML and Hampton, TH and Karagas, MR and Palumbo, PE and Foster, JA and Hibberd, PL and O'Toole, GA}, title = {Serial analysis of the gut and respiratory microbiome in cystic fibrosis in infancy: interaction between intestinal and respiratory tracts and impact of nutritional exposures.}, journal = {mBio}, volume = {3}, number = {4}, pages = {}, pmid = {22911969}, issn = {2150-7511}, support = {U01 AT002388/AT/NCCIH NIH HHS/United States ; 1P20ES018175-02/ES/NIEHS NIH HHS/United States ; 5P20RR018787/RR/NCRR NIH HHS/United States ; P30 GM106394/GM/NIGMS NIH HHS/United States ; P42 ES007373/ES/NIEHS NIH HHS/United States ; P20RR16448/RR/NCRR NIH HHS/United States ; UH3 DK083993/DK/NIDDK NIH HHS/United States ; P20 GM103413/GM/NIGMS NIH HHS/United States ; R01 AI059694/AI/NIAID NIH HHS/United States ; R01 AI59694/AI/NIAID NIH HHS/United States ; P20 RR016448/RR/NCRR NIH HHS/United States ; P42 ES7373/ES/NIEHS NIH HHS/United States ; K24 AT003683/AT/NCCIH NIH HHS/United States ; P20RR016454/RR/NCRR NIH HHS/United States ; P20 RR018787/RR/NCRR NIH HHS/United States ; R01 HL074175/HL/NHLBI NIH HHS/United States ; P20-RR01878/RR/NCRR NIH HHS/United States ; 4UH3DK083993-02/DK/NIDDK NIH HHS/United States ; 8 P20 GM103413/GM/NIGMS NIH HHS/United States ; P20 RR016454/RR/NCRR NIH HHS/United States ; 2K24AT003683/AT/NCCIH NIH HHS/United States ; P20 ES018175/ES/NIEHS NIH HHS/United States ; }, mesh = {Age Factors ; Bacteria/classification/genetics ; *Biota ; Cluster Analysis ; Cystic Fibrosis/*microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Infant ; Infant, Newborn ; *Metagenome ; Respiratory System/*microbiology ; }, abstract = {UNLABELLED: Pulmonary damage caused by chronic colonization of the cystic fibrosis (CF) lung by microbial communities is the proximal cause of respiratory failure. While there has been an effort to document the microbiome of the CF lung in pediatric and adult patients, little is known regarding the developing microflora in infants. We examined the respiratory and intestinal microbiota development in infants with CF from birth to 21 months. Distinct genera dominated in the gut compared to those in the respiratory tract, yet some bacteria overlapped, demonstrating a core microbiota dominated by Veillonella and Streptococcus. Bacterial diversity increased significantly over time, with evidence of more rapidly acquired diversity in the respiratory tract. There was a high degree of concordance between the bacteria that were increasing or decreasing over time in both compartments; in particular, a significant proportion (14/16 genera) increasing in the gut were also increasing in the respiratory tract. For 7 genera, gut colonization presages their appearance in the respiratory tract. Clustering analysis of respiratory samples indicated profiles of bacteria associated with breast-feeding, and for gut samples, introduction of solid foods even after adjustment for the time at which the sample was collected. Furthermore, changes in diet also result in altered respiratory microflora, suggesting a link between nutrition and development of microbial communities in the respiratory tract. Our findings suggest that nutritional factors and gut colonization patterns are determinants of the microbial development of respiratory tract microbiota in infants with CF and present opportunities for early intervention in CF with altered dietary or probiotic strategies.

IMPORTANCE: While efforts have been focused on assessing the microbiome of pediatric and adult cystic fibrosis (CF) patients to understand how chronic colonization by these microbes contributes to pulmonary damage, little is known regarding the earliest development of respiratory and gut microflora in infants with CF. Our findings suggest that colonization of the respiratory tract by microbes is presaged by colonization of the gut and demonstrated a role of nutrition in development of the respiratory microflora. Thus, targeted dietary or probiotic strategies may be an effective means to change the course of the colonization of the CF lung and thereby improve patient outcomes.}, } @article {pmid22908010, year = {2012}, author = {Armitage, DW and Gallagher, KL and Youngblut, ND and Buckley, DH and Zinder, SH}, title = {Millimeter-scale patterns of phylogenetic and trait diversity in a salt marsh microbial mat.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {293}, pmid = {22908010}, issn = {1664-302X}, abstract = {Intertidal microbial mats are comprised of distinctly colored millimeter-thick layers whose communities organize in response to environmental gradients such as light availability, oxygen/sulfur concentrations, and redox potential. Here, slight changes in depth correspond to sharp niche boundaries. We explore the patterns of biodiversity along this depth gradient as it relates to functional groups of bacteria, as well as trait-encoding genes. We used molecular techniques to determine how the mat's layers differed from one another with respect to taxonomic, phylogenetic, and trait diversity, and used these metrics to assess potential drivers of community assembly. We used a range of null models to compute the degree of phylogenetic and functional dispersion for each layer. The SSU-rRNA reads were dominated by Cyanobacteria and Chromatiales, but contained a high taxonomic diversity. The composition of each mat core was significantly different for developmental stage, year, and layer. Phylogenetic richness and evenness positively covaried with depth, and trait richness tended to decrease with depth. We found evidence for significant phylogenetic clustering for all bacteria below the surface layer, supporting the role of habitat filtering in the assembly of mat layers. However, this signal disappeared when the phylogenetic dispersion of particular functional groups, such as oxygenic phototrophs, was measured. Overall, trait diversity measured by orthologous genes was also lower than would be expected by chance, except for genes related to photosynthesis in the topmost layer. Additionally, we show how the choice of taxa pools, null models, spatial scale, and phylogenies can impact our ability to test hypotheses pertaining to community assembly. Our results demonstrate that given the appropriate physiochemical conditions, strong phylogenetic, and trait variation, as well as habitat filtering, can occur at the millimeter-scale.}, } @article {pmid22904045, year = {2012}, author = {Boujelben, I and Yarza, P and Almansa, C and Villamor, J and Maalej, S and Antón, J and Santos, F}, title = {Virioplankton community structure in Tunisian solar salterns.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {20}, pages = {7429-7437}, pmid = {22904045}, issn = {1098-5336}, mesh = {Base Composition ; *Biota ; Cloning, Molecular ; DNA, Viral/chemistry/genetics ; Electrophoresis, Gel, Pulsed-Field ; *Metagenome ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Seawater/*virology ; Sequence Analysis, DNA ; Tunisia ; Viral Load ; }, abstract = {The microbial community inhabiting Sfax solar salterns on the east coast of Tunisia has been studied by means of different molecular and culture-dependent tools that have unveiled the presence of novel microbial groups as well as a community structure different from that of other coastal hypersaline environments. We have focused on the study of the viral assemblages of these salterns and their changes along the salinity gradient and over time. Viruses from three ponds (C4, M1, and TS) encompassing salinities from moderately hypersaline to saturated (around 14, 19, and 35%, respectively) were sampled in May and October 2009 and analyzed by transmission electron microscopy (TEM) and pulsed-field gel electrophoresis (PFGE). Additionally, for all three October samples and the May TS sample, viral metagenomic DNA was cloned in fosmids, end sequenced, and analyzed. Viral concentration, as well as virus-to-cell ratios, increased along the salinity gradient, with around 10(10) virus-like particles (VLPs)/ml in close-to-saturation ponds, which represents the highest viral concentration reported so far for aquatic systems. Four distinct morphologies could be observed with TEM (spherical, tailed, spindled, and filamentous) but with various proportions in the different samples. Metagenomic analyses indicated that every pond harbored a distinct viral assemblage whose G+C content could be roughly correlated with that of the active part of the microbial community that may have constituted the putative hosts. As previously reported for hypersaline metaviromes, most sequences did not have matches in the databases, although some were conserved among the Sfax metaviromes. BLASTx, BLASTp, and dinucleotide frequency analyses indicated that (i) factors additional to salinity could be structuring viral communities and (ii) every metavirome had unique gene contents and dinucleotide frequencies. Comparison with hypersaline metaviromes available in the databases indicated that the viral assemblages present in close-to-saturation environments located thousands of kilometers apart presented some common traits among them in spite of their differences regarding the putative hosts. A small core metavirome for close-to-saturation systems was found that contained 7 sequences of around 100 nucleotides (nt) whose function was not hinted at by in silico search results, although it most likely represents properties essential for hyperhalophilic viruses.}, } @article {pmid22903086, year = {2013}, author = {Costa, R and Keller-Costa, T and Gomes, NC and da Rocha, UN and van Overbeek, L and van Elsas, JD}, title = {Evidence for selective bacterial community structuring in the freshwater sponge Ephydatia fluviatilis.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {232-244}, pmid = {22903086}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*classification/genetics/isolation & purification ; Biodiversity ; DNA, Bacterial/genetics ; Fresh Water/microbiology ; *Metagenome ; Netherlands ; *Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {To understand the functioning of sponges, knowledge of the structure of their associated microbial communities is necessary. However, our perception of sponge-associated microbiomes remains mainly restricted to marine ecosystems. Here, we report on the molecular diversity and composition of bacteria in the freshwater sponge Ephydatia fluviatilis inhabiting the artificial lake Vinkeveense Plassen, Utrecht, The Netherlands. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints revealed that the apparent diversities within the domain Bacteria and the phylum Actinobacteria were lower in E. fluviatilis than in bulk water. Enrichment of specific PCR-DGGE bands in E. fluviatilis was detected. Furthermore, sponge- and bulk water-derived bacterial clone libraries differed with respect to bacterial community composition at the phylum level. E. fluviatilis-derived sequences were affiliated with six recognized phyla, i.e., Proteobacteria, Planctomycetes, Actinobacteria, Bacteroidetes, Chlamydiae and Verrucomicrobia, in order of relative abundance; next to the uncultured candidate phylum TM7 and one deeply rooted bacterial lineage of undefined taxonomy (BLUT). Actinobacteria, Proteobacteria, and Bacteroidetes were the dominant bacterial phyla in the freshwater clone library whereas sequences affiliated with Planctomycetes, Verrucomicrobia, Acidobacteria and Armatimonadetes were found at lower frequencies. Fine-tuned phylogenetic inference showed no or negligible overlaps between the E. fluviatilis and water-derived phylotypes within bacterial taxa such as Alphaproteobacteria, Bacteroidetes and Actinobacteria. We also ascertained the status of two alphaproteobacterial lineages as freshwater sponge-specific phylogenetic clusters, and report on high distinctiveness of other E. fluviatilis specific phylotypes, especially within the Bacteroidetes, Planctomycetes and Chlamydia taxa. This study supports the contention that the composition and diversity of bacteria in E. fluviatilis is partially driven by the host organism.}, } @article {pmid22900048, year = {2012}, author = {Kraneveld, EA and Buijs, MJ and Bonder, MJ and Visser, M and Keijser, BJ and Crielaard, W and Zaura, E}, title = {The relation between oral Candida load and bacterial microbiome profiles in Dutch older adults.}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e42770}, pmid = {22900048}, issn = {1932-6203}, mesh = {Aged ; Aged, 80 and over ; Bacteria/classification/*genetics/growth & development ; Biodiversity ; Candida/classification/*genetics/growth & development ; DNA, Ribosomal Spacer/genetics ; Female ; Humans ; Male ; *Metagenome ; Middle Aged ; Mouth/*microbiology ; Netherlands ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; *White People ; }, abstract = {Currently there are no evidence-based ecological measures for prevention of overgrowth and subsequent infection by fungi in the oral cavity. The aim of this study was to increase our knowledge on fungal-bacterial ecological interactions. Salivary Candida abundance of 82 Dutch adults aged 58-80 years was established relative to the bacterial load by quantitative PCR analysis of the Internal Transcribed (ITS) region (Candida) and 16S rDNA gene (bacteria). The salivary microbiome was assessed using barcoded pyrosequencing of the bacterial hypervariable regions V5-V7 of 16S rDNA. Sequencing data was preprocessed by denoising and chimera removal, clustered in Operational Taxonomic Units (OTUs) and assigned to taxonomy. Both OTU-based (PCA, diversity statistics) and phylogeny-based analyses (UniFrac, PCoA) were performed. Saliva of Dutch older adults contained 0-4 × 10(8) CFU/mL Candida with a median Candida load of 0.06%. With increased Candida load the diversity of the salivary microbiome decreased significantly (p<0.001). Increase in the Candida load correlated positively with class Bacilli, and negatively with class Fusobacteria, Flavobacteria, and Bacteroidia. Microbiomes with high Candida load were less diverse and had a distinct microbial composition towards dominance by saccharolytic and acidogenic bacteria--streptococci. The control of the acidification of the oral environment may be a potential preventive measure for Candida outgrowth that should be evaluated in longitudinal clinical intervention trials.}, } @article {pmid22895161, year = {2013}, author = {Blaser, MJ and Dominguez-Bello, MG and Contreras, M and Magris, M and Hidalgo, G and Estrada, I and Gao, Z and Clemente, JC and Costello, EK and Knight, R}, title = {Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents.}, journal = {The ISME journal}, volume = {7}, number = {1}, pages = {85-95}, pmid = {22895161}, issn = {1751-7370}, support = {UH2 AR057056/AR/NIAMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; DK090989/DK/NIDDK NIH HHS/United States ; HG004872/HG/NHGRI NIH HHS/United States ; R01 DK090989/DK/NIDDK NIH HHS/United States ; HG004866/HG/NHGRI NIH HHS/United States ; U01 HG004866/HG/NHGRI NIH HHS/United States ; }, mesh = {Adult ; Bacteria/*classification/genetics/*isolation & purification ; Biodiversity ; Colorado ; DNA, Bacterial/genetics ; Feces/parasitology ; Female ; Humans ; Male ; *Metagenome ; Middle Aged ; New York ; Phylogeny ; Propionibacterium/genetics/isolation & purification ; Proteobacteria/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Skin/*microbiology ; Staphylococcus/genetics/isolation & purification ; Venezuela ; }, abstract = {The human skin harbors complex bacterial communities. Prior studies showing high inter-individual variation focused on subjects from developed countries. We therefore compared cutaneous bacterial communities of Amerindians in the Venezuelan Amazon with subjects in the United States. Forearm skin specimens were studied from healthy Amerindians in Platanillal village in Amazonas State, and from healthy persons in New York and Colorado. All skin sampling used similar swab/buffer techniques. Multiplexed V2-targeted 16S rRNA gene pyrosequencing yielded high quality sequences from 112 samples. The results show 20 phyla, with three (Proteobacteria, Firmicutes, Actinobacteria) predominating. US residents and Venezuelan Amerindians had significantly different forearm skin bacterial community compositions, with United States dominated by Propionibacterium. Among the Amerindians, there was a deep split based on bacterial community membership, with 30 and 42 samples, respectively, falling into each of the two groups, not associated with age, gender, or body mass index. One Amerindian group had diversity similar to the United States, but was dominated by Staphylococcus rather than Propionibacterium. The other Amerindian group was significantly more diverse and even than the US or the other Amerindian group, and featured a broad range of Proteobacteria. The results provide evidence that ethnicity, lifestyle and/or geography are associated with the structure of human cutaneous bacterial communities.}, } @article {pmid22861806, year = {2012}, author = {Ursell, LK and Metcalf, JL and Parfrey, LW and Knight, R}, title = {Defining the human microbiome.}, journal = {Nutrition reviews}, volume = {70 Suppl 1}, number = {Suppl 1}, pages = {S38-44}, pmid = {22861806}, issn = {1753-4887}, support = {HG4872/HG/NHGRI NIH HHS/United States ; T32 GM008759/GM/NIGMS NIH HHS/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; /HHMI_/Howard Hughes Medical Institute/United States ; }, mesh = {Bacteria/*classification/*genetics ; Biodiversity ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenome/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis ; }, abstract = {Rapidly developing sequencing methods and analytical techniques are enhancing our ability to understand the human microbiome, and, indeed, how the microbiome and its constituents are defined. This review highlights recent research that expands our ability to understand the human microbiome on different spatial and temporal scales, including daily time series datasets spanning months. Furthermore, emerging concepts related to defining operational taxonomic units, diversity indices, core versus transient microbiomes, and the possibility of enterotypes are discussed. Additional advances in sequencing technology and in our understanding of the microbiome will provide exciting prospects for exploiting the microbiota for personalized medicine.}, } @article {pmid22861804, year = {2012}, author = {Relman, DA}, title = {The human microbiome: ecosystem resilience and health.}, journal = {Nutrition reviews}, volume = {70 Suppl 1}, number = {Suppl 1}, pages = {S2-9}, pmid = {22861804}, issn = {1753-4887}, support = {DP1 OD000964/OD/NIH HHS/United States ; DP1 OD000964-05/OD/NIH HHS/United States ; DP1OD000964/OD/NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Biodiversity ; *Ecosystem ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome/drug effects ; Phylogeny ; Species Specificity ; Symbiosis ; }, abstract = {Given the importance of the microbiome for human health, both the stability and the response to disturbance of this microbial ecosystem are crucial issues. Yet, the current understanding of these factors is insufficient. Early data suggest there is relative stability in the microbiome of adults in the absence of gross perturbation, and that long-term stability of the human indigenous microbial communities is maintained not by inertia but by the action of restorative forces within a dynamic system. After brief exposures to some antibiotics, there is an immediate and substantial perturbation and at least a partial recovery of taxonomic composition. Responses to antibiotics are individualized and are influenced by prior experience with the same antibiotic. These findings suggest that the human microbiome has properties of resilience. Besides serving to reveal critical underlying functional attributes, microbial interactions, and keystone species within the indigenous microbiota, the response to disturbance may have value in predicting future instability and disease and in managing the human microbial ecosystem.}, } @article {pmid22885760, year = {2012}, author = {Naether, A and Foesel, BU and Naegele, V and Wüst, PK and Weinert, J and Bonkowski, M and Alt, F and Oelmann, Y and Polle, A and Lohaus, G and Gockel, S and Hemp, A and Kalko, EK and Linsenmair, KE and Pfeiffer, S and Renner, S and Schöning, I and Weisser, WW and Wells, K and Fischer, M and Overmann, J and Friedrich, MW}, title = {Environmental factors affect Acidobacterial communities below the subgroup level in grassland and forest soils.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {20}, pages = {7398-7406}, pmid = {22885760}, issn = {1098-5336}, mesh = {Acidobacteria/*classification/genetics/*isolation & purification ; *Biota ; Carbon/analysis ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; Germany ; Hydrogen-Ion Concentration ; Metagenome ; Molecular Sequence Data ; Nitrogen/analysis ; Phosphorus/analysis ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; Temperature ; Trees ; }, abstract = {In soil, Acidobacteria constitute on average 20% of all bacteria, are highly diverse, and are physiologically active in situ. However, their individual functions and interactions with higher taxa in soil are still unknown. Here, potential effects of land use, soil properties, plant diversity, and soil nanofauna on acidobacterial community composition were studied by cultivation-independent methods in grassland and forest soils from three different regions in Germany. The analysis of 16S rRNA gene clone libraries representing all studied soils revealed that grassland soils were dominated by subgroup Gp6 and forest soils by subgroup Gp1 Acidobacteria. The analysis of a large number of sites (n = 57) by 16S rRNA gene fingerprinting methods (terminal restriction fragment length polymorphism [T-RFLP] and denaturing gradient gel electrophoresis [DGGE]) showed that Acidobacteria diversities differed between grassland and forest soils but also among the three different regions. Edaphic properties, such as pH, organic carbon, total nitrogen, C/N ratio, phosphorus, nitrate, ammonium, soil moisture, soil temperature, and soil respiration, had an impact on community composition as assessed by fingerprinting. However, interrelations with environmental parameters among subgroup terminal restriction fragments (T-RFs) differed significantly, e.g., different Gp1 T-RFs correlated positively or negatively with nitrogen content. Novel significant correlations of Acidobacteria subpopulations (i.e., individual populations within subgroups) with soil nanofauna and vascular plant diversity were revealed only by analysis of clone sequences. Thus, for detecting novel interrelations of environmental parameters with Acidobacteria, individual populations within subgroups have to be considered.}, } @article {pmid22885757, year = {2012}, author = {Andrew, DR and Fitak, RR and Munguia-Vega, A and Racolta, A and Martinson, VG and Dontsova, K}, title = {Abiotic factors shape microbial diversity in Sonoran Desert soils.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {21}, pages = {7527-7537}, pmid = {22885757}, issn = {1098-5336}, mesh = {Archaea/*classification/*genetics ; Arizona ; Bacteria/*classification/*genetics ; Biodiversity ; Cactaceae/*microbiology ; DNA, Bacterial/genetics ; Desert Climate ; Geography ; *Metagenome ; Microbial Consortia ; RNA, Ribosomal, 16S ; Rhizosphere ; Sequence Analysis, DNA ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {High-throughput, culture-independent surveys of bacterial and archaeal communities in soil have illuminated the importance of both edaphic and biotic influences on microbial diversity, yet few studies compare the relative importance of these factors. Here, we employ multiplexed pyrosequencing of the 16S rRNA gene to examine soil- and cactus-associated rhizosphere microbial communities of the Sonoran Desert and the artificial desert biome of the Biosphere2 research facility. The results of our replicate sampling approach show that microbial communities are shaped primarily by soil characteristics associated with geographic locations, while rhizosphere associations are secondary factors. We found little difference between rhizosphere communities of the ecologically similar saguaro (Carnegiea gigantea) and cardón (Pachycereus pringlei) cacti. Both rhizosphere and soil communities were dominated by the disproportionately abundant Crenarchaeota class Thermoprotei, which comprised 18.7% of 183,320 total pyrosequencing reads from a comparatively small number (1,337 or 3.7%) of the 36,162 total operational taxonomic units (OTUs). OTUs common to both soil and rhizosphere samples comprised the bulk of raw sequence reads, suggesting that the shared community of soil and rhizosphere microbes constitute common and abundant taxa, particularly in the bacterial phyla Proteobacteria, Actinobacteria, Planctomycetes, Firmicutes, Bacteroidetes, Chloroflexi, and Acidobacteria. The vast majority of OTUs, however, were rare and unique to either soil or rhizosphere communities and differed among locations dozens of kilometers apart. Several soil properties, particularly soil pH and carbon content, were significantly correlated with community diversity measurements. Our results highlight the importance of culture-independent approaches in surveying microbial communities of extreme environments.}, } @article {pmid22883720, year = {2012}, author = {Renan, S and Speyer, E and Shahar, N and Gueta, T and Templeton, AR and Bar-David, S}, title = {A factorial design experiment as a pilot study for noninvasive genetic sampling.}, journal = {Molecular ecology resources}, volume = {12}, number = {6}, pages = {1040-1047}, doi = {10.1111/j.1755-0998.2012.03170.x}, pmid = {22883720}, issn = {1755-0998}, mesh = {Animals ; *Biota ; DNA, Mitochondrial/genetics/isolation & purification ; Equidae/microbiology ; Feces/*microbiology/*parasitology ; Israel ; Metagenomics/*methods ; Microsatellite Repeats ; Pilot Projects ; Preservation, Biological/methods ; Specimen Handling/*methods ; }, abstract = {Noninvasive genetic sampling has increasingly been used in ecological and conservation studies during the last decade. A major part of the noninvasive genetic literature is dedicated to the search for optimal protocols, by comparing different methods of collection, preservation and extraction of DNA from noninvasive materials. However, the lack of quantitative comparisons among these studies and the possibility that different methods are optimal for different systems make it difficult to decide which protocol to use. Moreover, most studies that have compared different methods focused on a single factor - collection, preservation or extraction - while there could be interactions between these factors. We designed a factorial experiment, as a pilot study, aimed at exploring the effect of several collection, preservation and extraction methods, and the interactions between them, on the quality and amplification success of DNA obtained from Asiatic wild ass (Equus hemionus) faeces in Israel. The amplification success rates of one mitochondrial DNA and four microsatellite markers differed substantially as a function of collection, preservation and extraction methods and their interactions. The most efficient combination for our system integrated the use of swabs as a collection method with preservation at -20 °C and with the Qiagen DNA Stool Kit with modifications as the DNA extraction method. The significant interaction found between the collection, preservation methods and the extraction methods reinforces the importance of conducting a factorial design experiment, rather than examining each factor separately, as a pilot study before initiating a full-scale noninvasive research project.}, } @article {pmid22864264, year = {2012}, author = {Reyes, A and Semenkovich, NP and Whiteson, K and Rohwer, F and Gordon, JI}, title = {Going viral: next-generation sequencing applied to phage populations in the human gut.}, journal = {Nature reviews. Microbiology}, volume = {10}, number = {9}, pages = {607-617}, pmid = {22864264}, issn = {1740-1534}, support = {GM007200/GM/NIGMS NIH HHS/United States ; P01 DK078669/DK/NIDDK NIH HHS/United States ; R01 DK030292/DK/NIDDK NIH HHS/United States ; R01 DK070977/DK/NIDDK NIH HHS/United States ; DK70977/DK/NIDDK NIH HHS/United States ; GM095384/GM/NIGMS NIH HHS/United States ; R01 GM095384/GM/NIGMS NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; DK78669/DK/NIDDK NIH HHS/United States ; T32 GM007200/GM/NIGMS NIH HHS/United States ; DK30292/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/*virology ; Bacterial Infections/therapy ; Bacteriophages/*classification/*genetics/isolation & purification ; *Biodiversity ; Biological Products/therapeutic use ; *Biota ; Complementary Therapies/methods ; Gastrointestinal Tract/microbiology/*virology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; }, abstract = {Over the past decade, researchers have begun to characterize viral diversity using metagenomic methods. These studies have shown that viruses, the majority of which infect bacteria, are probably the most genetically diverse components of the biosphere. Here, we briefly review the incipient rise of a phage biology renaissance, which has been catalysed by advances in next-generation sequencing. We explore how work characterizing phage diversity and lifestyles in the human gut is changing our view of ourselves as supra-organisms. Finally, we discuss how a renewed appreciation of phage dynamics may yield new applications for phage therapies designed to manipulate the structure and functions of our gut microbiomes.}, } @article {pmid22859207, year = {2012}, author = {Bulgarelli, D and Rott, M and Schlaeppi, K and Ver Loren van Themaat, E and Ahmadinejad, N and Assenza, F and Rauf, P and Huettel, B and Reinhardt, R and Schmelzer, E and Peplies, J and Gloeckner, FO and Amann, R and Eickhorst, T and Schulze-Lefert, P}, title = {Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota.}, journal = {Nature}, volume = {488}, number = {7409}, pages = {91-95}, pmid = {22859207}, issn = {1476-4687}, mesh = {Actinobacteria/isolation & purification ; Arabidopsis/classification/*microbiology ; Bacteria/classification/genetics/*isolation & purification/ultrastructure ; Bacteroidetes/isolation & purification ; Biodiversity ; Cell Wall/metabolism/microbiology ; Ecosystem ; Endophytes/classification/genetics/growth & development/isolation & purification ; Host Specificity ; In Situ Hybridization, Fluorescence ; *Metagenome ; Plant Cells/microbiology ; Plant Roots/*microbiology ; Proteobacteria/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Ribotyping ; Soil/analysis/chemistry ; Soil Microbiology ; }, abstract = {The plant root defines the interface between a multicellular eukaryote and soil, one of the richest microbial ecosystems on Earth. Notably, soil bacteria are able to multiply inside roots as benign endophytes and modulate plant growth and development, with implications ranging from enhanced crop productivity to phytoremediation. Endophytic colonization represents an apparent paradox of plant innate immunity because plant cells can detect an array of microbe-associated molecular patterns (also known as MAMPs) to initiate immune responses to terminate microbial multiplication. Several studies attempted to describe the structure of bacterial root endophytes; however, different sampling protocols and low-resolution profiling methods make it difficult to infer general principles. Here we describe methodology to characterize and compare soil- and root-inhabiting bacterial communities, which reveals not only a function for metabolically active plant cells but also for inert cell-wall features in the selection of soil bacteria for host colonization. We show that the roots of Arabidopsis thaliana, grown in different natural soils under controlled environmental conditions, are preferentially colonized by Proteobacteria, Bacteroidetes and Actinobacteria, and each bacterial phylum is represented by a dominating class or family. Soil type defines the composition of root-inhabiting bacterial communities and host genotype determines their ribotype profiles to a limited extent. The identification of soil-type-specific members within the root-inhabiting assemblies supports our conclusion that these represent soil-derived root endophytes. Surprisingly, plant cell-wall features of other tested plant species seem to provide a sufficient cue for the assembly of approximately 40% of the Arabidopsis bacterial root-inhabiting microbiota, with a bias for Betaproteobacteria. Thus, this root sub-community may not be Arabidopsis-specific but saprophytic bacteria that would naturally be found on any plant root or plant debris in the tested soils. By contrast, colonization of Arabidopsis roots by members of the Actinobacteria depends on other cues from metabolically active host cells.}, } @article {pmid22858232, year = {2012}, author = {Mayer, M and Abenthum, A and Matthes, JM and Kleeberger, D and Ege, MJ and Hölzel, C and Bauer, J and Schwaiger, K}, title = {Development and genetic influence of the rectal bacterial flora of newborn calves.}, journal = {Veterinary microbiology}, volume = {161}, number = {1-2}, pages = {179-185}, doi = {10.1016/j.vetmic.2012.07.023}, pmid = {22858232}, issn = {1873-2542}, mesh = {Animals ; Animals, Newborn ; Bacteria/*genetics/*growth & development/isolation & purification ; *Biodiversity ; Cattle ; Feces/microbiology ; Intestines/microbiology ; Metagenome ; Rectum/*microbiology ; Time Factors ; }, abstract = {The aim of the study was to investigate a dynamic change in the rectal flora of calves as well as to study a genetic influence on the intestinal microflora of calves. The bacterial community of fecal samples from calves was examined by PCR single strand conformation polymorphism (PCR-SSCP) in two independent studies. In study one 14 newborn calves of the same farm were examined. Sampling was conducted directly after delivery (meconium) and after 6 h, 12 h, 24 h, 48 h, 3 d, 7 d, 14 d and 42 d of life. In study two 6 twin calves and their coresident of the same age and farm were analysed in order to study for the first time whether genetic predisposition of the host may influence the fecal microflora. All calves were weaned directly after delivery and received pumped colostrum without direct contact to other farm animals. After delivery and during the first 12h of life the SSCP profiles were simple, but became more complex since the bacterial diversity increased with time in all calves. It became obvious that the intra-individual band-pattern similarity decreased over time and inter-individual similarity was low. The analysis of fecal samples from twin calves revealed higher similarity in SSCP profiles for twins compared to their coresident indicating that the individual microflora might be genetically or epigenetically influenced. The insight that there are several conformities between intestinal microfloras of healthy calves and that there might be genetic influence on the fecal flora could help to prevent diarrhoeal diseases in the future.}, } @article {pmid22857743, year = {2012}, author = {Bergström, A and Kristensen, MB and Bahl, MI and Metzdorff, SB and Fink, LN and Frøkiaer, H and Licht, TR}, title = {Nature of bacterial colonization influences transcription of mucin genes in mice during the first week of life.}, journal = {BMC research notes}, volume = {5}, number = {}, pages = {402}, pmid = {22857743}, issn = {1756-0500}, mesh = {Animals ; Animals, Newborn ; Escherichia coli/*physiology ; *Gene Expression Regulation, Developmental ; Germ-Free Life/genetics ; Intestine, Small/*metabolism/microbiology ; Lactobacillus acidophilus/*physiology ; Metagenome/*physiology ; Mice ; Microbial Consortia/genetics ; Mucin-1/genetics/metabolism ; Mucin-2/genetics/metabolism ; Mucin-3/genetics/metabolism ; Mucin-4/genetics/metabolism ; Mucins/genetics/metabolism ; Mucus/*metabolism/microbiology ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; *Transcription, Genetic ; Trefoil Factor-3 ; }, abstract = {BACKGROUND: Postnatal regulation of the small intestinal mucus layer is potentially important in the development of adult gut functionality. We hypothesized that the nature of bacterial colonization affects mucus gene regulation in early life.We thus analyzed the influence of the presence of a conventional microbiota as well as two selected monocolonizing bacterial strains on the transcription of murine genes involved in mucus layer development during the first week of life.Mouse pups (N = 8/group) from differently colonized dams: Germ-free (GF), conventional specific pathogen free (SPF), monocolonized with either Lactobacillus acidophilus NCFM (Lb) or Escherichia coli Nissle (Ec) were analyzed by qPCR on isolated ileal tissue sections from postnatal days 1 and 6 (PND1, PND6) after birth with respect to: (i) transcription of specific genes involved in mucus production (Muc1-4, Tff3) and (ii) amounts of 16S rRNA of Lactobacillus and E. coli. Quantification of 16S rRNA genes was performed to obtain a measure for amounts of colonized bacteria.

RESULTS: We found a microbiota-independent transcriptional increase of all five mucus genes from PND1 to PND6. Furthermore, the relative level of transcription of certain mucus genes on PND1 was increased by the presence of bacteria. This was observed for Tff3 in the SPF, Ec, and Lb groups; for Muc2 in SPF; and for Muc3 and Muc4 in Ec and Lb, respectively.Detection of bacterial 16S rRNA genes levels above the qPCR detection level occurred only on PND6 and only for some of the colonized animals. On PND6, we found significantly lower levels of Muc1, Muc2 and Muc4 gene transcription for Lb animals with detectable Lactobacillus levels as compared to animals with Lactobacillus levels below the detection limit.

CONCLUSIONS: In summary, our data show that development of the expression of genes encoding secreted (Muc2/Tff3) and membrane-bound (Muc1/Muc3/Muc4) mucus regulatory proteins, respectively, is distinct and that the onset of this development may be accelerated by specific groups of bacteria present or absent at the mucosal site.}, } @article {pmid22849830, year = {2012}, author = {Whiteley, AS and Jenkins, S and Waite, I and Kresoje, N and Payne, H and Mullan, B and Allcock, R and O'Donnell, A}, title = {Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform.}, journal = {Journal of microbiological methods}, volume = {91}, number = {1}, pages = {80-88}, doi = {10.1016/j.mimet.2012.07.008}, pmid = {22849830}, issn = {1872-8359}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; *Biota ; DNA Barcoding, Taxonomic/economics/methods ; Metagenomics/economics/*methods ; Polymerase Chain Reaction/economics/methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/economics/methods ; Wastewater/microbiology ; }, abstract = {Here we demonstrate a cost effective and scalable microbial ecology sequencing platform using the Ion Torrent Personal Genome Machine (PGM). We assessed both PCR amplified 16S rRNA and shotgun metagenomic approaches and generated 100,000+ to 1,000,000+ reads using 'post-light' based sequencing technology within different sized semi-conductor chips. Further development of Golay barcoded Ion Tags allowed multiplex analyses of microbial communities with substantially reduced costs compared with platforms such as 454/GS-FLX. Using these protocols we assessed the bacterial and archaeal dynamics within covered anaerobic digesters used to treat piggery wastes. Analysis of these sequence data showed that these novel methanogenic waste treatment systems are dominated by bacterial taxa, in particular Clostridium, Synergistia and Bacteroides that were maintained as a stable community over extended time periods. Archaeal community dynamics were more stochastic with the key methanogenic taxa more difficult to resolve, principally due to the poor congruence seen between community structures generated either by nested PCR or metagenomic approaches for archaeal analyses. Our results show that for microbial community structure and function analyses, the PGM platform provides a low cost, scalable and high throughput solution for both Tag sequencing and metagenomic analyses.}, } @article {pmid22848694, year = {2012}, author = {Wang, F and Li, Q and Wang, C and Tang, C and Li, J}, title = {Dynamic alteration of the colonic microbiota in intestinal ischemia-reperfusion injury.}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e42027}, pmid = {22848694}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Colon/*microbiology/pathology ; Intestinal Mucosa/microbiology ; Lactic Acid/blood ; Male ; *Metagenome ; Rats ; Rats, Sprague-Dawley ; Reperfusion Injury/blood/classification/*microbiology/pathology ; Time Factors ; }, abstract = {BACKGROUND: Intestinal ischemia-reperfusion (I/R) plays an important role in critical illnesses. Gut flora participate in the pathogenesis of the injury. This study is aimed at unraveling colonic microbiota alteration pattern and identifying specific bacterial species that differ significantly as well as observing colonic epithelium change in the same injury model during the reperfusion time course.

Denaturing gradient gel electrophoresis (DGGE) was used to monitor the colonic microbiota of control rats and experimental rats that underwent 0.5 hour ischemia and 1, 3, 6, 12, 24, and 72 hours following reperfusion respectively. The microbiota similarity, bacterial diversity and species that characterized the dysbiosis were estimated based on the DGGE profiles using a combination of statistical approaches. The interested bacterial species in the gel were cut and sequenced and were subsequently quantified and confirmed with real-time PCR. Meanwhile, the epithelial barrier was checked by microscopy and D-lactate analysis. Colonic flora changed early and differed significantly at 6 hours after reperfusion and then started to recover. The shifts were characterized by the increase of Escherichia coli and Prevotella oralis, and Lactobacilli proliferation together with epithelia healing.

CONCLUSION/SIGNIFICANCE: This study shows for the first time that intestinal ischemia-reperfusion results in colonic flora dysbiosis that follows epithelia damage, and identifies the bacterial species that contribute most.}, } @article {pmid22846661, year = {2012}, author = {Cardona, S and Eck, A and Cassellas, M and Gallart, M and Alastrue, C and Dore, J and Azpiroz, F and Roca, J and Guarner, F and Manichanh, C}, title = {Storage conditions of intestinal microbiota matter in metagenomic analysis.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {158}, pmid = {22846661}, issn = {1471-2180}, mesh = {*Biota ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrophoresis, Capillary ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenome/*genetics ; Metagenomics/*methods/standards ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Specimen Handling/*methods ; Temperature ; Time Factors ; }, abstract = {BACKGROUND: The structure and function of human gut microbiota is currently inferred from metagenomic and metatranscriptomic analyses. Recovery of intact DNA and RNA is therefore a critical step in these studies. Here, we evaluated how different storage conditions of fecal samples affect the quality of extracted nucleic acids and the stability of their microbial communities.

RESULTS: We assessed the quality of genomic DNA and total RNA by microcapillary electrophoresis and analyzed the bacterial community structure by pyrosequencing the 16S rRNA gene. DNA and RNA started to fragment when samples were kept at room temperature for more than 24 h. The use of RNAse inhibitors diminished RNA degradation but this protection was not consistent among individuals. DNA and RNA degradation also occurred when frozen samples were defrosted for a short period (1 h) before nucleic acid extraction. The same conditions that affected DNA and RNA integrity also altered the relative abundance of most taxa in the bacterial community analysis. In this case, intra-individual variability of microbial diversity was larger than inter-individual one.

CONCLUSIONS: Though this preliminary work explored a very limited number of parameters, the results suggest that storage conditions of fecal samples affect the integrity of DNA and RNA and the composition of their microbial community. For optimal preservation, stool samples should be kept at room temperature and brought at the laboratory within 24 h after collection or be stored immediately at -20°C in a home freezer and transported afterwards in a freezer pack to ensure that they do not defrost at any time. Mixing the samples with RNAse inhibitors outside the laboratory is not recommended since proper homogenization of the stool is difficult to monitor.}, } @article {pmid22845467, year = {2013}, author = {Hurwitz, BL and Deng, L and Poulos, BT and Sullivan, MB}, title = {Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics.}, journal = {Environmental microbiology}, volume = {15}, number = {5}, pages = {1428-1440}, pmid = {22845467}, issn = {1462-2920}, mesh = {Biodiversity ; *Metagenomics ; Reproducibility of Results ; Seawater/virology ; Viral Proteins/analysis/genetics ; Virology/*methods ; Viruses/*genetics/*isolation & purification ; *Water Microbiology ; }, abstract = {Viruses have global impact through mortality, nutrient cycling and horizontal gene transfer, yet their study is limited by complex methodologies with little validation. Here, we use triplicate metagenomes to compare common aquatic viral concentration and purification methods across four combinations as follows: (i) tangential flow filtration (TFF) and DNase + CsCl, (ii) FeCl3 precipitation and DNase, (iii) FeCl3 precipitation and DNase + CsCl and (iv) FeCl3 precipitation and DNase + sucrose. Taxonomic data (30% of reads) suggested that purification methods were statistically indistinguishable at any taxonomic level while concentration methods were significantly different at family and genus levels. Specifically, TFF-concentrated viral metagenomes had significantly fewer abundant viral types (Podoviridae and Phycodnaviridae) and more variability among Myoviridae than FeCl3 -precipitated viral metagenomes. More comprehensive analyses using protein clusters (66% of reads) and k-mers (100% of reads) showed 50-53% of these data were common to all four methods, and revealed trace bacterial DNA contamination in TFF-concentrated metagenomes and one of three replicates concentrated using FeCl3 and purified by DNase alone. Shared k-mer analyses also revealed that polymerases used in amplification impact the resulting metagenomes, with TaKaRa enriching for 'rare' reads relative to PfuTurbo. Together these results provide empirical data for making experimental design decisions in culture-independent viral ecology studies.}, } @article {pmid22845175, year = {2013}, author = {Dostal, A and Fehlbaum, S and Chassard, C and Zimmermann, MB and Lacroix, C}, title = {Low iron availability in continuous in vitro colonic fermentations induces strong dysbiosis of the child gut microbial consortium and a decrease in main metabolites.}, journal = {FEMS microbiology ecology}, volume = {83}, number = {1}, pages = {161-175}, pmid = {22845175}, issn = {1574-6941}, support = {U01 HD064921/HD/NICHD NIH HHS/United States ; U01HD0 64921/HD/NICHD NIH HHS/United States ; }, mesh = {Bacteria/*metabolism ; Cells, Immobilized/metabolism ; Child ; Colon/metabolism/*microbiology ; Culture Media/chemistry ; DNA, Bacterial/genetics ; Feces/microbiology ; *Fermentation ; Humans ; Iron/*metabolism ; Iron Deficiencies ; *Metagenome ; *Microbial Consortia ; Sequence Analysis, DNA ; }, abstract = {Iron (Fe) deficiency affects an estimated 2 billion people worldwide, and Fe supplements are a common corrective strategy. The impact of Fe deficiency and Fe supplementation on the complex microbial community of the child gut was studied using in vitro colonic fermentation models inoculated with immobilized fecal microbiota. Chyme media (all Fe chelated by 2,2'-dipyridyl to 26.5 mg Fe L(-1)) mimicking Fe deficiency and supplementation were continuously fermented. Fermentation effluent samples were analyzed daily on the microbial composition and metabolites by quantitative PCR, 16S rRNA gene 454-pyrosequencing, and HPLC. Low Fe conditions (1.56 mg Fe L(-1)) significantly decreased acetate concentrations, and subsequent Fe supplementation (26.5 mg Fe L(-1)) restored acetate production. High Fe following normal Fe conditions had no impact on the gut microbiota composition and metabolic activity. During very low Fe conditions (0.9 mg Fe L(-1) or Fe chelated by 2,2'-dipyridyl), a decrease in Roseburia spp./Eubacterium rectale, Clostridium Cluster IV members and Bacteroides spp. was observed, while Lactobacillus spp. and Enterobacteriaceae increased consistent with a decrease in butyrate (-84%) and propionate (-55%). The strong dysbiosis of the gut microbiota together with decrease in main gut microbiota metabolites observed with very low iron conditions could weaken the barrier effect of the microbiota and negatively impact gut health.}, } @article {pmid22843531, year = {2012}, author = {Wang, X and Hu, M and Xia, Y and Wen, X and Ding, K}, title = {Pyrosequencing analysis of bacterial diversity in 14 wastewater treatment systems in China.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {19}, pages = {7042-7047}, pmid = {22843531}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics ; *Biota ; China ; Cities ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electric Conductivity ; Hydrogen-Ion Concentration ; *Metagenome ; Oxygen/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Temperature ; Wastewater/chemistry/*microbiology ; Water Purification ; }, abstract = {To determine if there is a core microbial community in the microbial populations of different wastewater treatment plants (WWTPs) and to investigate the effects of wastewater characteristics, operational parameters, and geographic locations on microbial communities, activated sludge samples were collected from 14 wastewater treatment systems located in 4 cities in China. High-throughput pyrosequencing was used to examine the 16S rRNA genes of bacteria in the wastewater treatment systems. Our results showed that there were 60 genera of bacterial populations commonly shared by all 14 samples, including Ferruginibacter, Prosthecobacter, Zoogloea, Subdivision 3 genera incertae sedis, Gp4, Gp6, etc., indicating that there is a core microbial community in the microbial populations of WWTPs at different geographic locations. The canonical correspondence analysis (CCA) results showed that the bacterial community variance correlated most strongly with water temperature, conductivity, pH, and dissolved oxygen (DO) content. Variance partitioning analyses suggested that wastewater characteristics had the greatest contribution to the bacterial community variance, explaining 25.7% of the variance of bacterial communities independently, followed by operational parameters (23.9%) and geographic location (14.7%). Results of this study provided insights into the bacterial community structure and diversity in geographically distributed WWTPs and discerned the relationships between bacterial community and environmental variables in WWTPs.}, } @article {pmid22842661, year = {2012}, author = {Hentschel, U and Piel, J and Degnan, SM and Taylor, MW}, title = {Genomic insights into the marine sponge microbiome.}, journal = {Nature reviews. Microbiology}, volume = {10}, number = {9}, pages = {641-654}, pmid = {22842661}, issn = {1740-1534}, mesh = {Animals ; Aquatic Organisms ; *Biota ; Metagenome/*genetics/physiology ; Porifera/*microbiology/physiology ; Symbiosis ; }, abstract = {Marine sponges (phylum Porifera) often contain dense and diverse microbial communities, which can constitute up to 35% of the sponge biomass. The genome of one sponge, Amphimedon queenslandica, was recently sequenced, and this has provided new insights into the origins of animal evolution. Complementary efforts to sequence the genomes of uncultivated sponge symbionts have yielded the first glimpse of how these intimate partnerships are formed. The remarkable microbial and chemical diversity of the sponge-microorganism association, coupled with its postulated antiquity, makes sponges important model systems for the study of metazoan host-microorganism interactions, and their evolution, as well as for enabling access to biotechnologically important symbiont-derived natural products. In this Review, we discuss our current understanding of the interactions between marine sponges and their microbial symbiotic consortia, and highlight recent insights into these relationships from genomic studies.}, } @article {pmid22842102, year = {2012}, author = {Federici, E and Giubilei, MA and Covino, S and Zanaroli, G and Fava, F and D'Annibale, A and Petruccioli, M}, title = {Addition of maize stalks and soybean oil to a historically PCB-contaminated soil: effect on degradation performance and indigenous microbiota.}, journal = {New biotechnology}, volume = {30}, number = {1}, pages = {69-79}, doi = {10.1016/j.nbt.2012.07.007}, pmid = {22842102}, issn = {1876-4347}, mesh = {Bacteria/genetics/growth & development ; Biodegradation, Environmental ; Biomass ; Denaturing Gradient Gel Electrophoresis ; Fungi/genetics/growth & development ; Genetic Variation ; Heterotrophic Processes ; *Metagenome ; Polychlorinated Biphenyls/*metabolism ; RNA, Ribosomal, 16S/genetics ; Regression Analysis ; Soil Pollutants/*metabolism ; Soybean Oil/*metabolism ; Time Factors ; Zea mays/*metabolism ; }, abstract = {Objective of this study was to assess the single or combined effect of a plant oil and a lignocellulosic waste, namely soybean oil (SO) and maize stalks (MS), respectively, on resident microbiota and bioremediation performances of a soil historically contaminated by medium to highly chlorinated PCBs. Higher concentrations of both biphenyl- and chlorobenzoate-degrading cultivable bacteria were found in the MS-amended microcosms (MSM) than the non amended or SO-amended ones after 30 d incubation at 28°C. Fungal growth, instead, was strikingly stimulated in the microcosms that had undergone concomitant MS and SO supplementation (MS-SOM). Denaturing gradient gel electrophoresis analyses of 16S and 18S rRNA genes showed that both amendments promoted a remarkable increase in both bacterial and fungal biodiversity. The abundances of biphenyl-2,3-dioxygenase (bph) and that of catechol-2,3-dioxygenase (C230) genes in the non-amended contaminated soil were constant over time. Conversely, after 60 d incubation, bph and C230 abundances increased 2.8- and 61-fold in the MSM, respectively, and, in the MS-SOM, 1.4- and 46-fold, respectively, with respect to the zero time point. Although the overall PCB removal was not positively affected by the amendments, the concomitant presence of both MS and SO led to significantly higher depletions of hexa-, hepta-, octa- and nona-chlorinated congeners than in the non-amended microcosms (i.e. 24.6, 22, 20.5 and 9.5%, versus 19.4, 16.4, 14.7 and 6.1%, respectively). In all microcosms, PCB degradation was negatively correlated with hydrophobicity, organic matter/water partition coefficient, molecular weight and extent of chlorination of the pollutants with the notable exception of the MS-SOM ones where such a relationship was less stringent.}, } @article {pmid22841660, year = {2012}, author = {Liu, L and Chen, X and Skogerbø, G and Zhang, P and Chen, R and He, S and Huang, DW}, title = {The human microbiome: a hot spot of microbial horizontal gene transfer.}, journal = {Genomics}, volume = {100}, number = {5}, pages = {265-270}, doi = {10.1016/j.ygeno.2012.07.012}, pmid = {22841660}, issn = {1089-8646}, mesh = {*Biota ; Computational Biology ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Genomics/*methods ; Humans ; Metagenome/*genetics ; Molecular Sequence Annotation ; }, abstract = {The human body harbors numerous microbes, and here exists a close relationship between microbes and human health. The Human Microbiome Project has generated whole genome sequences of several hundred human microbes. In this study, we identified horizontal gene transfer (HGT) events in human microbes and tried to elucidate the relationships between the gene-transferring microbes. A total of 13,514 high confidence HGT genes were identified in 308 human microbes. The horizontally transferred genes were enriched for Gene Ontology terms pertaining to catalytic functions and metabolic processes. Construction of an HGT event network suggested that the human microbes could be divided into specific communities which only partly overlap their distribution in human body. Our research suggests that human microbiome may facilitate frequent horizontal gene transfer among bacteria in human body. Awareness of HGT in human microbiome may aid our understanding of the relationship between the human microbiome and human health.}, } @article {pmid22839737, year = {2012}, author = {Hsiao, WW and Li, KL and Liu, Z and Jones, C and Fraser-Liggett, CM and Fouad, AF}, title = {Microbial transformation from normal oral microbiota to acute endodontic infections.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {345}, pmid = {22839737}, issn = {1471-2164}, support = {DE015320-01-A1/DE/NIDCR NIH HHS/United States ; }, mesh = {Acute Disease ; Analysis of Variance ; Bacteria/*genetics ; Bacterial Infections/*microbiology ; Biodiversity ; Confidence Intervals ; DNA, Bacterial/classification/isolation & purification ; Dental Pulp Cavity/microbiology/pathology ; Female ; Humans ; Male ; Metagenome/*genetics ; Molecular Sequence Annotation ; Mouth Mucosa/*microbiology/pathology ; Periapical Abscess/microbiology ; Phylogeny ; Sequence Analysis, DNA ; Software ; Species Specificity ; }, abstract = {BACKGROUND: Endodontic infections are a leading cause of oro-facial pain and tooth loss in western countries, and may lead to severe life-threatening infections. These infections are polymicrobial with high bacterial diversity. Understanding the spatial transition of microbiota from normal oral cavities through the infected root canal to the acute periapical abscess can improve our knowledge of the pathogenesis of endodontic infections and lead to more effective treatment. We obtained samples from the oral cavity, infected root canal and periapical abscess of 8 patients (5 with localized and 3 with systemic infections). Microbial populations in these samples were analyzed using next-generation sequencing of 16S rRNA amplicons. Bioinformatics tools and statistical tests with rigorous criteria were used to elucidate the spatial transition of the microbiota from normal to diseased sites.

RESULTS: On average, 10,000 partial 16S rRNA gene sequences were obtained from each sample. All sequences fell into 11 different bacterial phyla. The microbial diversity in root canal and abscess samples was significantly lower than in the oral samples. Streptococcus was the most abundant genus in oral cavities while Prevotella and Fusobacterium were most abundant in diseased samples. The microbiota community structures of root canal and abscess samples were, however, more similar to each other than to the oral cavity microbiota. Using rigorous criteria and novel bioinformatics tools, we found that Granulicatella adiacens, Eubacterium yurii, Prevotella melaninogenica, Prevotella salivae, Streptococcus mitis, and Atopobium rimae were over-represented in diseased samples.

CONCLUSIONS: We used a novel approach and high-throughput methodologies to characterize the microbiota associated normal and diseased oral sites in the same individuals.}, } @article {pmid22832345, year = {2013}, author = {Guazzaroni, ME and Herbst, FA and Lores, I and Tamames, J and Peláez, AI and López-Cortés, N and Alcaide, M and Del Pozo, MV and Vieites, JM and von Bergen, M and Gallego, JL and Bargiela, R and López-López, A and Pieper, DH and Rosselló-Móra, R and Sánchez, J and Seifert, J and Ferrer, M}, title = {Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation.}, journal = {The ISME journal}, volume = {7}, number = {1}, pages = {122-136}, pmid = {22832345}, issn = {1751-7370}, mesh = {Bacteria/*classification/genetics/*isolation & purification/metabolism ; Biodegradation, Environmental ; Biodiversity ; Metagenomics ; Molecular Sequence Data ; Naphthalenes/metabolism/*toxicity ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/metabolism ; }, abstract = {Microbial metabolism in aromatic-contaminated environments has important ecological implications, and obtaining a complete understanding of this process remains a relevant goal. To understand the roles of biodiversity and aromatic-mediated genetic and metabolic rearrangements, we conducted 'OMIC' investigations in an anthropogenically influenced and polyaromatic hydrocarbon (PAH)-contaminated soil with (Nbs) or without (N) bio-stimulation with calcium ammonia nitrate, NH(4)NO(3) and KH(2)PO(4) and the commercial surfactant Iveysol, plus two naphthalene-enriched communities derived from both soils (CN2 and CN1, respectively). Using a metagenomic approach, a total of 52, 53, 14 and 12 distinct species (according to operational phylogenetic units (OPU) in our work equivalent to taxonomic species) were identified in the N, Nbs, CN1 and CN2 communities, respectively. Approximately 10 out of 95 distinct species and 238 out of 3293 clusters of orthologous groups (COGs) protein families identified were clearly stimulated under the assayed conditions, whereas only two species and 1465 COGs conformed to the common set in all of the mesocosms. Results indicated distinct biodegradation capabilities for the utilisation of potential growth-supporting aromatics, which results in bio-stimulated communities being extremely fit to naphthalene utilisation and non-stimulated communities exhibiting a greater metabolic window than previously predicted. On the basis of comparing protein expression profiles and metagenome data sets, inter-alia interactions among members were hypothesised. The utilisation of curated databases is discussed and used for first time to reconstruct 'presumptive' degradation networks for complex microbial communities.}, } @article {pmid22832344, year = {2013}, author = {Harris, JK and Caporaso, JG and Walker, JJ and Spear, JR and Gold, NJ and Robertson, CE and Hugenholtz, P and Goodrich, J and McDonald, D and Knights, D and Marshall, P and Tufo, H and Knight, R and Pace, NR}, title = {Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat.}, journal = {The ISME journal}, volume = {7}, number = {1}, pages = {50-60}, pmid = {22832344}, issn = {1751-7370}, support = {T32 GM084907/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Bacteria/*classification/genetics/*isolation & purification ; Biodiversity ; Cyanobacteria/genetics/isolation & purification/physiology ; Genes, rRNA ; High-Throughput Nucleotide Sequencing ; Mexico ; Molecular Sequence Data ; Phylogeny ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The microbial mats of Guerrero Negro (GN), Baja California Sur, Mexico historically were considered a simple environment, dominated by cyanobacteria and sulfate-reducing bacteria. Culture-independent rRNA community profiling instead revealed these microbial mats as among the most phylogenetically diverse environments known. A preliminary molecular survey of the GN mat based on only ∼1500 small subunit rRNA gene sequences discovered several new phylum-level groups in the bacterial phylogenetic domain and many previously undetected lower-level taxa. We determined an additional ∼119,000 nearly full-length sequences and 28,000 >200 nucleotide 454 reads from a 10-layer depth profile of the GN mat. With this unprecedented coverage of long sequences from one environment, we confirm the mat is phylogenetically stratified, presumably corresponding to light and geochemical gradients throughout the depth of the mat. Previous shotgun metagenomic data from the same depth profile show the same stratified pattern and suggest that metagenome properties may be predictable from rRNA gene sequences. We verify previously identified novel lineages and identify new phylogenetic diversity at lower taxonomic levels, for example, thousands of operational taxonomic units at the family-genus levels differ considerably from known sequences. The new sequences populate parts of the bacterial phylogenetic tree that previously were poorly described, but indicate that any comprehensive survey of GN diversity has only begun. Finally, we show that taxonomic conclusions are generally congruent between Sanger and 454 sequencing technologies, with the taxonomic resolution achieved dependent on the abundance of reference sequences in the relevant region of the rRNA tree of life.}, } @article {pmid22831283, year = {2012}, author = {Ismail, IH and Oppedisano, F and Joseph, SJ and Boyle, RJ and Licciardi, PV and Robins-Browne, RM and Tang, ML}, title = {Reduced gut microbial diversity in early life is associated with later development of eczema but not atopy in high-risk infants.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {23}, number = {7}, pages = {674-681}, doi = {10.1111/j.1399-3038.2012.01328.x}, pmid = {22831283}, issn = {1399-3038}, mesh = {Biodiversity ; DNA, Bacterial/*analysis ; Eczema/etiology/immunology/*microbiology/prevention & control ; Feces/chemistry/microbiology ; Follow-Up Studies ; Humans ; Hypersensitivity, Immediate/complications/diet therapy/immunology/*microbiology ; Infant ; Infant, Newborn ; Intestines/*microbiology ; *Metagenome/genetics/immunology ; Parents ; Probiotics ; Prospective Studies ; Risk ; }, abstract = {BACKGROUND: Alterations in intestinal microflora have been linked to the development of allergic disease. Recent studies suggest that healthy infant immune development may depend on the establishment of a diverse gut microbiota rather than the presence or absence of specific microbial strains.

OBJECTIVES: We investigated the relationship between diversity of gut microbiota in the early postnatal period and subsequent development of eczema and atopy in the first year of life.

METHODS: Fecal samples were collected 1 wk after birth from 98 infants at high risk of allergic disease, who were followed prospectively to age 12 months. Fecal microbial diversity was assessed by terminal restriction fragment length polymorphism (T-RFLP) using restriction enzymes Sau96I and AluI, with a greater number of peaks representing greater diversity of bacterial communities.

RESULTS: Microbial diversity at day 7 was significantly lower in infants with eczema at age 12 months as compared to infants without eczema (AluI mean number of peaks 13.1 vs. 15.5, p = 0.003, 95% CI for difference in means -3.9, -0.8; Sau96I 14.7 vs. 17.2, p = 0.03, 95% CI -4.9, -0.3). No differences were observed for atopic compared to non-atopic infants, or infants with two allergic parents compared to those with one or no allergic parent.

CONCLUSIONS: A more diverse intestinal microbiota in the first week of life is associated with a reduced risk of subsequent eczema in infants at increased risk of allergic disease. Interventions that enhance microbial diversity in early life may provide an effective means for the prevention of eczema in high-risk infants.}, } @article {pmid22828641, year = {2012}, author = {García-López, R and Pérez-Brocal, V and Diez-Domingo, J and Moya, A}, title = {Gut microbiota in children vaccinated with rotavirus vaccine.}, journal = {The Pediatric infectious disease journal}, volume = {31}, number = {12}, pages = {1300-1302}, doi = {10.1097/INF.0b013e318269e3ec}, pmid = {22828641}, issn = {1532-0987}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Infant ; Male ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Rotavirus Infections/*prevention & control ; Rotavirus Vaccines/*administration & dosage ; Sequence Analysis, DNA ; Vaccines, Attenuated/administration & dosage ; }, abstract = {To assess the effect that the rotavirus vaccine RotaTeq may have on the gut microbiota, this study searched for differences in intestinal bacterial composition between vaccinated and unvaccinated children. Bacterial diversity in fecal samples was evaluated by pyrosequencing of the 16S rRNA gene and taxonomic analyses using bioinformatics tools. No evidence of such differences was observed.}, } @article {pmid22827264, year = {2013}, author = {Smedile, F and Messina, E and La Cono, V and Tsoy, O and Monticelli, LS and Borghini, M and Giuliano, L and Golyshin, PN and Mushegian, A and Yakimov, MM}, title = {Metagenomic analysis of hadopelagic microbial assemblages thriving at the deepest part of Mediterranean Sea, Matapan-Vavilov Deep.}, journal = {Environmental microbiology}, volume = {15}, number = {1}, pages = {167-182}, doi = {10.1111/j.1462-2920.2012.02827.x}, pmid = {22827264}, issn = {1462-2920}, mesh = {Alteromonas/classification/enzymology/*genetics ; Archaea/classification/enzymology/*genetics ; Autotrophic Processes ; *Biodiversity ; Ecosystem ; *Environmental Microbiology ; Greece ; Mediterranean Sea ; *Metagenome ; *Metagenomics ; Oceans and Seas ; Phylogeny ; Seawater/microbiology ; Viruses/classification/genetics ; }, abstract = {The marine pelagic zone situated > 200 m below the sea level (bls) is the largest marine subsystem, comprising more than two-thirds of the oceanic volume. At the same time, it is one of the least explored ecosystems on Earth. Few large-scale environmental genomics studies have been undertaken to examine the phylogenetic diversity and functional gene repertoire of planktonic microbes present in mesopelagic and bathypelagic environments. Here, we present the description of the deep-sea microbial community thriving at > 4900 m depth in Matapan-Vavilov Deep (MVD). This canyon is the deepest site of Mediterranean Sea, with a deepest point located at approximately 5270 m, 56 km SW of city Pylos (Greece) in the Ionian Sea (36°34.00N, 21°07.44E). Comparative analysis of whole-metagenomic data revealed that unlike other deep-sea metagenomes, the prokaryotic diversity in MVD was extremely poor. The decline in the dark primary production rates, measured at 4908 m depth, was coincident with overwhelming dominance of copiotrophic Alteromonas macleodii'deep-ecotype' AltDE at the expense of other prokaryotes including those potentially involved in both autotrophic and anaplerotic CO(2) fixation. We also demonstrate the occurrence in deep-sea metagenomes of several clustered regularly interspaced short palindromic repeats systems.}, } @article {pmid22826704, year = {2012}, author = {Biller, SJ and Mosier, AC and Wells, GF and Francis, CA}, title = {Global Biodiversity of Aquatic Ammonia-Oxidizing Archaea is Partitioned by Habitat.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {252}, pmid = {22826704}, issn = {1664-302X}, abstract = {Archaea play an important role in nitrification and are, thus, inextricably linked to the global carbon and nitrogen cycles. Since the initial discovery of an ammonia monooxygenase α-subunit (amoA) gene associated with an archaeal metagenomic fragment, archaeal amoA sequences have been detected in a wide variety of nitrifying environments. Recent sequencing efforts have revealed extensive diversity of archaeal amoA sequences within different habitats. In this study, we have examined over 8000 amoA sequences from the literature and public databases in an effort to understand the ecological factors influencing the distribution and diversity of ammonia-oxidizing archaea (AOA), with a particular focus on sequences from aquatic habitats. This broad survey provides strong statistical support for the hypothesis that different environments contain distinct clusters of AOA amoA sequences, as surprisingly few sequences are found in more than one habitat type. Within aquatic environments, salinity, depth in the water column, and temperature were significantly correlated with the distribution of sequence types. These findings support the existence of multiple distinct aquatic AOA populations in the environment and suggest some possible selective pressures driving the partitioning of AOA amoA diversity.}, } @article {pmid22825498, year = {2012}, author = {Looft, T and Allen, HK}, title = {Collateral effects of antibiotics on mammalian gut microbiomes.}, journal = {Gut microbes}, volume = {3}, number = {5}, pages = {463-467}, pmid = {22825498}, issn = {1949-0984}, mesh = {Animals ; Anti-Bacterial Agents/*administration & dosage ; *Biota ; Escherichia coli/drug effects/growth & development ; Gastrointestinal Tract/*microbiology ; Gene Transfer, Horizontal/drug effects ; Humans ; Mammals ; Metagenome/*drug effects ; }, abstract = {Antibiotics are an essential component of the modern lifestyle. They improve our lives by treating disease, preventing disease, and in the case of agricultural animals by improving feed efficiency. However, antibiotic usage is not without collateral effects. The development and spread of antibiotic resistance is the most notorious concern associated with antibiotic use. New technologies have enabled the study of how the microbiota responds to the antibiotic disturbance, including how the community recovers after the antibiotic is removed. One common theme in studies of antibiotic effects is a rapid increase in Escherichia coli followed by a gradual decline. Increases in E. coli are also associated with systemic host stresses, and may be an indicator of ecosystem disturbances of the intestinal microbiota. Moreover, recent studies have shown additional effects mediated by antibiotics on the gut microbiota, such as the stimulation of gene transfer among gut bacteria and the reduction of immune responses in peripheral organs. Querying the microbiota after antibiotic treatment has led to intriguing hypotheses regarding predicting or mitigating unfavorable treatment outcomes. Here we explore the varied effects of antibiotics on human and animal microbiotas.}, } @article {pmid22817758, year = {2012}, author = {Pushalkar, S and Ji, X and Li, Y and Estilo, C and Yegnanarayana, R and Singh, B and Li, X and Saxena, D}, title = {Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {144}, pmid = {22817758}, issn = {1471-2180}, support = {DE019178/DE/NIDCR NIH HHS/United States ; DE020891/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/*classification/isolation & purification ; *Biodiversity ; Carcinoma, Squamous Cell/*microbiology/*pathology ; Cloning, Molecular ; Denaturing Gradient Gel Electrophoresis ; Female ; Humans ; Male ; Metagenome ; Middle Aged ; Mouth Mucosa/*microbiology ; Mouth Neoplasms/*microbiology/*pathology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Bacterial infections have been linked to malignancies due to their ability to induce chronic inflammation. We investigated the association of oral bacteria in oral squamous cell carcinoma (OSCC/tumor) tissues and compared with adjacent non-tumor mucosa sampled 5 cm distant from the same patient (n = 10). By using culture-independent 16S rRNA approaches, denaturing gradient gel electrophoresis (DGGE) and cloning and sequencing, we assessed the total bacterial diversity in these clinical samples.

RESULTS: DGGE fingerprints showed variations in the band intensity profiles within non-tumor and tumor tissues of the same patient and among the two groups. The clonal analysis indicated that from a total of 1200 sequences characterized, 80 bacterial species/phylotypes were detected representing six phyla, Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Actinobacteria and uncultivated TM7 in non-tumor and tumor libraries. In combined library, 12 classes, 16 order, 26 families and 40 genera were observed. Bacterial species, Streptococcus sp. oral taxon 058, Peptostreptococcus stomatis, Streptococcus salivarius, Streptococcus gordonii, Gemella haemolysans, Gemella morbillorum, Johnsonella ignava and Streptococcus parasanguinis I were highly associated with tumor site where as Granulicatella adiacens was prevalent at non-tumor site. Streptococcus intermedius was present in 70% of both non-tumor and tumor sites.

CONCLUSIONS: The underlying changes in the bacterial diversity in the oral mucosal tissues from non-tumor and tumor sites of OSCC subjects indicated a shift in bacterial colonization. These most prevalent or unique bacterial species/phylotypes present in tumor tissues may be associated with OSCC and needs to be further investigated with a larger sample size.}, } @article {pmid22815679, year = {2012}, author = {Tang, X and Freitak, D and Vogel, H and Ping, L and Shao, Y and Cordero, EA and Andersen, G and Westermann, M and Heckel, DG and Boland, W}, title = {Complexity and variability of gut commensal microbiota in polyphagous lepidopteran larvae.}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e36978}, pmid = {22815679}, issn = {1932-6203}, mesh = {Animal Feed/microbiology ; Animals ; Bacteria/*classification/genetics ; *Biodiversity ; In Situ Hybridization, Fluorescence ; Intestines/*microbiology ; Larva/growth & development/microbiology ; Lepidoptera/growth & development/*microbiology ; *Metagenome/genetics ; Oligonucleotide Array Sequence Analysis ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; Spatio-Temporal Analysis ; }, abstract = {BACKGROUND: The gut of most insects harbours nonpathogenic microorganisms. Recent work suggests that gut microbiota not only provide nutrients, but also involve in the development and maintenance of the host immune system. However, the complexity, dynamics and types of interactions between the insect hosts and their gut microbiota are far from being well understood.

METHODS/PRINCIPAL FINDINGS: To determine the composition of the gut microbiota of two lepidopteran pests, Spodoptera littoralis and Helicoverpa armigera, we applied cultivation-independent techniques based on 16S rRNA gene sequencing and microarray. The two insect species were very similar regarding high abundant bacterial families. Different bacteria colonize different niches within the gut. A core community, consisting of Enterococci, Lactobacilli, Clostridia, etc. was revealed in the insect larvae. These bacteria are constantly present in the digestion tract at relatively high frequency despite that developmental stage and diet had a great impact on shaping the bacterial communities. Some low-abundant species might become dominant upon loading external disturbances; the core community, however, did not change significantly. Clearly the insect gut selects for particular bacterial phylotypes.

CONCLUSIONS: Because of their importance as agricultural pests, phytophagous Lepidopterans are widely used as experimental models in ecological and physiological studies. Our results demonstrated that a core microbial community exists in the insect gut, which may contribute to the host physiology. Host physiology and food, nevertheless, significantly influence some fringe bacterial species in the gut. The gut microbiota might also serve as a reservoir of microorganisms for ever-changing environments. Understanding these interactions might pave the way for developing novel pest control strategies.}, } @article {pmid22806816, year = {2012}, author = {Liu, Y and Zuo, S and Zou, Y and Wang, J and Song, W}, title = {Investigation on diversity and population succession dynamics of indigenous bacteria of the maize spermosphere.}, journal = {World journal of microbiology & biotechnology}, volume = {28}, number = {1}, pages = {391-396}, pmid = {22806816}, issn = {1573-0972}, mesh = {Bacteria/classification/genetics/isolation & purification ; Base Sequence ; Biodiversity ; Ecosystem ; Endophytes/classification/genetics/*isolation & purification ; *Food Microbiology ; Genes, Bacterial ; Germination ; Metagenome ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seeds/microbiology ; Zea mays/growth & development/*microbiology ; }, abstract = {The spermosphere, an important habitat to the plant micro-ecosystem, has a unique significance to seed microbial ecology, but has been poorly researched. In this study, the mature seeds of reciprocal cross maize (Zea mays L., Nongda108) were collected to investigate the diversity and population succession dynamics of indigenous spermosphere bacteria at 12, 24 and 36 h into seed germination using 16S rDNA library construction. In the spermosphere of Nongda108A (Huang C × 178), the dominant bacteria genera identified were Pseudomonas and Burkholderia. The proportion of Pseudomonas increased from 59.60 to 75.00% then 82.61%; while Burkholderia decreased from 39.39 to 25.00% then 15.22% at 12, 24 and 36 h, respectively. Bacillus, Paenibacillus and Stenotrophomonas were the dominant genera in Nongda108B. The proportion of Paenibacillus after 12, 24 and 36 h into germination decreased from 68.00 to 46.15 to 13.27%, respectively. The proportion of non-Paenibacillus genera increased from 32.00 (Stenotrophomonas) to 53.85 (Bacillus) to 77.55% (Burkholderia) from 12 h to 24 h to 36 h, respectively. Some dominant bacteria genera identified from maize spermosphere have been identified as common PGPR.}, } @article {pmid22806799, year = {2012}, author = {Wu, L and Ge, G and Zhu, G and Gong, S and Li, S and Wan, J}, title = {Diversity and composition of the bacterial community of Poyang Lake (China) as determined by 16S rRNA gene sequence analysis.}, journal = {World journal of microbiology & biotechnology}, volume = {28}, number = {1}, pages = {233-244}, pmid = {22806799}, issn = {1573-0972}, mesh = {Bacteria/classification/*genetics/*isolation & purification ; Base Sequence ; Biodiversity ; China ; Ecosystem ; Genes, Bacterial ; Lakes/*microbiology ; Metagenome ; Phylogeny ; Plankton/genetics/isolation & purification ; Polymorphism, Restriction Fragment Length ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Poyang Lake is the largest fresh water lake in China. In this study, the objective was to examine the diversity of bacterial community in this environment. The phylogenetic composition of bacterioplankton communities from two sites and two dates (northern and southern sub-basins in October 2006 and in May 2007, respectively) in the water column of Poyang Lake were investigated by partially sequencing cloned 16SrRNA genes. Moreover, restriction fragment length polymorphism (RFLP) was applied in the 16SrRNA gene clones. In total, four clone libraries were constructed and 347 clones were screened by RFLP, yielding 153 operational taxonomic units, which mainly belonged to the proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Verrucomicrobia and Planctomycetes. Our results showed that Beta-proteobacteria was the most significant lineage, with dominant numbers of operational taxonomic units in the northern October 2006, southern October 2006 and May 2007 libraries. The highest bacterial diversity occurred in the library from the southern sub-basin in May 2007 and the lowest in the library from the northern sub-basin in May 2007. Horizontal and temporal differences associated with the concentration of total phosphorus, water temperature and pH suggested that the trophic state and the physicochemical properties of lake play key roles in sustaining bacterial community composition structure.}, } @article {pmid22806796, year = {2012}, author = {Chen, X and Su, Y and He, X and Wei, Y and Wei, W and Wu, J}, title = {Soil bacterial community composition and diversity respond to cultivation in Karst ecosystems.}, journal = {World journal of microbiology & biotechnology}, volume = {28}, number = {1}, pages = {205-213}, pmid = {22806796}, issn = {1573-0972}, mesh = {Agriculture ; Bacteria/classification/*genetics/*isolation & purification ; Biodiversity ; China ; *Ecosystem ; *Metagenome ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Soil/analysis ; *Soil Microbiology ; Trees ; }, abstract = {Soil microorganisms play vital roles in recovering and maintaining the health of ecosystems, particularly in fragile Karst ecosystems that are easily degraded after cultivation. We investigated the composition and diversity of soil bacterial communities, based on RFLP and 16S rDNA sequencing, in a cropland, a naturally revegetated land with former cultivation disturbance and a primeval forest in the subtropical Karst of southwest China. Our results illustrated that Proteobacteria accounted for 44.8% of the 600 tested clones, making it the most dominant phylum observed. This phylum was followed by Acidobacteria and Planctomycetes for the three Karst soils analyzed. Compared with the primeval forest soil, the proportions of Proteobacteria were decreased by 30.2 and 37.9%, while Acidobacteria increased by 93.9 and 87.9%, and the Shannon-Wiener diversity indices and the physicochemical parameters declined in the cropland and the revegetated land, respectively. Among the three soils, the proportion of dominant bacterial phyla and the diversity indices in the revegetated land were similar to the cropland, implying the bacterial community in the cropland was relatively stable, and the after-effects of cultivation were difficult to eliminate. However, similar distributions of the four Proteobacteria subphyla were observed between the revegetated land and the primeval forest soil. Furthermore, the proportion of Rhizobiales belonging to α-Proteobacteria was sharply decreased with cultivation compared to the primeval forest soil, while a small cluster of Rhizobiales recurred with vegetation recovery. These results indicated that although the subphyla of the dominant bacterial phylum had some positive responses to 20 years of vegetation recovery, it is a slow process. Our results suggest that priority should be given to conserve the primeval forest and inoculation of functional microorganisms on the basis of vegetation recovery may be more effective for the restoration of Karst ecosystems after cultivation.}, } @article {pmid22806049, year = {2012}, author = {Qi, X and Wang, E and Xing, M and Zhao, W and Chen, X}, title = {Rhizosphere and non-rhizosphere bacterial community composition of the wild medicinal plant Rumex patientia.}, journal = {World journal of microbiology & biotechnology}, volume = {28}, number = {5}, pages = {2257-2265}, pmid = {22806049}, issn = {1573-0972}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; China ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Molecular Sequence Data ; Phylogeny ; Plant Roots/*microbiology ; Plants, Medicinal/microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Rumex/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {To investigate bacterial communities between rhizosphere and non-rhizosphere soils of the wild medicinal plant Rumex patientia of Jilin, China, small subunit rRNAs (16S rDNA) from soil metagenome were amplified by polymerase chain reaction using primers specific to the domain bacteria and analysed by cloning and sequencing. The relative proportion of bacterial communities in rhizosphere soils was similar to non-rhizosphere soils in five phylogenetic groups (Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi and Planctomycetes). But there were differences in five other phylogenetic groups (Firmicutes, Bacteroidetes, Gemmatimonadetes, Verrucomicrobia and Unclassified bacteria). Over 97.24 % of the sequenced clones were found to be unique to rhizosphere and non-rhizosphere soils, while 2.76 % were shared by both of them. Our results indicate that there are differences in the composition and proportion of bacterial communities between rhizosphere and non-rhizosphere soils. Furthermore, the unique bacterial clones between rhizosphere and non-rhizosphere soils of the wild medicinal plant R. patientia have obvious differences.}, } @article {pmid22806023, year = {2012}, author = {Pangallo, D and Kraková, L and Chovanová, K and Simonovičová, A and De Leo, F and Urzì, C}, title = {Analysis and comparison of the microflora isolated from fresco surface and from surrounding air environment through molecular and biodegradative assays.}, journal = {World journal of microbiology & biotechnology}, volume = {28}, number = {5}, pages = {2015-2027}, pmid = {22806023}, issn = {1573-0972}, mesh = {Bacteria/classification/genetics/*isolation & purification/metabolism ; *Biota ; Biotransformation ; Cluster Analysis ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; *Environmental Microbiology ; Fungi/classification/genetics/*isolation & purification/metabolism ; Genetic Variation ; Metabolic Networks and Pathways ; Metagenome ; *Paintings ; Polymerase Chain Reaction ; Proteolysis ; }, abstract = {The aim of this study was to find a correlation among the environmental isolated microflora and the fresco colonizators through the investigation of their biodegradative abilities and DNA characteristics. A molecular technique named RAMP (Random Amplified Microsatellite Polymorphisms) was utilized in order to analyze the DNA diversity of bacterial and fungal species isolated from fresco as well as from air samples. The RAMP-PCR results were combined with the screening of some biodegradative properties obtained through the use of specific agar plate assays detecting the proteolytic, solubilization and biomineralization abilities of the isolated microflora. This comparative analysis showed that only in few cases a direct link among the fresco and airborne isolates of specific microbial group existed. The investigation clearly evidenced that colonization of surface of Ladislav's fresco occurred in different time and by different strains than those observed at the moment of sampling campaign. Furthermore, the microflora investigation permitted the identification of taxonomically interesting bacteria with particular biodegradative properties, which had been less studied until now.}, } @article {pmid22805147, year = {2012}, author = {Boutin, S and Sevellec, M and Pavey, SA and Bernatchez, L and Derome, N}, title = {A fast, highly sensitive double-nested PCR-based method to screen fish immunobiomes.}, journal = {Molecular ecology resources}, volume = {12}, number = {6}, pages = {1027-1039}, doi = {10.1111/j.1755-0998.2012.03166.x}, pmid = {22805147}, issn = {1755-0998}, mesh = {Animals ; Bacteria/*classification/*genetics ; Bacteriological Techniques/*methods ; *Biodiversity ; Kidney/microbiology ; Lakes ; Metagenomics/*methods ; Polymerase Chain Reaction/*methods ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Salmonidae/*microbiology ; Sensitivity and Specificity ; Sequence Analysis, DNA ; }, abstract = {Efficient methods for constructing 16S tag amplicon libraries for pyrosequencing are needed for the rapid and thorough screening of infectious bacterial diversity from host tissue samples. Here we have developed a double-nested PCR methodology that generates 16S tag amplicon libraries from very small amounts of bacteria/host samples. This methodology was tested for 133 kidney samples from the lake whitefish Coregonus clupeaformis (Salmonidae) sampled in five different lake populations. The double-nested PCR efficiency was compared with two other PCR strategies: single primer pair amplification and simple nested PCR. The double-nested PCR was the only amplification strategy to provide highly specific amplification of bacterial DNA. The resulting 16S amplicon libraries were synthesized and pyrosequenced using 454 FLX technology to analyse the variation of pathogenic bacteria abundance. The proportion of the community sequenced was very high (Good's coverage estimator; mean = 95.4%). Furthermore, there were no significant differences of sequence coverage among samples. Finally, the occurrence of chimeric amplicons was very low. Therefore, the double-nested PCR approach provides a rapid, informative and cost-effective method for screening fish immunobiomes and most likely applicable to other low-density microbiomes as well.}, } @article {pmid22798356, year = {2012}, author = {Young, W and Roy, NC and Lee, J and Lawley, B and Otter, D and Henderson, G and McCann, MJ and Tannock, GW}, title = {Changes in bowel microbiota induced by feeding weanlings resistant starch stimulate transcriptomic and physiological responses.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {18}, pages = {6656-6664}, pmid = {22798356}, issn = {1098-5336}, mesh = {Animals ; *Biodiversity ; Colon ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Diet/*methods ; Electrophoresis ; Gastrointestinal Tract/*microbiology ; Intestinal Mucosa ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; Sequence Analysis, DNA ; Starch/*metabolism ; *Transcriptome ; }, abstract = {The ability to predictably engineer the composition of bowel microbial communities (microbiota) using dietary components is important because of the reported associations of altered microbiota composition with medical conditions. In a synecological study, weanling conventional Sprague-Dawley rats (21 days old) were fed a basal diet (BD) or a diet supplemented with resistant starch (RS) at 5%, 2.5%, or 1.25% for 28 days. Pyrosequencing of 16S rRNA genes and temporal temperature gradient electrophoresis (TTGE) profiles in the colonic digesta showed that rats fed RS had altered microbiota compositions due to blooms of Bacteroidetes and Actinobacteria. The altered microbiota was associated with changes in colonic short-chain fatty acid (SCFA) concentrations, colonic-tissue gene expression (Gsta2 and Ela1), and host physiology (serum metabolite profiles and colonic goblet cell numbers). Comparisons between germ-free and conventional rats showed that transcriptional and serum metabolite differences were mediated by the microbiota and were not the direct result of diet composition. Altered transcriptomic and physiological responses may reflect the young host's attempts to maintain homeostasis as a consequence of exposure to a new collection of bacteria and their associated biochemistry.}, } @article {pmid22796884, year = {2012}, author = {Faust, K and Raes, J}, title = {Microbial interactions: from networks to models.}, journal = {Nature reviews. Microbiology}, volume = {10}, number = {8}, pages = {538-550}, pmid = {22796884}, issn = {1740-1534}, mesh = {*Biota ; Humans ; Metagenomics/*methods ; *Microbial Interactions ; }, abstract = {Metagenomics and 16S pyrosequencing have enabled the study of ecosystem structure and dynamics to great depth and accuracy. Co-occurrence and correlation patterns found in these data sets are increasingly used for the prediction of species interactions in environments ranging from the oceans to the human microbiome. In addition, parallelized co-culture assays and combinatorial labelling experiments allow high-throughput discovery of cooperative and competitive relationships between species. In this Review, we describe how these techniques are opening the way towards global ecosystem network prediction and the development of ecosystem-wide dynamic models.}, } @article {pmid22794922, year = {2012}, author = {Berlec, A}, title = {Novel techniques and findings in the study of plant microbiota: search for plant probiotics.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {193-194}, number = {}, pages = {96-102}, doi = {10.1016/j.plantsci.2012.05.010}, pmid = {22794922}, issn = {1873-2259}, mesh = {Bacteria/*genetics ; Biodiversity ; *Metagenome ; Molecular Sequence Data ; Plant Components, Aerial/microbiology ; Plants/*microbiology ; Probiotics/*analysis ; Proteomics ; Rhizosphere ; Soil Microbiology ; Symbiosis ; }, abstract = {Plants live in intimate relationships with numerous microorganisms present inside or outside plant tissues. The plant exterior provides two distinct ecosystems, the rhizosphere (below ground) and the phyllosphere (above ground), both populated by microbial communities. Most studies on plant microbiota deal with pathogens or mutualists. This review focuses on plant commensal bacteria, which could represent a rich source of bacteria beneficial to plants, alternatively termed plant probiotics. Plant commensal bacteria have been addressed only recently with culture-independent studies. These use next-generation sequencing, DNA microarray technologies and proteomics to decipher microbial community composition and function. Diverse bacterial populations are described in both rhizosphere and phyllosphere of different plants. The microorganisms can emerge from neighboring environmental ecosystems at random; however their survival is regulated by the plant. Influences from the environment, such as pesticides, farming practice and atmosphere, also affect the composition of microbial communities. Apart from community composition studies, some functional studies have also been performed. These include identification of broad-substrate surface receptors and methanol utilization enzymes by the proteomic approach, as well as identification of bacterial species that are important mediators of disease-suppressive soil phenomenon. Experience from more advanced human microbial studies could provide useful information and is discussed in the context of methodology and common trends. Administration of microbial mixtures of whole communities, rather than individual species, is highlighted and should be considered in future agricultural applications.}, } @article {pmid22791237, year = {2012}, author = {Taubert, M and Vogt, C and Wubet, T and Kleinsteuber, S and Tarkka, MT and Harms, H and Buscot, F and Richnow, HH and von Bergen, M and Seifert, J}, title = {Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing, benzene-degrading microbial consortium.}, journal = {The ISME journal}, volume = {6}, number = {12}, pages = {2291-2301}, pmid = {22791237}, issn = {1751-7370}, mesh = {Bacterial Proteins/analysis ; Benzene/*metabolism ; Biodegradation, Environmental ; *Carbon Cycle ; Carbon Isotopes/analysis ; Groundwater/microbiology ; Isotope Labeling/*methods ; *Microbial Consortia ; Oxidation-Reduction ; Phylogeny ; Proteomics/*methods ; Sulfur-Reducing Bacteria/*metabolism ; }, abstract = {Benzene is a major contaminant in various environments, but the mechanisms behind its biodegradation under strictly anoxic conditions are not yet entirely clear. Here we analyzed a benzene-degrading, sulfate-reducing enrichment culture originating from a benzene-contaminated aquifer by a metagenome-based functional metaproteomic approach, using protein-based stable isotope probing (protein-SIP). The time-resolved, quantitative analysis of carbon fluxes within the community supplied with either (13)C-labeled benzene or (13)C-labeled carbonate yielded different functional groups of organisms, with their peptides showing specific time dependencies of (13)C relative isotope abundance indicating different carbon utilization. Through a detailed analysis of the mass spectrometric (MS) data, it was possible to quantify the utilization of the initial carbon source and the metabolic intermediates. The functional groups were affiliated to Clostridiales, Deltaproteobacteria and Bacteroidetes/Chlorobi. The Clostridiales-related organisms were involved in benzene degradation, putatively by fermentation, and additionally used significant amounts of carbonate as a carbon source. The other groups of organisms were found to perform diverse functions, with Deltaproteobacteria degrading fermentation products and Bacteroidetes/Chlorobi being putative scavengers feeding on dead cells. A functional classification of identified proteins supported this allocation and gave further insights into the metabolic pathways and the interactions between the community members. This example shows how protein-SIP can be applied to obtain temporal and phylogenetic information about functional interdependencies within microbial communities.}, } @article {pmid22790926, year = {2012}, author = {Nguyen, NH and Maruset, L and Uengwetwanit, T and Mhuantong, W and Harnpicharnchai, P and Champreda, V and Tanapongpipat, S and Jirajaroenrat, K and Rakshit, SK and Eurwilaichitr, L and Pongpattanakitshote, S}, title = {Identification and characterization of a cellulase-encoding gene from the buffalo rumen metagenomic library.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {76}, number = {6}, pages = {1075-1084}, doi = {10.1271/bbb.110786}, pmid = {22790926}, issn = {1347-6947}, mesh = {Amino Acid Sequence ; Animal Feed ; Animals ; Bacterial Proteins/genetics/*isolation & purification/metabolism ; Buffaloes ; Cellulases/genetics/*isolation & purification/metabolism ; Cloning, Molecular ; Enzyme Stability ; Gene Library ; Genetic Vectors ; Hydrogen-Ion Concentration ; Lignin/*metabolism ; *Metagenome ; Metagenomics ; Microbial Consortia/genetics ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Rumen/enzymology/microbiology ; Sequence Analysis, DNA ; Temperature ; Xylans/metabolism ; }, abstract = {Microorganisms residing in the rumens of cattle represent a rich source of lignocellulose-degrading enzymes, since their diet consists of plant-based materials that are high in cellulose and hemicellulose. In this study, a metagenomic library was constructed from buffalo rumen contents using pCC1FOS fosmid vector. Ninety-three clones from the pooled library of approximately 10,000 clones showed degrading activity against AZCL-HE-Cellulose, whereas four other clones showed activity against AZCL-Xylan. Contig analysis of pyrosequencing data derived from the selected strongly positive clones revealed 15 ORFs that were closely related to lignocellulose-degrading enzymes belonging to several glycosyl hydrolase families. Glycosyl hydrolase family 5 (GHF5) was the most abundant glycosyl hydrolase found, and a majority of the GHF5s in our metagenomes were closely related to several ruminal bacteria, especially ones from other buffalo rumen metagenomes. Characterization of BT-01, a selected clone with highest cellulase activity from the primary plate screening assay, revealed a cellulase encoding gene with optimal working conditions at pH 5.5 at 50 °C. Along with its stability over acidic pH, the capability efficiently to hydrolyze cellulose in feed for broiler chickens, as exhibited in an in vitro digestibility test, suggests that BT-01 has potential application as a feed supplement.}, } @article {pmid22782251, year = {2012}, author = {Sirohi, SK and Singh, N and Dagar, SS and Puniya, AK}, title = {Molecular tools for deciphering the microbial community structure and diversity in rumen ecosystem.}, journal = {Applied microbiology and biotechnology}, volume = {95}, number = {5}, pages = {1135-1154}, doi = {10.1007/s00253-012-4262-2}, pmid = {22782251}, issn = {1432-0614}, mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biota ; Ciliophora/classification/genetics ; *Ecosystem ; Fungi/classification/genetics ; Metagenomics/*methods ; Rumen/*microbiology ; }, abstract = {Rumen microbial community comprising of bacteria, archaea, fungi, and protozoa is characterized not only by the high population density but also by the remarkable diversity and the most complex microecological interactions existing in the biological world. This unprecedented biodiversity is quite far from full elucidation as only about 15-20 % of the rumen microbes are identified and characterized till date using conventional culturing and microscopy. However, the last two decades have witnessed a paradigm shift from cumbersome and time-consuming classical methods to nucleic acid-based molecular approaches for deciphering the rumen microbial community. These techniques are rapid, reproducible and allow both the qualitative and quantitative assessment of microbial diversity. This review describes the different molecular methods and their applications in elucidating the rumen microbial community.}, } @article {pmid22778901, year = {2012}, author = {Ghai, R and Hernandez, CM and Picazo, A and Mizuno, CM and Ininbergs, K and Díez, B and Valas, R and DuPont, CL and McMahon, KD and Camacho, A and Rodriguez-Valera, F}, title = {Metagenomes of Mediterranean coastal lagoons.}, journal = {Scientific reports}, volume = {2}, number = {}, pages = {490}, pmid = {22778901}, issn = {2045-2322}, mesh = {Bacteria ; Bacteriophages/genetics ; Base Composition ; Biodiversity ; Chlorophyta/genetics ; Ecosystem ; Fresh Water/chemistry/*microbiology ; Mediterranean Region ; *Metagenome ; Phylogeny ; Phytoplankton/microbiology ; RNA, Ribosomal, 16S/genetics ; Rhodopsin/genetics ; Seawater/chemistry/*microbiology ; Verrucomicrobia/genetics ; }, abstract = {Coastal lagoons, both hypersaline and freshwater, are common, but still understudied ecosystems. We describe, for the first time, using high throughput sequencing, the extant microbiota of two large and representative Mediterranean coastal lagoons, the hypersaline Mar Menor, and the freshwater Albufera de Valencia, both located on the south eastern coast of Spain. We show there are considerable differences in the microbiota of both lagoons, in comparison to other marine and freshwater habitats. Importantly, a novel uncultured sulfur oxidizing Alphaproteobacteria was found to dominate bacterioplankton in the hypersaline Mar Menor. Also, in the latter prokaryotic cyanobacteria were almost exclusively comprised by Synechococcus and no Prochlorococcus was found. Remarkably, the microbial community in the freshwaters of the hypertrophic Albufera was completely in contrast to known freshwater systems, in that there was a near absence of well known and cosmopolitan groups of ultramicrobacteria namely Low GC Actinobacteria and the LD12 lineage of Alphaproteobacteria.}, } @article {pmid22773646, year = {2012}, author = {Hewson, I and Barbosa, JG and Brown, JM and Donelan, RP and Eaglesham, JB and Eggleston, EM and LaBarre, BA}, title = {Temporal dynamics and decay of putatively allochthonous and autochthonous viral genotypes in contrasting freshwater lakes.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {18}, pages = {6583-6591}, pmid = {22773646}, issn = {1098-5336}, mesh = {*Biota ; Fresh Water/*virology ; Genotype ; Lakes ; Metagenome ; Viruses/*classification/*genetics ; }, abstract = {Aquatic viruses play important roles in the biogeochemistry and ecology of lacustrine ecosystems; however, their composition, dynamics, and interactions with viruses of terrestrial origin are less extensively studied. We used a viral shotgun metagenomic approach to elucidate candidate autochthonous (i.e., produced within the lake) and allochthonous (i.e., washed in from other habitats) viral genotypes for a comparative study of their dynamics in lake waters. Based on shotgun metagenomes prepared from catchment soil and freshwater samples from two contrasting lakes (Cayuga Lake and Fayetteville Green Lake), we selected two putatively autochthonous viral genotypes (phycodnaviruses likely infecting algae and cyanomyoviruses likely infecting picocyanobacteria) and two putatively allochthonous viral genotypes (geminiviruses likely infecting terrestrial plants and circoviruses infecting unknown hosts but common in soil libraries) for analysis by genotype-specific quantitative PCR (TaqMan) applied to DNAs from viruses in the viral size fraction of lake plankton, i.e., 0.2 μm > virus > 0.02 μm. The abundance of autochthonous genotypes largely reflected expected host abundance, while the abundance of allochthonous genotypes corresponded with rainfall and storm events in the respective catchments, suggesting that viruses with these genotypes may have been transported to the lake in runoff. The decay rates of allochthonous and autochthonous genotypes, assessed in incubations where all potential hosts were killed, were generally lower (0.13 to 1.50% h(-1)) than those reported for marine virioplankton but similar to those for freshwater virioplankton. Both allochthonous and autochthonous viral genotypes were detected at higher concentrations in subsurface sediments than at the water-sediment interface. Our data indicate that putatively allochthonous viruses are present in lake plankton and sediments, where their temporal dynamics reflect active transport to the lake during hydrological events and then decay once there.}, } @article {pmid22773627, year = {2012}, author = {Emerson, JB and Thomas, BC and Andrade, K and Allen, EE and Heidelberg, KB and Banfield, JF}, title = {Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {17}, pages = {6309-6320}, pmid = {22773627}, issn = {1098-5336}, mesh = {Archaea/virology ; Bacteria/virology ; *Biodiversity ; Lakes ; *Metagenome ; *Salinity ; Victoria ; Viruses/*classification/*genetics ; Water/*chemistry ; *Water Microbiology ; }, abstract = {Viruses of the Bacteria and Archaea play important roles in microbial evolution and ecology, and yet viral dynamics in natural systems remain poorly understood. Here, we created de novo assemblies from 6.4 Gbp of metagenomic sequence from eight community viral concentrate samples, collected from 12 h to 3 years apart from hypersaline Lake Tyrrell (LT), Victoria, Australia. Through extensive manual assembly curation, we reconstructed 7 complete and 28 partial novel genomes of viruses and virus-like entities (VLEs, which could be viruses or plasmids). We tracked these 35 populations across the eight samples and found that they are generally stable on the timescale of days and transient on the timescale of years, with some exceptions. Cross-detection of the 35 LT populations in three previously described haloviral metagenomes was limited to a few genes, and most previously sequenced haloviruses were not detected in our samples, though 3 were detected upon reducing our detection threshold from 90% to 75% nucleotide identity. Similar results were obtained when we applied our methods to haloviral metagenomic data previously reported from San Diego, CA: 10 contigs that we assembled from that system exhibited a variety of detection patterns on a timescale of weeks to 1 month but were generally not detected in LT. Our results suggest that most haloviral populations have a limited or, possibly, a temporally variable global distribution. This study provides high-resolution insight into viral biogeography and dynamics and it places "snapshot" viral metagenomes, collected at a single time and location, in context.}, } @article {pmid22768370, year = {2012}, author = {Gilbert, JA and Bao, Y and Wang, H and Sansone, SA and Edmunds, SC and Morrison, N and Meyer, F and Schriml, LM and Davies, N and Sterk, P and Wilkening, J and Garrity, GM and Field, D and Robbins, R and Smith, DP and Mizrachi, I and Moreau, C}, title = {Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012.}, journal = {Standards in genomic sciences}, volume = {6}, number = {2}, pages = {276-286}, pmid = {22768370}, issn = {1944-3277}, abstract = {This report details the outcome of the 13(th) Meeting of the Genomic Standards Consortium. The three-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on March 5-7, 2012, and was hosted by the Beijing Genomics Institute. The meeting, titled From Genomes to Interactions to Communities to Models, highlighted the role of data standards associated with genomic, metagenomic, and amplicon sequence data and the contextual information associated with the sample. To this end the meeting focused on genomic projects for animals, plants, fungi, and viruses; metagenomic studies in host-microbe interactions; and the dynamics of microbial communities. In addition, the meeting hosted a Genomic Observatories Network session, a Genomic Standards Consortium biodiversity working group session, and a Microbiology of the Built Environment session sponsored by the Alfred P. Sloan Foundation.}, } @article {pmid22768172, year = {2012}, author = {Di Camillo, CG and Luna, GM and Bo, M and Giordano, G and Corinaldesi, C and Bavestrello, G}, title = {Biodiversity of prokaryotic communities associated with the ectoderm of Ectopleura crocea (Cnidaria, Hydrozoa).}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e39926}, pmid = {22768172}, issn = {1932-6203}, mesh = {Animals ; Archaea/genetics/*growth & development/ultrastructure ; Bacteria/genetics/*growth & development/ultrastructure ; *Biodiversity ; DNA, Ribosomal/genetics ; Epidermis/*microbiology/ultrastructure ; Genes, Bacterial/genetics ; Geography ; Hydrozoa/*microbiology ; Metagenome/genetics ; Microscopy, Fluorescence ; Time Factors ; }, abstract = {The surface of many marine organisms is colonized by complex communities of microbes, yet our understanding of the diversity and role of host-associated microbes is still limited. We investigated the association between Ectopleura crocea (a colonial hydroid distributed worldwide in temperate waters) and prokaryotic assemblages colonizing the hydranth surface. We used, for the first time on a marine hydroid, a combination of electron and epifluorescence microscopy and 16S rDNA tag pyrosequencing to investigate the associated prokaryotic diversity. Dense assemblages of prokaryotes were associated with the hydrant surface. Two microbial morphotypes were observed: one horseshoe-shaped and one fusiform, worm-like. These prokaryotes were observed on the hydrozoan epidermis, but not in the portions covered by the perisarcal exoskeleton, and their abundance was higher in March while decreased in late spring. Molecular analyses showed that assemblages were dominated by Bacteria rather than Archaea. Bacterial assemblages were highly diversified, with up to 113 genera and 570 Operational Taxonomic Units (OTUs), many of which were rare and contributed to <0.4%. The two most abundant OTUs, likely corresponding to the two morphotypes present on the epidermis, were distantly related to Comamonadaceae (genus Delftia) and to Flavobacteriaceae (genus Polaribacter). Epibiontic bacteria were found on E. crocea from different geographic areas but not in other hydroid species in the same areas, suggesting that the host-microbe association is species-specific. This is the first detailed report of bacteria living on the hydrozoan epidermis, and indeed the first study reporting bacteria associated with the epithelium of E. crocea. Our results provide a starting point for future studies aiming at clarifying the role of this peculiar hydrozoan-bacterial association.}, } @article {pmid22768065, year = {2012}, author = {Papa, E and Docktor, M and Smillie, C and Weber, S and Preheim, SP and Gevers, D and Giannoukos, G and Ciulla, D and Tabbaa, D and Ingram, J and Schauer, DB and Ward, DV and Korzenik, JR and Xavier, RJ and Bousvaros, A and Alm, EJ}, title = {Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease.}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e39242}, pmid = {22768065}, issn = {1932-6203}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 DK092405/DK/NIDDK NIH HHS/United States ; T32 GM087237/GM/NIGMS NIH HHS/United States ; 1-R21-A1084032-01A1//PHS HHS/United States ; }, mesh = {Adolescent ; Adult ; Anti-Bacterial Agents/therapeutic use ; Biodiversity ; Child ; Child, Preschool ; Cohort Studies ; Colitis, Ulcerative/diagnosis/microbiology/pathology ; Crohn Disease/diagnosis/microbiology/pathology ; Demography ; Diagnosis, Differential ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology/*pathology ; Humans ; Inflammatory Bowel Diseases/classification/*diagnosis/drug therapy/*microbiology ; Leukocyte L1 Antigen Complex/metabolism ; Male ; *Metagenome/genetics ; Remission Induction ; Reproducibility of Results ; Severity of Illness Index ; Software ; Young Adult ; }, abstract = {BACKGROUND: Pediatric inflammatory bowel disease (IBD) is challenging to diagnose because of the non-specificity of symptoms; an unequivocal diagnosis can only be made using colonoscopy, which clinicians are reluctant to recommend for children. Diagnosis of pediatric IBD is therefore frequently delayed, leading to inappropriate treatment plans and poor outcomes. We investigated the use of 16S rRNA sequencing of fecal samples and new analytical methods to assess differences in the microbiota of children with IBD and other gastrointestinal disorders.

We applied synthetic learning in microbial ecology (SLiME) analysis to 16S sequencing data obtained from i) published surveys of microbiota diversity in IBD and ii) fecal samples from 91 children and young adults who were treated in the gastroenterology program of Children's Hospital (Boston, USA). The developed method accurately distinguished control samples from those of patients with IBD; the area under the receiver-operating-characteristic curve (AUC) value was 0.83 (corresponding to 80.3% sensitivity and 69.7% specificity at a set threshold). The accuracy was maintained among data sets collected by different sampling and sequencing methods. The method identified taxa associated with disease states and distinguished patients with Crohn's disease from those with ulcerative colitis with reasonable accuracy. The findings were validated using samples from an additional group of 68 patients; the validation test identified patients with IBD with an AUC value of 0.84 (e.g. 92% sensitivity, 58.5% specificity).

CONCLUSIONS/SIGNIFICANCE: Microbiome-based diagnostics can distinguish pediatric patients with IBD from patients with similar symptoms. Although this test can not replace endoscopy and histological examination as diagnostic tools, classification based on microbial diversity is an effective complementary technique for IBD detection in pediatric patients.}, } @article {pmid22752167, year = {2012}, author = {Juottonen, H and Hynninen, A and Nieminen, M and Tuomivirta, TT and Tuittila, ES and Nousiainen, H and Kell, DK and Yrjälä, K and Tervahauta, A and Fritze, H}, title = {Methane-cycling microbial communities and methane emission in natural and restored peatlands.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {17}, pages = {6386-6389}, pmid = {22752167}, issn = {1098-5336}, mesh = {*Biota ; Metagenome ; Methane/*metabolism ; Molecular Sequence Data ; Sequence Analysis, DNA ; *Soil Microbiology ; Time Factors ; }, abstract = {We addressed how restoration of forestry-drained peatlands affects CH(4)-cycling microbes. Despite similar community compositions, the abundance of methanogens and methanotrophs was lower in restored than in natural sites and correlated with CH(4) emission. Poor establishment of methanogens may thus explain low CH(4) emissions on restored peatlands even 10 to 12 years after restoration.}, } @article {pmid22746335, year = {2012}, author = {Ma, B and Forney, LJ and Ravel, J}, title = {Vaginal microbiome: rethinking health and disease.}, journal = {Annual review of microbiology}, volume = {66}, number = {}, pages = {371-389}, pmid = {22746335}, issn = {1545-3251}, support = {U01 AI070921/AI/NIAID NIH HHS/United States ; U19 AI084044/AI/NIAID NIH HHS/United States ; UH2 AI083264/AI/NIAID NIH HHS/United States ; UO1 AI070921/AI/NIAID NIH HHS/United States ; }, mesh = {*Biota ; Female ; Humans ; *Metagenome ; Vagina/*microbiology ; Vaginosis, Bacterial/*microbiology ; }, abstract = {Vaginal microbiota form a mutually beneficial relationship with their host and have a major impact on health and disease. In recent years our understanding of vaginal bacterial community composition and structure has significantly broadened as a result of investigators using cultivation-independent methods based on the analysis of 16S ribosomal RNA (rRNA) gene sequences. In asymptomatic, otherwise healthy women, several kinds of vaginal microbiota exist, the majority often dominated by species of Lactobacillus, while others are composed of a diverse array of anaerobic microorganisms. Bacterial vaginosis is the most common vaginal condition and is vaguely characterized as the disruption of the equilibrium of the normal vaginal microbiota. A better understanding of normal and healthy vaginal ecosystems that is based on their true function and not simply on their composition would help better define health and further improve disease diagnostics as well as the development of more personalized regimens to promote health and treat diseases.}, } @article {pmid22743759, year = {2012}, author = {Collado, MC and Cernada, M and Baüerl, C and Vento, M and Pérez-Martínez, G}, title = {Microbial ecology and host-microbiota interactions during early life stages.}, journal = {Gut microbes}, volume = {3}, number = {4}, pages = {352-365}, pmid = {22743759}, issn = {1949-0984}, mesh = {*Biota ; Gastrointestinal Tract/*microbiology ; Humans ; Immune System/*physiology ; Infant, Newborn ; *Metagenome ; }, abstract = {The role of human microbiota has been redefined during recent years and its physiological role is now much more important than earlier understood. Intestinal microbial colonization is essential for the maturation of immune system and for the developmental regulation of the intestinal physiology. Alterations in this process of colonization have been shown to predispose and increase the risk to disease later in life. The first contact of neonates with microbes is provided by the maternal microbiota. Moreover, mode of delivery, type of infant feeding and other perinatal factors can influence the establishment of the infant microbiota. Taken into consideration all the available information it could be concluded that the exposure to the adequate microbes early in gestation and neonatal period seems to have a relevant role in health. Maternal microbial environment affects maternal and fetal immune physiology and, of relevance, this interaction with microbes at the fetal-maternal interface could be modulated by specific microbes administered to the pregnant mother. Indeed, probiotic interventions aiming to reduce the risk of immune-mediated diseases may appear effective during early life.}, } @article {pmid22737213, year = {2012}, author = {Andreote, FD and Jiménez, DJ and Chaves, D and Dias, AC and Luvizotto, DM and Dini-Andreote, F and Fasanella, CC and Lopez, MV and Baena, S and Taketani, RG and de Melo, IS}, title = {The microbiome of Brazilian mangrove sediments as revealed by metagenomics.}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e38600}, pmid = {22737213}, issn = {1932-6203}, mesh = {Biodiversity ; Brazil ; Carbon Dioxide/metabolism ; DNA, Ribosomal/metabolism ; Databases, Factual ; Deltaproteobacteria/genetics ; Ecosystem ; Formaldehyde/metabolism ; Gammaproteobacteria/genetics ; Geologic Sediments/*microbiology ; Hydrogen Sulfide/chemistry ; Metagenome ; *Metagenomics ; Methane/chemistry/metabolism ; Models, Genetic ; Phylogeny ; Sequence Analysis, DNA ; Soil Microbiology ; Sulfur/chemistry/metabolism ; }, abstract = {Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04) in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H(2)S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments.}, } @article {pmid22730762, year = {2012}, author = {Tikhonovich, IA and Provorova, NA}, title = {[Development of symbiogenetic approaches for studying variation and heredity of superspecies systems].}, journal = {Genetika}, volume = {48}, number = {4}, pages = {437-450}, pmid = {22730762}, issn = {0016-6758}, mesh = {*Biological Evolution ; Biota ; Ecology ; Endophytes/*genetics ; Metagenome/*genetics ; Plants/genetics/*microbiology ; Soil Microbiology ; Symbiosis/*genetics ; }, abstract = {Based on the knowledge on the structural and functional organization, ecological potential, and evolution of symbiotic complexes, we suggest to formulate the subject, aims, and methodology of symbiogenetics as a science studying the genetic control of interspecies interactions. It is based on the view on the superspecies system of variation and heredity (symbiogenome) controlling the development of novel properties lacking in the unitary organisms and radically extending their adaptive potentials. Investigation of symbiogenomes represents the first step toward genetic analysis of microbiomes and metagenomes, which are superspecies hereditary systems responsible for developing the multicomponent complexes of biocenotic type, such as rumen microflora, endophytic and rhizospheric communities, soil microbial consortia. The approaches of symbiogenetics can be used for developing biotechnologies of integration of plants or animals with beneficial microbes ensuring host nutrition and development as well as resistance to biotic and abiotic stresses.}, } @article {pmid22729545, year = {2012}, author = {Gomez-Alvarez, V and Revetta, RP and Santo Domingo, JW}, title = {Metagenomic analyses of drinking water receiving different disinfection treatments.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {17}, pages = {6095-6102}, pmid = {22729545}, issn = {1098-5336}, mesh = {Archaea/classification/drug effects/genetics ; Bacteria/classification/drug effects/genetics ; *Biodiversity ; Chlorine/*pharmacology ; Disinfectants/*pharmacology ; Disinfection/*methods ; Drinking Water/*microbiology ; Eukaryota/classification/drug effects/genetics ; *Metagenome ; Sequence Analysis, DNA ; Viruses/classification/drug effects/genetics ; Water Purification/*methods ; }, abstract = {A metagenome-based approach was used to assess the taxonomic affiliation and function potential of microbial populations in free-chlorine-treated (CHL) and monochloramine-treated (CHM) drinking water (DW). In all, 362,640 (averaging 544 bp) and 155,593 (averaging 554 bp) pyrosequencing reads were analyzed for the CHL and CHM samples, respectively. Most annotated proteins were found to be of bacterial origin, although eukaryotic, archaeal, and viral proteins were also identified. Differences in community structure and function were noted. Most notably, Legionella-like genes were more abundant in the CHL samples while mycobacterial genes were more abundant in CHM samples. Genes associated with multiple disinfectant mechanisms were identified in both communities. Moreover, sequences linked to virulence factors, such as antibiotic resistance mechanisms, were observed in both microbial communities. This study provides new insights into the genetic network and potential biological processes associated with the molecular microbial ecology of DW microbial communities.}, } @article {pmid22727216, year = {2012}, author = {Gomez-Alvarez, V and Revetta, RP and Santo Domingo, JW}, title = {Metagenome analyses of corroded concrete wastewater pipe biofilms reveal a complex microbial system.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {122}, pmid = {22727216}, issn = {1471-2180}, mesh = {Archaea/classification/genetics ; Bacteria/*classification/genetics ; *Biodiversity ; *Biofilms ; Cluster Analysis ; *Environmental Microbiology ; Humans ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Viruses/classification/genetics ; Wastewater/*microbiology ; }, abstract = {BACKGROUND: Concrete corrosion of wastewater collection systems is a significant cause of deterioration and premature collapse. Failure to adequately address the deteriorating infrastructure networks threatens our environment, public health, and safety. Analysis of whole-metagenome pyrosequencing data and 16S rRNA gene clone libraries was used to determine microbial composition and functional genes associated with biomass harvested from crown (top) and invert (bottom) sections of a corroded wastewater pipe.

RESULTS: Taxonomic and functional analysis demonstrated that approximately 90% of the total diversity was associated with the phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The top (TP) and bottom pipe (BP) communities were different in composition, with some of the differences attributed to the abundance of sulfide-oxidizing and sulfate-reducing bacteria. Additionally, human fecal bacteria were more abundant in the BP communities. Among the functional categories, proteins involved in sulfur and nitrogen metabolism showed the most significant differences between biofilms. There was also an enrichment of genes associated with heavy metal resistance, virulence (protein secretion systems) and stress response in the TP biofilm, while a higher number of genes related to motility and chemotaxis were identified in the BP biofilm. Both biofilms contain a high number of genes associated with resistance to antibiotics and toxic compounds subsystems.

CONCLUSIONS: The function potential of wastewater biofilms was highly diverse with level of COG diversity similar to that described for soil. On the basis of the metagenomic data, some factors that may contribute to niche differentiation were pH, aerobic conditions and availability of substrate, such as nitrogen and sulfur. The results from this study will help us better understand the genetic network and functional capability of microbial members of wastewater concrete biofilms.}, } @article {pmid22727142, year = {2012}, author = {Ritari, J and Koskinen, K and Hultman, J and Kurola, JM and Kymäläinen, M and Romantschuk, M and Paulin, L and Auvinen, P}, title = {Molecular analysis of meso- and thermophilic microbiota associated with anaerobic biowaste degradation.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {121}, pmid = {22727142}, issn = {1471-2180}, mesh = {Archaea/*classification ; Bacteria/*classification ; *Biota ; Fungi/*classification ; *Medical Waste Disposal ; *Metagenome ; Methane/metabolism ; Microarray Analysis ; Organic Chemicals/metabolism ; Sequence Analysis, DNA ; Temperature ; }, abstract = {BACKGROUND: Microbial anaerobic digestion (AD) is used as a waste treatment process to degrade complex organic compounds into methane. The archaeal and bacterial taxa involved in AD are well known, whereas composition of the fungal community in the process has been less studied. The present study aimed to reveal the composition of archaeal, bacterial and fungal communities in response to increasing organic loading in mesophilic and thermophilic AD processes by applying 454 amplicon sequencing technology. Furthermore, a DNA microarray method was evaluated in order to develop a tool for monitoring the microbiological status of AD.

RESULTS: The 454 sequencing showed that the diversity and number of bacterial taxa decreased with increasing organic load, while archaeal i.e. methanogenic taxa remained more constant. The number and diversity of fungal taxa increased during the process and varied less in composition with process temperature than bacterial and archaeal taxa, even though the fungal diversity increased with temperature as well. Evaluation of the microarray using AD sample DNA showed correlation of signal intensities with sequence read numbers of corresponding target groups. The sensitivity of the test was found to be about 1%.

CONCLUSIONS: The fungal community survives in anoxic conditions and grows with increasing organic loading, suggesting that Fungi may contribute to the digestion by metabolising organic nutrients for bacterial and methanogenic groups. The microarray proof of principle tests suggest that the method has the potential for semiquantitative detection of target microbial groups given that comprehensive sequence data is available for probe design.}, } @article {pmid22725615, year = {2012}, author = {Kumagai, H and Maisawa, S and Tanaka, M and Takahashi, M and Takasago, Y and Nishijima, A and Watanabe, S}, title = {Intestinal microbiota and secretory immunoglobulin A in feces of exclusively breast-fed infants with blood-streaked stools.}, journal = {Microbiology and immunology}, volume = {56}, number = {10}, pages = {657-663}, doi = {10.1111/j.1348-0421.2012.00487.x}, pmid = {22725615}, issn = {1348-0421}, mesh = {Bacteria/classification/genetics/isolation & purification ; Bacteriological Techniques/methods ; *Biota ; *Breast Feeding ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Enzyme-Linked Immunosorbent Assay/methods ; Feces/*chemistry/*microbiology ; Female ; Humans ; Immunoglobulin A, Secretory/*analysis ; Infant ; Male ; Metagenomics/methods ; Phylogeny ; Proctocolitis/*immunology/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Episodes of blood-streaked stools are not uncommon in exclusively breast-fed infants under 6 months of age. Such bleeding is thought to be associated with food protein-induced proctocolitis, however the pathomechanism remains unclear. The aim of this study was to investigate intestinal microbiota and secretory immunoglobulin A in the feces of exclusively breast-fed infants with blood-streaked stools. Fecal specimens from 15 full-term infants with blood-streaked stools and 15 breast-fed healthy infants were studied and the results compared. All infants had been delivered vaginally and exclusively breast-fed. The fecal microbiota were investigated by phylogenetic analysis combined with culture methods for some bacterial species, and feces were assessed for the presence of fecal secretory immunoglobulin A by enzyme-linked immunosorbent assay. Phylogenetic cluster analysis revealed four major clusters of fecal bacteria, cluster A being found only in healthy infants. The Bacteroides fragilis group was observed more frequently in controls than in patients (P < 0.05). In the controls, the predominant species belonging to the Enterobacteriaceae group was Escherichia coli, whereas in the patients it was Klebsiella (P < 0.05). Concentrations of secretory immunoglobulin A were high in one third of the healthy controls. In conclusion, the pathomechanism of rectal bleeding in exclusively breast-fed infants may be related to differences in the composition of their intestinal flora.}, } @article {pmid22719831, year = {2012}, author = {Martin, J and Sykes, S and Young, S and Kota, K and Sanka, R and Sheth, N and Orvis, J and Sodergren, E and Wang, Z and Weinstock, GM and Mitreva, M}, title = {Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities.}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e36427}, pmid = {22719831}, issn = {1932-6203}, support = {U54HG004969/HG/NHGRI NIH HHS/United States ; NIH-NHGRI U54HG003079//PHS HHS/United States ; U54 AI084844/AI/NIAID NIH HHS/United States ; U54AI084844/AI/NIAID NIH HHS/United States ; U54 HG004968/HG/NHGRI NIH HHS/United States ; U54 HG003079/HG/NHGRI NIH HHS/United States ; U54 HG004969/HG/NHGRI NIH HHS/United States ; UH3 AI083263/AI/NIAID NIH HHS/United States ; U54HG004968/HG/NHGRI NIH HHS/United States ; NIH-NIAID UH3AI083263//PHS HHS/United States ; }, mesh = {Biodiversity ; Databases, Factual ; Humans ; *Metagenome ; *Metagenomics ; Phylogeny ; }, abstract = {The Human Microbiome Project (HMP) aims to characterize the microbial communities of 18 body sites from healthy individuals. To accomplish this, the HMP generated two types of shotgun data: reference shotgun sequences isolated from different anatomical sites on the human body and shotgun metagenomic sequences from the microbial communities of each site. The alignment strategy for characterizing these metagenomic communities using available reference sequence is important to the success of HMP data analysis. Six next-generation aligners were used to align a community of known composition against a database comprising reference organisms known to be present in that community. All aligners report nearly complete genome coverage (>97%) for strains with over 6X depth of coverage, however they differ in speed, memory requirement and ease of use issues such as database size limitations and supported mapping strategies. The selected aligner was tested across a range of parameters to maximize sensitivity while maintaining a low false positive rate. We found that constraining alignment length had more impact on sensitivity than does constraining similarity in all cases tested. However, when reference species were replaced with phylogenetic neighbors, similarity begins to play a larger role in detection. We also show that choosing the top hit randomly when multiple, equally strong mappings are available increases overall sensitivity at the expense of taxonomic resolution. The results of this study identified a strategy that was used to map over 3 tera-bases of microbial sequence against a database of more than 5,000 reference genomes in just over a month.}, } @article {pmid22719823, year = {2012}, author = {Li, K and Bihan, M and Yooseph, S and Methé, BA}, title = {Analyses of the microbial diversity across the human microbiome.}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e32118}, pmid = {22719823}, issn = {1932-6203}, support = {U54 AI084844/AI/NIAID NIH HHS/United States ; #AI084844/AI/NIAID NIH HHS/United States ; }, mesh = {Biodiversity ; Humans ; *Metagenome ; }, abstract = {Analysis of human body microbial diversity is fundamental to understanding community structure, biology and ecology. The National Institutes of Health Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine microbial diversity within and across body habitats and individuals through pyrosequencing-based profiling of 16 S rRNA gene sequences (16 S) from habits of the oral, skin, distal gut, and vaginal body regions from over 200 healthy individuals enabling the application of statistical techniques. In this study, two approaches were applied to elucidate the nature and extent of human microbiome diversity. First, bootstrap and parametric curve fitting techniques were evaluated to estimate the maximum number of unique taxa, S(max), and taxa discovery rate for habitats across individuals. Next, our results demonstrated that the variation of diversity within low abundant taxa across habitats and individuals was not sufficiently quantified with standard ecological diversity indices. This impact from low abundant taxa motivated us to introduce a novel rank-based diversity measure, the Tail statistic, ("τ"), based on the standard deviation of the rank abundance curve if made symmetric by reflection around the most abundant taxon. Due to τ's greater sensitivity to low abundant taxa, its application to diversity estimation of taxonomic units using taxonomic dependent and independent methods revealed a greater range of values recovered between individuals versus body habitats, and different patterns of diversity within habitats. The greatest range of τ values within and across individuals was found in stool, which also exhibited the most undiscovered taxa. Oral and skin habitats revealed variable diversity patterns, while vaginal habitats were consistently the least diverse. Collectively, these results demonstrate the importance, and motivate the introduction, of several visualization and analysis methods tuned specifically for next-generation sequence data, further revealing that low abundant taxa serve as an important reservoir of genetic diversity in the human microbiome.}, } @article {pmid22717885, year = {2012}, author = {Mason, OU and Hazen, TC and Borglin, S and Chain, PS and Dubinsky, EA and Fortney, JL and Han, J and Holman, HY and Hultman, J and Lamendella, R and Mackelprang, R and Malfatti, S and Tom, LM and Tringe, SG and Woyke, T and Zhou, J and Rubin, EM and Jansson, JK}, title = {Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill.}, journal = {The ISME journal}, volume = {6}, number = {9}, pages = {1715-1727}, pmid = {22717885}, issn = {1751-7370}, mesh = {Archaea/genetics/physiology ; Bacteria/genetics ; Biodiversity ; Gulf of Mexico ; Hydrocarbons/*metabolism ; *Metagenome ; Oceanospirillaceae/*genetics/*metabolism ; *Petroleum Pollution ; RNA, Ribosomal, 16S ; Seawater/*microbiology ; *Single-Cell Analysis ; *Transcriptome ; }, abstract = {The Deepwater Horizon oil spill in the Gulf of Mexico resulted in a deep-sea hydrocarbon plume that caused a shift in the indigenous microbial community composition with unknown ecological consequences. Early in the spill history, a bloom of uncultured, thus uncharacterized, members of the Oceanospirillales was previously detected, but their role in oil disposition was unknown. Here our aim was to determine the functional role of the Oceanospirillales and other active members of the indigenous microbial community using deep sequencing of community DNA and RNA, as well as single-cell genomics. Shotgun metagenomic and metatranscriptomic sequencing revealed that genes for motility, chemotaxis and aliphatic hydrocarbon degradation were significantly enriched and expressed in the hydrocarbon plume samples compared with uncontaminated seawater collected from plume depth. In contrast, although genes coding for degradation of more recalcitrant compounds, such as benzene, toluene, ethylbenzene, total xylenes and polycyclic aromatic hydrocarbons, were identified in the metagenomes, they were expressed at low levels, or not at all based on analysis of the metatranscriptomes. Isolation and sequencing of two Oceanospirillales single cells revealed that both cells possessed genes coding for n-alkane and cycloalkane degradation. Specifically, the near-complete pathway for cyclohexane oxidation in the Oceanospirillales single cells was elucidated and supported by both metagenome and metatranscriptome data. The draft genome also included genes for chemotaxis, motility and nutrient acquisition strategies that were also identified in the metagenomes and metatranscriptomes. These data point towards a rapid response of members of the Oceanospirillales to aliphatic hydrocarbons in the deep sea.}, } @article {pmid22717882, year = {2012}, author = {Delmont, TO and Simonet, P and Vogel, TM}, title = {Describing microbial communities and performing global comparisons in the 'omic era.}, journal = {The ISME journal}, volume = {6}, number = {9}, pages = {1625-1628}, pmid = {22717882}, issn = {1751-7370}, mesh = {Biodiversity ; *Computational Biology ; *Ecosystem ; *Environmental Microbiology ; Metagenome/genetics/*physiology ; }, } @article {pmid22713270, year = {2012}, author = {Nagy-Szakal, D and Ross, MC and Dowd, SE and Mir, SA and Schaible, TD and Petrosino, JF and Kellermayer, R}, title = {Maternal micronutrients can modify colonic mucosal microbiota maturation in murine offspring.}, journal = {Gut microbes}, volume = {3}, number = {5}, pages = {426-433}, pmid = {22713270}, issn = {1949-0984}, support = {K12 HD041648/HD/NICHD NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; DK56338/DK/NIDDK NIH HHS/United States ; 5K12 HD041648/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification/*drug effects/genetics ; *Biota ; Colon/*microbiology ; Feces/microbiology ; Female ; Metagenome ; Mice ; Mice, Inbred C57BL ; Micronutrients/*metabolism ; }, abstract = {Epidemiologic data suggest that early nutritional exposures may inflict persistent changes in the developing mammalian "super-organism" (i.e., the host and its residing microbiota). Such persistent modifications could predispose young adults to inflammatory bowel diseases (IBD). We recently observed that the dietary supplementation of four micronutrients to dams augmented colitis susceptibility in murine offspring in association with mucosal microbiota composition changes. In this study the effects of the four micronutrients on the microbiota of dams and female mice was examined. Additionally, age dependent microbiota composition shifts during pediatric development were delineated from the previous offspring data sets. Maternal and adult female microbiota did not separate secondary to the nutritional intervention. Significant microbiota composition changes occurred from postnatal day 30 (P30) to P90 at the level of 1 phylum and 15 genera. Most of these changes were absent or opposite in the maternally supplemented offspring. Nutritionally induced alterations in mucosal microbiota maturation may be contributors to colitis susceptibility in mammals.}, } @article {pmid22712623, year = {2012}, author = {Fritz, JI and Franke-Whittle, IH and Haindl, S and Insam, H and Braun, R}, title = {Microbiological community analysis of vermicompost tea and its influence on the growth of vegetables and cereals.}, journal = {Canadian journal of microbiology}, volume = {58}, number = {7}, pages = {836-847}, doi = {10.1139/w2012-061}, pmid = {22712623}, issn = {1480-3275}, mesh = {Animals ; *Biodiversity ; Hordeum/*growth & development/microbiology ; Metagenome/genetics/*physiology ; Oligochaeta ; Soil/chemistry ; *Soil Microbiology ; Time Factors ; Triticum/*growth & development/microbiology ; Vegetables/*growth & development/microbiology ; }, abstract = {Vermicompost, the digestion product of organic material by earthworms, has been widely reported to have a more positive effect on plant growth and plant health than conventional compost. A study was conducted to investigate the effects of different vermicompost elutriates (aerated compost teas) on soils and plant growth. The teas were analyzed by chemical, microbiological, and molecular methods accompanied by plant growth tests at laboratory and field scale. The number of microorganisms in the teas increased during the extraction process and was affected by substrate addition. The vermicompost tea found to increase plant growth best under laboratory tests was applied to cereals (wheat and barley) and vegetables (Raphanus sativus, Rucola selvatica, and Pisum sativum) in a field study. The results revealed no effects of tea application on plant yield; however, sensoric tests indicated an improvement in crop quality. The soils from laboratory and field studies were investigated to detect possible microbial or chemical changes. The results indicated that minor changes to the soil microbial community occurred following tea application by foliar spray in both the laboratory-scale and field-scale experiments.}, } @article {pmid22711827, year = {2012}, author = {Engel, P and Martinson, VG and Moran, NA}, title = {Functional diversity within the simple gut microbiota of the honey bee.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {27}, pages = {11002-11007}, pmid = {22711827}, issn = {1091-6490}, mesh = {Animals ; Bacteria/classification/*genetics ; Bees/*microbiology ; *Biodiversity ; Biofilms/growth & development ; Biological Evolution ; Carbohydrate Metabolism/physiology ; Genetic Variation ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Metagenome/*genetics ; Metagenomics/methods ; Molecular Sequence Data ; Pectins/metabolism ; Phylogeny ; Polygalacturonase/metabolism ; Symbiosis/*physiology ; }, abstract = {Animals living in social communities typically harbor a characteristic gut microbiota important for nutrition and pathogen defense. Accordingly, in the gut of the honey bee, Apis mellifera, a distinctive microbial community, composed of a taxonomically restricted set of species specific to social bees, has been identified. Despite the ecological and economical importance of honey bees and the increasing concern about population declines, the role of their gut symbionts for colony health and nutrition is unknown. Here, we sequenced the metagenome of the gut microbiota of honey bees. Unexpectedly, we found a remarkable degree of genetic diversity within the few bacterial species colonizing the bee gut. Comparative analysis of gene contents suggests that different species harbor distinct functional capabilities linked to host interaction, biofilm formation, and carbohydrate breakdown. Whereas the former two functions could be critical for pathogen defense and immunity, the latter one might assist nutrient utilization. In a γ-proteobacterial species, we identified genes encoding pectin-degrading enzymes likely involved in the breakdown of pollen walls. Experimental investigation showed that this activity is restricted to a subset of strains of this species providing evidence for niche specialization. Long-standing association of these gut symbionts with their hosts, favored by the eusocial lifestyle of honey bees, might have promoted the genetic and functional diversification of these bee-specific bacteria. Besides revealing insights into mutualistic functions governed by the microbiota of this important pollinator, our findings indicate that the honey bee can serve as a model for understanding more complex gut-associated microbial communities.}, } @article {pmid22711811, year = {2012}, author = {Stukenbrock, EH and Christiansen, FB and Hansen, TT and Dutheil, JY and Schierup, MH}, title = {Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {27}, pages = {10954-10959}, pmid = {22711811}, issn = {1091-6490}, mesh = {Ascomycota/classification/*genetics ; Chimera/*genetics ; *Evolution, Molecular ; Genes, Fungal/genetics ; Genome, Fungal/genetics ; Haplotypes ; Metagenomics ; Molecular Sequence Data ; Plant Diseases/*microbiology ; Selection, Genetic/genetics ; Triticum/*microbiology ; }, abstract = {In a genome alignment of five individuals of the ascomycete fungus Zymoseptoria pseudotritici, a close relative of the wheat pathogen Z. tritici (synonym Mycosphaerella graminicola), we observed peculiar diversity patterns. Long regions up to 100 kb without variation alternate with similarly long regions of high variability. The variable segments in the genome alignment are organized into two main haplotype groups that have diverged ∼3% from each other. The genome patterns in Z. pseudotritici are consistent with a hybrid speciation event resulting from a cross between two divergent haploid individuals. The resulting hybrids formed the new species without backcrossing to the parents. We observe no variation in 54% of the genome in the five individuals and estimate a complete loss of variation for at least 30% of the genome in the entire species. A strong population bottleneck following the hybridization event caused this loss of variation. Variable segments in the Z. pseudotritici genome exhibit the two haplotypes contributed by the parental individuals. From our previously estimated recombination map of Z. tritici and the size distribution of variable chromosome blocks untouched by recombination we estimate that the hybridization occurred ∼380 sexual generations ago. We show that the amount of lost variation is explained by genetic drift during the bottleneck and by natural selection, as evidenced by the correlation of presence/absence of variation with gene density and recombination rate. The successful spread of this unique reproductively isolated pathogen highlights the strong potential of hybridization in the emergence of pathogen species with sexual reproduction.}, } @article {pmid22711422, year = {2012}, author = {Valverde, A and Tuffin, M and Cowan, DA}, title = {Biogeography of bacterial communities in hot springs: a focus on the actinobacteria.}, journal = {Extremophiles : life under extreme conditions}, volume = {16}, number = {4}, pages = {669-679}, pmid = {22711422}, issn = {1433-4909}, mesh = {*Actinobacteria/cytology/genetics/growth & development ; *Biodiversity ; Hot Springs/*microbiology ; Hot Temperature ; Hydrogen-Ion Concentration ; Phylogeography/methods ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; }, abstract = {Actinobacteria are ubiquitous in soil, freshwater and marine ecosystems. Although various studies have focused on the microbial ecology of this phylum, data are scant on the ecology of actinobacteria endemic to hot springs. Here, we have investigated the molecular diversity of eubacteria, with specific focus on the actinobacteria in hot springs in Zambia, China, New Zealand and Kenya. Temperature and pH values at sampling sites ranged between 44.5 and 86.5 °C and 5-10, respectively. Non-metric multidimensional scaling analysis of 16S rRNA gene T-RFLP patterns showed that samples could be separated by geographical location. Multivariate analysis showed that actinobacterial community composition was best predicted by changes in pH and temperature, whereas temperature alone was the most important variable explaining differences in bacterial community structure. Using 16S rRNA gene libraries, 28 major actinobacterial OTUs were found. Both molecular techniques indicated that many of the actinobacterial phylotypes were unique and exclusive to the respective sample. Collectively, these results support the view that both actinobacterial diversity and endemism are high in hot spring ecosystems.}, } @article {pmid22711164, year = {2013}, author = {Serino, M and Fernández-Real, JM and García-Fuentes, E and Queipo-Ortuño, M and Moreno-Navarrete, JM and Sánchez, A and Burcelin, R and Tinahones, F}, title = {The gut microbiota profile is associated with insulin action in humans.}, journal = {Acta diabetologica}, volume = {50}, number = {5}, pages = {753-761}, pmid = {22711164}, issn = {1432-5233}, mesh = {Adult ; Case-Control Studies ; DNA, Bacterial/analysis ; DNA, Fungal/analysis ; Diet, High-Fat ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Insulin/*metabolism ; *Insulin Resistance ; Male ; Metagenome/physiology ; Microarray Analysis ; Microbiota/*physiology ; Middle Aged ; Obesity/complications/metabolism/microbiology ; Transcriptome ; }, abstract = {The role of the gut microbiota in the induction of metabolic diseases has now been increasingly recognized worldwide. Indeed, a specific gut microbiota has been shown to characterize lean versus obese phenotypes both in humans and mice. We have also recently demonstrated that a precise gut microbiota is associated with the host's responsiveness to a high-fat diet. Therefore, we hypothesized that insulin resistance in humans could also be linked to a specific gut microbiota. To this aim, microbial DNA and RNA were extracted from the appendix contents of insulin-resistant versus insulin-sensitive obese subjects, matched for body mass index and age, and analyzed by DNA- and RNA-DGGE. Microbial DNA analysis showed that the patients fully segregated according to their degree of insulin action. Conversely, microbial RNA investigation showed that some degree of homology still existed between insulin-sensitive and insulin-resistant patients. Quantitative trait analysis, ordinary least squares regression, principal components regression, partial least squares, canonical correlation analysis, and canonical correspondence analysis also showed a net separation of the two phenotypes analyzed. We conclude that a specific gut microbial profile is associated with insulin action in humans.}, } @article {pmid22707521, year = {2012}, author = {Stressmann, FA and Rogers, GB and van der Gast, CJ and Marsh, P and Vermeer, LS and Carroll, MP and Hoffman, L and Daniels, TW and Patel, N and Forbes, B and Bruce, KD}, title = {Long-term cultivation-independent microbial diversity analysis demonstrates that bacterial communities infecting the adult cystic fibrosis lung show stability and resilience.}, journal = {Thorax}, volume = {67}, number = {10}, pages = {867-873}, doi = {10.1136/thoraxjnl-2011-200932}, pmid = {22707521}, issn = {1468-3296}, mesh = {Adult ; Anti-Bacterial Agents/pharmacology ; Bacterial Load/drug effects ; Biodiversity ; Cystic Fibrosis/drug therapy/*microbiology/physiopathology ; Disease Progression ; Female ; Humans ; Male ; Metagenome ; Polymorphism, Restriction Fragment Length ; Principal Component Analysis ; Respiratory System/*microbiology ; Sputum/*microbiology ; }, abstract = {BACKGROUND: Culture-independent analysis of the respiratory secretions of people with cystic fibrosis (CF) has identified many bacterial species not previously detected using culture in this context. However, little is known about their clinical significance or persistence in CF airways.

METHODS: The authors characterised the viable bacterial communities in the sputum collected from 14 patients at monthly intervals over 1 year using a molecular community profiling technique-terminal restriction fragment length polymorphism. Clinical characteristics were also collected, including lung function and medications. Ecological community measures were determined for each sample. Microbial community change over time within subjects was defined using ecological analytical tools, and these measures were compared between subjects and to clinical features.

RESULTS: Bacterial communities were stable within subjects over time but varied between subjects, despite similarities in clinical course. Antibiotic therapy temporarily perturbed these communities which generally returned to pretreatment configurations within 1 month. Species usually considered CF pathogens and those not previously regarded as such exhibited similar patterns of persistence. Less diverse sputum bacterial communities were correlated to lung disease severity and relative abundance of Pseudomonas aeruginosa.

CONCLUSION: Whilst not true in all cases, the microbial communities that chronically infect the airways of patients with CF can vary little over a year despite antibiotic perturbation. The species present tended to vary more between than within subjects, suggesting that each CF airway infection is unique, with relatively stable and resilient bacterial communities. The inverse relationship between community richness and disease severity is similar to findings reported in other mucosal infections.}, } @article {pmid22706066, year = {2012}, author = {Trias, R and Ruiz-Rueda, O and García-Lledó, A and Vilar-Sanz, A and López-Flores, R and Quintana, XD and Hallin, S and Bañeras, L}, title = {Emergent macrophytes act selectively on ammonia-oxidizing bacteria and archaea.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {17}, pages = {6352-6356}, pmid = {22706066}, issn = {1098-5336}, mesh = {Ammonia/*metabolism ; Archaea/*classification/*genetics/metabolism ; Bacteria/*classification/*genetics/metabolism ; Biodiversity ; Hydrogen-Ion Concentration ; Metagenome ; Oxidation-Reduction ; Plant Roots/*microbiology ; Wetlands ; }, abstract = {Ammonia-oxidizing bacteria (AOB) and archaea (AOA) were quantified in the sediments and roots of dominant macrophytes in eight neutral to alkaline coastal wetlands. The AOA dominated in most samples, but the bacterial-to-archaeal amoA gene ratios increased with increasing ammonium levels and pH in the sediments. For all plant species, the ratios increased on the root surface relative to the adjacent bulk sediment. This suggests that root surfaces in these environments provide conditions favoring enrichment of AOB.}, } @article {pmid22706048, year = {2012}, author = {Lee, HJ and Jung, JY and Oh, YK and Lee, SS and Madsen, EL and Jeon, CO}, title = {Comparative survey of rumen microbial communities and metabolites across one caprine and three bovine groups, using bar-coded pyrosequencing and [1]H nuclear magnetic resonance spectroscopy.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {17}, pages = {5983-5993}, pmid = {22706048}, issn = {1098-5336}, mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biota ; Cattle ; *DNA Barcoding, Taxonomic ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Goats ; Korea ; *Magnetic Resonance Spectroscopy ; *Metabolome ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; *Sequence Analysis, DNA ; }, abstract = {Pyrosequencing of 16S rRNA genes (targeting Bacteria and Archaea) and (1)H nuclear magnetic resonance were applied to investigate the rumen microbiota and metabolites of Hanwoo steers in the growth stage (HGS), Hanwoo steers in the late fattening stage (HFS), Holstein-Friesian dairy cattle (HDC), and Korean native goats (KNG) in the late fattening stage. This was a two-part investigation. We began by comparing metabolites and microbiota of Hanwoo steers at two stages of husbandry. Statistical comparisons of metabolites and microbial communities showed no significant differences between HFS and HGS (differing by a dietary shift at 24 months and age [67 months versus 12 months]). We then augmented the study by extending the investigation to HDC and KNG. Overall, pyrosequencing of 16S rRNA genes showed that the rumens had highly diverse microbial communities containing many previously undescribed microorganisms. Bioinformatic analysis revealed that the bacterial sequences were predominantly affiliated with four phyla-Bacteroidetes, Firmicutes, Fibrobacteres, and Proteobacteria-in all ruminants. However, interestingly, the bacterial reads belonging to Fibrobacteres were present at a very low abundance (<0.1%) in KNG. Archaeal community analysis showed that almost all of these reads fell into a clade related to, but distinct from, known cultivated methanogens. Statistical analyses showed that the microbial communities and metabolites of KNG were clearly distinct from those of other ruminants. In addition, bacterial communities and metabolite profiles of HGS and HDC, fed similar diets, were distinctive. Our data indicate that bovine host breeds override diet as the key factor that determines bacterial community and metabolite profiles in the rumen.}, } @article {pmid22705839, year = {2012}, author = {Ikuma, K and Gunsch, CK}, title = {Genetic bioaugmentation as an effective method for in situ bioremediation: functionality of catabolic plasmids following conjugal transfers.}, journal = {Bioengineered}, volume = {3}, number = {4}, pages = {236-241}, pmid = {22705839}, issn = {2165-5987}, mesh = {Base Composition ; Biodegradation, Environmental ; Biotransformation ; Carbon/metabolism ; Conjugation, Genetic ; Escherichia coli/*genetics/metabolism ; *Gene Transfer, Horizontal ; Genetic Engineering ; Metagenome ; Microbial Consortia/genetics ; Phylogeny ; Plasmids/*genetics/metabolism ; Pseudomonas putida/*genetics/metabolism ; Serratia marcescens/*genetics/metabolism ; Soil Pollutants/*metabolism ; Toluene/*metabolism ; }, abstract = {Genetic bioaugmentation is an in situ bioremediation method that stimulates horizontal transfer of catabolic plasmids between exogenous donor cells and indigenous bacteria to increase the biodegradation potential of contaminants. A critical outcome of genetic bioaugmentation is the expression of an active catabolic phenotype upon plasmid conjugation. Using a pWW0-derivative TOL plasmid, we showed that certain genetic characteristics of the recipient bacteria, including genomic guanine-cytosine (G + C) content and phylogeny, may limit the expression of the transferred catabolic pathway. However, such genetic limitations observed in transconjugants could be overcome by the presence of an additional carbon source. Glucose and Luria-Bertani broth were shown to enhance the toluene degradation rates of transconjugants; these enhancement effects were dependent on transconjugant genomic G + C contents. Based on these observations, thorough genetic characterization of the indigenous microbial community in the contaminated environment of interest may provide a predictive tool for assessing the success of genetic bioaugmentation.}, } @article {pmid22699611, year = {2012}, author = {Yatsunenko, T and Rey, FE and Manary, MJ and Trehan, I and Dominguez-Bello, MG and Contreras, M and Magris, M and Hidalgo, G and Baldassano, RN and Anokhin, AP and Heath, AC and Warner, B and Reeder, J and Kuczynski, J and Caporaso, JG and Lozupone, CA and Lauber, C and Clemente, JC and Knights, D and Knight, R and Gordon, JI}, title = {Human gut microbiome viewed across age and geography.}, journal = {Nature}, volume = {486}, number = {7402}, pages = {222-227}, pmid = {22699611}, issn = {1476-4687}, support = {K05 AA017688/AA/NIAAA NIH HHS/United States ; P01 DK078669/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; T32-HD049338/HD/NICHD NIH HHS/United States ; T32 HD049338-06/HD/NICHD NIH HHS/United States ; P01 DK078669-05/DK/NIDDK NIH HHS/United States ; DK078669/DK/NIDDK NIH HHS/United States ; T32 HD049338/HD/NICHD NIH HHS/United States ; K01 DK090285/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Bacteria/*classification/*genetics ; *Biodiversity ; Child ; Child, Preschool ; Feces/microbiology ; Female ; Geography ; Humans ; Infant ; Intestines/*microbiology ; Malawi ; Male ; *Metagenome ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Twins, Dizygotic ; Twins, Monozygotic ; United States ; Venezuela ; Young Adult ; }, abstract = {Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.}, } @article {pmid22699609, year = {2012}, author = {, }, title = {Structure, function and diversity of the healthy human microbiome.}, journal = {Nature}, volume = {486}, number = {7402}, pages = {207-214}, pmid = {22699609}, issn = {1476-4687}, support = {R01HG004856/HG/NHGRI NIH HHS/United States ; R01HG004908/HG/NHGRI NIH HHS/United States ; P30DE020751/DE/NIDCR NIH HHS/United States ; R21HG005811/HG/NHGRI NIH HHS/United States ; R01HG005172/HG/NHGRI NIH HHS/United States ; UH3DK083993/DK/NIDDK NIH HHS/United States ; R01 HG005969/HG/NHGRI NIH HHS/United States ; R01HG004900/HG/NHGRI NIH HHS/United States ; UH2 DK083990/DK/NIDDK NIH HHS/United States ; N01HG62088/HG/NHGRI NIH HHS/United States ; R01 HG004857/HG/NHGRI NIH HHS/United States ; U54 HG004973/HG/NHGRI NIH HHS/United States ; U01DE016937/DE/NIDCR NIH HHS/United States ; UH2 AR057504/AR/NIAMS NIH HHS/United States ; U54HG004969/HG/NHGRI NIH HHS/United States ; T32 AI007528/AI/NIAID NIH HHS/United States ; U54 HG003067/HG/NHGRI NIH HHS/United States ; U54HG003273/HG/NHGRI NIH HHS/United States ; R01HG004877/HG/NHGRI NIH HHS/United States ; R01 HG004900/HG/NHGRI NIH HHS/United States ; DP2OD001500/OD/NIH HHS/United States ; R01HG004885/HG/NHGRI NIH HHS/United States ; R01HG004872/HG/NHGRI NIH HHS/United States ; R01 HG004856/HG/NHGRI NIH HHS/United States ; R01 HG005171/HG/NHGRI NIH HHS/United States ; UH3AI083263/AI/NIAID NIH HHS/United States ; UH2 AR057506/AR/NIAMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; UH2AR057504/AR/NIAMS NIH HHS/United States ; U01HG004866/HG/NHGRI NIH HHS/United States ; U54HG003067/HG/NHGRI NIH HHS/United States ; U54 AI084844/AI/NIAID NIH HHS/United States ; UH3AR057504/AR/NIAMS NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; UH2AI083263/AI/NIAID NIH HHS/United States ; U01 HG004866/HG/NHGRI NIH HHS/United States ; U54AI084844/AI/NIAID NIH HHS/United States ; R01 HG005975/HG/NHGRI NIH HHS/United States ; R37 DE016937/DE/NIDCR NIH HHS/United States ; UH3 DK083993/DK/NIDDK NIH HHS/United States ; R01DE021574/DE/NIDCR NIH HHS/United States ; R01 HG004885/HG/NHGRI NIH HHS/United States ; U54 HG004968/HG/NHGRI NIH HHS/United States ; U54HG004973/HG/NHGRI NIH HHS/United States ; R01HG004857/HG/NHGRI NIH HHS/United States ; UH2 AI083263/AI/NIAID NIH HHS/United States ; R01HG005171/HG/NHGRI NIH HHS/United States ; T32AI007528/AI/NIAID NIH HHS/United States ; R01HG004906/HG/NHGRI NIH HHS/United States ; U54HG003079/HG/NHGRI NIH HHS/United States ; RC1 DE020298/DE/NIDCR NIH HHS/United States ; DP2 OD001500/OD/NIH HHS/United States ; R01 DE021574/DE/NIDCR NIH HHS/United States ; T32 GM087237/GM/NIGMS NIH HHS/United States ; R01 HG004908/HG/NHGRI NIH HHS/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; R21 CA139193/CA/NCI NIH HHS/United States ; R01HG005975/HG/NHGRI NIH HHS/United States ; U01 DE016937/DE/NIDCR NIH HHS/United States ; R21CA139193/CA/NCI NIH HHS/United States ; R21 HG005811/HG/NHGRI NIH HHS/United States ; U54 HG003079/HG/NHGRI NIH HHS/United States ; R01 HG004853/HG/NHGRI NIH HHS/United States ; N01AI30071/AI/NIAID NIH HHS/United States ; U54 HG004969/HG/NHGRI NIH HHS/United States ; R01HG004853/HG/NHGRI NIH HHS/United States ; UH3 AI083263/AI/NIAID NIH HHS/United States ; UH2DK083990/DK/NIDDK NIH HHS/United States ; U54HG004968/HG/NHGRI NIH HHS/United States ; RC1DE0202098/DE/NIDCR NIH HHS/United States ; R01 HG004906/HG/NHGRI NIH HHS/United States ; R01HG005969/HG/NHGRI NIH HHS/United States ; R01 HG004877/HG/NHGRI NIH HHS/United States ; P30 DE020751/DE/NIDCR NIH HHS/United States ; R01 HG005172/HG/NHGRI NIH HHS/United States ; UH2AR057506/AR/NIAMS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Bacteria/*classification/genetics ; *Biodiversity ; Ecosystem ; Female ; *Health ; Humans ; Male ; Metabolic Networks and Pathways/physiology ; *Metagenome ; Metagenomics ; Phenotype ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat's signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81-99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.}, } @article {pmid22699602, year = {2012}, author = {Relman, DA}, title = {Microbiology: Learning about who we are.}, journal = {Nature}, volume = {486}, number = {7402}, pages = {194-195}, pmid = {22699602}, issn = {1476-4687}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Female ; *Health ; Humans ; Male ; *Metagenome ; Metagenomics/*methods ; }, } @article {pmid22698087, year = {2012}, author = {Segata, N and Haake, SK and Mannon, P and Lemon, KP and Waldron, L and Gevers, D and Huttenhower, C and Izard, J}, title = {Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples.}, journal = {Genome biology}, volume = {13}, number = {6}, pages = {R42}, pmid = {22698087}, issn = {1474-760X}, support = {HG004969/HG/NHGRI NIH HHS/United States ; DE020751/DE/NIDCR NIH HHS/United States ; HG005969/HG/NHGRI NIH HHS/United States ; CA139193/CA/NCI NIH HHS/United States ; DE020298/DE/NIDCR NIH HHS/United States ; DE021574/DE/NIDCR NIH HHS/United States ; }, mesh = {Actinobacteria/classification/genetics/isolation & purification ; Adolescent ; Adult ; Bacterial Typing Techniques/methods ; Bacteroidetes/classification/genetics/isolation & purification ; *Biota ; Feces/*microbiology ; Female ; Genes, rRNA ; Humans ; Male ; *Metagenome ; Mouth/*microbiology ; Palatine Tonsil/*microbiology ; Pharynx/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/analysis/genetics ; Saliva/microbiology ; Veillonellaceae/classification/genetics/isolation & purification ; Young Adult ; }, abstract = {BACKGROUND: To understand the relationship between our bacterial microbiome and health, it is essential to define the microbiome in the absence of disease. The digestive tract includes diverse habitats and hosts the human body's greatest bacterial density. We describe the bacterial community composition of ten digestive tract sites from more than 200 normal adults enrolled in the Human Microbiome Project, and metagenomically determined metabolic potentials of four representative sites.

RESULTS: The microbiota of these diverse habitats formed four groups based on similar community compositions: buccal mucosa, keratinized gingiva, hard palate; saliva, tongue, tonsils, throat; sub- and supra-gingival plaques; and stool. Phyla initially identified from environmental samples were detected throughout this population, primarily TM7, SR1, and Synergistetes. Genera with pathogenic members were well-represented among this disease-free cohort. Tooth-associated communities were distinct, but not entirely dissimilar, from other oral surfaces. The Porphyromonadaceae, Veillonellaceae and Lachnospiraceae families were common to all sites, but the distributions of their genera varied significantly. Most metabolic processes were distributed widely throughout the digestive tract microbiota, with variations in metagenomic abundance between body habitats. These included shifts in sugar transporter types between the supragingival plaque, other oral surfaces, and stool; hydrogen and hydrogen sulfide production were also differentially distributed.

CONCLUSIONS: The microbiomes of ten digestive tract sites separated into four types based on composition. A core set of metabolic pathways was present across these diverse digestive tract habitats. These data provide a critical baseline for future studies investigating local and systemic diseases affecting human health.}, } @article {pmid22697249, year = {2012}, author = {Wang, M and Ye, Y and Tang, H}, title = {A de Bruijn graph approach to the quantification of closely-related genomes in a microbial community.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {19}, number = {6}, pages = {814-825}, pmid = {22697249}, issn = {1557-8666}, support = {1R01HG004908/HG/NHGRI NIH HHS/United States ; 1U01HL098960/HL/NHLBI NIH HHS/United States ; }, mesh = {*Algorithms ; Chromosome Mapping/*methods ; Escherichia coli/classification/*genetics ; *Genome, Bacterial ; Genomic Structural Variation ; Metagenomics ; Microbial Consortia ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Treponema/classification/*genetics ; }, abstract = {The wide applications of next-generation sequencing (NGS) technologies in metagenomics have raised many computational challenges. One of the essential problems in metagenomics is to estimate the taxonomic composition of a microbial community, which can be approached by mapping shotgun reads acquired from the community to previously characterized microbial genomes followed by quantity profiling of these species based on the number of mapped reads. This procedure, however, is not as trivial as it appears at first glance. A shotgun metagenomic dataset often contains DNA sequences from many closely-related microbial species (e.g., within the same genus) or strains (e.g., within the same species), thus it is often difficult to determine which species/strain a specific read is sampled from when it can be mapped to a common region shared by multiple genomes at high similarity. Furthermore, high genomic variations are observed among individual genomes within the same species, which are difficult to be differentiated from the inter-species variations during reads mapping. To address these issues, a commonly used approach is to quantify taxonomic distribution only at the genus level, based on the reads mapped to all species belonging to the same genus; alternatively, reads are mapped to a set of representative genomes, each selected to represent a different genus. Here, we introduce a novel approach to the quantity estimation of closely-related species within the same genus by mapping the reads to their genomes represented by a de Bruijn graph, in which the common genomic regions among them are collapsed. Using simulated and real metagenomic datasets, we show the de Bruijn graph approach has several advantages over existing methods, including (1) it avoids redundant mapping of shotgun reads to multiple copies of the common regions in different genomes, and (2) it leads to more accurate quantification for the closely-related species (and even for strains within the same species).}, } @article {pmid22694805, year = {2012}, author = {Rodrigues, DM and Sousa, AJ and Hawley, SP and Vong, L and Gareau, MG and Kumar, SA and Johnson-Henry, KC and Sherman, PM}, title = {Matrix metalloproteinase 9 contributes to gut microbe homeostasis in a model of infectious colitis.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {105}, pmid = {22694805}, issn = {1471-2180}, support = {IOP-92890//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; *Biodiversity ; Citrobacter rodentium/*pathogenicity ; Colitis/*microbiology/pathology ; Female ; Gastrointestinal Tract/*microbiology/pathology ; Homeostasis ; Immunohistochemistry ; Male ; Matrix Metalloproteinase 9/deficiency/*metabolism ; *Metagenome ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Permeability ; Real-Time Polymerase Chain Reaction ; Severity of Illness Index ; }, abstract = {BACKGROUND: Inflammatory bowel diseases are associated with increased expression of zinc-dependent Matrix Metalloproteinase 9 (MMP-9). A stark dysregulation of intestinal mucosal homeostasis has been observed in patients with chronic inflammatory bowel diseases. We therefore sought to determine the contribution of MMP-9 to the pathogenesis of Citrobacter rodentium-induced colitis and its effects on gut microbiome homeostasis.

RESULTS: Wild-type and MMP-9-/- mice aged 5-6 weeks were challenged with C. rodentium by orogastric gavage and sacrificed either 10 or 30 days post-infection. Disease severity was assessed by histological analysis of colonic epithelial hyperplasia and by using an in vivo intestinal permeability assay. Changes in the inflammatory responses were measured by using qPCR, and the composition of the fecal microbiome evaluated with both qPCR and terminal restriction fragment length polymorphism. Activation and localization of MMP-9 to the apical surface of the colonic epithelium in response to C. rodentium infection was demonstrated by both zymography and immunocytochemistry. The pro-inflammatory response to infection, including colonic epithelial cell hyperplasia and barrier dysfunction, was similar, irrespective of genotype. Nonmetric multidimensional scaling of terminal restriction fragments revealed a different fecal microbiome composition and C. rodentium colonization pattern between genotypes, with MMP-9-/- having elevated levels of protective segmented filamentous bacteria and interleukin-17, and lower levels of C. rodentium. MMP-9-/- but not wild-type mice were also protected from reductions in fecal microbial diversity in response to the bacterial enteric infection.

CONCLUSIONS: These results demonstrate that MMP-9 expression in the colon causes alterations in the fecal microbiome and has an impact on the pathogenesis of bacterial-induced colitis in mice.}, } @article {pmid22692220, year = {2012}, author = {Copeland, WK and Krishnan, V and Beck, D and Settles, M and Foster, JA and Cho, KC and Day, M and Hickey, R and Schütte, UM and Zhou, X and Williams, CJ and Forney, LJ and Abdo, Z}, title = {mcaGUI: microbial community analysis R-Graphical User Interface (GUI).}, journal = {Bioinformatics (Oxford, England)}, volume = {28}, number = {16}, pages = {2198-2199}, pmid = {22692220}, issn = {1367-4811}, support = {UH2 AI083264/AI/NIAID NIH HHS/United States ; P20 RR016448/RR/NCRR NIH HHS/United States ; U19 AI084044/AI/NIAID NIH HHS/United States ; R24 RR023344/RR/NCRR NIH HHS/United States ; P20 RR16448/RR/NCRR NIH HHS/United States ; 1UH2AI083264-01/AI/NIAID NIH HHS/United States ; R24 RR023344-01A2/RR/NCRR NIH HHS/United States ; }, mesh = {Biodiversity ; Cluster Analysis ; *Computer Graphics ; *Metagenome ; Multivariate Analysis ; Principal Component Analysis ; Sequence Analysis/methods ; *Software ; *User-Computer Interface ; }, abstract = {UNLABELLED: Microbial communities have an important role in natural ecosystems and have an impact on animal and human health. Intuitive graphic and analytical tools that can facilitate the study of these communities are in short supply. This article introduces Microbial Community Analysis GUI, a graphical user interface (GUI) for the R-programming language (R Development Core Team, 2010). With this application, researchers can input aligned and clustered sequence data to create custom abundance tables and perform analyses specific to their needs. This GUI provides a flexible modular platform, expandable to include other statistical tools for microbial community analysis in the future.

AVAILABILITY: The mcaGUI package and source are freely available as part of Bionconductor at http://www.bioconductor.org/packages/release/bioc/html/mcaGUI.html}, } @article {pmid22688727, year = {2012}, author = {Schloss, PD and Schubert, AM and Zackular, JP and Iverson, KD and Young, VB and Petrosino, JF}, title = {Stabilization of the murine gut microbiome following weaning.}, journal = {Gut microbes}, volume = {3}, number = {4}, pages = {383-393}, pmid = {22688727}, issn = {1949-0984}, support = {U54 HG004973/HG/NHGRI NIH HHS/United States ; U19 AI090871/AI/NIAID NIH HHS/United States ; R01 HG005975/HG/NHGRI NIH HHS/United States ; U54HG004973/HG/NHGRI NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; R01HG005975/HG/NHGRI NIH HHS/United States ; U19AI090871/AI/NIAID NIH HHS/United States ; T32 AI007528/AI/NIAID NIH HHS/United States ; P30DK034933/DK/NIDDK NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; R01 DK070875/DK/NIDDK NIH HHS/United States ; R01DK070875/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Biota ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Gastrointestinal Tract/*microbiology ; Male ; *Metagenome ; Mice ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Weaning ; }, abstract = {Ecologists hypothesize that community structure and stability affect productivity, sensitivity to invasion and extinction, and resilience and resistance to perturbations. Viewed in the context of the gut microbiome, the stability of the gut community is important for understanding the effects of antibiotics, diet change and other perturbations on host health and colonization resistance. Here we describe the dynamics of a self-contained community, the murine gut microbiome. Using 16S rRNA gene sequencing of fecal samples collected daily from individual mice, we characterized the community membership and structure to determine whether there were significant changes in the gut community during the first year of life. Based on analysis of molecular variance, we observed two community states. The first was observed in the 10 days following weaning and the second was observed by 15 days following weaning. Interestingly, these two states had the same bacterial populations, but those populations had different relative abundances in the two states. By calculating the root mean squared distances between samples collected in the early and late states for each mouse, we observed that the late state was more stable than the early state. This increase in stability was not correlated with increased taxonomic richness, taxonomic diversity, or phylogenetic diversity. In the absence of an experimentally induced perturbation, the second community state was relatively constant through 364 days post weaning. These results suggest a high degree of stability in the microbiome once the community reached the second state.}, } @article {pmid22688724, year = {2012}, author = {Rawls, JF}, title = {Special issue: gut microbial communities in health and disease.}, journal = {Gut microbes}, volume = {3}, number = {4}, pages = {277-278}, pmid = {22688724}, issn = {1949-0984}, mesh = {*Biota ; Disease ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; }, } @article {pmid22685152, year = {2012}, author = {Lei, F and Yin, Y and Wang, Y and Deng, B and Yu, HD and Li, L and Xiang, C and Wang, S and Zhu, B and Wang, X}, title = {Higher-level production of volatile fatty acids in vitro by chicken gut microbiotas than by human gut microbiotas as determined by functional analyses.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {16}, pages = {5763-5772}, pmid = {22685152}, issn = {1098-5336}, mesh = {Animals ; Bacteria/isolation & purification/*metabolism ; *Biodiversity ; Carbohydrate Metabolism ; Chickens ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fatty Acids, Volatile/*metabolism ; Feces/microbiology ; Fermentation ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenome ; Proteins/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The aim of this study was to determine the relationship between the composition and function of gut microbiota. Here, we compared the bacterial compositions and fermentation metabolites of human and chicken gut microbiotas. Results generated by quantitative PCR (qPCR) and 454 pyrosequencing of the 16S rRNA gene V3 region showed the compositions of human and chicken microbiotas to be markedly different, with chicken cecal microbiotas displaying more diversity than human fecal microbiotas. The nutrient requirements of each microbiota growing under batch and chemostat conditions were analyzed. The results showed that chicken cecal microbiotas required simple sugars and peptides to maintain balanced growth in vitro but that human fecal microbiotas preferred polysaccharides and proteins. Chicken microbiotas also produced higher concentrations of volatile fatty acids than did human microbiotas. Our data suggest that the availability of different fermentable substrates in the chicken cecum, which exist due to the unique anatomical structure of the cecum, may provide an environment favorable to the nourishment of microbiotas suited to the production of the higher-energy metabolites required by the bird. Therefore, gut structure, nutrition, immunity, and life-style all contribute to the selection of an exclusive bacterial community that produces types of metabolites beneficial to the host.}, } @article {pmid22683836, year = {2012}, author = {Tsuji, H and Oozeer, R and Matsuda, K and Matsuki, T and Ohta, T and Nomoto, K and Tanaka, R and Kawashima, M and Kawashima, K and Nagata, S and Yamashiro, Y}, title = {Molecular monitoring of the development of intestinal microbiota in Japanese infants.}, journal = {Beneficial microbes}, volume = {3}, number = {2}, pages = {113-125}, doi = {10.3920/BM2011.0038}, pmid = {22683836}, issn = {1876-2891}, mesh = {Asian People ; Bacteria/*classification/*genetics ; *Biota ; Carboxylic Acids/analysis ; Child, Preschool ; Feces/chemistry/*microbiology ; Female ; Gastrointestinal Tract/*physiology ; Humans ; Hydrogen-Ion Concentration ; Infant ; Infant, Newborn ; Japan ; Male ; *Metagenome ; Pregnancy ; }, abstract = {The faecal microbiota of 166 healthy Japanese newborns was analysed periodically from day 1 after birth until the age of 3 years by using the reverse transcription-quantitative PCR. Faecal pH and the organic acid concentration were also examined. Colonisation by both facultative anaerobes and strict anaerobes was confirmed in 95% of the meconium tested. Bifidobacterium-predominant microbiota was established subsequently in most of the infants by 3 months after birth. Bifidobacterium breve, Bifidobacterium longum, Bifidobacterium infantis, Bifidobacterium catenulatum group and Bifidobacterium bifidum were the species mainly detected. Intergroup correlation analysis revealed that the bifidobacterial population levels, but not other strict anaerobe groups, were found to be negatively correlated with those of the Enterobacteriaceae from 7 days until 3 months after birth. Faecal pH was maintained at about 6 until 6 months after birth and reached 6.6 at 3 years after birth. The initial concentration of faecal organic acids (19 μM/g of faeces) just after birth increased until 3 years after birth to the level of 111 μM/g of faeces. Early start of feeding formula milk promoted colonisation by obligate anaerobes such as the Clostridium coccoides group, the Clostridium leptum subgroup, Prevotella, and Atopobium cluster during the 3 months after birth. Population levels of the bifidobacteria until 1 month after birth and those of the Bacteroides fragilis group until 6 months after birth were lower in infants delivered by Caesarean section than in those delivered normally. The results suggested that both earlier start of feeding of formula milk and the mode of infant delivery were found to be important in the development of intestinal microbiota in early infancy.}, } @article {pmid22676058, year = {2012}, author = {Molina-Santiago, C and Udaondo, Z and Marin, A and García-Salamanca, A and Michán, C and Daniels, C and Molina, L and Ramos, JL}, title = {Evolution of antibiotic resistance, catabolic pathways and niche colonization.}, journal = {Microbial biotechnology}, volume = {5}, number = {4}, pages = {452-454}, pmid = {22676058}, issn = {1751-7915}, mesh = {Anti-Bacterial Agents/isolation & purification ; Bacteria/*drug effects/genetics/*metabolism ; Biodiversity ; Biotechnology/methods ; *Drug Resistance, Bacterial ; *Metabolic Networks and Pathways ; Metagenome ; }, } @article {pmid22674336, year = {2012}, author = {Mueller, K and Ash, C and Pennisi, E and Smith, O}, title = {The gut microbiota. Introduction.}, journal = {Science (New York, N.Y.)}, volume = {336}, number = {6086}, pages = {1245}, doi = {10.1126/science.336.6086.1245}, pmid = {22674336}, issn = {1095-9203}, mesh = {Gastrointestinal Tract/*microbiology/physiology ; Homeostasis ; Humans ; Immune System/physiology ; *Metagenome ; Microbial Consortia/physiology ; }, } @article {pmid22674335, year = {2012}, author = {Costello, EK and Stagaman, K and Dethlefsen, L and Bohannan, BJ and Relman, DA}, title = {The application of ecological theory toward an understanding of the human microbiome.}, journal = {Science (New York, N.Y.)}, volume = {336}, number = {6086}, pages = {1255-1262}, pmid = {22674335}, issn = {1095-9203}, support = {DP1 OD000964/OD/NIH HHS/United States ; R01 OD011116/OD/NIH HHS/United States ; R01 GM095385/GM/NIGMS NIH HHS/United States ; R01GM095385/GM/NIGMS NIH HHS/United States ; DP1OD000964/OD/NIH HHS/United States ; T32 GM007413/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/*therapeutic use ; Bacterial Infections/*microbiology ; Biodiversity ; Ecology ; *Ecosystem ; Gastrointestinal Tract/*microbiology ; *Host-Pathogen Interactions ; Humans ; Infant, Newborn ; *Metagenome ; Selection, Genetic ; Symbiosis ; }, abstract = {The human-microbial ecosystem plays a variety of important roles in human health and disease. Each person can be viewed as an island-like "patch" of habitat occupied by microbial assemblages formed by the fundamental processes of community ecology: dispersal, local diversification, environmental selection, and ecological drift. Community assembly theory, and metacommunity theory in particular, provides a framework for understanding the ecological dynamics of the human microbiome, such as compositional variability within and between hosts. We explore three core scenarios of human microbiome assembly: development in infants, representing assembly in previously unoccupied habitats; recovery from antibiotics, representing assembly after disturbance; and invasion by pathogens, representing assembly in the context of invasive species. Judicious application of ecological theory may lead to improved strategies for restoring and maintaining the microbiota and the crucial health-associated ecosystem services that it provides.}, } @article {pmid22674329, year = {2012}, author = {Hood, L}, title = {Tackling the microbiome.}, journal = {Science (New York, N.Y.)}, volume = {336}, number = {6086}, pages = {1209}, doi = {10.1126/science.1225475}, pmid = {22674329}, issn = {1095-9203}, mesh = {Genomics ; Humans ; *Metagenome ; Microbial Consortia/physiology ; Proteomics ; Systems Biology/*methods ; }, } @article {pmid22674326, year = {2012}, author = {Gordon, JI}, title = {Honor thy gut symbionts redux.}, journal = {Science (New York, N.Y.)}, volume = {336}, number = {6086}, pages = {1251-1253}, doi = {10.1126/science.1224686}, pmid = {22674326}, issn = {1095-9203}, mesh = {Animals ; Diet ; Food ; Gastrointestinal Tract/*microbiology ; Humans ; Interdisciplinary Communication ; *Metagenome ; Metagenomics ; Microbial Consortia ; Probiotics ; Sequence Analysis, DNA ; Symbiosis ; Synbiotics ; }, abstract = {Exploring our gut microbial communities with new tools is allowing us to revisit old questions; to develop new concepts about our evolution, postnatal development, systems physiology, individuality, and definitions of health; and to further delineate the impact of our changing life-styles. It is also allowing us to envision exciting new ways for addressing global health problems. This area is inherently interdisciplinary, offering a wealth of opportunities to create new fields, partnerships, and educational initiatives. It is captivating to the public and carries substantial expectations. As such, participating scientists need to sponsor proactive, solution-focused discussions of its societal implications.}, } @article {pmid22672413, year = {2012}, author = {Candela, M and Rampelli, S and Turroni, S and Severgnini, M and Consolandi, C and De Bellis, G and Masetti, R and Ricci, G and Pession, A and Brigidi, P}, title = {Unbalance of intestinal microbiota in atopic children.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {95}, pmid = {22672413}, issn = {1471-2180}, mesh = {Adolescent ; *Biota ; Child ; Child, Preschool ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Hypersensitivity/*microbiology ; Male ; *Metagenome ; Microarray Analysis ; }, abstract = {BACKGROUND: Playing a strategic role in the host immune function, the intestinal microbiota has been recently hypothesized to be involved in the etiology of atopy. In order to investigate the gastrointestinal microbial ecology of atopic disease, here we performed a pilot comparative molecular analysis of the faecal microbiota in atopic children and healthy controls.

RESULTS: Nineteen atopic children and 12 healthy controls aged 4-14 years were enrolled. Stools were collected and the faecal microbiota was characterized by means of the already developed phylogenetic microarray platform, HTF-Microbi.Array, and quantitative PCR. The intestinal microbiota of atopic children showed a significant depletion in members of the Clostridium cluster IV, Faecalibacterium prausnitzii, Akkermansia muciniphila and a corresponding increase of the relative abundance of Enterobacteriaceae.

CONCLUSION: Depleted in key immunomodulatory symbionts, the atopy-associated microbiota can represent an inflammogenic microbial consortium which can contribute to the severity of the disease. Our data open the way to the therapeutic manipulation of the intestinal microbiota in the treatment of atopy by means of pharmaceutical probiotics.}, } @article {pmid22672382, year = {2012}, author = {Mäkivuokko, H and Lahtinen, SJ and Wacklin, P and Tuovinen, E and Tenkanen, H and Nikkilä, J and Björklund, M and Aranko, K and Ouwehand, AC and Mättö, J}, title = {Association between the ABO blood group and the human intestinal microbiota composition.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {94}, pmid = {22672382}, issn = {1471-2180}, mesh = {*ABO Blood-Group System ; Adult ; *Biota ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; *Metagenome ; Middle Aged ; }, abstract = {BACKGROUND: The mucus layer covering the human intestinal epithelium forms a dynamic surface for host-microbial interactions. In addition to the environmental factors affecting the intestinal equilibrium, such as diet, it is well established that the microbiota composition is individually driven, but the host factors determining the composition have remained unresolved.

RESULTS: In this study, we show that ABO blood group is involved in differences in relative proportion and overall profiles of intestinal microbiota. Specifically, the microbiota from the individuals harbouring the B antigen (secretor B and AB) differed from the non-B antigen groups and also showed higher diversity of the Eubacterium rectale-Clostridium coccoides (EREC) and Clostridium leptum (CLEPT) -groups in comparison with other blood groups.

CONCLUSIONS: Our novel finding indicates that the ABO blood group is one of the genetically determined host factors modulating the composition of the human intestinal microbiota, thus enabling new applications in the field of personalized nutrition and medicine.}, } @article {pmid22671536, year = {2012}, author = {Grube, M and Köberl, M and Lackner, S and Berg, C and Berg, G}, title = {Host-parasite interaction and microbiome response: effects of fungal infections on the bacterial community of the Alpine lichen Solorina crocea.}, journal = {FEMS microbiology ecology}, volume = {82}, number = {2}, pages = {472-481}, doi = {10.1111/j.1574-6941.2012.01425.x}, pmid = {22671536}, issn = {1574-6941}, support = {I 882/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/classification/*genetics ; Biodiversity ; Cluster Analysis ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; Fungi/*pathogenicity ; Lichens/*microbiology ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The lichen symbiosis allows a self-sustained life under harsh environmental conditions, yet symbiotic integrity can be affected by fungal parasites. Nothing is known about the impact of these biologically diverse and often specific infections on the recently detected bacterial community in lichens. To address this question, we studied the arctic-alpine 'chocolate chip lichen' Solorina crocea, which is frequently infected by Rhagadostoma lichenicola. We sampled healthy and infected lichens at two different sites in the Eastern Alps. High abundances of Acidobacteria, Planctomycetes, and Proteobacteria were identified analyzing 16S rRNA gene regions obtained by barcoded pyrosequencing. At the phylum and genus level, no significant alterations were present among infected and healthy individuals. Yet, evidence for a differentiation of communities emerged, when data were analyzed at the strain level by detrended correspondence analysis. Further, a profile clustering network revealed strain-specific abundance shifts among Acidobacteria and other bacteria. Study of stability and change in host-associated bacterial communities requires a fine-grained analysis at strain level. No correlation with the infection was found by analysis of nifH genes responsible for nitrogen fixation.}, } @article {pmid22647051, year = {2012}, author = {Alcaraz, LD and Belda-Ferre, P and Cabrera-Rubio, R and Romero, H and Simón-Soro, A and Pignatelli, M and Mira, A}, title = {Identifying a healthy oral microbiome through metagenomics.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {18 Suppl 4}, number = {}, pages = {54-57}, doi = {10.1111/j.1469-0691.2012.03857.x}, pmid = {22647051}, issn = {1469-0691}, mesh = {Bacteria/classification/genetics ; Biodiversity ; DNA, Bacterial/chemistry/genetics ; Humans ; *Metagenome ; Metagenomics/*methods ; Mouth/*microbiology/*physiology ; Sequence Analysis, DNA/methods ; }, abstract = {We present the results of an exploratory study of the bacterial communities from the human oral cavity showing the advantages of pyrosequencing complex samples. Over 1.6 million reads from the metagenomes of eight dental plaque samples were taxonomically assigned through a binning procedure. We performed clustering analysis to discern if there were associations between non-caries and caries conditions in the community composition. Our results show a given bacterial consortium associated with cariogenic and non-cariogenic conditions, in agreement with the existence of a healthy oral microbiome and giving support to the idea of dental caries being a polymicrobial disease. The data are coherent with those previously reported in the literature by 16S rRNA amplification, thus giving the chance to link gene functions with taxonomy in further studies involving larger sample numbers.}, } @article {pmid22647049, year = {2012}, author = {Gosalbes, MJ and Abellan, JJ and Durbán, A and Pérez-Cobas, AE and Latorre, A and Moya, A}, title = {Metagenomics of human microbiome: beyond 16s rDNA.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {18 Suppl 4}, number = {}, pages = {47-49}, doi = {10.1111/j.1469-0691.2012.03865.x}, pmid = {22647049}, issn = {1469-0691}, mesh = {DNA, Ribosomal/chemistry/genetics ; Humans ; *Metagenome ; Metagenomics/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Transcriptome ; }, abstract = {The gut microbiota presents a symbiotic relationship with the human host playing a beneficial role in human health. Since its establishment, the bacterial community is subjected to the influence of many different factors that shape its composition within each individual. However, an important convergence is observed at functional level in the gut microbiota. A metatranscriptomic study of healthy individuals showed homogeneity in the composition of the active microbiota that increased further at functional level.}, } @article {pmid22647045, year = {2012}, author = {Gueimonde, M and Collado, MC}, title = {Metagenomics and probiotics.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {18 Suppl 4}, number = {}, pages = {32-34}, doi = {10.1111/j.1469-0691.2012.03873.x}, pmid = {22647045}, issn = {1469-0691}, mesh = {*Biota ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; Metagenomics/*methods ; Probiotics/*administration & dosage ; }, abstract = {The development of extensive sequencing methods has allowed metagenomic studies on the human gut microbiome to be carried out. This has tremendously increased our knowledge on gut microbiota composition and activity, allowing microbiota aberrations related to different diseases to be identified. These aberrations constitute targets for the development of probiotics directed to correct them. Probiotics are extensively used to modulate gut microbiota. Nevertheless, metagenomic studies on the effects of probiotics are still very scarce. In the near future, the use of metagenomics promises to expand our understanding of probiotic action.}, } @article {pmid22647044, year = {2012}, author = {Garmendia, L and Hernandez, A and Sanchez, MB and Martinez, JL}, title = {Metagenomics and antibiotics.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {18 Suppl 4}, number = {}, pages = {27-31}, doi = {10.1111/j.1469-0691.2012.03868.x}, pmid = {22647044}, issn = {1469-0691}, mesh = {Anti-Bacterial Agents/*administration & dosage ; Bacteria/*drug effects ; *Biota ; Drug Resistance, Bacterial ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; Metagenomics/*methods ; }, abstract = {Most of the bacterial species that form part of the biosphere have never been cultivated. In this situation, a comprehensive study of bacterial communities requires the utilization of non-culture-based methods, which have been named metagenomics. In this paper we review the use of different metagenomic techniques for understanding the effect of antibiotics on microbial communities, to synthesize new antimicrobial compounds and to analyse the distribution of antibiotic resistance genes in different ecosystems. These techniques include functional metagenomics, which serves to find new antibiotics or new antibiotic resistance genes, and descriptive metagenomics, which serves to analyse changes in the composition of the microbiota and to track the presence and abundance of already known antibiotic resistance genes in different ecosystems.}, } @article {pmid22647043, year = {2012}, author = {Vallès, Y and Gosalbes, MJ and de Vries, LE and Abellán, JJ and Francino, MP}, title = {Metagenomics and development of the gut microbiota in infants.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {18 Suppl 4}, number = {}, pages = {21-26}, doi = {10.1111/j.1469-0691.2012.03876.x}, pmid = {22647043}, issn = {1469-0691}, support = {R01DK066288/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; *Biota ; Drug Resistance, Bacterial ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Infant ; Infant, Newborn ; *Metagenome ; Metagenomics/*methods ; }, abstract = {The establishment of a balanced intestinal microbiota is essential for numerous aspects of human health, yet the microbial colonization of the gastrointestinal tract of infants is both complex and highly variable among individuals. In addition, the gastrointestinal tract microbiota is often exposed to antibiotics, and may be an important reservoir of resistant strains and of transferable resistance genes from early infancy. We are investigating by means of diverse metagenomic approaches several areas of microbiota development in infants, including the deployment of functional capabilities at the community level, the presence of antibiotic resistances and the population dynamics of the most abundant genera.}, } @article {pmid22647042, year = {2012}, author = {Salonen, A and Salojärvi, J and Lahti, L and de Vos, WM}, title = {The adult intestinal core microbiota is determined by analysis depth and health status.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {18 Suppl 4}, number = {}, pages = {16-20}, doi = {10.1111/j.1469-0691.2012.03855.x}, pmid = {22647042}, issn = {1469-0691}, mesh = {Adult ; *Biota ; Electronic Data Processing/methods ; Female ; Gastrointestinal Tract/*microbiology ; *Health Status ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; *Metagenome ; Metagenomics/methods ; Microarray Analysis/methods ; Phylogeny ; }, abstract = {High-throughput molecular methods are currently exploited to characterize the complex and highly individual intestinal microbiota in health and disease. Definition of the human intestinal core microbiota, i.e. the number and the identity of bacteria that are shared among different individuals, is currently one of the main research questions. Here we apply a high-throughput phylogenetic microarray, for a comprehensive and high-resolution microbiota analysis, and a novel computational approach in a quantitative study of the core microbiota in over 100 individuals. In the approach presented we study how the criteria for the phylotype abundance or prevalence influence the resulting core in parallel with biological variables, such as the number and health status of the study subjects. We observed that the core size is highly conditional, mostly depending on the depth of the analysis and the required prevalence of the core taxa. Moreover, the core size is also affected by biological variables, of which the health status had a larger impact than the number of studied subjects. We also introduce a computational method that estimates the expected size of the core, given the varying prevalence and abundance criteria. The approach is directly applicable to sequencing data derived from intestinal and other host-associated microbial communities, and can be modified to include more informative definitions of core microbiota. Hence, we anticipate its utilization will facilitate the conceptual definition of the core microbiota and its consequent characterization so that future studies yield conclusive views on the intestinal core microbiota, eliminating the current controversy.}, } @article {pmid22647040, year = {2012}, author = {Parfrey, LW and Knight, R}, title = {Spatial and temporal variability of the human microbiota.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {18 Suppl 4}, number = {}, pages = {8-11}, doi = {10.1111/j.1469-0691.2012.03861.x}, pmid = {22647040}, issn = {1469-0691}, support = {HG4872/HG/NHGRI NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; }, mesh = {*Biodiversity ; Geography ; Host-Pathogen Interactions ; Humans ; *Metagenome ; Time Factors ; }, abstract = {The knowledge that our bodies are home to microbes is not new; van Leeuwenhoek first saw the microbes of the mouth and gut over three centuries ago. However, next generation sequencing technologies are enabling us to characterize our microbial consortia on an unprecedented scale, and are providing new insights into the range of variability of our microbiota and their contributions to our health. The microbiota far outnumber the human component of our selves, with 10 times more cells and at least 100 times more genes. Moreover, while individuals share over 99.9% of their human genome sequence, there are vast differences in the microbiome (the collection of genes of our associated microbes). This raises the question of the extent to which our microbial community determines our human physiological responses and susceptibility to disease. In order to develop technologies that allow us to manipulate the microbiome to improve health we must first understand the factors that influence spatial and temporal variation, stability in response to perturbation, and conditions that induce community-wide changes.}, } @article {pmid22647038, year = {2012}, author = {Baquero, F and Nombela, C}, title = {The microbiome as a human organ.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {18 Suppl 4}, number = {}, pages = {2-4}, doi = {10.1111/j.1469-0691.2012.03916.x}, pmid = {22647038}, issn = {1469-0691}, mesh = {Biota ; Host-Pathogen Interactions ; Humans ; *Metagenome ; Metagenomics/*methods ; Probiotics ; }, abstract = {The human organism is a complex structure composed of cells belonging to all three domains of life on Earth, Eukarya, Bacteria and Archaea, as well as their viruses. Bacterial cells of more than a thousand taxonomic units are condensed in a particular functional collective domain, the intestinal microbiome. The microbiome constitutes the last human organ under active research. Like other organs, and despite its intrinsic complexity, the microbiome is readily inherited, in a process probably involving 'small world' power law dynamics of construction in newborns. Like any other organ, the microbiome has physiology and pathology, and the individual (and collective?) health might be damaged when its collective population structure is altered. The diagnostic of microbiomic diseases involves metagenomic studies. The therapeutics of microbiome-induced pathology include microbiota transplantation, a technique increasingly available. Perhaps a new medical specialty, microbiomology, is being born.}, } @article {pmid22647037, year = {2012}, author = {Raoult, D}, title = {Human microbiota. [corrected].}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {18 Suppl 4}, number = {}, pages = {1}, doi = {10.1111/j.1469-0691.2012.03915.x}, pmid = {22647037}, issn = {1469-0691}, mesh = {Biota ; Host-Pathogen Interactions ; Humans ; *Metagenome ; Metagenomics/*methods ; Probiotics ; }, } @article {pmid22666442, year = {2012}, author = {Illeghems, K and De Vuyst, L and Papalexandratou, Z and Weckx, S}, title = {Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e38040}, pmid = {22666442}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; Cacao/*metabolism/microbiology ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; *Fermentation ; Fungi/*classification/genetics ; Metagenome/*genetics ; *Phylogeny ; Quality Control ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {This is the first report on the phylogenetic analysis of the community diversity of a single spontaneous cocoa bean box fermentation sample through a metagenomic approach involving 454 pyrosequencing. Several sequence-based and composition-based taxonomic profiling tools were used and evaluated to avoid software-dependent results and their outcome was validated by comparison with previously obtained culture-dependent and culture-independent data. Overall, this approach revealed a wider bacterial (mainly γ-Proteobacteria) and fungal diversity than previously found. Further, the use of a combination of different classification methods, in a software-independent way, helped to understand the actual composition of the microbial ecosystem under study. In addition, bacteriophage-related sequences were found. The bacterial diversity depended partially on the methods used, as composition-based methods predicted a wider diversity than sequence-based methods, and as classification methods based solely on phylogenetic marker genes predicted a more restricted diversity compared with methods that took all reads into account. The metagenomic sequencing analysis identified Hanseniaspora uvarum, Hanseniaspora opuntiae, Saccharomyces cerevisiae, Lactobacillus fermentum, and Acetobacter pasteurianus as the prevailing species. Also, the presence of occasional members of the cocoa bean fermentation process was revealed (such as Erwinia tasmaniensis, Lactobacillus brevis, Lactobacillus casei, Lactobacillus rhamnosus, Lactococcus lactis, Leuconostoc mesenteroides, and Oenococcus oeni). Furthermore, the sequence reads associated with viral communities were of a restricted diversity, dominated by Myoviridae and Siphoviridae, and reflecting Lactobacillus as the dominant host. To conclude, an accurate overview of all members of a cocoa bean fermentation process sample was revealed, indicating the superiority of metagenomic sequencing over previously used techniques.}, } @article {pmid22661685, year = {2012}, author = {Stewart, EJ}, title = {Growing unculturable bacteria.}, journal = {Journal of bacteriology}, volume = {194}, number = {16}, pages = {4151-4160}, pmid = {22661685}, issn = {1098-5530}, mesh = {Bacteria/*growth & development/*isolation & purification ; Bacterial Infections/*microbiology ; Bacteriological Techniques/*methods/trends ; *Biodiversity ; *Environmental Microbiology ; }, abstract = {The bacteria that can be grown in the laboratory are only a small fraction of the total diversity that exists in nature. At all levels of bacterial phylogeny, uncultured clades that do not grow on standard media are playing critical roles in cycling carbon, nitrogen, and other elements, synthesizing novel natural products, and impacting the surrounding organisms and environment. While molecular techniques, such as metagenomic sequencing, can provide some information independent of our ability to culture these organisms, it is essentially impossible to learn new gene and pathway functions from pure sequence data. A true understanding of the physiology of these bacteria and their roles in ecology, host health, and natural product production requires their cultivation in the laboratory. Recent advances in growing these species include coculture with other bacteria, recreating the environment in the laboratory, and combining these approaches with microcultivation technology to increase throughput and access rare species. These studies are unraveling the molecular mechanisms of unculturability and are identifying growth factors that promote the growth of previously unculturable organisms. This minireview summarizes the recent discoveries in this area and discusses the potential future of the field.}, } @article {pmid22657530, year = {2012}, author = {Selvin, J and Kennedy, J and Lejon, DP and Kiran, GS and Dobson, AD}, title = {Isolation identification and biochemical characterization of a novel halo-tolerant lipase from the metagenome of the marine sponge Haliclona simulans.}, journal = {Microbial cell factories}, volume = {11}, number = {}, pages = {72}, pmid = {22657530}, issn = {1475-2859}, mesh = {Amino Acid Sequence ; Animals ; Calcium/chemistry ; Cloning, Molecular ; Haliclona/genetics/*metabolism ; Hydrogen-Ion Concentration ; Ions/chemistry ; Lipase/*chemistry/classification/genetics ; Metagenome ; Metals/chemistry ; Molecular Sequence Data ; Phylogeny ; Plasmids/genetics/metabolism ; Protein Stability ; Recombinant Proteins/biosynthesis/chemistry/isolation & purification ; Sequence Alignment ; Sodium Chloride/chemistry ; Substrate Specificity ; Temperature ; }, abstract = {BACKGROUND: Lipases (EC 3.1.1.3) catalyze the hydrolysis of triacyl glycerol to glycerol and are involved in the synthesis of both short chain and long chain acylglycerols. They are widely used industrially in various applications, such as baking, laundry detergents and as biocatalysts in alternative energy strategies. Marine ecosystems are known to represent a large reservoir of biodiversity with respect to industrially useful enzymes. However the vast majority of microorganisms within these ecosystems are not readily culturable. Functional metagenomic based approaches provide a solution to this problem by facilitating the identification of novel enzymes such as the halo-tolerant lipase identified in this study from a marine sponge metagenome.

RESULTS: A metagenomic library was constructed from the marine sponge Haliclona simulans in the pCC1fos vector, containing approximately 48,000 fosmid clones. High throughput plate screening on 1% tributyrin agar resulted in the identification of 58 positive lipase clones. Following sequence analysis of the 10 most highly active fosmid clones the pCC1fos53E1 clone was found to contain a putative lipase gene lpc53E1, encoded by 387 amino acids and with a predicted molecular mass of 41.87 kDa. Sequence analysis of the predicted amino acid sequence of Lpc53E1 revealed that it is a member of the group VIII family of lipases possessing the SXTK motif, related to type C β-lactamases. Heterologous expression of lpc53E1 in E. coli and the subsequent biochemical characterization of the recombinant protein, showed an enzyme with the highest substrate specificity for long chain fatty acyl esters. Optimal activity was observed with p- nitrophenyl palmitate (C16) at 40°C, in the presence of 5 M NaCl at pH 7; while in addition the recombinant enzyme displayed activity across broad pH (3-12) and temperature (4 -60°C) ranges and high levels of stability in the presence of various solvents at NaCl concentrations as high as 5 M and at temperatures ranging from 10 to 80°C. A maximum lipase activity of 2,700 U/mg was observed with 10 mM p-nitrophenyl palmitate as substrate, in the presence of 5 mM Ca2+ and 5 M NaCl, and a reaction time of 15 min at pH 7 and 40°C; while KM and Vmax values were calculated to be 1.093 mM-1 and 50 μmol/min, respectively.

CONCLUSION: We have isolated a novel halo tolerant lipase following a functional screen of a marine sponge fosmid metagenomic library. The activity and stability profile of the recombinant enzyme over a wide range of salinity, pH and temperature; and in the presence of organic solvent and metal ions suggests a utility for this enzyme in a variety of industrial applications.}, } @article {pmid22647069, year = {2012}, author = {Jespers, V and Menten, J and Smet, H and Poradosú, S and Abdellati, S and Verhelst, R and Hardy, L and Buvé, A and Crucitti, T}, title = {Quantification of bacterial species of the vaginal microbiome in different groups of women, using nucleic acid amplification tests.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {83}, pmid = {22647069}, issn = {1471-2180}, mesh = {Adolescent ; Adult ; Bacteria/*classification/*genetics ; Bacterial Load/methods ; *Biodiversity ; Ethnicity ; Female ; Humans ; *Metagenome ; Nucleic Acid Amplification Techniques/*methods ; Vagina/*microbiology ; Young Adult ; }, abstract = {BACKGROUND: The vaginal microbiome plays an important role in urogenital health. Quantitative real time Polymerase Chain Reaction (qPCR) assays for the most prevalent vaginal Lactobacillus species and bacterial vaginosis species G. vaginalis and A. vaginae exist, but qPCR information regarding variation over time is still very limited. We set up qPCR assays for a selection of seven species and defined the temporal variation over three menstrual cycles in a healthy Caucasian population with a normal Nugent score. We also explored differences in qPCR data between these healthy women and an 'at risk' clinic population of Caucasian, African and Asian women with and without bacterial vaginosis (BV), as defined by the Nugent score.

RESULTS: Temporal stability of the Lactobacillus species counts was high with L. crispatus counts of 108 copies/mL and L. vaginalis counts of 106 copies/mL. We identified 2 types of 'normal flora' and one 'BV type flora' with latent class analysis on the combined data of all women. The first group was particularly common in women with a normal Nugent score and was characterized by a high frequency of L. crispatus, L. iners, L. jensenii, and L. vaginalis and a correspondingly low frequency of L. gasseri and A. vaginae. The second group was characterized by the predominance of L. gasseri and L. vaginalis and was found most commonly in healthy Caucasian women. The third group was commonest in women with a high Nugent score but was also seen in a subset of African and Asian women with a low Nugent score and was characterized by the absence of Lactobacillus species (except for L. iners) but the presence of G. vaginalis and A. vaginae.

CONCLUSIONS: We have shown that the quantification of specific bacteria by qPCR contributes to a better description of the non-BV vaginal microbiome, but we also demonstrated that differences in populations such as risk and ethnicity also have to be taken into account. We believe that our selection of indicator organisms represents a feasible strategy for the assessment of the vaginal microbiome and could be useful for monitoring the microbiome in safety trials of vaginal products.}, } @article {pmid22645973, year = {2012}, author = {Kuz'mina, VV and Shalygin, MV and Skvortsova, EG}, title = {[Effect of temperature on proteinase activities of enteral microbiota and intestinal mucosa of fish of different ecological group].}, journal = {Zhurnal evoliutsionnoi biokhimii i fiziologii}, volume = {48}, number = {2}, pages = {129-134}, pmid = {22645973}, issn = {0044-4529}, mesh = {Adaptation, Physiological ; Animals ; Biota ; *Enzyme Stability ; Fishes/*metabolism/microbiology ; Intestinal Mucosa/*enzymology ; Metagenome/physiology ; Peptide Hydrolases/*metabolism ; Temperature ; }, abstract = {Effect of temperature on proteinases activities of enteral microbiota and of intestinal mucosa was studied in five fish species (roach Rutilus rutilus, crucian carp Carassius carassius, common perch Perca fluviatilis, pike-perch Zander lucioperca, and pike Esox lucius) belonging by the nutrition type to different ecological groups. Essential differences of temperature characteristics of proteinases of intestinal mucosa and of enteral microbiota are revealed in fish belonging by the nutrition type to different ecologic groups. The character of the t0-function of proteinases of intestinal mucosa and enteral microbiota by casein and hemoglobin as a rule is different. The highest values of relative proteinases activities for casein in the zone of low temperatures (38 and 45.3 % of the maximal activity) are found at study of proteinases of enteral microbiota in common perch and crucian carp. The latter indicates a significant adaptability of the enteral microbiota proteinases of common perch and crucial carp to functioning at low temperatures.}, } @article {pmid22630140, year = {2012}, author = {Barreto, MC and Houbraken, J and Samson, RA and Brito, D and Gadanho, M and San Romão, MV}, title = {Unveiling the fungal mycobiota present throughout the cork stopper manufacturing process.}, journal = {FEMS microbiology ecology}, volume = {82}, number = {1}, pages = {202-214}, doi = {10.1111/j.1574-6941.2012.01419.x}, pmid = {22630140}, issn = {1574-6941}, mesh = {Biodiversity ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Denaturing Gradient Gel Electrophoresis ; Fungi/*classification/isolation & purification ; Humidity ; Industry ; *Metagenome ; Penicillium/classification/isolation & purification ; Phylogeny ; Plant Bark/*microbiology ; Portugal ; Quercus/*microbiology ; Spain ; Temperature ; }, abstract = {A particular fungal population is present in the main stages of the manufacturing process of cork discs. Its diversity was studied using both dependent (isolation) and independent culture methods (denaturing gel gradient electrophoresis and cloning of the ITS1-5.8S-ITS2 region). The mycobiota in the samples taken in the stages before and after the first boiling seems to be distinct from the population in the subsequent manufacturing stages. Most isolated fungi belong to the genera Penicillium, Eurotium and Cladosporium. The presence of uncultivable fungi, Ascomycota and endophytes in raw cork was confirmed by sequencing. The samples taken after the first boiling contained uncultivable fungi, but in a few samples some isolated fungi were also detected. The main taxa present in the following stages were Chrysonilia sitophila, Penicillium glabrum and Penicillium spp. All applied techniques had complementary outcomes. The main factors driving the shift in cork fungal colonization seem to be the high levels of humidity and temperature to which the slabs are subjected during the boiling process.}, } @article {pmid22626027, year = {2012}, author = {Ward, NL and Pieretti, A and Dowd, SE and Cox, SB and Goldstein, AM}, title = {Intestinal aganglionosis is associated with early and sustained disruption of the colonic microbiome.}, journal = {Neurogastroenterology and motility}, volume = {24}, number = {9}, pages = {874-e400}, doi = {10.1111/j.1365-2982.2012.01937.x}, pmid = {22626027}, issn = {1365-2982}, mesh = {Animals ; Bacteria/classification/genetics ; Biodiversity ; Colon/*microbiology ; Disease Models, Animal ; Enterocolitis/etiology/*microbiology ; Feces/*chemistry ; Hirschsprung Disease/complications/*microbiology ; Magnetic Resonance Spectroscopy ; Metagenome/*physiology ; Mice ; Mice, Transgenic ; RNA, Ribosomal, 16S/*analysis ; }, abstract = {BACKGROUND: Congenital aganglionosis (Hirschsprung's disease) results in colonic dysmotility and a risk for Hirschsprung's-associated enterocolitis (HAEC), whose cause is unknown. We hypothesized that aganglionosis leads to microbiome changes that may contribute to HAEC risk.

METHODS: Colon and fecal samples were collected from endothelin receptor B-null (Ednrb(-/-)) mice, an established model of colorectal aganglionosis, at postnatal day 7 (P7), P20, and P24. We determined microbiome composition by 16S ribosomal RNA gene pyrosequencing and fecal metabolite profile by nuclear magnetic resonance spectroscopy.

KEY RESULTS: Wild-type (WT) mice exhibited increasing species diversity with age, with mutant mice possessing even greater diversity. WT and mutant microbiomes, both fecal and colonic, significantly segregated by principal coordinates analysis based on species composition at all ages examined. Importantly, mutant mice contained more Bacteroidetes and less Firmicutes than WT, with additional genus- and species-level differences observed. Notably, mutant P7 colon was dominated by coagulase-negative Staphylococcus species, which were rare in WT. Mutant fecal metabolite profiles also differed, particularly in the abundance of formate, a short-chain fatty acid product of microbial fermentation.

CONCLUSIONS & INFERENCES: Colorectal aganglionosis is associated with early and sustained disruption of the normal colonic and fecal microbiome, supporting the enteric nervous system as a determinant of microbiome composition. Furthermore, the differences observed suggest a potential contributory role for the microbiome in the etiology of HAEC. These findings provide a basis for further studies to determine the causative role of specific bacterial communities in HAEC and the potential to restore the normal microbiome in Hirschsprung's disease.}, } @article {pmid22616725, year = {2012}, author = {Magwira, CA and Kullin, B and Lewandowski, S and Rodgers, A and Reid, SJ and Abratt, VR}, title = {Diversity of faecal oxalate-degrading bacteria in black and white South African study groups: insights into understanding the rarity of urolithiasis in the black group.}, journal = {Journal of applied microbiology}, volume = {113}, number = {2}, pages = {418-428}, doi = {10.1111/j.1365-2672.2012.05346.x}, pmid = {22616725}, issn = {1365-2672}, mesh = {Adult ; Bifidobacterium/*metabolism ; Biodiversity ; *Black People ; Cluster Analysis ; Denaturing Gradient Gel Electrophoresis ; Feces/*microbiology ; Humans ; Lactobacillus/*metabolism ; Male ; Metagenome ; Oxalates/*metabolism ; Oxalobacter formigenes/*metabolism ; Real-Time Polymerase Chain Reaction ; South Africa/epidemiology ; Urolithiasis/epidemiology/microbiology ; *White People ; }, abstract = {AIM: To examine whether enhanced diversity or numbers of oxalate-degrading bacteria in the gastrointestinal tracts of black South Africans play a role in determining the rarity of urolithiasis in this group.

METHODS AND RESULTS: Fresh faecal samples collected from healthy black and white South African male volunteers were analysed in terms of bacterial oxalate-degrading activity, bacterial diversity and relative species abundance. Varied bacterial populations prepared from samples from the low-risk black group showed a significantly higher level of oxalate degradation. Denaturing gradient gel electrophoresis analyses of Lactobacillus and related spp. and Bifidobacterium spp. 16S rRNA PCR products revealed a significantly higher faecal Lactobacillus diversity for the low-risk black group relative to the higher-risk white group. Quantitative real-time PCR experiments did not show any significant differences between the study groups for Lactobacillus and related spp.. However, Bifidobacterium spp. were present at a significantly higher relative abundance in the black group. Oxalobacter formigenes was present only at very low levels in either group.

CONCLUSIONS: The low abundance of O. formigenes and increased diversity and abundance of oxalate-degrading Lactobacillus and Bifidobacterium spp. in the black South African population suggest that these strains rather than O. formigenes may protect this group against calcium oxalate kidney stone disease.

The South African black population harbours a pool of potential oxalate-degrading lactic acid bacteria, which is more abundant and diverse than that of white South Africans. This may be useful in developing probiotics for calcium oxalate kidney stone prophylaxis.}, } @article {pmid22615371, year = {2012}, author = {Johnson, PT and Hoverman, JT}, title = {Parasite diversity and coinfection determine pathogen infection success and host fitness.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {23}, pages = {9006-9011}, pmid = {22615371}, issn = {1091-6490}, mesh = {Animals ; Anura/growth & development/*parasitology ; *Biodiversity ; California ; *Ecosystem ; Genetic Fitness ; *Host-Parasite Interactions ; Metagenome/genetics/physiology ; Survival Analysis ; Trematoda/*pathogenicity ; Trematode Infections/*transmission/*veterinary ; Virulence ; }, abstract = {While the importance of changes in host biodiversity for disease risk continues to gain empirical support, the influence of natural variation in parasite diversity on epidemiological outcomes remains largely overlooked. Here, we combined field infection data from 2,191 amphibian hosts representing 158 parasite assemblages with mechanistic experiments to evaluate the influence of parasite richness on both parasite transmission and host fitness. Using a guild of larval trematode parasites (six species) and an amphibian host, our experiments contrasted the effects of parasite richness vs. composition, observed vs. randomized assemblages, and additive vs. replacement designs. Consistent with the dilution effect hypothesis extended to intrahost diversity, increases in parasite richness reduced overall infection success, including infections by the most virulent parasite. However, the effects of parasite richness on host growth and survival were context dependent; pathology increased when parasites were administered additively, even when the presence of the most pathogenic species was held constant, but decreased when added species replaced or reduced virulent species, emphasizing the importance of community composition and assembly. These results were similar or stronger when community structures were weighted by their observed frequencies in nature. The field data also revealed the highly nested structure of parasite assemblages, with virulent species generally occupying basal positions, suggesting that increases in parasite richness and antagonism in nature will decrease virulent infections. Our findings emphasize the importance of parasite biodiversity and coinfection in affecting epidemiological responses and highlight the value of integrating research on biodiversity and community ecology for understanding infectious diseases.}, } @article {pmid22615052, year = {2013}, author = {Chi Fru, E and Chen, M and Walshe, G and Penner, T and Weisener, C}, title = {Bioreactor studies predict whole microbial population dynamics in oil sands tailings ponds.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {7}, pages = {3215-3224}, doi = {10.1007/s00253-012-4137-6}, pmid = {22615052}, issn = {1432-0614}, mesh = {Archaea/classification/*growth & development ; Bacteria/classification/*growth & development ; Bioreactors/*microbiology ; *Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Metagenome ; *Oils ; Population Dynamics ; *Silicon Dioxide ; *Soil Microbiology ; Time Factors ; }, abstract = {Microorganisms in oil sands fluid fine tailings (FFT) are critical to biogeochemical elemental cycling as well as to the degradation of residual hydrocarbon constituents and subsequent methane and CO2 production. Microbial activity enhances particulate matter sedimentation rates and the dewatering of FFT materials, allowing water to be recycled back into bitumen extraction. A bulk of this evidence comes from bioreactor studies and has implications for engineering and environmental management of the FFT ponds. Yet, it is largely uncertain whether such laboratory populations are representative of whole field scale microbial communities. By using population ecology tools, we compared whole microbial communities present in FFT bioreactors to reference populations existing in Syncrude's West In Pit (WIP) tailings pond. Bacteria were found to be persistent in a sulfidic zone in both the oxic and anoxic bioreactors at all occasions tested. In contrast to the WIP, archaea only became predominant in bioreactors after 300 days, at which point analysis of similarity (global R statistic p<0.5) revealed no significant dissimilarities between the populations present in either system. A whole community succession pattern from bacterial dominated prevalence to a new assemblage predominated by archaea was suggested. These results have implications for the stepwise development of microbial model systems for predictive management of field scale FFT basins.}, } @article {pmid22612542, year = {2012}, author = {Jiménez-Pranteda, ML and Aguilera, M and McCartney, AL and Hoyles, L and Jiménez-Valera, M and Náder-Macías, ME and Ramos-Cormenzana, A and Monteoliva-Sánchez, M}, title = {Investigation of the impact of feeding Lactobacillus plantarum CRL 1815 encapsulated in microbially derived polymers on the rat faecal microbiota.}, journal = {Journal of applied microbiology}, volume = {113}, number = {2}, pages = {399-410}, doi = {10.1111/j.1365-2672.2012.05343.x}, pmid = {22612542}, issn = {1365-2672}, mesh = {Animals ; Bifidobacterium/genetics/growth & development ; Biodiversity ; Capsules ; Clostridium histolyticum/genetics/growth & development ; Drug Carriers/*chemistry ; Electrophoresis, Gel, Pulsed-Field ; Feces/*microbiology ; Female ; Gastrointestinal Tract/microbiology ; *Lactobacillus plantarum ; *Metagenome ; Polymers/chemistry ; Polysaccharides, Bacterial/chemistry ; Probiotics/*administration & dosage ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Wistar ; }, abstract = {AIMS: The aim of this study was to evaluate the impact of the administration of microencapsulated Lactobacillus plantarum CRL 1815 with two combinations of microbially derived polysaccharides, xanthan : gellan gum (1%:0·75%) and jamilan : gellan gum (1%:1%), on the rat faecal microbiota.

METHODS AND RESULTS: A 10-day feeding study was performed for each polymer combination in groups of 16 rats fed either with placebo capsules, free or encapsulated Lact. plantarum or water. The composition of the faecal microbiota was analysed by fluorescence in situ hybridization and temporal temperature gradient gel electrophoresis. Degradation of placebo capsules was detected, with increased levels of polysaccharide-degrading bacteria. Xanthan : gellan gum capsules were shown to reduce the Bifidobacterium population and increase the Clostridium histolyticum group levels, but not jamilan : gellan gum capsules. Only after administration of jamilan : gellan gum-probiotic capsules was detected a significant increase in Lactobacillus-Enterococcus group levels compared to controls (capsules and probiotic) as well as two bands were identified as Lact. plantarum in two profiles of ileum samples.

CONCLUSIONS: Exopolysaccharides constitute an interesting approach for colon-targeted delivery of probiotics, where jamilan : gellan gum capsules present better biocompatibility and promising results as a probiotic carrier.

This study introduces and highlights the importance of biological compatibility in the encapsulating material election, as they can modulate the gut microbiota by themselves, and the use of bacterial exopolysaccharides as a powerful source of new targeted-delivery coating material.}, } @article {pmid22611623, year = {2012}, author = {Clerc, O and Prod'hom, G and Petignat, C}, title = {[Uncomplicated urinary tract infections: impact of increasing antibiotic resistance in the community].}, journal = {Revue medicale suisse}, volume = {8}, number = {338}, pages = {878-881}, pmid = {22611623}, issn = {1660-9379}, mesh = {Anti-Bacterial Agents/therapeutic use ; *Biota ; Drug Resistance, Microbial/*physiology ; Humans ; Internal Medicine/methods/*trends ; Metagenome/physiology ; Practice Guidelines as Topic ; Practice Patterns, Physicians'/statistics & numerical data/trends ; Pyelonephritis/etiology/microbiology/therapy ; Urinary Tract Infections/epidemiology/microbiology/*therapy ; }, abstract = {Uncomplicated urinary tract infections are commonly encountered in primary care and frequently lead to empirical antibiotic prescriptions. The development of antibiotic resistance in the community explains treatment failures observed with commonly-prescribed drugs such as quinolones and co-trimoxazole. This article describes the epidemiology of antibiotic resistance among pathogens causing uncomplicated urinary tract infections and the consequences in terms of recommendations for empirical antibiotic therapy.}, } @article {pmid22610288, year = {2012}, author = {Dionisi, HM and Lozada, M and Olivera, NL}, title = {Bioprospection of marine microorganisms: biotechnological applications and methods.}, journal = {Revista Argentina de microbiologia}, volume = {44}, number = {1}, pages = {49-60}, doi = {10.1590/S0325-75412012000100010}, pmid = {22610288}, issn = {0325-7541}, mesh = {Agricultural Inoculants ; Argentina ; Biocatalysis ; Biodiversity ; Biotechnology/*methods/trends ; Drug Discovery ; Ecosystem ; *Environmental Microbiology ; Industrial Microbiology/methods/trends ; Marine Biology/*methods/trends ; Metagenomics/methods ; Microbial Consortia ; }, abstract = {Environmental microorganisms constitute an almost inexhaustible reserve of genetic and functional diversity, accumulated during millions of years of adaptive evolution to various selective pressures. In particular, the extent of microbial biodiversity in marine habitats seems to grow larger as new techniques emerge to measure it. This has resulted in novel and more complex approaches for the screening of molecules and activities of biotechnological interest in these environments. In this review, we explore the different partially overlapping biotechnological fields that make use of microorganisms and we describe the different marine habitats that are particularly attractive for bioprospection. In addition, we review the methodological approaches currently used for microbial bioprospection, from the traditional cultivation techniques to state of the art metagenomic approaches, with emphasis in the marine environment.}, } @article {pmid22608236, year = {2012}, author = {Zheng, XW and Yan, Z and Han, BZ and Zwietering, MH and Samson, RA and Boekhout, T and Robert Nout, MJ}, title = {Complex microbiota of a Chinese "Fen" liquor fermentation starter (Fen-Daqu), revealed by culture-dependent and culture-independent methods.}, journal = {Food microbiology}, volume = {31}, number = {2}, pages = {293-300}, doi = {10.1016/j.fm.2012.03.008}, pmid = {22608236}, issn = {1095-9998}, mesh = {Bacteria/classification/genetics/growth & development/*isolation & purification ; Biodiversity ; Colony Count, Microbial/*methods ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; Electrophoresis, Polyacrylamide Gel/*methods ; Fermentation ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; Wine/analysis/*microbiology ; Yeasts/classification/genetics/growth & development/*isolation & purification ; }, abstract = {Daqu is a traditional fermentation starter that is used for Chinese liquor production. Although partly mechanized, its manufacturing process has remained traditional. We investigated the microbial diversity of Fen-Daqu, a starter for light-flavour liquor, using combined culture-dependent and culture-independent approaches (PCR-DGGE). A total of 190 microbial strains, comprising 109 bacteria and 81 yeasts and moulds, were isolated and identified on the basis of the sequences of their 16S rDNA (bacteria) and 26S rDNA and ITS regions (fungi). DGGE of DNA extracted from Daqu was used to complement the culture-dependent method in order to include non-culturable microbes. Both approaches revealed that Bacillus licheniformis was an abundant bacterial species, and Saccharomycopsis fibuligera, Wickerhamomyces anomalus, and Pichia kudriavzevii were the most common yeasts encountered in Fen-Daqu. Six genera of moulds (Absidia, Aspergillus, Mucor, Rhizopus, Rhizomucor and Penicillium) were found. The potential function of these microorganisms in starters for alcoholic fermentation is discussed. In general the culture-based findings overlapped with those obtained by DGGE by a large extent. However, Weissella cibaria, Weissella confusa, Staphylococcus saprophyticus, Enterobacter aerogenes, Lactobacillus sanfranciscensis, Lactobacillus lactis, and Bacillus megaterium were only revealed by DGGE.}, } @article {pmid22584354, year = {2012}, author = {Hunter, P}, title = {The changing hypothesis of the gut. The intestinal microbiome is increasingly seen as vital to human health.}, journal = {EMBO reports}, volume = {13}, number = {6}, pages = {498-500}, pmid = {22584354}, issn = {1469-3178}, mesh = {Anti-Bacterial Agents/pharmacology ; Autoimmune Diseases/epidemiology/immunology/microbiology ; Bacteria/drug effects ; Biota ; Gastrointestinal Tract/*microbiology ; *Health ; Humans ; Hypersensitivity/epidemiology/immunology/microbiology ; *Metagenome/drug effects ; }, } @article {pmid22581327, year = {2012}, author = {Pandey, PK and Siddharth, J and Verma, P and Bavdekar, A and Patole, MS and Shouche, YS}, title = {Molecular typing of fecal eukaryotic microbiota of human infants and their respective mothers.}, journal = {Journal of biosciences}, volume = {37}, number = {2}, pages = {221-226}, pmid = {22581327}, issn = {0973-7138}, mesh = {Adult ; Biodiversity ; Blastocystis/genetics/isolation & purification ; Breast Feeding ; Feces/*microbiology ; Female ; Fungi/genetics/isolation & purification ; Gastrointestinal Tract/*microbiology ; Humans ; Infant ; Infant Formula ; *Metagenome ; Molecular Typing/methods ; Mothers ; RNA, Ribosomal, 18S/genetics ; }, abstract = {The micro-eukaryotic diversity from the human gut was investigated using universal primers directed towards 18S rRNA gene, fecal samples being the source of DNA. The subjects in this study included two breast-fed and two formula-milk-fed infants and their mothers. The study revealed that the infants did not seem to harbour any microeukaryotes in their gut. In contrast, there were distinct eukaryotic microbiota present in the mothers. The investigation is the first of its kind in the comparative study of the human feces to reveal the presence of micro-eukaryotic diversity variance in infants and adults from the Indian subcontinent. The micro-eukaryotes encountered during the investigation include known gut colonizers like Blastocystis and some fungi species. Some of these micro-eukaryotes have been speculated to be involved in clinical manifestations of various diseases. The study is an attempt to highlight the importance of micro-eukaryotes in the human gut.}, } @article {pmid22580321, year = {2012}, author = {Cydzik-Kwiatkowska, A and Zielińska, M and Bernat, K and Kulikowska, D and Wojnowska-Baryła, I}, title = {Changes in the ammonia-oxidizing bacteria community in response to operational parameters during the treatment of anaerobic sludge digester supernatant.}, journal = {Journal of microbiology and biotechnology}, volume = {22}, number = {7}, pages = {1005-1014}, doi = {10.4014/jmb.1111.11011}, pmid = {22580321}, issn = {1738-8872}, mesh = {Ammonia/*metabolism ; Anaerobiosis ; Bacteria/*classification/*isolation & purification ; Bioreactors/microbiology ; *Biota ; DNA, Bacterial/chemistry/genetics ; Metagenome ; Molecular Sequence Data ; Oxidation-Reduction ; Sequence Analysis, DNA ; Sewage/*microbiology ; Time Factors ; Water Purification/*methods ; }, abstract = {The understanding of the relationship between ammoniaoxidizing bacteria (AOB) communities in activated sludge and the operational treatment parameters supports the control of the treatment of ammonia-rich wastewater. The modifications of treatment parameters by alteration of the number and length of aerobic and anaerobic stages in the sequencing batch reactor (SBR) working cycle may influence the efficiency of ammonium oxidation and induce changes in the AOB community. Therefore, in the research, the impact of an SBR cycle mode with alternating aeration/ mixing conditions (7 h/1 h vs. 4 h/5.5 h) and volumetric exchange rate (n) on AOB abundance and diversity in activated sludge during the treatment of anaerobic sludge digester supernatant at limited oxygen concentration in the aeration stage (0.7 mg O2/l) was assessed. AOB diversity expressed by the Shannon-Wiener index (H') was determined by the cycle mode. At aeration/mixing stage lengths of 7 h/1 h, H' averaged 2.48 +/- 0.17, while at 4 h/ 5.5 h it was 2.35 +/- 0.16. At the given mode, AOB diversity decreased with increasing n. The cycle mode did not affect AOB abundance; however, a higher AOB abundance in activated sludge was promoted by decreasing the volumetric exchange rate. The sequences clustering with Nitrosospira sp. NpAV revealed the uniqueness of the AOB community and the simultaneously lower ability of adaptation of Nitrosospira sp. to the operational parameters applied in comparison with Nitrosomonas sp.}, } @article {pmid22576945, year = {2013}, author = {Ji, G and Wang, C and Guo, F}, title = {Characterisation of microbial floras and functional gene levels in an anaerobic/aerobic bio-reactor for the degradation of carboxymethyl cellulose.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {7}, pages = {3195-3206}, doi = {10.1007/s00253-012-4134-9}, pmid = {22576945}, issn = {1432-0614}, mesh = {Aerobiosis ; Anaerobiosis ; Archaea/*classification/genetics/growth & development/metabolism ; Bacteria/*classification/genetics/growth & development/metabolism ; Bioreactors/*microbiology ; *Biota ; Biotransformation ; Carboxymethylcellulose Sodium/*metabolism ; Denaturing Gradient Gel Electrophoresis ; *Gene Expression Profiling ; Metagenome ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {The current study determined the carboxymethyl cellulose (CMC) degradation efficiency, dominant microbial flora, eubacteria and archaebacteria characteristics, and expression levels of genes cel5A, cel6B, and bglC in an anaerobic/aerobic bio-reactor consisting of two-stage UASB (U1 and U2) and two-stage BAF (B1 and B2). The results showed that under three CMC loads, the CMC degradation efficiency of the UASB-BAF system was 91.25%, 80.44%, and 78.73%, respectively. At higher CMC loads, the degradation of cellulose and transformation to cellobiose in U1 was higher, while the transformation to glucose was lower. The results of DGGE and real-time PCR indicated that cellulose degradation bacteria are dominant in U1, cellulose degradation bacteria and cellulose degradation symbiosis bacteria are dominant in B1, and non-cellulose degradation symbiosis bacteria are dominant in both U2 and B2. The rate-limiting enzyme gene of cellulose degradation in U1, B1, and B2 is cel6B, but it is cel5A in U2.}, } @article {pmid22575897, year = {2012}, author = {Nielsen, JL and Nguyen, H and Meyer, RL and Nielsen, PH}, title = {Identification of glucose-fermenting bacteria in a full-scale enhanced biological phosphorus removal plant by stable isotope probing.}, journal = {Microbiology (Reading, England)}, volume = {158}, number = {Pt 7}, pages = {1818-1825}, doi = {10.1099/mic.0.058818-0}, pmid = {22575897}, issn = {1465-2080}, mesh = {Bacteria/*classification/*metabolism ; *Biodiversity ; Carbon Isotopes/metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fermentation ; Glucose/*metabolism ; In Situ Hybridization, Fluorescence ; Isotope Labeling ; Metagenome ; Molecular Sequence Data ; Phosphorus/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Microbiology ; Water Purification/methods ; }, abstract = {Microbiology in wastewater treatment has mainly been focused on problem-causing filamentous bacteria or bacteria directly involved in nitrogen and phosphorus removal, and to a lesser degree on flanking groups, such as hydrolysing and fermenting bacteria. However, these groups constitute important suppliers of readily degradable substrates for the overall processes in the plant. This study aimed to identify glucose-fermenting bacteria in a full-scale enhanced biological phosphorus removal (EBPR) wastewater treatment plant (WWTP), and to determine their abundance in similar WWTPs. Glucose-fermenting micro-organisms were identified by an in situ approach using RNA-based stable isotope probing. Activated sludge was incubated anaerobically with (13)C(6)-labelled glucose, and (13)C-enriched rRNA was subsequently reverse-transcribed and used to construct a 16S rRNA gene clone library. Phylogenetic analysis of the library revealed the presence of two major phylogenetic groups of gram-positive bacteria affiliating with the genera Tetrasphaera, Propionicimonas (Actinobacteria), and Lactococcus and Streptococcus (Firmicutes). Specific oligonucleotide probes were designed for fluorescence in situ hybridization (FISH) to specifically target the glucose-fermenting bacteria identified in this study. The combination of FISH with microautoradiography confirmed that Tetrasphaera, Propionicimonas and Streptococcus were the dominant glucose fermenters. The probe-defined fermenters were quantified in 10 full-scale EBPR plants and averaged 39 % of the total biovolume. Tetrasphaera and Propionicimonas were the most abundant glucose fermenters (average 33 and 4 %, respectively), while Streptococcus and Lactococcus were present only in some WWTPs (average 1 and 0.4 %, respectively). Thus the population of actively metabolizing glucose fermenters seems to occupy a relatively large component of the total biovolume.}, } @article {pmid22574119, year = {2012}, author = {Sanchez, LM and Wong, WR and Riener, RM and Schulze, CJ and Linington, RG}, title = {Examining the fish microbiome: vertebrate-derived bacteria as an environmental niche for the discovery of unique marine natural products.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e35398}, pmid = {22574119}, issn = {1932-6203}, support = {U01 TW006634/TW/FIC NIH HHS/United States ; 2R25GM05803-12/GM/NIGMS NIH HHS/United States ; TW006634/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/growth & development/*isolation & purification/*metabolism ; Biodiversity ; Biological Products/*metabolism ; Culture Techniques ; *Drug Discovery ; Fishes/*microbiology ; Intestines/microbiology ; *Metagenome ; Oceans and Seas ; Phylogeny ; }, abstract = {Historically, marine invertebrates have been a prolific source of unique natural products, with a diverse array of biological activities. Recent studies of invertebrate-associated microbial communities are revealing microorganisms as the true producers of many of these compounds. Inspired by the human microbiome project, which has highlighted the human intestine as a unique microenvironment in terms of microbial diversity, we elected to examine the bacterial communities of fish intestines (which we have termed the fish microbiome) as a new source of microbial and biosynthetic diversity for natural products discovery. To test the hypothesis that the fish microbiome contains microorganisms with unique capacity for biosynthesizing natural products, we examined six species of fish through a combination of dissection and culture-dependent evaluation of intestinal microbial communities. Using isolation media designed to enrich for marine Actinobacteria, we have found three main clades that show taxonomic divergence from known strains, several of which are previously uncultured. Extracts from these strains exhibit a wide range of activities against both gram-positive and gram-negative human pathogens, as well as several fish pathogens. Exploration of one of these extracts has identified the novel bioactive lipid sebastenoic acid as an anti-microbial agent, with activity against Staphylococcus aureus, Bacillus subtilis, Enterococcus faecium, and Vibrio mimicus.}, } @article {pmid22573274, year = {2013}, author = {Kim, TG and Moon, KE and Yun, J and Cho, KS}, title = {Comparison of RNA- and DNA-based bacterial communities in a lab-scale methane-degrading biocover.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {7}, pages = {3171-3181}, doi = {10.1007/s00253-012-4123-z}, pmid = {22573274}, issn = {1432-0614}, mesh = {Bacteria/*classification/genetics/metabolism ; Benzene/metabolism ; *Biota ; DNA, Bacterial/*genetics ; DNA, Ribosomal/genetics ; Metagenomics/*methods ; Methane/*metabolism ; RNA, Bacterial/*genetics ; RNA, Ribosomal/genetics ; *Soil Microbiology ; Sulfides/metabolism ; Toluene/metabolism ; }, abstract = {Methanotrophs must become established and active in a landfill biocover for successful methane oxidation. A lab-scale biocover with a soil mixture was operated for removal of methane and nonmethane volatile organic compounds, such as dimethyl sulfide (DMS), benzene (B), and toluene (T). The methane elimination capacity was 211±40 g m(-2) d(-1) at inlet loads of 330-516 g m(-2) d(-1). DMS, B, and T were completely removed at the bottom layer (40-50 cm) with inlet loads of 221.6±92.2, 99.6±19.5, and 23.4±4.9 mg m(-2) d(-1), respectively. The bacterial community was examined based on DNA and RNA using ribosomal tag pyrosequencing. Interestingly, methanotrophs comprised 80% of the active community (RNA) while 29% of the counterpart (DNA). Types I and II methanotrophs equally contributed to methane oxidation, and Methylobacter, Methylocaldum, and Methylocystis were dominant in both communities. The DNA vs. RNA comparison suggests that DNA-based analysis alone can lead to a significant underestimation of active members.}, } @article {pmid22566627, year = {2012}, author = {Hanski, I and von Hertzen, L and Fyhrquist, N and Koskinen, K and Torppa, K and Laatikainen, T and Karisola, P and Auvinen, P and Paulin, L and Mäkelä, MJ and Vartiainen, E and Kosunen, TU and Alenius, H and Haahtela, T}, title = {Environmental biodiversity, human microbiota, and allergy are interrelated.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {21}, pages = {8334-8339}, pmid = {22566627}, issn = {1091-6490}, support = {232826/ERC_/European Research Council/International ; }, mesh = {Acinetobacter/immunology ; Adolescent ; Alphaproteobacteria/immunology ; Bacillus/immunology ; Betaproteobacteria/immunology ; *Biodiversity ; Civilization ; Clostridium/immunology ; Environmental Exposure ; Finland/epidemiology ; Gammaproteobacteria/immunology ; Humans ; *Hygiene Hypothesis ; Hypersensitivity/epidemiology/*immunology/*microbiology ; Logistic Models ; Metagenome/*immunology ; Prevalence ; Random Allocation ; Skin/immunology/microbiology ; }, abstract = {Rapidly declining biodiversity may be a contributing factor to another global megatrend--the rapidly increasing prevalence of allergies and other chronic inflammatory diseases among urban populations worldwide. According to the "biodiversity hypothesis," reduced contact of people with natural environmental features and biodiversity may adversely affect the human commensal microbiota and its immunomodulatory capacity. Analyzing atopic sensitization (i.e., allergic disposition) in a random sample of adolescents living in a heterogeneous region of 100 × 150 km, we show that environmental biodiversity in the surroundings of the study subjects' homes influenced the composition of the bacterial classes on their skin. Compared with healthy individuals, atopic individuals had lower environmental biodiversity in the surroundings of their homes and significantly lower generic diversity of gammaproteobacteria on their skin. The functional role of the gram-negative gammaproteobacteria is supported by in vitro measurements of expression of IL-10, a key anti-inflammatory cytokine in immunologic tolerance, in peripheral blood mononuclear cells. In healthy, but not in atopic, individuals, IL-10 expression was positively correlated with the abundance of the gammaproteobacterial genus Acinetobacter on the skin. These results raise fundamental questions about the consequences of biodiversity loss for both allergic conditions and public health in general.}, } @article {pmid22566034, year = {2012}, author = {Wang, D and Yang, G and Li, X and Zheng, W and Wu, Y and Yang, Q and Zeng, G}, title = {Inducing mechanism of biological phosphorus removal driven by the aerobic/extended-idle regime.}, journal = {Biotechnology and bioengineering}, volume = {109}, number = {11}, pages = {2798-2807}, doi = {10.1002/bit.24543}, pmid = {22566034}, issn = {1097-0290}, mesh = {Aerobiosis ; Bacteria/classification/isolation & purification/*metabolism ; Biodiversity ; Biotransformation ; Glycogen/metabolism ; Metagenome ; Phosphorus/*metabolism ; Polyhydroxyalkanoates/*metabolism ; Sewage/*microbiology ; }, abstract = {Recently, it was found that excess phosphorus (Pi) removal could be achieved in activated sludge with an aerobic/extended-idle (AEI) process. In this study, batch tests were performed to further reveal the inducing mechanism of Pi removal involved in the AEI process. Unlike the classical anaerobic/aerobic process where an anaerobic Pi release along with a significant polyhydroxyalkanoate (PHA) accumulation drives polyphosphate (poly-P) accumulating organisms (PAOs) to over-store Pi as poly-P, an idle Pi release accompanied by a low-idle PHA production, which is usually considered to be detrimental for biological Pi removal, was observed to induce some cells to effectively uptake Pi in excess of metabolic requirement in the AEI process. With the increase of idle Pi release, Pi removal efficiency linearly increased. The results also showed that a long idle period with a low level of intracellular glycogen could significantly increase Pi release contents, thus remarkably enhancing Pi removal performances. Fluorescence in situ hybridization analysis further revealed that activated sludge in the AEI process contained 37.6% of Accumulibacter (PAOs) and 28.2% of Competibacter and Defluviicoccus-related organisms (glycogen accumulating organisms). This study revealed an actually existent, yet previously unrecognized, inducing mechanism of poly-P accumulation, and this mechanism behind the AEI regime may provide a scientific basis for the development of an alternative strategy for Pi removal from wastewaters.}, } @article {pmid22564556, year = {2012}, author = {Meng, X and Wang, L and Long, X and Liu, Z and Zhang, Z and Zed, R}, title = {Influence of nitrogen fertilization on diazotrophic communities in the rhizosphere of the Jerusalem artichoke (Helianthus tuberosus L.).}, journal = {Research in microbiology}, volume = {163}, number = {5}, pages = {349-356}, doi = {10.1016/j.resmic.2012.03.005}, pmid = {22564556}, issn = {1769-7123}, mesh = {*Biota ; *Fertilizers ; Helianthus/*microbiology ; Metagenome ; Nitrogen/*metabolism ; *Nitrogen Fixation ; Oxidoreductases/genetics ; Plant Roots/microbiology ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; *Rhizosphere ; }, abstract = {Diazotrophs in the soil may be influenced by plant factors as well as nitrogen (N) fertilization. In this study, we investigated potential diazotrophic communities in the rhizosphere of the Jerusalem artichoke (Helianthus tuberosus L.) supplied with differing amounts of N. The community structure of N(2)-fixing bacteria was profiled using the length heterogeneity polymerase chain reaction (LH-PCR) and terminal restriction fragment length polymorphism (T-RFLP) based on a variation in the nifH gene. Higher numbers of diazotrophs were detected by T-RFLP compared to LH-PCR. The lowest number of N(2)-fixing bacteria was observed in the rhizosphere soil with high N fertilization. T-RFLP was a better method than LH-PCR for profiling microbial diversity of diazotrophs using multidimensional scaling (MDS) and analysis of similarity (ANOSIM) of fingerprints as well as diversity measures. The supply of N fertilizer appeared to negatively influence the abundance of diazotrophs in the rhizophere of the Jerusalem artichoke.}, } @article {pmid22564542, year = {2012}, author = {Berendsen, RL and Pieterse, CM and Bakker, PA}, title = {The rhizosphere microbiome and plant health.}, journal = {Trends in plant science}, volume = {17}, number = {8}, pages = {478-486}, doi = {10.1016/j.tplants.2012.04.001}, pmid = {22564542}, issn = {1878-4372}, support = {269072/ERC_/European Research Council/International ; }, mesh = {Anti-Infective Agents/chemistry/immunology ; Biota ; Fungi/chemistry/immunology/pathogenicity ; Host-Pathogen Interactions ; *Metagenome ; Microbial Interactions ; Plant Diseases/immunology/microbiology ; Plant Roots/chemistry/microbiology ; Plants/chemistry/immunology/*microbiology ; Pseudomonas/chemistry/growth & development/immunology ; Rhizobiaceae/chemistry/growth & development/immunology ; *Rhizosphere ; *Soil Microbiology ; Species Specificity ; }, abstract = {The diversity of microbes associated with plant roots is enormous, in the order of tens of thousands of species. This complex plant-associated microbial community, also referred to as the second genome of the plant, is crucial for plant health. Recent advances in plant-microbe interactions research revealed that plants are able to shape their rhizosphere microbiome, as evidenced by the fact that different plant species host specific microbial communities when grown on the same soil. In this review, we discuss evidence that upon pathogen or insect attack, plants are able to recruit protective microorganisms, and enhance microbial activity to suppress pathogens in the rhizosphere. A comprehensive understanding of the mechanisms that govern selection and activity of microbial communities by plant roots will provide new opportunities to increase crop production.}, } @article {pmid22558432, year = {2012}, author = {Delhaes, L and Monchy, S and Fréalle, E and Hubans, C and Salleron, J and Leroy, S and Prevotat, A and Wallet, F and Wallaert, B and Dei-Cas, E and Sime-Ngando, T and Chabé, M and Viscogliosi, E}, title = {The airway microbiota in cystic fibrosis: a complex fungal and bacterial community--implications for therapeutic management.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e36313}, pmid = {22558432}, issn = {1932-6203}, mesh = {Adult ; Bacteria/classification/genetics ; Biodiversity ; Cystic Fibrosis/*microbiology/*therapy ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Female ; Fungi/classification/genetics ; Humans ; Male ; Metagenome/*genetics ; Respiratory System/*microbiology ; *Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Given the polymicrobial nature of pulmonary infections in patients with cystic fibrosis (CF), it is essential to enhance our knowledge on the composition of the microbial community to improve patient management. In this study, we developed a pyrosequencing approach to extensively explore the diversity and dynamics of fungal and prokaryotic populations in CF lower airways.

Fungi and bacteria diversity in eight sputum samples collected from four adult CF patients was investigated using conventional microbiological culturing and high-throughput pyrosequencing approach targeting the ITS2 locus and the 16S rDNA gene. The unveiled microbial community structure was compared to the clinical profile of the CF patients. Pyrosequencing confirmed recently reported bacterial diversity and observed complex fungal communities, in which more than 60% of the species or genera were not detected by cultures. Strikingly, the diversity and species richness of fungal and bacterial communities was significantly lower in patients with decreased lung function and poor clinical status. Values of Chao1 richness estimator were statistically correlated with values of the Shwachman-Kulczycki score, body mass index, forced vital capacity, and forced expiratory volume in 1 s (p = 0.046, 0.047, 0.004, and 0.001, respectively for fungal Chao1 indices, and p = 0.010, 0.047, 0.002, and 0.0003, respectively for bacterial Chao1 values). Phylogenetic analysis showed high molecular diversities at the sub-species level for the main fungal and bacterial taxa identified in the present study. Anaerobes were isolated with Pseudomonas aeruginosa, which was more likely to be observed in association with Candida albicans than with Aspergillus fumigatus.

CONCLUSIONS: In light of the recent concept of CF lung microbiota, we viewed the microbial community as a unique pathogenic entity. We thus interpreted our results to highlight the potential interactions between microorganisms and the role of fungi in the context of improving survival in CF.}, } @article {pmid22555912, year = {2013}, author = {Ye, L and Zhang, T}, title = {Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {6}, pages = {2681-2690}, pmid = {22555912}, issn = {1432-0614}, mesh = {Bacteria/*classification/*genetics ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Microbiology ; Water Purification ; }, abstract = {In this study, we successfully demonstrated that 454 pyrosequencing was a powerful approach for investigating the bacterial communities in the activated sludge, digestion sludge, influent, and effluent samples of a full scale wastewater treatment plant treating saline sewage. For each sample, 18,808 effective sequences were selected and utilized to do the bacterial diversity and abundance analysis. In total, 2,455, 794, 1,667, and 1,932 operational taxonomic units were obtained at 3 % distance cutoff in the activated sludge, digestion sludge, influent, and effluent samples, respectively. The corresponding most dominant classes in the four samples are Alphaproteobacteria, Thermotogae, Deltaproteobacteria, and Gammaproteobacteria. About 67 % sequences in the digestion sludge sample were found to be affiliated with the Thermotogales order. Also, these sequences were assigned into a recently proposed genus Kosmotoga by the Ribosomal Database Project classifier. In the effluent sample, we found high abundance of Mycobacterium and Vibrio, which are genera containing pathogenic bacteria. Moreover, in this study, we proposed a method to differentiate the "gene percentage" and "cell percentage" by using Ribosomal RNA Operon Copy Number Database.}, } @article {pmid22555633, year = {2012}, author = {Parnell, JA and Reimer, RA}, title = {Prebiotic fiber modulation of the gut microbiota improves risk factors for obesity and the metabolic syndrome.}, journal = {Gut microbes}, volume = {3}, number = {1}, pages = {29-34}, pmid = {22555633}, issn = {1949-0984}, support = {115076-1/CAPMC/CIHR/Canada ; }, mesh = {Animals ; Biota ; Dietary Fiber/*administration & dosage ; Disease Models, Animal ; Dose-Response Relationship, Drug ; Gastrointestinal Tract/microbiology ; Metabolic Syndrome/*prevention & control ; Metagenome/drug effects ; Obesity/*prevention & control ; Rats ; Risk Factors ; }, abstract = {Prebiotic fibers are non-digestible carbohydrates that promote the growth of beneficial bacteria in the gut. Prebiotic consumption may benefit obesity and associated co-morbidities by improving or normalizing the dysbiosis of the gut microbiota. We evaluated the dose response to a prebiotic diet on the gut microbiota, body composition and obesity associated risk factors in lean and genetically obese rats. Prebiotic fibers increased Firmicutes and decreased Bacteroidetes, a profile often associated with a leaner phenotype. Bifidobacteria and Lactobacillus numbers also increased. Changes in the gut microbiota correlated with energy intake, glucose, insulin, satiety hormones, and hepatic cholesterol and triglyceride accumulation. Here we provide a comprehensive analysis evaluating the results through the lens of the gut microbiota. Salient, new developments impacting the interpretation and significance of our data are discussed. We propose that prebiotic fibers have promise as a safe and cost-effective means of modulating the gut microbiota to promote improved host:bacterial interactions in obesity and insulin resistance. Human clinical trials should be undertaken to confirm these effects.}, } @article {pmid22555548, year = {2012}, author = {Toward, R and Montandon, S and Walton, G and Gibson, GR}, title = {Effect of prebiotics on the human gut microbiota of elderly persons.}, journal = {Gut microbes}, volume = {3}, number = {1}, pages = {57-60}, doi = {10.4161/gmic.19411}, pmid = {22555548}, issn = {1949-0984}, mesh = {Aged ; Aged, 80 and over ; Bifidobacterium/drug effects ; Biota ; Colon/*microbiology ; Diet/*methods ; Humans ; Metagenome/*drug effects ; Oligosaccharides/administration & dosage ; *Prebiotics ; }, abstract = {The colonic microbiota undergoes certain age related changes that may affect health. For example, above the age of 55-65 y, populations of bifidobacteria are known to decrease markedly. Bifidobacteria are known inhibitors of pathogenic microbes and a decrease in their activities may increase susceptibility to infections. There is therefore interest in trying to reverse their decline in aged persons. As the gut microbiota responds to dietary intervention, both probiotics and prebiotics have been tested in this regard. Probiotics are live microbes in the diet, whereas prebiotics are fermentable ingredients that specifically target components of the indigenous microbiota seen to be beneficial. We have published a recent paper demonstrating that prebiotic galactooligosaccharides can exert power effects upon bifidobacteria in the gut flora of elderly persons (both in vivo and in vitro). This addendum summarizes research that led up to this study and discusses the possible impact of prebiotics in impacting upon the gut health of aged persons.}, } @article {pmid22554309, year = {2012}, author = {Mao, DP and Zhou, Q and Chen, CY and Quan, ZX}, title = {Coverage evaluation of universal bacterial primers using the metagenomic datasets.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {66}, pmid = {22554309}, issn = {1471-2180}, mesh = {Bacteria/*classification/*genetics ; *Biota ; DNA Primers/*genetics ; Genes, rRNA ; Metagenomics/*methods ; RNA, Ribosomal, 16S/genetics ; Selection Bias ; }, abstract = {BACKGROUND: The coverage of universal primers for the bacterial 16S rRNA gene plays a crucial role in the correct understanding of microbial community structure. However, existing studies on primer coverage are limited by the lack of appropriate databases and are restricted to the domain level. Additionally, most studies do not account for the positional effect of single primer-template mismatches. In this study, we used 7 metagenomic datasets as well as the Ribosomal Database Project (RDP) to assess the coverage of 8 widely used bacterial primers.

RESULTS: The coverage rates for bacterial primers were found to be overestimated by previous studies that only investigated the RDP because of PCR amplification bias in the sequence composition of the dataset. In the RDP, the non-coverage rates for all primers except 27F were ≪6%, while in the metagenomic datasets, most were ≫10%. If one considers that a single mismatch near the 3' end of the primer might greatly reduce PCR efficiency, then some phylum non-coverage rates would change by more than 20%. Primer binding-site sequence variants that could not pair with their corresponding primers are discussed.

CONCLUSIONS: Our study revealed the potential bias introduced by the use of universal bacterial primers in the assessment of microbial communities. With the development of high-throughput, next-generation sequencing techniques, it will become feasible to sequence more of the hypervariable regions of the bacterial 16S rRNA gene. This, in turn, will lead to the more frequent use of the primers discussed here.}, } @article {pmid22554028, year = {2012}, author = {Bonilla-Rosso, G and Eguiarte, LE and Romero, D and Travisano, M and Souza, V}, title = {Understanding microbial community diversity metrics derived from metagenomes: performance evaluation using simulated data sets.}, journal = {FEMS microbiology ecology}, volume = {82}, number = {1}, pages = {37-49}, doi = {10.1111/j.1574-6941.2012.01405.x}, pmid = {22554028}, issn = {1574-6941}, mesh = {*Biodiversity ; Cluster Analysis ; *Computer Simulation ; Ecology/methods ; Genes, rRNA ; *Metagenome ; Metagenomics/*methods ; Phylogeny ; }, abstract = {Metagenomics holds the promise of greatly advancing the study of diversity in natural communities, but novel theoretical and methodological approaches must first be developed and adjusted for these data sets. We evaluated widely used macroecological metrics of taxonomic diversity on a simulated set of metagenomic samples, using phylogenetically meaningful protein-coding genes as ecological proxies. To our knowledge, this is the first approach of this kind to evaluate taxonomic diversity metrics derived from metagenomic data sets. We demonstrate that abundance matrices derived from protein-coding marker genes reproduce more faithfully the structure of the original community than those derived from SSU-rRNA gene. We also found that the most commonly used diversity metrics are biased estimators of community structure and differ significantly from their corresponding real parameters and that these biases are most likely caused by insufficient sampling and differences in community phylogenetic composition. Our results suggest that the ranking of samples using multidimensional metrics makes a good qualitative alternative for contrasting community structure and that these comparisons can be greatly improved with the incorporation of metrics for both community structure and phylogenetic diversity. These findings will help to achieve a standardized framework for community diversity comparisons derived from metagenomic data sets.}, } @article {pmid22547653, year = {2012}, author = {Jenq, RR and Ubeda, C and Taur, Y and Menezes, CC and Khanin, R and Dudakov, JA and Liu, C and West, ML and Singer, NV and Equinda, MJ and Gobourne, A and Lipuma, L and Young, LF and Smith, OM and Ghosh, A and Hanash, AM and Goldberg, JD and Aoyama, K and Blazar, BR and Pamer, EG and van den Brink, MR}, title = {Regulation of intestinal inflammation by microbiota following allogeneic bone marrow transplantation.}, journal = {The Journal of experimental medicine}, volume = {209}, number = {5}, pages = {903-911}, pmid = {22547653}, issn = {1540-9538}, support = {R01 HL069929/HL/NHLBI NIH HHS/United States ; P01 CA023766/CA/NCI NIH HHS/United States ; R01-AI34495/AI/NIAID NIH HHS/United States ; R01 AI034495/AI/NIAID NIH HHS/United States ; R01-HL069929/HL/NHLBI NIH HHS/United States ; R01-AI042135/AI/NIAID NIH HHS/United States ; R01-CA107096/CA/NCI NIH HHS/United States ; R01 HL056067/HL/NHLBI NIH HHS/United States ; R01 AI042135/AI/NIAID NIH HHS/United States ; P01 CA142106/CA/NCI NIH HHS/United States ; P01-CA023766/CA/NCI NIH HHS/United States ; UL1 TR000064/TR/NCATS NIH HHS/United States ; P01 AI056299/AI/NIAID NIH HHS/United States ; R01 CA107096/CA/NCI NIH HHS/United States ; K23 AI095398/AI/NIAID NIH HHS/United States ; R01 AI080455/AI/NIAID NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; R01-HL56067/HL/NHLBI NIH HHS/United States ; R01 AI100288/AI/NIAID NIH HHS/United States ; R37 AI039031/AI/NIAID NIH HHS/United States ; R01-AI080455/AI/NIAID NIH HHS/United States ; R37-AI039031/AI/NIAID NIH HHS/United States ; }, mesh = {Ampicillin ; Animals ; Base Sequence ; *Biodiversity ; Bone Marrow Transplantation/*adverse effects ; Dextran Sulfate ; Enterocolitis/etiology/*microbiology/pathology ; Feces/microbiology ; Graft vs Host Disease/*complications/microbiology ; Gram-Positive Bacteria/isolation & purification ; Humans ; Metagenome/*genetics ; Mice ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Transplantation, Homologous ; }, abstract = {Despite a growing understanding of the link between intestinal inflammation and resident gut microbes, longitudinal studies of human flora before initial onset of intestinal inflammation have not been reported. Here, we demonstrate in murine and human recipients of allogeneic bone marrow transplantation (BMT) that intestinal inflammation secondary to graft-versus-host disease (GVHD) is associated with major shifts in the composition of the intestinal microbiota. The microbiota, in turn, can modulate the severity of intestinal inflammation. In mouse models of GVHD, we observed loss of overall diversity and expansion of Lactobacillales and loss of Clostridiales. Eliminating Lactobacillales from the flora of mice before BMT aggravated GVHD, whereas reintroducing the predominant species of Lactobacillus mediated significant protection against GVHD. We then characterized gut flora of patients during onset of intestinal inflammation caused by GVHD and found patterns mirroring those in mice. We also identified increased microbial chaos early after allogeneic BMT as a potential risk factor for subsequent GVHD. Together, these data demonstrate regulation of flora by intestinal inflammation and suggest that flora manipulation may reduce intestinal inflammation and improve outcomes for allogeneic BMT recipients.}, } @article {pmid22544239, year = {2012}, author = {Köhler, T and Dietrich, C and Scheffrahn, RH and Brune, A}, title = {High-resolution analysis of gut environment and bacterial microbiota reveals functional compartmentation of the gut in wood-feeding higher termites (Nasutitermes spp.).}, journal = {Applied and environmental microbiology}, volume = {78}, number = {13}, pages = {4691-4701}, pmid = {22544239}, issn = {1098-5336}, mesh = {Animals ; Bacteria/*classification/*genetics ; *Biodiversity ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Diet ; Gastrointestinal Tract/chemistry/microbiology ; Hydrogen/analysis ; Hydrogen-Ion Concentration ; Isoptera/*microbiology ; Oxidation-Reduction ; Oxygen/analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Wood/metabolism ; }, abstract = {Higher termites are characterized by a purely prokaryotic gut microbiota and an increased compartmentation of their intestinal tract. In soil-feeding species, each gut compartment has different physicochemical conditions and is colonized by a specific microbial community. Although considerable information has accumulated also for wood-feeding species of the genus Nasutitermes, including cellulase activities and metagenomic data, a comprehensive study linking physicochemical gut conditions with the structure of the microbial communities in the different gut compartments is lacking. In this study, we measured high-resolution profiles of H(2), O(2), pH, and redox potential in the gut of Nasutitermes corniger termites, determined the fermentation products accumulating in the individual gut compartments, and analyzed the bacterial communities in detail by pyrotag sequencing of the V3-V4 region of the 16S rRNA genes. The dilated hindgut paunch (P3 compartment) was the only anoxic gut region, showed the highest density of bacteria, and accumulated H(2) to high partial pressures (up to 12 kPa). Molecular hydrogen is apparently produced by a dense community of Spirochaetes and Fibrobacteres, which also dominate the gut of other Nasutitermes species. All other compartments, such as the alkaline P1 compartment (average pH, 10.0), showed high redox potentials and comprised small but distinct populations characteristic for each gut region. In the crop and the posterior hindgut compartments, the community was even more diverse than in the paunch. Similarities in the communities of the posterior hindgut and crop suggested that proctodeal trophallaxis or coprophagy also occurs in higher termites. The large sampling depths of pyrotag sequencing in combination with the determination of important physicochemical parameters allow cautious conclusions concerning the functions of particular bacterial lineages in the respective gut sections to be drawn.}, } @article {pmid22537669, year = {2012}, author = {Poole, AM and Stouffer, DB and Tylianakis, JM}, title = {'Ecosystomics': ecology by sequencer.}, journal = {Trends in ecology & evolution}, volume = {27}, number = {6}, pages = {309-310}, doi = {10.1016/j.tree.2012.03.008}, pmid = {22537669}, issn = {1872-8383}, mesh = {Animals ; Bacteria/genetics ; Biodiversity ; Ecology/*trends ; *Ecosystem ; Metagenomics/*trends ; Sequence Analysis, DNA ; }, } @article {pmid22536450, year = {2012}, author = {Machida, RJ and Kweskin, M and Knowlton, N}, title = {PCR primers for metazoan mitochondrial 12S ribosomal DNA sequences.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e35887}, pmid = {22536450}, issn = {1932-6203}, mesh = {Animals ; Base Pair Mismatch ; Base Sequence ; Biodiversity ; Conserved Sequence ; DNA Primers/*genetics ; DNA, Mitochondrial/*genetics ; Metagenome ; Polymerase Chain Reaction ; RNA, Ribosomal/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {BACKGROUND: Assessment of the biodiversity of communities of small organisms is most readily done using PCR-based analysis of environmental samples consisting of mixtures of individuals. Known as metagenetics, this approach has transformed understanding of microbial communities and is beginning to be applied to metazoans as well. Unlike microbial studies, where analysis of the 16S ribosomal DNA sequence is standard, the best gene for metazoan metagenetics is less clear. In this study we designed a set of PCR primers for the mitochondrial 12S ribosomal DNA sequence based on 64 complete mitochondrial genomes and then tested their efficacy.

A total of the 64 complete mitochondrial genome sequences representing all metazoan classes available in GenBank were downloaded using the NCBI Taxonomy Browser. Alignment of sequences was performed for the excised mitochondrial 12S ribosomal DNA sequences, and conserved regions were identified for all 64 mitochondrial genomes. These regions were used to design a primer pair that flanks a more variable region in the gene. Then all of the complete metazoan mitochondrial genomes available in NCBI's Organelle Genome Resources database were used to determine the percentage of taxa that would likely be amplified using these primers. Results suggest that these primers will amplify target sequences for many metazoans.

CONCLUSIONS/SIGNIFICANCE: Newly designed 12S ribosomal DNA primers have considerable potential for metazoan metagenetic analysis because of their ability to amplify sequences from many metazoans.}, } @article {pmid22535224, year = {2012}, author = {Hesham, Ael-L and Khan, S and Tao, Y and Li, D and Zhang, Y and Yang, M}, title = {Biodegradation of high molecular weight PAHs using isolated yeast mixtures: application of meta-genomic methods for community structure analyses.}, journal = {Environmental science and pollution research international}, volume = {19}, number = {8}, pages = {3568-3578}, pmid = {22535224}, issn = {1614-7499}, mesh = {Biodegradation, Environmental ; *Biota ; Catechol 2,3-Dioxygenase/metabolism ; Industrial Waste ; Metagenomics/*methods ; Oil and Gas Fields/microbiology ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Sewage/analysis/microbiology ; Water Purification/methods ; Yeasts/*genetics/*metabolism ; }, abstract = {Bioaugmentation for the removal of polyaromatic hydrocarbons (PAHs) from wastewater using bacteria and yeasts is considered environment-friendly and a cost-effective technique. The effectiveness of this biodegradation system depends on the stability of inoculated microorganisms and the availability of nutrients. This study is aimed to investigate the removal of high molecular weight (HMW)-PAHs from biologically treated produced water using different biological systems. Three systems, inoculated with activated sludge (AS), the mixture of five yeast strains (MY), and the mixture of AS and the five yeast strains (SY), respectively, were constructed, and their performance for the removal of HMW-PAHs was compared over 10 weeks. The effluent of the biologically treated produced water from an oilfield was used as the influent after chrysene and benzo(a)pyrene were spiked as HMW-PAHs. Polymerase chain reaction-based denaturing gradient gel electrophoresis (PCR-DGGE) and fluorescent in situ hybridization (FISH) techniques were used to examine the changes in the structures and abundances of the bacterial and yeast communities in these three systems. Only SY and MY systems were capable to remove chrysene (90.7 % and 98.5 %, respectively) and benzo(a)pyrene (80.7 % and 95.2 %, respectively). PCR-DGGE analysis confirmed that all of the five yeast strains inoculated remained in the SY and MY systems, while FISH results showed that the relative abundance of yeast in the SY and MY systems (10.6 % to 21.9 %, respectively) were significantly higher than AS system (2.3 % to 7.8 %, respectively). The relative abundances of the catechol 2,3-dioxygenase (C23O) indicated that the copy number ratios of benzene ring cleavage gene C23O in the yeast amended systems were much higher than that in the AS system. In this study, all of the three systems were effective in removing the low molecular weight (LMW)-PAHs, while HMW-PAHs including chrysene and benzo(a)pyrene were efficiently removed by MY and SY systems, not by AS system. The high HMW-PAHs removal in the MY and SY bioaugmentation systems possibly attributed to the inoculation of the mixed yeast culture. By combining the PCR-DGGE results with the FISH analyses, it was found that yeast probably consisting mainly of the five inoculated strains inhabited in the two bioaugmentation systems as a dominant population. The relatively higher performance of the SY system might be attributed to the suspended growth type which permitted a more efficient contact between microbial cells and contaminants. The bioaugmentation systems (SY and MY) were successfully established by inoculating with five nonindigenous yeast strains and demonstrated high performance in removal of HMW-PAHs.}, } @article {pmid22530070, year = {2012}, author = {Waite, DW and Deines, P and Taylor, MW}, title = {Gut microbiome of the critically endangered New Zealand parrot, the kakapo (Strigops habroptilus).}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e35803}, pmid = {22530070}, issn = {1932-6203}, mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; *Endangered Species ; Gastrointestinal Tract/*microbiology ; *Metagenome ; Molecular Sequence Data ; New Zealand ; Parrots/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The kakapo, a parrot endemic to New Zealand, is currently the focus of intense research and conservation efforts with the aim of boosting its population above the current 'critically endangered' status. While virtually nothing is known about the microbiology of the kakapo, given the acknowledged importance of gut-associated microbes in vertebrate nutrition and pathogen defense, it should be of great conservation value to analyze the microbes associated with kakapo. Here we describe the first study of the bacterial communities that reside within the gastrointestinal tract (GIT) of both juvenile and adult kakapo. Samples from along the GIT, taken from the choana (≈ throat), crop and faeces, were subjected to 16 S rRNA gene library analysis. Phylogenetic analysis of >1000 16 S rRNA gene clones, derived from six birds, revealed low phylum-level diversity, consisting almost exclusively of Firmicutes (including lactic acid bacteria) and Gammaproteobacteria. The relative proportions of Firmicutes and Gammaproteobacteria were highly consistent among individual juveniles, irrespective of sampling location, but differed markedly among adult birds. Diversity at a finer phylogenetic resolution (i.e. operational taxonomic units (OTUs) of 99% sequence identity) was also low in all samples, with only one or two OTUs dominating each sample. These data represent the first analysis of the bacterial communities associated with the kakapo GIT, providing a baseline for further microbiological study, and facilitating conservation efforts for this unique bird.}, } @article {pmid22524615, year = {2012}, author = {Garcia-Garcerà, M and Coscollà, M and Garcia-Etxebarria, K and Martín-Caballero, J and González-Candelas, F and Latorre, A and Calafell, F}, title = {Staphylococcus prevails in the skin microbiota of long-term immunodeficient mice.}, journal = {Environmental microbiology}, volume = {14}, number = {8}, pages = {2087-2098}, doi = {10.1111/j.1462-2920.2012.02756.x}, pmid = {22524615}, issn = {1462-2920}, mesh = {Animals ; Base Sequence ; Biodiversity ; Male ; *Metagenome ; Mice ; Mice, Inbred C57BL ; Mice, SCID ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Skin/*microbiology ; Staphylococcus/genetics/immunology/*physiology ; Staphylococcus epidermidis/genetics ; }, abstract = {Host-commensal relationships in the skin are a complex system governed by variables related to the host, the bacteria and the environment. A disruption of this system may lead to new steady states, which, in turn, may lead to disease. We have studied one such disruption by characterizing the skin microbiota in healthy and immunodepressed (ID) mice. A detailed anatomopathological study failed to reveal any difference between the skin of healthy and ID mice. We sequenced the 16S rDNA V1-V2 gene region to saturation in 10 healthy and 10 ID 8 week-old mice, and found than all of the healthy and two of the ID mice had bacterial communities that were similar in composition to that of human skin, although, presumably because of the uniform raising conditions, less interindividual variation was found in mice. However, eight ID mice showed microbiota dominated by Staphylococcus epidermidis. Quantitative PCR amplification of 16S rDNA gene and of the Staphylococcus-specific TstaG region confirmed the previous results and indicated that the quantitative levels of Staphylococcus were similar in both groups while the total number of 16S copies was greater in the healthy mice. Thus, it is possible that, under long-term immunodeficiency, which removes the acquired but not the native immune system, S.epidermidis may inhibit the growth of other bacteria but does not cause a pathogenic state.}, } @article {pmid22520388, year = {2012}, author = {Diaz, PI and Dupuy, AK and Abusleme, L and Reese, B and Obergfell, C and Choquette, L and Dongari-Bagtzoglou, A and Peterson, DE and Terzi, E and Strausbaugh, LD}, title = {Using high throughput sequencing to explore the biodiversity in oral bacterial communities.}, journal = {Molecular oral microbiology}, volume = {27}, number = {3}, pages = {182-201}, pmid = {22520388}, issn = {2041-1014}, support = {R01 DE021578/DE/NIDCR NIH HHS/United States ; 5R01DE02157/DE/NIDCR NIH HHS/United States ; }, mesh = {Actinomyces/classification ; Bacteria/*classification/genetics ; Bias ; Biodiversity ; DNA, Bacterial/analysis ; Fusobacterium nucleatum/classification ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Lacticaseibacillus casei/classification ; Metagenome/genetics ; Mouth/*microbiology ; Mouth Mucosa/microbiology ; Porphyromonas gingivalis/classification ; RNA, Bacterial/*analysis ; RNA, Ribosomal, 16S/analysis ; Saliva/microbiology ; *Sequence Analysis, RNA ; Staphylococcaceae/classification ; Streptococcus mitis/classification ; Streptococcus mutans/classification ; Streptococcus oralis/classification ; Veillonella/classification ; Young Adult ; }, abstract = {High throughput sequencing of 16S ribosomal RNA gene amplicons is a cost-effective method for characterization of oral bacterial communities. However, before undertaking large-scale studies, it is necessary to understand the technique-associated limitations and intrinsic variability of the oral ecosystem. In this work we evaluated bias in species representation using an in vitro-assembled mock community of oral bacteria. We then characterized the bacterial communities in saliva and buccal mucosa of five healthy subjects to investigate the power of high throughput sequencing in revealing their diversity and biogeography patterns. Mock community analysis showed primer and DNA isolation biases and an overestimation of diversity that was reduced after eliminating singleton operational taxonomic units (OTUs). Sequencing of salivary and mucosal communities found a total of 455 OTUs (0.3% dissimilarity) with only 78 of these present in all subjects. We demonstrate that this variability was partly the result of incomplete richness coverage even at great sequencing depths, and so comparing communities by their structure was more effective than comparisons based solely on membership. With respect to oral biogeography, we found inter-subject variability in community structure was lower than site differences between salivary and mucosal communities within subjects. These differences were evident at very low sequencing depths and were mostly caused by the abundance of Streptococcus mitis and Gemella haemolysans in mucosa. In summary, we present an experimental and data analysis framework that will facilitate design and interpretation of pyrosequencing-based studies. Despite challenges associated with this technique, we demonstrate its power for evaluation of oral diversity and biogeography patterns.}, } @article {pmid22509283, year = {2012}, author = {Ray, J and Dondrup, M and Modha, S and Steen, IH and Sandaa, RA and Clokie, M}, title = {Finding a needle in the virus metagenome haystack--micro-metagenome analysis captures a snapshot of the diversity of a bacteriophage armoire.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e34238}, pmid = {22509283}, issn = {1932-6203}, mesh = {Bacteriophage lambda/genetics ; Bacteriophages/classification/*genetics ; *Biodiversity ; Culture Techniques ; Genome, Viral/*genetics ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Hydrothermal Vents/virology ; Metagenome/*genetics ; Phylogeny ; Seawater/virology ; }, abstract = {Viruses are ubiquitous in the oceans and critical components of marine microbial communities, regulating nutrient transfer to higher trophic levels or to the dissolved organic pool through lysis of host cells. Hydrothermal vent systems are oases of biological activity in the deep oceans, for which knowledge of biodiversity and its impact on global ocean biogeochemical cycling is still in its infancy. In order to gain biological insight into viral communities present in hydrothermal vent systems, we developed a method based on deep-sequencing of pulsed field gel electrophoretic bands representing key viral fractions present in seawater within and surrounding a hydrothermal plume derived from Loki's Castle vent field at the Arctic Mid-Ocean Ridge. The reduction in virus community complexity afforded by this novel approach enabled the near-complete reconstruction of a lambda-like phage genome from the virus fraction of the plume. Phylogenetic examination of distinct gene regions in this lambdoid phage genome unveiled diversity at loci encoding superinfection exclusion- and integrase-like proteins. This suggests the importance of fine-tuning lyosgenic conversion as a viral survival strategy, and provides insights into the nature of host-virus and virus-virus interactions, within hydrothermal plumes. By reducing the complexity of the viral community through targeted sequencing of prominent dsDNA viral fractions, this method has selectively mimicked virus dominance approaching that hitherto achieved only through culturing, thus enabling bioinformatic analysis to locate a lambdoid viral "needle" within the greater viral community "haystack". Such targeted analyses have great potential for accelerating the extraction of biological knowledge from diverse and poorly understood environmental viral communities.}, } @article {pmid22491358, year = {2012}, author = {Koropatkin, NM and Cameron, EA and Martens, EC}, title = {How glycan metabolism shapes the human gut microbiota.}, journal = {Nature reviews. Microbiology}, volume = {10}, number = {5}, pages = {323-335}, pmid = {22491358}, issn = {1740-1534}, support = {T32 GM007544/GM/NIGMS NIH HHS/United States ; DK034933/DK/NIDDK NIH HHS/United States ; DK084214/DK/NIDDK NIH HHS/United States ; GM07544/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biota ; *Diet ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenome/*physiology ; Polysaccharides/*metabolism ; }, abstract = {Symbiotic microorganisms that reside in the human intestine are adept at foraging glycans and polysaccharides, including those in dietary plants (starch, hemicellulose and pectin), animal-derived cartilage and tissue (glycosaminoglycans and N-linked glycans), and host mucus (O-linked glycans). Fluctuations in the abundance of dietary and endogenous glycans, combined with the immense chemical variation among these molecules, create a dynamic and heterogeneous environment in which gut microorganisms proliferate. In this Review, we describe how glycans shape the composition of the gut microbiota over various periods of time, the mechanisms by which individual microorganisms degrade these glycans, and potential opportunities to intentionally influence this ecosystem for better health and nutrition.}, } @article {pmid22486820, year = {2012}, author = {Shokralla, S and Spall, JL and Gibson, JF and Hajibabaei, M}, title = {Next-generation sequencing technologies for environmental DNA research.}, journal = {Molecular ecology}, volume = {21}, number = {8}, pages = {1794-1805}, doi = {10.1111/j.1365-294X.2012.05538.x}, pmid = {22486820}, issn = {1365-294X}, mesh = {DNA/*analysis/genetics ; Environmental Monitoring/*methods ; *High-Throughput Nucleotide Sequencing/instrumentation/methods ; *Metagenomics ; }, abstract = {Since 2005, advances in next-generation sequencing technologies have revolutionized biological science. The analysis of environmental DNA through the use of specific gene markers such as species-specific DNA barcodes has been a key application of next-generation sequencing technologies in ecological and environmental research. Access to parallel, massive amounts of sequencing data, as well as subsequent improvements in read length and throughput of different sequencing platforms, is leading to a better representation of sample diversity at a reasonable cost. New technologies are being developed rapidly and have the potential to dramatically accelerate ecological and environmental research. The fast pace of development and improvements in next-generation sequencing technologies can reflect on broader and more robust applications in environmental DNA research. Here, we review the advantages and limitations of current next-generation sequencing technologies in regard to their application for environmental DNA analysis.}, } @article {pmid22458294, year = {2013}, author = {Glurich, I and Acharya, A and Shukla, SK and Nycz, GR and Brilliant, MH}, title = {The oral-systemic personalized medicine model at Marshfield Clinic.}, journal = {Oral diseases}, volume = {19}, number = {1}, pages = {1-17}, pmid = {22458294}, issn = {1601-0825}, support = {1U01HG006389-01/HG/NHGRI NIH HHS/United States ; U01 HG006389-01/HG/NHGRI NIH HHS/United States ; U01 HG006389/HG/NHGRI NIH HHS/United States ; UL1 RR025011/RR/NCRR NIH HHS/United States ; 1UL1RR025011/RR/NCRR NIH HHS/United States ; UL1 RR025011-01/RR/NCRR NIH HHS/United States ; UL1 TR000427/TR/NCATS NIH HHS/United States ; }, mesh = {Delivery of Health Care, Integrated ; Dental Informatics ; Diabetes Mellitus/genetics/*physiopathology ; Humans ; Medical Informatics ; Metagenomics ; Microbiota/genetics ; Periodontal Diseases/genetics/*physiopathology ; *Precision Medicine ; United States ; Wisconsin ; }, abstract = {Periodontal disease and diabetes, two diseases that have achieved epidemic status, share a bidirectional relationship driven by micro-inflammatory processes. The present review frames the current understanding of the pathological processes that appear to link these diseases and advances the hypothesis that reversal of the epidemic is possible through application of interdisciplinary intervention and advancement of oral-systemic personalized medicine. An overview of how Marshfield Clinic's unique clinical, informatics and bio-repository resources and infrastructures are being aligned to advance oral-systemic personalized medicine is presented as an interventional model with the potential to reverse the epidemic trends seen for these two chronic diseases over the past several decades. The overall vision is to engineer a transformational shift in paradigm from 'personalized medicine' to 'personalized health'.}, } @article {pmid22456445, year = {2012}, author = {Stegen, JC and Lin, X and Konopka, AE and Fredrickson, JK}, title = {Stochastic and deterministic assembly processes in subsurface microbial communities.}, journal = {The ISME journal}, volume = {6}, number = {9}, pages = {1653-1664}, pmid = {22456445}, issn = {1751-7370}, mesh = {Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; Ecosystem ; Metagenome/genetics/*physiology ; Phylogeny ; Stochastic Processes ; *Water Microbiology ; }, abstract = {A major goal of microbial community ecology is to understand the forces that structure community composition. Deterministic selection by specific environmental factors is sometimes important, but in other cases stochastic or ecologically neutral processes dominate. Lacking is a unified conceptual framework aiming to understand why deterministic processes dominate in some contexts but not others. Here we work toward such a framework. By testing predictions derived from general ecological theory we aim to uncover factors that govern the relative influences of deterministic and stochastic processes. We couple spatiotemporal data on subsurface microbial communities and environmental parameters with metrics and null models of within and between community phylogenetic composition. Testing for phylogenetic signal in organismal niches showed that more closely related taxa have more similar habitat associations. Community phylogenetic analyses further showed that ecologically similar taxa coexist to a greater degree than expected by chance. Environmental filtering thus deterministically governs subsurface microbial community composition. More importantly, the influence of deterministic environmental filtering relative to stochastic factors was maximized at both ends of an environmental variation gradient. A stronger role of stochastic factors was, however, supported through analyses of phylogenetic temporal turnover. Although phylogenetic turnover was on average faster than expected, most pairwise comparisons were not themselves significantly non-random. The relative influence of deterministic environmental filtering over community dynamics was elevated, however, in the most temporally and spatially variable environments. Our results point to general rules governing the relative influences of stochastic and deterministic processes across micro- and macro-organisms.}, } @article {pmid22451929, year = {2012}, author = {Zhao, J and Schloss, PD and Kalikin, LM and Carmody, LA and Foster, BK and Petrosino, JF and Cavalcoli, JD and VanDevanter, DR and Murray, S and Li, JZ and Young, VB and LiPuma, JJ}, title = {Decade-long bacterial community dynamics in cystic fibrosis airways.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {15}, pages = {5809-5814}, pmid = {22451929}, issn = {1091-6490}, support = {P30DK034933/DK/NIDDK NIH HHS/United States ; P30 DK027651/DK/NIDDK NIH HHS/United States ; UL1RR024986/RR/NCRR NIH HHS/United States ; R01HG004906/HG/NHGRI NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; RC1 HL100809/HL/NHLBI NIH HHS/United States ; R01 HG004906/HG/NHGRI NIH HHS/United States ; 1RC1HL100809-01/HL/NHLBI NIH HHS/United States ; UL1 RR024986/RR/NCRR NIH HHS/United States ; R01 HG005975/HG/NHGRI NIH HHS/United States ; 1R01HG005975-01/HG/NHGRI NIH HHS/United States ; U01 HL098961/HL/NHLBI NIH HHS/United States ; U01HL098961/HL/NHLBI NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aging/drug effects ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/classification/drug effects/*growth & development ; Bacterial Load/drug effects ; Biodiversity ; Cystic Fibrosis/drug therapy/*microbiology/physiopathology ; Disease Progression ; Humans ; Lung/drug effects/*microbiology/*pathology/physiopathology ; Male ; Metagenome/drug effects ; Principal Component Analysis ; Respiratory Function Tests ; Sputum/drug effects/microbiology ; Young Adult ; }, abstract = {The structure and dynamics of bacterial communities in the airways of persons with cystic fibrosis (CF) remain largely unknown. We characterized the bacterial communities in 126 sputum samples representing serial collections spanning 8-9 y from six age-matched male CF patients. Sputum DNA was analyzed by bar-coded pyrosequencing of the V3-V5 hypervariable region of the 16S rRNA gene, defining 662 operational taxonomic units (OTUs) from >633,000 sequences. Bacterial community diversity decreased significantly over time in patients with typically progressive lung disease but remained relatively stable in patients with a mild lung disease phenotype. Antibiotic use, rather than patient age or lung function, was the primary driver of decreasing diversity. Interpatient variability in community structure exceeded intrapatient variability in serial samples. Antibiotic treatment was associated with pronounced shifts in community structure, but communities showed both short- and long-term resilience after antibiotic perturbation. There was a positive correlation between OTU occurrence and relative abundance, with a small number of persistent OTUs accounting for the greatest abundance. Significant changes in community structure, diversity, or total bacterial density at the time of pulmonary exacerbation were not observed. Despite decreasing community diversity in patients with progressive disease, total bacterial density remained relatively stable over time. These findings show the critical relationship between airway bacterial community structure, disease stage, and clinical state at the time of sample collection. These features are the key parameters with which to assess the complex ecology of the CF airway.}, } @article {pmid22443608, year = {2012}, author = {Durbán, A and Abellán, JJ and Jiménez-Hernández, N and Latorre, A and Moya, A}, title = {Daily follow-up of bacterial communities in the human gut reveals stable composition and host-specific patterns of interaction.}, journal = {FEMS microbiology ecology}, volume = {81}, number = {2}, pages = {427-437}, doi = {10.1111/j.1574-6941.2012.01368.x}, pmid = {22443608}, issn = {1574-6941}, mesh = {Adult ; Bacteria/*classification/genetics ; DNA, Bacterial/genetics ; Feces/*microbiology ; Humans ; Intestines/*microbiology ; Male ; *Metagenome ; Models, Statistical ; Multivariate Analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {In the last decade, an extensive effort has been made to characterize the human intestinal microbiota by means of SSU rRNA gene sequence and metagenomic analysis. Relatively few studies have followed intestinal bacterial communities over time to assess their stability in the absence of perturbation. In this study, we have monitored the faecal bacteria of three healthy subjects during 15 consecutive days. The global community structure was analysed through SSU rRNA gene sequencing. In agreement with previous studies, we found that the between-subject variation in community structure was larger than within. The composition was fairly stable throughout, although daily fluctuations were detected for all genera and phylotypes at 97% of sequence identity. While the core shared between subjects was very small, each subject harboured a stable high-abundance core composed of a small number of bacterial groups (9% of the phylotypes accounted for between 74% and 93% of the sequences). This may suggest that studies aimed at linking the microbiota composition with disease risk should be limited to the numerically most dominant phylotypes, as the rest appears transient. Networks of potential interactions between co-occurring genera were also subject-specific, even for the same bacterial genus, which might be reflecting host-specific selective pressures and historic events.}, } @article {pmid22437157, year = {2012}, author = {Meron, D and Rodolfo-Metalpa, R and Cunning, R and Baker, AC and Fine, M and Banin, E}, title = {Changes in coral microbial communities in response to a natural pH gradient.}, journal = {The ISME journal}, volume = {6}, number = {9}, pages = {1775-1785}, pmid = {22437157}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; Hydrogen-Ion Concentration ; Metagenome/genetics/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*chemistry ; }, abstract = {Surface seawater pH is currently 0.1 units lower than pre-industrial values and is projected to decrease by up to 0.4 units by the end of the century. This acidification has the potential to cause significant perturbations to the physiology of ocean organisms, particularly those such as corals that build their skeletons/shells from calcium carbonate. Reduced ocean pH could also have an impact on the coral microbial community, and thus may affect coral physiology and health. Most of the studies to date have examined the impact of ocean acidification on corals and/or associated microbiota under controlled laboratory conditions. Here we report the first study that examines the changes in coral microbial communities in response to a natural pH gradient (mean pH(T) 7.3-8.1) caused by volcanic CO(2) vents off Ischia, Gulf of Naples, Italy. Two Mediterranean coral species, Balanophyllia europaea and Cladocora caespitosa, were examined. The microbial community diversity and the physiological parameters of the endosymbiotic dinoflagellates (Symbiodinium spp.) were monitored. We found that pH did not have a significant impact on the composition of associated microbial communities in both coral species. In contrast to some earlier studies, we found that corals present at the lower pH sites exhibited only minor physiological changes and no microbial pathogens were detected. Together, these results provide new insights into the impact of ocean acidification on the coral holobiont.}, } @article {pmid22437156, year = {2012}, author = {Belzer, C and de Vos, WM}, title = {Microbes inside--from diversity to function: the case of Akkermansia.}, journal = {The ISME journal}, volume = {6}, number = {8}, pages = {1449-1458}, pmid = {22437156}, issn = {1751-7370}, support = {250172/ERC_/European Research Council/International ; }, mesh = {*Bacteria/classification/genetics/metabolism ; *Biodiversity ; Humans ; Intestines/*microbiology ; Metagenome/*physiology ; Phylogeny ; *Verrucomicrobia/classification/genetics/metabolism ; }, abstract = {The human intestinal tract is colonized by a myriad of microbes that have developed intimate interactions with the host. In healthy individuals, this complex ecosystem remains stable and resilient to stressors. There is significant attention on the understanding of the composition and function of this intestinal microbiota in health and disease. Current developments in metaomics and systems biology approaches allow to probe the functional potential and activity of the intestinal microbiota. However, all these approaches inherently suffer from the fact that the information on macromolecules (DNA, RNA and protein) is collected at the ecosystem level. Similarly, all physiological and other information collected from isolated strains relates to pure cultures grown in vitro or in gnotobiotic systems. It is essential to integrate these two worlds of predominantly chemistry and biology by linking the molecules to the cells. Here, we will address the integration of omics- and culture-based approaches with the complexity of the human intestinal microbiota in mind and the mucus-degrading bacteria Akkermansia spp. as a paradigm.}, } @article {pmid22435705, year = {2012}, author = {Wilson, SL and Grogan, P and Walker, VK}, title = {Prospecting for ice association: characterization of freeze-thaw selected enrichment cultures from latitudinally distant soils.}, journal = {Canadian journal of microbiology}, volume = {58}, number = {4}, pages = {402-412}, doi = {10.1139/w2012-010}, pmid = {22435705}, issn = {1480-3275}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Canada ; Cold Temperature ; Freezing ; Genes, rRNA ; Ice ; Metagenome/*physiology ; *Microbial Consortia ; Polymerase Chain Reaction ; Seasons ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Freeze-thaw stress has previously been shown to alter soil community structure and function. We sought to further investigate this stress on enriched microbial consortia with the aim of identifying microbes with ice-associating adaptations that facilitate survival. Enrichments were established to obtain culturable psychrotolerant microbes from soil samples from the latitudinal extremes of the Canadian Shield plateau. The resulting consortia were subjected to consecutive freeze-thaw cycles, and survivors were putatively identified by their 16S rRNA gene sequences. Even though the northerly site was exposed to longer, colder winters and large spring-time temperature fluctuations, the selective regime similarly affected both enriched consortia. Quantitative PCR and metagenomic sequencing were used to determine the frequency of a subset of the resistant microbes in the original enrichments. The metagenomes showed 22 initial genera, only 6 survived and these were not dominant prior to selection. When survivors were assayed for ice recrystallization inhibition and ice nucleation activities, over 60% had at least one of these properties. These phenotypes were not more prevalent in the northern enrichment, indicating that regarding these adaptations, the enrichment strategy yielded seemingly functionally similar consortia from each site.}, } @article {pmid22432919, year = {2012}, author = {Dugat-Bony, E and Biderre-Petit, C and Jaziri, F and David, MM and Denonfoux, J and Lyon, DY and Richard, JY and Curvers, C and Boucher, D and Vogel, TM and Peyretaillade, E and Peyret, P}, title = {In situ TCE degradation mediated by complex dehalorespiring communities during biostimulation processes.}, journal = {Microbial biotechnology}, volume = {5}, number = {5}, pages = {642-653}, pmid = {22432919}, issn = {1751-7915}, mesh = {*Biota ; DNA, Bacterial/chemistry/genetics ; Ethane/metabolism ; Groundwater/*microbiology ; Metagenome ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Sequence Analysis, DNA ; Trichloroethylene/*metabolism ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The bioremediation of chloroethene contaminants in groundwater polluted systems is still a serious environmental challenge. Many previous studies have shown that cooperation of several dechlorinators is crucial for complete dechlorination of trichloroethene to ethene. In the present study, we used an explorative functional DNA microarray (DechloArray) to examine the composition of specific functional genes in groundwater samples in which chloroethene bioremediation was enhanced by delivery of hydrogen-releasing compounds. Our results demonstrate for the first time that complete biodegradation occurs through spatial and temporal variations of a wide diversity of dehalorespiring populations involving both Sulfurospirillum, Dehalobacter, Desulfitobacterium, Geobacter and Dehalococcoides genera. Sulfurospirillum appears to be the most active in the highly contaminated source zone, while Geobacter was only detected in the slightly contaminated downstream zone. The concomitant detection of both bvcA and vcrA genes suggests that at least two different Dehalococcoides species are probably responsible for the dechlorination of dichloroethenes and vinyl chloride to ethene. These species were not detected on sites where cis-dichloroethene accumulation was observed. These results support the notion that monitoring dechlorinators by the presence of specific functional biomarkers using a powerful tool such as DechloArray will be useful for surveying the efficiency of bioremediation strategies.}, } @article {pmid22432637, year = {2012}, author = {Richardson, C and Hill, M and Marks, C and Runyen-Janecky, L and Hill, A}, title = {Experimental manipulation of sponge/bacterial symbiont community composition with antibiotics: sponge cell aggregates as a unique tool to study animal/microorganism symbiosis.}, journal = {FEMS microbiology ecology}, volume = {81}, number = {2}, pages = {407-418}, doi = {10.1111/j.1574-6941.2012.01365.x}, pmid = {22432637}, issn = {1574-6941}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Axenic Culture ; Bacteria/*classification/drug effects/genetics/growth & development ; Biodiversity ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; *Metagenome ; Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Marine sponges can harbor dense and diverse bacterial communities, yet we have a limited understanding of important aspects of this symbiosis. We developed an experimental methodology that permits manipulating the composition of the microbial community. Specifically, we evaluated sponge cell aggregates (SCA) from Clathria prolifera that had been treated with different classes of antibiotics to determine whether this system might offer novel experimental approaches to the study of sponge/bacterial symbioses. Microscopic analysis of the SCA demonstrated that two distinct morphological types of microbiota existed on the external surface vs. the internal regions of the SCA. Denaturing gradient gel electrophoresis and sequence analysis of 16S rRNA gene clone libraries indicated that we were unable to create entirely aposymbiotic SCA but that different classes of antibiotics produced distinctive shifts in the SCA-associated bacterial community. After exposure to antibiotics, some bacterial species were 'revealed', thus uncovering novel components of the sponge-associated community. The antibiotic treatments used here had little discernible effect on the formation of SCA or subsequent development of the adult. The experimental approach we describe offers empirical options for studying the role symbionts play in sponge growth and development and for ascertaining relationships among bacterial species in communities residing in sponges.}, } @article {pmid22432013, year = {2012}, author = {Jami, E and Mizrahi, I}, title = {Composition and similarity of bovine rumen microbiota across individual animals.}, journal = {PloS one}, volume = {7}, number = {3}, pages = {e33306}, pmid = {22432013}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Cattle ; *Genetic Variation ; Metagenome/*genetics ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The bovine rumen houses a complex microbiota which is responsible for cattle's remarkable ability to convert indigestible plant mass into food products. Despite this ecosystem's enormous significance for humans, the composition and similarity of bacterial communities across different animals and the possible presence of some bacterial taxa in all animals' rumens have yet to be determined. We characterized the rumen bacterial populations of 16 individual lactating cows using tag amplicon pyrosequencing. Our data showed 51% similarity in bacterial taxa across samples when abundance and occurrence were analyzed using the Bray-Curtis metric. By adding taxon phylogeny to the analysis using a weighted UniFrac metric, the similarity increased to 82%. We also counted 32 genera that are shared by all samples, exhibiting high variability in abundance across samples. Taken together, our results suggest a core microbiome in the bovine rumen. Furthermore, although the bacterial taxa may vary considerably between cow rumens, they appear to be phylogenetically related. This suggests that the functional requirement imposed by the rumen ecological niche selects taxa that potentially share similar genetic features.}, } @article {pmid22428950, year = {2012}, author = {Stomeo, F and Makhalanyane, TP and Valverde, A and Pointing, SB and Stevens, MI and Cary, CS and Tuffin, MI and Cowan, DA}, title = {Abiotic factors influence microbial diversity in permanently cold soil horizons of a maritime-associated Antarctic Dry Valley.}, journal = {FEMS microbiology ecology}, volume = {82}, number = {2}, pages = {326-340}, doi = {10.1111/j.1574-6941.2012.01360.x}, pmid = {22428950}, issn = {1574-6941}, mesh = {Altitude ; Antarctic Regions ; Bacteria/genetics/*growth & development ; *Biodiversity ; DNA, Bacterial/genetics ; Desiccation ; Environment ; Humidity ; Ice ; Metagenome ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; Temperature ; Water ; }, abstract = {The McMurdo Dry Valleys collectively comprise the most extensive ice-free region in Antarctica and are considered one of the coldest arid environments on Earth. In low-altitude maritime-associated valleys, mineral soil profiles show distinct horizontal structuring, with a surface arid zone overlying a moist and biologically active zone generated by seasonally melted permafrost. In this study, long-term microenvironmental monitoring data show that temperature and soil humidity regimes vary in the soil horizons of north- and south-facing slopes within the Miers Valley, a maritime valley in the McMurdo Dry Valleys. We found that soil bacterial communities varied from the north to the south. The microbial assemblages at the surface and shallow subsurface depths displayed higher metabolic activity and diversity compared to the permafrost soil interface. Multivariate analysis indicated that K, C, Ca and moisture influenced the distribution and structure of microbial populations. Furthermore, because of the large % RH gradient between the frozen subsurface and the soil surface we propose that water transported to the surface as water vapour is available to microbial populations, either as a result of condensation processes or by direct adsorption from the vapour phase.}, } @article {pmid22427492, year = {2012}, author = {Reddy, BV and Kallifidas, D and Kim, JH and Charlop-Powers, Z and Feng, Z and Brady, SF}, title = {Natural product biosynthetic gene diversity in geographically distinct soil microbiomes.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {10}, pages = {3744-3752}, pmid = {22427492}, issn = {1098-5336}, support = {R01 GM077516/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; GM077516/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/enzymology/*genetics ; Biodiversity ; Biological Products/*metabolism ; Biosynthetic Pathways/*genetics ; Genetic Variation ; Geography ; *Metagenome ; Polyketide Synthases/genetics ; *Soil Microbiology ; }, abstract = {The number of bacterial species estimated to exist on Earth has increased dramatically in recent years. This newly recognized species diversity has raised the possibility that bacterial natural product biosynthetic diversity has also been significantly underestimated by previous culture-based studies. Here, we compare 454-pyrosequenced nonribosomal peptide adenylation domain, type I polyketide ketosynthase domain, and type II polyketide ketosynthase alpha gene fragments amplified from cosmid libraries constructed using DNA isolated from three different arid soils. While 16S rRNA gene sequence analysis indicates these cloned metagenomes contain DNA from similar distributions of major bacterial phyla, we found that they contain almost completely distinct collections of secondary metabolite biosynthetic gene sequences. When grouped at 85% identity, only 1.5% of the adenylation domain, 1.2% of the ketosynthase, and 9.3% of the ketosynthase alpha sequence clusters contained sequences from all three metagenomes. Although there is unlikely to be a simple correlation between biosynthetic gene sequence diversity and the diversity of metabolites encoded by the gene clusters in which these genes reside, our analysis further suggests that sequences in one soil metagenome are so distantly related to sequences in another metagenome that they are, in many cases, likely to arise from functionally distinct gene clusters. The marked differences observed among collections of biosynthetic genes found in even ecologically similar environments suggest that prokaryotic natural product biosynthesis diversity is, like bacterial species diversity, potentially much larger than appreciated from culture-based studies.}, } @article {pmid22404795, year = {2012}, author = {Voorhies, AA and Biddanda, BA and Kendall, ST and Jain, S and Marcus, DN and Nold, SC and Sheldon, ND and Dick, GJ}, title = {Cyanobacterial life at low O(2): community genomics and function reveal metabolic versatility and extremely low diversity in a Great Lakes sinkhole mat.}, journal = {Geobiology}, volume = {10}, number = {3}, pages = {250-267}, doi = {10.1111/j.1472-4669.2012.00322.x}, pmid = {22404795}, issn = {1472-4669}, mesh = {*Biota ; Carbon Radioisotopes/metabolism ; Cluster Analysis ; Cyanobacteria/*classification/genetics/*isolation & purification/metabolism ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Energy Metabolism ; Fresh Water/*microbiology ; Geologic Sediments/*microbiology ; Isotope Labeling ; *Metagenomics ; Molecular Sequence Data ; Oxygen/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Cyanobacteria are renowned as the mediators of Earth's oxygenation. However, little is known about the cyanobacterial communities that flourished under the low-O(2) conditions that characterized most of their evolutionary history. Microbial mats in the submerged Middle Island Sinkhole of Lake Huron provide opportunities to investigate cyanobacteria under such persistent low-O(2) conditions. Here, venting groundwater rich in sulfate and low in O(2) supports a unique benthic ecosystem of purple-colored cyanobacterial mats. Beneath the mat is a layer of carbonate that is enriched in calcite and to a lesser extent dolomite. In situ benthic metabolism chambers revealed that the mats are net sinks for O(2), suggesting primary production mechanisms other than oxygenic photosynthesis. Indeed, (14)C-bicarbonate uptake studies of autotrophic production show variable contributions from oxygenic and anoxygenic photosynthesis and chemosynthesis, presumably because of supply of sulfide. These results suggest the presence of either facultatively anoxygenic cyanobacteria or a mix of oxygenic/anoxygenic types of cyanobacteria. Shotgun metagenomic sequencing revealed a remarkably low-diversity mat community dominated by just one genotype most closely related to the cyanobacterium Phormidium autumnale, for which an essentially complete genome was reconstructed. Also recovered were partial genomes from a second genotype of Phormidium and several Oscillatoria. Despite the taxonomic simplicity, diverse cyanobacterial genes putatively involved in sulfur oxidation were identified, suggesting a diversity of sulfide physiologies. The dominant Phormidium genome reflects versatile metabolism and physiology that is specialized for a communal lifestyle under fluctuating redox conditions and light availability. Overall, this study provides genomic and physiologic insights into low-O(2) cyanobacterial mat ecosystems that played crucial geobiological roles over long stretches of Earth history.}, } @article {pmid22403423, year = {2012}, author = {Rôças, IN and Siqueira, JF}, title = {Characterization of microbiota of root canal-treated teeth with posttreatment disease.}, journal = {Journal of clinical microbiology}, volume = {50}, number = {5}, pages = {1721-1724}, pmid = {22403423}, issn = {1098-660X}, mesh = {Adolescent ; Adult ; Aged ; Bacteria/*classification/genetics ; Bacterial Load ; *Biodiversity ; Dental Pulp Cavity/*microbiology ; Female ; Humans ; Male ; *Metagenome ; Middle Aged ; Real-Time Polymerase Chain Reaction ; *Root Canal Therapy ; Stomatognathic Diseases/*microbiology/*therapy ; Young Adult ; }, abstract = {This study evaluated the microbiota of root canals undergoing retreatment. The most prevalent taxa detected by checkerboard included Propionibacterium species, Fusobacterium nucleatum, streptococci, and Pseudoramibacter alactolyticus. Quantitative real-time PCR detected Enterococcus faecalis and streptococci in 38% and 41% of the cases, comprising 9.76% and 65.78% of the total bacterial counts, respectively. The findings call into question the status of E. faecalis as the main pathogen and suggest that other species can be candidate pathogens associated with persistent/secondary endodontic infections.}, } @article {pmid22369384, year = {2011}, author = {Ogura, A and Lin, M and Shigenobu, Y and Fujiwara, A and Ikeo, K and Nagai, S}, title = {Effective gene collection from the metatranscriptome of marine microorganisms.}, journal = {BMC genomics}, volume = {12 Suppl 3}, number = {Suppl 3}, pages = {S15}, pmid = {22369384}, issn = {1471-2164}, mesh = {Algorithms ; Aquatic Organisms/classification/*genetics ; Chloroplasts/genetics ; Gene Library ; Information Storage and Retrieval ; *Metagenomics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Metagenomic studies, accelerated by the evolution of sequencing technologies and the rapid development of genomic analysis methods, can reveal genetic diversity and biodiversity in various samples including those of uncultured or unknown species. This approach, however, cannot be used to identify active functional genes under actual environmental conditions. Metatranscriptomics, which is similar in approach to metagenomics except that it utilizes RNA samples, is a powerful tool for the transcriptomic study of environmental samples. Unlike metagenomic studies, metatranscriptomic studies have not been popular to date due to problems with reliability, repeatability, redundancy and cost performance. Here, we propose a normalized metatranscriptomic method that is suitable for the collection of genes from samples as a platform for comparative transcriptomics.

RESULTS: We constructed two libraries, one non-normalized and the other normalized library, from samples of marine microorganisms taken during daylight hours from Hiroshima bay in Japan. We sequenced 0.6M reads for each sample on a Roche GS FLX, and obtained 0.2M genes after quality control and assembly. A comparison of the two libraries showed that the number of unique genes was larger in the normalized library than in the non-normalized library. Functional analysis of genes revealed that a small number of gene groups, ribosomal RNA genes and chloroplast genes, were dominant in both libraries. Taxonomic distribution analysis of the libraries suggests that Stramenopiles form a major taxon that includes diatoms. The normalization technique thus increases unique genes, functional categories of genes, and taxonomic richness.

CONCLUSIONS: Normalization of the marine metatranscriptome could be useful in increasing the number of genes collected, and in reducing redundancies among highly expressed genes. Gene collection through the normalization method was effective in providing a foundation for comparative transcriptomic analysis.}, } @article {pmid22378537, year = {2012}, author = {Brisson, VL and West, KA and Lee, PK and Tringe, SG and Brodie, EL and Alvarez-Cohen, L}, title = {Metagenomic analysis of a stable trichloroethene-degrading microbial community.}, journal = {The ISME journal}, volume = {6}, number = {9}, pages = {1702-1714}, pmid = {22378537}, issn = {1751-7370}, support = {P42 ES004705/ES/NIEHS NIH HHS/United States ; ES04705-19/ES/NIEHS NIH HHS/United States ; }, mesh = {Biodiversity ; Chloroflexi/classification/*genetics/*metabolism ; Genes, Bacterial/genetics ; Hydrogen/metabolism ; *Metagenomics ; Phylogeny ; Trichloroethylene/*metabolism ; Vitamin B 12/genetics ; }, abstract = {Dehalococcoides bacteria are the only organisms known to completely reduce chlorinated ethenes to the harmless product ethene. However, Dehalococcoides dechlorinate these chemicals more effectively and grow more robustly in mixed microbial communities than in isolation. In this study, the phylogenetic composition and gene content of a functionally stable trichloroethene-degrading microbial community was examined using metagenomic sequencing and analysis. For phylogenetic classification, contiguous sequences (contigs) longer than 2500 bp were grouped into classes according to tetranucleotide frequencies and assigned to taxa based on rRNA genes and other phylogenetic marker genes. Classes were identified for Clostridiaceae, Dehalococcoides, Desulfovibrio, Methanobacterium, Methanospirillum, as well as a Spirochete, a Synergistete, and an unknown Deltaproteobacterium. Dehalococcoides contigs were also identified based on sequence similarity to previously sequenced genomes, allowing the identification of 170 kb on contigs shorter than 2500 bp. Examination of metagenome sequences affiliated with Dehalococcoides revealed 406 genes not found in previously sequenced Dehalococcoides genomes, including 9 cobalamin biosynthesis genes related to corrin ring synthesis. This is the first time that a Dehalococcoides strain has been found to possess genes for synthesizing this cofactor critical to reductive dechlorination. Besides Dehalococcoides, several other members of this community appear to have genes for complete or near-complete cobalamin biosynthesis pathways. In all, 17 genes for putative reductive dehalogenases were identified, including 11 novel ones, all associated with Dehalococcoides. Genes for hydrogenase components (271 in total) were widespread, highlighting the importance of hydrogen metabolism in this community. PhyloChip analysis confirmed the stability of this microbial community.}, } @article {pmid22378535, year = {2012}, author = {Aylward, FO and Burnum, KE and Scott, JJ and Suen, G and Tringe, SG and Adams, SM and Barry, KW and Nicora, CD and Piehowski, PD and Purvine, SO and Starrett, GJ and Goodwin, LA and Smith, RD and Lipton, MS and Currie, CR}, title = {Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens.}, journal = {The ISME journal}, volume = {6}, number = {9}, pages = {1688-1701}, pmid = {22378535}, issn = {1751-7370}, mesh = {Animals ; Ants/*microbiology ; Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; Enterobacter/classification/genetics ; Fungi/physiology ; *Metagenomics ; Phylogeny ; *Proteomics ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Herbivores gain access to nutrients stored in plant biomass largely by harnessing the metabolic activities of microbes. Leaf-cutter ants of the genus Atta are a hallmark example; these dominant neotropical herbivores cultivate symbiotic fungus gardens on large quantities of fresh plant forage. As the external digestive system of the ants, fungus gardens facilitate the production and sustenance of millions of workers. Using metagenomic and metaproteomic techniques, we characterize the bacterial diversity and physiological potential of fungus gardens from two species of Atta. Our analysis of over 1.2 Gbp of community metagenomic sequence and three 16S pyrotag libraries reveals that in addition to harboring the dominant fungal crop, these ecosystems contain abundant populations of Enterobacteriaceae, including the genera Enterobacter, Pantoea, Klebsiella, Citrobacter and Escherichia. We show that these bacterial communities possess genes associated with lignocellulose degradation and diverse biosynthetic pathways, suggesting that they play a role in nutrient cycling by converting the nitrogen-poor forage of the ants into B-vitamins, amino acids and other cellular components. Our metaproteomic analysis confirms that bacterial glycosyl hydrolases and proteins with putative biosynthetic functions are produced in both field-collected and laboratory-reared colonies. These results are consistent with the hypothesis that fungus gardens are specialized fungus-bacteria communities that convert plant material into energy for their ant hosts. Together with recent investigations into the microbial symbionts of vertebrates, our work underscores the importance of microbial communities in the ecology and evolution of herbivorous metazoans.}, } @article {pmid22377802, year = {2012}, author = {Nelson, A and De Soyza, A and Perry, JD and Sutcliffe, IC and Cummings, SP}, title = {Polymicrobial challenges to Koch's postulates: ecological lessons from the bacterial vaginosis and cystic fibrosis microbiomes.}, journal = {Innate immunity}, volume = {18}, number = {5}, pages = {774-783}, doi = {10.1177/1753425912439910}, pmid = {22377802}, issn = {1753-4267}, mesh = {Animals ; Coinfection/*immunology/microbiology ; Cystic Fibrosis/genetics/*immunology/microbiology ; Cystic Fibrosis Transmembrane Conductance Regulator/genetics ; Female ; *Gene-Environment Interaction ; Homeostasis ; Humans ; Metagenome ; *Microbial Consortia ; Microbial Interactions/immunology ; Vaginosis, Bacterial/*immunology/microbiology ; }, abstract = {Koch's postulates have shaped our understanding of infectious diseases; however, one of the tangential consequences of them has been the emergence of a predominantly monomicrobial perspective concerning disease aetiology. This orthodoxy has been undermined by the growing recognition that some important infectious diseases have a polymicrobial aetiology. A significant new development in our understanding of polymicrobial infections is the recognition that they represent functional ecosystems and that to understand such systems and the outcome and impact of therapeutic interventions requires an understanding of how these communities arise and develop. Therefore, it is timely to explore what we can learn from other fields. In particular, ecological theory may inform our understanding of how polymicrobial communities assemble their structure and their dynamics over time. Such work may also offer insights into how such communities move from stable to unstable states, as well as the role of invasive pathogens in the progression of the disease. Ecological theory offers a theoretical framework around which testable hypotheses can be developed to clarify the polymicrobial nature and dynamics of such infections in the face of environmental change and therapeutic interventions.}, } @article {pmid22367934, year = {2012}, author = {Li, X and Yu, Y and Feng, W and Yan, Q and Gong, Y}, title = {Host species as a strong determinant of the intestinal microbiota of fish larvae.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {50}, number = {1}, pages = {29-37}, pmid = {22367934}, issn = {1976-3794}, mesh = {Animals ; *Biodiversity ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; Fishes/*microbiology ; Gastrointestinal Tract/*microbiology ; Larva/microbiology ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Water Microbiology ; }, abstract = {We investigated the influence of host species on intestinal microbiota by comparing the gut bacterial community structure of four cohabitating freshwater fish larvae, silver carp, grass carp, bighead carp, and blunt snout bream, using denaturing gradient gel electrophoresis (DGGE) of the amplified 16S and 18S rRNA genes. Similarity clustering indicated that the intestinal microbiota derived from these four fish species could be divided into four groups based on 16S rRNA gene similarity, whereas the eukaryotic 18S rRNA genes showed no distinct groups. The water sample from the shared environment contained microbiota of an independent group as indicated by both 16S and 18S rRNA genes segments. The bacterial community structures were visualized using rank-abundance plots fitted with linear regression models. Results showed that the intestinal bacterial evenness was significantly different between species (P<0.05) and between species and the water sample (P<0.01). Thirty-five relatively dominant bands in DGGE patterns were sequenced and grouped into five major taxa: Proteobacteria (26), Actinobacteria (5), Bacteroidetes (1), Firmicutes (2), and Cyanobacterial (1). Six eukaryotes were detected by sequencing 18S rRNA genes segments. The present study suggests that the intestines of the four fish larvae, although reared in the same environment, contained distinct bacterial populations, while intestinal eukaryotic microorganisms were almost identical.}, } @article {pmid22367084, year = {2012}, author = {Buerger, S and Spoering, A and Gavrish, E and Leslin, C and Ling, L and Epstein, SS}, title = {Microbial scout hypothesis and microbial discovery.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {9}, pages = {3229-3233}, pmid = {22367084}, issn = {1098-5336}, mesh = {Bacteria/classification/*growth & development/*isolation & purification ; Bacteriological Techniques/*methods ; *Biodiversity ; Humans ; Metagenome ; Molecular Sequence Data ; Sequence Analysis, DNA ; Soil Microbiology ; Time Factors ; Water Microbiology ; }, abstract = {In this study, we examine the temporal pattern of colony appearance during cultivation experiments, and whether this pattern could inform on optimizing the process of microbial discovery. In a series of long-term cultivation experiments, we observed an expected gradual increase over time of the total number of microbial isolates, culminating in a 700-fold colony count increase at 18 months. Conventional thought suggests that long-term incubations result in a culture collection enriched with species that are slow growing or rare, may be unavailable from short-term experiments, and likely are novel. However, after we examined the phylogenetic novelty of the isolates as a function of the time of their isolation, we found no correlation between the two. The probability of discovering either a new or rare species late in the incubation matched that of species isolated earlier. These outcomes are especially notable because of their generality: observations were essentially identical for marine and soil bacteria as well as for spore formers and non-spore formers. These findings are consistent with the idea of the stochastic awakening of dormant cells, thus lending support to the scout model. The process of microbial discovery is central to the study of environmental microorganisms and the human microbiome. While long-term incubation does not appear to increase the probability of discovering novel species, the technology enabling such incubations, i.e., single-cell cultivation, may still be the method of choice. While it does not necessarily allow more species to grow from a given inoculum, it minimizes the overall isolation effort and supplies needed.}, } @article {pmid22363639, year = {2012}, author = {Gregoracci, GB and Nascimento, JR and Cabral, AS and Paranhos, R and Valentin, JL and Thompson, CC and Thompson, FL}, title = {Structuring of bacterioplankton diversity in a large tropical bay.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e31408}, pmid = {22363639}, issn = {1932-6203}, mesh = {Bacteria/classification/genetics/*growth & development/metabolism ; Bays/*microbiology ; *Biodiversity ; Brazil ; Colony Count, Microbial ; Flow Cytometry ; Geography ; Metabolome ; Metagenome/genetics ; Metagenomics ; Phylogeny ; Plankton/classification/genetics/*growth & development/metabolism ; Principal Component Analysis ; Prokaryotic Cells/cytology ; Regression Analysis ; Seawater/microbiology ; *Tropical Climate ; Vibrio/cytology/genetics/growth & development ; *Water Microbiology ; }, abstract = {Structuring of bacterioplanktonic populations and factors that determine the structuring of specific niche partitions have been demonstrated only for a limited number of colder water environments. In order to better understand the physical chemical and biological parameters that may influence bacterioplankton diversity and abundance, we examined their productivity, abundance and diversity in the second largest Brazilian tropical bay (Guanabara Bay, GB), as well as seawater physical chemical and biological parameters of GB. The inner bay location with higher nutrient input favored higher microbial (including vibrio) growth. Metagenomic analysis revealed a predominance of Gammaproteobacteria in this location, while GB locations with lower nutrient concentration favored Alphaproteobacteria and Flavobacteria. According to the subsystems (SEED) functional analysis, GB has a distinctive metabolic signature, comprising a higher number of sequences in the metabolism of phosphorus and aromatic compounds and a lower number of sequences in the photosynthesis subsystem. The apparent phosphorus limitation appears to influence the GB metagenomic signature of the three locations. Phosphorus is also one of the main factors determining changes in the abundance of planktonic vibrios, suggesting that nutrient limitation can be observed at community (metagenomic) and population levels (total prokaryote and vibrio counts).}, } @article {pmid22363439, year = {2012}, author = {Wu, S and Wang, G and Angert, ER and Wang, W and Li, W and Zou, H}, title = {Composition, diversity, and origin of the bacterial community in grass carp intestine.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e30440}, pmid = {22363439}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/*genetics ; Carps/*microbiology ; Cellulose/metabolism ; Environmental Microbiology ; Gene Library ; *Genetic Variation ; Intestines/*microbiology ; Metagenome/*genetics ; Phylogeny ; }, abstract = {Gut microbiota has become an integral component of the host, and received increasing attention. However, for many domestic animals, information on the microbiota is insufficient and more effort should be exerted to manage the gastrointestinal bacterial community. Understanding the factors that influence the composition of microbial community in the host alimentary canal is essential to manage or improve the microbial community composition. In the present study, 16S rRNA gene sequence-based comparisons of the bacterial communities in the grass carp (Ctenopharyngodon idellus) intestinal contents and fish culture-associated environments are performed. The results show that the fish intestinal microbiota harbors many cellulose-decomposing bacteria, including sequences related to Anoxybacillus, Leuconostoc, Clostridium, Actinomyces, and Citrobacter. The most abundant bacterial operational taxonomic units (OTUs) in the grass carp intestinal content are those related to feed digestion. In addition, the potential pathogens and probiotics are important members of the intestinal microbiota. Further analyses show that grass carp intestine holds a core microbiota composed of Proteobacteria, Firmicutes, and Actinobacteria. The comparison analyses reveal that the bacterial community in the intestinal contents is most similar to those from the culture water and sediment. However, feed also plays significant influence on the composition of gut microbiota.}, } @article {pmid22360453, year = {2012}, author = {Creer, S and Sinniger, F}, title = {Cosmopolitanism of microbial eukaryotes in the global deep seas.}, journal = {Molecular ecology}, volume = {21}, number = {5}, pages = {1033-1035}, doi = {10.1111/j.1365-294X.2012.05437.x}, pmid = {22360453}, issn = {1365-294X}, mesh = {Animals ; *Biodiversity ; Eukaryota/*classification ; *Geologic Sediments ; Metagenomics/*methods ; }, abstract = {Deep sea environments cover more than 65% of the earth's surface and fulfil a range of ecosystem functions, yet they are also amongst the least known habitats on earth. Whilst the discovery of key geological processes, combined with technological developments, has focused interest onto geologically active areas such as hydrothermal vents, most abyssal biodiversity remains to be discovered (Danovaro et al. 2010). However, as for terrestrial reservoirs of biodiversity, the world's largest biome is under threat from anthropogenic activities ranging from environmental change to the exploitation of minerals and rare-earth elements (Kato et al. 2011). It is therefore important to understand the magnitude, nature and composition of deep sea biological communities to inform us of levels of local adaptation, functionality and resilience with respect to future environmental perturbation. In this issue of Molecular Ecology, Bik et al. utilize 454 Roche metagenetic environmental sequencing to assess microbial metazoan community composition and phylogenetic identity across deep sea depth gradients and between ocean basins. The analyses suggest that although the majority of microbial eukaryotic taxa are regionally restricted, a small percentage might maintain cosmopolitan deep sea distributions, and an even smaller fraction appear to be eurybathic (live across depth gradients).}, } @article {pmid22355719, year = {2011}, author = {Ishak, HD and Miller, JL and Sen, R and Dowd, SE and Meyer, E and Mueller, UG}, title = {Microbiomes of ant castes implicate new microbial roles in the fungus-growing ant Trachymyrmex septentrionalis.}, journal = {Scientific reports}, volume = {1}, number = {}, pages = {204}, pmid = {22355719}, issn = {2045-2322}, mesh = {Animals ; Ants/*microbiology/*physiology ; Biodiversity ; Computational Biology ; Female ; Male ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; Symbiosis/genetics ; }, abstract = {Fungus-growing ants employ several defenses against diseases, including disease-suppressing microbial biofilms on their integument and in fungal gardens. Here, we compare the phenology of microbiomes in natural nests of the temperate fungus-growing ant Trachymyrmex septentrionalis using culture-dependent isolations and culture-independent 16S-amplicon 454-sequencing. 454-sequencing revealed diverse actinobacteria associated with ants, including most prominently Solirubrobacter (12.2-30.9% of sequence reads), Pseudonocardia (3.5-42.0%), and Microlunatus (0.4-10.8%). Bacterial abundances remained relatively constant in monthly surveys throughout the annual active period (late winter to late summer), except Pseudonocardia abundance declined in females during the reproductive phase. Pseudonocardia species found on ants are phylogenetically different from those in gardens and soil, indicating ecological separation of these Pseudonocardia types. Because the pathogen Escovopsis is not known to infect gardens of T. septentrionalis, the ant-associated microbes do not seem to function in Escovopsis suppression, but could protect against ant diseases, help in nest sanitation, or serve unknown functions.}, } @article {pmid22355685, year = {2011}, author = {Stearns, JC and Lynch, MD and Senadheera, DB and Tenenbaum, HC and Goldberg, MB and Cvitkovitch, DG and Croitoru, K and Moreno-Hagelsieb, G and Neufeld, JD}, title = {Bacterial biogeography of the human digestive tract.}, journal = {Scientific reports}, volume = {1}, number = {}, pages = {170}, pmid = {22355685}, issn = {2045-2322}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Adult ; Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; *Metagenome/genetics ; Organ Specificity ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {We present bacterial biogeography as sampled from the human gastrointestinal tract of four healthy subjects. This study generated >32 million paired-end sequences of bacterial 16S rRNA genes (V3 region) representing >95,000 unique operational taxonomic units (OTUs; 97% similarity clusters), with >99% Good's coverage for all samples. The highest OTU richness and phylogenetic diversity was found in the mouth samples. The microbial communities of multiple biopsy sites within the colon were highly similar within individuals and largely distinct from those in stool. Within an individual, OTU overlap among broad site definitions (mouth, stomach/duodenum, colon and stool) ranged from 32-110 OTUs, 25 of which were common to all individuals and included OTUs affiliated with Faecalibacterium prasnitzii and the TM7 phylum. This first comprehensive characterization of the abundant and rare microflora found along the healthy human digestive tract represents essential groundwork to investigate further how the human microbiome relates to health and disease.}, } @article {pmid22354366, year = {2013}, author = {Belila, A and Abbas, B and Fazaa, I and Saidi, N and Snoussi, M and Hassen, A and Muyzer, G}, title = {Sulfur bacteria in wastewater stabilization ponds periodically affected by the 'red-water' phenomenon.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {1}, pages = {379-394}, pmid = {22354366}, issn = {1432-0614}, mesh = {Bacteria/*classification/*genetics/metabolism ; Bacterial Proteins/genetics ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; Metagenome ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfur/*metabolism ; Tunisia ; Wastewater/*microbiology ; }, abstract = {Several wastewater stabilization ponds (WSP) in Tunisia suffer periodically from the 'red-water' phenomenon due to blooming of purple sulfur bacteria, indicating that sulfur cycle is one of the main element cycles in these ponds. In this study, we investigated the microbial diversity of the El Menzeh WSP and focused in particular on the different functional groups of sulfur bacteria. For this purpose, we used denaturing gradient gel electrophoresis of PCR-amplified fragments of the 16S rRNA gene and of different functional genes involved in microbial sulfur metabolism (dsrB, aprA, and pufM). Analyses of the 16S rRNA revealed a relatively high microbial diversity where Proteobacteria, Chlorobi, Bacteroidetes, and Cyanobacteria constitute the major bacterial groups. The dsrB and aprA gene analysis revealed the presence of deltaproteobacterial sulfate-reducing bacteria (i.e., Desulfobacter and Desulfobulbus), while the analysis of 16S rRNA, aprA, and pufM genes assigned the sulfur-oxidizing bacteria community to the photosynthetic representatives belonging to the Chlorobi (green sulfur bacteria) and the Proteobacteria (purple sulfur and non sulfur bacteria) phyla. These results point on the diversity of the metabolic processes within this wastewater plant and/or the availability of sulfate and diverse electron donors.}, } @article {pmid22353769, year = {2012}, author = {Sato, Y and Ohta, H and Yamagishi, T and Guo, Y and Nishizawa, T and Rahman, MH and Kuroda, H and Kato, T and Saito, M and Yoshinaga, I and Inubushi, K and Suwa, Y}, title = {Detection of anammox activity and 16S rRNA genes in ravine paddy field soil.}, journal = {Microbes and environments}, volume = {27}, number = {3}, pages = {316-319}, pmid = {22353769}, issn = {1347-4405}, mesh = {Ammonia/*metabolism ; Bacteria/*classification/genetics/*metabolism ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gas Chromatography-Mass Spectrometry ; Isotope Labeling ; Japan ; *Metagenome ; Nitrogen Isotopes ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {An anammox assay involving a [15]N tracer and gas chromatography-mass spectrometry revealed that the potential anammox activity accounted for 1 to 5% of total N2 production in a ravine paddy field, Japan. Among four 4-cm-deep layers, the top layer showed the highest activity. Clone libraries showed that the DNA in the top layer contained sequences related to those of Candidatus 'Brocadia fulgida', Ca. 'B. anammoxidans', and Ca. 'Kuenenia stuttgartiensis'. These results suggest that a specific population of anammox bacteria was present in paddy soils, although a small part of dinitrogen gas was emitted from the soil via anammox.}, } @article {pmid22350256, year = {2013}, author = {Brito, EM and Piñón-Castillo, HA and Guyoneaud, R and Caretta, CA and Gutiérrez-Corona, JF and Duran, R and Reyna-López, GE and Nevárez-Moorillón, GV and Fahy, A and Goñi-Urriza, M}, title = {Bacterial biodiversity from anthropogenic extreme environments: a hyper-alkaline and hyper-saline industrial residue contaminated by chromium and iron.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {1}, pages = {369-378}, doi = {10.1007/s00253-012-3923-5}, pmid = {22350256}, issn = {1432-0614}, mesh = {Bacteria/*classification/*genetics ; Chromium/*analysis ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Hydrogen-Ion Concentration ; *Industrial Waste ; Iron/*analysis ; Metagenome ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Sequence Analysis, DNA ; }, abstract = {Anthropogenic extreme environments are among the most interesting sites for the bioprospection of extremophiles since the selection pressures may favor the presence of microorganisms of great interest for taxonomical and astrobiological research as well as for bioremediation technologies and industrial applications. In this work, T-RFLP and 16S rRNA gene library analyses were carried out to describe the autochthonous bacterial populations from an industrial waste characterized as hyper-alkaline (pH between 9 and 14), hyper-saline (around 100 PSU) and highly contaminated with metals, mainly chromium (from 5 to 18 g kg(-1)) and iron (from 2 to 108 g kg(-1)). Due to matrix interference with DNA extraction, a protocol optimization step was required in order to carry out molecular analyses. The most abundant populations, as evaluated by both T-RFLP and 16S rRNA gene library analyses, were affiliated to Bacillus and Lysobacter genera. Lysobacter related sequences were present in the three samples: solid residue and lixiviate sediments from both dry and wet seasons. Sequences related to Thiobacillus were also found; although strains affiliated to this genus are known to have tolerance to metals, they have not previously been detected in alkaline environments. Together with Bacillus (already described as a metal reducer), such organisms could be of use in bioremediation technologies for reducing chromium, as well as for the prospection of enzymes of biotechnological interest.}, } @article {pmid22342609, year = {2012}, author = {Archambaud, C and de Wouters, T and Dobrijevic, D and Grompone, G and Pédron, T}, title = {Microbes for Health 2 Symposium: meeting report.}, journal = {Research in microbiology}, volume = {163}, number = {2}, pages = {151-155}, doi = {10.1016/j.resmic.2012.01.005}, pmid = {22342609}, issn = {1769-7123}, mesh = {*Bacteria/classification/immunology/pathogenicity ; Congresses as Topic ; Gastrointestinal Diseases/*microbiology ; Gastrointestinal Tract/*microbiology/pathology ; Health ; Humans ; Metagenome ; Microbial Consortia ; }, } @article {pmid22323793, year = {2012}, author = {Humphries, C}, title = {Indoor ecosystems.}, journal = {Science (New York, N.Y.)}, volume = {335}, number = {6069}, pages = {648-650}, doi = {10.1126/science.335.6069.648}, pmid = {22323793}, issn = {1095-9203}, mesh = {Air Microbiology ; Animals ; Bacteria/*isolation & purification ; Biodiversity ; Biota ; Databases, Genetic ; *Ecosystem ; *Environmental Microbiology ; Foundations ; Hospitals ; Housing ; Humans ; Metagenome ; Research Support as Topic ; Toilet Facilities ; Workplace ; }, } @article {pmid22322827, year = {2012}, author = {Balaji, K and Thenmozhi, R and Sundaravadivel, M and Pandian, SK}, title = {Comparison of bacterial communities in the throat swabs from healthy subjects and pharyngitis patients by terminal restriction fragment length polymorphism.}, journal = {Applied biochemistry and biotechnology}, volume = {167}, number = {5}, pages = {1459-1473}, doi = {10.1007/s12010-011-9508-4}, pmid = {22322827}, issn = {1559-0291}, mesh = {Bacteria/classification/*genetics/*isolation & purification/pathogenicity ; Biodiversity ; *Health ; Humans ; Metagenome/genetics ; Pharyngitis/*microbiology ; Pharynx/*microbiology ; Phylogeny ; *Polymorphism, Restriction Fragment Length ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Terminal restriction fragment length polymorphism (T-RFLP) analysis was applied to characterize bacterial flora present in the throats of healthy subjects and pharyngitis patients. The 16S rRNA genes of bacteria present in throat metagenome were amplified by PCR with 6-carboxy-fluorescein (6-FAM)-labeled universal forward primer (27 F) and a universal reverse primer (1513R). The 16S rDNAs were digested with restriction enzymes with 4-bp recognition sites (MspI or RsaI) and analyzed by using an automated DNA sequencer. T-RFLP patterns were numerically analyzed using computer programs. From analysis of the throat bacterial community, patterns derived from MspI and RsaI digested samples of healthy subjects and pharyngitis patients were grouped into different clusters, though RsaI digested samples showed some uncertainty. Pharyngitis throats generated an average species richness of 9 [±2.1 (SD)] and 10 (±2.9) for MspI and RsaI digests, respectively, whereas healthy throats generated 6.3 (±1.2) and 6.1 (±1.5) in MspI and RsaI digests, respectively. These results suggest that samples from pharyngitis patients contain an unexpected diversity of causative bacteria. The pharyngitis throats were colonized with a rich diversity of bacterial species than that of healthy throats. Using T-RFLP, we are able to detect a model bacterium, Streptococcus pyogenes SF370, and T-RF patterns were consistent with the Streptococcal T-RFLP patterns. Our study indicates that T-RFLP analysis is useful for the assessment of diversity of throat bacterial flora and rapid comparison of the community structure between subjects with and without pharyngitis.}, } @article {pmid22313738, year = {2012}, author = {Godoy-Vitorino, F and Leal, SJ and Díaz, WA and Rosales, J and Goldfarb, KC and García-Amado, MA and Michelangeli, F and Brodie, EL and Domínguez-Bello, MG}, title = {Differences in crop bacterial community structure between hoatzins from different geographical locations.}, journal = {Research in microbiology}, volume = {163}, number = {3}, pages = {211-220}, doi = {10.1016/j.resmic.2012.01.001}, pmid = {22313738}, issn = {1769-7123}, mesh = {Animals ; Bacteria/*classification/*genetics ; *Biota ; Birds/*microbiology ; Feces/*microbiology ; Feeding Behavior ; Geography ; *Metagenome ; Plant Development ; Venezuela ; }, abstract = {The hoatzin is the only known folivorous bird with foregut fermentation, and is distributed in Venezuela in rivers of the central savannas to the eastern Orinoco River. Differences in diet are expected to affect the digestive microbiota and we hypothesized that hoatzins from different habitats might have a different crop microbiota. We thus characterized the microbiota of six birds from the Cojedes and Orinoco Rivers using the G2 PhyloChip and, in parallel, we compared plant availability and foraging behavior of the hoatzins from the two locations. Plant composition differed between the 2 locations, which shared 5 out of 18 plant families and 1 plant genus--Coccoloba--that was highly consumed in both locations. The PhyloChip detected ∼1600 phylotypes from 42 phyla. There was a core microbiota with ~50% of the OTUs shared by at least 4 of the 6 individuals, but there were also differences in the crop microbiota of animals from the two regions. There existed a higher relative abundance of Alphaproteobacteria and Actinobacteria in the crops of birds from the Cojedes River and of Clostridia and Deltaproteobacteria in the crops of birds from the Orinoco River. The results showed both a core crop microbiota and also the bacterial taxa responsible for geographical differences among individuals from the two locations with different vegetation, suggesting an effect of both diet and geography in shaping the crop bacterial community of the hoatzin.}, } @article {pmid22309113, year = {2012}, author = {Jia, W and Whitehead, RN and Griffiths, L and Dawson, C and Bai, H and Waring, RH and Ramsden, DB and Hunter, JO and Cauchi, M and Bessant, C and Fowler, DP and Walton, C and Turner, C and Cole, JA}, title = {Diversity and distribution of sulphate-reducing bacteria in human faeces from healthy subjects and patients with inflammatory bowel disease.}, journal = {FEMS immunology and medical microbiology}, volume = {65}, number = {1}, pages = {55-68}, doi = {10.1111/j.1574-695X.2012.00935.x}, pmid = {22309113}, issn = {1574-695X}, support = {WT080238MA//Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacteria/*classification/genetics/*isolation & purification/metabolism ; *Biota ; DNA Primers/genetics ; DNA, Bacterial/genetics ; Feces/*microbiology ; High-Throughput Nucleotide Sequencing/methods ; Human Experimentation ; Humans ; Inflammatory Bowel Diseases/drug therapy/*microbiology ; *Metagenome ; Oxidation-Reduction ; Polymerase Chain Reaction/methods ; Sulfates/*metabolism ; }, abstract = {The relative abundance of different groups of sulphate-reducing bacteria (SRB) in faecal DNA collected before and after therapy from patients suffering from Crohn's disease (CD), irritable bowel syndrome (IBS) or ulcerative colitis (UC) has been compared with that from healthy controls. Growth tests revealed that SRB were not more abundant in samples from patients with CD before treatment than in the healthy control group. For most of the 128 samples available, these preliminary results were confirmed using degenerate PCR primers that amplify the dsrAB gene. However, some samples from patients with CD before treatment contained a growth inhibitor that was absent from IBS or UC samples. In-depth sequencing of PCR-generated dsrB fragments revealed that the diversity detected was surprisingly low, with only eight strains of SRB and the sulphite-reducing bacterium, Bilophila wadsworthia, detected above the 0.1% threshold. The proportion of the two major species detected, B. wadsworthia and Desulfovibrio piger, was as high as 93.5% of the total SRB population in the healthy control group and lower in all patient groups. Four previously undescribed species were found: it is impossible to predict whether they are sulphate or sulphite-reducing bacteria.}, } @article {pmid22307294, year = {2012}, author = {Perkins, GA and den Bakker, HC and Burton, AJ and Erb, HN and McDonough, SP and McDonough, PL and Parker, J and Rosenthal, RL and Wiedmann, M and Dowd, SE and Simpson, KW}, title = {Equine stomachs harbor an abundant and diverse mucosal microbiota.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {8}, pages = {2522-2532}, pmid = {22307294}, issn = {1098-5336}, support = {/WT_/Wellcome Trust/United Kingdom ; T32 AI070077/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification/*genetics ; *Biodiversity ; Biopsy ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gastric Mucosa/*microbiology ; Horses/*microbiology ; In Situ Hybridization, Fluorescence ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Stomach/*microbiology ; }, abstract = {Little is known about the gastric mucosal microbiota in healthy horses, and its role in gastric disease has not been critically examined. The present study used a combination of 16S rRNA bacterial tag-encoded pyrosequencing (bTEFAP) and fluorescence in situ hybridization (FISH) to characterize the composition and spatial distribution of selected gastric mucosal microbiota of healthy horses. Biopsy specimens of the squamous, glandular, antral, and any ulcerated mucosa were obtained from 6 healthy horses by gastroscopy and from 3 horses immediately postmortem. Pyrosequencing was performed on biopsy specimens from 6 of the horses and yielded 53,920 reads in total, with 631 to 4,345 reads in each region per horse. The microbiome segregated into two distinct clusters comprised of horses that were stabled, fed hay, and sampled at postmortem (cluster 1) and horses that were pastured on grass, fed hay, and biopsied gastroscopically after a 12-h fast (cluster 2). The types of bacteria obtained from different anatomic regions clustered by horse rather than region. The dominant bacteria in cluster 1 were Firmicutes (>83% reads/sample), mainly Streptococcus spp., Lactobacillus spp. and, Sarcina spp. Cluster 2 was more diverse, with predominantly Proteobacteria, Bacteroidetes, and Firmicutes, consisting of Actinobacillus spp. Moraxella spp., Prevotella spp., and Porphyromonas spp. Helicobacter sp. sequences were not identified in any of 53,920 reads. FISH (n = 9) revealed bacteria throughout the stomach in close apposition to the mucosa, with significantly more Streptococcus spp. present in the glandular region of the stomach. The equine stomach harbors an abundant and diverse mucosal microbiota that varies by individual.}, } @article {pmid22306331, year = {2012}, author = {Xing, MN and Zhang, XZ and Huang, H}, title = {Application of metagenomic techniques in mining enzymes from microbial communities for biofuel synthesis.}, journal = {Biotechnology advances}, volume = {30}, number = {4}, pages = {920-929}, doi = {10.1016/j.biotechadv.2012.01.021}, pmid = {22306331}, issn = {1873-1899}, mesh = {Bacteria/*enzymology/*genetics/isolation & purification ; *Biofuels ; Biomass ; Databases, Genetic ; Environmental Microbiology ; Enzymes ; Gene Library ; Genetic Engineering/*methods ; *Genome, Bacterial ; *Metagenomics ; Microbial Consortia ; }, abstract = {Feedstock for biofuel synthesis is transitioning to lignocelluosic biomass to address criticism over competition between first generation biofuels and food production. As microbial catalysis is increasingly applied for the conversion of biomass to biofuels, increased import has been placed on the development of novel enzymes. With revolutionary advances in sequencer technology and metagenomic sequencing, mining enzymes from microbial communities for biofuel synthesis is becoming more and more practical. The present article highlights the latest research progress on the special characteristics of metagenomic sequencing, which has been a powerful tool for new enzyme discovery and gene functional analysis in the biomass energy field. Critical enzymes recently developed for the pretreatment and conversion of lignocellulosic materials are evaluated with respect to their activity and stability, with additional explorations into xylanase, laccase, amylase, chitinase, and lipolytic biocatalysts for other biomass feedstocks.}, } @article {pmid22301318, year = {2012}, author = {Iverson, V and Morris, RM and Frazar, CD and Berthiaume, CT and Morales, RL and Armbrust, EV}, title = {Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota.}, journal = {Science (New York, N.Y.)}, volume = {335}, number = {6068}, pages = {587-590}, doi = {10.1126/science.1212665}, pmid = {22301318}, issn = {1095-9203}, mesh = {Archaeal Proteins/*genetics/metabolism ; Biota ; *Ecosystem ; Enzymes/genetics/metabolism ; Euryarchaeota/classification/*genetics/metabolism/*physiology ; Genes, Archaeal ; *Genome, Archaeal ; Genome, Bacterial ; Heterotrophic Processes ; Lipid Metabolism/genetics ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Microbial Consortia ; Molecular Sequence Data ; Pacific Ocean ; Peptide Hydrolases/genetics/metabolism ; Phylogeny ; Proteins/metabolism ; Rhodopsin/genetics ; Rhodopsins, Microbial ; Seawater/*microbiology ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Ecosystems are shaped by complex communities of mostly unculturable microbes. Metagenomes provide a fragmented view of such communities, but the ecosystem functions of major groups of organisms remain mysterious. To better characterize members of these communities, we developed methods to reconstruct genomes directly from mate-paired short-read metagenomes. We closed a genome representing the as-yet uncultured marine group II Euryarchaeota, assembled de novo from 1.7% of a metagenome sequenced from surface seawater. The genome describes a motile, photo-heterotrophic cell focused on degradation of protein and lipids and clarifies the origin of proteorhodopsin. It also demonstrates that high-coverage mate-paired sequence can overcome assembly difficulties caused by interstrain variation in complex microbial communities, enabling inference of ecosystem functions for uncultured members.}, } @article {pmid22297557, year = {2012}, author = {Liu, M and Fan, L and Zhong, L and Kjelleberg, S and Thomas, T}, title = {Metaproteogenomic analysis of a community of sponge symbionts.}, journal = {The ISME journal}, volume = {6}, number = {8}, pages = {1515-1525}, pmid = {22297557}, issn = {1751-7370}, mesh = {Animals ; Bacteria/classification/genetics/metabolism ; *Bacterial Physiological Phenomena ; Bacterial Proteins/genetics ; Biodiversity ; Biological Evolution ; Biological Transport, Active/genetics ; *Metagenomics ; Oxidoreductases/genetics ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; Stress, Physiological/genetics ; Symbiosis/genetics ; }, abstract = {Sponges harbour complex communities of diverse microorganisms, which have been postulated to form intimate symbiotic relationships with their host. Here we unravel some of these interactions by characterising the functional features of the microbial community of the sponge Cymbastela concentrica through a combined metagenomic and metaproteomic approach. We discover the expression of specific transport functions for typical sponge metabolites (for example, halogenated aromatics, dipeptides), which indicates metabolic interactions between the community and the host. We also uncover the simultaneous performance of aerobic nitrification and anaerobic denitrification, which would aid to remove ammonium secreted by the sponge. Our analysis also highlights the requirement for the microbial community to respond to variable environmental conditions and hence express an array of stress protection proteins. Molecular interactions between symbionts and their host might also be mediated by a set of expressed eukaryotic-like proteins and cell-cell mediators. Finally, some sponge-associated bacteria (for example, a Phyllobacteriaceae phylotype) appear to undergo an evolutionary adaptation process to the sponge environment as evidenced by active mobile genetic elements. Our data clearly show that a combined metaproteogenomic approach can provide novel information on the activities, physiology and interactions of sponge-associated microbial communities.}, } @article {pmid22297556, year = {2012}, author = {Delmont, TO and Prestat, E and Keegan, KP and Faubladier, M and Robe, P and Clark, IM and Pelletier, E and Hirsch, PR and Meyer, F and Gilbert, JA and Le Paslier, D and Simonet, P and Vogel, TM}, title = {Structure, fluctuation and magnitude of a natural grassland soil metagenome.}, journal = {The ISME journal}, volume = {6}, number = {9}, pages = {1677-1687}, pmid = {22297556}, issn = {1751-7370}, support = {BBS/E/C/00004961/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; Climate Change ; Cluster Analysis ; *Metagenome ; Metagenomics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The soil ecosystem is critical for human health, affecting aspects of the environment from key agricultural and edaphic parameters to critical influence on climate change. Soil has more unknown biodiversity than any other ecosystem. We have applied diverse DNA extraction methods coupled with high throughput pyrosequencing to explore 4.88 × 10(9) bp of metagenomic sequence data from the longest continually studied soil environment (Park Grass experiment at Rothamsted Research in the UK). Results emphasize important DNA extraction biases and unexpectedly low seasonal and vertical soil metagenomic functional class variations. Clustering-based subsystems and carbohydrate metabolism had the largest quantity of annotated reads assigned although <50% of reads were assigned at an E value cutoff of 10(-5). In addition, with the more detailed subsystems, cAMP signaling in bacteria (3.24±0.27% of the annotated reads) and the Ton and Tol transport systems (1.69±0.11%) were relatively highly represented. The most highly represented genome from the database was that for a Bradyrhizobium species. The metagenomic variance created by integrating natural and methodological fluctuations represents a global picture of the Rothamsted soil metagenome that can be used for specific questions and future inter-environmental metagenomic comparisons. However, only 1% of annotated sequences correspond to already sequenced genomes at 96% similarity and E values of <10(-5), thus, considerable genomic reconstructions efforts still have to be performed.}, } @article {pmid22286379, year = {2012}, author = {Franzolin, R and St-Pierre, B and Northwood, K and Wright, AD}, title = {Analysis of rumen methanogen diversity in water buffaloes (Bubalus bubalis) under three different diets.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {131-139}, pmid = {22286379}, issn = {1432-184X}, mesh = {Animal Feed/*analysis ; Animals ; Bacteria/classification/genetics/*isolation & purification/*metabolism ; *Biodiversity ; Buffaloes/genetics/*metabolism/*microbiology ; Diet ; Metagenome ; Methane/*metabolism ; Molecular Sequence Data ; Phylogeny ; Rumen/metabolism/*microbiology ; }, abstract = {The water buffalo (Bubalus bubalis) is a prominent livestock species for the production of milk and meat in many countries. We investigated the diversity of rumen methanogens in Mediterranean water buffaloes maintained in Brazil under different diets: corn silage, grazing pasture, or sugar cane. A total of 467 clones were isolated from three methanogen 16S rRNA gene clone libraries that each represented a distinct feed type. The 467 clones were assigned to 19 species-level operational taxonomic units (OTUs). Four OTUs were represented in all three libraries, eight OTUs were library-specific, six OTUs were found in only the corn silage and pasture grazing libraries, and one OTU was shared only between pasture grazing and sugar cane libraries. We found that Methanobrevibacter-related sequences were the most abundant in the water buffaloes sampled for our analysis, in contrast to previously reported studies showing that Methanomicrobium mobile-like methanogens were the most abundant methanogens in water buffaloes of Murrah and Surti breeds sampled in India. Considering the worldwide distribution of water buffaloes and the likely wide variety of diets provided, our results combined with studies from other groups support that larger scope analyses of microbiomes for this livestock species would provide great insight into the contribution of geographical location, breed, and diet in determining the population structure of rumen microorganisms.}, } @article {pmid22284965, year = {2012}, author = {Ishizuka, A and Tomizuka, K and Aoki, R and Nishijima, T and Saito, Y and Inoue, R and Ushida, K and Mawatari, T and Ikeda, T}, title = {Effects of administration of Bifidobacterium animalis subsp. lactis GCL2505 on defecation frequency and bifidobacterial microbiota composition in humans.}, journal = {Journal of bioscience and bioengineering}, volume = {113}, number = {5}, pages = {587-591}, doi = {10.1016/j.jbiosc.2011.12.016}, pmid = {22284965}, issn = {1347-4421}, mesh = {Adult ; Bifidobacterium/genetics/growth & development/*physiology ; Biodiversity ; Colony Count, Microbial ; Constipation/microbiology ; Cross-Over Studies ; *Defecation ; Double-Blind Method ; Feces/*microbiology ; Female ; Humans ; Intestines/microbiology ; Male ; Metagenome/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Young Adult ; }, abstract = {The aim of this study was to evaluate the changes in endogenous bifidobacteria and administered Bifidobacterium animalis subsp. lactis (B. lactis) GCL2505 (GCL2505) in the intestine after administration of GCL2505 by means of a randomized, placebo-controlled double-blind, cross-over study. An increase in the number of total bifidobacteria (the sum of B. bifidum, B. breve, B. longum subsp. longum, B. adolescentis, B. anglatum, B. catenulatum, B. pseudocatenulatum, B. dentium, B. longum subsp. infantis and B. lactis) in the feces were observed after administration of GCL2505 using species- and subspecies-specific real-time polymerase chain reaction analysis. However, the number of endogenous bifidobacteria species (excluding B. lactis) remained unchanged. B. lactis also became the predominant bifidobacterial species. Taking into account the number of GCL2505 administered, the findings further suggested that GCL2505 proliferated in the intestine. In addition, the defecation frequency increased during GCL2505 administration compared with the placebo. Moreover, a single administration study (n=17) clearly demonstrated that GCL2505 successfully reached the intestine before proliferating at least 10-fold. This is the first report to show an increase in intestinal bifidobacteria, with no changes to the endogenous species, and improvements in constipation following proliferation of administered bifidobacteria.}, } @article {pmid22279554, year = {2012}, author = {Kolmeder, CA and de Been, M and Nikkilä, J and Ritamo, I and Mättö, J and Valmu, L and Salojärvi, J and Palva, A and Salonen, A and de Vos, WM}, title = {Comparative metaproteomics and diversity analysis of human intestinal microbiota testifies for its temporal stability and expression of core functions.}, journal = {PloS one}, volume = {7}, number = {1}, pages = {e29913}, pmid = {22279554}, issn = {1932-6203}, mesh = {Adult ; Bacteria/classification/*genetics/metabolism ; Biodiversity ; Chromatography, Liquid ; Electrophoresis, Polyacrylamide Gel ; Feces/chemistry/microbiology ; Female ; Gene Expression Profiling ; Genetic Variation ; Humans ; Intestinal Mucosa/metabolism ; Intestines/microbiology ; *Metagenome ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Proteome/genetics/metabolism ; Proteomics/*methods ; Tandem Mass Spectrometry ; Young Adult ; }, abstract = {The human intestinal tract is colonized by microbial communities that show a subject-specific composition and a high-level temporal stability in healthy adults. To determine whether this is reflected at the functional level, we compared the faecal metaproteomes of healthy subjects over time using a novel high-throughput approach based on denaturing polyacrylamide gel electrophoresis and liquid chromatography-tandem mass spectrometry. The developed robust metaproteomics workflow and identification pipeline was used to study the composition and temporal stability of the intestinal metaproteome using faecal samples collected from 3 healthy subjects over a period of six to twelve months. The same samples were also subjected to DNA extraction and analysed for their microbial composition and diversity using the Human Intestinal Tract Chip, a validated phylogenetic microarray. Using metagenome and single genome sequence data out of the thousands of mass spectra generated per sample, approximately 1,000 peptides per sample were identified. Our results indicate that the faecal metaproteome is subject-specific and stable during a one-year period. A stable common core of approximately 1,000 proteins could be recognized in each of the subjects, indicating a common functional core that is mainly involved in carbohydrate transport and degradation. Additionally, a variety of surface proteins could be identified, including potential microbes-host interacting components such as flagellins and pili. Altogether, we observed a highly comparable subject-specific clustering of the metaproteomic and phylogenetic profiles, indicating that the distinct microbial activity is reflected by the individual composition.}, } @article {pmid22278883, year = {2012}, author = {Fonseca, VG and Nichols, B and Lallias, D and Quince, C and Carvalho, GR and Power, DM and Creer, S}, title = {Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses.}, journal = {Nucleic acids research}, volume = {40}, number = {9}, pages = {e66}, pmid = {22278883}, issn = {1362-4962}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Artifacts ; Base Sequence ; Genetic Variation ; *Metagenomics ; Molecular Sequence Data ; Nematoda/classification/genetics ; Phylogeny ; *Polymerase Chain Reaction ; RNA, Ribosomal, 18S/genetics ; Ribosome Subunits, Small, Eukaryotic/*genetics ; *Sequence Analysis, DNA ; }, abstract = {Eukaryotic diversity in environmental samples is often assessed via PCR-based amplification of nSSU genes. However, estimates of diversity derived from pyrosequencing environmental data sets are often inflated, mainly because of the formation of chimeric sequences during PCR amplification. Chimeras are hybrid products composed of distinct parental sequences that can lead to the misinterpretation of diversity estimates. We have analyzed the effect of sample richness, evenness and phylogenetic diversity on the formation of chimeras using a nSSU data set derived from 454 Roche pyrosequencing of replicated, large control pools of closely and distantly related nematode mock communities, of known intragenomic identity and richness. To further investigate how chimeric molecules are formed, the nSSU gene secondary structure was analyzed in several individuals. For the first time in eukaryotes, chimera formation proved to be higher in both richer and more genetically diverse samples, thus providing a novel perspective of chimera formation in pyrosequenced environmental data sets. Findings contribute to a better understanding of the nature and mechanisms involved in chimera formation during PCR amplification of environmentally derived DNA. Moreover, given the similarities between biodiversity analyses using amplicon sequencing and those used to assess genomic variation, our findings have potential broad application for identifying genetic variation in homologous loci or multigene families in general.}, } @article {pmid22278670, year = {2012}, author = {Kembel, SW and Jones, E and Kline, J and Northcutt, D and Stenson, J and Womack, AM and Bohannan, BJ and Brown, GZ and Green, JL}, title = {Architectural design influences the diversity and structure of the built environment microbiome.}, journal = {The ISME journal}, volume = {6}, number = {8}, pages = {1469-1479}, pmid = {22278670}, issn = {1751-7370}, mesh = {*Architecture ; Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; Environmental Microbiology ; Hospitals ; Humidity ; *Metagenome ; Phylogeny ; Temperature ; Ventilation ; }, abstract = {Buildings are complex ecosystems that house trillions of microorganisms interacting with each other, with humans and with their environment. Understanding the ecological and evolutionary processes that determine the diversity and composition of the built environment microbiome--the community of microorganisms that live indoors--is important for understanding the relationship between building design, biodiversity and human health. In this study, we used high-throughput sequencing of the bacterial 16S rRNA gene to quantify relationships between building attributes and airborne bacterial communities at a health-care facility. We quantified airborne bacterial community structure and environmental conditions in patient rooms exposed to mechanical or window ventilation and in outdoor air. The phylogenetic diversity of airborne bacterial communities was lower indoors than outdoors, and mechanically ventilated rooms contained less diverse microbial communities than did window-ventilated rooms. Bacterial communities in indoor environments contained many taxa that are absent or rare outdoors, including taxa closely related to potential human pathogens. Building attributes, specifically the source of ventilation air, airflow rates, relative humidity and temperature, were correlated with the diversity and composition of indoor bacterial communities. The relative abundance of bacteria closely related to human pathogens was higher indoors than outdoors, and higher in rooms with lower airflow rates and lower relative humidity. The observed relationship between building design and airborne bacterial diversity suggests that we can manage indoor environments, altering through building design and operation the community of microbial species that potentially colonize the human microbiome during our time indoors.}, } @article {pmid22276952, year = {2012}, author = {Anderson, KE and Russell, JA and Moreau, CS and Kautz, S and Sullam, KE and Hu, Y and Basinger, U and Mott, BM and Buck, N and Wheeler, DE}, title = {Highly similar microbial communities are shared among related and trophically similar ant species.}, journal = {Molecular ecology}, volume = {21}, number = {9}, pages = {2282-2296}, doi = {10.1111/j.1365-294X.2011.05464.x}, pmid = {22276952}, issn = {1365-294X}, support = {5K-12-GM000708/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Ants/classification/*microbiology/physiology ; Bacteria/*classification/*genetics ; Biodiversity ; Digestive System/microbiology ; Herbivory ; *Metagenome ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Ants dominate many terrestrial ecosystems, yet we know little about their nutritional physiology and ecology. While traditionally viewed as predators and scavengers, recent isotopic studies revealed that many dominant ant species are functional herbivores. As with other insects with nitrogen-poor diets, it is hypothesized that these ants rely on symbiotic bacteria for nutritional supplementation. In this study, we used cloning and 16S sequencing to further characterize the bacterial flora of several herbivorous ants, while also examining the beta diversity of bacterial communities within and between ant species from different trophic levels. Through estimating phylogenetic overlap between these communities, we tested the hypothesis that ecologically or phylogenetically similar groups of ants harbor similar microbial flora. Our findings reveal: (i) clear differences in bacterial communities harbored by predatory and herbivorous ants; (ii) notable similarities among communities from distantly related herbivorous ants and (iii) similar communities shared by different predatory army ant species. Focusing on one herbivorous ant tribe, the Cephalotini, we detected five major bacterial taxa that likely represent the core microbiota. Metabolic functions of bacterial relatives suggest that these microbes may play roles in fixing, recycling, or upgrading nitrogen. Overall, our findings reveal that similar microbial communities are harbored by ants from similar trophic niches and, to a greater extent, by related ants from the same colonies, species, genera, and tribes. These trends hint at coevolved histories between ants and microbes, suggesting new possibilities for roles of bacteria in the evolution of both herbivores and carnivores from the ant family Formicidae.}, } @article {pmid22276533, year = {2012}, author = {Brucker, RM and Bordenstein, SR}, title = {The roles of host evolutionary relationships (genus: Nasonia) and development in structuring microbial communities.}, journal = {Evolution; international journal of organic evolution}, volume = {66}, number = {2}, pages = {349-362}, doi = {10.1111/j.1558-5646.2011.01454.x}, pmid = {22276533}, issn = {1558-5646}, mesh = {Animals ; Bacteria/classification/genetics ; Bacterial Physiological Phenomena ; Biodiversity ; *Biological Evolution ; Female ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; Wasps/*microbiology/physiology ; }, abstract = {The comparative structure of bacterial communities among closely related host species remains relatively unexplored. For instance, as speciation events progress from incipient to complete stages, does divergence in the composition of the species' microbial communities parallel the divergence of host nuclear genes? To address this question, we used the recently diverged species of the parasitoid wasp genus Nasonia to test whether the evolutionary relationships of their bacterial microbiotas recapitulate the Nasonia phylogenetic history. We also assessed microbial diversity in Nasonia at different stages of development to determine the role that host age plays in microbiota structure. The results indicate that all three species of Nasonia share simple larval microbiotas dominated by the γ-proteobacteria class; however, bacterial species diversity increases as Nasonia develop into pupae and adults. Finally, under identical environmental conditions, the relationships of the microbial communities reflect the phylogeny of the Nasonia host species at multiple developmental stages, which suggests that the structure of an animal's microbial community is closely allied with divergence of host genes. These findings highlight the importance of host evolutionary relationships on microbiota composition and have broad implications for future studies of microbial symbiosis and animal speciation.}, } @article {pmid22266158, year = {2012}, author = {Braem, G and De Vliegher, S and Verbist, B and Heyndrickx, M and Leroy, F and De Vuyst, L}, title = {Culture-independent exploration of the teat apex microbiota of dairy cows reveals a wide bacterial species diversity.}, journal = {Veterinary microbiology}, volume = {157}, number = {3-4}, pages = {383-390}, doi = {10.1016/j.vetmic.2011.12.031}, pmid = {22266158}, issn = {1873-2542}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; Cattle/microbiology ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis/veterinary ; Female ; Mammary Glands, Animal/*microbiology ; Mastitis, Bovine/*microbiology ; *Metagenome ; Polymerase Chain Reaction/veterinary ; RNA, Ribosomal, 16S/genetics ; Skin/microbiology ; }, abstract = {Due to their close proximity to the mammary gland tissue, the bacterial communities lining the teat apex of the udders from lactating cows influence udder health. Denaturing gradient gel electrophoresis of the amplified V3 variable region of the 16S rRNA gene was used as a culture-independent method to reveal the bacterial composition of 48 samples originating from the teat apices of twelve Friesian-Holstein dairy cows suffering from clinical mastitis in one quarter. The microbiota belonged to four bacterial phyla: the Actinobacteria (32% of all genera), the Bacteroidetes (1%), the Firmicutes (42%), and the Proteobacteria (25%), encompassing 17 bacterial genera. Some differences in occurrence of these genera were seen when comparing quarters that were non-infected (n=22), subclinically infected (n=14), or clinically infected (n=12). Besides commensal skin-associated bacteria, opportunistic pathogenic bacteria, and mastitis-causing pathogens were found as well. The species diversity varied considerably among the most prevalent bacterial genera. While Corynebacterium and Staphylococcus displayed a large diversity among the recovered sequences, indicating the possible presence of a variety of different species, only a single bacterial species (represented by one sequence) was obtained for the genera Aerococcus, Acinetobacter, and Psychrobacter. In conclusion, introducing culture-independent analysis of teat apical skin swabs in mastitis research revealed an unexpected wide bacterial diversity, with variations between quarters with a different clinical status. In addition to potential mastitis-causing pathogens, it exposed the yet poorly mapped presence of skin-associated and other bacteria residing in close proximity to the mammary gland tissue. PCR-DGGE may thus be considered as a useful tool for the entanglement of animal skin microbiota, in casu the teat apices of dairy cows.}, } @article {pmid22265301, year = {2012}, author = {Park, EJ and Chun, J and Cha, CJ and Park, WS and Jeon, CO and Bae, JW}, title = {Bacterial community analysis during fermentation of ten representative kinds of kimchi with barcoded pyrosequencing.}, journal = {Food microbiology}, volume = {30}, number = {1}, pages = {197-204}, doi = {10.1016/j.fm.2011.10.011}, pmid = {22265301}, issn = {1095-9998}, mesh = {Bacteria/classification/*isolation & purification ; Brassica/*microbiology ; DNA, Bacterial/genetics/isolation & purification ; *Fermentation ; Food Contamination/analysis ; Food Microbiology/*methods ; Metagenomics/methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics/isolation & purification ; Sequence Analysis, DNA ; Vegetables/microbiology ; }, abstract = {Kimchi, a food made of fermented vegetables, is densely populated by indigenous microorganisms that originate from the raw ingredients under normal conditions. Most microbiological studies on kimchi have been on the most popular dish, baechu-kimchi (Chinese cabbage kimchi). Therefore, relatively little is known about the various other kinds of kimchi (depending on the region, season, main ingredient, starter culture inoculation and recipe). In this study, we collected 100 samples periodically during the fermentation of ten representative kinds of kimchi (including starter-inoculated kimchi) that were stored in the refrigerator (4 °C) during the 30-35 days fermentation period. The multiplex barcoded pyrosequencing of a hypervariable V1-V3 region of the 16S ribosomal RNA (rRNA) gene tagged with sample-specific barcodes for multiplex identifiers was employed for bacterial community profiling. We found that bacterial communities differed between starter-inoculated and non-inoculated kimchi at the early stages of fermentation, but overall there were no significant differences in the late phases. Also, the diversity and richness of bacterial communities varied depending on the various types of kimchi, and these differences could largely be explained by the major ingredients and the manufacture processes of each types of kimchi. This study provides the comprehensive understanding of the factors influencing the biodiversity of the kimchi ecosystem.}, } @article {pmid22253843, year = {2012}, author = {Gonzalez, JM and Portillo, MC and Belda-Ferre, P and Mira, A}, title = {Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities.}, journal = {PloS one}, volume = {7}, number = {1}, pages = {e29973}, pmid = {22253843}, issn = {1932-6203}, mesh = {Bacteria/classification/genetics ; Base Sequence ; *Biodiversity ; DNA, Bacterial/genetics ; Genes, Bacterial/genetics ; Genetic Variation ; Humans ; Metagenome/*genetics ; Mouth/microbiology ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; Templates, Genetic ; }, abstract = {The microbial world has been shown to hold an unimaginable diversity. The use of rRNA genes and PCR amplification to assess microbial community structure and diversity present biases that need to be analyzed in order to understand the risks involved in those estimates. Herein, we show that PCR amplification of specific sequence targets within a community depends on the fractions that those sequences represent to the total DNA template. Using quantitative, real-time, multiplex PCR and specific Taqman probes, the amplification of 16S rRNA genes from four bacterial species within a laboratory community were monitored. Results indicate that the relative amplification efficiency for each bacterial species is a nonlinear function of the fraction that each of those taxa represent within a community or multispecies DNA template. Consequently, the low-proportion taxa in a community are under-represented during PCR-based surveys and a large number of sequences might need to be processed to detect some of the bacterial taxa within the 'rare biosphere'. The structure of microbial communities from PCR-based surveys is clearly biased against low abundant taxa which are required to decipher the complete extent of microbial diversity in nature.}, } @article {pmid22253013, year = {2012}, author = {Feazel, LM and Robertson, CE and Ramakrishnan, VR and Frank, DN}, title = {Microbiome complexity and Staphylococcus aureus in chronic rhinosinusitis.}, journal = {The Laryngoscope}, volume = {122}, number = {2}, pages = {467-472}, pmid = {22253013}, issn = {1531-4995}, support = {R21 HG005964/HG/NHGRI NIH HHS/United States ; HG005964/HG/NHGRI NIH HHS/United States ; }, mesh = {Chronic Disease ; Cross-Sectional Studies ; Female ; Humans ; Male ; *Metagenome ; Middle Aged ; RNA, Bacterial/*genetics ; Retrospective Studies ; Rhinitis/complications/*microbiology ; Sequence Analysis, RNA ; Sinusitis/complications/*microbiology ; Staphylococcal Infections/*microbiology ; Staphylococcus aureus/*genetics/isolation & purification ; }, abstract = {OBJECTIVES/HYPOTHESIS: The aim of this study was to compare microbiological culture-based and culture-independent (16S rRNA gene sequencing) methodologies for pathogen identification in chronic rhinosinusitis (CRS) patients. We hypothesized that bacterial culture and DNA sequencing would yield largely concurrent results, although sequencing would detect greater bacterial diversity, and the sinonasal microbiomes of CRS patients would differ in composition and diversity compared with non-CRS controls.

STUDY DESIGN: Cross-sectional observational study.

METHODS: Middle meatus swabs from CRS patients collected during endoscopic sinus surgery were analyzed by both clinical culture and broad-range analysis of 16S rRNA gene pyrosequences.

RESULTS: A total of 21 swab samples from 15 CRS patients and five non-CRS controls were analyzed. One CRS patient was also swabbed 3 weeks postoperatively due to evidence of purulence during a clinical visit. All subjects had positive bacterial cultures, with a mean of 2.8 isolates per subject. The most prevalent cultivars were coagulase-negative staphylococci (15/20 specimens, 75%), Staphylococcus aureus (10/20, 50%), and Propionibacterium acnes (6/20, 30%). Among 57,407 pyrosequences generated, the most prevalent were from coagulase-negative staphylococci (21/21 specimens, 100%), Corynebacterium spp (18/21, 85.7%), P acnes (16/21, 76.2%), and S aureus (14/21, 66.7%). Bacterial diversity correlated with recent antibiotic use, asthma, prior sinus surgery, and relative abundance of S aureus.

CONCLUSIONS: DNA pyrosequencing revealed greater biodiversity than culture, although in most cases culture results represented a subset of the abundant DNA sequence types. CRS patients were characterized by altered microbial composition (P = .02) and greater abundance of S aureus (P = .03).}, } @article {pmid22251411, year = {2012}, author = {Ozok, AR and Persoon, IF and Huse, SM and Keijser, BJ and Wesselink, PR and Crielaard, W and Zaura, E}, title = {Ecology of the microbiome of the infected root canal system: a comparison between apical and coronal root segments.}, journal = {International endodontic journal}, volume = {45}, number = {6}, pages = {530-541}, pmid = {22251411}, issn = {1365-2591}, support = {UH2 DK083993/DK/NIDDK NIH HHS/United States ; 1UH2DK083993-01/DK/NIDDK NIH HHS/United States ; }, mesh = {Actinobacteria/classification ; Archaea/classification ; Bacteria/*classification ; Bacteria, Anaerobic/classification ; Biodiversity ; DNA, Ribosomal/classification ; Dental Pulp Cavity/*microbiology ; Dentin/microbiology ; Ecosystem ; Gram-Negative Bacteria/classification ; Gram-Positive Bacteria/classification ; Humans ; Metagenome/*physiology ; Periapical Periodontitis/*microbiology ; Proteobacteria/classification ; RNA, Bacterial/classification ; RNA, Ribosomal, 16S/classification ; Sequence Analysis, DNA ; Tooth Apex/*microbiology ; }, abstract = {AIM: To evaluate the microbial ecology of the coronal and apical segments of infected root canal systems using a complete sampling technique and next-generation sequencing.

METHODOLOGY: The roots of 23 extracted teeth with apical periodontitis were sectioned in half, horizontally, and cryo-pulverized. Bacterial communities were profiled using tagged 454 pyrosequencing of the 16S rDNA hypervariable V5-V6 region.

RESULTS: The sequences were classified into 606 taxa (species or higher taxon), representing 24 bacterial phyla or candidate divisions and one archaeal phylum. Proteobacteria were more abundant in the apical samples (P < 0.05), whilst Actinobacteria were in significantly higher proportions in the coronal samples. The apical samples harboured statistically significantly more taxa than the coronal samples (P = 0.01) and showed a higher microbial diversity. Several taxa belonging to fastidious obligate anaerobes were significantly more abundant in the apical segments of the roots compared with their coronal counterparts.

CONCLUSIONS: Endodontic infections are more complex than reported previously. The apical part of the root canal system drives the selection of a more diverse and more anaerobic community than the coronal part. The presence of a distinct ecological niche in the apical region explains the difficulty of eradication of the infection and emphasizes the need for new treatment approaches to be developed.}, } @article {pmid22249719, year = {2012}, author = {Stanley, D and Denman, SE and Hughes, RJ and Geier, MS and Crowley, TM and Chen, H and Haring, VR and Moore, RJ}, title = {Intestinal microbiota associated with differential feed conversion efficiency in chickens.}, journal = {Applied microbiology and biotechnology}, volume = {96}, number = {5}, pages = {1361-1369}, doi = {10.1007/s00253-011-3847-5}, pmid = {22249719}, issn = {1432-0614}, mesh = {Animals ; *Biota ; Cecum/*microbiology ; Chickens ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Diet ; Jejunum/*microbiology ; *Metagenome ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Analysis of model systems, for example in mice, has shown that the microbiota in the gastrointestinal tract can play an important role in the efficiency of energy extraction from diets. The study reported here aimed to determine whether there are correlations between gastrointestinal tract microbiota population structure and energy use in chickens. Efficiency in converting food into muscle mass has a significant impact on the intensive animal production industries, where feed represents the major portion of production costs. Despite extensive breeding and selection efforts, there are still large differences in the growth performance of animals fed identical diets and reared under the same conditions. Variability in growth performance presents management difficulties and causes economic loss. An understanding of possible microbiota drivers of these differences has potentially important benefits for industry. In this study, differences in cecal and jejunal microbiota between broiler chickens with extreme feed conversion capabilities were analysed in order to identify candidate bacteria that may influence growth performance. The jejunal microbiota was largely dominated by lactobacilli (over 99% of jejunal sequences) and showed no difference between the birds with high and low feed conversion ratios. The cecal microbial community displayed higher diversity, and 24 unclassified bacterial species were found to be significantly (<0.05) differentially abundant between high and low performing birds. Such differentially abundant bacteria represent target populations that could potentially be modified with prebiotics and probiotics in order to improve animal growth performance.}, } @article {pmid22247131, year = {2012}, author = {Santos, F and Yarza, P and Parro, V and Meseguer, I and Rosselló-Móra, R and Antón, J}, title = {Culture-independent approaches for studying viruses from hypersaline environments.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {6}, pages = {1635-1643}, pmid = {22247131}, issn = {1098-5336}, mesh = {Biodiversity ; Electrophoresis, Gel, Pulsed-Field ; *Environmental Microbiology ; Metagenomics ; Microscopy, Electron, Transmission ; Virology/*methods ; Viruses/classification/*genetics/*isolation & purification ; }, abstract = {Hypersaline close-to-saturation environments harbor an extremely high concentration of virus-like particles, but the number of haloviruses isolated so far is still very low. Haloviruses can be directly studied from natural samples by using different culture-independent techniques that include transmission electron microscopy, pulsed-field gel electrophoresis, and different metagenomic approaches. Here, we review the findings of these studies, with a main focus on the metagenomic approaches. The analysis of bulk viral nucleic acids directly retrieved from the environment allows estimations of viral diversity, activity, and dynamics and tentative host assignment. Results point to a diverse and active viral community in constant interplay with its hosts and to a "hypersalineness" quality common to viral assemblages present in hypersaline environments that are thousands of kilometers away from each other.}, } @article {pmid22238640, year = {2012}, author = {Wieczorek, J and Bloom, D and Guralnick, R and Blum, S and Döring, M and Giovanni, R and Robertson, T and Vieglais, D}, title = {Darwin Core: an evolving community-developed biodiversity data standard.}, journal = {PloS one}, volume = {7}, number = {1}, pages = {e29715}, pmid = {22238640}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; *Biota ; Data Collection/standards ; Databases, Factual/*standards ; Environment ; Evolution, Molecular ; Genetic Fitness/genetics/*physiology ; Guidelines as Topic ; Humans ; Information Storage and Retrieval/standards ; Models, Biological ; *Selection, Genetic ; Validation Studies as Topic ; }, abstract = {Biodiversity data derive from myriad sources stored in various formats on many distinct hardware and software platforms. An essential step towards understanding global patterns of biodiversity is to provide a standardized view of these heterogeneous data sources to improve interoperability. Fundamental to this advance are definitions of common terms. This paper describes the evolution and development of Darwin Core, a data standard for publishing and integrating biodiversity information. We focus on the categories of terms that define the standard, differences between simple and relational Darwin Core, how the standard has been implemented, and the community processes that are essential for maintenance and growth of the standard. We present case-study extensions of the Darwin Core into new research communities, including metagenomics and genetic resources. We close by showing how Darwin Core records are integrated to create new knowledge products documenting species distributions and changes due to environmental perturbations.}, } @article {pmid22226752, year = {2012}, author = {Scibetta, S and Schena, L and Chimento, A and Cacciola, SO and Cooke, DE}, title = {A molecular method to assess Phytophthora diversity in environmental samples.}, journal = {Journal of microbiological methods}, volume = {88}, number = {3}, pages = {356-368}, doi = {10.1016/j.mimet.2011.12.012}, pmid = {22226752}, issn = {1872-8359}, mesh = {*Biodiversity ; Classification/*methods ; DNA Primers/genetics ; DNA, Ribosomal Spacer/genetics ; *Environmental Microbiology ; Molecular Biology/*methods ; Molecular Sequence Data ; Phytophthora/*classification/*genetics ; Scotland ; Sequence Analysis, DNA ; }, abstract = {Current molecular detection methods for the genus Phytophthora are specific to a few key species rather than the whole genus and this is a recognized weakness of protocols for ecological studies and international plant health legislation. In the present study a molecular approach was developed to detect Phytophthora species in soil and water samples using novel sets of genus-specific primers designed against the internal transcribed spacer (ITS) regions. Two different rDNA primer sets were tested: one assay amplified a long product including the ITS1, 5.8S and ITS2 regions (LP) and the other a shorter product including the ITS1 only (SP). Both assays specifically amplified products from Phytophthora species without cross-reaction with the related Pythium s. lato, however the SP assay proved the more sensitive and reliable. The method was validated using woodland soil and stream water from Invergowrie, Scotland. On-site use of a knapsack sprayer and in-line water filters proved more rapid and effective than centrifugation at sampling Phytophthora propagules. A total of 15 different Phytophthora phylotypes were identified which clustered within the reported ITS-clades 1, 2, 3, 6, 7 and 8. The range and type of the sequences detected varied from sample to sample and up to three and five different Phytophthora phylotypes were detected within a single sample of soil or water, respectively. The most frequently detected sequences were related to members of ITS-clade 6 (i.e. P. gonapodyides-like). The new method proved very effective at discriminating multiple species in a given sample and can also detect as yet unknown species. The reported primers and methods will prove valuable for ecological studies, biosecurity and commercial plant, soil or water (e.g. irrigation water) testing as well as the wider metagenomic sampling of this fascinating component of microbial pathogen diversity.}, } @article {pmid22210205, year = {2012}, author = {Yoshida-Takashima, Y and Nunoura, T and Kazama, H and Noguchi, T and Inoue, K and Akashi, H and Yamanaka, T and Toki, T and Yamamoto, M and Furushima, Y and Ueno, Y and Yamamoto, H and Takai, K}, title = {Spatial distribution of viruses associated with planktonic and attached microbial communities in hydrothermal environments.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {5}, pages = {1311-1320}, pmid = {22210205}, issn = {1098-5336}, mesh = {Archaea/classification/genetics/*isolation & purification ; Bacteria/classification/genetics/*isolation & purification ; Biota ; *Cell Adhesion ; Cell Count ; Cluster Analysis ; Hydrothermal Vents/*microbiology/*virology ; Metagenome ; Molecular Sequence Data ; Phylogeny ; Plankton/*virology ; Seawater/microbiology/virology ; Sequence Analysis, DNA ; Viral Load ; Viruses/classification/genetics/*isolation & purification ; }, abstract = {Viruses play important roles in marine surface ecosystems, but little is known about viral ecology and virus-mediated processes in deep-sea hydrothermal microbial communities. In this study, we examined virus-like particle (VLP) abundances in planktonic and attached microbial communities, which occur in physical and chemical gradients in both deep and shallow submarine hydrothermal environments (mixing waters between hydrothermal fluids and ambient seawater and dense microbial communities attached to chimney surface areas or macrofaunal bodies and colonies). We found that viruses were widely distributed in a variety of hydrothermal microbial habitats, with the exception of the interior parts of hydrothermal chimney structures. The VLP abundance and VLP-to-prokaryote ratio (VPR) in the planktonic habitats increased as the ratio of hydrothermal fluid to mixing water increased. On the other hand, the VLP abundance in attached microbial communities was significantly and positively correlated with the whole prokaryotic abundance; however, the VPRs were always much lower than those for the surrounding hydrothermal waters. This is the first report to show VLP abundance in the attached microbial communities of submarine hydrothermal environments, which presented VPR values significantly lower than those in planktonic microbial communities reported before. These results suggested that viral lifestyles (e.g., lysogenic prevalence) and virus interactions with prokaryotes are significantly different among the planktonic and attached microbial communities that are developing in the submarine hydrothermal environments.}, } @article {pmid22202870, year = {2012}, author = {Janssens, M and Myter, N and De Vuyst, L and Leroy, F}, title = {Species diversity and metabolic impact of the microbiota are low in spontaneously acidified Belgian sausages with an added starter culture of Staphylococcus carnosus.}, journal = {Food microbiology}, volume = {29}, number = {2}, pages = {167-177}, doi = {10.1016/j.fm.2011.07.005}, pmid = {22202870}, issn = {1095-9998}, mesh = {Animals ; Belgium ; *Biodiversity ; Fermentation ; Lactobacillus/*metabolism ; Meat Products/analysis/*microbiology ; *Metagenome ; Staphylococcus/*metabolism ; Swine ; }, abstract = {Quality of fermented sausages is affected by acidifying lactic acid bacteria (LAB) and colour- and flavour-promoting coagulase-negative staphylococci (CNS), whether or not used as starter culture. Artisan fermented sausages are often perceived as superior to industrial variants, partially because of the specific microbiota due to spontaneous acidification, which may be considered as an artisan characteristic. Therefore, two kinds of spontaneously acidified Belgian sausages were prepared (Belgian-type salami and Boulogne sausage), but with addition of a Staphylococcus carnosus culture. The Belgian-type salami was made from pork and beef, whereas the Boulogne sausage contained pork and horse meat. In all cases, Lactobacillus sakei was the dominant LAB species present on the raw materials and during fermentation, whereas enterococci remained present in the background. Enterobacteriaceae vanished after fermentation. The CNS species diversity on the raw materials was large and differed between the pork, beef, and horse meat. Nevertheless, this species diversity was annihilated during fermentation by the added S. carnosus culture. The volatiles fraction was mainly composed of aldehydes that originated from lipid oxidation and spices-derived compounds. Aromatic compounds that are typically associated to CNS activity, such as end-products from the metabolism of branched-chain amino acids, were not present in the Belgian-type salami and only marginally present in the Boulogne sausage. In conclusion, spontaneous acidification of Belgian-type fermented sausages leads to dominance of L. sakei and is no guarantee for bacterial contribution to the aroma profile when S. carnosus is added as a starter culture.}, } @article {pmid22194782, year = {2011}, author = {Schloss, PD and Gevers, D and Westcott, SL}, title = {Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.}, journal = {PloS one}, volume = {6}, number = {12}, pages = {e27310}, pmid = {22194782}, issn = {1932-6203}, support = {R01 HG005975/HG/NHGRI NIH HHS/United States ; U54 HG004969/HG/NHGRI NIH HHS/United States ; NIHU54HG004969/HG/NHGRI NIH HHS/United States ; 1R01HG005975-01/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; *Artifacts ; Base Sequence ; Biodiversity ; Cluster Analysis ; DNA Primers/metabolism ; DNA, Bacterial/analysis/genetics ; Humans ; Metagenome/genetics ; Phylogeny ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/analysis/*genetics ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; }, abstract = {The advent of next generation sequencing has coincided with a growth in interest in using these approaches to better understand the role of the structure and function of the microbial communities in human, animal, and environmental health. Yet, use of next generation sequencing to perform 16S rRNA gene sequence surveys has resulted in considerable controversy surrounding the effects of sequencing errors on downstream analyses. We analyzed 2.7×10(6) reads distributed among 90 identical mock community samples, which were collections of genomic DNA from 21 different species with known 16S rRNA gene sequences; we observed an average error rate of 0.0060. To improve this error rate, we evaluated numerous methods of identifying bad sequence reads, identifying regions within reads of poor quality, and correcting base calls and were able to reduce the overall error rate to 0.0002. Implementation of the PyroNoise algorithm provided the best combination of error rate, sequence length, and number of sequences. Perhaps more problematic than sequencing errors was the presence of chimeras generated during PCR. Because we knew the true sequences within the mock community and the chimeras they could form, we identified 8% of the raw sequence reads as chimeric. After quality filtering the raw sequences and using the Uchime chimera detection program, the overall chimera rate decreased to 1%. The chimeras that could not be detected were largely responsible for the identification of spurious operational taxonomic units (OTUs) and genus-level phylotypes. The number of spurious OTUs and phylotypes increased with sequencing effort indicating that comparison of communities should be made using an equal number of sequences. Finally, we applied our improved quality-filtering pipeline to several benchmarking studies and observed that even with our stringent data curation pipeline, biases in the data generation pipeline and batch effects were observed that could potentially confound the interpretation of microbial community data.}, } @article {pmid22182607, year = {2011}, author = {Hail, D and Lauzìere, I and Dowd, SE and Bextine, B}, title = {Culture independent survey of the microbiota of the glassy-winged sharpshooter (Homalodisca vitripennis) using 454 pyrosequencing.}, journal = {Environmental entomology}, volume = {40}, number = {1}, pages = {23-29}, doi = {10.1603/EN10115}, pmid = {22182607}, issn = {1938-2936}, mesh = {Animals ; Bacteria/*classification/genetics ; Bacterial Typing Techniques ; Biodiversity ; DNA, Bacterial/genetics ; Gastrointestinal Tract/microbiology ; Hemiptera/*microbiology ; Hemolymph/microbiology ; *Metagenome ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {The glassy-winged sharpshooter, Homalodisca vitripennis (Germar), is an invasive pest that has spread across the southern and western United States. H. vitripennis is highly polyphagous and voracious, feeding on at least 100 plant species and consuming up to 100 times its weight in xylem fluid daily. The insect is a vector of the phytopathogen Xylella fastidiosa (Wells), which is the causative agent of Pierce's disease in grapevines. To evaluate the microbial flora associated with H. vitripennis, total DNA extracts from hemolymph, alimentary canal excretions, and whole insect bodies were subjected to 16S rDNA pyrosequencing using the bTEFAP methodology and the resulting sequences (370-520 bp in length) were compared with a curated high quality 16S database derived from GenBank http://www.ncbi.nlm.nih.gov. Species from the genera Wolbachia, Delftia (formerly Pseudomonas), Pectobacterium, Moraxella, Serratia, Bacillus, and many others were detected and a comprehensive picture of the microbiome associated with H. vitripennis was established. Some of the bacteria identified in this report are initial discoveries; providing a breadth of knowledge to the microbial flora of this insect pest can serve as a reservoir of information for developing biological control strategies.}, } @article {pmid22179250, year = {2012}, author = {Wang, IK and Lai, HC and Yu, CJ and Liang, CC and Chang, CT and Kuo, HL and Yang, YF and Lin, CC and Lin, HH and Liu, YL and Chang, YC and Wu, YY and Chen, CH and Li, CY and Chuang, FR and Huang, CC and Lin, CH and Lin, HC}, title = {Real-time PCR analysis of the intestinal microbiotas in peritoneal dialysis patients.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {4}, pages = {1107-1112}, pmid = {22179250}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics ; *Biota ; China ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; *Peritoneal Dialysis ; *Real-Time Polymerase Chain Reaction ; }, abstract = {Bifidobacterium and Lactobacillus can beneficially affect the host by producing acetic acid and lactic acid, which lower pH and thereby inhibit the growth of pathogens or allow the probiotic bacteria to compete with pathogens for epithelial adhesion sites and nutrients. The transmural migration of enteric organisms into the peritoneal cavity can cause peritonitis in peritoneal dialysis (PD) patients. We hypothesized that the composition of the intestinal microbiota with regard to Lactobacillus species and Bifidobacterium species differed between PD patients and healthy controls. The aim of the study was to investigate these differences by real-time PCR analysis of fecal samples. From 1 August 2009 to 31 March 2010, a total of 29 nondiabetic PD patients and 41 healthy controls from China Medical University Hospital were recruited after giving their informed consent. Fecal samples were collected from the PD patients and their age-matched counterparts in the morning using a standardized procedure. DNA extracted from these samples was analyzed by real-time PCR. All bifidobacteria, Bifidobacterium catenulatum, B. longum, B. bifidum, Lactobacillus plantarum, L. paracasei, and Klebsiella pneumoniae were less frequently detected in the patient samples. Dysbiosis (microbial imbalance) may impair intestinal barrier function and increase host vulnerability to pathogen invasion. Further studies are necessary to confirm our findings before clinical trials with probiotic supplementation in PD patients.}, } @article {pmid22179237, year = {2012}, author = {Waller, AS and Hug, LA and Mo, K and Radford, DR and Maxwell, KL and Edwards, EA}, title = {Transcriptional analysis of a Dehalococcoides-containing microbial consortium reveals prophage activation.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {4}, pages = {1178-1186}, pmid = {22179237}, issn = {1098-5336}, mesh = {Methanol/metabolism ; Microarray Analysis ; Microbial Consortia/*genetics ; Molecular Sequence Data ; Prophages/*genetics/*growth & development ; Sequence Analysis, DNA ; *Soil Microbiology ; *Transcriptome ; Vinyl Chloride/metabolism ; *Virus Activation ; }, abstract = {Chlorinated solvents are among the most prevalent groundwater contaminants in the industrialized world. Biodegradation with Dehalococcoides-containing mixed cultures is an effective remediation technology. To elucidate transcribed genes in a Dehalococcoides-containing mixed culture, a shotgun metagenome microarray was created and used to investigate gene transcription during vinyl chloride (VC) dechlorination and during starvation (no chlorinated compounds) by a microbial enrichment culture called KB-1. In both treatment conditions, methanol was amended as an electron donor. Subsequently, spots were sequenced that contained the genes most differentially transcribed between the VC-degrading and methanol-only conditions, as well as spots with the highest intensities. Sequencing revealed that during VC degradation Dehalococcoides genes involved in transcription, translation, metabolic energy generation, and amino acid and lipid metabolism and transport were overrepresented in the transcripts compared to the average Dehalococcoides genome. KB-1 rdhA14 (vcrA) was the only reductive dehalogenase homologous (RDH) gene with higher transcript levels during VC degradation, while multiple RDH genes had higher transcript levels in the absence of VC. Numerous hypothetical genes from Dehalococcoides also had higher transcript levels in methanol-only treatments, indicating that many uncharacterized proteins are involved in cell maintenance in the absence of chlorinated substrates. In addition, microarray results prompted biological experiments confirming that electron acceptor limiting conditions activated a Dehalococcoides prophage. Transcripts from Spirochaetes, Chloroflexi, Geobacter, and methanogens demonstrate the importance of non-Dehalococcoides organisms to the culture, and sequencing of identified shotgun clones of interest provided information for follow-on targeted studies.}, } @article {pmid22179233, year = {2012}, author = {Green, SJ and Prakash, O and Jasrotia, P and Overholt, WA and Cardenas, E and Hubbard, D and Tiedje, JM and Watson, DB and Schadt, CW and Brooks, SC and Kostka, JE}, title = {Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {4}, pages = {1039-1047}, pmid = {22179233}, issn = {1098-5336}, mesh = {*Biota ; DNA, Bacterial/genetics ; Denitrification ; Groundwater/chemistry/*microbiology ; Hydrogen-Ion Concentration ; Metagenome ; Metagenomics/methods ; Nitrogen/analysis ; Oxygen/analysis ; RNA, Bacterial/genetics ; Radioactive Waste ; Soil Pollutants, Radioactive/*metabolism ; Xanthomonadaceae/*classification/*isolation & purification/metabolism ; }, abstract = {The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower-pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution of Rhodanobacter bacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment.}, } @article {pmid22179208, year = {2011}, author = {Iebba, V and Aloi, M and Civitelli, F and Cucchiara, S}, title = {Gut microbiota and pediatric disease.}, journal = {Digestive diseases (Basel, Switzerland)}, volume = {29}, number = {6}, pages = {531-539}, doi = {10.1159/000332969}, pmid = {22179208}, issn = {1421-9875}, mesh = {Child ; Gastrointestinal Tract/*microbiology ; Humans ; Intestinal Diseases/*microbiology ; Metagenome/*physiology ; *Pediatrics ; }, abstract = {BACKGROUND: Researchers have made every effort to assess the role of gut microbiota in pediatric diseases like inflammatory bowel disease (IBD), celiac disease, asthma, allergy, and autism. The leading hypothesis is that an altered microbial composition is present (other than the presence of a specific pathogen) and that it could be involved in the pathogenesis or progression of such disorders.

METHODS: Cultural, molecular, metabolomic, and metagenomic approaches are trying to define the pediatric gut microbiota imbalances in different diseases.

RESULTS AND CONCLUSION: In pediatric IBD, a marked increase in aerobes and facultative anaerobes was found, along with an increase in Enterobacteriaceae members (Escherichia coli). In both pediatric IBD and celiac disease (Th1-mediated disorders), higher bacterial cell counts were observed, jointly with a general gain of biodiversity. A preponderance of Bacteroidetes and a parallel decrease of Firmicutes was also reported in IBD, celiac disease and autism. Contrarily, dietary changes due to Western lifestyles increase Firmicutes populations and lower short-chain fatty acids production, possibly exposing 'developed' children to the infectious challenge (Escherichia and Shigella spp.). Lactobacillus and Bifidobacterium species could be protective agents for atopic diseases, while Clostridia, Enterobacteriaceae, and staphylococci can be associated with an increased risk of such Th2-mediated disorders. In the brain-gut axis view, gut microbiota could also play a role in autism.}, } @article {pmid22919574, year = {2011}, author = {Georgiades, K and Merhej, V and Raoult, D}, title = {The influence of rickettsiologists on post-modern microbiology.}, journal = {Frontiers in cellular and infection microbiology}, volume = {1}, number = {}, pages = {8}, pmid = {22919574}, issn = {2235-2988}, mesh = {Archaea/classification/genetics ; Biodiversity ; Evolution, Molecular ; Humans ; Metagenomics/trends ; Microbiology/*trends ; Models, Biological ; Phylogeny ; *Rickettsia/classification/genetics/pathogenicity ; Species Specificity ; Virulence Factors/genetics ; Viruses/classification/genetics ; }, abstract = {Many of the definitions in microbiology are currently false. We have reviewed the great denominations of microbiology and attempted to free microorganisms from the theories of the twentieth century. The presence of compartmentation and a nucleoid in Planctomycetes clearly calls into question the accuracy of the definitions of eukaryotes and prokaryotes. Archaea are viewed as prokaryotes resembling bacteria. However, the name archaea, suggesting an archaic origin of lifestyle, is inconsistent with the lifestyle of this family. Viruses are defined as small, filterable infectious agents, but giant viruses challenge the size criteria used for the definition of a virus. Pathogenicity does not require the acquisition of virulence factors (except for toxins), and in many cases, gene loss is significantly inked to the emergence of virulence. Species classification based on 16S rRNA is useless for taxonomic purposes of human pathogens, as a 2% divergence would classify all Rickettsiae within the same species and would not identify bacteria specialized for mammal infection. The use of metagenomics helps us to understand evolution and physiology by elucidating the structure, function, and interactions of the major microbial communities, but it neglects the minority populations. Finally, Darwin's descent with modification theory, as represented by the tree of life, no longer matches our current genomic knowledge because genomics has revealed the occurrence of de novo-created genes and the mosaic structure of genomes, the Rhizome of life is therefore more appropriate.}, } @article {pmid22587826, year = {2011}, author = {Gilbert, JA and O'Dor, R and King, N and Vogel, TM}, title = {The importance of metagenomic surveys to microbial ecology: or why Darwin would have been a metagenomic scientist.}, journal = {Microbial informatics and experimentation}, volume = {1}, number = {1}, pages = {5}, pmid = {22587826}, issn = {2042-5783}, abstract = {Scientific discovery is incremental. The Merriam-Webster definition of 'Scientific Method' is "principles and procedures for the systematic pursuit of knowledge involving the recognition and formulation of a problem, the collection of data through observation and experiment, and the formulation and testing of hypotheses". Scientists are taught to be excellent observers, as observations create questions, which in turn generate hypotheses. After centuries of science we tend to assume that we have enough observations to drive science, and enable the small steps and giant leaps which lead to theories and subsequent testable hypotheses. One excellent example of this is Charles Darwin's Voyage of the Beagle, which was essentially an opportunistic survey of biodiversity. Today, obtaining funding for even small-scale surveys of life on Earth is difficult; but few argue the importance of the theory that was generated by Darwin from his observations made during this epic journey. However, these observations, even combined with the parallel work of Alfred Russell Wallace at around the same time have still not generated an indisputable 'law of biology'. The fact that evolution remains a 'theory', at least to the general public, suggests that surveys for new data need to be taken to a new level.}, } @article {pmid22174751, year = {2011}, author = {LaTuga, MS and Ellis, JC and Cotton, CM and Goldberg, RN and Wynn, JL and Jackson, RB and Seed, PC}, title = {Beyond bacteria: a study of the enteric microbial consortium in extremely low birth weight infants.}, journal = {PloS one}, volume = {6}, number = {12}, pages = {e27858}, pmid = {22174751}, issn = {1932-6203}, mesh = {Bacteria/classification/*genetics ; Base Sequence ; Demography ; Eukaryotic Cells/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Infant, Extremely Low Birth Weight/*physiology ; Infant, Newborn ; Male ; Metagenome/genetics ; Metagenomics ; Microbial Consortia/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Extremely low birth weight (ELBW) infants have high morbidity and mortality, frequently due to invasive infections from bacteria, fungi, and viruses. The microbial communities present in the gastrointestinal tracts of preterm infants may serve as a reservoir for invasive organisms and remain poorly characterized. We used deep pyrosequencing to examine the gut-associated microbiome of 11 ELBW infants in the first postnatal month, with a first time determination of the eukaryote microbiota such as fungi and nematodes, including bacteria and viruses that have not been previously described. Among the fungi observed, Candida sp. and Clavispora sp. dominated the sequences, but a range of environmental molds were also observed. Surprisingly, seventy-one percent of the infant fecal samples tested contained ribosomal sequences corresponding to the parasitic organism Trichinella. Ribosomal DNA sequences for the roundworm symbiont Xenorhabdus accompanied these sequences in the infant with the greatest proportion of Trichinella sequences. When examining ribosomal DNA sequences in aggregate, Enterobacteriales, Pseudomonas, Staphylococcus, and Enterococcus were the most abundant bacterial taxa in a low diversity bacterial community (mean Shannon-Weaver Index of 1.02 ± 0.69), with relatively little change within individual infants through time. To supplement the ribosomal sequence data, shotgun sequencing was performed on DNA from multiple displacement amplification (MDA) of total fecal genomic DNA from two infants. In addition to the organisms mentioned previously, the metagenome also revealed sequences for gram positive and gram negative bacteriophages, as well as human adenovirus C. Together, these data reveal surprising eukaryotic and viral microbial diversity in ELBW enteric microbiota dominated bytypes of bacteria known to cause invasive disease in these infants.}, } @article {pmid22174282, year = {2012}, author = {Zhang, Y and Sun, Y}, title = {MetaDomain: a profile HMM-based protein domain classification tool for short sequences.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {}, number = {}, pages = {271-282}, pmid = {22174282}, issn = {2335-6936}, mesh = {Algorithms ; Amino Acid Sequence ; Computational Biology ; Data Mining/statistics & numerical data ; Databases, Protein/statistics & numerical data ; Markov Chains ; Metagenomics/*statistics & numerical data ; Microbiota/*genetics ; *Protein Structure, Tertiary/genetics ; Sequence Alignment/statistics & numerical data ; Sequence Analysis, Protein/statistics & numerical data ; *Software ; Soil Microbiology ; Transcriptome/genetics ; }, abstract = {Protein homology search provides basis for functional profiling in metagenomic annotation. Profile HMM-based methods classify reads into annotated protein domain families and can achieve better sensitivity for remote protein homology search than pairwise sequence alignment. However, their sensitivity deteriorates with the decrease of read length. As a result, a large number of short reads cannot be classified into their native domain families. In this work, we introduce MetaDomain, a protein domain classification tool designed for short reads generated by next-generation sequencing technologies. MetaDomain uses relaxed position-specific score thresholds to align more reads to a profile HMM while using the distribution of alignment positions as an additional constraint to control false positive matches. In this work MetaDomain is applied to the transcriptomic data of a bacterial genome and a soil metagenomic data set. The experimental results show that it can achieve better sensitivity than the state-of-the-art profile HMM alignment tool in identifying encoded domains from short sequences. The source codes of MetaDomain are available at http://sourceforge.net/projects/metadomain/.}, } @article {pmid22174281, year = {2012}, author = {Zhang, Q and Doak, TG and Ye, Y}, title = {Artificial functional difference between microbial communities caused by length difference of sequencing reads.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {}, number = {}, pages = {259-270}, pmid = {22174281}, issn = {2335-6936}, support = {1R01HG004908/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/isolation & purification ; Bacterial Proteins/classification/genetics ; Computational Biology ; Feces/microbiology ; Metagenomics/*statistics & numerical data ; Mice ; Microbiota/*genetics ; Obesity/microbiology ; Sequence Analysis/*statistics & numerical data ; Thinness/microbiology ; }, abstract = {Homology-based approaches are often used for the annotation of microbial communities, providing functional profiles that are used to characterize and compare the content and the functionality of microbial communities. Metagenomic reads are the starting data for these studies, however considerable differences are observed between the functional profiles-built from sequencing reads produced by different sequencing techniques-for even the same microbial community. Using simulation experiments, we show that such functional differences are likely to be caused by the actual difference in read lengths, and are not the results of a sampling bias of the sequencing techniques. Furthermore, the functional differences derived from different sequencing techniques cannot be fully explained by the read-count bias, i.e. 1) the higher fraction of unannotated shorter reads (i.e., "read length matters"), and 2) the different lengths of proteins in different functional categories. Instead, we show here that specific functional categories are under-annotated, because similarity-search-based functional annotation tools tend to miss more reads from functional categories that contain less conserved genes/proteins. In addition, the accuracy of functional annotation of short reads for different functions varies, further skewing the functional profiles. To address these issues, we present a simple yet efficient method to improve the frequency estimates of different functional categories in the functional profiles of metagenomes, based on the functional annotation of simulated reads from complete microbial genomes.}, } @article {pmid22170749, year = {2012}, author = {Michail, S and Durbin, M and Turner, D and Griffiths, AM and Mack, DR and Hyams, J and Leleiko, N and Kenche, H and Stolfi, A and Wine, E}, title = {Alterations in the gut microbiome of children with severe ulcerative colitis.}, journal = {Inflammatory bowel diseases}, volume = {18}, number = {10}, pages = {1799-1808}, pmid = {22170749}, issn = {1536-4844}, support = {R21 AT003400/AT/NCCIH NIH HHS/United States ; R21 AT003400-01A2/AT/NCCIH NIH HHS/United States ; AT003400/AT/NCCIH NIH HHS/United States ; }, mesh = {Adolescent ; Bacteria/*pathogenicity ; Biomarkers/analysis ; Case-Control Studies ; Child ; Child, Preschool ; Colitis, Ulcerative/*diagnosis/genetics/microbiology ; Colon/*metabolism/pathology ; DNA, Bacterial/genetics ; Feces/*microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Gene Expression Profiling ; Genetic Variation/*genetics ; Humans ; Male ; *Metagenome ; Oligonucleotide Array Sequence Analysis ; Polymerase Chain Reaction ; Prospective Studies ; }, abstract = {BACKGROUND: Although the role of microbes in disease pathogenesis is well established, data describing the variability of the vast microbiome in children diagnosed with ulcerative colitis (UC) are lacking. This study characterizes the gut microbiome in hospitalized children with severe UC and determines the relationship between microbiota and response to steroid therapy.

METHODS: Fecal samples were collected from 26 healthy controls and 27 children hospitalized with severe UC as part of a prospective multicenter study. DNA extraction, polymerase chain reaction (PCR) amplification of bacterial 16S rRNA, and microarray hybridization were performed. Results were analyzed in GeneSpring GX 11.0 comparing healthy controls with children with UC, and steroid responsive (n = 17) with nonresponsive patients (n = 10).

RESULTS: Bacterial signal strength and distribution showed differences between UC and healthy controls (adjusted P < 0.05) for Phylum, Class, Order, Family, Genus, and Phylospecies levels with reduction in Clostridia and an increase in Gamma-proteobacteria. The number of microbial phylospecies was reduced in UC (266 ± 69) vs. controls (758 ± 3, P < 0.001), as was the Shannon Diversity Index (6.1 ± 0.23 vs. 6.49 ± 0.04, respectively; P < 0.0001). Steroid nonresponders harbored fewer phylospecies than responders (142 ± 49 vs. 338 ± 62, P = 0.013).

CONCLUSIONS: Richness, evenness, and biodiversity of the gut microbiome were remarkably reduced in children with UC compared with healthy controls. Children who did not respond to steroids harbored a microbiome that was even less rich than steroid responders. This study is the first to characterize the gut microbiome in a large cohort of pediatric patients with severe UC and describes changes in the gut microbiome as a potential prognostic feature.}, } @article {pmid22164261, year = {2011}, author = {Schmidt, B and Mulder, IE and Musk, CC and Aminov, RI and Lewis, M and Stokes, CR and Bailey, M and Prosser, JI and Gill, BP and Pluske, JR and Kelly, D}, title = {Establishment of normal gut microbiota is compromised under excessive hygiene conditions.}, journal = {PloS one}, volume = {6}, number = {12}, pages = {e28284}, pmid = {22164261}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Crosses, Genetic ; Gastrointestinal Tract/*microbiology ; Gene Library ; Hygiene ; Intestinal Mucosa/microbiology ; Metagenome/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Swine ; }, abstract = {BACKGROUND: Early gut colonization events are purported to have a major impact on the incidence of infectious, inflammatory and autoimmune diseases in later life. Hence, factors which influence this process may have important implications for both human and animal health. Previously, we demonstrated strong influences of early-life environment on gut microbiota composition in adult pigs. Here, we sought to further investigate the impact of limiting microbial exposure during early life on the development of the pig gut microbiota.

Outdoor- and indoor-reared animals, exposed to the microbiota in their natural rearing environment for the first two days of life, were transferred to an isolator facility and adult gut microbial diversity was analyzed by 16S rRNA gene sequencing. From a total of 2,196 high-quality 16S rRNA gene sequences, 440 phylotypes were identified in the outdoor group and 431 phylotypes in the indoor group. The majority of clones were assigned to the four phyla Firmicutes (67.5% of all sequences), Proteobacteria (17.7%), Bacteroidetes (13.5%) and to a lesser extent, Actinobacteria (0.1%). Although the initial maternal and environmental microbial inoculum of isolator-reared animals was identical to that of their naturally-reared littermates, the microbial succession and stabilization events reported previously in naturally-reared outdoor animals did not occur. In contrast, the gut microbiota of isolator-reared animals remained highly diverse containing a large number of distinct phylotypes.

CONCLUSIONS/SIGNIFICANCE: The results documented here indicate that establishment and development of the normal gut microbiota requires continuous microbial exposure during the early stages of life and this process is compromised under conditions of excessive hygiene.}, } @article {pmid22162545, year = {2012}, author = {Rea, MC and O'Sullivan, O and Shanahan, F and O'Toole, PW and Stanton, C and Ross, RP and Hill, C}, title = {Clostridium difficile carriage in elderly subjects and associated changes in the intestinal microbiota.}, journal = {Journal of clinical microbiology}, volume = {50}, number = {3}, pages = {867-875}, pmid = {22162545}, issn = {1098-660X}, mesh = {Aged ; Aged, 80 and over ; *Biodiversity ; Carrier State/epidemiology/*microbiology ; Clostridioides difficile/classification/genetics/*isolation & purification ; Clostridium Infections/epidemiology/*microbiology ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; *Metagenome ; Prevalence ; Ribotyping ; Sequence Analysis, DNA ; }, abstract = {Clostridium difficile is an important nosocomial pathogen associated particularly with diarrheal disease in elderly individuals in hospitals and long-term care facilities. We examined the carriage rate of Clostridium difficile by culture as a function of fecal microbiota composition in elderly subjects recruited from the community, including outpatient, short-term respite, and long-term hospital stay subjects. The carriage rate ranged from 1.6% (n = 123) for subjects in the community, to 9.5% (n = 43) in outpatient settings, and increasing to 21% (n = 151) for patients in short- or long-term care in hospital. The dominant 072 ribotype was carried by 43% (12/28) of subjects, while the hypervirulent strain R027 (B1/NAP1/027) was isolated from 3 subjects (11%), 2 of whom displayed C. difficile associated diarrhea (CDAD) symptoms at the time of sampling. Emerging ribotypes with enhanced virulence (078 and 018) were also isolated from two asymptomatic subjects. Pyrosequencing of rRNA gene amplicons was used to determine the composition of the fecal microbiota as a surrogate for the microbial population structure of the distal intestine. Asymptomatic subjects (n = 20) from whom C. difficile was isolated showed no dramatic difference at the phylum or family taxonomic level compared to those that were culture negative (n = 252). However, in contrast, a marked reduction in microbial diversity at genus level was observed in patients who had been diagnosed with CDAD at the time of sampling and from whom C. difficile R027 was isolated.}, } @article {pmid22156428, year = {2012}, author = {Hernandez-Sanabria, E and Goonewardene, LA and Wang, Z and Durunna, ON and Moore, SS and Guan, LL}, title = {Impact of feed efficiency and diet on adaptive variations in the bacterial community in the rumen fluid of cattle.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {4}, pages = {1203-1214}, pmid = {22156428}, issn = {1098-5336}, mesh = {Animals ; Bacteria/*genetics ; Bacterial Load ; *Biota ; Cattle ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Denaturing Gradient Gel Electrophoresis ; *Diet ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Rumen/*microbiology ; }, abstract = {Limited knowledge of the structure and activities of the ruminal bacterial community prevents the understanding of the effect of population dynamics on functional bacterial groups and on host productivity. This study aimed to identify particular bacteria associated with host feed efficiency in steers with differing diets and residual feed intake (RFI) using culture-independent methods: PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR analysis. PCR-DGGE profiles were generated from the ruminal fluid of 55 steers fed a low-energy-density diet and then switched to a high-energy-density diet. Bacterial profile comparisons by multivariate statistical analysis showed a trend only for RFI-related clusters on the high-energy diet. When steers (n = 19) belonging to the same RFI group under both diets were used to identify specific bacterial phylotypes related to feed efficiency traits, correlations were detected between dry matter intake, average daily gain, and copy numbers of the 16S rRNA gene of Succinivibrio sp. in low-RFI (efficient) steers, whereas correlations between Robinsoniella sp. and RFI (P < 0.05) were observed for high-RFI (inefficient) animals. Eubacterium sp. differed significantly (P < 0.05) between RFI groups that were only on the high-energy diet. Our work provides a comprehensive framework to understand how particular bacterial phylotypes contribute to differences in feed efficiency and ultimately influence host productivity, which may either depend on or be independent from diet factors.}, } @article {pmid22156414, year = {2012}, author = {Minervini, F and Di Cagno, R and Lattanzi, A and De Angelis, M and Antonielli, L and Cardinali, G and Cappelle, S and Gobbetti, M}, title = {Lactic acid bacterium and yeast microbiotas of 19 sourdoughs used for traditional/typical italian breads: interactions between ingredients and microbial species diversity.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {4}, pages = {1251-1264}, pmid = {22156414}, issn = {1098-5336}, mesh = {Amino Acids/analysis ; *Biodiversity ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Food Analysis ; *Food Microbiology ; Fructose/analysis ; Glucose/analysis ; Italy ; Lactobacillales/classification/genetics/isolation & purification/*physiology ; Maltose ; Metagenome ; *Microbial Interactions ; Molecular Sequence Data ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Yeasts/classification/genetics/isolation & purification/*physiology ; }, abstract = {The study of the microbiotas of 19 Italian sourdoughs used for the manufacture of traditional/typical breads allowed the identification, through a culture-dependent approach, of 20 and 4 species of lactic acid bacteria (LAB) and yeasts, respectively. Numerically, the most frequent LAB isolates were Lactobacillus sanfranciscensis (ca. 28% of the total LAB isolates), Lactobacillus plantarum (ca. 16%), and Lactobacillus paralimentarius (ca. 14%). Saccharomyces cerevisiae was identified in 16 sourdoughs. Candida humilis, Kazachstania barnettii, and Kazachstania exigua were also identified. As shown by principal component analysis (PCA), a correlation was found between the ingredients, especially the type of flour, the microbial community, and the biochemical features of sourdoughs. Triticum durum flours were characterized by the high level of maltose, glucose, fructose, and free amino acids (FAA) correlated with the sole or main presence of obligately heterofermentative LAB, the lowest number of facultatively heterofermentative strains, and the low cell density of yeasts in the mature sourdoughs. This study highlighted, through a comprehensive and comparative approach, the dominant microbiotas of 19 Italian sourdoughs, which determined some of the peculiarities of the resulting traditional/typical Italian breads.}, } @article {pmid22155131, year = {2012}, author = {Rashid, MU and Weintraub, A and Nord, CE}, title = {Effect of new antimicrobial agents on the ecological balance of human microflora.}, journal = {Anaerobe}, volume = {18}, number = {2}, pages = {249-253}, doi = {10.1016/j.anaerobe.2011.11.005}, pmid = {22155131}, issn = {1095-8274}, mesh = {Anti-Infective Agents/*pharmacology ; Biota ; Humans ; Metagenome/*drug effects ; }, abstract = {The human normal microflora is relatively stable at each ecological habitat under normal circumstances and acts as a barrier against colonization by potentially pathogenic microorganisms and against overgrowth of already present opportunistic microorganisms. Administration of antimicrobial agents causes disturbances in the ecological balance between the host and the normal microflora. The risk of emergence and spread of resistant strains between patients and dissemination of resistant determinants between microorganisms is reduced if colonization resistance is not disturbed by antimicrobial agents. In this article, the potential ecological effects of administration of new antimicrobial agents on the intestinal and oropharyngeal microflora are summarized. The review is based on clinical studies published during the past 10 years.}, } @article {pmid22154467, year = {2012}, author = {Gonzalez, A and King, A and Robeson, MS and Song, S and Shade, A and Metcalf, JL and Knight, R}, title = {Characterizing microbial communities through space and time.}, journal = {Current opinion in biotechnology}, volume = {23}, number = {3}, pages = {431-436}, pmid = {22154467}, issn = {1879-0429}, support = {U01 HG004866-05/HG/NHGRI NIH HHS/United States ; U01 HG004866/HG/NHGRI NIH HHS/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; R01 HG004872-03/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Bacteria/*classification/genetics ; Biodiversity ; *Environmental Microbiology ; Metagenomics/methods ; Models, Biological ; Spatio-Temporal Analysis ; }, abstract = {Until recently, the study of microbial diversity has mainly been limited to descriptive approaches, rather than predictive model-based analyses. The development of advanced analytical tools and decreasing cost of high-throughput multi-omics technologies has made the later approach more feasible. However, consensus is lacking as to which spatial and temporal scales best facilitate understanding of the role of microbial diversity in determining both public and environmental health. Here, we review the potential for combining these new technologies with both traditional and nascent spatio-temporal analysis methods. The fusion of proper spatio-temporal sampling, combined with modern multi-omics and computational tools, will provide insight into the tracking, development and manipulation of microbial communities.}, } @article {pmid22152152, year = {2011}, author = {Huang, S and Yang, F and Zeng, X and Chen, J and Li, R and Wen, T and Li, C and Wei, W and Liu, J and Chen, L and Davis, C and Xu, J}, title = {Preliminary characterization of the oral microbiota of Chinese adults with and without gingivitis.}, journal = {BMC oral health}, volume = {11}, number = {}, pages = {33}, pmid = {22152152}, issn = {1472-6831}, mesh = {Adult ; Bacteria/*genetics/isolation & purification ; Bacterial Typing Techniques ; Case-Control Studies ; China ; Cross-Sectional Studies ; DNA, Bacterial/analysis ; Dental Plaque/*microbiology ; Female ; Fusobacterium/genetics ; Genetic Variation ; Genome, Bacterial/genetics ; Gingivitis/*microbiology ; Humans ; Male ; Metagenome/*genetics ; Microbial Consortia ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Saliva/*microbiology ; Sequence Analysis, DNA/methods ; Statistics, Nonparametric ; Streptococcus/genetics ; Young Adult ; }, abstract = {BACKGROUND: Microbial communities inhabiting human mouth are associated with oral health and disease. Previous studies have indicated the general prevalence of adult gingivitis in China to be high. The aim of this study was to characterize in depth the oral microbiota of Chinese adults with or without gingivitis, by defining the microbial phylogenetic diversity and community-structure using highly paralleled pyrosequencing.

METHODS: Six non-smoking Chinese, three with and three without gingivitis (age range 21-39 years, 4 females and 2 males) were enrolled in the present cross-sectional study. Gingival parameters of inflammation and bleeding on probing were characterized by a clinician using the Mazza Gingival Index (MGI). Plaque (sampled separately from four different oral sites) and salivary samples were obtained from each subject. Sequences and relative abundance of the bacterial 16 S rDNA PCR-amplicons were determined via pyrosequencing that produced 400 bp-long reads. The sequence data were analyzed via a computational pipeline customized for human oral microbiome analyses. Furthermore, the relative abundances of selected microbial groups were validated using quantitative PCR.

RESULTS: The oral microbiomes from gingivitis and healthy subjects could be distinguished based on the distinct community structures of plaque microbiomes, but not the salivary microbiomes. Contributions of community members to community structure divergence were statistically accessed at the phylum, genus and species-like levels. Eight predominant taxa were found associated with gingivitis: TM7, Leptotrichia, Selenomonas, Streptococcus, Veillonella, Prevotella, Lautropia, and Haemophilus. Furthermore, 98 species-level OTUs were identified to be gingivitis-associated, which provided microbial features of gingivitis at a species resolution. Finally, for the two selected genera Streptococcus and Fusobacterium, Real-Time PCR based quantification of relative bacterial abundance validated the pyrosequencing-based results.

CONCLUSIONS: This methods study suggests that oral samples from this patient population of gingivitis can be characterized via plaque microbiome by pyrosequencing the 16 S rDNA genes. Further studies that characterize serial samples from subjects (longitudinal study design) with a larger population size may provide insight into the temporal and ecological features of oral microbial communities in clinically-defined states of gingivitis.}, } @article {pmid22151572, year = {2012}, author = {Caro-Quintero, A and Konstantinidis, KT}, title = {Bacterial species may exist, metagenomics reveal.}, journal = {Environmental microbiology}, volume = {14}, number = {2}, pages = {347-355}, doi = {10.1111/j.1462-2920.2011.02668.x}, pmid = {22151572}, issn = {1462-2920}, mesh = {Bacteria/classification/*genetics ; Biodiversity ; Classification ; Gene Transfer, Horizontal ; *Metagenomics ; Phylogeny ; Transformation, Bacterial ; }, abstract = {Whether or not bacterial species exist remains an unresolved issue of paramount theoretical as well as practical consequences. Here we review and synthesize the findings emerging from metagenomic surveys of natural microbial populations and argue that microbial communities are predominantly organized in genetically and ecologically discernible populations, which possess the attributes expected for species. These sequence-discrete populations represent a major foundation for beginning high-resolution investigations on how populations are organized, interact, and evolve within communities. We also attempt to reconcile these findings with those of previous studies that reported indiscrete species and a genetic continuum within bacterial taxa and discuss the implications for the current bacterial species definition.}, } @article {pmid22142955, year = {2012}, author = {Diaz, PI}, title = {Microbial diversity and interactions in subgingival biofilm communities.}, journal = {Frontiers of oral biology}, volume = {15}, number = {}, pages = {17-40}, doi = {10.1159/000329669}, pmid = {22142955}, issn = {1420-2433}, support = {R21 DE020166/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics/metabolism ; *Biodiversity ; *Biofilms/growth & development ; Biomass ; Dental Plaque/*microbiology ; Ecosystem ; Host-Pathogen Interactions/physiology ; Humans ; Metagenome/genetics ; Metagenomics ; *Microbial Consortia ; *Microbial Interactions ; Models, Biological ; Nucleic Acid Hybridization ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Tooth Root/microbiology ; }, abstract = {The human subgingival environment is a complex environmental niche where microorganisms from the three domains of life meet to form diverse biofilm communities that exist in close proximity to the host. Bacteria constitute the most abundant, diverse and ultimately well-studied component of these communities with about 500 bacterial taxa reported to occur in this niche. Cultivation and molecular approaches are revealing the breadth and depth of subgingival biofilm diversity as part of an effort to understand the subgingival microbiome, the collection of microorganisms that inhabit the gingival crevices. Although these investigations are constructing a pretty detailed taxonomical census of subgingival microbial communities, including inter-subject and temporal variability in community structure, as well as differences according to periodontal health status, we are still at the front steps in terms of understanding community function. Clinical studies that evaluate community structure need to be coupled with biologically relevant models that allow evaluation of the ecological determinants of subgingival biofilm maturation. Functional characteristics of subgingival biofilm communities that still need to be clarified include main metabolic processes that support microbial communities, identification of keystone species, microbial interactions and signaling events that lead to community maturation and the relationship of different communities with the host. This manuscript presents a summary of our current understanding of subgingival microbial diversity and an overview of experimental models used to dissect the functional characteristics of subgingival communities. Future coupling of 'omics'-based approaches with such models will facilitate a better understanding of subgingival ecology opening opportunities for community manipulation.}, } @article {pmid22128350, year = {2011}, author = {Allen, HK and Looft, T and Bayles, DO and Humphrey, S and Levine, UY and Alt, D and Stanton, TB}, title = {Antibiotics in feed induce prophages in swine fecal microbiomes.}, journal = {mBio}, volume = {2}, number = {6}, pages = {}, pmid = {22128350}, issn = {2150-7511}, mesh = {Animal Feed ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics/*virology ; Biota ; Carbadox/pharmacology ; Chlortetracycline/pharmacology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Drug Combinations ; Gastrointestinal Tract/*microbiology/*virology ; Metagenome ; Penicillin G/pharmacology ; Prophages/classification/*drug effects/genetics/*growth & development ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfamethazine/pharmacology ; Swine ; }, abstract = {UNLABELLED: Antibiotics are a cost-effective tool for improving feed efficiency and preventing disease in agricultural animals, but the full scope of their collateral effects is not understood. Antibiotics have been shown to mediate gene transfer by inducing prophages in certain bacterial strains; therefore, one collateral effect could be prophage induction in the gut microbiome at large. Here we used metagenomics to evaluate the effect of two antibiotics in feed (carbadox and ASP250 [chlortetracycline, sulfamethazine, and penicillin]) on swine intestinal phage metagenomes (viromes). We also monitored the bacterial communities using 16S rRNA gene sequencing. ASP250, but not carbadox, caused significant population shifts in both the phage and bacterial communities. Antibiotic resistance genes, such as multidrug resistance efflux pumps, were identified in the viromes, but in-feed antibiotics caused no significant changes in their abundance. The abundance of phage integrase-encoding genes was significantly increased in the viromes of medicated swine over that in the viromes of nonmedicated swine, demonstrating the induction of prophages with antibiotic treatment. Phage-bacterium population dynamics were also examined. We observed a decrease in the relative abundance of Streptococcus bacteria (prey) when Streptococcus phages (predators) were abundant, supporting the "kill-the-winner" ecological model of population dynamics in the swine fecal microbiome. The data show that gut ecosystem dynamics are influenced by phages and that prophage induction is a collateral effect of in-feed antibiotics.

IMPORTANCE: This study advances our knowledge of the collateral effects of in-feed antibiotics at a time in which the widespread use of "growth-promoting" antibiotics in agriculture is under scrutiny. Using comparative metagenomics, we show that prophages are induced by in-feed antibiotics in swine fecal microbiomes and that antibiotic resistance genes were detected in most viromes. This suggests that in-feed antibiotics are contributing to phage-mediated gene transfer, potentially of antibiotic resistance genes, in the swine gut. Additionally, the so-called "kill-the-winner" model of phage-bacterium population dynamics has been shown in aquatic ecosystems but met with conflicting evidence in gut ecosystems. The data support the idea that swine fecal Streptococcus bacteria and their phages follow the kill-the-winner model. Understanding the role of phages in gut microbial ecology is an essential component of the antibiotic resistance problem and of developing potential mitigation strategies.}, } @article {pmid22104273, year = {2011}, author = {Shao, ZY and Tang, ZS and Yan, C and Jiang, YT and Ma, R and Liu, Z and Huang, ZW}, title = {Effects of intensity-modulated radiotherapy on human oral microflora.}, journal = {Journal of radiation research}, volume = {52}, number = {6}, pages = {834-839}, doi = {10.1269/jrr.11085}, pmid = {22104273}, issn = {1349-9157}, mesh = {Dental Plaque/microbiology ; Head and Neck Neoplasms/radiotherapy ; Humans ; Metagenome/genetics/radiation effects ; Mouth/*microbiology/*radiation effects ; RNA, Ribosomal, 16S/genetics/isolation & purification ; Radiotherapy, Intensity-Modulated/*adverse effects ; Xerostomia/etiology/prevention & control ; }, abstract = {This study aimed to evaluate changes in the biodiversity of the oral microflora of patients with head and neck cancer treated with postoperative intensity-modulated radiotherapy (IMRT) or conventional radiotherapy (CRT). Pooled dental plaque samples were collected during the radiation treatment from patients receiving IMRT (n = 13) and CRT (n = 12). Denaturing gradient gel electrophoresis (DGGE) was used to analyze the temporal variation of these plaque samples. The stimulated and unstimulated salivary flow rates were also compared between IMRT and CRT patients. Reductions in the severity of hyposalivation were observed in IMRT patients compared with CRT patients. We also observed that the temporal stability of the oral ecosystem was significantly higher in the IMRT group (69.96 ± 7.82%) than in the CRT group (51.98 ± 10.45%) (P < 0.05). The findings of the present study suggest that IMRT is more conducive to maintaining the relative stability of the oral ecosystem than CRT.}, } @article {pmid22092522, year = {2012}, author = {Paliy, O and Agans, R}, title = {Application of phylogenetic microarrays to interrogation of human microbiota.}, journal = {FEMS microbiology ecology}, volume = {79}, number = {1}, pages = {2-11}, pmid = {22092522}, issn = {1574-6941}, support = {AT003423/AT/NCCIH NIH HHS/United States ; R21 AT003423/AT/NCCIH NIH HHS/United States ; R03 HD065575/HD/NICHD NIH HHS/United States ; R21 AT003423-02/AT/NCCIH NIH HHS/United States ; HD065575/HD/NICHD NIH HHS/United States ; R03 HD065575-01/HD/NICHD NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; Gene Expression Profiling ; Humans ; Ilium/microbiology ; Metagenome/*genetics ; Microbial Consortia/*genetics ; Oligonucleotide Array Sequence Analysis ; Oropharynx/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Human-associated microbiota is recognized to play vital roles in maintaining host health, and it is implicated in many disease states. While the initial surge in the profiling of these microbial communities was achieved with Sanger and next-generation sequencing, many oligonucleotide microarrays have also been developed recently for this purpose. Containing probes complementary to small ribosomal subunit RNA gene sequences of community members, such phylogenetic arrays provide direct quantitative comparisons of microbiota composition among samples and between sample groups. Some of the developed microarrays including PhyloChip, Microbiota Array, and HITChip can simultaneously measure the presence and abundance of hundreds and thousands of phylotypes in a single sample. This review describes the currently available phylogenetic microarrays that can be used to analyze human microbiota, delineates the approaches for the optimization of microarray use, and provides examples of recent findings based on microarray interrogation of human-associated microbial communities.}, } @article {pmid22081564, year = {2012}, author = {Varin, T and Lovejoy, C and Jungblut, AD and Vincent, WF and Corbeil, J}, title = {Metagenomic analysis of stress genes in microbial mat communities from Antarctica and the High Arctic.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {2}, pages = {549-559}, pmid = {22081564}, issn = {1098-5336}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Antarctic Regions ; Arctic Regions ; Bacteria/*classification/*genetics ; *Biota ; Geologic Sediments/*microbiology ; *Metagenome ; Sequence Analysis, DNA ; }, abstract = {Polar and alpine microbial communities experience a variety of environmental stresses, including perennial cold and freezing; however, knowledge of genomic responses to such conditions is still rudimentary. We analyzed the metagenomes of cyanobacterial mats from Arctic and Antarctic ice shelves, using high-throughput pyrosequencing to test the hypotheses that consortia from these extreme polar habitats were similar in terms of major phyla and subphyla and consequently in their potential responses to environmental stresses. Statistical comparisons of the protein-coding genes showed similarities between the mats from the two poles, with the majority of genes derived from Proteobacteria and Cyanobacteria; however, the relative proportions differed, with cyanobacterial genes more prevalent in the Antarctic mat metagenome. Other differences included a higher representation of Actinobacteria and Alphaproteobacteria in the Arctic metagenomes, which may reflect the greater access to diasporas from both adjacent ice-free lands and the open ocean. Genes coding for functional responses to environmental stress (exopolysaccharides, cold shock proteins, and membrane modifications) were found in all of the metagenomes. However, in keeping with the greater exposure of the Arctic to long-range pollutants, sequences assigned to copper homeostasis genes were statistically (30%) more abundant in the Arctic samples. In contrast, more reads matching the sigma B genes were identified in the Antarctic mat, likely reflecting the more severe osmotic stress during freeze-up of the Antarctic ponds. This study underscores the presence of diverse mechanisms of adaptation to cold and other stresses in polar mats, consistent with the proportional representation of major bacterial groups.}, } @article {pmid22080429, year = {2012}, author = {Reisberg, EE and Hildebrandt, U and Riederer, M and Hentschel, U}, title = {Phyllosphere bacterial communities of trichome-bearing and trichomeless Arabidopsis thaliana leaves.}, journal = {Antonie van Leeuwenhoek}, volume = {101}, number = {3}, pages = {551-560}, doi = {10.1007/s10482-011-9669-8}, pmid = {22080429}, issn = {1572-9699}, mesh = {Arabidopsis/genetics/*microbiology ; Arabidopsis Proteins/genetics ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Bacterial Adhesion ; Bacterial Load ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; DNA-Binding Proteins/deficiency/genetics ; Metagenome/*genetics ; *Microbial Consortia ; Molecular Sequence Data ; Phylogeny ; Plant Leaves/chemistry/*microbiology/ultrastructure ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Homology, Nucleic Acid ; Waxes/analysis ; }, abstract = {This study aimed to investigate whether the presence of trichomes as conspicuous physical attributes of the leaf surface affects the microbial community composition on Arabidopsis thaliana leaves. The A. thaliana ecotype Col-0 and its trichomeless gl1 mutant were grown in growth cabinets under climate-controlled conditions. The gl1 mutant showed a similar wax composition as the Col-0 wild type with slightly reduced amounts of C(29), C(31) and C(33) alkanes by GC/MS and GC/FID analyses. 120 bacterial isolates representing 39 bacterial genera were obtained from A. thaliana Col-0 leaf surfaces. Phylogenetic analysis of nearly full-length 16S rRNA sequences from 29 selected isolates confirmed their affiliation to the Proteobacteria (Alpha-, Beta-, Gamma-), Actinobacteria, Bacteroidetes and Firmicutes. The bacterial diversity on A. thaliana ecotype Col-0 and its gl1 mutant, devoid of trichomes, were further compared by denaturing gradient gel electrophoresis (DGGE). Banding patterns and sequencing of representative DGGE bands revealed the presence of phylotypes related to Sphingomonas (Alphaproteobacteria), Methylophilus (Betaproteobacteria) and Dyadobacter (Bacteroidetes) which are common phyllosphere inhabitants. Furthermore, wildtype and trichomeless mutant plants were exposed to outdoor conditions for 4-5 weeks. The DGGE gels showed only minor differences between the two plant lines, thus suggesting that trichomes per se do not affect bacterial diversity on Arabidopsis leaves under the experimental conditions tested.}, } @article {pmid22075025, year = {2012}, author = {Friedl, MA and Druzhinina, IS}, title = {Taxon-specific metagenomics of Trichoderma reveals a narrow community of opportunistic species that regulate each other's development.}, journal = {Microbiology (Reading, England)}, volume = {158}, number = {Pt 1}, pages = {69-83}, pmid = {22075025}, issn = {1465-2080}, mesh = {Biodiversity ; Ecosystem ; Hypocrea/classification/genetics/growth & development/isolation & purification ; *Metagenomics ; Molecular Sequence Data ; Phylogeny ; Soil/analysis ; *Soil Microbiology ; Trichoderma/*classification/genetics/*growth & development/isolation & purification ; }, abstract = {In this paper, we report on the in situ diversity of the mycotrophic fungus Trichoderma (teleomorph Hypocrea, Ascomycota, Dikarya) revealed by a taxon-specific metagenomic approach. We designed a set of genus-specific internal transcribed spacer (ITS)1 and ITS2 rRNA primers and constructed a clone library containing 411 molecular operational taxonomic units (MOTUs). The overall species composition in the soil of the two distinct ecosystems in the Danube floodplain consisted of 15 known species and two potentially novel taxa. The latter taxa accounted for only 1.5 % of all MOTUs, suggesting that almost no hidden or uncultivable Hypocrea/Trichoderma species are present at least in these temperate forest soils. The species were unevenly distributed in vertical soil profiles although no universal factors controlling the distribution of all of them (chemical soil properties, vegetation type and affinity to rhizosphere) were revealed. In vitro experiments simulating infrageneric interactions between the pairs of species that were detected in the same soil horizon showed a broad spectrum of reactions from very strong competition over neutral coexistence to the pronounced synergism. Our data suggest that only a relatively small portion of Hypocrea/Trichoderma species is adapted to soil as a habitat and that the interaction between these species should be considered in a screening for Hypocrea/Trichoderma as an agent(s) of biological control of pests.}, } @article {pmid22068488, year = {2011}, author = {Na, H and Kim, OS and Yoon, SH and Kim, Y and Chun, J}, title = {Comparative approach to capture bacterial diversity of coastal waters.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {49}, number = {5}, pages = {729-740}, pmid = {22068488}, issn = {1976-3794}, mesh = {Bacteria/*classification/genetics/growth & development/*isolation & purification ; Bacteriological Techniques/*methods ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Metagenomics/*methods ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Despite the revolutionary advancements in DNA sequencing technology and cultivation techniques, few studies have been done to directly compare these methods. In this study, a 16S rRNA gene-based, integrative approach combining culture-independent techniques with culture-dependent methods was taken to investigate the bacterial community structure of coastal seawater collected from the Yellow Sea, Korea. For culture-independent studies, we used the latest model pyrosequencer, Roche/454 Genome Sequencer FLX Titanium. Pyrosequencing captured a total of 52 phyla including 27 candidate divisions from the water column, whereas the traditional cloning approach captured only 15 phyla including 2 candidate divisions. In addition, of 878 genera retrieved, 92.1 % of the sequences were unique to pyrosequencing. For culture-dependent analysis, plate culturing, plate washing, enrichment, and high-throughput culturing (HTC) methods were applied. Phylogenetic analysis showed that the plate-washing clones formed a cluster devoid of any previously cultured representatives within the family Rhodobacteraceae. One HTC isolate (SF293) fell into the OM182 clade, which was not recovered by other culturing methods described here. By directly comparing the sequences obtained from cultures with those from culture-independent work, we found that only 33% of the culture sequences were identical to those from clone libraries and pyrosequences. This study presents a detailed comparison of common molecular and cultivation techniques available in microbial ecology. As different methods yielded different coverage, we suggest choosing the approach after carefully examining the scientific questions being asked.}, } @article {pmid22066608, year = {2011}, author = {Roux, S and Enault, F and Bronner, G and Debroas, D}, title = {Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems.}, journal = {FEMS microbiology ecology}, volume = {78}, number = {3}, pages = {617-628}, doi = {10.1111/j.1574-6941.2011.01190.x}, pmid = {22066608}, issn = {1574-6941}, mesh = {Archaea/classification/*genetics ; Archaeal Proteins/genetics ; Bacteria/classification/*genetics ; Bacterial Proteins/genetics ; *Biodiversity ; DNA Primers ; Metagenome ; Operon ; Phylogeny ; Polymerase Chain Reaction ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; *Water Microbiology ; }, abstract = {PCR amplification of the rRNA gene is the most popular method for assessing microbial diversity. However, this molecular marker is often present in multiple copies in cells presenting, in addition, an intragenomic heterogeneity. In this context, housekeeping genes may be used as taxonomic markers for ecological studies. However, the efficiency of these protein-coding genes compared to 16S rRNA genes has not been tested on environmental data. For this purpose, five protein marker genes for which primer sets are available, were selected (rplB, pyrG, fusA, leuS and rpoB) and compared with 16S rRNA gene results from PCR amplification or metagenomic data from aquatic ecosystems. Analysis of the major groups found in these ecosystems, such as Actinobacteria, Bacteroides, Proteobacteria and Cyanobacteria, showed good agreement between the protein markers and the results given by 16S rRNA genes from metagenomic reads. However, with the markers it was possible to detect minor groups among the microbial assemblages, providing more details compared to 16S rRNA results from PCR amplification. In addition, the use of a set of protein markers made it possible to deduce a mean copy number of rRNA operons. This average estimate is essentially lower than the one estimated in sequenced genomes.}, } @article {pmid22059529, year = {2012}, author = {Ma, Y and Paulsen, IT and Palenik, B}, title = {Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments.}, journal = {Environmental microbiology}, volume = {14}, number = {2}, pages = {453-466}, doi = {10.1111/j.1462-2920.2011.02633.x}, pmid = {22059529}, issn = {1462-2920}, mesh = {Base Sequence ; Biodiversity ; California ; DNA Replication ; Environment ; Genetic Variation ; Metagenome ; Metagenomics ; Oceans and Seas ; Phylogeny ; Plasmids/metabolism ; Polymerase Chain Reaction ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {Plasmid diversity is still poorly understood in pelagic marine environments. Metagenomic approaches have the potential to reveal the genetic diversity of microbes actually present in an environment and the contribution of mobile genetic elements such as plasmids. By searching metagenomic datasets from flow cytometry-sorted coastal California seawater samples dominated by cyanobacteria (SynMeta) and from the Global Ocean Survey (GOS) putative marine plasmid sequences were identified as well as their possible hosts in the same samples. Based on conserved plasmid replication protein sequences predicted from the SynMeta metagenomes, PCR primers were designed for amplification of one plasmid family and used to confirm that metagenomic contigs of this family were derived from plasmids. These results suggest that the majority of plasmids in SynMeta metagenomes were small and cryptic, encoding mostly their own replication proteins. In contrast, probable plasmid sequences identified in the GOS dataset showed more complexity, consistent with a much more diverse microbial population, and included genes involved in plasmid transfer, mobilization, stability and partitioning. Phylogenetic trees were constructed based on common replication protein functional domains and, even within one replication domain family, substantial diversity was found within and between different samples. However, some replication protein domain families appear to be rare in the marine environment.}, } @article {pmid22043282, year = {2011}, author = {Brulc, JM and Yeoman, CJ and Wilson, MK and Berg Miller, ME and Jeraldo, P and Jindou, S and Goldenfeld, N and Flint, HJ and Lamed, R and Borovok, I and Vodovnik, M and Nelson, KE and Bayer, EA and White, BA}, title = {Cellulosomics, a gene-centric approach to investigating the intraspecific diversity and adaptation of Ruminococcus flavefaciens within the rumen.}, journal = {PloS one}, volume = {6}, number = {10}, pages = {e25329}, pmid = {22043282}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Cattle ; Cellulose/genetics/*metabolism ; Diet ; Gram-Positive Bacterial Infections/microbiology ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S ; Rumen/*microbiology ; Ruminococcus/genetics/isolation & purification ; Species Specificity ; }, abstract = {BACKGROUND: The bovine rumen maintains a diverse microbial community that serves to break down indigestible plant substrates. However, those bacteria specifically adapted to degrade cellulose, the major structural component of plant biomass, represent a fraction of the rumen microbiome. Previously, we proposed scaC as a candidate for phylotyping Ruminococcus flavefaciens, one of three major cellulolytic bacterial species isolated from the rumen. In the present report we examine the dynamics and diversity of scaC-types both within and between cattle temporally, following a dietary switch from corn-silage to grass-legume hay. These results were placed in the context of the overall bacterial population dynamics measured using the 16S rRNA.

PRINCIPAL FINDINGS: As many as 117 scaC-types were estimated, although just nineteen were detected in each of three rumens tested, and these collectively accounted for the majority of all types present. Variation in scaC populations was observed between cattle, between planktonic and fiber-associated fractions and temporally over the six-week survey, and appeared related to scaC phylogeny. However, by the sixth week no significant separation of scaC populations was seen between animals, suggesting enrichment of a constrained set of scaC-types. Comparing the amino-acid translation of each scaC-type revealed sequence variation within part of the predicted dockerin module but strong conservation in the N-terminus, where the cohesin module is located.

CONCLUSIONS: The R. flavefaciens species comprises a multiplicity of scaC-types in-vivo. Enrichment of particular scaC-types temporally, following a dietary switch, and between fractions along with the phylogenetic congruence suggests that functional differences exist between types. Observed differences in dockerin modules suggest at least part of the functional heterogeneity may be conferred by scaC. The polymorphic nature of scaC enables the relative distribution of R. flavefaciens strains to be examined and represents a gene-centric approach to investigating the intraspecific adaptation of an important specialist population.}, } @article {pmid22039404, year = {2011}, author = {Belda-Ferre, P and Cabrera-Rubio, R and Moya, A and Mira, A}, title = {Mining virulence genes using metagenomics.}, journal = {PloS one}, volume = {6}, number = {10}, pages = {e24975}, pmid = {22039404}, issn = {1932-6203}, mesh = {Bacteria/genetics/*pathogenicity ; Genome, Bacterial ; *Metagenomics ; Virulence/*genetics ; }, abstract = {When a bacterial genome is compared to the metagenome of an environment it inhabits, most genes recruit at high sequence identity. In free-living bacteria (for instance marine bacteria compared against the ocean metagenome) certain genomic regions are totally absent in recruitment plots, representing therefore genes unique to individual bacterial isolates. We show that these Metagenomic Islands (MIs) are also visible in bacteria living in human hosts when their genomes are compared to sequences from the human microbiome, despite the compartmentalized structure of human-related environments such as the gut. From an applied point of view, MIs of human pathogens (e.g. those identified in enterohaemorragic Escherichia coli against the gut metagenome or in pathogenic Neisseria meningitidis against the oral metagenome) include virulence genes that appear to be absent in related strains or species present in the microbiome of healthy individuals. We propose that this strategy (i.e. recruitment analysis of pathogenic bacteria against the metagenome of healthy subjects) can be used to detect pathogenicity regions in species where the genes involved in virulence are poorly characterized. Using this approach, we detect well-known pathogenicity islands and identify new potential virulence genes in several human pathogens.}, } @article {pmid22030447, year = {2012}, author = {Thiennimitr, P and Winter, SE and Bäumler, AJ}, title = {Salmonella, the host and its microbiota.}, journal = {Current opinion in microbiology}, volume = {15}, number = {1}, pages = {108-114}, pmid = {22030447}, issn = {1879-0364}, support = {AI040124/AI/NIAID NIH HHS/United States ; R01 AI044170/AI/NIAID NIH HHS/United States ; R29 AI040124/AI/NIAID NIH HHS/United States ; R21 AI088122-01/AI/NIAID NIH HHS/United States ; R01 AI040124/AI/NIAID NIH HHS/United States ; AI076246/AI/NIAID NIH HHS/United States ; R21 AI088122-02/AI/NIAID NIH HHS/United States ; AI096528/AI/NIAID NIH HHS/United States ; AI044170/AI/NIAID NIH HHS/United States ; R01 AI076246-04/AI/NIAID NIH HHS/United States ; R01 AI096528-02/AI/NIAID NIH HHS/United States ; R01 AI096528-01/AI/NIAID NIH HHS/United States ; R21 AI088122/AI/NIAID NIH HHS/United States ; R01 AI076246/AI/NIAID NIH HHS/United States ; R01 AI076246-03/AI/NIAID NIH HHS/United States ; AI088122/AI/NIAID NIH HHS/United States ; R01 AI096528/AI/NIAID NIH HHS/United States ; }, mesh = {*Biota ; Gastroenteritis/*microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; Salmonella Infections/*microbiology ; Salmonella typhimurium/*growth & development/*pathogenicity ; }, abstract = {The intestine is host to a diverse bacterial community whose structure, at the phylum level, is maintained through unknown mechanisms. Acute inflammation triggered by enteric pathogens, such as Salmonella enterica serotype Typhimurium (S. Typhimurium), is accompanied by changes in the bacterial community structure marked by an outgrowth of the pathogen. Recent studies show that S. Typhimurium can harness benefit from the host response to edge out the beneficial bacterial species that dominate in the healthy gut. The elucidation of how S. Typhimurium alters the bacterial community structure during gastroenteritis is beginning to provide insights into mechanisms that dictate the balance between the host and its microbiota.}, } @article {pmid22022422, year = {2011}, author = {Carpi, G and Cagnacci, F and Wittekindt, NE and Zhao, F and Qi, J and Tomsho, LP and Drautz, DI and Rizzoli, A and Schuster, SC}, title = {Metagenomic profile of the bacterial communities associated with Ixodes ricinus ticks.}, journal = {PloS one}, volume = {6}, number = {10}, pages = {e25604}, pmid = {22022422}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/*genetics ; Base Sequence ; DNA, Complementary/genetics ; Genome, Bacterial/genetics ; Host-Pathogen Interactions/genetics ; Ixodes/*microbiology ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Software ; }, abstract = {Assessment of the microbial diversity residing in arthropod vectors of medical importance is crucial for monitoring endemic infections, for surveillance of newly emerging zoonotic pathogens, and for unraveling the associated bacteria within its host. The tick Ixodes ricinus is recognized as the primary European vector of disease-causing bacteria in humans. Despite I. ricinus being of great public health relevance, its microbial communities remain largely unexplored to date. Here we evaluate the pathogen-load and the microbiome in single adult I. ricinus by using 454- and Illumina-based metagenomic approaches. Genomic DNA-derived sequences were taxonomically profiled using a computational approach based on the BWA algorithm, allowing for the identification of known tick-borne pathogens at the strain level and the putative tick core microbiome. Additionally, we assessed and compared the bacterial taxonomic profile in nymphal and adult I. ricinus pools collected from two distinct geographic regions in Northern Italy by means of V6-16S rRNA amplicon pyrosequencing and community based ecological analysis. A total of 108 genera belonging to representatives of all bacterial phyla were detected and a rapid qualitative assessment for pathogenic bacteria, such as Borrelia, Rickettsia and Candidatus Neoehrlichia, and for other bacteria with mutualistic relationship or undetermined function, such as Wolbachia and Rickettsiella, was possible. Interestingly, the ecological analysis revealed that the bacterial community structure differed between the examined geographic regions and tick life stages. This finding suggests that the environmental context (abiotic and biotic factors) and host-selection behaviors affect their microbiome.Our data provide the most complete picture to date of the bacterial communities present within I. ricinus under natural conditions by using high-throughput sequencing technologies. This study further demonstrates a novel detection strategy for the microbiomes of arthropod vectors in the context of epidemiological and ecological studies.}, } @article {pmid22018236, year = {2011}, author = {Douglas, AE}, title = {Lessons from studying insect symbioses.}, journal = {Cell host & microbe}, volume = {10}, number = {4}, pages = {359-367}, pmid = {22018236}, issn = {1934-6069}, support = {R01 GM095372/GM/NIGMS NIH HHS/United States ; R01 GM095372-01/GM/NIGMS NIH HHS/United States ; 1R01GM095372-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biodiversity ; Host-Parasite Interactions ; Insecta/*microbiology/*physiology ; *Metagenome ; *Symbiosis ; }, abstract = {As in mammals, insect health is strongly influenced by the composition and activities of resident microorganisms. However, the microbiota of insects is generally less diverse than that of mammals, allowing microbial function in insects to be coupled to individual, identified microbial species. This trait of insect symbioses facilitates our understanding of the mechanisms that promote insect-microbial coexistence and the processes by which the microbiota affect insect well-being. As a result, insects are potentially ideal models to study various aspects of interactions between the host and its resident microorganisms that would be impractical or unfeasible in mammals and to generate hypotheses for subsequent testing in mammalian models.}, } @article {pmid22018229, year = {2011}, author = {Mathis, D and Benoist, C}, title = {Microbiota and autoimmune disease: the hosted self.}, journal = {Cell host & microbe}, volume = {10}, number = {4}, pages = {297-301}, doi = {10.1016/j.chom.2011.09.007}, pmid = {22018229}, issn = {1934-6069}, mesh = {Animals ; Autoimmune Diseases/*microbiology ; *Biodiversity ; Disease Models, Animal ; Humans ; *Metagenome ; }, abstract = {The trillions of microbial symbionts normally hosted by mammals have important influences on the development and function of the immune system. We highlight recently discovered cellular and molecular mechanisms by which they impact autoimmune diseases--in particular, gut-distal disorders. Besides provoking a reconsideration of the definition of immunological "self" and "nonself," these new findings evoke exciting possibilities for the discovery of a whole new class of immunomodulatory molecules.}, } @article {pmid22018228, year = {2011}, author = {Knights, D and Parfrey, LW and Zaneveld, J and Lozupone, C and Knight, R}, title = {Human-associated microbial signatures: examining their predictive value.}, journal = {Cell host & microbe}, volume = {10}, number = {4}, pages = {292-296}, pmid = {22018228}, issn = {1934-6069}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; T32 GM008759/GM/NIGMS NIH HHS/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; /HHMI_/Howard Hughes Medical Institute/United States ; U01 HG004866/HG/NHGRI NIH HHS/United States ; K01 DK090285/DK/NIDDK NIH HHS/United States ; }, mesh = {Artificial Intelligence ; *Biodiversity ; Humans ; *Metagenome ; Predictive Value of Tests ; }, abstract = {Host-associated microbial communities are unique to individuals, affect host health, and correlate with disease states. Although advanced technologies capture detailed snapshots of microbial communities, high within- and between-subject variation hampers discovery of microbial signatures in diagnostic or forensic settings. We suggest turning to machine learning and discuss key directions toward harnessing human-associated microbial signatures.}, } @article {pmid22018227, year = {2011}, author = {Proctor, LM}, title = {The Human Microbiome Project in 2011 and beyond.}, journal = {Cell host & microbe}, volume = {10}, number = {4}, pages = {287-291}, doi = {10.1016/j.chom.2011.10.001}, pmid = {22018227}, issn = {1934-6069}, mesh = {*Biodiversity ; Humans ; *Metagenome ; }, abstract = {The human microbiome comprises the genes and genomes of the microbiota that inhabit the body. We highlight Human Microbiome Project (HMP) resources, including 600 microbial reference genomes, 70 million 16S sequences, 700 metagenomes, and 60 million predicted genes from healthy adult microbiomes. Microbiome studies of specific diseases and future research directions are also discussed.}, } @article {pmid22008940, year = {2011}, author = {Marchesi, JR}, title = {Shifting from a gene-centric to metabolite-centric strategy to determine the core gut microbiome.}, journal = {Bioengineered bugs}, volume = {2}, number = {6}, pages = {309-314}, pmid = {22008940}, issn = {1949-1026}, mesh = {Gastrointestinal Tract/*microbiology ; Humans ; Metabolomics/*methods ; Metagenome/*physiology ; Metagenomics/*methods ; Microbial Consortia/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/analysis ; }, abstract = {A key challenge in the area of determining how the microbiome communicates with the host's karyome is deciding which microbial functions should be studied. Ideally we would wish to look at functions which are not only important to the microbial host, but which also play roles in host physiology. Selecting the key microbial functions is essential to developing robust strategies to either promote or demote them, with the aim to enhancing host health. This commentary argues that the bottom-up approach is not providing the necessary gene-set from which we can start to develop a robust core microbiome and in fact we should adopt a top-down strategy in order to indentify the functions that are important and need further study.}, } @article {pmid22006309, year = {2011}, author = {Wu, T and Ayres, E and Bardgett, RD and Wall, DH and Garey, JR}, title = {Molecular study of worldwide distribution and diversity of soil animals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {43}, pages = {17720-17725}, pmid = {22006309}, issn = {1091-6490}, mesh = {Animals ; Base Sequence ; *Biodiversity ; Computational Biology ; DNA Primers/genetics ; Demography ; Hydrogen-Ion Concentration ; Invertebrates/*genetics ; Metagenomics/*methods ; Molecular Sequence Data ; Nitrogen/analysis ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; *Soil ; Species Specificity ; }, abstract = {The global distribution of soil animals and the relationship of below-ground biodiversity to above-ground biodiversity are not well understood. We examined 17,516 environmental 18S rRNA gene sequences representing 20 phyla of soil animals sampled from 11 locations covering a range of biomes and latitudes around the world. No globally cosmopolitan taxa were found and only 14 of 2,259 operational taxonomic units (OTUs) found were common to four or more locations. Half of those were circumpolar and may reflect higher connectivity among circumpolar locations compared with other locations in the study. Even when OTU assembly criteria were relaxed to approximate the family taxonomic level, only 34 OTUs were common to four or more locations. A comparison of our diversity and community structure data to environmental factors suggests that below-ground animal diversity may be inversely related to above-ground biodiversity. Our data suggest that greater soil inorganic N and lower pH could explain the low below-ground biodiversity found at locations of high above-ground biodiversity. Our locations could also be characterized as being dominated by microarthropods or dominated by nematodes. Locations dominated by arthropods were primarily forests with lower soil pH, root biomass, mean annual temperature, low soil inorganic N and higher C:N, litter and moisture compared with nematode-dominated locations, which were mostly grasslands. Overall, our data indicate that small soil animals have distinct biogeographical distributions and provide unique evidence of the link between above-ground and below-ground biodiversity at a global scale.}, } @article {pmid22005039, year = {2011}, author = {Alain, K and Callac, N and Ciobanu, MC and Reynaud, Y and Duthoit, F and Jebbar, M}, title = {DNA extractions from deep subseafloor sediments: novel cryogenic-mill-based procedure and comparison to existing protocols.}, journal = {Journal of microbiological methods}, volume = {87}, number = {3}, pages = {355-362}, doi = {10.1016/j.mimet.2011.09.015}, pmid = {22005039}, issn = {1872-8359}, mesh = {Biodiversity ; Cold Temperature ; DNA, Archaeal/genetics/*isolation & purification ; DNA, Bacterial/genetics/*isolation & purification ; Geologic Sediments/*microbiology ; Liquid-Liquid Extraction/methods ; Metagenomics/*methods ; Specimen Handling/*methods ; }, abstract = {Extracting DNA from deep subsurface sediments is challenging given the complexity of sediments types, low biomasses, resting structures (spores, cysts) frequently encountered in deep sediments, and the potential presence of enzymatic inhibitors. Promising results for cell lysis efficiency were recently obtained by use of a cryogenic mill (Lipp et al., 2008). These findings encouraged us to devise a DNA extraction protocol using this tool. Thirteen procedures involving a combination of grinding in liquid nitrogen (for various durations and beating rates) with different chemical solutions (phenol, chloroform, SDS, sarkosyl, proteinase, GTC), or with use of DNA recovery kits (MagExtractor®) were compared. Effective DNA extraction was evaluated in terms of cell lysis efficiency, DNA extraction efficiency, DNA yield and determination of prokaryotic diversity. Results were compared to those obtained by standard protocols: the FastDNA®SPIN kit for soil and the Zhou protocol. For most sediment types grinding in a cryogenic mill at a low beating rate in combination with direct phenol-chloroform extraction resulted in much higher DNA yields than those obtained using classical procedures. In general (except for clay-rich sediments), this procedure provided high-quality crude extracts for direct downstream nested-PCR, from cell numbers as low as 1.1×10(6) cells/cm(3). This procedure is simple, rapid, low-cost, and could be used with minor modifications for large-scale DNA extractions for a variety of experimental goals.}, } @article {pmid22004549, year = {2012}, author = {Berg Miller, ME and Yeoman, CJ and Chia, N and Tringe, SG and Angly, FE and Edwards, RA and Flint, HJ and Lamed, R and Bayer, EA and White, BA}, title = {Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome.}, journal = {Environmental microbiology}, volume = {14}, number = {1}, pages = {207-227}, doi = {10.1111/j.1462-2920.2011.02593.x}, pmid = {22004549}, issn = {1462-2920}, mesh = {Animals ; Bacteria/genetics/isolation & purification/*virology ; Bacteriophages/*genetics/isolation & purification/metabolism ; Biodiversity ; Cattle ; Computational Biology ; DNA, Bacterial/genetics ; DNA, Viral/genetics ; Genotype ; Interspersed Repetitive Sequences ; Inverted Repeat Sequences ; Metabolome ; *Metagenome ; Rumen/*microbiology/*virology ; Sequence Analysis, DNA ; }, abstract = {Viruses are the most abundant biological entities on the planet and play an important role in balancing microbes within an ecosystem and facilitating horizontal gene transfer. Although bacteriophages are abundant in rumen environments, little is known about the types of viruses present or their interaction with the rumen microbiome. We undertook random pyrosequencing of virus-enriched metagenomes (viromes) isolated from bovine rumen fluid and analysed the resulting data using comparative metagenomics. A high level of diversity was observed with up to 28,000 different viral genotypes obtained from each environment. The majority (~78%) of sequences did not match any previously described virus. Prophages outnumbered lytic phages approximately 2:1 with the most abundant bacteriophage and prophage types being associated with members of the dominant rumen phyla (Firmicutes and Proteobacteria). Metabolic profiling based on SEED subsystems revealed an enrichment of sequences with putative functional roles in DNA and protein metabolism, but a surprisingly low proportion of sequences assigned to carbohydrate and amino acid metabolism. We expanded our analysis to include previously described metagenomic data and 14 reference genomes. Clustered regularly interspaced short palindromic repeats (CRISPR) were detected in most of the microbial genomes, suggesting previous interactions between viral and microbial communities.}, } @article {pmid22004523, year = {2012}, author = {Shade, A and Handelsman, J}, title = {Beyond the Venn diagram: the hunt for a core microbiome.}, journal = {Environmental microbiology}, volume = {14}, number = {1}, pages = {4-12}, doi = {10.1111/j.1462-2920.2011.02585.x}, pmid = {22004523}, issn = {1462-2920}, mesh = {*Ecosystem ; Genomics ; Metabolomics ; *Metagenome ; *Microbial Consortia ; *Phylogeny ; Proteomics ; }, abstract = {Discovering a core microbiome is important for understanding the stable, consistent components across complex microbial assemblages. A core is typically defined as the suite of members shared among microbial consortia from similar habitats, and is represented by the overlapping areas of circles in Venn diagrams, in which each circle contains the membership of the sample or habitats being compared. Ecological insight into core microbiomes can be enriched by 'omics approaches that assess gene expression, thereby extending the concept of the core beyond taxonomically defined membership to community function and behaviour. Parameters defined by traditional ecology theory, such as composition, phylogeny, persistence and connectivity, will also create a more complex portrait of the core microbiome and advance understanding of the role of key microorganisms and functions within and across ecosystems.}, } @article {pmid22003019, year = {2011}, author = {Turpin, W and Humblot, C and Guyot, JP}, title = {Genetic screening of functional properties of lactic acid bacteria in a fermented pearl millet slurry and in the metagenome of fermented starchy foods.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {24}, pages = {8722-8734}, pmid = {22003019}, issn = {1098-5336}, mesh = {Acids/toxicity ; Bile Acids and Salts/toxicity ; *Biota ; DNA, Bacterial/chemistry/genetics ; Feces/microbiology ; Fermentation ; Folic Acid/metabolism ; *Food Microbiology ; Lactobacillus/classification/genetics/*isolation & purification ; *Metagenome ; Microbial Viability/drug effects ; Molecular Sequence Data ; Pediococcus/classification/genetics/*isolation & purification ; Pennisetum/*microbiology ; Riboflavin/metabolism ; Sequence Analysis, DNA ; Starch/metabolism ; }, abstract = {Lactic acid bacteria (LAB) (n = 152) in African pearl millet slurries and in the metagenomes of amylaceous fermented foods were investigated by screening 33 genes involved in probiotic and nutritional functions. All isolates belonged to six species of the genera Pediococcus and Lactobacillus, and Lactobacillus fermentum was the dominant species. We screened the isolates for the abilities to survive passage through the gastrointestinal tract and to synthesize folate and riboflavin. The isolates were also tested in vitro for their abilities to survive exposure to bile salts and to survive at pH 2. Because the ability to hydrolyze starch confers an ecological advantage on LAB that grow in starchy matrixes as well as improving the nutritional properties of the gruels, we screened for genes involved in starch metabolism. The results showed that genes with the potential ability to survive passage through the gastrointestinal tract were widely distributed among isolates and metagenomes, whereas in vitro tests showed that only a limited set of isolates, mainly those belonging to L. fermentum, could tolerate a low pH. In contrast, the wide distribution of genes associated with bile salt tolerance, in particular bsh, is consistent with the high frequency of tolerance to bile salts observed. Genetic screening revealed a potential for folate and riboflavin synthesis in both isolates and metagenomes, as well as high variability among genes related to starch metabolism. Genetic screening of isolates and metagenomes from fermented foods is thus a promising approach for assessing the functional potential of food microbiotas.}, } @article {pmid21996482, year = {2011}, author = {Federici, E and Pepi, M and Esposito, A and Scargetta, S and Fidati, L and Gasperini, S and Cenci, G and Altieri, R}, title = {Two-phase olive mill waste composting: community dynamics and functional role of the resident microbiota.}, journal = {Bioresource technology}, volume = {102}, number = {23}, pages = {10965-10972}, doi = {10.1016/j.biortech.2011.09.062}, pmid = {21996482}, issn = {1873-2976}, mesh = {Bacteria/metabolism ; Biodegradation, Environmental ; Biodiversity ; Biotransformation ; Chemistry, Physical/methods ; DNA/chemistry ; Electrophoresis, Agar Gel ; Hydrogen-Ion Concentration ; Industrial Waste/*analysis ; Metagenome ; *Olea ; Organic Chemicals/chemistry ; Phenols/chemistry ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/metabolism ; Refuse Disposal/methods ; Soil ; Tannins/chemistry ; }, abstract = {In this study, physico-chemical modifications and community dynamics and functional role of the resident microbiota during composting of humid husk from a two-phase extraction system (TPOMW) were investigated. High mineralization and humification of carbon, low loss of nitrogen and complete degradation of polyphenols led to the waste biotransformation into a high-quality compost. Viable cell counts and denaturing gradient gel electrophoresis (DGGE) profiling of the 16S rRNA genes showed that the thermophilic phase was characterized by the strongest variations of cell number, the highest biodiversity and the most variable community profiles. The isolation of tannin-degrading bacteria (e.g. Lysinibacillus fusiformis, Kocuria palustris, Tetrathiobacter kashmirensis and Rhodococcus rhodochrous) suggested a role of this enzymatic activity during the process. Taken together, the results indicated that the composting process, particularly the thermophilic phase, was characterized by a rapid succession of specialized bacterial populations with key roles in the organic matter biotransformation.}, } @article {pmid21993395, year = {2012}, author = {Schmitt, S and Tsai, P and Bell, J and Fromont, J and Ilan, M and Lindquist, N and Perez, T and Rodrigo, A and Schupp, PJ and Vacelet, J and Webster, N and Hentschel, U and Taylor, MW}, title = {Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges.}, journal = {The ISME journal}, volume = {6}, number = {3}, pages = {564-576}, pmid = {21993395}, issn = {1751-7370}, support = {S06 GM044796/GM/NIGMS NIH HHS/United States ; S06-GM-44796/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification/genetics ; *Biodiversity ; DNA, Bacterial/genetics ; Genes, rRNA ; Geography ; *Metagenome ; Oceans and Seas ; Phylogeny ; Porifera/genetics/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Tropical Climate ; }, abstract = {Marine sponges are well known for their associations with highly diverse, yet very specific and often highly similar microbiota. The aim of this study was to identify potential bacterial sub-populations in relation to sponge phylogeny and sampling sites and to define the core bacterial community. 16S ribosomal RNA gene amplicon pyrosequencing was applied to 32 sponge species from eight locations around the world's oceans, thereby generating 2567 operational taxonomic units (OTUs at the 97% sequence similarity level) in total and up to 364 different OTUs per sponge species. The taxonomic richness detected in this study comprised 25 bacterial phyla with Proteobacteria, Chloroflexi and Poribacteria being most diverse in sponges. Among these phyla were nine candidate phyla, six of them found for the first time in sponges. Similarity comparison of bacterial communities revealed no correlation with host phylogeny but a tropical sub-population in that tropical sponges have more similar bacterial communities to each other than to subtropical sponges. A minimal core bacterial community consisting of very few OTUs (97%, 95% and 90%) was found. These microbes have a global distribution and are probably acquired via environmental transmission. In contrast, a large species-specific bacterial community was detected, which is represented by OTUs present in only a single sponge species. The species-specific bacterial community is probably mainly vertically transmitted. It is proposed that different sponges contain different bacterial species, however, these bacteria are still closely related to each other explaining the observed similarity of bacterial communities in sponges in this and previous studies. This global analysis represents the most comprehensive study of bacterial symbionts in sponges to date and provides novel insights into the complex structure of these unique associations.}, } @article {pmid21989224, year = {2012}, author = {Terrat, S and Christen, R and Dequiedt, S and Lelièvre, M and Nowak, V and Regnier, T and Bachar, D and Plassart, P and Wincker, P and Jolivet, C and Bispo, A and Lemanceau, P and Maron, PA and Mougel, C and Ranjard, L}, title = {Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure.}, journal = {Microbial biotechnology}, volume = {5}, number = {1}, pages = {135-141}, pmid = {21989224}, issn = {1751-7915}, mesh = {Bacteria/*classification/genetics/*isolation & purification ; Biodiversity ; Biomass ; DNA, Bacterial/genetics/*isolation & purification ; *Metagenomics ; Molecular Sequence Data ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Three soil DNA extraction procedures (homemade protocols and commercial kit) varying in their practicability were applied to contrasting soils to evaluate their efficiency in recovering: (i) soil DNA and (ii) bacterial diversity estimated by 16S rDNA pyrosequencing. Significant differences in DNA yield were systematically observed between tested procedures. For certain soils, 10 times more DNA was recovered with one protocol than with the others. About 15,000 sequences of 16S rDNA were obtained for each sample which were clustered to draw rarefaction curves. These curves, as well as the PCA ordination of community composition based on OTU clustering, did not reveal any significant difference between procedures. Nevertheless, significant differences between procedures were highlighted by the taxonomic identification of sequences obtained at the phylum to genus levels. Depending on the soil, differences in the number of genera detected ranged from 1% to 26% between the most and least efficient procedures, mainly due to a poorer capacity to recover populations belonging to Actinobacteria, Firmicutes or Crenarchaeota. This study enabled us to rank the relative efficiencies of protocols for their recovery of soil molecular microbial biomass and bacterial diversity and to help choosing an appropriate soil DNA extraction procedure adapted to novel sequencing technologies.}, } @article {pmid21985648, year = {2012}, author = {Bik, HM and Sung, W and De Ley, P and Baldwin, JG and Sharma, J and Rocha-Olivares, A and Thomas, WK}, title = {Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments.}, journal = {Molecular ecology}, volume = {21}, number = {5}, pages = {1048-1059}, pmid = {21985648}, issn = {1365-294X}, support = {P20 RR030360/RR/NCRR NIH HHS/United States ; P20 RR030360-01/RR/NCRR NIH HHS/United States ; 1P20RR030360-01/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; *Biodiversity ; Cluster Analysis ; Eukaryota/*classification ; *Geologic Sediments ; Metagenome ; Metagenomics/*methods ; Oceans and Seas ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {Microbial eukaryotes (nematodes, protists, fungi, etc., loosely referred to as meiofauna) are ubiquitous in marine sediments and probably play pivotal roles in maintaining ecosystem function. Although the deep-sea benthos represents one of the world's largest habitats, we lack a firm understanding of the biodiversity and community interactions amongst meiobenthic organisms in this ecosystem. Within this vast environment, key questions concerning the historical genetic structure of species remain a mystery, yet have profound implications for our understanding of global biodiversity and how we perceive and mitigate the impact of environmental change and anthropogenic disturbance. Using a metagenetic approach, we present an assessment of microbial eukaryote communities across depth (shallow water to abyssal) and ocean basins (deep-sea Pacific and Atlantic). Within the 12 sites examined, our results suggest that some taxa can maintain eurybathic ranges and cosmopolitan deep-sea distributions, but the majority of species appear to be regionally restricted. For Operationally Clustered Taxonomic Units (OCTUs) reporting wide distributions, there appears to be a taxonomic bias towards a small subset of taxa in most phyla; such bias may be driven by specific life history traits amongst these organisms. In addition, low genetic divergence between geographically disparate deep-sea sites suggests either a shorter coalescence time between deep-sea regions or slower rates of evolution across this vast oceanic ecosystem. While high-throughput studies allow for broad assessment of genetic patterns across microbial eukaryote communities, intragenomic variation in rRNA gene copies and the patchy coverage of reference databases currently present substantial challenges for robust taxonomic interpretations of eukaryotic data sets.}, } @article {pmid21972239, year = {2011}, author = {Cantalupo, PG and Calgua, B and Zhao, G and Hundesa, A and Wier, AD and Katz, JP and Grabe, M and Hendrix, RW and Girones, R and Wang, D and Pipas, JM}, title = {Raw sewage harbors diverse viral populations.}, journal = {mBio}, volume = {2}, number = {5}, pages = {}, pmid = {21972239}, issn = {2150-7511}, mesh = {*Biodiversity ; Genome, Viral ; Molecular Sequence Data ; Phylogeny ; Sewage/*virology ; Viruses/*classification/genetics/*isolation & purification ; }, abstract = {UNLABELLED: At this time, about 3,000 different viruses are recognized, but metagenomic studies suggest that these viruses are a small fraction of the viruses that exist in nature. We have explored viral diversity by deep sequencing nucleic acids obtained from virion populations enriched from raw sewage. We identified 234 known viruses, including 17 that infect humans. Plant, insect, and algal viruses as well as bacteriophages were also present. These viruses represented 26 taxonomic families and included viruses with single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), positive-sense ssRNA [ssRNA(+)], and dsRNA genomes. Novel viruses that could be placed in specific taxa represented 51 different families, making untreated wastewater the most diverse viral metagenome (genetic material recovered directly from environmental samples) examined thus far. However, the vast majority of sequence reads bore little or no sequence relation to known viruses and thus could not be placed into specific taxa. These results show that the vast majority of the viruses on Earth have not yet been characterized. Untreated wastewater provides a rich matrix for identifying novel viruses and for studying virus diversity.

IMPORTANCE: At this time, virology is focused on the study of a relatively small number of viral species. Specific viruses are studied either because they are easily propagated in the laboratory or because they are associated with disease. The lack of knowledge of the size and characteristics of the viral universe and the diversity of viral genomes is a roadblock to understanding important issues, such as the origin of emerging pathogens and the extent of gene exchange among viruses. Untreated wastewater is an ideal system for assessing viral diversity because virion populations from large numbers of individuals are deposited and because raw sewage itself provides a rich environment for the growth of diverse host species and thus their viruses. These studies suggest that the viral universe is far more vast and diverse than previously suspected.}, } @article {pmid21966276, year = {2011}, author = {Chandler, JA and Lang, JM and Bhatnagar, S and Eisen, JA and Kopp, A}, title = {Bacterial communities of diverse Drosophila species: ecological context of a host-microbe model system.}, journal = {PLoS genetics}, volume = {7}, number = {9}, pages = {e1002272}, pmid = {21966276}, issn = {1553-7404}, mesh = {Animals ; Bacteria/*classification/genetics/isolation & purification ; *Biodiversity ; Biological Evolution ; Diet ; Drosophila/genetics/*microbiology ; Metagenome ; Models, Biological ; Population ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; }, abstract = {Drosophila melanogaster is emerging as an important model of non-pathogenic host-microbe interactions. The genetic and experimental tractability of Drosophila has led to significant gains in our understanding of animal-microbial symbiosis. However, the full implications of these results cannot be appreciated without the knowledge of the microbial communities associated with natural Drosophila populations. In particular, it is not clear whether laboratory cultures can serve as an accurate model of host-microbe interactions that occur in the wild, or those that have occurred over evolutionary time. To fill this gap, we characterized natural bacterial communities associated with 14 species of Drosophila and related genera collected from distant geographic locations. To represent the ecological diversity of Drosophilids, examined species included fruit-, flower-, mushroom-, and cactus-feeders. In parallel, wild host populations were compared to laboratory strains, and controlled experiments were performed to assess the importance of host species and diet in shaping bacterial microbiome composition. We find that Drosophilid flies have taxonomically restricted bacterial communities, with 85% of the natural bacterial microbiome composed of only four bacterial families. The dominant bacterial taxa are widespread and found in many different host species despite the taxonomic, ecological, and geographic diversity of their hosts. Both natural surveys and laboratory experiments indicate that host diet plays a major role in shaping the Drosophila bacterial microbiome. Despite this, the internal bacterial microbiome represents only a highly reduced subset of the external bacterial communities, suggesting that the host exercises some level of control over the bacteria that inhabit its digestive tract. Finally, we show that laboratory strains provide only a limited model of natural host-microbe interactions. Bacterial taxa used in experimental studies are rare or absent in wild Drosophila populations, while the most abundant associates of natural Drosophila populations are rare in the lab.}, } @article {pmid21957972, year = {2012}, author = {Mühling, M}, title = {On the culture-independent assessment of the diversity and distribution of Prochlorococcus.}, journal = {Environmental microbiology}, volume = {14}, number = {3}, pages = {567-579}, doi = {10.1111/j.1462-2920.2011.02589.x}, pmid = {21957972}, issn = {1462-2920}, mesh = {*Biodiversity ; Genes, Bacterial ; Phylogeny ; Prochlorococcus/*classification/genetics ; Seawater/microbiology ; }, abstract = {Much of our current knowledge on Prochlorococcus has derived from research on various genetic strains that have successfully been brought into culture. In particular, analyses of the complete genomes of 12 of those isolates have revealed the extent to which these strains differ from each other and the genetic means by which they are adapted to specific environmental niches. However, based on culture-independent studies it is now clear that the strains currently available in diverse culture collections do not represent the true diversity of Prochlorococcus geno- and phenotypes. Potential alternatives to overcome the limitations caused by difficulties in isolating Prochlorococcus may be provided by the whole-genome amplification of flow cytometrically isolated individual cells. The new information obtained in this way on various genetic types would, in turn, facilitate the correct identification of Prochlorococcus-derived sequences within metagenomic sequence data sets. However, culture-independent molecular population genetic approaches have also greatly furthered our understanding of the ecology and physiological capability of Prochlorococcus genetic groups. Based on this, I support the notion that such population genetic approaches to reveal the Prochlorococcus microdiversity are still of great value if appropriate marker genes providing a high genetic resolution are used. The comparison of the results from those culture-independent analyses of environmental marine samples with those from the measurement of relevant environmental and biotic parameters still has potential to uncover further parameters that control Prochlorococcus diversity and distribution. In this context, I will discuss those markers that have so far been used in population genetic studies of Prochlorococcus, which is followed by outlining a general approach to evaluate their use for resolving microbial microdiversity and for phylogenetic identification.}, } @article {pmid21955991, year = {2012}, author = {McKenzie, VJ and Bowers, RM and Fierer, N and Knight, R and Lauber, CL}, title = {Co-habiting amphibian species harbor unique skin bacterial communities in wild populations.}, journal = {The ISME journal}, volume = {6}, number = {3}, pages = {588-596}, pmid = {21955991}, issn = {1751-7370}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Ambystoma/*microbiology ; Animals ; Anura/*microbiology ; Bacteria/*classification/genetics ; Biodiversity ; Colorado ; DNA, Bacterial/genetics ; *Metagenome ; Ponds/microbiology ; RNA, Ribosomal, 16S/genetics ; Ranidae/*microbiology ; Sequence Analysis, DNA ; Skin/*microbiology ; Species Specificity ; }, abstract = {Although all plant and animal species harbor microbial symbionts, we know surprisingly little about the specificity of microbial communities to their hosts. Few studies have compared the microbiomes of different species of animals, and fewer still have examined animals in the wild. We sampled four pond habitats in Colorado, USA, where multiple amphibian species were present. In total, 32 amphibian individuals were sampled from three different species including northern leopard frogs (Lithobates pipiens), western chorus frogs (Pseudacris triseriata) and tiger salamanders (Ambystoma tigrinum). We compared the diversity and composition of the bacterial communities on the skin of the collected individuals via barcoded pyrosequencing of the 16S rRNA gene. Dominant bacterial phyla included Acidobacteria, Actinobacteria, Bacteriodetes, Cyanobacteria, Firmicutes and Proteobacteria. In total, we found members of 18 bacterial phyla, comparable to the taxonomic diversity typically found on human skin. Levels of bacterial diversity varied strongly across species: L. pipiens had the highest diversity; A. tigrinum the lowest. Host species was a highly significant predictor of bacterial community similarity, and co-habitation within the same pond was not significant, highlighting that the skin-associated bacterial communities do not simply reflect those bacterial communities found in their surrounding environments. Innate species differences thus appear to regulate the structure of skin bacterial communities on amphibians. In light of recent discoveries that some bacteria on amphibian skin have antifungal activity, our finding suggests that host-specific bacteria may have a role in the species-specific resistance to fungal pathogens.}, } @article {pmid21938024, year = {2012}, author = {Godoy-Vitorino, F and Goldfarb, KC and Karaoz, U and Leal, S and Garcia-Amado, MA and Hugenholtz, P and Tringe, SG and Brodie, EL and Dominguez-Bello, MG}, title = {Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows.}, journal = {The ISME journal}, volume = {6}, number = {3}, pages = {531-541}, pmid = {21938024}, issn = {1751-7370}, mesh = {Animals ; Bacteria/*classification/genetics ; Biodiversity ; Biological Evolution ; Birds/*microbiology ; Cattle/*microbiology ; Cecum/*microbiology ; Cluster Analysis ; Crop, Avian/*microbiology ; Genes, rRNA ; *Metagenome ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Rumen/microbiology ; Species Specificity ; }, abstract = {Foregut fermentation occurs in mammalian ruminants and in one bird, the South American folivorous hoatzin. This bird has an enlarged crop with a function analogous to the rumen, where foregut microbes degrade the otherwise indigestible plant matter, providing energy to the host from foregut fermentation, in addition to the fermentation that occurs in their hindguts (cecum/colon). As foregut fermentation represents an evolutionary convergence between hoatzins and ruminants, our aim was to compare the community structure of foregut and hindgut bacterial communities in the cow and hoatzin to evaluate the influences of host phylogeny and organ function in shaping the gut microbiome. The approach used was to hybridize amplified bacterial ribosomal RNA genes onto a high-density microarray (PhyloChip). The results show that the microbial communities cluster primarily by functional environment (foreguts cluster separately from hindguts) and then by host. Bacterial community diversity was higher in the cow than in the hoatzin. Overall, compared with hindguts, foreguts have higher proportions of Bacteroidetes and Spirochaetes, and lower proportions of Firmicutes and Proteobacteria. The main host differences in gut bacterial composition include a higher representation of Spirochaetes, Synergistetes and Verrucomicrobia in the cow. Despite the significant differences in host phylogeny, body size, physiology and diet, the function seems to shape the microbial communities involved in fermentation. Regardless of the independent origin of foregut fermentation in birds and mammals, organ function has led to convergence of the microbial community structure in phylogenetically distant hosts.}, } @article {pmid21912589, year = {2011}, author = {Kembel, SW and Eisen, JA and Pollard, KS and Green, JL}, title = {The phylogenetic diversity of metagenomes.}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e23214}, pmid = {21912589}, issn = {1932-6203}, mesh = {Aquatic Organisms/classification/genetics/microbiology ; *Biodiversity ; Genetic Markers/genetics ; Metagenome/*genetics ; Metagenomics ; *Microbiology ; *Phylogeny ; RNA, Ribosomal/genetics ; Ribosome Subunits, Small/genetics ; }, abstract = {Phylogenetic diversity--patterns of phylogenetic relatedness among organisms in ecological communities--provides important insights into the mechanisms underlying community assembly. Studies that measure phylogenetic diversity in microbial communities have primarily been limited to a single marker gene approach, using the small subunit of the rRNA gene (SSU-rRNA) to quantify phylogenetic relationships among microbial taxa. In this study, we present an approach for inferring phylogenetic relationships among microorganisms based on the random metagenomic sequencing of DNA fragments. To overcome challenges caused by the fragmentary nature of metagenomic data, we leveraged fully sequenced bacterial genomes as a scaffold to enable inference of phylogenetic relationships among metagenomic sequences from multiple phylogenetic marker gene families. The resulting metagenomic phylogeny can be used to quantify the phylogenetic diversity of microbial communities based on metagenomic data sets. We applied this method to understand patterns of microbial phylogenetic diversity and community assembly along an oceanic depth gradient, and compared our findings to previous studies of this gradient using SSU-rRNA gene and metagenomic analyses. Bacterial phylogenetic diversity was highest at intermediate depths beneath the ocean surface, whereas taxonomic diversity (diversity measured by binning sequences into taxonomically similar groups) showed no relationship with depth. Phylogenetic diversity estimates based on the SSU-rRNA gene and the multi-gene metagenomic phylogeny were broadly concordant, suggesting that our approach will be applicable to other metagenomic data sets for which corresponding SSU-rRNA gene sequences are unavailable. Our approach opens up the possibility of using metagenomic data to study microbial diversity in a phylogenetic context.}, } @article {pmid21909446, year = {2011}, author = {McCarthy, CB and Diambra, LA and Rivera Pomar, RV}, title = {Metagenomic analysis of taxa associated with Lutzomyia longipalpis, vector of visceral leishmaniasis, using an unbiased high-throughput approach.}, journal = {PLoS neglected tropical diseases}, volume = {5}, number = {9}, pages = {e1304}, pmid = {21909446}, issn = {1935-2735}, mesh = {Animals ; Argentina ; *Biodiversity ; Brazil ; *Disease Vectors ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Latin America ; Male ; Metagenome/*genetics ; Plants/genetics ; Psychodidae/*parasitology ; RNA/genetics/isolation & purification ; }, abstract = {BACKGROUND: Leishmaniasis is one of the most diverse and complex of all vector-borne diseases worldwide. It is caused by parasites of the genus Leishmania, obligate intramacrophage protists characterised by diversity and complexity. Its most severe form is visceral leishmaniasis (VL), a systemic disease that is fatal if left untreated. In Latin America VL is caused by Leishmania infantum chagasi and transmitted by Lutzomyia longipalpis. This phlebotomine sandfly is only found in the New World, from Mexico to Argentina. In South America, migration and urbanisation have largely contributed to the increase of VL as a public health problem. Moreover, the first VL outbreak was recently reported in Argentina, which has already caused 7 deaths and 83 reported cases.

An inventory of the microbiota associated with insect vectors, especially of wild specimens, would aid in the development of novel strategies for controlling insect vectors. Given the recent VL outbreak in Argentina and the compelling need to develop appropriate control strategies, this study focused on wild male and female Lu. longipalpis from an Argentine endemic (Posadas, Misiones) and a Brazilian non-endemic (Lapinha Cave, Minas Gerais) VL location. Previous studies on wild and laboratory reared female Lu. longipalpis have described gut bacteria using standard bacteriological methods. In this study, total RNA was extracted from the insects and submitted to high-throughput pyrosequencing. The analysis revealed the presence of sequences from bacteria, fungi, protist parasites, plants and metazoans.

CONCLUSIONS/SIGNIFICANCE: This is the first time an unbiased and comprehensive metagenomic approach has been used to survey taxa associated with an infectious disease vector. The identification of gregarines suggested they are a possible efficient control method under natural conditions. Ongoing studies are determining the significance of the associated taxa found in this study in a greater number of adult male and female Lu. longipalpis samples from endemic and non-endemic locations. A particular emphasis is being given to those species involved in the biological control of this vector and to the etiologic agents of animal and plant diseases.}, } @article {pmid21908188, year = {2011}, author = {Chojnacka, A and Błaszczyk, MK and Szczęsny, P and Nowak, K and Sumińska, M and Tomczyk-Żak, K and Zielenkiewicz, U and Sikora, A}, title = {Comparative analysis of hydrogen-producing bacterial biofilms and granular sludge formed in continuous cultures of fermentative bacteria.}, journal = {Bioresource technology}, volume = {102}, number = {21}, pages = {10057-10064}, doi = {10.1016/j.biortech.2011.08.063}, pmid = {21908188}, issn = {1873-2976}, mesh = {Biodiversity ; Biofilms/*growth & development ; Bioreactors/microbiology ; Cell Culture Techniques/*methods ; Clostridium/cytology/growth & development/*physiology ; Fermentation/*physiology ; Hydrogen/*metabolism ; Leuconostocaceae/cytology/growth & development/*physiology ; Molasses ; Sewage/*microbiology ; }, abstract = {A system for biohydrogen production was developed based on long-term continuous cultures grown on sugar beet molasses in packed bed reactors. In two separate cultures, consortia of fermentative bacteria developed as biofilms on granitic stones. In one of the cultures, a granular sludge was also formed. Metagenomic analysis of the microbial communities by 454-pyrosequencing of amplified 16S rDNA fragments revealed that the overall biodiversity of the hydrogen-producing cultures was quite small. The stone biofilm from the culture without granular sludge was dominated by Clostridiaceae and heterolactic fermentation bacteria, mainly Leuconostocaeae. Representatives of the Leuconostocaeae and Enterobacteriaceae were dominant in both the granules and the stone biofilm formed in the granular sludge culture. The culture containing granular sludge produced hydrogen significantly more effectively than that containing only the stone biofilm: 5.43 vs. 2.8 mol H(2)/mol sucrose from molasses, respectively. The speculations that lactic acid bacteria may favor hydrogen production are discussed.}, } @article {pmid21900163, year = {2011}, author = {Shan, T and Li, L and Simmonds, P and Wang, C and Moeser, A and Delwart, E}, title = {The fecal virome of pigs on a high-density farm.}, journal = {Journal of virology}, volume = {85}, number = {22}, pages = {11697-11708}, pmid = {21900163}, issn = {1098-5514}, support = {095831/WT_/Wellcome Trust/United Kingdom ; R01 HL083254/HL/NHLBI NIH HHS/United States ; R01HL083254/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Animals, Domestic/virology ; *Biodiversity ; Diarrhea/*veterinary/virology ; Feces/*virology ; Humans ; Metagenome ; Molecular Sequence Data ; Sequence Analysis, DNA ; Swine/virology ; Swine Diseases/*virology ; Viruses/*classification/genetics/*isolation & purification ; }, abstract = {Swine are an important source of proteins worldwide but are subject to frequent viral outbreaks and numerous infections capable of infecting humans. Modern farming conditions may also increase viral transmission and potential zoonotic spread. We describe here the metagenomics-derived virome in the feces of 24 healthy and 12 diarrheic piglets on a high-density farm. An average of 4.2 different mammalian viruses were shed by healthy piglets, reflecting a high level of asymptomatic infections. Diarrheic pigs shed an average of 5.4 different mammalian viruses. Ninety-nine percent of the viral sequences were related to the RNA virus families Picornaviridae, Astroviridae, Coronaviridae, and Caliciviridae, while 1% were related to the small DNA virus families Circoviridae, and Parvoviridae. Porcine RNA viruses identified, in order of decreasing number of sequence reads, consisted of kobuviruses, astroviruses, enteroviruses, sapoviruses, sapeloviruses, coronaviruses, bocaviruses, and teschoviruses. The near-full genomes of multiple novel species of porcine astroviruses and bocaviruses were generated and phylogenetically analyzed. Multiple small circular DNA genomes encoding replicase proteins plus two highly divergent members of the Picornavirales order were also characterized. The possible origin of these viral genomes from pig-infecting protozoans and nematodes, based on closest sequence similarities, is discussed. In summary, an unbiased survey of viruses in the feces of intensely farmed animals revealed frequent coinfections with a highly diverse set of viruses providing favorable conditions for viral recombination. Viral surveys of animals can readily document the circulation of known and new viruses, facilitating the detection of emerging viruses and prospective evaluation of their pathogenic and zoonotic potentials.}, } @article {pmid21893414, year = {2011}, author = {Cowan, DA and Chown, SL and Convey, P and Tuffin, M and Hughes, K and Pointing, S and Vincent, WF}, title = {Non-indigenous microorganisms in the Antarctic: assessing the risks.}, journal = {Trends in microbiology}, volume = {19}, number = {11}, pages = {540-548}, doi = {10.1016/j.tim.2011.07.008}, pmid = {21893414}, issn = {1878-4380}, mesh = {Antarctic Regions ; Climate Change ; *Ecosystem ; *Environmental Microbiology ; Environmental Pollution ; Human Activities ; Humans ; *Introduced Species ; }, abstract = {The Antarctic continent is frequently cited as the last pristine continent on Earth. However, this view is misleading for several reasons. First, there has been a rapid increase in visitors to Antarctica, with large increases at research bases and their environs and to sites of major tourist interest (e.g. historical sites and concentrations of megafauna). Second, although substantial efforts are made to avoid physical disturbance and contamination by chemical, human and other wastes at these sites, little has been done to prevent the introduction of non-indigenous microorganisms. Here, we analyse the extent and significance of anthropogenic introduction of microbial 'contaminants' to the Antarctic continent. We conclude that such processes are unlikely to have any immediate gross impact on microbiological community structure or function, but that increased efforts are required to protect the unique ecosystems of Antarctica from microbial and genetic contamination and homogenisation.}, } @article {pmid21875444, year = {2011}, author = {Yap, GC and Chee, KK and Hong, PY and Lay, C and Satria, CD and Sumadiono, and Soenarto, Y and Haksari, EL and Aw, M and Shek, LP and Chua, KY and Zhao, Y and Leow, D and Lee, BW}, title = {Evaluation of stool microbiota signatures in two cohorts of Asian (Singapore and Indonesia) newborns at risk of atopy.}, journal = {BMC microbiology}, volume = {11}, number = {}, pages = {193}, pmid = {21875444}, issn = {1471-2180}, support = {08/1/21/19/566//Medical Research Council/United Kingdom ; }, mesh = {*Biodiversity ; Feces/*microbiology ; Humans ; Indonesia ; Infant ; Infant, Newborn ; Longitudinal Studies ; *Metagenome ; Singapore ; Socioeconomic Factors ; }, abstract = {BACKGROUND: Studies have suggested that demographic and lifestyle factors could shape the composition of fecal microbiota in early life. This study evaluated infant stool microbiota signatures in two Asian populations, Singapore (n = 42) and Indonesia (n = 32) with contrasting socioeconomic development, and examined the putative influences of demographic factors on these human fecal associated bacterial signatures.

RESULTS: Longitudinal analysis showed associations of geographical origin with Clostridium leptum, Atopobium and Bifidobacterium groups. Mode of delivery had the largest effect on stool microbiota signatures influencing the abundance of four bacterial groups. Significantly higher abundance of bacterial members belonging to the Bacteroides-Prevotella, Bifidobacterium and Atopobium groups, but lower abundance of Lactobacilli-Enterococci group members, were observed in vaginal delivered compared to caesarean delivered infants. Demographic factors influencing the structure of infants stool microbiota during the first year of life included breastfeeding, age of weaning, sibship size and exposure to antibiotics.

CONCLUSIONS: Differences in stool microbiota signatures were observed in relation to various demographic factors. These features may confound studies relating to the association of the structure of fecal microbiota and the predisposition to human modern disease.}, } @article {pmid21875091, year = {2011}, author = {Rath, CM and Janto, B and Earl, J and Ahmed, A and Hu, FZ and Hiller, L and Dahlgren, M and Kreft, R and Yu, F and Wolff, JJ and Kweon, HK and Christiansen, MA and Håkansson, K and Williams, RM and Ehrlich, GD and Sherman, DH}, title = {Meta-omic characterization of the marine invertebrate microbial consortium that produces the chemotherapeutic natural product ET-743.}, journal = {ACS chemical biology}, volume = {6}, number = {11}, pages = {1244-1256}, pmid = {21875091}, issn = {1554-8937}, support = {CA070375/CA/NCI NIH HHS/United States ; U01 TW007404/TW/FIC NIH HHS/United States ; R01 CA070375/CA/NCI NIH HHS/United States ; R01 CA070375-08/CA/NCI NIH HHS/United States ; C76HF00659//PHS HHS/United States ; U01 TW007404-08/TW/FIC NIH HHS/United States ; R01 DC002148/DC/NIDCD NIH HHS/United States ; }, mesh = {Animals ; Antineoplastic Agents/chemistry/*metabolism ; Biological Products/chemistry/*metabolism ; Dioxoles/chemistry/*metabolism ; Gene Library ; *Metagenome ; Microbial Consortia/genetics/*physiology ; Molecular Conformation ; Phylogeny ; Proteomics ; Sequence Analysis, DNA ; Tetrahydroisoquinolines/chemistry/*metabolism ; Trabectedin ; Urochordata/genetics/*microbiology ; }, abstract = {In many macroorganisms, the ultimate source of potent biologically active natural products has remained elusive due to an inability to identify and culture the producing symbiotic microorganisms. As a model system for developing a meta-omic approach to identify and characterize natural product pathways from invertebrate-derived microbial consortia, we chose to investigate the ET-743 (Yondelis) biosynthetic pathway. This molecule is an approved anticancer agent obtained in low abundance (10(-4)-10(-5) % w/w) from the tunicate Ecteinascidia turbinata and is generated in suitable quantities for clinical use by a lengthy semisynthetic process. On the basis of structural similarities to three bacterial secondary metabolites, we hypothesized that ET-743 is the product of a marine bacterial symbiont. Using metagenomic sequencing of total DNA from the tunicate/microbial consortium, we targeted and assembled a 35 kb contig containing 25 genes that comprise the core of the NRPS biosynthetic pathway for this valuable anticancer agent. Rigorous sequence analysis based on codon usage of two large unlinked contigs suggests that Candidatus Endoecteinascidia frumentensis produces the ET-743 metabolite. Subsequent metaproteomic analysis confirmed expression of three key biosynthetic proteins. Moreover, the predicted activity of an enzyme for assembly of the tetrahydroisoquinoline core of ET-743 was verified in vitro. This work provides a foundation for direct production of the drug and new analogues through metabolic engineering. We expect that the interdisciplinary approach described is applicable to diverse host-symbiont systems that generate valuable natural products for drug discovery and development.}, } @article {pmid21873488, year = {2011}, author = {Lee, S and Sung, J and Lee, J and Ko, G}, title = {Comparison of the gut microbiotas of healthy adult twins living in South Korea and the United States.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {20}, pages = {7433-7437}, pmid = {21873488}, issn = {1098-5336}, mesh = {Adult ; *Biodiversity ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; Phylogeography ; Republic of Korea ; Twins ; United States ; }, abstract = {We compared the composition of the fecal microbiotas of Korean and U.S. adult twins. Our data indicated that the gut microbiota shows some signature of biogeography, potentially mediated by differences in diet and/or other environmental factors; however, these regional differences may be masked by other phenotypic variations, such as obesity.}, } @article {pmid21869815, year = {2011}, author = {Gill, N and Finlay, BB}, title = {The gut microbiota: challenging immunology.}, journal = {Nature reviews. Immunology}, volume = {11}, number = {10}, pages = {636-637}, pmid = {21869815}, issn = {1474-1741}, support = {//Canadian Institutes of Health Research/Canada ; //Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; *Gastrointestinal Tract/immunology/microbiology ; Humans ; *Immunity ; Metagenome/*immunology ; Mice ; Microbial Consortia/*immunology ; }, abstract = {For several decades the intestinal microbiota was mainly studied by those investigating infections and diseases associated with gut health, usually from a microbiology point of view. In the past few years, however, it has become apparent that the intestinal microbiota has widespread implications in the field of immunology, and researchers are being compelled to explain how the microbiota contributes to and/or affects their studies.}, } @article {pmid21858083, year = {2011}, author = {Nasidze, I and Li, J and Schroeder, R and Creasey, JL and Li, M and Stoneking, M}, title = {High diversity of the saliva microbiome in Batwa Pygmies.}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e23352}, pmid = {21858083}, issn = {1932-6203}, mesh = {Bacteria/classification/genetics/growth & development ; Biodiversity ; DNA, Bacterial/analysis/genetics ; Democratic Republic of the Congo ; *Genetic Variation ; Geography ; Humans ; Metagenome/*genetics ; Polymerase Chain Reaction ; Population Dynamics ; Principal Component Analysis ; RNA, Ribosomal, 16S/*genetics ; Saliva/*microbiology ; Sequence Analysis, DNA ; Sierra Leone ; Species Specificity ; Uganda ; }, abstract = {We describe the saliva microbiome diversity in Batwa Pygmies, a former hunter-gatherer group from Uganda, using next-generation sequencing of partial 16S rRNA sequences. Microbial community diversity in the Batwa is significantly higher than in agricultural groups from Sierra Leone and the Democratic Republic of Congo. We found 40 microbial genera in the Batwa, which have previously not been described in the human oral cavity. The distinctive composition of the salvia microbiome of the Batwa may have been influenced by their recent different lifestyle and diet.}, } @article {pmid21850056, year = {2012}, author = {Wang, T and Cai, G and Qiu, Y and Fei, N and Zhang, M and Pang, X and Jia, W and Cai, S and Zhao, L}, title = {Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers.}, journal = {The ISME journal}, volume = {6}, number = {2}, pages = {320-329}, pmid = {21850056}, issn = {1751-7370}, mesh = {Acyl Coenzyme A/genetics ; Adult ; Aged ; Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; Coenzyme A-Transferases/genetics ; Colorectal Neoplasms/*microbiology ; Feces/microbiology ; Female ; Gastrointestinal Tract/chemistry/*microbiology ; Humans ; Male ; *Metagenome ; Middle Aged ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; }, abstract = {Despite a long-suspected role in the development of human colorectal cancer (CRC), the composition of gut microbiota in CRC patients has not been adequately described. In this study, fecal bacterial diversity in CRC patients (n=46) and healthy volunteers (n=56) were profiled by 454 pyrosequencing of the V3 region of the 16S ribosomal RNA gene. Both principal component analysis and UniFrac analysis showed structural segregation between the two populations. Forty-eight operational taxonomic units (OTUs) were identified by redundancy analysis as key variables significantly associated with the structural difference. One OTU closely related to Bacteroides fragilis was enriched in the gut microbiota of CRC patients, whereas three OTUs related to Bacteroides vulgatus and Bacteroides uniformis were enriched in that of healthy volunteers. A total of 11 OTUs belonging to the genera Enterococcus, Escherichia/Shigella, Klebsiella, Streptococcus and Peptostreptococcus were significantly more abundant in the gut microbiota of CRC patients, and 5 OTUs belonging to the genus Roseburia and other butyrate-producing bacteria of the family Lachnospiraceae were less abundant. Real-time quantitative PCR further validated the significant reduction of butyrate-producing bacteria in the gut microbiota of CRC patients by measuring the copy numbers of butyryl-coenzyme A CoA transferase genes (Mann-Whitney test, P<0.01). Reduction of butyrate producers and increase of opportunistic pathogens may constitute a major structural imbalance of gut microbiota in CRC patients.}, } @article {pmid21844636, year = {2012}, author = {Su, CH and Wang, TY and Hsu, MT and Weng, FC and Kao, CY and Wang, D and Tsai, HK}, title = {The impact of normalization and phylogenetic information on estimating the distance for metagenomes.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {9}, number = {2}, pages = {619-628}, doi = {10.1109/TCBB.2011.111}, pmid = {21844636}, issn = {1557-9964}, mesh = {*Cluster Analysis ; Databases, Genetic ; Environmental Microbiology ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/genetics ; Models, Genetic ; *Phylogeny ; }, abstract = {Metagenomics enables the study of unculturable microorganisms in different environments directly. Discriminating between the compositional differences of metagenomes is an important and challenging problem. Several distance functions have been proposed to estimate the differences based on functional profiles or taxonomic distributions; however, the strengths and limitations of such functions are still unclear. Initially, we analyzed three well-known distance functions and found very little difference between them in the clustering of samples. This motivated us to incorporate suitable normalizations and phylogenetic information into the functions so that we could cluster samples from both real and synthetic data sets. The results indicate significant improvement in sample clustering over that derived by rank-based normalization with phylogenetic information, regardless of whether the samples are from real or synthetic microbiomes. Furthermore, our findings suggest that considering suitable normalizations and phylogenetic information is essential when designing distance functions for estimating the differences between metagenomes. We conclude that incorporating rank-based normalization with phylogenetic information into the distance functions helps achieve reliable clustering results.}, } @article {pmid21841025, year = {2011}, author = {Reid, NM and Addison, SL and Macdonald, LJ and Lloyd-Jones, G}, title = {Biodiversity of active and inactive bacteria in the gut flora of wood-feeding huhu beetle larvae (Prionoplus reticularis).}, journal = {Applied and environmental microbiology}, volume = {77}, number = {19}, pages = {7000-7006}, pmid = {21841025}, issn = {1098-5336}, mesh = {Animals ; Bacteria/*classification/*genetics ; *Biodiversity ; Coleoptera/*microbiology ; DNA, Bacterial/chemistry/genetics ; Gastrointestinal Tract/microbiology ; Larva/microbiology ; Metagenome ; Molecular Sequence Data ; New Zealand ; Sequence Analysis, DNA ; }, abstract = {Huhu grubs (Prionoplus reticularis) are wood-feeding beetle larvae endemic to New Zealand and belonging to the family Cerambycidae. Compared to the wood-feeding lower termites, very little is known about the diversity and activity of microorganisms associated with xylophagous cerambycid larvae. To address this, we used pyrosequencing to evaluate the diversity of metabolically active and inactive bacteria in the huhu larval gut. Our estimate, that the gut harbors at least 1,800 phylotypes, is based on 33,420 sequences amplified from genomic DNA and reverse-transcribed RNA. Analysis of genomic DNA- and RNA-derived data sets revealed that 71% of all phylotypes (representing 95% of all sequences) were metabolically active. Rare phylotypes contributed considerably to the richness of the community and were also largely metabolically active, indicating their participation in digestive processes in the gut. The dominant families in the active community (RNA data set) included Acidobacteriaceae (24.3%), Xanthomonadaceae (16.7%), Acetobacteraceae (15.8%), Burkholderiaceae (8.7%), and Enterobacteriaceae (4.1%). The most abundant phylotype comprised 14% of the active community and affiliated with Dyella ginsengisoli (Gammaproteobacteria), suggesting that a Dyella-related organism is a likely symbiont. This study provides new information on the diversity and activity of gut-associated microorganisms that are essential for the digestion of the nutritionally poor diet consumed by wood-feeding larvae. Many huhu gut phylotypes affiliated with insect symbionts or with bacteria present in acidic environments or associated with fungi.}, } @article {pmid21829636, year = {2011}, author = {Ardura, A and Planes, S and Garcia-Vazquez, E}, title = {Beyond biodiversity: fish metagenomes.}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e22592}, pmid = {21829636}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Fishes/classification/*genetics ; *Genome ; }, abstract = {Biodiversity and intra-specific genetic diversity are interrelated and determine the potential of a community to survive and evolve. Both are considered together in Prokaryote communities treated as metagenomes or ensembles of functional variants beyond species limits.Many factors alter biodiversity in higher Eukaryote communities, and human exploitation can be one of the most important for some groups of plants and animals. For example, fisheries can modify both biodiversity and genetic diversity (intra specific). Intra-specific diversity can be drastically altered by overfishing. Intense fishing pressure on one stock may imply extinction of some genetic variants and subsequent loss of intra-specific diversity. The objective of this study was to apply a metagenome approach to fish communities and explore its value for rapid evaluation of biodiversity and genetic diversity at community level. Here we have applied the metagenome approach employing the barcoding target gene coi as a model sequence in catch from four very different fish assemblages exploited by fisheries: freshwater communities from the Amazon River and northern Spanish rivers, and marine communities from the Cantabric and Mediterranean seas.Treating all sequences obtained from each regional catch as a biological unit (exploited community) we found that metagenomic diversity indices of the Amazonian catch sample here examined were lower than expected. Reduced diversity could be explained, at least partially, by overexploitation of the fish community that had been independently estimated by other methods.We propose using a metagenome approach for estimating diversity in Eukaryote communities and early evaluating genetic variation losses at multi-species level.}, } @article {pmid21829583, year = {2011}, author = {Gómez-Hurtado, I and Santacruz, A and Peiró, G and Zapater, P and Gutiérrez, A and Pérez-Mateo, M and Sanz, Y and Francés, R}, title = {Gut microbiota dysbiosis is associated with inflammation and bacterial translocation in mice with CCl4-induced fibrosis.}, journal = {PloS one}, volume = {6}, number = {7}, pages = {e23037}, pmid = {21829583}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/*genetics/metabolism ; *Bacterial Translocation ; Biodiversity ; Biomarkers/metabolism ; Carbon Tetrachloride Poisoning ; DNA, Bacterial/genetics ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology/*pathology ; Gene Expression Profiling ; Inflammation/complications/*pathology ; Laparotomy ; Liver Cirrhosis/chemically induced/complications/*pathology/surgery ; Metagenome/*genetics ; Mice ; Mice, Inbred BALB C ; Real-Time Polymerase Chain Reaction ; }, abstract = {BACKGROUND: Gut is the major source of endogenous bacteria causing infections in advanced cirrhosis. Intestinal barrier dysfunction has been described in cirrhosis and account for an increased bacterial translocation rate.

HYPOTHESIS AND AIMS: We hypothesize that microbiota composition may be affected and change along with the induction of experimental cirrhosis, affecting the inflammatory response.

ANIMALS AND METHODS: Progressive liver damage was induced in Balb/c mice by weight-controlled oral administration of carbon tetrachloride. Laparotomies were performed at weeks 6, 10, 13 and 16 in a subgroup of treated mice (n = 6/week) and control animals (n = 4/week). Liver tissue specimens, mesenteric lymph nodes, intestinal content and blood were collected at laparotomies. Fibrosis grade, pro-fibrogenic genes expression, gut bacterial composition, bacterial translocation, host's specific butyrate-receptor GPR-43 and serum cytokine levels were measured.

RESULTS: Expression of pro-fibrogenic markers was significantly increased compared with control animals and correlated with the accumulated dose of carbon tetrachloride. Bacterial translocation episodes were less frequent in control mice than in treated animals. Gram-positive anaerobic Clostridia spp count was decreased in treated mice compared with control animals and with other gut common bacterial species, altering the aerobic/anaerobic ratio. This fact was associated with a decreased gene expression of GPR43 in neutrophils of treated mice and inversely correlated with TNF-alpha and IL-6 up-regulation in serum of treated mice along the study protocol. This pro-inflammatory scenario favoured blood bacterial translocation in treated animals, showing the highest bacterial translocation rate and aerobic/anaerobic ratio at the same weeks.

CONCLUSIONS: Gut microbiota alterations are associated with the development of an inflammatory environment, fibrosis progression and bacterial translocation in carbon tetrachloride-treated mice.}, } @article {pmid21829582, year = {2011}, author = {Jalanka-Tuovinen, J and Salonen, A and Nikkilä, J and Immonen, O and Kekkonen, R and Lahti, L and Palva, A and de Vos, WM}, title = {Intestinal microbiota in healthy adults: temporal analysis reveals individual and common core and relation to intestinal symptoms.}, journal = {PloS one}, volume = {6}, number = {7}, pages = {e23035}, pmid = {21829582}, issn = {1932-6203}, mesh = {Adult ; Bacteria/*classification/*genetics ; Biodiversity ; Biomarkers/metabolism ; DNA, Bacterial/genetics ; Double-Blind Method ; Feces/microbiology ; Female ; Gene Expression Profiling ; Humans ; Intestinal Diseases/diagnosis/*genetics/microbiology ; Intestines/*microbiology ; Longitudinal Studies ; Male ; Metagenome/*genetics ; Middle Aged ; *Oligonucleotide Array Sequence Analysis ; Phylogeny ; RNA, Messenger/genetics ; RNA, Ribosomal, 16S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {BACKGROUND: While our knowledge of the intestinal microbiota during disease is accumulating, basic information of the microbiota in healthy subjects is still scarce. The aim of this study was to characterize the intestinal microbiota of healthy adults and specifically address its temporal stability, core microbiota and relation with intestinal symptoms. We carried out a longitudinal study by following a set of 15 healthy Finnish subjects for seven weeks and regularly assessed their intestinal bacteria and archaea with the Human Intestinal Tract (HIT) Chip, a phylogenetic microarray, in conjunction with qPCR analyses. The health perception and occurrence of intestinal symptoms was recorded by questionnaire at each sampling point.

PRINCIPAL FINDINGS: A high overall temporal stability of the microbiota was observed. Five subjects showed transient microbiota destabilization, which correlated not only with the intake of antibiotics but also with overseas travelling and temporary illness, expanding the hitherto known factors affecting the intestinal microbiota. We identified significant correlations between the microbiota and common intestinal symptoms, including abdominal pain and bloating. The most striking finding was the inverse correlation between Bifidobacteria and abdominal pain: subjects who experienced pain had over five-fold less Bifidobacteria compared to those without pain. Finally, a novel computational approach was used to define the common core microbiota, highlighting the role of the analysis depth in finding the phylogenetic core and estimating its size. The in-depth analysis suggested that we share a substantial number of our intestinal phylotypes but as they represent highly variable proportions of the total community, many of them often remain undetected.

CONCLUSIONS/SIGNIFICANCE: A global and high-resolution microbiota analysis was carried out to determine the temporal stability, the associations with intestinal symptoms, and the individual and common core microbiota in healthy adults. The findings provide new approaches to define intestinal health and to further characterize the microbial communities inhabiting the human gut.}, } @article {pmid21829462, year = {2011}, author = {Peris-Bondia, F and Latorre, A and Artacho, A and Moya, A and D'Auria, G}, title = {The active human gut microbiota differs from the total microbiota.}, journal = {PloS one}, volume = {6}, number = {7}, pages = {e22448}, pmid = {21829462}, issn = {1932-6203}, mesh = {Adult ; Bacteria/classification/*genetics ; *Bacterial Typing Techniques ; *Biodiversity ; Feces/*microbiology ; Flow Cytometry ; Gastrointestinal Tract/*microbiology ; Humans ; In Situ Hybridization, Fluorescence ; Metagenome/*genetics ; Polymerase Chain Reaction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA ; }, abstract = {The human gut microbiota is considered one of the most fascinating reservoirs of microbial diversity hosting between 400 to 1000 bacterial species distributed among nine phyla with Firmicutes, Bacteroidetes and Actinobacteria representing around 75% of the diversity. One of the most intriguing issues relates to understanding which microbial groups are active players in the maintenance of the microbiota homeostasis.Here, we describe the diversity of active microbial fractions compared with the whole community from raw human fecal samples. We studied four healthy volunteers by 16S rDNA gene pyrosequencing. The fractions were obtained by cell sorting based on bacterial RNA concentration. Bacterial families were observed to appear or disappear on applying a cell sorting method in which flow cytometry was used to evaluate the active cells by pyronin-Y staining of RNA. This method was able to detect active bacteria, indicating that the active players differed from that observed in raw fecal material. Generally, observations showed that in the active fractions, the number of reads related to Bacteroidetes decreased whereas several families from Clostridiales (Firmicutes) were more highly represented. Moreover, a huge number of families appeared as part of the active fraction when cell sorting was applied, indicating reads that are simply statistically hidden by the total reads.}, } @article {pmid21825123, year = {2011}, author = {Burke, C and Steinberg, P and Rusch, D and Kjelleberg, S and Thomas, T}, title = {Bacterial community assembly based on functional genes rather than species.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {34}, pages = {14288-14293}, pmid = {21825123}, issn = {1091-6490}, mesh = {Bacteria/classification/*genetics/*growth & development ; *Biota ; Colony Count, Microbial ; Genes, Bacterial/*genetics ; Molecular Sequence Annotation ; Species Specificity ; Ulva/*microbiology ; }, abstract = {The principles underlying the assembly and structure of complex microbial communities are an issue of long-standing concern to the field of microbial ecology. We previously analyzed the community membership of bacterial communities associated with the green macroalga Ulva australis, and proposed a competitive lottery model for colonization of the algal surface in an attempt to explain the surprising lack of similarity in species composition across different algal samples. Here we extend the previous study by investigating the link between community structure and function in these communities, using metagenomic sequence analysis. Despite the high phylogenetic variability in microbial species composition on different U. australis (only 15% similarity between samples), similarity in functional composition was high (70%), and a core of functional genes present across all algal-associated communities was identified that were consistent with the ecology of surface- and host-associated bacteria. These functions were distributed widely across a variety of taxa or phylogenetic groups. This observation of similarity in habitat (niche) use with respect to functional genes, but not species, together with the relative ease with which bacteria share genetic material, suggests that the key level at which to address the assembly and structure of bacterial communities may not be "species" (by means of rRNA taxonomy), but rather the more functional level of genes.}, } @article {pmid21795334, year = {2011}, author = {Li, L and Shan, T and Wang, C and Côté, C and Kolman, J and Onions, D and Gulland, FM and Delwart, E}, title = {The fecal viral flora of California sea lions.}, journal = {Journal of virology}, volume = {85}, number = {19}, pages = {9909-9917}, pmid = {21795334}, issn = {1098-5514}, support = {R01 HL083254/HL/NHLBI NIH HHS/United States ; R01 HL105770/HL/NHLBI NIH HHS/United States ; R01HL083254/HL/NHLBI NIH HHS/United States ; R01HL105770/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; *Biodiversity ; Feces/*virology ; *Metagenome ; Molecular Sequence Data ; Sea Lions/*virology ; Sequence Analysis, DNA ; Viruses/*classification/genetics/*isolation & purification ; }, abstract = {California sea lions are one of the major marine mammal species along the Pacific coast of North America. Sea lions are susceptible to a wide variety of viruses, some of which can be transmitted to or from terrestrial mammals. Using an unbiased viral metagenomic approach, we surveyed the fecal virome in California sea lions of different ages and health statuses. Averages of 1.6 and 2.5 distinct mammalian viral species were shed by pups and juvenile sea lions, respectively. Previously undescribed mammalian viruses from four RNA virus families (Astroviridae, Picornaviridae, Caliciviridae, and Reoviridae) and one DNA virus family (Parvoviridae) were characterized. The first complete or partial genomes of sapeloviruses, sapoviruses, noroviruses, and bocavirus in marine mammals are reported. Astroviruses and bocaviruses showed the highest prevalence and abundance in California sea lion feces. The diversity of bacteriophages was higher in unweaned sea lion pups than in juveniles and animals in rehabilitation, where the phage community consisted largely of phages related to the family Microviridae. This study increases our understanding of the viral diversity in marine mammals, highlights the high rate of enteric viral infections in these highly social carnivores, and may be used as a baseline viral survey for comparison with samples from California sea lions during unexplained disease outbreaks.}, } @article {pmid21791581, year = {2011}, author = {Zhou, J and Deng, Y and Luo, F and He, Z and Yang, Y}, title = {Phylogenetic molecular ecological network of soil microbial communities in response to elevated CO2.}, journal = {mBio}, volume = {2}, number = {4}, pages = {}, pmid = {21791581}, issn = {2150-7511}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biodiversity ; Carbon/analysis ; Carbon Dioxide/*metabolism ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Ecosystem ; Genes, rRNA ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Minnesota ; Nitrogen/analysis ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Homology, Nucleic Acid ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {UNLABELLED: Understanding the interactions among different species and their responses to environmental changes, such as elevated atmospheric concentrations of CO(2), is a central goal in ecology but is poorly understood in microbial ecology. Here we describe a novel random matrix theory (RMT)-based conceptual framework to discern phylogenetic molecular ecological networks using metagenomic sequencing data of 16S rRNA genes from grassland soil microbial communities, which were sampled from a long-term free-air CO(2) enrichment experimental facility at the Cedar Creek Ecosystem Science Reserve in Minnesota. Our experimental results demonstrated that an RMT-based network approach is very useful in delineating phylogenetic molecular ecological networks of microbial communities based on high-throughput metagenomic sequencing data. The structure of the identified networks under ambient and elevated CO(2) levels was substantially different in terms of overall network topology, network composition, node overlap, module preservation, module-based higher-order organization, topological roles of individual nodes, and network hubs, suggesting that the network interactions among different phylogenetic groups/populations were markedly changed. Also, the changes in network structure were significantly correlated with soil carbon and nitrogen contents, indicating the potential importance of network interactions in ecosystem functioning. In addition, based on network topology, microbial populations potentially most important to community structure and ecosystem functioning can be discerned. The novel approach described in this study is important not only for research on biodiversity, microbial ecology, and systems microbiology but also for microbial community studies in human health, global change, and environmental management.

IMPORTANCE: The interactions among different microbial populations in a community play critical roles in determining ecosystem functioning, but very little is known about the network interactions in a microbial community, owing to the lack of appropriate experimental data and computational analytic tools. High-throughput metagenomic technologies can rapidly produce a massive amount of data, but one of the greatest difficulties is deciding how to extract, analyze, synthesize, and transform such a vast amount of information into biological knowledge. This study provides a novel conceptual framework to identify microbial interactions and key populations based on high-throughput metagenomic sequencing data. This study is among the first to document that the network interactions among different phylogenetic populations in soil microbial communities were substantially changed by a global change such as an elevated CO(2) level. The framework developed will allow microbiologists to address research questions which could not be approached previously, and hence, it could represent a new direction in microbial ecology research.}, } @article {pmid21786107, year = {2012}, author = {Denecke, M and Eilmus, S and Röder, N and Roesch, C and Bothe, H}, title = {Molecular identification of the microbial diversity in two sequencing batch reactors with activated sludge.}, journal = {Applied microbiology and biotechnology}, volume = {93}, number = {4}, pages = {1725-1734}, doi = {10.1007/s00253-011-3474-1}, pmid = {21786107}, issn = {1432-0614}, mesh = {Aerobiosis ; Biomass ; Bioreactors/*microbiology ; *Biota ; DNA Fingerprinting ; *Metagenome ; Nitrogen Compounds/metabolism ; Organic Chemicals/metabolism ; Polymorphism, Restriction Fragment Length ; Sewage/*microbiology ; *Water Purification ; }, abstract = {The diversity of the microbial community was identified in two lab-scale, ideally mixed sequencing batch reactors which were run for 115 days. One of the reactors was intermittently aerated (2 h aerobically/2 h anaerobically) whereas the other was consistently aerated. The amount of biomass as dry matter, the degradation of organic carbon determined by chemical oxygen demand and nitrogen-degradation activity were followed over the operation of the two reactors and did not show significant differences between the two approaches at the end of the experiment. At this point, the composition of the microbial community was determined by a terminal restriction fragment length polymorphism approach using multiple restriction enzymes by which organisms were retrieved to the lowest taxonomic level. The microbial composition was then significantly different. The species richness was at least five-fold higher in the intermittently aerated reactor than in the permanently kept aerobic approach which is in line with the observation that ecosystem disturbances result in higher diversity.}, } @article {pmid21776033, year = {2012}, author = {Baldrian, P and Kolařík, M and Stursová, M and Kopecký, J and Valášková, V and Větrovský, T and Zifčáková, L and Snajdr, J and Rídl, J and Vlček, C and Voříšková, J}, title = {Active and total microbial communities in forest soil are largely different and highly stratified during decomposition.}, journal = {The ISME journal}, volume = {6}, number = {2}, pages = {248-258}, pmid = {21776033}, issn = {1751-7370}, mesh = {Bacteria/*classification/enzymology/genetics ; Biodiversity ; Cellulose/metabolism ; Cellulose 1,4-beta-Cellobiosidase/genetics ; *Ecosystem ; Fungi/*classification/enzymology/genetics ; Metagenome ; Phylogeny ; Picea/physiology ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Trees/*microbiology ; }, abstract = {Soils of coniferous forest ecosystems are important for the global carbon cycle, and the identification of active microbial decomposers is essential for understanding organic matter transformation in these ecosystems. By the independent analysis of DNA and RNA, whole communities of bacteria and fungi and its active members were compared in topsoil of a Picea abies forest during a period of organic matter decomposition. Fungi quantitatively dominate the microbial community in the litter horizon, while the organic horizon shows comparable amount of fungal and bacterial biomasses. Active microbial populations obtained by RNA analysis exhibit similar diversity as DNA-derived populations, but significantly differ in the composition of microbial taxa. Several highly active taxa, especially fungal ones, show low abundance or even absence in the DNA pool. Bacteria and especially fungi are often distinctly associated with a particular soil horizon. Fungal communities are less even than bacterial ones and show higher relative abundances of dominant species. While dominant bacterial species are distributed across the studied ecosystem, distribution of dominant fungi is often spatially restricted as they are only recovered at some locations. The sequences of cbhI gene encoding for cellobiohydrolase (exocellulase), an essential enzyme for cellulose decomposition, were compared in soil metagenome and metatranscriptome and assigned to their producers. Litter horizon exhibits higher diversity and higher proportion of expressed sequences than organic horizon. Cellulose decomposition is mediated by highly diverse fungal populations largely distinct between soil horizons. The results indicate that low-abundance species make an important contribution to decomposition processes in soils.}, } @article {pmid21776031, year = {2012}, author = {Chaban, B and Hill, JE}, title = {A 'universal' type II chaperonin PCR detection system for the investigation of Archaea in complex microbial communities.}, journal = {The ISME journal}, volume = {6}, number = {2}, pages = {430-439}, pmid = {21776031}, issn = {1751-7370}, mesh = {Animals ; Archaea/*classification/*genetics/physiology ; Bacteria/classification/genetics ; Biodiversity ; Cattle ; Female ; Group II Chaperonins/*genetics ; Metagenomics/*methods ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Rumen/microbiology ; }, abstract = {Bacteria and Archaea are evolutionarily and biochemically distinct domains found together in many environments. Robust 'universal' PCR primer sets targeting both the bacterial 16S rRNA gene and the type I chaperonin gene have been established. However, 'universal' PCR primers for Archaea are currently limited to the 16S rRNA gene. We investigated the type II chaperonin (known as the thermosome, TF55, CCT or TCP-1) as a potential universal target (UT) for Archaea. Reproducible amplification of thermosome gene sequences from all major phyla tested was achieved through the application of a mixture or 'cocktail' of two forward and two reverse primers. Phylogenies based on the ∼750-bp thermosome UT were congruent with 16S rRNA gene phylogenies while exhibiting longer branch lengths, improving resolution of closely related taxa. 'Universal' thermosome primers were applied to profiling the archaeal community of dairy cow rumen and results compared with profiles based on the 16S rRNA gene and methyl co-enzyme M reductase (methanogen-specific) gene. Clone libraries generated from each target gene, as well as a pyrosequencing profile of one thermosome rumen library, revealed that all three targets consistently detected Methanobrevibacter smithii, Methanobrevibacter ruminantium and Methanosphaera stadtmanae as the dominant constituents; however, thermosome gene sequences were more diverse than either of the other targets providing a higher resolution description of the archaeal community. These findings demonstrate that a 'universal' thermosome PCR protocol is a powerful metagenomic tool for detecting and characterizing Archaea and archaeal communities.}, } @article {pmid21773777, year = {2011}, author = {Taylor, MW and Hill, RT and Hentschel, U}, title = {Meeting report: 1st international symposium on sponge microbiology.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {13}, number = {6}, pages = {1057-1061}, pmid = {21773777}, issn = {1436-2236}, mesh = {Animals ; *Biodiversity ; *Ecosystem ; Genomics/methods/*trends ; Host-Pathogen Interactions ; Porifera/*microbiology ; Research/*trends ; *Symbiosis ; }, abstract = {The success of the 1st International Symposium on Sponge Microbiology reflects the growing interest of the scientific community in this new and emerging field. Research themes of the symposium included symbiont diversity, physiology and function, secondary metabolites, metagenomics, single-cell genomics and other -omics approaches, sponge-symbiont interactions, sponge diseases, environmental stress, and many more. This article summarizes the major developments in the field and identifies future foci for research.}, } @article {pmid21764977, year = {2011}, author = {Lüke, C and Frenzel, P}, title = {Potential of pmoA amplicon pyrosequencing for methanotroph diversity studies.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {17}, pages = {6305-6309}, pmid = {21764977}, issn = {1098-5336}, mesh = {*Biodiversity ; Cluster Analysis ; *Environmental Microbiology ; Metagenomics/*methods ; Methylococcaceae/*classification/*genetics ; Oxygenases/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {We analyzed the potential of pmoA amplicon pyrosequencing compared to that of Sanger sequencing with paddy soils as a model environment. We defined operational taxonomic unit (OTU) cutoff values of 7% and 18%, reflecting methanotrophic species and major phylogenetic pmoA lineages, respectively. Major lineages were already well covered by clone libraries; nevertheless, pyrosequencing provided a higher level of diversity at the species level.}, } @article {pmid21764972, year = {2011}, author = {Bannert, A and Kleineidam, K and Wissing, L and Mueller-Niggemann, C and Vogelsang, V and Welzl, G and Cao, Z and Schloter, M}, title = {Changes in diversity and functional gene abundances of microbial communities involved in nitrogen fixation, nitrification, and denitrification in a tidal wetland versus paddy soils cultivated for different time periods.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {17}, pages = {6109-6116}, pmid = {21764972}, issn = {1098-5336}, mesh = {Agriculture/methods ; Archaea/genetics ; Archaeal Proteins/genetics ; Bacteria/genetics ; Bacterial Proteins/genetics ; *Biodiversity ; China ; *Denitrification ; Metabolic Networks and Pathways/*genetics ; Metagenome ; *Nitrification ; *Nitrogen Fixation ; Oryza ; Polymorphism, Restriction Fragment Length ; Real-Time Polymerase Chain Reaction ; *Soil Microbiology ; }, abstract = {In many areas of China, tidal wetlands have been converted into agricultural land for rice cultivation. However, the consequences of land use changes for soil microbial communities are poorly understood. Therefore, we investigated bacterial and archaeal communities involved in inorganic nitrogen turnover (nitrogen fixation, nitrification, and denitrification) based on abundances and relative species richness of the corresponding functional genes along a soil chronosequence ranging between 50 and 2,000 years of paddy soil management compared to findings for a tidal wetland. Changes in abundance and diversity of the functional groups could be observed, reflecting the different chemical and physical properties of the soils, which changed in terms of soil development. The tidal wetland was characterized by a low microbial biomass and relatively high abundances of ammonia-oxidizing microbes. Conversion of the tidal wetlands into paddy soils was followed by a significant increase in microbial biomass. Fifty years of paddy management resulted in a higher abundance of nitrogen-fixing microbes than was found in the tidal wetland, whereas dominant genes of nitrification and denitrification in the paddy soils showed no differences. With ongoing rice cultivation, copy numbers of archaeal ammonia oxidizers did not change, while that of their bacterial counterparts declined. The nirK gene, coding for nitrite reductase, increased with rice cultivation time and dominated its functionally redundant counterpart, nirS, at all sites under investigation. Relative species richness showed significant differences between all soils with the exception of the archaeal ammonia oxidizers in the paddy soils cultivated for 100 and 300 years. In general, changes in diversity patterns were more pronounced than those in functional gene abundances.}, } @article {pmid21764968, year = {2011}, author = {Oh, S and Caro-Quintero, A and Tsementzi, D and DeLeon-Rodriguez, N and Luo, C and Poretsky, R and Konstantinidis, KT}, title = {Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {17}, pages = {6000-6011}, pmid = {21764968}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics ; *Biodiversity ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; *Ecosystem ; Eukaryota/classification/genetics ; Fresh Water/*microbiology ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; *Plankton ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; Southeastern United States ; }, abstract = {Lake Lanier is an important freshwater lake for the southeast United States, as it represents the main source of drinking water for the Atlanta metropolitan area and is popular for recreational activities. Temperate freshwater lakes such as Lake Lanier are underrepresented among the growing number of environmental metagenomic data sets, and little is known about how functional gene content in freshwater communities relates to that of other ecosystems. To better characterize the gene content and variability of this freshwater planktonic microbial community, we sequenced several samples obtained around a strong summer storm event and during the fall water mixing using a random whole-genome shotgun (WGS) approach. Comparative metagenomics revealed that the gene content was relatively stable over time and more related to that of another freshwater lake and the surface ocean than to soil. However, the phylogenetic diversity of Lake Lanier communities was distinct from that of soil and marine communities. We identified several important genomic adaptations that account for these findings, such as the use of potassium (as opposed to sodium) osmoregulators by freshwater organisms and differences in the community average genome size. We show that the lake community is predominantly composed of sequence-discrete populations and describe a simple method to assess community complexity based on population richness and evenness and to determine the sequencing effort required to cover diversity in a sample. This study provides the first comprehensive analysis of the genetic diversity and metabolic potential of a temperate planktonic freshwater community and advances approaches for comparative metagenomics.}, } @article {pmid21764955, year = {2011}, author = {DeAngelis, KM and Wu, CH and Beller, HR and Brodie, EL and Chakraborty, R and DeSantis, TZ and Fortney, JL and Hazen, TC and Osman, SR and Singer, ME and Tom, LM and Andersen, GL}, title = {PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {18}, pages = {6313-6322}, pmid = {21764955}, issn = {1098-5336}, mesh = {*Biodiversity ; DNA, Complementary/genetics ; *Environmental Microbiology ; Metagenomics/*methods ; Microarray Analysis/*methods ; Oligonucleotide Array Sequence Analysis/*methods ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; }, abstract = {Environmental microbial community analysis typically involves amplification by PCR, despite well-documented biases. We have developed two methods of PCR-independent microbial community analysis using the high-density microarray PhyloChip: direct hybridization of 16S rRNA (dirRNA) or rRNA converted to double-stranded cDNA (dscDNA). We compared dirRNA and dscDNA communities to PCR-amplified DNA communities using a mock community of eight taxa, as well as experiments derived from three environmental sample types: chromium-contaminated aquifer groundwater, tropical forest soil, and secondary sewage in seawater. Community profiles by both direct hybridization methods showed differences that were expected based on accompanying data but that were missing in PCR-amplified communities. Taxon richness decreased in RNA compared to that in DNA communities, suggesting a subset of 20% in soil and 60% in groundwater that is active; secondary sewage showed no difference between active and inactive populations. Direct hybridization of dscDNA and RNA is thus a viable alternative to PCR-amplified microbial community analysis, providing identification of the active populations within microbial communities that attenuate pollutants, drive global biogeochemical cycles, or proliferate disease states.}, } @article {pmid21755290, year = {2011}, author = {Graças, DA and Miranda, PR and Baraúna, RA and McCulloch, JA and Ghilardi, R and Schneider, MP and Silva, A}, title = {Microbial diversity of an anoxic zone of a hydroelectric power station reservoir in Brazilian Amazonia.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {853-861}, pmid = {21755290}, issn = {1432-184X}, mesh = {Archaea/*classification/genetics ; *Biodiversity ; Brazil ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Gene Library ; Geologic Sediments/microbiology ; Phylogeny ; *Power Plants ; Proteobacteria/*classification/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Microbial diversity was evaluated in an anoxic zone of Tucuruí Hydroelectric Power Station reservoir in Brazilian Amazonia using a culture-independent approach by amplifying and sequencing fragments of the 16S rRNA gene using metagenomic DNA as a template. Samples obtained from the photic, aphotic (40 m) and sediment (60 m) layers were used to construct six 16S rDNA libraries containing a total of 1,152 clones. The sediment, aphotic and photic layers presented 64, 33 and 35 unique archaeal operational taxonomic units (OTUs). The estimated richness of these layers was evaluated to be 153, 106 and 79 archaeal OTUs, respectively, using the abundance-based coverage estimator (ACE) and 114, 83 and 77 OTUs using the Chao1 estimator. For bacterial sequences, 114, 69 and 57 OTUs were found in the sediment, aphotic and photic layers, which presented estimated richnesses of 1,414, 522 and 197 OTUs (ACE) and 1,059, 1,014 and 148 OTUs (Chao1), respectively. Phylogenetic analyses of the sequences obtained revealed a high richness of microorganisms which participate in the carbon cycle, namely, methanogenic archaea and methanotrophic proteobacteria. Most sequences obtained belong to non-culturable prokaryotes. The present study offers the first glimpse of the huge microbial diversity of an anoxic area of a man-made lacustrine environment in the tropics.}, } @article {pmid21748362, year = {2011}, author = {de Castro, AP and Quirino, BF and Allen, H and Williamson, LL and Handelsman, J and Krüger, RH}, title = {Construction and validation of two metagenomic DNA libraries from Cerrado soil with high clay content.}, journal = {Biotechnology letters}, volume = {33}, number = {11}, pages = {2169-2175}, doi = {10.1007/s10529-011-0693-6}, pmid = {21748362}, issn = {1573-6776}, mesh = {Aluminum Silicates ; *Biodiversity ; Brazil ; Clay ; *Gene Library ; Hydrogen-Ion Concentration ; Iron/analysis ; *Metagenome ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {A challenge of metagenomic studies is in the extraction and purification of DNA from environmental samples. The soils of the Cerrado region of Brazil present several technical difficulties to DNA extraction: high clay content (>55% w/w), low pH (4.7) and high iron levels (146 ppm). Here we describe for the first time the efficient recovery and purification of microbial DNA associated with these unusual soil characteristics and the construction and validation of two metagenomic libraries: a 150,000 clones library with insert size of approximately 8 kb and a 65,000 clones library with insert size of approximately 35 kb. The construction of these metagenomic libraries will allow the biotechnological exploitation of the microbial community present in the soil from this endangered biome.}, } @article {pmid21744288, year = {2011}, author = {Singh, KM and Tripathi, AK and Pandya, PR and Rank, DN and Kothari, RK and Joshi, CG}, title = {Dasytricha dominance in Surti buffalo rumen revealed by 18S rRNA sequences and real-time PCR assay.}, journal = {Current microbiology}, volume = {63}, number = {3}, pages = {281-288}, pmid = {21744288}, issn = {1432-0991}, mesh = {Animals ; *Biodiversity ; Buffaloes ; Ciliophora/*classification/*genetics/growth & development ; Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Diet ; Genes, rRNA ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; Rumen/*parasitology ; Sequence Analysis, DNA ; }, abstract = {The genetic diversity of protozoa in Surti buffalo rumen was studied by amplified ribosomal DNA restriction analysis, 18S rDNA sequence homology and phylogenetic and Real-time PCR analysis methods. Three animals were fed diet comprised green fodder Napier bajra 21 (Pennisetum purpureum), mature pasture grass (Dicanthium annulatum) and concentrate mixture (20% crude protein, 65% total digestible nutrients). A protozoa-specific primer (P-SSU-342f) and a eukarya-specific primer (Medlin B) were used to amplify a 1,360 bp fragment of DNA encoding protozoal small subunit (SSU) ribosomal RNA from rumen fluid. A total of 91 clones were examined and identified 14 different 18S RNA sequences based on PCR-RFLP pattern. These 14 phylotypes were distributed into four genera-based 18S rDNA database sequences and identified as Dasytricha (57 clones), Isotricha (14 clones), Ostracodinium (11 clones) and Polyplastron (9 clones). Phylogenetic analyses were also used to infer the makeup of protozoa communities in the rumen of Surti buffalo. Out of 14 sequences, 8 sequences (69 clones) clustered with the Dasytricha ruminantium-like clone and 4 sequences (13 clones) were also phylogenetically placed with the Isotricha prostoma-like clone. Moreover, 2 phylotypes (9 clones) were related to Polyplastron multivesiculatum-like clone. In addition, the number of 18S rDNA gene copies of Dasytricha ruminantium (0.05% to ciliate protozoa) was higher than Entodinium sp. (2.0 × 10(5) vs. 1.3 × 10(4)) in per ml ruminal fluid.}, } @article {pmid21742924, year = {2011}, author = {Constant, P and Chowdhury, SP and Hesse, L and Pratscher, J and Conrad, R}, title = {Genome data mining and soil survey for the novel group 5 [NiFe]-hydrogenase to explore the diversity and ecological importance of presumptive high-affinity H(2)-oxidizing bacteria.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {17}, pages = {6027-6035}, pmid = {21742924}, issn = {1098-5336}, mesh = {Bacteria/*classification/*enzymology/genetics/metabolism ; *Biodiversity ; Computational Biology ; *Genetic Variation ; Hydrogen/*metabolism ; Hydrogenase/*genetics ; Metagenome ; Oxidation-Reduction ; *Soil Microbiology ; }, abstract = {Streptomyces soil isolates exhibiting the unique ability to oxidize atmospheric H(2) possess genes specifying a putative high-affinity [NiFe]-hydrogenase. This study was undertaken to explore the taxonomic diversity and the ecological importance of this novel functional group. We propose to designate the genes encoding the small and large subunits of the putative high-affinity hydrogenase hhyS and hhyL, respectively. Genome data mining revealed that the hhyL gene is unevenly distributed in the phyla Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria. The hhyL gene sequences comprised a phylogenetically distinct group, namely, the group 5 [NiFe]-hydrogenase genes. The presumptive high-affinity H(2)-oxidizing bacteria constituting group 5 were shown to possess a hydrogenase gene cluster, including the genes encoding auxiliary and structural components of the enzyme and four additional open reading frames (ORFs) of unknown function. A soil survey confirmed that both high-affinity H(2) oxidation activity and the hhyL gene are ubiquitous. A quantitative PCR assay revealed that soil contained 10(6) to 10(8) hhyL gene copies g (dry weight)(-1). Assuming one hhyL gene copy per genome, the abundance of presumptive high-affinity H(2)-oxidizing bacteria was higher than the maximal population size for which maintenance energy requirements would be fully supplied through the H(2) oxidation activity measured in soil. Our data indicate that the abundance of the hhyL gene should not be taken as a reliable proxy for the uptake of atmospheric H(2) by soil, because high-affinity H(2) oxidation is a facultatively mixotrophic metabolism, and microorganisms harboring a nonfunctional group 5 [NiFe]-hydrogenase may occur.}, } @article {pmid21738787, year = {2011}, author = {Belda, E and Pedrola, L and Peretó, J and Martínez-Blanch, JF and Montagud, A and Navarro, E and Urchueguía, J and Ramón, D and Moya, A and Porcar, M}, title = {Microbial diversity in the midguts of field and lab-reared populations of the European corn borer Ostrinia nubilalis.}, journal = {PloS one}, volume = {6}, number = {6}, pages = {e21751}, pmid = {21738787}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Moths/*microbiology ; Phylogeny ; }, abstract = {BACKGROUND: Insects are associated with microorganisms that contribute to the digestion and processing of nutrients. The European Corn Borer (ECB) is a moth present world-wide, causing severe economical damage as a pest on corn and other crops. In the present work, we give a detailed view of the complexity of the microorganisms forming the ECB midgut microbiota with the objective of comparing the biodiversity of the midgut-associated microbiota and explore their potential as a source of genes and enzymes with biotechnological applications.

A high-throughput sequencing approach has been used to identify bacterial species, genes and metabolic pathways, particularly those involved in plant-matter degradation, in two different ECB populations (field-collected vs. lab-reared population with artificial diet). Analysis of the resulting sequences revealed the massive presence of Staphylococcus warneri and Weissella paramesenteroides in the lab-reared sample. This enabled us to reconstruct both genomes almost completely. Despite the apparently low diversity, 208 different genera were detected in the sample, although most of them at very low frequency. By contrast, the natural population exhibited an even higher taxonomic diversity along with a wider array of cellulolytic enzyme families. However, in spite of the differences in relative abundance of major taxonomic groups, not only did both metagenomes share a similar functional profile but also a similar distribution of non-redundant genes in different functional categories.

CONCLUSIONS/SIGNIFICANCE: Our results reveal a highly diverse pool of bacterial species in both O. nubilalis populations, with major differences: The lab-reared sample is rich in gram-positive species (two of which have almost fully sequenced genomes) while the field sample harbors mainly gram-negative species and has a larger set of cellulolytic enzymes. We have found a clear relationship between the diet and the midgut microbiota, which reveals the selection pressure of food on the community of intestinal bacteria.}, } @article {pmid21737778, year = {2011}, author = {Carroll, IM and Ringel-Kulka, T and Keku, TO and Chang, YH and Packey, CD and Sartor, RB and Ringel, Y}, title = {Molecular analysis of the luminal- and mucosal-associated intestinal microbiota in diarrhea-predominant irritable bowel syndrome.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {301}, number = {5}, pages = {G799-807}, pmid = {21737778}, issn = {1522-1547}, support = {DK-075621/DK/NIDDK NIH HHS/United States ; DK-084294/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Colon/*microbiology ; DNA, Bacterial/genetics ; Diarrhea/*microbiology ; Feces/microbiology ; Female ; Humans ; Intestinal Mucosa/*microbiology ; Irritable Bowel Syndrome/*microbiology ; Male ; Metagenome/*genetics ; Middle Aged ; }, abstract = {Alterations in the intestinal microbiota have been suggested as an etiological factor in the pathogenesis of irritable bowel syndrome (IBS). This study used a molecular fingerprinting technique to compare the composition and biodiversity of the microbiota within fecal and mucosal niches between patients with diarrhea-predominant IBS (D-IBS) and healthy controls. Terminal-restriction fragment (T-RF) length polymorphism (T-RFLP) fingerprinting of the bacterial 16S rRNA gene was used to perform microbial community composition analyses on fecal and mucosal samples from patients with D-IBS (n = 16) and healthy controls (n = 21). Molecular fingerprinting of the microbiota from fecal and colonic mucosal samples revealed differences in the contribution of T-RFs to the microbiota between D-IBS patients and healthy controls. Further analysis revealed a significantly lower (1.2-fold) biodiversity of microbes within fecal samples from D-IBS patients than healthy controls (P = 0.008). No difference in biodiversity in mucosal samples was detected between D-IBS patients and healthy controls. Multivariate analysis of T-RFLP profiles demonstrated distinct microbial communities between luminal and mucosal niches in all samples. Our findings of compositional differences in the luminal- and mucosal-associated microbiota between D-IBS patients and healthy controls and diminished microbial biodiversity in D-IBS fecal samples further support the hypothesis that alterations in the intestinal microbiota may have an etiological role in the pathogenesis of D-IBS and suggest that luminal and mucosal niches need to be investigated.}, } @article {pmid21734380, year = {2011}, author = {Marteau, P and Chaput, U}, title = {Bacteria as trigger for chronic gastrointestinal disorders.}, journal = {Digestive diseases (Basel, Switzerland)}, volume = {29}, number = {2}, pages = {166-171}, doi = {10.1159/000323879}, pmid = {21734380}, issn = {1421-9875}, mesh = {Animals ; *Bacterial Physiological Phenomena ; Chronic Disease ; Gastrointestinal Diseases/*microbiology ; Gastrointestinal Neoplasms/microbiology ; Humans ; Inflammatory Bowel Diseases/microbiology ; }, abstract = {Apart from acute infections, microorganisms may also induce or perpetuate chronic inflammatory diseases and reversible or irreversible proliferation of various cells in the gastrointestinal tract (the extreme being adenocarcinoma and lymphoma). Helicobacter pylori is not only involved in the pathogenesis of lymphoma and gastric adenocarcinoma. The steps and mechanisms of the carcinogenic process involve host predisposition, environmental factors, and strain virulence. The steps of lymphoma genesis include chronic inflammation, acquisition of mucosa-associated lymphoid tissue in the stomach, proliferation of the B lymphocytes in an inflammatory context, acquisition of genetic anomalies and dysregulation of the NF-κB pathway. The role of Campylobacter jejuni in immunoproliferative small bowel disease has also been shown and eradication of this bacterium can cure the lymphoma at its early stage. The evidence for the role of some bacteria in colon cancer development is discussed. Opportunistic pathogens are detected in the stools or mucosa of a proportion of subjects with Crohn's disease. They include Mycobacterium avium paratuberculosis, adherent invasive Escherichia coli, and Clostridium difficile. A dysbiosis has been repeatedly observed in patients with inflammatory bowel disease. Instability of the dominant microbiota and decreased biodiversity (especially in the firmicutes phylum) are major characteristics. The decrease of Faecalibacterium prausnitzii seems to have a prognostic value to predict relapse of Crohn's disease after surgery. Finally, important perspectives are opened by new tools such as metagenomics and metabolomics of the gastrointestinal ecosystems. Major tracks concern irritable bowel syndrome, colon cancer and obesity.}, } @article {pmid21731976, year = {2011}, author = {Erijman, L and Figuerola, EL and Guerrero, LD and Ayarza, JM}, title = {[Impact of the recent advances in the analysis of microbial communities on the control of the wastewater treatment process].}, journal = {Revista Argentina de microbiologia}, volume = {43}, number = {2}, pages = {127-135}, doi = {10.1590/S0325-75412011000200011}, pmid = {21731976}, issn = {0325-7541}, mesh = {Aerobiosis ; Biodiversity ; Biomass ; Ecosystem ; *Environmental Microbiology ; Forecasting ; Metagenomics ; *Microbial Consortia ; Sewage/*microbiology ; Soil Microbiology ; Waste Disposal, Fluid/*methods/standards ; Water Microbiology ; Water Purification/*methods ; }, abstract = {One of the main functions of environmental biotechnology is to address the study of microbial communities that provide essential services to society. Beyond the similarities with industrial and agricultural microbiology, the unique features exhibited by environmental biotechnology, such as process objectives, biomass characteristics and type and mode of feeding (substrates), allow a clear distinction from the other related disciplines. Recent advances in microbial ecology, ecophysiology, genomics and process engineering are herein reviewed to illustrate how the integration of the new knowledge can help overcome the shortcomings of classic microbiological analyses to understand, predict and optimize the performance of wastewater treatment.}, } @article {pmid21724886, year = {2011}, author = {Gladden, JM and Allgaier, M and Miller, CS and Hazen, TC and VanderGheynst, JS and Hugenholtz, P and Simmons, BA and Singer, SW}, title = {Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {16}, pages = {5804-5812}, pmid = {21724886}, issn = {1098-5336}, support = {L30 NS050030/NS/NINDS NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Bacteria/*enzymology/genetics/growth & development ; Bacterial Typing Techniques ; Base Sequence ; Biomass ; Enzyme Activation ; Fermentation ; Genes, rRNA ; Glycoside Hydrolases/*metabolism ; Lignin/metabolism ; *Microbial Consortia ; Molecular Sequence Data ; Panicum/*microbiology ; Phylogeny ; Protein Stability ; Sequence Analysis, DNA ; Soil/chemistry ; Temperature ; }, abstract = {Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60°C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene amplicon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low-diversity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli, Rhodothermus marinus, and Thermus thermophilus. At lower abundance, thermophilic Chloroflexi and an uncultivated lineage of the Gemmatimonadetes phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80°C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions.}, } @article {pmid21718534, year = {2011}, author = {Pandey, RV and Nolte, V and Boenigk, J and Schlötterer, C}, title = {CANGS DB: a stand-alone web-based database tool for processing, managing and analyzing 454 data in biodiversity studies.}, journal = {BMC research notes}, volume = {4}, number = {}, pages = {227}, pmid = {21718534}, issn = {1756-0500}, support = {P 19467/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {BACKGROUND: Next generation sequencing (NGS) is widely used in metagenomic and transcriptomic analyses in biodiversity. The ease of data generation provided by NGS platforms has allowed researchers to perform these analyses on their particular study systems. In particular the 454 platform has become the preferred choice for PCR amplicon based biodiversity surveys because it generates the longest sequence reads. Nevertheless, the handling and organization of massive amounts of sequencing data poses a major problem for the research community, particularly when multiple researchers are involved in data acquisition and analysis. An integrated and user-friendly tool, which performs quality control, read trimming, PCR primer removal, and data organization is desperately needed, therefore, to make data interpretation fast and manageable.

FINDINGS: We developed CANGS DB (Cleaning and Analyzing Next Generation Sequences DataBase) a flexible, stand alone and user-friendly integrated database tool. CANGS DB is specifically designed to organize and manage the massive amount of sequencing data arising from various NGS projects. CANGS DB also provides an intuitive user interface for sequence trimming and quality control, taxonomy analysis and rarefaction analysis. Our database tool can be easily adapted to handle multiple sequencing projects in parallel with different sample information, amplicon sizes, primer sequences, and quality thresholds, which makes this software especially useful for non-bioinformaticians. Furthermore, CANGS DB is especially suited for projects where multiple users need to access the data. CANGS DB is available at http://code.google.com/p/cangsdb/.

CONCLUSION: CANGS DB provides a simple and user-friendly solution to process, store and analyze 454 sequencing data. Being a local database that is accessible through a user-friendly interface, CANGS DB provides the perfect tool for collaborative amplicon based biodiversity surveys without requiring prior bioinformatics skills.}, } @article {pmid21694499, year = {2011}, author = {Nava, GM and Stappenbeck, TS}, title = {Diversity of the autochthonous colonic microbiota.}, journal = {Gut microbes}, volume = {2}, number = {2}, pages = {99-104}, pmid = {21694499}, issn = {1949-0984}, support = {P30 DK052574/DK/NIDDK NIH HHS/United States ; R01 AI084887/AI/NIAID NIH HHS/United States ; DK52574/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Biodiversity ; Cluster Analysis ; Colon/*microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Humans ; *Metagenome ; Mice ; Mucous Membrane/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {A longstanding hypothesis in intestinal microbial ecology is that autochthonous microbes (resident) play a role that is distinct from allochthonous microbes (transient microbes in the fecal stream). A challenge has been to identify this pool of microbes. We used laser capture microdissection to collect microbes from the mouse ascending colon. This area contains transverse folds that mimic human intestinal folds and contains a distinct population of intestinal microbes that is associated with the mucosa. Our analysis of bacterial 16S rRNA genes showed that this area was enriched for Lachnospiraceae and Ruminococcaceae. In this addendum, we further compare this community to studies of mucosa-associated microbes in humans. This analysis reveals common phylogenetic groups of bacteria that are present in both mouse and human. However, we found microorganisms at the genus and species levels including Faecalibacterium prausnitzii which appears to be specific for humans. We propose that that examination of the mucosa-associated microbes in wild type and genetically modified mice will be a valuable component to define host microbial interactions that are essential for homeostasis.}, } @article {pmid21677692, year = {2012}, author = {Degnan, PH and Ochman, H}, title = {Illumina-based analysis of microbial community diversity.}, journal = {The ISME journal}, volume = {6}, number = {1}, pages = {183-194}, pmid = {21677692}, issn = {1751-7370}, mesh = {Animals ; Bacteria/*classification/*genetics ; Biodiversity ; DNA Primers ; DNA, Bacterial/*analysis/genetics ; Intestines/microbiology ; *Metagenome ; Mice ; RNA, Ribosomal, 16S/*analysis/genetics ; }, abstract = {Microbes commonly exist in milieus of varying complexity and diversity. Although cultivation-based techniques have been unable to accurately capture the true diversity within microbial communities, these deficiencies have been overcome by applying molecular approaches that target the universally conserved 16S ribosomal RNA gene. The recent application of 454 pyrosequencing to simultaneously sequence thousands of 16S rDNA sequences (pyrotags) has revolutionized the characterization of complex microbial communities. To date, studies based on 454 pyrotags have dominated the field, but sequencing platforms that generate many more sequence reads at much lower costs have been developed. Here, we use the Illumina sequencing platform to design a strategy for 16S amplicon analysis (iTags), and assess its generality, practicality and potential complications. We fabricated and sequenced paired-end libraries of amplified hyper-variable 16S rDNA fragments from sets of samples that varied in their contents, ranging from a single bacterium to highly complex communities. We adopted an approach that allowed us to evaluate several potential sources of errors, including sequencing artifacts, amplification biases, non-corresponding paired-end reads and mistakes in taxonomic classification. By considering each source of error, we delineate ways to make biologically relevant and robust conclusions from the millions of sequencing reads that can be readily generated by this technology.}, } @article {pmid21674005, year = {2011}, author = {Ng, TF and Willner, DL and Lim, YW and Schmieder, R and Chau, B and Nilsson, C and Anthony, S and Ruan, Y and Rohwer, F and Breitbart, M}, title = {Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes.}, journal = {PloS one}, volume = {6}, number = {6}, pages = {e20579}, pmid = {21674005}, issn = {1932-6203}, mesh = {Animals ; Bacteriophages/classification/genetics ; *Biodiversity ; Culicidae/*virology ; DNA Viruses/classification/*genetics ; DNA, Viral/genetics ; Genome, Viral/genetics ; Humans ; Insect Vectors/virology ; Metagenomics/*methods ; Molecular Sequence Data ; Plant Viruses/classification/genetics ; Sequence Analysis, DNA ; }, abstract = {Viruses are the most abundant and diverse genetic entities on Earth; however, broad surveys of viral diversity are hindered by the lack of a universal assay for viruses and the inability to sample a sufficient number of individual hosts. This study utilized vector-enabled metagenomics (VEM) to provide a snapshot of the diversity of DNA viruses present in three mosquito samples from San Diego, California. The majority of the sequences were novel, suggesting that the viral community in mosquitoes, as well as the animal and plant hosts they feed on, is highly diverse and largely uncharacterized. Each mosquito sample contained a distinct viral community. The mosquito viromes contained sequences related to a broad range of animal, plant, insect and bacterial viruses. Animal viruses identified included anelloviruses, circoviruses, herpesviruses, poxviruses, and papillomaviruses, which mosquitoes may have obtained from vertebrate hosts during blood feeding. Notably, sequences related to human papillomaviruses were identified in one of the mosquito samples. Sequences similar to plant viruses were identified in all mosquito viromes, which were potentially acquired through feeding on plant nectar. Numerous bacteriophages and insect viruses were also detected, including a novel densovirus likely infecting Culex erythrothorax. Through sampling insect vectors, VEM enables broad survey of viral diversity and has significantly increased our knowledge of the DNA viruses present in mosquitoes.}, } @article {pmid21673982, year = {2011}, author = {Johnston-Monje, D and Raizada, MN}, title = {Conservation and diversity of seed associated endophytes in Zea across boundaries of evolution, ethnography and ecology.}, journal = {PloS one}, volume = {6}, number = {6}, pages = {e20396}, pmid = {21673982}, issn = {1932-6203}, mesh = {Acetoin/metabolism ; Anthropology, Cultural ; *Biodiversity ; Biomass ; Crops, Agricultural/microbiology ; *Ecology ; *Evolution, Molecular ; Genotype ; *Metagenome ; Nitrogen Fixation ; Phosphates/chemistry ; Phylogeny ; Plant Roots/growth & development/microbiology ; Plant Shoots/growth & development/microbiology ; Proteobacteria/genetics/metabolism ; Rhizosphere ; Seeds/*microbiology ; Solanum tuberosum/growth & development/microbiology ; Solubility ; Species Specificity ; Symbiosis ; Zea mays/*microbiology ; }, abstract = {Endophytes are non-pathogenic microbes living inside plants. We asked whether endophytic species were conserved in the agriculturally important plant genus Zea as it became domesticated from its wild ancestors (teosinte) to modern maize (corn) and moved from Mexico to Canada. Kernels from populations of four different teosintes and 10 different maize varieties were screened for endophytic bacteria by culturing, cloning and DNA fingerprinting using terminal restriction fragment length polymorphism (TRFLP) of 16S rDNA. Principle component analysis of TRFLP data showed that seed endophyte community composition varied in relation to plant host phylogeny. However, there was a core microbiota of endophytes that was conserved in Zea seeds across boundaries of evolution, ethnography and ecology. The majority of seed endophytes in the wild ancestor persist today in domesticated maize, though ancient selection against the hard fruitcase surrounding seeds may have altered the abundance of endophytes. Four TRFLP signals including two predicted to represent Clostridium and Paenibacillus species were conserved across all Zea genotypes, while culturing showed that Enterobacter, Methylobacteria, Pantoea and Pseudomonas species were widespread, with γ-proteobacteria being the prevalent class. Twenty-six different genera were cultured, and these were evaluated for their ability to stimulate plant growth, grow on nitrogen-free media, solubilize phosphate, sequester iron, secrete RNAse, antagonize pathogens, catabolize the precursor of ethylene, produce auxin and acetoin/butanediol. Of these traits, phosphate solubilization and production of acetoin/butanediol were the most commonly observed. An isolate from the giant Mexican landrace Mixteco, with 100% identity to Burkholderia phytofirmans, significantly promoted shoot potato biomass. GFP tagging and maize stem injection confirmed that several seed endophytes could spread systemically through the plant. One seed isolate, Enterobacter asburiae, was able to exit the root and colonize the rhizosphere. Conservation and diversity in Zea-microbe relationships are discussed in the context of ecology, crop domestication, selection and migration.}, } @article {pmid21671962, year = {2011}, author = {de Menezes, AB and Lewis, E and O'Donovan, M and O'Neill, BF and Clipson, N and Doyle, EM}, title = {Microbiome analysis of dairy cows fed pasture or total mixed ration diets.}, journal = {FEMS microbiology ecology}, volume = {78}, number = {2}, pages = {256-265}, doi = {10.1111/j.1574-6941.2011.01151.x}, pmid = {21671962}, issn = {1574-6941}, mesh = {Animal Husbandry/methods ; Animals ; Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Biodiversity ; Cattle ; Dairying/*methods ; Diet/methods/*veterinary ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Genome, Protozoan/genetics ; *Metagenome ; Methane/analysis/metabolism ; Rumen/microbiology/parasitology ; }, abstract = {Understanding rumen microbial ecology is essential for the development of feed systems designed to improve livestock productivity, health and for methane mitigation strategies from cattle. Although rumen microbial communities have been studied previously, few studies have applied next-generation sequencing technologies to that ecosystem. The aim of this study was to characterize changes in microbial community structure arising from feeding dairy cows two widely used diets: pasture and total mixed ration (TMR). Bacterial, archaeal and protozoal communities were characterized by terminal restriction fragment length polymorphism of the amplified SSU rRNA gene and statistical analysis showed that bacterial and archaeal communities were significantly affected by diet, whereas no effect was observed for the protozoal community. Deep amplicon sequencing of the 16S rRNA gene revealed significant differences in the bacterial communities between the diets and between rumen solid and liquid content. At the family level, some important groups of rumen bacteria were clearly associated with specific diets, including the higher abundance of the Fibrobacteraceae in TMR solid samples and members of the propionate-producing Veillonelaceae in pasture samples. This study will be relevant to the study of rumen microbial ecology and livestock feed management.}, } @article {pmid21651822, year = {2011}, author = {Steward, GF and Preston, CM}, title = {Analysis of a viral metagenomic library from 200 m depth in Monterey Bay, California constructed by direct shotgun cloning.}, journal = {Virology journal}, volume = {8}, number = {}, pages = {287}, pmid = {21651822}, issn = {1743-422X}, support = {P20RR016467/RR/NCRR NIH HHS/United States ; P20RR018727/RR/NCRR NIH HHS/United States ; U54RR026136/RR/NCRR NIH HHS/United States ; }, mesh = {*Biodiversity ; California ; Cloning, Molecular/methods ; Cluster Analysis ; DNA Viruses/*classification/*genetics ; DNA, Viral/chemistry/genetics ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Seawater/*virology ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Viruses have a profound influence on both the ecology and evolution of marine plankton, but the genetic diversity of viral assemblages, particularly those in deeper ocean waters, remains poorly described. Here we report on the construction and analysis of a viral metagenome prepared from below the euphotic zone in a temperate, eutrophic bay of coastal California.

METHODS: We purified viruses from approximately one cubic meter of seawater collected from 200 m depth in Monterey Bay, CA. DNA was extracted from the virus fraction, sheared, and cloned with no prior amplification into a plasmid vector and propagated in E. coli to produce the MBv200m library. Random clones were sequenced by the Sanger method. Sequences were assembled then compared to sequences in GenBank and to other viral metagenomic libraries using BLAST analyses.

RESULTS: Only 26% of the 881 sequences remaining after assembly had significant (E≤0.001) BLAST hits to sequences in the GenBank nr database, with most being matches to bacteria (15%) and viruses (8%). When BLAST analysis included environmental sequences, 74% of sequences in the MBv200m library had a significant match. Most of these hits (70%) were to microbial metagenome sequences and only 0.7% were to sequences from viral metagenomes. Of the 121 sequences with a significant hit to a known virus, 94% matched bacteriophages (Families Podo-, Sipho-, and Myoviridae) and 6% matched viruses of eukaryotes in the Family Phycodnaviridae (5 sequences) or the Mimivirus (2 sequences). The largest percentages of hits to viral genes of known function were to those involved in DNA modification (25%) or structural genes (17%). Based on reciprocal BLAST analyses, the MBv200m library appeared to be most similar to viral metagenomes from two other bays and least similar to a viral metagenome from the Arctic Ocean.

CONCLUSIONS: Direct cloning of DNA from diverse marine viruses was feasible and resulted in a distribution of virus types and functional genes at depth that differed in detail, but were broadly similar to those found in surface marine waters. Targeted viral analyses are useful for identifying those components of the greater marine metagenome that circulate in the subcellular size fraction.}, } @article {pmid21640948, year = {2011}, author = {Hättenschwiler, S and Fromin, N and Barantal, S}, title = {Functional diversity of terrestrial microbial decomposers and their substrates.}, journal = {Comptes rendus biologies}, volume = {334}, number = {5-6}, pages = {393-402}, doi = {10.1016/j.crvi.2011.03.001}, pmid = {21640948}, issn = {1768-3238}, mesh = {Bacterial Physiological Phenomena ; *Biodegradation, Environmental ; *Biodiversity ; Biomass ; Climate ; Ecosystem ; Fungi/physiology ; Plants ; *Soil Microbiology ; }, abstract = {The relationship between biodiversity and biogeochemical processes gained much interest in light of the rapidly decreasing biodiversity worldwide. In this article, we discuss the current status, challenges and prospects of functional concepts to plant litter diversity and microbial decomposer diversity. We also evaluate whether these concepts permit a better understanding of how biodiversity is linked to litter decomposition as a key ecosystem process influencing carbon and nutrient cycles. Based on a literature survey, we show that plant litter and microbial diversity matters for decomposition, but that considering numbers of taxonomic units appears overall as little relevant and less useful than functional diversity. However, despite easily available functional litter traits and the well-established theoretical framework for functional litter diversity, the impact of functional litter diversity on decomposition is not yet well enough explored. Defining functional diversity of microorganisms remains one of the biggest challenges for functional approaches to microbial diversity. Recent developments in microarray and metagenomics technology offer promising possibilities in the assessment of the functional structure of microbial communities. This might allow significant progress in measuring functional microbial diversity and ultimately in our ability to predict consequences of biodiversity loss in the decomposer system for biogeochemical processes.}, } @article {pmid21635673, year = {2011}, author = {Zurel, D and Benayahu, Y and Or, A and Kovacs, A and Gophna, U}, title = {Composition and dynamics of the gill microbiota of an invasive Indo-Pacific oyster in the eastern Mediterranean Sea.}, journal = {Environmental microbiology}, volume = {13}, number = {6}, pages = {1467-1476}, doi = {10.1111/j.1462-2920.2011.02448.x}, pmid = {21635673}, issn = {1462-2920}, mesh = {Animals ; Bacteria/classification/*genetics/isolation & purification ; Gills/*microbiology ; Introduced Species ; Mediterranean Sea ; *Metagenome ; Ostreidae/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; *Water Microbiology ; }, abstract = {Gill bacterial communities of Chama pacifica, an Indo-Pacific invasive oyster to the eastern Mediterranean Sea, were compared with those of Chama savignyi, its northern Red Sea congeneric species. Summer and winter bacterial populations were characterized and compared using 16S rDNA clone libraries, and seasonal population dynamics were monitored by automated ribosomal intergenic spacer analysis (ARISA). Clone libraries revealed a specific clade of bacteria, closely related to marine endosymbionts from the Indo-Pacific, found in both ecosystems, of which one taxon was conserved in oysters from both sites. This taxon was dominant in summer libraries and was weakly present in winter ones, where other members of this group were dominant. ARISA results revealed significant seasonal variation in bacterial populations of Mediterranean Sea oysters, as opposed to Red Sea ones that were stable throughout the year. We suggest that this conserved association between bacteria and oyster reflects either a symbiosis between the oyster host and some of its bacteria, a co-invasion of both parties, or both.}, } @article {pmid21631545, year = {2011}, author = {Lombard, N and Prestat, E and van Elsas, JD and Simonet, P}, title = {Soil-specific limitations for access and analysis of soil microbial communities by metagenomics.}, journal = {FEMS microbiology ecology}, volume = {78}, number = {1}, pages = {31-49}, doi = {10.1111/j.1574-6941.2011.01140.x}, pmid = {21631545}, issn = {1574-6941}, support = {R01ES016197-01/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/growth & development ; Biodiversity ; DNA, Bacterial/*analysis ; DNA, Fungal/*analysis ; Ecosystem ; Fungi/classification/genetics/growth & development ; Genetic Variation ; Metagenomics/*methods ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with. Its physicochemical properties affect microbial distributions inside the soil matrix, metagenome extraction and its subsequent analyses. To better understand the bias inherent to soil metagenome 'processing', we focus on soil physicochemical properties and their effects on the perceived bacterial distribution. In the light of this information, each step of soil metagenome processing is then discussed, with an emphasis on strategies for optimal soil sampling. Then, the interaction of cells and DNA with the soil matrix and the consequences for microbial DNA extraction are examined. Soil DNA extraction methods are compared and the veracity of the microbial profiles obtained is discussed. Finally, soil metagenomic sequence analysis and exploitation methods are reviewed.}, } @article {pmid21622781, year = {2011}, author = {Chistoserdova, L}, title = {Methylotrophy in a lake: from metagenomics to single-organism physiology.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {14}, pages = {4705-4711}, pmid = {21622781}, issn = {1098-5336}, mesh = {Aquatic Organisms/genetics ; Carbon/*metabolism ; Lakes/*microbiology ; Metagenomics ; Methylophilaceae/*genetics ; Microbial Consortia/*genetics ; United States ; Washington ; }, abstract = {This review provides a brief summary of ongoing studies in Lake Washington (Seattle, WA) directed at an understanding of the content and activities of microbial communities involved in methylotrophy. One of the findings from culture-independent approaches, including functional metagenomics, is the prominent presence of Methylotenera species in the site and their inferred activity in C(1) metabolism, highlighting the local environmental importance of this group. Comparative analyses of individual genomes of Methylophilaceae from Lake Washington provide insights into their genomic divergence and suggest significant metabolic flexibility.}, } @article {pmid21606604, year = {2011}, author = {Ghishan, FK and Kiela, PR}, title = {From probiotics to therapeutics: another step forward?.}, journal = {The Journal of clinical investigation}, volume = {121}, number = {6}, pages = {2149-2152}, pmid = {21606604}, issn = {1558-8238}, support = {R01 DK041274/DK/NIDDK NIH HHS/United States ; R01 DK067286/DK/NIDDK NIH HHS/United States ; 2R01DK041274/DK/NIDDK NIH HHS/United States ; 5R01DK067286/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/administration & dosage/pharmacology/*therapeutic use ; Colitis/chemically induced/prevention & control/therapy ; Drug Evaluation, Preclinical ; Enzyme Activation/drug effects ; ErbB Receptors/drug effects/physiology ; Food Microbiology ; Gastrointestinal Diseases/microbiology/prevention & control/*therapy ; Humans ; Inflammatory Bowel Diseases/therapy ; Lacticaseibacillus rhamnosus/physiology ; *Metagenome ; Mice ; Microbial Consortia/*physiology ; Microbial Interactions ; Opportunistic Infections/prevention & control ; Probiotics/*therapeutic use ; Protein Kinases/drug effects/physiology ; Recombinant Proteins/administration & dosage/pharmacology/therapeutic use ; }, abstract = {Preclinical studies with probiotics continue to unravel mechanisms of cytoprotection and suggest that approaches utilizing microbial products as therapeutics in acute and chronic gastrointestinal disorders could be effective. However, clinical trials using these bacteria have thus far been inconsistent. In this issue of the JCI, Yan et al. describe a novel mechanism of cytoprotection by p40, a soluble product of Lactobacillus rhamnosus GG, mediated via EGFR. The efficacy of p40 in three models of chemically induced colitis indicates tremendous therapeutic potential, though this finding will need to be verified in human patients.}, } @article {pmid21575735, year = {2011}, author = {Cunha, IS and Barreto, CC and Costa, OY and Bomfim, MA and Castro, AP and Kruger, RH and Quirino, BF}, title = {Bacteria and Archaea community structure in the rumen microbiome of goats (Capra hircus) from the semiarid region of Brazil.}, journal = {Anaerobe}, volume = {17}, number = {3}, pages = {118-124}, doi = {10.1016/j.anaerobe.2011.04.018}, pmid = {21575735}, issn = {1095-8274}, mesh = {Animals ; Archaea/classification/*genetics/isolation & purification ; Bacteria/classification/*genetics/isolation & purification ; Base Sequence ; Biota ; Brazil ; Female ; Gene Library ; Genes, Archaeal ; Genes, Bacterial ; Goats/*microbiology ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Most studies present in the literature about the rumen microbiome have focused on cattle and sheep. This is the first report of the characterization of the bacterial and archaeal communities present in the liquid and solid-associated fractions of the rumen from free ranging Moxotó breed goats using 16S rRNA gene libraries. PCR was used to amplify the 16S rRNA gene with bacterial and archaeal universal primers and sequences from each library constructed were obtained. Sequences of Bacteria from the phyla Bacteroidetes and Firmicutes were predominant. The overall dominant classes in the rumen were Clostridia and Bacteroidia, which are known to play a role in plant fiber degradation in other ruminants. Unclassified Bacteria accounted for 4.7% of the liquid fraction sequences and 16.4% of the solid fraction sequences. From the archaeal libraries only sequences from the phylum Euryarcheota were identified and were assigned to the class Methanobacteria of the genera Methanobrevibacter and Methanosphaera. A group of Archaea not previously known to be associated with the rumen was identified: uncultured methanogens belonging to the "uncultured marine bacteria" groups II and III. The local water contained high salt concentrations and this may explain the presence of these groups in the Moxotó goat rumen.}, } @article {pmid21575148, year = {2011}, author = {Lamendella, R and Domingo, JW and Ghosh, S and Martinson, J and Oerther, DB}, title = {Comparative fecal metagenomics unveils unique functional capacity of the swine gut.}, journal = {BMC microbiology}, volume = {11}, number = {}, pages = {103}, pmid = {21575148}, issn = {1471-2180}, mesh = {Animals ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biodiversity ; Feces/*microbiology ; Gastrointestinal Tract/microbiology ; Genes, rRNA ; *Metagenome ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Swine/*microbiology ; }, abstract = {BACKGROUND: Uncovering the taxonomic composition and functional capacity within the swine gut microbial consortia is of great importance to animal physiology and health as well as to food and water safety due to the presence of human pathogens in pig feces. Nonetheless, limited information on the functional diversity of the swine gut microbiome is available.

RESULTS: Analysis of 637, 722 pyrosequencing reads (130 megabases) generated from Yorkshire pig fecal DNA extracts was performed to help better understand the microbial diversity and largely unknown functional capacity of the swine gut microbiome. Swine fecal metagenomic sequences were annotated using both MG-RAST and JGI IMG/M-ER pipelines. Taxonomic analysis of metagenomic reads indicated that swine fecal microbiomes were dominated by Firmicutes and Bacteroidetes phyla. At a finer phylogenetic resolution, Prevotella spp. dominated the swine fecal metagenome, while some genes associated with Treponema and Anareovibrio species were found to be exclusively within the pig fecal metagenomic sequences analyzed. Functional analysis revealed that carbohydrate metabolism was the most abundant SEED subsystem, representing 13% of the swine metagenome. Genes associated with stress, virulence, cell wall and cell capsule were also abundant. Virulence factors associated with antibiotic resistance genes with highest sequence homology to genes in Bacteroidetes, Clostridia, and Methanosarcina were numerous within the gene families unique to the swine fecal metagenomes. Other abundant proteins unique to the distal swine gut shared high sequence homology to putative carbohydrate membrane transporters.

CONCLUSIONS: The results from this metagenomic survey demonstrated the presence of genes associated with resistance to antibiotics and carbohydrate metabolism suggesting that the swine gut microbiome may be shaped by husbandry practices.}, } @article {pmid21569081, year = {2011}, author = {Yung, PY and Kjelleberg, S and Thomas, T}, title = {A polyphasic approach to the exploration of collagenolytic activity in the bacterial community associated with the marine sponge Cymbastela concentrica.}, journal = {FEMS microbiology letters}, volume = {321}, number = {1}, pages = {24-29}, doi = {10.1111/j.1574-6968.2011.02306.x}, pmid = {21569081}, issn = {1574-6968}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/*enzymology/genetics/isolation & purification ; Biodiversity ; Collagen/*metabolism ; Collagenases/chemistry/genetics/*metabolism ; Gelatinases/metabolism ; Gene Library ; High-Throughput Screening Assays ; Metagenomics ; Molecular Sequence Data ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Collagen is an important, extracellular structural protein for metazoans and provides a rich nutrient source for bacteria that possess collagen-degrading enzymes. In a symbiotic host system, collagen degradation could benefit the bacteria, but would be harmful for the eukaryotic host. Using a polyphasic approach, we investigated the presence of collagenolytic activity in the bacterial community hosted by the marine sponge Cymbastela concentrica. Functional screening for collagenase activity using metagenomic library clones (227 Mbp) and cultured isolates of sponge's bacterial community, as well as bioinformatic analysis of metagenomic shotgun-sequencing data (106,679 predicted genes) were used. The results show that the abundant members of the bacterial community contain very few genes encoding for collagenolytic enzymes, while some low-abundance sponge isolates possess collagenolytic activities. These findings indicate that collagen is not a preferred nutrient source for the majority of the members of the bacterial community associated with healthy C. concentrica, and that some low-abundance bacteria have collagenase activities that have the potential to harm the sponge through tissue degradation.}, } @article {pmid21554340, year = {2011}, author = {Wang, HY and Gao, YB and Fan, QW and Xu, Y}, title = {Characterization and comparison of microbial community of different typical Chinese liquor Daqus by PCR-DGGE.}, journal = {Letters in applied microbiology}, volume = {53}, number = {2}, pages = {134-140}, doi = {10.1111/j.1472-765X.2011.03076.x}, pmid = {21554340}, issn = {1472-765X}, mesh = {Alcoholic Beverages/*microbiology ; Bacteria/classification/genetics ; DNA Primers/genetics ; DNA, Bacterial/analysis/genetics ; Denaturing Gradient Gel Electrophoresis ; *Ethanol ; Fungi/classification/genetics ; Metagenome ; Microbial Consortia/*genetics ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; Yeasts/classification/genetics ; }, abstract = {AIMS: To identify and compare microbiota in Chinese liquor Daqu, which were produced in the different regions using different production process.

METHODS AND RESULTS: The DNA exacted from Daqu samples was used as a template for PCR with universal primers of 16S rRNA, 26S rRNA and 18S rRNA, respectively. The amplicons were analysed using denaturing gradient gel electrophoresis (DGGE). It was observed that the bacterial DGGE profile indicated high diversity and predominance of lactic acid bacteria. The results showed that Saccharomycopsis fibuligera and Pichia anomal were dominant yeast species and that several non-Saccharomyces yeasts including Hanseniaspora guilliermondii, Debaryomyces hansenii, Issatchenkia orientalis and Trichosporon asahii were also detected. As for fungal DGGE, Aspergillus oryzae and Absidia blakesleeana were the most common species amongst different samples. Based on the DGGE analysis, a few differences in community structure were found between Daqu samples.

CONCLUSIONS: A variety of bacteria, yeast and moulds were identified in Daqu samples, in addition to the present knowledge obtained mainly through the traditional culture-dependent methods. Moreover, production temperature played a more decisive role on the formation of micro-organism composition in Daqu than geographical region.

PCR-DGGE technique was used in this study to fully observe and asses all microbial community (including bacteria, yeast and mould) in Chinese liquor Daqu for the first time and proved to be effective in profiling Daqu microbial diversity.}, } @article {pmid21551032, year = {2011}, author = {Mendes, R and Kruijt, M and de Bruijn, I and Dekkers, E and van der Voort, M and Schneider, JH and Piceno, YM and DeSantis, TZ and Andersen, GL and Bakker, PA and Raaijmakers, JM}, title = {Deciphering the rhizosphere microbiome for disease-suppressive bacteria.}, journal = {Science (New York, N.Y.)}, volume = {332}, number = {6033}, pages = {1097-1100}, doi = {10.1126/science.1203980}, pmid = {21551032}, issn = {1095-9203}, mesh = {Actinobacteria/genetics/isolation & purification/physiology ; *Antibiosis ; Archaea/classification/genetics/isolation & purification/physiology ; Bacteria/classification/genetics/isolation & purification ; Beta vulgaris/microbiology ; *Metagenome ; *Microbial Consortia ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Peptide Synthases/genetics/metabolism ; Plant Diseases/microbiology/*prevention & control ; Plant Roots/microbiology ; Proteobacteria/genetics/isolation & purification/physiology ; Pseudomonadaceae/genetics/isolation & purification/physiology ; Rhizoctonia/*physiology ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Disease-suppressive soils are exceptional ecosystems in which crop plants suffer less from specific soil-borne pathogens than expected owing to the activities of other soil microorganisms. For most disease-suppressive soils, the microbes and mechanisms involved in pathogen control are unknown. By coupling PhyloChip-based metagenomics of the rhizosphere microbiome with culture-dependent functional analyses, we identified key bacterial taxa and genes involved in suppression of a fungal root pathogen. More than 33,000 bacterial and archaeal species were detected, with Proteobacteria, Firmicutes, and Actinobacteria consistently associated with disease suppression. Members of the γ-Proteobacteria were shown to have disease-suppressive activity governed by nonribosomal peptide synthetases. Our data indicate that upon attack by a fungal root pathogen, plants can exploit microbial consortia from soil for protection against infections.}, } @article {pmid21549585, year = {2011}, author = {Li, C and Zhang, L and Ding, L and Ren, H and Cui, H}, title = {Effect of conductive polymers coated anode on the performance of microbial fuel cells (MFCs) and its biodiversity analysis.}, journal = {Biosensors & bioelectronics}, volume = {26}, number = {10}, pages = {4169-4176}, doi = {10.1016/j.bios.2011.04.018}, pmid = {21549585}, issn = {1873-4235}, mesh = {Aminophenols ; Aniline Compounds ; Biodiversity ; Bioelectric Energy Sources/*microbiology ; Electric Conductivity ; Electrodes ; Electron Transport ; Metagenome ; Microscopy, Electron, Scanning ; Reproducibility of Results ; Temperature ; }, abstract = {Conductive polymer, one of the most attractive electrode materials, has been applied to coat anode of MFC to improve its performance recently. In this paper, two conductive polymer materials, polyaniline (PANI) and poly(aniline-co-o-aminophenol) (PAOA) were used to modify carbon felt anode and physical and chemical properties of the modified anodes were studied. The power output and biodiversity of modified anodes, along with unmodified carbon anode were compared in two-chamber MFCs. Results showed that the maximum power density of PANI and PAOA MFC could reach 27.4 mW/m(2) and 23.8 mW/m(2), comparing with unmodified MFC, increased by 35% and 18% separately. Low temperature caused greatly decrease of the maximum voltage by 70% and reduced the sorts of bacteria on anodes in the three MFCs. Anode biofilm analysis showed different bacteria enrichment: a larger mount of bacteria and higher biodiversity were found on the two modified anodes than on the unmodified one. For PANI anode, the two predominant bacteria were phylogenetically closely related to Hippea maritima and an uncultured clone MEC_Bicarb_Ac-008; for PAOA, Clostridiales showed more enrichment. Compare PAOA with PANI, the former introduced phenolic hydroxyl group by copolymerization o-aminophenol with aniline, which led to a different microbial community and the mechanism of group effect was proposed.}, } @article {pmid21544196, year = {2011}, author = {Ng, TF and Duffy, S and Polston, JE and Bixby, E and Vallad, GE and Breitbart, M}, title = {Exploring the diversity of plant DNA viruses and their satellites using vector-enabled metagenomics on whiteflies.}, journal = {PloS one}, volume = {6}, number = {4}, pages = {e19050}, pmid = {21544196}, issn = {1932-6203}, mesh = {Animals ; Chenopodium ambrosioides/virology ; DNA Viruses/classification/*genetics ; Hemiptera/*virology ; Insect Vectors/*virology ; Metagenomics/*methods ; Phylogeny ; Plant Viruses/classification/*genetics ; Polymerase Chain Reaction ; }, abstract = {Current knowledge of plant virus diversity is biased towards agents of visible and economically important diseases. Less is known about viruses that have not caused major diseases in crops, or viruses from native vegetation, which are a reservoir of biodiversity that can contribute to viral emergence. Discovery of these plant viruses is hindered by the traditional approach of sampling individual symptomatic plants. Since many damaging plant viruses are transmitted by insect vectors, we have developed "vector-enabled metagenomics" (VEM) to investigate the diversity of plant viruses. VEM involves sampling of insect vectors (in this case, whiteflies) from plants, followed by purification of viral particles and metagenomic sequencing. The VEM approach exploits the natural ability of highly mobile adult whiteflies to integrate viruses from many plants over time and space, and leverages the capability of metagenomics for discovering novel viruses. This study utilized VEM to describe the DNA viral community from whiteflies (Bemisia tabaci) collected from two important agricultural regions in Florida, USA. VEM successfully characterized the active and abundant viruses that produce disease symptoms in crops, as well as the less abundant viruses infecting adjacent native vegetation. PCR assays designed from the metagenomic sequences enabled the complete sequencing of four novel begomovirus genome components, as well as the first discovery of plant virus satellites in North America. One of the novel begomoviruses was subsequently identified in symptomatic Chenopodium ambrosiodes from the same field site, validating VEM as an effective method for proactive monitoring of plant viruses without a priori knowledge of the pathogens. This study demonstrates the power of VEM for describing the circulating viral community in a given region, which will enhance our understanding of plant viral diversity, and facilitate emerging plant virus surveillance and management of viral diseases.}, } @article {pmid21538072, year = {2012}, author = {Heuer, W and Kettenring, A and Stumpp, SN and Eberhard, J and Gellermann, E and Winkel, A and Stiesch, M}, title = {Metagenomic analysis of the peri-implant and periodontal microflora in patients with clinical signs of gingivitis or mucositis.}, journal = {Clinical oral investigations}, volume = {16}, number = {3}, pages = {843-850}, pmid = {21538072}, issn = {1436-3771}, mesh = {Adult ; Aged ; Biodiversity ; Biofilms ; Dental Implants/microbiology ; Dental Plaque Index ; Dental Prosthesis, Implant-Supported ; Female ; Gingivitis/*microbiology ; Humans ; Jaw, Edentulous, Partially/*microbiology ; Male ; Metagenome/*genetics ; Middle Aged ; Molecular Typing ; Mucositis/microbiology ; Peri-Implantitis/*microbiology ; Periodontium/*microbiology ; Polymorphism, Single-Stranded Conformational ; Statistics, Nonparametric ; }, abstract = {The long-term success of osseointegrated oral implants is endangered by inflammation of peri-implant hard and soft tissues caused by bacterial biofilms that may have been initiated by bacterial transmission from the adjacent dentition. The present study aimed to compare the bacterial communities at inflamed implant and tooth sites by broad-range PCR techniques to evaluate the etiological processes of peri-implant and periodontal diseases and potential future therapeutic strategies. Eighteen samples of peri-implant and periodontal microflora were collected from nine partially edentulous patients with implant-retained crowns or bridges revealing clinical signs of gingivitis or mucositis. The clinical parameters plaque index (PI), probing depth (PD), and bleeding on probing were recorded. Amplified fragments of bacterial 16S rRNA genes were separated by use of single-strand conformation polymorphism analysis, and sequences were determined to identify the predominant bacterial genera. The clinical parameters PI and PD were significantly different at implants (PI = 0.4 ± 0.7, PD = 3.1 ± 0.6 mm) compared with teeth (PI = 1.8 ± 0.8, PD = 2.5 ± 0.2 mm). A total of 20 different genera were found at the inflamed tooth and implant sites. The microbial diversity of the microflora surrounding the remaining dentition (12.0 ± 3.8) was significantly higher (p = 0.01) than the diversity of the peri-implant microflora at implant-retained crowns or bridges (6.3 ± 2.3). Within the limitations of the present study, the microbial diversity of the investigated implants and teeth with clinical signs of mucositis or gingivitis exhibits substantial differences, demonstrating that transmission of the complete bacterial microflora from teeth to implants could be excluded. Furthermore, broad-range molecular biological detection methods specify bacterial genera and species in the peri-implant and periodontal microflora which were not in the focus of research interests so far.}, } @article {pmid21519906, year = {2011}, author = {Verma, D and Satyanarayana, T}, title = {An improved protocol for DNA extraction from alkaline soil and sediment samples for constructing metagenomic libraries.}, journal = {Applied biochemistry and biotechnology}, volume = {165}, number = {2}, pages = {454-464}, doi = {10.1007/s12010-011-9264-5}, pmid = {21519906}, issn = {1559-0291}, mesh = {2-Propanol/chemistry ; Archaea ; Bacteria ; Cell Extracts ; Charcoal/chemistry ; DNA, Archaeal/*analysis ; DNA, Bacterial/*analysis ; DNA, Fungal/*analysis ; DNA, Intergenic/analysis ; Fungi ; Genomic Library ; *Metagenome ; Metagenomics/*methods ; *Microbial Consortia ; Polyethylene Glycols/chemistry ; Polymerase Chain Reaction ; Povidone/analogs & derivatives/chemistry ; RNA, Ribosomal, 16S/analysis ; *Soil Microbiology ; Xylans/metabolism ; }, abstract = {An improved single-step protocol has been developed for extracting pure community humic substance-free DNA from alkaline soils and sediments. The method is based on direct cell lysis in the presence of powdered activated charcoal and polyvinylpolypyrrolidone followed by precipitation with polyethyleneglycol and isopropanol. The strategy allows simultaneous isolation and purification of DNA while minimizing the loss of DNA with respect to other available protocols for metagenomic DNA extraction. Moreover, the purity levels are significant, which are difficult to attain with any of the methods reported in the literature for DNA extraction from soils. The DNA thus extracted was free from humic substances and, therefore, could be processed for restriction digestion, PCR amplification as well as for the construction of metagenomic libraries.}, } @article {pmid21512891, year = {2011}, author = {Mardanov, AV and Gumerov, VM and Beletsky, AV and Perevalova, AA and Karpov, GA and Bonch-Osmolovskaya, EA and Ravin, NV}, title = {Uncultured archaea dominate in the thermal groundwater of Uzon Caldera, Kamchatka.}, journal = {Extremophiles : life under extreme conditions}, volume = {15}, number = {3}, pages = {365-372}, pmid = {21512891}, issn = {1433-4909}, mesh = {Acidithiobacillus/classification ; Archaea/*classification/genetics/isolation & purification ; Autotrophic Processes ; Bacteria/*classification/genetics/isolation & purification ; Biodiversity ; Crenarchaeota/classification ; DNA, Archaeal/isolation & purification ; DNA, Bacterial/isolation & purification ; Hot Springs/*microbiology ; Hot Temperature ; Hydrogen-Ion Concentration ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ribotyping ; Russia ; Thermoplasmales/classification ; *Water Microbiology ; }, abstract = {The thermoacidophilic microbial community inhabiting the groundwater with pH 4.0 and temperature 50°C at the East Thermal Field of Uzon Caldera, Kamchatka, was examined using pyrosequencing of the V3 region of the 16S rRNA gene. Bacteria comprise about 30% of microorganisms and are represented primarily by aerobic lithoautotrophs using the energy sources of volcanic origin--thermoacidophilic methanotrophs of the phylum Verrucomicrobia and Acidithiobacillus spp. oxidising metals and reduced sulfur compounds. More than 70% of microbial population in this habitat were represented by archaea, in majority affiliated with "uncultured" lineages. The most numerous group (39% of all archaea) represented a novel division in the phylum Euryarchaeota related to the order Thermoplasmatales. Another abundant group (33% of all archaea) was related to MCG1 lineage of the phylum Crenarchaeota, originally detected in the Yellowstone hot spring as the environmental clone pJP89. The organisms belonging to these two groups are widely spread in hydrothermal environments worldwide. These data indicate an important environmental role of these two archaeal groups and should stimulate the investigation of their metabolism by cultivation or metagenomic approaches.}, } @article {pmid21508958, year = {2011}, author = {Arumugam, M and Raes, J and Pelletier, E and Le Paslier, D and Yamada, T and Mende, DR and Fernandes, GR and Tap, J and Bruls, T and Batto, JM and Bertalan, M and Borruel, N and Casellas, F and Fernandez, L and Gautier, L and Hansen, T and Hattori, M and Hayashi, T and Kleerebezem, M and Kurokawa, K and Leclerc, M and Levenez, F and Manichanh, C and Nielsen, HB and Nielsen, T and Pons, N and Poulain, J and Qin, J and Sicheritz-Ponten, T and Tims, S and Torrents, D and Ugarte, E and Zoetendal, EG and Wang, J and Guarner, F and Pedersen, O and de Vos, WM and Brunak, S and Doré, J and , and Antolín, M and Artiguenave, F and Blottiere, HM and Almeida, M and Brechot, C and Cara, C and Chervaux, C and Cultrone, A and Delorme, C and Denariaz, G and Dervyn, R and Foerstner, KU and Friss, C and van de Guchte, M and Guedon, E and Haimet, F and Huber, W and van Hylckama-Vlieg, J and Jamet, A and Juste, C and Kaci, G and Knol, J and Lakhdari, O and Layec, S and Le Roux, K and Maguin, E and Mérieux, A and Melo Minardi, R and M'rini, C and Muller, J and Oozeer, R and Parkhill, J and Renault, P and Rescigno, M and Sanchez, N and Sunagawa, S and Torrejon, A and Turner, K and Vandemeulebrouck, G and Varela, E and Winogradsky, Y and Zeller, G and Weissenbach, J and Ehrlich, SD and Bork, P}, title = {Enterotypes of the human gut microbiome.}, journal = {Nature}, volume = {473}, number = {7346}, pages = {174-180}, pmid = {21508958}, issn = {1476-4687}, support = {/WT_/Wellcome Trust/United Kingdom ; 076964/WT_/Wellcome Trust/United Kingdom ; 082372/WT_/Wellcome Trust/United Kingdom ; K24 DK002800/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics ; Bacterial Typing Techniques ; Biodiversity ; Biomarkers/analysis ; Europe ; Feces/microbiology ; Female ; Humans ; Intestines/*microbiology ; Male ; *Metagenome ; Metagenomics ; Phylogeny ; }, abstract = {Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers.}, } @article {pmid21494865, year = {2011}, author = {Neveu, J and Regeard, C and DuBow, MS}, title = {Isolation and characterization of two serine proteases from metagenomic libraries of the Gobi and Death Valley deserts.}, journal = {Applied microbiology and biotechnology}, volume = {91}, number = {3}, pages = {635-644}, doi = {10.1007/s00253-011-3256-9}, pmid = {21494865}, issn = {1432-0614}, mesh = {Amino Acid Sequence ; Base Sequence ; Biomass ; California ; China ; Desert Climate ; Electrophoresis, Polyacrylamide Gel ; Gene Library ; *Metagenomics ; Microbial Consortia/*genetics ; Mongolia ; Nevada ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Serine Proteases/*genetics/*isolation & purification ; Silicon Dioxide/*analysis ; United States ; }, abstract = {The screening of environmental DNA metagenome libraries for functional activities can provide an important source of new molecules and enzymes. In this study, we identified 17 potential protease-producing clones from two metagenomic libraries derived from samples of surface sand from the Gobi and Death Valley deserts. Two of the proteases, DV1 and M30, were purified and biochemically examined. These two proteases displayed a molecular mass of 41.5 kDa and 45.7 kDa, respectively, on SDS polyacrylamide gels. Alignments with known protease sequences showed less than 55% amino acid sequence identity. These two serine proteases appear to belong to the subtilisin (S8A) family and displayed several unique biochemical properties. Protease DV1 had an optimum pH of 8 and an optimal activity at 55°C, while protease M30 had an optimum pH >11 and optimal activity at 40°C. The properties of these enzymes make them potentially useful for biotechnological applications and again demonstrate that metagenomic approaches can be useful, especially when coupled with the study of novel environments such as deserts.}, } @article {pmid21494150, year = {2011}, author = {Zemanick, ET and Sagel, SD and Harris, JK}, title = {The airway microbiome in cystic fibrosis and implications for treatment.}, journal = {Current opinion in pediatrics}, volume = {23}, number = {3}, pages = {319-324}, doi = {10.1097/MOP.0b013e32834604f2}, pmid = {21494150}, issn = {1531-698X}, mesh = {Bacteria, Anaerobic/genetics/*isolation & purification ; Biota ; Cystic Fibrosis/drug therapy/*microbiology ; DNA Barcoding, Taxonomic ; Humans ; *Metagenome ; Polymerase Chain Reaction ; }, abstract = {PURPOSE OF REVIEW: Lung disease in cystic fibrosis (CF) results from chronic airway infection and inflammation leading to progressive bronchiectasis and respiratory failure. Bacterial pathogens, including Pseudomonas aeruginosa, Staphylococcus aureus, and Burkholderia cepacia, are known contributors. Recent studies using culture-independent molecular techniques and anaerobic cultures have broadened our view of CF airway bacterial communities.

RECENT FINDINGS: Sanger sequencing, high-throughput pyrosequencing, and phylogenetic microarray analysis have been used to comprehensively examine the airway microbiome in CF. Findings confirm that CF airway bacterial communities are highly complex structures with anaerobes frequently present. Importantly, there is evidence that loss of community diversity and richness is associated with older age and decreased lung function in CF. Bacterial communities are also likely influenced by antibiotic use, chronic P. aeruginosa infection, host genetic background (ΔF508 CFTR mutation) and geographic variations. Quantitative anaerobic cultures also detect high quantities of anaerobes from CF airway samples, including during pulmonary exacerbations. The effect of antimicrobial therapy on the airway microbiome needs further investigation. In addition, probiotic approaches have been recently studied; whether probiotics act by altering microbial communities or by modulating host inflammatory response is unknown.

SUMMARY: Complex bacterial communities, including traditional CF-associated pathogens and anaerobic bacteria, are common in CF airways. Novel therapeutic approaches aimed at modulating airway bacterial communities may lead to improved treatment of CF lung disease.}, } @article {pmid21477358, year = {2011}, author = {Vael, C and Vanheirstraeten, L and Desager, KN and Goossens, H}, title = {Denaturing gradient gel electrophoresis of neonatal intestinal microbiota in relation to the development of asthma.}, journal = {BMC microbiology}, volume = {11}, number = {}, pages = {68}, pmid = {21477358}, issn = {1471-2180}, mesh = {Asthma/*etiology ; Bacteroides fragilis/genetics/isolation & purification/pathogenicity ; *Biodiversity ; Child, Preschool ; Clostridium/genetics/isolation & purification/pathogenicity ; Denaturing Gradient Gel Electrophoresis ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Infant ; Infant, Newborn ; Male ; *Metagenome ; Prospective Studies ; Severity of Illness Index ; }, abstract = {BACKGROUND: The extended 'hygiene hypothesis' suggests that the initial composition of the infant gut microbiota is a key determinant in the development of atopic disease. Several studies have demonstrated that the microbiota of allergic and non-allergic infants are different even before the development of symptoms, with a critical time window during the first 6 months of life. The aim of the study was to investigate the association between early intestinal colonisation and the development of asthma in the first 3 years of life using DGGE (denaturing gradient gel electrophoresis).

METHODS: In a prospective birth cohort, 110 children were classified according to the API (Asthma Predictive Index). A positive index included wheezing during the first three years of life combined with eczema in the child in the first years of life or with a parental history of asthma. A fecal sample was taken at the age of 3 weeks and analysed with DGGE using universal and genus specific primers.

RESULTS: The Asthma Predictive Index was positive in 24/110 (22%) of the children. Using universal V3 primers a band corresponding to a Clostridum coccoides XIVa species was significantly associated with a positive API. A Bacteroides fragilis subgroup band was also significantly associated with a positive API. A final DGGE model, including both bands, allowed correct classification of 73% (80/110) of the cases.

CONCLUSION: Fecal colonisation at age 3 weeks with either a Bacteroides fragilis subgroup or a Clostridium coccoides subcluster XIVa species is an early indicator of possible asthma later in life. These findings need to be confirmed in a new longitudinal follow-up study.}, } @article {pmid21468224, year = {2010}, author = {Salzman, NH}, title = {Paneth cell defensins and the regulation of the microbiome: détente at mucosal surfaces.}, journal = {Gut microbes}, volume = {1}, number = {6}, pages = {401-406}, pmid = {21468224}, issn = {1949-0984}, support = {R01 AI057757/AI/NIAID NIH HHS/United States ; R21 AI057757/AI/NIAID NIH HHS/United States ; AI057757/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification/growth & development/*immunology ; Bacterial Load ; *Biodiversity ; Defensins/*immunology/metabolism ; Humans ; *Immunity, Mucosal ; Intestine, Small/microbiology ; Metagenome/*immunology ; Mice ; Mice, Knockout ; Paneth Cells/*immunology/metabolism ; }, abstract = {Recently, our laboratory demonstrated that Paneth cell defensins, innate antimicrobial peptides that contribute to mucosal host defense, are able to regulate the composition of the intestinal bacterial microbiome. Using complementary mouse models of defensin deficiency (MMP7(-/-)) and surplus (HD5(+/+)), we noted defensin-dependent reciprocal shifts in the dominant bacterial species of the small intestine, without changes in total bacterial numbers. In addition, mice that expressed HD5 showed a significant loss of segemented filamentous bacteria (SFB), resulting in reduced numbers of Th17 cells in the lamina propria. This data showed a novel role for PC defensins in intestinal homeostasis, by regulation of the small intestinal microbiome. The microbiome plays an essential role in mediating host physiology, metabolism and immune response. The ability of PC defensins to regulate the composition of the biome suggests a much broader importance of these innate immune effectors than previously considered. In this addendum, the role of PC defensins in the regulation of the intestinal microbiome is reviewed, and discussed in the context of recent evidence that highlights the important role of PCs and defensins in the pathophysiology of inflammatory bowel disease.}, } @article {pmid21468215, year = {2010}, author = {Viswanathan, V}, title = {Self portraits. Gut microbiology.}, journal = {Gut microbes}, volume = {1}, number = {6}, pages = {357-358}, pmid = {21468215}, issn = {1949-0984}, mesh = {Anti-Bacterial Agents/pharmacology ; *Biodiversity ; Diet/methods ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; Metagenomics/methods ; }, abstract = {In dealing with gastric contents, faesces and urine, chemically and bacteriologically, no very complex apparatus is required, and with a brief preliminary training any practitioner possessing the instinct of research may in a very few years acquire the power of perceiving, in many of the chronic gastro-intestinal conditions coming before him daily, order—pathological order if you will—where before he saw nothing but chaos. David Sommerville, Lancet 1910.}, } @article {pmid21466489, year = {2011}, author = {Fries, W and Comunale, S}, title = {Ulcerative colitis: pathogenesis.}, journal = {Current drug targets}, volume = {12}, number = {10}, pages = {1373-1382}, doi = {10.2174/138945011796818261}, pmid = {21466489}, issn = {1873-5592}, mesh = {Animals ; Autoantibodies/immunology ; Colitis, Ulcerative/*etiology/immunology/microbiology/*pathology ; Epithelial Cells/immunology/microbiology/pathology ; Humans ; Intestinal Mucosa/immunology/microbiology/*pathology ; Metagenome/physiology ; }, abstract = {The pathogenesis of ulcerative is still poorly understood. With the introduction of new culture-independent techniques the research on the intestinal microbiota has revealed an important reduction of Bacteroidetes and Firmicutes leading to a reduced biodiversity and dysbiosis in these patients. Going in depth, the intestinal barrier is covered under physiologic conditions by a mostly sterile mucus layer. Besides a reduction of mucus thickness or an alteration in mucus composition hypothesized for human ulcerative colitis, new evidence coming from mouse models has introduced a novel concept based on cellular stress due to misfolded mucus-associated proteins opening a new research area for the epithelial cell lining. A dysregulated immune response involving the innate (e.g. toll-like receptors, dendritic cells, etc) and the adaptive immune system (e.g. effector T-cells, regulatory T-cells, eosinophils, neutrophils, etc) may follow or precede the macroscopic lesions. The immune response in ulcerative colitis is represented principally by secretion of interleukin-5 and -13 being the latter responsible for the direct cytotoxicity against the epithelial cells. In latter stages the role of interleukin-17 producing cells, apparently differently regulated compared with Crohn's disease, remains to be elucidated. Finally, human ulcerative colitis is characterized by the presence of various types of autoantibodies including pANCA, antibodies against goblet cells and the isoforms 1 and 5 of human tropomyosin. The pathogenic potential of these antibodies is still debated. The present review focus on new achievements in the various scenarios converging to the clinical and histopathological feature of ulcerative colitis.}, } @article {pmid21440432, year = {2011}, author = {Taupp, M and Mewis, K and Hallam, SJ}, title = {The art and design of functional metagenomic screens.}, journal = {Current opinion in biotechnology}, volume = {22}, number = {3}, pages = {465-472}, doi = {10.1016/j.copbio.2011.02.010}, pmid = {21440432}, issn = {1879-0429}, mesh = {DNA, Bacterial ; Escherichia coli/*genetics/metabolism ; Gene Library ; Genes, Bacterial ; Genetic Vectors ; Metagenomics/*methods ; Microbial Consortia ; Sequence Analysis, DNA ; }, abstract = {This article summarizes general design principles for functional metagenomics. The focus is on Escherichia coli as an expression host, although alternative host-vector systems are discussed in relation to optimizing gene recovery in activity-based screens. Examples of DNA isolation and enrichment approaches, library construction and phenotypic read-out are described with special emphasis on the use of high throughput technologies for rapid isolation of environmental clones encoding phenotypic traits of interest.}, } @article {pmid21437280, year = {2011}, author = {Lucero, ME and Unc, A and Cooke, P and Dowd, S and Sun, S}, title = {Endophyte microbiome diversity in micropropagated Atriplex canescens and Atriplex torreyi var griffithsii.}, journal = {PloS one}, volume = {6}, number = {3}, pages = {e17693}, pmid = {21437280}, issn = {1932-6203}, mesh = {Atriplex/cytology/*growth & development/*microbiology/ultrastructure ; Bacteria/*growth & development/isolation & purification ; Base Sequence ; Bayes Theorem ; *Biodiversity ; DNA, Intergenic/genetics ; Fungi/cytology/genetics/*growth & development/isolation & purification ; Germination ; *Metagenome ; Molecular Sequence Data ; Regeneration/physiology ; Seeds/cytology/microbiology ; Sequence Analysis, DNA ; }, abstract = {Microbial diversity associated with micropropagated Atriplex species was assessed using microscopy, isolate culturing, and sequencing. Light, electron, and confocal microscopy revealed microbial cells in aseptically regenerated leaves and roots. Clone libraries and tag-encoded FLX amplicon pyrosequencing (TEFAP) analysis amplified sequences from callus homologous to diverse fungal and bacterial taxa. Culturing isolated some seed borne endophyte taxa which could be readily propagated apart from the host. Microbial cells were observed within biofilm-like residues associated with plant cell surfaces and intercellular spaces. Various universal primers amplified both plant and microbial sequences, with different primers revealing different patterns of fungal diversity. Bacterial and fungal TEFAP followed by alignment with sequences from curated databases revealed 7 bacterial and 17 ascomycete taxa in A. canescens, and 5 bacterial taxa in A. torreyi. Additional diversity was observed among isolates and clone libraries. Micropropagated Atriplex retains a complex, intimately associated microbiome which includes diverse strains well poised to interact in manners that influence host physiology. Microbiome analysis was facilitated by high throughput sequencing methods, but primer biases continue to limit recovery of diverse sequences from even moderately complex communities.}, } @article {pmid21431767, year = {2011}, author = {Sun, Y and Wolcott, RD and Dowd, SE}, title = {Tag-encoded FLX amplicon pyrosequencing for the elucidation of microbial and functional gene diversity in any environment.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {733}, number = {}, pages = {129-141}, doi = {10.1007/978-1-61779-089-8_9}, pmid = {21431767}, issn = {1940-6029}, mesh = {Animals ; Bacteria/*genetics/isolation & purification ; Biodiversity ; DNA Primers/genetics ; DNA, Bacterial/*genetics/isolation & purification ; DNA, Ribosomal/genetics/isolation & purification ; *Genetic Variation ; Metagenome/genetics ; Microspheres ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; }, abstract = {Comprehensive evaluation of microbial diversity in almost any environment is now possible. Questions such as "Does the addition of fiber to the diet of humans change the gastrointestinal microbiota?" can now be answered easily and inexpensively. Tag-encoded FLX-amplicon pyrosequencing (TEFAP) has been utilized to evaluate bacterial, archaeal, fungal, algal, as well as functional genes. Using the new tag-encoded FLX amplicon pyrosequencing (bTEFAP) approach, we have evaluated the microbial diversity using a more cost-effective and largely reproducible method that would allow us to sequence the ribosomal RNA genes of microorganisms (hereafter focused on bacteria), without the need for the inherent bias of culture methods. These developments have ushered in a new age of microbial ecology studies, and we have utilized this technology to evaluate the microbiome in a wide range of systems in almost any conceivable environment.}, } @article {pmid21429530, year = {2011}, author = {Ramond, JB and Petit, F and Quillet, L and Ouddane, B and Berthe, T}, title = {Evidence of methylmercury production and modification of the microbial community structure in estuary sediments contaminated with wastewater treatment plant effluents.}, journal = {Marine pollution bulletin}, volume = {62}, number = {5}, pages = {1073-1080}, doi = {10.1016/j.marpolbul.2011.02.013}, pmid = {21429530}, issn = {1879-3363}, mesh = {Environmental Monitoring ; Fresh Water/chemistry/microbiology ; Geologic Sediments/*chemistry/microbiology ; Methylmercury Compounds/*analysis/metabolism ; Microbial Consortia ; Seawater/chemistry/microbiology ; Sulfur-Reducing Bacteria/classification/genetics/*metabolism ; *Waste Disposal, Fluid ; Water Pollutants, Chemical/*analysis/metabolism ; }, abstract = {The Seine's estuary (France) waters are the receptacle of effluents originating from wastewater treatment plants (WWTP). In this estuary, mudflats are deposition zones for sediments and their associated contaminants, and play an essential role in the mercury (Hg) biogeochemical cycle mainly due to indigenous microorganisms. Microcosms were used to assess the impact of WWTP-effluents on mercury methylation by monitoring Hg species (total dissolved Hg in porewater, methylmercury and total mercury) and on microbial communities in sediments. After effluent amendment, methylmercury (MeHg) concentrations increased in relation with the total Hg and organic matter content of the WWTP-effluents. A correlation was observed between MeHg and acid-volatile-sulfides concentrations. Quantification of sulfate-reducing microorganisms involved in Hg methylation showed no increase of their abundance but their activity was probably enhanced by the organic matter supplied with the effluents. WWTP-effluent spiking modified the bacterial community fingerprint, mainly influenced by Hg contamination and the organic matter amendment.}, } @article {pmid21420503, year = {2011}, author = {Dridi, B and Raoult, D and Drancourt, M}, title = {Archaea as emerging organisms in complex human microbiomes.}, journal = {Anaerobe}, volume = {17}, number = {2}, pages = {56-63}, doi = {10.1016/j.anaerobe.2011.03.001}, pmid = {21420503}, issn = {1095-8274}, mesh = {Anaerobiosis ; *Biodiversity ; Female ; Humans ; Intestinal Mucosa/microbiology ; *Metagenome ; Methanobacteriaceae/classification/*isolation & purification/metabolism ; Methanobrevibacter/classification/*isolation & purification/metabolism ; Mouth Mucosa/microbiology ; Vagina/microbiology ; }, abstract = {In this work, we review the state of knowledge of Archaea associated with the human microbiome. These prokaryotes, initially discovered in extreme environments, were named Archaea because these environments were thought to be the most primitive on Earth. Further research revealed that this terminology is misleading because these organisms were later found in various non-extreme environments, including the human host. Further examination of the human microbiome has enabled the isolation of three archaeal species, Methanobrevibacter smithii, Methanosphaera stadtmanae and Methanobrevibacter oralis, which are associated with oral, intestinal and vaginal mucosae in humans. Moreover, molecular studies including metagenomic analyses detected DNA sequences indicative of the presence of additional methanogenic and non-methanogenic Archaea in the human intestinal tract. All three culturable Archaea are strict anaerobes, although their potential role in human diseases remains to be established. Future research aims to detect and culture additional human mucosa-associated Archaea and to look for their presence in additional human tissues, to establish their role in human infections involving complex flora.}, } @article {pmid21414363, year = {2011}, author = {Vinten, AJ and Artz, RR and Thomas, N and Potts, JM and Avery, L and Langan, SJ and Watson, H and Cook, Y and Taylor, C and Abel, C and Reid, E and Singh, BK}, title = {Comparison of microbial community assays for the assessment of stream biofilm ecology.}, journal = {Journal of microbiological methods}, volume = {85}, number = {3}, pages = {190-198}, doi = {10.1016/j.mimet.2011.03.001}, pmid = {21414363}, issn = {1872-8359}, mesh = {*Biodiversity ; Biofilms/*growth & development ; Chemistry Techniques, Analytical ; Ecology/methods ; *Ecosystem ; *Metagenome ; Metagenomics/methods ; Rivers/chemistry/*microbiology ; Scotland ; }, abstract = {We investigated a range of microbiological community assays performed on scrapes of biofilms formed on artificial diffusing substrates deployed in 8 streams in eastern Scotland, with a view to using them to characterize ecological response to stream water quality. The assays considered were: Multiplex Terminal Restriction Fragment Length Polymorphism or M-TRFLP (a molecular method), Phospholipid Fatty Acid or PLFA analysis (a biochemical method) and MICRORESP™ (a physiological method) alongside TDI, diatom species, and chlorophyll a content. Four of the streams were classified as of excellent status (3-6μg/L Soluble Reactive Phosphorus (SRP)) with respect to soluble P content under the EU Water Framework Directive and four were of borderline good/moderate or moderate status (43-577μg/L SRP). At each site, 3 replicates of 3 solute diffusion treatments were deployed in a Latin square design. Solute diffusion treatments were: KCl (as a control solute), N and P (to investigate the effect of nutrient enrichment), or the herbicide isoproturon (as a "high impact" control, which aimed to affect biofilm growth in a way detectable by all assays). Biofilms were sampled after 4weeks deployment in a low flow period of early summer 2006. The chlorophyll a content of biofilms after 4weeks was 2.0±0.29mg/m(2) (mean±se). Dry matter content was 16.0±13.1g/m(2). The M-TRFLP was successfully used for generating community profiles of cyanobacteria, algae and bacteria and was much faster than diatom identification. The PFLA and TDI were successful after an increase in the sample size, due to low counts. The MICRORESP(™) assays were often below or near detection limit. We estimated the per-sample times for the successful assays as follows: M-TRFLP: 20min, PLFA 40min, TDI 90min. Using MANOVA on the first 5 principal co-ordinates, all the assays except MICRORESP(™) showed significant differences between sites, but none of the assays showed a significant effect of either initial stream trophic status (as classified by the EU Water Framework Directive using chemical standards for soluble P), or of the diffusing solute treatment. Multiple Procrustes analysis on the ordination results showed that the diatom and M-TRFLP data sets hold distinct, though as yet unexplored, information about the ecological factors affecting stream biofilms. The diatom data were subjected to principal components analysis, to identify which taxa were more strongly influenced by site variables, trophic status or treatment effects. These were Acnanthes lanceolata, A. minutissimma, Nitzchia spp., Coccineis spp. and Navicula spp. Further experimentation and data analysis on a larger number of sites, to identify specific M-TRFLP bands that could be used as indicators linked to specific taxa, are desirable. Results highlight the need for a multifactorial approach to understanding controls on stream ecology.}, } @article {pmid21408168, year = {2011}, author = {Gosalbes, MJ and Durbán, A and Pignatelli, M and Abellan, JJ and Jiménez-Hernández, N and Pérez-Cobas, AE and Latorre, A and Moya, A}, title = {Metatranscriptomic approach to analyze the functional human gut microbiota.}, journal = {PloS one}, volume = {6}, number = {3}, pages = {e17447}, pmid = {21408168}, issn = {1932-6203}, mesh = {Bacteria/classification/genetics ; Biodiversity ; DNA, Complementary/genetics ; Gastrointestinal Tract/*microbiology ; Gene Expression Profiling/*methods ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; RNA, Messenger/classification/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The human gut is the natural habitat for a large and dynamic bacterial community that has a great relevance for health. Metagenomics is increasing our knowledge of gene content as well as of functional and genetic variability in this microbiome. However, little is known about the active bacteria and their function(s) in the gastrointestinal tract. We performed a metatranscriptomic study on ten healthy volunteers to elucidate the active members of the gut microbiome and their functionality under conditions of health. First, the microbial cDNAs obtained from each sample were sequenced using 454 technology. The analysis of 16S transcripts showed the phylogenetic structure of the active microbial community. Lachnospiraceae, Ruminococcaceae, Bacteroidaceae, Prevotellaceae, and Rickenellaceae were the predominant families detected in the active microbiota. The characterization of mRNAs revealed a uniform functional pattern in healthy individuals. The main functional roles of the gut microbiota were carbohydrate metabolism, energy production and synthesis of cellular components. In contrast, housekeeping activities such as amino acid and lipid metabolism were underrepresented in the metatranscriptome. Our results provide new insights into the functionality of the complex gut microbiota in healthy individuals. In this RNA-based survey, we also detected small RNAs, which are important regulatory elements in prokaryotic physiology and pathogenicity.}, } @article {pmid21407244, year = {2011}, author = {Spor, A and Koren, O and Ley, R}, title = {Unravelling the effects of the environment and host genotype on the gut microbiome.}, journal = {Nature reviews. Microbiology}, volume = {9}, number = {4}, pages = {279-290}, pmid = {21407244}, issn = {1740-1534}, support = {U01 HG004866/HG/NHGRI NIH HHS/United States ; }, mesh = {Adaptive Immunity/genetics ; Animals ; Diet ; Environment ; Gastrointestinal Tract/*immunology/*microbiology ; *Genes ; Genotype ; Humans ; Immunity, Innate/genetics ; Metagenome/immunology/*physiology ; Mice ; Mice, Inbred Strains ; Microbial Consortia/immunology/*physiology ; Twins ; }, abstract = {To what extent do host genetics control the composition of the gut microbiome? Studies comparing the gut microbiota in human twins and across inbred mouse lines have yielded inconsistent answers to this question. However, candidate gene approaches, in which one gene is deleted or added to a model host organism, show that a single host gene can have a tremendous effect on the diversity and population structure of the gut microbiota. Now, quantitative genetics is emerging as a highly promising approach that can be used to better understand the overall architecture of host genetic influence on the microbiota, and to discover additional host genes controlling microbial diversity in the gut. In this Review, we describe how host genetics and the environment shape the microbiota, and how these three factors may interact in the context of chronic disease.}, } @article {pmid21407210, year = {2011}, author = {Raes, J and Letunic, I and Yamada, T and Jensen, LJ and Bork, P}, title = {Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data.}, journal = {Molecular systems biology}, volume = {7}, number = {}, pages = {473}, pmid = {21407210}, issn = {1744-4292}, mesh = {Adaptation, Physiological ; Algorithms ; Biodiversity ; *Climate ; Data Interpretation, Statistical ; *Ecology ; *Ecosystem ; Genetic Loci/*genetics ; Geography ; Metabolic Networks and Pathways ; *Metagenomics ; Molecular Sequence Annotation ; Oceans and Seas ; Regression Analysis ; Seawater/*microbiology ; Species Specificity ; }, abstract = {Using metagenomic 'parts lists' to infer global patterns on microbial ecology remains a significant challenge. To deduce important ecological indicators such as environmental adaptation, molecular trait dispersal, diversity variation and primary production from the gene pool of an ecosystem, we integrated 25 ocean metagenomes with geographical, meteorological and geophysicochemical data. We find that climatic factors (temperature, sunlight) are the major determinants of the biomolecular repertoire of each sample and the main limiting factor on functional trait dispersal (absence of biogeographic provincialism). Molecular functional richness and diversity show a distinct latitudinal gradient peaking at 20° N and correlate with primary production. The latter can also be predicted from the molecular functional composition of an environmental sample. Together, our results show that the functional community composition derived from metagenomes is an important quantitative readout for molecular trait-based biogeography and ecology.}, } @article {pmid21395625, year = {2011}, author = {Nacke, H and Will, C and Herzog, S and Nowka, B and Engelhaupt, M and Daniel, R}, title = {Identification of novel lipolytic genes and gene families by screening of metagenomic libraries derived from soil samples of the German Biodiversity Exploratories.}, journal = {FEMS microbiology ecology}, volume = {78}, number = {1}, pages = {188-201}, doi = {10.1111/j.1574-6941.2011.01088.x}, pmid = {21395625}, issn = {1574-6941}, mesh = {Amino Acid Sequence ; Bacteria/classification/enzymology/genetics ; Biodiversity ; Esterases/genetics/metabolism ; Gene Library ; Genes, Bacterial ; Lipase/chemistry/genetics/metabolism ; Lipolysis/*genetics ; *Metagenome ; Metagenomics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; Substrate Specificity ; }, abstract = {Microbial metagenomes derived from soils are rich sources for the discovery of novel genes and biocatalysts. Fourteen environmental plasmid and seven fosmid libraries obtained from 10 German forest soils (A horizons) and six grassland soils (A and B horizons) were screened for genes conferring lipolytic activity. The libraries comprised approximately 29.3 Gb of cloned soil DNA. Partial activity-based screening of the constructed libraries resulted in the identification of 37 unique lipolytic clones. The amino acid sequences of the 37 corresponding lipolytic gene products shared 29-90% identity to other lipolytic enzymes, which were mainly uncharacterized or derived from uncultured microorganisms. Multiple sequence alignments and phylogenetic tree analysis revealed that 35 of the predicted proteins were new members of known families of lipolytic enzymes. The remaining two gene products represent two putatively new families. In addition, sequence analysis indicated that two genes encode true lipases, whereas the other genes encode esterases. The determination of substrate specificity and chain-length selectivity using different triacylglycerides and p-nitrophenyl esters of fatty acids as substrates supported the classification of the esterases.}, } @article {pmid21383980, year = {2011}, author = {Caporaso, JG and Knight, R and Kelley, ST}, title = {Host-associated and free-living phage communities differ profoundly in phylogenetic composition.}, journal = {PloS one}, volume = {6}, number = {2}, pages = {e16900}, pmid = {21383980}, issn = {1932-6203}, support = {R01 HG004872/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; HG004872/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteriophages/*genetics/physiology ; Base Sequence ; Biodiversity ; *Biota ; Ecosystem ; *Genetic Variation/physiology ; Host-Pathogen Interactions/*genetics/physiology ; Humans ; Metagenome/physiology ; *Phylogeny ; }, abstract = {Phylogenetic profiling has been widely used for comparing bacterial communities, but has so far been impossible to apply to viruses because of the lack of a single marker gene analogous to 16S rRNA. Here we developed a reference tree approach for matching viral sequences and applied it to the largest viral datasets available. The resulting technique, Shotgun UniFrac, was used to compare host-associated and non-host-associated phage communities (130 total metagenomes), and revealed a profound split similar to that found with bacterial communities. This new informatics approach complements analysis of bacterial communities and promises to provide new insights into viral community dynamics, such as top-down versus bottom-up control of bacterial communities by viruses in a range of systems.}, } @article {pmid21380504, year = {2011}, author = {Haldar, S and Choudhury, SR and Sengupta, S}, title = {Genetic and functional diversities of bacterial communities in the rhizosphere of Arachis hypogaea.}, journal = {Antonie van Leeuwenhoek}, volume = {100}, number = {1}, pages = {161-170}, doi = {10.1007/s10482-011-9570-5}, pmid = {21380504}, issn = {1572-9699}, mesh = {Arachis/growth & development/*microbiology ; Bacteria/classification/*genetics/*isolation & purification ; Biodiversity ; Molecular Sequence Data ; Phylogeny ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Bioinoculants are environmentally friendly, energy efficient and economically viable resources in sustainable agriculture. Knowledge of the structure and activities of microbial population in the rhizosphere of a plant is essential to formulate an effective bioinoculant. In this study, the bacterial community present in the rhizosphere of an important oilseed legume, Arachis hypogaea (L.) was described with respect to adjoining bulk soil as a baseline control using a 16S rDNA based metagenomic approach. Significantly higher abundance of Gamma-proteobacteria, a prevalence of Bacillus and the Cytophaga-Flavobacteria group of Bacteroidetes and absence of the Rhizobiaceae family of Alpha-proteobacteria were the major features observed in the matured Arachis-rhizosphere. The functional characterization of the rhizosphere-competent bacteria was performed using culture-dependent determination of phenotypes. Most bacterial isolates from the groundnut-rhizosphere exhibited multiple biochemical activities associated with plant growth and disease control. Validation of the beneficial traits in candidate bioinoculants in pot-cultures and field trials is necessary before their targeted application in the groundnut production system.}, } @article {pmid21378055, year = {2011}, author = {Shanks, OC and Kelty, CA and Archibeque, S and Jenkins, M and Newton, RJ and McLellan, SL and Huse, SM and Sogin, ML}, title = {Community structures of fecal bacteria in cattle from different animal feeding operations.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {9}, pages = {2992-3001}, pmid = {21378055}, issn = {1098-5336}, mesh = {Animals ; Bacteria/*classification/*isolation & purification ; *Biodiversity ; Cattle ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Diet ; Feces/*microbiology ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Phylogeny ; }, abstract = {The fecal microbiome of cattle plays a critical role not only in animal health and productivity but also in food safety, pathogen shedding, and the performance of fecal pollution detection methods. Unfortunately, most published molecular surveys fail to provide adequate detail about variability in the community structures of fecal bacteria within and across cattle populations. Using massively parallel pyrosequencing of a hypervariable region of the rRNA coding region, we profiled the fecal microbial communities of cattle from six different feeding operations where cattle were subjected to consistent management practices for a minimum of 90 days. We obtained a total of 633,877 high-quality sequences from the fecal samples of 30 adult beef cattle (5 individuals per operation). Sequence-based clustering and taxonomic analyses indicate less variability within a population than between populations. Overall, bacterial community composition correlated significantly with fecal starch concentrations, largely reflected in changes in the Bacteroidetes, Proteobacteria, and Firmicutes populations. In addition, network analysis demonstrated that annotated sequences clustered by management practice and fecal starch concentration, suggesting that the structures of bovine fecal bacterial communities can be dramatically different in different animal feeding operations, even at the phylum and family taxonomic levels, and that the feeding operation is a more important determinant of the cattle microbiome than is the geographic location of the feedlot.}, } @article {pmid21377761, year = {2011}, author = {Guarner, F}, title = {[The intestinal microbiota and inflammatory bowel disease].}, journal = {Gastroenterologia y hepatologia}, volume = {34}, number = {3}, pages = {147-154}, doi = {10.1016/j.gastrohep.2010.11.009}, pmid = {21377761}, issn = {0210-5705}, mesh = {Animals ; Antigens, Bacterial/immunology ; Genetic Predisposition to Disease ; Germ-Free Life ; Homeostasis/immunology ; Humans ; Immune Tolerance ; Immunity, Mucosal/immunology ; Inflammatory Bowel Diseases/etiology/genetics/immunology/*microbiology/therapy ; Intestines/immunology/*microbiology ; Metagenome/genetics/immunology/*physiology ; Microbial Consortia/immunology/*physiology ; Microbial Interactions/immunology/*physiology ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Symbiosis ; T-Lymphocytes, Regulatory/immunology ; }, abstract = {The intestine hosts a complex ecosystem of microbial communities. Experimental data suggests that the microbiota has metabolic functions that contribute to nutrient and energy recovery from non-digestible substrates. Moreover, microbial colonization is essential for the normal development of the immune system and therefore seems to influence homeostasis between environmental antigen load and immune response. In genetically-susceptible individuals, an imbalance may give rise to diseases of immune dysregulation, including chronic inflammatory bowel diseases, in which there is an exaggerated immune response to harmless microbial antigens. Despite the availability of new molecular technologies, the normal composition of the human intestinal microbiota remains unknown. In the next few years, the results of international projects designed to determine the precise impact of the microbiota in various physiological and pathological processes will hopefully lead to major advances.}, } @article {pmid21376666, year = {2011}, author = {Kong, HH}, title = {Skin microbiome: genomics-based insights into the diversity and role of skin microbes.}, journal = {Trends in molecular medicine}, volume = {17}, number = {6}, pages = {320-328}, pmid = {21376666}, issn = {1471-499X}, support = {UH2 AR057504-01/AR/NIAMS NIH HHS/United States ; ZIA BC010938-02//Intramural NIH HHS/United States ; AR057504/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; Archaea/genetics ; *Bacteria/genetics/isolation & purification ; Biodiversity ; DNA, Bacterial/*isolation & purification ; Fungi/genetics ; Genomics/methods ; Humans ; Metagenome/*genetics ; Mites/genetics ; RNA, Ribosomal, 16S/*analysis ; Sequence Analysis, DNA ; Skin/*microbiology ; Viruses/genetics ; }, abstract = {Recent advances in DNA sequencing methodology have facilitated studies of human skin microbes that circumvent difficulties in isolating and characterizing fastidious microbes. Sequence-based approaches have identified a greater diversity of cutaneous bacteria than studies using traditional cultivation techniques. However, improved sequencing technologies and analytical methods are needed to study all skin microbes, including bacteria, archaea, fungi, viruses and mites, and how they interact with each other and their human hosts. This review discusses current skin microbiome research, with a primary focus on bacteria, and the challenges facing investigators striving to understand how skin microorganisms contribute to health and disease.}, } @article {pmid21376215, year = {2011}, author = {Carlisle, EM and Morowitz, MJ}, title = {Pediatric surgery and the human microbiome.}, journal = {Journal of pediatric surgery}, volume = {46}, number = {3}, pages = {577-584}, doi = {10.1016/j.jpedsurg.2010.12.018}, pmid = {21376215}, issn = {1531-5037}, mesh = {Adolescent ; Animals ; Bacterial Translocation ; Bariatric Surgery ; Child ; Child, Preschool ; Cross Infection/complications/microbiology ; Diet ; Disease Susceptibility ; Enterocolitis, Necrotizing/*microbiology/surgery ; *General Surgery ; Germ-Free Life ; Humans ; Infant ; Infant, Newborn ; Inflammatory Bowel Diseases/*microbiology/surgery ; Intensive Care Units, Neonatal ; Intestines/*microbiology ; *Metagenome ; Mice ; Microbial Consortia/*physiology ; Obesity/*microbiology/surgery ; *Pediatrics ; Postoperative Complications/etiology/microbiology/prevention & control ; Pouchitis/etiology/microbiology/prevention & control ; Probiotics/therapeutic use ; Species Specificity ; Virulence ; }, abstract = {Bold advances in the past decade have made it possible to carefully study the contributions of microbes to normal human development and to disease pathogenesis. The intestinal microbiota has been implicated in adult diseases ranging from obesity to cancer, but there have been relatively few investigations of bacteria in surgical diseases of infancy and childhood. In this review, we discuss how novel culture-independent approaches have been harnessed to profile microbes present within clinical specimens. Unique features of the pediatric microbiota and innovative approaches to manipulate the gut flora are also reviewed. Finally, we detail the contributions of gut microbes to 3 diseases relevant to pediatric surgeons: necrotizing enterocolitis, obesity, and inflammatory bowel disease. Current and future research regarding the pediatric microbiota is likely to translate to improved outcomes for infants and children with surgical diseases.}, } @article {pmid21371219, year = {2011}, author = {Lopez-Velasco, G and Welbaum, GE and Boyer, RR and Mane, SP and Ponder, MA}, title = {Changes in spinach phylloepiphytic bacteria communities following minimal processing and refrigerated storage described using pyrosequencing of 16S rRNA amplicons.}, journal = {Journal of applied microbiology}, volume = {110}, number = {5}, pages = {1203-1214}, doi = {10.1111/j.1365-2672.2011.04969.x}, pmid = {21371219}, issn = {1365-2672}, mesh = {Bacteria/classification/genetics/*growth & development ; Biodiversity ; Food Handling/*methods ; *Food Microbiology ; Gene Library ; Metagenome ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Refrigeration ; Sequence Analysis, DNA ; Spinacia oleracea/*microbiology ; }, abstract = {AIMS: To investigate the changes in bacterial diversity on fresh spinach phyllosphere associated with storage at refrigeration temperatures.

METHODS AND RESULTS:   Community structure and population dynamics of spinach phylloepiphytic bacteria associated with packaging and refrigeration of ready-to-eat fresh produce were evaluated using pyrosequencing of 16S rRNA gene amplicons. A diverse community responsive to storage at refrigerated temperatures was detected belonging to over 1000 operational taxonomic units, including many diverse members not previously described on the phyllosphere. Of the approx. 8800 unique sequences examined from fresh spinach leaves, 75% were from previously undescribed taxa. The classified sequences from the fresh spinach phyllosphere were assigned to 11 different phyla with the largest number of reads belonging to Proteobacteria and Firmicutes. Packaging and storage of spinach under refrigerated conditions decreased the richness, diversity and evenness of the bacterial community. Refrigeration at 4 and 10°C and storage resulted in a decrease in number of taxa represented from 11 phyla in fresh spinach to only 5 phyla after 1 day of storage. Sequences belonging to γ-Proteobacteria, particularly Pseudomonas spp. and members of the Enterobacteriaceae, were the most numerous after 15 days of storage at both temperatures. Growth inhibition of the genera Escherichia was achieved at 4°C but not at 10°C storage, thus highlighting the importance of temperature in fresh packaged spinach.

CONCLUSIONS: The application of pyrosequencing to describe composition and diversity of the phyllosphere on spinach leaves provided a broader outlook of the bacterial composition of this community complementing other phyllosphere studies that have used culture- and nonculture-dependent approaches.

Pyrosequencing allowed a broader description of the bacterial composition and diversity of the spinach leaf surface than previously obtained using culture-based detection and will be a powerful tool to help ensure the future safety and quality of packaged spinach.}, } @article {pmid21359229, year = {2011}, author = {Kristiansson, E and Fick, J and Janzon, A and Grabic, R and Rutgersson, C and Weijdegård, B and Söderström, H and Larsson, DG}, title = {Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements.}, journal = {PloS one}, volume = {6}, number = {2}, pages = {e17038}, pmid = {21359229}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/*adverse effects ; Bacteria/drug effects/genetics ; *Biota ; DNA Transposable Elements/physiology ; *Drug Resistance, Bacterial/drug effects/genetics ; Gene Transfer, Horizontal/*drug effects/physiology ; Geologic Sediments/chemistry/*microbiology ; Humans ; Rivers/chemistry ; Sequence Analysis, DNA/*methods ; Water Microbiology ; Water Pollutants, Chemical/*adverse effects ; }, abstract = {The high and sometimes inappropriate use of antibiotics has accelerated the development of antibiotic resistance, creating a major challenge for the sustainable treatment of infections world-wide. Bacterial communities often respond to antibiotic selection pressure by acquiring resistance genes, i.e. mobile genetic elements that can be shared horizontally between species. Environmental microbial communities maintain diverse collections of resistance genes, which can be mobilized into pathogenic bacteria. Recently, exceptional environmental releases of antibiotics have been documented, but the effects on the promotion of resistance genes and the potential for horizontal gene transfer have yet received limited attention. In this study, we have used culture-independent shotgun metagenomics to investigate microbial communities in river sediments exposed to waste water from the production of antibiotics in India. Our analysis identified very high levels of several classes of resistance genes as well as elements for horizontal gene transfer, including integrons, transposons and plasmids. In addition, two abundant previously uncharacterized resistance plasmids were identified. The results suggest that antibiotic contamination plays a role in the promotion of resistance genes and their mobilization from environmental microbes to other species and eventually to human pathogens. The entire life-cycle of antibiotic substances, both before, under and after usage, should therefore be considered to fully evaluate their role in the promotion of resistance.}, } @article {pmid21347361, year = {2011}, author = {Piganeau, G and Eyre-Walker, A and Jancek, S and Grimsley, N and Moreau, H}, title = {How and why DNA barcodes underestimate the diversity of microbial eukaryotes.}, journal = {PloS one}, volume = {6}, number = {2}, pages = {e16342}, pmid = {21347361}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal/genetics ; Eukaryota/classification/*genetics ; Evolution, Molecular ; Genome/genetics ; Humans ; Mice ; Plankton/classification/*genetics ; Proteome/genetics ; Rats ; }, abstract = {BACKGROUND: Because many picoplanktonic eukaryotic species cannot currently be maintained in culture, direct sequencing of PCR-amplified 18S ribosomal gene DNA fragments from filtered sea-water has been successfully used to investigate the astounding diversity of these organisms. The recognition of many novel planktonic organisms is thus based solely on their 18S rDNA sequence. However, a species delimited by its 18S rDNA sequence might contain many cryptic species, which are highly differentiated in their protein coding sequences.

PRINCIPAL FINDINGS: Here, we investigate the issue of species identification from one gene to the whole genome sequence. Using 52 whole genome DNA sequences, we estimated the global genetic divergence in protein coding genes between organisms from different lineages and compared this to their ribosomal gene sequence divergences. We show that this relationship between proteome divergence and 18S divergence is lineage dependent. Unicellular lineages have especially low 18S divergences relative to their protein sequence divergences, suggesting that 18S ribosomal genes are too conservative to assess planktonic eukaryotic diversity. We provide an explanation for this lineage dependency, which suggests that most species with large effective population sizes will show far less divergence in 18S than protein coding sequences.

CONCLUSIONS: There is therefore a trade-off between using genes that are easy to amplify in all species, but which by their nature are highly conserved and underestimate the true number of species, and using genes that give a better description of the number of species, but which are more difficult to amplify. We have shown that this trade-off differs between unicellular and multicellular organisms as a likely consequence of differences in effective population sizes. We anticipate that biodiversity of microbial eukaryotic species is underestimated and that numerous "cryptic species" will become discernable with the future acquisition of genomic and metagenomic sequences.}, } @article {pmid21338450, year = {2011}, author = {Ketabi, A and Dieleman, LA and Gänzle, MG}, title = {Influence of isomalto-oligosaccharides on intestinal microbiota in rats.}, journal = {Journal of applied microbiology}, volume = {110}, number = {5}, pages = {1297-1306}, doi = {10.1111/j.1365-2672.2011.04984.x}, pmid = {21338450}, issn = {1365-2672}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Biodiversity ; Denaturing Gradient Gel Electrophoresis ; *Diet ; Fatty Acids, Volatile/biosynthesis ; Feces/chemistry/microbiology ; Intestines/chemistry/*microbiology ; Inulin/administration & dosage/pharmacology ; Lactobacillus/drug effects/*growth & development ; Metagenome/*drug effects ; Oligosaccharides/administration & dosage/*pharmacology ; Polymerase Chain Reaction ; Rats ; Rats, Inbred F344 ; }, abstract = {AIMS: Isomalto-oligosaccharides (IMO) with α(1 --> 6) and α(1 --> 4) glucosidic linkages are produced by enzymatic conversion of starch. IMO are only partially digestible but data on their influence on intestinal microbiota are limited. It was the aim of this study to investigate the effect of IMO diet on intestinal microbiota and short-chain fatty acids production (SCFA) in rats.

METHODS AND RESULTS: Three groups of F344 rats, each consisting of six animals, were fed IMO, inulin or a control diets for six weeks. A qualitative assessment of the intestinal microbiota was achieved by PCR-denaturing gradient gel electrophoresis (DGGE). Major bacterial taxa were quantified by quantitative PCR (qPCR), and SCFA were measured using gas chromatography. Quantitative PCR demonstrated that lactobacilli were one of the dominant bacterial taxa in faecal samples from rats. IMO increased the number of lactobacilli and the total number of intestinal bacteria in rats fed IMO compared with animals receiving control and inulin diets. Furthermore, PCR-DGGE with lactobacilli-specific primers showed an altered biodiversity of lactobacilli in rats fed IMO compared with control diet.

CONCLUSIONS: IMO selectively stimulates lactobacilli and increases their diversity in rats.

  Isomalto-oligosaccharides specifically stimulate growth of intestinal lactobacilli in a rat model system.}, } @article {pmid21337248, year = {2011}, author = {Bae, H and Park, JH and Jun, KS and Jung, JY}, title = {The community analysis of ammonia-oxidizing bacteria in wastewater treatment plants revealed by the combination of double labeled T-RFLP and sequencing.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering}, volume = {46}, number = {4}, pages = {345-354}, doi = {10.1080/10934529.2011.542384}, pmid = {21337248}, issn = {1532-4117}, mesh = {Ammonia/metabolism ; Bacteria/metabolism ; Betaproteobacteria/*classification/genetics/isolation & purification/metabolism ; Biota ; *Metagenome ; Nitrosomonas/*classification/genetics/isolation & purification/metabolism ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Polymorphism, Restriction Fragment Length ; Sewage/*microbiology ; Waste Disposal, Fluid/methods ; }, abstract = {The functional gene of amoA, which produces the α-subunit of ammonia monooxygenase (AMO), has been analyzed to reveal the microbial community structure of ammonia-oxidizing bacteria (AOB) by culture-independent methods. In this study, the distribution of the amoA gene in 10 wastewater treatment plants (WWTPs) was revealed by the fingerprinting method of terminal restriction fragment length polymorphism (T-RFLP) and comparative sequencing. T-RFLP showed diverse communities of AOB in the modified Ludzack-Ettinger process, in the anaerobic-anoxic-oxic processes, in the hanging biological contactor, and in the sequencing batch reactor. In all of these environments, long solid retention time (SRT) was expected to be the critical factor for maintaining the diverse AOB community structure. Because T-RFLP does not offer sufficient information to confirm the phylogenetic information of AOB, the microbial community structures were analyzed by comparative sequencing for seven samples that were selected by the statistical categorization using principal component analysis (PCA) among 14 samples. The phylogenetic tree of 21 operational taxonomic units (OTUs) among 88 clones obtained in this study revealed that AOB of Nitrosomonas oligotropha and europaea lineages were predominant in WWTPs. Double labeled T-RFLP produced group-specific terminal restriction fragments (T-RFs) representing several groups of AOB and offered advanced resolution comparing with the single labeled T-RFLP.}, } @article {pmid21317261, year = {2011}, author = {Jung, JY and Lee, SH and Kim, JM and Park, MS and Bae, JW and Hahn, Y and Madsen, EL and Jeon, CO}, title = {Metagenomic analysis of kimchi, a traditional Korean fermented food.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {7}, pages = {2264-2274}, pmid = {21317261}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics ; Bacteriophages/classification/genetics ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Food Microbiology ; Korea ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Kimchi, a traditional food in the Korean culture, is made from vegetables by fermentation. In this study, metagenomic approaches were used to monitor changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation process. Metagenomic DNA was extracted from kimchi samples obtained periodically and was sequenced using a 454 GS FLX Titanium system, which yielded a total of 701,556 reads, with an average read length of 438 bp. Phylogenetic analysis based on 16S rRNA genes from the metagenome indicated that the kimchi microbiome was dominated by members of three genera: Leuconostoc, Lactobacillus, and Weissella. Assignment of metagenomic sequences to SEED categories of the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) server revealed a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates, which was supported by the detection of mannitol, lactate, acetate, and ethanol as fermentation products. When the metagenomic reads were mapped onto the database of completed genomes, the Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 and Lactobacillus sakei subsp. sakei 23K genomes were highly represented. These same two genera were confirmed to be important in kimchi fermentation when the majority of kimchi metagenomic sequences showed very high identity to Leuconostoc mesenteroides and Lactobacillus genes. Besides microbial genome sequences, a surprisingly large number of phage DNA sequences were identified from the cellular fractions, possibly indicating that a high proportion of cells were infected by bacteriophages during fermentation. Overall, these results provide insights into the kimchi microbial community and also shed light on fermentation processes carried out broadly by complex microbial communities.}, } @article {pmid21275452, year = {2010}, author = {Rogers, GB and Bruce, KD}, title = {Next-generation sequencing in the analysis of human microbiota: essential considerations for clinical application.}, journal = {Molecular diagnosis & therapy}, volume = {14}, number = {6}, pages = {343-350}, pmid = {21275452}, issn = {1179-2000}, mesh = {Bacterial Infections/diagnosis/*microbiology ; Biodiversity ; Cystic Fibrosis/complications ; Humans ; Metagenome/*genetics ; Quality Control ; Respiratory Tract Infections/complications/diagnosis/microbiology ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods/trends ; }, abstract = {The development of next-generation sequencing (NGS) presents an unprecedented opportunity to investigate the complex microbial communities that are associated with the human body. It offers for the first time a basis for detailed temporal and spatial analysis, with the potential to revolutionize our understanding of many clinically important systems. However, while advances continue to be made in areas such as PCR amplification for NGS, sequencing protocols, and data analysis, in many cases the quality of the data generated is undermined by a failure to address fundamental aspects of experimental design. While little is added in terms of time or cost by the analysis of repeat samples, the exclusion of DNA from dead bacterial cells and the extracellular matrix, the use of efficient nucleic acid extraction methodologies, and the implementation of safeguards to minimize the introduction of contaminating nucleic acids, such considerations are essential in achieving an accurate representation of the system being studied. In this review, the chronic bacterial infections that characterize lower respiratory tract infections in cystic fibrosis patients are used as an example system to examine the implications of a failure to address these issues when designing NGS-based analysis of human-associated microbiota. Further, ways in which the impact of these factors can be minimized are discussed.}, } @article {pmid21272046, year = {2011}, author = {Bibby, K and Viau, E and Peccia, J}, title = {Viral metagenome analysis to guide human pathogen monitoring in environmental samples.}, journal = {Letters in applied microbiology}, volume = {52}, number = {4}, pages = {386-392}, pmid = {21272046}, issn = {1472-765X}, support = {S10 RR019895/RR/NCRR NIH HHS/United States ; S10 RR019895-01/RR/NCRR NIH HHS/United States ; RR19895/RR/NCRR NIH HHS/United States ; }, mesh = {Biodiversity ; *Environmental Microbiology ; Environmental Monitoring/*methods ; Genome, Viral ; Metagenome ; Metagenomics/*methods ; Molecular Sequence Annotation ; Viruses/*classification/genetics/isolation & purification ; }, abstract = {AIMS: The aim of this study was to develop and demonstrate an approach for describing the diversity of human pathogenic viruses in an environmentally isolated viral metagenome.

METHODS AND RESULTS: In silico bioinformatic experiments were used to select an optimum annotation strategy for discovering human viruses in virome data sets and applied to annotate a class B biosolid virome. Results from the in silico study indicated that <1% errors in virus identification could be achieved when nucleotide-based search programs (BLASTn or tBLASTx), viral genome only databases and sequence reads >200 nt were considered. Within the 51,925 annotated sequences, 94 DNA and 19 RNA sequences were identified as human viruses. Virus diversity included environmentally transmitted agents such as parechovirus, coronavirus, adenovirus and aichi virus, as well as viruses associated with chronic human infections such as human herpes and hepatitis C viruses.

CONCLUSIONS: This study provided a bioinformatic approach for identifying pathogens in a virome data set and demonstrated the human virus diversity in a relevant environmental sample.

 As the costs of next-generation sequencing decrease, the pathogen diversity described by virus metagenomes will provide an unbiased guide for subsequent cell culture and quantitative pathogen analyses and ensures that highly enriched and relevant pathogens are not neglected in exposure and risk assessments.}, } @article {pmid21261774, year = {2011}, author = {Medina, RF and Nachappa, P and Tamborindeguy, C}, title = {Differences in bacterial diversity of host-associated populations of Phylloxera notabilis Pergande (Hemiptera: Phylloxeridae) in pecan and water hickory.}, journal = {Journal of evolutionary biology}, volume = {24}, number = {4}, pages = {761-771}, doi = {10.1111/j.1420-9101.2010.02215.x}, pmid = {21261774}, issn = {1420-9101}, mesh = {Animals ; Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; Carya/*microbiology ; Hemiptera/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Host-associated differentiation (HAD) is the presence of genetically divergent, host-associated populations. It has been suggested that microbial symbionts of insect herbivores may play a role in HAD by allowing their insect hosts to use different plant species. The objective of this study was to document if host-associated populations of Phylloxera notabilis Pergande (Hemiptera: Phylloxeridae) in pecan and water hickory corresponded with differences in the composition of their associated bacteria. To test this hypothesis, we characterized the symbionts present in P. notabilis associated with these two tree species through metagenomic analyses using 454 sequencing. Differences in bacterial diversity were found between P. notabilis populations associated with pecan and water hickory. The bacteria, Pantoea agglomerans and Serratia marcescens, were absent in the P. notabilis water hickory population, whereas both species accounted for more than 69.72% of bacterial abundance in the pecan population.}, } @article {pmid21256887, year = {2011}, author = {Töwe, S and Wallisch, S and Bannert, A and Fischer, D and Hai, B and Haesler, F and Kleineidam, K and Schloter, M}, title = {Improved protocol for the simultaneous extraction and column-based separation of DNA and RNA from different soils.}, journal = {Journal of microbiological methods}, volume = {84}, number = {3}, pages = {406-412}, doi = {10.1016/j.mimet.2010.12.028}, pmid = {21256887}, issn = {1872-8359}, mesh = {Bacteria/classification/genetics ; Biodiversity ; Chromatography/*methods ; DNA/*isolation & purification ; Metagenome ; RNA/*isolation & purification ; *Soil Microbiology ; }, abstract = {We developed an improved protocol, allowing the simultaneous extraction of DNA and RNA from soil using phenol-chloroform with subsequent column-based separation of DNA and RNA (PCS). We compared this new approach with the well established protocol published by Griffiths et al. (2000), where DNA and RNA are separated by selective enzymatic digestions and two commercial kits used for DNA or RNA extraction, respectively, using four different agricultural soils. We compared yield and purity of the nucleic acids as well as abundance and diversity profiles of the soil bacterial communities targeting the nosZ gene via quantitative real-time PCR and terminal restriction fragment length polymorphism on DNA and RNA level. The newly developed protocol provided purer nucleic acid extracts compared to the used kit-based protocols. All protocols were suitable for DNA- and RNA-based gene quantification, however high variations between replicates were obtained for RNA samples using the original Griffiths protocol. Diversity patterns of nosZ were highly influenced by the extraction protocol used both on the DNA and RNA level. Finally, our data showed that the new protocol allows a simultaneous and reproducible extraction and separation of DNA and RNA, which were suitable for reliable analyses of gene and transcript copy numbers and diversity pattern.}, } @article {pmid21253553, year = {2010}, author = {Horz, HP and Conrads, G}, title = {The discussion goes on: What is the role of Euryarchaeota in humans?.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2010}, number = {}, pages = {967271}, pmid = {21253553}, issn = {1472-3654}, mesh = {Archaea/classification/isolation & purification/pathogenicity/*physiology ; *Biodiversity ; Gastrointestinal Tract/microbiology ; Humans ; *Metagenome ; Mouth/microbiology ; }, abstract = {The human body (primarily the intestinal tract, the oral cavity, and the skin) harbours approximately 1,000 different bacterial species. However, the number of archaeal species known to colonize man seems to be confined to a handful of organisms within the class Euryarchaeota (including Methanobrevibacter smithii, M. oralis, and Methanosphaera stadtmanae). In contrast to this conspicuously low diversity of Archaea in humans their unique physiology in conjunction with the growing number of reports regarding their occurrence at sites of infection has made this issue an emerging field of study. While previous review articles in recent years have addressed the putative role of particularly methanogenic archaea for human health and disease, this paper compiles novel experimental data that have been reported since then. The aim of this paper is to inspire the scientific community of "Archaea experts" for those unique archaeal organisms that have successfully participated in the human-microbe coevolution.}, } @article {pmid21223325, year = {2011}, author = {Kim, M and Morrison, M and Yu, Z}, title = {Status of the phylogenetic diversity census of ruminal microbiomes.}, journal = {FEMS microbiology ecology}, volume = {76}, number = {1}, pages = {49-63}, doi = {10.1111/j.1574-6941.2010.01029.x}, pmid = {21223325}, issn = {1574-6941}, mesh = {Animals ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biodiversity ; Databases, Genetic ; Metagenome ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; }, abstract = {In this study, the collective microbial diversity in the rumen was examined by performing a meta-analysis of all the curated 16S rRNA gene (rrn) sequences deposited in the RDP database. As of November 2010, 13,478 bacterial and 3516 archaeal rrn sequences were found. The bacterial sequences were assigned to 5271 operation taxonomic units (OTUs) at species level (0.03 phylogenetic distance) representing 19 existing phyla, of which the Firmicutes (2958 OTUs), Bacteroidetes (1610 OTUs) and Proteobacteria (226 OTUs) were the most predominant. These bacterial sequences were grouped into more than 3500 OTUs at genus level (0.05 distance), but only 180 existing genera were represented. Nearly all the archaeal sequences were assigned to 943 species-level OTUs in phylum Euryarchaeota. Although clustered into 670 genus-level OTUs, only 12 existing archaeal genera were represented. Based on rarefaction analysis, the current percent coverage at species level reached 71% for bacteria and 65% for archaea. At least 78,218 bacterial and 24,480 archaeal sequences would be needed to reach 99.9% coverage. The results of this study may serve as a framework to assess the significance of individual populations to rumen functions and to guide future studies to identify the alpha and global diversity of ruminal microbiomes.}, } @article {pmid21221928, year = {2010}, author = {Jung, MY and Pham, V and Park, SJ and Kim, SJ and Chae, JC and Roh, Y and Rhee, SK}, title = {Metagenomic assessment of a sulfur-oxidizing enrichment culture derived from marine sediment.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {48}, number = {6}, pages = {739-747}, pmid = {21221928}, issn = {1976-3794}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/*microbiology ; *Metagenome ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Quinone Reductases/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfur/*metabolism ; }, abstract = {The biological oxidation of reduced sulfur compounds is a critically important process in global sulfur biogeochemistry. In this study, we enriched from marine sediments under denitrifying conditions, chemolithotrophic sulfur oxidizers that could oxidize a variety of reduced sulfur compounds: thiosulfate, tetrathionate, sulfide, and polysulfide. Two major phylotypes of 16S rRNA gene (>99% identity in each phylotype) were detected in this enrichment culture. In order to characterize sulfide oxidation, we sequenced and characterized one fosmid clone (43.6 kb) containing the group I sulfide-quinone reductase (sqr) gene. Interestingly, four putative rhodanese genes were found in this clone. Furthermore, comparative alignment with the closest genome of Thiomicrospira crunogena XCL2 revealed that three homologous genes were located within the vicinity of the sqr gene. Fosmid clones harboring carbon fixation (cbbL and cbbM) and denitrification (narG) genes were screened, and the phylogeny of the functional genes was analyzed. Along with the comparison between the sqr-containing fosmid clones and the relevant -proteobacteria, our phylogenetic study based on the 16S rRNA gene and carbon fixation genes suggest the prevalence of chemolithotrophic -proteobacteria in the denitrifying cultures. The findings of this study imply that a combination of cultivation and metagenomic approaches might provide us with a glimpse into the characteristics of sulfur oxidizers in marine sediments.}, } @article {pmid21221926, year = {2010}, author = {Liu, J and Li, J and Feng, L and Cao, H and Cui, Z}, title = {An improved method for extracting bacteria from soil for high molecular weight DNA recovery and BAC library construction.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {48}, number = {6}, pages = {728-733}, pmid = {21221926}, issn = {1976-3794}, mesh = {Bacteria/genetics/*isolation & purification ; Bacterial Typing Techniques ; Biodiversity ; Centrifugation, Density Gradient/methods ; Chromosomes, Artificial, Bacterial ; DNA, Bacterial/chemistry/genetics/*isolation & purification ; DNA, Ribosomal Spacer/genetics ; Gene Library ; Genetics, Microbial/*methods ; Molecular Biology/*methods ; Molecular Typing ; Molecular Weight ; *Soil Microbiology ; }, abstract = {Separation of bacterial cells from soil is a key step in the construction of metagenomic BAC libraries with large DNA inserts. Our results showed that when combined with sodium pyro-phosphate and homogenization for soil dispersion, sucrose density gradient centrifugation (SDGC) was more effective at separating bacteria from soil than was low speed centrifugation (LSC). More than 70% of the cells, along with some soil colloids, were recovered with one round of centrifugation. A solution of 0.8% NaCl was used to resuspend these cell and soil pellets for purification with nycodenz density gradient centrifugation (NDGC). After purification, more than 30% of the bacterial cells in the primary soil were extracted. This procedure effectively removed soil contamination and yielded sufficient cells for high molecular weight (HMW) DNA isolation. Ribosomal intergenic spacer analysis (RISA) showed that the microbial community structure of the extracted cells was similar to that of the primary soil, suggesting that this extraction procedure did not significantly change the the soil bacteria community structure. HMW DNA was isolated from bacterial cells extracted from red soil for metagenomic BAC library construction. This library contained DNA inserts of more than 200 Mb with an average size of 75 kb.}, } @article {pmid21217792, year = {2011}, author = {Nicolas, GG and Lavoie, MC}, title = {[Streptococcus mutans and oral streptococci in dental plaque].}, journal = {Canadian journal of microbiology}, volume = {57}, number = {1}, pages = {1-20}, doi = {10.1139/w10-095}, pmid = {21217792}, issn = {1480-3275}, mesh = {Bacterial Physiological Phenomena ; *Biofilms ; Biota ; Dental Plaque/*microbiology ; Genome, Bacterial/genetics ; Humans ; Metagenome/physiology ; Mouth/*microbiology ; Streptococcus/genetics/pathogenicity/*physiology ; Streptococcus mutans/genetics/pathogenicity/*physiology ; Virulence ; }, abstract = {The human oral microbial biota represents a highly diverse biofilm. Twenty-five species of oral streptococci inhabit the human oral cavity and represent about 20 % of the total oral bacteria. Taxonomy of these bacteria is complex and remains provisional. Oral streptococci encompass friends and foes bacteria. Each species has developed specific properties for colonizing the different oral sites subjected to constantly changing conditions, for competing against competitors, and for resisting external agressions (host immune system, physico-chemical shocks, and mechanical frictions). Imbalance in the indigenous microbial biota generates oral diseases, and under proper conditions, commensal streptococci can switch to opportunistic pathogens that initiate disease in and damage to the host. The group of "mutans streptococci" was described as the most important bacteria related to the formation of dental caries. Streptococcus mutans, although naturally present among the human oral microbiota, is the microbial species most strongly associated with carious lesions. This minireview describes the oral streptococci ecology and their biofilm life style by focusing on the mutans group, mainly S. mutans. Virulence traits, interactions in the biofilm, and influence of S. mutans in dental caries etiology are discussed.}, } @article {pmid21210935, year = {2012}, author = {Stewart, FJ and Ulloa, O and DeLong, EF}, title = {Microbial metatranscriptomics in a permanent marine oxygen minimum zone.}, journal = {Environmental microbiology}, volume = {14}, number = {1}, pages = {23-40}, doi = {10.1111/j.1462-2920.2010.02400.x}, pmid = {21210935}, issn = {1462-2920}, mesh = {Ammonia/metabolism ; Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; Biodiversity ; Chile ; Metagenome ; Nitrification ; Oxidation-Reduction ; Oxidoreductases/genetics ; Oxygen/metabolism ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics/metabolism ; Seawater/chemistry/*microbiology ; Sequence Analysis, DNA ; *Transcriptome ; }, abstract = {Simultaneous characterization of taxonomic composition, metabolic gene content and gene expression in marine oxygen minimum zones (OMZs) has potential to broaden perspectives on the microbial and biogeochemical dynamics in these environments. Here, we present a metatranscriptomic survey of microbial community metabolism in the Eastern Tropical South Pacific OMZ off northern Chile. Community RNA was sampled in late austral autumn from four depths (50, 85, 110, 200 m) extending across the oxycline and into the upper OMZ. Shotgun pyrosequencing of cDNA yielded 180,000 to 550,000 transcript sequences per depth. Based on functional gene representation, transcriptome samples clustered apart from corresponding metagenome samples from the same depth, highlighting the discrepancies between metabolic potential and actual transcription. BLAST-based characterizations of non-ribosomal RNA sequences revealed a dominance of genes involved with both oxidative (nitrification) and reductive (anammox, denitrification) components of the marine nitrogen cycle. Using annotations of protein-coding genes as proxies for taxonomic affiliation, we observed depth-specific changes in gene expression by key functional taxonomic groups. Notably, transcripts most closely matching the genome of the ammonia-oxidizing archaeon Nitrosopumilus maritimus dominated the transcriptome in the upper three depths, representing one in five protein-coding transcripts at 85 m. In contrast, transcripts matching the anammox bacterium Kuenenia stuttgartiensis dominated at the core of the OMZ (200 m; 1 in 12 protein-coding transcripts). The distribution of N. maritimus-like transcripts paralleled that of transcripts matching ammonia monooxygenase genes, which, despite being represented by both bacterial and archaeal sequences in the community DNA, were dominated (> 99%) by archaeal sequences in the RNA, suggesting a substantial role for archaeal nitrification in the upper OMZ. These data, as well as those describing other key OMZ metabolic processes (e.g. sulfur oxidation), highlight gene-specific expression patterns in the context of the entire community transcriptome, as well as identify key functional groups for taxon-specific genomic profiling.}, } @article {pmid21209889, year = {2010}, author = {Turque, AS and Batista, D and Silveira, CB and Cardoso, AM and Vieira, RP and Moraes, FC and Clementino, MM and Albano, RM and Paranhos, R and Martins, OB and Muricy, G}, title = {Environmental shaping of sponge associated archaeal communities.}, journal = {PloS one}, volume = {5}, number = {12}, pages = {e15774}, pmid = {21209889}, issn = {1932-6203}, mesh = {Ammonia/chemistry ; Animals ; Archaea/*metabolism ; Biodiversity ; Brazil ; Ecology ; Environment ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Plankton ; Porifera/*metabolism ; Principal Component Analysis ; RNA, Ribosomal, 16S/metabolism ; Seawater ; }, abstract = {BACKGROUND: Archaea are ubiquitous symbionts of marine sponges but their ecological roles and the influence of environmental factors on these associations are still poorly understood.

We compared the diversity and composition of archaea associated with seawater and with the sponges Hymeniacidon heliophila, Paraleucilla magna and Petromica citrina in two distinct environments: Guanabara Bay, a highly impacted estuary in Rio de Janeiro, Brazil, and the nearby Cagarras Archipelago. For this we used metagenomic analyses of 16S rRNA and ammonia monooxygenase (amoA) gene libraries. Hymeniacidon heliophila was more abundant inside the bay, while P. magna was more abundant outside and P. citrina was only recorded at the Cagarras Archipelago. Principal Component Analysis plots (PCA) generated using pairwise unweighted UniFrac distances showed that the archaeal community structure of inner bay seawater and sponges was different from that of coastal Cagarras Archipelago. Rarefaction analyses showed that inner bay archaeaoplankton were more diverse than those from the Cagarras Archipelago. Only members of Crenarchaeota were found in sponge libraries, while in seawater both Crenarchaeota and Euryarchaeota were observed. Although most amoA archaeal genes detected in this study seem to be novel, some clones were affiliated to known ammonia oxidizers such as Nitrosopumilus maritimus and Cenarchaeum symbiosum.

CONCLUSION/SIGNIFICANCE: The composition and diversity of archaeal communities associated with pollution-tolerant sponge species can change in a range of few kilometers, probably influenced by eutrophication. The presence of archaeal amoA genes in Porifera suggests that Archaea are involved in the nitrogen cycle within the sponge holobiont, possibly increasing its resistance to anthropogenic impacts. The higher diversity of Crenarchaeota in the polluted area suggests that some marine sponges are able to change the composition of their associated archaeal communities, thereby improving their fitness in impacted environments.}, } @article {pmid21205002, year = {2011}, author = {Pushalkar, S and Mane, SP and Ji, X and Li, Y and Evans, C and Crasta, OR and Morse, D and Meagher, R and Singh, A and Saxena, D}, title = {Microbial diversity in saliva of oral squamous cell carcinoma.}, journal = {FEMS immunology and medical microbiology}, volume = {61}, number = {3}, pages = {269-277}, pmid = {21205002}, issn = {1574-695X}, support = {R03-DE019178/DE/NIDCR NIH HHS/United States ; R03 DE019178-01A2/DE/NIDCR NIH HHS/United States ; U19-DE018385/DE/NIDCR NIH HHS/United States ; R01-DE020891/DE/NIDCR NIH HHS/United States ; U54 DE014257/DE/NIDCR NIH HHS/United States ; U54-DE14257/DE/NIDCR NIH HHS/United States ; R01 DE020891/DE/NIDCR NIH HHS/United States ; U19 DE018385/DE/NIDCR NIH HHS/United States ; R03 DE019178/DE/NIDCR NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Bacteria/*classification/*genetics ; *Biodiversity ; Carcinoma, Squamous Cell/*microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenome ; Middle Aged ; Molecular Sequence Data ; Mouth Neoplasms/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; }, abstract = {In the oral cavity, chronic inflammation has been observed at various stages of oral squamous cell carcinomas (OSCC). Such inflammation could result from persistent mucosal or epithelial cell colonization by microorganisms. There is increasing evidence of the involvement of oral bacteria in inflammation, warranting further studies on the association of bacteria with the progression of OSCC. The objective of this study was to evaluate the diversity and relative abundance of bacteria in the saliva of subjects with OSCC. Using 454 parallel DNA sequencing, ∼58,000 PCR amplicons that span the V4-V5 hypervariable region of rRNAs from five subjects were sequenced. Members of eight phyla (divisions) of bacteria were detected. The majority of classified sequences belonged to the phyla Firmicutes (45%) and Bacteroidetes (25%). Further, 52 different genera containing approximately 860 (16.51%) known species were identified and 1077 (67%) sequences belonging to various uncultured bacteria or unclassified groups. The species diversity estimates obtained with abundance-based coverage estimators and Chao1 were greater than published analyses of other microbial profiles from the oral cavity. Fifteen unique phylotypes were present in all three OSCC subjects.}, } @article {pmid21203913, year = {2010}, author = {Zhu, B and Wang, X and Li, L}, title = {Human gut microbiome: the second genome of human body.}, journal = {Protein & cell}, volume = {1}, number = {8}, pages = {718-725}, pmid = {21203913}, issn = {1674-8018}, mesh = {Animals ; Biota ; Cell Culture Techniques ; Digestive System/immunology/*microbiology ; Digestive System Diseases/microbiology ; Humans ; Immune System ; *Metagenome ; Obesity/microbiology ; Symbiosis ; }, abstract = {The human body is actually a super-organism that is composed of 10 times more microbial cells than our body cells. Metagenomic study of the human microbiome has demonstrated that there are 3.3 million unique genes in human gut, 150 times more genes than our own genome, and the bacterial diversity analysis showed that about 1000 bacterial species are living in our gut and a majority of them belongs to the divisions of Firmicutes and Bacteriodetes. In addition, most people share a core microbiota that comprises 50-100 bacterial species when the frequency of abundance at phylotype level is not considered, and a core microbiome harboring more than 6000 functional gene groups is present in the majority of human gut surveyed till now. Gut bacteria are not only critical for regulating gut metabolism, but also important for host immune system as revealed by animal studies.}, } @article {pmid21196114, year = {2011}, author = {Supaphol, S and Jenkins, SN and Intomo, P and Waite, IS and O'Donnell, AG}, title = {Microbial community dynamics in mesophilic anaerobic co-digestion of mixed waste.}, journal = {Bioresource technology}, volume = {102}, number = {5}, pages = {4021-4027}, doi = {10.1016/j.biortech.2010.11.124}, pmid = {21196114}, issn = {1873-2976}, mesh = {Bacteria/genetics/*metabolism ; *Biota ; Denaturing Gradient Gel Electrophoresis ; Metagenomics ; Methane/*biosynthesis ; Methanosarcinales/genetics/*metabolism ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Refuse Disposal/*methods ; Species Specificity ; Thailand ; }, abstract = {This paper identifies key components of the microbial community involved in the mesophilic anaerobic co-digestion (AD) of mixed waste at Rayong Biogas Plant, Thailand. The AD process is separated into three stages: front end treatment (FET); feed holding tank and the main anaerobic digester. The study examines how the microbial community structure was affected by the different stages and found that seeding the waste at the beginning of the process (FET) resulted in community stability. Also, co-digestion of mixed waste supported different bacterial and methanogenic pathways. Typically, acetoclastic methanogenesis was the major pathway catalysed by Methanosaeta but hydrogenotrophs were also supported. Finally, the three-stage AD process means that hydrolysis and acidogenesis is initiated prior to entering the main digester which helps improve the bioconversion efficiency. This paper demonstrates that both resource availability (different waste streams) and environmental factors are key drivers of microbial community dynamics in mesophilic, anaerobic co-digestion.}, } @article {pmid21185430, year = {2011}, author = {Müller, S and Strous, M}, title = {Continuous cultivation and thermodynamic aspects of niche definition in the nitrogen cycle.}, journal = {Methods in enzymology}, volume = {486}, number = {}, pages = {33-52}, doi = {10.1016/B978-0-12-381294-0.00002-X}, pmid = {21185430}, issn = {1557-7988}, mesh = {Biodiversity ; Calorimetry/methods ; Ecology/methods ; Environment ; Metagenomics/*methods ; Models, Biological ; Nitrification/*physiology ; Thermodynamics ; }, abstract = {The study of model organisms in pure culture has provided detailed information about the physiology and biochemistry of nitrification and related processes. Metagenomic sequencing of environmental samples is providing information to what extent this understanding also applies to natural microbial communities. Here, we outline a conceptual and experimental strategy that links these two approaches. It consists of the mathematical modeling of nitrification and related processes. The model predictions are subsequently validated experimentally by the study of natural microbial communities in continuous cultures under precisely defined environmental conditions. Combined with calorimetry and metagenomic monitoring this form of "experimental metagenomics" enables the answering of current questions in the ecology of the nitrogen cycle.}, } @article {pmid21183646, year = {2011}, author = {Delmont, TO and Robe, P and Cecillon, S and Clark, IM and Constancias, F and Simonet, P and Hirsch, PR and Vogel, TM}, title = {Accessing the soil metagenome for studies of microbial diversity.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {4}, pages = {1315-1324}, pmid = {21183646}, issn = {1098-5336}, mesh = {*Bacteria/classification/genetics/isolation & purification ; Biodiversity ; DNA/*analysis/genetics/isolation & purification ; DNA Fingerprinting ; DNA, Bacterial/analysis/genetics ; Ecosystem ; *Metagenome ; Microbial Consortia/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Soil microbial communities contain the highest level of prokaryotic diversity of any environment, and metagenomic approaches involving the extraction of DNA from soil can improve our access to these communities. Most analyses of soil biodiversity and function assume that the DNA extracted represents the microbial community in the soil, but subsequent interpretations are limited by the DNA recovered from the soil. Unfortunately, extraction methods do not provide a uniform and unbiased subsample of metagenomic DNA, and as a consequence, accurate species distributions cannot be determined. Moreover, any bias will propagate errors in estimations of overall microbial diversity and may exclude some microbial classes from study and exploitation. To improve metagenomic approaches, investigate DNA extraction biases, and provide tools for assessing the relative abundances of different groups, we explored the biodiversity of the accessible community DNA by fractioning the metagenomic DNA as a function of (i) vertical soil sampling, (ii) density gradients (cell separation), (iii) cell lysis stringency, and (iv) DNA fragment size distribution. Each fraction had a unique genetic diversity, with different predominant and rare species (based on ribosomal intergenic spacer analysis [RISA] fingerprinting and phylochips). All fractions contributed to the number of bacterial groups uncovered in the metagenome, thus increasing the DNA pool for further applications. Indeed, we were able to access a more genetically diverse proportion of the metagenome (a gain of more than 80% compared to the best single extraction method), limit the predominance of a few genomes, and increase the species richness per sequencing effort. This work stresses the difference between extracted DNA pools and the currently inaccessible complete soil metagenome.}, } @article {pmid21183639, year = {2011}, author = {Yung, PY and Burke, C and Lewis, M and Kjelleberg, S and Thomas, T}, title = {Novel antibacterial proteins from the microbial communities associated with the sponge Cymbastela concentrica and the green alga Ulva australis.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {4}, pages = {1512-1515}, pmid = {21183639}, issn = {1098-5336}, mesh = {Alphaproteobacteria/*enzymology ; Animals ; Anti-Bacterial Agents/*biosynthesis ; DNA Transposable Elements ; Gammaproteobacteria/*enzymology ; Metagenomics ; Microbial Consortia/genetics ; Mutation ; Porifera/*microbiology ; Ulva/*microbiology ; }, abstract = {The functional metagenomic screening of the microbial communities associated with a temperate marine sponge and a green alga identified three novel hydrolytic enzymes with antibacterial activities. The results suggest that uncultured alpha- and gammaproteobacteria contain new classes of proteins that may be a source of antibacterial agents.}, } @article {pmid21183634, year = {2011}, author = {Park, EJ and Kim, KH and Abell, GC and Kim, MS and Roh, SW and Bae, JW}, title = {Metagenomic analysis of the viral communities in fermented foods.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {4}, pages = {1284-1291}, pmid = {21183634}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification/isolation & purification ; Bacteriophages/*classification/*genetics/isolation & purification ; Caudovirales/genetics ; DNA/analysis ; *Fermentation ; Food/*virology ; Gene Library ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Microbial Consortia/genetics ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; }, abstract = {Viruses are recognized as the most abundant biological components on Earth, and they regulate the structure of microbial communities in many environments. In soil and marine environments, microorganism-infecting phages are the most common type of virus. Although several types of bacteriophage have been isolated from fermented foods, little is known about the overall viral assemblages (viromes) of these environments. In this study, metagenomic analyses were performed on the uncultivated viral communities from three fermented foods, fermented shrimp, kimchi, and sauerkraut. Using a high-throughput pyrosequencing technique, a total of 81,831, 70,591 and 69,464 viral sequences were obtained from fermented shrimp, kimchi and sauerkraut, respectively. Moreover, 37 to 50% of these sequences showed no significant hit against sequences in public databases. There were some discrepancies between the prediction of bacteriophages hosts via homology comparison and bacterial distribution, as determined from 16S rRNA gene sequencing. These discrepancies likely reflect the fact that the viral genomes of fermented foods are poorly represented in public databases. Double-stranded DNA viral communities were amplified from fermented foods by using a linker-amplified shotgun library. These communities were dominated by bacteriophages belonging to the viral order Caudovirales (i.e., Myoviridae, Podoviridae, and Siphoviridae). This study indicates that fermented foods contain less complex viral communities than many other environmental habitats, such as seawater, human feces, marine sediment, and soil.}, } @article {pmid21183039, year = {2011}, author = {Santos, TM and Gilbert, RO and Bicalho, RC}, title = {Metagenomic analysis of the uterine bacterial microbiota in healthy and metritic postpartum dairy cows.}, journal = {Journal of dairy science}, volume = {94}, number = {1}, pages = {291-302}, doi = {10.3168/jds.2010-3668}, pmid = {21183039}, issn = {1525-3198}, mesh = {Animals ; Bacteria/classification/*genetics ; Biodiversity ; Cattle/*microbiology ; Cattle Diseases/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Endometritis/microbiology/*veterinary ; Female ; *Metagenome ; Puerperal Disorders/*veterinary ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Uterus/*microbiology ; }, abstract = {At present, many bacterial species are validly known as etiological agents of dairy cattle metritis, yet the vast uncultured fraction has received no attention so far. The purpose of this study was to use culture-independent methods to describe and compare the uterine bacterial composition in healthy and metritic postpartum Holstein dairy cows. Both group-specific 16S ribosomal DNA PCR-denaturing gradient gel electrophoresis (DGGE) and clone library sequencing of broad-range 16S ribosomal DNA PCR revealed differences in the bacterial communities comparing healthy and metritic cows. Bacterial diversity in healthy and metritic uteri was greater and more complex than described previously by traditional culture methods. Sequences were assigned to 5 major groups (Gammaproteobacteria, Firmicutes, Fusobacteria, Bacteroidetes, and Tenericutes) and to uncultured bacteria. Additionally, DGGE suggested the presence of Actinobacteria. Most clone sequences in the metritic status libraries were affiliated with the phylum Fusobacteria. Many components, especially from other phyla, have not previously been isolated from cases of metritis. In the clone libraries from the healthy status dairy cows, Gammaproteobacteria was the most prominent group and most sequences showed high identity with Mannheimia varigena, Pasteurella hemolytica, and members of the phylum Tenericutes. Our data showed that the uterine bacterial community in postpartum dairy cows differed considerably between healthy and metritic cows and described the occurrence of a previously unrecognized extent of this diversity in the bovine intrauterine microbiota.}, } @article {pmid21177896, year = {2011}, author = {Rousseau, C and Levenez, F and Fouqueray, C and Doré, J and Collignon, A and Lepage, P}, title = {Clostridium difficile colonization in early infancy is accompanied by changes in intestinal microbiota composition.}, journal = {Journal of clinical microbiology}, volume = {49}, number = {3}, pages = {858-865}, pmid = {21177896}, issn = {1098-660X}, mesh = {*Biodiversity ; Clostridioides difficile/*growth & development ; Clostridium Infections/*microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Hot Temperature ; Humans ; Infant ; Infant, Newborn ; Male ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Clostridium difficile is a major enteric pathogen responsible for antibiotic-associated diarrhea. Host susceptibility to C. difficile infections results partly from inability of the intestinal microbiota to resist C. difficile colonization. During early infancy, asymptomatic colonization by C. difficile is common and the intestinal microbiota shows low complexity. Thus, we investigated the potential relationship between the microbiota composition and the implantation of C. difficile in infant gut. Fecal samples from 53 infants, ages 0 to 13 months, 27 negative and 26 positive for C. difficile, were studied. Dominant microbiota profiles were assessed by PCR-temporal temperature gradient gel electrophoresis (TTGE). Bacterial signatures of the intestinal microbiota associated with colonization by C. difficile were deciphered using principal component analysis (PCA). Resulting bands of interest in TTGE profiles were excised, sequenced, and analyzed by nucleotide BLAST (NCBI). While global biodiversity was not affected, interclass PCA on instrumental variables highlighted significant differences in dominant bacterial species between C. difficile-colonized and noncolonized infants (P = 0.017). Four bands were specifically associated with the presence or absence of C. difficile: 16S rRNA gene sequences related to Ruminococcus gnavus and Klebsiella pneumoniae for colonized infants and to Bifidobacterium longum for noncolonized infants. We demonstrated that the presence of C. difficile in the intestinal microbiota of infants was associated with changes in this ecosystem's composition. These results suggest that the composition of the gut microbiota might be crucial in the colonization process, although the chronology of events remains to be determined.}, } @article {pmid21169428, year = {2011}, author = {Simon, C and Daniel, R}, title = {Metagenomic analyses: past and future trends.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {4}, pages = {1153-1161}, pmid = {21169428}, issn = {1098-5336}, mesh = {Drug Discovery ; Ecosystem ; *Gene Library ; Humans ; Metagenomics/*trends ; Microbial Consortia/*genetics ; Proteomics/methods ; Sequence Analysis, DNA/methods ; Sequence Analysis, Protein/methods ; Sequence Analysis, RNA/methods ; }, abstract = {Metagenomics has revolutionized microbiology by paving the way for a cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. Metagenomics comprising construction and screening of metagenomic DNA libraries has proven to be a powerful tool to isolate new enzymes and drugs of industrial importance. So far, the majority of the metagenomically exploited habitats comprised temperate environments, such as soil and marine environments. Recently, metagenomes of extreme environments have also been used as sources of novel biocatalysts. The employment of next-generation sequencing techniques for metagenomics resulted in the generation of large sequence data sets derived from various environments, such as soil, the human body, and ocean water. Analyses of these data sets opened a window into the enormous taxonomic and functional diversity of environmental microbial communities. To assess the functional dynamics of microbial communities, metatranscriptomics and metaproteomics have been developed. The combination of DNA-based, mRNA-based, and protein-based analyses of microbial communities present in different environments is a way to elucidate the compositions, functions, and interactions of microbial communities and to link these to environmental processes.}, } @article {pmid21167876, year = {2011}, author = {Durso, LM and Harhay, GP and Bono, JL and Smith, TP}, title = {Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach.}, journal = {Journal of microbiological methods}, volume = {84}, number = {2}, pages = {278-282}, doi = {10.1016/j.mimet.2010.12.008}, pmid = {21167876}, issn = {1872-8359}, mesh = {Animals ; Bacterial Proteins/*genetics ; Biodiversity ; Cattle ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; *Drug Resistance, Bacterial ; Feces/*microbiology ; High-Throughput Nucleotide Sequencing ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Virulence Factors/*genetics ; }, abstract = {The bovine fecal microbiota impacts human food safety as well as animal health. Although the bacteria of cattle feces have been well characterized using culture-based and culture-independent methods, techniques have been lacking to correlate total community composition with community function. We used high throughput sequencing of total DNA extracted from fecal material to characterize general community composition and examine the repertoire of microbial genes present in beef cattle feces, including genes associated with antibiotic resistance and bacterial virulence. Results suggest that traditional 16S sequencing using "universal" primers to generate full-length sequence may under represent Acitinobacteria and Proteobacteria. Over eight percent (8.4%) of the sequences from our beef cattle fecal pool sample could be categorized as virulence genes, including a suite of genes associated with resistance to antibiotic and toxic compounds (RATC). This is a higher proportion of virulence genes found in Sargasso sea, chicken cecum, and cow rumen samples, but comparable to the proportion found in Antarctic marine derived lake, human fecal, and farm soil samples. The quantitative nature of metagenomic data, combined with the large number of RATC classes represented in samples from widely different habitats indicates that metagenomic data can be used to track relative amounts of antibiotic resistance genes in individual animals over time. Consequently, these data can be used to generate sample-specific and temporal antibiotic resistance gene profiles to facilitate an understanding of the ecology of the microbial communities in each habitat as well as the epidemiology of antibiotic resistant gene transport between and among habitats.}, } @article {pmid21160538, year = {2011}, author = {Weber, M and Teeling, H and Huang, S and Waldmann, J and Kassabgy, M and Fuchs, BM and Klindworth, A and Klockow, C and Wichels, A and Gerdts, G and Amann, R and Glöckner, FO}, title = {Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics.}, journal = {The ISME journal}, volume = {5}, number = {5}, pages = {918-928}, pmid = {21160538}, issn = {1751-7370}, mesh = {Algorithms ; *Biodiversity ; Cluster Analysis ; *Internet ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sensitivity and Specificity ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {Next-generation sequencing (NGS) technologies have enabled the application of broad-scale sequencing in microbial biodiversity and metagenome studies. Biodiversity is usually targeted by classifying 16S ribosomal RNA genes, while metagenomic approaches target metabolic genes. However, both approaches remain isolated, as long as the taxonomic and functional information cannot be interrelated. Techniques like self-organizing maps (SOMs) have been applied to cluster metagenomes into taxon-specific bins in order to link biodiversity with functions, but have not been applied to broad-scale NGS-based metagenomics yet. Here, we provide a novel implementation, demonstrate its potential and practicability, and provide a web-based service for public usage. Evaluation with published data sets mimicking varyingly complex habitats resulted into classification specificities and sensitivities of close to 100% to above 90% from phylum to genus level for assemblies exceeding 8 kb for low and medium complexity data. When applied to five real-world metagenomes of medium complexity from direct pyrosequencing of marine subsurface waters, classifications of assemblies above 2.5 kb were in good agreement with fluorescence in situ hybridizations, indicating that biodiversity was mostly retained within the metagenomes, and confirming high classification specificities. This was validated by two protein-based classifications (PBCs) methods. SOMs were able to retrieve the relevant taxa down to the genus level, while surpassing PBCs in resolution. In order to make the approach accessible to a broad audience, we implemented a feature-rich web-based SOM application named TaxSOM, which is freely available at http://www.megx.net/toolbox/taxsom. TaxSOM can classify reads or assemblies exceeding 2.5 kb with high accuracy and thus assists in linking biodiversity and functions in metagenome studies, which is a precondition to study microbial ecology in a holistic fashion.}, } @article {pmid21155911, year = {2011}, author = {Unterseher, M and Jumpponen, A and Opik, M and Tedersoo, L and Moora, M and Dormann, CF and Schnittler, M}, title = {Species abundance distributions and richness estimations in fungal metagenomics--lessons learned from community ecology.}, journal = {Molecular ecology}, volume = {20}, number = {2}, pages = {275-285}, doi = {10.1111/j.1365-294X.2010.04948.x}, pmid = {21155911}, issn = {1365-294X}, mesh = {*Biodiversity ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer ; Ecosystem ; Fungi/*genetics ; Glomeromycota/*genetics ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Mycorrhizae/*genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal ; Ribosome Subunits, Small ; Sampling Studies ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Results of diversity and community ecology studies strongly depend on sampling depth. Completely surveyed communities follow log-normal distribution, whereas power law functions best describe incompletely censused communities. It is arguable whether the statistics behind those theories can be applied to voluminous next generation sequencing data in microbiology by treating individual DNA sequences as counts of molecular taxonomic units (MOTUs). This study addresses the suitability of species abundance models in three groups of plant-associated fungal communities - phyllosphere, ectomycorrhizal and arbuscular mycorrhizal fungi. We tested the impact of differential treatment of molecular singletons on observed and estimated species richness and species abundance distribution models. The arbuscular mycorrhizal community of 48 MOTUs was exhaustively sampled and followed log-normal distribution. The ectomycorrhizal (153 MOTUs) and phyllosphere (327 MOTUs) communities significantly differed from log-normal distribution. The fungal phyllosphere community in particular was clearly undersampled. This undersampling bias resulted in strong sensitivity to the exclusion of molecular singletons and other rare MOTUs that may represent technical artefacts. The analysis of abundant (core) and rare (satellite) MOTUs clearly identified two species abundance distributions in the phyllosphere data - a log-normal model for the core group and a log-series model for the satellite group. The prominent log-series distribution of satellite phyllosphere fungi highlighted the ecological significance of an infrequent fungal component in the phyllosphere community.}, } @article {pmid21127032, year = {2011}, author = {Gori, F and Folino, G and Jetten, MS and Marchiori, E}, title = {MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks.}, journal = {Bioinformatics (Oxford, England)}, volume = {27}, number = {2}, pages = {196-203}, pmid = {21127032}, issn = {1367-4811}, mesh = {Algorithms ; Biodiversity ; Cluster Analysis ; Metagenome ; Metagenomics/*methods ; Phylogeny ; }, abstract = {MOTIVATION: Metagenomics is a recent field of biology that studies microbial communities by analyzing their genomic content directly sequenced from the environment. A metagenomic dataset consists of many short DNA or RNA fragments called reads. One interesting problem in metagenomic data analysis is the discovery of the taxonomic composition of a given dataset. A simple method for this task, called the Lowest Common Ancestor (LCA), is employed in state-of-the-art computational tools for metagenomic data analysis of very short reads (about 100 bp). However LCA has two main drawbacks: it possibly assigns many reads to high taxonomic ranks and it discards a high number of reads.

RESULTS: We present MTR, a new method for tackling these drawbacks using clustering at Multiple Taxonomic Ranks. Unlike LCA, which processes the reads one-by-one, MTR exploits information shared by reads. Specifically, MTR consists of two main phases. First, for each taxonomic rank, a collection of potential clusters of reads is generated, and each potential cluster is associated to a taxon at that rank. Next, a small number of clusters is selected at each rank using a combinatorial optimization algorithm. The effectiveness of the resulting method is tested on a large number of simulated and real-life metagenomes. Results of experiments show that MTR improves on LCA by discarding a significantly smaller number of reads and by assigning much more reads at lower taxonomic ranks. Moreover, MTR provides a more faithful taxonomic characterization of the metagenome population distribution.

AVAILABILITY: Matlab and C++ source codes of the method available at http://cs.ru.nl/gori/software/MTR.tar.gz.}, } @article {pmid21124487, year = {2011}, author = {Tucker, KP and Parsons, R and Symonds, EM and Breitbart, M}, title = {Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean.}, journal = {The ISME journal}, volume = {5}, number = {5}, pages = {822-830}, pmid = {21124487}, issn = {1751-7370}, mesh = {Atlantic Ocean ; Base Composition ; *Biodiversity ; DNA Helicases/genetics ; DNA, Single-Stranded/genetics ; DNA, Viral/genetics ; Genes, Viral ; *Genome, Viral ; Geography ; Metagenome ; Microviridae/classification/*genetics ; Seawater/virology ; Sequence Analysis, DNA ; Time Factors ; Trans-Activators/genetics ; *Water Microbiology ; }, abstract = {Knowledge of marine phages is highly biased toward double-stranded DNA (dsDNA) phages; however, recent metagenomic surveys have also identified single-stranded DNA (ssDNA) phages in the oceans. Here, we describe two complete ssDNA phage genomes that were reconstructed from a viral metagenome from 80 m depth at the Bermuda Atlantic Time-series Study (BATS) site in the northwestern Sargasso Sea and examine their spatial and temporal distributions. Both genomes (SARssφ1 and SARssφ2) exhibited similarity to known phages of the Microviridae family in terms of size, GC content, genome organization and protein sequence. PCR amplification of the replication initiation protein (Rep) gene revealed narrow and distinct depth distributions for the newly described ssDNA phages within the upper 200 m of the water column at the BATS site. Comparison of Rep gene sequences obtained from the BATS site over time revealed changes in the diversity of ssDNA phages over monthly time scales, although some nearly identical sequences were recovered from samples collected 4 years apart. Examination of ssDNA phage diversity along transects through the North Atlantic Ocean revealed a positive correlation between genetic distance and geographic distance between sampling sites. Together, the data suggest fundamental differences between the distribution of these ssDNA phages and the distribution of known marine dsDNA phages, possibly because of differences in host range, host distribution, virion stability, or viral evolution mechanisms and rates. Future work needs to elucidate the host ranges for oceanic ssDNA phages and determine their ecological roles in the marine ecosystem.}, } @article {pmid21104154, year = {2011}, author = {Yan, Q and Yu, Y}, title = {Metagenome-based analysis: a promising direction for plankton ecological studies.}, journal = {Science China. Life sciences}, volume = {54}, number = {1}, pages = {75-81}, doi = {10.1007/s11427-010-4103-4}, pmid = {21104154}, issn = {1869-1889}, mesh = {*Ecology ; *Ecosystem ; Marine Biology ; *Metagenome ; Plankton/*genetics ; Seawater ; }, abstract = {The plankton community plays an especially important role in the functioning of aquatic ecosystems and also in biogeochemical cycles. Since the beginning of marine research expeditions in the 1870 s, an enormous number of planktonic organisms have been described and studied. Plankton investigation has become one of the most important areas of aquatic ecological study, as well as a crucial component of aquatic environmental evaluation. Nonetheless, traditional investigations have mainly focused on morphospecies composition, abundances and dynamics, which primarily depend on morphological identification and counting under microscopes. However, for many species/groups, with few readily observable characteristics, morphological identification and counting have historically been a difficult task. Over the past decades, microbiologists have endeavored to apply and extend molecular techniques to address questions in microbial ecology. These culture-independent studies have generated new insights into microbial ecology. One such strategy, metagenome-based analysis, has also proved to be a powerful tool for plankton research. This mini-review presents a brief history of plankton research using morphological and metagenome-based approaches and the potential applications and further directions of metagenomic analyses in plankton ecological studies are discussed. The use of metagenome-based approaches for plankton ecological study in aquatic ecosystems is encouraged.}, } @article {pmid21103066, year = {2010}, author = {Yildirim, S and Yeoman, CJ and Sipos, M and Torralba, M and Wilson, BA and Goldberg, TL and Stumpf, RM and Leigh, SR and White, BA and Nelson, KE}, title = {Characterization of the fecal microbiome from non-human wild primates reveals species specific microbial communities.}, journal = {PloS one}, volume = {5}, number = {11}, pages = {e13963}, pmid = {21103066}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/genetics/growth & development ; Base Sequence ; Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; *Ecosystem ; Feces/*microbiology ; Gastrointestinal Tract/microbiology ; Genetic Variation ; Humans ; Metagenome/*genetics ; Molecular Sequence Data ; Phylogeny ; Primates/classification/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: Host-associated microbes comprise an integral part of animal digestive systems and these interactions have a long evolutionary history. It has been hypothesized that the gastrointestinal microbiome of humans and other non-human primates may have played significant roles in host evolution by facilitating a range of dietary adaptations. We have undertaken a comparative sequencing survey of the gastrointestinal microbiomes of several non-human primate species, with the goal of better understanding how these microbiomes relate to the evolution of non-human primate diversity. Here we present a comparative analysis of gastrointestinal microbial communities from three different species of Old World wild monkeys.

We analyzed fecal samples from three different wild non-human primate species (black-and-white colobus [Colubus guereza], red colobus [Piliocolobus tephrosceles], and red-tailed guenon [Cercopithecus ascanius]). Three samples from each species were subjected to small subunit rRNA tag pyrosequencing. Firmicutes comprised the vast majority of the phyla in each sample. Other phyla represented were Bacterioidetes, Proteobacteria, Spirochaetes, Actinobacteria, Verrucomicrobia, Lentisphaerae, Tenericutes, Planctomycetes, Fibrobacateres, and TM7. Bray-Curtis similarity analysis of these microbiomes indicated that microbial community composition within the same primate species are more similar to each other than to those of different primate species. Comparison of fecal microbiota from non-human primates with microbiota of human stool samples obtained in previous studies revealed that the gut microbiota of these primates are distinct and reflect host phylogeny.

CONCLUSION/SIGNIFICANCE: Our analysis provides evidence that the fecal microbiomes of wild primates co-vary with their hosts, and that this is manifested in higher intraspecies similarity among wild primate species, perhaps reflecting species specificity of the microbiome in addition to dietary influences. These results contribute to the limited body of primate microbiome studies and provide a framework for comparative microbiome analysis between human and non-human primates as well as a comparative evolutionary understanding of the human microbiome.}, } @article {pmid21097583, year = {2011}, author = {Howard, EC and Sun, S and Reisch, CR and del Valle, DA and Bürgmann, H and Kiene, RP and Moran, MA}, title = {Changes in dimethylsulfoniopropionate demethylase gene assemblages in response to an induced phytoplankton bloom.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {2}, pages = {524-531}, pmid = {21097583}, issn = {1098-5336}, mesh = {Bacteria/classification/*enzymology/*genetics ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Metagenome ; Mexico ; Molecular Sequence Data ; Phylogeny ; Phytoplankton/*genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sulfonium Compounds/*metabolism ; Sulfur/metabolism ; }, abstract = {Over half of the bacterioplankton cells in ocean surface waters are capable of carrying out a demethylation of the phytoplankton metabolite dimethylsulfoniopropionate (DMSP) that routes the sulfur moiety away from the climatically active gas dimethylsulfide (DMS). In this study, we tracked changes in dmdA, the gene responsible for DMSP demethylation, over the course of an induced phytoplankton bloom in Gulf of Mexico seawater microcosms. Analysis of >91,000 amplicon sequences indicated 578 different dmdA sequence clusters at a conservative clustering criterion of ≥90% nucleotide sequence identity over the 6-day study. The representation of the major clades of dmdA, several of which are linked to specific taxa through genomes of cultured marine bacterioplankton, remained fairly constant. However, the representation of clusters within these major clades shifted significantly in response to the bloom, including two Roseobacter-like clusters and a SAR11-like cluster, and the best correlate with shifts of the dominant dmdA clades was chlorophyll a concentration. Concurrent 16S rRNA amplification and sequencing indicated the presence of Roseobacter, SAR11, OM60, and marine Rhodospirillales populations, all of which are known to harbor dmdA genes, although the largest taxonomic change was an increase in Flavobacteriaceae, a group not yet demonstrated to have DMSP-demethylating capabilities. Sequence heterogeneity in dmdA and other functional gene populations is becoming increasingly evident with the advent of high-throughput sequencing technologies, and understanding the ecological implications of this heterogeneity is a major challenge for marine microbial ecology.}, } @article {pmid21097582, year = {2011}, author = {Brown, JF and Jones, DS and Mills, DB and Macalady, JL and Burgos, WD}, title = {Application of a depositional facies model to an acid mine drainage site.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {2}, pages = {545-554}, pmid = {21097582}, issn = {1098-5336}, mesh = {*Biodiversity ; Geography ; Geologic Sediments/chemistry/*microbiology/*parasitology ; Iron/metabolism ; *Metagenome ; Minerals/analysis ; Molecular Sequence Data ; Oxidation-Reduction ; Pennsylvania ; Sequence Analysis, DNA ; Water/chemistry ; }, abstract = {Lower Red Eyes is an acid mine drainage site in Pennsylvania where low-pH Fe(II) oxidation has created a large, terraced iron mound downstream of an anoxic, acidic, metal-rich spring. Aqueous chemistry, mineral precipitates, microbial communities, and laboratory-based Fe(II) oxidation rates for this site were analyzed in the context of a depositional facies model. Depositional facies were defined as pools, terraces, or microterracettes based on cm-scale sediment morphology, irrespective of the distance downstream from the spring. The sediments were composed entirely of Fe precipitates and cemented organic matter. The Fe precipitates were identified as schwertmannite at all locations, regardless of facies. Microbial composition was studied with fluorescence in situ hybridization (FISH) and transitioned from a microaerophilic, Euglena-dominated community at the spring, to a Betaproteobacteria (primarily Ferrovum spp.)-dominated community at the upstream end of the iron mound, to a Gammaproteobacteria (primarily Acidithiobacillus)-dominated community at the downstream end of the iron mound. Microbial community structure was more strongly correlated with pH and geochemical conditions than depositional facies. Intact pieces of terrace and pool sediments from upstream and downstream locations were used in flowthrough laboratory reactors to measure the rate and extent of low-pH Fe(II) oxidation. No change in Fe(II) concentration was observed with (60)Co-irradiated sediments or with no-sediment controls, indicating that abiotic Fe(II) oxidation was negligible. Upstream sediments attained lower effluent Fe(II) concentrations compared to downstream sediments, regardless of depositional facies.}, } @article {pmid21088127, year = {2011}, author = {Smith, AR and Macfarlane, S and Furrie, E and Ahmed, S and Bahrami, B and Reynolds, N and Macfarlane, GT}, title = {Microbiological and immunological effects of enteral feeding on the upper gastrointestinal tract.}, journal = {Journal of medical microbiology}, volume = {60}, number = {Pt 3}, pages = {359-365}, doi = {10.1099/jmm.0.026401-0}, pmid = {21088127}, issn = {1473-5644}, support = {//Medical Research Council/United Kingdom ; }, mesh = {Aged ; *Biodiversity ; Cytokines/biosynthesis ; *Enteral Nutrition ; Female ; Gastric Mucosa/immunology ; Gene Expression Profiling ; Humans ; Immunity, Mucosal ; In Situ Hybridization ; Intestinal Mucosa/immunology ; Male ; *Metagenome ; Middle Aged ; Polymerase Chain Reaction/methods ; Upper Gastrointestinal Tract/*immunology/*microbiology ; }, abstract = {Enteral feeding via a percutaneous endoscopic gastrostomy tube is required for nutritional support in patients with dysphagia. Enteral tube feeding bypasses the innate defence mechanisms in the upper gastrointestinal tract. This study examined the surface-associated microbial populations and immune response in the gastric and duodenal mucosae of eight enteral nutrition (EN) patients and ten controls. Real-time PCR and fluorescence in situ hybridization were employed to assess microbiota composition and mucosal pro-inflammatory cytokine expression. The results showed that EN patients had significantly higher levels of bacterial DNA in mucosal biopsies from the stomach and duodenum (P<0.05) than the controls, and that enterobacteria were the predominant colonizing species on mucosal surfaces in these individuals. Expression of the pro-inflammatory cytokines interleukin (IL)-1α, IL-6 and tumour necrosis factor-α was significantly higher in gastric and small intestinal mucosae from patients fed normal diets in comparison with those receiving EN (P<0.05). These results indicate that EN can lead to significant bacterial overgrowth on upper gastrointestinal tract mucosae and a significantly diminished pro-inflammatory cytokine response.}, } @article {pmid21083935, year = {2010}, author = {Weng, FC and Su, CH and Hsu, MT and Wang, TY and Tsai, HK and Wang, D}, title = {Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency.}, journal = {BMC bioinformatics}, volume = {11}, number = {}, pages = {565}, pmid = {21083935}, issn = {1471-2105}, mesh = {Algorithms ; Base Sequence ; Databases, Factual ; *Gene Order ; Metagenomics/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Investigation of metagenomes provides greater insight into uncultured microbial communities. The improvement in sequencing technology, which yields a large amount of sequence data, has led to major breakthroughs in the field. However, at present, taxonomic binning tools for metagenomes discard 30-40% of Sanger sequencing data due to the stringency of BLAST cut-offs. In an attempt to provide a comprehensive overview of metagenomic data, we re-analyzed the discarded metagenomes by using less stringent cut-offs. Additionally, we introduced a new criterion, namely, the evolutionary conservation of adjacency between neighboring genes. To evaluate the feasibility of our approach, we re-analyzed discarded contigs and singletons from several environments with different levels of complexity. We also compared the consistency between our taxonomic binning and those reported in the original studies.

RESULTS: Among the discarded data, we found that 23.7 ± 3.9% of singletons and 14.1 ± 1.0% of contigs were assigned to taxa. The recovery rates for singletons were higher than those for contigs. The Pearson correlation coefficient revealed a high degree of similarity (0.94 ± 0.03 at the phylum rank and 0.80 ± 0.11 at the family rank) between the proposed taxonomic binning approach and those reported in original studies. In addition, an evaluation using simulated data demonstrated the reliability of the proposed approach.

CONCLUSIONS: Our findings suggest that taking account of conserved neighboring gene adjacency improves taxonomic assignment when analyzing metagenomes using Sanger sequencing. In other words, utilizing the conserved gene order as a criterion will reduce the amount of data discarded when analyzing metagenomes.}, } @article {pmid21075899, year = {2011}, author = {Spear, GT and Gilbert, D and Landay, AL and Zariffard, R and French, AL and Patel, P and Gillevet, PM}, title = {Pyrosequencing of the genital microbiotas of HIV-seropositive and -seronegative women reveals Lactobacillus iners as the predominant Lactobacillus Species.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {1}, pages = {378-381}, pmid = {21075899}, issn = {1098-5336}, support = {M01 RR000079/RR/NCRR NIH HHS/United States ; U01 AI031834/AI/NIAID NIH HHS/United States ; P30 AI082151/AI/NIAID NIH HHS/United States ; U01 AI035004/AI/NIAID NIH HHS/United States ; U01 AI35004/AI/NIAID NIH HHS/United States ; U01 AI34993/AI/NIAID NIH HHS/United States ; M01 RR000071/RR/NCRR NIH HHS/United States ; P01 AI082971/AI/NIAID NIH HHS/United States ; M01-RR-00079/RR/NCRR NIH HHS/United States ; U01 34993//PHS HHS/United States ; M01 RR000083/RR/NCRR NIH HHS/United States ; U01 AI31834/AI/NIAID NIH HHS/United States ; U01 AI042590/AI/NIAID NIH HHS/United States ; U01 AI34994/AI/NIAID NIH HHS/United States ; U01 AI42590/AI/NIAID NIH HHS/United States ; U01 AI034989/AI/NIAID NIH HHS/United States ; M01-RR-00083/RR/NCRR NIH HHS/United States ; U01 AI034994/AI/NIAID NIH HHS/United States ; U01 AI34989/AI/NIAID NIH HHS/United States ; M01-RR-00071/RR/NCRR NIH HHS/United States ; U01 AI034993/AI/NIAID NIH HHS/United States ; U01 HD 23632/HD/NICHD NIH HHS/United States ; }, mesh = {*Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; *HIV Infections ; Humans ; Lactobacillus/classification/genetics/*isolation & purification ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vagina/*microbiology ; }, abstract = {The species of vaginal lactobacilli in HIV-seropositive and -seronegative women were determined by 16S gene pyrosequencing. Lactobacillus iners sequences were the predominant lactobacillus sequences in 66% of HIV(+) women and 90% of HIV(-) women. This has implications for resistance of HIV(+) and HIV(-) women to genital colonization by pathogenic organisms.}, } @article {pmid21073719, year = {2010}, author = {Day, JM and Ballard, LL and Duke, MV and Scheffler, BE and Zsak, L}, title = {Metagenomic analysis of the turkey gut RNA virus community.}, journal = {Virology journal}, volume = {7}, number = {}, pages = {313}, pmid = {21073719}, issn = {1743-422X}, mesh = {Animals ; *Biodiversity ; Caliciviridae/classification/genetics/isolation & purification ; Gastrointestinal Tract/*virology ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Molecular Sequence Data ; Picobirnavirus/classification/genetics/isolation & purification ; Picornaviridae/classification/genetics/isolation & purification ; RNA Viruses/*classification/*genetics/isolation & purification ; Turkeys ; United States ; }, abstract = {Viral enteric disease is an ongoing economic burden to poultry producers worldwide, and despite considerable research, no single virus has emerged as a likely causative agent and target for prevention and control efforts. Historically, electron microscopy has been used to identify suspect viruses, with many small, round viruses eluding classification based solely on morphology. National and regional surveys using molecular diagnostics have revealed that suspect viruses continuously circulate in United States poultry, with many viruses appearing concomitantly and in healthy birds. High-throughput nucleic acid pyrosequencing is a powerful diagnostic technology capable of determining the full genomic repertoire present in a complex environmental sample. We utilized the Roche/454 Life Sciences GS-FLX platform to compile an RNA virus metagenome from turkey flocks experiencing enteric disease. This approach yielded numerous sequences homologous to viruses in the BLAST nr protein database, many of which have not been described in turkeys. Our analysis of this turkey gut RNA metagenome focuses in particular on the turkey-origin members of the Picornavirales, the Caliciviridae, and the turkey Picobirnaviruses.}, } @article {pmid21069557, year = {2011}, author = {Eusébio, A and Tacão, M and Chaves, S and Tenreiro, R and Almeida-Vara, E}, title = {Molecular assessment of microbiota structure and dynamics along mixed olive oil and winery wastewaters biotreatment.}, journal = {Biodegradation}, volume = {22}, number = {4}, pages = {773-795}, doi = {10.1007/s10532-010-9434-0}, pmid = {21069557}, issn = {1572-9729}, mesh = {Bacteria/*classification/*genetics/isolation & purification/metabolism ; Bacterial Typing Techniques ; Biodegradation, Environmental ; Bioreactors ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Genes, rRNA ; Genetic Variation ; *Metagenome ; *Microbial Consortia ; Olive Oil ; Phylogeny ; Plant Oils/chemistry ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Waste Disposal, Fluid ; Wine/microbiology ; }, abstract = {The major parcel of the degradation occurring along wastewater biotreatments is performed either by the native microbiota or by added microbial inocula. The main aim of this study was to apply two fingerprinting methods, temperature gradient gel electrophoresis (TGGE) and length heterogeneity-PCR (LH-PCR) analysis of 16S rRNA gene fragments, in order to assess the microbiota structure and dynamics during mixed olive oil and winery wastewaters aerobic biotreatment performed in a jet-loop reactor (JLR). Sequence homology analysis showed the presence of bacterial genera Gluconacetobacter, Klebsiella, Lactobacillus, Novosphingobium, Pseudomonas, Prevotella, Ralstonia, Sphingobium and Sphingomonas affiliated with five main phylogenetic groups: alpha-, beta- and gamma-Proteobacteria, Firmicutes and Bacteroidetes. LH-PCR analysis distinguished eight predominant DNA fragments correlated with the samples showing highest performance (COD removal rates of 67 up to 75%). Cluster analysis of both TGGE and LH-PCR fingerprinting profiles established five main clusters, with similarity coefficients higher than 79% (TGGE) and 62% (LH-PCR), and related with hydraulic retention time, indicating that this was the main factor responsible for the shifts in the microbiota structure. Canonical correspondence analysis revealed that changes observed on temperature and O(2) level were also responsible for shifts in microbiota composition. Community level metabolic profile analysis was used to test metabolic activities in samples. Integrated data revealed that the microbiota structure corresponds to bacterial groups with high degradative potential and good suitability for this type of effluents biotreatments.}, } @article {pmid21058662, year = {2010}, author = {Callister, SJ and Wilkins, MJ and Nicora, CD and Williams, KH and Banfield, JF and VerBerkmoes, NC and Hettich, RL and N'Guessan, L and Mouser, PJ and Elifantz, H and Smith, RD and Lovley, DR and Lipton, MS and Long, PE}, title = {Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles.}, journal = {Environmental science & technology}, volume = {44}, number = {23}, pages = {8897-8903}, doi = {10.1021/es101029f}, pmid = {21058662}, issn = {1520-5851}, mesh = {Bacteria/classification/genetics/*metabolism ; Biodiversity ; Biomass ; Fresh Water/*microbiology ; Plankton/classification/genetics/*metabolism ; Proteome/*metabolism ; Water Microbiology ; }, abstract = {Stimulated by an acetate-amendment field experiment conducted in 2007, anaerobic microbial populations in the aquifer at the Rifle Integrated Field Research Challenge site in Colorado reduced mobile U(VI) to insoluble U(IV). During this experiment, planktonic biomass was sampled at various time points to quantitatively evaluate proteomes. In 2008, an acetate-amended field experiment was again conducted in a similar manner to the 2007 experiment. As there was no comprehensive metagenome sequence available for use in proteomics analysis, we systematically evaluated 12 different organism genome sequences to generate sets of aggregate genomes, or "pseudo-metagenomes", for supplying relative quantitative peptide and protein identifications. Proteomics results support previous observations of the dominance of Geobacteraceae during biostimulation using acetate as sole electron donor, and revealed a shift from an early stage of iron reduction to a late stage of iron reduction. Additionally, a shift from iron reduction to sulfate reduction was indicated by changes in the contribution of proteome information contributed by different organism genome sequences within the aggregate set. In addition, the comparison of proteome measurements made between the 2007 field experiment and 2008 field experiment revealed differences in proteome profiles. These differences may be the result of alterations in abundance and population structure within the planktonic biomass samples collected for analysis.}, } @article {pmid21058507, year = {2010}, author = {Math, RK and Islam, SM and Hong, SJ and Cho, KM and Kim, JM and Yun, MG and Cho, JJ and Kim, EJ and Lee, YH and Yun, HD}, title = {Metagenomic characterization of oyster shell dump reveals predominance of Firmicutes bacteria.}, journal = {Mikrobiologiia}, volume = {79}, number = {4}, pages = {532-542}, pmid = {21058507}, issn = {0026-3656}, mesh = {Animals ; Biodegradation, Environmental ; Gram-Positive Bacteria/classification/genetics/*isolation & purification ; *Metagenome ; Ostreidae/anatomy & histology/*microbiology ; Phylogeny ; Republic of Korea ; *Waste Products ; }, abstract = {Metagenomic analyses were conducted to evaluate the biodiversity of oyster shell bacteria, under storage conditions, on the basis of 16s rDNA sequences. Temperature was recorded during a one year storage period, and the highest temperature (about 60 degrees C) was observed after five months ofstorage. Bacterial diversity was greatest in the initial stage sample, with 33 different phylotypes classified under seven phyla (Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Planctomycetes, Verrucomicrobia and unclassified bacteria), with 42.22% ofphylotypes belonging to Proteobacteria. The lowest diversity was found in the high temperature (fermentation) stage sample, with 10 different phylotypes belonging to Firmicutes (78.57%) and Bacteroidetes. In the final stage sample, bacteria were found belonging to Proteobacteria, Bacteroidetes, and Firmicutes, and some were unclassified bacteria. Of the bacteria constituting the final stage metagenome, 69.70% belonged to Firmicutes. Our results show that bacteria belonging to phylum Firmicutes were predominant during fermentation, and during the final stages of oyster shell storage, which suggests that these bacteria supposed to be the key players for oyster shell biodegradation.}, } @article {pmid21057783, year = {2011}, author = {Kanokratana, P and Uengwetwanit, T and Rattanachomsri, U and Bunterngsook, B and Nimchua, T and Tangphatsornruang, S and Plengvidhya, V and Champreda, V and Eurwilaichitr, L}, title = {Insights into the phylogeny and metabolic potential of a primary tropical peat swamp forest microbial community by metagenomic analysis.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {518-528}, pmid = {21057783}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/metabolism ; Biodegradation, Environmental ; Biodiversity ; Biomass ; DNA, Bacterial/genetics ; Gene Library ; *Metabolome ; Metagenome ; *Metagenomics ; Molecular Sequence Annotation ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Thailand ; *Wetlands ; }, abstract = {A primary tropical peat swamp forest is a unique ecosystem characterized by long-term accumulation of plant biomass under high humidity and acidic water-logged conditions, and is regarded as an important terrestrial carbon sink in the biosphere. In this study, the microbial community in the surface peat layer in Pru Toh Daeng, a primary tropical peat swamp forest, was studied for its phylogenetic diversity and metabolic potential using direct shotgun pyrosequencing of environmental DNA, together with analysis of 16S rRNA gene library and key metabolic genes. The community was dominated by aerobic microbes together with a significant number of facultative and anaerobic microbial taxa. Acidobacteria and diverse Proteobacteria (mainly Alphaproteobacteria) constituted the major phylogenetic groups, with minor representation of archaea and eukaryotic microbes. Based on comparative pyrosequencing dataset analysis, the microbial community showed high metabolic versatility of plant polysaccharide decomposition. A variety of glycosyl hydrolases targeting lignocellulosic and starch-based polysaccharides from diverse bacterial phyla were annotated, originating mostly from Proteobacteria, and Acidobacteria together with Firmicutes, Bacteroidetes, Chlamydiae/Verrucomicrobia, and Actinobacteria, suggesting the key role of these microbes in plant biomass degradation. Pyrosequencing dataset annotation and direct mcrA gene analysis indicated the presence of methanogenic archaea clustering in the order Methanomicrobiales, suggesting the potential on partial carbon flux from biomass degradation through methanogenesis. The insights on the peat swamp microbial assemblage thus provide a valuable approach for further study on biogeochemical processes in this unique ecosystem.}, } @article {pmid21057016, year = {2011}, author = {Lin, W and Jogler, C and Schüler, D and Pan, Y}, title = {Metagenomic analysis reveals unexpected subgenomic diversity of magnetotactic bacteria within the phylum Nitrospirae.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {1}, pages = {323-326}, pmid = {21057016}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; China ; DNA, Bacterial/chemistry/genetics ; Fresh Water/*microbiology ; Gene Order ; In Situ Hybridization, Fluorescence ; *Metagenome ; Molecular Sequence Data ; Sequence Analysis, DNA ; }, abstract = {A targeted metagenomic approach was applied to investigate magnetotactic bacteria (MTB) within the phylum Nitrospirae in Lake Miyun near Beijing, China. Five fosmids containing rRNA operons were identified. Comparative sequence analysis of a total of 172 kb provided new insights into their genome organization and revealed unexpected subgenomic diversity of uncultivated MTB in the phylum Nitrospirae. In addition, affiliation of two novel MTB with the phylum Nitrospirae was verified by fluorescence in situ hybridization. One of them was morphologically similar to "Candidatus Magnetobacterium bavaricum," but the other differed substantially in cell shape and magnetosome organization from all previously described "Ca. Magnetobacterium bavaricum"-like bacteria.}, } @article {pmid21050115, year = {2010}, author = {Manges, AR and Labbe, A and Loo, VG and Atherton, JK and Behr, MA and Masson, L and Tellis, PA and Brousseau, R}, title = {Comparative metagenomic study of alterations to the intestinal microbiota and risk of nosocomial Clostridum difficile-associated disease.}, journal = {The Journal of infectious diseases}, volume = {202}, number = {12}, pages = {1877-1884}, doi = {10.1086/657319}, pmid = {21050115}, issn = {1537-6613}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Aged ; Anti-Bacterial Agents/adverse effects/therapeutic use ; Anti-Inflammatory Agents/adverse effects/therapeutic use ; Bacteria/classification/genetics ; Biodiversity ; Case-Control Studies ; Clostridioides difficile/*pathogenicity ; *Clostridium Infections ; DNA, Ribosomal/chemistry/genetics ; Feces/microbiology ; Female ; Hospitalization ; Humans ; Male ; *Metagenome ; Microarray Analysis ; Middle Aged ; Quebec ; RNA, Ribosomal, 16S/genetics ; *Risk Assessment ; }, abstract = {This study investigated the relationship between hospital exposures, intestinal microbiota, and subsequent risk of Clostridium difficile-associated disease (CDAD), with use of a nested case-control design. The study included 599 patients, hospitalized from September 2006 through May 2007 in Montreal, Quebec, from whom fecal samples were obtained within 72 h after admission; 25 developed CDAD, and 50 matched controls were selected for analysis. Nonsteroidal anti-inflammatory drugs and antibiotic use were associated with CDAD. Fecal specimens were evaluated by 16S ribosomal RNA microarray to characterize bacteria in the intestinal microbiota during the at-risk period. Probe intensities were higher for Firmicutes, Proteobacteria, and Actinobacteria in the patients with CDAD, compared with controls, whereas probe intensities for Bacteroidetes were lower. After epidemiologic factors were controlled for, only Bacteroidetes and Firmicutes remained significantly and independently associated with development of CDAD. Hospital exposures were associated with changes in the intestinal microbiota and risk of CDAD, and these changes were not driven exclusively by antimicrobial use.}, } @article {pmid21048761, year = {2010}, author = {Yooseph, S and Nealson, KH and Rusch, DB and McCrow, JP and Dupont, CL and Kim, M and Johnson, J and Montgomery, R and Ferriera, S and Beeson, K and Williamson, SJ and Tovchigrechko, A and Allen, AE and Zeigler, LA and Sutton, G and Eisenstadt, E and Rogers, YH and Friedman, R and Frazier, M and Venter, JC}, title = {Genomic and functional adaptation in surface ocean planktonic prokaryotes.}, journal = {Nature}, volume = {468}, number = {7320}, pages = {60-66}, pmid = {21048761}, issn = {1476-4687}, mesh = {Aquatic Organisms/classification/*genetics/isolation & purification/virology ; Biodiversity ; Biomass ; Databases, Protein ; Genome, Bacterial/genetics ; *Genomics ; *Metagenome ; Models, Biological ; Oceans and Seas ; Phylogeny ; Plankton/*genetics/growth & development/isolation & purification/metabolism ; Prokaryotic Cells/classification/*metabolism/virology ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; }, abstract = {The understanding of marine microbial ecology and metabolism has been hampered by the paucity of sequenced reference genomes. To this end, we report the sequencing of 137 diverse marine isolates collected from around the world. We analysed these sequences, along with previously published marine prokaryotic genomes, in the context of marine metagenomic data, to gain insights into the ecology of the surface ocean prokaryotic picoplankton (0.1-3.0 μm size range). The results suggest that the sequenced genomes define two microbial groups: one composed of only a few taxa that are nearly always abundant in picoplanktonic communities, and the other consisting of many microbial taxa that are rarely abundant. The genomic content of the second group suggests that these microbes are capable of slow growth and survival in energy-limited environments, and rapid growth in energy-rich environments. By contrast, the abundant and cosmopolitan picoplanktonic prokaryotes for which there is genomic representation have smaller genomes, are probably capable of only slow growth and seem to be relatively unable to sense or rapidly acclimate to energy-rich conditions. Their genomic features also lead us to propose that one method used to avoid predation by viruses and/or bacterivores is by means of slow growth and the maintenance of low biomass.}, } @article {pmid21047533, year = {2011}, author = {Kim, M and Morrison, M and Yu, Z}, title = {Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes.}, journal = {Journal of microbiological methods}, volume = {84}, number = {1}, pages = {81-87}, doi = {10.1016/j.mimet.2010.10.020}, pmid = {21047533}, issn = {1872-8359}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biodiversity ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Genes, rRNA ; *Metagenome ; Metagenomics/*methods ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Operational taxonomic units (OTUs) are conventionally defined at a phylogenetic distance (0.03--species, 0.05--genus, 0.10--family) based on full-length 16S rRNA gene sequences. However, partial sequences (700 bp or shorter) have been used in most studies. This discord may affect analysis of diversity and species richness because sequence divergence is not distributed evenly along the 16S rRNA gene. In this study, we compared a set each of bacterial and archaeal 16S rRNA gene sequences of nearly full length with multiple sets of different partial 16S rRNA gene sequences derived therefrom (approximately 440-700 bp), at conventional and alternative distance levels. Our objective was to identify partial sequence region(s) and distance level(s) that allow more accurate phylogenetic analysis of partial 16S rRNA genes. Our results showed that no partial sequence region could estimate OTU richness or define OTUs as reliably as nearly full-length genes. However, the V1-V4 regions can provide more accurate estimates than others. For analysis of archaea, we recommend the V1-V3 and the V4-V7 regions and clustering of species-level OTUs at 0.03 and 0.02 distances, respectively. For analysis of bacteria, the V1-V3 and the V1-V4 regions should be targeted, with species-level OTUs being clustered at 0.04 distance in both cases.}, } @article {pmid21046336, year = {2010}, author = {Jung, SW and Park, JS and Kown, OY and Kang, JH and Shim, WJ and Kim, YO}, title = {Effects of crude oil on marine microbial communities in short term outdoor microcosms.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {48}, number = {5}, pages = {594-600}, pmid = {21046336}, issn = {1976-3794}, mesh = {Animals ; Bacteria/drug effects/growth & development ; *Biodiversity ; Copepoda/drug effects/growth & development ; DNA Fingerprinting ; Electrophoresis, Polyacrylamide Gel ; *Metagenome ; Microalgae/drug effects/growth & development ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Petroleum/*metabolism ; Seawater/*microbiology/*parasitology ; Sequence Analysis, DNA ; Water Pollutants, Chemical/*metabolism ; }, abstract = {To assess the effects of crude oil spills on marine microbial communities, 10 L outdoor microcosms were manipulated over an exposure period of 8 days. The responses of microbial organisms exposed to five crude oil concentrations in 10 to 10,000 ppm (v/v) were monitored in the microcosms. The abundance of microalgae and copepods decreased rapidly upon the addition of crude oil at concentrations over 1,000 ppm, whereas the total density of heterotrophic bacteria increased dramatically at the higher concentrations. Bacterial diversity, determined by denaturing gradient gel electrophoresis, was increased at higher concentrations. In particular, the intensity of the bands representing Jannaschia sp. and Sulfitobacter brevis increased with the addition of oil. These results indicate that crude oil spills with concentrations over 1,000 ppm seriously affected the structure of the microbial communities.}, } @article {pmid21046333, year = {2010}, author = {Kim, YT and Cho, M and Jeong, JY and Lee, HB and Kim, SB}, title = {Application of terminal restriction fragment length polymorphism (T-RFLP) analysis to monitor effect of biocontrol agents on rhizosphere microbial community of hot pepper (Capsicum annuum L.).}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {48}, number = {5}, pages = {566-572}, pmid = {21046333}, issn = {1976-3794}, mesh = {Biodiversity ; Capsicum/*microbiology ; DNA Fingerprinting ; *Metagenome ; Pest Control, Biological/*methods ; Plant Leaves/microbiology ; Plant Roots/*microbiology ; Polymorphism, Restriction Fragment Length ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Microbial communities in hot pepper (Capsicum annuum L.) cultivation fields under different cultivation methods were investigated by terminal restriction fragment length polymorphism (T-RFLP) analysis. Rhizosphere soil and leaf samples were collected from control, conventional and nature-friendly cultivation fields between May and July, 2009. Two Bacillus subtilis strains were applied to nature-friendly cultivation fields as biocontrol agents during the sampling period. Relative abundances of bacteria and plant pathogenic fungi related T-RFs were also measured to monitor the effect of biocontrol agents on potential plant pathogenic fungi. In the principal component analysis (PCA) based on T-RFLP profiles, the microbial communities from rhizosphere soil samples in July, including bacteria and fungi, showed distinct difference between nature-friendly cultivation fields and other cultivation fields. However, there was no correlation between cultivation methods and leaf microbial communities at any sampling period. Changes in the abundance of bacteria related T-RF in the rhizosphere of nature-friendly cultivation fields were observed clearly two months after application of biocontrol agent, while the abundance of plant pathogenic fungi related T-RFs significantly decreased.}, } @article {pmid21044097, year = {2010}, author = {Kong, Y and Teather, R and Forster, R}, title = {Composition, spatial distribution, and diversity of the bacterial communities in the rumen of cows fed different forages.}, journal = {FEMS microbiology ecology}, volume = {74}, number = {3}, pages = {612-622}, doi = {10.1111/j.1574-6941.2010.00977.x}, pmid = {21044097}, issn = {1574-6941}, mesh = {Animal Feed ; Animals ; Bacteria/classification/*genetics ; *Biodiversity ; Cattle/*microbiology ; DNA, Bacterial/genetics ; Diet ; Medicago sativa ; Phylogeny ; Poaceae ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The species composition, distribution, and biodiversity of the bacterial communities in the rumen of cows fed alfalfa or triticale were investigated using 16S rRNA gene clone library analyses. The rumen bacterial community was fractionated and analyzed as three separate fractions: populations in the planktonic, loosely attached to rumen digesta particles, and tightly attached to rumen digesta particles. Six hundred and thirteen operational taxonomic units (OTUs) belonging to 32 genera, 19 families, and nine phyla of the domain Bacteria were identified from 1014 sequenced clones. Four hundred and fifty one of the 613 OTUs were identified as new species. These bacterial sequences were distributed differently among the three fractions in the rumen digesta of cows fed alfalfa or triticale. Chao 1 estimation revealed that, in both communities, the populations tightly attached to particulates were more diverse than the planktonic and those loosely attached to particulates. S-Libshuff detected significant differences in the composition between any two fractions in the rumen of cows with the same diet and between the communities fed alfalfa and triticale diets. The species richness estimated for the communities fed alfalfa and triticale is 1027 and 662, respectively. The diversity of the rumen bacterial community examined in this study is greater than previous studies have demonstrated and the differences in the community composition between two high-fiber diets have implications for sample selection for downstream metagenomics applications.}, } @article {pmid21039665, year = {2010}, author = {Alcántara-Hernández, RJ and Rodríguez-Álvarez, JA and Valenzuela-Encinas, C and Gutiérrez-Miceli, FA and Castañón-González, H and Marsch, R and Ayora-Talavera, T and Dendooven, L}, title = {The bacterial community in 'taberna' a traditional beverage of Southern Mexico.}, journal = {Letters in applied microbiology}, volume = {51}, number = {5}, pages = {558-563}, doi = {10.1111/j.1472-765X.2010.02934.x}, pmid = {21039665}, issn = {1472-765X}, mesh = {Arecaceae/*microbiology ; Bacteria/classification/genetics/*isolation & purification ; Beverages/*microbiology ; *Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Fermentation ; Mexico ; Molecular Sequence Data ; Phylogeny ; }, abstract = {AIMS: To characterize the bacterial community of taberna, an alcoholic traditional beverage from the Southern part of Mexico produced by the fermentation of the coyol palm sap (Acrocomia aculeate).

METHODS AND RESULTS: Bacterial 16S rDNA libraries were constructed from metagenomic DNA extracted during the fermentation process at 0, 60 and 108 h. A total of 154 clones were sequenced, and 13, 10 and nine unique sequences were found at each sampling time. At the onset of the fermentation, Zymomonas mobilis, Fructobacillus spp., Pantoea agglomerans and other Gammaproteobacteria were detected. After 60 h, lactic acid bacteria were found and 30% of clones in the library were related to Lactobacillus nagelii, L. sucicola and L. sp. By the end of the experiment, i.e. after 108 h, the bacterial community included Z. mobilis, Lact. nagelii and Acetobacter pasteurianus.

CONCLUSIONS: Our results suggest that Z. mobilis population represented an important proportion of the bacterial community (60-80%), as well as the lactobacilli during the fermentation process. The bacterial diversity was low and decreased as the fermentation progressed.

This culture-independent study suggests that Z. mobilis and lactobacilli play an important role in the alcoholic fermentation of the taberna beverage.}, } @article {pmid21039646, year = {2011}, author = {Knights, D and Costello, EK and Knight, R}, title = {Supervised classification of human microbiota.}, journal = {FEMS microbiology reviews}, volume = {35}, number = {2}, pages = {343-359}, doi = {10.1111/j.1574-6976.2010.00251.x}, pmid = {21039646}, issn = {1574-6976}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Bacteria/*classification/*genetics/isolation & purification ; Biodiversity ; Humans ; *Metagenome ; *Phylogeny ; }, abstract = {Recent advances in DNA sequencing technology have allowed the collection of high-dimensional data from human-associated microbial communities on an unprecedented scale. A major goal of these studies is the identification of important groups of microorganisms that vary according to physiological or disease states in the host, but the incidence of rare taxa and the large numbers of taxa observed make that goal difficult to obtain using traditional approaches. Fortunately, similar problems have been addressed by the machine learning community in other fields of study such as microarray analysis and text classification. In this review, we demonstrate that several existing supervised classifiers can be applied effectively to microbiota classification, both for selecting subsets of taxa that are highly discriminative of the type of community, and for building models that can accurately classify unlabeled data. To encourage the development of new approaches to supervised classification of microbiota, we discuss several structures inherent in microbial community data that may be available for exploitation in novel approaches, and we include as supplemental information several benchmark classification tasks for use by the community.}, } @article {pmid20971877, year = {2010}, author = {Chaucheyras-Durand, F and Masséglia, S and Fonty, G and Forano, E}, title = {Influence of the composition of the cellulolytic flora on the development of hydrogenotrophic microorganisms, hydrogen utilization, and methane production in the rumens of gnotobiotically reared lambs.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {24}, pages = {7931-7937}, pmid = {20971877}, issn = {1098-5336}, mesh = {Animals ; *Biodiversity ; Cellulose/*metabolism ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fibrobacter/growth & development/metabolism ; Fungi/growth & development/metabolism ; Germ-Free Life ; Hydrogen/*metabolism ; *Metagenome ; Methane/*metabolism ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Ruminococcus/growth & development/metabolism ; Sequence Analysis, DNA ; Sheep ; }, abstract = {We investigated the influence of the composition of the fibrolytic microbial community on the development and activities of hydrogen-utilizing microorganisms in the rumens of gnotobiotically reared lambs. Two groups of lambs were reared. The first group was inoculated with Fibrobacter succinogenes, a non-H(2)-producing species, as the main cellulolytic organism, and the second group was inoculated with Ruminococcus albus, Ruminococcus flavefaciens, and anaerobic fungi that produce hydrogen. The development of hydrogenotrophic bacterial communities, i.e., acetogens, fumarate and sulfate reducers, was monitored in the absence of methanogens and after inoculation of methanogens. Hydrogen production and utilization and methane production were measured in rumen content samples incubated in vitro in the presence of exogenous hydrogen (supplemented with fumarate or not supplemented with fumarate) or in the presence of ground alfalfa hay as a degradable substrate. Our results show that methane production was clearly reduced when the dominant fibrolytic species was a non-H(2)-producing species, such as Fibrobacter succinogenes, without significantly impairing fiber degradation and fermentations in the rumen. The addition of fumarate to the rumen contents stimulated H(2) utilization only by the ruminal microbiota inoculated with F. succinogenes, suggesting that these communities could play an important role in fumarate reduction in vivo.}, } @article {pmid20971872, year = {2010}, author = {Ollivier, J and Kleineidam, K and Reichel, R and Thiele-Bruhn, S and Kotzerke, A and Kindler, R and Wilke, BM and Schloter, M}, title = {Effect of sulfadiazine-contaminated pig manure on the abundances of genes and transcripts involved in nitrogen transformation in the root-rhizosphere complexes of maize and clover.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {24}, pages = {7903-7909}, pmid = {20971872}, issn = {1098-5336}, mesh = {Animals ; *Biodiversity ; Denitrification/genetics ; Gene Expression Profiling ; Genes, Archaeal ; Genes, Bacterial ; Manure/*microbiology ; Medicago/*microbiology ; Metabolic Networks and Pathways/*genetics ; Metagenome ; Nitrification/genetics ; Nitrogen Fixation/genetics ; Plant Roots/microbiology ; *Rhizosphere ; Sulfadiazine/*analysis ; Swine ; Time Factors ; Zea mays/*microbiology ; }, abstract = {The antibiotic sulfadiazine (SDZ) can enter the environment by application of manure from antibiotic-treated animals to arable soil. Because antibiotics are explicitly designed to target microorganisms, they likely affect microbes in the soil ecosystem, compromising important soil functions and disturbing processes in nutrient cycles. In a greenhouse experiment, we investigated the impact of sulfadiazine-contaminated pig manure on functional microbial communities involved in key processes of the nitrogen cycle in the root-rhizosphere complexes (RRCs) of maize (Zea mays) and clover (Trifolium alexandrinum). At both the gene and transcript level, we performed real-time PCR using nifH, amoA (in both ammonia-oxidizing bacteria and archaea), nirK, nirS, and nosZ as molecular markers for nitrogen fixation, nitrification, and denitrification. Sampling was performed 10, 20, and 30 days after the application. SDZ affected the abundance pattern of all investigated genes in the RRCs of both plant species (with stronger effects in the RRC of clover) 20 and 30 days after the addition. Surprisingly, effects on the transcript level were less pronounced, which might indicate that parts of the investigated functional groups were tolerant or resistant against SDZ or, as in the case of nifH and clover, have been protected by the nodules.}, } @article {pmid20962877, year = {2011}, author = {Zhou, HW and Li, DF and Tam, NF and Jiang, XT and Zhang, H and Sheng, HF and Qin, J and Liu, X and Zou, F}, title = {BIPES, a cost-effective high-throughput method for assessing microbial diversity.}, journal = {The ISME journal}, volume = {5}, number = {4}, pages = {741-749}, pmid = {20962877}, issn = {1751-7370}, mesh = {Biodiversity ; DNA Barcoding, Taxonomic/economics/*methods ; DNA Primers ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing/economics/*methods ; Metagenome ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Pyrosequencing of 16S rRNA (16S) variable tags has become the most popular method for assessing microbial diversity, but the method remains costly for the evaluation of large numbers of environmental samples with high sequencing depths. We developed a barcoded Illumina paired-end (PE) sequencing (BIPES) method that sequences each 16S V6 tag from both ends on the Illumina HiSeq 2000, and the PE reads are then overlapped to obtain the V6 tag. The average accuracy of Illumina single-end (SE) reads was only 97.9%, which decreased from ∼99.9% at the start of the read to less than 85% at the end of the read; nevertheless, overlapping of the PE reads significantly increased the sequencing accuracy to 99.65% by verifying the 3' end of each SE in which the sequencing quality was degraded. After the removal of tags with two or more mismatches within the medial 40-70 bases of the reads and of tags with any primer errors, the overall base sequencing accuracy of the BIPES reads was further increased to 99.93%. The BIPES reads reflected the amounts of the various tags in the initial template, but long tags and high GC tags were underestimated. The BIPES method yields 20-50 times more 16S V6 tags than does pyrosequencing in a single-flow cell run, and each of the BIPES reads costs less than 1/40 of a pyrosequencing read. As a laborsaving and cost-effective method, BIPES can be routinely used to analyze the microbial ecology of both environmental and human microbiomes.}, } @article {pmid20961641, year = {2010}, author = {Joseph, SJ and Read, TD}, title = {Bacterial population genomics and infectious disease diagnostics.}, journal = {Trends in biotechnology}, volume = {28}, number = {12}, pages = {611-618}, doi = {10.1016/j.tibtech.2010.09.001}, pmid = {20961641}, issn = {1879-3096}, mesh = {Bacteria/*classification/*genetics/isolation & purification ; Bacterial Infections/*diagnosis ; Bacteriological Techniques/*methods ; Biodiversity ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Molecular Diagnostic Techniques/*methods ; }, abstract = {New sequencing technologies have made the production of bacterial genome sequences increasingly easy, and it can be confidently forecasted that vast genomic databases will be generated in the next few years. Here, we detail how collections of bacterial genomes from a particular species (population genomics libraries) have already been used to improve the design of several diagnostic assays for bacterial pathogens. Genome sequencing itself is also becoming more commonly used for epidemiological, forensic and clinical investigations. There is an opportunity for the further development of bioinformatic tools to bring even further value to bacterial diagnostic genomics.}, } @article {pmid20961563, year = {2011}, author = {Jacquot, A and Neveu, D and Aujoulat, F and Mercier, G and Marchandin, H and Jumas-Bilak, E and Picaud, JC}, title = {Dynamics and clinical evolution of bacterial gut microflora in extremely premature patients.}, journal = {The Journal of pediatrics}, volume = {158}, number = {3}, pages = {390-396}, doi = {10.1016/j.jpeds.2010.09.007}, pmid = {20961563}, issn = {1097-6833}, mesh = {Bacteria/*growth & development ; *Biodiversity ; DNA Fingerprinting ; Digestion ; Feces/microbiology ; Humans ; *Infant, Extremely Low Birth Weight ; Infant, Newborn ; *Infant, Premature ; Intestines/*microbiology ; *Metagenome ; Prospective Studies ; }, abstract = {OBJECTIVE: To determine baseline clinical characteristics that influence bacterial gut flora dynamics in very preterm infants and the relationship between gut flora dynamics and clinical evolution.

STUDY DESIGN: Prospective, monocentric study enrolling 29 consecutive very preterm infants. We collected data about growth, digestive tolerance, nutrition, and antibiotic use. Microflora in stool samples, collected between 3 and 56 days of life, was identified with direct molecular fingerprinting.

RESULTS: Median (interquartile range) body weight and gestational age at birth were 950 g (760-1060 g) and 27 weeks (27-29 weeks), respectively. The diversity score (number of operational taxonomic units) increased 0.45 units/week (P < .0001), with staphylococci as the major group. Bifidobacterium was poorly represented. Gestational age (≥ 28 weeks) and caesarean delivery independently correlated with better diversity scores during follow-up (P < .05). The 6-week diversity score inversely correlated with the duration of antibiotherapy (P = .0184) and parenteral feeding (P = .013). The microflora dynamics was associated with the digestive tolerance profile. Weight gain increased with increasing diversity score (P = .0428).

CONCLUSION: Microflora diversity settled progressively in very preterm infants. Staphylococci were the major group, and few infants were colonized with Bifidobacterium spp. Measures that may improve microflora could have beneficial effects on digestive tolerance and growth.}, } @article {pmid20953417, year = {2010}, author = {Heidelberg, KB and Gilbert, JA and Joint, I}, title = {Marine genomics: at the interface of marine microbial ecology and biodiscovery.}, journal = {Microbial biotechnology}, volume = {3}, number = {5}, pages = {531-543}, pmid = {20953417}, issn = {1751-7915}, mesh = {Aquatic Organisms/classification/*genetics/*isolation & purification/metabolism ; *Biodiversity ; Biotechnology/trends ; *Genomics/history ; History, 20th Century ; History, 21st Century ; *Marine Biology/history ; Seawater/microbiology/virology ; }, abstract = {The composition and activities of microbes from diverse habitats have been the focus of intense research during the past decade with this research being spurred on largely by advances in molecular biology and genomic technologies. In recent years environmental microbiology has entered very firmly into the age of the 'omics' – (meta)genomics, proteomics, metabolomics, transcriptomics – with probably others on the rise. Microbes are essential participants in all biogeochemical processes on our planet, and the practical applications of what we are learning from the use of molecular approaches has altered how we view biological systems. In addition, there is considerable potential to use information about uncultured microbes in biodiscovery research as microbes provide a rich source of discovery for novel genes, enzymes and metabolic pathways. This review explores the brief history of genomic and metagenomic approaches to study environmental microbial assemblages and describes some of the future challenges involved in broadening our approaches – leading to new insights for understanding environmental problems and enabling biodiscovery research.}, } @article {pmid20950425, year = {2010}, author = {Fernàndez-Guerra, A and Buchan, A and Mou, X and Casamayor, EO and González, JM}, title = {T-RFPred: a nucleotide sequence size prediction tool for microbial community description based on terminal-restriction fragment length polymorphism chromatograms.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {262}, pmid = {20950425}, issn = {1471-2180}, mesh = {Amplified Fragment Length Polymorphism Analysis/*methods ; Bacteria/*classification/genetics ; Computational Biology/*methods ; DNA Fingerprinting/*methods ; DNA, Bacterial/analysis ; Gene Library ; Phylogeny ; Polymerase Chain Reaction ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S ; Restriction Mapping/*methods ; Seawater/*microbiology ; Sequence Analysis, RNA ; Software ; Water Microbiology ; }, abstract = {BACKGROUND: Terminal-Restriction Fragment Length Polymorphism (T-RFLP) is a technique used to analyze complex microbial communities. It allows for the quantification of unique or numerically dominant phylotypes in amplicon pools and it has been used primarily for comparisons between different communities. T-RFPred, Terminal-Restriction Fragment Prediction, was developed to identify and assign taxonomic information to chromatogram peaks of a T-RFLP fingerprint for a more comprehensive description of microbial communities. The program estimates the expected fragment size of representative 16S rRNA gene sequences (either from a complementary clone library or from public databases) for a given primer and restriction enzyme(s) and provides candidate taxonomic assignments.

RESULTS: To show the accuracy of the program, T-RFLP profiles of a marine bacterial community were described using artificial bacterioplankton clone libraries of sequences obtained from public databases. For all valid chromatogram peaks, a phylogenetic group could be assigned.

CONCLUSIONS: T-RFPred offers enhanced functionality of T-RFLP profile analysis over current available programs. In particular, it circumvents the need for full-length 16S rRNA gene sequences during taxonomic assignments of T-RF peaks. Thus, large 16S rRNA gene datasets from environmental studies, including metagenomes, or public databases can be used as the reference set. Furthermore, T-RFPred is useful in experimental design for the selection of primers as well as the type and number of restriction enzymes that will yield informative chromatograms from natural microbial communities.}, } @article {pmid20940022, year = {2011}, author = {Gantner, S and Andersson, AF and Alonso-Sáez, L and Bertilsson, S}, title = {Novel primers for 16S rRNA-based archaeal community analyses in environmental samples.}, journal = {Journal of microbiological methods}, volume = {84}, number = {1}, pages = {12-18}, doi = {10.1016/j.mimet.2010.10.001}, pmid = {20940022}, issn = {1872-8359}, mesh = {Archaea/*classification/*genetics ; *Biodiversity ; Computational Biology ; DNA Primers/*genetics ; DNA, Archaeal/chemistry/genetics ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; Molecular Sequence Data ; Polymerase Chain Reaction/methods ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/*genetics ; Sensitivity and Specificity ; }, abstract = {Next generation sequencing technologies for in depth analyses of complex microbial communities rely on rational primer design based on up-to-date reference databases. Most of the 16S rRNA-gene based analyses of environmental Archaea community composition use PCR primers developed from small data sets several years ago, making an update long overdue. Here we present a new set of archaeal primers targeting the 16S rRNA gene designed from 8500 aligned archaeal sequences in the SILVA database. The primers 340F-1000R showed a high archaeal specificity (<1% bacteria amplification) covering 93 and 97% of available sequences for Crenarchaeota and Euryarchaeota respectively. In silico tests of the primers revealed at least 38% higher coverage for Archaea compared to other commonly used primers. Empirical tests with clone libraries confirmed the high specificity of the primer pair to Archaea in three biomes: surface waters in the Arctic Ocean, the pelagic zone of a temperate lake and a methanogenic bioreactor. The clone libraries featured both Euryarchaeota and Crenarchaeota in variable proportions and revealed dramatic differences in the archaeal community composition and minimal phylogenetic overlap between samples.}, } @article {pmid20934523, year = {2010}, author = {Shen, Q and Chen, YA and Tuohy, KM}, title = {A comparative in vitro investigation into the effects of cooked meats on the human faecal microbiota.}, journal = {Anaerobe}, volume = {16}, number = {6}, pages = {572-577}, doi = {10.1016/j.anaerobe.2010.09.007}, pmid = {20934523}, issn = {1095-8274}, mesh = {Animals ; Bacterial Load ; *Biodiversity ; Cattle ; Chickens ; Feces/*microbiology ; *Feeding Behavior ; Fishes ; Humans ; Meat ; *Metagenome ; }, abstract = {Protein fermentation is one of the important microbial activities in the human colon. Meat foods rich in protein provide substantial resource for this metabolic activity. However, little information exists on the relative impact of different meats on the composition and activities of the human gut microbiota. Similarly, little information is available on the confounding effects of cooking on these activities. In this study, beef, chicken and fish (salmon) were examined in vitro for their impact on the human faecal microbiota. The influence of cooking method was also investigated by using either frying or boiling. Upon fermentation over 48 h the Clostridium perfringens/histolyticum group increased significantly in number in the beef fermentations, either fried (p = 0.023) or boiled (p = 0.017). Cooking method appeared to influence Clostridium spp. growth, with higher numbers in fried meat compared to boiled meats after 5 h (p = 0.024) and 48 h (p = 0.003) fermentation. Significant differences between meat types were also seen for numbers of Bifidobacterium spp. at 48 h (p = 0.028), Bacteroides group at 24 h (p = 0.016) as well as Coriobacterium/Atopobium group at 10 h (p = 0.038). Most types of short chain fatty acids increased significantly in concentration over the experiment (p < 0.05). Significant differences between meat types were found in n-butyric acid production at 24, 30 and 48 h (p = 0.015, p = 0.024 and p = 0.035 respectively) and in i-valeric acid production at 10, 24, 30 and 48 h (p = 0.026, p = 0.002, p = 0.019 and p = 0.022 respectively). The concentration of i-valeric acid differed significantly between cooking methods at 24 h (p = 0.042). These findings suggest that both the type of meat and cooking process can influence fermentation profiles within the human gut microbiota. Interactions between ingested cooked meats and the gut microbiota may represent a novel corollary to mechanisms underlying the observed increased risk of intestinal and systemic diseases associated with high intake of certain meats/processed meats.}, } @article {pmid20931185, year = {2010}, author = {Wang, Y and Antonopoulos, DA and Zhu, X and Harrell, L and Hanan, I and Alverdy, JC and Meyer, F and Musch, MW and Young, VB and Chang, EB}, title = {Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon.}, journal = {Applied microbiology and biotechnology}, volume = {88}, number = {6}, pages = {1333-1342}, pmid = {20931185}, issn = {1432-0614}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; UH3 UH3DK083993/DK/NIDDK NIH HHS/United States ; R21 HG004858/HG/NHGRI NIH HHS/United States ; UH3 DK083993/DK/NIDDK NIH HHS/United States ; R01 GM062344/GM/NIGMS NIH HHS/United States ; R01 5R01GM062344-11/GM/NIGMS NIH HHS/United States ; P30 DK42086/DK/NIDDK NIH HHS/United States ; R21HG004858/HG/NHGRI NIH HHS/United States ; R01 HG004906/HG/NHGRI NIH HHS/United States ; }, mesh = {*Biodiversity ; Cluster Analysis ; Colon/*microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; High-Throughput Nucleotide Sequencing ; Human Experimentation ; Humans ; Intestinal Mucosa/*microbiology ; *Metagenome ; Microdissection/*methods ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Metagenomic analysis of colonic mucosa-associated microbes has been complicated by technical challenges that disrupt or alter community structure and function. In the present study, we determined the feasibility of laser capture microdissection (LCM) of intact regional human colonic mucosa-associated microbes followed by phi29 multiple displacement amplification (MDA) and massively parallel sequencing for metagenomic analysis. Samples were obtained from the healthy human subject without bowel preparation and frozen sections immediately prepared. Regional mucosa-associated microbes were successfully dissected using LCM with minimal contamination by host cells, their DNA extracted and subjected to phi29 MDA with a high fidelity, prior to shotgun sequencing using the GS-FLX DNA sequencer. Metagenomic analysis of approximately 67 million base pairs of DNA sequences from two samples revealed that the metabolic functional profiles in mucosa-associated microbes were as diverse as those reported in feces, specifically the representation of functional genes associated with carbohydrate, protein, and nucleic acid utilization. In summary, these studies demonstrate the feasibility of the approach to study the structure and metagenomic profiles of human intestinal mucosa-associated microbial communities at small spatial scales.}, } @article {pmid20927138, year = {2011}, author = {Xie, W and Wang, F and Guo, L and Chen, Z and Sievert, SM and Meng, J and Huang, G and Li, Y and Yan, Q and Wu, S and Wang, X and Chen, S and He, G and Xiao, X and Xu, A}, title = {Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries.}, journal = {The ISME journal}, volume = {5}, number = {3}, pages = {414-426}, pmid = {20927138}, issn = {1751-7370}, mesh = {Autotrophic Processes/genetics ; Bacteria/classification/*genetics/metabolism ; Biodiversity ; Biofilms ; Carbon/metabolism ; Carbon Cycle/genetics ; Environment ; Gene Library ; Hydrothermal Vents/*chemistry/*microbiology ; Metagenome/*genetics ; *Metagenomics ; Molecular Sequence Data ; Nitrogen/metabolism ; Oceans and Seas ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfur/metabolism ; }, abstract = {Deep-sea hydrothermal vent chimneys harbor a high diversity of largely unknown microorganisms. Although the phylogenetic diversity of these microorganisms has been described previously, the adaptation and metabolic potential of the microbial communities is only beginning to be revealed. A pyrosequencing approach was used to directly obtain sequences from a fosmid library constructed from a black smoker chimney 4143-1 in the Mothra hydrothermal vent field at the Juan de Fuca Ridge. A total of 308,034 reads with an average sequence length of 227 bp were generated. Comparative genomic analyses of metagenomes from a variety of environments by two-way clustering of samples and functional gene categories demonstrated that the 4143-1 metagenome clustered most closely with that from a carbonate chimney from Lost City. Both are highly enriched in genes for mismatch repair and homologous recombination, suggesting that the microbial communities have evolved extensive DNA repair systems to cope with the extreme conditions that have potential deleterious effects on the genomes. As previously reported for the Lost City microbiome, the metagenome of chimney 4143-1 exhibited a high proportion of transposases, implying that horizontal gene transfer may be a common occurrence in the deep-sea vent chimney biosphere. In addition, genes for chemotaxis and flagellar assembly were highly enriched in the chimney metagenomes, reflecting the adaptation of the organisms to the highly dynamic conditions present within the chimney walls. Reconstruction of the metabolic pathways revealed that the microbial community in the wall of chimney 4143-1 was mainly fueled by sulfur oxidation, putatively coupled to nitrate reduction to perform inorganic carbon fixation through the Calvin-Benson-Bassham cycle. On the basis of the genomic organization of the key genes of the carbon fixation and sulfur oxidation pathways contained in the large genomic fragments, both obligate and facultative autotrophs appear to be present and contribute to biomass production.}, } @article {pmid20922382, year = {2011}, author = {Han, I and Congeevaram, S and Ki, DW and Oh, BT and Park, J}, title = {Bacterial community analysis of swine manure treated with autothermal thermophilic aerobic digestion.}, journal = {Applied microbiology and biotechnology}, volume = {89}, number = {3}, pages = {835-842}, doi = {10.1007/s00253-010-2893-8}, pmid = {20922382}, issn = {1432-0614}, mesh = {Aerobiosis ; Animal Husbandry/methods ; Animals ; Bacteria/*classification/*genetics ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Manure/*microbiology ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Swine/*microbiology ; Temperature ; }, abstract = {Due to the environmental problems associated with disposal of livestock sludge, many stabilization studies emphasizing on the sludge volume reduction were performed. However, little is known about the microbial risk present in sludge and its stabilized products. This study microbiologically explored the effects of anaerobic lagoon fermentation (ALF) and autothermal thermophilic aerobic digestion (ATAD) on pathogen-related risk of raw swine manure by using culture-independent 16S rDNA cloning and sequencing methods. In raw swine manure, clones closely related to pathogens such as Dialister pneumosintes, Erysipelothrix rhusiopathiae, Succinivibrioan dextrinosolvens, and Schineria sp. were detected. Meanwhile, in the mesophilic ALF-treated swine manure, bacterial community clones closely related to pathogens such as Schineria sp. and Succinivibrio dextrinosolvens were still detected. Interestingly, the ATAD treatment resulted in no detection of clones closely related to pathogens in the stabilized thermophilic bacterial community, with the predominance of novel Clostridia class populations. These findings support the superiority of ATAD in selectively reducing potential human and animal pathogens compared to ALF, which is a typical manure stabilization method used in livestock farms.}, } @article {pmid20922378, year = {2011}, author = {Sonthiphand, P and Limpiyakorn, T}, title = {Change in ammonia-oxidizing microorganisms in enriched nitrifying activated sludge.}, journal = {Applied microbiology and biotechnology}, volume = {89}, number = {3}, pages = {843-853}, doi = {10.1007/s00253-010-2902-y}, pmid = {20922378}, issn = {1432-0614}, mesh = {Ammonia/*metabolism ; Archaea/*growth & development/metabolism ; Archaeal Proteins/genetics ; Bacteria/*growth & development/metabolism ; *Biodiversity ; Bioreactors/microbiology ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; *Metagenome ; Molecular Sequence Data ; Nitrification ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Sewage/*microbiology ; }, abstract = {In this study, sludge was taken from a municipal wastewater treatment plant that contained a nearly equal number of archaeal amoA genes (5.70 × 10[6] ± 3.30 × 10[5] copies mg sludge[-1]) to bacterial amoA genes (8.60 × 10[6] ± 7.64 × 10[5] copies mg sludge[-1]) and enriched in three continuous-flow reactors receiving an inorganic medium containing different ammonium concentrations: 2, 10, and 30 mM NH (4) (+) -N (28, 140, and 420 mg N l[-1]). The abundance and communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in enriched nitrifying activated sludge (NAS) were monitored at days 60 and 360 of the operation. Early on, between day 0 and day 60 of reactor operation, comparative abundance of AOA amoA genes to AOB amoA genes varied among the reactors depending on the ammonium levels found in the reactors. As compared to the seed sludge, the number of AOA amoA genes was unchanged in the reactor with lower ammonium level (0.06 ± 0.04 mgN l[-1]), while in the reactors with higher ammonium levels (0.51 ± 0.33 and 0.25 ± 0.10 mgN l[-1]), the numbers of AOA amoA genes were deteriorated. By day 360, AOA disappeared from the ammonia-oxidizing consortiums in all reactors. The majority of the AOA sequences from all NASs at each sampling period fell into a single AOA cluster, however, suggesting that the ammonium did not affect the AOA communities under this operational condition. This result is contradictory to the case of AOB, where the communities varied significantly among the NASs. AOB with a high affinity for ammonia were present in the reactors with lower ammonium levels, whereas AOB with a low affinity to ammonia existed in the reactors with higher ammonium levels.}, } @article {pmid20890848, year = {2010}, author = {Kouridaki, I and Polymenakou, PN and Tselepides, A and Mandalakis, M and Smith, KL}, title = {Phylogenetic diversity of sediment bacteria from the deep Northeastern Pacific Ocean: a comparison with the deep Eastern Mediterranean Sea.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {13}, number = {3}, pages = {143-150}, doi = {10.2436/20.1501.01.119}, pmid = {20890848}, issn = {1618-1905}, mesh = {Bacteria/chemistry/*classification/*genetics ; *Biodiversity ; Carbon/analysis ; Chlorophyll/analysis ; Chlorophyll A ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics/isolation & purification ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/*microbiology ; Mediterranean Sea ; *Metagenome ; Molecular Sequence Data ; Nitrogen Compounds/analysis ; Pacific Ocean ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The variability of bacterial community composition and diversity was studied by comparative analysis of five 16S rRNA gene clone libraries from deep-sea sediments (water column depth: 4000 m) of the Northeastern Pacific Ocean and Eastern Mediterranean Sea. This is the first comparison of the bacterial communities living in these deep-sea ecosystems. The estimated chlorophyll a, organic carbon, and C/N ratio provided evidence of significant differences in the trophic state of the sediments between the Northeastern Pacific Ocean and the much warmer Eastern Mediterranean Sea. A diverse range of 16S rRNA gene phylotypes was found in the sediments of both regions. These were represented by 11 different taxonomic groups, with Gammaproteobacteria predominating in the Northeastern Pacific Ocean sediments and Acidobacteria in the Eastern Mediterranean microbial community. In addition, several 16S rRNA gene phylotypes only distantly related to any of the previously identified sequences (non-affiliated rRNA genes) represented a significant fraction of the total sequences. The potential diversity at the two sites differs but remains largely unexplored and remains of continuing scientific interest.}, } @article {pmid20890846, year = {2010}, author = {Martínez-Alonso, M and Escolano, J and Montesinos, E and Gaju, N}, title = {Diversity of the bacterial community in the surface soil of a pear orchard based on 16S rRNA gene analysis.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {13}, number = {3}, pages = {123-134}, doi = {10.2436/20.1501.01.117}, pmid = {20890846}, issn = {1618-1905}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics/isolation & purification ; DNA, Ribosomal/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; *Metagenome ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Spain ; }, abstract = {A cultivation-independent approach based on polymerase chain reaction (PCR)-amplified partial small subunit rRNA genes was used to characterize bacterial populations in the surface soil of a commercial pear orchard consisting of different pear cultivars during two consecutive growing seasons. Pyrus communis L. cvs Blanquilla, Conference, and Williams are among the most widely cultivated cultivars in Europe and account for the majority of pear production in Northeastern Spain. To assess the heterogeneity of the community structure in response to environmental variables and tree phenology, bacterial populations were examined using PCR-denaturing gradient gel electrophoresis (DGGE) followed by cluster analysis of the 16S ribosomal DNA profiles by means of the unweighted pair group method with arithmetic means. Similarity analysis of the band patterns failed to identify characteristic fingerprints associated with the pear cultivars. Both environmentally and biologically based principal-component analyses showed that the microbial communities changed significantly throughout the year depending on temperature and, to a lesser extent, on tree phenology and rainfall. Prominent DGGE bands were excised and sequenced to gain insight into the identities of the predominant bacterial populations. Most DGGE band sequences were related to bacterial phyla, such as Bacteroidetes, Cyanobacteria, Acidobacteria, Proteobacteria, Nitrospirae, and Gemmatimonadetes, previously associated with typical agronomic crop environments.}, } @article {pmid20890842, year = {2010}, author = {de Los Ríos, A and Valea, S and Ascaso, C and Davila, A and Kastovsky, J and McKay, CP and Gómez-Silva, B and Wierzchos, J}, title = {Comparative analysis of the microbial communities inhabiting halite evaporites of the Atacama Desert.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {13}, number = {2}, pages = {79-89}, doi = {10.2436/20.1501.01.113}, pmid = {20890842}, issn = {1618-1905}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; *Biodiversity ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Desert Climate ; Electrophoresis, Polyacrylamide Gel ; Genes, rRNA ; *Metagenome ; Microscopy ; Nucleic Acid Denaturation ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; *Soil Microbiology ; }, abstract = {Molecular biology and microscopy techniques were used to characterize the microbial communities inside halite evaporites from different parts of the Atacama Desert. Denaturing gradient gel electrophoresis (DGGE) analysis revealed that the evaporite rocks harbor communities predominantly made up of cyanobacteria, along with heterotrophic bacteria and archaea. Different DGGE profiles were obtained for the different sites, with the exception of the cyanobacterial profile, in which only one phylotype was detected across the three sites examined. Chroococcidiopsis-like cells were the only cyanobacterial components of the rock samples, although the phylogenetic study revealed their closer genetic affinity to Halothece genera. Gene sequences of the heterotrophic bacteria and archaea indicated their proximity to microorganisms found in other hypersaline environments. Microorganisms colonizing these halites formed microbial aggregates in the pore spaces between halite crystals, where microbial interactions occur. In this exceptional, salty, porous halite rock habitat, microbial consortia with a community structure probably conditioned by the environmental conditions occupy special microhabitats with physical and chemical properties that promote their survival.}, } @article {pmid20890841, year = {2010}, author = {Villaescusa, JA and Casamayor, EO and Rochera, C and Velázquez, D and Chicote, A and Quesada, A and Camacho, A}, title = {A close link between bacterial community composition and environmental heterogeneity in maritime Antarctic lakes.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {13}, number = {2}, pages = {67-77}, doi = {10.2436/20.1501.01.112}, pmid = {20890841}, issn = {1618-1905}, mesh = {Antarctic Regions ; Bacteria/*classification/*genetics ; *Biodiversity ; DNA Fingerprinting ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Electrophoresis, Polyacrylamide Gel ; Geography ; *Metagenome ; Nucleic Acid Denaturation ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; }, abstract = {Seven maritime Antarctic lakes located on Byers Peninsula (Livingston Island, South Shetland Islands) were surveyed to determine the relationship between planktonic bacterial community composition and environmental features. Specifically, the extent to which factors other than low temperature determine the composition of bacterioplankton assemblages of maritime Antarctic lakes was evaluated. Both deep and shallow lakes in the central plateau of the Peninsula, as well as a coastal lake, were studied in order to fully account for the environmental heterogeneity of the Peninsula's lakes. The results showed that shallow coastal lakes display eutrophic conditions, mainly due to the influence of marine animals, whereas plateau lakes are generally deeper and most are oligotrophic, with very limited inputs of nutrients and organic matter. Meso-eutrophic shallow lakes are also present on the Peninsula; they contain microbial mats and a higher trophic status because of the biologically mediated active nutrient release from the sediments. Diversity studies of the lakes' planktonic bacterial communities using molecular techniques showed that bacterial diversity is lower in eutrophic than in oligotrophic lakes. The former also differed in community composition with respect to dominant taxa. Multivariate statistical analyses of environmental data yielded the same clustering of lakes as obtained based on the DGGE band pattern after DNA extraction and amplification of 16S rRNA gene fragments. Thus, even in extremely cold lakes, the bacterial community composition parallels other environmental factors, such as those related to trophic status. This correspondence is not only mediated by the influence of marine fauna but also by processes including sediment and ice melting dynamics. The bacterial community can therefore be considered to be equally representative as environmental abiotic variables in demonstrating the environmental heterogeneity among maritime Antarctic lakes.}, } @article {pmid20890838, year = {2010}, author = {Aguilera, A and Souza-Egipsy, V and González-Toril, E and Rendueles, O and Amils, R}, title = {Eukaryotic microbial diversity of phototrophic microbial mats in two Icelandic geothermalhot springs.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {13}, number = {1}, pages = {21-32}, doi = {10.2436/20.1501.01.109}, pmid = {20890838}, issn = {1618-1905}, mesh = {*Biodiversity ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Eukaryota/*classification/cytology/*genetics/physiology ; Geologic Sediments/*microbiology ; Hot Springs/chemistry/*microbiology ; Hydrogen-Ion Concentration ; Iceland ; *Metagenome ; Metals, Heavy/analysis ; Microscopy, Electron ; Phototrophic Processes ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Temperature ; }, abstract = {The composition of the eukaryotic community and the three-dimensional structure of diverse phototrophic microbial mats from two hot springs in Iceland (Seltun and Hveradalir geothermal areas) were explored by comparing eukaryotic assemblages from microbial mats. Samples were collected in July 2007 from 15 sampling stations along thermal and pH gradients following both hot springs. Physicochemical data revealed high variability in terms of pH (ranging from 2.8 to 7), with high concentrations of heavy metals, including up to 20 g Fe/l, 80 mg Zn/l, 117 mg Cu/l, and 39 mg Ni/l at the most acidic sampling points. Phylogenetic analysis of 18S rDNA genes revealed a diversity of sequences related to several taxa, including members of the Bacillariophyta, Chlorophyta, Rhodophyta, and Euglenophyta phyla as well as ciliates, amoebae, and stramenopiles. The closest relatives to some of the sequences detected came from acidophilic organisms, even when the samples were collected at circumneutral water locations. Electron microscopy showed that most of the microecosystems analyzed were organized as phototrophic microbial mats in which filamentous cyanobacteria usually appeared as a major component. Deposits of amorphous minerals rich in silica, iron, and aluminium around the filaments were frequently detected.}, } @article {pmid20886741, year = {2010}, author = {Mardanov, AV and Gumerov, VM and Beletsky, AV and Bonch-Osmolovskaya, EA and Ravin, NV and Skryabin, KG}, title = {Characteristic of biodiversity of thermophilic microbial community by parallel pyrosequencing method.}, journal = {Doklady. Biochemistry and biophysics}, volume = {432}, number = {}, pages = {110-113}, pmid = {20886741}, issn = {1607-6729}, mesh = {Archaea/*classification/genetics/*isolation & purification ; Base Sequence ; *Biodiversity ; DNA Primers/genetics ; Fuel Oils/microbiology ; Hot Temperature ; Metagenome ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Russia ; }, } @article {pmid20870788, year = {2010}, author = {Pan, Y and Bodrossy, L and Frenzel, P and Hestnes, AG and Krause, S and Lüke, C and Meima-Franke, M and Siljanen, H and Svenning, MM and Bodelier, PL}, title = {Impacts of inter- and intralaboratory variations on the reproducibility of microbial community analyses.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {22}, pages = {7451-7458}, pmid = {20870788}, issn = {1098-5336}, mesh = {*Biodiversity ; Electrophoresis, Polyacrylamide Gel ; Italy ; Metagenomics/*methods/*standards ; Microarray Analysis ; Nucleic Acid Denaturation ; Oryza ; Polymerase Chain Reaction ; Reproducibility of Results ; *Soil Microbiology ; }, abstract = {With the advent of molecular biological techniques, especially next-generation sequencing and metagenomics, the number of microbial biogeography studies is rapidly increasing. However, these studies involve the synthesis of data generated by different laboratories using different protocols, chemicals, etc., all with inherent biases. The aim of this study was to assess inter- as well as intralaboratory variations in microbial community composition when standardized protocols are applied to a single soil sample. Aliquots from a homogenized soil sample from a rice field in Italy were sent to five participating laboratories. DNA was extracted by two investigators per laboratory using an identical protocol. All DNA samples were sent to one laboratory to perform DNA quantification, quantitative PCR (QPCR), and microarray and denaturing gradient gel electrophoresis (DGGE) analyses of methanotrophic communities. Yields, as well as purity of DNA, were significantly different between laboratories but in some cases also between investigators within the same laboratory. The differences in yield and quality of the extracted DNA were reflected in QPCR, microarray, and DGGE analysis results. Diversity indices (Shannon-Wiener, evenness, and richness) differed significantly between laboratories. The observed differences have implications for every project in which microbial communities are compared in different habitats, even if assessed within the same laboratory. To be able to make sensible comparisons leading to valid conclusions, intralaboratory variation should be assessed. Standardization of DNA extraction protocols and possible use of internal standards in interlaboratory comparisons may help in rendering a "quantifiable" bias.}, } @article {pmid20865128, year = {2010}, author = {Youssef, NH and Couger, MB and Elshahed, MS}, title = {Fine-scale bacterial beta diversity within a complex ecosystem (Zodletone Spring, OK, USA): the role of the rare biosphere.}, journal = {PloS one}, volume = {5}, number = {8}, pages = {e12414}, pmid = {20865128}, issn = {1932-6203}, mesh = {Bacteria/classification/genetics/*isolation & purification/metabolism ; *Biodiversity ; DNA, Bacterial/genetics ; Ecosystem ; Geologic Sediments/*microbiology ; Hot Springs/chemistry/*microbiology ; Molecular Sequence Data ; Oklahoma ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfides/metabolism ; Sulfur/metabolism ; United States ; }, abstract = {BACKGROUND: The adaptation of pyrosequencing technologies for use in culture-independent diversity surveys allowed for deeper sampling of ecosystems of interest. One extremely well suited area of interest for pyrosequencing-based diversity surveys that has received surprisingly little attention so far, is examining fine scale (e.g. micrometer to millimeter) beta diversity in complex microbial ecosystems.

We examined the patterns of fine scale Beta diversity in four adjacent sediment samples (1mm apart) from the source of an anaerobic sulfide and sulfur rich spring (Zodletone spring) in southwestern Oklahoma, USA. Using pyrosequencing, a total of 292,130 16S rRNA gene sequences were obtained. The beta diversity patterns within the four datasets were examined using various qualitative and quantitative similarity indices. Low levels of Beta diversity (high similarity indices) were observed between the four samples at the phylum-level. However, at a putative species (OTU(0.03)) level, higher levels of beta diversity (lower similarity indices) were observed. Further examination of beta diversity patterns within dominant and rare members of the community indicated that at the putative species level, beta diversity is much higher within rare members of the community. Finally, sub-classification of rare members of Zodletone spring community based on patterns of novelty and uniqueness, and further examination of fine scale beta diversity of each of these subgroups indicated that members of the community that are unique, but non novel showed the highest beta diversity within these subgroups of the rare biosphere.

CONCLUSIONS/SIGNIFICANCE: The results demonstrate the occurrence of high inter-sample diversity within seemingly identical samples from a complex habitat. We reason that such unexpected diversity should be taken into consideration when exploring gamma diversity of various ecosystems, as well as planning for sequencing-intensive metagenomic surveys of highly complex ecosystems.}, } @article {pmid20861337, year = {2010}, author = {Verma, R and Verma, AK and Ahuja, V and Paul, J}, title = {Real-time analysis of mucosal flora in patients with inflammatory bowel disease in India.}, journal = {Journal of clinical microbiology}, volume = {48}, number = {11}, pages = {4279-4282}, pmid = {20861337}, issn = {1098-660X}, mesh = {Adolescent ; Adult ; Aged ; Bacteria/*classification/genetics/*isolation & purification ; Bacterial Load ; *Biodiversity ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Humans ; India ; Inflammatory Bowel Diseases/*microbiology ; Intestinal Mucosa/*microbiology ; Male ; *Metagenome ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Mucosa-associated bacterial flora from control individuals and inflammatory bowel disease (IBD) patients were evaluated by real-time analysis using 16S rRNA-based genus-specific primers. Our data show a clear delineation in concentration of bacteria between the predominating and subdominating genera under disease conditions, indicating that the subsets of bacteria participating in the pathogenesis of ulcerative colitis (UC) and Crohn's disease (CD) are likely to be different.}, } @article {pmid20851965, year = {2010}, author = {Fernando, SC and Purvis, HT and Najar, FZ and Sukharnikov, LO and Krehbiel, CR and Nagaraja, TG and Roe, BA and Desilva, U}, title = {Rumen microbial population dynamics during adaptation to a high-grain diet.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {22}, pages = {7482-7490}, pmid = {20851965}, issn = {1098-5336}, mesh = {Animals ; Bacteria/*classification/*genetics ; *Biodiversity ; Cattle ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Diet/*methods ; Edible Grain ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {High-grain adaptation programs are widely used with feedlot cattle to balance enhanced growth performance against the risk of acidosis. This adaptation to a high-grain diet from a high-forage diet is known to change the rumen microbial population structure and help establish a stable microbial population within the rumen. Therefore, to evaluate bacterial population dynamics during adaptation to a high-grain diet, 4 ruminally cannulated beef steers were adapted to a high-grain diet using a step-up diet regimen containing grain and hay at ratios of 20:80, 40:60, 60:40, and 80:20. The rumen bacterial populations were evaluated at each stage of the step-up diet after 1 week of adaptation, before the steers were transitioned to the next stage of the diet, using terminal restriction fragment length polymorphism (T-RFLP) analysis, 16S rRNA gene libraries, and quantitative real-time PCR. The T-RFLP analysis displayed a shift in the rumen microbial population structure during the final two stages of the step-up diet. The 16S rRNA gene libraries demonstrated two distinct rumen microbial populations in hay-fed and high-grain-fed animals and detected only 24 common operational taxonomic units out of 398 and 315, respectively. The 16S rRNA gene libraries of hay-fed animals contained a significantly higher number of bacteria belonging to the phylum Fibrobacteres, whereas the 16S rRNA gene libraries of grain-fed animals contained a significantly higher number of bacteria belonging to the phylum Bacteroidetes. Real-time PCR analysis detected significant fold increases in the Megasphaera elsdenii, Streptococcus bovis, Selenomonas ruminantium, and Prevotella bryantii populations during adaptation to the high-concentrate (high-grain) diet, whereas the Butyrivibrio fibrisolvens and Fibrobacter succinogenes populations gradually decreased as the animals were adapted to the high-concentrate diet. This study evaluates the rumen microbial population using several molecular approaches and presents a broader picture of the rumen microbial population structure during adaptation to a high-grain diet from a forage diet.}, } @article {pmid20847294, year = {2011}, author = {Dethlefsen, L and Relman, DA}, title = {Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108 Suppl 1}, number = {Suppl 1}, pages = {4554-4561}, pmid = {20847294}, issn = {1091-6490}, support = {DP1 OD000964/OD/NIH HHS/United States ; DP1 OD000964-05/OD/NIH HHS/United States ; DP1OD000964/OD/NIH HHS/United States ; }, mesh = {Base Sequence ; *Biodiversity ; Ciprofloxacin/*pharmacology ; Colony Count, Microbial ; Feces/microbiology ; Humans ; Intestine, Large/*microbiology ; Metagenome/*drug effects/genetics ; Molecular Sequence Data ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {The indigenous human microbiota is essential to the health of the host. Although the microbiota can be affected by many features of modern life, we know little about its responses to disturbance, especially repeated disturbances, and how these changes compare with baseline temporal variation. We examined the distal gut microbiota of three individuals over 10 mo that spanned two courses of the antibiotic ciprofloxacin, analyzing more than 1.7 million bacterial 16S rRNA hypervariable region sequences from 52 to 56 samples per subject. Interindividual variation was the major source of variability between samples. Day-to-day temporal variability was evident but constrained around an average community composition that was stable over several months in the absence of deliberate perturbation. The effect of ciprofloxacin on the gut microbiota was profound and rapid, with a loss of diversity and a shift in community composition occurring within 3-4 d of drug initiation. By 1 wk after the end of each course, communities began to return to their initial state, but the return was often incomplete. Although broadly similar, community changes after ciprofloxacin varied among subjects and between the two courses within subjects. In all subjects, the composition of the gut microbiota stabilized by the end of the experiment but was altered from its initial state. As with other ecosystems, the human distal gut microbiome at baseline is a dynamic regimen with a stable average state. Antibiotic perturbation may cause a shift to an alternative stable state, the full consequences of which remain unknown.}, } @article {pmid20847007, year = {2010}, author = {Contreras, M and Costello, EK and Hidalgo, G and Magris, M and Knight, R and Dominguez-Bello, MG}, title = {The bacterial microbiota in the oral mucosa of rural Amerindians.}, journal = {Microbiology (Reading, England)}, volume = {156}, number = {Pt 11}, pages = {3282-3287}, doi = {10.1099/mic.0.043174-0}, pmid = {20847007}, issn = {1465-2080}, mesh = {Adolescent ; Adult ; Bacteria/classification/*genetics/isolation & purification ; Biodiversity ; DNA, Bacterial/genetics ; Female ; Humans ; *Indians, South American ; Male ; *Metagenome ; Middle Aged ; Mouth Mucosa/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rural Population ; Sequence Analysis, DNA ; Specimen Handling ; Venezuela ; Young Adult ; }, abstract = {The oral microbiota plays an important role in buccal health and in diseases such as periodontitis and meningitis. The study of the human oral bacteria has so far focused on subjects from Western societies, while little is known about subjects from isolated communities. This work determined the composition of the oral mucosa microbiota from six Amazon Amerindians, and tested a sample preservation alternative to freezing. Paired oral swabs were taken from six adults of Guahibo ethnicity living in the community of Platanillal, Amazonas State, Venezuela. Replicate swabs were preserved in liquid nitrogen and in Aware Messenger fluid (Calypte). Buccal DNA was extracted, and the V2 region of the 16S rRNA gene was amplified and pyrosequenced. A total of 17 214 oral bacterial sequences were obtained from the six subjects; these were binned into 1034 OTUs from 10 phyla, 30 families and 51 genera. The oral mucosa was highly dominated by four phyla: Firmicutes (mostly the genera Streptococcus and Veillonella), Proteobacteria (mostly Neisseria), Bacterioidetes (Prevotella) and Actinobacteria (Micrococcineae). Although the microbiota were similar at the phylum level, the Amerindians shared only 62 % of the families and 23 % of the genera with non-Amerindians from previous studies, and had a lower richness of genera (51 vs 177 reported in non-Amerindians). The Amerindians carried unidentified members of the phyla Bacteroidetes, Firmicutes and Proteobacteria and their microbiota included soil bacteria Gp1 (Acidobacteriaceae) and Xylanibacter (Prevotellaceae), and the rare genus Phocoenobacter (Pasteurellaceae). Preserving buccal swabs in the Aware Messenger oral fluid collection device substantially altered the bacterial composition in comparison to freezing, and therefore this method cannot be used to preserve samples for the study of microbial communities.}, } @article {pmid20838785, year = {2011}, author = {Rosewarne, CP and Pope, PB and Denman, SE and McSweeney, CS and O'Cuiv, P and Morrison, M}, title = {High-yield and phylogenetically robust methods of DNA recovery for analysis of microbial biofilms adherent to plant biomass in the herbivore gut.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {448-454}, pmid = {20838785}, issn = {1432-184X}, mesh = {Animals ; Biodiversity ; *Biofilms ; Biomass ; Cattle/microbiology ; DNA, Archaeal/*isolation & purification ; DNA, Bacterial/*isolation & purification ; Denaturing Gradient Gel Electrophoresis/methods ; Male ; Plants/*microbiology ; Polymerase Chain Reaction/methods ; Rumen/*microbiology ; }, abstract = {Recent studies have shown the microbial biofilms adherent to plant biomass in the gastrointestinal tracts of humans and other herbivores are quite different to planktonic populations. If these biofilm communities are to be properly characterized by metagenomics methods, then the microbial desorption methods used must ensure the phylogenetic diversity and genetic potential recovered is biologically valid. To that end, we describe here two different methods for desorbing microbes tightly adherent to plant biomass; and used PCR-DGGE analyses of the Bacteria and Archaea rrs genes to show both these desorption methods were effective in recovering the adherent microbial biofilm with no apparent biases in microbe recovery. We also present a derivation of the "repeated bead beating and column (RBB+C) purification" method of DNA extraction that results in the recovery of high molecular weight DNA. These DNA samples can be fragmented and size fractionated by sucrose density gradient centrifugation, bypassing the use of gel-plug lysis and pulsed-field gel electrophoresis separation of DNA for metagenomic library constructions.}, } @article {pmid20830554, year = {2010}, author = {Simon, C and Daniel, R}, title = {Construction of small-insert and large-insert metagenomic libraries.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {668}, number = {}, pages = {39-50}, doi = {10.1007/978-1-60761-823-2_2}, pmid = {20830554}, issn = {1940-6029}, mesh = {Biodiversity ; DNA/analysis/genetics ; *Gene Library ; *Genome, Bacterial ; Metagenome/*genetics ; Metagenomics/*methods ; }, abstract = {The vast majority of the Earth's biological diversity is hidden in uncultured and yet uncharacterized microbial genomes. The construction of metagenomic libraries is a cultivation-independent molecular approach to assess this unexplored genetic reservoir. In the last few years, a high number of novel biocatalysts have been identified by function-based or sequence-based screening of metagenomic libraries. Here, we describe detailed protocols for the construction of metagenomic small-insert and large-insert libraries in plasmids and fosmids, respectively, from environmental DNA.}, } @article {pmid20830553, year = {2010}, author = {Vieites, JM and Guazzaroni, ME and Beloqui, A and Golyshin, PN and Ferrer, M}, title = {Molecular methods to study complex microbial communities.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {668}, number = {}, pages = {1-37}, doi = {10.1007/978-1-60761-823-2_1}, pmid = {20830553}, issn = {1940-6029}, mesh = {Bacteria/*genetics ; Biodiversity ; Cosmids/genetics ; DNA/analysis/isolation & purification ; Environment ; Environmental Microbiology ; Gene Library ; *Metagenome/genetics ; Metagenomics/*methods ; RNA, Ribosomal, 16S/analysis/isolation & purification ; }, abstract = {Microbes, which constitute a major fraction of the total biomass, are the main source of biodiversity on our Planet and play an essential role in maintaining global processes, which ultimately regulate the functioning of the Biosphere. Recent emergence of "metagenomics" allows for the analysis of microbial communities without tedious cultivation efforts. Metagenomics approach is analogous to the genomics with the difference that it does not deal with the single genome from a clone or microbe cultured or characterized in laboratory, but rather with that from the entire microbial community present in an environmental sample; it is the community genome. Global understanding by metagenomics depends essentially on the possibility of isolating the entire bulk DNA and identifying the genomes, genes, and proteins more relevant to each of the environmental sample under investigation. Following on this, in this chapter, we provide an analysis of methods available to isolate environmental DNA and to establish metagenomic libraries that can further be used for extensive activity screens.}, } @article {pmid20829292, year = {2010}, author = {Roger, LC and McCartney, AL}, title = {Longitudinal investigation of the faecal microbiota of healthy full-term infants using fluorescence in situ hybridization and denaturing gradient gel electrophoresis.}, journal = {Microbiology (Reading, England)}, volume = {156}, number = {Pt 11}, pages = {3317-3328}, doi = {10.1099/mic.0.041913-0}, pmid = {20829292}, issn = {1465-2080}, mesh = {Bacteria/genetics/growth & development/*isolation & purification ; Biodiversity ; Breast Feeding ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Feces/*microbiology ; Female ; Humans ; In Situ Hybridization, Fluorescence ; Infant ; Infant Formula ; Longitudinal Studies ; Male ; *Metagenome ; Principal Component Analysis ; Time Factors ; Weaning ; }, abstract = {From birth onwards, the gastrointestinal (GI) tract of infants progressively acquires a complex range of micro-organisms. It is thought that by 2 years of age the GI microbial population has stabilized. Within the developmental period of the infant GI microbiota, weaning is considered to be most critical, as the infant switches from a milk-based diet (breast and/or formula) to a variety of food components. Longitudinal analysis of the biological succession of the infant GI/faecal microbiota is lacking. In this study, faecal samples were obtained regularly from 14 infants from 1 month to 18 months of age. Seven of the infants (including a set of twins) were exclusively breast-fed and seven were exclusively formula-fed prior to weaning, with 175 and 154 faecal samples, respectively, obtained from each group. Diversity and dynamics of the infant faecal microbiota were analysed by using fluorescence in situ hybridization and denaturing gradient gel electrophoresis. Overall, the data demonstrated large inter- and intra-individual differences in the faecal microbiological profiles during the study period. However, the infant faecal microbiota merged with time towards a climax community within and between feeding groups. Data from the twins showed the highest degree of similarity both quantitatively and qualitatively. Inter-individual variation was evident within the infant faecal microbiota and its development, even within exclusively formula-fed infants receiving the same diet. These data can be of help to future clinical trials (e.g. targeted weaning products) to organize protocols and obtain a more accurate outline of the changes and dynamics of the infant GI microbiota.}, } @article {pmid20826648, year = {2010}, author = {Gross, EL and Leys, EJ and Gasparovich, SR and Firestone, ND and Schwartzbaum, JA and Janies, DA and Asnani, K and Griffen, AL}, title = {Bacterial 16S sequence analysis of severe caries in young permanent teeth.}, journal = {Journal of clinical microbiology}, volume = {48}, number = {11}, pages = {4121-4128}, pmid = {20826648}, issn = {1098-660X}, support = {DE16125/DE/NIDCR NIH HHS/United States ; R01 DE016125/DE/NIDCR NIH HHS/United States ; T32DE14320/DE/NIDCR NIH HHS/United States ; F30 DE019339/DE/NIDCR NIH HHS/United States ; F30DE019339/DE/NIDCR NIH HHS/United States ; T32 DE014320/DE/NIDCR NIH HHS/United States ; }, mesh = {Adolescent ; Bacteria/*classification/*genetics/metabolism ; *Biodiversity ; Carboxylic Acids/metabolism ; Child ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Dental Caries/*microbiology ; Female ; Humans ; Male ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tooth/*microbiology ; }, abstract = {Previous studies have confirmed the association of the acid producers Streptococcus mutans and Lactobacillus spp. with childhood caries, but they also suggested these microorganisms are not sufficient to explain all cases of caries. In addition, health-associated bacterial community profiles are not well understood, including the importance of base production and acid catabolism in pH homeostasis. The bacterial community composition in health and in severe caries of the young permanent dentition was compared using Sanger sequencing of the ribosomal 16S rRNA genes. Lactobacillus species were dominant in severe caries, and levels rose significantly as caries progressed from initial to deep lesions. S. mutans was often observed at high levels in the early stages of caries but also in some healthy subjects and was not statistically significantly associated with caries progression in the overall model. Lactobacillus or S. mutans was found either at low levels or not present in several samples. Other potential acid producers observed at high levels in these subjects included strains of Selenomonas, Neisseria, and Streptococcus mitis. Propionibacterium FMA5 was significantly associated with caries progression but was not found at high levels. An overall loss of community diversity occurred as caries progressed, and species that significantly decreased included the Streptococcus mitis-S. pneumoniae-S. infantis group, Corynebacterium matruchotii, Streptococcus gordonii, Streptococcus cristatus, Capnocytophaga gingivalis, Eubacterium IR009, Campylobacter rectus, and Lachnospiraceae sp. C1. The relationship of acid-base metabolism to 16S rRNA gene-based species assignments appears to be complex, and metagenomic approaches that would allow functional profiling of entire genomes will be helpful in elucidating the microbial pathogenesis of caries.}, } @article {pmid20815238, year = {2010}, author = {Tian, X and Zhang, Q and Chen, G and Mao, Z and Yang, J and Xie, B}, title = {[Diversity of bacteria associated with pine wood nematode revealed by metagenome].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {50}, number = {7}, pages = {909-916}, pmid = {20815238}, issn = {0001-6209}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; *Biodiversity ; DNA, Bacterial/genetics ; *Metagenome ; Molecular Sequence Data ; Nematoda/*microbiology ; Phylogeny ; Pinus/parasitology ; Plant Diseases/parasitology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVE: The pine wood nematode (PWN), Bursaphlenchus xylophilus, which collaborates with its associated bacteria to form ecosystem and has interaction among them, is the pathogen of pine wilt disease. This study focused on revealing the bacterial diversity of ecosystem of pine wood nematode and its associated bacteria.

METHODS: The metagenome of ecosystem of bacteria associated with the PWN was analyzed by 16S rRNA gene library and 454 sequencing.

RESULTS: The results showed that 25 OTUs (Operational Taxonomic Units) were obtained from the library according to sequences similarity of 97%, which affiliated to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Bacteroidetes. The dominant bacteria were belonged to Gammaproteobacteria, especially Stenotrophomonas maltophilia in this class dominated the library. In terms of dominant bacteria, the results revealed by metagenome were similar to that of 16S rRNA gene library.

CONCLUSION: The diversity of bacteria associated with the PWN is high and these bacteria maybe have ecological role to the PWN.}, } @article {pmid20806900, year = {2010}, author = {Martin, FP and Sprenger, N and Montoliu, I and Rezzi, S and Kochhar, S and Nicholson, JK}, title = {Dietary modulation of gut functional ecology studied by fecal metabonomics.}, journal = {Journal of proteome research}, volume = {9}, number = {10}, pages = {5284-5295}, doi = {10.1021/pr100554m}, pmid = {20806900}, issn = {1535-3907}, mesh = {Animals ; Biodiversity ; Colony Count, Microbial ; Dietary Sucrose/*administration & dosage ; Ecology ; Feces/microbiology ; Female ; Gastrointestinal Tract/*metabolism/microbiology ; Glucose/administration & dosage ; Host-Pathogen Interactions ; Humans ; Infant, Newborn ; Lactobacillus/metabolism/physiology ; Lactose/administration & dosage ; Magnetic Resonance Spectroscopy ; Metabolomics/*methods ; Metagenome/physiology ; Mice ; Mice, Inbred C3H ; Prebiotics ; Probiotics/*administration & dosage ; Time Factors ; }, abstract = {A major source of intestinal metabolites results from both host and microbial processing of dietary nutrients. (1)H NMR-based metabolic profiling of mouse feces was carried out over time in different microbiome mouse models, including conventional (n = 9), conventionalized (n = 10), and "humanized" gnotobiotic mice inoculated with a model of human baby microbiota (HBM, n = 17). HBM mice were supplemented with Lactobacillus paracasei with (n = 10) and without (n = 7) prebiotics. Animals not supplemented with prebiotics received a diet enriched in glucose and lactose as placebo. In conventionalized animals, microbial populations and activities converged in term of multivariate mapping toward conventional mice. Both groups decreased bacterial processing of dietary proteins when switching to a diet enriched in glucose and lactose, as described with low levels of 5-aminovalerate, acetate, and propionate and high levels of lysine and arginine. The HBM model differs from conventional and conventionalized microbiota in terms of type, proportion, and metabolic activity of gut bacteria (lower short chain fatty acids (SCFAs), lactate, 5-aminovalerate, and oligosaccharides, higher bile acids and choline). The probiotics supplementation of HBM mice was associated with a specific amino acid pattern that can be linked to L. paracasei proteolytic activities. The combination of L. paracasei with the galactosyl-oligosaccharide prebiotics was related to the enhanced growth of bifidobacteria and lactobacilli, and a specific metabolism of carbohydrates, proteins, and SCFAs. The present study describes how the assessment of metabolic changes in feces may provide information for studying nutrient-microbiota relationships in different microbiome mouse models.}, } @article {pmid20803250, year = {2011}, author = {Lim, J and Woodward, J and Tulaczyk, S and Christoffersen, P and Cummings, SP}, title = {Analysis of the microbial community and geochemistry of a sediment core from Great Slave Lake, Canada.}, journal = {Antonie van Leeuwenhoek}, volume = {99}, number = {2}, pages = {423-430}, doi = {10.1007/s10482-010-9500-y}, pmid = {20803250}, issn = {1572-9699}, mesh = {Archaea/*classification/genetics/isolation & purification ; Bacteria/*classification/genetics/isolation & purification ; *Biodiversity ; Canada ; Geologic Sediments/*chemistry/*microbiology ; Metagenome ; Minerals/*analysis ; Statistics as Topic ; }, abstract = {Sediment cores taken from Great Slave Lake, Canada, were analysed to investigate their metabolically active microbial populations and geochemistry. The amplification of cDNA detected metabolically active bacterial (50 separate bands) and archaeal (49 separate band) communities. The bacterial communities were further resolved indicating active actinobacterial and γ-proteobacterial communities (36 and 43 individual bands respectively). Redundancy discriminate analysis and Monte Carlo permutation testing demonstrated the significant impact of geochemical parameters on microbial community structures. Geochemical analyses suggest that the upper 0.4 m represents soil weathering and erosion in the lake catchment. An increase in organic carbon in the lower core suggests either more primary productivity, indicating warmer climate conditions, associated with Holocene Climatic Optimum conditions pre 5,000 years BP or change from a reducing environment in the lower core to an oxidizing environment during more recent deposition. Drivers for bacterial, archaeal and actinobacterial community structures were sediment particle size, and its mineral composition. Depth also significantly affected γ- proteobacterial community structure. In contrast the organic carbon content did not significantly shape the microbial community structures within the sediment. This study indicates that geochemical parameters significantly contribute to microbial community structure in these sediments.}, } @article {pmid20802827, year = {2010}, author = {Lemon, KP and Klepac-Ceraj, V and Schiffer, HK and Brodie, EL and Lynch, SV and Kolter, R}, title = {Comparative analyses of the bacterial microbiota of the human nostril and oropharynx.}, journal = {mBio}, volume = {1}, number = {3}, pages = {}, pmid = {20802827}, issn = {2150-7511}, support = {R01 GM058213/GM/NIGMS NIH HHS/United States ; R01 GM082137/GM/NIGMS NIH HHS/United States ; GM082137/GM/NIGMS NIH HHS/United States ; GM58213/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Bacteria/classification/*genetics/*isolation & purification/metabolism ; Biodiversity ; Female ; Humans ; Male ; *Metagenome ; Middle Aged ; Molecular Sequence Data ; Nasal Cavity/*microbiology ; Oropharynx/*microbiology ; }, abstract = {The nose and throat are important sites of pathogen colonization, yet the microbiota of both is relatively unexplored by culture-independent approaches. We examined the bacterial microbiota of the nostril and posterior wall of the oropharynx from seven healthy adults using two culture-independent methods, a 16S rRNA gene microarray (PhyloChip) and 16S rRNA gene clone libraries. While the bacterial microbiota of the oropharynx was richer than that of the nostril, the oropharyngeal microbiota varied less among participants than did nostril microbiota. A few phyla accounted for the majority of the bacteria detected at each site: Firmicutes and Actinobacteria in the nostril and Firmicutes, Proteobacteria, and Bacteroidetes in the oropharynx. Compared to culture-independent surveys of microbiota from other body sites, the microbiota of the nostril and oropharynx show distinct phylum-level distribution patterns, supporting niche-specific colonization at discrete anatomical sites. In the nostril, the distribution of Actinobacteria and Firmicutes was reminiscent of that of skin, though Proteobacteria were much less prevalent. The distribution of Firmicutes, Proteobacteria, and Bacteroidetes in the oropharynx was most similar to that in saliva, with more Proteobacteria than in the distal esophagus or mouth. While Firmicutes were prevalent at both sites, distinct families within this phylum dominated numerically in each. At both sites there was an inverse correlation between the prevalences of Firmicutes and another phylum: in the oropharynx, Firmicutes and Proteobacteria, and in the nostril, Firmicutes and Actinobacteria. In the nostril, this inverse correlation existed between the Firmicutes family Staphylococcaceae and Actinobacteria families, suggesting potential antagonism between these groups.}, } @article {pmid20738373, year = {2011}, author = {Sime-Ngando, T and Lucas, S and Robin, A and Tucker, KP and Colombet, J and Bettarel, Y and Desmond, E and Gribaldo, S and Forterre, P and Breitbart, M and Prangishvili, D}, title = {Diversity of virus-host systems in hypersaline Lake Retba, Senegal.}, journal = {Environmental microbiology}, volume = {13}, number = {8}, pages = {1956-1972}, doi = {10.1111/j.1462-2920.2010.02323.x}, pmid = {20738373}, issn = {1462-2920}, mesh = {Archaea/classification/genetics/*virology ; Archaeal Viruses/*classification/genetics/*physiology/ultrastructure ; Bacteria/classification/genetics/*virology ; Bacteriophages/*classification/genetics/isolation & purification/*ultrastructure ; *Biodiversity ; Environmental Microbiology ; Lakes/microbiology/virology ; Metagenome ; Microscopy, Electron, Transmission ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; Senegal ; }, abstract = {Remarkable morphological diversity of virus-like particles was observed by transmission electron microscopy in a hypersaline water sample from Lake Retba, Senegal. The majority of particles morphologically resembled hyperthermophilic archaeal DNA viruses isolated from extreme geothermal environments. Some hypersaline viral morphotypes have not been previously observed in nature, and less than 1% of observed particles had a head-and-tail morphology, which is typical for bacterial DNA viruses. Culture-independent analysis of the microbial diversity in the sample suggested the dominance of extremely halophilic archaea. Few of the 16S sequences corresponded to known archeal genera (Haloquadratum, Halorubrum and Natronomonas), whereas the majority represented novel archaeal clades. Three sequences corresponded to a new basal lineage of the haloarchaea. Bacteria belonged to four major phyla, consistent with the known diversity in saline environments. Metagenomic sequencing of DNA from the purified virus-like particles revealed very few similarities to the NCBI non-redundant database at either the nucleotide or amino acid level. Some of the identifiable virus sequences were most similar to previously described haloarchaeal viruses, but no sequence similarities were found to archaeal viruses from extreme geothermal environments. A large proportion of the sequences had similarity to previously sequenced viral metagenomes from solar salterns.}, } @article {pmid20733077, year = {2010}, author = {Rusch, DB and Martiny, AC and Dupont, CL and Halpern, AL and Venter, JC}, title = {Characterization of Prochlorococcus clades from iron-depleted oceanic regions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {37}, pages = {16184-16189}, pmid = {20733077}, issn = {1091-6490}, mesh = {Biodiversity ; Genome, Bacterial ; Iron/*metabolism ; Oceans and Seas ; Phylogeny ; Prochlorococcus/genetics/*isolation & purification/metabolism ; }, abstract = {Prochlorococcus describes a diverse and abundant genus of marine photosynthetic microbes. It is primarily found in oligotrophic waters across the globe and plays a crucial role in energy and nutrient cycling in the ocean ecosystem. The abundance, global distribution, and availability of isolates make Prochlorococcus a model system for understanding marine microbial diversity and biogeochemical cycling. Analysis of 73 metagenomic samples from the Global Ocean Sampling expedition acquired in the Atlantic, Pacific, and Indian Oceans revealed the presence of two uncharacterized Prochlorococcus clades. A phylogenetic analysis using six different genetic markers places the clades close to known lineages adapted to high-light environments. The two uncharacterized clades consistently cooccur and dominate the surface waters of high-temperature, macronutrient-replete, and low-iron regions of the Eastern Equatorial Pacific upwelling and the tropical Indian Ocean. They are genetically distinct from each other and other high-light Prochlorococcus isolates and likely define a previously unrecognized ecotype. Our detailed genomic analysis indicates that these clades comprise organisms that are adapted to iron-depleted environments by reducing their iron quota through the loss of several iron-containing proteins that likely function as electron sinks in the photosynthetic pathway in other Prochlorococcus clades from high-light environments. The presence and inferred physiology of these clades may explain why Prochlorococcus populations from iron-depleted regions do not respond to iron fertilization experiments and further expand our understanding of how phytoplankton adapt to variations in nutrient availability in the ocean.}, } @article {pmid20729324, year = {2010}, author = {Will, C and Thürmer, A and Wollherr, A and Nacke, H and Herold, N and Schrumpf, M and Gutknecht, J and Wubet, T and Buscot, F and Daniel, R}, title = {Horizon-specific bacterial community composition of German grassland soils, as revealed by pyrosequencing-based analysis of 16S rRNA genes.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {20}, pages = {6751-6759}, pmid = {20729324}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Carbon/analysis ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Germany ; *Metagenome ; Molecular Sequence Data ; Nitrogen/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; }, abstract = {The diversity of bacteria in soil is enormous, and soil bacterial communities can vary greatly in structure. Here, we employed a pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to characterize the overall and horizon-specific (A and B horizons) bacterial community compositions in nine grassland soils, which covered three different land use types. The entire data set comprised 752,838 sequences, 600,544 of which could be classified below the domain level. The average number of sequences per horizon was 41,824. The dominant taxonomic groups present in all samples and horizons were the Acidobacteria, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, Firmicutes, and Bacteroidetes. Despite these overarching dominant taxa, the abundance, diversity, and composition of bacterial communities were horizon specific. In almost all cases, the estimated bacterial diversity (H') was higher in the A horizons than in the corresponding B horizons. In addition, the H' was positively correlated with the organic carbon content, the total nitrogen content, and the C-to-N ratio, which decreased with soil depth. It appeared that lower land use intensity results in higher bacterial diversity. The majority of sequences affiliated with the Actinobacteria, Bacteroidetes, Cyanobacteria, Fibrobacteres, Firmicutes, Spirochaetes, Verrucomicrobia, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria were derived from A horizons, whereas the majority of the sequences related to Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospira, TM7, and WS3 originated from B horizons. The distribution of some bacterial phylogenetic groups and subgroups in the different horizons correlated with soil properties such as organic carbon content, total nitrogen content, or microbial biomass.}, } @article {pmid20729323, year = {2010}, author = {Kielak, AM and van Veen, JA and Kowalchuk, GA}, title = {Comparative analysis of acidobacterial genomic fragments from terrestrial and aquatic metagenomic libraries, with emphasis on acidobacteria subdivision 6.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {20}, pages = {6769-6777}, pmid = {20729323}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics ; Base Composition ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, Bacterial ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Recombination, Genetic ; Sequence Analysis, DNA ; *Soil Microbiology ; Synteny ; *Water Microbiology ; }, abstract = {The bacterial phylum Acidobacteria has a widespread distribution and is one of the most common and diverse phyla in soil habitats. However, members of this phylum have often been recalcitrant to cultivation methods, hampering the study of this presumably important bacterial group. In this study, we used a cultivation-independent metagenomic approach to recover genomic information from soilborne members of this phylum. A soil metagenomic fosmid library was screened by PCR targeting acidobacterial 16S rRNA genes, facilitating the recovery of 17 positive clones. Recovered inserts appeared to originate from a range of Acidobacteria subdivisions, with dominance of subdivision 6 (10 clones). Upon full-length insert sequencing, gene annotation identified a total of 350 open reading frames (ORFs), representing a broad range of functions. Remarkably, six inserts from subdivision 6 contained a region of gene synteny, containing genes involved in purine de novo biosynthesis and encoding tRNA synthetase and conserved hypothetical proteins. Similar genomic regions had previously been observed in several environmental clones recovered from soil and marine sediments, facilitating comparisons with respect to gene organization and evolution. Comparative analyses revealed a general dichotomy between marine and terrestrial genes in both phylogeny and G+C content. Although the significance of this homologous gene cluster across subdivision 6 members is not known, it appears to be a common feature within a large percentage of all acidobacterial genomic fragments recovered from both of these environments.}, } @article {pmid20729318, year = {2010}, author = {Cardenas, E and Wu, WM and Leigh, MB and Carley, J and Carroll, S and Gentry, T and Luo, J and Watson, D and Gu, B and Ginder-Vogel, M and Kitanidis, PK and Jardine, PM and Zhou, J and Criddle, CS and Marsh, TL and Tiedje, JM}, title = {Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {20}, pages = {6778-6786}, pmid = {20729318}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics/metabolism ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil Pollutants, Radioactive/metabolism ; Sulfates/*metabolism ; Tennessee ; Uranium/*metabolism ; }, abstract = {Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared.}, } @article {pmid20717659, year = {2010}, author = {Terán-Ventura, E and Roca, M and Martin, MT and Abarca, ML and Martinez, V and Vergara, P}, title = {Characterization of housing-related spontaneous variations of gut microbiota and expression of toll-like receptors 2 and 4 in rats.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {691-702}, pmid = {20717659}, issn = {1432-184X}, mesh = {Animals ; Bacteria/genetics ; Biodiversity ; Cecum/*microbiology ; DNA, Bacterial/genetics ; Gene Expression ; *Housing, Animal ; In Situ Hybridization, Fluorescence ; Male ; Metagenome/*genetics ; Polymorphism, Restriction Fragment Length ; Rats ; Rats, Sprague-Dawley ; Toll-Like Receptor 2/*metabolism ; Toll-Like Receptor 4/*metabolism ; }, abstract = {Gut microbiota has been suggested as a key component of gut homeostasis, affecting immune responses within the gut. We determined changes in intestinal commensal bacteria and expression of toll-like receptors (TLR) 2 and 4 in rats bred under microbiologically controlled conditions (barrier), under standard conditions (conventional), and in barrier animals adapted to standard conditions (barrier/conventional). Cecal microbiota was analyzed by plate culture, and fluorescence in situ hybridization and microbial profiles were assessed by terminal restriction fragment length polymorphism. Cecal expression of TLR-2 and TLR-4 was determined by reverse transcription polymerase chain reaction (PCR). Total number of cecal bacteria was similar in the three groups. However, the barrier group showed a higher number of strict anaerobic bacteria (Bacteroides spp. and Clostridium spp.) while Bifidobacterium spp. were scarce. Re-housing the barrier-bred rats into conventional conditions led to a microbiota with intermediate characteristics between the barrier and conventional groups. Richness of the cecal microbial ecosystem was similar in the three groups, although a relative time-dependent variation, with highest homogeneity in the barrier group, was observed. Expression levels of TLR-2 and TLR-4 had no clear correlation with the microbiota. These results show that the relative composition of the cecal microbiota in rats varies spontaneously with changes in the environmental conditions, with minor impact in the expression of TLR-2 and TLR-4. These observations might be important in the understanding of variability in animal responses, particularly to immune-related stimuli, when assessed in the context of the environmental/microbiological conditions.}, } @article {pmid20709849, year = {2010}, author = {Hernandez-Sanabria, E and Guan, LL and Goonewardene, LA and Li, M and Mujibi, DF and Stothard, P and Moore, SS and Leon-Quintero, MC}, title = {Correlation of particular bacterial PCR-denaturing gradient gel electrophoresis patterns with bovine ruminal fermentation parameters and feed efficiency traits.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {19}, pages = {6338-6350}, pmid = {20709849}, issn = {1098-5336}, mesh = {*Animal Feed ; Animals ; Bacteria/*classification/*genetics/metabolism ; *Biodiversity ; Cattle/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Denaturing Gradient Gel Electrophoresis/methods ; Diet ; Fatty Acids/analysis ; Fermentation ; Male ; *Metagenome ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Rumen/chemistry/*microbiology ; }, abstract = {The influence of rumen microbial structure and functions on host physiology remains poorly understood. This study aimed to investigate the interaction between the ruminal microflora and the host by correlating bacterial diversity with fermentation measurements and feed efficiency traits, including dry matter intake, feed conversion ratio, average daily gain, and residual feed intake, using culture-independent methods. Universal bacterial partial 16S rRNA gene products were amplified from ruminal fluid collected from 58 steers raised under a low-energy diet and were subjected to PCR-denaturing gradient gel electrophoresis (DGGE) analysis. Multivariate statistical analysis was used to relate specific PCR-DGGE bands to various feed efficiency traits and metabolites. Analysis of volatile fatty acid profiles showed that butyrate was positively correlated with daily dry matter intake (P < 0.05) and tended to have higher concentration in inefficient animals (P = 0.10), while isovalerate was associated with residual feed intake (P < 0.05). Our results suggest that particular bacteria and their metabolism in the rumen may contribute to differences in host feed efficiency under a low-energy diet. This is the first study correlating PCR-DGGE bands representing specific bacteria to metabolites in the bovine rumen and to host feed efficiency traits.}, } @article {pmid20705353, year = {2010}, author = {Dolci, P and Alessandria, V and Rantsiou, K and Bertolino, M and Cocolin, L}, title = {Microbial diversity, dynamics and activity throughout manufacturing and ripening of Castelmagno PDO cheese.}, journal = {International journal of food microbiology}, volume = {143}, number = {1-2}, pages = {71-75}, doi = {10.1016/j.ijfoodmicro.2010.07.007}, pmid = {20705353}, issn = {1879-3460}, mesh = {Biodiversity ; Cheese/*microbiology ; DNA, Bacterial/analysis ; Food Handling/*methods ; *Food Microbiology ; Italy ; Lactobacillus/genetics/*isolation & purification ; Lactococcus/genetics/*isolation & purification ; Metagenome ; RNA, Bacterial/analysis ; Streptococcus/genetics/*isolation & purification ; }, abstract = {The diversity, dynamics and activity of Castelmagno PDO cheese microbiota were studied in three batches produced in a floor valley farm, in the Grana Valley (northwest Italy), during the wintertime. Samples of milk, curd and cheese (core and subsurface) at different ripening time were submitted to both culture-dependent and -independent analysis. In particular, DNA and RNA directly extracted from the matrices were studied by PCR-Denaturing gradient gel electrophoresis (DGGE) and reverse transcription (RT)-PCR-DGGE. Culture-dependent methods highlighted the initial dominance of a thermophilic streptococcal population with the species Streptococcus thermophilus and S. agalactiae. Then, mesophilic lactococci occurred among isolates during manufacturing, with Lactococcus lactis which was also well represented in the first month of Castelmagno PDO ripening. At this point and throughout the ripening, lactobacilli prevailed in cheese samples, represented from Lactobacillus plantarum and Lb. casei. Culture-independent analysis underlined the undoubted role of L. lactis, actively involved in both Castelmagno PDO manufacturing and ripening. Despite Lb. helveticus was never isolated on selective media, a DGGE band referred to this microorganism was detected, at RNA level, in samples from ripened cheeses. On the other hand, Lb. plantarum was widely isolated from the plates, among lactobacilli, but never detected by direct analysis. Due to the importance of microbiota in the sensory richness and properties of traditional cheeses, new information have been added, in this work, on microbial diversity of Castelmagno PDO cheese.}, } @article {pmid20693454, year = {2010}, author = {Cressman, MD and Yu, Z and Nelson, MC and Moeller, SJ and Lilburn, MS and Zerby, HN}, title = {Interrelations between the microbiotas in the litter and in the intestines of commercial broiler chickens.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {19}, pages = {6572-6582}, pmid = {20693454}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification/genetics ; *Biodiversity ; Cecum/*microbiology ; Chickens ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Diet ; Electrophoresis, Polyacrylamide Gel ; Feces/*microbiology ; Ileum/*microbiology ; Intestinal Mucosa/microbiology ; *Metagenome ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The intestinal microbiota of broiler chickens and the microbiota in the litter have been well studied, but the interactions between these two microbiotas remain to be determined. Therefore, we examined their reciprocal effects by analyzing the intestinal microbiotas of broilers reared on fresh pine shavings versus reused litter, as well as the litter microbiota over a 6-week cycle. Composite ileal mucosal and cecal luminal samples from birds (n = 10) reared with both litter conditions (fresh versus reused) were collected at 7, 14, 21, and 42 days of age. Litter samples were also collected at days 7, 14, 21, and 42. The microbiotas were profiled and compared within sample types based on litter condition using PCR and denaturing gradient gel electrophoresis (PCR-DGGE). The microbiotas were further analyzed using 16S rRNA gene clone libraries constructed from microbiota DNA extracted from both chick intestinal and litter samples collected at day 7. Results showed significant reciprocal effects between the microbiotas present in the litter and those in the intestines of broilers. Fresh litter had more environmental bacteria, while reused litter contained more bacteria of intestinal origin. Lactobacillus spp. dominated the ileal mucosal microbiota of fresh-litter chicks, while a group of bacteria yet to be classified within Clostridiales dominated in the ileal mucosal microbiota in the reused-litter chicks. The Litter condition (fresh versus reused) seemed to have a more profound impact on the ileal microbiota than on the cecal microbiota. The data suggest that the influence of fresh litter on ileal microbiota decreased as broilers grew, compared with temporal changes observed under reused-litter rearing conditions.}, } @article {pmid20693331, year = {2010}, author = {Caboche, S and Leclère, V and Pupin, M and Kucherov, G and Jacques, P}, title = {Diversity of monomers in nonribosomal peptides: towards the prediction of origin and biological activity.}, journal = {Journal of bacteriology}, volume = {192}, number = {19}, pages = {5143-5150}, pmid = {20693331}, issn = {1098-5530}, mesh = {Databases, Factual ; Models, Theoretical ; Peptide Synthases/metabolism ; Peptides/*chemistry/metabolism ; }, abstract = {Nonribosomal peptides (NRPs) are molecules produced by microorganisms that have a broad spectrum of biological activities and pharmaceutical applications (e.g., antibiotic, immunomodulating, and antitumor activities). One particularity of the NRPs is the biodiversity of their monomers, extending far beyond the 20 proteogenic amino acid residues. Norine, a comprehensive database of NRPs, allowed us to review for the first time the main characteristics of the NRPs and especially their monomer biodiversity. Our analysis highlighted a significant similarity relationship between NRPs synthesized by bacteria and those isolated from metazoa, especially from sponges, supporting the hypothesis that some NRPs isolated from sponges are actually synthesized by symbiotic bacteria rather than by the sponges themselves. A comparison of peptide monomeric compositions as a function of biological activity showed that some monomers are specific to a class of activities. An analysis of the monomer compositions of peptide products predicted from genomic information (metagenomics and high-throughput genome sequencing) or of new peptides detected by mass spectrometry analysis applied to a culture supernatant can provide indications of the origin of a peptide and/or its biological activity.}, } @article {pmid20686513, year = {2011}, author = {Walker, AW and Ince, J and Duncan, SH and Webster, LM and Holtrop, G and Ze, X and Brown, D and Stares, MD and Scott, P and Bergerat, A and Louis, P and McIntosh, F and Johnstone, AM and Lobley, GE and Parkhill, J and Flint, HJ}, title = {Dominant and diet-responsive groups of bacteria within the human colonic microbiota.}, journal = {The ISME journal}, volume = {5}, number = {2}, pages = {220-230}, pmid = {20686513}, issn = {1751-7370}, support = {/WT_/Wellcome Trust/United Kingdom ; 076964/WT_/Wellcome Trust/United Kingdom ; WT 76964/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Archaea/genetics/growth & development/physiology ; Bacteria/classification/genetics/*growth & development/metabolism ; *Biodiversity ; Colon/*microbiology ; Cross-Over Studies ; *Diet ; Diet, Reducing ; Dietary Carbohydrates/metabolism ; Dietary Proteins/metabolism ; Feces/microbiology ; Humans ; Male ; Metagenome/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; Starch/metabolism ; }, abstract = {The populations of dominant species within the human colonic microbiota can potentially be modified by dietary intake with consequences for health. Here we examined the influence of precisely controlled diets in 14 overweight men. Volunteers were provided successively with a control diet, diets high in resistant starch (RS) or non-starch polysaccharides (NSPs) and a reduced carbohydrate weight loss (WL) diet, over 10 weeks. Analysis of 16S rRNA sequences in stool samples of six volunteers detected 320 phylotypes (defined at >98% identity) of which 26, including 19 cultured species, each accounted for >1% of sequences. Although samples clustered more strongly by individual than by diet, time courses obtained by targeted qPCR revealed that 'blooms' in specific bacterial groups occurred rapidly after a dietary change. These were rapidly reversed by the subsequent diet. Relatives of Ruminococcus bromii (R-ruminococci) increased in most volunteers on the RS diet, accounting for a mean of 17% of total bacteria compared with 3.8% on the NSP diet, whereas the uncultured Oscillibacter group increased on the RS and WL diets. Relatives of Eubacterium rectale increased on RS (to mean 10.1%) but decreased, along with Collinsella aerofaciens, on WL. Inter-individual variation was marked, however, with >60% of RS remaining unfermented in two volunteers on the RS diet, compared to <4% in the other 12 volunteers; these two individuals also showed low numbers of R-ruminococci (<1%). Dietary non-digestible carbohydrate can produce marked changes in the gut microbiota, but these depend on the initial composition of an individual's gut microbiota.}, } @article {pmid20683720, year = {2010}, author = {Lee, MH and Hong, KS and Malhotra, S and Park, JH and Hwang, EC and Choi, HK and Kim, YS and Tao, W and Lee, SW}, title = {A new esterase EstD2 isolated from plant rhizosphere soil metagenome.}, journal = {Applied microbiology and biotechnology}, volume = {88}, number = {5}, pages = {1125-1134}, doi = {10.1007/s00253-010-2729-6}, pmid = {20683720}, issn = {1432-0614}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics/metabolism ; Biota ; Butyrates/*metabolism ; Caulobacteraceae/genetics ; Cloning, Molecular ; DNA, Bacterial/genetics ; Escherichia coli/enzymology/genetics/metabolism ; Esterases/chemistry/*isolation & purification/*metabolism ; Gene Expression ; Genome, Bacterial ; Genomic Library ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Plasmids/genetics ; Republic of Korea ; *Rhizosphere ; Sequence Alignment ; Sequence Analysis, DNA ; *Soil Microbiology ; Substrate Specificity ; }, abstract = {Soil metagenome constitutes a reservoir for discovering novel enzymes from the unculturable microbial diversity. From three plant rhizosphere metagenomic libraries comprising a total of 142,900 members of recombinant plasmids, we obtained 14 recombinant fosmids that exhibited lipolytic activity. A selected recombinant plasmid, pFLP-2, which showed maximum lipolytic activity, was further analyzed. DNA sequence analysis of the subclone in pUC119, pELP-2, revealed an open reading frame of 1,191 bp encoding a 397-amino-acid protein. Purified EstD2 exhibited maximum enzymatic activity towards p-nitrophenyl butyrate, indicating that it is an esterase. Purified EstD2 showed optimal activity at 35 °C and at pH 8.0. The K(m) and K(cat) values were determined to be 79.4 μM and 120.5/s, respectively. The esterase exhibited an increase in enzymatic activity in the presence of 15% butanol and 15% methanol. Phylogenetic analysis revealed that the lipolytic protein EstD2 may be a member of a novel family of lipolytic enzymes. Several hypothetical protein homologs of EstD2 were found in the database. A hypothetical protein from Phenylobacterium zucineum HLK1, a close homolog of EstD2, displayed lipolytic activity when the corresponding gene was expressed in Escherichia coli. Our results suggest that the other hypothetical protein homologs of EstD2 might also be members of this novel family.}, } @article {pmid20679230, year = {2010}, author = {De Filippo, C and Cavalieri, D and Di Paola, M and Ramazzotti, M and Poullet, JB and Massart, S and Collini, S and Pieraccini, G and Lionetti, P}, title = {Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {33}, pages = {14691-14696}, pmid = {20679230}, issn = {1091-6490}, mesh = {Bacteria/classification/*genetics/growth & development ; Biodiversity ; Burkina Faso ; Child ; Child, Preschool ; Cluster Analysis ; Feces/microbiology ; *Feeding Behavior ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Infant ; Italy ; Male ; Metagenome/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rural Population/statistics & numerical data ; Sequence Analysis, DNA ; Urban Population/statistics & numerical data ; }, abstract = {Gut microbial composition depends on different dietary habits just as health depends on microbial metabolism, but the association of microbiota with different diets in human populations has not yet been shown. In this work, we compared the fecal microbiota of European children (EU) and that of children from a rural African village of Burkina Faso (BF), where the diet, high in fiber content, is similar to that of early human settlements at the time of the birth of agriculture. By using high-throughput 16S rDNA sequencing and biochemical analyses, we found significant differences in gut microbiota between the two groups. BF children showed a significant enrichment in Bacteroidetes and depletion in Firmicutes (P < 0.001), with a unique abundance of bacteria from the genus Prevotella and Xylanibacter, known to contain a set of bacterial genes for cellulose and xylan hydrolysis, completely lacking in the EU children. In addition, we found significantly more short-chain fatty acids (P < 0.001) in BF than in EU children. Also, Enterobacteriaceae (Shigella and Escherichia) were significantly underrepresented in BF than in EU children (P < 0.05). We hypothesize that gut microbiota coevolved with the polysaccharide-rich diet of BF individuals, allowing them to maximize energy intake from fibers while also protecting them from inflammations and noninfectious colonic diseases. This study investigates and compares human intestinal microbiota from children characterized by a modern western diet and a rural diet, indicating the importance of preserving this treasure of microbial diversity from ancient rural communities worldwide.}, } @article {pmid20675448, year = {2010}, author = {Redmond, MC and Valentine, DL and Sessions, AL}, title = {Identification of novel methane-, ethane-, and propane-oxidizing bacteria at marine hydrocarbon seeps by stable isotope probing.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {19}, pages = {6412-6422}, pmid = {20675448}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/*metabolism ; *Biodiversity ; California ; Carbon Isotopes/metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics/metabolism ; DNA, Ribosomal/chemistry/genetics ; Ethane/*metabolism ; Fatty Acids/metabolism ; Geologic Sediments/*microbiology ; *Metagenome ; Methane/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Propane/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Staining and Labeling/methods ; }, abstract = {Marine hydrocarbon seeps supply oil and gas to microorganisms in sediments and overlying water. We used stable isotope probing (SIP) to identify aerobic bacteria oxidizing gaseous hydrocarbons in surface sediment from the Coal Oil Point seep field located offshore of Santa Barbara, California. After incubating sediment with (13)C-labeled methane, ethane, or propane, we confirmed the incorporation of (13)C into fatty acids and DNA. Terminal restriction fragment length polymorphism (T-RFLP) analysis and sequencing of the 16S rRNA and particulate methane monooxygenase (pmoA) genes in (13)C-DNA revealed groups of microbes not previously thought to contribute to methane, ethane, or propane oxidation. First, (13)C methane was primarily assimilated by Gammaproteobacteria species from the family Methylococcaceae, Gammaproteobacteria related to Methylophaga, and Betaproteobacteria from the family Methylophilaceae. Species of the latter two genera have not been previously shown to oxidize methane and may have been cross-feeding on methanol, but species of both genera were heavily labeled after just 3 days. pmoA sequences were affiliated with species of Methylococcaceae, but most were not closely related to cultured methanotrophs. Second, (13)C ethane was consumed by members of a novel group of Methylococcaceae. Growth with ethane as the major carbon source has not previously been observed in members of the Methylococcaceae; a highly divergent pmoA-like gene detected in the (13)C-labeled DNA may encode an ethane monooxygenase. Third, (13)C propane was consumed by members of a group of unclassified Gammaproteobacteria species not previously linked to propane oxidation. This study identifies several bacterial lineages as participants in the oxidation of gaseous hydrocarbons in marine seeps and supports the idea of an alternate function for some pmoA-like genes.}, } @article {pmid20673351, year = {2010}, author = {Bittner, L and Halary, S and Payri, C and Cruaud, C and de Reviers, B and Lopez, P and Bapteste, E}, title = {Some considerations for analyzing biodiversity using integrative metagenomics and gene networks.}, journal = {Biology direct}, volume = {5}, number = {}, pages = {47}, pmid = {20673351}, issn = {1745-6150}, mesh = {Animals ; *Biodiversity ; Gene Regulatory Networks/*genetics ; Humans ; Metagenomics/*methods ; Models, Theoretical ; }, abstract = {BACKGROUND: Improving knowledge of biodiversity will benefit conservation biology, enhance bioremediation studies, and could lead to new medical treatments. However there is no standard approach to estimate and to compare the diversity of different environments, or to study its past, and possibly, future evolution.

We argue that there are two conditions for significant progress in the identification and quantification of biodiversity. First, integrative metagenomic studies - aiming at the simultaneous examination (or even better at the integration) of observations about the elements, functions and evolutionary processes captured by the massive sequencing of multiple markers - should be preferred over DNA barcoding projects and over metagenomic projects based on a single marker. Second, such metagenomic data should be studied with novel inclusive network-based approaches, designed to draw inferences both on the many units and on the many processes present in the environments.

TESTING THE HYPOTHESIS: We reached these conclusions through a comparison of the theoretical foundations of two molecular approaches seeking to assess biodiversity: metagenomics (mostly used on prokaryotes and protists) and DNA barcoding (mostly used on multicellular eukaryotes), and by pragmatic considerations of the issues caused by the 'species problem' in biodiversity studies.

Evolutionary gene networks reduce the risk of producing biodiversity estimates with limited explanatory power, biased either by unequal rates of LGT, or difficult to interpret due to (practical) problems caused by type I and type II grey zones. Moreover, these networks would easily accommodate additional (meta)transcriptomic and (meta)proteomic data.}, } @article {pmid21966903, year = {2010}, author = {Webster, NS and Taylor, MW and Behnam, F and Lücker, S and Rattei, T and Whalan, S and Horn, M and Wagner, M}, title = {Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts.}, journal = {Environmental microbiology}, volume = {12}, number = {8}, pages = {2070-2082}, pmid = {21966903}, issn = {1462-2920}, mesh = {Animals ; Australia ; Bacteria/classification/*genetics/growth & development ; *Biodiversity ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; }, abstract = {Marine sponges contain complex bacterial communities of considerable ecological and biotechnological importance, with many of these organisms postulated to be specific to sponge hosts. Testing this hypothesis in light of the recent discovery of the rare microbial biosphere, we investigated three Australian sponges by massively parallel 16S rRNA gene tag pyrosequencing. Here we show bacterial diversity that is unparalleled in an invertebrate host, with more than 250,000 sponge-derived sequence tags being assigned to 23 bacterial phyla and revealing up to 2996 operational taxonomic units (95% sequence similarity) per sponge species. Of the 33 previously described 'sponge-specific' clusters that were detected in this study, 48% were found exclusively in adults and larvae - implying vertical transmission of these groups. The remaining taxa, including 'Poribacteria', were also found at very low abundance among the 135,000 tags retrieved from surrounding seawater. Thus, members of the rare seawater biosphere may serve as seed organisms for widely occurring symbiont populations in sponges and their host association might have evolved much more recently than previously thought.}, } @article {pmid20668488, year = {2011}, author = {Quaiser, A and Zivanovic, Y and Moreira, D and López-García, P}, title = {Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara.}, journal = {The ISME journal}, volume = {5}, number = {2}, pages = {285-304}, pmid = {20668488}, issn = {1751-7370}, mesh = {*Archaea/classification/genetics ; *Bacteria/classification/genetics ; Biodiversity ; Enzymes/genetics ; *Eukaryota/classification/genetics ; Genes, rRNA/genetics ; Geologic Sediments/*microbiology ; *Metagenome ; Metagenomics ; Molecular Sequence Data ; Oceans and Seas ; Phylogeny ; *Plankton/genetics/microbiology ; }, abstract = {To extend comparative metagenomic analyses of the deep-sea, we produced metagenomic data by direct 454 pyrosequencing from bathypelagic plankton (1000 m depth) and bottom sediment of the Sea of Marmara, the gateway between the Eastern Mediterranean and the Black Seas. Data from small subunit ribosomal RNA (SSU rRNA) gene libraries and direct pyrosequencing of the same samples indicated that Gamma- and Alpha-proteobacteria, followed by Bacteroidetes, dominated the bacterial fraction in Marmara deep-sea plankton, whereas Planctomycetes, Delta- and Gamma-proteobacteria were the most abundant groups in high bacterial-diversity sediment. Group I Crenarchaeota/Thaumarchaeota dominated the archaeal plankton fraction, although group II and III Euryarchaeota were also present. Eukaryotes were highly diverse in SSU rRNA gene libraries, with group I (Duboscquellida) and II (Syndiniales) alveolates and Radiozoa dominating plankton, and Opisthokonta and Alveolates, sediment. However, eukaryotic sequences were scarce in pyrosequence data. Archaeal amo genes were abundant in plankton, suggesting that Marmara planktonic Thaumarchaeota are ammonia oxidizers. Genes involved in sulfate reduction, carbon monoxide oxidation, anammox and sulfatases were over-represented in sediment. Genome recruitment analyses showed that Alteromonas macleodii 'surface ecotype', Pelagibacter ubique and Nitrosopumilus maritimus were highly represented in 1000 m-deep plankton. A comparative analysis of Marmara metagenomes with ALOHA deep-sea and surface plankton, whale carcasses, Peru subsurface sediment and soil metagenomes clustered deep-sea Marmara plankton with deep-ALOHA plankton and whale carcasses, likely because of the suboxic conditions in the deep Marmara water column. The Marmara sediment clustered with the soil metagenome, highlighting the common ecological role of both types of microbial communities in the degradation of organic matter and the completion of biogeochemical cycles.}, } @article {pmid20668241, year = {2010}, author = {Grice, EA and Snitkin, ES and Yockey, LJ and Bermudez, DM and , and Liechty, KW and Segre, JA}, title = {Longitudinal shift in diabetic wound microbiota correlates with prolonged skin defense response.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {33}, pages = {14799-14804}, pmid = {20668241}, issn = {1091-6490}, support = {DP2 DK083085/DK/NIDDK NIH HHS/United States ; R56 DK080672/DK/NIDDK NIH HHS/United States ; 1R56DK080672-01A1/DK/NIDDK NIH HHS/United States ; 7DP2DK083085-02./DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/growth & development ; Bacterial Infections/genetics/microbiology/*physiopathology ; Biodiversity ; Cluster Analysis ; Diabetes Mellitus, Type 2/genetics/*physiopathology ; Female ; Gene Expression Profiling ; Host-Pathogen Interactions ; Metagenome/genetics ; Mice ; Mice, Knockout ; Molecular Sequence Data ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; Receptors, Leptin/genetics/physiology ; Sequence Analysis, DNA ; Skin/metabolism/microbiology/*physiopathology ; Staphylococcus/genetics/physiology ; Time Factors ; *Wound Healing ; }, abstract = {Diabetics frequently suffer from chronic, nonhealing wounds. Although bacterial colonization and/or infection are generally acknowledged to negatively impact wound healing, the precise relationship between the microbial community and impaired wound healing remains unclear. Because the host cutaneous defense response is proposed to play a key role in modulating microbial colonization, we longitudinally examined the diabetic wound microbiome in tandem with host tissue gene expression. By sequencing 16S ribosomal RNA genes, we show that a longitudinal selective shift in wound microbiota coincides with impaired healing in diabetic mice (Lepr(db/db); db/db). We demonstrate a parallel shift in longitudinal gene expression that occurs in a cluster of genes related to the immune response. Further, we establish a correlation between relative abundance of Staphylococcus spp. and the expression of cutaneous defense response genes. Our data demonstrate that integrating two types of global datasets lends a better understanding to the dynamics governing host-microbe interactions.}, } @article {pmid20665239, year = {2011}, author = {Coman, C and Bica, A and Drugă, B and Barbu-Tudoran, L and Dragoş, N}, title = {Methodological constraints in the molecular biodiversity study of a thermomineral spring cyanobacterial mat: a case study.}, journal = {Antonie van Leeuwenhoek}, volume = {99}, number = {2}, pages = {271-281}, doi = {10.1007/s10482-010-9486-5}, pmid = {20665239}, issn = {1572-9699}, mesh = {*Biodiversity ; Cluster Analysis ; Cyanobacteria/*classification/genetics/isolation & purification ; DNA Fingerprinting/methods ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/genetics ; Geologic Sediments/*microbiology ; Hot Springs/*microbiology ; Metagenomics/*methods ; Microscopy/methods ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Romania ; Sequence Analysis, DNA ; }, abstract = {The biodiversity of a specific cyanobacterial mat associated to a thermomineral spring from the Western Plain of Romania was investigated. Light and electron microscopy, together with molecular tools (denaturing gradient gel electrophoresis-DGGE, automated ribosomal intergenic spacer analysis-ARISA and amplified ribosomal DNA restriction analysis-ARDRA), based on 16S rDNA and 16S-23S internal transcribed spacer markers were used. Based on the partial 16S rRNA fragments sequenced, eight cyanobacterial taxons were identified, all belonging to the Oscillatoriales order, Phormidium and Leptolyngbya being dominant. A significant difference was observed, in comparison with the morphological approach. In certain conditions, DGGE can provide misleading information due to multiple melting domains in the same sequence, to multiple rrn operons in the same genome and due to unspecific hybridization among closely related sequences. This can lead to an overestimated species abundance which can cause incorrect description of the microbial community investigated. Additional techniques, such as ARISA and ARDRA, can improve the microbial biodiversity studies, thus providing optimal results.}, } @article {pmid20664551, year = {2010}, author = {Faith, JJ and Rey, FE and O'Donnell, D and Karlsson, M and McNulty, NP and Kallstrom, G and Goodman, AL and Gordon, JI}, title = {Creating and characterizing communities of human gut microbes in gnotobiotic mice.}, journal = {The ISME journal}, volume = {4}, number = {9}, pages = {1094-1098}, pmid = {20664551}, issn = {1751-7370}, support = {R01 DK070977-07/DK/NIDDK NIH HHS/United States ; P01 DK078669/DK/NIDDK NIH HHS/United States ; R01 DK030292/DK/NIDDK NIH HHS/United States ; R01 DK070977/DK/NIDDK NIH HHS/United States ; DK30292/DK/NIDDK NIH HHS/United States ; DK70977/DK/NIDDK NIH HHS/United States ; P01 DK078669-04/DK/NIDDK NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; R37 DK030292-29/DK/NIDDK NIH HHS/United States ; DK78669/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Biota ; Gastrointestinal Tract/*microbiology ; *Germ-Free Life ; Humans ; *Metagenome ; Mice ; Models, Animal ; }, } @article {pmid20663617, year = {2011}, author = {Lowe, BA and Marsh, TL and Isaacs-Cosgrove, N and Kirkwood, RN and Kiupel, M and Mulks, MH}, title = {Microbial communities in the tonsils of healthy pigs.}, journal = {Veterinary microbiology}, volume = {147}, number = {3-4}, pages = {346-357}, doi = {10.1016/j.vetmic.2010.06.025}, pmid = {20663617}, issn = {1873-2542}, mesh = {Animals ; Bacteria/classification/genetics/growth & development/isolation & purification ; *Bacterial Physiological Phenomena ; Bacterial Typing Techniques ; Biodiversity ; Culture Techniques ; Metagenome/*physiology ; Palatine Tonsil/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Swine ; }, abstract = {The tonsils of mammals such as humans and pigs are colonized with an extensive microbiota and are frequently the site for asymptomatic carriage of bacterial pathogens. The goal of this study was to determine the composition of the microbial community of the tonsils in healthy pigs. Tonsils were collected from eight pigs from two different healthy herds. Samples of the tonsils from each pig were used for culture dependent and culture independent identification of the microbial community. Aerobic cultivation identified Pasteurella multocida, Actinobacillus spp., Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus suis, Streptococcus dysgalactiae, and Escherichia coli from ≥ 50% of the pigs in both herds. For culture independent studies, microbial community members were identified by 16S rRNA sequences using the Ribosomal Database Project Pipeline programs developed at Michigan State University. Dominant genera identified by 16S rRNA analysis in pigs from both herds included Actinobacillus, Haemophilus, Pasteurella, Porphyromonas, Fusobacterium, Bacteroides, and Prevotella. These genera were detected in nearly every pig regardless of herd. In contrast, there was an asymmetric distribution of minor genera between the two herds, suggesting herd-specific differences in the microbial communities. In addition, we demonstrated primer bias between two frequently used forward primers when targeting the tonsillar community. Our results suggest that the major bacterial community members found in porcine tonsils are the same regardless of herd, while the minor species are unique to each herd. This is the first analysis using 16S rRNA sequence libraries of the composition of microbial communities in the porcine upper respiratory tract.}, } @article {pmid20646876, year = {2010}, author = {Xenoulis, PG and Gray, PL and Brightsmith, D and Palculict, B and Hoppes, S and Steiner, JM and Tizard, I and Suchodolski, JS}, title = {Molecular characterization of the cloacal microbiota of wild and captive parrots.}, journal = {Veterinary microbiology}, volume = {146}, number = {3-4}, pages = {320-325}, doi = {10.1016/j.vetmic.2010.05.024}, pmid = {20646876}, issn = {1873-2542}, mesh = {Animals ; Animals, Wild/microbiology ; Bacteria/classification/*genetics ; Biodiversity ; Cloaca/*microbiology ; DNA, Bacterial/genetics ; Metagenome/*genetics ; Molecular Sequence Data ; Parrots/*microbiology ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The gastrointestinal microbiota plays a fundamental role in health and disease. Only limited data are available about the composition of the intestinal microbiota of captive animals compared to those of wild animals. The aim of the present study was to characterize the cloacal microbiota of apparently healthy wild and captive parrots. A total of 16 parrots, 8 wild and 8 captive, belonging to 3 different species, were used in this study. Cloacal material was collected via cloacal swabbing. DNA was extracted and 16S rRNA genes were amplified using universal bacterial primers. Constructed 16S rRNA gene clone libraries were compared between groups. A total of 518 clones were analyzed, and 49 operational taxonomic units (OTUs) were identified. The OTUs were classified in 4 bacterial phyla: Firmicutes (72.9%), Proteobacteria (14.9%), Actinobacteria (12%), and Bacteroidetes (0.2%). Bacterial diversity was significantly lower in wild birds than in captive birds. Principal component analysis based on the Unifrac distance metric indicated that the cloacal microbiota differed between wild and captive parrots. Staphylococcus saprophyticus was significantly more abundant in wild birds, while Escherichia coli was significantly more abundant in captive birds. In conclusion, wild and captive parrots appear to have differences in the composition of their cloacal bacterial microbiota. The clinical significance of these differences remains to be determined.}, } @article {pmid20639117, year = {2010}, author = {Liaw, RB and Cheng, MP and Wu, MC and Lee, CY}, title = {Use of metagenomic approaches to isolate lipolytic genes from activated sludge.}, journal = {Bioresource technology}, volume = {101}, number = {21}, pages = {8323-8329}, doi = {10.1016/j.biortech.2010.05.091}, pmid = {20639117}, issn = {1873-2976}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Bacteria/*genetics ; Bacterial Proteins/chemistry/genetics ; Biodiversity ; Cloning, Molecular ; Conserved Sequence ; Gene Library ; Genes, Bacterial/*genetics ; Lipolysis/*genetics ; Metagenomics/*methods ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; }, abstract = {The aims of this study were to access the bacterial diversity and isolate lipolytic genes using the metagenomic approach in activated sludge of a swine wastewater treatment facility. On the basis of BLASTN analysis of 16S rRNA gene clones, most of these communities (90%) were of uncultivated bacteria. The metagenomic library was constructed using a plasmid vector and DNA extracted directly from activated sludge samples. The average insert size was approximately 5.1 kb. A total of 12 unique and lipolytic clones were obtained using the tributyrin plate assay. The rate of discovering a lipolytic clone in this study was as high as 0.31%. Molecular analysis revealed that most of the 16 putative lipolytic enzymes showed 28-55% identity with non-redundant protein sequences in the database. Briefly, this study demonstrates that activated sludge is an ideal bioresource for isolating new lipolytic enzymes.}, } @article {pmid20629946, year = {2010}, author = {Nelson, A and De Soyza, A and Bourke, SJ and Perry, JD and Cummings, SP}, title = {Assessment of sample handling practices on microbial activity in sputum samples from patients with cystic fibrosis.}, journal = {Letters in applied microbiology}, volume = {51}, number = {3}, pages = {272-277}, doi = {10.1111/j.1472-765X.2010.02891.x}, pmid = {20629946}, issn = {1472-765X}, mesh = {Adult ; Bacteria/*classification/genetics/isolation & purification ; Bacterial Infections/diagnosis/microbiology ; *Biodiversity ; Cystic Fibrosis/*complications ; Electrophoresis, Polyacrylamide Gel ; Fungi/*classification/genetics/isolation & purification ; Humans ; Metagenome ; Molecular Sequence Data ; Mycoses/diagnosis/microbiology ; Nucleic Acid Denaturation ; Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Specimen Handling/*methods ; Sputum/*microbiology ; Temperature ; Time Factors ; }, abstract = {AIM: The aim of this study was to quantitatively and qualitatively assess the effect of sample storage on the metabolically active microbial community found in sputum samples from patients with cystic fibrosis (CF).

METHODS: Sputum samples were collected and split in two equal aliquots one of which was immersed in RNAlater and refrigerated immediately, the second stored at room temperature for 24 h and RNAlater was subsequently added. mRNA was extracted, and RT-PCR-DGGE and qPCR analysis of the bacterial and fungal communities was carried out.

RESULTS: Significant differences in the bacterial communities between the two protocols were observed but there were no significant difference seen in the fungal community analyses. Analysis by qPCR demonstrated that room temperature storage gave statistically significant increases in eubacteria and Pseudomonas spp. and a statistically significant decrease in those of Haemophilus influenzae.

CONCLUSIONS: The analysis of metabolically active microbial communities from CF sputum using molecular techniques indicated that samples should be stored at 4 degrees C upon addition of RNAlater to obtain an accurate depiction of the CF lung microbiota. Also, storing respiratory samples at room temperature may cause an over representation of Pseudomonas aeruginosa and mask the presence of other clinically significant organisms.}, } @article {pmid20622123, year = {2010}, author = {Beloqui, A and Nechitaylo, TY and López-Cortés, N and Ghazi, A and Guazzaroni, ME and Polaina, J and Strittmatter, AW and Reva, O and Waliczek, A and Yakimov, MM and Golyshina, OV and Ferrer, M and Golyshin, PN}, title = {Diversity of glycosyl hydrolases from cellulose-depleting communities enriched from casts of two earthworm species.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {17}, pages = {5934-5946}, pmid = {20622123}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification/*enzymology/genetics ; *Biota ; Cellulose/*metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Feces/microbiology ; Gene Library ; *Genetic Variation ; Glycoside Hydrolases/classification/*genetics/*metabolism ; Metagenome ; Molecular Sequence Data ; Oligochaeta/*microbiology ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {The guts and casts of earthworms contain microbial assemblages that process large amounts of organic polymeric substrates from plant litter and soil; however, the enzymatic potential of these microbial communities remains largely unexplored. In the present work, we retrieved carbohydrate-modifying enzymes through the activity screening of metagenomic fosmid libraries from cellulose-depleting microbial communities established with the fresh casts of two earthworm species, Aporrectodea caliginosa and Lumbricus terrestris, as inocula. Eight glycosyl hydrolases (GHs) from the A. caliginosa-derived community were multidomain endo-beta-glucanases, beta-glucosidases, beta-cellobiohydrolases, beta-galactosidase, and beta-xylosidases of known GH families. In contrast, two GHs derived from the L. terrestris microbiome had no similarity to any known GHs and represented two novel families of beta-galactosidases/alpha-arabinopyranosidases. Members of these families were annotated in public databases as conserved hypothetical proteins, with one being structurally related to isomerases/dehydratases. This study provides insight into their biochemistry, domain structures, and active-site architecture. The two communities were similar in bacterial composition but significantly different with regard to their eukaryotic inhabitants. Further sequence analysis of fosmids and plasmids bearing the GH-encoding genes, along with oligonucleotide usage pattern analysis, suggested that those apparently originated from Gammaproteobacteria (pseudomonads and Cellvibrio-like organisms), Betaproteobacteria (Comamonadaceae), and Alphaproteobacteria (Rhizobiales).}, } @article {pmid20613793, year = {2011}, author = {Giongo, A and Gano, KA and Crabb, DB and Mukherjee, N and Novelo, LL and Casella, G and Drew, JC and Ilonen, J and Knip, M and Hyöty, H and Veijola, R and Simell, T and Simell, O and Neu, J and Wasserfall, CH and Schatz, D and Atkinson, MA and Triplett, EW}, title = {Toward defining the autoimmune microbiome for type 1 diabetes.}, journal = {The ISME journal}, volume = {5}, number = {1}, pages = {82-91}, pmid = {20613793}, issn = {1751-7370}, mesh = {Age Factors ; Autoantibodies/blood ; Bacteria/*classification/genetics/isolation & purification ; Biodiversity ; Case-Control Studies ; Child ; Child, Preschool ; Diabetes Mellitus, Type 1/diagnosis/*microbiology ; Feces/microbiology ; Humans ; Infant ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Several studies have shown that gut bacteria have a role in diabetes in murine models. Specific bacteria have been correlated with the onset of diabetes in a rat model. However, it is unknown whether human intestinal microbes have a role in the development of autoimmunity that often leads to type 1 diabetes (T1D), an autoimmune disorder in which insulin-secreting pancreatic islet cells are destroyed. High-throughput, culture-independent approaches identified bacteria that correlate with the development of T1D-associated autoimmunity in young children who are at high genetic risk for this disorder. The level of bacterial diversity diminishes overtime in these autoimmune subjects relative to that of age-matched, genotype-matched, nonautoimmune individuals. A single species, Bacteroides ovatus, comprised nearly 24% of the total increase in the phylum Bacteroidetes in cases compared with controls. Conversely, another species in controls, represented by the human firmicute strain CO19, represented nearly 20% of the increase in Firmicutes compared with cases overtime. Three lines of evidence are presented that support the notion that, as healthy infants approach the toddler stage, their microbiomes become healthier and more stable, whereas, children who are destined for autoimmunity develop a microbiome that is less diverse and stable. Hence, the autoimmune microbiome for T1D may be distinctly different from that found in healthy children. These data also suggest bacterial markers for the early diagnosis of T1D. In addition, bacteria that negatively correlated with the autoimmune state may prove to be useful in the prevention of autoimmunity development in high-risk children.}, } @article {pmid20613791, year = {2011}, author = {Duhaime, MB and Wichels, A and Waldmann, J and Teeling, H and Glöckner, FO}, title = {Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1.}, journal = {The ISME journal}, volume = {5}, number = {1}, pages = {107-121}, pmid = {20613791}, issn = {1751-7370}, mesh = {Aquatic Organisms ; Bacteriophages/classification/*genetics/physiology ; Biodiversity ; Codon ; DNA Packaging ; Genome, Viral/*genetics ; Molecular Sequence Data ; Phylogeny ; Proteome/genetics ; Pseudoalteromonas/genetics/*virology ; Virus Integration ; Virus Replication ; }, abstract = {Marine phages have an astounding global abundance and ecological impact. However, little knowledge is derived from phage genomes, as most of the open reading frames in their small genomes are unknown, novel proteins. To infer potential functional and ecological relevance of sequenced marine Pseudoalteromonas phage H105/1, two strategies were used. First, similarity searches were extended to include six viral and bacterial metagenomes paired with their respective environmental contextual data. This approach revealed 'ecogenomic' patterns of Pseudoalteromonas phage H105/1, such as its estuarine origin. Second, intrinsic genome signatures (phylogenetic, codon adaptation and tetranucleotide (tetra) frequencies) were evaluated on a resolved intra-genomic level to shed light on the evolution of phage functional modules. On the basis of differential codon adaptation of Phage H105/1 proteins to the sequenced Pseudoalteromonas spp., regions of the phage genome with the most 'host'-adapted proteins also have the strongest bacterial tetra signature, whereas the least 'host'-adapted proteins have the strongest phage tetra signature. Such a pattern may reflect the evolutionary history of the respective phage proteins and functional modules. Finally, analysis of the structural proteome identified seven proteins that make up the mature virion, four of which were previously unknown. This integrated approach combines both novel and classical strategies and serves as a model to elucidate ecological inferences and evolutionary relationships from phage genomes that typically abound with unknown gene content.}, } @article {pmid20607404, year = {2011}, author = {Perumbakkam, S and Mitchell, EA and Craig, AM}, title = {Changes to the rumen bacterial population of sheep with the addition of 2,4,6-trinitrotoluene to their diet.}, journal = {Antonie van Leeuwenhoek}, volume = {99}, number = {2}, pages = {231-240}, doi = {10.1007/s10482-010-9481-x}, pmid = {20607404}, issn = {1572-9699}, mesh = {Animals ; Bacteria/*classification/*drug effects/isolation & purification ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Diet/*methods ; Metagenome ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; Sheep/*microbiology ; Trinitrotoluene/*administration & dosage/metabolism ; }, abstract = {Previous work has shown that bacterial isolates from the sheep rumen are capable of detoxifying 2,4,6-trinitrotoluene (TNT) into polar constituents. In this study, the dietary effects of TNT on the sheep rumen microbial community were evaluated using molecular microbiology ecology tools. Rumen samples were collected from sheep fed with and without TNT added to their diet, genomic DNA was extracted, and the 16S rRNA-V3 gene marker was used to quantify changes in the microbial population in the rumen. Control and treatment samples yielded 533 sequences. Phylogenetic analyses were performed to determine the microbial changes between the two conditions. Results indicated the predominant bacterial populations present in the rumen were comprised of the phyla Firmicutes and Bacteroidetes, irrespective of presence/absence of TNT in the diet. Significant differences (P < 0.001) were found between the community structure of the bacteria under TNT (-) and TNT (+) diets. Examination of the TNT (+) diet showed an increase in the clones belonging to family Ruminococcaceae, which have previously been shown to degrade TNT in pure culture experiments.}, } @article {pmid20601513, year = {2010}, author = {Lindsay, EA and Colloff, MJ and Gibb, NL and Wakelin, SA}, title = {The abundance of microbial functional genes in grassy woodlands is influenced more by soil nutrient enrichment than by recent weed invasion or livestock exclusion.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {16}, pages = {5547-5555}, pmid = {20601513}, issn = {1098-5336}, mesh = {Animals ; Animals, Domestic ; *Biodiversity ; Biomass ; Ecosystem ; *Gene Expression Profiling ; Genes ; Metabolic Networks and Pathways/*genetics ; *Metagenome ; Nitrogen/*metabolism ; Phosphorus/analysis ; Plants ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {A diverse soil microbial community is involved in nitrogen cycling, and these microbes can be affected by land management practices and weed invasion. We surveyed 20 woodlands with a history of livestock grazing, with livestock recently excluded from 10 sites. We investigated whether soil nutrients were lower when grazing was excluded and higher when exotic grasses dominated the understory. Second, using quantitative real-time PCR, we investigated whether microbial nitrogen functional gene (NFG) abundance was altered with soil nutrient enrichment, livestock exclusion, and exotic grass invasion. The target genes were chiA (decomposition-ammonification), nifH (nitrogen fixation), nirK and narG (denitrification), and bacterial amoA (nitrification). Woodland soils were enriched in phosphorus and nitrogen compared to reference condition sites, but soil nutrients were not lower following livestock exclusion. Total nitrogen and nifH were negatively correlated in grazed woodlands, suggesting that aboveground herbivory reduces the capacity for belowground nitrogen fixation. Woodlands dominated by exotic grasses had higher levels of nitrate, narG, and nirK than those dominated by native grasses. We hypothesize that the increase in potential for denitrification was due to increases in soil nitrate, rather than changes in plant composition. Overall, soil physicochemistry explained more variation in NFG abundance than livestock presence or plant invasion, particularly for chiA and bacterial amoA, with significant relationships between the abundance of all five NFGs and total nitrogen or nitrate. All woodlands investigated had a history of anthropogenic disturbance and nutrification, and soil nutrient levels and the abundance of NFGs are likely to be related to long-term land management practices.}, } @article {pmid20600268, year = {2010}, author = {Siddhapura, PK and Vanparia, S and Purohit, MK and Singh, SP}, title = {Comparative studies on the extraction of metagenomic DNA from the saline habitats of Coastal Gujarat and Sambhar Lake, Rajasthan (India) in prospect of molecular diversity and search for novel biocatalysts.}, journal = {International journal of biological macromolecules}, volume = {47}, number = {3}, pages = {375-379}, doi = {10.1016/j.ijbiomac.2010.06.004}, pmid = {20600268}, issn = {1879-0003}, mesh = {Bacterial Proteins/genetics ; *Biocatalysis ; *Biodiversity ; DNA/genetics/*isolation & purification ; *Ecosystem ; Electrophoresis, Agar Gel ; Endopeptidases/genetics ; *Fresh Water ; India ; *Metagenomics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics/isolation & purification ; Spectrophotometry ; }, abstract = {Extraction of total DNA from a given habitat assumes significance in metagenomics, due to the requirement of inhibitor free and high quality metagenome in good quantity for applications in molecular biology. DNA extraction and its quality assessment for PCR applications from saline soils of Coastal Gujarat and Sambhar Soda Lake, Rajasthan in India is described in a comparative manner. The mechanical and soft lysis methods were simple and efficient for rapid isolation of PCR amplifiable total genomic DNA. The results are significant as only few extreme environments, particularly saline habitats are explored for their metagenomic potential.}, } @article {pmid20599611, year = {2010}, author = {Dijkshoorn, L and De Vos, P and Dedeurwaerdere, T}, title = {Understanding patterns of use and scientific opportunities in the emerging global microbial commons.}, journal = {Research in microbiology}, volume = {161}, number = {6}, pages = {407-413}, doi = {10.1016/j.resmic.2010.06.001}, pmid = {20599611}, issn = {1769-7123}, mesh = {Access to Information ; Agriculture ; Animal Feed ; Biological Specimen Banks ; Food Microbiology ; *Information Dissemination ; *Information Management ; Information Seeking Behavior ; *International Cooperation ; *Microbiology ; Soil Microbiology ; *Technology Transfer ; }, abstract = {Rapidly growing global networking has induced and supported an increased interest in the life sciences in such general issues as health, climate change, food security and biodiversity. Therefore, the need to address and share research data and materials in a systematic way emerged almost simultaneously. This movement has been described as the so-called global research commons. Also in microbiology, where the sharing of microbiological materials is a key issue, microbial commons is attracting attention. Microbiology is currently facing great challenges with the advances of high throughput screening and next-generation whole genome sequencing. Furthermore, the exploration and use of microorganisms in agriculture and food production are increasing so as to safeguard global food and feed production. Further to several meetings on the subject, a special issue of Research in Microbiology is dedicated to Microbial Research Commons with a series of reviews elaborating its major pay-offs and needs in basic and applied microbiology. This paper gives an introduction to these articles covering a range of topics. These include the role of public culture collections and biological resource centers and legal aspects in the exchange of materials, microbial classification, an internet-based platform for data-sharing, applications in agriculture and food production, and challenges in metagenomics and extremophile research.}, } @article {pmid20582590, year = {2011}, author = {Mwirichia, R and Cousin, S and Muigai, AW and Boga, HI and Stackebrandt, E}, title = {Bacterial diversity in the haloalkaline Lake Elmenteita, Kenya.}, journal = {Current microbiology}, volume = {62}, number = {1}, pages = {209-221}, pmid = {20582590}, issn = {1432-0991}, mesh = {Bacteria/*classification/*genetics/isolation & purification ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Kenya ; Metagenome ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Lake Elmenteita is one of the alkaline saline lakes within the Kenyan Rift valley. The lake is situated on the floor of the Kenyan Rift Valley at 1,776 m above sea level and has no direct outlet. The microbial diversity of the lake was investigated using a culture-independent approach. Five different sampling points were selected randomly within the lake. Wet sediments and water samples were collected from each sampling point. In addition, dry mud cake was collected from three points where the lake had dried. DNA was extracted from the samples and the 16S rRNA genes amplified using universal primers for Bacteria. Thirteen clone libraries were constructed using the PCR amplified 16S rRNA genes. A total of 1,663 clones were picked. Representative clones were selected using ARDRA technique for sequencing. 655 partial and non-chimeric clone sequences indicated the presence of 37 orders in the Domain Bacteria. Cyanobacteria were the most abundant clones in terms of numbers whereas members of the phylum Firmicutes group were the second in terms of numbers but the most diverse in terms of genera represented. All clones affiliated to the class Betaproteobacteria originated from DNA obtained from the water samples. Analysis using BLAST showed that 93.1% of the sequenced clones had similarity values below 98% to both cultured and as yet uncultured bacteria, resulting in 596 phylotypes. Therefore, it can be concluded that Lake Elmenteita harbours phylogenetically diverse groups of bacteria involved in complex metabolic interactions within the Lake's ecosystem.}, } @article {pmid20581188, year = {2010}, author = {Hong, PY and Hwang, C and Ling, F and Andersen, GL and LeChevallier, MW and Liu, WT}, title = {Pyrosequencing analysis of bacterial biofilm communities in water meters of a drinking water distribution system.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {16}, pages = {5631-5635}, pmid = {20581188}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; *Biofilms ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Metagenome ; Microscopy, Electron, Scanning ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; *Water Microbiology ; }, abstract = {The applicability of 454 pyrosequencing to characterize bacterial biofilm communities from two water meters of a drinking water distribution system was assessed. Differences in bacterial diversity and composition were observed. A better understanding of the bacterial ecology of drinking water biofilms will allow for effective management of water quality in distribution systems.}, } @article {pmid20581179, year = {2010}, author = {Weckx, S and Van der Meulen, R and Allemeersch, J and Huys, G and Vandamme, P and Van Hummelen, P and De Vuyst, L}, title = {Community dynamics of bacteria in sourdough fermentations as revealed by their metatranscriptome.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {16}, pages = {5402-5408}, pmid = {20581179}, issn = {1098-5336}, mesh = {Bacteria/*classification/growth & development/*isolation & purification ; *Biodiversity ; Ecosystem ; Fermentation ; *Food Microbiology ; *Gene Expression Profiling ; *Metagenome ; Microarray Analysis/methods ; Time Factors ; Triticum ; }, abstract = {The lactic acid bacterial (LAB) community dynamics of two wheat and two spelt sourdough fermentations that were daily back-slopped were monitored during a period of 10 days by hybridizing time-related RNA samples, representing the metatranscriptome, to an LAB functional gene microarray. To indicate the species present in each hybridized sample, annotation information for the 2,269 oligonucleotides on the microarray was used. The overall hybridization data revealed that after a transition phase of 5 days, in which atypical sourdough LAB species, including Enterococcus species, were found, a stabilized ecosystem was established with Lactobacillus plantarum and Lactobacillus fermentum as the dominating LAB species. Compared with the combined outcome of culture-dependent and culture-independent identification techniques, the microarray data revealed a functional role for Lactococcus lactis in the early stage ecosystem and the dominance of Pediococcus pentosaceus in most of the fermentations, besides L. plantarum and L. fermentum. Consequently, metatranscriptome hybridization data obtained using an LAB functional gene microarray was shown to be an interesting alternative to microbiological analysis of the community dynamics of complex food ecosystems.}, } @article {pmid20562281, year = {2010}, author = {Van den Abbeele, P and Grootaert, C and Marzorati, M and Possemiers, S and Verstraete, W and Gérard, P and Rabot, S and Bruneau, A and El Aidy, S and Derrien, M and Zoetendal, E and Kleerebezem, M and Smidt, H and Van de Wiele, T}, title = {Microbial community development in a dynamic gut model is reproducible, colon region specific, and selective for Bacteroidetes and Clostridium cluster IX.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {15}, pages = {5237-5246}, pmid = {20562281}, issn = {1098-5336}, mesh = {Bacteroidetes/*growth & development ; *Biodiversity ; Clostridium/*growth & development ; Colon/*microbiology ; Humans ; *Metagenome ; Models, Biological ; Models, Theoretical ; *Selection, Genetic ; }, abstract = {Dynamic, multicompartment in vitro gastrointestinal simulators are often used to monitor gut microbial dynamics and activity. These reactors need to harbor a microbial community that is stable upon inoculation, colon region specific, and relevant to in vivo conditions. Together with the reproducibility of the colonization process, these criteria are often overlooked when the modulatory properties from different treatments are compared. We therefore investigated the microbial colonization process in two identical simulators of the human intestinal microbial ecosystem (SHIME), simultaneously inoculated with the same human fecal microbiota with a high-resolution phylogenetic microarray: the human intestinal tract chip (HITChip). Following inoculation of the in vitro colon compartments, microbial community composition reached steady state after 2 weeks, whereas 3 weeks were required to reach functional stability. This dynamic colonization process was reproducible in both SHIME units and resulted in highly diverse microbial communities which were colon region specific, with the proximal regions harboring saccharolytic microbes (e.g., Bacteroides spp. and Eubacterium spp.) and the distal regions harboring mucin-degrading microbes (e.g., Akkermansia spp.). Importantly, the shift from an in vivo to an in vitro environment resulted in an increased Bacteroidetes/Firmicutes ratio, whereas Clostridium cluster IX (propionate producers) was enriched compared to clusters IV and XIVa (butyrate producers). This was supported by proportionally higher in vitro propionate concentrations. In conclusion, high-resolution analysis of in vitro-cultured gut microbiota offers new insight on the microbial colonization process and indicates the importance of digestive parameters that may be crucial in the development of new in vitro models.}, } @article {pmid20562276, year = {2010}, author = {Shartau, SL and Yurkiw, M and Lin, S and Grigoryan, AA and Lambo, A and Park, HS and Lomans, BP and van der Biezen, E and Jetten, MS and Voordouw, G}, title = {Ammonium concentrations in produced waters from a mesothermic oil field subjected to nitrate injection decrease through formation of denitrifying biomass and anammox activity.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {15}, pages = {4977-4987}, pmid = {20562276}, issn = {1098-5336}, support = {232937/ERC_/European Research Council/International ; }, mesh = {Bacteria/classification/genetics/*metabolism ; *Biodiversity ; Biomass ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Metagenome ; Molecular Sequence Data ; Nitrates/*metabolism ; Nucleic Acid Denaturation ; Oxidation-Reduction ; Phylogeny ; Quaternary Ammonium Compounds/*analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Sulfides/metabolism ; Water/*chemistry ; }, abstract = {Community analysis of a mesothermic oil field, subjected to continuous field-wide injection of nitrate to remove sulfide, with denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA genes indicated the presence of heterotrophic and sulfide-oxidizing, nitrate-reducing bacteria (hNRB and soNRB). These reduce nitrate by dissimilatory nitrate reduction to ammonium (e.g., Sulfurospirillum and Denitrovibrio) or by denitrification (e.g., Sulfurimonas, Arcobacter, and Thauera). Monitoring of ammonium concentrations in producing wells (PWs) indicated that denitrification was the main pathway for nitrate reduction in the field: breakthrough of nitrate and nitrite in two PWs was not associated with an increase in the ammonium concentration, and no increase in the ammonium concentration was seen in any of 11 producing wells during periods of increased nitrate injection. Instead, ammonium concentrations in produced waters decreased on average from 0.3 to 0.2 mM during 2 years of nitrate injection. Physiological studies with produced water-derived hNRB microcosms indicated increased biomass formation associated with denitrification as a possible cause for decreasing ammonium concentrations. Use of anammox-specific primers and cloning of the resulting PCR product gave clones affiliated with the known anammox genera "Candidatus Brocadia" and "Candidatus Kuenenia," indicating that the anammox reaction may also contribute to declining ammonium concentrations. Overall, the results indicate the following: (i) that nitrate injected into an oil field to oxidize sulfide is primarily reduced by denitrifying bacteria, of which many genera have been identified by DGGE, and (ii) that perhaps counterintuitively, nitrate injection leads to decreasing ammonium concentrations in produced waters.}, } @article {pmid20561021, year = {2010}, author = {Santos, F and Yarza, P and Parro, V and Briones, C and Antón, J}, title = {The metavirome of a hypersaline environment.}, journal = {Environmental microbiology}, volume = {12}, number = {11}, pages = {2965-2976}, doi = {10.1111/j.1462-2920.2010.02273.x}, pmid = {20561021}, issn = {1462-2920}, mesh = {Archaeal Viruses/classification/*genetics/isolation & purification ; Bacteriophages/classification/*genetics/isolation & purification ; Bacteroidetes/virology ; Base Composition ; Base Sequence ; Biodiversity ; Contig Mapping ; DNA, Viral ; Dinucleoside Phosphates ; Genetic Variation ; Genome, Viral ; Halobacteriaceae/virology ; Lysogeny ; *Metagenome ; Metagenomics/methods ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; *Salinity ; *Salt Tolerance ; Seawater/*virology ; Sodium Chloride ; Spain ; Viruses/classification/*genetics/isolation & purification ; Water Microbiology ; }, abstract = {Hypersaline environments harbour the highest number of virus-like particles reported for planktonic systems. However, very little is known about the genomic diversity of these virus assemblages since most of the knowledge on halophages is based on the analysis of a few isolates infecting strains of hyperhalophilic Archaea that may not be representatives of the natural microbiota. Here, we report the characterization, through a metagenomic approach, of the viral assemblage inhabiting a crystallizer pond (CR30) from a multi-pond solar saltern in Santa Pola (SE Spain). A total of 1.35 Mbp were cloned that yielded a total of 620 kb sequenced viral DNA. The metavirome was highly diverse and different from virus communities of marine and other aquatic environments although it showed some similarities with metaviromes from high-salt ponds in solar salterns in San Diego (SW USA), indicating some common traits between high-salt viromes. A high degree of diversity was found in the halophages as revealed by the presence of 2479 polymorphic nucleotides. Dinucleotide frequency analysis of the CR30 metavirome showed a good correlation with GC content and enabled the establishment of different groups, and even the assignment of their putative hosts: the archaeon Haloquadratum walsbyi and the bacterium Salinibacter ruber.}, } @article {pmid20561018, year = {2010}, author = {Sauvadet, AL and Gobet, A and Guillou, L}, title = {Comparative analysis between protist communities from the deep-sea pelagic ecosystem and specific deep hydrothermal habitats.}, journal = {Environmental microbiology}, volume = {12}, number = {11}, pages = {2946-2964}, doi = {10.1111/j.1462-2920.2010.02272.x}, pmid = {20561018}, issn = {1462-2920}, mesh = {Animals ; *Aquatic Organisms/classification/genetics/isolation & purification ; Biodiversity ; *Biota ; Bivalvia/classification/genetics ; Cytogenetic Analysis ; *Ecosystem ; *Eukaryota/classification/genetics/isolation & purification ; Gene Library ; Genetic Variation ; Hot Temperature ; Metagenomics ; Molecular Sequence Data ; Oceans and Seas ; Pacific Ocean ; Phylogeny ; Plankton/classification/genetics/isolation & purification ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/classification ; *Seawater ; }, abstract = {Protist communities associated with deep seawater and bivalves from six hydrothermal sites in the Pacific Ocean were characterized by microscopy and molecular rRNA gene surveys (18S rRNA) and compared with planktonic communities from Pacific deep-pelagic seawater (from 500 to 3000 m in depth). Genetic libraries from larger size fractions (>3 µm) of deep-pelagic water were mainly dominated by Dinophyceae, whereas small size fractions (<3 µm) mainly revealed radiolarians and Syndiniales. In contrast, more specific opportunistic detritivores and grazers, mostly belonging to Stramenopiles and Cercozoa, were detected from water surrounding vent chimneys. Protist communities were different in the pallial cavity of the giant hydrothermal bivalves Bathymodiolus thermophilus and Calyptogena magnifica, dominated by Ciliophora (primarily belonging to Phyllopharyngea, Oligohymenophorea and Oligotrichea) and Cercozoa. Interestingly, protist communities retrieved from the pallial cavity liquid of hydrothermal bivalves were remarkably homogeneous along the Southern East Pacific Rise, in contrast to bivalves collected on the Mid-Atlantic Ridge hydrothermal vents and cold seeps from the Gulf of Mexico. Hence, complex protist communities seem to occur inside hydrothermal bivalves, and these metazoa may constitute a stable micro-niche for micro-eukaryotes, including grazers, detritivores, symbionts and potential parasites. From these communities, new lineages within the ciliates may emerge.}, } @article {pmid20559826, year = {2010}, author = {Garcia-Armisen, T and Papalexandratou, Z and Hendryckx, H and Camu, N and Vrancken, G and De Vuyst, L and Cornelis, P}, title = {Diversity of the total bacterial community associated with Ghanaian and Brazilian cocoa bean fermentation samples as revealed by a 16 S rRNA gene clone library.}, journal = {Applied microbiology and biotechnology}, volume = {87}, number = {6}, pages = {2281-2292}, doi = {10.1007/s00253-010-2698-9}, pmid = {20559826}, issn = {1432-0614}, mesh = {Bacteria/genetics/*isolation & purification/*metabolism ; *Biodiversity ; Brazil ; Cacao/*microbiology ; DNA Fingerprinting ; DNA, Bacterial/genetics ; *Fermentation ; Fruit/microbiology ; Gene Library ; Ghana ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cocoa bean fermentation is a spontaneous process involving a succession of microbial activities, starting with yeasts, followed by lactic acid bacteria and acetic acid bacteria. So far, all microbiological studies about cocoa bean fermentation were based on culture-dependent (isolation, cultivation, and identification), or, more recently, culture-independent (PCR-DGGE, or polymerase chain reaction denaturing gradient gel electrophoresis) methods. Using a metagenomic approach, total DNA was extracted from heap and box fermentations at different time points and from different locations (Ghana and Brazil, respectively) to generate a 16 S rDNA clone library that was sequenced. The sequencing data revealed a low bacterial diversity in the fermentation samples and were in accordance with the results obtained through culture-dependent and a second, culture-independent analysis (PCR-DGGE), suggesting that almost all bacteria involved in the fermentation process are cultivable. One exception was the identification by 16 S rDNA library sequencing of Gluconacetobacter species of acetic acid bacteria that were not detected by the two other approaches. The presence of Enterobacteriaceae related to Erwinia/Pantoea/Tatumella, as revealed by 16 S rDNA library sequencing, suggests an impact of these bacteria on fermentation.}, } @article {pmid20553905, year = {2010}, author = {Beards, E and Tuohy, K and Gibson, G}, title = {Bacterial, SCFA and gas profiles of a range of food ingredients following in vitro fermentation by human colonic microbiota.}, journal = {Anaerobe}, volume = {16}, number = {4}, pages = {420-425}, doi = {10.1016/j.anaerobe.2010.05.006}, pmid = {20553905}, issn = {1095-8274}, mesh = {Bacterial Load ; Biodiversity ; Chromatography, Gas ; Fatty Acids, Volatile/*analysis ; Fermentation ; *Food Analysis ; *Food Microbiology ; Gases/*analysis ; Humans ; In Situ Hybridization, Fluorescence ; *Metagenome ; }, abstract = {It is now apparent that there is a strong link between health and nutrition and this can be seen clearly when we talk of obesity. The food industry is trying to capitalise on this by adapting high sugar/fat foods to become healthier alternatives. In confectionery food ingredients can be used for a range of purposes including sucrose replacement. Many of these ingredients may also evade digestion in the upper gut and be fermented by the gut microbiota upon entering the colon. This study was designed to screen a range of ingredients and their activities on the gut microbiota. In this study we screened a range of these ingredients in triplicate batch culture fermentations with known prebiotics as controls. Changes in bacteriology were monitored using FISH. SCFA were measured by GC and gas production was assessed during anaerobic batch fermentations. Bacterial enumeration showed significant increases (P < or = 0.05) in bifidobacteria and lactobacilli with polydextrose and most polyols with no significant increases in Clostridium histolyticum/perfringens. SCFA and gas formation indicated that the substrates added to the fermenters were being utilised by the gut microbiota. It therefore appears these ingredients exert some prebiotic activity in vitro. Further studies, particularly in human volunteers, are necessary.}, } @article {pmid20549533, year = {2010}, author = {Raoult, D}, title = {The globalization of intestinal microbiota.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {29}, number = {9}, pages = {1049-1050}, pmid = {20549533}, issn = {1435-4373}, mesh = {*Biodiversity ; *Food Microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; *Internationality ; *Metagenome ; }, abstract = {Many microorganisms reside in human mucosa, specifically in the gut. There are many sources of the microorganisms that colonize our gut, and these sources are mainly environmental. Indeed, food is a major source of bacteria and viruses. Food also modifies the equilibrium of microorganisms in our gut, with vegetables favoring a wider diversity. The increasing role of industrial food in our alimentation is generating a globalization of our gut microbiota that may influence our health and aid the diffusion of clonal bacteria.}, } @article {pmid20541022, year = {2010}, author = {Rougé, C and Goldenberg, O and Ferraris, L and Berger, B and Rochat, F and Legrand, A and Göbel, UB and Vodovar, M and Voyer, M and Rozé, JC and Darmaun, D and Piloquet, H and Butel, MJ and de La Cochetière, MF}, title = {Investigation of the intestinal microbiota in preterm infants using different methods.}, journal = {Anaerobe}, volume = {16}, number = {4}, pages = {362-370}, doi = {10.1016/j.anaerobe.2010.06.002}, pmid = {20541022}, issn = {1095-8274}, mesh = {*Biodiversity ; Birth Weight ; DNA Fingerprinting/methods ; Electrophoresis, Polyacrylamide Gel ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Infant, Newborn ; Intensive Care Units, Neonatal ; *Metagenome ; Nucleic Acid Denaturation ; *Premature Birth ; Sequence Analysis, DNA/methods ; }, abstract = {Modifications in microbial colonization of the human gut are believed to affect intestinal homeostasis and increase the risk of gastrointestinal diseases. The present study examined different methods for investigating the dynamic characterization of the intestinal microbiota in preterm infants. Fecal samples were collected weekly from ten preterm infants during their stay in a neonatal intensive care unit. The infants had a mean gestational age of 29 weeks (range: 28-32 weeks) and a mean birth weight of 1233g (range: 935-1450g). Bacterial colonization was assessed using conventional culture techniques and molecular biological methods. More specifically, the recently developed denaturing high performance liquid chromatography (dHPLC) technique was compared to established methods such as temporal temperature gradient gel electrophoresis (TTGE) and rRNA gene library sequencing. Our results indicate that the gastrointestinal tract of preterm infants, born at a gestational age of less than 33 weeks, has a low biodiversity of mainly, culturable bacteria. Finally, dHPLC was evaluated in terms of speed, labor and sensitivity for its use as a tool to analyze microbial colonization in preterm infants. We found that this technique provided major improvements over gel-based fingerprinting methods, such as TTGE, that are commonly used for studying microbial ecology. As such, it may become a common analytical tool for this purpose.}, } @article {pmid20530908, year = {2010}, author = {Hongoh, Y}, title = {Diversity and genomes of uncultured microbial symbionts in the termite gut.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {74}, number = {6}, pages = {1145-1151}, doi = {10.1271/bbb.100094}, pmid = {20530908}, issn = {1347-6947}, mesh = {Animals ; Bacteria/classification/*genetics/*isolation & purification ; *Biodiversity ; Gastrointestinal Tract/*microbiology ; Gene Expression Profiling ; Isoptera/*microbiology ; Metagenome/*genetics ; *Symbiosis ; }, abstract = {Termites play a key role in the global carbon cycle as decomposers. Their ability to thrive solely on dead plant matter is chiefly attributable to the activities of gut microbes, which comprise protists, bacteria, and archaea. Although the majority of the gut microbes are as yet unculturable, molecular analyses have gradually been revealing their diversity and symbiotic mechanisms. Culture-independent studies indicate that a single termite species harbors several hundred species of gut microbes unique to termites, and that the microbiota is consistent within a host termite species. To elucidate the functions of these unculturable symbionts, environmental genomics has recently been applied. Particularly, single-species-targeting metagenomics has provided a breakthrough in the understanding of symbiotic roles, such as the nitrogen fixation, of uncultured, individual microbial species. A combination of single-species-targeting metagenomics, conventional metagenomics, and metatranscriptomics should be a powerful tool to dissect this complex, multi-layered symbiotic system.}, } @article {pmid20520652, year = {2010}, author = {Costello, EK and Gordon, JI and Secor, SM and Knight, R}, title = {Postprandial remodeling of the gut microbiota in Burmese pythons.}, journal = {The ISME journal}, volume = {4}, number = {11}, pages = {1375-1385}, pmid = {20520652}, issn = {1751-7370}, support = {R01 HG004872-01/HG/NHGRI NIH HHS/United States ; R01 DK030292/DK/NIDDK NIH HHS/United States ; R01 DK070977/DK/NIDDK NIH HHS/United States ; DK30292/DK/NIDDK NIH HHS/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; DK70977/DK/NIDDK NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; HG004872/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Bacteria/*classification/genetics ; *Biodiversity ; Boidae/*microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gastrointestinal Tract/*microbiology/physiology ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Postprandial Period ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The vertebrate gut microbiota evolved in an environment typified by periodic fluctuations in nutrient availability, yet little is known about its responses to host feeding and fasting. As many model species (for example, mice) are adapted to lifestyles of frequent small meals, we turned to the Burmese python, a sit-and-wait foraging snake that consumes large prey at long intervals (>1 month), to examine the effects of a dynamic nutrient milieu on the gut microbiota. We used multiplexed 16S rRNA gene pyrosequencing to characterize bacterial communities harvested from the intestines of fasted and digesting snakes, and from their rodent meal. In this unprecedented survey of a reptilian host, we found that Bacteroidetes and Firmicutes numerically dominated the python gut. In the large intestine, fasting was associated with increased abundances of the genera Bacteroides, Rikenella, Synergistes and Akkermansia, and with reduced overall diversity. A marked postprandial shift in bacterial community configuration occurred. Between 12 h and 3 days after feeding, Firmicutes, including the taxa Clostridium, Lactobacillus and Peptostreptococcaceae, gradually outnumbered the fasting-dominant Bacteroidetes, and overall 'species'-level diversity increased significantly. Most lineages seemed to be indigenous to the python rather than ingested with the meal, but a dietary source of Lactobacillus could not be ruled out. Thus, the observed large-scale alterations of the gut microbiota that accompany the Burmese python's own dramatic physiological and morphological changes during feeding and fasting emphasize the need to consider both microbial and host cellular responses to nutrient flux. The Burmese python may provide a unique model for dissecting these interrelationships.}, } @article {pmid20511433, year = {2010}, author = {Dang, H and Li, J and Chen, R and Wang, L and Guo, L and Zhang, Z and Klotz, MG}, title = {Diversity, abundance, and spatial distribution of sediment ammonia-oxidizing Betaproteobacteria in response to environmental gradients and coastal eutrophication in Jiaozhou Bay, China.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {14}, pages = {4691-4702}, pmid = {20511433}, issn = {1098-5336}, mesh = {Ammonia/*metabolism ; Bacterial Proteins/genetics ; *Biodiversity ; China ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Eutrophication ; Geologic Sediments/*microbiology ; *Metagenome ; Molecular Sequence Data ; Nitrates/metabolism ; Nitrites/metabolism ; Nitrosomonadaceae/*classification/genetics/isolation & purification/*metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Ongoing anthropogenic eutrophication of Jiaozhou Bay offers an opportunity to study the influence of human activity on bacterial communities that drive biogeochemical cycling. Nitrification in coastal waters appears to be a sensitive indicator of environmental change, suggesting that function and structure of the microbial nitrifying community may be associated closely with environmental conditions. In the current study, the amoA gene was used to unravel the relationship between sediment aerobic obligate ammonia-oxidizing Betaproteobacteria (Beta-AOB) and their environment in Jiaozhou Bay. Protein sequences deduced from amoA gene sequences grouped within four distinct clusters in the Nitrosomonas lineage, including a putative new cluster. In addition, AmoA sequences belonging to three newly defined clusters in the Nitrosospira lineage were also identified. Multivariate statistical analyses indicated that the studied Beta-AOB community structures correlated with environmental parameters, of which nitrite-N and sediment sand content had significant impact on the composition, structure, and distribution of the Beta-AOB community. Both amoA clone library and quantitative PCR (qPCR) analyses indicated that continental input from the nearby wastewater treatment plants and polluted rivers may have significant impact on the composition and abundance of the sediment Beta-AOB assemblages in Jiaozhou Bay. Our work is the first report of a direct link between a sedimentological parameter and the composition and distribution of the sediment Beta-AOB and indicates the potential for using the Beta-AOB community composition in general and individual isolates or environmental clones in the Nitrosomonas oligotropha lineage in particular as bioindicators and biotracers of pollution or freshwater or wastewater input in coastal environments.}, } @article {pmid20509028, year = {2011}, author = {Zhao, L and Xu, W and Ibrahim, SA and Jin, J and Feng, J and Jiang, J and Meng, J and Ren, F}, title = {Effects of age and region on fecal microflora in elderly subjects living in Bama, Guangxi, China.}, journal = {Current microbiology}, volume = {62}, number = {1}, pages = {64-70}, pmid = {20509028}, issn = {1432-0991}, mesh = {Age Factors ; Aged ; Aged, 80 and over ; Bacteria/*classification/isolation & purification ; *Biodiversity ; China ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Feces/*microbiology ; Geography ; Humans ; *Metagenome ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Intestinal microflora analysis was performed on 52 healthy elderly subjects of different ages and in different regions in Bama County, Guangxi, China. The participants were assigned to three groups depending on their age and location: longevous (group M; mean age = 98 years; n = 21); rural younger elderly (group S; mean age = 70 years; n = 18); and urban elderly (group C; mean age = 82 years; n = 13). Ten groups of bacteria were quantified using real-time PCR. Age-related differences were observed in the number of Clostridium coccoides-Eubacterium rectale--there were more in longevous participants. Region affected the numbers of Bacteroides--Prevotella and Clostridium perfringens subgroup, and longevous participants had significantly more of the two bacterial groups than urban elderly participants. Region-related effects were also observed for the relative abundance of E. coli, and rural elderly participants had a lower proportion. Both age and regional effects were observed in the amount of total bacteria, and longevous participants had higher numbers than urban elderly participants. A significantly higher proportion of lactobacilli was observed in rural younger elderly participants than urban elderly participants, but independent age or regional effects did not contribute to this difference. This study suggests that age and region can affect the intestinal microflora of elderly people.}, } @article {pmid20498722, year = {2010}, author = {Frank, DN and Feazel, LM and Bessesen, MT and Price, CS and Janoff, EN and Pace, NR}, title = {The human nasal microbiota and Staphylococcus aureus carriage.}, journal = {PloS one}, volume = {5}, number = {5}, pages = {e10598}, pmid = {20498722}, issn = {1932-6203}, mesh = {Adult ; Bacterial Typing Techniques ; Biodiversity ; Colony Count, Microbial ; DNA, Ribosomal/genetics ; Health ; Hospitalization ; Humans ; Inpatients ; Longitudinal Studies ; *Metagenome/genetics ; Molecular Sequence Data ; Nasal Cavity/microbiology ; Nose/*microbiology ; Residence Characteristics ; Sequence Analysis, DNA ; Staphylococcus aureus/classification/genetics/*growth & development/*isolation & purification ; Staphylococcus epidermidis/genetics ; Time Factors ; }, abstract = {BACKGROUND: Colonization of humans with Staphylococcus aureus is a critical prerequisite of subsequent clinical infection of the skin, blood, lung, heart and other deep tissues. S. aureus persistently or intermittently colonizes the nares of approximately 50% of healthy adults, whereas approximately 50% of the general population is rarely or never colonized by this pathogen. Because microbial consortia within the nasal cavity may be an important determinant of S. aureus colonization we determined the composition and dynamics of the nasal microbiota and correlated specific microorganisms with S. aureus colonization.

Nasal specimens were collected longitudinally from five healthy adults and a cross-section of hospitalized patients (26 S. aureus carriers and 16 non-carriers). Culture-independent analysis of 16S rRNA sequences revealed that the nasal microbiota of healthy subjects consists primarily of members of the phylum Actinobacteria (e.g., Propionibacterium spp. and Corynebacterium spp.), with proportionally less representation of other phyla, including Firmicutes (e.g., Staphylococcus spp.) and Proteobacteria (e.g. Enterobacter spp). In contrast, inpatient nasal microbiotas were enriched in S. aureus or Staphylococcus epidermidis and diminished in several actinobacterial groups, most notably Propionibacterium acnes. Moreover, within the inpatient population S. aureus colonization was negatively correlated with the abundances of several microbial groups, including S. epidermidis (p = 0.004).

CONCLUSIONS/SIGNIFICANCE: The nares environment is colonized by a temporally stable microbiota that is distinct from other regions of the integument. Negative association between S. aureus, S. epidermidis, and other groups suggests microbial competition during colonization of the nares, a finding that could be exploited to limit S. aureus colonization.}, } @article {pmid20495046, year = {2010}, author = {Ottesen, EA and Leadbetter, JR}, title = {Diversity of formyltetrahydrofolate synthetases in the guts of the wood-feeding cockroach Cryptocercus punctulatus and the omnivorous cockroach Periplaneta americana.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {14}, pages = {4909-4913}, pmid = {20495046}, issn = {1098-5336}, support = {R01 HG002644/HG/NHGRI NIH HHS/United States ; T32 GM007616/GM/NIGMS NIH HHS/United States ; 5T32GM07616/GM/NIGMS NIH HHS/United States ; R01-HG002644/HG/NHGRI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Bacteria/*classification/*genetics ; *Biodiversity ; Cluster Analysis ; Cockroaches/*microbiology ; DNA, Bacterial/chemistry/genetics ; Formate-Tetrahydrofolate Ligase/*genetics ; Gastrointestinal Tract/microbiology ; *Metagenome ; Molecular Sequence Data ; Periplaneta/*microbiology ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {We examined the diversity of a marker gene for homoacetogens in two cockroach gut microbial communities. Formyltetrahydrofolate synthetase (FTHFS or fhs) libraries prepared from a wood-feeding cockroach, Cryptocercus punctulatus, were dominated by sequences that affiliated with termite gut treponemes. No spirochete-like sequences were recovered from the omnivorous roach Periplaneta americana, which was dominated by Firmicutes-like sequences.}, } @article {pmid20495045, year = {2010}, author = {Ding, GC and Heuer, H and Zühlke, S and Spiteller, M and Pronk, GJ and Heister, K and Kögel-Knabner, I and Smalla, K}, title = {Soil type-dependent responses to phenanthrene as revealed by determining the diversity and abundance of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase genes by using a novel PCR detection system.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {14}, pages = {4765-4771}, pmid = {20495045}, issn = {1098-5336}, mesh = {Bacteria/*classification/genetics ; Bacterial Proteins/*genetics ; *Biodiversity ; Cloning, Molecular ; Cluster Analysis ; DNA Primers/genetics ; Dioxygenases/*genetics ; *Metagenome ; Molecular Sequence Data ; Phenanthrenes/*metabolism ; Phylogeny ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Sequence Homology ; *Soil Microbiology ; }, abstract = {A novel PCR primer system that targets a wide range of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD(alpha)) genes of both Gram-positive and Gram-negative bacteria was developed and used to study their abundance and diversity in two different soils in response to phenanthrene spiking. The specificities and target ranges of the primers predicted in silico were confirmed experimentally by cloning and sequencing of PAH-RHD(alpha) gene amplicons from soil DNA. Cloning and sequencing showed the dominance of phnAc genes in the contaminated Luvisol. In contrast, high diversity of PAH-RHD(alpha) genes of Gram-positive and Gram-negative bacteria was observed in the phenanthrene-spiked Cambisol. Quantitative real-time PCR based on the same primers revealed that 63 days after phenanthrene spiking, PAH-RHD(alpha) genes were 1 order of magnitude more abundant in the Luvisol than in the Cambisol, while they were not detected in both control soils. In conclusion, sequence analysis of the amplicons obtained confirmed the specificity of the novel primer system and revealed a soil type-dependent response of PAH-RHD(alpha) gene-carrying soil bacteria to phenanthrene spiking.}, } @article {pmid20489017, year = {2010}, author = {, and Nelson, KE and Weinstock, GM and Highlander, SK and Worley, KC and Creasy, HH and Wortman, JR and Rusch, DB and Mitreva, M and Sodergren, E and Chinwalla, AT and Feldgarden, M and Gevers, D and Haas, BJ and Madupu, R and Ward, DV and Birren, BW and Gibbs, RA and Methe, B and Petrosino, JF and Strausberg, RL and Sutton, GG and White, OR and Wilson, RK and Durkin, S and Giglio, MG and Gujja, S and Howarth, C and Kodira, CD and Kyrpides, N and Mehta, T and Muzny, DM and Pearson, M and Pepin, K and Pati, A and Qin, X and Yandava, C and Zeng, Q and Zhang, L and Berlin, AM and Chen, L and Hepburn, TA and Johnson, J and McCorrison, J and Miller, J and Minx, P and Nusbaum, C and Russ, C and Sykes, SM and Tomlinson, CM and Young, S and Warren, WC and Badger, J and Crabtree, J and Markowitz, VM and Orvis, J and Cree, A and Ferriera, S and Fulton, LL and Fulton, RS and Gillis, M and Hemphill, LD and Joshi, V and Kovar, C and Torralba, M and Wetterstrand, KA and Abouellleil, A and Wollam, AM and Buhay, CJ and Ding, Y and Dugan, S and FitzGerald, MG and Holder, M and Hostetler, J and Clifton, SW and Allen-Vercoe, E and Earl, AM and Farmer, CN and Liolios, K and Surette, MG and Xu, Q and Pohl, C and Wilczek-Boney, K and Zhu, D}, title = {A catalog of reference genomes from the human microbiome.}, journal = {Science (New York, N.Y.)}, volume = {328}, number = {5981}, pages = {994-999}, pmid = {20489017}, issn = {1095-9203}, support = {U54-HG004969/HG/NHGRI NIH HHS/United States ; U54-HG003079/HG/NHGRI NIH HHS/United States ; U54 HG004973-02/HG/NHGRI NIH HHS/United States ; U54 HG003273-04S1/HG/NHGRI NIH HHS/United States ; /CAPMC/CIHR/Canada ; U54 HG003273/HG/NHGRI NIH HHS/United States ; U54 HG003273-05S2/HG/NHGRI NIH HHS/United States ; U54 HG003273-08/HG/NHGRI NIH HHS/United States ; U54 HG003273-04/HG/NHGRI NIH HHS/United States ; U54 HG003273-06S1/HG/NHGRI NIH HHS/United States ; U54-AI084844/AI/NIAID NIH HHS/United States ; U54 HG003079/HG/NHGRI NIH HHS/United States ; U54 HG003273-06S2/HG/NHGRI NIH HHS/United States ; U54-HG003273/HG/NHGRI NIH HHS/United States ; U54 HG004973/HG/NHGRI NIH HHS/United States ; U54 HG003067/HG/NHGRI NIH HHS/United States ; U54 HG003273-05S1/HG/NHGRI NIH HHS/United States ; U54 AI084844/AI/NIAID NIH HHS/United States ; U54 HG003273-05/HG/NHGRI NIH HHS/United States ; U54 HG004973-01/HG/NHGRI NIH HHS/United States ; U54-HG004968/HG/NHGRI NIH HHS/United States ; U54 HG004968/HG/NHGRI NIH HHS/United States ; U54 HG004969/HG/NHGRI NIH HHS/United States ; N01 AI30071/AI/NIAID NIH HHS/United States ; U54 HG003273-07/HG/NHGRI NIH HHS/United States ; U54-HG004973/HG/NHGRI NIH HHS/United States ; HHSN272200900017C/AI/NIAID NIH HHS/United States ; U54 HG003273-06/HG/NHGRI NIH HHS/United States ; N01 AI030071/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics ; Bacterial Proteins/chemistry/genetics ; Biodiversity ; Computational Biology ; Databases, Genetic ; Gastrointestinal Tract/microbiology ; Genes, Bacterial ; Genetic Variation ; Genome, Archaeal ; *Genome, Bacterial ; Humans ; Metagenome/*genetics ; Metagenomics/methods/standards ; Mouth/microbiology ; Peptides/chemistry/genetics ; Phylogeny ; Respiratory System/microbiology ; *Sequence Analysis, DNA/standards ; Skin/microbiology ; Urogenital System/microbiology ; }, abstract = {The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented.}, } @article {pmid20485386, year = {2010}, author = {De Corte, D and Sintes, E and Winter, C and Yokokawa, T and Reinthaler, T and Herndl, GJ}, title = {Links between viral and prokaryotic communities throughout the water column in the (sub)tropical Atlantic Ocean.}, journal = {The ISME journal}, volume = {4}, number = {11}, pages = {1431-1442}, doi = {10.1038/ismej.2010.65}, pmid = {20485386}, issn = {1751-7370}, mesh = {Archaea/classification/*isolation & purification ; Atlantic Ocean ; Bacteria/classification/*isolation & purification ; Bacterial Load ; *Biodiversity ; Cluster Analysis ; DNA Fingerprinting ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; DNA, Viral/genetics ; Genotype ; Metagenome ; Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length ; Random Amplified Polymorphic DNA Technique ; Seawater/*microbiology/*virology ; Tropical Climate ; Viral Load ; Viruses/classification/*isolation & purification ; }, abstract = {Viral and prokaryotic abundance, production and diversity were determined throughout the water column of the subtropical Atlantic Ocean to assess potential variations in the relation between viruses and prokaryotes. Prokaryotic abundance and heterotrophic activity decreased by one and three orders of magnitude, respectively, from the epi- to the abyssopelagic layer. Although the lytic viral production (VP) decreased with depth, lysogenic VP was variable throughout the water column and did not show any trend with depth. The bacterial, archaeal and viral community composition were depth-stratified as determined by the automated ribosomal intergenic spacer analysis, terminal-restriction fragment length polymorphism and randomly amplified polymorphic DNA-PCR, respectively. Generally, the number of operational taxonomic units (OTUs) did not reveal consistent trends throughout the water column. Viral and prokaryotic abundance were strongly related to heterotrophic prokaryotic production, suggesting similar linkage strength between the viral and prokaryotic communities from the lower epi- to the abyssopelagic layer in the Atlantic Ocean. Strikingly, the prokaryotic and viral parameters exhibited a similar variability throughout the water column down to the abyssopelagic layers, suggesting that the dark ocean is as dynamic a system as is the lower epipelagic layer. It also indicates that viruses are apparently having a similar role for prokaryotic mortality in the dark oceanic realm as in surface waters. The more than twofold increase in bacterial OTUs from 2750 m depth to >5000 m depth and the concurrent decrease in viral OTUs, however, suggests that viruses might exhibit a wider host range in deep waters than in surface waters.}, } @article {pmid20477961, year = {2010}, author = {Guglielmo, F and Gonthier, P and Garbelotto, M and Nicolotti, G}, title = {Optimization of sampling procedures for DNA-based diagnosis of wood decay fungi in standing trees.}, journal = {Letters in applied microbiology}, volume = {51}, number = {1}, pages = {90-97}, doi = {10.1111/j.1472-765X.2010.02860.x}, pmid = {20477961}, issn = {1472-765X}, mesh = {Biodiversity ; DNA, Fungal/*isolation & purification ; Fungi/*classification/genetics/isolation & purification ; Metagenomics/*methods ; Mycology/*methods ; Polymerase Chain Reaction/*methods ; Trees/*microbiology ; }, abstract = {AIMS: To develop fast and reliable sampling procedures for DNA-based diagnosis of wood decay fungi in standing trees.

METHODS AND RESULTS: A total of 250 trees were tested for the presence of a suite of wood decay fungi by collecting wood frass obtained by drilling each tree once with a 4-mm-diameter, 43-cm-long bit. We identified at least one of 11 target wood decay fungi in 56 trees through multiplex PCR assays. The presence of target wood decay taxa was further investigated in these 56 trees, by analysing independently wood from each of six drillings. Results were then compared with those obtained using sampling schemes differing in terms of number and position of drillings. Samples of 1-4 drillings were either analysed separately, and the results were combined, or pooled together before analysis was performed. In comparison with taxa identified by the analysis of six drillings, diagnostic efficiency ranged from 56.6% for the scheme based on a single drill to 96.8% for the scheme based on four drillings analysed separately. Both schemes significantly differ (P < 0.05) from those based on two and three drillings, whose efficiency was 72.6% and 83.9%, respectively. Diagnostic efficiency of pooled samples was comparable to that of samples analysed separately.

CONCLUSIONS: Highest diagnostic efficiency was obtained by analysing wood from four drillings. It is advisable to pool samples deriving from different drillings to reduce laboratory costs.

Fast and reliable sampling procedures make DNA-based diagnosis more suitable for tree inspection procedures.}, } @article {pmid20472731, year = {2010}, author = {Durso, LM and Harhay, GP and Smith, TP and Bono, JL and Desantis, TZ and Harhay, DM and Andersen, GL and Keen, JE and Laegreid, WW and Clawson, ML}, title = {Animal-to-animal variation in fecal microbial diversity among beef cattle.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {14}, pages = {4858-4862}, pmid = {20472731}, issn = {1098-5336}, mesh = {Animals ; *Biodiversity ; Cattle/*microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Feces/*microbiology ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The intestinal microbiota of beef cattle are important for animal health, food safety, and methane emissions. This full-length sequencing survey of 11,171 16S rRNA genes reveals animal-to-animal variation in communities that cannot be attributed to breed, gender, diet, age, or weather. Beef communities differ from those of dairy. Core bovine taxa are identified.}, } @article {pmid20463765, year = {2010}, author = {Huang, S and Wilhelm, SW and Jiao, N and Chen, F}, title = {Ubiquitous cyanobacterial podoviruses in the global oceans unveiled through viral DNA polymerase gene sequences.}, journal = {The ISME journal}, volume = {4}, number = {10}, pages = {1243-1251}, doi = {10.1038/ismej.2010.56}, pmid = {20463765}, issn = {1751-7370}, mesh = {Biodiversity ; Cluster Analysis ; Cyanobacteria/*virology ; DNA, Viral/chemistry/*genetics ; DNA-Directed DNA Polymerase/*genetics ; Geography ; Molecular Sequence Data ; Oceans and Seas ; Phylogeny ; Podoviridae/*genetics/*isolation & purification ; Polymorphism, Genetic ; Seawater/*virology ; Sequence Analysis, DNA ; Viral Proteins/*genetics ; }, abstract = {As a major cyanophage group, cyanobacterial podoviruses are important in regulating the biomass and population structure of picocyanobacteria in the ocean. However, little is known about their biogeography in the open ocean. This study represents the first survey of the biodiversity of cyanopodoviruses in the global oceans based on the viral encoded DNA polymerase (pol) gene. A total of 303 DNA pol sequences were amplified by PCR from 10 virus communities collected in the Atlantic and Pacific oceans and the South China Sea. At least five subclusters of cyanopodoviruses were identified in these samples, and one subcluster (subcluster VIII) was found in all sampling sites and comprised approximately 50% of total sequences. The diversity index based on the DNA pol gene sequences recovered through PCR suggests that cyanopodoviruses are less diverse in these oceanic samples than in a previously studied estuarine environment. Although diverse podoviruses were present in the global ocean, each sample was dominated by one major group of cyanopodoviruses. No clear biogeographic patterns were observed using statistical analysis. A metagenomic analysis based on the Global Ocean Sampling database indicates that other types of cyanopodovirus-like DNA pol sequences were present in the global ocean. Together, our study results suggest that cyanopodoviruses are widely distributed in the ocean but their community composition varies with local environments.}, } @article {pmid20463763, year = {2010}, author = {Vila-Costa, M and Rinta-Kanto, JM and Sun, S and Sharma, S and Poretsky, R and Moran, MA}, title = {Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate.}, journal = {The ISME journal}, volume = {4}, number = {11}, pages = {1410-1420}, doi = {10.1038/ismej.2010.62}, pmid = {20463763}, issn = {1751-7370}, mesh = {Acetyl Coenzyme A/metabolism ; Acyl Coenzyme A/metabolism ; Atlantic Ocean ; Bacteria/*classification/genetics/*metabolism ; Bermuda ; *Biodiversity ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Gene Expression Profiling ; Metabolic Networks and Pathways/genetics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sulfonium Compounds/*metabolism ; }, abstract = {Dimethylsulfoniopropionate (DMSP) is an important source of reduced sulfur and carbon for marine microbial communities, as well as the precursor of the climate-active gas dimethylsulfide (DMS). In this study, we used metatranscriptomic sequencing to analyze gene expression profiles of a bacterial assemblage from surface waters at the Bermuda Atlantic Time-series Study (BATS) station with and without a short-term enrichment of DMSP (25 nM for 30 min). An average of 303 143 reads were obtained per treatment using 454 pyrosequencing technology, of which 51% were potential protein-encoding sequences. Transcripts from Gammaproteobacteria and Bacteroidetes increased in relative abundance on DMSP addition, yet there was little change in the contribution of two bacterioplankton groups whose cultured members harbor known DMSP degradation genes, Roseobacter and SAR11. The DMSP addition led to an enrichment of transcripts supporting heterotrophic activity, and a depletion of those encoding light-related energy generation. Genes for the degradation of C3 compounds were significantly overrepresented after DMSP addition, likely reflecting the metabolism of the C3 component of DMSP. Mapping these transcripts to known biochemical pathways indicated that both acetyl-CoA and succinyl-CoA may be common entry points of this moiety into the tricarboxylic acid cycle. In a short time frame (30 min) in the extremely oligotrophic Sargasso Sea, different gene expression patterns suggest the use of DMSP by a diversity of marine bacterioplankton as both carbon and sulfur sources.}, } @article {pmid20452420, year = {2010}, author = {Mocali, S and Benedetti, A}, title = {Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology.}, journal = {Research in microbiology}, volume = {161}, number = {6}, pages = {497-505}, doi = {10.1016/j.resmic.2010.04.010}, pmid = {20452420}, issn = {1769-7123}, mesh = {Biodiversity ; Databases, Genetic ; Gene Library ; Industrial Microbiology ; Internationality ; *Metagenomics/trends ; Phylogeny ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Soil is one of the most complex and challenging environments for microbiologists. In fact, although it contains the largest microbial diversity on the planet, the majority of these microbes are still uncharacterized and represent an enormous unexplored reservoir of genetic and metabolic diversity. Metagenomics, the study of the entire genome of soil biota, currently represents a powerful tool for assessing the diversity of complex microbial communities, providing access to a number of new species, genes or novel molecules that are relevant for biotechnology and agricultural applications. In this paper, the onset of new high-throughput metagenomic approaches and new perspectives in soil microbial ecology and data handling are discussed.}, } @article {pmid20445636, year = {2010}, author = {Rousk, J and Bååth, E and Brookes, PC and Lauber, CL and Lozupone, C and Caporaso, JG and Knight, R and Fierer, N}, title = {Soil bacterial and fungal communities across a pH gradient in an arable soil.}, journal = {The ISME journal}, volume = {4}, number = {10}, pages = {1340-1351}, doi = {10.1038/ismej.2010.58}, pmid = {20445636}, issn = {1751-7370}, mesh = {Bacteria/*classification/*isolation & purification ; *Biodiversity ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; Fungi/*classification/*isolation & purification ; Hydrogen-Ion Concentration ; Metagenome ; Metagenomics/methods ; North America ; Polymerase Chain Reaction/methods ; Polymorphism, Genetic ; Sequence Analysis, DNA/methods ; Soil/*analysis ; *Soil Microbiology ; South America ; }, abstract = {Soils collected across a long-term liming experiment (pH 4.0-8.3), in which variation in factors other than pH have been minimized, were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria. We hypothesized that bacterial communities would be more strongly influenced by pH than fungal communities. To determine the relative abundance of bacteria and fungi, we used quantitative PCR (qPCR), and to analyze the composition and diversity of the bacterial and fungal communities, we used a bar-coded pyrosequencing technique. Both the relative abundance and diversity of bacteria were positively related to pH, the latter nearly doubling between pH 4 and 8. In contrast, the relative abundance of fungi was unaffected by pH and fungal diversity was only weakly related with pH. The composition of the bacterial communities was closely defined by soil pH; there was as much variability in bacterial community composition across the 180-m distance of this liming experiment as across soils collected from a wide range of biomes in North and South America, emphasizing the dominance of pH in structuring bacterial communities. The apparent direct influence of pH on bacterial community composition is probably due to the narrow pH ranges for optimal growth of bacteria. Fungal community composition was less strongly affected by pH, which is consistent with pure culture studies, demonstrating that fungi generally exhibit wider pH ranges for optimal growth.}, } @article {pmid20437144, year = {2010}, author = {Pan, WZ and Huang, XW and Wei, KB and Zhang, CM and Yang, DM and Ding, JM and Zhang, KQ}, title = {Diversity of thermophilic fungi in Tengchong Rehai National Park revealed by ITS nucleotide sequence analyses.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {48}, number = {2}, pages = {146-152}, pmid = {20437144}, issn = {1976-3794}, mesh = {*Biodiversity ; China ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Fungi/*classification/cytology/genetics/growth & development ; Hot Springs/*microbiology ; Metagenome ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The geothermal sites near neutral and alkalescent thermal springs in Tengchong Rehai National Park were examined through cultivation-dependent approach to determine the diversity of thermophilic fungi in these environments. Here, we collected soils samples in this area, plated on agar media conducive for fungal growth, obtained pure cultures, and then employed the method of internal transcribed spacer (ITS) sequencing combined with morphological analysis for identification of thermophilic fungi to the species level. In total, 102 strains were isolated and identified as Rhizomucor miehei, Chaetomium sp., Talaromyces thermophilus, Talaromyces byssochlamydoides, Thermoascus aurantiacus Miehe var. levisporus, Thermomyces lanuginosus, Scytalidium thermophilum, Malbranchea flava, Myceliophthora sp. 1, Myceliophthora sp. 2, Myceliophthora sp. 3, and Coprinopsis sp. Two species, T. lanuginosus and S. thermophilum were the dominant species, representing 34.78% and 28.26% of the sample, respectively. Our results indicated a greater diversity of thermophilic fungi in neutral and alkaline geothermal sites than acidic sites around hot springs reported in previous studies. Most of our strains thrived at alkaline growth conditions.}, } @article {pmid20437143, year = {2010}, author = {Zhou, ZX and Jiang, H and Yang, C and Yang, MZ and Zhang, HB}, title = {Microbial community on healthy and diseased leaves of an invasive plant Eupatorium adenophorum in Southwest China.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {48}, number = {2}, pages = {139-145}, pmid = {20437143}, issn = {1976-3794}, mesh = {Ageratina/*microbiology ; Bacteria/*classification/genetics/growth & development/*isolation & purification ; *Biodiversity ; China ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fungi/*classification/genetics/growth & development/*isolation & purification ; Metagenomics ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/*microbiology ; Plant Leaves/microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {Invasive plants have caused great economic losses and environmental problems worldwide. Eupatorium adenophorum is one of the most invasive weeds in China. To better understand its invasive mechanisms, in the present paper, the microbial communities of healthy and diseased leaves of E. adenophorum were obtained using both culture-independent and -dependent methods and their diversities were compared. The bacteria obtained from culture-independent method belong to Proteobacteria (95.8%), Actinobacteria (2.1%), and Firmicutes (2.1%) and fungi belong to Ascomycota (65.2%) and Basidiomycota (34.8%). Very few overlapped microbial species were found by culture-dependent and -independent methods. Healthy leaves display higher bacterial diversity than diseased leaves. Phylogenetic structures are very different between healthy and diseased phyllosphere microbial communities. Bacteria close to Acinetobacter and Pseudomonas were dominant on healthy leaves, whereas those close to Shigella were dominant on diseased leaves. 52.9% of fungal clones from healthy leaves were Ustilaginomycetes, close to Rhodotorula phylloplana and uncultured basidomycete; by contrast, 60% of clones from diseased leaves were Lecanoromycetes, close to Umbilicaria muehlenbergii. No bacteria but four fungal strains phylogenetically close to Myrothecium sp. and Alternaria alternate were pathogenic to seedlings and detached leaves of the invasive plant. Therefore, this plant may be resistant to pathogens from bacteria but not fungi in its introduced range.}, } @article {pmid20434786, year = {2010}, author = {Maphosa, F and de Vos, WM and Smidt, H}, title = {Exploiting the ecogenomics toolbox for environmental diagnostics of organohalide-respiring bacteria.}, journal = {Trends in biotechnology}, volume = {28}, number = {6}, pages = {308-316}, doi = {10.1016/j.tibtech.2010.03.005}, pmid = {20434786}, issn = {1879-3096}, mesh = {Bacteria/classification/genetics/*isolation & purification/*metabolism ; Biodegradation, Environmental ; *Environmental Microbiology ; Environmental Pollutants/*metabolism ; Halogenated Diphenyl Ethers/*metabolism ; *Metagenome ; Oxidation-Reduction ; }, abstract = {Various 'omics' methods have enabled environmental probing at the molecular level and have created an important new paradigm in bioremediation design and management. Ecogenomics - the application of genomics to ecological and environmental sciences - defines phylogenetic and functional biodiversity at the DNA, RNA and protein levels. It capitalizes on this knowledge to elucidate functions and interactions of organisms at the ecosystem level in relation to ecological and evolutionary processes. Effective bioremediation of widespread halo-organic pollutants in anaerobic environments requires knowledge of catabolic potential and in situ dynamics of organohalide-respiring and co-metabolizing microorganisms. Here, we discuss the potential of ecogenomics approaches in developing high-throughput methods for detecting and monitoring organohalide respirers, and for providing improvements to selection, specificity and sensitivity of target biomarkers and their application to evaluate bioremediation strategies.}, } @article {pmid20428223, year = {2010}, author = {He, Z and Deng, Y and Van Nostrand, JD and Tu, Q and Xu, M and Hemme, CL and Li, X and Wu, L and Gentry, TJ and Yin, Y and Liebich, J and Hazen, TC and Zhou, J}, title = {GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity.}, journal = {The ISME journal}, volume = {4}, number = {9}, pages = {1167-1179}, doi = {10.1038/ismej.2010.46}, pmid = {20428223}, issn = {1751-7370}, mesh = {Bacteria/classification/genetics ; *Biota ; Computational Biology/methods ; DNA Gyrase/genetics ; Drug Resistance, Bacterial ; *Environmental Microbiology ; Metabolic Networks and Pathways/genetics ; Metagenomics/*methods ; Microarray Analysis/*methods ; Oligonucleotide Array Sequence Analysis/methods ; Oligonucleotide Probes/genetics ; Phylogeny ; Sensitivity and Specificity ; Software ; }, abstract = {A new generation of functional gene arrays (FGAs; GeoChip 3.0) has been developed, with approximately 28 000 probes covering approximately 57 000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance and organic contaminant degradation. GeoChip 3.0 also has several other distinct features, such as a common oligo reference standard (CORS) for data normalization and comparison, a software package for data management and future updating and the gyrB gene for phylogenetic analysis. Computational evaluation of probe specificity indicated that all designed probes would have a high specificity to their corresponding targets. Experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036-0.025% false-positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which showed that the structure, composition and potential activity of soil microbial communities significantly changed with the plant species diversity. As expected, GeoChip 3.0 is a high-throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning.}, } @article {pmid20426769, year = {2009}, author = {Lillis, L and Doyle, E and Clipson, N}, title = {Comparison of DNA- and RNA-based bacterial community structures in soil exposed to 2,4-dichlorophenol.}, journal = {Journal of applied microbiology}, volume = {107}, number = {6}, pages = {1883-1893}, doi = {10.1111/j.1365-2672.2009.04369.x}, pmid = {20426769}, issn = {1365-2672}, mesh = {Bacteria/*classification/genetics/isolation & purification ; Biodegradation, Environmental ; Biodiversity ; Chlorophenols/*pharmacology ; DNA, Bacterial/*genetics ; Metagenome/*drug effects ; Molecular Sequence Data ; Polymorphism, Restriction Fragment Length ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Soil Pollutants/*pharmacology ; }, abstract = {AIMS: To examine the effect of the pollutant 2,4-dichlorophenol on DNA- and RNA-based bacterial communities in soil.

METHODS AND RESULTS: Soil was exposed to 100 mg kg(-1) of 2,4-dichlorophenol (2,4-DCP), and degradation was monitored over 35 days. DNA and RNA were coextracted, and terminal restriction fragment length polymorphism (T-RFLP) was used to report changes in bacterial communities in response to the presence of the chlorophenol. The phylogenetic composition of the soil during degradation was determined by creating a clone library of amplified 16S rRNA sequences from both DNA and reverse-transcribed RNA from exposed soil. Resulting clones were sequenced, and putative identities were assigned.

CONCLUSIONS: A significant difference between active (RNA-based) and total (DNA-based) bacterial community structure was observed for both T-RFLP and phylogenetic analyses in response to 2,4-DCP, with more pronounced changes seen in RNA-based communities. Phylogenetic analysis indicated the dominance of Proteobacteria in both profiles.

This study describes the response of soil bacterial communities to the addition of the xenobiotic compound 2,4-DCP, and highlights the importance of including RNA-based 16S rRNA analysis to complement any molecular study in a perturbed soil.}, } @article {pmid20418436, year = {2010}, author = {Zhou, M and Hernandez-Sanabria, E and Guan, LL}, title = {Characterization of variation in rumen methanogenic communities under different dietary and host feed efficiency conditions, as determined by PCR-denaturing gradient gel electrophoresis analysis.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {12}, pages = {3776-3786}, pmid = {20418436}, issn = {1098-5336}, mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biodiversity ; Cattle ; Cluster Analysis ; DNA Fingerprinting ; *Diet ; Electrophoresis, Polyacrylamide Gel/methods ; *Metagenome ; Methane/*metabolism ; Nucleic Acid Denaturation ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; }, abstract = {Understanding ruminal methanogens is essential for greenhouse gas mitigation, as well as for improving animal performance in the livestock industry. It has been speculated that ruminal methanogenic diversity affects host feed efficiency and results in differences in methane production. This study examined methanogenic profiles in the rumen using culture-independent PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analysis for 56 beef cattle which differed in feed efficiency, as well as diet (the cattle were fed a low-energy diet or a high-energy diet). The methanogenic PCR-DGGE profiles detected were greatly affected by diet, and the major pattern changed from a community containing predominantly Methanobrevibacter ruminantium NT7 with the low-energy diet to a community containing predominantly Methanobrevibacter smithii, Methanobrevibacter sp. AbM4, and/or M. ruminantium NT7 with the high-energy diet. For each diet, the methanogenic PCR-DGGE pattern was strongly associated with the feed efficiency of the host. Diet-associated bands for Methanobrevibacter sp. AbM4 and M. smithii SM9 and a feed efficiency-related band for M. smithii PS were identified. The abundance of total methanogens was estimated by determining the numbers of copies of the 16S rRNA genes of methanogens. However, the size of the methanogen population did not correlate with differences in feed efficiency, diet, or metabolic measurements. Thus, the structure of the methanogenic community at the species or strain level may be more important for determining host feed efficiency under different dietary conditions.}, } @article {pmid20410934, year = {2010}, author = {Handley, KM and Boothman, C and Mills, RA and Pancost, RD and Lloyd, JR}, title = {Functional diversity of bacteria in a ferruginous hydrothermal sediment.}, journal = {The ISME journal}, volume = {4}, number = {9}, pages = {1193-1205}, doi = {10.1038/ismej.2010.38}, pmid = {20410934}, issn = {1751-7370}, mesh = {Acetates/metabolism ; Anaerobiosis ; Arsenic/metabolism ; Bacteria/classification/*isolation & purification/*metabolism ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Greece ; Hot Springs/*microbiology ; Iron/*metabolism ; Lactic Acid/metabolism ; Manganese/metabolism ; Metagenome ; Molecular Sequence Data ; Nitrates/metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfates/metabolism ; }, abstract = {A microbial community showing diverse respiratory processes was identified within an arsenic-rich, ferruginous shallow marine hydrothermal sediment (20-40 degrees C, pH 6.0-6.3) in Santorini, Greece. Analyses showed that ferric iron reduction with depth was broadly accompanied by manganese and arsenic reduction and FeS accumulation. Clone library analyses indicated the suboxic-anoxic transition zone sediment contained abundant Fe(III)- and sulfate-reducing Deltaproteobacteria, whereas the overlying surface sediment was dominated by clones related to the Fe(II)-oxidizing zetaproteobacterium, Mariprofundus ferroxydans. Cultures obtained from the transition zone were enriched in bacteria that reduced Fe(III), nitrate, sulfate and As(V) using acetate or lactate as electron donors. In the absence of added organic carbon, bacteria were enriched that oxidized Fe(II) anaerobically or microaerobically, sulfide microaerobically and aerobically and As(III) aerobically. According to 16S rRNA gene analyses, enriched bacteria represented a phylogenetically wide distribution. Most probable number counts indicated an abundance of nitrate-, As(V)- and Fe(III)((s,aq))-reducers, and dissolved sulfide-oxidizers over sulfate-reducers, and FeS-, As(III)- and nitrate-dependent Fe(II)-oxidisers in the transition zone. It is noteworthy that the combined community and geochemical data imply near-surface microbial iron and arsenic redox cycling were dominant biogeochemical processes.}, } @article {pmid20409657, year = {2010}, author = {Santos, F and Peña, A and Nogales, B and Soria-Soria, E and Del Cura, MA and González-Martín, JA and Antón, J}, title = {Bacterial diversity in dry modern freshwater stromatolites from Ruidera Pools Natural Park, Spain.}, journal = {Systematic and applied microbiology}, volume = {33}, number = {4}, pages = {209-221}, doi = {10.1016/j.syapm.2010.02.006}, pmid = {20409657}, issn = {1618-0984}, mesh = {Bacteria/*classification/*growth & development ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Metagenome ; Microscopy ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Spain ; }, abstract = {Ruidera Pools Natural Park, Spain, constitutes one of the most representative systems of carbonate precipitation in Europe. The prokaryotic community of a dry modern stromatolite recovered from the park has been analyzed by molecular techniques that included denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library analysis, together with microscopic observations from the sample and cultures. Ribosomal RNA was directly extracted to study the putatively active part of the microbial community present in the sample. A total of 295 16S rRNA gene sequences were analyzed. Libraries were dominated by sequences related to Cyanobacteria, most frequently to the genus Leptolyngbya. A diverse and abundant assemblage of non-cyanobacterial sequences was also found, including members of Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Acidobacteria,Planctomycetes and Chloroflexi groups. No amplification was obtained when using archaeal primers. The results showed that at the time of sampling, when the pool was dry, the bacterial community of the stromatolites was dominated by groups of highly related Cyanobacteria, including new groups that had not been previously reported, although a high diversity outside this phylogenetic group was also found. The results indicated that part of the Cyanobacteria assemblage was metabolically active and could thus play a role in the mineralization processes inside the stromatolites.}, } @article {pmid20403728, year = {2010}, author = {Corsaro, D and Pages, GS and Catalan, V and Loret, JF and Greub, G}, title = {Biodiversity of amoebae and amoeba-associated bacteria in water treatment plants.}, journal = {International journal of hygiene and environmental health}, volume = {213}, number = {3}, pages = {158-166}, doi = {10.1016/j.ijheh.2010.03.002}, pmid = {20403728}, issn = {1618-131X}, mesh = {Amoeba/*classification/genetics/isolation & purification/microbiology ; Bacteria/*classification/genetics/isolation & purification ; Biodiversity ; Coculture Techniques ; Genes, Bacterial ; Genes, rRNA ; Metagenome ; Symbiosis ; *Water Microbiology ; Water Purification ; *Water Supply ; }, abstract = {In this study, we enlarged our previous investigation focusing on the biodiversity of chlamydiae and amoebae in a drinking water treatment plant, by the inclusion of two additional plants and by searching also for the presence of legionellae and mycobacteria. Autochthonous amoebae were recovered onto non-nutritive agar, identified by 18S rRNA gene sequencing, and screened for the presence of bacterial endosymbionts. Bacteria were also searched for by Acanthamoeba co-culture. From a total of 125 samples, we recovered 38 amoebae, among which six harboured endosymbionts (three chlamydiae and three legionellae). In addition, we recovered by amoebal co-culture 11 chlamydiae, 36 legionellae (no L. pneumophila), and 24 mycobacteria (all rapid-growers). Two plants presented a similar percentage of samples positive for chlamydiae (11%), mycobacteria (20%) and amoebae (27%), whereas in the third plant the number of recovered bacteria was almost twice higher. Each plant exhibited a relatively high specific microbiota. Amoebae were mainly represented by various Naegleria species, Acanthamoeba species and Hartmannella vermiformis. Parachlamydiaceae were the most abundant chlamydiae (8 strains in total), and in this study we recovered a new genus-level strain, along with new chlamydiae previously reported. Similarly, about 66% of the recovered legionellae and 47% of the isolated mycobacteria could represent new species. Our work highlighted a high species diversity among legionellae and mycobacteria, dominated by putative new species, and it confirmed the presence of chlamydiae in these artificial water systems.}, } @article {pmid20393573, year = {2010}, author = {Yergeau, E and Hogues, H and Whyte, LG and Greer, CW}, title = {The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses.}, journal = {The ISME journal}, volume = {4}, number = {9}, pages = {1206-1214}, doi = {10.1038/ismej.2010.41}, pmid = {20393573}, issn = {1751-7370}, mesh = {Arctic Regions ; *Biota ; Canada ; Carbon/metabolism ; DNA/chemistry/genetics/isolation & purification ; *Genetic Variation ; Metabolic Networks and Pathways/*genetics ; *Metagenome ; Microarray Analysis ; Molecular Sequence Data ; Nitrogen/metabolism ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The fate of the carbon stocked in permafrost following global warming and permafrost thaw is of major concern in view of the potential for increased CH(4) and CO(2) emissions from these soils. Complex carbon compound degradation and greenhouse gas emissions are due to soil microbial communities, but no comprehensive study has yet addressed their composition and functional potential in permafrost. Here, a 2-m deep permafrost sample and its overlying active layer soil were subjected to metagenomic sequencing, quantitative PCR (qPCR) and microarray analyses. The active layer soil and the 2-m permafrost microbial community structures were very similar, with Actinobacteria being the dominant phylum. The two samples also possessed a highly similar spectrum of functional genes, especially when compared with other already published metagenomes. Key genes related to methane generation, methane oxidation and organic matter degradation were highly diverse for both samples in the metagenomic libraries and some (for example, pmoA) showed relatively high abundance in qPCR assays. Genes related to nitrogen fixation and ammonia oxidation, which could have important roles following climatic change in these nitrogen-limited environments, showed low diversity but high abundance. The 2-m permafrost showed lower abundance and diversity for all the assessed genes and taxa. Experimental biases were also evaluated using qPCR and showed that the whole-community genome amplification technique used caused representational biases in the metagenomic libraries by increasing the abundance of Bacteroidetes and decreasing the abundance of Actinobacteria. This study describes for the first time the detailed functional potential of permafrost-affected soils.}, } @article {pmid20393571, year = {2010}, author = {Ghai, R and Martin-Cuadrado, AB and Molto, AG and Heredia, IG and Cabrera, R and Martin, J and Verdú, M and Deschamps, P and Moreira, D and López-García, P and Mira, A and Rodriguez-Valera, F}, title = {Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing.}, journal = {The ISME journal}, volume = {4}, number = {9}, pages = {1154-1166}, doi = {10.1038/ismej.2010.44}, pmid = {20393571}, issn = {1751-7370}, mesh = {*Biota ; DNA/chemistry/*genetics/*isolation & purification ; Gene Library ; *Genetic Variation ; Mediterranean Sea ; *Metagenome ; Molecular Sequence Data ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The deep chlorophyll maximum (DCM) is a zone of maximal photosynthetic activity, generally located toward the base of the photic zone in lakes and oceans. In the tropical waters, this is a permanent feature, but in the Mediterranean and other temperate waters, the DCM is a seasonal phenomenon. The metagenome from a single sample of a mature Mediterranean DCM community has been 454 pyrosequenced both directly and after cloning in fosmids. This study is the first to be carried out at this sequencing depth (ca. 600 Mb combining direct and fosmid sequencing) at any DCM. Our results indicate a microbial community massively dominated by the high-light-adapted Prochlorococcus marinus subsp. pastoris, Synechococcus sp., and the heterotroph Candidatus Pelagibacter. The sequences retrieved were remarkably similar to the existing genome of P. marinus subsp. pastoris with a nucleotide identity over 98%. Besides, we found a large number of cyanophages that could prey on this microbe, although sequence conservation was much lower. The high abundance of phage sequences in the cellular size fraction indicated a remarkably high proportion of cells suffering phage lytic attack. In addition, several fosmids clearly belonging to Group II Euryarchaeota were retrieved and recruited many fragments from the total direct DNA sequencing suggesting that this group might be quite abundant in this habitat. The comparison between the direct and fosmids sequencing revealed a bias in the fosmid libraries against low-GC DNA and specifically against the two most dominant members of the community, Candidatus Pelagibacter and P. marinus subsp. pastoris, thus unexpectedly providing a feasible method to obtain large genomic fragments from other less prevalent members of this community.}, } @article {pmid20376100, year = {2010}, author = {Reeve, JR and Schadt, CW and Carpenter-Boggs, L and Kang, S and Zhou, J and Reganold, JP}, title = {Effects of soil type and farm management on soil ecological functional genes and microbial activities.}, journal = {The ISME journal}, volume = {4}, number = {9}, pages = {1099-1107}, doi = {10.1038/ismej.2010.42}, pmid = {20376100}, issn = {1751-7370}, mesh = {Agriculture/*methods ; *Biota ; Cellulose/metabolism ; DNA/genetics/isolation & purification ; Fragaria ; *Genetic Variation ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Microarray Analysis ; Quaternary Ammonium Compounds/metabolism ; Soil/*analysis ; *Soil Microbiology ; Sulfur/metabolism ; }, abstract = {Relationships between soil microbial diversity and soil function are the subject of much debate. Process-level analyses have shown that microbial function varies with soil type and responds to soil management. However, such measurements cannot determine the role of community structure and diversity in soil function. The goal of this study was to investigate the role of gene frequency and diversity, measured by microarray analysis, on soil processes. The study was conducted in an agro-ecosystem characterized by contrasting management practices and soil types. Eight pairs of adjacent commercial organic and conventional strawberry fields were matched for soil type, strawberry variety, and all other environmental conditions. Soil physical, chemical and biological analyses were conducted including functional gene microarrays (FGA). Soil physical and chemical characteristics were primarily determined by soil textural type (coarse vs fine-textured), but biological and FGA measures were more influenced by management (organic vs conventional). Organically managed soils consistently showed greater functional activity as well as FGA signal intensity (SI) and diversity. Overall FGA SI and diversity were correlated to total soil microbial biomass. Functional gene group SI and/or diversity were correlated to related soil chemical and biological measures such as microbial biomass, cellulose, dehydrogenase, ammonium and sulfur. Management was the dominant determinant of soil biology as measured by microbial gene frequency and diversity, which paralleled measured microbial processes.}, } @article {pmid20370919, year = {2010}, author = {Chun, J and Kim, KY and Lee, JH and Choi, Y}, title = {The analysis of oral microbial communities of wild-type and toll-like receptor 2-deficient mice using a 454 GS FLX Titanium pyrosequencer.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {101}, pmid = {20370919}, issn = {1471-2180}, mesh = {Animals ; Bacteria/*classification/*genetics ; *Biodiversity ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Metagenome ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Molecular Sequence Data ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Toll-Like Receptor 2/*deficiency/*immunology ; }, abstract = {BACKGROUND: Although mice have long served as an animal model for periodontitis, information on the composition of their indigenous oral microbiota is limited. The aim of the current study was to characterize mouse oral bacterial flora by applying extensive parallel pyrosequencing using the latest model pyrosequencer, a Roche/454 Genome Sequencer FLX Titanium. In addition, the effect of Toll-like receptor (TLR) 2 deficiency on oral microbiota was evaluated.

RESULTS: Eight oral bacterial communities of wild-type (n = 4) and TLR2 knock-out (n = 4) C57BL/6 mice were characterized by analyzing 80,046 reads of 16S rRNA genes obtained by pyrosequencing. Excluding the PCR primers, the average length of each sequencing product was 443 bp. The average species richness of the murine oral bacterial communities was estimated to be about 200, but the communities were dominated by only two main phyla and several species. Therefore, the bacterial communities were relatively simple. The bacterial composition of the murine oral microbiota was significantly different from that of humans, and the lack of TLR2 had a negligible effect on the murine oral microbiota.

CONCLUSION: Pyrosequencing using the Roche/454 FLX Titanium successfully characterized mouse oral bacterial communities. The relatively simple oral bacterial communities of mice were not affected by TLR2 deficiency. These findings will provide a basis for future studies on the role of periodontal pathogens in the murine model of periodontitis.}, } @article {pmid20331772, year = {2010}, author = {Roossinck, MJ and Saha, P and Wiley, GB and Quan, J and White, JD and Lai, H and Chavarría, F and Shen, G and Roe, BA}, title = {Ecogenomics: using massively parallel pyrosequencing to understand virus ecology.}, journal = {Molecular ecology}, volume = {19 Suppl 1}, number = {}, pages = {81-88}, doi = {10.1111/j.1365-294X.2009.04470.x}, pmid = {20331772}, issn = {1365-294X}, mesh = {DNA, Complementary/genetics ; Ecology ; *Metagenomics ; Plant Viruses/classification/*genetics/isolation & purification ; RNA, Double-Stranded/genetics/isolation & purification ; RNA, Viral/genetics/isolation & purification ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; }, abstract = {Environmental samples have been analysed for viruses in metagenomic studies, but these studies have not linked individual viruses to their hosts. We designed a strategy to isolate double-stranded RNA, a hallmark of RNA virus infection, from individual plants and convert this to cDNA with a unique four nucleotide Tag at each end. Using 96 different Tags allowed us to pool samples and still retain the link to the original sample. We then analysed the sequence of pooled samples using massively parallel sequencing with Roche 454 pyrosequencing such that 384 samples could be assessed per picotiter plate. Using this method we have been able to analyse thousands of plants, and we have discovered several thousand new plant viruses, all linked to their specific plant hosts. Here we describe the method in detail, including the results and analysis for eight pools of samples. This technology will be extremely useful in understanding the full scope of plant virus biodiversity.}, } @article {pmid20331766, year = {2010}, author = {Creer, S and Fonseca, VG and Porazinska, DL and Giblin-Davis, RM and Sung, W and Power, DM and Packer, M and Carvalho, GR and Blaxter, ML and Lambshead, PJ and Thomas, WK}, title = {Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises.}, journal = {Molecular ecology}, volume = {19 Suppl 1}, number = {}, pages = {4-20}, doi = {10.1111/j.1365-294X.2009.04473.x}, pmid = {20331766}, issn = {1365-294X}, support = {G0900740/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Biodiversity ; Computational Biology ; DNA/isolation & purification ; Ecosystem ; Evolution, Molecular ; Metagenomics/*methods ; *Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 18S/genetics ; Ribosome Subunits, Small, Eukaryotic ; Sequence Analysis, DNA/*methods ; }, abstract = {Biodiversity assessment is the key to understanding the relationship between biodiversity and ecosystem functioning, but there is a well-acknowledged biodiversity identification gap related to eukaryotic meiofaunal organisms. Meiofaunal identification is confounded by the small size of taxa, morphological convergence and intraspecific variation. However, the most important restricting factor in meiofaunal ecological research is the mismatch between diversity and the number of taxonomists that are able to simultaneously identify and catalogue meiofaunal diversity. Accordingly, a molecular operational taxonomic unit (MOTU)-based approach has been advocated for en mass meiofaunal biodiversity assessment, but it has been restricted by the lack of throughput afforded by chain termination sequencing. Contemporary pyrosequencing offers a solution to this problem in the form of environmental metagenetic analyses, but this represents a novel field of biodiversity assessment. Here, we provide an overview of meiofaunal metagenetic analyses, ranging from sample preservation and DNA extraction to PCR, sequencing and the bioinformatic interrogation of multiple, independent samples using 454 Roche sequencing platforms. We report two examples of environmental metagenetic nuclear small subunit 18S (nSSU) analyses of marine and tropical rainforest habitats and provide critical appraisals of the level of putative recombinant DNA molecules (chimeras) in metagenetic data sets. Following stringent quality control measures, environmental metagenetic analyses achieve MOTU formation across the eukaryote domain of life at a fraction of the time and cost of traditional approaches. The effectiveness of Roche 454 sequencing brings substantial advantages to studies aiming to elucidate the molecular genetic richness of not only meiofaunal, but also all complex eukaryotic communities.}, } @article {pmid20337064, year = {2010}, author = {Xue, J and Xiao, LY and Zhou, XD}, title = {[The latest progress in studies of human oral microbiome].}, journal = {Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology}, volume = {28}, number = {1}, pages = {5-8}, pmid = {20337064}, issn = {1000-1182}, mesh = {Humans ; *Metagenome ; *Microbiota ; Mouth/*microbiology ; }, abstract = {With the successful implementation of Human Genome Project, more and more scientists started to pay attention on the second genome of human body: Microbiome. This paper will briefly introduce the latest developments of the Human Microbiome Project, the human oral microbiome research, and new technologies of microbial gene research.}, } @article {pmid20307274, year = {2010}, author = {Tamames, J and Abellán, JJ and Pignatelli, M and Camacho, A and Moya, A}, title = {Environmental distribution of prokaryotic taxa.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {85}, pmid = {20307274}, issn = {1471-2180}, mesh = {Archaea/classification/*genetics/*growth & development ; Bacteria/classification/*genetics/*growth & development ; Bayes Theorem ; Biodiversity ; DNA, Bacterial/genetics ; Databases, Genetic ; *Environmental Microbiology ; Genes, Bacterial ; Poisson Distribution ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The increasing availability of gene sequences of prokaryotic species in samples extracted from all kind of locations allows addressing the study of the influence of environmental patterns in prokaryotic biodiversity. We present a comprehensive study to address the potential existence of environmental preferences of prokaryotic taxa and the commonness of the specialist and generalist strategies. We also assessed the most significant environmental factors shaping the environmental distribution of taxa.

RESULTS: We used 16S rDNA sequences from 3,502 sampling experiments in natural and artificial sources. These sequences were taxonomically assigned, and the corresponding samples were also classified into a hierarchical classification of environments. We used several statistical methods to analyze the environmental distribution of taxa. Our results indicate that environmental specificity is not very common at the higher taxonomic levels (phylum to family), but emerges at lower taxonomic levels (genus and species). The most selective environmental characteristics are those of animal tissues and thermal locations. Salinity is another very important factor for constraining prokaryotic diversity. On the other hand, soil and freshwater habitats are the less restrictive environments, harboring the largest number of prokaryotic taxa. All information on taxa, samples and environments is provided at the envDB online database, http://metagenomics.uv.es/envDB.

CONCLUSIONS: This is, as far as we know, the most comprehensive assessment of the distribution and diversity of prokaryotic taxa and their associations with different environments. Our data indicate that we are still far from characterizing prokaryotic diversity in any environment, except, perhaps, for human tissues such as the oral cavity and the vagina.}, } @article {pmid20237576, year = {2010}, author = {Taok, M and Mundo, J and Sarde, CO and Schoefs, O and Cochet, N}, title = {Monitoring the impact of hydrocarbon contamination and nutrient addition on microbial density, activity, and diversity in soil.}, journal = {Canadian journal of microbiology}, volume = {56}, number = {2}, pages = {145-155}, doi = {10.1139/w09-119}, pmid = {20237576}, issn = {1480-3275}, mesh = {Alkanes/*toxicity ; Bacteria/*classification/*drug effects/growth & development/metabolism ; *Biodiversity ; Cluster Analysis ; DNA/biosynthesis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Metagenomics ; Molecular Sequence Data ; Nitrogen/metabolism ; Oxygen Consumption ; Phosphorus/metabolism ; Phylogeny ; RNA/biosynthesis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The development of optimal in situ bioremediation strategies requires a better knowledge of their impact on the soil microbial communities. We have evaluated the impact of hexadecane contamination and different nutrient amendments on soil microbial density and activity. Microbial density was measured via total DNA quantification, and microbial activity via respiration and RNA variation. The RNA/DNA ratio was also determined, as it is a potential indicator of microbial activity. PCR-amplified 16S rRNA genes were cloned and sequenced to analyze the diversity of bacterial communities. Nutrient addition significantly increased respiration and DNA and RNA concentrations in contaminated soil, indicating a limitation of degradation and growth by the availability of nitrogen and phosphorus in unamended microcosms. Hexadecane treatment slightly affected the diversity of the bacterial community, while it was dramatically reduced by nutrient treatments, particularly the addition of nitrogen and phosphorus. Microbial community composition was also altered with the enrichment of populations related to Nocardia in bioremediated soils, while uncultured Proteobacteria were mostly detected in uncontaminated soil.}, } @article {pmid20236171, year = {2010}, author = {Huse, SM and Welch, DM and Morrison, HG and Sogin, ML}, title = {Ironing out the wrinkles in the rare biosphere through improved OTU clustering.}, journal = {Environmental microbiology}, volume = {12}, number = {7}, pages = {1889-1898}, pmid = {20236171}, issn = {1462-2920}, support = {UH2 DK083993/DK/NIDDK NIH HHS/United States ; 1UH2DK083993-01/DK/NIDDK NIH HHS/United States ; }, mesh = {*Biodiversity ; *Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Escherichia coli/genetics ; Metagenomics/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment/*methods ; Sequence Analysis, DNA ; Staphylococcus epidermidis/genetics ; }, abstract = {Deep sequencing of PCR amplicon libraries facilitates the detection of low-abundance populations in environmental DNA surveys of complex microbial communities. At the same time, deep sequencing can lead to overestimates of microbial diversity through the generation of low-frequency, error-prone reads. Even with sequencing error rates below 0.005 per nucleotide position, the common method of generating operational taxonomic units (OTUs) by multiple sequence alignment and complete-linkage clustering significantly increases the number of predicted OTUs and inflates richness estimates. We show that a 2% single-linkage preclustering methodology followed by an average-linkage clustering based on pairwise alignments more accurately predicts expected OTUs in both single and pooled template preparations of known taxonomic composition. This new clustering method can reduce the OTU richness in environmental samples by as much as 30-60% but does not reduce the fraction of OTUs in long-tailed rank abundance curves that defines the rare biosphere.}, } @article {pmid20227843, year = {2010}, author = {Simonato, F and Gómez-Pereira, PR and Fuchs, BM and Amann, R}, title = {Bacterioplankton diversity and community composition in the Southern Lagoon of Venice.}, journal = {Systematic and applied microbiology}, volume = {33}, number = {3}, pages = {128-138}, doi = {10.1016/j.syapm.2009.12.006}, pmid = {20227843}, issn = {1618-0984}, mesh = {Bacteria/*classification/*genetics/isolation & purification ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; In Situ Hybridization, Fluorescence ; Italy ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The Lagoon of Venice is a large water basin that exchanges water with the Northern Adriatic Sea through three large inlets. In this study, the 16S rRNA approach was used to investigate the bacterial diversity and community composition within the southern basin of the Lagoon of Venice and at one inlet in October 2007 and June 2008. Comparative sequence analysis of 645 mostly partial 16S rRNA gene sequences indicated high diversity and dominance of Alphaproteobacteria, Gammaproteobacteria and Bacteroidetes at the lagoon as well as at the inlet station, therefore pointing to significant mixing. Many of these sequences were close to the 16S rRNA of marine, often coastal, bacterioplankton, such as the Roseobacter clade, the family Vibrionaceae, and class Flavobacteria. Sequences of Actinobacteria were indicators of a freshwater input. The composition of the bacterioplankton was quantified by catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) with a set of rRNA-targeted oligonucleotide probes. CARD-FISH counts corroborated the dominance of members of the phyla Alphaproteobacteria, Gammaproteobacteria and Bacteroidetes. When assessed by a probe set for the quantification of selected clades within Alphaproteobacteria and Gammaproteobacteria, bacterioplankton composition differed between October 2007 and June 2008, and also between the inlet and the lagoon. In particular, members of the readily culturable copiotrophic gammaproteobacterial genera Vibrio, Alteromonas and Pseudoalteromonas were enriched in the southern basin of the Lagoon of Venice. Interestingly, the alphaproteobacterial SAR11 clade and related clusters were also present in high abundances at the inlet and within the lagoon, which was indicative of inflow of water from the open sea.}, } @article {pmid20202856, year = {2010}, author = {Bution, ML and C Bresil, and Destéfano, RH and Tango, MF and da Silveira, WD and Paulino, LC and Caetano, FH and Solferini, VN}, title = {Molecular and ultrastructural profiles of the symbionts in Cephalotes ants.}, journal = {Micron (Oxford, England : 1993)}, volume = {41}, number = {5}, pages = {484-489}, doi = {10.1016/j.micron.2010.01.011}, pmid = {20202856}, issn = {1878-4291}, mesh = {Animals ; Bacteria/*genetics/*ultrastructure ; *Bacterial Physiological Phenomena ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Gastrointestinal Tract/microbiology ; Geography ; Hymenoptera/*microbiology ; Metagenome ; Microscopy, Electron, Transmission ; Nucleic Acid Denaturation ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {The molecular and ultrastructural profiles of the symbionts found in the midgut and ileum of Cephalotes atratus, Cephalotes clypeatus, and Cephalotes pusillus were determined using the V3 region of the bacterial 16S rDNA gene and transmission electron microscopy (T.E.M.). Two samples of C. atratus, three of C. clypeatus, and six of C. pusillus were analyzed. The coefficients of similarity ranged from 80% to 94% for the samples of symbionts from C. clypeatus and C. atratus, despite being collected in geographically distant sites. The variability within symbionts found in the samples of C. pusillus varied from 29% to 55%, in samples geographically close as well as distant. PCR-DGGE was effective for the purpose of this study and can be considered a versatile tool to analyze gut microbiota. Details of the ultrastructural aspect of these bacteria are presented.}, } @article {pmid20202776, year = {2010}, author = {Filteau, M and Lagacé, L and LaPointe, G and Roy, D}, title = {Seasonal and regional diversity of maple sap microbiota revealed using community PCR fingerprinting and 16S rRNA gene clone libraries.}, journal = {Systematic and applied microbiology}, volume = {33}, number = {3}, pages = {165-173}, doi = {10.1016/j.syapm.2010.02.003}, pmid = {20202776}, issn = {1618-0984}, mesh = {Acer/*microbiology ; Bacteria/*classification/*genetics ; *Biodiversity ; Cloning, Molecular ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gene Library ; Geography ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Quebec ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; }, abstract = {An arbitrary primed community PCR fingerprinting technique based on capillary electrophoresis was developed to study maple sap microbial community characteristics among 19 production sites in Québec over the tapping season. Presumptive fragment identification was made with corresponding fingerprint profiles of bacterial isolate cultures. Maple sap microbial communities were subsequently compared using a representative subset of 13 16S rRNA gene clone libraries followed by gene sequence analysis. Results from both methods indicated that all maple sap production sites and flow periods shared common microbiota members, but distinctive features also existed. Changes over the season in relative abundance of predominant populations showed evidence of a common pattern. Pseudomonas (64%) and Rahnella (8%) were the most abundantly and frequently represented genera of the 2239 sequences analyzed. Janthinobacterium, Leuconostoc, Lactococcus, Weissella, Epilithonimonas and Sphingomonas were revealed as occasional contaminants in maple sap. Maple sap microbiota showed a low level of deep diversity along with a high variation of similar 16S rRNA gene sequences within the Pseudomonas genus. Predominance of Pseudomonas is suggested as a typical feature of maple sap microbiota across geographical regions, production sites, and sap flow periods.}, } @article {pmid20200290, year = {2010}, author = {Forney, LJ and Gajer, P and Williams, CJ and Schneider, GM and Koenig, SS and McCulle, SL and Karlebach, S and Brotman, RM and Davis, CC and Ault, K and Ravel, J}, title = {Comparison of self-collected and physician-collected vaginal swabs for microbiome analysis.}, journal = {Journal of clinical microbiology}, volume = {48}, number = {5}, pages = {1741-1748}, pmid = {20200290}, issn = {1098-660X}, support = {U01 AI070921/AI/NIAID NIH HHS/United States ; AI-U01070921/AI/NIAID NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; *Biodiversity ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ego ; Female ; Humans ; *Metagenome ; Phylogeny ; *Physicians ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; *Self-Examination ; Sequence Analysis, DNA ; Vagina/*microbiology ; Young Adult ; }, abstract = {To our knowledge, no data are available on whether the microbial species composition and abundance sampled with self-collected vaginal swabs are comparable to those of swabs collected by clinicians. Twenty healthy women were recruited to the study during a routine gynecological visit. Eligible women were between 18 and 40 years old with regular menstrual cycles. Participants self-collected a vaginal swab using a standardized protocol and then were examined by a physician, who collected an additional five swabs from the lateral wall of the mid-vagina. In this study, the self-collected and three physician-obtained swabs were analyzed and compared using terminal restriction fragment length polymorphism and sequence analyses of the 16S rRNA genes. Vaginal microbial community comparative statistical analyses of both T-RFLP and 16S rRNA gene sequence datasets revealed that self-collected vaginal swabs sampled the same microbial diversity as physician collected swabs of the mid-vagina. These findings enable large-scale, field-based studies of the vaginal microbiome.}, } @article {pmid20190018, year = {2011}, author = {Gaget, V and Gribaldo, S and Tandeau de Marsac, N}, title = {An rpoB signature sequence provides unique resolution for the molecular typing of cyanobacteria.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {61}, number = {Pt 1}, pages = {170-183}, doi = {10.1099/ijs.0.019018-0}, pmid = {20190018}, issn = {1466-5034}, mesh = {Bacterial Proteins/*genetics ; Bacterial Typing Techniques/*methods ; Cyanobacteria/*classification/*genetics ; DNA, Bacterial/genetics ; DNA-Directed RNA Polymerases/*genetics ; INDEL Mutation ; Molecular Typing/*methods ; }, abstract = {The use of morphological characters for the classification of cyanobacteria has often led to ambiguous strain assignment. In the past two decades, the availability of sequences, such as those of the 16S rRNA, nif, cpc and rpoC1 genes, and the use of metagenomics, has steadily increased and has made the reconstruction of evolutionary relationships of some cyanobacterial groups possible in addition to improving strain assignment. Conserved indels (insertions/deletions) are present in all cyanobacterial RpoB (β subunit of RNA polymerase) sequences presently available in public databases. These indels are located in the Rpb2_6 domain of RpoB, which is involved in DNA binding and DNA-directed RNA polymerase activity. They are variable in length (6-44 aa) and sequence, and form part of what appears to be a longer signature sequence (43-81 aa). Indeed, a number of these sequences turn out to be distinctive among several strains of a given genus and even among strains of a given species. These signature sequences can thus be used to identify cyanobacteria at a subgenus level and can be useful molecular markers to establish the taxonomic positions of cyanobacterial isolates in laboratory cultures, and/or to assess cyanobacterial biodiversity in space and time in natural ecosystems.}, } @article {pmid20189795, year = {2010}, author = {Lee, HS and Kwon, KK and Kang, SG and Cha, SS and Kim, SJ and Lee, JH}, title = {Approaches for novel enzyme discovery from marine environments.}, journal = {Current opinion in biotechnology}, volume = {21}, number = {3}, pages = {353-357}, doi = {10.1016/j.copbio.2010.01.015}, pmid = {20189795}, issn = {1879-0429}, mesh = {Biodiversity ; Biotechnology/*methods ; *Enzymes ; Marine Biology/*methods ; }, abstract = {The enormous pool of biodiversity in marine ecosystems is an excellent natural reservoir for acquiring an inventory of enzymes with potential for biotechnological applications. Moreover, the opportunity for sustainable resource management has been greatly enhanced by recent advances in culturing methods for recalcitrant microbes. In this review, we will focus primarily on successful examples in culturing marine microbes and provide an overview of work examining the biotechnological potential of the marine reservoir, mainly through genomic strategies, such as activity-based functional screening of genomic and metagenomic libraries and homology-driven screening of enormous amounts of sequence data.}, } @article {pmid20182523, year = {2010}, author = {Hemme, CL and Deng, Y and Gentry, TJ and Fields, MW and Wu, L and Barua, S and Barry, K and Tringe, SG and Watson, DB and He, Z and Hazen, TC and Tiedje, JM and Rubin, EM and Zhou, J}, title = {Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community.}, journal = {The ISME journal}, volume = {4}, number = {5}, pages = {660-672}, doi = {10.1038/ismej.2009.154}, pmid = {20182523}, issn = {1751-7370}, mesh = {Bacteria/*classification/genetics/*isolation & purification/metabolism ; *Biodiversity ; Fresh Water/*microbiology ; Humans ; *Metagenomics ; Metals, Heavy/toxicity ; Nitric Acid/toxicity ; Organic Chemicals/toxicity ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents (approximately 50 years) has resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying gamma- and beta-proteobacterial populations. The resulting community is overabundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could have a key function in rapid response and adaptation to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.}, } @article {pmid20172578, year = {2010}, author = {Coetzee, B and Freeborough, MJ and Maree, HJ and Celton, JM and Rees, DJ and Burger, JT}, title = {Deep sequencing analysis of viruses infecting grapevines: Virome of a vineyard.}, journal = {Virology}, volume = {400}, number = {2}, pages = {157-163}, doi = {10.1016/j.virol.2010.01.023}, pmid = {20172578}, issn = {1096-0341}, mesh = {*Biodiversity ; Metagenome ; Phylogeny ; Plant Viruses/*classification/*genetics ; RNA, Double-Stranded/genetics/isolation & purification ; RNA, Viral/genetics/isolation & purification ; *Sequence Analysis, DNA ; South Africa ; Vitis/*virology ; }, abstract = {Double stranded RNA, isolated from 44 pooled randomly selected vines from a diseased South African vineyard, has been used in a deep sequencing analysis to build a census of the viral population. The dsRNA was sequenced in an unbiased manner using the sequencing-by-synthesis technology offered by the Illumina Genome Analyzer II and yielded 837 megabases of metagenomic sequence data. Four known viral pathogens were identified. It was found that Grapevine leafroll-associated virus 3 (GLRaV-3) is the most prevalent species, constituting 59% of the total reads, followed by Grapevine rupestris stem pitting-associated virus and Grapevine virus A. Grapevine virus E, a virus not previously reported in South African vineyards, was identified in the census. Viruses not previously identified in grapevine were also detected. The second most prevalent virus detected was a member of the Chrysoviridae family similar to Penicillium chrysogenum virus. Sequences aligning to two other mycoviruses were also detected.}, } @article {pmid20171997, year = {2010}, author = {Salonen, A and Nikkilä, J and Jalanka-Tuovinen, J and Immonen, O and Rajilić-Stojanović, M and Kekkonen, RA and Palva, A and de Vos, WM}, title = {Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis.}, journal = {Journal of microbiological methods}, volume = {81}, number = {2}, pages = {127-134}, doi = {10.1016/j.mimet.2010.02.007}, pmid = {20171997}, issn = {1872-8359}, mesh = {Adult ; Biodiversity ; DNA, Archaeal/genetics/*isolation & purification ; DNA, Bacterial/genetics/*isolation & purification ; Feces/*microbiology ; Humans ; Metagenomics/*methods ; Microarray Analysis/*methods ; Young Adult ; }, abstract = {Several different protocols are used for fecal DNA extraction, which is an integral step in all phylogenetic and metagenomic approaches to characterize the highly diverse intestinal ecosystem. We compared four widely used methods, and found their DNA yields to vary up to 35-fold. Bacterial, archaeal and human DNA was quantified by real-time PCR, and a compositional analysis of different extracts was carried out using the Human Intestinal Tract Chip, a 16S rRNA gene-based phylogenetic microarray. The overall microbiota composition was highly similar between the methods in contrast to the profound differences between the subjects (Pearson correlations >0.899 and 0.735, respectively). A detailed comparative analysis of mechanical and enzymatic methods showed that despite their overall similarity, the mechanical cell disruption by repeated bead beating showed the highest bacterial diversity and resulted in significantly improved DNA extraction efficiency of archaea and some bacteria, including Clostridium cluster IV. By applying the mechanical disruption method a high prevalence (67%) of methanogenic archaea was detected in healthy subjects (n=24), exceeding the typical values reported previously. The assessment of performance differences between different methodologies serves as a concrete step towards the comparison and reliable meta-analysis of the results obtained in different laboratories.}, } @article {pmid20154108, year = {2010}, author = {Parsley, LC and Consuegra, EJ and Thomas, SJ and Bhavsar, J and Land, AM and Bhuiyan, NN and Mazher, MA and Waters, RJ and Wommack, KE and Harper, WF and Liles, MR}, title = {Census of the viral metagenome within an activated sludge microbial assemblage.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {8}, pages = {2673-2677}, pmid = {20154108}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics/isolation & purification ; Bacteriophages/classification/genetics/isolation & purification ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Viral/chemistry/genetics ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*virology ; Virus Cultivation ; Viruses/*classification/*genetics/isolation & purification ; }, abstract = {The viral metagenome within an activated sludge microbial assemblage was sampled using culture-dependent and culture-independent methods and compared to the diversity of activated sludge bacterial taxa. A total of 70 unique cultured bacterial isolates, 24 cultured bacteriophages, 829 bacterial metagenomic clones of 16S rRNA genes, and 1,161 viral metagenomic clones were subjected to a phylogenetic analysis.}, } @article {pmid20144707, year = {2010}, author = {Singh, SK and Verma, P and Ramaiah, N and Chandrashekar, AA and Shouche, YS}, title = {Phylogenetic diversity of archaeal 16S rRNA and ammonia monooxygenase genes from tropical estuarine sediments on the central west coast of India.}, journal = {Research in microbiology}, volume = {161}, number = {3}, pages = {177-186}, doi = {10.1016/j.resmic.2010.01.008}, pmid = {20144707}, issn = {1769-7123}, mesh = {Archaea/*classification/*genetics ; Archaeal Proteins/genetics ; *Biodiversity ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/*microbiology ; India ; *Metagenome ; Molecular Sequence Data ; Oxidoreductases/genetics ; Pacific Ocean ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Phylogenetic diversity analyses of archaeal 16S rRNA and ammonia monooxygenase subunit A (AamoA) genes were carried out on sediment samples from the Mandovi and Zuari estuaries on the central west coast of India. The 16S rRNA gene libraries revealed quite high diversity of archaea in these sediments compared to previous reports from tropical and temperate estuarine sediments. Uncultured members of Crenarchaeota accounted for approximately 78% of 433 archaeal 16S rRNA gene clones from both of the estuaries. We detected archaeal 16S and amoA gene-related organisms capable of ammonia oxidation. Among Crenarchaeota, marine group I (MG I) was the most predominant. Clones matching the uncultured methanobacteria were predominant among the ribogroups of Euryarchaeota. Our results indicate that archaeal diversity in tropical estuarine sediments is influenced by the mangrove vegetation bordering the lower stretches of both estuaries. Higher diversity may be related to elevated land drainage during the monsoon, particularly in the Mandovi estuary sediments. Also, the diversity of AamoA sequences was higher in Mandovi sediments than those from Zuari and other tropical and/or temperate estuaries studied previously.}, } @article {pmid20139317, year = {2010}, author = {Manter, DK and Weir, TL and Vivanco, JM}, title = {Negative effects of sample pooling on PCR-based estimates of soil microbial richness and community structure.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {7}, pages = {2086-2090}, pmid = {20139317}, issn = {1098-5336}, mesh = {Bacteria/classification/*isolation & purification ; *Biodiversity ; Cluster Analysis ; DNA, Ribosomal Spacer/chemistry/genetics ; Fungi/classification/*isolation & purification ; Metagenomics/*methods ; Phylogeny ; Polymerase Chain Reaction/*methods ; *Soil Microbiology ; }, abstract = {In this study, we examined the effect of various pooling strategies on the characterization of soil microbial community composition and phylotype richness estimates. Automated ribosomal intergenic spacer analysis (ARISA) profiles were determined from soil samples that were (i) unpooled (extracted and amplified individually), (ii) pooled prior to PCR amplification, or (iii) pooled prior to DNA extraction. Regression analyses suggest that the less even the soil microbial community (i.e., low Shannon equitability, E(H)), the greater was the impact of either pooling strategy on microbial detection (R(2) = 0.766). For example, at a tropical rainforest site, which had the most uneven fungal (E(H) of 0.597) and bacterial communities (E(H) of 0.822), the unpooled procedure detected an additional 67 fungal and 115 bacterial phylotypes relative to either of the pooled procedures. Phylotype rarity, resulting in missed detection upon pooling, differed between the fungal and bacterial communities. Fungi were typified by locally abundant but spatially rare phylotypes, and the bacteria were typified by locally rare but spatially ubiquitous phylotypes. As a result, pooling differentially influenced plot comparisons, leading to an increase in similarity for the bacterial community and a decrease in the fungal community. In conclusion, although pooling reduces sample numbers and variability, it could mask a significant portion of the detectable microbial community, particularly for fungi due to their higher spatial heterogeneity.}, } @article {pmid20138146, year = {2010}, author = {Baudoin, E and Lerner, A and Mirza, MS and El Zemrany, H and Prigent-Combaret, C and Jurkevich, E and Spaepen, S and Vanderleyden, J and Nazaret, S and Okon, Y and Moënne-Loccoz, Y}, title = {Effects of Azospirillum brasilense with genetically modified auxin biosynthesis gene ipdC upon the diversity of the indigenous microbiota of the wheat rhizosphere.}, journal = {Research in microbiology}, volume = {161}, number = {3}, pages = {219-226}, doi = {10.1016/j.resmic.2010.01.005}, pmid = {20138146}, issn = {1769-7123}, mesh = {Azospirillum brasilense/genetics/growth & development/*metabolism ; Bacterial Proteins/genetics ; *Biodiversity ; Biomass ; Biosynthetic Pathways/genetics ; Carboxy-Lyases/genetics ; DNA Fingerprinting/methods ; DNA, Ribosomal Spacer/genetics ; Electrophoresis, Polyacrylamide Gel ; Gene Dosage ; Genetic Engineering ; Indoleacetic Acids/*metabolism ; Metagenome ; Nucleic Acid Denaturation ; Organisms, Genetically Modified/genetics/growth & development/metabolism ; Plant Roots/*microbiology ; Plant Shoots/growth & development ; Plasmids ; *Soil Microbiology ; Triticum/*microbiology ; }, abstract = {The phytostimulatory properties of Azospirillum inoculants, which entail production of the phytohormone indole-3-acetic acid (IAA), can be enhanced by genetic means. However, it is not known whether this could affect their interactions with indigenous soil microbes. Here, wheat seeds were inoculated with the wild-type strain Azospirillum brasilense Sp245 or one of three genetically modified (GM) derivatives and grown for one month. The GM derivatives contained a plasmid vector harboring the indole-3-pyruvate/phenylpyruvate decarboxylase gene ipdC (IAA production) controlled either by the constitutive promoter PnptII or the root exudate-responsive promoter PsbpA, or by an empty vector (GM control). All inoculants displayed equal rhizosphere population densities. Only inoculation with either ipdC construct increased shoot biomass compared with the non-inoculated control. At one month after inoculation, automated ribosomal intergenic spacer analysis (ARISA) revealed that the effect of the PsbpA construct on bacterial community structure differed from that of the GM control, which was confirmed by 16S rDNA-based denaturing gradient gel electrophoresis (DGGE). The fungal community was sensitive to inoculation with the PsbpA construct and especially the GM control, based on ARISA data. Overall, fungal and bacterial communities displayed distinct responses to inoculation of GM A. brasilense phytostimulators, whose effects could differ from those of the wild-type.}, } @article {pmid20138144, year = {2010}, author = {Kovacs, A and Yacoby, K and Gophna, U}, title = {A systematic assessment of automated ribosomal intergenic spacer analysis (ARISA) as a tool for estimating bacterial richness.}, journal = {Research in microbiology}, volume = {161}, number = {3}, pages = {192-197}, doi = {10.1016/j.resmic.2010.01.006}, pmid = {20138144}, issn = {1769-7123}, mesh = {Animals ; Automation/methods ; Bacteria/*classification/genetics ; Bacteriological Techniques/*methods ; *Biodiversity ; Computer Simulation ; DNA Fingerprinting/*methods ; DNA Primers/genetics ; DNA, Bacterial/*genetics ; DNA, Ribosomal Spacer/*genetics ; Metagenomics/*methods ; Mice ; Polymorphism, Genetic ; Sensitivity and Specificity ; }, abstract = {ARISA (automated ribosomal intergenic spacer analysis) is a commonly used method for microbial community analysis that provides estimates of microbial richness and diversity. Here we investigated the potential biases of ARISA in richness estimation by performing computer simulations using 722 complete genomes. Our simulations based on in silico PCR demonstrated that over 8% of bacterial strains represented by complete genomes will never yield a PCR fragment using ARISA primers, usually because their ribosomal RNA genes are not organized in an operon. Despite the tendency of ARISA to overestimate species richness, a strong linear correlation exists between the observed number of fragments, even after binning, and the actual number of species in the sample. This linearity is fairly robust to the taxon sampling in the database as it is also observed on subsets of the 722 genome database using a jackknife approach. However, this linearity disappears when the species richness is high and binned fragment lengths gradually become saturated. We suggest that for ARISA-based richness estimates, where the number of binned lengths observed ranges between 10 and 116, a correction should be used in order to obtain more accurate "species richness" results comparable to 16S rRNA clone-library data.}, } @article {pmid20127458, year = {2009}, author = {Sattin, SR and Cleveland, CC and Hood, E and Reed, SC and King, AJ and Schmidt, SK and Robeson, MS and Ascarrunz, N and Nemergut, DR}, title = {Functional shifts in unvegetated, perhumid, recently-deglaciated soils do not correlate with shifts in soil bacterial community composition.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {47}, number = {6}, pages = {673-681}, pmid = {20127458}, issn = {1976-3794}, mesh = {*Biodiversity ; Cluster Analysis ; DNA, Ribosomal/genetics ; Hydrogen-Ion Concentration ; Metagenome ; Molecular Sequence Data ; Nitrogen/analysis ; Nitrogen Fixation ; Organic Chemicals/analysis ; Phosphorus/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Soil/*analysis ; *Soil Microbiology ; United States ; }, abstract = {Past work in recently deglaciated soils demonstrates that microbial communities undergo shifts prior to plant colonization. To date, most studies have focused on relatively 'long' chronosequences with the ability to sample plant-free sites over at least 50 years of development. However, some recently deglaciated soils feature rapid plant colonization and questions remain about the relative rate of change in the microbial community in the unvegetated soils of these chronosequences. Thus, we investigated the forelands of the Mendenhall Glacier near Juneau, AK, USA, where plants rapidly establish. We collected unvegetated samples representing soils that had been ice-free for 0, 1, 4, and 8 years. Total nitrogen (N) ranged from 0.00 approximately 0.14 mg/g soil, soil organic carbon pools ranged from 0.6 approximately 2.3 mg/g soil, and both decreased in concentration between the 0 and 4 yr soils. Biologically available phosphorus (P) and pH underwent similar dynamics. However, both pH and available P increased in the 8 yr soils. Nitrogen fixation was nearly undetectable in the most recently exposed soils, and increased in the 8 yr soils to approximately 5 ng N fixed/cm(2)/h, a trend that was matched by the activity of the soil N-cycling enzymes urease and beta-l,4-N-acetyl-glucosa-minidase. 16S rRNA gene clone libraries revealed no significant differences between the 0 and 8 yr soils; however, 8 yr soils featured the presence of cyanobacteria, a division wholly absent from the 0 yr soils. Taken together, our results suggest that microbes are consuming allochtonous organic matter sources in the most recently exposed soils. Once this carbon source is depleted, a competitive advantage may be ceded to microbes not reliant on in situ nutrient sources.}, } @article {pmid20118356, year = {2010}, author = {Cuhel, J and Simek, M and Laughlin, RJ and Bru, D and Chèneby, D and Watson, CJ and Philippot, L}, title = {Insights into the effect of soil pH on N(2)O and N(2) emissions and denitrifier community size and activity.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {6}, pages = {1870-1878}, pmid = {20118356}, issn = {1098-5336}, mesh = {*Biodiversity ; DNA, Ribosomal/genetics ; Hydrogen-Ion Concentration ; *Metagenome ; Nitrites/metabolism ; Nitrogen/*metabolism ; Nitrogen Isotopes/metabolism ; Nitrous Oxide/*metabolism ; RNA, Ribosomal, 16S/genetics ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {The objective of this study was to investigate how changes in soil pH affect the N(2)O and N(2) emissions, denitrification activity, and size of a denitrifier community. We established a field experiment, situated in a grassland area, which consisted of three treatments which were repeatedly amended with a KOH solution (alkaline soil), an H(2)SO(4) solution (acidic soil), or water (natural pH soil) over 10 months. At the site, we determined field N(2)O and N(2) emissions using the (15)N gas flux method and collected soil samples for the measurement of potential denitrification activity and quantification of the size of the denitrifying community by quantitative PCR of the narG, napA, nirS, nirK, and nosZ denitrification genes. Overall, our results indicate that soil pH is of importance in determining the nature of denitrification end products. Thus, we found that the N(2)O/(N(2)O + N(2)) ratio increased with decreasing pH due to changes in the total denitrification activity, while no changes in N(2)O production were observed. Denitrification activity and N(2)O emissions measured under laboratory conditions were correlated with N fluxes in situ and therefore reflected treatment differences in the field. The size of the denitrifying community was uncoupled from in situ N fluxes, but potential denitrification was correlated with the count of NirS denitrifiers. Significant relationships were observed between nirS, napA, and narG gene copy numbers and the N(2)O/(N(2)O + N(2)) ratio, which are difficult to explain. However, this highlights the need for further studies combining analysis of denitrifier ecology and quantification of denitrification end products for a comprehensive understanding of the regulation of N fluxes by denitrification.}, } @article {pmid20112227, year = {2009}, author = {Berlanga, M and Paster, BJ and Guerrero, R}, title = {The taxophysiological paradox: changes in the intestinal microbiota of the xylophagous cockroach Cryptocercus punctulatus depending on the physiological state of the host.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {12}, number = {4}, pages = {227-236}, pmid = {20112227}, issn = {1618-1905}, support = {DE-10374/DE/NIDCR NIH HHS/United States ; DE-11443/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; *Biodiversity ; Cluster Analysis ; Cockroaches/*microbiology/*physiology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gastrointestinal Tract/microbiology ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The phylogenetic relationships of symbiotic bacteria from the xylophagous cockroach Cryptocercus (Cryptocercidae, Blattaria) were compared to those described in previous reports in lower termites. The 16S rDNA bacterial genes were PCR-amplified from DNA isolated from the entire hindgut using Bacteria-selective primers, and the 16S rDNA amplicons were cloned into Escherichia coli. The changes in the gut microbiota of Cryptocercus under three physiological conditions, "active," "fasting," and "dead," were studied. Analysis of the active-clone library revealed 45 new phylotypes (clones sharing >97% sequence identity were grouped into the same phylotype) from 54 analyzed clones. The clones were affiliated with the phyla Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes, Synergistetes, Verrucomicrobia, and candidate phylum Termite Group 1 (TG1). Clones belonging to Spirochaetes, Bacteroidetes, and TG1 phyla clustered with previously reported sequences obtained from the guts of several termites, suggesting that these clones are common constituents of the intestinal microbiota of lower termites and Cryptocercus. In the fasting-clone library, 19 new phylotypes, from 49 clones studied, were distinguished. The new phylotypes were affiliated with the phyla Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, Spirochaetes, Synergistetes, and the candidate phylum TM7. Finally, in the dead-clone library, 24 new phylotypes from 50 studied clones were found. The new phylotypes were affiliated with the phyla Firmicutes, Actinobacteria, and Proteobacteria. Thus, from active, to fasting, to dead physiological states, a decrease in the number of phyla present in the whole microbial gut was evident. However, in the dead physiological state, each phylum conserved contained more new phylotypes. This poses a taxophysiological paradox, because a stable, active physiological state of Cryptocercus-due to a continuous input of wood-supports a higher diversity of bacterial phyla, probably necessary to maintain a sharp O(2)-H(2) gradient in the gut. By contrast, in the dead state, nutrient input is limited to the residual gut microbiota that is killed by the newly oxic environment, thus providing a food source for other, aerobic or facultative anaerobic bacteria. This results in an increase in the internal diversity of the few remaining phyla.}, } @article {pmid20107988, year = {2010}, author = {Li, M and Hong, Y and Klotz, MG and Gu, JD}, title = {A comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sediments.}, journal = {Applied microbiology and biotechnology}, volume = {86}, number = {2}, pages = {781-790}, doi = {10.1007/s00253-009-2361-5}, pmid = {20107988}, issn = {1432-0614}, mesh = {Bacteria/*classification/enzymology/genetics/*isolation & purification ; Bacterial Proteins/genetics ; Biodiversity ; Cluster Analysis ; DNA Primers/*genetics ; DNA, Bacterial/chemistry/genetics ; Geologic Sediments/*microbiology ; Metagenomics/*methods ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Polymerase Chain Reaction/*methods ; Quaternary Ammonium Compounds/metabolism ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {Published polymerase chain reaction primer sets for detecting the genes encoding 16S rRNA gene and hydrazine oxidoreductase (hzo) in anammox bacteria were compared by using the same coastal marine sediment samples. While four previously reported primer sets developed to detect the 16S rRNA gene showed varying specificities between 12% and 77%, an optimized primer combination resulted in up to 98% specificity, and the recovered anammox 16S rRNA gene sequences were >95% sequence identical to published sequences from anammox bacteria in the Candidatus "Scalindua" group. Furthermore, four primer sets used in detecting the hzo gene of anammox bacteria were highly specific (up to 92%) and efficient, and the newly designed primer set in this study amplified longer hzo gene segments suitable for phylogenetic analysis. The optimized primer set for the 16S rRNA gene and the newly designed primer set for the hzo gene were successfully applied to identify anammox bacteria from marine sediments of aquaculture zone, coastal wetland, and deep ocean where the three ecosystems form a gradient of anthropogenic impact. Results indicated a broad distribution of anammox bacteria with high niche-specific community structure within each marine ecosystem.}, } @article {pmid20107985, year = {2010}, author = {Zhang, F and She, Y and Zheng, Y and Zhou, Z and Kong, S and Hou, D}, title = {Molecular biologic techniques applied to the microbial prospecting of oil and gas in the Ban 876 gas and oil field in China.}, journal = {Applied microbiology and biotechnology}, volume = {86}, number = {4}, pages = {1183-1194}, doi = {10.1007/s00253-009-2426-5}, pmid = {20107985}, issn = {1432-0614}, mesh = {Bacteria/*classification/genetics/growth & development/*isolation & purification ; *Biodiversity ; China ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fossil Fuels/*analysis ; *Metagenome ; Molecular Sequence Data ; Oils/*analysis/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Currently, molecular biologic techniques achieve a great development in studies of soil samples. The objective of this research is to improve methods for microbial prospecting of oil and gas by applying culture-independent techniques to soil sampled from above a known oil and gas field. Firstly, the community structure of soil bacteria above the Ban 876 Gas and Oil Field was analyzed based on 16S rRNA gene clone libraries. The soil bacteria communities were consistently different along the depth; however, Chloroflexi and Gemmatimonadetes were predominant and methanotrophs were minor in both bacteria libraries (DGS1 and DGS2). Secondly, the numbers of methane-oxidizing bacteria, quantified using a culture-dependent procedure and culture-independent group-specific real-time PCR (RT-PCR), respectively, were inconsistent with a quantify variance of one or two orders of magnitude. Special emphasis was given to the counting advantages of RT-PCR based on the methanotrophic pmoA gene. Finally, the diversity and distribution of methanotrophic communities in the soil samples were analyzed by constructing clone libraries of functional gene. All 508-bp inserts in clones phylogenetically belonged to the methanotrophic pmoA gene with similarities from 83% to 100%. However, most of the similarities were below 96%. Five clone libraries of methanotrophs clearly showed that the anomalous methanotrophs (Methylosinus and Methylocystis) occupy the studied area.}, } @article {pmid20097807, year = {2010}, author = {Koopman, MM and Fuselier, DM and Hird, S and Carstens, BC}, title = {The carnivorous pale pitcher plant harbors diverse, distinct, and time-dependent bacterial communities.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {6}, pages = {1851-1860}, pmid = {20097807}, issn = {1098-5336}, mesh = {Bacteria/*classification/genetics/*isolation & purification ; *Biodiversity ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Metagenome ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Sarraceniaceae/*microbiology ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {The ability of American carnivorous pitcher plants (Sarracenia) to digest insect prey is facilitated by microbial associations. Knowledge of the details surrounding this interaction has been limited by our capability to characterize bacterial diversity in this system. To describe microbial diversity within and between pitchers of one species, Sarracenia alata, and to explore how these communities change over time as pitchers accumulate and digest insect prey, we collected and analyzed environmental sequence tag (454 pyrosequencing) and genomic fingerprint (automated ribosomal intergenic spacer analysis and terminal restriction fragment length polymorphism) data. Microbial richness associated with pitcher plant fluid is high; more than 1,000 unique phylogroups were identified across at least seven phyla and 50 families. We documented an increase in bacterial diversity and abundance with time and observed repeated changes in bacterial community composition. Pitchers from different plants harbored significantly more similar bacterial communities at a given time point than communities coming from the same genetic host over time. The microbial communities in pitcher plant fluid also differ significantly from those present in the surrounding soil. These findings indicate that the bacteria associated with pitcher plant leaves are far from random assemblages and represent an important step toward understanding this unique plant-microbe interaction.}, } @article {pmid20069462, year = {2010}, author = {Krishnani, KK and Kathiravan, V and Natarajan, M and Kailasam, M and Pillai, SM}, title = {Diversity of sulfur-oxidizing bacteria in greenwater system of coastal aquaculture.}, journal = {Applied biochemistry and biotechnology}, volume = {162}, number = {5}, pages = {1225-1237}, doi = {10.1007/s12010-009-8886-3}, pmid = {20069462}, issn = {1559-0291}, mesh = {Amino Acid Sequence ; Animals ; Aquaculture/*methods ; Bacteria/*genetics/*metabolism ; Bacterial Proteins/chemistry ; Biodegradation, Environmental ; *Biodiversity ; Fishes/growth & development ; Genes, Bacterial/genetics ; Genetic Variation/*genetics ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sulfur/*metabolism ; Waste Disposal, Fluid/standards ; }, abstract = {Reduced sulfur compounds produced by the metabolism are the one of the major problems in aquaculture. In the present study, herbivorous fishes have been cultured as biomanipulators for secretions of slime, which enhanced the production of greenwater containing beneficial bacteria. The genes encoding soxB which is largely unique to sulfur-oxidizing bacteria (SOB) due to its hydrolytic function has been targeted for examining the diversity of SOB in the green water system of coastal aquaculture. Novel sequences obtained based on the sequencing of metagenomic clone libraries for soxB genes revealed the abundance of SOB in green water system. Phylogenetic tree constructed from aligned amino acid sequences demonstrated that different clusters have only 82-93% match with Roseobacter sp., Phaeobacter sp., Roseovarius sp., Sulfitobacter sp., Ruegeria sp., and Oceanibulbus sp. The level of conservation of the soxB amino acid sequences ranged from 42% to 71%. 16S rRNA gene analyses of enrichment culture from green water system revealed the presence of Pseudoxanthomonas sp., which has 97% similarity with nutritionally fastidious Indian strain of Pseudoxanthomonas mexicana-a sulfur chemolithotrophic gamma-proteobacterium. Our results illustrate the relevance of SOB in the functioning of the green water system of coastal shrimp aquaculture for oxidation of reduced sulfur compounds, which in turn maintain the sulfide concentration well within the prescribed safe levels.}, } @article {pmid20067591, year = {2009}, author = {Dawson, SC and Hagen, KD}, title = {Mapping the protistan 'rare biosphere'.}, journal = {Journal of biology}, volume = {8}, number = {12}, pages = {105}, pmid = {20067591}, issn = {1475-4924}, mesh = {Archaea/genetics/physiology ; Bacteria/classification/genetics ; Biodiversity ; Biological Evolution ; DNA, Protozoan/*analysis ; DNA, Ribosomal/*analysis ; *Ecosystem ; Eukaryota/physiology ; Genetic Variation/*immunology ; *Metagenome ; *Models, Biological ; Phylogeny ; RNA, Bacterial/analysis ; RNA, Protozoan/analysis ; }, abstract = {The use of cultivation-independent approaches to map microbial diversity, including recent work published in BMC Biology, has now shown that protists, like bacteria/archaea, are much more diverse than had been realized. Uncovering eukaryotic diversity may now be limited not by access to samples or cost but rather by the availability of full-length reference sequence data.}, } @article {pmid20064769, year = {2010}, author = {Sapkota, AR and Berger, S and Vogel, TM}, title = {Human pathogens abundant in the bacterial metagenome of cigarettes.}, journal = {Environmental health perspectives}, volume = {118}, number = {3}, pages = {351-356}, pmid = {20064769}, issn = {1552-9924}, mesh = {Bacteria/classification/*genetics/*isolation & purification ; Biodiversity ; Environmental Exposure/*adverse effects ; Humans ; *Metagenome ; Oligonucleotide Array Sequence Analysis ; RNA, Ribosomal, 16S/analysis/genetics ; Respiratory Tract Infections/*etiology/*microbiology ; Risk Assessment ; Smoking/*adverse effects ; Time Factors ; }, abstract = {BACKGROUND: Many studies have evaluated chemical, heavy metal, and other abiotic substances present in cigarettes and their roles in the development of lung cancer and other diseases, yet no studies have comprehensively evaluated bacterial diversity of cigarettes and the possible impacts of these microbes on respiratory illnesses in smokers and exposed nonsmokers.

OBJECTIVES: The goal of this study was to explore the bacterial metagenomes of commercially available cigarettes.

METHODS: A 16S rRNA-based taxonomic microarray and cloning and sequencing were used to evaluate total bacterial diversity of four brands of cigarettes. Normalized microarray data were compared using principal component analysis and hierarchical cluster analysis to evaluate potential differences in microbial diversity across cigarette brands.

RESULTS: Fifteen different classes of bacteria and a broad range of potentially pathogenic organisms were detected in all cigarette samples. Most notably, we detected Acinetobacter, Bacillus, Burkholderia, Clostridium, Klebsiella, Pseudomonas aeruginosa, and Serratia in > or = 90% of all cigarette samples. Other pathogenic bacteria detected included Campylobacter, Enterococcus, Proteus, and Staphylococcus. No significant variability in bacterial diversity was observed across the four different cigarette brands.

CONCLUSIONS: Previous studies have shown that smoking is associated with colonization by pathogenic bacteria and an increased risk of lung infections. However, this is the first study to show that cigarettes themselves could be the direct source of exposure to a wide array of potentially pathogenic microbes among smokers and other people exposed to secondhand smoke. The overall public health implications of these findings are unclear at this time, and future studies are necessary to determine whether bacteria in cigarettes could play important roles in the development of both infectious and chronic respiratory diseases.}, } @article {pmid20045332, year = {2010}, author = {Raina, JB and Dinsdale, EA and Willis, BL and Bourne, DG}, title = {Do the organic sulfur compounds DMSP and DMS drive coral microbial associations?.}, journal = {Trends in microbiology}, volume = {18}, number = {3}, pages = {101-108}, doi = {10.1016/j.tim.2009.12.002}, pmid = {20045332}, issn = {1878-4380}, mesh = {Animals ; Anthozoa/*metabolism/*microbiology ; Bacteria/*growth & development/*metabolism ; Biodiversity ; *Ecosystem ; Metagenome ; Sulfides/*metabolism ; Sulfonium Compounds/*metabolism ; Viruses/genetics ; }, abstract = {Dimethylsulfoniopropionate (DMSP) and dimethylsulfide (DMS) are key compounds in the global sulfur cycle. Moreover, DMS is particularly important in climate regulation owing to its role in cloud formation. Reef building corals are major contributors to the production of these two compounds and also form diverse and complex associations with bacteria, which are known to play a crucial role in the degradation of DMSP and DMS. Here, we highlight an extensive overlap between bacterial species implicated in DMSP/DMS degradation and those associated with corals, leading to the hypothesis that these two compounds play a major role in structuring coral-associated bacterial communities, with important consequences for coral health and the resilience of coral reefs. We also explore the publically available metagenome databases and show that genes implicated in DMSP metabolism are abundant in the viral component of coral-reef-derived metagenomes, indicating that viruses can act as a reservoir for such genes.}, } @article {pmid22129346, year = {2010}, author = {Smid, EJ and Hugenholtz, J}, title = {Functional genomics for food fermentation processes.}, journal = {Annual review of food science and technology}, volume = {1}, number = {}, pages = {497-519}, doi = {10.1146/annurev.food.102308.124143}, pmid = {22129346}, issn = {1941-1413}, mesh = {Fermentation ; *Food Handling ; *Food Microbiology ; Genomics/*methods ; Lactobacillales/genetics/metabolism ; Metagenomics/methods ; Models, Biological ; Probiotics/metabolism ; }, abstract = {This review describes recent scientific and technological drivers of food fermentation research. In addition, a number of practical implications of the results of this development will be highlighted. The first part of the manuscript elaborates on the message that genome sequence information gives us an unprecedented view on the biodiversity of microbes in food fermentation. This information can be made applicable for tailoring relevant characteristics of food products through fermentation. The second part deals with the integration of genome sequence data into metabolic models and the use of these models for a number of topics that are relevant for food fermentation processes. The final part will be about metagenomics approaches to reveal the complexity and understand the functionality of undefined complex microbial consortia used in a diverse range of food fermentation processes.}, } @article {pmid20033072, year = {2010}, author = {Bodaker, I and Sharon, I and Suzuki, MT and Feingersch, R and Shmoish, M and Andreishcheva, E and Sogin, ML and Rosenberg, M and Maguire, ME and Belkin, S and Oren, A and Béjà, O}, title = {Comparative community genomics in the Dead Sea: an increasingly extreme environment.}, journal = {The ISME journal}, volume = {4}, number = {3}, pages = {399-407}, doi = {10.1038/ismej.2009.141}, pmid = {20033072}, issn = {1751-7370}, mesh = {Archaea/*classification/*genetics ; *Biodiversity ; Cations/metabolism ; Cluster Analysis ; DNA Transposable Elements ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; *Metagenome ; *Metagenomics ; Molecular Sequence Data ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Owing to the extreme salinity (approximately 10 times saltier than the oceans), near toxic magnesium levels (approximately 2.0 M Mg(2+)), the dominance of divalent cations, acidic pH (6.0) and high-absorbed radiation flux rates, the Dead Sea represents a unique and harsh ecosystem. Measures of microbial presence (microscopy, pigments and lipids) indicate that during rare bloom events after exceptionally rainy seasons, the microbial communities can reach high densities. However, most of the time, when the Dead Sea level is declining and halite is precipitating from the water column, it is difficult to reliably measure the presence of microorganisms and their activities. Although a number of halophilic Archaea have been previously isolated from the Dead Sea, polar lipid analyses of biomass collected during Dead Sea blooms suggested that these isolates were not the major components of the microbial community of these blooms. In this study, in an effort to characterize the perennial microbial community of the Dead Sea and compare it with bloom assemblages, we performed metagenomic analyses of concentrated biomass from hundreds of liters of brine and of microbial material from the last massive Dead Sea bloom. The difference between the two conditions was reflected in community composition and diversity, in which the bloom was different and less diverse from the residual brine population. The distributional patterns of microbial genes suggested Dead Sea community trends in mono- and divalent cation metabolisms as well as in transposable elements. This may indicate possible mechanisms and pathways enabling these microbes to survive in such a harsh environment.}, } @article {pmid20033071, year = {2010}, author = {Sawicka, JE and Robador, A and Hubert, C and Jørgensen, BB and Brüchert, V}, title = {Effects of freeze-thaw cycles on anaerobic microbial processes in an Arctic intertidal mud flat.}, journal = {The ISME journal}, volume = {4}, number = {4}, pages = {585-594}, doi = {10.1038/ismej.2009.140}, pmid = {20033071}, issn = {1751-7370}, mesh = {Arctic Regions ; Bacteria, Anaerobic/chemistry/classification/metabolism/*physiology ; Biodiversity ; DNA, Bacterial/genetics ; Fatty Acids, Volatile/analysis ; *Freezing ; Geologic Sediments/*microbiology ; Metagenome ; Nucleic Acid Denaturation ; Oxidation-Reduction ; Seasons ; *Soil Microbiology ; Sulfates/metabolism ; Svalbard ; }, abstract = {Insight into the effects of repeated freezing and thawing on microbial processes in sediments and soils is important for understanding sediment carbon cycling at high latitudes acutely affected by global warming. Microbial responses to repeated freeze-thaw conditions were studied in three complementary experiments using arctic sediment collected from an intertidal flat that is exposed to seasonal freeze-thaw conditions (Ymerbukta, Svalbard, Arctic Ocean). The sediment was subjected to oscillating freeze-thaw incubations, either gradual, from -5 to 4 degrees C, or abrupt, from -20 to 10 degrees C. Concentrations of low-molecular weight carboxylic acids (volatile fatty acids) were measured and sulfate reduction was assessed by measuring (35)S sulfate reduction rates (SRRs). Gradual freeze-thaw incubation decreased microbial activity in the frozen state to 0.25 % of initial levels at 4 degrees C, but activity resumed rapidly reaching >60 % of initial activity in the thawed state. Exposure of sediments to successive large temperature changes (-20 versus 10 degrees C) decreased SRR by 80% of the initial activity, suggesting that a fraction of the bacterial community recovered rapidly from extreme temperature fluctuations. This is supported by 16S rRNA gene-based denaturing gradient gel electrophoresis profiles that revealed persistence of the dominant microbial taxa under repeated freeze-thaw cycles. The fast recovery of the SRRs suggests that carbon mineralization in thawing arctic sediment can resume without delay or substantial growth of microbial populations.}, } @article {pmid20030730, year = {2010}, author = {Ciric, L and Philp, JC and Whiteley, AS}, title = {Hydrocarbon utilization within a diesel-degrading bacterial consortium.}, journal = {FEMS microbiology letters}, volume = {303}, number = {2}, pages = {116-122}, doi = {10.1111/j.1574-6968.2009.01871.x}, pmid = {20030730}, issn = {1574-6968}, mesh = {Bacteria/*classification/genetics/isolation & purification/*metabolism ; Bacterial Typing Techniques ; *Biodiversity ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Gasoline/*microbiology ; Hydrocarbons/*metabolism ; Metagenome ; Nucleic Acid Denaturation ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Diesel fuel is a common environmental pollutant comprised of a large number of both aromatic and aliphatic hydrocarbons. The microbial degradation of individual hydrocarbons has been well characterized, however, the community dynamics within a system degrading a complex pollutant such as diesel fuel are still poorly understood. The growth capabilities of a diesel-degrading consortium, along with organisms isolated from a contaminated site, were investigated using molecular profiling, isolation, and physiological methods using 10 of the fuel's most abundant constituents as sole carbon sources. The results indicated that the degradation of the fuel's constituents may be shared among the diverse microbial community. Some organisms were capable of growth on the majority of the hydrocarbons tested, whereas others seemed specialized to only a few of the substrates.}, } @article {pmid20010634, year = {2010}, author = {Humbert, S and Tarnawski, S and Fromin, N and Mallet, MP and Aragno, M and Zopfi, J}, title = {Molecular detection of anammox bacteria in terrestrial ecosystems: distribution and diversity.}, journal = {The ISME journal}, volume = {4}, number = {3}, pages = {450-454}, doi = {10.1038/ismej.2009.125}, pmid = {20010634}, issn = {1751-7370}, mesh = {Anaerobiosis ; Bacteria/*classification/*genetics ; Bacterial Proteins/genetics ; *Biodiversity ; DNA, Bacterial/chemistry/*genetics/isolation & purification ; DNA, Ribosomal/chemistry/genetics ; *Ecosystem ; Metagenome ; Oxidation-Reduction ; Quaternary Ammonium Compounds/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Anaerobic oxidation of ammonium (anammox) is recognized as an important process in the marine nitrogen cycle yet nothing is known about the distribution, diversity and activity of anammox bacteria in the terrestrial realm. In this study, we report on the detection of anammox sequences of Candidatus 'Brocadia', 'Kuenenia', 'Scalindua' and 'Jettenia' in marshes, lakeshores, a contaminated porous aquifer, permafrost soil, agricultural soil and in samples associated with nitrophilic or nitrogen-fixing plants. This suggests a higher diversity of anammox bacteria in terrestrial than in marine ecosystems and could be a consequence of the larger variety of suitable niches in soils. Anammox bacteria were not ubiquitously present but were only detected in certain soil types and at particular depths, thus reflecting specific ecological requirements. As opposed to marine water column habitats where Candidatus 'Scalindua' dominates anammox guilds, 'Kuenenia' and 'Brocadia' appear to be the most common representatives in terrestrial environments.}, } @article {pmid19940845, year = {2010}, author = {Hill, DA and Hoffmann, C and Abt, MC and Du, Y and Kobuley, D and Kirn, TJ and Bushman, FD and Artis, D}, title = {Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis.}, journal = {Mucosal immunology}, volume = {3}, number = {2}, pages = {148-158}, pmid = {19940845}, issn = {1935-3456}, support = {R01 AI074878/AI/NIAID NIH HHS/United States ; T32 AI060516-01A2/AI/NIAID NIH HHS/United States ; DK50306/DK/NIDDK NIH HHS/United States ; P30 DK050306/DK/NIDDK NIH HHS/United States ; S10 RR024525/RR/NCRR NIH HHS/United States ; R01 AI074878-01A1/AI/NIAID NIH HHS/United States ; AI074878/AI/NIAID NIH HHS/United States ; R21 AI083480-01/AI/NIAID NIH HHS/United States ; T32 AI060516/AI/NIAID NIH HHS/United States ; T32 AI05528/AI/NIAID NIH HHS/United States ; R21 AI083480/AI/NIAID NIH HHS/United States ; S10 RR024525-01/RR/NCRR NIH HHS/United States ; R01 AI061570-01/AI/NIAID NIH HHS/United States ; T32 AI055428/AI/NIAID NIH HHS/United States ; R01 AI095466/AI/NIAID NIH HHS/United States ; R01 AI061570/AI/NIAID NIH HHS/United States ; T32 AI055428-01/AI/NIAID NIH HHS/United States ; S10RR024525/RR/NCRR NIH HHS/United States ; AI61570/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics/immunology ; *Biodiversity ; CD4-Positive T-Lymphocytes/immunology ; Homeostasis/*drug effects ; Humans ; Intestines/drug effects/immunology/*microbiology ; *Metagenomics ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Despite widespread use of antibiotics, few studies have measured their effects on the burden or diversity of bacteria in the mammalian intestine. We developed an oral antibiotic treatment protocol and characterized its effects on murine intestinal bacterial communities and immune cell homeostasis. Antibiotic administration resulted in a 10-fold reduction in the amount of intestinal bacteria present and sequencing of 16S rDNA segments revealed significant temporal and spatial effects on luminal and mucosal-associated communities including reductions in luminal Firmicutes and mucosal-associated Lactobacillus species, and persistence of bacteria belonging to the Bacteroidetes and Proteobacteria phyla. Concurrently, antibiotic administration resulted in reduced RELM beta production, and reduced production of interferon-gamma and interleukin-17A by mucosal CD4(+) T lymphocytes. This comprehensive temporal and spatial metagenomic analyses will provide a resource and framework to test the influence of bacterial communities in murine models of human disease.}, } @article {pmid19926862, year = {2009}, author = {Luo, H and Benner, R and Long, RA and Hu, J}, title = {Subcellular localization of marine bacterial alkaline phosphatases.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {50}, pages = {21219-21223}, pmid = {19926862}, issn = {1091-6490}, mesh = {Alkaline Phosphatase/analysis/genetics/*metabolism ; Bacteria/enzymology ; Bacterial Proteins/analysis/genetics ; Biodiversity ; Biological Transport ; Computational Biology ; Cytosol/chemistry ; Databases, Nucleic Acid ; *Ecosystem ; Extracellular Matrix/chemistry ; Marine Biology ; Oceans and Seas ; Phosphates/*metabolism ; }, abstract = {Bacterial alkaline phosphatases (APases) are important enzymes in organophosphate utilization in the ocean. The subcellular localization of APases has significant ecological implications for marine biota but is largely unknown. The extensive metagenomic sequence databases from the Global Ocean Sampling Expedition provide an opportunity to address this question. A bioinformatics pipeline was developed to identify marine bacterial APases from the metagenomic databases, and a consensus classification algorithm was designed to predict their subcellular localizations. We identified 3,733 bacterial APase sequences (including PhoA, PhoD, and PhoX) and found that cytoplasmic (41%) and extracellular (30%) APases exceed their periplasmic (17%), outer membrane (12%), and inner membrane (0.9%) counterparts. The unexpectedly high abundance of cytoplasmic APases suggests that the transport and intracellular hydrolysis of small organophosphate molecules is an important mechanism for bacterial acquisition of phosphorus (P) in the surface ocean. On average, each marine bacterium possessed at least one suite of uptake of glycerol phosphate (ugp) genes (e.g., ugpA, ugpB, ugpC, ugpE) for dissolved organic phosphorus (DOP) transport, but only half of them had ugpQ, which hydrolyzes transported DOP, indicating that cytoplasmic APases play a role in hydrolyzing transported DOP. The most abundant heterotrophic marine bacteria, alpha- and gamma-Proteobacteria, might hydrolyze DOP outside the cytoplasmic membrane, but the former could also transport and hydrolyze DOP in the cytoplasm. The abundant extracellular APases could provide bioavailable P for organisms that cannot directly access organophosphates, and thereby increase marine biological productivity and diversity.}, } @article {pmid19906901, year = {2010}, author = {Rogers, GB and Skelton, S and Serisier, DJ and van der Gast, CJ and Bruce, KD}, title = {Determining cystic fibrosis-affected lung microbiology: comparison of spontaneous and serially induced sputum samples by use of terminal restriction fragment length polymorphism profiling.}, journal = {Journal of clinical microbiology}, volume = {48}, number = {1}, pages = {78-86}, pmid = {19906901}, issn = {1098-660X}, mesh = {Adult ; Bacteria/*classification/genetics ; Bacterial Infections/*microbiology ; *Biodiversity ; Cystic Fibrosis/*complications ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Female ; Humans ; Lung/*microbiology ; Male ; *Metagenomics ; *Polymorphism, Restriction Fragment Length ; Sputum/microbiology ; Young Adult ; }, abstract = {Sampling of the lower airways of the adult cystic fibrosis (CF) lung has received insufficient detailed consideration, with the importance of sampling strategies for bacteriological outcome not known. Although spontaneously expectorated sputum (SES) samples are often used for diagnostic bacteriological analysis, induced sputum (IS) methods have advantages. This study examined whether significant differences in bacterial content were detected when using a culture-independent, molecular profiling technique to analyze SES or IS samples. Moreover, this work examined what trends relating to bacterial species distributions and reproducibility were found in sequentially induced sputum samples and what implications this has for pathogen detection. Terminal restriction fragment length polymorphism (T-RFLP) analysis was performed on a SES sample and 4 subsequent IS samples taken at 5-min intervals from 10 clinically stable, adult CF patients. This was repeated over 3 sampling days, with variability between samples, induction periods, and sampling days determined. A diverse range of bacterial species, including potentially novel pathogens, was found. No significant difference in bacterial content was observed for either SES or serial IS samples. On average, the analysis of a single sample from any time point resolved approximately 58% of total bacterial diversity achieved by analysis of an SES sample and 4 subsequent IS samples. The reliance on analysis of a single respiratory sample was not sufficient for the detection of recognized CF pathogens in all instances. Close correlation between T-RFLP and microbiological data in the detection of key species indicates the importance of these findings in routine diagnostics for the detection of recognized and novel CF pathogens.}, } @article {pmid19898553, year = {2009}, author = {Lin, B and Monreal, CM and Tambong, JT and Miguez, CB and Carrasco-Medina, L}, title = {Phylogenetic analysis of methanotrophic communities in cover soils of a landfill in Ontario.}, journal = {Canadian journal of microbiology}, volume = {55}, number = {9}, pages = {1103-1112}, doi = {10.1139/w09-069}, pmid = {19898553}, issn = {1480-3275}, mesh = {Bacterial Proteins/genetics ; *Biodiversity ; Carbon/analysis ; Cluster Analysis ; DNA Fingerprinting ; Electrophoresis, Polyacrylamide Gel ; *Metagenome ; Methane/*metabolism ; Molecular Sequence Data ; Nitrogen/analysis ; Nucleic Acid Denaturation ; Ontario ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology ; Soil/analysis ; *Soil Microbiology ; }, abstract = {We examined the methanotrophs in the Trail Road Landfill soils, Ottawa, Ontario, through cultivation-independent molecular assay and the culturing approach. Denaturing gradient gel electrophoresis (DGGE) analysis of amplified methanotroph-specific 16S rDNA gene fragments revealed a more diverse type I (RuMP pathway) methanotrophic community than type II (serine pathway) in 17 soil samples taken along a 50 m transect. The type II methanotrophic community was less diverse, with the dominance of Methylocystis in almost all samples, and clustering with high similarity (85%-88%). Also, the results showed that the C/N ratio of soil organic matter could significantly affect the methanotrophic community structures. The DGGE results were supported by sequence analysis of cloned pmoA. Members of the genera Methylobacter (type I), Methylocaldum (type X), and Methylocystis (type II) appeared to be the dominant methanotrophs. From methanotrophic enrichments, we isolated type I Methylobacter sp., and 3 type II Methylocystis spp.,which appeared to be one of the dominant bacteria species in the soil sample from which isolates were obtained.}, } @article {pmid19898551, year = {2009}, author = {Ndaw, SM and Gama-Rodrigues, AC and Gama-Rodrigues, EF and Sales, KR and Rosado, AS}, title = {Relationships between bacterial diversity, microbial biomass, and litter quality in soils under different plant covers in northern Rio de Janeiro State, Brazil.}, journal = {Canadian journal of microbiology}, volume = {55}, number = {9}, pages = {1089-1095}, doi = {10.1139/w09-066}, pmid = {19898551}, issn = {1480-3275}, mesh = {*Biodiversity ; Biomass ; Brazil ; Carbon/analysis ; DNA Fingerprinting ; DNA, Bacterial/isolation & purification ; Electrophoresis, Polyacrylamide Gel ; Metagenome ; Nitrogen/analysis ; Nucleic Acid Denaturation ; *Plant Development ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {Microbial populations are primarily responsible for the decomposition of organic residues, the nutrients cycle, and the flow of energy inside of soil. The present study was undertaken to link soil microbiological and soil biochemical parameters with soil- and litter-quality conditions in the surface layer from 5 sites differing in plant cover, in stand age, and in land-use history. The aim was to see how strongly these differences affect the soil microbial attributes and to identify how microbiological processes and structures can be influenced by soil and litter quality. Soil and litter samples were collected from 5 sites according to different land use: preserved forest, nonpreserved forest, secondary forest, pasture, and eucalyptus plantation. Soil and litter microbial biomass and activity were analysed and DNA was extracted from soil. The DNA concentrations and soil microbial C and N correlated positively and significantly, suggesting that these are decisive nutrients for microbial growth and time required for microbial biomass renewal. The litter microbial biomass represented a source of C and N higher than soil microbial biomass and can be an important layer to contribute to tropical soil with low C and N availability. The litter quality influenced the litter and soil microbial biomass and activity and the soil bacterial diversity. The chemical and nutritional quality of the litter influenced the structure and microbial community composition in the eucalyptus plantation.}, } @article {pmid19892985, year = {2009}, author = {López-Bueno, A and Tamames, J and Velázquez, D and Moya, A and Quesada, A and Alcamí, A}, title = {High diversity of the viral community from an Antarctic lake.}, journal = {Science (New York, N.Y.)}, volume = {326}, number = {5954}, pages = {858-861}, doi = {10.1126/science.1179287}, pmid = {19892985}, issn = {1095-9203}, mesh = {Animals ; Antarctic Regions ; Biodiversity ; Cold Climate ; DNA Viruses/classification/*genetics/isolation & purification/physiology ; DNA, Circular/genetics ; DNA, Single-Stranded/genetics ; DNA, Viral/genetics ; *Ecosystem ; Freezing ; Fresh Water/microbiology/parasitology/*virology ; Genes, Viral ; *Genetic Variation ; *Genome, Viral ; Ice Cover ; *Metagenome ; Molecular Sequence Data ; Seasons ; Virus Physiological Phenomena ; Virus Replication ; Viruses/classification/*genetics/isolation & purification ; }, abstract = {Viruses are the most abundant biological entities and can control microbial communities, but their identity in terrestrial and freshwater Antarctic ecosystems is unknown. The genetic structure of an Antarctic lake viral community revealed unexpected genetic richness distributed across the highest number of viral families that have been found to date in aquatic viral metagenomes. In contrast to other known aquatic viromes, which are dominated by bacteriophage sequences, this Antarctic virus assemblage had a large proportion of sequences related to eukaryotic viruses, including phycodnaviruses and single-stranded DNA (ssDNA) viruses not previously identified in aquatic environments. We also observed that the transition from an ice-covered lake in spring to an open-water lake in summer led to a change from a ssDNA- to a double-stranded DNA-virus-dominated assemblage, possibly reflecting a seasonal shift in host organisms.}, } @article {pmid19892944, year = {2009}, author = {Costello, EK and Lauber, CL and Hamady, M and Fierer, N and Gordon, JI and Knight, R}, title = {Bacterial community variation in human body habitats across space and time.}, journal = {Science (New York, N.Y.)}, volume = {326}, number = {5960}, pages = {1694-1697}, pmid = {19892944}, issn = {1095-9203}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; T32 GM065103-08/GM/NIGMS NIH HHS/United States ; DK64540/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; P50 DK064540/DK/NIDDK NIH HHS/United States ; DK78669/DK/NIDDK NIH HHS/United States ; T32 GM065103/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; Cluster Analysis ; DNA, Bacterial/analysis/genetics/isolation & purification ; DNA, Ribosomal/analysis/genetics/isolation & purification ; Ear Canal/*microbiology ; Feces/*microbiology ; Female ; Genes, rRNA ; Hair/*microbiology ; Humans ; Male ; *Metagenome ; Middle Aged ; Mouth/*microbiology ; Nose/*microbiology ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Skin/*microbiology ; Time Factors ; }, abstract = {Elucidating the biogeography of bacterial communities on the human body is critical for establishing healthy baselines from which to detect differences associated with diseases. To obtain an integrated view of the spatial and temporal distribution of the human microbiota, we surveyed bacteria from up to 27 sites in seven to nine healthy adults on four occasions. We found that community composition was determined primarily by body habitat. Within habitats, interpersonal variability was high, whereas individuals exhibited minimal temporal variability. Several skin locations harbored more diverse communities than the gut and mouth, and skin locations differed in their community assembly patterns. These results indicate that our microbiota, although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome changes cause or prevent disease.}, } @article {pmid19844706, year = {2010}, author = {Ramos, CG and Grilo, AM and Sousa, SA and Barbosa, ML and Nadais, H and Leitão, JH}, title = {A new methodology combining PCR, cloning, and sequencing of clones discriminated by RFLP for the study of microbial populations: application to an UASB reactor sample.}, journal = {Applied microbiology and biotechnology}, volume = {85}, number = {3}, pages = {801-806}, doi = {10.1007/s00253-009-2268-1}, pmid = {19844706}, issn = {1432-0614}, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; Bioreactors/microbiology ; *Cloning, Molecular ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Metagenomics/*methods ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {This work describes a methodology combining DNA extraction, polymerase chain reaction amplification with primers targeting 16S ribosomal RNA genes, cloning, and sequencing of clones previously analyzed by restriction fragment length polymorphism (RFLP), which can be applied to study the microbial diversity in a given habitat. The methodology allows the minimization of the sequencing effort, which is particularly relevant when analyzing large numbers of clones. The methodology does not require particularly skilled personnel and can easily be adaptable to the molecular characterization of virtually any particular microbial population, provided that both adequate primers and suitable restriction enzymes for RFLP analysis of the clone library have been chosen. An example of application is presented, in which a sample taken from a continuously operating upflow anaerobic sludge blanket reactor was analyzed. RFLP analysis of the initial 162 clones with HaeIII allowed the identification of only 28 distinct profiles. As expected, identical RFLP profiles corresponded to identical nucleotide sequences.}, } @article {pmid19830416, year = {2010}, author = {Korenblum, E and Valoni, E and Penna, M and Seldin, L}, title = {Bacterial diversity in water injection systems of Brazilian offshore oil platforms.}, journal = {Applied microbiology and biotechnology}, volume = {85}, number = {3}, pages = {791-800}, doi = {10.1007/s00253-009-2281-4}, pmid = {19830416}, issn = {1432-0614}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*classification/drug effects/*genetics ; *Biodiversity ; Brazil ; Cluster Analysis ; Corrosion ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Metagenomics ; Molecular Sequence Data ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; *Water Microbiology ; }, abstract = {Biogenic souring and microbial-influenced corrosion is a common scenario in water-flooded petroleum reservoirs. Water injection systems are continuously treated to control bacterial contamination, but some bacteria that cause souring and corrosion can persist even after different treatments have been applied. Our aim was to increase our knowledge of the bacterial communities that persist in the water injection systems of three offshore oil platforms in Brazil. To achieve this goal, we used a culture-independent molecular approach (16S ribosomal RNA gene clone libraries) to analyze seawater samples that had been subjected to different treatments. Phylogenetic analyses revealed that the bacterial communities from the different platforms were taxonomically different. A predominance of bacterial clones affiliated with Gammaproteobacteria, mostly belonging to the genus Marinobacter (60.7%), were observed in the platform A samples. Clones from platform B were mainly related to the genera Colwellia (37.9%) and Achromobacter (24.6%), whereas clones obtained from platform C were all related to unclassified bacteria. Canonical correspondence analyses showed that different treatments such as chlorination, deoxygenation, and biocide addition did not significantly influence the bacterial diversity in the platforms studied. Our results demonstrated that the injection water used in secondary oil recovery procedures contained potentially hazardous bacteria, which may ultimately cause souring and corrosion.}, } @article {pmid19826809, year = {2010}, author = {Cabrol, L and Malhautier, L and Poly, F and Lepeuple, AS and Fanlo, JL}, title = {Assessing the bias linked to DNA recovery from biofiltration woodchips for microbial community investigation by fingerprinting.}, journal = {Applied microbiology and biotechnology}, volume = {85}, number = {3}, pages = {779-790}, doi = {10.1007/s00253-009-2253-8}, pmid = {19826809}, issn = {1432-0614}, mesh = {Biodiversity ; Cluster Analysis ; DNA/*genetics/*isolation & purification ; DNA Fingerprinting/*methods ; Electrophoresis, Polyacrylamide Gel ; Filtration/methods ; Metagenomics/*methods ; Nucleic Acid Denaturation ; Polymerase Chain Reaction ; Wood/*microbiology ; }, abstract = {In this study, we explored methodological aspects of nucleic acid recovery from microbial communities involved in a gas biofilter filled with pine bark woodchips. DNA was recovered indirectly in two steps, comparing different methods: cell dispersion (crushing, shaking, and sonication) and DNA extraction (three commercial kits and a laboratory protocol). The objectives were (a) to optimize cell desorption from the packing material and (b) to compare the 12 combinations of desorption and extraction methods, according to three relevant criteria: DNA yield, DNA purity, and community structure representation by denaturing gradient gel electrophoresis (DGGE). Cell dispersion was not influenced by the operational parameters tested for shaking and blending, while it increased with time for sonication. DNA extraction by the laboratory protocol provided the highest DNA yields, whereas the best DNA purity was obtained by a commercial kit designed for DNA extraction from soil. After successful PCR amplification, the 12 methods did not generate the same bias in microbial community representation. Eight combinations led to high diversity estimation, independently of the experimental procedure. Among them, six provided highly similar DGGE profiles. Two protocols generated a significantly dissimilar community profile, with less diversity. This study highlighted the crucial importance of DNA recovery bias evaluation.}, } @article {pmid19801464, year = {2009}, author = {Schloss, PD and Westcott, SL and Ryabin, T and Hall, JR and Hartmann, M and Hollister, EB and Lesniewski, RA and Oakley, BB and Parks, DH and Robinson, CJ and Sahl, JW and Stres, B and Thallinger, GG and Van Horn, DJ and Weber, CF}, title = {Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {23}, pages = {7537-7541}, pmid = {19801464}, issn = {1098-5336}, mesh = {*Biodiversity ; Computational Biology/*methods ; Environmental Microbiology ; Metagenomics/*methods ; Sequence Analysis, DNA ; *Software ; }, abstract = {mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.}, } @article {pmid19801459, year = {2009}, author = {Simon, C and Wiezer, A and Strittmatter, AW and Daniel, R}, title = {Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {23}, pages = {7519-7526}, pmid = {19801459}, issn = {1098-5336}, mesh = {Archaea/classification/genetics/isolation & purification/metabolism ; Bacteria/*classification/genetics/isolation & purification/*metabolism ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Eukaryota/classification/genetics/isolation & purification/metabolism ; Germany ; Ice Cover/*microbiology ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Viruses ; }, abstract = {The largest part of the Earth's microbial biomass is stored in cold environments, which represent almost untapped reservoirs of novel species, processes, and genes. In this study, the first metagenomic survey of the metabolic potential and phylogenetic diversity of a microbial assemblage present in glacial ice is presented. DNA was isolated from glacial ice of the Northern Schneeferner, Germany. Pyrosequencing of this DNA yielded 1,076,539 reads (239.7 Mbp). The phylogenetic composition of the prokaryotic community was assessed by evaluation of a pyrosequencing-derived data set and sequencing of 16S rRNA genes. The Proteobacteria (mainly Betaproteobacteria), Bacteroidetes, and Actinobacteria were the predominant phylogenetic groups. In addition, isolation of psychrophilic microorganisms was performed, and 13 different bacterial isolates were recovered. Analysis of the 16S rRNA gene sequences of the isolates revealed that all were affiliated to the predominant groups. As expected for microorganisms residing in a low-nutrient environment, a high metabolic versatility with respect to degradation of organic substrates was detected by analysis of the pyrosequencing-derived data set. The presence of autotrophic microorganisms was indicated by identification of genes typical for different ways of carbon fixation. In accordance with the results of the phylogenetic studies, in which mainly aerobic and facultative aerobic bacteria were detected, genes typical for central metabolism of aerobes were found. Nevertheless, the capability of growth under anaerobic conditions was indicated by genes involved in dissimilatory nitrate/nitrite reduction. Numerous characteristics for metabolic adaptations associated with a psychrophilic lifestyle, such as formation of cryoprotectants and maintenance of membrane fluidity by the incorporation of unsaturated fatty acids, were detected. Thus, analysis of the glacial metagenome provided insights into the microbial life in frozen habitats on Earth, thereby possibly shedding light onto microbial life in analogous extraterrestrial environments.}, } @article {pmid19787059, year = {2009}, author = {Not, F and del Campo, J and Balagué, V and de Vargas, C and Massana, R}, title = {New insights into the diversity of marine picoeukaryotes.}, journal = {PloS one}, volume = {4}, number = {9}, pages = {e7143}, pmid = {19787059}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Ciliophora/physiology ; Cloning, Molecular ; Computational Biology ; DNA, Ribosomal/analysis/*genetics ; Environment ; Eukaryota ; Genetic Variation ; Marine Biology/*methods ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/*genetics ; Seawater ; Sequence Analysis, DNA ; }, abstract = {Over the last decade, culture-independent surveys of marine picoeukaryotic diversity based on 18S ribosomal DNA clone libraries have unveiled numerous sequences of novel high-rank taxa. This newfound diversity has significantly altered our understanding of marine microbial food webs and the evolution of eukaryotes. However, the current picture of marine eukaryotic biodiversity may be significantly skewed by PCR amplification biases, occurrence of rDNA genes in multiple copies within a single cell, and the capacity of DNA to persist as extracellular material. In this study we performed an analysis of the metagenomic dataset from the Global Ocean Survey (GOS) expedition, seeking eukaryotic ribosomal signatures. This PCR-free approach revealed similar phylogenetic patterns to clone library surveys, suggesting that PCR steps do not impose major biases in the exploration of environmental DNA. The different cell size fractions within the GOS dataset, however, displayed a distinct picture. High protistan diversity in the <0.8 microm size fraction, in particular sequences from radiolarians and ciliates (and their absence in the 0.8-3 microm fraction), suggest that most of the DNA in this fraction comes from extracellular material from larger cells. In addition, we compared the phylogenetic patterns from rDNA and reverse transcribed rRNA 18S clone libraries from the same sample harvested in the Mediterranean Sea. The libraries revealed major differences, with taxa such as pelagophytes or picobiliphytes only detected in the 18S rRNA library. MAST (Marine Stramenopiles) appeared as potentially prominent grazers and we observed a significant decrease in the contribution of alveolate and radiolarian sequences, which overwhelmingly dominated rDNA libraries. The rRNA approach appears to be less affected by taxon-specific rDNA copy number and likely better depicts the biogeochemical significance of marine protists.}, } @article {pmid19786749, year = {2009}, author = {Cucchiara, S and Iebba, V and Conte, MP and Schippa, S}, title = {The microbiota in inflammatory bowel disease in different age groups.}, journal = {Digestive diseases (Basel, Switzerland)}, volume = {27}, number = {3}, pages = {252-258}, doi = {10.1159/000228558}, pmid = {19786749}, issn = {1421-9875}, mesh = {Age Distribution ; *Aging ; Gastrointestinal Tract/microbiology/pathology ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Metagenome/*physiology ; }, abstract = {BACKGROUND: Many efforts were made in the past decades to assess the role of gut microbiota in inflammatory bowel diseases (IBD), leading to the hypothesis that an altered microbial composition, other than the presence of a specific pathogen, could be involved in the pathogenesis of the disease. On the other hand, existing differences in gut microbial community between distinct classes of age make sense of an increasing research in microbial shifts in IBD.

METHODS: Cultural, molecular, metabolomic and metagenomic approaches are trying to define the human gut microbiota in different age groups.

RESULTS AND CONCLUSION: An increase in anaerobic bacteria (Bacteroidesvulgatus, Streptococcus faecalis) was observed in adult IBD, whereas an increase in aerobic and facultative-anaerobic (Escherichia coli) was found in pediatric IBD. Overall higher bacterial cell counts were observed in IBD, jointly with a general loss of biodiversity and a preponderance of Bacteroidetes and a parallel decrease of Firmicutes phylum: a predominance of potential harmful members of Proteobacteria (E. coli) and low abundance of beneficial species (Faecalibacterium prausnitzii) was also reported in pediatric and adult age groups, respectively. Microbial community of elderly subjects contains a wider range of different species than those of children and adults, both in healthy and IBD status.}, } @article {pmid19783747, year = {2009}, author = {Khafipour, E and Li, S and Plaizier, JC and Krause, DO}, title = {Rumen microbiome composition determined using two nutritional models of subacute ruminal acidosis.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {22}, pages = {7115-7124}, pmid = {19783747}, issn = {1098-5336}, mesh = {Acidosis/microbiology/*veterinary ; Animal Nutritional Physiological Phenomena ; Animals ; Bacteria/classification/genetics/growth & development ; *Bacterial Physiological Phenomena ; Biodiversity ; Cattle ; Cattle Diseases/*microbiology ; Diet/veterinary ; Discriminant Analysis ; Female ; Gastrointestinal Contents/chemistry/*microbiology ; Haptoglobins/analysis ; Hydrogen-Ion Concentration ; Lipopolysaccharides/analysis/blood ; Medicago sativa/metabolism ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Time Factors ; }, abstract = {Subacute ruminal acidosis (SARA) is a metabolic disease in dairy cattle that occurs during early and mid-lactation and has traditionally been characterized by low rumen pH, but lactic acid does not accumulate as in acute lactic acid acidosis. It is hypothesized that factors such as increased gut permeability, bacterial lipopolysaccharides, and inflammatory responses may have a role in the etiology of SARA. However, little is known about the nature of the rumen microbiome during SARA. In this study, we analyzed the microbiome of 64 rumen samples taken from eight lactating Holstein dairy cattle using terminal restriction fragment length polymorphisms (TRFLP) of 16S rRNA genes and real-time PCR. We used rumen samples from two published experiments in which SARA had been induced with either grain or alfalfa pellets. The results of TRFLP analysis indicated that the most predominant shift during SARA was a decline in gram-negative Bacteroidetes organisms. However, the proportion of Bacteroidetes organisms was greater in alfalfa pellet-induced SARA than in mild or severe grain-induced SARA (35.4% versus 26.0% and 16.6%, respectively). This shift was also evident from the real-time PCR data for Prevotella albensis, Prevotella brevis, and Prevotella ruminicola, which are members of the Bacteroidetes. The real-time PCR data also indicated that severe grain-induced SARA was dominated by Streptococcus bovis and Escherichia coli, whereas mild grain-induced SARA was dominated by Megasphaera elsdenii and alfalfa pellet-induced SARA was dominated by P. albensis. Using discriminant analysis, the severity of SARA and degree of inflammation were highly correlated with the abundance of E. coli and not with lipopolysaccharide in the rumen. We thus suspect that E. coli may be a contributing factor in disease onset.}, } @article {pmid19763412, year = {2009}, author = {Bulgari, D and Casati, P and Brusetti, L and Quaglino, F and Brasca, M and Daffonchio, D and Bianco, PA}, title = {Endophytic bacterial diversity in grapevine (Vitis vinifera L.) leaves described by 16S rRNA gene sequence analysis and length heterogeneity-PCR.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {47}, number = {4}, pages = {393-401}, pmid = {19763412}, issn = {1976-3794}, mesh = {Bacteria/classification/*genetics/*isolation & purification ; *Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Molecular Sequence Data ; Plant Leaves/microbiology ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Vitis/*microbiology ; }, abstract = {Diversity of bacterial endophytes associated with grapevine leaf tissues was analyzed by cultivation and cultivation-independent methods. In order to identify bacterial endophytes directly from metagenome, a protocol for bacteria enrichment and DNA extraction was optimized. Sequence analysis of 16S rRNA gene libraries underscored five diverse Operational Taxonomic Units (OTUs), showing best sequence matches with gamma-Proteobacteria, family Enterobacteriaceae, with a dominance of the genus Pantoea. Bacteria isolation through cultivation revealed the presence of six OTUs, showing best sequence matches with Actinobacteria, genus Curtobacterium, and with Firmicutes genera Bacillus and Enterococcus. Length Heterogeneity-PCR (LH-PCR) electrophoretic peaks from single bacterial clones were used to setup a database representing the bacterial endophytes identified in association with grapevine tissues. Analysis of healthy and phytoplasma-infected grapevine plants showed that LH-PCR could be a useful complementary tool for examining the diversity of bacterial endophytes especially for diversity survey on a large number of samples.}, } @article {pmid19747599, year = {2009}, author = {De Vuyst, L and Vrancken, G and Ravyts, F and Rimaux, T and Weckx, S}, title = {Biodiversity, ecological determinants, and metabolic exploitation of sourdough microbiota.}, journal = {Food microbiology}, volume = {26}, number = {7}, pages = {666-675}, doi = {10.1016/j.fm.2009.07.012}, pmid = {19747599}, issn = {1095-9998}, mesh = {Animals ; Bacterial Physiological Phenomena ; *Biodiversity ; Bread/*microbiology ; Cooking ; *Ecosystem ; Fermentation ; Flour ; *Food Microbiology ; Gene Expression Profiling ; Humans ; Lactobacillus/*genetics/isolation & purification ; Metagenome ; Yeasts/*genetics/isolation & purification ; }, abstract = {Sourdough is a microbial ecosystem of lactic acid bacteria (LAB) and yeasts in a matrix of mainly cereal flour and water. Culture-dependent and culture-independent microbiological analysis together with metabolite target analyses of different sourdoughs enabled to understand this complex fermentation process. It is difficult to link the species diversity of the sourdough microbiota with the (geographical) type of sourdough and the flour used, although the type and quality of the latter is the main source of autochthonous LAB in spontaneous sourdough fermentations and plays a key role in establishing stable microbial consortia within a short time. Carbohydrate fermentation targeted towards maltose catabolism, the use of external alternative electron acceptors, amino acid transamination reactions, and/or the arginine deiminase pathway are metabolic activities that favour energy production, cofactor (re)cycling, and/or tolerance towards acid stress, and hence contribute to the competitiveness and dominance of certain species of LAB found in sourdoughs. Also, microbial interactions play an important role. The availability of genome sequences for several LAB species that are of importance in sourdough as well as technological advances in the fields of functional genomics, transcriptomics, and proteomics enable new approaches to study sourdough fermentations beyond the single species level and will allow an integral analysis of the metabolic activities and interactions taking place in sourdough. Finally, the implementation of selected starter cultures in sourdough technology is of pivotal importance for the industrial production of sourdoughs to be used as flavour carrier, texture-improving, or health-promoting dough ingredient.}, } @article {pmid19735330, year = {2010}, author = {Coda, R and Nionelli, L and Rizzello, CG and De Angelis, M and Tossut, P and Gobbetti, M}, title = {Spelt and emmer flours: characterization of the lactic acid bacteria microbiota and selection of mixed starters for bread making.}, journal = {Journal of applied microbiology}, volume = {108}, number = {3}, pages = {925-935}, doi = {10.1111/j.1365-2672.2009.04497.x}, pmid = {19735330}, issn = {1365-2672}, mesh = {Bread/analysis/*microbiology ; Fermentation ; Flour/*microbiology ; *Food Microbiology ; Genes, Bacterial ; Lactic Acid/metabolism ; Lactobacillus plantarum/*genetics/isolation & purification ; *Metagenome ; Random Amplified Polymorphic DNA Technique ; Triticum/microbiology ; }, abstract = {AIMS: This study aimed at characterizing the lactic acid bacteria microbiota and selecting mixed endogenous starters to be used for sourdough fermentation of spelt or emmer flours.

METHODS AND RESULTS: Identification of lactic acid bacteria was carried out by partial sequencing of the 16S rRNA, recA, 16S/23S rRNA spacer region and pheS genes. Spelt flour showed the largest biodiversity, while Lactobacillus plantarum dominated in emmer flour. Isolates were subjected to RAPD-PCR analysis and screened based on the kinetics of growth and acidification, quotient of fermentation and liberation of free amino acids (FAA) during sourdough fermentation. After selection, mixed starters were used according to a two-step fermentation process. Wheat flour was fermented by the same starters. Spelt and emmer sourdoughs had slightly higher pH than wheat sourdoughs but titratable acidity, concentration of FAA and phytase activity were higher. Specific volume and crumb grain of emmer and, especially, spelt breads approached those of wheat breads. Sensory analysis confirmed the suitability of spelt and emmer for bread making.

CONCLUSIONS: The sourdough biotechnology was indispensable to completely exploit the potential of spelt and emmer flours.

Results filled up the lack of knowledge on the lactic acid bacteria microbiota and technological performances of spelt and emmer flours.}, } @article {pmid19710652, year = {2009}, author = {Sharon, I and Alperovitch, A and Rohwer, F and Haynes, M and Glaser, F and Atamna-Ismaeel, N and Pinter, RY and Partensky, F and Koonin, EV and Wolf, YI and Nelson, N and Béjà, O}, title = {Photosystem I gene cassettes are present in marine virus genomes.}, journal = {Nature}, volume = {461}, number = {7261}, pages = {258-262}, pmid = {19710652}, issn = {1476-4687}, support = {Z99 LM999999/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Adhesins, Bacterial/chemistry/genetics ; Amino Acid Sequence ; Bacteriophages/*genetics/metabolism ; Biodiversity ; Genes, Bacterial/genetics ; Genes, Viral/*genetics ; Genome, Bacterial/genetics ; Genome, Viral/*genetics ; Geography ; Lipoproteins/chemistry/genetics ; Models, Molecular ; Molecular Sequence Data ; Oceans and Seas ; Open Reading Frames/genetics ; Oxidation-Reduction ; Photosynthesis/genetics ; Photosystem I Protein Complex/chemistry/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Prochlorococcus/*virology ; Protein Conformation ; Seawater/*microbiology ; Synechococcus/*virology ; Viral Proteins/chemistry/genetics/metabolism ; Water Microbiology ; }, abstract = {Cyanobacteria of the Synechococcus and Prochlorococcus genera are important contributors to photosynthetic productivity in the open oceans. Recently, core photosystem II (PSII) genes were identified in cyanophages and proposed to function in photosynthesis and in increasing viral fitness by supplementing the host production of these proteins. Here we show evidence for the presence of photosystem I (PSI) genes in the genomes of viruses that infect these marine cyanobacteria, using pre-existing metagenomic data from the global ocean sampling expedition as well as from viral biomes. The seven cyanobacterial core PSI genes identified in this study, psaA, B, C, D, E, K and a unique J and F fusion, form a cluster in cyanophage genomes, suggestive of selection for a distinct function in the virus life cycle. The existence of this PSI cluster was confirmed with overlapping and long polymerase chain reaction on environmental DNA from the Northern Line Islands. Potentially, the seven proteins encoded by the viral genes are sufficient to form an intact monomeric PSI complex. Projection of viral predicted peptides on the cyanobacterial PSI crystal structure suggested that the viral-PSI components might provide a unique way of funnelling reducing power from respiratory and other electron transfer chains to the PSI.}, } @article {pmid19703219, year = {2009}, author = {Chen, F and Wang, K and Huang, S and Cai, H and Zhao, M and Jiao, N and Wommack, KE}, title = {Diverse and dynamic populations of cyanobacterial podoviruses in the Chesapeake Bay unveiled through DNA polymerase gene sequences.}, journal = {Environmental microbiology}, volume = {11}, number = {11}, pages = {2884-2892}, doi = {10.1111/j.1462-2920.2009.02033.x}, pmid = {19703219}, issn = {1462-2920}, mesh = {*Biodiversity ; Cluster Analysis ; Cyanobacteria/*virology ; DNA Primers/genetics ; DNA, Viral/chemistry/genetics/isolation & purification ; DNA-Directed DNA Polymerase/genetics ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Podoviridae/*classification/genetics/*isolation & purification ; Polymerase Chain Reaction/methods ; Seasons ; Seawater/*virology ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Sequence Homology ; Viral Proteins/genetics ; }, abstract = {Many podoviruses have been isolated which infect marine picocyanobacteria, and they may play a potentially important role in regulating the biomass and population composition of picocyanobacteria. However, little is known about the diversity and population dynamics of autochthonous cyanopodoviruses in marine environments. Using a set of newly designed PCR primers which specifically amplify the DNA pol from cyanopodoviruses, a total of 221 DNA pol sequences were retrieved from eight Chesapeake Bay virioplankton communities collected at different times and locations. All DNA pol sequences clustered with the eight known podoviruses that infect different marine picocyanobacteria, and could be divided into at least 10 different subclusters (I-X). The presence of these cyanopodovirus genotypes based on PCR-amplification of DNA pol gene sequences was supported by the existence of similar DNA pol genotypes with metagenome libraries of Chesapeake Bay virioplankton assemblages. The composition of cyanopodoviruses in the Bay also exhibited distinct winter and summer patterns which were likely related to corresponding seasonal changes in the composition of cyanobacterial populations. Our study suggests that diverse and dynamic populations of cyanopodoviruses are present in the estuarine environment. The PCR method developed in this study provides a specific and sensitive tool to explore the abundance, distribution and phylogenetic diversity of cyanopodoviruses in aquatic environments. Linking the dynamics of host and viral populations in the natural environment is critical to broader characterization of the ecological role of virioplankton within microbial communities.}, } @article {pmid19693101, year = {2009}, author = {Hong, S and Bunge, J and Leslin, C and Jeon, S and Epstein, SS}, title = {Polymerase chain reaction primers miss half of rRNA microbial diversity.}, journal = {The ISME journal}, volume = {3}, number = {12}, pages = {1365-1373}, doi = {10.1038/ismej.2009.89}, pmid = {19693101}, issn = {1751-7370}, mesh = {Bacteria/classification/genetics/isolation & purification ; *Biodiversity ; DNA Primers/*genetics ; DNA, Bacterial/genetics/isolation & purification ; DNA, Ribosomal/*genetics/*isolation & purification ; *Diagnostic Errors ; *Environmental Microbiology ; Metagenomics/*methods ; Polymerase Chain Reaction/*methods ; }, abstract = {The rRNA approach is the principal tool to study microbial diversity, but it has important biases. These include polymerase chain reaction (PCR) primers bias, and relative inefficiency of DNA extraction techniques. Such sources of potential undersampling of microbial diversity are well known, but the scale of the undersampling has not been quantified. Using a marine tidal flat bacterial community as a model, we show that even with unlimited sampling and sequencing effort, a single combination of PCR primers/DNA extraction technique enables theoretical recovery of only half of the richness recoverable with three such combinations. This shows that different combinations of PCR primers/DNA extraction techniques recover in principle different species, as well as higher taxa. The majority of earlier estimates of microbial richness seem to be underestimates. The combined use of multiple PCR primer sets, multiple DNA extraction techniques, and deep community sequencing will minimize the biases and recover substantially more species than prior studies, but we caution that even this--yet to be used--approach may still leave an unknown number of species and higher taxa undetected.}, } @article {pmid19675595, year = {2010}, author = {Engel, AS and Meisinger, DB and Porter, ML and Payn, RA and Schmid, M and Stern, LA and Schleifer, KH and Lee, NM}, title = {Linking phylogenetic and functional diversity to nutrient spiraling in microbial mats from Lower Kane Cave (USA).}, journal = {The ISME journal}, volume = {4}, number = {1}, pages = {98-110}, doi = {10.1038/ismej.2009.91}, pmid = {19675595}, issn = {1751-7370}, mesh = {Archaea/*classification/genetics/*metabolism ; Bacteria, Anaerobic/*classification/genetics/*metabolism ; *Biodiversity ; Carbon/metabolism ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/*microbiology ; In Situ Hybridization, Fluorescence ; *Metagenomics ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Soil Microbiology ; Sulfates/metabolism ; Sulfides/metabolism ; Water/analysis ; Wyoming ; }, abstract = {Microbial mats in sulfidic cave streams offer unique opportunities to study redox-based biogeochemical nutrient cycles. Previous work from Lower Kane Cave, Wyoming, USA, focused on the aerobic portion of microbial mats, dominated by putative chemolithoautotrophic, sulfur-oxidizing groups within the Epsilonproteobacteria and Gammaproteobacteria. To evaluate nutrient cycling and turnover within the whole mat system, a multidisciplinary strategy was used to characterize the anaerobic portion of the mats, including application of the full-cycle rRNA approach, the most probable number method, and geochemical and isotopic analyses. Seventeen major taxonomic bacterial groups and one archaeal group were retrieved from the anaerobic portions of the mats, dominated by Deltaproteobacteria and uncultured members of the Chloroflexi phylum. A nutrient spiraling model was applied to evaluate upstream to downstream changes in microbial diversity based on carbon and sulfur nutrient concentrations. Variability in dissolved sulfide concentrations was attributed to changes in the abundance of sulfide-oxidizing microbial groups and shifts in the occurrence and abundance of sulfate-reducing microbes. Gradients in carbon and sulfur isotopic composition indicated that released and recycled byproduct compounds from upstream microbial activities were incorporated by downstream communities. On the basis of the type of available chemical energy, the variability of nutrient species in a spiraling model may explain observed differences in microbial taxonomic affiliations and metabolic functions, thereby spatially linking microbial diversity to nutrient spiraling in the cave stream ecosystem.}, } @article {pmid19641535, year = {2010}, author = {Gao, Z and Johnson, ZI and Wang, G}, title = {Molecular characterization of the spatial diversity and novel lineages of mycoplankton in Hawaiian coastal waters.}, journal = {The ISME journal}, volume = {4}, number = {1}, pages = {111-120}, doi = {10.1038/ismej.2009.87}, pmid = {19641535}, issn = {1751-7370}, mesh = {Ascomycota/*classification/*genetics ; Basidiomycota/*classification/*genetics ; *Biodiversity ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Genes, rRNA ; Hawaii ; *Metagenomics ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Phylogeny ; RNA, Fungal/genetics ; RNA, Ribosomal, 18S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Microbial community diversity and composition have critical biogeochemical roles in the functioning of marine ecosystems. Large populations of planktonic fungi exist in coastal ocean waters, yet their diversity and role in carbon and nutrient cycling remain largely unknown. Lack of information on critical functional microbial groups limits our understanding of their ecological roles in coastal oceans and hence our understanding of its functioning in the ocean's carbon and nutrient cycles. To address this gap, this study applied the molecular approach denaturing gradient gel electrophoresis (DGGE) coupled with clone library construction to investigate mycoplankton communities in Hawaiian coastal waters. Mycoplankton communities displayed distinct lateral and vertical variations in diversity and composition. Compared with the open ocean, surface (<100 m) near-shore waters had the greatest diversity and species richness of mycoplankton, whereas no differences were found among stations at depths below 150 m. Vertical diversity profiles in the coastal waters suggested that diversity and species richness were positively correlated to phytoplankton biomass in the coastal waters, but not in offshore waters. A total of 46 species were identified and belonging to two phyla Basidiomycota and Ascomycota, with the basidiomycetes as the dominant group (n=42). The majority (n=27) of the basidiomycetes are novel phylotypes showing less than 98% identity in the 18S rRNA gene with any sequence in GenBank. This study provides insight into mycoplankton ecology and is the first molecular analysis of planktonic fungi in the oceans.}, } @article {pmid19635847, year = {2009}, author = {Parks, DH and Porter, M and Churcher, S and Wang, S and Blouin, C and Whalley, J and Brooks, S and Beiko, RG}, title = {GenGIS: A geospatial information system for genomic data.}, journal = {Genome research}, volume = {19}, number = {10}, pages = {1896-1904}, pmid = {19635847}, issn = {1549-5469}, mesh = {Africa ; Biodiversity ; Classification ; DNA, Mitochondrial/analysis/genetics ; *Databases, Genetic ; Genetic Variation ; Genomics/*methods ; *Geographic Information Systems ; HIV-1/classification/genetics/metabolism ; Humans ; Oceans and Seas ; Phylogeny ; *Software ; Specimen Handling/methods ; }, abstract = {The increasing availability of genetic sequence data associated with explicit geographic and ecological information is offering new opportunities to study the processes that shape biodiversity. The generation and testing of hypotheses using these data sets requires effective tools for mathematical and visual analysis that can integrate digital maps, ecological data, and large genetic, genomic, or metagenomic data sets. GenGIS is a free and open-source software package that supports the integration of digital map data with genetic sequences and environmental information from multiple sample sites. Essential bioinformatic and statistical tools are integrated into the software, allowing the user a wide range of analysis options for their sequence data. Data visualizations are combined with the cartographic display to yield a clear view of the relationship between geography and genomic diversity, with a particular focus on the hierarchical clustering of sites based on their similarity or phylogenetic proximity. Here we outline the features of GenGIS and demonstrate its application to georeferenced microbial metagenomic, HIV-1, and human mitochondrial DNA data sets.}, } @article {pmid19632349, year = {2010}, author = {Matsui, H and Kato, Y and Chikaraishi, T and Moritani, M and Ban-Tokuda, T and Wakita, M}, title = {Microbial diversity in ostrich ceca as revealed by 16S ribosomal RNA gene clone library and detection of novel Fibrobacter species.}, journal = {Anaerobe}, volume = {16}, number = {2}, pages = {83-93}, doi = {10.1016/j.anaerobe.2009.07.005}, pmid = {19632349}, issn = {1095-8274}, mesh = {Animals ; Bacteria/*classification/*genetics ; *Biodiversity ; Cecum/*microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Struthioniformes/*microbiology ; }, abstract = {The ostrich (Struthio camelus) is a herbivorous bird and although the hindgut is known as the site for fiber digestion, little is known about the microbial diversity in the ostrich hindgut. Our aim was to analyze the microbial diversity in ostrich ceca using a 16S ribosomal RNA gene (rDNA) clone library approach. A total of 310 clones were sequenced and phylogenetically analyzed and were classified into 110 operational taxonomy units (OTUs) based on a 98% similarity criterion. The similarity of the sequences ranged from 86 to 99% and 95 OTUs had less than 98% similarity to the sequences in the public databases. Coverage and the Shannon-Wiener index (H') of the library were 83.9% and 4.29, respectively. The sequences were assigned to the following 6 phyla: Firmicutes (50.9% of the total number of sequences), Bacteroidetes (39.4%), Fibrobacteres (6.5%), Euryarchaeota (1.9%), Spirochaetes (1.0%), and Verrucomicrobia (0.3%); approximately 90% of the sequences were affiliated with Firmicutes and Bacteroidetes. The only OTU of Fibrobacteres (OTU 107), had 93 and 90% similarity to Fibrobacter succinogenes and F. intestinalis, respectively, suggesting a new species of Fibrobacter in ostrich ceca. Clostridium coccoides and C. leptum formed major groups within the Firmicutes. There was no OTU with high similarity (> or =98%) to the 16S rDNA of cultivated fibrolytic bacteria in our library. Although two OTUs were affiliated with Euryarchaeota, no sequence was affiliated with methanogenic Archaea. This study presents the very complex ostrich cecal microbial community, in which the majority of the bacterial species have not yet been cultivated.}, } @article {pmid19627515, year = {2010}, author = {Parahitiyawa, NB and Scully, C and Leung, WK and Yam, WC and Jin, LJ and Samaranayake, LP}, title = {Exploring the oral bacterial flora: current status and future directions.}, journal = {Oral diseases}, volume = {16}, number = {2}, pages = {136-145}, doi = {10.1111/j.1601-0825.2009.01607.x}, pmid = {19627515}, issn = {1601-0825}, mesh = {Bacteria/*classification/growth & development ; Bacteriological Techniques ; Biodiversity ; Humans ; Metagenome ; Metagenomics ; Mouth/*microbiology ; Mouth Diseases/microbiology ; Tooth Diseases/microbiology ; }, abstract = {OBJECTIVE: The oral cavity forms an indispensable part of the human microbiome, for its unique and diverse microflora distributed within various niches. While majority of these organisms exhibit commensalism, shifts in bacterial community dynamics cause pathological changes within oral cavity and distant sites. The aim of this review was to appraise the current and emerging methods of detecting bacteria of the oral cavity paying particular attention to the cultivation independent methods.

DESIGN: Literature pertaining to cultivation based and cultivation independent methods of oral bacterial identification was reviewed.

METHODS: The specific advantages and disadvantages of cultivation based, microscopic, immunological and metagenomic identification methods were appraised.

RESULTS: Because of their fastidious and exacting growth requirements, cultivation based studies grossly underestimate the extent of bacterial diversity in these polymicrobial infections. Culture independent methods deemed more sensitive in identifying difficult to culture and novel bacterial species.

CONCLUSION: Apart from characterizing potentially novel bacterial species, the nucleic acid sequence data analyzed using various bioinformatics protocols have revealed that there are in excess of 700 bacterial species inhabiting the mouth. Moreover, the latest pyrosequencing based methods have further broadened the extent of bacterial diversity in oral niches.}, } @article {pmid19571895, year = {2009}, author = {Brazelton, WJ and Baross, JA}, title = {Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm.}, journal = {The ISME journal}, volume = {3}, number = {12}, pages = {1420-1424}, doi = {10.1038/ismej.2009.79}, pmid = {19571895}, issn = {1751-7370}, mesh = {Atlantic Ocean ; *Biodiversity ; *Biofilms ; Gene Transfer, Horizontal ; Geologic Sediments/*microbiology ; *Hot Springs ; *Metagenome ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Transposases/*genetics ; }, abstract = {The carbonate chimneys of the Lost City Hydrothermal Field on the Mid-Atlantic Ridge are coated in thick microbial biofilms consisting of just a few dominant species. We report a preliminary analysis of a biofilm metagenome that revealed a remarkable abundance and diversity of genes potentially involved in lateral gene transfer (LGT). More than 8% of all metagenomic reads showed significant sequence similarity to transposases; all available metagenomic data sets from other environments contained at least an order of magnitude fewer transposases. Furthermore, the sequence diversity of transposase genes in the biofilm was much greater than that of 16S rRNA genes. The small size and high sequencing coverage of contigs containing transposases indicate that they are located on small but abundant extragenomic molecules. These results suggest that rampant LGT among members of the Lost City biofilm may serve as a generator of phenotypic diversity in a community with very low organismal diversity.}, } @article {pmid19566421, year = {2009}, author = {Straight, PD and Kolter, R}, title = {Interspecies chemical communication in bacterial development.}, journal = {Annual review of microbiology}, volume = {63}, number = {}, pages = {99-118}, doi = {10.1146/annurev.micro.091208.073248}, pmid = {19566421}, issn = {1545-3251}, mesh = {Bacteria/*growth & development/*metabolism ; *Bacterial Physiological Phenomena ; Models, Biological ; *Quorum Sensing ; *Signal Transduction ; }, abstract = {Our view of bacteria, from the earliest observations through the heyday of antibiotic discovery, has shifted dramatically. We recognize communities of bacteria as integral and functionally important components of diverse habitats, ranging from soil collectives to the human microbiome. To function as productive communities, bacteria coordinate metabolic functions, often requiring shifts in growth and development. The hallmark of cellular development, which we characterize as physiological change in response to environmental stimuli, is a defining feature of many bacterial interspecies interactions. Bacterial communities rely on chemical exchanges to provide the cues for developmental change. Traditional methods in microbiology focus on isolation and characterization of bacteria in monoculture, separating the organisms from the surroundings in which interspecies chemical communication has relevance. Developing multispecies experimental systems that incorporate knowledge of bacterial physiology and metabolism with insights from biodiversity and metagenomics shows great promise for understanding interspecies chemical communication in the microbial world.}, } @article {pmid19558513, year = {2009}, author = {Debroas, D and Humbert, JF and Enault, F and Bronner, G and Faubladier, M and Cornillot, E}, title = {Metagenomic approach studying the taxonomic and functional diversity of the bacterial community in a mesotrophic lake (Lac du Bourget--France).}, journal = {Environmental microbiology}, volume = {11}, number = {9}, pages = {2412-2424}, doi = {10.1111/j.1462-2920.2009.01969.x}, pmid = {19558513}, issn = {1462-2920}, mesh = {Bacteria/*classification/genetics/metabolism ; Base Sequence ; Biodiversity ; France ; Fresh Water/*microbiology ; Genes, Bacterial ; Genomics ; Metabolic Networks and Pathways ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/analysis ; }, abstract = {The main goals of this work were to identify the metabolic pathways of the bacterial community in a lacustrine ecosystem and to establish links between taxonomic composition and the relative abundances of these metabolic pathways. For this purpose, we analysed a 16S rRNA gene library obtained by gene amplification together with a sequence library of both insert ends on c. 7700 fosmids. Whatever the library used, Actinobacteria was the most abundant bacterial group, followed by Proteobacteria and Bacteroidetes. Specific aquatic clades such as acI and acIV (Actinobacteria) or LD12 and GOBB-C201 (Alphaproteobacteria) were found in both libraries. From comparative analysis of metagenomic libraries, the metagenome of this lake was characterized by overrepresentation of genes involved in the degradation of xenobiotics mainly associated with Alphaproteobacteria. Actinobacteria were mainly related to metabolic pathways involved in nucleotide metabolism, cofactors, vitamins, energy, replication and repair. Betaproteobacteria appeared to be characterized by the presence of numerous genes implicated in environmental information processing (membrane transport and signal transduction) whereas glycan and carbohydrate metabolism pathways were overrepresented in Bacteroidetes. These results prompted us to propose hypotheses on the ecological role of these bacterial classes in lacustrine ecosystems.}, } @article {pmid19552772, year = {2009}, author = {Berdoulay, M and Salvado, JC}, title = {Genetic characterization of microbial communities living at the surface of building stones.}, journal = {Letters in applied microbiology}, volume = {49}, number = {3}, pages = {311-316}, doi = {10.1111/j.1472-765X.2009.02660.x}, pmid = {19552772}, issn = {1472-765X}, mesh = {Bacteria/*classification/*isolation & purification ; *Biodiversity ; Calcium Carbonate ; Cluster Analysis ; DNA, Algal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Environmental Microbiology ; Eukaryota/*classification/*isolation & purification ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {AIMS: The aim of the present study was to reveal the microbial genetic diversity of epilithic biofilms using a DNA-based procedure.

METHODS AND RESULTS: A DNA extraction protocol was first selected to obtain PCR-amplifiable metagenomic DNA from a limestone biofilm. Extracted DNA was used to amplify either 16S rRNA genes or ITS regions from prokaryotic and eukaryotic genomes, respectively. Amplified DNAs were subsequently cloned, amplified by colony PCR and screened by restriction analysis [restriction analyses of amplified ribosomal DNA (ARDRA)] for DNA sequencing. Phylogenetic analysis using 16S rDNA sequences showed that predominating bacteria were Alphaproteobacteria belonging to the genera Sphingomonas, Erythrobacter, Porphyrobacter, Rhodopila and Jannashia; Cyanobacteria and Actinobacteria were also identified. Analysis of ITS rDNA sequences revealed the presence of algae of the Chlorophyceae family and fungi related either to Rhinocladiella or to a melanized ascomycete. Statistical analysis showed that the specific richness evidenced was representative of the original sampled biofilm.

CONCLUSIONS: The molecular methodology developed here constitutes a valuable tool to investigate the genetic diversity of microbial biofilms from building stone.

The easy-to-run molecular method described here has practical importance to establish microbiological diagnosis and to define strategies for protection and restoration of stone surfaces.}, } @article {pmid19543937, year = {2009}, author = {Morales-Jiménez, J and Zúñiga, G and Villa-Tanaca, L and Hernández-Rodríguez, C}, title = {Bacterial community and nitrogen fixation in the red turpentine beetle, Dendroctonus valens LeConte (Coleoptera: Curculionidae: Scolytinae).}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {879-891}, pmid = {19543937}, issn = {1432-184X}, mesh = {Acetylene/metabolism ; Animals ; Bacteria/classification/*genetics/isolation & purification ; Biodiversity ; Coleoptera/*metabolism/*microbiology ; DNA, Bacterial/genetics ; Gastrointestinal Tract/microbiology ; Gene Library ; *Nitrogen Fixation ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The red turpentine beetle, Dendroctonus valens LeConte (Coleoptera: Curculionidae: Scolytinae), colonizes all pines species within its native range throughout North and Central America. Recently, this species was accidentally introduced to China, where it has caused severe damage in pine forests. It belongs to a group of beetles that spend most of their lives between the tree bark and sapwood, where it feeds on phloem: a poor substrate with very low nutritional value of nitrogen and toxic properties due to its high content of secondary defensive compounds. The aim of this study was to characterize the bacterial community of the D. valens gut by culture-dependent and -independent methods. Polymerase chain reaction denaturing gradient gel electrophoresis and ribosomal gene library analyses revealed that species diversity in the D. valens gut was relatively low, containing between six and 17 bacterial species. The bacterial community associated with larvae and adults was dominated by members of the following genera: Lactococcus, Acinetobacter, Pantoea, Rahnella, Stenothrophomonas, Erwinia, Enterobacter, Serratia, Janibacter, Leifsonia, Cellulomonas, and Cellulosimicrobium. The members of the last four genera showed cellulolytic activity in vitro and could be involved in cellulose breakdown in the insect gut. Finally, nitrogen fixation was demonstrated in live larvae and adults; however, capacity of nitrogen fixing in vitro was not found among enterobacterial species isolated in nitrogen-free media; neither were nifD nor nifH genes detected. In contrast, nifD gen was detected in metagenomic DNA from insect guts. The identification of bacterial species and their potential physiological capacities will allow exploring the role of gut symbiotic bacteria in the adaptation and survival of D. valens in a harsh chemical habitat poor in nitrogen sources.}, } @article {pmid19508561, year = {2009}, author = {Orcutt, B and Bailey, B and Staudigel, H and Tebo, BM and Edwards, KJ}, title = {An interlaboratory comparison of 16S rRNA gene-based terminal restriction fragment length polymorphism and sequencing methods for assessing microbial diversity of seafloor basalts.}, journal = {Environmental microbiology}, volume = {11}, number = {7}, pages = {1728-1735}, pmid = {19508561}, issn = {1462-2920}, mesh = {Biodiversity ; Geologic Sediments/*microbiology ; *Metagenome ; Metagenomics/*methods ; Polymorphism, Genetic ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; *Silicates ; }, abstract = {We present an interlaboratory comparison between full-length 16S rRNA gene sequence analysis and terminal restriction fragment length polymorphism (TRFLP) for microbial communities hosted on seafloor basaltic lavas, with the goal of evaluating how similarly these two different DNA-based methods used in two independent labs would estimate the microbial diversity of the same basalt samples. Two samples were selected for these analyses based on differences detected in the overall levels of microbial diversity between them. Richness estimators indicate that TRFLP analysis significantly underestimates the richness of the relatively high-diversity seafloor basalt microbial community: at least 50% of species from the high-diversity site are missed by TRFLP. However, both methods reveal similar dominant species from the samples, and they predict similar levels of relative diversity between the two samples. Importantly, these results suggest that DNA-extraction or PCR-related bias between the two laboratories is minimal. We conclude that TRFLP may be useful for relative comparisons of diversity between basalt samples, for identifying dominant species, and for estimating the richness and evenness of low-diversity, skewed populations of seafloor basalt microbial communities, but that TRFLP may miss a majority of species in relatively highly diverse samples.}, } @article {pmid19508560, year = {2009}, author = {Rajilić-Stojanović, M and Heilig, HG and Molenaar, D and Kajander, K and Surakka, A and Smidt, H and de Vos, WM}, title = {Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults.}, journal = {Environmental microbiology}, volume = {11}, number = {7}, pages = {1736-1751}, pmid = {19508560}, issn = {1462-2920}, mesh = {Adult ; Aged ; *Biodiversity ; DNA, Ribosomal/genetics ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Genetic Variation ; Humans ; *Metagenome ; Microarray Analysis/*methods ; Microbiological Techniques/*methods ; Oligonucleotide Probes/genetics ; Reproducibility of Results ; }, abstract = {In this paper we present the in silico assessment of the diversity of variable regions of the small subunit ribosomal RNA (SSU rRNA) gene based on an ecosystem-specific curated database, describe a probe design procedure based on two hypervariable regions with minimal redundancy and test the potential of such probe design strategy for the design of a flexible microarray platform. This resulted in the development and application of a phylogenetic microarray for studying the human gastrointestinal microbiota--referred as the human intestinal tract chip (HITChip). Over 4800 dedicated tiling oligonucleotide probes were designed based on two hypervariable regions of the SSU rRNA gene of 1140 unique microbial phylotypes (< 98% identity) following analysis of over 16,000 human intestinal SSU rRNA sequences. These HITChip probes were hybridized to a diverse set of human intestinal samples and SSU rRNA clones to validate its fingerprinting and quantification potential. Excellent reproducibility (median Pearson's correlation of 0.99) was obtained following hybridization with T7 polymerase transcripts generated in vitro from SSU rRNA gene amplicons. A linear dose-response was observed with artificial mixtures of 40 different representative amplicons with relative abundances as low as 0.1% of total microbiota. Analysis of three consecutively collected faecal samples from ten individuals (five young and five elderly adults) revealed temporal dynamics and confirmed that the adult intestinal microbiota is an individual-specific and relatively stable ecosystem. Further analysis of the stable part allowed for the identification of a universal microbiota core at the approximate genus level (90% sequence similarity). This core consists of members of Actinobacteria, Bacteroidetes and Firmicutes. Used as a phylogenetic fingerprinting tool with the possibility for relative quantification, the HITChip has the potential to bridge the gaps in our knowledge in the quantitative and qualitative description of the human gastrointestinal microbiota composition.}, } @article {pmid19508556, year = {2009}, author = {Conrad, R and Klose, M and Noll, M}, title = {Functional and structural response of the methanogenic microbial community in rice field soil to temperature change.}, journal = {Environmental microbiology}, volume = {11}, number = {7}, pages = {1844-1853}, doi = {10.1111/j.1462-2920.2009.01909.x}, pmid = {19508556}, issn = {1462-2920}, mesh = {Archaea/classification/*growth & development/*metabolism ; *Biodiversity ; Carbon Dioxide/metabolism ; Carbon Isotopes/metabolism ; DNA Fingerprinting ; Metagenome ; Methane/*metabolism ; Oryza/microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Staining and Labeling ; *Temperature ; }, abstract = {The microbial community in anoxic rice field soil produces CH(4) over a wide temperature range up to 55°C. However, at temperatures higher than about 40°C, the methanogenic path changes from CH(4) production by hydrogenotrophic plus acetoclastic methanogenesis to exclusively hydrogenotrophic methanogenesis and simultaneously, the methanogenic community consisting of Methanosarcinaceae, Methanoseataceae, Methanomicrobiales, Methanobacteriales and Rice Cluster I (RC-1) changes to almost complete dominance of RC-1. We studied changes in structure and function of the methanogenic community with temperature to see whether microbial members of the community were lost or their function impaired by exposure to high temperature. We characterized the function of the community by the path of CH(4) production measuring δ(13)C in CH(4) and CO(2) and calculating the apparent fractionation factor (α(app)) and the structure of the community by analysis of the terminal restriction fragment length polymorphism (T-RFLP) of the microbial 16S rRNA genes. Shift of the temperature from 45°C to 35°C resulted in a corresponding shift of function and structure, especially when some 35°C soil was added to the 45°C soil. The bacterial community (T-RFLP patterns), which was much more diverse than the archaeal community, changed in a similar manner upon temperature shift. Incubation of a mixture of 35°C and 50°C pre-incubated methanogenic rice field soil at different temperatures resulted in functionally and structurally well-defined communities. Although function changed from a mixture of acetoclastic and hydrogenotrophic methanogenesis to exclusively hydrogenotrophic methanogenesis over a rather narrow temperature range of 42-46°C, each of these temperatures also resulted in only one characteristic function and structure. Our study showed that temperature conditions defined structure and function of the methanogenic microbial community.}, } @article {pmid19478181, year = {2009}, author = {Grice, EA and Kong, HH and Conlan, S and Deming, CB and Davis, J and Young, AC and , and Bouffard, GG and Blakesley, RW and Murray, PR and Green, ED and Turner, ML and Segre, JA}, title = {Topographical and temporal diversity of the human skin microbiome.}, journal = {Science (New York, N.Y.)}, volume = {324}, number = {5931}, pages = {1190-1192}, pmid = {19478181}, issn = {1095-9203}, support = {Z01 HG000180-08/ImNIH/Intramural NIH HHS/United States ; ZIA BC010938-02/ImNIH/Intramural NIH HHS/United States ; ZIA HG000180-09/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Actinobacteria/classification/genetics/isolation & purification ; Adult ; Bacteria/classification/genetics/*isolation & purification ; Bacteroidetes/classification/genetics/isolation & purification ; Biodiversity ; Female ; Genes, rRNA ; Humans ; Male ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Proteobacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S ; Skin/*microbiology ; Time Factors ; Young Adult ; }, abstract = {Human skin is a large, heterogeneous organ that protects the body from pathogens while sustaining microorganisms that influence human health and disease. Our analysis of 16S ribosomal RNA gene sequences obtained from 20 distinct skin sites of healthy humans revealed that physiologically comparable sites harbor similar bacterial communities. The complexity and stability of the microbial community are dependent on the specific characteristics of the skin site. This topographical and temporal survey provides a baseline for studies that examine the role of bacterial communities in disease states and the microbial interdependencies required to maintain healthy skin.}, } @article {pmid19465140, year = {2010}, author = {Nicholson, MJ and McSweeney, CS and Mackie, RI and Brookman, JL and Theodorou, MK}, title = {Diversity of anaerobic gut fungal populations analysed using ribosomal ITS1 sequences in faeces of wild and domesticated herbivores.}, journal = {Anaerobe}, volume = {16}, number = {2}, pages = {66-73}, doi = {10.1016/j.anaerobe.2009.05.003}, pmid = {19465140}, issn = {1095-8274}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Animals, Domestic/*microbiology ; Animals, Wild/*microbiology ; *Biodiversity ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Feces/*microbiology ; Fungi/*classification/*genetics ; Gastrointestinal Tract/*microbiology ; Metagenome ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Gut fungal-specific PCR primers have been used to selectively amplify the ITS1 region of gut fungal rDNA recovered from faeces of domestic and wild animals to investigate population diversity. Two different gel-based methods are described for separating populations of gut fungal rDNA amplicons, namely (1) denaturing gradient gel electrophoresis (DGGE) and (2) separation according to small size differences using Spreadex, a proprietary matrix for electrophoresis. Gut fungal populations were characterised by analysis of rDNA in faeces of seventeen domesticated and ten wild herbivores. Sequences derived from these gel-based characterisations were analysed and classified using a hidden Markov model-based fingerprint matching algorithm. Faecal samples contained a broad spectrum of fungi and sequences from five of the six recognised genera were identified, including Cyllamyces, the most recently described gut fungal genus, which was found to be widely distributed in the samples. Furthermore, four other novel groupings of gut fungal sequences were identified that did not cluster with sequences from any of the previously described genera. Both gel- and sequence- based profiles for gut fungal populations suggested a lack of geographical restriction on occurrence of any individual fungal type.}, } @article {pmid19460451, year = {2010}, author = {Michelland, RJ and Combes, S and Monteils, V and Cauquil, L and Gidenne, T and Fortun-Lamothe, L}, title = {Molecular analysis of the bacterial community in digestive tract of rabbit.}, journal = {Anaerobe}, volume = {16}, number = {2}, pages = {61-65}, doi = {10.1016/j.anaerobe.2009.05.002}, pmid = {19460451}, issn = {1095-8274}, mesh = {Ammonia/analysis ; Animals ; Bacteria/*classification/genetics/metabolism ; *Biodiversity ; Cecum/chemistry/*microbiology ; Electrophoresis, Capillary ; Fatty Acids, Volatile/analysis ; Feces/chemistry/*microbiology ; Hydrogen-Ion Concentration ; *Metagenome ; Oxidation-Reduction ; *Polymorphism, Single-Stranded Conformational ; Rabbits ; }, abstract = {This work aimed to study the stability over time of the bacterial community in caecum and faeces of the rabbit (diversity index and structure) without experimental disturbance and to evaluate its relationships with environmental parameters. Soft and hard faeces of 14 rabbits were sampled for 5 weeks while caecal content was sampled on the 3rd week (by surgery) and the 5th week (at slaughter). Bacterial communities were assessed by studying CE-SSCP profiles of 16S rRNA genes fragments. Redox potential, pH, NH3-N concentration and volatile fatty acid concentrations were measured in the caecum. Data showed that bacterial communities of soft and hard faeces barely differed from that of the caecum (ANOSIM-R<0.25; p<0.05). Without disturbance, the bacterial communities of faeces were stable over time (ANOSIM-R<0.25; p<0.001). However, the bacterial communities of caecum and faeces were affected by the surgery (ANOSIM-R=0.22-0.33; p<0.001). The caecal content was an acidic (pH=6.03+/-0.33) and an anaerobic environment (redox potential=-160+/-43 mV). Only the redox potential was correlated with the diversity index of the bacterial community of the caecum (R(2)=0.35; p<0.05) and no environmental parameters were correlated to its structure.}, } @article {pmid19453611, year = {2009}, author = {Dumont, M and Harmand, J and Rapaport, A and Godon, JJ}, title = {Towards functional molecular fingerprints.}, journal = {Environmental microbiology}, volume = {11}, number = {7}, pages = {1717-1727}, doi = {10.1111/j.1462-2920.2009.01898.x}, pmid = {19453611}, issn = {1462-2920}, mesh = {*Biodiversity ; DNA Fingerprinting/*methods ; Ecology/*methods ; Mathematics/methods ; Metagenomics/*methods ; Nitrates/metabolism ; Nitrites/metabolism ; Nitrogen/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {One of the most important challenges in microbial ecology is to determine the ecological function of dominant microbial populations in their environment. In this paper we propose a generic method coupling fingerprinting and mathematical tools to achieve the functional assigning of bacteria detected in microbial consortia. This approach was tested on a nitrification bioprocess where two functions carried out by two different communities could be clearly distinguished. The mathematical theory of observers of dynamical systems has been used to design a dynamic estimator of the active biomass concentration of each functional community from the available measurements on nitrifying performance. Then, the combination of phylotypes obtained by fingerprinting that best approximated the estimated trajectories of each functional biomass was selected through a random optimization method. By this way, a nitritation or nitratation function was assigned to each phylotype detected in the ecosystem by means of functional molecular fingerprints. The results obtained by this approach were successfully compared with the information obtained from 16S rDNA identification. This original approach can be used on any biosystem involving n successive cascading bioreactions performed by n communities.}, } @article {pmid19446029, year = {2010}, author = {Uyeno, Y and Sekiguchi, Y and Tajima, K and Takenaka, A and Kurihara, M and Kamagata, Y}, title = {An rRNA-based analysis for evaluating the effect of heat stress on the rumen microbial composition of Holstein heifers.}, journal = {Anaerobe}, volume = {16}, number = {1}, pages = {27-33}, doi = {10.1016/j.anaerobe.2009.04.006}, pmid = {19446029}, issn = {1095-8274}, mesh = {Animals ; Bacteria/*classification/*genetics ; *Biodiversity ; Cattle ; DNA, Bacterial/genetics ; Hot Temperature ; Humidity ; *Metagenome ; Rumen/*microbiology ; *Stress, Physiological ; }, abstract = {We performed a set of heifer feeding trials to investigate the effect of heat and humidity stresses on the rumen bacterial molecular diversity of Holstein heifers (Tajima K, Nonaka I, Higuchi K, Takusari N, Kurihara M, Takenaka A, et al. Anaerobe 2007;13:57-64). To further characterize the response of the microbial community to the physiological changes caused by the stresses, we evaluated changes in the ruminal bacterial community composition in the same trials by applying an RNA-based method (sequence-specific small-subunit (SSU) rRNA cleavage method), which was optimized for a comprehensive description of the predominant bacterial groups inhabiting the rumen. Four Holstein heifers were kept at three temperatures (20 degrees C, 28 degrees C, 33 degrees C) in a climatic chamber for two weeks each, and rumen fluid samples were obtained on the last day of each temperature experiment. For quantitative detection, we applied a set of 15 oligonucleotide probes, including those targeting taxa comprised of uncultured rumen bacteria (URB) belonging to phylum Firmicutes, to the RNAs extracted from the fluid samples. The relative populations of the Clostridium coccoides-Eubacterium rectale group, and the genus Streptococcus increased, and that of the genus Fibrobacter decreased in response to increasing temperature both in the first (nine months old, 80% relative humidity) and second (15 months old, 60% relative humidity) experiments. In addition, the population of a defined URB group was higher at 33 degrees C than at 20 degrees C in the second trial, whereas one of the other URB groups showed a decreasing trend with the temperature rise. These results indicate that the exposure to heat affects the population levels of specific bacterial groups in the ruminal microbial community.}, } @article {pmid19445183, year = {2009}, author = {Liu, L and Tang, J and Feng, J}, title = {[Bacterial diversity in Guangxi buffalo rumen].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {49}, number = {2}, pages = {251-256}, pmid = {19445183}, issn = {0001-6209}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; *Biodiversity ; Buffaloes/*microbiology ; China ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; }, abstract = {OBJECTIVE: To analyze the diversity of bacterial community in Guangxi buffalo rumen and to identify the possible cellulolytic bacterial group.

METHODS: Metagenomic DNAs were isolated directly from a buffalo rumen and its enriched culture, and were used as PCR templates to amplify 16S rRNA genes. Two libraries carrying 16S rRNA genes of bacteria in the two samples were constructed. The bacterial community composition was revealed by the constructed phylogenetic tree of known sequences and the sequences randomly selected from the libraries.

RESULTS: We found that both samples contained low G + C Gram-positive bacteria (LGCGPB) and Cytophaga-Flexibacter-Bacteroides (CFB) phyla as the majorities, and Spirochaetes as the minorities. LGCGPB accounts for 56.66% and 73.33% of the bacterial communities in buffalo rumen and its enriched culture. We detected Fibrobacteres in the rumen sample (3.33%) but not in the enriched sample. Furthermore, we found Proteobacteria as a major component in the enrichment (13.33%) but not in the rumen sample. Clone R46 was not clustered into any known phyla and might belong to a novel taxonomic group.

CONCLUSION: The LGCGPB and Proteobacteria may play important roles in the hydrolysis of cellulose in buffalo rumen. The bacterial composition in the rumen of buffalo is quite similar to those in the rumen of yak, cattle and sheep.}, } @article {pmid19442689, year = {2009}, author = {Chew, YV and Holmes, AJ}, title = {Suppression subtractive hybridisation allows selective sampling of metagenomic subsets of interest.}, journal = {Journal of microbiological methods}, volume = {78}, number = {2}, pages = {136-143}, doi = {10.1016/j.mimet.2009.05.003}, pmid = {19442689}, issn = {1872-8359}, mesh = {Animals ; Bacteria/genetics/*isolation & purification ; *Biodiversity ; DNA, Bacterial/genetics/*isolation & purification ; Electrophoresis, Polyacrylamide Gel ; Feces/*microbiology ; Male ; Nucleic Acid Denaturation ; Nucleic Acid Hybridization/*methods ; Sensitivity and Specificity ; Swine/*microbiology ; }, abstract = {Metagenomic studies bypass the requirement of a pure culture for analysis, focusing instead on the genetic information present in a given sample. Metagenomics have been applied to various studies, with objectives ranging from genome reconstruction, gene prospecting and ecology. However, the use of metagenomics in comparative studies has been constrained by sequencing costs and computational limitations. Efforts are underway to improve current sequencing methods and reduce the expense involved. We suggest an alternative approach - pretreatment of the sample of interest to enrich for desired subsets prior to deep sequencing. In this study, we tested the use of suppression subtractive hybridisation (SSH) for in vitro separation of metagenomic samples based on temporal variance. Faecal samples were taken from pigs at different timepoints and extracted DNA was whole genome-amplified using multiple displacement amplification (MDA). A sample collected at 31 days of age was designated the tester while a 24 day sample was denoted the driver. Following hybridisation and subtraction, tester-specific sequences are expected to be enriched in the final sample while driver-specific and common sequences are removed. Using denaturing gel gradient electrophoresis (DGGE), we found that driver-specific bands were completely removed from all final profiles while an average of 70% of common bands were successfully subtracted. Final profiles retained an average of 70% of tester-specific sequences and new sequences contributed an average of 36% of the band mobilities found in the final profiles. Tester-unique sequences were inferred to make up 78% of the final profile after SSH. We expect that using subtractive hybridisation for separation of metagenomic samples into desired subsets will provide a more effective and targeted approach to comparative studies.}, } @article {pmid19417062, year = {2009}, author = {Sun, Y and Cai, Y and Liu, L and Yu, F and Farrell, ML and McKendree, W and Farmerie, W}, title = {ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences.}, journal = {Nucleic acids research}, volume = {37}, number = {10}, pages = {e76}, pmid = {19417062}, issn = {1362-4962}, mesh = {Air Microbiology ; *Algorithms ; *Biodiversity ; *Environmental Microbiology ; Genes, rRNA ; RNA, Ribosomal, 16S/*genetics ; Seawater/microbiology ; Sequence Alignment ; *Sequence Analysis, DNA ; }, abstract = {Recent metagenomics studies of environmental samples suggested that microbial communities are much more diverse than previously reported, and deep sequencing will significantly increase the estimate of total species diversity. Massively parallel pyrosequencing technology enables ultra-deep sequencing of complex microbial populations rapidly and inexpensively. However, computational methods for analyzing large collections of 16S ribosomal sequences are limited. We proposed a new algorithm, referred to as ESPRIT, which addresses several computational issues with prior methods. We developed two versions of ESPRIT, one for personal computers (PCs) and one for computer clusters (CCs). The PC version is used for small- and medium-scale data sets and can process several tens of thousands of sequences within a few minutes, while the CC version is for large-scale problems and is able to analyze several hundreds of thousands of reads within one day. Large-scale experiments are presented that clearly demonstrate the effectiveness of the newly proposed algorithm. The source code and user guide are freely available at http://www.biotech.ufl.edu/people/sun/esprit.html.}, } @article {pmid19411599, year = {2009}, author = {Doolittle, WF and Zhaxybayeva, O}, title = {On the origin of prokaryotic species.}, journal = {Genome research}, volume = {19}, number = {5}, pages = {744-756}, doi = {10.1101/gr.086645.108}, pmid = {19411599}, issn = {1088-9051}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Biodiversity ; Ecosystem ; *Evolution, Molecular ; Genetic Speciation ; Genetic Variation ; Genomics ; Species Specificity ; }, abstract = {The notion that all prokaryotes belong to genomically and phenomically cohesive clusters that we might legitimately call "species" is a contentious one. At issue are (1) whether such clusters actually exist; (2) what species definition might most reliably identify them, if they do; and (3) what species concept -- by which is meant a genetic and ecological theory of speciation -- might best explain species existence and rationalize a species definition, if we could agree on one. We review existing theories and some relevant data. We conclude that microbiologists now understand in some detail the various genetic, population, and ecological processes that effect the evolution of prokaryotes. There will be on occasion circumstances under which these, working together, will form groups of related organisms sufficiently like each other that we might all agree to call them "species," but there is no reason that this must always be so. Thus, there is no principled way in which questions about prokaryotic species, such as how many there are, how large their populations are, or how globally they are distributed, can be answered. These questions can, however, be reformulated so that metagenomic methods and thinking will meaningfully address the biological patterns and processes whose understanding is our ultimate target.}, } @article {pmid19406095, year = {2009}, author = {Nasidze, I and Quinque, D and Li, J and Li, M and Tang, K and Stoneking, M}, title = {Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches.}, journal = {Analytical biochemistry}, volume = {391}, number = {1}, pages = {64-68}, doi = {10.1016/j.ab.2009.04.034}, pmid = {19406095}, issn = {1096-0309}, mesh = {Biodiversity ; Cloning, Molecular ; Humans ; Metagenome/*genetics ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Metagenomic studies traditionally rely on cloning polymerase chain reaction (PCR) products and sequencing multiple clones. However, this approach is tedious and expensive, thereby limiting the range and scale of questions that can be addressed. Recent developments in DNA sequencing technologies enable a dramatic increase in throughput via parallel in-depth analysis of many samples with limited sample processing and lower costs. We directly compared the traditional cloning approach with a barcoded pyrosequencing method to see whether the latter accurately describes microbiome diversity in human saliva. Our results indicate that despite the shorter read lengths, the pyrosequencing approach provides a description of the human salivary microbiome that is in good agreement with results based on the traditional cloning and sequencing approach.}, } @article {pmid19390573, year = {2009}, author = {Woyke, T and Xie, G and Copeland, A and González, JM and Han, C and Kiss, H and Saw, JH and Senin, P and Yang, C and Chatterji, S and Cheng, JF and Eisen, JA and Sieracki, ME and Stepanauskas, R}, title = {Assembling the marine metagenome, one cell at a time.}, journal = {PloS one}, volume = {4}, number = {4}, pages = {e5299}, pmid = {19390573}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Genes, Bacterial/*genetics ; Genome, Bacterial ; Genomics/*methods ; Marine Biology ; Phylogeny ; Plankton ; RNA, Ribosomal, 16S/genetics/metabolism ; Rhodopsin/genetics ; Rhodopsins, Microbial ; Sequence Analysis, DNA ; }, abstract = {The difficulty associated with the cultivation of most microorganisms and the complexity of natural microbial assemblages, such as marine plankton or human microbiome, hinder genome reconstruction of representative taxa using cultivation or metagenomic approaches. Here we used an alternative, single cell sequencing approach to obtain high-quality genome assemblies of two uncultured, numerically significant marine microorganisms. We employed fluorescence-activated cell sorting and multiple displacement amplification to obtain hundreds of micrograms of genomic DNA from individual, uncultured cells of two marine flavobacteria from the Gulf of Maine that were phylogenetically distant from existing cultured strains. Shotgun sequencing and genome finishing yielded 1.9 Mbp in 17 contigs and 1.5 Mbp in 21 contigs for the two flavobacteria, with estimated genome recoveries of about 91% and 78%, respectively. Only 0.24% of the assembling sequences were contaminants and were removed from further analysis using rigorous quality control. In contrast to all cultured strains of marine flavobacteria, the two single cell genomes were excellent Global Ocean Sampling (GOS) metagenome fragment recruiters, demonstrating their numerical significance in the ocean. The geographic distribution of GOS recruits along the Northwest Atlantic coast coincided with ocean surface currents. Metabolic reconstruction indicated diverse potential energy sources, including biopolymer degradation, proteorhodopsin photometabolism, and hydrogen oxidation. Compared to cultured relatives, the two uncultured flavobacteria have small genome sizes, few non-coding nucleotides, and few paralogous genes, suggesting adaptations to narrow ecological niches. These features may have contributed to the abundance of the two taxa in specific regions of the ocean, and may have hindered their cultivation. We demonstrate the power of single cell DNA sequencing to generate reference genomes of uncultured taxa from a complex microbial community of marine bacterioplankton. A combination of single cell genomics and metagenomics enabled us to analyze the genome content, metabolic adaptations, and biogeography of these taxa.}, } @article {pmid19389737, year = {2009}, author = {Pignatelli, M and Serras, F and Moya, A and Guigó, R and Corominas, M}, title = {CROC: finding chromosomal clusters in eukaryotic genomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {25}, number = {12}, pages = {1552-1553}, doi = {10.1093/bioinformatics/btp248}, pmid = {19389737}, issn = {1367-4811}, mesh = {Algorithms ; Chromosomes/*genetics ; *Genome ; Genomics/*methods ; Internet ; *Software ; }, abstract = {SUMMARY: There is increasing evidence showing that co-expression of genes that cluster along the genome is a common characteristic of eukaryotic transcriptomes. Several algorithms have been used to date in the identification of these kinds of gene organization. Here, we present a web tool called CROC that aims to help in the identification and analysis of genomic gene clusters. This method has been successfully used before in the identification of chromosomal clusters in different eukaryotic species.

AVAILABILITY: The web server is freely available to non-commercial users at the following address: http://metagenomics.uv.es/CROC/.}, } @article {pmid19352371, year = {2009}, author = {Tschöp, MH and Hugenholtz, P and Karp, CL}, title = {Getting to the core of the gut microbiome.}, journal = {Nature biotechnology}, volume = {27}, number = {4}, pages = {344-346}, pmid = {19352371}, issn = {1546-1696}, mesh = {Adult ; Africa/ethnology ; Biodiversity ; Environment ; Europe/ethnology ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Genotype ; Humans ; Metagenome/genetics/*physiology ; Missouri ; Molecular Sequence Data ; Mothers ; Obesity/*microbiology ; RNA, Ribosomal, 16S/analysis/genetics ; Thinness/*microbiology ; Twins, Dizygotic ; Twins, Monozygotic ; }, } @article {pmid19340085, year = {2009}, author = {Temperton, B and Field, D and Oliver, A and Tiwari, B and Mühling, M and Joint, I and Gilbert, JA}, title = {Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing.}, journal = {The ISME journal}, volume = {3}, number = {7}, pages = {792-796}, doi = {10.1038/ismej.2009.32}, pmid = {19340085}, issn = {1751-7370}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; *Gene Library ; Genetic Vectors ; Norway ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA/*methods ; }, abstract = {On the basis of 16S rRNA gene sequencing, the SAR11 clade of marine bacteria has an almost universal distribution, being detected as abundant sequences in all marine provinces. Yet, SAR11 sequences are rarely detected in fosmid libraries, suggesting that the widespread abundance may be an artefact of PCR cloning and that SAR11 has a relatively low abundance. Here the relative abundance of SAR11 is explored in both a fosmid library and a metagenomic sequence data set from the same biological community taken from fjord surface water from Bergen, Norway. Pyrosequenced data and 16S clone data confirmed an 11-15% relative abundance of SAR11 within the community. In contrast, not a single SAR11 fosmid was identified in a pooled shotgun sequence data set of 100 fosmid clones. This underrepresentation was evidenced by comparative abundances of SAR11 sequences assessed by taxonomic annotation and fragment recruitment. Analysis revealed a similar underrepresentation of low-GC Flavobacteriaceae. We speculate that a contributing factor towards the fosmid bias may be DNA fragmentation during preparation because of the low GC content of SAR11 sequences and other underrepresented taxa. This study suggests that, although fosmid libraries can be extremely useful, caution must be taken when directly inferring community composition from metagenomic fosmid libraries.}, } @article {pmid19288513, year = {2009}, author = {Singh, J and Behal, A and Singla, N and Joshi, A and Birbian, N and Singh, S and Bali, V and Batra, N}, title = {Metagenomics: Concept, methodology, ecological inference and recent advances.}, journal = {Biotechnology journal}, volume = {4}, number = {4}, pages = {480-494}, doi = {10.1002/biot.200800201}, pmid = {19288513}, issn = {1860-7314}, mesh = {Archaea/genetics ; Bacteria/genetics ; Biodiversity ; DNA, Bacterial/analysis/*isolation & purification ; Ecology/*methods/trends ; *Genome, Bacterial ; *Genomic Library ; Genomics/*methods/trends ; Viruses/genetics ; }, abstract = {Microorganisms constitute two third of the Earth's biological diversity. As many as 99% of the microorganisms present in certain environments cannot be cultured by standard techniques. Culture-independent methods are required to understand the genetic diversity, population structure and ecological roles of the majority of organisms. Metagenomics is the genomic analysis of microorganisms by direct extraction and cloning of DNA from their natural environment. Protocols have been developed to capture unexplored microbial diversity to overcome the existing barriers in estimation of diversity. New screening methods have been designed to select specific functional genes within metagenomic libraries to detect novel biocatalysts as well as bioactive molecules applicable to mankind. To study the complete gene or operon clusters, various vectors including cosmid, fosmid or bacterial artificial chromosomes are being developed. Bioinformatics tools and databases have added much to the study of microbial diversity. This review describes the various methodologies and tools developed to understand the biology of uncultured microbes including bacteria, archaea and viruses through metagenomic analysis.}, } @article {pmid19278445, year = {2009}, author = {Babalola, OO and Kirby, BM and Le Roes-Hill, M and Cook, AE and Cary, SC and Burton, SG and Cowan, DA}, title = {Phylogenetic analysis of actinobacterial populations associated with Antarctic Dry Valley mineral soils.}, journal = {Environmental microbiology}, volume = {11}, number = {3}, pages = {566-576}, doi = {10.1111/j.1462-2920.2008.01809.x}, pmid = {19278445}, issn = {1462-2920}, mesh = {Actinobacteria/*classification/*isolation & purification ; Antarctic Regions ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Molecular Sequence Data ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; *Soil Microbiology ; }, abstract = {Despite the apparent severity of the environmental conditions in the McMurdo Dry Valleys, Eastern Antarctica, recent phylogenetic studies conducted on mineral soil samples have revealed the presence of a wide diversity of microorganisms, with actinobacteria representing one of the largest phylotypic groups. Previous metagenomic studies have shown that the majority of Antarctic actinobacterial populations are classified as 'uncultured'. In this study, we assessed the diversity of actinobacteria in Antarctic cold desert soils by complementing traditional culture-based techniques with a metagenomic study. Phylogenetic analysis of clones generated with actinobacterium- and streptomycete-specific PCR primers revealed that the majority of the phylotypes were most closely related to uncultured Pseudonocardia and Nocardioides species. Phylotypes most closely related to a number of rarer actinobacteria genera, including Geodermatophilus, Modestobacter and Sporichthya, were also identified. While complementary culture-dependent studies isolated a number of Nocardia and Pseudonocardia species, the majority of the cultured isolates (> 80%) were Streptomyces species--although phylotypes affiliated to the genus Streptomyces were detected at a low frequency in the metagenomic study. This study confirms that Antarctic Dry Valley desert soil harbours highly diverse actinobacterial communities and suggests that many of the phylotypes identified may represent novel, uncultured species.}, } @article {pmid19273267, year = {2009}, author = {Ventura, M and Turroni, F and Canchaya, C and Vaughan, EE and O'Toole, PW and van Sinderen, D}, title = {Microbial diversity in the human intestine and novel insights from metagenomics.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {14}, number = {9}, pages = {3214-3221}, doi = {10.2741/3445}, pmid = {19273267}, issn = {2768-6698}, mesh = {Bacteria/*classification/genetics/isolation & purification ; *Genome, Bacterial ; Humans ; Intestines/*microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bacterial communities reside in very different ecological niches on and within the human host, such as those associated with the alimentary tract. The human gastrointestinal tract is populated with as many as 100 trillion bacterial cells, whose collective genome likely reflects the co-evolution between the microbial community and its host. Recent progress has highlighted the intriguing diversity of these bacterial populations and their important contributions to human physiology. Thus, a thorough understanding of the autochthonous component of the intestinal microbiota is expected to provide crucial information not only on how to develop therapies for various gastrointestinal diseases but also on how to choose the next generation of probiotic bacteria as part of novel functional foods. Recently, novel culture-independent approaches such as metagenomics-based techniques were shown to be crucially important for the exploration of the biodiversity of the human intestinal microbiota.}, } @article {pmid19251737, year = {2009}, author = {Nasidze, I and Li, J and Quinque, D and Tang, K and Stoneking, M}, title = {Global diversity in the human salivary microbiome.}, journal = {Genome research}, volume = {19}, number = {4}, pages = {636-643}, pmid = {19251737}, issn = {1088-9051}, mesh = {*Biodiversity ; *Genetic Variation ; Humans ; *Metagenome ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; Saliva/*microbiology ; }, abstract = {The human salivary microbiome may play a role in diseases of the oral cavity and interact with microbiomes from other parts of the human body (in particular, the intestinal tract), but little is known about normal variation in the salivary microbiome. We analyzed 14,115 partial (approximately 500 bp) 16S ribosomal RNA (rRNA) sequences from saliva samples from 120 healthy individuals (10 individuals from each of 12 worldwide locations). These sequences could be assigned to 101 known bacterial genera, of which 39 were not previously reported from the human oral cavity; phylogenetic analysis suggests that an additional 64 unknown genera are present. There is high diversity in the salivary microbiome within and between individuals, but little geographic structure. Overall, approximately 13.5% of the total variance in the composition of genera is due to differences among individuals, which is remarkably similar to the fraction of the total variance in neutral genetic markers that can be attributed to differences among human populations. Investigation of some environmental variables revealed a significant association between the genetic distances among locations and the distance of each location from the equator. Further characterization of the enormous diversity revealed here in the human salivary microbiome will aid in elucidating the role it plays in human health and disease, and in the identification of potentially informative species for studies of human population history.}, } @article {pmid19217233, year = {2009}, author = {Smith, SA and Benardini, JN and Strap, JL and Crawford, RL}, title = {Diversity of aerobic and facultative alkalitolerant and halotolerant endospore formers in soil from the Alvord Basin, Oregon.}, journal = {Systematic and applied microbiology}, volume = {32}, number = {4}, pages = {233-244}, doi = {10.1016/j.syapm.2008.09.008}, pmid = {19217233}, issn = {1618-0984}, mesh = {Alkalies ; Bacillus/*classification/genetics/isolation & purification ; Bacteria, Aerobic/classification/genetics/isolation & purification ; Base Sequence ; *Biodiversity ; DNA Primers ; Endospore-Forming Bacteria/*classification/genetics/isolation & purification ; Molecular Sequence Data ; Oregon ; Phylogeny ; RNA, Ribosomal, 16S/classification/genetics ; Salt Tolerance ; *Soil Microbiology ; }, abstract = {Many proteins produced by Bacillus species isolated from extreme environments have been utilized for industrial purposes, as these extreme environments often promote evolution of unique protein properties. The Borax Lake area is unusual due to its geothermal activity, elevated pH, and high arsenic and salt concentrations in its soils. Soils from this region are likely to harbor alkalitolerant, halotolerant, endospore-forming strains that may be of potential ecological and/or commercial interest. The objectives of this study were to develop new PCR primers that could target Bacillus or closely related 16S rRNA genes, to characterize the diversity of alkalitolerant, halotolerant, endospore-forming organisms in the soils surrounding Borax Lake, and to identify novel organisms that may ultimately provide new enzymes for applied use. A three-pronged approach was used to identify such bacteria in soil samples. Organisms were isolated using two different techniques. Finally, metagenomic DNA from soil samples was subjected to 16S rRNA gene amplification using the newly designed primers. Assays were performed to characterize the halotolerance and alkalitolerance of isolates. Four different endospore-forming genera and 22 different species were identified by sequencing their 16S rRNA genes. Twenty-five organisms had 96% or less identity to known organisms. Thus, the newly designed Bacillus-related PCR primer sets proved useful for the detection of new species of endospore-forming bacteria in these unique soils. Results indicate that the collection of strains obtained from the Borax Lake region represents a rich source of alkalitolerant, halotolerant, endospore formers.}, } @article {pmid19201952, year = {2009}, author = {Biers, EJ and Sun, S and Howard, EC}, title = {Prokaryotic genomes and diversity in surface ocean waters: interrogating the global ocean sampling metagenome.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {7}, pages = {2221-2229}, pmid = {19201952}, issn = {1098-5336}, mesh = {Bacteria/*classification/genetics/*isolation & purification ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/*genetics ; DNA, Ribosomal/chemistry/genetics ; Ecosystem ; Genotype ; Oceans and Seas ; Phylogeny ; Ribotyping ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The Sorcerer II Global Ocean Sampling (GOS) sequencing effort has vastly expanded the landscape of metagenomics, providing an opportunity to study the genetic potential of surface ocean water bacterioplankton on a global scale. Here we describe the habitat-based microbial diversity, both taxon evenness and taxon richness, for each GOS site and estimate genome characteristics of a typical free-living, surface ocean water bacterium. While Alphaproteobacteria and particularly SAR11 dominate the 0.1- to 0.8-mum size fraction of surface ocean water bacteria (43% and 31%, respectively), the proportions of other taxa varied with ocean habitat type. Within each habitat type, lower-bound estimates of phylum richness ranged between 18 and 59 operational taxonomic units (OTUs). However, OTU richness was relatively low in the hypersaline lagoon community at every taxonomic level, and open-ocean communities had much more microdiversity than any other habitat. Based on the abundance of single-copy eubacterial genes from the same data set, we estimate that the genome of an average free-living surface ocean water bacterium (sized between 0.1 and 0.8 mum) contains approximately 1,019 genes and 1.8 copies of the 16S rRNA gene, suggesting that these bacteria have relatively streamlined genomes in comparison to those of cultured bacteria and bacteria from other habitats (e.g., soil or acid mine drainage).}, } @article {pmid21304642, year = {2009}, author = {Wooley, JC and Field, D and Glöckner, FO}, title = {Extending Standards for Genomics and Metagenomics Data: A Research Coordination Network for the Genomic Standards Consortium (RCN4GSC).}, journal = {Standards in genomic sciences}, volume = {1}, number = {1}, pages = {87-90}, pmid = {21304642}, issn = {1944-3277}, abstract = {Through a newly established Research Coordination Network for the Genomic Standards Consortium (RCN4GSC), the GSC will continue its leadership in establishing and integrating genomic standards through community-based efforts. These efforts, undertaken in the context of genomic and metagenomic research aim to ensure the electronic capture of all genomic data and to facilitate the achievement of a community consensus around collecting and managing relevant contextual information connected to the sequence data. The GSC operates as an open, inclusive organization, welcoming inspired biologists with a commitment to community service. Within the collaborative framework of the ongoing, international activities of the GSC, the RCN will expand the range of research domains engaged in these standardization efforts and sustain scientific networking to encourage active participation by the broader community. The RCN4GSC, funded for five years by the US National Science Foundation, will primarily support outcome-focused working meetings and the exchange of early-career scientists between GSC research groups in order to advance key standards contributions such as GCDML. Focusing on the timely delivery of the extant GSC core projects, the RCN will also extend the pioneering efforts of the GSC to engage researchers active in developing ecological, environmental and biodiversity data standards. As the initial goals of the GSC are increasingly achieved, promoting the comprehensive use of effective standards will be essential to ensure the effective use of sequence and associated data, to provide access for all biologists to all of the information, and to create interdisciplinary opportunities for discovery. The RCN will facilitate these implementation activities through participation in major scientific conferences and presentations on scientific advances enabled by community usage of genomic standards.}, } @article {pmid20203504, year = {2009}, author = {Marteau, P}, title = {Bacterial flora in inflammatory bowel disease.}, journal = {Digestive diseases (Basel, Switzerland)}, volume = {27 Suppl 1}, number = {}, pages = {99-103}, doi = {10.1159/000268128}, pmid = {20203504}, issn = {1421-9875}, mesh = {Animals ; Bacteria/*metabolism ; Humans ; Inflammation/complications ; Inflammatory Bowel Diseases/complications/*microbiology ; Intestines/microbiology/pathology ; Metagenome ; }, abstract = {The pathogenesis of inflammatory bowel disease (IBD) involves an interaction between host susceptibility (which is partly genetically determined), mucosal immunity and the intestinal milieu. Micro-organisms have physiological effects on mucosal structure, epithelial turnover, the intestinal immune cells and, thus, on many intestinal functions. Toll-like receptors and nucleotide oligomerisation-binding domain proteins in host cells recognise specific bacterial molecules and modify the immune response. Human studies have repeatedly shown that the microbiota of patients with IBD differs from that of controls and is unstable, both in the intestinal lumen and at the surface of the mucosa. A single pathogen has not been identified, but potentially pro-inflammatory micro-organisms have been found in samples from IBD patients more often than from healthy controls. These include Mycobacterium paratuberculosis, and enteroadherent and invasive Escherichia coli in Crohn's disease (CD). Ecological descriptions of the microbiota present in patients with IBD (either in the faeces or adherent to the mucosa) have repeatedly reported a decrease in usually dominant bacteria, especially those from the dominant phylum Firmicutes. A decrease in the biodiversity of Firmicutes has been observed in CD, while a recent study has shown that a decrease in Firmicutes, especially Faecalibacterium prausnitzii, was associated with CD and the post-operative recurrence of CD lesions in the ileum. Taken together, these results suggest that dysbiosis, or an imbalance within the (dominant) intestinal microbiota, may favour IBD.}, } @article {pmid19082562, year = {2009}, author = {Wommack, KE and Bench, SR and Bhavsar, J and Mead, D and Hanson, T}, title = {Isolation independent methods of characterizing phage communities 2: characterizing a metagenome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {502}, number = {}, pages = {279-289}, doi = {10.1007/978-1-60327-565-1_16}, pmid = {19082562}, issn = {1064-3745}, mesh = {Bacteriophages/classification/*genetics/isolation & purification ; Biodiversity ; Computational Biology/methods ; DNA, Viral/chemistry/genetics/isolation & purification ; Databases, Genetic ; Genetic Variation ; Genome, Viral/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Current appreciation of the vast expanse of prokaryotic diversity has largely come through molecular phylogenetic exploration of sequence diversity within the universally conserved gene for small subunit ribosomal RNA (16S rDNA). A plethora of methodologies for characterizing the diversity and composition of bacterial communities is based on sequence polymorphisms within this single gene. By comparison, no gene is universally shared among viruses or bacteriophages, which has prevented broad scale characterization of viral diversity within microbial ecosystems. With the reduction in DNA sequencing costs and wide availability of bioinformatics software, the tools of whole genome shotgun sequencing are now beginning to be applied to the characterization of genetic diversity within whole microbial communities. Such metagenomic approaches are ideally suited to the characterization of natural assemblages of viruses, because of the typically small, coding-dense nature of viral genomes. Data from a limited number of characterized viral metagenome libraries within a range of microbial ecosystems indicates that viral assemblages are comprised of between approximately 1,000 to a million different genotypes. Furthermore, viral assemblages typically contain a large proportion of completely novel genes and are likely to be the largest reservoir of unexplored genetic diversity on earth. Here, we present a conceptual framework for characterization of viral assemblages through metagenomic approaches.}, } @article {pmid19054115, year = {2009}, author = {Vieites, JM and Guazzaroni, ME and Beloqui, A and Golyshin, PN and Ferrer, M}, title = {Metagenomics approaches in systems microbiology.}, journal = {FEMS microbiology reviews}, volume = {33}, number = {1}, pages = {236-255}, doi = {10.1111/j.1574-6976.2008.00152.x}, pmid = {19054115}, issn = {0168-6445}, mesh = {Animals ; Biodiversity ; *Environmental Microbiology ; Gene Expression Regulation ; Genome ; *Genomics ; Humans ; Metabolomics ; Systems Biology/*methods ; }, abstract = {The world of microorganisms comprises a vast diversity of live organisms, each with its individual set of genes, cellular components and metabolic reactions that interact within the cell and communicate with the environment in many different ways. There is a strong imperative to gain a broader view of the wired and interconnected cellular and environmental processes as a whole via the systems microbiology approach in order to understand and predict ecosystem functioning. On the other hand, currently we experience a rise of metagenomics as an emerging tool to study communities of uncultured microorganisms. In this review, we conducted a survey of important methodologies in metagenomics and describe systems microbiology-like approaches for gaining a mechanistic understanding of complex microbial systems to interrogate compositional, evolutionary and metabolic properties. The review also discusses how metagenomics can be used as a holistic indicator for ecosystem response in terms of matter, nutrient and energy sources and functional networking.}, } @article {pmid19043404, year = {2009}, author = {Turnbaugh, PJ and Hamady, M and Yatsunenko, T and Cantarel, BL and Duncan, A and Ley, RE and Sogin, ML and Jones, WJ and Roe, BA and Affourtit, JP and Egholm, M and Henrissat, B and Heath, AC and Knight, R and Gordon, JI}, title = {A core gut microbiome in obese and lean twins.}, journal = {Nature}, volume = {457}, number = {7228}, pages = {480-484}, pmid = {19043404}, issn = {1476-4687}, support = {AA09022/AA/NIAAA NIH HHS/United States ; R01 HD049024-01/HD/NICHD NIH HHS/United States ; K05 AA017688/AA/NIAAA NIH HHS/United States ; P01 DK078669/DK/NIDDK NIH HHS/United States ; P01 DK078669-01/DK/NIDDK NIH HHS/United States ; R01 AA009022/AA/NIAAA NIH HHS/United States ; T32 GM065103-07/GM/NIGMS NIH HHS/United States ; R01 AA009022-10/AA/NIAAA NIH HHS/United States ; P50 ES012742/ES/NIEHS NIH HHS/United States ; UL1 TR000448/TR/NCATS NIH HHS/United States ; HD049024/HD/NICHD NIH HHS/United States ; R01 HD049024/HD/NICHD NIH HHS/United States ; ES012742/ES/NIEHS NIH HHS/United States ; P30 DK056341-08/DK/NIDDK NIH HHS/United States ; P30 DK056341/DK/NIDDK NIH HHS/United States ; P30 DK056341-07/DK/NIDDK NIH HHS/United States ; DK78669/DK/NIDDK NIH HHS/United States ; T32 GM065103/GM/NIGMS NIH HHS/United States ; P50 ES012742-049001/ES/NIEHS NIH HHS/United States ; }, mesh = {Adult ; Africa/ethnology ; Biodiversity ; Environment ; Europe/ethnology ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Genotype ; Humans ; Metagenome/genetics/*physiology ; Missouri ; Molecular Sequence Data ; Mothers ; Obesity/*microbiology ; RNA, Ribosomal, 16S/analysis/genetics ; Thinness/*microbiology ; Twins, Dizygotic ; Twins, Monozygotic ; }, abstract = {The human distal gut harbours a vast ensemble of microbes (the microbiota) that provide important metabolic capabilities, including the ability to extract energy from otherwise indigestible dietary polysaccharides. Studies of a few unrelated, healthy adults have revealed substantial diversity in their gut communities, as measured by sequencing 16S rRNA genes, yet how this diversity relates to function and to the rest of the genes in the collective genomes of the microbiota (the gut microbiome) remains obscure. Studies of lean and obese mice suggest that the gut microbiota affects energy balance by influencing the efficiency of calorie harvest from the diet, and how this harvested energy is used and stored. Here we characterize the faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers, to address how host genotype, environmental exposure and host adiposity influence the gut microbiome. Analysis of 154 individuals yielded 9,920 near full-length and 1,937,461 partial bacterial 16S rRNA sequences, plus 2.14 gigabases from their microbiomes. The results reveal that the human gut microbiome is shared among family members, but that each person's gut microbial community varies in the specific bacterial lineages present, with a comparable degree of co-variation between adult monozygotic and dizygotic twin pairs. However, there was a wide array of shared microbial genes among sampled individuals, comprising an extensive, identifiable 'core microbiome' at the gene, rather than at the organismal lineage, level. Obesity is associated with phylum-level changes in the microbiota, reduced bacterial diversity and altered representation of bacterial genes and metabolic pathways. These results demonstrate that a diversity of organismal assemblages can nonetheless yield a core microbiome at a functional level, and that deviations from this core are associated with different physiological states (obese compared with lean).}, } @article {pmid19023400, year = {2008}, author = {Huse, SM and Dethlefsen, L and Huber, JA and Mark Welch, D and Relman, DA and Sogin, ML}, title = {Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing.}, journal = {PLoS genetics}, volume = {4}, number = {11}, pages = {e1000255}, pmid = {19023400}, issn = {1553-7404}, support = {DP1 OD000964/OD/NIH HHS/United States ; DP1 OD000964-03/OD/NIH HHS/United States ; P50 ES012742/ES/NIEHS NIH HHS/United States ; 1 P50 ES012742-01/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics ; Biodiversity ; Classification/methods ; Humans ; Metagenome/genetics ; RNA, Ribosomal/*genetics ; Sequence Analysis, DNA ; Sequence Tagged Sites ; }, abstract = {Massively parallel pyrosequencing of hypervariable regions from small subunit ribosomal RNA (SSU rRNA) genes can sample a microbial community two or three orders of magnitude more deeply per dollar and per hour than capillary sequencing of full-length SSU rRNA. As with full-length rRNA surveys, each sequence read is a tag surrogate for a single microbe. However, rather than assigning taxonomy by creating gene trees de novo that include all experimental sequences and certain reference taxa, we compare the hypervariable region tags to an extensive database of rRNA sequences and assign taxonomy based on the best match in a Global Alignment for Sequence Taxonomy (GAST) process. The resulting taxonomic census provides information on both composition and diversity of the microbial community. To determine the effectiveness of using only hypervariable region tags for assessing microbial community membership, we compared the taxonomy assigned to the V3 and V6 hypervariable regions with the taxonomy assigned to full-length SSU rRNA sequences isolated from both the human gut and a deep-sea hydrothermal vent. The hypervariable region tags and full-length rRNA sequences provided equivalent taxonomy and measures of relative abundance of microbial communities, even for tags up to 15% divergent from their nearest reference match. The greater sampling depth per dollar afforded by massively parallel pyrosequencing reveals many more members of the "rare biosphere" than does capillary sequencing of the full-length gene. In addition, tag sequencing eliminates cloning bias and the sequences are short enough to be completely sequenced in a single read, maximizing the number of organisms sampled in a run while minimizing chimera formation. This technique allows the cost-effective exploration of changes in microbial community structure, including the rare biosphere, over space and time and can be applied immediately to initiatives, such as the Human Microbiome Project.}, } @article {pmid19020558, year = {2009}, author = {Kielak, A and Pijl, AS and van Veen, JA and Kowalchuk, GA}, title = {Phylogenetic diversity of Acidobacteria in a former agricultural soil.}, journal = {The ISME journal}, volume = {3}, number = {3}, pages = {378-382}, doi = {10.1038/ismej.2008.113}, pmid = {19020558}, issn = {1751-7370}, mesh = {Bacteria/*classification/*isolation & purification ; *Biodiversity ; Cloning, Molecular ; DNA Primers/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gene Library ; Genes, rRNA ; Molecular Sequence Data ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; *Soil Microbiology ; }, abstract = {Although Acidobacteria represent the most abundant bacterial phylum in many soils, knowledge of acidobacterial diversity is still rather incomplete. We, therefore, examined the diversity of 16S rRNA genes affiliated with this phylum in a former arable soil via three independent approaches: (1) screening of a fosmid metagenome library for inserts containing Acidobacteria-like 16S rRNA genes; (2) PCR-cloning using general bacterial primers; and (3) PCR-cloning with acidobacterial-specific primers. Bacterial-specific libraries compared rhizosphere versus bulk soil samples, revealing a higher proportion of acidobacterial sequences in bulk soil libraries (P<0.001). Bacterial libraries recovered the greatest diversity, and sequence examination suggested that sequence mismatches with the Acidobacteria-specific primers limited the coverage of the metagenome library screening and specific library approaches. Together, these results expand knowledge of the distribution and diversity of Acidobacteria in soil environments and highlight important technical considerations in the molecular analysis of Acidobacteria diversity.}, } @article {pmid18841700, year = {2008}, author = {Manson, JM and Rauch, M and Gilmore, MS}, title = {The commensal microbiology of the gastrointestinal tract.}, journal = {Advances in experimental medicine and biology}, volume = {635}, number = {}, pages = {15-28}, doi = {10.1007/978-0-387-09550-9_2}, pmid = {18841700}, issn = {0065-2598}, mesh = {Animals ; Bacteria/cytology/*metabolism ; Biodiversity ; Colony Count, Microbial ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenome ; }, abstract = {The gastrointestinal (GI) tract is a dynamic environment and therefore the stability of the commensal community, or microbiota, is under constant challenge. Microscopic observations have revealed that the majority of bacteria present in the GI tract are not detected using standard culturing techniques, however with the application of culture-independent techniques it has been estimated that between 500 to 1000 bacterial species inhabit the human GI tract. Numerically predominant organisms in the microbiota belong to two eubacterial divisions, the Cytophaga-Flavobacterium-Bacteroides (CFB) and the Firmicutes, and fall into three main groups; Clostridium rRNA subcluster XIVa, Clostridium rRNA subcluster IV and Bacteroides. The prevalence and diversity of bacteria in different areas of the GI tract is influenced by the different conditions at these sites and thus the microbiota of the stomach and jejunum varies with that of the large intestine. Additionally, host genotype, age and diet have all been shown to affect microbial diversity in the GI tract. The distal intestine harbours the highest bacterial cell densities for any known ecosystem. Characterizing the species composition of the healthy microbiota may be a key step in identifying bacterial or associated physiological conditions that are present or absent in an unhealthy microbiota.}, } @article {pmid18840282, year = {2008}, author = {Frank, DN}, title = {XplorSeq: a software environment for integrated management and phylogenetic analysis of metagenomic sequence data.}, journal = {BMC bioinformatics}, volume = {9}, number = {}, pages = {420}, pmid = {18840282}, issn = {1471-2105}, mesh = {Artificial Intelligence ; Base Sequence ; *Database Management Systems ; Genes, rRNA ; *Genome ; Information Storage and Retrieval ; Meta-Analysis as Topic ; *Phylogeny ; Sequence Analysis, DNA/*methods ; Systems Integration ; *User-Computer Interface ; }, abstract = {BACKGROUND: Advances in automated DNA sequencing technology have accelerated the generation of metagenomic DNA sequences, especially environmental ribosomal RNA gene (rDNA) sequences. As the scale of rDNA-based studies of microbial ecology has expanded, need has arisen for software that is capable of managing, annotating, and analyzing the plethora of diverse data accumulated in these projects.

RESULTS: XplorSeq is a software package that facilitates the compilation, management and phylogenetic analysis of DNA sequences. XplorSeq was developed for, but is not limited to, high-throughput analysis of environmental rRNA gene sequences. XplorSeq integrates and extends several commonly used UNIX-based analysis tools by use of a Macintosh OS-X-based graphical user interface (GUI). Through this GUI, users may perform basic sequence import and assembly steps (base-calling, vector/primer trimming, contig assembly), perform BLAST (Basic Local Alignment and Search Tool; 123) searches of NCBI and local databases, create multiple sequence alignments, build phylogenetic trees, assemble Operational Taxonomic Units, estimate biodiversity indices, and summarize data in a variety of formats. Furthermore, sequences may be annotated with user-specified meta-data, which then can be used to sort data and organize analyses and reports. A document-based architecture permits parallel analysis of sequence data from multiple clones or amplicons, with sequences and other data stored in a single file.

CONCLUSION: XplorSeq should benefit researchers who are engaged in analyses of environmental sequence data, especially those with little experience using bioinformatics software. Although XplorSeq was developed for management of rDNA sequence data, it can be applied to most any sequencing project. The application is available free of charge for non-commercial use at http://vent.colorado.edu/phyloware.}, } @article {pmid18818648, year = {2008}, author = {Hugenholtz, P and Tyson, GW}, title = {Microbiology: metagenomics.}, journal = {Nature}, volume = {455}, number = {7212}, pages = {481-483}, doi = {10.1038/455481a}, pmid = {18818648}, issn = {1476-4687}, mesh = {Biodiversity ; Computational Biology/trends ; *Ecosystem ; *Environmental Microbiology ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; *Genetics, Microbial/methods ; Genome/genetics ; *Genomics/economics/methods/trends ; Humans ; Marine Biology ; Prokaryotic Cells/metabolism ; Sequence Analysis, DNA/economics ; Time Factors ; Viruses/genetics ; }, } @article {pmid18817891, year = {2008}, author = {Tringe, SG and Hugenholtz, P}, title = {A renaissance for the pioneering 16S rRNA gene.}, journal = {Current opinion in microbiology}, volume = {11}, number = {5}, pages = {442-446}, doi = {10.1016/j.mib.2008.09.011}, pmid = {18817891}, issn = {1369-5274}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Culture-independent molecular surveys using the 16S rRNA gene have become a mainstay for characterizing microbial community structure over the past quarter century. More recently this approach has been overshadowed by metagenomics, which provides a global overview of a community's functional potential rather than just an inventory of its inhabitants. However, the pioneering 16S rRNA gene is making a comeback in its own right thanks to a number of methodological advancements including higher resolution (more sequences), analysis of multiple related samples (e.g. spatial and temporal series) and improved metadata, and use of metadata. The standard conclusion that microbial ecosystems are remarkably complex and diverse is now being replaced by detailed insights into microbial ecology and evolution based only on this one historically important marker gene.}, } @article {pmid18786627, year = {2008}, author = {Rajendhran, J and Gunasekaran, P}, title = {Strategies for accessing soil metagenome for desired applications.}, journal = {Biotechnology advances}, volume = {26}, number = {6}, pages = {576-590}, doi = {10.1016/j.biotechadv.2008.08.002}, pmid = {18786627}, issn = {1873-1899}, mesh = {Bacteriophages/genetics ; Biodiversity ; Biotechnology/*methods ; Cloning, Molecular ; DNA Transposable Elements ; DNA, Bacterial/*isolation & purification ; *Genome, Bacterial ; Genome, Viral ; Genomic Library ; Genomics ; Humic Substances/analysis ; Plasmids ; *Soil Microbiology ; }, abstract = {Most of the microorganisms in nature are inaccessible as they are uncultivable in the laboratory. Metagenomic approaches promise the accessibility of the genetic resources and their potential applications. Genetic resources from terrestrial environments can be accessed by exploring the soil metagenome. Soil metagenomic analyses are usually initiated by the isolation of environmental DNAs. Several methods have been described for the direct isolation of environmental DNAs from soil and sediments. Application of metagenomics largely depends on the construction of genomic DNA libraries and subsequent high-throughput sequencing or library screening. Thus, obtaining large quantities of pure cloneable DNA from the environment is a prerequisite. This review discusses the recent developments related to efficient extraction and purification of soil metagenome highlighting the considerations for various metagenomic applications.}, } @article {pmid18764874, year = {2009}, author = {Breitbart, M and Hoare, A and Nitti, A and Siefert, J and Haynes, M and Dinsdale, E and Edwards, R and Souza, V and Rohwer, F and Hollander, D}, title = {Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico.}, journal = {Environmental microbiology}, volume = {11}, number = {1}, pages = {16-34}, doi = {10.1111/j.1462-2920.2008.01725.x}, pmid = {18764874}, issn = {1462-2920}, mesh = {*Biodiversity ; Carbonates/metabolism ; Fresh Water/*chemistry/*microbiology ; Geologic Sediments/*chemistry/*microbiology ; *Isotope Labeling ; Mexico ; Polymers/metabolism ; Sequence Analysis, DNA ; }, abstract = {Ancient biologically mediated sedimentary carbonate deposits, including stromatolites and other microbialites, provide insight into environmental conditions on early Earth. The primary limitation to interpreting these records is our lack of understanding regarding microbial processes and the preservation of geochemical signatures in contemporary microbialite systems. Using a combination of metagenomic sequencing and isotopic analyses, this study describes the identity, metabolic potential and chemical processes of microbial communities from living microbialites from Cuatro Ciénegas, Mexico. Metagenomic sequencing revealed a diverse, redox-dependent microbial community associated with the microbialites. The microbialite community is distinct from other marine and freshwater microbial communities, and demonstrates extensive environmental adaptation. The microbialite metagenomes contain a large number of genes involved in the production of exopolymeric substances and the formation of biofilms, creating a complex, spatially structured environment. In addition to the spatial complexity of the biofilm, microbial activity is tightly controlled by sensory and regulatory systems, which allow for coordination of autotrophic and heterotrophic processes. Isotopic measurements of the intracrystalline organic matter demonstrate the importance of heterotrophic respiration of photoautotrophic biomass in the precipitation of calcium carbonate. The genomic and stable isotopic data presented here significantly enhance our evolving knowledge of contemporary biomineralization processes, and are directly applicable to studies of ancient microbialites.}, } @article {pmid18717988, year = {2008}, author = {Kennedy, J and Marchesi, JR and Dobson, AD}, title = {Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments.}, journal = {Microbial cell factories}, volume = {7}, number = {}, pages = {27}, pmid = {18717988}, issn = {1475-2859}, abstract = {Metagenomic based strategies have previously been successfully employed as powerful tools to isolate and identify enzymes with novel biocatalytic activities from the unculturable component of microbial communities from various terrestrial environmental niches. Both sequence based and function based screening approaches have been employed to identify genes encoding novel biocatalytic activities and metabolic pathways from metagenomic libraries. While much of the focus to date has centred on terrestrial based microbial ecosystems, it is clear that the marine environment has enormous microbial biodiversity that remains largely unstudied. Marine microbes are both extremely abundant and diverse; the environments they occupy likewise consist of very diverse niches. As culture-dependent methods have thus far resulted in the isolation of only a tiny percentage of the marine microbiota the application of metagenomic strategies holds great potential to study and exploit the enormous microbial biodiversity which is present within these marine environments.}, } @article {pmid18708511, year = {2008}, author = {Kim, KH and Chang, HW and Nam, YD and Roh, SW and Kim, MS and Sung, Y and Jeon, CO and Oh, HM and Bae, JW}, title = {Amplification of uncultured single-stranded DNA viruses from rice paddy soil.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {19}, pages = {5975-5985}, pmid = {18708511}, issn = {1098-5336}, mesh = {Biodiversity ; Cloning, Molecular ; DNA Viruses/*classification/genetics/*isolation & purification ; DNA, Single-Stranded/*genetics ; DNA, Viral/chemistry/*genetics ; Genome, Viral ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques/*methods ; Oryza/*virology ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; *Soil Microbiology ; Viral Proteins/genetics ; }, abstract = {Viruses are known to be the most numerous biological entities in soil; however, little is known about their diversity in this environment. In order to explore the genetic diversity of soil viruses, we isolated viruses by centrifugation and sequential filtration before performing a metagenomic investigation. We adopted multiple-displacement amplification (MDA), an isothermal whole-genome amplification method with phi29 polymerase and random hexamers, to amplify viral DNA and construct clone libraries for metagenome sequencing. By the MDA method, the diversity of both single-stranded DNA (ssDNA) viruses and double-stranded DNA viruses could be investigated at the same time. On the contrary, by eliminating the denaturing step in the MDA reaction, only ssDNA viral diversity could be explored selectively. Irrespective of the denaturing step, more than 60% of the soil metagenome sequences did not show significant hits (E-value criterion, 0.001) with previously reported viral sequences. Those hits that were considered to be significant were also distantly related to known ssDNA viruses (average amino acid similarity, approximately 34%). Phylogenetic analysis showed that replication-related proteins (which were the most frequently detected proteins) related to those of ssDNA viruses obtained from the metagenomic sequences were diverse and novel. Putative circular genome components of ssDNA viruses that are unrelated to known viruses were assembled from the metagenomic sequences. In conclusion, ssDNA viral diversity in soil is more complex than previously thought. Soil is therefore a rich pool of previously unknown ssDNA viruses.}, } @article {pmid18682527, year = {2008}, author = {Manichanh, C and Chapple, CE and Frangeul, L and Gloux, K and Guigo, R and Dore, J}, title = {A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.}, journal = {Nucleic acids research}, volume = {36}, number = {16}, pages = {5180-5188}, pmid = {18682527}, issn = {1362-4962}, mesh = {Bacteria/*classification/genetics/isolation & purification ; Base Sequence ; *Biodiversity ; Crohn Disease/microbiology ; DNA, Ribosomal/chemistry ; Gastrointestinal Tract/microbiology ; *Genomic Library ; Genomics/*methods ; Humans ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Alignment ; }, abstract = {The construction of metagenomic libraries has permitted the study of microorganisms resistant to isolation and the analysis of 16S rDNA sequences has been used for over two decades to examine bacterial biodiversity. Here, we show that the analysis of random sequence reads (RSRs) instead of 16S is a suitable shortcut to estimate the biodiversity of a bacterial community from metagenomic libraries. We generated 10,010 RSRs from a metagenomic library of microorganisms found in human faecal samples. Then searched them using the program BLASTN against a prokaryotic sequence database to assign a taxon to each RSR. The results were compared with those obtained by screening and analysing the clones containing 16S rDNA sequences in the whole library. We found that the biodiversity observed by RSR analysis is consistent with that obtained by 16S rDNA. We also show that RSRs are suitable to compare the biodiversity between different metagenomic libraries. RSRs can thus provide a good estimate of the biodiversity of a metagenomic library and, as an alternative to 16S, this approach is both faster and cheaper.}, } @article {pmid18667859, year = {2008}, author = {Wang, Q and Shao, Y and Huong, VT and Park, WJ and Park, JM and Jeon, CO}, title = {Fine-scale population structure of Accumulibacter phosphatis in enhanced biological phosphorus removal sludge.}, journal = {Journal of microbiology and biotechnology}, volume = {18}, number = {7}, pages = {1290-1297}, pmid = {18667859}, issn = {1017-7825}, mesh = {Acyltransferases/genetics ; Bacterial Proteins/genetics ; Betaproteobacteria/*classification/genetics/isolation & purification/*metabolism ; Biodegradation, Environmental ; Biodiversity ; Bioreactors ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Phosphorus/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; }, abstract = {To investigate the diversities of Accumulibacter phosphatis and its polyhydroxyalkanoate (PHA) synthase gene (phaC) in enhanced biological phosphorus removal (EBPR) sludge, an acetate-fed sequencing batch reactor was operated. Analysis of microbial communities using fluorescence in situ hybridization and 16S rRNA gene clone libraries showed that the population of Accumulibacter phosphatis in the EBPR sludge comprised more than 50% of total bacteria, and was clearly divided into two subgroups with about 97.5% sequence identity of the 16S rRNA genes. PAO phaC primers targeting the phaC genes of Accumulibacter phosphatis were designed and applied to retrieve fragments of putative phaC homologs of Accumulibacter phosphatis from EBPR sludge. PAO phaC primers targeting G 1PAO, G 2PAO, and G 3PAO groups produced PCR amplicons successfully; the resulting sequences of the phaC gene homologs were diverse, and were distantly related to metagenomic phaC sequences of Accumulibacter phosphatis with 75-98% DNA sequence identities. Degenerate NPAO (non-PAO) phaC primers targeting phaC genes of non- Accumulibacter phosphatis bacteria were also designed and applied to the EBPR sludge. Twenty-four phaC homologs retrieved from NPAO phaC primers were different from the phaC gene homologs derived from Accumulibacter phosphatis, which suggests that the PAO phaC primers were specific for the amplification of phaC gene homologs of Accumulibacter phosphatis, and the putative phaC gene homologs by PAO phaC primers were derived from Accumulibacter phosphatis in the EBPR sludge. Among 24 phaC homologs, a phaC homolog (G1NPAO-2), which was dominant in the NPAO phaC clone library, showed the strongest signal in slot hybridization and shared approximately 60% nucleotide identity with the G4PAO group of Accumulibacter phosphatis, which suggests that G1NPAO-2 might be derived from Accumulibacter phosphatis. In conclusion, analyses of the 16S rRNA and phaC genes showed that Accumulibacter phosphatis might be phylogenetically and metabolically diverse.}, } @article {pmid18650928, year = {2008}, author = {Quince, C and Curtis, TP and Sloan, WT}, title = {The rational exploration of microbial diversity.}, journal = {The ISME journal}, volume = {2}, number = {10}, pages = {997-1006}, doi = {10.1038/ismej.2008.69}, pmid = {18650928}, issn = {1751-7370}, mesh = {Bacteria/genetics/*isolation & purification ; *Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Genome, Bacterial ; Models, Statistical ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The exploration of the microbial world has been an exciting series of unanticipated discoveries despite being largely uninformed by rational estimates of the magnitude of task confronting us. However, in the long term, more structured surveys can be achieved by estimating the diversity of microbial communities and the effort required to describe them. The rates of recovery of new microbial taxa in very large samples suggest that many more taxa remain to be discovered in soils and the oceans. We apply a robust statistical method to large gene sequence libraries from these environments to estimate both diversity and the sequencing effort required to obtain a given fraction of that diversity. In the upper ocean, we predict some 1400 phylotypes, and a mere fivefold increase in shotgun reads could yield 90% of the metagenome, that is, all genes from all taxa. However, at deep ocean, hydrothermal vents and diversities in soils can be up to two orders of magnitude larger, and hundreds of times the current number of samples will be required just to obtain 90% of the taxonomic diversity based on 3% difference in 16S rDNA. Obtaining 90% of the metagenome will require tens of thousands of times the current sequencing effort. Although the definitive sequencing of hyperdiverse environments is not yet possible, we can, using taxa-abundance distributions, begin to plan and develop the required methods and strategies. This would initiate a new phase in the exploration of the microbial world.}, } @article {pmid18642606, year = {2008}, author = {Galbraith, EA and Antonopoulos, DA and White, BA}, title = {Application of suppressive subtractive hybridization to uncover the metagenomic diversity of environmental samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {410}, number = {}, pages = {295-333}, doi = {10.1007/978-1-59745-548-0_16}, pmid = {18642606}, issn = {1064-3745}, mesh = {Animals ; *Biodiversity ; Environment ; *Genetic Variation ; Genomics/*methods ; Nucleic Acid Hybridization/*methods ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Metagenomics addresses the collective genetic structure and functional composition of a microbial environmental sample without the bias or necessity for culturing the microorganisms from the community in question. Metagenomic studies are now beginning to take advantage of the plethora of complete genome sequences and the associated tools, such as bacterial artificial chromosome (BAC) and fosmid vectors, to discover novel genes and survey the structure and function of microbial communities. Complementary and less expensive methods to compare genomes from individual microbes have been utilized in comparative genomic studies. Suppressive subtractive hybridization (SSH) is one such approach, which has been utilized to compare the genomic content of closely related species of bacteria. Recently, SSH has also been used as a comparative method to examine the microbial diversity (i.e., species composition) and functional differences (i.e., gene composition) in the genomic content of two different rumen environmental communities. Through a series of hybridizations and pblymerase chain reaction (PCR) amplifications, metagenomic differences between two environmental samples can be isolated by SSH. Subsequent DNA sequencing and bioinformatic analyses allow the putative identification of these differences.}, } @article {pmid18631363, year = {2008}, author = {Wang, HX and Geng, ZL and Zeng, Y and Shen, YM}, title = {Enriching plant microbiota for a metagenomic library construction.}, journal = {Environmental microbiology}, volume = {10}, number = {10}, pages = {2684-2691}, doi = {10.1111/j.1462-2920.2008.01689.x}, pmid = {18631363}, issn = {1462-2920}, mesh = {Bacteria/*growth & development/*isolation & purification ; Biodiversity ; DNA, Bacterial/chemistry/*genetics ; DNA, Ribosomal/chemistry/genetics ; *Gene Library ; Genes, rRNA ; Genotype ; Molecular Sequence Data ; Phylogeny ; Plants/*microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Ribotyping ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Plant microbiota (the microorganisms that live in any associations with plant tissues) represents a rather unexplored area of metagenomic research compared with soils and oceans. Constructing a metagenomic library for plant microbiota is technically challenging. Using all the biomass without pre-enrichment could lead to vast proportions of the host plant DNA in the metagenomic library, doubtless obliterating the microbial contribution. Therefore, the first and essential step is to enrich for the constituent microorganisms from plant tissues. Here, a strong enrichment for plant microbiota was achieved by coupling SDS (sodium dodecyl sulfate) with NaCl, creating a predominantly microbial metagenomic library that contains 88% bacterial inserts. 16S rDNA sequence analysis revealed that the metagenomic DNA of enrichments originates from very diverse microorganisms. At least 74 distinct ribotypes (at a 97% threshold) from seven different bacterial phyla were identified and mainly distributed among Actinobacteria and Proteobacteria. Additionally, a simplified version of Amplified Ribosomal DNA Restriction Analysis (ARDRA) was developed for a quick and efficient assessment of the enriching procedures. This work opens further insight into the great biotechnical potential of plant microbiota, holding more potential for drug discovery through a metagenomic strategy, and paving the way for recovery and biochemical characterization of functional gene repertoire from plant microbiota.}, } @article {pmid18625611, year = {2008}, author = {Pignatelli, M and Aparicio, G and Blanquer, I and Hernández, V and Moya, A and Tamames, J}, title = {Metagenomics reveals our incomplete knowledge of global diversity.}, journal = {Bioinformatics (Oxford, England)}, volume = {24}, number = {18}, pages = {2124-2125}, pmid = {18625611}, issn = {1367-4811}, mesh = {Biodiversity ; Ecosystem ; *Genetic Variation ; Genomics/*methods ; }, abstract = {Contact: Javier.tamames@uv.es}, } @article {pmid18604648, year = {2009}, author = {Sundset, MA and Edwards, JE and Cheng, YF and Senosiain, RS and Fraile, MN and Northwood, KS and Praesteng, KE and Glad, T and Mathiesen, SD and Wright, AD}, title = {Molecular diversity of the rumen microbiome of Norwegian reindeer on natural summer pasture.}, journal = {Microbial ecology}, volume = {57}, number = {2}, pages = {335-348}, pmid = {18604648}, issn = {0095-3628}, support = {BBS/E/W/00003135A/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/W/00003135B/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biodiversity ; DNA, Archaeal/genetics ; DNA, Fungal/genetics ; DNA, Protozoan/genetics ; Eukaryota/classification/genetics ; Female ; Gene Library ; *Metagenome ; Neocallimastigales/classification/genetics ; Norway ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Reindeer/*microbiology ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The molecular diversity of the rumen microbiome was investigated in five semi-domesticated adult female Norwegian reindeer (Rangifer tarandus tarandus) grazing on natural summer pastures on the coast of northern Norway (71.00 degrees N, 25.30 degrees E). Mean population densities (numbers per gram wet weight) of methanogenic archaea, rumen bacteria and ciliate protozoa, estimated using quantitative real-time polymerase chain reaction (PCR), were 3.17x10(9), 5.17x10(11) and 4.02x10(7), respectively. Molecular diversity of rumen methanogens was revealed using a 16S rRNA gene library (54 clones) constructed using pooled PCR products from the whole rumen contents of the five individual reindeer. Based upon a similarity criterion of <97%, a total of 19 distinct operational taxonomic units (OTUs) were identified, nine of which are potential new species. The 16S rRNA sequences generated from the reindeer rumen exhibited a high degree of sequence similarity to methanogens affiliated with the families Methanobacteriaceae (14 OTUs) and Methanosarcinaceae (one OTU). Four of the OTUs detected belonged to a group of uncultivated archaea previously found in domestic ruminants and thought to be dominant in the rumen together with Methanobrevibacter spp. Denaturing gradient gel electrophoresis profiling of the rumen bacterial 16S rRNA gene and the protozoal 18S rRNA gene indicated a high degree of animal variation, although some bands were common to all individuals. Automated ribosomal intergenic spacer analysis (ARISA) profiling of the ruminal Neocallimastigales population indicated that the reindeer are likely to contain more than one type of anaerobic fungus. The ARISA profile from one animal was distinct from the other four. This is the first molecular investigation of the ruminal methanogenic archaea in reindeer, revealing higher numbers than expected based on methane emission data available. Also, many of the reindeer archaeal 16S rRNA gene sequences were similar to those reported in domesticated ruminants in Australia, Canada, China, New Zealand and Venezuela, supporting previous findings that there seems to be no host type or geographical effect on the methanogenic archaea community structure in ruminants.}, } @article {pmid18584522, year = {2008}, author = {Ott, SJ and Kühbacher, T and Musfeldt, M and Rosenstiel, P and Hellmig, S and Rehman, A and Drews, O and Weichert, W and Timmis, KN and Schreiber, S}, title = {Fungi and inflammatory bowel diseases: Alterations of composition and diversity.}, journal = {Scandinavian journal of gastroenterology}, volume = {43}, number = {7}, pages = {831-841}, doi = {10.1080/00365520801935434}, pmid = {18584522}, issn = {1502-7708}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Base Sequence ; Colitis, Ulcerative/microbiology ; Crohn Disease/microbiology ; Feces/microbiology ; Female ; Fungi/*isolation & purification ; Humans ; In Situ Hybridization ; In Situ Hybridization, Fluorescence ; Inflammatory Bowel Diseases/*microbiology ; Intestinal Mucosa/*microbiology ; Male ; Middle Aged ; Molecular Sequence Data ; Polymerase Chain Reaction ; }, abstract = {OBJECTIVE: Altered bacterial diversity of the intestinal mucosa-associated microbiota may reflect the net influence of lifestyle factors associated with the development of chronic inflammatory bowel diseases (IBD). While a reduced bacterial diversity has been reported in IBD, little is known about the fungal microbiota. The aim of this study was to carry out a systematic analysis of intestinal fungal microbiota in IBD.

MATERIAL AND METHODS: The mucosa-associated fungal microbiota of 104 colonic biopsy tissues from 47 controls and 57 IBD patients was investigated using metagenomic 18S rDNA-based denaturing gradient gel electrophoresis (DGGE), clone libraries, sequencing, and in situ hybridization techniques.

RESULTS: Fungi-specific 18S rDNA signatures could be detected in all 104 patients, accounting for only a small proportion of the intestinal microbiota (0.02% of the mucosal and 0.03% of the fecal microbiota). An overall fungal biodiversity of 43 different operational taxonomic units (OTUs) was found in the clone libraries. The qualitative composition of fungal microbiota was different between patients with IBD and controls. The DGGE profiles showed a higher mean fungal diversity in patients with Crohn's disease (CD) in comparison with controls (10.8+/-3.1 versus 6.2+/-2.4 for CD, p
CONCLUSIONS: Diverse fungal species are part of the normal enteric microbiota, but diversity is increased and composition of the fungal communities varies in IBD. Further work is needed to investigate whether the alteration of the fungal flora in IBD is secondary to an imbalanced bacterial microbiota or an independent etiologic factor.}, } @article {pmid18554975, year = {2008}, author = {Allen, MJ and Wilson, WH}, title = {Aquatic virus diversity accessed through omic techniques: a route map to function.}, journal = {Current opinion in microbiology}, volume = {11}, number = {3}, pages = {226-232}, doi = {10.1016/j.mib.2008.05.004}, pmid = {18554975}, issn = {1369-5274}, mesh = {Archaea/virology ; *Biodiversity ; Ecosystem ; Eukaryotic Cells/virology ; *Genomics ; Oligonucleotide Array Sequence Analysis ; Prokaryotic Cells/virology ; *Proteomics ; Sequence Analysis, DNA ; Viruses/*classification/genetics ; *Water Microbiology ; }, abstract = {Viruses are arguably the simplest form of life yet they play a crucial role in regulating planetary processes. From shuttling genes to 'lubricating' microbial loop dynamics, viruses are integral in shaping microbial ecology. In every environment on Earth the role of viruses goes far beyond the simple infect-replicate-kill cycle. Their enormous abundance and seemingly infinite diversity provide the vital clues to the true function of viruses. New 'omic' approaches are now allowing researchers to gain extraordinary insights into virus diversity and inferred function, particularly within aquatic environments. The development of molecular markers and application of techniques including microarrays, metagenomic sequencing and proteomic analysis are now being applied to virus communities. Despite this shift towards culture-independent approaches it has proved difficult to derive useful information about infection strategies since so much of the sequence information has no database matches. Future advances will involve tools such as microarrays to help determine the functionality of unknown genes. Sequence information should be considered as a starting point for asking questions and developing hypotheses about the role of viruses. It is an exciting new era for virus ecology and when used in combination with more traditional approaches, virus genomics will give us access to their ecological function on an unprecedented scale.}, } @article {pmid18543030, year = {2008}, author = {Ahmad, N and Sharma, S and Khan, FG and Kumar, R and Johri, S and Abdin, MZ and Qazi, GN}, title = {Phylogenetic analyses of archaeal ribosomal DNA sequences from salt pan sediment of Mumbai, India.}, journal = {Current microbiology}, volume = {57}, number = {2}, pages = {145-152}, pmid = {18543030}, issn = {0343-8651}, mesh = {Archaea/*classification/genetics/*isolation & purification ; *Biodiversity ; DNA Fingerprinting ; DNA Primers/genetics ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Genotype ; Geologic Sediments/*microbiology ; India ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction/methods ; Polymorphism, Restriction Fragment Length ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {The archaeal diversity in salt pan sediment from Mumbai, India, was investigated by 16S rDNA-dependent molecular phylogeny. Small-subunit rRNA (16S rDNA) from salt pan sediment metagenome were amplified by polymerase chain reaction (PCR) using primers specific to the domain archaea. Thirty-two unique phylotypes were obtained by PCR-based RFLP of 16S rRNA genes using endonucleases Hae111 and Msp1, which were most suitable to score the genetic diversity. These phylotypes spanned a wide range within the domain Archaea including both Crenarchaeota and Euryarcheaota. However, none of the retrieved Crenarchaeota sequences could be grouped with previously cultured Crenarchaeota. Of all the Euryarcheaota sequences, three sequences were related to Haloarchaea, two were related to cultured Methanosarcina sp., and the remaining sequences were affiliated with uncultured Methanosarcina sp., Methanogenium sp., and Methanolobus sp. Most of the sequences determined were closely related to the sequences that had been previously obtained from metagenome of a variety of marine environments. The phylogenetic study of a site investigated for the first time revealed the presence of a highly diverse archaeal population and may represent novel sequences and organisms specially adapted to the salt pan sediment of Mumbai. These findings are of fundamental value for understanding the complexity of salt pan ecosystems.}, } @article {pmid18541415, year = {2008}, author = {Breitbart, M and Haynes, M and Kelley, S and Angly, F and Edwards, RA and Felts, B and Mahaffy, JM and Mueller, J and Nulton, J and Rayhawk, S and Rodriguez-Brito, B and Salamon, P and Rohwer, F}, title = {Viral diversity and dynamics in an infant gut.}, journal = {Research in microbiology}, volume = {159}, number = {5}, pages = {367-373}, doi = {10.1016/j.resmic.2008.04.006}, pmid = {18541415}, issn = {0923-2508}, mesh = {*Biodiversity ; DNA Viruses/*classification/genetics/*isolation & purification/ultrastructure ; DNA, Viral/genetics ; Feces/virology ; Gastrointestinal Tract/*virology ; Humans ; Infant ; Infant Food/analysis ; Male ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; }, abstract = {Metagenomic sequencing of DNA viruses from the feces of a healthy week-old infant revealed a viral community with extremely low diversity. The identifiable sequences were dominated by phages, which likely influence the diversity and abundance of co-occurring microbes. The most abundant fecal viral sequences did not originate from breast milk or formula, suggesting a non-dietary initial source of viruses. Certain sequences were stable in the infant's gut over the first 3 months of life, but microarray experiments demonstrated that the overall viral community composition changed dramatically between 1 and 2 weeks of age.}, } @article {pmid18541218, year = {2008}, author = {Peterson, DA and Frank, DN and Pace, NR and Gordon, JI}, title = {Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases.}, journal = {Cell host & microbe}, volume = {3}, number = {6}, pages = {417-427}, pmid = {18541218}, issn = {1934-6069}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; P01 DK078669-03/DK/NIDDK NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; R37 DK030292-29/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/immunology/*isolation & purification ; Biodiversity ; *Host-Pathogen Interactions ; Humans ; Immunoglobulin A/immunology ; Inflammatory Bowel Diseases/*immunology/*microbiology/therapy ; Intestinal Mucosa/immunology/microbiology/physiopathology ; Mice ; Probiotics/administration & dosage ; }, abstract = {The human gastrointestinal tract is home to immense and complex populations of microorganisms. Using recent technical innovations, the diversity present in this human body habitat is now being analyzed in detail. This review focuses on the microbial ecology of the gut in inflammatory bowel diseases and on how recent studies provide an impetus for using carefully designed, comparative metagenomic approaches to delve into the structure and activities of the gut microbial community and its interrelationship with the immune system.}, } @article {pmid18510552, year = {2008}, author = {Howard, EC and Sun, S and Biers, EJ and Moran, MA}, title = {Abundant and diverse bacteria involved in DMSP degradation in marine surface waters.}, journal = {Environmental microbiology}, volume = {10}, number = {9}, pages = {2397-2410}, doi = {10.1111/j.1462-2920.2008.01665.x}, pmid = {18510552}, issn = {1462-2920}, mesh = {Bacteria/*genetics/metabolism ; Bacterial Proteins/genetics ; Base Composition ; Biodegradation, Environmental ; Biodiversity ; Computational Biology ; DNA, Bacterial/genetics ; Databases, Nucleic Acid ; Genes, Bacterial ; Genome, Bacterial ; Molecular Sequence Data ; Oxidoreductases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sulfonium Compounds/*metabolism ; *Water Microbiology ; }, abstract = {An expanded analysis of oceanic metagenomic data indicates that the majority of prokaryotic cells in marine surface waters have the genetic capability to demethylate dimethylsulfoniopropionate (DMSP). The 1701 homologues of the DMSP demethylase gene, dmdA, identified in the (2007) Global Ocean Sampling (GOS) metagenome, are sufficient for 58% (+/-9%) of sampled cells to participate in this critical step in the marine sulfur cycle. This remarkable frequency of DMSP-demethylating cells is in accordance with biogeochemical data indicating that marine phytoplankton direct up to 10% of fixed carbon to DMSP synthesis, and that most of this DMSP is subsequently degraded by bacteria via demethylation. The GOS metagenomic data also revealed a new cluster of dmdA sequences (designated Clade E) that implicates marine gammaproteobacteria in DMSP demethylation, along with previously recognized alphaproteobacterial groups Roseobacter and SAR11. Analyses of G+C content and gene order indicate that lateral gene transfer is likely responsible for the wide distribution of dmdA among diverse taxa, contributing to the homogenization of biogeochemical roles among heterotrophic marine bacterioplankton. Candidate genes for the competing bacterial degradation process that converts DMSP to the climate-active gas dimethylsulfide (DMS) (dddD and dddL) occur infrequently in the (2007) GOS metagenome, suggesting either that the key DMS-producing bacterial genes are yet to be identified or that DMS formation by free-living bacterioplankton is insignificant relative to their demethylation activity.}, } @article {pmid18509446, year = {2008}, author = {Blow, N}, title = {Metagenomics: exploring unseen communities.}, journal = {Nature}, volume = {453}, number = {7195}, pages = {687-690}, doi = {10.1038/453687a}, pmid = {18509446}, issn = {1476-4687}, mesh = {Benchmarking ; Biodiversity ; Computational Biology/methods/standards/*trends ; Databases, Genetic ; Genomics/economics/*methods/standards/*trends ; Humans ; Intestines/microbiology ; Microbiology/economics/*trends ; Sequence Analysis, DNA/*methods/trends ; }, } @article {pmid18500568, year = {2008}, author = {Jensen, PR and Lauro, FM}, title = {An assessment of actinobacterial diversity in the marine environment.}, journal = {Antonie van Leeuwenhoek}, volume = {94}, number = {1}, pages = {51-62}, pmid = {18500568}, issn = {0003-6072}, support = {U01 TW007401/TW/FIC NIH HHS/United States ; U19 TW007401/TW/FIC NIH HHS/United States ; U01-TW007401-01/TW/FIC NIH HHS/United States ; }, mesh = {Actinobacteria/*classification/*genetics/isolation & purification ; *Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Databases, Nucleic Acid ; Genome, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {The 16S rRNA gene sequence diversity within the Phylum Actinobacteria was assessed from four sources: PCR-generated V6 sequence tags derived from seawater samples, metagenomic data from the Global Ocean Sampling (GOS) expedition, marine-derived sequences maintained in the Ribosomal Database Project (RDP), and select cultured strains for which sequence data is not yet available in the RDP. This meta-analysis revealed remarkable levels of phylogenetic diversity and confirms the existence of major, deeply rooted, and as of yet uncharacterized lineages within the phylum. A dramatic incongruence among cultured strains and those detected using culture-independent techniques was also revealed. Redundancy among the actinobacteria detected using culture-independent techniques suggests that greater sequence coverage or improved DNA extraction efficiencies may be required to detect the rare phylotypes that can be readily cultured from marine samples. Conversely, new strategies need to be developed for the cultivation of frequently observed but yet to be cultured marine actinobacteria.}, } @article {pmid18479440, year = {2008}, author = {Marhaver, KL and Edwards, RA and Rohwer, F}, title = {Viral communities associated with healthy and bleaching corals.}, journal = {Environmental microbiology}, volume = {10}, number = {9}, pages = {2277-2286}, pmid = {18479440}, issn = {1462-2920}, mesh = {Animals ; Anthozoa/*virology ; *Biodiversity ; DNA, Viral/genetics ; Ecology ; *Genome, Viral ; Genomic Library ; Sequence Alignment ; Sequence Analysis, DNA ; Symbiosis ; Viruses/*genetics/isolation & purification ; *Water Microbiology ; }, abstract = {The coral holobiont is the integrated assemblage of the coral animal, its symbiotic algae, protists, fungi and a diverse consortium of Bacteria and Archaea. Corals are a model system for the study of symbiosis, the breakdown of which can result in disease and mortality. Little is known, however, about viruses that infect corals and their symbionts. Here we present metagenomic analyses of the viral communities associated with healthy and partially bleached specimens of the Caribbean reef-building coral Diploria strigosa. Surprisingly, herpes-like sequences accounted for 4-8% of the total sequences in each metagenome; this abundance of herpes-like sequences is unprecedented in other marine viral metagenomes. Viruses similar to those that infect algae and plants were also present in the coral viral assemblage. Among the phage identified, cyanophages were abundant in both healthy and bleaching corals and vibriophages were also present. Therefore, coral-associated viruses could potentially infect all components of the holobiont--coral, algal and microbial. Thus, we expect viruses to figure prominently in the preservation and breakdown of coral health.}, } @article {pmid18463691, year = {2008}, author = {Martin-Cuadrado, AB and Rodriguez-Valera, F and Moreira, D and Alba, JC and Ivars-Martínez, E and Henn, MR and Talla, E and López-García, P}, title = {Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions.}, journal = {The ISME journal}, volume = {2}, number = {8}, pages = {865-886}, doi = {10.1038/ismej.2008.40}, pmid = {18463691}, issn = {1751-7370}, mesh = {Animals ; Archaea/*classification/genetics/*isolation & purification ; Archaeal Proteins/genetics ; *Biodiversity ; Cloning, Molecular ; Conserved Sequence ; DNA, Archaeal/chemistry/genetics/*isolation & purification ; DNA, Ribosomal/chemistry/genetics ; Gene Library ; Genome, Archaeal ; Molecular Sequence Data ; Phylogeny ; Plankton/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Synteny ; }, abstract = {Marine planktonic archaea are widespread and abundant in deep oceanic waters but, despite their obvious ecological importance, little is known about them. Metagenomic analyses of large genome fragments allow access to both gene content and genome structure from single individuals of these cultivation-reluctant organisms. We present the comparative analysis of 22 archaeal genomic clones containing 16S rRNA genes that were selected from four metagenomic libraries constructed from meso- and bathypelagic plankton of different oceanic regions (South Atlantic, Antarctic Polar Front, Adriatic and Ionian Sea; depths from 500 to 3000 m). We sequenced clones of the divergent archaeal lineages Group 1A (Crenarchaeota) and Group III (Euryarchaeota) as well as clones from the more frequent Group I Crenarchaeota and Group II Euryarchaeota. Whenever possible, we analysed clones that had identical or nearly identical 16S rRNA genes and that were retrieved from distant geographical locations, that is, that defined pan-oceanic operational taxonomic units (OTUs). We detected genes involved in nitrogen fixation in Group 1A Crenarchaeota, and genes involved in carbon fixation pathways and oligopeptide importers in Group I Crenarchaeota, which could confirm the idea that these are mixotrophic. A two-component system resembling that found in ammonia-oxidizing bacteria was found in Group III Euryarchaeota, while genes for anaerobic respiratory chains were detected in Group II Euryarchaeota. Whereas gene sequence conservation was high, and recombination and gene shuffling extensive within and between OTUs in Group I Crenarchaeota, gene sequence conservation was low and global synteny maintained in Group II Euryarchaeota. This implies remarkable differences in genome dynamics in Group I Crenarchaeota and Group II Euryarchaeota with recombination and mutation being, respectively, the dominant genome-shaping forces. These observations, along with variations in GC content, led us to hypothesize that the two groups of organisms have fundamentally different lifestyles.}, } @article {pmid18461319, year = {2008}, author = {Mayumi, D and Akutsu-Shigeno, Y and Uchiyama, H and Nomura, N and Nakajima-Kambe, T}, title = {Identification and characterization of novel poly(DL-lactic acid) depolymerases from metagenome.}, journal = {Applied microbiology and biotechnology}, volume = {79}, number = {5}, pages = {743-750}, doi = {10.1007/s00253-008-1477-3}, pmid = {18461319}, issn = {0175-7598}, mesh = {Bacteria/chemistry/classification/*enzymology/genetics ; Bacterial Proteins/*chemistry/*genetics/isolation & purification/metabolism ; Biodiversity ; Cloning, Molecular ; Enzyme Stability ; Esterases/*chemistry/*genetics/isolation & purification/metabolism ; Gene Library ; *Genome, Bacterial ; Lactic Acid/*metabolism ; Lipase/chemistry/genetics/isolation & purification/metabolism ; Molecular Sequence Data ; Phylogeny ; Polyesters ; Polymers/*metabolism ; Sequence Analysis, DNA ; Soil Microbiology ; Substrate Specificity ; }, abstract = {Many poly(lactic acid) (PLA)-degrading microorganisms have been isolated from the natural environment by culture-based methods, but there is no study about unculturable PLA-degrading microorganisms. In this study, we constructed a metagenomic library consisting of the DNA extracted from PLA disks buried in compost. We identified three PLA-degrading genes encoding lipase or hydrolase. The purified enzymes degraded not only PLA, but also various aliphatic polyesters, tributyrin, and p-nitrophenyl esters. From their substrate specificities, the PLA depolymerases were classified into an esterase rather than a lipase. Among the PLA depolymerases, PlaM4 exhibited thermophilic properties; that is, it showed the highest activity at 70 degrees C and was stable even after incubation for 1 h at 50 degrees C. PlaM4 had absorption and degradation activities for solid PLA at 60 degrees C, which indicates that the enzyme can effectively degrade PLA in a high-temperature environment. On the other hand, the enzyme classification based on amino acid sequences showed that the other PLA depolymerases, PlaM7 and PlaM9, were not classified into known lipases or esterases. This is the first report on the identification and characterization of PLA depolymerase from a metagenome.}, } @article {pmid18451062, year = {2008}, author = {Chhour, KL and Hinds, LA and Deane, EM and Jacques, NA}, title = {The microbiome of the cloacal openings of the urogenital and anal tracts of the tammar wallaby, Macropus eugenii.}, journal = {Microbiology (Reading, England)}, volume = {154}, number = {Pt 5}, pages = {1535-1543}, doi = {10.1099/mic.0.2007/014803-0}, pmid = {18451062}, issn = {1350-0872}, mesh = {Animals ; Biodiversity ; Cloaca/*microbiology ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Gastrointestinal Tract/*microbiology ; Macropodidae/*microbiology ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Urogenital System/*microbiology ; }, abstract = {The bacterial diversity of the openings of the urogenital and anal tracts of the adult female tammar wallaby, Macropus eugenii, was determined in order to ascertain whether the physical proximity of the openings of these tracts within the cloaca affected the two populations of bacteria. Terminal restriction fragment length polymorphism (T-RFLP) analyses of 42 wallabies identified 81 different terminal fragments, indicative of diverse and complex microbiomes at these anatomical locations. Subsequent amplified rDNA restriction analysis (ARDRA) identified 72 phylotypes from the urogenital tract and 50 from the anal tract. Twenty-two of these phylotypes were common to both tracts. Phylogenetic analysis of sequenced 16S rDNA showed that 83 % of the phylotypes were unidentified species based on the premise that any sequence possessing <97 % homology to a known bacterial species or phylotype was novel. Thus, despite the close proximity of the openings of the urogenital and anal tracts within the cloaca, the two sites retained a diverse range of distinct bacteria, with only a small percentage of overlapping species.}, } @article {pmid18442374, year = {2008}, author = {Chan, CK and Hsu, AL and Halgamuge, SK and Tang, SL}, title = {Binning sequences using very sparse labels within a metagenome.}, journal = {BMC bioinformatics}, volume = {9}, number = {}, pages = {215}, pmid = {18442374}, issn = {1471-2105}, mesh = {Algorithms ; Artificial Intelligence ; Base Sequence ; Confidence Intervals ; *Database Management Systems ; Databases, Genetic ; Genes, rRNA ; Genomics/methods ; Information Storage and Retrieval/methods/statistics & numerical data ; Pattern Recognition, Automated/*methods/statistics & numerical data ; *Phylogeny ; RNA, Archaeal/analysis/*classification ; RNA, Bacterial/analysis/*classification ; Sample Size ; Sequence Analysis, RNA ; Species Specificity ; Uncertainty ; }, abstract = {BACKGROUND: In metagenomic studies, a process called binning is necessary to assign contigs that belong to multiple species to their respective phylogenetic groups. Most of the current methods of binning, such as BLAST, k-mer and PhyloPythia, involve assigning sequence fragments by comparing sequence similarity or sequence composition with already-sequenced genomes that are still far from comprehensive. We propose a semi-supervised seeding method for binning that does not depend on knowledge of completed genomes. Instead, it extracts the flanking sequences of highly conserved 16S rRNA from the metagenome and uses them as seeds (labels) to assign other reads based on their compositional similarity.

RESULTS: The proposed seeding method is implemented on an unsupervised Growing Self-Organising Map (GSOM), and called Seeded GSOM (S-GSOM). We compared it with four well-known semi-supervised learning methods in a preliminary test, separating random-length prokaryotic sequence fragments sampled from the NCBI genome database. We identified the flanking sequences of the highly conserved 16S rRNA as suitable seeds that could be used to group the sequence fragments according to their species. S-GSOM showed superior performance compared to the semi-supervised methods tested. Additionally, S-GSOM may also be used to visually identify some species that do not have seeds. The proposed method was then applied to simulated metagenomic datasets using two different confidence threshold settings and compared with PhyloPythia, k-mer and BLAST. At the reference taxonomic level Order, S-GSOM outperformed all k-mer and BLAST results and showed comparable results with PhyloPythia for each of the corresponding confidence settings, where S-GSOM performed better than PhyloPythia in the >/= 10 reads datasets and comparable in the > or = 8 kb benchmark tests.

CONCLUSION: In the task of binning using semi-supervised learning methods, results indicate S-GSOM to be the best of the methods tested. Most importantly, the proposed method does not require knowledge from known genomes and uses only very few labels (one per species is sufficient in most cases), which are extracted from the metagenome itself. These advantages make it a very attractive binning method. S-GSOM outperformed the binning methods that depend on already-sequenced genomes, and compares well to the current most advanced binning method, PhyloPythia.}, } @article {pmid18430018, year = {2008}, author = {Kennedy, J and Codling, CE and Jones, BV and Dobson, AD and Marchesi, JR}, title = {Diversity of microbes associated with the marine sponge, Haliclona simulans, isolated from Irish waters and identification of polyketide synthase genes from the sponge metagenome.}, journal = {Environmental microbiology}, volume = {10}, number = {7}, pages = {1888-1902}, doi = {10.1111/j.1462-2920.2008.01614.x}, pmid = {18430018}, issn = {1462-2920}, mesh = {Animals ; *Biodiversity ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis/chemistry/genetics ; Gammaproteobacteria/*enzymology/*genetics/growth & development ; Genomic Library ; Haliclona/*microbiology ; Molecular Sequence Data ; Peptide Synthases/metabolism ; Polyketide Synthases/*genetics/metabolism ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seawater ; }, abstract = {Samples of the sponge Haliclona simulans were collected from Irish waters and subjected to a culture-independent analysis to determine the microbial, polyketide synthase (PKS) and non-ribosomal peptide synthase (NRPS) diversity. 16S rRNA gene libraries were prepared from total sponge, bacterial enriched sponge and seawater samples. Eight phyla from the Bacteria were detected in the sponge by phylogenetic analyses of the 16S rRNA gene libraries. The most abundant phylum in the total sponge library was the Proteobacteria (86%), with the majority of these clones being from the gamma-Proteobacteria (77%); two groups of clones were dominant and together made up 69% of the total. Both of these groups were related to other sponge-derived microbes and comprised novel genera. Within the other bacterial phyla groups of clones representing novel candidate genera within the phyla Verrucomicrobia and Lentisphaerae were also found. Selective enrichment of the bacterial component of the sponge prior to 16S rRNA gene analysis resulted in a 16S rRNA gene library dominated by a novel genus of delta-Proteobacteria, most closely related to the Bdellovibrio. The potential for the sponge microbiota to produce secondary metabolites was also analysed by polymerase chain reaction amplification of PKS and NRPS genes. While no NRPS sequences were isolated seven ketosynthase (KS) sequences were obtained from the sponge metagenome. Analyses of these clones revealed a diverse collection of PKS sequences which were most closely affiliated with PKS from members of the Cyanobacteria, Myxobacteria and Dinoflagellata.}, } @article {pmid18421492, year = {2008}, author = {Marco, D}, title = {Metagenomics and the niche concept.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {127}, number = {3}, pages = {241-247}, pmid = {18421492}, issn = {1611-7530}, mesh = {Biodiversity ; Biological Evolution ; *Ecology/methods ; Environment ; Genetics, Microbial ; Genome ; *Genomics ; Hydrogen-Ion Concentration ; Models, Biological ; Models, Genetic ; Models, Theoretical ; Oxygen/chemistry ; Phenotype ; Plasmids/metabolism ; }, abstract = {The metagenomics approach has revolutionised the fields of bacterial diversity, ecology and evolution, as well as derived applications like bioremediation and obtaining bioproducts. A further associated conceptual change has also occurred since in the metagenomics methodology the species is no longer the unit of study, but rather partial genome arrangements or even isolated genes. In spite of this, concepts coming from ecological and evolutionary fields traditionally centred on the species, like the concept of niche, are still being applied without further revision. A reformulation of the niche concept is necessary to deal with the new operative and epistemological challenges posed by the metagenomics approach. To contribute to this end, I review past and present uses of the niche concept in ecology and in microbiological studies, showing that a new, updated definition need to be used in the context of the metagenomics. Finally, I give some insights into a more adequate conceptual background for the utilisation of the niche concept in metagenomic studies. In particular, I raise the necessity of including the microbial genetic background as another variable into the niche space.}, } @article {pmid18311127, year = {2008}, author = {Desnues, C and Rodriguez-Brito, B and Rayhawk, S and Kelley, S and Tran, T and Haynes, M and Liu, H and Furlan, M and Wegley, L and Chau, B and Ruan, Y and Hall, D and Angly, FE and Edwards, RA and Li, L and Thurber, RV and Reid, RP and Siefert, J and Souza, V and Valentine, DL and Swan, BK and Breitbart, M and Rohwer, F}, title = {Biodiversity and biogeography of phages in modern stromatolites and thrombolites.}, journal = {Nature}, volume = {452}, number = {7185}, pages = {340-343}, doi = {10.1038/nature06735}, pmid = {18311127}, issn = {1476-4687}, mesh = {Bacteriophages/classification/genetics/*isolation & purification/*physiology ; Bahamas ; *Biodiversity ; Capsid/chemistry ; Computational Biology ; DNA, Viral/analysis/genetics ; *Ecosystem ; Fresh Water/microbiology/virology ; Genome, Viral/genetics ; Genomics ; *Geography ; Geologic Sediments/microbiology/virology ; Mexico ; Molecular Sequence Data ; Phylogeny ; Proteome/metabolism ; Seawater/microbiology/virology ; *Water Microbiology ; }, abstract = {Viruses, and more particularly phages (viruses that infect bacteria), represent one of the most abundant living entities in aquatic and terrestrial environments. The biogeography of phages has only recently been investigated and so far reveals a cosmopolitan distribution of phage genetic material (or genotypes). Here we address this cosmopolitan distribution through the analysis of phage communities in modern microbialites, the living representatives of one of the most ancient life forms on Earth. On the basis of a comparative metagenomic analysis of viral communities associated with marine (Highborne Cay, Bahamas) and freshwater (Pozas Azules II and Rio Mesquites, Mexico) microbialites, we show that some phage genotypes are geographically restricted. The high percentage of unknown sequences recovered from the three metagenomes (>97%), the low percentage similarities with sequences from other environmental viral (n = 42) and microbial (n = 36) metagenomes, and the absence of viral genotypes shared among microbialites indicate that viruses are genetically unique in these environments. Identifiable sequences in the Highborne Cay metagenome were dominated by single-stranded DNA microphages that were not detected in any other samples examined, including sea water, fresh water, sediment, terrestrial, extreme, metazoan-associated and marine microbial mats. Finally, a marine signature was present in the phage community of the Pozas Azules II microbialites, even though this environment has not been in contact with the ocean for tens of millions of years. Taken together, these results prove that viruses in modern microbialites display biogeographical variability and suggest that they may be derived from an ancient community.}, } @article {pmid18283556, year = {2008}, author = {Holmes, AJ and Coleman, NV}, title = {Evolutionary ecology and multidisciplinary approaches to prospecting for monooxygenases as biocatalysts.}, journal = {Antonie van Leeuwenhoek}, volume = {94}, number = {1}, pages = {75-84}, doi = {10.1007/s10482-008-9227-1}, pmid = {18283556}, issn = {0003-6072}, mesh = {Bacteria/*enzymology/genetics/isolation & purification ; Bacterial Proteins/*genetics/metabolism ; Biodiversity ; *Biological Evolution ; Catalysis ; *Ecology ; *Environmental Microbiology ; Industrial Microbiology ; Mixed Function Oxygenases/*genetics/metabolism ; Multigene Family ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {New techniques to explore microbial diversity have led to resurgent interest in prospecting for natural products (bioprospecting or biodiscovery). Although many bioprospecting projects may share little in common at first glance, the vast majority share one particular challenge. Their targets are rare to very rare members of complex natural assemblages. Despite the advances made in bringing new organisms into cultivation and application of culture-independent techniques to isolation of novel genes there remain systematic biases against relatively rare organisms with specific growth requirements. These can frequently be overcome by application of multidisciplinary approaches that take into account principles of evolutionary ecology. Our experiences with prospecting for soluble di-iron monooxygenases (SDIMO) indicate that conventional approaches to organism isolation and metagenomic cloning systematically under-sample diversity in this enzyme family. This reflects that SDIMO-containing organisms are typically relatively low-abundance members of natural assemblages (thus biased against by direct cloning) and SDIMOs have discrete physiological roles in each organism (thus are not amenable to generic enrichment culture strategies). We have sought to overcome this by a PCR-based survey of gene diversity to guide evaluation of subsequent culture or cloning studies. A surprising outcome of this survey was that conventional PCR approaches using degenerate primers also systematically under-sampled diversity, but nested PCR strategies revealed unprecedented diversity. We conclude that many PCR-based gene-prospecting studies are likely to have under-estimated the impact of target:competitor ratios on their success.}, } @article {pmid18207371, year = {2008}, author = {López-García, P and Moreira, D}, title = {Tracking microbial biodiversity through molecular and genomic ecology.}, journal = {Research in microbiology}, volume = {159}, number = {1}, pages = {67-73}, doi = {10.1016/j.resmic.2007.11.019}, pmid = {18207371}, issn = {0923-2508}, mesh = {Animals ; Archaea/*classification/isolation & purification ; Bacteria/*classification/isolation & purification ; *Biodiversity ; *Ecosystem ; *Environmental Microbiology ; Eukaryota/*classification/isolation & purification ; Evolution, Molecular ; }, abstract = {Molecular ecology and metagenomics applied to the study of microbial biodiversity are changing our comprehension of the biosphere. An impressive diversity of archaea, bacteria and, more recently, protists has been uncovered by molecular tools. Efforts to couple function to the phylogenetic diversity observed in natural environments are leading to the discovery of novel metabolisms and to a re-evaluation of the global ecological impact of known ones. Interesting questions relating to mechanisms of speciation and evolutionary trends at the smallest and largest phylogenetic scales are emerging.}, } @article {pmid18179699, year = {2008}, author = {Piganeau, G and Desdevises, Y and Derelle, E and Moreau, H}, title = {Picoeukaryotic sequences in the Sargasso sea metagenome.}, journal = {Genome biology}, volume = {9}, number = {1}, pages = {R5}, pmid = {18179699}, issn = {1474-760X}, mesh = {Base Composition ; *Biodiversity ; Eukaryota/*genetics ; *Genome ; Genomics ; Oceans and Seas ; Phylogeny ; Seawater ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: With genome sequencing becoming more and more affordable, environmental shotgun sequencing of the microorganisms present in an environment generates a challenging amount of sequence data for the scientific community. These sequence data enable the diversity of the microbial world and the metabolic pathways within an environment to be investigated, a previously unthinkable achievement when using traditional approaches. DNA sequence data assembled from extracts of 0.8 microm filtered Sargasso seawater unveiled an unprecedented glimpse of marine prokaryotic diversity and gene content. Serendipitously, many sequences representing picoeukaryotes (cell size <2 microm) were also present within this dataset. We investigated the picoeukaryotic diversity of this database by searching sequences containing homologs of eight nuclear anchor genes that are well conserved throughout the eukaryotic lineage, as well as one chloroplastic and one mitochondrial gene.

RESULTS: We found up to 41 distinct eukaryotic scaffolds, with a broad phylogenetic spread on the eukaryotic tree of life. The average eukaryotic scaffold size is 2,909 bp, with one gap every 1,253 bp. Strikingly, the AT frequency of the eukaryotic sequences (51.4%) is significantly lower than the average AT frequency of the metagenome (61.4%). This represents 4% to 18% of the estimated prokaryotic diversity, depending on the average prokaryotic versus eukaryotic genome size ratio.

CONCLUSION: Despite similar cell size, eukaryotic sequences of the Sargasso Sea metagenome have higher GC content, suggesting that different environmental pressures affect the evolution of their base composition.}, } @article {pmid18097633, year = {2008}, author = {Valenzuela-Encinas, C and Neria-González, I and Alcántara-Hernández, RJ and Enríquez-Aragón, JA and Estrada-Alvarado, I and Hernández-Rodríguez, C and Dendooven, L and Marsch, R}, title = {Phylogenetic analysis of the archaeal community in an alkaline-saline soil of the former lake Texcoco (Mexico).}, journal = {Extremophiles : life under extreme conditions}, volume = {12}, number = {2}, pages = {247-254}, pmid = {18097633}, issn = {1431-0651}, mesh = {*Biodiversity ; DNA, Archaeal/*genetics ; Halobacteriaceae/*physiology ; Hydrogen-Ion Concentration ; Mexico ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Salinity ; *Soil Microbiology ; }, abstract = {The soil of the former lake Texcoco is an extreme environment localized in the valley of Mexico City, Mexico. It is highly saline and alkaline, where Na+, Cl(-), HCO3(-) and CO3(2-) are the predominant ions, with a pH ranging from 9.8 to 11.7 and electrolytic conductivities in saturation extracts from 22 to 150 dS m(-1). Metagenomic DNA from the archaeal community was extracted directly from soil and used as template to amplify 16S ribosomal gene by PCR. PCR products were used to construct gene libraries. The ribosomal library showed that the archaeal diversity included Natronococcus sp., Natronolimnobius sp., Natronobacterium sp., Natrinema sp., Natronomonas sp., Halovivax sp., "Halalkalicoccus jeotgali" and novel clades within the family of Halobacteriaceae. Four clones could not be classified. It was found that the archaeal diversity in an alkaline-saline soil of the former lake Texcoco, Mexico, was low, but showed yet uncharacterized and unclassified species.}, } @article {pmid18084915, year = {2008}, author = {Singh, SB and Pelaez, F}, title = {Biodiversity, chemical diversity and drug discovery.}, journal = {Progress in drug research. Fortschritte der Arzneimittelforschung. Progres des recherches pharmaceutiques}, volume = {65}, number = {}, pages = {141, 143-74}, doi = {10.1007/978-3-7643-8117-2_4}, pmid = {18084915}, issn = {0071-786X}, mesh = {Bacteria/chemistry/genetics/*metabolism ; Bacteriological Techniques ; *Biodiversity ; Biological Factors/chemistry/isolation & purification/*metabolism ; Cloning, Molecular ; *Drug Design ; Genome, Bacterial ; Industrial Microbiology/methods ; *Metabolic Networks and Pathways/genetics ; Molecular Structure ; Pharmaceutical Preparations/chemistry/isolation & purification/*metabolism ; Soil Microbiology ; Structure-Activity Relationship ; Water Microbiology ; }, abstract = {Drugs developed from microbial natural products are in the fundaments of modern pharmaceutical companies. Despite decades of research, all evidences suggest that there must remain many interesting natural molecules with potential therapeutic application yet to be discovered. Any efforts to successfully exploit the chemical diversity of microbial secondary metabolites need to rely heavily on a good understanding of microbial diversity, being the working hypothesis that maximizing biological diversity is the key strategy to maximizing chemical diversity. This chapter presents an overview of diverse topics related with this basic principle, always in relation with the discovery of novel secondary metabolites. The types of microorganisms more frequently used for natural products discovery are briefly reviewed, as well as the differences between terrestrial and marine habitats as sources of bioactive secondary metabolite producers. The concepts about microbial diversity as applied to prokaryotes have evolved in the last years, but recent data suggest the existence of true biogeographic patterns of bacterial diversity, which are also discussed. Special attention is dedicated to the existing strategies to exploit the microbial diversity that is not easy to tackle by conventional approaches. This refers explicitly to the current attempts to isolate and cultivate the previously uncultured bacteria, including the application of high throughput techniques. Likewise, the advances of microbial molecular biology has allowed the development of metagenomic approaches, i.e., the expression of biosynthetic pathways directly obtained from environmental DNA and cloned in a suitable host, as another way of accessing microbial genetic resources. Also, approaches relying on the genomics of metabolite producers are reviewed.}, } @article {pmid18059494, year = {2007}, author = {Bhaya, D and Grossman, AR and Steunou, AS and Khuri, N and Cohan, FM and Hamamura, N and Melendrez, MC and Bateson, MM and Ward, DM and Heidelberg, JF}, title = {Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses.}, journal = {The ISME journal}, volume = {1}, number = {8}, pages = {703-713}, doi = {10.1038/ismej.2007.46}, pmid = {18059494}, issn = {1751-7362}, mesh = {Bacterial Proteins/genetics/metabolism ; *Biodiversity ; Cyanobacteria/classification/*genetics/growth & development ; Genetic Variation/genetics ; *Genome, Bacterial ; Genomics/*methods ; Iron/metabolism ; Models, Genetic ; Species Specificity ; Synechococcus/genetics/growth & development ; }, abstract = {In microbial mat communities of Yellowstone hot springs, ribosomal RNA (rRNA) sequence diversity patterns indicate the presence of closely related bacterial populations along environmental gradients of temperature and light. To identify the functional bases for adaptation, we sequenced the genomes of two cyanobacterial (Synechococcus OS-A and OS-B') isolates representing ecologically distinct populations that dominate at different temperatures and are major primary producers in the mat. There was a marked lack of conserved large-scale gene order between the two Synechococcus genomes, indicative of extensive genomic rearrangements. Comparative genomic analyses showed that the isolates shared a large fraction of their gene content at high identity, yet, differences in phosphate and nitrogen utilization pathways indicated that they have adapted differentially to nutrient fluxes, possibly by the acquisition of genes by lateral gene transfer or their loss in certain populations. Comparisons of the Synechococcus genomes to metagenomic sequences derived from mats where these Synechococcus stains were originally isolated, revealed new facets of microbial diversity. First, Synechococcus populations at the lower temperature regions of the mat showed greater sequence diversity than those at high temperatures, consistent with a greater number of ecologically distinct populations at the lower temperature. Second, we found evidence of a specialized population that is apparently very closely related to Synechococcus OS-B', but contains genes that function in the uptake of reduced ferrous iron. In situ expression studies demonstrated that these genes are differentially expressed over the diel cycle, with highest expression when the mats are anoxic and iron may be in the reduced state. Genomic information from these mat-specific isolates and metagenomic information can be coupled to detect naturally occurring populations that are associated with different functionalities, not always represented by isolates, but which may nevertheless be important for niche partitioning and the establishment of microbial community structure.}, } @article {pmid18054096, year = {2008}, author = {Zinger, L and Gury, J and Alibeu, O and Rioux, D and Gielly, L and Sage, L and Pompanon, F and Geremia, RA}, title = {CE-SSCP and CE-FLA, simple and high-throughput alternatives for fungal diversity studies.}, journal = {Journal of microbiological methods}, volume = {72}, number = {1}, pages = {42-53}, doi = {10.1016/j.mimet.2007.10.005}, pmid = {18054096}, issn = {0167-7012}, mesh = {*Biodiversity ; DNA Fingerprinting/methods ; DNA, Fungal/analysis/isolation & purification ; Ecosystem ; Electrophoresis, Capillary/*methods ; Fungi/*classification/genetics/isolation & purification ; *Polymorphism, Restriction Fragment Length ; *Polymorphism, Single-Stranded Conformational ; Reproducibility of Results ; Sensitivity and Specificity ; *Soil Microbiology ; }, abstract = {Fungal communities are key components of soil, but the study of their ecological significance is limited by a lack of appropriated methods. For instance, the assessment of fungi occurrence and spatio-temporal variation in soil requires the analysis of a large number of samples. The molecular signature methods provide a useful tool to monitor these microbial communities and can be easily adapted to capillary electrophoresis (CE) allowing high-throughput studies. Here we assess the suitability of CE-FLA (Fragment Length Polymorphism, denaturing conditions) and CE-SSCP (Single-Stranded Conformation Polymorphism, native conditions) applied to environmental studies since they require a short molecular marker and no post-PCR treatments. We amplified the ITS1 region from 22 fungal strains isolated from an alpine ecosystem and from total genomic DNA of alpine and infiltration basin soils. The CE-FLA and CE-SSCP separated 17 and 15 peaks respectively from a mixture of 19 strains. For the alpine soil-metagenomic DNA, the FLA displayed more peaks than the SSCP and the converse result was found for infiltration basin sediments. We concluded that CE-FLA and CE-SSCP of ITS1 region provided complementary information. In order to improve CE-SSCP sensitivity, we tested its resolution according to migration temperature and found 32 degrees C to be optimal. Because of their simplicity, quickness and reproducibility, we found that these two methods were promising for high-throughput studies of soil fungal communities.}, } @article {pmid18053937, year = {2007}, author = {Dupré, J and O'Malley, MA}, title = {Metagenomics and biological ontology.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {38}, number = {4}, pages = {834-846}, doi = {10.1016/j.shpsc.2007.09.001}, pmid = {18053937}, issn = {1369-8486}, mesh = {*Biodiversity ; Biology ; *Environmental Microbiology ; *Genome, Bacterial ; *Genomics ; Humans ; Models, Theoretical ; Systems Analysis ; Systems Biology ; }, abstract = {Metagenomics is an emerging microbial systems science that is based on the large-scale analysis of the DNA of microbial communities in their natural environments. Studies of metagenomes are revealing the vast scope of biodiversity in a wide range of environments, as well as new functional capacities of individual cells and communities, and the complex evolutionary relationships between them. Our examination of this science focuses on the ontological implications of these studies of metagenomes and metaorganisms, and what they mean for common sense and philosophical understandings of multicellularity, individuality and organism. We show how metagenomics requires us to think in different ways about what human beings are and what their relation to the microbial world is. Metagenomics could also transform the way in which evolutionary processes are understood, with the most basic relationship between cells from both similar and different organisms being far more cooperative and less antagonistic than is widely assumed. In addition to raising fundamental questions about biological ontology, metagenomics generates possibilities for powerful technologies addressed to issues of climate, health and conservation. We conclude with reflections about process-oriented versus entity-oriented analysis in light of current trends towards systems approaches.}, } @article {pmid18043628, year = {2007}, author = {Nealson, KH and Venter, JC}, title = {Metagenomics and the global ocean survey: what's in it for us, and why should we care?.}, journal = {The ISME journal}, volume = {1}, number = {3}, pages = {185-187}, doi = {10.1038/ismej.2007.43}, pmid = {18043628}, issn = {1751-7362}, mesh = {*Biodiversity ; *Ecosystem ; Genomics ; Oceans and Seas ; Seawater/*microbiology ; }, } @article {pmid18043225, year = {2008}, author = {Frank, DN and Pace, NR}, title = {Gastrointestinal microbiology enters the metagenomics era.}, journal = {Current opinion in gastroenterology}, volume = {24}, number = {1}, pages = {4-10}, doi = {10.1097/MOG.0b013e3282f2b0e8}, pmid = {18043225}, issn = {1531-7056}, mesh = {Bacteria/*genetics ; Biodiversity ; Gastrointestinal Diseases/*microbiology ; Gastrointestinal Tract/*microbiology ; *Genome, Bacterial ; *Genomics ; Host-Pathogen Interactions ; Humans ; Metagenome/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {PURPOSE OF REVIEW: Advances in DNA sequence-based technologies now permit genetic analysis of complex microbial populations without the need for prior cultivation. This review summarizes the molecular methods of culture-independent microbiology ('metagenomics') and their recent application to studies of the human gastrointestinal tract in both health and disease.

RECENT FINDINGS: Culture-independent metagenomic surveys reveal unprecedented microbial biodiversity in the human intestine. Upwards of 40,000 bacterial species are estimated to comprise the collective gastrointestinal microbiome, most of which have not been characterized by culture. Diverse conditions such as antibiotic-associated diarrhea, Crohn's disease, ulcerative colitis, obesity, and pouchitis have been correlated with large-scale imbalances in gastrointestinal microbiota, or 'dysbiosis'. These findings demonstrate the importance of commensal microorganisms in maintaining gastrointestinal health.

SUMMARY: Through technological and conceptual innovations in metagenomics, the complex microbial habitat of the human gastrointestinal tract is now amenable to detailed ecological analysis. Large-scale shifts in gut commensal populations, rather than occurrence of particular microorganisms, are associated with several gastroenterological conditions; redress of these imbalances may ameliorate the conditions.}, } @article {pmid17951101, year = {2007}, author = {D'Costa, VM and Griffiths, E and Wright, GD}, title = {Expanding the soil antibiotic resistome: exploring environmental diversity.}, journal = {Current opinion in microbiology}, volume = {10}, number = {5}, pages = {481-489}, doi = {10.1016/j.mib.2007.08.009}, pmid = {17951101}, issn = {1369-5274}, mesh = {Anti-Bacterial Agents/metabolism ; Bacteria/classification/*drug effects/genetics/metabolism ; Biodiversity ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genomics ; Phylogeny ; *Soil Microbiology ; }, abstract = {Antibiotic resistance has largely been studied in the context of failure of the drugs in clinical settings. There is now growing evidence that bacteria that live in the environment (e.g. the soil) are multi-drug-resistant. Recent functional screens and the growing accumulation of metagenomic databases are revealing an unexpected density of resistance genes in the environment: the antibiotic resistome. This challenges our current understanding of antibiotic resistance and provides both barriers and opportunities for antimicrobial drug discovery.}, } @article {pmid17943116, year = {2007}, author = {Turnbaugh, PJ and Ley, RE and Hamady, M and Fraser-Liggett, CM and Knight, R and Gordon, JI}, title = {The human microbiome project.}, journal = {Nature}, volume = {449}, number = {7164}, pages = {804-810}, pmid = {17943116}, issn = {1476-4687}, support = {P30 DK056341/DK/NIDDK NIH HHS/United States ; P30 DK056341-06/DK/NIDDK NIH HHS/United States ; P30 DK056341-07/DK/NIDDK NIH HHS/United States ; T32 GM065103/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biodiversity ; Genome, Bacterial/genetics ; Genomics ; Humans ; Intestines/cytology/immunology/*microbiology ; *Metagenome/genetics/immunology ; Mice ; Sequence Analysis, DNA ; }, abstract = {A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease.}, } @article {pmid17936679, year = {2007}, author = {Raes, J and Foerstner, KU and Bork, P}, title = {Get the most out of your metagenome: computational analysis of environmental sequence data.}, journal = {Current opinion in microbiology}, volume = {10}, number = {5}, pages = {490-498}, doi = {10.1016/j.mib.2007.09.001}, pmid = {17936679}, issn = {1369-5274}, mesh = {Aminohydrolases/chemistry/classification/genetics ; Biodiversity ; Computational Biology ; *Environmental Microbiology ; Genomics/*methods/standards ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {New advances in sequencing technologies bring random shotgun sequencing of ecosystems within reach of smaller labs, but the complexity of metagenomics data can be overwhelming. Recently, many novel computational tools have been developed to unravel ecosystem properties starting from fragmented sequences. In addition, the so-called 'comparative metagenomics' approaches have allowed the discovery of specific genomic and community adaptations to environmental factors. However, many of the parameters extracted from these data to describe the environment at hand (e.g. genomic features, functional complement, phylogenetic composition) are interdependent and influenced by technical aspects of sample preparation and data treatment, leading to various pitfalls during analysis. To avoid this and complement existing initiatives in data standards, we propose a minimal standard for metagenomics data analysis ('MINIMESS') to be able to take full advantage of the power of comparative metagenomics in understanding microbial life on earth.}, } @article {pmid17933580, year = {2007}, author = {McHardy, AC and Rigoutsos, I}, title = {What's in the mix: phylogenetic classification of metagenome sequence samples.}, journal = {Current opinion in microbiology}, volume = {10}, number = {5}, pages = {499-503}, doi = {10.1016/j.mib.2007.08.004}, pmid = {17933580}, issn = {1369-5274}, mesh = {Animals ; Archaea/chemistry/genetics ; Bacteria/classification/genetics ; Base Sequence ; Biodiversity ; Biofilms/classification ; Computational Biology ; DNA/chemistry/classification ; *Environmental Microbiology ; *Genomics ; *Phylogeny ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {Metagenomics is a novel field which deals with the sequencing and study of microbial organisms or viruses isolated directly from a particular environment. This has already provided a wealth of information and new insights for the inhabitants of various environmental niches. For a given sample, one would like to determine the phylogenetic provenance of the obtained fragments, the relative abundance of its different members, their metabolic capabilities, and the functional properties of the community as a whole. To this end, computational analyses are becoming increasingly indispensable tools. In this review, we focus on the problem of determining the phylogenetic identity of the sample fragments, a procedure known as 'binning'. This step is essential for the reconstruction of the metabolic capabilities of individual organisms or phylogenetic clades of a community, and the study of their interactions.}, } @article {pmid17923430, year = {2007}, author = {Lasken, RS}, title = {Single-cell genomic sequencing using Multiple Displacement Amplification.}, journal = {Current opinion in microbiology}, volume = {10}, number = {5}, pages = {510-516}, doi = {10.1016/j.mib.2007.08.005}, pmid = {17923430}, issn = {1369-5274}, mesh = {Bacteria/classification/*genetics ; Biodiversity ; Electrophoresis, Agar Gel ; Gene Library ; Genomics/*methods ; *Nucleic Acid Amplification Techniques ; }, abstract = {Single microbial cells can now be sequenced using DNA amplified by the Multiple Displacement Amplification (MDA) reaction. The few femtograms of DNA in a bacterium are amplified into micrograms of high molecular weight DNA suitable for DNA library construction and Sanger sequencing. The MDA-generated DNA also performs well when used directly as template for pyrosequencing by the 454 Life Sciences method. While MDA from single cells loses some of the genomic sequence, this approach will greatly accelerate the pace of sequencing from uncultured microbes. The genetically linked sequences from single cells are also a powerful tool to be used in guiding genomic assembly of shotgun sequences of multiple organisms from environmental DNA extracts (metagenomic sequences).}, } @article {pmid17921274, year = {2007}, author = {Bench, SR and Hanson, TE and Williamson, KE and Ghosh, D and Radosovich, M and Wang, K and Wommack, KE}, title = {Metagenomic characterization of Chesapeake Bay virioplankton.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {23}, pages = {7629-7641}, pmid = {17921274}, issn = {1098-5336}, mesh = {Biodiversity ; Cluster Analysis ; Electrophoresis, Gel, Pulsed-Field ; Genetic Variation ; *Genome, Viral ; Molecular Sequence Data ; Phylogeny ; Plankton ; Seawater/*virology ; Sequence Analysis, DNA ; United States ; Viruses/classification/*genetics/growth & development ; *Water Microbiology ; }, abstract = {Viruses are ubiquitous and abundant throughout the biosphere. In marine systems, virus-mediated processes can have significant impacts on microbial diversity and on global biogeocehmical cycling. However, viral genetic diversity remains poorly characterized. To address this shortcoming, a metagenomic library was constructed from Chesapeake Bay virioplankton. The resulting sequences constitute the largest collection of long-read double-stranded DNA (dsDNA) viral metagenome data reported to date. BLAST homology comparisons showed that Chesapeake Bay virioplankton contained a high proportion of unknown (homologous only to environmental sequences) and novel (no significant homolog) sequences. This analysis suggests that dsDNA viruses are likely one of the largest reservoirs of unknown genetic diversity in the biosphere. The taxonomic origin of BLAST homologs to viral library sequences agreed well with reported abundances of cooccurring bacterial subphyla within the estuary and indicated that cyanophages were abundant. However, the low proportion of Siphophage homologs contradicts a previous assertion that this family comprises most bacteriophage diversity. Identification and analyses of cyanobacterial homologs of the psbA gene illustrated the value of metagenomic studies of virioplankton. The phylogeny of inferred PsbA protein sequences suggested that Chesapeake Bay cyanophage strains are endemic in that environment. The ratio of psbA homologous sequences to total cyanophage sequences in the metagenome indicated that the psbA gene may be nearly universal in Chesapeake Bay cyanophage genomes. Furthermore, the low frequency of psbD homologs in the library supports the prediction that Chesapeake Bay cyanophage populations are dominated by Podoviridae.}, } @article {pmid17853905, year = {2007}, author = {Karl, DM}, title = {Microbial oceanography: paradigms, processes and promise.}, journal = {Nature reviews. Microbiology}, volume = {5}, number = {10}, pages = {759-769}, doi = {10.1038/nrmicro1749}, pmid = {17853905}, issn = {1740-1534}, mesh = {Bacteria/*genetics/*isolation & purification ; Biodiversity ; *Marine Biology ; Oceans and Seas ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {Life on Earth most likely originated as microorganisms in the sea. Over the past approximately 3.5 billion years, microorganisms have shaped and defined Earth's biosphere and have created conditions that have allowed the evolution of macroorganisms and complex biological communities, including human societies. Recent advances in technology have highlighted the vast and previously unknown genetic information that is contained in extant marine microorganisms, from new protein families to novel metabolic processes. Now there is a unique opportunity, using recent advances in molecular ecology, metagenomics, remote sensing of microorganisms and ecological modelling, to achieve a comprehensive understanding of marine microorganisms and their susceptibility to environmental variability and climate change. Contemporary microbial oceanography is truly a sea of opportunity and excitement.}, } @article {pmid17672325, year = {2007}, author = {Li, X and Qin, L and Dai, SK and Jiang, SM and Liu, ZH}, title = {[Marine microbial metagenomics: progress and prospect].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {47}, number = {3}, pages = {548-553}, pmid = {17672325}, issn = {0001-6209}, mesh = {Bacteria/*genetics/isolation & purification ; Biodiversity ; Cloning, Molecular ; *Genome, Bacterial ; Seawater/*microbiology ; }, abstract = {Preliminary statistics showed that there are more than one million species of microbes in marine environments that formed a dynamic genetic reservoir, among which the majority are not revealed and categorized due to barrier in cultivation techniques. However, the situation has changed in recent years because of the rapid development of phylogenetic studies based on small ribosomal RNA and rDNA sequencing independent to standard laboratory cultivation. These changes have significantly altered our understanding about microbial diversity and microbial ecology. In this review, we highlight some of recent progress and innovation in research on microbial diversity, and propose a metagenomic scheme as an alternative to overcome some of the barriers that still remain for exploitation of marine microbial diversity for its enormous potential in pharmaceutical applications. We believe that rapid progress in marine metagenomics allows direct access to the genomes of numerous non-cultivable microorganisms for their associated chemical prosperity.}, } @article {pmid17664828, year = {2001}, author = {Shivaji, S}, title = {Microbial biodiversity: Shotgun Libraries to Metagenome.}, journal = {Indian journal of medical microbiology}, volume = {19}, number = {4}, pages = {171}, pmid = {17664828}, issn = {0255-0857}, } @article {pmid17564605, year = {2007}, author = {Santos, F and Meyerdierks, A and Peña, A and Rosselló-Mora, R and Amann, R and Antón, J}, title = {Metagenomic approach to the study of halophages: the environmental halophage 1.}, journal = {Environmental microbiology}, volume = {9}, number = {7}, pages = {1711-1723}, doi = {10.1111/j.1462-2920.2007.01289.x}, pmid = {17564605}, issn = {1462-2912}, mesh = {Bacteriophages/*genetics/ultrastructure ; Base Composition ; Base Sequence ; *Biodiversity ; Blotting, Southern ; Cluster Analysis ; Codon/genetics ; DNA Primers/genetics ; Genome Components ; Genome, Viral/*genetics ; Halobacteriaceae/*virology ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; *Phylogeny ; Restriction Mapping ; Seawater/*microbiology/virology ; Sequence Analysis, DNA ; Spain ; *Water Microbiology ; }, abstract = {Hypersaline environments, such as crystallizer ponds of solar salterns, show one of the highest concentration of viruses reported for aquatic systems. All the halophages characterized so far are isolates obtained by cultivation from described haloarchaeal species that have only low abundance in the environment. We employed a culture-independent metagenomic approach to analyse for the first time complete genomes in the halophage community and explored the in situ diversity by transmission electron microscopy and pulsed-field gel electrophoresis. We report the genomic sequence of a not yet isolated halophage (named as environmental halophage 1 'EHP-1') whose DNA was obtained from crystallizer samples with a salinity of 31%. The sequenced genome has a size of 35 kb and a G + C content around 51%. The G + C content is lower than that of previously characterized halophages. However, G + C content and codon usage in EHP-1 are similar to the recently cultivated and sequenced Haloquadratum walsbyi, the major prokaryotic component in solar salterns around the world. Forty open reading frames have been predicted, including genes that putatively code for proteins involved in DNA replication (ribonucleotide reductases, thymidylate kinase) normally found in lytic viruses.}, } @article {pmid17504484, year = {2007}, author = {Yutin, N and Suzuki, MT and Teeling, H and Weber, M and Venter, JC and Rusch, DB and Béjà, O}, title = {Assessing diversity and biogeography of aerobic anoxygenic phototrophic bacteria in surface waters of the Atlantic and Pacific Oceans using the Global Ocean Sampling expedition metagenomes.}, journal = {Environmental microbiology}, volume = {9}, number = {6}, pages = {1464-1475}, doi = {10.1111/j.1462-2920.2007.01265.x}, pmid = {17504484}, issn = {1462-2912}, mesh = {Aerobiosis/*physiology ; Atlantic Ocean ; Bacteria, Aerobic/*classification/genetics/isolation & purification/metabolism ; *Bacterial Physiological Phenomena ; Biodiversity ; Pacific Ocean ; Phototrophic Processes/*physiology ; Pigments, Biological/metabolism ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Aerobic anoxygenic photosynthetic bacteria (AAnP) were recently proposed to be significant contributors to global oceanic carbon and energy cycles. However, AAnP abundance, spatial distribution, diversity and potential ecological importance remain poorly understood. Here we present metagenomic data from the Global Ocean Sampling expedition indicating that AAnP diversity and abundance vary in different oceanic regions. Furthermore, we show for the first time that the composition of AAnP assemblages change between different oceanic regions, with specific bacterial assemblages adapted to open ocean or coastal areas respectively. Our results support the notion that marine AAnP populations are complex and dynamic, and compose an important fraction of bacterioplankton assemblages in certain oceanic areas.}, } @article {pmid17476541, year = {2007}, author = {Pontes, DS and Lima-Bittencourt, CI and Chartone-Souza, E and Amaral Nascimento, AM}, title = {Molecular approaches: advantages and artifacts in assessing bacterial diversity.}, journal = {Journal of industrial microbiology & biotechnology}, volume = {34}, number = {7}, pages = {463-473}, pmid = {17476541}, issn = {1367-5435}, mesh = {Bacteria/classification/*genetics/*growth & development ; Bacteriological Techniques/methods/trends ; Biodiversity ; DNA, Bacterial/genetics ; Genetic Variation ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bacteria account for a major proportion of Earth's biological diversity. They play essential roles in quite diverse environments and there has been an increasing interest in bacterial biodiversity. Research using novel and efficient tools to identify and characterize bacterial communities has been the key for elucidating biological activities with potential for industrial application. The current approach used for defining bacterial species is based on phenotypic and genomic properties. Traditional and novel DNA-based molecular methods are improving our knowledge of bacterial diversity in nature. Advances in molecular biology have been important for studies of diversity, considerably improving our knowledge of morphological, physiological, and ecological features of bacterial taxa. DNA-DNA hybridization, which has been used for many years, is still considered the golden standard for bacteria species identification. PCR-based methods investigating 16S rRNA gene sequences, and other approaches, such as the metagenome, have been used to study the physiology and diversity of bacteria and to identify novel genes with potential pharmaceutical and other biotechnological applications. We examined the advantages and limitations of molecular methods currently used to analyze bacterial diversity; these are mainly based on the 16S rRNA gene. These methods have allowed us to examine microorganisms that cannot be cultivated by routine methods and have also been useful for phylogenetic studies. We also considered the importance of improvements in microbe culture techniques and how we can combine different methods to allow a more appropriate assessment of bacterial diversity and to determine their real potential for industrial applications.}, } @article {pmid17363641, year = {2007}, author = {Bohannon, J}, title = {Metagenomics. Ocean study yields a tidal wave of microbial DNA.}, journal = {Science (New York, N.Y.)}, volume = {315}, number = {5818}, pages = {1486-1487}, doi = {10.1126/science.315.5818.1486}, pmid = {17363641}, issn = {1095-9203}, mesh = {Atlantic Ocean ; Bacteria/*classification/*genetics ; *Biodiversity ; Computational Biology ; DNA, Bacterial/*analysis/genetics ; Databases, Nucleic Acid ; *Genomics ; Pacific Ocean ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, } @article {pmid17255551, year = {2007}, author = {Huson, DH and Auch, AF and Qi, J and Schuster, SC}, title = {MEGAN analysis of metagenomic data.}, journal = {Genome research}, volume = {17}, number = {3}, pages = {377-386}, pmid = {17255551}, issn = {1088-9051}, mesh = {Atlantic Ocean ; *Biodiversity ; Computational Biology/methods ; *Ecosystem ; *Genetic Variation ; Genome/*genetics ; Genomics/*methods ; *Phylogeny ; *Software ; Species Specificity ; }, abstract = {Metagenomics is the study of the genomic content of a sample of organisms obtained from a common habitat using targeted or random sequencing. Goals include understanding the extent and role of microbial diversity. The taxonomical content of such a sample is usually estimated by comparison against sequence databases of known sequences. Most published studies use the analysis of paired-end reads, complete sequences of environmental fosmid and BAC clones, or environmental assemblies. Emerging sequencing-by-synthesis technologies with very high throughput are paving the way to low-cost random "shotgun" approaches. This paper introduces MEGAN, a new computer program that allows laptop analysis of large metagenomic data sets. In a preprocessing step, the set of DNA sequences is compared against databases of known sequences using BLAST or another comparison tool. MEGAN is then used to compute and explore the taxonomical content of the data set, employing the NCBI taxonomy to summarize and order the results. A simple lowest common ancestor algorithm assigns reads to taxa such that the taxonomical level of the assigned taxon reflects the level of conservation of the sequence. The software allows large data sets to be dissected without the need for assembly or the targeting of specific phylogenetic markers. It provides graphical and statistical output for comparing different data sets. The approach is applied to several data sets, including the Sargasso Sea data set, a recently published metagenomic data set sampled from a mammoth bone, and several complete microbial genomes. Also, simulations that evaluate the performance of the approach for different read lengths are presented.}, } @article {pmid17174002, year = {2007}, author = {Pohn, B and Gerlach, J and Scheideler, M and Katz, H and Uray, M and Bischof, H and Klimant, I and Schwab, H}, title = {Micro-colony array based high throughput platform for enzyme library screening.}, journal = {Journal of biotechnology}, volume = {129}, number = {1}, pages = {162-170}, doi = {10.1016/j.jbiotec.2006.11.002}, pmid = {17174002}, issn = {0168-1656}, mesh = {Calibration ; Enzymes/*genetics/*metabolism ; Escherichia coli/*cytology/*metabolism ; Esterases/genetics/metabolism ; Mutant Proteins/metabolism ; *Protein Engineering ; Reproducibility of Results ; }, abstract = {Enzymes are becoming increasingly important tools for synthesizing and modifying fine and bulk chemicals. The availability of biocatalysts which fulfil the requirements of industrial processes is often limited. Recruiting suited enzymes from natural (e.g. metagenomes) and artificial (e.g. directed evolution) biodiversity is based on screening libraries of microbial clones expressing enzyme variants. However, exploring the complex diversity of such libraries needs efficient screening methods. Overcoming the "screening bottleneck" requires rapid high throughput technology allowing the analysis of a large diversity of different enzymes and applying different screening conditions. Facing these facts an efficient and cost effective method for high throughput screening of large enzyme libraries at the colony level was developed. Therefore, ordered high density micro-colony arrays were combined with optical sensor technology and automated image analysis. The system generally allows the simultaneous monitoring of enzyme activities reflected by up to 7000 micro-colonies spotted on a filter in the size of a micro-titer plate. A developed replica option also allows the analysis of clones under varying external conditions. The method was verified by a model screening using esterases and was proved to provide reliable enzyme activity measurements within single micro-colonies allowing the discrimination of activity differences in the range of 10-20%.}, } @article {pmid17124705, year = {2007}, author = {Meyer, QC and Burton, SG and Cowan, DA}, title = {Subtractive hybridization magnetic bead capture: a new technique for the recovery of full-length ORFs from the metagenome.}, journal = {Biotechnology journal}, volume = {2}, number = {1}, pages = {36-40}, doi = {10.1002/biot.200600156}, pmid = {17124705}, issn = {1860-7314}, mesh = {Chromosome Mapping/*methods ; DNA/*genetics/*isolation & purification ; Gene Targeting/methods ; Genomics/methods ; In Situ Hybridization/*methods ; *Magnetics ; Microspheres ; Open Reading Frames/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {A new method for the recovery of full-length open reading frames from metagenomic nucleic acid samples is reported. This technique, based on subtractive hybridization magnetic bead capture technology, has the potential to access multiple gene variants from a single amplification reaction. It is now widely accepted that classical microbiological methods provide only limited access to the true microbial biodiversity (less than 1%). The desire to access a higher proportion of the metagenome has led to the development of efficient environmental nucleic acid extraction technologies and to a range of sequence-dependent and sequence-independent gene discovery techniques. These methods avoid many of the limitations of culture-dependent gene targeting.}, } @article {pmid17090214, year = {2006}, author = {Angly, FE and Felts, B and Breitbart, M and Salamon, P and Edwards, RA and Carlson, C and Chan, AM and Haynes, M and Kelley, S and Liu, H and Mahaffy, JM and Mueller, JE and Nulton, J and Olson, R and Parsons, R and Rayhawk, S and Suttle, CA and Rohwer, F}, title = {The marine viromes of four oceanic regions.}, journal = {PLoS biology}, volume = {4}, number = {11}, pages = {e368}, pmid = {17090214}, issn = {1545-7885}, mesh = {Bacteriophages/isolation & purification ; Biodiversity ; DNA, Single-Stranded/isolation & purification ; Genetic Variation ; *Genome, Viral ; Marine Biology ; Molecular Sequence Data ; Oceans and Seas ; Phylogeny ; Seawater/*virology ; Selection Bias ; Specimen Handling ; Viruses/classification/*genetics/isolation & purification ; }, abstract = {Viruses are the most common biological entities in the marine environment. There has not been a global survey of these viruses, and consequently, it is not known what types of viruses are in Earth's oceans or how they are distributed. Metagenomic analyses of 184 viral assemblages collected over a decade and representing 68 sites in four major oceanic regions showed that most of the viral sequences were not similar to those in the current databases. There was a distinct "marine-ness" quality to the viral assemblages. Global diversity was very high, presumably several hundred thousand of species, and regional richness varied on a North-South latitudinal gradient. The marine regions had different assemblages of viruses. Cyanophages and a newly discovered clade of single-stranded DNA phages dominated the Sargasso Sea sample, whereas prophage-like sequences were most common in the Arctic. However most viral species were found to be widespread. With a majority of shared species between oceanic regions, most of the differences between viral assemblages seemed to be explained by variation in the occurrence of the most common viral species and not by exclusion of different viral genomes. These results support the idea that viruses are widely dispersed and that local environmental conditions enrich for certain viral types through selective pressure.}, } @article {pmid17035189, year = {2006}, author = {Hu, TT and Jiang, CJ and Liang, X and Long, WJ and Wu, B}, title = {[Cloning and diversity analysis of microorganism genes from alkalescence soil].}, journal = {Yi chuan = Hereditas}, volume = {28}, number = {10}, pages = {1287-1293}, doi = {10.1360/yc-006-1287}, pmid = {17035189}, issn = {0253-9772}, mesh = {Amino Acid Sequence ; Bacteria/*genetics/*isolation & purification ; Bacterial Proteins/genetics ; Base Sequence ; Cloning, Molecular ; Computational Biology ; DNA, Ribosomal/genetics ; Endopeptidases/genetics ; Gene Expression Regulation, Bacterial ; Gene Library ; Genes, Bacterial/*genetics ; *Genetic Variation ; Genome, Bacterial/genetics ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Phylogeny ; Soil/*analysis ; *Soil Microbiology ; beta-Glucosidase/chemistry/genetics ; }, abstract = {The metagenomic DNAs were extracted and purified from alkalescence environmental samples directly. On the basis of the metagenomic DNA, the alkaline soil 16S rDNA library composed of 5,562 positive clones was constructed. The phylogenic tree indicated that the bacteria from the alkaline soils were bio-diversity. The metagenomic DNA library named AL01 was constructed by inserting restriction fragments of the purified DNAs into plasmids pGEM-3Zf(+) vector. This library contained 23,650 positive clones and the average foreign DNA fragments were about 3.2 kb. The length of the library covered 75.68 Mb. The efficiency of the metagenomic library was approximately 6,000 clones from 1g dry soil samples. After screening AL01 DNA library with the screening tactics of enzymes, we confirmed that a positive clone, designated pGXAA2011, contained an alkaline protease gene AP01. Enzymatic analysis proved that its reaction optimum pH was 9.5 and the optimum temperature was 40 degrees C. Furthermore, a clone, designated pGXAG142 was screened from metagenomic DNA library, which expresses beta-glucosidase. DNA sequence indicated that the potential ORF of pGXAG142, which was named unglu01, there was no DNA or amino acids identity with the known beta-glucosidase genes in the Genbank. The integrated ORF was cloned into pETBlue-2 vector and was then transformed into Tuner(DE3)pLacI. The recombinant expression clone could express beta-glucosidase on the screening plate clearly and the analysis of SDS-PAGE indicated that the target protein was about 29 kDa.}, } @article {pmid17014489, year = {2006}, author = {Gros, R and Jocteur Monrozier, L and Faivre, P}, title = {Does disturbance and restoration of alpine grassland soils affect the genetic structure and diversity of bacterial and N2-fixing populations?.}, journal = {Environmental microbiology}, volume = {8}, number = {11}, pages = {1889-1901}, doi = {10.1111/j.1462-2920.2006.01106.x}, pmid = {17014489}, issn = {1462-2912}, mesh = {Bacteria/*genetics ; Biodiversity ; DNA, Ribosomal Spacer/genetics ; *Ecosystem ; Genes, rRNA ; Nitrogen Fixation ; Oxidoreductases/genetics ; Plant Roots/*microbiology ; Poaceae/*microbiology ; Polymorphism, Restriction Fragment Length ; *Soil Microbiology ; }, abstract = {Responses of bacterial communities to disturbance and restoration processes were investigated on alpine grassland soil. Bulk soil, rhizosphere soil and two soil separates, i.e. sand-size (2000-200 microm) and silt-size (50-2 microm) were sampled from undisturbed grassland soil to soil under restoration for 1 month, 1 year, 4 years and 13 years after disturbance. Automated ribosomal intergenic spacer analysis (ARISA) and restriction fragment length polymorphism (RFLP) of nifH gene pools were used to assay genetic structure of the bacterial communities and N2-fixing guild. According to the distribution of ARISA band length in bacterial phyla, the dominance of ARISA bands below 400 bp showed that Gram-positive bacteria would be predominant in the studied grassland soil when not disturbed. Disturbance affected the genetic structure of bacterial community and of N2-fixing guild in relation to their location within the selected habitats. Shifts in IGS and nifH profiles of bulk soil metagenome were larger than those observed from sand-size- and silt-size-fractions, accounting for 40-50% of the variance in the profiles. Restoration of the genetic structure of telluric bacteria community and N2-fixing populations was found to be influenced by the spatial heterogeneity of the soil and niche diversification. Particular bacterial genetic structure within distinct habitats were evidenced and must be defined as subdivisions of the meta-community of bulk soil. Scale of soil microbial diversity/stability relationships is discussed with special attention to disconnected bacterial habitat compared with whole soil with multiple niches.}, } @article {pmid16907762, year = {2006}, author = {Mills, DK and Entry, JA and Voss, JD and Gillevet, PM and Mathee, K}, title = {An assessment of the hypervariable domains of the 16S rRNA genes for their value in determining microbial community diversity: the paradox of traditional ecological indices.}, journal = {FEMS microbiology ecology}, volume = {57}, number = {3}, pages = {496-503}, doi = {10.1111/j.1574-6941.2006.00135.x}, pmid = {16907762}, issn = {0168-6496}, mesh = {Biodiversity ; Complementarity Determining Regions/*genetics ; Ecology/*methods ; RNA, Ribosomal, 16S/*genetics ; *Soil Microbiology ; }, abstract = {Amplicon length heterogeneity PCR (LH-PCR) was investigated for its ability to distinguish between microbial community patterns from the same soil type under different land management practices. Natural sagebrush and irrigated mouldboard-ploughed soils from Idaho were queried as to which hypervariable domains, or combinations of 16S rRNA gene domains, were the best molecular markers. Using standard ecological indices to measure richness, diversity and evenness, the combination of three domains, V1, V3 and V1+V2, or the combined V1 and V3 domains were the markers that could best distinguish the undisturbed natural sagebrush communities from the mouldboard-ploughed microbial communities. Bray-Curtis similarity and multidimensional scaling were found to be better metrics to ordinate and cluster the LH-PCR community profiling data. The use/misuse of traditional ecological indices such as diversity and evenness to study microbial community profiles will remain a major point to consider when performing metagenomic studies.}, } @article {pmid16897828, year = {2006}, author = {Langer, M and Gabor, EM and Liebeton, K and Meurer, G and Niehaus, F and Schulze, R and Eck, J and Lorenz, P}, title = {Metagenomics: an inexhaustible access to nature's diversity.}, journal = {Biotechnology journal}, volume = {1}, number = {7-8}, pages = {815-821}, doi = {10.1002/biot.200600111}, pmid = {16897828}, issn = {1860-7314}, mesh = {Biodiversity ; Biotechnology/*methods/*trends ; Conservation of Natural Resources/*methods/*trends ; Genomics/*methods/trends ; Industry/*methods/*trends ; }, abstract = {The chemical industry has an enormous need for innovation. To save resources, energy and time, currently more and more established chemical processes are being switched to biotechnological routes. This requires white biotechnology to discover and develop novel enzymes, biocatalysts and applications. Due to a limitation in the cultivability of microbes living in certain habitats, technologies have to be established which give access to the enormous resource of uncultivated microbial diversity. Metagenomics promises to provide new and diverse enzymes and biocatalysts as well as bioactive molecules and has the potential to make industrial biotechnology an economic, sustainable success.}, } @article {pmid16879649, year = {2006}, author = {Yang, H and To, KH and Aguila, SJ and Miller, JH}, title = {Metagenomic DNA fragments that affect Escherichia coli mutational pathways.}, journal = {Molecular microbiology}, volume = {61}, number = {4}, pages = {960-977}, doi = {10.1111/j.1365-2958.2006.05268.x}, pmid = {16879649}, issn = {0950-382X}, support = {ES0110875/ES/NIEHS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Biodiversity ; California ; Computational Biology ; DNA Repair/genetics ; DNA Replication/genetics ; Escherichia coli/classification/*genetics ; *Gene Library ; *Genome, Bacterial ; Molecular Sequence Data ; Mutation/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Recombination, Genetic ; Sequence Alignment ; *Soil Microbiology ; }, abstract = {A multicopy cloning approach was used to search for metagenomic DNA fragments that affect Escherichia coli mutational pathways. Soil metagenomic expression libraries were constructed with DNA samples prepared directly from soil samples collected from the UCLA Botanical Garden. Using frameshift mutator screening, we obtained a total of 26 unique metagenomic fragments that stimulate frameshift rates in an E. coli wild-type host. Mutational enhancer strains such as an ndk-deficient strain and a temperature sensitive mutS strain (mutS60) were used to further verify the mutator phenotype. We found that the presence of multiple copies of certain types of metagenomic DNA sequence repeats cause general genome instability in the wild-type E. coli host and the effect can be suppressed by overproducing a DNA mismatch component MutL. In addition, we identified nine metagenomic mutator genes (designated as smu genes) that encode proteins that have not been linked to mutator phenotypes prior to this study including a putative RNA methyltransferase Smu10A. The strain overproducing Smu10A displays one prominent base substitution hotspot in the rpoB gene, which coincides with the base substitution hotspot we have observed in cells that are partially deficient in the proofreading function carried out by the DNA polymerase III epsilon subunit. Based on the structural conservation of DNA replication/recombination/repair machineries among microorganisms, this approach would allow us to both identify new mutational pathways in E. coli and to find genes involved in DNA replication, recombination or DNA repair from vast unculturable microbes.}, } @article {pmid16817924, year = {2006}, author = {Yokouchi, H and Fukuoka, Y and Mukoyama, D and Calugay, R and Takeyama, H and Matsunaga, T}, title = {Whole-metagenome amplification of a microbial community associated with scleractinian coral by multiple displacement amplification using phi29 polymerase.}, journal = {Environmental microbiology}, volume = {8}, number = {7}, pages = {1155-1163}, doi = {10.1111/j.1462-2920.2006.01005.x}, pmid = {16817924}, issn = {1462-2912}, mesh = {Animals ; Anthozoa/*microbiology ; Bacillus Phages/enzymology ; Bacteriological Techniques/*methods ; Biodiversity ; DNA Primers ; DNA-Directed DNA Polymerase/*genetics ; Ecosystem ; Gene Library ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques/*methods ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Limitations in obtaining sufficient specimens and difficulties in extracting high quality DNA from environmental samples have impeded understanding of the structure of microbial communities. In this study, multiple displacement amplification (MDA) using phi29 polymerase was applied to overcome these hindrances. Optimization of the reaction conditions for amplification of the bacterial genome and evaluation of the MDA product were performed using cyanobacterium Synechocystis sp. strain PCC6803. An 8-h MDA reaction yielded a sufficient quantity of DNA from an initial amount of 0.4 ng, which is equivalent to approximately 10(5) cells. Uniform amplification of genes randomly selected from the cyanobacterial genome was confirmed by real-time polymerase chain reaction. The metagenome from bacteria associated with scleractinian corals was used for whole-genome amplification using phi29 polymerase to analyse the microbial diversity. Unidentified bacteria with less than 93% identity to the closest 16S rDNA sequences deposited in DNA Data Bank of Japan were predominantly detected from the coral-associated bacterial community before and after the MDA procedures. Sequencing analysis indicated that alpha-Proteobacteria was the dominant group in Pocillopora damicornis. This study demonstrates that MDA techniques are efficient for genome wide investigation to understand the actual microbial diversity in limited bacterial samples.}, } @article {pmid16765858, year = {2006}, author = {Neria-González, I and Wang, ET and Ramírez, F and Romero, JM and Hernández-Rodríguez, C}, title = {Characterization of bacterial community associated to biofilms of corroded oil pipelines from the southeast of Mexico.}, journal = {Anaerobe}, volume = {12}, number = {3}, pages = {122-133}, doi = {10.1016/j.anaerobe.2006.02.001}, pmid = {16765858}, issn = {1075-9964}, mesh = {Bacteria/*classification/genetics/isolation & purification/metabolism ; *Bacterial Physiological Phenomena ; Biodiversity ; *Biofilms ; Corrosion ; DNA, Bacterial/genetics ; *Environmental Monitoring ; *Industrial Microbiology ; *Industrial Oils ; Industry ; Mexico ; Oxidation-Reduction ; Phylogeny ; Polymerase Chain Reaction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Steel/analysis/chemistry ; Sulfates/metabolism ; Templates, Genetic ; }, abstract = {Microbial communities associated to biofilms promote corrosion of oil pipelines. The community structure of bacteria in the biofilm formed in oil pipelines is the basic knowledge to understand the complexity and mechanisms of metal corrosion. To assess bacterial diversity, biofilm samples were obtained from X52 steel coupons corroded after 40 days of exposure to normal operation and flow conditions. The biofilm samples were directly used to extract metagenomic DNA, which was used as template to amplify 16S ribosomal gene by PCR. The PCR products of 16S ribosomal gene were also employed as template for sulfate-reducing bacteria (SRB) specific nested-PCR and both PCR products were utilized for the construction of gene libraries. The V3 region of the 16S rRNA gene was also amplified to analyse the bacterial diversity by analysis of denaturing gradient gel electrophoresis (DGGE). Ribosomal library and DGGE profiles exhibited limited bacterial diversity, basically including Citrobacter spp., Enterobacter spp. and Halanaerobium spp. while Desulfovibrio alaskensis and a novel clade within the genus Desulfonatronovibrio were detected from the nested PCR library. The biofilm samples were also taken for the isolation of SRB. Desulfovibrio alaskensis and Desulfovibrio capillatus, as well as some strains related to Citrobacter were isolated. SRB consists in a very small proportion of the community and Desulfovibrio spp. were the relatively abundant groups among the SRB. This is the first study directly exploring bacterial diversity in corrosive biofilms associated to steel pipelines subjected to normal operation conditions.}, } @article {pmid16675292, year = {2006}, author = {Ward, AC and Bora, N}, title = {Diversity and biogeography of marine actinobacteria.}, journal = {Current opinion in microbiology}, volume = {9}, number = {3}, pages = {279-286}, doi = {10.1016/j.mib.2006.04.004}, pmid = {16675292}, issn = {1369-5274}, mesh = {Actinobacteria/*classification/genetics/*growth & development ; Animals ; Culture Media ; Ecosystem ; *Genetic Variation ; Geologic Sediments/microbiology ; *Marine Biology ; Seawater/microbiology ; }, abstract = {The actinomycetes, although not all the Actinobacteria, are easy to isolate from the marine environment. However, their ecological role in the marine ecosystem is largely neglected and various assumptions meant there was little incentive to isolate strains for search and discovery of new drugs. However, the marine environment has become a prime resource in search and discovery for novel natural products and biological diversity, and marine actinomycetes turn out to be important contributors. Similarly, striking advances have been made in marine microbial ecology using molecular techniques and metagenomics, and actinobacteria emerge as an often significant, sometimes even dominant, environmental clade. Both approaches - cultivation methods and molecular techniques - are leading to new insights into marine actinobacterial biodiversity and biogeography. Very different views of actinobacterial diversity emerge from these, however, and the true extent and biogeography of this are still not clear. These are important for developing natural product search and discovery strategies, and biogeography is a hot topic for microbial ecologists.}, } @article {pmid16672469, year = {2006}, author = {Abulencia, CB and Wyborski, DL and Garcia, JA and Podar, M and Chen, W and Chang, SH and Chang, HW and Watson, D and Brodie, EL and Hazen, TC and Keller, M}, title = {Environmental whole-genome amplification to access microbial populations in contaminated sediments.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {5}, pages = {3291-3301}, pmid = {16672469}, issn = {0099-2240}, mesh = {Bacillus Phages ; Bacteria/*classification/genetics ; Bacterial Proteins/genetics ; DNA, Bacterial/analysis/isolation & purification ; Genes, rRNA ; Genome, Bacterial ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques/*methods ; Phylogeny ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; *Soil Pollutants ; }, abstract = {Low-biomass samples from nitrate and heavy metal contaminated soils yield DNA amounts that have limited use for direct, native analysis and screening. Multiple displacement amplification (MDA) using phi29 DNA polymerase was used to amplify whole genomes from environmental, contaminated, subsurface sediments. By first amplifying the genomic DNA (gDNA), biodiversity analysis and gDNA library construction of microbes found in contaminated soils were made possible. The MDA method was validated by analyzing amplified genome coverage from approximately five Escherichia coli cells, resulting in 99.2% genome coverage. The method was further validated by confirming overall representative species coverage and also an amplification bias when amplifying from a mix of eight known bacterial strains. We extracted DNA from samples with extremely low cell densities from a U.S. Department of Energy contaminated site. After amplification, small-subunit rRNA analysis revealed relatively even distribution of species across several major phyla. Clone libraries were constructed from the amplified gDNA, and a small subset of clones was used for shotgun sequencing. BLAST analysis of the library clone sequences showed that 64.9% of the sequences had significant similarities to known proteins, and "clusters of orthologous groups" (COG) analysis revealed that more than half of the sequences from each library contained sequence similarity to known proteins. The libraries can be readily screened for native genes or any target of interest. Whole-genome amplification of metagenomic DNA from very minute microbial sources, while introducing an amplification bias, will allow access to genomic information that was not previously accessible. The reported SSU rRNA sequences and library clone end sequences are listed with their respective GenBank accession numbers, DQ 404590 to DQ 404652, DQ 404654 to DQ 404938, and DX 385314 to DX 389173.}, } @article {pmid16524840, year = {2006}, author = {Foerstner, KU and von Mering, C and Bork, P}, title = {Comparative analysis of environmental sequences: potential and challenges.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {361}, number = {1467}, pages = {519-523}, pmid = {16524840}, issn = {0962-8436}, mesh = {*Biodiversity ; *Environmental Microbiology ; *Evolution, Molecular ; Genomics/*methods ; }, abstract = {Environmental sequencing, also dubbed metagenomics, is increasingly being used to obtain insights into organismal communities in diverse habitats, and has a variety of potential applications foreseeable in biotechnology and medicine. The first public large-scale data provide already a wealth of information hidden in vast amounts of fragmented pieces of DNA from unknown species residing in these environments. Comparative sequence analysis is essential for the interpretation of such data. However, different layers of complexity that are intrinsic to each sample require the establishment of some baselines for comparison: how to normalize for the differences in phylogenetic and functional diversity, how to avoid biases from incomplete data, and how to deal with differences in species dominance or genome sizes? Here we discuss a few of these items and delineate some simple discriminative sequence properties for four distinct habitats.}, } @article {pmid16309396, year = {2005}, author = {Ferrer, M and Golyshina, OV and Chernikova, TN and Khachane, AN and Reyes-Duarte, D and Santos, VA and Strompl, C and Elborough, K and Jarvis, G and Neef, A and Yakimov, MM and Timmis, KN and Golyshin, PN}, title = {Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora.}, journal = {Environmental microbiology}, volume = {7}, number = {12}, pages = {1996-2010}, doi = {10.1111/j.1462-2920.2005.00920.x}, pmid = {16309396}, issn = {1462-2912}, mesh = {Animals ; Bacterial Proteins/*genetics ; Biodiversity ; Cattle ; Female ; Fungal Proteins/*genetics ; Genes, Bacterial ; Genes, Fungal ; Genes, Helminth ; Helminth Proteins/genetics ; Hydrolases/*genetics ; Molecular Sequence Data ; New Zealand ; Rumen/*microbiology/parasitology ; }, abstract = {A metagenome expression library of bulk DNA extracted from the rumen content of a dairy cow was established in a phage lambda vector and activity-based screening employed to explore the functional diversity of the microbial flora. Twenty-two clones specifying distinct hydrolytic activities (12 esterases, nine endo-beta-1,4-glucanases and one cyclodextrinase) were identified in the library and characterized. Sequence analysis of the retrieved enzymes revealed that eight (36%) were entirely new and formed deep-branched phylogenetic lineages with no close relatives among known ester- and glycosyl-hydrolases. Bioinformatic analyses of the hydrolase gene sequences, and the sequences and contexts of neighbouring genes, suggested tentative phylogenetic assignments of the rumen organisms producing the retrieved enzymes. The phylogenetic novelty of the hydrolases suggests that some of them may have potential for new applications in biocatalysis.}, } @article {pmid16309389, year = {2005}, author = {Kalyuzhnaya, MG and Nercessian, O and Lapidus, A and Chistoserdova, L}, title = {Fishing for biodiversity: novel methanopterin-linked C transfer genes deduced from the Sargasso Sea metagenome.}, journal = {Environmental microbiology}, volume = {7}, number = {12}, pages = {1909-1916}, doi = {10.1111/j.1462-2920.2005.00798.x}, pmid = {16309389}, issn = {1462-2912}, mesh = {*Biodiversity ; Biological Transport ; Carbon/*metabolism ; Computational Biology/*methods ; Formaldehyde/metabolism ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; *Marine Biology ; Oceans and Seas ; Oxidation-Reduction ; Plankton/genetics ; Pterins/*metabolism ; *Water Microbiology ; }, abstract = {The recently generated database of microbial genes from an oligotrophic environment populated by a calculated 1800 major phylotypes (the Sargasso Sea metagenome-SSM) presents a great source for expanding local databases of genes indicative of a specific function. In this article we analyse the SSM for the presence of methanopterin-linked C1 transfer genes that are signature for methylotrophy. We conclude that more than 10 phylotypes possessing genes of interest are present in this environment. The sequences representative of these major phylotypes do not appear to belong to any known microbial group capable of methanopterin-linked C1 transfer. Instead, these sequences separate from all known sequences on phylogenetic trees, pointing toward their affiliation with novel microbial phyla. These data imply a broader distribution of methanopterin-linked functions in the microbial world than has been previously known.}, } @article {pmid16309387, year = {2005}, author = {Cottrell, MT and Waidner, LA and Yu, L and Kirchman, DL}, title = {Bacterial diversity of metagenomic and PCR libraries from the Delaware River.}, journal = {Environmental microbiology}, volume = {7}, number = {12}, pages = {1883-1895}, doi = {10.1111/j.1462-2920.2005.00762.x}, pmid = {16309387}, issn = {1462-2912}, mesh = {Actinobacteria/genetics/isolation & purification ; Bacteria/genetics/*isolation & purification ; Betaproteobacteria/genetics/isolation & purification ; *Biodiversity ; Burkholderiaceae/genetics/isolation & purification ; Cytophaga/genetics/isolation & purification ; Delaware ; Fresh Water/*microbiology ; *Genomic Library ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; *Polymerase Chain Reaction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; *Water Microbiology ; }, abstract = {To determine whether metagenomic libraries sample adequately the dominant bacteria in aquatic environments, we examined the phylogenetic make-up of a large insert metagenomic library constructed with bacterial DNA from the Delaware River, a polymerase chain reaction (PCR) library of 16S rRNA genes, and community structure determined by fluorescence in situ hybridization (FISH). The composition of the libraries and community structure determined by FISH differed for the major bacterial groups in the river, which included Actinobacteria, beta-proteobacteria and Cytophaga-like bacteria. Beta-proteobacteria were underrepresented in the metagenomic library compared with the PCR library and FISH, while Cytophaga-like bacteria were more abundant in the metagenomic library than in the PCR library and in the actual community according to FISH. The Delaware River libraries contained bacteria belonging to several widespread freshwater clusters, including clusters of Polynucleobacter necessarius, Rhodoferax sp. Bal47 and LD28 beta-proteobacteria, the ACK-m1 and STA2-30 clusters of Actinobacteria, and the PRD01a001B Cytophaga-like bacteria cluster. Coverage of bacteria with > 97% sequence identity was 65% and 50% for the metagenomic and PCR libraries respectively. Rarefaction analysis of replicate PCR libraries and of a library constructed with re-conditioned amplicons indicated that heteroduplex formation did not substantially impact the composition of the PCR library. This study suggests that although it may miss some bacterial groups, the metagenomic approach can sample other groups (e.g. Cytophaga-like bacteria) that are potentially underrepresented by other culture-independent approaches.}, } @article {pmid16270658, year = {2005}, author = {Bornscheuer, UT}, title = {Trends and challenges in enzyme technology.}, journal = {Advances in biochemical engineering/biotechnology}, volume = {100}, number = {}, pages = {181-203}, doi = {10.1007/b136413}, pmid = {16270658}, issn = {0724-6145}, mesh = {Biotechnology/*trends ; Enzymes/*biosynthesis/*genetics ; Forecasting ; Protein Engineering/*methods/*trends ; Recombinant Proteins/*biosynthesis ; }, abstract = {Several major developments took place in the field of biocatalysis over the past few years. These include the invention of directed evolution as an extremely useful method for biocatalyst improvement on the molecular level in combination with high-throughput screening systems, methods for accessing "nonculturable" biodiversity using metagenome approaches and progress in sequence-based biocatalyst discovery. In addition, new carriers and tools for immobilization of enzymes have been developed. For the synthesis of optically active compounds impressive examples using new enzymes and major progress in dynamic kinetic resolutions of racemates took place. These achievements are summarized in this review.}, } @article {pmid16171989, year = {2005}, author = {Ferrer, M and Martínez-Abarca, F and Golyshin, PN}, title = {Mining genomes and 'metagenomes' for novel catalysts.}, journal = {Current opinion in biotechnology}, volume = {16}, number = {6}, pages = {588-593}, doi = {10.1016/j.copbio.2005.09.001}, pmid = {16171989}, issn = {0958-1669}, mesh = {Biotechnology/trends ; Catalysis ; *DNA Shuffling/trends ; *Directed Molecular Evolution/trends ; Environmental Microbiology ; Enzymes/*genetics ; Genome, Bacterial/*genetics ; *Genomic Library ; }, abstract = {Advances in the field of genomics and 'metagenomics' have dramatically revised our view of microbial biodiversity and its potential for biotechnological applications. Considering the estimation that >99% of microorganisms in most environments are not amenable to culturing, very little is known about their genomes, genes and encoded enzymatic activities. The isolation, archiving and analysis of environmental DNA (or so-called 'metagenomes') has enabled us to mine microbial diversity, allowing us to access their genomes, identify protein coding sequences and even to reconstruct biochemical pathways, providing insights into the properties and functions of these organisms. The generation and analysis of (meta)genomic libraries is thus a powerful approach to harvest and archive environmental genetic resources. It will enable us to identify which organisms are present, what they do, and how their genetic information can be beneficial to mankind.}, } @article {pmid16043354, year = {2005}, author = {Johnston, AW and Li, Y and Ogilvie, L}, title = {Metagenomic marine nitrogen fixation--feast or famine?.}, journal = {Trends in microbiology}, volume = {13}, number = {9}, pages = {416-420}, doi = {10.1016/j.tim.2005.07.002}, pmid = {16043354}, issn = {0966-842X}, mesh = {Bacteria/*genetics ; Biodiversity ; Computational Biology ; Databases, Genetic ; Genome, Bacterial ; *Genomics ; Nitrogen Fixation/*genetics ; Seawater/*microbiology ; Water Microbiology ; }, abstract = {Natural populations of bacteria in different environments can be astonishingly diverse, as was revealed graphically by large-scale sequencing of samples of their so-called metagenomes. Among the sequence datasets from four different samples of marine bacterial metagenomes, we noted that nitrogen fixation (nif) genes were conspicuous by their absence from three of them. However, in one sample, more than one-third of the bacteria appeared to have a complement of these genes. Here, some reasons behind this site-to-site variability and their implications for how molecular methods, involving large-scale sequencing and/or functional metagenomics, can best be used to describe bacterial diversity in natural environments are discussed.}, } @article {pmid16039858, year = {2005}, author = {Remington, KA and Heidelberg, K and Venter, JC}, title = {Taking metagenomic studies in context.}, journal = {Trends in microbiology}, volume = {13}, number = {9}, pages = {404}, doi = {10.1016/j.tim.2005.07.001}, pmid = {16039858}, issn = {0966-842X}, mesh = {Bacteria/*genetics ; Biodiversity ; Computational Biology ; Databases, Genetic ; *Genomics ; Nitrogen Fixation/*genetics ; *Water Microbiology ; }, } @article {pmid15936660, year = {2005}, author = {Breitbart, M and Rohwer, F}, title = {Here a virus, there a virus, everywhere the same virus?.}, journal = {Trends in microbiology}, volume = {13}, number = {6}, pages = {278-284}, doi = {10.1016/j.tim.2005.04.003}, pmid = {15936660}, issn = {0966-842X}, mesh = {Bacteriophages/genetics/physiology ; *Biodiversity ; Gene Transfer, Horizontal ; Genes, Viral ; *Genome, Viral ; *Virus Physiological Phenomena ; Viruses/*genetics ; }, abstract = {There are an estimated 10(31) viruses on Earth, most of which are phages that infect bacteria. Metagenomic analyses have shown that environmental viral communities are incredibly diverse. There are an estimated 5000 viral genotypes in 200 liters of seawater and possibly a million different viral genotypes in one kilogram of marine sediment. By contrast, some culturing and molecular studies have found that viruses move between different biomes. Together, these findings suggest that viral diversity could be high on a local scale but relatively limited globally. Also, by moving between environments, viruses can facilitate horizontal gene transfer.}, } @article {pmid15931168, year = {2005}, author = {Lorenz, P and Eck, J}, title = {Metagenomics and industrial applications.}, journal = {Nature reviews. Microbiology}, volume = {3}, number = {6}, pages = {510-516}, doi = {10.1038/nrmicro1161}, pmid = {15931168}, issn = {1740-1526}, mesh = {Bacteria/enzymology/genetics ; Biodiversity ; Catalysis ; Ecosystem ; Enzymes/*genetics ; *Genomics ; *Industry ; Plasmids/genetics ; }, abstract = {Different industries have different motivations to probe the enormous resource that is uncultivated microbial diversity. Currently, there is a global political drive to promote white (industrial) biotechnology as a central feature of the sustainable economic future of modern industrialized societies. This requires the development of novel enzymes, processes, products and applications. Metagenomics promises to provide new molecules with diverse functions, but ultimately, expression systems are required for any new enzymes and bioactive molecules to become an economic success. This review highlights industrial efforts and achievements in metagenomics.}, } @article {pmid15922085, year = {2005}, author = {Cowan, D and Meyer, Q and Stafford, W and Muyanga, S and Cameron, R and Wittwer, P}, title = {Metagenomic gene discovery: past, present and future.}, journal = {Trends in biotechnology}, volume = {23}, number = {6}, pages = {321-329}, doi = {10.1016/j.tibtech.2005.04.001}, pmid = {15922085}, issn = {0167-7799}, mesh = {Bacteria/*genetics ; Biodiversity ; *Cloning, Molecular/methods ; *Environmental Microbiology ; Genetics, Microbial/methods/*trends ; *Genome, Bacterial ; }, abstract = {It is now widely accepted that the application of standard microbiological methods for the recovery of microorganisms from the environment has had limited success in providing access to the true extent of microbial biodiversity. It follows that much of the extant microbial genetic diversity (collectively termed the metagenome) remains unexploited, an issue of considerable relevance to a wider understanding of microbial communities and of considerable importance to the biotechnology industry. The recent development of technologies designed to access this wealth of genetic information through environmental nucleic acid extraction has provided a means of avoiding the limitations of culture-dependent genetic exploitation.}, } @article {pmid15865958, year = {2005}, author = {Valentin, K and John, U and Medlin, L}, title = {Nucleic acid isolation from environmental aqueous samples.}, journal = {Methods in enzymology}, volume = {395}, number = {}, pages = {15-37}, doi = {10.1016/S0076-6879(05)95002-7}, pmid = {15865958}, issn = {0076-6879}, mesh = {Biodiversity ; Chemical Precipitation ; DNA/genetics/isolation & purification ; DNA Restriction Enzymes ; Ecosystem ; Fresh Water ; Marine Biology ; Methods ; Nucleic Acid Hybridization ; Nucleic Acids/genetics/*isolation & purification ; Plankton/chemistry/genetics/isolation & purification ; Polymerase Chain Reaction ; Quality Control ; RNA/genetics/isolation & purification ; }, abstract = {The application of molecular techniques has revolutionized freshwater and marine ecology, especially for plankton research. Methods, such as denatured gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), and single-strand conformation polymorphism (SSCP), together with environmental clone libraries, have unraveled an unexpected biodiversity of organisms in the water column. Molecular probes are just entering the field of commercialization for monitoring toxic algal blooms. Genomics and metagenomics were recently introduced into marine biology. At the basis of all molecular approaches is the isolation of nucleic acids from cultures, tissue, or environmental samples. Here, we summarize methods, quality controls, and hints for sample treatment to reliably isolate nucleic acids, both DNA and RNA, from environmental aqueous samples. This chapter not only is directed to researchers inexperienced with such methods but also is an aid to those already working in the field. It may be used as a step-by-step guide for nucleic acid isolation from field samples, and we make suggestions for subsequent use of the DNA/RNA.}, } @article {pmid15845853, year = {2005}, author = {Tringe, SG and von Mering, C and Kobayashi, A and Salamov, AA and Chen, K and Chang, HW and Podar, M and Short, JM and Mathur, EJ and Detter, JC and Bork, P and Hugenholtz, P and Rubin, EM}, title = {Comparative metagenomics of microbial communities.}, journal = {Science (New York, N.Y.)}, volume = {308}, number = {5721}, pages = {554-557}, doi = {10.1126/science.1107851}, pmid = {15845853}, issn = {1095-9203}, mesh = {Animals ; Archaea/classification/genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Biofilms ; Bone and Bones/microbiology ; Computational Biology ; *Ecosystem ; Energy Metabolism ; Eukaryotic Cells/metabolism ; Gene Library ; Genes ; Genes, Bacterial ; *Genome ; Genome, Bacterial ; *Genomics ; Molecular Sequence Data ; Operon ; Phylogeny ; Polymerase Chain Reaction ; Proteins/genetics/metabolism ; Proteome ; Seawater/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; Whales/*microbiology ; }, abstract = {The species complexity of microbial communities and challenges in culturing representative isolates make it difficult to obtain assembled genomes. Here we characterize and compare the metabolic capabilities of terrestrial and marine microbial communities using largely unassembled sequence data obtained by shotgun sequencing DNA isolated from the various environments. Quantitative gene content analysis reveals habitat-specific fingerprints that reflect known characteristics of the sampled environments. The identification of environment-specific genes through a gene-centric comparative analysis presents new opportunities for interpreting and diagnosing environments.}, } @article {pmid15743531, year = {2005}, author = {Angly, F and Rodriguez-Brito, B and Bangor, D and McNairnie, P and Breitbart, M and Salamon, P and Felts, B and Nulton, J and Mahaffy, J and Rohwer, F}, title = {PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information.}, journal = {BMC bioinformatics}, volume = {6}, number = {}, pages = {41}, pmid = {15743531}, issn = {1471-2105}, mesh = {Algorithms ; Bacteriophages/metabolism ; Biodiversity ; Computational Biology/*methods ; Contig Mapping ; DNA/chemistry ; DNA Viruses ; Databases, Genetic ; Genes, Viral ; Genetic Variation ; Genome, Viral ; Genotype ; Internet ; Models, Genetic ; Models, Statistical ; Protein Interaction Mapping/*methods ; Sequence Analysis, DNA ; *Software ; Viruses/*metabolism ; }, abstract = {BACKGROUND: Phages, viruses that infect prokaryotes, are the most abundant microbes in the world. A major limitation to studying these viruses is the difficulty of cultivating the appropriate prokaryotic hosts. One way around this limitation is to directly clone and sequence shotgun libraries of uncultured viral communities (i.e., metagenomic analyses). PHACCS http://phage.sdsu.edu/phaccs, Phage Communities from Contig Spectrum, is an online bioinformatic tool to assess the biodiversity of uncultured viral communities. PHACCS uses the contig spectrum from shotgun DNA sequence assemblies to mathematically model the structure of viral communities and make predictions about diversity.

RESULTS: PHACCS builds models of possible community structure using a modified Lander-Waterman algorithm to predict the underlying contig spectrum. PHACCS finds the most appropriate structure model by optimizing the model parameters until the predicted contig spectrum is as close as possible to the experimental one. This model is the basis for making estimates of uncultured viral community richness, evenness, diversity index and abundance of the most abundant genotype.

CONCLUSION: PHACCS analysis of four different environmental phage communities suggests that the power law is an important rank-abundance form to describe uncultured viral community structure. The estimates support the fact that the four phage communities were extremely diverse and that phage community biodiversity and structure may be correlated with that of their hosts.}, } @article {pmid15568985, year = {2004}, author = {Riesenfeld, CS and Schloss, PD and Handelsman, J}, title = {Metagenomics: genomic analysis of microbial communities.}, journal = {Annual review of genetics}, volume = {38}, number = {}, pages = {525-552}, doi = {10.1146/annurev.genet.38.072902.091216}, pmid = {15568985}, issn = {0066-4197}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Bacteriophages/*genetics ; Biodiversity ; *Environmental Microbiology ; Gene Library ; Genome, Archaeal ; *Genome, Bacterial ; Genomic Library ; Microscopy ; Phylogeny ; Rhodopsin/genetics ; Rhodopsins, Microbial ; Sequence Analysis ; }, abstract = {Uncultured microorganisms comprise the majority of the planet's biological diversity. Microorganisms represent two of the three domains of life and contain vast diversity that is the product of an estimated 3.8 billion years of evolution. In many environments, as many as 99% of the microorganisms cannot be cultured by standard techniques, and the uncultured fraction includes diverse organisms that are only distantly related to the cultured ones. Therefore, culture-independent methods are essential to understand the genetic diversity, population structure, and ecological roles of the majority of microorganisms. Metagenomics, or the culture-independent genomic analysis of an assemblage of microorganisms, has potential to answer fundamental questions in microbial ecology. This review describes progress toward understanding the biology of uncultured Bacteria, Archaea, and viruses through metagenomic analyses.}, } @article {pmid15156913, year = {2004}, author = {Breitbart, M and Felts, B and Kelley, S and Mahaffy, JM and Nulton, J and Salamon, P and Rohwer, F}, title = {Diversity and population structure of a near-shore marine-sediment viral community.}, journal = {Proceedings. Biological sciences}, volume = {271}, number = {1539}, pages = {565-574}, pmid = {15156913}, issn = {0962-8452}, mesh = {*Biodiversity ; California ; Gene Library ; Geologic Sediments/*virology ; *Models, Genetic ; *Phylogeny ; Seawater ; Sequence Analysis, DNA ; Viruses/classification/*genetics ; }, abstract = {Viruses, most of which are phage, are extremely abundant in marine sediments, yet almost nothing is known about their identity or diversity. We present the metagenomic analysis of an uncultured near-shore marine-sediment viral community. Three-quarters of the sequences in the sample were not related to anything previously reported. Among the sequences that could be identified, the majority belonged to double-stranded DNA phage. Temperate phage were more common than lytic phage, suggesting that lysogeny may be an important lifestyle for sediment viruses. Comparisons between the sediment sample and previously sequenced seawater viral communities showed that certain phage phylogenetic groups were abundant in all marine viral communities, while other phage groups were under-represented or absent. This 'marineness' suggests that marine phage are derived from a common set of ancestors. Several independent mathematical models, based on the distribution of overlapping shotgun sequence fragments from the library, were used to show that the diversity of the viral community was extremely high, with at least 10(4) viral genotypes per kilogram of sediment and a Shannon index greater than 9 nats. Based on these observations we propose that marine-sediment viral communities are one of the largest unexplored reservoirs of sequence space on the planet.}, } @article {pmid12713464, year = {2003}, author = {Holmes, AJ and Gillings, MR and Nield, BS and Mabbutt, BC and Nevalainen, KM and Stokes, HW}, title = {The gene cassette metagenome is a basic resource for bacterial genome evolution.}, journal = {Environmental microbiology}, volume = {5}, number = {5}, pages = {383-394}, doi = {10.1046/j.1462-2920.2003.00429.x}, pmid = {12713464}, issn = {1462-2912}, mesh = {Base Sequence ; *Evolution, Molecular ; *Genes, Bacterial ; *Genome, Bacterial ; Integrons ; Molecular Sequence Data ; *Recombination, Genetic ; Sequence Alignment ; Soil Microbiology ; }, abstract = {Lateral gene transfer has been proposed as a fundamental process underlying bacterial diversity. Transposons, plasmids and phage are widespread and have been shown to significantly contribute to lateral gene transfer. However, the processes by which disparate genes are assembled and integrated into the host regulatory network to yield new phenotypes are poorly known. Recent discoveries about the integron/gene cassette system indicate it has the potential to play a role in this process. Gene cassettes are small mobile elements typically consisting of a promoterless orf and a recombination site. Integrons are capable of acquisition and re-arrangement of gene cassettes and of the expression of their associated genes. The potential of the integron/gene cassette system is thus largely determined by the diversity contained within the cassette pool and the rate at which integrons sample this pool. We show here using a polymerase chain reaction (PCR) approach by which the environmental gene cassette (EGC) metagenome can be directly sampled that this metagenome contains both protein-coding and non-protein coding genes. Environmental gene cassette-associated recombination sites showed greater diversity than previously seen in integron arrays. Class 1 integrons were shown to be capable of accessing this gene pool through tests of recombinational activity with a representative range of EGCs. We propose that gene cassettes represent a vast, prepackaged genetic resource that could be thought of as a metagenomic template for bacterial evolution.}, } @article {pmid12460270, year = {2002}, author = {Rodríguez-Valera, F}, title = {Approaches to prokaryotic biodiversity: a population genetics perspective.}, journal = {Environmental microbiology}, volume = {4}, number = {11}, pages = {628-633}, doi = {10.1046/j.1462-2920.2002.00354.x}, pmid = {12460270}, issn = {1462-2912}, mesh = {Biological Evolution ; *Genetic Variation ; Genetics, Population ; Genomics ; *Microbiology ; }, abstract = {The study of prokaryotic diversity has blossomed during the last 10-15 years as a result of the introduction of molecular identification, mostly based on direct 16S rRNA gene polymerase chain reaction (PCR) amplification and sequencing from natural samples. A large amount of information exists about the diversity of this specific gene. However, data from the field of bacterial population genetics and genomics make questionable the value of information regarding just one gene. Even if we accept 16S rRNA genes as useful for species identification, intraspecific variation in bacteria is so high that species catalogues are often of little value. The gene pools represented by an operational species are yet impossible to predict. On the other hand, adaptive features in prokaryotes are often coded in gene clusters (genomic islands) that can be cloned directly from the environment, sequenced and even expressed in a surrogate host. Thus, the study of the environmental genome or metagenome appears as an alternative that could eventually lead to a more realistic understanding of prokaryotic biodiversity, provide biotechnology with new tools and maybe even contribute to develop a model of prokaryotic evolution.}, }